# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanosaeta_concilii_GP6_uid66207/NC_015416.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanosaeta_concilii_GP6_uid66207/NC_015416.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanosaeta_concilii_GP6_uid66207/NC_015416.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|330506320|ref|YP_004382748.1|  [L=980]
Description: peptidase families S8 and S53 [Methanosaeta concilii GP6]
Scores for complete 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-28   98.7   0.3    1.8e-27   96.4   0.3    2.1  1  Peptidase_S8  Subtilase family
  ------ inclusion threshold ------
        4.5    7.5   4.6         34    4.7   0.4    3.4  3  EF-hand_6     EF-hand 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 !   96.4   0.3     2e-31   1.8e-27       1     298 []      30     457 ..      30     458 .. 0.76

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 2e-31
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegag..................................... 40 
                                       gkgv +a++D G+d   pdl  t       v+  +   +g                                     
  gi|330506320|ref|YP_004382748.1|  30 GKGVNIAIIDFGIDFATPDLMGTQAR----VSNVSSPYYGwpividleslsyyqdgtsgfsshyanttsmdvrdyqv 102
                                       899****************9955322....22233334458999999999999999999997777777777777777 PP

                                       .....................................................GGEETT-SS-TT-SC-S....... CS
                                       .....................................................xxxxxxxxxxxxxxxxx....... RF
                      Peptidase_S8  41 .....................................................fngadsettstnwardd....... 57 
                                                                                                            d       
  gi|330506320|ref|YP_004382748.1| 103 tgtsksgiyhigdhpdqhiaqfygqqvkvlvvdesvssvydtvyvdlnnnhdfR---------------Ddkpcrkg 164
                                       777777777777777777777777777777766666666666665555555541...............03444445 PP

                                       ..................................................SS...........HHHHHHHHHH-B.. CS
                                       ..................................................xxxxxx.......xxxxxxxxxxxxxx RF
                      Peptidase_S8  58 ..................................................ngnsie.......HGthvAGiaaanap 77 
                                                                                              +       HGt +A+++aa+  
  gi|330506320|ref|YP_004382748.1| 165 deasywdrdndgypdesggmvyfiadgktplplsrmlygekakipksgelI----AfecdgdfHGTMCASLIAAQ-- 235
                                       555555556677778899999999999999999999999999999966550....34455556************.. PP

                                       SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHH..CT-SEEEE-EESCETTCHHCHHHHHH...HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxx RF
                      Peptidase_S8  78 eegekngvapgakilsvkvldtsggsmetgteliraieeaae..dkvdvinmslgestslpktgrsieal...ainr 149
                                         +++ g+ap+a+i+sv+ ++t++         + + + + +  d++dv++ s g    + + g +   +    + +
  gi|330506320|ref|YP_004382748.1| 236 -GKNVMGIAPDARIISVRLGKTEELLWLL---AVLGYDGVPNtgDEADVVSRSGG-FMYRLNKGADEGSAfleYLST 307
                                       .*******************999877632...3333444444468999*******.444444444444454644445 PP

                                       HH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES........TTSSB-TT--B-TT.......-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 150 avnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayt........tegkiapfSsrGpssdgklkpdiv 218
                                        v +  + +++ +GN+g      +   + + ps+ + +i vga+           g++  fSsrGp++ g++kp ++
  gi|330506320|ref|YP_004382748.1| 308 NV-SPSTAMIFVSGNDG------SGYGTCNPPSG-EHAINVGATYdqwwnnssYRGDVTCFSSRGPNALGQVKPNVL 376
                                       55.7899999999****......55566666665.459*****999******999********************** PP

                                       EE-S-...CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT.....--HHHHHHHHHCCS-EE... CS
                                       xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 219 apGgn...ivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpk.....ltpetvraallntAqdlgka 287
                                       apG     +++ w ++s ++  + + +   GTS A+P+aa+++Al+ +a+++      t e+ r++l+ +A+d+   
  gi|330506320|ref|YP_004382748.1| 377 APGYRtpeSLPLWITHSGKA--AWD-NHGGGTSGATPHAAAVVALIYQAYKEahgefPTSEKARDILMSSATDI--- 447
                                       *****99*********9333..333.56899*********************9***99*************998... PP

                                       ...SSSSSSTT CS
                                       xxxxxxxxxxx RF
                      Peptidase_S8 288 dniesfaqGaG 298
                                        n e faqG G
  gi|330506320|ref|YP_004382748.1| 448 -NEEIFAQGSG 457
                                       .4567888877 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.09     8e+02       8      16 ..     169     177 ..     168     181 .. 0.81
   2 ?    1.3   0.0     0.049   4.4e+02      10      24 ..     573     587 ..     569     596 .. 0.84
   3 ?    4.7   0.4    0.0038        34       9      20 ..     923     934 ..     922     934 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.09
                         EF-hand_6   8 lfDkdgdGk 16 
                                       ++D+d+dG+
  gi|330506320|ref|YP_004382748.1| 169 YWDRDNDGY 177
                                       57******9 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.049
                         EF-hand_6  10 DkdgdGkidaeElrk 24 
                                       D + dG+i  +El+ 
  gi|330506320|ref|YP_004382748.1| 573 DMNEDGEIQNDELKI 587
                                       6689*********87 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0038
                         EF-hand_6   9 fDkdgdGkidae 20 
                                       fD +++G+id++
  gi|330506320|ref|YP_004382748.1| 923 FDSNRNGTIDRD 934
                                       9*********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (980 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 6341.54
//
Query:       gi|330506321|ref|YP_004382749.1|  [L=375]
Description: transposase, Mutator family [Methanosaeta concilii GP6]
Scores for complete 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-101  338.3   0.1   6.1e-101  338.0   0.1    1.0  1  Transposase_mut  Transposase, Mutator family
    1.2e-09   38.4   0.0    2.1e-09   37.7   0.0    1.4  1  MULE             MULE transposase domain
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.094   13.2   0.0    2.2  2  HTH_26           Cro/C1-type HTH DNA-binding domain
      0.076   13.0   0.9       0.29   11.1   0.1    2.4  3  HTH_12           Ribonuclease R winged-helix domain
       0.16   11.7   0.0        4.7    7.0   0.0    2.7  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus


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 !  338.0   0.1  1.7e-104  6.1e-101      21     380 ..      13     365 ..       6     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 338.0 bits;  conditional E-value: 1.7e-104
                   Transposase_mut  21 gkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspalleryk 97 
                                       + +  lk++++ +l++++  e+  + ga  yers++r+ +RnG r+r+l+Tr+g+l+l+ P+ R+  F+  ++ery 
  gi|330506321|ref|YP_004382749.1|  13 DPNSGLKQVITEFLNAVMLFEAYLQSGALPYERSPQRKAHRNGTRSRTLKTRVGELTLNKPQFREFPFESSVFERYC 89 
                                       567789*********************************************************************** PP

                   Transposase_mut  98 RrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkv 174
                                       R e+al  +++e y++Gvstrk+e+lv++++  + +S+sevS+++k lde+ve+f +R++e k   +l++Da+y kv
  gi|330506321|ref|YP_004382749.1|  90 RVEQALLMTIAESYIQGVSTRKMEELVKNFGL-NRLSASEVSRLCKILDEKVEEFLKRPIEVK-IRYLLVDATYFKV 164
                                       ********************************.77**************************99.************* PP

                   Transposase_mut 175 ReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaa 251
                                       R   + +++a l+ +g+  dG reiLg ++a+sE+   W +++++Lk+rGl+gvelv+sDahkG++ka++ +f +a+
  gi|330506321|ref|YP_004382749.1| 165 RCGAQYKNRALLVVVGIREDGLREILGASIAESEDSGYWMTLFRNLKDRGLEGVELVISDAHKGIQKAVESSFVGAS 241
                                       ***************************************************************************** PP

                   Transposase_mut 252 vQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgk.kypkvaelldeaaedvlaflafp 327
                                       +Q C  H +r +l+ +p k+++++a++lk    a+d e+  ++l++   +l +  y  +ae++d+ + d+ ++ a+p
  gi|330506321|ref|YP_004382749.1| 242 WQYCHFHHSRAVLESIPNKDKQEIADKLKE---ASDDEMKMQELAK---ELRDrGYDPAAETIDRFRFDLWNYKAYP 312
                                       ****************************95...7777776666554...444448********************** PP

                   Transposase_mut 328 eqirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                       ++++++i++tN++Er+Nke++Rr+r vg FP ++s++rl g ++ + ++ew +
  gi|330506321|ref|YP_004382749.1| 313 KAHWKRIRTTNIIERINKELKRRSRPVGAFPSDQSLMRLAGCIMININEEWVT 365
                                       ***************************************************75 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   5.8e-13   2.1e-09       2      94 ..     155     250 ..     154     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 5.8e-13
                              MULE   2 vvlDgTyktnkyklp.....lltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekal 73 
                                       +++D+Ty + ++  +     ll vvg+ + g   +l+  + ese++  +  l+++l+++    +  + +i+D +k++
  gi|330506321|ref|YP_004382749.1| 155 LLVDATYFKVRCGAQyknraLLVVVGIREDGLREILGASIAESEDSGYWMTLFRNLKDRGL--EGVELVISDAHKGI 229
                                       689999998887543333339999**********************************644..69************ PP

                              MULE  74 lnaleevfpeakhrlClfHia 94 
                                       ++a+e+ f +a  + C+fH  
  gi|330506321|ref|YP_004382749.1| 230 QKAVESSFVGASWQYCHFHHS 250
                                       *******************75 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.6e-05     0.094      21      59 ..     106     145 ..     100     147 .. 0.91
   2 ?   -1.1   0.0      0.75   2.7e+03       8      19 ..     274     285 ..     270     302 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.6e-05
                            HTH_26  21 gisaatlsrlvkgk.pervsldtLdkiCdaLgctpgDLle 59 
                                       g+s  +++ lvk+   +r+s+++ +++C++L+ ++++ l+
  gi|330506321|ref|YP_004382749.1| 106 GVSTRKMEELVKNFgLNRLSASEVSRLCKILDEKVEEFLK 145
                                       78999*******97589****************9999875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.75
                            HTH_26   8 drgitkseLarg 19 
                                       d +++ +eLa+ 
  gi|330506321|ref|YP_004382749.1| 274 DDEMKMQELAKE 285
                                       778999999863 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       0.9   3.2e+03      12      45 ..     105     139 ..      95     148 .. 0.62
   2 ?   11.1   0.1   8.2e-05      0.29      10      35 ..     273     298 ..     262     305 .. 0.79
   3 ?   -3.5   0.0       2.9     1e+04       5      15 ..     330     340 ..     326     341 .. 0.46

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.9
                            HTH_12  12 kpigakeiaeeLkkrg.ydigeravRyrLrkleer 45 
                                       + ++ ++++e +k+ g   +++  v +  ++l+e+
  gi|330506321|ref|YP_004382749.1| 105 QGVSTRKMEELVKNFGlNRLSASEVSRLCKILDEK 139
                                       55777777777777741446666677777777776 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8.2e-05
                            HTH_12  10 sdkpigakeiaeeLkkrgydigerav 35 
                                       sd+ +  +e+a+eL++rgyd  ++++
  gi|330506321|ref|YP_004382749.1| 273 SDDEMKMQELAKELRDRGYDPAAETI 298
                                       5778999*************999988 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.9
                            HTH_12   5 kilaesdkpig 15 
                                       k l+++++p+g
  gi|330506321|ref|YP_004382749.1| 330 KELKRRSRPVG 340
                                       33445555555 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 ?    1.3   0.0     0.075   2.7e+02       4      23 ..       2      20 ..       1      28 [. 0.88
   2 ?    7.0   0.0    0.0013       4.7      16      51 ..     102     137 ..      91     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.075
                   Cation_ATPase_N  4 lsleevlekLetdlenGLtq 23
                                      ++le v++ L  d+ +GL+q
  gi|330506321|ref|YP_004382749.1|  2 QPLEPVINYLV-DPNSGLKQ 20
                                      79999*****6.******98 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0013
                   Cation_ATPase_N  16 dlenGLtqaeaaerlkkyGpNelkekkkkslwvkll 51 
                                       +  +G ++   +e+ k +G N+l++ +   l+++l 
  gi|330506321|ref|YP_004382749.1| 102 SYIQGVSTRKMEELVKNFGLNRLSASEVSRLCKILD 137
                                       556899999**************8887777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2612.89
//
Query:       gi|330506322|ref|YP_004382750.1|  [L=1256]
Description: hypothetical protein MCON_0003 [Methanosaeta concilii GP6]
Scores for 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-28   98.2   0.3    8.4e-28   97.5   0.3    1.3  1  Peptidase_S8  Subtilase family
     0.0053   17.0   0.1      0.031   14.6   0.1    2.4  1  Invasin_D3    Invasin, domain 3
     0.0053   17.0   2.3      0.012   15.9   0.1    2.8  4  DUF4959       Domain of unknown function (DUF4959)
     0.0089   16.4   0.6      0.026   14.9   0.2    2.0  2  fn3           Fibronectin type III domain
  ------ inclusion threshold ------
        0.2   11.7   2.8        4.9    7.3   0.0    3.3  3  EF-hand_6     EF-hand domain
       0.67    9.6   2.3         38    4.1   0.0    3.3  3  EF-hand_1     EF hand


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 !   97.5   0.3   2.8e-31   8.4e-28      57     298 .]     175     459 ..      81     459 .. 0.76

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 2.8e-31
                                       S...........................................SS....HHHHHHHHHH-B..SSSSSB-SSTTSE CS
                                       x...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  57 d...........................................ngnsieHGthvAGiaaanapeegekngvapgak 90 
                                       +                                           + ++  HGt +AGi+aa+    ++++g+ap+a+
  gi|330506322|ref|YP_004382750.1| 175 KdgypdesggmvyfiadgkmplplartlygenakipkngelvafHYDDGSHGTMCAGIIAAQ---GKNIKGIAPDAR 248
                                       24455555555555555555555555555555555553333333333334************...************ PP

                                       EEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHH..HHHHHH.CCT-EEEEE--SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  91 ilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsieal..ainravnkkgvlvviSaGNn 165
                                       i  v++  +++   +  + +      +  d++d+i+ s g  + l + g +   +  ++ +++ +  + +v ++GN+
  gi|330506322|ref|YP_004382750.1| 249 IMPVQNSAENDMILCLLASIGYDGVPESGDEADIISRSGG-FSYLFNKGADEGSAflEYLTTNVSPSTTIVYANGND 324
                                       ***********9999986555555555667**********.5555555555555545444555578*********** PP

                                       -T-HHEEE-TTCEECTTTSTTCEEEEEES........TTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 166 gktgsslqagspvgtpstsknvitvgayt........tegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnn 234
                                       g      +   + ++ps s+ vi  ga+           g++  fSsrGp++ g++kp ++a G   ++ +   s++
  gi|330506322|ref|YP_004382750.1| 325 G------SGYGTCQSPS-SEHVINAGAIYdlwwnsssYSGDVICFSSRGPNVLGQVKPNVLATGYL-APRVLPLSET 393
                                       *......8999999**9.677******999******9999************************98.4444444444 PP

                                       HTTTHH.EEEE-SHHHCHHHHHHHHHHHHHHHTT.....--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 235 saglss.yqsmsGTSmAsPnaagaaAlllsalpk.....ltpetvraallntAqdlgkadniesfaqGaG 298
                                       + g+    ++  GTS A+P++a+++Al+ +a+++      t e+ r++l+ +A+d+      e+faqG G
  gi|330506322|ref|YP_004382750.1| 394 HSGKAAwNDMGGGTSSATPHVAAVIALIYQAYKDahgefPTSEKARDILMSSATDI----DEEVFAQGSG 459
                                       444444568999*********************99***99*************998....4589999988 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.1e-05     0.031      22      79 ..    1061    1118 ..    1045    1131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                        Invasin_D3   22 stltvtlkDangnpvsgltvtfsttsagtlsavtdngdGtytatLta.ttagtatitpt 79  
                                          +++ ++D++gn v ++t t   + +gt+++v d  +G  +  Lta +++g ++i+++
  gi|330506322|ref|YP_004382750.1| 1061 FEVKLEVQDKFGNLVENDTATAVIEFNGTTKNV-DLVKGKDSINLTApEKTGIYKIKAQ 1118
                                        5799***************99999999999998.8889******************997 PP

>> DUF4959  Domain of unknown function (DUF4959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.9   5.7e+03      65      90 ..      87     114 ..      76     117 .. 0.74
   2 ?   -2.5   0.0       2.2   6.6e+03      89     106 .]     839     856 ..     813     856 .. 0.76
   3 ?   -3.8   0.0       5.4   1.6e+04      26      52 ..    1092    1118 ..    1087    1123 .. 0.78
   4 !   15.9   0.1     4e-06     0.012      10     106 .]    1160    1256 .]    1153    1256 .] 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.9
                           DUF4959  65 aSvykds..ltveGFgdtkeyevklyav 90 
                                        S+y+d+  +   GF++t++ +  +y +
  gi|330506322|ref|YP_004382750.1|  87 QSRYADTssIDTTGFQTTGTSKSGIYHI 114
                                       5778776336678****99988777765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.2
                           DUF4959  89 avsrseneSepvevkitP 106
                                        vs  ++++e v+vk++P
  gi|330506322|ref|YP_004382750.1| 839 VVSGGNKYGENVTVKVSP 856
                                       467778899999999998 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 5.4
                           DUF4959   26 kvknlpGgavisytlPddedLlyvkae 52  
                                        +v  ++G+  i+ t P+   +  +ka+
  gi|330506322|ref|YP_004382750.1| 1092 NVDLVKGKDSINLTAPEKTGIYKIKAQ 1118
                                        666778999999999998888888875 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 4e-06
                           DUF4959   10 epietd..kaaPgkvtnvkvknlpGgavisytlPddedLlyvkaeYklknGkerevkaSvykdsltveGFgdtke 82  
                                        +p++t+  k+ P+kv+ v+   ++G+  ++++ ++d d   v   Y+lk G + e+ a v + + t++G +  k+
  gi|330506322|ref|YP_004382750.1| 1160 GPASTEqiKDLPKKVESVSSILTSGNISLTWQASEDADYYNV---YRLK-GASLEKLAEVKSPEYTLKG-ELWKS 1229
                                        55555545788***************************8765...9985.*******************.7899* PP

                           DUF4959   83 yevklyavsrseneSe...pvevkitP 106 
                                        y+++++av+r++neSe   pv + +tP
  gi|330506322|ref|YP_004382750.1| 1230 YTFRVSAVNREGNESElsdPVGIVVTP 1256
                                        ************998622266666655 PP

>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.7   5.2e+03      15      33 ..     739     754 ..     738     755 .. 0.87
   2 !   14.9   0.2   8.7e-06     0.026       7      83 ..    1176    1245 ..    1171    1247 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.7
                                       EEEEEEE-CSSSSSTEEEE CS
                               fn3  15 sltvsWeppkdgggpitgY 33 
                                       ++ v We p   + +i+ Y
  gi|330506322|ref|YP_004382750.1| 739 TVEVAWEDP---NTDIDVY 754
                                       6899*****...9999988 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 8.7e-06
                                        EEEEE.SSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEETSE CS
                               fn3    7 svsev.tstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavnggg 80  
                                        svs++ ts +++++W+++     + ++Y+v yr kg    ++   v++++  +tl+g +  + Y++rV avn++g
  gi|330506322|ref|YP_004382750.1| 1176 SVSSIlTSGNISLTWQAS----EDADYYNV-YRLKGASL-EKLAEVKSPE--YTLKG-ELWKSYTFRVSAVNREG 1241
                                        57778899**********....79999**9.88887776.7777888888..*****.8899************8 PP

                                        .EEE CS
                               fn3   81 .egp 83  
                                         e++
  gi|330506322|ref|YP_004382750.1| 1242 nESE 1245
                                        6655 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.32   9.7e+02       8      16 ..     170     178 ..     169     182 .. 0.81
   2 ?    7.3   0.0    0.0017       4.9      10      27 ..     576     593 ..     570     600 .. 0.88
   3 ?    1.7   0.2      0.11   3.2e+02       9      19 ..     926     936 ..     925     937 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.32
                         EF-hand_6   8 lfDkdgdGk 16 
                                       ++D+d+dG+
  gi|330506322|ref|YP_004382750.1| 170 YWDRDKDGY 178
                                       57******9 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0017
                         EF-hand_6  10 DkdgdGkidaeElrkalr 27 
                                       D+d+dG+i   El ++ +
  gi|330506322|ref|YP_004382750.1| 576 DTDRDGEIQELELESIVS 593
                                       9************99987 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.11
                         EF-hand_6   9 fDkdgdGkida 19 
                                       fD +g+G+ d+
  gi|330506322|ref|YP_004382750.1| 926 FDSNGNGTMDW 936
                                       9*******985 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.22   6.7e+02       9      16 ..     171     178 ..     167     178 .. 0.84
   2 ?    4.1   0.0     0.013        38      10      26 ..     576     592 ..     576     594 .. 0.89
   3 ?    2.5   0.1     0.042   1.3e+02       9      18 ..     926     935 ..     925     937 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.22
                                       HTTTSSSE CS
                         EF-hand_1   9 fDkDgdGk 16 
                                        D+D+dG+
  gi|330506322|ref|YP_004382750.1| 171 WDRDKDGY 178
                                       6******8 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.013
                                       TTTSSSEEEHHHHHHHH CS
                         EF-hand_1  10 DkDgdGkIdfeEfkell 26 
                                       D+D+dG I   E+ +++
  gi|330506322|ref|YP_004382750.1| 576 DTDRDGEIQELELESIV 592
                                       9********99998876 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.042
                                       HTTTSSSEEE CS
                         EF-hand_1   9 fDkDgdGkId 18 
                                       fD +g+G++d
  gi|330506322|ref|YP_004382750.1| 926 FDSNGNGTMD 935
                                       9*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.80u 0.31s 00:00:01.11 Elapsed: 00:00:00.45
# Mc/sec: 8297.61
//
Query:       gi|330506323|ref|YP_004382751.1|  [L=694]
Description: acylamino-acid-releasing enzyme [Methanosaeta concilii GP6]
Scores for complete 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  153.7   0.0    6.2e-45  153.3   0.0    1.2  1  Peptidase_S9   Prolyl oligopeptidase family
    3.4e-12   46.5   0.0    3.7e-09   36.6   0.0    2.2  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
      3e-10   40.2   1.9    1.6e-07   31.2   0.3    2.7  3  Abhydrolase_1  alpha/beta hydrolase fold
    4.7e-09   36.1   0.0    2.3e-08   33.9   0.0    2.0  1  DLH            Dienelactone hydrolase family
      5e-08   32.5   0.1     0.0023   17.2   0.1    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
    1.3e-07   32.4   0.1    7.8e-07   29.9   0.1    2.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    0.00036   19.9   0.0     0.0016   17.8   0.0    1.9  2  LIP            Secretory lipase
    0.00054   19.9   0.0     0.0016   18.4   0.0    1.7  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
      0.003   17.5   0.0     0.0089   15.9   0.0    1.7  1  Abhydrolase_3  alpha/beta hydrolase fold
     0.0038   16.0   0.0      0.041   12.6   0.0    2.2  1  AXE1           Acetyl xylan esterase (AXE1)
  ------ inclusion threshold ------
      0.037   13.7   0.0      0.063   12.9   0.0    1.3  1  Esterase       Putative esterase
      0.077   12.2   0.0       0.23   10.6   0.1    1.7  2  DUF2920        Protein of unknown function (DUF2920)


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   0.0   4.2e-48   6.2e-45       3     211 ..     437     650 ..     435     651 .. 0.90

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 4.2e-48
                                       --HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHH CS
                      Peptidase_S9   3 fsselqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltg 79 
                                       ++s  qlla+rGy+v+ +n+rGs+g+G++f++agk ++g +   D+i+++++++k+g++d++r++i+GgSyGGy t+
  gi|330506323|ref|YP_004382751.1| 437 LNSIHQLLANRGYAVLSINFRGSTGFGKNFTNAGKFEYGRKMQYDLIDGVDWAVKKGIADPDRVGIMGGSYGGYATL 513
                                       567789*********************************************************************** PP

                                       HHHHH-GGG-SEEEEESE---CCCHHCSTTS.....THH.HCCCC--TTTCHHHHHHHHHH-CGGG--.---EEEEE CS
                      Peptidase_S9  80 aalnqrpdlFkaavaevpvvdvlrydsdtdl.....lte.eymewgnpeeneegykelspyspldnvk.aypplLli 149
                                       aal+  p++F+++v  +++++++++  +  +     + + +++++  + + +eg++ ls+ spl+  + +  plL+ 
  gi|330506323|ref|YP_004382751.1| 514 AALAFTPEIFACGVDICGMSNLTSSEEN--IppydhWDRvRWTNFVGNISTKEGRELLSERSPLNYANrVRRPLLIA 588
                                       ***********************99988..44467788887776665556666666666666655544599****** PP

                                       EETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHHHCT- CS
                      Peptidase_S9 150 hGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlkealgk 211
                                       +G +D  v  +e++++v a+q+++  v ++ fpdegHg+ +p+++++ +a   aF++++lg 
  gi|330506323|ref|YP_004382751.1| 589 QGANDPIVNQSESAQMVLAMQERNLSVTYVLFPDEGHGFVRPKNNIAFYAVAEAFFAKHLGG 650
                                       ***********************************************************985 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   2.5e-12   3.7e-09      52     139 ..     418     536 ..     354     542 .. 0.76
   2 !    7.8   0.0    0.0015       2.2     209     257 ..     563     612 ..     549     630 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 2.5e-12
                                       H.........................HHHTT-EEEEEE-TTSTT......S-S---TTTTTHHHHHHHHHHHHHHC. CS
                     Peptidase_S15  52 v.........................fvarGYavVvqdvrGtgg......SeGeftvgdsdeaedgadvidWlakq. 96 
                                       +                         +++rGYav+  + rG+ g        G+f+  +++ + d  d +dW++k+ 
  gi|330506323|ref|YP_004382751.1| 418 PlpmvllvhggpegrdywglnsihqlLANRGYAVLSINFRGSTGfgknftNAGKFEY-GRKMQYDLIDGVDWAVKKg 493
                                       055555555555555556666666669**************8651111115566666.9****************** PP

                                       TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TC CS
                     Peptidase_S15  97 pwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdly 139
                                           ++Vg +G SY+G+  l+a+a  ++  ++ v ++++s+l 
  gi|330506323|ref|YP_004382751.1| 494 IADPDRVGIMGGSYGGYATLAALAFTPEIFACGVDICGMSNLT 536
                                       ****************************999999999999876 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0015
                                       -SSSHHHHTT-HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT CS
                     Peptidase_S15 209 gdydafWkdrnlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapg 257
                                       ++ ++   +r++ + a++v+ p+l+++G nD +v   ++ ++  a+++++
  gi|330506323|ref|YP_004382751.1| 563 KEGRELLSERSPLNYANRVRRPLLIAQGANDPIVNqSESAQMVLAMQERN 612
                                       55667788999********************8888888999999999886 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.9   2.8e+03     158     199 ..     109     148 ..      96     153 .. 0.80
   2 !   31.2   0.3   1.1e-10   1.6e-07       1     129 [.     420     554 ..     420     570 .. 0.76
   3 !    7.7   0.0    0.0016       2.4     194     250 ..     571     625 ..     548     628 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.9
                                       HHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHH CS
                     Abhydrolase_1 158 vdalkfpdkskrfpssgsdnasslatgalksieqwpttdsak 199
                                       +d++   d++++ +s +  n++ + +++l+ +++  + +s+k
  gi|330506323|ref|YP_004382751.1| 109 QDKN--GDWNWQVYSVNLSNEKIKNFTHLNGVQTTIQALSFK 148
                                       3444..899999999999999999999999998887777665 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 1.1e-10
                                       SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETT...STTSSSTTTGB.CHHSHHHHHHHHH...HH..HHH CS
                     Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrG...vgySspapacinddygtasvaddld...ri..lda 69 
                                       p ++++hG+p++ d+w  +++ + La +g+ v+ ++ rG   +g+  +   +   +yg  +  d +d   ++  +  
  gi|330506323|ref|YP_004382751.1| 420 PMVLLVHGGPEGRDYWGLNSIHQLLANRGYAVLSINFRGstgFGKNFTNAGK--FEYGRKMQYDLIDgvdWAvkKGI 494
                                       679***********************************82224555555555..77755444444444447766666 PP

                                       CTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHC CS
                     Abhydrolase_1  70 lgddkltlvGhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffd 129
                                        + d++ ++G+S+GG   la++a  pe  ++ v ++++++  s +e  + +++++   + 
  gi|330506323|ref|YP_004382751.1| 495 ADPDRVGIMGGSYGGYATLAALAFTPEIFACGVDICGMSNLTSSEENIPPYDHWDRVRWT 554
                                       6666677***********************999999977766666666666666555555 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0016
                                       HCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHC.HTS....EEEEEEETCSS CS
                     Abhydrolase_1 194 ttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaql.lpk....krlvvisdagH 250
                                       ++   ++ +r r+      p l+ +g++Dp+v  +++ ++  +   +    +++v ++d+gH
  gi|330506323|ref|YP_004382751.1| 571 ERSPLNYANRVRR------PLLIAQGANDPIVNQSESAQMVLAmQ-ErnlsVTYVLFPDEGH 625
                                       4455556666666......**************988888876641.2345699999999999 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   1.5e-11   2.3e-08      21     195 ..     433     633 ..     413     647 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.5e-11
                               DLH  21 eifGvndnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavaylksvpevst 97 
                                       + +G+n+      + la+ GY++l  ++    ++  ++ ++a +   e ++     k+  dl + v+++ +++ +++
  gi|330506323|ref|YP_004382751.1| 433 DYWGLNSI----HQLLANRGYAVLSINFRGSTGF-GKNFTNAGKF--EYGR-----KMQYDLIDGVDWAVKKGIADP 497
                                       56776654....4789999999998776655552.2233333322..3333.....445677778888888888888 PP

                               DLH  98 kkvgvvGfCmGGalalllaaev.pevdaavafYG.....................................lspeke 136
                                       ++vg++G   GG  +l+  a   + +++ v   G                                     ls  ++
  gi|330506323|ref|YP_004382751.1| 498 DRVGIMGGSYGGYATLAALAFTpEIFACGVDICGmsnltsseenippydhwdrvrwtnfvgnistkegrelLSERSP 574
                                       ************99987655554889999*****************************************9999*** PP

                               DLH 137 leeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsre 195
                                       l++a+++  p+l+  g +D++++++e  ++  a++++n  +  +++p+ gH+F++++++
  gi|330506323|ref|YP_004382751.1| 575 LNYANRVRRPLLIAQGANDPIVNQSESAQMVLAMQERNLSVTYVLFPDEGHGFVRPKNN 633
                                       *******************************************************9987 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.5e-06    0.0023       5     102 ..     420     524 ..     416     551 .. 0.85
   2 !   13.1   0.0   2.9e-05     0.044     186     232 ..     577     625 ..     558     630 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-06
                       Hydrolase_4   5 avvvlvHGlae..hsgryaelaeaLaaqGfavyalDhrG...hGrsegkrghvpsfddyvdDlaafvekvkeehpel 76 
                                         v+lvHG  e   ++  + + + La++G+av+ ++ rG   +G++  + g+++   ++  Dl   v+ ++++    
  gi|330506323|ref|YP_004382751.1| 420 PMVLLVHGGPEgrDYWGLNSIHQLLANRGYAVLSINFRGstgFGKNFTNAGKFEYGRKMQYDLIDGVDWAVKKGIAD 496
                                       6799****966336888999****************99544489999**********************99888777 PP

                       Hydrolase_4  77 ..plfllGhSmGGliallyllrypdkva 102
                                         ++ ++G S GG+ +l++l+  p+ +a
  gi|330506323|ref|YP_004382751.1| 497 pdRVGIMGGSYGGYATLAALAFTPEIFA 524
                                       78899************99988887555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.9e-05
                       Hydrolase_4 186 raakitlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyH 232
                                        a++++ Pll+ +G++D++v++++s++++ +++ +   +t+ l+p   H
  gi|330506323|ref|YP_004382751.1| 577 YANRVRRPLLIAQGANDPIVNQSESAQMVLAMQERnlSVTYVLFPDEGH 625
                                       588999*******************999988888745666666666555 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   5.2e-10   7.8e-07       1     102 [.     422     535 ..     422     639 .. 0.63

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 5.2e-10
                                       EEEE--GC.....GCHHHHHHHHCCT.CEEEEE--TTS.T....S-GGCS--HHH......CHHHHHHHCCTT..TT CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaag.vhvlapDlpGh.G....rsdpppldled......ladlaalldelaaggg 65 
                                       vll+HG++ +++ W   +++ lla + ++vl++ ++G  G    ++    +++ +      ++ ++ ++ + +a+++
  gi|330506323|ref|YP_004382751.1| 422 VLLVHGGPEGRDYWGLNSIHQLLANRgYAVLSINFRGStGfgknFTNAGKFEYGRkmqydlIDGVDWAVKKGIADPD 498
                                       89************5568888888888999******88864455333333333333332214555888888888*** PP

                                       SEEEEEETCHHHHHHHHHHCC....EE.EEES-..----T CS
                     Abhydrolase_6  66 pvvlvGHSlGGalalaaapla..lvvg.vlldppptalpa 102
                                       +v ++G S+GG+  laa++ +  + ++ v +++++    +
  gi|330506323|ref|YP_004382751.1| 499 RVGIMGGSYGGYATLAALAFTpeIFACgVDICGMS---NL 535
                                       ***********977775555565444467777733...22 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.1e-06    0.0016      19     104 ..     440     532 ..     436     543 .. 0.87
   2 ?   -1.7   0.0      0.98   1.5e+03     216     252 ..     583     618 ..     575     627 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                               LIP  19 ivplL.keGyyVvvpDyeGpks.........tftvgrqsgkavLdsiraalksekvtgiksdakvalwGYSgGslAs 85 
                                       i +lL ++Gy+V +  + G  +          f  gr+  +  +d++  a+k     gi++  +v+++G S+G+ A+
  gi|330506323|ref|YP_004382751.1| 440 IHQLLaNRGYAVLSINFRGSTGfgknftnagKFEYGRKMQYDLIDGVDWAVK----KGIADPDRVGIMGGSYGGYAT 512
                                       66666258***********9999999999999999************99994....48999**************** PP

                               LIP  86 awAaelqpe.YAPelelvGa 104
                                        +A +  pe +A  +++ G 
  gi|330506323|ref|YP_004382751.1| 513 LAALAFTPEiFACGVDICGM 532
                                       ****9999867888888774 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.98
                               LIP 216 iPvlvyhgvidelipikdakklaknwcdkgiaslefa 252
                                        P+l+++g  d +++ +++ ++     ++   s++++
  gi|330506323|ref|YP_004382751.1| 583 RPLLIAQGANDPIVNQSESAQMVLAMQERNL-SVTYV 618
                                       699***********99999887766666654.66665 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 !   18.4   0.0   1.1e-06    0.0016      10     167 ..     486     631 ..     483     654 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                                       HHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEEETTE..EE----B-GGG-EE-T CS
                            BAAT_C  10 inyllrhpkvkkdkigllGiSkGgelalllasflkkisavvlingsavvvegklvykdeskvlpelklsmeklkvnk 86 
                                       +++  ++     d++g++G S Gg  +l+  +f ++i a+ +  ++  +        +e   +p+ ++  +   +n 
  gi|330506323|ref|YP_004382751.1| 486 VDWAVKKGIADPDRVGIMGGSYGGYATLAALAFTPEIFACGVDICGMSNL----TSSEE--NIPPYDHWDRVRWTNF 556
                                       6666677777889***********99999999999998875555554443....22333..5888888766655688 PP

                                       TS-EE-TT-B--TTTGGGCCCB--GGG--SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S-- CS
                            BAAT_C  87 nglldivdvlallkeklaekalipvekakgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGHli 163
                                        g + +++ ++ll e         + + + p+l+++g +D +++ +esa   ++ L+ ++++ +v+++ +p+ GH +
  gi|330506323|ref|YP_004382751.1| 557 VGNISTKEGRELLSERSPL---NYANRVRRPLLIAQGANDPIVNQSESA---QMVLAMQERNLSVTYVLFPDEGHGF 627
                                       8888888888888655444...46789999***************9999...455777777788***********98 PP

                                       -STT CS
                            BAAT_C 164 epPy 167
                                         P 
  gi|330506323|ref|YP_004382751.1| 628 VRPK 631
                                       8875 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.9e-06    0.0089      51     210 ..     481     628 ..     475     629 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.9e-06
                                       HHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHTT CS
                     Abhydrolase_3  51 dalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepkvagqvliyPvtdlertesesikkaeela 127
                                       d ++ + w++++     adp+r+ ++G S GG  ++a al++  e     a  v i+ + +l ++++e+i      +
  gi|330506323|ref|YP_004382751.1| 481 DLIDGVDWAVKKG---IADPDRVGIMGGSYGGYATLA-ALAFTPE---IFACGVDICGMSNL-TSSEENI-P---PY 545
                                       5666677777774...49**************85554.5566665...57888888888866.3333333.2...22 PP

                                       TSSSSCHHHHHHHHHHHSSGGGGG.STTTSGGGC.S-SST---EEEEEETT-TTHHHHHH..HHHHHHHTT--EEEE CS
                     Abhydrolase_3 128 dgplltraaldlfwrlylpeadrd.dplasplla.edlsglpptlvvvaefDplrdegea..yaerlraagveveli 200
                                       d   + r +   f+  +  ++ r+     spl   ++++   p l++ + +Dp+ +++e   +  ++++ + +v+++
  gi|330506323|ref|YP_004382751.1| 546 D--HWDRVRWTNFVGNISTKEGRElLSERSPLNYaNRVR--RPLLIAQGANDPIVNQSESaqMVLAMQERNLSVTYV 618
                                       3..455444444554444333333234567776624676..9************988776115556668999***** PP

                                       EETTEETTGG CS
                     Abhydrolase_3 201 eyegmvHgfa 210
                                        ++++ Hgf+
  gi|330506323|ref|YP_004382751.1| 619 LFPDEGHGFV 628
                                       *********7 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   2.7e-05     0.041     152     201 ..     476     525 ..     413     602 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEE CS
                              AXE1 152 rrvflDavrlveivaslpevDeeRvavlGasqGGalalavaalekrikav 201
                                       r++  D +  v+ +      D++Rv+++G+s GG  +la+ a+ ++i a 
  gi|330506323|ref|YP_004382751.1| 476 RKMQYDLIDGVDWAVKKGIADPDRVGIMGGSYGGYATLAALAFTPEIFAC 525
                                       67777888888989999999**********************99988665 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.2e-05     0.063     111     211 ..     494     609 ..     467     628 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.2e-05
                                       SEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC.............HCHHHC.TTCCHHHCC-CCCC CS
                          Esterase 111 rtapdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnps.............namWgq.eekeawqendpvll 173
                                         +pd+  ++G S GG++ L + +  p+ F++     ++ n++              + W + + + + +e++++l+
  gi|330506323|ref|YP_004382751.1| 494 IADPDRVGIMGGSYGGYATLAALAFTPEIFACGVDICGMSNLTsseenippydhwdRVRWTNfVGNISTKEGRELLS 570
                                       45677799**********************99888888888888999999955555444444844444446666655 PP

                                       HC..HHCHTTSEEEEEEEECTTBCCCHTSCHHHHHHHHHH CS
                          Esterase 174 ak..elsaslkalriyldvGtseddlgeqlsveilevlar 211
                                       +    ++a++ +   ++ +G +++ +++  s++    + +
  gi|330506323|ref|YP_004382751.1| 571 ERspLNYANRVRRPLLIAQGANDPIVNQSESAQMVL-AMQ 609
                                       531145667777778889999998777655554433.333 PP

>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00015      0.23     161     212 ..     480     530 ..     468     537 .. 0.79
   2 ?   -2.6   0.0       1.6   2.4e+03     293     325 ..     590     623 ..     571     625 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                           DUF2920 161 lDiinalkdlvkrfpkeadlpviliGgsyGGYlalLiaKiaPwyvdgvlDns 212
                                        D+i  ++ +vk+   +  + v ++GgsyGGY +l +  + P ++   +D  
  gi|330506323|ref|YP_004382751.1| 480 YDLIDGVDWAVKKGIADP-DRVGIMGGSYGGYATLAALAFTPEIFACGVDIC 530
                                       699999999999988887.55666799*****98888899999987776655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                           DUF2920 293 sekDklapaeeKiqlakilkklgfdveleli.de 325
                                         +D+++   e  q++ +++++++ v+  l+ de
  gi|330506323|ref|YP_004382751.1| 590 GANDPIVNQSESAQMVLAMQERNLSVTYVLFpDE 623
                                       56899999999999999****9999998888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (694 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 4544.97
//
Query:       gi|330506324|ref|YP_004382752.1|  [L=102]
Description: hypothetical protein MCON_0005 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.0   0.0      0.089   12.5   0.0    1.5  1  TRAM1     TRAM1-like protein


Domain annotation for each model (and alignments):
>> TRAM1  TRAM1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     5e-06     0.089      14      34 ..      54      74 ..       5      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-06
                             TRAM1 14 sansetglYgkGlkDlafvff 34
                                      + ++++g Yg+Gl+D a+++f
  gi|330506324|ref|YP_004382752.1| 54 EVPTGPGSYGIGLNDTAYIVF 74
                                      556799*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 786.90
//
Query:       gi|330506325|ref|YP_004382753.1|  [L=315]
Description: hypothetical protein MCON_0006 [Methanosaeta concilii GP6]
Scores for complete 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  138.4   9.4    8.8e-06   25.3   0.0    8.3  8  TPR_1            Tetratricopeptide repeat
    2.1e-35  118.0  11.1    0.00012   22.0   0.0    9.3  8  TPR_8            Tetratricopeptide repeat
    2.2e-35  117.9  13.0    5.6e-05   23.0   0.0    8.4  8  TPR_2            Tetratricopeptide repeat
    3.7e-31  106.5  10.2     0.0001   21.9   0.1    7.3  7  TPR_11           TPR repeat
    5.1e-31  104.8   9.5    4.7e-06   26.6   0.4    7.2  7  TPR_17           Tetratricopeptide repeat
    2.8e-28   98.2   9.7    2.4e-09   37.6   0.1    5.1  5  TPR_19           Tetratricopeptide repeat
    1.1e-26   93.2  12.2    2.2e-07   31.4   0.0    5.3  5  TPR_16           Tetratricopeptide repeat
    8.9e-26   88.4  12.3    1.1e-05   25.9   0.3    8.0  8  TPR_14           Tetratricopeptide repeat
    1.7e-20   73.0   9.5    7.8e-05   22.9   0.0    5.5  5  TPR_12           Tetratricopeptide repeat
    2.1e-20   72.7   1.9    1.1e-05   25.5   0.3    4.1  4  TPR_9            Tetratricopeptide repeat
    5.1e-18   65.1   4.9    4.5e-06   26.8   0.2    4.1  4  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    4.1e-15   55.3  10.1       0.26   12.0   0.0    8.4  8  TPR_6            Tetratricopeptide repeat
    1.2e-11   44.5   2.3     0.0061   16.6   0.0    4.5  5  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    2.3e-10   40.1   2.0     0.0056   15.7   0.0    4.0  4  NARP1            NMDA receptor-regulated protein 1
    2.7e-10   40.5   1.8       0.11   12.9   0.1    4.6  5  TPR_20           Tetratricopeptide repeat
    5.2e-09   36.7   6.5      9e-05   22.9   2.9    3.3  3  BTAD             Bacterial transcriptional activator domain
      1e-08   35.3   8.4          1    9.4   0.0    6.1  5  DUF3856          Domain of Unknown Function (DUF3856)
    4.9e-08   32.9   2.7      0.023   15.3   0.0    6.0  5  TPR_4            Tetratricopeptide repeat
    1.1e-06   28.2   6.2         23    5.3   0.0    7.7  8  TPR_7            Tetratricopeptide repeat
    1.4e-06   27.9  13.7        4.7    7.2   0.0    7.2  7  TPR_10           Tetratricopeptide repeat
      3e-06   27.7   4.0       0.31   11.5   0.1    4.5  5  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    3.7e-05   23.7   0.3      0.018   15.0   0.0    2.9  4  SRP_TPR_like     Putative TPR-like repeat
    0.00011   21.3   0.3       0.01   14.8   0.0    2.5  3  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
    0.00091   19.0   2.1       0.63    9.7   0.2    4.1  3  RPN7             26S proteasome subunit RPN7
     0.0028   17.6   1.0         34    4.6   0.0    4.5  4  TPR_3            Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.018   15.2   0.4        3.4    7.9   0.0    3.1  3  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
      0.019   14.8   1.5          2    8.2   0.0    3.8  4  DUF5113          Domain of unknown function (DUF5113)
       0.02   14.1   8.5        4.6    6.4   7.2    2.8  2  TPR_15           Tetratricopeptide repeat
      0.027   14.2   2.3        6.2    6.5   0.1    3.2  3  YfiO             Outer membrane lipoprotein
      0.036   13.8   3.7       0.19   11.4   0.1    3.0  2  DUF2225          Uncharacterized protein conserved in bacteri
      0.044   13.4   0.1        0.2   11.3   0.0    2.1  2  HrpB1_HrpK       Bacterial type III secretion protein (HrpB1_
      0.097   12.8   0.4         52    4.0   0.0    3.9  4  ANAPC5           Anaphase-promoting complex subunit 5


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 !   12.1   0.0   0.00024      0.14      19      33 ..      56      70 ..      54      71 .. 0.91
   2 !   24.8   0.0   2.2e-08   1.3e-05       3      32 ..      74     103 ..      72     105 .. 0.96
   3 !   16.3   0.0   1.1e-05    0.0064       1      33 [.     106     138 ..     106     139 .. 0.97
   4 !   25.3   0.0   1.6e-08   8.8e-06       2      33 ..     141     172 ..     140     173 .. 0.96
   5 !   10.3   0.1   0.00088      0.49      19      34 .]     202     217 ..     201     217 .. 0.91
   6 !   21.9   0.1   1.9e-07   0.00011       1      32 [.     218     249 ..     218     251 .. 0.96
   7 !   18.7   0.0     2e-06    0.0011       2      34 .]     253     285 ..     252     285 .. 0.95
   8 !    7.2   0.0    0.0087       4.9       2      26 ..     287     311 ..     286     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                                      HHHHHHHHHHHHSTT CS
                             TPR_1 19 eAleyyekALelnPn 33
                                      +A+e yekA++++P+
  gi|330506325|ref|YP_004382753.1| 56 DAVESYEKAIQIEPH 70
                                      8*************7 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 2.2e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                       a+  ++ ayf++g+y eAl+  ++ +e++P
  gi|330506325|ref|YP_004382753.1|  74 AWLKKAIAYFEMGNYIEALDSVNRSIEIDP 103
                                       9****************************9 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+aly ++  y + g+  +Al+++++ Le++P+
  gi|330506325|ref|YP_004382753.1| 106 ADALYMKAGFYGETGRTRDALQAFNETLEVDPE 138
                                       89******************************6 PP

  == domain 4  score: 25.3 bits;  conditional E-value: 1.6e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                       +a++ ++  + ++g y+eAl +y++ +e++P+
  gi|330506325|ref|YP_004382753.1| 141 DAWFWKADFLASMGSYEEALNAYNRTIEIDPE 172
                                       89*****************************7 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00088
                                       HHHHHHHHHHHHSTTH CS
                             TPR_1  19 eAleyyekALelnPnn 34 
                                        A e y+kA+e nPn+
  gi|330506325|ref|YP_004382753.1| 202 MAAETYDKAIEQNPND 217
                                       5999**********97 PP

  == domain 6  score: 21.9 bits;  conditional E-value: 1.9e-07
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+a++++G  +  +g+ydeA  + ++ +el P
  gi|330506325|ref|YP_004382753.1| 218 ANAWFGKGCNLNDQGRYDEAAVALNRSVELAP 249
                                       79****************************99 PP

  == domain 7  score: 18.7 bits;  conditional E-value: 2e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +a+y +++a+   g+y+eA+   +k Le nP++
  gi|330506325|ref|YP_004382753.1| 253 NAWYFRAVALNATGRYEEAVRSLDKFLEANPEH 285
                                       79**************************99986 PP

  == domain 8  score: 7.2 bits;  conditional E-value: 0.0087
                                       HHHHHHHHHHHHTT-HHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyek 26 
                                        a++ +G a+  lg+ +eA  ++e 
  gi|330506325|ref|YP_004382753.1| 287 LAWKLKGEALSALGRDKEAQSAFEM 311
                                       59*****************999985 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0     0.004       2.2      19      32 ..      56      69 ..      54      71 .. 0.89
   2 !   17.5   0.0     6e-06    0.0034       3      33 ..      74     104 ..      72     105 .. 0.95
   3 !   12.2   0.0   0.00031      0.17       1      33 [.     106     138 ..     106     139 .. 0.96
   4 !   22.0   0.0   2.2e-07   0.00012       2      33 ..     141     172 ..     140     173 .. 0.96
   5 ?    6.4   0.5     0.021        12       2      23 ..     178     199 ..     177     217 .. 0.56
   6 !   19.1   0.0   1.9e-06    0.0011       1      33 [.     218     250 ..     218     251 .. 0.95
   7 !   20.5   0.0   6.7e-07   0.00037       2      34 .]     253     285 ..     252     285 .. 0.95
   8 ?    5.8   0.1     0.033        18       6      25 ..     291     310 ..     288     310 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.004
                                      HHHHHHHHHHHHHH CS
                             TPR_8 19 eAkeyyekaleldp 32
                                       A+e+yeka++++p
  gi|330506325|ref|YP_004382753.1| 56 DAVESYEKAIQIEP 69
                                      59**********99 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 6e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+++++ +y+++g+y eA  + ++ +e+dp 
  gi|330506325|ref|YP_004382753.1|  74 AWLKKAIAYFEMGNYIEALDSVNRSIEIDPV 104
                                       89***************************96 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00031
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+a+y+++  y ++g+   A +++++ le dp+
  gi|330506325|ref|YP_004382753.1| 106 ADALYMKAGFYGETGRTRDALQAFNETLEVDPE 138
                                       789****************************96 PP

  == domain 4  score: 22.0 bits;  conditional E-value: 2.2e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a++++++ + ++g yeeA  +y++ +e+dp+
  gi|330506325|ref|YP_004382753.1| 141 DAWFWKADFLASMGSYEEALNAYNRTIEIDPE 172
                                       79*****************************7 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.021
                                       CHHHHHHHHHHHTT-HHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkey 23 
                                       +++  ++++++k+g  ++Ak++
  gi|330506325|ref|YP_004382753.1| 178 RSWDSKSYVLKKMGLEDQAKSA 199
                                       6666677777777777777654 PP

  == domain 6  score: 19.1 bits;  conditional E-value: 1.9e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a a++ +g+ + ++g+y+eA  ++++ +el+p+
  gi|330506325|ref|YP_004382753.1| 218 ANAWFGKGCNLNDQGRYDEAAVALNRSVELAPA 250
                                       679****************************97 PP

  == domain 7  score: 20.5 bits;  conditional E-value: 6.7e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        a+y  + ++  +g+yeeA+ ++ k le++p++
  gi|330506325|ref|YP_004382753.1| 253 NAWYFRAVALNATGRYEEAVRSLDKFLEANPEH 285
                                       69*****************************86 PP

  == domain 8  score: 5.8 bits;  conditional E-value: 0.033
                                       HHHHHHHHTT-HHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyye 25 
                                       ++g +++ lg+ +eA++++e
  gi|330506325|ref|YP_004382753.1| 291 LKGEALSALGRDKEAQSAFE 310
                                       799***************97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0032       1.8      19      33 ..      56      70 ..      53      71 .. 0.90
   2 !   21.0   0.0   4.3e-07   0.00024       2      32 ..      73     103 ..      72     103 .. 0.96
   3 !   12.7   0.0   0.00018       0.1       1      33 [.     106     138 ..     106     139 .. 0.95
   4 !   23.0   0.0     1e-07   5.6e-05       2      33 ..     141     172 ..     140     173 .. 0.96
   5 !    8.1   0.1    0.0055       3.1      19      34 .]     202     217 ..     179     217 .. 0.94
   6 !   18.1   0.1   3.6e-06     0.002       1      33 [.     218     250 ..     218     251 .. 0.95
   7 !   19.2   0.1   1.6e-06    0.0009       3      34 .]     254     285 ..     252     285 .. 0.96
   8 !    8.4   0.0    0.0045       2.5       2      25 ..     287     310 ..     286     312 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0032
                             TPR_2 19 eAleafekAleldPn 33
                                      +A+e +ekA++++P+
  gi|330506325|ref|YP_004382753.1| 56 DAVESYEKAIQIEPH 70
                                      8************97 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 4.3e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                        a+   + ay+++g+y eAl+  ++++e+dP
  gi|330506325|ref|YP_004382753.1|  73 LAWLKKAIAYFEMGNYIEALDSVNRSIEIDP 103
                                       5899**************************9 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00018
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+aly+ +  y + g+  +Al+af++ le dP+
  gi|330506325|ref|YP_004382753.1| 106 ADALYMKAGFYGETGRTRDALQAFNETLEVDPE 138
                                       789*****************************7 PP

  == domain 4  score: 23.0 bits;  conditional E-value: 1e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +a+++ ++ ++ +g yeeAl+a+++ +e+dP+
  gi|330506325|ref|YP_004382753.1| 141 DAWFWKADFLASMGSYEEALNAYNRTIEIDPE 172
                                       69*****************************7 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0055
                             TPR_2  19 eAleafekAleldPnn 34 
                                        A+e ++kA+e +Pn+
  gi|330506325|ref|YP_004382753.1| 202 MAAETYDKAIEQNPND 217
                                       599***********97 PP

  == domain 6  score: 18.1 bits;  conditional E-value: 3.6e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a++  G+ +  +g+y+eA+ a+++++el+P 
  gi|330506325|ref|YP_004382753.1| 218 ANAWFGKGCNLNDQGRYDEAAVALNRSVELAPA 250
                                       689****************************95 PP

  == domain 7  score: 19.2 bits;  conditional E-value: 1.6e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+y ++ a+ + g+yeeA++ ++k le +P++
  gi|330506325|ref|YP_004382753.1| 254 AWYFRAVALNATGRYEEAVRSLDKFLEANPEH 285
                                       9*****************************86 PP

  == domain 8  score: 8.4 bits;  conditional E-value: 0.0045
                             TPR_2   2 ealynlGlayyklgdyeeAleafe 25 
                                        a+   G+a+ +lg+ +eA  afe
  gi|330506325|ref|YP_004382753.1| 287 LAWKLKGEALSALGRDKEAQSAFE 310
                                       5899******************98 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.3e-07   0.00013      11      42 .]      55      86 ..      54      86 .. 0.96
   2 !   17.9   0.1   3.2e-06    0.0018       3      32 ..      81     110 ..      79     113 .. 0.97
   3 !   10.1   0.0   0.00087      0.49       6      40 ..     118     152 ..     116     154 .. 0.85
   4 !   21.9   0.1   1.8e-07    0.0001       4      29 ..     150     175 ..     147     176 .. 0.88
   5 !   18.0   0.1     3e-06    0.0017      13      35 ..     203     225 ..     201     226 .. 0.93
   6 !   20.0   0.1   7.4e-07   0.00042       5      39 ..     229     263 ..     227     266 .. 0.90
   7 !    7.9   0.0    0.0042       2.3       4      42 .]     262     300 ..     261     300 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.3e-07
                            TPR_11 11 eeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      ++A+e+Y+kA+++ P +  a+++ + ay+++G
  gi|330506325|ref|YP_004382753.1| 55 TDAVESYEKAIQIEPHSSLAWLKKAIAYFEMG 86
                                      78****************************99 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.2e-06
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayy 32 
                                       ay+e G+y eA+ + ++ +++dP na+a+y
  gi|330506325|ref|YP_004382753.1|  81 AYFEMGNYIEALDSVNRSIEIDPVNADALY 110
                                       8***************************99 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00087
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       e G+  +A++a+++ l+ dP+  +a+++ ++ ++ 
  gi|330506325|ref|YP_004382753.1| 118 ETGRTRDALQAFNETLEVDPERIDAWFWKADFLAS 152
                                       5689999********************98776655 PP

  == domain 4  score: 21.9 bits;  conditional E-value: 1.8e-07
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnae 29 
                                       + + G yeeA++aY++ +++dP++ +
  gi|330506325|ref|YP_004382753.1| 150 LASMGSYEEALNAYNRTIEIDPESMN 175
                                       5689******************9865 PP

  == domain 5  score: 18.0 bits;  conditional E-value: 3e-06
                            TPR_11  13 AieaYkkAlkldPdnaeayynLG 35 
                                       A e Y kA++ +P++a+a+++ G
  gi|330506325|ref|YP_004382753.1| 203 AAETYDKAIEQNPNDANAWFGKG 225
                                       889****************9876 PP

  == domain 6  score: 20.0 bits;  conditional E-value: 7.4e-07
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                        +qG+y+eA  a+++ ++l P + +a+y +++a+ 
  gi|330506325|ref|YP_004382753.1| 229 NDQGRYDEAAVALNRSVELAPAFINAWYFRAVALN 263
                                       68**************************9999875 PP

  == domain 7  score: 7.9 bits;  conditional E-value: 0.0042
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       + + G+yeeA+ ++ k l+ +P+   a+   G+a+ ++G
  gi|330506325|ref|YP_004382753.1| 262 LNATGRYEEAVRSLDKFLEANPEHSLAWKLKGEALSALG 300
                                       6688***********999999988777777777776665 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   3.2e-06    0.0018       2      33 ..      61      92 ..      60      93 .. 0.96
   2 !   17.8   0.0   5.3e-06     0.003       4      34 .]      97     127 ..      96     127 .. 0.96
   3 !   12.5   0.0   0.00027      0.15       2      33 ..     129     160 ..     128     161 .. 0.93
   4 ?    5.5   0.0     0.045        25       1      32 [.     162     196 ..     162     198 .. 0.85
   5 !   26.6   0.4   8.4e-09   4.7e-06       1      32 [.     206     237 ..     206     238 .. 0.97
   6 ?    6.2   0.0     0.028        16       3      33 ..     242     272 ..     240     273 .. 0.92
   7 !   17.1   0.0   9.2e-06    0.0051       3      33 ..     276     306 ..     275     307 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.2e-06
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      y+ka++++P ++ a+  +A ++ + G++ +A+
  gi|330506325|ref|YP_004382753.1| 61 YEKAIQIEPHSSLAWLKKAIAYFEMGNYIEAL 92
                                      9***************************9996 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 5.3e-06
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +++e+dP nada++++A ++ + G++++A+q
  gi|330506325|ref|YP_004382753.1|  97 RSIEIDPVNADALYMKAGFYGETGRTRDALQ 127
                                       89***************************87 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00027
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + + le dP   da++ +A +l++ G +++A+
  gi|330506325|ref|YP_004382753.1| 129 FNETLEVDPERIDAWFWKADFLASMGSYEEAL 160
                                       67889************************995 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.045
                            TPR_17   1 lylkaleldPnn...adaynnLAelllknGdlmtA 32 
                                       +y + +e+dP +   a ++  + ++l+k G  ++A
  gi|330506325|ref|YP_004382753.1| 162 AYNRTIEIDPESmnaARSWDSKSYVLKKMGLEDQA 196
                                       599*********99999999999999998877766 PP

  == domain 5  score: 26.6 bits;  conditional E-value: 8.4e-09
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y ka+e++Pn+a+a++ ++  l  +G++++A
  gi|330506325|ref|YP_004382753.1| 206 TYDKAIEQNPNDANAWFGKGCNLNDQGRYDEA 237
                                       69****************************98 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.028
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtAr 33 
                                        +++el P   +a++ +A++l   G++++A+
  gi|330506325|ref|YP_004382753.1| 242 NRSVELAPAFINAWYFRAVALNATGRYEEAV 272
                                       6899*************************96 PP

  == domain 7  score: 17.1 bits;  conditional E-value: 9.2e-06
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtAr 33 
                                        k+le +P ++ a+ +++e+l+ +G+ ++A+
  gi|330506325|ref|YP_004382753.1| 276 DKFLEANPEHSLAWKLKGEALSALGRDKEAQ 306
                                       699**************************98 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.2e-09   1.2e-06       8      61 ..      55     108 ..      54     114 .. 0.91
   2 !   26.2   0.0   1.5e-08   8.4e-06       5      58 ..     120     173 ..     118     179 .. 0.92
   3 ?    6.7   0.2     0.019        11       8      29 ..     201     222 ..     187     225 .. 0.84
   4 !   37.6   0.1   4.3e-12   2.4e-09       3      65 ..     230     292 ..     228     294 .. 0.96
   5 !    9.4   0.1    0.0026       1.5      18      49 ..     279     310 ..     277     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.2e-09
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       ++A++ +e+a+q +p+++ a+l  A+a++++g++ eA + +++  e dp +a++
  gi|330506325|ref|YP_004382753.1|  55 TDAVESYEKAIQIEPHSSLAWLKKAIAYFEMGNYIEALDSVNRSIEIDPVNADA 108
                                       79********************************************99986655 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 1.5e-08
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       g+  +Al+++ + l+ dp+  +a+ + A+ l ++g ++eA ++ ++  e dp +
  gi|330506325|ref|YP_004382753.1| 120 GRTRDALQAFNETLEVDPERIDAWFWKADFLASMGSYEEALNAYNRTIEIDPES 173
                                       8999******************************************99999985 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.019
                            TPR_19   8 aeAlalleqalqedpknaearl 29 
                                       a A++ + +a++++p++a+a+ 
  gi|330506325|ref|YP_004382753.1| 201 AMAAETYDKAIEQNPNDANAWF 222
                                       457999999*********9986 PP

  == domain 4  score: 37.6 bits;  conditional E-value: 4.3e-12
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLl 65 
                                       ++g+y+eA+ +l +  + +p   +a++  A al a+g+++eA + Ld+ +e++p ++ +++L+
  gi|330506325|ref|YP_004382753.1| 230 DQGRYDEAAVALNRSVELAPAFINAWYFRAVALNATGRYEEAVRSLDKFLEANPEHSLAWKLK 292
                                       89*******************************************************999998 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.0026
                            TPR_19  18 lqedpknaearllLAeallalgqldeAealLd 49 
                                       l+++p+++ a+ l  eal alg+ +eA+ + +
  gi|330506325|ref|YP_004382753.1| 279 LEANPEHSLAWKLKGEALSALGRDKEAQSAFE 310
                                       678************************98766 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00015     0.085      14      65 ..      55     103 ..      49     106 .. 0.93
   2 !   13.5   0.0   0.00015     0.086       1      41 [.      76     113 ..      76     116 .. 0.94
   3 !   31.4   0.0     4e-10   2.2e-07       2      65 ..     111     171 ..     110     173 .. 0.88
   4 !   24.1   1.4   7.2e-08   4.1e-05      16      65 ..     203     249 ..     195     251 .. 0.91
   5 !   26.1   1.1   1.8e-08     1e-05      10      54 ..     265     306 ..     258     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00015
                            TPR_16  14 ddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +dA++ +e a+      P    A+l ++ a+++ g++ eA++ +++ ++ +p
  gi|330506325|ref|YP_004382753.1|  55 TDAVESYEKAIQIE---PHSSLAWLKKAIAYFEMGNYIEALDSVNRSIEIDP 103
                                       79************...99999*******************99999999998 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00015
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllg 41 
                                       l++a a+++ g+y +A+   ++ ++ d   P++a+Al+ ++
  gi|330506325|ref|YP_004382753.1|  76 LKKAIAYFEMGNYIEALDSVNRSIEID---PVNADALYMKA 113
                                       6899***********************...********887 PP

  == domain 3  score: 31.4 bits;  conditional E-value: 4e-10
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       ++a  + + g+ +dA+ a++++l+ d   P++ +A+++++d ++  g ++eA+ +y++ ++ +p
  gi|330506325|ref|YP_004382753.1| 111 MKAGFYGETGRTRDALQAFNETLEVD---PERIDAWFWKADFLASMGSYEEALNAYNRTIEIDP 171
                                       666668889*****************...************************66666668887 PP

  == domain 4  score: 24.1 bits;  conditional E-value: 7.2e-08
                            TPR_16  16 AaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       Aa+ ++ a++++   P +a A++++g  +  qgr++eAa ++++ ++ ap
  gi|330506325|ref|YP_004382753.1| 203 AAETYDKAIEQN---PNDANAWFGKGCNLNDQGRYDEAAVALNRSVELAP 249
                                       999*********...************************66666668887 PP

  == domain 5  score: 26.1 bits;  conditional E-value: 1.8e-08
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                                        g+y++A++ l+ +l+++   P++  A+ l+g+a+ ++gr +eA 
  gi|330506325|ref|YP_004382753.1| 265 TGRYEEAVRSLDKFLEAN---PEHSLAWKLKGEALSALGRDKEAQ 306
                                       69****************...*********************995 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0016      0.91      17      42 ..      54      79 ..      39      80 .. 0.89
   2 !   16.8   0.0   1.5e-05    0.0085       3      42 ..      74     113 ..      72     114 .. 0.94
   3 !   15.8   0.1   3.3e-05     0.018       2      43 ..     107     148 ..     106     149 .. 0.94
   4 !   14.1   0.0   0.00011     0.062       2      36 ..     141     175 ..     140     180 .. 0.90
   5 !   10.6   0.0    0.0015      0.82      19      40 ..     202     223 ..     188     225 .. 0.86
   6 !   13.8   0.2   0.00015     0.081      12      42 ..     229     259 ..     228     260 .. 0.91
   7 !   25.9   0.3   1.9e-08   1.1e-05       2      43 ..     253     294 ..     252     295 .. 0.95
   8 ?    4.8   0.1      0.11        63       3      26 ..     288     311 ..     288     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0016
                            TPR_14 17 pdeAiallrralalaPddaeawllla 42
                                      + +A++ +++a++  P +  awl  a
  gi|330506325|ref|YP_004382753.1| 54 LTDAVESYEKAIQIEPHSSLAWLKKA 79
                                      579*******************9876 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.5e-05
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       a+l+ a a+++ G++ eA++  +r ++ +P +a+a+++ a
  gi|330506325|ref|YP_004382753.1|  74 AWLKKAIAYFEMGNYIEALDSVNRSIEIDPVNADALYMKA 113
                                       8*****************************9999998876 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 3.3e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +al++ a ++ + G++++A++++++ l+ +P+  +aw+  a+
  gi|330506325|ref|YP_004382753.1| 107 DALYMKAGFYGETGRTRDALQAFNETLEVDPERIDAWFWKAD 148
                                       799**********************************98875 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 0.00011
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddae 36 
                                       +a+   a++l+  G ++eA+++++r ++ +P++  
  gi|330506325|ref|YP_004382753.1| 141 DAWFWKADFLASMGSYEEALNAYNRTIEIDPESMN 175
                                       699999*************************9864 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.0015
                            TPR_14  19 eAiallrralalaPddaeawll 40 
                                        A++ +++a++++P+da aw+ 
  gi|330506325|ref|YP_004382753.1| 202 MAAETYDKAIEQNPNDANAWFG 223
                                       4999****************86 PP

  == domain 6  score: 13.8 bits;  conditional E-value: 0.00015
                            TPR_14  12 lalGdpdeAiallrralalaPddaeawllla 42 
                                         +G++deA+ +l+r ++laP++  aw++ a
  gi|330506325|ref|YP_004382753.1| 229 NDQGRYDEAAVALNRSVELAPAFINAWYFRA 259
                                       579************************8876 PP

  == domain 7  score: 25.9 bits;  conditional E-value: 1.9e-08
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +a++ +a al a G+++eA++ l++ l+++P++  aw l ++
  gi|330506325|ref|YP_004382753.1| 253 NAWYFRAVALNATGRYEEAVRSLDKFLEANPEHSLAWKLKGE 294
                                       79***********************************99886 PP

  == domain 8  score: 4.8 bits;  conditional E-value: 0.11
                            TPR_14   3 allalaeallalGdpdeAiallrr 26 
                                       a+++ +eal alG+ +eA  +++ 
  gi|330506325|ref|YP_004382753.1| 288 AWKLKGEALSALGRDKEAQSAFEM 311
                                       79999*************999885 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00011     0.064       5      74 ..      74     101 ..      54     103 .. 0.55
   2 !   22.9   0.0   1.4e-07   7.8e-05       5      76 ..      74     137 ..      70     138 .. 0.91
   3 !   15.1   0.4   3.9e-05     0.022       8      75 ..     145     207 ..     139     209 .. 0.89
   4 !   20.7   0.3   6.5e-07   0.00037      10      76 ..     184     249 ..     175     250 .. 0.89
   5 !   19.4   0.2   1.7e-06   0.00093       4      70 ..     253     311 ..     251     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       a+ + a +++++g+y eAl+  +++                                          ++i
  gi|330506325|ref|YP_004382753.1|  74 AWLKKAIAYFEMGNYIEALDSVNRS------------------------------------------IEI 101
                                       3334555555555555555555555..........................................554 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.4e-07
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a+ + a +++++g+y eAl+  ++++ei      p +   a +l+  +  y ++gr+++Al++++e+l++++
  gi|330506325|ref|YP_004382753.1|  74 AWLKKAIAYFEMGNYIEALDSVNRSIEID-----PVN---ADALYMKAGFYGETGRTRDALQAFNETLEVDP 137
                                       66689************************.....765...999*************************9875 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 3.9e-05
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                         a++l+ +g y+eAl  +++ +ei      p++ ++a++    + ++ ++g  ++A ++   a + +
  gi|330506325|ref|YP_004382753.1| 145 WKADFLASMGSYEEALNAYNRTIEID-----PESMNAARSWDSKSYVLKKMGLEDQAKSAAAMAAETY 207
                                       57999*********************.....99**********9999999999999999888887766 PP

  == domain 4  score: 20.7 bits;  conditional E-value: 6.5e-07
                            TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                         vl ++g  d+A +    a e + ++  +++p+ a++ ++ g  +  +gry+eA  +l++++++a+
  gi|330506325|ref|YP_004382753.1| 184 SYVLKKMGLEDQAKSAAAMAAETYDKAI-EQNPNDANAWFGKGCNLNDQGRYDEAAVALNRSVELAP 249
                                       5689999*****************6664.89*********************************986 PP

  == domain 5  score: 19.4 bits;  conditional E-value: 1.7e-06
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlellee 70 
                                       +a++ +a++l++ gry+eA + l+k le+      p+h   + +    g++++algr +eA++++e 
  gi|330506325|ref|YP_004382753.1| 253 NAWYFRAVALNATGRYEEAVRSLDKFLEAN-----PEH---SLAWKLKGEALSALGRDKEAQSAFEM 311
                                       678899************************.....999...779999999999**********9996 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0     3e-07   0.00017      14      69 ..      57     112 ..      53     115 .. 0.93
   2 !   20.9   0.0   5.4e-07    0.0003      10      66 ..     121     177 ..     114     179 .. 0.92
   3 !   10.3   0.1    0.0011       0.6      12      61 ..     201     250 ..     195     254 .. 0.90
   4 !   25.5   0.3   1.9e-08   1.1e-05       8      63 ..     231     286 ..     228     294 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3e-07
                             TPR_9  14 alavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeair 69 
                                       a + +e  +++ P++   ++  +++++++G++ +Al+  ++ ++++p ++da  ++
  gi|330506325|ref|YP_004382753.1|  57 AVESYEKAIQIEPHSSLAWLKKAIAYFEMGNYIEALDSVNRSIEIDPVNADALYMK 112
                                       77889999***************************************999998776 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.4e-07
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                                       +   al++ +  l ++P++++ ++  +  la +G +++Al++ ++ ++++p+   a+
  gi|330506325|ref|YP_004382753.1| 121 RTRDALQAFNETLEVDPERIDAWFWKADFLASMGSYEEALNAYNRTIEIDPESMNAA 177
                                       66789**********************************************988776 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0011
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       + a ++++  +  +P+d+  ++  G  l  +G++ +A+ +L++ ++lap+
  gi|330506325|ref|YP_004382753.1| 201 AMAAETYDKAIEQNPNDANAWFGKGCNLNDQGRYDEAAVALNRSVELAPA 250
                                       5678889999999*********************************9995 PP

  == domain 4  score: 25.5 bits;  conditional E-value: 1.9e-08
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       + ++++a  +++r + laP  +  ++ R+++l   G++++A++ L+ +l+ +p+  
  gi|330506325|ref|YP_004382753.1| 231 QGRYDEAAVALNRSVELAPAFINAWYFRAVALNATGRYEEAVRSLDKFLEANPEHS 286
                                       568999**********************************************9865 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.5e-06   0.00083       7      81 ..      56     131 ..      51     132 .. 0.89
   2 !   18.7   0.0   2.8e-06    0.0015       2      59 ..     119     177 ..     118     191 .. 0.90
   3 !   20.8   0.3     6e-07   0.00033       8      81 ..     203     277 ..     193     278 .. 0.84
   4 !   26.8   0.2   8.1e-09   4.5e-06       1      80 [.     230     310 ..     230     312 .. 0.97

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3   7 nAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +A+  +e++ + e++s+ + + +A +++++g+y +A++ ++++ ++++ +  ++y +A  + + ++  +A++a+ +
  gi|330506325|ref|YP_004382753.1|  56 DAVESYEKAIQIEPHSSLAWLKKAIAYFEMGNYIEALDSVNRSiEIDPVNADALYMKAGFYGETGRTRDALQAFNE 131
                                       78888999996666666666667*************************************************9976 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.8e-06
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcr 59 
                                       ++++++A+  ++  l+ ++e+ ++ +++A  l ++g y++A++ ++++ +++++s++++
  gi|330506325|ref|YP_004382753.1| 119 TGRTRDALQAFNETLEVDPERIDAWFWKADFLASMGSYEEALNAYNRTiEIDPESMNAA 177
                                       678999******************************************9*999999876 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 6e-07
                                       HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3   8 AiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       A   ++++ +++++++++ + ++  l  +g+y++A   l+++ +l++  ++++y  A +l + ++yeeA++ L+k
  gi|330506325|ref|YP_004382753.1| 203 AAETYDKAIEQNPNDANAWFGKGCNLNDQGRYDEAAVALNRSvELAPAFINAWYFRAVALNATGRYEEAVRSLDK 277
                                       444555566677777777777899999*********************************************998 PP

  == domain 4  score: 26.8 bits;  conditional E-value: 8.1e-09
                                       HTT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                            ANAPC3   1 dqnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76 
                                       dq++y++A   ++r ++  +   ++ y+ A +l  +g+y++A + l+k+ + n+++  ++ l++++l +L++ +eA 
  gi|330506325|ref|YP_004382753.1| 230 DQGRYDEAAVALNRSVELAPAFINAWYFRAVALNATGRYEEAVRSLDKFlEANPEHSLAWKLKGEALSALGRDKEAQ 306
                                       699*************************************************************************9 PP

                                       HHH- CS
                            ANAPC3  77 aaLe 80 
                                       +a+e
  gi|330506325|ref|YP_004382753.1| 307 SAFE 310
                                       9987 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.14        79      16      33 .]      54      71 ..      47      71 .. 0.85
   2 ?    6.6   0.0     0.025        14       2      21 ..      74      93 ..      73     102 .. 0.92
   3 !    8.7   0.0    0.0052       2.9       1      28 [.     107     134 ..     107     138 .. 0.88
   4 !   11.7   0.0    0.0006      0.33       1      33 []     141     173 ..     141     173 .. 0.95
   5 ?    4.1   0.2      0.15        87      18      32 ..     202     216 ..     184     217 .. 0.73
   6 ?    3.8   0.0      0.19     1e+02      10      31 ..     227     249 ..     220     250 .. 0.77
   7 !   12.0   0.0   0.00047      0.26       2      32 ..     254     284 ..     253     285 .. 0.90
   8 ?    2.2   0.0      0.61   3.4e+02       7      26 ..     293     312 ..     291     314 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.14
                                      HHHHHHHHHHHHHH-TT- CS
                             TPR_6 16 tdkAlealerlikeYPdS 33
                                       ++A+e +e+ i+  P S
  gi|330506325|ref|YP_004382753.1| 54 LTDAVESYEKAIQIEPHS 71
                                      578**********99987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.025
                                      HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  2 AlyklalsyrklgdtdkAle 21
                                      A +k a +y+++g++ +Al+
  gi|330506325|ref|YP_004382753.1| 74 AWLKKAIAYFEMGNYIEALD 93
                                      7899************9986 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0052
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                       dAly+ a  y ++g+t++Al+a+++ ++
  gi|330506325|ref|YP_004382753.1| 107 DALYMKAGFYGETGRTRDALQAFNETLE 134
                                       79**********99*********98776 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.0006
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPdS 33 
                                       dA ++ a  + ++g +++Al a++r i+  P+S
  gi|330506325|ref|YP_004382753.1| 141 DAWFWKADFLASMGSYEEALNAYNRTIEIDPES 173
                                       799999**9999*****************9998 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHH-TT CS
                             TPR_6  18 kAlealerlikeYPd 32 
                                        A e++++ i++ P+
  gi|330506325|ref|YP_004382753.1| 202 MAAETYDKAIEQNPN 216
                                       467789999988887 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.19
                                       HHH.HHHHHHHHHHHHHHHHH-T CS
                             TPR_6  10 yrk.lgdtdkAlealerlikeYP 31 
                                        ++ +g++d+A  al+r ++  P
  gi|330506325|ref|YP_004382753.1| 227 NLNdQGRYDEAAVALNRSVELAP 249
                                       445599*********99776655 PP

  == domain 7  score: 12.0 bits;  conditional E-value: 0.00047
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       A y +a ++ ++g++++A++ l+++++  P+
  gi|330506325|ref|YP_004382753.1| 254 AWYFRAVALNATGRYEEAVRSLDKFLEANPE 284
                                       6788899999999**************9997 PP

  == domain 8  score: 2.2 bits;  conditional E-value: 0.61
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerl 26 
                                       ++++ +lg+  +A  a+e +
  gi|330506325|ref|YP_004382753.1| 293 GEALSALGRDKEAQSAFEMV 312
                                       7888899999*******988 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 !   16.6   0.0   1.1e-05    0.0061       8      38 ..      79     109 ..      78     113 .. 0.93
   2 ?   -1.7   0.0       5.8   3.3e+03      19      33 ..     124     138 ..     121     142 .. 0.86
   3 !    8.3   0.0    0.0044       2.4      14      38 ..     153     177 ..     150     178 .. 0.92
   4 ?   -2.2   0.0       7.9   4.4e+03      15      34 ..     232     251 ..     231     255 .. 0.78
   5 !   15.9   0.0   1.8e-05      0.01       4      41 ..     255     292 ..     252     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHT-HHHHHHHHHHHHHHTTS-HHHH CS
                        Fis1_TPR_C   8 AlGhyklgeYseArryvdalLeiEPenrQaq 38 
                                       A++++ +g+Y eA+  v++ +ei+P n  a+
  gi|330506325|ref|YP_004382753.1|  79 AIAYFEMGNYIEALDSVNRSIEIDPVNADAL 109
                                       8**************************9986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.8
                                       HHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  19 eArryvdalLeiEPe 33 
                                       +A++  +  Le++Pe
  gi|330506325|ref|YP_004382753.1| 124 DALQAFNETLEVDPE 138
                                       689999999****98 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0044
                                       HT-HHHHHHHHHHHHHHTTS-HHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaq 38 
                                       +g Y+eA++  ++ +ei+Pe ++a+
  gi|330506325|ref|YP_004382753.1| 153 MGSYEEALNAYNRTIEIDPESMNAA 177
                                       899*****************99886 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 7.9
                                       T-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPen 34 
                                       g+Y+eA   +++  e+ P +
  gi|330506325|ref|YP_004382753.1| 232 GRYDEAAVALNRSVELAPAF 251
                                       89999998888888887766 PP

  == domain 5  score: 15.9 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHH CS
                        Fis1_TPR_C   4 lYylAlGhyklgeYseArryvdalLeiEPenrQaqsLk 41 
                                        Y+ A++    g+Y+eA r +d +Le  Pe + a +Lk
  gi|330506325|ref|YP_004382753.1| 255 WYFRAVALNATGRYEEAVRSLDKFLEANPEHSLAWKLK 292
                                       6****************************988777776 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0074       4.2     209     256 ..      55     102 ..      42     107 .. 0.90
   2 !   15.7   0.0   9.9e-06    0.0056     195     256 ..     109     170 ..     105     174 .. 0.93
   3 !    6.1   0.1    0.0076       4.3     209     262 ..     200     252 ..     185     255 .. 0.82
   4 !    8.5   0.1    0.0015      0.84       9      62 ..     257     310 ..     253     313 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0074
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 209 ekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       + A+e  +kai+ +p +   +l Ka  +  +G+  +A + ++++ ++D
  gi|330506325|ref|YP_004382753.1|  55 TDAVESYEKAIQIEPHSSLAWLKKAIAYFEMGNYIEALDSVNRSIEID 102
                                       5799999******************************99999988877 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 9.9e-06
                                       HHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 195 lyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       ly+ A +y ++g++  Al+  ++ +e +p+ ++ +  Ka +l  +G  ++A ++ +++ ++D
  gi|330506325|ref|YP_004382753.1| 109 LYMKAGFYGETGRTRDALQAFNETLEVDPERIDAWFWKADFLASMGSYEEALNAYNRTIEID 170
                                       788999***********************************************999887777 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0076
                                       H.HHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHH CS
                             NARP1 209 e.kAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyi 262
                                          A e+ dkaie++p+  + +  K+  l  +G  ++Aa +++++ +  la  +i
  gi|330506325|ref|YP_004382753.1| 200 AaMAAETYDKAIEQNPNDANAWFGKGCNLNDQGRYDEAAVALNRSVE--LAPAFI 252
                                       34789999*******************************99986544..444455 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHH CS
                             NARP1   9 yknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatye 62 
                                       +++  ++ +g++eeA+  L++  +   ++    + k+e l +Lgr +eA++++e
  gi|330506325|ref|YP_004382753.1| 257 FRAVALNATGRYEEAVRSLDKFLEANPEHSLAWKLKGEALSALGRDKEAQSAFE 310
                                       677788999999999999999888888877777899999999999999999987 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.11        64       7      51 ..      57     101 ..      55     108 .. 0.87
   2 ?    6.8   0.0     0.016       8.7       8      50 ..      92     134 ..      89     136 .. 0.90
   3 !   10.4   0.0    0.0011      0.61       6      53 ..     124     171 ..     119     179 .. 0.87
   4 !   12.9   0.1   0.00019      0.11       3      48 ..     199     244 ..     197     251 .. 0.88
   5 !    9.6   0.1     0.002       1.1      12      53 ..     242     283 ..     239     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkr 51 
                                        +++ e+a++ +p    a l+ A a+++ g+y eAl+   + ++ 
  gi|330506325|ref|YP_004382753.1|  57 AVESYEKAIQIEPHSSLAWLKKAIAYFEMGNYIEALDSVNRSIEI 101
                                       578889999***************************987666665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                            TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                       l+++ + ++ +p + da +  A  + + gr ++Al+++ e l+
  gi|330506325|ref|YP_004382753.1|  92 LDSVNRSIEIDPVNADALYMKAGFYGETGRTRDALQAFNETLE 134
                                       677889999***************************9988886 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0011
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                                         l+++ ++l+ +p+ +da +  A+ l++ g yeeAl++  + ++ d 
  gi|330506325|ref|YP_004382753.1| 124 DALQAFNETLEVDPERIDAWFWKADFLASMGSYEEALNAYNRTIEIDP 171
                                       578999*******************************98777777665 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 0.00019
                            TPR_20   3 adapelaeleaalaanpddldarldlAlallaagryeeAleqLlei 48 
                                       a+a   ++ ++a+++np+d +a +     l+ +gry+eA+ +L + 
  gi|330506325|ref|YP_004382753.1| 199 AAAMAAETYDKAIEQNPNDANAWFGKGCNLNDQGRYDEAAVALNRS 244
                                       5667788999*****************************9988665 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.002
                            TPR_20  12 eaalaanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                                        + ++ +p+ ++a +  A al+a gryeeA+  L ++l+++ 
  gi|330506325|ref|YP_004382753.1| 242 NRSVELAPAFINAWYFRAVALNATGRYEEAVRSLDKFLEANP 283
                                       56667777788899999*****************99999876 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0026       1.5      71     124 ..      81     134 ..      70     142 .. 0.83
   2 !    9.1   0.1    0.0029       1.6      74     123 ..     118     167 ..     104     174 .. 0.88
   3 !   22.9   2.9   1.6e-07     9e-05      10     123 ..     195     313 ..     190     314 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0026
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       a +++G + eal+  ++ ++ +P++ ++       +  +Gr+ +AL++++++ +
  gi|330506325|ref|YP_004382753.1|  81 AYFEMGNYIEALDSVNRSIEIDPVNADALYMKAGFYGETGRTRDALQAFNETLE 134
                                       4689999*****************98887766666889***********99865 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0029
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       + Gr ++al+  ++ ++ +P r +++      la +G  +eAL++Y+r+ 
  gi|330506325|ref|YP_004382753.1| 118 ETGRTRDALQAFNETLEVDPERIDAWFWKADFLASMGSYEEALNAYNRTI 167
                                       57999999999999999999999999999999999***********9975 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTT.....STTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHH CS
                              BTAD  10 vaagraalaagdpeeaaelleaAlalwrGpaladlea.....gewleaererleelrlealealaeaelrlGraeea 81 
                                       +a+++aa aa+  ++a+e+  + ++ w G+  +  ++        +  + ++l   ++ a   +a a+ + Gr+eea
  gi|330506325|ref|YP_004382753.1| 195 QAKSAAAMAAETYDKAIEQNPNDANAWFGKGCNLNDQgrydeAAVALNRSVELAPAFINAWYFRAVALNATGRYEEA 271
                                       4667788888899999999999999998776654444567767778888999999********************** PP

                                       HHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  82 laelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       ++ l++ ++++P +  ++++  +Al ++Gr  eA  ++e +r
  gi|330506325|ref|YP_004382753.1| 272 VRSLDKFLEANPEHSLAWKLKGEALSALGRDKEAQSAFEMVR 313
                                       ***********************************9999876 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1     0.003       1.7      23     129 ..      39     135 ..      23     141 .. 0.68
   2 ?    5.8   0.0     0.024        13     100     129 ..     140     169 ..     138     178 .. 0.86
   3 ?    5.0   0.2     0.044        24      66     129 ..     188     247 ..     177     250 .. 0.76
   4 !    9.4   0.0    0.0018         1      99     128 ..     251     280 ..     248     286 .. 0.86
   5 ?    3.4   0.1      0.13        73     106     126 ..     292     312 ..     287     314 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.003
                                       T-HHHHHHHHHHHHHHHTTS.-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHH CS
                           DUF3856  23 gayeeaaasyrkalevsrti.paeeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGkl 98 
                                       +a++e+ + + + l ++ ++ + e a   e   +l++   + a+ ++g+y eal s+++++       e++  +   
  gi|330506325|ref|YP_004382753.1|  39 EAFNESGNMTLRNLILTDAVeSYEKAIQIEPHSSLAWLKKAIAYFEMGNYIEALDSVNRSI-------EIDPVN--- 105
                                       4577777776667777766624577889999999999999999999999999999986655.......333322... PP

                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  99 WiaavfsravaleelGrkdealkafrmagem 129
                                          a++ +a  + e+Gr+ +al+af+ + e+
  gi|330506325|ref|YP_004382753.1| 106 -ADALYMKAGFYGETGRTRDALQAFNETLEV 135
                                       .346666777777777777777777766665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 100 iaavfsravaleelGrkdealkafrmagem 129
                                       i a f +a  l+++G+++eal+a++ + e+
  gi|330506325|ref|YP_004382753.1| 140 IDAWFWKADFLASMGSYEEALNAYNRTIEI 169
                                       66778899999*************998886 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.044
                                       HHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  66 aklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                        k+g  d+a ++a+ a + +++  e + ++ + W    f ++  l++ Gr+dea  a++ ++e+
  gi|330506325|ref|YP_004382753.1| 188 KKMGLEDQAKSAAAMAAETYDKAIEQNPNDANAW----FGKGCNLNDQGRYDEAAVALNRSVEL 247
                                       5566666777777777777777777777777777....7899999999***9999999988886 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  99 WiaavfsravaleelGrkdealkafrmage 128
                                       +i+a + raval+ +Gr++ea++++ +  e
  gi|330506325|ref|YP_004382753.1| 251 FINAWYFRAVALNATGRYEEAVRSLDKFLE 280
                                       6899999***************99877655 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.13
                                       HHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 106 ravaleelGrkdealkafrma 126
                                       ++ al+ lGr +ea  af+m+
  gi|330506325|ref|YP_004382753.1| 292 KGEALSALGRDKEAQSAFEMV 312
                                       799***************997 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.76   4.3e+02       7      22 ..      78      93 ..      72      97 .. 0.84
   2 ?    1.7   0.1         1   5.8e+02       3      23 ..     108     128 ..     106     131 .. 0.83
   3 ?    6.3   0.0     0.032        18      11      24 ..     228     241 ..     227     243 .. 0.84
   4 !   15.3   0.0   4.2e-05     0.023       3      25 ..     254     276 ..     253     277 .. 0.91
   5 ?    1.2   0.0       1.4   7.9e+02       8      24 ..     293     309 ..     291     311 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.76
                             TPR_4  7 LArallalGdldeAra 22
                                       A a+++ G++ eA++
  gi|330506325|ref|YP_004382753.1| 78 KAIAYFEMGNYIEALD 93
                                      699***********96 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1
                             TPR_4   3 allaLArallalGdldeAral 23 
                                       al++ A  + ++G+  +A+++
  gi|330506325|ref|YP_004382753.1| 108 ALYMKAGFYGETGRTRDALQA 128
                                       77888888999*******987 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.032
                             TPR_4  11 llalGdldeArall 24 
                                       l ++G++deA+ +l
  gi|330506325|ref|YP_004382753.1| 228 LNDQGRYDEAAVAL 241
                                       668*******9887 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 4.2e-05
                             TPR_4   3 allaLArallalGdldeAralle 25 
                                       a +++A al a+G+++eA + l+
  gi|330506325|ref|YP_004382753.1| 254 AWYFRAVALNATGRYEEAVRSLD 276
                                       6799***************9886 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 1.4
                             TPR_4   8 ArallalGdldeArall 24 
                                       ++al alG+  eA+ ++
  gi|330506325|ref|YP_004382753.1| 293 GEALSALGRDKEAQSAF 309
                                       79999999988888766 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.85   4.8e+02      17      27 ..      56      66 ..      54      72 .. 0.78
   2 ?    3.6   0.0      0.15        84       4      20 ..      77      93 ..      74     103 .. 0.75
   3 ?    3.3   0.0      0.18     1e+02       2      33 ..     109     138 ..     108     141 .. 0.84
   4 ?    3.5   0.0      0.15        85       6      34 ..     147     173 ..     146     175 .. 0.81
   5 ?    1.4   0.0      0.76   4.2e+02      17      35 ..     202     218 ..     201     219 .. 0.85
   6 ?    1.2   0.0      0.82   4.6e+02      11      19 ..     230     238 ..     228     249 .. 0.81
   7 ?    5.3   0.0     0.041        23       2      26 ..     255     279 ..     254     284 .. 0.80
   8 ?    2.5   0.0      0.32   1.8e+02       5      24 ..     292     311 ..     288     312 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.85
                             TPR_7 17 eAielyeqsLa 27
                                      +A+e ye++++
  gi|330506325|ref|YP_004382753.1| 56 DAVESYEKAIQ 66
                                      799****9655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.15
                             TPR_7  4 nLarlysrlGdyeeAie 20
                                        a +y+++G+y eA++
  gi|330506325|ref|YP_004382753.1| 77 KKAIAYFEMGNYIEALD 93
                                      55889999999999986 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.18
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       L+  a  y + G++++A++ + +   l+ dpe
  gi|330506325|ref|YP_004382753.1| 109 LYMKAGFYGETGRTRDALQAFNE--TLEVDPE 138
                                       6666788999*************..9998887 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.15
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                       a+   ++G yeeA+  y +   ++ dpe 
  gi|330506325|ref|YP_004382753.1| 147 ADFLASMGSYEEALNAYNR--TIEIDPES 173
                                       566778999********99..88888776 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.76
                             TPR_7  17 eAielyeqsLaltkdpeda 35 
                                        A+e y +  a++  p+da
  gi|330506325|ref|YP_004382753.1| 202 MAAETYDK--AIEQNPNDA 218
                                       59999999..999999987 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 0.82
                             TPR_7  11 rlGdyeeAi 19 
                                       ++G+y+eA+
  gi|330506325|ref|YP_004382753.1| 230 DQGRYDEAA 238
                                       69*****97 PP

  == domain 7  score: 5.3 bits;  conditional E-value: 0.041
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsL 26 
                                       ++  a++  + G+yeeA++ + + L
  gi|330506325|ref|YP_004382753.1| 255 WYFRAVALNATGRYEEAVRSLDKFL 279
                                       56668888899*******9887755 PP

  == domain 8  score: 2.5 bits;  conditional E-value: 0.32
                             TPR_7   5 LarlysrlGdyeeAielyeq 24 
                                        +++ s+lG+ +eA + +e 
  gi|330506325|ref|YP_004382753.1| 292 KGEALSALGRDKEAQSAFEM 311
                                       68999*********999885 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.89     5e+02      19      31 ..      55      67 ..      54      68 .. 0.86
   2 !    7.2   0.0    0.0084       4.7       9      23 ..      79      93 ..      78     101 .. 0.84
   3 ?    3.0   0.1      0.18        99       8      30 ..     112     134 ..     106     135 .. 0.82
   4 ?    4.5   0.0     0.059        33      12      31 ..     150     169 ..     147     170 .. 0.83
   5 ?    6.7   0.1     0.012       6.7      10      30 ..     226     246 ..     225     248 .. 0.81
   6 ?    6.4   0.1     0.015       8.6       9      25 ..     259     275 ..     258     281 .. 0.86
   7 ?    1.6   0.0       0.5   2.8e+02       9      26 ..     293     310 ..     293     312 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.89
                            TPR_10 19 deAealleealai 31
                                      ++A++ +e+a++i
  gi|330506325|ref|YP_004382753.1| 55 TDAVESYEKAIQI 67
                                      6899999**9997 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0084
                            TPR_10  9 analrqrgrydeAea 23
                                      a+a++++g+y eA++
  gi|330506325|ref|YP_004382753.1| 79 AIAYFEMGNYIEALD 93
                                      89***********97 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.18
                            TPR_10   8 LanalrqrgrydeAealleeala 30 
                                        a  + ++gr  +A++ + e+l+
  gi|330506325|ref|YP_004382753.1| 112 KAGFYGETGRTRDALQAFNETLE 134
                                       57889***********9999987 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.059
                            TPR_10  12 lrqrgrydeAealleealai 31 
                                       l ++g y+eA++ + ++++i
  gi|330506325|ref|YP_004382753.1| 150 LASMGSYEEALNAYNRTIEI 169
                                       77899999999999998886 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.012
                            TPR_10  10 nalrqrgrydeAealleeala 30 
                                       + l ++grydeA   l ++++
  gi|330506325|ref|YP_004382753.1| 226 CNLNDQGRYDEAAVALNRSVE 246
                                       6689********988877776 PP

  == domain 6  score: 6.4 bits;  conditional E-value: 0.015
                            TPR_10   9 analrqrgrydeAeall 25 
                                       a+al ++gry+eA++ l
  gi|330506325|ref|YP_004382753.1| 259 AVALNATGRYEEAVRSL 275
                                       799**********9866 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.5
                            TPR_10   9 analrqrgrydeAealle 26 
                                       + al+++gr +eA   +e
  gi|330506325|ref|YP_004382753.1| 293 GEALSALGRDKEAQSAFE 310
                                       679**********87665 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       7.7   4.3e+03     119     135 ..      43      59 ..      34      63 .. 0.79
   2 ?    6.7   0.0     0.016       9.1      73     123 ..      76     126 ..      61     131 .. 0.91
   3 ?    7.3   0.0     0.011       6.1      76     127 ..     113     164 ..     106     172 .. 0.86
   4 ?    3.3   0.5      0.18     1e+02      74     123 ..     189     238 ..     171     248 .. 0.77
   5 !   11.5   0.1   0.00055      0.31      79     124 ..     262     307 ..     253     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.7
                                       H-SSHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr 119 qaesatwRniYlsgake 135
                                       ++ ++t Rn+ l+ a e
  gi|330506325|ref|YP_004382753.1|  43 ESGNMTLRNLILTDAVE 59 
                                       5678999****999987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.016
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  73 lekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       l+ka ++++ g+y  a+  +n  ++ dp na+a  +ka  + + g+   + 
  gi|330506325|ref|YP_004382753.1|  76 LKKAIAYFEMGNYIEALDSVNRSIEIDPVNADALYMKAGFYGETGRTRDAL 126
                                       789999***********************************9999987665 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.011
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHH CS
                   Alkyl_sulf_dimr  76 akealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRn 127
                                       a  + + g  r a++  n  ++ dpe+ +a   kad l ++g  +e+ ++ n
  gi|330506325|ref|YP_004382753.1| 113 AGFYGETGRTRDALQAFNETLEVDPERIDAWFWKADFLASMGSYEEALNAYN 164
                                       555567899999*********************************9998765 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.18
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  74 ekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       ++  e+ ++  + +aae  +++++++p++a+a   k   l+  g+  e+a
  gi|330506325|ref|YP_004382753.1| 189 KMGLEDQAKSAAAMAAETYDKAIEQNPNDANAWFGKGCNLNDQGRYDEAA 238
                                       5566778889999**************99988776666666666655555 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00055
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  79 alkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                         + g y+ a+  l++ ++a+pe++ a +lk +al +lg+ +e+  
  gi|330506325|ref|YP_004382753.1| 262 LNATGRYEEAVRSLDKFLEANPEHSLAWKLKGEALSALGRDKEAQS 307
                                       457899**********************************999765 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 !   15.0   0.0   3.3e-05     0.018       3      98 ..      59     163 ..      57     179 .. 0.80
   2 ?    2.5   0.0      0.25   1.4e+02       6      58 ..     130     190 ..     127     206 .. 0.64
   3 ?   -1.7   0.0         5   2.8e+03      20      35 ..     197     212 ..     176     243 .. 0.58
   4 ?    5.9   0.0     0.022        12      19      40 ..     257     278 ..     203     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-05
                      SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkveae 74 
                                       e+yek +++e +    +  k++a+ +++ y eaL  ++       ++ d  + ka  +  + + ++al+ ++++ ++
  gi|330506325|ref|YP_004382753.1|  59 ESYEKAIQIEPHSSLAWlkKAIAYFEMGNYIEALDSVNRSIeidPVNADALYMKAGFYGETGRTRDALQAFNETLEV 135
                                       78999999997766666689***************998765455799************************998776 PP

                      SRP_TPR_like  75 e..kvk..vlksqvlYrlgsyekAYklL 98 
                                       +  +++    k+  l  +gsye+A +  
  gi|330506325|ref|YP_004382753.1| 136 DpeRIDawFWKADFLASMGSYEEALNAY 163
                                       6445552257999999999999996654 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.25
                      SRP_TPR_like   6 ekilrlegkelkkf..kvvaliklekyeeaLkllkkgs.....alsedvrfE.kaYvlYkl 58 
                                       ++ l+++ + ++ +  k+  l +++ yeeaL++ + +      +++    ++ k+Yvl k+
  gi|330506325|ref|YP_004382753.1| 130 NETLEVDPERIDAWfwKADFLASMGSYEEALNAYNRTIeidpeSMNAARSWDsKSYVLKKM 190
                                       5556666666666555777888999999999988766544444444444443256666555 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5
                      SRP_TPR_like  20 kvvaliklekyeeaLk 35 
                                       k  a + +e y+ a++
  gi|330506325|ref|YP_004382753.1| 197 KSAAAMAAETYDKAIE 212
                                       4445555555555544 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.022
                      SRP_TPR_like  19 fkvvaliklekyeeaLkllkkg 40 
                                       f++val   ++yeea++ l+k 
  gi|330506325|ref|YP_004382753.1| 257 FRAVALNATGRYEEAVRSLDKF 278
                                       6999999999***999998875 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.9e-05      0.01     209     292 ..      81     164 ..      52     182 .. 0.91
   2 ?    3.3   0.1     0.059        33     247     292 ..     197     242 ..     179     250 .. 0.80
   3 ?    3.2   0.2     0.063        35     222     273 ..     206     257 ..     197     285 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                                       HHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HH CS
                             ChAPs 209 vllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledie 285
                                        ++ + + ++a++ +n+++e ++ +a+ L ++a f  +  +++ Al++ +++ ++ P     W+  ++   +++ +e
  gi|330506325|ref|YP_004382753.1|  81 AYFEMGNYIEALDSVNRSIEIDPVNADALYMKAGFYGETGRTRDALQAFNETLEVDPERIDAWFWKADFLASMGSYE 157
                                       58899999********************************************************************* PP

                                       HHHHHHH CS
                             ChAPs 286 nALltLN 292
                                       +AL + N
  gi|330506325|ref|YP_004382753.1| 158 EALNAYN 164
                                       ***9988 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.059
                                       SS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                             ChAPs 247 kkkeelAlevakravksaPsefktWalLvkvYikledienALltLN 292
                                       k+   +A e+ ++a++  P++ + W+       +++ +++A ++LN
  gi|330506325|ref|YP_004382753.1| 197 KSAAAMAAETYDKAIEQNPNDANAWFGKGCNLNDQGRYDEAAVALN 242
                                       444589999****************987777777777777777776 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.063
                                       HHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHH CS
                             ChAPs 222 llneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWal 273
                                       +  +++e++++da+    +   l ++ +++ A  + +r+v++aP   + W+ 
  gi|330506325|ref|YP_004382753.1| 206 TYDKAIEQNPNDANAWFGKGCNLNDQGRYDEAAVALNRSVELAPAFINAWYF 257
                                       3344455555555555555555555555555555556666666666666655 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.13        70      36      65 ..      72     102 ..      52     110 .. 0.79
   2 ?    3.4   0.0     0.096        54      36      64 ..     106     134 ..     100     139 .. 0.89
   3 !    9.7   0.2    0.0011      0.63      38      65 ..     142     169 ..     134     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHCT-HHHHHHHHHT.CCCC CS
                              RPN7  36 rrakldlaehYlkigdleeAlkaysr.irey 65 
                                         a+l++a  Y+++g++ eAl  ++r i ++
  gi|330506325|ref|YP_004382753.1|  72 SLAWLKKAIAYFEMGNYIEALDSVNRsIEID 102
                                       5689999*****************9955555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.096
                                       HHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  36 rrakldlaehYlkigdleeAlkaysrire 64 
                                       ++a + +a +Y ++g ++ Al+a+++++e
  gi|330506325|ref|YP_004382753.1| 106 ADALYMKAGFYGETGRTRDALQAFNETLE 134
                                       57788999******************987 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHCT-HHHHHHHHHTCCCC CS
                              RPN7  38 akldlaehYlkigdleeAlkaysrirey 65 
                                       a+  +a++ +++g +eeAl+ay+r++e 
  gi|330506325|ref|YP_004382753.1| 142 AWFWKADFLASMGSYEEALNAYNRTIEI 169
                                       566699******************9874 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.061        34       8      22 ..      79      93 ..      72      94 .. 0.89
   2 ?    3.7   0.0      0.12        65      12      27 ..     151     164 ..     150     172 .. 0.76
   3 ?    3.8   0.0       0.1        59       8      23 ..     225     240 ..     219     242 .. 0.76
   4 ?   -1.0   0.0       3.3   1.8e+03      14      21 ..     265     272 ..     257     279 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.061
                                      HHHHHHTT-HHHHHH CS
                             TPR_3  8 AaefynkkkyqeAre 22
                                      A +++ +++y eA++
  gi|330506325|ref|YP_004382753.1| 79 AIAYFEMGNYIEALD 93
                                      779**********86 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.12
                                       HHTT-HHHHHHH..HH CS
                             TPR_3  12 ynkkkyqeArelfsYa 27 
                                        +++ y+eA+++  Y 
  gi|330506325|ref|YP_004382753.1| 151 ASMGSYEEALNA--YN 164
                                       57999*******..64 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.1
                                       HHHHHHTT-HHHHHHH CS
                             TPR_3   8 AaefynkkkyqeArel 23 
                                       ++ + ++++y+eA+ +
  gi|330506325|ref|YP_004382753.1| 225 GCNLNDQGRYDEAAVA 240
                                       667778*******876 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 3.3
                                       TT-HHHHH CS
                             TPR_3  14 kkkyqeAr 21 
                                        ++y+eA+
  gi|330506325|ref|YP_004382753.1| 265 TGRYEEAV 272
                                       79*****8 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 ?    7.9   0.0    0.0061       3.4      14      49 ..     146     181 ..     143     199 .. 0.88
   2 ?   -1.6   0.0       5.8   3.2e+03      17      30 ..     200     213 ..     188     243 .. 0.66
   3 ?    3.8   0.0      0.12        68      14      33 ..     258     277 ..     253     311 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0061
                         NRBF2_MIT  14 kadrllaaGkyeeaischkkaaaylseamkltkseq 49 
                                       kad l + G yeea+  ++++ ++  e+m+ ++s  
  gi|330506325|ref|YP_004382753.1| 146 KADFLASMGSYEEALNAYNRTIEIDPESMNAARSWD 181
                                       899999*******************9*999988855 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.8
                         NRBF2_MIT  17 rllaaGkyeeaisc 30 
                                         +aa  y++ai  
  gi|330506325|ref|YP_004382753.1| 200 AAMAAETYDKAIEQ 213
                                       45677777777754 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.12
                         NRBF2_MIT  14 kadrllaaGkyeeaischkk 33 
                                       +a  l a+G+yeea+    k
  gi|330506325|ref|YP_004382753.1| 258 RAVALNATGRYEEAVRSLDK 277
                                       677799********976555 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.45   2.5e+02      12      37 ..      76     101 ..      61     149 .. 0.76
   2 ?   -1.2   0.0       2.7   1.5e+03      15      35 ..     147     167 ..     138     176 .. 0.73
   3 ?    1.6   0.0      0.37   2.1e+02       7      36 ..     217     246 ..     211     259 .. 0.77
   4 ?    8.2   0.0    0.0035         2       9      54 ..     253     297 ..     247     312 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.45
                           DUF5113  12 anlayylnvegeyeeALeyldsaley 37 
                                        + a +++  g+y eAL+ ++  +e+
  gi|330506325|ref|YP_004382753.1|  76 LKKAIAYFEMGNYIEALDSVNRSIEI 101
                                       55677788888888888888877654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.7
                           DUF5113  15 ayylnvegeyeeALeyldsal 35 
                                       a +l   g+yeeAL+  +  +
  gi|330506325|ref|YP_004382753.1| 147 ADFLASMGSYEEALNAYNRTI 167
                                       555667788999998877665 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.37
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsale 36 
                                        an++   +++ln +g+y+eA   l+  +e
  gi|330506325|ref|YP_004382753.1| 217 DANAWFGKGCNLNDQGRYDEAAVALNRSVE 246
                                       5888999999**********9887776655 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0035
                           DUF5113   9 ndYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtld 54 
                                       n++   a +ln++g+yeeA++ ld+ le   +h   +  k  + l+
  gi|330506325|ref|YP_004382753.1| 253 NAWYFRAVALNATGRYEEAVRSLDKFLEANPEHSLAWKLKG-EALS 297
                                       666677889******************99888877776665.4555 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.015       8.4     115     178 ..      78     138 ..      70     147 .. 0.68
   2 ?    6.4   7.2    0.0083       4.6     111     269 ..     148     307 ..     141     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                            TPR_15 115 salellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapd 178
                                       +a+ + e  + +++++++ +s+e ++    +a  l++ a +y ++g+t +Al+++ e l+++p+
  gi|330506325|ref|YP_004382753.1|  78 KAIAYFEMGNYIEALDSVNRSIEIDP---VNADALYMKAGFYGETGRTRDALQAFNETLEVDPE 138
                                       55554444444444444444433333...345678899***********************997 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0083
                            TPR_15 111 rlLssalellerakdydriaellksle.eeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselraal 186
                                       ++L s+  + e++++y+r+ e+  + + +     + +++l  ++   +++++ + A + y +A++ +p+++++  + 
  gi|330506325|ref|YP_004382753.1| 148 DFLASMGSYEEALNAYNRTIEIDPESMnAARSWDSKSYVLKKMGLEDQAKSAAAMAAETYDKAIEQNPNDANAWFGK 224
                                       677778888888888887666655544145558899999999999999***************************** PP

                            TPR_15 187 lWlliDlgrraeLrellkawkaraesdasLwgplaaAlllLgrpkkALeylrkqakenrk.dplwllaYADaleqag 262
                                         +l+D gr++e+  +l +  + a +  + w   a Al + gr+++A + l k +++n++ + +w+l+  +al + g
  gi|330506325|ref|YP_004382753.1| 225 GCNLNDQGRYDEAAVALNRSVELAPAFINAWYFRAVALNATGRYEEAVRSLDKFLEANPEhSLAWKLK-GEALSALG 300
                                       ************9999998888888888889999999999*************888887615667776.78888888 PP

                            TPR_15 263 radeAwr 269
                                       r  eA++
  gi|330506325|ref|YP_004382753.1| 301 RDKEAQS 307
                                       8887775 PP

>> YfiO  Outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.011       6.2      10      80 ..      43     110 ..      34     116 .. 0.77
   2 ?    0.0   0.1       1.1     6e+02      57      68 ..     196     207 ..     141     244 .. 0.59
   3 ?    5.5   0.0     0.022        13      54      76 ..     264     286 ..     216     307 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                                       HHHHHHHHHT-HHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-SSSTTHHH CS
                              YfiO  10 ekgqealqkgdyaeAikklealdsryPfspyaeqaqldliyAyykdadyaealasaerFlrlyPthknvdy 80 
                                       e+g   l++   ++A++  e++ ++    p++  a l+ + Ay++ ++y+eal+s++r ++  P   ++ y
  gi|330506325|ref|YP_004382753.1|  43 ESGNMTLRNLILTDAVESYEKAIQI---EPHSSLAWLKKAIAYFEMGNYIEALDSVNRSIEIDPVNADALY 110
                                       4566666666777777777777665...4566778999*********************999998777555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.1
                                       -HHHHHHHHHHH CS
                              YfiO  57 dyaealasaerF 68 
                                         ++a+ +ae++
  gi|330506325|ref|YP_004382753.1| 196 AKSAAAMAAETY 207
                                       333333333333 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.022
                                       HTT-HHHHHHHHHHHHHH-SSST CS
                              YfiO  54 kdadyaealasaerFlrlyPthk 76 
                                        ++ y+ea+ s+++Fl+ +P+h 
  gi|330506325|ref|YP_004382753.1| 264 ATGRYEEAVRSLDKFLEANPEHS 286
                                       567899***************95 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 ?   11.4   0.1   0.00033      0.19     116     193 ..      31     134 ..       6     140 .. 0.78
   2 ?    1.8   0.7       0.3   1.7e+02     116     158 ..     175     217 ..     146     299 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00033
                           DUF2225 116 kkAklalrlAWlyrdkedeekeklflkkAlelykeayekesfpvegideat.......................... 166
                                        k+  + + A  ++++++ + ++l l+ A+e y++a++ e  ++    ++                           
  gi|330506325|ref|YP_004382753.1|  31 DKGNESCKEA--FNESGNMTLRNLILTDAVESYEKAIQIEPHSSLAWLKKAiayfemgnyiealdsvnrsieidpvn 105
                                       5555555555..899999**********************9987766666668888999999999999999999999 PP

                           DUF2225 167 ..vlYLiaeLerrlgnkeealrwlskvig 193
                                          lY+ a     +g++++al++++++++
  gi|330506325|ref|YP_004382753.1| 106 adALYMKAGFYGETGRTRDALQAFNETLE 134
                                       99999999999999999999999888765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.3
                           DUF2225 116 kkAklalrlAWlyrdkedeekeklflkkAlelykeayekesfp 158
                                       + A  +   +++ ++ + e++ k     A+e+y++a+e++ ++
  gi|330506325|ref|YP_004382753.1| 175 NAARSWDSKSYVLKKMGLEDQAKSAAAMAAETYDKAIEQNPND 217
                                       4455555555555555557777777778888888888776655 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         3   1.7e+03      58      73 ..     119     134 ..     101     178 .. 0.67
   2 ?   11.3   0.0   0.00035       0.2      25      93 ..     232     300 ..     220     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3
                        HrpB1_HrpK  58 rgrweeAlrlLrevea 73 
                                        gr  +Al++++e  +
  gi|330506325|ref|YP_004382753.1| 119 TGRTRDALQAFNETLE 134
                                       5566666666665443 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00035
                        HrpB1_HrpK  25 edtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyakaLlAlcLaalr 93 
                                       ++ ++a++ L+    L P + ++  + +v l + gr+eeA+r L +  +++++  +a  L   +L+al+
  gi|330506325|ref|YP_004382753.1| 232 GRYDEAAVALNRSVELAPAFINAWYFRAVALNATGRYEEAVRSLDKFLEANPEHSLAWKLKGEALSALG 300
                                       5566677777777789*****************************************999999999875 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.14        79      42      77 ..      73     108 ..      56     114 .. 0.87
   2 ?   -0.6   0.0       2.5   1.4e+03      53      75 ..     118     140 ..     108     144 .. 0.75
   3 ?    4.0   0.0     0.093        52      46      73 ..     145     172 ..     140     180 .. 0.82
   4 ?   -1.7   0.0       5.6   3.1e+03      55      71 ..     232     248 ..     226     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.14
                            ANAPC5  42 yalLnlaslhadfghneeAvkaleeairlArenkDk 77 
                                        a L+ a+   ++g++ eA+++++ +i++   n+D 
  gi|330506325|ref|YP_004382753.1|  73 LAWLKKAIAYFEMGNYIEALDSVNRSIEIDPVNADA 108
                                       688999999***************999998877775 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.5
                            ANAPC5  53 dfghneeAvkaleeairlArenk 75 
                                       + g   +A++a++e+ ++  e+ 
  gi|330506325|ref|YP_004382753.1| 118 ETGRTRDALQAFNETLEVDPERI 140
                                       5588899*******998876665 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.093
                            ANAPC5  46 nlaslhadfghneeAvkaleeairlAre 73 
                                         a + a++g +eeA++a + +i++  e
  gi|330506325|ref|YP_004382753.1| 145 WKADFLASMGSYEEALNAYNRTIEIDPE 172
                                       56778899************99998655 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 5.6
                            ANAPC5  55 ghneeAvkaleeairlA 71 
                                       g ++eA  al+ +++lA
  gi|330506325|ref|YP_004382753.1| 232 GRYDEAAVALNRSVELA 248
                                       77899999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 1813.93
//
Query:       gi|330506326|ref|YP_004382754.1|  [L=414]
Description: LVIVD repeat family [Methanosaeta concilii GP6]
Scores for complete 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-41  136.8  22.0    1.8e-14   52.7   0.5    7.8  7  LVIVD        LVIVD repeat
    7.2e-07   28.4   0.0      0.023   13.6   0.0    2.6  2  Beta_propel  Beta propeller domain


Domain annotation for each model (and alignments):
>> LVIVD  LVIVD repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1     0.097   8.7e+02       2      37 ..      29      66 ..      28      68 .. 0.75
   2 !   17.0   1.0   3.1e-07    0.0027       5      35 ..      78     116 ..      76     122 .. 0.80
   3 !   12.6   0.0   7.2e-06     0.065       9      42 .]     131     164 ..     124     164 .. 0.91
   4 !   52.7   0.5     2e-18   1.8e-14       1      34 [.     165     198 ..     165     203 .. 0.92
   5 !   27.8   0.0   1.3e-10   1.2e-06      10      35 ..     291     316 ..     285     322 .. 0.87
   6 !   24.4   0.3   1.4e-09   1.3e-05      19      40 ..     350     371 ..     328     372 .. 0.83
   7 !   10.7   0.0   2.7e-05      0.24       2      34 ..     375     407 ..     374     412 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.097
                             LVIVD  2 GdaqdvavsGn.YaYvAdqdngLvIvDI.SNpSsptlk 37
                                      G++ dva s + Y++   +d g+ I    SN S + ++
  gi|330506326|ref|YP_004382754.1| 29 GYTFDVASSDDgYVFAVEGDRGMKIFQLdSNRSRLDMV 66
                                      78888888864499988888888887777888887665 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.1e-07
                             LVIVD   5 qdvavsGnYaYvA........dqdngLvIvDISNpSspt 35 
                                       +++++ GnYa+vA        + +++L I+ ISNp +p 
  gi|330506326|ref|YP_004382754.1|  78 RNIKLAGNYAFVAslpngndpFVKGELAIINISNPYYPM 116
                                       79***********5555555546789*********8886 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 7.2e-06
                             LVIVD   9 vsGnYaYvAdqdngLvIvDISNpSsptlkgsydT 42 
                                       ++  YaYvA +  gL I  I + S+   +g++ T
  gi|330506326|ref|YP_004382754.1| 131 IKDSYAYVAAGTEGLHIYEIGDSSAVRIVGKCET 164
                                       7789*************************99988 PP

  == domain 4  score: 52.7 bits;  conditional E-value: 2e-18
                             LVIVD   1 gGdaqdvavsGnYaYvAdqdngLvIvDISNpSsp 34 
                                       +G a+dv+ sGnYaY+Ad++ngL +vD+SNp  p
  gi|330506326|ref|YP_004382754.1| 165 PGTAWDVWSSGNYAYIADNENGLAVVDVSNPVLP 198
                                       699****************************766 PP

  == domain 5  score: 27.8 bits;  conditional E-value: 1.3e-10
                             LVIVD  10 sGnYaYvAdqdngLvIvDISNpSspt 35 
                                        GnY+YvA +  gL+++D+SNp  p 
  gi|330506326|ref|YP_004382754.1| 291 EGNYVYVAAGPQGLIVIDVSNPFRPE 316
                                       59********************7776 PP

  == domain 6  score: 24.4 bits;  conditional E-value: 1.4e-09
                             LVIVD  19 qdngLvIvDISNpSsptlkgsy 40 
                                       +dngL ++D SNpS+p l+g++
  gi|330506326|ref|YP_004382754.1| 350 KDNGLLVIDMSNPSNPKLIGKC 371
                                       69*****************987 PP

  == domain 7  score: 10.7 bits;  conditional E-value: 2.7e-05
                             LVIVD   2 GdaqdvavsGnYaYvAdqdngLvIvDISNpSsp 34 
                                       G ++ v + ++ a vA  d g  I+D+S+   p
  gi|330506326|ref|YP_004382754.1| 375 GWVEGVTLFEDMAIVANTDRGVAIIDVSDVRDP 407
                                       667889999*******************96555 PP

>> Beta_propel  Beta propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   7.2e-06     0.065      15     208 ..      33     249 ..      32     279 .. 0.76
   2 !   13.6   0.0   2.6e-06     0.023      14     117 ..     285     376 ..     284     394 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-06
                       Beta_propel  15 DivktDGkyiyvvsg.skvvivd..aeaeelklvseikleekfkieelyldgdrLvvisseeeeeeseaeeeeepil 88 
                                       D+  +D+ y+++v+g + + i +  ++ + l+ vs +  ++  +++++ l g+  +v s  + +++  +   e +i+
  gi|330506326|ref|YP_004382754.1|  33 DVASSDDGYVFAVEGdRGMKIFQldSNRSRLDMVSVLYPPKGLYFRNIKLAGNYAFVASLPNGNDPFVKG--ELAII 107
                                       78889999*****884446666655888888999999999999999999999999999988777776554..33333 PP

                       Beta_propel  89 skee...............................tkvliyDisdkenpkllreleldGsyvssRkigdklylvssk 134
                                       + ++                                 ++iy+i d ++ ++++++e  G+  +    g+++y+  + 
  gi|330506326|ref|YP_004382754.1| 108 NISNpyypmvsyisdmgsgfglfikdsyayvaagtEGLHIYEIGDSSAVRIVGKCETPGTAWDVWSSGNYAYIADN- 183
                                       333345677789999999*************9998889************************************99. PP

                       Beta_propel 135 eaeeeeenekeaeeakleellPkvseeeeklvacediylpdesesss.ylvvtsldlak.dkavdskavlgsgeev 208
                                              ++  a  +  + +lPk+    ++ + +  iyl++  ++s  yl+  +++    +k  ++ + l +g+++
  gi|330506326|ref|YP_004382754.1| 184 -------ENGLAVVDVSNPVLPKY---LGQAIWSGMIYLFSMGPESGkYLINGTIEKHIlNKFHQNGFSLENGDTI 249
                                       .......45566666678999999...7777788888888766555437766666666655555555555555555 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.6e-06
                       Beta_propel  14 aDivktDGkyiyvvsg.skvvivd.aeaeelklvseikleekfkieelyldgdrLvvisseeeeeeseaeeeeepil 88 
                                       a iv+ +G+y+yv+ g + ++++d +++   +++s+++  ++   e l + ++ L +   + e++++          
  gi|330506326|ref|YP_004382754.1| 285 AEIVRGEGNYVYVAAGpQGLIVIDvSNPFRPEVISQFRSGNNACAEGLAIRDNILYLANGNHEDSKD---------- 351
                                       689*************999*****6666777**********999*******9999987777555553.......... PP

                       Beta_propel  89 skeetkvliyDisdkenpkllreleldGs 117
                                             +l++D+s+++npkl++++ ++G 
  gi|330506326|ref|YP_004382754.1| 352 ----NGLLVIDMSNPSNPKLIGKCPFSGW 376
                                       ....358***************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 2411.08
//
Query:       gi|330506327|ref|YP_004382755.1|  [L=444]
Description: hypothetical protein MCON_0008 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0026   17.1   0.0      0.027   13.7   0.0    2.0  2  Hydrolase_4   Serine aminopeptidase, S33
     0.0048   16.4   0.1      0.011   15.3   0.1    1.6  1  Peptidase_S9  Prolyl oligopeptidase family


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   3.1e-06     0.027      58     106 ..     151     203 ..     141     221 .. 0.76
   2 ?    0.8   0.0     0.027   2.4e+02     182     228 ..     357     401 ..     343     406 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.1e-06
                       Hydrolase_4  58 yvdDlaafvekvkeehpel...plfllGhSmGGliallyllrypdkva.glil 106
                                        +dD++a+ + ++++       +++++G S GG+++++yl++y d+v+ +li 
  gi|330506327|ref|YP_004382755.1| 151 QIDDIEAIRRDMQKKGLLPkngKIMVYGRSGGGVLVQQYLDKYGDHVSrALIE 203
                                       56777777666665442223359************************955553 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.027
                       Hydrolase_4 182 rleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklyp 228
                                       +++ + ++++  +++ +G+ D+v+  e  + + ++ +    +l++++
  gi|330506327|ref|YP_004382755.1| 357 QINLNRSRYKGEVMVWSGTGDQVCAVEMGQWVSDSYPY--SRLAVFD 401
                                       56666777778899************999998888774..5555555 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   0.1   1.2e-06     0.011      42     119 ..     149     227 ..     134     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHHHHHHHHHTT.S--GGGEEEEEETHHHHHHHHHHHH-GG.G-SEEEEESE---CCCHHCSTTSTHH.HC CS
                      Peptidase_S9  42 qnefdDfiaaaealakeg.yvdserlaitGgSyGGyltgaalnqrpd.lFkaavaevpvvdvlrydsdtdllte.ey 115
                                       ++++dD+ a+ + + k+g + ++ +++++G S GG+l+   l + +d + +a++ + +  d+ r + +t  +++  y
  gi|330506327|ref|YP_004382755.1| 149 NEQIDDIEAIRRDMQKKGlLPKNGKIMVYGRSGGGVLVQQYLDKYGDhVSRALIEASGGPDLAREHNTT--FNKnTY 223
                                       456899999999******99**********************966651567777888888999988888..888556 PP

                                       CCC- CS
                      Peptidase_S9 116 mewg 119
                                       + ++
  gi|330506327|ref|YP_004382755.1| 224 ESNP 227
                                       5544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 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:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3202.21
//
Query:       gi|330506328|ref|YP_004382756.1|  [L=95]
Description: hypothetical protein MCON_0011 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   0.3       0.19   11.7   0.3    1.4  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3     1e-05      0.19     111     148 ..       3      40 ..       1      60 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1e-05
                                       EEEE-HHHHHHHHHHHHHSHHHHHEECS.EEE--TTSHH CS
                               LCM 111 fEvDqpevlefKretlkelgaepkaelr.yvpvDlrddd 148
                                       +EvD p+ lefK++  kel+a++k + +  ++ D++ +d
  gi|330506328|ref|YP_004382756.1|   3 IEVDIPKELEFKIKANKELNALVKRRIErQISTDIK-ND 40 
                                       8***********************876636999998.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 703.37
//
Query:       gi|330506329|ref|YP_004382757.1|  [L=368]
Description: 4Fe-4S ferredoxin, iron-sulfur binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-44  150.9   0.0    7.4e-44  150.4   0.0    1.2  1  DUF362    Domain of unknown function (DUF362)
    1.1e-13   50.4   9.1    8.3e-07   28.6   0.3    2.3  2  Fer4      4Fe-4S binding domain
      1e-10   41.2   9.6    5.9e-06   26.1   0.4    2.4  2  Fer4_6    4Fe-4S binding domain
    1.8e-09   38.0  19.7    6.5e-08   33.1  10.7    1.7  2  Fer4_7    4Fe-4S dicluster domain
    6.5e-09   35.8  17.9    6.7e-06   26.1  11.1    2.2  2  Fer4_10   4Fe-4S dicluster domain
    1.9e-08   35.1   6.8     0.0015   19.4   2.0    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
    2.4e-08   33.6  11.0    0.00034   20.5   1.0    2.4  2  Fer4_2    4Fe-4S binding domain
    5.9e-08   32.7   8.2    1.2e-07   31.8   8.2    1.6  1  Fer4_9    4Fe-4S dicluster domain
    1.9e-05   24.7  10.1    5.2e-05   23.3  10.1    1.7  2  Fer4_21   4Fe-4S dicluster domain
    4.3e-05   23.7   8.8      0.028   14.9   0.5    2.3  2  Fer4_4    4Fe-4S binding domain
    0.00018   22.0  11.8       0.01   16.4   1.6    2.4  2  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   16.5   9.8      0.026   15.3   1.3    2.5  2  Fer4_22   4Fe-4S dicluster domain
      0.029   13.6   0.3      0.045   12.9   0.3    1.3  1  Lar_N     Lactate racemase N-terminal domain
      0.034   14.7   7.0       0.58   10.8   0.6    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.063   14.0  11.6       0.12   13.2   1.0    2.7  2  Fer4_15   4Fe-4S single cluster domain
       0.12   12.9  12.6       0.87   10.1   2.2    2.3  2  Fer4_8    4Fe-4S dicluster domain
       0.16   12.9  18.8       0.33   12.0   5.2    2.6  2  Fer4_3    4Fe-4S binding 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 !  150.4   0.0     7e-47   7.4e-44       2     203 .]      43     313 ..      42     313 .. 0.91

  Alignments for each domain:
  == domain 1  score: 150.4 bits;  conditional E-value: 7e-47
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..xxxxxxxxxxxxxxxxx..xxx RF
                            DUF362   2 aiKpNlgeagnpegatthpevvravvellkeagagkiivgdspglyv.srgka..hrevaeeagydelaega..dia 73 
                                       aiK+++ge+gn+++  ++p +vr+v++ +++ag g+++++d+++ly  sr++a  h+++aee+g+ + + ga  +ia
  gi|330506329|ref|YP_004382757.1|  43 AIKIHFGEQGNSSY--VNPVLVRPVADKIRSAG-GQPFLTDTNTLYGgSRSNAvrHLQTAEEHGFGRTVAGApvIIA 116
                                       8**********999..***************99.9**********8557777788************9998888*** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx....... RF
                            DUF362  74 dglegedevvvpvkgkhlkkelkiakavleaDviInlpklKgHalagvtgalKn.lfGcisgsgkaeiHs....... 142
                                       dgl+g+++++v ++gkh+++ +kia +++ a ++I+++++KgH  ag++ga+Kn ++Gc+++ gk+++Hs       
  gi|330506329|ref|YP_004382757.1| 117 DGLQGDNYREVAISGKHFQR-VKIAGEIASAQSMIVVSHFKGHLPAGFGGAIKNlGMGCAPALGKSDQHSarpifna 192
                                       ***********999*9*988.******************************************************** PP

                                       ..................................................xx.xxxxxxxxxxxxxxx.x....xxx RF
                            DUF362 143 ..................................................kr.dsekfaekiadlaka.l....kpd 163
                                                                                         +  +   f+e+++++a + +    ++ 
  gi|330506329|ref|YP_004382757.1| 193 elcegcracadgcpnqaitvkkkitqidyslctgcgkclrlcpahaldfdWIvEVPPFMERMVEYALGaVtgkeGKV 269
                                       *************************************************95545778***********888754233 PP

                                       ..xxxxxxx.....xxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxx RF
                            DUF362 164 ..lnvvdgi.....kamegegpsggskelglv.....laStDpvalDaaaad 203
                                         +n++ +i     ++ + + p         v     laS+Dpva+D+a++d
  gi|330506329|ref|YP_004382757.1| 270 gfFNFLLNItpdcdCVPWSDTPI--------VpdigiLASKDPVAIDQASYD 313
                                       777******78777555557773........333346***********9875 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   3.3   9.3e-09   9.8e-06       1      24 []     188     211 ..     188     211 .. 0.94
   2 !   28.6   0.3   7.9e-10   8.3e-07       2      23 ..     218     239 ..     217     240 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 9.3e-09
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       ++++ e+C gC aC++ CP+ AIt
  gi|330506329|ref|YP_004382757.1| 188 PIFNAELCEGCRACADGCPNQAIT 211
                                       5799*******************7 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 7.9e-10
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       +id+++C+gCG+C   CP  A+
  gi|330506329|ref|YP_004382757.1| 218 QIDYSLCTGCGKCLRLCPAHAL 239
                                       79*****************997 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   3.3   1.2e-06    0.0012       2      24 .]     188     210 ..     187     210 .. 0.94
   2 !   26.1   0.4   5.6e-09   5.9e-06       3      24 .]     218     239 ..     216     239 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       + +++++C gC++C++ CP +ai
  gi|330506329|ref|YP_004382757.1| 188 PIFNAELCEGCRACADGCPNQAI 210
                                       569******************98 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 5.6e-09
                            Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                       +id+++C+gCg+C r CP+ a+
  gi|330506329|ref|YP_004382757.1| 218 QIDYSLCTGCGKCLRLCPAHAL 239
                                       59*****************986 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1  10.7   6.1e-11   6.5e-08       2      52 .]     195     238 ..     194     238 .. 0.93
   2 !   18.0   1.6     3e-06    0.0032       2      20 ..     224     242 ..     223     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 6.1e-11
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       C gC+aC++ Cp++ai+++++        ++id++ C+gCg+C + CP+ a
  gi|330506329|ref|YP_004382757.1| 195 CEGCRACADGCPNQAITVKKK-------ITQIDYSLCTGCGKCLRLCPAHA 238
                                       ******************886.......689*****************865 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3e-06
                            Fer4_7   2 CigCgaCvaaCpvkaield 20 
                                       C+gCg+C + Cp++a+++d
  gi|330506329|ref|YP_004382757.1| 224 CTGCGKCLRLCPAHALDFD 242
                                       ****************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 !   26.1  11.1   6.3e-09   6.7e-06       3      56 .]     189     235 ..     187     235 .. 0.90
   2 !   21.6   0.5   1.7e-07   0.00017       3      24 ..     218     247 ..     216     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.3e-09
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +++++ C +C++C + CP        ++++ +++  +++++ Ctgcg+C + CP
  gi|330506329|ref|YP_004382757.1| 189 IFNAELCEGCRACADGCPN-------QAITVKKKITQIDYSLCTGCGKCLRLCP 235
                                       78999**************.......777777788888***************9 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.7e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPadl........t 24 
                                       +id + C++CgkC + CPa++         
  gi|330506329|ref|YP_004382757.1| 218 QIDYSLCTGCGKCLRLCPAHAldfdwiveV 247
                                       6899***************87666654440 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   2.0   1.4e-06    0.0015       2      22 ..     195     215 ..     194     222 .. 0.84
   2 !   17.9   0.2   4.2e-06    0.0045       2      20 ..     224     242 ..     223     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.4e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                       C +C++Ca+ CP +ai+ kk+
  gi|330506329|ref|YP_004382757.1| 195 CEGCRACADGCPNQAITVKKK 215
                                       *****************9833 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 4.2e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++CgkC+  CP++a++ +
  gi|330506329|ref|YP_004382757.1| 224 CTGCGKCLRLCPAHALDFD 242
                                       ***************9876 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   3.3     3e-06    0.0031       2      22 .]     187     207 ..     186     207 .. 0.92
   2 !   20.5   1.0   3.2e-07   0.00034       4      22 .]     218     236 ..     215     236 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       ++ ++++ C gC+aC + CP+
  gi|330506329|ref|YP_004382757.1| 187 RPIFNAELCEGCRACADGCPN 207
                                       799*****************5 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.2e-07
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                       ++d   C+gCg+C+  CPa
  gi|330506329|ref|YP_004382757.1| 218 QIDYSLCTGCGKCLRLCPA 236
                                       68999*************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 !   31.8   8.2   1.1e-10   1.2e-07       2      50 ..     195     238 ..     181     239 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.1e-10
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       C gC+aC + Cp+++++ +++ + + +       C+gCg+C+  Cp +a
  gi|330506329|ref|YP_004382757.1| 195 CEGCRACADGCPNQAITVKKKITQIDYS-----LCTGCGKCLRLCPAHA 238
                                       ****************999999998884.....6************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 !   12.1   2.2   0.00016      0.16      37      58 ..     191     211 ..     178     212 .. 0.78
   2 !   23.3  10.1   4.9e-08   5.2e-05       4      53 ..     191     236 ..     186     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                           Fer4_21  37 vedeCvGCnlCssvCPvedcie 58 
                                        ++ C GC  C++ CP +++i+
  gi|330506329|ref|YP_004382757.1| 191 NAELCEGCRACADGCP-NQAIT 211
                                       4799************.69987 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 4.9e-08
                           Fer4_21   4 dedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                       + + C gC  C+  C++   qai+++ k+++++  + C+GC  C+  CP 
  gi|330506329|ref|YP_004382757.1| 191 NAELCEGCRACADGCPN---QAITVK-KKITQIDYSLCTGCGKCLRLCPA 236
                                       7789************5...***986.67779999**************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 !   12.4   2.3   0.00017      0.18       2      16 ..     193     207 ..     192     215 .. 0.90
   2 !   14.9   0.5   2.7e-05     0.028       3      15 ..     223     235 ..     221     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e C gC++C + CP 
  gi|330506329|ref|YP_004382757.1| 193 ELCEGCRACADGCPN 207
                                       78************5 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.7e-05
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                        C+gCg+C + CP
  gi|330506329|ref|YP_004382757.1| 223 LCTGCGKCLRLCP 235
                                       6***********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 !   10.5   3.0   0.00064      0.67      36      59 ..     183     208 ..     166     210 .. 0.75
   2 !   16.4   1.6   9.5e-06      0.01      37      59 ..     215     237 ..     208     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00064
                           Fer4_17  36 eaeke..ekaslCieCgeCerkCPqg 59 
                                       +++++   +a+lC +C+ C+  CP++
  gi|330506329|ref|YP_004382757.1| 183 QHSARpiFNAELCEGCRACADGCPNQ 208
                                       44444334899*************85 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 9.5e-06
                           Fer4_17  37 aekeekaslCieCgeCerkCPqg 59 
                                        +++   slC++Cg+C r CP++
  gi|330506329|ref|YP_004382757.1| 215 KITQIDYSLCTGCGKCLRLCPAH 237
                                       45556789*************98 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.8      0.03        31      76      95 ..     189     208 ..     178     210 .. 0.83
   2 ?   15.3   1.3   2.5e-05     0.026      72      95 ..     214     237 ..     208     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.03
                           Fer4_22  76 kfgesgCvGCgRCieacpvk 95 
                                        f+++ C GC  C + cp++
  gi|330506329|ref|YP_004382757.1| 189 IFNAELCEGCRACADGCPNQ 208
                                       578999***********976 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.5e-05
                           Fer4_22  72 efkekfgesgCvGCgRCieacpvk 95 
                                       +  ++++ s C+GCg+C + cp++
  gi|330506329|ref|YP_004382757.1| 214 KKITQIDYSLCTGCGKCLRLCPAH 237
                                       55678899*************975 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 ?   12.9   0.3   4.3e-05     0.045     143     189 ..     135     181 ..      90     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.3e-05
                             Lar_N 143 tpveinklvaeadlviltGfiepHyfaGfsGGrKsilpGvasretim 189
                                       ++v+i  ++a+a+ +i++   + H  aGf+G  K +  G+a +    
  gi|330506329|ref|YP_004382757.1| 135 QRVKIAGEIASAQSMIVVSHFKGHLPAGFGGAIKNLGMGCAPALGKS 181
                                       5799************************************9765555 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   1.0    0.0084       8.8      39      58 .]     193     212 ..     181     212 .. 0.74
   2 ?   10.8   0.6   0.00055      0.58       1      18 [.     219     236 ..     219     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0084
                           Fer4_13  39 eekadaeeAadaCPvesIgv 58 
                                       e+ + +++ ad+CP ++I+v
  gi|330506329|ref|YP_004382757.1| 193 ELCEGCRACADGCPNQAITV 212
                                       55566777788888888875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00055
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       +D + C++cg+C  l+P 
  gi|330506329|ref|YP_004382757.1| 219 IDYSLCTGCGKCLRLCPA 236
                                       68889************7 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   3.8     0.059        62       5      20 ..     192     207 ..     189     212 .. 0.83
   2 ?   13.2   1.0   0.00011      0.12       3      20 ..     219     236 ..     218     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.059
                           Fer4_15   5 rdaCigcglCvaeape 20 
                                        ++C+gc +C++ +p+
  gi|330506329|ref|YP_004382757.1| 192 AELCEGCRACADGCPN 207
                                       6899999999999985 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00011
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       +D ++C+gcg C++++p 
  gi|330506329|ref|YP_004382757.1| 219 IDYSLCTGCGKCLRLCPA 236
                                       8***************95 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.6    0.0042       4.4      48      63 ..     192     207 ..     176     209 .. 0.81
   2 ?   10.1   2.2   0.00083      0.87      48      64 ..     221     237 ..     208     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0042
                            Fer4_8  48 lwsCttcgaCtevCpv 63 
                                       ++ C +c+aC++ Cp+
  gi|330506329|ref|YP_004382757.1| 192 AELCEGCRACADGCPN 207
                                       5789999999999997 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00083
                            Fer4_8  48 lwsCttcgaCtevCpvg 64 
                                          Ct+cg+C + Cp +
  gi|330506329|ref|YP_004382757.1| 221 YSLCTGCGKCLRLCPAH 237
                                       56899999999999986 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.6      0.02        21       1      15 []     195     209 ..     195     209 .. 0.91
   2 ?   12.0   5.2   0.00031      0.33       1      15 []     224     238 ..     224     238 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.02
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gC+aC + CP+ A
  gi|330506329|ref|YP_004382757.1| 195 CEGCRACADGCPNQA 209
                                       99**********865 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00031
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       CtgCg C++ CP +A
  gi|330506329|ref|YP_004382757.1| 224 CTGCGKCLRLCPAHA 238
                                       ************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2640.55
//
Query:       gi|330506330|ref|YP_004382758.1|  [L=191]
Description: iron-sulfur flavoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-30  105.4   0.0    2.6e-30  105.2   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    1.6e-10   41.0   0.0    1.9e-10   40.8   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
      0.046   13.4   0.0       0.16   11.7   0.0    1.8  2  IpaB_EvcA     IpaB/EvcA family


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.0   4.4e-34   2.6e-30       1     152 [.       1     157 [.       1     160 [. 0.88

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 4.4e-34
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--...---HCHGHT...CGGSHHHHHHHHHHHH- CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladlilpc.alcdkdlese...gqtsddvaellekiaaa 73 
                                       mk+++++GS+r+++nt +l+ +++++l+ +g+e+el++l +  ++c a +++++ ++    q++d +++++ek+aaa
  gi|330506330|ref|YP_004382758.1|   1 MKVIAFNGSPRRDGNTATLLAAVLRELESQGIETELVHLIGTLAGCkACFKCKEMKNgrcIQDKDMINQCIEKMAAA 77 
                                       9*************************************98888999755555555558877788888********** PP

                                       SCEEEEEEECTTCE-HHHHHHHHCHT-...SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEE CS
                           FMN_red  74 daliivtPeYngsysgllKnalDrlsr..trgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraav 148
                                       d++ii++P++++  ++  K+++Dr+++  ++++ +++ K++a+v+++  r+g+ ++  +  +++ + ++i+ +++++
  gi|330506330|ref|YP_004382758.1|  78 DGIIIGSPTHFADLTPETKALIDRAGFvaMANGYMFKRKVGAAVVAV-RRAGAIHVFDSINHLFLISQMIIAGSSYW 153
                                       ********************************************666.66777666666666666*********999 PP

                                       EETS CS
                           FMN_red 149 avgk 152
                                       ++g 
  gi|330506330|ref|YP_004382758.1| 154 NIGM 157
                                       9886 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   3.1e-14   1.9e-10       1     110 [.       1     106 [.       1     155 [. 0.79

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 3.1e-14
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTT...CHHHHHHH.HH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeek...padveseq.ie 73 
                                       mk+   n++pr  + ++  l++a++++le++g  e + ++L  +     +++++++k +++++   + +   +q ie
  gi|330506330|ref|YP_004382758.1|   1 MKVIAFNGSPRR-DGNTATLLAAVLRELESQG-IETELVHLIGT--LAGCKACFKCK-EMKNGrciQDKDMINQcIE 72 
                                       9999********.5999***************.9*********6..33444566655.44444546666678999** PP

                                       HHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSC CS
                      Flavodoxin_2  74 kllaadaivlqfPlwwfgvPailKgwiDrvltagfaf 110
                                       k++aad i++++P ++  + +  K+ iDr   agf  
  gi|330506330|ref|YP_004382758.1|  73 KMAAADGIIIGSPTHFADLTPETKALIDR---AGFVA 106
                                       ****************************9...57744 PP

>> IpaB_EvcA  IpaB/EvcA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.6e-05      0.16      43      63 ..      64      84 ..      30      90 .. 0.86
   2 ?   -1.0   0.0      0.22   1.3e+03      90     106 ..     135     154 ..     131     168 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.6e-05
                         IpaB_EvcA 43 ssvvnrsidklaiensvvltd 63
                                        ++n++i+k+a+ ++  +++
  gi|330506330|ref|YP_004382758.1| 64 KDMINQCIEKMAAADGIIIGS 84
                                      67****************998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.22
                         IpaB_EvcA  90 sishlalne...vassslrk 106
                                       si+hl l     +a+ss+ +
  gi|330506330|ref|YP_004382758.1| 135 SINHLFLISqmiIAGSSYWN 154
                                       89998764323389999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1511.15
//
Query:       gi|330506331|ref|YP_004382759.1|  [L=383]
Description: phosphoserine phosphatase [Methanosaeta concilii GP6]
Scores for complete 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-18   65.5   0.1    1.3e-17   64.8   0.1    1.3  1  HAD              haloacid dehalogenase-like hydrolase
    2.8e-16   60.5   0.2    5.4e-16   59.5   0.2    1.5  1  Hydrolase        haloacid dehalogenase-like hydrolase
    3.4e-11   42.7   0.5    4.3e-05   23.2   0.1    2.7  2  ACT              ACT domain
      2e-09   37.6   3.1    4.5e-09   36.4   0.2    2.5  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
    7.1e-09   35.5   0.1     0.0031   17.5   0.0    2.5  2  ACT_6            ACT domain
    4.4e-07   30.4   0.3      0.009   16.6   0.0    2.6  2  ACT_4            ACT domain
    5.8e-07   29.1   1.2    0.00013   21.5   0.1    2.8  3  Put_Phosphatase  Putative Phosphatase
    6.4e-07   29.6   2.8    1.5e-05   25.1   2.8    2.7  1  HAD_2            Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.043   13.3   0.1       0.32   10.5   0.0    2.0  2  S6PP             Sucrose-6F-phosphate phosphohydrolase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.1   6.5e-21   1.3e-17       1     186 [.     172     338 ..     172     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 6.5e-21
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerf 76 
                                       ++fD+D T++d     +++  +l+++a    + +++ ++ a+    +++d ++  ++  +ll+g++   l + ++++
  gi|330506331|ref|YP_004382759.1| 172 IVFDMDMTIVDF----EIIN-RLASFAGV-DEQVKAITDRAM---NGEMDFKESLRQRVRLLKGMPfSTLQEIAADL 239
                                       79**********....5555.44443333.466666666666...677888899999999******99999999999 PP

                               HAD  77 vaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrge 152
                                       +        l+pg  el+++ ++ G++++++Sgg+ +++  l ++lg+d+  a++le +d +ltge  + g ++  e
  gi|330506331|ref|YP_004382759.1| 240 Q--------LTPGSEELIHHLKQVGYKIALISGGFTYFTDVLKERLGFDYAFANDLEIEDgVLTGE--IKGEIIDAE 306
                                       9........78********999********************************************..********* PP

                               HAD 153 gkvaalrewlaaegegidleevvayGDspsDlpl 186
                                       +k + + +   ae e+i+++++va+GD+ +D  +
  gi|330506331|ref|YP_004382759.1| 307 AKGRIIYD--LAEREKISPDNIVAVGDGANDCLM 338
                                       ********..888889999************766 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.2   2.7e-19   5.4e-16       2     210 .]     170     343 ..     169     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 2.7e-19
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewlt 78 
                                       +++vfD+d T+++ e     +i+++                     a + ++ ++++ ++      +++ g+ ++ +
  gi|330506331|ref|YP_004382759.1| 170 RLIVFDMDMTIVDFE-----IINRL---------------------ASFAGVDEQVKAITD-----RAMNGEMDFKE 215
                                       689************.....*****.....................***************.....*********** PP

                                       HHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  79 aldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanql 155
                                       +l               + r   l+      + +ia  l++ p+ +e++++Lk+ g++++l++g++  + + + ++l
  gi|330506331|ref|YP_004382759.1| 216 SL---------------RQRVRLLKGMPFSTLQEIAADLQLTPGSEELIHHLKQVGYKIALISGGFTYFTDVLKERL 277
                                       **...............77777777666666677777777*******************************99999* PP

                                       T.......GGGE.SEEEEHHCES...STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       x.......xxxx.xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 156 G.......ddyf.daviasdiet...vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       G       d  + d+v++++i++    a+++ ++   ++++ +++p ++++VGDg+nD  ++++Ag
  gi|330506331|ref|YP_004382759.1| 278 GfdyafanDLEIeDGVLTGEIKGeiiDAEAKGRIIYDLAEREKISPDNIVAVGDGANDCLMIKNAG 343
                                       *955555522233555555555588888888888888888888*********************98 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.6e-06    0.0031       8      56 ..       3      47 ..       1      55 [. 0.88
   2 !   23.2   0.1   2.2e-08   4.3e-05       1      38 [.      87     124 ..      87     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.6e-06
                                      ESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHH CS
                               ACT  8 pDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedle 56
                                      +Dr Gl+ ++++  a  ++Ni+ + q+ +     gi+++++v+d e+++
  gi|330506331|ref|YP_004382759.1|  3 RDRSGLIRDILSEPAMQNVNIVDMDQKVMQ----GISVMTVVADFESAK 47
                                      7****************************5....6*******9988876 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 2.2e-08
                                       EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEEST CS
                               ACT   1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssed 38 
                                       +++ ++++DrPG++ +v+ + a++g+N+++++++  ++
  gi|330506331|ref|YP_004382759.1|  87 YIVTILAKDRPGIIRDVAEVAARNGVNLERASVTARGE 124
                                       67899****************************99977 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.3       3.5     7e+03       1      11 [.     172     182 ..     172     184 .. 0.88
   2 ?    1.3   0.0      0.12   2.3e+02      13      55 ..     238     280 ..     231     306 .. 0.76
   3 !   36.4   0.2   2.3e-12   4.5e-09     187     251 ..     307     370 ..     293     374 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.5
                                       EEEEIIIIIS- CS
                       Hydrolase_3   1 ialDlDGTLln 11 
                                       i++D+D T+++
  gi|330506331|ref|YP_004382759.1| 172 IVFDMDMTIVD 182
                                       89*****9986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.12
                                       TS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                       Hydrolase_3  13 dkkisektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                       d ++++ + e i+ lk+ g+k+++ +G  ++++  + e lg+d
  gi|330506331|ref|YP_004382759.1| 238 DLQLTPGSEELIHHLKQVGYKIALISGGFTYFTDVLKERLGFD 280
                                       567889999******************8888888888888887 PP

  == domain 3  score: 36.4 bits;  conditional E-value: 2.3e-12
                                       SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHH CS
                       Hydrolase_3 187 sKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGV 251
                                        Kg  + +la++ +is+++++a+GDg ND  M++ aglgvA  na+e +kk++d      n  G+
  gi|330506331|ref|YP_004382759.1| 307 AKGRIIYDLAEREKISPDNIVAVGDGANDCLMIKNAGLGVAF-NAKEVLKKVSDGSLSRENLLGL 370
                                       59999************************************7.9999999999876666665555 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.5e-06     0.011       8      75 ..       1      70 [.       1      70 [. 0.88
   2 !   17.5   0.0   1.6e-06    0.0031       4      74 ..      88     158 ..      85     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.5e-06
                             ACT_6  8 tGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgped..alarlekaLlflakelgltvef 75
                                      +G dr Gl+ +++s  a  +vni+D  q v  g  + +++ + ++   + ++lek  +  a+ l+++++f
  gi|330506331|ref|YP_004382759.1|  1 MGRDRSGLIRDILSEPAMQNVNIVDMDQKVMQGISVMTVVADFESAkvTPQKLEKWYRDNAESLAIDFSF 70
                                      7***************************************999955358888998888888888887765 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.6e-06
                             ACT_6   4 litvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgpedalarlekaLlflakelgltve 74 
                                       ++t++ +drpG++ ++++v a++gvn+    +   ++  s+  l +  +      +++L + ++ lgl+v+
  gi|330506331|ref|YP_004382759.1|  88 IVTILAKDRPGIIRDVAEVAARNGVNLERASVTARGELISIEFLMDFADCSADDCRSQLKKECEGLGLDVV 158
                                       89************************999988888888888888888888888888888888888888876 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00022      0.44      13      48 ..       2      35 ..       1      44 [. 0.84
   2 !   16.6   0.0   4.5e-06     0.009      10      52 ..      90     130 ..      85     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                             ACT_4 13 aedrkglLaditqviseekanivsvnaktrkkdgla 48
                                      ++dr+gl++di++  + +++niv++  k  +  g+ 
  gi|330506331|ref|YP_004382759.1|  2 GRDRSGLIRDILSEPAMQNVNIVDMDQKVMQ--GIS 35
                                      79**********************9998844..444 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.5e-06
                             ACT_4  10 eveaedrkglLaditqviseekanivsvnaktrkkdglaeiki 52 
                                       ++ a+dr+g+++d+++v + +++n++  ++++r   +l +i++
  gi|330506331|ref|YP_004382759.1|  90 TILAKDRPGIIRDVAEVAARNGVNLERASVTAR--GELISIEF 130
                                       6899*************************9995..55777665 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.39   7.8e+02       4      65 ..      23      85 ..      20     144 .. 0.67
   2 !   21.5   0.1   6.4e-08   0.00013       2     117 ..     171     284 ..     170     289 .. 0.87
   3 !    5.2   0.0    0.0059        12     151     188 ..     308     341 ..     304     359 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.39
                   Put_Phosphatase  4 vfDFDktiidedsdnwvv.delpatelfeelretlrkglwnelmdrvlkelheqgvseadikk 65
                                      ++D D+ +++  s  +vv d   a+ ++++l++ +r++     +d  +  l++++ + +  k+
  gi|330506331|ref|YP_004382759.1| 23 IVDMDQKVMQGISVMTVVaDFESAKVTPQKLEKWYRDNAESLAIDFSFLPLEKHQGRRQTAKE 85
                                      678888888877765444155667778888888888776666666666666555544444443 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 6.4e-08
                   Put_Phosphatase   2 lvvfDFDktiidedsdnwvvdelpatelfeelretlrkgl..wnelmdrvlkelheqgvseadikkvlrsiplspgl 76 
                                       l+vfD D ti+d +  n + + ++ +e+ + + +   +g   ++e + + ++ l+  g   + ++++   + l+pg 
  gi|330506331|ref|YP_004382759.1| 171 LIVFDMDMTIVDFEIINRLASFAGVDEQVKAITDRAMNGEmdFKESLRQRVRLLK--GMPFSTLQEIAADLQLTPGS 245
                                       89******************************99877653237788888788885..677788999999999***** PP

                   Put_Phosphatase  77 velikslakkkleldliiiSDaNsffieeileaagledlFs 117
                                        eli++l  k+ ++ + +iS   ++f + + e +g+   F+
  gi|330506331|ref|YP_004382759.1| 246 EELIHHL--KQVGYKIALISGGFTYFTDVLKERLGFDYAFA 284
                                       *******..5789***************9999999988886 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0059
                   Put_Phosphatase 151 KgkvleelvaeqaregveyerliYvGDganDlCpvlkl 188
                                       Kg+++ +l +   re+++ + ++ vGDganD C + k 
  gi|330506331|ref|YP_004382759.1| 308 KGRIIYDLAE---REKISPDNIVAVGDGAND-CLMIKN 341
                                       5566655554...478899************.555554 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   2.8   7.8e-09   1.5e-05       1     175 [.     172     346 ..     172     348 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 7.8e-09
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkke 77 
                                       i+FD+D T++d      +++n+l+   g++e  +   ++ ++ ++ + ++++  + ++  +    +++ +e   +  
  gi|330506331|ref|YP_004382759.1| 172 IVFDMDMTIVDF-----EIINRLASFAGVDEQVKAITDRAMNGEM-D-FKESLRQ-RVRLLKGMPFSTLQEIAAD-- 238
                                       79*********5.....5677777666776666666666666666.3.3333332.2333555666788898999.. PP

                             HAD_2  78 vkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyF.......dvivtsedvekk......KPdpevi 141
                                       +++ +g +el++ Lk+ gyk+++++ + +  ++   e+lg++  F       d ++t+e  + +      K   ++i
  gi|330506331|ref|YP_004382759.1| 239 LQLTPGSEELIHHLKQVGYKIALISGGFTYFTDVLKERLGFDYAFandleieDGVLTGEIKG-EiidaeaK--GRII 312
                                       ******************************************99943333322344444322.22333234..8899 PP

                             HAD_2 142 ekaleklklkkeeviyvGDsptDieaakkagikv 175
                                         + e+ k+++++++ vGD  +D    k+ag+ v
  gi|330506331|ref|YP_004382759.1| 313 YDLAEREKISPDNIVAVGDGANDCLMIKNAGLGV 346
                                       9999999************************876 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       0.2     4e+02       2      27 ..     169     192 ..     168     215 .. 0.77
   2 ?   10.5   0.0   0.00016      0.32     166     208 ..     308     349 ..     302     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.2
                                       SEEEEE-TBTTTB.S-HHHHHHHHHH CS
                              S6PP   2 klllvsdLDntlvdgdnealarlnel 27 
                                       k+l+v d+D t+v  d e ++rl ++
  gi|330506331|ref|YP_004382759.1| 169 KRLIVFDMDMTIV--DFEIINRLASF 192
                                       689**********..65566665554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT CS
                              S6PP 166 kgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgn 208
                                       kg+ +  La++ ++ +++i+ +Gd  nD  ++++  lgV   n
  gi|330506331|ref|YP_004382759.1| 308 KGRIIYDLAEREKISPDNIVAVGDGANDCLMIKNAGLGVAF-N 349
                                       777788899***********************999999975.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2687.22
//
Query:       gi|330506332|ref|YP_004382760.1|  [L=62]
Description: hypothetical protein MCON_0016 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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      0.012   15.7   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.0   6.6e-07     0.012      23      51 ..      17      45 ..       4      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.6e-07
                   HicB_lk_antitox 23 cfsagdtleeaianakeaielhleglied 51
                                      ++  gdt  ea+a+ k+ai++h+e+   +
  gi|330506332|ref|YP_004382760.1| 17 VIGEGDTYGEALADVKSAIQFHIETFGRE 45
                                      4668********************97555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 462.50
//
Query:       gi|330506333|ref|YP_004382761.1|  [L=59]
Description: YHS domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-18   64.2   0.7    9.3e-18   64.1   0.7    1.0  1  YHS              YHS domain
     0.0032   17.8   0.3      0.005   17.1   0.3    1.4  1  Arc_trans_TRASH  Archaeal TRASH domain
  ------ inclusion threshold ------
      0.012   16.3   0.1      0.014   16.1   0.1    1.1  1  ATPase-cat_bd    Putative metal-binding domain of cation tran


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.7   1.6e-21   9.3e-18       2      46 ..       3      47 ..       2      49 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.6e-21
                               YHS  2 tdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYat 46
                                      +dP c+m vd ++a+  seYkGk+YyFc +gCk +F+++Pek ++
  gi|330506333|ref|YP_004382761.1|  3 IDPICKMAVDEKTAKLVSEYKGKKYYFCAPGCKKAFDQNPEKHLG 47
                                      8*****************************************887 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   8.4e-07     0.005      13      33 ..      18      38 ..      11      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.4e-07
                   Arc_trans_TRASH 13 ivyklknkvYyvCCktCksel 33
                                      +v ++k k Yy+C + Ck+ +
  gi|330506333|ref|YP_004382761.1| 18 LVSEYKGKKYYFCAPGCKKAF 38
                                      5778999***********998 PP

>> ATPase-cat_bd  Putative metal-binding domain of cation transport ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   0.1   2.3e-06     0.014       5      36 ..       7      39 ..       6      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.3e-06
                     ATPase-cat_bd  5 Cglpveesa.klkaeiegeerefCCkGCqavaq 36
                                      C+  v+e++ kl +e++g++ +fC +GC+  ++
  gi|330506333|ref|YP_004382761.1|  7 CKMAVDEKTaKLVSEYKGKKYYFCAPGCKKAFD 39
                                      8888876654999***************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 432.81
//
Query:       gi|330506334|ref|YP_004382762.1|  [L=829]
Description: copper-translocating P-type ATPase [Methanosaeta concilii GP6]
Scores for complete 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-58  196.1   4.4    2.3e-57  193.4   1.5    2.5  2  E1-E2_ATPase  E1-E2 ATPase
    3.5e-46  158.1   1.2    1.8e-45  155.8   2.1    1.8  2  Hydrolase     haloacid dehalogenase-like hydrolase
    1.4e-29  102.3   0.6    1.7e-14   54.0   0.0    2.6  2  HMA           Heavy-metal-associated domain
    2.2e-05   24.3   1.0      0.013   15.3   0.3    2.3  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
     0.0056   16.7   0.1       0.49   10.5   0.0    2.5  2  RRM_3         RNA binding motif
  ------ inclusion threshold ------
       0.14   11.9   0.1       0.14   11.9   0.1    2.1  2  DUF443        Protein of unknown function (DUF443)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.025        76     106     169 ..     156     221 ..     136     231 .. 0.64
   2 !  193.4   1.5   7.8e-61   2.3e-57       2     179 ..     301     479 ..     300     481 .. 0.99

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.025
                                       ----HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHH..HHHHHHHHS-TTHHHHHHH CS
                      E1-E2_ATPase 106 skktplqkkldklgkvlvpvvlliallvflialllgkslaeallr..alallvaaiPcaLplavpl 169
                                        ++++l  k ++++  +++ +ll+a++ + ++ ++  ++ +a+ +  +l +lv+++P    +  p+
  gi|330506334|ref|YP_004382762.1| 156 LREKDLSDKKRRIIIGFAASILLMAMMYIPLHRIIPSGISTAVPNlmSLLMLVVSLPVFVYVSHPI 221
                                       455666667777777777777777777777777777777777777334555667777666555444 PP

  == domain 2  score: 193.4 bits;  conditional E-value: 7.8e-61
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvs 78 
                                       l+p++a+v+rdg++ e++a e+ ++D+vl+++g++vpaDg +veg++ vdes++TGE +p+ k +g++v +Gt++++
  gi|330506334|ref|YP_004382762.1| 301 LQPRQATVLRDGRQIEVAAVEVMVDDLVLVRPGEKVPADGLVVEGESYVDESMITGEPVPAFKAAGEKVVGGTMNKN 377
                                       79*************************************************************************** PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HHHHHHHHH CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.eallralal 154
                                       g++++++t++g+dt l+ i++lv+ea+ +++ +q+++d+++++++p++l+ia+++f++++++ +++  ++l+  +++
  gi|330506334|ref|YP_004382762.1| 378 GSLTFKATRVGKDTVLAGIIALVQEAQGSRPAMQRIADRIVAYFIPTILAIAAAAFVYWYFVAHNTLlFSLTALISV 454
                                       *****************************************************************999********* PP

                                       HHHHS-TTHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 155 lvaaiPcaLplavplalalgarrla 179
                                       lv+a+PcaL+la p+a+++g++r a
  gi|330506334|ref|YP_004382762.1| 455 LVVACPCALGLASPTAITVGIGRGA 479
                                       **********************988 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.3     7e+03      38      54 ..     217     233 ..     202     252 .. 0.75
   2 !  155.8   2.1   6.1e-49   1.8e-45       2     210 .]     498     714 ..     497     714 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                                       HHCHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                         Hydrolase  38 sehpigkalvaaakars 54 
                                         hpi+ka ++a  +r+
  gi|330506334|ref|YP_004382762.1| 217 VSHPIFKAATRALRNRT 233
                                       479*****999988873 PP

  == domain 2  score: 155.8 bits;  conditional E-value: 6.1e-49
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHHHHHH...HHHHHETTTE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx.. RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakarsgal...tgfatfigrg.. 67 
                                       ++v+fDk+GTLt g+p v+d+++   +++++ l+++      sehp+++a+v+ ak+ +++l   ++f++f+g+g  
  gi|330506334|ref|YP_004382762.1| 498 DVVAFDKTGTLTIGRPDVVDLFAWE-MDERKLLRLAasaekpSEHPLAEAVVRRAKEDGFDLlpaEQFEAFPGKGvv 573
                                       79***********************.9999999999999*******************6666566************ PP

                                       ......HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTT CS
                                       ......xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ......ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaag 134
                                              +a g++ +++++   +p+ l ++   ++++g+t++l+  +++a +v++i+d   +k+  a av++Lk+++
  gi|330506334|ref|YP_004382762.1| 574 ariagmSVAAGNRILFDEMdiAMPDGLLQKAIGYEEEGKTAMLVavDGKASGVLAISDR--LKDSSAYAVEELKKMN 648
                                       *******************9999*********************99*************..**************** PP

                                       EEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 135 ievvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       +evv++tgdnp+ a r+a+++G          + +t ++++pe k + +r+L++ +++v +VGDg+nDa+ala+A+
  gi|330506334|ref|YP_004382762.1| 649 LEVVMITGDNPRSAARVAEKIG----------IQKTLSEVLPEEKAHEVRRLKEAGSRVGFVGDGINDAPALAEAD 714
                                       **********************..........7777***************************************8 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   5.7e-18   1.7e-14       2      62 .]       9      69 ..       8      69 .. 0.98
   2 !   46.3   0.1   1.4e-15   4.2e-12       2      61 ..      77     136 ..      76     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 5.7e-18
                               HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                      ++v+gm Ca+C +++ek+L++l+gV+ v v+l+  t+t ++d++++kl +i +ai+++gy+
  gi|330506334|ref|YP_004382762.1|  9 LKVEGMMCAACTSAIEKALQNLDGVSWVRVNLGGETATAKYDPSKIKLVDIEKAIRDLGYD 69
                                      68**********************************************************7 PP

  == domain 2  score: 46.3 bits;  conditional E-value: 1.4e-15
                               HMA   2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61 
                                       +++ gm Ca C++++e +L +l+gV +v v+la+ ++ V++++ ++ l++ ++ai ++gy
  gi|330506334|ref|YP_004382762.1|  77 LKIGGMACAMCVGAIEAALRKLDGVVDVQVNLAAEKARVTYNPGMVGLEDMKKAIIESGY 136
                                       7899******************************************************99 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0011       3.2      15      56 ..     632     673 ..     626     678 .. 0.90
   2 !   15.3   0.3   4.2e-06     0.013     200     252 ..     691     744 ..     683     746 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0011
                                       ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCS CS
                       Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgldl 56 
                                       +++++++ a+++lk+ + +vv  TG ++r++ +v+e++g++ 
  gi|330506334|ref|YP_004382762.1| 632 RLKDSSAYAVEELKKMNLEVVMITGDNPRSAARVAEKIGIQK 673
                                       67889999*******************************985 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.2e-06
                                       T--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGG.THHH CS
                       Hydrolase_3 200 nisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnne.dGVa 252
                                       +   ++v  +GDg ND + L  a++g+A+g++++ +++  d v  + +  d+Va
  gi|330506334|ref|YP_004382762.1| 691 KEAGSRVGFVGDGINDAPALAEADVGIAIGSGTDVAIETGDIVLMKDDLlDAVA 744
                                       5566788899*****************************999999988888887 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00017      0.49       4      47 ..       9      52 ..       7      66 .. 0.91
   2 ?    3.5   0.1     0.024        71       3      81 ..      76     148 ..      75     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                                      EEEEE-SSS--HHHHHHHCHCCS-ECEEEE-TTSSEEEEEESSH CS
                             RRM_3  4 lklsGlnkelsredikellsklgevayvdyekgdkegevrFked 47
                                      lk++G+  + + + i ++l++l+ v +v ++ g ++++ +++ +
  gi|330506334|ref|YP_004382762.1|  9 LKVEGMMCAACTSAIEKALQNLDGVSWVRVNLGGETATAKYDPS 52
                                      789999999******************************99866 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.024
                                       EEEEEE-SSS--HHHHHHHCHCCS-ECEEEE-TTSSEEEEEESSHHHHHHHHHHHHHC-B-CCTSSEEEEE--HHHH CS
                             RRM_3   3 ilklsGlnkelsredikellsklgevayvdyekgdkegevrFkedeeakkalekateaklkikdaevtlelLeGeeE 79 
                                       +lk+ G+  ++++  i  +l+kl+ v  v ++  ++++ v ++        +  + ++k+ i +   ++  + Gee 
  gi|330506334|ref|YP_004382762.1|  76 VLKIGGMACAMCVGAIEAALRKLDGVVDVQVNLAAEKARVTYNPG------MVGLEDMKKAIIESGYQFIGVAGEET 146
                                       799999***********************************9976......33333333334444555555555555 PP

                                       HH CS
                             RRM_3  80 ke 81 
                                       +e
  gi|330506334|ref|YP_004382762.1| 147 EE 148
                                       55 PP

>> DUF443  Protein of unknown function (DUF443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   4.7e-05      0.14      50     123 ..     153     227 ..     139     283 .. 0.81
   2 ?   -4.3   1.2       4.3   1.3e+04     153     180 ..     424     451 ..     410     460 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
                            DUF443  50 klklnivkkakkks.igllalGsavllgnllrklidvfniqlsklvnliillivlllvlvlriyiskklkkklyn 123
                                       + +l++++  +kk  i +  ++s++l++ +  +l  +++  +s+ v  ++ l++l++ l +++y+s+   k  ++
  gi|330506334|ref|YP_004382762.1| 153 ERELREKDLSDKKRrIIIGFAASILLMAMMYIPLHRIIPSGISTAVPNLMSLLMLVVSLPVFVYVSHPIFKAATR 227
                                       344555554444440445556668999**************************************9876666555 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 4.3
                            DUF443 153 lfflglvilalvalietqniiilivlll 180
                                       ++++    ++++ ++ ++n++++ ++ l
  gi|330506334|ref|YP_004382762.1| 424 TILAIAAAAFVYWYFVAHNTLLFSLTAL 451
                                       3333333333344445555555544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (829 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); 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):               6  [number of targets reported over threshold]
# CPU time: 0.75u 0.28s 00:00:01.03 Elapsed: 00:00:00.45
# Mc/sec: 5591.10
//
Query:       gi|330506335|ref|YP_004382763.1|  [L=177]
Description: hypothetical protein MCON_0019 [Methanosaeta concilii GP6]
Scores for 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-25   86.9   0.1    1.2e-24   86.3   0.1    1.2  1  FeThRed_B  Ferredoxin thioredoxin reductase catalytic beta ch
  ------ inclusion threshold ------
      0.015   15.6   0.3      0.015   15.6   0.3    1.1  1  zf-C4H2    Zinc finger-containing protein
      0.032   14.6   0.0      0.057   13.8   0.0    1.4  1  FHA        FHA domain


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 !   86.3   0.1     2e-28   1.2e-24       2      94 ..      13     103 ..      12     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 2e-28
                                       HHHHHHHHHHHHHHTT-B-BSSHHHHHHHHHHHHHHHHHHSS-B-SSC--S-HHHHHHH-TTBSS-HHHHHH....- CS
                         FeThRed_B   2 lektrkflekvakklgtkfnpdeevtevvieglarnkeeyGkrlCPCrlvedkeeeekkavwnCPCvplreeldeek 78 
                                       ++ +++ l k ak+ g+++npd ++++++i+gl+ n+++yG++ CPCrl  d++ e+ +++  CPC +++ ++ e++
  gi|330506335|ref|YP_004382763.1|  13 IDRMHARLAKDAKQGGYYLNPDIDFVKGLINGLIVNERRYGYQACPCRLAADDRSEDLDII--CPCNYRDADITESG 87 
                                       6889999******************************************************..************** PP

                                       --TTSSSB-TTSTTB- CS
                         FeThRed_B  79 eChCglfvtkdnaeek 94 
                                       +C+C l+v+k + e k
  gi|330506335|ref|YP_004382763.1|  88 ACYCALYVSKAVIEGK 103
                                       *********9876655 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.3   2.6e-06     0.015     130     200 ..      84     168 ..       2     173 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-06
                           zf-C4H2 130 k...........aaavelkkesstapappapptsllskssqapsapstatasfr.qqpPPMKsClsChqqIHRNAP. 193
                                       +           ++av ++k++ ++ +   pp +  +k++++ ++p + +a +  + + P   C  C     R  P 
  gi|330506335|ref|YP_004382763.1|  84 TesgacycalyvSKAVIEGKQELSSIPERRPPLEERQKLQSQGETPGSRAAILGqKLSVPVWRCVVCGYLCGRDGPp 160
                                       05555555555433444445555555555577777777776666655555555516689****************99 PP

                           zf-C4H2 194 .iCPlCKa 200
                                        +CP+CKa
  gi|330506335|ref|YP_004382763.1| 161 eVCPICKA 168
                                       99*****8 PP

>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.6e-06     0.057       9      54 ..       3      54 ..       1      67 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.6e-06
                                      SSEETT.STTSTTTEEEEEEETTCEEEEEEE.....ESSSSSEEETTEEEST CS
                               FHA  9 cdivld.dpsiSrkHalikfdkgsgkvyleD.....lgSknGtfvNgqrigk 54
                                      +di+ + +++i r Ha++  d ++g++yl        g  nG  vN++r g 
  gi|330506335|ref|YP_004382763.1|  3 NDIQEPtQEEIDRMHARLAKDAKQGGYYLNPdidfvKGLINGLIVNERRYGY 54
                                      7888774577********************9888876688******999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1235.11
//
Query:       gi|330506336|ref|YP_004382764.1|  [L=87]
Description: glutaredoxin [Methanosaeta concilii GP6]
Scores for complete 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-11   42.1   0.0    1.1e-10   41.6   0.0    1.2  1  Glutaredoxin   Glutaredoxin
     0.0019   18.6   0.0     0.0025   18.2   0.0    1.1  1  GST_N_3        Glutathione S-transferase, N-terminal domain
  ------ inclusion threshold ------
      0.013   15.9   0.1      0.031   14.7   0.1    1.6  1  Thioredoxin_2  Thioredoxin-like domain
      0.034   14.5   0.0      0.038   14.3   0.0    1.1  1  GST_N_2        Glutathione S-transferase, N-terminal domain


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   2.4e-14   1.1e-10       1      60 []       9      73 ..       9      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.4e-14
                                      EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSH.HHHHHHHHHH....TSSSSSEEEETTEEE CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkde.eireelkels....gvrtvPqvfidgkhv 60
                                      ++l+  +tC +Ckk+k++L + gv+f++i vd  + e+r++  + +    +  ++P++++++k +
  gi|330506336|ref|YP_004382764.1|  9 IMLYALSTCIWCKKTKEFLSSVGVAFDYIYVDLLKgEERAKAIASVkrfnPSTSFPTLVVNDKAI 73
                                      799**********************999999998775555555555577799*********9965 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   5.5e-07    0.0025       1      57 [.      11      73 ..      11      75 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.5e-07
                                      EES-TTSHHHHHHHHHHHHHT--EEE..E---TTTT....HHHHHHH-TT--SSEEETTS-EE CS
                           GST_N_3  1 LygfpaSpyarrvrlaLnekglpvev..vevtpgeh....deellaknplgkvPvLeddgeal 57
                                      Ly   ++ ++++ +++L   g+++ +  v++ +ge      +++++ np   +P+L+ +++a+
  gi|330506336|ref|YP_004382764.1| 11 LYALSTCIWCKKTKEFLSSVGVAFDYiyVDLLKGEErakaIASVKRFNPSTSFPTLVVNDKAI 73
                                      8999******************98862266667775233467777777********9887766 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1     7e-06     0.031       3      90 ..       3      72 ..       1      85 [. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7e-06
                     Thioredoxin_2  3 gngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgt 81
                                      g+ k  +++++ ++C  Ckk k+ l+++ +v            f+ ++v++ + +e++ka+        + r  + +++
  gi|330506336|ref|YP_004382764.1|  3 GKDKGKIMLYALSTCIWCKKTKEFLSSV-GVA-----------FDYIYVDLLKGEERAKAIAS------VKRFNPSTSF 63
                                      667889999999********99999999.554...........55566666666666533333......3333456666 PP

                     Thioredoxin_2 82 Ptivfldgk 90
                                      Pt+v+ d+ 
  gi|330506336|ref|YP_004382764.1| 64 PTLVVNDKA 72
                                      666666655 PP

>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.5e-06     0.038       2      56 ..      17      73 ..      16      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.5e-06
                                      -HHHHHHHHHHHHCT--EEEEEE..H...-TTSHHHHHHHHCTTTSSSEEE-CTTEE CS
                           GST_N_2  2 CPwahRvlialalkglediisvv..vlepkgfekseefprlnprgtVPvLwdkdgqv 56
                                      C w+ ++  +l   g+ + ++ v  + +++  ++ + ++r+np+++ P+L++ d  +
  gi|330506336|ref|YP_004382764.1| 17 CIWCKKTKEFLSSVGVAFDYIYVdlLKGEERAKAIASVKRFNPSTSFPTLVVNDKAI 73
                                      99**************9998888545666666777788*************976554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 621.77
//
Query:       gi|330506337|ref|YP_004382765.1|  [L=252]
Description: hypothetical protein MCON_0021 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1705.29
//
Query:       gi|330506338|ref|YP_004382766.1|  [L=387]
Description: hypothetical protein MCON_0023 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-82  277.8   0.0    1.7e-82  277.3   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    1.3e-36  124.8   0.0    2.1e-36  124.2   0.0    1.4  1  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.3   0.0   1.9e-86   1.7e-82      11     264 ..      10     262 ..       4     264 .. 0.97

  Alignments for each domain:
  == domain 1  score: 277.3 bits;  conditional E-value: 1.9e-86
                             Nre_N  11 eklravekakkkisskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwl..glslediiklrlslvr 85 
                                       +kl+a+  + +++ +kel+Gs+pPsvf+G+ +YPkV +gp+++p +gd+ v+d+pe+w+  +++ e+ii++rl+l+r
  gi|330506338|ref|YP_004382766.1|  10 KKLTASMYIPSQEVGKELDGSTPPSVFIGSWNYPKVLAGPMISPLHGDTMVMDHPESWIpeNKTQEEIIRYRLNLIR 86 
                                       666666777777789*********************************************9**************** PP

                             Nre_N  86 gekkvkvkkakedklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkvprkveklv 162
                                       g+++vkv++ + ++++e+++ ++ls++++++e+++ +   + ++fd+v +P+Gpsa+le++++ +n++++r++ek++
  gi|330506338|ref|YP_004382766.1|  87 GKRSVKVTDIE-NRFIEKLRDISLSSSSIESEAQFIQA-PKGMSFDDVHTPFGPSAPLERFEI-GNSRWDRDLEKVY 160
                                       **********9.*************************9.6899********************.************* PP

                             Nre_N 163 eDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpeidevevfsg 239
                                        D dlkA++av +L+++g+  ++iq+++SvG++G kkkrrlVPTrWsITA+d+++g++l+++++d++ id +++ + 
  gi|330506338|ref|YP_004382766.1| 161 FDGDLKAADAVEDLHQRGLPFSSIQKAFSVGAMGMKKKRRLVPTRWSITACDSALGDRLLQKVRDYDIIDCCQIREF 237
                                       ***************************************************************************** PP

                             Nre_N 240 eylgNrflviLaPgkwsfelvEawa 264
                                         l+N+++v+L+P++w++e++Ea+ 
  gi|330506338|ref|YP_004382766.1| 238 ASLNNYYAVLLLPTAWQYEWMEAFL 262
                                       **********************986 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.2   0.0   2.4e-40   2.1e-36       1     110 []     276     386 ..     276     386 .. 0.96

  Alignments for each domain:
  == domain 1  score: 124.2 bits;  conditional E-value: 2.4e-40
                             Nre_C   1 egyegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleeal 77 
                                       e++ g+k+ys+++G+Yy++++avle Le+++rqa++i+lre++ +Y +P+Gv++vRe+vr+a+++kp efe++++al
  gi|330506338|ref|YP_004382766.1| 276 ETNGGKKGYSRVGGCYYSCKMAVLEGLERERRQAGAIILREAYAGY-VPLGVFNVRENVRNAMHQKPLEFEDMRAAL 351
                                       56789*****************************************.9***************************** PP

                             Nre_C  78 eevseklklplkkllkkskllkelk..kqktLddF 110
                                        ++s++l+lp+k+++++s+ll++    +q+tL++F
  gi|330506338|ref|YP_004382766.1| 352 GYISTRLELPVKSFIRQSDLLRGELksRQTTLSSF 386
                                       *********************98665799999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2848.35
//
Query:       gi|330506339|ref|YP_004382767.1|  [L=283]
Description: hypothetical protein MCON_0024 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.077   13.0   0.0       0.13   12.3   0.0    1.4  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 ?   12.3   0.0   7.1e-06      0.13      53     106 ..     198     246 ..     162     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-06
                                       HHHHHHHHHC-SEEEEE--SSSSSS--HHHHHHHHHHHHCT-EEEEE-S-GCGH CS
                   Nuc_deoxyrib_tr  53 yeadialirqaDavianldpfrgpeaDsGtafEvGyavalgkpvlayttdarel 106
                                       ++   + i+qa ++ia+l++     aD+ +++ +G+a  lgk +++   +  ++
  gi|330506339|ref|YP_004382767.1| 198 VRDLWRSINQAALIIADLTG-----ADPQVMYALGIAHTLGKDTILIHPQGSKY 246
                                       55556789************.....9****************999888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2158.49
//
Query:       gi|330506340|ref|YP_004382768.1|  [L=379]
Description: Myo-inositol-1-phosphate synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-32  109.5   0.0    1.8e-31  108.6   0.0    1.5  1  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
  ------ inclusion threshold ------
      0.044   13.2   0.0      0.072   12.5   0.0    1.3  1  NAD_binding_5   Myo-inositol-1-phosphate synthase


Domain annotation for each model (and alignments):
>> Inos-1-P_synth  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.6   0.0     2e-35   1.8e-31       1     109 []     196     304 ..     196     304 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 2e-35
                                       SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE...EE CS
                    Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi...kY 74 
                                       G+T+++++L++l+++r++ ++++++lNi+Gn+D++n+ ++er+ksKkisK+++v++i+++ +l   d  ++i   +Y
  gi|330506340|ref|YP_004382768.1| 196 GATIVHRALTQLFKDRACIMDRTYQLNIGGNTDFLNMLNRERLKSKKISKTEAVQSILDT-PL--CDDDIHIgpsDY 269
                                       9**********************************************************9.55..3568******** PP

                                       -GGGTTEEEEEEEEEEEEGGGEEEEEEEEEEEEH. CS
                    Inos-1-P_synth  75 vpylgDsKvaldeieseiflggkntielkleceDS 109
                                       vp+ +D+Kv++ ++e++if+++++++el+l++eDS
  gi|330506340|ref|YP_004382768.1| 270 VPWQKDNKVCFLRMEGRIFGDTPINLELRLSVEDS 304
                                       **********************************9 PP

>> NAD_binding_5  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     8e-06     0.072     207     258 ..     148     258 ..     124     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8e-06
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx............................... RF
                     NAD_binding_5 207 tiyavAailegvpyingsPqntl.vpglvelAekkgvfiaGdDfKt............................... 251
                                         ya Aa+ +gv ++n  P      p   +  +  g++i+GdD+K+                               
  gi|330506340|ref|YP_004382768.1| 148 RFYAQAALDAGVGFVNCMPVFIAsNPEWAKKFQVAGIPIVGDDIKSqigativhraltqlfkdracimdrtyqlnig 224
                                       67*****************766655666666666899*********8888888888888888888888888888877 PP

                                       ...........................xxxxxxx RF
                     NAD_binding_5 252 ...........................lLAaPli 258
                                                                  +L +Pl+
  gi|330506340|ref|YP_004382768.1| 225 gntdflnmlnrerlkskkiskteavqsILDTPLC 258
                                       7777777777777777777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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: 00:00:00.38
# Mc/sec: 2998.75
//
Query:       gi|330506341|ref|YP_004382769.1|  [L=108]
Description: cupin 2 barrel domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-15   55.0   0.0    5.9e-15   54.7   0.0    1.2  1  Cupin_2        Cupin domain
    3.9e-06   26.8   0.1    4.9e-06   26.5   0.1    1.1  1  AraC_binding   AraC-like ligand binding domain
    7.4e-05   22.4   0.0     0.0001   21.9   0.0    1.2  1  Cupin_3        Protein of unknown function (DUF861)
     0.0011   18.6   0.0     0.0014   18.2   0.0    1.2  1  Cupin_1        Cupin
     0.0015   18.1   0.2       0.38   10.2   0.0    2.0  2  PCO_ADO        PCO_ADO
     0.0019   18.3   0.0     0.0023   18.1   0.0    1.2  1  CENP-C_C       Mif2/CENP-C like
  ------ inclusion threshold ------
      0.018   14.7   0.0      0.019   14.6   0.0    1.1  1  DMSP_lyase     Dimethlysulfonioproprionate lyase
      0.084   13.1   0.0        0.1   12.8   0.0    1.1  1  Ectoine_synth  Ectoine synthase


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.0   2.6e-18   5.9e-15       3      61 ..      33      90 ..      31      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 2.6e-18
                                      EEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-S CS
                           Cupin_2  3 velppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtg 61
                                      + l+ G ++p+h+Hp+  + +yV++G++ +t+dg+  el++Gds+  p+g+ H  r  +
  gi|330506341|ref|YP_004382769.1| 33 FDLESGVQIPEHSHPHD-QAGYVVSGRIQITIDGNSLELGPGDSYCAPPGVLHSARALE 90
                                      56788889********8.***********************************998765 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 !   26.5   0.1   2.2e-09   4.9e-06      15      63 ..      40      88 ..      28      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.2e-09
                                      SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE CS
                      AraC_binding 15 sfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyes 63
                                        p+h h++ + +yv++G+ +++++g+  +lgpGd    ppg++H+ ++
  gi|330506341|ref|YP_004382769.1| 40 QIPEHSHPHDQAGYVVSGRIQITIDGNSLELGPGDSYCAPPGVLHSARA 88
                                      5799*****************************************9875 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 !   21.9   0.0   4.5e-08    0.0001      26      63 ..      49      85 ..      40      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.5e-08
                                      EEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEEEC CS
                           Cupin_3 26 dEfcyileGevkvtpeggetvelraGDlvvlpkglsgt 63
                                      d+  y+++G++++t  +g+  el++GD+   p+g    
  gi|330506341|ref|YP_004382769.1| 49 DQAGYVVSGRIQITI-DGNSLELGPGDSYCAPPGVLHS 85
                                      6666***********.******************8333 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   6.4e-07    0.0014      32     109 ..      27      94 ..      19     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.4e-07
                                       TEEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEE CS
                           Cupin_1  32 gisaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepav 108
                                       ++ + r+dle g +++ h h    +  yv+ G+    +++ gn     + +l +Gd    P+g+ h + + +   +v
  gi|330506341|ref|YP_004382769.1|  27 ALMICRFDLESGVQIPEHSH-PHDQAGYVVSGRIQ--ITIDGN-----SLELGPGDSYCAPPGVLHSARALE--ATV 93 
                                       5678899*************.8899********99..677776.....689*****************9994..333 PP

                                       E CS
                           Cupin_1 109 a 109
                                       +
  gi|330506341|ref|YP_004382769.1|  94 V 94 
                                       3 PP

>> PCO_ADO  PCO_ADO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00017      0.38      37      78 ..      21      61 ..       7      67 .. 0.82
   2 !    6.5   0.0    0.0023       5.1     123     145 ..      81     102 ..      64     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                           PCO_ADO 37 tlyetdsfslgvFvlppgaviPLHdHPgMtvlskllyGslhi 78
                                      tl   +++ ++ F l++g  iP H HP+ +    ++ G+++i
  gi|330506341|ref|YP_004382769.1| 21 TLVSGKALMICRFDLESGVQIPEHSHPHDQA-GYVVSGRIQI 61
                                      566778899******************8554.4577777776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0023
                           PCO_ADO 123 gnlHeitaitgpaaflDilsPPY 145
                                       g+lH  +a++ +++++D  sPP 
  gi|330506341|ref|YP_004382769.1|  81 GVLHSARALE-ATVVVDTFSPPR 102
                                       89********.***********5 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     1e-06    0.0023      25      66 ..      40      81 ..      20      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1e-06
                                      EEEEE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT CS
                          CENP-C_C 25 KkkknskkatlvFyViqGrvevtvsktsfvigkgsvFqvPag 66
                                        +++s+ +  + yV+ Gr+++t+ ++s  +g+g+++  P g
  gi|330506341|ref|YP_004382769.1| 40 QIPEHSHPHDQAGYVVSGRIQITIDGNSLELGPGDSYCAPPG 81
                                      5677888888899************************99965 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   8.5e-06     0.019     106     162 ..      39      94 ..      19      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.5e-06
                        DMSP_lyase 106 vrYPdHhhaaeelYlvlsggaefrqgeaewlsrgiGevifnepgikhamrsaeePll 162
                                       v+ P+H+h+++ + +v+sg + +  +++  l+ g G+++ ++pg+ h  r+ e+ ++
  gi|330506341|ref|YP_004382769.1|  39 VQIPEHSHPHDQAGYVVSGRIQITIDGNS-LELGPGDSYCAPPGVLHSARALEATVV 94 
                                       788*******999999***9888777775.9*****************999877665 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.6e-05       0.1      44     110 ..      37     101 ..      23     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.6e-05
                                       TT--EEEE-TT-EEEEEEEE--EEEEETTT--EEEE-TTEEEEETTT-EEEEEESS-EEEEEEEES- CS
                     Ectoine_synth  44 agtetelkYknHleavycieGegeveeledgevyeikpgtlYlldkhdkHllrakkelrlvcvFnPp 110
                                       +g +   + + H  a y+++G+ +++   dg+  e+ pg+ Y+      H  ra +   +v  F+Pp
  gi|330506341|ref|YP_004382769.1|  37 SGVQIPEHSHPHDQAGYVVSGRIQITI--DGNSLELGPGDSYCAPPGVLHSARALEATVVVDTFSPP 101
                                       55566666778999******9888875..8************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       160  (0.00892409); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); 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):               8  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 816.51
//
Query:       gi|330506342|ref|YP_004382770.1|  [L=395]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-08   35.6   0.0    2.2e-08   34.7   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
    2.9e-08   33.8   0.2    5.6e-07   29.7   0.0    2.6  2  HHH_3        Helix-hairpin-helix motif
     0.0052   17.1   0.1     0.0092   16.3   0.1    1.4  1  Fer4_12      4Fe-4S single cluster domain
     0.0054   17.3   0.0      0.021   15.4   0.0    2.1  1  HHH_5        Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.035   14.2   0.0      0.071   13.2   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain
       0.12   12.3   0.0       0.43   10.5   0.0    2.0  1  HHH          Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   7.4e-12   2.2e-08       4     160 ..      75     239 ..      72     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 7.4e-12
                                       ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgir 79 
                                       t+ C+++C++C++ +  +r +   s +++e++++  +l ++ + +++++l++g    +++     ++l  l   ++r
  gi|330506342|ref|YP_004382770.1|  75 TNHCSHQCNYCINATNCSRKVQTFSYTPDELARITLSL-YRSNyIEGLFLSSG--AGRDEDLIMERMLETL--QKLR 146
                                       789*************99********************.67777*******99..4444444444444444..6788 PP

                                       EEEEECSSCHG.......HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET..... CS
                                       xxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                       Radical_SAM  80 itvetngtlpd.......eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr..... 144
                                         +  +g+ +        + +++   el  drvs++leaa+  +  +++  +    ++l+  +++r+++ ++     
  gi|330506342|ref|YP_004382770.1| 147 KQYDFPGYIHLkilpgssKNHIQQAMELA-DRVSINLEAASASQLNEICATKSYENDILQRQRYIRDLRTDEnlpag 222
                                       88888888876777777788999999999.*************8888888888899************98889999* PP

                                       .EEEEEEEBTTTSHHHH CS
                                       .xxxxxxxxxxxxxxxx RF
                       Radical_SAM 145 .vvdrivglpGendeel 160
                                        ++  +vg  Ge+d+++
  gi|330506342|ref|YP_004382770.1| 223 qTTQLVVGAAGESDQDI 239
                                       9*************996 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.19   5.6e+02       3      19 ..     177     193 ..     175     195 .. 0.86
   2 !   29.7   0.0   1.9e-10   5.6e-07       5      45 ..     326     365 ..     324     371 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.19
                             HHH_3   3 avgvdiNtAsaeeLqkl 19 
                                       +v +++  Asa++L+ +
  gi|330506342|ref|YP_004382770.1| 177 RVSINLEAASASQLNEI 193
                                       57899*********875 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 1.9e-10
                             HHH_3   5 gvdiNtAsaeeLqklpGlgpklAknIvayReknGpfksree 45 
                                       +vd N+A + eL ++pG+gp+ Ak+I+a R  +  + s  e
  gi|330506342|ref|YP_004382770.1| 326 PVDPNSAAYRELIRVPGIGPRSAKRIIALRMRKN-IVSKRE 365
                                       79****************************6554.444444 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   3.1e-06    0.0092       9      61 ..      72     126 ..      62     171 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.1e-06
                           Fer4_12   9 slfvsgCnlsCkgCfnketwsfk.sgkeft.kelleeiiedlkkesiegltllGG 61 
                                       +l+++ C+++C++C+n    s k +   +t +el++  +     ++iegl l+ G
  gi|330506342|ref|YP_004382770.1|  72 TLYTNHCSHQCNYCINATNCSRKvQTFSYTpDELARITLSLYRSNYIEGLFLSSG 126
                                       899************9877766623445563555555556666789999988766 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     7e-06     0.021      35      52 ..     335     352 ..     316     358 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7e-06
                                       HHHHTSTTS-HHHHHHHH CS
                             HHH_5  35 eeLakipGiGkktAerii 52 
                                        eL ++pGiG++ A+rii
  gi|330506342|ref|YP_004382770.1| 335 RELIRVPGIGPRSAKRII 352
                                       578888888888888887 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.4e-05     0.071       5      56 ..      75     126 ..      72     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpq.teelleqilkdlkkseikiqglvltGG 56 
                                       ++ C+++C  C n ++ + ++++ + t ++l +i+ +l+ s++ i+gl l+ G
  gi|330506342|ref|YP_004382770.1|  75 TNHCSHQCNYCINATNCSRKVQTFSyTPDELARITLSLYRSNY-IEGLFLSSG 126
                                       599************9999998876155556566658888888.888988765 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00014      0.43      12      28 ..     336     352 ..     331     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                                       HHHTSTT-SHHHHHHHH CS
                               HHH  12 eLlalPGVGpktAeaIl 28 
                                       eL  +PG+Gp  A +I+
  gi|330506342|ref|YP_004382770.1| 336 ELIRVPGIGPRSAKRII 352
                                       999***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2730.54
//
Query:       gi|330506343|ref|YP_004382771.1|  [L=210]
Description: hypothetical protein MCON_0028 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-20   71.8   0.0    8.4e-20   71.3   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 !   71.3   0.0   4.7e-24   8.4e-20      25     139 ..      36     186 ..      20     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 4.7e-24
                           DUF4130  25 ladpdvlrleelarkvsreahrmkgfvRFreledgiyvakiePkhnvlellaehFadRfadekwlIldekrklalvy 101
                                        + p+ ++l++++ +v +e hrmk+fvR r l d+++ + ++P+h++ e ++ehFa+R + +  ++ + + +  +++
  gi|330506343|ref|YP_004382771.1|  36 STSPEAVSLRRMVYAVMSEVHRMKAFVRLRPLGDRVLWGYMKPRHKIGEHTSEHFARRNPGTIIVLGNGAESWTAFF 112
                                       67899999****************************************************99888887777777776 PP

                           DUF4130 102 d....................................lseeedefeelWktyfksiaikeRknpklqrqemPkr 139
                                       +                                     + ++++++++W+ty++s   +eRkn ++ rq mP r
  gi|330506343|ref|YP_004382771.1| 113 RqdrmmrihgaglnetldrlksalkiseeekgadaegARANAQDIDDIWQTYYDSQYCPERKNLQAFRQRMPAR 186
                                       667777777888889999999999999999999999888889******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 00:00:00.40
# Mc/sec: 1575.89
//
Query:       gi|330506344|ref|YP_004382772.1|  [L=103]
Description: hypothetical protein MCON_0029 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 773.85
//
Query:       gi|330506345|ref|YP_004382773.1|  [L=745]
Description: M6 family metalloprotease domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-34  116.1   0.0    1.1e-15   57.3   0.0    2.3  2  P_proprotein  Proprotein convertase P-domain
    0.00034   19.1   3.1       0.63    8.3   0.1    3.5  2  Peptidase_M6  Immune inhibitor A peptidase M6


Domain annotation for each model (and alignments):
>> P_proprotein  Proprotein convertase P-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   2.1e-19   1.9e-15       4      85 ..     529     613 ..     526     614 .. 0.93
   2 !   57.3   0.0   1.3e-19   1.1e-15       2      85 ..     654     740 ..     653     741 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 2.1e-19
                                       EEEEEEEEESSGGGEEEEEE-TTS-EEEEE---TT---SS-EEEEEEE......ESTTTTS---EEEEEEEEESSTT CS
                      P_proprotein   4 vqvsvnithtrrgdlritLvsPsGtrsvLlnrrgkdksrsgfldwtfm......sthlwgeraeGeWkLevkdseee 74 
                                       + ++++i+h+++ dl+++L+sPsG+r +++nr+g     +g+l +t+       + +l+g++ +GeW L+v d ++ 
  gi|330506345|ref|YP_004382773.1| 529 IYLNLDISHSYISDLKVELISPSGKRAMIHNREGG---GEGNLIKTYDsnslpsLGDLVGSPINGEWSLTVADVAAI 602
                                       66789******************************...999***99997777777789******************* PP

                                       --EEEEEEEEE CS
                      P_proprotein  75 dtgtlkswkLr 85 
                                       d+g l++w++ 
  gi|330506345|ref|YP_004382773.1| 603 DKGVLNRWSIE 613
                                       ********986 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 1.3e-19
                                       EEEEEEEEEEESSGGGEEEEEE-TTS-EEEEE---TT---SS-EEEEEEE......ESTTTTS---EEEEEEEEESS CS
                      P_proprotein   2 ehvqvsvnithtrrgdlritLvsPsGtrsvLlnrrgkdksrsgfldwtfm......sthlwgeraeGeWkLevkdse 72 
                                       ++v   v+ith+ +gdlr+++ sPsG++  +++r g     +++ld+t+       +++++g++aeG+W L+  d +
  gi|330506345|ref|YP_004382773.1| 654 QRVVTMVDITHPFIGDLRVEILSPSGKTAIIHDRGGF---DQDNLDKTYDsqinpeLQAFVGQPAEGNWILRAMDLS 727
                                       678899*******************************...5667777777677899********************* PP

                                       TT--EEEEEEEEE CS
                      P_proprotein  73 eedtgtlkswkLr 85 
                                       + d+g +++w++r
  gi|330506345|ref|YP_004382773.1| 728 RLDKGIINKWNMR 740
                                       **********987 PP

>> Peptidase_M6  Immune inhibitor A peptidase M6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.4    0.0001      0.92      59     104 ..     158     201 ..     124     214 .. 0.85
   2 !    8.3   0.1   7.1e-05      0.63     222     347 ..     275     399 ..     235     403 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0001
                      Peptidase_M6  59 ytgpdgenvkslkqyyekqsggsysvdGevadWlkvpknaaryGsn 104
                                       y   +g n+ s+++yy k s g+ +   ev++ ++ +kn+ +y  n
  gi|330506345|ref|YP_004382773.1| 158 Y--NEGGNFCSVRDYYLKMSNGKLDYTNEVVGPITLKKNKMYYHFN 201
                                       3..4699***********************************9766 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 7.1e-05
                      Peptidase_M6 222 edgavGvfaheyGhDLG.LPDeyDtkytGkg....epvgyWslmssGsWaGkiaGteptdfsaqakeflqkqlGGnW 293
                                       +d a+G ++he Gh L  +PD yD     ++       g + lms G  +   +       ++   +++++  G  W
  gi|330506345|ref|YP_004382773.1| 275 DDLAIGTICHETGHLLCrFPDLYDYGRRDEDlvesAGLGLYCLMSVGDHLDDWK------TPSPVCAYFRNLAG--W 343
                                       6889**********99658****9754444322113467899999999887777......34455678888888..8 PP

                      Peptidase_M6 294 lnieeldlaklea...nkgkkltldeasekskrpdvvkvtlpkksveiikPaeGeta 347
                                        + + +dl+k ++   ++g   t+ +++++  ++ +   ++ +   +   P++G   
  gi|330506345|ref|YP_004382773.1| 344 CD-NVVDLNKPGKyeaKHGDYRTVMKYATDRANEYFLVENRSQMGLDRALPSSGLAI 399
                                       87.778887654411044555666666666666666655666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (745 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.42
# Mc/sec: 5290.67
//
Query:       gi|330506346|ref|YP_004382774.1|  [L=150]
Description: fkbp-type peptidyl-prolyl cis-trans isomerase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-24   84.9   0.1    4.6e-24   84.6   0.1    1.2  1  FKBP_C      FKBP-type peptidyl-prolyl cis-trans isomerase
  ------ inclusion threshold ------
      0.036   14.0   0.0      0.072   13.0   0.0    1.6  1  Tudor_FRX1  Fragile X mental retardation Tudor 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 !   84.6   0.1   5.2e-28   4.6e-24       4      94 .]       3     139 ..       1     139 [. 0.79

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 5.2e-28
                                       BB-TTCEEEEEEEEEETTSSEEEEHCCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTTT....... CS
                            FKBP_C   4 eakegdtVtvhykgkledgkvfdssrsrakplefkvGsgqvikGfeealegmkvGekrtltippelaYge....... 73 
                                       +ak gdtV+vhy+gkl  g +fd+s +   plef++Gsg +i+Gfeea++gm+ Ge +++ ippe +Yg+       
  gi|330506346|ref|YP_004382774.1|   3 QAKMGDTVKVHYTGKLGTGVIFDTS-EGCDPLEFEIGSGSFIPGFEEAVVGMSPGESKKVQIPPEKGYGNykedrai 78 
                                       4899*********************.9*******************************************7777777 PP

                                       ..............................TTBCTTTB.TT...................SEEEEEEEEE CS
                            FKBP_C  74 ..............................kglaggvippn...................atLvFeveLl 94 
                                                                               +                   +tL+F++ Ll
  gi|330506346|ref|YP_004382774.1|  79 tmdkkdfpsdlvpvegmsleictsegtyvpA---------QitdvtettvtldanhplveQTLYFDIMLL 139
                                       7666666666666655555555444444440.........255555556666666777779999999885 PP

>> Tudor_FRX1  Fragile X mental retardation Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     8e-06     0.072       3      27 ..      97     121 ..      95     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8e-06
                        Tudor_FRX1   3 VEVrGsnGafykafvkdvhedsltv 27 
                                        E++ s+G++  a ++dv e  +t 
  gi|330506346|ref|YP_004382774.1|  97 LEICTSEGTYVPAQITDVTETTVTL 121
                                       79******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1146.10
//
Query:       gi|330506347|ref|YP_004382775.1|  [L=293]
Description: HtpX protease [Methanosaeta concilii GP6]
Scores for complete sequence (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  135.9   0.0    1.4e-39  135.9   0.0    1.5  2  Peptidase_M48  Peptidase family M48
      2e-07   30.5   0.5      2e-07   30.5   0.5    2.0  2  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.024   14.8   0.1      0.045   14.0   0.1    1.4  1  DUF4157        Domain of unknown function (DUF4157)
       0.12   12.2   0.0       0.17   11.7   0.0    1.2  1  SprT-like      SprT-like family
       0.16   11.5   0.1       0.24   10.9   0.1    1.3  1  DUF2268        Predicted Zn-dependent protease (DUF2268)
        4.4    6.6   8.8         18    4.7   8.8    1.9  2  DUF373         Domain of unknown function (DUF373)
        8.9    6.2  10.5         10    6.0   0.6    2.4  2  DUF2721        Protein of unknown function (DUF2721)


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 ?   -2.5   0.3       1.4   3.7e+03      88     110 ..      18      40 ..      10      59 .. 0.43
   2 !  135.9   0.0   5.5e-43   1.4e-39       2     195 ..      73     287 ..      72     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHTT-SHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  88 llasillllglallisraeedaa 110
                                        +   +l++++++++ +++ d++
  gi|330506347|ref|YP_004382775.1|  18 MILLAVLYMAFLAVLVSQGVDNI 40 
                                       22233333333333333333333 PP

  == domain 2  score: 135.9 bits;  conditional E-value: 5.5e-43
                                       --SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   2 lreaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikh 77 
                                       ++++el+++v++l + a+l  p++k++vvns+  NAFa+g+++++  +++t+g++ q+l+++el+aVl+HEl H+k+
  gi|330506347|ref|YP_004382775.1|  73 SEAPELHQIVSRLCAIADL--PMPKIAVVNSSMPNAFATGRNQKNaVVAVTTGIM-QKLDHSELEAVLAHELTHVKN 146
                                       6899***************..*********************99989********.********************* PP

                                       THHHHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---H...HHHHHHHHHTT...HHHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  78 rhsvvslivsllasillllglallisraeedaagafldalav...liglliillfl...alSRkrEyqADeagvell 148
                                       r+++v++i + l+s+++ l++++ +   ++ +   ++++  v   + +++ +l+f+   alSR+rE+ AD+ ++ ++
  gi|330506347|ref|YP_004382775.1| 147 RDMMVMTIATFLSSMAQILVRSMPFMGGGGGRDRDSGGSFIVifvVSLAVWVLSFIliqALSRYREFAADRGAAIIT 223
                                       ******99999999999998887655444444333333333300033334444444777****************** PP

                                       T.HHHHHHHHHHHHHHTT--S---HHHH..................HHS-SS--HHHHHHHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 149 krakdlvraliklakdlerqdvsaslrs..................ellstHPplleRiqalkel 195
                                        ++ +lv+al+k++     +++  +  +                  +l+stHP l+ Ri+al+++
  gi|330506347|ref|YP_004382775.1| 224 GQPSNLVSALMKISGFRVPTEDLRKV-EgpvsalfivpafsrssimNLFSTHPTLEARIEALQRI 287
                                       *************9865443333322.2368889999999999999****************986 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.5   7.7e-11     2e-07      96     222 ..      32     159 ..      24     165 .. 0.67
   2 ?   -0.7   0.2      0.25   6.5e+02       8      33 ..     187     212 ..     184     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 7.7e-11
                     Peptidase_M56  96 vewktilkillliWivgalilllyliaall.vlkkr.fvrklgklraeelkeaLkeakeemqlkrnikirlsssids 170
                                       + ++ +++i+++++i g+++l  y    +  +   + +v+++++ + ++++++L ++        +   +++ss+ +
  gi|330506347|ref|YP_004382775.1|  32 LVSQGVDNIIIILFIGGFMLLQYYYSDKMIlSTMGAkMVSESEAPELHQIVSRLCAIADLPM---PKIAVVNSSMPN 105
                                       56778899999999999999776654333302222225555555555556666555544433...322334555555 PP

                     Peptidase_M56 171 Pavlgllkp..rIvlPadflkklsdeeleyillHElaHlkrkDllvnllvavlq 222
                                        + +g  +   ++ + + +++kl+  ele +l+HEl+H+k++D++v  ++++l+
  gi|330506347|ref|YP_004382775.1| 106 AFATGRNQKnaVVAVTTGIMQKLDHSELEAVLAHELTHVKNRDMMVMTIATFLS 159
                                       555554432225667899*******************************99997 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.25
                     Peptidase_M56   8 iaaaiavllvlllrrilrrllsaiaa 33 
                                       i   ++ l+v++l +il + ls  ++
  gi|330506347|ref|YP_004382775.1| 187 IVIFVVSLAVWVLSFILIQALSRYRE 212
                                       55567889999999999888877665 PP

>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.8e-05     0.045      55      74 ..     127     146 ..     103     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                           DUF4157  55 qpesaagrellaHELtHvvq 74 
                                       + + ++ +++laHELtHv  
  gi|330506347|ref|YP_004382775.1| 127 KLDHSELEAVLAHELTHVKN 146
                                       446677789*********76 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.8e-05      0.17      42      77 ..     111     146 ..      51     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.8e-05
                         SprT-like  42 tvrhhasIeLseklldsrsedrllntLaHElcHlal 77 
                                       +++++a +   + ++++ ++++l+ +LaHEl H+ +
  gi|330506347|ref|YP_004382775.1| 111 RNQKNAVVAVTTGIMQKLDHSELEAVLAHELTHVKN 146
                                       345668888999999******************876 PP

>> DUF2268  Predicted Zn-dependent protease (DUF2268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   9.6e-05      0.24      42      79 ..     109     147 ..      77     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.6e-05
                           DUF2268  42 kgglaipdkiflfl.leneyskerlaallaHEyhHvvrl 79 
                                       +g+   +  + ++  + ++ + ++l+a+laHE+ Hv   
  gi|330506347|ref|YP_004382775.1| 109 TGRNQKNAVVAVTTgIMQKLDHSELEAVLAHELTHVKNR 147
                                       55556666677777788999***************9655 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   8.8    0.0069        18     155     328 ..      13     192 ..      10     222 .. 0.67
   2 ?   -0.8   0.0      0.33   8.4e+02      49      86 ..     203     237 ..     200     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0069
                            DUF373 155 ktiLvplGlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvallll 231
                                       +++L+++ l++l +a+l++l ++++  +ii+l++G+++ll+ +  d+++    +   ++++e++   +  +v+ l +
  gi|330506347|ref|YP_004382775.1|  13 RMLLTMILLAVLYMAFLAVLVSQGVDNIIIILFIGGFMLLQYYYSDKMIL--STMGAKMVSESEAPELHQIVSRLCA 87 
                                       678889999999999999998889999***************99999764..3445666666666666777777776 PP

                            DUF373 232 ligiisgyislesvssasvssglltlilafiygavewlalailtaslgkiideylkre....ekdiarllllpflvl 304
                                       +  +    i++ ++s          ++     +av  ++ +i+  +  + ++++l++e    +++   ++++  ++ 
  gi|330506347|ref|YP_004382775.1|  88 IADLPMPKIAVVNSSM-----PNAFATGRNQKNAVVAVTTGIMQKLDHSELEAVLAHElthvKNRDMMVMTIATFLS 159
                                       6666655444333333.....11222233344555555555555555555555555555443444456677888888 PP

                            DUF373 305 aiglvlygasaylls............lsilalslv 328
                                       +++++l++++ ++              +   ++++v
  gi|330506347|ref|YP_004382775.1| 160 SMAQILVRSMPFMGGgggrdrdsggsfI---VIFVV 192
                                       8888888888888548888888874432...33332 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.33
                            DUF373  49 lfgaikvydeLkaegedvevavvtGdekvgveadrkia 86 
                                       l +a+  y+e +a   d   a++tG++++ v+a +ki+
  gi|330506347|ref|YP_004382775.1| 203 LIQALSRYREFAA---DRGAAIITGQPSNLVSALMKIS 237
                                       5677777777775...4556899********9999996 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   3.7     0.018        46      73     109 ..      18      52 ..      11      56 .. 0.79
   2 ?    6.0   0.6     0.004        10      41     115 ..     129     203 ..     111     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.018
                           DUF2721  73 sallvvlvvlllflsallsldlsllaailfvlallll 109
                                        +ll+vl +++l++  l+s  ++ ++ ilf+ + +ll
  gi|330506347|ref|YP_004382775.1|  18 MILLAVLYMAFLAV--LVSQGVDNIIIILFIGGFMLL 52 
                                       35667777777777..89**************99987 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.004
                           DUF2721  41 eeeeedeelakeiknlrrRarlirrailllvlsallvvlvvlllflsallsldlsllaailfvlalllllvslll 115
                                       +++e ++ la+e+ +++ R  ++    ++l   a ++v ++ ++  +   + d      ++fv++l+  ++s +l
  gi|330506347|ref|YP_004382775.1| 129 DHSELEAVLAHELTHVKNRDMMVMTIATFLSSMAQILVRSMPFMGGGGGRDRDSGGSFIVIFVVSLAVWVLSFIL 203
                                       23344689999********99999988888888888889999999999999*****************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); 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):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1991.80
//
Query:       gi|330506348|ref|YP_004382776.1|  [L=187]
Description: hypothetical protein MCON_0033 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1442.18
//
Query:       gi|330506349|ref|YP_004382777.1|  [L=281]
Description: hypothetical protein MCON_0034 [Methanosaeta concilii GP6]
Scores for complete 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-48  164.2  41.9    4.7e-48  163.9  41.9    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 !  163.9  41.9   2.6e-52   4.7e-48       1     236 []      17     272 ..      17     272 .. 0.93

  Alignments for each domain:
  == domain 1  score: 163.9 bits;  conditional E-value: 2.6e-52
                              TauE   1 lllagllaGfvagllGiGggliavPlLll.ll........ppavavatsllavvatslsgalahrrrgnvdwrllll 68 
                                       lll+g+++Gf  g+lG+Ggg+i+vP+ ++ l+        + +va +tsl+++++tsl g   h  +g v wr +++
  gi|330506349|ref|YP_004382777.1|  17 LLLTGMVVGFACGMLGVGGGFIMVPVQIWaLTsmgvdptlSTRVAFGTSLAVILPTSLCGCHGHNCQGVVLWRPGVT 93 
                                       5799************************9663568999999************************************ PP

                              TauE  69 lllgsliGallGallllllpsellkllfgvlllllallmllrkkrsrakgrerrptaillvligglvGllsGllGiG 145
                                       l+l++l+Ga+lG+ ++++ p+ell+++fg++++  al+m++ +  +r++  e  ++++  +l+g++vG++sGl GiG
  gi|330506349|ref|YP_004382777.1|  94 LGLSGLVGAFLGGTIASHAPGELLRMIFGIIIIGGALRMIYARDLRRGR-PEVVSSLLPYILWGVVVGVISGLAGIG 169
                                       ***************************************9988766666.5566666667788888*********** PP

                              TauE 146 gGfllvpllllllglplkkavatslllilvislagalgyal............agavdwpllllllpgallGallGa 210
                                       gG++lvp++++ +g+++ +av+ts+++i+++++ g+++ya+             g++d+  ++ll+ +++l+a +G+
  gi|330506349|ref|YP_004382777.1| 170 GGVILVPAMVIAMGFTMYQAVGTSTVAIAFNAVGGTIAYAIngwgvaglpaycVGYIDLFQFVLLAGASMLTAHWGV 246
                                       ***************************************66677777888899*****999999************* PP

                              TauE 211 rlarrlsertlrrlfallllvlgvkl 236
                                        +++++se++l+r+f++l++++g+k+
  gi|330506349|ref|YP_004382777.1| 247 NVTHKMSEEKLKRIFIALMILIGLKM 272
                                       ************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1919.79
//
Query:       gi|330506350|ref|YP_004382778.1|  [L=399]
Description: beta-lactamase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-12   46.4   0.1    7.3e-12   45.7   0.1    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
    4.7e-05   23.0   0.0    8.2e-05   22.2   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.018   15.3   0.0    1.4  1  Flavodoxin_1   Flavodoxin
      0.048   13.9   0.0        0.1   12.8   0.0    1.5  1  Flavodoxin_5   Flavodoxin domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.1   1.6e-15   7.3e-12       4     154 ..      34     170 ..      31     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.6e-15
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       ++ nsyl++g+++  LiD+  st a+ +     ++ l++k++d++i+ H+  DH+G lg lve ++  ++a ++   
  gi|330506350|ref|YP_004382778.1|  34 TSYNSYLVRGKNKIALIDAVDSTMADVLI--ENLNALGIKKIDYIIVQHAEQDHTGSLGRLVELYPDSTVAGSARCL 108
                                       567************************98..699******************************************* PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSS CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDalla 154
                                       +l+ e +             v+++  ++ ++++ +++gg  ++ +    +h ++ +  ++  +++lf+ D+l +
  gi|330506350|ref|YP_004382778.1| 109 ELLVEFGL------------VDKKRTQELKDGDVIDLGGKSLQIISAPWVHWPDTILSYLAADRILFSCDFLGS 170
                                       *******4............55555667888877788888888888888*********************9975 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.8e-08   8.2e-05       4     131 ..      49     158 ..      48     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.8e-08
                                       EES--TTHHHH....HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGH CS
                     Lactamase_B_2   4 LiDagpdlrqq....alralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvy 76 
                                       LiDa+ ++++      l a         +++id +++ ha+ DH+  l  l el+p+  ++ +++++l+ l + +  
  gi|330506350|ref|YP_004382778.1|  49 LIDAVDSTMADvlieNLNA-------LGIKKIDYIIVQHAEQDHTGSLGRLVELYPD-STVAGSARCLELLVEFGLV 117
                                       7888888554432111333.......3578***********************9996.6999*********999753 PP

                                       HHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE CS
                     Lactamase_B_2  77 laleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie 131
                                       +      + +++el+ g+ ++lg+  l+i   p  h+  +        +l+++ +
  gi|330506350|ref|YP_004382778.1| 118 D------KKRTQELKDGDVIDLGGKSLQIISAPWVHWPDT--------ILSYLAA 158
                                       3......34678**********988888888888888776........6666555 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   3.9e-06     0.018       3      62 ..     252     313 ..     250     367 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.9e-06
                                       EETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSC..GGGGGTHSEEEEEEEEETTTBEE CS
                      Flavodoxin_1   3 YgSetGnteklAkqlaeelgehgfnadvvslsdydes..lseieeealllvvtsTfgnGdpp 62 
                                       + S+ G+t+++   +a+ l ++g++++ ++l + d+   ++ + +   ++++t+T+  G  p
  gi|330506350|ref|YP_004382778.1| 252 FVSMHGSTKAMTDYIADALIARGIEVKRFDLTNSDIGllAEALVDASTIVIGTPTMLSGAHP 313
                                       78*********************************999999999999999999999999877 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.3e-05       0.1       4      53 ..     252     306 ..     249     330 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                      Flavodoxin_5   4 YsSrdGqTkkiaeriaeelree...gelvdved..vekesedlesydavvigasv 53 
                                       + S +G+Tk   ++ia++l ++   ++ +d+++  +   +e+l ++  +vig++ 
  gi|330506350|ref|YP_004382778.1| 252 FVSMHGSTKAMTDYIADALIARgieVKRFDLTNsdIGLLAEALVDASTIVIGTPT 306
                                       89********************544444455542222445688888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.24s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2740.03
//
Query:       gi|330506351|ref|YP_004382779.1|  [L=105]
Description: Rubredoxin-type Fe(Cys)4 protein [Methanosaeta concilii GP6]
Scores for complete 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-24   83.4   4.2    1.1e-23   83.0   4.2    1.2  1  Rubredoxin       Rubredoxin
    0.00092   19.3   0.1     0.0014   18.7   0.1    1.3  1  PHD_4            PHD-finger
     0.0098   16.0   2.8      0.055   13.6   2.8    2.0  1  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.012   15.1   0.3        1.6    8.3   0.0    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.019   14.9   2.5        2.4    8.1   0.1    2.3  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
      0.023   14.8   0.3        8.1    6.6   0.0    2.5  3  zf-Sec23_Sec24   Sec23/Sec24 zinc finger
      0.059   13.8   2.0        3.2    8.4   0.1    2.3  2  zf-H2C2_2        Zinc-finger double domain
      0.085   12.7   3.3        5.3    7.0   1.2    2.2  2  zf-HIT           HIT zinc finger
      0.096   12.3   1.3       0.17   11.5   0.4    1.8  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.11   12.5   0.0       0.14   12.2   0.0    1.3  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.16   12.0   2.3        1.6    8.8   0.7    2.2  2  Ribosomal_L37ae  Ribosomal L37ae protein family
        0.2   12.6   2.6        8.6    7.5   0.1    2.4  2  zf-C2H2_4        C2H2-type zinc finger
       0.24   11.2   2.4        2.6    7.9   0.2    2.3  2  zinc_ribbon_2    zinc-ribbon domain
       0.32   11.0   1.8        4.4    7.4   0.4    2.2  2  ADK_lid          Adenylate kinase, active site lid
       0.56   10.3   4.9        8.3    6.6   0.2    2.3  2  UPF0547          Uncharacterised protein family UPF0547
       0.63    9.7   0.1       0.63    9.7   0.1    2.0  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
        2.4    8.0   7.4          3    7.6   1.5    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
        8.6    5.9   7.5       0.54    9.7   0.9    2.0  2  zf-ribbon_3      zinc-ribbon domain
        9.4    5.7   8.1       0.45    9.9   0.7    2.3  3  zf-RanBP         Zn-finger in Ran binding protein and others


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 !   83.0   4.2   1.2e-26   1.1e-23       1      47 []      55     101 ..      55     101 .. 0.99

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 1.2e-26
                                       EEEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                        Rubredoxin   1 kyeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47 
                                       ky+C++Cgy+Ydp+ Gdpd+giap+T+Fe+lPd W+CP+Cg++k++F
  gi|330506351|ref|YP_004382779.1|  55 KYKCTLCGYIYDPEIGDPDSGIAPNTPFEELPDSWTCPQCGASKSDF 101
                                       7********************************************99 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.5e-06    0.0014      28      67 ..      53      94 ..      37      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
                             PHD_4 28 sslmeCsvCyeivHpeClkek..egegvvnedlpnsWeCpkC 67
                                       +   C++C  i  pe  +     ++++  e+lp sW Cp+C
  gi|330506351|ref|YP_004382779.1| 53 AKKYKCTLCGYIYDPEIGDPDsgIAPNTPFEELPDSWTCPQC 94
                                      56678**********9887763334557778*********** PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   2.8   5.9e-05     0.055       6      34 ..      56      96 ..      55     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-05
                       Zn-ribbon_8  6 YrCeeCghefe...........vlqsisdaplta.CPeCgs 34
                                      Y+C+ Cg  ++           +  ++ + p+   CP+Cg+
  gi|330506351|ref|YP_004382779.1| 56 YKCTLCGYIYDpeigdpdsgiaPNTPFEELPDSWtCPQCGA 96
                                      ***********999999998887777778889999*****8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0017       1.6      16      37 ..      52      73 ..      44      76 .. 0.83
   2 ?    4.8   0.1     0.021        20       2       9 ..      90      97 ..      89     103 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0017
                                      STTCEEESSSSBEEEECCCCCC CS
                      TF_Zn_Ribbon 16 ergelvCtdCGlVlednsideg 37
                                      +   + Ct CG++ + ++ d+ 
  gi|330506351|ref|YP_004382779.1| 52 MAKKYKCTLCGYIYDPEIGDPD 73
                                      566778*********9999986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.021
                                      EETTTTCE CS
                      TF_Zn_Ribbon  2 kCPnCgst 9 
                                      +CP Cg +
  gi|330506351|ref|YP_004382779.1| 90 TCPQCGAS 97
                                      58888875 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0026       2.4       4      15 ..      55      64 ..      55      73 .. 0.82
   2 ?    6.6   0.3    0.0075         7       5      11 ..      89      95 ..      86      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0026
                    Zn_ribbon_SprT  4 vYrCtgCgreyt 15
                                      +Y+Ct Cg  y 
  gi|330506351|ref|YP_004382779.1| 55 KYKCTLCG--YI 64
                                      7*******..44 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0075
                    Zn_ribbon_SprT  5 YrCtgCg 11
                                      ++C++Cg
  gi|330506351|ref|YP_004382779.1| 89 WTCPQCG 95
                                      9*****9 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 ?   -2.6   0.0       6.5   6.1e+03      12      20 ..       9      17 ..       8      22 .. 0.73
   2 ?    5.8   0.0     0.015        14      18      31 ..      50      63 ..      44      66 .. 0.86
   3 ?    6.6   0.0    0.0086       8.1      22      32 ..      87      97 ..      76     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.5
                    zf-Sec23_Sec24 12 Npfckidfg 20
                                      N +++i  +
  gi|330506351|ref|YP_004382779.1|  9 NAYTQIETS 17
                                      889998654 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.015
                    zf-Sec23_Sec24 18 dfggkrwiCnfCnh 31
                                       f +k+++C +C+ 
  gi|330506351|ref|YP_004382779.1| 50 VFMAKKYKCTLCGY 63
                                      68899*******86 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0086
                    zf-Sec23_Sec24 22 krwiCnfCnhk 32
                                       +w+C+ C+ +
  gi|330506351|ref|YP_004382779.1| 87 DSWTCPQCGAS 97
                                      68******975 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0034       3.2      13      22 ..      54      63 ..      47      66 .. 0.88
   2 ?    5.1   0.2     0.037        35      15      21 ..      89      95 ..      78      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0034
                         zf-H2C2_2 13 kpyeCplCdk 22
                                      k+y+C lC++
  gi|330506351|ref|YP_004382779.1| 54 KKYKCTLCGY 63
                                      78******99 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.037
                         zf-H2C2_2 15 yeCplCd 21
                                      ++Cp C+
  gi|330506351|ref|YP_004382779.1| 89 WTCPQCG 95
                                      69****8 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.2    0.0056       5.3      11      22 ..      53      64 ..      51      65 .. 0.82
   2 ?    5.6   0.0     0.015        14      13      21 ..      88      96 ..      83      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0056
                                      B-SEE-TTT--E CS
                            zf-HIT 11 pakYkCpkCntr 22
                                       +kYkC  C+  
  gi|330506351|ref|YP_004382779.1| 53 AKKYKCTLCGYI 64
                                      58*******975 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.015
                                      SEE-TTT-- CS
                            zf-HIT 13 kYkCpkCnt 21
                                        +Cp+C++
  gi|330506351|ref|YP_004382779.1| 88 SWTCPQCGA 96
                                      679****96 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00018      0.17       5      15 ..      54      64 ..      51      66 .. 0.86
   2 ?   -1.5   0.0       2.2   2.1e+03       7      13 ..      89      95 ..      86      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                      -EEE-TTT--E CS
                   Desulfoferrod_N  5 evYkCevCGni 15
                                       +YkC++CG i
  gi|330506351|ref|YP_004382779.1| 54 KKYKCTLCGYI 64
                                      68*******77 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                                      EE-TTT- CS
                   Desulfoferrod_N  7 YkCevCG 13
                                      + C  CG
  gi|330506351|ref|YP_004382779.1| 89 WTCPQCG 95
                                      5699999 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.14      66      98 ..      51     100 ..       7     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                       EE--EEEETTTS-EEECHH.HHH.................S-TTTSSS-EE CS
                              HypA  66 evpvkvrCreCgkefelee.kal.................rCpkCgsadve 98 
                                        +  k++C+ Cg+ ++ e  +                   +Cp+Cg+++ +
  gi|330506351|ref|YP_004382779.1|  51 FMAKKYKCTLCGYIYDPEIgD-PdsgiapntpfeelpdswTCPQCGASKSD 100
                                       4566899*******9977543.2347899*****************98765 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.7    0.0017       1.6      14      40 ..      34      62 ..      32      65 .. 0.84
   2 ?    2.4   0.0      0.17   1.6e+02      33      43 ..      88      98 ..      83     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                                      SS-HHHHHHH..HHHHHHHHS-BEESSSS CS
                   Ribosomal_L37ae 14 rYGaslrkrv..kkieisqhakytCpfcg 40
                                      rY  s++kr+  k+i + + +ky+C+ cg
  gi|330506351|ref|YP_004382779.1| 34 RYLESAKKRIsrKRIVVFMAKKYKCTLCG 62
                                      788888888744789999**********9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.17
                                      -BEESSSSSSE CS
                   Ribosomal_L37ae 33 kytCpfcgktk 43
                                      ++tCp+cg +k
  gi|330506351|ref|YP_004382779.1| 88 SWTCPQCGASK 98
                                      57899998765 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3     0.049        46       1      10 [.      56      65 ..      56      68 .. 0.82
   2 ?    7.5   0.1    0.0091       8.6       2      16 ..      90     104 ..      89     105 .] 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.049
                         zf-C2H2_4  1 fkCpiCgksF 10
                                      +kC++Cg  +
  gi|330506351|ref|YP_004382779.1| 56 YKCTLCGYIY 65
                                      8*****8655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0091
                         zf-C2H2_4   2 kCpiCgksFsskkaL 16 
                                       +Cp+Cg+s s+ ++L
  gi|330506351|ref|YP_004382779.1|  90 TCPQCGASKSDFEEL 104
                                       7*****999888776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.11     1e+02       1       7 [.      57      63 ..      57      68 .. 0.74
   2 ?    7.9   0.2    0.0027       2.6       2       7 ..      91      96 ..      90     101 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.11
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +C+ CG+
  gi|330506351|ref|YP_004382779.1| 57 KCTLCGY 63
                                      7999997 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0027
                     zinc_ribbon_2  2 CpnCGa 7 
                                      Cp+CGa
  gi|330506351|ref|YP_004382779.1| 91 CPQCGA 96
                                      666665 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 ?    2.8   0.0      0.12   1.2e+02       4      12 ..      58      66 ..      56      84 .. 0.81
   2 ?    7.4   0.4    0.0047       4.4       2      10 ..      89      97 ..      89      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                                      -TTT--EEE CS
                           ADK_lid  4 CpkCGrsYh 12
                                      C  CG +Y 
  gi|330506351|ref|YP_004382779.1| 58 CTLCGYIYD 66
                                      999999996 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0047
                                      EE-TTT--E CS
                           ADK_lid  2 rvCpkCGrs 10
                                      ++Cp+CG+s
  gi|330506351|ref|YP_004382779.1| 89 WTCPQCGAS 97
                                      9******97 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2    0.0088       8.3      16      25 ..      57      66 ..      56      67 .. 0.85
   2 ?    5.5   0.8      0.02        19       2       8 ..      90      96 ..      90      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0088
                           UPF0547 16 fCphCGyvFq 25
                                      +C +CGy+++
  gi|330506351|ref|YP_004382779.1| 57 KCTLCGYIYD 66
                                      7******986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.02
                           UPF0547  2 vCPeCea 8 
                                      +CP+C a
  gi|330506351|ref|YP_004382779.1| 90 TCPQCGA 96
                                      6999975 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3       1.3   1.3e+03       2       9 ..      55      62 ..      54      65 .. 0.86
   2 ?    9.7   0.1   0.00067      0.63       1      11 [.      87      97 ..      87     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                            zf_UBZ  2 tylCerCg 9 
                                       y C  Cg
  gi|330506351|ref|YP_004382779.1| 55 KYKCTLCG 62
                                      699*9998 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00067
                            zf_UBZ  1 dtylCerCgke 11
                                      d+++C++Cg++
  gi|330506351|ref|YP_004382779.1| 87 DSWTCPQCGAS 97
                                      79*******97 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.4     0.056        53       1       9 [.      56      64 ..      56      66 .. 0.88
   2 ?    7.6   1.5    0.0032         3      15      22 ..      89      96 ..      88      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.056
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      Y C  CG+ 
  gi|330506351|ref|YP_004382779.1| 56 YKCTLCGYI 64
                                      99*****96 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0032
                      Rubredoxin_2 15 GrCpsCgs 22
                                      + Cp+Cg+
  gi|330506351|ref|YP_004382779.1| 89 WTCPQCGA 96
                                      99****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 ?   -1.0   0.8       1.4   1.3e+03      18      24 ..      57      63 ..      56      63 .. 0.78
   2 ?    9.7   0.9   0.00057      0.54       4      14 ..      90      99 ..      90     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
                       zf-ribbon_3 18 vCpyCGt 24
                                      +C+ CG+
  gi|330506351|ref|YP_004382779.1| 57 KCTLCGY 63
                                      5888996 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00057
                       zf-ribbon_3  4 rCPnCGaplss 14
                                      +CP+CGa  +s
  gi|330506351|ref|YP_004382779.1| 90 TCPQCGAS-KS 99
                                      5*****96.55 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       7.5   7.1e+03      24      27 ..       6       9 ..       6      11 .. 0.72
   2 ?    0.3   0.2      0.45   4.3e+02       6      12 ..      57      63 ..      55      64 .. 0.84
   3 ?    9.9   0.7   0.00048      0.45       3      12 ..      87      96 ..      85     100 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.5
                                      T--B CS
                          zf-RanBP 24 Cqap 27
                                      C+a 
  gi|330506351|ref|YP_004382779.1|  6 CWAN 9 
                                      9985 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.45
                                      E-SSS-- CS
                          zf-RanBP  6 dCskClv 12
                                      +C+ C++
  gi|330506351|ref|YP_004382779.1| 57 KCTLCGY 63
                                      6999986 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00048
                                      SSEE-SSS-- CS
                          zf-RanBP  3 gdWdCskClv 12
                                      ++W+C+ C++
  gi|330506351|ref|YP_004382779.1| 87 DSWTCPQCGA 96
                                      5777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 719.24
//
Query:       gi|330506352|ref|YP_004382780.1|  [L=146]
Description: hypothetical protein MCON_0038 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1055.74
//
Query:       gi|330506353|ref|YP_004382781.1|  [L=844]
Description: hypothetical protein MCON_0039 [Methanosaeta concilii GP6]
Scores for complete 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   31.1   0.0    0.00021   20.0   0.0    2.3  2  DUF853         Bacterial protein of unknown function (DUF853)
    5.7e-07   29.9   0.0    5.7e-07   29.9   0.0    3.4  3  DUF87          Helicase HerA, central domain
    4.8e-05   22.4   0.1     0.0049   15.8   0.0    2.3  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    0.00016   20.7   0.0       0.18   10.7   0.0    2.3  2  AAA_10         AAA-like domain
     0.0098   15.3   0.0      0.065   12.6   0.1    2.1  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
  ------ inclusion threshold ------
        3.3    8.0   6.8         22    5.4   0.5    2.7  2  KxDL           Uncharacterized conserved protein
        7.1    5.9   7.7         12    5.2   7.7    1.3  1  DUF4407        Domain of unknown function (DUF4407)
        8.7    6.6  10.5        5.7    7.2   1.9    2.4  2  Spc24          Spc24 subunit of Ndc80


Domain annotation for each model (and alignments):
>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   9.4e-08   0.00021       9      64 ..      30      85 ..      24      88 .. 0.81
   2 !    8.6   0.0   0.00027       0.6     199     317 ..     279     395 ..     270     528 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.4e-08
                            DUF853  9 aeqelalalklanrhGliaGatGtGktv.tLqvlaeslseaGvpvfladvkGdLsgi 64
                                       ++++   ++    hG+i G tG Gkt   + +l e+ls  G+p ++ d kGd+ ++
  gi|330506353|ref|YP_004382781.1| 30 MQRDIIYDARNLTTHGIIVGMTGSGKTGlGIVMLEEALS-SGIPCLILDPKGDMGNL 85
                                      56677778888899*************615666666666.7************9876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00027
                            DUF853 199 ePaLdledllrtdadGrGvislLaadkllqsPklyatfLlWllseLfeeLP.evGdldkPklvfffdeahLLfn.da 273
                                        P Ld+e +l  + +G+   s++   +l ++ + +   L  +ls L + +  + G +d   lv ++de   +    a
  gi|330506353|ref|YP_004382781.1| 279 GPPLDIERMLYSS-RGQPQASIIYLAHLSEAERQFVVTL--ILSRLITWMRrQSGTPDLRALV-YMDEVFGFAPpTA 351
                                       5777887777665.8888888888888888888877766..5788888775245777766665.5688765443145 PP

                            DUF853 274 pkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrv 317
                                            +++  +++  r+ GvG+ + tqnP dl  + ++  G+ +
  gi|330506353|ref|YP_004382781.1| 352 EPPSKKQILTILKQGRAYGVGMVLSTQNPVDLDYKAMSNAGTWM 395
                                       55677889999999******************999998888755 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   2.5e-10   5.7e-07      17      68 ..      37      86 ..      25     143 .. 0.83
   2 ?   -1.2   0.0      0.78   1.7e+03     200     226 ..     294     320 ..     256     321 .. 0.78
   3 ?   -3.3   4.7       3.4   7.7e+03     130     148 ..     722     741 ..     642     838 .. 0.56

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.5e-10
                             DUF87 17 dlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal 68
                                      d+ +l t H  i+g+TGsGK+ +  v+lee+l + g++ lilDp G+ g++l
  gi|330506353|ref|YP_004382781.1| 37 DARNL-TTHGIIVGMTGSGKTGLGIVMLEEAL-SSGIPCLILDPKGDMGNLL 86
                                      66666.9*************************.99************88887 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.78
                             DUF87 200 egkitiidlsgvdelaqqlvvsvilrr 226
                                       + + +ii l+ ++e + q vv++il r
  gi|330506353|ref|YP_004382781.1| 294 QPQASIIYLAHLSEAERQFVVTLILSR 320
                                       3467899****************9987 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.4
                             DUF87 130 a.keekeklssdepveklle 148
                                       + ++++ +l++d+   + +e
  gi|330506353|ref|YP_004382781.1| 722 NaDRRVRELNTDTRQRQQEE 741
                                       12222233333332222222 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.2e-06    0.0049      12      55 ..      39      82 ..      32      91 .. 0.91
   2 !    4.2   0.0    0.0076        17     224     285 ..     315     383 ..     292     451 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.2e-06
                     TrwB_AAD_bind 12 eretqhilivGttGsGKtqalekllrairargdraivlDltGaf 55
                                      ++ t h +ivG tGsGKt     +l+++ + g  +++lD++G++
  gi|330506353|ref|YP_004382781.1| 39 RNLTTHGIIVGMTGSGKTGLGIVMLEEALSSGIPCLILDPKGDM 82
                                      56689*************************************97 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0076
                     TrwB_AAD_bind 224 sawldlaikallslpesrerrlWfflDEl.......paLgrleelksllaegRkfGgavvlglqsiaql 285
                                       +++l+  i  + + + + + r  + +DE+       ++ +  +++ ++l++gR +G+ +vl  q+   l
  gi|330506353|ref|YP_004382781.1| 315 TLILSRLITWMRRQSGTPDLRALVYMDEVfgfapptAEPPSKKQILTILKQGRAYGVGMVLSTQNPVDL 383
                                       44455555555555556677777777776333321122234578999*****************97766 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0007       1.6      21      70 ..      42      91 ..      31     107 .. 0.87
   2 !   10.7   0.0   7.9e-05      0.18     241     314 ..     335     410 ..     306     429 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0007
                            AAA_10 21 asasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpe 70
                                        + +i+G +G GK  l  ++   ++  g   li+Dpk ++ +   ++p 
  gi|330506353|ref|YP_004382781.1| 42 TTHGIIVGMTGSGKTGLGIVMLEEALSSGIPCLILDPKGDMGNLLLNFPS 91
                                      56779***********************************9988777765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.9e-05
                            AAA_10 241 fkvvifDEawift...ssaeGkkllkelvRiGRsynaavylvtqsadDvlkeelknniglklaFretdkeeikkvLe 314
                                        + v +DE+  f+     +  kk +  ++++GR+y   ++l tq++ D++ + ++n  g+ ++ r ++++++ ++Le
  gi|330506353|ref|YP_004382781.1| 335 RALVYMDEVFGFApptAEPPSKKQILTILKQGRAYGVGMVLSTQNPVDLDYKAMSN-AGTWMIGRLQTERDKARILE 410
                                       56678888888862213445678888999********************9887765.57777777777666666665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   2.9e-05     0.065      27      54 ..      30      57 ..      21      72 .. 0.84
   2 ?   -0.7   0.0      0.32   7.2e+02     164     186 ..     357     379 ..     336     410 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                                      TS-EEEEEGGGS-.SEEEE--TTSSHHH CS
                      FtsK_SpoIIIE 27 sgnplvldlkkmashllvaGatgsGKSt 54
                                      + + ++ d+++ + h++++G tgsGK+ 
  gi|330506353|ref|YP_004382781.1| 30 MQRDIIYDARNLTTHGIIVGMTGSGKTG 57
                                      6677889999999*************95 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.32
                                       ............----------- CS
                      FtsK_SpoIIIE 164 eritsLsnqgpsygvhvlvtagr 186
                                       ++i  + +qg +ygv ++++++ 
  gi|330506353|ref|YP_004382781.1| 357 KQILTILKQGRAYGVGMVLSTQN 379
                                       38999999999999998888764 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.0     0.012        27      51      80 ..     707     736 ..     687     741 .. 0.82
   2 ?    5.4   0.5    0.0097        22      26      74 ..     788     836 ..     771     838 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.012
                              KxDL  51 kqgtkllkevkkdLesifkkirslkaklak 80 
                                        ++   ++++k++L++  +++r l++ +++
  gi|330506353|ref|YP_004382781.1| 707 DKHESSINRIKSQLNNADRRVRELNTDTRQ 736
                                       46778999*****************98776 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0097
                              KxDL  26 nkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirsl 74 
                                       ++k+reL+el +++ e+ + +++r k  +  + e+k  Le+    ++ +
  gi|330506353|ref|YP_004382781.1| 788 EEKERELEELEDKLAEEISLISDRWKVAADQIEEIKIPLEKADVDVEEM 836
                                       7899********************************9999887776665 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   7.7    0.0052        12     110     208 ..     688     808 ..     683     835 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0052
                           DUF4407 110 aelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk............... 171
                                       ++ ++ ++++a+   ++l+++ ++ ++++++q++++++ +++++++ ++ ++e   +  g+                
  gi|330506353|ref|YP_004382781.1| 688 RRCFQAAEDKADIEMAKLKDKHESSINRIKSQLNNADRRVRELNTDTRQRQQEELLHGAGDLlsgllggrrrslslg 764
                                       566677777777778888888999***********************999999998888888888776444444443 PP

                           DUF4407 172 ..gtgttgvaGkgpaakekkaqldaaqaelaelkakld.....a 208
                                          ++ + + +  ++ ++++++ +++++el+el++kl       
  gi|330506353|ref|YP_004382781.1| 765 gaASRRSMTIRTQERLRSAEEKKEEKERELEELEDKLAeeislI 808
                                       33222222333333333355555555555555555533222221 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.9    0.0025       5.7       4      46 ..     697     739 ..     695     751 .. 0.85
   2 ?    3.7   1.6     0.032        73       9      43 ..     776     803 ..     770     832 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0025
                             Spc24   4 nekfriakelsdleselesleselaelkeeleeleeeseekes 46 
                                       +  +++ak  ++ es++++++s+l++  ++++el++   ++++
  gi|330506353|ref|YP_004382781.1| 697 KADIEMAKLKDKHESSINRIKSQLNNADRRVRELNTDTRQRQQ 739
                                       6678999****************************99888333 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.032
                             Spc24   9 iakelsdleselesleselaelkeeleeleeesee 43 
                                       +++        l s e++++e+++eleele++  e
  gi|330506353|ref|YP_004382781.1| 776 TQE-------RLRSAEEKKEEKERELEELEDKLAE 803
                                       444.......4455555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (844 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1395  (0.0778069); expected 358.6 (0.02)
Passed bias filter:                      865  (0.0482459); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); 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: 0.86u 0.30s 00:00:01.15 Elapsed: 00:00:00.44
# Mc/sec: 5744.24
//
Query:       gi|330506354|ref|YP_004382782.1|  [L=299]
Description: hypothetical protein MCON_0042, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-09   37.8   0.1    2.2e-09   37.3   0.1    1.3  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.022   14.6   0.3      0.054   13.4   0.3    1.6  1  AT_hook    AT hook motif


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 !   37.3   0.1   2.5e-13   2.2e-09     125     213 ..     112     216 ..      39     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.5e-13
                         DDE_Tnp_1 125 lrkhdrnkiltksqkrrnk........................skkekgdvyyvtntnsellsaeevaelyrlRwqi 177
                                       ++k+ +++          +                         + +k+ + +v+  n  +l++e + ++y+ +  +
  gi|330506354|ref|YP_004382782.1| 112 MEKAEKKRG---------RpkkdelltasymiqgeiklneealIEARKNLGRFVLASNQVDLDPEVMLNYYKGQQAV 179
                                       333333333.........24455555558888888889999999999****************************** PP

                         DDE_Tnp_1 178 ErvFkwlkrk.fgldrlryrglnrveaqllllllaln 213
                                       Er F++lk+k f+   +++++ +r+ea  +++ l+l+
  gi|330506354|ref|YP_004382782.1| 180 ERGFRFLKDKsFHVSEVYLKKEERIEALCMIMVLSLL 216
                                       *******************************999986 PP

>> AT_hook  AT hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3     6e-06     0.054       2      10 ..     117     125 ..     116     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-06
                           AT_hook   2 RkRGRPrKa 10 
                                       +kRGRP+K+
  gi|330506354|ref|YP_004382782.1| 117 KKRGRPKKD 125
                                       9*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2315.30
//
Query:       gi|330506355|ref|YP_004382783.1|  [L=450]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-25   89.8   0.0    3.3e-25   89.0   0.0    1.4  1  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
      0.014   14.7   0.3      0.021   14.1   0.3    1.3  1  DDE_Tnp_2    Archaeal putative transposase ISC1217
      0.019   13.3   0.0       0.03   12.6   0.0    1.2  1  DDE_Tnp_1_4  Transposase DDE domain group 1
      0.075   13.0   1.0        1.4    8.9   0.1    2.8  3  Tudor_FRX1   Fragile X mental retardation Tudor 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 !   89.0   0.0   7.3e-29   3.3e-25       2     212 ..     133     371 ..     132     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 7.3e-29
                         DDE_Tnp_1   2 skrevlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkq..lldelrprk 76 
                                       s+r+v i D+t +r +++ +d+++     k  +g+k+  ++++    + s+ i p n++d+k+lk   ++      k
  gi|330506355|ref|YP_004382783.1| 133 SFRDVMIQDSTIIRLHKSLADKWPATRSRKVAAGVKVAFLTSAIANSPKSISILPENTNDVKTLKIgpWV------K 203
                                       6899***************9999988899999********************************995555......7 PP

                         DDE_Tnp_1  77 gklvlaDaGYasaelldtleekgvdyiirlkkntklyrk.............gaeskrrgrlrkhdrnkiltksqkr 140
                                       + ++l D G+ +++l+ ++ e+g+++++rlk+n++ ++              + +++++ +l+k d    ++ + ++
  gi|330506355|ref|YP_004382783.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVgtnqvrntrgvdlNGKHLKDIKLEKSDDIFDVNVEVSF 280
                                       789************************************99777666666663444444444444444444444444 PP

                         DDE_Tnp_1 141 rnk...................skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrgl 198
                                       +++                    +++++++ y+tn++s+ l a+eva+ y+ Rw++E +Fk+lk+++ ld   ++++
  gi|330506355|ref|YP_004382783.1| 281 DRRsyrgeskkdnkifrlvaiyNTEAEEHHFYLTNISSDILNASEVAAVYSGRWEVELIFKELKSRYALDQITTKSP 357
                                       4447777777777799999999999**************************************************** PP

                         DDE_Tnp_1 199 nrveaqllllllal 212
                                        ++ea ++  +l+l
  gi|330506355|ref|YP_004382783.1| 358 YAIEALIWVSILTL 371
                                       *******9998876 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   4.6e-06     0.021     219     288 ..     274     346 ..     202     384 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                         DDE_Tnp_2 219 rhvpvaelPeGeylveyl.dtvikllvlddykkdgrrylfstdln...dtdediittWenrWdievlirelkal 288
                                        +v+v+ + + +y  e   d+ i  lv +   + +  +++ t++    + + ++ + +  rW++e +++elk+ 
  gi|330506355|ref|YP_004382783.1| 274 VNVEVS-FDRRSYRGESKkDNKIFRLVAIYNTEAEEHHFYLTNISsdiLNASEVAAVYSGRWEVELIFKELKSR 346
                                       445543.7777888887767777767777777888999**999973335799********************73 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.6e-06      0.03     217     368 ..     204     372 ..     197     399 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.6e-06
                       DDE_Tnp_1_4 217 kilvRgDSafarpellkwceergvdYviglaknsrlealiaelvekakteaaekkek................erey 277
                                       +i++  D +f + +l++ + e+g ++v +l++n++     ++ v +++  + + k+                 e+++
  gi|330506355|ref|YP_004382783.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVGTNQVRNTRGVDLNGKHLkdikleksddifdvnvEVSF 280
                                       578889999**********************999877766666666666666654436799999999**99999999 PP

                       DDE_Tnp_1_4 278 refayqaesWskerrVvakaerpaeglnlrfvvTsla..klspeelyeqlYcaRGemEnrIKeakldlaadrtsshs 352
                                        +  y+ es + ++   + a +++e  +++f +T+++   l+++e+   +Y  R e+E  +Ke k+  a+d++ ++s
  gi|330506355|ref|YP_004382783.1| 281 DRRSYRGESKKDNKIFRLVAIYNTEAEEHHFYLTNISsdILNASEVA-AVYSGRWEVELIFKELKSRYALDQITTKS 356
                                       99999999855444333334455556667999****99888999999.9*************************999 PP

                       DDE_Tnp_1_4 353 faaNqlrlllsalAyn 368
                                         a ++ +++s l   
  gi|330506355|ref|YP_004382783.1| 357 PYAIEALIWVSILTLL 372
                                       9999988888887654 PP

>> Tudor_FRX1  Fragile X mental retardation Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00031       1.4      17      36 ..      22      41 ..      18      44 .. 0.88
   2 ?    1.1   0.0     0.085   3.8e+02      18      31 ..     269     282 ..     257     291 .. 0.89
   3 ?   -2.6   0.0       1.2   5.4e+03      13      36 ..     313     337 ..     311     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00031
                        Tudor_FRX1 17 vkdvhedsltvaFennWqpe 36
                                       kd+ e++lt +Fe +W  +
  gi|330506355|ref|YP_004382783.1| 22 EKDIVEQELTRMFESKWIRD 41
                                      59***************765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.085
                        Tudor_FRX1  18 kdvhedsltvaFen 31 
                                        d+++ ++ v+F+ 
  gi|330506355|ref|YP_004382783.1| 269 DDIFDVNVEVSFDR 282
                                       59**********96 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.2
                        Tudor_FRX1  13 ykafvkdvhed.sltvaFennWqpe 36 
                                       +  +  d+++  ++ +++   W  e
  gi|330506355|ref|YP_004382783.1| 313 LTNISSDILNAsEVAAVYSGRWEVE 337
                                       5566778888526888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3154.90
//
Query:       gi|330506356|ref|YP_004382784.1|  [L=249]
Description: hypothetical protein MCON_0043, partial [Methanosaeta concilii GP6]
Scores for complete 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-42  142.5   0.0    1.5e-41  141.1   0.0    1.7  2  DUF4277   Domain of unknown function (DUF4277)


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   0.0   8.6e-46   1.5e-41       3     109 .]       7     113 ..       5     113 .. 0.97
   2 ?   -1.8   0.0      0.22     4e+03      43      54 ..     168     179 ..     150     221 .. 0.56

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 8.6e-46
                           DUF4277   3 vksldhlglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfpeffedkplerLlgegve 79 
                                       +  ++hlg+vag +d+l+la++id+++pk+ ++++ ++ ++ka+ilngLg++ ++Lylfp+ff+++p+e+Llg+g+ 
  gi|330506356|ref|YP_004382784.1|   7 SYLIGHLGIVAGSFDALNLADVIDRVLPKRGSRNLPHSVIIKAMILNGLGYTGQRLYLFPNFFKTIPTEKLLGKGIC 83 
                                       5669************************************************************************* PP

                           DUF4277  80 aehlnddrlgrtLDklyeagvtklfteial 109
                                       +++lndd++grtLD++y++g+t+lf+ei+l
  gi|330506356|ref|YP_004382784.1|  84 PTDLNDDVVGRTLDAIYKYGATELFNEISL 113
                                       ***************************985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.22
                           DUF4277  43 vkalilngLgfv 54 
                                       v  ++ n +g+ 
  gi|330506356|ref|YP_004382784.1| 168 VLGMVTNQFGLP 179
                                       555666655533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1769.16
//
Query:       gi|330506357|ref|YP_004382785.1|  [L=47]
Description: hypothetical protein MCON_0045 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.6   0.3      0.015   15.4   0.3    1.1  1  MRP-L47   Mitochondrial 39-S ribosomal protein L47 (MRP-L47)


Domain annotation for each model (and alignments):
>> MRP-L47  Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.3   8.1e-07     0.015       3      38 ..       6      41 ..       4      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.1e-07
                           MRP-L47  3 effddkkdlkseeevkvgraWaaeeLrkksfedLhk 38
                                       f++++  +   ++ k+   W++eeL kk  edLh+
  gi|330506357|ref|YP_004382785.1|  6 SFWENESFVVVTDRTKPAMKWTIEELEKKRKEDLHR 41
                                      6899977776777789*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 325.60
//
Query:       gi|330506358|ref|YP_004382786.1|  [L=100]
Description: hypothetical protein MCON_0046 [Methanosaeta concilii GP6]
Scores for complete sequence (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   25.7   0.0    5.4e-05   23.7   0.0    1.7  2  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0     3e-09   5.4e-05      48     114 ..      12      78 ..       3      80 .. 0.88
   2 ?    1.6   0.0     0.021   3.7e+02      21      43 ..      77      99 ..      75     100 .] 0.89

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3e-09
                                       --T.....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  48 slaed.pepvdlvdvftppeatpeivkealalgakavwlqpgsedeeaaelaeeagirvvgdrCilve 114
                                       + + d   ++d++++ +  ++ +  v+e++++g+k +w+   +e + + ++ ++a + ++  rC+++ 
  gi|330506358|ref|YP_004382786.1|  12 QFS-DlSPEIDCAVIGLTKKDPAHAVEELKTIGIKNFWIHWRTETDGTKKMSQDAVVHYIAGRCPMMY 78 
                                       333.13479*******************************************************9985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.021
                                      HHHHHHT--EEEESSS-SEETTE CS
                     CoA_binding_2 21 ryllehglpvvpVnpkeeeilge 43
                                       yl ++g++++ ++    +ilg+
  gi|330506358|ref|YP_004382786.1| 77 MYLADKGFNMHSIHRAVAKILGK 99
                                      58999*************99994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 753.38
//
Query:       gi|330506359|ref|YP_004382787.1|  [L=53]
Description: hypothetical protein MCON_0047 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 396.51
//
Query:       gi|330506360|ref|YP_004382788.1|  [L=66]
Description: hypothetical protein MCON_0048 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 483.61
//
Query:       gi|330506361|ref|YP_004382789.1|  [L=37]
Description: hypothetical protein MCON_0049 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   0.4      0.045   13.5   0.4    1.1  1  DUF3039      Protein of unknown function (DUF3039)
      0.062   13.4   1.4      0.081   13.0   1.4    1.3  1  Zn-ribbon_8  Zinc ribbon domain
       0.19   12.1   0.2       0.24   11.9   0.2    1.2  1  DUF983       Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> DUF3039  Protein of unknown function (DUF3039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   7.6e-06     0.045      29      51 ..       1      23 [.       1      27 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.6e-06
                           DUF3039 29 LCGkvwvptrdpkkfPvCpeCke 51
                                      +CG +w+ + + +  P C +C +
  gi|330506361|ref|YP_004382789.1|  1 MCGSMWIAHNENNPKPECETCGQ 23
                                      6********************65 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.4   1.4e-05     0.081      23      38 ..      12      27 ..       1      28 [. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                       Zn-ribbon_8 23 dapltaCPeCgsevrr 38
                                       +p+++C +Cg+++r+
  gi|330506361|ref|YP_004382789.1| 12 NNPKPECETCGQKLRK 27
                                      566777********99 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   3.9e-05      0.24       7      24 ..      14      31 ..       9      35 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                            DUF983  7 vadaCeaCgldlsharad 24
                                       +++Ce+Cg++l++ + +
  gi|330506361|ref|YP_004382789.1| 14 PKPECETCGQKLRKRENG 31
                                      689*********998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 297.00
//
Query:       gi|330506362|ref|YP_004382790.1|  [L=42]
Description: hypothetical protein MCON_0050 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 305.64
//
Query:       gi|330506363|ref|YP_004382791.1|  [L=67]
Description: hypothetical protein MCON_0051 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 506.37
//
Query:       gi|330506364|ref|YP_004382792.1|  [L=302]
Description: aldo/keto reductase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-15   57.3   0.0      4e-13   49.2   0.0    2.1  2  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   2.3e-17     4e-13      17     194 ..      52     226 ..      37     237 .. 0.83
   2 !    6.4   0.0   0.00025       4.4     245     275 ..     239     268 ..     228     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.3e-17
                                       HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTSSSS-HHHHHHHHHHH CS
                      Aldo_ket_red  17 keealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeiksglskenireslees 93 
                                         +al++++ a  +Gi +fD+A++Y    s+ ++G +  + +++r +++ ++K         +  +  + r+ l e+
  gi|330506364|ref|YP_004382792.1|  52 GRDALQVIEEAATRGISYFDSAKAY--AGSQGYYGSFYRSHQENRSTIFQTSKS--------AAREYHEARADLFET 118
                                       57899********************..***************************........778888999****** PP

                                       HHHHT-S-EEEEEE-S--TTS-......HHHHHHHHHHHHHTTSEEEEEEES--.HHHHHHHHHTTT--EEEEE-B- CS
                      Aldo_ket_red  94 lkrLgtdyvDllllHrpdpslp.....sieevldaleelvkeGkiraiGvSnfs.veqlekakkkkkvkivavqvey 164
                                       l+ +g++ +Dl+++H+     +     s   +l+a+ e +++G+ ++iGv+++   e + +a   +  ++ av    
  gi|330506364|ref|YP_004382792.1| 119 LEVMGLKSLDLWQIHDLRTRREkeeieSSNGALKAFIEARDSGLTKYIGVTGHHdPEVILAA--IESWPLDAVLLPV 193
                                       ****************9998886655555555577777777**********98889999888..6777777777777 PP

                                       BTT...-HHHHTTHHHHHHHTT-EEEEBSTTGG CS
                      Aldo_ket_red 165 nll...releeegllelckkkgvpliaysplgg 194
                                       n+       +   ++ ++ +kg+++i + +lg 
  gi|330506364|ref|YP_004382792.1| 194 NPAeaiIGGFMDRVITAALDKGIAVIGMKVLGA 226
                                       777334444667777788888999999999886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00025
                                       HHHHHHHTTSTT-SEEEE--SSHHHHHHHHG CS
                      Aldo_ket_red 245 qlalryalsqpavgivipgasnieqlednld 275
                                       +l +r+al +   +++i+g+s++e++++ ++
  gi|330506364|ref|YP_004382792.1| 239 ELLIRFAL-SRDITTAIVGCSSPEEVQQLAR 268
                                       6889****.588999************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 1889.52
//
Query:       gi|330506365|ref|YP_004382793.1|  [L=348]
Description: hypothetical protein MCON_0054 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 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:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2315.99
//
Query:       gi|330506366|ref|YP_004382794.1|  [L=67]
Description: hypothetical protein MCON_0056 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 523.04
//
Query:       gi|330506367|ref|YP_004382795.1|  [L=167]
Description: hypothetical protein MCON_0057 [Methanosaeta concilii GP6]
Scores for complete 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-05   23.2   0.0    9.6e-05   22.9   0.0    1.2  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.4e-09   9.6e-05      23     117 ..      34     144 ..       6     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.4e-09
                                       HHHHTS.....SEEEEEHHHHHHHHHHHHS....SCHCHHHHHHHHHHHHHHHTSEEEE..BCHHHHHHHHHHHHHH CS
                               PIN  23 klleel.....eelvtsalvlaEllyvlar....rkskrekaaelvelllllsalkilp..idaeiaeeaaeialky 88 
                                       k l +l       l++++ vl E+++++      +++++  ++el+el +++s+l+i     ++++a + + ++++ 
  gi|330506367|ref|YP_004382795.1|  34 KFLFHLsshpdISLCVPISVLGEVVIICVEgewkGREDKHNREELHELIDIWSGLRISFlhPNEAVATTCYNLYNHS 110
                                       55555555566789****************99976666666666666666677766643449999999999999998 PP

                                       H.....SBHHHHHHHHHHHHHT-EEE.ESSTHHH CS
                               PIN  89 g.....llpnDaliaAtAkehgikliatfDedfr 117
                                       +     ++p+D++++  A++++ + ++t D+ +r
  gi|330506367|ref|YP_004382795.1| 111 KykdsrIKPADLVHLGYALAYDVDFFITTDRILR 144
                                       899***************************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1337.69
//
Query:       gi|330506368|ref|YP_004382796.1|  [L=280]
Description: nitrogenase MoFe cofactor biosynthesis domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-53  181.9   0.2      3e-53  181.0   0.2    1.4  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
  ------ inclusion threshold ------
      0.088   12.8   0.0       0.42   10.7   0.0    1.9  2  Gly_rich_SFCGS  Glycine-rich SFCGS


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 !  181.0   0.2   3.4e-57     3e-53       1     258 [.      23     271 ..      23     276 .. 0.89

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 3.4e-57
                                       -HHHHHHHHHTTBTTEEEEEES-HHH...HHCCCCHHHCHHSS-HS-EEEE--HHHHSSSSHHHHHHHHHHHHHHC- CS
                    Oxidored_nitro   1 CaplGAalvllgikdalplvhGpqGC...atyaralltrhfrepiplastdltekdavfGgeekLkeaikeivkryk 74 
                                       Ca+  A  vl++i+da+++v+Gp  C   atya++++++ +++p+ +     + +++ f+     ++ ++e++++ k
  gi|330506368|ref|YP_004382796.1|  23 CAYSRAISVLNPIADAMHVVQGPLECatcATYAWNARGSISSQPMLHG----KRDKIFFDNLGLSAQVMRELAAACK 95 
                                       9**********************9987778999999999999888555....45678888777778999******** PP

                                       TSEEEEEE-HHHHHTTTTHHHHHHHHHHHHTSSEEEEEE--TTSSSHHHHHHHHHHHHHHHCTT.-TT---SSEEEE CS
                    Oxidored_nitro  75 pkaIgVittClteliGdDieavareaeeelgeipvipvstpgfggsqseGydaalealvrklvg.kkgekeprkvni 150
                                       p+aI+V++tC+te++G D+  v++ a ++l + pvipv + gf  + ++Gy+aa++al+r +     ++ +p +vni
  gi|330506368|ref|YP_004382796.1|  96 PQAIFVYSTCMTETMGCDVSEVCESAAKDLRI-PVIPVGSMGF--QAETGYEAACNALLRLIGSrSYKPISPYSVNI 169
                                       ******************************77.9999988888..5689***********9944322334455**** PP

                                       EEETTCGHGHHHHHHHHHHHHTEEEEEEECTSB-HHHHGGGGG-SEEEEESHHCHHHHHHHHHHHH---EEEEE-SS CS
                    Oxidored_nitro 151 lgeynlgpgdlrelkelleklGlevnavftggtsleelraagraklnlvlcprsanyaaelleekfgvpyiklvspi 227
                                       lg+yn++ gdl+ ++ +le+lG+ev   +tg+++++e+++a+ a+lnlv+c++s+ ++a+ +ee++g+py + vs+ 
  gi|330506368|ref|YP_004382796.1| 170 LGDYNIA-GDLWPIRSYLEELGIEVISAITGDSRVAEIQRAHCADLNLVQCSSSIGSLARRFEEEYGIPYRN-VSFL 244
                                       *******.****************************************************************.**** PP

                                       SHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH CS
                    Oxidored_nitro 228 Gleatdaflrelakllgkevaperiaeerar 258
                                       G+e+t+  lr+ a++++++     i+ee++r
  gi|330506368|ref|YP_004382796.1| 245 GIEETSSALRTAAEFFENPG----IIEESER 271
                                       ****************9443....5555555 PP

>> Gly_rich_SFCGS  Glycine-rich SFCGS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.15   1.3e+03      31      72 ..     109     147 ..      75     156 .. 0.55
   2 ?   10.7   0.0   4.6e-05      0.42      27      89 ..     192     256 ..     183     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.15
                    Gly_rich_SFCGS  31 glaadlklgdvmkkeeadlgisfcgsggagaltaqtkygyka 72 
                                        +++   + +v ++   dl i     g  g + a+t y   +
  gi|330506368|ref|YP_004382796.1| 109 TMGC--DVSEVCESAAKDLRIPVIPVGSMG-FQAETGYEAAC 147
                                       2332..356777888888888887766665.45666665555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4.6e-05
                    Gly_rich_SFCGS  27 ivipglaadlklgdvmkkeeadlgisfcgsg.gagaltaqtkygykaky.glrsveegvtaikeg 89 
                                        vi+ ++ d ++ ++ + + adl +  c s  g+ a   ++ yg + +   +  +ee  +a++  
  gi|330506368|ref|YP_004382796.1| 192 EVISAITGDSRVAEIQRAHCADLNLVQCSSSiGSLARRFEEEYGIPYRNvSFLGIEETSSALRTA 256
                                       58999***********************8753777778889999987642567788888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2066.37
//
Query:       gi|330506369|ref|YP_004382797.1|  [L=60]
Description: hypothetical protein MCON_0061 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 453.75
//
Query:       gi|330506370|ref|YP_004382798.1|  [L=216]
Description: alpha/beta hydrolase fold protein [Methanosaeta concilii GP6]
Scores for complete 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-23   81.2   0.0    1.7e-17   63.9   0.0    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    7.3e-15   54.9   0.0    1.2e-14   54.2   0.0    1.3  1  Hydrolase_4    Serine aminopeptidase, S33
    1.8e-14   54.9   0.3    2.2e-14   54.6   0.3    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
     0.0027   17.4   0.0     0.0037   16.9   0.0    1.3  1  Esterase       Putative esterase
     0.0038   17.4   0.0     0.0071   16.5   0.0    1.4  1  Thioesterase   Thioesterase domain
  ------ inclusion threshold ------
      0.023   14.2   0.0        2.7    7.4   0.0    2.1  2  Peptidase_S9   Prolyl oligopeptidase family
      0.076   12.9   0.0       0.23   11.3   0.0    1.9  1  Abhydrolase_3  alpha/beta hydrolase fold
      0.079   11.7   0.0       0.12   11.1   0.0    1.1  1  Ndr            Ndr family


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 !   63.9   0.0   7.7e-21   1.7e-17      33     113 ..       2      82 ..       1      98 [. 0.88
   2 !   15.6   0.0   4.3e-06    0.0096     195     255 ..     148     202 ..     124     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 7.7e-21
                                       EEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE... CS
                     Abhydrolase_1  33 illDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmGGmialayaaeyperVkalvllga... 106
                                       il+D rG g+S+ +p +     ++  +a+d   +ldalg+d+ ++ G+SmGGmial++a++yp+ V++lvl g+   
  gi|330506370|ref|YP_004382798.1|   2 ILFDNRGAGRSDQPPGP----LTIGQMAKDAAGLLDALGIDHAHVFGGSMGGMIALQMALDYPKQVDKLVLGGTtag 74 
                                       89*************86....78999*********************************************999777 PP

                                       .CSSCCHH CS
                     Abhydrolase_1 107 .idpaasl 113
                                        ++  + +
  gi|330506370|ref|YP_004382798.1|  75 gSSRTNPP 82 
                                       74433333 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 4.3e-06
                                       CCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHH CS
                     Abhydrolase_1 195 tdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafle 255
                                        d   +l+++r       pt+vi+g  D l+pp ++ ++a+++p+++ + i++agH+  + 
  gi|330506370|ref|YP_004382798.1| 148 FDVEGRLGFIRA------PTMVIIGKRDVLIPPPNSFEIARKIPGAQMREIEGAGHIFWIS 202
                                       334444555555......***************99999******************97665 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   5.1e-18   1.2e-14      36     232 ..       3     197 ..       1     201 [. 0.85

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 5.1e-18
                       Hydrolase_4  36 alDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPalk 112
                                        +D+rG Grs+   g    + ++ +D+a +++++  +h      ++G SmGG+ial+++l+yp++v++l+l ++  +
  gi|330506370|ref|YP_004382798.1|   3 LFDNRGAGRSDQPPG-PLTIGQMAKDAAGLLDALGIDHA----HVFGGSMGGMIALQMALDYPKQVDKLVLGGTTAG 74 
                                       69*********9999.6689**************97775....56******************************** PP

                       Hydrolase_4 113 ikaklk.appllklllkllgkllpklqv...snnlkadslsrdpevvaayeadplvhgkitvrlllelldamk.rle 184
                                         ++++ +p+++k +   +   + ++          ++++  +p+ v++  +  l   ++ +   ++l    + ++e
  gi|330506370|ref|YP_004382798.1|  75 GSSRTNpPPEIQKYFYPRTDLSAHDYLWwtgAVCYPPEFIEAHPDIVERKIQANLAFPGTLAAYEAQLKAFNEfDVE 151
                                       ***99989999999776666666655555557888999999999999999998888766666666666555553578 PP

                       Hydrolase_4 185 eraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyH 232
                                        r   i++P+++++G++D +++p +s e++++++    +++ ++g+ H
  gi|330506370|ref|YP_004382798.1| 152 GRLGFIRAPTMVIIGKRDVLIPPPNSFEIARKIP--GAQMREIEGAGH 197
                                       8899999***************************..699999999999 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.3   9.8e-18   2.2e-14      31     218 ..       3     208 ..       1     208 [. 0.64

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 9.8e-18
                                       EE--TTSTS-GGCS--HHH...CHHHHHHHCCTT..TTSEEEEEETCHHHHHHHHHHCC.......EE.EEES-..- CS
                     Abhydrolase_6  31 apDlpGhGrsdpppldled...ladlaalldelaagggpvvlvGHSlGGalalaaapla.....lvvg.vlldpppt 98 
                                        +D +G Grsd pp  l+    + d a lld+l+   + ++++G S+GG++al+    a     +v + vl  +   
  gi|330506370|ref|YP_004382798.1|   3 LFDNRGAGRSDQPPGPLTIgqmAKDAAGLLDALG--IDHAHVFGGSMGGMIALQ---MAldypkQVDKlVLGGT--- 71 
                                       69******88777766655547899999*****5..9999**************...55555597777455555... PP

                                       ---TTT....S----TTHHHHHHTT-C.CCCHCCH.S-HSCCCCHHH........CCCCHCHCCCGHHHHCCHHCHT CS
                     Abhydrolase_6  99 alpagl....laaalelllallallrl.lawlsre.plprlfladed........adaawrarlarlaallaglgll 161
                                       +++ +     ++ + +++ ++++l ++ + w +++  +p++f++  +        a  a+  +la+  a+l+++ ++
  gi|330506370|ref|YP_004382798.1|  72 TAGGSSrtnpPPEIQKYFYPRTDLSAHdYLWWTGAvCYPPEFIEAHPdiverkiqANLAFPGTLAAYEAQLKAFNEF 148
                                       44444433335555555555555555546777887966668888555343332222444444444444444444433 PP

                                       T.CCHHTT-TTGCEEE.CTT-CHHH.HCHHCCCH.STTEEETCE...SSS-HHHHSHHHHH CS
                     Abhydrolase_6 162 p.aaawadlpvpllvl.ggeDplvp.rllerlla.qagarlpvvlpgaGHlphleepdeva 218
                                           ++  +++p++v+ g++D l+p +   ++++ ++ga++  +++gaGH +++++p+e++
  gi|330506370|ref|YP_004382798.1| 149 DvEGRLGFIRAPTMVIiGKRDVLIPpPNSFEIARkIPGAQM-REIEGAGHIFWISHPEETV 208
                                       22335555555554444*****77732233777788*****.*********9**9**9875 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.7e-06    0.0037     118     140 ..      41      63 ..      31     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.7e-06
                                       EEEEETHHHHHHHHHHHCSTTTC CS
                          Esterase 118 avaGqSmGGlgALilalkhpdrF 140
                                        v+G SmGG++AL +al++p++ 
  gi|330506370|ref|YP_004382798.1|  41 HVFGGSMGGMIALQMALDYPKQV 63 
                                       589*****************986 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.1e-06    0.0071      37      87 ..      10      59 ..       3      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.1e-06
                                      TSTSHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHHHHHH CS
                      Thioesterase 37 grerdepplesieelaaeyaealrqiqpegPyalfGhSlGgllAfevArqL 87
                                      gr+++ p + +i+++a   a  l +   +   ++fG S+Gg++A ++A  +
  gi|330506370|ref|YP_004382798.1| 10 GRSDQPPGPLTIGQMAKDAAGLLDALGID-HAHVFGGSMGGMIALQMALDY 59
                                      44455555679**********99999888.8999999**********9865 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0081        18      65      86 ..      39      60 ..      26      69 .. 0.85
   2 ?    7.4   0.0    0.0012       2.7     128     186 ..     138     197 ..     121     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0081
                                      GEEEEEETHHHHHHHHHHHH-G CS
                      Peptidase_S9 65 rlaitGgSyGGyltgaalnqrp 86
                                      +  ++GgS GG+ ++ ++ + p
  gi|330506370|ref|YP_004382798.1| 39 HAHVFGGSMGGMIALQMALDYP 60
                                      56799********999988766 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0012
                                       HHHHHHH-CGGG--.....---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-S CS
                      Peptidase_S9 128 ykelspyspldnvk.....aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegH 186
                                       y+++ ++ +   v+     + +p+++i G  D  +pp ++++++++       ++++   ++gH
  gi|330506370|ref|YP_004382798.1| 138 YEAQLKAFNEFDVEgrlgfIRAPTMVIIGKRDVLIPPPNSFEIARKIPG----AQMREIEGAGH 197
                                       5555555555555567778899********************9988653....55666666666 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0001      0.23      72     115 ..      39      98 ..      21     201 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                                       EEEEEEETHHHHHHHHHHHHHHHTT---................EEEEEEESE-SSTSST CS
                     Abhydrolase_3  72 rivlaGdSaGGnlaaavalrardegepk................vagqvliyPvtdlert 115
                                       +  ++G S GG +a+++al   ++                    ++ q  +yP tdl+++
  gi|330506370|ref|YP_004382798.1|  39 HAHVFGGSMGGMIALQMALDYPKQVDKLvlggttaggssrtnppPEIQKYFYPRTDLSAH 98 
                                       45689*************998887433357778888888888888888888887777333 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.1e-05      0.12      81     134 ..      20      73 ..      11      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.1e-05
                                       -HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES--- CS
                               Ndr  81 slddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinits 134
                                       ++ ++a++   +ld + ++++  +G   G  i ++ al +p++v  lvL  +t+
  gi|330506370|ref|YP_004382798.1|  20 TIGQMAKDAAGLLDALGIDHAHVFGGSMGGMIALQMALDYPKQVDKLVLGGTTA 73 
                                       8899********************************************966655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1572.63
//
Query:       gi|330506371|ref|YP_004382799.1|  [L=79]
Description: hypothetical protein MCON_0066 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 590.52
//
Query:       gi|330506372|ref|YP_004382800.1|  [L=149]
Description: hypothetical protein MCON_0067 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.19   11.4   0.1       0.79    9.4   0.0    1.9  2  DUF4222   Domain of unknown function (DUF4222)


Domain annotation for each model (and alignments):
>> DUF4222  Domain of unknown function (DUF4222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   4.4e-05      0.79       7      33 ..      60      89 ..      57      95 .. 0.81
   2 ?   -0.9   0.0     0.074   1.3e+03      27      46 ..     128     145 ..     114     146 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 4.4e-05
                           DUF4222  7 diYrDkrGvvVkvisvden...rVtFrRdG 33
                                      d+ +D r v+  v+ +d+    ++tF+RdG
  gi|330506372|ref|YP_004382800.1| 60 DLVEDDRIVLAVVEQTDRLftgNITFMRDG 89
                                      6677888888888888888889******** PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.074
                           DUF4222  27 VtFrRdGYehpcvaplerFn 46 
                                       +++   G   p +a + +F 
  gi|330506372|ref|YP_004382800.1| 128 MFYLEHG--TPAIAAIDQFH 145
                                       4555566..78888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1133.71
//
Query:       gi|330506373|ref|YP_004382801.1|  [L=86]
Description: hypothetical protein MCON_0068 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 682.88
//
Query:       gi|330506374|ref|YP_004382802.1|  [L=2872]
Description: glycosyl transferase family protein [Methanosaeta concilii GP6]
Scores for complete 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-160  530.5   0.0    1.8e-79  266.7   0.0    2.2  2  Glyco_transf_36  Glycosyltransferase family 36
   1.6e-116  389.5   0.0   2.3e-116  388.9   0.0    1.3  1  Glyco_hydro_36   Glycosyl hydrolase 36 superfamily, catalytic
    4.7e-15   55.8   0.0    8.9e-15   54.8   0.0    1.5  1  Glycoamylase     Putative glucoamylase
  ------ inclusion threshold ------
      0.081   13.0   0.0       0.28   11.2   0.0    2.0  1  DUF772           Transposase domain (DUF772)
       0.17   11.9   0.1          2    8.5   0.0    2.5  2  DUF2025          Protein of unknown function (DUF2025)


Domain annotation for each model (and alignments):
>> Glyco_transf_36  Glycosyltransferase family 36
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.7   0.0   5.1e-83   1.8e-79       3     251 .]    1600    1848 ..    1599    1848 .. 0.96
   2 !  261.8   0.0   1.5e-81   5.5e-78       1     251 []    2105    2344 ..    2105    2344 .. 0.95

  Alignments for each domain:
  == domain 1  score: 266.7 bits;  conditional E-value: 5.1e-83
                   Glyco_transf_36    3 pwinvlsngdygvlisetGgGyswyknsrenrltrwsndvvrdppGeyiYirDedsgevwsatwqpv.kkeldey 76  
                                        p +++lsng+y v+i+ +G+G s++k+ +   +trw+ d++ d+ G+++YirD +++++wsa++qp+ +   d+ 
  gi|330506374|ref|YP_004382802.1| 1600 PNVHLLSNGNYNVMITGSGAGISRWKDIA---VTRWHGDATLDNEGQFFYIRDLENNDFWSAGYQPAcR---DSR 1668
                                        899**************************...***********************************88...778 PP

                   Glyco_transf_36   77 kyecrhglgytefesekngietelevfVpkedpveirrlkLtNtsererelsvtsyaefvlgnaeadaanpafsr 151 
                                        +y++ ++ +++e++s   gi+++ e++V++ed+ve+r+++LtN+s+ +r++++tsyae+vl   +ada++pafs+
  gi|330506374|ref|YP_004382802.1| 1669 TYQVIFEGSKAEIRSMIWGIDARSEIVVSPEDDVELRTISLTNRSSAKRKIELTSYAEVVLTALAADATHPAFSN 1743
                                        *************************************************************************** PP

                   Glyco_transf_36  152 lfseteietelgegilaarnpyseeekkrvafltlsaev.....tsfetdreeFiGrngslsnPaalergk.lsn 220 
                                        lf+et+i +++++ il++r+p+se+ek++++++ +++++      sfetdr++FiGr++++++P a+   + lsn
  gi|330506374|ref|YP_004382802.1| 1744 LFVETKILPKNSA-ILCTRRPRSEDEKTPWMLHMMASKNvaddsISFETDRSRFIGRGRDVADPVAMTGTAsLSN 1817
                                        *********9999.*******************86644467888***********************76557*** PP

                   Glyco_transf_36  221 segagldpcaalqtkitLepgeekevvfllG 251 
                                        seg +ldp++++++ ++++pge+ +v f++G
  gi|330506374|ref|YP_004382802.1| 1818 SEGPVLDPIVSIRCIVSIDPGETMRVNFITG 1848
                                        *****************************98 PP

  == domain 2  score: 261.8 bits;  conditional E-value: 1.5e-81
                   Glyco_transf_36    1 PapwinvlsngdygvlisetGgGyswyknsrenrltrwsndvvrdppGeyiYirDedsgevwsatwqpvkkelde 75  
                                        Papw+nv++n+++g++ise G++y+w +ns++ rlt+w+nd+v+d++Ge++YirDe sg++ws+++ p++ +   
  gi|330506374|ref|YP_004382802.1| 2105 PAPWSNVIANHNFGTVISECGSSYTWSENSQQFRLTPWYNDPVSDHSGEALYIRDELSGDFWSPSALPARGKT-- 2177
                                        9********************************************************************9455.. PP

                   Glyco_transf_36   76 ykyecrhglgytefesekngietelevfVpkedpveirrlkLtNtsererelsvtsyaefvlgnaeadaanpafs 150 
                                          y+crhg+gy++fe+++ gi +el v+V +++pv++ rl ++N+s   r+ls+t y+e vlg            
  gi|330506374|ref|YP_004382802.1| 2178 -PYTCRHGFGYSVFEHKEFGIASELWVYVAMDAPVKFCRLVVRNESGIFRQLSLTCYIEQVLG----------DL 2241
                                        .9*************************************************************..........55 PP

                   Glyco_transf_36  151 rlfseteietel.ge.gilaarnpyseeekkrvafltlsaevtsfetdreeFiGrngslsnPaalergklsnseg 223 
                                        r ++ ++++te+  + g+l++rnp++ ++ +r++f +++++++sf++dr+eF+G+ngs+++Paal+r++lsn++g
  gi|330506374|ref|YP_004382802.1| 2242 RSKTGMHVVTEIdPRtGALFSRNPFNTDFPGRIVFSDVNTKINSFTGDRTEFLGKNGSMTRPAALDRETLSNRIG 2316
                                        666666666666444568********************************************************* PP

                   Glyco_transf_36  224 agldpcaalqtkitLepgeekevvfllG 251 
                                        a  dpcaa+q++i L+ +e +e++f+ G
  gi|330506374|ref|YP_004382802.1| 2317 AAMDPCAAIQVRIDLQDKEDVEIIFTCG 2344
                                        *************************987 PP

>> Glyco_hydro_36  Glycosyl hydrolase 36 superfamily, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.9   0.0  6.5e-120  2.3e-116       1     422 [.    2375    2801 ..    2375    2802 .. 0.93

  Alignments for each domain:
  == domain 1  score: 388.9 bits;  conditional E-value: 6.5e-120
                    Glyco_hydro_36    1 yWddilekvqvktpdesldrminiWnlYqalitfvlsRsasfiesGgrrGlGfRDtaqDilgvvhvnPektrkri 75  
                                        yW++ l  v+v+t+d+ ld + n+W lYq+l++++++R+  +++s g+  +GfRD++qD +++++++Pe  r+++
  gi|330506374|ref|YP_004382802.1| 2375 YWNHTLGVVHVETEDKALDVLTNGWLLYQTLSCRMWARTG-YYQSSGA--YGFRDQLQDSMALIYAEPEIFREHL 2446
                                        9**************************************9.9999888..9************************ PP

                    Glyco_hydro_36   76 ldllsgqveeGsalhlfdPlv...ikpsksdd.ldtpk.dedkikGiedlssdDelWivltieayvketGdlsil 145 
                                        l  +s+q++eG++lh+++P +   ++++ sdd l++p   + +++ ++d+ + +e      i+  +    ++s +
  gi|330506374|ref|YP_004382802.1| 2447 LRCASHQFVEGDVLHWWHPPFergVRTHSSDDrLWLPLaAHRYVTTTGDVGVLNE--STHFITGGLLAPDEDSCY 2519
                                        ********************99999999999999999855667888888888887..556666777777888888 PP

                    Glyco_hydro_36  146 devipysddkkatvyehlkkaldfsleklGkhglpligraDWnDclnl....gkgesvfvsfllylalkeflela 216 
                                        +  +p    +++t+yeh+ ++++ sl++ G+hglpl+g +DWnD++n     g gesv+ +f+ly +l +f+++a
  gi|330506374|ref|YP_004382802.1| 2520 H--LPARSAESGTLYEHCVRSIKRSLQF-GRHGLPLMGTGDWNDGMNHvgyqGLGESVWNAFFLYDVLAKFKDIA 2591
                                        8..8888889*****************9.******************9877677********************* PP

                    Glyco_hydro_36  217 kkkgeeeeaekaekaadklreaiekyaWdGewflRaytkdgekiGskeneegkiflesqslavlsGigkderakv 291 
                                        +  g+ + ae    +a++lre+i + +WdG+w+lRay+++g+++Gs  nee++i++ +qs++vlsG+g  er++ 
  gi|330506374|ref|YP_004382802.1| 2592 HLFGDSAFAELCASEAATLRENIRQSGWDGHWYLRAYFDNGDPLGSIANEECQIDSIPQSWSVLSGAGDPERSRE 2666
                                        *************************************************************************** PP

                    Glyco_hydro_36  292 aldsvekyLdte.yGlv.lqqPafsklklelgeissyvpGvkenagifchanpWvivaetklGrGdrafklyrki 364 
                                        a++ v++ L++    ++ l qP+f+++ l++g+i+ y pGv+en+g+++ha+ Wvi+a + lG+  ra++l + i
  gi|330506374|ref|YP_004382802.1| 2667 AMEEVDHRLVNRdNSVIqLLQPPFDRSSLNPGYIKGYLPGVRENGGQYTHAAIWVIMAFASLGDSARAWELLDLI 2741
                                        ******99987745555699******************************************************* PP

                    Glyco_hydro_36  365 nPanle...dkieirkaePYvyaqfvagkdakrhGraknsWltGtagwayvaiteyiLGlr 422 
                                        nP+ +    +++ i+++ePY+ a+++ +  + + Gr+ ++W+tG +gw+y++i+e +LG+ 
  gi|330506374|ref|YP_004382802.1| 2742 NPVMHGstpNQVAIYRVEPYIVAADICALPP-NAGRGGWTWYTGASGWMYRLILESLLGIT 2801
                                        ***9862224569**************9876.9**************************95 PP

>> Glycoamylase  Putative glucoamylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.0   2.5e-18   8.9e-15      30     221 .]    1356    1547 ..    1335    1547 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 2.5e-18
                      Glycoamylase   30 yea.watierdwenyegeevlksesgpLFvhqyshawldfrgiqdkygvdYfensrratlaqreYaeenpkkfkg 103 
                                         ++ w+++ r  +  +g   l s++g++F ++++ +++  +g     ++ + ++  + ++ q eY+++       
  gi|330506374|ref|YP_004382802.1| 1356 RQEhWFALGRMLTIAGGDFALLSWGGTMFEYLMPLLIMPTYG-----NTLLDQTCISIVKRQIEYGQQ------- 1418
                                        44458788899999999999999******************9.....7777888899999*******9....... PP

                      Glycoamylase  104 ygedlWGltasdspeeekke..gYaargaplee......ddGtisPtaalsslpfapeealaalrelykelkdql 170 
                                          +  WG+++s ++  + ++  +Y+a+g+p         +d +++P+a+ ++l + p+e+  +l+ l     +  
  gi|330506374|ref|YP_004382802.1| 1419 -RKVPWGISESGYSVVDVNQiyQYRAFGVPGLGlkrglaNDLVVAPYASAMALMVLPQESCVNLKRLA---DEGY 1489
                                        .7889*****998887766678*******98878999*******************************...899* PP

                      Glycoamylase  171 lgrygfydafnpte......kegwvakrylgidqGpillmieNy.rsgllwklfmksp 221 
                                        lg+ygfy+a+++t       ++ +++++++ ++qG++ll++  +  ++ ++++fm++p
  gi|330506374|ref|YP_004382802.1| 1490 LGEYGFYEAIDYTPsrlaqhQRSAIVQSFMSHHQGMSLLSLAYVlLDRPMQRRFMANP 1547
                                        ***********98889**9999******************998867888888888875 PP

>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.9e-05      0.28       6      43 ..     122     159 ..     120     197 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.9e-05
                            DUF772   6 ppelmlkllllqylyglSdreleealrenlsfrwflgl 43 
                                        +++ml+l l+ +l ++S r + +++ ++l+ rw++++
  gi|330506374|ref|YP_004382802.1| 122 AVAIMLRLALIENLRNISLRIIQDRIDRDLANRWAVQI 159
                                       6799******************************9875 PP

>> DUF2025  Protein of unknown function (DUF2025)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00056         2      27      69 ..     548     591 ..     532     599 .. 0.78
   2 ?   -0.2   0.1      0.27   9.8e+02      59      92 ..    1865    1899 ..    1855    1903 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00056
                                       EEEEE.S-GGG-SSSS-GGG-EEHHHHTEEESSSSEEEE-TTHH CS
                           DUF2025  27 kyivr.fsedsfGldvaddsitpasefvwaveeaqlmtlkrerl 69 
                                       ++++r  se+sf +   d si p  ++v +v+e+++m ++  r+
  gi|330506374|ref|YP_004382802.1| 548 NFLLRgGSENSFSVITGDVSILPGVKYVITVDEDTMMPFESARI 591
                                       46666349*****************************9876654 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.27
                                        SSEEEE-TTHHHHHHHHT-HHHHT--HH.HHHHTT CS
                           DUF2025   59 aqlmtlkrerlellleqniddrlnlsep.lrvylr 92  
                                        + +m+ + ++l++  +q i ++ln+s+  ++ y+r
  gi|330506374|ref|YP_004382802.1| 1865 DVRMAERVHNLAWTHNQMIMQQLNISDGdVHLYMR 1899
                                        55677777899***************953778888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2872 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 1.26u 0.36s 00:00:01.62 Elapsed: 00:00:00.53
# Mc/sec: 16430.92
//
Query:       gi|330506375|ref|YP_004382803.1|  [L=156]
Description: small multidrug export protein [Methanosaeta concilii GP6]
Scores for complete 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  125.2   4.0    2.8e-36  124.8   4.0    1.2  1  Sm_multidrug_ex  Putative small multi-drug export protein


Domain annotation for each model (and alignments):
>> Sm_multidrug_ex  Putative small multi-drug export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.8   4.0   1.6e-40   2.8e-36       1     121 []      21     143 ..      21     143 .. 0.95

  Alignments for each domain:
  == domain 1  score: 124.8 bits;  conditional E-value: 1.6e-40
                   Sm_multidrug_ex   1 Elrgaiplgi.llgldpllallvsvlgnllpvplillflrkllellkkkkllkklfekleekaek.ksekiekygfl 75 
                                       E+rgaipl+i ++g+++++a+l+svlgnllpv+ +llfl +++++l+++++ +++f++l +++++ + +k e++g++
  gi|330506375|ref|YP_004382803.1|  21 EVRGAIPLAIgYYGYSWYQAFLISVLGNLLPVVPLLLFLGPVSDYLRRYTIGDRFFTWLFARTRSkYIQKHENFGLI 97 
                                       99********777**************************************************994566668***** PP

                   Sm_multidrug_ex  76 GLllFvaiPLpgTGawtGsliasllglkkkkallaillGvliaglI 121
                                       +L++FvaiPLp+TGawtG++ia+llg+++  al+a+++G+lia+ I
  gi|330506375|ref|YP_004382803.1|  98 ALIIFVAIPLPMTGAWTGCAIAFLLGFRFLPALAAVATGILIAASI 143
                                       *******************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1107.32
//
Query:       gi|330506376|ref|YP_004382804.1|  [L=172]
Description: hypothetical protein MCON_0071 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1205.92
//
Query:       gi|330506377|ref|YP_004382805.1|  [L=352]
Description: putative methanogenesis marker protein 9 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2616.12
//
Query:       gi|330506378|ref|YP_004382806.1|  [L=308]
Description: triphosphoribosyl-dephospho-CoA synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-67  227.8   0.1    2.3e-67  227.6   0.1    1.0  1  CitG      ATP:dephospho-CoA triphosphoribosyl transferase


Domain annotation for each model (and alignments):
>> CitG  ATP:dephospho-CoA triphosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.6   0.1   1.3e-71   2.3e-67       1     280 [.       2     300 ..       2     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 227.6 bits;  conditional E-value: 1.3e-71
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHH CS
                              CitG   1 aelavlAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekaml 77 
                                       a++avlA+l E+s +pKPG+Vdr++++  +D++f++Fl Sa++++p+f++aa          ++++s G l+ + ++
  gi|330506378|ref|YP_004382806.1|   2 AQCAVLAMLFELSSSPKPGNVDRCHDF--SDIRFHHFLTSAVSAYPVFRKAA----------SGEGSPGSLILEGVA 66 
                                       79*************************..***********************..........99************* PP

                                       HH...------HHHHHHHHHHHHTTTTS-...............................SHHHHHHHHHHHHHT-- CS
                              CitG  78 aa...tggvNThkGaifllgllaaaagrraa........................eeeeasleelveeaaevlaelt 127
                                       a+       NTh+G + ll++la aagr a+                          ++   + l ee+a+vl+++t
  gi|330506378|ref|YP_004382806.1|  67 AWgdwNLRSNTHFGSLVLLIPLALAAGRMAGheraghehgqetkqdesqengpddGVDDGVDDGLEEELARVLRSTT 143
                                       ****8889*******************8877**********************98455556678999********** PP

                                       HHHHHHH.HHHHHH--......---.......HHHHHH.TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH.... CS
                              CitG 128 vedavaf.rairlakv......eel.......kdelvekksltlgevlelsygvdgirgeaasgFpsvfeialpalr 190
                                       v+da++f ra++la +      +         +++l++  +++l+e ++ls ++d +++e+a+ F+++f++a  +lr
  gi|330506378|ref|YP_004382806.1| 144 VQDALDFyRAFDLAGArvvqvdD-FslkdpdwERKLID-GNQSLLELMRLSLDHDIVAREWATDFERSFQLAG-RLR 217
                                       ****************9998762.14656667778888.89*****************************888.799 PP

                                       ....HH.-SSHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHHHHH..........H-SHHHHHHHHHHHHHHT-- CS
                              CitG 191 ealasg.adlndalvqallallaelpDtnilrrgGaegaeevqeeArallaaggvaaeaglealeeldrelvernis 266
                                       e++  + ++lnd +v+++l+ lae+pD++i  ++G+e a ev+++A + l        ++l++++++d el +r+++
  gi|330506378|ref|YP_004382806.1| 218 EMV--SiYGLNDGVVRTFLEALAEVPDSLISAKFGRERAVEVSRMAVDALLD------STLNKARKMDCELNNRDMN 286
                                       985..449**************************************955554......3799*************** PP

                                       -HHHHHHHHHHHHH CS
                              CitG 267 PGgsADllaatlfl 280
                                       PG++ADl+aa+lf+
  gi|330506378|ref|YP_004382806.1| 287 PGSTADLIAASLFI 300
                                       *************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2397.71
//
Query:       gi|330506379|ref|YP_004382807.1|  [L=199]
Description: hypothetical protein MCON_0074 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-49  166.9   0.0    4.2e-49  166.7   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 !  166.7   0.0   2.3e-53   4.2e-49       1     175 [.      20     189 ..      20     190 .. 0.97

  Alignments for each domain:
  == domain 1  score: 166.7 bits;  conditional E-value: 2.3e-53
                                       EEEEEEEE-TT-EEEEEEEEEESSSEEEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEEETTT CS
                            DUF447   1 yEvivtTksekrpnaaPiGvivkgdkvvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfdsetkp 77 
                                       +E+i+tT+   r naaP+G+i+++d++ +rlf g++T+eN+l+++++v+nvt+D+ +fa++al+dl++++f++ +  
  gi|330506379|ref|YP_004382807.1|  20 NEIIATTETGGRVNAAPLGIIRSEDSLYIRLFLGTHTYENILTRKWFVANVTHDAWIFAETALEDLPQEYFTHCD-- 94 
                                       79*******88************************************************************8888.. PP

                                       CTT.EETT-SEEEEEEEEEECTCECCEEEEEEEEEEEEETTB---B-HHHHHHHHHHHHHHCCCCSHHHHHHHHHHH CS
                            DUF447  78 akiavlksaeawveveveevegdsealelelepvkeeileervkpfnRgdaaviEaaVlatRldiedkeklleeiey 154
                                         +++lk++eaw+ ++++     s+ +++++epvk e+l++ ++++nRg ++v+EaaV+atR+  ++ +++ ee+ +
  gi|330506379|ref|YP_004382807.1|  95 -GLPILKDTEAWLLFKCDPF--ASDIIIANIEPVKGELLRKDFRAVNRGANLVVEAAVAATRYMSLRSDNYFEELMK 168
                                       .589**************98..8899*************************************99************ PP

                                       HHHHHHHH--HHHHHHHHHHH CS
                            DUF447 155 lssvikktggerekealellk 175
                                        +++i+++g++re+ea+e+l+
  gi|330506379|ref|YP_004382807.1| 169 TQRIINRCGNPREREAMERLM 189
                                       *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1504.29
//
Query:       gi|330506380|ref|YP_004382808.1|  [L=223]
Description: DNA repair and recombination protein RadB [Methanosaeta concilii GP6]
Scores for complete 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  108.1   0.0    5.2e-31  107.8   0.0    1.1  1  Rad51            Rad51
    4.8e-09   36.1   0.1    5.8e-09   35.8   0.1    1.2  1  RecA             recA bacterial DNA recombination protein
      6e-09   35.6   1.9    4.5e-07   29.5   1.9    2.3  1  ATPase           KaiC
    4.3e-08   33.0   0.1    8.9e-08   31.9   0.1    1.5  1  AAA_25           AAA domain
    8.3e-06   25.7   0.0    1.2e-05   25.1   0.0    1.2  1  AAA_24           AAA domain
    1.4e-05   24.8   0.0    1.9e-05   24.4   0.0    1.2  1  Zot              Zonular occludens toxin (Zot)
    0.00013   22.1   0.0    0.00016   21.7   0.0    1.5  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00022   20.3   0.1    0.00047   19.2   0.0    1.5  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
    0.00089   19.0   0.0     0.0018   18.0   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
     0.0025   18.2   0.2     0.0048   17.3   0.2    1.5  1  AAA_16           AAA ATPase domain
      0.007   16.8   0.0      0.012   16.1   0.0    1.3  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.015   14.9   0.1       0.09   12.3   0.1    2.0  1  CobU             Cobinamide kinase / cobinamide phosphate gua
      0.039   14.1   0.0      0.064   13.3   0.0    1.4  1  DUF87            Helicase HerA, central domain
      0.039   13.2   0.0      0.064   12.5   0.0    1.4  1  MipZ             ATPase MipZ
      0.043   13.5   0.4          1    9.1   0.1    2.1  2  Cytidylate_kin   Cytidylate kinase
      0.045   12.9   0.0      0.093   11.9   0.0    1.5  2  DUF815           Protein of unknown function (DUF815)
      0.048   13.8   0.0        1.4    9.1   0.0    2.1  2  Isochorismatase  Isochorismatase family
      0.049   13.9   0.1       0.15   12.4   0.1    1.8  1  AAA_22           AAA domain
      0.051   13.3   0.1      0.077   12.7   0.1    1.3  1  AAA_30           AAA domain
      0.057   13.3   0.0       0.08   12.8   0.0    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
      0.068   12.8   0.0      0.091   12.4   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
       0.07   12.3   0.1       0.19   10.9   0.0    1.6  2  DAP3             Mitochondrial ribosomal death-associated pro
      0.097   12.4   0.0       0.18   11.6   0.0    1.4  1  AAA_29           P-loop containing region of 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 !  107.8   0.0   6.7e-34   5.2e-31      16     251 ..       4     221 ..       1     223 [] 0.89

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 6.7e-34
                                       S-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHH CS
                             Rad51  16 llqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveia 92 
                                       l +l  G+++lD lLgGG+e+g ite++Ge++sGk+ +  +l+v++           ++++idteg f +er  +ia
  gi|330506380|ref|YP_004382808.1|   4 LERLPVGCQSLDLLLGGGFESGIITELYGESGSGKSNIVLQLAVAAVA------RGFRVIFIDTEG-FSAERFKQIA 73 
                                       567889********************************9999998743......4569*******6.9********* PP

                                       HHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHH CS
                             Rad51  93 erykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtL 169
                                              +++  ++++    + e+q+  +++a+ ++a   ++l+i+Ds+t+lyR+  +  +   +R   l+  l++L
  gi|330506380|ref|YP_004382808.1|  74 G---PGAADIAAKIMIFEPMSLEQQAMAIREAS-KIAGRDLGLVILDSATSLYRMLLEAEDSRPARR-ALTVQLSEL 145
                                       5...567789999999999****9999998876.577888****************99999988886.688999*** PP

                                       HHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-.EEEE CS
                             Rad51 170 rkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpel.eavf 245
                                       +++a ++++ vvitnqv  +++        ++ +P gG  l h+ +  + l k  +  R +++++  +lpe+  a f
  gi|330506380|ref|YP_004382808.1| 146 QEIARRHRIPVVITNQVYTDIES-------NSLRPLGGTYLEHMCKAIIFLEKAGEGLRRARLMKHRSLPENrTAEF 215
                                       *******************9998.......899********************999999999999999999624678 PP

                                       EEETTE CS
                             Rad51 246 aigeeG 251
                                        ++ +G
  gi|330506380|ref|YP_004382808.1| 216 RLTARG 221
                                       887777 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.1   7.5e-12   5.8e-09      31     193 ..       4     166 ..       1     194 [. 0.80

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 7.5e-12
                                       --EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHTT...-- CS
                              RecA  31 vetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakklG...vd 104
                                       +e ++ G  +ld+ lG GG+  G i+e+yG   sGk+ + l++ + a  +g  + fid+e     ++ +  G    d
  gi|330506380|ref|YP_004382808.1|   4 LERLPVGCQSLDLLLG-GGFESGIITELYGESGSGKSNIVLQLAVAAVARGFRVIFIDTEGFSAERFKQIAGpgaAD 79 
                                       678999**********.**************************99999************88877777766633357 PP

                                       GG.G-EEE--SSHH.HHHHHHHH.HHTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTT CS
                              RecA 105 id.ellvsqpdtGe.qaleiada.lvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisk 178
                                       i  ++++ +p + e qa+ i +a  +    + l+++ds ++l  +  +e   +ds+ + +a  ++  l  l+   ++
  gi|330506380|ref|YP_004382808.1|  80 IAaKIMIFEPMSLEqQAMAIREAsKIAGRDLGLVILDSATSLY-RMLLE--AEDSRPARRA--LTVQLSELQEIARR 151
                                       643689999988763699999872467778999*****99886.44444..4466666544..55567777777777 PP

                                       T--EEEEEEE----- CS
                              RecA 179 sntvvifinqireki 193
                                        ++ v+  nq+ + i
  gi|330506380|ref|YP_004382808.1| 152 HRIPVVITNQVYTDI 166
                                       788888888876655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   1.9   5.7e-10   4.5e-07       2      83 ..       8      84 ..       7     221 .. 0.60

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 5.7e-10
                            ATPase  2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleee 80
                                      + g + lD +l gG+ +g ++ ++Ge+G+GK+ ++lq ++  +++ g +++f+ +e  + +  ++++  G    ++ ++
  gi|330506380|ref|YP_004382808.1|  8 PVGCQSLDLLLGGGFESGIITELYGESGSGKSNIVLQLAVAAVAR-GFRVIFIDTEGFSAERFKQIAGPG--AADIAAK 83
                                      679999************************************999.*******99986654444444333..3444455 PP

                            ATPase 81 gkl 83
                                        +
  gi|330506380|ref|YP_004382808.1| 84 --I 84
                                      ..4 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   1.1e-10   8.9e-08      22     187 ..      14     160 ..       3     164 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.1e-10
                            AAA_25  22 rrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealr 98 
                                       ++ l++g    g ++ l+G +g+GK+ ++l+la+a +           +  +V+++++E+     ++R++++     
  gi|330506380|ref|YP_004382808.1|  14 LDLLLGGGFESGIITELYGESGSGKSNIVLQLAVAAVA----------RGFRVIFIDTEGFS---AERFKQIA---- 73 
                                       5667777778999999*****************99884..........2349**********...99999654.... PP

                            AAA_25  99 ddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg..densnsdv....galv 169
                                          +  + d+a +  +++f++++ ++++  ++++   +i    +++lv++D+ +++++   + ++++ +    +  +
  gi|330506380|ref|YP_004382808.1|  74 ---GPGAADIAAK--IMIFEPMSLEQQAM-AIREAS-KIAG-RDLGLVILDSATSLYRMllEAEDSRPArralTVQL 142
                                       ...3334444443..67777666565533.343433.3333.46*************99985555555421135556 PP

                            AAA_25 170 ealeriarrtgaavllvh 187
                                       + l++iarr+++ v+++ 
  gi|330506380|ref|YP_004382808.1| 143 SELQEIARRHRIPVVITN 160
                                       789999999999999876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.6e-08   1.2e-05       7      83 ..      30     127 ..      25     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.6e-08
                            AAA_24   7 iyGpsgiGKTtlakel.......gpkplfidtek.Glksldadkfpdie............swedfldevvel.... 59 
                                       +yG+sg+GK+ ++++l       g +++fidte+ ++ + + + +p +             s          l    
  gi|330506380|ref|YP_004382808.1|  30 LYGESGSGKSNIVLQLavaavarGFRVIFIDTEGfSAERFKQIAGPGAAdiaakimifepmS----------Leqqa 96 
                                       8*********************************8887777777776655555555544444..........04555 PP

                            AAA_24  60 .......aaeladyktlviDtideleelcla 83 
                                              + + +d+  +++D+++ l+++ l+
  gi|330506380|ref|YP_004382808.1|  97 maireasKIAGRDLGLVILDSATSLYRMLLE 127
                                       55565588899****************9876 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.4e-08   1.9e-05       6     130 ..      31     166 ..      27     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.4e-08
                               Zot   6 tGapGsgKtsgavkkdllpalkegRkiitnidGlrlerieqvlgekvs..tarliridnpegaetl.kefakwatid 79 
                                       +G+ GsgK+  +++  +    +  R+i+ + +G+  er++q+ g      +a+++  + p + e++ ++++   +i+
  gi|330506380|ref|YP_004382808.1|  31 YGESGSGKSNIVLQLAVAAVARGFRVIFIDTEGFSAERFKQIAGPGAAdiAAKIMIFE-PMSLEQQaMAIREASKIA 106
                                       8**************88888889999999************99887777888887777.444333303333334445 PP

                               Zot  80 ..kgallviDEcqeifpvrakegrkd......pevinafte.hRhlgwDivlltqdiski 130
                                           +l+++D +  ++    + + ++         + +++e +R++   +v++ q  + i
  gi|330506380|ref|YP_004382808.1| 107 grDLGLVILDSATSLYRMLLEAEDSRparralTVQLSELQEiARRHRIPVVITNQVYTDI 166
                                       53559**********998776533333343332222333222455555566655555555 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.1e-07   0.00016       6      35 ..      32      61 ..      27     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-07
                                      SSTTSSHHHHHHHHHHHHHHTT--EEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  6 tkGGvGKTtlaanLaralarrglrVllvDa 35
                                      + +G+GK+ +++ La+a   rg+rV+ +D+
  gi|330506380|ref|YP_004382808.1| 32 GESGSGKSNIVLQLAVAAVARGFRVIFIDT 61
                                      78***************************7 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 !   19.2   0.0     6e-07   0.00047      20      62 ..      30      81 ..      25      95 .. 0.83
   2 ?   -2.6   0.0       2.5     2e+03     137     159 ..     135     157 ..     118     180 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6e-07
                     TrwB_AAD_bind 20 ivGttGsGKtqalekllrairargdraivlDltGafvsrfyd.........e 62
                                      + G  GsGK++ + +l  a+ arg r+i +D++G   +rf +         +
  gi|330506380|ref|YP_004382808.1| 30 LYGESGSGKSNIVLQLAVAAVARGFRVIFIDTEGFSAERFKQiagpgaadiA 81
                                      7899************************************986665555444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                     TrwB_AAD_bind 137 ralltadleeLkellagteaaal 159
                                       r+ lt +l+eL+e+++++ +  +
  gi|330506380|ref|YP_004382808.1| 135 RRALTVQLSELQEIARRHRIPVV 157
                                       44455555555555555544433 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.3e-06    0.0018      52      85 ..      30      63 ..      23      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.3e-06
                         IstB_IS21 52 llGpsGvGKshlaialgveavraglsvlfvrved 85
                                      l G sG GKs +   l+v+av++g++v+f+ +e 
  gi|330506380|ref|YP_004382808.1| 30 LYGESGSGKSNIVLQLAVAAVARGFRVIFIDTEG 63
                                      78***************************99875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   6.2e-06    0.0048      29     107 ..      30     126 ..      17     172 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.2e-06
                            AAA_16  29 lsGesGvGKsslvrellralekdggiflrgkcdql..esaipy.sa.laqalareellrqlldeaesaeleawrekl 101
                                       l+GesG+GKs +v +l+ a+ ++g+ ++  +++ +  e+      +  a+++a+  +++ +  e+++ + +++++  
  gi|330506380|ref|YP_004382808.1|  30 LYGESGSGKSNIVLQLAVAAVARGFRVIFIDTEGFsaERFKQIaGPgAADIAAKIMIFEPMSLEQQAMAIREASKIA 106
                                       89***************9***99877766666666112222223222333332223444444443333333333333 PP

                            AAA_16 102 eeala..............a 107
                                        + l+               
  gi|330506380|ref|YP_004382808.1| 107 GRDLGlvildsatslyrmlL 126
                                       33333555555555544442 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   1.5e-05     0.012       3     117 ..      30     168 ..      29     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-05
                                       EESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS.......................STTHHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel...gvefleisgsellsk.......................yvgesekkirelfkea 53 
                                       lyG  G GK+ ++ ++a  +   g++++ i+   +  +                        ++++++ ire  k a
  gi|330506380|ref|YP_004382808.1|  30 LYGESGSGKSNIVLQLAVAAvarGFRVIFIDTEGFSAErfkqiagpgaadiaakimifepmSLEQQAMAIREASKIA 106
                                       8*************999998666566666666666644566777777777899999866655666666666666655 PP

                                       HHTSTSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS.GGGSTH CS
                               AAA  54 kekakpsilfiDEidalaksr.sgseseeeervvnqLlteldgvkkkeskvivigatnr.pdkldp 117
                                        +      +++D + +l +   + ++s+ ++r++ + l+el++  ++ +++  +++tn+ + ++++
  gi|330506380|ref|YP_004382808.1| 107 GRD--LGLVILDSATSLYRMLlEAEDSRPARRALTVQLSELQEIARR-HRIP-VVITNQvYTDIES 168
                                       554..49**********999888889999999999999999999996.4355.5555553666655 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00012      0.09      63     131 ..      99     167 ..      28     193 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                              CobU  63 laealkeeek.kevvLvDcltlwltnllleeeaekveekleeeveellealkelkatvvlVsnEvglgvv 131
                                       ++ea k + +    v++D+ t +   ll +e+++ ++++l+ +++el e++++++ +vv ++n v  ++ 
  gi|330506380|ref|YP_004382808.1|  99 IREASKIAGRdLGLVILDSATSLYRMLLEAEDSRPARRALTVQLSELQEIARRHRIPVV-ITNQVYTDIE 167
                                       333332222245789**************998777999999999999999999988876.6898887775 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.2e-05     0.064      29      81 ..      31      89 ..      30     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.2e-05
                             DUF87 29 lgsTGsGKSntvavLleellekkgatililDpHGEYgkal........ekllsekvkvitp 81
                                       g++GsGKSn v  L   ++  +g +++ +D  G +++ +        +  ++ k+++++p
  gi|330506380|ref|YP_004382808.1| 31 YGESGSGKSNIVLQLAVAAV-ARGFRVIFIDTEG-FSAERfkqiagpgAADIAAKIMIFEP 89
                                      599*****************.9*********999.33333355556665555555555555 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.2e-05     0.064      10      38 ..      34      62 ..      30     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.2e-05
                                      TTSSHHHHHHHHHHHHHTTT--EEEEE-- CS
                              MipZ 10 GGsGksttavhvavaLlkkGarvaaidld 38
                                       GsGks + + +ava +++G+rv  id +
  gi|330506380|ref|YP_004382808.1| 34 SGSGKSNIVLQLAVAAVARGFRVIFIDTE 62
                                      69*********************999965 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0       0.1        82       5      21 ..      32      48 ..      29      64 .. 0.81
   2 ?    9.1   0.1    0.0013         1      89     151 ..      77     140 ..      55     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.1
                                      -STTSSHHHHHHHHHHH CS
                    Cytidylate_kin  5 GPagsGKssvaralaek 21
                                      G +gsGKs +  +la  
  gi|330506380|ref|YP_004382808.1| 32 GESGSGKSNIVLQLAVA 48
                                      88********9999865 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                                       HHHHTTSHHHHHHHHHHHHTT-BSSBEEEEESSIIIIISTT-S..EEEEEE--HHHHHHHHHHHH CS
                    Cytidylate_kin  89 vSavaaipavRailvkklrelvkkarvvveGRDigtvvfpdae..lKifldAsveeRakRRlkql 151
                                       +  +aa   + + +   +++++ ++   + GRD+g v++  a    ++ l+A  + R +RR+  +
  gi|330506380|ref|YP_004382808.1|  77 AADIAAKIMIFEPMSLEQQAMAIREASKIAGRDLGLVILDSATslYRMLLEAE-DSRPARRALTV 140
                                       566788888889999999999999999999*********99863235556654.66777776654 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012     0.093      58      91 ..      30      63 ..      26     102 .. 0.85
   2 ?   -2.8   0.0       3.6   2.8e+03      16      40 ..     131     155 ..     120     170 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                            DUF815 58 LwGarGtGKSslvkallneyaeegLrlieveked 91
                                      L+G+ G+GKS +v  l  ++ ++g r+i ++ e 
  gi|330506380|ref|YP_004382808.1| 30 LYGESGSGKSNIVLQLAVAAVARGFRVIFIDTEG 63
                                      8***************************999875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.6
                            DUF815  16 lepveevdevklddLvgidkqkeal 40 
                                        +p +++ +v+l++L++i ++++  
  gi|330506380|ref|YP_004382808.1| 131 SRPARRALTVQLSELQEIARRHRIP 155
                                       5677777788888888887776654 PP

>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.17   1.3e+02     127     144 ..      42      59 ..      40      63 .. 0.92
   2 ?    9.1   0.0    0.0018       1.4      15      53 ..     127     166 ..     111     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.17
                   Isochorismatase 127 VeatardaldlGyevvvv 144
                                       V++ a++a+ +G++v+ +
  gi|330506380|ref|YP_004382808.1|  42 VLQLAVAAVARGFRVIFI 59 
                                       8999***********987 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0018
                   Isochorismatase  15 egvkeseeisavveninkllkaarkagipviftrdvhe.l 53 
                                       e+ ++ ++ +a+  + ++l + ar+++ipv++t++v+  +
  gi|330506380|ref|YP_004382808.1| 127 EAEDSRPARRALTVQLSELQEIARRHRIPVVITNQVYTdI 166
                                       55566677778888999******************99952 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00019      0.15       8     126 ..      28     157 ..      23     162 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka.....erlssee 77 
                                       + ++GesG+GK+  + +l+  ++++      + +v+f++  + +    k+++   + ++     a     e+ s+e+
  gi|330506380|ref|YP_004382808.1|  28 TELYGESGSGKSNIVLQLAVAAVAR------GFRVIFIDTEGFSaeRFKQIAGPGAADIA----AkimifEPMSLEQ 94 
                                       6699****************99987......99999999998884444444444444444....2344576777777 PP

                            AAA_22  78 llealeqalrarav.ielliiDEaqhlr........s.......eealeeLrsllnlsrkgvqli 126
                                          a+++a++ +++  +l+i+D a  l         s         +l+eL +++   r+ ++++
  gi|330506380|ref|YP_004382808.1|  95 QAMAIREASKIAGRdLGLVILDSATSLYrmlleaedSrparralTVQLSELQEIAR--RHRIPVV 157
                                       77777777777777778888888887765555443314555566666666666666..6666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   9.9e-05     0.077      21     102 ..      28     107 ..      22     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.9e-05
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk....grarlepgtlli 93 
                                       + l G  G+GK+ ++ +l+ a+ a+g+rvi +  +g  A++ ++ +g  a+ ia  +   +    +      ++ + 
  gi|330506380|ref|YP_004382808.1|  28 TELYGESGSGKSNIVLQLAVAAVARGFRVIFIDTEGFSAERFKQIAGPGAADIAAKIMIFEpmslE------QQAMA 98 
                                       55789**************************************99887666666655455534331......24445 PP

                            AAA_30  94 vDEagmvdt 102
                                       + Ea+ ++ 
  gi|330506380|ref|YP_004382808.1|  99 IREASKIAG 107
                                       555555544 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0    0.0001      0.08      22      68 ..      27      72 ..      21     186 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                          ATPase_2 22 iyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68
                                      i  +YG  gsGK+ ++ +++      +++vi+++  ++ s +++++ 
  gi|330506380|ref|YP_004382808.1| 27 ITELYGESGSGKSNIVLQLAVAAVARGFRVIFID-TEGFSAERFKQI 72
                                      5568***************************985.455566666654 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012     0.091       6      92 ..      30     118 ..      26     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                       EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHH...TTEEEEESSTTSCHHHHHHHHHHHH CS
                             SRP54   6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaek...lgvpvikkkeeadpaavakeaveka 79 
                                       l G  G+GK   + +La    ++g +v+++ +  f a  ++Q++  +     +++ +++  +  ++ a+a ++ +k 
  gi|330506380|ref|YP_004382808.1|  30 LYGESGSGKSNIVLQLAVAAVARGFRVIFIDTEGFSAERFKQIAGPGAAdiaAKIMIFEPMSL-EQQAMAIREASKI 105
                                       7899***************************************98766443355555554333.5566666777777 PP

                                       HHTTSSEEEEEE- CS
                             SRP54  80 keekidvvlvDTa 92 
                                         ++  +v++D+a
  gi|330506380|ref|YP_004382808.1| 106 AGRDLGLVILDSA 118
                                       777999****998 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00024      0.19      28      57 ..      30      59 ..      28      63 .. 0.92
   2 ?   -2.0   0.0         2   1.5e+03     123     161 ..     120     158 ..     114     160 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                                      EE-SSSSSTTTTHHHHHHHGGGS--EEEEE CS
                              DAP3 28 ltGekgsGKSvlLlqalayAlekgwvvlhv 57
                                      l+Ge gsGKS  +lq+   A+ +g+ v+ +
  gi|330506380|ref|YP_004382808.1| 30 LYGESGSGKSNIVLQLAVAAVARGFRVIFI 59
                                      89********************99988866 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                                       EHHHHHHHHHH-SSSHHHHHHHHHHHHHHHTT.SS--EEE CS
                              DAP3 123 tLleLvklgikdaksawdvfqallkeLkaqsk.grvpvlv 161
                                       +L++++   ++d++ a  ++ + l+eL++ ++ +r+pv++
  gi|330506380|ref|YP_004382808.1| 120 SLYRMLL-EAEDSRPARRALTVQLSELQEIARrHRIPVVI 158
                                       5555554.56777777777888888888877766677765 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   0.00023      0.18      22      39 ..      24      42 ..      21      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            AAA_29 22 kg.atlltGpsGsGKSTll 39
                                      +g +t l G+sGsGKS ++
  gi|330506380|ref|YP_004382808.1| 24 SGiITELYGESGSGKSNIV 42
                                      5667889*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 1661.91
//
Query:       gi|330506381|ref|YP_004382809.1|  [L=166]
Description: ribosomal-protein-alanine acetyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-15   55.0   0.1    1.1e-14   54.7   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    6.3e-11   42.3   0.0    7.2e-11   42.1   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.3e-10   39.9   0.1    6.5e-10   39.3   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.6e-08   32.9   0.0    6.7e-08   32.4   0.0    1.2  1  FR47             FR47-like protein
    0.00021   21.3   0.0     0.0077   16.3   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0036   18.0   0.1     0.0076   16.9   0.1    1.5  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.032   14.4   0.0    1.5  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
      0.036   14.2   0.0      0.067   13.3   0.0    1.5  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.1   4.9e-18   1.1e-14      20     117 .]      52     143 ..      32     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 4.9e-18
                                       HHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTE.S CS
                    Acetyltransf_1  20 seeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegi.k 95 
                                        +++f+e+   ++ ++l+a+ +gel+Gf+ ++k  +    ++ +  la++p y+g+G+G +L+ a+++ +r+ g+  
  gi|330506381|ref|YP_004382809.1|  52 IFAAFYEY---HPATTLAAKVNGELAGFVLGFKHAP---FEGRVFWLAIRPRYQGRGIGMRLMLAVLKSFRNLGAlG 122
                                       33346666...999********************99...8899999**********************999999956 PP

                                       EEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  96 kivlaveedndaairlYeklGF 117
                                       +  l+v+++n++a+ lY  lGF
  gi|330506381|ref|YP_004382809.1| 123 A-TLEVRVSNRKAQSLYSNLGF 143
                                       6.9**************66**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   3.2e-14   7.2e-11      29     108 ..      60     145 ..      35     166 .] 0.86

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 3.2e-14
                   Acetyltransf_10  29 gealllvaeeggkivGvi.elrdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavp 99 
                                       + a++l+a+++g+++G++ + +      ++  l+++p y+g+Gig +L+ av++ +++ g    +l+v+ s+ +a++
  gi|330506381|ref|YP_004382809.1|  60 HPATTLAAKVNGELAGFVlGFKHAPfegRVFWLAIRPRYQGRGIGMRLMLAVLKSFRNLGALGaTLEVRVSNrKAQS 136
                                       467899************6335554677****************************99998889************* PP

                   Acetyltransf_10 100 fYeklGFka 108
                                       +Y +lGF+ 
  gi|330506381|ref|YP_004382809.1| 137 LYSNLGFQI 145
                                       *******96 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.1   2.9e-13   6.5e-10       4      75 ..      63     144 ..      50     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 2.9e-13
                                       EEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH.....TT...SEEEEE.EEEETHHHHHHH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea.....ae...kgiile.qlelnaekaikf 68 
                                       +++ a+ +g+  Gf+    ++   +   +la++p y+g+GiG +L+ a     ++    g   + +++++++ka+++
  gi|330506381|ref|YP_004382809.1|  63 TTLAAKVNGELAGFVLGFKHApfeGRVFWLAIRPRYQGRGIGMRLMLAvlksfRNlgaLGA--TlEVRVSNRKAQSL 137
                                       45668888999999998888877666666*****************864544422233332..2334556569**** PP

                                       HHHTTEE CS
                    Acetyltransf_7  69 YeklGFe 75 
                                       Y  lGF+
  gi|330506381|ref|YP_004382809.1| 138 YSNLGFQ 144
                                       ******8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0     3e-11   6.7e-08      18      80 ..      82     146 ..      67     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 3e-11
                                       E-TT.SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  18 rkdg.gelgalqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfeki 80 
                                       + ++ g ++ l ++p  ++rG g rl  a+ k  ++ g   ++l v+ sN ++++ly+ lGf+ +
  gi|330506381|ref|YP_004382809.1|  82 HAPFeGRVFWLAIRPRYQGRGIGMRLMLAVLKSFRNLGAlGATLEVRVSNRKAQSLYSNLGFQIR 146
                                       566669999***************************8863699*******************965 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.4e-06    0.0077       2     108 ..      26     121 ..      25     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.4e-06
                                       EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEE.EEEE CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlka.agvt 77 
                                       ir++  +dl+++le+ +++F+  ++ +    ++  + + ++ +l a  ngel+g +  +++         +  + v 
  gi|330506381|ref|YP_004382809.1|  26 IRRMSASDLNAALEIDREVFGGYDPNI----FAAFYEYHPATTLAAKVNGELAGFVLGFKHA--------PFeGRVF 90 
                                       899**********************96....78889999***************98877764........3325688 PP

                                       EEEE-CCGTTS-HHHHHHHHHHHHHHHTT-- CS
                    Acetyltransf_9  78 gVavapehrgrgvlskLlaraleemreegqp 108
                                       + a  p ++grg+  +L+ ++l+  r  g+ 
  gi|330506381|ref|YP_004382809.1|  91 WLAIRPRYQGRGIGMRLMLAVLKSFRNLGAL 121
                                       99****************9999988876655 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   3.4e-06    0.0076      63     138 .]      70     144 ..      23     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.4e-06
                    Acetyltransf_3  63 tgv.iGsv.glrdleeedeeaelgym.lapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklG 136
                                       +g+  G+v g+ +++ e   + + ++ ++p ++g+G++   + a+l+ + ++lg+     ++  +N++ + ++  lG
  gi|330506381|ref|YP_004382809.1|  70 NGElAGFVlGFKHAPFE---GRVFWLaIRPRYQGRGIGMRLMLAVLKSF-RNLGALGATLEVRVSNRKAQSLYSNLG 142
                                       33338999777777766...67776636678*****************9.9999999******************** PP

                    Acetyltransf_3 137 fe 138
                                       f+
  gi|330506381|ref|YP_004382809.1| 143 FQ 144
                                       *6 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.9   4.2e+03       4      25 ..      18      38 ..      15      49 .. 0.56
   2 ?   14.4   0.0   1.4e-05     0.032      83     146 ..      91     155 ..      88     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.9
                    Acetyltransf_4  4 ateeDakeilaiyaeyvvntai 25
                                      a ++Da  i+++ a  ++n a+
  gi|330506381|ref|YP_004382809.1| 18 AVLKDAVIIRRMSAS-DLNAAL 38
                                      555566656555553.444443 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.4e-05
                    Acetyltransf_4  83 yla.erdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikk 146
                                       +la +   + +g+g  l+ a+ + +++ + +  + e+ ++n +++ ++++lGF++ gi   ++ +
  gi|330506381|ref|YP_004382809.1|  91 WLAiRPRYQGRGIGMRLMLAVLKSFRNLGALGATLEVRVSNRKAQSLYSNLGFQIRGICPSYYSD 155
                                       5555555677899999999999*********************************9998777665 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     3e-05     0.067      32      55 ..      94     117 ..      72     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                   Acetyltransf_CG  32 VpeelrGkGiAkkLvkaalddare 55 
                                       + ++++G+Gi+++L+ a+l+  r+
  gi|330506381|ref|YP_004382809.1|  94 IRPRYQGRGIGMRLMLAVLKSFRN 117
                                       7899***************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1201.78
//
Query:       gi|330506382|ref|YP_004382810.1|  [L=57]
Description: hypothetical protein MCON_0077 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 440.44
//
Query:       gi|330506383|ref|YP_004382811.1|  [L=367]
Description: hypothetical protein MCON_0078 [Methanosaeta concilii GP6]
Scores for complete 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  201.1   0.0    1.2e-59  200.6   0.0    1.2  1  YhcG_C     YhcG PDDEXK nuclease domain
    6.9e-48  162.3   0.5    1.8e-46  157.7   0.4    2.1  2  DUF1016_N  DUF1016 N-terminal domain


Domain annotation for each model (and alignments):
>> YhcG_C  YhcG PDDEXK nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.6   0.0   1.3e-63   1.2e-59       2     155 .]     195     350 ..     194     350 .. 0.99

  Alignments for each domain:
  == domain 1  score: 200.6 bits;  conditional E-value: 1.3e-63
                            YhcG_C   2 eilkdpyvldflelkeeykErelekalieklkkfllelGkgFafvgrqyrleveekefyidLlfYhlklkcyvvieL 78 
                                       +i+kdpy++dfl+ ++  +Ere+ek li+++++fllelG+gFafvgrq++le+ +k++y+dLlfYhlkl++yvv+eL
  gi|330506383|ref|YP_004382811.1| 195 QIFKDPYLFDFLGTADPRREREVEKGLIDHIQRFLLELGEGFAFVGRQVHLEFATKDYYLDLLFYHLKLRSYVVVEL 271
                                       799************************************************************************** PP

                            YhcG_C  79 KvgefkpedagklnlYlsaldeelkkeednptiGiilckekdktvveyalkeinkpigvseY..elpkelpeelkek 153
                                       K  +f+p ++g ln+Ylsa+d+ l++++d+p+iG++lc++ ++++veyal+ i+kp+gv+ +  +l k+lpeel++k
  gi|330506383|ref|YP_004382811.1| 272 KSVSFDPGFVGTLNMYLSAVDDLLRHPDDKPSIGLLLCRKGSRIEVEYALRGIQKPMGVAGWetKLVKTLPEELQSK 348
                                       **************************************************************999***********9 PP

                            YhcG_C 154 lp 155
                                       lp
  gi|330506383|ref|YP_004382811.1| 349 LP 350
                                       96 PP

>> DUF1016_N  DUF1016 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.7   0.4     2e-50   1.8e-46       1     137 []      37     173 ..      37     173 .. 0.99
   2 ?    2.5   0.0     0.016   1.5e+02      38      60 ..     330     352 ..     322     360 .. 0.85

  Alignments for each domain:
  == domain 1  score: 157.7 bits;  conditional E-value: 2e-50
                         DUF1016_N   1 eikelieqarqkaakavnselvelyweiGkrivekqeraeyGkkvikkLsedLkkefpevkGFsernlknmrqfyea 77 
                                       eike+i++ r ++++++ns++v lyw+iG++i ++qe++++G+kvi++Ls+dL+++fp+++G s rnlk+mr+f+ a
  gi|330506383|ref|YP_004382811.1|  37 EIKERIQKERLRVVMSANSSMVLLYWDIGRTIIDRQEKEGWGAKVIDRLSADLREAFPDMQGLSPRNLKYMRAFAAA 113
                                       69*************************************************************************** PP

                         DUF1016_N  78 ykeeeilqqlvaqlsWshnllllekvkdeeerefYleeaieegWsrreLerqiksklyer 137
                                       ++++ei+q+++aq++W hn++llekv d++ r +Y+++ +eegWsr++L  qi++kl++r
  gi|330506383|ref|YP_004382811.1| 114 WPDREIVQEVLAQITWYHNIALLEKVADSQVRLWYAKKGLEEGWSRSVLVMQIERKLHDR 173
                                       *********************************************************987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.016
                         DUF1016_N  38 raeyGkkvikkLsedLkkefpev 60 
                                        a++ +k++k+L e+L+++ p+v
  gi|330506383|ref|YP_004382811.1| 330 VAGWETKLVKTLPEELQSKLPSV 352
                                       589***************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2661.14
//
Query:       gi|330506384|ref|YP_004382812.1|  [L=436]
Description: restriction modification system DNA specificity domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (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  142.7   0.1    8.9e-24   84.6   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 !   84.6   0.0     5e-28   8.9e-24      25     168 .]      55     216 ..      49     216 .. 0.80
   2 !   56.3   0.0   2.4e-19   4.3e-15       1     142 [.     244     394 ..     244     420 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 5e-28
                                       GGTTT--EEEE-HHHCCT..........EE-HHHHCCTT---B-.TT-EEEE-SSSTT-EEEESS-.....BEE-TT CS
                       Methylase_S  25 elkengkypyiragilnn..........kvvkdglgykkkyilp.kgdilissratiGkvayrdkk.....yylnqs 85 
                                        ++ + ++p+ir + lnn           v+ + + ++   +l   gd+++++r+t G va+++k+     y+++qs
  gi|330506384|ref|YP_004382812.1|  55 RDYSDQGIPVIRGSNLNNgrfldmnefvYVSDSKVRKDLSGNLAkPGDLVFTQRGTLGQVAIIPKEgisdrYVVSQS 131
                                       45566778999999777779999999874444444444444444489******************555556****** PP

                                       EEEEEEST.TT--HHHHHHHHH..HCHHHHHHHCCSSTTT---HHHHCC-EEEE--HHHHHHHHHHHHHHHHHHHHH CS
                       Methylase_S  86 vivlipkn.kkkineflylyll..lklkklkslsvgstqpkltkenlkkikIplPpleeQkkIakiLsqldntiele 159
                                        ++l++ + k ++  fly+y++      ++++++ +s+ p+++++ l++++Ip+Pple+Qk Ia+iLs++d++ie +
  gi|330506384|ref|YP_004382812.1| 132 QMKLTVDDtKADQ-FFLYYYFSsrEVIDRITNFTSSSGVPHINLTVLRNFEIPVPPLEIQKSIASILSAYDDLIENN 207
                                       ******8855544.6666666655444599999******************************************** PP

                                       HHHHHHHHH CS
                       Methylase_S 160 kkikneier 168
                                       +++++ +e+
  gi|330506384|ref|YP_004382812.1| 208 RRRIQLLEQ 216
                                       ***999986 PP

  == domain 2  score: 56.3 bits;  conditional E-value: 2.4e-19
                                       ETT-EEEEHHHHEEEEE-----TT.GGTTT--EEEE-HHHCCT.........EE-HHHHCCTT---B-TT-EEEE-S CS
                       Methylase_S   1 pedwevvkLgdvfeikkgktpkkk.elkengkypyiragilnn.........kvvkdglgykkkyilpkgdilissr 67 
                                       pe+we ++  d  +i +g tpk+   +++ng++p+++++++ +           +++gl +++ +++pk++i i++r
  gi|330506384|ref|YP_004382812.1| 244 PEGWERKTAFDEMDILSGGTPKTGvPDYWNGDIPFFTPKDSMDyayalatekRLTEEGLRNCNSKLYPKDTIFITAR 320
                                       7999999999999**************************66566********************************* PP

                                       SSTT-EEEESS-BEE-TTEEEEEESTTT--HHHHHHHHHHCHHHHHHHCCSSTTT---HHHHCC-EEEE--HHHH CS
                       Methylase_S  68 atiGkvayrdkkyylnqsvivlipknkkkineflylylllklkklkslsvgstqpkltkenlkkikIplPpleeQ 142
                                       +t+Gk++++     +nqs++ li k+  ++ ++ly+ l   ++++ s  vg  +  +  e++ +i++ +P  ++ 
  gi|330506384|ref|YP_004382812.1| 321 GTVGKINLAQTAMAMNQSCYALIGKPPLNQ-YYLYFALVDGVEQFRSRAVGAVFDAIIRETFNQIPFIVPDDKII 394
                                       *************************95555.999999999999***************************87763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3155.70
//
Query:       gi|330506385|ref|YP_004382813.1|  [L=441]
Description: hypothetical protein MCON_0080 [Methanosaeta concilii GP6]
Scores for complete sequence (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   54.5   0.0    2.3e-13   50.5   0.0    2.2  2  SIR2_2    SIR2-like domain


Domain annotation for each model (and alignments):
>> SIR2_2  SIR2-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.014   2.6e+02      57     114 ..      48     116 ..      36     149 .. 0.67
   2 !   50.5   0.0   1.3e-17   2.3e-13       3     138 ..     214     392 ..     212     396 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.014
                            SIR2_2  57 pesivltesdYeell.....arktpiptllkallrskslLfl...GySfsD...pnirelleellkesg 114
                                       p++  ++++  ++ +     + k+++ ++l ++l+ ++l++l   G+S++D   p +++l++ +++++ 
  gi|330506385|ref|YP_004382813.1|  48 PDTARISDKNKKNEIdgkakEAKRTLDEMLLSSLQMSNLVILsgsGTSLGDvggPSMKDLWNYAINNEL 116
                                       566656666654444343322478899999999988888887899999999443466666655555555 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 1.3e-17
                            SIR2_2   3 iiTTNYDdllekaleesgkpvsd................aavskedler.elseaesgrtllyklhGslsrp..... 57 
                                       ++TTNYD ++e+a   +   + d                + +   +l+  e+    +g  +l+klhGs+++      
  gi|330506385|ref|YP_004382813.1| 214 VFTTNYDLCFERAASLQSLIINDgfsytqprifdprffgYDTVRRSLAAaERGDYLEGVFHLLKLHGSVNWArssng 290
                                       8*************99999999999999999999988884444444444678999**************76655444 PP

                            SIR2_2  58 ....esivltesd................Yeell.a.rktpiptllkallrskslLfl.GySfsDpnirelleellk 111
                                           +                        Y+  + +   + i+++l++l++ +++L++ G++f+D+++ e + +++k
  gi|330506385|ref|YP_004382813.1| 291 rieeK-------NnpeppeacliypakgkYQLSYiQpHLELISQYLTSLREPNTCLIVtGFGFNDDHLSEPILAAVK 360
                                       44440.......45555555555555555876665633455889999999988999999****************** PP

                            SIR2_2 112 esgnarrhyaflpede......keeeekllekk 138
                                        +++  r +++  ++e      +ee  ++++++
  gi|330506385|ref|YP_004382813.1| 361 INPR-LRLIVVDFKAEdsiekpSEETSRYWKEF 392
                                       ****.6666655555566766666666677665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 3107.87
//
Query:       gi|330506386|ref|YP_004382814.1|  [L=580]
Description: hypothetical protein MCON_0081 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-22   80.1   0.0    4.1e-22   79.4   0.0    1.4  1  DUF87          Helicase HerA, central domain
    5.1e-08   32.2   0.1    0.00016   20.8   0.0    2.2  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    5.4e-07   28.6   0.1     0.0007   18.3   0.0    2.1  2  DUF853         Bacterial protein of unknown function (DUF853)
    3.1e-05   24.1   0.1      0.095   12.7   0.0    2.2  2  ResIII         Type III restriction enzyme, res subunit
    3.1e-05   23.1   0.0      0.015   14.2   0.0    2.7  3  AAA_10         AAA-like domain
    0.00015   22.0   0.3       0.22   11.8   0.0    2.5  2  AAA_22         AAA domain
     0.0059   16.3   0.0      0.011   15.4   0.0    1.4  1  Zot            Zonular occludens toxin (Zot)
  ------ inclusion threshold ------
      0.027   14.3   0.0       0.98    9.2   0.0    2.2  2  DEAD           DEAD/DEAH box helicase
       0.11   13.1   0.0       0.21   12.1   0.0    1.4  1  ABC_tran       ABC transporter


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 !   79.4   0.0   2.1e-25   4.1e-22       2     129 ..     160     282 ..     159     427 .. 0.78

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 2.1e-25
                             DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal...ekllsek 75 
                                       e+G + +++e +v++  +kl+ rH+Ailg TG GKS+t+a ++ee + k++++i++lD+ GEYg ++    ++    
  gi|330506386|ref|YP_004382814.1| 160 ELGAVGDANESKVSITPEKLFGRHCAILGATGGGKSWTTARIIEECI-KHKGKIILLDATGEYGEFSgdeVMHCYLG 235
                                       789999999**************************************.*******************7777777777 PP

                             DUF87  76 vkvitpspsakdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqak 129
                                       + v++p+        +++p s++  +++ l+      + +vq   l+ea+++++
  gi|330506386|ref|YP_004382814.1| 236 MPVYKPE---TSIACSLPPTSFQESDFMALFLP----SGKVQGPKLREAIRSLR 282
                                       7777776...79999************999988....34444444444444444 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 !   20.8   0.0   7.8e-08   0.00016      12      55 ..     178     221 ..     168     229 .. 0.87
   2 !    9.2   0.0   0.00026      0.52     256     327 ..     467     530 ..     464     535 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7.8e-08
                     TrwB_AAD_bind  12 eretqhilivGttGsGKtqalekllrairargdraivlDltGaf 55 
                                       +   +h +i+G+tG GK+ ++  ++++  + + ++i lD+tG++
  gi|330506386|ref|YP_004382814.1| 178 KLFGRHCAILGATGGGKSWTTARIIEECIKHKGKIILLDATGEY 221
                                       55569*************************************98 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00026
                     TrwB_AAD_bind 256 grleelksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsdaetAeelsellGeqev 327
                                        rl++++ +++egRkfG ++ l+ q           d ++ +ls ++t ++ r ++ + +e +++  Ge ++
  gi|330506386|ref|YP_004382814.1| 467 SRLDAFELIAKEGRKFGLCICLATQRPR--------DITEGVLSQMGTLVVHRLTNDRDREIVERACGEIDL 530
                                       7999*********************975........556677778888888887777777777777777666 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 !    8.1   0.0   0.00043      0.85      13      59 ..     173     219 ..     163     227 .. 0.67
   2 !   18.3   0.0   3.5e-07    0.0007     249     322 ..     435     513 ..     430     547 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00043
                            DUF853  13 lalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkG 59 
                                            kl  rh  i GatG Gk  t   + e+  +    ++l d  G
  gi|330506386|ref|YP_004382814.1| 173 SITPEKLFGRHCAILGATGGGKSWTTARIIEECIKHKGKIILLDATG 219
                                       344567889*************9887666655444444555556555 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3.5e-07
                            DUF853 249 PevGdldkPklvfffdeahLLfn.d.apkal...lekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqha 320
                                          Gd      v+  deah ++  +  ++ +   l+  e + +  r  G  + + tq P d+ + vL+q+G+ v h 
  gi|330506386|ref|YP_004382814.1| 435 ARKGDFKANPAVVVVDEAHHFLGrQiGSEDMfsrLDAFELIAKEGRKFGLCICLATQRPRDITEGVLSQMGTLVVHR 511
                                       567887777778889999865531212333312267789999999*******************************8 PP

                            DUF853 321 lr 322
                                       l 
  gi|330506386|ref|YP_004382814.1| 512 LT 513
                                       75 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   4.8e-05     0.095      26      60 ..     183     215 ..     166     220 .. 0.82
   2 !    9.1   0.0    0.0006       1.2     127     147 ..     434     458 ..     372     482 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                                       EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                            ResIII  26 rglikmaTGtGKTlvaaklierllkkgkeekflfl 60 
                                       +  i  aTG GK+++ a++ie++ k+++  k+++l
  gi|330506386|ref|YP_004382814.1| 183 HCAILGATGGGKSWTTARIIEECIKHKG--KIILL 215
                                       455889******************9766..66655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0006
                                       HHHTTT-S....EEEEETGGGTTS. CS
                            ResIII 127 ellrdrfd....viiiDEaHrlgak 147
                                        ++++ f+    v+++DEaH++ + 
  gi|330506386|ref|YP_004382814.1| 434 LARKGDFKanpaVVVVDEAHHFLGR 458
                                       344444446667*********9874 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   7.8e-06     0.015      22      64 ..     182     224 ..     170     244 .. 0.90
   2 ?   -0.5   0.0      0.23   4.5e+02     124     170 ..     388     437 ..     369     442 .. 0.83
   3 !    5.0   0.0    0.0049       9.7     242     304 ..     445     513 ..     438     523 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.8e-06
                            AAA_10  22 sasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekf 64 
                                        +++i+G +G+GKS ++  ++  +   +gk++++D + e  +f
  gi|330506386|ref|YP_004382814.1| 182 RHCAILGATGGGKSWTTARIIEECIKHKGKIILLDATGEYGEF 224
                                       69************************************98887 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.23
                            AAA_10 124 kaalseaveavlegkqrgllavieelrke...dekvareiarhlesvvkk 170
                                        +a+ +a+++ l+++qr l  ++  +++e    e +a+ i+r+l  +++k
  gi|330506386|ref|YP_004382814.1| 388 DKAITDAISEFLREDQRLLCICLSGIQHEfnaREIIANTIGRYLLYLARK 437
                                       34799*********************96655588899999*999887765 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0049
                            AAA_10 242 kvvifDEawiftssaeGkk.......llkelvRiGRsynaavylvtqsadDvlkeelknniglklaFret 304
                                       +vv++DEa  f   + G +         + + + GR++   + l+tq + D+ +     ++g+ ++ r t
  gi|330506386|ref|YP_004382814.1| 445 AVVVVDEAHHFLGRQIGSEdmfsrldAFELIAKEGRKFGLCICLATQRPRDITEGV-LSQMGTLVVHRLT 513
                                       7899999999999999975322221123456799*****************97543.3344444444433 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0018       3.6       6      28 ..     182     204 ..     181     239 .. 0.83
   2 !   11.8   0.0   0.00011      0.22      84     114 ..     429     471 ..     378     526 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                            AAA_22   6 gilvvtGesGtGKTtllrrlleq 28 
                                       +++++ G +G GK+++ +r+ e+
  gi|330506386|ref|YP_004382814.1| 182 RHCAILGATGGGKSWTTARIIEE 204
                                       6889**************99887 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00011
                            AAA_22  84 qalrarav.......ielliiDEaqhlr.....seealeeLrs 114
                                       ++l   a+       ++++++DEa+h+      se++++ L  
  gi|330506386|ref|YP_004382814.1| 429 RYLLYLARkgdfkanPAVVVVDEAHHFLgrqigSEDMFSRLDA 471
                                       44444444455677799*********55576655999998833 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.5e-06     0.011      35     134 ..     409     500 ..     385     514 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.5e-06
                               Zot  35 nidGlrlerieqvlgekvstarliridnpegaetlkefakwatidkgallviDEcqeifpvrakegrkdpevinaf. 110
                                        + G++ e  ++         ++i   n  g+ +l  ++k++  ++ a++v+DE++++   + +  +++  +++af 
  gi|330506386|ref|YP_004382814.1| 409 CLSGIQHEFNAR---------EIIA--NTIGRYLLYLARKGDFKANPAVVVVDEAHHFLGRQIG-SEDMFSRLDAFe 473
                                       555555544444.........5665..66777777888888887899*************9999.577888888883 PP

                               Zot 111 ...tehRhlgwDivlltqdiskihkev 134
                                          +e R++g  i+l tq +  i + v
  gi|330506386|ref|YP_004382814.1| 474 liaKEGRKFGLCICLATQRPRDITEGV 500
                                       333478**************9998766 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     0.042        85       9      39 ..     176     206 ..     170     246 .. 0.82
   2 ?    9.2   0.0   0.00049      0.98      98     149 ..     420     472 ..     390     498 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.042
                                       HHHHTTCEEEEEESTTSSHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   9 plilgggdvlvaaeTGsGKTlaflipvlqiv 39 
                                       p+ l g+++ + ++TG GK+   +  + +++
  gi|330506386|ref|YP_004382814.1| 176 PEKLFGRHCAILGATGGGKSWTTARIIEECI 206
                                       566779999**********998777766666 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00049
                                       CSEEEEEHHHHHHHH.HCTSSHCTTEEEEEEETHHHHHHT..TTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                              DEAD  98 vdivvgtpgrlddll.stgklnlsqvrflVlDEadrlldq..gfsdfinrilnql 149
                                        +i+  t gr +  l ++g ++  +  ++V+DEa+ +l    g +d  +r l ++
  gi|330506386|ref|YP_004382814.1| 420 REIIANTIGRYLLYLaRKGDFK-ANPAVVVVDEAHHFLGRqiGSEDMFSR-LDAF 472
                                       5788899999988663555533.34579**********985455554444.4444 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   0.00011      0.21      11      45 ..     181     215 ..     173     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                                       TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilld 45 
                                       g+  ai+G +G GKS   + ++++  + +G+i l 
  gi|330506386|ref|YP_004382814.1| 181 GRHCAILGATGGGKSWTTARIIEECIKHKGKIILL 215
                                       6789*************99999**9******9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4081.39
//
Query:       gi|330506387|ref|YP_004382815.1|  [L=700]
Description: hypothetical protein MCON_0083 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-31  110.0   0.1      4e-31  108.9   0.1    1.5  1  DUF262           Protein of unknown function DUF262
    1.2e-26   93.2   0.1    2.3e-26   92.3   0.1    1.4  1  DUF1524          Protein of unknown function (DUF1524)
  ------ inclusion threshold ------
       0.18   11.8   0.0       0.55   10.2   0.0    1.8  1  Phage_sheath_1C  Phage tail sheath C-terminal domain


Domain annotation for each model (and alignments):
>> DUF262  Protein of unknown function DUF262
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.9   0.1   6.7e-35     4e-31       3     220 ..      10     222 ..       7     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 6.7e-35
                            DUF262   3 dllskskrglriPdfQRpyvWeeeqveeLiedlla......lkgyplGsivlw...skaads...ageleviDGQQR 67 
                                       d+l+ks + ++iP++QR y+W+e+++ +L++d+l+       + +++Gsiv          +    + l+viDGQQR
  gi|330506387|ref|YP_004382815.1|  10 DFLKKSPQ-FVIPIYQRTYSWTERECLQLWDDILRtgsndaIAAHFIGSIVYIqkgL---YQisgMSPLLVIDGQQR 82 
                                       67777777.9******************************************85542...33445999********* PP

                            DUF262  68 ltTltlllaa...tkeesekriknleaeiek...............ekeeededrlkrreresdkellqkllrsekl 126
                                       ltTl+l+++a   +           ++   +               + +e  e  +k+   ++dk+ l  ll+++ l
  gi|330506387|ref|YP_004382815.1|  83 LTTLMLIIEAlarN--------LGETE---PvdgfsakklrnyyllNPLEDGERAFKLLLGQTDKQSLLALLQQKPL 148
                                       **********3221........22222...23331111111111223333334444444444444444444444443 PP

                            DUF262 127 sleekeelaelnsltkkdlakeekrneeknlikayevieeilksa......llsalktklslieieleseddedqay 197
                                                               ++   ++++++ ++ee ++        l + l  kl ++ i l+   d+d  +
  gi|330506387|ref|YP_004382815.1| 149 P-----------------------TEPSLRIQDNFAFFEEHVRALgldlapLCNGL-AKLVVVDIALS--RDKDNPQ 199
                                       3.......................56667777888888775555577655544444.55567777777..78889** PP

                            DUF262 198 eiFerlNsrGvpLtasellkall 220
                                        iFe++Ns+G++L++++l+++++
  gi|330506387|ref|YP_004382815.1| 200 LIFESMNSTGRELSQADLIRNFI 222
                                       *********************87 PP

>> DUF1524  Protein of unknown function (DUF1524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.1   3.8e-30   2.3e-26       2     137 ..     415     548 ..     414     549 .. 0.91

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 3.8e-30
                           DUF1524   2 prdeefrrallnaklysssrkklryilakelesalreedeeegeakkltiEHilPqslae..kw.egagqedeekre 75 
                                       p deef+r+l+ ++ly+ ++++  y l+ +le++ r+e+   +   ++tiEHi+Pq+ +   kw e+ g + ++  e
  gi|330506387|ref|YP_004382815.1| 415 PGDEEFKRELMVRDLYNFRSRS--YWLR-RLENHGRNERVPVD---EYTIEHIMPQNENLpvKWrESLGPDCQRVWE 485
                                       679***************9876..9999.***99995544444...467*********99756699999******** PP

                           DUF1524  76 elvndlgNLtlltkslNsslsnkpfleKrd...lykksslrlnrklaekdewdeeaiearqeaLa 137
                                        ++++lgNLtl+   +Ns +s++pf eKrd   ++k+s l ln++l + d w+e++i++r+e La
  gi|330506387|ref|YP_004382815.1| 486 TWLHTLGNLTLTG--YNSRYSDHPFIEKRDmegGFKESPLHLNKELGTLDGWNETKIKQRAERLA 548
                                       *************..***********************************************997 PP

>> Phage_sheath_1C  Phage tail sheath C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   9.2e-05      0.55      36      64 ..     193     221 ..     186     231 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 9.2e-05
                                       TSHHHHHHHHHHHHHHHHHHHHTTSB-S- CS
                   Phage_sheath_1C  36 nnddgralvksalnaylkelqregaienf 64 
                                        ++d+++l+++ +n++ +el ++++i nf
  gi|330506387|ref|YP_004382815.1| 193 RDKDNPQLIFESMNSTGRELSQADLIRNF 221
                                       589************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (700 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.22s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 5302.29
//
Query:       gi|330506388|ref|YP_004382816.1|  [L=1078]
Description: type I site-specific deoxyribonuclease, HsdR family [Methanosaeta concilii GP6]
Scores for complete 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-70  235.2   1.8    2.3e-69  233.5   0.0    2.4  2  SWI2_SNF2  SWI2/SNF2 ATPase
    8.2e-29  100.9   1.5    1.8e-28   99.9   0.1    2.3  2  HSDR_N     Type I restriction enzyme R protein N terminus (HS
    1.3e-23   83.9   9.2    1.3e-23   83.9   9.2    1.9  2  DUF3387    Domain of unknown function (DUF3387)
    9.7e-17   61.5   1.4    2.2e-16   60.3   0.0    2.4  3  ResIII     Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
       0.65    8.7   4.4       0.35    9.6   2.0    1.7  2  UPF0061    Uncharacterized ACR, YdiU/UPF0061 family


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 !  233.5   0.0   6.5e-73   2.3e-69       1     218 [.     270     491 ..     270     497 .. 0.91
   2 ?   -0.2   0.4      0.18   6.5e+02     165     216 ..     810     861 ..     797     870 .. 0.79

  Alignments for each domain:
  == domain 1  score: 233.5 bits;  conditional E-value: 6.5e-73
                         SWI2_SNF2   1 qQyravekavervke...gdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfaka.. 72 
                                       +Q+ +v++a+e+v +    + k Gv+WHtqG+GKs++mv++++k++++   n++++v+tDR+dLd+Q++ktfa +  
  gi|330506388|ref|YP_004382816.1| 270 HQFLGVNRAIEAVCKrkeLHGKLGVFWHTQGAGKSYSMVMFTRKVHRKLGGNFTFLVLTDRDDLDTQIYKTFAGCgv 346
                                       8************885554489*************************6679***********************965 PP

                         SWI2_SNF2  73 ..geekpkqaesrkeLkellekesekiifttiqKfeeeekeklevlsereniivlvDEaHRsqygelakklrkalpn 147
                                         +++ + +a+s+++L +ll +e++  if++iqKf+++  +  e +++r++iiv++DEaHR+qyg+la+++r+alp+
  gi|330506388|ref|YP_004382816.1| 347 vdNDQVQCRASSGSHLSRLL-AEHKAFIFSLIQKFNQKI-DPGEGYTQRDDIIVITDEAHRTQYGTLAENMRNALPH 421
                                       544666779***********.6699**********8753.357899******************************* PP

                         SWI2_SNF2 148 aafigFTGTPilkkdkktkevFgeyidkYtikeaveDgavvpilYesrlaklelkeeekldeefeeiteel 218
                                       a+figFTGTP++k+d+ t++vFg+y+++Y++++aveD+a+vp++Y +r +kl +   + l+e++ e  ee 
  gi|330506388|ref|YP_004382816.1| 422 ASFIGFTGTPLFKEDQITRKVFGDYVSTYDFQRAVEDKATVPLYYDARGEKLGVAIGD-LNERVAEKLEEF 491
                                       ****************************************************999987.888887777665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.18
                         SWI2_SNF2 165 tkevFgeyidkYtikeaveDgavvpilYesrlaklelkeeekldeefeeite 216
                                         ++F  +i   +i+   +D+  v+i+Y+s  ++ e  + +++ ++++++++
  gi|330506388|ref|YP_004382816.1| 810 VFKKFRACITLQDINAYRDDRDAVNIVYKSLQQDREKADITDIMRQLQHLVD 861
                                       5678889999999999999*********999888887776666666666554 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 !   99.9   0.1   4.9e-32   1.8e-28       2     191 ..       4     212 ..       3     215 .. 0.93
   2 ?   -2.2   0.2      0.93   3.3e+03      42      83 ..     915     941 ..     878     986 .. 0.56

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 4.9e-32
                                       SSHHHHHH.HHHHHH.HHTT-EE................----SHHHHHHHHHHHHHHHH...........-HHHHH CS
                            HSDR_N   2 lsEaeleqelidell.relGyqvlskkdveiegrrpe.vrkskaevaleknlreqlgaln...........ikkltk 65 
                                       ++E +l+q+   ++l ++lG++     + e  g +    r+s +ev+l+  lr++l++ln           ++++t+
  gi|330506388|ref|YP_004382816.1|   4 YTEDTLVQQTTADYLeQQLGWESVYAYNSEDFGPKSLlGRASDREVVLTRILRQKLAELNpglpgaayddaVRQITA 80 
                                       6899999999999999******99988777666555599*************************************9 PP

                                       HHH...TT--HHHHHHHHHTS.-EEEE....TS-EEEEESS-SSSGGGS-EEEEE----S.SSS---EEEEEEETTE CS
                            HSDR_N  66 rla...lsdgnkefyellkeg.kvkfk....egrkknikLiDkknlenNrfqvvnQvtvt.gnqkrrpDivlfvngl 133
                                        +a   l + n+e+y  ++eg +v f+    e  k++++L D++++ nN+f +v++++++ +   rr+Div fvngl
  gi|330506388|ref|YP_004382816.1|  81 TIAsqtLASTNREKYGQIREGvQVAFRndegELVKERMQLFDFNEPGNNHFLAVRELWIRgDLYRRRADIVGFVNGL 157
                                       999**********************7779888889*************************88999************ PP

                                       EEEEEEE--T.T-HHHHHHH.HTSS---.---SSSGGGGG--EEEEE-SS-EEEEE--SS CS
                            HSDR_N 134 plvviElKrp.gtieeAinQ.ikryrkeksdvsipqlfrYlqfgvisngketrfyaktkr 191
                                       pl++iE+K+  ++++ A++  + +y ++     ip +f+ +++++  ng ++++++ t +
  gi|330506388|ref|YP_004382816.1| 158 PLLFIECKNIhKNLKAAFEKnFSDYLDT-----IPHIFHHNAIVMFGNGQQAKIGTITSK 212
                                       *********955*******99*****77.....9*********************98876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.93
                                       -SHHHHHHHHHHHHHHHH-HHHHHHHHTT--HHHHHHHHHTS CS
                            HSDR_N  42 kaevaleknlreqlgalnikkltkrlalsdgnkefyellkeg 83 
                                       +++++l ++++++++++               ++ y++ k+ 
  gi|330506388|ref|YP_004382816.1| 915 LQQNPLRTDFQQHYEKI---------------VAEYNREKDR 941
                                       23333333333333333...............3333332222 PP

>> DUF3387  Domain of unknown function (DUF3387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.39   1.4e+03     130     187 ..     454     514 ..     452     526 .. 0.75
   2 !   83.9   9.2   3.8e-27   1.3e-23       3     306 ..     738    1035 ..     736    1049 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.39
                           DUF3387 130 kaiaseevvdifaaaglekp..disiLseefleevkkmkeknlavel.LkklLadeikars 187
                                       +a++ +  v ++ +a  ek    i +L+e + e++++ +  ++ ve  L+k L++e + ++
  gi|330506388|ref|YP_004382816.1| 454 RAVEDKATVPLYYDARGEKLgvAIGDLNERVAEKLEEFEIDDINVEQrLEKELKREYHIIT 514
                                       6777777777776666666545788999999999999999999997448888888876655 PP

  == domain 2  score: 83.9 bits;  conditional E-value: 3.8e-27
                           DUF3387    3 gkgkptedieeavavlkeklevvrell..hgfdyskfftadpkeklellleaaehilsleegkkrFlklvkaLkk 75  
                                        g+ +p++ +ee+++ l e ++ vr++l   +  + ++ +++  e+ +++++  e   +++e++krF  + +++ k
  gi|330506388|ref|YP_004382816.1|  738 GEIDPARPEEELLSDLAEAISFVRAFLdeRNAPLDDIIHKTGFERNAAIAACKEAANENDETRKRFEIMCREVFK 812 
                                        6778999999*****************44467788**************************************** PP

                           DUF3387   76 ayalcapseeaeelrdevaffqavrailvKltaaeegkspdteeleaavrqlidkaiaseevvdifaaaglekpd 150 
                                         +  c++ ++++++rd+   ++ v + l +    ++ +++d+++++++++ l+d+ai+ +   d   + g+   d
  gi|330506388|ref|YP_004382816.1|  813 KFRACITLQDINAYRDDRDAVNIVYKSLQQ----DR-EKADITDIMRQLQHLVDEAIDVQS--DTATKPGEP-YD 879 
                                        *****************9877766666555....33.456899*************96543..434444443.46 PP

                           DUF3387  151 isiLseefleevkkmkeknlavelLkklLadeikarsrkNlvkskkFserLeelikkYnnra..ltsaevieeLi 223 
                                        is ++   l++    ++kn+ v+ L+++++  +++  ++N  + ++F++  e+++++Yn+++   t ++ +e L+
  gi|330506388|ref|YP_004382816.1|  880 ISKIDFVRLKQEF-ERYKNTVVQNLRQAVEIRLQRLLQQNPLR-TDFQQHYEKIVAEYNREKdrATIEQTFEALL 952 
                                        6666655554432.468************************99.9**************99888999******** PP

                           DUF3387  224 elakeikeekkrgeelgLseeElAFYdaLaenesavevmgddkLkelAkelvetvrk.nati.DWtkresvrAkl 296 
                                        +l + + ee++r+ + gL+ee lA +d+L++ + +   ++ +++k++A el++t+++ ++++  W+ +e  r  +
  gi|330506388|ref|YP_004382816.1|  953 KLVQGLDEEESRAVREGLDEESLAIFDLLKKPDLK--GVDIKRIKKVAAELLKTLKEeKLRVdQWRDKEATRDAV 1025
                                        ********************************998..779999************972567777*********** PP

                           DUF3387  297 rvavkrlLrk 306 
                                        rv +   L +
  gi|330506388|ref|YP_004382816.1| 1026 RVTIHNFLWN 1035
                                        ****998865 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 ?   -2.7   0.0       1.4   5.1e+03      59      85 ..     160     192 ..     159     257 .. 0.64
   2 !   60.3   0.0   6.1e-20   2.2e-16      11     169 ..     278     431 ..     267     433 .. 0.86
   3 ?   -2.8   0.2       1.5   5.5e+03      78     118 ..     928     962 ..     888     979 .. 0.49

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.4
                                       EEESSHHHHHHHHHHGGGGTGG..........G CS
                            ResIII  59 flvprkslleqtleefkkflseayke......i 85 
                                       +++  k++ + ++ +f+k +s++ +       +
  gi|330506388|ref|YP_004382816.1| 160 LFIECKNIHKNLKAAFEKNFSDYLDTiphifhH 192
                                       566667888888888888888876663333331 PP

  == domain 2  score: 60.3 bits;  conditional E-value: 6.1e-20
                                       HHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S......-EEEEESSHHHHHHHHHHGGGGTGG.....G CS
                            ResIII  11 aienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee.kflflvprkslleqtleefkkflseayke.i 85 
                                       aie++  k+k+ + k g+++++ G+GK++ ++ +++++++k + +  fl+l +r +l  q +++f+ +   ++++ +
  gi|330506388|ref|YP_004382816.1| 278 AIEAVC-KRKELHGKLGVFWHTQGAGKSYSMVMFTRKVHRKLGGNfTFLVLTDRDDLDTQIYKTFAGCGVVDNDQvQ 353
                                       566665.33436667899*********************9988777**********************999887778 PP

                                       EEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---SEE CS
                            ResIII  86 gkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfkeavl 162
                                       +   sg + ++    +++k ++++ iq++++++       e + +    ++i DEaHr+++ +  ++  +++++a  
  gi|330506388|ref|YP_004382816.1| 354 CRASSGSHLSR--LLAEHKAFIFSLIQKFNQKI----DPGEGYTQRDDIIVITDEAHRTQYGTLAENMRNALPHASF 424
                                       88888888877..88999***************....555666666677************9888889999999*** PP

                                       EEEESS- CS
                            ResIII 163 lglTATp 169
                                       +g+T+Tp
  gi|330506388|ref|YP_004382816.1| 425 IGFTGTP 431
                                       ******9 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.5
                                       TGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH CS
                            ResIII  78 lseaykeigkkvsgdkkkakekdstnkkilvttiqsldads 118
                                       ++    +i  +++ +k++a    +++ + l+  +q ld+++
  gi|330506388|ref|YP_004382816.1| 928 YE----KIVAEYNREKDRA--TIEQTFEALLKLVQGLDEEE 962
                                       22....1333333333333..33444455555555555444 PP

>> UPF0061  Uncharacterized ACR, YdiU/UPF0061 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       0.7   2.5e+03     301     332 ..     505     536 ..     497     568 .. 0.81
   2 ?    9.6   2.0   9.8e-05      0.35     351     465 ..     829     949 ..     763     953 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.7
                           UPF0061 301 qlaeplallieaeeleealeeykevyttkYaq 332
                                       +l+++ +++ + ++l++  +++ ++y+t++++
  gi|330506388|ref|YP_004382816.1| 505 ELKREYHIITAEKRLDQVARDFVQHYSTAWEN 536
                                       56777788889999999999999999999976 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 9.8e-05
                           UPF0061 351 dselleellelLqe..tqvdYneffveLaeskskkwrdeaesileese....keleeekleeWrelYkklleeleed 421
                                       d + ++ + + Lq+  +++d ++ +++L++  ++ ++ ++++  +  e    ++++  +l++  e+Yk+++ ++ ++
  gi|330506388|ref|YP_004382816.1| 829 DRDAVNIVYKSLQQdrEKADITDIMRQLQHLVDEAIDVQSDTATKPGEpydiSKIDFVRLKQEFERYKNTVVQNLRQ 905
                                       466677777777752268999**********9999998877776666677676677799999999**9999999999 PP

                           UPF0061 422 eleeraerlkkvNpktvllrplieeviekiaeeddlsplkklle 465
                                        +e r +rl + Np+ +  ++  e+++ + ++e+d  ++++ +e
  gi|330506388|ref|YP_004382816.1| 906 AVEIRLQRLLQQNPLRTDFQQHYEKIVAEYNREKDRATIEQTFE 949
                                       ********************************999988887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1078 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1277  (0.0712254); expected 358.6 (0.02)
Passed bias filter:                      773  (0.0431145); 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: 0.87u 0.29s 00:00:01.15 Elapsed: 00:00:00.46
# Mc/sec: 7076.62
//
Query:       gi|330506389|ref|YP_004382817.1|  [L=1070]
Description: carbamoyl-phosphate synthase, large subunit [Methanosaeta concilii GP6]
Scores for complete 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  318.0   1.6    3.8e-58  196.4   0.1    2.3  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    3.2e-26   92.1   0.1    2.2e-25   89.4   0.0    2.5  2  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    2.5e-24   85.3   0.1    3.6e-23   81.6   0.1    3.0  3  MGS              MGS-like domain
    2.9e-24   85.5   0.2      3e-11   43.2   0.0    2.4  2  ATP-grasp        ATP-grasp domain
    8.6e-16   58.1   0.3    7.9e-08   32.1   0.1    2.6  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    7.5e-13   48.4   0.0    7.1e-06   25.8   0.1    2.4  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    6.6e-09   36.0   0.1     0.0006   19.9   0.1    2.5  2  ATP-grasp_3      ATP-grasp domain
    3.4e-08   33.5   0.3      0.012   15.4   0.0    3.0  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    1.1e-05   25.1   0.0       0.12   11.8   0.0    2.7  2  ATP-grasp_5      ATP-grasp domain
    1.8e-05   24.4   0.0      0.026   14.1   0.0    2.6  2  ATP-grasp_2      ATP-grasp domain
  ------ inclusion threshold ------
      0.024   14.7   0.0        2.7    8.1   0.0    2.9  2  DUF4176          Domain of unknown function (DUF4176)
      0.068   13.1   0.0       0.16   11.8   0.0    1.6  1  QSregVF_b        Putative quorum-sensing-regulated virulence 


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 !  196.4   0.1   2.6e-61   3.8e-58       1     210 [.     128     333 ..     128     334 .. 0.99
   2 !  120.8   0.2   3.6e-38   5.4e-35       1     210 [.     669     871 ..     669     872 .. 0.96

  Alignments for each domain:
  == domain 1  score: 196.4 bits;  conditional E-value: 2.6e-61
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D+  +ke+++ ++++v +s+a    t+e+a ++a ++gyPv++++a+++GG+G+++++n eel+ +v++++a++   
  gi|330506389|ref|YP_004382817.1| 128 DRIIFKETMNSLGIEVPKSTAI--YTVEDAEKVALDLGYPVVVRPAYTMGGTGGGLVYNAEELRTVVSRGIAASL-- 200
                                       999******************9..*************************************************95.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                           qvl+e+s++g+ e+E+ev+rD+k+ +itvc +en++++  +t+++   AP  t+++e  ++l+  + ++v+++
  gi|330506389|ref|YP_004382817.1| 201 --IGQVLIEESVAGWEELELEVVRDSKNHMITVCFIENVDAMgvHTGDSFCTAPMLTISQELQDKLQDYSYRIVEAI 275
                                       ..89************************************************************************* PP

                                       T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 153 gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       +v+g+ +++f+ dpk+++ +viE+N+R s++sala+kaTG++++ ++ak+a+g +++e
  gi|330506389|ref|YP_004382817.1| 276 KVIGGTNIQFAHDPKTGRVVVIEINPRTSRSSALASKATGFPIALISAKLASGLTMDE 333
                                       *****************************************************99987 PP

  == domain 2  score: 120.8 bits;  conditional E-value: 3.6e-38
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D+++++ +++++++p+ +s  a  ++l++al++ak+igyP ++++++ lGG+Gm v+++ee l+  v++a++ ++  
  gi|330506389|ref|YP_004382817.1| 669 DRDRFRMMMEELDIPMPESGMA--SNLDQALEVAKRIGYPLMVRPSYVLGGRGMEVIYDEEMLERYVAAAVDVTP-- 741
                                       9******************999..**************************************************6.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                         ++ +l++++l++  e E++ l+D k+  +    +e + q   + +++  v P   ++ e+ q+++e + k+++++
  gi|330506389|ref|YP_004382817.1| 742 --ERPILIDRFLENALETEADALSDGKEAFVPA-VMEHIEQAgiHSGDSACVIPPVSISGEHLQTIEEYTRKIAQKL 815
                                       ..99***********************998875.5888888888********************************* PP

                                       T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 153 gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       +vvg  ++++++++  +  yv+E N+R s+  +l +k+  + ++ +a ++ ++++++e
  gi|330506389|ref|YP_004382817.1| 816 HVVGLMNMQYAISH--DVVYVLEANPRASRTVPLVSKVCNVSMARIATQMMMNKRMDE 871
                                       *************5..999*************************99999988887765 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 !   89.4   0.0   1.4e-28   2.2e-25       3     122 .]     424     543 ..     422     543 .. 0.96
   2 ?   -1.5   0.0       2.1   3.2e+03      43      98 ..     951    1006 ..     947    1042 .. 0.68

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1.4e-28
                       CPSase_L_D3   3 lkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkk....eldeellreakklGfsDkq 75 
                                       lke ++eR f+++ea+r+g++++++++lt+i+pwFL++++elv+le+e+ ++k     +l++ell +akk Gf D++
  gi|330506389|ref|YP_004382817.1| 424 LKETSSERQFILYEAIRKGADIQKLYQLTHIKPWFLQQMKELVQLEEEILAYKGkplvDLPDELLSQAKKDGFADRY 500
                                       78999********************************************9999899********************* PP

                       CPSase_L_D3  76 iaelleeeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                       +++ll+   e+e+r+ rk+lgi   ++ v     e   +  Y+YstY
  gi|330506389|ref|YP_004382817.1| 501 LSKLLA-VPEAEIRARRKSLGIVQGWEPVPVSGVE---NAFYYYSTY 543
                                       ****86.77888*********************99...899*****9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                       CPSase_L_D3   43 elvelekelkkkkk..eldeellreakklGfsDkqiaelleeeeeeevrelrkklgil 98  
                                        elve+++e++k       ++ +   +k+ G++ + i+++ e   + ++ ++ k+++i+
  gi|330506389|ref|YP_004382817.1|  951 ELVEVAREFQKLGFriMATSGTRAVLKENGIPSEMIKKIYE--GRPNIDDAIKNKEIQ 1006
                                        67777777777766544455556678999999999999963..333455555554444 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.1   6.1e+03       5      17 ..      33      45 ..      30      57 .. 0.85
   2 ?   -1.1   0.0       1.4   2.2e+03       5      20 ..     645     660 ..     623     685 .. 0.74
   3 !   81.6   0.1   2.4e-26   3.6e-23       1      95 []     951    1037 ..     951    1037 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.1
                                      HHHHHHHTTCEEE CS
                               MGS  5 lakklkelgfell 17
                                       +k+lk+lg++++
  gi|330506389|ref|YP_004382817.1| 33 ACKALKALGYKIV 45
                                      5789999999986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                                       HHHHHHHTTCEEEEEH CS
                               MGS   5 lakklkelgfellATg 20 
                                       + ++l+++g+++l T+
  gi|330506389|ref|YP_004382817.1| 645 ISRELEDAGVKILGTS 660
                                       5566777777777664 PP

  == domain 3  score: 81.6 bits;  conditional E-value: 2.4e-26
                                        THHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHH CS
                               MGS    1 glvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatv 75  
                                        +lve+a+++++lgf+++AT+GT ++lke+gip  e+++k+ eg r++    i daikn+ei+lvint+ +++++ 
  gi|330506389|ref|YP_004382817.1|  951 ELVEVAREFQKLGFRIMATSGTRAVLKENGIP-SEMIKKIYEG-RPN----IDDAIKNKEIQLVINTPIGKASQY 1019
                                        689*****************************.**********.***....***********************9 PP

                                        HCHHHHHHHHHHHTTSHEES CS
                               MGS   76 akdgykirraaenidIplpt 95  
                                          d+  ir+aa+++++p++t
  gi|330506389|ref|YP_004382817.1| 1020 --DDSYIRKAAIKYKVPYIT 1037
                                        ..8999************98 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.1   1.9e-13   2.9e-10       2     161 ..     137     304 ..     136     312 .. 0.90
   2 !   43.2   0.0     2e-14     3e-11       2     160 ..     678     841 ..     677     844 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.9e-13
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE---- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpf 74 
                                       ++lg++vp+ +a+ + e++e++a +lg+pvvv+ +     G G  +v ++e+l+++++        ++v++Ee v  
  gi|330506389|ref|YP_004382817.1| 137 NSLGIEVPKSTAIYTVEDAEKVALDLGYPVVVR-PAYTMGGTGGGLVYNAEELRTVVSRGiaasLIGQVLIEESVAG 212
                                       5799*****************************.999999***************9987766667799********* PP

                                       SEEEEEEEEEETTC-EEE--EEEEEEETTEEE...EEEECE.E-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEE. CS
                         ATP-grasp  75 ekElsvlvvrsaeGetafypvvetvqedgilr...lsvapa.evsekaqkkaeeiakkiveeLggvGvfavElFvl. 146
                                         El + vvr+ + ++ ++  +e+v   g+      + ap+ ++s++ q k +++  +ive++ ++G   + +    
  gi|330506389|ref|YP_004382817.1| 213 WEELELEVVRDSKNHMITVCFIENVDAMGVHTgdsFCTAPMlTISQELQDKLQDYSYRIVEAIKVIGGTNIQFAHDp 289
                                       **************************9999853336788863578899***********************987765 PP

                                       TTCTEEEEEEESS-- CS
                         ATP-grasp 147 edgellvnElapRpH 161
                                       ++g+++v E+ pR+ 
  gi|330506389|ref|YP_004382817.1| 290 KTGRVVVIEINPRTS 304
                                       7788*********85 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 2e-14
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE---- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpf 74 
                                       e+l +p+p+  ++++ +++ e+a+++g+p++v+ +     G+G  v+ +ee le+ ++a+     e+++++  f + 
  gi|330506389|ref|YP_004382817.1| 678 EELDIPMPESGMASNLDQALEVAKRIGYPLMVR-PSYVLGGRGMEVIYDEEMLERYVAAAvdvtPERPILIDRFLEN 753
                                       6899*****************************.99999****************999998998999********98 PP

                                       SEEEEEEEEEETTC-EEE--.EEEEEEETTEE....EEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEE CS
                         ATP-grasp  75 ekElsvlvvrsaeGetafyp.vvetvqedgil....rlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvl 146
                                         E  + +    +G+ af+p v+e++++ gi       ++ p ++s ++++++ee+++ki+++L +vG++ +   + 
  gi|330506389|ref|YP_004382817.1| 754 ALETEADAL--SDGKEAFVPaVMEHIEQAGIHsgdsACVIPPVSISGEHLQTIEEYTRKIAQKLHVVGLMNMQYAIS 828
                                       888776555..5677777762568898877652221688999******************************98777 PP

                                       TTCTEEEEEEESS- CS
                         ATP-grasp 147 edgellvnElapRp 160
                                        ++ ++v E  pR 
  gi|330506389|ref|YP_004382817.1| 829 -HDVVYVLEANPRA 841
                                       .4449999999885 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.1   5.3e-11   7.9e-08      26     174 ..     153     301 ..     137     306 .. 0.84
   2 !   23.1   0.0   2.9e-08   4.3e-05      26     174 ..     694     839 ..     682     862 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 5.3e-11
                                       HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHH..HHTT-SCEEEEE--.ESEEEEEEEEETSSCEEE CS
                   Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseeelkeaiee..afkydekvlvEeai.egreievavlgneklevs 99 
                                       e  ekv   lgypv+V+pa +    G   v ++eel+  +++  a++   +vl+Ee +   +e+e  v+ + k+++ 
  gi|330506389|ref|YP_004382817.1| 153 EDAEKVALDLGYPVVVRPAYTMGGTGGGLVYNAEELRTVVSRgiAASLIGQVLIEESVaGWEELELEVVRDSKNHMI 229
                                       456899999**********99999999*************9844667789********77799*******8888877 PP

                                       EEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEE.ETTTEEEEEEEES CS
                   Dala_Dala_lig_C 100 evgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDffl.teegeivlnEvNt 174
                                       +v  i   +++      +++d+       ++++e ++k+q+++ ++ +a+++ G + + f    ++g++v+ E+N+
  gi|330506389|ref|YP_004382817.1| 230 TVCFIENVDAM----GVHTGDSFCTAPMLTISQELQDKLQDYSYRIVEAIKVIGGTNIQFAHdPKTGRVVVIEINP 301
                                       77766554433....23345566666667899******************************7799*********6 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 2.9e-08
                                       HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-..SCEEEEE--.ESEEEEEEEEETSS.CEE CS
                   Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd..ekvlvEeai.egreievavlgnek.lev 98 
                                       +   +v +++gyp++V+p+      G++ +  ee l++++++a+  +  + +l+++++ ++ e e   l ++k   v
  gi|330506389|ref|YP_004382817.1| 694 DQALEVAKRIGYPLMVRPSYVLGGRGMEVIYDEEMLERYVAAAVDVTpeRPILIDRFLeNALETEADALSDGKeAFV 770
                                       45678999***********999999******************98862267*******99******99998883456 PP

                                       EEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C  99 sevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                         v e++ + g+       s+d+a +  p++++ e  ++i+e+  k+ + l++ Gl  + + ++ ++ +++ E N+
  gi|330506389|ref|YP_004382817.1| 771 PAVMEHIEQAGIH------SGDSACVIPPVSISGEHLQTIEEYTRKIAQKLHVVGLMNMQYAIS-HDVVYVLEANP 839
                                       6678888888875......6799999**********************************9998.78999999996 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 !   19.9   0.0   3.2e-07   0.00048      46     121 ..     261     339 ..     254     346 .. 0.84
   2 !   25.8   0.1   4.8e-09   7.1e-06      47     115 ..     802     871 ..     793     883 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.2e-07
                      ATPgrasp_Ter  46 deelielaerlaeefgldglvnvQvrededg..pkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeveep 119
                                       +++l +++ r++e++++ g +n+Q+ +d ++   +++EiNpR s      s ++G  ++ +++kl+ gl ++e++ +
  gi|330506389|ref|YP_004382817.1| 261 QDKLQDYSYRIVEAIKVIGGTNIQFAHDPKTgrVVVIEINPRTSRSSAlASKATGFPIALISAKLASGLTMDEIPYW 337
                                       5678899******************9997776899********96555156677**********9999988887766 PP

                      ATPgrasp_Ter 120 ee 121
                                       +e
  gi|330506389|ref|YP_004382817.1| 338 KE 339
                                       65 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 4.8e-09
                      ATPgrasp_Ter  47 eelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgy.salaGvnlpylalklllgletee 115
                                       + + e+++++a+++++ gl+n+Q+   +d  ++LE NpRas ++ + s +++v ++++a ++++++ ++e
  gi|330506389|ref|YP_004382817.1| 802 QTIEEYTRKIAQKLHVVGLMNMQYAISHDVVYVLEANPRASRTVPLvSKVCNVSMARIATQMMMNKRMDE 871
                                       567899**************************************8538899***********99975544 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1     4e-07    0.0006       6     158 ..     131     303 ..     127     306 .. 0.72
   2 !   13.6   0.0   3.4e-05      0.05       9     158 ..     675     841 ..     667     844 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4e-07
                                       HHHHHHTTT.S---....-EESS--.......SSSEEEEESS-------B--SS--TTE...............EEE CS
                       ATP-grasp_3   6 ktykkLkeagvkvPtkleaeeleee.......ekklvvKprdGaggesvrvveekeeaeaaieeve........lvq 67 
                                        + + ++  g++vP+ +  + +e +        +++vv p++ +gg++  +v + ee+ + +            l+ 
  gi|330506389|ref|YP_004382817.1| 131 IFKETMNSLGIEVPKSTAIYTVEDAekvaldlGYPVVVRPAYTMGGTGGGLVYNAEELRTVVSRGIaasligqvLIE 207
                                       556677788999994444444444444567789**********************9988666654478999999999 PP

                                       E---S.EEEEEEEEE.SSSEEEEEEE.EEEEET........TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEE CS
                       ATP-grasp_3  68 efieG.kplSvsllsdgekvlvlavn.rqliekaeke....fvyaGnvtpietelkeevvelaeevvekleglaGyv 138
                                       e + G ++l ++++ d  k+++++v+  + ++  + +    f+ a  +  i +el++++++   ++ve++ ++ G  
  gi|330506389|ref|YP_004382817.1| 208 ESVAGwEELELEVVRDS-KNHMITVCfIENVDAMGVHtgdsFCTA-PMLTISQELQDKLQDYSYRIVEAI-KVIGGT 281
                                       99999668899999866.555555541333333222245434433.455667799***************.888888 PP

                                       EEEEEESS...SEEEEEEESS- CS
                       ATP-grasp_3 139 GvDlvlkd..eepyviEvNPRl 158
                                        + +      +  +viE+NPR 
  gi|330506389|ref|YP_004382817.1| 282 NIQFAHDPktGRVVVIEINPRT 303
                                       899986545589*********6 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.4e-05
                                       HHHTTT.S---.........-..EESS--SSSEEEEESS-------B--SS--TTE...............EEEE-- CS
                       ATP-grasp_3   9 kkLkeagvkvP.....tklea..eeleeeekklvvKprdGaggesvrvveekeeaeaaieeve........lvqefi 70 
                                         ++e  +++P     ++l +  e +++  ++l v p++  gg ++ v+ ++e +e+ ++           l+ +f+
  gi|330506389|ref|YP_004382817.1| 675 MMMEELDIPMPesgmaSNLDQalEVAKRIGYPLMVRPSYVLGGRGMEVIYDEEMLERYVAAAVdvtperpiLIDRFL 751
                                       456777899997766633322114455559**********************99998888777899*********** PP

                                       -SE.EEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES...----HHHHHHHHHHHHHTTSTT--EEEEEEEE CS
                       ATP-grasp_3  71 eGk.plSvsllsdgekvlvlavnrqliekaekefvyaGnvtp...ietelkeevvelaeevvekleglaGyvGvDlv 143
                                       e   +  +++lsdg+++ v av + + + + ++   + +v+p   i  e+ + ++e  +++ +kl  ++G++     
  gi|330506389|ref|YP_004382817.1| 752 ENAlETEADALSDGKEAFVPAVMEHIEQAGIHS-GDSACVIPpvsISGEHLQTIEEYTRKIAQKL-HVVGLMNMQYA 826
                                       9763888*******9998888877666553333.2222222211144566778888888888889.99999999999 PP

                                       ESS.SEEEEEEESS- CS
                       ATP-grasp_3 144 lkdeepyviEvNPRl 158
                                       ++ +  yv+E NPR 
  gi|330506389|ref|YP_004382817.1| 827 ISHDVVYVLEANPRA 841
                                       **************6 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.4e-05      0.02       6     148 ..     132     266 ..     128     284 .. 0.82
   2 !   15.4   0.0   7.7e-06     0.012       7     148 ..     674     806 ..     669     842 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSS CS
                            GARS_A   6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagek 82 
                                        k+ ++  gi+ ++ +a+  +e+a+++  +++ ++ Vv+++   +g g  ++ ++ee  ++v+  +     G    +
  gi|330506389|ref|YP_004382817.1| 132 FKETMNSLGIEVPKSTAIYTVEDAEKVALDLGYPV-VVRPAYTMGGTGGGLVYNAEELRTVVSRGIAASLIG----Q 203
                                       5899*******************************.***************************999999999....9 PP

                                       EEEEE---S.EEEEEEEEECTTEEEE---BEEEEEEECCC.EEEEECECEEEES-TTS-HHHHHHHHH CS
                            GARS_A  83 vviEelleG.eEvsllalvdgktvkplplaqdhkrvlegD.kgpnTGGmGayspapvvteellekike 148
                                       v+iEe + G eE+ l ++ d k+++ +    +     + D  g+ TG   + +p+ ++++el++k ++
  gi|330506389|ref|YP_004382817.1| 204 VLIEESVAGwEELELEVVRDSKNHMITVCFIE-----NVDaMGVHTGDSFCTAPMLTISQELQDKLQD 266
                                       *********66789999999888765544322.....2221477777777777777777777776665 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 7.7e-06
                                       HHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSE CS
                            GARS_A   7 kdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekv 83 
                                       + ++++ +ip +e    ++ ++a e+ ++ + +   v+++ + +g+g+ v  +ee   ++v+  ++     + ++ +
  gi|330506389|ref|YP_004382817.1| 674 RMMMEELDIPMPESGMASNLDQALEVAKRIGYPL-MVRPSYVLGGRGMEVIYDEEMLERYVAAAVD----VTPERPI 745
                                       679*******************************.99************************99997....45789** PP

                                       EEEE---S.EEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEES-TTS-HHHHHHHHH CS
                            GARS_A  84 viEelleG.eEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGayspapvvteellekike 148
                                       +i+ +le   E    al+dgk+   +p++ +h        g   G   ++ p   ++ e l++i+e
  gi|330506389|ref|YP_004382817.1| 746 LIDRFLENaLETEADALSDGKEAF-VPAVMEHIE----QAGIHSGDSACVIPPVSISGEHLQTIEE 806
                                       ******86269*********9975.455555532....2355555555555555555555555555 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00025      0.37      16      52 ..     133     169 ..     128     173 .. 0.92
   2 !   11.8   0.0   7.9e-05      0.12      18      51 ..     676     709 ..     668     712 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00025
                       ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvlK 52 
                                       ke ++ +gi+v+++  + ++e+a ++a  +gypvv++
  gi|330506389|ref|YP_004382817.1| 133 KETMNSLGIEVPKSTAIYTVEDAEKVALDLGYPVVVR 169
                                       5677899****************************96 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.9e-05
                       ATP-grasp_5  18 lleaygipvvetrlassaeeaveaaeeigypvvl 51 
                                       ++e ++ip++e+ +as+ ++a+e+a++igyp  +
  gi|330506389|ref|YP_004382817.1| 676 MMEELDIPMPESGMASNLDQALEVAKRIGYPLMV 709
                                       67899**************************765 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.8e-05     0.026       8     120 ..     133     229 ..     131     236 .. 0.78
   2 !    7.4   0.0    0.0019       2.8      10      54 ..     676     719 ..     672     739 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                       HHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE-TT CS
                       ATP-grasp_2   8 keilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelvtkq 84 
                                       ke +++ g++vp+++   + e+ae++a +lg  + vv+    +GG G  gG  lv+++ee+++++++ + ++l+   
  gi|330506389|ref|YP_004382817.1| 133 KETMNSLGIEVPKSTAIYTVEDAEKVALDLGYPV-VVRPAYTMGGTG--GG--LVYNAEELRTVVSRGIAASLI--- 201
                                       7889999*************************99.999999***977..55..577788888888887777777... PP

                                       S-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEE CS
                       ATP-grasp_2  85 tgkeGkkvekvlveealdikkElYlsivlDraskkv 120
                                                +vl+ee++   +El l +v D +++++
  gi|330506389|ref|YP_004382817.1| 202 --------GQVLIEESVAGWEELELEVVRDSKNHMI 229
                                       ........3466666666666666666666666555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0019
                                       HHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCC CS
                       ATP-grasp_2  10 ilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRG 54 
                                       ++++ ++++pe+ +a++ ++a e+ak++g    +v+     GGRG
  gi|330506389|ref|YP_004382817.1| 676 MMEELDIPMPESGMASNLDQALEVAKRIGYPL-MVRPSYVLGGRG 719
                                       78999************************998.88888889***9 PP

>> DUF4176  Domain of unknown function (DUF4176)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0018       2.7      13      38 ..       6      31 ..       4      34 .. 0.91
   2 ?    3.1   0.0     0.065        98      13      38 ..     553     578 ..     551     581 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0018
                           DUF4176 13 gtkkvmiigrrqieeeekkiydYvgc 38
                                      + +k+miig  +i+ ++ + +dY+g 
  gi|330506389|ref|YP_004382817.1|  6 DINKIMIIGSGPIVIGQACEFDYSGT 31
                                      5689*******************995 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.065
                           DUF4176  13 gtkkvmiigrrqieeeekkiydYvgc 38 
                                       +++kvm++g  +++ +++  +dY+ +
  gi|330506389|ref|YP_004382817.1| 553 SRRKVMVLGGGPNRIGQGIEFDYCCV 578
                                       689********************965 PP

>> QSregVF_b  Putative quorum-sensing-regulated virulence factor
   #    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       4      49 ..     461     506 ..     459     513 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                         QSregVF_b   4 lleelvktkmPFGkYkgrllidlPeeYlvWfarkGFPkgkLGella 49 
                                       +++elv+ +     Ykg+ l+dlP e l   +++GF +  L +lla
  gi|330506389|ref|YP_004382817.1| 461 QMKELVQLEEEILAYKGKPLVDLPDELLSQAKKDGFADRYLSKLLA 506
                                       67888888888889**********************9999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1070 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); 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: 0.84u 0.31s 00:00:01.14 Elapsed: 00:00:00.49
# Mc/sec: 6631.51
//
Query:       gi|330506390|ref|YP_004382818.1|  [L=145]
Description: hypothetical protein MCON_0087 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-05   24.4   0.7      2e-05   24.0   0.7    1.1  1  DDE_Tnp_2  Archaeal putative transposase ISC1217
    4.2e-05   23.3   0.1    5.1e-05   23.0   0.1    1.1  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.7   2.2e-09     2e-05     240     307 ..       7      75 ..       3      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.2e-09
                         DDE_Tnp_2 240 ikllvlddykkdgrrylfstdlndtdediittWenrWdievlirel.kalGledssflkrvrnkGflll 307
                                       +kl + +  k+   +y+ st+  ++  +i + +e rWdie  +re  + lG++d  +  +   + f+ +
  gi|330506390|ref|YP_004382818.1|   7 VKLVISKRKKDSTTKYIISTNGSLSLKEILSIYEDRWDIETAHREAnQKLGFKDYQLRDKHSIERFIQM 75 
                                       56666667788899******************************9835799998877777666666654 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   5.7e-09   5.1e-05     149     212 ..      18      80 ..       2      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.7e-09
                         DDE_Tnp_1 149 gdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                        ++ y+ +tn  +ls +e+  +y  Rw iE+ +++  +k+g+   ++r++  +e+++ +++ ++
  gi|330506390|ref|YP_004382818.1|  18 STTKYIISTNG-SLSLKEILSIYEDRWDIETAHREANQKLGFKDYQLRDKHSIERFIQMVFSVW 80 
                                       23335555555.78999*****************************************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1058.93
//
Query:       gi|330506391|ref|YP_004382819.1|  [L=292]
Description: transposase IS3 family protein integrase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-25   89.8   0.0    2.2e-25   89.1   0.0    1.3  1  rve            Integrase core domain
    2.7e-19   69.1   0.3    1.9e-18   66.3   0.3    2.1  2  HTH_21         HTH-like domain
    3.8e-16   58.6   0.1    9.1e-16   57.4   0.1    1.7  1  rve_3          Integrase core domain
    4.7e-08   33.1   3.6    9.4e-08   32.1   2.4    2.1  2  rve_2          Integrase core domain
    0.00016   21.9   0.3    0.00028   21.1   0.3    1.4  1  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.027   14.6   0.1         12    6.1   0.0    2.4  2  GP3_package    DNA-packaging protein gp3
      0.041   14.1   0.0       0.11   12.7   0.0    1.7  1  HTH_Tnp_Tc3_2  Transposase
      0.049   13.8   0.1       0.17   12.0   0.0    1.9  2  HTH_Tnp_1_2    Helix-turn-helix of insertion element transpos


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.0   9.9e-29   2.2e-25       5     117 ..     127     239 ..     124     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 9.9e-29
                               rve   5 gelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve..pervlsDngseyt 79 
                                       ++ w +D+t+v++      ++l+v++d +sr ++++ ls+++ ++++  +l +a++++ ++    ++++sD+g +y+
  gi|330506391|ref|YP_004382819.1| 127 NQAWASDITYVQLQHE--HIFLAVILDLYSRKCIGWELSRSIRSDLAMSALAKALKNRSKESleGLIHHSDQGVQYA 201
                                       899*********6655..5*****************************************8899************* PP

                               rve  80 skafrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                       sk++ + l+ ++i++s++r+g+p+dn+ +E+f++tlk 
  gi|330506391|ref|YP_004382819.1| 202 SKDYVDCLKAHDIQISMSRKGNPYDNAFAESFIKTLKV 239
                                       ************************************95 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.3   8.5e-22   1.9e-18       6      58 ..      49      99 ..      45     101 .. 0.90
   2 ?   -0.0   0.0      0.45     1e+03      13      33 ..     257     277 ..     248     292 .] 0.66

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 8.5e-22
                            HTH_21  6 llalireifeeskgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgvqrr 58
                                      l ++i+ei  e  + YGyrri+aeL+++g+ +vnhkrV RlMr+++L+++ ++
  gi|330506391|ref|YP_004382819.1| 49 LVNQIQEIALEF-PYYGYRRITAELQNRGY-AVNHKRVLRLMRQEKLLCYKKK 99
                                      7899********.9**************87.5*****************9544 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.45
                            HTH_21  13 ifeeskgrYGyrriwaeLrre 33 
                                       i++    +Y ++r++ +L+ +
  gi|330506391|ref|YP_004382819.1| 257 ICNFIENVYNHKRLHSALNYR 277
                                       555445577788888888854 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1   4.1e-19   9.1e-16       1      67 []     212     279 ..     212     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 4.1e-19
                             rve_3   1 lgielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawred.YNteRPHssLgykTP 67 
                                       ++i++s+++ g P++N+++Esf++tl+ e ++ + ++++++a +++ +++e  YN++R Hs+L+y++P
  gi|330506391|ref|YP_004382819.1| 212 HDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHSALNYRSP 279
                                       689***************************************99999999866*************99 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.4     3e+03      21      33 ..     196     208 ..     184     209 .. 0.74
   2 !   32.1   2.4   4.2e-11   9.4e-08       1      48 [.     231     283 ..     231     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                             rve_2  21 eeleaaiedYIew 33 
                                       + ++ a +dY+++
  gi|330506391|ref|YP_004382819.1| 196 QGVQYASKDYVDC 208
                                       556788999*986 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 4.2e-11
                             rve_2   1 EsfFgsLKtElvygetfktleeleaaiedYIew.YNnkRlk....glsPvqYr 48 
                                       Esf ++LK+E vy  +++t+e +   i ++Ie  YN+kRl+    + sPvq++
  gi|330506391|ref|YP_004382819.1| 231 ESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHsalnYRSPVQFE 283
                                       9******************************988*****988888*******8 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   1.3e-07   0.00028       2     139 ..     128     271 ..     127     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                     DDE_Tnp_IS240   2 kswrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkek.lepeeivtDkasayasalke 76 
                                       ++w+ D Tyv+ + +  +l  ++D  +r  +++ +s     + a  +l kalk+ + ++ e ++    +  + a k 
  gi|330506391|ref|YP_004382819.1| 128 QAWASDITYVQLQHEHIFLAVILDLYSRkCIGWELSRSIRSDLAMSALAKALKNRSkESLEGLIHHSDQGVQYASKD 204
                                       68************************************999************998455555665555555555555 PP

                     DDE_Tnp_IS240  77 lkr...egelfdevshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktl.agfeavknlrkgh 139
                                         +     + + ++s+   +y n   Es  +tlK++  + +  ++++ a + + + +e v+n+++ h
  gi|330506391|ref|YP_004382819.1| 205 YVDclkAHDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNIcNFIENVYNHKRLH 271
                                       44411123556788899999***************************99877625679999999977 PP

>> GP3_package  DNA-packaging protein gp3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0053        12      49      78 ..      19      55 ..      15      63 .. 0.82
   2 ?    6.1   0.0    0.0052        12      51      90 ..     236     275 ..     199     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0053
                                      HHHHT--HHHHHHHGG..SHHH.......HHHHHHHH CS
                       GP3_package 49 alyLgisrstlkeyekrkrefs.......etierikq 78
                                      +l+L++srs  +e+ kr+++f        +++++i++
  gi|330506391|ref|YP_004382819.1| 19 CLALDVSRSGYYEWLKRSEKFTaensessDLVNQIQE 55
                                      899***************9998666666666666555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0052
                                       HHT--HHHHHHHGG..SHHHHHHHHHHHHHHHHHHHHHHT CS
                       GP3_package  51 yLgisrstlkeyekrkrefsetierikqivenqqiegala 90 
                                        L + + +l+eye+ +  f ++ + i+++ +++++  al 
  gi|330506391|ref|YP_004382819.1| 236 TLKVEEVYLNEYETFEDAFRNICNFIENVYNHKRLHSALN 275
                                       6889999*******999****************9999876 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.9e-05      0.11       3      56 ..      52     105 ..      50     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                     HTH_Tnp_Tc3_2   3 rIvrlvrkdPritlreLanelkeeGksvsreTirrrLrkaglkkrkprkkplLs 56 
                                       +I +++ + P+  +r++++el+++G  v ++ + r +r+++l  +k + kp+ +
  gi|330506391|ref|YP_004382819.1|  52 QIQEIALEFPYYGYRRITAELQNRGYAVNHKRVLRLMRQEKLLCYKKKFKPVTT 105
                                       68888889999**********************************999999755 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.7e-05      0.17      33      61 ..      19      48 ..      13      58 .. 0.83
   2 ?   -2.7   0.1       2.7   6.1e+03      55      72 ..     225     243 ..     224     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.7e-05
                                      HHHHTS-HHHHHHHH.H-HHHHHHHHHHHH CS
                       HTH_Tnp_1_2 33 aeevgvsrsTlykWk.kkkeFieyvnelae 61
                                      +  + vsrs +y+W+ + ++F+++ +e ++
  gi|330506391|ref|YP_004382819.1| 19 CLALDVSRSGYYEWLkRSEKFTAENSESSD 48
                                      56789*********9889999999888765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHT.THHHHH CS
                       HTH_Tnp_1_2  55 yvnelaeeflee.eraevy 72 
                                       y n  ae+f+++ +++evy
  gi|330506391|ref|YP_004382819.1| 225 YDNAFAESFIKTlKVEEVY 243
                                       7899999999873557777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.40
# Mc/sec: 2189.16
//
Query:       gi|330506392|ref|YP_004382820.1|  [L=109]
Description: IS3/IS66 family element, Orf1 protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-10   39.8   0.1    6.4e-10   39.2   0.1    1.5  1  HTH_Tnp_1  Transposase
     0.0043   16.8   0.0     0.0089   15.8   0.0    1.7  1  HTH_23     Homeodomain-like domain
      0.005   16.9   0.0      0.011   15.8   0.0    1.6  1  HTH_28     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.033   14.0   0.3      0.074   12.9   0.3    1.6  1  PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein k
      0.058   13.9   0.1       0.12   12.8   0.0    1.5  2  DUF4733    Domain of unknown function (DUF4733)


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.1   1.8e-13   6.4e-10       2      74 ..       3      75 ..       2     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.8e-13
                         HTH_Tnp_1  2 rrrrrwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyr.egeeaspaefeltaleeenrelkrel 74
                                      ++rrr+++ fK+++++e  e+gk+ +++Ar++g++p+   +W+ +     e+a   +    + +++++el+r+l
  gi|330506392|ref|YP_004382820.1|  3 KTRRRYDRDFKISVLAEL-EAGKPLAQIAREYGIHPSLPCRWKVELAeNPEKAFMGNGNKYKDQAKIAELERLL 75
                                      79***************9.***********************99886433333333333344466777777765 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   2.5e-06    0.0089       8      33 ..      14      39 ..       2      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-06
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrT 33
                                      +++l  l  G++ ++IAre+g++++ 
  gi|330506392|ref|YP_004382820.1| 14 ISVLAELEAGKPLAQIAREYGIHPSL 39
                                      567888888**************985 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.1e-06     0.011       1      27 [.      12      38 ..      12      39 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.1e-06
                            HTH_28  1 qRleiikllaaGhsvreaArelgisrr 27
                                      +++ ++ +l aG++ +++Are+gi+++
  gi|330506392|ref|YP_004382820.1| 12 FKISVLAELEAGKPLAQIAREYGIHPS 38
                                      7999********************996 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.1e-05     0.074       9      28 ..      67      86 ..      61      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                         PKcGMP_CC  9 RIRELEkrlaekdeEIqELr 28
                                      +I+ELE+ l + ++EI  L+
  gi|330506392|ref|YP_004382820.1| 67 KIAELERLLGQAHAEIDLLK 86
                                      9***************9888 PP

>> DUF4733  Domain of unknown function (DUF4733)
   #    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      29      67 ..       4      42 ..       1      52 [. 0.88
   2 ?   -2.0   0.0       1.4     5e+03      32      32 ..      91      91 ..      64     106 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.4e-05
                           DUF4733 29 qplrpqravleelsaplelsqplsgllddyGilPkhPrp 67
                                        +r+ r +   + a le  +pl+++  +yGi+P  P +
  gi|330506392|ref|YP_004382820.1|  4 TRRRYDRDFKISVLAELEAGKPLAQIAREYGIHPSLPCR 42
                                      56899999999***********************99976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                           DUF4733 32 r 32
                                       
  gi|330506392|ref|YP_004382820.1| 91 M 91
                                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 856.77
//
Query:       gi|330506393|ref|YP_004382821.1|  [L=291]
Description: hypothetical protein MCON_0090 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-14   53.3   0.0    4.1e-14   52.6   0.0    1.3  1  DDE_5      DDE superfamily endonuclease
    9.1e-07   28.4   0.3    4.4e-05   22.9   0.1    2.1  2  DDE_Tnp_2  Archaeal putative transposase ISC1217


Domain annotation for each model (and alignments):
>> DDE_5  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   4.5e-18   4.1e-14       5     214 ..      31     232 ..      27     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 4.5e-18
                             DDE_5   5 altradrrrglllylrgllldggrksvepmaarl...ehdg.shqalqrflsrspwddaklrrrlarlvl.pllape 76 
                                        +t+ +  + ++ ++ +l  + + k+v ++  ++   + +  s+ ++  f+s+++wd+ ++ +r  +l +  l+ +e
  gi|330506393|ref|YP_004382821.1|  31 LFTKPSYGS-FRDLCGALSVCDKSKTVSNLCDTMadcSKGKkSRSSYNWFFSDANWDENEVAQRKVDLFIdSLCLKE 106
                                       555444444.67777777777777***********9955555999*****************999999997777776 PP

                             DDE_5  77 aav..laiDdTgfpkdGkasvgvarqycgalgkadncqvavslglatervsapldwrlylpeswaqdlsarrrragv 151
                                       +    l+iDdT   k G ++ gv+++y++++   + ++ +v+  + ++  ++p +   y++              ++
  gi|330506393|ref|YP_004382821.1| 107 NDKllLIIDDTYNEKEGNQTDGVGKFYDHSKEAYIWGNNFVTSVVQSKGLFIPHKAKMYIK--------------ND 169
                                       66679************************************99999999999999999999..............34 PP

                             DDE_5 152 pddvtaktkpeial.elldraraagvplqvvvaDagYgdaaalrqglrelglhyvvrvrsdral 214
                                       ++   +ktk eia  e+++ ++  +  + ++v+D++  +++ +      lg ++v +++sd+++
  gi|330506393|ref|YP_004382821.1| 170 DENENFKTKMEIAFeEIIKPLVVPKSIDLYIVFDSWWFSSDLF-SKCLKLGHNIVCQIKSDKKV 232
                                       56669********96677888888888889*******9*****.888889***********987 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   0.0    0.0036        33      84     106 ..     109     131 ..      98     142 .. 0.82
   2 !   22.9   0.1   4.9e-09   4.4e-05     147     226 ..     157     245 ..     143     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0036
                         DDE_Tnp_2  84 Pvlliiddtfdhklyaralpvsr 106
                                        +lliiddt++ k   ++ +v +
  gi|330506393|ref|YP_004382821.1| 109 KLLLIIDDTYNEKEGNQTDGVGK 131
                                       5789*********8877777766 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 4.9e-09
                         DDE_Tnp_2 147 yiprkvaeilkerGeksefktkiellle.ileilkeefnva.avvfdsWyvnskl....lk..gnvvgelksnarv. 214
                                       +ip+k +  +k+  e+ +fktk+e++ e i++ l     +   +vfdsW+++s l    lk   n+v ++ks+++v 
  gi|330506393|ref|YP_004382821.1| 157 FIPHKAKMYIKNDDENENFKTKMEIAFEeIIKPLVVPKSIDlYIVFDSWWFSSDLfskcLKlgHNIVCQIKSDKKVg 233
                                       7999*999****************98752777776655554279******998652222433369999***999986 PP

                         DDE_Tnp_2 215 vegerhvpvael 226
                                       ++ +   +v +l
  gi|330506393|ref|YP_004382821.1| 234 INRDMYFQVRDL 245
                                       666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2366.18
//
Query:       gi|330506394|ref|YP_004382822.1|  [L=417]
Description: hypothetical protein MCON_0092 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-44  151.8   0.0    1.9e-44  151.3   0.0    1.2  1  Lar_N     Lactate racemase N-terminal 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 !  151.3   0.0     1e-48   1.9e-44       1     204 []      12     201 ..      12     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 151.3 bits;  conditional E-value: 1e-48
                             Lar_N   1 ygkkkleleipeenllgvlepkevkeekdeeeaieeaLenpigsekleelvkekekvvivvsDiTRptpskiilpll 77 
                                       yg++ l+l   ee  ++v+ p+e+++  + e  +e++L++ +g  +le+++  +++  i vsDiTRp ps+ +lp l
  gi|330506394|ref|YP_004382822.1|  12 YGQGCLDLLAGEE--AKVVLPQELPPAGSGE--VERSLDQAVGR-RLEDFAG-ARSASILVSDITRPAPSHLMLPPL 82 
                                       6666666666666..4999999999887776..*********98.9***998.6899******************** PP

                             Lar_N  78 leelkeagvkdeditilvAtGlHrkqteeelkkilGeevvkrikvvnhdaedksslvklGttskGtpveinklvaea 154
                                       +++++e g+  + + +++A+G+Hr++t +e +++l + +     ++ h ++d++ +v lG t++Gtpve+ ++va++
  gi|330506394|ref|YP_004382822.1|  83 VKRIRELGI--RSLFVVFALGTHRRMTVAEEEYLLKDCI-----CLPHVQHDSKGCVPLGWTERGTPVEVLEAVASS 152
                                       *********..67******************98888666.....9999999************************** PP

                             Lar_N 155 dlviltGfiepHyfaGfsGGrKsilpGvasretimanHkavlaepraalg 204
                                       dl+++tG+ie+Hy+aGfsGG+K+ilpGv+s+ ++  nH+++  +p+a++g
  gi|330506394|ref|YP_004382822.1| 153 DLIVATGNIEYHYYAGFSGGAKAILPGVSSEPSVVRNHELMR-DPAATTG 201
                                       ****************************************88.9888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.40
# Mc/sec: 3108.73
//
Query:       gi|330506395|ref|YP_004382823.1|  [L=285]
Description: hypothetical protein MCON_0093 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-15   54.7   0.0      2e-14   53.6   0.0    1.5  1  DUF58     Protein of unknown function DUF58


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   1.1e-18     2e-14       1      84 [.      36     115 ..      36     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.1e-18
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarql 77 
                                       g+++ g ReY+ gD+++ +dWk++ Rt +l++re e+er+  v ++ld s++m  +     k+ ++ ++aa  a+ +
  gi|330506395|ref|YP_004382823.1|  36 GISPVGYREYRKGDDFKLVDWKVYGRTEKLFIREHEEERSLVVHILLDSSASMGYA----GKYAYSSRLAAGFAYLA 108
                                       57899************************************************985....68888888888888888 PP

                             DUF58  78 ldegdrv 84 
                                         e+ ++
  gi|330506395|ref|YP_004382823.1| 109 TMENEKY 115
                                       8777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2001.11
//
Query:       gi|330506396|ref|YP_004382824.1|  [L=318]
Description: ATPase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-62  208.9   0.0    3.6e-62  208.0   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
    3.8e-18   65.1   0.0    7.8e-18   64.1   0.0    1.6  1  AAA_lid_2        AAA lid domain
    2.2e-11   43.9   0.0    3.6e-11   43.2   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    1.7e-05   24.0   0.0    4.8e-05   22.6   0.0    1.8  2  MCM              MCM P-loop domain
      0.001   19.5   0.0     0.0025   18.2   0.0    1.7  1  AAA              ATPase family associated with various cellul
     0.0021   17.5   0.1       0.22   10.9   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0062   16.3   0.0      0.096   12.4   0.0    2.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.016   14.9   0.0       0.03   14.0   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.0   0.0   1.6e-65   3.6e-62       1     131 []      46     178 ..      46     178 .. 0.98

  Alignments for each domain:
  == domain 1  score: 208.0 bits;  conditional E-value: 1.6e-65
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke..kefefkkGpvfanllladeinrap 75 
                                       h lle+ PGlaktllvk+ a++++l+f+riq+tpdl+P+di+Gt++++e    k+f+f++Gpvf+n++ladeinra+
  gi|330506396|ref|YP_004382824.1|  46 HALLESNPGLAKTLLVKTTASCMGLDFSRIQCTPDLMPADITGTTIIDEIGggKKFRFEPGPVFSNIVLADEINRAS 122
                                       99**********************************************987779*********************** PP

                             AAA_3  76 pktqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                       pktqsalleam+e+qvtv+++t++l++pf++latqnPie+eGt+plpeaqldrfll
  gi|330506396|ref|YP_004382824.1| 123 PKTQSALLEAMQEKQVTVGNKTYALDRPFFILATQNPIEMEGTFPLPEAQLDRFLL 178
                                       ******************************************************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 !   64.1   0.0   3.5e-21   7.8e-18       1      71 [.     239     310 ..     239     312 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 3.5e-21
                         AAA_lid_2   1 latrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeive 71 
                                       latr+   +++g+s+r a++ l+  A+A+A+l+gr+yV++eD+  +a +VL+HR++   e+e++g t +++v 
  gi|330506396|ref|YP_004382824.1| 239 LATRNWDGVQYGASPR-ASIGLILSAKARAFLQGRNYVSKEDLHVMAYPVLRHRIIlgFEAERKGLTRDQVVG 310
                                       5899999*********.***************************************99999999988888775 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 !   43.2   0.0   1.6e-14   3.6e-11       3     138 .]      48     176 ..      46     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 1.6e-14
                                       EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.............--------G-SEEEEESGG CS
                             AAA_5   3 lLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEve 75 
                                       lL  +pG +K+ l++  a+ ++  +  +q+t d+ ++d++g + i+    +++ +++++p+      + i++ DE++
  gi|330506396|ref|YP_004382824.1|  48 LLESNPGLAKTLLVKTTASCMGLDFSRIQCTPDLMPADITGTTIIDeiggGKKFRFEPGPVF-----SNIVLADEIN 119
                                       66668*******************************************999999********.....9********* PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra+++++++Ll  + e+++ + + +     +++     f ++at np +  +  +l +a ++Rf
  gi|330506396|ref|YP_004382824.1| 120 RASPKTQSALLEAMQEKQVTVGNKTYAL--DRP-----FFILATQNPIEmEGTFPLPEAQLDRF 176
                                       ********************55554444..333.....99********9999999999999998 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.2e-08   4.8e-05      42     175 ..      29     161 ..       3     181 .. 0.79
   2 ?   -3.9   0.0       2.7   6.1e+03      20      42 ..     218     240 ..     214     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.2e-08
                                       ---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHS..SSEEEEESSSSSSSHSSSEEEEESSSSS..EEEEE CS
                               MCM  42 ggvkkkledktklrgdinvllvgdpgtaKsqlLkyvekla..pravytsgkgssaagLtaavvrdeetge..fvlea 114
                                       g  +  ++  +++++  + ll ++pg+aK+ l+k++++++  + +   +      a++t +   de  g   f +e 
  gi|330506396|ref|YP_004382824.1|  29 GQDRAIEQLLVSIIAGGHALLESNPGLAKTLLVKTTASCMglDFSRIQCTPDLMPADITGTTIIDEIGGGkkFRFEP 105
                                       4444444445667777899****************9877522567778888889999999988888765445***** PP

                                       THHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SS CS
                               MCM 115 GalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpka 175
                                       G +      +++ De+++ + +++sal+Eam ++++++      + L+    +la  np++
  gi|330506396|ref|YP_004382824.1| 106 GPVFS---NIVLADEINRASPKTQSALLEAMQEKQVTVGNKT--YALDRPFFILATQNPIE 161
                                       *9986...49**************************997655..88888889999999874 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.7
                                       HHSSTTSSS-HHHHHHHHHHHH- CS
                               MCM  20 ksiapsiyghedvkkaillqlfg 42 
                                       +++++ i   +d k+a++ ++++
  gi|330506396|ref|YP_004382824.1| 218 QKLCRDIPIADDLKRAVVNLVLA 240
                                       56777788888888888765554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.1e-06    0.0025       2     129 ..      48     181 ..      47     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.1e-06
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.......STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHH CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk.......yvgesekkirelfkeakekakpsilfiDEidala 71 
                                       ll  +pG  KTll+k  a+ +g +f +i+++  l         ++ e     +  f+     +   i++ DEi +  
  gi|330506396|ref|YP_004382824.1|  48 LLESNPGLAKTLLVKTTASCMGLDFSRIQCTPDLMPaditgttIIDEIGGGKKFRFEPGPVFS--NIVLADEINRAS 122
                                       78889************************9755512245555555555555555555544444..9**********9 PP

                                       HHHTTCCCHHHHHHHHHHHHHHHHTTTS.......SSTEEEEEEESS......GGGSTHHHHSTTSSEEEE CS
                               AAA  72 ksrsgseseeeervvnqLlteldgvkkk.......eskvivigatnr......pdkldpallrgRfdrkie 129
                                       ++            +++Ll+++++ +          ++ ++i+at++         l++a l +Rf  ki+
  gi|330506396|ref|YP_004382824.1| 123 PKT-----------QSALLEAMQEKQVTvgnktyaLDRPFFILATQNpiemegTFPLPEAQL-DRFLLKIF 181
                                       999...........***********9999999999555677777777333322223455555.66666666 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   9.6e-05      0.22       5      44 ..      27      66 ..      24      77 .. 0.83
   2 !    4.4   0.0    0.0093        21      91     158 ..      95     159 ..      81     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.6e-05
                      Mg_chelatase  5 vkGqeeakraleiaa.aGgHnlllvGppGsGKtmlakrlps 44
                                      ++Gq++a + l +++ aGgH  ll  +pG  Kt+l k  +s
  gi|330506396|ref|YP_004382824.1| 27 IVGQDRAIEQLLVSIiAGGH-ALLESNPGLAKTLLVKTTAS 66
                                      89**********99725555.56899*********998665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0093
                      Mg_chelatase  91 vGggs..kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                       +Ggg+  + +pG +      +++ DE+   + k+  +L e +++++vt+  +++ ++ p  f ++a+ Np
  gi|330506396|ref|YP_004382824.1|  95 IGGGKkfRFEPGPVF---SNIVLADEINRASPKTQSALLEAMQEKQVTVGNKTYALDRP--FFILATQNP 159
                                       677764556788875...458889*************************9888777655..667777777 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   4.3e-05     0.096      10     113 ..      28     138 ..      19     149 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                            RuvB_N  10 igqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlekagdlaa..lltnl. 82 
                                       +gq++  e+l + i a         h ll   PGl kt l k  a+ +g ++ +i ++P l  ++d+++  ++ ++ 
  gi|330506396|ref|YP_004382824.1|  28 VGQDRAIEQLLVSIIAG-------GHALLESNPGLAKTLLVKTTASCMGLDFsRIQCTPDLM-PADITGttIIDEIg 96 
                                       67777777777766654.......69***********************9984567778775.55665322555552 PP

                            RuvB_N  83 .......ee....kdvlfideihrlsraveevlysamedfrl 113
                                              e+    +++++ dei r s++++  l  am++ ++
  gi|330506396|ref|YP_004382824.1|  97 ggkkfrfEPgpvfSNIVLADEINRASPKTQSALLEAMQEKQV 138
                                       221111122222246778888888888888888888887776 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.4e-05      0.03      97     146 ..     113     161 ..     109     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                                       EEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-HH CS
                   Sigma54_activat  97 lfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedle 146
                                       ++ Dei++ ++++Q+ Ll+++qe++v+ vG+++       +i at++ +e
  gi|330506396|ref|YP_004382824.1| 113 VLADEINRASPKTQSALLEAMQEKQVT-VGNKTYALDRPFFILATQNPIE 161
                                       667*********************996.8988777667777888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2255.88
//
Query:       gi|330506397|ref|YP_004382825.1|  [L=110]
Description: hypothetical protein MCON_0096 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-11   43.9   4.3    2.6e-11   43.5   4.3    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 !   43.5   4.3   1.4e-15   2.6e-11       4      69 ..       2      69 ..       1      83 [. 0.84

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.4e-15
                        Spore_YtfJ  4 gdgtviiPvskvsfGfgaGgsefkskkekepfgggsgaGvsitPvAfLvikkg.....evkllpvkk..ssld 69
                                      +d ++iiP++k+++Gfg+G++ +    e+e  +  +g+Gv++ P+A++v+ kg     +vk++p++   s  +
  gi|330506397|ref|YP_004382825.1|  2 ED-KIIIPITKMGMGFGTGQEPG----ESEAIKVKAGGGVGVIPIAIVVVFKGipgedGVKVIPLSGhiSGNQ 69
                                      45.9*******************....67789999***************99999999*******87774433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 850.56
//
Query:       gi|330506398|ref|YP_004382826.1|  [L=303]
Description: hypothetical protein MCON_0097 [Methanosaeta concilii GP6]
Scores for complete 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-08   32.2   0.0    1.6e-07   31.3   0.0    1.5  1  DUF2953   Protein of unknown function (DUF2953)
  ------ inclusion threshold ------
      0.078   13.3   0.0        0.2   12.0   0.0    1.6  1  DUF1772   Domain of unknown function (DUF1772)
       0.12   12.1   0.9       0.21   11.3   0.9    1.3  1  TRH       Thyrotropin-releasing hormone (TRH)


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 !   31.3   0.0   2.7e-11   1.6e-07       1      53 []     221     265 ..     221     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.7e-11
                           DUF2953   1 leiGleDaadTgilyGliwaikgllygllsnlfnikkpeievtPvFneevfeg 53 
                                       l++Gl D++ T+il+G +w+i ++l + l         +i+++P F+ee +eg
  gi|330506398|ref|YP_004382826.1| 221 LQLGLDDPSETAILTGRLWSIAAFL-SYL-------GADIQIEPFFEEERLEG 265
                                       589*********************9.555.......88***********9996 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.3e-05       0.2      50     125 ..      30     107 ..       4     108 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.3e-05
                           DUF1772  50 fa.ylaaraasrgarllylaaaallllsivpyTllvmvPtNnkLaal.........keedakekedeaevrelle.r 115
                                          +l+     ++a  l+l +a+ll+l i+p++l ++   + +L +          +   a  +   +e++ ll   
  gi|330506398|ref|YP_004382826.1|  30 SPsLLT-----SAALILMLFIALLLILLIIPLSLCLFLCKEGQLVEGklrgswlgiS---AGGDLRSKETQ-LLGrL 97 
                                       221222.....3333344344555666666666666644443433336666665441...33444557777.5555* PP

                           DUF1772 116 WgrlnlvRav 125
                                       W  ++++R +
  gi|330506398|ref|YP_004382826.1|  98 WISWHNIRLL 107
                                       ********75 PP

>> TRH  Thyrotropin-releasing hormone (TRH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.9   3.5e-05      0.21      50      99 ..     128     177 ..     116     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.5e-05
                               TRH  50 klqeedeeneelssqlewlsKRqHPGKryeedlekrqhPgkrdeeeeesy 99 
                                       k ++e++e +++++    ++KR  P Kr  ++ ++  hPg  ++  e ++
  gi|330506398|ref|YP_004382826.1| 128 KEKDEEKEIKKVKKGSAGIAKRGSPDKRKYKEGQDESHPGSDEKGGELEV 177
                                       456667777778889999**********98888888*****998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.37
# Mc/sec: 2444.24
//
Query:       gi|330506399|ref|YP_004382827.1|  [L=847]
Description: alpha glucan phosphorylase [Methanosaeta concilii GP6]
Scores for complete 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   98.4   0.0    4.9e-20   71.4   0.0    3.2  2  Phosphorylase  Carbohydrate phosphorylase
    4.6e-24   85.0   0.3    1.3e-23   83.6   0.3    1.8  1  DUF3417        Protein of unknown function (DUF3417)
  ------ inclusion threshold ------
      0.037   13.5   0.0      0.066   12.7   0.0    1.3  1  Capsule_synth  Capsule polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Phosphorylase  Carbohydrate phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.8e-09   2.9e-05      22      67 ..     117     163 ..      95     179 .. 0.94
   2 !   71.4   0.0   8.1e-24   4.9e-20     218     577 ..     262     612 ..     235     619 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.8e-09
                                       SSHHHHHHHHHHHHHHHTT-EEEEEEE--SCESEEEEE.ETTEEEEE CS
                     Phosphorylase  22 nGGLGRLAacfldslatlelpavGygirYeyGlFkQki.edgaqvee 67 
                                        GGLG LA  +l +++ l++p vG+g+ Y+ G F+Q + +dg q+e+
  gi|330506399|ref|YP_004382827.1| 117 SGGLGILAGDHLKTASDLGVPLVGVGLLYQQGYFRQVLaQDGSQIEA 163
                                       69***********************************9899***996 PP

  == domain 2  score: 71.4 bits;  conditional E-value: 8.1e-24
                                       EEEEEESSTTTTHHHHHHHHHHHCC---HHHHHHHHCCCEEEEE--SSGGGS-EEEHHHHHHHSHHHHHHHHHHHHH CS
                     Phosphorylase 218 vaiqlnDtHPalaipelmriLvdeeglewdeaweitkktfaytnhtvlpealekwpvellekllprhleiieeiner 294
                                       ++ ++n+ H a+++      +++eeg+++ ea+  t++   +t ht ++   ++++ +ll+k    h++  + +   
  gi|330506399|ref|YP_004382827.1| 262 IVCHMNEGHAAFVVLARAYSFMHEEGCSFLEALWATRAGNVFTTHTPVEAGFDRFDRDLLKKYAK-HYTDAQGL--- 334
                                       688*********************************************************99865.44333333... PP

                                       HHHHHHHHSTT-HHHHHHHSSEETSCEEEHHHHHHHCCSEEEESSHHHHHHHHHTTTHHHHHHSGGG...EEE---- CS
                     Phosphorylase 295 fleevekklpedeeklerlsiieeekkvrmanlaivgshsvngvaalhsellkkevlkdfyelypek...fnnktnG 368
                                       f +++     ++  + +       ++  ++a lai gs  vngv++lh+++  k+++++ y  +pe    +  +tnG
  gi|330506399|ref|YP_004382827.1| 335 FPNDLVIMGLKT--EKD------YSSPFNIAFLAISGSCFVNGVSRLHAQV-SKRIFQSRYPRWPENevpIDYITNG 402
                                       222222221111..111......2345679******************985.6789********9975557899*** PP

                                       B.........-CHHHCCCT....SHHHHHHHHHHCSSGGCCSGGGGGGGGGGCCSHHHH..HHHHHHHHHHHHHHHH CS
                     Phosphorylase 369 i.........tprrwllla....npelaelitekigeewvkdleeLkkLekladdkefl..eelaeikqenKerlae 430
                                       +         ++r w l +     pe  ++ + ki ++  +d+ ++++L++   ++ +   ++ ++ + ++  +  e
  gi|330506399|ref|YP_004382827.1| 403 VhiptwdspvAQRLWSLSCptgcGPESIDYEAGKIARQSDQDIWNFRALAR---KDLIDyaRRRHARQMQEHGASPE 476
                                       733333333357778777622113444444445555555555555555544...33332002222222233334445 PP

                                       HHHHHHSS---TTSEEEEEES-SCCCCTHHHHHHHHHHHHHHHHHSTTS----EEEEEE----TT-HHHHHHHHHHH CS
                     Phosphorylase 431 likekegvevdpeslfdvqvkRlheYkRqlLnvLhiitlYneikenpekkvvprtvifggkaapgYalAkkiiklin 507
                                        i++  +  +dp++l     +R   YkR  L  L+  ++  +i +n+     p  +++++ka p+    k+++k + 
  gi|330506399|ref|YP_004382827.1| 477 EIEAA-RHVLDPNTLTIGFARRATAYKRTNLL-LRDEEKLVSILTNH---DRPVQLLMAAKAHPADIAGKEMVKQMA 548
                                       56655.6789*****9999**********995.45555555555553...5899*******************9998 PP

                                       HHHHHHCC-TTTCCCEEEEEETT-SHHHHHHHGGG-SEEEE---TTTSSS-SHHHHHHHTT-EEEEESST CS
                     Phosphorylase 508 svaevvnndpevkdklkvvflenynvslaekiipaadlseqistagkeASGTgnmkfmlnGaltigtlDG 577
                                       + a+     p+++d+  v+fle+y++ la+++ ++ dl  +  +  +eA GT+ mk+  nG+l ++tlDG
  gi|330506399|ref|YP_004382827.1| 549 NFAD----RPDITDR--VIFLEDYDIDLAQHLQAGVDLWINTPLRPNEACGTSGMKVLANGGLNLSTLDG 612
                                       8886....5999996..9***************************************************9 PP

>> DUF3417  Protein of unknown function (DUF3417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.3   2.1e-27   1.3e-23       1     109 []       9     113 ..       9     113 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 2.1e-27
                           DUF3417   1 lpeeLekLeeLaknlwwswneeareLFksldpelweevghnPvklLeevsqerleelaedeeflarleavveefeey 77 
                                       lp+ Le L++La +l+w+ + +++++++ ldpe+we+ ++nP  +L+++s++rl+ela+d+++ +++++  e+ ++ 
  gi|330506399|ref|YP_004382827.1|   9 LPSGLEGLADLALDLRWTVRLTTDRVWELLDPEAWEK-TKNPYLILQNISKSRLNELAQDDALRTEIRDWQERNTKF 84 
                                       899**********************************.99************************************* PP

                           DUF3417  78 leektwfqkkaeeekkeaiAYFsaEfGlhesL 109
                                       l+++ w++++    + +++AYFs+EfGl+e+L
  gi|330506399|ref|YP_004382827.1|  85 LAQPGWCEEHF---NLDSVAYFSMEFGLSEAL 113
                                       *******9998...899************997 PP

>> Capsule_synth  Capsule polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.1e-05     0.066     182     231 ..     521     569 ..     510     581 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                     Capsule_synth 182 eeapadaeliiKtHPldeglikyrrvikgyltelaalkkrvllvedvnlp 231
                                       ++ p +  ++ K HP d ++++  + +++++   +++ +rv+++ed++++
  gi|330506399|ref|YP_004382827.1| 521 HDRPVQLLMAAKAHPADIAGKEMVKQMANFADR-PDITDRVIFLEDYDID 569
                                       55688889999*******************998.8***********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (847 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 5529.35
//
Query:       gi|330506400|ref|YP_004382828.1|  [L=116]
Description: hypothetical protein MCON_0099 [Methanosaeta concilii GP6]
Scores for complete 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-05   22.4   0.0    0.00012   22.2   0.0    1.2  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
        0.2   12.1   0.1         12    6.3   0.0    2.3  2  Jag_N            Jag N-terminus


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.3e-08   0.00012      11      57 ..      23      69 ..      15     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.3e-08
                   HicB_lk_antitox 11 saygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipe 57
                                      + y   vP+l+G++ +g t+e+a +n  ea+e ++ + ++ g  ip 
  gi|330506400|ref|YP_004382828.1| 23 EPYFADVPELDGVWATGHTVEDARRNFIEALEEWIAARLQWGLLIPP 69
                                      467778*****************************999988888875 PP

>> Jag_N  Jag N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.01        92      22      32 ..      11      21 ..       4      26 .. 0.85
   2 ?    6.3   0.0    0.0013        12       2      17 ..      38      53 ..      37      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.01
                             Jag_N 22 deveieVleeg 32
                                      ++v+++V+++g
  gi|330506400|ref|YP_004382828.1| 11 EKVQYKVIDNG 21
                                      89******998 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0013
                             Jag_N  2 eGkTveeAiekAlkeL 17
                                      +G Tve+A ++ ++ L
  gi|330506400|ref|YP_004382828.1| 38 TGHTVEDARRNFIEAL 53
                                      9**********99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 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:                        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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 881.90
//
Query:       gi|330506401|ref|YP_004382829.1|  [L=69]
Description: hypothetical protein MCON_0100 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 528.65
//
Query:       gi|330506402|ref|YP_004382830.1|  [L=172]
Description: hypothetical protein MCON_0101 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00012   22.5   1.1    0.00018   22.0   1.1    1.4  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   1.1   9.8e-09   0.00018      40     120 ..      78     150 ..      30     152 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 9.8e-09
                                       HHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHH CS
                               PIN  40 EllyvlarrkskrekaaelvelllllsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedf 116
                                       E+ ++  +     e++ +++    + ++  i  +d++i+ +++ei  +  ++p Dal++A+A+++ +  + t D+++
  gi|330506402|ref|YP_004382830.1|  78 EISRIPDA-----ERRSKVEQIASISREKTI--VDESIVSRVREIEMQGLIKPMDALHLACAERSADVML-TTDDEI 146
                                       33333333.....222222222222333333..67999999999999888*****************766.999988 PP

                                       HHHH CS
                               PIN 117 rrva 120
                                        r+a
  gi|330506402|ref|YP_004382830.1| 147 LRAA 150
                                       7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1239.19
//
Query:       gi|330506403|ref|YP_004382831.1|  [L=50]
Description: hypothetical protein MCON_0102 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 387.20
//
Query:       gi|330506404|ref|YP_004382832.1|  [L=65]
Description: hypothetical protein MCON_0103 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       132  (0.00736237); expected 358.6 (0.02)
Passed bias filter:                      119  (0.00663729); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 460.18
//
Query:       gi|330506405|ref|YP_004382833.1|  [L=96]
Description: hypothetical protein MCON_0104 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-11   41.9   0.1    9.6e-11   41.7   0.1    1.1  1  DUF2188   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2188  Uncharacterized protein conserved in bacteria (DUF2188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.1   5.3e-15   9.6e-11       4      60 ..       2      57 ..       1      59 [. 0.89

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 5.3e-15
                           DUF2188  4 vPkddggWavkreGgsrasktfdTqeeAieaArelAkeqggselvihgrdGqirern 60
                                      v++  +gW +k+  + r+  +  T++eAi  Are+ +++ ++e +ih +dG+++  +
  gi|330506405|ref|YP_004382833.1|  2 VKNSRNGWDIKKPHAWRPCGHAQTKAEAIRLAREICRKE-KAECIIHSEDGKFEVYD 57
                                      5567799*****************************886.************97555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 715.20
//
Query:       gi|330506406|ref|YP_004382834.1|  [L=297]
Description: zinc finger, swim domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-07   29.6   0.2    7.7e-07   28.7   0.2    1.5  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.2   4.3e-11   7.7e-07      10      38 ..     141     166 ..     131     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 4.3e-11
                              SWIM  10 vrlnkatCsCpefqkngipCkHalAvlla 38 
                                        r  k++CsCp++   + pCkH++Av++ 
  gi|330506406|ref|YP_004382834.1| 141 GRDLKTDCSCPDW---SNPCKHIAAVYYL 166
                                       57789*******9...7*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2047.92
//
Query:       gi|330506407|ref|YP_004382835.1|  [L=1035]
Description: SNF2 family helicase [Methanosaeta concilii GP6]
Scores for complete 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-63  213.0   0.0    8.1e-63  212.3   0.0    1.4  1  SNF2_N      SNF2 family N-terminal domain
    2.4e-39  134.3   0.1    4.8e-39  133.3   0.1    1.6  1  DUF3670     SNF2 Helicase protein
    1.9e-18   66.8   0.0    4.1e-18   65.7   0.0    1.6  1  Helicase_C  Helicase conserved C-terminal domain
    0.00042   20.1   0.0    0.00094   19.0   0.0    1.6  1  DEAD        DEAD/DEAH box helicase
     0.0021   18.1   0.0     0.0036   17.3   0.0    1.4  1  ResIII      Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.3   0.0   2.3e-66   8.1e-63       8     349 ..     466     835 ..     461     836 .. 0.80

  Alignments for each domain:
  == domain 1  score: 212.3 bits;  conditional E-value: 2.3e-66
                                       HH........................................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxx........................................................ RF
                            SNF2_N   8 wmlkReqnlqdleaalrkllk........................................................ 28 
                                       wm   e  +qd+eaa+++++k                                                        
  gi|330506407|ref|YP_004382835.1| 466 WM---ELRPQDIEAAIDFFHKnrnhemtlaealqlglnpaghplpeakttlpvhgieaegkikemlsalsdpsghme 539
                                       66...556666666666666666666666666666666666666666666666666666666666666666666666 PP

                                       .......................HHHHHTT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  29 ...tldgekiyvnpatgevveesaeakqsvrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLiv 102
                                            + ++  + p++   v+  + +++   G  LaD+mGLGKT++++a++l++r+            +  gptL++
  gi|330506407|ref|YP_004382835.1| 540 qlpSPRDFQGTLRPYQLRGVSWLMYLNRLGLGACLADDMGLGKTIELIAFLLHERE---T-------MKGPGPTLLI 606
                                       6655555555666666666666666777788999******************3332...2.......24569***** PP

                                       --HHHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 103 vPaslldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewk 179
                                       +P+s++ +We+eier++++ ++  l+++g         + ++k ++++dvvittY+  +r+       ++l++v+w 
  gi|330506407|ref|YP_004382835.1| 607 CPMSVAGNWEREIERFAPGLKV--LMHHGLG---RLSGQDFEKAAEKADVVITTYSLAQRDE------EELNAVSWG 672
                                       *******************986..5555544...34466899*****************999......9******** PP

                                       EEEES-GGGT--TTSHHHHHHHH---S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHH.HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                            SNF2_N 180 rvvlDEghtlknstskaaeavskLstsnrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpie.aqaek 255
                                        +vlDE++ +kn+ ++ ++ +++L++ +++ ltGTP+ n l++l+++++fL+++ +g++++f++ +  pie  ++++
  gi|330506407|ref|YP_004382835.1| 673 HIVLDEAQSIKNQSARQTQSIKRLKATQKIALTGTPVENRLSELWSIMDFLNPGYLGSFESFRRDFVLPIErYNNRA 749
                                       ***********************************************************************667889 PP

                                       HHHHHHTT-STTEE---GGGT..--S---EEEEEEEEE--HHHHHHHH....................HHHHHH-HH CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 256 grsrLlqllqrlmlrrakkdv..eknlPpkteeiiflklskverksYnrllevlrkkalakllkrseaalksssksk 330
                                        ++ L++l+q+++lrr k+d+   k+lP+kte+ +  +l+++++++Y  + e++           s+++ +++ k +
  gi|330506407|ref|YP_004382835.1| 750 HSEALRSLIQPFVLRRLKTDTtvIKDLPEKTEMKVGYNLTPEQASLYAAVVEDM----------LSRIESSEGMKRR 816
                                       999*****************987889**********************333333..........3334444444444 PP

                                       H-HHHHHHHHHHHHH---X CS
                                       xxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 331 ekilelllelrqacnhpql 349
                                        +il  l++l+q+cnhp l
  gi|330506407|ref|YP_004382835.1| 817 GQILAALTKLKQICNHPAL 835
                                       679**************87 PP

>> DUF3670  SNF2 Helicase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.3   0.1   1.3e-42   4.8e-39       2     135 ..     362     497 ..     361     499 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 1.3e-42
                           DUF3670   2 vpdalelddeeaaefLkeaaeaLeaaGvgVllPrwlkkrarprltlklavkgp...asaakesklgldalldfdwel 75 
                                       +p++le++++ea++fL+++a+ Le++G+gV+lP+w+ +r   rl++kl+ + +   + +a+++++gl++++++dw+l
  gi|330506407|ref|YP_004382835.1| 362 RPAELEMETTEAYSFLRQSAPLLEQNGFGVMLPAWW-QRPGTRLGVKLQLRDAprkEGNAGSAFFGLNSVVEYDWQL 437
                                       899*********************************.8889999999988888787778889*************** PP

                           DUF3670  76 alGdeeLseeEldrLaeakrpLvrlrgqWvevdpeelrraleflkrreekkltladaLra 135
                                       +lGd  +s+eE+++L   k pL+++rg+W+e++p+++++a +f+++++++++tla+aL++
  gi|330506407|ref|YP_004382835.1| 438 SLGDYVISREEFAQLSHLKIPLIQIRGEWMELRPQDIEAAIDFFHKNRNHEMTLAEALQL 497
                                       ************************************************99********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 !   65.7   0.0   1.2e-21   4.1e-18       2     111 .]     849     961 ..     848     961 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 1.2e-21
                                       HHHHHHHHH.HHTTTTSEEEEEESSHH...HHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEES CS
                        Helicase_C   2 kleallell.kleeeggkilifvntid...rlekvklllekkgikvavlhgelpqnereeileqfnkgesd.vLiat 73 
                                       kl++l e+l +  ++g+++lif+++     +l   + l+ek g++v+ lhg+++ ++ree++++f++g+s  ++++ 
  gi|330506407|ref|YP_004382835.1| 849 KLSRLEEMLdEAISVGDRALIFTQFAGmgaML--RHQLQEKLGVEVLFLHGKTSRKQREEMIQRFQQGSSPiFILSL 923
                                       67788888888889*************65555..48888888*****************************9***** PP

                                       GGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  74 dvaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                       ++++ G++++ +n+V++fd ++n++  +q+ +R+ R+g
  gi|330506407|ref|YP_004382835.1| 924 KAGGFGLNLTAANHVFHFDRWWNPAVENQATDRAFRIG 961
                                       ************************************97 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.6e-07   0.00094      19     168 ..     574     707 ..     560     716 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.6e-07
                                       EEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET.TSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                              DEAD  19 vaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig.gvaardqlskl 94 
                                       +a + G GKT   +  +l++  e + k    +l+++P+   a +  +++++f     l+vl+  g g    ++ +k 
  gi|330506407|ref|YP_004382835.1| 574 LADDMGLGKTIELIAFLLHER-E-TMKGPGPTLLICPMS-VAGNWEREIERFAPG--LKVLMHHGlGRLSGQDFEKA 645
                                       5667799***98777777555.3.455555799999985.7999********997..66776666566667777888 PP

                                       HTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  95 dngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSAT 168
                                        +++d+v++t +  ++  ++++ln  +   +VlDEa+ + +q   ++ ++ +++l       k   q i+l+ T
  gi|330506407|ref|YP_004382835.1| 646 AEKADVVITTYSLAQR--DEEELNAVSWGHIVLDEAQSIKNQ-SARQTQS-IKRL-------K-ATQKIALTGT 707
                                       799********88887..778888888888***********9.3333333.4555.......1.2235555555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   9.9e-07    0.0036      26     169 ..     571     708 ..     548     710 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.9e-07
                                       EEEEEESTTSTHHHHHHHHHHHH-S......-EEEEESSHHHHHHHHHHGGGGTGG........GEEEESSS-B--. CS
                            ResIII  26 rglikmaTGtGKTlvaaklierllkkgkee.kflflvprkslleqtleefkkflseayke....igkkvsgdkkkak 97 
                                        ++++   G GKT+ ++++  + ++  k    +l+++p  s+   +++e+++f++  +       g  +sg+    +
  gi|330506407|ref|YP_004382835.1| 571 GACLADDMGLGKTIELIAFLLHERETMKGPgPTLLICPM-SVAGNWEREIERFAPGLKVLmhhgLGR-LSGQD---F 642
                                       67888889*****98866555555544444599999985.89*************975435332222.33322...3 PP

                                       ......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHH..HHT---SEEEEEESS- CS
                            ResIII  98 ekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswrei..lekfkeavllglTATp 169
                                       ek+++++++++tt++ +++d+       eel   +   i+ DEa  ++ + s r+   ++ +k+  +++lT+Tp
  gi|330506407|ref|YP_004382835.1| 643 EKAAEKADVVITTYSLAQRDE-------EELNAVSWGHIVLDEAQSIKNQ-SARQTqsIKRLKATQKIALTGTP 708
                                       557************999999.......899999999*******999995.4444333788899*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1035 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.79u 0.27s 00:00:01.06 Elapsed: 00:00:00.44
# Mc/sec: 7072.20
//
Query:       gi|330506408|ref|YP_004382836.1|  [L=182]
Description: YeeE/YedE family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-16   59.3  13.6    4.6e-16   59.3  13.6    1.3  1  Sulf_transp  Sulphur transport


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3  13.6   2.6e-20   4.6e-16       8     148 ..      37     177 ..      30     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 2.6e-20
                       Sulf_transp   8 gairdivvekdgrllralllaiavaavgfqllaaaglidlpksafpvvglivGGllFGvGMalaGgCasgtlyrvGe 84 
                                       g i  ++   d++ +r++l+ai+v ++g++++ +agl++l  ++ ++ ++++GGl+FG+G a+ G C++++ +  G+
  gi|330506408|ref|YP_004382836.1|  37 GVIVGQLQLTDFTVVRVMLTAILVGMIGIHIMRYAGLVRLHIKPGSIGSTVIGGLIFGAGFAILGYCPGTAAAAFGS 113
                                       6777888999******************************98888889***************************** PP

                       Sulf_transp  85 Gslralitllffilgavalltgilsswleqlles.tvskeslyetlglsplllialllliallll 148
                                       G + al+ ++++i+ga ++++ + + +++++l+  +  + +++e++g+ p+++ia ++++ +++l
  gi|330506408|ref|YP_004382836.1| 114 GAIDALVGMVGIIIGAGMFAR-LYPVLNRSVLKWgPLPEGTIPELIGIRPIIVIAAVAVLIVAVL 177
                                       ***************998655.7777777766552678899**********99998877755544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1307.70
//
Query:       gi|330506409|ref|YP_004382837.1|  [L=174]
Description: YeeE/YedE family protein [Methanosaeta concilii GP6]
Scores for complete 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   88.2  12.2    7.2e-25   88.2  12.2    1.5  2  Sulf_transp  Sulphur transport


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2  12.2     4e-29   7.2e-25     171     308 ..       4     161 ..       1     164 [. 0.78
   2 ?    0.9   0.5     0.015   2.7e+02      54      68 ..     159     173 ..     157     174 .] 0.85

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 4e-29
                       Sulf_transp 171 klfrkpwslvlgavllgllavlawllsak.tgrsfglg.........ftvpgakilqylvlgtskflnwgvvlvlGi 237
                                        ++  +ws+++ +  +g+l+++a+lls   +g s++++         +    a+ ++y+  + +  ++w+ ++v+G 
  gi|330506409|ref|YP_004382837.1|   4 WITMDSWSPYVVGAGIGVLSWIAFLLSDRpLGASTAFAksagmiesaINRENADQMSYYQ-KIKPKIDWQWMIVFGM 79 
                                       567889********************9764677765532111212114444444444442.445669********** PP

                       Sulf_transp 238 ilGaflaallsgefkleapkar...........ellaallGGllMGfGarlAgGCniGaglsgiaslslsgwlalvf 303
                                       i+G++l++ lsg++++ + ++            +++ al+GG+l G Gar+A GC++G+g+sg+ +lsl +w+a+v+
  gi|330506409|ref|YP_004382837.1|  80 IIGSLLSSFLSGRLAVLIVPPIfaeafgadalfRFAIALIGGILIGLGARWADGCTSGHGISGTLQLSLVSWIAVVC 156
                                       ***************997666334566666677******************************************** PP

                       Sulf_transp 304 lllGa 308
                                       +++ +
  gi|330506409|ref|YP_004382837.1| 157 FFVSG 161
                                       **955 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.015
                       Sulf_transp  54 vvglivGGllFGvGM 68 
                                       v g++v +l+FG+G+
  gi|330506409|ref|YP_004382837.1| 159 VSGIAVAALIFGLGI 173
                                       57899********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1300.37
//
Query:       gi|330506410|ref|YP_004382838.1|  [L=459]
Description: metallo-beta-lactamase family protein [Methanosaeta concilii GP6]
Scores for complete 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-20   71.5   0.0      4e-10   40.2   0.0    2.5  2  Rhodanese      Rhodanese-like domain
    6.4e-11   42.6   0.7    2.1e-10   41.0   0.7    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.053   13.0   0.3       0.15   11.5   0.3    1.7  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0     2e-10   1.2e-06       2     104 ..     257     347 ..     256     350 .. 0.83
   2 !   40.2   0.0   6.6e-14     4e-10       5     106 ..     365     451 ..     361     452 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2e-10
                         Rhodanese   2 akelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr 78 
                                       +k + + ++++k+a+lDvR+ ++++  hIpg+ ++          + a + ++ + +      +kk + ++ +g+++
  gi|330506410|ref|YP_004382838.1| 257 PKAFSNSIKSEKAAILDVRSYPAFSGLHIPGSWHI----------DLAGSFATQAGWVI---PPKKDIFLVVEGNEQ 320
                                       67778888899989*********************..........55555555555555...588999999999999 PP

                         Rhodanese  79 aaaaaallkklGykn.vsvldGGfkaw 104
                                         +aa++l++ G+     +l+ G+ aw
  gi|330506410|ref|YP_004382838.1| 321 VDEAAMQLRRVGLDSvEAFLERGMLAW 347
                                       8999999999**988889999999999 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 6.6e-14
                         Rhodanese   5 lkellekgkvallDvRppeeYek.ghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraa 80 
                                       + +l +++k++++DvR++ee ++   + g++ +             p  +l ++ +el  +++++ +v c+gg+ra+
  gi|330506410|ref|YP_004382838.1| 365 ANDLVASEKAVIIDVRSAEE-KTdDCVIGSIQI-------------PWHDLRTRHKEL--SRDRKYIVMCRGGQRAS 425
                                       55667778878*********.5559********.............777777888887..88*************99 PP

                         Rhodanese  81 aaaallkklGyknvsvldGGfkawke 106
                                        aa +lk  G++nv+++ GGf+a+++
  gi|330506410|ref|YP_004382838.1| 426 IAASILKMNGFNNVFNMAGGFTAYQK 451
                                       9999******999**********986 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.7   3.5e-14   2.1e-10       5     184 ..      13     170 ..       9     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 3.5e-14
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                        ++sy + g++ + +iD+   +++ r    l ++++ ++++++++ THlH+D i+g  +l eat++ ++a a + +a
  gi|330506410|ref|YP_004382838.1|  13 AHSSYMVAGNNICAVIDP---ERNIRPY--LDSAKKMGLKITHILETHLHADFISGHLDLEEATGARIYAPASANCA 84 
                                       578999999999999998...5555554..5789******************************************* PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCE......EEECTTT CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkv......lftGDal 152
                                       +++e +                        e+d + +++  + v+ +pgh++ h+++ + + +       lf+GD+l
  gi|330506410|ref|YP_004382838.1|  85 FPHEPL-----------------------KEGDRIKLEDIIFSVIETPGHTPEHISYIAADTSRaddpvsLFCGDTL 138
                                       ******.......................778888888888888888888888888765554422222229****** PP

                                       SSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHH CS
                       Lactamase_B 153 lagetgridltlrgaevrdpsdaekyldsllk 184
                                       ++g+ gr dl ++ ae +  s+++++ +++lk
  gi|330506410|ref|YP_004382838.1| 139 FVGDVGRPDLFPGRAEELASSLYDSLHEKILK 170
                                       **********7777777766666666655554 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   2.5e-05      0.15      30      67 ..      47      82 ..      27     159 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.5e-05
                                      SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHH CS
                     Lactamase_B_2 30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvl 67
                                      +i  +l th H+D + g l+l e ++  +++yap++  
  gi|330506410|ref|YP_004382838.1| 47 KITHILETHLHADFISGHLDLEEATG--ARIYAPASAN 82
                                      7999*******************554..6788886543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 3356.82
//
Query:       gi|330506411|ref|YP_004382839.1|  [L=591]
Description: citrate transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-51  173.1  16.3    1.4e-50  172.2  16.3    1.4  1  CitMHS         Citrate transporter
    1.9e-13   50.0   0.0    5.3e-06   26.2   0.0    2.5  2  TrkA_C         TrkA-C domain
    1.6e-12   47.2  40.9    4.4e-08   32.6  14.2    3.1  3  Na_sulph_symp  Sodium:sulfate symporter transmembrane region


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.2  16.3   2.4e-54   1.4e-50       1     300 []      16     539 ..      16     539 .. 0.80

  Alignments for each domain:
  == domain 1  score: 172.2 bits;  conditional E-value: 2.4e-54
                                       xxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   1 lvllileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd 73 
                                       lvl+i  ++rld+va+++ ++l    ++++ ea+sg+as++++ ++ +mi+g ++e+tG+  rla ++++ ag++++
  gi|330506411|ref|YP_004382839.1|  16 LVLFISNRIRLDLVAIVACLALawlsLISPLEAISGFASNAVVAMASVMILGYGIERTGVTSRLASTIIKYAGTNEK 92 
                                       69**************888888******************************************************* PP

                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  74 .llvllvlltallsafvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaarpglsl 148
                                        ++  ++++++lls++++n g++++++p++ +++++ + +p++ l++p+++aa +gg++t+iG              
  gi|330506411|ref|YP_004382839.1|  93 rIISTVSMTVGLLSSVMQNIGAAALFLPAIRRIGQQ-TSIPTShLMMPMGFAAILGGTVTMIGSG------------ 156
                                       ***********************************7.****************************............ PP

                                       xxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxx RF
                            CitMHS 149 pnlll.....................lalllvgllplvllfmfgvalalpvnap.................kvkkqk 187
                                       p ++l                     l+ll++g++ ++l++       +++n                         
  gi|330506411|ref|YP_004382839.1| 157 PLIVLndllrqngmepfsmfavtpvgLPLLIAGVALFALAG-----SRIFPNKKekkcqltvaeiwgidyaI----- 223
                                       66666666666666666655554555777888788878877.....44444443444445444444444440..... PP

                                       xxxxxxxxxxxxx................................................................ RF
                            CitMHS 188 aiieaiarsllpv................................................................ 200
                                                   +                                                                
  gi|330506411|ref|YP_004382839.1| 224 ------------Ktcilprssnlsgktreeasfkikydlnllairkntevtvapsryarlesgqelaflgskedfnd 288
                                       ............04555556666666666666666666666666666666666666677777788888888888888 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|330506411|ref|YP_004382839.1| 289 fisasgcvptenrsrlksildsggfglaelivrpkasiidktlreigfrqkfsiepivhyskmresrsdfydtplaa 365
                                       88888888888888888888888888888888888888888999999999999999999999999999999999999 PP

                                       ...............................................................xxxxxxx....... RF
                            CitMHS 201 ...............................................................atillla....... 207
                                                                                                                    
  gi|330506411|ref|YP_004382839.1| 366 gdtiiafgswdtlrllashqdllllthpegeeirykkgplavmifiaslaltftgmpisiallT-----Gavamila 437
                                       9888888888888888888888888888888888888888666666555555555555555551.....05555566 PP

                                       ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 208 ........ykkveWsvlllfaGvfllvgaleqtGilealadllga...g.gplvalalvlgliallsafisnvavaa 272
                                               y++++W+ ++l++G+++++ a+e+tG + ++a+++ +   g  p+++++ +++l+++ls++isnva+++
  gi|330506411|ref|YP_004382839.1| 438 eiltpdeaYHAIDWKSVILIGGLIPFGIAMENTGASRLIASSFVDllaGaHPIAVMLSLAILTTALSLIISNVAATV 514
                                       99********************************6666666664455544565666777888888************ PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 273 lmapialgmapalgllspsplalalavg 300
                                       l++p++l +++++g   ++p alal+v+
  gi|330506411|ref|YP_004382839.1| 515 LLVPLVLLLSAGIG---ADPRALALLVA 539
                                       ********999999...99999999986 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.6e-08   0.00016       7      67 ..     229     291 ..     227     294 .. 0.93
   2 !   26.2   0.0   8.8e-10   5.3e-06       1      67 [.     315     383 ..     315     386 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.6e-08
                                       E--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   7 pagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       p +s l Gkt  e+ ++ + + +++air++ ++ + ps   +Le+G +l ++gs++d +++ +
  gi|330506411|ref|YP_004382839.1| 229 PRSSNLSGKTREEASFKIKyDLNLLAIRKNtEVTVAPSRYARLESGQELAFLGSKEDFNDFIS 291
                                       56899*************************999999999******************999865 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 8.8e-10
                                       CEEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T...-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrargvlvvairRg...geliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       l+e+ v++ + +++ktl+e+++r+ ++ +  i++     e  +   dt L +GD+++ +gs ++l+ l++
  gi|330506411|ref|YP_004382839.1| 315 LAELIVRPKASIIDKTLREIGFRQ-KFSIEPIVHYskmRESRSDFYDTPLAAGDTIIAFGSWDTLRLLAS 383
                                       6899********************.666666655554455666666******************999876 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   9.3   7.3e-07    0.0043      33     135 ..       8     107 ..       1     116 [. 0.89
   2 !   10.0   2.6   5.2e-05      0.31     385     462 ..     115     197 ..     109     201 .. 0.80
   3 !   32.6  14.2   7.4e-12   4.4e-08     295     462 ..     425     587 ..     402     590 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.3e-07
                     Na_sulph_symp  33 llaifiaaivglileplplavialialsllavligvlaakalsevlsgfssdttlLvfaalliaaavektgLgkRiA 109
                                       l  +++a+ v +i + + l  +a++a   la l+ + +     e++sgf s++++ +++ ++++ ++e tg   R+A
  gi|330506411|ref|YP_004382839.1|   8 LSMVIAAMLVLFISNRIRLDLVAIVACLALAWLSLISP----LEAISGFASNAVVAMASVMILGYGIERTGVTSRLA 80 
                                       667999*********************99999999999....899******************************** PP

                     Na_sulph_symp 110 lvlvkivGkrt.liLgyalvladllla 135
                                        +++k  G++  +i++ + +++ ll +
  gi|330506411|ref|YP_004382839.1|  81 STIIKYAGTNEkRIISTVSMTVGLLSS 107
                                       ********9987888888888887655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 5.2e-05
                     Na_sulph_symp 385 taallpillavaqaipgappllvalllalatslagfllpyatgpnpivf......gagylkvkdywrlGfilsiigl 455
                                        a +lp +  ++q +  +p+  +++++++a  l+g+++ +++gp  ++       g++ +++     +G++l i g+
  gi|330506411|ref|YP_004382839.1| 115 AALFLPAIRRIGQQT-SIPTSHLMMPMGFAAILGGTVTMIGSGPLIVLNdllrqnGMEPFSMFAVTPVGLPLLIAGV 190
                                       5789**********9.9***************************988642223236666666666677888888888 PP

                     Na_sulph_symp 456 lillllg 462
                                       ++++l+g
  gi|330506411|ref|YP_004382839.1| 191 ALFALAG 197
                                       8887776 PP

  == domain 3  score: 32.6 bits;  conditional E-value: 7.4e-12
                     Na_sulph_symp 295 tvaivvlvillllrvldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslf 371
                                       +  + + v ++l ++l+ +    +   W  ++l ggli +   +e++g +  ++ +++ +l+g++p ++++ +  ++
  gi|330506411|ref|YP_004382839.1| 425 IALLTGAVAMILAEILTPD-EAYHAIDWKSVILIGGLIPFGIAMENTGASRLIASSFVDLLAGAHPIAVMLSL-AIL 499
                                       33455677799999***99.7778899***********************************99997666554.555 PP

                     Na_sulph_symp 372 vlvhylfaSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGf 448
                                        ++  l+ S++A t+ l+p++l ++ +i ga+p  +all+a+++    f+lp     n+++   g   ++dy ++G 
  gi|330506411|ref|YP_004382839.1| 500 TTALSLIISNVAATVLLVPLVLLLSAGI-GADPRALALLVAVSSQNS-FILPTHQ-VNALLMDPGGYTIRDYLKAGG 573
                                       56667889********************.999999999999887766.****876.677888889999********* PP

                     Na_sulph_symp 449 ilsiigllillllg 462
                                       +++++++ i  +++
  gi|330506411|ref|YP_004382839.1| 574 VMTVLFICIETTFI 587
                                       *******9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3590.51
//
Query:       gi|330506412|ref|YP_004382840.1|  [L=361]
Description: hypothetical protein MCON_0111 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2269.23
//
Query:       gi|330506413|ref|YP_004382841.1|  [L=651]
Description: acetyl-CoA hydrolase/transferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-57  193.9   0.0    2.4e-57  193.2   0.0    1.4  1  AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal 
    1.5e-38  132.7   0.0    3.7e-38  131.5   0.0    1.6  1  AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal 
    1.4e-06   28.5   0.0    3.3e-06   27.3   0.0    1.6  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    5.5e-06   25.9   0.0      0.013   14.9   0.0    2.5  2  CoA_trans        Coenzyme A transferase
    1.6e-05   25.6   0.0      3e-05   24.7   0.0    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    2.8e-05   24.3   0.0    5.1e-05   23.5   0.0    1.4  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    8.3e-05   22.9   0.1    0.00021   21.7   0.1    1.7  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00031   20.6   0.0     0.0008   19.3   0.0    1.6  1  FR47             FR47-like protein
    0.00034   20.5   0.0     0.0022   18.0   0.0    2.1  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0035   15.8   0.1        1.4    7.2   0.0    2.2  2  Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, trans
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.035   14.1   0.0    1.7  2  DeoRC            DeoR C terminal sensor domain


Domain annotation for each model (and alignments):
>> AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.2   0.0   1.5e-60   2.4e-57       1     154 []     293     460 ..     293     460 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.2 bits;  conditional E-value: 1.5e-60
                                       S-HHHHHHHTT-TTEEE-BHHHHT-HHHHTTSTTEEEEEE-SEEETTS-EESSECTTCCTCGGTTHHHHHHHHHHST CS
                   AcetylCoA_hyd_C   1 GskklydfldenpkielrpveyvndpeviaqnkkvvsinsalevdltGqvnseslggrvvsGvGgqldFvrgaalsk 77 
                                       G ++ ydfl +n++ie+r ++y+n+p +iaqn+k+++insale+dltGq+++eslg++++sG+Ggq dF+rg+a ++
  gi|330506413|ref|YP_004382841.1| 293 GHRSTYDFLRNNDSIEFRTIDYTNNPLIIAQNSKMIAINSALEIDLTGQATAESLGHSFYSGIGGQADFMRGTAIAP 369
                                       78999************************************************************************ PP

                                       T-EEEEE--SEET..............TTTEESEESS-STTSSECE-TTT-SEEEETTEEEE-TT--HHHHHHHHHT CS
                   AcetylCoA_hyd_C  78 ggksiialpStak..............kgeiSrIvpslkegahvtttrhdvdyvvTEyGiadLrgkslreraealik 140
                                       ggk+++alpSta                g++SrIvp+l+ega+vt tr d++yvvTEyGia+L+gks+rera+ali+
  gi|330506413|ref|YP_004382841.1| 370 GGKTVLALPSTALvtcadssddeasqkGGRVSRIVPFLGEGAGVTLTRGDIHYVVTEYGIAYLHGKSIRERAMALIA 446
                                       ***********97778888888877633579********************************************** PP

                                       TS-HHHHHHHHHHH CS
                   AcetylCoA_hyd_C 141 iAhpdfreeLleea 154
                                       iAhp fr +L+eea
  gi|330506413|ref|YP_004382841.1| 447 IAHPLFRLWLIEEA 460
                                       ***********997 PP

>> AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.5   0.0   2.3e-41   3.7e-38      22     190 ..      35     201 ..      19     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 2.3e-41
                   AcetylCoA_hydro  22 gshielsgftavgtakaipkylakrkvekenvkkkllidlavgavlsagPeeevleekdavlyrpapkqvgellrka 98 
                                       ++ i  +++++vgt +++p+ l++   e ++ ++k ++d++  +++++g  +++++ek+  ++r +++++g+++r a
  gi|330506413|ref|YP_004382841.1|  35 FQEIRPGNRIFVGTGCGEPQHLVRSLLEFVKERPKAFLDAELINIVTLG-VAPYTDEKFQSNFRLNSFFIGDHTRNA 110
                                       788999*******************************************.*************************** PP

                   AcetylCoA_hydro  99 inqglvsfvdkhlsevpqklekgfvpiDvalieataldedGylnlGvgvrakKviiEvaelvvivvkknpPrvngyd 175
                                       +n g +++++++ls++pq++  + +p+Dvali++t +d+dG lnlGv+v++++ ++E a++v+++ ++++P +ng d
  gi|330506413|ref|YP_004382841.1| 111 VNRGEADYTPIFLSNLPQLIRSERIPLDVALIQTTLPDKDGRLNLGVSVDIVRTAVEKAGIVIAQPNSHMPAING-D 186
                                       ***************************************************************************.* PP

                   AcetylCoA_hydro 176 elialdkvdyivvdp 190
                                       + i +d vdy++  +
  gi|330506413|ref|YP_004382841.1| 187 GWIRMDDVDYLIPWD 201
                                       **********87544 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0     2e-09   3.3e-06      34     117 .]     550     633 ..     511     633 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2e-09
                                       EEEE.EEET..TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHH CS
                    Acetyltransf_1  34 gllv.aeed..geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveednda 107
                                        l++ +eed  + + G  ++ ++ d     ++   l+V+ +++++G+G +Ll +l   a+++g+    ++v + nd+
  gi|330506413|ref|YP_004382841.1| 550 VLVAtVEEDgiESICGLGQYGINSD---MFTADVALVVRDDCQNHGIGGELLAYLTYLAKRQGLLGFTAEVLAGNDP 623
                                       3333667776677999999999999...56666799****************************66678**9***** PP

                                       HHHHHHHTTE CS
                    Acetyltransf_1 108 airlYeklGF 117
                                         +l++k+GF
  gi|330506413|ref|YP_004382841.1| 624 VFHLFKKMGF 633
                                       *****88**9 PP

>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0007       1.1       8      38 ..      34      62 ..      27      91 .. 0.85
   2 !   14.9   0.0   8.3e-06     0.013       3      67 ..     218     276 ..     216     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0007
                                      HCTT--TTEEEEE-SBTTBTHHHHHHHHHHH CS
                         CoA_trans  8 vakeikdGmtvavGGFgligiPealiaalar 38
                                      + +ei+ G  ++vG  +++g+P++l+++l++
  gi|330506413|ref|YP_004382841.1| 34 IFQEIRPGNRIFVG--TGCGEPQHLVRSLLE 62
                                      6679**********..************997 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 8.3e-06
                                       HHHHHHCTT--TTEEEEE-SBTTBT.HHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTTTEEE CS
                         CoA_trans   3 taaeavakeikdGmtvavGGFglig.iPealiaalarsgvkdltviiseagvlglgplllngsvkk 67 
                                       ++ + va+ ++dG+t+ vG     g iP+a++ +l +   k++  ++se    g+  l+++g v++
  gi|330506413|ref|YP_004382841.1| 218 RIGKYVARIVEDGSTIQVG----YGsIPNAIVSSLKK---KKHLGVHSELLSDGIAGLIRDGVVDN 276
                                       56788999***********....888**777777766...59999999999999999999999986 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.9e-08     3e-05       2     137 ..     496     633 ..     496     634 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.9e-08
                    Acetyltransf_3   2 LlLrplteeD...lealfelrsdpe.vmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdl 74 
                                       +lLrp++ +D   l+++f  +sd+   +r+++    ++  ++ l+++ a ++ ++ +  a  ++++g+  ++gl ++
  gi|330506413|ref|YP_004382841.1| 496 ILLRPVKISDeplLKDFFYSLSDESmYQRFISA--RRDIPHQELQKFAAVDYFQKMVLVAT-VEEDGIESICGLGQY 569
                                       68*******944444443347788877788644..34455555555444444444544444.356656666666666 PP

                    Acetyltransf_3  75 eeedee..aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                         +++   a++ ++++++++++G++ e ++ l+ +a +++gl  + a++ + N   + +++k+Gf
  gi|330506413|ref|YP_004382841.1| 570 GINSDMftADVALVVRDDCQNHGIGGELLAYLTYLA-KRQGLLGFTAEVLAGNDPVFHLFKKMGF 633
                                       66655566*******************987766666.9999***********************9 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   3.1e-08   5.1e-05      58     139 ..     558     638 ..     520     645 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.1e-08
                    Acetyltransf_4  58 drivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGF 134
                                       d i  ++ lgq         a +   + + d+++ g+g el+++l   +k+q+++ ++ae+ + n++   ++k++GF
  gi|330506413|ref|YP_004382841.1| 558 DGIESICGLGQYGINSDMFTADVALVV-RDDCQNHGIGGELLAYLTYLAKRQGLLGFTAEVLAGNDPVFHLFKKMGF 633
                                       555555555544441233334444444.689***************999**************************** PP

                    Acetyltransf_4 135 elvgi 139
                                        + ++
  gi|330506413|ref|YP_004382841.1| 634 AVSKR 638
                                       98765 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   1.3e-07   0.00021       7      75 ..     552     634 ..     544     635 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                                       EEEET....TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH....TT.SEEEEE.EEEE...THHHHHH CS
                    Acetyltransf_7   7 Vaedd....gkivGfialslld...aeitrlaVdpeyrgkGiGraLlea....ae.kgiile.qlel...naekaik 67 
                                       Va  +    + i+G   + +++   +    l+V+ +++++GiG +Ll++    a+ +g+    ++e+   n+ +  +
  gi|330506413|ref|YP_004382841.1| 552 VATVEedgiESICGLGQYGINSdmfTADVALVVRDDCQNHGIGGELLAYltylAKrQGLL-GfTAEVlagND-PVFH 626
                                       44444335555566555555555444444499****************756652256632.33333334433.6788 PP

                                       HHHHTTEE CS
                    Acetyltransf_7  68 fYeklGFe 75 
                                       +++k+GF 
  gi|330506413|ref|YP_004382841.1| 627 LFKKMGFA 634
                                       *******6 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.9e-07    0.0008      25      80 ..     580     636 ..     571     640 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.9e-07
                                       EEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  25 galqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfeki 80 
                                        al v+++ ++ G g+ l + l++   ++g    ++ v a+N+p  +l++k+Gf + 
  gi|330506413|ref|YP_004382841.1| 580 VALVVRDDCQNHGIGGELLAYLTYLAKRQGLlGFTAEVLAGNDPVFHLFKKMGFAVS 636
                                       5899********************9999886257899*****************875 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.71   1.2e+03      16      72 ..     207     269 ..     193     283 .. 0.73
   2 !   18.0   0.0   1.3e-06    0.0022      31     111 ..     549     638 ..     519     642 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.71
                   Acetyltransf_10  16 fisp..ealrerieegealllvaeeggkiv.Gvielrdgs.....hisllfVdpeyrgqGigkaL 72 
                                       +i++   ++++ri  g+++  ++e+g +i  G++++ +       +  +l V++e  + Gi+  +
  gi|330506413|ref|YP_004382841.1| 207 YIEDvpGEIAQRI--GKYVARIVEDGSTIQvGYGSIPNAIvsslkKKKHLGVHSELLSDGIAGLI 269
                                       5555556777777..88888888888776448887766666666688899999999999998665 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.3e-06
                   Acetyltransf_10  31 alllvaeeggkivGvielrdgs.......hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yav 98 
                                       ++l++  e++ i  +++l + +           l+V+++++  Gig +Ll ++   a+++g+   + +v a +    
  gi|330506413|ref|YP_004382841.1| 549 MVLVATVEEDGIESICGLGQYGinsdmftADVALVVRDDCQNHGIGGELLAYLTYLAKRQGLLGfTAEVLAGNdPVF 625
                                       44555555554544444433333333554334579**********************9999999********99999 PP

                   Acetyltransf_10  99 pfYeklGFkavge 111
                                        +++k+GF + ++
  gi|330506413|ref|YP_004382841.1| 626 HLFKKMGFAVSKR 638
                                       ********98865 PP

>> Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0017       2.7     139     207 ..     138     203 ..     130     213 .. 0.78
   2 !    7.2   0.0   0.00086       1.4     448     482 ..     415     448 ..     409     456 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0017
                   Mal_decarbox_Al 139 nvalvaaekadreGnlytGantedtPaiveatafkdgiviaqvneivdklpr.vdiPadwvdfvveadkp 207
                                       +val+ ++  d++G l  G++ +    iv ++  k giviaq n  +  +     i  d vd+++  d+p
  gi|330506413|ref|YP_004382841.1| 138 DVALIQTTLPDKDGRLNLGVSVD----IVRTAVEKAGIVIAQPNSHMPAINGdGWIRMDDVDYLIPWDEP 203
                                       69******************987....777777799*******988776653133666777777766666 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00086
                   Mal_decarbox_Al 448 iygddvthvvteeGiayllkaesleereqairava 482
                                       +   d+ +vvte Giayl+  +s+ er  a+ a+a
  gi|330506413|ref|YP_004382841.1| 415 LTRGDIHYVVTEYGIAYLH-GKSIRERAMALIAIA 448
                                       55679************97.678899998888887 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       5.8   9.5e+03      14      28 ..      35      49 ..      32      52 .. 0.84
   2 ?   14.1   0.0   2.1e-05     0.035       7      46 ..     217     256 ..     214     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.8
                             DeoRC 14 aeliedgdtifldaG 28
                                       + i++g+ if+++G
  gi|330506413|ref|YP_004382841.1| 35 FQEIRPGNRIFVGTG 49
                                      67899******9988 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.1e-05
                             DeoRC   7 rrIAkaAaeliedgdtifldaGtTtlelaraLaekknltv 46 
                                       +rI+k++a+++edg+ti ++ G+   ++++ L++kk+l v
  gi|330506413|ref|YP_004382841.1| 217 QRIGKYVARIVEDGSTIQVGYGSIPNAIVSSLKKKKHLGV 256
                                       79*********************************99977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); 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:                        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 0.32s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 4209.54
//
Query:       gi|330506414|ref|YP_004382842.1|  [L=368]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-22   77.3   0.0    1.6e-21   76.0   0.0    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.7e-19   69.0   2.2    3.6e-19   68.0   2.2    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
      5e-17   62.2   0.0    1.2e-16   61.0   0.0    1.7  1  OrfB_IS605      Probable transposase
      0.007   16.4   0.2      0.012   15.6   0.2    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
        0.2   11.2   3.0        6.4    6.4   0.1    3.1  3  RecR            RecR protein
       0.76    9.3   3.1        4.5    6.8   3.1    2.1  1  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.0   5.2e-25   1.6e-21       1      68 [.     285     352 ..     285     353 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 5.2e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++ l +  +yka+ +G  v++v+p++TSk Cs+Cg  + ++ls+r+++Cp+Cg+++drD+nAaiNil+
  gi|330506414|ref|YP_004382842.1| 285 WNMLVTLTSYKAESAGSMVVLVDPRNTSKMCSRCGILVGKTLSDRVHNCPQCGLSMDRDWNAAINILR 352
                                       667777889*********************************************************97 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   2.2   1.2e-22   3.6e-19       1      47 []       1      46 [.       1      46 [. 0.99

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.2e-22
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkayk+r+yPT+ Q++k++rt++ +R+ YN+ La+rk+a+e+egk
  gi|330506414|ref|YP_004382842.1|  1 M-LKAYKFRIYPTKSQRTKMERTIDLCRWTYNQTLAYRKDAWEKEGK 46
                                      8.*******************************************98 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   4.2e-20   1.2e-16       3     117 ..     165     271 ..     163     273 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 4.2e-20
                        OrfB_IS605   3 pveveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        ve+e++ +p+ k ++ +g+D+G++ +at+++++          +++++k+la+ +++l++  k++  +kka r + 
  gi|330506414|ref|YP_004382842.1| 165 SVEIEDQlKPPWKVGSLVGVDVGLESFATLSNGE---------TFREEEKELARVQRKLSKAPKGTPERKKALRMVE 232
                                       689999966677999****************999.........8999****************************** PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       r+h++++++r +++hk++++l+++   ++ e+L ++nm 
  gi|330506414|ref|YP_004382842.1| 233 RVHERIANKRYDFAHKVSRYLVNRFGLIAFEDLSIQNML 271
                                       *************************************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   4.1e-06     0.012      10      44 ..     310     346 ..     306     349 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.1e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + +++Cs+Cg  + ++ +   ++Cp+Cg ++d +++ 
  gi|330506414|ref|YP_004382842.1| 310 NTSKMCSRCGILVGKTLSdrVHNCPQCGLSMDRDWNA 346
                                       6789******9998776689************99986 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.29   8.6e+02       5      16 ..      71      82 ..      69      84 .. 0.89
   2 ?    3.5   0.1     0.018        53      13      25 ..     309     321 ..     304     326 .. 0.78
   3 ?    6.4   0.1    0.0021       6.4      12      26 ..     326     340 ..     324     344 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.29
                                      HHHHHHHHHHH- CS
                              RecR  5 LaeaLqeakekv 16
                                      ++++Lq+a e+v
  gi|330506414|ref|YP_004382842.1| 71 FSQTLQNAQERV 82
                                      89*******998 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.018
                                       HHH-EE-TTT--E CS
                              RecR  13 kekvrhCsrCgnl 25 
                                       +++ + CsrCg l
  gi|330506414|ref|YP_004382842.1| 309 RNTSKMCSRCGIL 321
                                       667799****976 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0021
                                       HHHH-EE-TTT--EE CS
                              RecR  12 akekvrhCsrCgnlt 26 
                                       + ++v+ C++Cg   
  gi|330506414|ref|YP_004382842.1| 326 LSDRVHNCPQCGLSM 340
                                       6799*******9655 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.1    0.0015       4.5       5      24 ..     315     338 ..     312     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0015
                       zf-ribbon_3   5 CPnCG....aplssddnvCpyCGt 24 
                                       C++CG    + ls+++ +Cp CG 
  gi|330506414|ref|YP_004382842.1| 315 CSRCGilvgKTLSDRVHNCPQCGL 338
                                       6666422226369*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2619.43
//
Query:       gi|330506415|ref|YP_004382843.1|  [L=258]
Description: hypothetical protein MCON_0114 [Methanosaeta concilii GP6]
Scores for complete 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   50.4   0.0    2.1e-13   50.1   0.0    1.1  1  RsmJ      Ribosomal RNA large subunit methyltransferase D, Rl


Domain annotation for each model (and alignments):
>> RsmJ  Ribosomal RNA large subunit methyltransferase D, RlmJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   1.2e-17   2.1e-13       2     141 ..      34     173 ..      33     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.2e-17
                                       S--EEEESS--SSEEETTSHHHHHHSGGGGTGGGTTT-TT--GGGHHHHHHHHHTTTTSS.....--EEE-HHHHHH CS
                              RsmJ   2 kpfavlDthaGvGrYdLsseeaektgeaeeGiaRliaqadlpaeleryldvvrklnkgek.....lryYpGspllar 73 
                                        ++++ ++h G+ +Y L+      +g++e+Gi+R++ +  l++++ +y +++ ++n+ e+     ++ YpGs+ll++
  gi|330506415|ref|YP_004382843.1|  34 SSLVYAESHVGRPKYALK-----PSGDWESGIGRIWPALPLLKDF-PYFNILAEFNSIESlsslqIEFYPGSALLVA 104
                                       6789************96.....58****************9999.7*********99988888899********** PP

                                       HHS-TT-EEEEE---TTHHHH..HHHHTTT-TTEEEESS-HHHHHHHS-S-TTS-EEEEE----SSCCHH CS
                              RsmJ  74 rllReqDrlvlteLhpkdaal..LkaelakdkrvrvkkadGfaalkaklppkekRglvliDPPyeakdey 141
                                       +l + +   +l+++ + d a+    +e  +++ ++ + +dGf+ +   l  ++  gl++iDPP+   +e 
  gi|330506415|ref|YP_004382843.1| 105 ELAKRKKADLLINIWDIDPAVgaAWNECLDHSPISFHLDDGFSGVMSLLKSSS-PGLLFIDPPFTSPEEK 173
                                       *998887777777777665541134566677889**********998887666.9*********887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1763.68
//
Query:       gi|330506416|ref|YP_004382844.1|  [L=148]
Description: hypothetical protein MCON_0115 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1123.20
//
Query:       gi|330506417|ref|YP_004382845.1|  [L=566]
Description: iron transport protein [Methanosaeta concilii GP6]
Scores for complete 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-49  167.4   0.8    2.3e-49  166.9   0.8    1.2  1  FeoB_N     Ferrous iron transport protein B
    3.9e-24   85.1  17.4      5e-13   49.3   5.3    2.5  2  Gate       Nucleoside recognition
    1.5e-16   60.5   0.1    2.3e-16   59.9   0.1    1.3  1  MMR_HSR1   50S ribosome-binding GTPase
    1.1e-12   47.4   1.0    1.1e-12   47.4   1.0    2.5  2  FeoB_C     Ferrous iron transport protein B C terminus
    0.00036   20.0   0.0    0.00054   19.4   0.0    1.2  1  SRPRB      Signal recognition particle receptor beta subunit
  ------ inclusion threshold ------
      0.016   14.5   0.0       0.05   12.9   0.0    1.8  2  Gtr1_RagA  Gtr1/RagA G protein conserved region
      0.035   14.3   0.1       0.37   11.0   0.0    2.2  2  Roc        Ras of Complex, Roc, domain of DAPkinase
        0.2   11.0   0.1       0.29   10.4   0.1    1.2  1  AIG1       AIG1 family


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 !  166.9   0.8     1e-52   2.3e-49       2     156 .]       2     155 ..       1     155 [. 0.97

  Alignments for each domain:
  == domain 1  score: 166.9 bits;  conditional E-value: 1e-52
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleee 78 
                                       ++ l+GnpnvGk+++f +ltg +   +N+pG+t+e +eg++kl +k ++++D PG+Ysl+++s+ e+v+ ++l e+ 
  gi|330506417|ref|YP_004382845.1|   2 KILLMGNPNVGKSVIFSRLTGIEVVSANYPGTTIEYTEGRMKLGEKMATLIDPPGVYSLEPTSKVEEVTGHIL-EQG 77 
                                       799*****************************************************************98876.678 PP

                                       SSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N  79 pdvvvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellka 155
                                       +dvvvnv+d+tnlernL Ltl++le g+p+v+aln++d+a++kgieid++ L+e+Lgv+v++t+a +++gi +l++a
  gi|330506417|ref|YP_004382845.1|  78 ADVVVNVIDSTNLERNLNLTLKILEKGLPTVVALNLWDVATRKGIEIDTAILAEALGVDVIPTVAVSGQGIYDLVEA 154
                                       9*************************************************************************998 PP

                                       H CS
                            FeoB_N 156 i 156
                                       i
  gi|330506417|ref|YP_004382845.1| 155 I 155
                                       6 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   4.2   7.1e-14   1.6e-10       4     109 ..     287     378 ..     284     381 .. 0.96
   2 !   49.3   5.3   2.2e-16     5e-13       1     110 [.     442     539 ..     442     541 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 7.1e-14
                              Gate   4 agpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfd 80 
                                       ++p+++++ +l+++l++ ++l r++ +l+ +++++g  l++ a+ ++++g++   + v+++ +++           +
  gi|330506417|ref|YP_004382845.1| 287 VLPFLIPFYLLLGILEDIGYLPRLSVILDAFMHRIG--LHGAAILPCVLGMG---CSVPAVLSVR---------ILE 349
                                       79**********************************..**************...*********9.........*** PP

                              Gate  81 tpksalafllfvllytpcvatlavivrel 109
                                       + k+++ +  ++++++pc ++ a+i+++l
  gi|330506417|ref|YP_004382845.1| 350 SAKQRYLAATLMTMAIPCASQSAMIFGIL 378
                                       ************************99886 PP

  == domain 2  score: 49.3 bits;  conditional E-value: 2.2e-16
                              Gate   1 llkagpiillasiliwflssssllgrigkllepvfap.lgqeldwkatvslltgfaakevvvgtlgtlytsalgell 76 
                                       l+ a+p+i l++i+++f++ ++l+  ig  l+pv++  lg  l+  a+++l+ gf+ k v++g+++ l         
  gi|330506417|ref|YP_004382845.1| 442 LKEAVPYIGLGMIIMNFFYLTGLMHLIGEELKPVVSGlLG--LPSDAATALIIGFLRKDVGIGMFAPL--------- 507
                                       6889******************************999899..***********************888......... PP

                              Gate  77 qgfdtpksalafllfvllytpcvatlavivrelg 110
                                           tp++ +++ +++++y+pcvat+ v+ +elg
  gi|330506417|ref|YP_004382845.1| 508 --DMTPVQYVIAAVVLAMYMPCVATFMVMLKELG 539
                                       ..79****************************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 !   59.9   0.1     1e-19   2.3e-16       1     113 [.       2     112 ..       2     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 1e-19
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHC CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflalee 75 
                                       +++++G+pNvGKS ++++ltg ++  +++pgtT++ +egr+kl++k  +l+D pG+++    s+ ++++ ++l+  +
  gi|330506417|ref|YP_004382845.1|   2 KILLMGNPNVGKSVIFSRLTGIEVVSANYPGTTIEYTEGRMKLGEKMATLIDPPGVYSlePTSKVEEVTGHILE--Q 76 
                                       5899**************************************9999*********8853222333345555554..3 PP

                                       .TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                          MMR_HSR1  76 .adlillvvdaseeklkpldeeleelleeakkplilvln 113
                                        ad+++ v+d++ + l+++ +   ++l e++ p++++ln
  gi|330506417|ref|YP_004382845.1|  77 gADVVVNVIDST-N-LERNLNLTLKIL-EKGLPTVVALN 112
                                       59********55.4.555544444444.35667777766 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 !   47.4   1.0   5.1e-16   1.1e-12       1      53 []     386     437 ..     386     437 .. 0.97
   2 ?   -2.4   1.0       1.8   4.1e+03       7      21 ..     549     563 ..     547     565 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 5.1e-16
                            FeoB_C   1 lfslYllgilvallvalllkkttlkgepspfvmELPpYrlPslknvliktweR 53 
                                       +f++Y++ +l ++++++ll+++ + ge++  ++E+PpYr+P+l+ +l+kt+ R
  gi|330506417|ref|YP_004382845.1| 386 IFIVYATLFLSFVITGYLLHRF-IGGESPEIFLEIPPYRMPNLQALLKKTFIR 437
                                       699******************8.***************************977 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                            FeoB_C   7 lgilvallvalllkk 21 
                                       l +++al+v+  l+ 
  gi|330506417|ref|YP_004382845.1| 549 LRLVAALVVGTALNL 563
                                       5679999**999986 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 !   19.4   0.0   2.4e-07   0.00054       5      95 ..       2      97 ..       1     111 [. 0.77

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.4e-07
                                      EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT-GCC....SHHHHHHHHHHGGEEE CS
                             SRPRB  5 avllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGhekl....rqklleklkaksslkg 78
                                      ++ll+G  + GK  +f rLt  +v ++       + ++   +  +++ tliD PG  +l    + + ++ ++ ++ +  
  gi|330506417|ref|YP_004382845.1|  2 KILLMGNPNVGKSVIFSRLTGIEVVSANYPGtTIEYTEGRMKLGEKMATLIDPPGVYSLeptsKVEEVTGHILEQGADV 80
                                      599*****************8866655443324455554456788999**********944222344567788899*** PP

                                      EEEEEETTS-HHHHHHH CS
                             SRPRB 79 lvfvvDStidpkevkev 95
                                      +v v+DSt  +++++ +
  gi|330506417|ref|YP_004382845.1| 81 VVNVIDSTNLERNLNLT 97
                                      ********999998766 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 ?   12.9   0.0   2.2e-05      0.05       1     101 [.       2     100 ..       2     114 .. 0.73
   2 ?   -2.1   0.0       0.9     2e+03     163     178 ..     236     251 ..     234     266 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                         Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtl...rlgatidveksevrflgnltlnlwDcgGqeafvee.ylssqkeei 73 
                                       k+LLmG+ + GK+    +iF+ ++  +++   + g+ti+ ++ ++++ +++   l+D +G  ++  + ++++   +i
  gi|330506417|ref|YP_004382845.1|   2 KILLMGNPNVGKS----VIFSRLTGIEVVsanYPGTTIEYTEGRMKLGEKM-ATLIDPPGVYSLEPTsKVEEVTGHI 73 
                                       89**********7....6666666666651115689*********866655.68******99886553677888899 PP

                         Gtr1_RagA  74 frn.vgvliyVfDvesreleedletlkei 101
                                       +++  +v++ V+D++  +le++l+   +i
  gi|330506417|ref|YP_004382845.1|  74 LEQgADVVVNVIDST--NLERNLNLTLKI 100
                                       876367*******99..555555544444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.9
                         Gtr1_RagA 163 slykAfssivqklipn 178
                                        l+ A+s+ +++l+  
  gi|330506417|ref|YP_004382845.1| 236 PLFIAYSNFITDLVHR 251
                                       6999********9965 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00017      0.37       1      35 [.       2      36 ..       2      50 .. 0.77
   2 ?    0.7   0.0      0.26   5.9e+02      54      66 ..     107     119 ..      79     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                                      EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEE CS
                               Roc  1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvd 35
                                      K++l+G+ +vGK+ +++r++  ++ + + + + ++
  gi|330506417|ref|YP_004382845.1|  2 KILLMGNPNVGKSVIFSRLTGIEVVSANYPGTTIE 36
                                      9******************9877665555544555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.26
                                       TCEEEEEEEE-SG CS
                               Roc  54 kkvklniWDtaGq 66 
                                       + v ln+WD+a  
  gi|330506417|ref|YP_004382845.1| 107 TVVALNLWDVATR 119
                                       4589******975 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00013      0.29       2     103 ..       2      97 ..       1     105 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrcll 78 
                                       +i+l+G   +GkS     + g ++ + +    + t + ++ + +  +k    iD Pg+ +l+ + +   +e++   +
  gi|330506417|ref|YP_004382845.1|   2 KILLMGNPNVGKSVIFSRLTGIEVVSAN--YPGTTIEYTEGRMKLGEKMATLIDPPGVYSLEPTSK--VEEVTG--H 72 
                                       79*********************99888..578888999999999999*************98765..556664..6 PP

                                       HCTT-ESEEEEEEETTB-SHHHHHH CS
                              AIG1  79 lseegihalllvlslgrfteedeka 103
                                       + e+g ++++ v++ ++++++ + +
  gi|330506417|ref|YP_004382845.1|  73 ILEQGADVVVNVIDSTNLERNLNLT 97 
                                       77899*****999988777665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 4302.74
//
Query:       gi|330506418|ref|YP_004382846.1|  [L=369]
Description: hypothetical protein MCON_0118 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0022   18.5   2.2     0.0031   18.1   0.5    1.9  2  Transmemb_17  Predicted membrane protein
  ------ inclusion threshold ------
       0.26   12.4   0.6        2.7    9.1   0.6    2.3  1  PPC           Bacterial pre-peptidase C-terminal domain
        4.5    7.0  10.9       0.62    9.8   5.8    2.0  2  DUF2157       Predicted membrane protein (DUF2157)


Domain annotation for each model (and alignments):
>> Transmemb_17  Predicted membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.4      0.14   8.6e+02      34      84 ..     230     282 ..     218     285 .. 0.74
   2 !   18.1   0.5   5.2e-07    0.0031      18      82 ..     277     342 ..     266     359 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.14
                      Transmemb_17  34 yllldvvllvlllllEvlRlylgykgNltekvpelalfllltlpvllpl..vy 84 
                                       + ++ ++ ++++l++ +l ++ g++ +l   + +la+fl+l   +l+++  +y
  gi|330506418|ref|YP_004382846.1| 230 SVIMIFIPYLVALIAGGLIYWRGSRRSLFSLTGTLAGFLFLGTSSLVITqmIY 282
                                       55666666777777778888888999999999999999999999988886444 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 5.2e-07
                      Transmemb_17  18 lllliykgkllpy.psnyllldvvllvlllllEvlRlylgykgNltekvpelalfllltlpvllpl 82 
                                       +  +iy ++  py p++y+++ ++l+ +ll++  +Rl  g +g l+ + +++++ ++l   + ++l
  gi|330506418|ref|YP_004382846.1| 277 ITQMIYSLSRAPYgPEVYITMAIILFHALLGVASIRLARGEAGILQRSLLAVIGTIALLGGSGVIL 342
                                       566899999**********************************************99987777666 PP

>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.6   0.00046       2.7       2      69 ..      50     173 ..      49     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00046
                                       EEEEEEEE-TT-EEEEEES-TT........SEEEEE-TT..-SS-EE-ST..T-TT..................... CS
                               PPC   2 vDvysfevpagdsltididggti......dldLylldsngtsvaaydans..apsg..................... 49 
                                       v+++sf+v++g ++   +   t         dL l  +  ++ + ++a +     +                     
  gi|330506418|ref|YP_004382846.1|  50 VHYFSFDVREGERIYMGLLKSTDpadegfLPDLLLIGPGIGVQSGSSAQQpeG--Ntslegavllensaipkniilp 124
                                       78888888888888877755555222222344667777766555544444322..2357777777777777777777 PP

                                       .............................S-TTS-EE-SSSEEEEEEE. CS
                               PPC  50 .............................sdeyieftapqaGtYyvaVs 69 
                                                                        i+ +apq G Yy a++
  gi|330506418|ref|YP_004382846.1| 125 eslkdlgalaadgregiatyepfgpssfiGLAEINLSAPQSGRYYAAIY 173
                                       77777777777777777777777776677447788999*******9998 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   5.8    0.0001      0.62      66     134 ..     230     299 ..     224     311 .. 0.73
   2 ?   -0.7   1.5      0.18   1.1e+03      69     106 ..     297     334 ..     290     352 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0001
                           DUF2157  66 kfllllvllllslllg.avlwrdrrvpprlgeallllaalllgaaialv..gqifqlsgdaysllllwalll 134
                                        +++++++ l++l++g ++ wr   +++ l  + ++la++l+++   lv  + i+ ls  +y+  +   +++
  gi|330506418|ref|YP_004382846.1| 230 SVIMIFIPYLVALIAGgLIYWR--GSRRSLFSLTGTLAGFLFLGTSSLVitQMIYSLSRAPYGPEVYITMAI 299
                                       478999**999999999*****..888999999999999999886544322778999999887643333333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.18
                           DUF2157  69 lllvllllslllg.avlwrdrrvpprlge.allllaalll 106
                                       ++++l+ + l+++ ++l r   +   l++ +l+++++++l
  gi|330506418|ref|YP_004382846.1| 297 MAIILFHALLGVAsIRLAR--GEAGILQRsLLAVIGTIAL 334
                                       4444444444444444444..2222222202223333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2970.80
//
Query:       gi|330506419|ref|YP_004382847.1|  [L=313]
Description: fasciclin domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-41  141.0   0.0    4.1e-22   78.8   0.0    2.1  2  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 !   78.8   0.0   2.3e-26   4.1e-22       3     128 .]      43     167 ..      41     167 .. 0.94
   2 !   60.4   0.0   1.1e-20     2e-16       4     128 .]     185     308 ..     183     308 .. 0.87

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 2.3e-26
                                       GHHHHHHHHTTTCCCCCTCSSS.......SEEEEEE-HHHHCCCHHHHHHHHHTCHHHHHHHHHTTEEESSS-HHHH CS
                         Fasciclin   3 lstfvsllekaglaeeLnkkdg.......glTvFaPtneAfaklppellakllndkkklkeiLkyHvvpetvsssal 72 
                                       l++f++l e++g+a++L +++g       ++ +FaP+++Af++++    + l +++ +l+++L yH v ++ s  ++
  gi|330506419|ref|YP_004382847.1|  43 LTEFSELAESTGFASTL-DNQGvllfdsgSFVIFAPSDDAFSAIDDMDMNILIENQTELERVLSYHAVWNSGSFVNI 118
                                       89***************.66567888888************************************************ PP

                                       HHHHEEEECCTTSSEEEEEEEGGTTEEEETTEEEEEEEEEEESSEEEEEESS-TSX CS
                         Fasciclin  73 kkasetlatllegaklrvniekgngtvtvngkarvvrsdieatngvihvidkvLlp 128
                                       ++   + +t l+g++l++n +   + ++vng a+v+   i+ +ngvi+vidkvL+p
  gi|330506419|ref|YP_004382847.1| 119 SDI-DSART-LQGENLSINST---DGLMVNG-ANVT-ESIQYDNGVIYVIDKVLMP 167
                                       **9.999**.***********...68*****.***9.66***************98 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 1.1e-20
                                       HHHHHHHHTTTCCCCCTCSSS..........SEEEEEE-HHHHCCCHHHHHHHHHTCHHHHHHHHHTTEEESSS-HH CS
                         Fasciclin   4 stfvsllekaglaeeLnkkdg..........glTvFaPtneAfaklppellakllndkkklkeiLkyHvvpetvsss 70 
                                       ++f+s++ + gl++ Ln ++g          ++T+FaP++eAf++  +++ +++++++  + ++L yH+v+ +   +
  gi|330506419|ref|YP_004382847.1| 185 KDFASAIVAEGLEDRLN-GQGlmgittlgegPFTIFAPSDEAFDAA-KSTVDSIKKQDMGMIDLLGYHMVEAKDLIN 259
                                       68999***********5.4355667777777************777.9999*******************9988777 PP

                                       HHHHHHEEEECCTTSSEEEEEEEGGTTEEEETTEEEEEEEEEEESSEEEEEESS-TSX CS
                         Fasciclin  71 alkkasetlatllegaklrvniekgngtvtvngkarvvrsdieatngvihvidkvLlp 128
                                         ++  ++ +t l+g++l v+      t +v   arv       +ngv++ id+vL+p
  gi|330506419|ref|YP_004382847.1| 260 MTES--GSAKT-LQGESLAVDSA----TGYVSM-ARVS-GSERYSNGVVYLIDQVLVP 308
                                       7776..58999.***********....668888.9997.7899*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2427.93
//
Query:       gi|330506420|ref|YP_004382848.1|  [L=246]
Description: hypothetical protein MCON_0120 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1815.26
//
Query:       gi|330506421|ref|YP_004382849.1|  [L=135]
Description: hypothetical protein MCON_0122 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.27   11.2   0.4       0.27   11.2   0.4    2.0  2  Zap1_zf2  Zap1 zinc finger 2


Domain annotation for each model (and alignments):
>> Zap1_zf2  Zap1 zinc finger 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   1.5e-05      0.27       5      15 ..      43      53 ..      42      57 .. 0.83
   2 ?   -2.3   1.2      0.27   4.9e+03       1       4 [.      83      86 ..      83      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.5e-05
                          Zap1_zf2  5 DCdFegeDicS 15
                                       CdF+g+Di +
  gi|330506421|ref|YP_004382849.1| 43 TCDFQGDDINT 53
                                      6********88 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.27
                          Zap1_zf2  1 CnWk 4 
                                      C+W+
  gi|330506421|ref|YP_004382849.1| 83 CKWE 86
                                      ***6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1010.75
//
Query:       gi|330506422|ref|YP_004382850.1|  [L=250]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1862.95
//
Query:       gi|330506423|ref|YP_004382851.1|  [L=59]
Description: hypothetical protein MCON_0124 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 435.90
//
Query:       gi|330506424|ref|YP_004382852.1|  [L=185]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   44.5   1.7    1.9e-10   40.9   1.3    2.6  2  Fer4_14      4Fe-4S single cluster domain
    1.3e-08   35.2   1.4    3.8e-08   33.7   1.0    1.9  2  Fer4_12      4Fe-4S single cluster domain
    2.1e-08   34.7   0.2    3.4e-08   34.0   0.2    1.4  1  Radical_SAM  Radical SAM superfamily


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 !   40.9   1.3   3.2e-14   1.9e-10       1      96 [.       6      87 ..       6     104 .. 0.76
   2 ?    0.0   0.0      0.15     9e+02      56      92 ..     123     155 ..     111     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3.2e-14
                           Fer4_14  1 lfvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeyp 79
                                      lf+rlsgCnl+C gCd+  + +      ++ ell       k  e + + + +tGGeP    + +el++l+ rl  ++ 
  gi|330506424|ref|YP_004382852.1|  6 LFIRLSGCNLNCEGCDTDLKPS---LDLSVLELL-------KRIEGQGKRVIITGGEPT--LQMNELVDLICRLYSRG- 71
                                      7***************988333...334445555.......33334444599******9..67899************. PP

                           Fer4_14 80 ekkiwletngtleiele 96
                                       ++i++e+ngt  i l+
  gi|330506424|ref|YP_004382852.1| 72 -MEIHIESNGTNTIPLD 87
                                      .**********998777 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.15
                           Fer4_14  56 GePLhyenkkellklvkrlkeeypekkiwletngtle 92 
                                       G P   +n+kel +l+  l +e     +w+   gt +
  gi|330506424|ref|YP_004382852.1| 123 GKPDWCWNEKELKQLIPILDRER----VWIMAYGTDQ 155
                                       66666788888888888777766....6666655555 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   1.0   6.3e-12   3.8e-08       8      95 ..       6      82 ..       2      99 .. 0.84
   2 ?   -2.4   0.0      0.87   5.2e+03      88     100 ..     126     138 ..     111     151 .. 0.61

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 6.3e-12
                           Fer4_12  8 lslfvsgCnlsCkgCfnketwsfksgkeft.kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpe 85
                                      l++++sgCnl+C+gC      + k + + +  ell++i       + + ++++GGEP l  + ++l++l+ +++++++e
  gi|330506424|ref|YP_004382852.1|  6 LFIRLSGCNLNCEGCD----TDLKPSLDLSvLELLKRIEG-----QGKRVIITGGEPTL--QMNELVDLICRLYSRGME 73
                                      5788**********87....56666666665888888864.....5699**********..9****************6 PP

                           Fer4_12 86 kdiwlytgyt 95
                                        +++++g+ 
  gi|330506424|ref|YP_004382852.1| 74 -IHIESNGTN 82
                                      .8******86 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.87
                           Fer4_12  88 iwlytgytleels 100
                                        w+++   l++l 
  gi|330506424|ref|YP_004382852.1| 126 DWCWNEKELKQLI 138
                                       4555555555554 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.2   5.7e-12   3.4e-08       3      89 ..       9      83 ..       7     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 5.7e-12
                                      EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgirit 81
                                       + gCnl+C  C++       +++ +lsv e+l+ ++       +k vi++ggep+l+    el++ +++l ++g++i+
  gi|330506424|ref|YP_004382852.1|  9 RLSGCNLNCEGCDTD-----LKPSLDLSVLELLKRIEGQ-----GKRVIITGGEPTLQM--NELVDLICRLYSRGMEIH 75
                                      678************.....5899999999999888666.....89***********55..7899999999999***** PP

                                      EEECSSCH CS
                                      xxxxxxxx RF
                       Radical_SAM 82 vetngtlp 89
                                      +e+ngt  
  gi|330506424|ref|YP_004382852.1| 76 IESNGTNT 83
                                      *****984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1372.23
//
Query:       gi|330506425|ref|YP_004382853.1|  [L=119]
Description: hypothetical protein MCON_0126 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-31  107.5   0.0      4e-31  107.3   0.0    1.0  1  Cyclophil_like   Cyclophilin-like
    3.2e-10   40.0   0.0    3.4e-10   39.9   0.0    1.1  1  Cyclophil_like2  Cyclophilin-like family
     0.0013   18.4   0.0     0.0022   17.7   0.0    1.6  1  DUF3830          Protein of unknown function (DUF3830)


Domain annotation for each model (and alignments):
>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.3   0.0   6.7e-35     4e-31       5     119 .]       6     115 ..       2     115 .. 0.92

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 6.7e-35
                                       EEET.TEEEEEEEETT..HHHHHHHHC-SEEEEEEECTTEEEEE-S-----SSSEESSB-TTEEEEECCCTEEEEES CS
                    Cyclophil_like   5 idie.sseveveLddt..etaraikealPiesrvntWgeEiYfstpvklekeenakevveagdiaywppGkalclff 78 
                                       i++  ++++ +e+d++   + +ai++alPie+r+ +WgeE+Yf+ ++kl+ +en++++ eagdi yw pG alc+ff
  gi|330506425|ref|YP_004382853.1|   6 IEVYgKGSALAEMDERnpIIREAIWQALPIEGRAILWGEEVYFDLDMKLK-DENPSASSEAGDICYWSPGPALCIFF 81 
                                       5554588889999999778899****************************.************************** PP

                                       S--TT-TTSB--SSSEEEEEEEEC-GGGGGG--TTEEEEEE CS
                    Cyclophil_like  79 GktPisddeirpaspvnviGrivedlellkkvkdgekvrve 119
                                       G+t       +p+s vn+iG++v++l+l+ +++++++++++
  gi|330506425|ref|YP_004382853.1|  82 GQT-------QPYSRVNHIGKVVQGLDLFERINAADRIVLR 115
                                       ***.......**************************99875 PP

>> Cyclophil_like2  Cyclophilin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   5.8e-14   3.4e-10      22     104 ..      30     106 ..      10     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 5.8e-14
                   Cyclophil_like2  22 leklPltltmedyngnEkiaylpeklptddapegssikaGdlayyapwgnlvlfykdfeesysygltrlGrieedae 98 
                                       ++ lP++ +     g E +++l+ kl++++   ++s +aGd++y++p++ l++f+++++   ++ + ++G++ + + 
  gi|330506425|ref|YP_004382853.1|  30 WQALPIEGRAIL-WGEEVYFDLDMKLKDENP--SASSEAGDICYWSPGPALCIFFGQTQP--YSRVNHIGKVVQ-GL 100
                                       555555555443.369************998..88999********************66..89*******955.77 PP

                   Cyclophil_like2  99 elaeal 104
                                       +l e +
  gi|330506425|ref|YP_004382853.1| 101 DLFERI 106
                                       776655 PP

>> DUF3830  Protein of unknown function (DUF3830)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.7e-07    0.0022      15      76 ..      18      72 ..       6     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.7e-07
                                      -TTTSHHHHHHHHHH--EEEE-EE-SSSSSEEEEEEE--SSS---S-SEESS--TTEEEEEE CS
                           DUF3830 15 ledkAPetcaavwealplssdviHakyagneiyvllpefaatelpaENaTvtPipGdvvlfs 76
                                      ++++ P   +a+w+alp+++ +i     g+e+y  l+     +l  EN+    + Gd++++s
  gi|330506425|ref|YP_004382853.1| 18 MDERNPIIREAIWQALPIEGRAI---LWGEEVYFDLDM----KLKDENPSASSEAGDICYWS 72
                                      478889999***********976...569*****9984....579***************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 923.00
//
Query:       gi|330506426|ref|YP_004382854.1|  [L=444]
Description: glutamine synthetase, type I [Methanosaeta concilii GP6]
Scores for complete 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-132  441.6   0.0   2.1e-132  441.4   0.0    1.1  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    2.3e-30  104.1   0.0    5.1e-30  103.0   0.0    1.6  1  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
    0.00092   19.0   0.0     0.0054   16.6   0.0    2.1  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 !  441.4   0.0  3.4e-136  2.1e-132       2     345 .]     108     440 ..     107     440 .. 0.98

  Alignments for each domain:
  == domain 1  score: 441.4 bits;  conditional E-value: 3.4e-136
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHH CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrrei 78 
                                       +dPR+vlkr l+r+++ G++++vgpElEFf f+ e++++                 ++ggyf+++++d+a+dlrr+ 
  gi|330506426|ref|YP_004382854.1| 108 GDPRNVLKRNLSRIKDDGYSFLVGPELEFFYFKGENNTD---------------VLDNGGYFDLTTADNATDLRRDT 169
                                       79*******************************988855...............4678******************* PP

                                       HHHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEE CS
                        Gln-synt_C  79 vealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlS 155
                                       + al+++gi+ve shhEva++Q+Ei+l+++dal++aD+v+t+K +vke+Ar++g++a+FmpKp++g+nGsgmHvh+S
  gi|330506426|ref|YP_004382854.1| 170 ILALDSMGIDVEYSHHEVAPSQHEIDLRYKDALSMADTVMTYKITVKEIARRYGYHASFMPKPIFGQNGSGMHVHQS 246
                                       ***************************************************************************** PP

                                       EEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-. CS
                        Gln-synt_C 156 lwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa. 231
                                       l+ + ++n+++d+++e +ls+ +r++i+Gll+ha+++ta+t+++vnSYkRlvpgyeaPv++aw+ rNRs l+R+p+ 
  gi|330506426|ref|YP_004382854.1| 247 LF-QGKRNVMFDPGNEFNLSDEGRYYIAGLLRHAPEITAVTNQWVNSYKRLVPGYEAPVYIAWARRNRSSLVRVPMy 322
                                       **.888*********************************************************************** PP

                                       ..TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHH CS
                        Gln-synt_C 232 ..skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAleal 304
                                         +ke a+rvE+R+pd++aNPYLa++++laAgl Gi nk++++ p e+d+y++++e+r  +gi++lP sl++A++  
  gi|330506426|ref|YP_004382854.1| 323 kpGKEAATRVEYRSPDPAANPYLAFSVMLAAGLAGIANKYDLPSPQEQDIYHMTDEQRakAGITSLPGSLNDAIHIT 399
                                       9999*****************************************************9999**************** PP

                                       HCSHHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 305 eedellkevlgeevieaylalkraEleeleeevsdwelery 345
                                       e+++l++e+lge+v++a++a kraE+++++++v++wel+ry
  gi|330506426|ref|YP_004382854.1| 400 EKSTLVREALGEHVFRAFIANKRAEWDAYRMNVTQWELNRY 440
                                       **************************************998 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.0   8.5e-34   5.1e-30       1      83 []      19     101 ..      19     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 8.5e-34
                                       T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-..EEEE CS
                        Gln-synt_N   1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek.ktarv 76 
                                       +v+fv+++FtDi g +k+++i+ +el + a++eg++FDGSsiegfa+i+eSDm+ kPd++t+ ++P+r+++ ++ar+
  gi|330506426|ref|YP_004382854.1|  19 NVRFVRIWFTDILGIPKSFAINPNEL-DGAFSEGMGFDGSSIEGFARIHESDMVAKPDPTTFQLIPWRQQEnAVARM 94 
                                       699***********************.******************************************999***** PP

                                       EEEEE-T CS
                        Gln-synt_N  77 icdvydp 83 
                                       +cd+ +p
  gi|330506426|ref|YP_004382854.1|  95 FCDIQNP 101
                                       ****876 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 !   16.6   0.0     9e-07    0.0054       2     107 .]       7     106 ..       6     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9e-07
                                       -........------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-GGGGG--TTS---TT-S-SSS--EEEEE CS
                      Gln-synt_N_2   2 adeavveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGltkatlalserdlidevedlgpvGelrLvp 78 
                                       ++e v e ++e +v++++  ++d  G+ +  a+   +L+  + +G+G+    ++++    i+e++ ++        p
  gi|330506426|ref|YP_004382854.1|   7 NKEEVFEAIDEFNVRFVRIWFTDILGIPKSFAINPNELDGAFSEGMGFDG--SSIEGFARIHESDMVA-------KP 74 
                                       568899*****************************************975..6778888899886554.......5* PP

                                       -GGG-EEE---SSTTS...EEEEEE-TTS-B- CS
                      Gln-synt_N_2  79 dPasavalpyaPdaaa...llgdlvevdgtPy 107
                                       dP+++  +p   +  a   ++ d+++ dgtPy
  gi|330506426|ref|YP_004382854.1|  75 DPTTFQLIPWRQQENAvarMFCDIQNPDGTPY 106
                                       ********97665433334************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3128.94
//
Query:       gi|330506427|ref|YP_004382855.1|  [L=372]
Description: glutamine amidotransferase, class-II [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-16   60.3   0.0    1.8e-14   53.3   0.0    2.0  1  GATase_2     Glutamine amidotransferases class-II
    7.6e-08   32.6   0.1    5.4e-07   29.9   0.0    2.3  3  GATase_6     Glutamine amidotransferase domain
    2.3e-05   24.3   0.0      0.027   14.4   0.0    2.6  2  GATase_7     Glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0     3e-18   1.8e-14      32     374 ..      20     345 ..      11     372 .] 0.81

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 3e-18
                                       S-B-TTSSSBSEEEEEEE--HHHHHHH.....HHHTT-----GGG-EEEEEEE-SSHHHHHHHHHHHHHHHHHTT-E CS
                          GATase_2  32 GavgadektGDGaGillqiPdeflrke.....akekgielpeageyavgmlflpkdeekaeeakkileeiveeegle 103
                                       Ga++ d +  + aG++ +i +  +r +     +++ gi  + ++ ya   +f  k  +++ +ak+++e+ +++  ++
  gi|330506427|ref|YP_004382855.1|  20 GAMNRDGERFNAAGVMKAIANMHVRGNglgggFAAYGIYPQYRDYYAFHLMFNGKTLQSQISAKAEFEQYLNQ-RFD 95 
                                       6777777777788888888777776552222245566777778899999999999999999999999999875.689 PP

                                       EEEEEE--B-GGGS-HHHHHH--EEEEEEEE-TT---HHHHHHHHHHHHHHHGGG.....-BTTBEEEEEESSEEEE CS
                          GATase_2 104 vlgwRevpvdksvlgeaakesePsieqvfvekkedlseeelerklyviRkriekeiakkkaekefYicslssrtivY 180
                                       v+   e+p   +    + ++  P i + f + k+  ++++l  + yv+R  ++++      +++ Yi s   +   +
  gi|330506427|ref|YP_004382855.1|  96 VVHDEEIPHRPQ----TQLRDPPLIWRYFASPKKMGEDASLSDDEYVVRTVMQTNS----RAEDAYIFSSGMNMGCF 164
                                       999999999875....678899**********999999***********9988875....589************** PP

                                       EESS-GGGHHHHBHGGGSTT--BSEEEEEE---SSSS--GGGSSS-SSE....EEEE--TTHHHHHHHHHHHCTT-- CS
                          GATase_2 181 kglltseqlkefykdlkdeelesalalvHsRfstntfPsWelaqPlRll....aHnGEintlrGnknwmkareaelk 253
                                       kg+  +e+++e++  + d+ ++++    H Rf tnt   W  a+P+ ll     HnGEi    G ++w         
  gi|330506427|ref|YP_004382855.1| 165 KGVGYPEEIGEYF--MLDQLYSAYAWTAHGRFPTNTQAWWGGAHPFSLLdtsvVHNGEISSY-GTNRWYL------- 231
                                       *************..57899999999********************87533338*****986.5556642....... PP

                                       BT-HH.HHHTC--S--TTS-HHHHHHHHHHHHHHTT--HHHHH.HHHS----TT-GGGTHHHHHHHHHHTTT---.. CS
                          GATase_2 254 sellgdelekllPivneegsDsasldnvlellvlsgrslaeal.mlliPeawennksldkekkafyeyasalmep.. 327
                                        e++g           + + D++ +  + +ll++  r ++e +  +l P+ w++ ++++++ k+++    ++  p  
  gi|330506427|ref|YP_004382855.1| 232 -EMYG--------YACTLQTDTEVIAYAADLLLRRQRIPMEIVaKILAPPIWNAIDTMNEKEKKLFTTLRMVYGPll 299
                                       .3333........2334568999**********999877776527999******************99999999944 PP

                                       --SSEEEEE.E-SSEEEEEE-TT--S--EEEEETT--EEEESSTTSS- CS
                          GATase_2 328 WDGPalivf.tdGkvvgavLDRnGLRPaRylvtkddlvvlasEvGvld 374
                                        +GP +i++ + G+ +g   DR  LRP     t+ ++++l+sE   + 
  gi|330506427|ref|YP_004382855.1| 300 MNGPFAIIIgQTGRLIGL-TDRIRLRPIT-AATRGEMFYLSSEEASIR 345
                                       59**88777256888886.5*******86.678999999999976555 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.66     4e+03      40      62 ..      65      88 ..      32     101 .. 0.67
   2 !   29.9   0.0     9e-11   5.4e-07       9      83 ..     182     259 ..     174     301 .. 0.82
   3 ?   -0.6   0.0      0.24   1.4e+03      98     134 .]     304     340 ..     298     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.66
                          GATase_6 40 grlllvhNGeiynyk.elreelpa 62
                                        + l++NG+  + + + ++e+++
  gi|330506427|ref|YP_004382855.1| 65 YAFHLMFNGKTLQSQiSAKAEFEQ 88
                                      456688899888877655555555 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 9e-11
                          GATase_6   9 lvedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.... 81 
                                       l+++ ++ aH R  ++  a   ga+Pf  +    ++vhNGei+ y++ r  l+   g+a+  ++Dtev++ ++    
  gi|330506427|ref|YP_004382855.1| 182 LYSAYAWTAHGRFPTNTQAWWGGAHPF--SLLDTSVVHNGEISSYGTNRWYLEM-YGYACTLQTDTEVIAYAAdlll 255
                                       556668889999999999999999***..99999************88888888.***************9885555 PP

                          GATase_6  82 ..ee 83 
                                         ++
  gi|330506427|ref|YP_004382855.1| 256 rrQR 259
                                       5544 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.24
                          GATase_6  98 faiwdkrentlilardrlgvkplyyavdesglafase 134
                                       fai+  ++++li ++dr+  +p + a+ ++ ++ +se
  gi|330506427|ref|YP_004382855.1| 304 FAIIIGQTGRLIGLTDRIRLRPITAATRGEMFYLSSE 340
                                       556666789999999***********99999999998 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   4.4e-06     0.027      14      61 ..     206     250 ..     198     268 .. 0.83
   2 !    7.0   0.0    0.0009       5.4      74     120 ..     300     343 ..     294     345 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.4e-06
                          GATase_7  14 QPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllal 61 
                                        P++     +  +v+nGei  y   r  Le  g++++ ++Dtev++ +
  gi|330506427|ref|YP_004382855.1| 206 HPFSL---LDTSVVHNGEISSYGTNRWYLEMYGYACTLQTDTEVIAYA 250
                                       55552...34679*******************************9544 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0009
                          GATase_7  74 lnGmfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelka 120
                                       +nG fA++i ++ +  l+   Dr+  +P+  +++ g+ ++++Se  +
  gi|330506427|ref|YP_004382855.1| 300 MNGPFAIIIGQTGR--LIGLTDRIRLRPITAATR-GEMFYLSSEEAS 343
                                       68999998877666..****************99.89******9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2566.24
//
Query:       gi|330506428|ref|YP_004382856.1|  [L=504]
Description: glutamate synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-140  468.8   0.1   1.9e-140  468.2   0.1    1.3  1  Glu_synthase     Conserved region in glutamate synthase
      6e-15   55.5   0.1    4.1e-07   29.8   0.1    2.3  2  Glu_syn_central  Glutamate synthase central domain
    6.5e-09   35.2   7.8    4.1e-07   29.3   5.0    2.3  2  IMPDH            IMP dehydrogenase / GMP reductase domain
    2.9e-07   29.9   7.6    5.8e-07   28.9   3.2    2.8  3  FMN_dh           FMN-dependent dehydrogenase
    1.8e-06   28.0  10.4    1.8e-06   28.0  10.4    2.4  2  Fer4_9           4Fe-4S dicluster domain
    1.5e-05   25.0  14.8    0.00038   20.5   0.6    3.4  3  Fer4_10          4Fe-4S dicluster domain
    1.8e-05   24.3   2.8    1.8e-05   24.3   2.8    3.5  3  Fer4             4Fe-4S binding domain
    0.00014   21.4   2.8    0.00032   20.2   2.8    1.5  1  NMO              Nitronate monooxygenase
    0.00017   22.5   0.5    0.00017   22.5   0.5    3.3  3  Fer4_16          4Fe-4S double cluster binding domain
    0.00036   20.6   8.8    0.00036   20.6   8.8    2.5  2  Fer4_21          4Fe-4S dicluster domain
     0.0022   18.5  22.9     0.0045   17.6  11.8    2.9  3  Fer4_7           4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   16.1   2.3      0.012   16.1   2.3    3.5  3  Fer4_4           4Fe-4S binding domain
      0.043   13.0   4.1       0.16   11.2   3.4    2.2  2  DHO_dh           Dihydroorotate dehydrogenase
      0.061   12.8   0.3       0.14   11.6   0.3    1.5  1  His_biosynth     Histidine biosynthesis protein
       0.22   11.6  24.9      0.039   14.0   4.4    3.5  3  Fer4_6           4Fe-4S binding domain
        1.9    9.0  19.0          4    8.0   2.9    3.3  3  Fer4_8           4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.2   0.1  1.7e-143  1.9e-140       4     368 .]     108     472 ..     105     472 .. 0.99

  Alignments for each domain:
  == domain 1  score: 468.2 bits;  conditional E-value: 1.7e-143
                                       -HHHHHHHHHHHHH---HHHHHHHHHHHTS.-S-SGGGGEEE--SS--.--GGGS--HHHHHTTEE---B-TTTS-H CS
                      Glu_synthase   4 eievikllqkavqveskesidkyrekleerevlkakrdlleldaaeealikleevepalkikkriltsamSyGalse 80 
                                       +i++++++ +a+qv +++sid +re++e r++l+ak+dl++++ ++e ++  +++ p+l ++ +i++samS+Ga+s 
  gi|330506428|ref|YP_004382856.1| 108 RIYWDHMVLNASQV-TNPSIDPLREPMELRTFLGAKPDLMDFKVKNEEVEIATQLSPNLMVEMPIVFSAMSFGAISY 183
                                       6899**********.******************************999999************************** PP

                                       HHHHHHHHHHHHHT-B-EETTS---GGGGS-----SEEEE-TT-TT--HHHHHH-SEEEEE---TTSTTS--EE-GG CS
                      Glu_synthase  81 eahealakamnrlgtksntGEGGedeerlktakdvaikQvasgrFGvteeyLnnakaleikiaQGakpgeGgqlpge 157
                                       +a  +la+a+++lgt +ntGEGG+++e +++  + ai+QvasgrFG+++eyLn a+a+eik++QGakpg+Gg+lpge
  gi|330506428|ref|YP_004382856.1| 184 NAFLSLATAASKLGTYFNTGEGGLPREMREKFGKHAIVQVASGRFGIDAEYLNCAAAVEIKVGQGAKPGIGGHLPGE 260
                                       ******************************999999***************************************** PP

                                       G--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-.TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEE CS
                      Glu_synthase 158 KvseeiakiRkikpgvdliSPaphhdiysiedlaqliedLkevn.keakvsvKlvaeagvetiaagvakanadiili 233
                                       Kvs +++++R+i+ g+d+iSPaphhdiysiedl++li+++ke++ +e++vsvK++a ++  +iaag+++a+adii+i
  gi|330506428|ref|YP_004382856.1| 261 KVSVSVSATRMIPVGTDAISPAPHHDIYSIEDLSMLIHAIKEATnYEKPVSVKIAAVHNFAAIAAGIVHAGADIIAI 337
                                       *******************************************99******************************** PP

                                       E-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHHHHT CS
                      Glu_synthase 234 dGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaalial 310
                                       dGl+GGTGA+pk++++++G+P+ela++  d++l++ g+r+r s+ia+Gg++++adv+ka+alGAda +ig+aalia+
  gi|330506428|ref|YP_004382856.1| 338 DGLRGGTGAAPKVIRDNVGIPIELAISSLDRRLRQDGIRNRCSIIAAGGIRCSADVIKAIALGADATYIGSAALIAM 414
                                       ***************************************************************************** PP

                                       T--S---GGGT--TTSSS---HHHH..TT----HHHHHHHHHHHHHHHHHHHHHHT-S CS
                      Glu_synthase 311 gCimarvChtntCpvGvatqdpeLrkrlkveekaervvnyikalaeevrellaalgin 368
                                       gC  +++C+t++C++G++tqdp+L  rl+v+ + +r+vn+i a+++e++e+l+ +gin
  gi|330506428|ref|YP_004382856.1| 415 GCNLCQKCYTGKCNWGICTQDPRLAGRLNVDIASQRLVNLISAWSHEIQEMLGGMGIN 472
                                       *******************************************************986 PP

>> Glu_syn_central  Glutamate synthase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0     3e-08   3.3e-05      49      91 ..     112     152 ..      76     197 .. 0.73
   2 !   29.8   0.1   3.7e-10   4.1e-07     134     270 ..     314     480 ..     268     489 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3e-08
                                       GGEEE----SSS----TTTTGGG-B--EEES----SSS--GGG CS
                   Glu_syn_central  49 dYFkqlfAqVTNPpiDpiREelvmsletllGkegnlleeeeeq 91 
                                       d++  + +qVTNP+iDp+RE   m l+t+lG++++l++ + ++
  gi|330506428|ref|YP_004382856.1| 112 DHMVLNASQVTNPSIDPLREP--MELRTFLGAKPDLMDFKVKN 152
                                       45555679************6..89***********9944322 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 3.7e-10
                                       HHHHHHHHHHHHHHHHTT-SEEEEESS........--STTEEE--HHHHHHHHHHHHHHTT-GGG-EEEEEESS--S CS
                   Glu_syn_central 134 eealerlceeaeeavregaeilvLsDr........kvseervpipslLavgavhhhLvrkglrtkvslvvesgeare 202
                                        +a+++ ++ a+  v++ga+i+ ++          kv +++v ip  La+++++++L + g r+++s++  +g +r 
  gi|330506428|ref|YP_004382856.1| 314 IAAVHNFAAIAAGIVHAGADIIAIDGLrggtgaapKVIRDNVGIPIELAISSLDRRLRQDGIRNRCSIIA-AGGIRC 389
                                       467777788888888899999998876677777777889****************************986.677999 PP

                                       HHHHHHHHHTT-SEEEEHHHHHHH..HHHHTTT..............S-.......----HHHHHHHHHHHHHHHHH CS
                   Glu_syn_central 203 vhhfavllgyGadavnPylaleti..eklveeg..............al.......aeeeleknyrkavekGllKim 256
                                         +++  +++Gada +   a  ++   +l+++               +l        +++   n+++a ++ +   +
  gi|330506428|ref|YP_004382856.1| 390 SADVIKAIALGADATYIGSAALIAmgCNLCQKCytgkcnwgictqdpRLagrlnvdIASQRLVNLISAWSHEIQEML 466
                                       99*********9997644333333333444443455555555555551144444332333349************** PP

                                       HHTT--BHHHHHHS CS
                   Glu_syn_central 257 skmGistlqSYkga 270
                                         mGi  l+S +g 
  gi|330506428|ref|YP_004382856.1| 467 GGMGINALESLRGN 480
                                       **********9986 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0     0.004       4.5      15      43 ..     149     177 ..     142     193 .. 0.90
   2 !   29.3   5.0   3.6e-10   4.1e-07     136     238 ..     297     409 ..     268     416 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.004
                                       -S-GGGSB--EESSTTEEESSSEEE-SST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  15 evlpkevdlktkltkkiklniPlvsaamd 43 
                                       +v+ +ev+++t+l+ ++ +++P+v +am 
  gi|330506428|ref|YP_004382856.1| 149 KVKNEEVEIATQLSPNLMVEMPIVFSAMS 177
                                       67889**********************96 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 3.6e-10
                                       HHHHHHHTT..T.SEEEEEEE-SHHH.HHHHHHTT-SEEEE.-SS-STTBHHHHHC.SB---HHHHHHHHHHHHCTC CS
                                       xxxxxxxxx..x.xxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 136 vkeikkkve..e.veviaGnvataeg.akaLieagadavkv.GiGpGsiCttrvva.gvGvpqltAvaevaeaakka 206
                                       +++ik++++  + v+v    v + ++ a+ +++agad++ + G+  G     +v+   vG+p   A+++  +  ++ 
  gi|330506428|ref|YP_004382856.1| 297 IHAIKEATNyeKpVSVKIAAVHNFAAiAAGIVHAGADIIAIdGLRGGTGAAPKVIRdNVGIPIELAISSLDRRLRQD 373
                                       44444443311225554444444444156689********989988888888887538*****************99 PP

                                       T....-EEEEES---SHHHHHHHHHTT-SEEEESCC CS
                                       x....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 207 g....vpviaDGGikysgdivkAlaaGadavmlGsl 238
                                       g      +ia GGi+ s d++kA+a+Gada  +Gs 
  gi|330506428|ref|YP_004382856.1| 374 GirnrCSIIAAGGIRCSADVIKAIALGADATYIGSA 409
                                       9555568***************************85 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.14   1.5e+02      57      91 ..     167     200 ..     149     206 .. 0.84
   2 !   28.9   3.2   5.2e-10   5.8e-07     266     308 ..     373     415 ..     324     418 .. 0.87
   3 ?   -0.4   0.0      0.42   4.7e+02     315     342 ..     451     478 ..     447     485 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.14
                                       ESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-E CS
                            FMN_dh  57 lslPvliaPvglaklahpdgelalaraaakagipf 91 
                                       +++P++++++++  +   ++ l la aa+k+g+ f
  gi|330506428|ref|YP_004382856.1| 167 VEMPIVFSAMSFGAISY-NAFLSLATAASKLGTYF 200
                                       79**********98887.999**********9977 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 5.2e-10
                                       HHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHH CS
                            FMN_dh 266 eavggrievlvDgGirrGsDvlkAlalGAdavllGRpflygla 308
                                       + +++r+ +++ gGir  +Dv+kA+alGAda  +G ++l ++ 
  gi|330506428|ref|YP_004382856.1| 373 DGIRNRCSIIAAGGIRCSADVIKAIALGADATYIGSAALIAMG 415
                                       456789*******************************999876 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHHHHHHHT-SBHHHHH CS
                            FMN_dh 315 vervleilraelertmallGvksvaeld 342
                                       + ++++ +++e+++ +  +G++ +++l+
  gi|330506428|ref|YP_004382856.1| 451 LVNLISAWSHEIQEMLGGMGINALESLR 478
                                       5678999****************99985 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0  10.4   1.6e-09   1.8e-06       1      51 []      17      64 ..      17      64 .. 0.93
   2 ?    3.8   1.5     0.058        65       2      17 ..     416     432 ..     388     448 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.6e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC +C+ C+++C +g++++d +      +    ++C+gC++C+  Cp++ai
  gi|330506428|ref|YP_004382856.1| 17 KCGQCRGCERQCAFGTHTYDPVSDRLISDD---NKCVGCQRCAIFCPRDAI 64
                                      7*********************99999865...48*************997 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.058
                            Fer4_9   2 CtgCgaCvea.Cpagvv 17 
                                       C+ C++C +  C+ g++
  gi|330506428|ref|YP_004382856.1| 416 CNLCQKCYTGkCNWGIC 432
                                       66777774333665555 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   1.3   0.00097       1.1       2      19 ..      11      28 ..      10      39 .. 0.87
   2 !   20.5   0.6   3.4e-07   0.00038       3      24 ..      43      80 ..      41     103 .. 0.68
   3 ?    3.2   0.6     0.084        95       8      19 ..     415     427 ..     409     461 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00097
                           Fer4_10  2 vvidddtCirCgkCvkaC 19
                                      +++d+ +C +C+ C + C
  gi|330506428|ref|YP_004382856.1| 11 IIRDEAKCGQCRGCERQC 28
                                      688999************ PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.4e-07
                           Fer4_10  3 vidddtCirCgkCvkaCPadl................t 24
                                      + dd++C++C++C  +CP d+                +
  gi|330506428|ref|YP_004382856.1| 43 ISDDNKCVGCQRCAIFCPRDAivvrpnpsfyrpnaswS 80
                                      789***************98877777777777666663 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.084
                           Fer4_10   8 tCirCgkCvka.C 19 
                                        C  C+kC +  C
  gi|330506428|ref|YP_004382856.1| 415 GCNLCQKCYTGkC 427
                                       5888999988557 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   2.9     0.017        19       2      18 ..      12      28 ..      11      30 .. 0.92
   2 !   24.3   2.8   1.6e-08   1.8e-05       4      23 ..      45      64 ..      42      65 .. 0.93
   3 ?   -0.9   1.7       1.5   1.7e+03       8      14 ..     416     422 ..     414     424 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.017
                                      EEETTTSSS-THHHHHS CS
                              Fer4  2 videekCigCGaCvevC 18
                                      + de kC  C  C+  C
  gi|330506428|ref|YP_004382856.1| 12 IRDEAKCGQCRGCERQC 28
                                      679***********999 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 1.6e-08
                                      ETTTSSS-THHHHHSTTTEE CS
                              Fer4  4 deekCigCGaCvevCPvgAI 23
                                      d +kC+gC +C+  CP +AI
  gi|330506428|ref|YP_004382856.1| 45 DDNKCVGCQRCAIFCPRDAI 64
                                      889****************9 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.5
                                       SSS-THH CS
                              Fer4   8 CigCGaC 14 
                                       C  C +C
  gi|330506428|ref|YP_004382856.1| 416 CNLCQKC 422
                                       6666666 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   2.8   2.9e-07   0.00032     141     232 ..     312     417 ..     295     422 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-07
                               NMO 141 ptissvkeark....vearGaDalivqGpeaG.GhqGtpevgdkglfaLvpqvldavd...........iPviAaGG 201
                                       + i++v++  +    + ++GaD++ ++G  +G G    p+v   +    ++ + + +d             +iAaGG
  gi|330506428|ref|YP_004382856.1| 312 VKIAAVHNFAAiaagIVHAGADIIAIDGLRGGtGAA--PKVIRDNVGIPIELAISSLDrrlrqdgirnrCSIIAAGG 386
                                       555555554430001446789999999988773333..455444444445556666666777888889999****** PP

                               NMO 202 iidrrgvaaaLalGAsgvqigtrfLltkesd 232
                                       i    +v  a+alGA + +ig++ L++  ++
  gi|330506428|ref|YP_004382856.1| 387 IRCSADVIKAIALGADATYIGSAALIAMGCN 417
                                       *************************998776 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.0      0.11   1.3e+02       1      13 [.      17      29 ..      17      40 .. 0.86
   2 !   22.5   0.5   1.5e-07   0.00017       1      58 [.      48     102 ..      48     103 .. 0.74
   3 ?    0.8   0.4      0.89     1e+03      55      62 ..     414     421 ..     390     430 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.11
                           Fer4_16  1 rCgtCgkCaevCP 13
                                      +Cg+C+ C   C 
  gi|330506428|ref|YP_004382856.1| 17 KCGQCRGCERQCA 29
                                      5********9996 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.5e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCd 58 
                                       +C++C++Ca  CP +ai  + ++++  r + s++ ++ +d+++++e+      +tgC+
  gi|330506428|ref|YP_004382856.1|  48 KCVGCQRCAIFCPRDAIVVRPNPSFY-RPNASWSREKLEDVKKQAETGG--VILTGCG 102
                                       5*****************99888876.5555775666677766666544..4458887 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.89
                           Fer4_16  55 tgCdiCqd 62 
                                       +gC+ Cq+
  gi|330506428|ref|YP_004382856.1| 414 MGCNLCQK 421
                                       56666664 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   8.8   3.3e-07   0.00036       4      57 ..      14      64 ..      11      66 .. 0.78
   2 ?    2.1   3.2       0.2   2.2e+02      16      49 ..     387     421 ..     376     427 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.3e-07
                           Fer4_21  4 dedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                      de+kC +C  C   C  ++h+   + ++ +l   +++CvGC+ C++ CP  d+i
  gi|330506428|ref|YP_004382856.1| 14 DEAKCGQCRGCERQCAFGTHTYDPV-SD-RLISDDNKCVGCQRCAIFCP-RDAI 64
                                      799*************766654333.33.3446789*************.6887 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.2
                           Fer4_21  16 iaCedtshqaieid.aktvlkvvedeCvGCnlCss 49 
                                       i C+   ++ai +  ++t++   +   +GCnlC +
  gi|330506428|ref|YP_004382856.1| 387 IRCSADVIKAIALGaDATYIGSAALIAMGCNLCQK 421
                                       56888888888654155667777778899999975 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  11.8     4e-06    0.0045       1      52 []      17      63 ..      17      63 .. 0.93
   2 !   14.9   3.2   2.7e-05      0.03       1      21 [.      48      68 ..      48      94 .. 0.81
   3 ?    1.8   1.9      0.33   3.6e+02      29      51 ..     407     430 ..     387     432 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4e-06
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C +C+ C++ C  ++ ++d++      +++  d +kC+gC++C+  CP +a
  gi|330506428|ref|YP_004382856.1| 17 KCGQCRGCERQCAFGTHTYDPV-----SDRLISDDNKCVGCQRCAIFCPRDA 63
                                      7********************9.....4578999***************987 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.7e-05
                            Fer4_7  1 rCigCgaCvaaCpvkaielde 21
                                      +C+gC++C+  Cp +ai +++
  gi|330506428|ref|YP_004382856.1| 48 KCVGCQRCAIFCPRDAIVVRP 68
                                      7*************9998875 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.33
                            Fer4_7  29 ekveidpekClgCgaCva.vCPtg 51 
                                        ++++ ++ C  C++C +  C +g
  gi|330506428|ref|YP_004382856.1| 407 GSAALIAMGCNLCQKCYTgKCNWG 430
                                       555667788999999987567776 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   4.9      0.31   3.4e+02       3      15 ..      17      29 ..      15      31 .. 0.82
   2 ?   16.1   2.3   1.1e-05     0.012       2      16 ..      47      61 ..      46      71 .. 0.92
   3 ?    0.2   3.7       1.2   1.4e+03       4      12 ..     416     424 ..     413     428 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.31
                            Fer4_4  3 rCigCgsCvaaCP 15
                                      +C +C+ C++ C 
  gi|330506428|ref|YP_004382856.1| 17 KCGQCRGCERQCA 29
                                      6889999*****5 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.1e-05
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++C+gC +C ++CP 
  gi|330506428|ref|YP_004382856.1| 47 NKCVGCQRCAIFCPR 61
                                      69************5 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.2
                            Fer4_4   4 CigCgsCva 12 
                                       C+ C +C+ 
  gi|330506428|ref|YP_004382856.1| 416 CNLCQKCYT 424
                                       9******95 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.6   2.9e+03      51      83 ..     102     132 ..     100     169 .. 0.67
   2 ?   11.2   3.4   0.00014      0.16     241     285 ..     375     420 ..     284     425 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.6
                                       -S-S--EEEETTCTEEEE---S-BS-HHHHHHH CS
                            DHO_dh  51 GnpkPrvfrlkedrsvlNslGlnneGldavlek 83 
                                       Gn+kP  fr++ d+ vlN+  + n+ +d + e 
  gi|330506428|ref|YP_004382856.1| 102 GNDKP--FRIYWDHMVLNASQVTNPSIDPLREP 132
                                       66666..66677777777777777766655544 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00014
                                       TTT.S-EEEESS--SHHHHHHHHHHTECEEEESHH.HHHHGTCHHH CS
                            DHO_dh 241 lkkeipiIgvGGiesgeDalekieaGAslvqvyta.lvfegpkiak 285
                                       ++++  iI+ GGi  + D++  i  GA +  +++a l+  g  +++
  gi|330506428|ref|YP_004382856.1| 375 IRNRCSIIAAGGIRCSADVIKAIALGADATYIGSAaLIAMGCNLCQ 420
                                       567899***************************9724555666665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00012      0.14     192     223 ..     379     410 ..     370     415 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                       SEEEEESS--SHHHHHHHHHTTCSEEEESHHH CS
                      His_biosynth 192 ipviasGGvgsledlkelksegvdavivgsal 223
                                        ++ia+GG++  +d+ ++ + g+da  +gsa 
  gi|330506428|ref|YP_004382856.1| 379 CSIIAAGGIRCSADVIKAIALGADATYIGSAA 410
                                       45667777777777777777777666666664 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.0   0.00079      0.89       5      22 ..      14      31 ..      11      32 .. 0.89
   2 ?   14.0   4.4   3.5e-05     0.039       5      24 .]      45      64 ..      44      64 .. 0.95
   3 ?   -1.5   3.2       2.7   3.1e+03       9      17 ..     416     424 ..     416     430 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00079
                            Fer4_6  5 dpdkCigCgdCvrvCPeg 22
                                      d+ kC +C+ C+r C +g
  gi|330506428|ref|YP_004382856.1| 14 DEAKCGQCRGCERQCAFG 31
                                      99*************875 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.5e-05
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      d++kC+gC +C++ CP +ai
  gi|330506428|ref|YP_004382856.1| 45 DDNKCVGCQRCAIFCPRDAI 64
                                      89**************9997 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.7
                            Fer4_6   9 CigCgdCvr 17 
                                       C+ C +C++
  gi|330506428|ref|YP_004382856.1| 416 CNLCQKCYT 424
                                       888888886 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  13.9     0.057        64       4      63 ..      17      61 ..      14      63 .. 0.79
   2 ?    8.0   2.9    0.0036         4       4      63 ..      48      61 ..      45     102 .. 0.61
   3 ?    3.9   0.2     0.067        76       4      15 ..     415     427 ..     392     462 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.057
                            Fer4_8  4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      kC++C  C+ +C     ++ h +d+  ++      ++        ++C++c++C+  Cp 
  gi|330506428|ref|YP_004382856.1| 17 KCGQCRGCERQCA----FGTHTYDPVSDRLI----SDD-------NKCVGCQRCAIFCPR 61
                                      8***********6....55556777777666....444.......69************7 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0036
                            Fer4_8  4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      kC++C++C   Cp                                               
  gi|330506428|ref|YP_004382856.1| 48 KCVGCQRCAIFCP----------------------------------------------R 61
                                      5666666666665..............................................3 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.067
                            Fer4_8   4 kCieCgaCq.saC 15 
                                        C+ C+ C   +C
  gi|330506428|ref|YP_004382856.1| 415 GCNLCQKCYtGKC 427
                                       3555555543334 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3459.26
//
Query:       gi|330506429|ref|YP_004382857.1|  [L=272]
Description: glutamate synthase subunit alpha domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (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  119.5   3.6    1.7e-34  119.1   3.6    1.1  1  GXGXG     GXGXG motif


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   3.6   9.3e-39   1.7e-34      12     185 ..      52     223 ..      33     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 9.3e-39
                                       HHHHHHHHHHHTTT---....-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--TT-SS-G CS
                             GXGXG  12 tilsneiakrygeeglpe...dtikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpskeskfka 85 
                                        i+ n++++ry+ + l +   ++++i++ G++G++l+afl  G +l ++G+a+d vG+++++G+ivi++ +      
  gi|330506429|ref|YP_004382857.1|  52 VIIRNVCGQRYIGTRLYSperHRMEIDIFGTPGNDLAAFL-FGHRLVVHGNAQDGVGNTMDDGEIVIEGRA------ 121
                                       48999********99954333899****************.9*****************************...... PP

                                       GGSB-S-SSTTTT--SEEEEESSB--SSTTTT-.....SS-EEEESEB.-SSTTTT-EEEEEEE-S-B.....-SSB CS
                             GXGXG  86 eeniivGnvvlygatgGklfirgkageRfavrn.....sgatavvegv.gdhgceYmtGGvvvvLgkt.....grnf 151
                                             G+v+ ++++gG++++r+  g+R+a ++     +++ +v++g+  d+++eYm+GG+v++L  +     ++ +
  gi|330506429|ref|YP_004382857.1| 122 ------GDVLGFSMRGGTIYVRDGCGYRTALHMkeyegKKPALVIGGTaQDFLGEYMAGGTVILLDLKgqghrANFI 192
                                       ......***************************9999999********99***************988555545678 PP

                                       TTT--EEEEEEE-SSSTHHHHB-TTT-EEEES-S CS
                             GXGXG 152 aaGmsgGiayvldedekfekklnkelvelekved 185
                                       ++Gm+gG++y++ + ++   +   e ve++ +++
  gi|330506429|ref|YP_004382857.1| 193 GSGMHGGTIYLRGSVNR---SQVSEQVEISPIDE 223
                                       ***********955544...34455566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1994.09
//
Query:       gi|330506430|ref|YP_004382858.1|  [L=145]
Description: 4Fe-4S binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   47.1  36.6    2.9e-06   27.1   1.2    4.3  4  Fer4_6    4Fe-4S binding domain
    2.5e-12   46.0  35.1    8.6e-08   31.7   1.5    5.7  6  Fer4      4Fe-4S binding domain
    1.3e-10   41.6  31.1    2.3e-05   24.9  14.2    3.5  3  Fer4_7    4Fe-4S dicluster domain
    2.3e-08   33.6  36.5    3.3e-06   26.8   1.6    4.5  4  Fer4_2    4Fe-4S binding domain
    4.8e-08   33.0  16.4    4.8e-08   33.0  16.4    1.9  2  Fer4_11   4Fe-4S dicluster domain
    1.4e-07   31.5  30.2     0.0037   17.4  11.0    3.4  4  Fer4_9    4Fe-4S dicluster domain
    0.00017   22.4  32.2      0.029   15.3   2.0    4.6  5  Fer4_16   4Fe-4S double cluster binding domain
    0.00046   20.3  35.6     0.0019   18.3  12.1    3.6  4  Fer4_10   4Fe-4S dicluster domain
    0.00057   20.6  15.3      0.069   13.9   0.6    3.2  2  Fer4_15   4Fe-4S single cluster domain
    0.00057   20.2  39.4     0.0032   17.8   2.5    4.6  4  Fer4_4    4Fe-4S binding domain
     0.0033   17.5  35.0     0.0056   16.8  12.7    3.5  3  Fer4_21   4Fe-4S dicluster domain
     0.0064   17.0   1.0     0.0064   17.0   1.0    4.2  4  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.013   16.4  47.2      0.015   16.2   5.1    4.3  4  Fer4_3    4Fe-4S binding domain
        0.1   13.4   1.4        0.1   13.4   1.4    3.9  4  Fer4_22   4Fe-4S dicluster domain
       0.17   12.4  36.2        1.3    9.5  11.6    4.1  2  Fer4_8    4Fe-4S dicluster domain
       0.19   12.3   1.0       0.19   12.3   1.0    3.6  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   4.4   1.8e-06     0.002       2      19 ..       3      20 ..       2      24 .. 0.94
   2 !    7.6   6.0    0.0037       4.1       9      24 .]      45      62 ..      42      62 .. 0.93
   3 !   27.1   1.2   2.6e-09   2.9e-06       3      23 ..      70      90 ..      68      91 .. 0.93
   4 !   11.9   2.2   0.00017      0.19       7      24 .]      98     120 ..      96     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-06
                            Fer4_6  2 veidpdkCigCgdCvrvC 19
                                      v +d ++CigC+ C+++C
  gi|330506430|ref|YP_004382858.1|  3 VYVDISRCIGCRSCEVAC 20
                                      789*************** PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0037
                            Fer4_6  9 CigCgd..CvrvCPegai 24
                                      C +C+d  C++vC +ga+
  gi|330506430|ref|YP_004382858.1| 45 CHHCEDacCTMVCSTGAL 62
                                      9***99999*******97 PP

  == domain 3  score: 27.1 bits;  conditional E-value: 2.6e-09
                            Fer4_6  3 eidpdkCigCgdCvrvCPega 23
                                      ++d dkC+gCg C  +CP+g+
  gi|330506430|ref|YP_004382858.1| 70 AFDVDKCTGCGLCQLACPFGV 90
                                      69****************997 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00017
                            Fer4_6   7 dkCigC.gd....CvrvCPegai 24 
                                        kC+ C g     Cv+ CP++a+
  gi|330506430|ref|YP_004382858.1|  98 HKCDLCsGQemptCVMTCPANAL 120
                                       59****8889***********97 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   4.5   1.9e-06    0.0022       1      18 [.       3      20 ..       3      22 .. 0.94
   2 ?    3.7   1.1     0.054        61       9      18 ..      43      52 ..      43      52 .. 0.92
   3 ?    3.1   0.0     0.082        92      14      23 ..      53      62 ..      53      63 .. 0.92
   4 !   31.7   1.5   7.7e-11   8.6e-08       3      23 ..      71      91 ..      69      92 .. 0.91
   5 ?   -1.0   0.2       1.6   1.8e+03       7      11 ..      99     103 ..      96     104 .. 0.68
   6 !    9.8   0.3   0.00063      0.71      13      23 ..     110     120 ..     110     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.9e-06
                                      EEEETTTSSS-THHHHHS CS
                              Fer4  1 vvideekCigCGaCvevC 18
                                      v++d ++CigC  C+ +C
  gi|330506430|ref|YP_004382858.1|  3 VYVDISRCIGCRSCEVAC 20
                                      689*************** PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.054
                                      SS-THHHHHS CS
                              Fer4  9 igCGaCvevC 18
                                      ++C  C+++C
  gi|330506430|ref|YP_004382858.1| 43 VFCHHCEDAC 52
                                      68******** PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.082
                                      HHHHSTTTEE CS
                              Fer4 14 CvevCPvgAI 23
                                      C +vC +gA+
  gi|330506430|ref|YP_004382858.1| 53 CTMVCSTGAL 62
                                      99******97 PP

  == domain 4  score: 31.7 bits;  conditional E-value: 7.7e-11
                                      EETTTSSS-THHHHHSTTTEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAI 23
                                      +d +kC+gCG+C  +CP+g+ 
  gi|330506430|ref|YP_004382858.1| 71 FDVDKCTGCGLCQLACPFGVV 91
                                      799***************986 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 1.6
                                       TSSS- CS
                              Fer4   7 kCigC 11 
                                       kC  C
  gi|330506430|ref|YP_004382858.1|  99 KCDLC 103
                                       66666 PP

  == domain 6  score: 9.8 bits;  conditional E-value: 0.00063
                                       HHHHHSTTTEE CS
                              Fer4  13 aCvevCPvgAI 23 
                                       +Cv+ CP +A+
  gi|330506430|ref|YP_004382858.1| 110 TCVMTCPANAL 120
                                       5*********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 !    9.7  18.0    0.0011       1.3       1      52 []       9      61 ..       9      61 .. 0.78
   2 !   24.9  14.2     2e-08   2.3e-05       5      52 .]      45      90 ..      43      90 .. 0.88
   3 !   12.1   0.3    0.0002      0.22       1      23 [.      99     126 ..      99     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga..CvavCPtga 52
                                      rCigC+ C++aC  ++   + + n   + +++ +p  C +C+   C  vC tga
  gi|330506430|ref|YP_004382858.1|  9 RCIGCRSCEVACD-RVHGGKGHVNVHFVGSLASVPVFCHHCEDacCTMVCSTGA 61
                                      8***********9.3333333333334479999********9889*******97 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 2e-08
                            Fer4_7  5 CgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C+ C++aC + + ++     +k+ +k+++d +kC+gCg C+ +CP+g+
  gi|330506430|ref|YP_004382858.1| 45 CHHCEDACCTMVCSTGAL--HKEGDKTAFDVDKCTGCGLCQLACPFGV 90
                                      999999999999998887..456699********************96 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.0002
                            Fer4_7   1 rCigCg.....aCvaaCpvkaieldeee 23 
                                       +C  C       Cv +Cp++a++ld + 
  gi|330506430|ref|YP_004382858.1|  99 KCDLCSgqempTCVMTCPANALSLDFDL 126
                                       688886666779**********999653 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   3.5   4.1e-06    0.0046       2      20 ..       2      20 ..       1      20 [. 0.94
   2 ?   -0.9   6.4         2   2.3e+03      10      20 ..      45      57 ..      43      59 .. 0.64
   3 !   26.8   1.6     3e-09   3.3e-06       4      21 ..      70      87 ..      67      88 .. 0.92
   4 !    8.2   2.2    0.0026       2.9       9      22 .]      99     117 ..      93     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.1e-06
                            Fer4_2  2 pvvvdtdrCigCgaCvsaC 20
                                      pv+vd  rCigC++C  aC
  gi|330506430|ref|YP_004382858.1|  2 PVYVDISRCIGCRSCEVAC 20
                                      689999***********9* PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                            Fer4_2 10 CigCg..aCvsaC 20
                                      C +C+   C+ +C
  gi|330506430|ref|YP_004382858.1| 45 CHHCEdaCCTMVC 57
                                      4466555678887 PP

  == domain 3  score: 26.8 bits;  conditional E-value: 3e-09
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      ++d d+C+gCg C+ aCP
  gi|330506430|ref|YP_004382858.1| 70 AFDVDKCTGCGLCQLACP 87
                                      79**************** PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0026
                            Fer4_2   9 rCigCg.....aCvsaCPa 22 
                                       +C  C+     +Cv  CPa
  gi|330506430|ref|YP_004382858.1|  99 KCDLCSgqempTCVMTCPA 117
                                       79999778999*******8 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.3      0.83   9.3e+02      69      84 ..      14      29 ..       5      39 .. 0.72
   2 !   33.0  16.4   4.3e-11   4.8e-08       6      97 ..      41     122 ..      36     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.83
                           Fer4_11 69 ekCdmcldrveaGllp 84
                                      + C++  drv+ G+  
  gi|330506430|ref|YP_004382858.1| 14 RSCEVACDRVHGGKGH 29
                                      5677778888877655 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 4.3e-11
                           Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGl 82 
                                       +p  C+hC+++ C +++ ++a++k+ +     +d +++  ++  ++ acP+ +vr+++    ++kCd+c  +     
  gi|330506430|ref|YP_004382858.1|  41 VPVFCHHCEDACCTMVCSTGALHKEGDKT--AFDVDKCT-GCGLCQLACPFGVVRTDKI---AHKCDLCSGQEM--- 108
                                       7899********************99665..57778887.99*************9865...56*****98765... PP

                           Fer4_11  83 lpacvescptgalnf 97 
                                        p+cv +cp++al++
  gi|330506430|ref|YP_004382858.1| 109 -PTCVMTCPANALSL 122
                                       .*********99875 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0  13.1   3.7e-05     0.041       1      50 [.       9      61 ..       9      62 .. 0.74
   2 !   16.1  15.6   8.5e-06    0.0096       5      49 ..      45      89 ..      43      91 .. 0.86
   3 !   17.4  11.0   3.3e-06    0.0037       1      50 [.      75     119 ..      75     120 .. 0.86
   4 !    7.5   1.5     0.004       4.5       1      20 [.      99     123 ..      99     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                            Fer4_9  1 kCtgCgaCveaC.....pagvvvedaaerkarlraaseeaCigCga..CveaCpkga 50
                                      +C+gC++C+ aC      +g+v+ + ++  a++       C++C++  C+ +C +ga
  gi|330506430|ref|YP_004382858.1|  9 RCIGCRSCEVACdrvhgGKGHVNVHFVGSLASVPV----FCHHCEDacCTMVCSTGA 61
                                      6***********66655445555555555555544....5*************9987 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 8.5e-06
                            Fer4_9  5 CgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                      C+ C++aC ++v++  a +++   +a++ ++C+gCg C  aCp g
  gi|330506430|ref|YP_004382858.1| 45 CHHCEDACCTMVCSTGALHKEGDKTAFDVDKCTGCGLCQLACPFG 89
                                      9999999999999988888888888888899************87 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 3.3e-06
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.....CveaCpkga 50 
                                       kCtgCg C+ aCp+gvv+ d+ + k          C  C       Cv  Cp +a
  gi|330506430|ref|YP_004382858.1|  75 KCTGCGLCQLACPFGVVRTDKIAHK----------CDLCSGqemptCVMTCPANA 119
                                       7****************99988777..........77777668888999999886 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.004
                            Fer4_9   1 kCtgC.....gaCveaCpagvvved 20 
                                       kC  C      +Cv  Cpa++ + d
  gi|330506430|ref|YP_004382858.1|  99 KCDLCsgqemPTCVMTCPANALSLD 123
                                       6888854443349999999988655 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.0     0.037        41       1      12 [.       9      20 ..       6      23 .. 0.79
   2 ?    6.3   7.5     0.017        19       1      30 [.      44      76 ..      44      77 .. 0.82
   3 !   15.3   2.0   2.6e-05     0.029      51      66 ..      73      88 ..      64      89 .. 0.79
   4 !   10.1   6.6    0.0011       1.2       2      20 ..      76      94 ..      75     106 .. 0.71
   5 !   10.5   0.7   0.00084      0.94       7      31 ..     110     132 ..      99     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.037
                           Fer4_16  1 rCgtCgkCaevC 12
                                      rC++C+ C  +C
  gi|330506430|ref|YP_004382858.1|  9 RCIGCRSCEVAC 20
                                      588888888888 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.017
                           Fer4_16  1 rCgtCgk..CaevCPtnaikek.kekeiearec 30
                                      +C+ C+   C++vC t+a++++  ++ ++ ++c
  gi|330506430|ref|YP_004382858.1| 44 FCHHCEDacCTMVCSTGALHKEgDKTAFDVDKC 76
                                      6****9999**********99855566676666 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 2.6e-05
                           Fer4_16 51 qeaitgCdiCqdvCPa 66
                                        ++tgC+ Cq +CP+
  gi|330506430|ref|YP_004382858.1| 73 VDKCTGCGLCQLACPF 88
                                      5789***********9 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0011
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++Cg C  +CP ++++++
  gi|330506430|ref|YP_004382858.1| 76 CTGCGLCQLACPFGVVRTD 94
                                      7777777777777776666 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.00084
                           Fer4_16   7 kCaevCPtnaikekkekeieareci 31 
                                        C+++CP+na++ +  + +++r+  
  gi|330506430|ref|YP_004382858.1| 110 TCVMTCPANALSLD--FDLASRRAR 132
                                       5***********99..777666654 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0  16.9       0.2   2.2e+02       3      55 ..       4      57 ..       2      58 .. 0.65
   2 !   11.1  16.2    0.0003      0.33       8      56 .]      44      87 ..      39      87 .. 0.81
   3 !   18.3  12.1   1.7e-06    0.0019       4      56 .]      71     116 ..      68     116 .. 0.76
   4 !    6.3   2.1    0.0093        10       8      21 ..      99     117 ..      91     142 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.2
                           Fer4_10  3 vidddtCirCgkCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcg..aCveaC 55
                                      ++d ++Ci+C+ C  aC  d  ++ ++       +    ++  C++c+   C+ +C
  gi|330506430|ref|YP_004382858.1|  4 YVDISRCIGCRSCEVAC--DRvHGGKGHVNVHFVGSLASVPVFCHHCEdaCCTMVC 57
                                      67889************..5544444444444455555566677777554666666 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0003
                           Fer4_10  8 tCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       C +C+   C+ +C       ++ +  +e+++   +v+kCtgcg C+ aCP
  gi|330506430|ref|YP_004382858.1| 44 FCHHCEdaCCTMVC-------STGALHKEGDKTAFDVDKCTGCGLCQLACP 87
                                      47777764455567.......578889999999999**************9 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.7e-06
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg.....aCveaCP 56 
                                       +d d+C++Cg C+ aCP+            +  + +k   kC+ c       Cv  CP
  gi|330506430|ref|YP_004382858.1|  71 FDVDKCTGCGLCQLACPF------------GVVRTDKIAHKCDLCSgqempTCVMTCP 116
                                       799***************............445555555566666444477******9 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0093
                           Fer4_10   8 tCirCg.....kCvkaCPa 21 
                                       +C  C      +Cv  CPa
  gi|330506430|ref|YP_004382858.1|  99 KCDLCSgqempTCVMTCPA 117
                                       4555544445566666666 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.6   6.2e-05     0.069       1      23 [.       3      25 ..       3      43 .. 0.81
   2 !    9.1   8.2    0.0019       2.2       3      23 ..      71      91 ..      70     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.2e-05
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfe 23
                                      V+vD ++Cigc  C  ++++v  
  gi|330506430|ref|YP_004382858.1|  3 VYVDISRCIGCRSCEVACDRVHG 25
                                      89****************86644 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0019
                           Fer4_15  3 vDrdaCigcglCvaeapevfe 23
                                      +D d+C+gcglC  ++p  ++
  gi|330506430|ref|YP_004382858.1| 71 FDVDKCTGCGLCQLACPFGVV 91
                                      799*************83333 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   5.4   7.9e-05     0.088       2      14 ..       8      20 ..       7      21 .. 0.94
   2 ?    2.8   4.7       0.2   2.2e+02       4      16 ..      45      59 ..      44      60 .. 0.78
   3 !   17.8   2.5   2.9e-06    0.0032       2      17 .]      74      89 ..      74      89 .. 0.94
   4 ?    3.4   3.4      0.12   1.4e+02       8      16 ..     109     117 ..      97     118 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-05
                            Fer4_4  2 erCigCgsCvaaC 14
                                      +rCigC+sC+ aC
  gi|330506430|ref|YP_004382858.1|  8 SRCIGCRSCEVAC 20
                                      59*********** PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.2
                            Fer4_4  4 CigCg..sCvaaCPq 16
                                      C +C   +C+ +C++
  gi|330506430|ref|YP_004382858.1| 45 CHHCEdaCCTMVCST 59
                                      888887779999986 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 2.9e-06
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++C+gCg C  aCP+g
  gi|330506430|ref|YP_004382858.1| 74 DKCTGCGLCQLACPFG 89
                                      79************86 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.12
                            Fer4_4   8 gsCvaaCPq 16 
                                       + Cv +CP 
  gi|330506430|ref|YP_004382858.1| 109 PTCVMTCPA 117
                                       36******7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9  17.7      0.45     5e+02       3      52 ..       5      53 ..       3      57 .. 0.58
   2 !   16.8  12.7     5e-06    0.0056       8      55 ..      45      89 ..      38      93 .. 0.70
   3 ?    0.8   3.2      0.48   5.4e+02      38      56 ..     100     119 ..      90     122 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.45
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52
                                      +d ++CigC +C +aC+   h      + + +  +++  v C+ C + C 
  gi|330506430|ref|YP_004382858.1|  5 VDISRCIGCRSCEVACDR-VHGGKGHVNVHFVGSLASVPVFCHHCEDACC 53
                                      67899***********95.3332222222233334555566666666664 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 5e-06
                           Fer4_21  8 CigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPved 55
                                      C +C+   C+++C+   + a++++++++ +   d+C+GC lC   CP  +
  gi|330506430|ref|YP_004382858.1| 45 CHHCEDacCTMVCS---TGALHKEGDKT-AFDVDKCTGCGLCQLACPF-G 89
                                      44443222555555...57777776665.67889*************6.5 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.48
                           Fer4_21  38 edeCvGCnl..CssvCPvedc 56 
                                        d C G ++  C+  CP  ++
  gi|330506430|ref|YP_004382858.1| 100 CDLCSGQEMptCVMTCPA-NA 119
                                       455666553338888884.54 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   1.8   0.00029      0.33      43      56 ..       7      20 ..       4      23 .. 0.87
   2 ?    4.2   5.7     0.058        65       1      20 [.      44      65 ..      44      72 .. 0.81
   3 !   17.0   1.0   5.7e-06    0.0064      38      60 ..      68      90 ..      62      91 .. 0.79
   4 ?    3.0   2.7      0.14   1.5e+02      39      59 ..      96     118 ..      90     120 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                           Fer4_17 43 aslCieCgeCerkC 56
                                      +s+Ci+C+ Ce +C
  gi|330506430|ref|YP_004382858.1|  7 ISRCIGCRSCEVAC 20
                                      78999999999999 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.058
                           Fer4_17  1 rCiqCg..yClpeCpsyeaydn 20
                                      +C++C+  +C+ +C++++ +++
  gi|330506430|ref|YP_004382858.1| 44 FCHHCEdaCCTMVCSTGALHKE 65
                                      6****9667******9988876 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 5.7e-06
                           Fer4_17 38 ekeekaslCieCgeCerkCPqgl 60
                                      ++   +++C++Cg+C+ +CP g+
  gi|330506430|ref|YP_004382858.1| 68 KTAFDVDKCTGCGLCQLACPFGV 90
                                      4456789*************875 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.14
                           Fer4_17  39 keekaslCie..CgeCerkCPqg 59 
                                         +k++lC++  +  C++ CP++
  gi|330506430|ref|YP_004382858.1|  96 IAHKCDLCSGqeMPTCVMTCPAN 118
                                       45677888751145799***986 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.5    0.0043       4.9       1      11 [.      10      20 ..      10      24 .. 0.95
   2 ?    3.6   9.5      0.14   1.6e+02       1      15 []      45      61 ..      45      61 .. 0.90
   3 ?   16.2   5.1   1.3e-05     0.015       1      14 [.      76      89 ..      76      90 .. 0.95
   4 ?    7.1   4.2     0.011        12       1      15 []     100     119 ..     100     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0043
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+gC+ C+++C
  gi|330506430|ref|YP_004382858.1| 10 CIGCRSCEVAC 20
                                      *********** PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.14
                            Fer4_3  1 CtgCg..aCvevCPvgA 15
                                      C++C+   C  vC +gA
  gi|330506430|ref|YP_004382858.1| 45 CHHCEdaCCTMVCSTGA 61
                                      ****8767*****9998 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.3e-05
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      CtgCg+C  +CP g
  gi|330506430|ref|YP_004382858.1| 76 CTGCGLCQLACPFG 89
                                      ************87 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.011
                            Fer4_3   1 CtgCg.....aCvevCPvgA 15 
                                       C+ C+     +Cv  CP +A
  gi|330506430|ref|YP_004382858.1| 100 CDLCSgqempTCVMTCPANA 119
                                       ****8889989******987 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.8     0.011        13      80      93 ..       8      21 ..       2      24 .. 0.69
   2 ?   -0.4   7.0         2   2.2e+03       5      19 ..      45      59 ..      42      70 .. 0.59
   3 ?   13.4   1.4   9.3e-05       0.1      74      94 ..      68      88 ..      61      90 .. 0.82
   4 ?   -0.1   0.3       1.6   1.8e+03       7      14 ..     110     117 ..      96     137 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                           Fer4_22 80 sgCvGCgRCieacp 93
                                      s C+GC  C+ ac 
  gi|330506430|ref|YP_004382858.1|  8 SRCIGCRSCEVACD 21
                                      56777777777774 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2
                           Fer4_22  5 CgaCtlvCptCsCfd 19
                                      C +C  +C t +C +
  gi|330506430|ref|YP_004382858.1| 45 CHHCEDACCTMVCST 59
                                      666666666666654 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 9.3e-05
                           Fer4_22 74 kekfgesgCvGCgRCieacpv 94
                                      k+ f+  +C+GCg C+ acp 
  gi|330506430|ref|YP_004382858.1| 68 KTAFDVDKCTGCGLCQLACPF 88
                                      5678999************96 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.6
                           Fer4_22   7 aCtlvCpt 14 
                                       +C ++Cp+
  gi|330506430|ref|YP_004382858.1| 110 TCVMTCPA 117
                                       35555553 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  26.5     0.011        12       2      65 .]       7      90 ..       6      90 .. 0.65
   2 ?    9.5  11.6    0.0012       1.3       2      19 ..      73      92 ..      72     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.011
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtk.khlldargeaae......................dvqeeqvlee.....eealwsCt 52
                                      +++Ci+C  C+ aC  ++  k + + +  g  a                                +     +  +++Ct
  gi|330506430|ref|YP_004382858.1|  7 ISRCIGCRSCEVACDRVHGGKgHVNVHFVGSLASvpvfchhcedacctmvcstgalH--------KegdktAFDVDKCT 77
                                      689***********8666666333334444433366666666655565555553221........1333337789**** PP

                            Fer4_8 53 tcgaCtevCpvgi 65
                                      +cg C+ +Cp g+
  gi|330506430|ref|YP_004382858.1| 78 GCGLCQLACPFGV 90
                                      **********875 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                            Fer4_8  2 lekCieCgaCqsaCp..vlr 19
                                      ++kC++Cg+Cq aCp  v+r
  gi|330506430|ref|YP_004382858.1| 73 VDKCTGCGLCQLACPfgVVR 92
                                      789********99*944333 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9  10.2      0.14   1.6e+02       1      32 [.       5      36 ..       5      63 .. 0.74
   2 ?   12.3   1.0   0.00017      0.19       3      17 ..      73      87 ..      72      95 .. 0.92
   3 ?    0.1   1.4       1.1   1.2e+03      11      18 ..     110     117 ..      99     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.14
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvva 32
                                      VD ++Ci+c +C  ++  v   + + + ++v 
  gi|330506430|ref|YP_004382858.1|  5 VDISRCIGCRSCEVACDRVHGGKGHVNVHFVG 36
                                      8999************9988777766666665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00017
                           Fer4_13  3 rdtCiacgaCvelaP 17
                                       d+C++cg+C  ++P
  gi|330506430|ref|YP_004382858.1| 73 VDKCTGCGLCQLACP 87
                                      57************9 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.1
                           Fer4_13  11 aCvelaPd 18 
                                       +Cv+++P 
  gi|330506430|ref|YP_004382858.1| 110 TCVMTCPA 117
                                       79999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); 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):              16  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1096.63
//
Query:       gi|330506431|ref|YP_004382859.1|  [L=139]
Description: 4Fe-4S ferredoxin, iron-sulfur binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-08   32.1  19.6    1.4e-05   25.1  10.9    2.7  3  Fer4_10   4Fe-4S dicluster domain
    4.7e-07   30.3  30.6    0.00013   22.5  10.8    2.7  4  Fer4_7    4Fe-4S dicluster domain
    2.7e-06   27.5   9.2    2.7e-06   27.5   9.2    2.5  4  Fer4_9    4Fe-4S dicluster domain
    1.1e-05   25.0   2.6    1.1e-05   25.0   2.6    3.4  4  Fer4      4Fe-4S binding domain
    4.5e-05   24.3  11.7      0.034   15.1   3.6    2.8  2  Fer4_16   4Fe-4S double cluster binding domain
    6.7e-05   22.9  10.3    6.7e-05   22.9  10.3    2.3  3  Fer4_21   4Fe-4S dicluster domain
    8.4e-05   22.4   2.0    8.4e-05   22.4   2.0    3.9  4  Fer4_2    4Fe-4S binding domain
    0.00034   20.6   1.9    0.00034   20.6   1.9    3.4  4  Fer4_6    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.032   14.7   8.3       0.13   12.8   1.2    4.0  4  Fer4_4    4Fe-4S binding domain
       0.34   11.5  12.3       0.23   12.0   1.5    3.1  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        2.9    8.5  19.3        4.5    7.9   4.0    3.3  3  Fer4_17   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> 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  10.9   8.5e-09   1.4e-05       2      56 .]       2      52 ..       1      52 [. 0.88
   2 !   18.6   1.4   9.5e-07    0.0016       7      49 ..      38      81 ..      33      86 .. 0.90
   3 ?   -1.9   0.1       2.2   3.7e+03       9      13 ..     114     118 ..     110     122 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 8.5e-09
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg.cgaCveaCP 56
                                      +++d+ +C++C  C ++CP      +++      ++  +  +kC + c  Cve CP
  gi|330506431|ref|YP_004382859.1|  2 IKVDPGKCLGCLSCSNVCPN-----QNIVLLQSADTRTVHWKKCKEeCDLCVEFCP 52
                                      6789****************.....7788888888888889999988********9 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 9.5e-07
                           Fer4_10  7 dtCi.rCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg 49
                                      ++C  +C  Cv++CPa++ + +a++e  +e++++  + +C  cg
  gi|330506431|ref|YP_004382859.1| 38 KKCKeECDLCVEFCPAKALALVAYDELVPESEISFELVACRVCG 81
                                      678549***********************************998 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.2
                           Fer4_10   9 CirCg 13 
                                       C +C+
  gi|330506431|ref|YP_004382859.1| 114 CSQCR 118
                                       66665 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   2.5     5e-06    0.0081      32      50 ..       3      21 ..       2      23 .. 0.87
   2 !   22.5  10.8     8e-08   0.00013       1      52 []       8      55 ..       8      55 .. 0.87
   3 !   15.0   2.0   1.8e-05     0.029       4      42 ..      43      81 ..      39      86 .. 0.88
   4 ?   -1.9   0.0       3.2   5.2e+03      38      41 ..     114     117 ..      99     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5e-06
                            Fer4_7 32 eidpekClgCgaCvavCPt 50
                                      ++dp kClgC +C +vCP 
  gi|330506431|ref|YP_004382859.1|  3 KVDPGKCLGCLSCSNVCPN 21
                                      68999************97 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 8e-08
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekC.lgCgaCvavCPtga 52
                                      +C gC  C ++Cp++ i l +++     ++ +++  kC   C+ Cv+ CP++a
  gi|330506431|ref|YP_004382859.1|  8 KCLGCLSCSNVCPNQNIVLLQSA-----DTRTVHWKKCkEECDLCVEFCPAKA 55
                                      7*****************99884.....44579999**668*********986 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 1.8e-05
                            Fer4_7  4 gCgaCvaaCpvkaieldeeenekgtekveidpekClgCg 42
                                      +C  Cv+ Cp+ka+ l  +++  +  ++ ++   C  Cg
  gi|330506431|ref|YP_004382859.1| 43 ECDLCVEFCPAKALALVAYDELVPESEISFELVACRVCG 81
                                      7***************99988888899999999999998 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 3.2
                            Fer4_7  38 ClgC 41 
                                       C++C
  gi|330506431|ref|YP_004382859.1| 114 CSQC 117
                                       4444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   9.2   1.6e-09   2.7e-06       1      50 [.       8      55 ..       8      56 .. 0.91
   2 ?   -1.5   0.2       1.8   2.9e+03      35      40 ..      76      81 ..      62      84 .. 0.70
   3 ?   -1.1   2.0       1.4   2.3e+03      36      39 ..     114     117 ..      75     122 .. 0.52
   4 ?    0.0   0.3      0.61   9.9e+02       8      15 ..     114     120 ..     112     136 .. 0.53

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.6e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaC.igCgaCveaCpkga 50
                                      kC gC +C ++Cp++ +v  +++ ++ ++++   +C  +C  Cve Cp +a
  gi|330506431|ref|YP_004382859.1|  8 KCLGCLSCSNVCPNQNIVLLQSADTRTVHWK---KCkEECDLCVEFCPAKA 55
                                      7************************999775...7*667*********986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.8
                            Fer4_9 35 aCigCg 40
                                      aC  Cg
  gi|330506431|ref|YP_004382859.1| 76 ACRVCG 81
                                      455554 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.4
                            Fer4_9  36 CigC 39 
                                       C +C
  gi|330506431|ref|YP_004382859.1| 114 CSQC 117
                                       3333 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.61
                            Fer4_9   8 CveaCpag 15 
                                       C + C  +
  gi|330506431|ref|YP_004382859.1| 114 CSQ-CRRD 120
                                       333.4444 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   2.6   6.9e-09   1.1e-05       1      23 [.       2      24 ..       2      25 .. 0.90
   2 !   12.3   2.0   7.1e-05      0.12      11      23 ..      44      56 ..      34      57 .. 0.92
   3 ?   -1.5   0.4       1.6   2.6e+03      10      14 ..      76      80 ..      75      82 .. 0.59
   4 ?   -3.7   0.4       8.2   1.3e+04      11      14 ..     114     117 ..     114     118 .. 0.49

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 6.9e-09
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      +++d+ kC gC  C +vCP+  I
  gi|330506431|ref|YP_004382859.1|  2 IKVDPGKCLGCLSCSNVCPNQNI 24
                                      689****************9765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.1e-05
                                      -THHHHHSTTTEE CS
                              Fer4 11 CGaCvevCPvgAI 23
                                      C +Cve CP  A+
  gi|330506431|ref|YP_004382859.1| 44 CDLCVEFCPAKAL 56
                                      **********996 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.6
                                      S-THH CS
                              Fer4 10 gCGaC 14
                                      +C  C
  gi|330506431|ref|YP_004382859.1| 76 ACRVC 80
                                      56666 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 8.2
                                       -THH CS
                              Fer4  11 CGaC 14 
                                       C +C
  gi|330506431|ref|YP_004382859.1| 114 CSQC 117
                                       4445 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   2.8    0.0002      0.33       1      20 [.       8      27 ..       8      42 .. 0.75
   2 !   15.1   3.6   2.1e-05     0.034       4      60 ..      43     117 ..      39     120 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C +C  C +vCP + i   
  gi|330506431|ref|YP_004382859.1|  8 KCLGCLSCSNVCPNQNIVLL 27
                                      59999999999999999865 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.1e-05
                           Fer4_16   4 tCgkCaevCPtnaikekkekeiearecisy.................ntaekkdlaedeekckkq.eaitgCdiC 60 
                                       +C  C+e CP++a+   ++ e+ ++ +is                    + + +l+   +++ ++ e+i  C  C
  gi|330506431|ref|YP_004382859.1|  43 ECDLCVEFCPAKALALVAYDELVPESEISFelvacrvcgsryatlpmLMKVEASLPAGMQEDASGlEWIRICSQC 117
                                       5**************999999999998887777777777777777765555555555555555334777778777 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9  10.3   4.1e-08   6.7e-05       3      55 ..       4      54 ..       2      59 .. 0.78
   2 !    6.5   5.3    0.0054       8.9      10      47 ..      43      80 ..      34      83 .. 0.52
   3 ?   -2.9   0.1       4.9     8e+03      11      14 ..     114     117 ..     112     131 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.1e-08
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCv.GCnlCssvCPved 55
                                      +d+ kC+gC +C  +C++   + + ++++ + +v  ++C   C+lC++ CP  +
  gi|330506431|ref|YP_004382859.1|  4 VDPGKCLGCLSCSNVCPN--QNIVLLQSADTRTVHWKKCKeECDLCVEFCPA-K 54
                                      8999*************6..3444556666667888999736*********6.4 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0054
                           Fer4_21 10 gCgkCliaCedtshqaieidaktvlkvvedeCvGCnlC 47
                                      +C +C+  C+ ++   + +d+      ++ e v+C +C
  gi|330506431|ref|YP_004382859.1| 43 ECDLCVEFCPAKALALVAYDELVPESEISFELVACRVC 80
                                      46666666666555555555444444455555555555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.9
                           Fer4_21  11 CgkC 14 
                                       C +C
  gi|330506431|ref|YP_004382859.1| 114 CSQC 117
                                       3333 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   2.0   5.1e-08   8.4e-05       3      22 .]       2      21 ..       1      21 [. 0.93
   2 !   11.7   1.3   0.00013      0.21       9      22 .]      39      53 ..      31      53 .. 0.87
   3 ?   -0.5   0.5         1   1.7e+03      12      16 ..      76      80 ..      75      82 .. 0.71
   4 ?    0.2   0.5      0.62     1e+03       9      14 ..     113     118 ..     111     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.1e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      ++vd+ +C+gC +C ++CP+
  gi|330506431|ref|YP_004382859.1|  2 IKVDPGKCLGCLSCSNVCPN 21
                                      689****************5 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00013
                            Fer4_2  9 rCi.gCgaCvsaCPa 22
                                      +C  +C  Cv  CPa
  gi|330506431|ref|YP_004382859.1| 39 KCKeECDLCVEFCPA 53
                                      89757*********8 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1
                            Fer4_2 12 gCgaC 16
                                      +C+ C
  gi|330506431|ref|YP_004382859.1| 76 ACRVC 80
                                      67777 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.62
                            Fer4_2   9 rCigCg 14 
                                       +C +C+
  gi|330506431|ref|YP_004382859.1| 113 ICSQCR 118
                                       699997 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   1.9   2.1e-07   0.00034       2      23 ..       2      23 ..       1      24 [. 0.90
   2 !   10.8   2.3   0.00025      0.41       8      24 .]      39      56 ..      38      56 .. 0.88
   3 ?   -1.7   0.1       2.3   3.7e+03       9      12 ..      77      80 ..      72      82 .. 0.66
   4 ?   -0.8   0.4       1.1   1.8e+03       9      14 ..     114     119 ..     112     119 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                                      + +dp kC+gC  C +vCP + 
  gi|330506431|ref|YP_004382859.1|  2 IKVDPGKCLGCLSCSNVCPNQN 23
                                      789****************875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00025
                            Fer4_6  8 kCi.gCgdCvrvCPegai 24
                                      kC   C+ Cv  CP++a+
  gi|330506431|ref|YP_004382859.1| 39 KCKeECDLCVEFCPAKAL 56
                                      78857**********996 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.3
                            Fer4_6  9 CigC 12
                                      C  C
  gi|330506431|ref|YP_004382859.1| 77 CRVC 80
                                      5555 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.1
                            Fer4_6   9 CigCgd 14 
                                       C +C++
  gi|330506431|ref|YP_004382859.1| 114 CSQCRR 119
                                       999985 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.2   8.1e-05      0.13       3      16 ..       8      21 ..       6      28 .. 0.90
   2 ?   12.4   1.0   0.00011      0.18       2      16 ..      38      53 ..      36      61 .. 0.87
   3 ?   -0.2   0.5       1.2     2e+03       6      10 ..      76      80 ..      75      81 .. 0.83
   4 ?    0.6   0.1      0.68   1.1e+03       4       8 ..     114     118 ..     108     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.1e-05
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      +C+gC sC ++CP 
  gi|330506431|ref|YP_004382859.1|  8 KCLGCLSCSNVCPN 21
                                      8************5 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00011
                            Fer4_4  2 erCi.gCgsCvaaCPq 16
                                      ++C  +C+ Cv +CP 
  gi|330506431|ref|YP_004382859.1| 38 KKCKeECDLCVEFCPA 53
                                      578669*********6 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.2
                            Fer4_4  6 gCgsC 10
                                       C++C
  gi|330506431|ref|YP_004382859.1| 76 ACRVC 80
                                      69999 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.68
                            Fer4_4   4 CigCg 8  
                                       C +C+
  gi|330506431|ref|YP_004382859.1| 114 CSQCR 118
                                       66665 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 ?   12.0   1.5   0.00014      0.23       1      18 [.       4      21 ..       4      22 .. 0.95
   2 ?    4.7   1.6     0.027        44       8      18 ..      43      53 ..      38      54 .. 0.88
   3 ?   -0.6   0.0       1.3     2e+03       8      14 ..      76      82 ..      73      93 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      VD  +C +c +C +++P+
  gi|330506431|ref|YP_004382859.1|  4 VDPGKCLGCLSCSNVCPN 21
                                      8999*************7 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.027
                           Fer4_13  8 acgaCvelaPd 18
                                      +c++Cve++P 
  gi|330506431|ref|YP_004382859.1| 43 ECDLCVEFCPA 53
                                      6*********5 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.3
                           Fer4_13  8 acgaCve 14
                                      ac +C++
  gi|330506431|ref|YP_004382859.1| 76 ACRVCGS 82
                                      5666653 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.0    0.0028       4.5      45      58 ..       8      21 ..       4      24 .. 0.85
   2 ?    5.4   2.3     0.017        27      42      58 ..      36      53 ..      23      56 .. 0.74
   3 ?    4.1   0.2     0.041        67       8      50 ..      77     118 ..      74     119 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0028
                           Fer4_17 45 lCieCgeCerkCPq 58
                                      +C++C  C+ +CP+
  gi|330506431|ref|YP_004382859.1|  8 KCLGCLSCSNVCPN 21
                                      79999999999997 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.017
                           Fer4_17 42 kaslCi.eCgeCerkCPq 58
                                       +++C  eC +C++ CP+
  gi|330506431|ref|YP_004382859.1| 36 HWKKCKeECDLCVEFCPA 53
                                      577785369999999997 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.041
                           Fer4_17   8 ClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCg 50 
                                       C+  C s +a+    +k+ + + +g+ e+a+  e +  C++C+
  gi|330506431|ref|YP_004382859.1|  77 CRV-CGSRYATLPMLMKVEASLPAGMQEDASGLEWIRICSQCR 118
                                       666.666666666666777777777777776669999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 981.90
//
Query:       gi|330506432|ref|YP_004382860.1|  [L=357]
Description: sugar kinase [Methanosaeta concilii GP6]
Scores for complete 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   23.7   0.0    7.6e-05   22.9   0.0    1.4  1  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   4.2e-09   7.6e-05      11      66 .]     130     194 ..     120     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.2e-09
                                       TSSSCHHHHHHHHHHHHHHHHTTEHH.HH.......HHHHHHHH.HHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N  11 gaGLGSSAAlavalvaAllallglsl.ee.......aklaleae.rlaqggngsggDvaasvyGg 66 
                                       + GLGS +++ +al  A++++lg +l +e       ++   e e   +  g   g+  aa++yGg
  gi|330506432|ref|YP_004382860.1| 130 HVGLGSTGSVLLALGHAMNSALGSPLnREqirmligNNYVEETEdGRVTNGFETGVGPAAATYGG 194
                                       57*********************99863358889999999999988999999************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2690.17
//
Query:       gi|330506433|ref|YP_004382861.1|  [L=119]
Description: hypothetical protein MCON_0136 [Methanosaeta concilii GP6]
Scores for complete 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   21.8   0.0    0.00022   21.2   0.0    1.4  1  DUF2148   Uncharacterized protein containing a ferredoxin dom


Domain annotation for each model (and alignments):
>> DUF2148  Uncharacterized protein containing a ferredoxin domain (DUF2148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.2e-08   0.00022      48      68 .]      96     117 ..      80     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.2e-08
                           DUF2148  48 e.asvvlgiplsvsgKsifFDR 68 
                                       +   v++gipl++sgK+i+F R
  gi|330506433|ref|YP_004382861.1|  96 QeRVVAYGIPLKASGKNIYFGR 117
                                       337899**************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 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:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 908.52
//
Query:       gi|330506434|ref|YP_004382862.1|  [L=136]
Description: hypothetical protein MCON_0137 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1024.35
//
Query:       gi|330506435|ref|YP_004382863.1|  [L=78]
Description: hypothetical protein MCON_0138 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0076   16.1   0.2      0.011   15.6   0.2    1.2  1  ANTAR     ANTAR domain


Domain annotation for each model (and alignments):
>> ANTAR  ANTAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2     6e-07     0.011      15      42 ..      36      63 ..      29      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6e-07
                                      HHHHHHHHHHT--HHHHHHHHHHHHCTT CS
                             ANTAR 15 qAkgiLmeryglsedeAfrlLrklSmds 42
                                      +Ak iL e   ++ +eA +++ + S+++
  gi|330506435|ref|YP_004382863.1| 36 AAKEILAEVFDITIAEAEDMIKQRSQER 63
                                      7*************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 564.35
//
Query:       gi|330506436|ref|YP_004382864.1|  [L=89]
Description: translation elongation factor aEF-1 beta [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-19   70.5   0.3    1.1e-19   70.4   0.3    1.0  1  EF1_GNE         EF-1 guanine nucleotide exchange domain
     0.0038   17.7   0.2       0.19   12.2   0.0    2.2  2  HMA             Heavy-metal-associated domain
     0.0096   16.1   0.6      0.039   14.1   0.1    2.0  2  FeS_assembly_P  Iron-sulfur cluster assembly protein
  ------ inclusion threshold ------
      0.033   14.2   0.2      0.071   13.2   0.2    1.6  1  P2              P2 response regulator binding domain
      0.061   13.0   0.0      0.062   13.0   0.0    1.1  1  Ribosomal_L4    Ribosomal protein L4/L1 family
      0.087   13.2   0.0      0.094   13.1   0.0    1.1  1  TINF2_N         TERF1-interacting nuclear factor 2 N-terminus
       0.11   12.9   0.0       0.33   11.3   0.0    1.7  2  POTRA_1         POTRA domain, FtsQ-type


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 !   70.4   0.3   4.3e-23   1.1e-19       2      88 ..       6      87 ..       5      89 .] 0.94

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 4.3e-23
                                      EEEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEESSS-G.GGGHHHHHHTTS-S..... CS
                           EF1_GNE  2 vvlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvieddkv.stdeleekieeiegeledl 78
                                      v ++v+Pe++++dle+l++ +++ +++  + ++ a++ +piafGlk+L +  +++d+ + s de+ee+++++ g     
  gi|330506436|ref|YP_004382864.1|  6 VRMKVMPESTDVDLEKLAEDIRK-AVPSfARMH-AIEQKPIAFGLKALIVVTIMDDKGGrSPDEIEEAVRKLPG----- 77
                                      679********************.999978888.7*******************99999999************..... PP

                                      SEEEEEEEEE CS
                           EF1_GNE 79 Vqsveivsfn 88
                                      V+sve++++ 
  gi|330506436|ref|YP_004382864.1| 78 VESVEVEEVG 87
                                      ******9986 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.033        85      38      59 ..       8      29 ..       4      32 .. 0.78
   2 !   12.2   0.0   7.5e-05      0.19      14      32 ..      66      84 ..      61      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.033
                               HMA 38 vtVegdaestklrkiieaieka 59
                                      + V+ + ++++l+k+ e i+ka
  gi|330506436|ref|YP_004382864.1|  8 MKVMPESTDVDLEKLAEDIRKA 29
                                      5677777777789999999987 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.5e-05
                               HMA 14 akvekvLselpgVesvkvd 32
                                        +e+++ +lpgVesv+v 
  gi|330506436|ref|YP_004382864.1| 66 DEIEEAVRKLPGVESVEVE 84
                                      579*************995 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 ?    0.0   0.0      0.39   9.9e+02      50      61 ..      19      30 ..       2      40 .. 0.60
   2 !   14.1   0.1   1.5e-05     0.039      55      73 ..      66      84 ..      62      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.39
                                      HHHHHHHHHHHH CS
                    FeS_assembly_P 50 aeairadaeaal 61
                                      +e +++d+++a+
  gi|330506436|ref|YP_004382864.1| 19 LEKLAEDIRKAV 30
                                      445555555555 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHC.STT--EEEEE CS
                    FeS_assembly_P 55 adaeaalralpgvevveVe 73
                                      +++e+a+r+lpgve+veVe
  gi|330506436|ref|YP_004382864.1| 66 DEIEEAVRKLPGVESVEVE 84
                                      689*********8877775 PP

>> P2  P2 response regulator binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   2.8e-05     0.071      26      81 .]      19      85 ..      17      85 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                                      HHHTT.EEEEEES...-HHHHHTT-SSSEEEEEE.......EESS-HHHHHHHHHTSSS-SEEEEEE CS
                                P2 26 Leelg.eiiksiP...svedieeekfdegfevvl.......ltkeskeeikealasiseiesvevee 81
                                      Le+l+ +i k +P    + +ie++ + +g++ ++       +   s++ei+ea+++++ +esvevee
  gi|330506436|ref|YP_004382864.1| 19 LEKLAeDIRKAVPsfaRMHAIEQKPIAFGLKALIvvtimddKGGRSPDEIEEAVRKLPGVESVEVEE 85
                                      66676345577883333445555556666666665466554456799******************86 PP

>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.4e-05     0.062     137     169 ..      42      87 ..       3      89 .] 0.60

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                       S......SEEEEES.......SSSCHHHHHHTT-TTEEEEESTT-- CS
                      Ribosomal_L4 137 k......svLivvs.......ekdenlvlaarnlpgvevievesln 169
                                       k      ++Livv        ++ +++ +a+r lpgve +eve++ 
  gi|330506436|ref|YP_004382864.1|  42 KpiafglKALIVVTimddkggRSPDEIEEAVRKLPGVESVEVEEVG 87 
                                       1233333778888755555554445******************985 PP

>> TINF2_N  TERF1-interacting nuclear factor 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.7e-05     0.094      15      69 ..      19      75 ..       9      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                           TINF2_N 15 leefvslvteavPeL..lssrqkakLilGLrarlilellrkekaadlkaiqshlerl 69
                                      le++ + +++avP    ++  +++ +++GL+a ++++++ ++   + ++i++ + +l
  gi|330506436|ref|YP_004382864.1| 19 LEKLAEDIRKAVPSFarMHAIEQKPIAFGLKALIVVTIMDDKGGRSPDEIEEAVRKL 75
                                      4555667899999764477889999**************999988888888777665 PP

>> POTRA_1  POTRA domain, FtsQ-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.6     4e+03      34      46 ..      17      30 ..      15      33 .. 0.63
   2 ?   11.3   0.0   0.00013      0.33      35      55 ..      64      84 ..      61      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.6
                                      S-HHHHHHHHHH.- CS
                           POTRA_1 34 ldleaieqrlek.l 46
                                      +dle++++ ++k  
  gi|330506436|ref|YP_004382864.1| 17 VDLEKLAEDIRKaV 30
                                      56666666666544 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00013
                                      -HHHHHHHHHH-TTEEEEEEE CS
                           POTRA_1 35 dleaieqrleklpwvksasVr 55
                                      ++++ie++++klp v+s++V+
  gi|330506436|ref|YP_004382864.1| 64 SPDEIEEAVRKLPGVESVEVE 84
                                      689*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 690.12
//
Query:       gi|330506437|ref|YP_004382865.1|  [L=56]
Description: hypothetical protein MCON_0141 [Methanosaeta concilii GP6]
Scores for 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-06   26.4   4.1      5e-06   26.4   4.1    2.2  2  DUF1610         Domain of unknown function (DUF1610)
  ------ inclusion threshold ------
      0.015   15.1   2.0      0.015   15.1   2.0    2.3  2  HscB_4_cys      Co-chaperone HscB tetracysteine metal binding
      0.029   14.3   8.5      0.096   12.6   0.3    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.035   14.1   6.6      0.053   13.5   6.6    1.3  1  zinc-ribbons_6  zinc-ribbons
      0.038   14.3   9.7        3.1    8.2   7.9    2.1  2  C1_2            C1 domain
      0.064   13.8  10.4      0.055   14.0   6.5    2.0  2  zf-CHY          CHY zinc finger
      0.077   13.2   5.8      0.092   13.0   5.8    1.0  1  FYVE_2          FYVE-type zinc finger
        0.1   13.0   7.5       0.12   12.7   7.5    1.2  1  Rhodanese_C     Rhodanase C-terminal
       0.11   12.4   9.8         70    3.4   9.8    2.2  1  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.26   10.8   0.3       0.26   10.8   0.3    3.4  3  zf-ribbon_3     zinc-ribbon domain
       0.27   11.2  11.7       0.87    9.6   0.1    3.8  4  Nudix_N_2       Nudix N-terminal
       0.34   10.7   0.3       0.34   10.7   0.3    3.9  4  Rubredoxin_2    Rubredoxin metal binding domain
       0.36   10.9  10.4        1.3    9.1   0.2    2.0  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.42   10.7   9.0        0.9    9.6   9.0    1.6  1  Zn_Tnp_IS91     Transposase zinc-binding domain
       0.47   10.3   0.3       0.47   10.3   0.3    3.6  4  Fer4            4Fe-4S binding domain
       0.72   10.0   8.2        1.8    8.7   0.2    3.0  3  DUF2752         Protein of unknown function (DUF2752)
        0.8    9.8   0.1        0.8    9.8   0.1    4.0  3  zf-ACC          Acetyl-coA carboxylase zinc finger domain
       0.84    9.7  11.9       0.27   11.3   5.5    2.2  2  zf-C2HC5        Putative zinc finger motif, C2HC5-type
       0.97    8.2   4.2          1    8.2   4.2    1.0  1  NMDAR2_C        N-methyl D-aspartate receptor 2B3 C-terminus
        1.4    9.1  13.3        6.5    6.9   2.4    2.9  3  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
        1.4    6.6   6.5        1.5    6.6   6.5    1.0  1  PolC_DP2        DNA polymerase II large subunit DP2
        1.9    8.1  15.9      0.085   12.4   5.7    2.7  3  zn-ribbon_14    Zinc-ribbon
        2.5    8.1  16.5        7.2    6.6   1.1    3.9  4  zinc_ribbon_4   zinc-ribbon domain
        2.7    8.4   9.9       0.35   11.2   3.1    2.4  2  zf-UBP          Zn-finger in ubiquitin-hydrolases and other p
        5.6    7.6  12.6        8.7    7.0   0.6    3.6  4  zf-H2C2_2       Zinc-finger double domain
        6.9    6.1   9.6          8    5.8   9.6    1.0  1  NMD3            NMD3 family
          7    6.5  19.8        0.5   10.2   3.7    3.2  2  zinc_ribbon_2   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 !   26.4   4.1   7.6e-09     5e-06       1      23 [.       9      30 ..       9      31 .. 0.99
   2 ?   -0.8   0.2       2.4   1.6e+03       1       5 [.      48      52 ..      48      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 7.6e-09
                           DUF1610  1 CtSCGaelaprEravvFpCPNCG 23
                                      C+SCG+ l++ + +  FpCP CG
  gi|330506437|ref|YP_004382865.1|  9 CISCGITLTGVG-GARFPCPSCG 30
                                      ************.*********9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.4
                           DUF1610  1 CtSCG 5 
                                      C +CG
  gi|330506437|ref|YP_004382865.1| 48 CKACG 52
                                      78898 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   2.0   2.3e-05     0.015       2      23 ..       8      29 ..       7      31 .. 0.97
   2 ?   -1.4   0.3       3.2   2.1e+03       3       7 ..      48      52 ..      47      55 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-05
                                      B-SSS--B--SS-S---B-TTT CS
                        HscB_4_cys  2 rCWnCGgpgapgrgdefFCpqC 23
                                      rC +CG  + + +g++f Cp C
  gi|330506437|ref|YP_004382865.1|  8 RCISCGITLTGVGGARFPCPSC 29
                                      899******************* PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.2
                                      -SSS- CS
                        HscB_4_cys  3 CWnCG 7 
                                      C  CG
  gi|330506437|ref|YP_004382865.1| 48 CKACG 52
                                      55677 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   0.00014     0.096      30      58 ..       8      35 ..       6      35 .. 0.92
   2 ?    9.2   7.2    0.0016       1.1      31      55 ..      26      54 ..      26      55 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfeadr 58
                                      +C  Cg +++  + g +f Cp+Cg+++ r
  gi|330506437|ref|YP_004382865.1|  8 RCISCGITLTG-VGGARFPCPSCGTVIAR 35
                                      799********.************99765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0016
                    OrfB_Zn_ribbon 31 CseCgsknke....alsgrtfkCpnCgfe 55
                                      C+ Cg +  +    ++++++++C++Cgf+
  gi|330506437|ref|YP_004382865.1| 26 CPSCGTVIARcnkcKKQSNVYTCKACGFT 54
                                      *********99999*************96 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   6.6   7.9e-05     0.053       2      46 ..       8      52 ..       7      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.9e-05
                                      --SSS-S--E.E-SSEEE-TTT--EEEEEEE-SSS-S-..--EEEETT CS
                    zinc-ribbons_6  2 kCpeCqqele.krgeqyhCeaCqedlkkealCpeCeqe..levlkaCg 46
                                       C +C   l+   g+++ C +C +     a C++C+++  + ++kaCg
  gi|330506437|ref|YP_004382865.1|  8 RCISCGITLTgVGGARFPCPSCGTV---IARCNKCKKQsnVYTCKACG 52
                                      5999999999888899******975...56677776541167799999 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.012       7.8      19      40 ..       7      31 ..       1      34 [. 0.72
   2 ?    8.2   7.9    0.0046       3.1      19      41 ..      34      54 ..      21      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                              C1_2 19 fnCsaCgrkidgff...YsCseCdf 40
                                       +C  Cg + +g     + C+ C  
  gi|330506437|ref|YP_004382865.1|  7 ERCISCGITLTGVGgarFPCPSCGT 31
                                      68999*9995555555599999975 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0046
                              C1_2 19 fnCsaCgrkidgffYsCseCdfs 41
                                       +C+ C++++  + Y+C+ C f+
  gi|330506437|ref|YP_004382865.1| 34 ARCNKCKKQS--NVYTCKACGFT 54
                                      5799999996..55***99*995 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.032        21      52      73 ..       4      30 ..       1      32 [. 0.68
   2 ?   14.0   6.5   8.3e-05     0.055      43      74 ..      25      53 ..      16      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.032
                            zf-CHY 52 ekavlCkkCkk.....efaeyfCpiCk 73
                                      e  + C +C+        a++ Cp C 
  gi|330506437|ref|YP_004382865.1|  4 EMPERCISCGItltgvGGARFPCPSCG 30
                                      456789999985555445666899996 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 8.3e-05
                            zf-CHY 43 lcllCeteqekavlCkkCkkefaeyfCpiCkl 74
                                       c  C t   +   C+kCkk+ + y+C+ C +
  gi|330506437|ref|YP_004382865.1| 25 PCPSCGT---VIARCNKCKKQSNVYTCKACGF 53
                                      5777777...5899****************75 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   5.8   0.00014     0.092      55     100 ..       7      51 ..       2      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                            FYVE_2  55 thCilCleefkllvnskrqCldCklnvCkkCsvenkkekvwlCkiC 100
                                       ++Ci C  +++ +   +  C  C +    +C + +k+ +v+ Ck+C
  gi|330506437|ref|YP_004382865.1|   7 ERCISCGITLTGVGGARFPCPSCGTV-IARCNKCKKQSNVYTCKAC 51 
                                       68*********************975.56799999*********** PP

>> Rhodanese_C  Rhodanase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   7.5   0.00018      0.12      17      63 ..       5      51 ..       1      52 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00018
                       Rhodanese_C 17 vvgkCieCgkpvdelrkrnCanedCnelvlvCeeCaeklkgvcseeC 63
                                      +  +Ci Cg   + +   +  +++C + +  C++C+++ + + +++C
  gi|330506437|ref|YP_004382865.1|  5 MPERCISCGITLTGVGGARFPCPSCGTVIARCNKCKKQSNVYTCKAC 51
                                      5579*****999988855555579*************9999977799 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 ?    3.4   9.8      0.11        70      12      34 ..      34      51 ..       1      54 [. 0.43

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.11
                                      -B-TTT-SB--SSSS-EEEETTT CS
                              C1_1 12 tfCkhCgeflwgkekqglkCswC 34
                                      ++C++C+     k +  ++C++C
  gi|330506437|ref|YP_004382865.1| 34 ARCNKCK-----KQSNVYTCKAC 51
                                      2233333.....33355555555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.46     3e+02      19      23 ..       9      13 ..       7      16 .. 0.61
   2 ?   10.8   0.3   0.00039      0.26       5      12 ..      26      33 ..      24      35 .. 0.64
   3 ?    4.5   6.6     0.036        24       4      23 ..      35      52 ..      34      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.46
                       zf-ribbon_3 19 CpyCG 23
                                      C +CG
  gi|330506437|ref|YP_004382865.1|  9 CISCG 13
                                      55566 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00039
                       zf-ribbon_3  5 CPnCGapl 12
                                      CP+CG+++
  gi|330506437|ref|YP_004382865.1| 26 CPSCGTVI 33
                                      77777643 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.036
                       zf-ribbon_3  4 rCPnCGaplssddnvCpyCG 23
                                      rC++C+++  s + +C+ CG
  gi|330506437|ref|YP_004382865.1| 35 RCNKCKKQ--SNVYTCKACG 52
                                      8******8..99*******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 ?    1.9   0.1      0.33   2.2e+02      25      30 ..       9      14 ..       4      17 .. 0.72
   2 ?    9.6   0.1    0.0013      0.87      22      31 ..      23      32 ..      20      33 .. 0.88
   3 ?    0.6   0.3      0.82   5.5e+02      24      29 ..      35      40 ..      34      42 .. 0.71
   4 ?    5.2   0.3     0.031        21      23      30 ..      46      53 ..      46      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.33
                                      ETTTTE CS
                         Nudix_N_2 25 CpaCgt 30
                                      C +Cg 
  gi|330506437|ref|YP_004382865.1|  9 CISCGI 14
                                      777775 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                                      EEEETTTTEE CS
                         Nudix_N_2 22 RlvCpaCgti 31
                                      R+ Cp+Cgt+
  gi|330506437|ref|YP_004382865.1| 23 RFPCPSCGTV 32
                                      899*****98 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.82
                                      EETTTT CS
                         Nudix_N_2 24 vCpaCg 29
                                      +C++C 
  gi|330506437|ref|YP_004382865.1| 35 RCNKCK 40
                                      688885 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.031
                                      EEETTTTE CS
                         Nudix_N_2 23 lvCpaCgt 30
                                      ++C+aCg+
  gi|330506437|ref|YP_004382865.1| 46 YTCKACGF 53
                                      57999998 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.27   1.8e+02       2       7 ..       8      13 ..       8      18 .. 0.72
   2 ?    4.4   0.6     0.048        32      17      21 ..      26      30 ..      24      31 .. 0.86
   3 ?    3.0   0.6      0.13        88       2       8 ..      35      41 ..      35      45 .. 0.66
   4 ?   10.7   0.3   0.00051      0.34       1      10 [.      46      55 ..      46      56 .] 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.27
                      Rubredoxin_2  2 vCsqCG 7 
                                      +C +CG
  gi|330506437|ref|YP_004382865.1|  8 RCISCG 13
                                      577777 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.048
                      Rubredoxin_2 17 CpsCg 21
                                      CpsCg
  gi|330506437|ref|YP_004382865.1| 26 CPSCG 30
                                      99998 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.13
                      Rubredoxin_2  2 vCsqCGf 8 
                                      +C++C  
  gi|330506437|ref|YP_004382865.1| 35 RCNKCKK 41
                                      6777755 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00051
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      Y C++CGf+ 
  gi|330506437|ref|YP_004382865.1| 46 YTCKACGFTG 55
                                      99******96 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2    0.0019       1.3      69      94 ..       5      31 ..       1      34 [. 0.77
   2 ?    6.3   4.7     0.014       9.2      69      93 ..      32      52 ..      31      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0019
                                      -EEEETTTS-EEECHH.HHHS-TTTSS CS
                              HypA 69 vkvrCreCgkefelee.kalrCpkCgs 94
                                      +  rC +Cg + +    +++ Cp+Cg+
  gi|330506437|ref|YP_004382865.1|  5 MPERCISCGITLTGVGgARFPCPSCGT 31
                                      5669*****999955435899****96 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                                      -EEEETTTS-EEECHHHHHS-TTTS CS
                              HypA 69 vkvrCreCgkefeleekalrCpkCg 93
                                      v +rC++C+k+ ++     +C++Cg
  gi|330506437|ref|YP_004382865.1| 32 VIARCNKCKKQSNVY----TCKACG 52
                                      5689*****888854....8****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   9.0    0.0014       0.9      25      63 ..       7      51 ..       2      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                       Zn_Tnp_IS91 25 ekilrCrtaa..lGfaryeCeeCghekivyfsCksrh....CpsC 63
                                      e+ ++C+      G+ar+ C++Cg     +++Ck+++    C+ C
  gi|330506437|ref|YP_004382865.1|  7 ERCISCGITLtgVGGARFPCPSCGTVIARCNKCKKQSnvytCKAC 51
                                      567788875423799*******************98553346666 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   0.3   0.00071      0.47       5      13 ..       6      14 ..       3      14 .. 0.88
   2 ?   -1.5   0.7       3.9   2.6e+03       8      12 ..      26      30 ..      26      31 .. 0.70
   3 ?    1.3   0.4      0.52   3.4e+02       7      12 ..      35      40 ..      34      41 .. 0.64
   4 ?    2.1   0.2      0.29   1.9e+02       8      12 ..      48      52 ..      44      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00071
                                      TTTSSS-TH CS
                              Fer4  5 eekCigCGa 13
                                      +e+Ci CG+
  gi|330506437|ref|YP_004382865.1|  6 PERCISCGI 14
                                      8*******5 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.9
                                      SSS-T CS
                              Fer4  8 CigCG 12
                                      C  CG
  gi|330506437|ref|YP_004382865.1| 26 CPSCG 30
                                      77788 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.52
                                      TSSS-T CS
                              Fer4  7 kCigCG 12
                                      +C +C+
  gi|330506437|ref|YP_004382865.1| 35 RCNKCK 40
                                      577775 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.29
                                      SSS-T CS
                              Fer4  8 CigCG 12
                                      C +CG
  gi|330506437|ref|YP_004382865.1| 48 CKACG 52
                                      88888 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2      0.15     1e+02      11      17 ..       9      15 ..       7      17 .. 0.91
   2 ?    8.7   0.2    0.0027       1.8       9      16 ..      24      31 ..      22      35 .. 0.88
   3 ?    2.2   0.4      0.29   1.9e+02       9      17 ..      46      54 ..      44      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.15
                           DUF2752 11 CPGCGlt 17
                                      C  CG+t
  gi|330506437|ref|YP_004382865.1|  9 CISCGIT 15
                                      *****98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0027
                           DUF2752  9 ipCPGCGl 16
                                      +pCP CG+
  gi|330506437|ref|YP_004382865.1| 24 FPCPSCGT 31
                                      8******7 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.29
                           DUF2752  9 ipCPGCGlt 17
                                      + C +CG t
  gi|330506437|ref|YP_004382865.1| 46 YTCKACGFT 54
                                      57*****98 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.27   1.8e+02       3       8 ..       8      13 ..       8      16 .. 0.82
   2 ?    9.8   0.1    0.0012       0.8       4      12 ..      26      34 ..      24      35 .. 0.88
   3 ?   -2.7   7.7       9.7   6.4e+03      18      25 ..      43      50 ..      34      51 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.27
                            zf-ACC  3 KCpsCg 8 
                                      +C sCg
  gi|330506437|ref|YP_004382865.1|  8 RCISCG 13
                                      6****9 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                            zf-ACC  4 CpsCgemly 12
                                      CpsCg+++ 
  gi|330506437|ref|YP_004382865.1| 26 CPSCGTVIA 34
                                      ******996 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 9.7
                            zf-ACC 18 rnlyVCPk 25
                                       n y+C  
  gi|330506437|ref|YP_004382865.1| 43 SNVYTCKA 50
                                      35555555 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 ?   11.3   5.5    0.0004      0.27      19      46 ..       8      35 ..       3      46 .. 0.85
   2 ?    1.5   9.0      0.47   3.1e+02      20      41 ..      26      52 ..      26      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0004
                          zf-C2HC5 19 nClnCGkiiCakeglskpCsfCgsplls 46
                                       C++CG  +    g   pC++Cg+ +  
  gi|330506437|ref|YP_004382865.1|  8 RCISCGITLTGVGGARFPCPSCGTVIAR 35
                                      6**********************98765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.47
                          zf-C2HC5 20 ClnCGkii.....CakeglskpCsfCg 41
                                      C +CG +i     C+k+  + +C  Cg
  gi|330506437|ref|YP_004382865.1| 26 CPSCGTVIarcnkCKKQSNVYTCKACG 52
                                      99*****97755555565559999997 PP

>> NMDAR2_C  N-methyl D-aspartate receptor 2B3 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.2    0.0015         1     383     422 ..       5      47 ..       1      50 [. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                                       XXXXXXXXXXXXXXX.XXXX...XXXXXX.XXXXXXXXXXXXX CS
                          NMDAR2_C 383 ksthCRsClsklsaygagss...svrspykrCdaCkklgnLYd 422
                                        +  C sC   l+++g + +   s ++ ++rC+ Ckk +n+Y 
  gi|330506437|ref|YP_004382865.1|   5 MPERCISCGITLTGVGGARFpcpSCGTVIARCNKCKKQSNVYT 47 
                                       456688887777666555542225668899************6 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 ?    1.4   0.1      0.53   3.5e+02      18      25 ..       8      15 ..       2      18 .. 0.80
   2 ?    2.1   8.2      0.31   2.1e+02      15      29 ..      22      36 ..       9      40 .. 0.78
   3 ?    6.9   2.4    0.0098       6.5       2      24 ..      36      53 ..      35      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.53
                          zf-Mss51 18 eCpdCGip 25
                                       C  CGi 
  gi|330506437|ref|YP_004382865.1|  8 RCISCGIT 15
                                      7*****96 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.31
                          zf-Mss51 15 vdfeCpdCGiptycs 29
                                       +f Cp CG ++  +
  gi|330506437|ref|YP_004382865.1| 22 ARFPCPSCGTVIARC 36
                                      78*******988765 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0098
                          zf-Mss51  2 CPvpkhkqtapkhvdfeCpdCGi 24
                                      C+ +k     +++  ++C+ CG+
  gi|330506437|ref|YP_004382865.1| 36 CNKCK-----KQSNVYTCKACGF 53
                                      88885.....67789*******8 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 ?    6.6   6.5    0.0023       1.5     629     662 ..      22      52 ..       3      55 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0023
                          PolC_DP2 629 learCeeCgekteeklvCkkceeeveeekcekce 662
                                        ++ C++Cg+ +     C+kc+++++  +c+ c+
  gi|330506437|ref|YP_004382865.1|  22 ARFPCPSCGTVIAR---CNKCKKQSNVYTCKACG 52 
                                       44555555555554...55555555555555554 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3      0.21   1.4e+02       2       8 ..       8      14 ..       7      15 .. 0.84
   2 ?   -0.3   0.1       1.2   8.1e+02       3       8 ..      26      31 ..      25      32 .. 0.82
   3 ?   12.4   5.7   0.00013     0.085       2      18 ..      35      51 ..      34      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.21
                      zn-ribbon_14  2 kCerCGy 8 
                                      +C  CG 
  gi|330506437|ref|YP_004382865.1|  8 RCISCGI 14
                                      8****95 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                      zn-ribbon_14  3 CerCGy 8 
                                      C  CG 
  gi|330506437|ref|YP_004382865.1| 26 CPSCGT 31
                                      999*96 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00013
                      zn-ribbon_14  2 kCerCGylSSqkiCkAC 18
                                      +C++C   S+   CkAC
  gi|330506437|ref|YP_004382865.1| 35 RCNKCKKQSNVYTCKAC 51
                                      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 ?    1.7   0.1      0.39   2.6e+02      27      32 ..       8      13 ..       5      17 .. 0.69
   2 ?    6.5   0.2     0.012       7.9       5      11 ..      26      32 ..      23      33 .. 0.64
   3 ?    6.6   1.1     0.011       7.2       3      14 ..      34      45 ..      33      47 .. 0.77
   4 ?    2.9   0.5      0.16   1.1e+02      27      32 ..      47      52 ..      44      54 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.39
                     zinc_ribbon_4 27 rCskCg 32
                                      rC  Cg
  gi|330506437|ref|YP_004382865.1|  8 RCISCG 13
                                      566665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.012
                     zinc_ribbon_4  5 CpsCkak 11
                                      CpsC+++
  gi|330506437|ref|YP_004382865.1| 26 CPSCGTV 32
                                      7777664 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.011
                     zinc_ribbon_4  3 itCpsCkakyei 14
                                       +C +Ck++ ++
  gi|330506437|ref|YP_004382865.1| 34 ARCNKCKKQSNV 45
                                      689999988775 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.16
                     zinc_ribbon_4 27 rCskCg 32
                                      +C++Cg
  gi|330506437|ref|YP_004382865.1| 47 TCKACG 52
                                      466665 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 ?    0.7   0.6         1   6.7e+02      11      19 ..      23      31 ..       9      34 .. 0.48
   2 ?   11.2   3.1   0.00053      0.35       1      21 [.      36      55 ..      36      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1
                                      EEEETTT-- CS
                            zf-UBP 11 lWlCLkCgh 19
                                       + C +Cg+
  gi|330506437|ref|YP_004382865.1| 23 RFPCPSCGT 31
                                      344666665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00053
                                      -TTTH--.SSEEEETTT--EE CS
                            zf-UBP  1 CseCnsenknlWlCLkCghvg 21
                                      C++C+++ +n++ C  Cg+ g
  gi|330506437|ref|YP_004382865.1| 36 CNKCKKQ-SNVYTCKACGFTG 55
                                      9****88.**********875 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 ?   -0.0   0.1       2.1   1.4e+03      16      21 ..       8      13 ..       1      16 [. 0.81
   2 ?    5.9   0.0     0.029        20      14      21 ..      23      30 ..      17      32 .. 0.84
   3 ?    2.2   0.8      0.43   2.8e+02      16      23 ..      35      42 ..      33      45 .. 0.84
   4 ?    7.0   0.6     0.013       8.7      13      23 ..      44      54 ..      40      55 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 2.1
                         zf-H2C2_2 16 eCplCd 21
                                       C +C+
  gi|330506437|ref|YP_004382865.1|  8 RCISCG 13
                                      599996 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.029
                         zf-H2C2_2 14 pyeCplCd 21
                                      ++ Cp+C+
  gi|330506437|ref|YP_004382865.1| 23 RFPCPSCG 30
                                      699****7 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.43
                         zf-H2C2_2 16 eCplCdka 23
                                       C +C+k 
  gi|330506437|ref|YP_004382865.1| 35 RCNKCKKQ 42
                                      6****996 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.013
                         zf-H2C2_2 13 kpyeCplCdka 23
                                      + y+C++C+ +
  gi|330506437|ref|YP_004382865.1| 44 NVYTCKACGFT 54
                                      45******975 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   9.6     0.012         8       1      42 [.       9      52 ..       9      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                              NMD3  1 CcrCGkeieeling...lCedCllkevditegiekievevCkeCg 42
                                      C+ CG++ +  + g    C++C +   +  +++++ +v  Ck Cg
  gi|330506437|ref|YP_004382865.1|  9 CISCGITLT-GVGGarfPCPSCGTVIARCNKCKKQSNVYTCKACG 52
                                      ********6.55667999**************************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 ?   10.2   3.7   0.00075       0.5       1      21 [.       8      31 ..       8      33 .. 0.79
   2 ?    0.3   8.2      0.97   6.5e+02       1      21 [.      35      53 ..      35      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00075
                     zinc_ribbon_2  1 fCpnCGael.q.dnakF.CpyCGt 21
                                      +C +CG +l    +a+F Cp CGt
  gi|330506437|ref|YP_004382865.1|  8 RCISCGITLtGvGGARFpCPSCGT 31
                                      58888888853359*********9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.97
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGt 21
                                      +C +C ++   n+  C  CG+
  gi|330506437|ref|YP_004382865.1| 35 RCNKCKKQ--SNVYTCKACGF 53
                                      69999998..99999****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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):              27  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 369.32
//
Query:       gi|330506438|ref|YP_004382866.1|  [L=222]
Description: hypothetical protein MCON_0142 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-11   44.9   0.0    2.5e-05   24.0   0.0    2.1  2  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.81   10.0   0.0    2.1  2  PucR       Purine catabolism regulatory protein-like 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 !   24.0   0.0   2.8e-09   2.5e-05       4      63 ..      11      68 ..       8      91 .. 0.81
   2 !   19.0   0.0   9.3e-08   0.00083     136     186 ..      98     151 ..      92     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.8e-09
                                      EEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC CS
                         AA_kinase  4 VvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllal..ksglssgela 63
                                      V+KlGGs++++  +  l r++  +a+   +++   vV Ggg+f+d + ++  k+gl ++ ++
  gi|330506438|ref|YP_004382866.1| 11 VLKLGGSLIETSRD--LMRVLISLANE--EDYSFLVVPGGGPFADLIREInaKRGLGDEAAH 68
                                      9*********9989..88888888887..77888****************888888888877 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 9.3e-08
                                       HTT-EEEEESEEEEETTTE....EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCE CS
                         AA_kinase 136 eagvvpvltgfigldeege....lgrgssDtiaallAealgAdkliiltdVdGVy 186
                                       e+++v vl ++ +l+e+      ++  +sD ia l+A+ lg   li +tdVdGV+
  gi|330506438|ref|YP_004382866.1|  98 EKREVNVLLPYRALTEDDFcpehSWDYTSDSIALLVAARLGL-PLIKATDVDGVL 151
                                       6678999999999999999999999*****************.***********7 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   9.1e-05      0.81      75     115 ..      18      58 ..      11      59 .. 0.90
   2 ?   -0.3   0.0      0.14   1.3e+03      89      99 ..     133     143 ..     125     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 9.1e-05
                              PucR  75 viklgreipeelieaadelglPlielpeevpfveiieevle 115
                                        i++ r++ + li++a+e +   +++p   pf+++i+e++ 
  gi|330506438|ref|YP_004382866.1|  18 LIETSRDLMRVLISLANEEDYSFLVVPGGGPFADLIREINA 58 
                                       57888899******************************986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.14
                              PucR  89 aadelglPlie 99 
                                       +a +lglPli+
  gi|330506438|ref|YP_004382866.1| 133 VAARLGLPLIK 143
                                       7999*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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: 00:00:00.41
# Mc/sec: 1608.42
//
Query:       gi|330506439|ref|YP_004382867.1|  [L=142]
Description: ADP-ribose pyrophosphatase [Methanosaeta concilii GP6]
Scores for complete 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-22   78.7   0.0    4.7e-22   78.4   0.0    1.0  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
       0.18   11.3   0.0       0.84    9.1   0.0    1.8  2  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 !   78.4   0.0   5.3e-26   4.7e-22       5     127 ..      12     125 ..       8     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 5.3e-26
                                       EEEEEEEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   5 avgvvllnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd 80 
                                       a +v+l+++   ++l+rr++ p +g ++lPgG+ve gEt+eeAA+RE++EEtGl+ +ll l+g    ++++++++++
  gi|330506439|ref|YP_004382867.1|  12 ADAVILFQDG--IVLIRRNNPPYQGcYALPGGFVEIGETVEEAAIREAREETGLDINLLGLVG----VYSDPARDPR 82 
                                       3445577777..*******999999778**************************999999999....8888899999 PP

                                       EEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHH CS
                             NUDIX  81 eheilyvfleevegelepndenevsevrwvpleellkeklaaesrkl 127
                                        h +++ fl++  g+l+ +   + ++++ +p+eel  ++l  +++++
  gi|330506439|ref|YP_004382867.1|  83 GHVVSVAFLARGSGRLQSG--SDARSAEVFPPEEL--TRLSFDHEQI 125
                                       *********9999999998..55567777******..6666666655 PP

>> DUF4916  Domain of unknown function (DUF4916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0     0.063   5.7e+02      56      79 ..      39      62 ..      19      69 .. 0.82
   2 ?    9.1   0.0   9.4e-05      0.84     106     152 ..      77     123 ..      71     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.063
                                      EEEE--TT--HHHHHHHHHHHHH- CS
                           DUF4916 56 vsGrvlyhetvreallrhiekdlG 79
                                        G v   etv ea +r+  ++ G
  gi|330506439|ref|YP_004382867.1| 39 PGGFVEIGETVEEAAIREAREETG 62
                                      568899999999999998877655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 9.4e-05
                                       SEE-TT-EEEEEEEEEEB-S-----TTEEEEEEE-HHHHTSHHHHHT CS
                           DUF4916 106 eytdprqhavslayvvpvaGdceprqdaleleWltpeealseevlae 152
                                       +  dpr h vs+a++   +G  ++ +da   e + pee ++ ++ +e
  gi|330506439|ref|YP_004382867.1|  77 PARDPRGHVVSVAFLARGSGRLQSGSDARSAEVFPPEELTRLSFDHE 123
                                       678********************************999987776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1023.25
//
Query:       gi|330506440|ref|YP_004382868.1|  [L=559]
Description: glutamyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-65  219.2   0.0    7.6e-65  218.9   0.0    1.1  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    2.8e-23   82.7   0.0    4.6e-23   82.0   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 !  218.9   0.0   8.5e-69   7.6e-65       2     310 ..     100     403 ..      99     407 .. 0.95

  Alignments for each domain:
  == domain 1  score: 218.9 bits;  conditional E-value: 8.5e-69
                                       -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC-..-HHHHHHHHHHHHHTT---SSEEEEGGG CS
                      tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdpere..keeaeesiledlkwlgikwdekptyqsd 76 
                                       V+ RfaP+P+G + +G+a+ +++n  + k+++Gkfi+R++DTdp ++   +ea    led +wl  k+ ++++ +s+
  gi|330506440|ref|YP_004382868.1| 100 VVMRFAPNPNGPPTLGSARGIIVNSEYVKKYGGKFIIRFDDTDPVKKrpMPEAYGWYLEDCQWLAAKP-DQVIVASE 175
                                       899****************************************9776225799999************.67****** PP

                                       GHHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTT CS
                      tRNA-synt_1c  77 rfdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkidee 153
                                       r ++++ +aeeLi++G AYvc c++   +e++e+   +++  r +++eenl+l+ ++m +g+ ++++av+R+k d++
  gi|330506440|ref|YP_004382868.1| 176 RIEQYYPIAEELIRRGGAYVCRCPQAAFKEHKEK--GIECIDRGQSIEENLDLW-KKMLDGTLKEGEAVLRVKTDMH 249
                                       ********************************99..99****************.89******************** PP

                                       SS.GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-E CS
                      tRNA-synt_1c 154 ss.vefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevpp 229
                                       ++  ++rD  + ri  +p   h+lv++++++ P  df  ++ D+l + th++r+++  d+ +++  l+ +lg+e p+
  gi|330506440|ref|YP_004382868.1| 250 HKdPAIRDWPAFRIVTAP---HPLVGDRYRVWPLLDFESAVEDHLLGTTHIIRGKDLADSGSRQRYLYSYLGWEYPR 323
                                       999***************...******************************************************** PP

                                       EEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHH CS
                      tRNA-synt_1c 230 fiheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnreskslea 306
                                       +ih   +   +    S  kl   ++  ++ +wdd+r ++++++r +G+ pe+ r+++   ++ + + ++ +++s+ a
  gi|330506440|ref|YP_004382868.1| 324 VIHWGRVKIHQFGSFSTSKLRKAIEAGEYSGWDDPRVPTVRAMRCRGIRPEALRKFMIDLGVGETD-ISLSMDSIYA 399
                                       ***9888888888888889999999*************************************9999.9999999888 PP

                                       HHHH CS
                      tRNA-synt_1c 307 fdrk 310
                                        +rk
  gi|330506440|ref|YP_004382868.1| 400 ENRK 403
                                       7776 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 !   82.0   0.0   5.1e-27   4.6e-23       1     173 [.     409     545 ..     409     546 .. 0.92

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 5.1e-27
                    tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelynikveev 77 
                                       A+R+++V++pv ++ie+   + +  +++plhp   ++g r++p +++++i r+D++ +  g+++rLk+l+n+++++ 
  gi|330506440|ref|YP_004382868.1| 409 ANRRFFVWEPVALEIEG---DVPPLARAPLHPT-DDRGFREIPAGNRLFICRSDLEGFRAGDNIRLKDLCNVEITSL 481
                                       89**************5...35579********.6****************************************99 PP

                    tRNA-synt_1c_C  78 ekdesgevtelkleydgesleearkkkgiihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepal 154
                                       e          ++++ g+++    k ++iihW +  + v++                 +++pd+    +eg++e  +
  gi|330506440|ref|YP_004382868.1| 482 E--------PARARFLGKDM---GKRTKIIHWAPL-DGVRV----------------IVMKPDGV---DEGIGETGI 527
                                       4........24699999999...47899******5.89999................99*****8...79******* PP

                    tRNA-synt_1c_C 155 anlkkgdivQfeRiGyfrv 173
                                       a+ + g++vQfeR+G++rv
  gi|330506440|ref|YP_004382868.1| 528 AE-ELGKVVQFERYGFVRV 545
                                       *9.**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 4063.96
//
Query:       gi|330506441|ref|YP_004382869.1|  [L=96]
Description: hypothetical protein MCON_0145, partial [Methanosaeta concilii GP6]
Scores for complete 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   94.8   0.2    6.4e-27   94.7   0.2    1.0  1  CHAT      CHAT domain


Domain annotation for each model (and alignments):
>> CHAT  CHAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   0.2   3.6e-31   6.4e-27     192     289 ..       1      95 [.       1      96 [] 0.97

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 3.6e-31
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                              CHAT 192 lVvLsACqtglgevidgegvlgLaralllaGarsviaslwpVddeatalLmkrfyqnlla.glskaeALreaqlkll 267
                                       +++LsAC+tg+   +  ++v++L +a+++aG   +i+slw V++++ta+Lm rfyq ++a g+++ +AL++aq +l+
  gi|330506441|ref|YP_004382869.1|   1 MATLSACETGVPGARLPDEVVSLPSAFIRAGFAGAIGSLWTVSEKSTAMLMIRFYQLWRAeGKQPVQALARAQKELR 77 
                                       689*******99899************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxx RF
                              CHAT 268 sgkrdqkpshapyyWaaFiliG 289
                                       ++ r    + +p+yWaaF+++G
  gi|330506441|ref|YP_004382869.1|  78 EDTR----FWHPFYWAAFYMTG 95 
                                       **99....677*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 785.39
//
Query:       gi|330506442|ref|YP_004382870.1|  [L=262]
Description: acylphosphatase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-19   69.9   0.1    5.8e-19   68.3   0.1    2.0  2  Acylphosphatase  Acylphosphatase
    3.4e-06   27.4   3.1       0.14   12.6   0.1    4.4  4  Snapin_Pallidin  Snapin/Pallidin
    0.00029   20.8   1.1      0.016   15.1   1.1    2.4  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
     0.0012   18.6   0.1      0.034   13.8   0.1    2.1  1  DUF4559          Domain of unknown function (DUF4559)
     0.0041   17.2   0.0        4.1    7.4   0.0    2.9  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
  ------ inclusion threshold ------
      0.012   15.9   0.0        1.2    9.5   0.0    2.8  3  DUF948           Bacterial protein of unknown function (DUF94
      0.013   15.5   3.2          1    9.4   0.1    2.8  4  DUF1664          Protein of unknown function (DUF1664)
      0.013   14.8   1.5      0.024   14.0   1.5    1.4  1  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
      0.039   14.1   0.1        1.9    8.7   0.0    3.1  4  CREPT            Cell-cycle alteration and expression-elevate
      0.072   13.4   0.7        1.7    9.0   0.0    2.8  2  KxDL             Uncharacterized conserved protein
      0.075   11.9   1.2       0.15   10.9   1.2    1.5  1  Spc7             Spc7 kinetochore protein
      0.092   12.8   0.0       0.13   12.3   0.0    1.4  1  DUF1115          Protein of unknown function (DUF1115)
        0.1   10.4   0.8        1.4    6.6   0.1    1.9  2  Nup88            Nuclear pore component
        0.1   11.8   0.7        3.9    6.6   0.0    2.1  2  TMPIT            TMPIT-like protein
       0.11   10.4   0.1          3    5.7   0.0    1.8  2  Prominin         Prominin
       0.18   12.2   2.3        2.9    8.3   0.1    3.5  4  UPF0184          Uncharacterised protein family (UPF0184)
       0.52   10.8   5.0        9.7    6.7   0.5    2.7  4  DUF5610          Domain of unknown function (DUF5610)
       0.59   10.3   3.4        2.1    8.6   0.8    3.0  3  DUF5446          Family of unknown function (DUF5446)


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 !   68.3   0.1   5.9e-22   5.8e-19       2      83 ..       5      86 ..       4      89 .. 0.96
   2 ?   -2.9   0.0       9.2   9.1e+03      49      70 ..     105     128 ..      93     144 .. 0.63

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 5.9e-22
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      +++v+G+VQ  g+R  +  +A+ +glkGyv+Nl+d +V+ivaeg e+++e+fle+++ +++ + v+e++++ +e+++ +
  gi|330506442|ref|YP_004382870.1|  5 TAYVSGKVQMAGYRSKIATIARVFGLKGYVMNLPDSRVKIVAEGHEADLERFLEAVRIKNTLIDVEEIKADFSEANGSY 83
                                      689**************************************************************************99 PP

                   Acylphosphatase 81 kdF 83
                                      ++F
  gi|330506442|ref|YP_004382870.1| 84 EEF 86
                                      777 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.2
                   Acylphosphatase  49 kvekfleelksgppk..arvdeve 70 
                                        ++++++++++g +   ++ d+++
  gi|330506442|ref|YP_004382870.1| 105 YLKELISAVREGFKDngSKLDSMS 128
                                       566677777765554455555555 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1    0.0089       8.9      13      38 ..     122     147 ..     120     151 .. 0.91
   2 ?    2.4   0.0      0.21     2e+02      17      38 ..     151     172 ..     148     176 .. 0.87
   3 ?    2.5   0.0       0.2     2e+02      17      38 ..     176     197 ..     172     201 .. 0.87
   4 !   12.6   0.1   0.00014      0.14      17      80 ..     201     261 ..     198     262 .] 0.92

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0089
                   Snapin_Pallidin  13 pkldeldeklkelrqsQeeLleqldr 38 
                                       +kld + ++lk++  +Q++L++++++
  gi|330506442|ref|YP_004382870.1| 122 SKLDSMSSSLKDISGKQDDLKKSITE 147
                                       5899******************9975 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.21
                   Snapin_Pallidin  17 eldeklkelrqsQeeLleqldr 38 
                                       e+ + lk++  +Q++L++++++
  gi|330506442|ref|YP_004382870.1| 151 ETGSYLKDISGKQDDLKKSITE 172
                                       667899************9975 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.2
                   Snapin_Pallidin  17 eldeklkelrqsQeeLleqldr 38 
                                       e+ + lk++  +Q++L++++++
  gi|330506442|ref|YP_004382870.1| 176 ETGSYLKDISGKQDDLKKSITE 197
                                       667899************9975 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00014
                   Snapin_Pallidin  17 eldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeya.kKLvnikkrmsslnerlq 80 
                                       e+ ++lk++  +Q++  +++d  +e++  ++e+    + +dlk    ++L++i+ ++++++ r++
  gi|330506442|ref|YP_004382870.1| 201 ETGSSLKDISGKQDQIIDRIDCAREEI--VSEVSG--MRSDLKGRTeERLQRIESDVTEIKARMR 261
                                       67789**********************..899999..9*****98879*************9986 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.1   1.6e-05     0.016     103     141 ..     167     260 ..      47     262 .] 0.52

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                                       H.......................................................HHHHHHHHHHHHHHHHCHHHH CS
                    Apolipoprotein 103 e.......................................................lrerlerhvealkarlapyve 124
                                       +                                                       +re++ ++v+ +++ l+  +e
  gi|330506442|ref|YP_004382870.1| 167 KksitegfretgsylkdisgkqddlkksitegfretgsslkdisgkqdqiidridcAREEIVSEVSGMRSDLKGRTE 243
                                       03333333335555555555555544444444444666655555555555555555555555555555555555555 PP

                                       HHHHHHHHHHHHHHH-- CS
                    Apolipoprotein 125 elrqklaerleelkesl 141
                                       e  q++++ + e+k ++
  gi|330506442|ref|YP_004382870.1| 244 ERLQRIESDVTEIKARM 260
                                       55555555555555444 PP

>> DUF4559  Domain of unknown function (DUF4559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   3.4e-05     0.034     139     300 ..      52     226 ..      24     262 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-05
                           DUF4559 139 dvekvknvievRNklMHSpdlkvssqdmkeymkkilrLledlktvpeleeaeeaieellkilkqefeislke.ddev 214
                                       d e + + ++++N+l+   ++k +  +++   ++ ++++ + +t++ l +a e  +el   +++ f+ + ++ d  +
  gi|330506442|ref|YP_004382870.1|  52 DLERFLEAVRIKNTLIDVEEIKADFSEANGSYEEFFKIAGEGETDARLDQAAEYLKELISAVREGFKDNGSKlDSMS 128
                                       55677788889999999999999999999999999999999889999999999999999999999999888856666 PP

                           DUF4559 215 rvltdvllslqklkeleeellkedatkldelvlraeeqkiskeel.lkelqvlkeflnknkdLkenlkedv...... 284
                                       ++l d+  ++ +lk+  +e ++e +  l+++  ++++ k s  e  +++   lk++  k  dLk+  +e        
  gi|330506442|ref|YP_004382870.1| 129 SSLKDISGKQDDLKKSITEGFRETGSYLKDISGKQDDLKKSITEGfRETGSYLKDISGKQDDLKKSITEGFretgss 205
                                       77888888888899999999999899999997777777777777767788888888888888998888877777766 PP

                           DUF4559 285 .....kklqeieekldklded 300
                                             k+++i +++d++ e+
  gi|330506442|ref|YP_004382870.1| 206 lkdisGKQDQIIDRIDCAREE 226
                                       666664555555555555444 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 !    7.4   0.0    0.0041       4.1      14      96 ..      49     133 ..      42     148 .. 0.56
   2 ?    1.6   0.0      0.27   2.6e+02      18      63 ..     127     172 ..     119     187 .. 0.51
   3 ?    6.2   0.0      0.01        10      20      99 ..     179     258 ..     155     261 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0041
                      Baculo_PEP_C  14 qfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksl.laeldtrldtlltnLtdalnalq...dtlrne 86 
                                       +  dL   L+a+r +n+ i  ++++++++  +  ++ +e +k +   e d+rld++++ L++ + a+    ++  ++
  gi|330506442|ref|YP_004382870.1|  49 HEADLERFLEAVRIKNTLI--DVEEIKADFSEANGSYEEFFKIAgEGETDARLDQAAEYLKELISAVRegfKDNGSK 123
                                       5678888888888888887..44444444444333332222222024556688888888888888888555222234 PP

                      Baculo_PEP_C  87 Ltnlnsiltn 96 
                                       L+++ s l +
  gi|330506442|ref|YP_004382870.1| 124 LDSMSSSLKD 133
                                       4444444433 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.27
                      Baculo_PEP_C  18 LtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt 63 
                                       ++  L++i  ++  +   +++ + +  + L+++s +  +l +++++
  gi|330506442|ref|YP_004382870.1| 127 MSSSLKDISGKQDDLKKSITEGFRETGSYLKDISGKQDDLKKSITE 172
                                       3444445544444455555555555555555555555554444444 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.01
                      Baculo_PEP_C  20 nvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltn 96 
                                         L++i  ++  +   +++ + +  ++L+++s +  + +  +d + ++ +++++     l+   +++L+ ++s++t+
  gi|330506442|ref|YP_004382870.1| 179 SYLKDISGKQDDLKKSITEGFRETGSSLKDISGKQDQIIDRIDCAREEIVSEVSGMRSDLKGRTEERLQRIESDVTE 255
                                       56666666666666666666777777777777777777777777777777777777777777777777777777776 PP

                      Baculo_PEP_C  97 Lls 99 
                                       + +
  gi|330506442|ref|YP_004382870.1| 256 IKA 258
                                       655 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0012       1.2      25      86 ..     121     183 ..      93     186 .. 0.86
   2 ?    9.5   0.0    0.0012       1.2      23      87 ..     144     209 ..     141     211 .. 0.89
   3 ?    5.1   0.0     0.028        27      23      70 ..     169     216 ..     166     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvd.plteavadlgesvse 86 
                                       ++ ld+++++++++  + d + k +++  +++   l+d+++k ++++ ++te ++++g  +++
  gi|330506442|ref|YP_004382870.1| 121 GSKLDSMSSSLKDISGKQDDLKKSITEGFRETGSYLKDISGKQDDLKkSITEGFRETGSYLKD 183
                                       6679999************************************99972577777777776665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvd.plteavadlgesvsel 87 
                                       ++++ ++e+ + ++++  + d + k +++  +++   l+d+++k ++++ ++te ++++g s++++
  gi|330506442|ref|YP_004382870.1| 144 SITEGFRETGSYLKDISGKQDDLKKSITEGFRETGSYLKDISGKQDDLKkSITEGFRETGSSLKDI 209
                                       567778999999***********************************9736899999999999887 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.028
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekv 70 
                                       ++++ ++e+ + ++++  + d + k +++  +++   l+d+++k +++
  gi|330506442|ref|YP_004382870.1| 169 SITEGFRETGSYLKDISGKQDDLKKSITEGFRETGSSLKDISGKQDQI 216
                                       456667788888888888888888888888888888888888887765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       6.1   6.1e+03      83     104 ..      63      84 ..      54      92 .. 0.65
   2 ?    2.1   0.1      0.18   1.8e+02      73     110 ..     101     138 ..      93     147 .. 0.38
   3 ?    9.4   0.1     0.001         1      38     124 .]     126     213 ..     106     213 .. 0.91
   4 ?    8.5   0.5     0.002         2      47     109 ..     196     259 ..     190     262 .] 0.60

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.1
                           DUF1664  83 keikeevtevredlseigedve 104
                                       k++  +v+e++ d se +   e
  gi|330506442|ref|YP_004382870.1|  63 KNTLIDVEEIKADFSEANGSYE 84 
                                       4555566777776666655555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.18
                           DUF1664  73 kkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                       +  +  ke++++++e  ++  ++l+++++ ++ ++   
  gi|330506442|ref|YP_004382870.1| 101 QAAEYLKELISAVREGFKDNGSKLDSMSSSLKDISGKQ 138
                                       33333333333333333333333333333333333333 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.001
                           DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedve.svkeavegl 113
                                       s+s+ ++++s + +++++s+++  r+  s ++ +  k+d+ k+ ++e  +e  +  +d+s  ++d++ s+ e +++ 
  gi|330506442|ref|YP_004382870.1| 126 SMSSSLKDISGKQDDLKKSITEGFRETGSYLKDISGKQDDLKKSITEGFRETGSYLKDISGKQDDLKkSITEGFRET 202
                                       799999999999999999***999**************999999999999999999999999999853799999999 PP

                           DUF1664 114 esklerieekQ 124
                                       +s+l++i++kQ
  gi|330506442|ref|YP_004382870.1| 203 GSSLKDISGKQ 213
                                       9***9999998 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.002
                           DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevte.vredlseigedvesvkea 109
                                       ++   +  +sl++   +  + idr+d+  +e     + ++++++   +e l++i++dv+++k+ 
  gi|330506442|ref|YP_004382870.1| 196 TEGFRETGSSLKDISGKQDQIIDRIDCAREEIVSEVSGMRSDLKGrTEERLQRIESDVTEIKAR 259
                                       5555555566666666666667777777777777677777776641455667777777776654 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 ?   14.0   1.5   2.4e-05     0.024      84     257 ..      83     256 ..      63     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                    ALIX_LYPXL_bnd  84 yreileeAsesDkivrqklqenkedlelL.sgpeeeleaalpssssaaa..sesveeqirklrsllekldelkaere 157
                                       y+e ++ A+e    + ++l++  e l++L s+ +e  ++  +    + +  s+s ++  +k  +l + + e  +e  
  gi|330506442|ref|YP_004382870.1|  83 YEEFFKIAGEG--ETDARLDQAAEYLKELiSAVREGFKDNGS----KLDsmSSSLKDISGKQDDLKKSITEGFRETG 153
                                       55555555543..34455666666666664544444444432....2222256777777777788888888889999 PP

                    ALIX_LYPXL_bnd 158 qllkdlkekaendDitpklltekkr......diaanefealfeeelekydplqeqleqslakqeellkeiqeaneef 228
                                       + lkd+    ++dD ++ + + +++      di+ ++ ++l ++  e +++  + l++   kq++++ +i+ a ee+
  gi|330506442|ref|YP_004382870.1| 154 SYLKDIS--GKQDDLKKSITEGFREtgsylkDISGKQ-DDLKKSITEGFRETGSSLKDISGKQDQIIDRIDCAREEI 227
                                       9999997..8999999999988888999998777444.888777777****************************** PP

                    ALIX_LYPXL_bnd 229 eqskksdseqsqrqreevlqkleaaydky 257
                                        ++ +  +++ + ++ee lq++e+ ++++
  gi|330506442|ref|YP_004382870.1| 228 VSEVSGMRSDLKGRTEERLQRIESDVTEI 256
                                       ***99999778999*******99987765 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 ?   -2.0   0.0       3.6   3.6e+03      99     125 ..      14      39 ..       7      50 .. 0.73
   2 ?    8.7   0.0    0.0019       1.9      70     120 ..      94     145 ..      67     147 .. 0.89
   3 ?   -0.9   0.0       1.7   1.7e+03      81     120 ..     156     195 ..     150     210 .. 0.64
   4 ?    0.5   0.1      0.61   6.1e+02      80     106 ..     234     260 ..     226     262 .] 0.56

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.6
                             CREPT  99 leelkeklekvksvrkelkshiqsLPd 125
                                       ++ +++k++++  v   lk  + +LPd
  gi|330506442|ref|YP_004382870.1|  14 MAGYRSKIATIARVF-GLKGYVMNLPD 39 
                                       566788888887764.58888899998 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0019
                             CREPT  70 eleeR.kklakmledfleaqkellakaeekleelkeklekvksvrkelkshi 120
                                       e++ R  + a++l+++++a++e  +++ +kl+++ + l+ ++ ++++lk+ i
  gi|330506442|ref|YP_004382870.1|  94 ETDARlDQAAEYLKELISAVREGFKDNGSKLDSMSSSLKDISGKQDDLKKSI 145
                                       66667457899**************************************987 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.7
                             CREPT  81 ledfleaqkellakaeekleelkeklekvksvrkelkshi 120
                                       l+d+   q +l +   e  +e+ + l+ ++ ++++lk+ i
  gi|330506442|ref|YP_004382870.1| 156 LKDISGKQDDLKKSITEGFRETGSYLKDISGKQDDLKKSI 195
                                       5555555555555566666666666666666666666655 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.61
                             CREPT  80 mledfleaqkellakaeekleelkekl 106
                                       m +d++    e+l++ e+ ++e+k ++
  gi|330506442|ref|YP_004382870.1| 234 MRSDLKGRTEERLQRIESDVTEIKARM 260
                                       555555555555555555555555554 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0017       1.7      28      80 ..      95     147 ..      93     151 .. 0.93
   2 ?    1.7   0.1      0.32   3.2e+02      46      70 ..     234     259 ..     194     262 .] 0.53

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                              KxDL  28 knreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkaklak 80 
                                       + ++L +  ++++e  + +r+ fk++   l ++ + L+ i  k + lk+ +++
  gi|330506442|ref|YP_004382870.1|  95 TDARLDQAAEYLKELISAVREGFKDNGSKLDSMSSSLKDISGKQDDLKKSITE 147
                                       778999******************************************98875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.32
                              KxDL  46 lrarfkqgt.kllkevkkdLesifkk 70 
                                       +r+++k  t + l+++ +d   i+ +
  gi|330506442|ref|YP_004382870.1| 234 MRSDLKGRTeERLQRIESDVTEIKAR 259
                                       33333333333334444444444333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.2   0.00015      0.15     135     279 ..     108     257 ..      93     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                              Spc7 135 qllegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelael 211
                                       +l++ ++eg ++n ++l++ ++ L++   + d+l+++++e + e  + l+++  ++++l+++  e  +e+ + l+++
  gi|330506442|ref|YP_004382870.1| 108 ELISAVREGFKDNGSKLDSMSSSLKDISGKQDDLKKSITEGFRETGSYLKDISGKQDDLKKSITEGFRETGSYLKDI 184
                                       6889999************************************9999999999999999999999999999999999 PP

                              Spc7 212 kaeieekkkelae....lqeqleeleekieelkeqkseleeei.aeaervleeckgwsesevsrlkeevkale 279
                                       + + + +kk ++e      + l++++ k +++ ++++ ++eei +e   ++   kg +e+ ++r+++ v +++
  gi|330506442|ref|YP_004382870.1| 185 SGKQDDLKKSITEgfreTGSSLKDISGKQDQIIDRIDCAREEIvSEVSGMRSDLKGRTEERLQRIESDVTEIK 257
                                       9999888888876211155678888999999999999888887366788999999999999999999999886 PP

>> DUF1115  Protein of unknown function (DUF1115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014      0.13      11      62 ..      15      65 ..       6     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                           DUF1115 11 pkhrfkvdknAkqlsltGvvllg.pkfnlvvveGgekaikkYkklmlrrikWt 62
                                         r k+ + A   +l+G v+   ++   +v+eG e +++++ + +  rik t
  gi|330506442|ref|YP_004382870.1| 15 AGYRSKIATIARVFGLKGYVMNLpDSRVKIVAEGHEADLERFLEAV--RIKNT 65
                                      55799*************88877544578*************9988..77755 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0038       3.8     630     709 ..     113     195 ..      41     196 .. 0.77
   2 ?    6.6   0.1    0.0014       1.4     579     648 ..     190     260 ..     178     262 .] 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0038
                             Nup88 630 mkkelekikeklkslknalkqvkkkldkqrkqiakskeeekksslelsekq...kktikeiLkeegeeieelikqvk 703
                                       +++ ++   +kl+s+  +lk++  k+d  +k i+++  e+ +    +s kq   kk i+e  +e+g+ ++++  +  
  gi|330506442|ref|YP_004382870.1| 113 VREGFKDNGSKLDSMSSSLKDISGKQDDLKKSITEGFRETGSYLKDISGKQddlKKSITEGFRETGSYLKDISGKQD 189
                                       45566777789999999999999999999999999866655555455544433378999999999999999988888 PP

                             Nup88 704 dikkiv 709
                                       d+kk +
  gi|330506442|ref|YP_004382870.1| 190 DLKKSI 195
                                       888765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0014
                             Nup88 579 eerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklp.vlseaeremkkelekikeklkslknal 648
                                       + +ks++e   +    + +i+ kQ++++ r++   +++ s++  + s+ +   ++ l++i++++ ++k+++
  gi|330506442|ref|YP_004382870.1| 190 DLKKSITEGFRETGSSLKDISGKQDQIIDRIDCAREEIVSEVSgMRSDLKGRTEERLQRIESDVTEIKARM 260
                                       56999**************************9999998887761556777788899999999999999886 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0039       3.9       5      86 ..     104     185 ..      93     191 .. 0.71
   2 ?    3.9   0.1     0.026        26      12      82 ..     193     260 ..     183     262 .] 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0039
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkv 81 
                                       e l++ + +++e +k   +kl+++s++ +++s + +  kk ++e  ++  ++ k+++ ++++  ++++e ++e+ ++
  gi|330506442|ref|YP_004382870.1| 104 EYLKELISAVREGFKDNGSKLDSMSSSLKDISGKQDDLKKSITEGFRETGSYLKDISGKQDDLKKSITEGFRETGSY 180
                                       44556666677777777777777777777777777777777777777777777777777788888888888777777 PP

                             TMPIT  82 lkeve 86 
                                       lk+++
  gi|330506442|ref|YP_004382870.1| 181 LKDIS 185
                                       77776 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.026
                             TMPIT  12 keleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvl 82 
                                       k++ e ++e  ++l+++s  q+++  +i+  +++   + s+++ +++++k ++ee+++++++++ e+k+ +
  gi|330506442|ref|YP_004382870.1| 193 KSITEGFRETGSSLKDISGKQDQIIDRIDCAREE---IVSEVSGMRSDLKGRTEERLQRIESDVTEIKARM 260
                                       5677888888889999999999999888887765...5667777777888899999999999999998876 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.027        27     613     696 ..      56     147 ..      45     163 .. 0.55
   2 ?    5.7   0.0     0.003         3     173     269 ..     165     260 ..     157     262 .] 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.027
                          Prominin 613 yleqlckkltkvnletlaekleelanelsngk.....knlkqslkneaqdlraiqqelvlple...ssvkklkksvk 681
                                       +le ++ k t +++e+++++  e   + ++        +   +l ++a+ l+++ +   +  +   s+++++ +s+k
  gi|330506442|ref|YP_004382870.1|  56 FLEAVRIKNTLIDVEEIKADFSEANGSYEEFFkiageGETDARLDQAAEYLKELISAVREGFKdngSKLDSMSSSLK 132
                                       55555555555555555555555555443322455555555566666666665555554444311144555555666 PP

                          Prominin 682 kldeensdlqesikk 696
                                       +++ ++ dl++si++
  gi|330506442|ref|YP_004382870.1| 133 DISGKQDDLKKSITE 147
                                       666666777766665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.003
                          Prominin 173 esketvkrgledlrtflkdvp...qhidhvlvqnyeelekhvsddLddagkhlgldladtlesnvlpaLaelerlle 246
                                       + k+++++g++++ ++lkd++   + +++ + + ++e+    ++d+++ ++++++++  + e+     ++e+  +  
  gi|330506442|ref|YP_004382870.1| 165 DLKKSITEGFRETGSYLKDISgkqDDLKKSITEGFRETG-SSLKDISGKQDQIIDRIDCAREEI----VSEVSGMRS 236
                                       567899999**********98333456666778899999.667889999999999997766655....899999999 PP

                          Prominin 247 nlk.eakeqLeqvnklekeLrksg 269
                                       +lk +++e L+ +++  +e++  +
  gi|330506442|ref|YP_004382870.1| 237 DLKgRTEERLQRIESDVTEIKARM 260
                                       998458889999999999998766 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0029       2.9      29      58 ..     118     147 ..     111     152 .. 0.85
   2 ?   -0.3   0.0       1.5   1.5e+03      40      58 ..     154     172 ..     149     177 .. 0.81
   3 ?    0.3   0.0      0.97   9.7e+02      39      58 ..     178     197 ..     168     215 .. 0.82
   4 ?   -0.8   0.1       2.1   2.1e+03      34      49 ..     205     220 ..     185     255 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0029
                           UPF0184  29 eainsmLDqinsaLDalEernDdlnskLrE 58 
                                       ++  s LD ++s L ++  ++Ddl+  + E
  gi|330506442|ref|YP_004382870.1| 118 KDNGSKLDSMSSSLKDISGKQDDLKKSITE 147
                                       566799******************987766 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                           UPF0184  40 saLDalEernDdlnskLrE 58 
                                       s+L ++  ++Ddl+  + E
  gi|330506442|ref|YP_004382870.1| 154 SYLKDISGKQDDLKKSITE 172
                                       8999999999999877665 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.97
                           UPF0184  39 nsaLDalEernDdlnskLrE 58 
                                        s+L ++  ++Ddl+  + E
  gi|330506442|ref|YP_004382870.1| 178 GSYLKDISGKQDDLKKSITE 197
                                       58899999999999877665 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2.1
                           UPF0184  34 mLDqinsaLDalEern 49 
                                       +L  i+   D++ +r 
  gi|330506442|ref|YP_004382870.1| 205 SLKDISGKQDQIIDRI 220
                                       3444444333333333 PP

>> DUF5610  Domain of unknown function (DUF5610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.5    0.0097       9.7      59     116 ..      93     150 ..      81     152 .. 0.86
   2 ?    3.7   0.1     0.085        85      74     117 ..     140     183 ..     128     184 .. 0.84
   3 ?    4.6   0.1     0.043        43      74     117 ..     165     208 ..     150     209 .. 0.87
   4 ?    4.1   0.1     0.063        63      74     112 ..     190     228 ..     175     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0097
                                       -TTS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHHHHHH CS
                           DUF5610  59 kadgaseeklqslleqarkGvekGfkeAreiLeglgvlngeiaegidktydlvqegld 116
                                        +  a  ++++++l+   ++v  Gfk+   +L++++    +i+ + d+ ++ + eg+ 
  gi|330506442|ref|YP_004382870.1|  93 GETDARLDQAAEYLKELISAVREGFKDNGSKLDSMSSSLKDISGKQDDLKKSITEGFR 150
                                       555677788999999999***********************************99987 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.085
                                       HHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHHHHHHH CS
                           DUF5610  74 qarkGvekGfkeAreiLeglgvlngeiaegidktydlvqegldd 117
                                         +k ++ Gf e    L++ +  ++++++ i +    + + l+d
  gi|330506442|ref|YP_004382870.1| 140 DLKKSITEGFRETGSYLKDISGKQDDLKKSITEGFRETGSYLKD 183
                                       5678999************************9988877666665 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.043
                                       HHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHHHHHHH CS
                           DUF5610  74 qarkGvekGfkeAreiLeglgvlngeiaegidktydlvqegldd 117
                                         +k ++ Gf e    L++ +  ++++++ i +    + + l+d
  gi|330506442|ref|YP_004382870.1| 165 DLKKSITEGFRETGSYLKDISGKQDDLKKSITEGFRETGSSLKD 208
                                       567899**************************999988888877 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.063
                                       HHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHH CS
                           DUF5610  74 qarkGvekGfkeAreiLeglgvlngeiaegidktydlvq 112
                                         +k ++ Gf e    L++ +  +++i + id +++ + 
  gi|330506442|ref|YP_004382870.1| 190 DLKKSITEGFRETGSSLKDISGKQDQIIDRIDCAREEIV 228
                                       567899**************************9999886 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.2   1.2e+03      41      59 ..      93     111 ..      69     124 .. 0.82
   2 ?    1.4   0.1      0.37   3.7e+02      14      51 ..     181     221 ..     179     232 .. 0.71
   3 ?    8.6   0.8    0.0021       2.1      19      57 ..     218     256 ..     213     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.2
                           DUF5446  41 ekeeerldllekElkdLvl 59 
                                        + ++rld+  + lk+L +
  gi|330506442|ref|YP_004382870.1|  93 GETDARLDQAAEYLKELIS 111
                                       5678899999999999876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.37
                           DUF5446  14 LeeiEeeltevEkelseavneteae...keekeeerldlle 51 
                                       L++i  + +   k+++e  +et         k+++++d+++
  gi|330506442|ref|YP_004382870.1| 181 LKDISGKQDDLKKSITEGFRETGSSlkdISGKQDQIIDRID 221
                                       67788888888889999888886541114468999999998 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0021
                           DUF5446  19 eeltevEkelseavneteaekeekeeerldllekElkdL 57 
                                       + ++ + +e+ + v   +   +   eerl+++e+ + ++
  gi|330506442|ref|YP_004382870.1| 218 DRIDCAREEIVSEVSGMRSDLKGRTEERLQRIESDVTEI 256
                                       77899999****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.40
# Mc/sec: 1977.32
//
Query:       gi|330506443|ref|YP_004382871.1|  [L=269]
Description: UbiA family prenyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-38  132.7  18.3    1.8e-38  132.3  18.3    1.1  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
      0.034   14.3   0.4        1.3    9.2   0.1    2.5  2  DUF1378   Protein of unknown function (DUF1378)
        9.7    5.4   6.9         14    4.9   0.0    2.5  3  S_4TM     SMODS-associating 4TM effector 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 !  132.3  18.3   3.1e-42   1.8e-38       5     244 ..      20     250 ..      15     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 3.1e-42
                              UbiA   5 alvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgl 81 
                                       a++gl++a  +      +l+++ +++l+++a+n++Ndy+Dr+iDa+  ++p+RP++s r+ p++a+ ++i+l+++g+
  gi|330506443|ref|YP_004382871.1|  20 AIIGLLIAMVQD--MHAALIIAGAVFLITGAGNVINDYYDRQIDAI--NRPDRPIPSKRVRPQTAFYYSIALFAAGC 92 
                                       677788885554..445899999999********************..***************************** PP

                              UbiA  82 lllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgsl.sllalllalavflltw 157
                                       +l+  l++  ++++++++ ll+++Y    lK +++lg++ ++   g  +l+g a+++ ++  l+  +++ + fl ++
  gi|330506443|ref|YP_004382871.1|  93 ILA-GLAGRICLAIAAFNSLLLFFYA-RNLKATPILGNLSVSYLTGSTFLFGGAVAG-FMgILANQVPFGLSFLASM 166
                                       ***.**********************.6******************99999988854.44355666777777999** PP

                              UbiA 158 aialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraarlv 234
                                       +  +a+d++d+ gD+++g +tlp+++G++aa+  la l  v+ +a  l lla ++ lyll+++++ +l+ll  ++++
  gi|330506443|ref|YP_004382871.1| 167 SREIAKDIEDMVGDQQGGARTLPILAGERAAAA-LAGLFGVAGVA--LSLLAPFGRLYLLIVAVADLLLLLSVYKVI 240
                                       ********************************9.66677777766..788899999999998888888888877777 PP

                              UbiA 235 rrrdakkaak 244
                                       r++ a + ++
  gi|330506443|ref|YP_004382871.1| 241 RKDAAGSQKA 250
                                       7766655554 PP

>> DUF1378  Protein of unknown function (DUF1378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00022       1.3      16      38 ..      40      62 ..      34      65 .. 0.90
   2 ?    2.5   0.1     0.027   1.6e+02      13      30 ..     226     242 ..     218     253 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00022
                           DUF1378 16 cvLYLvsGGYkviRnyiRrkiDk 38
                                       +++L+ G   vi +y+ r+iD+
  gi|330506443|ref|YP_004382871.1| 40 GAVFLITGAGNVINDYYDRQIDA 62
                                      5899******************7 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.027
                           DUF1378  13 tvvcvLYLvsGGYkviRn 30 
                                       + v+ L L+   YkviR 
  gi|330506443|ref|YP_004382871.1| 226 A-VADLLLLLSVYKVIRK 242
                                       3.5566677778****96 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 ?    4.9   0.0    0.0023        14     174     225 ..      16      67 ..       9      73 .. 0.87
   2 ?   -2.6   0.3      0.45   2.7e+03      31      53 ..      96     118 ..      82     140 .. 0.61
   3 ?    3.4   1.0    0.0068        41      38      88 ..     198     248 ..     195     250 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0023
                             S_4TM 174 lvlwillvlvvgliknlslsdlllsvivpllpllllalkeyreqresakele 225
                                       +++  +++l++++++++  + +++ +++ ++++  ++ + y +q +++++ +
  gi|330506443|ref|YP_004382871.1|  16 ASAAAIIGLLIAMVQDMHAALIIAGAVFLITGAGNVINDYYDRQIDAINRPD 67 
                                       5667899999***********************9999999999999998766 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.45
                             S_4TM  31 alrvilsvvlaivlsvlavlvps 53 
                                       +l   +++++a++ s+l +++ +
  gi|330506443|ref|YP_004382871.1|  96 GLAGRICLAIAAFNSLLLFFYAR 118
                                       44444566666666666665555 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.0068
                             S_4TM  38 vvlaivlsvlavlvpslktylallgllwllldvlvldrlqkkekekAAkiQ 88 
                                       ++la ++ v++v+++ l+++  l+ l+++++d+l+l ++ k  +++AA  Q
  gi|330506443|ref|YP_004382871.1| 198 AALAGLFGVAGVALSLLAPFGRLYLLIVAVADLLLLLSVYKVIRKDAAGSQ 248
                                       6788899999999999********************************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1971.37
//
Query:       gi|330506444|ref|YP_004382872.1|  [L=289]
Description: hypothetical protein MCON_0148 [Methanosaeta concilii GP6]
Scores for complete 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   0.1    0.00037   20.3   0.1    1.6  1  MarR_2          MarR family
    0.00025   21.1   0.0    0.00046   20.3   0.0    1.4  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
     0.0015   18.4   0.0     0.0041   17.0   0.0    1.7  1  MarR            MarR family
  ------ inclusion threshold ------
       0.13   12.7   0.0       0.29   11.7   0.0    1.5  1  HTH_27          Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   8.3e-08   0.00037      15      57 ..      25      66 ..      18      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.3e-08
                                      HCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                            MarR_2 15 grrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgp 57
                                      + rp++ + +++l r l+++ s  s++++rL+   L++r++ p
  gi|330506444|ref|YP_004382872.1| 25 ALRPEG-IYQSDLRRLLKIDSSKCSKVVARLQGSELIRRESVP 66
                                      555655.89******************************9665 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 !   20.3   0.0     1e-07   0.00046      14      59 ..      26      71 ..      19      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1e-07
                    B-block_TFIIIC 14 sRysGitqsdLakeskqdprslfyrlksLekkgLIvkqsiidsatk 59
                                       R +Gi qsdL +++k+d+++  +++  L+ + LI + s++ s t+
  gi|330506444|ref|YP_004382872.1| 26 LRPEGIYQSDLRRLLKIDSSKCSKVVARLQGSELIRRESVPASSTY 71
                                      599*************************************866554 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   9.1e-07    0.0041      16      51 ..      29      64 ..      17      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.1e-07
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      +++++s+L + l++++s  ++v+ rL   +li+R+ 
  gi|330506444|ref|YP_004382872.1| 29 EGIYQSDLRRLLKIDSSKCSKVVARLQGSELIRRES 64
                                      4599******************************86 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   0.0   6.4e-05      0.29      22      54 ..      34      66 ..      23      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.4e-05
                            HTH_27 22 adlcgrlnvedshisyslkkLtekGLvertgde 54
                                      +dl++ l++++s  s+++ +L   +L+ r+  +
  gi|330506444|ref|YP_004382872.1| 34 SDLRRLLKIDSSKCSKVVARLQGSELIRRESVP 66
                                      8**************************777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 00:00:00.42
# Mc/sec: 2067.23
//
Query:       gi|330506445|ref|YP_004382873.1|  [L=208]
Description: hypothetical protein MCON_0150 [Methanosaeta concilii GP6]
Scores for complete 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-49  168.2   0.0    1.9e-49  168.0   0.0    1.0  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.0   0.0   1.1e-53   1.9e-49       8     204 ..       2     192 ..       1     193 [. 0.95

  Alignments for each domain:
  == domain 1  score: 168.0 bits;  conditional E-value: 1.1e-53
                                       EEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGG.GGSTT-EEEE--S-SS----- CS
                    tRNA_deacylase   8 iiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkia.ekleefevtlEatHHGPtelk 83 
                                       i++ +rH+++++ p +  H+tG l+    G  + +l+ aaP+ l+++l ++++i   + +++ v+ EatHHGP++++
  gi|330506445|ref|YP_004382873.1|   2 IVLPCRHEAKAALPWFGGHFTGILEV---GEGKSRLSAAAPAGLRSFLYNVSAIVsLSMPGYIVSAEATHHGPVDVR 75 
                                       8999******************7765...667889******************998899****************** PP

                                       S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH------EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGGGGG- CS
                    tRNA_deacylase  84 vPslFvEiGSteeeWkdedaaeavaeavlelleseeekekvlvgiGGgHYaprftklvletevavGhilskyaleel 160
                                       +Ps+F+EiGSt+e+W d +a+eava+a+l l  +e    +v++g+GGgHY++r+t+l++++++a+Gh++s+y++ +l
  gi|330506445|ref|YP_004382873.1|  76 TPSFFAEIGSTKEQWVDLKAGEAVARAILALGPEE---LPVFLGFGGGHYVQRQTELIFNSRIAFGHMFSSYQVPDL 149
                                       ******************************95555...*************************************** PP

                                       -HHHHHHHHHHH.T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                    tRNA_deacylase 161 keevikqaleksegadvalidkkslkseqkeaieelleelgiev 204
                                       + e+++ a e s +a++a+id+ksl+s +++++e ++ee g+++
  gi|330506445|ref|YP_004382873.1| 150 DLEAVEIARESS-NATYAYIDRKSLRSAERKRLEGMVEEIGLPM 192
                                       ********9999.**************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1506.38
//
Query:       gi|330506446|ref|YP_004382874.1|  [L=353]
Description: hypothetical protein MCON_0151 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-07   29.3   0.0      0.029   14.3   0.0    3.2  3  MarR_2          MarR family
    0.00013   21.9   0.1        3.6    7.6   0.0    3.8  4  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0004   20.2   0.0        1.1    9.3   0.0    2.4  2  MarR            MarR family
    0.00054   20.1   0.0       0.12   12.6   0.0    3.1  3  B-block_TFIIIC  B-block binding subunit of TFIIIC
  ------ inclusion threshold ------
      0.013   15.6   0.0          3    8.0   0.0    3.4  5  HTH_3           Helix-turn-helix
      0.015   15.1   0.1         19    5.2   0.0    3.3  3  TrmB            Sugar-specific transcriptional regulator TrmB
      0.074   13.3   0.0        5.5    7.3   0.0    2.4  2  ACBP            Acyl CoA binding protein
       0.16   11.6   0.0       0.84    9.2   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
       0.18   11.8   0.2        5.8    7.0   0.0    2.9  2  HTH_36          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.4e-05     0.029       3      52 ..       5      52 ..       3      91 .. 0.85
   2 !    6.7   0.0    0.0033       6.5      26      54 ..     209     237 ..     201     240 .. 0.90
   3 ?    4.6   0.0     0.016        31      36      55 ..     303     322 ..     302     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      lt  ++ vL+ L+r pg  ++  +la   g+++s++ +  +++ +  L+ 
  gi|330506446|ref|YP_004382874.1|  5 LTSKERLVLYGLARYPG--FSDIDLASNIGVDRSTIFKSKRKFRDWKLIK 52
                                      7899*************..************************9999994 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0033
                                       HHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  26 elarrlglsksavsrilkrLvaaGLverr 54 
                                       el rr+g+s++++s    ++ + GL++r+
  gi|330506446|ref|YP_004382874.1| 209 ELSRRTGISRPTISGKRTKFFQSGLLTRE 237
                                       89************998888888888887 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  36 savsrilkrLvaaGLverrp 55 
                                       s++ + l+ L+++GL+++rp
  gi|330506446|ref|YP_004382874.1| 303 SRLDQELRNLSSQGLITERP 322
                                       55567799*********996 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0054        11      23      52 ..      23      52 ..      10      58 .. 0.89
   2 !    7.6   0.0    0.0018       3.6      22      54 ..     205     237 ..     187     244 .. 0.87
   3 ?    2.9   0.0     0.054   1.1e+02      40      59 ..     307     326 ..     303     331 .. 0.78
   4 ?   -1.7   0.0       1.5     3e+03      28      36 ..     344     352 ..     342     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0054
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglis 52
                                      +  +lAs +G+ r+t+ +  +++++ +li+
  gi|330506446|ref|YP_004382874.1| 23 SDIDLASNIGVDRSTIFKSKRKFRDWKLIK 52
                                      5569*********************99997 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglisrg 54 
                                       l+  el+++ G++r t+s   +++ + gl++r+
  gi|330506446|ref|YP_004382874.1| 205 LSDLELSRRTGISRPTISGKRTKFFQSGLLTRE 237
                                       78889***********************99975 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.054
                                       HHHHHHHHTTSEEETEEEEE CS
                         HTH_Crp_2  40 rilseLkreglisrgrriri 59 
                                       ++l+ L+ +gli+ +  ++i
  gi|330506446|ref|YP_004382874.1| 307 QELRNLSSQGLITERPMVVI 326
                                       789**********7752444 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.5
                                       HHHTTSSHH CS
                         HTH_Crp_2  28 AsmlGltre 36 
                                       A+mlG+ re
  gi|330506446|ref|YP_004382874.1| 344 ADMLGIGRE 352
                                       9*****998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00053       1.1       1      36 [.       5      40 ..       5      45 .. 0.91
   2 !    8.5   0.0   0.00096       1.9      22      50 ..     209     237 ..     200     239 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00053
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHH CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtr 36
                                      lt  + ++L+ l++ ++ s ++La+ +gv++st+ +
  gi|330506446|ref|YP_004382874.1|  5 LTSKERLVLYGLARYPGFSDIDLASNIGVDRSTIFK 40
                                      67888899*************************975 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00096
                                       HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  22 eLakklgvskstvtrvldrLekkGlieRs 50 
                                       eL ++ g+s++t++   ++  + Gl++R+
  gi|330506446|ref|YP_004382874.1| 209 ELSRRTGISRPTISGKRTKFFQSGLLTRE 237
                                       899*************************7 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   5.8e-05      0.12      12      55 ..      15      63 ..       7     105 .. 0.82
   2 ?    1.8   0.0      0.13   2.7e+02      24      58 ..     210     244 ..     206     265 .. 0.84
   3 ?    1.5   0.0      0.17   3.4e+02      39      54 ..     309     324 ..     302     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.8e-05
                    B-block_TFIIIC 12 assRysGitqsdLakeskqdprslfyrlksLekkgLIvkqsii.....d 55
                                      + +Ry G    dLa+ ++ d + +f+  ++  + +LI+ ++++      
  gi|330506446|ref|YP_004382874.1| 15 GLARYPGFSDIDLASNIGVDRSTIFKSKRKFRDWKLIKLLNVPsgeavG 63
                                      678***********************************99997644440 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.13
                    B-block_TFIIIC  24 LakeskqdprslfyrlksLekkgLIvkqsiidsat 58 
                                       L++ ++++   + + + + +++gL ++ ++id ++
  gi|330506446|ref|YP_004382874.1| 210 LSRRTGISRPTISGKRTKFFQSGLLTREAYIDWQK 244
                                       67778888888889999999*********986655 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.17
                    B-block_TFIIIC  39 lksLekkgLIvkqsii 54 
                                       l+ L+++gLI+ ++++
  gi|330506446|ref|YP_004382874.1| 309 LRNLSSQGLITERPMV 324
                                       6789*******99986 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.045        90      10      26 ..      22      38 ..      20      40 .. 0.85
   2 ?   -1.8   0.0       1.7   3.4e+03      42      52 ..      48      58 ..      48      60 .. 0.83
   3 ?    8.0   0.0    0.0015         3      10      27 ..     205     222 ..     204     223 .. 0.88
   4 ?   -2.8   0.0       3.6   7.1e+03       8      18 ..     259     269 ..     258     270 .. 0.82
   5 ?   -3.4   0.0       5.2     1e+04      15      23 ..     343     351 ..     342     351 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.045
                                      HHHHHHHHHHTSSHHHH CS
                             HTH_3 10 lsqeeLAeklGvsrsti 26
                                       s  +LA  +Gv rsti
  gi|330506446|ref|YP_004382874.1| 22 FSDIDLASNIGVDRSTI 38
                                      56679***********9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                                      HHHHHHHTSEH CS
                             HTH_3 42 kklakaLgvsl 52
                                      +kl k L+v+ 
  gi|330506446|ref|YP_004382874.1| 48 WKLIKLLNVPS 58
                                      6999****986 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHTSSHHHHH CS
                             HTH_3  10 lsqeeLAeklGvsrstis 27 
                                       ls  eL++++G+sr tis
  gi|330506446|ref|YP_004382874.1| 205 LSDLELSRRTGISRPTIS 222
                                       56679************9 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 3.6
                                       TTHHHHHHHHH CS
                             HTH_3   8 lglsqeeLAek 18 
                                       +g ++e+LA++
  gi|330506446|ref|YP_004382874.1| 259 HGHDREDLAKV 269
                                       68899***996 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 5.2
                                       HHHHHTSSH CS
                             HTH_3  15 LAeklGvsr 23 
                                       +A++lG+ r
  gi|330506446|ref|YP_004382874.1| 343 VADMLGIGR 351
                                       899***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 ?    5.2   0.0    0.0096        19       6      45 ..       5      44 ..       2      54 .. 0.83
   2 ?    5.0   0.0     0.011        22       6      40 ..     188     222 ..     185     238 .. 0.87
   3 ?   -0.3   0.0      0.51     1e+03      38      55 ..     304     321 ..     302     327 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0096
                                      HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHH CS
                              TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrs 45
                                      L++ E  v   L ++   +  ++a+++gv+rs++ ++ r+
  gi|330506446|ref|YP_004382874.1|  5 LTSKERLVLYGLARYPGFSDIDLASNIGVDRSTIFKSKRK 44
                                      777888888889999999999*************987655 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
                                       HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHH CS
                              TrmB   6 LseyEakvYlaLlklgpatadeiaeelgvprskvY 40 
                                       L+e +  +  a +k+  ++  e+++++g++r+++ 
  gi|330506446|ref|YP_004382874.1| 188 LTEKDKLTLYAFVKYPMLSDLELSRRTGISRPTIS 222
                                       7888899999999999*****************96 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.51
                                       CHHHHHHHHHHCTSEEEE CS
                              TrmB  38 kvYevLrsLedkGlVere 55 
                                       +  + Lr+L++ Gl++ +
  gi|330506446|ref|YP_004382874.1| 304 RLDQELRNLSSQGLITER 321
                                       556679********9877 PP

>> ACBP  Acyl CoA binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.039        77      21      65 ..       4      52 ..       1      62 [. 0.70
   2 ?    7.3   0.0    0.0027       5.5      19      50 ..     185     217 ..     175     245 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.039
                                      ---HHHHHHHHHHHHHHHTSS--S......----TTSHHHHHHHHHHHHTT CS
                              ACBP 21 kpsneeklelYglyKqateGdvnt......srPsaldfkgkaKwdaWkalk 65
                                      k++ +e+l lYgl +     d++       +r  +  fk k K + Wk  k
  gi|330506446|ref|YP_004382874.1|  4 KLTSKERLVLYGLARYPGFSDIDLasnigvDRSTI--FKSKRKFRDWKLIK 52
                                      578999*******9999988883321222233333..78999999998765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0027
                                       TS---HHHHHHHHHHHHHHHTSS--S-.---TT CS
                              ACBP  19 kkkpsneeklelYglyKqateGdvnts.rPsal 50 
                                        +++++++kl lY++ K  +  d + s r ++ 
  gi|330506446|ref|YP_004382874.1| 185 DSRLTEKDKLTLYAFVKYPMLSDLELSrRTGIS 217
                                       345899***********9999998555344554 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         1   2.1e+03      21      34 ..      25      38 ..      16      40 .. 0.83
   2 ?    9.2   0.0   0.00042      0.84      16      35 ..     203     222 ..     183     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1
                            HTH_24 21 reLAerlglSpstv 34
                                       +LA  +g+ +st+
  gi|330506446|ref|YP_004382874.1| 25 IDLASNIGVDRSTI 38
                                      599*******9996 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00042
                            HTH_24  16 prisqreLAerlglSpstvn 35 
                                       p +s  eL++r+g+S++t++
  gi|330506446|ref|YP_004382874.1| 203 PMLSDLELSRRTGISRPTIS 222
                                       557778************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 ?    7.0   0.0    0.0029       5.8       3      48 ..       5      44 ..       3      51 .. 0.81
   2 ?    1.4   0.0      0.15   3.1e+02      31      43 ..     210     222 ..     186     225 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0029
                            HTH_36  3 LspsaklllgslasfanknggcfpsqetlakrlglsknTvsraike 48
                                      L+ +++l+l  la++ +       s  +la++ g++++T+ + +++
  gi|330506446|ref|YP_004382874.1|  5 LTSKERLVLYGLARYPGF------SDIDLASNIGVDRSTIFKSKRK 44
                                      788888888888888833......5569************998876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.15
                            HTH_36  31 lakrlglsknTvs 43 
                                       l++r+g+s+ T+s
  gi|330506446|ref|YP_004382874.1| 210 LSRRTGISRPTIS 222
                                       6778888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2596.44
//
Query:       gi|330506447|ref|YP_004382875.1|  [L=551]
Description: thermosome subunit alpha [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.2e-179  598.1  23.5   1.3e-179  597.9  23.5    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.065   13.2   0.4       0.32   11.0   0.0    2.3  2  DUF3924     Protein of unknown function (DUF3924)
       0.19   11.2   0.9       0.25   10.8   0.1    1.6  2  TrwC        TrwC relaxase


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  597.9  23.5  2.2e-183  1.3e-179       2     490 ..      37     523 ..      36     524 .. 0.99

  Alignments for each domain:
  == domain 1  score: 597.9 bits;  conditional E-value: 2.2e-183
                                       HHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   2 adivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeae 78 
                                       a +v+ttlGPkGmdKm v+ +g+vv+TnDG+tilke++iehPaak++ve+a++qd+evGDGTtt+viLageLl+++e
  gi|330506447|ref|YP_004382875.1|  37 AGAVRTTLGPKGMDKMMVDTMGDVVITNDGVTILKEMDIEHPAAKMMVEIAKTQDTEVGDGTTTAVILAGELLKQSE 113
                                       679************************************************************************** PP

                                       HHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCC CS
                        Cpn60_TCP1  79 kliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvkliee 155
                                       +l+++++hpt+i  gy+ a++k++e+L++ a+++    +d++ L ++a t++++k +++ +e+l++++v+Av+++ +
  gi|330506447|ref|YP_004382875.1| 114 ELLEQDIHPTVIAAGYRAAADKCMEILQSLAKNVTA--NDQDLLNSIAITAMTGKGSQAAREKLADIAVRAVQAVVD 188
                                       ******************************666665..58999999**************************99999 PP

                                       CSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHH CS
                        Cpn60_TCP1 156 nekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeelek 232
                                       +++++d ++i v+k+ ggs++ds++v+G+v+dk+ l+p+mpkk+++ak++ll+  +eiekte++++++++++++l++
  gi|330506447|ref|YP_004382875.1| 189 EDGSVDTDNITVEKKVGGSISDSKIVQGVVIDKDRLHPSMPKKVTDAKIALLNAAVEIEKTEVDAKIQITSPAQLQS 265
                                       99*************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC- CS
                        Cpn60_TCP1 233 lekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeel 309
                                       ++++ee +l+ ++++i+++g+nv+++qkgiddla+h+lak+gi ++rrvkk+d+e+la+atG+++v+sl +++ ++l
  gi|330506447|ref|YP_004382875.1| 266 FLDQEESMLKGMVDRIAATGANVLFVQKGIDDLAQHYLAKAGIYTVRRVKKSDMEKLARATGGRVVTSLHEISVDDL 342
                                       ***************************************************************************** PP

                                       EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHH CS
                        Cpn60_TCP1 310 GtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakk 386
                                       G+a+ vee+k+++ek+t++e+++++k+++i+l g t++v+de+ ra edAl+vv  aied+ +v+GGGa e+ela++
  gi|330506447|ref|YP_004382875.1| 343 GKAGLVEERKVSDEKMTFVEDCNNPKSVSIILHGGTEHVVDELDRAMEDALRVVGVAIEDKMLVAGGGAPEVELASR 419
                                       ***************************************************************************** PP

                                       HHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEH CS
                        Cpn60_TCP1 387 lkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDpl 463
                                       l++ya++v g+eqlaie fa+A+e+ipktLaeNaGld+i++l  lr++h+kg +++g+d++sg+++d+++ gvv+pl
  gi|330506447|ref|YP_004382875.1| 420 LRSYASTVGGREQLAIESFANAMEIIPKTLAENAGLDQIDTLVALRSQHEKGVMTAGLDMDSGKPVDMMQIGVVEPL 496
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 464 kvkrqalksAteaastiLrideiikak 490
                                       +vk+qa++sA+eaa +iLrid++i  k
  gi|330506447|ref|YP_004382875.1| 497 RVKSQAISSAAEAAVMILRIDDVIASK 523
                                       ************************976 PP

>> DUF3924  Protein of unknown function (DUF3924)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.3e-05      0.32      23      41 ..     200     218 ..     192     229 .. 0.84
   2 ?   -1.1   0.0      0.32   1.9e+03      46      58 ..     255     267 ..     222     271 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.3e-05
                           DUF3924  23 yekktGasisestlvqtli 41 
                                        ekk G sis+s +vq ++
  gi|330506447|ref|YP_004382875.1| 200 VEKKVGGSISDSKIVQGVV 218
                                       69**************764 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.32
                           DUF3924  46 iqaitPfdlqqfv 58 
                                       iq   P  lq f+
  gi|330506447|ref|YP_004382875.1| 255 IQITSPAQLQSFL 267
                                       5666666666665 PP

>> TrwC  TrwC relaxase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.72   4.3e+03      90      90 ..     157     157 ..     115     191 .. 0.56
   2 ?   10.8   0.1   4.2e-05      0.25      59     125 ..     332     404 ..     245     417 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.72
                              TrwC  90 S 90 
                                       S
  gi|330506447|ref|YP_004382875.1| 157 S 157
                                       2 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.2e-05
                              TrwC  59 d.....tgerlgrakesaere.rkavagfDltfsaPKSvSllalvgdderraaieaahdaAvkaalalleeea 125
                                             + + lg+a    er+ +++++ f   ++ PKSvS++   g++++  ++ +a+++A + +   +e+++
  gi|330506447|ref|YP_004382875.1| 332 TslheiSVDDLGKAGLVEERKvSDEKMTFVEDCNNPKSVSIILHGGTEHVVDELDRAMEDALRVVGVAIEDKM 404
                                       13333345555554444444446666666667888******98877777777777777777776666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 4088.81
//
Query:       gi|330506448|ref|YP_004382876.1|  [L=411]
Description: proteasome-activating nucleotidase [Methanosaeta concilii GP6]
Scores for complete 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  151.4   1.3    3.7e-44  150.3   0.1    2.2  2  AAA              ATPase family associated with various cellul
      4e-11   42.5   1.0    1.2e-10   41.0   1.0    1.9  1  AAA_lid_3        AAA+ lid domain
    1.4e-05   24.9   0.2    7.8e-05   22.5   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      3e-05   24.5   0.2     0.0012   19.3   0.1    2.4  2  AAA_16           AAA ATPase domain
    0.00019   21.4   0.3     0.0029   17.6   0.3    2.8  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00032   21.0   0.3      0.014   15.6   0.3    2.7  1  AAA_22           AAA domain
    0.00041   20.5   1.5    0.00059   20.0   0.0    2.0  2  AAA_2            AAA domain (Cdc48 subfamily)
     0.0014   18.7   0.0     0.0038   17.3   0.0    1.7  1  AAA_14           AAA domain
     0.0014   17.9   0.4     0.0037   16.5   0.0    1.8  2  TIP49            TIP49 P-loop domain
     0.0017   18.8   0.5      0.028   14.8   0.0    2.6  2  AAA_17           AAA domain
     0.0027   17.9   0.1     0.0098   16.1   0.0    2.1  2  AAA_33           AAA domain
      0.008   16.7   0.2      0.072   13.6   0.0    2.4  2  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.012   14.8   0.0      0.024   13.8   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
      0.014   15.8   0.0      0.027   14.9   0.0    1.5  1  RNA_helicase     RNA helicase
      0.023   14.1   0.1      0.046   13.1   0.1    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.023   14.4   0.1       0.27   10.9   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
      0.026   14.2   0.0      0.066   12.9   0.0    1.7  1  AAA_24           AAA domain
      0.029   14.3   0.1       0.16   11.9   0.1    2.2  1  NACHT            NACHT domain
      0.042   13.6   0.0      0.086   12.6   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
        0.1   12.4   1.6       0.32   10.8   1.6    1.8  1  SKA2             Spindle and kinetochore-associated protein 2
        0.1   12.9   0.8        1.3    9.3   0.1    2.5  2  baeRF_family11   Bacterial archaeo-eukaryotic release factor 
       0.26   11.7   2.1         17    5.9   0.5    2.9  2  FlaC_arch        Flagella accessory protein C (FlaC)
       0.34   10.2   5.6       0.36   10.1   0.0    3.0  4  ATPase           KaiC
       0.41   10.8   4.6       0.57   10.4   1.2    2.5  2  JIP_LZII         JNK-interacting protein  leucine zipper II
        1.6    9.4   3.6        3.8    8.2   1.4    2.5  3  YabA             Initiation control protein YabA


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 ?   -1.4   0.0       4.1     3e+03      75      97 ..      96     118 ..      29     138 .. 0.69
   2 !  150.3   0.1   5.2e-47   3.7e-44       1     131 [.     191     323 ..     191     324 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.1
                                       TTCCCHHHHHHHHHHHHHHHHTT CS
                               AAA  75 sgseseeeervvnqLlteldgvk 97 
                                       +g+++e+ ++v+++++++l+  +
  gi|330506448|ref|YP_004382876.1|  96 HGNNQEFITTVAPEMMEQLQPNS 118
                                       45566666666666666666554 PP

  == domain 2  score: 150.3 bits;  conditional E-value: 5.2e-47
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       vllyG pGtGKT+lakava+e++++f+ +sgsel+ k++ge+++ +r++f+ a+eka psi+fiDEida+++ r   
  gi|330506448|ref|YP_004382876.1| 191 VLLYGLPGTGKTMLAKAVAHESKATFIHMSGSELVHKFIGEGAQLVRDIFQMAREKA-PSIIFIDEIDAVGSIRthd 266
                                       79******************************************************9.****************987 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        ++ s e +r++ qLl+e+dg++++ +++ +i+atnr+d ldpallr gRfdr+iei+
  gi|330506448|ref|YP_004382876.1| 267 GTTGSAEVNRTMMQLLAEMDGFRTR-GDIRIIAATNRIDILDPALLRpGRFDRIIEIP 323
                                       66789999****************7.66****************************97 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   1.0   1.7e-13   1.2e-10       1      45 []     346     390 ..     346     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.7e-13
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfee 45 
                                       dv+l+e+A  T+  SGADl+++  eA+++Alrr+ + ++++df++
  gi|330506448|ref|YP_004382876.1| 346 DVNLAEIATVTDEASGADLKSIAVEAGMNALRRNATIVSKDDFDK 390
                                       9******************************************75 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.4   1.7e+03      62      84 ..     125     147 ..      89     170 .. 0.59
   2 !   22.5   0.0   1.1e-07   7.8e-05      35      95 ..     190     258 ..     183     264 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.4
                            RuvB_N  62 kitsgPvlekagdlaalltnlee 84 
                                         t   +le++ d+ a +++l e
  gi|330506448|ref|YP_004382876.1| 125 SLTVVRILERSVDVRAKVMELVE 147
                                       33444556666666665555544 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.1e-07
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvleka..gdlaalltnl......eekdvlfideihr 95 
                                        vllyG PG Gkt lak +a+e ++++ + sg  l ++  g+ a l+ ++      ++  ++fidei  
  gi|330506448|ref|YP_004382876.1| 190 GVLLYGLPGTGKTMLAKAVAHESKATFIHMSGSELVHKfiGEGAQLVRDIfqmareKAPSIIFIDEIDA 258
                                       59***********************999999887655433444444443311122134479*****975 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   1.6e-06    0.0012      24      55 ..     187     216 ..     156     245 .. 0.70
   2 ?    2.7   0.0       0.2   1.4e+02     120     147 ..     233     259 ..     218     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.6e-06
                            AAA_16  24 p.elvllsGesGvGKsslvrellralekdggif 55 
                                       p + vll+G +G+GK+ l+++++++ +++   f
  gi|330506448|ref|YP_004382876.1| 187 PpRGVLLYGLPGTGKTMLAKAVAHESKAT---F 216
                                       159********************866655...3 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.2
                            AAA_16 120 lellkrllallsrderplvlvlDdlqwa 147
                                       ++l++++++ +++ + p ++++D+++ +
  gi|330506448|ref|YP_004382876.1| 233 AQLVRDIFQMARE-KAPSIIFIDEIDAV 259
                                       5677777777777.778*******9954 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3     4e-06    0.0029       1     124 [.     190     304 ..     190     313 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                       +vlL G pGtgK++la+ +a+  ++++  + ++      +l+ +    +g +  +d   +   + ++i+++DE++ +
  gi|330506448|ref|YP_004382876.1| 190 GVLLYGLPGTGKTMLAKAVAHESKATFIHMSGS------ELVHKFI-GEGAQLVRDIFQMAREKAPSIIFIDEIDAV 259
                                       59******************9887777665554......5666666.244445555555555558889999999877 PP

                                       -.HHHHHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS-- CS
                             AAA_5  78 e.sevlnsLlslleerrllleeggelvkaknddller..frviatanpld 124
                                           + +      e +r ++  + e  +++      r  +r+ia++n+ d
  gi|330506448|ref|YP_004382876.1| 260 GsIRTHDGTTGSAEVNRTMMQLLAEMDGFRT-----RgdIRIIAATNRID 304
                                       6444555555555555555444444443333.....22366666666666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3     2e-05     0.014       8      45 ..     191     219 ..     186     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfv 45 
                                       ++++G +GtGKT+l++ ++++          +++++++
  gi|330506448|ref|YP_004382876.1| 191 VLLYGLPGTGKTMLAKAVAHES---------KATFIHM 219
                                       689*****************97.........4444444 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   8.2e-07   0.00059       7     103 ..     192     282 ..     187     297 .. 0.86
   2 ?   -2.8   0.1       8.1   5.8e+03      57      80 ..     360     391 ..     327     405 .. 0.46

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.2e-07
                                       EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG-- CS
                             AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKih 81 
                                       ll g  g+Gkt+laka+a   ++    ++i +  sel      + + +  +  ++  + a e+   i+++DEid + 
  gi|330506448|ref|YP_004382876.1| 192 LLYGLPGTGKTMLAKAVAHESKA----TFIHMSGSELVH----KFIGEGAQLVRDIFQMAREKApsIIFIDEIDAVG 260
                                       678889************99985....9**9999**999....77777788888888888888889**********9 PP

                                       -----------HHHHHHHHHHH CS
                             AAA_2  82 pkessgadvSregVqrdLLqil 103
                                       + ++      + +V r ++q+l
  gi|330506448|ref|YP_004382876.1| 261 SIRTHDGTTGSAEVNRTMMQLL 282
                                       9766666677889999999998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.1
                                       HHHTTT-HHHHTTS........EEEEETGGG- CS
                             AAA_2  57 igappgyvgaeegG........ivllDEidKi 80 
                                        ga    +++e g         iv  D+ dK 
  gi|330506448|ref|YP_004382876.1| 360 SGADLKSIAVEAGMnalrrnatIVSKDDFDKG 391
                                       22222222222222334444445555555554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.3e-06    0.0038       5      79 ..     191     262 ..     188     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.3e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpew 79 
                                       +++ G+  +GKT+l+k +++e+      ++ ++  +   k + + ++l + i+++++e+  +++f+DEi  v ++
  gi|330506448|ref|YP_004382876.1| 191 VLLYGLPGTGKTMLAKAVAHESK---ATFIHMSGSELVHKFIGEGAQLVRDIFQMAREKAPSIIFIDEIDAVGSI 262
                                       6899999************8888...889999888877766666557888888886667899*******988655 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.2e-06    0.0037      51      90 ..     189     226 ..     183     243 .. 0.88
   2 ?   -2.8   0.1       3.8   2.7e+03      96     119 ..     334     357 ..     330     383 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                       r+vLl G +gtGkt la a+++e  ++  f+++sgse+  
  gi|330506448|ref|YP_004382876.1| 189 RGVLLYGLPGTGKTMLAKAVAHE--SKATFIHMSGSELVH 226
                                       89*******************99..5689********865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.8
                                       XXXXXXXXXXXXXXXXXX-S-EEE CS
                             TIP49  96 tevltqalrksigvrikeekevle 119
                                        e+ t+++rk+  v + e+ +v +
  gi|330506448|ref|YP_004382876.1| 334 LEIHTRKMRKAEDVNLAEIATVTD 357
                                       688899999999999999988864 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.66   4.7e+02      38     112 ..      52     126 ..      37     141 .. 0.64
   2 !   14.8   0.0   3.9e-05     0.028       1      37 [.     194     232 ..     194     270 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.66
                                       TSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH...HSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE-- CS
                            AAA_17  38 glakardemrklpleekkelqkeaaekiaeea...kkkgvlvdghprikeqagfldglpkevleelkpdaiillead 111
                                       +l+ +++++r+++  +k+ l+ + +     +    + + vl+  h    ++++f+ ++  e+ e+l+p+  + ++ +
  gi|330506448|ref|YP_004382876.1|  52 SLIANKKYLREVERLKKENLLLKRMPLFLATVvemGPDYVLLRQHG---NNQEFITTVAPEMMEQLQPNSRVAINNS 125
                                       4566777777776666666554433332222212266678888887...5688899999999999999988888766 PP

                                       H CS
                            AAA_17 112 p 112
                                        
  gi|330506448|ref|YP_004382876.1| 126 L 126
                                       5 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.9e-05
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTT CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeakrg 37 
                                       +G+PG GK+ +++ ++++    f h+s ++l+ + + +g
  gi|330506448|ref|YP_004382876.1| 194 YGLPGTGKTMLAKAVAHESkaTFIHMSGSELVHKFIGEG 232
                                       7***********999976533788888777777666544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.7   3.4e+03      18      48 ..      30      60 ..      18     101 .. 0.69
   2 !   16.1   0.0   1.4e-05    0.0098       2      32 ..     191     223 ..     191     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.7
                            AAA_33 18 rllkklgavllssdtlrrrlfgtdqqsktdy 48
                                      +l+++l +++ +  ++r +lf++   +k+++
  gi|330506448|ref|YP_004382876.1| 30 SLAEELETTRMEREEVRAKLFESLIANKKYL 60
                                      5666666666666667777766444444433 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.4e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdt 32 
                                       vll GlpG+GK+ la+ ++ + +  +++ s  +
  gi|330506448|ref|YP_004382876.1| 191 VLLYGLPGTGKTMLAKAVAHESKatFIHMSGSE 223
                                       7899**************999885566666555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       1.6   1.2e+03      33      72 ..      33      66 ..       8     102 .. 0.56
   2 !   13.6   0.0    0.0001     0.072       1      25 [.     191     223 ..     191     267 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.6
                            AAA_18 33 kenglllevdpealdeskrldedkldklldaleenss.....ale 72
                                       e           l+ ++ ++e++++kl++ l +n +      + 
  gi|330506448|ref|YP_004382876.1| 33 EE-----------LETTRMEREEVRAKLFESLIANKKylrevERL 66
                                      33...........34444444445555555554444444433222 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.0001
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf........g 25 
                                       +ll G pG+GKt lak+++ + +          
  gi|330506448|ref|YP_004382876.1| 191 VLLYGLPGTGKTMLAKAVAHESKAtfihmsgsE 223
                                       799***************665322345555442 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.3e-05     0.024      51     115 ..     186     255 ..     134     258 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                            DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegLrl..ievekedlkelpklvellr...erperfilfvDD 115
                                       +p + vLL+G  GtGK  l ka+ +e +++ +++   e+ ++ + e  +lv+ +    +++   i+f+D 
  gi|330506448|ref|YP_004382876.1| 186 EPPRGVLLYGLPGTGKTMLAKAVAHESKATFIHMsgSELVHKFIGEGAQLVRDIFqmaREKAPSIIFIDE 255
                                       67788*********************99998766224777777777777766554111445556888876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.8e-05     0.027       1      69 [.     191     251 ..     191     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.8e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenps.d 69 
                                       ++lyG +g+GK++lak            ++++ ++++ + ++ ++++ g+ + ++ D+ q+  e+ ps +
  gi|330506448|ref|YP_004382876.1| 191 VLLYGLPGTGKTMLAKA---------VAHESKATFIHMSGSELVHKFIGEGAQLVRDIFQMAREKAPSiI 251
                                       689**************.........34566788899***********************9988777643 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.4e-05     0.046      25      42 ..     191     208 ..     183     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.4e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +ll+G pG+GKtmlak++
  gi|330506448|ref|YP_004382876.1| 191 VLLYGLPGTGKTMLAKAV 208
                                       89*************987 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00037      0.27      24      51 ..     190     214 ..     178     230 .. 0.81
   2 ?   -0.1   0.0      0.94   6.8e+02     132     143 ..     291     302 ..     276     321 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
                                       -EEEECSTTSSHHHHHHHHHHHSTTTTS CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheaskrkek 51 
                                        vl+ G  GtGK++la+a+ ++sk   +
  gi|330506448|ref|YP_004382876.1| 190 GVLLYGLPGTGKTMLAKAVAHESK---A 214
                                       69****************987776...3 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.94
                                       E--EEEEEEESS CS
                   Sigma54_activat 132 kvdvriiaatne 143
                                       + d+riiaatn+
  gi|330506448|ref|YP_004382876.1| 291 RGDIRIIAATNR 302
                                       5699******97 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   9.2e-05     0.066       5      76 ..     191     258 ..     188     280 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.2e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtide 76 
                                       +l+yG +g+GKT+lak    + k+ fi + ++    +++     e+ + ++d ++  +++ +  ++++iD id 
  gi|330506448|ref|YP_004382876.1| 191 VLLYGLPGTGKTMLAKAVahESKATFIHMSGSELVHKFIG----EGAQLVRDIFQMAREKAP--SIIFIDEIDA 258
                                       79**************999888888887766443333333....233333333333333333..5666666665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00022      0.16       3      25 ..     191     213 ..     189     287 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                                       EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                       v+l G +G GKT+L++ +a++ +
  gi|330506448|ref|YP_004382876.1| 191 VLLYGLPGTGKTMLAKAVAHESK 213
                                       899**************998765 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   0.00012     0.086      48      71 ..     189     212 ..     176     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                        +++l G +G+GK+ la a+++e 
  gi|330506448|ref|YP_004382876.1| 189 RGVLLYGLPGTGKTMLAKAVAHES 212
                                       6799****************9975 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 ?   10.8   1.6   0.00045      0.32      44      90 ..      18      64 ..      14      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00045
                              SKA2 44 lerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLq 90
                                      l+r++++ ++ ++L e++e    e++e+  k+  +l+an++ l++ +
  gi|330506448|ref|YP_004382876.1| 18 LKRIAALESDTKSLAEELETTRMEREEVRAKLFESLIANKKYLREVE 64
                                      89***************************************998765 PP

>> baeRF_family11  Bacterial archaeo-eukaryotic release factor family 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0019       1.3      32     100 ..      23      91 ..      14     124 .. 0.71
   2 ?    1.5   0.1      0.49   3.5e+02      13      42 ..     128     157 ..     116     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0019
                    baeRF_family11  32 glpkdaasaagkssindrsesgrlqga.egqkvrleqYarkvdkalrpvLagrdlPLiLaaaeplaslyr 100
                                        l +d +s a++ +++  +   +++++     +  ++Y+r+v++  ++ L  +++PL+La++ ++ + y 
  gi|330506448|ref|YP_004382876.1|  23 ALESDTKSLAEELETTRMER-EEVRAKlFESLIANKKYLREVERLKKENLLLKRMPLFLATVVEMGPDYV 91 
                                       56666666666655543333.3333331344578899***********************9998887665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.49
                    baeRF_family11  13 svrLvevtadlpaeevkvpglpkdaasaag 42 
                                        vr++e + d +a+ +++ +lp+   + +g
  gi|330506448|ref|YP_004382876.1| 128 VVRILERSVDVRAKVMELVELPDVSYDQVG 157
                                       59********************97777665 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 ?    5.9   0.5     0.024        17       1      29 [.      20      48 ..      20      53 .. 0.93
   2 ?    4.1   0.0     0.086        62       8      31 ..     147     171 ..     141     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.024
                         FlaC_arch  1 ridelEnklsklsteletvkkeneelsks 29
                                      ri  lE++ ++l  elet + e ee++ +
  gi|330506448|ref|YP_004382876.1| 20 RIAALESDTKSLAEELETTRMEREEVRAK 48
                                      8999**********************976 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.086
                         FlaC_arch   8 klsklst.eletvkkeneelsksve 31 
                                       +l+++s  +++ ++++++e++++ve
  gi|330506448|ref|YP_004382876.1| 147 ELPDVSYdQVGGLEAQIQEVRETVE 171
                                       567777778999***********98 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       5.3   3.8e+03      69      85 ..      23      39 ..      11      69 .. 0.50
   2 ?   -3.0   0.1         5   3.6e+03     113     149 ..     109     147 ..      93     148 .. 0.64
   3 ?   10.1   0.0    0.0005      0.36      13      38 ..     182     207 ..     176     216 .. 0.82
   4 ?    1.5   0.0      0.22   1.6e+02     105     151 ..     233     285 ..     207     291 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.3
                            ATPase 69 slGwdlekleeegklai 85
                                      +l  d++ l ee + + 
  gi|330506448|ref|YP_004382876.1| 23 ALESDTKSLAEELETTR 39
                                      44444444444422222 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5
                            ATPase 113 eaikeika.krvviD.sitglayeekeavaReilrqlvr 149
                                       e++++++  +rv i  s+t++   e++  +R+ +++lv+
  gi|330506448|ref|YP_004382876.1| 109 EMMEQLQPnSRVAINnSLTVVRILERSVDVRAKVMELVE 147
                                       555666655667664266666666777778888888875 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0005
                            ATPase  13 kgGipegrvvlitGepGtGKtifalq 38 
                                       + Gi   r vl++G pGtGKt++a+ 
  gi|330506448|ref|YP_004382876.1| 182 DIGIEPPRGVLLYGLPGTGKTMLAKA 207
                                       458888899**************986 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.22
                            ATPase 105 eelieelaeaikeikakrvviDsitgl.ayeek.....eavaReilrqlvrvl 151
                                        +l++++ ++ +e+  + + iD i+++ + +++     +a++ ++++ql+ ++
  gi|330506448|ref|YP_004382876.1| 233 AQLVRDIFQMAREKAPSIIFIDEIDAVgSIRTHdgttgSAEVNRTMMQLLAEM 285
                                       57889999999999999999998887753222201111344555566665555 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 ?   10.4   1.2   0.00079      0.57      26      63 ..      12      49 ..      10      52 .. 0.90
   2 ?    0.7   0.1      0.85   6.1e+02       5      19 ..      61      75 ..      54      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00079
                          JIP_LZII 26 vvkddLIarvdeLtsereiLreEleslqkakerlesri 63
                                      + ++  ++r+  L s+ ++L eEle++++++e+++ ++
  gi|330506448|ref|YP_004382876.1| 12 TIQESFLKRIAALESDTKSLAEELETTRMEREEVRAKL 49
                                      6778899**************************99987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.85
                          JIP_LZII  5 kevenLikENteLle 19
                                      +eve L kEN  L+ 
  gi|330506448|ref|YP_004382876.1| 61 REVERLKKENLLLKR 75
                                      688888888877765 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.4    0.0053       3.8      18      61 ..      15      58 ..       5      76 .. 0.72
   2 ?   -2.2   0.0         9   6.5e+03      21      46 ..     100     125 ..      92     148 .. 0.69
   3 ?   -0.3   0.0       2.4   1.7e+03      17      41 ..     149     172 ..     135     249 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0053
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....XXXXXXXXX CS
                              YabA 18 eelleeleelkeelaelleenaeLeleneklrerl.....eeeekkeke 61
                                      e++l+++++l++++++l ee ++ ++e e++r +l     +     +k+
  gi|330506448|ref|YP_004382876.1| 15 ESFLKRIAALESDTKSLAEELETTRMEREEVRAKLfesliA-----NKK 58
                                      56789999************************999544331.....222 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  21 leeleelkeelaelleenaeLelene 46 
                                       +e ++++  e+ e l+ n+++ ++n+
  gi|330506448|ref|YP_004382876.1| 100 QEFITTVAPEMMEQLQPNSRVAINNS 125
                                       55566777778888888888888776 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  17 leelleeleelkeelaelleenaeL 41 
                                        +  +++++ l+++++e+  e  eL
  gi|330506448|ref|YP_004382876.1| 149 PDVSYDQVGGLEAQIQEVR-ETVEL 172
                                       5555566666666665543.33444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1032  (0.0575604); expected 358.6 (0.02)
Passed bias filter:                      745  (0.0415528); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 2683.89
//
Query:       gi|330506449|ref|YP_004382877.1|  [L=106]
Description: hypothetical protein MCON_0156 [Methanosaeta concilii GP6]
Scores for complete sequence (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  100.0   1.4    1.3e-28   99.9   1.4    1.0  1  DUF5611      Domain of unknown function (DUF5611)
  ------ inclusion threshold ------
      0.059   13.2   0.0      0.085   12.7   0.0    1.3  1  RACo_linker  RACo linker region


Domain annotation for each model (and alignments):
>> DUF5611  Domain of unknown function (DUF5611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   1.4   1.4e-32   1.3e-28       3     103 .]       2      97 ..       1      97 [. 0.97

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1.4e-32
                                       EE---SSS--SH.HHHHHHHHHHT.-EEEEETTEEEEE-TTBS-EEEEE..-SS-EEEEE--.B...-TTS-HHHHH CS
                           DUF5611   3 eYkiKrGfkkeeeerlkelleeyfggeveeegdllvvsfgaikklevkisskkkklvvdteerdaeeeddeaaldtv 79 
                                       +Y++KrGfk++  er++++lee f+ e++e +++l  sfga+k+++v+i  ++kkl v+te+   ++++d+++ldt+
  gi|330506449|ref|YP_004382877.1|   2 DYSFKRGFKPDM-ERIRKVLEEEFPAEIKELDGMLSLSFGALKSIQVSI--NNKKLNVTTESY--SDAKDDQILDTN 73 
                                       7***********.************************************..***********3..689********* PP

                                       HHHHHHHHHHH---GGGHHHHH-- CS
                           DUF5611  80 kkfndFLeeaTGydaKeRkkkakk 103
                                       k+f++FLe+aTGy+aK+R ++akk
  gi|330506449|ref|YP_004382877.1|  74 KRFRNFLEKATGYTAKQRLQMAKK 97 
                                       *********************997 PP

>> RACo_linker  RACo linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.5e-06     0.085      28      77 ..      10      71 ..       8      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.5e-06
                       RACo_linker 28 sgDleRLkeaLekqw.....d....leidlsvLrkLpevLrkgnwkVtval...hede..eiia 77
                                      ++D+eR+++ Le+++     +    l+ ++ +L+ ++  +  ++ +Vt         +  +i++
  gi|330506449|ref|YP_004382877.1| 10 KPDMERIRKVLEEEFpaeikEldgmLSLSFGALKSIQVSINNKKLNVTTESysdA--KddQILD 71
                                      58*************87665166899*********************98774332..1346766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 791.35
//
Query:       gi|330506450|ref|YP_004382878.1|  [L=416]
Description: Enolase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.4e-106  356.1   0.0   1.7e-106  355.8   0.0    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    4.3e-59  198.4   0.0    7.3e-59  197.6   0.0    1.4  1  Enolase_N  Enolase, N-terminal domain
    0.00063   19.4   0.0     0.0011   18.6   0.0    1.4  1  MR_MLE_C   Enolase C-terminal domain-like
  ------ inclusion threshold ------
        0.1   11.7   0.2        0.7    9.0   0.0    2.1  2  MAAL_C     Methylaspartate ammonia-lyase C-terminus
       0.22   11.2   0.0       0.37   10.4   0.0    1.4  1  FlaA       Flagellar filament outer layer protein Flaa


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 !  355.8   0.0  4.9e-110  1.7e-106       2     288 ..     139     414 ..     138     416 .] 0.98

  Alignments for each domain:
  == domain 1  score: 355.8 bits;  conditional E-value: 4.9e-110
                                       -EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SS CS
                         Enolase_C   2 lvlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqs 78 
                                       ++lP+P++nv+nGG+hagn+l++qefmi+P+ga++f+e lr+ ae+yh l ++l+ kyg  atnvG eGG+aP l +
  gi|330506450|ref|YP_004382878.1| 139 VTLPIPSFNVLNGGKHAGNELSIQEFMIQPTGAKTFSEGLRMAAETYHALGKILQGKYGVGATNVGYEGGYAPPLIK 215
                                       68*************************************************************************** PP

                                       HHHHHHHHHHHHHHCT-TCTBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEE CS
                         Enolase_C  79 nkealdliveaiekaGykgkvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsie 155
                                       +++ald i++a + +Gy +++ki+ld+a+s fy   ++ y +d++         l+  +l d+y++lv+ yPi+ +e
  gi|330506450|ref|YP_004382878.1| 216 TRDALDAIMSAFDVSGYGDEIKIGLDAAASSFY--MEGGYSVDGNR--------LSPGELIDYYVDLVNTYPIILLE 282
                                       *********************************..66799999877........9********************** PP

                                       S-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEE CS
                         Enolase_C 156 dpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvv 232
                                       dp++e+ ++ +++lt++l     ivGddl+vtn krl+++i+  a+nalllk+nqiG+++e+++a++++ ++g+ v+
  gi|330506450|ref|YP_004382878.1| 283 DPFEEEAYDDFARLTAKLP-GTIIVGDDLYVTNIKRLEKGIKMCAGNALLLKLNQIGTVSEAFDAARMSFRSGWKVM 358
                                       ******************9.567****************************************************** PP

                                       EE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE- CS
                         Enolase_C 233 vshrsGetedttiadlavglsaGqiktGaparserlakynqllrieeelgekakya 288
                                        shrs eted+ +ad+av+l +  +ktGaparser akynqllri+e+lge+a+ya
  gi|330506450|ref|YP_004382878.1| 359 ASHRSAETEDSALADVAVALGCELLKTGAPARSERTAKYNQLLRIQEDLGEAARYA 414
                                       *******************************************************8 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.6   0.0     2e-62   7.3e-59       1     131 []       5     133 ..       5     133 .. 0.99

  Alignments for each domain:
  == domain 1  score: 197.6 bits;  conditional E-value: 2e-62
                                       EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHT CS
                         Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapali 77 
                                       I+k++areildSrGnpTvev+v+t  g +graavpsGaStg++ealelrDg  +ry gkgv+kav+nvne+iap+l+
  gi|330506450|ref|YP_004382878.1|   5 IEKIHAREILDSRGNPTVEVDVYTCCG-FGRAAVPSGASTGTHEALELRDG-GDRYDGKGVLKAVKNVNEVIAPELL 79 
                                       89**********************877.8*********************9.89*********************** PP

                                       TSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                         Enolase_N  78 gldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                       g+d++ q+eiD+l+i++Dgt nk++lGaN+il+vS+A+akaaA ++++ply+yl
  gi|330506450|ref|YP_004382878.1|  80 GMDASCQREIDDLMINMDGTANKANLGANSILGVSIAMAKAAAMSSGVPLYKYL 133
                                       *****************************************************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 !   18.6   0.0   2.9e-07    0.0011      28     156 ..     217     361 ..     179     400 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.9e-07
                                       HHHHHHHHHHHHHHTTTSTSEEEEE-TTTS..............BHHHHHHHHHHHGG.GTESEEESSSSTTTHHHH CS
                          MR_MLE_C  28 aedvervravreavgpgddvdlmvDanqaw..............dlatAirvarelee.ldllwlEEPvppeddleg 89 
                                       ++ ++ +  + ++ g gd++++ +Da ++               ++ + i +   l   + + +lE+P+  e  +++
  gi|330506450|ref|YP_004382878.1| 217 RDALDAIMSAFDVSGYGDEIKIGLDAAASSfymeggysvdgnrlSPGELIDYYVDLVNtYPIILLEDPFEEE-AYDD 292
                                       5666666666677788889999999888844577777777777799999999988856599*********95.6*** PP

                                       HHHHHHHH..SSEEEEST..TSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBS CS
                          MR_MLE_C  90 laelrara..sipiaagE..slysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHs 156
                                        a+l+a +  +  i++g   ++++++++++ ++  a  ++ ++++++g ++ea + a++    g++v+  +
  gi|330506450|ref|YP_004382878.1| 293 FARLTA-KlpG-TIIVGDdlYVTNIKRLEKGIKMCAGNALLLKLNQIGTVSEAFDAARMSFRSGWKVMASH 361
                                       *****6.4443.444444124567***************************************99987765 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.11   3.8e+02     190     220 ..      91     121 ..      80     127 .. 0.79
   2 ?    9.0   0.0    0.0002       0.7     134     217 ..     297     381 ..     275     387 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.11
                            MAAL_C 190 gvgaylGGscnetdvsarvsvhvalatrpaq 220
                                       ++ + + G++n  + +a+ +  v++a+  a 
  gi|330506450|ref|YP_004382878.1|  91 DLMINMDGTANKANLGANSILGVSIAMAKAA 121
                                       5666788***********9999999986554 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0002
                            MAAL_C 134 kekgikvelvaDe.WcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvsarvs 209
                                       ++k     +v D+ +  +++ +++ +   a++++ +k   +G+++++ +a  ++ ++g +++    + et+ sa + 
  gi|330506450|ref|YP_004382878.1| 297 TAKLPGTIIVGDDlYVTNIKRLEKGIKMCAGNALLLKLNQIGTVSEAFDAARMSFRSGWKVMASHRSAETEDSALAD 373
                                       5555566677665356667888888899999*******************************************999 PP

                            MAAL_C 210 vhvalatr 217
                                       v val ++
  gi|330506450|ref|YP_004382878.1| 374 VAVALGCE 381
                                       99999765 PP

>> FlaA  Flagellar filament outer layer protein Flaa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0001      0.37      95     123 ..      47      73 ..      23     120 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                              FlaA  95 feiplygkasGgrfdGkGvvknvgviksi 123
                                        +++l+    G r+dGkGv+k v+++ ++
  gi|330506450|ref|YP_004382878.1|  47 EALELRD--GGDRYDGKGVLKAVKNVNEV 73 
                                       5666776..67*************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2907.17
//
Query:       gi|330506451|ref|YP_004382879.1|  [L=353]
Description: cation diffusion facilitator family transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-47  161.2  11.1    3.1e-47  160.9  11.1    1.1  1  Cation_efflux  Cation efflux family
      2e-24   85.5   0.4    3.1e-24   84.9   0.4    1.3  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
          2    8.9   7.1         11    6.5   0.6    2.6  2  MerC           MerC mercury resistance protein


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 !  160.9  11.1   5.2e-51   3.1e-47       2     199 .]      28     228 ..      27     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 160.9 bits;  conditional E-value: 5.2e-51
                     Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsglll 78 
                                       +ls+++n++l + ++ivg++ +S++++++a+hs  dl++ +++++a+k s kp+de++pfG+g++e++ +   +ll+
  gi|330506451|ref|YP_004382879.1|  28 LLSVFSNTSLVFLKIIVGMMIGSVSVISEAIHSGMDLIAAVIAFFAVKTSAKPADEDHPFGHGKVENISGTAEALLI 104
                                       689************************************************************************** PP

                     Cation_efflux  79 lglavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlv 155
                                       l++a ++++eai +l  +++++++++l l+v+lvs++ n+++ ++l  +g+++ s+alka+a+h ++D++tslgvl 
  gi|330506451|ref|YP_004382879.1| 105 LIAAGWIIYEAIGRLR-NPVPLDEPALGLAVMLVSVAANIFVSRKLFIVGEETDSIALKADAWHLRTDVYTSLGVLA 180
                                       ****************.************************************************************ PP

                     Cation_efflux 156 salvillfnlksg....plaDpvaslligliilysalkllkeslseLl 199
                                       ++l+i l+ + s     +++Dp+a+++++l i+ ++++l+ es ++L+
  gi|330506451|ref|YP_004382879.1| 181 GLLIIVLGGYISPstnlQWVDPIAAIVVALHIARTSYHLILESARDLI 228
                                       99999998665558899****************************995 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 !   84.9   0.4   5.2e-28   3.1e-24       2      79 .]     233     310 ..     232     310 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 5.2e-28
                                       ...HHHHHHHHHTT.-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEE CS
                          ZT_dimer   2 deeeeeeireiiks.vpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHve 77 
                                       + +e+ee+r+ i++  p v+gvh+lrtrk+G ++fv++h++vd ++sv e+H+i+d +  +ik+++pg + v+iH+e
  gi|330506451|ref|YP_004382879.1| 233 PNDEIEEVRRHIAAfAPTVRGVHRLRTRKAGGNRFVEFHLRVDSSMSVDESHRITDMIACAIKQHYPG-TTVTIHIE 308
                                       77899999999977699***************************************************.89****** PP

                                       E. CS
                          ZT_dimer  78 Pe 79 
                                       P+
  gi|330506451|ref|YP_004382879.1| 309 PC 310
                                       *7 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.1     0.004        24      15      58 ..      34      78 ..      25      92 .. 0.72
   2 ?    6.5   0.6    0.0018        11      44     107 ..     102     184 ..      85     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.004
                              MerC 15 ClllPvllallpllglsf.lasellhqvllilvvaigllalvvgy 58
                                       + l +l +++ ++  s+ + se++h  + +++++i+++a+  ++
  gi|330506451|ref|YP_004382879.1| 34 NTSLVFLKIIVGMMIGSVsVISEAIHSGMDLIAAVIAFFAVKTSA 78
                                      555555555555544445255******************997665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0018
                              MerC  44 ilvvaigllalvvgyrrhrktsvlvlgalGllillvalflg...............teaeetl.........lfgsl 96 
                                       +l+++ +++ ++ +  r r++ +l   alGl+++lv++ ++               +     +          ++++
  gi|330506451|ref|YP_004382879.1| 102 LLILIAAGWIIYEAIGRLRNPVPLDEPALGLAVMLVSVAANifvsrklfivgeetdS-----IalkadawhlRTDVY 173
                                       4566778899999999*********************99997777777766544330.....144444433223333 PP

                              MerC  97 wqvltvlGaal 107
                                        +  +++G+++
  gi|330506451|ref|YP_004382879.1| 174 TSLGVLAGLLI 184
                                       44444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2607.46
//
Query:       gi|330506452|ref|YP_004382880.1|  [L=149]
Description: universal stress protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-30  106.0   0.1    2.5e-30  105.8   0.1    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.8   0.1   1.4e-34   2.5e-30       1     141 []       1     145 [.       1     145 [. 0.94

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 1.4e-34
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.....HH CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.....ak 72 
                                       m+k+I+Va+Dgs++s + +e A++la+ +g+ +i+++v+d  + ++ + ++     ++   e++++e +      ++
  gi|330506452|ref|YP_004382880.1|   1 MFKKIMVATDGSQTSIRTAELAVDLARLSGGSIIAIYVVDIYRLAHLPGYAAFPSLSSRLMELMQREGELaisevEN 77 
                                       9***************************************************9999999999999999999***555 PP

                                       HHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  73 aaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +a+ ++gv    ++ egdp++ei++   + +adl+V+G+ grs l+++llG v+e+v+rh+++pVl+V+
  gi|330506452|ref|YP_004382880.1|  78 MAC-DAGVPFSSIIAEGDPSQEIVKRSHKSGADLLVLGRIGRSDLEKILLGCVAEKVVRHSKIPVLIVP 145
                                       555.555666778999****************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1229.42
//
Query:       gi|330506453|ref|YP_004382881.1|  [L=283]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-21   76.2   0.0    7.5e-21   74.6   0.0    1.7  2  OrfB_IS605      Probable transposase
    1.9e-19   69.3   0.1    3.9e-19   68.3   0.1    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0068   15.3   0.1     0.0088   14.9   0.1    1.1  1  Pestivirus_E2   Pestivirus envelope glycoprotein E2
  ------ inclusion threshold ------
      0.024   14.7   0.2      0.039   14.0   0.2    1.3  1  DZR             Double zinc ribbon
      0.026   14.1   0.0      0.035   13.7   0.0    1.1  1  OpuAC           Substrate binding domain of ABC-type glycine 
       0.12   12.9   0.2       0.33   11.5   0.2    1.7  1  FeoB_Cyto       FeoB cytosolic helical domain
       0.58    9.8   3.4         13    5.5   0.5    2.6  2  RecR            RecR protein


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   3.7e+03      88     113 ..      21      46 ..      15      49 .. 0.82
   2 !   74.6   0.0   2.9e-24   7.5e-21      10     117 ..      82     186 ..      70     188 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                        OrfB_IS605  88 rkhllhklathliktlkevgvetLnv 113
                                       r   l+k +++++++++   ++++++
  gi|330506453|ref|YP_004382881.1|  21 RSPILRKGSRSILERMYLSKIGDIKI 46 
                                       55678899999999999999999987 PP

  == domain 2  score: 74.6 bits;  conditional E-value: 2.9e-24
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +p+ k ++ +g+D+G++ +at+++++   ++ ++r++++++ +la+ +++l++  k++  +kka + + r+h+++++
  gi|330506453|ref|YP_004382881.1|  82 KPPWKDGSLVGVDVGLESFATLSNGE---KIANPRFFREEEHELARVQRILSRAPKGTPERKKALEIVERVHERIAN 155
                                       566688999*****************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r +++h+++++l++++  ++ e+Ln+++m+
  gi|330506453|ref|YP_004382881.1| 156 KRYEFAHQISNQLVNRYGLIAFEDLNIKGMM 186
                                       ******************************9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.1   1.5e-22   3.9e-19       1      67 [.     200     266 ..     200     268 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1.5e-22
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       ++ l +  +yka  +G  v++v+p++TSk Cs+Cg  ++++ls+r+++C++Cg+++d D+nAaiNi 
  gi|330506453|ref|YP_004382881.1| 200 WNMLVTLTSYKAASAGSMVVLVDPRNTSKMCSRCGILVQKDLSERVHNCTQCGLSIDGDWNAAINIH 266
                                       667777889*********************************************************6 PP

>> Pestivirus_E2  Pestivirus envelope glycoprotein E2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   3.4e-06    0.0088     125     184 ..     192     252 ..     177     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.4e-06
                                       EEESS-CT--EEEEEEEE-SSS--EEEEEEE.EE-S-B---TT---EEEETTEEEEEEE-S CS
                     Pestivirus_E2 125 fqmvcpigwtgtvsctsfnmdtlattvvrty.rrskpfphrqgcitqknlgedlhncilgg 184
                                        + +  ++w   v+ ts++  +  + vv    r +  +  r g++ qk+l e +hnc   g
  gi|330506453|ref|YP_004382881.1| 192 AKSIGDVAWNMLVTLTSYKAASAGSMVVLVDpRNTSKMCSRCGILVQKDLSERVHNCTQCG 252
                                       55677899***********99998888876526677899******************8655 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   1.5e-05     0.039      10      44 ..     225     261 ..     221     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + +++Cs+Cg  +++  +   ++C +Cg ++d +++ 
  gi|330506453|ref|YP_004382881.1| 225 NTSKMCSRCGILVQKDLSerVHNCTQCGLSIDGDWNA 261
                                       6789********997666899*******999998886 PP

>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.3e-05     0.035     119     215 ..     149     244 ..     132     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                                       EEHHCCHSTTSHHCCHHHHHHHHHHT-TTCEEEGSCEEEEHH..HHHHHHHTTCSSEEEEETTSTHHHHTTEEE-B- CS
                             OpuAC 119 akgeflgrpdgwgcekvtegllkaYgldkvelvegseaamda..elyaaykrgepvvvyawtPdwaikkydlvvLed 193
                                       +  ++ +    ++ ++++++l++ Ygl  +e++  + ++m++   l++++ +  +++  + t   a ++  +vvL d
  gi|330506453|ref|YP_004382881.1| 149 VHERIANKRYEFA-HQISNQLVNRYGLIAFEDL--NIKGMMQnhNLAKSIGDVAWNMLVTLTSYKAASAGSMVVLVD 222
                                       5566667777777.999**********667776..889999989********************************* PP

                                       TTSTS-SSEEEEEEEEHHHHHH CS
                             OpuAC 194 pkglfppaynvvpvvrkefaek 215
                                       p++++  +++  ++v+k++ e+
  gi|330506453|ref|YP_004382881.1| 223 PRNTSKMCSRCGILVQKDLSER 244
                                       ******************9987 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00013      0.33      66      90 ..     145     169 ..     113     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                         FeoB_Cyto  66 lgedledvIvdarykfiegilrevv 90 
                                       + e + + I+++ry+f+++i+++ v
  gi|330506453|ref|YP_004382881.1| 145 IVERVHERIANKRYEFAHQISNQLV 169
                                       3468999***************987 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0064        16      13      29 ..     224     240 ..     219     241 .. 0.74
   2 ?    5.5   0.5     0.005        13      11      23 ..     240     252 ..     239     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0064
                                       HHH-EE-TTT--EESSS CS
                              RecR  13 kekvrhCsrCgnlteed 29 
                                       +++ + CsrCg l  +d
  gi|330506453|ref|YP_004382881.1| 224 RNTSKMCSRCGILVQKD 240
                                       667799*****986665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.005
                                       HHHHH-EE-TTT- CS
                              RecR  11 eakekvrhCsrCg 23 
                                       ++ e+v+ C +Cg
  gi|330506453|ref|YP_004382881.1| 240 DLSERVHNCTQCG 252
                                       6889********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2168.88
//
Query:       gi|330506454|ref|YP_004382882.1|  [L=489]
Description: catalase [Methanosaeta concilii GP6]
Scores for complete 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-189  627.9   0.3   8.1e-189  627.6   0.3    1.1  1  Catalase      Catalase
    3.5e-22   78.4   0.0      7e-22   77.4   0.0    1.5  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 !  627.6   0.3    9e-193  8.1e-189       1     382 [.      11     392 ..      11     393 .. 0.99

  Alignments for each domain:
  == domain 1  score: 627.6 bits;  conditional E-value: 9e-193
                                       B-TTS-B-S-SSS-EEESTTS-BBTT-HHHHHHHHHHHT------SS--SEEEEEEEEEESS--TTT---GGGSSTT CS
                          Catalase   1 ttseGapvsdnqnsltagerGplllqdvhlieklahfdreripeRvvhAkGagahgeFevtkdisdltkakllskvg 77 
                                       tt+ Gapv+dnqn+ltag+rGp+llqdv+++eklahfdre ipeR +hAkG+ga+g+F+vt+di+++t+a ++sk+g
  gi|330506454|ref|YP_004382882.1|  11 TTNVGAPVADNQNVLTAGQRGPMLLQDVWYLEKLAHFDREVIPERRMHAKGSGAYGTFTVTHDITRFTRAMIFSKIG 87 
                                       8999************************************************************************* PP

                                       -EEEEEEEEE-SS--TT--SSSSS--EEEEEEEETTEEEEEEEESSSS-S-S-GGGHHHHHHHHSB-TTT-SB-HHH CS
                          Catalase  78 kktpvlvRfStvagekgsadtaRdvrGfavkfyTeeGnwDlvgnntpvFfirDpikfpdlihsqkrepqtnlkdaam 154
                                       kkt++++RfStvage+g+ad++Rd+rGfavkfyTeeGnwDlvgnntpvFf+rDp+kfpdl+h+ kr+p+t +++a++
  gi|330506454|ref|YP_004382882.1|  88 KKTDLFARFSTVAGERGAADAERDIRGFAVKFYTEEGNWDLVGNNTPVFFLRDPLKFPDLNHAIKRDPKTGMRSAKN 164
                                       ***************************************************************************** PP

                                       HHHHHHT-GGGHHHHHHHHSGGGSBS-GGGS-EE--S-EEEE-TT--EEEEEEEEEETT---B--HHHHHHHHHH-T CS
                          Catalase 155 fwdflslnpeslhqvlilfsdrgipksyrhmngygvhtfklvnkegevvyvkfhfktkqgvknltaeeaeklagedp 231
                                        wdf+++ pe+lhqv+i++sdrgip s+rhm+g+g+htf+++n+++e+v+vkfh+ t+qg+knlt++eae++ ++d+
  gi|330506454|ref|YP_004382882.1| 165 NWDFWTSLPEALHQVTITMSDRGIPYSFRHMHGFGSHTFSMINTKNERVWVKFHWVTQQGIKNLTDAEAEAIIAKDR 241
                                       ***************************************************************************** PP

                                       THHHHHHHHHHHTT---EEEEEEEEEEHHHHTTTHHHHT-TT----TTTS--EEEEEEEEEE--S-HHHHTTT---- CS
                          Catalase 232 dyatrdLyeaiekgeypewelyvqvmteeeaeklrfnilDlTkvwpekevplrevGkltLnrnpenyFaevEqvafs 308
                                       ++++rdL+++iekg+yp+w+l++qvm+e+ea+++ ++++DlTkvw + ++pl+evG ++Lnrnpen+FaevEq+af+
  gi|330506454|ref|YP_004382882.1| 242 ESHQRDLFDSIEKGDYPRWKLFIQVMPEKEAQTVPYHPFDLTKVWYHGDYPLIEVGVMELNRNPENFFAEVEQAAFN 318
                                       ***************************************************************************** PP

                                       TT---TTEE--S-HHHHHHHHHHHHHHHHHT-TTGGGSGGG---..---S----TT-.....S-S---SS-S-T CS
                          Catalase 309 psnlvpGiepseDklLqgRlfsYadtqryRlGvnyqqlpvNrpkakvanyqrdGamrveankgkepnYepnsle 382
                                       p+n+vpGi++s+D++LqgRlfsY d+qryRlGvn++ +pvNr++++++ y+rdG+mrv++n+g +  Yepns++
  gi|330506454|ref|YP_004382882.1| 319 PANIVPGIGFSPDRMLQGRLFSYGDAQRYRLGVNHHLIPVNRARCPTNIYHRDGMMRVDDNQGCTLAYEPNSYG 392
                                       ***********************************************************************975 PP

>> Catalase-rel  Catalase-related immune-responsive
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0   7.9e-26     7e-22       3      65 .]     419     480 ..     417     480 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 7.9e-26
                                       GG--SSHHHHHHHHHS-HHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH-HHHHHHHHHHH CS
                      Catalase-rel   3 dfddhfsQagllyrsmseeekerlvnniafelskvedeeiqerqlehfakvDpdlgqrVaeal 65 
                                       d dd+++Q+g+l+r+m++e+++ l++n+a+++++++ + i+ r++ +++k+Dp++g++Va al
  gi|330506454|ref|YP_004382882.1| 419 DDDDYYTQPGKLFRLMKPEQQQALFENTARAMGDAP-KMIKIRHIGNCYKADPAYGEGVARAL 480
                                       558********************************9.***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 3155.49
//
Query:       gi|330506455|ref|YP_004382883.1|  [L=191]
Description: rubrerythrin [Methanosaeta concilii GP6]
Scores for complete 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  118.1   1.3    5.1e-34  117.6   1.3    1.2  1  Rubrerythrin    Rubrerythrin
    8.7e-07   29.0   0.4    1.6e-06   28.1   0.4    1.4  1  Ferritin        Ferritin-like domain
     0.0074   16.3   1.0      0.015   15.3   1.0    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.037   13.9   0.3      0.059   13.2   0.3    1.3  1  MCM_OB          MCM OB domain
      0.095   12.7   0.2       0.18   11.8   0.2    1.3  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type
       0.18   11.7   0.1       0.18   11.7   0.1    2.6  4  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.18   11.7   3.3        2.1    8.4   0.1    3.1  3  Nudix_N_2       Nudix N-terminal
       0.19   11.9   2.8       0.45   10.7   2.8    1.6  1  Zn-ribbon_8     Zinc ribbon domain
       0.98    9.8   5.5        3.1    8.2   5.5    2.0  1  DUF4379         Probable Zinc-ribbon domain
        1.5    8.8   6.8       0.81    9.6   0.3    2.6  3  HalOD2          Halobacterial output domain 2
        1.8    8.3   5.5        0.7    9.7   0.3    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 !  117.6   1.3   3.2e-37   5.1e-34       1     137 []      11     139 ..      11     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 3.2e-37
                                       HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS------- CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakp 76 
                                       ++L  ++agEs+ar++Y ++ ++ak egy+qia++F+++A++E+eHak+++klle  e+e +           +++ 
  gi|330506455|ref|YP_004382883.1|  11 KNLLLSFAGESQARNRYSYFGSQAKkEGYEQIAAIFLDTADNEKEHAKVFFKLLEGGELEIN---------GSFPAG 78 
                                       6899****************************************************888888.........889*** PP

                                       TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  77 kflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkll 137
                                        +  t+ nL ea+eg+  e+++my++++  a+keg++e+++ f+++++ Ek+He+r+r+ll
  gi|330506455|ref|YP_004382883.1|  79 VIGDTKANLMEAAEGEKFENTKMYPQFAATADKEGFPEIAEKFRNVCKVEKGHEDRYRALL 139
                                       **********************************************************995 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.4   9.9e-10   1.6e-06       7     140 ..      16     143 ..      10     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 9.9e-10
                                       HHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCS.SHH CS
                          Ferritin   7 qladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkefg.sve 82 
                                        +a e +a + y ++ + +k +g+e++a+ f + a+ e eha+ +++ +   Gg     + e+    +    g +  
  gi|330506455|ref|YP_004382883.1|  16 SFAGESQARNRYSYFGSQAKKEGYEQIAAIFLDTADNEKEHAKVFFKLLE--GG-----ELEINGSFPAGVIGdTKA 85 
                                       578899*************************************9999765..56.....666666555555584555 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  83 evleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekle 140
                                       + +eaa   + + t+++ + ++ a++eg p  a+ + ++ + +  he+  +all+++e
  gi|330506455|ref|YP_004382883.1|  86 NLMEAAEGEKFENTKMYPQFAATADKEGFPEIAEKFRNVCKVEKGHEDRYRALLKNVE 143
                                       666666666669******************************************9875 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 !   15.3   1.0   9.3e-06     0.015      64      97 ..     149     182 ..     118     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.3e-06
                                       EEEE--EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                              HypA  64 ieevpvkvrCreCgkefeleekalrCpkCgsadv 97 
                                        ++++v  rCr+Cg+  e +e+  +Cp+C +++ 
  gi|330506455|ref|YP_004382883.1| 149 KKDTKVAWRCRNCGYIHEGTEAPDECPACAHEQA 182
                                       4678999*******99996654347****98875 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   3.6e-05     0.059      25      65 ..     146     184 ..     142     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                                       --EEEEEEEEEEETTT-.-EEES----SB-..TTT-HHH.-E CS
                            MCM_OB  25 evkpklkkavfeckkcgktveveleePrkCeekeCeskd.pf 65 
                                       +v++k +k++ +c++cg+ +e  +e P +C  ++C +++  f
  gi|330506455|ref|YP_004382883.1| 146 KVFKKDTKVAWRCRNCGYIHE-GTEAPDEC--PACAHEQaYF 184
                                       7889999**********9666.7889****..99*9666244 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 ?   11.8   0.2   0.00011      0.18      15      43 ..     153     180 ..     151     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                          zf-C2HC5  15 eaapnClnCGkiiCakeglskpCsfCgsp 43 
                                       ++a  C nCG i    e++  +C+ C+++
  gi|330506455|ref|YP_004382883.1| 153 KVAWRCRNCGYIHEGTEAP-DECPACAHE 180
                                       56788**************.******965 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 ?   -3.4   0.0       5.7   9.4e+03       8      14 ..      11      17 ..      11      22 .. 0.72
   2 ?   -1.1   0.0       1.1   1.8e+03       9      18 ..      86      95 ..      85      99 .. 0.84
   3 ?   11.7   0.1   0.00011      0.18      19      32 ..     152     166 ..     148     170 .. 0.71
   4 ?   -3.8   0.7         8   1.3e+04       4       7 ..     174     177 ..     173     178 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.7
                                      TSBEEEE CS
                    RNA_POL_M_15KD  8 gNlLlpk 14
                                      +NlLl+ 
  gi|330506455|ref|YP_004382883.1| 11 KNLLLSF 17
                                      6999975 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                                      SBEEEEECSC CS
                    RNA_POL_M_15KD  9 NlLlpkedke 18
                                      Nl++ +e+++
  gi|330506455|ref|YP_004382883.1| 86 NLMEAAEGEK 95
                                      9***999986 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00011
                                       CCE.EEESSSS-EEE CS
                    RNA_POL_M_15KD  19 gkn.feCrqCgYeep 32 
                                       +k+   Cr+CgY+ +
  gi|330506455|ref|YP_004382883.1| 152 TKVaWRCRNCGYIHE 166
                                       344466******998 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 8
                                       ESTT CS
                    RNA_POL_M_15KD   4 CpkC 7  
                                       Cp C
  gi|330506455|ref|YP_004382883.1| 174 CPAC 177
                                       7777 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.47   7.7e+02      15      26 ..     115     126 ..     109     127 .. 0.82
   2 ?    8.4   0.1    0.0013       2.1      18      32 ..     151     165 ..     144     166 .. 0.79
   3 ?    1.4   0.4      0.19   3.1e+02       3       9 ..     174     180 ..     174     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.47
                                       -TT-SS-EEEET CS
                         Nudix_N_2  15 pdgDnreRlvCp 26 
                                       p+  ++ R vC+
  gi|330506455|ref|YP_004382883.1| 115 PEIAEKFRNVCK 126
                                       7778999****6 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0013
                                       -SS-EEEETTTTEEE CS
                         Nudix_N_2  18 DnreRlvCpaCgtih 32 
                                       D++   +C +Cg+ih
  gi|330506455|ref|YP_004382883.1| 151 DTKVAWRCRNCGYIH 165
                                       6666668*******9 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.19
                                       -TTT--B CS
                         Nudix_N_2   3 CsqCGtp 9  
                                       C++C+++
  gi|330506455|ref|YP_004382883.1| 174 CPACAHE 180
                                       8888875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.8   0.00028      0.45       7      34 ..     157     179 ..     155     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs 34 
                                       rC++Cg  +e       a + +CP+C +
  gi|330506455|ref|YP_004382883.1| 157 RCRNCGYIHEGTE----A-PDECPACAH 179
                                       9*****9999443....2.345****76 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   5.5    0.0019       3.1      24      45 ..     150     166 ..     115     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                           DUF4379  24 skkkvwWkCakCgheWeasvsn 45 
                                       + +kv W+C++Cg+     +++
  gi|330506455|ref|YP_004382883.1| 150 KDTKVAWRCRNCGY-----IHE 166
                                       478**********4.....333 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.3   5.4e+03      19      29 ..      34      44 ..      27      45 .. 0.74
   2 ?    9.6   0.3    0.0005      0.81      29      44 ..     153     168 ..     143     170 .. 0.75
   3 ?    1.9   0.8      0.13   2.1e+02       2      10 ..     171     179 ..     170     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.3
                            HalOD2 19 glGeGyrqLGa 29
                                      +  eGy+q+ a
  gi|330506455|ref|YP_004382883.1| 34 AKKEGYEQIAA 44
                                      55579999865 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0005
                            HalOD2  29 ayvWkCtrCGevqaaA 44 
                                          W+C +CG +  + 
  gi|330506455|ref|YP_004382883.1| 153 KVAWRCRNCGYIHEGT 168
                                       568*******998776 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.13
                            HalOD2   2 PekCseCsl 10 
                                       P++C++C  
  gi|330506455|ref|YP_004382883.1| 171 PDECPACAH 179
                                       9******75 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00043       0.7       1       8 [.     156     163 ..     152     166 .. 0.68
   2 ?    0.5   0.8      0.33   5.3e+02      17      21 ..     174     178 ..     173     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00043
                      Rubredoxin_2   1 YvCsqCGf 8  
                                       ++C++CG+
  gi|330506455|ref|YP_004382883.1| 156 WRCRNCGY 163
                                       56666666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.33
                      Rubredoxin_2  17 CpsCg 21 
                                       Cp+C 
  gi|330506455|ref|YP_004382883.1| 174 CPACA 178
                                       9**96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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):              11  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1386.05
//
Query:       gi|330506456|ref|YP_004382884.1|  [L=100]
Description: hypothetical protein MCON_0164 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.048   13.9   0.0       0.08   13.2   0.0    1.4  1  Toast_rack_N  N-terminal domain of toast_rack, DUF2154


Domain annotation for each model (and alignments):
>> Toast_rack_N  N-terminal domain of toast_rack, DUF2154
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.5e-06      0.08       9      50 ..      51      92 ..      44      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.5e-06
                      Toast_rack_N  9 nlelgaGeltvsggaeellegkveynakewepevkyevkgkr 50
                                      ++ +++G++++s + e  ++++ve +++e+e+e+k + k+ +
  gi|330506456|ref|YP_004382884.1| 51 EVSVKYGSINISINPEPPIKVEVECEKDELEIEIKLKAKKDK 92
                                      6899*******************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 755.90
//
Query:       gi|330506457|ref|YP_004382885.1|  [L=250]
Description: TPR repeat-containing protein [Methanosaeta concilii GP6]
Scores for 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   98.7  18.7    1.2e-06   28.2   0.1    6.3  6  TPR_2        Tetratricopeptide repeat
    1.8e-27   94.0  20.5    4.9e-07   29.3   0.2    6.6  7  TPR_1        Tetratricopeptide repeat
    2.7e-21   74.9  30.2    2.7e-05   23.8   0.2    6.0  6  TPR_11       TPR repeat
    9.5e-21   74.1  13.6    4.5e-08   33.5   1.2    4.1  4  TPR_19       Tetratricopeptide repeat
    6.2e-20   71.6  12.7    1.5e-09   38.3   0.9    4.2  4  TPR_16       Tetratricopeptide repeat
    1.3e-18   65.5  17.6     0.0015   18.6   0.1    6.2  6  TPR_8        Tetratricopeptide repeat
    5.3e-16   57.9   7.5     0.0011   19.7   0.0    5.8  6  TPR_14       Tetratricopeptide repeat
    2.4e-13   49.5  15.7     0.0067   16.7   0.1    6.4  6  TPR_17       Tetratricopeptide repeat
    7.8e-10   38.9  15.2     0.0005   20.3   2.3    5.1  5  TPR_12       Tetratricopeptide repeat
    8.6e-08   32.1   2.4    0.00041   20.4   0.2    4.2  4  Fis1_TPR_C   Fis1 C-terminal tetratricopeptide repeat
    2.7e-07   30.2   2.9      0.025   14.6   0.0    4.8  5  TPR_7        Tetratricopeptide repeat
    1.6e-06   28.4  13.0       0.05   14.3   0.1    5.0  4  TPR_6        Tetratricopeptide repeat
    6.3e-06   26.3  11.0      7e-05   23.0   1.1    3.1  3  ANAPC3       Anaphase-promoting complex, cyclosome, subunit 3
    4.3e-05   23.6   1.4       0.79    9.9   0.1    3.5  4  TPR_9        Tetratricopeptide repeat
    0.00016   21.9   0.2        2.7    8.9   0.0    3.7  3  TPR_4        Tetratricopeptide repeat
    0.00027   20.7   3.8       0.36   10.5   0.0    3.7  3  TOM20_plant  Plant specific mitochondrial import receptor sub
    0.00061   19.6   5.9        1.7    8.6   0.1    4.1  4  TPR_10       Tetratricopeptide repeat
     0.0011   18.9   0.0       0.44   10.6   0.0    2.5  2  RNase_PH_C   3' exoribonuclease family, domain 2
     0.0016   17.5   1.6        3.2    6.6   0.0    2.9  3  NARP1        NMDA receptor-regulated protein 1
  ------ inclusion threshold ------
      0.077   13.1   3.0        1.2    9.2   1.1    3.3  3  DUF3856      Domain of Unknown Function (DUF3856)
       0.12   12.8   1.5        1.5    9.3   0.1    2.8  3  BTAD         Bacterial transcriptional activator domain
          2    8.5  14.7        1.5    9.0   0.1    5.0  6  MIT          MIT (microtubule interacting and transport) doma


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.7   1.4e-07   0.00012       3      34 .]      24      55 ..      22      55 .. 0.91
   2 ?    4.6   0.0      0.05        41       2      33 ..      57      88 ..      56      89 .. 0.90
   3 !    9.4   0.0    0.0015       1.2       1      32 [.      90     121 ..      90     123 .. 0.94
   4 !   23.3   0.2   5.1e-08   4.2e-05       3      34 .]     126     157 ..     125     157 .. 0.97
   5 !   28.2   0.1   1.4e-09   1.2e-06       2      34 .]     159     191 ..     158     191 .. 0.97
   6 !   20.3   0.5   4.9e-07    0.0004       3      33 ..     194     224 ..     193     225 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.4e-07
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                                      +  + G  +y++++y +Al++f++A++ dPn+
  gi|330506457|ref|YP_004382885.1| 24 YFDWKGSQLYAAKNYTDALAYFNQAVAQDPNY 55
                                      56788999**********************96 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.05
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPn 33
                                       a+   G+  + l+dy+  ++ +  Al+ld  
  gi|330506457|ref|YP_004382885.1| 57 NAWVHKGDTERILKDYNVSIQSYYNALQLDGS 88
                                      589999**********************9965 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0015
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       a a+  ++++y++ + y  A  a  kA el+ 
  gi|330506457|ref|YP_004382885.1|  90 AAAWSGIAESYMAVKSYSNATIAASKATELNN 121
                                       689***************************97 PP

  == domain 4  score: 23.3 bits;  conditional E-value: 5.1e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++y+ G+++  +g yee ++ f+ A++ldPn+
  gi|330506457|ref|YP_004382885.1| 126 YWYREGRLLQLQGMYEESVAKFDGAIALDPNY 157
                                       8*****************************96 PP

  == domain 5  score: 28.2 bits;  conditional E-value: 1.4e-09
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ealy  G   ++lg+ye+A+++f++Al  dPn+
  gi|330506457|ref|YP_004382885.1| 159 EALYLKGITQMALGNYEDAKALFDQALVVDPNY 191
                                       79*****************************96 PP

  == domain 6  score: 20.3 bits;  conditional E-value: 4.9e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+   Gla+ + g++ eA + ++kAle+dP+
  gi|330506457|ref|YP_004382885.1| 194 AYLGKGLALHADGKLVEAQQEYDKALEIDPG 224
                                       78899*************************7 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.4     8e-07   0.00065       8      34 .]      29      55 ..      27      55 .. 0.92
   2 !   10.1   0.0   0.00072      0.59       2      34 .]      57      89 ..      56      89 .. 0.93
   3 !    8.7   0.0    0.0019       1.6       1      31 [.      90     120 ..      90     123 .. 0.94
   4 !   15.3   0.2   1.6e-05     0.013       3      34 .]     126     157 ..     125     157 .. 0.96
   5 !   29.3   0.2     6e-10   4.9e-07       2      34 .]     159     191 ..     159     191 .. 0.97
   6 !   21.8   0.5   1.4e-07   0.00011       3      34 .]     194     225 ..     193     225 .. 0.96
   7 ?   -2.1   0.0         5   4.1e+03       9      20 ..     234     245 ..     234     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8e-07
                                      HHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  8 GnayfklgkydeAleyyekALelnPnn 34
                                      G  ++  ++y +Al+y+++A+  +Pn+
  gi|330506457|ref|YP_004382885.1| 29 GSQLYAAKNYTDALAYFNQAVAQDPNY 55
                                      777899*******************97 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00072
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                      +a+  +G + + l++y+  ++ y  AL+l+ +n
  gi|330506457|ref|YP_004382885.1| 57 NAWVHKGDTERILKDYNVSIQSYYNALQLDGSN 89
                                      79***************************9765 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                       a a+ +++  y+  + y  A  + +kA eln
  gi|330506457|ref|YP_004382885.1|  90 AAAWSGIAESYMAVKSYSNATIAASKATELN 120
                                       78*************************9998 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                        +y+ G +++ +g+y+e ++ ++ A+ l+Pn+
  gi|330506457|ref|YP_004382885.1| 126 YWYREGRLLQLQGMYEESVAKFDGAIALDPNY 157
                                       6*****************************97 PP

  == domain 5  score: 29.3 bits;  conditional E-value: 6e-10
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +aly +G + + lg+y++A + +++AL ++Pn+
  gi|330506457|ref|YP_004382885.1| 159 EALYLKGITQMALGNYEDAKALFDQALVVDPNY 191
                                       69*****************************97 PP

  == domain 6  score: 21.8 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+ ++G+a++  gk+ eA + y+kALe++P +
  gi|330506457|ref|YP_004382885.1| 194 AYLGKGLALHADGKLVEAQQEYDKALEIDPGY 225
                                       9*****************************76 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 5
                                       HHHHHTT-HHHH CS
                             TPR_1   9 nayfklgkydeA 20 
                                       +a++ ++k+ eA
  gi|330506457|ref|YP_004382885.1| 234 HALMAMNKPREA 245
                                       58999***9998 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.5   6.5e-07   0.00053       1      35 [.      29      63 ..      29      65 .. 0.92
   2 !   20.4   0.4   3.7e-07    0.0003       1      39 [.      63     101 ..      63     104 .. 0.95
   3 ?    1.5   0.0      0.29   2.3e+02      19      42 .]     115     138 ..     114     138 .. 0.88
   4 !   23.8   0.2   3.3e-08   2.7e-05       4      42 .]     134     172 ..     131     172 .. 0.91
   5 !   23.6   1.1   3.8e-08   3.1e-05       6      42 .]     170     206 ..     167     206 .. 0.96
   6 !   16.2   0.5   7.4e-06     0.006       1      25 [.     199     223 ..     199     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.5e-07
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLG 35
                                      G  +y+  +y++A++ +++A++ dP++++a+ + G
  gi|330506457|ref|YP_004382885.1| 29 GSQLYAAKNYTDALAYFNQAVAQDPNYVNAWVHKG 63
                                      7789**************************98777 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 3.7e-07
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       Gd  + + +y+ +i++Y +Al+ld +na a++++++ y+
  gi|330506457|ref|YP_004382885.1|  63 GDTERILKDYNVSIQSYYNALQLDGSNAAAWSGIAESYM 101
                                       8999999****************************9997 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.29
                            TPR_11  19 kAlkldPdnaeayynLGlayykqG 42 
                                       kA +l++++ + +y  G +++ qG
  gi|330506457|ref|YP_004382885.1| 115 KATELNNQSKNYWYREGRLLQLQG 138
                                       9*************9988888887 PP

  == domain 4  score: 23.8 bits;  conditional E-value: 3.3e-08
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +  qG yee+++++  A++ldP++ ea+y  G +++++G
  gi|330506457|ref|YP_004382885.1| 134 LQLQGMYEESVAKFDGAIALDPNYKEALYLKGITQMALG 172
                                       5569*****************************999988 PP

  == domain 5  score: 23.6 bits;  conditional E-value: 3.8e-08
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ++G+ye+A + + +Al  dP++  ay++ Gla+++ G
  gi|330506457|ref|YP_004382885.1| 170 ALGNYEDAKALFDQALVVDPNYKQAYLGKGLALHADG 206
                                       79********************************987 PP

  == domain 6  score: 16.2 bits;  conditional E-value: 7.4e-06
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldP 25 
                                       G a+++ Gk+ eA ++Y kAl++dP
  gi|330506457|ref|YP_004382885.1| 199 GLALHADGKLVEAQQEYDKALEIDP 223
                                       8899********************9 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   4.9e-06     0.004       1      29 [.      32      60 ..      32      65 .. 0.92
   2 !   10.7   0.2   0.00074       0.6       6      61 ..      71     126 ..      67     129 .. 0.84
   3 !   33.5   1.2   5.5e-11   4.5e-08       4      60 ..     137     193 ..     134     199 .. 0.92
   4 !   19.4   0.1   1.4e-06    0.0011       2      44 ..     203     245 ..     202     249 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.9e-06
                            TPR_19  1 llaegdyaeAlalleqalqedpknaearl 29
                                      l+a+++y++Ala++ qa ++dp++ +a+ 
  gi|330506457|ref|YP_004382885.1| 32 LYAAKNYTDALAYFNQAVAQDPNYVNAWV 60
                                      7899********************99986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00074
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       dy   ++ + +alq d  na+a+ + Ae ++a + +  A  + +++ e + ++ +y
  gi|330506457|ref|YP_004382885.1|  71 DYNVSIQSYYNALQLDGSNAAAWSGIAESYMAVKSYSNATIAASKATELNNQSKNY 126
                                       7778889999**********************999999987777777777776555 PP

  == domain 3  score: 33.5 bits;  conditional E-value: 5.5e-11
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                       +g y+e +a +  a++ dp++ ea++l  + ++alg++++A+al d+++  dp+  +
  gi|330506457|ref|YP_004382885.1| 137 QGMYEESVAKFDGAIALDPNYKEALYLKGITQMALGNYEDAKALFDQALVVDPNYKQ 193
                                       899**********************************************99999633 PP

  == domain 4  score: 19.4 bits;  conditional E-value: 1.4e-06
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeA 44 
                                        a+g++ eA++ + +al+ dp+++ a++  + al+a++ + eA
  gi|330506457|ref|YP_004382885.1| 203 HADGKLVEAQQEYDKALEIDPGYSSAKISKMHALMAMNKPREA 245
                                       689************************************9999 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.3   3.4e-09   2.7e-06       7      60 ..      32      83 ..      28      90 .. 0.90
   2 ?    5.1   0.1     0.043        35      12      55 ..      71     111 ..      69     123 .. 0.80
   3 !   11.0   0.1   0.00066      0.54       1      44 [.     128     168 ..     128     172 .. 0.89
   4 !   38.3   0.9   1.9e-12   1.5e-09       7      67 ..     168     225 ..     164     226 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.4e-09
                            TPR_16  7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyraa 60
                                      +++a++y+dA+a++++a+++d   P  + A+ ++gd    ++++   +  +y+a+
  gi|330506457|ref|YP_004382885.1| 32 LYAAKNYTDALAYFNQAVAQD---PNYVNAWVHKGDTERILKDYNVSIqSYYNAL 83
                                      899******************...********************99997777775 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.043
                            TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaa 55 
                                       dy   +  +  al +d     +a+A+ + ++++ + + +  A  
  gi|330506457|ref|YP_004382885.1|  71 DYNVSIQSYYNALQLD---GSNAAAWSGIAESYMAVKSYSNATI 111
                                       6666777777788888...789***************9998864 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00066
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaa 44 
                                       + ++r++  +g y++ +a ++ a+++d   P   eAl+l+g   
  gi|330506457|ref|YP_004382885.1| 128 YREGRLLQLQGMYEESVAKFDGAIALD---PNYKEALYLKGITQ 168
                                       678999999999***************...*********99765 PP

  == domain 4  score: 38.3 bits;  conditional E-value: 1.9e-12
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                        +++g+y+dA a++++al  d   P   +A+l++g+a+ + g l eA + y++al+ +p++
  gi|330506457|ref|YP_004382885.1| 168 QMALGNYEDAKALFDQALVVD---PNYKQAYLGKGLALHADGKLVEAQQEYDKALEIDPGY 225
                                       6789*****************...***********************************97 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.2    0.0044       3.6      13      33 ..      34      54 ..      23      55 .. 0.85
   2 !   13.2   0.0   9.7e-05     0.079       2      33 ..      57      88 ..      56      89 .. 0.93
   3 !    6.9   0.2      0.01       8.1       2      33 ..      91     122 ..      90     123 .. 0.92
   4 !   12.0   0.1   0.00024      0.19       3      34 .]     126     157 ..     125     157 .. 0.95
   5 !   18.6   0.1   1.9e-06    0.0015       2      33 ..     159     190 ..     158     191 .. 0.94
   6 !   15.8   0.2   1.4e-05     0.012       2      32 ..     193     223 ..     192     225 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0044
                                      HTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8 13 klgdyeeAkeyyekaleldpd 33
                                        ++y  A +y+++a+  dp+
  gi|330506457|ref|YP_004382885.1| 34 AAKNYTDALAYFNQAVAQDPN 54
                                      5689*************9998 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 9.7e-05
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                                       a++++g++ + l+dy+ ++++y  al+ld +
  gi|330506457|ref|YP_004382885.1| 57 NAWVHKGDTERILKDYNVSIQSYYNALQLDGS 88
                                      69***************************965 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.01
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        a+  ++  y+  + y +A  +  ka+el+ +
  gi|330506457|ref|YP_004382885.1|  91 AAWSGIAESYMAVKSYSNATIAASKATELNNQ 122
                                       68999************************976 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++y+ g++++ +g yee+++ +  a+ ldp++
  gi|330506457|ref|YP_004382885.1| 126 YWYREGRLLQLQGMYEESVAKFDGAIALDPNY 157
                                       7*****************************85 PP

  == domain 5  score: 18.6 bits;  conditional E-value: 1.9e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ea+y++g + + lg+ye Ak+ + +al  dp+
  gi|330506457|ref|YP_004382885.1| 159 EALYLKGITQMALGNYEDAKALFDQALVVDPN 190
                                       799************************99997 PP

  == domain 6  score: 15.8 bits;  conditional E-value: 1.4e-05
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +ay+ +g++++  g++ eA++ y kale+dp
  gi|330506457|ref|YP_004382885.1| 193 QAYLGKGLALHADGKLVEAQQEYDKALEIDP 223
                                       69****************************9 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.3e-06    0.0011       8      42 ..      29      63 ..      23      65 .. 0.91
   2 ?    3.3   0.0      0.23   1.8e+02      14      39 ..      69      94 ..      62      99 .. 0.79
   3 !   11.4   0.1   0.00059      0.48       3      41 ..     126     164 ..     124     167 .. 0.91
   4 !   19.2   0.1   1.8e-06    0.0015       2      40 ..     159     197 ..     158     201 .. 0.92
   5 !    9.5   0.1    0.0024         2       3      37 ..     194     228 ..     193     233 .. 0.88
   6 ?   -1.0   0.0       5.6   4.5e+03       9      24 ..     234     249 ..     232     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-06
                            TPR_14  8 aeallalGdpdeAiallrralalaPddaeawllla 42
                                      ++ l+a+ ++ +A+a++++a+a++P+   aw + +
  gi|330506457|ref|YP_004382885.1| 29 GSQLYAAKNYTDALAYFNQAVAQDPNYVNAWVHKG 63
                                      67899**************************9987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.23
                            TPR_14 14 lGdpdeAiallrralalaPddaeawl 39
                                      l d+  +i+ +  al+l+ ++a+aw 
  gi|330506457|ref|YP_004382885.1| 69 LKDYNVSIQSYYNALQLDGSNAAAWS 94
                                      5566667999999************5 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00059
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                        +++ +++l  +G ++e++a ++ a+al+P+  ea++l 
  gi|330506457|ref|YP_004382885.1| 126 YWYREGRLLQLQGMYEESVAKFDGAIALDPNYKEALYLK 164
                                       589999***************************999876 PP

  == domain 4  score: 19.2 bits;  conditional E-value: 1.8e-06
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       eal++ +   +alG++++A al+++al  +P+  +a+l 
  gi|330506457|ref|YP_004382885.1| 159 EALYLKGITQMALGNYEDAKALFDQALVVDPNYKQAYLG 197
                                       789999**************************9999976 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0024
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaea 37 
                                       a+l  + al a G++ eA + +++al+ +P+   a
  gi|330506457|ref|YP_004382885.1| 194 AYLGKGLALHADGKLVEAQQEYDKALEIDPGYSSA 228
                                       6777789999********************98766 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 5.6
                            TPR_14   9 eallalGdpdeAiall 24 
                                       +al+a  +p+eA  +l
  gi|330506457|ref|YP_004382885.1| 234 HALMAMNKPREAFGML 249
                                       689999******9887 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00018      0.15       2      29 ..      45      72 ..      44      73 .. 0.90
   2 ?    3.5   0.2      0.14   1.1e+02       2      24 ..      79     101 ..      78     109 .. 0.86
   3 ?    2.9   0.2      0.21   1.7e+02       4      32 ..     115     143 ..     112     145 .. 0.89
   4 !   16.7   0.1   8.2e-06    0.0067       5      33 ..     150     178 ..     147     179 .. 0.94
   5 !   14.1   0.1   5.6e-05     0.046       1      34 []     180     213 ..     180     213 .. 0.97
   6 ?    6.1   0.0      0.02        16       2      14 ..     215     227 ..     214     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdl 29
                                      + +a+++dPn+++a+  ++ + + ++d+
  gi|330506457|ref|YP_004382885.1| 45 FNQAVAQDPNYVNAWVHKGDTERILKDY 72
                                      889****************999988886 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                            TPR_17   2 ylkaleldPnnadaynnLAelll 24 
                                       y +al+ld +na a+   Ae + 
  gi|330506457|ref|YP_004382885.1|  79 YYNALQLDGSNAAAWSGIAESYM 101
                                       779************99999886 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.21
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtA 32 
                                       ka el+  + + ++  ++ll  +G +++ 
  gi|330506457|ref|YP_004382885.1| 115 KATELNNQSKNYWYREGRLLQLQGMYEES 143
                                       8999999999**************99875 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 8.2e-06
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmtAr 33 
                                       a++ldPn+ +a+++++ ++  +G++++A+
  gi|330506457|ref|YP_004382885.1| 150 AIALDPNYKEALYLKGITQMALGNYEDAK 178
                                       89*************************98 PP

  == domain 5  score: 14.1 bits;  conditional E-value: 5.6e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       l+ +al  dPn+  ay  ++ +l+  G+l +A+q
  gi|330506457|ref|YP_004382885.1| 180 LFDQALVVDPNYKQAYLGKGLALHADGKLVEAQQ 213
                                       6899****************************98 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.02
                            TPR_17   2 ylkaleldPnnad 14 
                                       y kale+dP ++ 
  gi|330506457|ref|YP_004382885.1| 215 YDKALEIDPGYSS 227
                                       9********9985 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.7   0.00035      0.28      10      69 ..      29      80 ..      24      85 .. 0.70
   2 ?    6.0   0.1     0.018        15       4      33 ..      57      86 ..      54     102 .. 0.87
   3 !    7.7   0.4    0.0052       4.2       4      74 ..      91     153 ..      88     156 .. 0.63
   4 !   16.8   0.6   7.8e-06    0.0064      10      72 ..     131     185 ..     125     190 .. 0.83
   5 !   20.3   2.3   6.1e-07    0.0005       5      75 ..     160     222 ..     157     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00035
                            TPR_12 10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelle 69
                                      ++ l+++++y++Al+++++a+++      p+   ++++    g++ r l++y   ++ + 
  gi|330506457|ref|YP_004382885.1| 29 GSQLYAAKNYTDALAYFNQAVAQD-----PN---YVNAWVHKGDTERILKDYNVSIQSYY 80
                                      666888999999999999996554.....43...56777777777777777777766665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.018
                            TPR_12  4 talnnlaavlrrlgrydeAlellekaleia 33
                                      +a+++ ++++r l++y  +++ +  al++ 
  gi|330506457|ref|YP_004382885.1| 57 NAWVHKGDTERILKDYNVSIQSYYNALQLD 86
                                      688999*********************986 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0052
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +a++ +a+ +++ + y  A     ka e+ +++         ++ +  grl++++g yee ++ +  a+a+
  gi|330506457|ref|YP_004382885.1|  91 AAWSGIAESYMAVKSYSNATIAASKATELNNQS--------KNYWYREGRLLQLQGMYEESVAKFDGAIAL 153
                                       666677777777777777777777776666554........334566677777777777766666555555 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 7.8e-06
                            TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       + +l+ +g y+e+ + ++ a+++      p++    ++l+  g+++ alg+ye+A +l+ +al
  gi|330506457|ref|YP_004382885.1| 131 GRLLQLQGMYEESVAKFDGAIALD-----PNY---KEALYLKGITQMALGNYEDAKALFDQAL 185
                                       78999***************8888.....875...5566666666668*************98 PP

  == domain 5  score: 20.3 bits;  conditional E-value: 6.1e-07
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       al+  + + ++lg+y++A +l+++al +      p+   + +++ + g +++a g++ eA++ + +al+i+
  gi|330506457|ref|YP_004382885.1| 160 ALYLKGITQMALGNYEDAKALFDQALVVD-----PN---YKQAYLGKGLALHADGKLVEAQQEYDKALEID 222
                                       5668899999***************8888.....76...589***************************96 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.025        20      14      34 ..      35      55 ..      32      59 .. 0.86
   2 ?    4.4   0.0     0.048        39      15      42 ..     138     165 ..     135     170 .. 0.90
   3 !   20.4   0.2     5e-07   0.00041       2      37 ..     159     194 ..     158     196 .. 0.96
   4 ?    2.4   0.0      0.21   1.7e+02      19      37 ..     210     228 ..     206     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.025
                                      HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPen 34
                                       ++Y++A+ y ++  + +P+ 
  gi|330506457|ref|YP_004382885.1| 35 AKNYTDALAYFNQAVAQDPNY 55
                                      69*************999986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.048
                                       T-HHHHHHHHHHHHHHTTS-HHHHHHHH CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenrQaqsLke 42 
                                       g Y+e+    d  ++++P+ + a+ Lk 
  gi|330506457|ref|YP_004382885.1| 138 GMYEESVAKFDGAIALDPNYKEALYLKG 165
                                       67**********************9996 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 5e-07
                                       HHHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C   2 eclYylAlGhyklgeYseArryvdalLeiEPenrQa 37 
                                       e lY+  + ++ lg+Y++A+ + d+ L ++P+ +Qa
  gi|330506457|ref|YP_004382885.1| 159 EALYLKGITQMALGNYEDAKALFDQALVVDPNYKQA 194
                                       89*********************************9 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  19 eArryvdalLeiEPenrQa 37 
                                       eA +  d  Lei+P+ + a
  gi|330506457|ref|YP_004382885.1| 210 EAQQEYDKALEIDPGYSSA 228
                                       7889999999999998877 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.093        76      14      33 ..      37      54 ..      33      54 .. 0.91
   2 ?   -2.4   0.0         8   6.6e+03       7      19 ..      57      69 ..      57      72 .. 0.77
   3 ?    5.4   0.0     0.027        22       6      32 ..     131     155 ..     131     158 .. 0.87
   4 !   14.6   0.0   3.1e-05     0.025       1      32 [.     160     189 ..     160     190 .. 0.89
   5 ?    2.6   0.0       0.2   1.7e+02      10      20 ..     210     220 ..     194     224 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.093
                             TPR_7 14 dyeeAielyeqsLaltkdpe 33
                                      +y +A+ ++ q  a++ dp+
  gi|330506457|ref|YP_004382885.1| 37 NYTDALAYFNQ--AVAQDPN 54
                                      799********..9999985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8
                             TPR_7  7 rlysrlGdyeeAi 19
                                      ++++  Gd+e+ +
  gi|330506457|ref|YP_004382885.1| 57 NAWVHKGDTERIL 69
                                      5789999999865 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.027
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdp 32 
                                       +rl + +G yee +  +    a++ dp
  gi|330506457|ref|YP_004382885.1| 131 GRLLQLQGMYEESVAKFDG--AIALDP 155
                                       789999************9..777776 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 3.1e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       aL+  + ++ +lG+ye+A  l+ q  al  dp
  gi|330506457|ref|YP_004382885.1| 160 ALYLKGITQMALGNYEDAKALFDQ--ALVVDP 189
                                       67888999****************..888887 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.2
                             TPR_7  10 srlGdyeeAie 20 
                                       +++++y++A+e
  gi|330506457|ref|YP_004382885.1| 210 EAQQEYDKALE 220
                                       56788888876 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.3    0.0018       1.4      10      32 ..      32      54 ..      26      55 .. 0.84
   2 ?    5.7   0.1     0.032        26       4      32 ..     128     156 ..     126     157 .. 0.90
   3 !   14.3   0.1   6.1e-05      0.05       1      31 [.     159     189 ..     159     191 .. 0.90
   4 ?    4.7   0.2      0.07        57       1      31 [.     193     223 ..     193     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0018
                                      HHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6 10 yrklgdtdkAlealerlikeYPd 32
                                      +++++++++Al+++++ + + P+
  gi|330506457|ref|YP_004382885.1| 32 LYAAKNYTDALAYFNQAVAQDPN 54
                                      45567***************998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                                       y+ +++++ +g ++++++ ++  i   P+
  gi|330506457|ref|YP_004382885.1| 128 YREGRLLQLQGMYEESVAKFDGAIALDPN 156
                                       899******9**********999988887 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 6.1e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                       +Aly+ +  + +lg++++A++++++ +   P
  gi|330506457|ref|YP_004382885.1| 159 EALYLKGITQMALGNYEDAKALFDQALVVDP 189
                                       7***********9***********9886666 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                       +A++  +l++ + g+  +A + +++ ++  P
  gi|330506457|ref|YP_004382885.1| 193 QAYLGKGLALHADGKLVEAQQEYDKALEIDP 223
                                       6999999999997799999999999998877 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.8     0.013        11      28      76 ..      27      76 ..      17      82 .. 0.83
   2 !   23.0   1.1   8.6e-08     7e-05       3      80 ..     104     182 ..     102     184 .. 0.89
   3 ?    3.2   0.1      0.12     1e+02      20      78 ..     188     248 ..     179     250 .] 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                                      HHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                            ANAPC3 28 llAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76
                                      +++  ly +++y+ A+ ++++a  ++++  ++++ ++ +   Lk y+  i
  gi|330506457|ref|YP_004382885.1| 27 WKGSQLYAAKNYTDALAYFNQAvAQDPNYVNAWVHKGDTERILKDYNVSI 76
                                      778899****************9999999999999988888787777655 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 8.6e-08
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       + y nA + a+++ + +++s +  y  +  l l+g y++    ++ a  l+++ ++++yl++ ++ +L++ye+A a+
  gi|330506457|ref|YP_004382885.1| 104 KSYSNATIAASKATELNNQSKNYWYREGRLLQLQGMYEESVAKFDGAiALDPNYKEALYLKGITQMALGNYEDAKAL 180
                                       5799**********6666666666666***********************************************988 PP

                                       H- CS
                            ANAPC3  79 Le 80 
                                       ++
  gi|330506457|ref|YP_004382885.1| 181 FD 182
                                       76 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.12
                                       H--HHHHHH.HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  20 tespedayl.lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                         +++ ayl ++l+l  +g+  +A++ ++ka ++++    + + + ++l +++k  eA   
  gi|330506457|ref|YP_004382885.1| 188 DPNYKQAYLgKGLALHADGKLVEAQQEYDKAlEIDPGYSSAKISKMHALMAMNKPREAFGM 248
                                       45677788867999************99999999999999999999999999999998765 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.098        80       9      59 ..      36      86 ..      29      92 .. 0.61
   2 !    7.4   0.0    0.0059       4.8       4      65 ..      99     160 ..      96     169 .. 0.84
   3 !    8.6   0.0    0.0025       2.1      22      66 ..     151     195 ..     150     198 .. 0.90
   4 !    9.9   0.1   0.00097      0.79       9      61 ..     172     226 ..     163     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.098
                             TPR_9  9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59
                                      +++  ala+ +  ++ +P+ +  +   G  +  l ++++ ++    +l+l+
  gi|330506457|ref|YP_004382885.1| 36 KNYTDALAYFNQAVAQDPNYVNAWVHKGDTERILKDYNVSIQSYYNALQLD 86
                                      455566666666666666666666666666666666666666665555555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0059
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                        ++  + ++ a  ++     l+ ++   ++  G+ll+ +G +++ +a ++ ++al+p+  +a
  gi|330506457|ref|YP_004382885.1|  99 SYMAVKSYSNATIAASKATELNNQSKNYWYREGRLLQLQGMYEESVAKFDGAIALDPNYKEA 160
                                       5777777788888888888888899999999**************************76555 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0025
                             TPR_9  22 lllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                                       ++l+P+  e ++  G+ ++ lG+++ A a ++++l ++p+  +a+
  gi|330506457|ref|YP_004382885.1| 151 IALDPNYKEALYLKGITQMALGNYEDAKALFDQALVVDPNYKQAY 195
                                       5789999999999**************************887776 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00097
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap..d 61 
                                        ++e a a  +  l+++P+  + ++  Gl+l+  G l +A ++ + +l+++p  +
  gi|330506457|ref|YP_004382885.1| 172 GNYEDAKALFDQALVVDPNYKQAYLGKGLALHADGKLVEAQQEYDKALEIDPgyS 226
                                       5677788889999*************************************99553 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.59   4.8e+02       7      20 ..     130     143 ..     126     145 .. 0.83
   2 !    8.9   0.0    0.0033       2.7       3      26 .]     160     183 ..     159     183 .. 0.92
   3 ?    6.7   0.1     0.016        13       3      24 ..     194     215 ..     193     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.59
                             TPR_4   7 LArallalGdldeA 20 
                                        +r+l+++G ++e 
  gi|330506457|ref|YP_004382885.1| 130 EGRLLQLQGMYEES 143
                                       589*******9985 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0033
                             TPR_4   3 allaLArallalGdldeAraller 26 
                                       al++ + ++ alG++++A al+++
  gi|330506457|ref|YP_004382885.1| 160 ALYLKGITQMALGNYEDAKALFDQ 183
                                       7899999**************986 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.016
                             TPR_4   3 allaLArallalGdldeArall 24 
                                       a+l+ + al+a G l eA++  
  gi|330506457|ref|YP_004382885.1| 194 AYLGKGLALHADGKLVEAQQEY 215
                                       788999************9865 PP

>> TOM20_plant  Plant specific mitochondrial import receptor subunit TOM20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.2     0.017        14      91     112 ..      33      54 ..      16     120 .. 0.80
   2 !   10.5   0.0   0.00045      0.36      49      99 ..     138     184 ..     132     187 .. 0.82
   3 ?    5.0   0.0     0.023        18      52      98 ..     175     217 ..     170     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHH-TT CS
                       TOM20_plant  91 eakenfekatqffqqavdedPd 112
                                        a +n+  a  +f+qav++dP+
  gi|330506457|ref|YP_004382885.1|  33 YAAKNYTDALAYFNQAVAQDPN 54 
                                       6889999**************7 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHH CS
                       TOM20_plant  49 qmiqdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfeka 99 
                                        m +++++k++ a+ +dP+ ++al++ g + ++ + +    e+ak  f++a
  gi|330506457|ref|YP_004382885.1| 138 GMYEESVAKFDGAIALDPNYKEALYLKGITQMALGNY----EDAKALFDQA 184
                                       6999**********************99888877665....5666667666 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHH CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfek 98 
                                       +da + +++al++dP+ ++a    g a  + + l++ ++e    ++k
  gi|330506457|ref|YP_004382885.1| 175 EDAKALFDQALVVDPNYKQAYLGKGLALHADGKLVEAQQE----YDK 217
                                       68888999*********99998888888888877755544....444 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.037        30      12      30 ..      32      50 ..      32      50 .. 0.92
   2 !    8.6   0.1    0.0021       1.7       9      29 ..     165     185 ..     159     187 .. 0.92
   3 !    6.6   0.2    0.0087       7.1       9      31 ..     199     221 ..     194     221 .. 0.94
   4 ?   -2.4   0.0       6.2   5.1e+03      11      22 ..     235     246 ..     234     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.037
                            TPR_10 12 lrqrgrydeAealleeala 30
                                      l++ ++y++A+a++ +a+a
  gi|330506457|ref|YP_004382885.1| 32 LYAAKNYTDALAYFNQAVA 50
                                      68999***********996 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0021
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       +++  ++g+y++A al+++al
  gi|330506457|ref|YP_004382885.1| 165 GITQMALGNYEDAKALFDQAL 185
                                       788999**************8 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0087
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al++ g++ eA + +++al+i
  gi|330506457|ref|YP_004382885.1| 199 GLALHADGKLVEAQQEYDKALEI 221
                                       789******************97 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 6.2
                            TPR_10  11 alrqrgrydeAe 22 
                                       al ++++  eA 
  gi|330506457|ref|YP_004382885.1| 235 ALMAMNKPREAF 246
                                       788899999986 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 !   10.6   0.0   0.00055      0.44       7      35 ..     143     171 ..     143     180 .. 0.81
   2 ?    6.0   0.0     0.015        12       9      29 ..     179     199 ..     177     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00055
                                       EEEEETTEEEES--HHHHHHSSEEEEEEE CS
                        RNase_PH_C   7 tvgkvddqfvlDptkeEedlsegdltlav 35 
                                       +v+k+d+ + lDp+++E ++ +g   +a+
  gi|330506457|ref|YP_004382885.1| 143 SVAKFDGAIALDPNYKEALYLKGITQMAL 171
                                       69***************999888555554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.015
                                       EEETTEEEES--HHHHHHSSE CS
                        RNase_PH_C   9 gkvddqfvlDptkeEedlseg 29 
                                       +++d  +v+Dp++++  l++g
  gi|330506457|ref|YP_004382885.1| 179 ALFDQALVVDPNYKQAYLGKG 199
                                       578889*********999887 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0039       3.2     205     240 ..      35      70 ..      23      91 .. 0.78
   2 ?    2.4   0.0     0.069        56     198     256 ..      96     154 ..      86     158 .. 0.93
   3 !    6.4   0.1    0.0044       3.6     204     256 ..     170     222 ..     157     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0039
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaG 240
                                        ++++ Al y ++a++++p+ v+ ++ K+   +   
  gi|330506457|ref|YP_004382885.1|  35 AKNYTDALAYFNQAVAQDPNYVNAWVHKGDTERILK 70 
                                       467899**********************95444444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.069
                                       HHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 198 lAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       +A  y  ++s+++A+   +ka e + ++ +++++ +r+l+ +G  ++ ++  + a +lD
  gi|330506457|ref|YP_004382885.1|  96 IAESYMAVKSYSNATIAASKATELNNQSKNYWYREGRLLQLQGMYEESVAKFDGAIALD 154
                                       67889999******************************************999999998 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0044
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                        lg++e A  + d+a+  +p+  + yl K+  l   G l +A +  ++a ++D
  gi|330506457|ref|YP_004382885.1| 170 ALGNYEDAKALFDQALVVDPNYKQAYLGKGLALHADGKLVEAQQEYDKALEID 222
                                       5788999******************************************9988 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.5   2.9e+03      79      87 ..      39      47 ..      27      61 .. 0.70
   2 ?    9.2   1.1    0.0015       1.2      46      98 ..      81     133 ..      41     181 .. 0.82
   3 ?    1.5   0.0      0.34   2.8e+02     104     128 ..     196     220 ..     190     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.5
                                      HHHHHHHHH CS
                           DUF3856 79 dkalryfnr 87
                                        al yfn+
  gi|330506457|ref|YP_004382885.1| 39 TDALAYFNQ 47
                                      457778876 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0015
                                       S---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHH CS
                           DUF3856  46 eafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGkl 98 
                                       +a+  +G +a +++g++e+++ +++y +a  +a ka +  n+  +    eG+l
  gi|330506457|ref|YP_004382885.1|  81 NALQLDGSNAAAWSGIAESYMAVKSYSNATIAASKATELNNQSKNYWYREGRL 133
                                       678899*************************9999987666555555544443 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.34
                                       HHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmage 128
                                       + ++ al+  G+  ea +++ +a e
  gi|330506457|ref|YP_004382885.1| 196 LGKGLALHADGKLVEAQQEYDKALE 220
                                       5677788888888888888877776 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.9     4e+03      26      41 ..      35      50 ..      27      62 .. 0.52
   2 ?    9.3   0.1    0.0018       1.5     104     135 ..     159     190 ..      90     200 .. 0.85
   3 ?    1.6   0.0      0.41   3.3e+02      76     115 ..     206     245 ..     193     248 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.9
                                      HHHHHHHHTT--SSTT CS
                              BTAD 26 aelleaAlalwrGpal 41
                                      a+ + +Ala ++  + 
  gi|330506457|ref|YP_004382885.1| 35 AKNYTDALAYFNQAVA 50
                                      3333333333333333 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0018
                                       HHHHHTT-HHHHHHHHHHHHHHHHHHHS---- CS
                              BTAD 104 rAlarsGrqaeALevYerlrrlLaeeLgvepg 135
                                       +Al+  G ++ AL+ Ye++++l ++ L v+p 
  gi|330506457|ref|YP_004382885.1| 159 EALYLKGITQMALGNYEDAKALFDQALVVDPN 190
                                       79****************************97 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.41
                                       T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHH CS
                              BTAD  76 GraeealaelealvaehPlrErlhrqlmrAlarsGrqaeA 115
                                       G+  ea++e++++++ +P    +    m Al+++++  eA
  gi|330506457|ref|YP_004382885.1| 206 GKLVEAQQEYDKALEIDPGYSSAKISKMHALMAMNKPREA 245
                                       5556777788888888888888888888888888877777 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   0.1    0.0018       1.5      23      42 ..      34      52 ..      23      64 .. 0.82
   2 ?    0.0   0.1       1.1   9.3e+02      18      33 ..      70      85 ..      68      85 .. 0.89
   3 ?   -2.0   0.1       4.9     4e+03       3      16 ..     108     121 ..     101     126 .. 0.58
   4 ?    0.4   0.0      0.85   6.9e+02      26      49 ..     139     161 ..     138     169 .. 0.66
   5 ?    4.4   0.1     0.047        38      21      48 ..     168     194 ..     163     201 .. 0.78
   6 ?    0.5   0.1      0.81   6.6e+02      18      32 ..     206     220 ..     196     221 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0018
                               MIT 23 AlelYkealelLlqalkekn 42
                                      A ++Y++al +++qa+++ +
  gi|330506457|ref|YP_004382885.1| 34 AAKNYTDALAYFNQAVAQ-D 52
                                      8899***********983.3 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.1
                               MIT 18 gnyeeAlelYkealel 33
                                      ++y   ++ Y +al+l
  gi|330506457|ref|YP_004382885.1| 70 KDYNVSIQSYYNALQL 85
                                      789999*******986 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.9
                               MIT   3 kAlelvkkAveeDn 16 
                                       +A   ++kA+e+ n
  gi|330506457|ref|YP_004382885.1| 108 NATIAASKATELNN 121
                                       45555666666554 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.85
                               MIT  26 lYkealelLlqalkekneerrell 49 
                                       +Y+e++  +  a++  +++ +e+l
  gi|330506457|ref|YP_004382885.1| 139 MYEESVAKFDGAIA-LDPNYKEAL 161
                                       57777777777776.455566655 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.047
                               MIT  21 eeAlelYkealelLlqalkekneerrel 48 
                                       + Al +Y++a  l+ qal   +++ +++
  gi|330506457|ref|YP_004382885.1| 168 QMALGNYEDAKALFDQALV-VDPNYKQA 194
                                       7799999999999999997.55566655 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 0.81
                               MIT  18 gnyeeAlelYkeale 32 
                                       g+  eA + Y +ale
  gi|330506457|ref|YP_004382885.1| 206 GKLVEAQQEYDKALE 220
                                       566666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1715.47
//
Query:       gi|330506458|ref|YP_004382886.1|  [L=229]
Description: glucosamine--fructose-6-phosphate aminotransferase [Methanosaeta concilii GP6]
Scores for complete 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-22   78.5   0.0    7.2e-22   78.0   0.0    1.2  1  GATase_6  Glutamine amidotransferase domain
    6.3e-20   71.3   0.0    1.5e-19   70.1   0.0    1.6  2  GATase_7  Glutamine amidotransferase domain
    2.5e-05   23.3   0.0    3.1e-05   23.0   0.0    1.2  1  GATase_4  Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0   1.2e-25   7.2e-22       7     134 .]      58     191 ..      50     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 1.2e-25
                          GATase_6   7 aslvedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.. 81 
                                       ++ +e+++++aH+R+a++g    + a+P +  + r+++vhNG i+n+kel+eel + +g+ f s +D+ev+++l+  
  gi|330506458|ref|YP_004382886.1|  58 LKEFEGNIGIAHTRRATHGHICVANAHPHTDCKNRVAIVHNGVIENHKELKEELLS-RGHIFTSSTDSEVIAHLIee 133
                                       4557889*************988888******************************.******************66 PP

                          GATase_6  82 .eelG.......eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                         ++G        ++++rl+G +a  +++ ++++l+  r +    pl+++v e+g++fas+
  gi|330506458|ref|YP_004382886.1| 134 gLKAGrsfiaacMDAFKRLQGCYALLVISPDARRLVAFRKD---LPLVVGVAEGGIIFASD 191
                                       64455888866666667*************99999999555...69*************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      0.28   1.7e+03      65      88 ..      52      75 ..      27      84 .. 0.69
   2 !   70.1   0.0   2.5e-23   1.5e-19      12     122 ..      82     196 ..      69     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.28
                          GATase_7 65 ewgeealerlnGmfAfaiwdeeek 88
                                        ++++l++++G   +a   ++++
  gi|330506458|ref|YP_004382886.1| 52 GAIDDLLKEFEGNIGIAHTRRATH 75
                                      467889999999999988877665 PP

  == domain 2  score: 70.1 bits;  conditional E-value: 2.5e-23
                          GATase_7  12 gaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGmfA 79 
                                       +a P + + ++r++iv+nG i N+kel+eeL ++gh f++++D+ev+++l+e+         + + +a++rl+G +A
  gi|330506458|ref|YP_004382886.1|  82 NAHPHT-DCKNRVAIVHNGVIENHKELKEELLSRGHIFTSSTDSEVIAHLIEEglkagrsfiAACMDAFKRLQGCYA 157
                                       566777.57899***********************************************99999999********** PP

                          GATase_7  80 faiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       ++++  + +rl++ R      PL +g ++g +++faS  + ll
  gi|330506458|ref|YP_004382886.1| 158 LLVISPDARRLVAFRKD---LPLVVGVAEG-GIIFASDASVLL 196
                                       ***************95...8*******86.******999887 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   5.2e-09   3.1e-05      57     136 ..      51     130 ..      29     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.2e-09
                          GATase_4  57 esplaelvreypiksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlke...ykpkl.egrfePvGsTD 129
                                       + ++  l++e  ++ ++ +aH R+at+G++  +n+hp +    +++  + HnG +++   +k++l +  +    sTD
  gi|330506458|ref|YP_004382886.1|  51 DGAIDDLLKE--FEGNIGIAHTRRATHGHICVANAHPHTDC--KNRVAIVHNGVIENhkeLKEELlSRGHIFTSSTD 123
                                       5667778887..7899*********************9853..4556668****97722344555544455568999 PP

                          GATase_4 130 sElafCe 136
                                       sE++   
  gi|330506458|ref|YP_004382886.1| 124 SEVIAHL 130
                                       9987544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1663.64
//
Query:       gi|330506459|ref|YP_004382887.1|  [L=135]
Description: hypothetical protein MCON_0167 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-59  198.6   0.5    2.9e-59  198.4   0.5    1.0  1  DUF1699         Protein of unknown function (DUF1699)
  ------ inclusion threshold ------
      0.058   13.4   0.0      0.089   12.8   0.0    1.3  1  Merozoite_SPAM  Merozoite surface protein (SPAM)
      0.086   13.0   0.1       0.16   12.1   0.1    1.4  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
        0.1   12.4   1.8       0.82    9.5   0.1    2.1  2  SKA2            Spindle and kinetochore-associated protein 2


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.4   0.5   6.5e-63   2.9e-59       1     130 []       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 198.4 bits;  conditional E-value: 6.5e-63
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       mk+rvvssk+ei++ln+ne++vHlafr+sn+d+++lv++cp+l+a+q+p+Sy++t+s++a++fleiqg++ll+gdvw
  gi|330506459|ref|YP_004382887.1|   1 MKLRVVSSKKEITDLNRNEQLVHLAFRASNMDVMNLVQSCPRLRAVQIPPSYHETMSRAAQQFLEIQGVQLLKGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                       ghrkdi+eyy++ e++++ri++l+seg s ee ++kl++etkls+dli+++lk
  gi|330506459|ref|YP_004382887.1|  78 GHRKDIDEYYAIGEQIVNRISTLMSEGNSIEETVRKLQRETKLSEDLIRYILK 130
                                       ***************************************************86 PP

>> Merozoite_SPAM  Merozoite surface protein (SPAM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.089     139     175 ..      81     117 ..      68     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                    Merozoite_SPAM 139 kdnekskkaaetlvntlisLleekNelDstlknLkke 175
                                       kd ++     e++vn +  L+ e+N++ +t+++L++e
  gi|330506459|ref|YP_004382887.1|  81 KDIDEYYAIGEQIVNRISTLMSEGNSIEETVRKLQRE 117
                                       67777777789***********************987 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.5e-05      0.16      19      48 ..      97     129 ..      89     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHSS...BEHHHHHHHHSSTHHHHHHHH CS
                             HTH_9  19 vetLlrkgr...ltlrelvkktkLsldqVkksL 48 
                                       ++tL+++g     t+r+l+++tkLs d+++ +L
  gi|330506459|ref|YP_004382887.1|  97 ISTLMSEGNsieETVRKLQRETKLSEDLIRYIL 129
                                       4678877752226****************9776 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.024   1.1e+02      53     105 ..       4      59 ..       1      64 [. 0.70
   2 ?    9.5   0.1   0.00018      0.82      42      82 ..      92     132 ..      83     135 .] 0.93

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.024
                              SKA2  53 elqaLkeqceellaekkelidkirttlvanrellqqLqasa..elppls.eeeqea 105
                                       ++ + k+++++l  + + +  ++r++ ++ ++l+q++ +    ++pp   e+  +a
  gi|330506459|ref|YP_004382887.1|   4 RVVSSKKEITDLNRNEQLVHLAFRASNMDVMNLVQSCPRLRavQIPPSYhETMSRA 59 
                                       66677888888888888888999999999999999886533346666554444444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00018
                              SKA2  42 kLlerlkkvkeelqaLkeqceellaekkelidkirttlvan 82 
                                       ++++r++ + +e ++++e +++l+ e k + d ir+ l ++
  gi|330506459|ref|YP_004382887.1|  92 QIVNRISTLMSEGNSIEETVRKLQRETKLSEDLIRYILKEQ 132
                                       699******************************99999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 1006.81
//
Query:       gi|330506460|ref|YP_004382888.1|  [L=323]
Description: hypothetical protein MCON_0168 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.2   0.0        0.3   11.2   0.0    1.4  1  IFNGR1    Interferon gamma receptor (IFNGR1)


Domain annotation for each model (and alignments):
>> IFNGR1  Interferon gamma receptor (IFNGR1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.7e-05       0.3      14      58 ..     153     199 ..     147     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.7e-05
                                       EEEEEETTE.EEE.EESSSSSSB-SSEEEEEEE--..SEEEEEEEEEE CS
                            IFNGR1  14 tvyvkfndskeil.eysvkeedCdevqCelaiess..envCvsvvgvs 58 
                                       + +++f+++ ei+  +++  + C+ ++Ce+ ++s    + C  v g++
  gi|330506460|ref|YP_004382888.1| 153 NSNIIFSEE-EIQeALEIASRPCQGMHCEVHLHSPlyAELCAHVSGID 199
                                       567888888.78879*****************998889******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2283.66
//
Query:       gi|330506461|ref|YP_004382889.1|  [L=449]
Description: threonine synthase [Methanosaeta concilii GP6]
Scores for complete 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   89.6   0.0    9.2e-25   87.6   0.0    1.9  2  PALP         Pyridoxal-phosphate dependent enzyme
    2.3e-21   75.8   0.1    9.8e-21   73.8   0.0    2.2  3  Thr_synth_N  Threonine synthase N terminus
  ------ inclusion threshold ------
       0.15   11.8   0.0        2.2    8.1   0.0    2.6  2  CUE          CUE 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 !   87.6   0.0   1.5e-28   9.2e-25      25     290 ..      97     394 ..      88     398 .. 0.76
   2 ?   -3.4   0.0      0.83     5e+03     182     201 ..     403     424 ..     401     433 .. 0.76

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 1.5e-28
                                       EEEEGGGSTTSBTTHHHHH...HHHHH....HHTTTTTSEEEEEBSSHHHHHHHHHHHHH.T-EEEEEEETTS-.HH CS
                              PALP  25 flKlEslnptgSfKdRgae...yllar....lkegtgaktvveassGNhgralAaaaall.Glkvtivvpadas.pe 92 
                                       +l + +  pt+SfKd +a             lke+ + + +++a+sG++g a+A+a   l ++kv++++p+    + 
  gi|330506461|ref|YP_004382889.1|  97 YLLRLDRGPTCSFKDFAARlmgR---LmqyfLKEEGRSMIILTATSGDTGSAVAHAFYGLeNIKVIVLFPEREVtER 170
                                       56677899***********5541...2445677777**********************9999*******99988468 PP

                                       HHHHHHHTT-EEEEE..CCHHHHHHHHHHHHHHH.STTCEE--TTT..SHHHHHHHHTHHHHHHHHTT..TTEEEEE CS
                              PALP  93 kvallrllGaevvev..ggdydeavaaaaelaae.gegaylvsqfd..nptviegygtiglEileqlg..gkpdavv 162
                                       +++++  lG ++      g +d+++a+++++  + + + + +s+ +  n+ + + ++   +  ++++   g+  ++ 
  gi|330506461|ref|YP_004382889.1| 171 QRRQMTTLGENIYPLavTGKFDDCQALVKQAFVDpELKGLELSSANsiNVGRLLPQAVYYFYAHSRVApgGEEVVFS 247
                                       889**********9999999*********988884444444444444455555557777777776666443333689 PP

                                       EE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.....................SSS.CC CS
                              PALP 163 vpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvs....................dtiadg 219
                                       vp G+ g ++G   +lk + p  + +++ ++++d + r++++g ++++ +s                    +     
  gi|330506461|ref|YP_004382889.1| 248 VPSGNFGDLMGGLIALKMGLPV-KKFVAATNENDEFPRFMQTGVYEPIRPSkncisnamnvghpsnlarlfS----- 318
                                       999999***************6.555555777*******************866666666666544444431..... PP

                                       STCSCGTTCCHHHHSEEEE..................EEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHH CS
                              PALP 220 lavgspselafelldrlvd..................eivtvsdeealeamrllarregivvepssaaalaalklre 278
                                                   l+ ++ d                  ++v++sdee+ +++r+ ++  ++++ep++a++ a+l  r 
  gi|330506461|ref|YP_004382889.1| 319 ------------LYGGQMDetgqvarqpdlsamreeiYAVSISDEETRQTIREAYSQYKVLLEPHGAVGWAGL-VRY 382
                                       ............442222222223333334444444469**********************************.999 PP

                                       HHCCTTCEEEEE CS
                              PALP 279 agelkegdrvvv 290
                                         e++++++ v 
  gi|330506461|ref|YP_004382889.1| 383 LDEFGDWSPAVS 394
                                       999888877775 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.83
                                       STT..-EEEEEEECTTCGGTTC CS
                              PALP 182 rpd..vrvigvepegsdalars 201
                                       +pd  vr+ gv+p+  +a+a+ 
  gi|330506461|ref|YP_004382889.1| 403 FPDeiVRLTGVNPSLPPAMASL 424
                                       566779999****988888765 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 !   73.8   0.0   1.6e-24   9.8e-21       1      79 []       5      83 ..       5      83 .. 0.99
   2 ?   -3.8   0.0       2.7   1.6e+04      48      62 ..     107     121 ..     102     129 .. 0.68
   3 ?   -2.8   0.1       1.3   7.6e+03      64      79 .]     346     361 ..     342     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1.6e-24
                       Thr_synth_N  1 kYiSTRgeaeklsfeeallkGlAeDgGLyvPeeiPklsaeeleelrklsYaelafevlklfiedeipeedLkeliekaY 79
                                      k++ST g+ ++++f+ all+G A+D GLy+Pe +P+ls e+++++ ++sY+++a++v+k++++d ++e+ L++++++aY
  gi|330506461|ref|YP_004382889.1|  5 KFFSTNGHLDRVDFKGALLAGQAPDKGLYMPEMFPSLSPETIRNFPQMSYHQIAYQVIKPYLGDLVEESALEDMLKDAY 83
                                      699***************************************************************************9 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.7
                       Thr_synth_N  48 lsYaelafevlklfi 62 
                                       +s+++ a++++ + +
  gi|330506461|ref|YP_004382889.1| 107 CSFKDFAARLMGRLM 121
                                       678888888776554 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.3
                       Thr_synth_N  64 deipeedLkeliekaY 79 
                                        +i++e+ ++ i++aY
  gi|330506461|ref|YP_004382889.1| 346 VSISDEETRQTIREAY 361
                                       5799999999999999 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00037       2.2      10      21 ..      36      47 ..      36      48 .. 0.95
   2 ?    0.1   0.0      0.11   6.8e+02      12      22 ..      49      59 ..      49      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00037
                                      HHSTTS-HHHHH CS
                               CUE 10 emFPdldeevIr 21
                                      emFP+l++e+Ir
  gi|330506461|ref|YP_004382889.1| 36 EMFPSLSPETIR 47
                                      8**********8 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.11
                                      STTS-HHHHHH CS
                               CUE 12 FPdldeevIra 22
                                      FP+++  +I++
  gi|330506461|ref|YP_004382889.1| 49 FPQMSYHQIAY 59
                                      9********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2975.39
//
Query:       gi|330506462|ref|YP_004382890.1|  [L=286]
Description: CBS domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-40  135.1  13.4    1.5e-12   47.7   0.5    4.2  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.066   13.8   0.0         11    6.6   0.0    2.5  2  GAF       GAF domain
       0.09   12.7   0.1       0.25   11.2   0.1    1.8  1  RuvB_C    RuvB C-terminal winged helix domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.5   3.8e-13   2.2e-09       1      53 [.       5      56 ..       5      60 .. 0.95
   2 !   47.7   0.5   2.6e-16   1.5e-12       4      54 ..      66     115 ..      62     118 .. 0.92
   3 !   23.4   0.0     1e-08     6e-05       7      54 ..     131     178 ..     123     180 .. 0.87
   4 !   33.5   0.2     7e-12   4.2e-08       8      56 ..     230     278 ..     219     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3.8e-13
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                      V+d+m r+v ++    +  ++l+++ +++vs+lPVV + g++vGi+t++Dllr
  gi|330506462|ref|YP_004382890.1|  5 VRDVMVREVAYAEIPGNRDDVLKTLQDRKVSGLPVV-KKGEVVGIITRSDLLR 56
                                      89***********************8888*******.8**************9 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 2.6e-16
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       +mtrd+v+++pd ++ ea +l+++++++rlPVV e ++lvG+vt  D++r+
  gi|330506462|ref|YP_004382890.1|  66 LMTRDPVVISPDRSIVEASKLLIQHKIRRLPVV-EGKELVGLVTVADIVRV 115
                                       5********************99**********.5667**********997 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 1e-08
                                       SSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   7 rdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllra 54 
                                       ++ v++  +++l  a  +m e + v + PV+d d klvG++++rDl++a
  gi|330506462|ref|YP_004382890.1| 131 KETVVLWSEMPLPVAGSIM-EFAaVEACPVIDTDLKLVGMISDRDLIKA 178
                                       566899999**********.76669999***9888************98 PP

  == domain 4  score: 33.5 bits;  conditional E-value: 7e-12
                                       SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   8 dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       ++ t+  ++ +++++  mr+++++++PVV  + kl G++ ++D+lral+
  gi|330506462|ref|YP_004382890.1| 230 PPKTAFKTDKVSDCAAVMRKNRIDQMPVVKTSRKLMGMLKDTDILRALV 278
                                       6679999***********8888*******9999**************97 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0069        41      76     106 ..      18      50 ..       3      61 .. 0.82
   2 ?    6.6   0.0    0.0019        11      54     109 ..      64     111 ..      51     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0069
                                       T..HHHHHHHHTTESEEEEEEEEETTEEEEEEE CS
                               GAF  76 y..nrrdllenmgirsslvvPlvndgelwGllv 106
                                          nr d+l+  + r + ++P+v +ge++G+++
  gi|330506462|ref|YP_004382890.1|  18 IpgNRDDVLKTLQDRKVSGLPVVKKGEVVGIIT 50 
                                       355778889999999999************997 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0019
                                       HHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE CS
                               GAF  54 qvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhn 109
                                       + l t++p+vi+   pd    +   ++ll ++ ir    +P+v + el+Gl+++ +
  gi|330506462|ref|YP_004382890.1|  64 ALLMTRDPVVIS---PDRSIVE--ASKLLIQHKIR---RLPVVEGKELVGLVTVAD 111
                                       4577999*****...9999999..77899999999...99************9976 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 ?   11.2   0.1   4.2e-05      0.25      21      51 ..     101     132 ..      89     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.2e-05
                                       T--B-HHHHHHHTT--HH.HHHHTTHHHHHHT CS
                            RuvB_C  21 ggpvglktlaailgeeke.tiedviEPyLlke 51 
                                       ++ vgl t+a i+++ +  +ie+ iEPyL ke
  gi|330506462|ref|YP_004382890.1| 101 KELVGLVTVADIVRVAEGmNIEESIEPYLEKE 132
                                       5679**********987538********9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2189.88
//
Query:       gi|330506463|ref|YP_004382891.1|  [L=145]
Description: universal stress protein [Methanosaeta concilii GP6]
Scores for complete 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   0.3      3e-33  115.3   0.3    1.0  1  Usp            Universal stress protein family
  ------ inclusion threshold ------
       0.01   15.5   0.2       0.05   13.2   0.0    1.8  2  SRP54          SRP54-type protein, GTPase domain
      0.085   13.1   0.5         11    6.3   0.0    2.8  3  SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate bi


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   0.3   5.1e-37     3e-33       1     141 []       1     141 [.       1     141 [. 0.99

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 5.1e-37
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       m+++Il a+Dgse+  +A++ A+el k +g+++++++v d+++ ++ +d +     +el l+e +++ ++ +++ae+
  gi|330506463|ref|YP_004382891.1|   1 MFEKILAATDGSEHGLRAAKVAVELGKISGGKVYAVYVADTQRTAHLPDDMLLFSIKELLLKEGKEAIKQVQELAEK 77 
                                       99*************************************************************9999999******* PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        gv+ +  v+eg+p++ei+ +a++++a+ i+vG+ gr+gl+++llGSv+e+v+r++ +pVl V+
  gi|330506463|ref|YP_004382891.1|  78 NGVDFDGAVVEGNPSDEIISYAKKKGANVIIVGAVGRTGLDKFLLGSVAEKVVRNSRIPVLTVP 141
                                       *************************************************************997 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1     0.093   5.6e+02      10      43 ..      10      45 ..       4      48 .. 0.76
   2 ?   13.2   0.0   8.4e-06      0.05      44     103 ..      67     123 ..      65     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.093
                                      TTSSHHHHHHHHHHHHHHT..TS-EEEEEESTSSTT CS
                             SRP54 10 qGaGKTttlaKLaallkke..gkkvllvaaDtfRaa 43
                                       G+     +aK+a  l k   gk  ++  aDt R a
  gi|330506463|ref|YP_004382891.1| 10 DGSEHGLRAAKVAVELGKIsgGKVYAVYVADTQRTA 45
                                      566666778999998888776777788999999987 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.4e-06
                                       HHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHH CS
                             SRP54  44 AveQLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTaGrlqndkelme 103
                                       A++Q+++laek gv++ ++  e +p     e ++ ak+++++v++v   Gr   dk l+ 
  gi|330506463|ref|YP_004382891.1|  67 AIKQVQELAEKNGVDFDGAVVEGNPS---DEIISYAKKKGANVIIVGAVGRTGLDKFLLG 123
                                       99***********9987777666665...578999****************999987765 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0019        11      18      45 ..      56      81 ..      51      84 .. 0.88
   2 ?    3.9   0.0     0.011        67      33      49 ..      93     109 ..      85     111 .. 0.82
   3 ?   -2.0   0.0      0.73   4.4e+03      42      53 ..     133     144 ..     126     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0019
                     SpoU_sub_bind 18 iekllvtegradkrleellklakkrgik 45
                                      i++ll++eg+++ +  ++ +la+k+g+ 
  gi|330506463|ref|YP_004382891.1| 56 IKELLLKEGKEAIK--QVQELAEKNGVD 81
                                      89*******77777..*********985 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.011
                     SpoU_sub_bind  33 eellklakkrgikvelv 49 
                                        e++++akk+g  v++v
  gi|330506463|ref|YP_004382891.1|  93 DEIISYAKKKGANVIIV 109
                                       49************998 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.73
                     SpoU_sub_bind  42 rgikvelvdkek 53 
                                        +i+v +v++e+
  gi|330506463|ref|YP_004382891.1| 133 SRIPVLTVPREE 144
                                       589999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1126.62
//
Query:       gi|330506464|ref|YP_004382892.1|  [L=374]
Description: amidohydrolase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-35  123.1   0.0    1.5e-33  116.5   0.0    2.6  1  Amidohydro_1  Amidohydrolase family
    4.2e-12   46.3   0.1    3.4e-11   43.3   0.0    2.1  2  Amidohydro_3  Amidohydrolase family
    1.5e-05   24.5   0.0    2.3e-05   23.9   0.0    1.2  1  A_deaminase   Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.5   0.0   2.6e-37   1.5e-33       1     319 [.      71     346 ..      71     371 .. 0.85

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 2.6e-37
                                       EEEE-EEEEEEECETTECSSS...GHHHHH............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga...tledwl............vppetaaealesgiktalksGtttvadmgattstg 62 
                                       iv+P ++++H+Hl +s+++++   +l +++            +p e + e++++ +++++ sGt  +ad+++  + g
  gi|330506464|ref|YP_004382892.1|  71 IVCPRFVNSHIHLGDSAFKDPpflPLSELVgpkglkisllseTPRERLIEGMRRSLAQMVDSGTYAFADFREGGEAG 147
                                       69999****************999999999******************************************99989 PP

                                       HHHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHH CS
                      Amidohydro_1  63 iealleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealk 139
                                       ++ l eaa+++pl +ri+g         + + ++++ +    +              +l+ ++   f +++++ ++ 
  gi|330506464|ref|YP_004382892.1| 148 VRMLQEAAKDMPLLVRIFGR--------PAQGETETPEG---C-------------YGLGISSTRDFDPSLIQRMIL 200
                                       999999************66........44444444444...6.............89999**************** PP

                                       HHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE.HHHHHHHHHHHHHHCE CS
                      Amidohydro_1 140 eakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt.pteaellkerlkeagv 215
                                       ea+++++ +aiHa+e+  +  d+ +af        +l +               h vh++ ++e+ l  ++ k++ +
  gi|330506464|ref|YP_004382892.1| 201 EARRAGKALAIHAGESARD--DIPDAFS-------LLPD---------------HLVHMSrAEESDLRSAAQKGIAL 253
                                       *************887766..6677777.......2222...............77888854455554444335555 PP

                                       EHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHH CS
                      Amidohydro_1 216 ahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTin 292
                                       + cp+sn+i +sg+++++++++ G+ vg+gtD + + ns+n++ e+ l     r+ll+       +  ++++m+T+n
  gi|330506464|ref|YP_004382892.1| 254 VICPRSNLITGSGLPNVKRMIELGITVGVGTD-NVMLNSPNMFMEMHLIS---RALLH-------DDRQVFKMCTLN 319
                                       59******************************.*********99999888...54444.......4578******** PP

                                       HHHHTT-TTTSSSS-TTSB--EEEECC CS
                      Amidohydro_1 293 gAkalglddkvGsievGkdADlvvvdl 319
                                       gA+++gld+k+Gsi +Gk+A   v+++
  gi|330506464|ref|YP_004382892.1| 320 GAEIMGLDQKLGSIREGKEAKVMVING 346
                                       *********************999965 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.05     3e+02       8      21 ..      70      83 ..      66      91 .. 0.84
   2 !   43.3   0.0   5.7e-15   3.4e-11     255     446 ..     185     345 ..     110     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.05
                      Amidohydro_3  8 rlvlPGFvDsHtHl 21
                                      ++v P Fv sH+Hl
  gi|330506464|ref|YP_004382892.1| 70 GIVCPRFVNSHIHL 83
                                      3799*********6 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 5.7e-15
                      Amidohydro_3 255 tgwpdfedealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegvtesqiervaalqva 331
                                       ++++df+   + +++ +a+ +g  +aiha g++a dd++daf          d   l h +   es+++ +a  ++a
  gi|330506464|ref|YP_004382892.1| 185 SSTRDFDPSLIQRMILEARRAGKALAIHA-GESARDDIPDAFSLL------PD--HLVHMSRAEESDLRSAAQKGIA 252
                                       68899998889*****************8.8889999*****666......34..57888888************** PP

                      Amidohydro_3 332 agvqpvfnfedelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeel 408
                                         ++p++n              ++g+++vk++++ g++v  g+D      + +     ++m   +   ++  +   +
  gi|330506464|ref|YP_004382892.1| 253 LVICPRSNL-----------ITGSGLPNVKRMIELGITVGVGTD------NVMLNSPNMFM--EM---HLISRALLH 307
                                       *********...........678999******************......66666666666..22...777777888 PP

                      Amidohydro_3 409 sleealalyTrgpAkalgledrkGtLevGadADlvvld 446
                                       + +++++++T ++A+++gl+++ G++++G++A ++v++
  gi|330506464|ref|YP_004382892.1| 308 DDRQVFKMCTLNGAEIMGLDQKLGSIREGKEAKVMVIN 345
                                       889*********************************98 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.8e-09   2.3e-05     165     319 ..     182     328 ..     174     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.8e-09
                                       CCCCC-TTSTTGGGHHHHHCCCCHTT-EEEEEESSSS-CHHHHHHHHCS--SCECE-GGGGGSHHHHHHHHHCT-EE CS
                       A_deaminase 165 ldllndekiepaslflklraeagkstllltpHaGEagglehvveAllllkaerigHGvrlrkdpvLqyllalaqipl 241
                                       l++++  + + +sl +++  ea+ ++  l++HaGE +  + + +A+ ll  + + H  r+ +  +L    a++ i l
  gi|330506464|ref|YP_004382892.1| 182 LGISS-TRDFDPSLIQRMILEARRAGKALAIHAGESAR-DDIPDAFSLL-PDHLVHMSRAEE-SDL-RSAAQKGIAL 253
                                       56666.677888889999999**************875.789*****95.688888555544.455.567899**** PP

                                       EE-HHHHCCCSST-TTTT-C.HHHHHHTT-EEEE--BSCCCCT-SHHHHHHHHHHHHT--HHH.HHHHHHHHHHCSS CS
                       A_deaminase 242 evcPlSNvalgafleyaenP.lkeflerglnvslntDDPlqfgttLieeYaiaaqvfklseed.laelarNsvkqsf 316
                                        +cP SN  +g        P +k+ +e g+ v ++tD+ ++ + ++  e++ +++++  ++++ ++  + N+++  +
  gi|330506464|ref|YP_004382892.1| 254 VICPRSNLITGS-----GLPnVKRMIELGITVGVGTDNVMLNSPNMFMEMHLISRALLHDDRQvFKMCTLNGAEIMG 325
                                       **********44.....4444899******************************99966665515556667777666 PP

                                       S-H CS
                       A_deaminase 317 lsa 319
                                       l++
  gi|330506464|ref|YP_004382892.1| 326 LDQ 328
                                       665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2743.97
//
Query:       gi|330506465|ref|YP_004382893.1|  [L=220]
Description: diaminohydroxyphosphoribosylaminopyrimidine reductase [Methanosaeta concilii GP6]
Scores for complete 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-53  179.3   0.0    8.4e-53  179.2   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 !  179.2   0.0   4.7e-57   8.4e-53       1     200 []       4     215 ..       4     215 .. 0.97

  Alignments for each domain:
  == domain 1  score: 179.2 bits;  conditional E-value: 4.7e-57
                                       -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHH.HTT.GSS CS
                            RibD_C   1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreae.adaearq 76 
                                       p+v +++a+S+DGk++ +++ + +i+g+e+  +v+elra +dai+vG+gtvlad+p l v+ +  re++ ++++ ++
  gi|330506465|ref|YP_004382893.1|   4 PFVFINSAMSADGKISSRDRRQIRISGKEDLMRVDELRAASDAIMVGVGTVLADDPGLRVKSRILREKRkDMGQLKE 80 
                                       89*******************************************************************888888** PP

                                       -EEEEEETTS-S-TTSHHHHSSS-EEEEESSCSCHHHHHHCC.....E.....SE-HHHHHHHHHHTT--EEEEEET CS
                            RibD_C  77 pvrvVvdstlrvpldakvltddaptlvatteeadkekveklk.....v.....rvdlkelleeLkergirsllveGG 143
                                       p r+V+ds  r+p +ak+l  +   ++a++ +a++e++++l+     +      vdl+ l+eeL+ rg+r+l+veGG
  gi|330506465|ref|YP_004382893.1|  81 PFRIVADSNARTPANAKILGPG--CMIAVSYSAPEERLDRLRsgceiIkcgteMVDLPGLMEELYNRGVRRLMVEGG 155
                                       ********************87..******************99875277889************************ PP

                                       HHHHHHHHHTTT-SEEEEEEESCE--T.TSBCSSSSST-SS..EEEEEEEEEEETTEEEE CS
                            RibD_C 144 atLagsllraglvDelrlyiaPkllGg.agktlfdgegfka..lklklvksealgegvvl 200
                                       a L++sl++ glvDe+ +yi  +++Gg  +++l+dg gf++  ++l l ++++l+eg++l
  gi|330506465|ref|YP_004382893.1| 156 ARLNWSLIELGLVDEIYIYIGGLIIGGeRAPSLVDGPGFRNsfPRLSLQSVQRLDEGLLL 215
                                       ********************************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1589.70
//
Query:       gi|330506466|ref|YP_004382894.1|  [L=59]
Description: hypothetical protein MCON_0174 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0022   17.4   2.0     0.0025   17.3   2.0    1.0  1  DUF3387   Domain of unknown function (DUF3387)
  ------ inclusion threshold ------
      0.025   14.7   0.0      0.035   14.2   0.0    1.3  1  SAM_Exu   Exuperantia SAM-like domain


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 !   17.3   2.0   2.8e-07    0.0025     150     206 ..       2      57 ..       1      58 [. 0.96

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.8e-07
                           DUF3387 150 disiLseefleevkkmkeknlavelLkklLadeikarsrkNlvkskkFserLeelik 206
                                       dis ++ + l+++ + ++kn+  e L  ++++ + ++ + N ++  ++ e+++++i+
  gi|330506466|ref|YP_004382894.1|   2 DISKIDFDKLKDIFRRNRKNTVTESLVSAIESRLSQMVNLNRTR-IDYLEKFQKMID 57 
                                       8*****************************************99.99*******997 PP

>> SAM_Exu  Exuperantia SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     4e-06     0.035      29      57 ..       5      33 ..       3      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4e-06
                           SAM_Exu 29 gidyesLkeiweekkkeGlekllkekits 57
                                      +id+++Lk+i+  ++k+ +++ l + i+s
  gi|330506466|ref|YP_004382894.1|  5 KIDFDKLKDIFRRNRKNTVTESLVSAIES 33
                                      79******************999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 457.69
//
Query:       gi|330506467|ref|YP_004382895.1|  [L=412]
Description: hypothetical protein MCON_0175 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3086.59
//
Query:       gi|330506468|ref|YP_004382896.1|  [L=631]
Description: hypothetical protein MCON_0176 [Methanosaeta concilii GP6]
Scores for complete 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   24.8   0.0    4.9e-05   23.2   0.0    1.8  2  PLDc_2    PLD-like domain


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.37   6.6e+03      79      90 ..     107     119 ..      87     144 .. 0.65
   2 !   23.2   0.0   2.7e-09   4.9e-05      79     120 ..     314     360 ..     281     370 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.37
                            PLDc_2  79 l.gslHaKlylid 90 
                                       + + +H K+++ +
  gi|330506468|ref|YP_004382896.1| 107 EgSVFHPKAWVLR 119
                                       2578999999987 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 2.7e-09
                            PLDc_2  79 l..gslHaKlylid...gktvivGSsNltkrgldlnlElnvviedke 120
                                       +  + lHaKly+ d   +    +GS+N t++++++n E++v++ +++
  gi|330506468|ref|YP_004382896.1| 314 EnpQGLHAKLYVADaggQGRIWTGSANATDAAFQGNIEFLVELRGRK 360
                                       135789********98544888*******************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 4481.07
//
Query:       gi|330506469|ref|YP_004382897.1|  [L=1111]
Description: hypothetical protein MCON_0177 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.6e-06   27.7   0.0    8.4e-06   26.1   0.0    1.9  1  Helicase_C  Helicase conserved C-terminal domain
    0.00025   20.9   0.0       0.12   12.2   0.0    2.4  2  DEAD        DEAD/DEAH box helicase
     0.0017   18.3   0.0       0.05   13.6   0.0    2.3  1  ResIII      Type III restriction enzyme, res subunit
     0.0051   17.2   0.1       0.65   10.4   0.1    2.5  2  AAA         ATPase family associated with various cellular ac
     0.0055   15.6   0.0          1    8.2   0.0    2.2  2  AAA_34      P-loop containing NTP hydrolase pore-1
  ------ inclusion threshold ------
      0.022   15.0   0.0          1    9.6   0.0    2.9  2  AAA_22      AAA domain
      0.031   13.6   0.0      0.061   12.6   0.0    1.4  1  AGOG        N-glycosylase/DNA lyase
       0.13   11.0   0.0       0.23   10.2   0.0    1.3  1  UPF0061     Uncharacterized ACR, YdiU/UPF0061 family
       0.15   10.8   0.0        9.8    4.8   0.0    2.2  2  SNF2_N      SNF2 family N-terminal 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 !   26.1   0.0   4.2e-09   8.4e-06      56     110 ..     923     985 ..     882     986 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.2e-09
                                       H......HHHHHHHTTSSS.EEEESGGGTSSSTST.TESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  56 e......eileqfnkgesd.vLiatdvaerGidip.kvnlVinfdlprnvtsyiqriGRtgRa 110
                                       +      ++ ++fn+     vL +t+++++G+d+   ++ +++ +lp n+ ++ qr GR++R+
  gi|330506469|ref|YP_004382897.1| 923 RsvnrisQVRQAFNSPFWPfVLATTSIGQEGLDFHaYCHAIVHWNLPSNPVDLEQREGRIHRF 985
                                       333333366677777666779999**********94588899********************7 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   5.9e-05      0.12      15     110 ..      51     145 ..      29     177 .. 0.72
   2 !    6.1   0.1    0.0042       8.4     115     170 ..     268     330 ..     233     335 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.9e-05
                                       CEEEEEESTTSSHHHHHHHHHHHHHHHS.TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyet.kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardq 90 
                                       + +lva e+G GKTl++   + +++ +  k+ ++  +++++    +a+q + +l+ +++     +++ i+       
  gi|330506469|ref|YP_004382897.1|  51 RRFLVADEVGLGKTLVARGVIAKTIDHLwKTVHRIDIIYICSNSNIAKQNIARLNVLGDDNA-HCSSRIS--LLPTI 124
                                       6788************99988888855599************************99999532.2333333..23334 PP

                                       HHHHH.TTCSEEEEEHHHHHH CS
                                       xxxxx.xxxxxxxxxxxxxxx RF
                              DEAD  91 lskld.ngvdivvgtpgrldd 110
                                       +++l+ +++++v  tpg  ++
  gi|330506469|ref|YP_004382897.1| 125 IKNLEeRKINFVSLTPGTSFE 145
                                       555542347777777776655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0042
                                       TSSHCTTEEEEEEETHHHHHHTTTHHHHHH....HHHHSHHHCTTSTTT.......SEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx.......xxxxxxxxxxx RF
                              DEAD 115 gklnlsqvrflVlDEadrlldqgfsdfinr....ilnqlpqitcdgklq.......rqvivlSATlp 170
                                         l+  +  +++lDE +r+    +sd+ +      +++l+q       +        +v++lSAT+ 
  gi|330506469|ref|YP_004382897.1| 268 SCLKALEPDLIILDEFQRFKHLMYSDDDEDastiSARELAQELF----DyadenskARVLLLSATPY 330
                                       4444555589********99998888766511112333333332....1333333367*******85 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 !   13.6   0.0   2.5e-05      0.05       6     170 ..      30     330 ..      14     331 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHT........TTSEEEEEESTTSTHHHHH....HHHHHHH-S.....-EEEEESSHHHHHHHHHHG.. CS
                            ResIII   6 eyQeeaienlleklks..krdkrglikmaTGtGKTlva....aklierllkkgkeekflflvprkslleqtleef.. 74 
                                       + Q e ++ +   l    +  +r+l++ + G GKTlva    ak+i++l+k  ++  ++ ++ + ++ +q + ++  
  gi|330506469|ref|YP_004382897.1|  30 DFQRETVDYVFRRLYTdeDCTRRFLVADEVGLGKTLVArgviAKTIDHLWKTVHRIDIIYICSNSNIAKQNIARLnv 106
                                       445555555554443233445699************87433366777777777777****************99966 PP

                                       ............................................................................. CS
                            ResIII  75 ............................................................................. 74 
                                                                                                                    
  gi|330506469|ref|YP_004382897.1| 107 lgddnahcssrisllptiiknleerkinfvsltpgtsfevssgtgianerallywmlkeewklegeghkrvfcgsmk 183
                                       66666666666666666666666666666666666666666666666666555555555555555555555554444 PP

                                       ........GGGTGG.............GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-S CS
                            ResIII  75 ........kkflseayke.........igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfd 134
                                               k    e+                +++dk+ +   ds+++  l  ++q+l+++    +e+s +++r+r+ 
  gi|330506469|ref|YP_004382897.1| 184 lmnfkrlvK----EYPRHkidahlkacFLSLLQDDKDVS---DSNSCIALRRKVQELSSAF---SEMSLSASRKREM 250
                                       444422210....11111111222111111122222222...3333333333334444444...3333333333333 PP

                                       ..........................EEEEETGGGTTS.......T.....TTHHH.......HHT---SEEEEEES CS
                            ResIII 135 ..........................viiiDEaHrlgak......k.....swrei.......lekfkeavllglTA 167
                                                                 +ii DE  r++        +     s re+       ++ +++a +l l+A
  gi|330506469|ref|YP_004382897.1| 251 ikesnrcvselrrllvrsclkalepdLIILDEFQRFKHLmysdddEdastiSARELaqelfdyADENSKARVLLLSA 327
                                       33444455555555555556666666777777766666544444403444433332222233334445577777777 PP

                                       S-S CS
                            ResIII 168 Tpe 170
                                       Tp+
  gi|330506469|ref|YP_004382897.1| 328 TPY 330
                                       775 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 ?    4.0   0.0     0.031        61       7      22 ..      59      74 ..      53     124 .. 0.74
   2 !   10.4   0.1   0.00033      0.65      19     111 ..     230     328 ..     224     339 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.031
                                      TTSSHHHHHHHHHHHH CS
                               AAA  7 pGtGKTllakavakel 22
                                       G GKTl+a+ v+ ++
  gi|330506469|ref|YP_004382897.1| 59 VGLGKTLVARGVIAKT 74
                                      69*********99885 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00033
                                       HHHHTHEEEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHH CS
                               AAA  19 akelgvefleisgsell.skyvgesekkirelfkeakeka....kpsilfiDEidalaksr.sgseseeeervvnqL 89 
                                       ++el++ f e+s+s  +  ++++es++ ++el + + ++     +p  +++DE+ ++     s+++++ ++  + +L
  gi|330506469|ref|YP_004382897.1| 230 VQELSSAFSEMSLSASRkREMIKESNRCVSELRRLLVRSClkalEPDLIILDEFQRFKHLMySDDDEDASTISAREL 306
                                       578999999999999997789999999888887775332245688**********9966667445555555555666 PP

                                       HHHHHHTTTSSSTEEEEEEESS CS
                               AAA  90 lteldgvkkkeskvivigatnr 111
                                        +el ++ +++sk  v++ + +
  gi|330506469|ref|YP_004382897.1| 307 AQELFDYADENSKARVLLLSAT 328
                                       6666666665555555555444 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 !    8.2   0.0    0.0005         1      33      85 ..      25      75 ..       3     115 .. 0.80
   2 !    5.0   0.0    0.0048       9.6     154     221 ..     255     329 ..     237     334 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0005
                            AAA_34 33 egklSalQleavvyacqrheellpdgkRaGfllGDgaGvGkgrqiagiilenl 85
                                       g+l + Q e+v y  +r  ++ + + R  fl+ D+ G+Gk+    g+i++ +
  gi|330506469|ref|YP_004382897.1| 25 LGSLKDFQRETVDYVFRRLYTDEDCTRR--FLVADEVGLGKTLVARGVIAKTI 75
                                      4789999*********999887766665..************99999998765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0048
                            AAA_34 154 kkkkksrleql.veWlgedfdG.vivfDEchkaknlakse......ekkatktgkavlelqkklpkArvvYvsaTg 221
                                       +++  s l++l v+ + + ++  +i++DE  + k+l+ s+      + +a + ++  ++  ++  kArv+ +saT 
  gi|330506469|ref|YP_004382897.1| 255 NRCV-SELRRLlVRSCLKALEPdLIILDEFQRFKHLMYSDddedasTISARELAQELFDYADENSKARVLLLSATP 329
                                       4443.5555541556667776559***********99876443332223355666777888999**********95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.11   2.2e+02      13      46 ..      58      91 ..      53     136 .. 0.74
   2 ?    9.6   0.0   0.00052         1      70     106 ..     236     295 ..     146     335 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.11
                            AAA_22 13 esGtGKTtllrrlleqldeeakaee...erpevvfvt 46
                                      e+G GKT+++r +  +    +++ +   +r ++++++
  gi|330506469|ref|YP_004382897.1| 58 EVGLGKTLVARGVIAKT---IDHLWktvHRIDIIYIC 91
                                      78*********999986...33333446666655554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00052
                            AAA_22  70 a.................erlsseellealeqalraravielliiDEaqhlr....s..e 106
                                       a                 ++   +el+++l + + ++  + l+i+DE+q++     s  +
  gi|330506469|ref|YP_004382897.1| 236 AfsemslsasrkremikeSNRCVSELRRLLVRSCLKALEPDLIILDEFQRFKhlmySddD 295
                                       3444444444455555556667888887777777777779**********9544442442 PP

>> AGOG  N-glycosylase/DNA lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.1e-05     0.061      55     139 ..     823     908 ..     807     919 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.1e-05
                                       T-HHHHHHHHHHHHCTS--SSHHHHHHHHHHH-TTS-TTHHHHHH.HHHHHCCHHHTTTHHHHHHHHHTHHHHHHHH CS
                              AGOG  55 grGEewWkefskyfsekeiknileefikflekskgnrrlreakik.Riekivefledleleelksylenleelleel 130
                                       + G ++W+++ +y+ +  ++ +l e+++fl++s+g+    ++ i  +++ +v+ + +l++++l+    ++++ le++
  gi|330506469|ref|YP_004382897.1| 823 QDGQAYWRQVLDYCLDGGLQAVLDEYVHFLKESEGLFGKEKVEIAgKLSEVVSEAMSLRTASLDVDKIKIDQRLESM 899
                                       4699*******************************988777777546777777777788777777777777777777 PP

                                       HHHHTS-TT CS
                              AGOG 131 akilgskke 139
                                       ++++++ ++
  gi|330506469|ref|YP_004382897.1| 900 SRSIKKMRT 908
                                       777766655 PP

>> UPF0061  Uncharacterized ACR, YdiU/UPF0061 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00011      0.23     133     216 ..     754     835 ..     751     858 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                           UPF0061 133 vlasealhklgvrtsralslietgekllRedePspersavvvRlarshiRfGtferlkylkrldllkkLldyvieey 209
                                       vla  al+  g++  rals ++ g  +    +P  e s   +R++rs+iR+  f++ + +  l++l +L d   + y
  gi|330506469|ref|YP_004382897.1| 754 VLAKLALAGPGITCLRALSRVTGGLPANNPWHPFYEISMSSIRMSRSFIRL--FNLSTSIALLRGLYSLEDQDGQAY 828
                                       5677799999****************************************9..777777788888888888888888 PP

                           UPF0061 210 ypelade 216
                                       + ++ d 
  gi|330506469|ref|YP_004382897.1| 829 WRQVLDY 835
                                       8777554 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 ?    3.7   0.0     0.011        21      59      77 ..      54      72 ..      36     142 .. 0.80
   2 ?    4.8   0.0    0.0049       9.8     168     239 ..     265     364 ..     209     413 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.011
                                      EE---TTS--HHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 59 iLaDemGLGKTvqvlalil 77
                                      + aDe GLGKT+ +  +i+
  gi|330506469|ref|YP_004382897.1| 54 LVADEVGLGKTLVARGVIA 72
                                      78*********87666666 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0049
                                       ...TTS-S-S-SEEEES-GGGT--T...T..............SHHHHHHHH---S-EEEE-S--SSS......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx...x..............xxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                            SNF2_N 168 kkrsvlkqvewkrvvlDEghtlkns...t..............skaaeavskLstsnrwiltGTPiqn......... 218
                                        +rs lk++e + ++lDE +++k     +              +++   + + s  + ++l++TP +          
  gi|330506469|ref|YP_004382897.1| 265 LVRSCLKALEPDLIILDEFQRFKHLmysDddedastisarelaQELFDYADENSKARVLLLSATPYKMyttadesgi 341
                                       68999*****************9885541556666644433333333333333455667889999887777788877 PP

                                       ..-HHHHHHHHHHH-TTTT--HH CS
                                       ..xxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 219 ..sledlygLlkfLreepfgekq 239
                                           +d+   lkfL+ +     +
  gi|330506469|ref|YP_004382897.1| 342 edHYKDFLRTLKFLMQDTAAVEK 364
                                       77777888888888877766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); 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:                         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: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.45
# Mc/sec: 7459.28
//
Query:       gi|330506470|ref|YP_004382898.1|  [L=169]
Description: hypothetical protein MCON_0178 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.0   0.1      0.072   12.6   0.1    1.1  1  DUF5087   Domain of unknown function (DUF5087)


Domain annotation for each model (and alignments):
>> DUF5087  Domain of unknown function (DUF5087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     4e-06     0.072      37     103 ..      42     109 ..      29     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-06
                           DUF5087  37 kyvktnlkkilkyllkniNtlelekicttlllisneleyeeklvil.hDiilfledlskllfiisalf 103
                                        ++  n  +il  l +ni +l++++ +t + l+ +  e+++  +i+ hD +l+ ++   + +++ al 
  gi|330506470|ref|YP_004382898.1|  42 LFISGNYSRILSRLNRNITELDVRRAFTSFQLMTILEENHHSFLIVeHDPLLYEDSQGMVGYLAQALK 109
                                       6999**************************99999999999887776******999999999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1211.01
//
Query:       gi|330506471|ref|YP_004382899.1|  [L=124]
Description: PIN domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-18   66.0   0.0    6.3e-18   65.4   0.0    1.3  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.0   3.5e-22   6.3e-18      29     121 ..       3     116 ..       1     117 [. 0.97

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 3.5e-22
                                       SEEEEEHHHHHHHHHHHHS......................SCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHHH CS
                               PIN  29 eelvtsalvlaEllyvlar......................rkskrekaaelvelllllsalkilpidaeiaeeaae 83 
                                       ++l+ts+ vl+El++v  r                      ++   +++ +l+ +l++ ++++ilp   +++ e++ 
  gi|330506471|ref|YP_004382899.1|   3 SDLATSSTVLSELVFVSLRklskerygtknysefrkaivqrGYGPFKEDLDLLFRLIEEREVSILP-INDDLNEWKG 78 
                                       6899**************************************************************.778899**** PP

                                       HHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  84 ialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                       i+ +y+llpnDalia+t+++h i++iatfD+df+rv++
  gi|330506471|ref|YP_004382899.1|  79 IMIRYNLLPNDALIASTCLKHEISKIATFDSDFSRVDW 116
                                       ************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 894.99
//
Query:       gi|330506472|ref|YP_004382900.1|  [L=366]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete 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-24   84.9   0.4    4.8e-24   84.1   0.4    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    5.4e-21   75.0   0.0    1.2e-20   74.0   0.0    1.5  1  OrfB_IS605      Probable transposase
    7.3e-14   51.0   1.9    1.6e-13   49.9   1.9    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.038   13.2   0.1      0.055   12.6   0.1    1.4  1  RuvC_1          RuvC nuclease domain
      0.041   13.9   2.4      0.072   13.1   2.4    1.3  1  DZR             Double zinc ribbon
      0.046   13.6   3.0       0.09   12.7   3.0    1.5  1  Zn_ribbon_SprT  SprT-like 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 !   84.1   0.4   1.6e-27   4.8e-24       1      68 [.     290     357 ..     290     358 .. 0.99

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 1.6e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++kl ++ +yka e+G+kv++vnp +TS+ Cs+Cg+++k++ls r++ Cp Cg+++drD+nAa Nil+
  gi|330506472|ref|YP_004382900.1| 290 WNKLVQYTSYKAVEAGRKVVLVNPLNTSQMCSCCGQTVKKDLSVRVHSCPYCGLSMDRDLNAAKNILR 357
                                       99****************************************************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0   3.9e-24   1.2e-20      10     117 ..     172     276 ..     163     278 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 3.9e-24
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +  +++ k++giD+Gi n+a++++++   f+ ++r+l +d+  l+k++ + +++ k+s+ + ka + +  l++++++
  gi|330506472|ref|YP_004382900.1| 172 HVIEPSDKVVGIDVGITNFAVLSNGE---FIENPRFLLADEGMLKKAQSKRDKLPKGSQERNKANKSVNHLYERIAN 245
                                       5567889*******************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       rr +++++l++ l+  +  +  e+Ln++nm+
  gi|330506472|ref|YP_004382900.1| 246 RREDFAQQLSHMLVTSYGIICFEDLNIKNMT 276
                                       ******************************8 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   1.9   5.3e-17   1.6e-13       1      46 [.       1      45 [.       1      46 [. 0.97

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 5.3e-17
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeeg 46
                                      M  k ++yrl PT+ Q +kl++ ++ +R+VYN  La+rk+a e+eg
  gi|330506472|ref|YP_004382900.1|  1 M-AKVFRYRLRPTKAQVTKLNEQLELCRWVYNETLAMRKNAFEQEG 45
                                      7.899***************************************98 PP

>> RuvC_1  RuvC nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.8e-05     0.055      22     160 ..     179     316 ..     156     365 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                            RuvC_1  22 kiiGidRgeknLlYvsvvdekgeileqkslNeing......vdYrelLderekerekarknWqki.ekikelKegYl 91 
                                       k++Gid g  n + +    ++ge +e+  +   ++         r++L + ++er+ka k+ +++ e+i + +e + 
  gi|330506472|ref|YP_004382900.1| 179 KVVGIDVGITNFAVL----SNGEFIENPRFLLADEgmlkkaQSKRDKLPKGSQERNKANKSVNHLyERIANRREDFA 251
                                       677777777776533....4566666554444333344344567899999999999999988775367888888775 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RuvC_1  92 sqvvhkiaklaikynaivvlEdLnlgFkrgrqkvekqvyqkfEkaLidklnylvdkkkkeeeaggllka 160
                                           ++++++++    i+ +EdLn++ + + +++ k++  +  ++L++  +y + +  ++    + l++
  gi|330506472|ref|YP_004382900.1| 252 ----QQLSHMLVTSYGIICFEDLNIKNMTQNHNLAKSILDASWNKLVQYTSYKAVEAGRKVVLVNPLNT 316
                                       ....57899999999************************999999998777765554444444444444 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.4   2.4e-05     0.072      11      44 ..     316     351 ..     312     354 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                               DZR  11 darfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                        +++Cs Cg+++k+  +   + Cp Cg ++d + + 
  gi|330506472|ref|YP_004382900.1| 316 TSQMCSCCGQTVKKDLSvrVHSCPYCGLSMDRDLNA 351
                                       6899********97777999*******999887665 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.0     3e-05      0.09       7      31 ..     320     342 ..     319     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                    Zn_ribbon_SprT   7 CtgCgreythhlsirrhnYrCrrCk 31 
                                       C  Cg++++  ls+r h+  C++C+
  gi|330506472|ref|YP_004382900.1| 320 CSCCGQTVKKDLSVRVHS--CPYCG 342
                                       555***************..****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2472.79
//
Query:       gi|330506473|ref|YP_004382901.1|  [L=63]
Description: hypothetical protein MCON_0181 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-19   68.3   0.7    6.6e-19   68.1   0.7    1.0  1  DUF104    Protein of unknown function DUF104


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.7   3.7e-23   6.6e-19       2      59 .]       4      59 ..       3      59 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 3.7e-23
                            DUF104  2 skvIeavYEnGvLKPLekvdLkEGeevkikIeeakeilkklkgilkeadeeeleelle 59
                                      sk+Ie++YE GvLKPL++vd+kEGe++k++I++    + ++ g ++e + ee+ee++e
  gi|330506473|ref|YP_004382901.1|  4 SKTIECIYERGVLKPLHEVDFKEGERLKLTIKR--FNISDFLGAFGEGSVEEFEEFEE 59
                                      79*******************************..9999999*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 499.11
//
Query:       gi|330506474|ref|YP_004382902.1|  [L=528]
Description: hypothetical protein MCON_0184 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-10   41.0   0.0    3.4e-10   40.0   0.0    1.5  1  Intein_splicing  Intein splicing domain
    1.4e-06   28.4   0.4      8e-06   26.0   0.1    2.2  2  Hom_end_hint     Hom_end-associated Hint
    1.4e-05   25.4   0.0    3.7e-05   24.0   0.0    1.8  1  PT-HINT          Pretoxin HINT domain
    0.00019   21.0   0.0     0.0008   19.0   0.0    2.0  2  Hint             Hint module
  ------ inclusion threshold ------
      0.035   13.9   0.0      0.058   13.2   0.0    1.3  1  Vint             Hint-domain
       0.14   12.5   0.0         22    5.4   0.1    2.3  2  Hint_2           Hint domain


Domain annotation for each model (and alignments):
>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   1.2e-13   3.4e-10      34     132 ..     399     491 ..     370     494 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.2e-13
                                       EEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEEHSCEEEEEEEEEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  34 evksvkkliklklkelyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdliavpdadvvwdkvksievede 110
                                       +  sv++++    ke+++i +e+g++i aT +H++++   eg+  k    L+ gd + + d++  +  + +   e +
  gi|330506474|ref|YP_004382902.1| 399 KSLSVTNVWTGMEKEILRIIMEKGNEISATEKHPFMTR--EGM--KPIISLSIGDELLMEDGN--YSAIDQCYPEPY 469
                                       3446999***99**************************..999..*************76666..************ PP

                                       EEEEEEEEETTT-EEEECTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing 111 eeyVYdltvednhNFvangiiv 132
                                        ++VY l ve+   F+ ng++v
  gi|330506474|ref|YP_004382902.1| 470 GRTVYNLDVEGGGPFICNGFVV 491
                                       *******************996 PP

>> Hom_end_hint  Hom_end-associated Hint
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   2.7e-09     8e-06       1      46 [.     367     412 ..     367     435 .. 0.87
   2 ?   -0.7   0.0      0.39   1.2e+03      15      34 ..     439     458 ..     433     463 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.7e-09
                                       CEETT-EEEBTTS-EEEGGG--TT-EEEBTTSSEEEEEE--EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hom_end_hint   1 cFakgTevlmadGsdksiedievgekvmGkdGkpreVvalprgvet 46 
                                       c+a++  v m dGs k+i  i++g++vmG  Gk+ +V+++ +g+e+
  gi|330506474|ref|YP_004382902.1| 367 CLAEDSLVRMVDGSTKTIRAIAIGDRVMGLGGKSLSVTNVWTGMEK 412
                                       8999999*********************************999986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.39
                                       EEEGGG--TT-EEEBTTSSE CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                      Hom_end_hint  15 dksiedievgekvmGkdGkp 34 
                                        k i ++++g++++ +dG+ 
  gi|330506474|ref|YP_004382902.1| 439 MKPIISLSIGDELLMEDGNY 458
                                       57888999999999999975 PP

>> PT-HINT  Pretoxin HINT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.3e-08   3.7e-05       1     115 [.     373     479 ..     373     498 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.3e-08
                           PT-HINT   1 lvktadG.ykaiarikaGdrvlakdeasgkvaekpvlarygneyqelvylkisdgignsevlisnkihPfyskgkfi 76 
                                       lv+ +dG  k+i  i  Gdrv+    +s      +v++ ++   +e++ + ++   gn   + ++++hPf ++ ++ 
  gi|330506474|ref|YP_004382902.1| 373 LVRMVDGsTKTIRAIAIGDRVMGLGGKSL-----SVTNVWTGMEKEILRIIMEK--GN--EISATEKHPFMTREGMK 440
                                       68999994589***********9877765.....57888999999****99998..44..58999***********9 PP

                           PT-HINT  77 eakelkvGdklldesGkvlvveeiklkdePlkaynlkva 115
                                           l  Gd+ll e G+  ++++   ++    +ynl v+
  gi|330506474|ref|YP_004382902.1| 441 PIISLSIGDELLMEDGNYSAIDQCYPEPYGRTVYNLDVE 479
                                       ************************************997 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.7e-07    0.0008       9      83 ..     364     431 ..     357     441 .. 0.78
   2 ?   -1.5   0.0       0.5   1.5e+03      22      42 ..     435     455 ..     433     461 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.7e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              Hint   9 kggCFpgestvtvedgeqkslseLepGdkVlavdesgevvfsevllfldrdseqraefveietengekltlTpaH 83 
                                       + gC   +s+v++ dg++k+++ +++Gd+V+ + + +++ +++v + +      ++e + i  e+g++++ T++H
  gi|330506474|ref|YP_004382902.1| 364 QWGCLAEDSLVRMVDGSTKTIRAIAIGDRVMGLGG-KSLSVTNVWTGM------EKEILRIIMEKGNEISATEKH 431
                                       579*****************************984.445555565544......445677777777777777777 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.5
                                       XXXXXXXXXXXXXXXXXXXXX CS
                              Hint  22 edgeqkslseLepGdkVlavd 42 
                                         ++ k++ +L++Gd+ l  d
  gi|330506474|ref|YP_004382902.1| 435 TREGMKPIISLSIGDELLMED 455
                                       567899*********998766 PP

>> Vint  Hint-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.9e-05     0.058       1      67 [.     366     436 ..     366     444 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                              Vint   1 pCfagesrvklaegktvkiselrkgmkvqtpkgarkvaavlktkveeeelcrl....gellvTpwHPvrle 67 
                                       +C+a +s v++ +g+t++i+ +  g++v+   g+   ++ + t +e+e l+ +    +e+  T +HP  ++
  gi|330506474|ref|YP_004382902.1| 366 GCLAEDSLVRMVDGSTKTIRAIAIGDRVMGLGGKSLSVTNVWTGMEKEILRIImekgNEISATEKHPFMTR 436
                                       6****************************999666544445555555544444555479********8665 PP

>> Hint_2  Hint domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0072        22       2      37 ..     367     403 ..     366     416 .. 0.82
   2 ?    4.6   0.0     0.012        36      10      38 ..     434     462 ..     428     473 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0072
                            Hint_2   2 CflagtliatpeGev.aveeLrvGdlVvtadgglqpv 37 
                                       C+++++l++  +G    + ++++Gd+V+   g+   v
  gi|330506474|ref|YP_004382902.1| 367 CLAEDSLVRMVDGSTkTIRAIAIGDRVMGLGGKSLSV 403
                                       9************8626**********9887776555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.012
                            Hint_2  10 atpeGevaveeLrvGdlVvtadgglqpvr 38 
                                       +t eG  ++ +L +Gd+++ +dg++  + 
  gi|330506474|ref|YP_004382902.1| 434 MTREGMKPIISLSIGDELLMEDGNYSAID 462
                                       799*******************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3765.26
//
Query:       gi|330506475|ref|YP_004382903.1|  [L=120]
Description: hypothetical protein MCON_0185 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 882.10
//
Query:       gi|330506476|ref|YP_004382904.1|  [L=411]
Description: transposase, IS4 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-14   53.4   7.1    5.4e-13   48.9   7.1    2.5  1  DDE_Tnp_2        Archaeal putative transposase ISC1217
    9.2e-13   48.1   0.0      2e-12   47.0   0.0    1.5  1  DDE_5            DDE superfamily endonuclease
      5e-11   42.6   0.5    7.9e-11   42.0   0.5    1.2  1  DDE_Tnp_1        Transposase DDE domain
  ------ inclusion threshold ------
      0.028   14.6   0.8       0.24   11.6   0.2    2.7  3  Bac_DNA_binding  Bacterial DNA-binding protein


Domain annotation for each model (and alignments):
>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   7.1   1.2e-16   5.4e-13     146     308 ..     146     342 ..      77     353 .. 0.75

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.2e-16
                         DDE_Tnp_2 146 pyiprkvaeilkerGeksefktkielll.eileilkeefnv.aavvfdsWyvnskllk......gnvvgelksnarv 214
                                        +ip+k +  +k++ e ++fktk+e++  ei+e lk    +   +vfdsW+ ++ l++       +vv ++ks+++v
  gi|330506476|ref|YP_004382904.1| 146 LFIPHKAKMYFKNSDECVNFKTKLEIAFdEIIEPLKVPKGMnLCIVFDSWWSSEELINkcinlgHSVVCQIKSDRKV 222
                                       4799999999***************97548999998544331469********99876233232589********99 PP

                         DDE_Tnp_2 215 .ve...................gerhvpvaelPeGeylveyl...dtvikllvlddykkdg..rrylfstdlndtde 266
                                        ++                   ++  ++v    +  y  e     d++ ++++++  +k +   +y+ std  +++ 
  gi|330506476|ref|YP_004382904.1| 223 gINnimnfqvremanqidekhfTKTIINVRGKKKTYYTFEKNviiDRIGEVKLVISKRKRDgvTKYIISTDKSLSPK 299
                                       544999**********98888766666777777777777754445776667666654443213799*********** PP

                         DDE_Tnp_2 267 diittWenrWdievlirelk.alGledssflkrvrnkGflllk 308
                                       ++i+ +e rWdie  +re+   lG++d  +  +   + f+ l 
  gi|330506476|ref|YP_004382904.1| 300 EVISIYEDRWDIETAHREINqKLGFKDYQLRDKNTIERFIQLV 342
                                       *******************6369*9999888888888888774 PP

>> DDE_5  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   4.4e-16     2e-12      15     214 ..      30     222 ..      17     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 4.4e-16
                             DDE_5  15 lllylrgllldggrksvepmaarl...ehdg.shqalqrflsrspwddaklrrrlarlvl.pllapeaav..laiDd 84 
                                       ++ ++ +l  + + k+v+++  ++   + +  s+ ++  fls+++wd+ ++ +r  +l + +l+ +++    l+iDd
  gi|330506476|ref|YP_004382904.1|  30 FRDLCGALSVCDKSKTVANLCDTMadcSKGKkSRSSYNWFLSDANWDENEVAQRKVDLFIdKLCLKSNDKilLIIDD 106
                                       66667677777777***********9955555999*****************99999999777766555559***** PP

                             DDE_5  85 TgfpkdGkasvgvarqycgalgkadncqvavslglatervsapldwrlylpeswaqdlsarrrragvpddvtaktkp 161
                                       T   k G ++ gv+r+y++++   + ++ +v+    ++  ++p +   y +              + ++ v +ktk 
  gi|330506476|ref|YP_004382904.1| 107 TYKEKNGIQTDGVGRFYDHSKESYIWGNNFVTSVIQSKGLFIPHKAKMYFK--------------NSDECVNFKTKL 169
                                       *******************************99999999999988888888..............446889****** PP

                             DDE_5 162 eial.elldra.raagvplqvvvaDagYgdaaalrqglrelglhyvvrvrsdral 214
                                       eia  e+++ + + +g+ l ++v+D++ ++ + +      lg  +v +++sdr++
  gi|330506476|ref|YP_004382904.1| 170 EIAFdEIIEPLkVPKGMNL-CIVFDSWWSSEELI-NKCINLGHSVVCQIKSDRKV 222
                                       ****455666655555544.7*******776666.888999***********987 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.5   1.8e-14   7.9e-11      80     211 ..     190     345 ..     171     347 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.8e-14
                         DDE_Tnp_1  80 vlaDaGYasaelldtleekgvdyiirlkkntklyrk.....gaeskrrgrlrkhdrnkiltksqkrrnk........ 143
                                       ++ D++ +s+el+ ++   g + + ++k++ k+ +         +  +++ +kh+++ i++ + k++++        
  gi|330506476|ref|YP_004382904.1| 190 IVFDSWWSSEELINKCINLGHSVVCQIKSDRKVGINnimnfQVREMANQIDEKHFTKTIINVRGKKKTYytfeknvi 266
                                       789*********************************9999967777899999************************* PP

                         DDE_Tnp_1 144 ..........skkekgdvyyvtntn.sellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqlllll 209
                                                   k+k d+++ + ++ +++ls++ev+ +y  Rw iE+ ++++ +k+g+   ++r++n +e+++ l++
  gi|330506476|ref|YP_004382904.1| 267 idrigevklvISKRKRDGVTKYIIStDKSLSPKEVISIYEDRWDIETAHREINQKLGFKDYQLRDKNTIERFIQLVF 343
                                       **********66666666666665515689*******************************************9998 PP

                         DDE_Tnp_1 210 la 211
                                        +
  gi|330506476|ref|YP_004382904.1| 344 SV 345
                                       65 PP

>> Bac_DNA_binding  Bacterial DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.41   1.8e+03      28      57 ..     100     129 ..      91     164 .. 0.73
   2 ?   11.6   0.2   5.4e-05      0.24      32      85 ..     212     265 ..     199     267 .. 0.91
   3 ?   -2.9   0.0       1.8     8e+03      56      66 ..     358     368 ..     353     373 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHTT-EEEETTTEEEEEEEE-- CS
                   Bac_DNA_binding  28 fldtikeaLkkgekvelsgFGtfkvkerka 57 
                                       +l +i ++ k+++ ++  g G f+ + ++ 
  gi|330506476|ref|YP_004382904.1| 100 ILLIIDDTYKEKNGIQTDGVGRFYDHSKES 129
                                       666778888888889999999988666655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.4e-05
                                       HHHHHHTT-EEEETTTEEEEEEEE--BS-B-TTT--B--B--EEEEEEEE-HHH CS
                   Bac_DNA_binding  32 ikeaLkkgekvelsgFGtfkvkerkartgrnpkTgekvkiparkvvkFkpskel 85 
                                       +  ++k+++kv ++++ +f+v+e +  +    +T+  +++  +k+ ++++ k++
  gi|330506476|ref|YP_004382904.1| 212 VVCQIKSDRKVGINNIMNFQVREMANQIDEKHFTKTIINVRGKKKTYYTFEKNV 265
                                       5668999**************************************999999986 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.8
                                       --BS-B-TTT- CS
                   Bac_DNA_binding  56 kartgrnpkTg 66 
                                       +a+ g np+T 
  gi|330506476|ref|YP_004382904.1| 358 PAKDGSNPRTM 368
                                       6899*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.22s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2988.76
//
Query:       gi|330506477|ref|YP_004382905.1|  [L=514]
Description: hypothetical protein MCON_0187 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.1e-12   45.4   0.0    1.5e-11   44.7   0.0    1.4  1  Laminin_G_3  Concanavalin A-like lectin/glucanases superfamil
     0.0053   15.7   0.5     0.0091   15.0   0.5    1.4  1  MFS_1        Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.036   13.7   0.1       0.06   13.0   0.1    1.3  1  TraT         Enterobacterial TraT complement resistance prote


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 !   44.7   0.0   2.5e-15   1.5e-11       8     151 ..      71     218 ..      64     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.5e-15
                       Laminin_G_3   8 tlpdaslp.tssfTvsaWvkpdslpsaaqiiis.sssdgrgfelgldgsg..rlrfsvnagngaeesvtsgasvpag 80 
                                       +l +++ +  ++fTv   v+p  +++++++i + +s ++ g+ + l+++   ++r+ ++a+      + s ++v+a+
  gi|330506477|ref|YP_004382905.1|  71 QLKNKVSKnYDEFTVLGKVYPLFTSNDEMVIYTsRSATD-GYTVLLRRQEdyNYRLVFKAAS---GELISLKEVRAN 143
                                       555544442679999999999999998888886555445.9999996555356666666664...57899******* PP

                       Laminin_G_3  81 eWtHvavtydggtlrlYvNGvevgsatltggllsatsgplviGrdp.gg....ddpfdGlidevriynralsaaeI 151
                                       +W   a+t+ +g+++lY++G+ +g+ + ++  l +++++  iG  + +g    ++ f G+id ++ +++al ++ I
  gi|330506477|ref|YP_004382905.1| 144 RWFDFAITLLSGKITLYIDGANAGEMSISSINL-KGDANALIGTGYdDGymdyKKGFSGYIDYIAEFEKALDSTRI 218
                                       **************************9999866.5666677888875224556*****************998877 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.5   1.5e-06    0.0091     124     189 ..     384     474 ..     379     513 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-06
                             MFS_1 124 gllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeee............ 188
                                       g+ +a  + +a++g++++g ++ s+ + a+  +++++   a+vlf +++ +++p ++  + k ++            
  gi|330506477|ref|YP_004382905.1| 384 GFNGAVGGGAAAMGAGAAGSVSGSGTFVAAVAAIGVFVTAAVVLFTIFYDRPEPVKSDIRIKSLRfnsdgdstigsl 460
                                       88899999999*******************************************99999888887776666666666 PP

                             MFS_1 189 .............k 189
                                                    +
  gi|330506477|ref|YP_004382905.1| 461 ncrkdsattvpvrA 474
                                       65555544444442 PP

>> TraT  Enterobacterial TraT complement resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1     1e-05      0.06      76     126 ..     372     424 ..     353     445 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                              TraT  76 tdkaaaegalkaGfggalagaa..agaaigaanggsagaalggglvGglvgai 126
                                        +++++  + ++Gf+ga+ g+a  +ga+++++ +gs + +++++++G  v a+
  gi|330506477|ref|YP_004382905.1| 372 IQNRRVPRIPHNGFNGAVGGGAaaMGAGAAGSVSGSGTFVAAVAAIGVFVTAA 424
                                       67788888889******777651156666666888888888888888777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 3522.10
//
Query:       gi|330506478|ref|YP_004382906.1|  [L=406]
Description: transposase [Methanosaeta concilii GP6]
Scores for 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-76  255.6   1.2    9.9e-76  254.6   0.6    1.7  2  DDE_Tnp_ISL3  Transposase
    3.3e-14   52.0   0.1    6.3e-14   51.1   0.1    1.5  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
    1.9e-10   41.2   6.3      5e-10   39.9   6.3    1.7  1  zf-ISL3       zinc-finger of transposase IS204/IS1001/IS1096/


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 ?   -1.1   0.0      0.21   1.3e+03     185     211 ..     121     147 ..     102     150 .. 0.81
   2 !  254.6   0.6   1.7e-79   9.9e-76       1     240 []     159     393 ..     159     393 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.21
                      DDE_Tnp_ISL3 185 efkklaktlknhreeIlnyfdsrlsng 211
                                        +  +a+++++h ++I +++++++  +
  gi|330506478|ref|YP_004382906.1| 121 TVTAIAEMIDEHDTRIWRVLQHYVAEA 147
                                       567789999999999999999987766 PP

  == domain 2  score: 254.6 bits;  conditional E-value: 1.7e-79
                      DDE_Tnp_ISL3   1 lgiDEislkkghkyvtvvvdllvdggrlldilpgRkketlkafleslsek..erekveavvmDmsaayksavkealP 75 
                                       +g+DE+s  kghkyv+v++dl  d++r++++++g++++t+ +f ++l+++    e++e +++Dms+a++s +++ +P
  gi|330506478|ref|YP_004382906.1| 159 IGVDETSRAKGHKYVSVFIDL--DESRVIHVCEGKDASTIGSFKDDLEQHngSSENIENFCCDMSPAFISGIENSFP 233
                                       8********************..************************8888899*********************** PP

                      DDE_Tnp_ISL3  76 nAkivvDrFHvvklanealdevRrreqkelreekrkklkrsrrlllknpenlteeqkqrldelleaspelekaYelk 152
                                       nA+i++D+FHv+kl+nea+d+vRr+eq++        lkr+r+++lknpenlt +q + l  l +   ++ +aY++k
  gi|330506478|ref|YP_004382906.1| 234 NASITFDKFHVMKLMNEAVDKVRREEQSHNA-----LLKRTRYIWLKNPENLTANQNKMLTPLKSIRLKTMRAYNIK 305
                                       ****************************865.....6***********************99*************** PP

                      DDE_Tnp_ISL3 153 eelrevfrkkdkeearkalkewiekaersglkefkklaktlknhreeIlnyfdsrlsngpvEgiNnkikaikrrayG 229
                                        +lr+++ ++ +++a+ +lk+w+ +a++s+l+++ ++ak++knh+++++ny+++++ ng++Eg+N+ i+a+k +a+G
  gi|330506478|ref|YP_004382906.1| 306 LALRDFWSYEYRKSAEDYLKRWYYWATHSRLDPVIECAKMIKNHWNGVTNYIKTKIDNGILEGTNSLIQAAKDSARG 382
                                       ********99*******************************************99********************** PP

                      DDE_Tnp_ISL3 230 frnfenfrlri 240
                                       fr+++nf+++i
  gi|330506478|ref|YP_004382906.1| 383 FRSTKNFITII 393
                                       ********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 !   51.1   0.1   1.1e-17   6.3e-14       2      52 .]      95     144 ..      94     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.1e-17
                      HTH_Tnp_ISL3   2 elPwarrrsriTlrleayilelllesrsvkavArqlgvSwtTVwrildryv 52 
                                       ++Pwar++s++Tl+++  i+ +++ + +v+a+A++ + ++t++wr+l +yv
  gi|330506478|ref|YP_004382906.1|  95 KVPWARKGSGFTLLMDSLIVLMAQYM-TVTAIAEMIDEHDTRIWRVLQHYV 144
                                       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 !   39.9   6.3   8.4e-14     5e-10       5      47 .]      47      89 ..      44      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 8.4e-14
                           zf-ISL3  5 CPnCgsktvvkhgkkerrvrhlpiggkrvyLrlrkrRyrCkeC 47
                                      C +Cg++   +h++ er++rhl+++++++y+++r++R  C +C
  gi|330506478|ref|YP_004382906.1| 47 CAKCGNPGCSVHDTIERTWRHLNFFQFKTYIHCRVPRTICEDC 89
                                      *******99*********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2777.17
//
Query:       gi|330506479|ref|YP_004382907.1|  [L=583]
Description: hypothetical protein MCON_0189 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.1   0.0       0.15   12.8   0.0    1.6  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 ?   12.8   0.0   8.2e-06      0.15      56      90 ..      26      59 ..       9      70 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.2e-06
                             fn3_5 56 eaaltfetskvtvpAnssktvtvtldlpsdakkkn 90
                                      +   ++++ ++t++A+ +k++t+++d+ + +k+++
  gi|330506479|ref|YP_004382907.1| 26 PIIGDLTSDEFTINAGDTKNITINIDAAK-LKDAS 59
                                      34788999*******************55.55533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 4283.22
//
Query:       gi|330506480|ref|YP_004382908.1|  [L=110]
Description: hypothetical protein MCON_0190 [Methanosaeta concilii GP6]
Scores for complete 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-10   40.4   0.0      3e-10   40.3   0.0    1.0  1  GDPD            Glycerophosphoryl diester phosphodiesterase f
  ------ inclusion threshold ------
      0.081   12.2   0.0      0.087   12.1   0.0    1.1  1  Glyco_hydro_97  Glycoside hydrolase 97


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   3.3e-14     3e-10     198     258 ..      23     100 ..       6     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 3.3e-14
                                       CTCCCCHHCCCHCCCE........B.CHHHHHHHTT-EEEEBSB-THS.........HHHHHHHHCCC-SEEEES-H CS
                              GDPD 198 adallgevsavaeglg........dpdlVkraksrglvvhvytvnned.........eeemkrlleagvdgvitDfp 257
                                       +++ l+e++++a+g+g        +p+lV+ a++ gl+vh++t + ++         ee  +++  +gvdg++tDf+
  gi|330506480|ref|YP_004382908.1|  23 TQEGLKEIATFADGVGpykmyieaNPELVQWAHDDGLQVHTWTMRADSlpekysdftEELNQFYFVYGVDGLFTDFT 99 
                                       5667889999999999999999999********************************99999**************9 PP

                                       H CS
                              GDPD 258 d 258
                                       d
  gi|330506480|ref|YP_004382908.1| 100 D 100
                                       8 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.7e-06     0.087      83     137 ..      48     101 ..      25     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.7e-06
                    Glyco_hydro_97  83 eelvaYakekgvgvelwlhsetsgnvanlekqldkafklyeklGvkgvKvdfvgr 137
                                       +elv++a++ g +v+ w+     +  +++++  ++  ++y  +Gv+g+ +df +r
  gi|330506480|ref|YP_004382908.1|  48 PELVQWAHDDGLQVHTWTMRAD-SLPEKYSDFTEELNQFYFVYGVDGLFTDFTDR 101
                                       69***************99997.6667788889*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 788.65
//
Query:       gi|330506481|ref|YP_004382909.1|  [L=96]
Description: hypothetical protein MCON_0191 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   12.6   0.1       0.52   10.3   0.0    1.9  2  MarR      MarR family


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 ?   -0.1   0.1     0.049   8.8e+02      26      39 ..      20      33 ..      18      34 .. 0.85
   2 ?   10.3   0.0   2.9e-05      0.52       5      28 ..      38      61 ..      35      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.049
                                      HHTS-HHHHHHHHH CS
                              MarR 26 klgvskstvtrvld 39
                                      k++++k+t+ r+++
  gi|330506481|ref|YP_004382909.1| 20 KSSLQKATLVRTAK 33
                                      78999****99987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 2.9e-05
                                      HHHHHHHHHHSTTEEHHHHHHHHT CS
                              MarR  5 qfviLrilyeqgplsvseLakklg 28
                                      ++++ ++++e ++l+v eLak++ 
  gi|330506481|ref|YP_004382909.1| 38 EWDLCEKISEAPSLNVYELAKRMD 61
                                      6777789***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 713.63
//
Query:       gi|330506482|ref|YP_004382910.1|  [L=523]
Description: cation transport protein [Methanosaeta concilii GP6]
Scores for complete 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-52  176.0  27.3    4.3e-29  101.3   7.7    3.0  3  TrkH        Cation transport protein
  ------ inclusion threshold ------
      0.069   12.7   0.6       0.19   11.3   0.6    1.8  1  TRAP-gamma  Translocon-associated protein, gamma subunit (TRA


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 !   16.6   0.0   2.3e-07     0.002      12     103 ..      40     129 ..      32     153 .. 0.83
   2 !   64.6   9.7   6.6e-22   5.9e-18      74     276 ..     152     319 ..     147     331 .. 0.86
   3 !  101.3   7.7   4.8e-33   4.3e-29     315     491 ..     338     517 ..     334     523 .] 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.3e-07
                              TrkH  12 tialgavllfldkeskyplalkddfqivkaaeialsvdgtlklllesaslafldalfeavsgltttglsvivveesl 88 
                                       +i ++a+l +++  +k ++  k++f+iv  a++  +  g+l+ +     l+ +d+lfe++sg+tttg++  ++++s 
  gi|330506482|ref|YP_004382910.1|  40 FITISAGLIIRRIGEKGEVTNKEAFVIVALAWLLATIFGSLPFI--FLGLDETDSLFETMSGFTTTGATILTESDSH 114
                                       67777888888888888999999*******************87..677888************************* PP

                              TrkH  89 prsgltlraqlqqiG 103
                                       ++++ +  a+ +++ 
  gi|330506482|ref|YP_004382910.1| 115 GYWIINSTAADNSLA 129
                                       ***988877766554 PP

  == domain 2  score: 64.6 bits;  conditional E-value: 6.6e-22
                              TrkH  74 ltttglsvivveeslprsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkelrslselikil 150
                                        +++g++++v+++   +  l++ra++q +Gg++++ l  ++lp lg  + +ly    ++e      ++++++++ki 
  gi|330506482|ref|YP_004382910.1| 152 TSDSGFNNYVEST--FYGLLFWRAFTQLLGGMSIILLFIAILPHLGVAGRQLYYVDTSRE----ALTPRVRSTAKIF 222
                                       5778888888744..55689**************************99999999999555....569********** PP

                              TrkH 151 vvyyvgleilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivillvaiifi 227
                                       + +y+g+ +l  +ll         +s+++      +l++ +++s+++++++Gfs +++ ++ +++ ++i++++iif+
  gi|330506482|ref|YP_004382910.1| 223 WGIYLGFVALQTILL---------WSAGM------SLYDSLCTSFTTISTAGFSPLSAGIVAYDS-VLIEAILIIFM 283
                                       ***************.........*****......******************************.*********** PP

                              TrkH 228 ilGnigFpillrviiaikkkilrdlkqikeslsflldlprrcftLllas 276
                                       i+G+++F +++++i + ++              +++d+++r   L l+ 
  gi|330506482|ref|YP_004382910.1| 284 IVGATNFILHYQFIYKNDFLC------------YFKDPEFRLY-LFLQA 319
                                       **************9988866............4455555555.33333 PP

  == domain 3  score: 101.3 bits;  conditional E-value: 4.8e-33
                              TrkH 315 rvlkalFqsvstrta.GFs.vvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkav 389
                                       r++ a F +vs  t+ GF+ ++d++ ++ a  +++++ m igg++g taggI+ ++v+ + +  ++e+ +  +pkav
  gi|330506482|ref|YP_004382910.1| 338 RIRLAGFHVVSVGTTtGFTnTFDYAHWSSAANMVIIMLMLIGGCAGATAGGIKVLRVLLIKKYARRELMKMLHPKAV 414
                                       777889******9999**659******************************************************** PP

                              TrkH 390 skksidgkhlerqllvdlwslflvlliililegl..klsdvqepdfsffdiLfevvSaygtvGLSlGaknaslsaql 464
                                        ++++    + + +l+++ ++ +++lii+++++l   +++ ++ +f+++ ++ +v+ +++ vG++lG   a  + q+
  gi|330506482|ref|YP_004382910.1| 415 IPIKLNDISVSEGVLISVLFFTIIYLIIFFACSLllTITESGNQNFDLLSAISAVATCMASVGPGLG-VVALDFSQV 490
                                       ******************************998722567888899**********************.8888899** PP

                              TrkH 465 ttisklvlialmirGrlrglpvlldra 491
                                       t+++k++ i+ m +Gr+++lpv+l+++
  gi|330506482|ref|YP_004382910.1| 491 TPVGKMIAIFCMYIGRMEILPVMLLFI 517
                                       *************************98 PP

>> TRAP-gamma  Translocon-associated protein, gamma subunit (TRAP-gamma)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   2.1e-05      0.19     107     165 ..     414     470 ..     396     477 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.1e-05
                        TRAP-gamma 107 rilwkknevadyEsttfsifynNalflalllvlsfyllksfsptvnyilsvvvasglva 165
                                        i  k n+++  E + +s+++  +++l++++ +s  ll +++ + n  + ++ a ++va
  gi|330506482|ref|YP_004382910.1| 414 VIPIKLNDISVSEGVLISVLFFTIIYLIIFFACS--LLLTITESGNQNFDLLSAISAVA 470
                                       567899**********************999999..45555555565555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 3075.18
//
Query:       gi|330506483|ref|YP_004382911.1|  [L=199]
Description: hypothetical protein MCON_0193 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.6   4.8        2.5    7.9   0.3    3.6  3  YL1_C     YL1 nuclear protein C-terminal domain
      0.083   13.5   0.3       0.17   12.5   0.3    1.5  1  PepSY     Peptidase propeptide and YPEB domain


Domain annotation for each model (and alignments):
>> YL1_C  YL1 nuclear protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3   0.00028       2.5      11      19 ..     107     115 ..     106     115 .. 0.95
   2 ?    2.0   0.0      0.02   1.8e+02      11      17 ..     119     125 ..     118     127 .. 0.90
   3 ?    3.7   0.1    0.0058        52      11      17 ..     158     164 ..     151     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00028
                             YL1_C  11 YrDPkTgLp 19 
                                       Y+DP TgLp
  gi|330506483|ref|YP_004382911.1| 107 YTDPDTGLP 115
                                       ********8 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.02
                             YL1_C  11 YrDPkTg 17 
                                       Y+DP Tg
  gi|330506483|ref|YP_004382911.1| 119 YMDPFTG 125
                                       ******8 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.0058
                             YL1_C  11 YrDPkTg 17 
                                       Y DP Tg
  gi|330506483|ref|YP_004382911.1| 158 YIDPLTG 164
                                       ******9 PP

>> PepSY  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   1.9e-05      0.17      15      59 ..     123     166 ..     116     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                                       STTEEEEEEEEEEETTEEEEEEEEE.EE.TTEEEEEEEETTT--E CS
                             PepSY  15 vpgkiieielededdgrlvYevelstaepegpeyevfiDAkTGkv 59 
                                       ++gk+++++l+++ + ++++    + ++++g++ + +iD+ TGk 
  gi|330506483|ref|YP_004382911.1| 123 FTGKKTYTYLNPD-TQHPIFTYYSYQDDKTGRTAYSYIDPLTGKA 166
                                       579**********.******96655499***************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1332.85
//
Query:       gi|330506484|ref|YP_004382912.1|  [L=171]
Description: hypothetical protein MCON_0194 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-08   33.8   0.1    6.2e-08   32.6   0.1    1.7  1  HTH_3           Helix-turn-helix
     0.0019   18.6   0.0     0.0048   17.3   0.0    1.7  1  HTH_26          Cro/C1-type HTH DNA-binding domain
     0.0047   16.9   0.0     0.0097   15.9   0.0    1.5  1  HTH_19          Helix-turn-helix domain
     0.0053   16.3   0.5     0.0081   15.7   0.5    1.3  1  PrpR_N          Propionate catabolism activator
  ------ inclusion threshold ------
      0.041   14.2   0.3       0.26   11.7   0.0    2.2  2  HTH_31          Helix-turn-helix domain
      0.059   13.1   0.3       0.63    9.8   0.0    2.3  2  HTH_psq         helix-turn-helix, Psq domain
       0.11   13.1   0.0       0.11   13.1   0.0    1.9  3  Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
       0.13   12.2   0.0       0.33   10.9   0.0    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   2.8e-11   6.2e-08       1      47 [.      22      68 ..      22      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.8e-11
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklaka 47
                                      lke   +lgls +e+++ + +++st+++i +G+r+P+++tl  + k+
  gi|330506484|ref|YP_004382912.1| 22 LKEVIGELGLSAREFSRISEIPQSTLYKILSGHREPNITTLRQIVKT 68
                                      6788889************************************9986 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.1e-06    0.0048       2      47 ..      22      66 ..      21      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-06
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiC 47
                                      L+e++ + g+++ e++r ++i ++tl+++++g  + ++++tL  i 
  gi|330506484|ref|YP_004382912.1| 22 LKEVIGELGLSAREFSRISEIPQSTLYKILSGH-REPNITTLRQIV 66
                                      99******************************7.799999998875 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.3e-06    0.0097       4      50 ..      22      67 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.3e-06
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiae 50
                                      Lke++ elgl+ +e ++   i +s +++i +g + +p++ +l++i++
  gi|330506484|ref|YP_004382912.1| 22 LKEVIGELGLSAREFSRISEIPQSTLYKILSGHR-EPNITTLRQIVK 67
                                      9****************99999**********99.*********986 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.5   3.6e-06    0.0081      60     159 ..      65     168 ..      60     171 .] 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-06
                            PrpR_N  60 ilralkqakklg.ekialvgfeniikglktlselld...ldieiytinseeeaeaavkelkaegvevvvGdgvvadl 132
                                       i++ ++q++  g + ia+++ + +++++++ +  ++   l+++ y+ ++ eea  a  ++ ++g +++v+  +v+ +
  gi|330506484|ref|YP_004382912.1|  65 IVKTIRQMEGSGgDFIAIIAARPVLDKISEKKMKIGdrlLTLREYSATNIEEAIIAAVRAERDGASALVCAPIVSPT 141
                                       7889999999997789*****99999998877766512255666777777777777778899*************** PP

                            PrpR_N 133 AekaGlksvlltsgkesvrqAieeAle 159
                                       +ek+    v     +esv +Aie A +
  gi|330506484|ref|YP_004382912.1| 142 VEKLLTIPVATIIPQESVVRAIEVAAR 168
                                       ***77666666666*********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 ?   11.7   0.0   0.00012      0.26      12      51 ..      28      66 ..       9      72 .. 0.87
   2 ?    0.4   0.1      0.38   8.6e+02       3      13 ..     100     110 ..      98     168 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                            HTH_31 12 raGLsqeevAerlgvsestlsrlEqGrrgrpspavleala 51
                                      + GLs +e  + + + +stl ++ +G r +p   +l++++
  gi|330506484|ref|YP_004382912.1| 28 ELGLSAREFSRISEIPQSTLYKILSGHR-EPNITTLRQIV 66
                                      66**************************.8****999986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.38
                            HTH_31   3 GalLralRera 13 
                                       G++L +lRe +
  gi|330506484|ref|YP_004382912.1| 100 GDRLLTLREYS 110
                                       67777777755 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00028      0.63      15      40 ..      30      54 ..      14      56 .. 0.80
   2 ?    0.7   0.3       0.2   4.4e+02       2      12 ..     115     125 ..     114     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00028
                           HTH_psq 15 GkmSirkAArkYgiPrsTLwrrkrgk 40
                                      G +S r+ +r+ +iP sTL++ ++g+
  gi|330506484|ref|YP_004382912.1| 30 G-LSAREFSRISEIPQSTLYKILSGH 54
                                      3.9999999999*********99997 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.2
                           HTH_psq   2 pealaaAleav 12 
                                       +ea+ aA++a 
  gi|330506484|ref|YP_004382912.1| 115 EEAIIAAVRAE 125
                                       89******985 PP

>> Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.1e-05      0.11      32      68 ..       6      42 ..       3      46 .. 0.90
   2 ?   -3.0   0.1       5.5   1.2e+04       5      17 ..     112     124 ..     107     133 .. 0.65
   3 ?   -3.7   0.1         8   1.8e+04       9      19 ..     157     167 ..     154     170 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-05
                    Mg_chelatase_C 32 eelrevceldeeaeelleeaierlglsaRaydrilkv 68
                                      + +r++++ de+ +++l+e+i +lglsaR ++ri  +
  gi|330506484|ref|YP_004382912.1|  6 RVMRSAFQSDESLRDTLKEVIGELGLSAREFSRISEI 42
                                      56789999*************************9765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.5
                    Mg_chelatase_C   5 aevrerVaaArei 17 
                                       ++++e ++aA ++
  gi|330506484|ref|YP_004382912.1| 112 TNIEEAIIAAVRA 124
                                       4566666666554 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 8
                    Mg_chelatase_C   9 erVaaAreiqk 19 
                                       e V++A e+++
  gi|330506484|ref|YP_004382912.1| 157 ESVVRAIEVAA 167
                                       45566655554 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00015      0.33      23      44 ..      31      52 ..      22      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                                      CHHCHHCCCTTSSCHCHHHHHH CS
                              TrmB 23 atadeiaeelgvprskvYevLr 44
                                      ++a+e ++++++p+s+ Y++L+
  gi|330506484|ref|YP_004382912.1| 31 LSAREFSRISEIPQSTLYKILS 52
                                      6899****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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: 1188.72
//
Query:       gi|330506485|ref|YP_004382913.1|  [L=407]
Description: hypothetical protein MCON_0195 [Methanosaeta concilii GP6]
Scores for complete 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  107.5   0.0      1e-30  107.1   0.0    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   0.0   5.9e-35     1e-30      31     294 .]      97     372 ..      62     372 .. 0.89

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 5.9e-35
                                       GSTTSBTTHHHHHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHTT-.EEE CS
                              PALP  31 lnptgSfKdRgaeyllar.lkegtgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrllGa.evv 105
                                         pt+SfKd+ a+  ++  l++g ++  +v+as+GN++ra A++a+l G +++++vp++a  e+   +   G  +++
  gi|330506485|ref|YP_004382913.1|  97 SLPTCSFKDLEAAPTMQMlLDKG-ERSSLVVASAGNTARAFAHIASLTGQELVLFVPEKAL-ERMWTIVPPGRiTLI 171
                                       569**********8888868888.************************************9.99********55999 PP

                                       EECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEEE-SSS.HHHHHHHHHHHH. CS
                              PALP 106 evggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavvvpvGgG.gliaGiaaglke. 180
                                        v+gdy +a ++a+++ ++ +g++      n ++ +g+gt++l  +  +g+ pd+ + +vG+G g i+++ a l+  
  gi|330506485|ref|YP_004382913.1| 172 AVKGDYLDAIQMAEKVQSR-KGFTPEGGARNIARRDGMGTVMLDAAVTIGRTPDHYFQAVGSGtGGISAWEASLRLk 247
                                       99***********999999.9998888888**********************************************7 PP

                                       .......HSTT-EEEEEEECTTCGGTTCCS..S.SS..B.......SSS.CCSTCS.....CGTTCCHHHHSEEEEE CS
                              PALP 181 .......rrpdvrvigvepegsdalarslragrrvtvpvs......dtiadglavg.....spselafelldrlvde 239
                                              + p +r+  +++  +++++ +++a ++++++++               +          + ++l+++ + 
  gi|330506485|ref|YP_004382913.1| 248 ndgrfhpELPLPRLHLAQNIPNAPIYYAWKALEPEPYQEEmfddvlF--------NrkpplDMPGGVRDALKATEGM 316
                                       77655444444******************999999999765544442........223334445778889999999* PP

                                       EEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 240 ivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                       +++++d ea +a  l+ + e i +  + a+a+aal k+ ea++++ +d +++ +tg
  gi|330506485|ref|YP_004382913.1| 317 VYGITDREASKARDLFEQSEEIDILNAPAVAVAALqKAIEAKSVSSKDIILLNITG 372
                                       ***********************************************999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2789.56
//
Query:       gi|330506486|ref|YP_004382914.1|  [L=247]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   55.1   0.0    1.7e-14   54.5   0.0    1.2  1  ABC_tran     ABC transporter
    2.4e-09   37.5   0.3    0.00055   19.9   0.0    2.4  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    7.2e-06   26.5   0.0    1.2e-05   25.7   0.0    1.3  1  AAA_16       AAA ATPase domain
    8.1e-06   25.4   0.3      3e-05   23.6   0.3    1.9  1  SMC_N        RecF/RecN/SMC N terminal domain
    9.9e-05   22.0   0.1    0.00024   20.8   0.1    1.7  1  AAA_29       P-loop containing region of AAA domain
    0.00014   22.4   0.0    0.00019   22.0   0.0    1.4  1  AAA_23       AAA domain
    0.00027   21.2   0.3     0.0034   17.6   0.3    2.1  1  AAA_22       AAA domain
    0.00085   19.4   0.0       0.17   11.9   0.0    2.9  2  AAA_14       AAA domain
     0.0057   16.4   0.1      0.025   14.3   0.1    2.0  1  AAA_30       AAA domain
     0.0089   16.0   1.0        3.3    7.6   0.1    2.2  2  NTPase_1     NTPase
  ------ inclusion threshold ------
      0.011   15.6   1.1       0.15   12.0   1.1    2.1  1  ATPase_2     ATPase domain predominantly from Archaea
      0.022   14.6   0.2      0.081   12.8   0.2    2.0  1  RsgA_GTPase  RsgA GTPase
      0.025   13.8   0.0      0.047   12.9   0.0    1.4  1  NB-ARC       NB-ARC domain
       0.04   14.5   0.0       0.12   12.9   0.0    1.9  2  AAA_18       AAA domain
      0.043   13.9   0.9       0.13   12.4   0.7    2.3  1  MMR_HSR1     50S ribosome-binding GTPase
       0.06   13.5   0.0       0.19   11.9   0.0    1.8  1  AAA_2        AAA domain (Cdc48 subfamily)
      0.074   12.6   0.0       0.13   11.8   0.0    1.5  1  AAA_25       AAA domain
      0.079   12.7   0.0       0.13   12.0   0.0    1.5  1  AAA_24       AAA domain
      0.086   11.6   0.1       0.13   11.0   0.1    1.2  1  Adeno_IVa2   Adenovirus IVa2 protein
      0.086   12.8   0.1        4.7    7.2   0.0    2.4  2  AAA_5        AAA domain (dynein-related subfamily)
       0.12   12.1   0.0       0.23   11.2   0.0    1.4  1  ATP_bind_1   Conserved hypothetical ATP binding protein
       0.15   11.5   0.1       0.78    9.2   0.0    1.9  2  AAA_7        P-loop containing dynein motor region
       0.23   11.9   1.9        4.8    7.6   1.9    2.4  1  AAA          ATPase family associated with various cellular a


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   2.2e-17   1.7e-14       6     135 ..      21     164 ..      19     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 2.2e-17
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS...--SEEEEEETTCEGGGB-HHHCCHC.EEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagll...kpteGeilldgkdlkeqeleslrke.igvlpqepqlfpeltvre 78 
                                       +++++ge+++ivG++G+GKStL++ + +     +pt  +il++g+  k++++   rk+ ++ l+q+ ++  +++v+e
  gi|330506486|ref|YP_004382914.1|  21 IEISRGEIIGIVGPTGSGKSTLISDIEQFAlgdTPTGRSILINGQVPKNEQRYDPRKKlVAQLSQNMHFLADMQVGE 97 
                                       6899*******************9988764222679999****99999966655555527889************** PP

                                       H.........HHHTCHHHHHHHSTTGGTTCBGESTTS..GGS-HHHHHHHHHHH.HHHHTSSEEEEEST CS
                                       x.........xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                          ABC_tran  79 n.........esdeeiekalsklglkelkdtvvkssp..ssLSgGqkqrvalar.allkkpkllllDEp 135
                                                 ++ ++++k+++  +      ++++ +   + LSgGq + +++a  a++++++++l+DE 
  gi|330506486|ref|YP_004382914.1|  98 FlrmhaksrgKDPNQADKVIELANTLT--GEPISPEFqlTILSGGQSRALMVADiAVISDSPIVLIDEI 164
                                       ****99988844445555555544433..333322223499************737899********95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     7e-07   0.00055       2      63 ..      29      84 ..      28     108 .. 0.86
   2 !   16.3   0.0   8.5e-06    0.0066     165     268 ..     100     166 ..      81     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 7e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie 63
                                       +++Gp gsGKS+L+  ++ +      + g+t++ +++  ++ +p+   +ydp+++ + +++
  gi|330506486|ref|YP_004382914.1| 29 IGIVGPTGSGKSTLISDIEQF------ALGDTPTGRSILINGQVPKNEQRYDPRKKLVAQLS 84
                                      68****************555......69************************999887776 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 8.5e-06
                            AAA_21 165 rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGt 241
                                       r+   +  +d    +k+++l+  l++++  +e+ l+ l                                   S G+
  gi|330506486|ref|YP_004382914.1| 100 RMHAKSRGKDPNQADKVIELANTLTGEPISPEFQLTIL-----------------------------------SGGQ 141
                                       55555566666667777788888888888888888888...................................**** PP

                            AAA_21 242 krllalltallralkkgsllliDEpEn 268
                                        r+  +++ ++   ++ +++liDE+En
  gi|330506486|ref|YP_004382914.1| 142 SRA-LMVADIAVISDS-PIVLIDEIEN 166
                                       ***.************.*********9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.6e-08   1.2e-05      13     161 ..      15     181 ..      14     189 .. 0.63

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.6e-08
                            AAA_16  13 lsalervrsgrpelvllsGesGvGKsslvrellralekd....ggiflrgkcdql.esaipysalaqalareellrq 84 
                                       +++++ +  +r+e++ ++G+ G+GKs+l+  + + + +d    + i+++g+  ++ ++  p+  l+ +l   + +  
  gi|330506486|ref|YP_004382914.1|  15 QDLVHEIEISRGEIIGIVGPTGSGKSTLISDIEQFALGDtptgRSILINGQVPKNeQRYDPRKKLVAQL-S-QNMHF 89 
                                       578889999999**********************99999999669999999999933223333344444.2.34444 PP

                            AAA_16  85 llde.........aesaeleawrekleeala.........avpelagaea......srllellkrllallsrderpl 137
                                       l+d+         a  ++++ ++ + +++++         +    +++         + ++l+ + +a +s   +  
  gi|330506486|ref|YP_004382914.1|  90 LADMqvgeflrmhA--KSRGKDPNQADKVIElantltgepI----SPEFQltilsgGQSRALMVADIAVISD--S-P 157
                                       44445555555431..2333333333444444445644442....333335554664555555555545554..3.6 PP

                            AAA_16 138 vlvlDdlqwadeaslqllaaLlrl 161
                                       ++++D+++ a    +++l++L  +
  gi|330506486|ref|YP_004382914.1| 158 IVLIDEIENAGIKKQEALRLLSGE 181
                                       888999999999999999988776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.3   3.8e-08     3e-05      25     170 ..      27     167 ..      18     211 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.8e-08
                                       SEEEEEESTTSSHHHHHHHH.HHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAi.lFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsis 100
                                       ++  ivGp GSGKs l+  i +F LG++   + rs  ++  + k++++    k  v+ + +n    + ++  e  ++
  gi|330506486|ref|YP_004382914.1|  27 EIIGIVGPTGSGKSTLISDIeQFALGDTP--TGRSILINGQVPKNEQRYDPRKKLVAQLSQNMHFLADMQVGE-FLR 100
                                       4678*************99956****654..478888888888867777777777776533333332223333.333 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT....CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiske....lLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                        ++k+ g+      ++  +  e+++ l  + is+e     LSgG+   +++a    i  ++ +p++l+Dei+ a
  gi|330506486|ref|YP_004382914.1| 101 MHAKSRGK----DPNQADKVIELANTLTGEPISPEfqltILSGGQSRALMVAD---IAVISDSPIVLIDEIENA 167
                                       33333333....2344444467777777766666555559*****88666654...577899*********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 !   20.8   0.1   3.1e-07   0.00024      15      39 ..      19      43 ..      13      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.1e-07
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                      h+iei++ +++ ++Gp+GsGKSTl+
  gi|330506486|ref|YP_004382914.1| 19 HEIEISRGEIIGIVGPTGSGKSTLI 43
                                      8999997779**************9 PP

>> AAA_23  AAA 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   0.00019      14      52 ..      20      59 ..      13     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.5e-07
                            AAA_23 14 eidFsk.gltlItGpNGaGKTTildAiklaLygetprlsr 52
                                      ei+ s+  +  I+Gp+G+GK+T++  i     g+tp+ ++
  gi|330506486|ref|YP_004382914.1| 20 EIEISRgEIIGIVGPTGSGKSTLISDIEQFALGDTPTGRS 59
                                      58887735999*************8887555555554433 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   4.4e-06    0.0034       5     117 ..      26     180 ..      21     195 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.4e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee....................erpevvfvtlpsstsskdllrell 61 
                                         i+ ++G++G+GK+tl+  + + +  +    +                    +                  +++l+
  gi|330506486|ref|YP_004382914.1|  26 GEIIGIVGPTGSGKSTLISDIEQFALGD----TptgrsilingqvpkneqrydP------------------RKKLV 80 
                                       67888****************9998432....2232344444444444444440..................55555 PP

                            AAA_22  62 ralglelka................................................erlsseell.ealeqalrar 89 
                                        +l ++ +                                                 ++++s++l+ + ++      
  gi|330506486|ref|YP_004382914.1|  81 AQLSQNMHFladmqvgeflrmhaksrgkdpnqadkvielantltgepispefqltilSGGQSRALMvADIAVI---S 154
                                       5555444444455555555555555555555555555555555555555677776665555555553333333...3 PP

                            AAA_22  90 avielliiDEaqhlrseealeeLrslln 117
                                       +  ++++iDE+++    +  e Lr l+ 
  gi|330506486|ref|YP_004382914.1| 155 DS-PIVLIDEIENA-GIKKQEALRLLSG 180
                                       33.67799999998.5444444444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00022      0.17       3      50 ..      27      76 ..      25      99 .. 0.78
   2 ?    3.6   0.0     0.083        65      62      87 ..     211     240 ..     135     247 .] 0.56

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                            AAA_14  3 kilvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpe 50
                                      +i+ i+G+  +GK+tl+ ++ +  l  ++  + + in + ++++++ dp+
  gi|330506486|ref|YP_004382914.1| 27 EIIGIVGPTGSGKSTLISDIEQFALgdTPTGRSILINGQVPKNEQRYDPR 76
                                      7999*************999877778888999999999998887766664 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.083
                            AAA_14  62 e.....ekktylflDEiqevpewekalkslv 87 
                                       +     ++++ +flD i +v++w + l++ +
  gi|330506486|ref|YP_004382914.1| 211 KvistsNEEQRIFLD-IERVDGWLTGLRETI 240
                                       111122345556665.666666666666655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   3.3e-05     0.025       9     108 ..      17     175 ..      13     193 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.3e-05
                            AAA_30   9 avealltsgdrvavltGpAGtGKttalkalreaweaag.............grviglAptgkaAkvLaeelgi.eas 71 
                                       +v ++  s+  +  ++Gp G+GK+t+++ +++ +  +              ++   + p +k  ++L++++ + + +
  gi|330506486|ref|YP_004382914.1|  17 LVHEIEISRGEIIGIVGPTGSGKSTLISDIEQFALGDTptgrsilingqvpKNEQRYDPRKKLVAQLSQNMHFlADM 93 
                                       66777778888999****************88766553466776666555544455666666666666666653445 PP

                            AAA_30  72 tiakllkrlk.............................................grarlepgtllivDEagmvdtk 103
                                        + ++l+ ++                                             + a ++++ ++++DE+  +++k
  gi|330506486|ref|YP_004382914.1|  94 QVGEFLRMHAksrgkdpnqadkvielantltgepispefqltilsggqsralmvaDIAVISDSPIVLIDEIENAGIK 170
                                       56666665556666666666666666666677777777777777777777777765555666677777777777777 PP

                            AAA_30 104 qlaal 108
                                       + +al
  gi|330506486|ref|YP_004382914.1| 171 KQEAL 175
                                       66655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0042       3.3       2      20 ..      29      47 ..      28      53 .. 0.87
   2 !    7.0   0.1    0.0063       4.9      93     159 ..     153     217 ..     133     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0042
                                      EEEE--TTSSHHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvl 20
                                      + i Gp G+GK+Tl++ + 
  gi|330506486|ref|YP_004382914.1| 29 IGIVGPTGSGKSTLISDIE 47
                                      6799***********9875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0063
                                       HHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE--TTT CS
                          NTPase_1  93 lseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrk.dlalveeirerkdvkvfevteen 159
                                       +s++ +++iDEi   E    k +ea++ +  ++k+v++v h +   l  +++i  ++++ +  ++ +n
  gi|330506486|ref|YP_004382914.1| 153 ISDSPIVLIDEI---ENAGIKKQEALRLLSGEGKIVVVVTHDPMlALMATRRIVMKNGGMTKVISTSN 217
                                       3777799****9...8888888888876666**********997777777788877665555555554 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 ?   12.0   1.1   0.00019      0.15      12      44 ..      18      50 ..      15     221 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                          ATPase_2 12 eeilerepneiyfiYGpegsGKtaLlkeiienl 44
                                       + +e ++ ei+ i Gp gsGK++L+  i +  
  gi|330506486|ref|YP_004382914.1| 18 VHEIEISRGEIIGIVGPTGSGKSTLISDIEQFA 50
                                      5667778899****************9876544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2    0.0001     0.081      98     121 ..      25      48 ..       8     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                                       TTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallp 121
                                       +++++ +vG++G GKStLi  + +
  gi|330506486|ref|YP_004382914.1|  25 RGEIIGIVGPTGSGKSTLISDIEQ 48 
                                       568999*************98865 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     6e-05     0.047      21      40 ..      27      46 ..      13      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6e-05
                                      EEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqi 40
                                       ++++vG  G+GK+tl+++i
  gi|330506486|ref|YP_004382914.1| 27 EIIGIVGPTGSGKSTLISDI 46
                                      59***************998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00015      0.12       1      20 [.      29      48 ..      29     123 .. 0.71
   2 ?   -1.3   0.0       3.8   2.9e+03      70      95 ..     178     203 ..     148     241 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                            AAA_18  1 IlltGtpGvGKttlakeLsk 20
                                      I++ G+ G+GK+tl   +++
  gi|330506486|ref|YP_004382914.1| 29 IGIVGPTGSGKSTLISDIEQ 48
                                      89************999843 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.8
                            AAA_18  70 aleegknlvidghlaeleseaakdik 95 
                                        ++egk +v+  h   l  +a ++i+
  gi|330506486|ref|YP_004382914.1| 178 LSGEGKIVVVVTHDPMLALMATRRIV 203
                                       45666666666665555555444444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.7   0.00017      0.13       2      19 ..      29      46 ..      28     190 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                                      EEEEESTTSSHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                      ++ivG + +GKStLi+ +
  gi|330506486|ref|YP_004382914.1| 29 IGIVGPTGSGKSTLISDI 46
                                      89*************876 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00024      0.19      39      94 ..     112     182 ..      26     188 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                                       EGGG-------THHHHHHHHHTTT-HHHHTTS.................EEEEETGGG----.---------HH CS
                             AAA_2  39 daselleeeevehlvsrligappgyvgaeegG.................ivllDEidKihpk.essgadvSreg 94 
                                        a +++   e++++++ + ++p++      gG                 ivl+DEi+ +  k +++ +  S+eg
  gi|330506486|ref|YP_004382914.1| 112 QADKVI---ELANTLTGEPISPEFQLTILSGGqsralmvadiavisdspIVLIDEIENAGIKkQEALRLLSGEG 182
                                       333333...4778888888888888888888899999999999999999**********988777777777776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.13      30      58 ..      23      51 ..      14     126 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava 58
                                      + +ge++ ++G++g+GK+tl +d+    +
  gi|330506486|ref|YP_004382914.1| 23 ISRGEIIGIVGPTGSGKSTLISDIEQFAL 51
                                      679999***************99765555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017      0.13       5      44 ..      29      67 ..      25     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                            AAA_24  5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfp 44
                                      i i+Gp g+GK+tl++ + +++++ dt  G   l + ++p
  gi|330506486|ref|YP_004382914.1| 29 IGIVGPTGSGKSTLISDI-EQFALGDTPTGRSILINGQVP 67
                                      88****************.999998887776655555555 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00017      0.13      81     107 ..      21      46 ..      12      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                        Adeno_IVa2  81 lnyglqPviGviyGPtGsGksqllrnl 107
                                       +++ +  +iG++ GPtGsGks l+ ++
  gi|330506486|ref|YP_004382914.1|  21 IEISRGEIIGIV-GPTGSGKSTLISDI 46 
                                       666677899975.**********9876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.006       4.7       4      21 ..      31      48 ..      29      70 .. 0.86
   2 ?    3.5   0.0     0.085        66      65     122 ..     155     218 ..     116     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.006
                                      EE--SSSSHHHHHHHGGG CS
                             AAA_5  4 LvGppGtgKselaerlaa 21
                                      +vGp+G+gKs+l+  + +
  gi|330506486|ref|YP_004382914.1| 31 IVGPTGSGKSTLISDIEQ 48
                                      69**********988876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.085
                                       G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---..............-EEEEEESS CS
                             AAA_5  65 egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddller........frviatanp 122
                                        + i+++DE+e+a  + +++L  l  e ++ +   +  + a   +  +r        + vi t+n+
  gi|330506486|ref|YP_004382914.1| 155 DSPIVLIDEIENAGIKKQEALRLLSGEGKIVVVVTHDPMLALMAT--RRivmknggmTKVISTSNE 218
                                       67799********99989988666666666666666666555543..1123356666666666666 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00029      0.23       1      19 [.      31      49 ..      31      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                        ATP_bind_1  1 vvGpaGsGKttfvgalsei 19
                                      +vGp GsGK+t+++ + ++
  gi|330506486|ref|YP_004382914.1| 31 IVGPTGSGKSTLISDIEQF 49
                                      79************99887 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 ?    9.2   0.0     0.001      0.78      31      53 ..      24      46 ..      13      51 .. 0.81
   2 ?   -0.8   0.0       1.2   9.2e+02      39      58 ..      51      70 ..      46      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.001
                             AAA_7 31 knkkpvllvGptGtGKtviikdl 53
                                      +++  + +vGptG+GK+++i+d+
  gi|330506486|ref|YP_004382914.1| 24 SRGEIIGIVGPTGSGKSTLISDI 46
                                      56666779************986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                             AAA_7 39 vGptGtGKtviikdllkkld 58
                                       G+t tG++++i+  + k +
  gi|330506486|ref|YP_004382914.1| 51 LGDTPTGRSILINGQVPKNE 70
                                      79999******998554444 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 ?    7.6   1.9    0.0062       4.8       3      75 ..      31     179 ..      29     230 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0062
                                       EESSTTSSHHHHHHHHHHHH......THE...............................EEEEETTTCSSS..... CS
                               AAA   3 lyGppGtGKTllakavakel......gve...............................fleisgsellsk..... 37 
                                       ++Gp G GK++l++ + + +      g +                               +  +++ e+l +     
  gi|330506486|ref|YP_004382914.1|  31 IVGPTGSGKSTLISDIEQFAlgdtptG-RsilingqvpkneqrydprkklvaqlsqnmhfLADMQVGEFLRMhaksr 106
                                       679999999999988888754433331.1233333333444444445555555555555423333333332255555 PP

                                       .............................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.......T CS
                               AAA  38 .............................yvgesekkirelfkeakekakpsilfiDEidalaksr.......s 75 
                                                                    +++ ++++  ++ + a   ++  i++iDEi++ + ++       s
  gi|330506486|ref|YP_004382914.1| 107 gkdpnqadkvielantltgepispefqltILSGGQSRALMVADIA-VISDSPIVLIDEIENAGIKKqealrllS 179
                                       556777777777777777777777777743333333333333333.3333589999999888766645555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 1779.15
//
Query:       gi|330506487|ref|YP_004382915.1|  [L=232]
Description: hypothetical protein MCON_0197 [Methanosaeta concilii GP6]
Scores for complete 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-09   36.0   0.0    1.2e-08   34.8   0.0    1.6  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00023   21.5   0.1    0.00037   20.8   0.1    1.3  1  AAA_19           AAA domain
     0.0017   18.9   0.0      0.003   18.1   0.0    1.4  1  AAA_18           AAA domain
      0.005   17.2   0.0      0.031   14.7   0.0    1.9  2  AAA_16           AAA ATPase domain
     0.0056   16.0   0.0     0.0071   15.6   0.0    1.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.019   14.3   0.0    1.3  1  Zeta_toxin       Zeta toxin
       0.02   14.4   0.3      0.027   14.0   0.3    1.1  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
      0.076   12.0   0.1       0.21   10.5   0.1    1.6  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.092   12.5   0.1       0.13   12.0   0.1    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.12   12.4   0.0       0.24   11.4   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
       0.12   12.2   0.0       0.19   11.6   0.0    1.3  1  MobB             Molybdopterin guanine dinucleotide synthesis
       0.13   12.3   0.0       0.13   12.3   0.0    1.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.16   11.8   0.1        0.3   11.0   0.1    1.4  1  NACHT            NACHT domain
       0.19   11.4   0.2       0.29   10.8   0.2    1.3  1  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0     9e-12   1.2e-08       2     176 ..       3     164 ..       2     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 9e-12
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT..EEEETTTTECCHCTT-HHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgve.ivelenGciCctlredllkelea 75 
                                       ++v++G +GsGKT++l h +    +ag   a++  +     +D  + ++ g + +v l++  ++   +   + e+  
  gi|330506487|ref|YP_004382915.1|   3 MVVVAGTPGSGKTSVLMHAVkdLIKAGAAPALVKIDCM-WTEDDLRFKRLGLPvAVGLSKDMCPDHYAIYNVDEMLG 78 
                                       589*****************87779*************.8888888888877769*****99998877777777777 PP

                                       HHHHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HH CS
                              cobW  76 leereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtD 151
                                        ++++    ++l Et G  +  ap                 ++v+D+    + + +++ k++  l++ad  v++K D
  gi|330506487|ref|YP_004382915.1|  79 WAKEQ-GAGILLNETAGlCLRCAPY----------PDQALAICVIDV----TTGPNSPLKVGPLLTTADAAVMTKGD 140
                                       77777.69999******87888888..........456788******....99************************ PP

                                       HHCHC..HHHHHHHHHHHHTTS-EE CS
                              cobW 152 lldeeallekleerlrqlnpeakvl 176
                                       l+++++  e+++er+ + np+ +++
  gi|330506487|ref|YP_004382915.1| 141 LVSQAER-EVFRERILEANPGCRII 164
                                       *****88.9********99998876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   2.9e-07   0.00037      11      41 ..       2      32 ..       1      43 [. 0.87

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.9e-07
                            AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggvk 41
                                      k+++v + pG+GKT vl+h+v+ l+++g  +
  gi|330506487|ref|YP_004382915.1|  2 KMVVVAGTPGSGKTSVLMHAVKDLIKAGAAP 32
                                      689999*******************998664 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.3e-06     0.003       1      76 [.       4      86 ..       4     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.3e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf.....gvnlrdvakenglllevdpe...aldeskrldedkldklldaleenssa 70
                                      ++++GtpG+GKt++  +  k l +       v++ ++++e++l++ +         +++   +++  +++d++ ++++ 
  gi|330506487|ref|YP_004382915.1|  4 VVVAGTPGSGKTSVLMHAVKDLiKAgaapaLVKIDCMWTEDDLRFKRLGLpvaVGLSKDMCPDHYAIYNVDEMLGWAK- 81
                                      78***************9999856599999999999999999999887776644444555566666777777777765. PP

                            AAA_18 71 leegkn 76
                                       e+g  
  gi|330506487|ref|YP_004382915.1| 82 -EQGAG 86
                                      .55555 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   2.4e-05     0.031      26      52 ..       3      29 ..       1      56 [. 0.85
   2 ?    0.4   0.0      0.57   7.3e+02      72     123 ..     127     181 ..      99     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                            AAA_16 26 lvllsGesGvGKsslvrellralekdg 52
                                      +v++ G +G+GK+s++ ++ + l k+g
  gi|330506487|ref|YP_004382915.1|  3 MVVVAGTPGSGKTSVLMHAVKDLIKAG 29
                                      799*************99999888885 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.57
                            AAA_16  72 laqalareellrqlldeaesaeleawrekleeala.....avpelagaeasrllell 123
                                       l++++++  ++++ +  +++ e+e +re+++ea       +++ l+g+++s ++el+
  gi|330506487|ref|YP_004382915.1| 127 LLTTADA-AVMTKGDLVSQA-EREVFRERILEANPgcriiEANGLTGKGSSEFAELI 181
                                       5555544.566666666555.999999999998888888888888888887777766 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   5.5e-06    0.0071       2      25 ..       2      25 ..       1      45 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.5e-06
                           DUF2075  2 avvlVtGvaGtGKtvvllnllael 25
                                      ++v+V G +G+GKt vl++++ +l
  gi|330506487|ref|YP_004382915.1|  2 KMVVVAGTPGSGKTSVLMHAVKDL 25
                                      689******************998 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.5e-05     0.019      17      44 ..       2      29 ..       2      48 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                        Zeta_toxin 17 klillgGqpGAGKselaellkdelerqg 44
                                      k+++++G pG+GK++++  + ++l ++g
  gi|330506487|ref|YP_004382915.1|  2 KMVVVAGTPGSGKTSVLMHAVKDLIKAG 29
                                      689************9988888776444 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   2.1e-05     0.027      16      41 ..       4      29 ..       1      36 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                                      EEEEE-TTSSHHHHHHHHHHHHHHTS CS
                     UvrD-helicase 16 ilveAsAGsGKTfvlaerilrlikee 41
                                      ++v+  +GsGKT vl++ +  lik++
  gi|330506487|ref|YP_004382915.1|  4 VVVAGTPGSGKTSVLMHAVKDLIKAG 29
                                      5667779*****************98 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 ?   10.5   0.1   0.00016      0.21      31      66 ..       3      38 ..       1      43 [. 0.91
   2 ?   -1.8   0.0      0.92   1.2e+03     168     185 ..     130     148 ..     118     188 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                      +v + G+PG+Gk  ++ + +  l+++G   a++ +D
  gi|330506487|ref|YP_004382915.1|  3 MVVVAGTPGSGKTSVLMHAVKDLIKAGAAPALVKID 38
                                      57799***************************9999 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.92
                                       H-SEEEEE---.HHHHHHH CS
                              MeaB 168 iaDiivvnkaD.kkeaeka 185
                                        aD  v+ k D  ++ae+ 
  gi|330506487|ref|YP_004382915.1| 130 TADAAVMTKGDlVSQAERE 148
                                       5566666666633333332 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1    0.0001      0.13       2      21 ..       5      24 ..       4      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrt 21
                                      vv+G pG+GK++++ +++++
  gi|330506487|ref|YP_004382915.1|  5 VVAGTPGSGKTSVLMHAVKD 24
                                      9*************999998 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.24       2      44 ..       4      49 ..       3      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                      EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH-- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgr 44
                                      v++ G pG+gK+++ ++  + l   ++    v +   +te+dl+ +
  gi|330506487|ref|YP_004382915.1|  4 VVVAGTPGSGKTSVLMHAVKDLikaGAAPALVKIDCMWTEDDLRFK 49
                                      6789*************98888899999999999999999999876 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.19       2      35 ..       4      37 ..       3      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKh 35
                                      + ++g+ gsGKT+ l + ++ l + g   +++K 
  gi|330506487|ref|YP_004382915.1|  4 VVVAGTPGSGKTSVLMHAVKDLIKAGAAPALVKI 37
                                      6789************************999996 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.13       2      42 ..       4      44 ..       3     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannl 42
                                      ++++++ G+GKT+++ +  + l ++g   +lv+ D + + +
  gi|330506487|ref|YP_004382915.1|  4 VVVAGTPGSGKTSVLMHAVKDLIKAGAAPALVKIDCMWTED 44
                                      6899999****************************986555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00023       0.3       2      26 ..       3      28 ..       2      37 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                                      CEEEEC-TTTCHHHHHHHHH.HHHCT CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla.lawae 26
                                      +v++ G +GsGKT  l + + +++++
  gi|330506487|ref|YP_004382915.1|  3 MVVVAGTPGSGKTSVLMHAVkDLIKA 28
                                      699*********98666554044454 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00022      0.29      20      43 ..       3      26 ..       1      38 [. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                            AAA_30 20 vavltGpAGtGKttalkalreawe 43
                                      ++v+ G +G+GKt +l ++++ + 
  gi|330506487|ref|YP_004382915.1|  3 MVVVAGTPGSGKTSVLMHAVKDLI 26
                                      789**********99887755443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1475.54
//
Query:       gi|330506488|ref|YP_004382916.1|  [L=226]
Description: Fe-S cluster domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-10   38.0   1.0    9.3e-10   38.0   1.0    2.2  2  FeS       Putative Fe-S cluster


Domain annotation for each model (and alignments):
>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   1.0   5.2e-14   9.3e-10       1      23 [.      26      48 ..      26      57 .. 0.87
   2 ?   -0.1   0.1     0.041   7.4e+02      10      15 ..     101     106 ..     101     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 5.2e-14
                               FeS  1 LPgtNCgaCGypgCmafAealve 23
                                      LPg+NCg+CG+ +C++fA +lv 
  gi|330506488|ref|YP_004382916.1| 26 LPGYNCGECGFSSCREFAGKLVD 48
                                      9********************96 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.041
                               FeS  10 GypgCm 15 
                                       G+p+C+
  gi|330506488|ref|YP_004382916.1| 101 GEPSCR 106
                                       9****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1541.17
//
Query:       gi|330506489|ref|YP_004382917.1|  [L=355]
Description: hypothetical protein MCON_0199 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2566.20
//
Query:       gi|330506490|ref|YP_004382918.1|  [L=54]
Description: hypothetical protein MCON_0200 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 429.76
//
Query:       gi|330506491|ref|YP_004382919.1|  [L=451]
Description: hypothetical protein MCON_0202 [Methanosaeta concilii GP6]
Scores for complete 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-114  382.3   0.0   2.7e-114  382.1   0.0    1.0  1  HI0933_like    HI0933-like protein
      5e-11   42.4   0.0    7.1e-05   22.2   0.0    2.9  3  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    5.3e-06   25.9   0.0    3.8e-05   23.1   0.0    2.1  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    4.5e-05   22.7   0.2     0.0035   16.5   0.0    2.9  3  FAD_binding_2  FAD binding domain
     0.0003   20.5   0.0    0.00046   19.9   0.0    1.2  1  DAO            FAD dependent oxidoreductase
     0.0003   20.9   0.0     0.0008   19.6   0.0    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00058   19.0   0.0       0.59    9.1   0.0    2.6  3  GIDA           Glucose inhibited division protein A
      0.006   16.6   0.0        0.1   12.6   0.0    2.5  2  NAD_binding_9  FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.018   14.3   0.0      0.035   13.3   0.0    1.4  1  Thi4           Thi4 family


Domain annotation for each model (and alignments):
>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.1   0.0  1.3e-117  2.7e-114       2     408 ..      31     440 ..      30     441 .. 0.95

  Alignments for each domain:
  == domain 1  score: 382.1 bits;  conditional E-value: 1.3e-117
                                       SEEEE--SHHHHHHHHHH.........HHTT--EEEE-SSSSS-HHHHHCGGGT-EEEETT-SGGGEEES...STTT CS
                       HI0933_like   2 dviviGgGaAGlmaAisa.........akrgkrVlllekakklgrKilisGgGrcNvTnlseepeellsrypenpkf 69 
                                       d+iviG+G+AGl++Ai++         ++ ++r+l+lek+ ++grK+l+sG G+cN+T+ + e++++l++y e ++f
  gi|330506491|ref|YP_004382919.1|  31 DLIVIGAGPAGLFCAINCrqnarnddhRRDNRRILILEKKGSPGRKLLLSGSGQCNITH-EGEIRNFLNHYGEHGRF 106
                                       89***************9665554443445789**************************.***************** PP

                                       THHHHHHS-HHHHHHHHHHTT--EEE-STTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEE CS
                       HI0933_like  70 lksalsrftnedlialveelgvelkeedsgrlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvk 146
                                       l+ a+  ftn+dli +++++g+e+  e sg++Fp++++++d++d+l++ +k+a+++++ +++v++v++ edg f + 
  gi|330506491|ref|YP_004382919.1| 107 LRPAIMGFTNQDLIYYFKAKGLEMASEPSGKIFPQTRRSKDVLDILIEDCKKADIEIQCRKDVRTVNRIEDG-FALL 182
                                       ************************************************************************.7777 PP

                                       E.TTEEEEESEEEE----SS-GGGT--SHHHHHHHHTT--EEEEEEES--EE--HHHHHCGGGTT-EEEEEEE.... CS
                       HI0933_like 147 tkseeeleadklvlAtGGlSiPklGstgkgyklaeqfghtivplrpalvpltlkesklklkelsGvslkavvlsl.k 222
                                         ++ +++++ lv+AtGG S+P +Gs+g+gy++a+++gh+++++ pal p  +k+  +  ++l+G+s++++++sl +
  gi|330506491|ref|YP_004382919.1| 183 G-DGFSYRSSILVIATGGCSYPATGSSGDGYRFARSLGHRVTEIGPALTPVIIKDYPF--HDLAGISFENIKISLnN 256
                                       7.89*************************************************98766..8**************77 PP

                                       ECTTEEEEEEEEE-SSEEESHHHHHHTTT-......-TT--EEEECSTTS-...HHHHHHHHHHHTTTSBHHHHHTT CS
                       HI0933_like 223 kkkkatekgellfThrGlsGpailqlSsyvakalekkeeetleidllPdldaeelkaalekekekeskkslknalae 299
                                        kk+++ +g++l+Th GlsGpail lS+y+      ++e+tl++ ++P+ ++++l+ ++ +  +ke ++++k+ l++
  gi|330506491|ref|YP_004382919.1| 257 LKKTREGQGDILLTHEGLSGPAILDLSRYI------QPEDTLKLSFVPKEKRAALEGWILELSGKEGSRTVKSLLSS 327
                                       7888999***********************......*******************************9***999877 PP

                                       T.....S-HHHHHHHHHC..TTT-TTBGGG--HHHHHHHHHHHHSEEE--SEE--TTT-SEEEEEE-GGGB-TTT-B CS
                       HI0933_like 300 l.....lpkrlvevlleealieeedkklaqlskkelkklaealkaltvkvngteglrkaevTaGGVdlkevssktme 371
                                       +     lp rl+ +++e ++i ++d  l+ql+++e+ +l++ l  l+++v++  g++ a+vT GGVd +ev++ktm+
  gi|330506491|ref|YP_004382919.1| 328 IpcsvpLPYRLIGRIIEICGI-DPDLGLSQLRRRERMHLVDILVGLPLTVSRPDGFEAAMVTRGGVDWREVNPKTMQ 403
                                       555555***************.******************************************************* PP

                                       BTTSTTEEE-GGGBSEEE-TTTHHHHHHHHHHHHHHH CS
                       HI0933_like 372 skkvpgLffaGEvlDvegvtGGynlqaAwasgyaAGk 408
                                       s+ v+gL++aGEvlDv+g+tGGynlq++++++++A++
  gi|330506491|ref|YP_004382919.1| 404 SRLVKGLYLAGEVLDVDGDTGGYNLQSCFSTAMLAAR 440
                                       ***********************************97 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.7e-06    0.0054       1      22 [.      33      54 ..      33      76 .. 0.81
   2 !   22.2   0.0   3.6e-08   7.1e-05      26     139 ..      87     204 ..      74     214 .. 0.85
   3 ?    0.2   0.0      0.18   3.5e+02     285     305 .]     393     414 ..     381     414 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.7e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagle 22
                                      i+iGaGPaGl +ai+++++  +
  gi|330506491|ref|YP_004382919.1| 33 IVIGAGPAGLFCAINCRQNARN 54
                                      89***************98774 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 3.6e-08
                       Pyr_redox_3  26 ilEkgnignsiyrypkemtfispsftsekleipdlnaiseets......pafslkeeklsrkealeYlrevaksfel 96 
                                       i   g+i n++ +y ++ +f+ p+    +++ +dl   ++ +       p+ ++  +  + k++l+ l e +k+ ++
  gi|330506491|ref|YP_004382919.1|  87 ITHEGEIRNFLNHYGEHGRFLRPA--IMGFTNQDLIYYFKAKGlemasePSGKIFPQTRRSKDVLDILIEDCKKADI 161
                                       6678999***************97..4677777776666544334444477777788888999************** PP

                       Pyr_redox_3  97 piklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPn 139
                                       +i+  ++V++v++ ++gf +  +  +y+++ ++iAtG  ++P 
  gi|330506491|ref|YP_004382919.1| 162 EIQCRKDVRTVNRIEDGFALLGDGFSYRSSILVIATGGCSYPA 204
                                       *************************************999997 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.18
                       Pyr_redox_3 285 grpvlteeteet.nvpglflaG 305
                                        + +++++t+++  v+gl+laG
  gi|330506491|ref|YP_004382919.1| 393 DWREVNPKTMQSrLVKGLYLAG 414
                                       566788988866279******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 !   23.1   0.0   1.9e-08   3.8e-05       1     111 [.      30     201 ..      30     225 .. 0.74
   2 ?   -0.2   0.0      0.23   4.6e+02     259     279 ..     396     421 ..     375     434 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.9e-08
                                       CSEEEE--SHHHHHHHHHHHH.........HTS-EEEEETTHCHHHCSHHHHC.HHHHHHHHHHHHH.......... CS
                                       xxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx.......... RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq.........agakvtlvelegtclnggcllsk.allgvaedaeias.......... 57 
                                       +d++viG+GpAGl +a++ +q          + +++++ +++  ++++ lls    +++ +++ei+           
  gi|330506491|ref|YP_004382919.1|  30 YDLIVIGAGPAGLFCAINCRQnarnddhrrDNRRILIL-EKKGSPGRKLLLSGsGQCNITHEGEIRNflnhygehgr 105
                                       689********************999988779999999.8888999999997546666666666666888999999* PP

                                       ..................................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC........ CS
                                       ..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                       Pyr_redox_2  58 ..................................evvkklnqgielllgeevvkidpgkkkvklekkke........ 92 
                                                                          ++++ +  ++ l +  + k d + ++ k+    +        
  gi|330506491|ref|YP_004382919.1| 106 flrpaimgftnqdliyyfkakglemasepsgkifPQTRRSKDVLDILIE-DCKKADIEIQCRKDV---Rtvnriedg 178
                                       ****999999999999999999999888887777444444444555544.333333332222222...133366689 PP

                                       ....TCEEEEEESEEEE---EEE CS
                                       ....xxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  93 ....gdeekiaydklvlAtGssp 111
                                           gd++++    lv+AtG+ +
  gi|330506491|ref|YP_004382919.1| 179 fallGDGFSYRSSILVIATGGCS 201
                                       9999****************644 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.23
                                       E--T.TSBES.STTEEE-GGGC...T CS
                                       xxxx.xxxxx.xxxxxxxxxxx...x RF
                       Pyr_redox_2 259 vvde.flrtn.vpgiyaiGDva...g 279
                                       +v++ ++++  v+g+y++G v    g
  gi|330506491|ref|YP_004382919.1| 396 EVNPkTMQSRlVKGLYLAGEVLdvdG 421
                                       45541568888*********986653 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.8e-06    0.0035       1      22 [.      31      52 ..      31      88 .. 0.92
   2 ?    0.0   0.0      0.17   3.4e+02     141     172 ..     146     178 ..     130     223 .. 0.75
   3 ?    2.1   0.0     0.042        84     386     410 ..     401     427 ..     381     432 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                                      SEEEE--SHHHHHHHHHHHHTT CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaG 22
                                      D+iViG+G AGL +A++++++ 
  gi|330506491|ref|YP_004382919.1| 31 DLIVIGAGPAGLFCAINCRQNA 52
                                      89****************9875 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHTCTEEEEESEEEEEEEE.CTT CS
                     FAD_binding_2 141 hallarlvesarkagvdfqerteadeLiv.edg 172
                                       + +l  l+e ++ka++++q r +++++++ edg
  gi|330506491|ref|YP_004382919.1| 146 KDVLDILIEDCKKADIEIQCRKDVRTVNRiEDG 178
                                       568889999999999999999999999763333 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.042
                                       TTEEESSBTEEE-STCE..ESSSSTTS CS
                     FAD_binding_2 386 dadgqpipGLYAaGeva..aggvhgan 410
                                         + + ++GLY aGev+   g+ +g+n
  gi|330506491|ref|YP_004382919.1| 401 TMQSRLVKGLYLAGEVLdvDGDTGGYN 427
                                       456789**********97666666666 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.3e-07   0.00046       1     156 [.      31     222 ..      31     228 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.3e-07
                                       EEEEECTSHHHHHHHHHH...HHTT..........EEEEESSSSTTSSGGGSSEEEEESSS.........STHHSTH CS
                               DAO   1 dvviiGGGiiGlstAyeL...arrg..........VtllekgdiagsgaSgrnsgllhsgl.........rylpeas 55 
                                       d+++iG+G +Gl++A      a             +++lek+  +g+      sg++   +         +y +++ 
  gi|330506491|ref|YP_004382919.1|  31 DLIVIGAGPAGLFCAINCrqnA--RnddhrrdnrrILILEKKGSPGRKLLLSGSGQCNITHegeirnflnHYGEHGR 105
                                       789***************4432..12345567899*******99995555555555544333336655665555551 PP

                                       ....HHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEE.EEEHHHHHHHSTT CS
                               DAO  56 ....elarlslealeelreleeelgididyrrtGllslaadeeelealdkllallleagldae.lldaeevrelepa 127
                                           +   + +  +++++ + ++ g+++  +++G+++   ++++++ ld+l++++++a+++ +   d + v+++e +
  gi|330506491|ref|YP_004382919.1| 106 flrpA--IMGFTNQDLIYYFKAK-GLEMASEPSGKIFPQ-TRRSKDVLDILIEDCKKADIEIQcRKDVRTVNRIEDG 178
                                       33222..2444444777888887.99************7.556799*********9999988733444678888876 PP

                                       ST..............TTSEEEEETTEEEE.EHHHHHHHHHHHH CS
                               DAO 128 lp..............gllgalfypdtgqv.dpakltaalaraa 156
                                        +                +g++ yp tg   d ++++++l +++
  gi|330506491|ref|YP_004382919.1| 179 FAllgdgfsyrssilvIATGGCSYPATGSSgDGYRFARSLGHRV 222
                                       22345678888899966569999999999999999999887765 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 !   19.6   0.0     4e-07    0.0008       1      40 [.      34      82 ..      34     108 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4e-07
                                      EE--SHHHHHHHHHHHC......C...TEEEEEE-SSSSSSGGG-EECE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLak......a...gfdvlllekrdrlGGraasyev 40
                                      ++GaG +Gl +A  +++      +   ++++l+lek  ++G ++     
  gi|330506491|ref|YP_004382919.1| 34 VIGAGPAGLFCAINCRQnarnddHrrdNRRILILEKKGSPGRKLLLSGS 82
                                      8***************64444431345889*********9966554444 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0013       2.5       1      20 [.      31      50 ..      31      54 .. 0.88
   2 ?   -2.1   0.0      0.76   1.5e+03     131     150 ..     180     199 ..     149     213 .. 0.75
   3 !    9.1   0.0    0.0003      0.59     333     369 ..     384     421 ..     355     449 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0013
                                      CEEEE-SSHHHHHHHHHHHH CS
                              GIDA  1 dviViGgGhAGceAAlaaar 20
                                      d+iViG+G AG+ +A+++ +
  gi|330506491|ref|YP_004382919.1| 31 DLIVIGAGPAGLFCAINCRQ 50
                                      689************98765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.76
                                       EEETTS-EEEECEEEE--TT CS
                              GIDA 131 vvtedgetikakavviatGt 150
                                        ++ dg  +++++ viatG 
  gi|330506491|ref|YP_004382919.1| 180 ALLGDGFSYRSSILVIATGG 199
                                       567789999999******96 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0003
                                       -EEEEEEEE-GGGB-T.TSBBSSSBTEEE-CGGGTB-S CS
                              GIDA 333 Gyaieydyvdprqlln.tLetkkvkgLflAGqinGteG 369
                                       + ++    vd r++++ t++++ vkgL+lAG++  + G
  gi|330506491|ref|YP_004382919.1| 384 AAMVTRGGVDWREVNPkTMQSRLVKGLYLAGEVLDVDG 421
                                       56677777888889988**************9754433 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   5.1e-05       0.1       2     154 ..      34     198 ..      33     200 .. 0.59
   2 ?   -3.3   0.0         4   7.9e+03      83     101 ..     395     413 ..     385     415 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.1e-05
                     NAD_binding_9   2 ivGaGprGlavlerLlara....kkkspleitlfdpsep.gagrvwrtdqseelllNvpasemslftddp....... 66 
                                       ++GaGp+Gl ++ +  ++a    +++++ +i + +++++ g++   + + + +    ++ +e+  f ++        
  gi|330506491|ref|YP_004382919.1|  34 VIGAGPAGLFCAINCRQNArnddHRRDNRRILILEKKGSpGRKLLLSGSGQCNI---THEGEIRNFLNHYgehgrfl 107
                                       8*****************9987666778********655597777666654332...33344444444443345666 PP

                     NAD_binding_9  67 .........ptfaeWlrergaleeaeeldpddfvpRalyGrYlrdlfeellarl.pegvtvevhraevvdleeradg 133
                                                +++  + +++g  e a e +++ f++ +      +d+++ l++++ +++++++ +r++v  +++ +dg
  gi|330506491|ref|YP_004382919.1| 108 rpaimgftnQDLIYYFKAKGL-EMASEPSGKIFPQTRRS----KDVLDILIEDCkKADIEIQ-CRKDVRTVNRIEDG 178
                                       666666666666666666553.22344455555554443....3444444444423334444.35666666666666 PP

                     NAD_binding_9 134 qavlladgaslaadaVvLAlG 154
                                       +a+ l dg s++   +v+A+G
  gi|330506491|ref|YP_004382919.1| 179 FAL-LGDGFSYRSSILVIATG 198
                                       533.66666666666666666 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4
                     NAD_binding_9  83 eeldpddfvpRalyGrYlr 101
                                       +e++p+++ +R + G Yl+
  gi|330506491|ref|YP_004382919.1| 395 REVNPKTMQSRLVKGLYLA 413
                                       5788999999999999985 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.8e-05     0.035      18      80 ..      30     100 ..      26     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                                       EEEEEE--SHHHHHHHHHH...HHCT.....TS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHT CS
                              Thi4  18 sDvvivGaGssGLtaayyl...akkp.....dlkvailersvspGGGawlGGqlfsaivvrkpakelLdel 80 
                                        D++++GaG++GL +a      a++      + +++ile++ spG    l G    +i  + + +++L+  
  gi|330506491|ref|YP_004382919.1|  30 YDLIVIGAGPAGLFCAINCrqnARNDdhrrdNRRILILEKKGSPGRKLLLSGSGQCNITHEGEIRNFLNHY 100
                                       59*************97652224433122225689**********99999999988888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3059.01
//
Query:       gi|330506492|ref|YP_004382920.1|  [L=172]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-26   89.0   8.5    5.3e-09   35.5   0.2    4.0  4  TPR_1         Tetratricopeptide repeat
    1.3e-21   76.0   2.3    3.9e-12   45.7   0.1    3.2  3  TPR_11        TPR repeat
    3.1e-20   70.6   5.6    6.5e-07   29.0   0.1    4.0  4  TPR_2         Tetratricopeptide repeat
      4e-19   67.2   4.0    3.2e-06   26.9   0.1    4.1  4  TPR_8         Tetratricopeptide repeat
    1.4e-13   51.3   0.0    2.7e-06   27.9   0.0    2.9  3  TPR_16        Tetratricopeptide repeat
    1.1e-11   44.4   0.0     0.0075   17.0   0.0    3.4  3  TPR_14        Tetratricopeptide repeat
    1.4e-11   44.7   0.4    0.00015   22.2   0.0    2.1  2  TPR_19        Tetratricopeptide repeat
    3.7e-11   42.6   4.6    0.00014   22.0   0.5    3.8  4  TPR_17        Tetratricopeptide repeat
    2.6e-07   30.8   4.7      2e-05   24.7   0.4    2.2  2  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    3.1e-07   30.4   0.1     0.0025   17.9   0.0    2.3  2  TPR_9         Tetratricopeptide repeat
      2e-06   28.0   0.5     0.0051   17.1   0.0    2.9  3  TPR_12        Tetratricopeptide repeat
     0.0005   20.1   1.3       0.28   11.3   0.1    3.2  3  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
     0.0006   19.7   1.7       0.71    9.7   0.2    2.7  3  DUF5113       Domain of unknown function (DUF5113)
      0.001   18.8   1.0         12    6.0   0.0    3.9  4  TPR_10        Tetratricopeptide repeat
      0.008   15.1   0.2       0.12   11.2   0.3    2.1  2  NARP1         NMDA receptor-regulated protein 1
  ------ inclusion threshold ------
      0.011   15.8   0.2        8.9    6.4   0.1    3.0  2  DUF3856       Domain of Unknown Function (DUF3856)
      0.011   16.1   0.1       0.05   14.0   0.1    2.0  1  BTAD          Bacterial transcriptional activator domain
      0.016   15.2   0.5       0.11   12.6   0.1    2.0  2  SRP_TPR_like  Putative TPR-like repeat
      0.024   14.6   0.0        8.5    6.7   0.0    3.1  4  TPR_7         Tetratricopeptide repeat
      0.034   14.2   0.3       0.48   10.5   0.0    2.6  3  MIT           MIT (microtubule interacting and transport) dom
      0.034   13.9   0.0      0.063   13.0   0.0    1.4  1  YfiO          Outer membrane lipoprotein


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 !   35.5   0.2   6.2e-12   5.3e-09       3      33 ..      39      69 ..      37      70 .. 0.95
   2 !   30.0   0.1   3.4e-10   2.9e-07       1      34 []      71     104 ..      71     104 .. 0.96
   3 !   26.1   0.0   5.9e-09     5e-06       3      34 .]     107     138 ..     105     138 .. 0.94
   4 ?    0.5   0.2      0.72   6.2e+02       3      20 ..     141     158 ..     139     168 .. 0.56

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 6.2e-12
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  3 alynlGnayfklgkydeAleyyekALelnPn 33
                                       + n+G+ + k+g y++A+ +y++AL+lnPn
  gi|330506492|ref|YP_004382920.1| 39 QWVNKGHELVKKGSYKDAINCYNEALKLNPN 69
                                      699***************************9 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 3.4e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++a++ +G+a+ kl+ky+e  ++ ++AL++nP +
  gi|330506492|ref|YP_004382920.1|  71 PRAWCSKGYALIKLKKYKESHACLDEALRINPRH 104
                                       58******************************75 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 5.9e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++  +G a+  ++k+++Al y ++A+el+P++
  gi|330506492|ref|YP_004382920.1| 107 CWTIKGWAFNCQNKHKDALVYLDRAIELDPHY 138
                                       7999**************************97 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.72
                                       HHHHHHHHHHHTT-HHHH CS
                             TPR_1   3 alynlGnayfklgkydeA 20 
                                       a+y++ +a+  l++  eA
  gi|330506492|ref|YP_004382920.1| 141 AWYQKHLALNDLNRKAEA 158
                                       566555566666666666 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.1   4.5e-15   3.9e-12       1      40 [.      44      83 ..      44      85 .. 0.95
   2 !   12.8   0.0   8.7e-05     0.074       1      26 [.      78     103 ..      78     108 .. 0.94
   3 !   21.0   0.2   2.3e-07    0.0002       6      38 ..     117     149 ..     112     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 4.5e-15
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40
                                      G++++++G y++Ai++Y++Alkl+P+ ++a++  G+a+ k
  gi|330506492|ref|YP_004382920.1| 44 GHELVKKGSYKDAINCYNEALKLNPNLPRAWCSKGYALIK 83
                                      899*********************************9876 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.7e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPd 26 
                                       G+a+ ++ ky+e+ +++ +Al+++P 
  gi|330506492|ref|YP_004382920.1|  78 GYALIKLKKYKESHACLDEALRINPR 103
                                       899**********************6 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 2.3e-07
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                        q+k ++A+  + +A++ldP +++a+y  +la+
  gi|330506492|ref|YP_004382920.1| 117 CQNKHKDALVYLDRAIELDPHYVDAWYQKHLAL 149
                                       599************************998886 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.9e-09   1.6e-06       4      33 ..      40      69 ..      37      70 .. 0.94
   2 !   29.0   0.1   7.6e-10   6.5e-07       1      34 []      71     104 ..      71     104 .. 0.96
   3 !   14.1   0.0   4.6e-05     0.039      13      34 .]     117     138 ..     106     138 .. 0.83
   4 ?   -0.5   0.2       2.1   1.8e+03      14      30 ..     152     168 ..     146     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.9e-09
                             TPR_2  4 lynlGlayyklgdyeeAleafekAleldPn 33
                                      + n G  + k+g y++A++++++Al+l+Pn
  gi|330506492|ref|YP_004382920.1| 40 WVNKGHELVKKGSYKDAINCYNEALKLNPN 69
                                      899**************************9 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 7.6e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++a++  G+a++kl++y+e ++++++Al+++P++
  gi|330506492|ref|YP_004382920.1|  71 PRAWCSKGYALIKLKKYKESHACLDEALRINPRH 104
                                       589*****************************86 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 4.6e-05
                             TPR_2  13 klgdyeeAleafekAleldPnn 34 
                                        ++++++Al ++++A+eldP++
  gi|330506492|ref|YP_004382920.1| 117 CQNKHKDALVYLDRAIELDPHY 138
                                       6899****************85 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.1
                             TPR_2  14 lgdyeeAleafekAlel 30 
                                       l++ +eA  a+ kA el
  gi|330506492|ref|YP_004382920.1| 152 LNRKAEADVALAKAREL 168
                                       67888888888888776 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.1   3.7e-09   3.2e-06       4      33 ..      40      69 ..      40      70 .. 0.97
   2 !   24.9   0.1   1.6e-08   1.4e-05       2      34 .]      72     104 ..      71     104 .. 0.95
   3 !    9.6   0.0    0.0013       1.1       3      33 ..     107     137 ..     105     138 .. 0.88
   4 ?    4.7   0.2     0.048        41       2      27 ..     140     165 ..     139     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.7e-09
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  4 yynlgsiylklgdyeeAkeyyekaleldpd 33
                                      ++n+g+ + k+g y+ A+ +y++al+l+p+
  gi|330506492|ref|YP_004382920.1| 40 WVNKGHELVKKGSYKDAINCYNEALKLNPN 69
                                      89***************************8 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.6e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +a++ +g++++kl++y+e+ +++ +al+++p +
  gi|330506492|ref|YP_004382920.1|  72 RAWCSKGYALIKLKKYKESHACLDEALRINPRH 104
                                       89*****************************75 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        +  +g++   +++++ A  y+ +a+eldp 
  gi|330506492|ref|YP_004382920.1| 107 CWTIKGWAFNCQNKHKDALVYLDRAIELDPH 137
                                       6778888888899****************96 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.048
                                       CHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyeka 27 
                                       +a+y++ +++ +l+++ eA  ++ ka
  gi|330506492|ref|YP_004382920.1| 140 DAWYQKHLALNDLNRKAEADVALAKA 165
                                       789999999**********9999998 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.8e-08   1.6e-05       2      52 ..      42      89 ..      41      89 .. 0.94
   2 !   27.9   0.0   3.1e-09   2.7e-06       2      66 ..      76     137 ..      75     139 .. 0.96
   3 !   10.4   0.6   0.00097      0.83      10      53 ..     118     158 ..     118     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.8e-08
                            TPR_16  2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlae 52
                                      ++++++++ g y dA++ +++alk++   P  ++A+  +g a+ +++ ++e
  gi|330506492|ref|YP_004382920.1| 42 NKGHELVKKGSYKDAINCYNEALKLN---PNLPRAWCSKGYALIKLKKYKE 89
                                      689***********************...99999*********99999976 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 3.1e-09
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                        +++a++++++y +  a l++al+ +   P+++  +  +g+a+  q+ +++A+ ++++a++ +p 
  gi|330506492|ref|YP_004382920.1|  76 SKGYALIKLKKYKESHACLDEALRIN---PRHVSCWTIKGWAFNCQNKHKDALVYLDRAIELDPH 137
                                       5799**********************...*******************************99996 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00097
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeA 53 
                                       +++  dA+ +l++a+++d   P  ++A++ + +a+  ++r aeA
  gi|330506492|ref|YP_004382920.1| 118 QNKHKDALVYLDRAIELD---PHYVDAWYQKHLALNDLNRKAEA 158
                                       6788899999********...********999999999999998 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   8.7e-06    0.0075       9      39 ..      45      75 ..      37      80 .. 0.84
   2 !    8.9   0.0    0.0036       3.1       8      39 ..      78     109 ..      76     114 .. 0.89
   3 !   16.0   0.0   1.9e-05     0.016       8      40 ..     112     144 ..     106     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.7e-06
                            TPR_14  9 eallalGdpdeAiallrralalaPddaeawl 39
                                      + l   G +++Ai+++++al+l+P+ ++aw 
  gi|330506492|ref|YP_004382920.1| 45 HELVKKGSYKDAINCYNEALKLNPNLPRAWC 75
                                      5677889**********************95 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0036
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawl 39 
                                       + al  l +++e+ a+l++al+ +P +   w+
  gi|330506492|ref|YP_004382920.1|  78 GYALIKLKKYKESHACLDEALRINPRHVSCWT 109
                                       5789999******************9988775 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 1.9e-05
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawll 40 
                                       ++a+  + ++++A+ +l+ra++l+P   +aw++
  gi|330506492|ref|YP_004382920.1| 112 GWAFNCQNKHKDALVYLDRAIELDPHYVDAWYQ 144
                                       678888999*********************965 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.8e-07   0.00015       1      57 [.      47     103 ..      47     109 .. 0.95
   2 !   19.3   1.6   1.4e-06    0.0012       4      53 ..     118     167 ..     118     169 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.8e-07
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       l++ g y +A++ + +al+ +p+ ++a+     al++l+ ++e  a+Ld++++ +p 
  gi|330506492|ref|YP_004382920.1|  47 LVKKGSYKDAINCYNEALKLNPNLPRAWCSKGYALIKLKKYKESHACLDEALRINPR 103
                                       5788***********************************************999886 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.4e-06
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       ++++ +Al +l +a++ dp++ +a+++   al  l++ +eA  +L+++ e
  gi|330506492|ref|YP_004382920.1| 118 QNKHKDALVYLDRAIELDPHYVDAWYQKHLALNDLNRKAEADVALAKARE 167
                                       67899***************************************998865 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       6.3   5.4e+03      16      33 ..      40      57 ..      33      57 .. 0.75
   2 !   22.0   0.5   1.6e-07   0.00014       1      33 [.      59      91 ..      59      92 .. 0.94
   3 !    8.5   0.0    0.0033       2.8       1      32 [.      93     124 ..      93     125 .. 0.91
   4 !   11.3   0.2   0.00044      0.37       2      19 ..     128     145 ..     127     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.3
                            TPR_17 16 ynnLAelllknGdlmtAr 33
                                      + n++  l k+G +++A+
  gi|330506492|ref|YP_004382920.1| 40 WVNKGHELVKKGSYKDAI 57
                                      788888888899888885 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.6e-07
                            TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      +y +al+l+Pn + a++ ++++l k++++++ +
  gi|330506492|ref|YP_004382920.1| 59 CYNEALKLNPNLPRAWCSKGYALIKLKKYKESH 91
                                      8***************************99875 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0033
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       ++ +al+++P ++  ++ +++++  ++++++A
  gi|330506492|ref|YP_004382920.1|  93 CLDEALRINPRHVSCWTIKGWAFNCQNKHKDA 124
                                       6789*******************999998888 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00044
                            TPR_17   2 ylkaleldPnnadaynnL 19 
                                       + +a+eldP ++da++++
  gi|330506492|ref|YP_004382920.1| 128 LDRAIELDPHYVDAWYQK 145
                                       679*************85 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 !   24.7   0.4   2.3e-08     2e-05       2      62 ..      50     111 ..      49     117 .. 0.90
   2 !    8.0   0.3    0.0039       3.3      36      81 ..     118     164 ..     110     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.3e-08
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylf 62 
                                       ++ yk+Ai +++ +l+ +++ p +   ++++l ++++yk+ +  l++a ++n+++  c+ ++
  gi|330506492|ref|YP_004382920.1|  50 KGSYKDAINCYNEALKLNPNLPRAWCSKGYALIKLKKYKESHACLDEAlRINPRHVSCWTIK 111
                                       67899999999999999999999999999999999999999999999999999999999886 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0039
                                       TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++++k A+ +l++a +l+++   ++y +  +l +L++  eA  aL k
  gi|330506492|ref|YP_004382920.1| 118 QNKHKDALVYLDRAiELDPHYVDAWYQKHLALNDLNRKAEADVALAK 164
                                       78999999999999999999999999999999999999999877765 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.9e-06    0.0025      10      61 ..      52     103 ..      46     106 .. 0.93
   2 !   10.2   0.3   0.00076      0.65       2      48 ..     111     158 ..     110     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.9e-06
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                        +  a+ +++  l l+P+ p+ +   G +l +l  +++  a+L+ +l+++p 
  gi|330506492|ref|YP_004382920.1|  52 SYKDAINCYNEALKLNPNLPRAWCSKGYALIKLKKYKESHACLDEALRINPR 103
                                       67889******************************************99985 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00076
                             TPR_9   2 kaia.ireedweralavverllllaPddpeerrdRGlllaqlGclsaA 48 
                                       k +a   ++++  al +++r + l+P+ ++ ++   l+l  l++ ++A
  gi|330506492|ref|YP_004382920.1| 111 KGWAfNCQNKHKDALVYLDRAIELDPHYVDAWYQKHLALNDLNRKAEA 158
                                       5566334789999*******************9988888777776666 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0048       4.1      55      74 ..      47      66 ..      40      69 .. 0.72
   2 !   17.1   0.0     6e-06    0.0051       5      75 ..      73     135 ..      69     137 .. 0.92
   3 !    7.7   0.0     0.005       4.3      52      75 ..     112     135 ..     106     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0048
                            TPR_12 55 yralgryeeAlelleealai 74
                                      + + g y++A++ ++eal++
  gi|330506492|ref|YP_004382920.1| 47 LVKKGSYKDAINCYNEALKL 66
                                      45667888888888888876 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 6e-06
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a+   + +l +l++y e+ ++l++al+i      p h   +++    g+++  ++++++Al +l +a++++
  gi|330506492|ref|YP_004382920.1|  73 AWCSKGYALIKLKKYKESHACLDEALRIN-----PRH---VSCWTIKGWAFNCQNKHKDALVYLDRAIELD 135
                                       666689999********************.....999...899999**********************986 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.005
                            TPR_12  52 grlyralgryeeAlelleealaia 75 
                                       g+++  ++++++Al +l +a++++
  gi|330506492|ref|YP_004382920.1| 112 GWAFNCQNKHKDALVYLDRAIELD 135
                                       778888888888888888888875 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.13   1.1e+02      13      33 ..      49      69 ..      47      73 .. 0.88
   2 !   11.3   0.1   0.00032      0.28       9      33 ..      79     103 ..      78     106 .. 0.92
   3 ?    3.1   0.0      0.12     1e+02      16      33 ..     120     137 ..     118     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.13
                                      HHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C 13 klgeYseArryvdalLeiEPe 33
                                      k g Y++A ++ +  L++ P+
  gi|330506492|ref|YP_004382920.1| 49 KKGSYKDAINCYNEALKLNPN 69
                                      7799************99997 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00032
                                       HHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPe 33 
                                       ++ +kl++Y+e+  ++d  L+i P+
  gi|330506492|ref|YP_004382920.1|  79 YALIKLKKYKESHACLDEALRINPR 103
                                       5889*******************97 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.12
                                       -HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPe 33 
                                       ++++A+ y+d+ +e++P 
  gi|330506492|ref|YP_004382920.1| 120 KHKDALVYLDRAIELDPH 137
                                       6899*************7 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0023         2       7      37 ..      36      66 ..      34      96 .. 0.78
   2 ?    0.7   0.0      0.48   4.1e+02      11      42 ..      74     105 ..      68     112 .. 0.81
   3 !    9.7   0.2   0.00083      0.71      15      59 ..     112     155 ..     103     168 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0023
                           DUF5113  7 iandYanlayylnvegeyeeALeyldsaley 37
                                      i n+++n + +l  +g+y++A+++ ++al++
  gi|330506492|ref|YP_004382920.1| 36 IPNQWVNKGHELVKKGSYKDAINCYNEALKL 66
                                      66899************************86 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.48
                           DUF5113  11 YanlayylnvegeyeeALeyldsaleylNahy 42 
                                       + + +y+l   ++y+e+ ++ld+al++  +h 
  gi|330506492|ref|YP_004382920.1|  74 WCSKGYALIKLKKYKESHACLDEALRINPRHV 105
                                       5667888888899************9866665 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00083
                           DUF5113  15 ayylnvegeyeeALeyldsaleylNahyekYakkkadtldklkml 59 
                                       + + n ++++++AL yld a+e+  ++ + +++k+   l+ l+ +
  gi|330506492|ref|YP_004382920.1| 112 GWAFNCQNKHKDALVYLDRAIELDPHYVDAWYQKHL-ALNDLNRK 155
                                       56789****************744444444554442.44444444 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.22   1.9e+02      25      37 ..      53      65 ..      44      69 .. 0.73
   2 ?    5.6   0.0     0.018        15       9      31 ..      78     100 ..      77     101 .. 0.91
   3 ?    6.0   0.0     0.014        12      13      30 ..     116     133 ..     112     134 .. 0.86
   4 ?    0.2   0.2       0.9   7.7e+02      11      28 ..     148     165 ..     147     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.22
                            TPR_10 25 leealairrrllG 37
                                      +++a++++ ++l 
  gi|330506492|ref|YP_004382920.1| 53 YKDAINCYNEALK 65
                                      5677777777765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.018
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al ++++y+e+ a l+eal+i
  gi|330506492|ref|YP_004382920.1|  78 GYALIKLKKYKESHACLDEALRI 100
                                       6788999**************97 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.014
                            TPR_10  13 rqrgrydeAealleeala 30 
                                         ++++++A+ +l++a++
  gi|330506492|ref|YP_004382920.1| 116 NCQNKHKDALVYLDRAIE 133
                                       579*************98 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.9
                            TPR_10  11 alrqrgrydeAealleea 28 
                                       al +++r +eA   l +a
  gi|330506492|ref|YP_004382920.1| 148 ALNDLNRKAEADVALAKA 165
                                       788999999998777776 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.088        75     205     252 ..      50      97 ..      45     101 .. 0.79
   2 !   11.2   0.3   0.00014      0.12     190     253 ..     105     166 ..      83     171 .. 0.48

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.088
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                        gs++ A+++ ++a++ +p+l   +  K+  l +    k+  ++++ea
  gi|330506492|ref|YP_004382920.1|  50 KGSYKDAINCYNEALKLNPNLPRAWCSKGYALIKLKKYKESHACLDEA 97 
                                       578999***************999999987766666666666666665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             NARP1 190 allwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeear 253
                                       + +w+    A  ++  ++ + Al y+d+aie +p  v+ +++K   l       +A  ++ +ar
  gi|330506492|ref|YP_004382920.1| 105 VSCWTIKGWA--FNCQNKHKDALVYLDRAIELDPHYVDAWYQKHLALNDLNRKAEADVALAKAR 166
                                       3333333222..3444455556666666666666666666666555555555555555555555 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.032        27      62      83 ..      78      99 ..      39     105 .. 0.59
   2 ?    6.4   0.1      0.01       8.9      77     128 ..     120     167 ..     105     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.032
                                      HHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 62 sealaklgrydealesadkalr 83
                                        al+kl++y+e+  + d+alr
  gi|330506492|ref|YP_004382920.1| 78 GYALIKLKKYKESHACLDEALR 99
                                      3466777777777777777776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  77 sadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                         + al y++r  el+      ++ a +++  al++l rk+ea  a+ +a e
  gi|330506492|ref|YP_004382920.1| 120 KHKDALVYLDRAIELDPH----YVDAWYQKHLALNDLNRKAEADVALAKARE 167
                                       567899999999999865....6777799**************999888887 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.8e-05      0.05      10     117 ..      41     160 ..      37     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-05
                                       HHHHHHHHHTT-HHHHHHHHHHHHTT.......-..-SSTTGGGTT...STTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BTAD  10 vaagraalaagdpeeaaelleaAlal.......w..rGpaladlea...gewleaererleelrlealealaeaelr 74 
                                       v++g ++ ++g  + a++++++Al+l       w  +G al +l++   ++ + +e+ r++ + +++ +    a   
  gi|330506492|ref|YP_004382920.1|  41 VNKGHELVKKGSYKDAINCYNEALKLnpnlpraWcsKGYALIKLKKykeSHACLDEALRINPRHVSCWTIKGWAFNC 117
                                       56777788888888888888888877333333333345555555557778999999999999999999999998888 PP

                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALe 117
                                        +++++al +l+++++++P+  +++ q  +Al  ++r+aeA  
  gi|330506492|ref|YP_004382920.1| 118 QNKHKDALVYLDRAIELDPHYVDAWYQKHLALNDLNRKAEADV 160
                                       88**************************************955 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00012      0.11      25      71 ..      48      97 ..      38     108 .. 0.77
   2 ?    0.6   0.0      0.65   5.5e+02      28      45 ..     119     136 ..     110     167 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                      SRP_TPR_like 25 iklekyeeaLkllkkgsalsed...vrfEkaYvlYklkkykkalkilkkv 71
                                      +k + y++a++  +++ +l+ +       k Y+l klkkyk++   l+++
  gi|330506492|ref|YP_004382920.1| 48 VKKGSYKDAINCYNEALKLNPNlprAWCSKGYALIKLKKYKESHACLDEA 97
                                      66667777777777777777651115689**************9988765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.65
                      SRP_TPR_like  28 ekyeeaLkllkkgsalse 45 
                                       +k+++aL +l+ + +l+ 
  gi|330506492|ref|YP_004382920.1| 119 NKHKDALVYLDRAIELDP 136
                                       789999999988764443 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0      0.01       8.5      11      32 ..      49      68 ..      41      72 .. 0.79
   2 ?   -1.8   0.0         5   4.3e+03       2      26 ..      74      98 ..      73     104 .. 0.64
   3 ?    4.1   0.0     0.068        58       6      32 ..     112     136 ..     107     138 .. 0.83
   4 ?   -2.2   0.0       6.6   5.7e+03      22      29 ..     143     150 ..     140     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
                             TPR_7 11 rlGdyeeAielyeqsLaltkdp 32
                                      + G y++Ai +y +  al   p
  gi|330506492|ref|YP_004382920.1| 49 KKGSYKDAINCYNE--ALKLNP 68
                                      5677**********..665555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5
                             TPR_7  2 LlnLarlysrlGdyeeAielyeqsL 26
                                      ++  + +  +l +y+e   ++ ++L
  gi|330506492|ref|YP_004382920.1| 74 WCSKGYALIKLKKYKESHACLDEAL 98
                                      5555666777777887777777744 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.068
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdp 32 
                                       + ++  ++++++A+ ++ +  a++ dp
  gi|330506492|ref|YP_004382920.1| 112 GWAFNCQNKHKDALVYLDR--AIELDP 136
                                       56677799***********..777776 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 6.6
                             TPR_7  22 yeqsLalt 29 
                                       y+++Lal 
  gi|330506492|ref|YP_004382920.1| 143 YQKHLALN 150
                                       88888775 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 ?   10.5   0.0   0.00056      0.48      10      32 ..      43      65 ..      39      66 .. 0.68
   2 ?   -0.9   0.0         2   1.7e+03      24      39 ..      84      99 ..      84     105 .. 0.78
   3 ?   -0.3   0.0       1.3   1.1e+03      30      62 ..     124     133 ..     118     146 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00056
                               MIT 10 kAveeDnagnyeeAlelYkeale 32
                                      k  e+ ++g y++A+++Y eal+
  gi|330506492|ref|YP_004382920.1| 43 KGHELVKKGSYKDAINCYNEALK 65
                                      45555567888888888888876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                               MIT 24 lelYkealelLlqalk 39
                                      l++Yke+   L +al+
  gi|330506492|ref|YP_004382920.1| 84 LKKYKESHACLDEALR 99
                                      5789999988888886 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.3
                               MIT  30 alelLlqalkekneerrellrekieeYleRaee 62 
                                       al +L  a+                       e
  gi|330506492|ref|YP_004382920.1| 124 ALVYLDRAI-----------------------E 133
                                       444444444.......................3 PP

>> YfiO  Outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.4e-05     0.063       6      77 ..      38     106 ..      34     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.4e-05
                                       HHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-SSSTT CS
                              YfiO   6 selYekgqealqkgdyaeAikklealdsryPfspyaeqaqldliyAyykdadyaealasaerFlrlyPthkn 77 
                                       ++  +kg e ++kg+y++Ai+  +++ +  P+ p   +a     yA  k + y e +a +++ lr +P+h +
  gi|330506492|ref|YP_004382920.1|  38 NQWVNKGHELVKKGSYKDAINCYNEALKLNPNLP---RAWCSKGYALIKLKKYKESHACLDEALRINPRHVS 106
                                       566689999*******************998866...5667779**************************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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):              21  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1199.22
//
Query:       gi|330506493|ref|YP_004382921.1|  [L=310]
Description: ribose-1,5-bisphosphate isomerase, e2b2 family [Methanosaeta concilii GP6]
Scores for complete 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-83  278.1   7.2    8.1e-83  277.9   7.2    1.0  1  IF-2B      Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.083   13.4   0.0       0.16   12.5   0.0    1.5  1  Rhodanese  Rhodanese-like domain


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 !  277.9   7.2     9e-87   8.1e-83       1     282 []      18     290 ..      18     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 277.9 bits;  conditional E-value: 9e-87
                                       SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHH CS
                             IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakk 77 
                                       ++rG+ +ia aa+ +l+e++ + +++  +++ ++   a+dlL k+rPtavsl+nair+++k      +  d + a++
  gi|330506493|ref|YP_004382921.1|  18 EIRGAGRIATAAAASLKEYALAVQAESFEDFNQKTAVAADLLLKTRPTAVSLSNAIRMVMK-----YKADDIDGARQ 89 
                                       589**********************************************************.....67999****** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHH CS
                             IF-2B  78 sliekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeL 154
                                       ++  +++++i++ ++a ekig+i++++i +gdt+lT+cns+++++v+ aa+k++k++kVi++EsrPr+qG  t+  L
  gi|330506493|ref|YP_004382921.1|  90 AIATNADRFIENSQKAVEKIGQIGSKRIREGDTVLTHCNSNAAISVISAAHKSGKNIKVIATESRPRFQGITTIGML 166
                                       ***************************************************************************** PP

                                       HHTTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGG CS
                             IF-2B 155 vqagipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqlded 231
                                        q gi++ li+dsav+ vm+  vd v+vGAd i++nG+++nkiGT+++A++A+e+++ ++v+ae++kfs+++ l+e 
  gi|330506493|ref|YP_004382921.1| 167 DQMGIETELIVDSAVRSVMND-VDLVVVGADVITANGTLVNKIGTAQIALCAREARTSFMVAAETYKFSPETILGEL 242
                                       *********************.******************************************************* PP

                                       SSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 232 ifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       + ieer++ e+l   ++ +    ++v+npafDvtP+++I+li Te G++ p
  gi|330506493|ref|YP_004382921.1| 243 VTIEEREATEVLADISKYK---HVRVRNPAFDVTPHQYIDLICTEAGAISP 290
                                       ************9999887...9*************************987 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.8e-05      0.16      20      96 ..      74     148 ..      42     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                         Rhodanese  20 RppeeYekghIpgAvnvskdtlsrakkseapllelpeellel...gidnkktvvvycdgggraaaaaallkklGykn 93 
                                       R   +Y++  I gA+     ++++a++  +++++ +e++ +     i++++tv ++c+++    ++  ++ k G kn
  gi|330506493|ref|YP_004382921.1|  74 RMVMKYKADDIDGARQA---IATNADRFIENSQKAVEKIGQIgskRIREGDTVLTHCNSNAA-ISVISAAHKSG-KN 145
                                       4445599999*******...6666666666666666666666666************88777.55533444477.77 PP

                         Rhodanese  94 vsv 96 
                                       ++v
  gi|330506493|ref|YP_004382921.1| 146 IKV 148
                                       766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2245.25
//
Query:       gi|330506494|ref|YP_004382922.1|  [L=157]
Description: hypothetical protein MCON_0207 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-12   45.1   0.5    1.8e-06   28.0   0.0    2.1  2  PurS      Phosphoribosylformylglycinamidine (FGAM) synthase


Domain annotation for each model (and alignments):
>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   7.2e-07     0.013      11      67 ..      10      64 ..       3      74 .. 0.74
   2 !   28.0   0.0   9.8e-11   1.8e-06       6      75 ..      86     155 ..      83     157 .] 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.2e-07
                                      TS--HHHHHHHHHHHHT.THTT.EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS- CS
                              PurS 11 gvlDpqGkavkkalksl.gyee.vedvrvgkyieleleaedeeeaeeeveemceklLaN 67
                                      ++ D+++ +vk++l +   y +  edv+  ++i++++++ d ee    +++++++ L+N
  gi|330506494|ref|YP_004382922.1| 10 KIPDAEAATVKNTLVRRlSYGKvLEDVKKERLISIQVDSGDPEE---LARAFARE-LVN 64
                                      389**********976549988579*************998775...33444443.455 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 9.8e-11
                                       EEE-TTS--HHHHHHHHHHHHT.THTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEE CS
                              PurS   6 VtlKkgvlDpqGkavkkalksl.gyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyei 75 
                                       V++  ++ D ++ a+++ l++  gy++v dv+ + + +l ++   + eae +++e++eklL+Np   +yei
  gi|330506494|ref|YP_004382922.1|  86 VKVALHIEDGEAIAIRDRLRKRlGYQNVVDVKKATVWKLYFRL-LRPEAEITAREIAEKLLINPHKDSYEI 155
                                       44445699***********7644******************96.56789****************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1120.37
//
Query:       gi|330506495|ref|YP_004382923.1|  [L=269]
Description: phosphoribosylformylglycinamidine synthase I [Methanosaeta concilii GP6]
Scores for complete 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-54  182.2   0.0    1.2e-53  181.9   0.0    1.1  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
    3.2e-09   36.8   0.1    5.7e-09   36.0   0.1    1.6  1  GATase         Glutamine amidotransferase class-I
    1.9e-07   30.9   0.0    3.2e-07   30.1   0.0    1.4  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    1.8e-06   27.8   0.0    4.9e-06   26.4   0.0    1.7  2  DJ-1_PfpI      DJ-1/PfpI family
    0.00048   20.0   0.0     0.0011   18.8   0.0    1.6  2  SNO            SNO glutamine amidotransferase family
     0.0035   17.1   0.1     0.0065   16.2   0.1    1.5  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 !  181.9   0.0   3.9e-57   1.2e-53       3     260 .]       2     264 ..       1     264 [. 0.84

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 3.9e-57
                          GATase_5   3 kvailreeGvngeyemaaafekaGfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklr 79 
                                       k+a++ ++G+n+e e+  a+++ G+e + +      + +++l+ f ++++pGGfsy D   +g++++k     e + 
  gi|330506495|ref|YP_004382923.1|   2 KIAVMQFPGTNCEFETLVAVKEVGMEGEIFRW---NRPEEELSGFDGFIIPGGFSYQDRVRAGAVASK-----EPVL 70 
                                       89*************************88755...455889**********************98884.....5667 PP

                          GATase_5  80 ealekflnredtlaLGiCnGfqlLvklglvpggeieea......eksptltrNksgr..fesrlvsvvvsekspsvf 148
                                       +al++  +  ++ +LGiCnGfq+Lv+ gl+pg    +       ++++   + ++ r  + + +v+++ +++s+   
  gi|330506495|ref|YP_004382923.1|  71 KALNEEAAL-GKPILGICNGFQILVEAGLLPGLVPGTGkvqmalAQNVMVSEGEIVRrgYYCDWVYLRHDASSRRCS 146
                                       777777777.899*****************99544444011123555555555554456********7766665443 PP

                          GATase_5 149 l....kgmeglslpvahGeGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvla 221
                                            + ++ l++p+ahGeG++v++s+  +k+l++++qv++rY+d +g++  e+p+N NgS+e+ia+i++p+G vl+
  gi|330506495|ref|YP_004382923.1| 147 GsyqiEMGALLKIPIAHGEGNLVTASPGLIKKLNDQEQVVFRYCDRNGRVIDEFPVNVNGSTESIAAICNPEGNVLG 223
                                       3211144469******************************************************************* PP

                          GATase_5 222 lmpHpervveavqksiipeeeee..evspwlrlFenavkyv 260
                                       +mpHper++ a+q + +++++++  e +p+ r+Fe++ +y+
  gi|330506495|ref|YP_004382923.1| 224 MMPHPERAFFAWQLPSFDPRKHRpnEPGPGRRIFESMKRYI 264
                                       *****************9988864349**********9995 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.1   1.9e-12   5.7e-09      16      87 ..      20      96 ..      16     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.9e-12
                                      HHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT......TTTHHHHHHHHCT...STS-EEEETHHHHHHH CS
                            GATase 16 alvelgvkvevvpidasaeeilellknpdgilvsgGpgspg......vegkieaikeare...nkiPiLGICLGmQlla 85
                                      a+ e+g++ e+++++ + ee     +++dg +++gG+ +        v  k  ++k + e    ++PiLGIC G+Q+l+
  gi|330506495|ref|YP_004382923.1| 20 AVKEVGMEGEIFRWNRPEEEL----SGFDGFIIPGGFSYQDrvragaVASKEPVLKALNEeaaLGKPILGICNGFQILV 94
                                      578899999******987777....79************9999999855666666665556669**************9 PP

                                      HH CS
                            GATase 86 ie 87
                                      ++
  gi|330506495|ref|YP_004382923.1| 95 EA 96
                                      87 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   1.1e-10   3.2e-07      25      90 ..      29      95 ..       2     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.1e-10
                          GATase_3 25 vrvrfvplkdeslgedadlvilpGgkdt...iqdlallresgldeaikeaaeaggpvlgiCGGlqmLGe 90
                                      + +r+ + ++e+l    d  i+pGg+++   +++ a++ ++ + +a++e a+ g+p+lgiC G+q+L e
  gi|330506495|ref|YP_004382923.1| 29 EIFRWNR-PEEELSG-FDGFIIPGGFSYqdrVRAGAVASKEPVLKALNEEAALGKPILGICNGFQILVE 95
                                      4566777.9999955.*********766111566788899999************************76 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.6e-09   4.9e-06      59     115 ..      40     101 ..      16     128 .. 0.82
   2 ?   -3.1   0.0         2   5.9e+03     115     128 ..     166     179 ..     156     197 .. 0.62

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.6e-09
                                       CCG-SEEEE--BHHHHHHHHT.....SHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTT CS
                         DJ-1_PfpI  59 aaeyDalvlpGGragperlre.....nekvvelvkefaekgklvaaICagpqlLaaagvlkg 115
                                        + +D  ++pGG +  +r+r+     +e v++ + e a  gk++  IC g q+L++ag+l+g
  gi|330506495|ref|YP_004382923.1|  40 LSGFDGFIIPGGFSYQDRVRAgavasKEPVLKALNEEAALGKPILGICNGFQILVEAGLLPG 101
                                       5679**********99988752222267999*****************************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                                       TSEE--SGGGHHHH CS
                         DJ-1_PfpI 115 grrvTsypavkdkl 128
                                       g  vT+ p++ +kl
  gi|330506495|ref|YP_004382923.1| 166 GNLVTASPGLIKKL 179
                                       34445555555555 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.8e-07    0.0011      13      82 ..      19      94 ..       8     117 .. 0.79
   2 ?   -2.4   0.0       1.2   3.6e+03     136     170 ..     194     229 ..     174     231 .. 0.49

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.8e-07
                                      HHHHHTTSEE...EEE-SGGGGCC-SEEEE-SS-HHH....HHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHC CS
                               SNO 13 eaikkclaen...ktvkrkedlaevdaliiPGGesta....mskliertglyedllefvknsekvvlGtCaGlills 82
                                       a+k++++e+   +  + +e+l + d++iiPGG s       + ++ +  ++++l e ++ + k++lG C G+ +l 
  gi|330506495|ref|YP_004382923.1| 19 VAVKEVGMEGeifRWNRPEEELSGFDGFIIPGGFSYQdrvrAGAVASKEPVLKALNEEAALG-KPILGICNGFQILV 94
                                      567777777744333456789************99642222668999999********9999.*********96664 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                                       EEE-.TTTCEEEEECTT.EEEEEEETTEEEESS-GG CS
                               SNO 136 eeilddeavkvlyeldg.eivvakqkkilatsfhPe 170
                                        +++d+  v+v   ++    ++   +++l++  hPe
  gi|330506495|ref|YP_004382923.1| 194 GRVIDEFPVNVNGSTESiAAICNPEGNVLGMMPHPE 229
                                       444444444444444422223333567777777777 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.2e-06    0.0065      97     120 ..      72      94 ..      34     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-06
                     Peptidase_C26  97 LiraalergvPilgiCrGlqllnv 120
                                        ++++ + g+PilgiC G+q+l v
  gi|330506495|ref|YP_004382923.1|  72 ALNEEAALGKPILGICNGFQIL-V 94 
                                       45677889*************9.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1811.17
//
Query:       gi|330506496|ref|YP_004382924.1|  [L=777]
Description: phosphoribosylformylglycinamidine synthase II [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-39  134.0   0.2    3.4e-19   69.5   0.1    2.5  2  AIRS_C          AIR synthase related protein, C-terminal doma
    1.6e-32  112.0   1.2    1.7e-15   57.5   0.3    2.7  2  AIRS            AIR synthase related protein, N-terminal doma
    1.8e-13   50.8   0.0    4.7e-13   49.5   0.0    1.8  2  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0     1e-20   6.2e-17       4     153 ..     217     378 ..     215     381 .. 0.82
   2 !   69.5   0.1   5.6e-23   3.4e-19       2     154 ..     602     750 ..     601     752 .. 0.88

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1e-20
                                       EEEEEEET...SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH...HTTECEEEE--TTHHHH CS
                            AIRS_C   4 dvliltgs...lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal...kglvkaahDvTgGGLlg 74 
                                       dv+++ ++   +Glgg+++++ +   e+e++++ avq+ d++l++ l +++  l ++   +g   +++D++gGG+++
  gi|330506496|ref|YP_004382924.1| 217 DVILVGKPtdaSGLGGVTFASEALREEDEETNRGAVQIPDPFLKNVLFKANSDLFRMvreSGIEIGFKDLGGGGFTC 293
                                       78889999**********7776655555555555*************************8777789*********** PP

                                       HHHHHHHTTTEEEEEECGTHHHHHHHH.HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHH........HTTCCCEEEE CS
                            AIRS_C  75 alaemapasgvgaeidldkvpifdele.splemllsensGrllvavppeeadavlaile........eeglpeaavI 142
                                       a++em +a+g+g+eidld  +  + +   p+ + ++e+++r l+++p+e ++++l+i +         eg   a+v+
  gi|330506496|ref|YP_004382924.1| 294 ATSEMGAAGGFGMEIDLD--EMHKAADfPPEVLSIAETQERFLIIAPEELREKILNIYNedwdlpnvYEGA-RASVV 367
                                       ******************..4444444366677777********************999544444433444.68888 PP

                                       EEEEESSSEEE CS
                            AIRS_C 143 Gevtakeelsv 153
                                       G++  +++  v
  gi|330506496|ref|YP_004382924.1| 368 GKINTGDRFVV 378
                                       88888877666 PP

  == domain 2  score: 69.5 bits;  conditional E-value: 5.6e-23
                                       TTEEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHH CS
                            AIRS_C   2 pGdvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgal 76 
                                       +G  l+l+g+  + lgg+ ++    ++  + ++     ++   le+ +iy++  ++ + gl+ aahD+++GGL+ ++
  gi|330506496|ref|YP_004382924.1| 602 AGEELYLIGPrfDELGGSEYYQTILGVMGANVP-----RVRFDLERSMIYAVIDAIDE-GLIAAAHDISNGGLAATA 672
                                       799****************99987777777766.....*******************8.****************** PP

                                       HHHH..HTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSE CS
                            AIRS_C  77 aema..pasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeel 151
                                       +ema  + +++g+e+dld v   d      ++l+se+sG ll a ++ +++++ ++l++++l+  a IG+vtak++ 
  gi|330506496|ref|YP_004382924.1| 673 MEMAvtRPAKFGLELDLDGVVCGDLDLRTDKLLFSESSGFLLEA-KAGKEKRLEELLKSYDLL-PAKIGRVTAKRRI 747
                                       ***9554589********88888877788999999999976555.666666***********6.89********998 PP

                                       EEE CS
                            AIRS_C 152 svi 154
                                       +++
  gi|330506496|ref|YP_004382924.1| 748 RIT 750
                                       875 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.3   2.8e-19   1.7e-15       4      94 .]      92     197 ..      75     197 .. 0.93
   2 !   52.4   0.0   1.1e-17   6.4e-14       2      94 .]     460     588 ..     459     588 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 2.8e-19
                                       EEEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC............HHHHHHHHHHHHHHH CS
                              AIRS   4 avvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp............wleevvrglaeaaee 68 
                                       +vv++ +shn+p+ + p ++ +a++++++++D+ +mGA+ +a  + l ++             +e+vv+g+ +++++
  gi|330506496|ref|YP_004382924.1|  92 CVVISHESHNHPSQILPNEG-AATGIGGIVRDVNCMGATVVATADPLRFGdpfgpkankvrwVAEGVVDGIWQYGNA 167
                                       369*****************.****************************************88899*********** PP

                                       TT-EEEEEEEEEESS....EEEEEEEEEEE CS
                              AIRS  69 lgvplvgGdtsfsne....ptisvtavGlv 94 
                                       lgvp + Gd+ fs++    ++++v+ +G+v
  gi|330506496|ref|YP_004382924.1| 168 LGVPNIAGDVVFSESfddnCLVNVVSLGIV 197
                                       ************98899999*******997 PP

  == domain 2  score: 52.4 bits;  conditional E-value: 1.1e-17
                                       SSE...........EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHH CS
                              AIRS   2 Daa...........vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleev 58 
                                       Da+           v++++ds++ +  ++p+ + Ga++va++++++aa GA+P  l+++l+ +         +++e 
  gi|330506496|ref|YP_004382924.1| 460 DAGliapvrgekfgVALAVDSNPFYGRISPYWG-GATSVAEAMRNVAAIGATPATLTDCLNYGnpekpeafwEFREG 535
                                       56644444444444699****************.**************************************9**** PP

                                       HHHHHHHHHHTT-..........EEEEEEEEEESS.......EEEEEEEEEEE CS
                              AIRS  59 vrglaeaaeelgv..........plvgGdtsfsne.......ptisvtavGlv 94 
                                       v+glae ++ l            p+v+G++sf+ne       p++++++vG++
  gi|330506496|ref|YP_004382924.1| 536 VKGLAESCKNLWLkdykderipvPIVSGNVSFYNEspqgsvdPSPVIACVGII 588
                                       *******8776544444455555**********999***************86 PP

>> FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransferase linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   7.9e-17   4.7e-13       8      50 .]      18      57 ..      11      57 .. 0.94
   2 ?   -3.8   0.0         3   1.8e+04       9      21 ..     305     317 ..     304     319 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 7.9e-17
                    FGAR-AT_linker  8 lglaLsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrHK 50
                                       g ++s +E + ++++   lgr+Pt +El+++ ++wSEHC++K
  gi|330506496|ref|YP_004382924.1| 18 AGIGMSVDEARSIAQV---LGRDPTLTELFCYDAMWSEHCSYK 57
                                      689*************...9**********************9 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3
                    FGAR-AT_linker   9 glaLsdeEidylq 21 
                                       g+ ++++E+++ +
  gi|330506496|ref|YP_004382924.1| 305 GMEIDLDEMHKAA 317
                                       688899**99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (777 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 5081.47
//
Query:       gi|330506497|ref|YP_004382925.1|  [L=93]
Description: hypothetical protein MCON_0210 [Methanosaeta concilii GP6]
Scores for 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   34.4   2.3    2.4e-08   34.1   2.3    1.2  1  2TM       2TM domain


Domain annotation for each model (and alignments):
>> 2TM  2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   2.3   1.4e-12   2.4e-08       7      54 ..      18      72 ..      13      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.4e-12
                               2TM  7 vkeikgFyrhlvvYlivniflilinl.......gsswf...lwpilfWgiglllhalk 54
                                      +++ k F+ h+++Yl+vni+ +++n+           +   ++  ++Wgi +++h++ 
  gi|330506497|ref|YP_004382925.1| 18 ADQMKLFKLHIAIYLVVNIIWLILNMmgyikidP---AlamWYSPVGWGILVIVHYWF 72
                                      578999*************999999887776641...133356889***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 646.35
//
Query:       gi|330506498|ref|YP_004382926.1|  [L=224]
Description: hypothetical protein MCON_0211 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.8   2.3       0.11   12.9   0.8    1.8  2  PEMT      Phospholipid methyltransferase


Domain annotation for each model (and alignments):
>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.19   3.5e+03      70      86 ..      90     105 ..      70     119 .. 0.64
   2 ?   12.9   0.8   6.3e-06      0.11      41     103 ..     136     195 ..      96     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.19
                              PEMT  70 tgsaaglllallvllvy 86 
                                         s++ ++la+ +++v+
  gi|330506498|ref|YP_004382926.1|  90 LPSPW-IWLAFAAQIVV 105
                                       45666.55555555554 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 6.3e-06
                              PEMT  41 klvtsGiYrylnnPeyvgstlgflGlaLitgsaaglllallvllvylialkfvEephlakiYg 103
                                       +l  +GiY ++++P  + ++l ++ + ++t++++ + l+++++l++   +  +E + l k++g
  gi|330506498|ref|YP_004382926.1| 136 ALGIRGIYCWIRDPFLLSGFLLIWLTPFMTENLLLVYLLTTAYLFM-GSVH-WESR-LIKQFG 195
                                       67789**************************999444444333333.2233.5544.445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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: 1572.11
//
Query:       gi|330506499|ref|YP_004382927.1|  [L=163]
Description: pyridoxamine 5'-phosphate oxidase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-20   73.8   0.0    1.5e-20   73.7   0.0    1.1  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    6.3e-05   23.1   0.0    9.4e-05   22.5   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.0   1.6e-24   1.5e-20       2     115 ..      10     118 ..       9     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.6e-24
                                       HHHHHHHHHC-SEEEEEEEETTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGEE CS
                      Pyridox_ox_2   2 reeilalLdegevgrlafvddgepvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfnsl 77 
                                       ++e+++l++e+ ++r+af+ +++p++ P+ yv+dg+ +yf ++k+++++ ++r++p v+v+v++   + ++ s    
  gi|330506499|ref|YP_004382927.1|  10 KQEYDRLIEEEFICRIAFNGESHPHVAPFLYVFDGKFMYFLSTKYGKKVLHFRKNPaVTVEVER---YSPDLS---- 79 
                                       79***************************************************88889999999...444666.... PP

                                       EEEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTT.GGC CS
                      Pyridox_ox_2  78 nyrSVvvrGraeevtdeeekaealellvekivpgr.wen 115
                                       ++ +V + Gr+ ev+d+e k+ ++e++ve i+ ++ + n
  gi|330506499|ref|YP_004382927.1|  80 SFSFVALPGRLVEVEDPETKSLVRERFVELIQKKNlSSN 118
                                       5889***************************88775444 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     1e-08   9.4e-05       3      87 ..      11      96 ..       9      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1e-08
                                      HHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT....GSEEEEE CS
                    Putative_PNPOx  3 eelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde....lgrgvri 77
                                      +e+  +++e+ ++++A    + +P+v p l++ +dg+  ++f + +  +k+ + ++np v++ +  ++    +   v +
  gi|330506499|ref|YP_004382927.1| 11 QEYDRLIEEEFICRIAFN-GESHPHVAPFLYV-FDGK-FMYFLSTKYGKKVLHFRKNPAVTVEVERYSpdlsSFSFVAL 86
                                      688899999999999976.7788*********.7777.7***********************99888887887788888 PP

                                      EEEEEEESCH CS
                    Putative_PNPOx 78 eGtaelvsdg 87
                                       G+   v+d+
  gi|330506499|ref|YP_004382927.1| 87 PGRLVEVEDP 96
                                      8887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1248.95
//
Query:       gi|330506500|ref|YP_004382928.1|  [L=445]
Description: deoxyribodipyrimidine photo-lyase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-29  102.0   0.0    5.4e-29  101.3   0.0    1.3  1  DNA_photolyase  DNA photolyase


Domain annotation for each model (and alignments):
>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.0     3e-33   5.4e-29       2     162 ..      22     180 ..      21     187 .. 0.93

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 3e-33
                                       EEEESS---STT-HHHHHH....HCTTSEEEEEEEE-HHHHTCGS-CHHHHHHHHHHHHHHHHHHHHTT--EEEEES CS
                    DNA_photolyase   2 lvWfrrDlRlhDNpALaaA....aasgepvipvfvldpekahklrvgaarvdfllesLadLdeeLrelgirLvvrrg 74 
                                        +W++r++R++DN+ L  A    +++++p++++f+++p+ + +    + + +f+l++L++ +++L+el+i+L++++g
  gi|330506500|ref|YP_004382928.1|  22 FYWMSREQRVADNWPLLFAqelaIREKSPLAVLFCISPQ-FLEA--TSSQYKFMLKGLEEVETDLAELNIPLYLLSG 95 
                                       69***************6655559999************.6666..899999************************* PP

                                       SHHHHHHHHHHHCTECEEEEE---SHHHHHHHHHHHHHHHHCTSEEEEE--SSSS-HHHHHTTTSSSHSSHHHHHHC CS
                    DNA_photolyase  75 dpadvlpelakelgasavvanreyepdererdeavkealrkagievesfddhtlvepgevktkkgkpykvFtpfrkr 151
                                       dpa+++p+++++++a  +v ++++ + +  +++ +++ ++   i++ ++d+h++v+++++  k++ ++  F+p+++r
  gi|330506500|ref|YP_004382928.1|  96 DPAKEIPQFLQSHEAGILVSDFSPLRIKMIWQRSIAKEVN---IPCYEVDGHNIVPCWQASLKQEWAAYSFRPKIHR 169
                                       **********************************999986...*****************9999999999******* PP

                                       HHHHHCS-TTS CS
                    DNA_photolyase 152 wlkelkeplpa 162
                                        l+e+++++pa
  gi|330506500|ref|YP_004382928.1| 170 LLDEYLTDFPA 180
                                       ***99988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 3405.38
//
Query:       gi|330506501|ref|YP_004382929.1|  [L=495]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete 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   87.1   0.0    1.6e-24   86.0   0.0    1.6  1  Transposase_20  Transposase IS116/IS110/IS902 family
    1.3e-22   80.3   0.2    4.7e-22   78.5   0.0    1.9  2  DEDD_Tnp_IS110  Transposase
     0.0073   16.1   0.1      0.018   14.8   0.1    1.7  1  YfkB            YfkB-like domain


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.0   2.7e-28   1.6e-24       2      86 ..     305     390 ..     304     391 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 2.7e-28
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaai.r 77 
                                       ++++sipGi ++  +++l+eig+ r f++++qla+++Gl+p en+S++kkr+ +i+krG++++R +L+eaA++++  
  gi|330506501|ref|YP_004382929.1| 305 AIVMSIPGIAFISGSVILSEIGNYRDFQTPEQLAKWCGLNPGENESAGKKRKCGITKRGSKYIRVVLVEAAQTIAnM 381
                                       589********************************************************************999955 PP

                    Transposase_20  78 anpelrayy 86 
                                       +n  l ++y
  gi|330506501|ref|YP_004382929.1| 382 KNTGLSRFY 390
                                       569999888 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   7.9e-26   4.7e-22       1     151 [.      65     206 ..      65     208 .. 0.93
   2 ?   -1.8   0.0      0.42   2.5e+03      30      70 ..     382     422 ..     369     425 .. 0.62

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 7.9e-26
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G Dv+kd ++a+++  ++   ++e++ +++++l+++ ++ +a+ ++ +v++eatg y+ +++ + l++ i+++v n
  gi|330506501|ref|YP_004382929.1|  65 CGADVHKDLIVATITG-DEVPSIRENFGTTKSELDRFRNW-LADNKCEQVAFEATGVYWIPIYDV-LSRTIDTIVAN 138
                                       799******9999984.66666778999999999999999.88999*************999998.6789******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLd 151
                                       pl++k +      ++K+D+kD+k IA l +  ++++ +++ +++ +eLr+ltr+r+ +vk+rt++knr+++ L 
  gi|330506501|ref|YP_004382929.1| 139 PLQIKSIP-----NDKSDSKDSKRIATLCL-NNQIKRSRVFSDEDRELRNLTRARSGYVKTRTQFKNRIHKYLS 206
                                       ******95.....8****************.****************************************996 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.42
                    DEDD_Tnp_IS110  30 deeglealleklaakagevlvvveatghygallvaflleag 70 
                                       +  gl+++ ++l++k+++   +v    +   l++++l +++
  gi|330506501|ref|YP_004382929.1| 382 KNTGLSRFYKRLSKKKEHNVAIVAVARKLICLIYHLLINQE 422
                                       44578888888666666655556666666666666666665 PP

>> YfkB  YfkB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   3.1e-06     0.018      91     150 ..     373     433 ..     362     434 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-06
                              YfkB  91 gdeealgnikeekledvfekwke.sklakslnchcpavkclGpnvlvknayykevdfkkrk 150
                                         +++++n+k++ l+  +++ ++ ++ +  +     ++ cl   +l+++ +y+evd +krk
  gi|330506501|ref|YP_004382929.1| 373 EAAQTIANMKNTGLSRFYKRLSKkKEHNVAIVAVARKLICLIYHLLINQEFYQEVDCRKRK 433
                                       56789***************9873567788999999**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.23s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 3789.01
//
Query:       gi|330506502|ref|YP_004382930.1|  [L=339]
Description: hypothetical protein MCON_0215 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-07   31.4   0.0    0.00034   20.3   0.0    2.9  3  TM1586_NiRdase  Putative TM nitroreductase
    7.7e-06   26.1   1.9       0.54   10.3   0.0    3.7  3  Nitroreductase  Nitroreductase family


Domain annotation for each model (and alignments):
>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.8e-08   0.00034     156     195 ..      21      59 ..      13      68 .. 0.83
   2 !    7.1   0.1    0.0004       3.6       2      34 ..     126     159 ..     125     186 .. 0.78
   3 ?   -0.3   0.0     0.076   6.8e+02      74      98 ..     258     284 ..     234     287 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.8e-08
                                       S-HHHHHHHHHHHTS--GGG----EEE.E-SSEE.....E CS
                    TM1586_NiRdase 156 lpewfkeileaarlAPsAlNqqpwrfelkdddeikikasv 195
                                       l +++k +l+ a lAPs  N+qpw++ +++ +e++++a+ 
  gi|330506502|ref|YP_004382930.1|  21 LCDQIKGLLKYAVLAPSGPNTQPWKLAIDG-NEVSVIADF 59 
                                       568999*********************888.699987655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0004
                                       HHHHHHH--B---.B--S---HHHHHHHHH---- CS
                    TM1586_NiRdase   2 lyeaiekRhsvRk.Ykdealeeelleelkeaiee 34 
                                       l+ +i+ Rh+ Rk ++++a+e+++l elk+++++
  gi|330506502|ref|YP_004382930.1| 126 LFSQITRRHTNRKeFEKRAIEDAKLRELKACVKR 159
                                       7889******9966************99987754 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.076
                                       --SSHHHHH..HHHHHHHHHHHHHHHT CS
                    TM1586_NiRdase  74 gekkedlee..kaGYygeqlvLkltal 98 
                                       + +++d+++  kaG++ e l Lk+t+ 
  gi|330506502|ref|YP_004382930.1| 258 STDQDDMMTwlKAGFLFEILFLKATEM 284
                                       4444444433399*********99975 PP

>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0     6e-05      0.54      18      41 ..      23      46 ..      22      62 .. 0.89
   2 !    4.5   0.0    0.0037        33     111     136 ..      69      94 ..      52     112 .. 0.89
   3 !    8.4   0.2   0.00023         2       1     170 []     130     321 ..     130     321 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6e-05
                                      HHHHHHHHHHHTS--GGG---EEE CS
                    Nitroreductase 18 eelekileaarraPsagnlqpwrf 41
                                      ++++ +l+ a  aPs+ n+qpw++
  gi|330506502|ref|YP_004382930.1| 23 DQIKGLLKYAVLAPSGPNTQPWKL 46
                                      578899****************97 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0037
                                       HHHHHHHHHHHHHHHHHHHHHHTT-E CS
                    Nitroreductase 111 ayryalldagaaaqnllLaAtalGlg 136
                                       ++r+ +l++g+ + n+l+aA+ +G+g
  gi|330506502|ref|YP_004382930.1|  69 SNRTLYLSHGCLLANILMAAEHFGFG 94 
                                       5678899*****************99 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00023
                                       HHH--B--.-B-S----HHHHHHHHHHH...............HTS--GGG---EEEEEE.-CCCHHHHHHHHHHHH CS
                    Nitroreductase   1 irkRrSiR.kFddepvpkeelekileaa...............rraPsagnlqpwrfvvvqdkelryklaeaalell 61 
                                       i +R++ R +F+++ +++++l+++ ++                  a s   +q+ ++ +  +k+ r++la ++++++
  gi|330506502|ref|YP_004382930.1| 130 ITRRHTNRkEFEKRAIEDAKLRELKACVkrdgfdlnilideagKSAMSEILAQSHKIQLG-NKAFRKELASWVRSNT 205
                                       678999999999999999999999999977777777766666555777777777777777.9999999999999999 PP

                                       HHHHTT-SS-GGGGGG.................HHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHH CS
                    Nitroreductase  62 lkaeaqaelaqryrke.................elklkaqkalagapvlivivatldkserkaaerayryalldaga 121
                                         ++  +   +    +                 ++   + + ++ +p++ v+          + +++++ ++l ag 
  gi|330506502|ref|YP_004382930.1| 206 GGEKDGLPGYSFGYSDfqsyfgafvfgtfdmstSRARVETAYMKASPAVGVL----------STDQDDMMTWLKAGF 272
                                       9999888888887777899999999999999887777777778888888888..........999************ PP

                                       HHHHHHHHHHHTT-EEEEE-GGG.....GGHHHHHHHHT-S..SEEEEEEEEE- CS
                    Nitroreductase 122 aaqnllLaAtalGlgscpiggfd.....eaaeevrkllglpdeeeivvliavGy 170
                                         + l L+At++++ +   +++      ++   ++++l ++    +++li++Gy
  gi|330506502|ref|YP_004382930.1| 273 LFEILFLKATEMDVRFDLFSQPIaipelRE--DMARILKVK---YPQLLIRMGY 321
                                       **********99988766666664442333..488888888...5778888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2452.86
//
Query:       gi|330506503|ref|YP_004382931.1|  [L=48]
Description: hypothetical protein MCON_0216 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 381.23
//
Query:       gi|330506504|ref|YP_004382932.1|  [L=48]
Description: hypothetical protein MCON_0217 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 397.95
//
Query:       gi|330506505|ref|YP_004382933.1|  [L=74]
Description: hypothetical protein MCON_0218 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 618.99
//
Query:       gi|330506506|ref|YP_004382934.1|  [L=156]
Description: hypothetical protein MCON_0219 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-13   48.3   0.0    1.3e-12   47.9   0.0    1.1  1  F420H2_quin_red  F420H(2)-dependent quinone reductase


Domain annotation for each model (and alignments):
>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   7.5e-17   1.3e-12       8     103 ..      22     113 ..      16     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 7.5e-17
                                       XXXXXXXXXTTXTTS---EEEEEE-TTT-SEEEEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEEETTE CS
                   F420H2_quin_red   8 iyrrtegkvgrrlegvpvllLtttGrktgkprktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevqvgak 84 
                                       ++r+ +  + + + g ++++++t+Grktgk r tp++ +  g+s        G   + +wylN+ anP+vev     
  gi|330506506|ref|YP_004382934.1|  22 FQRNLGKYISNPIIG-NIMVIKTRGRKTGKTRFTPVYHALIGESIYCYQ---GKHLKGQWYLNVLANPDVEVLLPSG 94 
                                       445555577777777.899************************977643...45579******************** PP

                                       EEEEEEEE--HHHHHHHHH CS
                   F420H2_quin_red  85 kldvtAreveddekarlwk 103
                                       +l++ A+ev+d++ a +  
  gi|330506506|ref|YP_004382934.1|  95 TLKGIAEEVSDPKEAAYAI 113
                                       ***********99998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1377.37
//
Query:       gi|330506507|ref|YP_004382935.1|  [L=103]
Description: hypothetical protein MCON_0221 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00056   19.6   0.0    0.00064   19.5   0.0    1.2  1  SoxZ             Sulphur oxidation protein SoxZ
  ------ inclusion threshold ------
      0.021   14.8   0.5      0.029   14.4   0.5    1.1  1  Mucin_bdg        Putative mucin or carbohydrate-binding modul
       0.06   14.0   0.0      0.071   13.7   0.0    1.1  1  Desulfoferrodox  Desulfoferrodoxin


Domain annotation for each model (and alignments):
>> SoxZ  Sulphur oxidation protein SoxZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.1e-07   0.00064      30      83 ..      35      88 ..      13     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-07
                                      .S-B---B-EEEEEEEETTEEEEEE---SS--SS-EEEEEEE.--S-EEEEEEE CS
                              SoxZ 30 tgklipahfIqevevtlngkevleaelgiaiSknPylrfkfkgakkgdtlkvtw 83
                                      +  + p h+++ev v+ ng +vl+ e    +++n +   +  +a++gd lk+t+
  gi|330506507|ref|YP_004382935.1| 35 HTSTNPSHYVREVVVQKNGDDVLRKEYANQTAANTFSYYYQINATAGDILKATA 88
                                      466789****************************76665555599999999887 PP

>> Mucin_bdg  Putative mucin or carbohydrate-binding module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.5   4.8e-06     0.029      15      79 ..      22      85 ..      13      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-06
                         Mucin_bdg 15 ldqakkklnvtvtskkphyyfedetYasievkdkdGneklrkeieG.tekqtae..keisfkeGdvlk 79
                                       d+++++ln+tvt++ ++ +     Y++  v +k+G ++lrke    t ++t     +i+ + Gd+lk
  gi|330506507|ref|YP_004382935.1| 22 YDNTNQTLNATVTHTSTNPSH----YVREVVVQKNGDDVLRKEYANqTAANTFSyyYQINATAGDILK 85
                                      388999999999999888776....99999*************99953333333699********997 PP

>> Desulfoferrodox  Desulfoferrodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05     0.071      34      91 ..      33      94 ..      12      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                                      SS--BS.SSS-EEEEEEEEEETTSSEEEE-TBS...ESEEEEEEEESSSEEEEEEEEETTTE CS
                   Desulfoferrodox 34 ipHpne.eeHyIewielyleeegekrvelsaed...epevtftvklkkekklvalsyCnlHG 91
                                      ++H ++  +Hy++ + +  + ++  r+e+++++   + + + +++++    l+a++yC + G
  gi|330506507|ref|YP_004382935.1| 33 VTHTSTnPSHYVREVVVQKNGDDVLRKEYANQTaanTFSYYYQINATAGDILKATAYCSISG 94
                                      667665169****999999888888999988884323556778888888**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 872.84
//
Query:       gi|330506508|ref|YP_004382936.1|  [L=150]
Description: hypothetical protein MCON_0222 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-25   88.1   0.1    7.8e-25   86.8   0.0    1.7  2  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    1.5e-16   60.1   0.2    2.6e-16   59.3   0.2    1.3  1  PUA       PUA domain
  ------ inclusion threshold ------
      0.023   15.0   0.0      0.034   14.4   0.0    1.3  1  UPF0113   UPF0113 PUA domain
      0.049   14.1   0.0      0.072   13.5   0.0    1.3  1  Tex_YqgF  Tex protein YqgF-like domain
      0.068   13.2   0.1       0.11   12.5   0.1    1.4  1  DUF2388   Protein of unknown function (DUF2388)
       0.08   12.8   0.0       0.14   11.9   0.0    1.4  1  PUA_3     PUA-like domain


Domain annotation for each model (and alignments):
>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.8   0.0   2.6e-28   7.8e-25       2      71 .]       4      73 ..       3      73 .. 0.96
   2 ?   -1.7   0.0       1.1   3.4e+03      40      54 ..     107     121 ..      95     126 .. 0.62

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 2.6e-28
                            TGT_C2  2 rlraiadYqFGagagdaLfpedvtitrsatgrirqvlvdgerlatlraqdgrltLsleGarrlheslppP 71
                                      r r+iadYqFG+g g+aLfp+  t  +s+t r+r++++++er+at+ra+d++ltLs+ Ga+rlh+ +  P
  gi|330506508|ref|YP_004382936.1|  4 RARTIADYQFGRGSGSALFPDGTTYSLSKTRRLRYLYWEEERVATVRARDNLLTLSMIGAKRLHDLFCSP 73
                                      679*************************************************************998665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                            TGT_C2  40 dgerlatlraqdgrl 54 
                                        ge ++ +  qd +l
  gi|330506508|ref|YP_004382936.1| 107 SGEEVLVVDSQDRLL 121
                                       477777777777776 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.2   8.8e-20   2.6e-16       2      71 ..      76     145 ..      75     147 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 8.8e-20
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveie 71 
                                       rvv  d A+ ++++g +L+a  v+ v+ +++ g++V +vd +++l+a G a +  ee+++ik+g +v+ +
  gi|330506508|ref|YP_004382936.1|  76 RVVASDDAAPFIAKGGNLFARHVIAVDPEIRSGEEVLVVDSQDRLLATGTAVLAPEEMMQIKRGLAVQAR 145
                                       79999*************************************************************9976 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.1e-05     0.034      15      51 ..      90     126 ..      77     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                           UPF0113  15 GrdvlkesilkitesvkenqvvvVlnengeplGiGki 51 
                                       G +++  +++ +++++++++ v+V++ ++++l+ G +
  gi|330506508|ref|YP_004382936.1|  90 GGNLFARHVIAVDPEIRSGEEVLVVDSQDRLLATGTA 126
                                       899*****************************99987 PP

>> Tex_YqgF  Tex protein YqgF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.4e-05     0.072       2      35 ..      97     130 ..      96     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.4e-05
                                       -EEEEE--STT-EEEEEE-TTS-EEEEEEE--ST CS
                          Tex_YqgF   2 vvlglDPgyrtGcKlavvdetgkvletaviyphe 35 
                                        v+++DP +r G  + vvd++ ++l+t +  +  
  gi|330506508|ref|YP_004382936.1|  97 HVIAVDPEIRSGEEVLVVDSQDRLLATGTAVLAP 130
                                       699**********************998876653 PP

>> DUF2388  Protein of unknown function (DUF2388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   3.6e-05      0.11      20      65 ..      75     122 ..      60     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
                           DUF2388  20 lvlaArdDAasFVASdGairGarLEaaLqelRsenpel..qasDleLA 65 
                                       l + A dDAa F+A  G++ + ++ a   e+Rs +  l  +++D+ LA
  gi|330506508|ref|YP_004382936.1|  75 LRVVASDDAAPFIAKGGNLFARHVIAVDPEIRSGEEVLvvDSQDRLLA 122
                                       55779*************999888888888888777665566677777 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.8e-05      0.14      18      50 ..      93     125 ..      84     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.8e-05
                             PUA_3  18 vfsneiasvegeledGdvVdvfsekgkflGtGy 50 
                                       +f+  +  v+ e+++G+ V v++++++ l+tG 
  gi|330506508|ref|YP_004382936.1|  93 LFARHVIAVDPEIRSGEEVLVVDSQDRLLATGT 125
                                       577788889999*******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.48
# Mc/sec: 942.74
//
Query:       gi|330506509|ref|YP_004382937.1|  [L=414]
Description: serine hydroxymethyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.1e-164  547.9   0.2   1.3e-164  547.6   0.2    1.0  1  SHMT             Serine hydroxymethyltransferase
    4.3e-08   32.7   0.0      6e-08   32.3   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    5.3e-07   29.2   0.2    2.3e-06   27.1   0.1    1.9  2  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.085   12.1   0.1       0.13   11.5   0.1    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


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 !  547.6   0.2  2.8e-168  1.3e-164       3     399 .]       6     380 ..       4     380 .. 0.99

  Alignments for each domain:
  == domain 1  score: 547.6 bits;  conditional E-value: 2.8e-168
                                       HHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHC CS
                              SHMT   3 esdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelf 79 
                                        +dpe+a +i++e erq+++i liasenfts+av+ea+  v+tnkyaeGyPGkryy G+  vd +e+la++r+ +lf
  gi|330506509|ref|YP_004382937.1|   6 IVDPEIAAAIQSELERQRNNIILIASENFTSRAVMEAQSCVMTNKYAEGYPGKRYYRGTGCVDLAENLARERCIKLF 82 
                                       58*************************************************************************** PP

                                       T-STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB CS
                              SHMT  80 kldpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketgli 156
                                       +++    +vnvqp+sG+qan+a y a+l+ gd+i+g++la+GGhl+hG++v++     s+k++++v+y+v++et+++
  gi|330506509|ref|YP_004382937.1|  83 GAE----HVNVQPHSGTQANMAAYFAVLNAGDTIMGMNLAHGGHLSHGSPVNF-----SGKMYKIVPYNVSRETEML 150
                                       ***....**********************************************.....******************* PP

                                       -HHHHHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESSST CS
                              SHMT 157 dydelekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttthkt 233
                                       dy e+   a++ +P+liv G+s+y+r+id++ +reiad+vga +++d+ahiaG+ a g +psP++yad+vtttthkt
  gi|330506509|ref|YP_004382937.1| 151 DYSEMADIARKSRPQLIVVGASSYPRTIDFKAVREIADDVGALVMADIAHIAGMCAVGAHPSPVPYADIVTTTTHKT 227
                                       ***************************************************************************** PP

                                       T-S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHH CS
                              SHMT 234 lrGprgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknak 310
                                       lrGprg++il++              eel++ i+ +vfPg+qGGP++  iaakava+keal+pefk+yq qv++na+
  gi|330506509|ref|YP_004382937.1| 228 LRGPRGAIILCK--------------EELASAIDRSVFPGTQGGPFMNSIAAKAVAFKEALTPEFKEYQFQVIRNAR 290
                                       ************..............89************************************************* PP

                                       HHHHHHHHTT-EEGGGS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS.STTTT-SEEEEESHHHHHTT CS
                              SHMT 311 alaealkekgyklvsgGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgd.ksalvtsGlrlGtpaltsrg 386
                                       alae l ++ ++lvsgGtdnhl+lv+l ++g++Gk a++ le++ it nkn +P+d   ++vtsG+r+Gtpa+t+rg
  gi|330506509|ref|YP_004382937.1| 291 ALAERLLKNDFDLVSGGTDNHLLLVKLLKEGITGKVADETLERAGITLNKNMIPFDpATPFVTSGIRIGTPAMTTRG 367
                                       ***************************************************************************** PP

                                       --HHHHHHHHHHH CS
                              SHMT 387 fkeedlekvakfi 399
                                       ++e+++ ++a++i
  gi|330506509|ref|YP_004382937.1| 368 MQEKQMAQIADMI 380
                                       **********987 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 !   32.3   0.0   1.3e-11     6e-08      31     356 ..      51     368 ..      24     371 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.3e-11
                                       HHHHTSTTST-BTTHHHHHHHHHH.....HHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS CS
                     Aminotran_1_2  31 alaggtlneygpidglpeleeala.....kflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdpt 102
                                        ++g + ++y   +g  +l e+la     k++g       ++  +v+  sG++a+ +a +++l  n+gd i   ++ 
  gi|330506509|ref|YP_004382937.1|  51 YAEGYPGKRYYRGTGCVDLAENLArerciKLFG------AEHV-NVQPHSGTQANMAAYFAVL--NAGDTIMGMNLA 118
                                       466666677777777777777777776669999......6666.*********9999888888..5*********99 PP

                                       -THH.....HHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHH CS
                     Aminotran_1_2 103 yasy.....knilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleelekll 174
                                       ++ +       ++     ++v+y+++  e+  ld  ++ +  ++      ++++i+v   + P    ++ + ++++ 
  gi|330506509|ref|YP_004382937.1| 119 HGGHlshgsPVNFSGKMYKIVPYNVS-RETEMLDYSEMADIARKS-----RPQLIVVGASSYPRT--IDFKAVREI- 186
                                       98773333335666677778888854.577799999999977764.....668999998888865..455678888. PP

                                       HHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTT.SSGGG-EEEEEEEHHHHHHHHHHHHHH CS
                     Aminotran_1_2 175 dlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKaf.GlaGeRvGyilgnaavvsqlrklsrpf 250
                                         a+  ++l++ D a+ +++      v +++   ++ + +++++  K + G  G   ++il++++++s++ + + p+
  gi|330506509|ref|YP_004382937.1| 187 --ADDVGALVMADIAHIAGMCA----VGAHPSPVPYAD-IVTTTTHKTLrGPRG---AIILCKEELASAIDRSVFPG 253
                                       ..*******************8....334777778777.888888887635555...88999**********99999 PP

                                       TS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..TEEEECCSCSSEEEEEETHH.....CHHH CS
                     Aminotran_1_2 251 ls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael..glkvlasqsgmflltdlsae.....take 319
                                       +     +  ++a+a+  ++    e++e + +++++++ l ++L +   +l   + +++++l+ +l++      +++ 
  gi|330506509|ref|YP_004382937.1| 254 TQgGPFMNSIAAKAVAFKEALTPEFKEYQFQVIRNARALAERLLKNdfDLVSGGTDNHLLLVKLLKEGitgkvADET 330
                                       99888889999999999999999********************9985556666667888888777777777655555 PP

                                       HHHH..HHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHH CS
                     Aminotran_1_2 320 lskk..LleevgvyvtpgtsftvpgrlRitvAglteeel 356
                                       l ++   l++  +   p t+f  ++ +Ri  +++t+  +
  gi|330506509|ref|YP_004382937.1| 331 LERAgiTLNKNMIPFDPATPFV-TSGIRIGTPAMTTRGM 368
                                       5555654444244444444444.5559999999998766 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   5.1e-10   2.3e-06      38     241 ..      75     304 ..      35     346 .. 0.78
   2 ?   -2.0   0.0      0.37   1.7e+03     177     195 ..     365     383 ..     349     386 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 5.1e-10
                                       HHHHHHHTT-SEE.EEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT...TBE- CS
                   Beta_elim_lyase  38 edavaelfgkeaa.lfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea...Gkmd 110
                                        +++ +lfg+e++ +  ++Gt+An  ++ ++l+ g+ ++  + ah+     g ++ ++g + + ++ +       +d
  gi|330506509|ref|YP_004382937.1|  75 RERCIKLFGAEHVnVQPHSGTQANMAAYFAVLNAGDTIMGMNLAHGGHLSHGSPVNFSGKMYKIVPYNVSretEMLD 151
                                       3556669***98625788******************9999999**************99988877755443336677 PP

                                       HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHT CS
                   Beta_elim_lyase 111 lekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfs 187
                                         +++++ ++      +++li++          +      ++v++ia++ g  ++ D A +a  + ++g++++  + 
  gi|330506509|ref|YP_004382937.1| 152 YSEMADIARK-----SRPQLIVVGASSY-----P-RTIDFKAVREIADDVGALVMADIAHIAGMC-AVGAHPSP-VP 215
                                       7777766666.....6789998877665.....3.455689************************.78888875.68 PP

                                       TSSEEEEESSSTT--SS-EEEEE-HH.......................................HHHHHHHHHHHH CS
                   Beta_elim_lyase 188 yvDsvtmslkKdllanvGgvlafrddel...................................edylaerveqrkyl 229
                                       y+D+vt    K l  + G++++ +++ +                                   ++y  + ++ +++l
  gi|330506509|ref|YP_004382937.1| 216 YADIVTTTTHKTLRGPRGAIILCKEELAsaidrsvfpgtqggpfmnsiaakavafkealtpefKEYQFQVIRNARAL 292
                                       **************************8899**************977777777777777777755545666666777 PP

                                       T---SSTHHHHH CS
                   Beta_elim_lyase 230 ggglrqagvlaa 241
                                       +++l + ++  +
  gi|330506509|ref|YP_004382937.1| 293 AERLLKNDFDLV 304
                                       777766666555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.37
                                       HHTS-CHHHHTTSSEEEEE CS
                   Beta_elim_lyase 177 slgeivkemfsyvDsvtms 195
                                       + g + k+m++ +D++tm 
  gi|330506509|ref|YP_004382937.1| 365 TRGMQEKQMAQIADMITMV 383
                                       5567779999999999996 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.9e-05      0.13      44     152 ..      91     205 ..      66     264 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.9e-05
                                       ESSHHHHHHHHHHH.TTTTTT-EEEEESS...S-THHHHHHHHTT..-EEEEE-B-TTTSSB-GGGCGGG--TTE.. CS
                   DegT_DnrJ_EryC1  44 vssGtaAlhlaLra.lgvgpgdeVIvpsl...tFvatanavlelg..akpvfvDvdpdtynidpaaieaaitert.. 112
                                         sGt+A++ a+ a l++  gd++    l   + ++  ++v  +g  +k v+ +v ++t ++d ++++    + +  
  gi|330506509|ref|YP_004382937.1|  91 PHSGTQANMAAYFAvLNA--GDTIMGMNLahgGHLSHGSPVNFSGkmYKIVPYNVSRETEMLDYSEMADIARKSRpq 165
                                       567777777776663333..466654444111344445555555433688999999999999999998877777732 PP

                                       EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-E CS
                   DegT_DnrJ_EryC1 113 kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGat 152
                                         ++ +  y +  d++a+++ia++ g  v+ D Ah  G  
  gi|330506509|ref|YP_004382937.1| 166 LIVVGASSYPRTIDFKAVREIADDVGALVMADIAHIAGMC 205
                                       3344456677788**********************87754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 2880.58
//
Query:       gi|330506510|ref|YP_004382938.1|  [L=287]
Description: bifunctional protein FolD [Methanosaeta concilii GP6]
Scores for complete 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-65  217.1   0.9    1.2e-64  216.4   0.9    1.3  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
    2.2e-33  115.0   0.0    3.5e-33  114.3   0.0    1.3  1  THF_DHG_CYH      Tetrahydrofolate dehydrogenase/cyclohydrolas
  ------ inclusion threshold ------
      0.065   12.2   0.1      0.088   11.7   0.1    1.2  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil


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 !  216.4   0.9   2.1e-68   1.2e-64       1     159 [.     125     282 ..     125     283 .. 0.99

  Alignments for each domain:
  == domain 1  score: 216.4 bits;  conditional E-value: 2.1e-68
                                       SHHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHH CS
                     THF_DHG_CYH_C   1 hplnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeit 77 
                                       hp n+g l++g e l+pctp g++  l++ + +leg +vv+vG+sn+vgkpla+++l++natV+vch  t+dlae+t
  gi|330506510|ref|YP_004382938.1| 125 HPRNMGALLLGAERLVPCTPLGIIYALERLDKKLEGTEVVIVGHSNVVGKPLAAMMLNRNATVQVCHVFTRDLAEHT 201
                                       799************************************************************************** PP

                                       CCSSEEEE-SS-TT-B-GGGS-TT-EEEE---EEC-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHHHHHHHHHHH CS
                     THF_DHG_CYH_C  78 readivvvavGkpelikaemvkegavviDvGinrvekgklvGDvdfeevkevasaitPvpgGVGpmTvamllkntle 154
                                       r adi+vva+G+p+lik+emv++ga + DvGinrv ++k+vGDvd+eev+++a+aitPvpgGVGp+Tvamll++tl+
  gi|330506510|ref|YP_004382938.1| 202 RDADILVVAAGVPGLIKKEMVRPGAYIFDVGINRV-GDKTVGDVDYEEVSQIAGAITPVPGGVGPLTVAMLLRQTLN 277
                                       ***********************************.9**************************************** PP

                                       HHHCH CS
                     THF_DHG_CYH_C 155 aakrq 159
                                       a++ q
  gi|330506510|ref|YP_004382938.1| 278 ATEDQ 282
                                       99876 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 !  114.3   0.0   5.9e-37   3.5e-33       1     116 []       7     122 ..       7     122 .. 0.99

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 5.9e-37
                                       E--HHHHHHHHHHHHHHHHHHHHHHT---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHH CS
                       THF_DHG_CYH   1 lldGkalakeireelkeeveklkekgvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellkl 77 
                                       ++dGkala e+++e+ e+++kl +k + p+La++lvg++pas++Y+r k+ ac+++Gi+se + lpe+ +eee++++
  gi|330506510|ref|YP_004382938.1|   7 IIDGKALAGEVEAETLERAKKLANKAIVPGLATVLVGENPASQMYIRLKHSACSRAGIRSENVLLPESSTEEEIIAK 83 
                                       79*********************9999************************************************** PP

                                       HHHHHH-TT--EEEE-SS-STTS-HHHHHCCS-GGGBTT CS
                       THF_DHG_CYH  78 ieelneddsvdGilvqlPlpkhidekaileaispeKDVD 116
                                       ieeln +++++Gil+qlPlp  ++ ++++ +i peKDVD
  gi|330506510|ref|YP_004382938.1|  84 IEELNLREDINGILLQLPLPGGLNPQRAMMSILPEKDVD 122
                                       **************************************9 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 ?   11.7   0.1   1.5e-05     0.088     185     232 ..     195     241 ..     157     283 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.5e-05
                                       CSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB CS
                   OCD_Mu_crystall 185 kseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteL 232
                                        + +e   +adi+v + a    ++k+e+v pGa+i  vg ++ g++  
  gi|330506510|ref|YP_004382938.1| 195 RDLAEHTRDADILVVA-AGVPGLIKKEMVRPGAYIFDVGINRVGDKTV 241
                                       57789999****9965.4556899*****************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 00:00:00.43
# Mc/sec: 1993.23
//
Query:       gi|330506511|ref|YP_004382939.1|  [L=198]
Description: hypothetical protein MCON_0225 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-63  213.2   0.1      3e-63  212.9   0.1    1.0  1  DUF2121   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2121  Uncharacterized protein conserved in archaea (DUF2121)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.9   0.1   1.7e-67     3e-63       1     195 [.       1     187 [.       1     188 [. 0.99

  Alignments for each domain:
  == domain 1  score: 212.9 bits;  conditional E-value: 1.7e-67
                           DUF2121   1 MslviayigkkgaviagDkReiafrgdeeerekLEeeLYsGeiktdeeLkkkaeelgvkikitddreKvrkvgdvlv 77 
                                       Mslv+a +++k+avi+gD+R+i+f g++ e   LEeeLY+G+i++de L++ka+e+g+ +++td+r+Kv+++gd+lv
  gi|330506511|ref|YP_004382939.1|   1 MSLVVALTKSKEAVIGGDRRSITFLGSWPE---LEEELYCGRISDDEALLAKAMEIGAILQVTDGRDKVWRRGDLLV 74 
                                       9*****************************...******************************************** PP

                           DUF2121  78 GEVkeisaketkrrRiYatkgayaivelegsevtkkkkgesslivfGnkvtkeiankllkkevkkklslkeiekllk 154
                                       GEV+ei+++ ++rrRiY+++g++ +v+++g+ev+++++g++ +i++Gn++t++ia +++      +++ +  e+l++
  gi|330506511|ref|YP_004382939.1|  75 GEVTEITPQLERRRRIYLAPGSQLQVDITGKEVRIRDRGAMGCIIYGNRFTQQIAVSIV-----VQADGRVDEALIR 146
                                       **********************************************************9.....568899******* PP

                           DUF2121 155 eileevaektasvskeydllkkkkkldkkeaalekaikkDi 195
                                       +i++e+ae+tasvs+e+++lk++++l+++++aleka+++D+
  gi|330506511|ref|YP_004382939.1| 147 KIFQEAAERTASVSQEHVILKSERMLSNPQKALEKALEEDC 187
                                       ****************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1426.69
//
Query:       gi|330506512|ref|YP_004382940.1|  [L=222]
Description: molybdopterin-guanine dinucleotide biosynthesis protein [Methanosaeta concilii GP6]
Scores for complete 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   99.7   0.3    2.9e-28   99.2   0.3    1.1  1  NTP_transf_3  MobA-like NTP transferase domain
    1.2e-05   25.4   0.0    2.1e-05   24.6   0.0    1.4  1  CTP_transf_3  Cytidylyltransferase
  ------ inclusion threshold ------
      0.023   14.4   0.0      0.039   13.7   0.0    1.2  1  IspD          2-C-methyl-D-erythritol 4-phosphate cytidylyltr


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   0.3   4.8e-32   2.9e-28       1     154 [.       4     173 ..       4     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 4.8e-32
                                       EEEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHH...............HHTTCTS-E CS
                      NTP_transf_3   1 aviLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggdeevla...............alarlgvrv 62 
                                       a+iLAGG+S R+g +Kall++gg+pl+ +++++l +a +de+vvv++d++ ++               + +r ++++
  gi|330506512|ref|YP_004382940.1|   4 AIILAGGNSHRLGVEKALLEFGGRPLICWMAKTLLSA-ADELVVVARDQKHAKrlaeivsdrtlldqtHSDRVRIHF 79 
                                       79***********************************.9*********8777745555555555554444666999* PP

                                       EE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHH.HHTSSEEEEESSSEEEECC..EEEGG CS
                      NTP_transf_3  63 vededpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaa.asgadvvvptyegerghpl..lfrar 136
                                       ++d+ +g gp+a+l a+l  a +   ++ +acD+P+l+  +++rl++ a+  +g++++vp+  +++ +pl  ++ ++
  gi|330506512|ref|YP_004382940.1|  80 TWDRVSGFGPVAGLEAGLGMA-RGRFAFAAACDLPFLNGMVIQRLFELADpGRGYEAAVPVQPNGYFEPLhsVYERE 155
                                       *******************98.9**************************845668***************9999999 PP

                                       GHHHHHHHCTHTTHHHCH CS
                      NTP_transf_3 137 llsalaallgdqgarrll 154
                                        ++a  + + ++g+rr+ 
  gi|330506512|ref|YP_004382940.1| 156 KMQASCQRALESGERRIH 173
                                       998888888899**9986 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   3.5e-09   2.1e-05       2      57 ..       4      59 ..       3      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.5e-09
                                      EEEEE-SSSSSS.TTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHH CS
                      CTP_transf_3  2 aIipARsgSkRl.pgKnlldlggkpliayvleaalkskafekvivaTDseeiknvak 57
                                      aIi+A  +S Rl  +K+ll++gg+pli ++ + +l+++  e v+va D++  k +a+
  gi|330506512|ref|YP_004382940.1|  4 AIILAGGNSHRLgVEKALLEFGGRPLICWMAKTLLSAAD-ELVVVARDQKHAKRLAE 59
                                      8***********559*****************9999555.88********9998886 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.4e-06     0.039       3      66 ..       4      64 ..       3      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.4e-06
                                      EEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGGC CS
                              IspD  3 vvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllldk 66
                                      ++i A G+ +R++  ++K++le  g++l+ +  ++ll+  a + +vv+ ++++ ++ +++ +d+
  gi|330506512|ref|YP_004382940.1|  4 AIILAGGNSHRLG--VEKALLEFGGRPLICWMAKTLLS-AADELVVVARDQKHAKRLAEIVSDR 64
                                      7999999999985..679*******************9.4445666666666777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.42
# Mc/sec: 1578.48
//
Query:       gi|330506513|ref|YP_004382941.1|  [L=319]
Description: tyrosyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete 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  182.9   0.0    9.3e-54  182.7   0.0    1.0  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.094   11.6   0.0        1.3    7.8   0.0    2.0  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 !  182.7   0.0     1e-57   9.3e-54       5     292 ..      29     310 ..      25     311 .. 0.93

  Alignments for each domain:
  == domain 1  score: 182.7 bits;  conditional E-value: 1e-57
                                       --EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCH CS
                      tRNA-synt_1b   5 plrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgld 81 
                                       + r+y+G +++gk+HlG+++  +kl++lq+ag +v++l+aDlhA+++++   +++++r+ +++        +a gld
  gi|330506513|ref|YP_004382941.1|  29 RPRAYVGYETSGKVHLGHMLTANKLLDLQRAGFDVVVLLADLHAFLNEKG--TLEEVRQIADYNRDC---FMALGLD 100
                                       689*********************************************99..999999999999999...******* PP

                                       TTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHH.CCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEE CS
                      tRNA-synt_1b  82 pekaevvlqsewlehlelaellrdlgklgslnrmlqfks.vkkrleegegislgeftYplLqaaDilllkadlvpgG 157
                                       pe++e+v++++++ + + +  + ++++ +slnr  +  + v++++e+ +   +++++Ypl+qa Di+ lk dl +gG
  gi|330506513|ref|YP_004382941.1| 101 PERTEFVYGTDYQLQPDFMLKILQMARNTSLNRARRSMDeVSRNAEN-P--MVSQMIYPLMQAVDIADLKIDLAVGG 174
                                       ****************988888888888******8766626666666.5..8************************* PP

                                       GGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..S CS
                      tRNA-synt_1b 158 sDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..e 232
                                        DQ+++  l+r+ ++r++       p++l +pl++gl+Ge KmS+S+gn  I  d+  ++v+kki++a++  +   +
  gi|330506513|ref|YP_004382941.1| 175 IDQRKIHMLAREELPRLGLP----APVCLHTPLIPGLNGE-KMSSSKGN-NIAVDEPAQDVEKKIKSAFCPAKVveN 245
                                       *****************876....****************.********.**********************99986 PP

                                       HHHHHHHHHTHHH.....CHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 233 vekllklktelsn.....elierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                       +  l   k+ +++      +i+r e+++g   + ++e+l+a++v++ +h++dlkk  ae ++e+l
  gi|330506513|ref|YP_004382941.1| 246 NPVLAICKYHVFPrmevgMTISRPEKFGGDVHYASYEQLEADFVSGAMHPMDLKKSCAECMIEIL 310
                                       66666677777777777999*********999****************************99998 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.013   1.2e+02      29      42 ..      34      47 ..      13      55 .. 0.86
   2 ?    7.8   0.0   0.00015       1.3     261     297 ..     191     227 ..     180     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.013
                      tRNA-synt_1f 29 sGispSGliHiGnl 42
                                       G+ +SG++H+G +
  gi|330506513|ref|YP_004382941.1| 34 VGYETSGKVHLGHM 47
                                      59**********86 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00015
                      tRNA-synt_1f 261 lggeaPekvvYelillkggekmssSkGnvltledwle 297
                                       lg +aP+ +   li   +gekmssSkGn +++++  +
  gi|330506513|ref|YP_004382941.1| 191 LGLPAPVCLHTPLIPGLNGEKMSSSKGNNIAVDEPAQ 227
                                       56777888888888878899***********998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2255.63
//
Query:       gi|330506514|ref|YP_004382942.1|  [L=423]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-110  368.4   0.0   4.7e-110  368.2   0.0    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


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 !  368.2   0.0  2.6e-114  4.7e-110       5     417 .]       8     413 ..       5     413 .. 0.92

  Alignments for each domain:
  == domain 1  score: 368.2 bits;  conditional E-value: 2.6e-114
                                       S--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE- CS
                     EPSP_synthase   5 krlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeap 81 
                                       ++++gev +p+sks+++ra+l+ +L+ g   +  +L s+D+++++ a  ++ga+i k+ e+k+ + + g g   ++p
  gi|330506514|ref|YP_004382942.1|   8 SAVSGEVYAPPSKSYTHRAILITSLGPGGRVL-RPLLSADTLATISASEAFGAKIGKE-EKKDDLFIDGVGDLPQTP 82 
                                       689************************98655.68889**************999999.568888888977777787 PP

                                       HHHHTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS-BEE CS
                     EPSP_synthase  82 eelvldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lklkgv 157
                                        e+v+d+ nsgt+lr+  a++al     vLtGd sir+RP  +lld+Lr+lGa+  + ++++kapl ++g   ++++
  gi|330506514|ref|YP_004382942.1|  83 -ENVIDVLNSGTTLRFCSAVAALT-DGAVLTGDSSIRTRPNGPLLDSLRELGADAFSIKNNGKAPLVIRGkMLGGTA 157
                                       .7********************97.6799*****************************************888999* PP

                                       EEETSSTTHHHHHHHHHHHTTSBS.EEEEES.-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE- CS
                     EPSP_synthase 158 eikaevsSqqvtsllllaallaeg.ttelee.lasepsiddtlkmlkkfgikietsgteesitvkGkeklpgteyvv 232
                                       ++++ +sSq++++l ++++l   + ++++++ l+s+p+ ++tl+ml ++gi+ie+   e+++ v G+++ +  +y++
  gi|330506514|ref|YP_004382942.1| 158 HLQGGLSSQFLSALFIASPLAEREtRIRIVGeLKSRPYAEITLDMLHDAGITIEE--GEQEFIVPGGQSFDLERYTI 232
                                       *******************7777799999*9************************..5556********55558*** PP

                                       -B-HHHHHHHHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEE.STSEEEEEETTS--BEEEEEBGST CS
                     EPSP_synthase 233 egDassAayflvaAaitggevtvenvginslqGdiealdeilekmgaeitqe.edasivvgpsglklkdvdietlpd 308
                                       +gD ssA+y+l+aAa+tg+ev+v+++ + s qGd +++d il  mga+++++ e+ +++ +  +l+++++d  + pd
  gi|330506514|ref|YP_004382942.1| 233 PGDFSSASYPLAAAAVTGSEVMVKGILP-SRQGDSAIID-ILTLMGAQVSWNrESGDLRIKGGELEGIEIDAGRTPD 307
                                       **************************87.6789*77777.**********8724567888888************** PP

                                       TSBHGGGHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTTH CS
                     EPSP_synthase 309 eaptlavlaafaegttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRiam 385
                                       ++pt+avl a+a+gtt++ +++++r ketdrl+ama eL k+Ga+v+e++dgl+i+++ k l+ga v+ y+DhRi m
  gi|330506514|ref|YP_004382942.1| 308 LVPTIAVLGAVAKGTTTVVNAEHVRHKETDRLHAMAVELTKMGAKVKERPDGLEITGG-K-LHGASVHGYHDHRIVM 382
                                       ******************************************************8777.3.9*************** PP

                                       HHHHHHHHSBSEEEEETTHHHHHHSSSHHHHH CS
                     EPSP_synthase 386 alalaglvaegeveiddiectdksfpefeekL 417
                                       al++ag +++ge++id +e++d+s+p+f++++
  gi|330506514|ref|YP_004382942.1| 383 ALTVAG-LVAGETRIDTAEAVDVSYPGFFREM 413
                                       ******.56677*****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2949.74
//
Query:       gi|330506515|ref|YP_004382943.1|  [L=127]
Description: hypothetical protein MCON_0231 [Methanosaeta concilii GP6]
Scores for complete sequence (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   51.5   0.1    1.5e-13   51.3   0.1    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.1   8.5e-18   1.5e-13       1     121 [.       2     118 ..       2     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 8.5e-18
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHH CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidae 76 
                                       ivlDTs+li+l+rg e+    +  +   +++ t+++ ++E+  +++r     ++++++++ + +  s+++il+++  
  gi|330506515|ref|YP_004382943.1|   2 IVLDTSALIDLFRGGEEV---KGVIG--GDVTTTIINYYEIFVGIRR-----YRSKTEEKFFRRfFSDIRILDFNLT 68 
                                       79**********888866...99998..9******************.....66666666666669*********** PP

                                       HHHHHHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  77 iaeeaaeialkyg.....llpnDaliaAtAkehgikliatfDedfrrvak 121
                                       +ae+ +ei++++      ++++D li   A ++g + ++t+D+df  +ak
  gi|330506515|ref|YP_004382943.1|  69 AAERSSEIMARLMdlgisINAFDILISGIAVASGGETLMTKDRDFLSIAK 118
                                       *********************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 932.15
//
Query:       gi|330506516|ref|YP_004382944.1|  [L=72]
Description: hypothetical protein MCON_0232 [Methanosaeta concilii GP6]
Scores for 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   80.8   5.3      1e-22   80.7   5.3    1.0  1  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   5.3   5.6e-27     1e-22       1      69 []       4      69 ..       4      69 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 5.6e-27
                      VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgilseeea.deiekaskelrkefk 69
                                      KtIsI+d+vY+ Lk++Kre+eSFsd+IerLl+k k++    l e+fg l+e+ + d++e +sk++r++++
  gi|330506516|ref|YP_004382944.1|  4 KTISIRDDVYKLLKDAKREEESFSDAIERLLKKDKVN----LSEYFGALKEDPIlDRLEADSKRIREMAR 69
                                      9*******************************99999....**************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 557.52
//
Query:       gi|330506517|ref|YP_004382945.1|  [L=450]
Description: ADP-specific phosphofructokinase/glucokinase [Methanosaeta concilii GP6]
Scores for complete 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-80  269.9   0.0    3.6e-80  269.6   0.0    1.1  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 !  269.6   0.0     2e-84   3.6e-80       2     423 ..       7     439 ..       6     440 .. 0.83

  Alignments for each domain:
  == domain 1  score: 269.6 bits;  conditional E-value: 2e-84
                                       EEEEES--EEEEE.....HHHHHHHHCC-HH.HHHHHHC--SSBSSHHHHHHHHHHHHHHT--EEEEB--HHHHHHH CS
                        ADP_PFK_GK   2 kvavGynanvDai.....vdavelleklgleevkekseedhdeikskedlletfayffkkGaaaErfvenkelfeel 73 
                                       k++++y +n+Da+     +++++++++ + + +k   +e + +i+s+edl+++++y++++G++aE++ve+ +l ee+
  gi|330506517|ref|YP_004382945.1|   7 KIICAYPVNLDALydlgeERISRFIQSADPSGIK---SEMKGSIRSREDLISSLLYCIQQGSGAEILVESLQLAEEI 80 
                                       89************99999999999988877655...8999************************************ PP

                                       H....CC--SEEEEESHHHHHHHHHCCTT-EEEEE-.---HHHHTTS-SS....EEEEEEGGG-S-........--- CS
                        ADP_PFK_GK  74 vkaakklkkaelrmGGnagimanrlakegakvllga.klskklkellsek....ivvlgkpseaske.......kde 138
                                       ++   +++++ +r+GGnagiman+la++ga+ +l+a +l+++l +ll++     +   g+ +e s          + 
  gi|330506517|ref|YP_004382945.1|  81 EA---SFPWS-FRLGGNAGIMANLLAELGARPILNApALEPRLGALLHPGvgipV--SGRLIEPSLAaerpdlsSEV 151
                                       *9...99999.6**************************************66441..33333322222223454458 PP

                                       EEEEEEE-TT-EE....TEEE-SS-EEEEEE--STCGGTS--HHHCTTHHHHH..-SEEEE--GGG--TB-TTSTCH CS
                        ADP_PFK_GK 139 iHlIlEykkgekw....geieapraNRfIissdpenlrlsileefkealkefk..pdllvlsGlqmleeqykegker 209
                                       +H+++++k+ +++    g+i+a ++NRfI+++dp n+r++++++f+++++++   +++++lsG+++   +     ++
  gi|330506517|ref|YP_004382945.1| 152 LHFVFQFKESDRIpspqGPISAAKDNRFIATYDPVNTRMVSNQDFDAYCQDHIqeIEGAILSGFHLAPLD-----RY 223
                                       9***************888******************************99888************9884.....69 PP

                                       HHHHHHHHHHHHHHC..C.T-EEEEE----S-HHHHHHHHHHCGGG-SEEEE-HHHHHHHHHH...TT-...HHHCC CS
                        ADP_PFK_GK 210 eerlekvkeqlkslk..n.kikiHlElAsfqdeellkeilekilpyvdslGlnEqElanllsv...lgg...eekel 277
                                       +e +    eq++s+k  n +i iH+E++sfq++ +++++l+ +l+++dslGlnE+El++ +     +g+     + l
  gi|330506517|ref|YP_004382945.1| 224 REIFPPRIEQIRSWKeaNpNIYIHVEMGSFQSPGIARHFLR-LLEKADSLGLNEDELETATAEysaIGSstvLSTVL 299
                                       99***************88*********************9.***************77654412266566666667 PP

                                       SS...CC--HHHHHHHHHHHHH.....HHTT-SEEEEEETTEEEEEEETTSSS-HHHHHHHHHHHHHHHHHHHHH.- CS
                        ADP_PFK_GK 278 tevsdkepriakvlealrkllkllkkskkrkltrihvHtlayqiiltkkesewkneaakkalakaallAarkacn.s 353
                                       ++++ k++++++ ++++  l +     +  ++ r+ vHt++y+++++++++ ++ ++++ +l+k+a +Aa+ a++ s
  gi|330506517|ref|YP_004382945.1| 300 STARPKMSQWQERMQKAAGLRE-----HL-GIFRVSVHTRDYILSIMEEGK-ITAKEELLSLQKGADAAAALAATgS 369
                                       7777777777777777777777.....78.*****************7655.8888888**************9962 PP

                                       ....SHHHHHHHH...........HS-B-TTHHHHHHHHCCEETTEEEEEEE-B--SS-S--TTHHHHHHHHHHH CS
                        ADP_PFK_GK 354 ....dleklelklddsfsvsks.kkiplnekepvscweeeieleevevclaPvlvckkpkkTvGlGDtISaaglv 423
                                            +++++ +    ++ +++  ++  ++   v + + ++ ++++ v l+P+l+ ++p+ TvGlGDt +aa+++
  gi|330506517|ref|YP_004382945.1| 370 akgmPPNEVNPRG---LEAQREfCRLGAEA-AGVGRGAFHK-RDGLVVSLMPSLLAREPRITVGLGDTATAATFY 439
                                       3344333333333...23333333333333.3444433333.679***************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3542.87
//
Query:       gi|330506518|ref|YP_004382946.1|  [L=376]
Description: hypothetical protein MCON_0233 [Methanosaeta concilii GP6]
Scores for complete 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  209.4   0.2    5.9e-62  208.9   0.2    1.2  1  DUF2117   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2117  Uncharacterized protein conserved in archaea (DUF2117)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.9   0.2   3.3e-66   5.9e-62       1     212 []      79     288 ..      79     288 .. 0.95

  Alignments for each domain:
  == domain 1  score: 208.9 bits;  conditional E-value: 3.3e-66
                           DUF2117   1 DivfLlnygksketGhvFgkiVverskekkpliqierpgekdgeiilwn.........ekaeklakklseelglkiv 68 
                                       Div++ln++ks+etG +Fg++V++ +  +kpliqi++ g+  ++++l +         e+   +a++l+ +lgl+++
  gi|330506518|ref|YP_004382946.1|  79 DIVIILNQAKSRETGLAFGTMVARLAGIDKPLIQIDCGGRFVADLTLSHfasdsedinEEGLAVAARLAADLGLDLL 155
                                       9**********************************************99*****999666666************** PP

                           DUF2117  69 kpeevekeiveskgkrvvrkiagvspgenilvnGiviGkaeseevtivaedgkivdikggeiKehGvekLgkvdlek 145
                                       +p++ + +++  +g++v r ++gv pge i vnG+viG+a ++ev+i a++gki+d+kg+e K hG+ekL++vdlek
  gi|330506518|ref|YP_004382946.1| 156 RPRPRDCTLI--QGDTVRRIMTGVIPGELISVNGTVIGRAIGAEVEIKAKGGKIIDLKGAEPKMHGLEKLHRVDLEK 230
                                       ********99..8**************************************************************** PP

                           DUF2117 146 aivktgllRrskvkekllkkkklkkkkekkvgkvvlidHaaedvlelakkadlvvtvGDDTTavagd 212
                                       ai+++g++Rrs+v+++          +e+++  +++idH+aed++e+a +a +++tvGDDTTa+agd
  gi|330506518|ref|YP_004382946.1| 231 AIIRSGSIRRSTVRPR---------IGENRGEGAAFIDHCAEDAFEAAGGAAVALTVGDDTTAIAGD 288
                                       **********554444.........456678899********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 3024.90
//
Query:       gi|330506519|ref|YP_004382947.1|  [L=93]
Description: hypothetical protein MCON_0235 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-27   95.5   1.6      2e-27   95.4   1.6    1.0  1  DUF2098   Uncharacterized protein conserved in archaea (DUF20
  ------ inclusion threshold ------
      0.089   12.9   0.1       0.14   12.2   0.1    1.3  1  MerR_1    MerR HTH family regulatory protein


Domain annotation for each model (and alignments):
>> DUF2098  Uncharacterized protein conserved in archaea (DUF2098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   1.6   2.2e-31     2e-27       1      94 []       3      93 .]       3      93 .] 0.98

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 2.2e-31
                           DUF2098  1 eievGsvVrYinTgTvGkVvdikkeedgevwvkLdstdLyYrvdtLevidekekkkekeekekedleelekkekeleee 79
                                      ei+ +s+VrY++TgT+GkV+ +k+e+dg+vw+ Ldst+LyY+ dtLe+i+   k  e++e e ++le+++++ k+++e+
  gi|330506519|ref|YP_004382947.1|  3 EIREDSLVRYMGTGTIGKVKVLKTEDDGTVWAYLDSTGLYYKLDTLELIE---KPPERKELEGMTLEQIQERFKQTQEM 78
                                      68999*********************************************...89************************ PP

                           DUF2098 80 vdeeketdesceGGG 94
                                      +d++k++de++e+GG
  gi|330506519|ref|YP_004382947.1| 79 MDAAKMQDENLETGG 93
                                      *************99 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.6e-05      0.14      34      68 ..      40      74 ..      34      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                                      S-EEEEHHHHHHHHHHHHHHH.TT--GGG---XXXX CS
                            MerR_1 34 grryYtdedierLklikyLlk.rGltlkgikkllns 68
                                      g  yY  +++e +++  + ++ +G+tl++i++ +++
  gi|330506519|ref|YP_004382947.1| 40 G-LYYKLDTLELIEKPPERKElEGMTLEQIQERFKQ 74
                                      5.79***************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 679.34
//
Query:       gi|330506520|ref|YP_004382948.1|  [L=155]
Description: hypothetical protein MCON_0236 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1144.67
//
Query:       gi|330506521|ref|YP_004382949.1|  [L=50]
Description: hypothetical protein MCON_0237 [Methanosaeta concilii GP6]
Scores for complete 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   1.4      4e-05   23.7   1.4    1.3  1  Zn-ribbon_8  Zinc ribbon domain
     0.0021   18.1   0.6     0.0022   18.0   0.6    1.1  1  HypA         Hydrogenase/urease nickel incorporation, metallo
  ------ inclusion threshold ------
      0.015   15.3   0.9      0.019   15.0   0.9    1.1  1  DZR          Double zinc ribbon
      0.018   14.9   3.2          1    9.3   0.2    2.2  2  TFIIS_C      Transcription factor S-II (TFIIS)
      0.051   13.5   0.1       0.08   12.9   0.1    1.4  1  zf-LYAR      LYAR-type C2HC zinc finger
      0.093   13.4   1.0       0.11   13.2   1.0    1.1  1  FYDLN_acid   Protein of unknown function (FYDLN_acid)


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   1.4   1.3e-08     4e-05       5      37 ..      20      48 ..      19      50 .] 0.80

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.3e-08
                       Zn-ribbon_8  5 eYrCeeCghefevlqsisdapltaCPeCgs.evr 37
                                      +Y+C +C+++f  + +      + CP+C+s +v+
  gi|330506521|ref|YP_004382949.1| 20 DYECLDCNNKFQGMGR-----RPMCPSCKSrNVK 48
                                      8*******88876653.....567******8876 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.6   7.4e-07    0.0022      68      99 ..      18      49 ..      11      50 .] 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.4e-07
                                      --EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                              HypA 68 pvkvrCreCgkefeleekalrCpkCgsadvei 99
                                         ++C +C+++f+   ++  Cp+C+s++v+ 
  gi|330506521|ref|YP_004382949.1| 18 AKDYECLDCNNKFQGMGRRPMCPSCKSRNVKA 49
                                      55689*********6656678*******9986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.9   6.3e-06     0.019      11      37 ..      19      45 ..      13      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.3e-06
                               DZR 11 darfCseCgtklkavaaedrCpsCgek 37
                                      ++  C +C++k + + +  +CpsC++ 
  gi|330506521|ref|YP_004382949.1| 19 KDYECLDCNNKFQGMGRRPMCPSCKSR 45
                                      5677********************987 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2   0.00033         1      29      39 .]      21      31 ..      18      31 .. 0.92
   2 ?    6.5   0.2    0.0025       7.4       3      11 ..      39      47 ..      38      50 .] 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00033
                           TFIIS_C 29 ykCtkCghrWr 39
                                      y+C++C+++++
  gi|330506521|ref|YP_004382949.1| 21 YECLDCNNKFQ 31
                                      9********96 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0025
                           TFIIS_C  3 CpkCgsrea 11
                                      Cp+C+sr++
  gi|330506521|ref|YP_004382949.1| 39 CPSCKSRNV 47
                                      ******986 PP

>> zf-LYAR  LYAR-type C2HC zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.7e-05      0.08       1      12 [.      21      32 ..      21      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                           zf-LYAR  1 fsCiDCsktFdg 12
                                      + C+DC+++F+g
  gi|330506521|ref|YP_004382949.1| 21 YECLDCNNKFQG 32
                                      67********98 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.0   3.7e-05      0.11      12      34 ..      23      44 ..      17      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-05
                        FYDLN_acid 12 CpscgakFYDLnkdPivcpkcge 34
                                      C +c++kF  ++++P+ cp+c++
  gi|330506521|ref|YP_004382949.1| 23 CLDCNNKFQGMGRRPM-CPSCKS 44
                                      ***************6.****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 0.31u 0.28s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 383.71
//
Query:       gi|330506522|ref|YP_004382950.1|  [L=436]
Description: formylmethanofuran dehydrogenase subunit B [Methanosaeta concilii GP6]
Scores for complete sequence (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   60.7   0.0    7.9e-16   58.0   0.0    2.0  1  Molybdopterin  Molybdopterin oxidoreductase


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 !   58.0   0.0   4.4e-20   7.9e-16       1     416 [.      49     412 ..      49     418 .. 0.70

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 4.4e-20
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       R+k P+vR     +G+++r+sWdeA e+ a+ l +      p    +   g+ +s+e++ ++  +++ lgg      
  gi|330506522|ref|YP_004382950.1|  49 RIKEPLVR---V-DGDLRRASWDEAIEMTARILAN---SERP----LLFMGSETSTEAMEVGIHMAEFLGG----IA 110
                                       9*******...7.9****************99999...7788....8888999******************....89 PP

                                       ECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHH........HHHHHHHHHTTC..... CS
                     Molybdopterin  78 dwyadlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpil........narirkaalkkk..... 141
                                       d++  ++++ +  t+g +++   +  ++ ++   +dl + wGsN+ e +p                     +     
  gi|330506522|ref|YP_004382950.1| 111 DSNSTVCHGPT--TMGIQEA-GRVGATAGQSKSRADLTVYWGSNPLESMPRHmsryavypR----------Gywtqr 174
                                       99999999985..7776655.777777888899***************9999555533332..........123334 PP

                                       ....-EEEEECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHH CS
                     Molybdopterin 142 ....akvivigpryaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetg 214
                                             vi+++pr + +++ ad+++ ++p+td +l+ a+  ++l      +       +                ++
  gi|330506522|ref|YP_004382950.1| 175 grfdRTVICVDPRRSITAENADLHIQLNPNTDYELLSALL-TLLHGKRPHQ-------T----------------VE 227
                                       477788*****************************55544.4333333333.......1................12 PP

                                       HHHHCCHHHHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHH CS
                     Molybdopterin 215 kkkevvariarelarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaek 291
                                       + ++v +    ++ + + +++   +i vG g+  ++    + + ++nL++ ++   +     + + G   l g+ + 
  gi|330506522|ref|YP_004382950.1| 228 EVTGVSISEMERMLEMMKSCNY-GAIYVGLGIASSYGKHRNAELAFNLVKELNSHTK-----FVI-G--ALRGHCNV 295
                                       2334444444555555666666.8888999999999999999999999887665544.....222.2..45554444 PP

                                       HTCCTTCCCCCCCTTHHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSE CS
                     Molybdopterin 292 vgalpvllsvkslkeekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldl 368
                                       +g +    ++ s+ ++ ++  +  +g   ++p++      ++l++ ++++ ++l   + v+h  +     +      
  gi|330506522|ref|YP_004382950.1| 296 AGFN----QIASYLYGFPFGLDFARGYPRYNPGEYTA--VDVLRDRDVDAAFILS-ADLVSHFPAACS--EYLAQIP 363
                                       5555....33333444444444455555555544443..5778888888888888.444444444444..2447788 PP

                                       EEEEESCSSHHHHTSSEEEEBE-.CCGSEEEEE-TTSEEEEEEESSS-S CS
                     Molybdopterin 369 vvvldgrltstalyaDiiLPaat.wyEkedlytndegrfqhlkqavspp 416
                                       v ++d+    t  ++D++LP+    +E ++++   +   + +++++s+p
  gi|330506522|ref|YP_004382950.1| 364 VACIDIAPCPTTMISDVVLPGVIdAMECDGTFYRLDDVPIYFQPFTSSP 412
                                       8888888888888888888875426677777766666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2968.67
//
Query:       gi|330506523|ref|YP_004382951.1|  [L=132]
Description: formylmethanofuran dehydrogenase subunit D [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-09   36.3   0.0      6e-09   35.9   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 !   35.9   0.0   3.3e-13     6e-09       1     109 [.       5     103 ..       5     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 3.3e-13
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTE.EEEEEEEEESSB-TTEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrG.svevrakvtervrpGvvfm 76 
                                       + L+tg++ ++        +   ++ +e++v+e+n +d  a+G    d+V+v+sr G sv+v a   e +  G+vfm
  gi|330506523|ref|YP_004382951.1|   5 FLLNTGSTIEEGRLAKGGSKLTDDYTRECAVCEMNLADFLAMG--SPDRVKVTSRDGhSVVVYAYGAEKLSSGQVFM 79 
                                       57888888888888888888889999999**************..******************************** PP

                                       ESSHCC.....S-GHCTS--SCSTTT--CSTT- CS
                   Molydop_binding  77 pfgwweagekggnaNaltddatdplsgtpefks 109
                                       p + w+        N+++ d+ +  sg+p +k+
  gi|330506523|ref|YP_004382951.1|  80 PRAIWS--------NVVV-DPETFSSGSPLYKG 103
                                       ******........9999.55556677777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1042.68
//
Query:       gi|330506524|ref|YP_004382952.1|  [L=269]
Description: formylmethanofuran dehydrogenase subunit C [Methanosaeta concilii GP6]
Scores for complete sequence (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  21.7    4.9e-06   26.3  12.5    2.6  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 !   12.0   1.8   6.3e-06      0.11     132     164 ..      79     111 ..      59     117 .. 0.72
   2 !   26.3  12.5   2.7e-10   4.9e-06      34     154 ..     107     221 ..     106     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-06
                                       TTTT-EEEEEEE-S-B-SSBTTT--EEEEEEE- CS
                             GXGXG 132 gceYmtGGvvvvLgktgrnfaaGmsgGiayvld 164
                                       +++ m  G++ +Lg  g++ +a m+gG + v+ 
  gi|330506524|ref|YP_004382952.1|  79 IGQGMNSGMIEILGPAGMYTGAEMTGGKILVRG 111
                                       556688888888888888888888888888873 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 2.7e-10
                                       EEEEEEE-TTTTTT--TTEEEEEEEEE-STTT.......TT-ESSEEEEE--TT-SS-GGGSB-S-SSTTTT--SEE CS
                             GXGXG  34 iklkGsaGqslgaflakGltleleGdandyvG.......kglsgGkivikpskeskfkaeeniivGnvvlygatgGk 103
                                       i ++G aG   g+ l kG  l+++G+a d vG        g++gG+i+i+++++s+            +  g  gG+
  gi|330506524|ref|YP_004382952.1| 107 ILVRGDAGSWSGMEL-KGGLLQISGNAGDHVGsayrgswRGMTGGQIIIQGDARSQ------------LGGGLAGGS 170
                                       667899999999988.8888999999999999444444448999999999999443............455888999 PP

                                       EEESSB--SSTTTT-SS-EEEESEB.-SSTTTT-EEEEEEE-S-B-SSBTTT CS
                             GXGXG 104 lfirgkageRfavrnsgatavvegv.gdhgceYmtGGvvvvLgktgrnfaaG 154
                                       + ++g++ + +a+r  g  ++++g+    ++  m GG+vv+Lg++ +nf+ G
  gi|330506524|ref|YP_004382952.1| 171 ITVEGNVENFCAIRQAGGLLIIKGNaVRGLGAEMSGGTVVILGEV-KNFSPG 221
                                       999999999999999999999999966677888999999999987.455544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); 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 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1903.20
//
Query:       gi|330506525|ref|YP_004382953.1|  [L=594]
Description: formylmethanofuran dehydrogenase subunit A [Methanosaeta concilii GP6]
Scores for complete 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-90  302.9   0.8    7.5e-90  302.7   0.8    1.0  1  Amidohydro_3  Amidohydrolase family
    3.2e-07   30.0   0.1     0.0015   17.9   0.0    2.4  2  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.7   0.8   8.3e-94   7.5e-90       2     473 .]      51     523 ..      50     523 .. 0.97

  Alignments for each domain:
  == domain 1  score: 302.7 bits;  conditional E-value: 8.3e-94
                      Amidohydro_3   2 viDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerfp 77 
                                       viDa+G++v+PG+vD+H+H+ag++vn+ rl+r++d++++        vr++        +++g+G++++++++++++
  gi|330506525|ref|YP_004382953.1|  51 VIDARGKTVMPGGVDAHSHVAGTKVNAgRLMRPEDHYKS--------VRKKTDI-----THSGSGYTVPSVYKQGYD 114
                                       9**********************************7775........7777766.....47**************** PP

                      Amidohydro_3  78 yalaeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllregafhlvldlapla 154
                                       ya +++++v+e+a+++l+a++tH+++r +++ld+            g++++++n+++++++l++g           +
  gi|330506525|ref|YP_004382953.1| 115 YAAMGYTTVFEAAMPPLEARHTHEEMRATPILDM------------GAYMVFGNNWFVMRYLKDG-----------D 168
                                       *********************************8............*******************...........* PP

                      Amidohydro_3 155 reaeaaavaaalaalasyGitsv.......eagggnvsslddleplfeltaeeklplrviikelldaaerlglpls. 223
                                       +e+ aa+va++++ +++yGi++v       +++++nv +ld+++++fe+t +e      ii +l++++e lglp s 
  gi|330506525|ref|YP_004382953.1| 169 IEKAAAYVAWMMRTHKAYGIKCVnpagvenWGWAKNVKGLDEPNIHFEVTSRE------IIRGLAEVNELLGLPMSl 239
                                       *****************************************************......9****************9 PP

                      Amidohydro_3 224 .........pgseeltigavklfadgvl................gsrtalltepyf.....tgwpdfedea..lael 268
                                                pg+ e+  +++ +   +++                + +t++l++ +f     ++w+df ++a  la++
  gi|330506525|ref|YP_004382953.1| 240 hlhannlghPGNWETARDSLMITSSLEPnsktelewaqtresakRKQTVYLAHAQFnsyggSSWRDFCSGApdLAKY 316
                                       99999999999999999999999997778888888899999999********************************* PP

                      Amidohydro_3 269 vaaadergldvaihaigdaavd..dvldafeaa...aekngnqdrrrlehaegv...tesqiervaalqvaagvqpv 337
                                       +++  ++ +d + + +g a+++  d++++ + +   ++k++n+d  ++e ++gv    + + ++v+a  +a+g++  
  gi|330506525|ref|YP_004382953.1| 317 INQTENVVIDSGSVPFGPATTMtgDGPAQHDLYmltGQKWSNCDI-EMECGSGVlslMYLKSSPVHATMWAIGLE-- 390
                                       *****************************9999999*********.*****************************.. PP

                      Amidohydro_3 338 fnfedelldsrlgperargstpvkellnagvkvalgsD.apvgpfdpwprigaavmrktrrgg.............e 400
                                                             v +l+++++k+++++D +++g f  +p ++a++m++++r+               
  gi|330506525|ref|YP_004382953.1| 391 ----------------------VLLLIDDPWKTIMTTDhPNGGLFSQYPQVIAWLMSRKARDDtakechkwaydksS 445
                                       ......................******************************************************* PP

                      Amidohydro_3 401 vlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear.....vrltvvdGrvv 472
                                       + + d+e+sl++++ l+++++A+++g+ +rkG+L+vGad+D++++d+dp d+  ++  +++     + lt++dG++v
  gi|330506525|ref|YP_004382953.1| 446 LGGVDREMSLYDIAILTRANSARTIGMAHRKGHLGVGADGDVTIYDIDPGDLNVNDPSYIVsrfsrPDLTIKDGQIV 522
                                       ******************************************************999999999*************9 PP

                      Amidohydro_3 473 y 473
                                       +
  gi|330506525|ref|YP_004382953.1| 523 A 523
                                       5 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   5.1e-05      0.46       1      18 [.      58      75 ..      58     154 .. 0.78
   2 !   17.9   0.0   1.7e-07    0.0015     273     344 .]     447     522 ..     394     522 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 5.1e-05
                                      EEEE-EEEEEEECETTEC CS
                      Amidohydro_1  1 ivlPGlIDaHvHleqsll 18
                                      +v+PG++DaH H+ ++ +
  gi|330506525|ref|YP_004382953.1| 58 TVMPGGVDAHSHVAGTKV 75
                                      69***********97754 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.7e-07
                                       TTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT......CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 273 yedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldi......laafvglkkdgnvkkvivkGkl 343
                                        ++ +  +sl+++  ++  n A+ +g+++++G + vG d D ++ d d+       +++  +     ++ +i++G++
  gi|330506525|ref|YP_004382953.1| 447 GGV-DREMSLYDIAILTRANSARTIGMAHRKGHLGVGADGDVTIYDIDPgdlnvnDPSYIVSRF-SRPDLTIKDGQI 521
                                       333.455999998888889**************************9977777885555555544.459999999998 PP

                                       E CS
                      Amidohydro_1 344 v 344
                                       v
  gi|330506525|ref|YP_004382953.1| 522 V 522
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); 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:                         2  (0.000111551); expected 0.2 (1e-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: 3872.19
//
Query:       gi|330506526|ref|YP_004382954.1|  [L=343]
Description: formylmethanofuran dehydrogenase subunit F [Methanosaeta concilii GP6]
Scores for complete 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  157.4  83.1    1.6e-09   37.2   2.2    8.2  8  Fer4      4Fe-4S binding domain
    1.4e-36  124.8  63.1    1.7e-10   41.4  12.3    5.5  7  Fer4_7    4Fe-4S dicluster domain
    3.1e-34  116.9  56.5    2.4e-09   37.1   3.2    6.3  6  Fer4_10   4Fe-4S dicluster domain
    3.2e-30  104.8  59.6    2.4e-06   28.4  12.2    7.9  8  Fer4_16   4Fe-4S double cluster binding domain
      2e-28   97.2  85.4    2.5e-05   24.1   1.5    8.2  8  Fer4_6    4Fe-4S binding domain
    3.2e-28   97.6  65.7    8.9e-09   35.4   5.1    6.3  6  Fer4_9    4Fe-4S dicluster domain
    5.8e-27   93.6  68.1    6.7e-07   29.3   7.5    6.6  6  Fer4_21   4Fe-4S dicluster domain
    9.8e-23   78.8  83.9    2.5e-06   27.2   2.5    8.3  8  Fer4_2    4Fe-4S binding domain
    8.3e-16   58.2  69.4    3.1e-06   27.6  11.8    6.3  6  Fer4_8    4Fe-4S dicluster domain
    4.5e-13   49.5  67.7    0.00026   21.4   8.4    6.8  6  Fer4_17   4Fe-4S dicluster domain
    7.5e-13   47.9  84.7    0.00024   21.4   1.8    8.3  8  Fer4_4    4Fe-4S binding domain
    2.7e-07   31.0 115.5     0.0025   18.6   6.9    8.4  8  Fer4_3    4Fe-4S binding domain
    1.2e-06   29.2  64.3       0.04   14.6   0.3    8.7  7  Fer4_15   4Fe-4S single cluster domain
    6.3e-06   26.4  63.7        0.1   12.8   1.5    8.0  8  Fer4_18   4Fe-4S dicluster domain
    1.6e-05   25.3  84.5      0.055   14.0   2.5    8.2  8  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0036   18.1  75.2        0.1   13.5   0.5    8.1 11  Fer4_22   4Fe-4S dicluster domain
  ------ inclusion threshold ------
        1.7    8.8  37.1       0.42   10.8   3.7    5.9  7  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   3.6   8.3e-10   8.8e-07       5      21 ..      18      34 ..      15      34 .. 0.91
   2 !   18.0   1.8   1.7e-06    0.0018       7      24 .]      61      78 ..      57      78 .. 0.91
   3 !   18.4  10.3   1.3e-06    0.0014       2      24 .]     100     122 ..      99     122 .. 0.94
   4 !   37.2   2.2   1.5e-12   1.6e-09       2      24 .]     141     163 ..     140     163 .. 0.95
   5 !   18.9   0.9   9.2e-07   0.00097       4      23 ..     175     194 ..     172     195 .. 0.91
   6 !   31.3   4.1   1.1e-10   1.1e-07       4      23 ..     211     230 ..     208     231 .. 0.91
   7 !   27.2   3.1   2.1e-09   2.2e-06       4      23 ..     267     286 ..     264     287 .. 0.89
   8 !   20.8   3.6   2.3e-07   0.00024       2      24 .]     314     336 ..     313     336 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 8.3e-10
                                      TTTSSS-THHHHHSTTT CS
                              Fer4  5 eekCigCGaCvevCPvg 21
                                      +++CigCG+Cv+vCP g
  gi|330506526|ref|YP_004382954.1| 18 PDRCIGCGTCVQVCPKG 34
                                      8**************76 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.7e-06
                                      TSSS-THHHHHSTTTEEE CS
                              Fer4  7 kCigCGaCvevCPvgAIt 24
                                       C +C +C  vCP+gA++
  gi|330506526|ref|YP_004382954.1| 61 ACAFCALCSRVCPTGALE 78
                                      79**************85 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.3e-06
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       v+d ekC++CG+C +vCP  +I+
  gi|330506526|ref|YP_004382954.1| 100 VVDSEKCVHCGLCCDVCPQACIE 122
                                       89*****************9996 PP

  == domain 4  score: 37.2 bits;  conditional E-value: 1.5e-12
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       +id e+C++CG C++vCP+gAI+
  gi|330506526|ref|YP_004382954.1| 141 IIDLERCVHCGWCASVCPTGAIS 163
                                       79*******************96 PP

  == domain 5  score: 18.9 bits;  conditional E-value: 9.2e-07
                                       ETTTSSS-THHHHHSTTTEE CS
                              Fer4   4 deekCigCGaCvevCPvgAI 23 
                                       d + C +C++Cv  CP +A+
  gi|330506526|ref|YP_004382954.1| 175 DDNVCQACKTCVHTCPANAL 194
                                       7789***************8 PP

  == domain 6  score: 31.3 bits;  conditional E-value: 1.1e-10
                                       ETTTSSS-THHHHHSTTTEE CS
                              Fer4   4 deekCigCGaCvevCPvgAI 23 
                                        ++ Ci+CGaC+++CPv AI
  gi|330506526|ref|YP_004382954.1| 211 RPDACIYCGACAQACPVRAI 230
                                       59*****************9 PP

  == domain 7  score: 27.2 bits;  conditional E-value: 2.1e-09
                                       ETTTSSS-THHHHHSTTTEE CS
                              Fer4   4 deekCigCGaCvevCPvgAI 23 
                                       de  C gCG+Cv +CPv+A+
  gi|330506526|ref|YP_004382954.1| 267 DEIACLGCGNCVIACPVNAL 286
                                       7778***************8 PP

  == domain 8  score: 20.8 bits;  conditional E-value: 2.3e-07
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       v+d+e C  C +C ++CP +AI+
  gi|330506526|ref|YP_004382954.1| 314 VVDQEVCGSCATCSMICPADAIR 336
                                       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 !   23.0   0.4   8.6e-08   9.1e-05      34      51 ..      17      34 ..       3      36 .. 0.81
   2 !   13.3   2.7   8.8e-05     0.092      36      52 .]      60      76 ..      50      76 .. 0.86
   3 !   26.9  16.9     5e-09   5.2e-06       2      50 ..      62     118 ..      61     120 .. 0.79
   4 !   41.4  12.3   1.6e-13   1.7e-10       1      52 []     105     161 ..     105     161 .. 0.85
   5 !   34.6  13.1     2e-11   2.2e-08       2      52 .]     179     229 ..     178     229 .. 0.92
   6 !   31.3   7.3   2.2e-10   2.3e-07       1      52 []     270     334 ..     270     334 .. 0.67
   7 !   12.2   2.5    0.0002      0.21       2      22 ..     320     340 ..     319     342 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8.6e-08
                            Fer4_7 34 dpekClgCgaCvavCPtg 51
                                       p++C+gCg Cv+vCP+g
  gi|330506526|ref|YP_004382954.1| 17 LPDRCIGCGTCVQVCPKG 34
                                      589999999999999987 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.8e-05
                            Fer4_7 36 ekClgCgaCvavCPtga 52
                                        C +C  C +vCPtga
  gi|330506526|ref|YP_004382954.1| 60 GACAFCALCSRVCPTGA 76
                                      46*************98 PP

  == domain 3  score: 26.9 bits;  conditional E-value: 5e-09
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenek........gtekveidpekClgCgaCvavCPt 50 
                                       C  C  C ++Cp++a+e+++   ++         ++++++d+ekC++Cg C +vCP 
  gi|330506526|ref|YP_004382954.1|  62 CAFCALCSRVCPTGALEFRKNGIAEmdnsylsvAIKSTVVDSEKCVHCGLCCDVCPQ 118
                                       999***************98633333333444444888******************7 PP

  == domain 4  score: 41.4 bits;  conditional E-value: 1.6e-13
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek.gt....ekveidpekClgCgaCvavCPtga 52 
                                       +C++Cg C ++Cp+ +iel++++ ++ g      ++ id e+C++Cg C++vCPtga
  gi|330506526|ref|YP_004382954.1| 105 KCVHCGLCCDVCPQACIELEDRHLAEdGSlkvgGRTIIDLERCVHCGWCASVCPTGA 161
                                       7******************9986555422444478899*****************98 PP

  == domain 5  score: 34.6 bits;  conditional E-value: 2e-11
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       C  C+ Cv +Cp++a+  +e +  ++ ekv ++p+ C++CgaC+++CP+ a
  gi|330506526|ref|YP_004382954.1| 179 CQACKTCVHTCPANALFNREWKAGERGEKVSHRPDACIYCGACAQACPVRA 229
                                       99**************99988777777*********************976 PP

  == domain 6  score: 31.3 bits;  conditional E-value: 2.2e-10
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek............gtekv.eidpekClgCgaCvavCPtga 52 
                                       +C gCg+Cv aCpv+a++ ++ +               +  +v ++d+e C +C  C   CP++a
  gi|330506526|ref|YP_004382954.1| 270 ACLGCGNCVIACPVNALSDPYLAAGHlneleikpllevRDGTVkVVDQEVCGSCATCSMICPADA 334
                                       5*****************664322222222222333321133336789**************987 PP

  == domain 7  score: 12.2 bits;  conditional E-value: 0.0002
                            Fer4_7   2 CigCgaCvaaCpvkaieldee 22 
                                       C  C  C   Cp++ai+l ++
  gi|330506526|ref|YP_004382954.1| 320 CGSCATCSMICPADAIRLVPR 340
                                       9****************9887 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   3.2   2.3e-12   2.4e-09       6      56 .]      18      73 ..      14      89 .. 0.96
   2 !   16.4   3.9     7e-06    0.0074       3      21 ..     100     118 ..      98     136 .. 0.82
   3 !   19.9   0.6   5.6e-07   0.00059       3      21 ..     141     159 ..     139     169 .. 0.85
   4 !   35.7  10.9   6.6e-12     7e-09       4      56 .]     174     226 ..     171     226 .. 0.96
   5 !   20.5   0.5   3.7e-07   0.00039       4      23 ..     266     285 ..     263     310 .. 0.77
   6 !   14.7   1.7   2.4e-05     0.025       3      22 ..     314     333 ..     312     341 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.3e-12
                           Fer4_10  6 ddtCirCgkCvkaCPadl.....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +d+Ci+Cg+Cv++CP         + +++g ++++  ++  +++C +c  C ++CP
  gi|330506526|ref|YP_004382954.1| 18 PDRCIGCGTCVQVCPKGEliigsVGAVVRGLIDKDFIEKRMSGACAFCALCSRVCP 73
                                      79**************889***9999*****************************9 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 7e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPa 21 
                                       v+d+++C++Cg C ++CP+
  gi|330506526|ref|YP_004382954.1| 100 VVDSEKCVHCGLCCDVCPQ 118
                                       7899**************9 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 5.6e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPa 21 
                                       +id ++C++Cg C ++CP+
  gi|330506526|ref|YP_004382954.1| 141 IIDLERCVHCGWCASVCPT 159
                                       89****************9 PP

  == domain 4  score: 35.7 bits;  conditional E-value: 6.6e-12
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +dd+ C  C++Cv  CPa++  ++  ++ +++e+v++ +++C+ cgaC++aCP
  gi|330506526|ref|YP_004382954.1| 174 RDDNVCQACKTCVHTCPANALFNREWKAGERGEKVSHRPDACIYCGACAQACP 226
                                       799***************99999999**************************9 PP

  == domain 5  score: 20.5 bits;  conditional E-value: 3.7e-07
                           Fer4_10   4 idddtCirCgkCvkaCPadl 23 
                                        d+  C++Cg+Cv aCP+++
  gi|330506526|ref|YP_004382954.1| 266 TDEIACLGCGNCVIACPVNA 285
                                       57889************965 PP

  == domain 6  score: 14.7 bits;  conditional E-value: 2.4e-05
                           Fer4_10   3 vidddtCirCgkCvkaCPad 22 
                                       v+d++ C  C++C   CPad
  gi|330506526|ref|YP_004382954.1| 314 VVDQEVCGSCATCSMICPAD 333
                                       6899***************5 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 !   17.5   0.3   5.7e-06     0.006      45      66 ..      12      33 ..       5      37 .. 0.69
   2 !   16.2   0.2   1.4e-05     0.015       2      25 ..      62      85 ..      56     103 .. 0.79
   3 !   14.6   5.0   4.7e-05     0.049       1      21 [.     105     125 ..     105     136 .. 0.84
   4 !   22.6   0.5   1.5e-07   0.00016       1      21 [.     146     166 ..     146     176 .. 0.88
   5 !   15.8   1.4   1.9e-05      0.02       2      27 ..     179     201 ..     178     212 .. 0.79
   6 !   28.4  12.2   2.3e-09   2.4e-06       2      67 .]     215     284 ..     214     284 .. 0.61
   7 !   17.4   1.4   6.2e-06    0.0066       2      20 ..     271     289 ..     270     302 .. 0.87
   8 !   15.3   2.1   2.7e-05     0.029       2      20 ..     320     338 ..     319     343 .] 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.7e-06
                           Fer4_16 45 eekckkqeaitgCdiCqdvCPa 66
                                      +++ +   +++gC++C++vCP 
  gi|330506526|ref|YP_004382954.1| 12 RAQFYLPDRCIGCGTCVQVCPK 33
                                      5555556777777777777774 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.4e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekei 25
                                      C  C  C  vCPt+a++ +k+  +
  gi|330506526|ref|YP_004382954.1| 62 CAFCALCSRVCPTGALEFRKNGIA 85
                                      999************999854433 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 4.7e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikekk 21 
                                       +C+ Cg C +vCP+++i+ + 
  gi|330506526|ref|YP_004382954.1| 105 KCVHCGLCCDVCPQACIELED 125
                                       5****************9884 PP

  == domain 4  score: 22.6 bits;  conditional E-value: 1.5e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekk 21 
                                       rC+ Cg Ca+vCPt+ai+ +k
  gi|330506526|ref|YP_004382954.1| 146 RCVHCGWCASVCPTGAISFEK 166
                                       6****************9874 PP

  == domain 5  score: 15.8 bits;  conditional E-value: 1.9e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiea 27 
                                       C+ C+ C+ +CP+na+ ++   e++a
  gi|330506526|ref|YP_004382954.1| 179 CQACKTCVHTCPANALFNR---EWKA 201
                                       ***************9877...4444 PP

  == domain 6  score: 28.4 bits;  conditional E-value: 2.3e-09
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy.ntaekkd...laedeekckkq..eaitgCdiCqdvCPan 67 
                                       C+ Cg+Ca++CP++ai   k + i  +e + + + ++k      +++  +c +    a+ gC++C+ +CP+n
  gi|330506526|ref|YP_004382954.1| 215 CIYCGACAQACPVRAIVVSKTAII--PEMKGKgAFEKKLAlplPRPTLTSCLETdeIACLGCGNCVIACPVN 284
                                       *****************9943333..333233122222221113333444554333667***********98 PP

  == domain 7  score: 17.4 bits;  conditional E-value: 6.2e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C +Cg+C+ +CP+na++ +
  gi|330506526|ref|YP_004382954.1| 271 CLGCGNCVIACPVNALSDP 289
                                       99**************988 PP

  == domain 8  score: 15.3 bits;  conditional E-value: 2.7e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       Cg+C  C ++CP++ai+  
  gi|330506526|ref|YP_004382954.1| 320 CGSCATCSMICPADAIRLV 338
                                       ****************976 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   1.5   2.4e-08   2.5e-05       6      22 ..      18      34 ..      15      38 .. 0.90
   2 !   10.3   2.9   0.00057       0.6       9      24 .]      62      77 ..      59      77 .. 0.86
   3 !   14.5  10.0   2.6e-05     0.027       3      21 ..     100     118 ..      99     122 .. 0.90
   4 !   23.0   2.2   5.3e-08   5.6e-05       4      24 .]     142     162 ..     141     162 .. 0.96
   5 !   15.7   2.1   1.1e-05     0.011       5      24 .]     175     194 ..     171     194 .. 0.91
   6 !   16.5   4.5   6.3e-06    0.0067       2      24 .]     208     230 ..     207     230 .. 0.91
   7 !   21.4   3.8   1.7e-07   0.00018       8      24 .]     270     286 ..     265     286 .. 0.92
   8 !   14.6   4.3   2.5e-05     0.026       3      24 .]     314     335 ..     312     335 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.4e-08
                            Fer4_6  6 pdkCigCgdCvrvCPeg 22
                                      pd+CigCg Cv vCP g
  gi|330506526|ref|YP_004382954.1| 18 PDRCIGCGTCVQVCPKG 34
                                      8**************75 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00057
                            Fer4_6  9 CigCgdCvrvCPegai 24
                                      C  C  C rvCP+ga+
  gi|330506526|ref|YP_004382954.1| 62 CAFCALCSRVCPTGAL 77
                                      55599*********97 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2.6e-05
                            Fer4_6   3 eidpdkCigCgdCvrvCPe 21 
                                       ++d +kC++Cg C +vCP 
  gi|330506526|ref|YP_004382954.1| 100 VVDSEKCVHCGLCCDVCPQ 118
                                       79****************5 PP

  == domain 4  score: 23.0 bits;  conditional E-value: 5.3e-08
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       id ++C++Cg C++vCP+gai
  gi|330506526|ref|YP_004382954.1| 142 IDLERCVHCGWCASVCPTGAI 162
                                       799*****************8 PP

  == domain 5  score: 15.7 bits;  conditional E-value: 1.1e-05
                            Fer4_6   5 dpdkCigCgdCvrvCPegai 24 
                                       d++ C  C  Cv  CP++a+
  gi|330506526|ref|YP_004382954.1| 175 DDNVCQACKTCVHTCPANAL 194
                                       8999**************97 PP

  == domain 6  score: 16.5 bits;  conditional E-value: 6.3e-06
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       v + pd+Ci Cg+C+ +CP  ai
  gi|330506526|ref|YP_004382954.1| 208 VSHRPDACIYCGACAQACPVRAI 230
                                       7788***************9997 PP

  == domain 7  score: 21.4 bits;  conditional E-value: 1.7e-07
                            Fer4_6   8 kCigCgdCvrvCPegai 24 
                                       +C+gCg+Cv++CP +a+
  gi|330506526|ref|YP_004382954.1| 270 ACLGCGNCVIACPVNAL 286
                                       7*************997 PP

  == domain 8  score: 14.6 bits;  conditional E-value: 2.5e-05
                            Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                       ++d++ C +C  C ++CP++ai
  gi|330506526|ref|YP_004382954.1| 314 VVDQEVCGSCATCSMICPADAI 335
                                       79******************98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   5.1   8.5e-12   8.9e-09       1      50 [.      20      76 ..      20      77 .. 0.96
   2 !   17.9  16.7   2.4e-06    0.0025       1      51 []      61     121 ..      61     121 .. 0.80
   3 !   19.2   0.3   9.3e-07   0.00098      34      51 .]     145     162 ..     123     162 .. 0.77
   4 !   31.0  11.7     2e-10   2.1e-07       2      51 .]     179     230 ..     178     230 .. 0.78
   5 !   16.3   2.8   7.6e-06     0.008      28      50 ..     263     285 ..     248     286 .. 0.79
   6 !   18.8  11.4   1.3e-06    0.0013       1      51 []     270     335 ..     270     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 8.5e-12
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.......eaCigCgaCveaCpkga 50
                                      +C+gCg+Cv++Cp+g  +  +++  +r  ++++        aC +C  C  +Cp+ga
  gi|330506526|ref|YP_004382954.1| 20 RCIGCGTCVQVCPKGELIIGSVGAVVRGLIDKDfiekrmsGACAFCALCSRVCPTGA 76
                                      6***************************99999*******99*************97 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.4e-06
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase............eaCigCgaCveaCpkgai 51 
                                       +C+ C  C ++Cp+g+ + ++++     +   +            e+C++Cg C ++Cp+ +i
  gi|330506526|ref|YP_004382954.1|  61 ACAFCALCSRVCPTGALEFRKNGIAEMDNS--YlsvaikstvvdsEKCVHCGLCCDVCPQACI 121
                                       5*************9996555544433322..23579999********************976 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 9.3e-07
                            Fer4_9  34 eaCigCgaCveaCpkgai 51 
                                       e+C++Cg C+ +Cp+gai
  gi|330506526|ref|YP_004382954.1| 145 ERCVHCGWCASVCPTGAI 162
                                       79*************997 PP

  == domain 4  score: 31.0 bits;  conditional E-value: 2e-10
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase..eaCigCgaCveaCpkgai 51 
                                       C  C++Cv+ Cpa++  +++ +   r ++ s   +aCi CgaC++aCp  ai
  gi|330506526|ref|YP_004382954.1| 179 CQACKTCVHTCPANALFNREWKAGERGEKVSHrpDACIYCGACAQACPVRAI 230
                                       **************9844444444444444445789************9887 PP

  == domain 5  score: 16.3 bits;  conditional E-value: 7.6e-06
                            Fer4_9  28 lraaseeaCigCgaCveaCpkga 50 
                                       + +++e aC+gCg Cv aCp +a
  gi|330506526|ref|YP_004382954.1| 263 CLETDEIACLGCGNCVIACPVNA 285
                                       55556689************986 PP

  == domain 6  score: 18.8 bits;  conditional E-value: 1.3e-06
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase...............eaCigCgaCveaCpkgai 51 
                                       +C gCg+Cv aCp ++ ++   +    ++ + +               e C +C +C  +Cp +ai
  gi|330506526|ref|YP_004382954.1| 270 ACLGCGNCVIACPVNALSDPYLAAGHLNELEIKpllevrdgtvkvvdqEVCGSCATCSMICPADAI 335
                                       6****************888877776665544478*************99*************987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   2.5   2.7e-06    0.0028      34      53 ..      14      33 ..       5      38 .. 0.75
   2 !   27.4   9.6   2.6e-09   2.8e-06       6      57 ..      19      77 ..      16      79 .. 0.76
   3 !   18.7   5.8   1.3e-06    0.0014      34      58 ..      99     122 ..      84     123 .. 0.80
   4 !   29.3   7.5   6.4e-10   6.7e-07       2      53 ..     141     191 ..     140     195 .. 0.81
   5 !   17.2   0.4   3.9e-06    0.0041       5      31 ..     212     235 ..     203     250 .. 0.75
   6 !   20.0  14.3   5.1e-07   0.00054       4      58 ..     267     336 ..     264     337 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.7e-06
                           Fer4_21 34 lkvvedeCvGCnlCssvCPv 53
                                        ++ d+C+GC  C++vCP 
  gi|330506526|ref|YP_004382954.1| 14 QFYLPDRCIGCGTCVQVCPK 33
                                      44568999999999999995 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.6e-09
                           Fer4_21  6 dkCigCgkCliaCedtshqai.........eidaktvlkvvedeCvGCnlCssvCPvedci 57
                                      d+CigCg C+++C++ +   i          id++ + k ++  C  C+lCs vCP+ +++
  gi|330506526|ref|YP_004382954.1| 19 DRCIGCGTCVQVCPK-GELIIgsvgavvrgLIDKDFIEKRMSGACAFCALCSRVCPT-GAL 77
                                      89************7.33333555555765566666778889**************6.665 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 1.3e-06
                           Fer4_21  34 lkvvedeCvGCnlCssvCPvedcie 58 
                                       + v +++Cv C lC +vCP + cie
  gi|330506526|ref|YP_004382954.1|  99 TVVDSEKCVHCGLCCDVCP-QACIE 122
                                       356799*************.79998 PP

  == domain 4  score: 29.3 bits;  conditional E-value: 6.4e-10
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidak..tvlkvvedeCvGCnlCssvCPv 53 
                                       +id ++C++Cg C+ +C+   + ai++++    ++   ++ C +C+ C++ CP 
  gi|330506526|ref|YP_004382954.1| 141 IIDLERCVHCGWCASVCP---TGAISFEKPfaGTFSRDDNVCQACKTCVHTCPA 191
                                       6999**************...57887775511455667889************6 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 3.9e-06
                           Fer4_21   5 edkCigCgkCliaCedtshqaieidak 31 
                                       +d Ci Cg C++aC+   + ai +++ 
  gi|330506526|ref|YP_004382954.1| 212 PDACIYCGACAQACP---VRAIVVSKT 235
                                       577888888888888...566666555 PP

  == domain 6  score: 20.0 bits;  conditional E-value: 5.1e-07
                           Fer4_21   4 dedkCigCgkCliaCedtshqai...................eidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       de  C+gCg+C+iaC+ +   a+                   e+ + tv  v ++ C  C+ Cs +CP  d+i+
  gi|330506526|ref|YP_004382954.1| 267 DEIACLGCGNCVIACPVN---ALsdpylaaghlneleikpllEVRDGTVKVVDQEVCGSCATCSMICPA-DAIR 336
                                       6778************65...5544467778888777766665666666677799*************5.9997 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   2.5   2.4e-09   2.5e-06       4      21 ..      15      32 ..      12      33 .. 0.91
   2 ?    2.3   4.2       0.2   2.1e+02      13      22 .]      65      74 ..      57      74 .. 0.83
   3 !   15.7   6.2   1.1e-05     0.012       4      22 .]     100     118 ..      97     118 .. 0.89
   4 !   18.9   2.3   1.1e-06    0.0012       4      22 .]     141     159 ..     138     159 .. 0.92
   5 !   11.8   4.2   0.00019       0.2       6      22 .]     175     191 ..     172     191 .. 0.90
   6 !   16.8   3.6   4.9e-06    0.0052       7      21 ..     212     226 ..     206     227 .. 0.89
   7 !   16.3   2.7   7.2e-06    0.0076       9      21 ..     270     282 ..     264     283 .. 0.84
   8 !   13.2   3.4   6.9e-05     0.073       4      22 .]     314     332 ..     312     332 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.4e-09
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      ++ +drCigCg+Cv++CP
  gi|330506526|ref|YP_004382954.1| 15 FYLPDRCIGCGTCVQVCP 32
                                      788**************9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.2
                            Fer4_2 13 CgaCvsaCPa 22
                                      C  C  +CP+
  gi|330506526|ref|YP_004382954.1| 65 CALCSRVCPT 74
                                      999******7 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.1e-05
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                       vvd+++C++Cg C ++CP+
  gi|330506526|ref|YP_004382954.1| 100 VVDSEKCVHCGLCCDVCPQ 118
                                       79*********777****6 PP

  == domain 4  score: 18.9 bits;  conditional E-value: 1.1e-06
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                        +d +rC++Cg C s+CP+
  gi|330506526|ref|YP_004382954.1| 141 IIDLERCVHCGWCASVCPT 159
                                       589***************7 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 0.00019
                            Fer4_2   6 dtdrCigCgaCvsaCPa 22 
                                       d + C +C++Cv+ CPa
  gi|330506526|ref|YP_004382954.1| 175 DDNVCQACKTCVHTCPA 191
                                       6689************8 PP

  == domain 6  score: 16.8 bits;  conditional E-value: 4.9e-06
                            Fer4_2   7 tdrCigCgaCvsaCP 21 
                                       +d+Ci CgaC +aCP
  gi|330506526|ref|YP_004382954.1| 212 PDACIYCGACAQACP 226
                                       89************* PP

  == domain 7  score: 16.3 bits;  conditional E-value: 7.2e-06
                            Fer4_2   9 rCigCgaCvsaCP 21 
                                       +C+gCg Cv aCP
  gi|330506526|ref|YP_004382954.1| 270 ACLGCGNCVIACP 282
                                       8************ PP

  == domain 8  score: 13.2 bits;  conditional E-value: 6.9e-05
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                       vvd + C +C +C   CPa
  gi|330506526|ref|YP_004382954.1| 314 VVDQEVCGSCATCSMICPA 332
                                       79****************8 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   3.0   0.00013      0.13      49      63 ..      19      33 ..       5      35 .. 0.74
   2 !   15.7   9.8   1.5e-05     0.016       3      64 ..      19      75 ..      17      76 .. 0.68
   3 !   27.6  11.8   2.9e-09   3.1e-06       2      64 ..     103     160 ..     102     161 .. 0.87
   4 ?    5.2   5.6     0.027        29      51      64 ..     179     192 ..     174     193 .. 0.85
   5 !   24.8   8.9   2.2e-08   2.3e-05       3      64 ..     213     284 ..     211     285 .. 0.71
   6 !   10.7  11.0   0.00052      0.55       4      63 ..     270     332 ..     267     334 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                            Fer4_8 49 wsCttcgaCtevCpv 63
                                      ++C +cg C++vCp+
  gi|330506526|ref|YP_004382954.1| 19 DRCIGCGTCVQVCPK 33
                                      678888888888887 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.5e-05
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      ++Ci+Cg C + Cp  +          rg   + +  e     +++ ++C  c  C++vCp+g
  gi|330506526|ref|YP_004382954.1| 19 DRCIGCGTCVQVCPKGELIIgSVGAVVRGLIDK-DFIE-----KRMSGACAFCALCSRVCPTG 75
                                      58************5555542333333333333.2222.....345899************87 PP

  == domain 3  score: 27.6 bits;  conditional E-value: 2.9e-09
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                        ekC++Cg+C + Cp +  + ++++ a+++  + v  +        l++C++cg C++vCp+g
  gi|330506526|ref|YP_004382954.1| 103 SEKCVHCGLCCDVCPQACIELEDRHLAEDGSLK-VGGRTI----IDLERCVHCGWCASVCPTG 160
                                       689************988888888888888888.777777....56***************87 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.027
                            Fer4_8  51 CttcgaCtevCpvg 64 
                                       C++c+ C+  Cp +
  gi|330506526|ref|YP_004382954.1| 179 CQACKTCVHTCPAN 192
                                       99999999999976 PP

  == domain 5  score: 24.8 bits;  conditional E-value: 2.2e-08
                            Fer4_8   3 ekCieCgaCqsaCp....vlrrtk.khlldargeaae.............dvqeeqvleeeealwsCttcgaCtevC 61 
                                       ++Ci CgaC +aCp    v+++t+    ++ +g  ++             +         e+   +C++cg+C+ +C
  gi|330506526|ref|YP_004382954.1| 213 DACIYCGACAQACPvraiVVSKTAiIPEMKGKGAFEKklalplprptltsC-L-------ETDEIACLGCGNCVIAC 281
                                       58************7777677776555555555555566666666444422.2.......555579*********** PP

                            Fer4_8  62 pvg 64 
                                       pv+
  gi|330506526|ref|YP_004382954.1| 282 PVN 284
                                       *97 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.00052
                            Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaae..............dvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       +C +Cg C  aCpv   ++  ++ a g  +e              +v++++v         C +c  C+  Cp 
  gi|330506526|ref|YP_004382954.1| 270 ACLGCGNCVIACPVNALSD--PYLAAGHLNEleikpllevrdgtvKVVDQEV---------CGSCATCSMICPA 332
                                       7************554443..2223333333235554433322212444444.........9999999999997 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.5   1.6e-05     0.017      41      59 ..      16      34 ..       1      35 [. 0.71
   2 !   21.4   8.4   2.5e-07   0.00026       1      59 [.      20      75 ..      20      77 .. 0.81
   3 !    9.4  17.0    0.0015       1.5       1      58 [.      61     118 ..      61     121 .. 0.73
   4 !   14.1  15.6   5.1e-05     0.054       1      59 [.     105     160 ..     105     162 .. 0.79
   5 !   10.7  13.7   0.00055      0.58       2      57 ..     179     226 ..     178     229 .. 0.82
   6 !   13.3   7.8   8.6e-05      0.09       1      59 [.     270     333 ..     270     334 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                           Fer4_17 41 ekaslCieCgeCerkCPqg 59
                                         ++Ci+Cg C+++CP+g
  gi|330506526|ref|YP_004382954.1| 16 YLPDRCIGCGTCVQVCPKG 34
                                      4568899999999999975 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2.5e-07
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleea.ekeekaslCieCgeCerkCPqg 59
                                      rCi+Cg C+++Cp +e +      ++r     l+++  +++++ + C+ C +C+r+CP g
  gi|330506526|ref|YP_004382954.1| 20 RCIGCGTCVQVCPKGELIIGSVGAVVRG----LIDKDfIEKRMSGACAFCALCSRVCPTG 75
                                      7***************987766666665....444432667899**************86 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0015
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekee..kaslCieCgeCerkCPq 58 
                                       +C+ C+ C ++Cp+++   + +k+ ++++ ++ l  a+k++    ++C++Cg+C  +CPq
  gi|330506526|ref|YP_004382954.1|  61 ACAFCALCSRVCPTGAL--EFRKNGIAEMDNSYLSVAIKSTvvDSEKCVHCGLCCDVCPQ 118
                                       59***********9877..233455555555555555555422679*************8 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 5.1e-05
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       +C +Cg C ++Cp+  +  +  + l+++ +l+  +++      ++C++Cg C+++CP g
  gi|330506526|ref|YP_004382954.1| 105 KCVHCGLCCDVCPQACIELE-DRHLAEDGSLKVGGRT--IIDLERCVHCGWCASVCPTG 160
                                       6************9777665.5568888667544443..4689**************86 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00055
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57 
                                       C+ C+ C+  Cp ++  +        ++k+g+ +e + +++ + Ci Cg C+++CP
  gi|330506526|ref|YP_004382954.1| 179 CQACKTCVHTCPANALFNR-------EWKAGERGE-KVSHRPDACIYCGACAQACP 226
                                       9************999886.......566653333.45799*************** PP

  == domain 6  score: 13.3 bits;  conditional E-value: 8.6e-05
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepk.kllraaklglleeaeke....ekaslCieCgeCerkCPqg 59 
                                       +C +Cg C+ +Cp ++  d + +   l++++++ l e+ +        + C +C  C++ CP++
  gi|330506526|ref|YP_004382954.1| 270 ACLGCGNCVIACPVNALSDPYLAaGHLNELEIKPLLEVRDGtvkvVDQEVCGSCATCSMICPAD 333
                                       5**************99887754258888888544444443332146688************86 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   1.8   2.3e-07   0.00024       1      16 [.      18      33 ..      18      40 .. 0.93
   2 ?    1.5   3.5      0.53   5.6e+02       4      17 .]      62      75 ..      59      75 .. 0.83
   3 !    8.3  10.6    0.0034       3.6       1      16 [.     103     118 ..     103     121 .. 0.93
   4 !   16.6   2.5   7.8e-06    0.0082       2      17 .]     145     160 ..     144     160 .. 0.93
   5 !   12.5   2.4   0.00015      0.16       3      16 ..     178     191 ..     176     195 .. 0.90
   6 !   10.2   3.8   0.00087      0.91       1      16 [.     212     227 ..     212     229 .. 0.91
   7 !   16.8   1.9   6.8e-06    0.0072       4      17 .]     271     284 ..     265     285 .. 0.92
   8 ?    2.7   4.0      0.22   2.3e+02       1      16 [.     317     332 ..     317     333 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.3e-07
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      ++rCigCg Cv +CP 
  gi|330506526|ref|YP_004382954.1| 18 PDRCIGCGTCVQVCPK 33
                                      69*************6 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.53
                            Fer4_4  4 CigCgsCvaaCPqg 17
                                      C  C  C ++CP+g
  gi|330506526|ref|YP_004382954.1| 62 CAFCALCSRVCPTG 75
                                      666999******86 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0034
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       +e+C++Cg C ++CPq
  gi|330506526|ref|YP_004382954.1| 103 SEKCVHCGLCCDVCPQ 118
                                       69*************7 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 7.8e-06
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       erC++Cg C ++CP+g
  gi|330506526|ref|YP_004382954.1| 145 ERCVHCGWCASVCPTG 160
                                       9*************86 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 0.00015
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        C+ C+ Cv +CP 
  gi|330506526|ref|YP_004382954.1| 178 VCQACKTCVHTCPA 191
                                       6************6 PP

  == domain 6  score: 10.2 bits;  conditional E-value: 0.00087
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       ++ Ci Cg+C  aCP+
  gi|330506526|ref|YP_004382954.1| 212 PDACIYCGACAQACPV 227
                                       689************7 PP

  == domain 7  score: 16.8 bits;  conditional E-value: 6.8e-06
                            Fer4_4   4 CigCgsCvaaCPqg 17 
                                       C+gCg Cv+aCP++
  gi|330506526|ref|YP_004382954.1| 271 CLGCGNCVIACPVN 284
                                       ************75 PP

  == domain 8  score: 2.7 bits;  conditional E-value: 0.22
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       qe C  C  C  +CP 
  gi|330506526|ref|YP_004382954.1| 317 QEVCGSCATCSMICPA 332
                                       577888999******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 !   18.6   6.9   2.4e-06    0.0025       1      14 [.      21      34 ..      21      34 .. 0.97
   2 !   11.0   5.5   0.00065      0.68       1      15 []      62      76 ..      62      76 .. 0.93
   3 ?   -0.6  15.1       3.2   3.4e+03       1      12 [.     106     117 ..     106     120 .. 0.94
   4 !   14.2   6.9   6.3e-05     0.067       1      15 []     147     161 ..     147     161 .. 0.98
   5 ?    3.6   7.2      0.15   1.6e+02       1      15 []     179     193 ..     179     193 .. 0.92
   6 !   14.3   6.5   5.7e-05      0.06       1      15 []     215     229 ..     215     229 .. 0.97
   7 !   14.1   6.6   6.8e-05     0.072       1      15 []     271     285 ..     271     285 .. 0.98
   8 ?    0.4   4.9       1.5   1.6e+03       3      15 .]     322     334 ..     320     334 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-06
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+gCg+Cv+vCP+g
  gi|330506526|ref|YP_004382954.1| 21 CIGCGTCVQVCPKG 34
                                      ************98 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00065
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C  C +C +vCP+gA
  gi|330506526|ref|YP_004382954.1| 62 CAFCALCSRVCPTGA 76
                                      778***********9 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.2
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C++Cg+C +vCP
  gi|330506526|ref|YP_004382954.1| 106 CVHCGLCCDVCP 117
                                       ************ PP

  == domain 4  score: 14.2 bits;  conditional E-value: 6.3e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C++Cg C  vCP+gA
  gi|330506526|ref|YP_004382954.1| 147 CVHCGWCASVCPTGA 161
                                       **************9 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.15
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C +Cv  CP +A
  gi|330506526|ref|YP_004382954.1| 179 CQACKTCVHTCPANA 193
                                       889*9*******987 PP

  == domain 6  score: 14.3 bits;  conditional E-value: 5.7e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ CgaC ++CPv+A
  gi|330506526|ref|YP_004382954.1| 215 CIYCGACAQACPVRA 229
                                       9************98 PP

  == domain 7  score: 14.1 bits;  conditional E-value: 6.8e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCg Cv +CPv+A
  gi|330506526|ref|YP_004382954.1| 271 CLGCGNCVIACPVNA 285
                                       *************99 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 1.5
                            Fer4_3   3 gCgaCvevCPvgA 15 
                                        C +C   CP +A
  gi|330506526|ref|YP_004382954.1| 322 SCATCSMICPADA 334
                                       4889******877 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 !   14.6   0.3   3.8e-05      0.04       6      21 ..      19      34 ..      18      57 .. 0.83
   2 !    8.8   0.2    0.0025       2.7       7      33 ..      61      88 ..      59      97 .. 0.86
   3 !    8.1  16.0    0.0042       4.4       2      65 ..     100     163 ..      99     164 .. 0.77
   4 ?    4.8   0.7     0.045        48       4      20 ..     175     191 ..     173     207 .. 0.83
   5 ?    4.5   5.8     0.056        59       6      19 ..     213     226 ..     211     232 .. 0.89
   6 !    7.9   0.1    0.0047         5       4      19 ..     267     282 ..     265     305 .. 0.86
   7 ?    3.7   3.5       0.1   1.1e+02       2      19 ..     314     331 ..     314     337 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.8e-05
                           Fer4_15  6 daCigcglCvaeapev 21
                                      d+Cigcg Cv+++p+ 
  gi|330506526|ref|YP_004382954.1| 19 DRCIGCGTCVQVCPKG 34
                                      8************985 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0025
                           Fer4_15  7 aCigcglCvaea.pevfeldedglasvl 33
                                      aC  c+lC +++ +   e+ ++g+a+++
  gi|330506526|ref|YP_004382954.1| 61 ACAFCALCSRVCpTGALEFRKNGIAEMD 88
                                      7***********446899999***9987 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0042
                           Fer4_15   2 vvDrdaCigcglCvaeape.vfeldedglasvllddgeiaeg...evpddeeeaaqeAaraCPvdAIr 65 
                                       vvD ++C  cglC +++p+  +el++++la    d g ++ g    ++ ++  +    a++CP++AI+
  gi|330506526|ref|YP_004382954.1| 100 VVDSEKCVHCGLCCDVCPQaCIELEDRHLA---ED-GSLKVGgrtIIDLERCVHCGWCASVCPTGAIS 163
                                       69***************652799999****...23.3333334337777777777789*********7 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.045
                           Fer4_15   4 DrdaCigcglCvaeape 20 
                                       D + C+ c  Cv  +p 
  gi|330506526|ref|YP_004382954.1| 175 DDNVCQACKTCVHTCPA 191
                                       6778**********986 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.056
                           Fer4_15   6 daCigcglCvaeap 19 
                                       daCi cg+C++++p
  gi|330506526|ref|YP_004382954.1| 213 DACIYCGACAQACP 226
                                       89*********998 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.0047
                           Fer4_15   4 DrdaCigcglCvaeap 19 
                                       D+ aC gcg+Cv ++p
  gi|330506526|ref|YP_004382954.1| 267 DEIACLGCGNCVIACP 282
                                       7889*********998 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.1
                           Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                       vvD++ C +c+ C   +p
  gi|330506526|ref|YP_004382954.1| 314 VVDQEVCGSCATCSMICP 331
                                       69************9998 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   1.5    0.0001       0.1      58      74 ..      18      34 ..       2      42 .. 0.76
   2 !   12.4   0.2   0.00013      0.14      49      74 ..      50      75 ..      34      88 .. 0.83
   3 ?    3.9   7.3     0.057        61      57      73 ..     102     118 ..      86     127 .. 0.79
   4 !   10.2   1.3   0.00062      0.65      58      74 ..     144     160 ..     122     166 .. 0.83
   5 ?   -0.3  11.8       1.2   1.2e+03      57      95 ..     175     225 ..     166     225 .. 0.63
   6 !    8.1   1.3    0.0027       2.9      52      74 ..     206     228 ..     194     238 .. 0.77
   7 !    6.6   0.6    0.0083       8.7      58      73 ..     268     283 ..     247     287 .. 0.78
   8 ?    3.9   0.4     0.054        57      56      74 ..     315     333 ..     295     337 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                           Fer4_18 58 agdcidcescvkvcPtg 74
                                         ci c++cv+vcP g
  gi|330506526|ref|YP_004382954.1| 18 PDRCIGCGTCVQVCPKG 34
                                      467************87 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00013
                           Fer4_18 49 ekeerkekgagdcidcescvkvcPtg 74
                                      +k+  +++ +g c  c  c +vcPtg
  gi|330506526|ref|YP_004382954.1| 50 DKDFIEKRMSGACAFCALCSRVCPTG 75
                                      5677788899***************8 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.057
                           Fer4_18  57 gagdcidcescvkvcPt 73 
                                       ++ +c++c+ c +vcP 
  gi|330506526|ref|YP_004382954.1| 102 DSEKCVHCGLCCDVCPQ 118
                                       56789999999999996 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00062
                           Fer4_18  58 agdcidcescvkvcPtg 74 
                                          c++c+ c +vcPtg
  gi|330506526|ref|YP_004382954.1| 144 LERCVHCGWCASVCPTG 160
                                       567*************8 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 1.2
                           Fer4_18  57 gagdcidcescvkvcPtgi....dirk...Glqle.....ciscllcidac 95 
                                       +++ c +c++cv+ cP +     + +    G +++     ci c+ c  ac
  gi|330506526|ref|YP_004382954.1| 175 DDNVCQACKTCVHTCPANAlfnrEWKAgerGEKVShrpdaCIYCGACAQAC 225
                                       5667************97522212233111333323333488888888888 PP

  == domain 6  score: 8.1 bits;  conditional E-value: 0.0027
                           Fer4_18  52 erkekgagdcidcescvkvcPtg 74 
                                       e+ ++    ci c++c + cP+ 
  gi|330506526|ref|YP_004382954.1| 206 EKVSHRPDACIYCGACAQACPVR 228
                                       445556678***********985 PP

  == domain 7  score: 6.6 bits;  conditional E-value: 0.0083
                           Fer4_18  58 agdcidcescvkvcPt 73 
                                       +  c+ c+ cv  cP+
  gi|330506526|ref|YP_004382954.1| 268 EIACLGCGNCVIACPV 283
                                       4457777777777776 PP

  == domain 8  score: 3.9 bits;  conditional E-value: 0.054
                           Fer4_18  56 kgagdcidcescvkvcPtg 74 
                                        ++  c +c +c  +cP +
  gi|330506526|ref|YP_004382954.1| 315 VDQEVCGSCATCSMICPAD 333
                                       45667999*********75 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   2.5   5.2e-05     0.055       4      18 ..      19      33 ..      18      34 .. 0.93
   2 ?    1.0   3.0      0.59   6.2e+02       5      17 ..      61      73 ..      59      75 .. 0.90
   3 !    8.2   7.8    0.0033       3.5       1      18 [.     101     118 ..     101     123 .. 0.96
   4 !   10.6   2.1   0.00063      0.66       1      17 [.     142     158 ..     142     160 .. 0.94
   5 !   12.5   2.2   0.00016      0.17       3      18 ..     176     191 ..     175     201 .. 0.88
   6 !    6.9   5.0    0.0088       9.3       4      17 ..     213     226 ..     212     228 .. 0.93
   7 ?    6.2   3.0     0.014        15       2      17 ..     267     282 ..     266     284 .. 0.90
   8 !    8.7   4.5    0.0024       2.6       1      17 [.     315     331 ..     315     332 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.2e-05
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      d+Ci+cg+Cv+++P+
  gi|330506526|ref|YP_004382954.1| 19 DRCIGCGTCVQVCPK 33
                                      79************6 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.59
                           Fer4_13  5 tCiacgaCvelaP 17
                                       C  c++C  ++P
  gi|330506526|ref|YP_004382954.1| 61 ACAFCALCSRVCP 73
                                      5999********* PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0033
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VD ++C+ cg+C++++P+
  gi|330506526|ref|YP_004382954.1| 101 VDSEKCVHCGLCCDVCPQ 118
                                       9****************7 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00063
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       +D ++C+ cg C++++P
  gi|330506526|ref|YP_004382954.1| 142 IDLERCVHCGWCASVCP 158
                                       899************** PP

  == domain 5  score: 12.5 bits;  conditional E-value: 0.00016
                           Fer4_13   3 rdtCiacgaCvelaPd 18 
                                        + C ac++Cv+++P 
  gi|330506526|ref|YP_004382954.1| 176 DNVCQACKTCVHTCPA 191
                                       588************6 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.0088
                           Fer4_13   4 dtCiacgaCvelaP 17 
                                       d Ci cgaC++++P
  gi|330506526|ref|YP_004382954.1| 213 DACIYCGACAQACP 226
                                       78***********9 PP

  == domain 7  score: 6.2 bits;  conditional E-value: 0.014
                           Fer4_13   2 DrdtCiacgaCvelaP 17 
                                       D+  C +cg+Cv ++P
  gi|330506526|ref|YP_004382954.1| 267 DEIACLGCGNCVIACP 282
                                       6678***********9 PP

  == domain 8  score: 8.7 bits;  conditional E-value: 0.0024
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD++ C +c++C +++P
  gi|330506526|ref|YP_004382954.1| 315 VDQEVCGSCATCSMICP 331
                                       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 !   13.5   0.5   9.7e-05       0.1      78      94 ..      17      33 ..       1      35 [. 0.73
   2 ?    3.8   2.8     0.097     1e+02       2      15 ..      62      75 ..      61      94 .. 0.88
   3 ?    3.5   7.3      0.12   1.3e+02      76      94 ..     100     118 ..      77     120 .. 0.75
   4 ?    5.6   6.4     0.027        28       1      24 [.     105     127 ..     105     140 .. 0.80
   5 !    8.5   3.7    0.0034       3.6       1      15 [.     146     160 ..     146     169 .. 0.90
   6 ?    2.0   3.5      0.36   3.8e+02      80      94 ..     177     191 ..     163     193 .. 0.70
   7 ?    2.6   4.3      0.23   2.5e+02       2      24 ..     179     201 ..     177     216 .. 0.66
   8 ?    5.8   3.1     0.024        25      81      94 ..     214     227 ..     207     230 .. 0.64
   9 ?    5.7   3.2     0.025        26       2      14 ..     215     227 ..     214     250 .. 0.79
  10 !   11.3   2.1   0.00045      0.48      76      95 ..     265     284 ..     257     285 .. 0.83
  11 ?    5.2   2.0     0.035        37       2      14 ..     320     332 ..     310     335 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.7e-05
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                          C+GCg C+++cp+
  gi|330506526|ref|YP_004382954.1| 17 LPDRCIGCGTCVQVCPK 33
                                      55689999999999987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.097
                           Fer4_22  2 ClsCgaCtlvCptC 15
                                      C  C+ C+ vCpt 
  gi|330506526|ref|YP_004382954.1| 62 CAFCALCSRVCPTG 75
                                      999*********95 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.12
                           Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                        +++++Cv Cg C ++cp+
  gi|330506526|ref|YP_004382954.1| 100 VVDSEKCVHCGLCCDVCPQ 118
                                       4578889999999999986 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.027
                           Fer4_22   1 rClsCgaCtlvCptCsCfdvedet 24 
                                       +C++Cg C  vCp   C+++ed+ 
  gi|330506526|ref|YP_004382954.1| 105 KCVHCGLCCDVCPQ-ACIELEDRH 127
                                       7***********97.699998887 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0034
                           Fer4_22   1 rClsCgaCtlvCptC 15 
                                       rC++Cg C+ vCpt 
  gi|330506526|ref|YP_004382954.1| 146 RCVHCGWCASVCPTG 160
                                       7************95 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.36
                           Fer4_22  80 sgCvGCgRCieacpv 94 
                                       ++C  C  C+++cp+
  gi|330506526|ref|YP_004382954.1| 177 NVCQACKTCVHTCPA 191
                                       566667777777765 PP

  == domain 7  score: 2.6 bits;  conditional E-value: 0.23
                           Fer4_22   2 ClsCgaCtlvCptCsCfdvedet 24 
                                       C +C +C  +Cp+   f+ e ++
  gi|330506526|ref|YP_004382954.1| 179 CQACKTCVHTCPANALFNREWKA 201
                                       88999999999988777766555 PP

  == domain 8  score: 5.8 bits;  conditional E-value: 0.024
                           Fer4_22  81 gCvGCgRCieacpv 94 
                                       +C+ Cg C +acpv
  gi|330506526|ref|YP_004382954.1| 214 ACIYCGACAQACPV 227
                                       45555555555554 PP

  == domain 9  score: 5.7 bits;  conditional E-value: 0.025
                           Fer4_22   2 ClsCgaCtlvCpt 14 
                                       C+ CgaC+ +Cp 
  gi|330506526|ref|YP_004382954.1| 215 CIYCGACAQACPV 227
                                       8888888888875 PP

  == domain 10  score: 11.3 bits;  conditional E-value: 0.00045
                           Fer4_22  76 kfgesgCvGCgRCieacpvk 95 
                                       +++e +C GCg C+ acpv+
  gi|330506526|ref|YP_004382954.1| 265 ETDEIACLGCGNCVIACPVN 284
                                       56788999999999999985 PP

  == domain 11  score: 5.2 bits;  conditional E-value: 0.035
                           Fer4_22   2 ClsCgaCtlvCpt 14 
                                       C sC++C+++Cp+
  gi|330506526|ref|YP_004382954.1| 320 CGSCATCSMICPA 332
                                       7778888888874 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.2   1.3e+03      73      83 ..      19      29 ..       4      37 .. 0.75
   2 ?   10.8   3.7    0.0004      0.42      41      83 ..      63     114 ..      48     125 .. 0.69
   3 ?    8.9   2.2    0.0015       1.6      50      97 ..     116     169 ..     112     173 .. 0.70
   4 ?   -0.8   0.7       1.6   1.6e+03      71      81 ..     175     185 ..     168     191 .. 0.76
   5 ?    2.6   5.2      0.14   1.5e+02      45      90 ..     184     230 ..     173     240 .. 0.78
   6 ?   -1.7   1.0       3.1   3.2e+03      68      88 ..     264     284 ..     259     288 .. 0.78
   7 ?    4.1   0.1     0.047        50      69      94 ..     314     339 ..     301     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                                      CC--S--HHHH CS
                            ETF_QO 73 qnCvhCktCdi 83
                                        C+ C tC  
  gi|330506526|ref|YP_004382954.1| 19 DRCIGCGTCVQ 29
                                      57*******65 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0004
                                       HHS-THHHH-TTS-EEEEETT..T.......TSSEEEEE-CCC--S--HHHH CS
                            ETF_QO  41 kyagpeqryCPagvyeivede..e.......akekklqinaqnCvhCktCdi 83 
                                       ++ + ++r+CP g  e+ ++   e          k  +++++ CvhC  C  
  gi|330506526|ref|YP_004382954.1|  63 AFCALCSRVCPTGALEFRKNGiaEmdnsylsVAIKSTVVDSEKCVHCGLCCD 114
                                       688899***********995532222333334445667899******87643 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0015
                                       -TTS-EEEEETTT......TSSEEEEE-CCC--S--HHHHH-TT--EEE---ST CS
                            ETF_QO  50 CPagvyeivedee......akekklqinaqnCvhCktCdikdpsqniewvvPeG 97 
                                       CP +  e+ +++       + + +  i+ + CvhC  C    p+  i+++ P  
  gi|330506526|ref|YP_004382954.1| 116 CPQACIELEDRHLaedgslKVGGRTIIDLERCVHCGWCASVCPTGAISFEKPFA 169
                                       777766666644311112233445668899*******************99965 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.6
                                       -CCC--S--HH CS
                            ETF_QO  71 naqnCvhCktC 81 
                                       + + C  CktC
  gi|330506526|ref|YP_004382954.1| 175 DDNVCQACKTC 185
                                       56679999999 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.14
                                       THHHH-TTS-.EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--E CS
                            ETF_QO  45 peqryCPagv.yeivedeeakekklqinaqnCvhCktCdikdpsqni 90 
                                        + + CPa+  ++   ++ ++++k+      C++C +C    p + i
  gi|330506526|ref|YP_004382954.1| 184 TCVHTCPANAlFNREWKAGERGEKVSHRPDACIYCGACAQACPVRAI 230
                                       56789**986144444557789999*************887777766 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 3.1
                                       EEE-CCC--S--HHHHH-TT- CS
                            ETF_QO  68 lqinaqnCvhCktCdikdpsq 88 
                                       l+ +   C+ C  C i  p +
  gi|330506526|ref|YP_004382954.1| 264 LETDEIACLGCGNCVIACPVN 284
                                       5566778*******9988865 PP

  == domain 7  score: 4.1 bits;  conditional E-value: 0.047
                                       EE-CCC--S--HHHHH-TT--EEE-- CS
                            ETF_QO  69 qinaqnCvhCktCdikdpsqniewvv 94 
                                       +++ + C  C tC++  p + i+ v+
  gi|330506526|ref|YP_004382954.1| 314 VVDQEVCGSCATCSMICPADAIRLVP 339
                                       46778899***********9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2435.69
//
Query:       gi|330506527|ref|YP_004382955.1|  [L=74]
Description: hypothetical protein MCON_0243 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-05   25.1   0.1    2.4e-05   24.9   0.1    1.1  1  ThiS            ThiS family
  ------ inclusion threshold ------
      0.057   13.3   0.0      0.057   13.3   0.0    1.0  1  Thioredoxin_15  Thioredoxin-like 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 !   24.9   0.1   2.7e-09   2.4e-05      14      77 .]      20      74 .]      10      74 .] 0.89

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.7e-09
                                      EEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                              ThiS 14 eelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                      ++++ a +  ++e+l++L+ +       + v+v +Ng+iv +   ++     De+ i+ +V GG
  gi|330506527|ref|YP_004382955.1| 20 RVELAAKDRLIEEILKELKINS------EEVIVTLNGRIVAE---EETAGGSDELKIFRIVHGG 74
                                      556666778899**********......**************...8888**************9 PP

>> Thioredoxin_15  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.4e-06     0.057     128     158 ..      24      54 ..       7      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.4e-06
                                       ..HHHHHHHHHHHTT--TT-EEEEETTEEEE CS
                    Thioredoxin_15 128 kdylkalqkflrvlglepgqnavilNGRvvg 158
                                       +++ +  +++l++l++++++  v lNGR+v 
  gi|330506527|ref|YP_004382955.1|  24 AAKDRLIEEILKELKINSEEVIVTLNGRIVA 54 
                                       556677899********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 583.47
//
Query:       gi|330506528|ref|YP_004382956.1|  [L=241]
Description: moeB/thiF molybdopterin or thiamine synthase protein [Methanosaeta concilii GP6]
Scores for complete 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-63  214.4   0.0    1.7e-63  214.2   0.0    1.0  1  ThiF             ThiF family
  ------ inclusion threshold ------
       0.12   12.4   0.1       0.22   11.6   0.0    1.5  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.18   11.5   0.0        6.4    6.4   0.0    2.1  2  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
       0.18   11.7   0.0       0.29   11.1   0.0    1.2  1  T3SS_needle_reg  YopR, type III needle-polymerisation regulat
       0.21   11.4   0.0       0.31   10.9   0.0    1.2  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.2   0.0   4.8e-67   1.7e-63       1     240 [.      10     235 ..      10     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 214.2 bits;  conditional E-value: 4.8e-67
                                       THHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   1 ysrqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaeva 77 
                                       ysrq++l++e+gqe+L++++v++ GaGglGs +  ++a+sG+g+++++D D ++lsNlnRq+l+++ d G++Ka++a
  gi|330506528|ref|YP_004382956.1|  10 YSRQIRLFAEEGQERLKKKRVFIAGAGGLGSVISLYMAASGFGRIRIADCDSVDLSNLNRQILHGSLDLGRSKAQSA 86 
                                       89*************************************************************************** PP

                                       HHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  78 aealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviip 154
                                        e l++inp+ e+ea++e+i++e++ + l++++D+++da+Dn++ar+l+n+a+ +++ipl +++ +gf+gq+++i+p
  gi|330506528|ref|YP_004382956.1|  87 LETLSDINPEGEIEALQEKISAENI-NALVQGCDMIMDAMDNFPARYLLNHAALERRIPLFHGAISGFQGQATTILP 162
                                       **********************996.5************************************************** PP

                                       CCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 155 gktgcyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfen 231
                                       g+t+c++C +p   + p+ ++ p+          +++t++v+++++++e++k+  g+ +l +++l   d+l+s++e+
  gi|330506528|ref|YP_004382956.1| 163 GRTACLRCIFP---RAPPAQESPA----------LGSTCGVIGSIQVNEAIKFALGRGELLKNRLLLWDGLSSTLEE 226
                                       **********9...8887776555..........59******************999999999999*********** PP

                                       ECCEEEEEE CS
                                       xxxxxxxxx RF
                              ThiF 232 velerakks 240
                                       v +e++  +
  gi|330506528|ref|YP_004382956.1| 227 VSCEKSMSC 235
                                       **9887655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.1e-05      0.22       3      44 ..      18      59 ..      16      88 .. 0.86
   2 ?   -3.7   0.0       3.3   1.2e+04      64      80 ..     106     122 ..     100     127 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.1e-05
                                      HHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEES CS
                      Shikimate_DH  3 akkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNR 44
                                      a++  e+lk+k+v + GaG +++ +  +++a+g+ ++ +a  
  gi|330506528|ref|YP_004382956.1| 18 AEEGQERLKKKRVFIAGAGGLGSVISLYMAASGFGRIRIADC 59
                                      5666779******************************99875 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.3
                                       EEGCGHHHHHHT-SEEE CS
                      Shikimate_DH  64 lkleelkellaeadvvi 80 
                                       ++ e++++l++ +d+++
  gi|330506528|ref|YP_004382956.1| 106 ISAENINALVQGCDMIM 122
                                       44556666666666665 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0018       6.4      26      62 ..      21      57 ..      12      64 .. 0.78
   2 ?    2.9   0.0     0.021        75     121     145 ..     101     124 ..     100     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0018
                                      TTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEE CS
                     ELFV_dehydrog 26 kldslegkrvaisGsGnvgsyaallltelgakvvavs 62
                                      ++++l++krv i G G +gs+  l ++  g   + + 
  gi|330506528|ref|YP_004382956.1| 21 GQERLKKKRVFIAGAGGLGSVISLYMAASGFGRIRIA 57
                                      56689***************99998887776555555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.021
                                       SSTTSB-HHHHTHTHHTT-SEEE-S CS
                     ELFV_dehydrog 121 AtqneideenakalikngvklvvEg 145
                                       A+q++i++en++al++ g+++++ +
  gi|330506528|ref|YP_004382956.1| 101 ALQEKISAENINALVQ-GCDMIMDA 124
                                       89**********9999.9*999875 PP

>> T3SS_needle_reg  YopR, type III needle-polymerisation regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.2e-05      0.29      64     136 ..      51     125 ..      41     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.2e-05
                                       HTT--S---HHHHHHHH.HHHHHHHS-SSHHHHHHHHHHHHT----H...HHHHHHHHH.HHHH-XXXXXXXXXX CS
                   T3SS_needle_reg  64 fgglqgsvkPplDlpeL.rkvlrqfaplGkqkeavLlevleeikplPeneylsdLirke.Lkilipknamvdnll 136
                                       fg  +     ++Dl++L r++l+ +  lG+ k +  le l++i p  e e l + i  e ++ l++   m+ + +
  gi|330506528|ref|YP_004382956.1|  51 FGRIRIADCDSVDLSNLnRQILHGSLDLGRSKAQSALETLSDINPEGEIEALQEKISAEnINALVQGCDMIMDAM 125
                                       55555555668999999789**********************************998653788888888876666 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   0.0   8.7e-05      0.31       2      85 ..      30     124 ..      29     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.7e-05
                                       EEEE--SCCHHHHHHHHHHTT-.EEEEE-S-HHHHHHHHHHHHH...HHHCCTTTTSS-.......HHHHCCCHHCE CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagl.eVvlvdiseealekalekiek...sleklvekgklk.......eeeveaalari 67 
                                       v + GaG +G+ i   +a++g+ ++++ d+++  l + +++i +    l + +++ +l+       e e+ea+ ++i
  gi|330506528|ref|YP_004382956.1|  30 VFIAGAGGLGSVISLYMAASGFgRIRIADCDSVDLSNLNRQILHgslDLGRSKAQSALEtlsdinpEGEIEALQEKI 106
                                       7799*****************978******99999999998877545555555555555666777777777777777 PP

                                       EEES-HHHHH.C-SEEEE- CS
                           3HCDH_N  68 sfttdleeav.dadlviEa 85 
                                       s+ ++++++v ++d+++ a
  gi|330506528|ref|YP_004382956.1| 107 SA-ENINALVqGCDMIMDA 124
                                       74.4566666688887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1740.00
//
Query:       gi|330506529|ref|YP_004382957.1|  [L=132]
Description: hypothetical protein MCON_0246 [Methanosaeta concilii GP6]
Scores for complete sequence (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  148.8   0.1    1.4e-43  148.6   0.1    1.0  1  DUF1890   Domain of unknown function (DUF1890)


Domain annotation for each model (and alignments):
>> DUF1890  Domain of unknown function (DUF1890)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.6   0.1   7.9e-48   1.4e-43      11     139 .]       1     130 [.       1     130 [. 0.98

  Alignments for each domain:
  == domain 1  score: 148.6 bits;  conditional E-value: 7.9e-48
                                       THHHHHHHHHHHHHCTTEEEEEEE-HHHHHHHHHHSTT-SS-SEEEEHHHHHHH--TT..S-SEEEEEESSHHHHHH CS
                           DUF1890  11 vqtplalylanklkkkgievvvagnpaalkLlkvaDpekhYvkelvdldkaleeieek..dvdlllgfvhnDagvsy 85 
                                       +q+++++yla+klkk+g +v+vag++a  kLlk+aDpe++Yv+++ dld +++ei+ek  d+d +++f+h+Dag++y
  gi|330506529|ref|YP_004382957.1|   1 MQISIVIYLAHKLKKEGWDVTVAGTNAPIKLLKTADPEGYYVQKTADLDWIIQEIVEKkmDFDACFAFMHSDAGMAY 77 
                                       59*******************************************************99****************** PP

                                       HHHHHHHH-.SEEEEEEE-S-HHHHHHHHHH--EEEEE--SS--HHHHHHHHHH CS
                           DUF1890  86 avtlkavlnkakliaivfgkdaeelaeliefdaeviaaravHnpkplkkkldev 139
                                        +t++a+ + a  +a+vfgk+ae l e i++++e+i+a+a+Hnp plk k+d+v
  gi|330506529|ref|YP_004382957.1|  78 GATFSAISK-AVHYAVVFGKNAEALGESIDYPTEKIVAKATHNPGPLKSKIDKV 130
                                       ******666.******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 976.95
//
Query:       gi|330506530|ref|YP_004382958.1|  [L=124]
Description: hypothetical protein MCON_0247 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.5e-30  102.8   0.1    1.3e-29  102.4   0.1    1.2  1  DUF1894    Domain of unknown function (DUF1894)
  ------ inclusion threshold ------
      0.089   12.4   0.0        6.6    6.3   0.0    2.0  2  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


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 !  102.4   0.1   1.5e-33   1.3e-29       7      88 .]       1      82 [.       1      82 [. 0.98

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 1.5e-33
                                      H--S-SS-EEESSHHHHHHHHTTSEEEEES--EEES.SS---SS----EEEE--S-EEEE---SS-EEEEE-SS-GGGH CS
                           DUF1894  7 lkyeillkeasfkeceeyikkkakevyevepgykil.gvrliGvppipvgideekilfpytkPCyGtfvlkvkeseeei 84
                                      +ky+++l+++sfke++e+i+k+++evy+vepgy+i+ ++ +iGvpp+++gi+++++lf+y+kPC+Gtfv+ v +s+eei
  gi|330506530|ref|YP_004382958.1|  1 MKYKLYLERTSFKEAREFIEKNSEEVYYVEPGYRIFkDYFIIGVPPVALGIRGDEVLFTYVKPCHGTFVMGV-DSSEEI 78
                                      689*********************************9***********************************.999*** PP

                                      HHHH CS
                           DUF1894 85 eklr 88
                                      ++lr
  gi|330506530|ref|YP_004382958.1| 79 ARLR 82
                                      *998 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 ?    6.3   0.0   0.00073       6.6      10      39 ..      10      39 ..       5      47 .. 0.90
   2 ?    4.2   0.0    0.0031        27     150     196 ..      67     112 ..      60     121 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00073
                                      SSHHHHHHHHHHHGGGSSEEEEEHHHHHHH CS
                         OMPdecase 10 atarelleladkvgpsivvlKthydlvegw 39
                                      ++ +e+ e+++k  +++ +++++y +++++
  gi|330506530|ref|YP_004382958.1| 10 TSFKEAREFIEKNSEEVYYVEPGYRIFKDY 39
                                      67799**********************987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0031
                                       TTESEEECCCHTHHHHHH.TTCSCEEEHHHTTEEEEECTTCCGGGHHH CS
                         OMPdecase 150 dfvmGfvaqetlnateed.addfihltpgigleqggdgkgqqyntpek 196
                                        fvmG+ ++e+ ++++e+ ++++++  +  +  ++g  k+  + +++ 
  gi|330506530|ref|YP_004382958.1|  67 TFVMGVDSSEEIARLREKeEKKIKKTLKEGQ--KQGSEKDRTEADTKT 112
                                       69*********99555552233333333222..345555544444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1671  (0.093201); expected 358.6 (0.02)
Passed bias filter:                      808  (0.0450667); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 812.90
//
Query:       gi|330506531|ref|YP_004382959.1|  [L=92]
Description: MoaD family protein [Methanosaeta concilii GP6]
Scores for complete 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   55.8   0.0    6.1e-15   55.6   0.0    1.0  1  ThiS      ThiS family
  ------ inclusion threshold ------
      0.035   14.1   0.0      0.056   13.4   0.0    1.4  1  Med10     Transcription factor subunit Med10 of Mediator comp


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 !   55.6   0.0   6.9e-19   6.1e-15       1      77 []       5      92 .]       5      92 .] 0.97

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 6.9e-19
                                      EEETTCCHHHHT.CEEEEESSTSBHHHHHHHHHHHTCHHG.........TTTTEEEEETTEEEGC.CTTTSB--TTCEE CS
                              ThiS  1 vllfaelrelag.eeelelaegstvaelleaLgerypela.........lerrvavavNgeivpr.lwldtelkdgDev 68
                                      v+ fa+ re+ g e    ++egstv  ll+++g+  p+            ++ + +++N + +++ + l+ +l+dgDe+
  gi|330506531|ref|YP_004382959.1|  5 VRAFAQFREILGkEMDMNIPEGSTVLSLLRSIGASSPAFReqafsgsggPNDYILLMINRKRIDPlNDLSIPLNDGDEL 83
                                      5679*********************************999*********88**************88************ PP

                                      EEEESTTC- CS
                              ThiS 69 ailppVaGG 77
                                      ailppVaGG
  gi|330506531|ref|YP_004382959.1| 84 AILPPVAGG 92
                                      ********9 PP

>> Med10  Transcription factor subunit Med10 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.3e-06     0.056      93     115 ..       4      26 ..       1      31 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-06
                                       HHHHHHHHHHHHHHHHHHH-GGG CS
                             Med10  93 kmeafkkfrdvLaeelekalPel 115
                                       k++af++fr++L +e+  ++Pe 
  gi|330506531|ref|YP_004382959.1|   4 KVRAFAQFREILGKEMDMNIPEG 26 
                                       899******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 725.38
//
Query:       gi|330506532|ref|YP_004382960.1|  [L=131]
Description: molybdopterin converting factor subunit 2 [Methanosaeta concilii GP6]
Scores for complete 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-31  107.6   1.9    4.7e-31  107.4   1.9    1.0  1  MoaE        MoaE protein
  ------ inclusion threshold ------
       0.16   11.8   0.0       0.29   11.0   0.0    1.4  1  Baculo_E25  Occlusion-derived virus envelope protein E25


Domain annotation for each model (and alignments):
>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.4   1.9   5.3e-35   4.7e-31       1     113 []       4     112 ..       4     112 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 5.3e-35
                                       EESS---HHHHHHHH--TT--EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE- CS
                              MoaE   1 lteepldvaeiealvaspkaGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerwelervavvHrl 77 
                                       +t+e+++++e+ +  ++++ GA+v F+GtvRd+     ++ +e ea ++ ae++le+i  ea er++l++v ++Hr+
  gi|330506532|ref|YP_004382960.1|   4 ITAEEISIEEMIQRAKREDSGATVAFLGTVRDD----GIQMMEVEAFTEAAEAELEQIRLEAIERFGLTSVQIAHRT 76 
                                       6899******99999****************55....59************************************** PP

                                       EEEETTSEEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                              MoaE  78 GelevgeasvvvavssahRkeafeaceylidelKkr 113
                                       G+l vge +v +++++ahR+eaf+ c+y+idelKkr
  gi|330506532|ref|YP_004382960.1|  77 GRLAVGESIVAIVCTAAHRAEAFDGCRYIIDELKKR 112
                                       **********************************96 PP

>> Baculo_E25  Occlusion-derived virus envelope protein E25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.2e-05      0.29      39      77 ..       3      42 ..       1      56 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.2e-05
                        Baculo_E25 39 svaekplsiddivkeGs.dkvGansvflGvvydeglksvn 77
                                       ++ + +si++++++   +  Ga   flG+v d+g++ ++
  gi|330506532|ref|YP_004382960.1|  3 KITAEEISIEEMIQRAKrEDSGATVAFLGTVRDDGIQMME 42
                                      5788899******9874266899999*********98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 835.87
//
Query:       gi|330506533|ref|YP_004382961.1|  [L=101]
Description: CutA1 divalent ion tolerance protein [Methanosaeta concilii GP6]
Scores for complete 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  111.2   0.1    1.8e-32  111.1   0.1    1.0  1  CutA1     CutA1 divalent ion tolerance protein


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.1   0.1     1e-36   1.8e-32       3      98 ..       2      95 ..       1      96 [. 0.95

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 1e-36
                                      EEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEE CS
                             CutA1  3 vlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpeii 81
                                      vl+ta s ++ + +a++l++e+laACvni + ++S+Y W+gk++ d+E+ll+ikt++++++e+ +r++elh+ye+peii
  gi|330506533|ref|YP_004382961.1|  2 VLCTA-SPDNGEMIAKSLIKEHLAACVNISS-VNSCYLWEGKLNLDREALLIIKTEQTRIKEMISRIRELHSYELPEII 78
                                      55555.5899******************998.*********************************************** PP

                                      EEEESEEEHHHHHHHHH CS
                             CutA1 82 alpieagseaYlkWiee 98
                                      +lpi +g ++Yl+Wi++
  gi|330506533|ref|YP_004382961.1| 79 VLPIIDGYQPYLDWISQ 95
                                      ***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 783.06
//
Query:       gi|330506534|ref|YP_004382962.1|  [L=115]
Description: hypothetical protein MCON_0251 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0025   16.1   0.1     0.0033   15.7   0.1    1.1  1  EzrA      Septation ring formation regulator, EzrA


Domain annotation for each model (and alignments):
>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.8e-07    0.0033     229     288 ..      14      74 ..       5      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-07
                                       HHHHHHHHHSTTS--SGGGSSSSSHH.HHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHH CS
                              EzrA 229 eelkegykemkeegYaleelniekei.eelekkieeilerlkeleledveeelktieeeid 288
                                       ++l   + em+++gY++e++ni   + ++l+  +++  +rlk+l ++d++   + i + ++
  gi|330506534|ref|YP_004382962.1|  14 RKLAPEIVEMERHGYQIEYMNILPPLaNHLSRGLADFEQRLKKLSVDDMQYLTDMILQGME 74 
                                       66777889*************998763689********************99998887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 879.20
//
Query:       gi|330506535|ref|YP_004382963.1|  [L=267]
Description: alpha/beta fold family hydrolase [Methanosaeta concilii GP6]
Scores for complete 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   77.0   0.1    1.3e-20   74.1   0.1    1.9  2  Abhydrolase_1  alpha/beta hydrolase fold
    2.3e-20   74.2   2.5    2.8e-20   73.9   2.5    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.1e-09   37.9   0.0    1.5e-09   37.5   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
    2.8e-05   24.0   0.0    5.6e-05   23.1   0.0    1.6  1  Ser_hydrolase  Serine hydrolase
    0.00028   19.7   0.0     0.0006   18.6   0.0    1.5  2  Ndr            Ndr family
    0.00092   19.0   0.0     0.0015   18.3   0.0    1.3  1  Abhydrolase_5  Alpha/beta hydrolase family
     0.0036   16.8   0.0     0.0069   15.9   0.0    1.4  1  DUF676         Putative serine esterase (DUF676)
  ------ inclusion threshold ------
       0.02   14.6   1.1        5.3    6.7   0.0    2.4  3  PGAP1          PGAP1-like protein
      0.046   13.4   0.0      0.065   12.9   0.0    1.3  1  Esterase       Putative esterase
      0.058   13.3   0.1       0.12   12.2   0.0    1.7  2  Lipase_3       Lipase (class 3)
       0.15   11.5   0.0        1.7    8.0   0.0    2.1  2  Peptidase_S9   Prolyl oligopeptidase family
       0.21   10.7   0.0        0.3   10.2   0.0    1.2  1  LCAT           Lecithin:cholesterol acyltransferase


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 !   74.1   0.1   8.7e-24   1.3e-20       2     125 ..      23     144 ..      23     166 .. 0.90
   2 ?    0.7   0.0      0.22   3.3e+02     229     256 ..     213     240 ..     195     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 8.7e-24
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       ++v++h l+g++  w      ++L k + + +++D+rG+g S+p+++    dy   ++a+d+  +  +l++++++lv
  gi|330506535|ref|YP_004382963.1|  23 PVVFVHSLAGNASQWSM--QLDHLRK-ERRAVAFDMRGHGLSDPSSD---GDYWVETLAKDIGIVARSLDLERFVLV 93 
                                       79***********9999..999**99.********************...9************************** PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESE....CSSCCHHHHHHHHHHHHHH CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllga....idpaaslieaqrqqaksfp 125
                                       GhS+GG  + aya e+p+rV++l l+++     + ++++ie  + +++s+ 
  gi|330506535|ref|YP_004382963.1|  94 GHSLGGSASIAYAGENPHRVRGLLLVDPsgdgRMLPNEIIEPFLAALQSDD 144
                                       ****************************98886666666666666666665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.22
                                       HHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                     Abhydrolase_1 229 aledlaqllpkkrlvvisdagHlafleg 256
                                       a + l +l ++   ++is++gH+++++ 
  gi|330506535|ref|YP_004382963.1| 213 APYSLHNLVSDLPFIKISGTGHWLQMDQ 240
                                       5556666666666789*********986 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   2.5   1.8e-23   2.8e-20       1     217 [.      24     244 ..      24     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 1.8e-23
                                       EEEE--GC.....G.CHHHHHHHHCCTCEEEEE--TTST..S-GGCS--HHH..CHHHHHHHCCTT..TTSEEEEEE CS
                     Abhydrolase_6   1 vlllHGagssassW.lvapLaallaagvhvlapDlpGhG..rsdpppldled..ladlaalldelaagggpvvlvGH 72 
                                       v+++H + ++as+W    +L  l+ ++ + +a+D +GhG  +++++ + + +  + d+  ++++l  +  ++vlvGH
  gi|330506535|ref|YP_004382963.1|  24 VVFVHSLAGNASQWsM--QLDHLRKER-RAVAFDMRGHGlsDPSSDGDYWVEtlAKDIGIVARSL--DLERFVLVGH 95 
                                       8*************54..999999999.669*******964444444555444456666677777..48999***** PP

                                       TCHHHHHHHHHHCC.......EE.EEES-..----TTT.S----TTHHHHHH...TT-C..CCCHCCH......S-H CS
                     Abhydrolase_6  73 SlGGalalaaapla.....lvvg.vlldppptalpagl.laaalelllalla...llrl..lawlsre......plp 131
                                       SlGG+ + a   +a     +v+g +l+dp   +++ ++ ++ ++e++la+l+    lr+  ++w ++        + 
  gi|330506535|ref|YP_004382963.1|  96 SLGGSASIA---YAgenphRVRGlLLVDP---SGDGRMlPNEIIEPFLAALQsddYLRTirDYWQTLLvgssqvVAE 166
                                       *****9999...77777998899999999...555555566666666666664434444668888643333333333 PP

                                       SCCCCHHHCCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE..CTT-CHHHHCHHCCCHSTTEEETCE...SS CS
                     Abhydrolase_6 132 rlfladedadaawrarlarlaallaglgllpaaawadlpvpllvl..ggeDplvprllerllaqagarlpvvlpgaG 206
                                       r +      d + ++ +  + a++++l + p++ + ++  p l +  + +D+ +   l  l   +     + + g+G
  gi|330506535|ref|YP_004382963.1| 167 RVMN-----DLYATPKDVVAGAFRDSLLFDPVSMLQRYSGPKLSVisHLNDAPYS--LHNLVS-DLPF--IKISGTG 233
                                       3444.....4888888888889999999999999999999997554557777666..556665.5555..66***** PP

                                       S-HHHHSHHHH CS
                     Abhydrolase_6 207 Hlphleepdev 217
                                       H++++++pde+
  gi|330506535|ref|YP_004382963.1| 234 HWLQMDQPDEF 244
                                       *********98 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   9.7e-13   1.5e-09       7     116 ..      24     128 ..      23     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 9.7e-13
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGh 83 
                                       vv+vH la  +++ +   ++L ++  a +a+D rGhG s++       ++++ +D+  + + +      ++++l+Gh
  gi|330506535|ref|YP_004382963.1|  24 VVFVHSLAGNASQWSMQLDHLRKERRA-VAFDMRGHGLSDPSSDGDYWVETLAKDIGIVARSLD----LERFVLVGH 95 
                                       788888888888888888998877665.59*********9666555567778888877765555....457899*** PP

                       Hydrolase_4  84 SmGGliallyllrypdkvaglilsaPalkikak 116
                                       S+GG  +++y+ ++p++v+gl l+ P  + +  
  gi|330506535|ref|YP_004382963.1|  96 SLGGSASIAYAGENPHRVRGLLLVDPSGDGRML 128
                                       ************************999877743 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.7e-08   5.6e-05      38      91 ..      66     123 ..      25     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.7e-08
                                       -HHHHHHHHHHHHHC-STT.....EEEEEETCHHHHHHHHHHHTTSSSEEEEEEET--S CS
                     Ser_hydrolase  38 dledWvaaleaaveaaeek.....vvlvAHSlgclavlhaaelqlakkvagalLVapad 91 
                                       d + Wv++l++ +  + +       vlv HSlg  a++++a  + +++v+g lLV p  
  gi|330506535|ref|YP_004382963.1|  66 DGDYWVETLAKDIGIVARSldlerFVLVGHSLGGSASIAYA-GENPHRVRGLLLVDPSG 123
                                       4568999999998877766566669****************.*************9975 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     4e-07    0.0006      82     163 ..      71     151 ..      59     174 .. 0.83
   2 ?   -2.8   0.0       1.3     2e+03     250     276 ..     226     252 ..     222     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4e-07
                                       HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---S---HHHHHHHHHH.......TTT CS
                               Ndr  82 lddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinitskaagwvewakeKlsskllkkvglt 158
                                       ++ la+++  v+  ++l+ ++ +G   G      +a ++p rv gl+L+++ +  + + + + e +    l+++   
  gi|330506535|ref|YP_004382963.1|  71 VETLAKDIGIVARSLDLERFVLVGHSLGGSASIAYAGENPHRVRGLLLVDPSGDGRMLPNEIIEPFL-AALQSDDYL 146
                                       789***********************************************99887776666666666.355555555 PP

                                       S-HHH CS
                               Ndr 159 dllkd 163
                                        ++ d
  gi|330506535|ref|YP_004382963.1| 147 RTIRD 151
                                       55555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.3
                                       EEEETT-TT-HHHH-HHHHHHHHHHHH CS
                               Ndr 250 llkvadsgglvleeqPdklaeslklfl 276
                                       ++k++ +g   + +qPd     l  fl
  gi|330506535|ref|YP_004382963.1| 226 FIKISGTGHWLQMDQPDEFNWILDQFL 252
                                       799999999999****99887777776 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     1e-06    0.0015      50      92 ..      81     124 ..      73     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1e-06
                     Abhydrolase_5  50 ikeapklekfvvgGhslGGvvasrfaaee.ekiegvvflasYPe 92 
                                       +    +le+fv+ GhslGG ++  +a e+ +++ g++++    +
  gi|330506535|ref|YP_004382963.1|  81 VARSLDLERFVLVGHSLGGSASIAYAGENpHRVRGLLLVDPSGD 124
                                       5556689********************9956****998765444 PP

>> DUF676  Putative serine esterase (DUF676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.6e-06    0.0069       8      92 ..      24     101 ..      23     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.6e-06
                            DUF676   8 vVlvHGlqgnsaDlelikeqlekikeklpeekieflmsennesktfkgidvlgerlaeevlevvkkkkdknkkiSfv 84 
                                       vV+vH l gn + + +  ++l+k     +++++ f m     s+  ++ d+  e la+ +  v+++   +  +  +v
  gi|330506535|ref|YP_004382963.1|  24 VVFVHSLAGNASQWSMQLDHLRK-----ERRAVAFDMRGHGLSDPSSDGDYWVETLAKDIGIVARSLDLE--RFVLV 93 
                                       8**********************.....57899**************************98777777666..***** PP

                            DUF676  85 ghSlGgli 92 
                                       ghSlGg  
  gi|330506535|ref|YP_004382963.1|  94 GHSLGGSA 101
                                       *****964 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0036       5.3       3      21 ..      20      38 ..      19      78 .. 0.90
   2 ?    6.1   0.2    0.0054       8.1      91     105 ..      88     102 ..      81     121 .. 0.78
   3 ?   -2.2   0.0       1.8   2.7e+03     169     187 ..     180     198 ..     135     254 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0036
                             PGAP1  3 sGipVlFvpGnagsykqvr 21
                                      +G pV+Fv+ +ag+  q+ 
  gi|330506535|ref|YP_004382963.1| 20 GGLPVVFVHSLAGNASQWS 38
                                      699**************94 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0054
                             PGAP1  91 tsviliGHSmGGiva 105
                                       ++ +l+GHS+GG  +
  gi|330506535|ref|YP_004382963.1|  88 ERFVLVGHSLGGSAS 102
                                       5679********876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.8
                             PGAP1 169 itggirdsmvpaeysslee 187
                                       ++g  rds++ +  s+l+ 
  gi|330506535|ref|YP_004382963.1| 180 VAGAFRDSLLFDPVSMLQR 198
                                       4444444444444444444 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.3e-05     0.065     117     140 ..      90     113 ..      70     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.3e-05
                                       EEEEEETHHHHHHHHHHHCSTTTC CS
                          Esterase 117 ravaGqSmGGlgALilalkhpdrF 140
                                        +++G+S+GG++++ +a ++p r 
  gi|330506535|ref|YP_004382963.1|  90 FVLVGHSLGGSASIAYAGENPHRV 113
                                       589******************875 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.2e-05      0.12      65      80 ..      88     103 ..      27     108 .. 0.85
   2 ?   -3.1   0.0       4.2   6.3e+03      54      72 ..     216     234 ..     202     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.2e-05
                                       EEEEEEEETHHHHHHH CS
                          Lipase_3  65 ysivvtGHSLGgalAl 80 
                                        ++v++GHSLGg+ ++
  gi|330506535|ref|YP_004382963.1|  88 ERFVLVGHSLGGSASI 103
                                       589*********9876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.2
                                       HHHHHHHHTT-EEEEEEEE CS
                          Lipase_3  54 elkrllekypeysivvtGH 72 
                                       +l++l++  p ++i  tGH
  gi|330506535|ref|YP_004382963.1| 216 SLHNLVSDLPFIKISGTGH 234
                                       6778888888888888888 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.17   2.5e+02     161     201 ..      33      74 ..      29      76 .. 0.86
   2 ?    8.0   0.0    0.0012       1.7      61     103 ..      85     127 ..      80     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.17
                                       HHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHH.HHHHHH CS
                      Peptidase_S9 161 ealklvaaLqkkgknvlllifpdegHgvgkprakv.eelarl 201
                                       +a ++  +L+   k+ + + f   gHg+++p++   +++++l
  gi|330506535|ref|YP_004382963.1|  33 NASQWSMQLDHLRKERRAVAFDMRGHGLSDPSSDGdYWVETL 74 
                                       67788889999999999999************9998888765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0012
                                       --GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE---CCC CS
                      Peptidase_S9  61 vdserlaitGgSyGGyltgaalnqrpdlFkaavaevpvvdvlr 103
                                        d er ++ G+S GG  + a ++++p++ ++++ ++p  d ++
  gi|330506535|ref|YP_004382963.1|  85 LDLERFVLVGHSLGGSASIAYAGENPHRVRGLLLVDPSGDGRM 127
                                       6899***********************9999999999888665 PP

>> LCAT  Lecithin:cholesterol acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0002       0.3      83     134 ..      46     101 ..      27     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                              LCAT  83 knktvvaapYDWRls.....leerdkYfskLkelieealk.lsgkkvvliaHSmGnll 134
                                       k++  +a+++D R         + d + + L++ i  + + l+ ++ vl++HS+G+  
  gi|330506535|ref|YP_004382963.1|  46 KER--RAVAFDMRGHglsdpSSDGDYWVETLAKDIGIVARsLDLERFVLVGHSLGGSA 101
                                       445..899*****87777956666777789******999989*************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1993.90
//
Query:       gi|330506536|ref|YP_004382964.1|  [L=270]
Description: NADP oxidoreductase coenzyme F420-dependent [Methanosaeta concilii GP6]
Scores for complete 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-21   75.8   0.1    9.2e-21   74.2   0.0    1.8  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    1.1e-15   57.7   0.3    2.2e-15   56.7   0.3    1.5  1  P5CR_dimer       Pyrroline-5-carboxylate reductase dimerisati
    2.3e-08   34.4   0.0    4.1e-08   33.6   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    2.8e-07   30.7   0.0    1.1e-06   28.8   0.0    1.9  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    1.7e-05   25.1   0.1    6.9e-05   23.1   0.1    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    5.8e-05   22.9   0.1    0.00012   22.0   0.1    1.5  1  Rossmann-like    Rossmann-like domain
  ------ inclusion threshold ------
      0.012   16.4   0.0      0.025   15.4   0.0    1.6  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.013   14.9   0.0      0.028   13.8   0.0    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.059   12.4   0.0       0.11   11.4   0.0    1.4  1  PDH              Prephenate dehydrogenase
      0.063   12.9   0.3       0.29   10.8   0.3    1.9  1  ApbA             Ketopantoate reductase PanE/ApbA
       0.11   12.4   0.3        2.6    8.0   0.3    2.3  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge


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 !   74.2   0.0   5.7e-24   9.2e-21       2      96 ..       4      96 ..       3      97 .. 0.95
   2 ?   -2.0   0.0       3.5   5.7e+03      60      81 ..     233     254 ..     221     261 .. 0.65

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 5.7e-24
                                      EEEETTSHHHHHHHHHHHHTTS.-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaaga.qpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevls 79
                                       giiG+G+mg+ la+ ++++ga + +e++v  +r++eka++la++lgv++    n ++ae++dv++l+v+p d++ v++
  gi|330506536|ref|YP_004382964.1|  4 YGIIGTGHMGSMLAEEFIRRGAiNREELWVS-NRSQEKAQKLARKLGVRAAD--NLKVAERSDVLFLCVRPVDLKGVIA 79
                                      59***************************66.**************966665..************************* PP

                                      HCGHHHHTTSEEEEESS CS
                     F420_oxidored 80 elakdalkgklvisvla 96
                                      e  + +  +kl++sv++
  gi|330506536|ref|YP_004382964.1| 80 ETSELLTPEKLIVSVAV 96
                                      **999*********986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                                       HH-SEEEE-S-HHHHHHHHHHC CS
                     F420_oxidored  60 eeadvvvlavkpedveevlsel 81 
                                       ee   v+ a+ pe++ ++ s+ 
  gi|330506536|ref|YP_004382964.1| 233 EEGAKVIEALSPEMFRQLFSAT 254
                                       5556666677777777666655 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 !   56.7   0.3   1.4e-18   2.2e-15       1      82 [.     158     241 ..     158     260 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 1.4e-18
                                       CCHHHHHHHHTTTHHHHHHHHHHHHHHHHHH..TT--HHHHHHHHHHHHHHHHHHHHCHSHHHHHHHH--TTSHHHH CS
                        P5CR_dimer   1 EkqldavtalsGsgpAyvflliealadagvk..lGlsreeArelaaqtvaGaaklllesepaelrdkvtspgGtTia 75 
                                       E+ql++++ l++sgpAy+  ++ ++a  + +  +G++++ A++l+++t++G+a+ll+++++++l+++v++ gG+T++
  gi|330506536|ref|YP_004382964.1| 158 EEQLEVLSDLTSSGPAYISAILREFALEASMrgAGVDKDLAEQLIKKTLIGTAALLEDESFDDLIAMVATRGGITEE 234
                                       89*********************999888884469********************98666***************** PP

                                       HHHHHHH CS
                        P5CR_dimer  76 glkelee 82 
                                       g k++e+
  gi|330506536|ref|YP_004382964.1| 235 GAKVIEA 241
                                       **99997 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   2.5e-11   4.1e-08       2      89 ..       4      94 ..       3     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.5e-11
                                      EEEE--SHHHHHHHHHHHHTT....-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSH CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkag....ykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegl 76
                                      +g+iG+G MGs +a++++++g     ++ v nr++ek+++l+ +  + a++  +++++ dv +++v+   + + vi + 
  gi|330506536|ref|YP_004382964.1|  4 YGIIGTGHMGSMLAEEFIRRGainrEELWVSNRSQEKAQKLARKLGVRAADNLKVAERSDVLFLCVRP-VDLKGVIAET 81
                                      79***************8877333369****************976666666679***********85.8899*****9 PP

                                      CCC--TT-EEEE- CS
                     NAD_binding_2 77 lealkkgdilidg 89
                                       e l ++++++ +
  gi|330506536|ref|YP_004382964.1| 82 SELLTPEKLIVSV 94
                                      9999999999865 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   6.6e-10   1.1e-06      17      83 ..       6      69 ..       2      97 .. 0.83
   2 ?   -1.6   0.0       1.6   2.6e+03      79      92 ..     250     263 ..     246     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 6.6e-10
                                      EES-SHHHHHHHHHHHCCT-...CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-S CS
                      Shikimate_DH 17 liGaGemaelvakhLlakgv...kkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisat 83
                                      +iG+G m++ +a+ ++++g+   +++ v NR++e+a++la++l+       + ++lk + +++dv++ ++
  gi|330506536|ref|YP_004382964.1|  6 IIGTGHMGSMLAEEFIRRGAinrEELWVSNRSQEKAQKLARKLGVR-----AADNLK-VAERSDVLFLCV 69
                                      9****************97644489******************544.....444444.777888888775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                                       EEE-SSSSS-SB-H CS
                      Shikimate_DH  79 visataseepilek 92 
                                       ++sat++++ +++ 
  gi|330506536|ref|YP_004382964.1| 250 LFSATSAKHRLVKD 263
                                       79******999875 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   4.2e-08   6.9e-05       3      95 ..       6     113 ..       4     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.2e-08
                                       EE--SHHHHHHHHHHHCTCCT-G.EEEEEESSHHHHHHHHCHH..............TTTCEEEEE--TTTHHHHHH CS
                   Sacchrp_dh_NADP   3 iiGaGsvGqavaellarhfdvda.eitvadrskeklealaaka..............lgvrfeaialdaenyeavLa 64 
                                       iiG G +G+ +ae+  r++ + + e+ v  rs+ek+++la k+                  +  + +d + + a ++
  gi|330506536|ref|YP_004382964.1|   6 IIGTGHMGSMLAEEFIRRGAINReELWVSNRSQEKAQKLARKLgvraadnlkvaersDVLFLCVRPVDLKGVIAETS 82 
                                       9********************99*****************999********99965333333456788888888899 PP

                                       HHHTTSSEEEE-SSGGGHHHHHHHHHHHT-E CS
                   Sacchrp_dh_NADP  65 allkegdlvvnlsppissldvlkaCietgvh 95 
                                       +ll+  +l+v++++++s +++  +C+++ ++
  gi|330506536|ref|YP_004382964.1|  83 ELLTPEKLIVSVAVDFSLRQLESLCRARAAR 113
                                       99***********************998776 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   7.1e-08   0.00012      13     103 ..       4      94 ..       2     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.1e-08
                     Rossmann-like  13 vGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlP..dvpvlevedvaaraellllavPdaelpglvkg 87 
                                        Gii++G++G+ l++ + r g +      +s+ s+e+a++     +v  ++  +va+r+++l l+v   +l g++++
  gi|330506536|ref|YP_004382964.1|   4 YGIIGTGHMGSMLAEEFIRRGAINREELWVSNRSQEKAQKLARklGVRAADNLKVAERSDVLFLCVRPVDLKGVIAE 80 
                                       59********************999999**********97655114555666689********************98 PP

                     Rossmann-like  88 laatgavraGtivaht 103
                                        ++   + + ++++ +
  gi|330506536|ref|YP_004382964.1|  81 TSEL--LTPEKLIVSV 94 
                                       7654..5555555555 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 ?   15.4   0.0   1.5e-05     0.025       3      72 ..       4      71 ..       2      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                                      EEEETTSHHHHHHHHHHHHTTTTE.EEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-G CS
                      GFO_IDH_MocA  3 vaiiGaGkigskhlrplnesqrle.evvalldpdaeraeavaesfgveaysdleelladpeidavivatpn 72
                                      ++iiG+G +gs+ ++ + ++     e   + ++++e+a+++a+++gv a ++l+      + d+++ ++++
  gi|330506536|ref|YP_004382964.1|  4 YGIIGTGHMGSMLAEEFIRRGAINrEELWVSNRSQEKAQKLARKLGVRAADNLKVAE---RSDVLFLCVRP 71
                                      79***********999999854336555599*****************998876443...36666666665 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 ?   13.8   0.0   1.7e-05     0.028      39     100 ..       4      70 ..       2      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                                       EEEES-SHHHHHHHHHHHHTT-....EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S- CS
                      2-Hacid_dh_C  39 vGiiGlGrIGqavakrlkafgm....kviaydrskkkee.eeeelgvelvsleellaesDivslhlp 100
                                        GiiG+G++G+ +a+ +   g+    ++ + +rs++k +  +++lgv+ ++  ++ ++sD+++l++ 
  gi|330506536|ref|YP_004382964.1|   4 YGIIGTGHMGSMLAEEFIRRGAinreELWVSNRSQEKAQkLARKLGVRAADNLKVAERSDVLFLCVR 70 
                                       69*********999877655554444788888887777767889999****************9885 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.9e-05      0.11      19      78 ..      36      94 ..      20     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.9e-05
                                      SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE- CS
                               PDH 19 ideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitDv 78
                                      +++eka++ l++ l+  a+d+++ ++  d+ +l+v +  ++ v++e ++ l ++ li+ v
  gi|330506536|ref|YP_004382964.1| 36 RSQEKAQK-LARKLGVRAADNLKVAERSDVLFLCVRPVDLKGVIAETSELLTPEKLIVSV 94
                                      44444433.35555556666699************888899999**99999999999866 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00018      0.29       2     101 ..       5      94 ..       4      95 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETT..CEEEEEECEEECCH.SCCCCS-ESEEEE- CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseg..geeilrppealsae.ekselepidlvivt 75 
                                        i+G+G +Gs+la +  + g         +    ++++ l ++ ++  + ++l  +  ++a+ + + +e  d+++++
  gi|330506536|ref|YP_004382964.1|   5 GIIGTGHMGSMLAEEFIRRG---------A----INREELWVSNRSqeKAQKLARKLGVRAAdNLKVAERSDVLFLC 68 
                                       58888888888888884432.........2....3333333333332222222222222222233466778****** PP

                                       SSGGGHHHHHHHHGGGECTCEEEEEE CS
                              ApbA  76 vKayqteealeeikplldpntvvlll 101
                                       v   +++ +++e  +ll+p+  ++++
  gi|330506536|ref|YP_004382964.1|  69 VRPVDLKGVIAETSELLTPEKLIVSV 94 
                                       ********************999986 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 ?    8.0   0.3    0.0016       2.6       4     102 ..       6      94 ..       4     108 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                                       EE--SHHHHHHHHHHHTTT..--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE--- CS
                    NAD_Gly3P_dh_N   4 vlGaGswGtalAkvlaeng..hevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvP 78 
                                       ++G+G  G+ lA  + ++g  ++  lwv +        +++e  + L        ++a ++l ++++++d+++l v 
  gi|330506536|ref|YP_004382964.1|   6 IIGTGHMGSMLAEEFIRRGaiNREELWVSN--------RSQEKAQKLAR---KLGVRAADNL-KVAERSDVLFLCVR 70 
                                       788888888888888888844344444433........33333333332...3345555444.56677888888888 PP

                                       HHHHHHHHHHHCCC--TT-EEEE- CS
                    NAD_Gly3P_dh_N  79 sqalrevlkklkgllkkkailvsl 102
                                          l+ v+++ ++ll++++ +vs+
  gi|330506536|ref|YP_004382964.1|  71 PVDLKGVIAETSELLTPEKLIVSV 94 
                                       888888888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1708.83
//
Query:       gi|330506537|ref|YP_004382965.1|  [L=723]
Description: AAA family ATPase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-99  329.5   0.0    4.4e-49  166.3   0.0    2.3  2  AAA              ATPase family associated with various cellul
    2.1e-29  101.5   0.5    1.2e-28   99.0   0.1    2.5  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    7.1e-28   96.2   4.0    1.8e-14   53.2   0.4    3.0  2  AAA_lid_3        AAA+ lid domain
    1.9e-16   60.6   0.0    1.3e-07   31.9   0.0    2.4  2  AAA_2            AAA domain (Cdc48 subfamily)
    3.9e-16   59.2   0.0    2.9e-08   33.6   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.6e-15   56.7   0.0    3.6e-06   27.5   0.0    3.5  3  AAA_16           AAA ATPase domain
    1.5e-14   54.2   1.1    1.8e-06   28.0   0.2    3.8  2  AAA_5            AAA domain (dynein-related subfamily)
    8.9e-13   48.6   0.0      2e-05   24.8   0.0    3.6  3  AAA_33           AAA domain
    6.1e-12   46.0   1.4     0.0014   18.9   0.1    4.1  4  AAA_22           AAA domain
    3.6e-11   42.9   0.0    0.00017   20.9   0.0    2.6  2  TIP49            TIP49 P-loop domain
    1.8e-09   37.2   1.2    6.7e-09   35.4   0.0    2.6  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    9.8e-09   35.3   0.0     0.0044   17.1   0.0    2.4  2  AAA_14           AAA domain
    1.1e-08   35.5   0.0     0.0025   18.2   0.0    2.8  2  RNA_helicase     RNA helicase
    1.9e-08   34.0   0.0     0.0045   16.4   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.9e-08   34.3   0.0     0.0043   16.8   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    2.3e-08   34.7   0.0     0.0049   17.4   0.0    2.8  2  AAA_18           AAA domain
    4.9e-08   33.4   0.1     0.0024   18.1   0.0    2.6  2  AAA_28           AAA domain
    1.5e-07   31.4   0.0      0.019   14.7   0.0    2.4  2  AAA_24           AAA domain
    2.3e-07   30.7   0.1      0.036   13.8   0.0    3.9  3  Sigma54_activat  Sigma-54 interaction domain
    7.7e-07   29.2   0.0      0.048   13.7   0.0    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    9.6e-07   28.9   0.3       0.11   12.4   0.0    3.6  3  NACHT            NACHT domain
    1.2e-06   28.3   7.4       0.31   10.6   0.2    4.4  4  AAA_25           AAA domain
    1.7e-06   27.9   0.0      0.043   13.7   0.0    2.8  2  AAA_3            ATPase family associated with various cellul
    2.7e-06   27.0   0.0      0.062   12.8   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
    3.5e-06   27.0   0.0      0.074   12.9   0.0    2.6  2  Bac_DnaA         Bacterial dnaA  protein
    5.1e-06   27.0   0.0       0.14   12.7   0.0    2.7  2  ABC_tran         ABC transporter
    5.5e-06   25.9   0.8       0.51    9.6   0.0    3.5  3  ATPase           KaiC
    6.6e-06   25.5   0.0      0.034   13.3   0.0    2.5  2  DUF815           Protein of unknown function (DUF815)
    8.4e-06   25.2   0.0      0.044   13.1   0.0    2.5  2  Zeta_toxin       Zeta toxin
    1.8e-05   24.2   0.0        0.3   10.5   0.0    3.7  4  TniB             Bacterial TniB protein
      2e-05   23.8   0.1       0.19   10.8   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    2.4e-05   23.9   0.1       0.14   11.6   0.0    2.5  2  PhoH             PhoH-like protein
    2.8e-05   24.6   0.1       0.46   10.9   0.0    2.9  2  AAA_17           AAA domain
    3.5e-05   23.8   0.0       0.34   10.8   0.0    2.6  2  ATPase_2         ATPase domain predominantly from Archaea
    0.00014   21.7   0.0       0.43   10.3   0.0    2.3  2  AAA_11           AAA domain
    0.00016   21.5   0.0       0.58    9.8   0.0    2.8  2  AAA_30           AAA domain
    0.00017   21.5   0.2       0.36   10.9   0.0    3.1  2  Vps4_C           Vps4 C terminal oligomerisation domain
     0.0002   20.6   0.0       0.42    9.7   0.0    2.8  3  NB-ARC           NB-ARC domain
    0.00051   19.4   0.1        3.2    6.9   0.0    3.7  4  KAP_NTPase       KAP family P-loop domain
    0.00059   20.2   1.8        1.9    8.8   0.0    3.7  3  AAA_19           AAA domain
    0.00084   18.7   0.0       0.52    9.5   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00085   18.3   0.0        0.3    9.9   0.0    2.5  2  AFG1_ATPase      AFG1-like ATPase
     0.0011   19.1   0.0       0.53   10.4   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0026   17.5   0.1        6.9    6.3   0.0    3.7  4  Guanylate_kin    Guanylate kinase
     0.0063   16.5   0.1        6.9    6.6   0.0    3.1  3  Rad17            Rad17 P-loop domain
     0.0068   16.2   0.1        3.7    7.2   0.0    2.5  2  Cytidylate_kin   Cytidylate kinase
  ------ inclusion threshold ------
      0.014   14.4   0.0        2.9    6.9   0.0    2.4  2  T2SSE            Type II/IV secretion system protein
      0.018   14.8   0.0       0.55    9.9   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.019   14.9   0.0        5.4    7.0   0.0    2.6  2  ResIII           Type III restriction enzyme, res subunit
      0.025   14.0   0.0        2.9    7.3   0.0    2.4  2  SRPRB            Signal recognition particle receptor beta su
      0.036   13.4   0.1        8.5    5.7   0.0    2.5  2  IPT              Isopentenyl transferase
       0.04   13.6   0.0        8.7    6.2   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
       0.05   12.8   0.0        7.7    5.6   0.0    2.3  2  PIF1             PIF1-like helicase
       0.06   13.2   0.0        7.1    6.4   0.0    2.7  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.069   12.9   0.1         11    5.7   0.0    2.6  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.073   12.8   0.0        0.2   11.4   0.0    1.7  1  cIII             cIII protein family
      0.074   13.3   0.0         18    5.6   0.0    2.5  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.086   12.7   5.9        3.7    7.4   0.1    4.4  4  NTPase_1         NTPase
       0.14   11.3   0.0        5.1    6.2   0.0    2.3  2  DAP3             Mitochondrial ribosomal death-associated pro
       0.22   10.3   0.0        6.7    5.4   0.0    2.1  2  PPV_E1_C         Papillomavirus 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 !  166.3   0.0   1.5e-51   4.4e-49       1     131 [.     215     344 ..     215     345 .. 0.98
   2 !  161.1   0.0   5.8e-50   1.7e-47       1     131 [.     488     619 ..     488     620 .. 0.97

  Alignments for each domain:
  == domain 1  score: 166.3 bits;  conditional E-value: 1.5e-51
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vllyGppGtGKTllaka+a+e++++f ++sg+e++sky gese+k+r+lfk+a+e+a psi++iDEid++a++r++ 
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASETNAHFETLSGPEIMSKYYGESEEKLRQLFKTAEEQA-PSIILIDEIDSIAPKREEV 290
                                       79******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLl+ +dg++++ +kv+vi+atnrpd++dpal+r gRfdr+iei+
  gi|330506537|ref|YP_004382965.1| 291 TGEVERRVVAQLLALMDGMETR-GKVVVIAATNRPDSIDPALRRpGRFDREIEIG 344
                                       *********************6.77***************************996 PP

  == domain 2  score: 161.1 bits;  conditional E-value: 5.8e-50
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..T CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..s 75 
                                       +llyGppGtGKT+lakava+e++++f++i+g+e+lsk+vgesek +re+f++a++ a ps++f+DEid++a+sr   
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATESQANFISIKGPEFLSKWVGESEKAVRETFRKARQAA-PSVVFLDEIDSIAPSRggM 563
                                       69******************************************************9.****************988 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       +s+s ++erv++q+lteldg+++  ++v+vi+atnrpd +d allr gRfdr iei+
  gi|330506537|ref|YP_004382965.1| 564 SSDSHVTERVISQILTELDGLESL-NDVMVIAATNRPDIIDAALLRpGRFDRLIEIS 619
                                       88999******************7.66***************************997 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.0   0.1   4.2e-31   1.2e-28       1      83 [.       6      88 ..       6      90 .. 0.96
   2 ?   -1.5   0.0       9.5   2.9e+03      29      52 ..     122     146 ..     115     153 .. 0.70

  Alignments for each domain:
  == domain 1  score: 99.0 bits;  conditional E-value: 4.2e-31
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVt 79
                                      +L+V ea+++dvgrgi+r+dp++++++g++ gdvv i+gk+kT+a+vwp++ped+g g++r+dg+tR+nagvsi+dkV 
  gi|330506537|ref|YP_004382965.1|  6 TLKVIEARPTDVGRGIARVDPQVLNDMGWQAGDVVSIQGKKKTAALVWPGYPEDTGHGVVRLDGNTRRNAGVSIDDKVP 84
                                      69****************************************************************************8 PP

                                      EEEE CS
                           CDC48_N 80 Vrka 83
                                       + a
  gi|330506537|ref|YP_004382965.1| 85 LKIA 88
                                      8766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 9.5
                                       S-TTSEEEEEC.CCCEEEEEEEBST CS
                           CDC48_N  29 lepgdvveieg.krkTvaivwpaep 52 
                                       + +gd++ei+   rk+  ++ + +p
  gi|330506537|ref|YP_004382965.1| 122 ITRGDIIEISVmGRKIELMATRVAP 146
                                       7899999999867766666666555 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.2   8.1e-14   2.4e-11       1      40 [.     367     406 ..     367     428 .. 0.89
   2 !   53.2   0.4     6e-17   1.8e-14       1      45 []     642     699 ..     642     699 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 8.1e-14
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitm 40 
                                       dv+ ++ A  T+G++GADlaal reAa++A+rr+++ei+ 
  gi|330506537|ref|YP_004382965.1| 367 DVNQEKFADVTHGFVGADLAALAREAAMRAIRRVLPEIDL 406
                                       6777899999***********************9988765 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 6e-17
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr.........gik....eitmedfee 45 
                                       d+dl+++A+rT+ +SGADl a+++eA++lA+r+         +++    ++++++fee
  gi|330506537|ref|YP_004382965.1| 642 DIDLDDIAKRTDKFSGADLGAVVNEAVMLAIREyvlsgqckaDEEiceyKVSKKHFEE 699
                                       89*******************************8888777773334443699999986 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   4.4e-10   1.3e-07       6     105 ..     215     308 ..     212     320 .. 0.88
   2 !   26.2   0.0   2.4e-08   7.2e-06       6      96 ..     488     574 ..     483     585 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 4.4e-10
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+lakala+  ++    ++ ++   e++     + + ++++  ++  + aee+   i+l+DEid i
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASETNA----HFETLSGPEIMS----KYYGESEEKLRQLFKTAEEQApsIILIDEIDSI 283
                                       5789******************96....999999999999....99989999999999999999899********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk e+ + +v r  V+  LL +++g
  gi|330506537|ref|YP_004382965.1| 284 APKrEEVTGEVERR-VVAQLLALMDG 308
                                       **988888888886.67778999998 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 2.4e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ill gp g+Gkt+laka+a   ++    ++i +   e+l     + + ++++  ++   +a +    +v+lDEid i
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATESQA----NFISIKGPEFLS----KWVGESEKAVRETFRKARQAApsVVFLDEIDSI 556
                                       8999****************9995....************....66666667777777777777789********** PP

                                       ---...---------HHHH CS
                             AAA_2  81 hpk...essgadvSregVq 96 
                                       +p+    ss + v  e V 
  gi|330506537|ref|YP_004382965.1| 557 APSrggMSSDSHV-TERVI 574
                                       **76422222223.33333 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   9.8e-11   2.9e-08      31     103 ..     210     290 ..     188     332 .. 0.85
   2 !   22.5   0.0   2.6e-07   7.7e-05      35      69 ..     487     521 ..     454     563 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 9.8e-11
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsra 99 
                                       ea   vllyGpPG Gkt lak +a+e ++++++ sgP +      e +  l  l+++ ee+   +++idei  ++++
  gi|330506537|ref|YP_004382965.1| 210 EAPKGVLLYGPPGTGKTLLAKALASETNAHFETLSGPEImskyygESEEKLRQLFKTAEEQapSIILIDEIDSIAPK 286
                                       566789*******************************994433333456788888777665337************9 PP

                            RuvB_N 100 veev 103
                                        eev
  gi|330506537|ref|YP_004382965.1| 287 REEV 290
                                       9998 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.6e-07
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                        +llyGpPG Gkt lak +a+e ++++ +  gP  
  gi|330506537|ref|YP_004382965.1| 487 GILLYGPPGTGKTMLAKAVATESQANFISIKGPEF 521
                                       69*************************99999964 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.2e-08   3.6e-06      16     140 ..     204     318 ..     199     319 .. 0.70
   2 !   22.2   0.0     5e-07   0.00015      15      63 ..     476     521 ..     472     527 .. 0.81
   3 ?    1.9   0.0      0.87   2.6e+02     123     148 ..     533     557 ..     528     593 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.2e-08
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysa.laqalareellrqlldea 89 
                                       +er+    p  vll+G++G+GK+ l+++l+    +++++f  l+g    +     y+    + l r +l++  +++ 
  gi|330506537|ref|YP_004382965.1| 204 FERLGVEAPKGVLLYGPPGTGKTLLAKALAS---ETNAHFetLSGPEIMS----KYYGeSEEKL-R-QLFKTAEEQ- 270
                                       66666667899******************96...3335674244433333....4444377777.6.777777777. PP

                            AAA_16  90 esaeleawrekleealaavpelagaeasrllellkrllallsrderplvlv 140
                                         a      +++++ +    e++g+ ++r+ ++l +l++ ++++++ +v++
  gi|330506537|ref|YP_004382965.1| 271 --APSIILIDEIDSIAPKREEVTGEVERRVVAQLLALMDGMETRGK-VVVI 318
                                       ..3444444556666667777888888****************888.6654 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 5e-07
                            AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                       ++e   +  p+ +ll+G++G+GK+ l+++++++ +++   f++ k  ++
  gi|330506537|ref|YP_004382965.1| 476 LFEHMDAKPPRGILLYGPPGTGKTMLAKAVATESQAN---FISIKGPEF 521
                                       56666666679********************988877...777777666 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.87
                            AAA_16 123 lkrllallsrderplvlvlDdlqwad 148
                                       +++ ++++++ + p v++lD+++ + 
  gi|330506537|ref|YP_004382965.1| 533 VRETFRKARQ-AAPSVVFLDEIDSIA 557
                                       6677788999.889********9554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.2   6.1e-09   1.8e-06       1     136 [.     214     333 ..     214     335 .. 0.75
   2 !   21.6   0.1   5.6e-07   0.00017       2     132 ..     488     604 ..     487     609 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 6.1e-09
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                       +vlL GppGtgK+ la+ la+ +n+ +e+  +++ +++        + +++++l++   + + + ++i+++DE++ +
  gi|330506537|ref|YP_004382965.1| 214 GVLLYGPPGTGKTLLAKALASETNAHFETLSGPEIMSKY-------YGESEEKLRQLFKTAEEQAPSIILIDEIDSI 283
                                       59*******************************966653.......23445555555555555699*********98 PP

                                       -...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  78 e...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                            ev++++ +    + l l++g e  ++        + via++n++d    +++palr+
  gi|330506537|ref|YP_004382965.1| 284 ApkrEEVTGEVERRVVAQLLALMDGMETRGK--------VVVIAATNRPD----SIDPALRR 333
                                       7222356666655555555555555555544........99*********....99999987 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 5.6e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       +lL GppGtgK++la+ +a   ++++  + +++++++      +   ++ ++ v     r+ar   +++++lDE++ 
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATESQANFISIKGPEFLSK------WV--GESEKAVRET-FRKARqaAPSVVFLDEIDS 555
                                       89****************************9997664......54..2222334444.4455547899********9 PP

                                       --.HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTH CS
                             AAA_5  77 ae.sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelsp 132
                                       +  s   +s  s   er ++   ++el + ++   l++++via++n++d     +++
  gi|330506537|ref|YP_004382965.1| 556 IApSRGGMSSDSHVTERVIS-QILTELDGLES---LNDVMVIAATNRPD----IIDA 604
                                       99555556666777777776.33333333333...33399999999888....4444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   6.5e-08     2e-05       2      80 ..     215     323 ..     215     349 .. 0.78
   2 !   19.1   0.0   3.9e-06    0.0012       2     111 ..     488     639 ..     488     654 .. 0.68
   3 ?   -1.2   0.0         7   2.1e+03     104     123 ..     681     700 ..     677     717 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.5e-08
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       vll G+pG+GK+ la+ l+ ++   +++ls ++++++++g+ +++++                              
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASETNahFETLSGPEIMSKYYGESEEKLRqlfktaeeqapsiilideidsiapkreeVT 291
                                       7899***************99999***************97777666566667777777777777777777655433 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatnl 80 
                                        +v+ r+ ++l +l + + ++g+ v++ atn+
  gi|330506537|ref|YP_004382965.1| 292 GEVERRVVAQLLALMDGMETRGKVVVIAATNR 323
                                       34666677777777777778888888888775 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.9e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt.............................. 46 
                                       +ll G+pG+GK+ la+ ++ + +  ++ +  ++++++ +g+ ++  +                              
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATESQanFISIKGPEFLSKWVGESEKAVRetfrkarqaapsvvfldeidsiapsrggms 564
                                       6789***************9999778888888866666663333222235555556666777777777778888877 PP

                            AAA_33  47 ............dytrvldrlyqilnelarkalsagrnvildatnlsrrerarflkl.arrlgvpvrivvvetdeet 110
                                                        + +  + ln++    ++ +r+ i+da +l++ +++r++++ +++ +++++i+ ++t+ + 
  gi|330506537|ref|YP_004382965.1| 565 sdshvtervisqI--LTELDGLESLNDVM-VIAATNRPDIIDAALLRPGRFDRLIEIsLPDEEARREILKIHTSKKP 638
                                       5555444443221..11111233455555.34556667777888999999999999977888889999988888765 PP

                            AAA_33 111 l 111
                                       l
  gi|330506537|ref|YP_004382965.1| 639 L 639
                                       5 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 7
                            AAA_33 104 vetdeetlkeRlakRaangd 123
                                       +++dee ++ ++ k+ +++ 
  gi|330506537|ref|YP_004382965.1| 681 CKADEEICEYKVSKKHFEEA 700
                                       89************999863 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   4.6e-06    0.0014       8      58 ..     215     265 ..     210     270 .. 0.77
   2 ?    6.1   0.0     0.042        13      76     118 ..     257     308 ..     248     323 .. 0.62
   3 !   17.2   0.0   1.6e-05    0.0048       8      30 ..     488     510 ..     481     526 .. 0.80
   4 ?    0.9   0.0       1.7     5e+02      78     105 ..     533     559 ..     526     584 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.6e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.erpevv.fvtlpsstsskdllr 58 
                                       ++++G++GtGKT+l++ l+++ +++ +  +  +pe++ +++  s++++++l++
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASETNAHFE--TlSGPEIMsKYYGESEEKLRQLFK 265
                                       689*****************9864433..346777777888888888888776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.042
                            AAA_22  76 eellealeqalraravielliiDEaqhlr..s........eealeeLrsllnl 118
                                       ee l++l + ++++a  ++++iDE++ +   +         +++ +L  l++ 
  gi|330506537|ref|YP_004382965.1| 257 EEKLRQLFKTAEEQAP-SIILIDEIDSIApkReevtgeveRRVVAQLLALMDG 308
                                       4444555556666666.8*********98762344455556666666666665 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 1.6e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                       ++++G++GtGKT+l++ ++ + +
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATESQ 510
                                       89****************99873 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.7
                            AAA_22  78 llealeqalraravielliiDEaqhlr.s 105
                                       ++e++++a +a+  ++++ +DE++ +  s
  gi|330506537|ref|YP_004382965.1| 533 VRETFRKARQAA--PSVVFLDEIDSIApS 559
                                       444444444444..56********98652 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.3e-06   0.00067      50     103 ..     212     264 ..     206     284 .. 0.86
   2 !   20.9   0.0   5.6e-07   0.00017      51     106 ..     486     540 ..     479     547 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.3e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX CS
                             TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqal 103
                                        ++vLl Gp+gtGkt la a++ e +   +f +lsg e+ s     +e  l q +
  gi|330506537|ref|YP_004382965.1| 212 PKGVLLYGPPGTGKTLLAKALASETN--AHFETLSGPEIMSKYYGESEeKLRQLF 264
                                       599********************977..89**********998776651455555 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.6e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                       r++Ll Gp+gtGkt la a++ e   +  f++++g e+ s  v  +e ++ +++rk+
  gi|330506537|ref|YP_004382965.1| 486 RGILLYGPPGTGKTMLAKAVATES--QANFISIKGPEFLSKWVGESEkAVRETFRKA 540
                                       89*******************985..689**************99985688999998 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       7.8   2.3e+03      32      46 ..       3      21 ..       1      27 [. 0.73
   2 !   35.4   0.0   2.2e-11   6.7e-09       2      63 ..     106     167 ..     105     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 7.8
                                      CCEEEEEEEECCCC....S CS
                           CDC48_2 32 qeiklvVvstePkg....p 46
                                      + i+l+V +  P +    +
  gi|330506537|ref|YP_004382965.1|  3 GDITLKVIEARPTDvgrgI 21
                                      5799********9955544 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 2.2e-11
                                       .SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCC..SCEEECTSCCEEESTTCC CS
                           CDC48_2   2 idgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkg..pvgitetTeielgtkpve 63 
                                       i g+ ++ylkr+ +gr++t Gd++ ++++g+ i+l ++ + P    + +i e T i++ +kp++
  gi|330506537|ref|YP_004382965.1| 106 ITGG-EEYLKRYMEGRVITRGDIIEISVMGRKIELMATRVAPPKegT-VIGERTRIDITDKPAK 167
                                       7788.88***********************************99755.5*************98 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.5e-05    0.0044       4      84 ..     214     291 ..     211     328 .. 0.73
   2 !   15.8   0.0   3.7e-05     0.011       5      76 ..     488     556 ..     485     586 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-05
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqevpew 79 
                                        +++ G+  +GKT l+k l++e      ++  ++  +   k + ++e kl +l++   +e+  +++++DEi  +   
  gi|330506537|ref|YP_004382965.1| 214 GVLLYGPPGTGKTLLAKALASETN---AHFETLSGPEIMSKYYGESEeKLRQLFKTA-EEQAPSIILIDEIDSIAPK 286
                                       57899***************9988...888888888888777666552555555554.455899*******999444 PP

                            AAA_14  80 ekalk 84 
                                       ++ + 
  gi|330506537|ref|YP_004382965.1| 287 REEVT 291
                                       44443 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.7e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekll.elileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT+l+k ++ e+     +++ i+  +   k   ++ek   e +++  ++   +++flDEi  +
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATESQ---ANFISIKGPEFLSKWVGESEKAVrETFRKA-RQAAPSVVFLDEIDSI 556
                                       6899**************98887...666666666655555555554441555554.445899*******876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   8.4e-06    0.0025       1      36 [.     215     250 ..     215     286 .. 0.86
   2 !   14.4   0.0   0.00013     0.038       1      31 [.     488     518 ..     488     597 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.4e-06
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                       ++lyGp+g+GK++lak La++   ++++ + ++++s
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASETNAHFETLSGPEIMS 250
                                       689********************9997776666655 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 0.00013
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkk 31 
                                       i+lyGp+g+GK++lak +a++ + ++ ++k 
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATESQANFISIKG 518
                                       789**************98887766633333 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.5e-05     0.013      25      44 ..     215     234 ..     208     262 .. 0.90
   2 !   16.4   0.0   1.5e-05    0.0045      25      43 ..     488     506 ..     481     557 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.5e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlps 44 
                                       +ll+GppG+GKt+lak+l+s
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALAS 234
                                       89**************9975 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.5e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKtmlak+++
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVA 506
                                       89*************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 !   16.8   0.0   1.5e-05    0.0043      44      71 ..     209     236 ..     193     280 .. 0.91
   2 !   15.0   0.0   5.1e-05     0.015      49      74 ..     487     512 ..     478     555 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-05
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                                       +e+ ++++l Gp+G+GK+ la al+ e+
  gi|330506537|ref|YP_004382965.1| 209 VEAPKGVLLYGPPGTGKTLLAKALASET 236
                                       5677899*****************9875 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.1e-05
                         IstB_IS21  49 nivllGpsGvGKshlaialgveavra 74 
                                       +i+l Gp+G+GK+ la a+++e  ++
  gi|330506537|ref|YP_004382965.1| 487 GILLYGPPGTGKTMLAKAVATESQAN 512
                                       699****************9987555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.6e-05    0.0049       1      25 [.     215     250 ..     215     322 .. 0.66
   2 !   14.6   0.0   0.00012     0.037       1      22 [.     488     509 ..     488     631 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf...........g 25 
                                       +ll G+pG+GKt lak+L+++++            +
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASETNAhfetlsgpeimS 250
                                       799***************999744454444333330 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 0.00012
                            AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                       Ill G+pG+GKt lak+++ + 
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATES 509
                                       99***************97664 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   7.9e-06    0.0024       2      44 ..     215     262 ..     214     304 .. 0.78
   2 !   12.7   0.0   0.00039      0.12       2      35 ..     488     526 ..     487     552 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.9e-06
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakged 44 
                                       + + G+++tGKT l++aLa++    ++++  pE++ +++ e  +k ++
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASEtnaHFETLsgPEIMSKYYGESEEKLRQ 262
                                       6799***************54455666666899999999887776665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00039
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareil 35 
                                       i + G+++tGKT l++a a +   ++  +  pE+  + +
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATEsqaNFISIkgPEFLSKWV 526
                                       7899***************55434333333666655554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   6.3e-05     0.019       4      75 ..     214     281 ..     211     293 .. 0.65
   2 !   14.2   0.0   8.9e-05     0.027       5      23 ..     488     508 ..     485     558 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.3e-05
                            AAA_24   4 kiliyGpsgiGKTtlakel.gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtid 75 
                                        +l+yGp+g+GKT lak l  ++ + + t  G   +    ++   s e++++ +++ +++ +  +++ iD id
  gi|330506537|ref|YP_004382965.1| 214 GVLLYGPPGTGKTLLAKALaSETNAHFETLSGPEIMSKYYGE---SEEKLRQLFKTAEEQAP--SIILIDEID 281
                                       589**************9965554555555554444433333...66666666666655555..566666666 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 8.9e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..g 23 
                                       il+yGp+g+GKT+lak    +
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVatE 508
                                       89*************987553 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0012      0.36      21      47 ..     211     237 ..     193     248 .. 0.85
   2 ?   -1.4   0.0       5.4   1.6e+03      95     143 ..     273     323 ..     252     327 .. 0.58
   3 !   13.8   0.0   0.00012     0.036      22     108 ..     485     559 ..     472     620 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0012
                                       SSS-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraiheask 47 
                                        +  vl+ G  GtGK+lla+a+ ++++
  gi|330506537|ref|YP_004382965.1| 211 APKGVLLYGPPGTGKTLLAKALASETN 237
                                       56789***************9977655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.4
                                       SEEEEETGGGS-HHHHHHHHHHHHHSEEESBT...SSSEEE--EEEEEEESS CS
                   Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqegevervG...sskeikvdvriiaatne 143
                                       +++++Dei ++ ++   ++   ++++ v ++    +  e++ +v +iaatn+
  gi|330506537|ref|YP_004382965.1| 273 SIILIDEIDSIAPKRE-EVTGEVERRVVAQLLalmDGMETRGKVVVIAATNR 323
                                       5677788877776643.34444455555444311133455566777777765 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 0.00012
                                       SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEE CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlf 98 
                                       +  +l+ G  GtGK++la+a+ ++s+   ++f+++   ++      s+  G ++ a     +e   + ++a  +++f
  gi|330506537|ref|YP_004382965.1| 485 PRGILLYGPPGTGKTMLAKAVATESQ---ANFISIKGPEF-----LSKWVGESEKAV----RETFRKARQAAPSVVF 549
                                       4679****************998876...77888765433.....244455555444....3444455778888888 PP

                                       EETGGGS-HH CS
                   Sigma54_activat  99 LDeigelple 108
                                       LDei ++ ++
  gi|330506537|ref|YP_004382965.1| 550 LDEIDSIAPS 559
                                       8888877654 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0    0.0003      0.09      11      49 ..     204     244 ..     188     264 .. 0.74
   2 !   13.7   0.0   0.00016     0.048      21      53 ..     482     521 ..     453     524 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0003
                                       HHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--..--- CS
                              TsaE  11 gkklakalgdvilLeGdLGaGKTtlvrglakalgve..evk 49 
                                        ++l+ ++ + +lL+G+ G+GKT l+++la++ + +  + +
  gi|330506537|ref|YP_004382965.1| 204 FERLGVEAPKGVLLYGPPGTGKTLLAKALASETNAHfeTLS 244
                                       44555444567*******************99987763344 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00016
                                       E.....EEEEESTTSSHHHHHHHHHHHTT--..----TTT CS
                              TsaE  21 v.....ilLeGdLGaGKTtlvrglakalgve..evkSPTF 53 
                                       +     ilL+G+ G+GKT+l++++a + + +  ++k P F
  gi|330506537|ref|YP_004382965.1| 482 AkpprgILLYGPPGTGKTMLAKAVATESQANfiSIKGPEF 521
                                       1344459*******************99998888999887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0017      0.52       3      23 ..     215     235 ..     213     242 .. 0.90
   2 ?    1.6   0.0      0.79   2.3e+02      61     130 ..     252     322 ..     241     344 .. 0.64
   3 !   12.4   0.0   0.00038      0.11       3      23 ..     488     508 ..     486     514 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0017
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G GKT L++ la++
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASE 235
                                       799***************987 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.79
                                       CCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEEEEECC CS
                             NACHT  61 qlpepaapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasllltvrpr 130
                                        + e++++ ++ ++   e++ ++ +++D +D ++ + ++   + +++v   L  l+ + + ++ ++++++ ++
  gi|330506537|ref|YP_004382965.1| 252 YYGESEEKLRQLFKTAEEQAPSI-ILIDEIDSIAPKREEvtgEVERRVVAQLLALMDG-METRGKVVVIAATN 322
                                       55666677777666655555555.678******9988889884444444455578777.44444444444444 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00038
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++l G++G GKT+L++ +a++
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATE 508
                                       799**************9987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.2     0.001      0.31      36      55 ..     215     234 ..     208     245 .. 0.89
   2 ?    7.2   0.1     0.011       3.4     128     186 ..     258     318 ..     247     326 .. 0.85
   3 !   10.3   0.1    0.0013      0.38      36      54 ..     488     506 ..     485     509 .. 0.87
   4 ?    0.5   0.0       1.3   3.9e+02     128     172 ..     531     577 ..     514     586 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.001
                            AAA_25  36 allaGapgtGKttlaldlal 55 
                                       +ll+G+pgtGKt la  la 
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALAS 234
                                       69*************99986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.011
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar..rtgaavllv 186
                                       +++++l +++ee   +  + iD ++++ +  e+   +v +++v++l  + +  +t+  v+++
  gi|330506537|ref|YP_004382965.1| 258 EKLRQLFKTAEE-QAPSIILIDEIDSIAPKREEVTGEVeRRVVAQLLALMDgmETRGKVVVI 318
                                       6789999*****.77**********************99*******9998755666666665 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0013
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pgtGKt+la  +a
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVA 506
                                       69************97666 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.3
                            AAA_25 128 advdaleaaieevegvrlvviDplsralgg..densnsdv.galveal 172
                                        +v++  +++++ + + +v +D ++++ +   +  s+s v +++++++
  gi|330506537|ref|YP_004382965.1| 531 KAVRETFRKARQ-AAPSVVFLDEIDSIAPSrgGMSSDSHVtERVISQI 577
                                       567777888899.56********9999888666666666667777765 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 !   13.7   0.0   0.00014     0.043       2      78 ..     215     287 ..     214     326 .. 0.70
   2 !   11.3   0.0   0.00077      0.23       2      39 ..     488     524 ..     487     615 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00014
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappkt 78 
                                       vll g PG++ktll+kala+  +++f+ +   p+++     G +  eek +++  ++     +++l dei+  +pk 
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASETNAHFETLS-GPEIMS-KYYGES--EEKLRQLFKTAEEQAPSIILIDEIDSIAPKR 287
                                       7999**********************9874.566664.344543..2233333333333445677777777777765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00077
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPs 39 
                                       +ll g PG++kt+l+ka+a+  +++f  i+  p++l  
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATESQANFISIK-GPEFLSK 524
                                       7999******************99998886.4666544 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00021     0.062      30      58 ..     209     237 ..     201     246 .. 0.83
   2 !   11.4   0.0   0.00058      0.17      33      61 ..     485     512 ..     457     524 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00021
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkld 58 
                                       +++ k vll+Gp GtGKt+++k l ++ +
  gi|330506537|ref|YP_004382965.1| 209 VEAPKGVLLYGPPGTGKTLLAKALASETN 237
                                       677899****************9988877 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00058
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldkek 61 
                                        + +ll+Gp GtGKt+++k + ++ +  +
  gi|330506537|ref|YP_004382965.1| 485 PRGILLYGPPGTGKTMLAKAVATESQ-AN 512
                                       4679***************9877766.44 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00025     0.074      37     176 ..     215     356 ..     209     400 .. 0.71
   2 !   11.3   0.0   0.00077      0.23      37     111 ..     488     558 ..     479     654 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00025
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagk 112
                                       +++yg+ G Gkt L ka++ e+ +++       l++ e +++     ++k  + fk     +  ++liD+i  +a k
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASETNAHF-----ETLSGPEIMSKYYGESEEKLRQLFKTAEEqAPSIILIDEIDSIAPK 286
                                       79************999988776655.....56899999999999989999999998776256899********988 PP

                                       HH.....HHH....HHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHH CS
                          Bac_DnaA 113 ek.....tqe....elfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailk 176
                                        +     ++     +l+ +++ +   gk vv+++   P +++        rf++ +  +i  p+++ rl++l+
  gi|330506537|ref|YP_004382965.1| 287 REevtgeVERrvvaQLLALMDGMETRGKVVVIAATNRPDSIDPALR-RPGRFDREI--EIGVPNRQSRLEVLQ 356
                                       5322111222111145555555566789999999999998865433.345666544..444456666666654 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00077
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflag 111
                                       +++yg+ G Gkt L ka++ e ++n+     + +++ eFl++ v   ++   e+f++  + +  v+ +D+i  +a 
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATESQANF-----ISIKGPEFLSKWVGESEKAVRETFRKARQaAPSVVFLDEIDSIAP 558
                                       79***************998877666.....557799999999999999999999987662557888899888764 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00046      0.14       7      51 ..     208     250 ..     206     341 .. 0.73
   2 !   11.5   0.0    0.0011      0.32      13      67 ..     487     539 ..     479     596 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00046
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51 
                                        +++ + v + G+ G+GK+ L+k+la +++   +++   g ++ +
  gi|330506537|ref|YP_004382965.1| 208 GVEAPKGVLLYGPPGTGKTLLAKALASETNAHFETL--SGPEIMS 250
                                       567777899*******************99877776..3333333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0011
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                        + + G+ G+GK+ L+k++a +++  +  i ++g ++ ++   +++k ++  + +
  gi|330506537|ref|YP_004382965.1| 487 GILLYGPPGTGKTMLAKAVATESQ--ANFISIKGPEFLSKWVGESEKAVRETFRK 539
                                       57899****************986..57777787777774444444444444444 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0017      0.51      15      38 ..     208     231 ..     201     242 .. 0.81
   2 ?    4.2   0.1     0.081        24     108     155 ..     260     310 ..     241     323 .. 0.71
   3 !    8.3   0.0    0.0043       1.3      21      42 ..     487     508 ..     483     538 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0017
                            ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                       G+   + vl++G pGtGKt++a+ 
  gi|330506537|ref|YP_004382965.1| 208 GVEAPKGVLLYGPPGTGKTLLAKA 231
                                       55566779*************986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.081
                            ATPase 108 ieelaeaikeikakrvviDsitgl...ayeekeavaReilrqlvrvlkklg 155
                                       +++l +  +e   + ++iD i+++    +e + +v R+ + ql+  + +++
  gi|330506537|ref|YP_004382965.1| 260 LRQLFKTAEEQAPSIILIDEIDSIapkREEVTGEVERRVVAQLLALMDGME 310
                                       445555556666678888888887432455556778999999999998775 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0043
                            ATPase  21 vvlitGepGtGKtifalqFlik 42 
                                        +l++G pGtGKt++a+  + +
  gi|330506537|ref|YP_004382965.1| 487 GILLYGPPGTGKTMLAKAVATE 508
                                       589************9876665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0016      0.49      54      88 ..     213     249 ..     203     327 .. 0.67
   2 !   13.3   0.0   0.00011     0.034      21      81 ..     444     513 ..     425     522 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0016
                            DUF815  54 nnvLLwGarGtGKSslvkallneyaeeg..Lrlieve 88 
                                       + vLL+G  GtGK  l kal +e++++   L   e+ 
  gi|330506537|ref|YP_004382965.1| 213 KGVLLYGPPGTGKTLLAKALASETNAHFetLSGPEIM 249
                                       579******************9998765445555554 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00011
                            DUF815  21 evdevklddLvgidkqkealvente.........qfleglpannvLLwGarGtGKSslvkallneyaeeg 81 
                                       e  +v++d++ g+ + k++l+e +e         ++++ +p + +LL+G  GtGK  l ka+ +e +++ 
  gi|330506537|ref|YP_004382965.1| 444 ESPNVHWDEIGGLAEVKQQLIESVEwpltyarlfEHMDAKPPRGILLYGPPGTGKTMLAKAVATESQANF 513
                                       45578888888888888888887653333332224677788899******************99988765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0     0.002      0.59      14      41 ..     210     237 ..     201     243 .. 0.87
   2 !   13.1   0.0   0.00015     0.044      13      51 ..     482     518 ..     473     524 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.002
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdele 41 
                                       e Pk +ll G pG GK+ la++l+ e++
  gi|330506537|ref|YP_004382965.1| 210 EAPKGVLLYGPPGTGKTLLAKALASETN 237
                                       89*********************99975 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00015
                        Zeta_toxin  13 qerPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                        + P  ill G pG GK+ la+++++e   q n++ +++
  gi|330506537|ref|YP_004382965.1| 482 AKPPRGILLYGPPGTGKTMLAKAVATES--QANFISIKG 518
                                       577999*********************8..999999986 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.016       4.7      25      62 ..     202     239 ..     190     249 .. 0.84
   2 ?    2.0   0.0      0.39   1.2e+02     104     132 ..     256     284 ..     247     310 .. 0.77
   3 !   10.5   0.0     0.001       0.3      25      59 ..     475     509 ..     468     518 .. 0.87
   4 ?   -2.5   0.0       9.3   2.8e+03     107     132 ..     532     557 ..     526     566 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.016
                              TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekFarlhppe 62 
                                       eL+e+   + ++ +ll+G++ +GKt +++  a++ +++
  gi|330506537|ref|YP_004382965.1| 202 ELFERLGVEAPKGVLLYGPPGTGKTLLAKALASETNAH 239
                                       5777777888999***************9988877765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.39
                              TniB 104 vskleqqvlrllrelkvrvLiiDEihnll 132
                                        +++ +q  ++ +e  + +++iDEi+++ 
  gi|330506537|ref|YP_004382965.1| 256 SEEKLRQLFKTAEEQAPSIILIDEIDSIA 284
                                       45666777788899999*********986 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.001
                              TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekFarlh 59 
                                       +L+e+ ++k ++ +ll+G++ +GKtm+++  a + 
  gi|330506537|ref|YP_004382965.1| 475 RLFEHMDAKPPRGILLYGPPGTGKTMLAKAVATES 509
                                       68999999999****************99877665 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 9.3
                              TniB 107 leqqvlrllrelkvrvLiiDEihnll 132
                                       + +++ r  r+  + v+ +DEi+++ 
  gi|330506537|ref|YP_004382965.1| 532 AVRETFRKARQAAPSVVFLDEIDSIA 557
                                       4455666778889999******9986 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   0.00071      0.21     117     136 ..     215     234 ..     213     239 .. 0.90
   2 !   10.8   0.0   0.00064      0.19     117     137 ..     488     508 ..     479     512 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00071
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v++yGp+ tGkt la+a+a 
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALAS 234
                                       899***************97 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00064
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       +++yGp+ tGkt+la+a a+ 
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATE 508
                                       899**************9975 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00047      0.14      22      46 ..     215     239 ..     205     320 .. 0.71
   2 !    9.6   0.0    0.0019      0.56      23      43 ..     489     509 ..     477     515 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00047
                                       EEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH  22 vfaiGpaGtGKtylavalavealkk 46 
                                       v   Gp GtGKt+la ala e   +
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASETNAH 239
                                       6789************999876554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0019
                                       EEE--TTSSTTHHHHHHHHHH CS
                              PhoH  23 faiGpaGtGKtylavalavea 43 
                                          Gp GtGKt+la a+a e 
  gi|330506537|ref|YP_004382965.1| 489 LLYGPPGTGKTMLAKAVATES 509
                                       568*************99875 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0    0.0018      0.54       1      65 [.     218     283 ..     218     306 .. 0.72
   2 !   10.9   0.0    0.0015      0.46       1     107 [.     491     594 ..     491     648 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0018
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeakrgglakardemrklpleekkelqkeaaeki 65 
                                       +G+PG GK+ +++ l+ +   +f+ ls  +++ +   +++ +k r+ +++++++    ++   +++i
  gi|330506537|ref|YP_004382965.1| 218 YGPPGTGKTLLAKALASETnaHFETLSGPEIMSKYYGESE-EKLRQLFKTAEEQAPSIILIDEIDSI 283
                                       7***************887457999997777766654444.45666666666555555554444445 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0015
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlv 76 
                                       +G+PG GK+ +++ ++ + +  ++s  G  + +    ++ +  r+ +rk+ +     +    +++ia   +++g+  
  gi|330506537|ref|YP_004382965.1| 491 YGPPGTGKTMLAKAVATESQANFISIkGPEFLSKWVGESEKAVRETFRKARQAAPSVVFLDEIDSIAP--SRGGMSS 565
                                       7**************99987777766566666555555445678888888777666655555556665..4677777 PP

                                       EE-SEEEETTEEEESSHHHHHHHH..SEEEE CS
                            AAA_17  77 dghprikeqagfldglpkevleelkpdaiil 107
                                       d h + +  +++l +l+   le+l+  ++i 
  gi|330506537|ref|YP_004382965.1| 566 DSHVTERVISQILTELDG--LESLNDVMVIA 594
                                       777776666666666654..55554444444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0    0.0011      0.34      21     122 ..     213     318 ..     202     322 .. 0.60
   2 !   10.1   0.0    0.0019      0.57      15      45 ..     480     510 ..     474     579 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0011
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdk.......yviyyialreesiskldefieeeeekkklekalgiavpkae 90 
                                       + +++YGp g GKt L k ++++ + + +          yy +  ee++ +l ++ ee+  +  l + + +  pk  
  gi|330506537|ref|YP_004382965.1| 213 KGVLLYGPPGTGKTLLAKALASETNAHFEtlsgpeiMSKYYGES-EEKLRQLFKTAEEQAPSIILIDEIDSIAPK-- 286
                                       55789***************999844333355444222233333.333333333324444444444444444444.. PP

                          ATPase_2  91 leeilkeksklvfkaielllekikkkgkkiii 122
                                        ee+  e  + v +++ +l++ ++ +gk ++i
  gi|330506537|ref|YP_004382965.1| 287 REEVTGEVERRVVAQLLALMDGMETRGKVVVI 318
                                       44566678888888888888888888876665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0019
                          ATPase_2  15 lerepneiyfiYGpegsGKtaLlkeiienle 45 
                                       ++ +p + +++YGp g GKt L k ++++++
  gi|330506537|ref|YP_004382965.1| 480 MDAKPPRGILLYGPPGTGKTMLAKAVATESQ 510
                                       5667777899**************9998874 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0014      0.43      17      44 ..     212     239 ..     202     277 .. 0.70
   2 !    9.0   0.0    0.0038       1.1      20      42 ..     488     510 ..     476     570 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0014
                            AAA_11  17 seitliqGPPGtgKTktivellsqllsr 44 
                                       ++ +l+ GPPGtgKT    +l s+ + +
  gi|330506537|ref|YP_004382965.1| 212 PKGVLLYGPPGTGKTLLAKALASETNAH 239
                                       556899*********9988888888633 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0038
                            AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                        l+ GPPGtgKT    ++  +  
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATESQ 510
                                       5899********77666666663 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0049       1.5      21      42 ..     215     236 ..     202     283 .. 0.88
   2 !    9.8   0.0    0.0019      0.58      10      40 ..     477     507 ..     474     518 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0049
                            AAA_30  21 avltGpAGtGKttalkalreaw 42 
                                       ++l Gp+GtGKt + kal+   
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASET 236
                                       6789**********99997655 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0019
                            AAA_30  10 vealltsgdrvavltGpAGtGKttalkalre 40 
                                       +e++ +++ r  +l Gp+GtGKt++ ka++ 
  gi|330506537|ref|YP_004382965.1| 477 FEHMDAKPPRGILLYGPPGTGKTMLAKAVAT 507
                                       566666666778899**********999976 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 ?    6.8   0.0     0.023       6.7      15      44 ..     407     436 ..     403     441 .. 0.88
   2 !   10.9   0.0    0.0012      0.36      21      51 ..     684     714 ..     680     718 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.023
                            Vps4_C  15 twmdipsdkllePpvtlkDflkalkkarpt 44 
                                        ++ ip + l + +v+ +Dfl+al++  p+
  gi|330506537|ref|YP_004382965.1| 407 EVESIPVETLNKIEVNNEDFLAALREMEPS 436
                                       67789999******************9998 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0012
                            Vps4_C  21 sdkllePpvtlkDflkalkkarptVskeDLe 51 
                                        +++ e +v+ k+f++alkk+ pt  + DL 
  gi|330506537|ref|YP_004382965.1| 684 DEEICEYKVSKKHFEEALKKVTPTAIELDLY 714
                                       578999******************8888775 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0063       1.9      22      52 ..     214     241 ..     201     257 .. 0.80
   2 ?   -2.3   0.0       6.8     2e+03     120     153 ..     340     373 ..     338     378 .. 0.82
   3 !    9.7   0.0    0.0014      0.42      17      45 ..     485     510 ..     472     592 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0063
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCCCBT CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFd 52 
                                        v l+G +G GKt lak   ++   ++ +F+
  gi|330506537|ref|YP_004382965.1| 214 GVLLYGPPGTGKTLLAKALASE---TNAHFE 241
                                       4789***********9988777...555665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.8
                                       ....HHHHCHTTSEEE.EEESBCCCCCCS-S-EEE CS
                            NB-ARC 120 kigvvlparenrlrvl.lTTRdeevanavsatsek 153
                                       +i + +p+r++rl+vl + TR + +a+ v++ +++
  gi|330506537|ref|YP_004382965.1| 340 EIEIGVPNRQSRLEVLqIHTRGMPLAKDVNQ-EKF 373
                                       789999********99678999999999998.444 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0014
                                       TSCSEEEEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  17 elqslvvalvGmgGvGKttlakqilnksd 45 
                                         +   + l+G +G GKt lak +  +s+
  gi|330506537|ref|YP_004382965.1| 485 PRG---ILLYGPPGTGKTMLAKAVATESQ 510
                                       344...889**************998854 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.18        54      23      47 ..     215     239 ..     198     244 .. 0.88
   2 ?    6.9   0.0     0.011       3.2     154     196 ..     253     294 ..     238     301 .. 0.79
   3 ?    3.6   0.0      0.11        32       9      43 ..     474     508 ..     471     524 .. 0.84
   4 ?   -0.4   0.0       1.8   5.4e+02     170     189 ..     539     560 ..     528     563 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.18
                        KAP_NTPase  23 vgLygkWGsGKssllnkledelkef 47 
                                       v Lyg+ G+GK+ l + l +e + +
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASETNAH 239
                                       89****************9998865 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                        KAP_NTPase 154 qteveelladmektLdalqkrlVvviDdLDrceteevlqllea 196
                                         e ee+l +++kt ++ q + +++iD++D++ +++   + e+
  gi|330506537|ref|YP_004382965.1| 253 YGESEEKLRQLFKTAEE-QAPSIILIDEIDSIAPKREEVTGEV 294
                                       55777789999999988.99************99987776666 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.11
                        KAP_NTPase   9 adilseptlatpivvgLygkWGsGKssllnklede 43 
                                       a +  ++++++p  + Lyg+ G+GK+ l + +  e
  gi|330506537|ref|YP_004382965.1| 474 ARLFEHMDAKPPRGILLYGPPGTGKTMLAKAVATE 508
                                       55667788899999************999887665 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.8
                        KAP_NTPase 170 a..lqkrlVvviDdLDrcetee 189
                                       +  +  + Vv++D++D++ +++
  gi|330506537|ref|YP_004382965.1| 539 KarQAAPSVVFLDEIDSIAPSR 560
                                       34566788*********98875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2     0.017       5.1      12      31 ..     214     233 ..     209     249 .. 0.81
   2 ?   -0.6   0.0         5   1.5e+03      96     126 ..     265     295 ..     248     308 .. 0.66
   3 !    8.8   0.0    0.0064       1.9      10      32 ..     485     507 ..     478     556 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.017
                            AAA_19  12 vllvtaGpGtGKTrvlkhiv 31 
                                        +l+ ++pGtGKT + k+  
  gi|330506537|ref|YP_004382965.1| 214 GVLLYGPPGTGKTLLAKALA 233
                                       5899*********8877655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 5
                            AAA_19  96 eekklqeeellivDEfqdvdelqyrLlkall 126
                                       ++ + q+  ++++DE+  + +   ++  ++ 
  gi|330506537|ref|YP_004382965.1| 265 KTAEEQAPSIILIDEIDSIAPKREEVTGEVE 295
                                       3334445669*****9999877766666555 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0064
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhiva 32 
                                        + +l+ ++pGtGKT + k++ +
  gi|330506537|ref|YP_004382965.1| 485 PRGILLYGPPGTGKTMLAKAVAT 507
                                       566899*********98776654 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   0.0    0.0018      0.52       4      25 ..     215     236 ..     212     291 .. 0.72
   2 !    7.1   0.0    0.0091       2.7       4      25 ..     488     509 ..     485     548 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0018
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       vl  G +GtGKt+++ +l+ e 
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASET 236
                                       6789**************9998 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0091
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       +l  G +GtGKt+++ ++++e 
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATES 509
                                       6789***********9999997 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0      0.02       6.1      58      79 ..     208     229 ..     180     244 .. 0.84
   2 !    9.9   0.0     0.001       0.3      49      79 ..     474     502 ..     433     509 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.02
                       AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                        ve+++g+ l+G+ G GKt l 
  gi|330506537|ref|YP_004382965.1| 208 GVEAPKGVLLYGPPGTGKTLLA 229
                                       5789***************885 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.001
                       AFG1_ATPase  49 gklfgrkrksvepvrglYlwGgvGrGKtylm 79 
                                        +lf +   + +p+rg+ l+G+ G GKt+l 
  gi|330506537|ref|YP_004382965.1| 474 ARLFEH--MDAKPPRGILLYGPPGTGKTMLA 502
                                       456653..4789*****************96 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0018      0.53      22      47 ..     213     238 ..     202     289 .. 0.68
   2 ?    6.0   0.0     0.041        12      24      47 ..     488     511 ..     475     560 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0018
                                       S-EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  22 lpvfltGekGsgkelvArlLhknsgp 47 
                                         v+l G++G+gk+l A++L+++   
  gi|330506537|ref|YP_004382965.1| 213 KGVLLYGPPGTGKTLLAKALASETNA 238
                                       569*****************987654 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.041
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       ++l G++G+gk++ A++ + +s+ 
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATESQA 511
                                       89***************9987765 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.037        11       3      31 ..     213     241 ..     211     249 .. 0.87
   2 ?    0.3   0.0       1.7     5e+02      75      95 ..     249     269 ..     244     287 .. 0.79
   3 ?    6.3   0.0     0.023       6.9       3      30 ..     486     513 ..     484     519 .. 0.88
   4 ?   -1.4   0.0       5.6   1.7e+03      74      99 ..     521     551 ..     509     556 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.037
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekfg 31 
                                       + v l gp g+Gk  l kaL se + +f 
  gi|330506537|ref|YP_004382965.1| 213 KGVLLYGPPGTGKTLLAKALASETNAHFE 241
                                       66899******************999985 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.7
                                       TTEEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                        +++yg+s e+ ++ ++++ +
  gi|330506537|ref|YP_004382965.1| 249 MSKYYGESEEKLRQLFKTAEE 269
                                       579************999876 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.023
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       r + l gp g+Gk +l ka+ +e + +f
  gi|330506537|ref|YP_004382965.1| 486 RGILLYGPPGTGKTMLAKAVATESQANF 513
                                       6789****************99998888 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 5.6
                                       ETTEEEEEEHHHHHHHHHTTSE.....EEEE CS
                     Guanylate_kin  74 fsgnlygtsveaieevlekgki.....viLD 99 
                                       f ++  g+s +a++e + k+++     v+LD
  gi|330506537|ref|YP_004382965.1| 521 FLSKWVGESEKAVRETFRKARQaapsvVFLD 551
                                       667888999999**99999998666656665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.023       6.9      48      82 ..     215     249 ..     192     291 .. 0.76
   2 ?    6.0   0.0     0.035        10      40      74 ..     480     514 ..     455     552 .. 0.77
   3 ?   -2.0   0.0       9.3   2.8e+03     131     176 ..     543     597 ..     529     603 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.023
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvsl 82 
                                       +L+ GP+G gk+   k L+ e   +++  + p  +
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASETNAHFETLSGPEIM 249
                                       5789***************9998888777766543 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.035
                             Rad17  40 LesrkkriLLisGPsGCgkstvvkvLskelgiklr 74 
                                       ++ ++ r +L+ GP+G gk+   k ++ e   +++
  gi|330506537|ref|YP_004382965.1| 480 MDAKPPRGILLYGPPGTGKTMLAKAVATESQANFI 514
                                       455666678899********999988887766555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 9.3
                             Rad17 131 tdkklilvedlP......nkfyrdsdalrevirkylrsseal...plilviteie 176
                                       +  ++++++++            ds+  + vi + l+  + l     ++vi+  +
  gi|330506537|ref|YP_004382965.1| 543 AAPSVVFLDEIDsiapsrGGMSSDSHVTERVISQILTELDGLeslNDVMVIAATN 597
                                       5556677777643223222356677788888888887766555224477777655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.023       6.9       4      26 ..     218     240 ..     215     245 .. 0.89
   2 ?    7.2   0.0     0.012       3.7       3      28 ..     490     515 ..     488     517 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.023
                                       E-STTSSHHHHHHHHHHHHT-EE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglky 26 
                                        GP g+GK  +a+ala++ ++++
  gi|330506537|ref|YP_004382965.1| 218 YGPPGTGKTLLAKALASETNAHF 240
                                       6*****************99876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                                       EE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                       + GP g+GK  +a+a+a++ ++++++
  gi|330506537|ref|YP_004382965.1| 490 LYGPPGTGKTMLAKAVATESQANFIS 515
                                       67******************999985 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0096       2.9     126     156 ..     209     239 ..     140     246 .. 0.85
   2 ?    5.1   0.0     0.034        10     130     154 ..     486     510 ..     379     519 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0096
                             T2SSE 126 vrerglilvsGgTgsGKttllyallkeinks 156
                                       v++ + +l+ G+ g+GKt l+ al +e n++
  gi|330506537|ref|YP_004382965.1| 209 VEAPKGVLLYGPPGTGKTLLAKALASETNAH 239
                                       556678999****************999988 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.034
                             T2SSE 130 glilvsGgTgsGKttllyallkein 154
                                         il+ G+ g+GKt l+ a+ +e +
  gi|330506537|ref|YP_004382965.1| 486 RGILLYGPPGTGKTMLAKAVATESQ 510
                                       45999***********999887655 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0       0.3        90       5      71 ..     219     280 ..     215     285 .. 0.72
   2 ?    9.9   0.0    0.0019      0.55       4      71 ..     491     553 ..     488     558 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.3
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+ l + l+++   ++ + +   e+ ++   +++ +    ++++++++       i+++DE+
  gi|330506537|ref|YP_004382965.1| 219 GPPGTGKTLLAKALASETnAHFETLSG-PEIMSKYYGESEEKLRQLFKTAEEQAP-----SIILIDEI 280
                                       78************9997655555555.666666666666666777777777653.....48888886 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0019
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                        G pG GK+ l + ++ +s  ++ +++   e l++++ ++++   +t++++ +a+       +++lDE+
  gi|330506537|ref|YP_004382965.1| 491 YGPPGTGKTMLAKAVATESqANFISIKG-PEFLSKWVGESEKAVRETFRKARQAAP-----SVVFLDEI 553
                                       588*************999*99999999.9*******9999999999999998875.....489***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 ?    5.0   0.0     0.074        22      22      48 ..     210     236 ..     183     243 .. 0.72
   2 ?    7.0   0.0     0.018       5.4      15      47 ..     476     508 ..     430     522 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.074
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierl 48 
                                       +  k +l+  + GtGKTl+a +l+ + 
  gi|330506537|ref|YP_004382965.1| 210 EAPKGVLLYGPPGTGKTLLAKALASET 236
                                       6778899999*********98877665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.018
                                       HT......TTSEEEEEESTTSTHHHHHHHHHHH CS
                            ResIII  15 lleklkskrdkrglikmaTGtGKTlvaaklier 47 
                                       l e++++k  + +l+  + GtGKT++a +++ +
  gi|330506537|ref|YP_004382965.1| 476 LFEHMDAKPPRGILLYGPPGTGKTMLAKAVATE 508
                                       22555547777888************9555544 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 ?    7.3   0.0    0.0097       2.9       5      47 ..     214     256 ..     210     267 .. 0.79
   2 ?    4.2   0.0     0.086        26       5      35 ..     487     516 ..     483     534 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0097
                                       EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...G CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksek 47 
                                        vll G+  +GKT+l + L +++  +  t   +++  k+ +e 
  gi|330506537|ref|YP_004382965.1| 214 GVLLYGPPGTGKTLLAKALASETNAHFETLSGPEIMSKYYGES 256
                                       699*****************99888777776777777764444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.086
                                       EEEEE-STTSSHHHHHHHHHHSS---B---S CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSq 35 
                                        +ll G+  +GKT+l + + t+s  +  +S+
  gi|330506537|ref|YP_004382965.1| 487 GILLYGPPGTGKTMLAKAVATESQAN-FISI 516
                                       699************99998886543.4444 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.044        13       5      27 ..     216     238 ..     212     243 .. 0.90
   2 ?    5.7   0.0     0.028       8.5       5      31 ..     489     515 ..     486     539 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.044
                               IPT   5 lifGatttGKtaeaiklaketga 27 
                                       l++G+ +tGKt  a +la et a
  gi|330506537|ref|YP_004382965.1| 216 LLYGPPGTGKTLLAKALASETNA 238
                                       89****************99975 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.028
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       l++G+ +tGKt  a ++a e  a  i+
  gi|330506537|ref|YP_004382965.1| 489 LLYGPPGTGKTMLAKAVATESQANFIS 515
                                       89*****************99988877 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.087        26      21      39 ..     212     229 ..     204     239 .. 0.82
   2 ?    6.2   0.0     0.029       8.7      21      42 ..     485     505 ..     463     508 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.087
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                       +kg +ll Gp G+GK+ l 
  gi|330506537|ref|YP_004382965.1| 212 PKG-VLLYGPPGTGKTLLA 229
                                       567.9**********8765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.029
                            AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                       ++g +ll Gp G+GK+ l  A+
  gi|330506537|ref|YP_004382965.1| 485 PRG-ILLYGPPGTGKTMLAKAV 505
                                       355.9**********9887666 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.049        15      19      45 ..     209     235 ..     200     243 .. 0.82
   2 ?    5.6   0.0     0.026       7.7      14      44 ..     477     507 ..     471     514 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.049
                                       .HCTS-EEEEESTTSSCHHHHHHHHHH CS
                              PIF1  19 nekgklfFvtGsgGtgKtflwkallkk 45 
                                        e +k + ++G  GtgKt l kal + 
  gi|330506537|ref|YP_004382965.1| 209 VEAPKGVLLYGPPGTGKTLLAKALASE 235
                                       567888899*************99876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.026
                                       ......HCTS-EEEEESTTSSCHHHHHHHHH CS
                              PIF1  14 ieavlnekgklfFvtGsgGtgKtflwkallk 44 
                                        e + ++ ++ + ++G  GtgKt+l ka+ +
  gi|330506537|ref|YP_004382965.1| 477 FEHMDAKPPRGILLYGPPGTGKTMLAKAVAT 507
                                       56777888999**************999876 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.17        50       4      32 ..     215     243 ..     213     319 .. 0.85
   2 ?    6.4   0.0     0.024       7.1       4      40 ..     488     524 ..     486     547 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.17
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhl 32 
                                       +lL G + +GK+ la+al + +++ +  l
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASETNAHFETL 243
                                       89****************99888877655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafvea 40 
                                       ilL G + +GK+ la+a+ + +++ ++ ++  +f+ +
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATESQANFISIKGPEFLSK 524
                                       99************************99987777765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.037        11       2      25 ..     213     236 ..     212     244 .. 0.86
   2 ?    4.3   0.0       0.1        31       4      24 ..     488     508 ..     485     513 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.037
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkgee 25 
                                       k +ll G+ g+GKt L++al  e+
  gi|330506537|ref|YP_004382965.1| 213 KGVLLYGPPGTGKTLLAKALASET 236
                                       5699****************9875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.1
                         PduV-EutP   4 illiGkvgsGKttLtqalkge 24 
                                       ill G+ g+GKt L++a+  e
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATE 508
                                       89**************99765 PP

>> cIII  cIII protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00066       0.2       5      34 ..     243     269 ..     241     271 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00066
                              cIII   5 LaGsGvMSAYYPtESELskkiRrLIRAArk 34 
                                       L+G  +MS YY  ESE   k+R+L + A  
  gi|330506537|ref|YP_004382965.1| 243 LSGPEIMSKYY-GESE--EKLRQLFKTAEE 269
                                       9**********.5888..89****999876 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.059        18       2      40 ..     215     252 ..     214     268 .. 0.75
   2 ?    5.2   0.0     0.081        24       2      39 ..     488     524 ..     487     541 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.059
                                       EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEE CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltke 40 
                                       v+l G  g+GKt l+k + +++   + ++  g ++++k 
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASETN-AHFETLSGPEIMSKY 252
                                       6899************9996654.555666676666664 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.081
                                       EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEE CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltk 39 
                                       ++l G  g+GKt l+k + +++ + +  s+ g +fl+k
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATES-QANFISIKGPEFLSK 524
                                       6899**********99988554.455666677777666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.22        65       2      22 ..     215     235 ..     214     248 .. 0.83
   2 ?    1.3   0.1      0.92   2.7e+02      82     117 ..     257     293 ..     244     306 .. 0.68
   3 ?   -1.6   0.1       7.2   2.1e+03      87     119 ..     436     468 ..     404     472 .. 0.66
   4 ?    7.4   0.1     0.012       3.7       2      32 ..     488     518 ..     487     593 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.22
                                       EEEE--TTSSHHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlel 22 
                                       v++ GppG+GKt l k ++++
  gi|330506537|ref|YP_004382965.1| 215 VLLYGPPGTGKTLLAKALASE 235
                                       6788********998887765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.92
                                       HHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHH CS
                          NTPase_1  82 eelalealrkal.seadviviDEiGkmElkskkfkea 117
                                       ee   + +++a  + + +i+iDEi ++  k +++  +
  gi|330506537|ref|YP_004382965.1| 257 EEKLRQLFKTAEeQAPSIILIDEIDSIAPKREEVTGE 293
                                       44445555666535566*******7766665555555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 7.2
                                       HHHHHHHHHH-EEEE---STTGGG-HHHHHHHH CS
                          NTPase_1  87 ealrkalseadviviDEiGkmElkskkfkeave 119
                                       +a+r+ + e+  +  DEiG +    ++++e+ve
  gi|330506537|ref|YP_004382965.1| 436 SAMREVMVESPNVHWDEIGGLAEVKQQLIESVE 468
                                       444555545555567999998888888877775 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.012
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       +++ GppG+GKt l k v+ + + + ++++G
  gi|330506537|ref|YP_004382965.1| 488 ILLYGPPGTGKTMLAKAVATESQANFISIKG 518
                                       6788**************9999888888887 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.22        66      25      41 ..     214     229 ..     203     240 .. 0.80
   2 ?    6.2   0.0     0.017       5.1      19      56 ..     481     517 ..     472     540 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.22
                                       EEEEE-SSSSSTTTTHH CS
                              DAP3  25 rlvltGekgsGKSvlLl 41 
                                        ++l+G +g+GK++l +
  gi|330506537|ref|YP_004382965.1| 214 GVLLYGPPGTGKTLL-A 229
                                       579*********974.4 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.017
                                       SSS---EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEE CS
                              DAP3  19 kkkkvkrlvltGekgsGKSvlLlqalayAlekgwvvlh 56 
                                       ++k+   ++l+G +g+GK++ L++a+a   +++++ ++
  gi|330506537|ref|YP_004382965.1| 481 DAKPPRGILLYGPPGTGKTM-LAKAVATESQANFISIK 517
                                       566777789*********97.67777666666666555 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.16        48     264     283 ..     214     233 ..     204     240 .. 0.86
   2 ?    5.4   0.0     0.022       6.7     230     283 ..     449     506 ..     428     517 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.16
                          PPV_E1_C 264 clvllGppntGkslfamsli 283
                                        ++l+Gpp tGk+l+a++l 
  gi|330506537|ref|YP_004382965.1| 214 GVLLYGPPGTGKTLLAKALA 233
                                       5799***********99986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.022
                          PPV_E1_C 230 dWkei..vkflryqgvelisfltalkef...LkgvPkknclvllGppntGkslfamsli 283
                                       +W ei  +  ++ q +e +++  +  ++   +  +P +  ++l+Gpp tGk+++a+++ 
  gi|330506537|ref|YP_004382965.1| 449 HWDEIggLAEVKQQLIESVEWPLTYARLfehMDAKPPR-GILLYGPPGTGKTMLAKAVA 506
                                       56666222335666667766644433330004444444.6899**********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (723 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); 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):              60  [number of targets reported over threshold]
# CPU time: 0.85u 0.32s 00:00:01.17 Elapsed: 00:00:00.47
# Mc/sec: 4614.59
//
Query:       gi|330506538|ref|YP_004382966.1|  [L=152]
Description: hypothetical protein MCON_0257 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.067   13.7   0.1       0.11   13.0   0.1    1.4  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1     6e-06      0.11      53      96 ..      11      69 ..       4      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6e-06
                                      HHHHHHHHHHHHHH................S-SSS--TTSHHHHHHHHHHTTSSSSTTHH CS
                                      xxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD 53 rKakyikelArilv................gkpdvlivvDvhvrrilkrlrsikekktkk 96
                                       + k+i+ +  +++                +    l +vD+++rri++ l+  +e  + +
  gi|330506538|ref|YP_004382966.1| 11 DRLKRIRGVGNKIAslflrdvavnynltpiKDRWLLQPVDIWIRRIVQSLNNSSEM-DNR 69
                                      68899999999999999999999999***94447899*************999885.433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1100.76
//
Query:       gi|330506539|ref|YP_004382967.1|  [L=170]
Description: hypothetical protein MCON_0258 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.072   13.0   0.0       0.11   12.4   0.0    1.2  1  Mrr_cat_2  Restriction endonuclease


Domain annotation for each model (and alignments):
>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     6e-06      0.11      26      58 ..      30      62 ..      20      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6e-06
                         Mrr_cat_2 26 gkkDtGIDlVakerkegeywAIQcKfYaedeki 58
                                      +++  GID+Va + + + +  IQ+K   + +++
  gi|330506539|ref|YP_004382967.1| 30 ARNARGIDIVAYNSDGSCFKGIQVKSLRKRNSV 62
                                      46678********9999999*****98887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1252.45
//
Query:       gi|330506540|ref|YP_004382968.1|  [L=235]
Description: hypothetical protein MCON_0259 [Methanosaeta concilii GP6]
Scores for complete 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-52  176.0   0.3    1.1e-51  175.8   0.3    1.0  1  Nmad3     Nucleotide modification associated domain 3


Domain annotation for each model (and alignments):
>> Nmad3  Nucleotide modification associated domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.8   0.3   6.4e-56   1.1e-51      58     249 ..      17     214 ..       4     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 175.8 bits;  conditional E-value: 6.4e-56
                             Nmad3  58 dltegk....lkaestvHlDPdlaeetle....wrptyGqhgaaqghlrnqgveeGDlflFfglfrrvekenerlrf 126
                                       ++++++    l+++ ++HlDPd+ +++++    wrp++Gq++aaqghl++q+v+ +DlflFfg+fr++ + +++l++
  gi|330506540|ref|YP_004382968.1|  17 SIKSSNeridLSNDFGCHLDPDIFKNAIHrepnWRPLFGQVDAAQGHLQKQDVRRDDLFLFFGSFRKTRNDDGKLAY 93 
                                       4444222332444447***********999*********************************************** PP

                             Nmad3 127 vkgaewghylfGylqvdevlkveedevpeaewar.hphnahkkran.dntlyvase.......kegsglfdrlealp 194
                                       ++ ++++h++fGylq+++++ + +++ +  ew++ hph+ + +++n +nt+yva++        +g+g+f ++++l+
  gi|330506540|ref|YP_004382968.1|  94 DPHEKEMHVIFGYLQIGDII-KVDQKFDVPEWMSyHPHANNARKSNeTNTIYVARDhlswsesLPGAGRFIFSDRLV 169
                                       ********************.44555655699999****999998889*****999***************99**** PP

                             Nmad3 195 LskpeagkesnwklpsffkkelvtelsyhsgkgrWwrreedaalksaargqefvl 249
                                       L+k + +k s+w lp++fk+    ++syh+++  W    +d ++ksa+rgqefv+
  gi|330506540|ref|YP_004382968.1| 170 LTKRGYSK-SKWALPDCFKE---AKISYHKKP--W----KDGYFKSAGRGQEFVI 214
                                       *****666.77********8...69****988..9....567***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 00:00:00.45
# Mc/sec: 1581.09
//
Query:       gi|330506541|ref|YP_004382969.1|  [L=563]
Description: hypothetical protein MCON_0260 [Methanosaeta concilii GP6]
Scores for complete 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   1.8    8.4e-09   35.4   1.8    1.5  1  DDE_Tnp_1     Transposase DDE domain
  ------ inclusion threshold ------
       0.11   12.8   0.4          1    9.7   0.4    2.6  2  MADF_DNA_bdg  Alcohol dehydrogenase transcription factor Myb/


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 !   35.4   1.8   9.3e-13   8.4e-09      26     212 ..     208     487 ..     183     489 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 9.3e-13
                         DDE_Tnp_1  26 gykggk.ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYasaelldtleekg 99 
                                       gy+ ++ +++  +l i+v+ r +++ls  + +g++h + ++k ll++l ++  ++ +++ D+G  s+++++ ++e+g
  gi|330506541|ref|YP_004382969.1| 208 GYNPDRiRRRQANLAILVSKRDRYPLSHFVYNGSRHSISTVKNLLNRLSKMaiEPGTLIWDRGNVSKKHVQMVDESG 284
                                       888788899999************9999999********************************************** PP

                         DDE_Tnp_1 100 vdyiirlkkntklyrk.......gaeskrrgrlrkhdrnkiltksqkrrnk.......................... 143
                                       ++ i  ++k +k+ +        +++     r   +++  ++++++++++k                          
  gi|330506541|ref|YP_004382969.1| 285 WKLICGVPKTSKEAKEiigktkiPISPDSLVRSSHAGHIYAIKTENELFGKerstivyanrersvkdadarnealsv 361
                                       *******9999999889999999455555555566666666666666666666666668888888999999999*** PP

                         DDE_Tnp_1 144 .........................................................skkekgdvyyvtntnsells 163
                                                                                                +  ek+d+  + + ++ +l 
  gi|330506541|ref|YP_004382969.1| 362 igeslnelsqtgkdwsekrlhdriknivgqwsgfidasvrrkkdgpriewsydrqrlRSAEKYDGKWLILSTDYSLN 438
                                       *******************************************************99999999999999999999** PP

                         DDE_Tnp_1 164 aeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                       a   +++y  +  iE vF+ lk++   + +r+r   rv+a+l+ ++la+
  gi|330506541|ref|YP_004382969.1| 439 ANNAVNMYLEKDFIEKVFRVLKTHEEVEPVRHRLEHRVKAYLFVCMLAY 487
                                       ************************************************9 PP

>> MADF_DNA_bdg  Alcohol dehydrogenase transcription factor Myb/SANT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.28   2.5e+03       9      37 ..     264     293 ..     259     306 .. 0.70
   2 ?    9.7   0.4   0.00011         1       7      57 ..     337     393 ..     335     417 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.28
                      MADF_DNA_bdg   9 pvLwdrshpdyrnkek.rekaweeiaeeln 37 
                                       +++wdr + + ++++   e  w+ i+   +
  gi|330506541|ref|YP_004382969.1| 264 TLIWDRGNVSKKHVQMvDESGWKLICGVPK 293
                                       679***997777666636778988886655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00011
                      MADF_DNA_bdg   7 khpvLwdrshpdyrnkekrekaweeiaeelnekvd......veeckkkwknLRdryr 57 
                                       + ++ + ++ ++ ++ ++r++a++ i e+lne  +      +++++ ++kn+  + +
  gi|330506541|ref|YP_004382969.1| 337 RSTIVYANRERSVKDADARNEALSVIGESLNELSQtgkdwsEKRLHDRIKNIVGQWS 393
                                       56789*************************843333333324446667776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3942.49
//
Query:       gi|330506542|ref|YP_004382970.1|  [L=129]
Description: glyoxalase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-15   56.1   0.0    4.7e-15   55.9   0.0    1.0  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
      5e-07   30.0   0.0    4.2e-05   23.8   0.0    1.5  2  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    0.00043   21.0   0.0    0.00064   20.5   0.0    1.2  1  Glyoxalase_6  Glyoxalase-like domain
     0.0036   17.2   0.2      0.011   15.7   0.2    1.7  1  Glyoxalase_2  Glyoxalase-like domain
  ------ inclusion threshold ------
      0.041   14.1   0.0       0.05   13.8   0.0    1.2  1  Glyoxalase_5  Hydroxyphenylpyruvate dioxygenase, HPPD, N-term
       0.13   12.8   0.2         10    6.7   0.0    2.1  2  3-dmu-9_3-mt  3-demethylubiquinone-9 3-methyltransferase


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 !   55.9   0.0   1.6e-18   4.7e-15       2     128 .]       3     125 ..       2     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 1.6e-18
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCC.BSCTSEEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkk.ieetvhhv 77 
                                       i ++ ++v+d +k+l+FYt++LGf    +++   ++  +   +  ++++  el+l++++++aak ++k i+e  + +
  gi|330506542|ref|YP_004382970.1|   3 IIYTKVFVNDQDKALKFYTQILGFVKKSDIG--AGDYRWLTVVSPEDQNGTELILERNDNPAAKNYQKaIFE--QSI 75 
                                       667889*****************95555555..6666666689999********************996445..79* PP

                                       EEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  78 afialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                         i + v dv + ++rlk  gvk+++ p  ++++++ +++f D  G+l+++
  gi|330506542|ref|YP_004382970.1|  76 PAINFGVSDVHAEYERLKNLGVKFTMQP-SEVMENVTIAVFDDTCGNLIQL 125
                                       ***************************9.56666666677********986 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.4e-08   4.2e-05       5     104 ..       8     110 ..       6     115 .. 0.75
   2 !   10.4   0.0    0.0002       0.6       4      50 ..      79     125 ..      77     128 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.4e-08
                                       EE-S-HHHHHHHHHH.TT-EESS--.E.EETTTTEEEEEEEETTEEEEEEEESSTT...-THHH..TS-EEEEEEEE CS
                      Glyoxalase_4   5 ivVeDleaavarfsallGvgpwqry.rdepqevdlafallgsgsvqieLieplegp...eflae..hgeglhhlayw 75 
                                       + V+D ++a+++++++lG+ +  ++   + ++ ++   + ++g    eLi  ++++   + +++   +  +  + + 
  gi|330506542|ref|YP_004382970.1|   8 VFVNDQDKALKFYTQILGFVKKSDIgAGDYRWLTVVSPEDQNG---TELILERNDNpaaKNYQKaiFEQSIPAINFG 81 
                                       579***************9866555055555666666555555...577766666633544444888999999**** PP

                                       ES-HHHHHHHHCTTTEEEEEEEE-GGGTT CS
                      Glyoxalase_4  76 vddldaavarleeqGfevvqkgvragaag 104
                                       v+d++a  +rl++ G++++++ +++ ++ 
  gi|330506542|ref|YP_004382970.1|  82 VSDVHAEYERLKNLGVKFTMQPSEVMENV 110
                                       *******************9998877654 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0002
                                       EEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETT.EEE CS
                      Glyoxalase_4   4 givVeDleaavarfsallGvgpwqryrdepqevdlafallgsgs.vqi 50 
                                        + V D++a  +r+++ lGv+++ + ++  ++v++a+++   g+ +q+
  gi|330506542|ref|YP_004382970.1|  79 NFGVSDVHAEYERLKN-LGVKFTMQPSEVMENVTIAVFDDTCGNlIQL 125
                                       5677777777777777.7777777766667777777777777665555 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.1e-07   0.00064       7     104 ..      11     123 ..       6     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.1e-07
                      Glyoxalase_6   7 adpaalaaFwaaalgweveree..aaledpegvgpaaedaatllfqrvpe...........paknrvHldlavedld 70 
                                       +d +++ +F+ ++lg++++++      +   +v+p++++++ l ++r ++           + +    +++ v+d++
  gi|330506542|ref|YP_004382970.1|  11 NDQDKALKFYTQILGFVKKSDIgaGDYRWLTVVSPEDQNGTELILERNDNpaaknyqkaifE-QSIPAINFGVSDVH 86 
                                       6889999**************98844455566777888888999999999976666556542.2237899******* PP

                      Glyoxalase_6  71 aevarlvalGArvlreprdgthgr...vlaDPeGneF 104
                                       ae +rl +lG +   +p +  +     v+ D  Gn  
  gi|330506542|ref|YP_004382970.1|  87 AEYERLKNLGVKFTMQPSEVMENVtiaVFDDTCGNLI 123
                                       **********998888888765557888888888865 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   3.6e-06     0.011       6     112 ..       8     124 ..       3     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-06
                                       -EES-HHHHHHHHHHTT---EEEE-SS.......EEEE..TTS-EE...EEHHHHHH-------S--SS-EEEEEES CS
                      Glyoxalase_2   6 lvvkdieeskkFYedvlelkikldfGe.......nvsf..etgfal...kedlkelinldesiaeqsnnfeLyFeve 70 
                                       ++v+d +++ kFY ++l    k d G         vs   ++g++l   ++d  +  n+++ i eqs    + F v 
  gi|330506542|ref|YP_004382970.1|   8 VFVNDQDKALKFYTQILGFVKKSDIGAgdyrwltVVSPedQNGTELileRNDNPAAKNYQKAIFEQSI-PAINFGVS 83 
                                       79****************99999998522222112333113455555555666666677777777775.4699**** PP

                                       -HHHHHHHH..GGGS-EEEEEEE-TTS-EEEEEE-TT--EEE CS
                      Glyoxalase_2  71 dvdaflqklkeaeniellhelkekpWgqrvirfyDpDkhiiE 112
                                       dv+a  ++lk+ + +++  ++ e     +++ f D  +++i 
  gi|330506542|ref|YP_004382970.1|  84 DVHAEYERLKNLG-VKFTMQPSEVMENVTIAVFDDTCGNLIQ 124
                                       *********9999.***********999***99999999886 PP

>> Glyoxalase_5  Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.7e-05      0.05      47     111 ..      47     113 ..       7     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                      Glyoxalase_5  47 rqGginfilneepdsaaakfare.hGpsacalafrvkdakkayeralekGakpveketgvme.lkiP 111
                                        q g ++il+++ + aa+++ ++   +s+ a+ f v d ++ yer+ + G k  +++++vme ++i 
  gi|330506542|ref|YP_004382970.1|  47 DQNGTELILERNDNPAAKNYQKAiFEQSIPAINFGVSDVHAEYERLKNLGVKFTMQPSEVMEnVTIA 113
                                       588999******9999999988637899************************999998888724444 PP

>> 3-dmu-9_3-mt  3-demethylubiquinone-9 3-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0033        10       2      24 ..       2      24 ..       1      38 [. 0.83
   2 ?    4.5   0.1     0.016        49       5      59 ..      51     107 ..      47     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0033
                      3-dmu-9_3-mt  2 kitpcLlfdgeaeeAaefYvsvf 24
                                      ki+ + +f ++ ++A++fY++++
  gi|330506542|ref|YP_004382970.1|  2 KIIYTKVFVNDQDKALKFYTQIL 24
                                      7888889*************996 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.016
                      3-dmu-9_3-mt   5 pcLlfdgeaeeAaefYvsvfenseilsvarypeeeps..kegkvltveFtlagqefv 59 
                                       + L+ + + + Aa++Y + + + +i +++  +++ ++  ++ k l v+Ft++ +e++
  gi|330506542|ref|YP_004382970.1|  51 TELILERNDNPAAKNYQKAIFEQSIPAINFGVSDVHAeyERLKNLGVKFTMQPSEVM 107
                                       567788888999999999888888999888888876535666777788888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 935.44
//
Query:       gi|330506543|ref|YP_004382971.1|  [L=254]
Description: hypothetical protein MCON_0262 [Methanosaeta concilii GP6]
Scores for complete 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  181.0   2.1    3.3e-24   85.3   0.3    3.0  3  S-layer   S-layer protein
    0.00038   20.8   0.9         10    6.6   0.0    4.0  3  CBM60     Ca-dependent carbohydrate-binding module xylan-bind
     0.0063   16.5   0.0         11    6.1   0.0    3.1  3  NPM1-C    Nucleophosmin C-terminal domain
      0.009   15.8   0.0        1.1    9.1   0.1    2.5  3  TIMP      Tissue inhibitor of metalloproteinase
  ------ inclusion threshold ------
      0.028   14.4   0.0         34    4.4   0.0    3.1  3  PDDEXK_7  PD-(D/E)XK nuclease superfamily


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 !   17.5   0.0   4.6e-07    0.0016     180     206 ..      21      47 ..       4      53 .. 0.87
   2 !   85.3   0.3   9.2e-28   3.3e-24     103     206 ..      52     152 ..      48     156 .. 0.96
   3 !   77.1   0.1   3.1e-25   1.1e-21     103     201 ..     157     252 ..     153     253 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.6e-07
                           S-layer 180 iavhvdevfrgtedslvviegifqisd 206
                                       i vh+++ frg++++l++i+g++q s+
  gi|330506543|ref|YP_004382971.1|  21 IRVHFKNSFRGADQNLATIDGLWQTSE 47 
                                       89***********************96 PP

  == domain 2  score: 85.3 bits;  conditional E-value: 9.2e-28
                           S-layer 103 kvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska.dstyvyekdlgdeddvv 178
                                       k+li +++++t+ sg+ + Lee Yel i++iD+dg++v+leL+kdg  +dsk+i + ++ d+t++y+    +++   
  gi|330506543|ref|YP_004382971.1|  52 KMLIADSQSHTVASGTLMALEEVYELVIQSIDIDGNRVYLELYKDGIVIDSKIIMPANKvDDTFIYSSPGTSQE--- 125
                                       88999***************************************************9989*******9999988... PP

                           S-layer 179 iiavhvdevfrgtedslvviegifqisd 206
                                        i vh+++ frg++++l++i+g++q s+
  gi|330506543|ref|YP_004382971.1| 126 -IRVHFKNSFRGADQNLATIDGLWQTSE 152
                                       .************************996 PP

  == domain 3  score: 77.1 bits;  conditional E-value: 3.1e-25
                           S-layer 103 kvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska.dstyvyekdlgdeddvv 178
                                        +li ++ ++t++sg+ l LeegYel i++iD+dg+k  leL kdg  vds+vi s+k+ d+t++y++   +++   
  gi|330506543|ref|YP_004382971.1| 157 PILIADSRSRTMNSGTPLGLEEGYELLIQSIDIDGNKLHLELCKDGMVVDSQVIISEKEvDDTFIYSRPETSQK--- 230
                                       68999************************************************9998889*******9877765... PP

                           S-layer 179 iiavhvdevfrgtedslvviegi 201
                                        i+v+++++frg+e+sl++i+ i
  gi|330506543|ref|YP_004382971.1| 231 -IKVRFKNAFRGAEQSLATIDNI 252
                                       .*******************976 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 !    5.5   0.0    0.0065        23      41      71 ..       9      36 ..       3      52 .. 0.83
   2 ?    4.7   0.1     0.011        41      37      71 ..     110     141 ..      76     146 .. 0.70
   3 !    6.6   0.0    0.0029        10      14      62 ..     192     240 ..     181     247 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0065
                             CBM60 41 tftadltagahklqirylNDlyvgagqDRnL 71
                                      tf+   + + +++++++ N + +    D nL
  gi|330506543|ref|YP_004382971.1|  9 TFNYSSPGTSQEIRVHFKNSFRGA---DQNL 36
                                      788888888**********97665...8888 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.011
                             CBM60  37 aktytftadltagahklqirylNDlyvgagqDRnL 71 
                                         + tf    + + +++++++ N + +    D nL
  gi|330506543|ref|YP_004382971.1| 110 KVDDTFIYSSPGTSQEIRVHFKNSFRGA---DQNL 141
                                       455566667677799********97665...8887 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0029
                             CBM60  14 eppefrllvdGqkvgeadvasteaktytftadltagahklqirylNDly 62 
                                       ++ +++l  dG +v +  + s++  + tf    +++ +k+++r+ N + 
  gi|330506543|ref|YP_004382971.1| 192 NKLHLELCKDGMVVDSQVIISEKEVDDTFIYSRPETSQKIKVRFKNAFR 240
                                       4678999999***99888788899999999999999**********765 PP

>> NPM1-C  Nucleophosmin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0     0.003        11      28      46 ..      25      45 ..      12      47 .. 0.80
   2 !    6.0   0.0    0.0033        12      28      46 ..     130     150 ..     118     152 .. 0.82
   3 ?   -0.1   0.0      0.25   9.1e+02      18      37 ..     225     244 ..     222     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.003
                            NPM1-C 28 vkncFkmtDqe..viqdLwqw 46
                                       kn+F+  Dq+   i  Lwq 
  gi|330506543|ref|YP_004382971.1| 25 FKNSFRGADQNlaTIDGLWQT 45
                                      6*********84469999995 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0033
                            NPM1-C  28 vkncFkmtDqe..viqdLwqw 46 
                                        kn+F+  Dq+   i  Lwq 
  gi|330506543|ref|YP_004382971.1| 130 FKNSFRGADQNlaTIDGLWQT 150
                                       69********84469999995 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.25
                            NPM1-C  18 PkveaKFinyvkncFkmtDq 37 
                                       P++ +K     kn F+   q
  gi|330506543|ref|YP_004382971.1| 225 PETSQKIKVRFKNAFRGAEQ 244
                                       88889999999****98776 PP

>> TIMP  Tissue inhibitor of metalloproteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.76   2.7e+03      44      77 ..      18      50 ..       5      75 .. 0.65
   2 !    6.6   0.0    0.0017       6.1      19     107 ..      98     200 ..      94     200 .. 0.82
   3 !    9.1   0.1    0.0003       1.1      14      60 ..     198     244 ..     195     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.76
                                      EEEEEEEEEEEEE-CSCSSTTTS-SEEEEESSGG CS
                              TIMP 44 vlkyevkitkmfkgaekvrkakkiqavateeses 77
                                       ++ +v+ ++ f+ga++ + a+     +t+e ++
  gi|330506543|ref|YP_004382971.1| 18 SQEIRVHFKNSFRGADQ-NLATIDGLWQTSEANP 50
                                      56677888888999888.4444444455555554 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0017
                                       EEEEEEEESSEEEETTT.......TEEEEEEEEEEEEE-CSCSSTTTS-SEEEEESSGGG...............T- CS
                              TIMP  19 lvirakvvekkeveesesiaakkrkvlkyevkitkmfkgaekvrkakkiqavateesesl...............Cg 80 
                                       +vi +k++   ++ +++ i+ ++   ++ +v+ ++ f+ga++ + a+     +t+e ++                 +
  gi|330506543|ref|YP_004382971.1|  98 IVIDSKIIMPANKVDDTFIYSSPGTSQEIRVHFKNSFRGADQ-NLATIDGLWQTSEVDPNpiliadsrsrtmnsgTP 173
                                       79999**999999999999*999999**************99.5555555666766665566899999999996666 PP

                                       ----S-SEEEEEEEEE.TTEEE--TTS CS
                              TIMP  81 vklelnkeyliagklvddgklevslCd 107
                                         le + e li     d++kl+++lC+
  gi|330506543|ref|YP_004382971.1| 174 LGLEEGYELLIQSIDIDGNKLHLELCK 200
                                       667888999999988889999999995 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0003
                                       HHH-SEEEEEEEESSEEEETTT.......TEEEEEEEEEEEEE-CSC CS
                              TIMP  14 fCnadlvirakvvekkeveesesiaakkrkvlkyevkitkmfkgaek 60 
                                        C+  +v+ ++v+ +++  +++ i+ ++   +k +v+ ++ f+gae+
  gi|330506543|ref|YP_004382971.1| 198 LCKDGMVVDSQVIISEKEVDDTFIYSRPETSQKIKVRFKNAFRGAEQ 244
                                       7999********888888888889**999***************998 PP

>> PDDEXK_7  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.035   1.3e+02      47      78 ..       9      44 ..       2      65 .. 0.75
   2 ?    3.9   0.0     0.014        49      46      78 ..     113     149 ..      94     168 .. 0.76
   3 ?    4.4   0.0    0.0096        34      43      73 ..     215     245 ..     197     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.035
                          PDDEXK_7 47 kllferlsdgeeielaynprfsrkeekq....ssyt 78
                                      ++ ++++++++ei++ ++++f+++ ++     ++++
  gi|330506543|ref|YP_004382971.1|  9 TFNYSSPGTSQEIRVHFKNSFRGADQNLatidGLWQ 44
                                      6899999***************88777666665554 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.014
                          PDDEXK_7  46 akllferlsdgeeielaynprfsrkeekq....ssyt 78 
                                        +++++++++++ei++ ++++f+++ ++     ++++
  gi|330506543|ref|YP_004382971.1| 113 DTFIYSSPGTSQEIRVHFKNSFRGADQNLatidGLWQ 149
                                       5899*******************88777666665554 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0096
                          PDDEXK_7  43 graakllferlsdgeeielaynprfsrkeek 73 
                                       + + +++++r++++++i++++++ f+++e++
  gi|330506543|ref|YP_004382971.1| 215 EVDDTFIYSRPETSQKIKVRFKNAFRGAEQS 245
                                       444689*******************976654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 1929.80
//
Query:       gi|330506544|ref|YP_004382972.1|  [L=148]
Description: hypothetical protein MCON_0264 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-07   30.8   0.0    2.3e-07   30.6   0.0    1.2  1  dUTPase   dUTPase


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 !   30.6   0.0   1.3e-11   2.3e-07      30     114 ..      57     137 ..      35     148 .] 0.88

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.3e-11
                                       EEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEEEEEEBEC CS
                           dUTPase  30 etvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiAqLifarilt 106
                                       + +lv+++  + +p ++aal   RS l + g   ++ ++d  yrG  +  l++++ +  ++kk++R+ qL+f+r+++
  gi|330506544|ref|YP_004382972.1|  57 GAYLVTFNEIVNIPGDVAALARARSTLLRCGASLETALWDPGYRGRSQSLLVVHNPSGLRLKKNARLMQLVFMRLEN 133
                                       56899****************************************9999999999999****************999 PP

                                       GEEEEESS CS
                           dUTPase 107 aeleevet 114
                                           e e+
  gi|330506544|ref|YP_004382972.1| 134 ----EAEK 137
                                       ....3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1207.78
//
Query:       gi|330506545|ref|YP_004382973.1|  [L=269]
Description: CAAX amino terminal protease family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-11   42.9   7.0    4.8e-11   42.9   7.0    2.1  3  CPBP      CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
      0.034   14.2   0.6      0.034   14.2   0.6    3.2  3  PsbX      Photosystem II reaction centre X protein (PsbX)
        2.8    6.1  10.6       0.51    8.6   7.2    1.4  2  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.92   5.5e+03      19      19 ..      33      33 ..      11      68 .. 0.51
   2 !   42.9   7.0     8e-15   4.8e-11       5      91 ..     123     221 ..     118     222 .. 0.85
   3 ?   -3.4   0.2       2.2   1.3e+04      12      12 ..     245     245 ..     232     255 .. 0.47

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.92
                                      H CS
                              CPBP 19 E 19
                                      E
  gi|330506545|ref|YP_004382973.1| 33 E 33
                                      0 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 8e-15
                                       HHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG........HHHH.....HHHHHHHHH CS
                              CPBP   5 llvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn........gpsv.....llaalaGlv 68 
                                       l  f++++++++++EE+++ g+    lq+r+  + a +i +i+++++H+++           +      +a+++ ++
  gi|330506545|ref|YP_004382973.1| 123 LPAFFILFFVGGVGEEIGWTGYATDPLQARRTALEASIILGIIWAIWHAIPyiqghnapL--WilgqcEAAVMLRVL 197
                                       678999************************66699****************666666441..145554788889999 PP

                                       HHHHHHHT.T-HHHHHHHHHHHHH CS
                              CPBP  69 lgylylkt.gsllaaillHallnl 91 
                                       + ++y +t +sl+aai++Ha +nl
  gi|330506545|ref|YP_004382973.1| 198 IVWIYNNTgKSLFAAIAFHASVNL 221
                                       99****99669***********97 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.2
                                       H CS
                              CPBP  12 l 12 
                                       +
  gi|330506545|ref|YP_004382973.1| 245 V 245
                                       1 PP

>> PsbX  Photosystem II reaction centre X protein (PsbX)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.6   5.6e-06     0.034      10      30 ..      40      60 ..      40      62 .. 0.95
   2 ?   -2.0   0.6      0.64   3.8e+03      18      30 ..     120     132 ..     119     134 .. 0.77
   3 ?   -1.1   2.3      0.32   1.9e+03       8      20 ..     241     253 ..     239     255 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.6e-06
                                      HHHHHHH.HHHHHHHHHHHHH CS
                              PsbX 10 lSLvaGalvVvipiaaaLifv 30
                                      +SL aGalv v p aaaLi+v
  gi|330506545|ref|YP_004382973.1| 40 FSLPAGALVLVCPMAAALILV 60
                                      59*****************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHHHH CS
                              PsbX  18 vVvipiaaaLifv 30 
                                       ++ +p++  L+fv
  gi|330506545|ref|YP_004382973.1| 120 FIALPAFFILFFV 132
                                       5778888888887 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.32
                                       HHHHHHHHH.HHH CS
                              PsbX   8 fllSLvaGalvVv 20 
                                       fll   a+a+v++
  gi|330506545|ref|YP_004382973.1| 241 FLLAVTAAAVVIL 253
                                       7888888885554 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.26   1.6e+03     134     174 ..      18      61 ..       7      68 .. 0.53
   2 ?    8.6   7.2   8.6e-05      0.51      18     170 ..      93     252 ..      75     264 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.26
                           DUF2070 134 aliqpllailllvly..........fspesfllllllslifalavylfivv 174
                                        ++ ++        +          ++  ++l++ +l+l+  +a++l++v+
  gi|330506545|ref|YP_004382973.1|  18 LFALSVP-------FwlaggmaeqeLPLPFSLPAGALVLVCPMAAALILVY 61 
                                       2222222.......2334444466655566666666666666666666665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 8.6e-05
                           DUF2070  18 llliillalligllaflssk............lfgillfglpalvaflltlpvlrilggr......ltykrslfl.a 75 
                                       +l+ +l+al ++++     k            +     + lpa++ ++++  v + +g +      l+ +r ++  +
  gi|330506545|ref|YP_004382973.1|  93 FLMPLLMALEYTVM-----KltgmpvpdpqftF-----IALPAFFILFFVGGVGEEIGWTgyatdpLQARRTALEaS 159
                                       23333333333333.....23345588543333.....444433333333333222222223355799999966515 PP

                           DUF2070  76 lltelivviisllaillsallqalvllalvlslalvfalrllvlvavsde..sllkavlpaliqpllailllvlyfs 150
                                       ++  +i++i+  ++++  +      +l ++  + ++++lr+l+++++ ++  sl+ a++  +  +l+ ++l+ +y s
  gi|330506545|ref|YP_004382973.1| 160 IILGIIWAIWHAIPYIQGH----NAPLWILGQCEAAVMLRVLIVWIYNNTgkSLFAAIAFHASVNLSELVLFPIYGS 232
                                       6667888898888888775....557777788999999******999876226666666666677777777777755 PP

                           DUF2070 151 pesfllllllslifalavyl 170
                                       +++ +++++l+++ a+av++
  gi|330506545|ref|YP_004382973.1| 233 YYDPIIAFFLLAVTAAAVVI 252
                                       55555555555555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2168.11
//
Query:       gi|330506546|ref|YP_004382974.1|  [L=217]
Description: hypothetical protein MCON_0267 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.041   13.8   0.1       0.27   11.2   0.0    1.9  2  Glycos_transf_4  Glycosyl transferase family 4


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.5e-05      0.27      20      83 ..      30      91 ..      23      93 .. 0.71
   2 ?    0.2   0.0     0.036   6.4e+02      23      44 ..     120     141 ..     113     174 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.5e-05
                   Glycos_transf_4 20 vlglkarlKlilqilaalililtldlslttlgllltqvlielglilavll..tllvivgvtNavNl 83
                                      ++ l++  K ++++ ++l+l++t+   lt ++l+     + lg i+a+++  +l++i+++  ++N+
  gi|330506546|ref|YP_004382974.1| 30 LKTLNEDAKGLATLGSSLLLVYTGA--LTLFKLPENASYLGLG-IMAIPIvlWLVCIFFA-SSINF 91
                                      6789999999***999999998886..7777777776677777.4444332255555555.89998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.036
                   Glycos_transf_4  23 lkarlKlilqilaalililtld 44 
                                       l +  +l++  +aa  ++l+l+
  gi|330506546|ref|YP_004382974.1| 120 LIWSRRLFIMSIAASAIVLFLG 141
                                       6677777666666555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1552.60
//
Query:       gi|330506547|ref|YP_004382975.1|  [L=317]
Description: hypothetical protein MCON_0268 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-24   86.5   0.0    1.4e-17   64.2   0.0    2.0  2  Peptidase_C11  Clostripain family


Domain annotation for each model (and alignments):
>> Peptidase_C11  Clostripain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.5e-08   0.00027       1     103 [.      46     148 ..      46     158 .. 0.82
   2 !   64.2   0.0   7.9e-22   1.4e-17     120     241 ..     193     313 ..     169     316 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.5e-08
                     Peptidase_C11   1 vymvgdnsleeyaskDleEmiegaksvndnnilvlvdgi.aeedklerlsedgei.eeitrtadaeansgdaaeLek 75 
                                       +ym+++  l  +  +D+ Em+   +  ++ ni v + g  +      rl++   + e+i+ +  + +   + + L++
  gi|330506547|ref|YP_004382975.1|  46 IYMAANCDLAAHLFEDILEMKAIGSD-ENVNICVFFVGPlITDSFFARLNKGTPLgEDIIFRFLT-LSASEPKILKE 120
                                       5999999*************964444.45588887655516666678999988888898887655.5899******* PP

                     Peptidase_C11  76 fleyirenyeadsyllilwdHGdawkdd 103
                                       +++     y+a++ l+il  HG +wk+ 
  gi|330506547|ref|YP_004382975.1| 121 VISNNLILYPAENNLVILAGHGLGWKGA 148
                                       *************************875 PP

  == domain 2  score: 64.2 bits;  conditional E-value: 7.9e-22
                     Peptidase_C11 120 drleipelsdaLeasdekvdllgfDAClMgslEvayelrpeadylvaSsseepgeGwdY.svlgevsetkessaeev 195
                                       +r++   ++d    +++k++++ fDAClMg++E + ++++  + +v S+ + pg G++Y ++l++++  ++ ++  +
  gi|330506547|ref|YP_004382975.1| 193 NRMAKDSIND---GNKSKINIIAFDACLMGNIEAINHFKDLSEIIVTSEDVFPGSGYPYdKILQKLKADPNIDPNVM 266
                                       3344444444...35699*********************************************************** PP

                     Peptidase_C11 196 grkivdsyresyssvrve.elsLsvydlskveevlksvdalaedlvk 241
                                       + +i+++ +++y++ + +   + + +d  +++ + + + +la+++ k
  gi|330506547|ref|YP_004382975.1| 267 AINIINQTKDYYKNKFGNiVITQAALDCHELKGLNQMIYNLANKMTK 313
                                       ***********999775566778899999999999999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2485.06
//
Query:       gi|330506548|ref|YP_004382976.1|  [L=436]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete 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   27.8   0.6    2.7e-05   23.8   0.6    2.1  1  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
       0.14   12.7   4.6       0.18   12.3   2.2    2.4  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.15   12.2   0.7        7.5    6.8   0.1    2.4  2  Zn-ribbon_8      Zinc ribbon domain
       0.21   11.2   0.6         12    5.6   0.1    2.4  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.27   11.3   2.8        1.3    9.1   3.1    1.9  2  DZR              Double zinc ribbon
       0.66   10.0   2.5        7.3    6.7   0.3    2.6  2  YhfH             YhfH-like protein
        6.2    6.4   5.5         77    2.9   5.5    2.4  1  TF_Zn_Ribbon     TFIIB zinc-binding


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 !   23.8   0.6     1e-08   2.7e-05     111     259 ..     188     381 ..     146     393 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1e-08
                      DDE_Tnp_IS66 111 sRggevaealLag.....fkGvlvsDgyagYnklae....eqvthalCwaHlrRkfvdaeeakkksqaaaealar.. 176
                                       s  ++++e +L        + ++v+D y gY+++ +    ++v h++C+ Hl   +v+   +k   ++ +e l++  
  gi|330506548|ref|YP_004382976.1| 188 SKDADTIEGFLRRnldtqKQIFIVTDLYRGYSNVFKrvfgNKVIHQFCLLHLNKLIVNDFPRKT--SIEQELLKYkm 262
                                       55566666666655554445699**********9999***************999887776643..44444444442 PP

                      DDE_Tnp_IS66 177 igklya.............ierearea...........eae.........erlalrqeesrpllaelea.wleeql. 218
                                       ++ +++              e+ +r +           e           + + +r++es+ l+++ ++  l++ + 
  gi|330506548|ref|YP_004382976.1| 263 LNIFFNreleieflstlieEEKMMR-QrsnkeykswiaE-AkhlfydfvrRLELRRRRESKNLEQRTYHeALNNFKf 337
                                       4444445555555555543233332.1233344334331.0333333442555666777788877655504444448 PP

                      DDE_Tnp_IS66 219 ...kkvlpksklgkairyllkrweallrfledgrvpidNNaaER 259
                                          ++ +    ++k ++++ + w++l+ f    + p +NN +E+
  gi|330506548|ref|YP_004382976.1| 338 lkmQSDSFMISVRKRLDKIEELWPNLTAFYFTDNAPATNNPIEN 381
                                       777666677789*******************************9 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2     7e-05      0.18       8      51 ..      44     118 ..      43     123 .. 0.62
   2 ?   -1.0   0.0      0.99   2.5e+03      14      29 ..     284     299 ..     282     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7e-05
                   Zn_ribbon_recom   8 CgeCGspmtr......rkrkgkr.......hyYrCstyrrkgk..................k.Csnh...sireekl 49 
                                       C eCG+pm++      +    kr         Y C+++ ++ +                  + C+     ++++e++
  gi|330506548|ref|YP_004382976.1|  44 CPECGHPMSHngfntcQ----KRhlgganvGKYLCGACGKSTEedrdfwiklktdffgivtEiCTRLrlnHVSYEVI 116
                                       **********5543322....22355558889999988766655556666666666665531466544556666666 PP

                   Zn_ribbon_recom  50 ee 51 
                                       e+
  gi|330506548|ref|YP_004382976.1| 117 ES 118
                                       65 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.99
                   Zn_ribbon_recom  14 pmtrrkrkgkrhyYrC 29 
                                       +m r+++++++  ++ 
  gi|330506548|ref|YP_004382976.1| 284 KMMRQRSNKEYKSWIA 299
                                       7999999999988875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0029       7.5      26      35 ..      40      50 ..      25      53 .. 0.60
   2 ?    3.3   0.1     0.035        90       6      17 ..      72      83 ..      71      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                       Zn-ribbon_8 26 lta.CPeCgse 35
                                       ++ CPeCg++
  gi|330506548|ref|YP_004382976.1| 40 VPPlCPECGHP 50
                                      3444****986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.035
                       Zn-ribbon_8  6 YrCeeCghefev 17
                                      Y C +Cg+  e+
  gi|330506548|ref|YP_004382976.1| 72 YLCGACGKSTEE 83
                                      89*****99885 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0046        12       4      14 ..      43      53 ..      43      57 .. 0.86
   2 ?    3.5   0.1     0.021        54       2      15 ..      71      84 ..      70      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0046
                            zf_UBZ  4 lCerCgkeipe 14
                                      lC++Cg+++++
  gi|330506548|ref|YP_004382976.1| 43 LCPECGHPMSH 53
                                      6*******987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.021
                            zf_UBZ  2 tylCerCgkeipes 15
                                       ylC  Cgk+ +e+
  gi|330506548|ref|YP_004382976.1| 71 KYLCGACGKSTEED 84
                                      69*******97765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.9     0.002         5      30      46 ..      43      60 ..      26      63 .. 0.76
   2 ?    9.1   3.1   0.00049       1.3      15      43 ..      44      86 ..      41     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.002
                               DZR 30 rCpsCgek.vdpearfCp 46
                                       Cp+Cg++  ++++++C+
  gi|330506548|ref|YP_004382976.1| 43 LCPECGHPmSHNGFNTCQ 60
                                      688888886666777775 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00049
                               DZR 15 CseCgtklkavaa................edrCpsCgekvdpear 43
                                      C+eCg++++   +                ++ C +Cg++++++  
  gi|330506548|ref|YP_004382976.1| 44 CPECGHPMSH--NgfntcqkrhlgganvgKYLCGACGKSTEEDRD 86
                                      5556655552..123555555555556669999999998877665 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0028       7.3       7      24 ..      35      52 ..      31      61 .. 0.85
   2 ?    2.6   0.1     0.055   1.4e+02      15      26 ..      73      84 ..      67      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0028
                              YhfH  7 FfrnLPkKkCteCGkeie 24
                                      +fr++ +  C+eCG  + 
  gi|330506548|ref|YP_004382976.1| 35 IFRKIVPPLCPECGHPMS 52
                                      799999999*****9986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.055
                              YhfH 15 kCteCGkeieEq 26
                                       C  CGk  eE 
  gi|330506548|ref|YP_004382976.1| 73 LCGACGKSTEED 84
                                      6******99995 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   5.5      0.03        77       3      32 ..      44      84 ..      43      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.03
                                      ETTTTCEEC...........HEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon  3 CPnCgstnl...........veDpergelvCtdCGlVledn 32
                                      CP+Cg+++            +  ++ g ++C++CG   e++
  gi|330506548|ref|YP_004382976.1| 44 CPECGHPMShngfntcqkrhLGGANVGKYLCGACGKSTEED 84
                                      99999987458888888777777999999999999877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3098.02
//
Query:       gi|330506549|ref|YP_004382977.1|  [L=144]
Description: hypothetical protein MCON_0270 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1087.42
//
Query:       gi|330506550|ref|YP_004382978.1|  [L=118]
Description: glyoxalase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-05   25.2   0.0    4.8e-05   23.6   0.0    1.8  1  Glyoxalase      Glyoxalase/Bleomycin resistance protein/Dioxy
    0.00042   21.1   0.0    0.00073   20.3   0.0    1.4  1  Glyoxalase_6    Glyoxalase-like domain
  ------ inclusion threshold ------
        0.1   12.9   0.0        0.3   11.4   0.0    1.7  2  Transposase_20  Transposase IS116/IS110/IS902 family


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 !   23.6   0.0     8e-09   4.8e-05       2      57 ..       4      56 ..       3     109 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8e-09
                                      EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEE...EESTEEEEEEEEETTTSEEEEEEE CS
                        Glyoxalase  2 idhvallvgdleksldFYtkvLGfklvkktdn...teeteglriaffhaggghielvln 57
                                      i h+ ++++d++++  FY + +G+++    ++   +        +f+  ggg+ + ++ 
  gi|330506550|ref|YP_004382978.1|  4 IVHFEIPADDIQRAKTFYSDLFGWRMESMPGMdytM------IDTFGAPGGGMMKRMHP 56
                                      88************************9998855542......44444444444433333 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.2e-07   0.00073       6     105 ..      11     108 ..       5     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.2e-07
                      Glyoxalase_6   6 aadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpepaknrvHldlavedldaevarlvalGAr 82 
                                       a+d +++ +F+++++gw+ e+ +      +     + +a+   + ++  p+ +++   + v+++d+ +a++++lG++
  gi|330506550|ref|YP_004382978.1|  11 ADDIQRAKTFYSDLFGWRMESMP----GMDYTMIDTFGAPGGGMMKRMHPE-QQIINYIGVPSVDEYAAKAEKLGGK 82 
                                       89*********************....333333333344444444444432.3588899****************** PP

                      Glyoxalase_6  83 vlreprdgthgr...vlaDPeGneFc 105
                                        + ++ +  + +   v+ D e n F 
  gi|330506550|ref|YP_004382978.1|  83 IIVPKMSVPGMGyfvVCLDTENNAFG 108
                                       99888887766699999999999995 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     5e-05       0.3       4      56 ..      29      83 ..      27      85 .. 0.86
   2 ?   -1.6   0.0      0.57   3.4e+03       5      13 ..      88      96 ..      88      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5e-05
                    Transposase_20  4 LesipGiGpvtaaallaeigdl.rrfksakqlaayaGlapvenqSGkkkr.rgri 56
                                       es+pG++ ++  ++ a  g + +r + ++q+++y+G+  v++  +k ++  g+i
  gi|330506550|ref|YP_004382978.1| 29 MESMPGMDYTMIDTFGAPGGGMmKRMHPEQQIINYIGVPSVDEYAAKAEKlGGKI 83
                                      68*****************5555***************99998888888766655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.57
                    Transposase_20  5 esipGiGpv 13
                                      +s+pG+G  
  gi|330506550|ref|YP_004382978.1| 88 MSVPGMGYF 96
                                      79****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 864.49
//
Query:       gi|330506551|ref|YP_004382979.1|  [L=261]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-63  208.2   8.3    1.5e-11   43.6   0.2    7.0  7  TPR_1            Tetratricopeptide repeat
      5e-58  188.6  15.2    3.4e-10   39.3   0.6    7.0  7  TPR_2            Tetratricopeptide repeat
    1.6e-54  181.3  15.3    2.5e-13   49.4   0.1    6.4  6  TPR_11           TPR repeat
    6.4e-44  144.5   8.8    1.2e-06   28.3   0.1    7.2  7  TPR_8            Tetratricopeptide repeat
    4.2e-43  145.7  19.5    2.2e-13   50.6   0.1    4.2  4  TPR_16           Tetratricopeptide repeat
      3e-34  114.9   2.8    8.3e-06   25.8   0.1    7.1  7  TPR_17           Tetratricopeptide repeat
    3.7e-32  110.6   9.7    3.3e-10   40.3   0.1    4.1  4  TPR_19           Tetratricopeptide repeat
      4e-32  108.2  23.0    1.9e-07   31.3   0.1    7.0  7  TPR_14           Tetratricopeptide repeat
    3.4e-26   91.3  34.9    1.3e-07   31.7   0.5    6.0  6  TPR_12           Tetratricopeptide repeat
    1.3e-22   79.8   1.0    5.8e-07   29.6   0.0    3.7  4  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    2.3e-21   75.7  17.4    1.2e-06   28.6   3.4    4.7  5  TPR_9            Tetratricopeptide repeat
    2.2e-20   71.1  16.0     0.0007   19.4   0.1    7.3  7  TPR_7            Tetratricopeptide repeat
    1.3e-19   69.4  11.6       0.18   12.5   0.0    7.2  7  TPR_6            Tetratricopeptide repeat
    3.5e-14   52.6   0.1       0.34   11.0   0.0    6.2  6  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    1.5e-13   50.1  27.0      0.095   12.6   0.2    7.4  7  TPR_10           Tetratricopeptide repeat
      1e-11   44.6   5.1      0.022   14.7   0.0    5.6  5  TPR_3            Tetratricopeptide repeat
      4e-11   42.5   0.4    0.00012   21.2   0.0    3.6  5  NARP1            NMDA receptor-regulated protein 1
    1.2e-10   40.9  15.6        0.8   10.5   0.6    7.5  7  TPR_4            Tetratricopeptide repeat
      1e-09   39.0   6.7    4.5e-05   23.9   0.2    3.2  2  BTAD             Bacterial transcriptional activator domain
    2.2e-09   37.3   0.7          2    8.5   0.1    6.0  6  ANAPC5           Anaphase-promoting complex subunit 5
    5.3e-08   32.4   6.5     0.0068   15.6   1.6    3.4  3  TPR_15           Tetratricopeptide repeat
    7.2e-08   32.4  10.8      0.054   13.2   3.5    4.3  5  TPR_21           Tetratricopeptide repeat-like domain
    1.4e-07   31.5   0.2        3.3    7.5   0.0    5.4  6  DUF5113          Domain of unknown function (DUF5113)
    7.7e-07   29.1   0.0     0.0012   18.8   0.0    3.2  2  SRP_TPR_like     Putative TPR-like repeat
    8.2e-07   29.6   0.2        1.6    9.2   0.0    4.0  4  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    8.4e-07   29.2   7.3        0.2   11.7   0.3    6.1  5  DUF3856          Domain of Unknown Function (DUF3856)
    1.9e-06   27.5   0.1      0.044   13.4   0.0    2.8  3  HrpB1_HrpK       Bacterial type III secretion protein (HrpB1_
    2.2e-06   27.7   1.5        2.1    8.6   0.0    5.0  6  DUF1510          Domain of unknown function (DUF1510)
    1.3e-05   25.5   6.4       0.45   10.9   0.1    4.5  5  TPR_20           Tetratricopeptide repeat
    0.00037   20.0   3.5      0.021   14.2   0.9    3.4  3  TPR_MalT         MalT-like TPR region
     0.0021   18.2   0.1         25    5.4   0.0    5.0  4  PPR              PPR repeat
     0.0039   17.2   0.0         11    6.0   0.0    3.7  4  Mo-co_dimer      Mo-co oxidoreductase dimerisation domain
     0.0064   16.0   5.8        6.8    6.4   0.1    5.3  4  HTH_Bact         Helix-turn-helix bacterial domain
     0.0071   16.4  13.3        0.3   11.2   0.9    6.2  7  MIT              MIT (microtubule interacting and transport) 
  ------ inclusion threshold ------
      0.016   15.4   0.7         49    4.2   0.0    4.8  5  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
      0.017   14.4   0.9         10    5.2   0.1    3.3  3  FAT              FAT domain
       0.02   13.5   0.5       0.22   10.0   0.0    2.0  2  DUF1347          Protein of unknown function (DUF1347)
      0.023   14.8   1.9       0.14   12.3   0.0    2.8  2  DUF357           Protein of unknown function (DUF357)
      0.031   14.2   1.6        4.7    7.2   0.0    3.7  3  Clathrin_H_link  Clathrin-H-link
      0.039   14.1   0.3         10    6.3   0.0    4.3  5  MAS20            MAS20 protein import receptor
       0.04   13.6   2.3        3.3    7.4   0.1    3.5  3  YfiO             Outer membrane lipoprotein
      0.049   13.7   0.1         11    6.1   0.0    3.3  2  TPR_18           Tetratricopeptide repeat
      0.055   13.5   0.0        8.9    6.4   0.0    3.3  3  DUF627           Protein of unknown function (DUF627)
       0.15   12.0   4.8          6    6.7   0.1    3.9  4  Wzy_C_2          Virulence factor membrane-bound polymerase, 
       0.19   12.0   0.1         74    3.7   0.0    3.5  3  PPR_2            PPR repeat family
       0.19   12.4   0.4       0.19   12.4   0.4    4.3  4  DUF4398          Domain of unknown function (DUF4398)
       0.22   11.2   3.5         19    4.9   0.0    4.0  4  RPN7             26S proteasome subunit RPN7
       0.24    9.5   1.5         13    3.8   0.0    3.0  3  EzrA             Septation ring formation regulator, EzrA
        2.3    8.4   9.3        2.2    8.4   0.2    4.0  4  HEPN             HEPN 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 !   43.6   0.2     4e-14   1.5e-11       1      34 []      24      57 ..      24      57 .. 0.97
   2 !   33.9   0.0   4.8e-11   1.8e-08       2      33 ..      59      90 ..      58      91 .. 0.96
   3 !   28.3   0.1   2.8e-09     1e-06       1      34 []      92     125 ..      92     125 .. 0.97
   4 !   26.9   0.0   7.9e-09   2.9e-06       3      33 ..     128     158 ..     127     159 .. 0.95
   5 !   21.1   0.0     5e-07   0.00018       3      34 .]     162     193 ..     160     193 .. 0.95
   6 !   29.1   0.0   1.5e-09   5.6e-07       2      33 ..     195     226 ..     194     227 .. 0.95
   7 !   23.8   0.5   7.5e-08   2.8e-05       1      30 [.     228     257 ..     228     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 4e-14
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a+ +  +Gn +f++g+y+eA+e+y++AL+l+P+n
  gi|330506551|ref|YP_004382979.1| 24 AEEWLERGNELFSQGDYEEAIEAYDEALRLDPEN 57
                                      789*****************************97 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 4.8e-11
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPn 33
                                       a+ n+G a+ ++ +y+eA+++++++++++P+
  gi|330506551|ref|YP_004382979.1| 59 VAWSNKGTALINQRRYEEAIQAFDEVIRIDPE 90
                                      69*****************************7 PP

  == domain 3  score: 28.3 bits;  conditional E-value: 2.8e-09
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a+  +G a+++lg+ydeA+ + ++A+ l+P+n
  gi|330506551|ref|YP_004382979.1|  92 ASAWSYKGGALHELGEYDEAIVALDQAIGLEPEN 125
                                       68******************************97 PP

  == domain 4  score: 26.9 bits;  conditional E-value: 7.9e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       ++  +G a++ +g+ydeAl + e+A++l+P+
  gi|330506551|ref|YP_004382979.1| 128 IWSLKGSALYFQGEYDEALTAIEEAIRLEPD 158
                                       6999**************************8 PP

  == domain 5  score: 21.1 bits;  conditional E-value: 5e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+  ++ +++++g+y+eA+ + +++++l P++
  gi|330506551|ref|YP_004382979.1| 162 AWSLKADILYEQGDYQEAITAVDEVIRLMPDY 193
                                       9***************************9987 PP

  == domain 6  score: 29.1 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                        a+ n+G ++ +l++yde le+ ++A++l+ +
  gi|330506551|ref|YP_004382979.1| 195 AAWSNRGELLWRLERYDESLEALDRAIQLDSD 226
                                       79***************************986 PP

  == domain 7  score: 23.8 bits;  conditional E-value: 7.5e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a+a+yn+G a+  +g+ +eA  +y +A el
  gi|330506551|ref|YP_004382979.1| 228 ADAWYNRGEALKAQGRDEEADVAYTRAKEL 257
                                       89*************************887 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.6   9.2e-13   3.4e-10       1      34 []      24      57 ..      24      57 .. 0.97
   2 !   29.4   0.0   1.4e-09     5e-07       3      33 ..      60      90 ..      58      91 .. 0.95
   3 !   22.6   0.1     2e-07   7.3e-05       1      34 []      92     125 ..      92     125 .. 0.96
   4 !   26.9   0.0   8.4e-09   3.1e-06       3      33 ..     128     158 ..     126     159 .. 0.95
   5 !   26.9   0.0   8.5e-09   3.1e-06       3      34 .]     162     193 ..     160     193 .. 0.95
   6 !   27.5   0.1   5.3e-09   1.9e-06       1      33 [.     194     226 ..     194     227 .. 0.94
   7 !   20.6   0.9   8.4e-07   0.00031       1      30 [.     228     257 ..     228     258 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 9.2e-13
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      ae + ++G+ ++ +gdyeeA+ea+++Al+ldP+n
  gi|330506551|ref|YP_004382979.1| 24 AEEWLERGNELFSQGDYEEAIEAYDEALRLDPEN 57
                                      799*****************************97 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1.4e-09
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPn 33
                                      a+ n G a++++ +yeeA++af++++++dP+
  gi|330506551|ref|YP_004382979.1| 60 AWSNKGTALINQRRYEEAIQAFDEVIRIDPE 90
                                      9*****************************7 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 2e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a a+ + G a+ +lg+y+eA+ a+++A+ l+P+n
  gi|330506551|ref|YP_004382979.1|  92 ASAWSYKGGALHELGEYDEAIVALDQAIGLEPEN 125
                                       679****************************997 PP

  == domain 4  score: 26.9 bits;  conditional E-value: 8.4e-09
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       ++   G a+y +g+y+eAl a e+A++l+P+
  gi|330506551|ref|YP_004382979.1| 128 IWSLKGSALYFQGEYDEALTAIEEAIRLEPD 158
                                       6999**************************8 PP

  == domain 5  score: 26.9 bits;  conditional E-value: 8.5e-09
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+   ++++y++gdy+eA+ a +++++l P++
  gi|330506551|ref|YP_004382979.1| 162 AWSLKADILYEQGDYQEAITAVDEVIRLMPDY 193
                                       89****************************85 PP

  == domain 6  score: 27.5 bits;  conditional E-value: 5.3e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       + a+ n+G+++++l +y+e lea+++A++ld +
  gi|330506551|ref|YP_004382979.1| 194 PAAWSNRGELLWRLERYDESLEALDRAIQLDSD 226
                                       579***************************965 PP

  == domain 7  score: 20.6 bits;  conditional E-value: 8.4e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a+a+yn+G+a+ ++g+ eeA  a+ +A el
  gi|330506551|ref|YP_004382979.1| 228 ADAWYNRGEALKAQGRDEEADVAYTRAKEL 257
                                       79*************************887 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.1     7e-16   2.5e-13       1      38 [.      31      68 ..      31      71 .. 0.95
   2 !   26.4   0.1   1.1e-08     4e-06       9      42 .]      73     106 ..      66     106 .. 0.94
   3 !   27.2   0.1     6e-09   2.2e-06       3      39 ..     101     137 ..      99     137 .. 0.94
   4 !   20.6   0.1   7.3e-07   0.00027       1      31 [.     133     163 ..     133     166 .. 0.92
   5 !   36.2   0.0   9.6e-12   3.5e-09       2      41 ..     168     207 ..     167     208 .. 0.96
   6 !   37.8   0.4   2.9e-12   1.1e-09       8      42 .]     208     242 ..     206     242 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 7e-16
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                                      G+++++qG+yeeAieaY +Al+ldP+n+ a++n G a+
  gi|330506551|ref|YP_004382979.1| 31 GNELFSQGDYEEAIEAYDEALRLDPENPVAWSNKGTAL 68
                                      9*********************************9887 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 1.1e-08
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +yeeAi+a+ + +++dP+ a+a++  G a++++G
  gi|330506551|ref|YP_004382979.1|  73 RYEEAIQAFDEVIRIDPELASAWSYKGGALHELG 106
                                       8******************************998 PP

  == domain 3  score: 27.2 bits;  conditional E-value: 6e-09
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       a++e+G+y+eAi a+ +A+ l P+n ++++  G a+y
  gi|330506551|ref|YP_004382979.1| 101 ALHELGEYDEAIVALDQAIGLEPENGSIWSLKGSALY 137
                                       89******************************99987 PP

  == domain 4  score: 20.6 bits;  conditional E-value: 7.3e-07
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeay 31 
                                       G a+y qG+y+eA++a ++A++l Pd+  a+
  gi|330506551|ref|YP_004382979.1| 133 GSALYFQGEYDEALTAIEEAIRLEPDSTIAW 163
                                       8899**********************87766 PP

  == domain 5  score: 36.2 bits;  conditional E-value: 9.6e-12
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       d++yeqG+y eAi+a  + ++l Pd++ a++n+G++++++
  gi|330506551|ref|YP_004382979.1| 168 DILYEQGDYQEAITAVDEVIRLMPDYPAAWSNRGELLWRL 207
                                       9***********************************9986 PP

  == domain 6  score: 37.8 bits;  conditional E-value: 2.9e-12
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                        +y+e++ea+ +A++ld+d a+a+yn+G+a+ +qG
  gi|330506551|ref|YP_004382979.1| 208 ERYDESLEALDRAIQLDSDLADAWYNRGEALKAQG 242
                                       69*******************************99 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   3.2e-09   1.2e-06       4      34 .]      27      57 ..      24      57 .. 0.94
   2 !   24.0   0.0   7.4e-08   2.7e-05       3      33 ..      60      90 ..      58      91 .. 0.96
   3 !   18.3   0.0   4.9e-06    0.0018       4      34 .]      95     125 ..      92     125 .. 0.88
   4 !   21.1   0.0   6.5e-07   0.00024       3      33 ..     128     158 ..     126     159 .. 0.95
   5 !   15.3   0.0   4.5e-05     0.017       3      33 ..     162     192 ..     161     193 .. 0.91
   6 !   19.8   0.0   1.7e-06   0.00063       3      33 ..     196     226 ..     194     227 .. 0.94
   7 !   17.0   0.2   1.3e-05    0.0047       1      30 [.     228     257 ..     228     257 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.2e-09
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  4 yynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      ++  g+ ++++gdyeeA+e+y +al+ldp+n
  gi|330506551|ref|YP_004382979.1| 27 WLERGNELFSQGDYEEAIEAYDEALRLDPEN 57
                                      78899************************86 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 7.4e-08
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      a+ n+g +++++ +yeeA++++ +++++dp+
  gi|330506551|ref|YP_004382979.1| 60 AWSNKGTALINQRRYEEAIQAFDEVIRIDPE 90
                                      799**************************96 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 4.9e-06
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +  +g ++++lg+y+eA+ ++ +a+ l+p+n
  gi|330506551|ref|YP_004382979.1|  95 WSYKGGALHELGEYDEAIVALDQAIGLEPEN 125
                                       55578899*********************86 PP

  == domain 4  score: 21.1 bits;  conditional E-value: 6.5e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++ ++gs++  +g+y+eA  ++e+a++l+pd
  gi|330506551|ref|YP_004382979.1| 128 IWSLKGSALYFQGEYDEALTAIEEAIRLEPD 158
                                       7999**************************8 PP

  == domain 5  score: 15.3 bits;  conditional E-value: 4.5e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+ ++++i+ ++gdy+eA+ +  ++++l pd
  gi|330506551|ref|YP_004382979.1| 162 AWSLKADILYEQGDYQEAITAVDEVIRLMPD 192
                                       7999********************9998666 PP

  == domain 6  score: 19.8 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+ n g +++ l++y+e+ e++ +a++ld d
  gi|330506551|ref|YP_004382979.1| 196 AWSNRGELLWRLERYDESLEALDRAIQLDSD 226
                                       899*************************976 PP

  == domain 7  score: 17.0 bits;  conditional E-value: 1.3e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+a+yn g +++ +g+ eeA  +y +a el
  gi|330506551|ref|YP_004382979.1| 228 ADAWYNRGEALKAQGRDEEADVAYTRAKEL 257
                                       79***********************99876 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.1   6.1e-16   2.2e-13       1      65 [.      28      89 ..      28      89 .. 0.94
   2 !   42.9   0.3   1.6e-13   5.8e-11       2      61 ..      63     119 ..      62     125 .. 0.90
   3 !   48.1   0.2   3.6e-15   1.3e-12       3      68 .]     132     194 ..     131     196 .. 0.94
   4 !   33.8   4.8   1.1e-10   3.9e-08       3      59 ..     200     253 ..     198     258 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 6.1e-16
                            TPR_16  1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65
                                      l+++++++ +gdy++A++a+++al++dp+ P+   A+ ++g a+  q r++eA++++++ +r +p
  gi|330506551|ref|YP_004382979.1| 28 LERGNELFSQGDYEEAIEAYDEALRLDPENPV---AWSNKGTALINQRRYEEAIQAFDEVIRIDP 89
                                      5789***********************66666...************************999988 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 1.6e-13
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       ++++a++++++y++A+ a++++++ d   P+ a A+ ++g a+ ++g+++eA+ +++ a+
  gi|330506551|ref|YP_004382979.1|  63 NKGTALINQRRYEEAIQAFDEVIRID---PELASAWSYKGGALHELGEYDEAIVALDQAI 119
                                       5799**********************...************************5555555 PP

  == domain 3  score: 48.1 bits;  conditional E-value: 3.6e-15
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       ++ a++ +g+yd+A+ a e+a+++    Pd   A+ l++d++++qg+++eA+ ++++ +r  pd+p
  gi|330506551|ref|YP_004382979.1| 132 KGSALYFQGEYDEALTAIEEAIRLE---PDSTIAWSLKADILYEQGDYQEAITAVDEVIRLMPDYP 194
                                       5889*********************...****************************9998888766 PP

  == domain 4  score: 33.8 bits;  conditional E-value: 1.1e-10
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyra 59 
                                       ++ +++r+ +yd+ ++al++a+ +d   +d a+A++++g+a+ +qgr +eA  +y +
  gi|330506551|ref|YP_004382979.1| 200 RGELLWRLERYDESLEALDRAIQLD---SDLADAWYNRGEALKAQGRDEEADVAYTR 253
                                       7899*********************...**********************9655544 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.036        13      10      34 .]      21      45 ..      18      45 .. 0.91
   2 !   25.8   0.1   2.3e-08   8.3e-06       1      34 []      46      79 ..      46      79 .. 0.97
   3 !   14.6   0.0   8.5e-05     0.031       2      33 ..      81     112 ..      80     113 .. 0.95
   4 !   12.2   0.0    0.0005      0.18       3      33 ..     116     146 ..     114     147 .. 0.92
   5 !   21.3   0.0   6.5e-07   0.00024       2      33 ..     149     180 ..     148     181 .. 0.95
   6 ?    4.3   0.0      0.17        61       7      30 ..     188     211 ..     184     215 .. 0.75
   7 !   23.4   0.1   1.3e-07   4.8e-05       2      32 ..     217     247 ..     216     248 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.036
                            TPR_17 10 PnnadaynnLAelllknGdlmtArq 34
                                        na+ + ++++ l ++Gd+++A++
  gi|330506551|ref|YP_004382979.1| 21 QENAEEWLERGNELFSQGDYEEAIE 45
                                      579999*****************86 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 2.3e-08
                            TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtArq 34
                                      +y +al+ldP n++a+ n++++l ++ ++++A+q
  gi|330506551|ref|YP_004382979.1| 46 AYDEALRLDPENPVAWSNKGTALINQRRYEEAIQ 79
                                      599*****************************98 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 8.5e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + +++++dP  a a+ +++ +l+++G++++A+
  gi|330506551|ref|YP_004382979.1|  81 FDEVIRIDPELASAWSYKGGALHELGEYDEAI 112
                                       7899**************************96 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.0005
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtAr 33 
                                        +a+ l+P n   + +++ +l+ +G++++A+
  gi|330506551|ref|YP_004382979.1| 116 DQAIGLEPENGSIWSLKGSALYFQGEYDEAL 146
                                       678999***********************96 PP

  == domain 5  score: 21.3 bits;  conditional E-value: 6.5e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                        ++a++l+P++  a+ ++A +l+++Gd+++A+
  gi|330506551|ref|YP_004382979.1| 149 IEEAIRLEPDSTIAWSLKADILYEQGDYQEAI 180
                                       589***************************97 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.17
                            TPR_17   7 eldPnnadaynnLAelllknGdlm 30 
                                       +l P+++ a+ n++ell ++ +++
  gi|330506551|ref|YP_004382979.1| 188 RLMPDYPAAWSNRGELLWRLERYD 211
                                       5559***********996555555 PP

  == domain 7  score: 23.4 bits;  conditional E-value: 1.3e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       + +a++ld + ada++n++e+l+ +G+ ++A
  gi|330506551|ref|YP_004382979.1| 217 LDRAIQLDSDLADAWYNRGEALKAQGRDEEA 247
                                       579************************9998 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.1   9.1e-13   3.3e-10       1      59 [.      34      92 ..      34      99 .. 0.92
   2 !   34.8   0.1   4.8e-11   1.8e-08       3      68 .]     104     169 ..     102     169 .. 0.95
   3 !   32.6   0.3   2.3e-10   8.3e-08       1      57 [.     170     226 ..     170     228 .. 0.95
   4 !   16.6   1.9   2.3e-05    0.0083       6      50 ..     209     253 ..     209     259 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 9.1e-13
                            TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59
                                      l+ +gdy+eA++++ +al  dp+n+ a+ +   al+++ +++eA+++ d++ + dp  a
  gi|330506551|ref|YP_004382979.1| 34 LFSQGDYEEAIEAYDEALRLDPENPVAWSNKGTALINQRRYEEAIQAFDEVIRIDPELA 92
                                      688**************************************************999854 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 4.8e-11
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAkl 68 
                                       + g y+eA+ +l qa+  +p+n+ ++ l   al+ +g++deA  +++++ + +pd+  ++sL+A +
  gi|330506551|ref|YP_004382979.1| 104 ELGEYDEAIVALDQAIGLEPENGSIWSLKGSALYFQGEYDEALTAIEEAIRLEPDSTIAWSLKADI 169
                                       679****************************************************99999***975 PP

  == domain 3  score: 32.6 bits;  conditional E-value: 2.3e-10
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       l+++gdy+eA+ +  +++   p++++a+ +  e+l+ l ++de  ++Ld++ + d d
  gi|330506551|ref|YP_004382979.1| 170 LYEQGDYQEAITAVDEVIRLMPDYPAAWSNRGELLWRLERYDESLEALDRAIQLDSD 226
                                       789***********************************************9887766 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 2.3e-05
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLda 50 
                                       +y+e l++l +a+q d + a+a+++  eal a+g+ +eA  +  +
  gi|330506551|ref|YP_004382979.1| 209 RYDESLEALDRAIQLDSDLADAWYNRGEALKAQGRDEEADVAYTR 253
                                       69999**********************************876655 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   5.1e-10   1.9e-07       2      38 ..      25      61 ..      24      66 .. 0.94
   2 !   17.5   0.1   1.4e-05    0.0052       8      39 ..      65      96 ..      60      99 .. 0.88
   3 !   17.9   0.1   1.1e-05    0.0039       3      40 ..      94     131 ..      92     135 .. 0.90
   4 !   21.4   0.1   8.2e-07    0.0003       4      43 ..     129     168 ..     127     169 .. 0.91
   5 !   20.0   0.1   2.2e-06   0.00081       3      43 ..     162     202 ..     161     203 .. 0.91
   6 !   22.8   3.1   2.8e-07    0.0001       1      43 [.     194     236 ..     194     237 .. 0.94
   7 ?    7.1   0.7     0.031        11       2      27 ..     229     254 ..     228     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 5.1e-10
                            TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeaw 38
                                      e +l+++  l+ +Gd++eAi+++++al+l+P++++aw
  gi|330506551|ref|YP_004382979.1| 25 EEWLERGNELFSQGDYEEAIEAYDEALRLDPENPVAW 61
                                      78**********************************9 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.4e-05
                            TPR_14  8 aeallalGdpdeAiallrralalaPddaeawl 39
                                      + al ++++++eAi++++++++ +P+ a aw 
  gi|330506551|ref|YP_004382979.1| 65 GTALINQRRYEEAIQAFDEVIRIDPELASAWS 96
                                      7899************************9995 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 1.1e-05
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       a+   + al +lG++deAi +l++a+ l P++  +w l
  gi|330506551|ref|YP_004382979.1|  94 AWSYKGGALHELGEYDEAIVALDQAIGLEPENGSIWSL 131
                                       7888999*************************999965 PP

  == domain 4  score: 21.4 bits;  conditional E-value: 8.2e-07
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       + + ++al+ +G++deA+++ ++a++l Pd+  aw l a+
  gi|330506551|ref|YP_004382979.1| 129 WSLKGSALYFQGEYDEALTAIEEAIRLEPDSTIAWSLKAD 168
                                       6677999****************************88876 PP

  == domain 5  score: 20.0 bits;  conditional E-value: 2.2e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       a+ + a++l+++Gd++eAi++ +++++l Pd ++aw   ++
  gi|330506551|ref|YP_004382979.1| 162 AWSLKADILYEQGDYQEAITAVDEVIRLMPDYPAAWSNRGE 202
                                       78899*******************************76665 PP

  == domain 6  score: 22.8 bits;  conditional E-value: 2.8e-07
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       p+a+  ++e+l++l+++de++++l+ra++l+ d a+aw+  ++
  gi|330506551|ref|YP_004382979.1| 194 PAAWSNRGELLWRLERYDESLEALDRAIQLDSDLADAWYNRGE 236
                                       789***********************************98775 PP

  == domain 7  score: 7.1 bits;  conditional E-value: 0.031
                            TPR_14   2 eallalaeallalGdpdeAiallrra 27 
                                       +a++ ++eal a+G+ +eA  ++ ra
  gi|330506551|ref|YP_004382979.1| 229 DAWYNRGEALKAQGRDEEADVAYTRA 254
                                       79****************97777666 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   5.3e-05     0.019      54      75 ..      33      54 ..      27      56 .. 0.68
   2 !   21.2   0.4   7.4e-07   0.00027       5      72 ..      60     119 ..      56     121 .. 0.91
   3 !   22.1   1.2   3.8e-07   0.00014       2      74 ..      91     155 ..      90     155 .. 0.84
   4 !   28.1   0.2     5e-09   1.8e-06       5      75 ..     128     190 ..     124     192 .. 0.88
   5 !   31.7   0.5   3.7e-10   1.3e-07       4      75 ..     161     224 ..     158     226 .. 0.93
   6 !   28.4   2.9   4.1e-09   1.5e-06       4      71 ..     195     254 ..     192     257 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.3e-05
                            TPR_12 54 lyralgryeeAlelleealaia 75
                                       ++ +g+yeeA+e++ eal+++
  gi|330506551|ref|YP_004382979.1| 33 ELFSQGDYEEAIEAYDEALRLD 54
                                      4566777777777777777765 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 7.4e-07
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       a++n +++l  + ry+eA++ ++++++i      p+   +a++    g ++++lg+y+eA+ +l +a+
  gi|330506551|ref|YP_004382979.1|  60 AWSNKGTALINQRRYEEAIQAFDEVIRID-----PE---LASAWSYKGGALHELGEYDEAIVALDQAI 119
                                       7899*********************9999.....75...8999999999999*********9999986 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 3.8e-07
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +a+a++  + +l++lg+ydeA+  l++a+ +      p++ + +++l   g +++ +g+y+eAl + eea+++
  gi|330506551|ref|YP_004382979.1|  91 LASAWSYKGGALHELGEYDEAIVALDQAIGLE-----PEN-GSIWSLK--GSALYFQGEYDEALTAIEEAIRL 155
                                       6899999*********************6666.....877.5555555..566667**************985 PP

  == domain 4  score: 28.1 bits;  conditional E-value: 5e-09
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +++  +++l+ +g+ydeAl+  e+a+++      pd+    ++    +++++++g+y+eA+ +  e+++++
  gi|330506551|ref|YP_004382979.1| 128 IWSLKGSALYFQGEYDEALTAIEEAIRLE-----PDS---TIAWSLKADILYEQGDYQEAITAVDEVIRLM 190
                                       78889********************7777.....998...35677789***************99999986 PP

  == domain 5  score: 31.7 bits;  conditional E-value: 3.7e-10
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +a++  a++l+++g+y+eA++  +++++++     pd+p+   +  n g+l+++l+ry+e le+l +a++++
  gi|330506551|ref|YP_004382979.1| 161 IAWSLKADILYEQGDYQEAITAVDEVIRLM-----PDYPA---AWSNRGELLWRLERYDESLEALDRAIQLD 224
                                       577789************************.....**977...8************************9985 PP

  == domain 6  score: 28.4 bits;  conditional E-value: 4.1e-09
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                       +a++n++++l+rl+ryde+le l++a+++       d   +a + +n g+++ a+gr eeA  ++++a
  gi|330506551|ref|YP_004382979.1| 195 AAWSNRGELLWRLERYDESLEALDRAIQLD-----SD---LADAWYNRGEALKAQGRDEEADVAYTRA 254
                                       7899**********************8888.....55...899******************9999998 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   3.7e-08   1.4e-05      23      81 ..      22      83 ..       7      84 .. 0.87
   2 !   23.4   0.1   1.4e-07   5.1e-05      28      81 ..      97     151 ..      86     152 .. 0.90
   3 !   29.6   0.0   1.6e-09   5.8e-07      28      81 ..     131     185 ..     121     186 .. 0.92
   4 !   17.9   0.0   7.6e-06    0.0028      25      81 ..     162     219 ..     151     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.7e-08
                                      HHHHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3 23 pedayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                      +++  +l  +  l+++g+y++A+e +++a +l+++++ ++  ++ +l+ + +yeeAi+a+++
  gi|330506551|ref|YP_004382979.1| 22 ENAEEWLerGNELFSQGDYEEAIEAYDEAlRLDPENPVAWSNKGTALINQRRYEEAIQAFDE 83
                                      4555555558889**********************************************987 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  28 llAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +++ +l ++g+y++A+  l++a +l++++  ++ l++ +l+ +++y+eA++a+e+
  gi|330506551|ref|YP_004382979.1|  97 YKGGALHELGEYDEAIVALDQAiGLEPENGSIWSLKGSALYFQGEYDEALTAIEE 151
                                       567788999********************************************97 PP

  == domain 3  score: 29.6 bits;  conditional E-value: 1.6e-09
                                       HHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  28 llAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       l++ +ly +g+y++A++ +++a +l++ s  ++ l+A  l++++ y+eAi+a ++
  gi|330506551|ref|YP_004382979.1| 131 LKGSALYFQGEYDEALTAIEEAiRLEPDSTIAWSLKADILYEQGDYQEAITAVDE 185
                                       56899**********************************************9876 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 7.6e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  25 dayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +  l+A  ly++g+y++A++ +++  +l +  ++++   ++ l  L++y+e + aL++
  gi|330506551|ref|YP_004382979.1| 162 AWSLKADILYEQGDYQEAITAVDEViRLMPDYPAAWSNRGELLWRLERYDESLEALDR 219
                                       45678********************99999999*********************9986 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   3.4e-06    0.0012      28      65 ..      23      60 ..      19      61 .. 0.94
   2 !   25.4   0.1   3.2e-08   1.2e-05       4      62 ..      67     125 ..      64     133 .. 0.93
   3 !   22.0   0.2   3.6e-07   0.00013       9      65 ..     140     196 ..     131     198 .. 0.92
   4 !   28.6   3.4   3.2e-09   1.2e-06       6      65 ..     171     230 ..     169     232 .. 0.94
   5 !   16.3   2.7   2.1e-05    0.0078       4      48 ..     203     247 ..     201     254 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.4e-06
                             TPR_9 28 dpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                                       +ee+++RG  l+ +G++++A+++ + +l+l+p++p a
  gi|330506551|ref|YP_004382979.1| 23 NAEEWLERGNELFSQGDYEEAIEAYDEALRLDPENPVA 60
                                      689*******************************9976 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 3.2e-08
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       ++i+++++e+a+++ + ++ ++P+ ++ +   G +l++lG + +A+ +L++++ l+p++
  gi|330506551|ref|YP_004382979.1|  67 ALINQRRYEEAIQAFDEVIRIDPELASAWSYKGGALHELGEYDEAIVALDQAIGLEPEN 125
                                       469***************************************************99986 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 3.6e-07
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                        ++++al ++e  + l Pd+   +   + +l+++G++++A+ + +  ++l pd p+a
  gi|330506551|ref|YP_004382979.1| 140 GEYDEALTAIEEAIRLEPDSTIAWSLKADILYEQGDYQEAITAVDEVIRLMPDYPAA 196
                                       5799****************************************9999999998776 PP

  == domain 4  score: 28.6 bits;  conditional E-value: 3.2e-09
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                        ++ d+++a+ +v+ ++ l Pd p  +  RG ll +l+++ + l++L+++++l+ d +da
  gi|330506551|ref|YP_004382979.1| 171 YEQGDYQEAITAVDEVIRLMPDYPAAWSNRGELLWRLERYDESLEALDRAIQLDSDLADA 230
                                       5789*************************************************9988776 PP

  == domain 5  score: 16.3 bits;  conditional E-value: 2.1e-05
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaA 48 
                                       +++r e++++ l++++r ++l++d ++ ++ RG +l  +G+ ++A
  gi|330506551|ref|YP_004382979.1| 203 LLWRLERYDESLEALDRAIQLDSDLADAWYNRGEALKAQGRDEEA 247
                                       68999******************************9999987776 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.9e-06    0.0007      10      35 ..      35      58 ..      22      59 .. 0.91
   2 !   10.8   0.0    0.0011      0.39       1      33 [.      60      90 ..      60      93 .. 0.85
   3 !   10.3   0.0    0.0016      0.57       2      30 ..      95     123 ..      94     128 .. 0.79
   4 !   10.0   0.0     0.002      0.75       8      33 ..     135     158 ..     129     161 .. 0.76
   5 !    9.9   0.0    0.0022      0.79       2      21 ..     163     182 ..     162     192 .. 0.81
   6 !   10.9   0.6   0.00099      0.36       1      34 [.     196     229 ..     196     230 .. 0.92
   7 ?    5.7   0.2     0.049        18       1      25 [.     230     254 ..     230     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.9e-06
                             TPR_7 10 srlGdyeeAielyeqsLaltkdpeda 35
                                      +++GdyeeAie y +  al+ dpe++
  gi|330506551|ref|YP_004382979.1| 35 FSQGDYEEAIEAYDE--ALRLDPENP 58
                                      689************..999999875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0011
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33
                                      a++n + +  ++++yeeAi+ + +  +++ dpe
  gi|330506551|ref|YP_004382979.1| 60 AWSNKGTALINQRRYEEAIQAFDE--VIRIDPE 90
                                      689999****************99..6666654 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0016
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       +++ + + ++lG+y+eAi  + q+++l+ 
  gi|330506551|ref|YP_004382979.1|  95 WSYKGGALHELGEYDEAIVALDQAIGLEP 123
                                       67778899**********99999555544 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.002
                             TPR_7   8 lysrlGdyeeAielyeqsLaltkdpe 33 
                                       +   +G+y+eA++  e+  a++ +p+
  gi|330506551|ref|YP_004382979.1| 135 ALYFQGEYDEALTAIEE--AIRLEPD 158
                                       54458************..6666654 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.0022
                             TPR_7   2 LlnLarlysrlGdyeeAiel 21 
                                       ++  a++  ++Gdy+eAi+ 
  gi|330506551|ref|YP_004382979.1| 163 WSLKADILYEQGDYQEAITA 182
                                       667799999*********85 PP

  == domain 6  score: 10.9 bits;  conditional E-value: 0.00099
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       a++n ++l  rl +y+e +e + ++++l++d  d
  gi|330506551|ref|YP_004382979.1| 196 AWSNRGELLWRLERYDESLEALDRAIQLDSDLAD 229
                                       7899********************9999999866 PP

  == domain 7  score: 5.7 bits;  conditional E-value: 0.049
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqs 25 
                                       a++n +++  ++G+ eeA   y+++
  gi|330506551|ref|YP_004382979.1| 230 AWYNRGEALKAQGRDEEADVAYTRA 254
                                       7899**************9999995 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00061      0.22      10      32 ..      34      56 ..      27      57 .. 0.84
   2 !   11.7   0.0   0.00087      0.32       7      31 ..      65      89 ..      60      90 .. 0.90
   3 ?    8.3   0.0     0.011       4.1       8      31 ..      95     123 ..      91     125 .. 0.73
   4 !   12.5   0.0   0.00048      0.18       8      33 .]     134     159 ..     131     159 .. 0.87
   5 ?    7.4   0.0     0.022       7.9       7      28 ..     167     188 ..     162     193 .. 0.83
   6 ?    6.5   0.1     0.041        15       5      28 ..     199     222 ..     195     226 .. 0.86
   7 !   12.4   0.5   0.00054       0.2       1      27 [.     229     255 ..     229     259 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00061
                                      HHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6 10 yrklgdtdkAlealerlikeYPd 32
                                      ++++gd+++A+ea+++ ++  P+
  gi|330506551|ref|YP_004382979.1| 34 LFSQGDYEEAIEAYDEALRLDPE 56
                                      67899************999886 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00087
                                      HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  7 alsyrklgdtdkAlealerlikeYP 31
                                      + +++++ ++++A++a++++i+  P
  gi|330506551|ref|YP_004382979.1| 65 GTALINQRRYEEAIQAFDEVIRIDP 89
                                      88999999*************9888 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.011
                                       HHHHHH.....HHHHHHHHHHHHHHHH-T CS
                             TPR_6   8 lsyrkl.....gdtdkAlealerlikeYP 31 
                                       +sy+ +     g++d+A+ al++ i   P
  gi|330506551|ref|YP_004382979.1|  95 WSYKGGalhelGEYDEAIVALDQAIGLEP 123
                                       555543455558***********997666 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00048
                                       HHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   8 lsyrklgdtdkAlealerlikeYPdS 33 
                                        +++ +g++d+Al+a e+ i+  PdS
  gi|330506551|ref|YP_004382979.1| 134 SALYFQGEYDEALTAIEEAIRLEPDS 159
                                       5666688******************9 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.022
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       a  ++++gd+++A++a +++i+
  gi|330506551|ref|YP_004382979.1| 167 ADILYEQGDYQEAITAVDEVIR 188
                                       77889999*******9888776 PP

  == domain 6  score: 6.5 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                       ++++++ +l ++d++leal+r i+
  gi|330506551|ref|YP_004382979.1| 199 NRGELLWRLERYDESLEALDRAIQ 222
                                       6799999978***********998 PP

  == domain 7  score: 12.4 bits;  conditional E-value: 0.00054
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerli 27 
                                       dA y+++++++++g+ ++A  a+ r  
  gi|330506551|ref|YP_004382979.1| 229 DAWYNRGEALKAQGRDEEADVAYTRAK 255
                                       89*********************9975 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0     0.004       1.5      14      34 ..      37      57 ..      35      61 .. 0.93
   2 ?    6.3   0.0     0.027       9.9      11      35 ..      68      92 ..      65      96 .. 0.86
   3 !   10.6   0.0    0.0013      0.46      14      41 ..     105     132 ..     100     135 .. 0.92
   4 !   11.0   0.0   0.00092      0.34      12      42 ..     137     167 ..     133     169 .. 0.86
   5 ?    2.7   0.0      0.35   1.3e+02      12      33 ..     171     192 ..     170     196 .. 0.88
   6 ?    4.4   0.0      0.11        40      13      31 ..     206     224 ..     204     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.004
                                      HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPen 34
                                      +g+Y+eA +  d  L+++Pen
  gi|330506551|ref|YP_004382979.1| 37 QGDYEEAIEAYDEALRLDPEN 57
                                      69******************9 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.027
                                      HHHHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C 11 hyklgeYseArryvdalLeiEPenr 35
                                       + +++Y+eA +  d +++i+Pe  
  gi|330506551|ref|YP_004382979.1| 68 LINQRRYEEAIQAFDEVIRIDPELA 92
                                      56789*****************965 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0013
                                       HT-HHHHHHHHHHHHHHTTS-HHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaqsLk 41 
                                       lgeY+eA   +d+ + +EPen    sLk
  gi|330506551|ref|YP_004382979.1| 105 LGEYDEAIVALDQAIGLEPENGSIWSLK 132
                                       8********************9999887 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00092
                                       HHHT-HHHHHHHHHHHHHHTTS-HHHHHHHH CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQaqsLke 42 
                                       y +geY+eA+  ++  +++EP+   a sLk+
  gi|330506551|ref|YP_004382979.1| 137 YFQGEYDEALTAIEEAIRLEPDSTIAWSLKA 167
                                       6689******************988888875 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.35
                                       HHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPe 33 
                                       y +g+Y+eA   vd ++++ P+
  gi|330506551|ref|YP_004382979.1| 171 YEQGDYQEAITAVDEVIRLMPD 192
                                       678***********99999887 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.11
                                       HHT-HHHHHHHHHHHHHHT CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiE 31 
                                       +l +Y+e+++ +d+ ++++
  gi|330506551|ref|YP_004382979.1| 206 RLERYDESLEALDRAIQLD 224
                                       89************99987 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.4   0.00057      0.21       9      30 ..      31      52 ..      28      53 .. 0.91
   2 !   11.0   0.1   0.00084      0.31       7      31 ..      63      87 ..      62      87 .. 0.92
   3 !    8.4   0.1    0.0055         2       9      29 ..      99     119 ..      91     121 .. 0.90
   4 !   12.6   0.2   0.00026     0.095       9      30 ..     133     154 ..     133     156 .. 0.92
   5 !    7.8   0.1    0.0081         3      11      30 ..     169     188 ..     167     190 .. 0.86
   6 !    9.3   0.2    0.0028         1       7      30 ..     199     222 ..     197     223 .. 0.93
   7 ?    4.8   0.4     0.073        27       7      25 ..     233     251 ..     227     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00057
                            TPR_10  9 analrqrgrydeAealleeala 30
                                      +n l+++g+y+eA + ++eal+
  gi|330506551|ref|YP_004382979.1| 31 GNELFSQGDYEEAIEAYDEALR 52
                                      77899***************97 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00084
                            TPR_10  7 NLanalrqrgrydeAealleealai 31
                                      N + al +++ry+eA + ++e+++i
  gi|330506551|ref|YP_004382979.1| 63 NKGTALINQRRYEEAIQAFDEVIRI 87
                                      7799******************986 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0055
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       + al+++g+ydeA   l++a+
  gi|330506551|ref|YP_004382979.1|  99 GGALHELGEYDEAIVALDQAI 119
                                       789*************99998 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00026
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       + al+ +g+ydeA+   eea++
  gi|330506551|ref|YP_004382979.1| 133 GSALYFQGEYDEALTAIEEAIR 154
                                       679*****************97 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0081
                            TPR_10  11 alrqrgrydeAealleeala 30 
                                       +l+++g+y+eA    +e+++
  gi|330506551|ref|YP_004382979.1| 169 ILYEQGDYQEAITAVDEVIR 188
                                       79*********999888886 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.0028
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N + +l+++ ryde+++ l++a++
  gi|330506551|ref|YP_004382979.1| 199 NRGELLWRLERYDESLEALDRAIQ 222
                                       88999*****************98 PP

  == domain 7  score: 4.8 bits;  conditional E-value: 0.073
                            TPR_10   7 NLanalrqrgrydeAeall 25 
                                       N + al ++gr +eA   +
  gi|330506551|ref|YP_004382979.1| 233 NRGEALKAQGRDEEADVAY 251
                                       7899***********7665 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   6.1e-05     0.022      10      36 .]      33      57 ..      31      57 .. 0.88
   2 ?    3.5   0.0       0.2        73      13      25 ..      70      82 ..      67      84 .. 0.88
   3 !    8.8   0.0    0.0043       1.6      10      36 .]     101     125 ..      96     125 .. 0.89
   4 ?    5.7   0.0      0.04        15       7      22 ..     131     147 ..     127     148 .. 0.82
   5 !    9.3   0.1     0.003       1.1      11      23 ..     170     182 ..     164     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.1e-05
                                      HHHHTT-HHHHHHH..HHHHHHH-TT- CS
                             TPR_3 10 efynkkkyqeArelfsYallaildken 36
                                      e++++++y+eA+e+++   +  ld+en
  gi|330506551|ref|YP_004382979.1| 33 ELFSQGDYEEAIEAYD--EALRLDPEN 57
                                      689***********77..999998887 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.2
                                      HTT-HHHHHHH.. CS
                             TPR_3 13 nkkkyqeArelfs 25
                                      n+ +y+eA+++f+
  gi|330506551|ref|YP_004382979.1| 70 NQRRYEEAIQAFD 82
                                      5669*******98 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0043
                                       HHHHTT-HHHHHHH..HHHHHHH-TT- CS
                             TPR_3  10 efynkkkyqeArelfsYallaildken 36 
                                       +++  ++y+eA+ +++  ++  l++en
  gi|330506551|ref|YP_004382979.1| 101 ALHELGEYDEAIVALD--QAIGLEPEN 125
                                       6899***********9..999998887 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.04
                                       H.HHHHHHTT-HHHHHH CS
                             TPR_3   7 y.AaefynkkkyqeAre 22 
                                       + + ++y +++y+eA+ 
  gi|330506551|ref|YP_004382979.1| 131 LkGSALYFQGEYDEALT 147
                                       557899*********87 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.003
                                       HHHTT-HHHHHHH CS
                             TPR_3  11 fynkkkyqeArel 23 
                                       +y +++yqeA+ +
  gi|330506551|ref|YP_004382979.1| 170 LYEQGDYQEAITA 182
                                       8*********976 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.4   5.2e+02     239     256 ..      37      54 ..      24      66 .. 0.64
   2 ?    1.2   0.0      0.36   1.3e+02     206     251 ..      38      83 ..      33      88 .. 0.68
   3 !    8.8   0.0    0.0018      0.68     206     254 ..      72     120 ..      63     125 .. 0.92
   4 !   21.2   0.0   3.1e-07   0.00012     205     252 ..     139     186 ..     119     191 .. 0.87
   5 !    8.1   0.0     0.003       1.1     205     255 ..     207     257 ..     202     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                                       TT-HHHHHHHHHHHHHCT CS
                             NARP1 239 aGdlkkAaevmeearklD 256
                                       +Gd ++A+e+ +ea +lD
  gi|330506551|ref|YP_004382979.1|  37 QGDYEEAIEAYDEALRLD 54 
                                       455555555555555555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.36
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmee 251
                                       g++e+A+e  d+a++ +p+    + +K++ l  +   ++A+++ +e
  gi|330506551|ref|YP_004382979.1|  38 GDYEEAIEAYDEALRLDPENPVAWSNKGTALINQRRYEEAIQAFDE 83 
                                       5677777777777777777777777777766666666666666665 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0018
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeeark 254
                                       +++e+A++  d+ i+ +p+l   +  K+  l   G+ ++A+ ++++a  
  gi|330506551|ref|YP_004382979.1|  72 RRYEEAIQAFDEVIRIDPELASAWSYKGGALHELGEYDEAIVALDQAIG 120
                                       6799****************************************99965 PP

  == domain 4  score: 21.2 bits;  conditional E-value: 3.1e-07
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                        g++++Al+ i++ai+ +p ++  +  Ka il  +Gd ++A+++++e 
  gi|330506551|ref|YP_004382979.1| 139 QGEYDEALTAIEEAIRLEPDSTIAWSLKADILYEQGDYQEAITAVDEV 186
                                       4799***************************************99986 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.003
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                       l++++++le +d+ai+ +  l + ++++++ lk +G  ++A  +  +a++l
  gi|330506551|ref|YP_004382979.1| 207 LERYDESLEALDRAIQLDSDLADAWYNRGEALKAQGRDEEADVAYTRAKEL 257
                                       67899***********************************99999999887 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.52   1.9e+02      11      24 ..      34      47 ..      28      49 .. 0.77
   2 ?   -0.7   0.0         9   3.3e+03       1      24 [.      58      81 ..      58      83 .. 0.77
   3 ?    7.7   0.1     0.018       6.6       8      26 .]      99     117 ..      92     117 .. 0.80
   4 !   10.3   0.0    0.0026      0.94       9      26 .]     134     151 ..     129     151 .. 0.87
   5 ?    6.7   0.0     0.037        14       4      24 ..     163     183 ..     161     185 .. 0.82
   6 !   10.5   0.6    0.0022       0.8       1      26 []     194     219 ..     194     219 .. 0.95
   7 ?    6.2   0.5     0.054        20       3      20 ..     230     247 ..     228     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.52
                             TPR_4 11 llalGdldeArall 24
                                      l+ +Gd++eA ++ 
  gi|330506551|ref|YP_004382979.1| 34 LFSQGDYEEAIEAY 47
                                      6679******7665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 9
                             TPR_4  1 arallaLArallalGdldeArall 24
                                      ++a ++ + al  + +++eA +++
  gi|330506551|ref|YP_004382979.1| 58 PVAWSNKGTALINQRRYEEAIQAF 81
                                      578888899999888999996665 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.018
                             TPR_4   8 ArallalGdldeAraller 26 
                                       + al++lG++deA  +l++
  gi|330506551|ref|YP_004382979.1|  99 GGALHELGEYDEAIVALDQ 117
                                       569**********887775 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.0026
                             TPR_4   9 rallalGdldeAraller 26 
                                        al+ +G++deA+++ e+
  gi|330506551|ref|YP_004382979.1| 134 SALYFQGEYDEALTAIEE 151
                                       599***********9886 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.037
                             TPR_4   4 llaLArallalGdldeArall 24 
                                        ++ A  l+++Gd+ eA +++
  gi|330506551|ref|YP_004382979.1| 163 WSLKADILYEQGDYQEAITAV 183
                                       5677999**********7766 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.0022
                             TPR_4   1 arallaLArallalGdldeAraller 26 
                                       ++a ++++++l++l ++de +++l+r
  gi|330506551|ref|YP_004382979.1| 194 PAAWSNRGELLWRLERYDESLEALDR 219
                                       6899*******************997 PP

  == domain 7  score: 6.2 bits;  conditional E-value: 0.054
                             TPR_4   3 allaLArallalGdldeA 20 
                                       a +++++al a+G+ +eA
  gi|330506551|ref|YP_004382979.1| 230 AWYNRGEALKAQGRDEEA 247
                                       789***********8887 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.2   1.2e-07   4.5e-05      10     122 ..      28     152 ..      22     159 .. 0.78
   2 !   13.4   1.7   0.00022     0.079      51     124 ..     183     256 ..     170     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.2e-07
                                       HHHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTT............STTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BTAD  10 vaagraalaagdpeeaaelleaAlalwrGpaladlea............gewleaererleelrlealealaeaelr 74 
                                        ++g+++ ++gd eea+e++++Al+l  + ++a  ++               + +e+ r++ +  +a      a+ +
  gi|330506551|ref|YP_004382979.1|  28 LERGNELFSQGDYEEAIEAYDEALRLDPENPVAWSNKgtalinqrryeeAIQAFDEVIRIDPELASAWSYKGGALHE 104
                                       57999********************977777777666334444344422222334455555566666666666**** PP

                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       lG+++ea+  l++++ ++P +   + +   Al+ +G+  eAL++ e++
  gi|330506551|ref|YP_004382979.1| 105 LGEYDEAIVALDQAIGLEPENGSIWSLKGSALYFQGEYDEALTAIEEA 152
                                       ******************************************997776 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00022
                                       HHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  51 eaererleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                        +e+ rl  +  +a   + e+++rl+r++e l+ l+++++++    +++    +Al ++Gr +eA  +Y r+++
  gi|330506551|ref|YP_004382979.1| 183 VDEVIRLMPDYPAAWSNRGELLWRLERYDESLEALDRAIQLDSDLADAWYNRGEALKAQGRDEEADVAYTRAKE 256
                                       56666777777788999*****************************************************9986 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0       0.3   1.1e+02      55      71 ..      38      54 ..      32      59 .. 0.83
   2 ?    4.5   0.0       0.1        37      56      70 ..      73      87 ..      63      95 .. 0.88
   3 ?    5.3   0.0     0.056        20      52      79 ..     103     130 ..      99     137 .. 0.85
   4 !    8.5   0.1    0.0054         2      55      70 ..     140     155 ..     133     162 .. 0.87
   5 ?    4.8   0.0     0.081        30      52      70 ..     171     189 ..     160     192 .. 0.83
   6 ?    3.6   0.0      0.19        70      40      70 ..     193     223 ..     190     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.3
                            ANAPC5 55 ghneeAvkaleeairlA 71
                                      g++eeA++a  ea rl 
  gi|330506551|ref|YP_004382979.1| 38 GDYEEAIEAYDEALRLD 54
                                      899**********9985 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.1
                            ANAPC5 56 hneeAvkaleeairl 70
                                       +eeA++a+ e+ir+
  gi|330506551|ref|YP_004382979.1| 73 RYEEAIQAFDEVIRI 87
                                      689**********98 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.056
                            ANAPC5  52 adfghneeAvkaleeairlArenkDksc 79 
                                       +++g+++eA+ al  ai l  en++  +
  gi|330506551|ref|YP_004382979.1| 103 HELGEYDEAIVALDQAIGLEPENGSIWS 130
                                       579**************99888877655 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0054
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                       g+++eA+ a+eeairl
  gi|330506551|ref|YP_004382979.1| 140 GEYDEALTAIEEAIRL 155
                                       99************97 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.081
                            ANAPC5  52 adfghneeAvkaleeairl 70 
                                       ++ g+++eA+ a+ e+irl
  gi|330506551|ref|YP_004382979.1| 171 YEQGDYQEAITAVDEVIRL 189
                                       55699************97 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.19
                            ANAPC5  40 yqyalLnlaslhadfghneeAvkaleeairl 70 
                                       y+ a  n   l  +++ ++e+++al  ai+l
  gi|330506551|ref|YP_004382979.1| 193 YPAAWSNRGELLWRLERYDESLEALDRAIQL 223
                                       6667777778888899999999999999987 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.2    0.0011      0.42     142     233 ..      20     111 ..       9     117 .. 0.75
   2 !    8.5   0.0    0.0028         1     144     180 ..     124     160 ..     100     165 .. 0.79
   3 !   15.6   1.6   1.9e-05    0.0068      15      77 ..     167     227 ..     160     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                            TPR_15 142 aeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwg 218
                                        +++a  +l r++    +g+ ++A+++y eAl+l+p++  + ++   +li+  r++e   +++a+ +  + d++L  
  gi|330506551|ref|YP_004382979.1|  20 CQENAEEWLERGNELFSQGDYEEAIEAYDEALRLDPENPVAWSNKGTALINQRRYEE---AIQAFDEVIRIDPELAS 93 
                                       67778889999999999********************99999998889998888886...77777766655555544 PP

                            TPR_15 219 pl...aaAlllLgrpkkA 233
                                       +    + Al  Lg++++A
  gi|330506551|ref|YP_004382979.1|  94 AWsykGGALHELGEYDEA 111
                                       431115566666666665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0028
                            TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapdss 180
                                       ++  ++++ +++   +g+ d+Al++++eA++l+pds+
  gi|330506551|ref|YP_004382979.1| 124 ENGSIWSLKGSALYFQGEYDEALTAIEEAIRLEPDST 160
                                       455689999999999********************86 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.9e-05
                            TPR_15  15 atllykqgdvkkAlevLkeaaqkaapskdteyWrtladLAwalqqedearkAyrqLlasgkar 77 
                                       a +ly+qgd+++A  + +e   +   ++  + W ++++L w l+++de+ +A+ + ++ +   
  gi|330506551|ref|YP_004382979.1| 167 ADILYEQGDYQEAITAVDEV-IRL-MPDYPAAWSNRGELLWRLERYDESLEALDRAIQLDSDL 227
                                       99***************765.444.4788999*********************9999988764 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0031       1.1     152     177 ..      30      55 ..      21      63 .. 0.88
   2 ?   -0.6   0.0       2.5   9.3e+02     152     173 ..      64      85 ..      58      93 .. 0.78
   3 ?    2.8   0.0      0.22        82     124     174 ..      69     120 ..      66     135 .. 0.76
   4 !   10.0   0.0    0.0014      0.51     124     175 ..     103     155 ..      99     164 .. 0.85
   5 !   13.2   3.5   0.00015     0.054      82     174 ..     166     256 ..     160     261 .] 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0031
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaale 177
                                       rG+ l++qg+ +eA +aY++Al+   
  gi|330506551|ref|YP_004382979.1|  30 RGNELFSQGDYEEAIEAYDEALRLDP 55 
                                       89999****************98665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.5
                            TPR_21 152 rGDilvaqgkldeAraaYqaAl 173
                                       +G +l++q + +eA +a+++ +
  gi|330506551|ref|YP_004382979.1|  64 KGTALINQRRYEEAIQAFDEVI 85 
                                       7888888888888888887755 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.22
                            TPR_21 124 laekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       +++  y+eA+++ +++ + +   a++   +G +l + g+ deA  a ++A+ 
  gi|330506551|ref|YP_004382979.1|  69 INQRRYEEAIQAFDEVIRiDPELASAWSYKGGALHELGEYDEAIVALDQAIG 120
                                       6777888888888776541444567778999999999999999999999986 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0014
                            TPR_21 124 laekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAlaa 175
                                        + ++ydeA+ +L+++   e  ++++  l+G +l+ qg+ deA +a ++A++ 
  gi|330506551|ref|YP_004382979.1| 103 HELGEYDEAIVALDQAIGlEPENGSIWSLKGSALYFQGEYDEALTAIEEAIRL 155
                                       56799********877652667899************************9975 PP

  == domain 5  score: 13.2 bits;  conditional E-value: 0.00015
                            TPR_21  82 lAkaaveagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLeakke.eafaalvaelrGDilv 157
                                       +A+  +e+gd+++A ++ ++v+   +d      a     ++l   + yde l++L+++ + ++  a +   rG++l 
  gi|330506551|ref|YP_004382979.1| 166 KADILYEQGDYQEAITAVDEVIRLMPDYP---AAWSNRGELLWRLERYDESLEALDRAIQlDSDLADAWYNRGEALK 239
                                       67888999999999999999999998873...3444447889999**********8665415666777788****** PP

                            TPR_21 158 aqgkldeAraaYqaAla 174
                                       aqg+ +eA  aY++A +
  gi|330506551|ref|YP_004382979.1| 240 AQGRDEEADVAYTRAKE 256
                                       **************976 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0     0.009       3.3       7      36 ..      23      52 ..      19      54 .. 0.91
   2 ?    2.8   0.0      0.24        89      11      36 ..      61      86 ..      56      88 .. 0.87
   3 ?    1.5   0.0      0.63   2.3e+02       8      35 ..      92     119 ..      89     121 .. 0.86
   4 ?    4.6   0.0     0.072        26      15      36 ..     133     154 ..     126     156 .. 0.87
   5 ?    7.0   0.0     0.013       4.6      15      59 ..     167     210 ..     159     220 .. 0.81
   6 ?    0.8   0.0         1   3.8e+02      15      46 ..     201     232 ..     193     253 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.009
                           DUF5113  7 iandYanlayylnvegeyeeALeyldsale 36
                                       a+++ + +++l+ +g+yeeA+e  d+al+
  gi|330506551|ref|YP_004382979.1| 23 NAEEWLERGNELFSQGDYEEAIEAYDEALR 52
                                      68899999********************97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.24
                           DUF5113 11 YanlayylnvegeyeeALeyldsale 36
                                      + n +++l  +++yeeA++ +d++++
  gi|330506551|ref|YP_004382979.1| 61 WSNKGTALINQRRYEEAIQAFDEVIR 86
                                      67888899999***********9986 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.63
                           DUF5113   8 andYanlayylnvegeyeeALeyldsal 35 
                                       a+++   + +l   gey+eA+  ld+a+
  gi|330506551|ref|YP_004382979.1|  92 ASAWSYKGGALHELGEYDEAIVALDQAI 119
                                       77788888889999************98 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.072
                           DUF5113  15 ayylnvegeyeeALeyldsale 36 
                                       +++l+++gey+eAL+ +++a++
  gi|330506551|ref|YP_004382979.1| 133 GSALYFQGEYDEALTAIEEAIR 154
                                       667899**************96 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.013
                           DUF5113  15 ayylnvegeyeeALeyldsaleylNahyekYakkkadtldklkml 59 
                                       a  l+ +g+y+eA++ +d++++++  +   ++++  + l +l+ +
  gi|330506551|ref|YP_004382979.1| 167 ADILYEQGDYQEAITAVDEVIRLMPDYPAAWSNRG-ELLWRLERY 210
                                       5667899*****************99999998887.566666554 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 1
                           DUF5113  15 ayylnvegeyeeALeyldsaleylNahyekYa 46 
                                       +  l   ++y+e+Le ld a+++     + ++
  gi|330506551|ref|YP_004382979.1| 201 GELLWRLERYDESLEALDRAIQLDSDLADAWY 232
                                       55555667899999999999886555555555 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 !   18.8   0.0   3.4e-06    0.0012       3      98 ..      45     149 ..      41     190 .. 0.65
   2 ?    2.7   0.0      0.33   1.2e+02      25      46 ..     205     226 ..     196     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.4e-06
                      SRP_TPR_like   3 eeyekilrle..gkelkkfkvvaliklekyeeaLkllkkgsalsedvrfEkaY...vlYklkkykkalkilkkv... 71 
                                       e+y++ lrl+  +++    k +ali+  +yeea+++ ++   ++ ++    +Y   +l  l +y +a   l+++   
  gi|330506551|ref|YP_004382979.1|  45 EAYDEALRLDpeNPVAWSNKGTALINQRRYEEAIQAFDEVIRIDPELASAWSYkggALHELGEYDEAIVALDQAigl 121
                                       56777777751144444558888888888888888888887555554444444333777788888887777765222 PP

                      SRP_TPR_like  72 eaee.kvkvlksqvlYrlgsyekAYklL 98 
                                       e e+  +  lk   lY+ g+y++A   +
  gi|330506551|ref|YP_004382979.1| 122 EPENgSIWSLKGSALYFQGEYDEALTAI 149
                                       4444456677777888888888776655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.33
                      SRP_TPR_like  25 iklekyeeaLkllkkgsalsed 46 
                                        +le+y+e+L++l+ + +l++d
  gi|330506551|ref|YP_004382979.1| 205 WRLERYDESLEALDRAIQLDSD 226
                                       5789999999999887755544 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    0.0099       3.6      69     107 ..      24      62 ..      18      68 .. 0.87
   2 ?    6.6   0.0     0.027       9.7      75     123 ..      64     112 ..      60     116 .. 0.90
   3 !    9.2   0.0    0.0045       1.6      78     124 ..     135     181 ..     129     190 .. 0.90
   4 ?    1.2   0.0       1.3   4.8e+02      88     117 ..     213     242 ..     179     251 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0099
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHH CS
                   Alkyl_sulf_dimr  69 aekvlekakealkegdyrwaaellnhlvfadpenaeake 107
                                       ae+ le+ +e +++gdy+ a+e  + ++  dpen  a +
  gi|330506551|ref|YP_004382979.1|  24 AEEWLERGNELFSQGDYEEAIEAYDEALRLDPENPVAWS 62 
                                       6788999**************************976655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.027
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  75 kakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       k ++ +++  y+ a++  + ++  dpe a+a + k  al +lg+  e+ 
  gi|330506551|ref|YP_004382979.1|  64 KGTALINQRRYEEAIQAFDEVIRIDPELASAWSYKGGALHELGEYDEAI 112
                                       567788999**********************************988865 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0045
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                       + + +g+y  a++ ++ ++  +p+ + a +lkad+l + g  +e+ t
  gi|330506551|ref|YP_004382979.1| 135 ALYFQGEYDEALTAIEEAIRLEPDSTIAWSLKADILYEQGDYQEAIT 181
                                       56789*******************************99999988876 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHSTT-HHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  88 aaellnhlvfadpenaeakelkadaleqlg 117
                                       ++e l+ +++ d++ a+a   + +al++ g
  gi|330506551|ref|YP_004382979.1| 213 SLEALDRAIQLDSDLADAWYNRGEALKAQG 242
                                       555555555555555555555555555555 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.21        77      56      56 ..      59      59 ..      31      88 .. 0.47
   2 ?    6.0   0.0     0.032        12      62      82 ..      99     119 ..      91     130 .. 0.72
   3 ?    3.6   0.0      0.18        66      63      83 ..     134     154 ..     127     160 .. 0.85
   4 ?    0.7   0.0       1.4     5e+02      58      83 ..     163     188 ..     156     203 .. 0.79
   5 !   11.7   0.3   0.00055       0.2      63     129 ..     202     257 ..     195     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.21
                                      H CS
                           DUF3856 56 l 56
                                      +
  gi|330506551|ref|YP_004382979.1| 59 V 59
                                      2 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.032
                                       HHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  62 sealaklgrydealesadkal 82 
                                        +al +lg+ydea+ + d+a+
  gi|330506551|ref|YP_004382979.1|  99 GGALHELGEYDEAIVALDQAI 119
                                       567777888888877777775 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.18
                                       HHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  63 ealaklgrydealesadkalr 83 
                                       +al   g+ydeal+++++a+r
  gi|330506551|ref|YP_004382979.1| 134 SALYFQGEYDEALTAIEEAIR 154
                                       6788889**********9987 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  58 haglsealaklgrydealesadkalr 83 
                                       ++  ++ l + g+y+ea++++d+ +r
  gi|330506551|ref|YP_004382979.1| 163 WSLKADILYEQGDYQEAITAVDEVIR 188
                                       55567778888999999999998776 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.00055
                                       HHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  63 ealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                       e l++l ryde+le+ d+a+       +l++d    W    ++r+ al+  Gr +ea  a+  a+e+
  gi|330506551|ref|YP_004382979.1| 202 ELLWRLERYDESLEALDRAI-------QLDSDLADAW----YNRGEALKAQGRDEEADVAYTRAKEL 257
                                       56889999999999999887.......5899988888....89**************9999999885 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00051      0.19      25      78 ..      38      91 ..      26     107 .. 0.81
   2 !   13.4   0.0   0.00012     0.044      25      95 ..     106     176 ..      91     195 .. 0.87
   3 ?    0.7   0.0         1   3.8e+02      26      68 ..     175     217 ..     172     230 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00051
                        HrpB1_HrpK 25 edtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgt 78
                                      +d e+a +  d+  +L Pe++ +    g  li+++r+eeA++++ ev    ++ 
  gi|330506551|ref|YP_004382979.1| 38 GDYEEAIEAYDEALRLDPENPVAWSNKGTALINQRRYEEAIQAFDEVIRIDPEL 91
                                      55566666666677799******************************8666655 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00012
                        HrpB1_HrpK  25 edtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyakaLlAlcLaalrDe 95 
                                       ++ ++a + Ld    L Pe+  +  l g  l  +g+++eAl +++e    ++   +a +L A  L+ ++D 
  gi|330506551|ref|YP_004382979.1| 106 GEYDEAIVALDQAIGLEPENGSIWSLKGSALYFQGEYDEALTAIEEAIRLEPDSTIAWSLKADILYEQGDY 176
                                       566777778899999*****************************************************996 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1
                        HrpB1_HrpK  26 dtedaellLdalrvLrPevaeldllegvlliergrweeAlrlL 68 
                                       d ++a + +d++ +L P  +++    g ll + +r++e l +L
  gi|330506551|ref|YP_004382979.1| 175 DYQEAITAVDEVIRLMPDYPAAWSNRGELLWRLERYDESLEAL 217
                                       3344444455555666666666666666666666666666666 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0       0.1        38      26      52 ..      38      64 ..      29      77 .. 0.88
   2 ?   -0.7   0.0       4.4   1.6e+03      28      53 ..      74      99 ..      69     104 .. 0.83
   3 ?    6.3   0.0     0.029        11      27      53 ..     107     133 ..     103     136 .. 0.90
   4 !    8.6   0.0    0.0057       2.1      27      64 ..     141     183 ..     136     190 .. 0.79
   5 ?   -0.5   0.0       3.8   1.4e+03      26      45 ..     174     193 ..     168     201 .. 0.77
   6 ?    2.4   0.0      0.46   1.7e+02      28      52 ..     210     234 ..     207     252 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.1
                           DUF1510 26 vDwnEmekavskatglsednmivwwlg 52
                                       D++E  +a  +a  l+ +n + w  +
  gi|330506551|ref|YP_004382979.1| 38 GDYEEAIEAYDEALRLDPENPVAWSNK 64
                                      59******************9999754 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4.4
                           DUF1510 28 wnEmekavskatglsednmivwwlgn 53
                                      ++E  +a+ +++ ++ +    w  + 
  gi|330506551|ref|YP_004382979.1| 74 YEEAIQAFDEVIRIDPELASAWSYKG 99
                                      89999*********999888887765 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.029
                           DUF1510  27 DwnEmekavskatglsednmivwwlgn 53 
                                       +++E   a+ +a+gl+ +n  +w l+ 
  gi|330506551|ref|YP_004382979.1| 107 EYDEAIVALDQAIGLEPENGSIWSLKG 133
                                       689999*****************9975 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0057
                           DUF1510  27 DwnEmekavskatglsednmivwwl.....gnggspqkaigtv 64 
                                       +++E + a+++a+ l+ d+ i w l      ++g+ q+ai+ v
  gi|330506551|ref|YP_004382979.1| 141 EYDEALTAIEEAIRLEPDSTIAWSLkadilYEQGDYQEAITAV 183
                                       689********************99333333457777777666 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 3.8
                           DUF1510  26 vDwnEmekavskatglsedn 45 
                                        D++E   av +++ l  d 
  gi|330506551|ref|YP_004382979.1| 174 GDYQEAITAVDEVIRLMPDY 193
                                       59999999999999887765 PP

  == domain 6  score: 2.4 bits;  conditional E-value: 0.46
                           DUF1510  28 wnEmekavskatglsednmivwwlg 52 
                                       ++E ++a+ +a++l++d    w+ +
  gi|330506551|ref|YP_004382979.1| 210 YDESLEALDRAIQLDSDLADAWYNR 234
                                       7899***********9988888754 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.37   1.4e+02      21      44 ..      23      46 ..      18      54 .. 0.80
   2 !   10.9   0.1    0.0012      0.45       6      53 ..      42      89 ..      37      94 .. 0.91
   3 ?    3.8   0.0       0.2        73       7      50 ..     111     154 ..     107     159 .. 0.85
   4 !    8.4   0.1    0.0071       2.6       6      50 ..     144     188 ..     139     200 .. 0.88
   5 ?    4.8   0.6       0.1        37       6      41 ..     212     247 ..     208     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.37
                            TPR_20 21 dldarldlAlallaagryeeAleq 44
                                      + +  l+  + l+++g+yeeA+e+
  gi|330506551|ref|YP_004382979.1| 23 NAEEWLERGNELFSQGDYEEAIEA 46
                                      666678888999**********97 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0012
                            TPR_20  6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdr 53
                                      + +++ ++al  +p++  a  +  +al+ + ryeeA++++ e+++ d 
  gi|330506551|ref|YP_004382979.1| 42 EAIEAYDEALRLDPENPVAWSNKGTALINQRRYEEAIQAFDEVIRIDP 89
                                      56899999*********************************9999886 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.2
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                        + +l++a+  +p++  +      al+ +g+y+eAl+++ e ++
  gi|330506551|ref|YP_004382979.1| 111 AIVALDQAIGLEPENGSIWSLKGSALYFQGEYDEALTAIEEAIR 154
                                       567889999999999999999999************99877765 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0071
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                       + l+++e+a+  +pd   a    A+ l+++g+y+eA+++  e+++
  gi|330506551|ref|YP_004382979.1| 144 EALTAIEEAIRLEPDSTIAWSLKADILYEQGDYQEAITAVDEVIR 188
                                       67899***********9999999**************98777765 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.1
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeA 41 
                                       ++l++l++a++ + d  da ++  +al a+gr eeA
  gi|330506551|ref|YP_004382979.1| 212 ESLEALDRAIQLDSDLADAWYNRGEALKAQGRDEEA 247
                                       6799999******9999*****************99 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0       0.2        74      87     109 ..      31      53 ..      19      61 .. 0.66
   2 ?    3.6   0.0     0.098        36      12      68 ..      35      86 ..      30     120 .. 0.65
   3 !   14.2   0.9   5.6e-05     0.021      42     190 ..     128     257 ..     123     261 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.2
                          TPR_MalT  87 aeilvaqGrLheAletyeqalql 109
                                       ++ l+ qG+ +eA+e y +al+l
  gi|330506551|ref|YP_004382979.1|  31 GNELFSQGDYEEAIEAYDEALRL 53 
                                       44456677777777777777766 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.098
                          TPR_MalT 12 iasgdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaek 68
                                      +++gd e+a+e   +AL l pe+      +a ++ G+a   q + e+A qa+ e+++
  gi|330506551|ref|YP_004382979.1| 35 FSQGDYEEAIEAYDEALRLDPENP-----VAWSNKGTALINQRRYEEAIQAFDEVIR 86
                                      456666667776677776666666.....3444555555556666666666666665 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 5.6e-05
                          TPR_MalT  42 atavlGeasllqGdleaAlqalqeaeklarqadslhva.llallqqaeilvaqGrLheAletyeqalqlateqglqq 117
                                       + ++ G a   qG+ ++Al a +ea++l      ++ + +++l   a+il +qG+ +eA+    + ++l+++   + 
  gi|330506551|ref|YP_004382979.1| 128 IWSLKGSALYFQGEYDEALTAIEEAIRLE-----PDSTiAWSLK--ADILYEQGDYQEAITAVDEVIRLMPDYPAA- 196
                                       55677999999**************9997.....4333178877..**********************88776555. PP

                          TPR_MalT 118 lplvgfllvlladllyEwndLeeAeqhlqeGielleqlepeaaldayvllarialaqGdleeAetllekaeel 190
                                                 +++ll+   + +e  ++l+++i+l  +l  ++  + ++l      aqG+ eeA+ +  +a+el
  gi|330506551|ref|YP_004382979.1| 197 -------WSNRGELLWRLERYDESLEALDRAIQLDSDLADAWYNRGEALK-----AQGRDEEADVAYTRAKEL 257
                                       .......34789*************************9888888899986.....689999999999988887 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.069        25      12      27 ..      36      51 ..      32      54 .. 0.84
   2 ?    4.3   0.0      0.16        57      10      28 ..      68      86 ..      66      88 .. 0.83
   3 ?    0.8   0.0       2.1   7.6e+02      10      25 ..     136     151 ..     134     155 .. 0.75
   4 ?   -0.6   0.0       5.5     2e+03      12      27 ..     172     187 ..     168     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.069
                               PPR 12 knGkleeAlelfkeMk 27
                                      + G++eeA+e ++e +
  gi|330506551|ref|YP_004382979.1| 36 SQGDYEEAIEAYDEAL 51
                                      68**********9965 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.16
                               PPR 10 ycknGkleeAlelfkeMke 28
                                      +   +++eeA++ f+e ++
  gi|330506551|ref|YP_004382979.1| 68 LINQRRYEEAIQAFDEVIR 86
                                      567789*********9876 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 2.1
                               PPR  10 ycknGkleeAlelfke 25 
                                       +   G+++eAl  ++e
  gi|330506551|ref|YP_004382979.1| 136 LYFQGEYDEALTAIEE 151
                                       556799****988777 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 5.5
                               PPR  12 knGkleeAlelfkeMk 27 
                                         G+++eA+   +e +
  gi|330506551|ref|YP_004382979.1| 172 EQGDYQEAITAVDEVI 187
                                       579*****98887765 PP

>> Mo-co_dimer  Mo-co oxidoreductase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.4   5.2e+02     103     124 ..      43      65 ..      36      74 .. 0.82
   2 ?    1.2   0.0      0.91   3.3e+02     103     124 ..      77      99 ..      61     103 .. 0.84
   3 ?    3.9   0.0      0.13        49     103     125 ..     111     134 ..      94     144 .. 0.82
   4 ?    6.0   0.0     0.031        11      85     125 ..     161     202 ..     139     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.4
                                       EEEEEETT--B--S.HHH--TT- CS
                       Mo-co_dimer 103 lvravDealnvqPe.emiwnvlg 124
                                       ++ a Deal + Pe  + w+  g
  gi|330506551|ref|YP_004382979.1|  43 AIEAYDEALRLDPEnPVAWSNKG 65 
                                       5789**********667798766 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.91
                                       EEEEEETT--B--S.HHH--TT- CS
                       Mo-co_dimer 103 lvravDealnvqPe.emiwnvlg 124
                                       +++a+De + + Pe ++ w+  g
  gi|330506551|ref|YP_004382979.1|  77 AIQAFDEVIRIDPElASAWSYKG 99 
                                       689***********999999776 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.13
                                       EEEEEETT--B--S.HHH--TT-- CS
                       Mo-co_dimer 103 lvravDealnvqPe.emiwnvlgm 125
                                       ++ a+D+a+ + Pe  +iw++ g 
  gi|330506551|ref|YP_004382979.1| 111 AIVALDQAIGLEPEnGSIWSLKGS 134
                                       5669**********889****996 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.031
                                       EEEEEEEEESS...E.EEEEEEEETT--B--S.HHH--TT-- CS
                       Mo-co_dimer  85 vfweldvevselakekeilvravDealnvqPe.emiwnvlgm 125
                                         w+l++++   + + + ++ avDe + ++P+  + w+ +g 
  gi|330506551|ref|YP_004382979.1| 161 IAWSLKADILYEQGDYQEAITAVDEVIRLMPDyPAAWSNRGE 202
                                       569999999988889999999***********8899998885 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       4.3   1.6e+03       2      13 ..      40      51 ..      39      54 .. 0.77
   2 ?   -0.7   0.0       2.9   1.1e+03       1      15 [.      73      87 ..      73      93 .. 0.81
   3 ?    6.0   0.1     0.025         9       2      46 ..     108     153 ..     107     155 .. 0.68
   4 ?    6.4   0.1     0.019       6.8       1      15 [.     209     223 ..     209     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.3
                                      HHHHHHHHHHHH CS
                          HTH_Bact  2 YeeaLeqvnkAi 13
                                      Yeea+e  + A+
  gi|330506551|ref|YP_004382979.1| 40 YEEAIEAYDEAL 51
                                      899998888776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.9
                                      -HHHHHHHHHHHHHH CS
                          HTH_Bact  1 rYeeaLeqvnkAiei 15
                                      rYeea++  +  i i
  gi|330506551|ref|YP_004382979.1| 73 RYEEAIQAFDEVIRI 87
                                      7*****998887766 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHHHHHHTTB-.TTHHHHHHHHHHHHHHTT--HHHH CS
                          HTH_Bact   2 YeeaLeqvnkAieiSirinsM.sLlGQLyYqkgecleklgfseeeI 46 
                                       Y+ea+   ++Ai +  ++ s  sL G   Y +ge  e l   ee I
  gi|330506551|ref|YP_004382979.1| 108 YDEAIVALDQAIGLEPENGSIwSLKGSALYFQGEYDEALTAIEEAI 153
                                       8888888888888777777764566777777777777666666555 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.019
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rY+e+Le  ++Ai++
  gi|330506551|ref|YP_004382979.1| 209 RYDESLEALDRAIQL 223
                                       7************86 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       3.7   1.4e+03      50      63 ..      21      34 ..      18      36 .. 0.83
   2 !   11.2   0.9   0.00082       0.3      17      32 ..      37      52 ..      24      53 .. 0.91
   3 ?    2.0   0.0      0.62   2.3e+02      26      38 ..      73      85 ..      63      94 .. 0.71
   4 ?    0.2   0.0       2.2   8.2e+02      18      32 ..     106     120 ..     102     126 .. 0.64
   5 ?    0.6   0.1       1.7   6.2e+02      18      32 ..     140     154 ..     139     169 .. 0.70
   6 ?   -0.1   0.0       2.7     1e+03      16      25 ..     172     181 ..     166     185 .. 0.84
   7 ?    3.5   0.1       0.2        73      24      42 ..     207     226 ..     207     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.7
                               MIT 50 rekieeYleRaeeL 63
                                      +e++ee+leR +eL
  gi|330506551|ref|YP_004382979.1| 21 QENAEEWLERGNEL 34
                                      68999*****8887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00082
                               MIT 17 agnyeeAlelYkeale 32
                                      +g+yeeA+e+Y eal+
  gi|330506551|ref|YP_004382979.1| 37 QGDYEEAIEAYDEALR 52
                                      79************97 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.62
                               MIT 26 lYkealelLlqal 38
                                       Y+ea++ + +++
  gi|330506551|ref|YP_004382979.1| 73 RYEEAIQAFDEVI 85
                                      4666666666655 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 2.2
                               MIT  18 gnyeeAlelYkeale 32 
                                       g+y+eA+ +  +a++
  gi|330506551|ref|YP_004382979.1| 106 GEYDEAIVALDQAIG 120
                                       566666655555554 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 1.7
                               MIT  18 gnyeeAlelYkeale 32 
                                       g+y+eAl + +ea++
  gi|330506551|ref|YP_004382979.1| 140 GEYDEALTAIEEAIR 154
                                       566666666555554 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 2.7
                               MIT  16 nagnyeeAle 25 
                                       ++g+y+eA+ 
  gi|330506551|ref|YP_004382979.1| 172 EQGDYQEAIT 181
                                       5699***985 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.2
                               MIT  24 lelYkealelLlqalk.ekn 42 
                                       le Y e+le L  a++  ++
  gi|330506551|ref|YP_004382979.1| 207 LERYDESLEALDRAIQlDSD 226
                                       68899999999999994333 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 ?    4.2   0.0      0.13        49      14      34 ..      30      50 ..      21      57 .. 0.84
   2 ?   -0.0   0.0       2.9   1.1e+03      13      30 ..      63      80 ..      59      86 .. 0.79
   3 ?   -0.2   0.0       3.2   1.2e+03       7      31 ..      91     115 ..      88     121 .. 0.76
   4 ?    2.9   0.0      0.34   1.3e+02      12      30 ..     164     182 ..     158     192 .. 0.87
   5 ?   -0.2   0.0       3.4   1.2e+03       7      35 ..     227     255 ..     223     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.13
                         NRBF2_MIT 14 kadrllaaGkyeeaischkka 34
                                      + + l++ G yeeai  +  a
  gi|330506551|ref|YP_004382979.1| 30 RGNELFSQGDYEEAIEAYDEA 50
                                      678899*********987766 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2.9
                         NRBF2_MIT 13 rkadrllaaGkyeeaisc 30
                                       k   l+   +yeeai  
  gi|330506551|ref|YP_004382979.1| 63 NKGTALINQRRYEEAIQA 80
                                      56667888899****976 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 3.2
                         NRBF2_MIT   7 lahqqsrkadrllaaGkyeeaisch 31 
                                       la   s k   l   G y+eai   
  gi|330506551|ref|YP_004382979.1|  91 LASAWSYKGGALHELGEYDEAIVAL 115
                                       566667777788889******9765 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.34
                         NRBF2_MIT  12 srkadrllaaGkyeeaisc 30 
                                       s kad l   G y+eai+ 
  gi|330506551|ref|YP_004382979.1| 164 SLKADILYEQGDYQEAITA 182
                                       679**************86 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 3.4
                         NRBF2_MIT   7 lahqqsrkadrllaaGkyeeaischkkaa 35 
                                       la     + + l a G+ eea   +++a 
  gi|330506551|ref|YP_004382979.1| 227 LADAWYNRGEALKAQGRDEEADVAYTRAK 255
                                       5566667889999*******988888876 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       0.3   1.1e+02     251     291 ..      24      63 ..      15      73 .. 0.79
   2 ?    4.3   0.0     0.051        19     265     291 ..      71      97 ..      61     114 .. 0.82
   3 ?    5.2   0.1     0.028        10     251     303 ..     200     245 ..     139     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.3
                                       CCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 251 kGewqealqkldwseekieeilqsysaateidpswykawht 291
                                         ew+e+ ++l  s+ + ee+ ++y +a ++dp+   aw +
  gi|330506551|ref|YP_004382979.1|  24 AEEWLERGNEL-FSQGDYEEAIEAYDEALRLDPENPVAWSN 63 
                                       55788888885.4666799*******************986 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.051
                                       ...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 265 eekieeilqsysaateidpswykawht 291
                                       +++ ee+ q++ +  +idp+++ aw +
  gi|330506551|ref|YP_004382979.1|  71 QRRYEEAIQAFDEVIRIDPELASAWSY 97 
                                       56689********************97 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.028
                                       CCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHH CS
                               FAT 251 kGewqealqkldwseekieeilqsysaateidpswykawhtwalfnfevvske 303
                                       +Ge +++l++        +e l++  +a ++d ++++aw++ + +   + ++e
  gi|330506551|ref|YP_004382979.1| 200 RGELLWRLER-------YDESLEALDRAIQLDSDLADAWYNRGEALKAQGRDE 245
                                       4555555555.......99********************99777776666655 PP

>> DUF1347  Protein of unknown function (DUF1347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00061      0.22     446     520 ..       9      84 ..       3      98 .. 0.83
   2 ?    1.8   0.1      0.19        68     461     515 ..     161     215 ..     134     234 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00061
                           DUF1347 446 lvevGlnkilvseeeianfladaeylyakGdyklsi.lyslwlakiapstealrllalslveqkeyaealevfsll 520
                                       +  + +    +++e+  + l   + l+++Gdy  +i  y   l      + a+   + +l++q+ y ea++ f+ +
  gi|330506551|ref|YP_004382979.1|   9 ILIIAIAAPSTCQENAEEWLERGNELFSQGDYEEAIeAYDEALRLDPENPVAWSNKGTALINQRRYEEAIQAFDEV 84 
                                       55566677778999999999999**********9994577777555557899*******************99865 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.19
                           DUF1347 461 ianfladaeylyakGdyklsilyslwlakiaps.tealrllalslveqkeyaeale 515
                                       ia  l  a+ ly +Gdy+ +i     + ++ p  + a+   +  l     y e+le
  gi|330506551|ref|YP_004382979.1| 161 IAWSL-KADILYEQGDYQEAITAVDEVIRLMPDyPAAWSNRGELLWRLERYDESLE 215
                                       44333.46778888888777776666666666424445555555555555555555 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00038      0.14      27      56 ..      17      46 ..      12      48 .. 0.88
   2 ?    0.3   0.2       2.1   7.6e+02      31      54 ..     225     248 ..     207     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00038
                                      HHHHHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                            DUF357 27 aeevlemaesYleDakyflekgdlvnAlas 56
                                       + + e+ae +le +++ +++gd+++A+ +
  gi|330506551|ref|YP_004382979.1| 17 PSTCQENAEEWLERGNELFSQGDYEEAIEA 46
                                      56789**********************876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHHHTT-HHHHH CS
                            DUF357  31 lemaesYleDakyflekgdlvnAl 54 
                                        ++a ++++ ++   ++g  ++A 
  gi|330506551|ref|YP_004382979.1| 225 SDLADAWYNRGEALKAQGRDEEAD 248
                                       578999999999999999998885 PP

>> Clathrin_H_link  Clathrin-H-link
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.013       4.7      14      27 ..      32      45 ..      24      52 .. 0.89
   2 ?    0.5   0.0       1.6     6e+02      15      27 ..      67      79 ..      64      83 .. 0.87
   3 ?    2.5   0.0      0.37   1.4e+02      16      28 ..     170     182 ..     168     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.013
                   Clathrin_H_link 14 eqllaqgnykeAak 27
                                      ++l++qg+y+eA++
  gi|330506551|ref|YP_004382979.1| 32 NELFSQGDYEEAIE 45
                                      89**********97 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.6
                   Clathrin_H_link 15 qllaqgnykeAak 27
                                       l++q++y+eA++
  gi|330506551|ref|YP_004382979.1| 67 ALINQRRYEEAIQ 79
                                      5899*******97 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.37
                   Clathrin_H_link  16 llaqgnykeAakv 28 
                                       l++qg+y+eA++ 
  gi|330506551|ref|YP_004382979.1| 170 LYEQGDYQEAITA 182
                                       789*******976 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.027        10      77     106 ..      26      55 ..      13      59 .. 0.83
   2 ?   -0.7   0.0         4   1.5e+03      81     104 ..      64      87 ..      62      91 .. 0.84
   3 ?   -1.7   0.0       8.1     3e+03      85     110 ..     102     127 ..      98     132 .. 0.77
   4 ?    0.2   0.0       2.1   7.7e+02      82     106 ..     133     157 ..     130     160 .. 0.86
   5 ?   -0.0   0.0       2.4   8.7e+02      81     104 ..     200     223 ..     198     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.027
                             MAS20  77 eevqlGEellaqgeeeeaaehlynAlkvcp 106
                                       e +++G+el++qg++eea+e+   Al++ p
  gi|330506551|ref|YP_004382979.1|  26 EWLERGNELFSQGDYEEAIEAYDEALRLDP 55 
                                       56789****************999998765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4
                             MAS20  81 lGEellaqgeeeeaaehlynAlkv 104
                                       +G  l++q+++eea++++   +++
  gi|330506551|ref|YP_004382979.1|  64 KGTALINQRRYEEAIQAFDEVIRI 87 
                                       7889999********999877765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 8.1
                             MAS20  85 llaqgeeeeaaehlynAlkvcpqPqe 110
                                       l + ge++ea+ +l +A+ + p+ ++
  gi|330506551|ref|YP_004382979.1| 102 LHELGEYDEAIVALDQAIGLEPENGS 127
                                       555599*********99988887765 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 2.1
                             MAS20  82 GEellaqgeeeeaaehlynAlkvcp 106
                                       G  l  qge++ea++++  A+++ p
  gi|330506551|ref|YP_004382979.1| 133 GSALYFQGEYDEALTAIEEAIRLEP 157
                                       7788999*************99866 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 2.4
                             MAS20  81 lGEellaqgeeeeaaehlynAlkv 104
                                       +GE l + ++++e++e+l +A+++
  gi|330506551|ref|YP_004382979.1| 200 RGELLWRLERYDESLEALDRAIQL 223
                                       79999999*************975 PP

>> YfiO  Outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.14        51       9      41 ..      28      60 ..      21      97 .. 0.57
   2 ?    7.4   0.1    0.0089       3.3      18      75 ..     139     193 ..     132     197 .. 0.78
   3 ?   -1.5   0.1       4.6   1.7e+03      46      76 ..     225     255 ..     208     260 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.14
                                      HHHHHHHHHHT-HHHHHHHHHHHHHHSTTSTTH CS
                              YfiO  9 YekgqealqkgdyaeAikklealdsryPfspya 41
                                       e g e  ++gdy+eAi++ +++    P  p a
  gi|330506551|ref|YP_004382979.1| 28 LERGNELFSQGDYEEAIEAYDEALRLDPENPVA 60
                                      555666666666666666666665555555544 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0089
                                       HT-HHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-SSS CS
                              YfiO  18 kgdyaeAikklealdsryPfspyaeqaqldliyAyykdadyaealasaerFlrlyPth 75 
                                       +g+y eA +++e++    P s  a + + d+    y+++dy+ea+ ++++ +rl P  
  gi|330506551|ref|YP_004382979.1| 139 QGEYDEALTAIEEAIRLEPDSTIAWSLKADIL---YEQGDYQEAITAVDEVIRLMPDY 193
                                       67888888888888888888887777777665...79999999999999999999875 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.6
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH-SSST CS
                              YfiO  46 ldliyAyykdadyaealasaerFlrlyPthk 76 
                                        dl++A y++++  +a+   e+    y+++k
  gi|330506551|ref|YP_004382979.1| 225 SDLADAWYNRGEALKAQGRDEEADVAYTRAK 255
                                       5778888888888777766655555555555 PP

>> TPR_18  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.51   1.9e+02      58     107 ..      35      83 ..      32      96 .. 0.70
   2 ?    6.1   0.0      0.03        11      26      81 ..     142     194 ..     139     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.51
                            TPR_18  58 ykskdyelavasidrfirlnPahpkiDyvlYlrglanmaldksslqslvs 107
                                       + + dye a  + d  +rl P++p + +     +l+n+   ++++q + +
  gi|330506551|ref|YP_004382979.1|  35 FSQGDYEEAIEAYDEALRLDPENP-VAWSNKGTALINQRRYEEAIQAFDE 83 
                                       677899999999999999999988.4566666666666666666555555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.03
                            TPR_18  26 yltaieqLealdtryPfGaYaeqaqLDLiYakykskdyelavasidrfirlnPahp 81 
                                       y +a + +e+     P  + a   + D++   y++ dy+ a +++d  irl P  p
  gi|330506551|ref|YP_004382979.1| 142 YDEALTAIEEAIRLEPDSTIAWSLKADIL---YEQGDYQEAITAVDEVIRLMPDYP 194
                                       55555555555555555555556666666...57899***************9987 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.33   1.2e+02       3      31 ..      32      60 ..      30      76 .. 0.80
   2 ?    6.4   0.0     0.024       8.9       4      47 ..     135     175 ..     132     183 .. 0.81
   3 ?    1.2   0.0      0.99   3.6e+02       2      23 ..     167     188 ..     166     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.33
                            DUF627  3 kdllargnhikALeiiedlisrhgedeks 31
                                      ++l+ +g++ +A+e  +++++   e+ ++
  gi|330506551|ref|YP_004382979.1| 32 NELFSQGDYEEAIEAYDEALRLDPENPVA 60
                                      578999******99999998777665554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                            DUF627   4 dllargnhikALeiiedlisrhgedeksallhrlqGtifvklak 47 
                                       +l+ +g++ +AL  ie++i+ + +   s +   l+++i++++ +
  gi|330506551|ref|YP_004382979.1| 135 ALYFQGEYDEALTAIEEAIRLEPD---STIAWSLKADILYEQGD 175
                                       57889**************99999...56666667788888765 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.99
                            DUF627   2 AkdllargnhikALeiiedlis 23 
                                       A  l+++g++ +A+  ++++i+
  gi|330506551|ref|YP_004382979.1| 167 ADILYEQGDYQEAITAVDEVIR 188
                                       667899*********9999986 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.29   1.1e+02     122     180 ..      36      95 ..      26     102 .. 0.78
   2 ?    3.2   0.0       0.2        74     133     180 ..     115     163 ..     104     169 .. 0.76
   3 ?    6.7   0.1     0.016         6     127     181 ..     143     198 ..     139     205 .. 0.83
   4 ?    0.6   0.1       1.3   4.8e+02     151     170 ..     236     255 ..     227     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.29
                           Wzy_C_2 122 spenlaaklalarklihlsPepavi.erlilslallGdedeAeqilararalfpeedakw 180
                                       s+ ++++ ++++ ++++l Pe  v  ++   +l  + + +eA q  ++++ + pe + +w
  gi|330506551|ref|YP_004382979.1|  36 SQGDYEEAIEAYDEALRLDPENPVAwSNKGTALINQRRYEEAIQAFDEVIRIDPELASAW 95 
                                       567788889999999999998777426777888888888999998888888777777776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.2
                           Wzy_C_2 133 arklihlsPepavierli.lslallGdedeAeqilararalfpeedakw 180
                                         ++i l Pe   i  l   +l ++G  deA++ +++a+ l p++  +w
  gi|330506551|ref|YP_004382979.1| 115 LDQAIGLEPENGSIWSLKgSALYFQGEYDEALTAIEEAIRLEPDSTIAW 163
                                       566777777777776665256789**************99988888877 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.016
                           Wzy_C_2 127 aaklalarklihlsPepavierl.ilslallGdedeAeqilararalfpeedakwv 181
                                       ++ l + +++i+l P  ++   l ++ l  +Gd +eA + +++++ l p++ a+w+
  gi|330506551|ref|YP_004382979.1| 143 DEALTAIEEAIRLEPDSTIAWSLkADILYEQGDYQEAITAVDEVIRLMPDYPAAWS 198
                                       667777788888888888765543888999*************************5 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.3
                           Wzy_C_2 151 lslallGdedeAeqilarar 170
                                       ++l ++G+++eA+  + ra+
  gi|330506551|ref|YP_004382979.1| 236 EALKAQGRDEEADVAYTRAK 255
                                       68999********9999997 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.22        81      13      28 ..      34      49 ..      32      53 .. 0.87
   2 ?    3.7   0.0       0.2        74      12      28 ..      67      83 ..      66      86 .. 0.89
   3 ?   -1.3   0.0         7   2.6e+03      12      24 ..     169     181 ..     168     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.22
                             PPR_2 13 lckkgkveeAfklfne 28
                                      l+ +g++eeA++ ++e
  gi|330506551|ref|YP_004382979.1| 34 LFSQGDYEEAIEAYDE 49
                                      7889*********998 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.2
                             PPR_2 12 glckkgkveeAfklfne 28
                                      +l +++++eeA++ f+e
  gi|330506551|ref|YP_004382979.1| 67 ALINQRRYEEAIQAFDE 83
                                      68899**********98 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 7
                             PPR_2  12 glckkgkveeAfk 24 
                                        l+++g+++eA+ 
  gi|330506551|ref|YP_004382979.1| 169 ILYEQGDYQEAIT 181
                                       6889*******85 PP

>> DUF4398  Domain of unknown function (DUF4398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   0.00052      0.19      27      58 ..      22      54 ..      14      81 .. 0.74
   2 ?   -1.0   0.1       7.6   2.8e+03      38      62 ..      67      92 ..      63      95 .. 0.69
   3 ?    0.3   0.1         3   1.1e+03      42      58 ..     139     158 ..     132     188 .. 0.61
   4 ?    0.8   4.1       2.2   7.9e+02      29      56 ..     228     255 ..     192     257 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00052
                           DUF4398 27 eeAreaLaqAeaamaekdyeeAdhlaylAer.d 58
                                      e A+e L++++++ +++dyeeA +++ +A r d
  gi|330506551|ref|YP_004382979.1| 22 ENAEEWLERGNELFSQGDYEEAIEAYDEALRlD 54
                                      67***************************9952 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 7.6
                           DUF4398 38 aamaekdyeeAdhlaylAer.daelA 62
                                      a+ ++ +yeeA ++  +  r d elA
  gi|330506551|ref|YP_004382979.1| 67 ALINQRRYEEAIQAFDEVIRiDPELA 92
                                      66778888888888887777666666 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 3
                           DUF4398  42 ekdyeeAdhlaylAer...d 58 
                                       +++y+eA  + ++A r   d
  gi|330506551|ref|YP_004382979.1| 139 QGEYDEALTAIEEAIRlepD 158
                                       55666666666666664442 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 2.2
                           DUF4398  29 AreaLaqAeaamaekdyeeAdhlaylAe 56 
                                       A    +++ea++a++++eeAd ++ +A+
  gi|330506551|ref|YP_004382979.1| 228 ADAWYNRGEALKAQGRDEEADVAYTRAK 255
                                       5555667777777888888877777776 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.051        19      34      63 ..      22      51 ..      17      54 .. 0.85
   2 ?    2.2   0.0      0.36   1.3e+02     119     138 ..      64      83 ..      61      98 .. 0.85
   3 ?    1.6   0.0      0.55     2e+02      39      62 ..     163     186 ..     139     190 .. 0.82
   4 ?   -1.6   0.2         5   1.8e+03      19      60 ..     217     252 ..     206     257 .. 0.52

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.051
                                      HHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7 34 eirrakldlaehYlkigdleeAlkaysrir 63
                                      e ++ +l++++  ++ gd+eeA++ay +++
  gi|330506551|ref|YP_004382979.1| 22 ENAEEWLERGNELFSQGDYEEAIEAYDEAL 51
                                      556778889999999***********9976 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.36
                                       HHHHHHHTT-HHHHHHHHCT CS
                              RPN7 119 eGlallairkfkeAaellld 138
                                       +G+al+ +r+++eA + + +
  gi|330506551|ref|YP_004382979.1|  64 KGTALINQRRYEEAIQAFDE 83 
                                       79************998855 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.55
                                       HHHHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7  39 kldlaehYlkigdleeAlkaysri 62 
                                       +  +a+  ++ gd++eA+ a+ ++
  gi|330506551|ref|YP_004382979.1| 163 WSLKADILYEQGDYQEAITAVDEV 186
                                       55689999999*******999885 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 5
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHH CS
                              RPN7  19 LdaelkdakenlgkeeirrakldlaehYlkigdleeAlkays 60 
                                       Ld+ ++       +++ ++a+++++e     g  eeA  ay 
  gi|330506551|ref|YP_004382979.1| 217 LDRAIQ------LDSDLADAWYNRGEALKAQGRDEEADVAYT 252
                                       444444......355555555555555555555555555555 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.035        13     516     542 ..      25      51 ..      20      55 .. 0.82
   2 ?    2.3   0.1     0.099        36     524     549 ..     135     159 ..     130     162 .. 0.84
   3 ?    0.4   0.0      0.38   1.4e+02     521     541 ..     166     186 ..     160     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.035
                                       HHHHHHHHTSS-SSTTTTHHHHTTSSS CS
                              EzrA 516 aealteAeklFrkgeYkkaleiaatal 542
                                       +e l++  +lF++g+Y++a+e   +al
  gi|330506551|ref|YP_004382979.1|  25 EEWLERGNELFSQGDYEEAIEAYDEAL 51 
                                       5668888999*********99887776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.099
                                       TSS-SSTTTTHHHHTTSSS-TTHHHH CS
                              EzrA 524 klFrkgeYkkaleiaatalekvepGa 549
                                        l+ +geY++al  + +a+ ++ep++
  gi|330506551|ref|YP_004382979.1| 135 ALYFQGEYDEALTAIEEAI-RLEPDS 159
                                       6999**************9.567765 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.38
                                       HHHTSS-SSTTTTHHHHTTSS CS
                              EzrA 521 eAeklFrkgeYkkaleiaata 541
                                       +A  l+++g+Y++a+  + ++
  gi|330506551|ref|YP_004382979.1| 166 KADILYEQGDYQEAITAVDEV 186
                                       788999999999998776655 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0061       2.2       6      34 ..      22      50 ..      18      53 .. 0.87
   2 ?   -0.4   0.0       3.2   1.2e+03      19      35 ..     103     119 ..     101     121 .. 0.87
   3 ?    2.7   0.1      0.35   1.3e+02      95     114 ..     167     189 ..     137     193 .. 0.67
   4 ?   -1.1   0.1       5.2   1.9e+03      58      92 ..     202     235 ..     194     257 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0061
                                      HHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              HEPN  6 rrAeedleaAellleegdydlacfhaqqa 34
                                      ++Aee le  ++l+++gdy+ a+ ++ +a
  gi|330506551|ref|YP_004382979.1| 22 ENAEEWLERGNELFSQGDYEEAIEAYDEA 50
                                      89********************9877666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.2
                                       HHTT-HHHHHHHHHHHH CS
                              HEPN  19 leegdydlacfhaqqaa 35 
                                        e g+yd a+ +  qa+
  gi|330506551|ref|YP_004382979.1| 103 HELGEYDEAIVALDQAI 119
                                       6889**********997 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.35
                                       S...--HHHHHHHHHHHHHHHHH CS
                              HEPN  95 e...yteedaeealkdaeevlel 114
                                           y++ d++ea+  + ev++l
  gi|330506551|ref|YP_004382979.1| 167 AdilYEQGDYQEAITAVDEVIRL 189
                                       03447888888888888888865 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 5.2
                                       HHHCCHHHT...-HHHHHHHHHHHCCCHHCCCTSS CS
                              HEPN  58 eLleelkkelkeseelreeleeLekayiesrYpda 92 
                                       eLl +l+++++ s e  + +  L+    ++ Y   
  gi|330506551|ref|YP_004382979.1| 202 ELLWRLERYDE-SLEALDRAIQLDSDLADAWYNRG 235
                                       57777777776.55555555555555444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        49  (0.002733); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              49  [number of targets reported over threshold]
# CPU time: 0.80u 0.31s 00:00:01.11 Elapsed: 00:00:00.56
# Mc/sec: 1391.42
//
Query:       gi|330506552|ref|YP_004382980.1|  [L=71]
Description: hypothetical protein MCON_0280 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0039   17.6   0.0     0.0043   17.4   0.0    1.1  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 !   17.4   0.0   2.4e-07    0.0043       1      59 [.       6      58 ..       6      69 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.4e-07
                                      -TTEEEEEEE-S--TTS--SEEEEEE-S-HHHHCHSEEEEEEEESSSTSSGCSTTEEEE CS
                        PemK_toxin  1 krGeIvlvdldpsrgseqgkrRpvvVvsndafnekntvivvpltskdkdkkklpfhvel 59
                                      k+G+Ivl++l+ s     +k Rp +V+ +d+  +   ++v+ ++sk + +   p  + +
  gi|330506552|ref|YP_004382980.1|  6 KKGDIVLAPLSYS-DLVNDKLRPSLVLYHDIDVR--QLTVAYISSKVPAN---PSLCDI 58
                                      78********544.333458**********5444..79********9755...444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 622.22
//
Query:       gi|330506553|ref|YP_004382981.1|  [L=364]
Description: cell surface glycoprotein [Methanosaeta concilii GP6]
Scores for complete 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-52  176.8  51.6    6.1e-49  166.5  36.8    2.0  2  NosD             Periplasmic copper-binding protein (NosD)
    1.5e-25   89.9  45.3    2.6e-19   69.6  22.5    2.2  2  Beta_helix       Right handed beta helix region
    0.00079   19.3  18.0       0.11   12.3   5.0    3.2  3  Pectate_lyase_3  Pectate lyase superfamily protein
  ------ inclusion threshold ------
       0.46   10.2   2.7        8.8    6.0   0.4    2.6  2  PGM_PMM_I        Phosphoglucomutase/phosphomannomutase, alpha


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 !   24.0   6.7   4.5e-09     2e-05     107     168 ..      94     153 ..      85     156 .. 0.87
   2 !  166.5  36.8   1.4e-52   6.1e-49       2     240 ..     102     347 ..     101     348 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.5e-09
                              NosD 107 GillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNy 168
                                       G    +++n++is+ +i+  n++Gi +++ s+nti++N+ie++ +  i+ l  s++n+i+nN+
  gi|330506553|ref|YP_004382981.1|  94 GSVFMTANNSQISGFRIVnPNGDGIDVTS-SHNTISNNTIEAC-GAAIY-LMVSDKNKIVNNN 153
                                       56667789999***99999999****999.699**********.9****.9999999999996 PP

  == domain 2  score: 166.5 bits;  conditional E-value: 1.4e-52
                              NosD   2 nnaisgdevlvsargngiqlensegseisnneisnsrdgilldnssnntitgntienl.........ryGihlense 69 
                                       n++isg + +v  +g+gi + + ++++isnn+i+   ++i+l  s++n+i +n  +           + Gi+l  s+
  gi|330506553|ref|YP_004382981.1| 102 NSQISGFR-IVNPNGDGIDVTS-SHNTISNNTIEACGAAIYLMVSDKNKIVNNNASVRcqgvmgllsSDGIMLAHSD 176
                                       66777777.46779******65.6778*************************944444467799999********** PP

                              NosD  70 sntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflens.ssntitgNr 144
                                       +n+ie+nt+s+ ++Gi+l++s+nnt+ nN + +n+  Gi +++s++n i++N++  ++++Gi l n  s+nt+t+N+
  gi|330506553|ref|YP_004382981.1| 177 ENIIEGNTASGASMGIYLYYSHNNTILNNAALSNDH-GIAIKGSRDNIIQENRAIgSKEEGIGLLNGcSGNTVTKNN 252
                                       **********************************87.*************************998888********* PP

                              NosD 145 iesnqkiGilllsssegntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylg..GNyWsdydgeDadgDG 219
                                       +++n +iGi+ l +s++ntiy N+Fi+n +n+  ++s +n W+++++  +   g +y+g  GNyWsdy+g+D+dg+G
  gi|330506553|ref|YP_004382981.1| 253 VTGN-SIGIY-LRESNQNTIYLNDFIDNLQNALSSDS-ENIWHSPEQISYSSAGKSYTGllGNYWSDYKGNDSDGNG 326
                                       ****.*****.*********************99886.*************************************** PP

                              NosD 220 igDtpYeindgviDylplvnp 240
                                       +gD +Y+ + +  D +pl++p
  gi|330506553|ref|YP_004382981.1| 327 LGDASYSFEYDGQDDHPLMTP 347
                                       ********97778******99 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6  22.5   5.7e-23   2.6e-19       3     149 ..      96     244 ..      93     244 .. 0.94
   2 !   33.9  14.8   5.9e-12   2.6e-08      22      98 ..     210     286 ..     208     342 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 5.7e-23
                                       EEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---........SEE CS
                        Beta_helix   3 isingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnn........ggg 71 
                                       ++++ +++ +i+++ i n++g+Gi + +s+n +i+nn+i+   g  iy+  s++n+i nn+ s           ++g
  gi|330506553|ref|YP_004382981.1|  96 VFMTANNS-QISGFRIVNPNGDGIDVTSSHN-TISNNTIEA-CGAAIYLMVSDKNKIVNNNASVRCqgvmgllsSDG 169
                                       67777888.9*********************.*********.**************999999844478999999*** PP

                                       E-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-S CS
                        Beta_helix  72 ialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgss 148
                                       i+l  ++ n+ie+n+ +  +  Giyl+ys+nnti nN + +n  +Gi i  s  ++ ++ N++ ++k +Gi + +++
  gi|330506553|ref|YP_004382981.1| 170 IMLAHSDENIIEGNTASGASM-GIYLYYSHNNTILNNAALSND-HGIAIKGSR-DNIIQENRAIGSKEEGIGLLNGC 243
                                       *******************88.*********************.*********.999**************999987 PP

                                       S CS
                        Beta_helix 149 s 149
                                       s
  gi|330506553|ref|YP_004382981.1| 244 S 244
                                       5 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 5.9e-12
                                       SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT.-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE- CS
                        Beta_helix  22 ggyGiylrgssnvvienneiannsgsGiyilgs.snntisnntisdnngggialfgasnnlienneitdnggsGiyl 97 
                                       +++Gi ++gs++++i++n+  ++ ++Gi++l++ s+nt+++n++++n   gi+l+++++n+i+ n+++dn ++ ++ 
  gi|330506553|ref|YP_004382981.1| 210 NDHGIAIKGSRDNIIQENRAIGSKEEGIGLLNGcSGNTVTKNNVTGNS-IGIYLRESNQNTIYLNDFIDNLQNALSS 285
                                       69**************9999999********999***********999.*********************8876644 PP

                                       T CS
                        Beta_helix  98 n 98 
                                       +
  gi|330506553|ref|YP_004382981.1| 286 D 286
                                       3 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 !    5.7   0.2    0.0026        11      21      84 ..      43     102 ..      39     112 .. 0.79
   2 !    8.7   2.6   0.00032       1.4     163     211 ..     110     159 ..      94     165 .. 0.69
   3 !   12.3   5.0   2.5e-05      0.11     132     214 ..     177     260 ..     166     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0026
                                       HHHHH......HTSS-EEE-SEEEEESS-EEE-SSEEEEE..S-TTTEEEEE-TT-SS--SEEES- CS
                   Pectate_lyase_3  21 iqkaiscasatttgavVYfPaGtYlvsspiilksgvqLvG..dgngrpvlkaaaafvgaglidgdp 84 
                                       iq+ai   ++ +tg+++ + +GtY  +  i  k++v L+G   g g+pv+ a + + g+  +++++
  gi|330506553|ref|YP_004382981.1|  43 IQEAI---DQARTGDIIEVMSGTYQGTLDI--KKEVALMGidSGEGMPVIDAGS-ILGSVFMTANN 102
                                       9****...9999************766665..99*****976689999999955.56655555555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00032
                                       EES-SS-SEEES-EEEEEES-EEE-S--SEEE-T.T-EEEEEEEEEESSS CS
                   Pectate_lyase_3 163 fsglgdigiavgnqqftvrnitfnnattgievlw.gwgwtlknvkinnce 211
                                       + +  ++gi v++ + t++n+t++ ++ +i++   +++ +++n+    c+
  gi|330506553|ref|YP_004382981.1| 110 IVNPNGDGIDVTSSHNTISNNTIEACGAAIYLMVsDKNKIVNNNASVRCQ 159
                                       3335899************************9984555444455445555 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 2.5e-05
                                       S-SSEEE-SSS---TT---SS--EEEE.ES-EEES-SS-SEEE.S.-EEEEEES-EEE-S--SEEE-TT-E.EEEEE CS
                   Pectate_lyase_3 132 nvefemseasgtkhqgifiengsggfl.ndlvfsglgdigiav.g.nqqftvrnitfnnattgievlwgwg.wtlkn 204
                                       ++++e ++asg    gi++ ++ ++++ n++  s+  d+gia+ g +++++ +n ++ + ++gi +l g +  t+  
  gi|330506553|ref|YP_004382981.1| 177 ENIIEGNTASG-ASMGIYLYYSHNNTIlNNAALSN--DHGIAIkGsRDNIIQENRAIGSKEEGIGLLNGCSgNTVTK 250
                                       45688888995.788*****999999989999999..999999656888888999*************7666**999 PP

                                       EEEESSSEEE CS
                   Pectate_lyase_3 205 vkinncegGi 214
                                       +++ +   Gi
  gi|330506553|ref|YP_004382981.1| 251 NNVTGNSIGI 260
                                       9999998888 PP

>> 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 ?    3.7   0.1     0.011        48      93     114 ..     116     137 ..      92     158 .. 0.78
   2 ?    6.0   0.4     0.002       8.8      90     129 ..     187     226 ..     161     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.011
                                       EEEEE--TTS-TTCCCEEEEET CS
                         PGM_PMM_I  93 agimitaSHnppeyngiKvyls 114
                                       +gi +t SHn    n i  + +
  gi|330506553|ref|YP_004382981.1| 116 DGIDVTSSHNTISNNTIEACGA 137
                                       5899999999999999988776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.002
                                       CECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHH CS
                         PGM_PMM_I  90 kadagimitaSHnppeyngiKvylsnGgpispeveekIea 129
                                       +a+ gi++  SHn    n+  + + +G+ i+ + ++ I++
  gi|330506553|ref|YP_004382981.1| 187 GASMGIYLYYSHNNTILNNAALSNDHGIAIKGSRDNIIQE 226
                                       5899***************************999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2524.69
//
Query:       gi|330506554|ref|YP_004382982.1|  [L=166]
Description: N-acetyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-13   49.3   0.1    6.3e-13   49.0   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.2e-10   40.8   0.0    4.4e-10   39.8   0.0    1.5  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    8.8e-10   38.6   0.0      1e-09   38.4   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    0.00054   20.0   0.0      0.006   16.7   0.0    2.0  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00077   19.4   0.0     0.0013   18.7   0.0    1.3  1  FR47             FR47-like protein
     0.0022   18.1   0.0     0.0044   17.1   0.0    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
     0.0028   17.4   0.0      0.004   16.9   0.0    1.3  1  PanZ             Acetyltransferase (GNAT) domain, PanZ


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.1   2.5e-16   6.3e-13      20     117 .]      49     142 ..      22     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 2.5e-16
                                       HHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESE CS
                    Acetyltransf_1  20 seeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikk 96 
                                       +++ef++s   + e++++ +++++++G + +    +   ++a ++ l   pe rg+G+G+ L+e+++++ r  g++ 
  gi|330506554|ref|YP_004382982.1|  49 PLAEFAQS-QSPQERIWILKDGDRIAGSMAIVRHSQ---KEAQLRWLLLEPEIRGRGIGRWLVEEALDFSRISGYES 121
                                       44443333.2266699999999*******8888888...*****************************99999**** PP

                                       EEEEEETTEHHHHHHHHH.TTE CS
                    Acetyltransf_1  97 ivlaveedndaairlYek.lGF 117
                                       i+l++ e    a +lY + +GF
  gi|330506554|ref|YP_004382982.1| 122 IFLWTVEALYIAANLY-RsVGF 142
                                       ***9*9**********.65**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.7     7e+03      14      24 ..      20      30 ..       8      47 .. 0.53
   2 !   39.8   0.0   1.7e-13   4.4e-10       2      75 ..      60     143 ..      59     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.7
                                      EEEEEEEEEES CS
                    Acetyltransf_7 14 ivGfialslld 24
                                      ++G+i +++  
  gi|330506554|ref|YP_004382982.1| 20 DIGYITYMHAV 30
                                      45666555444 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 1.7e-13
                                       TEEEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH.....TTSEEEEE.EEEETHH..HHHH CS
                    Acetyltransf_7   2 kgevfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea.....aekgiile.qlelnae..kaik 67 
                                       ++++++++d+++i G +a+++++   a++ +l   pe rg+GiGr L+e      +++g++ +  l++++    a++
  gi|330506554|ref|YP_004382982.1|  60 QERIWILKDGDRIAGSMAIVRHSqkeAQLRWLLLEPEIRGRGIGRWLVEEaldfsRISGYE-SiFLWTVEAlyIAAN 135
                                       689*************999999998888888*****************9535544327754.22334422235899* PP

                                       HHHHTTEE CS
                    Acetyltransf_7  68 fYeklGFe 75 
                                       +Y++ GF+
  gi|330506554|ref|YP_004382982.1| 136 LYRSVGFV 143
                                       *******8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   3.9e-13     1e-09      27     115 ..      57     151 ..      33     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 3.9e-13
                   Acetyltransf_10  27 eegealllvaeeggkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl..eltvnaspya 97 
                                       ++++  ++++++g++i+G  ++ r ++   ++  l  +pe rg+Gig+ L+e++++  +  g++     tv+a   a
  gi|330506554|ref|YP_004382982.1|  57 QSPQERIWILKDGDRIAGSMAIvRHSQkeaQLRWLLLEPEIRGRGIGRWLVEEALDFSRISGYESifLWTVEALYIA 133
                                       3788999*************99887779999**************************999999988999******** PP

                   Acetyltransf_10  98 vpfYeklGFkavgeeqee 115
                                        ++Y+++GF++ ++ + e
  gi|330506554|ref|YP_004382982.1| 134 ANLYRSVGFVQRERLTHE 151
                                       **********99877665 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.3e-06     0.006      41     125 ..      60     142 ..      36     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.3e-06
                                       TSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--... CS
                    Acetyltransf_9  41 esrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemreegqplsllfP... 114
                                       ++r++++ d+++++g++a+++++        k a++ +    pe rgrg+ + L+++al+  r  g++ ++l+    
  gi|330506554|ref|YP_004382982.1|  60 QERIWILKDGDRIAGSMAIVRHS-------QKEAQLRWLLLEPEIRGRGIGRWLVEEALDFSRISGYESIFLWTvea 129
                                       6899***********99999985.......5678999999**********************************777 PP

                                       ..SSHHHHHTTT- CS
                    Acetyltransf_9 115 ..ssipiYrrfGy 125
                                         +++++Yr+ G+
  gi|330506554|ref|YP_004382982.1| 130 lyIAANLYRSVGF 142
                                       7777799999998 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.9e-07    0.0013      17      81 ..      81     146 ..      69     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.9e-07
                                       EE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEEE CS
                              FR47  17 lrkdggelgalqvlpehrrrGlgsrlvkalakeiaerg.ktvllvvvasNtpsirlyeklGfekie 81 
                                         ++  +l  l ++pe r+rG g+ lv++     +  g + ++l++v++   + +ly ++Gf ++e
  gi|330506554|ref|YP_004382982.1|  81 HSQKEAQLRWLLLEPEIRGRGIGRWLVEEALDFSRISGyESIFLWTVEALYIAANLYRSVGFVQRE 146
                                       4445589999*****************9876655556615689999****************8873 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.7e-06    0.0044      22      58 ..      83     119 ..      62     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-06
                   Acetyltransf_CG  22 egvldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                       +++ ++     ++e+rG+Gi++ Lv++ald+ r  g+
  gi|330506554|ref|YP_004382982.1|  83 QKEAQLRWLLLEPEIRGRGIGRWLVEEALDFSRISGY 119
                                       4556666666789*****************9997765 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.5e-06     0.004      43      88 ..      66     112 ..      43     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.5e-06
                              PanZ  43 arFNdRlLgAvkv.eledkeaelsdlcVRevTRrRGVgsyLleearr 88 
                                        +  dR  g++++ + ++kea+l+ l    + R RG+g+ L+eea++
  gi|330506554|ref|YP_004382982.1|  66 LKDGDRIAGSMAIvRHSQKEAQLRWLLLEPEIRGRGIGRWLVEEALD 112
                                       55568888887751556779************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.40
# Mc/sec: 1252.96
//
Query:       gi|330506555|ref|YP_004382983.1|  [L=166]
Description: acetyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-14   54.2   0.1      2e-14   53.8   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    7.4e-13   48.5   0.0    9.1e-13   48.3   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.3e-10   41.5   0.0    2.7e-10   40.5   0.0    1.5  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.1e-05   25.5   0.0    0.00015   21.8   0.0    2.0  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00016   21.5   0.0    0.00026   20.9   0.0    1.3  1  FR47             FR47-like protein
    0.00027   20.6   0.0    0.00034   20.3   0.0    1.2  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
     0.0017   18.4   0.0     0.0032   17.6   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 !   53.8   0.1   7.8e-18     2e-14      20     117 .]      49     142 ..      30     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 7.8e-18
                                       HHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESE CS
                    Acetyltransf_1  20 seeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikk 96 
                                       +++ef++s     e +++ ee+++++G + + k+++   ++a ++ l   pe rg+G+G+ L+e+++++ r+  ++ 
  gi|330506555|ref|YP_004382983.1|  49 PLAEFAQS-KSSREKIWILEEGDRIAGSVAIVKRTE---EEAQLRWLLLEPEIRGRGIGRWLVEEALDFSRDMRYES 121
                                       44443333.2266699********************...89************************************ PP

                                       EEEEEETTEHHHHHHHHH.TTE CS
                    Acetyltransf_1  97 ivlaveedndaairlYek.lGF 117
                                       ivl++ e+   a +lY + +GF
  gi|330506555|ref|YP_004382983.1| 122 IVLWTAESLPIAEKLY-RsVGF 142
                                       ****************.65**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   3.6e-16   9.1e-13      21     119 ..      52     155 ..      30     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 3.6e-16
                   Acetyltransf_10  21 alrerieegealllvaeeggkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl..eltv 91 
                                       ++++   +++ +++++eeg++i+G +++ ++++   ++  l  +pe rg+Gig+ L+e++++  ++++++     t+
  gi|330506555|ref|YP_004382983.1|  52 EFAQSK-SSREKIWILEEGDRIAGSVAIvKRTEeeaQLRWLLLEPEIRGRGIGRWLVEEALDFSRDMRYESivLWTA 127
                                       444443.88999**************9998888899*********************************99988899 PP

                   Acetyltransf_10  92 naspyavpfYeklGFkavgeeqeenGir 119
                                       ++ p a+++Y+++GF+++ +++ e + +
  gi|330506555|ref|YP_004382983.1| 128 ESLPIAEKLYRSVGFEQILRVRHERWGS 155
                                       9999*************97777776655 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.1   7.8e+03      15      25 ..      21      36 ..      17      48 .. 0.45
   2 !   40.5   0.0   1.1e-13   2.7e-10       2      75 ..      60     143 ..      59     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.1
                                      EEEEEEEEES.....T CS
                    Acetyltransf_7 15 vGfialslld.....a 25
                                      +G+i++++        
  gi|330506555|ref|YP_004382983.1| 21 IGYIIYMHGIfhaleQ 36
                                      5655544443444330 PP

  == domain 2  score: 40.5 bits;  conditional E-value: 1.1e-13
                                       TEEEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH.....TTSEEEEE..EEEETHH..HHH CS
                    Acetyltransf_7   2 kgevfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea.....aekgiile..qlelnae..kai 66 
                                       +++++++e++++i G +a++ +    a++ +l   pe rg+GiGr L+e      +   ++ e  +l+++++   a+
  gi|330506555|ref|YP_004382983.1|  60 REKIWILEEGDRIAGSVAIVKRTeeeAQLRWLLLEPEIRGRGIGRWLVEEaldfsR--DMRYEsiVLWTAESlpIAE 134
                                       579*************999999887777777*****************95244331..222122344553324599* PP

                                       HHHHHTTEE CS
                    Acetyltransf_7  67 kfYeklGFe 75 
                                       k+Y++ GFe
  gi|330506555|ref|YP_004382983.1| 135 KLYRSVGFE 143
                                       ********9 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     6e-08   0.00015      31     127 ..      50     144 ..      26     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6e-08
                                       HHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT- CS
                    Acetyltransf_9  31 ireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemreegq 107
                                       + e+ + + ++++++++e++++++g++a+++++        + a++ +    pe rgrg+ + L+++al+  r++++
  gi|330506555|ref|YP_004382983.1|  50 LAEFAQSKSSREKIWILEEGDRIAGSVAIVKRT-------EEEAQLRWLLLEPEIRGRGIGRWLVEEALDFSRDMRY 119
                                       556677788899**************9999864.......5678999999*************************** PP

                                       -EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9 108 plsllfP.....ssipiYrrfGyei 127
                                       + ++l+      +++++Yr+ G+e+
  gi|330506555|ref|YP_004382983.1| 120 ESIVLWTaeslpIAEKLYRSVGFEQ 144
                                       ****99766666888********97 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     1e-07   0.00026      22      81 ..      86     149 ..      72     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1e-07
                                       SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEE...E CS
                              FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfeki...e 81 
                                        +l  l ++pe r+rG g+ lv++     +  r + ++l++++s   +++ly ++Gfe+i   +
  gi|330506555|ref|YP_004382983.1|  86 AQLRWLLLEPEIRGRGIGRWLVEEALDFSRDmRYESIVLWTAESLPIAEKLYRSVGFEQIlrvR 149
                                       6788999***************9988888886777777777888888***********995444 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.3e-07   0.00034      46     120 ..      69     142 ..      41     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                              PanZ  46 NdRlLgAvk.veledkeaelsdlcVRevTRrRGVgsyLleearrqaPevkswvlaeedvkeldlavlqaflealgf 120
                                        dR  g+v+ v+++++ea+l+ l    + R RG+g+ L+eea++   +++   +   + +  +l++++++ +++gf
  gi|330506555|ref|YP_004382983.1|  69 GDRIAGSVAiVKRTEEEAQLRWLLLEPEIRGRGIGRWLVEEALDFSRDMRYESIVLWTAE--SLPIAEKLYRSVGF 142
                                       5899999873688899**************************998766665555554433..45555555555555 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.2e-06    0.0032      20      57 ..      81     118 ..      63     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-06
                   Acetyltransf_CG  20 rkegvldfthTeVpeelrGkGiAkkLvkaalddareeg 57 
                                       r e++ ++     ++e+rG+Gi++ Lv++ald+ r+ +
  gi|330506555|ref|YP_004382983.1|  81 RTEEEAQLRWLLLEPEIRGRGIGRWLVEEALDFSRDMR 118
                                       555566666666789******************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1274.67
//
Query:       gi|330506556|ref|YP_004382984.1|  [L=621]
Description: alpha-amylase [Methanosaeta concilii GP6]
Scores for complete 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   95.3   0.9    3.6e-17   62.9   0.1    2.9  2  Alpha-amylase    Alpha amylase, catalytic domain
     0.0066   16.9   0.0      0.018   15.5   0.0    1.7  1  Alpha-amylase_C  Alpha amylase, C-terminal all-beta domain
  ------ inclusion threshold ------
       0.05   13.7   0.0        0.1   12.7   0.0    1.5  1  Malt_amylase_C   Maltogenic Amylase, C-terminal domain


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.1     6e-21   3.6e-17       1      79 [.     163     242 ..     163     253 .. 0.95
   2 !   28.8   0.1   1.5e-10   8.7e-07     154     329 ..     283     482 ..     266     485 .. 0.66

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 6e-21
                                       --CHHHHCTCCCCCCCT-SCEEE-B-CE.-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC CS
                     Alpha-amylase   1 GDLkGiiekLdYlkeLGvtaiwlsPifk.spqadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNH 76 
                                       GD++  + +L+Yl++LGv+ i + P+++ s++ d g+    y  +d++fG   d+++Li+ ah+kgi vilD+V  H
  gi|330506556|ref|YP_004382984.1| 163 GDMRTATRHLEYLQDLGVNCIEIMPVTNiSNTTDWGFLPIGYFGVDERFGKRRDMQRLIDSAHQKGIAVILDMVYGH 239
                                       999999**********************999********************************************** PP

                                       --T CS
                     Alpha-amylase  77 tsd 79 
                                       t +
  gi|330506556|ref|YP_004382984.1| 240 TDS 242
                                       966 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 1.5e-10
                                       CCCCCCCCCCTTT.-SEEEETTCCCTTTCCCC.................HCCHCCHHHHHHHHHHHTCCGTT-..EE CS
                     Alpha-amylase 154 elkdvvkfwlekg.idGfRlDvvkhvskveal.................esngeflheftqalnetvasrkev..mt 210
                                         + v ++wl +  +dGfR D v+ +   ++                  + + ++++ f         + +e+  + 
  gi|330506556|ref|YP_004382984.1| 283 FFYTVNHHWLSTYhVDGFRYDCVPNYWDGPTGlgyanlvyqtyklvfgmRGSQDHWQRFF--------EGDEIhlIQ 351
                                       45779999*99988*********9998855558999999655544444433333333333........333330044 PP

                                       EEE-TT-SCCCHCCCC-CGG-SICECCITTCGGGCC-CTSTTSB-SS-HHHHHHHHHHHHHHS-C..CCTTCEEES- CS
                     Alpha-amylase 211 vgEvssdasedlrvyttearlelemvldfphldvaqkakikeqlksisakklkellkkwlkalee..aaeeavtflg 285
                                        +E  ++  e+l++  + +  +++ ++d     ++ +a++     ++  + l  +    +++++e   +++a  +++
  gi|330506556|ref|YP_004382984.1| 352 CAEQLEEPVEVLEKTYSSSTWQNQ-TFDAAIAVARAEASELAGRLTYLGHRLGLVGYPAKEKINEdtIQKSALQYIE 427
                                       456666555555544444444444.5555555555544442222222344444444444455554446789999*** PP

                                       -TTS--HHHHTTSSTTTT...........HHHHHHHHHCCCTSSSEEEEETTCCC CS
                     Alpha-amylase 286 nHDqeRilsrlgddsaea...........ekklklaaillltlrGvpviYyGeEi 329
                                       nHD  R++ ++   s++            + k++ ++i+++t rG+p i++G+E+
  gi|330506556|ref|YP_004382984.1| 428 NHDHYRFVCNFCTISRDDndllkegdrryWYKVQPYLIAIMTARGIPLIWQGQEL 482
                                       ********99988887667999********************************7 PP

>> Alpha-amylase_C  Alpha amylase, C-terminal all-beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.1e-06     0.018       9      95 ..     548     617 ..     544     618 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-06
                                       SSEEEEEECTTT.EEEEEEE-SSSSEEECEEESSSSSEEEEETTCTTSGCCTTT-SSTSS-EEEECTTCBSEEEEEE CS
                   Alpha-amylase_C   9 nkviaFeRgdge.kllvvfNfhpsnsrqdyrvgvpaagkyrdvlntdaeeyggsglgntgkvvtvdddgransltlt 84 
                                       + ++ F+R++g+   lv++Nf++s+   +  +++p +g y + ++++++                +  g  ++l++ 
  gi|330506556|ref|YP_004382984.1| 548 RGLLLFSRRAGDaFSLVALNFTDSDQ--KAYFSFPLGGDYYEEIHGEDSF-------------RAGA-G--EWLEIC 606
                                       56789****98889********9666..5555569999999999888763.............3333.2..477777 PP

                                       ESTTEEEEEEE CS
                   Alpha-amylase_C  85 lpprsalvlkv 95 
                                       +p++   +++v
  gi|330506556|ref|YP_004382984.1| 607 IPSNYGRIWTV 617
                                       77777777765 PP

>> Malt_amylase_C  Maltogenic Amylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05       0.1      11      68 ..     548     607 ..     544     615 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                                       TTEEEEEEEETTEEEEEEEE..SS-EEEEE--GGGTT-EEEETTTTEE-----SS.EEEEE CS
                    Malt_amylase_C  11 rkvlaYlReyedetilvvaN..rsaqaveldlselagrvpvelfggeefpaigel.ytltL 68 
                                       r  l + R+ +d   lv++N   s+q++ ++++ l g    e+ g++ f+a +++ + + +
  gi|330506556|ref|YP_004382984.1| 548 RGLLLFSRRAGDAFSLVALNftDSDQKAYFSFP-LGGDYYEEIHGEDSFRAGAGEwLEICI 607
                                       7899****************9999999999999.****************99988776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 4320.90
//
Query:       gi|330506557|ref|YP_004382985.1|  [L=192]
Description: hypothetical protein MCON_0286 [Methanosaeta concilii GP6]
Scores for complete 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-32  111.3   0.0    5.7e-32  111.0   0.0    1.1  1  DUF1638   Protein of unknown function (DUF1638)
  ------ inclusion threshold ------
       0.03   13.3   0.0      0.053   12.5   0.0    1.3  1  MukE      MukE-like family


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 !  111.0   0.0   6.3e-36   5.7e-32       2     160 ..      30     182 ..      29     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 6.3e-36
                           DUF1638   2 leaglHnrpeeLrealqeeidrak.adydqIllgYGlCggalaglrsdecpveilkgddCislllgseeayaeelkd 77 
                                       l +glH +++eL++al+ee++ra+ +++++I+++YG+C+++++ +  + ++  ++ +++C+++++++++    e+k+
  gi|330506557|ref|YP_004382985.1|  30 LGPGLHVDFDELKDALEEELKRASsDGSQGIIVAYGQCHPKMDAI-LKPYHAALMDCQNCVDAFISRQAV---EKKA 102
                                       678********************97999*****************.********************9999...4445 PP

                           DUF1638  78 ekg.tffltpgwvkewdrlvleky.g.eelarmifgkllkgYkrlvyidtgltddpeleeraeefaarlglelevip 151
                                       ++g +f+l+pgw+  w++++ +++ + +e ar  +g     +k  vyidt ++d +e ee++ ef+++++l+++++p
  gi|330506557|ref|YP_004382985.1| 103 REGlFFYLSPGWLDAWKDIF-KRLgWdPEIARLHMGS----FKGSVYIDT-MKDAQEREEELLEFFDFTNLPFTIMP 173
                                       5667***************7.445455**********....*******99.8999999******************* PP

                           DUF1638 152 gglgllekl 160
                                       ++l+++++l
  gi|330506557|ref|YP_004382985.1| 174 MELDHFKSL 182
                                       ******987 PP

>> MukE  MukE-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.9e-06     0.053      35      68 ..      79     112 ..      68     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-06
                              MukE  35 haflldfqeeleefyrrynvelirapeG.ffylrp 68 
                                       ha l+d q+ ++ f +r  ve  +a eG ffyl p
  gi|330506557|ref|YP_004382985.1|  79 HAALMDCQNCVDAFISRQAVEK-KAREGlFFYLSP 112
                                       9********************6.899997889988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1402.50
//
Query:       gi|330506558|ref|YP_004382986.1|  [L=135]
Description: thioredoxin [Methanosaeta concilii GP6]
Scores for complete 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   91.5   0.0    3.9e-26   91.0   0.0    1.3  1  Thioredoxin    Thioredoxin
    7.2e-06   26.4   0.0    8.9e-05   22.9   0.0    2.2  1  Thioredoxin_2  Thioredoxin-like domain
    8.3e-05   22.8   0.0      0.088   13.2   0.0    2.4  2  Thioredoxin_8  Thioredoxin-like
    0.00015   21.6   0.0    0.00017   21.3   0.0    1.3  1  Thioredoxin_9  Thioredoxin
    0.00037   19.9   0.0    0.00045   19.7   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
     0.0057   16.4   0.0      0.011   15.4   0.0    1.4  1  KaiB           KaiB domain
     0.0093   14.9   0.0       0.01   14.8   0.0    1.3  1  Phosducin      Phosducin
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.018   15.0   0.0    1.3  1  HyaE           Hydrogenase-1 expression protein HyaE
      0.012   15.8   0.0      0.025   14.8   0.0    1.5  1  Thioredoxin_7  Thioredoxin-like
      0.026   14.4   0.0      0.038   13.9   0.0    1.5  1  Thioredoxin_6  Thioredoxin-like domain
       0.14   12.1   0.0       0.24   11.3   0.0    1.6  1  AhpC-TSA       AhpC/TSA family


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   0.0   2.4e-29   3.9e-26      12     103 .]      43     133 ..      32     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 2.4e-29
                                       HHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEE CS
                       Thioredoxin  12 eevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkky 88 
                                       ++ ++   l++++++A+wCg+C+++ P +e+la e+k++v++ k++vden+++a+++ +++iPtl++fk+gk ++k+
  gi|330506558|ref|YP_004382986.1|  43 AASNQ-YPLLILDCWAEWCGPCRMIGPIIEELAAEMKGRVVFGKLNVDENPQTANRFRISAIPTLMVFKDGKLIDKL 118
                                       44444.778999***************************************************************** PP

                                       ESS-HHHHHHHHHHH CS
                       Thioredoxin  89 egarekeklaaflkk 103
                                       +ga +k +l+a+++k
  gi|330506558|ref|YP_004382986.1| 119 VGAYPKPSLVAKIQK 133
                                       **********99975 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.4e-08   8.9e-05       9     105 ..      52     127 ..      43     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.4e-08
                     Thioredoxin_2   9 lvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt.i 84 
                                       +++ ++++C+ C+ +   ++el           +k  +++   +++ +++              a+++++++ Pt +
  gi|330506558|ref|YP_004382986.1|  52 ILDCWAEWCGPCRMIGPIIEEL---AAE-----MKGRVVFGKLNVDENPQ-------------TANRFRISAIPTlM 107
                                       3444588888888888877777...222.....44445555555555555.............57**********88 PP

                     Thioredoxin_2  85 vfldgkeivarlpGyvpaeel 105
                                       vf dgk  +++l+G++p+  l
  gi|330506558|ref|YP_004382986.1| 108 VFKDGK-LIDKLVGAYPKPSL 127
                                       8*****.99*******98766 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   5.4e-05     0.088       4      43 ..      51      88 ..      49      94 .. 0.81
   2 !    7.8   0.0    0.0025       4.1      71      90 ..      91     110 ..      85     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.4e-05
                                      EEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE- CS
                     Thioredoxin_8  4 vlLyfgaswcppckaftpklkelyeklkkkkkveivyvsl 43
                                      ++L ++a+wc pc+ + p + el  ++k   +v++  +++
  gi|330506558|ref|YP_004382986.1| 51 LILDCWAEWCGPCRMIGPIIEELAAEMK--GRVVFGKLNV 88
                                      789********************99998..6666555555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0025
                                       HHHHTT-S--TT-SEEEEE- CS
                     Thioredoxin_8  71 rnklkkkynvkaiPtlvvld 90 
                                       + + +++++++aiPtl+v +
  gi|330506558|ref|YP_004382986.1|  91 NPQTANRFRISAIPTLMVFK 110
                                       557799***********986 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.1e-07   0.00017      37     107 ..      42     112 ..       4     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.1e-07
                                       HT--S-EEEEEE..--TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT CS
                     Thioredoxin_9  37 ksiekklkilvl..tedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildee 107
                                        + ++++ +l+l   ++wCg ++++ P+++++a e + ++ +  l  den+++ ++++     aiPtl++++++
  gi|330506558|ref|YP_004382986.1|  42 DAASNQYPLLILdcWAEWCGPCRMIGPIIEELAaEMKGRVVFGKLNVDENPQTANRFRI---SAIPTLMVFKDG 112
                                       44555555555522589*************998466778999999999*******9976...9****9888654 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 !   19.7   0.0   2.8e-07   0.00045      46     104 ..      60     111 ..      42     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.8e-07
                         OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfpp 104
                                       C +Cr + p +e +a  ++         ++F+k+++de++++ ++++++ +P l++f+ 
  gi|330506558|ref|YP_004382986.1|  60 CGPCRMIGPIIEELAAEMKGR-------VVFGKLNVDENPQTANRFRISAIPTLMVFKD 111
                                       999999999999999888777.......9****************************87 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.8e-06     0.011      29      56 ..      80     107 ..      66     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.8e-06
                                       TEEEEEEETTTSHCHHCCTCEESCCCCC CS
                              KaiB  29 qyeLqvvdvleqPelaeedrlvatPaLi 56 
                                       ++    ++v e+P+ a  +r+ a+P+L+
  gi|330506558|ref|YP_004382986.1|  80 RVVFGKLNVDENPQTANRFRISAIPTLM 107
                                       55555579******************96 PP

>> Phosducin  Phosducin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   6.2e-06      0.01     170     215 ..      72     119 ..       2     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.2e-06
                                       HHHHH-T.TSEEEEEEHH.HH--TTSS-TTT-SEEEEEETTEEEEEET CS
                         Phosducin 170 claaeyp.tvkfckvkas.vigasdrfsrdvlpallvykagellsnfv 215
                                        laae    v f k++   +  +++rf   ++p+l+v+k g+l+  +v
  gi|330506558|ref|YP_004382986.1|  72 ELAAEMKgRVVFGKLNVDeNPQTANRFRISAIPTLMVFKDGKLIDKLV 119
                                       5788864268899998652667899*******************9877 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.1e-05     0.018      49     100 ..      69     119 ..      64     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                                       HHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEEEE CS
                              HyaE  49 vlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgvla 100
                                       ++ El ++ + +     ++  +++ + a+rf+++  P+l++++dg+++  l 
  gi|330506558|ref|YP_004382986.1|  69 IIEELAAEMKGRVVFGKLN-VDENPQTANRFRISAIPTLMVFKDGKLIDKLV 119
                                       4556666666655555555.66777899******************987775 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.5e-05     0.025       9      81 ..      39     109 ..      35     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHT--EEE.EE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---SSEEEEE CS
                     Thioredoxin_7   9 alakaaergkpvlv.ffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqgvPvvafl 81 
                                       a+  aa+++ p+l+ +  a+wc++C+ +    ++    ++ +++++v+ +++v+e+ +   +++ + +P+++++
  gi|330506558|ref|YP_004382986.1|  39 ATVDAASNQYPLLIlDCWAEWCGPCRMIGPIIEEL--AAE-MKGRVVFGKLNVDENPQTANRFRISAIPTLMVF 109
                                       6667899999999989***********99877655..556.9***********999886645555889999988 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.3e-05     0.038     116     159 ..      69     110 ..       2     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEE CS
                     Thioredoxin_6 116 aiekvakefkdkinfaladaksfkrpleylglsssdlPvivivd 159
                                       +ie++a+e+k+++ f  ++++++++  +++++s  ++P++ +++
  gi|330506558|ref|YP_004382986.1|  69 IIEELAAEMKGRVVFGKLNVDENPQTANRFRIS--AIPTLMVFK 110
                                       699***************************999..****99887 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.24      26      58 ..      49      80 ..      23     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                      SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCT CS
                          AhpC-TSA 26 kpvvlffypkdwcpvCttelpalaklyeefker 58
                                        ++l ++++ wc +C+   p +++l+ e+k r
  gi|330506558|ref|YP_004382986.1| 49 PLLILDCWAE-WCGPCRMIGPIIEELAAEMKGR 80
                                      568999****.***************9999954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); 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:                        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 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 970.05
//
Query:       gi|330506559|ref|YP_004382987.1|  [L=161]
Description: hypothetical protein MCON_0288 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1153.20
//
Query:       gi|330506560|ref|YP_004382988.1|  [L=369]
Description: hypothetical protein MCON_0289 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0042   17.1   0.0        0.1   12.6   0.0    2.6  3  Wzt_C     Wzt C-terminal domain
  ------ inclusion threshold ------
      0.021   14.8   0.0        1.3    9.1   0.0    2.4  2  BsuPI     Intracellular proteinase inhibitor
      0.041   14.9   0.0         20    6.3   0.0    2.5  2  CopC      CopC domain


Domain annotation for each model (and alignments):
>> Wzt_C  Wzt C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.056   3.4e+02      79     112 ..      67     101 ..      51     117 .. 0.72
   2 ?   -2.7   0.0      0.88   5.3e+03      76      96 ..     196     215 ..     172     219 .. 0.60
   3 !   12.6   0.0   1.7e-05       0.1      71     125 ..     275     324 ..     264     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.056
                             Wzt_C  79 elkagervevefef.klpLapGeYlltvaledrdg 112
                                       +l+  + +++ ++  +l+  +G+Y++ + l+d + 
  gi|330506560|ref|YP_004382988.1|  67 KLDIDGPGTYVVRWpNLKVDKGSYSVCATLRDDGT 101
                                       45555667777888666777*********966554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.88
                             Wzt_C  76 eleelkagervevefefklpL 96 
                                        ++ l++g+++e ++++   L
  gi|330506560|ref|YP_004382988.1| 196 WKPILENGQTYEGRVKIV-EL 215
                                       356668888888777773.44 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 1.7e-05
                             Wzt_C  71 ekksfeleelkagervevefefklpLapGeYlltvaledrdgeeneiydwlddal 125
                                       ++  +++++l  g+  +ve++ +  L pG Y l+ al + dg+   i+d  ++++
  gi|330506560|ref|YP_004382988.1| 275 TE--KKTPVLLSGDDETVEITWNSTLEPGVYQLQTALIGQDGS---IVDLQENII 324
                                       33..44899999**********889************999998...888777554 PP

>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.014        85      62      97 ..      62      98 ..      60     101 .. 0.84
   2 ?    9.1   0.0   0.00021       1.3      68      98 ..     282     312 ..     275     314 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.014
                                      --EEEEE-TT-EEEEEEEE.S.---SEEEEEEEEE-- CS
                             BsuPI 62 alssetlepgesatyeetwde.dlepGeYtleaelva 97
                                      +l s++l+ +   ty  +w++ ++ +G+Y++ a+l+ 
  gi|330506560|ref|YP_004382988.1| 62 VLNSRKLDIDGPGTYVVRWPNlKVDKGSYSVCATLRD 98
                                      67888888888999*****9559********999875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00021
                                       E-TT-EEEEEEEE.S---SEEEEEEEEE--E CS
                             BsuPI  68 lepgesatyeetwdedlepGeYtleaelvae 98 
                                       l +g+  t+e tw+++lepG Y+l+  l+++
  gi|330506560|ref|YP_004382988.1| 282 LLSGDDETVEITWNSTLEPGVYQLQTALIGQ 312
                                       668999*******99*********9998876 PP

>> CopC  CopC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0033        20      52      80 ..      60      86 ..      22      91 .. 0.63
   2 ?    6.2   0.0    0.0037        22      38      84 ..     275     317 ..     201     320 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0033
                              CopC 52 ktveaelkvplpelaaGtYtVewrvvsaD 80
                                      +  ++  + +l+   +GtY V+w  +  D
  gi|330506560|ref|YP_004382988.1| 60 N--KVLNSRKLDIDGPGTYVVRWPNLKVD 86
                                      2..2233344555699*******988887 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0037
                              CopC  38 tdpdgkeevetvdaktveaelkvplpelaaGtYtVewrvvsaDGHpv 84 
                                       t+++ +  + ++d++tve + + +l+   +G Y+++   + +DG  v
  gi|330506560|ref|YP_004382988.1| 275 TEKKTP-VLLSGDDETVEITWNSTLE---PGVYQLQTALIGQDGSIV 317
                                       433332.3447788887888887787...**************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 2391.65
//
Query:       gi|330506561|ref|YP_004382989.1|  [L=543]
Description: peptidase M50 [Methanosaeta concilii GP6]
Scores for complete 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      1e-21   77.4   0.0    1.6  1  Peptidase_M50  Peptidase family M50
    3.5e-11   43.3   0.0    1.1e-06   28.9   0.0    2.3  2  PDZ_2          PDZ domain
    5.6e-10   38.9   0.1      0.001   18.8   0.0    2.4  2  PDZ_6          PDZ domain
    2.1e-05   24.8   0.6     0.0045   17.3   0.1    2.6  2  PDZ            PDZ domain
  ------ inclusion threshold ------
        4.9    7.5  13.5        2.2    8.6   1.3    3.5  3  DUF3267        Putative zincin peptidase


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0   2.8e-25     1e-21       4     247 ..     124     521 ..     121     524 .. 0.86

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 2.8e-25
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   4 lllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakafl 80 
                                       ++l++ ++vHE++H+++ + +gv+v++++i                 + + p+ ++V+ ++e+   ++     ++ +
  gi|330506561|ref|YP_004382989.1| 124 IALFVTMLVHEFAHGILSRVEGVRVKSMGIVT---------------LLVAPIAAFVEPDEEDLFGTK-----NKPS 180
                                       89*************************99999...............99999*********9955443.....3346 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX................................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................. RF
                     Peptidase_M50  81 kkspwqrllivlAGplanfilailvfvv................................................. 108
                                         +  +r++i+ AG +anf++a l++++                                                 
  gi|330506561|ref|YP_004382989.1| 181 LVNRAARIRILSAGVIANFMVAALAMALffgpvlgsispvdrliavgvqedsiaeeagfesgmvllqvngenaikie 257
                                       677889*******************9999************************************************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M50 109 ............................................................................. 108
                                                                                                                    
  gi|330506561|ref|YP_004382989.1| 258 elysnlgstmvemevlhngqkeifnlpgqaargimvasifpdspadsvglpagsvisridgkevvdvegfrremnlt 334
                                       ***************************************************************************** PP

                                       ............................-EEECECTTTSCEE-SEEEC-...............XXXXXXXXXX.XX CS
                                       ............................xxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxx.xx RF
                     Peptidase_M50 109 ............................pkkskeseeekrgviGvspkp...............vkkeglleal.ke 141
                                                                    ++++es+  ++g+iG++ +                 +  g+l+++ k+
  gi|330506561|ref|YP_004382989.1| 335 rpgqiitittgsgksyqvnltsaagqgeEEQNEESDAAGTGFIGIEMSGnaiyaggvafqeapaSEFLGILKTIpKR 411
                                       *************************998667777**************97888888877776665555555555334 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 142 gvektlkvvvltvkalgklitgkls.....lktlggpisiaqlaseaaeagls...sflqllalisvnLgilNLlPi 210
                                       gve +  +  l ++ + ++ ++ ++     l  +  p++ a+  +e +        ++l ++ +i++  g++N lP 
  gi|330506561|ref|YP_004382989.1| 412 GVEGFAYMLNLPFSGIPGFTQKGFPgfsgwLTAVYEPVGWAEPLGERF----FwiaNLLLWIGWINLYAGLFNCLPA 484
                                       555555555555555555554432211122344555555555555544....13559******************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 211 pvLDGghllfalleairrkplserkeevanlvglall 247
                                        +LDGgh+++ l++   ++ ++ +k e ++++ +a+ 
  gi|330506561|ref|YP_004382989.1| 485 GPLDGGHIFRDLVQTGFERLVPPEKAEKLTRTAVAIF 521
                                       **************99999999999999999888875 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   4.2e-05      0.15      15      76 ..     222     279 ..     212     284 .. 0.81
   2 !   28.9   0.0     3e-10   1.1e-06      13      68 ..     288     343 ..     268     349 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.2e-05
                                       -EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEE CS
                             PDZ_2  15 gvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkk 76 
                                       +++ v V+e++ a++ag+++g v+l+v+g    + e+l s+l ++     V+ +vl++g+k+
  gi|330506561|ref|YP_004382989.1| 222 RLIAVGVQEDSIAEEAGFESGMVLLQVNGENAIKIEELYSNLGST----MVEMEVLHNGQKE 279
                                       567788**************************9999999998764....4666666666665 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 3e-10
                                       ..-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEE CS
                             PDZ_2  13 tggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVklt 68 
                                       ++g+ v+s+ +++Pa+  gl ag vi  +dgk+v + e ++++++ ++pG+ +++t
  gi|330506561|ref|YP_004382989.1| 288 ARGIMVASIFPDSPADSVGLPAGSVISRIDGKEVVDVEGFRREMNLTRPGQIITIT 343
                                       78*************************************************99998 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.9e-07     0.001       4      38 ..     227     259 ..     224     265 .. 0.88
   2 !   17.8   0.0     6e-07    0.0022       2      53 ..     293     343 ..     292     344 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.9e-07
                             PDZ_6   4 aVdpgsPAdrAGlrvGDiilsvNGqpveglsladv 38 
                                        V+++s+A++AG++ G ++l+vNG++    +++++
  gi|330506561|ref|YP_004382989.1| 227 GVQEDSIAEEAGFESGMVLLQVNGENA--IKIEEL 259
                                       79***********************97..677666 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 6e-07
                             PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallr.gsagesvvlv 53 
                                       V ++ p+sPAd  Gl +G +i  ++G++v   +++ +++ +  +++g++++++
  gi|330506561|ref|YP_004382989.1| 293 VASIFPDSPADSVGLPAGSVISRIDGKEV--VDVEGFRREMNlTRPGQIITIT 343
                                       667779***********************..9999998888877777777765 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.1     0.008        29      33      63 ..     228     258 ..     221     263 .. 0.89
   2 !   17.3   0.1   1.3e-06    0.0045      24      73 ..     287     336 ..     261     344 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.008
                                       ECTTSHHHHHTSSTTEEEEEETTEETTTSHH CS
                               PDZ  33 vlpggaaeadglkvGDkIlsvNgvdvenvsh 63 
                                       v++++ ae +g + G ++l+vNg++  ++++
  gi|330506561|ref|YP_004382989.1| 228 VQEDSIAEEAGFESGMVLLQVNGENAIKIEE 258
                                       77889999999*************9988865 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.3e-06
                                       SSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTT CS
                               PDZ  24 gdkgifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgs 73 
                                       +++gi v+++ p+++a+  gl +G +I +++g+ v++v+  +    ++ +
  gi|330506561|ref|YP_004382989.1| 287 AARGIMVASIFPDSPADSVGLPAGSVISRIDGKEVVDVEGFRREMNLTRP 336
                                       557**********9999999************887777655555555555 PP

>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.8    0.0047        17      48      81 ..      62      92 ..      43      97 .. 0.83
   2 ?    8.6   1.3   0.00062       2.2       1      28 [.     126     150 ..     126     218 .. 0.79
   3 ?   -2.0   0.2       1.3   4.5e+03      53      73 ..     518     538 ..     509     542 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0047
                           DUF3267 48 kqfiiillaPfvllgilllllalllpsstlllll 81
                                      ++  +    P+v+l+++++l+++ll  +   l++
  gi|330506561|ref|YP_004382989.1| 62 WRTAVTIGIPLVILSMATFLILVLLMTY---LMI 92
                                      788888889**************97775...333 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00062
                           DUF3267   1 llvlvilHEllHglffklfgkkpkkkvk 28 
                                       l+v++++HE++Hg++ ++ g+++k   +
  gi|330506561|ref|YP_004382989.1| 126 LFVTMLVHEFAHGILSRVEGVRVK---S 150
                                       589**************9766543...2 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.3
                           DUF3267  53 illaPfvllgilllllalllp 73 
                                       ++++  v+l+ ll+ +++++ 
  gi|330506561|ref|YP_004382989.1| 518 VAIFTWVILTSLLISIIAPFT 538
                                       556666677666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        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):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3720.31
//
Query:       gi|330506562|ref|YP_004382990.1|  [L=180]
Description: hypothetical protein MCON_0291 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-12   45.7   1.9    1.2e-05   25.0   0.0    2.3  2  KH_1      KH domain
    0.00047   20.2   0.0    0.00079   19.5   0.0    1.4  1  KH_8      Krr1 KH1 domain
     0.0027   17.5   1.7       0.56   10.1   0.0    2.5  2  KH_2      KH domain
  ------ inclusion threshold ------
       0.14   12.2   0.1        2.5    8.3   0.1    2.4  2  KH_5      NusA-like KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   2.7e-09   1.2e-05       4      59 ..       3      54 ..       1      61 [. 0.77
   2 !   20.1   0.5   9.3e-08   0.00042      10      65 ..     100     147 ..      97     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.7e-09
                                      EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE..SHHHHHH CS
                              KH_1  4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG..speavek 59
                                      i++P + +g ++G++Gs+ + I+e+t+++  ++ s+       ++ ++   +p +v +
  gi|330506562|ref|YP_004382990.1|  3 IKIPEERIGVLVGPNGSMKHFIEEKTKTSLEID-SD-----TGTISVTSaeDPLQVLR 54
                                      89*****************************76.54.....46888854144445555 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 9.3e-08
                                       HHHHHHTGGGHHHHHHHHH.HT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
                              KH_1  10 lvgriIGkgGsnIkeIree.tgakIkvpksedegsderevtisGspeavekAkelie 65 
                                       l griIGk G++ +eI+e+ +g+k+ v  +       ++v i G pe++  A+++ie
  gi|330506562|ref|YP_004382990.1| 100 LKGRIIGKDGRS-REIMERlSGTKVSVY-G-------KTVAILGYPEQIRVARAAIE 147
                                       679********7.66666526*****87.5.......58*****9999*****9996 PP

>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.8e-07   0.00079      21      81 .]      19      77 ..       2      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.8e-07
                              KH_8 21 kikkll.eekklklevdlkerslkvsTtekTrDPyiilkardlikLisrgvpleeakkvleD 81
                                      ++k+ + e+ k +le+d + +++ v       DP  +l+  dl+k i+rg + e+a  +l+D
  gi|330506562|ref|YP_004382990.1| 19 SMKHFIeEKTKTSLEIDSDTGTISVTSA---EDPLQVLRVMDLVKAIGRGFSPERALAILDD 77
                                      6677773455788999999999988655...6****************************99 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00012      0.56      29      59 ..       3      33 ..       1      45 [. 0.88
   2 !    6.1   0.4    0.0021       9.5      36      67 ..     101     131 ..      97     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                                      EEEEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                              KH_2 29 iviresqpgivIGkgGsnikkigkelrkdie 59
                                      i i e++ g+++G +Gs+   i+++ +  +e
  gi|330506562|ref|YP_004382990.1|  3 IKIPEERIGVLVGPNGSMKHFIEEKTKTSLE 33
                                      78889******************99999887 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0021
                                       HHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEE CS
                              KH_2  36 pgivIGkgGsnikkigkelrkdieklegkkVk 67 
                                       +g++IGk G+  + ++   + ++  + gk V 
  gi|330506562|ref|YP_004382990.1| 101 KGRIIGKDGRSREIMERLSGTKVS-VYGKTVA 131
                                       8*********99999999999885.7777765 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.084   3.8e+02      18      35 ..       9      26 ..       5      35 .. 0.83
   2 ?    8.3   0.1   0.00055       2.5      19      44 ..     101     125 ..      93     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.084
                              KH_5 18 pvGaivgkkGsrikavss 35
                                       +G +vg +Gs  + +++
  gi|330506562|ref|YP_004382990.1|  9 RIGVLVGPNGSMKHFIEE 26
                                      5999******98777666 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00055
                              KH_5  19 vGaivgkkGsrikavsseLkgekidv 44 
                                        G i+gk G r++++++ L+g+k+ v
  gi|330506562|ref|YP_004382990.1| 101 KGRIIGKDG-RSREIMERLSGTKVSV 125
                                       599*****9.68************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1311.70
//
Query:       gi|330506563|ref|YP_004382991.1|  [L=266]
Description: kinase RIO1 family protein [Methanosaeta concilii GP6]
Scores for complete 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-61  205.7   0.0    6.4e-61  205.2   0.0    1.1  1  RIO1      RIO1 family
    0.00011   21.6   0.0    0.00017   21.1   0.0    1.3  1  Pkinase   Protein kinase domain
     0.0012   18.9   0.0     0.0036   17.3   0.0    1.7  2  APH       Phosphotransferase enzyme family
     0.0019   17.6   0.0      0.015   14.6   0.0    2.0  1  Kdo       Lipopolysaccharide kinase (Kdo/WaaP) family
  ------ inclusion threshold ------
      0.015   15.4   0.3      0.052   13.6   0.3    2.0  1  UvsW      ATP-dependant DNA helicase UvsW
       0.08   11.8   0.1       0.14   11.0   0.1    1.4  1  DUF759    Borrelia burgdorferi protein of unknown function (D


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.2   0.0   2.1e-64   6.4e-61       2     180 ..      66     242 ..      65     249 .. 0.95

  Alignments for each domain:
  == domain 1  score: 205.2 bits;  conditional E-value: 2.1e-64
                                       EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEE CS
                              RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpiel 78 
                                       ++ a     +e+a+Kiy++st++F+ ++ y +g++rf +   k  +r++v +w++kE+rnL+r+ee gv+vP+pi++
  gi|330506563|ref|YP_004382991.1|  66 IFRALV-GSRELALKIYRISTSNFNVMQDYLHGDPRFGSV--KGTKRAIVAAWTRKEYRNLMRAEEVGVRVPHPITM 139
                                       666655.4457*************************9966..9********************************** PP

                                       ETTEEEEE--EETTEEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEE CS
                              RIO1  79 krhvlvmefigedgvaapklkdve.eeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQave 154
                                       k+++lvm++ig+ ++ ap lkdve +++eae++y++++e++  l ++aglvHaDLSe+N+l+d++++viID++Q+v+
  gi|330506563|ref|YP_004382991.1| 140 KENILVMDLIGKGDYVAPPLKDVElDSAEAEQIYQKIVEYISLLCNQAGLVHADLSEFNILYDDGEPVIIDMGQSVT 216
                                       ************************779************************************************** PP

                                       TTSTTHHHHHHHHHHHHHHHHHTTC- CS
                              RIO1 155 ldhpnalefLerDveniikfFrrkgv 180
                                       ldhp+a++fLerD++ni+++F++k+ 
  gi|330506563|ref|YP_004382991.1| 217 LDHPMARKFLERDISNIVHYFQKKYS 242
                                       ***********************975 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   5.7e-08   0.00017      71     150 ..     140     219 ..     118     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.7e-08
                                       SEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-SGGGEEEETTTEEEE-SGTTSE CS
                           Pkinase  71 delylvleyveggeladllerkgslseeeakkiakqilegleylH.skgiiHrDlKpeNiLidekgelKitDFGlak 146
                                       +e +lv++++ +g++     +++ l+++ea++i ++i+e ++ l  ++g++H Dl   NiL+d +ge  i+D G + 
  gi|330506563|ref|YP_004382991.1| 140 KENILVMDLIGKGDYVAPPLKDVELDSAEAEQIYQKIVEYISLLCnQAGLVHADLSEFNILYD-DGEPVIIDMGQSV 215
                                       556789999999985555557899******************9875788**************.**********998 PP

                                       ESSS CS
                           Pkinase 147 eles 150
                                        l++
  gi|330506563|ref|YP_004382991.1| 216 TLDH 219
                                       8766 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.41   1.2e+03      37      59 ..     116     138 ..      65     180 .. 0.77
   2 !   17.3   0.0   1.2e-06    0.0036     153     196 ..     176     214 ..     148     222 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHTT-B--B-CT CS
                               APH  37 irrevallrlLakagvpvPevla 59 
                                       +r+e++ l   ++ gv+vP ++ 
  gi|330506563|ref|YP_004382991.1| 116 TRKEYRNLMRAEEVGVRVPHPIT 138
                                       56777777777777778887776 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.2e-06
                                       HHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                               APH 153 laalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                                       + +   ll    +++l+H Dl+  N+l d d+ +v  +iD + +
  gi|330506563|ref|YP_004382991.1| 176 IVEYISLLC--NQAGLVHADLSEFNILYD-DGEPV--IIDMGQS 214
                                       333334444..699***************.88999..***8654 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.2e-06     0.015      59     191 ..     117     238 ..     108     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.2e-06
                               Kdo  59 vrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkavgrliakl. 134
                                       ++E+r+l r ee+gv+vp p+ ++++        +l++  + +   ++  l++  el+ +  +++++++   i+ l 
  gi|330506563|ref|YP_004382991.1| 117 RKEYRNLMRAEEVGVRVPHPITMKEN--------ILVMDLIGKGDYVAPPLKD-VELDSAEAEQIYQKIVEYISLLc 184
                                       6899*****************98764........4555544444444445554.66899999999999999999886 PP

                               Kdo 135 hragvnHadlyaknillqqeeeeeaeiwliDldkarlrlr..adrwrekdLarLkrsfl 191
                                       ++ag+ Hadl   nil + +e      ++iD+ ++ +     a++  e+d+ ++  +f+
  gi|330506563|ref|YP_004382991.1| 185 NQAGLVHADLSEFNILYDDGE-----PVIIDMGQSVTLDHpmARKFLERDISNIVHYFQ 238
                                       89***************9997.....899999988776554567777777777776666 PP

>> UvsW  ATP-dependant DNA helicase UvsW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   1.8e-05     0.052      24      48 ..      17      41 ..       9      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                      ..S--TTHHHHHHHHHHHHHHHHHH CS
                              UvsW 24 lGaelkdtdDIrVRDAlrGKiaeld 48
                                      l + +kd dD+ V DA+  K++ +d
  gi|330506563|ref|YP_004382991.1| 17 LRTRIKDSDDLNVQDAVFDKRTLMD 41
                                      7799******************987 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 ?   11.0   0.1   4.6e-05      0.14      12      49 ..     216     252 ..     210     266 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.6e-05
                            DUF759  12 ildhaatkkaieqdiskmekylkpkksslgstkdivkn 49 
                                        ldh  ++k +e+dis++ +y++ kk s+gs+ +i   
  gi|330506563|ref|YP_004382991.1| 216 TLDHPMARKFLERDISNIVHYFQ-KKYSIGSSEEIYAR 252
                                       59*******************97.7899***9998644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1926.40
//
Query:       gi|330506564|ref|YP_004382992.1|  [L=56]
Description: translation initiation factor eIF-1A [Methanosaeta concilii GP6]
Scores for complete 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-13   48.5   1.9    6.7e-13   48.2   1.9    1.1  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   1.9   3.7e-17   6.7e-13      28      64 .]       1      37 [.       1      37 [. 0.98

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 3.7e-17
                                      EEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                            eIF-1a 28 laeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                      +a+ipgk++++iwi++Gd+V++ +++++ +k+++v+r
  gi|330506564|ref|YP_004382992.1|  1 MARIPGKMKKRIWIREGDVVIIIPWEFQNEKADVVWR 37
                                      69*********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 496.36
//
Query:       gi|330506565|ref|YP_004382993.1|  [L=259]
Description: di-trans,poly-cis-decaprenylcistransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-65  221.3   0.0    1.4e-65  221.0   0.0    1.0  1  Prenyltransf    Putative undecaprenyl diphosphate synthase
  ------ inclusion threshold ------
      0.065   13.9   0.2       0.13   12.9   0.2    1.5  1  Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
       0.38   10.3   1.6       0.75    9.3   1.6    1.5  1  UBM             Ubiquitin binding region


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 !  221.0   0.0   2.3e-69   1.4e-65       1     219 [.      33     255 ..      33     258 .. 0.90

  Alignments for each domain:
  == domain 1  score: 221.0 bits;  conditional E-value: 2.3e-69
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHHHHHHHHH.H CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellkeellkee.l 76 
                                       i DGNrR+A+++gl+++  Gh+ Gae+ +++ ++cle+gv+++t+YafSteNf+R+++e +++++l+k+++ + +  
  gi|330506565|ref|YP_004382993.1|  33 IQDGNRRYARQKGLAKTL-GHSLGAETSERVSDWCLEVGVRHLTLYAFSTENFSREDSEKRYIFDLIKKKFNELRnS 108
                                       78***********66655.************************************************9665543325 PP

                                       HHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHS CS
                      Prenyltransf  77 kellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeid 152
                                       k+++ ++vrvr+iG+le+lp+d++e+++ +eeatk+ +k + ln+a++Yg+++e+v+a+r+l++ ++e + + +++d
  gi|330506565|ref|YP_004382993.1| 109 KKIHFNRVRVRAIGRLEMLPDDLQEEIRLTEEATKDYKK-MYLNVALAYGGQRELVDAARSLAHLVEEGRIRsKDLD 184
                                       799999*****************************5555.**********************555544444325678 PP

                                       HHHHHCTSTT..T..SSS-SEEEEESS--S-TTSSTTTTTT-E..EEEESSSGGG--HHHHHHHHHHHHHC CS
                      Prenyltransf 153 eetlekhlytaka..lpdpDlliRtsGeeRlSnFllwqlayse..lyfldvlWPdfskedllealleyqkr 219
                                       e+ +++hly ++   +p++Dl+iRt+G+ R SnFl wq+  +e   yf+  +WP+f+k d+l+a+++ q+r
  gi|330506565|ref|YP_004382993.1| 185 ETIIAQHLYPQDGisVPKVDLIIRTAGDFRTSNFLPWQANGNEcaAYFCAPFWPEFRKIDFLRAIRTAQTR 255
                                       99*******8777889**********************99999999*******************988776 PP

>> Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   2.2e-05      0.13      25      90 ..     119     187 ..      99     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                    Mg_chelatase_C  25 e...naelsgeelrevceldeeaeelleeaierlglsaRaydrilkvArTiADLegseeieeehlaeAl 90 
                                       +     e+ +++l+e ++l+eea++  ++++ +  l   +   ++  Ar++A L ++ +i++++l e +
  gi|330506565|ref|YP_004382993.1| 119 RaigRLEMLPDDLQEEIRLTEEATKDYKKMYLNVALAYGGQRELVDAARSLAHLVEEGRIRSKDLDETI 187
                                       24566799999******************************************************9976 PP

>> UBM  Ubiquitin binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.6   0.00013      0.75      14      30 ..     124     140 ..     124     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00013
                               UBM  14 LaaLPpdLReEVLaqqd 30 
                                       L++LP+dL+eE+ ++++
  gi|330506565|ref|YP_004382993.1| 124 LEMLPDDLQEEIRLTEE 140
                                       89*********977765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); 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 0.33s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1383.47
//
Query:       gi|330506566|ref|YP_004382994.1|  [L=267]
Description: 5'/3'-nucleotidase SurE [Methanosaeta concilii GP6]
Scores for complete 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  180.6   0.2    3.3e-53  180.4   0.2    1.0  1  SurE      Survival protein SurE


Domain annotation for each model (and alignments):
>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.4   0.2   1.8e-57   3.3e-53       1     193 [.      10     204 ..      10     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: 180.4 bits;  conditional E-value: 1.8e-57
                                       EEEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHH CS
                              SurE   1 iLltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvkla 77 
                                       iL++NDDG+ a+g++a +++++  g ev+v+aP+ ++Sg+g+++++ eplr+ +++  ++ ++yav+GtP+d v ++
  gi|330506566|ref|YP_004382994.1|  10 ILVSNDDGVYASGLEAAAKSVRGLG-EVTVAAPSGQKSGVGRSISVFEPLRFAEVNL-NGFKAYAVTGTPVDSVIIG 84 
                                       8*********************888.*************************985544.8****************** PP

                                       HHTTTTTS.SSEEEEEEEES---GGGG.GG-HHHHHHHHHHHTTSEEEEEEEESSS.....SS-SSS---HHHHHHH CS
                              SurE  78 leellkekkpdlVvSGiNhGaNlgtdv.lySGTvgAaleaalegipaiAvSlaskk.....eeekkeedtfeaaakv 148
                                       + ++lke  pdlV+SGiN G+N++td+ ++SGT+gAaleaa  gipaiA S++  +     + ++  ++ f+ aa +
  gi|330506566|ref|YP_004382994.1|  85 IFAILKE-MPDLVISGINVGENISTDTvTTSGTIGAALEAASYGIPAIAASIQAVDqgdkfDMHHGAKHSFDVAALF 160
                                       *****86.6******************9************************998899999666678888******* PP

                                       HHHHHTTETTS-...SS-EEEEEEESS.GCG-SEEEE-B--CCSC CS
                              SurE 149 aaklveklieklllekvellnvNvPeleeeeikgvkvtrlgrrry 193
                                       +++++++++e+ l e v+lln+NvP   +ee + +kvtrl+++ +
  gi|330506566|ref|YP_004382994.1| 161 LRRVATRVLEHGLPEGVDLLNLNVPVGASEETE-IKVTRLAKKIF 204
                                       *************************54455544.77***998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2004.67
//
Query:       gi|330506567|ref|YP_004382995.1|  [L=188]
Description: imidazoleglycerol-phosphate dehydratase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-40  136.8   0.0    8.7e-40  136.3   0.0    1.2  1  IGPD      Imidazoleglycerol-phosphate dehydratase


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.3   0.0   4.9e-44   8.7e-40       2     143 ..      34     169 ..      33     170 .. 0.97

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 4.9e-44
                                       ...HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEEE CS
                              IGPD   2 gigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaevald 78 
                                       g gfldhmL +la+ +++dl  + +  l+       + +g a+G al++algd++gi R+gsa +pmDe+la vald
  gi|330506567|ref|YP_004382995.1|  34 GSGFLDHMLLALARTANIDLVAESEEGLW-----RAQTLGRAIGLALDDALGDRSGICRYGSASVPMDESLADVALD 105
                                       789**********************9999.....4669*************************************** PP

                                       --SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHH CS
                              IGPD  79 lsgrpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafara 143
                                       + grpyl++++e++ e+ig++++ l+e f+e l +aag+t+h++   gen+hh++e++fKa++ a
  gi|330506567|ref|YP_004382995.1| 106 FRGRPYLIVSGEFRGERIGDFEAMLLEPFLEELFNAAGMTVHIRFY-GENDHHKMECIFKALGLA 169
                                       ********************************************77.****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1405.12
//
Query:       gi|330506568|ref|YP_004382996.1|  [L=241]
Description: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-71  239.8   2.2    2.8e-71  239.6   2.2    1.0  1  His_biosynth    Histidine biosynthesis protein
    7.6e-09   35.1   0.4    0.00042   19.5   0.0    2.1  2  Dus             Dihydrouridine synthase (Dus)
    1.7e-06   27.4   1.1    0.00026   20.3   0.1    2.1  2  DHO_dh          Dihydroorotate dehydrogenase
    2.9e-06   26.9   7.0    0.00026   20.5   2.1    2.1  2  NMO             Nitronate monooxygenase
    6.8e-06   25.6   2.4    0.00075   18.9   0.1    2.2  2  ThiG            Thiazole biosynthesis protein ThiG
    1.5e-05   24.6   1.0    1.8e-05   24.3   0.1    1.5  2  PcrB            PcrB family
    3.6e-05   23.2   1.2      0.005   16.2   0.1    2.2  2  TMP-TENI        Thiamine monophosphate synthase
     0.0023   17.2   0.1       0.77    8.9   0.0    2.3  2  IGPS            Indole-3-glycerol phosphate synthase
     0.0032   16.9   0.8        1.7    8.0   0.1    2.2  2  G3P_antiterm    Glycerol-3-phosphate responsive antiterminato
  ------ inclusion threshold ------
      0.013   14.7   0.4       0.17   11.1   0.0    2.2  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
      0.039   12.9   5.8      0.083   11.9   2.6    1.9  2  IMPDH           IMP dehydrogenase / GMP reductase domain
      0.074   12.7   1.2       0.19   11.3   0.3    2.0  3  DeoC            DeoC/LacD family aldolase
       0.11   11.9   2.3        4.4    6.6   0.1    2.3  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
       0.36    9.8   7.6       0.93    8.4   0.5    2.1  2  FMN_dh          FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.6   2.2   2.2e-74   2.8e-71       3     228 ..       6     230 ..       4     231 .. 0.99

  Alignments for each domain:
  == domain 1  score: 239.6 bits;  conditional E-value: 2.2e-74
                                       EEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEE CS
                      His_biosynth   3 ipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvG 79 
                                       +pa+Dl+ Gk+V+lv G+  +e +  ++p+++a+r+ +egad lh++Dld+a +g++an +++++i++e+++ +qvG
  gi|330506568|ref|YP_004382996.1|   6 FPAVDLRGGKCVQLVGGVPGTEVVALDNPLAQAERWIDEGADHLHIIDLDGAIQGKRANASILAQIVKELDVYIQVG 82 
                                       6**************************************************************************** PP

                                       SSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHH CS
                      His_biosynth  80 GGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakkl 156
                                       GGIrs e+++++l++g+d+vi+gtaa+k+p++i +lae++g+++i+va+D++rg +v+++gw+++ g  a+el + +
  gi|330506568|ref|YP_004382996.1|  83 GGIRSEEEARDVLRLGVDRVILGTAALKDPDMIAQLAEEHGRERIMVALDVKRG-DVTTEGWQKTLGKRAMELGRLF 158
                                       ******************************************************.********************** PP

                                       HHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                      His_biosynth 157 eelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegel 228
                                       e++gag+il+t+id +G + G+d++ t+el +a++ipv+a+GGv+s++d+ +l+++g++++++g+a+y+g+l
  gi|330506568|ref|YP_004382996.1| 159 EDKGAGSILFTNIDVEGRERGIDIQPTRELVAALRIPVVAAGGVTSIDDVLALRDAGAAGAVAGTAIYTGKL 230
                                       *********************************************************************997 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.3e-07   0.00042     169     226 ..      62     119 ..      56     136 .. 0.86
   2 !   13.8   0.1   1.7e-05     0.022     140     216 ..     151     225 ..     138     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.3e-07
                                       G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.H CS
                               Dus 169 tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.s 226
                                       +a+ +  +++ +++ + + + G+I++ e+a+++l+  G+d v+ g +al++P ++a+  
  gi|330506568|ref|YP_004382996.1|  62 RANASILAQIVKELDVYIQVGGGIRSEEEARDVLRL-GVDRVILGTAALKDPDMIAQlA 119
                                       88889999**************************99.******************9532 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHH CS
                               Dus 140 alelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrga 216
                                       a+el++  e++Ga  + +      +++e  +d++  +e+  a++ipv+a G++++++d+ a  +  Ga g ++g + 
  gi|330506568|ref|YP_004382996.1| 151 AMELGRLFEDKGAGSI-LFTNIDVEGRERGIDIQPTRELVAALRIPVVAAGGVTSIDDVLALRDA-GAAGAVAGTAI 225
                                       5666666666666654.44556778889999****************************998777.99999999776 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0044       5.6     233     290 ..      67     121 ..      55     125 .. 0.81
   2 !   20.3   0.1     2e-07   0.00026     232     290 ..     183     238 ..     177     241 .] 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0044
                                       HHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHH CS
                            DHO_dh 233 virelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikke 290
                                       ++ ++ k+l+  + i   GGi s e a + ++ G   v ++ta   ++p ++ ++ +e
  gi|330506568|ref|YP_004382996.1|  67 ILAQIVKELD--VYIQVGGGIRSEEEARDVLRLGVDRVILGTAA-LKDPDMIAQLAEE 121
                                       5566666666..6666789************************9.7778877777665 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 2e-07
                                       HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHH CS
                            DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikke 290
                                       +  rel + l+  ip+++ GG++s +D+l    aGA+    +ta+ ++g  +++   + 
  gi|330506568|ref|YP_004382996.1| 183 QPTRELVAALR--IPVVAAGGVTSIDDVLALRDAGAAGAVAGTAI-YTGKLSVSATLQA 238
                                       55677777777..*************************999**99.9999888776665 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.2   0.00054      0.69     171     226 ..      59     109 ..      35     130 .. 0.85
   2 !   20.5   2.1     2e-07   0.00026     188     225 ..     188     225 ..     175     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00054
                               NMO 171 qGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfL 226
                                       qG     ++   ++++q+++ +d+ +   GGi  +++   +L+lG   v +gt+ L
  gi|330506568|ref|YP_004382996.1|  59 QG-----KRANASILAQIVKELDVYIQVGGGIRSEEEARDVLRLGVDRVILGTAAL 109
                                       44.....2346799***************************************987 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2e-07
                               NMO 188 vldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                        + a+ iPv+AaGG+    +v a   +GA+g+  gt+ 
  gi|330506568|ref|YP_004382996.1| 188 LVAALRIPVVAAGGVTSIDDVLALRDAGAAGAVAGTAI 225
                                       567899******************************96 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   5.9e-07   0.00075     158     214 ..      58     115 ..      31     139 .. 0.83
   2 !    6.9   0.4    0.0028       3.5     156     210 ..     175     228 ..     150     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.9e-07
                                       ----.S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHH CS
                              ThiG 158 glGl.lnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpv 214
                                        +G  +n+  l  i++e++v + v  Gi+s ++a  ++ lG+d v+l ta  +  d +
  gi|330506568|ref|YP_004382996.1|  58 IQGKrANASILAQIVKELDVYIQVGGGIRSEEEARDVLRLGVDRVILGTAALKDPDMI 115
                                       4554146788999************************************976555544 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0028
                                       TS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTS CS
                              ThiG 156 GsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaea 210
                                       G  +G+  +   + +++ +++Pv+   G+ s  d+ +  + Ga + +  ta+ + 
  gi|330506568|ref|YP_004382996.1| 175 GRERGIDIQ-PTRELVAALRIPVVAAGGVTSIDDVLALRDAGAAGAVAGTAIYTG 228
                                       556666544.346788999********************************9765 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   1.4e-08   1.8e-05     134     221 ..      29     117 ..      15     122 .. 0.76
   2 ?   -2.2   0.1       1.8   2.4e+03     183     213 ..     196     227 ..     181     237 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.4e-08
                                       B-TTHHHHHHHHHHHHHHTT-SEEEEE-..TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE CS
                              PcrB 134 vdlnkediaayallaakllglrliYlEa..sGaledveevialkkklekarlivGGGirsaEkAkevvea.ADvivv 207
                                       v l+ + + a   + +    l +i l+    G   +   +++++k l+   + vGGGirs+E+A++v++   D ++ 
  gi|330506568|ref|YP_004382996.1|  29 VALDNPLAQAERWIDEGADHLHIIDLDGaiQGKRANASILAQIVKELD-VYIQVGGGIRSEEEARDVLRLgVDRVIL 104
                                       566666666666666666677777777546788888889999999997.5789*****************9****** PP

                                       -CHHHHHHHCHHHH CS
                              PcrB 208 Gnvveekderkida 221
                                       G++  ++++ +i +
  gi|330506568|ref|YP_004382996.1| 105 GTAALKDPD-MIAQ 117
                                       ***999994.5554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.8
                                       EEEESS--SHHHHHHHHCC.SSEEEE-CHHHH CS
                              PcrB 183 livGGGirsaEkAkevvea.ADvivvGnvvee 213
                                       ++  GG+ s ++      a A   v G++++ 
  gi|330506568|ref|YP_004382996.1| 196 VVAAGGVTSIDDVLALRDAgAAGAVAGTAIYT 227
                                       55678888887766666666666778888885 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.1    0.0052       6.6     141     177 ..      67     104 ..      36     108 .. 0.65
   2 !   16.2   0.1   3.9e-06     0.005     121     180 ..     162     224 ..     151     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0052
                          TMP-TENI 141 glkelaealeiPvvaiGGitl.envaevleagadgvav 177
                                        l++++++l + + + GGi+  e++ +vl+ g+d+v +
  gi|330506568|ref|YP_004382996.1|  67 ILAQIVKELDVYIQVGGGIRSeEEARDVLRLGVDRVIL 104
                                       55555566666666666665313455566666655543 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.9e-06
                          TMP-TENI 121 gvGpifpTdtKkdaeplg..leglkelaealeiPvvaiGGitl.envaevleagadgvavvsa 180
                                       g+G+i  T+   + + +g  ++  +el++al+iPvva GG+t  ++v ++++aga+g    +a
  gi|330506568|ref|YP_004382996.1| 162 GAGSILFTNIDVEGRERGidIQPTRELVAALRIPVVAAGGVTSiDDVLALRDAGAAGAVAGTA 224
                                       5778888888777755550055679****************8548999999****99876665 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0039       4.9     202     250 ..      68     117 ..      24     120 .. 0.85
   2 !    8.9   0.0    0.0006      0.77     194     242 ..     180     226 ..     176     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0039
                                       HCHCC-TT.SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHH CS
                              IGPS 202 Laklvpkd.vllvaeSGiktredveklkeegvnafLvGeslmrqedveka 250
                                       La+ v++  v +    Gi+++e+++++ + gv+ ++ G++ ++++d+ ++
  gi|330506568|ref|YP_004382996.1|  68 LAQIVKELdVYIQVGGGIRSEEEARDVLRLGVDRVILGTAALKDPDMIAQ 117
                                       66666643255556689***********************9999987655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0006
                                       E-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHH CS
                              IGPS 194 vdlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslm 242
                                       +d++ t+eL++ ++  + +va  G+++ +dv +l+++g+ +   G+++ 
  gi|330506568|ref|YP_004382996.1| 180 IDIQPTRELVAALR--IPVVAAGGVTSIDDVLALRDAGAAGAVAGTAIY 226
                                       79999999999998..99***************************9986 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 !    8.0   0.1    0.0014       1.7     129     169 ..      66     106 ..      62     109 .. 0.89
   2 !    7.4   0.1    0.0021       2.7     132     165 ..     186     219 ..     179     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0014
                                       HHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE-- CS
                      G3P_antiterm 129 kvikeikkelkipiiaGGLietkedveealkaGaiavstsn 169
                                       +++++i kel++ i  GG i+++e+ +++l+ G++ v  ++
  gi|330506568|ref|YP_004382996.1|  66 SILAQIVKELDVYIQVGGGIRSEEEARDVLRLGVDRVILGT 106
                                       688999****************************9997665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0021
                                       CTSTTS...EEEEESS--SHHHHHHHCTT.SSEE CS
                      G3P_antiterm 132 keikkelkipiiaGGLietkedveealkaGaiav 165
                                       +e+  +l+ip++a+G +++ +dv ++ +aGa + 
  gi|330506568|ref|YP_004382996.1| 186 RELVAALRIPVVAAGGVTSIDDVLALRDAGAAGA 219
                                       6788899***********************9865 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00013      0.17     138     183 ..      70     116 ..      43     123 .. 0.78
   2 ?    1.8   0.1     0.091   1.2e+02     132     177 ..     180     226 ..     163     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                       HHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HH.HH-HHHHH CS
                              NanE 138 kalseaglkviaeGrintPekakkaieiGvdavvvGsa.itrleeia 183
                                       + ++e ++ + + G i + e+a++++++Gvd v++G+a +  ++ ia
  gi|330506568|ref|YP_004382996.1|  70 QIVKELDVYIQVGGGIRSEEEARDVLRLGVDRVILGTAaLKDPDMIA 116
                                       3345567889999***********************87144555555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.091
                                       --HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SEEEE-HHHH CS
                              NanE 132 pDfalvkalsea.glkviaeGrintPekakkaieiGvdavvvGsait 177
                                        D++  ++l++a  + v+a G + + +      + G++  v G+ai 
  gi|330506568|ref|YP_004382996.1| 180 IDIQPTRELVAAlRIPVVAAGGVTSIDDVLALRDAGAAGAVAGTAIY 226
                                       5666677777663688999999999999999999****999999984 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3     0.001       1.3     106     173 ..      35     105 ..      23     109 .. 0.62
   2 ?   11.9   2.6   6.5e-05     0.083     105     237 ..      87     223 ..      81     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.001
                                       HHHHHHHHHTT-SEEEE...E-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE- CS
                                       xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 106 lervkalveagvdvlvv...dsahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvG 173
                                       l+++++ +++g+d l +   d a   ++   + +++i k+++    ++G + ++e a+++++ g+d v  G
  gi|330506568|ref|YP_004382996.1|  35 LAQAERWIDEGADHLHIidlDGAIQGKRANASILAQIVKELDVYIQVGGGIRSEEEARDVLRLGVDRVILG 105
                                       56666667777775543111455444455556666666666444457888888888888888888877666 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.5e-05
                                       HHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHH..HHTTT.SEEEEEEE-SHHHHHHHHHTT-SEEEE..-SS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                             IMPDH 105 alervkalveagvdvlvvdsahghsekvleavkeik..kkvee.veviaGnvataegakaLieagadavkv..GiGp 176
                                       ++e+++ +++ gvd +++ +a  +   ++ +++e +  +++   ++v  G+v+t+   k+L +   +  +     G+
  gi|330506568|ref|YP_004382996.1|  87 SEEEARDVLRLGVDRVILGTAALKDPDMIAQLAEEHgrERIMVaLDVKRGDVTTEGWQKTLGKRAMELGRLfeDKGA 163
                                       5788999999************99999999887654114444348999******999999999888877763368** PP

                                       STTBHHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 177 GsiCttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGs 237
                                       Gsi  t +    G+ +   +  + e ++   +pv+a GG+++  d+     aGa   + G 
  gi|330506568|ref|YP_004382996.1| 164 GSILFTNI-DVEGRERGIDIQPTRELVAALRIPVVAAGGVTSIDDVLALRDAGAAGAVAGT 223
                                       ******86.5679999**************************9999866667777766665 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.5   1.9e+03      82      99 ..      34      51 ..      17      76 .. 0.75
   2 ?   -1.9   0.0       1.7   2.1e+03     182     216 ..      63      97 ..      55     111 .. 0.70
   3 ?   11.3   0.3   0.00015      0.19     185     233 ..     183     226 ..     173     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
                                      TTCHHHHHHHTT-SEEEE CS
                              DeoC 82 evasveeakalGAdavkv 99
                                      ++a++e+ +  GAd + +
  gi|330506568|ref|YP_004382996.1| 34 PLAQAERWIDEGADHLHI 51
                                      678999999999998766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHCHSSTEEEEETTS.SHHHHHHHHHH CS
                              DeoC 182 edaevfkdvikaapvpgvvlsGGv.seedfletved 216
                                         a +  + +k+ +v  + + GG+ see+ +++++ 
  gi|330506568|ref|YP_004382996.1|  63 ANASILAQIVKELDVY-IQVGGGIrSEEEARDVLRL 97 
                                       5566666777766665.8899999888887777765 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00015
                                       HHHHHHHHCHSSTEEEEETTSSHHHHHHHHHHHHH..HHTHCEEEESHHHH CS
                              DeoC 185 evfkdvikaapvpgvvlsGGvseedfletvedAvk..eagasGvlsGRaif 233
                                       +  +++++a ++p vv +GGv        ++d ++  +aga+G+++G ai+
  gi|330506568|ref|YP_004382996.1| 183 QPTRELVAALRIP-VVAAGGV------TSIDDVLAlrDAGAAGAVAGTAIY 226
                                       5678999******.*******......6677666666999*******9998 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 ?    6.6   0.1    0.0034       4.4     163     196 ..      73     107 ..      61     109 .. 0.82
   2 ?    4.9   0.2     0.012        15     158     198 .]     187     226 ..     180     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0034
                                       HT---EEEEESS--T.TTCHHHHHHT--EEEESHH CS
                    Ribul_P_3_epim 163 keldlkievDGGvkl.dnieqiaeagadvlVagsa 196
                                       keld+ i+v GG++  + ++ + + g+d ++ g+a
  gi|330506568|ref|YP_004382996.1|  73 KELDVYIQVGGGIRSeEEARDVLRLGVDRVILGTA 107
                                       3699*********86267999***********998 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.012
                                       HHHHHHT---EEEEESS--.TTTCHHHHHHT--EEEESHHHH CS
                    Ribul_P_3_epim 158 klidekeldlkievDGGvk.ldnieqiaeagadvlVagsavf 198
                                       +l+++  l + + + GGv+  d + ++ +aga   Vag+a++
  gi|330506568|ref|YP_004382996.1| 187 ELVAA--LRIPVVAAGGVTsIDDVLALRDAGAAGAVAGTAIY 226
                                       55554..6677888999973699*****************98 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5   0.00073      0.93     248     304 ..      56     109 ..      35     131 .. 0.81
   2 ?    5.3   1.4    0.0068       8.7     263     306 ..     187     228 ..     174     241 .] 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00073
                                       GTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHH CS
                            FMN_dh 248 GRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpfl 304
                                       G  + g  a  ++L +iv++++  + + v gGir+ + +   l lG d v+lG ++l
  gi|330506568|ref|YP_004382996.1|  56 G-AIQGKRANASILAQIVKELD--VYIQVGGGIRSEEEARDVLRLGVDRVILGTAAL 109
                                       4.4667788899999**99997..99**************************98765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0068
                                       HHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHH CS
                            FMN_dh 263 eiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyg 306
                                       e+v+a+  ri+v++ gG+++  Dvl     GA + + G ++  g
  gi|330506568|ref|YP_004382996.1| 187 ELVAAL--RIPVVAAGGVTSIDDVLALRDAGAAGAVAGTAIYTG 228
                                       455555..6*************************9999888555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1654.04
//
Query:       gi|330506569|ref|YP_004382997.1|  [L=231]
Description: phage shock protein A [Methanosaeta concilii GP6]
Scores for complete 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   83.6  32.0    1.6e-23   83.4  32.0    1.0  1  PspA_IM30      PspA/IM30 family
      0.003   17.7   7.7      0.003   17.7   7.7    2.4  2  COG5           Golgi transport complex subunit 5
     0.0074   16.3   4.8     0.0074   16.3   4.8    2.7  2  Baculo_PEP_C   Baculovirus polyhedron envelope protein, PEP, 
  ------ inclusion threshold ------
      0.012   15.9   5.9      0.012   15.9   5.9    3.2  3  DUF5082        Domain of unknown function (DUF5082)
      0.018   15.4  13.7       0.21   12.0   0.1    3.9  4  Flagellin_C    Bacterial flagellin C-terminal helical region
       0.02   15.0  20.1        0.1   12.7   2.0    3.1  3  GCN5L1         GCN5-like protein 1 (GCN5L1)
      0.067   13.2  17.4       0.23   11.5   5.0    3.2  4  DUF1664        Protein of unknown function (DUF1664)
       0.24   11.4   6.0       0.15   12.1   0.6    2.7  3  DUF1910        Domain of unknown function (DUF1910)
       0.25   10.9  26.1       0.91    9.0   4.7    3.0  2  Filament       Intermediate filament protein
       0.49    9.2  26.3      0.065   12.1  19.6    2.0  2  Spc7           Spc7 kinetochore protein
       0.58    9.1   9.4        2.7    7.0   9.2    2.1  1  DUF1501        Protein of unknown function (DUF1501)
       0.96    8.7  22.4          2    7.7  21.9    1.8  1  DUF4407        Domain of unknown function (DUF4407)
        1.3    9.7  17.7        3.8    8.2   2.8    3.1  3  YabA           Initiation control protein YabA
        1.5    8.7   9.8        2.9    7.9   2.7    2.8  3  Sec20          Sec20
        2.1    6.2  12.1        2.5    5.9  11.5    1.5  1  Prominin       Prominin
        2.9    5.7  16.0        5.6    4.8  11.2    2.0  2  V_ATPase_I     V-type ATPase 116kDa subunit family
        2.9    7.9  21.9          4    7.5  16.7    3.0  2  DUF1640        Protein of unknown function (DUF1640)
        4.7    7.1   9.4        4.3    7.2   4.7    2.5  2  EMP24_GP25L    emp24/gp25L/p24 family/GOLD


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 !   83.4  32.0   1.6e-26   1.6e-23       3     219 ..       4     229 ..       2     231 .] 0.93

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 1.6e-26
                         PspA_IM30   3 fkrllrllraniselldkaeDPekileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaALt 79 
                                       ++r++++++a++++ +  +eDP  +le   +   + l+++++ +a+v +++k+le + ++ +  + kl  +Ak+A +
  gi|330506569|ref|YP_004382997.1|   4 LERMSAVVQAKMNKIMNRIEDPREVLEVSYEKQLQLLQNVKRGVAEVTTSKKRLELQKAKLQMNIDKLDGQAKEAIS 80 
                                       89****************************999999***************************************** PP

                         PspA_IM30  80 kgeeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaakaqeavqkslg 156
                                       + +e+LAr+al++++ ++ q++ le + ++++ + ++l+++ ++l+tk+e++++kke++ka+  aa aq ++++s+ 
  gi|330506569|ref|YP_004382997.1|  81 ASREDLARKALESKALMQAQLNTLEGEINELNNQQQKLQAAETRLATKVEAFRTKKETIKAQYTAADAQVKITESVT 157
                                       ***************************************************************************** PP

                         PspA_IM30 157 kls..tesatdslerieeKieerearadaaaelae....saqd......ldakleaagiqkevseqvlarlkaeq 219
                                       ++s   ++   + +r eeK e+++ar+ a  el e    +  d       + +l+ ++++  v +++ arlkae 
  gi|330506569|ref|YP_004382997.1| 158 GISeeMADVGLAVQRAEEKTEDMKARSAALDELLEsgtlT--DysggdeIESELARVKAKNTV-DDEMARLKAEM 229
                                       ***55555566779*******************9776552..144677899999999999999.********986 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.74   7.4e+02      84     114 ..      11      41 ..       4      48 .. 0.70
   2 !   17.7   7.7     3e-06     0.003      25     105 ..      51     132 ..      38     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.74
                                       XXXXXXXXX-TTHHHHHHHHHHHHHHHHHHH CS
                              COG5  84 Lsasyerlkskvlepyeeaeklqsalkrlhq 114
                                       ++a ++++ + + +p e +e +++++ +l q
  gi|330506569|ref|YP_004382997.1|  11 VQAKMNKIMNRIEDPREVLEVSYEKQLQLLQ 41 
                                       5677788888888888888777666655554 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHH CS
                              COG5  25 ddteldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslss.vlselksslesLsasyerlkskvlepye 100
                                       ++++  l+ + ++l+  i++ld + ++ i+++ ++L  ++ +sk l +  l++l++++++L++  ++l+   ++  +
  gi|330506569|ref|YP_004382997.1|  51 TTSKKRLELQKAKLQMNIDKLDGQAKEAISASREDLARKALESKALMQaQLNTLEGEINELNNQQQKLQAAETRLAT 127
                                       567788999*******************************999999999*******************976444444 PP

                                       HHHHH CS
                              COG5 101 eaekl 105
                                       ++e  
  gi|330506569|ref|YP_004382997.1| 128 KVEAF 132
                                       44444 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 ?    2.9   1.2       0.1     1e+02      45      89 ..      35      81 ..       4      93 .. 0.61
   2 !   16.3   4.8   7.5e-06    0.0074      42     114 ..      96     169 ..      89     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.1
                      Baculo_PEP_C 45 tqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtn 89
                                      +qL+   +++k+ +ae++t   rl+ + ++L+  + +l  + ++++ +
  gi|330506569|ref|YP_004382997.1| 35 KQLQL-LQNVKRGVAEVTTskkRLELQKAKLQMNIDKLDGQAKEAISA 81
                                      44443.344666666666666677777777777777776555555554 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 7.5e-06
                      Baculo_PEP_C  42 aietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstLnnllqa 114
                                        ++ qLn+l+ ++++ l++++++l+++ t+L +++ a+    +t++ + t+ ++++  ++ svt+i + ++ +  a
  gi|330506569|ref|YP_004382997.1|  96 LMQAQLNTLEGEINE-LNNQQQKLQAAETRLATKVEAFRtkkETIKAQYTAADAQVK-ITESVTGISEEMADVGLA 169
                                       5799***********.778999****************999**************95.999*****9887766555 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.7     0.058        58       2      28 ..      51      77 ..      50      90 .. 0.70
   2 ?   15.9   5.9   1.2e-05     0.012       4      92 ..      93     183 ..      90     186 .. 0.84
   3 ?   -0.7   0.1       1.6   1.6e+03      31      46 ..     213     228 ..     203     231 .] 0.60

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.058
                           DUF5082  2 ktkisklqaqiaelrseiaaleekIer 28
                                      +t++++l+ q+a+l+ +i++l+ + ++
  gi|330506569|ref|YP_004382997.1| 51 TTSKKRLELQKAKLQMNIDKLDGQAKE 77
                                      577777888888888888877777554 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.2e-05
                           DUF5082   4 kisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGk.eennydgirs.nless 78 
                                       +++ +qaq   l++ei+ l+ + ++L++a t+l ++ e++ +kk+ ++ +    ++  +  e+ + ++++  ++  +
  gi|330506569|ref|YP_004382997.1|  93 SKALMQAQLNTLEGEINELNNQQQKLQAAETRLATKVEAFRTKKETIKAQYTAADAQVKItESVTGISEEMaDVGLA 169
                                       78889******************************************988888775554424444444444799*** PP

                           DUF5082  79 yqtyvdkldelida 92 
                                       +q+ ++k+++++++
  gi|330506569|ref|YP_004382997.1| 170 VQRAEEKTEDMKAR 183
                                       *******9998875 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.6
                           DUF5082  31 eaktklsdekeslkqk 46 
                                       +ak +++de ++lk++
  gi|330506569|ref|YP_004382997.1| 213 KAKNTVDDEMARLKAE 228
                                       4666666666666654 PP

>> Flagellin_C  Bacterial flagellin C-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.4      0.77   7.7e+02      16      62 ..      13      63 ..       6      68 .. 0.45
   2 ?    2.3   0.9      0.22   2.2e+02       8      43 ..      40      75 ..      34     102 .. 0.72
   3 ?    6.8   2.2    0.0088       8.8      23      47 ..     102     126 ..      85     146 .. 0.65
   4 ?   12.0   0.1   0.00021      0.21       3      40 ..     151     188 ..     149     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.77
                                      HHHHHHHHHHHHHHHHHH....HHHCHHHHHHCHHCCHHHHHHHHHHHHHH CS
                       Flagellin_C 16 selGavqnRlesaitnlk....aqsenlkaaesrledvDpaeestrvtklq 62
                                      +++  ++nR+e+  + l+    +q ++l++ ++   +v + +   +++k++
  gi|330506569|ref|YP_004382997.1| 13 AKMNKIMNRIEDPREVLEvsyeKQLQLLQNVKRGVAEVTTSKKRLELQKAK 63
                                      555555555555555443111133344444444444444444444444444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.22
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHH CS
                       Flagellin_C  8 itdldkvrselGavqnRlesaitnlkaqsenlkaae 43
                                      +++++   +e+ ++++Rle + ++l+  ++ l+ + 
  gi|330506569|ref|YP_004382997.1| 40 LQNVKRGVAEVTTSKKRLELQKAKLQMNIDKLDGQA 75
                                      566666667777777777777777777777666544 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0088
                                       HHHHHHHHHHHHHHCHHHHHHCHHC CS
                       Flagellin_C  23 nRlesaitnlkaqsenlkaaesrle 47 
                                       n le  i++l++q++ l+aae+rl 
  gi|330506569|ref|YP_004382997.1| 102 NTLEGEINELNNQQQKLQAAETRLA 126
                                       5566677777777777777777764 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH CS
                       Flagellin_C   3 ivdeaitdldkvrselGavqnRlesaitnlkaqsenlk 40 
                                       +++e +t+++++ +++G++ +R e+ ++ +ka s  l+
  gi|330506569|ref|YP_004382997.1| 151 KITESVTGISEEMADVGLAVQRAEEKTEDMKARSAALD 188
                                       68999***************************998876 PP

>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.0    0.0001       0.1      22      73 ..      27      78 ..      10      84 .. 0.83
   2 ?    8.7   8.0    0.0018       1.8      15      85 ..      82     151 ..      74     157 .. 0.81
   3 ?    0.9   0.1      0.48   4.8e+02      20      61 ..     173     214 ..     160     231 .] 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                            GCN5L1 22 eaiesaaaltealvdklnsgvaeayanqkklekeakalqanvakfakqtdqW 73
                                      e++e   + + +l++++++gvae+ + +k+le +  +lq n++k+  q+++ 
  gi|330506569|ref|YP_004382997.1| 27 EVLEVSYEKQLQLLQNVKRGVAEVTTSKKRLELQKAKLQMNIDKLDGQAKEA 78
                                      55666666777899*******************************9998875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0018
                            GCN5L1  15 eqekakkeaiesaaaltealvdklnsgvaeayanqkklekeakalqanvakfakqtdqWlalvesfnsalk 85 
                                       + e + ++a+ + +al +a +++l+ +++e+ ++q+kl +   +l+++v++f+ + +   a + + + ++k
  gi|330506569|ref|YP_004382997.1|  82 SREDLARKAL-ESKALMQAQLNTLEGEINELNNQQQKLQAAETRLATKVEAFRTKKETIKAQYTAADAQVK 151
                                       3445555555.5688999999********************************999988888887777766 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.48
                            GCN5L1  20 kkeaiesaaaltealvdklnsgvaeayanqkklekeakalqa 61 
                                        +e +e ++a + al + l+sg  + y+   ++e+e+ +++a
  gi|330506569|ref|YP_004382997.1| 173 AEEKTEDMKARSAALDELLESGTLTDYSGGDEIESELARVKA 214
                                       344444555555555555666666666666666655555444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   3.7     0.018        18      50     117 ..       4      75 ..       3      78 .. 0.81
   2 ?    6.3   3.6    0.0091       9.1      50     123 ..      50     114 ..      38     115 .. 0.47
   3 ?    9.7   4.2   0.00082      0.81      46     111 ..      86     151 ..      74     157 .. 0.65
   4 ?   11.5   5.0   0.00023      0.23      48     121 ..     109     181 ..      97     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.018
                           DUF1664  50 leqvseslaatkrhLssridr....vdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                       le++s+ ++a  +++++ri+     ++ + ++q ++ +++k+ v+ev    ++++ +  +++  + +l+++ 
  gi|330506569|ref|YP_004382997.1|   4 LERMSAVVQAKMNKIMNRIEDprevLEVSYEKQLQLLQNVKRGVAEVTTSKKRLELQKAKLQMNIDKLDGQA 75 
                                       678888888888899999975333377788899999999999999999999999999999999999999875 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0091
                           DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesv.keaveglesklerieek 123
                                       +++ ++ l+ +k +L+ +id++d +           ke +++ redl++   +++++ ++  ++le+++++++++
  gi|330506569|ref|YP_004382997.1|  50 VTTSKKRLELQKAKLQMNIDKLDGQA----------KEAISASREDLARKALESKALmQAQLNTLEGEINELNNQ 114
                                       33334455555555555555555554..........445555555555554444443133455555555555554 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00082
                           DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       ++++  + ++ ++a+ + L+ +i+++++++++ +++ + ++ +v++ r + ++i+ + ++ ++ v+
  gi|330506569|ref|YP_004382997.1|  86 LARKALESKALMQAQLNTLEGEINELNNQQQKLQAAETRLATKVEAFRTKKETIKAQYTAADAQVK 151
                                       444444445556666777777788888888888888888888888888887777777766666555 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00023
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       ++l++ +++l+a+  +L+ +++   +k +  k+  ++ +++v ++ e ++ i+e++  v  av+  e+k e+++
  gi|330506569|ref|YP_004382997.1| 109 NELNNQQQKLQAAETRLATKVEAFRTKKETIKAQYTAADAQV-KITESVTGISEEMADVGLAVQRAEEKTEDMK 181
                                       5788899999**************999999999999999998.5889999999999999999999999998886 PP

>> DUF1910  Domain of unknown function (DUF1910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.4   1.4e+03      19      42 ..      20      43 ..       8      72 .. 0.54
   2 ?   12.1   0.6   0.00015      0.15       1      85 [.      88     166 ..      88     191 .. 0.83
   3 ?    1.1   0.1      0.39   3.9e+02      59      70 ..     196     207 ..     169     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                           DUF1910 19 eriaklkekieelsedeeksiqae 42
                                      +ri++ +e +e + e++ + +q++
  gi|330506569|ref|YP_004382997.1| 20 NRIEDPREVLEVSYEKQLQLLQNV 43
                                      444444444444444444444433 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00015
                           DUF1910   1 RdpllseeyykesiefdkeriaklkekieelsedeeksiqaeikilklsifkykleliiakYSlGesieeleadyee 77 
                                       R +l s++  +++++  + +i++l+++ ++l+ +e++       ++k + f+ k e+i+a+Y++ +   ++++++  
  gi|330506569|ref|YP_004382997.1|  88 RKALESKALMQAQLNTLEGEINELNNQQQKLQAAETR------LATKVEAFRTKKETIKAQYTAADAQVKITESVTG 158
                                       6677777788888888888899999888888888888......45689****************9999999999888 PP

                           DUF1910  78 likeleel 85 
                                       + +e+ ++
  gi|330506569|ref|YP_004382997.1| 159 ISEEMADV 166
                                       88877766 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.39
                           DUF1910  59 iakYSlGesiee 70 
                                       ++ YS+G++ie+
  gi|330506569|ref|YP_004382997.1| 196 LTDYSGGDEIES 207
                                       678*****9985 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.7   0.00091      0.91      22      94 ..       3      78 ..       1      85 [. 0.84
   2 ?    4.6  14.9      0.02        20      34     127 ..      79     178 ..      73     231 .] 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00091
                                      XXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 22 aLEqenkeLeakieeleekksaevsklkelyekel...eelrkqldeltkerarlqleldnlreeledlrkkyeke 94
                                      +LE+  + ++ak+++  ++ +  ++ l+  yek+l   +++++ + e+t+ ++rl+l+  +l++++++l  + ++ 
  gi|330506569|ref|YP_004382997.1|  3 FLERMSAVVQAKMNKIMNRIEDPREVLEVSYEKQLqllQNVKRGVAEVTTSKKRLELQKAKLQMNIDKLDGQAKEA 78
                                      799999999******99998888888999999987222577899***********************998776665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.02
                                       XXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                          Filament  34 ieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalr. 109
                                       i++ +e   ++  + k+l +++l+ l  +++el++++++lq+   +l++++e +r+k e+  ++ ++++a++k    
  gi|330506569|ref|YP_004382997.1|  79 ISASREDLARKALESKALMQAQLNTLEGEINELNNQQQKLQAAETRLATKVEAFRTKKETIKAQYTAADAQVKITEs 155
                                       6677777788888999*******************************************998888888888776554 PP

                                       .....XXXXXXXXXXXXXXXXXX CS
                          Filament 110 .....kdldeatlarvdLekkve 127
                                             ++ +  la    e+k e
  gi|330506569|ref|YP_004382997.1| 156 vtgisEEMADVGLAVQRAEEKTE 178
                                       44444444444444444444444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  19.6   6.5e-05     0.065     137     257 ..      36     157 ..       6     163 .. 0.88
   2 ?    8.4  10.4   0.00087      0.87     144     275 ..     104     229 ..     103     231 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.5e-05
                              Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeeka.eleeeleklqeaaeelesidkeeLeelreelaelk 212
                                       + +L +++++ ++++++ k++Le q+++l+   ++l+ + + ++++  e+l ++a e +++ +++L++l  e++el+
  gi|330506569|ref|YP_004382997.1|  36 QLQLLQNVKRGVAEVTTSKKRLELQKAKLQMNIDKLDGQAKeAISASREDLARKALESKALMQAQLNTLEGEINELN 112
                                       55778888899999****************99999997654389*************9******************* PP

                              Spc7 213 aeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervl 257
                                       ++ +++++  ++l +++e+ ++k e++k+q++ + ++++  e+v+
  gi|330506569|ref|YP_004382997.1| 113 NQQQKLQAAETRLATKVEAFRTKKETIKAQYTAADAQVKITESVT 157
                                       ****99999999999999999999999999999999999888775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00087
                              Spc7 144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkk 220
                                       le ++++l++++++L++ e  l + +++++++k++++++++   ++++       e++  + ee+a++   +++ ++
  gi|330506569|ref|YP_004382997.1| 104 LEGEINELNNQQQKLQAAETRLATKVEAFRTKKETIKAQYTAADAQVKI-----TESVTGISEEMADVGLAVQRAEE 175
                                       5666777777777777777777777777777777777777777776665.....67788999999999999999999 PP

                              Spc7 221 elaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeev 275
                                       ++++++++ ++l+e +e+ +    +  +ei+ +e  + + k+  ++e  rlk+e+
  gi|330506569|ref|YP_004382997.1| 176 KTEDMKARSAALDELLESGTLTDYSGGDEIE-SELARVKAKNTVDDEMARLKAEM 229
                                       9999999999999999999988888888888.45555556777778888888876 PP

>> DUF1501  Protein of unknown function (DUF1501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   9.2    0.0027       2.7     130     225 ..       2      96 ..       1     195 [. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0027
                           DUF1501 130 Gflgralqgltlrssadpvldlsppagvteerqrrrldllkklnqehl.qrkndeeleariasyelafralmqseap 205
                                       Gfl r+  +++++  ++ +  +++p +v e++ +++l+ll+++++  +  ++++++le + a++++  +  + ++a+
  gi|330506569|ref|YP_004382997.1|   2 GFLERMSAVVQAK-MNKIMNRIEDPREVLEVSYEKQLQLLQNVKRGVAeVTTSKKRLELQKAKLQMNID-KLDGQAK 76 
                                       99****9999994.445689***************************999999999***********99.9****** PP

                           DUF1501 206 eafdlsdeteatreaygrda 225
                                       ea+  s+e+ a +++ +++ 
  gi|330506569|ref|YP_004382997.1|  77 EAISASREDLARKALESKAL 96 
                                       ********988777666655 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  21.9     0.002         2     115     256 ..      34     193 ..      25     231 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.002
                           DUF4407 115 eqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.......gtgttgvaGkgpa 184
                                       e+q +  ++ ++  a+ t+  ++le q a+lq +id+++ +++++  + ++ l  +        +++ +  +G+  +
  gi|330506569|ref|YP_004382997.1|  34 EKQLQLLQNVKRGVAEVTTSKKRLELQKAKLQMNIDKLDGQAKEAISASREDLARKAleskalmQAQLNTLEGEINE 110
                                       233333334444444599999***********************999999999998899999998899999999999 PP

                           DUF4407 185 akekkaqldaaqaelaelkakld...........atarlaalraelaeleaerakeraasqaaaaaddGllarleal 250
                                         + +++l+aa+++la+  +  +           a++++ +  +  +++ +e+a+   a q+a+++  ++ ar  al
  gi|330506569|ref|YP_004382997.1| 111 LNNQQQKLQAAETRLATKVEAFRtkketikaqytAADAQVKITESVTGISEEMADVGLAVQRAEEKTEDMKARSAAL 187
                                       999999999999999886666668999999999988889999999999999999999999***************** PP

                           DUF4407 251 drltke 256
                                       d+l ++
  gi|330506569|ref|YP_004382997.1| 188 DELLES 193
                                       *99875 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.8    0.0038       3.8      12      74 ..      28      87 ..      14      93 .. 0.78
   2 ?    5.3   6.7      0.03        30       7      53 ..      98     148 ..      87     195 .. 0.55
   3 ?    2.5   0.1      0.23   2.3e+02      12      53 ..     151     202 ..     145     230 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0038
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA 12 eleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLa 74
                                       le + e+ l+ l+++k+ +ae++   ++Lel++ kl+ +++   k + + k+++s ++e La
  gi|330506569|ref|YP_004382997.1| 28 VLEVSYEKQLQLLQNVKRGVAEVTTSKKRLELQKAKLQMNID---KLDGQAKEAISASREDLA 87
                                      578888899999***************************994...444555556666666665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.03
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....X CS
                              YabA   7 fdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl....e 53 
                                        ++l++le +++el+++ ++l+++ ++l  + +++++ +e+++ +     +
  gi|330506569|ref|YP_004382997.1|  98 QAQLNTLEGEINELNNQQQKLQAAETRLATKVEAFRTKKETIKAQYtaadA 148
                                       234444444444444444444444444444444444444444444433330 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........X CS
                              YabA  12 eleeqleelleeleelkeelaelleenaeLeleneklrerl..........e 53 
                                       +++e+++ ++ee++++  ++++  e+ +++++    l e+l           
  gi|330506569|ref|YP_004382997.1| 151 KITESVTGISEEMADVGLAVQRAEEKTEDMKARSAALDELLesgtltdysgG 202
                                       5667777888888888888888888888888888888888855555555441 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         4     4e+03      17      36 ..      57      76 ..      47      84 .. 0.58
   2 ?    7.9   2.7    0.0029       2.9       4      61 ..      84     141 ..      81     151 .. 0.87
   3 ?    4.9   0.2     0.025        25       5      41 ..     151     190 ..     147     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4
                             Sec20 17 lsqevqqSeenleeldastk 36
                                      l  +  + + n+++ld ++k
  gi|330506569|ref|YP_004382997.1| 57 LELQKAKLQMNIDKLDGQAK 76
                                      44444455566777766665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0029
                             Sec20   4 kqiTeslraisqllsqevqqSeenleeldastkslekleeeykqvedvlsrskklvkk 61 
                                       +++  + +++++l++++ +  e  ++el+++ ++l+++e  +    + +++ k+ +k 
  gi|330506569|ref|YP_004382997.1|  84 EDLARKALESKALMQAQLNTLEGEINELNNQQQKLQAAETRLATKVEAFRTKKETIKA 141
                                       677788899*********************************9999999999988875 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.025
                             Sec20   5 qiTeslraisqllsq...evqqSeenleeldastkslekl 41 
                                       +iTes+  is+ +++   +vq+ ee  e+++a +  l +l
  gi|330506569|ref|YP_004382997.1| 151 KITESVTGISEEMADvglAVQRAEEKTEDMKARSAALDEL 190
                                       79***********975557*************99999876 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  11.5    0.0025       2.5     604     702 ..      46     137 ..       4     166 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0025
                          Prominin 604 glskihsslyleqlckkltkvnletlaekleelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksv 680
                                       g+ ++ +s+   +l+k   ++n     +kl+  a+e     +  ++ l ++a + +a+ q +  +le ++++l+++ 
  gi|330506569|ref|YP_004382997.1|  46 GVAEVTTSKKRLELQKAKLQMN----IDKLDGQAKEAI---SASREDLARKALESKALMQAQLNTLEGEINELNNQQ 115
                                       3344444433334444433333....355555555553...357899999999999999999999999999999999 PP

                          Prominin 681 kkldeensdlqesikkllaave 702
                                       +kl++ ++ l+++++ + ++ e
  gi|330506569|ref|YP_004382997.1| 116 QKLQAAETRLATKVEAFRTKKE 137
                                       9999999999999888776644 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 ?    3.8   0.9     0.011        11     243     287 ..      10      54 ..       4      68 .. 0.81
   2 ?    4.8  11.2    0.0056       5.6      42     138 ..      64     163 ..      51     212 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.011
                        V_ATPase_I 243 ereeklkeveeriedlekvleqteealkevleeiakeleewklkv 287
                                         + k++++++ried ++vle + e++ ++l+++++ ++e+++  
  gi|330506569|ref|YP_004382997.1|  10 VVQAKMNKIMNRIEDPREVLEVSYEKQLQLLQNVKRGVAEVTTSK 54 
                                       568899****************************88777766554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0056
                        V_ATPase_I  42 leeeieklekavikeeea.eesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefle 117
                                       l+ +i+kl+ +  ++ +a  e+l+++  ++   ++++l++le e++eln++++kl++  ++l  + + +++ ke ++
  gi|330506569|ref|YP_004382997.1|  64 LQMNIDKLDGQAKEAISAsREDLARKALESKALMQAQLNTLEGEINELNNQQQKLQAAETRLATKVEAFRTKKETIK 140
                                       4444444444444444332345555555555667899**************************************99 PP

                        V_ATPase_I 118 ee.eeeeeeeeseeeeee..keee 138
                                       ++ ++ +++ + +e+  +  +ee 
  gi|330506569|ref|YP_004382997.1| 141 AQyTAADAQVKITES-VTgiSEEM 163
                                       884444444333333.33332222 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  16.7     0.004         4      58     154 ..      39     144 ..       3     159 .. 0.63
   2 ?    1.4   0.2      0.29   2.9e+02     127     147 ..     208     230 ..     159     231 .] 0.57

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.004
                           DUF1640  58 alselrkevqisersefaalrseteklqreleklkqkLreeidklkadirldlnleKgrireelakleakiqelnnk 134
                                        l++++  v   + s+ + l+ ++ klq +++kl+ + +e i+  ++d   +  + K+ ++++l+ le +i+elnn+
  gi|330506569|ref|YP_004382997.1|  39 LLQNVKRGVAEVTTSK-KRLELQKAKLQMNIDKLDGQAKEAISASREDLARKALESKALMQAQLNTLEGEINELNNQ 114
                                       4455555554444433.455677778888888888888888877777766666666666666666666666555444 PP

                           DUF1640 135 ..........idrevsalrteiEsvKldvi 154
                                                 + ++v+a rt+ E +K + +
  gi|330506569|ref|YP_004382997.1| 115 qqklqaaetrLATKVEAFRTKKETIKAQYT 144
                                       4444444444***********999998865 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.29
                           DUF1640 127 ki..qelnnkidrevsalrteiE 147
                                       ++   + +n +d e++ l++e++
  gi|330506569|ref|YP_004382997.1| 208 ELarVKAKNTVDDEMARLKAEMN 230
                                       22222335558888888888885 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.7    0.0043       4.3     111     150 ..      92     131 ..      12     144 .. 0.73
   2 ?    2.2   0.3      0.15   1.5e+02     104     150 ..     147     193 ..     132     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0043
                       EMP24_GP25L 111 eklet.leselkkleekldsikreqkylrereerlrdtnes 150
                                       e+ +  ++ +l++le  ++++ ++q+ l++ e+rl   +e 
  gi|330506569|ref|YP_004382997.1|  92 ES-KAlMQAQLNTLEGEINELNNQQQKLQAAETRLATKVEA 131
                                       22.22478899999999999999999999999999888876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                       EMP24_GP25L 104 ykdsakkekletleselkkleekldsikreqkylrereerlrdtnes 150
                                       +++++ +e+++ + +e+  +   ++  +++ + +++r + l +++es
  gi|330506569|ref|YP_004382997.1| 147 DAQVKITESVTGISEEMADVGLAVQRAEEKTEDMKARSAALDELLES 193
                                       34455578888888888888888888888888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2304  (0.128507); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.84u 0.29s 00:00:01.12 Elapsed: 00:00:00.57
# Mc/sec: 1220.77
//
Query:       gi|330506570|ref|YP_004382998.1|  [L=92]
Description: hypothetical protein MCON_0305 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.5   0.0      0.036   14.2   0.0    1.2  1  DUF4839   Domain of unknown function (DUF4839)


Domain annotation for each model (and alignments):
>> DUF4839  Domain of unknown function (DUF4839)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     2e-06     0.036      69      96 ..      10      37 ..       6      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-06
                           DUF4839 69 aFkfedvnvsdlnltgeeipdtlgegdn 96
                                      +F+f+d n+ dln  +++i+d +++gd+
  gi|330506570|ref|YP_004382998.1| 10 QFRFDDSNLGDLNKIDNQIVDHVKNGDQ 37
                                      7************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.58
# Mc/sec: 479.35
//
Query:       gi|330506571|ref|YP_004382999.1|  [L=329]
Description: cation diffusion facilitator family transporter [Methanosaeta concilii GP6]
Scores for complete 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-45  154.0  14.7    4.8e-45  153.7  14.7    1.1  1  Cation_efflux  Cation efflux family
    0.00067   19.7   1.8     0.0012   18.9   1.8    1.4  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
       0.73   10.0   7.5       0.19   11.9   0.3    2.3  2  DUF3180        Protein of unknown function (DUF3180)


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 !  153.7  14.7   8.1e-49   4.8e-45       2     199 .]      14     214 ..      13     214 .. 0.96

  Alignments for each domain:
  == domain 1  score: 153.7 bits;  conditional E-value: 8.1e-49
                     Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsglll 78 
                                       +l++l++ ++++ve i+ ++t+Slall+da h ++d+++ ll++la++ls +p+der+++G++r+ev+++l +gl+l
  gi|330506571|ref|YP_004382999.1|  14 LLAILLTCTILIVEAIGSWWTGSLALLSDAAHVFLDIFAILLSWLAIRLSTMPADERYSYGFHRFEVIASLANGLTL 90 
                                       578999999******************************************************************** PP

                     Cation_efflux  79 lglavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrkl........rsaalkaaalhvlgDa 147
                                        ++ + +l+ea+++l+   ++ +    +l++a ++l+vnl++++il ++  ++        ++ ++++a lhvlgDa
  gi|330506571|ref|YP_004382999.1|  91 GFVSLGILVEAYKRLL--VPAPVKGLDLLLLATFGLIVNLIVAYILGGGHLHRhdhgphhsEDLNIRSARLHVLGDA 165
                                       ****************..889999999999****************99888779*********************** PP

                     Cation_efflux 148 ltslgvlvsalvillfnlksgplaDpvaslligliilysalkllkeslseLl 199
                                       ++slgv+v+ ++i+ +   +++ aDp+as++i+lii+ s+++l+k+s+++++
  gi|330506571|ref|YP_004382999.1| 166 AASLGVIVAGIIIWQT---GWTQADPIASIIISLIIFASSYRLIKDSFRIMM 214
                                       ***************9...4477*************************9986 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 !   18.9   1.8     2e-07    0.0012       7      77 ..     224     293 ..     222     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-07
                                       HHHHHHHTT-SS-EEEEEEEEE.-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEE CS
                          ZT_dimer   7 eeireiiksvpgvkgvhdlrtr.ksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHve 77 
                                       e++ ++i svpgv++vhdl++      +++ + h +++++  ++++ +i++e++  +++ f g+++ +i +e
  gi|330506571|ref|YP_004382999.1| 224 EDVSRAIGSVPGVLQVHDLHVWgVCSAHVILSAHAVIEDQ-MISQGEAIMEEIKGILHDLF-GIEHTTIQLE 293
                                       67888999**************66668**********888.7*******************.99*****998 PP

>> DUF3180  Protein of unknown function (DUF3180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   2.4      0.11   6.3e+02       2      50 ..      16      64 ..      14      85 .. 0.79
   2 ?   11.9   0.3   3.1e-05      0.19      34      92 ..     125     182 ..      84     190 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.11
                           DUF3180  2 vaaavvaavagwllvrvsygslpplpwlaavvllvlavvelvlAlqvrr 50
                                      ++++ ++ ++  ++ ++++gsl  l+  a v l ++a+++ +lA+++ +
  gi|330506571|ref|YP_004382999.1| 16 AILLTCTILIVEAIGSWWTGSLALLSDAAHVFLDIFAILLSWLAIRLST 64
                                      4555555556666666699999999999999999999999999999865 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.1e-05
                           DUF3180  34 llvlavvelvlAlqvrrrirgrpgarqlepltaarllvlAkAsalvGAllaGvyaGllv 92 
                                       ++ l v+ ++ +  ++r+ +g p++++   ++ arl vl+ A+a +G ++aG+ + ++ 
  gi|330506571|ref|YP_004382999.1| 125 IVNLIVAYILGGGHLHRHDHG-PHHSEDLNIRSARLHVLGDAAASLGVIVAGIIIWQTG 182
                                       112222222333334444333.5667777899********************9876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1868.68
//
Query:       gi|330506572|ref|YP_004383000.1|  [L=453]
Description: hypothetical protein MCON_0307 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-43  147.4   0.0    7.9e-43  147.0   0.0    1.1  1  GSDH      Glucose / Sorbosone dehydrogenase
  ------ inclusion threshold ------
      0.077   13.3   0.0         58    4.4   0.0    4.3  4  Reg_prop  Two component regulator propeller
      0.093   12.8   0.0      0.093   12.8   0.0    3.0  3  NHL       NHL repeat


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.0   0.0   1.3e-46   7.9e-43       4     325 ..      61     430 ..      58     442 .. 0.78

  Alignments for each domain:
  == domain 1  score: 147.0 bits;  conditional E-value: 1.3e-46
                                       EEEEEE-TTS-EEEEETTTEEEEEE.TTEE..EEEEE-..--....--STT-SEEEEEE-TTTTTS-EEEEEEEE-. CS
                              GSDH   4 PwslaflpdgrlLvtersGrlrlvkadgkl.kepiagvp.ev....vakgqgGlldvalhpdfaenrlvYltyaea. 73 
                                       P +     dgr++   ++G ++++++dg++ + p  ++  ++        + Gll++a+hpdf +n+ v++ y+   
  gi|330506572|ref|YP_004383000.1|  61 PVQYISSDDGRMFAVDQTGMVEVFDEDGRMqEGPFMDLRdRMvdlsPGYDERGLLGMAFHPDFVKNGRVFVFYSVPl 137
                                       666666789*********************8788888863332333345789**********************886 PP

                                       ......TTSSEEEEEEEEE-SS.....-EEEEEEEEEEE---TT-------EEE-TTS-EEEE---TT-GG...... CS
                              GSDH  74 ...eeekggagtavararlsed...eaaledlevifrqepkvesgahfGsrlafgpdgtLfvtvGdrskre...... 138
                                          + e+   +++++ +++sed   +  +++++vif+ +    + +h+G+ ++fgpdg+L++ +Gd + ++      
  gi|330506572|ref|YP_004383000.1| 138 rsgAPEGYSCTNRLSLFTVSEDdpdAVDMSRERVIFQIDKP--QMNHNGGAITFGPDGYLYLPLGDGGGANdqgpgh 212
                                       655333334456777777777655678899999***98655..689********************99833356777 PP

                                       ....GGG-TT-SSSEEEEE-....TTS.SB-TT-TTTT-TTS-TTEEEE--SCE---EE-TTT--EEEEEE--SSSE CS
                              GSDH 139 ....eaqdlsselGkilrln....kdG.svpadnpfvgkagakpeiwsyGhRnpqGlaldpdtgeLwesEhGprggD 206
                                           +aqd+ss +Gkilr+     +dG  +p dnpf++++   peiw +G Rnp+G+a+d++ g+L+  + G++   
  gi|330506572|ref|YP_004383000.1| 213 seggNAQDTSSLFGKILRIDvdsaADGyAIPLDNPFINDSAYLPEIWILGLRNPYGIAFDSQ-GRLFVADAGQNLWE 288
                                       7888***************833223454589******************************9.************** PP

                                       EEEEE-TT-B--TTT-S......S-.............-S-TTS---SEEETT-..--EEEEEEE........TTEE CS
                              GSDH 207 elnlieaGknYGWplvsygeeYsgk.......kiges.etreglekpvlvwtps..iapsglafytgdafpewkgdl 273
                                       e++l+e+G+nYGW++ +  + ++ +       + +e   + e l +p++ ++    + + g  +y+g+ ++++ g++
  gi|330506572|ref|YP_004383000.1| 289 EVDLVEKGGNYGWNIREGTHCFDPEspndspaSCPEVgAKGEPLIDPIIEYDHDnhTVVVGGYLYEGQDLTDLVGSY 365
                                       **************99866666633445566555555688888******998766678888899************* PP

                                       EEEETT........TTEEEEEEEEEEEEEEEEEEEE......ESS-.-EEEEEE-TTS-EEEEE-T CS
                              GSDH 274 lvggLk........sqsllrleldegekvveeerll......eelgeriRdVeqgpdGalyvltde 325
                                       l++  +          +l+r e +++  + ++e++        ++ge iR+   + +G +y+lt+e
  gi|330506572|ref|YP_004383000.1| 366 LFADWSsnfdqgdgRLYLARQEASDE-GLWKAEEISiagrpdGRIGEFIRAFGRDGEGEIYLLTSE 430
                                       **999855555533334555555422.344444433355666788999999999999999999986 PP

>> Reg_prop  Two component regulator propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.2   7.4e+03       9      20 ..     186     197 ..     185     197 .. 0.81
   2 ?    4.4   0.0    0.0097        58       8      21 ..     267     280 ..     261     283 .. 0.84
   3 ?   -2.0   0.0       1.2   7.4e+03      16      21 ..     379     384 ..     377     394 .. 0.49
   4 ?    3.1   0.0     0.027   1.6e+02       3      23 ..     409     429 ..     407     430 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                                       EEEE-TTSCEEE CS
                          Reg_prop   9 aileDsdGrlWv 20 
                                       ai   +dG+l++
  gi|330506572|ref|YP_004383000.1| 186 AITFGPDGYLYL 197
                                       577789***986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0097
                                       EEEEE-TTSCEEEE CS
                          Reg_prop   8 taileDsdGrlWvG 21 
                                       + i+ Ds+Grl v+
  gi|330506572|ref|YP_004383000.1| 267 YGIAFDSQGRLFVA 280
                                       6899*******997 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.2
                                       SCEEEE CS
                          Reg_prop  16 GrlWvG 21 
                                       Grl+++
  gi|330506572|ref|YP_004383000.1| 379 GRLYLA 384
                                       555543 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.027
                                       SSSCEEEEEE-TTSCEEEEES CS
                          Reg_prop   3 psnnvtaileDsdGrlWvGte 23 
                                       ++++++a+ +D +G +++ t+
  gi|330506572|ref|YP_004383000.1| 409 IGEFIRAFGRDGEGEIYLLTS 429
                                       578899***********9886 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.28   1.7e+03      20      28 .]     124     132 ..     122     132 .. 0.74
   2 ?   12.8   0.0   1.6e-05     0.093       1      21 [.     263     283 ..     263     286 .. 0.89
   3 ?   -1.5   0.7      0.53   3.2e+03      19      27 ..     340     348 ..     340     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.28
                                       CCCTEEEEE CS
                               NHL  20 senhrvqvF 28 
                                        +n rv+vF
  gi|330506572|ref|YP_004383000.1| 124 VKNGRVFVF 132
                                       578888888 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.6e-05
                                       BSSEEEEEEETTTEEEEEECC CS
                               NHL   1 fnyPhGvavdsnGdiyVaDse 21 
                                       +++P G+a ds+G+++VaD +
  gi|330506572|ref|YP_004383000.1| 263 LRNPYGIAFDSQGRLFVADAG 283
                                       67899**************64 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.53
                                       ECCCTEEEE CS
                               NHL  19 Dsenhrvqv 27 
                                       D  nh+v+v
  gi|330506572|ref|YP_004383000.1| 340 DHDNHTVVV 348
                                       889****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3142.05
//
Query:       gi|330506573|ref|YP_004383001.1|  [L=446]
Description: hypothetical protein MCON_0309 [Methanosaeta concilii GP6]
Scores for complete 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-18   64.5   0.0    1.4e-17   63.7   0.0    1.4  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.4e-17   64.1   0.0    3.5e-17   62.8   0.0    1.6  1  Amino_oxidase   Flavin containing amine oxidoreductase
    6.3e-10   38.7   0.4    2.7e-07   30.0   0.5    2.2  2  FAD_binding_2   FAD binding domain
    5.2e-09   36.1   0.4    2.5e-07   30.6   0.5    2.2  2  DAO             FAD dependent oxidoreductase
    3.8e-08   33.1   0.0    1.2e-07   31.4   0.1    1.7  2  FAD_oxidored    FAD dependent oxidoreductase
    5.6e-07   28.6   0.1    9.6e-05   21.3   0.2    2.1  2  HI0933_like     HI0933-like protein
    3.4e-06   26.5   0.0     0.0003   20.1   0.0    2.1  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      4e-05   24.1   1.1     0.0032   18.0   0.2    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    5.5e-05   22.6   0.1    0.00011   21.5   0.1    1.4  2  FAD_binding_3   FAD binding domain
    5.9e-05   21.8   1.1      0.018   13.6   0.3    2.1  2  GDI             GDP dissociation inhibitor
    0.00012   21.4   0.2    0.00021   20.6   0.2    1.4  1  Thi4            Thi4 family
    0.00041   19.7   0.1      0.012   14.9   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0044   16.2   0.1     0.0094   15.1   0.1    1.5  2  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.098   11.4   0.0       0.16   10.8   0.0    1.3  1  MCRA            MCRA family
      0.099   11.5   0.2       0.15   10.9   0.2    1.2  1  Trp_halogenase  Tryptophan halogenase
       0.13   11.3   0.2       0.19   10.7   0.2    1.2  1  Lycopene_cycl   Lycopene cyclase protein
       0.18   11.8   0.0        1.5    8.8   0.0    2.1  2  NAD_binding_9   FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0   1.3e-20   1.4e-17       1      67 [.       8      73 ..       8      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.3e-20
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHHCC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrllre 67
                                      ++G+G+sGl++A +L+++g++vl+lek d +GG ++syev+g+r+d+g+h+++  + +  ++ l+++
  gi|330506573|ref|YP_004383001.1|  8 VIGSGISGLLTALALSREGKKVLILEKEDCIGGVCRSYEVDGYRLDTGPHAITRLK-SGPLKVLMDR 73
                                      8***************************************************9974.7888877776 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.0   3.3e-20   3.5e-17       1     366 [.      13     371 ..      13     375 .. 0.76

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 3.3e-20
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET.TTHHHHHHHHHTTCCCCEEEESCCGCE CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg.agnpllellkelgledslslpdpgapk 76 
                                       ++GL +A  L++ G +V++lE +d++GG +r+++ dGy +++G++ +t+ +  pl  l+++  +  ++++  +g  k
  gi|330506573|ref|YP_004383001.1|  13 ISGLLTALALSREGKKVLILEKEDCIGGVCRSYEVDGYRLDTGPHAITRlKSGPLKVLMDR-YFRVVPQFAPFG--K 86 
                                       8************************************************999999999999.677767777777..5 PP

                                       EEEETTEECC.................TTEECHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHH CS
                     Amino_oxidase  77 rvlskggref.................pgdlspvpaewealleqgalsaellsleeklrlgleallqktldeldlds 136
                                       +++  g ++                  + +l  + a++++l            l++   ++  +l    ++ l   +
  gi|330506573|ref|YP_004383001.1|  87 YYVRIGDEVKpfpwsinswltfslipmTDRLLLMRALFNTLYL----------LNSGKDFSNIPLSAVLPNALSSTT 153
                                       5555444444777777777755544444444444444444444..........3444444444444668999999** PP

                                       HHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETTHTHHHH CS
                     Amino_oxidase 137 kslaesleelgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllprgGlsqlp 213
                                        +++++l  +    + d +  +r+i+        +++ +     s  + +  ++l   +  ++++  +p+gGl++++
  gi|330506573|ref|YP_004383001.1| 154 RRFLDWLCYFMVGTSADNAPISRFIDN------KIHNTH-----SVPYVGKLYDLFITDGAKDQG--YPKGGLQSII 217
                                       **********9999999888******5......344444.....667888888877777777777..89******** PP

                                       HHHHH..TTTTEEEETSEEEEEEEE...ETTC..EEEEETTSTEEEESEEEE-S-HHHHHSSEEESCCSHHHHHHHH CS
                     Amino_oxidase 214 ealae..elrgldirlntrVkeikr...egdg..vtvtledgevveaDaVvvTvplgvlkailfsPplpdekaeair 283
                                       +++++   +++++i +n+rV +i+    e+        +++ +++e+D Vv     + l    ++  lp e +e + 
  gi|330506573|ref|YP_004383001.1| 218 NSVTSsfPEGRVKIITNERVVKIEGirrEDQVfrADQVITNRDSYECDTVVYSGFSSRLP--DLVDDLPSEYTENLS 292
                                       *****9999999************998633334455556799999***************..777789999999999 PP

                                       HSEEEEEEEEEEEESSGGSGCSTSECE.CECCCEEETTTEEEEECCECCCSTTTEEEEEEEEECHHHHHHHTTS-HH CS
                     Amino_oxidase 284 nlgfgsvnkvilefdrkfwednalgqg.vlvseltttlgeafissdfpsrappgkglvllvyvggdaaneleslsde 359
                                       +++ + +  + l   ++ +++ ++  + +  s+ + +   +  +   p  ap g++lv ++++ + +++ ++++ ++
  gi|330506573|ref|YP_004383001.1| 293 SIKKVKSLTIWLGLTKRLFLNYGS--EmWVDSDPYAWVVPTTNY--DPTLAPKGNHLVGFAFTLDGEYD-MAKIKKK 364
                                       998888888888888888888442..344444444444444444..77889999999999999844443.4677776 PP

                                       HHHHHHH CS
                     Amino_oxidase 360 elvqavl 366
                                       +  + v+
  gi|330506573|ref|YP_004383001.1| 365 AFQSIVQ 371
                                       6666655 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.5   2.5e-10   2.7e-07       1      36 [.       5      40 ..       5      44 .. 0.93
   2 !    6.4   0.0    0.0038         4     389     412 ..     405     428 ..     402     431 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.5e-10
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      Dv+ViGsG++GL  Al+++++G+kv+++eke+  gg
  gi|330506573|ref|YP_004383001.1|  5 DVVVIGSGISGLLTALALSREGKKVLILEKEDCIGG 40
                                      9*****************************987665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0038
                                       EESSBTEEE-STCEESSSSTTS-- CS
                     FAD_binding_2 389 gqpipGLYAaGevaaggvhganrl 412
                                        +p+++LY++G ++     g+nr 
  gi|330506573|ref|YP_004383001.1| 405 RTPVKNLYCVGTDTEKRSAGVNRS 428
                                       469***********9999999986 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.5   2.3e-10   2.5e-07       1      33 [.       5      39 ..       5      44 .. 0.92
   2 ?    3.3   0.0     0.047        50     156     267 ..     224     348 ..     214     412 .. 0.58

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.3e-10
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      dvv+iG+Gi Gl tA++L+r+g  V++lek+d +g
  gi|330506573|ref|YP_004383001.1|  5 DVVVIGSGISGLLTALALSREGkkVLILEKEDCIG 39
                                      9********************99*******96555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.047
                                       HHHTT-EEEESECEEEEEE..EETCEEEEE....EECT.EEEEEEEEEEE--GGGHH..HHHTTCTT......T.SE CS
                               DAO 156 aealGveilegtevtglee..edgkvwgve....rttp.gendaadavVnaaGawsd..llgllkel......d.lp 216
                                       + ++ v+i+++++v+++e   +     +v+    + t+  +  ++d+vV + G  s+     l+ +l      +   
  gi|330506573|ref|YP_004383001.1| 224 FPEGRVKIITNERVVKIEGirR---EDQVFradqVITNrDS-YECDTVVYS-GFSSRlpD--LVDDLpseyteNlSS 293
                                       556779********99944222...3444433242332222.245777776.45554331..223333333321345 PP

                                       EEEEEEEEEEEEECCTHSTGSGCSEEEEE..EEETTTTEEEEEE........TTSEEEEEE CS
                               DAO 217 ispvrgqvlvlkplseklvspaailpvpe..tdddgrgvyvtpr........kdgrvlvGg 267
                                       i+ v++  + l  l++ l  ++         ++d + +  v+p+        ++g++lvG 
  gi|330506573|ref|YP_004383001.1| 294 IKKVKSLTIWL-GLTKRLFLNY--G---SemWVDSDPYAWVVPTtnydptlaPKGNHLVGF 348
                                       55566666666.4444333332..1...112666666666666555555555445566555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1   1.2e-10   1.2e-07       1      38 [.       5      42 ..       5      61 .. 0.95
   2 ?   -1.3   0.0         1   1.1e+03     119     223 ..     236     345 ..     214     389 .. 0.60

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.2e-10
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38
                                      DvvV+G+g++G+  A+a  r+G+kvl++e+++++GG  
  gi|330506573|ref|YP_004383001.1|  5 DVVVIGSGISGLLTALALSREGKKVLILEKEDCIGGVC 42
                                      9***********************************75 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1
                      FAD_oxidored 119 riesvtveskegrktirAkvfiDA..TgdGdlaalaGvpyrvGresreetgep.aagtlmfrlegveg..geedekv 190
                                       r+ +++   +++++++rA+ +i    ++++d +  +G + r+ +  ++   e  ++ + + +++ ++   g +++ +
  gi|330506573|ref|YP_004383001.1| 236 RVVKIEGI-RREDQVFRADQVITNrdSYECDTVVYSGFSSRLPDLVDDLPSEYtENLSSIKKVKSLTIwlGLTKRLF 311
                                       55555553.33577777777775333777777777777777766655533333222333333333333666666666 PP

                      FAD_oxidored 191 qaynkrlcltskp.enrvpfekkpegydparyel 223
                                        +y ++++ +s+p +  vp+++ ++ ++p+ ++l
  gi|330506573|ref|YP_004383001.1| 312 LNYGSEMWVDSDPyAWVVPTTNYDPTLAPKGNHL 345
                                       6677777777777666667766666666666665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2   9.1e-08   9.6e-05       2      36 ..       5      39 ..       4      41 .. 0.94
   2 !    5.1   0.0    0.0073       7.7      98     161 ..     204     270 ..     194     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9.1e-08
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      dv+viG G +Gl++A++++++gk+Vl+lek++ +g
  gi|330506573|ref|YP_004383001.1|  5 DVVVIGSGISGLLTALALSREGKKVLILEKEDCIG 39
                                      8*****************************98776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0073
                                       TTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEE..ECETTE.EEEEE...TTEEEEESEEEE- CS
                       HI0933_like  98 sgrlFpvsdkaedivdallkelkeagvklrletevksv..ekeedgkfrvkt..kseeeleadklvlA 161
                                       +++ +p+    ++i++  ++   e +vk+ ++++v ++   ++ed++fr +   ++++++e+d++v +
  gi|330506573|ref|YP_004383001.1| 204 KDQGYPKG-GLQSIINSVTSSFPEGRVKIITNERVVKIegIRREDQVFRADQviTNRDSYECDTVVYS 270
                                       55667777.7789***********************9955467888888765567999*****99976 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.9e-07    0.0003       2      42 ..       5      44 ..       4      82 .. 0.83
   2 ?    4.5   0.0     0.017        18      65     234 ..     226     270 ..     174     301 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.9e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll 42
                                      dvvviG+G+ Gl +al l++ g kv+++ +++ c +g c  
  gi|330506573|ref|YP_004383001.1|  5 DVVVIGSGISGLLTALALSREGKKVLIL-EKEDCIGGVCRS 44
                                      8***************************.777888877754 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.017
                                       HHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  65 qgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkll 141
                                       +                                                                            
  gi|330506573|ref|YP_004383001.1| 226 E---------------------------------------------------------------------------- 226
                                       3............................................................................ PP

                                       TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                       Pyr_redox_2 142 pkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.... 214
                                                                                               v++ ++++v++i+g  +    
  gi|330506573|ref|YP_004383001.1| 227 ------------------------------------------------------GRVKIITNERVVKIEGIRRedqv 249
                                       ......................................................34666666666666554444443 PP

                                       .EEEEEETTSCEEEESEEEE- CS
                                       .xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 215 .klevvledgeeidadlvvva 234
                                        +++ v ++ +++++d+vv++
  gi|330506573|ref|YP_004383001.1| 250 fRADQVITNRDSYECDTVVYS 270
                                       333355555555666666654 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2     3e-06    0.0032       2      35 ..       6      39 ..       5      45 .. 0.93
   2 ?    4.4   0.0     0.053        56      46      70 ..     220     244 ..     214     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      vvv+G+G +gl  A al++ gkkV ++e +d + 
  gi|330506573|ref|YP_004383001.1|  6 VVVIGSGISGLLTALALSREGKKVLILEKEDCIG 39
                                      8****************************99886 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.053
                                       HHHHHHHTTEEEECSEEEEEEEEET CS
                         Pyr_redox  46 lqeklekngievllntkveeiegse 70 
                                       ++ ++ +  +++++n++v++ieg  
  gi|330506573|ref|YP_004383001.1| 220 VTSSFPEGRVKIITNERVVKIEGIR 244
                                       666666778*************855 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   1.1e-07   0.00011       3      33 ..       5      35 ..       3      38 .. 0.94
   2 ?   -3.4   0.0       4.2   4.5e+03     299     324 ..     392     417 ..     389     422 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.1e-07
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      dV+++G+G +Gl++al Ls+ G +v+++ek 
  gi|330506573|ref|YP_004383001.1|  5 DVVVIGSGISGLLTALALSREGKKVLILEKE 35
                                      8****************************96 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.2
                                       TTSHHHHHHHHHHHHHHHHHHHHHTT CS
                     FAD_binding_3 299 tgGqGlNtaiqDavnLawkLaavlkG 324
                                       ++  GlN++  D+ + ++ L +v + 
  gi|330506573|ref|YP_004383001.1| 392 KASWGLNLGFGDVRTPVKNLYCVGTD 417
                                       56679*******99988888888665 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.3   1.7e-05     0.018       4      45 ..       3      44 ..       1      52 [. 0.90
   2 !    7.0   0.0    0.0017       1.8     241     291 ..     215     267 ..     176     297 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                                      EECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG-E CS
                               GDI  4 eydvivlGtGlkecilsGllsvdgkkvlhldrndyyGgesas 45
                                      + dv+v+G+G+   + +  ls +gkkvl l+++d  Gg + s
  gi|330506573|ref|YP_004383001.1|  3 KNDVVVIGSGISGLLTALALSREGKKVLILEKEDCIGGVCRS 44
                                      57**********9999999******************98776 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0017
                                       HHHTT-EEETS--ECEEEE-TT.S-EEEEEETTEEEEECEEEE-.GGG-CCCE CS
                               GDI 241 saiyGGtymlnkpvdevvlded.gkvvGvkseeevakakkvicd.psylpekv 291
                                       s i+  t  + +  ++++ +e   k+ G++ e++v++a++vi++  sy  + v
  gi|330506573|ref|YP_004383001.1| 215 SIINSVTSSFPEGRVKIITNERvVKIEGIRREDQVFRADQVITNrDSYECDTV 267
                                       55666677777777888888876799****************87246766665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2     2e-07   0.00021      17      55 ..       3      40 ..       1      44 [. 0.94

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2e-07
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                      + Dvv++G+G sGL +a  l+++ + kv+ile++  +GG
  gi|330506573|ref|YP_004383001.1|  3 KNDVVVIGSGISGLLTALALSRE-GKKVLILEKEDCIGG 40
                                      57*********************.**********99999 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 !   14.9   0.0   1.1e-05     0.012       1      43 [.       7      49 ..       7      63 .. 0.89
   2 ?    2.5   0.0     0.067        70      97     265 ..     230     270 ..     203     293 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nignsiyrypkem 43
                                      ++iG G  Gl +a++l + g  ++lilEk+ +ig   + y  + 
  gi|330506573|ref|YP_004383001.1|  7 VVIGSGISGLLTALALSREGK-KVLILEKEdCIGGVCRSYEVDG 49
                                      79******************9.7*******9***9999997665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.067
                       Pyr_redox_3  97 piklfeeV...esvkkedegf...evetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkyagqkv 167
                                       +i ++e+V   e + +ed+ f   +v t++++ye+++v+                                      
  gi|330506573|ref|YP_004383001.1| 230 KIITNERVvkiEGIRREDQVFradQVITNRDSYECDTVV-------------------------------------- 268
                                       333333331113333444444333355555555555555...................................... PP

                       Pyr_redox_3 168 vViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeee 244
                                                                                                                    
  gi|330506573|ref|YP_004383001.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                       Pyr_redox_3 245 ykvktedgkkvevkddvvlat 265
                                                            
  gi|330506573|ref|YP_004383001.1| 269 -------------------YS 270
                                       ...................44 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   8.9e-06    0.0094       1      37 [.       5      40 ..       5      49 .. 0.84
   2 ?   -3.2   0.0       3.2   3.4e+03     283     310 ..     250     277 ..     223     280 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.9e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiae 37
                                      dv+ViG G +G+  Ala++r G kvl++ +k d i+ 
  gi|330506573|ref|YP_004383001.1|  5 DVVVIGSGISGLLTALALSREGKKVLIL-EKEDCIGG 40
                                      79***********************998.55555544 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.2
                                       -S--EEEEEESSTT--EEEEET----S- CS
                              GIDA 283 keshqvfLepegleteliylvgfstslp 310
                                         ++qv  ++++ e ++++  gfs++lp
  gi|330506573|ref|YP_004383001.1| 250 FRADQVITNRDSYECDTVVYSGFSSRLP 277
                                       4567888888888888999999998887 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00015      0.16       3      59 ..       5      55 ..       3      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                                      EEEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS-----------------CCC-- CS
                              MCRA  3 kaylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldgagdpekGyvlrgg 59
                                      ++ ++GsGi++L +A+ L r+    g+++ ile+++  gg + ++  + +Gy l +g
  gi|330506573|ref|YP_004383001.1|  5 DVVVIGSGISGLLTALALSRE----GKKVLILEKEDCIGGVCRSY--EVDGYRLDTG 55
                                      6789**************997....67**************9985..4567776665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00014      0.15       1      35 [.       5      36 ..       5      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                      ++v++G G++G l+A al++ +k   +v+++e+e+
  gi|330506573|ref|YP_004383001.1|  5 DVVVIGSGISGLLTALALSREGK---KVLILEKED 36
                                      69********************4...599999886 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00018      0.19       1      33 [.       5      35 ..       5      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieas 33
                                      DvvviG+G  gl+ A  l  ++ g kv+++e  
  gi|330506573|ref|YP_004383001.1|  5 DVVVIGSGISGLLTALAL--SREGKKVLILEKE 35
                                      9*****************..9*******99865 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 ?    8.8   0.0    0.0014       1.5       1      61 [.       7      61 ..       7      88 .. 0.81
   2 ?    0.5   0.0      0.51   5.4e+02     101     150 ..     214     268 ..     213     270 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrtdqseelllNvpasemsl 61
                                      +++G G++Gl+++ +L ++       ++ + +++    g+v r+ + + ++l +  ++++ 
  gi|330506573|ref|YP_004383001.1|  7 VVIGSGISGLLTALALSREG-----KKVLILEKEDCI-GGVCRSYEVDGYRLDTGPHAITR 61
                                      69**************9995.....788999998887.78888887777777776666665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.51
                     NAD_binding_9 101 rdlfeellarlpegvtvevh.raevvdleeradgqavll.....adgaslaadaVv 150
                                       +++++++++++peg +v+++ +++vv++e  +++ +v       ++ +s+++d Vv
  gi|330506573|ref|YP_004383001.1| 214 QSIINSVTSSFPEG-RVKIItNERVVKIEGIRREDQVFRadqviTNRDSYECDTVV 268
                                       66677888888886.88887477999999866554444311222666778888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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 0.30s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2848.22
//
Query:       gi|330506574|ref|YP_004383002.1|  [L=93]
Description: glutamyl-tRNA(Gln) amidotransferase subunit C [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-21   76.8   0.5    3.2e-21   75.4   0.5    1.6  2  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
  ------ inclusion threshold ------
      0.061   13.9   0.0      0.072   13.7   0.0    1.3  1  YjbR         YjbR
       0.19   11.6   0.2       0.29   11.0   0.2    1.4  1  zf-C2H2_9    C2H2 type zinc-finger (1 copy)


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 ?   -1.2   0.0      0.44   2.6e+03      39      50 ..       3      14 ..       2      17 .. 0.66
   2 !   75.4   0.5   5.4e-25   3.2e-21       1      61 [.      18      88 ..      18      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.44
                                      EB-S--HHHHHT CS
                       Glu-tRNAGln 39 lReDevreelLk 50
                                      +ReD+++  +L+
  gi|330506574|ref|YP_004383002.1|  3 TREDVEHISWLA 14
                                      599976555555 PP

  == domain 2  score: 75.4 bits;  conditional E-value: 5.4e-25
                                      --HHHHHHHHHHHHHHHHHHTTCGCS--TT----S.......-EB-S--.....HHHHHTT-SSEETTEEE CS
                       Glu-tRNAGln  1 lseeEleklakelnsildyveqLqevdttgveplthp.....vlReDev.....reelLknApetedgyfv 61
                                      ++eeE+++l +++nsil+y+ qL+ vdt+gvep++++      +ReD +     ++e+L nAp +e+gyf+
  gi|330506574|ref|YP_004383002.1| 18 IEEEEKDELVEQFNSILEYFHQLDLVDTEGVEPTYRVvdlanIFREDIArgsltQDEALFNAPRRENGYFK 88
                                      589********************************************7578999999*************8 PP

>> YjbR  YjbR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05     0.072      34      60 ..       9      39 ..       1      65 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                                      G....EEEES-HHHHHHHHHSSTTEEE-TST CS
                              YjbR 34 s....lnlkcdpeeaeaLreqypaiapgyhk 60
                                      +    +++k ++ee+++L+eq+ +i+ ++h+
  gi|330506574|ref|YP_004383002.1|  9 HiswlASIKIEEEEKDELVEQFNSILEYFHQ 39
                                      36677899**************99*****95 PP

>> zf-C2H2_9  C2H2 type zinc-finger (1 copy)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   4.9e-05      0.29      26      55 ..       3      31 ..       1      38 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.9e-05
                                      SSS--HHHHHHHHHT-SS---HHHHHHHHH CS
                         zf-C2H2_9 26 sksdaeHvmWLNRniskkrlskdELekkle 55
                                      ++ d eH++WL   i  ++ +kdEL ++++
  gi|330506574|ref|YP_004383002.1|  3 TREDVEHISWLA-SIKIEEEEKDELVEQFN 31
                                      5789*******7.79999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 700.30
//
Query:       gi|330506575|ref|YP_004383003.1|  [L=472]
Description: glutamyl-tRNA(Gln) amidotransferase subunit A [Methanosaeta concilii GP6]
Scores for 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-152  507.3   0.0   4.6e-152  507.1   0.0    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.1   0.0  2.5e-156  4.6e-152       2     451 .]      17     451 ..      16     451 .. 0.98

  Alignments for each domain:
  == domain 1  score: 507.1 bits;  conditional E-value: 2.5e-156
                                       HHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B- CS
                           Amidase   2 lveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypa 78 
                                        ++++++rie+   klna+ t++ e+al++A++ d++      kg L+GvPi++K++i++kg+++ ++s++l +y++
  gi|330506575|ref|YP_004383003.1|  17 YLSQLYERIER--GKLNAFTTLARETALREAKSFDQNPG----KGLLAGVPIAIKECISTKGIESNCSSRILQGYIP 87 
                                       67889999999..9*********************9996....********************************** PP

                                       SS--HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSST CS
                           Amidase  79 ekDatvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGS 155
                                       ++Da+v+erL+++Ga+i+gkTnmdefamg+ste+s+fgptrNPwd + +pGGSSGGsAA vA g +p ++G+DtGGS
  gi|330506575|ref|YP_004383003.1|  88 PYDAHVIERLRAEGAIIMGKTNMDEFAMGTSTETSAFGPTRNPWDIDCVPGGSSGGSAACVAGGEAPCSLGSDTGGS 164
                                       ***************************************************************************** PP

                                       THHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT CS
                           Amidase 156 iRiPAsfcglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeelk 232
                                       +R+PAsfcg+vGlKPtyg+vSr+g++a+++sl+++Gpl+r+v+d+alll+vi+g+d +dsts+     + ++ + l 
  gi|330506575|ref|YP_004383003.1| 165 VRCPASFCGIVGLKPTYGLVSRYGLIAYANSLEQIGPLTRTVKDTALLLEVIAGHDWRDSTSAE----KSSYLPDLD 237
                                       **********************************************************999997....578999999 PP

                                       ---TT-EEEEEGGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS. CS
                           Amidase 233 kslkglriGvvkedgvasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvry. 308
                                           g++iG++ke++ + ++++v+++v +a+  Le +G+   ev+lp+ ++al++yy i+++eassnlar++g ry 
  gi|330506575|ref|YP_004383003.1| 238 RGIYGMKIGIPKEYFGEGVNEKVEKSVWDAISVLEGLGASWQEVSLPHTQYALAAYYVIAMSEASSNLARFDGLRYg 314
                                       999************************************************************************** PP

                                       .---SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSS CS
                           Amidase 309 .erlsetkvlsellpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtapt 384
                                        +++ e+++++++++++r++++g+evkrri lg+yalsa++++ yylka kvr+l++++f +af+++D+l+sPt+p+
  gi|330506575|ref|YP_004383003.1| 315 lRQAGEDRDWHTTFSEIRSKGFGPEVKRRILLGTYALSAGYYGRYYLKALKVRTLIKEDFLQAFKQVDLLASPTMPI 391
                                       99999************************************************************************ PP

                                       S--BCCCCCHHHCSHHHHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
                           Amidase 385 paprlgekdktidsytvlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                                       pa+r+ge+    +++++ly+ + ft   vp nlag pa+s+p+g+    lP+G+q+ig++f e+++L
  gi|330506575|ref|YP_004383003.1| 392 PAFRIGERI---NDPLSLYKADIFT---VPINLAGVPAISLPCGFAG-QLPIGLQLIGPHFGEAAVL 451
                                       ******996...89***********...*****************85.8***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3592.81
//
Query:       gi|330506576|ref|YP_004383004.1|  [L=471]
Description: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B [Methanosaeta concilii GP6]
Scores for 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-101  338.4   0.0   4.2e-101  337.9   0.0    1.1  1  GatB_N           GatB/GatE catalytic domain
    2.3e-39  134.7   0.0    3.6e-39  134.0   0.0    1.2  1  GatB_Yqey        GatB domain
  ------ inclusion threshold ------
      0.073   13.1   0.0       0.15   12.1   0.0    1.4  1  L_lactis_RepB_C  Lactococcus lactis RepB C-terminus
       0.12   12.5   0.1       0.21   11.7   0.1    1.4  1  YqeY             Yqey-like protein


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.9   0.0  9.3e-105  4.2e-101       1     268 [.       4     281 ..       4     284 .. 0.97

  Alignments for each domain:
  == domain 1  score: 337.9 bits;  conditional E-value: 9.3e-105
                                       EEEEEEEEEEB--.SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEE CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N   1 lviGlEiHaqlkt.ksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRK 76 
                                       ++iGlEiH+ql+  +sK+F+++st+ +++epns++++v+l+lPG+lPv+n++ave+ ik++lalnc+i+ee+ f+RK
  gi|330506576|ref|YP_004383004.1|   4 VIIGLEIHVQLNRlESKMFCGCSTKYHNSEPNSHTCPVCLGLPGSLPVINRKAVESGIKVGLALNCKIEEETLFYRK 80 
                                       58*********998*********8889999*********************************************** PP

                                       E-TCTTCTTSEEEEESSS.SEEEEEEEE......TEEEEEEEEEEEE---EEEE....EETTEEEEETTSTT-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                            GatB_N  77 nyfypdlpkgyQitqkeeplakeGslel......ekkvrierihlEeDaaksvh....eekeeslvdlnRaGvpLiE 143
                                       ny+ypdlpkg+Qi+q++ pla++G++ +      e+++ri+r+h+EeD ++ vh    +++++++vd+nR+G+pL+E
  gi|330506576|ref|YP_004383004.1|  81 NYYYPDLPKGFQISQYDYPLATGGHIMIlgdddqERNIRINRAHMEEDPGRLVHagtiDKAKYTMVDYNRCGMPLLE 157
                                       ***************************9****99999*****************99987888*************** PP

                                       EEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 144 ivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaiey 220
                                       +vtepdl+sp+eara+++kl+++l++l+v dg++ eG++R+D+N+S++        g r E+Kn++ +k +eka++y
  gi|330506576|ref|YP_004383004.1| 158 VVTEPDLHSPKEARAFLDKLKSILEYLDVFDGSL-EGAMRVDANISLKG-------GDRSEVKNISGFKGVEKALSY 226
                                       **********************************.7************4.......48******************* PP

                                       HHHHHHHHH.......-EEEEEETTTTEEEEECC----...-EEE-TTS--EE-- CS
                                       xxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 221 eierqiell.......qeTrkfdedkgetvslRskeeaedYryfpepdlppleis 268
                                       ei+rq +l        qeTr+fde ++ tvs+Rsk  a+dYryfpe dl++l+i 
  gi|330506576|ref|YP_004383004.1| 227 EITRQRNLArrnikvvQETRHFDELRNITVSIRSKVGAHDYRYFPECDLVTLRIA 281
                                       ***************************************************9996 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.0   0.0   8.1e-43   3.6e-39       2     146 ..     325     466 ..     324     468 .. 0.95

  Alignments for each domain:
  == domain 1  score: 134.0 bits;  conditional E-value: 8.1e-43
                                       HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHH CS
                         GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspe 77 
                                       f+e  v+++a+++ aa w+++ l geln+++l ie+  ++pe+++e+++l+ e+kI++  a ev++ ll++ g+sp+
  gi|330506576|ref|YP_004383004.1| 325 FYE-FVAARASPRMAAVWIADVLKGELNYRDLGIES--FSPEHMVEIVQLLGENKITEHGAVEVIRDLLDKkGSSPQ 398
                                       455.555667**************************..9******************************988***** PP

                                       HHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHH CS
                         GatB_Yqey  78 eiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellke 146
                                       eii+ +gL  ++d + + ++v+e++ae ++av+dyk+g e+al+++vGqvMkkt+Gka p +v +l++ 
  gi|330506576|ref|YP_004383004.1| 399 EIIKSRGLGRAED-DVVARAVAEAVAECSAAVADYKAGSERALNYIVGQVMKKTRGKASPGEVHNLVRA 466
                                       *************.***************************************************9985 PP

>> L_lactis_RepB_C  Lactococcus lactis RepB C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.3e-05      0.15      73     102 ..     210     239 ..     206     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.3e-05
                   L_lactis_RepB_C  73 eLkelrGlkgvkkhlsYvaakqedyskkni 102
                                       e+k++ G+kgv+k lsY   +q + +++ni
  gi|330506576|ref|YP_004383004.1| 210 EVKNISGFKGVEKALSYEITRQRNLARRNI 239
                                       89**************************98 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   4.7e-05      0.21      95     142 ..     420     467 ..     388     468 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.7e-05
                                       HHHHHHHHHHHHTT--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH CS
                              YqeY  95 eiealvkeaiaevgaesmkdmGkvmkalkpkvkGkaDgkkvsalvkek 142
                                       e  a +++a+a+ +a s +++  +++++++k++Gka  ++v +lv+++
  gi|330506576|ref|YP_004383004.1| 420 EAVAECSAAVADYKAGSERALNYIVGQVMKKTRGKASPGEVHNLVRAQ 467
                                       2333445555666666*****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3305.60
//
Query:       gi|330506577|ref|YP_004383005.1|  [L=384]
Description: hypothetical protein MCON_0315 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-22   79.3   0.0    7.2e-22   78.1   0.0    1.6  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    3.2e-17   63.1   0.0    1.5e-16   61.0   0.0    2.0  2  eRF1_2          eRF1 domain 2
    1.8e-13   50.9   0.0    3.4e-13   50.0   0.0    1.5  1  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    6.4e-11   42.7   0.0    1.7e-10   41.3   0.0    1.7  2  eRF1_3          eRF1 domain 3
      4e-06   26.9   0.0    1.1e-05   25.5   0.0    1.7  2  baeRF_family2   Bacterial archaeo-eukaryotic release factor f
     0.0012   19.5   0.0      0.009   16.6   0.0    2.3  1  baeRF_family12  Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
      0.021   15.0   0.0      0.041   14.0   0.0    1.4  1  DUF1525         Protein of unknown function (DUF1525)
      0.048   13.8   1.3       0.11   12.7   1.3    1.6  1  Zn-ribbon_8     Zinc ribbon domain
        0.1   12.6   0.1        0.2   11.7   0.1    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.15   12.6   0.0       0.35   11.4   0.0    1.6  1  Host_attach     Protein required for attachment to host cells


Domain annotation for each model (and alignments):
>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.0     4e-25   7.2e-22       1     130 [.     127     255 ..     127     264 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 4e-25
                    baeRF_family10   1 PylapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevA 77 
                                       P+l pL+++ d+y  +g++l+d ++a+lf+++ + +ee ++ + +  +++k+ggw sq+rf r ++  ++ ++ +vA
  gi|330506577|ref|YP_004383005.1| 127 PFLLPLARLRDDYLDWGLLLLDSQEAKLFVIRSRIMEEMSRSSIDLMNKHKKGGW-SQMRFDRLRKGAIKSFFTQVA 202
                                       9*************************************9999999999*******.********************* PP

                    baeRF_family10  78 ellaklleergverlvlgGdeeetaalldrlpkalrarvvgtlplpvdasaaa 130
                                       e la+l + +g++ lvl+G+ e++++l+++lp + r+rv g l++p++  +++
  gi|330506577|ref|YP_004383005.1| 203 EDLANLDNLQGMRGLVLAGPGEAKSQLKELLPPQARDRVLGLLDVPMGTVPSE 255
                                       ***********************************************664444 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   8.1e-20   1.5e-16       2     112 ..     142     247 ..     141     254 .. 0.91
   2 ?   -0.9   0.0         1   1.9e+03      37      59 ..     258     280 ..     250     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 8.1e-20
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTES CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklk 78 
                                        gl++ld +eA++++++++ +e +++ + ++  Khk+Gg s+ rf+Rlr+ ++++f+ +vae + +     + + ++
  gi|330506577|ref|YP_004383005.1| 142 WGLLLLDSQEAKLFVIRSRIMEEMSRSSIDLMNKHKKGGWSQMRFDRLRKGAIKSFFTQVAEDLANL---DNLQGMR 215
                                       6999**************************************************************9...9****** PP

                                       EEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE- CS
                            eRF1_2  79 giilagpgfvkeefldkdlldaelkkkviklvdv 112
                                       g++lagpg++k+++ +  ll  +++++v+ l+dv
  gi|330506577|ref|YP_004383005.1| 216 GLVLAGPGEAKSQLKE--LLPPQARDRVLGLLDV 247
                                       *************954..6666666777777766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                                       STTBSCCCCHHHHHHHHHHHHHH CS
                            eRF1_2  37 krGgqsarrfeRlreekleeflk 59 
                                       k+G+q a  +eR   +k+ e lk
  gi|330506577|ref|YP_004383005.1| 258 KMGDQVALDYERSVSKKRAEELK 280
                                       6899********99999988777 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   1.9e-16   3.4e-13       4     110 ..     143     248 ..     141     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.9e-16
                           acVLRF1   4 gvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae.vvl 79 
                                       g+ll  +   ++ v++++ ++++++ + d ++++++GGwSq Rf+R r + +++ +++vae++a+l + +  + +vl
  gi|330506577|ref|YP_004383005.1| 143 GLLLLDSQEAKLFVIRSRIMEEMSRSSIDLMNKHKKGGWSQMRFDRLRKGAIKSFFTQVAEDLANLDNLQGMRgLVL 219
                                       555555666589999999999999****************************************9874333337*** PP

                           acVLRF1  80 gGdrslvaevledarlaplatlareelldvp 110
                                       +G+ ++ ++++e     p a+ ++  lldvp
  gi|330506577|ref|YP_004383005.1| 220 AGPGEAKSQLKELLP--PQARDRVLGLLDVP 248
                                       ***********9933..44444444455554 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         8   1.4e+04       6      18 ..     192     204 ..     190     207 .. 0.82
   2 !   41.3   0.0   9.6e-14   1.7e-10       6     111 ..     274     384 .]     270     384 .] 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8
                                       HHHHHHHHHHHCT CS
                            eRF1_3   6 klleefleelakd 18 
                                        +++ f++++a+d
  gi|330506577|ref|YP_004383005.1| 192 GAIKSFFTQVAED 204
                                       6799999999998 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 9.6e-14
                                       HHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSH.HHHHS..........-HHH-HHHHHHHH CS
                            eRF1_3   6 klleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdt.lkekv..........ketgeelelveli 71 
                                       k  ee+ +++ k+ ++  YG++ v++al  g v+tL+++ ++    ++ +k+++          +++g  +++v+++
  gi|330506577|ref|YP_004383005.1| 274 KRAEELKSNVLKG-QLSSYGIDPVRDALTHGRVNTLVMLSDYVVPGWIcEKCQHfqegarpeicPQCGGRTSQVNVL 349
                                       5567777788887.999*********************9999999988888888*********************** PP

                                       HHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS CS
                            eRF1_3  72 eelvenveesgakveiisseseeGeqlvkafgGiaaiLRy 111
                                       eel+e ++ +ga+ve++ +      +++++ gG++aiLRy
  gi|330506577|ref|YP_004383005.1| 350 EELYELAQRTGAEVEFVEE-----DEFLQSIGGVGAILRY 384
                                       ****************954.....3566***********9 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 !   25.5   0.0   6.4e-09   1.1e-05      33     104 ..     171     242 ..     144     251 .. 0.88
   2 ?   -3.0   0.0       3.8   6.8e+03       7      17 ..     356     366 ..     348     370 .. 0.58

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 6.4e-09
                     baeRF_family2  33 dpvhkvraggwshrryqrraeeswerNaeavAeevdrlvresgaelVvlaGDvrarsllrdeLpervrelvv 104
                                       d ++k ++ggws+ r+ r  + +++   ++vAe ++ l   +g + +vlaG  +a s l++ Lp+++r++v 
  gi|330506577|ref|YP_004383005.1| 171 DLMNKHKKGGWSQMRFDRLRKGAIKSFFTQVAEDLANLDNLQGMRGLVLAGPGEAKSQLKELLPPQARDRVL 242
                                       5678999***************************************************************95 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.8
                     baeRF_family2   7 vDrtGadltlv 17 
                                       + rtGa++++v
  gi|330506577|ref|YP_004383005.1| 356 AQRTGAEVEFV 366
                                       34555655555 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 !   16.6   0.0     5e-06     0.009      63     120 ..     185     243 ..     142     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5e-06
                    baeRF_family12  63 etdfkeq.eeerFakeladeLkkrakegkferlvlvappetlgelrkhlhkevkkrlvg 120
                                       ++d   + + + F+ ++a++L +  + + +  lvl +p e+  +l++ l+ ++++r+ g
  gi|330506577|ref|YP_004383005.1| 185 RFDRLRKgAIKSFFTQVAEDLANLDNLQGMRGLVLAGPGEAKSQLKELLPPQARDRVLG 243
                                       455555558899********************************************976 PP

>> DUF1525  Protein of unknown function (DUF1525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.3e-05     0.041      29      91 ..      61     125 ..      39     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                           DUF1525  29 erleeelsaelpadpeqaaalvrqrlnspdwaaleeqieqay..qgvadawqlgikkiPAVvvdr 91 
                                         +e++l +el+++ ++   l+++ ++sp+w+ +++++  a+  +   +++++g++  P Vv+d 
  gi|330506577|ref|YP_004383005.1|  61 RAMEKSLPSELRESFQKTVSLAQEAIESPSWKGERSRVILASspESFLHVYRMGLEAEPLVVLDT 125
                                       568999***************************9999755542289****************996 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.3     6e-05      0.11       8      38 ..     321     345 ..     313     346 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6e-05
                       Zn-ribbon_8   8 CeeCghefevlqsisdaplta.CPeCgsevrr 38 
                                       Ce+C+  f       + + ++ CP+Cg+++ +
  gi|330506577|ref|YP_004383005.1| 321 CEKCQ-HFQ------EGARPEiCPQCGGRTSQ 345
                                       77777.333......4556677******7665 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00011       0.2      70     102 ..     318     349 ..     280     354 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                       EEEETTTS-EEECHHHHHS-TTTSSS-EEEEES CS
                              HypA  70 kvrCreCgkefeleekalrCpkCgsadveivsG 102
                                          C++C++  e ++  + Cp+Cg++  ++   
  gi|330506577|ref|YP_004383005.1| 318 GWICEKCQHFQEGARP-EICPQCGGRTSQVNVL 349
                                       568*****76665543.46*****998877655 PP

>> Host_attach  Protein required for attachment to host cells
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.35      70     122 ..     193     245 ..     161     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                       Host_attach  70 eeerfarevadrLekaraagkferlvlvApPrflGlLrealskelkklvvkev 122
                                       + ++f  +va++L+++ + + ++ lvl+ p ++  +L+e l ++ +++v + +
  gi|330506577|ref|YP_004383005.1| 193 AIKSFFTQVAEDLANLDNLQGMRGLVLAGPGEAKSQLKELLPPQARDRVLGLL 245
                                       4689********************************************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2670.56
//
Query:       gi|330506578|ref|YP_004383006.1|  [L=267]
Description: alpha-acetolactate decarboxylase [Methanosaeta concilii GP6]
Scores for complete 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-87  291.9   0.0    2.8e-87  291.7   0.0    1.0  1  AAL_decarboxy  Alpha-acetolactate decarboxylase
  ------ inclusion threshold ------
      0.097   13.0   0.0       0.24   11.8   0.0    1.6  1  PapD_C         Pili assembly chaperone PapD, C-terminal domai


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 !  291.7   0.0   3.1e-91   2.8e-87       1     218 [.      34     251 ..      34     252 .. 0.99

  Alignments for each domain:
  == domain 1  score: 291.7 bits;  conditional E-value: 3.1e-91
                     AAL_decarboxy   1 lyqvstlsaLmegvyegtltvsellkhGdfGlGTfeeldGEliildgkvYqlksdgsvrevddeektPFavvtkfep 77 
                                       lyq+st+ aLm+gvy+gt+t++el ++GdfGlGT+++ldGE++++dg++Yq+ksdg ++ ++d+  tPF vvt+f++
  gi|330506578|ref|YP_004383006.1|  34 LYQISTIGALMQGVYDGTMTFGELGERGDFGLGTVQALDGEMVAVDGRFYQVKSDGVAYSLSDSMITPFSVVTFFDA 110
                                       7**************************************************************************** PP

                     AAL_decarboxy  78 ektvklkealskeeleealeellpskNlfyairidGtfksvkvRsvpkqekpyeplaevakkqsefefenveGtlvG 154
                                       e+t++l  + + +el+  l++ l+s+NlfyairidGtf++vk+Rsvp+qekpy+pl e++k q++fef++veGt+vG
  gi|330506578|ref|YP_004383006.1| 111 EETINLGGRYNLSELQGYLDNSLESDNLFYAIRIDGTFDYVKTRSVPAQEKPYPPLEEAIKGQEIFEFHDVEGTVVG 187
                                       *******99******************************************************************** PP

                     AAL_decarboxy 155 frtPeylqginvaGlHlHFisddrkfGGHvldfeleeveveiakisklelelpedeeFeeadlk 218
                                       fr+P+y++g+nv+G+HlHFi+ drk+GGH+ld+e+e+++++++ is +e++lpe+++F +adl+
  gi|330506578|ref|YP_004383006.1| 188 FRCPDYVEGVNVPGYHLHFITLDRKAGGHLLDLEIEDASAKVDSISGFEMDLPENKQFYQADLS 251
                                       **************************************************************96 PP

>> PapD_C  Pili assembly chaperone PapD, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.6e-05      0.24      15      43 ..      84     113 ..      82     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                                       EEEETTEEEEEEEEEE-TTEEEEE.TT--S CS
                            PapD_C  15 evkgggkslaleagmvaPfssatf.akkaa 43 
                                       +vk++g++++l ++m+ Pfs +tf  +  +
  gi|330506578|ref|YP_004383006.1|  84 QVKSDGVAYSLSDSMITPFSVVTFfDAEET 113
                                       689999*****99***********744444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1865.53
//
Query:       gi|330506579|ref|YP_004383007.1|  [L=369]
Description: DJ-1/PfpI family/rubredoxin fusion protein [Methanosaeta concilii GP6]
Scores for complete 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  124.6   0.1    4.4e-36  124.2   0.1    1.1  1  DJ-1_PfpI       DJ-1/PfpI family
    9.9e-09   35.1   7.1    9.9e-09   35.1   7.1    3.6  3  Rubredoxin      Rubredoxin
    0.00051   20.1   3.9      0.081   13.0   0.2    2.9  2  PHD_4           PHD-finger
     0.0095   16.0   2.0       0.95    9.5   0.1    2.3  2  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.016   14.9   0.1        2.1    8.0   0.0    2.3  2  ThiJ_like       ThiJ/PfpI family-like
       0.21   11.6   3.4          2    8.5   1.1    2.4  2  DZR             Double zinc ribbon
       0.34   10.7   7.9       0.35   10.7   1.4    3.2  3  Cys_rich_CPCC   Cysteine-rich CPCC
       0.47   10.5   2.1        1.3    9.1   0.0    2.6  4  CpXC            CpXC protein
       0.49   10.5   3.3        1.9    8.6   0.2    3.2  3  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.54   10.1   4.8        1.3    8.9   0.0    2.9  3  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO
       0.57   10.2   7.4        6.5    6.8   0.9    2.9  3  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        1.5    8.8  10.6        4.2    7.4   0.3    3.9  4  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        1.8    8.3  10.0        2.7    7.8   0.5    3.3  3  zf-MIZ          MIZ/SP-RING zinc finger
          3    8.3  11.3         17    5.8   0.6    3.1  2  DUF4379         Probable Zinc-ribbon 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 !  124.2   0.1   3.4e-39   4.4e-36       2     164 ..     132     294 ..     131     295 .. 0.96

  Alignments for each domain:
  == domain 1  score: 124.2 bits;  conditional E-value: 3.4e-39
                                       EEEEEEE.TTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHH.HHH CS
                         DJ-1_PfpI   2 kvlvlla.dgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGrag.per 76 
                                       k+l++l  d++++ El vp d++++ g++v+++s++ ++ +g++G+++ vd  ld+vk ++y a+v +GG+   +++
  gi|330506579|ref|YP_004383007.1| 132 KILMVLPpDQYQEEELNVPRDYFQSMGYQVHLASKGVKTATGMSGERTEVDLDLDEVKLSDYIAVVFVGGEGIySQE 208
                                       88999888**************************************************************9743889 PP

                                       HHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEEEESSGG CS
                         DJ-1_PfpI  77 lrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlvTsrgpg 153
                                       l +++ +++++k++  ++k+v+aIC gp++La+ag+lkg+++T+  +  d ++ +ga ++d+ vv+dg+++T++gp 
  gi|330506579|ref|YP_004383007.1| 209 LNRDPDYQKIAKSANAQKKIVGAICLGPWILADAGLLKGKKATASET--DHIKSKGAIVSDDAVVQDGKIITANGPS 283
                                       9999****************************************999..99************************** PP

                                       GHHHHHHHHHH CS
                         DJ-1_PfpI 154 aaiefalelle 164
                                       a+ efa+++++
  gi|330506579|ref|YP_004383007.1| 284 ASQEFAEAVVA 294
                                       *******9987 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.5     0.025        32      35      42 ..      33      40 ..      27      43 .. 0.78
   2 ?   -0.7   0.2       1.2   1.5e+03      36      41 ..      57      62 ..      53      68 .. 0.81
   3 !   35.1   7.1   7.7e-12   9.9e-09       2      47 .]     329     366 ..     328     366 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.025
                                      -BBTTTB- CS
                        Rubredoxin 35 WvCPdCgv 42
                                      W+CP+Cg 
  gi|330506579|ref|YP_004383007.1| 33 WQCPVCGY 40
                                      77777764 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                                      BBTTTB CS
                        Rubredoxin 36 vCPdCg 41
                                       CP+C 
  gi|330506579|ref|YP_004383007.1| 57 LCPNCY 62
                                      599994 PP

  == domain 3  score: 35.1 bits;  conditional E-value: 7.7e-12
                                       EEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                        Rubredoxin   2 yeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47 
                                       ++CkvCgyvYdpa+ d       g +FedlP +W+CP Cg++k++F
  gi|330506579|ref|YP_004383007.1| 329 WRCKVCGYVYDPAEND-------GVAFEDLPGTWKCP-CGAPKSKF 366
                                       9************966.......779***********.******99 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.5    0.0049       6.3      52      67 ..      23      38 ..      15      39 .. 0.82
   2 !   13.0   0.2   6.4e-05     0.081      21      65 ..     319     358 ..     304     360 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0049
                             PHD_4 52 gvvnedlpnsWeCpkC 67
                                       ++++   ++W+Cp C
  gi|330506579|ref|YP_004383007.1| 23 QTASDTDYTCWQCPVC 38
                                      47788899*******9 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.4e-05
                             PHD_4  21 eeesetpsslmeCsvCyeivHpeClkekegegvvnedlpnsWeCp 65 
                                       ++++ ++ +   C+vC  +  p+     e++gv+ edlp  W+Cp
  gi|330506579|ref|YP_004383007.1| 319 SSNAASQAAAWRCKVCGYVYDPA-----ENDGVAFEDLPGTWKCP 358
                                       44466677788999999999884.....679*************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 ?    5.7   0.3     0.011        14      70      95 ..      32      64 ..      14      70 .. 0.75
   2 !    9.5   0.1   0.00074      0.95      60      99 ..     318     366 ..     286     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                                      EEEETTTS-EEECHHHHH.......S-TTTSSS CS
                              HypA 70 kvrCreCgkefeleekal.......rCpkCgsa 95
                                        +C +Cg+++ l+ +++        Cp+C sa
  gi|330506579|ref|YP_004383007.1| 32 CWQCPVCGYTVILTPAEAesidpytLCPNCYSA 64
                                      568******99977532235677789****875 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00074
                                       -EEEEEEE--EEEETTTS-EEECHH.HHH..........S-TTTSSS-EEE CS
                              HypA  60 aeLeieevpvkvrCreCgkefelee.kal..........rCpkCgsadvei 99 
                                       a+ +  ++ +  rC++Cg+ ++ +e +            +Cp Cg+ + ++
  gi|330506579|ref|YP_004383007.1| 318 ASSNAASQAAAWRCKVCGYVYDPAEnD-GvafedlpgtwKCP-CGAPKSKF 366
                                       55567789999***********77633.12468999999***.99988765 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.017        21       6      33 ..     142     169 ..     137     179 .. 0.85
   2 ?    8.0   0.0    0.0016       2.1     113     141 ..     214     242 ..     178     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.017
                         ThiJ_like   6 ydvtevaipwkvlkdagfsveFvtekgk 33 
                                       y+ +e+ +p ++++  g++v+ +++  k
  gi|330506579|ref|YP_004383007.1| 142 YQEEELNVPRDYFQSMGYQVHLASKGVK 169
                                       889******************9987655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0016
                         ThiJ_like 113 eylklvkrekepskvlgaicqgvlalafa 141
                                       +y k  k +++++k++gaic g   la a
  gi|330506579|ref|YP_004383007.1| 214 DYQKIAKSANAQKKIVGAICLGPWILADA 242
                                       6888888888************9988877 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.1    0.0016         2      14      36 ..      34      63 ..      23      70 .. 0.84
   2 ?    2.7   0.0      0.11   1.3e+02      28      42 ..     328     342 ..     307     347 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                               DZR 14 fCseCgtklkavaa.......edrCpsCge 36
                                       C+ Cg ++  ++a        + Cp+C +
  gi|330506579|ref|YP_004383007.1| 34 QCPVCGYTVILTPAeaesidpYTLCPNCYS 63
                                      6*******887777889***999*****76 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.11
                               DZR  28 edrCpsCgekvdpea 42 
                                       + rC  Cg+  dp +
  gi|330506579|ref|YP_004383007.1| 328 AWRCKVCGYVYDPAE 342
                                       678999999888766 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.4   0.00027      0.35       2      25 ..      34      62 ..      33      71 .. 0.81
   2 ?   -0.5   0.1      0.85   1.1e+03       5      34 ..      74     104 ..      70     114 .. 0.68
   3 ?    2.0   0.0      0.15   1.9e+02       2      29 ..     330     339 ..     317     349 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                     Cys_rich_CPCC  2 qCpcCgyltl....eeee.gsydiCpvCf 25
                                      qCp+Cgy+++    e e+   y +Cp C+
  gi|330506579|ref|YP_004383007.1| 34 QCPVCGYTVIltpaEAESiDPYTLCPNCY 62
                                      8*******998875444557799***998 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.85
                     Cys_rich_CPCC   5 cCgyltleeee.gsydiCpvCfWedDlvqlk 34 
                                       c gy+  ++++   y+  +  +W++D+++ +
  gi|330506579|ref|YP_004383007.1|  74 CSGYVPKDDQSdDPYQDNEQPYWQEDEMNSQ 104
                                       6666666555556666677779999988744 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.15
                     Cys_rich_CPCC   2 qCpcCgyltleeeegsydiCpvCfWedD 29 
                                       +C +Cgy+                  +D
  gi|330506579|ref|YP_004383007.1| 330 RCKVCGYV------------------YD 339
                                       46666665..................44 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0     0.001       1.3      12      50 ..       7      45 ..       2      53 .. 0.85
   2 ?   -3.3   0.3       7.1     9e+03      40      44 ..      58      62 ..      55      74 .. 0.66
   3 ?   -3.6   0.0       8.9   1.1e+04      60      74 ..     131     145 ..     114     165 .. 0.57
   4 ?   -0.5   0.0      0.96   1.2e+03      32      46 ..     323     337 ..     306     342 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.001
                              CpXC 12 aeiwtsidadedpelkeklldgslfeatCpkCgatakle 50
                                      +++  ++ a+ +p  ++   d +++ ++Cp Cg+t+ l+
  gi|330506579|ref|YP_004383007.1|  7 TPLILILLAAMSPASAQTASDTDYTCWQCPVCGYTVILT 45
                                      5667788888899999999999************98875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.1
                              CpXC 40 CpkCg 44
                                      Cp+C 
  gi|330506579|ref|YP_004383007.1| 58 CPNCY 62
                                      55553 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 8.9
                              CpXC  60 kellillvpeserse 74 
                                       +++l++l p++ ++e
  gi|330506579|ref|YP_004383007.1| 131 EKILMVLPPDQYQEE 145
                                       333333334333333 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.96
                              CpXC  32 dgslfeatCpkCgat 46 
                                       + +   ++C  Cg+ 
  gi|330506579|ref|YP_004383007.1| 323 ASQAAAWRCKVCGYV 337
                                       56677899****985 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0015       1.9       1      16 [.      34      49 ..      34      52 .. 0.79
   2 ?   -0.3   0.1      0.87   1.1e+03       2       8 ..      58      64 ..      57      66 .. 0.87
   3 ?   -0.8   0.0       1.2   1.6e+03      16      20 ..     327     331 ..     315     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                    DNA_ligase_ZBD  1 hCPvCGsavvReegea 16
                                      +CPvCG  v+ ++ ea
  gi|330506579|ref|YP_004383007.1| 34 QCPVCGYTVILTPAEA 49
                                      5*****9998666555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.87
                    DNA_ligase_ZBD  2 CPvCGsa 8 
                                      CP C sa
  gi|330506579|ref|YP_004383007.1| 58 CPNCYSA 64
                                      ****876 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.2
                    DNA_ligase_ZBD  16 aiyRC 20 
                                       a++RC
  gi|330506579|ref|YP_004383007.1| 327 AAWRC 331
                                       88*** PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4       0.2   2.5e+02      12      20 ..      31      39 ..      24      41 .. 0.74
   2 ?   -1.7   0.1       2.2   2.8e+03      15      20 ..      56      62 ..      49      66 .. 0.70
   3 ?    8.9   0.0   0.00099       1.3      12      27 ..     327     342 ..     318     347 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.2
                         zf-C2H2_3 12 gasqCkeCg 20
                                      +  qC++Cg
  gi|330506579|ref|YP_004383007.1| 31 TCWQCPVCG 39
                                      4478****9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                         zf-C2H2_3 15 q.CkeCg 20
                                      + C++C 
  gi|330506579|ref|YP_004383007.1| 56 TlCPNCY 62
                                      34****6 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00099
                         zf-C2H2_3  12 gasqCkeCgMvYnpgs 27 
                                        a +Ck+Cg vY p +
  gi|330506579|ref|YP_004383007.1| 327 AAWRCKVCGYVYDPAE 342
                                       3567********9976 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.9    0.0051       6.5      23      52 ..      27      61 ..      22      66 .. 0.68
   2 ?    4.7   0.0     0.022        28      42      57 ..     324     339 ..     315     351 .. 0.81
   3 ?    4.9   0.8     0.019        24      30      54 ..     330     361 ..     329     363 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0051
                    OrfB_Zn_ribbon 23 npayTSktCseCgsknke.....alsgrtfkCpnC 52
                                      +  yT  +C++Cg+++       +  +    CpnC
  gi|330506579|ref|YP_004383007.1| 27 DTDYTCWQCPVCGYTVILtpaeaESIDPYTLCPNC 61
                                      6679999*******987655543333334446666 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.022
                    OrfB_Zn_ribbon  42 lsgrtfkCpnCgfead 57 
                                        +   ++C+ Cg+++d
  gi|330506579|ref|YP_004383007.1| 324 SQAAAWRCKVCGYVYD 339
                                       5677899****99987 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.019
                    OrfB_Zn_ribbon  30 tCseCgsknke........alsgrtfkCpnCgf 54 
                                       +C +Cg++ ++        ++ + t+kCp Cg+
  gi|330506579|ref|YP_004383007.1| 330 RCKVCGYVYDPaendgvafEDLPGTWKCP-CGA 361
                                       59999999998888999888889999999.985 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.3    0.0033       4.2       5      19 ..      33      45 ..      32      55 .. 0.90
   2 ?    1.2   0.1      0.27   3.5e+02       7      15 ..      58      66 ..      56      69 .. 0.82
   3 ?    4.2   0.1     0.033        42      22      31 ..     326     335 ..     315     339 .. 0.79
   4 ?   -0.3   0.1      0.79     1e+03       4      11 ..     354     360 ..     354     368 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0033
                    Zn_ribbon_SprT  5 YrCtgCgreythhls 19
                                      ++C+ Cg  yt++l+
  gi|330506579|ref|YP_004383007.1| 33 WQCPVCG--YTVILT 45
                                      9******..888876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.27
                    Zn_ribbon_SprT  7 CtgCgreyt 15
                                      C++C++ y 
  gi|330506579|ref|YP_004383007.1| 58 CPNCYSAYA 66
                                      ****98875 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.033
                    Zn_ribbon_SprT  22 rhnYrCrrCk 31 
                                        +++rC+ C+
  gi|330506579|ref|YP_004383007.1| 326 AAAWRCKVCG 335
                                       4569999996 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.79
                    Zn_ribbon_SprT   4 vYrCtgCg 11 
                                       +++C  Cg
  gi|330506579|ref|YP_004383007.1| 354 TWKC-PCG 360
                                       79**.999 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 ?    7.8   0.5    0.0021       2.7      40      47 ..      31      38 ..      20      41 .. 0.74
   2 ?    4.4   0.1     0.025        31      37      47 ..     324     334 ..     316     336 .. 0.84
   3 ?    0.4   0.6      0.45   5.7e+02      41      46 ..     354     359 ..     349     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0021
                                      ---B-TTT CS
                            zf-MIZ 40 etWnCPvC 47
                                        W+CPvC
  gi|330506579|ref|YP_004383007.1| 31 TCWQCPVC 38
                                      34****** PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.025
                                       HHS---B-TTT CS
                            zf-MIZ  37 ertetWnCPvC 47 
                                       +++ +W+C vC
  gi|330506579|ref|YP_004383007.1| 324 SQAAAWRCKVC 334
                                       67889****** PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.45
                                       --B-TT CS
                            zf-MIZ  41 tWnCPv 46 
                                       tW+CP 
  gi|330506579|ref|YP_004383007.1| 354 TWKCPC 359
                                       8****4 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.6     0.013        17      21      38 ..      24      41 ..      15      61 .. 0.64
   2 ?    5.1   4.5     0.023        30      22      40 ..     321     339 ..     307     359 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.013
                           DUF4379 21 tpgskkkvwWkCakCghe 38
                                      t++ +   +W+C+ Cg++
  gi|330506579|ref|YP_004383007.1| 24 TASDTDYTCWQCPVCGYT 41
                                      444577889*******76 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.023
                           DUF4379  22 pgskkkvwWkCakCgheWe 40 
                                        + ++ + W+C+ Cg+ + 
  gi|330506579|ref|YP_004383007.1| 321 NAASQAAAWRCKVCGYVYD 339
                                       4567899********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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):              14  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2768.11
//
Query:       gi|330506580|ref|YP_004383008.1|  [L=183]
Description: hypothetical protein MCON_0319 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.15   12.1   0.0    1.2  1  Spore_III_AF  Stage III sporulation protein AF (Spore_III_AF)


Domain annotation for each model (and alignments):
>> Spore_III_AF  Stage III sporulation protein AF (Spore_III_AF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.1e-06      0.15      21      85 ..       2      67 ..       1      73 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-06
                      Spore_III_AF 21 kYvklvlGLllilailsPvlsllnkdldlelaaesesleeeleeikeegeelkeenkke.aleeye 85
                                      +Yv+l++ Ll+  + + P ls+ +++++l++ a++ ++  +++ ++e++ +l+++ + + + + ye
  gi|330506580|ref|YP_004383008.1|  2 RYVRLFAALLVACISIVPALSMQDNGIALKECAKQMESPCQKSLMSEKAPDLQQQGRTNaMADNYE 67
                                      9*****************************988888888888888888888776655442666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1479.16
//
Query:       gi|330506581|ref|YP_004383009.1|  [L=94]
Description: AsnC family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-08   34.8   0.1    1.4e-08   34.6   0.1    1.1  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.17   12.0   0.0    1.6  1  sCache_3_2      Single cache domain 3


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 !   34.6   0.1   1.6e-12   1.4e-08       2      67 ..       1      62 [.       1      70 [. 0.93

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.6e-12
                                      EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEE CS
                    AsnC_trans_reg  2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvart 67
                                      +v++ +gh    +e+   l+++  V+e+yr+ G+y++++ + +++++al+ ++   ++s+p+ +++
  gi|330506581|ref|YP_004383009.1|  1 MVKVVRGH---EDEAYLDLRKVSGVKEAYRILGEYQFFVVMQAKSVAALQGLIGG-VRSIPDATNI 62
                                      58999999...9******************************************9.*****99987 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.9e-05      0.17      34      63 ..      40      72 ..       5      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
                        sCache_3_2 34 rapesglqalvddvrritgvd...yvvitDeeg 63
                                      ++  ++lq+l+  vr+i++++   +v itD++ 
  gi|330506581|ref|YP_004383009.1| 40 AKSVAALQGLIGGVRSIPDATnicHVLITDRDA 72
                                      455689*****9999999999999******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 772.90
//
Query:       gi|330506582|ref|YP_004383010.1|  [L=201]
Description: hypothetical protein MCON_0321 [Methanosaeta concilii GP6]
Scores for complete 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   1.7      0.033   14.4   0.1    2.2  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.021   13.9   0.1      0.088   11.8   0.0    1.9  2  Lipoprotein_1    Borrelia lipoprotein
      0.069   12.9   0.3        6.1    6.7   0.1    2.3  2  DUF5516          Family of unknown function (DUF5516)
      0.072   13.0   0.1        1.1    9.1   0.0    2.1  2  LT-IIB           Type II heat-labile enterotoxin , B subunit 


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   7.4e-06     0.033      16      68 ..      50      99 ..      33     111 .. 0.77
   2 !   13.4   0.1   1.6e-05     0.071      11      64 ..     132     183 ..     123     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.4e-06
                   CarboxypepD_reg 16 gatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevt 68
                                      ++ +t + ++tg +   +td+dG   ++  +pgt +  ++++Gy+  + +  +
  gi|330506582|ref|YP_004383010.1| 50 EVLITGS-DGTGNEFAGVTDSDGVAVIS-GTPGTWQFSFQKDGYDDLNLQ-YD 99
                                      4445545.478889999**********8.577*************99964.43 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.6e-05
                   CarboxypepD_reg  11 gapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr 64 
                                       g  ++ +++t + +++g + s tt+++G   ++g+p gt +  ++++Gy++   
  gi|330506582|ref|YP_004383010.1| 132 GPILSDVQITGQ-DGDGNEFSGTTNSTGVAIISGIP-GTWQFAFQKAGYDSLYL 183
                                       555677777777.488999**************988.9************9886 PP

>> Lipoprotein_1  Borrelia lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     2e-05     0.088     110     145 ..      38      73 ..      28      79 .. 0.89
   2 ?   -1.8   0.0      0.29   1.3e+03     119     143 ..     134     158 ..     123     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                                       EEEEEETTSCEEEEEEEETTS-EEEEECESSTTSEE CS
                     Lipoprotein_1 110 iteeklkknkldekkltradGtrleysqitdadnat 145
                                       + ee l+   l+e  +t +dGt  e++++td+d+ +
  gi|330506582|ref|YP_004383010.1|  38 VHEEALDGPLLSEVLITGSDGTGNEFAGVTDSDGVA 73 
                                       5699999999***********************965 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.29
                                       CEEEEEEEETTS-EEEEECESSTTS CS
                     Lipoprotein_1 119 kldekkltradGtrleysqitdadn 143
                                        l++ ++t  dG   e+s+ t++ +
  gi|330506582|ref|YP_004383010.1| 134 ILSDVQITGQDGDGNEFSGTTNSTG 158
                                       5777888999999999999888765 PP

>> DUF5516  Family of unknown function (DUF5516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0089        40      15      27 ..      71      85 ..      70      93 .. 0.75
   2 ?    6.7   0.1    0.0014       6.1      15      34 ..     158     178 ..     156     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0089
                           DUF5516 15 GVgLISW..GlWdla 27
                                      GV  IS   G+W+++
  gi|330506582|ref|YP_004383010.1| 71 GVAVISGtpGTWQFS 85
                                      888888444****96 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0014
                           DUF5516  15 GVgLISW..GlWdlakiiKSkf 34 
                                       GV +IS   G+W++a + K  +
  gi|330506582|ref|YP_004383010.1| 158 GVAIISGipGTWQFA-FQKAGY 178
                                       899999555*****9.666555 PP

>> LT-IIB  Type II heat-labile enterotoxin , B subunit (LT-IIB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00025       1.1      55      81 ..      67      93 ..      59     120 .. 0.81
   2 ?    1.8   0.0     0.048   2.1e+02      55      76 ..     154     175 ..     134     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00025
                                      TTT-EEEEEETTS-EEEE---SSTTHH CS
                            LT-IIB 55 tntdgiyvvsstggvwrisrakdypdn 81
                                      t++dg+ v+s t g w+ s  kd  d+
  gi|330506582|ref|YP_004383010.1| 67 TDSDGVAVISGTPGTWQFSFQKDGYDD 93
                                      6789*****************995554 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.048
                                       TTT-EEEEEETTS-EEEE---S CS
                            LT-IIB  55 tntdgiyvvsstggvwrisrak 76 
                                       tn+ g+ ++s   g w+ +  k
  gi|330506582|ref|YP_004383010.1| 154 TNSTGVAIISGIPGTWQFAFQK 175
                                       7889999999999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1464.96
//
Query:       gi|330506583|ref|YP_004383011.1|  [L=154]
Description: cytosine deaminase [Methanosaeta concilii GP6]
Scores for 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   76.7   0.0    1.4e-21   76.3   0.0    1.2  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    1.3e-20   73.6   0.0    1.4e-20   73.4   0.0    1.1  1  MafB19-deam      MafB19-like deaminase
    0.00014   21.9   0.2       0.01   15.9   0.4    2.2  2  Bd3614-deam      Bd3614-like deaminase
     0.0035   17.4   0.0     0.0065   16.6   0.0    1.4  1  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4
  ------ inclusion threshold ------
      0.061   13.4   0.0      0.098   12.7   0.0    1.3  1  APOBEC2          APOBEC2
      0.091   12.4   0.0       0.18   11.4   0.0    1.4  1  ATP-synt_J       ATP synthase j chain


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 !   76.3   0.0   4.6e-25   1.4e-21       7     100 ..       4      95 ..       1      96 [. 0.95

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 4.6e-25
                                       HHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEEEE--BH CS
                   dCMP_cyt_deam_1   7 llelalkaakeaqkcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyvtlePCs 83 
                                       +++ al++a++ + +  +++Gav+v++g+ii++g n++ ++ ++++HAE+ ++++a  +gg+++  a+ly+tl PC 
  gi|330506583|ref|YP_004383011.1|   4 FMQAALDEARKGSREGGIPIGAVLVEEGRIIGRGRNRRVQQRDQMMHAEIDCLRNARLTGGYHN--AVLYTTLMPCY 78 
                                       8*******************************************************98877665..*********** PP

                                       HHHHHHHHHT-SEEEEE CS
                   dCMP_cyt_deam_1  84 mCakaiiqsgikkvvvg 100
                                       mCa a++ +gikkvvvg
  gi|330506583|ref|YP_004383011.1|  79 MCAGAVVYFGIKKVVVG 95 
                                       ***************98 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.0   4.8e-24   1.4e-20       5     102 ..       3      97 ..       1     134 [. 0.86

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 4.8e-24
                       MafB19-deam   5 kafrkalaevekatkikedkigavivkdkkviargsnekelnakataHaEiaalqqAakklkskrlddatlyvtlep 81 
                                        +++ al e++k++  ++ +igav v+++++i+rg n++ ++ +   HaEi+ l+ A   +++    +a+ly+tl p
  gi|330506583|ref|YP_004383011.1|   3 IFMQAALDEARKGSREGGIPIGAVLVEEGRIIGRGRNRRVQQRDQMMHAEIDCLRNAR-LTGGY--HNAVLYTTLMP 76 
                                       689999***************************************************4.33433..7********** PP

                       MafB19-deam  82 CdmCagaivqaglkklvygag 102
                                       C mCaga+v+ g+kk+v g +
  gi|330506583|ref|YP_004383011.1|  77 CYMCAGAVVYFGIKKVVVGEA 97 
                                       *****************9977 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.016        48      13      44 ..      25      58 ..      16      65 .. 0.78
   2 !   15.9   0.4   3.5e-06      0.01      77      99 ..      67      89 ..      64     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.016
                       Bd3614-deam 13 alvsdqGelldaavn..tnaenkvLHAEvnLlap 44
                                      a++ ++G ++  ++n  +    +++HAE+  l  
  gi|330506583|ref|YP_004383011.1| 25 AVLVEEGRIIGRGRNrrVQQRDQMMHAEIDCLRN 58
                                      45567899999999933456789*****998865 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.5e-06
                       Bd3614-deam 77 garllvtlqcCkmCAalvvaaad 99
                                      +a+l+ tl +C mCA+ vv ++ 
  gi|330506583|ref|YP_004383011.1| 67 NAVLYTTLMPCYMCAGAVVYFGI 89
                                      699**************998765 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 !   16.6   0.0   2.2e-06    0.0065      15      63 ..      41      87 ..      31      94 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.2e-06
                             SNAD4 15 gvlknkke.haEllflekikseldpsqeyrvtwylswsPCaeCaekiaef 63
                                      +v + ++  haE+  l++   +l      + ++y++  PC+ Ca +++ f
  gi|330506583|ref|YP_004383011.1| 41 RVQQRDQMmHAEIDCLRNA--RLTGG-YHNAVLYTTLMPCYMCAGAVVYF 87
                                      343343336**********..66644.456678*************9988 PP

>> APOBEC2  APOBEC2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.3e-05     0.098      44      92 ..      43      87 ..      29      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.3e-05
                           APOBEC2 44 enkekkcHaEllflskvkkkkleekkeykvtwyvswsPCaeCaeevaef 92
                                      +++++ +HaE+  l++ +     +   ++  +y++  PC+ Ca  v+ f
  gi|330506583|ref|YP_004383011.1| 43 QQRDQMMHAEIDCLRNARL----TGGYHNAVLYTTLMPCYMCAGAVVYF 87
                                      4456788****99999888....455677899**************988 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 ?   11.4   0.0     6e-05      0.18      12      37 ..      77     102 ..      72     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6e-05
                                       HHHHHHHHHHHHHHHHHHHSTTSSSS CS
                        ATP-synt_J  12 PFfaaglivlygvnkaqnammnsdEf 37 
                                        ++ ag++v++g+ k+    ++s++ 
  gi|330506583|ref|YP_004383011.1|  77 CYMCAGAVVYFGIKKVVVGEARSAPA 102
                                       4899***********98777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1133.49
//
Query:       gi|330506584|ref|YP_004383012.1|  [L=226]
Description: hypothetical protein MCON_0323 [Methanosaeta concilii GP6]
Scores for complete 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-07   29.7   0.0    7.6e-07   29.1   0.0    1.2  1  Peptidase_C93   Bacterial transglutaminase-like cysteine prot
    7.3e-07   29.6   0.0    1.2e-06   29.0   0.0    1.3  1  Transglut_core  Transglutaminase-like superfamily
     0.0094   15.5   0.0      0.032   13.7   0.0    1.9  1  DUF553          Transglutaminase-like domain
  ------ inclusion threshold ------
        0.1   12.4   0.0       0.25   11.2   0.0    1.6  1  Imm31           Immunity protein 31
       0.14   12.0   0.0       0.27   11.1   0.0    1.4  1  PDEase_I_N      3'5'-cyclic nucleotide phosphodiesterase N-te


Domain annotation for each model (and alignments):
>> Peptidase_C93  Bacterial transglutaminase-like cysteine proteinase BTLCP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.1e-10   7.6e-07      48     126 ..      76     161 ..      65     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.1e-10
                     Peptidase_C93  48 svNeeikpvtdkelygveerWeypkd....gaGdCedyallKrkeLieaGlpasalll..tvvrdekge.gHavLtv 117
                                        v ++i+ vtdk+ +g e+ W +p++    g+GdCed   l    L+++G++++ +++    v ++ g  gHa ++ 
  gi|330506584|ref|YP_004383012.1|  76 YVTRSIDYVTDKSSFGLEDLWLFPEEtlmlGKGDCEDTSFLLASLLLASGISEQCVRVvlGRVASPAGSyGHAWVVY 152
                                       58899*******************98666689*********************987751145777776569**9999 PP

                     Peptidase_C93 118 rtdrGdlvL 126
                                       + ++G+  L
  gi|330506584|ref|YP_004383012.1| 153 QCESGQWCL 161
                                       999998766 PP

>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   3.2e-10   1.2e-06      21     109 ..      73     161 ..      55     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 3.2e-10
                    Transglut_core  21 iyewvrknveysaprrtpgsrd....aeavletgkGncedfaslfvallRalGi...paRvvtgylsgeeekeqsva 90 
                                         ++v  +++y++++++ g +d    +e++l  gkG+ced++ l+++ll a+Gi     Rvv g + ++       a
  gi|330506584|ref|YP_004383012.1|  73 SWDYVTRSIDYVTDKSSFGLEDlwlfPEETLMLGKGDCEDTSFLLASLLLASGIseqCVRVVLGRVASP-------A 142
                                       568999******999999999999******************************554489999999975.......8 PP

                    Transglut_core  91 sedaHawvevylegygWvp 109
                                       +++ Hawv +  e ++W+ 
  gi|330506584|ref|YP_004383012.1| 143 GSYGHAWVVYQCESGQWCL 161
                                       9999****99999999975 PP

>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   9.1e-06     0.032      66     102 ..      98     134 ..      33     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.1e-06
                            DUF553  66 tpkeilktkkgiCrDYaiLTaalLlnlniskvylvsv 102
                                        p+e+l+  kg C+D ++L a lLl+++is+  +  v
  gi|330506584|ref|YP_004383012.1|  98 FPEETLMLGKGDCEDTSFLLASLLLASGISEQCVRVV 134
                                       79***************************98544322 PP

>> Imm31  Immunity protein 31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.1e-05      0.25      27      62 ..     133     168 ..     123     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.1e-05
                             Imm31  27 vvlGrseddqGefeyavfiyadeniCWsleedelea 62 
                                       vvlGr     G +++a  +y+ e   W l e  le+
  gi|330506584|ref|YP_004383012.1| 133 VVLGRVASPAGSYGHAWVVYQCESGQWCLLETTLES 168
                                       89******************************9986 PP

>> PDEase_I_N  3'5'-cyclic nucleotide phosphodiesterase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.6e-05      0.27      17      31 ..      32      46 ..      31      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.6e-05
                        PDEase_I_N 17 VPseVrdWLastFtr 31
                                      +P++VrdWL+ t ++
  gi|330506584|ref|YP_004383012.1| 32 IPTDVRDWLSHTHSK 46
                                      7**********9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1634.06
//
Query:       gi|330506585|ref|YP_004383013.1|  [L=187]
Description: hypothetical protein MCON_0324 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-29  103.3   6.4    4.6e-28   98.2   6.4    2.1  1  Mut7-C          Mut7-C RNAse domain
    0.00044   19.5   0.8    0.00099   18.4   0.8    1.6  1  zf-TFIIB        Transcription factor zinc-finger
    0.00077   19.2   0.0     0.0017   18.1   0.0    1.5  1  DUF5615         Domain of unknown function (DUF5615)
     0.0042   17.0   1.0     0.0042   17.0   1.0    2.3  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.022   14.7   0.0    1.4  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.054   13.4   0.2       0.11   12.5   0.2    1.4  1  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.13   12.5   1.2       0.36   11.0   1.2    1.9  1  zf-RING_7       C4-type zinc ribbon domain
       0.16   11.4   0.1       0.27   10.6   0.1    1.3  1  MtrF            Tetrahydromethanopterin S-methyltransferase, 
       0.17   11.7   0.0       0.24   11.2   0.0    1.2  1  DUF3346         Protein of unknown function (DUF3346)


Domain annotation for each model (and alignments):
>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   6.4   2.3e-31   4.6e-28       2     146 .]      34     164 ..      33     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 2.3e-31
                            Mut7-C   2 rfllDamlgklakyLRllGydalyasdvedeellalaakekrillTrdreLlkraklkkg..vlltsrdveeqlrev 76 
                                        fl+D ml +la++LRllG d++  ++ +d++ll +a++e+ril+Trd++L ++ +++    +l++s+++ eq+ e+
  gi|330506585|ref|YP_004383013.1|  34 SFLVDLMLLRLARWLRLLGQDVANPESDSDKALLGQAKRENRILVTRDKRLFSSCSAAGVegILIRSSRICEQILEM 110
                                       59************************99*************************988876577*************** PP

                            Mut7-C  77 iarlglklslkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrkvfWkGshwerveell 146
                                        a+ g++l+++p  +rC+ Cn+ l+e+e  +              e++ C++C++++W+Gshw+++e++l
  gi|330506585|ref|YP_004383013.1| 111 -AEKGIALRIDP--QRCTLCNSSLKEAEGRDG-------------EIWICPNCQRLYWRGSHWKNMEKML 164
                                       .88889999998..**********99887765.............8********************9975 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.8     5e-07   0.00099       2      26 ..     124     148 ..     123     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5e-07
                          zf-TFIIB   2 CPkCqdeleeserggveidyCpqCr 26 
                                       C  C+++l+e+e ++ ei+ Cp+C+
  gi|330506585|ref|YP_004383013.1| 124 CTLCNSSLKEAEGRDGEIWICPNCQ 148
                                       999*********************6 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   8.5e-07    0.0017      11      59 ..      42      86 ..      34      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.5e-07
                           DUF5615 11 prlvellreaghdvlhvrelglegasDeeileyAkeedriivTkD.kDFg 59
                                       rl+++lr +g dv        e+ sD++ l  Ak+e+ri+vT+D + F+
  gi|330506585|ref|YP_004383013.1| 42 LRLARWLRLLGQDVANP-----ESDSDKALLGQAKRENRILVTRDkRLFS 86
                                      48899999999977777.....3458*******************66665 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.0   2.1e-06    0.0042       4      26 ..     123     148 ..     117     149 .. 0.89
   2 ?   -1.6   0.2       1.4   2.7e+03       6      11 ..     179     184 ..     179     186 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.1e-06
                    PhnA_Zn_Ribbon   4 kCplCaSeytY...edgallvCpeCa 26 
                                        C lC+S+       dg++++Cp+C 
  gi|330506585|ref|YP_004383013.1| 123 RCTLCNSSLKEaegRDGEIWICPNCQ 148
                                       599***98666999***********5 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                    PhnA_Zn_Ribbon   6 plCaSe 11 
                                       ++C+ e
  gi|330506585|ref|YP_004383013.1| 179 EECKGE 184
                                       455555 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 ?   14.7   0.0   1.1e-05     0.022       5      33 ..     122     154 ..     119     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                       Prok-RING_1   5 kkCpvCgkelkee....dDiVvCpeCgtpyHra 33 
                                       ++C++C+  lke+      i +Cp+C   y r 
  gi|330506585|ref|YP_004383013.1| 122 QRCTLCNSSLKEAegrdGEIWICPNCQRLYWRG 154
                                       78*********98777689*******9988874 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   5.3e-05      0.11      10      38 ..     120     151 ..     116     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-05
                                       S--B-TTT-SB-...-SSSS-EEEETTT--EE CS
                              C1_1  10 qptfCkhCgefl...wgkekqglkCswCkllv 38 
                                       +p++C+ C+++l   +g    ++ C +C++l+
  gi|330506585|ref|YP_004383013.1| 120 DPQRCTLCNSSLkeaEGRDGEIWICPNCQRLY 151
                                       689*********7755577788*******986 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 ?   11.0   1.2   0.00018      0.36      14      32 ..     131     150 ..     123     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                       HHHHCCS.TB-EE-TTT--E CS
                         zf-RING_7  14 lselrag.devvtCpeCGRI 32 
                                       l+e  +  +e+  Cp+C+R+
  gi|330506585|ref|YP_004383013.1| 131 LKEAEGRdGEIWICPNCQRL 150
                                       5666666799*********6 PP

>> MtrF  Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00014      0.27      26      47 ..      77      98 ..      74      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                              MtrF 26 LiaReqkLdSGvsatgivGfai 47
                                      L++R+++L+S  sa+g+ G+ i
  gi|330506585|ref|YP_004383013.1| 77 LVTRDKRLFSSCSAAGVEGILI 98
                                      89*****************976 PP

>> DUF3346  Protein of unknown function (DUF3346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.24      33      67 ..     125     159 ..     110     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                       EEEEESS--EE-TTSSEE--EEEEEEEE-HHHHHH CS
                           DUF3346  33 titaseeapkegkdgeirikpnlyilvwepsffde 67 
                                       t+  s     eg dgei i pn   l w  s +++
  gi|330506585|ref|YP_004383013.1| 125 TLCNSSLKEAEGRDGEIWICPNCQRLYWRGSHWKN 159
                                       5666777789*******************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1321.80
//
Query:       gi|330506586|ref|YP_004383014.1|  [L=641]
Description: hypothetical protein MCON_0325 [Methanosaeta concilii GP6]
Scores for complete 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-68  229.0   0.0    1.2e-67  228.6   0.0    1.1  1  FbpA       Fibronectin-binding protein A N-terminus (FbpA)
    8.6e-24   84.3   0.0    1.5e-23   83.5   0.0    1.4  1  NFACT-R_1  NFACT protein RNA binding domain


Domain annotation for each model (and alignments):
>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.6   0.0   1.4e-71   1.2e-67       2     408 ..       7     414 ..       6     421 .. 0.92

  Alignments for each domain:
  == domain 1  score: 228.6 bits;  conditional E-value: 1.4e-71
                                       HHHHHHHHHHHHHHHTTXEEEEEEEEETTEEEEEEE.ETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHH CS
                              FbpA   2 glvlaavvaELqkellggridkiyqpekdelvltlr.anrgrhkLllsahpsyarihltekpkenpkeppnFcmlLR 77 
                                       ++++aa+v+ELq+++lgg   k yq  +d + l+++   +gr +Lll+    + r+h+t+ +++  k+pp+F+ +LR
  gi|330506586|ref|YP_004383014.1|   7 NVDVAAMVKELQDRILGGFMGKAYQQSSDRIWLSVQsPAEGRLDLLLET---GRRVHITKAERPASKTPPQFPTMLR 80 
                                       789*********************************99999999*****...************************* PP

                                       HHHTTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBST CS
                              FbpA  78 kyLkgarivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilp 154
                                        +L+g+riv+i+q++fdR++e+++e+       + + LivE++ + + +iL+de+++I+  ++++  +    R+   
  gi|330506586|ref|YP_004383014.1|  81 SHLSGGRIVDIRQHQFDRVLEIKVERS-----GTARYLIVELFPK-GSMILLDESRNILSMLRKMLYR---GRKMAA 148
                                       ***************************.....89999********.*******************777...9***** PP

                                       TXBXXXSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH............... CS
                              FbpA 155 gekYelPpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerl 231
                                       ge+Y + p   +l+P ++ + +e+   l  + +dlv+ Lv+ + ++++++ ee++  ag+dk+++a +l+  +++r+
  gi|330506586|ref|YP_004383014.1| 149 GEPYLYHPG--QLDPRTIAR-DELALWLASSGQDLVRSLVRGL-NMGGTYGEEVCLVAGVDKNKEAIDLDPGEIDRV 221
                                       *********..999997766.55555555589***********.********************************* PP

                                       HHHHHHHHTXXX....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHHH CS
                              FbpA 232 yealqelleeleeekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkaerdrveqkrsdlekrv 308
                                       ++al+e++ + +   + p++v+++  p ++ + plk +s+lek+ f ++seald+++ ++++++  +     le+r+
  gi|330506586|ref|YP_004383014.1| 222 HQALSEVFLNET---LDPHIVIEDGAPIDVLPRPLKLYSGLEKKRFVTFSEALDAFFVEREKETTRQ---DPLEHRI 292
                                       ********9766...9********9888888888***********************9998877654...5777777 PP

                                       HHHHHHHHHHHHHHHHHHHCCGGH..HHHHCCHH-----------------------.--................. CS
                              FbpA 309 eneleklekklkklekelekaeka..enyrligelltaylyaikkgmsevelenyydege................. 366
                                       e +++  e+ ++ +e+el +  +   + y  ++++lt ++ a+++g s  ++ + ++ g+                 
  gi|330506586|ref|YP_004383014.1| 293 ELQRKAIEEFRS-QEAELVRKGELiyQLYGSVEQILTLMNDARARGFSYNQIWERIS-GSglpqaktilsldgrgem 367
                                       777666665544.45555555555689999999************************.77889************** PP

                                       .....---------------HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FbpA 367 .....evtIpLdprkspsenAqkyfkkykKlkraveaveeqieetke 408
                                            + + +L+ ++ +++nAq+y++k+k + r++++++ +++ t+e
  gi|330506586|ref|YP_004383014.1| 368 rvfldGEELELNAELAVPQNAQRYYDKAKDMVRKARGAQSALAITEE 414
                                       ***9999************************************9987 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   0.0   1.7e-27   1.5e-23       2     109 .]     443     552 ..     442     552 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 1.7e-27
                         NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia. 77 
                                       ++wF ssdg+lv++G+D+ +nee++ kyle++d+ +h d  +++ + ++ +eg+  e+pe++l+eaa +a+++S+  
  gi|330506586|ref|YP_004383014.1| 443 FRWFYSSDGFLVLGGRDADSNEEIYAKYLERRDLAMHTDAPGAPLTAIK-TEGK--EVPESTLQEAAGFAVSYSSLw 516
                                       99***********************************************.7777..8******************** PP

                         NFACT-R_1  78 gnklssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                       ++ l ++d++ v+ +++skt++    l++G+++++g
  gi|330506586|ref|YP_004383014.1| 517 KSGLAAADCYLVKGDQVSKTPEsgefLKKGAFVIRG 552
                                       ********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 4438.58
//
Query:       gi|330506587|ref|YP_004383015.1|  [L=493]
Description: hypothetical protein MCON_0326 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0019   18.3   2.0      0.005   17.0   2.0    1.6  1  HNH       HNH endonuclease
     0.0087   16.3   0.0      0.022   15.1   0.0    1.7  1  ParBc     ParB-like nuclease 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 !   17.0   2.0   5.6e-07     0.005       9      41 ..      34      66 ..      29      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.6e-07
                               HNH  9 hksealevdHiipisqggaddieNlqllCksCH 41
                                      ++ ++   +Hi p+ + g+++i+N++++Ck+ H
  gi|330506587|ref|YP_004383015.1| 34 EDISQVDFHHISPRCERGPTTIDNMAPVCKDHH 66
                                      55567789*********************9866 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.4e-06     0.022       3      73 ..     151     221 ..     149     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-06
                             ParBc   3 vplseir.pnplqprkdspekieelvasIkkkGllqPiivrktrqgryeiiaGerRlrAakrlglkevpviv 73 
                                       +p++ i+   +lqpr  + +++ el + +    +l P+i r ++  +  +++G++   A  ++g k+v++ +
  gi|330506587|ref|YP_004383015.1| 151 IPIEYIKnDFELQPRPLESKRMWELYRHFLRYTQLAPAICRLVD-RQVLLFDGQHKTAAQIWAGRKYVDCKI 221
                                       67777775568999999999***********************7.*******************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3510.06
//
Query:       gi|330506588|ref|YP_004383016.1|  [L=303]
Description: Ion transport protein [Methanosaeta concilii GP6]
Scores for 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   66.5  17.7    2.6e-18   66.2  17.7    1.1  1  Ion_trans      Ion transport protein
    7.2e-16   57.9   4.7    7.2e-16   57.9   4.7    2.8  3  Ion_trans_2    Ion channel
  ------ inclusion threshold ------
      0.011   15.8   0.9      0.018   15.1   0.9    1.3  1  DZR            Double zinc ribbon
      0.038   13.7   4.7       0.22   11.3   5.3    2.0  2  zinc_ribbon_2  zinc-ribbon domain
       0.12   11.9   0.9          6    6.4   0.1    2.3  2  zf-ribbon_3    zinc-ribbon domain
       0.18   11.9   0.0       0.26   11.3   0.0    1.3  1  HypA           Hydrogenase/urease nickel incorporation, metal
        1.4    8.9   3.5       0.92    9.5   0.3    2.1  2  YhfH           YhfH-like protein


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 !   66.2  17.7     1e-21   2.6e-18       3     226 ..      51     252 ..      49     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 1e-21
                                       HHHHHHHHHHHHHHHHHHCCCSSSSHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHCHSHHHHHHHHHHH CS
                         Ion_trans   3 vfelfilllillncvflaletyfpedelektileilelvftaiftlemllkilalgllikkrYlrdpwnilDflvvl 79 
                                        +++fi+ll ll ++++ +ety+ +  +  +il   e++ + +f++e ll++++++   ++ Y++d   i+D+++++
  gi|330506588|ref|YP_004383016.1|  51 AIDIFIILLNLLVVMLFVIETYPLSAGTQ-EILWRTEVAAVSLFIIEYLLRLYGAPD--RWAYVKDGYSIIDIVAIM 124
                                       5789999999999999999******8888.***************************..****************** PP

                                       HHHHHHHHHH....HHHHHHHHHHHHGGGGGGHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Ion_trans  80 psllslvlse....esllllsvlrlfrvlrllklisrleglrtlvtalirsvkdllnvlllllvvlfifaligvqlf 152
                                       p+l+ +vl        +  ++ +r++  +r++++++ + +   l  ++   + ++ +++  ++++lf+++ ++  +f
  gi|330506588|ref|YP_004383016.1| 125 PTLVLMVLPAtfftHDIRFIQTIRVMAAFRIFRFLRFMAKDHLLFGMISPGMINVARLVASIFIILFVYSGLF--YF 199
                                       ****995544555566788888888888888888888888888666666666666666666666666666555..66 PP

                                       TTSCCCCCCSCCSTSSSTTTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHH CS
                         Ion_trans 153 kgklreknecaktwenpnngntnFdnfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsflll 226
                                                     e+p n  + ++nf++a++++++  +t+g+gdi++    ++      ++ + +i+++++++
  gi|330506588|ref|YP_004383016.1| 200 -------------VEEPLN--PDVQNFGDAFYFVVVAVSTVGFGDIVPSSSAGR------LVTVAMIISGIIFI 252
                                       .............345544..4677*****************************......77777777777654 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.6     0.046   1.2e+02      47      70 ..      45      68 ..      39      71 .. 0.88
   2 ?    3.1   0.4     0.037        95      41      70 ..     169     200 ..     169     202 .. 0.79
   3 !   57.9   4.7   2.8e-19   7.2e-16       2      75 ..     186     261 ..     185     265 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.046
                                      T-----HHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2 47 etdagrlftivyillGlalfalfl 70
                                      +t++g+++ i++ill l++++lf+
  gi|330506588|ref|YP_004383016.1| 45 RTPLGKAIDIFIILLNLLVVMLFV 68
                                      588999************999987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.037
                                       ---SSTT.-----HHH.HHHHHHHHHHHHHHH CS
                       Ion_trans_2  41 YGdivpe.tdagrlft.ivyillGlalfalfl 70 
                                       +G i+p+  ++ rl++ i++il+ ++ +++f+
  gi|330506588|ref|YP_004383016.1| 169 FGMISPGmINVARLVAsIFIILFVYSGLFYFV 200
                                       78899999888899998888888777777666 PP

  == domain 3  score: 57.9 bits;  conditional E-value: 2.8e-19
                                       HHHHTCHHHHHHHHT......T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2   2 vlllvlifgaviysleeg..wekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgk 75 
                                       +++++++++ ++y++ee      ++f da+Yf++v ++T+G+Gdivp + agrl+t++ i+ G++++ +  a +++
  gi|330506588|ref|YP_004383016.1| 186 IFIILFVYSGLFYFVEEPlnPDVQNFGDAFYFVVVAVSTVGFGDIVPSSSAGRLVTVAMIISGIIFIPFQAARIFR 261
                                       577888888888888666434499************************9999***************998887766 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.9     7e-06     0.018       1      24 [.     275     299 ..     268     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7e-06
                               DZR   1 CpqCgee.lppdarfCseCgtklka 24 
                                       C +Cg + ++ d+++C++Cg++l++
  gi|330506588|ref|YP_004383016.1| 275 CTNCGLDrHDVDSKYCKKCGEALPE 299
                                       9999988467799999999999975 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3    0.0064        16      10      20 ..     269     279 ..     267     281 .. 0.78
   2 ?   11.3   5.3   8.5e-05      0.22       2      23 .]     275     297 ..     274     297 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0064
                     zinc_ribbon_2  10 qdnakFCpyCG 20 
                                       qd+ + C++CG
  gi|330506588|ref|YP_004383016.1| 269 QDRTVICTNCG 279
                                       67777888887 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 8.5e-05
                     zinc_ribbon_2   2 CpnCGaelqd.nakFCpyCGtpl 23 
                                       C+nCG    d ++k+C +CG+ l
  gi|330506588|ref|YP_004383016.1| 275 CTNCGLDRHDvDSKYCKKCGEAL 297
                                       ********888*********975 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0023         6      13      24 ..     269     280 ..     266     282 .. 0.80
   2 ?    3.8   0.1     0.016        41      17      24 ..     288     295 ..     283     301 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0023
                       zf-ribbon_3  13 ssddnvCpyCGt 24 
                                       +++ ++C++CG 
  gi|330506588|ref|YP_004383016.1| 269 QDRTVICTNCGL 280
                                       567789*****7 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.016
                       zf-ribbon_3  17 nvCpyCGt 24 
                                       + C++CG+
  gi|330506588|ref|YP_004383016.1| 288 KYCKKCGE 295
                                       45666664 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0001      0.26      60      95 ..     262     296 ..     236     303 .] 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                                       -EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  60 aeLeieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       a L+ ++++ +v C++Cg + +   ++  C+kCg+a
  gi|330506588|ref|YP_004383016.1| 262 AWLRASSQDRTVICTNCGLDRHDV-DSKYCKKCGEA 296
                                       6788899999********776633.3457*****87 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.46   1.2e+03      16      20 ..     275     279 ..     274     281 .. 0.86
   2 ?    9.5   0.3   0.00036      0.92      12      26 ..     286     300 ..     282     303 .] 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.46
                              YhfH  16 CteCG 20 
                                       Ct+CG
  gi|330506588|ref|YP_004383016.1| 275 CTNCG 279
                                       9***9 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00036
                              YhfH  12 PkKkCteCGkeieEq 26 
                                        +K C +CG+ + E 
  gi|330506588|ref|YP_004383016.1| 286 DSKYCKKCGEALPET 300
                                       58********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2020.58
//
Query:       gi|330506589|ref|YP_004383017.1|  [L=403]
Description: threonine dehydratase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-79  267.5   6.4    1.5e-79  267.5   5.6    1.4  2  PALP      Pyridoxal-phosphate dependent enzyme
    0.00051   19.8   0.2     0.0031   17.3   0.0    2.3  2  ACT       ACT domain
  ------ inclusion threshold ------
       0.11   13.1   0.0       0.25   12.0   0.0    1.6  1  ACT_4     ACT domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.5   5.6   2.5e-83   1.5e-79       4     294 .]      17     305 ..      14     305 .. 0.98
   2 ?   -3.0   0.0      0.62   3.7e+03     122     150 ..     349     378 ..     341     386 .. 0.78

  Alignments for each domain:
  == domain 1  score: 267.5 bits;  conditional E-value: 2.5e-83
                                       CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                              PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlk 80 
                                        + +TPlv +p +s+  +++++lKlEsl+ +gSfK+Rga+y l++  e+    +v++as GNh++++A+aa ++G++
  gi|330506589|ref|YP_004383017.1|  17 RVIRTPLVYSPTFSRLANAEVYLKLESLQMGGSFKVRGATYKLQSNLEK-IHSGVIAASVGNHAQGVALAACAAGVP 92 
                                       5789*****************************************8888.89************************* PP

                                       EEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTT CS
                              PALP  81 vtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggk 157
                                       +ti +p +as +k++++r++Gaev++ g++  e+ ++ +++a+e +++++++++d++ vi+g+gt+glEile+l ++
  gi|330506589|ref|YP_004383017.1|  93 ATIIMPVWASISKQEATRAYGAEVRLMGKSLVESIEIGRRMAQE-TNRIFIHPYDDEEVIAGQGTVGLEILEDL-PD 167
                                       ********************************************.*****************************.6* PP

                                       EEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B...SSS.CCSTCSCGTTCCHHH CS
                              PALP 158 pdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvs..dtiadglavgspselafel 232
                                        d ++vpvGgGgliaGia + k+ rp+ rv+gv+++ +++  ++l+ gr+ +v+ +   +iad++ v +++e  f+l
  gi|330506589|ref|YP_004383017.1| 168 ADLIIVPVGGGGLIAGIALAAKAIRPEARVVGVQAASCPSARKALELGRPAEVQAEerGSIADAIMVTQVGEAPFPL 244
                                       **************************************************999999889****************** PP

                                       HSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 233 ldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       l++lvd+iv v+++++++a+ +l +r +i++e ++aa laal l    +++eg+rvv++++g
  gi|330506589|ref|YP_004383017.1| 245 LQKLVDDIVLVDEDQIASAVLKLLERKRILAEGAAAAPLAAL-LGGSLQVAEGSRVVLVVSG 305
                                       ******************************************.*****************98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.62
                                       HHHSTTCEE--TTTSHHHHHH.HHTHHHHH CS
                              PALP 122 aaegegaylvsqfdnptvieg.ygtiglEi 150
                                       a ++ +++++++  n+ +++  y+ + lE+
  gi|330506589|ref|YP_004383017.1| 349 ADQEANVVHIHHARNESGVAInYTRVDLEL 378
                                       455688999999999999999888888887 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.27   1.6e+03      42      59 ..     247     264 ..     223     271 .. 0.71
   2 !   17.3   0.0   5.2e-07    0.0031       4      42 ..     331     369 ..     329     385 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.27
                                       EEEEEEEEEEHHHHHHHH CS
                               ACT  42 givfvvivvdeedleevl 59 
                                       ++v+ +++vde+++++++
  gi|330506589|ref|YP_004383017.1| 247 KLVDDIVLVDEDQIASAV 264
                                       566677777777777665 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.2e-07
                                       EEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECE CS
                               ACT   4 rvgvpDrPGlLarvfgaladrgiNidsieqrssedkvag 42 
                                       +v++ D PG La ++g+lad   N+++i++++ e +va 
  gi|330506589|ref|YP_004383017.1| 331 SVSLVDSPGSLACLLGLLADQEANVVHIHHARNESGVAI 369
                                       68999*************************998886444 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.1e-05      0.25       8      66 ..     329     390 ..     324     396 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
                             ACT_4   8 rleveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkdvehLsrvi 66 
                                       + +v   d++g La ++ ++++++an+v+++   +++    +++++++++e +  eh++ + 
  gi|330506589|ref|YP_004383017.1| 329 HFSVSLVDSPGSLACLLGLLADQEANVVHIHHARNESgvaINYTRVDLELETRGFEHIKGIE 390
                                       568999************************98887766776699999999999999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.42
# Mc/sec: 2851.14
//
Query:       gi|330506590|ref|YP_004383018.1|  [L=391]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (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   79.8   0.1    3.9e-22   78.0   0.1    2.0  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    3.1e-07   30.6   0.3    3.1e-07   30.6   0.3    1.9  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.033   14.2   0.3      0.089   12.8   0.3    1.7  1  DZR             Double zinc ribbon
      0.089   12.8   0.1       0.22   11.6   0.1    1.7  1  HypA            Hydrogenase/urease nickel incorporation, meta


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.1   8.6e-26   3.9e-22       1      67 [.     288     352 ..     288     353 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 8.6e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       f +lke+l+yka  +G+++++v+payTS+tC++Cg+ + +  +g+ fkCp Cg + d+D+n+a Ni+
  gi|330506590|ref|YP_004383018.1| 288 FCQLKEFLSYKALAAGVPLVLVDPAYTSQTCHQCGEHGIR--NGKSFKCPVCGWSGDADFNGAKNIA 352
                                       5689************************************..************************7 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2      0.54   2.4e+03      42      70 ..      92     120 ..      67     137 .. 0.71
   2 !   30.6   0.3     7e-11   3.1e-07       2     106 ..     154     255 ..     153     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.54
                        OrfB_IS605  42 kgrrlksdykylakeiaelqsklkkskny 70 
                                        +  ++++ ++++++  e++ +l +s+++
  gi|330506590|ref|YP_004383018.1|  92 TSIDYDTRIFAFREKDEEVSVTLLRSRQR 120
                                       45566777788888888888888888752 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 7e-11
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn..ykkasrk 76 
                                       ipv+ e  +++    +++g+DlGi ++a++++++     + g+ +k  +  +a  +a lq+k+ k ++  ++++++ 
  gi|330506590|ref|YP_004383018.1| 154 IPVKSEA-PEQIHVDTVLGVDLGITDIAVTSEGQ----KFGGKTIKLIKHHYASMRAVLQQKAVKGTRssRRRCREL 225
                                       6777665.777788899****************9....889999****************9998888889******* PP

                        OrfB_IS605  77 larlhrkrsrrrkhllhklathliktlkev 106
                                       ++rl+ k +r  +   h+++++++ + +e+
  gi|330506590|ref|YP_004383018.1| 226 QQRLSGKEARYQRQINHEISKAIVTRAQEI 255
                                       ************************999987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3     2e-05     0.089      28      49 .]     315     338 ..     282     349 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                               DZR  28 edrCpsCgek.vdpearf.CpeCG 49 
                                       +++C +Cge  + ++++f Cp CG
  gi|330506590|ref|YP_004383018.1| 315 SQTCHQCGEHgIRNGKSFkCPVCG 338
                                       566777777766666666777776 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 ?   11.6   0.1   4.9e-05      0.22      57      95 ..     301     340 ..     242     351 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.9e-05
                                       TTT-EEE.EEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  57 legaeLe.ieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       ++g  L  ++    + +C++Cg+++  + k+++Cp Cg +
  gi|330506590|ref|YP_004383018.1| 301 AAGVPLVlVDPAYTSQTCHQCGEHGIRNGKSFKCPVCGWS 340
                                       45555543444556789*****9998777789*****965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2797.11
//
Query:       gi|330506591|ref|YP_004383019.1|  [L=114]
Description: hypothetical protein MCON_0331 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 861.81
//
Query:       gi|330506592|ref|YP_004383020.1|  [L=156]
Description: hypothetical protein MCON_0332 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 992.73
//
Query:       gi|330506593|ref|YP_004383021.1|  [L=73]
Description: hypothetical protein MCON_0333 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.1   0.0      0.037   13.9   0.0    1.1  1  DUF4939   Domain of unknown function (DUF4939)


Domain annotation for each model (and alignments):
>> DUF4939  Domain of unknown function (DUF4939)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.1e-06     0.037      70     104 ..       3      37 ..       1      47 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-06
                           DUF4939  70 rltGealewvlpyikkdspllndyraflaemkrvf 104
                                       rlt + ++ +++yi+ d pl ++yr +l e kr+ 
  gi|330506593|ref|YP_004383021.1|   3 RLTEREQQEIIRYIEADKPLPDKYRFLLFEDKREV 37 
                                       899999**********************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 557.58
//
Query:       gi|330506594|ref|YP_004383022.1|  [L=97]
Description: hypothetical protein MCON_0334 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   0.0        0.2   11.4   0.0    1.4  1  KRTDAP    Keratinocyte differentiation-associated


Domain annotation for each model (and alignments):
>> KRTDAP  Keratinocyte differentiation-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.1e-05       0.2      45      76 ..      56      85 ..      41      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.1e-05
                            KRTDAP 45 halfealkkklpflnWdafPklkGlRsaiPDa 76
                                      hal+e  k    f+  + + k +GlR a PD+
  gi|330506594|ref|YP_004383022.1| 56 HALIELEKD--DFISLEEYAKRRGLRCARPDS 85
                                      999998776..59999***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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: 748.60
//
Query:       gi|330506595|ref|YP_004383023.1|  [L=38]
Description: hypothetical protein MCON_0335 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00019   21.4   0.0    0.00024   21.1   0.0    1.2  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.3e-08   0.00024       1      29 [.       9      37 ..       9      38 .] 0.91

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-08
                                      -HCHHHHHHHTT-EEEEEETTEEEEE-TT CS
                        HicA_toxin  1 wreviklLeklGfevvrqkGSHvrfkhpd 29
                                      ++e+ik++ k+G  v+r kG+Hv  k p+
  gi|330506595|ref|YP_004383023.1|  9 GKEAIKAFIKAGGIVRRGKGDHVNIKMPN 37
                                      69*********************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 297.57
//
Query:       gi|330506596|ref|YP_004383024.1|  [L=75]
Description: hypothetical protein MCON_0337 [Methanosaeta concilii GP6]
Scores for complete sequence (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   44.9   0.0    1.2e-11   44.8   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   6.4e-16   1.2e-11       1      56 [.       3      58 ..       3      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 6.4e-16
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeip 56
                                      y i+i++ e+  +   vP lpGc+s g+t+++ ++n+keaie hl +l ed  + p
  gi|330506596|ref|YP_004383024.1|  3 YTILIHQAEEGGFWSEVPALPGCYSQGETIDQTLQNTKEAIESHLIALKEDLVAAP 58
                                      99*******************************************99988866666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 578.02
//
Query:       gi|330506597|ref|YP_004383025.1|  [L=585]
Description: PUA domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-51  172.6   0.0    8.4e-51  171.9   0.0    1.3  1  DUF5591      Domain of unknown function (DUF5591)
    4.5e-14   52.2   0.1    1.9e-13   50.2   0.1    2.1  2  PUA          PUA domain
    5.9e-09   35.5   0.0    1.2e-08   34.5   0.0    1.5  2  TGT          Queuine tRNA-ribosyltransferase
    3.6e-06   27.0   0.0    8.6e-06   25.8   0.0    1.6  1  TGT_C2       Patch-forming domain C2 of tRNA-guanine transgly
     0.0056   16.8   0.6      0.013   15.6   0.6    1.7  1  Octopine_DH  NAD/NADP octopine/nopaline dehydrogenase, alpha-


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 !  171.9   0.0   2.3e-54   8.4e-51       1     150 [.     293     434 ..     293     438 .. 0.92

  Alignments for each domain:
  == domain 1  score: 171.9 bits;  conditional E-value: 2.3e-54
                                       X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT------- CS
                           DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqY 77 
                                       v+rf+ervlerY+ p+ ++vl+LlPcsa+kPys+s+shr faeai+++++ +he+iltsPl++vPrelee YPaa+Y
  gi|330506597|ref|YP_004383025.1| 293 VTRFAERVLERYQAPQ-SDVLLLLPCSARKPYSTSRSHRLFAEAIGSARRYLHELILTSPLALVPRELEEAYPAASY 368
                                       89*************7.************************************************************ PP

                                       ---------HHHHHHHHHHHHHHHHHHT-SEEEE---THHHHHHHHHHTT-SSEEEE--.SS-TTSHHHHHHH CS
                           DUF5591  78 diavtgewseeeiefvaellakylektkyekviahleeeyreiveevaeelgleiiytvvedkptskeslknL 150
                                       d++vtg+w++ee++++a +l+ yl+k++y +++ahl++e +e+v+e     g++++yt      t+  +l++L
  gi|330506597|ref|YP_004383025.1| 369 DVPVTGRWDREERAWLAGCLKAYLKKNRYVRIVAHLDGELEELVRES----GIDAVYTG---GGTNGPALARL 434
                                       ***************************************99999886....48888887...34555556555 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.9   6.8e+03      18      35 ..      24      41 ..      19      42 .. 0.80
   2 !   50.2   0.1   5.2e-17   1.9e-13      17      73 ..     528     582 ..     521     583 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.9
                                      EEEGGGEEEEETT--TTS CS
                               PUA 18 sLlapGvvevegdfeegd 35
                                      ++  pGv+  ++ +++g 
  gi|330506597|ref|YP_004383025.1| 24 QISTPGVITPDDYLSAGS 41
                                      57789****999988886 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 5.2e-17
                                       -EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA  17 asLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                        sLlapGvv++++++++gd+V +  e  ++ ++G+a++s+ e+    +g++vei+++
  gi|330506597|ref|YP_004383025.1| 528 GSLLAPGVVDADEEIRPGDEVIVEGE--QAFGIGRAKMSGWEMVASRRGVAVEIRHI 582
                                       49*******************77777..***************************97 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       1.9   6.8e+03       3      20 ..      14      30 ..      12      33 .. 0.82
   2 !   34.5   0.0   3.3e-12   1.2e-08     190     346 ..     106     249 ..      98     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1.9
                                      EEEEEEEETTEEEEESEE CS
                               TGT  3 aRlGklelphgtietPaf 20
                                      aR+Gkl l++ +i+tP +
  gi|330506597|ref|YP_004383025.1| 14 ARMGKLLLNR-QISTPGV 30
                                      8*******88.5***955 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 3.3e-12
                                       -SEEEE-SSSSSSHHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEE CS
                               TGT 190 fdgyaigGlsvgeekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsege 266
                                       +d+y  g     ++ ++l++ +  v+++   d   y     tP +l+ +v lG+D++d + ++  +  gr+ t++g 
  gi|330506597|ref|YP_004383025.1| 106 ADVYLMGNAGSLKNPRDLVKAIIGVRDKTAPDSALYAPALATPANLALLVYLGIDLIDGTRMIADGLLGRYHTRDGV 182
                                       56666666443344556666666788888888999*****************************************8 PP

                                       EETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                               TGT 267 lnlknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiHNlhyylelfkriReaIkegtfeefvee 343
                                       ++ k+   +++       C C+ C+      +++    +e   + Ll  HNl+ + e++ ++Rea+++ t  e+ve+
  gi|330506597|ref|YP_004383025.1| 183 WSAKELAERDE-----LFCLCPHCQ-----KMREKETRQE---TDLLVAHNLQKLDEELLAVREAVRTQTIREYVER 246
                                       87774433322.....35******9.....4555555566...89*******************************9 PP

                                       HHH CS
                               TGT 344 far 346
                                        +r
  gi|330506597|ref|YP_004383025.1| 247 QMR 249
                                       887 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 !   25.8   0.0   2.4e-09   8.6e-06       4      65 ..     457     512 ..     455     515 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.4e-09
                            TGT_C2   4 raiadYqFGagagdaLfpedvtitrsatgrirqvlv.dgerlatlraqdgrltLsleGarrlh 65 
                                       ra ad+ FG+gagdaL  +  +i      r r++++ ++  lat    +g + Ls++Ga+rl 
  gi|330506597|ref|YP_004383025.1| 457 RAHADFYFGQGAGDALLAG--KIV----VRGREIQDeNKRPLATW-TINGNMALSMAGAKRLE 512
                                       788**************88..555....4699****555557775.9**************96 PP

>> Octopine_DH  NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6   3.7e-06     0.013      40     109 ..     210     276 ..     177     345 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.7e-06
                       Octopine_DH  40 yegitpsvaevlealdeErlaiakalglevlplaerlldaYgdeikdksslaevirtneaykgikaPmsl 109
                                       +++++  va+ l++ldeE+la+++a++   ++++e+++++ + + ++++   + + +++ y   ++P s 
  gi|330506597|ref|YP_004383025.1| 210 RQETDLLVAHNLQKLDEELLAVREAVRT--QTIREYVERQMRVTPDQTA-ALRLLDAEHRYLERRTPVSR 276
                                       6788999*******************98..59********986555444.55556777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 4221.11
//
Query:       gi|330506598|ref|YP_004383026.1|  [L=479]
Description: archaeosine tRNA-ribosyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-78  263.1   0.0    5.1e-78  262.7   0.0    1.1  1  TGT           Queuine tRNA-ribosyltransferase
  ------ inclusion threshold ------
      0.092   13.1   0.2         25    5.3   0.0    2.5  2  TGT_C1        C1 domain of tRNA-guanine transglycosylase dime
       0.13   12.5   0.0       0.48   10.7   0.0    1.9  2  Mur_ligase_C  Mur ligase family, glutamate ligase domain


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.7   0.0   8.6e-82   5.1e-78       3     349 ..      14     334 ..      11     335 .. 0.95

  Alignments for each domain:
  == domain 1  score: 262.7 bits;  conditional E-value: 8.6e-82
                                       EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EE CS
                               TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpil 79 
                                       +R+G+l++ hgt+etP++mpv  +++++ + pdel+ ++ga+++++n+y++++ p  +  a ++glh++lg+++pi+
  gi|330506598|ref|YP_004383026.1|  14 GRIGRLSTLHGTVETPLLMPV-INPHLPLIPPDELA-SMGAEMVITNSYIINQDPDLREGAIEQGLHHLLGFPGPIM 88 
                                       8********************.999**********5.89********************99**************** PP

                                       EE-SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHH CS
                               TGT  80 tdsggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwld 156
                                       tdsg+fq   l           s + G+ + + p e++++q +++sDi ++ld ++p++ s++r+e +++ T+++l+
  gi|330506598|ref|YP_004383026.1|  89 TDSGAFQ---L-----------SVY-GD-IDVLPLEILDFQFAIKSDISVPLDIPTPPDVSRERAESELNITEERLR 149
                                       *******...3...........336.**.************************************************ PP

                                       HHHHHH.SE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEETT CS
                               TGT 157 rcleah.qa.lfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkprylmG 228
                                       ++   + +a l g+vqG++y+dlre++ + +++++fd y+igG ++++e  + ++l++vv ++++ l +  p++l+G
  gi|330506598|ref|YP_004383026.1| 150 EAAGLKrDAlLAGPVQGSTYPDLRERAGRFARELGFDLYPIGGvVPLMEayRFRDLVDVVVSAKKGLGSGVPVHLFG 226
                                       **97667666*********************************888***8888************************ PP

                                       B-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT CS
                               TGT 229 vgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhllktk 305
                                       +g+P+ ++ a a+G+D+fd+++++++ar+gr+lt +g+ +l++ k+     p    CsC++C +yt+++l    +  
  gi|330506598|ref|YP_004383026.1| 227 AGHPMIFALAAAMGCDLFDSAAYALYAREGRYLTVQGTRKLEEMKHL----P----CSCPVCLKYTQQELMDSPQR- 294
                                       *****************************************988888....9....******88*****9988744. PP

                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                               TGT 306 emlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                           ++ l+ HNl++ l+++k +R++I++g+++++ e+++r+++
  gi|330506598|ref|YP_004383026.1| 295 ----SRELARHNLYVSLQEIKLVRQSIRDGSLWDLLETRCRSHP 334
                                       ....4579*********************************997 PP

>> TGT_C1  C1 domain of tRNA-guanine transglycosylase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0044        26       4      34 ..     357     387 ..     355     394 .. 0.90
   2 ?    5.3   0.0    0.0041        25      42      59 ..     411     428 ..     405     440 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0044
                            TGT_C1   4 kksaffkvseealkwpiverakeraekvkak 34 
                                        ks+ff +s e+   p v r   r e++  k
  gi|330506598|ref|YP_004383026.1| 357 SKSTFFYLSPESASRPEVIRHGRRIERISLK 387
                                       589***********************99765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0041
                            TGT_C1  42 pifGeipkylslsypfaq 59 
                                       p fG  p  ls +ypf  
  gi|330506598|ref|YP_004383026.1| 411 PPFGPYPTQLSETYPFNA 428
                                       88**************64 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 ?   -2.7   0.0       1.2   7.4e+03      39      75 ..     153     187 ..     144     191 .. 0.72
   2 ?   10.7   0.0     8e-05      0.48       3      32 ..     379     408 ..     377     412 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                                       SSSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEE CS
                      Mur_ligase_C  39 pdkrlilvfgpggelgertrtfhdefgrlasaladsl 75 
                                         kr  l++gp    g+   +++++ gr a +l  +l
  gi|330506598|ref|YP_004383026.1| 153 GLKRDALLAGP--VQGSTYPDLRERAGRFARELGFDL 187
                                       55666777887..557888899999999988877665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8e-05
                                       TSSEEEEETTTEEEEEET--SHHHHHHHHH CS
                      Mur_ligase_C   3 gRlevvgeadgvtvidDyahnpdslsaalk 32 
                                       +R+e+++ ++ v++ dD ++np ++ ++l+
  gi|330506598|ref|YP_004383026.1| 379 RRIERISLKGEVLITDDPNANPSGYDNVLN 408
                                       8*************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 3167.70
//
Query:       gi|330506599|ref|YP_004383027.1|  [L=663]
Description: aconitate hydratase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.3e-103  347.5   1.5   4.9e-100  335.7   4.7    2.8  2  Aconitase    Aconitase family (aconitate hydratase)
    6.9e-19   68.5   0.0    1.6e-18   67.3   0.0    1.6  1  Aconitase_C  Aconitase C-terminal domain
  ------ inclusion threshold ------
      0.018   13.8   0.0      0.031   13.0   0.0    1.3  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 !  335.7   4.7  8.3e-104  4.9e-100       1     461 []       7     406 ..       7     406 .. 0.91
   2 ?   -2.6   0.0      0.34     2e+03     202     234 ..     416     449 ..     416     450 .. 0.84

  Alignments for each domain:
  == domain 1  score: 335.7 bits;  conditional E-value: 8.3e-104
                         Aconitase   1 ekiwdahlvee.....egiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeeal 72 
                                       eki+++hl +      ++i  + d+ l+qd+tg +a  ++++++ +          i +  +v+  +dh+       
  gi|330506599|ref|YP_004383027.1|   7 EKILREHLADGsyelgKEIGIKIDQTLTQDATGTMAYLQFESMGLSD---------IATELSVS-YVDHNT------ 67 
                                       78999998844444443366779*********************999.........44455555.444554...... PP

                         Aconitase  73 eknledefernkeryefLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgie 149
                                          ++  fe+ +   + L+s ak++gi +  pg+GI+Hqv lE  +a pgkt++g+DSHT+++gg+G la+G Gg +
  gi|330506599|ref|YP_004383027.1|  68 ---IQVGFEN-ADDHAYLESIAKKYGIYFSRPGNGICHQVHLER-FARPGKTLLGSDSHTPTAGGVGSLAMGAGGLD 139
                                       ...3444444.667799***************************.******************************** PP

                         Aconitase 150 aeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaE 226
                                       ++ ++ g  ++l +pkv+ v+l G+l+++ takD++l+v ++l +kg vg v E++G+g++ L++ +raTi+NM+aE
  gi|330506599|ref|YP_004383027.1| 140 VAVAMGGGAYYLAAPKVIDVHLMGNLQPWSTAKDVALKVLQILSTKGNVGFVSEYTGHGIAGLTVPERATITNMGAE 216
                                       ***************************************************************************** PP

                         Aconitase 227 vGAttglfpvdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavpl 303
                                       +G tt++fp d +t ++L+a++re++       +       laad+da+yd+ le+dl+++ep  a p++P + +++
  gi|330506599|ref|YP_004383027.1| 217 TGVTTSIFPSDLQTKRFLAAQERESQW------K------PLAADKDATYDRSLEIDLAEIEPLAAAPHSPGNIIKV 281
                                       *******************77773332......2......4889********************************* PP

                         Aconitase 304 selvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsv 380
                                        ++                             d +vd+++igSCTNss+ d++ +a++++     g++  +g+++ +
  gi|330506599|ref|YP_004383027.1| 282 -GDL----------------------------DLAVDQVMIGSCTNSSYVDLMTVARMVR-----GKRLPEGISLGI 324
                                       .333............................2459************************.....************ PP

                         Aconitase 381 aPGSevvkayleaeGlleiLekaGfevvgagCstCignsdrleegeaivsssNRNFegRqg.pntrayLaSPelvva 456
                                       aPGS++v + + ++G l++L + G+ ++++ C+ Cigns    +++++v +sNRNF gR g p+++ yL+SP +++a
  gi|330506599|ref|YP_004383027.1| 325 APGSRQVLNAIAKNGALSDLIAFGARILESSCGFCIGNSMSPCTNSVSVRTSNRNFMGRSGtPSANVYLTSPVVAAA 401
                                       *****************************************99*****************9566777********** PP

                         Aconitase 457 aAlaG 461
                                       aAl+G
  gi|330506599|ref|YP_004383027.1| 402 AALTG 406
                                       ***98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.34
                         Aconitase 202 vEffG.egvesLsledraTiaNMaaEvGAttglf 234
                                       +Ef G +  ++  ++dr+ i  +++E  A+++++
  gi|330506599|ref|YP_004383027.1| 416 MEFPGiQMPDHFDIDDRMIIPPLSPEQRARATIC 449
                                       5788845557899*****************9986 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.0   2.6e-22   1.6e-18      48     130 ..     497     580 ..     473     581 .. 0.85

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 2.6e-22
                                       BSEEEETTTTE.EEEHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT- CS
                       Aconitase_C  48 ankttdlddge.kedvvdaaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennlikngl 123
                                       ++k+ ++  ++ ++d++  a   +++g + +++ag  +G+GSSRehAA+ +  lG+k via+S erI+  nl++ g+
  gi|330506599|ref|YP_004383027.1| 497 VPKYAEFVFEPlDKDFFSRASSLRDQGFHNLIVAGLSYGQGSSREHAAMCPMYLGVKGVIAKSIERIHAANLVNFGI 573
                                       555555443331459************************************************************** PP

                                       EEEEEST CS
                       Aconitase_C 124 Lplefke 130
                                       +p +f++
  gi|330506599|ref|YP_004383027.1| 574 VPFTFEK 580
                                       ****986 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.1e-06     0.031     291     365 ..     288     369 ..     277     384 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.1e-06
                            DUF521 291 vdlvalG.cPhlsleElrelaellkgkkkkvkvelwvt.tsrevkeeaerlglveklekaGvkvlsdtCmvv..... 360
                                       vd v++G c   s+ +l+++a++++gk+  +++ l +   sr+v +++ + g ++ l ++G+++l+++C ++     
  gi|330506599|ref|YP_004383027.1| 288 VDQVMIGsCTNSSYVDLMTVARMVRGKRLPEGISLGIApGSRQVLNAIAKNGALSDLIAFGARILESSCGFCignsm 364
                                       7888887688899*********************988725899**************************76657444 PP

                            DUF521 361 splik 365
                                       sp+++
  gi|330506599|ref|YP_004383027.1| 365 SPCTN 369
                                       44443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (663 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 4550.51
//
Query:       gi|330506600|ref|YP_004383028.1|  [L=75]
Description: YcfA family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-19   69.4   0.2    2.2e-19   69.2   0.2    1.1  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.2   1.2e-23   2.2e-19       2      58 .]      10      66 ..       9      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.2e-23
                                      HCHHHHHHHTT-EEEEEETTEEEEE-TTSS-EEEEE.S-SSS--CCCHHHHHHHCC- CS
                        HicA_toxin  2 reviklLeklGfevvrqkGSHvrfkhpdkrgivtvppHpgkelkpgtlksIlkqaGl 58
                                      ++vi+++ek Gf+++r +GSH +f hp+++++vtvp H+++++ +gtl +Il++aG+
  gi|330506600|ref|YP_004383028.1| 10 QKVIAIIEKKGFVLKRVTGSHYIFAHPETKRRVTVPSHSDQDIARGTLIQILEDAGI 66
                                      68******************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 509.24
//
Query:       gi|330506601|ref|YP_004383029.1|  [L=77]
Description: hypothetical protein MCON_0347 [Methanosaeta concilii GP6]
Scores for complete 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-17   61.3   0.0      1e-16   61.1   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
      0.079   13.3   0.0       0.12   12.7   0.0    1.3  1  Jag_N            Jag N-terminus


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0   1.2e-20     1e-16       1      63 [.       6      68 ..       6      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.2e-20
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipepssiee 63
                                      y i++ k+ +  y+v+vP lpGc++ g+t+eeai++a++ai+ ++e+liedge+ip  +++ e
  gi|330506601|ref|YP_004383029.1|  6 YRITLRKEPEGGYTVLVPALPGCITYGKTVEEAIEMARDAINGYIESLIEDGEAIPVEEDLIE 68
                                      88999999************************************************8877755 PP

>> Jag_N  Jag N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.4e-05      0.12       2      14 ..      31      43 ..      30      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                             Jag_N  2 eGkTveeAiekAl 14
                                       GkTveeAie A 
  gi|330506601|ref|YP_004383029.1| 31 YGKTVEEAIEMAR 43
                                      6*********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 587.20
//
Query:       gi|330506602|ref|YP_004383030.1|  [L=68]
Description: hypothetical protein MCON_0348 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-12   47.5   0.0      2e-12   47.3   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
      0.027   14.5   0.0      0.029   14.4   0.0    1.2  1  DUF1902          Domain of unknown function (DUF1902)


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   2.3e-16     2e-12       3      57 ..       4      58 ..       3      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.3e-16
                   HicB_lk_antitox  3 iaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipe 57
                                      ++i ++ed ++   vP lpGc+s g t eea++n+keai++++++l edg ++pe
  gi|330506602|ref|YP_004383030.1|  4 VIIYPGEDGCWVAEVPSLPGCISQGRTKEEALNNTKEAIQAYIDALKEDGIAVPE 58
                                      678899*********************************************9997 PP

>> DUF1902  Domain of unknown function (DUF1902)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.2e-06     0.029       6      44 ..       5      43 ..       3      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-06
                                      EEEETTTTEEEEE-SSSTT---EESSHHHHHHHHHHHHH CS
                           DUF1902  6 vvwDeeAgVWvaesddipGlvteaetleeLlkkleamip 44
                                      + + +e g Wvae   +pG + +  t ee l+  + +i+
  gi|330506602|ref|YP_004383030.1|  5 IIYPGEDGCWVAEVPSLPGCISQGRTKEEALNNTKEAIQ 43
                                      578899***********************9999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      698  (0.0389313); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 492.80
//
Query:       gi|330506603|ref|YP_004383031.1|  [L=197]
Description: plasmid pRiA4b ORF-3-like protein [Methanosaeta concilii GP6]
Scores for complete 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-66  221.9   0.2    4.9e-66  221.7   0.2    1.0  1  PRiA4_ORF3  Plasmid pRiA4b ORF-3-like protein


Domain annotation for each model (and alignments):
>> PRiA4_ORF3  Plasmid pRiA4b ORF-3-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.7   0.2   2.7e-70   4.9e-66       2     173 ..      17     187 ..      16     188 .. 0.98

  Alignments for each domain:
  == domain 1  score: 221.7 bits;  conditional E-value: 2.7e-70
                        PRiA4_ORF3   2 ayqlkveLkdvepkiwRrlevpeditlarLhevlqaafgwedyHlheFeieekrygeeeeedeeeeeevldeskvkl 78 
                                       +yqlkv+L++++p+iwRr++v++di+l +Lh++lq+++gw+d+Hlh+F i++++y++ + e++  +++ +de+k++l
  gi|330506603|ref|YP_004383031.1|  17 IYQLKVTLDRIRPPIWRRIQVRGDISLFKLHKILQEVMGWYDCHLHQFLIDGESYSIISREADMLGDDFKDEKKFRL 93 
                                       8**************************************************************************** PP

                        PRiA4_ORF3  79 ddvlkekgkkltyeYDfgdsWeheielekvledkeearyprclagegacppEDvgGvgGyeelleiladpeheeyee 155
                                       d ++  ++ k+ yeYDfgdsW+h+i +ek+++ +ee ++p+cl+g++ +ppED+gG +Gy++ll++l+d++h+e+++
  gi|330506603|ref|YP_004383031.1|  94 DRIIPGEKFKFVYEYDFGDSWSHTILVEKIFKPEEELEHPVCLKGKRSAPPEDCGGESGYYHLLKTLRDRSHPEHKD 170
                                       ************************************999************************************** PP

                        PRiA4_ORF3 156 mrewlgeqefdpeafdle 173
                                       m+ w+g++ fdpe fd +
  gi|330506603|ref|YP_004383031.1| 171 MLMWVGGK-FDPEYFDAD 187
                                       *******5.******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1339.74
//
Query:       gi|330506604|ref|YP_004383032.1|  [L=296]
Description: hypothetical protein MCON_0350 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-08   35.3   0.1    1.3e-08   34.9   0.1    1.1  1  dCache_1  Cache domain


Domain annotation for each model (and alignments):
>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   7.5e-13   1.3e-08      19     208 ..      64     244 ..      54     283 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 7.5e-13
                          dCache_1  19 anniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvylvdadGqviassdpssp 95 
                                       ++++++ ++++e+ ++      s++ + + +   +  + +++ ++l+   +  + i+ v++ d+ G+v  +  pss 
  gi|330506604|ref|YP_004383032.1|  64 SDAVNANFTKIETALMDA----SIALSDTGI---DGPDAREILSRLML--ADSSAIDCVTI-DPTGTVREV-EPSSF 129
                                       667788888887655544....343333333...35667777777773..34557999998.******754.33322 PP

                          dCache_1  96 pnleg..tddpadrdwykealaggggkpvisdpy.vdqtggkpvitiavpiyddsgkfiGvlaadldldnlqd.lls 168
                                       +      +++  +++ +++++++g    ++s ++ + +++g++ i   +p++d++g+ iG++ + ++ +++ d  ls
  gi|330506604|ref|YP_004383032.1| 130 E---SvkGENLKNQEHINNTIDTG----LYSGFHlIKAVEGVYAIDSEMPVFDRNGTLIGTVSFLFNNSQFFDnVLS 199
                                       2...244567888999******99....689999877779*********************************9*** PP

                          dCache_1 169 niklgetgyvfivdsdG.niiahpdkdllgknlrdelkaq....e 208
                                        +++g++++++i   d+ + ++++d++++  n +++ ++      
  gi|330506604|ref|YP_004383032.1| 200 PFQPGGNSKIWIARADDaTKLYDTDPSQILLNKSSQIYQNfpqlL 244
                                       **************7776********9986666665543353332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2102.85
//
Query:       gi|330506605|ref|YP_004383033.1|  [L=139]
Description: hypothetical protein MCON_0351 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.12   12.6   0.1       0.23   11.7   0.0    1.5  2  Orthopox_F6  Orthopoxvirus F6 protein


Domain annotation for each model (and alignments):
>> Orthopox_F6  Orthopoxvirus F6 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.3e-05      0.23       7      69 ..      39      98 ..      34     100 .. 0.88
   2 ?   -3.6   0.0      0.74   1.3e+04      18      60 ..     109     115 ..     104     121 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.3e-05
                       Orthopox_F6  7 fvknkiidlikndqikysrvitieesdsllsvdevyanhGfdcvemideniinenleqyktes 69
                                      fv +   dl+++d++    +i++e++d l++ +  y   G + ve     i  +n   y +es
  gi|330506605|ref|YP_004383033.1| 39 FVGDGAYDLVEDDRVT---LIVVEQTDRLITGNITYMHEGEEIVEAFAGAIGADNKTFYIAES 98
                                      7777888999999985...79***************************999999988887776 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.74
                       Orthopox_F6  18 ndqikysrvitieesdsllsvdevyanhGfdcvemideniine 60 
                                       +d+i                                       
  gi|330506605|ref|YP_004383033.1| 109 DDEIE------------------------------------MS 115
                                       33333....................................33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1049.40
//
Query:       gi|330506606|ref|YP_004383034.1|  [L=58]
Description: FeoA domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-11   43.3   0.1    3.6e-11   43.2   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 !   43.2   0.1     2e-15   3.6e-11      21      70 ..       4      53 ..       1      56 [. 0.93

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 2e-15
                                      .SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTE CS
                              FeoA 21 dpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaI 70
                                      +++l+ r++emGlv+Ga++evv+ ap g+p+ + +++  +aL+++eA +I
  gi|330506606|ref|YP_004383034.1|  4 SGALRCRMMEMGLVKGAELEVVRLAPSGDPVEILLKGYSLALRKREAVNI 53
                                      478999*****************************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       174  (0.00970495); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 443.22
//
Query:       gi|330506607|ref|YP_004383035.1|  [L=87]
Description: FeoA family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-16   59.6   0.1    2.9e-16   59.5   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 !   59.5   0.1   1.6e-20   2.9e-16       2      73 ..      13      82 ..      12      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.6e-20
                                      EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA  2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                      pL++l+eG +g++ +i+   +   r L++mG+ p ar+ v++  p  g ++v v+d+r+aLgr++A++IlV+
  gi|330506607|ref|YP_004383035.1| 13 PLAFLPEGRAGTVLEIRGG-HGAVRHLEDMGFAPPARVLVLKSCP-PGAMLVMVKDSRIALGRGIAMKILVK 82
                                      9****************97.889******************6555.599**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       148  (0.00825478); expected 358.6 (0.02)
Passed bias filter:                      134  (0.00747392); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 663.63
//
Query:       gi|330506608|ref|YP_004383036.1|  [L=96]
Description: hypothetical protein MCON_0356 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.57
# Mc/sec: 510.95
//
Query:       gi|330506609|ref|YP_004383037.1|  [L=176]
Description: iron-dependent repressor [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-19   68.3   0.0    1.1e-18   67.2   0.1    1.6  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      3e-15   56.0   0.1    7.1e-15   54.9   0.1    1.6  1  Fe_dep_repr_C    Iron dependent repressor, metal binding and 
    3.6e-05   23.6   0.0    6.8e-05   22.7   0.0    1.4  1  MarR_2           MarR family
     0.0018   18.5   0.0     0.0031   17.8   0.0    1.3  1  ANT              Phage antirepressor protein KilAC domain
     0.0023   17.8   0.0     0.0046   16.9   0.0    1.5  1  MarR             MarR family
     0.0058   17.1   0.1      0.013   15.9   0.0    1.6  2  HTH_27           Winged helix DNA-binding domain
     0.0093   15.5   0.0       0.04   13.5   0.0    1.9  2  HTH_24           Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.011   16.0   0.0       0.02   15.3   0.0    1.4  1  Rrf2             Transcriptional regulator
      0.029   14.3   0.0       0.14   12.2   0.0    2.1  2  HTH_36           Helix-turn-helix domain
      0.088   12.6   0.0       0.16   11.8   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
      0.091   12.7   0.1       0.15   11.9   0.1    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
        0.1   12.6   0.0       0.37   10.8   0.0    2.0  1  Nitrate_red_del  Nitrate reductase delta subunit
        0.1   12.4   0.0       0.24   11.3   0.0    1.6  1  IF2_N            Translation initiation factor IF-2, N-termin


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 !   67.2   0.1   7.9e-22   1.1e-18       1      60 []       4      63 ..       4      63 .. 0.98
   2 ?   -2.8   0.0       5.7   7.9e+03      20      33 ..     145     158 ..     138     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 7.9e-22
                                      X--HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  1 dLvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      dL++++EdYLe++Y +s ek+ v+  d+ ++L+ +p+sV em+kkL++ Gy++y+k  gl
  gi|330506609|ref|YP_004383037.1|  4 DLSRKAEDYLEAVYVISQEKGHVRIRDICKELGTKPPSVVEMVKKLNDRGYLIYKKNEGL 63
                                      799*****************************************************9996 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.7
                                       HSSB-HHHHHHHHT CS
                    Fe_dep_repress  20 kkvvktkdlaerLn 33 
                                       +  +k ++l++ ++
  gi|330506609|ref|YP_004383037.1| 145 HPCIKDARLSQTMA 158
                                       55688899999885 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 !   54.9   0.1   5.1e-18   7.1e-15       1      65 [.      66     129 ..      66     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 5.1e-18
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhg 65 
                                       T +G+e+++ +++rh ++  fL +++gv+++ a+e+A+ +Eh l+ +++e++  l++f+e+ P+ 
  gi|330506609|ref|YP_004383037.1|  66 TAEGEEIGRIIKDRHDTIFAFL-KFIGVPEQVADEDACVIEHELHTKTVEQIKSLVSFIETAPDH 129
                                       99********************.99************************************9964 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   4.9e-08   6.8e-05      13      56 ..      18      60 ..      12      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.9e-08
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      ++  + g  +++++++++lg ++++v  ++k+L ++G++ ++++
  gi|330506609|ref|YP_004383037.1| 18 VISQEKGH-VRIRDICKELGTKPPSVVEMVKKLNDRGYLIYKKN 60
                                      56666765.89***************************988876 PP

>> ANT  Phage antirepressor protein KilAC 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    0.0031      12      62 ..      14      68 ..       6      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.2e-06
                               ANT 12 eyaDrvlesdgsititeiAkllgigen...rlfelLrekgilyrqkgsg.qnlpy 62
                                      e++  +++ +g + i++i+k+lg++++   ++++ L+++g+l+++k++g ++++ 
  gi|330506609|ref|YP_004383037.1| 14 EAVYVISQEKGHVRIRDICKELGTKPPsvvEMVKKLNDRGYLIYKKNEGlYLTAE 68
                                      555567899**************776633378899*********87643244443 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.3e-06    0.0046      14      48 ..      22      56 ..      13      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.3e-06
                                      HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 14 eqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      e+g  ++ ++ k lg+++++v +++++L ++G++ 
  gi|330506609|ref|YP_004383037.1| 22 EKGHVRIRDICKELGTKPPSVVEMVKKLNDRGYLI 56
                                      45568999************************985 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.6e-06     0.013      11      48 ..      18      55 ..      12      69 .. 0.79
   2 ?   -3.1   0.0       8.2   1.1e+04      11      25 ..     103     117 ..     102     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.6e-06
                            HTH_27 11 lirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                      +i  + + ++++d+c+ l +   ++++++kkL  +G++
  gi|330506609|ref|YP_004383037.1| 18 VISQEKGHVRIRDICKELGTKPPSVVEMVKKLNDRGYL 55
                                      455788999****************************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.2
                            HTH_27  11 lirhrrrrkkladlc 25 
                                       +i+h++++k+ +++ 
  gi|330506609|ref|YP_004383037.1| 103 VIEHELHTKTVEQIK 117
                                       678888888888875 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   2.9e-05      0.04      13      47 ..      21      55 ..      19      56 .. 0.96
   2 ?   -0.9   0.0      0.91   1.3e+03      14      20 ..     149     155 ..     135     156 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                            HTH_24 13 qknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      q++++  +r+++++lg  p+ v + +k+L + G++
  gi|330506609|ref|YP_004383037.1| 21 QEKGHVRIRDICKELGTKPPSVVEMVKKLNDRGYL 55
                                      789999***************************96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.91
                            HTH_24  14 knprisq 20 
                                       k++r+sq
  gi|330506609|ref|YP_004383037.1| 149 KDARLSQ 155
                                       4555555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.4e-05      0.02       3      70 ..       5      68 ..       1      73 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                                      --HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSH CS
                              Rrf2  3 lsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakp 70
                                      ls+k e  l a++++++e++  +v++++i ++ +++p+ +  +++kL+  g++  ++    G+ L+ +
  gi|330506609|ref|YP_004383037.1|  5 LSRKAEDYLEAVYVISQEKG--HVRIRDICKELGTKPPSVVEMVKKLNDRGYLIYKKN--EGLYLTAE 68
                                      78899999999999999988..49***************************9876653..35555555 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   9.9e-05      0.14      28      55 .]      28      55 ..      19      55 .. 0.92
   2 ?   -1.3   0.0       1.6   2.3e+03       8      18 ..     136     146 ..     134     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.9e-05
                            HTH_36 28 qetlakrlglsknTvsraikeLeqlGyi 55
                                       ++++k lg +  +v+  +k+L + Gy+
  gi|330506609|ref|YP_004383037.1| 28 IRDICKELGTKPPSVVEMVKKLNDRGYL 55
                                      689************************8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.6
                            HTH_36   8 klllgslasfa 18 
                                       ++++++l ++ 
  gi|330506609|ref|YP_004383037.1| 136 FAIFCELGKHP 146
                                       67888888875 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.16      13      48 ..      20      55 ..      17      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                      CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR 13 aeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      +++ + ++++++++++g  +++v  +++ L  +Gy+
  gi|330506609|ref|YP_004383037.1| 20 SQEKGHVRIRDICKELGTKPPSVVEMVKKLNDRGYL 55
                                      5677789****************************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 ?   11.9   0.1   0.00011      0.15      19      54 ..      22      57 ..      12      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      ++g  ++++i +elg   ++v e++++L d+G+   
  gi|330506609|ref|YP_004383037.1| 22 EKGHVRIRDICKELGTKPPSVVEMVKKLNDRGYLIY 57
                                      789999**************************8655 PP

>> Nitrate_red_del  Nitrate reductase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00027      0.37      78     110 ..     124     156 ..      59     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                   Nitrate_red_del  78 evaeefneppDHlaveLeflahLaereaeaeea 110
                                       e a + ++  DH+a+++e+  h + + a   ++
  gi|330506609|ref|YP_004383037.1| 124 ETAPDHPQWLDHFAIFCELGKHPCIKDARLSQT 156
                                       57889999****************998864443 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.24       4      30 ..      26      54 ..      24      63 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                             IF2_N  4 irVyeLAkeLgvkskevikkLfkel...Gi 30
                                      +r+++++keLg+k+  v++   k+l   G+
  gi|330506609|ref|YP_004383037.1| 26 VRIRDICKELGTKPPSVVEMV-KKLndrGY 54
                                      79*********9988777766.32433366 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 960.42
//
Query:       gi|330506610|ref|YP_004383038.1|  [L=317]
Description: cache, type 2 domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-41  142.3   0.1    8.5e-20   71.2   0.0    2.1  2  sCache_2         Single Cache domain 2
    1.4e-31  109.8   0.1    5.6e-17   61.8   0.1    2.3  2  dCache_2         Cache domain
      0.002   17.4   0.0      0.074   12.3   0.0    2.1  2  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain


Domain annotation for each model (and alignments):
>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.0   1.4e-23   8.5e-20       4     145 ..      28     164 ..      26     166 .. 0.89
   2 !   69.0   0.1   6.6e-23   3.9e-19      30     148 ..     184     303 ..     180     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 1.4e-23
                          sCache_2   4 qkeaelknqvetaislieavykqvesgkiteeeaqeevkelvnglkfgdGkgYffvldedgtllvhPfnpqleGkna 80 
                                       +k  ++++ +++++ ++++ ++ +++   ++e a +++ ++  +   gd   Y++++d +g++++hPf+p+++G++ 
  gi|330506610|ref|YP_004383038.1|  28 SKSMNNSSSISELVDFVKEARDYAREE--DRESACQQFSNKTGEFVRGD--LYIYAYDFQGINVAHPFRPDFIGEDK 100
                                       566777778888888888887766655..88888888888888777777..9************************* PP

                          sCache_2  81 snlkDanGkyiirelvkeakkkgggfvtylwkkpge.geveeklayvkyfepWdwvigtgvylddi 145
                                       +nl+D+nG+ +i++l +  +  g+  +++ +++p+  +e e k+ y++++ + +w++g+gvyl+d+
  gi|330506610|ref|YP_004383038.1| 101 INLTDPNGVALIKDLADCSR-RGEDSTYFIFPNPDHgSEDELKIGYAAKVDE-NWWVGSGVYLSDL 164
                                       ********************.***************889999*******986.***********96 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 6.6e-23
                          sCache_2  30 gkiteeeaqeevkelvng..lkfgdGkgYffvldedgtllvhPfnpqleGknasnlkDanGkyiirelvkeakkkgg 104
                                        k+ ee+ ++ + ++ n+    f  G+ Y+f++d +gt+l  P++p+l G+++ + kD nG++++++ +++ak  g 
  gi|330506610|ref|YP_004383038.1| 184 AKYAEENGRDAALQAFNDrnSSFVRGNLYIFAYDFNGTVLSLPYQPELLGSDRLDAKDENGVRFVQNSIDQAK-RGR 259
                                       5666777777777777641144567799*********************************************.*** PP

                          sCache_2 105 gfvtylwkkpge.geveeklayvkyfepWdwvigtgvylddinka 148
                                       g+ +yl+ +p++  e+e kl yv+ + + +w++g+g+y ++ n++
  gi|330506610|ref|YP_004383038.1| 260 GYLYYLYANPSKnMEEELKLGYVRSVDN-NWWLGAGIYASESNAT 303
                                       ************899999********98.9**********99886 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   8.3e-16     5e-12      89     184 ..      67     163 ..      19     165 .. 0.61
   2 !   61.8   0.1   9.4e-21   5.6e-17      71     185 ..     185     300 ..     179     311 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 8.3e-16
                          dCache_2  89 r..ydggegyyfiidskgtlilhpdspsleGknlldlkdkdGryiiremiklakkkgeGfveytwpkp.dekkprkk 162
                                       +  +++g+ y++++d +g +++hp++p+  G + ++l d +G  +i+++++   ++ge    + +p+p    +++ k
  gi|330506610|ref|YP_004383038.1|  67 TgeFVRGDLYIYAYDFQGINVAHPFRPDFIGEDKINLTDPNGVALIKDLADCS-RRGEDSTYFIFPNPdHGSEDELK 142
                                       33455666666666666666666666666666666666666666666666654.55555555666666555566666 PP

                          dCache_2 163 isyvkyfepldwiIGtgayldd 184
                                       i+y+++  + +w +G+g+yl+d
  gi|330506610|ref|YP_004383038.1| 143 IGYAAKVDE-NWWVGSGVYLSD 163
                                       666666666.666666666665 PP

  == domain 2  score: 61.8 bits;  conditional E-value: 9.4e-21
                          dCache_2  71 elseeeakklikealrsir..ydggegyyfiidskgtlilhpdspsleGknlldlkdkdGryiiremiklakkkgeG 145
                                       + +ee+ +  +++a ++ +  +++g+ y+f++d +gt++  p +p+l G + ld kd++G  ++++ i++a k+g G
  gi|330506610|ref|YP_004383038.1| 185 KYAEENGRDAALQAFNDRNssFVRGNLYIFAYDFNGTVLSLPYQPELLGSDRLDAKDENGVRFVQNSIDQA-KRGRG 260
                                       677788888888888665556**************************************************.9999* PP

                          dCache_2 146 fveytwpkp.dekkprkkisyvkyfepldwiIGtgaylddi 185
                                       ++ y + +p ++ +++ k++yv+   + +w +G+g+y ++ 
  gi|330506610|ref|YP_004383038.1| 261 YLYYLYANPsKNMEEELKLGYVRSVDN-NWWLGAGIYASES 300
                                       ************************987.9********9875 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 !    2.9   0.0    0.0088        53     198     282 ..      76     164 ..      64     166 .. 0.81
   2 !   12.3   0.0   1.2e-05     0.074     210     286 ..     220     304 ..     207     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0088
                   Cache_3-Cache_2 198 ylyvldgkgdkkgkliihptlk...gknvldlkdadgesvvkkllkk.....ksgsleyelk.kdekgreklavfty 265
                                       y+y++d +    g  ++hp +    g++ ++l+d +g + +k+l +      +s ++ ++     ++ + k+ ++ +
  gi|330506610|ref|YP_004383038.1|  76 YIYAYDFQ----GINVAHPFRPdfiGEDKINLTDPNGVALIKDLADCsrrgeDSTYFIFPNPdHGSEDELKIGYAAK 148
                                       77777777....9999999999999*******************999888765555556555666666777777777 PP

                   Cache_3-Cache_2 266 fepwdWvivasvyedef 282
                                       +++ +W ++++vy +++
  gi|330506610|ref|YP_004383038.1| 149 VDE-NWWVGSGVYLSDL 164
                                       776.8999999999885 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.2e-05
                   Cache_3-Cache_2 210 gkliihptlk...gknvldlkdadgesvvkkllkk...ksgsleyelk..kdekgreklavftyfepwdWvivasvy 278
                                       g+++  p +    g + ld+kd++g  +v++ +++     g+l+y +   +++ ++e +  +++    +W ++a+ y
  gi|330506610|ref|YP_004383038.1| 220 GTVLSLPYQPellGSDRLDAKDENGVRFVQNSIDQakrGRGYLYYLYAnpSKNMEEELKLGYVRSVDNNWWLGAGIY 296
                                       55555444444669999*****************99888899999999995555555555566666679******** PP

                   Cache_3-Cache_2 279 edefqeev 286
                                        +e +++ 
  gi|330506610|ref|YP_004383038.1| 297 ASESNATN 304
                                       ***98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); 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: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.56
# Mc/sec: 1715.49
//
Query:       gi|330506611|ref|YP_004383039.1|  [L=374]
Description: transposase, Mutator family [Methanosaeta concilii GP6]
Scores for complete 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-105  352.7   1.9   2.6e-105  352.4   1.9    1.0  1  Transposase_mut  Transposase, Mutator family
    4.9e-08   33.3   0.1    1.3e-07   31.9   0.0    1.8  2  MULE             MULE transposase domain
  ------ inclusion threshold ------
      0.016   14.9   0.2      0.041   13.6   0.2    1.7  1  DDE_Tnp_ISL3     Transposase
        0.4   11.3   4.9        3.1    8.5   0.1    3.7  4  DUF5499          Family of unknown function (DUF5499)


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 !  352.4   1.9  5.8e-109  2.6e-105      21     380 ..      13     365 ..       2     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 352.4 bits;  conditional E-value: 5.8e-109
                   Transposase_mut  21 gkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspalleryk 97 
                                       + ++ +k+l+  +l+e+++ e++++++a  yer+++r+ +RnG r+rkl+T +g++el  P+ R+  F++a++er+ 
  gi|330506611|ref|YP_004383039.1|  13 DRKEGMKKLTAGFLNEVMQLEAENQIQARPYERTGKRRAHRNGTRSRKLKTIYGEIELDKPQIREFPFETAVFERFS 89 
                                       4568999********************************************************************** PP

                   Transposase_mut  98 RrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkv 174
                                       R e+ l  +v+e y +Gvstrkvek++ +++  k++S+sevS+i+k+ld+ v+ f +R++e +  p++f+Da y kv
  gi|330506611|ref|YP_004383039.1|  90 RVEDSLRVAVAESYFEGVSTRKVEKVFSKFGL-KNISASEVSRIAKKLDKLVKDFLNRPIEGS-IPYIFVDASYFKV 164
                                       *******************************9.88****************************.************* PP

                   Transposase_mut 175 ReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaa 251
                                       R +gr v+ka l+ ++++ dG+reiL+ +v+dsE+e+ W++ +esLk+rGlkgv+lv+sDahkG+++a++++f +a+
  gi|330506611|ref|YP_004383039.1| 165 RTDGRYVNKALLVVVAIHDDGYREILSATVDDSEDESCWENCFESLKARGLKGVKLVISDAHKGIQAAVQKSFLGAS 241
                                       ***************************************************************************** PP

                   Transposase_mut 252 vQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaedvlaflafpe 328
                                       +Q C vH++r +l+++pkk++++va +lk    a + e   ++l+ +l+   k ++k a+++d+ + d+ ++ +fp+
  gi|330506611|ref|YP_004383039.1| 242 WQMCNVHFMRAVLKNIPKKEKKEVAYMLKD---AIEDEFKMQELAVILD--DKGFKKSADTIDSFRFDLWNYKSFPR 313
                                       ****************************95...6677888889999998..56899********************* PP

                   Transposase_mut 329 qirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                        ++++i++tN+lEr+Nke++Rr+rv g + n++s+lr+ + ++++ +++w++
  gi|330506611|ref|YP_004383039.1| 314 SHWKRIRTTNVLERINKELKRRSRVAGAYSNDQSLLRVAVCIMMDINEDWIT 365
                                       **************************************************86 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0     3e-11   1.3e-07      14      95 ..     172     251 ..     154     252 .. 0.87
   2 ?   -3.6   0.0       3.6   1.6e+04      61      70 ..     351     360 ..     341     364 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3e-11
                              MULE  14 klplltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlCl 90 
                                       +  ll vv+++d g   +l  ++ +se+e+++e  +++l+++    +  k +i+D +k+++ a+++ f +a  ++C 
  gi|330506611|ref|YP_004383039.1| 172 NKALLVVVAIHDDGYREILSATVDDSEDESCWENCFESLKARGL--KGVKLVISDAHKGIQAAVQKSFLGASWQMCN 246
                                       56789999********************************9644..69***************************** PP

                              MULE  91 fHiak 95 
                                        H+++
  gi|330506611|ref|YP_004383039.1| 247 VHFMR 251
                                       ***96 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.6
                              MULE  61 spkviitDke 70 
                                         ++i++D +
  gi|330506611|ref|YP_004383039.1| 351 VAVCIMMDIN 360
                                       4578888865 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   9.1e-06     0.041      23     105 ..     183     268 ..     162     351 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.1e-06
                      DDE_Tnp_ISL3  23 vdg.grlldilpg..RkketlkafleslsekerekveavvmDmsaayksavkealPnAkivvDrFHvvklanealde 96 
                                        dg +++l ++ +   ++++ ++++esl+++  + v+ v+ D ++++++av++ +  A+  + + H+++ + + + +
  gi|330506611|ref|YP_004383039.1| 183 DDGyREILSATVDdsEDESCWENCFESLKARGLKGVKLVISDAHKGIQAAVQKSFLGASWQMCNVHFMRAVLKNIPK 259
                                       3446677666544115667889*******9***************************************99998877 PP

                      DDE_Tnp_ISL3  97 vRrreqkel 105
                                         ++e+  +
  gi|330506611|ref|YP_004383039.1| 260 KEKKEVAYM 268
                                       766666555 PP

>> DUF5499  Family of unknown function (DUF5499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.7   3.1e+03       9      25 ..      37      53 ..      33      68 .. 0.74
   2 ?    8.5   0.1   0.00069       3.1      25      64 ..     113     152 ..      94     187 .. 0.83
   3 ?    1.9   0.0     0.076   3.4e+02      29      54 ..     199     224 ..     179     238 .. 0.78
   4 ?   -1.0   0.3      0.63   2.8e+03      36      61 ..     310     333 ..     276     346 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.7
                           DUF5499  9 dlkvrdydyfgkrkapd 25
                                      +++ r y+  gkr+a  
  gi|330506611|ref|YP_004383039.1| 37 QIQARPYERTGKRRAHR 53
                                      57789999999999864 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00069
                           DUF5499  25 dgvshkdmvenifrsdkwrrmkgidsevkdelnrqlrgev 64 
                                       + v  k  ++ni  s+  r  k +d  vkd lnr + g +
  gi|330506611|ref|YP_004383039.1| 113 EKVFSKFGLKNISASEVSRIAKKLDKLVKDFLNRPIEGSI 152
                                       4556677789*************************99987 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.076
                           DUF5499  29 hkdmvenifrsdkwrrmkgidsevkd 54 
                                        +   en f s k r +kg+   + d
  gi|330506611|ref|YP_004383039.1| 199 DESCWENCFESLKARGLKGVKLVISD 224
                                       556779*************9877666 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.63
                           DUF5499  36 ifrsdkwrrmkgidsevkdelnrqlr 61 
                                        f   +w+r++  +  v + +n++l+
  gi|330506611|ref|YP_004383039.1| 310 SFPRSHWKRIRTTN--VLERINKELK 333
                                       45566788877643..3344444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2601.88
//
Query:       gi|330506612|ref|YP_004383040.1|  [L=225]
Description: hypothetical protein MCON_0360 [Methanosaeta concilii GP6]
Scores for complete 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-12   45.5   0.4    5.9e-08   32.8   0.1    2.1  2  ZinT      ZinT (YodA) periplasmic lipocalin-like zinc-recruit


Domain annotation for each model (and alignments):
>> ZinT  ZinT (YodA) periplasmic lipocalin-like zinc-recruitment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.1   3.3e-12   5.9e-08      46     169 ..      24     148 ..      16     159 .. 0.83
   2 !   10.9   0.0   1.7e-05       0.3      19      51 ..     184     216 ..     167     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.3e-12
                                       HHHH-TTS-HHHHHHHHHHHH--SEEEEEEETTEEEEE..ETTEEEEEE-EEEEEEEEE-TTS-EEEEEEEE---TT CS
                              ZinT  46 kakekkdktaeeykeyYekGYktdvdkikieddtieft..kngkkkkaeYkydGykiltyekGnrgvrylfeakdke 120
                                        a+e+++ t++++ +++++  ktd   i+i++++i+f+  ++  k k+eY+y G k ++++ G     ++f+ ++++
  gi|330506612|ref|YP_004383040.1|  24 AADESSNFTVDDISNFFHAMQKTDFGDIEISGNNITFYspEGSVKCKGEYDYVGSKTIDFQ-GYPVEWHMFNLRSDK 99 
                                       57889999******************************54444556789***********6.88888899******* PP

                                       --S-SEEEEESS--SS--.-SSEEEEEESS-HHHHHT--S---EEEETTS CS
                              ZinT 121 sgapkyiqfsDheiapek.aehfhiylgnesqealleelenwPtyypsel 169
                                       +g  +y ++   +++ e   +h+h+ +g+   + +l e   +  +yp+  
  gi|330506612|ref|YP_004383040.1| 100 EGCLEYKHVIATAVHDEAgLTHWHMRYGKLCFD-ILMENPAYGMWYPTMA 148
                                       **9999999888888765379***********9.7778888999998643 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 1.7e-05
                                       -GGGG-EEEEESHHHHHTTTTHHHHHHHHHH-T CS
                              ZinT  19 elsdweGewqsvypylkdGtldevfekkakekk 51 
                                       +l+ w+G+w   + +l d  +d+v+e+ a++ +
  gi|330506612|ref|YP_004383040.1| 184 SLEKWSGRWVNTEQLLDDPLMDPVYEAAANTAN 216
                                       6899**********************9997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1623.19
//
Query:       gi|330506613|ref|YP_004383041.1|  [L=577]
Description: multi-domain sirohydrochlorin cobaltochelatase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-41  141.4   0.0    1.2e-16   60.9   0.0    4.6  4  CbiX            CbiX
     0.0017   17.5   0.0      0.033   13.3   0.0    2.8  3  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 !   60.9   0.0   1.4e-20   1.2e-16       1     106 [.      55     166 ..      55     167 .. 0.93
   2 !   11.4   0.0   3.4e-05      0.31      49     105 ..     257     306 ..     235     310 .. 0.80
   3 !   40.5   0.0   3.2e-14   2.8e-10       1     106 [.     326     443 ..     326     444 .. 0.81
   4 !   22.9   0.0   8.8e-09   7.9e-05       7     106 ..     471     568 ..     464     569 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.4e-20
                                       -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCE.CCSCCSSHHHHC-SBSEEEEEEESS.SSSHHHHTHHHHH CS
                              CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgflelee.psleealrelaeqgvkrivvvPlfl.faGvhvkeDIpee 75 
                                       HGS ++ + ++v+++++++    p +pvelgfle++  +s+++a+++l++qg+++i+++Plf+ + + h++e I++ 
  gi|330506613|ref|YP_004383041.1|  55 HGSDEDLWCQQVRQVVANVSL--P-YPVELGFLEFVPnESIDDAVERLESQGIRDIIAIPLFVsSYSSHIQE-IEYV 127
                                       9******************98..8.**********988*************************6678*****.***9 PP

                                       CT--SSSS-........TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  76 leeaeeahp........kdveieytepLGthplvaevlk 106
                                       l++ e+ +          +++i++t++L++h lva +l+
  gi|330506613|ref|YP_004383041.1| 128 LRLRETLPSgedlarvnTTANITMTRALDDHSLVAYILA 166
                                       9987777778889999999****************9997 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.4e-05
                                       C-SBSEEEEEEESSSSSHHHHTHHHHHCT--SSSS-TTEEEEE---CCCSCCHHHHH CS
                              CbiX  49 eqgvkrivvvPlflfaGvhvkeDIpeeleeaeeahpkdveieytepLGthplvaevl 105
                                       e g   ++v+Pl+++ G  +++ Ip++le +  +++       +  L +hp +a+++
  gi|330506613|ref|YP_004383041.1| 257 EDGNGGVIVLPLMVAGGSITDSQIPKLLEGYSCRYD-------RATLASHPNLARWI 306
                                       347788***********************9999988.......56666666666655 PP

  == domain 3  score: 40.5 bits;  conditional E-value: 3.2e-14
                                       -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESC..CCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHH CS
                              CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfle..leepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpee 75 
                                       HGS+dp+  e+v++la ++ ++ +  pv ++f+e  +ee++++ ++++l +qg++ri++v lf   G+ v++  +e+
  gi|330506613|ref|YP_004383041.1| 326 HGSSDPKRAEAVRELAGQVNQMLSSMPVAVAFAEnaAEEETIPGGIARLLDQGARRIIAVTLFT--GNTVDH--EEA 398
                                       ********************************99435679********************6665..555555..333 PP

                                       CT--SSSS-..............TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  76 leeaeeahp..............kdveieytepLGthplvaevlk 106
                                        +e+ +a +              +++  e+  p+++h l+a+++ 
  gi|330506613|ref|YP_004383041.1| 399 RDEVYSAMQsinqtkilitaplyEGICAEVKGPIDDHLLIADLIL 443
                                       333333333333677799999999999999999999999999885 PP

  == domain 4  score: 22.9 bits;  conditional E-value: 8.8e-09
                                       CHHHHHHHHHHHHHHHCCSCCCEECESCCCE.CCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTH.HHHHCT--SS CS
                              CbiX   7 esneeveklaeelrekgpfkpvelgflelee.psleealrelaeqgvkrivvvPlflfaGvhvkeD.Ipeeleeaee 81 
                                       es+  +  l+e+++++++fk v  gf+e++  p+++ea++++   + + ++vv    ++G  + +D I e le ++ 
  gi|330506613|ref|YP_004383041.1| 471 ESELLAKSLVERIKASSEFKDVGFGFMEYQGsPNIREAVEKA---QGEAVIVV-TVNSMGTKYVDDlIAERLEGLNY 543
                                       556667889*********************99*******998...44444444.57899966655526889999999 PP

                                       SS-TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  82 ahpkdveieytepLGthplvaevlk 106
                                       +h ++  + y+e L++hp +a++++
  gi|330506613|ref|YP_004383041.1| 544 THNGKGFYGYSENLDPHPNIARWIE 568
                                       999777899************9986 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   3.7e-06     0.033      77     193 ..      65     188 ..      49     215 .. 0.74
   2 ?   -0.1   0.0     0.043   3.9e+02      72     124 ..     338     389 ..     329     416 .. 0.70
   3 ?   -1.1   0.0     0.084   7.5e+02      63     114 ..     464     517 ..     439     529 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-06
                                       HHHHHHHHH---EEEEEEESSSSS..BHHHHHHHHHCTT-SEEEEEES-SS--TTTHHHHHHHHHHHHHH....... CS
                    Ferrochelatase  77 alekelaergidvkvylamryweP..siedaleelkadgvervvvlplyPqysasttgssleeleralkk....... 144
                                       ++++ +a+ + +++v+l++    P  si+da+e+l+++g+++++++pl+ ++s+s+  + +e + r ++        
  gi|330506613|ref|YP_004383041.1|  65 QVRQVVANVSLPYPVELGFLEFVPneSIDDAVERLESQGIRDIIAIPLF-VSSYSSHIQEIEYVLRLRETlpsgedl 140
                                       4555555556789999999776653379********************9.578999988888888887655555556 PP

                                       ..TT-SSEEEEE---TT-HHHHHHHHHHHHHHHTTS-HC.C-EEEEEEE-- CS
                    Ferrochelatase 145 ..kreapevrvirqfydhpgyiealaesikealeelpeekkakllfsaHgl 193
                                          + + ++++ r   dh     +la+ + +   +   ++ +++++  Hg+
  gi|330506613|ref|YP_004383041.1| 141 arVNTTANITMTRALDDHSLVAYILADWVSQMSSDP--SN-ETVVILSHGT 188
                                       545555566666666666666666666666554443..44.6677777776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.043
                                       HHHHHHHHHHHHHH---EEEEEEESSS.SSBHHHHHHHHHCTT-SEEEEEES-S CS
                    Ferrochelatase  72 rkqaealekelaergidvkvylamryw.ePsiedaleelkadgvervvvlplyP 124
                                       r++a ++++ l++  ++v v++a +   e  i   +++l ++g +r+++++l+ 
  gi|330506613|ref|YP_004383041.1| 338 RELAGQVNQMLSS--MPVAVAFAENAAeEETIPGGIARLLDQGARRIIAVTLFT 389
                                       5666677777765..477777775554156679999999999999999999874 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.084
                                       SS-SHHHHHHHHHHHHHHHHHHH-..--EEEEEEESSSSSBHHHHHHHHHCTT- CS
                    Ferrochelatase  63 ggSPlneitrkqaealekelaerg..idvkvylamrywePsiedaleelkadgv 114
                                       g S   e ++ +a+ l +++++++   dv + +    ++P i++a+e+ + + v
  gi|330506613|ref|YP_004383041.1| 464 GSSTYFEESELLAKSLVERIKASSefKDVGFGFMEYQGSPNIREAVEKAQGEAV 517
                                       567777888888888888888877555555555555689999999999886544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 3674.54
//
Query:       gi|330506614|ref|YP_004383042.1|  [L=175]
Description: hypothetical protein MCON_0362 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1219.40
//
Query:       gi|330506615|ref|YP_004383043.1|  [L=163]
Description: shikimate kinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-36  125.0   0.0    3.2e-36  124.9   0.0    1.0  1  SKI              Shikimate kinase
    1.3e-06   29.0   0.0    2.6e-06   28.0   0.0    1.5  1  AAA_18           AAA domain
    1.7e-05   25.0   0.0    8.1e-05   22.8   0.0    1.9  1  AAA_33           AAA domain
    0.00017   22.0   0.0    0.00042   20.8   0.0    1.6  1  AAA_17           AAA domain
    0.00073   19.4   0.1       0.38   10.6   0.0    2.2  2  dNK              Deoxynucleoside kinase
     0.0014   18.8   0.0     0.0018   18.4   0.0    1.4  1  Cytidylate_kin2  Cytidylate kinase-like family
     0.0023   17.7   0.0     0.0031   17.3   0.0    1.3  1  Cytidylate_kin   Cytidylate kinase
      0.009   15.7   0.1      0.016   14.9   0.1    1.4  1  CoaE             Dephospho-CoA kinase
  ------ inclusion threshold ------
      0.011   15.4   0.2       0.03   14.1   0.1    1.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.018   15.5   0.0      0.028   14.8   0.0    1.3  1  AAA              ATPase family associated with various cellul
      0.031   14.4   0.0        1.7    8.7   0.0    2.2  2  ADK              Adenylate kinase
      0.037   13.7   0.0      0.049   13.4   0.0    1.2  1  IstB_IS21        IstB-like ATP binding protein
       0.04   13.8   0.0      0.062   13.2   0.0    1.3  1  Ploopntkinase3   P-loop Nucleotide Kinase3
        0.1   12.8   0.0       0.15   12.3   0.0    1.4  1  AAA_28           AAA domain
       0.11   12.7   0.0       0.15   12.4   0.0    1.2  1  Hydin_ADK        Hydin Adenylate kinase-like domain
       0.12   12.3   0.0       0.21   11.6   0.0    1.3  1  AAA_5            AAA domain (dynein-related subfamily)


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 !  124.9   0.0   2.8e-39   3.2e-36       1     154 [.      10     160 ..      10     163 .] 0.94

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 2.8e-39
                                       TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGSHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsevlkelleeeglViatGGGavlsee 77 
                                       +GaGKstvG +lAk+lg++f+D+D +i++rtg + + i++++g +gF + E+e++ +l+ + ++ViatGG++v+s++
  gi|330506615|ref|YP_004383043.1|  10 PGAGKSTVGVILAKALGMNFVDADLVIQERTGLRLQAIIDRDGPAGFLKAEEEAVLSLSCR-NSVIATGGSVVMSPR 85 
                                       6************************************************************.9************** PP

                                       HHHHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCSSCEEEECTSSHHHHHHHHH CS
                               SKI  78 nrellkekgiviyLdvsleellerlkadkeRPllqekskeeelleela.ereplyeeaadvvvdeseeskeevaeei 153
                                       ++e+l + g+v+yL+v++ee+ +rl + + R ++    +    l+ ++ +r +lye++ad+++d +  + e+v+ ++
  gi|330506615|ref|YP_004383043.1|  86 AMEHLISAGTVVYLKVPFEEIEKRLGNISGRGIVLFAGQ---SLRMMYdQRVSLYEQYADITIDCAGLDFETVVGQV 159
                                       *************************99999988888777...5566666***************9999888888877 PP

                                       H CS
                               SKI 154 l 154
                                       l
  gi|330506615|ref|YP_004383043.1| 160 L 160
                                       6 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   2.3e-09   2.6e-06       1     110 [.       4     110 ..       4     114 .. 0.63

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.3e-09
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf......gvnlrdvakenglllevdpealdeskrldedkldklldaleenssal 71 
                                       I+l G+pG+GK+t++  L+k lg+       v+   +    +  +++d +    +++++e+ + +l+  +  ++   
  gi|330506615|ref|YP_004383043.1|   4 IVLIGMPGAGKSTVGVILAKALGMnfvdadLVIQERTGLRLQAIIDRDGP--AGFLKAEEEAVLSLSCRNSVIA--- 75 
                                       89*******************97754554433333333333333333333..5555666666555555555554... PP

                            AAA_18  72 eegknlvidghlaeleseaakdikkvvLtaspeelleRl 110
                                         g+++v++ +  e++  a +    v+L+++ ee  +Rl
  gi|330506615|ref|YP_004383043.1|  76 -TGGSVVMSPRAMEHLISAGTV---VYLKVPFEEIEKRL 110
                                       .366667776666666665553...99999999999997 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   7.2e-08   8.1e-05       2      40 ..       4      42 ..       4     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.2e-08
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgt 40
                                      ++l+G+pG+GKst+   l+k+lg+ +++ d +++  +g 
  gi|330506615|ref|YP_004383043.1|  4 IVLIGMPGAGKSTVGVILAKALGMNFVDADLVIQERTGL 42
                                      689***************************999887773 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.7e-07   0.00042       1     121 [.       7     112 ..       7     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.7e-07
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvd 77 
                                       +G+PG+GK+t+   l++ +g  ++   dl+++e  r gl    +++   + +    ++k  +e++   ++++ v+ +
  gi|330506615|ref|YP_004383043.1|   7 IGMPGAGKSTVGVILAKALGMNFVD-ADLVIQE--RTGL--RLQAI--IDRDGPAGFLKAEEEAVLSLSCRNSVIAT 76 
                                       6************************.7***998..5666..23444..45667788888889999999999999999 PP

                                       E-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHH CS
                            AAA_17  78 ghprikeqagfldglpkevleelkpdaiilleadpeeilerrlk 121
                                       g  ++          p+ +++ ++  ++++l+++ eei +r+ +
  gi|330506615|ref|YP_004383043.1|  77 GGSVVMS--------PRAMEHLISAGTVVYLKVPFEEIEKRLGN 112
                                       9988755........45555666777999999999998877654 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00034      0.38       1      27 [.       4      30 ..       4      39 .. 0.89
   2 !    6.9   0.0    0.0044       4.9     116     142 ..      86     112 ..      81     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                                      EEEEESTTSSHHHHHHHHHCCSTCEEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvf 27
                                      iv+ G  gaGKst+  +L+k+lg++++
  gi|330506615|ref|YP_004383043.1|  4 IVLIGMPGAGKSTVGVILAKALGMNFV 30
                                      6778999****************9987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0044
                                       HHHHCCH-SEEEEEE--HHHHHHHHHH CS
                               dNK 116 lleelakpdlliYLkasletclerikk 142
                                       ++e+l +   ++YLk++ e++++r+ +
  gi|330506615|ref|YP_004383043.1|  86 AMEHLISAGTVVYLKVPFEEIEKRLGN 112
                                       4667777889**************854 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.6e-06    0.0018       6      33 ..       8      35 ..       3      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                   Cytidylate_kin2  6 reyGsgGetigeaLAekLglpfydreii 33
                                      +  G+g++t+g  LA+ Lg++f+d +++
  gi|330506615|ref|YP_004383043.1|  8 GMPGAGKSTVGVILAKALGMNFVDADLV 35
                                      568**********************886 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.7e-06    0.0031       5      67 ..       8      70 ..       4     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.7e-06
                                      -STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHHHTT--TT-HHHHHHHHHT--EEEEEE CS
                    Cytidylate_kin  5 GPagsGKssvaralaeklglkyldtgalYRalalaalrrkvdlldeaalvelakevelsfeae 67
                                      G  g+GKs+v+ +la+ lg++++d+  +    +   l++ +d    a +++  +e+ ls++ +
  gi|330506615|ref|YP_004383043.1|  8 GMPGAGKSTVGVILAKALGMNFVDADLVIQERTGLRLQAIIDRDGPAGFLKAEEEAVLSLSCR 70
                                      6679***********************999999999999666655555555555555544443 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.4e-05     0.016       5      36 ..       6      38 ..       3      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                      EEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHH CS
                              CoaE  5 ltGgiasGKstvanlfad.lgvpivDaDlvArq 36
                                      l G  ++GKstv  ++a+ lg++ vDaDlv ++
  gi|330506615|ref|YP_004383043.1|  6 LIGMPGAGKSTVGVILAKaLGMNFVDADLVIQE 38
                                      667779**********999*********99665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.6e-05      0.03      35      64 ..       3      32 ..       1      50 [. 0.81
   2 ?   -3.0   0.0       4.9   5.5e+03      87     114 ..     119     146 ..     109     148 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                            RuvB_N 35 hvllyGpPGlGkttlakiiakelgvklkit 64
                                       ++l+G PG Gk+t+  i+ak lg+++  +
  gi|330506615|ref|YP_004383043.1|  3 NIVLIGMPGAGKSTVGVILAKALGMNFVDA 32
                                      5899********************998655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.9
                            RuvB_N  87 vlfideihrlsraveevlysamedfrld 114
                                       vlf  +  r+       ly    d+++d
  gi|330506615|ref|YP_004383043.1| 119 VLFAGQSLRMMYDQRVSLYEQYADITID 146
                                       6677777777777777788888887777 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.5e-05     0.028       1      30 [.       4      33 ..       4      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                                      EEEESSTTSSHHHHHHHHHHHHTHEEEEEE CS
                               AAA  1 vllyGppGtGKTllakavakelgvefleis 30
                                      ++l+G pG GK+++   +ak lg++f+  +
  gi|330506615|ref|YP_004383043.1|  4 IVLIGMPGAGKSTVGVILAKALGMNFVDAD 33
                                      579**********************99765 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0015       1.7       1      27 [.       6      32 ..       6      52 .. 0.81
   2 ?    3.7   0.0     0.053        60     100     123 ..      90     125 ..      81     154 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                                      EEESTTSSHHHHHHHHHHHHTSEEEEH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlst 27
                                      l+G PgaGK t+   l+k +g++ + +
  gi|330506615|ref|YP_004383043.1|  6 LIGMPGAGKSTVGVILAKALGMNFVDA 32
                                      79**************99999887654 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.053
                                       TSEESEEEEEE--HHHHHHHHHT............G CS
                                       xxxxxxxxxxxxxxxxxxxxxxx............x RF
                               ADK 100 kvkldlvleldvpeevlveRltg............D 123
                                        ++  +v++l+vp e + +Rl +             
  gi|330506615|ref|YP_004383043.1|  90 LISAGTVVYLKVPFEEIEKRLGNisgrgivlfagqS 125
                                       466789**************9886667666666652 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 ?   13.4   0.0   4.4e-05     0.049      48      78 ..       2      36 ..       1      63 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-05
                         IstB_IS21 48 enivllGpsGvGKsh....laialgveavraglsv 78
                                       nivl+G +G+GKs     la alg++ v a+l +
  gi|330506615|ref|YP_004383043.1|  2 RNIVLIGMPGAGKSTvgviLAKALGMNFVDADLVI 36
                                      59***********9644448999999999888765 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.5e-05     0.062       4      33 ..       2      31 ..       1      48 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.5e-05
                    Ploopntkinase3  4 rliylvGqPGaGkstlmaeltkgfdrskve 33
                                      r i l+G PGaGkst+   l+k++  + v+
  gi|330506615|ref|YP_004383043.1|  2 RNIVLIGMPGAGKSTVGVILAKALGMNFVD 31
                                      7899************99999998877776 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   0.00014      0.15       1      27 [.       3      30 ..       3      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                            AAA_28  1 kivitGgestGKTtlleaLaar.gypvv 27
                                      +iv++G +++GK+t+   La+  g++ v
  gi|330506615|ref|YP_004383043.1|  3 NIVLIGMPGAGKSTVGVILAKAlGMNFV 30
                                      69**************999987688776 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013      0.15       2      36 ..       4      38 ..       3      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                         Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsvvle 36
                                      i++ G P +GK++  v Lak+ +  ++  D v++e
  gi|330506615|ref|YP_004383043.1|  4 IVLIGMPGAGKSTVGVILAKALGMNFVDADLVIQE 38
                                      7889****************************987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019      0.21       1      27 [.       3      29 ..       3      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                                      EEEEE--SSSSHHHHHHHGGGGBS--E CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaalnrev 27
                                      +++L+G pG gKs++   la+al+ ++
  gi|330506615|ref|YP_004383043.1|  3 NIVLIGMPGAGKSTVGVILAKALGMNF 29
                                      589*******************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1199.72
//
Query:       gi|330506616|ref|YP_004383044.1|  [L=259]
Description: iron compound ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-33  116.5   0.0    2.2e-33  115.7   0.0    1.4  1  ABC_tran        ABC transporter
    8.6e-16   58.6   0.7      2e-07   31.1   0.1    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    5.3e-08   32.6   0.9    4.2e-06   26.4   0.9    2.4  1  SMC_N           RecF/RecN/SMC N terminal domain
    3.4e-06   26.7   0.0    6.6e-06   25.8   0.0    1.4  1  AAA_29          P-loop containing region of AAA domain
    3.7e-06   27.6   0.1    5.2e-06   27.1   0.1    1.2  1  AAA_23          AAA domain
    2.8e-05   24.0   0.1     0.0082   15.9   0.0    2.1  2  AAA_15          AAA ATPase domain
    0.00024   21.1   0.0    0.00047   20.1   0.0    1.4  1  RsgA_GTPase     RsgA GTPase
     0.0021   18.5   0.1       0.04   14.3   0.1    2.5  2  AAA             ATPase family associated with various cellula
     0.0022   17.8   0.4      0.016   14.9   0.0    2.2  3  AAA_30          AAA domain
     0.0023   18.4   0.2     0.0064   16.9   0.2    1.9  1  AAA_16          AAA ATPase domain
  ------ inclusion threshold ------
      0.016   14.6   0.0      0.028   13.8   0.0    1.4  1  Mg_chelatase    Magnesium chelatase, subunit ChlI
      0.021   14.8   0.1      0.081   12.8   0.0    1.9  2  NACHT           NACHT domain
      0.024   14.9   1.0       0.17   12.2   0.4    2.5  2  AAA_22          AAA domain
      0.027   13.3   0.1        1.3    7.8   0.0    2.5  3  ABC_ATPase      Predicted ATPase of the ABC class
      0.048   14.0   0.4       0.21   11.9   0.4    2.2  1  AAA_19          AAA domain
      0.066   12.8   0.0       0.12   11.9   0.0    1.3  1  AAA_27          AAA domain
        0.1   11.0   0.0       0.14   10.6   0.0    1.1  1  Cellulose_synt  Cellulose synthase
       0.14   12.1   0.0       0.26   11.2   0.0    1.4  1  ATPase_2        ATPase domain predominantly from Archaea
       0.14   11.8   0.1       0.22   11.2   0.1    1.3  1  AAA_24          AAA domain
       0.15   12.0   0.1       0.51   10.3   0.1    1.9  2  AAA_5           AAA domain (dynein-related subfamily)
       0.19   10.5   0.0       0.27   10.0   0.0    1.1  1  DLIC            Dynein light intermediate chain (DLIC)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   0.0   2.6e-36   2.2e-33       2     137 .]      21     169 ..      20     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 2.6e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvr 77 
                                       +nvs++l+ ge++ i+G+nG+GKStL+k++ag  kp+ G++++ g+++ +    +  ++ig++pq+ + +fp + v 
  gi|330506616|ref|YP_004383044.1|  21 ENVSFSLRSGEVMCILGPNGSGKSTLIKCIAGIFKPATGSVHIMGENTASLGAGKIARRIGYVPQQnEVVFPFT-VL 96 
                                       79****************************************************************55566665.99 PP

                                       HH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +                  ++ + + + l+ +g+ +l+++++     sLSgGq+q+v +aral+++p+llllDEpta
  gi|330506616|ref|YP_004383044.1|  97 DFvvmgrtphisifaspgaKDMKIARESLEMVGIGDLAERTL----GSLSGGQRQMVLIARALAQEPTLLLLDEPTA 169
                                       999***********9998444444899999999999999999....*****************************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 !   26.3   0.1   7.2e-09   6.1e-06       1      43 [.      32      77 ..      32     100 .. 0.75
   2 !   31.1   0.1   2.4e-10     2e-07     226     299 ..     130     200 ..     103     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 7.2e-09
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl...drdvegltdelsggggir 43
                                      ++++ GpNgsGKS+L++++ +++       ++ g+++ + g g+i+
  gi|330506616|ref|YP_004383044.1| 32 VMCILGPNGSGKSTLIKCIAGIFKPatgSVHIMGENTASLGAGKIA 77
                                      5789*****************9887666666666665555555554 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 2.4e-10
                            AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                        gd  e+++ +lS G++++  ++ al++ +   +lll+DEp ++L+   +  +le + +l++ g+ +++ TH p
  gi|330506616|ref|YP_004383044.1| 130 IGDLAERTLGSLSGGQRQMVLIARALAQEP---TLLLLDEPTAHLDFGNQVLVLEAVQKLASSGISIVMNTHMP 200
                                       688999*************55555555555...************************777777*********55 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.9   4.9e-09   4.2e-06      24     190 ..      30     190 ..      13     204 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.9e-09
                                       SSEEEEEESTTSSHHHHHHHHH..........HHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEES CS
                                       xxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAil..........FvLGersakklrseklsdlihkskekasvkkaeveitfdnedkkl 90 
                                        ++ +i+GpNGSGKs l+  i           +++Ge++a +l + k+ + i +       ++ ev   f+  d  +
  gi|330506616|ref|YP_004383044.1|  30 GEVMCILGPNGSGKSTLIKCIAgifkpatgsvHIMGENTA-SLGAGKIARRIGY-----VPQQNEVVFPFTVLDFVV 100
                                       46789**************996332222222245554444.5555555555555.....555566666666666655 PP

                                       SSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  91 kiekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDei 167
                                         +++++si  +    g  ++ki +++ +   + +l e++     +LSgG++++v +a  +A    +   l llDe 
  gi|330506616|ref|YP_004383044.1| 101 MGRTPHISIFASP---GAKDMKIARESLEMVGIGDLAERT---LGSLSGGQRQMVLIARALA----QEPTLLLLDEP 167
                                       5555777776554...445679999999999999987775...458********98887766....566799***** PP

                                       TTTS-HHHHHHHHHHHHHHCTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 168 daaLDeknvkkvaellkekskna 190
                                        a+LD+ n   v e +++  ++ 
  gi|330506616|ref|YP_004383044.1| 168 TAHLDFGNQVLVLEAVQKLASSG 190
                                       *************9999887554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   7.7e-09   6.6e-06      12      50 ..      20      58 ..      16      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 7.7e-09
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      f++ +++++  +++ + Gp+GsGKSTl+  i+ ++ pa+
  gi|330506616|ref|YP_004383044.1| 20 FENVSFSLRSGEVMCILGPNGSGKSTLIKCIAGIFKPAT 58
                                      777888888666****************99999999987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   6.1e-09   5.2e-06      10      41 ..      20      52 ..      13      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 6.1e-09
                            AAA_23 10 frdqeidF.skgltlItGpNGaGKTTildAikl 41
                                      f+++++ + s  + +I GpNG+GK+T++ +i  
  gi|330506616|ref|YP_004383044.1| 20 FENVSFSLrSGEVMCILGPNGSGKSTLIKCIAG 52
                                      5667777777789******************75 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.6e-06    0.0082      21      48 ..      27      55 ..      19      92 .. 0.83
   2 !    6.8   0.0    0.0058       4.9     322     366 ..     157     200 ..      75     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.6e-06
                            AAA_15 21 lsee.ltvliGkNnsGKSsilealdlFln 48
                                      l +  ++++ G+N+sGKS++++ +  +++
  gi|330506616|ref|YP_004383044.1| 27 LRSGeVMCILGPNGSGKSTLIKCIAGIFK 55
                                      444459****************9987776 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0058
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                       +++ +ll++EP ahL   +q  + ++ ++la+++   +++ TH p
  gi|330506616|ref|YP_004383044.1| 157 QEPTLLLLDEPTAHLDFGNQVLVLEAVQKLASSGI-SIVMNTHMP 200
                                       45689*****************************9.9*****965 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.5e-07   0.00047      77     131 ..       7      62 ..       4      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.5e-07
                                       SEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  77 yevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       ++ l  s  +++ +e+++  l++ ++++++G+ G GKStLi+ +++  + +tg+v 
  gi|330506616|ref|YP_004383044.1|   7 VDSLSYSYGKENVFENVSFSLRSgEVMCILGPNGSGKSTLIKCIAGIFKPATGSVH 62 
                                       566777888889999******999********************999888888875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   4.7e-05      0.04       1      35 [.      33      69 ..      33     172 .. 0.60
   2 ?   -0.4   0.0       1.6   1.4e+03      47      47 ..     202     202 ..     150     255 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.7e-05
                                      EEEESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTCS CS
                               AAA  1 vllyGppGtGKTllakavakelg.....vefleisgsell 35
                                      +++ Gp G GK++l+k +a  ++     v+   i g +  
  gi|330506616|ref|YP_004383044.1| 33 MCILGPNGSGKSTLIKCIAGIFKpatgsVH---IMGENTA 69
                                      7899****************9863322233...3232222 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                                       H CS
                               AAA  47 r 47 
                                       +
  gi|330506616|ref|YP_004383044.1| 202 H 202
                                       1 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.9e-05     0.016      15      53 ..      28      65 ..      21      86 .. 0.84
   2 ?   -1.0   0.0       1.5   1.3e+03      72      97 ..     137     167 ..     107     197 .. 0.57
   3 ?   -0.3   0.0      0.86   7.4e+02      81     100 ..     203     227 ..     168     239 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaaggrviglA 53
                                       sg+ v+++ Gp G+GK+t++k ++ +++ a g+v+++ 
  gi|330506616|ref|YP_004383044.1| 28 RSGE-VMCILGPNGSGKSTLIKCIAGIFKPATGSVHIMG 65
                                      5665.9*********************999977777654 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                            AAA_30  72 tiakllkrlk.....grarlepgtllivDEa 97 
                                       t+ +l   ++     +ra  ++ tll+ DE 
  gi|330506616|ref|YP_004383044.1| 137 TLGSLSGGQRqmvliARALAQEPTLLLLDEP 167
                                       4444444444666654333444488888884 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.86
                            AAA_30  81 k.....grarlepgtllivDEagmv 100
                                       +     ++a+l +++ll vDE++ v
  gi|330506616|ref|YP_004383044.1| 203 AflvgsRAAALCNRRLLAVDEVAAV 227
                                       1334444467778899999998776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   7.5e-06    0.0064      21      62 ..      29      69 ..      14     196 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.5e-06
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdq 62
                                      sg  e++ + G+ G+GKs+l+++++  ++ + g + + g+++ 
  gi|330506616|ref|YP_004383044.1| 29 SG--EVMCILGPNGSGKSTLIKCIAGIFKPATGSVhIMGENTA 69
                                      33..7899***************99777666433334444444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.3e-05     0.028      18      55 ..      26      63 ..      10      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                      Mg_chelatase 18 aaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55
                                      +   g  + ++Gp GsGK+ l+k++++++ p + +  +
  gi|330506616|ref|YP_004383044.1| 26 SLRSGEVMCILGPNGSGKSTLIKCIAGIFKPATGSVHI 63
                                      55556678899*****************9998876555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.4e-05     0.081       2      21 ..      32      51 ..      31      58 .. 0.90
   2 ?   -0.6   0.0       1.3   1.1e+03      72      88 ..     149     165 ..      81     224 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.4e-05
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      ++++ G++GsGK+tL++ +a
  gi|330506616|ref|YP_004383044.1| 32 VMCILGPNGSGKSTLIKCIA 51
                                      79**************9887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                                       CHHHHCCSCCCEEEEEE CS
                             NACHT  72 vwavllelperlLlilD 88 
                                       v + ++  +e +Ll+lD
  gi|330506616|ref|YP_004383044.1| 149 VLIARALAQEPTLLLLD 165
                                       44555555666666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   0.00019      0.17       5      28 ..      30      53 ..      27     195 .. 0.87
   2 ?    0.7   0.0      0.67   5.7e+02      83     103 ..     205     227 ..     178     251 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                            AAA_22  5 agilvvtGesGtGKTtllrrlleq 28
                                        ++++ G+ G+GK+tl++ ++  
  gi|330506616|ref|YP_004383044.1| 30 GEVMCILGPNGSGKSTLIKCIAGI 53
                                      66899*************987765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.67
                            AAA_22  83 eqalrarav..ielliiDEaqhl 103
                                          +ra+a   ++ll +DE+  +
  gi|330506616|ref|YP_004383044.1| 205 LVGSRAAALcnRRLLAVDEVAAV 227
                                       5555555557789******9885 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0015       1.3     242     265 ..      27      51 ..      23      60 .. 0.85
   2 ?    2.3   0.0     0.068        58     323     351 ..     141     169 ..     132     173 .. 0.88
   3 ?   -1.3   0.0      0.85   7.3e+02     109     144 ..     175     211 ..     170     248 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0015
                                       E-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAle 265
                                       ++ G v+ I G++  GKsTL++ ++
  gi|330506616|ref|YP_004383044.1|  27 LRSGeVMCILGPNGSGKSTLIKCIA 51 
                                       677889****************995 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.068
                                       --HHHHHHHHHHHHHHTT-SEEEEEGGGS CS
                        ABC_ATPase 323 ASGStsqAanimealeagakllLiDEDts 351
                                        SG   q + i++al  + +llL+DE t+
  gi|330506616|ref|YP_004383044.1| 141 LSGGQRQMVLIARALAQEPTLLLLDEPTA 169
                                       59999999******************886 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.85
                                       SEE--BSSEE.E--EEEEEEEEE---EETTSE-HHHH CS
                        ABC_ATPase 109 qevlersave.lsdekielrlrvgLPaegrrilgkea 144
                                       ++vl   av+ l +++i++ ++ ++P +   + +++a
  gi|330506616|ref|YP_004383044.1| 175 NQVLVLEAVQkLASSGISIVMNTHMPDHAFLVGSRAA 211
                                       5555555554268889999999999987655544443 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   0.00024      0.21      10      37 ..      30      57 ..      22     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvel 37
                                       +v++++++ G+GK++++k+i  +++ +
  gi|330506616|ref|YP_004383044.1| 30 GEVMCILGPNGSGKSTLIKCIAGIFKPA 57
                                      689*****************99887755 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   0.00014      0.12      15      47 ..      21      51 ..      12      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                            AAA_27 15 tdrsldfsaeeadlhliyGpNEAGKstalrAis 47
                                      ++  ++fs  + ++  i+GpN +GKst+++ i 
  gi|330506616|ref|YP_004383044.1| 21 EN--VSFSLRSGEVMCILGPNGSGKSTLIKCIA 51
                                      44..45555588999*************99886 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00017      0.14     458     524 ..      47     111 ..      34     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00017
                    Cellulose_synt 458 sdrlhqvlrwalGsveiffsrnnalfagykkklkllerlayl...nviiypftsifllvycilpalslls 524
                                          +  +++ a+Gsv i+  + ++l ag     k+ +r+ y+   n +++pft + ++v    p +s+++
  gi|330506616|ref|YP_004383044.1|  47 IKCIAGIFKPATGSVHIMGENTASLGAG-----KIARRIGYVpqqNEVVFPFTVLDFVVMGRTPHISIFA 111
                                       5556678899*******99999999888.....78888888766699********************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 ?   11.2   0.0    0.0003      0.26      20      41 ..      30      51 ..      24      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeii 41
                                       e++ i Gp gsGK++L+k i+
  gi|330506616|ref|YP_004383044.1| 30 GEVMCILGPNGSGKSTLIKCIA 51
                                      57899*************9876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00025      0.22       4      22 ..      32      50 ..      29      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                       ++i Gp+g+GK+tl+k +
  gi|330506616|ref|YP_004383044.1| 32 VMCILGPNGSGKSTLIKCI 50
                                      79*************9976 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   0.1    0.0006      0.51       2      24 ..      33      58 ..      32      82 .. 0.82
   2 ?   -1.2   0.0       2.2   1.9e+03     101     119 ..     176     196 ..     151     235 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0006
                                      EEEE--SSSSHHHHHHHGGGGB...S CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal...n 24
                                      ++++Gp G+gKs+l++ +a  +   +
  gi|330506616|ref|YP_004383044.1| 33 MCILGPNGSGKSTLIKCIAGIFkpaT 58
                                      699************99998886433 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.2
                                       SEEE---........-EEEEE CS
                             AAA_5 101 elvkakndd.ller.frviat 119
                                       ++   ++ + l++  +++++ 
  gi|330506616|ref|YP_004383044.1| 176 QVLVLEAVQkLASSgISIVMN 196
                                       444433333333323333333 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00031      0.27      19      55 ..      24      60 ..      12      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00031
                              DLIC 19 ssklPsgksvlvlGedgsGkttliaklqGveeekkGr 55
                                      s  l sg  + +lG +gsGk+tli  + G+ ++  G+
  gi|330506616|ref|YP_004383044.1| 24 SFSLRSGEVMCILGPNGSGKSTLIKCIAGIFKPATGS 60
                                      567899999********************98887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1680.25
//
Query:       gi|330506617|ref|YP_004383045.1|  [L=339]
Description: iron compounds ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete 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-91  304.7  31.8    6.8e-91  304.5  31.8    1.0  1  FecCD     FecCD transport family
    3.2e-06   26.8  17.7    3.2e-06   26.8  17.7    1.7  1  ABC-3     ABC 3 transport family
  ------ inclusion threshold ------
       0.44   10.7  14.4       0.11   12.7   1.5    3.3  3  PIG-F     GPI biosynthesis protein family Pig-F
        1.6    8.2   6.1        5.9    6.3   6.1    2.0  1  DUF1129   Protein of unknown function (DUF1129)


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 !  304.5  31.8   1.5e-94   6.8e-91       4     312 .]      18     333 ..      14     333 .. 0.97

  Alignments for each domain:
  == domain 1  score: 304.5 bits;  conditional E-value: 1.5e-94
                             FecCD   4 lllllslllgavkispsevfeallgka..........dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNp 70 
                                       l+l++sl++g +++++s +++ +++             s+++++++++rlpr+laa+lvG aL+vaG+++Q+v+rNp
  gi|330506617|ref|YP_004383045.1|  18 LMLIVSLFMGRYQVPVSVLIDDIMNTItalffgtaipASTHHTVLFSVRLPRILAAMLVGCALSVAGVSFQGVFRNP 94 
                                       67899****************9999889999******9*************************************** PP

                             FecCD  71 LadPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsal 147
                                       L++P+ilG+ sga++ga+l++ll+    + + + l+af+++lla++  + + + +kg+ +l l+L+Gi+vs++++al
  gi|330506617|ref|YP_004383045.1|  95 LVSPYILGVGSGAGFGACLGILLF---DNHIMIQLLAFIFGLLAMFAAISMDKASKGTGTLVLVLSGIIVSSIFTAL 168
                                       **********************98...677889******************************************** PP

                             FecCD 148 tsllllll.neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrll 223
                                       +sl ++ +   ++l +i+fwl+Gsls++++s+++++ v +++++l+l+ll+ ++++l+lgde+A+slGvnv ++rl+
  gi|330506617|ref|YP_004383045.1| 169 ISLAKYAAdPYDELPEIVFWLMGSLSSIRYSDLIWITVPMFIGMLVLFLLRWRINILSLGDEEARSLGVNVDKMRLI 245
                                       ********8899***************************************************************** PP

                             FecCD 224 llllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtal 300
                                       ++++++l+t++av+++G+ig+vGL+vPhi r++vg+++ +llp+s+++Ga ++ll+d lar++ s te+p+gi+t+l
  gi|330506617|ref|YP_004383045.1| 246 IIICATLVTSAAVSISGVIGWVGLVVPHISRMIVGPNYNRLLPMSMVCGASFMLLVDDLARTV-SVTEIPLGIITSL 321
                                       ***************************************************************.58*********** PP

                             FecCD 301 iGapffiylllr 312
                                       +Gap+f+yl+ r
  gi|330506617|ref|YP_004383045.1| 322 VGAPIFAYLIKR 333
                                       *********976 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8  17.7   7.1e-10   3.2e-06      44     226 ..     109     299 ..      63     327 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 7.1e-10
                             ABC-3  44 pGvalayllgvn...lllgailvgliaavalellkrktk...lkedtaigivlsvflalglvlvslikk...skvdl 111
                                        G +l++ll  n   + l a+++gl+a +a   + +++k   +   ++ gi++s+++   + l +++ +      ++
  gi|330506617|ref|YP_004383045.1| 109 FGACLGILLFDNhimIQLLAFIFGLLAMFAAISMDKASKgtgTLVLVLSGIIVSSIFTALISLAKYAADpydELPEI 185
                                       4778887776555556667788887766655555555551005556778*******997777777776675556678 PP

                             ABC-3 112 dsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavG 188
                                         +L+G++ +i   dli i++   + +l+l+l++  + ++++  e A++ g++v+ ++l++++   l  ++a+ + G
  gi|330506617|ref|YP_004383045.1| 186 VFWLMGSLSSIRYSDLIWITVPMFIGMLVLFLLRWRINILSLGDEEARSLGVNVDKMRLIIIICATLVTSAAVSISG 262
                                       88899********************99999999999***************************************** PP

                             ABC-3 189 viLvialliiPaatArrltrslesllivAillglvsvv 226
                                       vi  + l ++P +  + ++ + ++ll +++++g+ +++
  gi|330506617|ref|YP_004383045.1| 263 VIGWVGL-VVPHISRMIVGPNYNRLLPMSMVCGASFML 299
                                       **98885.679999999999999999999999987765 PP

>> PIG-F  GPI biosynthesis protein family Pig-F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.5   2.4e-05      0.11      65     146 ..      33     115 ..      17     117 .. 0.88
   2 ?    1.2   0.3     0.081   3.6e+02      23      74 ..     121     169 ..     116     176 .. 0.62
   3 ?    4.5   1.0    0.0077        34      50      90 ..     291     331 ..     185     334 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                             PIG-F  65 ltlllatlllaillvlfGApllthlleTlllalhls.lltvlpllyvlgvdaeawkevvsleepldevlggllgtvv 140
                                       +++l+  ++++i++++fG  +  ++++T+l+++ l  +l+++ + ++l v +  ++ v+    +   +lg   g+ +
  gi|330506617|ref|YP_004383045.1|  33 VSVLIDDIMNTITALFFGTAIPASTHHTVLFSVRLPrILAAMLVGCALSVAGVSFQGVFRNPLVSPYILGVGSGAGF 109
                                       5667788999************************96378888888**************999888889999999999 PP

                             PIG-F 141 GaWlGa 146
                                       Ga lG+
  gi|330506617|ref|YP_004383045.1| 110 GACLGI 115
                                       999997 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.081
                             PIG-F  23 stLlsslivlallqvlyvvlclekkkkkskkskivlallsllltlllatlll 74 
                                       + +++ l++++ l ++++++ +   k+++ + ++vl l  ++++++  t l+
  gi|330506617|ref|YP_004383045.1| 121 HIMIQLLAFIFGLLAMFAAISMD--KASKGTGTLVLVLSGIIVSSI-FTALI 169
                                       56788888999999999999993..232344555544444444444.44433 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0077
                             PIG-F  50 kskkskivlallsllltlllatlllaillvlfGApllthll 90 
                                         + ++++l++  l  t+ ++ ++l i++ l+GAp++ +l 
  gi|330506617|ref|YP_004383045.1| 291 MVCGASFMLLVDDLARTVSVTEIPLGIITSLVGAPIFAYLI 331
                                       6788899999999999999*****************99875 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.1    0.0013       5.9      87     170 ..     122     213 ..     113     224 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0013
                           DUF1129  87 lllalfallfgilalfskkkqtas...iGlitlllvalvgGlamvlvyrlltre.kkkkkrpplwkrllilllll.. 157
                                       +++ l+a++fg+la+f   ++ ++   +G ++l+l+++++  +++ +  l +   ++ ++ p+++  l+ +l ++  
  gi|330506617|ref|YP_004383045.1| 122 IMIQLLAFIFGLLAMFAAISMDKAskgTGTLVLVLSGIIVSSIFTALISLAKYAaDPYDELPEIVFWLMGSLSSIry 198
                                       5667777777777777665555444559****************999888876555666666655555444443322 PP

                           DUF1129 158 ..vvwlvlftlvall 170
                                         ++w+ + +++++l
  gi|330506617|ref|YP_004383045.1| 199 sdLIWITVPMFIGML 213
                                       225666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2362.80
//
Query:       gi|330506618|ref|YP_004383046.1|  [L=590]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   31.3   0.0      5e-07   30.2   0.0    1.5  1  Radical_SAM   Radical SAM superfamily
     0.0003   21.1   0.2    0.00065   20.0   0.2    1.5  1  Fer4_12       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.026   13.9   0.2       0.13   11.7   0.0    2.3  2  zf-ribbon_3   zinc-ribbon domain
       0.18   11.4   0.0       0.33   10.5   0.0    1.4  1  Peripla_BP_2  Periplasmic binding 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 !   30.2   0.0   1.1e-10     5e-07       2     150 ..      63     201 ..      63     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.1e-10
                                       EEESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       v++ gCn+ C  C  +   + r   + +ls+ ++++++ e      + +v+++  ep +++ + ++l+  ak+  + 
  gi|330506618|ref|YP_004383046.1|  63 VFSTGCNFECQGCVARLLaSNRSFGWPTLSPTQVVAKALEQE----CQGVVSTLNEPAANYYIFRELAVQAKE--NS 133
                                       5899************999999****************9997....***************999999999999..8* PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                       + + ++tn +   ee le+l  l  d v++g++ +++  + + + + ++   v +++  l e g++ v + +v
  gi|330506618|ref|YP_004383046.1| 134 LLVGCSTNCYFT-EETLEELGGLI-DFVNVGVKGYSNS-IYRTC-GAKSSTPVFRNIAGLLEMGVH-VETSVV 201
                                       ***********8.*********99.*************.*****.889999999999999999999.554444 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   1.4e-07   0.00065       8     117 ..      61     165 ..      55     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.4e-07
                           Fer4_12   8 lslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekp 84 
                                       l +f +gCn++C+gC++  +   +++  +++    ++++++ +++ +g++ +  EP +  n+ ++ el+ + ke+ +
  gi|330506618|ref|YP_004383046.1|  61 LQVFSTGCNFECQGCVA-RLLASNRSFGWPTLSPTQVVAKALEQECQGVVSTLNEPAA--NYYIFRELAVQAKENSL 134
                                       6799************5.5666666666666666677777779999************..**************999 PP

                           Fer4_12  85 ekdiwlytgytleelskkekeellkeidvlvdG 117
                                         +  +++ y  ee ++ e   l++ ++v v+G
  gi|330506618|ref|YP_004383046.1| 135 -LVGCSTNCYFTEETLE-ELGGLIDFVNVGVKG 165
                                       .4455555555555554.466666666666665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.9e-05      0.13       2      14 ..     274     286 ..     273     288 .. 0.81
   2 ?   -2.1   0.0      0.65   2.9e+03       8      13 ..     308     313 ..     307     315 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.9e-05
                       zf-ribbon_3   2 tvrCPnCGaplss 14 
                                       +++CP+CG++l++
  gi|330506618|ref|YP_004383046.1| 274 HTYCPQCGSLLAE 286
                                       689******7666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.65
                       zf-ribbon_3   8 CGapls 13 
                                       CG++++
  gi|330506618|ref|YP_004383046.1| 308 CGHNVQ 313
                                       999765 PP

>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   7.4e-05      0.33      96     236 ..     381     518 ..     367     519 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.4e-05
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EES CS
                      Peripla_BP_2  96 slkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsnsyigdlldalgieni 172
                                       s+ e ir +++  g e ++e+l ++i ++++++ s +++  +  v + +g++    +    + + + l+  +g+++i
  gi|330506618|ref|YP_004383046.1| 381 SYLEFIRLIAKKAGAEHQGEELSSFIGKRMESVLSLAAENSDHSVYYCMGSPL---FALNAGRMENNLVTFAGGKSI 454
                                       67889***********************************8888888886666...777778888888888****** PP

                                       TTT--..STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTS..HHHHTT-EEEE-H CS
                      Peripla_BP_2 173 aaesk..kseyeeisaEqilasdpdvifvsgraeadnktgleflkenpllael..pAvkngrVyalds 236
                                        +  +  ++ + ++s+  i++ +p+ if+sg      +  l+++     + ++   Avk+ rVy +++
  gi|330506618|ref|YP_004383046.1| 455 NKVLQreGKPGVNVSPAFINEHNPQTIFISGF----LSRPLDEFYGLCRYYGIeaDAVKEQRVYVIPP 518
                                       888878899999******************98....77777777777667666556788888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 4136.13
//
Query:       gi|330506619|ref|YP_004383047.1|  [L=205]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete 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   63.8   0.0    9.3e-17   61.5   0.0    1.9  2  Methyltransf_11  Methyltransferase domain
    4.4e-16   59.4   0.0    1.3e-15   57.9   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
    3.2e-12   46.5   0.0    4.3e-12   46.1   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.4e-08   35.3   0.1    6.7e-08   33.2   0.0    1.9  2  Methyltransf_12  Methyltransferase domain
    4.8e-08   32.6   0.0    8.6e-08   31.8   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.1e-08   32.9   0.0    8.2e-08   32.3   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
     0.0005   19.7   0.0      0.001   18.7   0.0    1.6  1  MTS              Methyltransferase small domain
    0.00062   19.2   0.0    0.00099   18.6   0.0    1.4  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.005   16.2   0.0     0.0057   16.0   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0051   16.7   0.0      0.058   13.2   0.0    2.1  1  Methyltransf_8   Hypothetical methyltransferase
     0.0079   14.8   0.0     0.0091   14.6   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
  ------ inclusion threshold ------
       0.04   13.9   0.5       0.22   11.5   0.0    1.9  2  Methyltransf_32  Methyltransferase domain
       0.11   11.5   0.0       0.16   11.0   0.0    1.2  1  GcpE             GcpE protein


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   6.7e-20   9.3e-17       1      95 [.      41     138 ..      41     139 .. 0.94
   2 ?    0.3   0.0      0.85   1.2e+03       6      55 ..     140     186 ..     137     194 .. 0.61

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 6.7e-20
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       Ld+GcG  +l   +a+   +r++gvDls em +l++ek+   ++  kv  + ad++ lpf+++  Dl+vs+ +++++
  gi|330506619|ref|YP_004383047.1|  41 LDLGCGIASLGISIAQITeMRTYGVDLSREMCRLSQEKVLHHRIadKVVPLIADVHVLPFQNGCADLIVSRGSVFFW 117
                                       8*****9999999998889*************9999999998888977889************************** PP

                                       CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                       +d+ +a++eiaRvL pgG   
  gi|330506619|ref|YP_004383047.1| 118 NDLPAAFNEIARVLAPGGQAW 138
                                       ******************875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.85
                                       TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT CS
                   Methyltransf_11   6 GtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaekl 55 
                                       G+G  +++l ++  ++  +++  ++  + +ke+ s+e+   +++++ ae++
  gi|330506619|ref|YP_004383047.1| 140 GGGFGTKELREQIsEKMAAIN--PQWQNNSKERLSPEN--QKVIEEAAEQT 186
                                       667777777766645555544..455555666666665..45677766665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   9.3e-19   1.3e-15       2      97 .]      41     135 ..      40     135 .. 0.94
   2 ?   -1.2   0.0       2.5   3.4e+03      55      55 ..     168     168 ..     139     201 .. 0.53

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 9.3e-19
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       LdlGcG   l + +a+   + + +gvD+s em++  +e++ ++++  +v  + +d++ lpf++g  Dl+vs+g++  
  gi|330506619|ref|YP_004383047.1|  41 LDLGCGIASLGISIAQIT-EMRTYGVDLSREMCRLSQEKVLHHRIadKVVPLIADVHVLPFQNGCADLIVSRGSVF- 115
                                       9**************996.7********************99999999***********************88744. PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       ++ +dl++a++eiarvL pgG
  gi|330506619|ref|YP_004383047.1| 116 FW-NDLPAAFNEIARVLAPGG 135
                                       44.59***************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.5
                                       C CS
                   Methyltransf_25  55 a 55 
                                        
  gi|330506619|ref|YP_004383047.1| 168 K 168
                                       2 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   3.1e-15   4.3e-12       6     133 ..      39     164 ..      36     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 3.1e-15
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsn 81 
                                       r lDlGCG   l++ +a+  +++ + +G+D s e+ +l++e+  ++ +   v   ++d++ l+  ++  + Dli+s+
  gi|330506619|ref|YP_004383047.1|  39 RCLDLGCGIASLGISIAQ--ITEMRTYGVDLSREMCRLSQEKVLHHRIAdKVVPLIADVHVLP--FQNGCADLIVSR 111
                                       78***************4..456778***************9999999879************..************ PP

                   Methyltransf_31  82 evlnaladpdkileeiervlkpggilliedprllaelpakveeeskay.evve 133
                                       + +   +d++++++ei rvl pgg   i    + +el+++++e++ a   +++
  gi|330506619|ref|YP_004383047.1| 112 GSVFFWNDLPAAFNEIARVLAPGGQAWIGGGFGTKELREQISEKMAAInPQWQ 164
                                       ****************************************9999995443332 PP

>> Methyltransf_12  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   6.7e-08       1      98 [.      41     136 ..      41     137 .. 0.78
   2 ?   -0.4   0.0       1.5     2e+03      39      70 ..     159     189 ..     146     192 .. 0.56

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 4.8e-11
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennn.nnnvelealdlldldggssfDlvvasnvl 76 
                                       L++GcG +sl   +++   + + +gvD+s++++   +ek  +++  + +  +  ++  l   ++++  Dl+v+ + +
  gi|330506619|ref|YP_004383047.1|  41 LDLGCGIASLGISIAQI-TEMRTYGVDLSREMCRLSQEKVLHHRIADkVVPLIADVHVLP--FQNGCADLIVSRGSV 114
                                       8*************776.9**************666666555554330333333333333..33369*******999 PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGr 98 
                                         ++d+ +++++i+++L+pgG+
  gi|330506619|ref|YP_004383047.1| 115 FFWNDLPAAFNEIARVLAPGGQ 136
                                       999******************8 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.5
                   Methyltransf_12  39 klakrennnnnnvelealdlldldggssfDlv 70 
                                          +++nn+ +++  e++ +++++  ++ Dlv
  gi|330506619|ref|YP_004383047.1| 159 INPQWQNNSKERLSPENQKVIEEAA-EQTDLV 189
                                       3445555555555555555554444.477777 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   6.2e-11   8.6e-08      48     149 ..      37     137 ..      25     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 6.2e-11
                                       TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEEEE CS
                   Ubie_methyltran  48 gakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvtvs 123
                                       + + lD+ +G + l +++++  + +    ++D++ +m + +++k+ ++    ++  l a+   Lpf+++  D++   
  gi|330506619|ref|YP_004383047.1|  37 SGRCLDLGCGIASLGISIAQITEMR--TYGVDLSREMCRLSQEKVLHHRIAdKVVPLIADVHVLPFQNGCADLIVSR 111
                                       4478**************9987765..689**************998887769999****************98655 PP

                                       S-GGG-S-HHHHHHHHHHHEEEEEEE CS
                   Ubie_methyltran 124 fGlrnvtDklkaLkeayrvlkpGGrl 149
                                         +    D + a++e+ rvl pGG+ 
  gi|330506619|ref|YP_004383047.1| 112 GSVFFWNDLPAAFNEIARVLAPGGQA 137
                                       5577889*****************86 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0     6e-11   8.2e-08      22     117 ..      36     139 ..      26     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 6e-11
                   Methyltransf_23  22 aggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae.......kakkaqkdqfdeqeaaepqgkfdlIvlre 90 
                                       ++gr+Ld+GcG  +l  ++++      +gvDls+e+  + +        a+k ++  +d +  ++++g  dlIv+r 
  gi|330506619|ref|YP_004383047.1|  36 KSGRCLDLGCGIASLGISIAQITEmRTYGVDLSREMCRLSQekvlhhrIADKVVPLIADVHVLPFQNGCADLIVSRG 112
                                       789************9999888655*********9999877888877766666666666667888************ PP

                   Methyltransf_23  91 vlehvpdppellrqiatllkpgGylll 117
                                       +     d+p++++ ia+ l+pgG + +
  gi|330506619|ref|YP_004383047.1| 113 SVFFWNDLPAAFNEIARVLAPGGQAWI 139
                                       ***********************8765 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   7.3e-07     0.001      27     102 ..      29     109 ..      23     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.3e-07
                                       CHCC...TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-ST.TTTSTTS- CS
                               MTS  27 lpke...lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdv.leeveekk 97 
                                       + +e   +sg+ lDlGcG+  lg+++a+ ++ ++   vd + +  ++++e + +++++  v  +  dv +  ++++ 
  gi|330506619|ref|YP_004383047.1|  29 IVTEsgiKSGRCLDLGCGIASLGISIAQITE-MRTYGVDLSREMCRLSQEKVLHHRIAdkVVPLIADVhVLPFQNGC 104
                                       55555668899****************9665.58999**************99999985532233333133445556 PP

                                       EEEEE CS
                               MTS  98 fdliv 102
                                        dliv
  gi|330506619|ref|YP_004383047.1| 105 ADLIV 109
                                       66666 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   7.2e-07   0.00099     164     256 ..      39     137 ..      29     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.2e-07
                              PrmA 164 evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell....keekadvivaN... 233
                                       + lD+G+G + L i  a++   + ++vD+     + ++e +   ++++k+ v l +++     +++ ad+iv+    
  gi|330506619|ref|YP_004383047.1|  39 RCLDLGCGIASLGISIAQITEMRTYGVDLSREMCRLSQEKVLHHRIADKV-VPLIADVHvlpfQNGCADLIVSRgsv 114
                                       679*********************************************99.77777776445558999999974222 PP

                              PrmA 234 ILaevlielaedikklvkeggll 256
                                          + l    ++i++++++gg++
  gi|330506619|ref|YP_004383047.1| 115 FFWNDLPAAFNEIARVLAPGGQA 137
                                       34455555555566666666655 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.1e-06    0.0057      57     162 ..      32     137 ..      25     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.1e-06
                                       TTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SE CS
                              CMAS  57 klelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdr 130
                                         ++k G + Ld+GcG  sl +  ++  + +  g+ lS+e  +l++++v +  +++kv  +++d + l+      d 
  gi|330506619|ref|YP_004383047.1|  32 ESGIKSG-RCLDLGCGIASLGISIAQITEMRTYGVDLSREMCRLSQEKVLHHRIADKVVPLIADVHVLPFqngCADL 107
                                       5566666.579****************************************99999998888877765432246788 PP

                                       EEEES-GGGTSGGGHHHHHHHHHHHS-TT-EE CS
                              CMAS 131 vvsvgafehvgkenydtffkklkkllkedGll 162
                                       +vs g +  +  + +++ f+++ ++l ++G  
  gi|330506619|ref|YP_004383047.1| 108 IVSRGSV--FFWNDLPAAFNEIARVLAPGGQA 137
                                       8888865..66677888888888888888765 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   4.2e-05     0.058      77     156 ..      41     139 ..      18     159 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                                       EEES-TT-HHHHH--S-..EEEE..ES..............S-SSTTEEE..S-TTS-S--TT-EEEEEEES---.S CS
                    Methyltransf_8  77 adlGcGeakiaeavrekekvrsf..dl..............vavnervva..cdlakvPledesvdvavfclslm.g 134
                                        dlGcG a +  ++ + +++r++  dl              + + ++vv+   d+  +P +++ +d++v   s+   
  gi|330506619|ref|YP_004383047.1|  41 LDLGCGIASLGISIAQITEMRTYgvDLsremcrlsqekvlhHRIADKVVPliADVHVLPFQNGCADLIVSRGSVFfW 117
                                       56666666666555555554443224422222211111111234556664337999**************9998626 PP

                                       S-HHHHHHHHHHHEEEEEEEEE CS
                    Methyltransf_8 135 tnladflkeanrvlkvGGllkv 156
                                       ++l    +e+ rvl +GG  ++
  gi|330506619|ref|YP_004383047.1| 118 NDLPAAFNEIARVLAPGGQAWI 139
                                       8899***************998 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 !   14.6   0.0   6.6e-06    0.0091     113     220 ..      32     143 ..       7     202 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.6e-06
                   Methyltransf_29 113 aaggkvrtvlDvGCgvasfg...ayllsrdvltlslapkDeheaqvqfaLeRgvpailavlgt.krlpyPsrsfdli 185
                                       ++g k    lD+GCg+as+g   a++ +     + l+ +    +q ++   R    ++ +++  + lp+     dli
  gi|330506619|ref|YP_004383047.1|  32 ESGIKSGRCLDLGCGIASLGisiAQITEMRTYGVDLSREMCRLSQEKVLHHRIADKVVPLIADvHVLPFQNGCADLI 108
                                       455566679**********933333444455555666666666666666667777788888862569*********9 PP

                   Methyltransf_29 186 hCsrCridwteedgilllevdRvlRpgGy.fvlsap 220
                                         sr  + + ++  + + e+ Rvl pgG  ++  + 
  gi|330506619|ref|YP_004383047.1| 109 -VSRGSVFFWNDLPAAFNEIARVLAPGGQaWIGGGF 143
                                       .69999999999999*************62443333 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016      0.22      21      68 ..      32      76 ..      15      88 .. 0.78
   2 ?    0.4   0.2      0.41   5.7e+02      58      93 ..     147     182 ..     143     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                   Methyltransf_32 21 akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekae 68
                                      ++  ++ + +D+G+G + L+  +a+     +++ +g+d+++e+++ ++
  gi|330506619|ref|YP_004383047.1| 32 ESGIKSGRCLDLGCGIASLGISIAQ---ITEMRTYGVDLSREMCRLSQ 76
                                      3455667899**************9...779*********99987665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.41
                   Methyltransf_32  58 dakeelvekaekraeklgkkfnkrlsfaelsieeat 93 
                                       +++e+ +ek  +++ + +++ ++rls +++++ e+ 
  gi|330506619|ref|YP_004383047.1| 147 ELREQISEKMAAINPQWQNNSKERLSPENQKVIEEA 182
                                       567777777777777777777777776666655544 PP

>> GcpE  GcpE protein
   #    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      33      83 ..      53      97 ..      45     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                      HHHHHHHHHHCT-SEEEEEE-SHHHHHHHHHHHHHHHHTT-SS-EEEEE-S CS
                              GcpE 33 tvkqikrlaeaGaelvRvtvqdeeeaealkeikeklkkkglkvplvaDihf 83
                                      +++qi+++ ++G++l R  ++ ++e    ++i +k+      vpl+aD+h 
  gi|330506619|ref|YP_004383047.1| 53 SIAQITEMRTYGVDLSREMCRLSQEKVLHHRIADKV------VPLIADVHV 97
                                      699*********************************......********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      737  (0.0411066); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 1529.16
//
Query:       gi|330506620|ref|YP_004383048.1|  [L=362]
Description: ABC transporter substrate-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-21   77.4   0.0    1.5e-21   77.1   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.0   8.4e-26   1.5e-21      44     237 ..     100     295 ..      54     296 .. 0.80

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 8.4e-26
                                       SBESSSB-HHHHHHH--SEEEE-GGG....GGGHHHHHH...HS-EEE----TTS.HHHHHHHHHHHHHTT-HHHHH CS
                      Peripla_BP_2  44 vgadgeidvEklaalkPDlvilskgl.gltdedeellks...giptvivessntg.eslkeqiralgellgledeae 115
                                         + ++ ++E+++++ PD+vi  ++  g ++e+++++++    ip+v+ + s  +  +   +i+ +g+ll+++d+ae
  gi|330506620|ref|YP_004383048.1| 100 WYGTQTGNYETMINMSPDIVIEGYTTdGEVQETINRRQEkfgSIPVVAIDGSIIFvTKSDPTIEYVGKLLDCKDQAE 176
                                       4568899********************8888888877762336*****99998779********************* PP

                                       HHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--...STT-EEE-HHH CS
                      Peripla_BP_2 116 klvaeidsklaaaksaidse.kpkpvlvfggadeggyvvagsnsyigdlldalgieniaaesk...kseyeeisaEq 188
                                       kl ++  s l ++++ ++ +  +++v v++   + g     s+s  ++++d+ g+ n+a+  +   +++  ++s Eq
  gi|330506620|ref|YP_004383048.1| 177 KLLEFRSSILTKINETVKDIpEDEKVRVYYAEGPTGLATDPSGSQHSQVIDICGGINVADC-PltpGNGMTQVSIEQ 252
                                       ********************7667777777666677777788999999****999999554.4579*********** PP

                                       HHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-HH CS
                      Peripla_BP_2 189 ilasdpdvifvsgraeadnktgleflkenpllaelpAvkngrVyaldss 237
                                       + +++p++i+ s+       ++++ + ++p++ +++Av+n+rVy  +++
  gi|330506620|ref|YP_004383048.1| 253 VMNWNPEAIITSSP------QFYKTVYSDPIWTSVEAVQNKRVYLAPQN 295
                                       **************......9***********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2673.46
//
Query:       gi|330506621|ref|YP_004383049.1|  [L=303]
Description: MerR family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-16   61.2   0.0    5.7e-16   59.2   0.0    2.1  1  GyrI-like      GyrI-like small molecule binding domain
    9.2e-11   41.7   1.0    1.1e-09   38.2   0.0    2.4  2  MerR_1         MerR HTH family regulatory protein
    8.7e-08   31.8   1.9    2.1e-07   30.6   1.9    1.7  1  MerR           MerR family regulatory protein
     0.0013   19.2   0.2     0.0028   18.1   0.2    1.5  1  MerR-DNA-bind  MerR, DNA binding


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 !   59.2   0.0   1.3e-19   5.7e-16       2     155 .]     123     300 ..     122     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.3e-19
                                       CEEEEEE--EEEEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHCTT....--SSEEEEEEEEE-..STTCCCEEEEEE CS
                         GyrI-like   2 eveivelpafrvvgirhrgdyneeggipklweelyawaseiklsn....avspligvssdepe..etedeelkydig 72 
                                       e+ ++++pa+rv+  + +g  + +  i+kl++el+ +++    +     +  p+i++++ +    ++ d e  ++++
  gi|330506621|ref|YP_004383049.1| 123 EPAVKDVPALRVICRKETGILSPT--IEKLIGELFSFVDLPASKRnqlkVIGPVIAIYHEDCAkgNENDRERGDEHV 197
                                       899********************9..888888888887655544445669999999999887766444444444443 PP

                                       EECCCCC.....................CGBTTSEEEEE-SEEEEEEEEECEGGGHHHHHHHHHHTHHHHTT-EEEE CS
                         GyrI-like  73 vtveirv.....................egpeglefleipageyAvfrhkGpyddlqatyaklygewlpesgyerrd 128
                                        +  ++                       + +g+e++++pa ++++  hkG+y +l ++y+ +++ +++  g+ + +
  gi|330506621|ref|YP_004383049.1| 198 SVEAEAIsdwsekevsievalpiagkveGEGSGIEVKSLPAARMLSMIHKGSYPTLHKSYQSVFK-YMAGAGL-EVA 272
                                       333333358999***************9999**********************************.*******.*** PP

                                       SEEEEEEECCCTS.SCGCEEEEEEEEEC CS
                         GyrI-like 129 gpsiEiYlsdpre.reeelkteiyipvk 155
                                       gp +E+Ylsdp++  eeel tei+ip++
  gi|330506621|ref|YP_004383049.1| 273 GPIRELYLSDPCKtAEEELLTEIQIPYR 300
                                       **************************96 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   2.5e-13   1.1e-09       3      68 ..       8      75 ..       6      76 .. 0.93
   2 ?    1.7   0.2     0.061   2.7e+02      42      57 ..      98     114 ..      96     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 2.5e-13
                                      HHHHHHHHTS-HHHHHHHHHHTT-S-EE..-TTS-EEEEHHHHHHHHHHHHHHHTT--GGG---XXXX CS
                            MerR_1  3 igevakilgvtthtlrywekegllkpkr..teggrryYtdedierLklikyLlkrGltlkgikkllns 68
                                      i  ++ i+ ++++ lry+++   l+p+     +g+ryYt +++e   +ik+  + G++l++ k++l++
  gi|330506621|ref|YP_004383049.1|  8 IARFSAITRISQRALRYYDRLEILVPEArdPFTGYRYYTSSQMELGVKIKAICSLGFSLEDLKTYLQA 75
                                      77899******************777776999**********************************97 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.061
                                       HHHHHHHHHHHHH.TT- CS
                            MerR_1  42 dierLklikyLlk.rGl 57 
                                       +i rLk+i +Llk +  
  gi|330506621|ref|YP_004383049.1|  98 EILRLKRIEALLKeERT 114
                                       589*********95554 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   1.9   4.7e-11   2.1e-07       2      38 .]       8      45 ..       7      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4.7e-11
                                      HHHHHHHHTTTHHHHHHHHHTT.SSTSEEETTTSSEEE CS
                              MerR  2 IgevAeltGvsprtLRyYEreG.LipppeRtegGyRlY 38
                                      I  ++ +t +s r+LRyY+r   L+p+++++ +GyR+Y
  gi|330506621|ref|YP_004383049.1|  8 IARFSAITRISQRALRYYDRLEiLVPEARDPFTGYRYY 45
                                      777899****************8888888888*****9 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   6.3e-07    0.0028      12      63 ..      61     110 ..      56     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.3e-07
                                       HTT--HHHHHHHHHHHHSTTTBHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind  12 rlGFsLdeIrelLalyddrappcqdvr...allarklaeleeriaeLqalraeLa 63 
                                       +lGFsL++ ++ L     +a +c d++    l + +l  ++  i +L++++a L+
  gi|330506621|ref|YP_004383049.1|  61 SLGFSLEDLKTYL-----QAEACGDWDtvdSLMEGRLSAVRLEILRLKRIEALLK 110
                                       69***********.....779999999999********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2148.30
//
Query:       gi|330506622|ref|YP_004383050.1|  [L=541]
Description: hypothetical protein MCON_0372 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-16   61.3   0.0    2.4e-16   60.6   0.0    1.4  1  DUF362    Domain of unknown function (DUF362)


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 !   60.6   0.0   1.3e-20   2.4e-16       1     200 [.     116     375 ..     116     377 .. 0.64

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 1.3e-20
                                       xxxxxxxxx.....xxxxx....xxxxxxxxxxxxxxxxxxx.xx...xxxxxxxxxxxxx......xxxxxxxxx. RF
                            DUF362   1 VaiKpNlge.....agnpe....gatthpevvravvellkea.ga...gkiivgdspglyv......srgkahrev. 57 
                                       V+iK+N++      +        g++ +p++vr v+  ++e  g    ++  v+d++  ++      +         
  gi|330506622|ref|YP_004383050.1| 116 VVIKVNVVGpsqglP---GekgrGIISDPRIVRYVAGKVREIiGFdgsADLKVIDATFTPEknpsdkN-------Np 182
                                       9*******5443433...26669****************88422234466777777775433432220.......13 PP

                                       ........................xxxxxxxxxxxxx...xxxxxxxxxxxxxx...xxx..xxxxxxxxxxxxxxx RF
                            DUF362  58 ........................aeeagydelaega...diadglegedevvv...pvk..gkhlkkelkiakavl 102
                                                               +++ g+ +   ga    ++  +++++   v   p++   +     + ++k + 
  gi|330506622|ref|YP_004383050.1| 183 qsfyyarlqrsagnsveandicydYDADGILDGGSGAklvNLDSVQKSDRFLAVvdePIRgrSE-----VWLPKFLR 254
                                       5556777777777788877777774444444433333332222222221111112222223222.....44444333 PP

                                       ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx.xxxxxxxxxxxxxxxxxxxx RF
                            DUF362 103 ..........eaDviInlpklKgHalagvtgalKnlfGcisgsgkaeiHs....kr.dsekfaekiadlakalkpdl 164
                                                  +Dv+I +p lK H l+g tgalK + G++ g   ++ H+     + d + f + ++ l++a + dl
  gi|330506622|ref|YP_004383050.1| 255 tkdqaqgeseYCDVYIGIPILKSHGLCGTTGALKLHWGSMLGLLEKQEHAgygfGTgDIRMFLDYLCALNRARGFDL 331
                                       44445577779****************************9999544456657763323567888888888887788* PP

                                       xxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxx RF
                            DUF362 165 nvvdgikamegegpsggs.........kelglvlaStDpvalDaa 200
                                       +++d++++ ++ gp+++          + ++ +l+S+D va+D++
  gi|330506622|ref|YP_004383050.1| 332 VIMDALTG-NRSGPANKVedkdaktdfILVNAILCSRDSVAIDTV 375
                                       ******76.558887776777744445555555**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 3954.49
//
Query:       gi|330506623|ref|YP_004383051.1|  [L=439]
Description: hypothetical protein MCON_0373 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00028   21.1   5.3    0.00028   21.1   5.3    6.7  6  DUF308        Short repeat of unknown function (DUF308)
  ------ inclusion threshold ------
       0.87    9.4  13.9        9.1    6.0   0.0    4.8  4  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr


Domain annotation for each model (and alignments):
>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.7     0.014   1.2e+02      27      40 ..      37      50 ..      27      76 .. 0.61
   2 !   21.1   5.3   3.2e-08   0.00028       1      63 [.      95     154 ..      95     165 .. 0.82
   3 ?   -0.9   6.2      0.23   2.1e+03       7      34 ..     169     199 ..     163     215 .. 0.82
   4 ?   -1.5   5.7      0.37   3.4e+03       3      16 ..     248     261 ..     246     284 .. 0.89
   5 !   10.7   6.4   5.7e-05      0.51       2      42 ..     306     346 ..     305     357 .. 0.92
   6 !    6.0   7.7    0.0017        15      22      73 .]     374     423 ..     365     423 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.014
                            DUF308 27 lfGilllvsGivqi 40
                                      + G+++l++G++ +
  gi|330506623|ref|YP_004383051.1| 37 VGGVFFLLFGALLF 50
                                      22444444444333 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 3.2e-08
                            DUF308   1 llGillivlGilalllPvaallalvllfGilllvsGivqiiaafaarkknrggrwlglllGil 63 
                                       ++G+l++ lG la+++Pv   +++ ++ G+++l++G v++++ f +++k r   +++ + Gil
  gi|330506623|ref|YP_004383051.1|  95 VIGLLAAMLGTLAIFYPVHLNATIRIIAGLMVLIAGTVGMLQLFISEDKAR---VWMKVPGIL 154
                                       68******************************************5555444...344445554 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.23
                            DUF308   7 ivlGilal...llPvaallalvllfGilllv 34 
                                       ivlGi+ l   ++P   ++++ llfG+ ll+
  gi|330506623|ref|YP_004383051.1| 169 IVLGIITLlpgIMPNPLTAVFLLLFGASLLF 199
                                       7888888844459999999999999998887 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.37
                            DUF308   3 GillivlGilalll 16 
                                       G lli+lGil+ll+
  gi|330506623|ref|YP_004383051.1| 248 GYLLILLGILVLLM 261
                                       78999999999987 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 5.7e-05
                            DUF308   2 lGillivlGilalllPvaallalvllfGilllvsGivqiia 42 
                                       lGil++++G++  ++P++ + ++  l+G+  ++sG++ +++
  gi|330506623|ref|YP_004383051.1| 306 LGILFAAIGFFSCIVPGILTGVIQPLIGLQNIISGVLLLAT 346
                                       8***********************************99875 PP

  == domain 6  score: 6.0 bits;  conditional E-value: 0.0017
                            DUF308  22 lalvllfGilllvsGivqiiaafaarkknrggrwlglllGilyliaGllllf 73 
                                       + + ++ Gi+ +++Gi  ++  +   +  +    + lll +l +i+Gl++l+
  gi|330506623|ref|YP_004383051.1| 374 TLVLTVTGIVTILFGINMLAPLL-LPGLFGM-IAYALLLPLLIIIMGLMVLI 423
                                       4555788************8777.7777776.4599*************985 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 ?    6.0   0.0     0.001       9.1      97     140 ..      12      53 ..       4      61 .. 0.72
   2 ?    1.5   5.9     0.025   2.3e+02      62      90 ..      88     116 ..      86     227 .. 0.80
   3 ?    2.1   0.4     0.017   1.5e+02     124     157 ..     185     218 ..     116     264 .. 0.50
   4 ?    1.0   0.7     0.037   3.3e+02      50      84 ..     286     320 ..     277     393 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.001
                      Trp_oprn_chp  97 raaaaaatgvasaaaaveltawpvlalaggvllllagvllllra 140
                                       ++++ +++    ++a+++l+  +vl ++ggv  ll g+ll+l  
  gi|330506623|ref|YP_004383051.1|  12 AQQQLQSN--IMKKAQIDLSIEVVLLIVGGVFFLLFGALLFLID 53 
                                       33333323..3466666788899****************98765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.025
                      Trp_oprn_chp  62 vrglgrrvvgvllalagagaavaalsllt 90 
                                       +r ++ +v+g+l+a++g +a++ +++l +
  gi|330506623|ref|YP_004383051.1|  88 LRSWLVVVIGLLAAMLGTLAIFYPVHLNA 116
                                       78999999999999999999999998755 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.017
                      Trp_oprn_chp 124 aggvllllagvllllrarswpamssrYerpaarr 157
                                       + +v lll g+ ll  ar  +  +++Y++++a+r
  gi|330506623|ref|YP_004383051.1| 185 LTAVFLLLFGASLLFLARCIHMAAHQYRSTEAKR 218
                                       3344444444444444444444445555554444 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.037
                      Trp_oprn_chp  50 lvllAaavAvlavrglgrrvvgvllalagagaava 84 
                                       l++l  ++   + r +  +++g+l a++g+  ++ 
  gi|330506623|ref|YP_004383051.1| 286 LLALGEFMGKEMSRSWPAIALGILFAAIGFFSCIV 320
                                       55555555555667777777777777777655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 2912.89
//
Query:       gi|330506624|ref|YP_004383052.1|  [L=272]
Description: short-chain dehydrogenase/reductase [Methanosaeta concilii GP6]
Scores for complete 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-48  163.0   0.2    7.3e-48  162.6   0.2    1.1  1  adh_short        short chain dehydrogenase
    2.5e-34  118.8   0.1    3.3e-34  118.5   0.1    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    4.5e-11   43.0   0.1      8e-11   42.2   0.1    1.3  1  KR               KR domain
    4.9e-05   22.9   0.1     0.0011   18.5   0.1    2.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00015   21.0   0.0    0.00018   20.8   0.0    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.011   15.7   0.2       0.03   14.3   0.1    1.8  2  ADH_zinc_N       Zinc-binding dehydrogenase
      0.074   12.0   0.0       0.11   11.5   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
       0.11   11.8   0.0        2.2    7.6   0.0    2.1  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.6   0.2   3.3e-51   7.3e-48       1     187 [.      11     200 ..      11     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 162.6 bits;  conditional E-value: 3.3e-51
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHH CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkee.gakalaiqvDvtdreevealvekavkkl 75 
                                       kv++vtG++sGIG+a++++++++Ga+ v+ +d+++ekl +  + l+ e   ++l + +Dvt++e+v++l++k ++  
  gi|330506624|ref|YP_004383052.1|  11 KVAVVTGGASGIGLALCEAMLASGANKVIlADINKEKLDRERARLEVEyPGRVLGLMCDVTSEESVKDLIAKSAAFG 87 
                                       89***********************87777****************99999*******************9986655 PP

                                       .SSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHH CS
                         adh_short  76 .gkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsA 151
                                        g++d+L nNAG+  sg f++ ++e we+ +++N+ +++  +ra++p m +q +G+I+nv S +++ p+a++++YsA
  gi|330506624|ref|YP_004383052.1|  88 eGRIDILFNNAGVGLSGLFEQQTNEIWEKAFAINFYSAIYGIRAAIPIMRAQGGGHIINVISGIAFSPMAQQSMYSA 164
                                       7*************9************************************************************** PP

                                       HHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHH CS
                         adh_short 152 sKaavagltrslakelaptgirvnavaPGlvdTdma 187
                                       +Kaa++glt +l+ e+ +++i  ++ +PG ++T++ 
  gi|330506624|ref|YP_004383052.1| 165 TKAALNGLTLALRYEYWDENICFTSATPGTTKTGIW 200
                                       *********************************986 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 !  118.5   0.1   1.5e-37   3.3e-34       1     182 [.      17     205 ..      17     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 1.5e-37
                                       TTTTSHHHHHHHHHHHTT-E.EEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHH.SSEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGae.vvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekf.gklDi 72 
                                       G asgIG a+ +a+ + Ga+ v+l+d+n+e+ +++ ++l+ e++ +v  l cDVt+ee+v++l+++ ++   g++Di
  gi|330506624|ref|YP_004383052.1|  17 GGASGIGLALCEAMLASGANkVILADINKEKlDRERARLEVEYPGRVlgLMCDVTSEESVKDLIAKSAAFGeGRIDI 93 
                                       669****************77**********9999999999***99779****************9887768***** PP

                                       EEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHH CS
                      adh_short_C2  73 lvnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaa 147
                                       l+nnag+  +  g f++ + e +++a+++n+ys+++ ++aa+p+m+++  g i+n+ s  a   ++++++y+a+Kaa
  gi|330506624|ref|YP_004383052.1|  94 LFNNAGVGLS--GLFEQQTNEIWEKAFAINFYSAIYGIRAAIPIMRAQggGHIINVISGIAFSPMAQQSMYSATKAA 168
                                       *********9..*******************************99887789*******99*9*************** PP

                                       HHHHHHHHHHHHGGGTEEEEEEEE--BHCTG..GGGS CS
                      adh_short_C2 148 lealtrylAvelgpkgiRvNavspgpikTla..asgi 182
                                       l++lt +l +e+ +++i   +  pg +kT +  a gi
  gi|330506624|ref|YP_004383052.1| 169 LNGLTLALRYEYWDENICFTSATPGTTKTGIwaAGGI 205
                                       *****************************98433334 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.1   3.6e-14     8e-11       4     160 ..      14     173 ..      12     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 3.6e-14
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS. CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee. 79 
                                       ++tGG+ g+Gl+l++ ++++ga++++l   ++++ ++++a+++   ++  +v  + +Dv+++++v+ l+++  a + 
  gi|330506624|ref|YP_004383052.1|  14 VVTGGASGIGLALCEAMLASGANKVILADINKEKLDRERARLE--VEYPGRVLGLMCDVTSEESVKDLIAKSAAFGe 88 
                                       89**************************999544444443333..45577999*******************99889 PP

                                       S---EEEE---------TTT--HHHHHHHHT....TTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvla....pKvkGawnLhelledesldffvlfSSiagllgsagqanYaaa 152
                                       ++i   ++ Agv   +l+e++t+e +e+++a    + + G++    +++ +   +++ + S  ++  +a+q+ Y+a+
  gi|330506624|ref|YP_004383052.1|  89 GRIDILFNNAGVGLSGLFEQQTNEIWEKAFAinfySAIYGIRAAIPIMRAQGGGHIINVISGIAFSPMAQQSMYSAT 165
                                       ****************************9983333456677777777788889999999999999999999999999 PP

                                       HHHHHHHH CS
                                KR 153 NaflDala 160
                                        a l++l 
  gi|330506624|ref|YP_004383052.1| 166 KAALNGLT 173
                                       99998875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   4.8e-07    0.0011       2     160 ..      14     180 ..      13     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.8e-07
                                       EEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC.........EEEE--TT-HH......HHHHHHHH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgye.vigldrlssasntarledl.........elveldltdrs......alerlfke 62 
                                       +VtG++  iG al++a+l+ g + vi  d ++++  ++r                 +d+t ++      a  ++f e
  gi|330506624|ref|YP_004383052.1|  14 VVTGGASGIGLALCEAMLASGANkVILADINKEKLDRERA--RleveypgrvLGLMCDVTSEEsvkdliAKSAAFGE 88 
                                       8********************7758888877554444443..24689***995566666666611211144555667 PP

                                       HT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----S CS
                         Epimerase  63 eqpdavihlAavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpn 139
                                        ++d+ ++ A+vg  +   ++ ++++ek ++++   + +  +a +     +  ++  G ++ +   + +  +p++++
  gi|330506624|ref|YP_004383052.1|  89 GRIDILFNNAGVGLSGLFEQQTNEIWEKAFAINFYSAIYGIRAAI----PIMRAQ--GGGHIINVISGIAFSPMAQQ 159
                                       799************************999887644443333433....222211..22222234444555677777 PP

                                       SHHHHHHHHHHHHHHHHHHHH CS
                         Epimerase 140 spYaaaKlageklveayaaqy 160
                                       s Y+a+K+a   l+ a++ +y
  gi|330506624|ref|YP_004383052.1| 160 SMYSATKAALNGLTLALRYEY 180
                                       777777777777777777766 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     8e-08   0.00018       2      96 ..      14     109 ..      13     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8e-08
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.... CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel.. 76 
                                       +vtG++  iG +l++ +l++ ++k+il + +  kl++ + +le e+       +++ +++dv+ +e++++++ +   
  gi|330506624|ref|YP_004383052.1|  14 VVTGGASGIGLALCEAMLASGANKVILADINKEKLDRERARLEVEYPG-----RVLGLMCDVTSEESVKDLIAKSaa 85 
                                       69**********************************999999877777.....345789999999999987764311 PP

                                       ....T-SEEEE------HHHHHHS CS
                   Polysacc_synt_2  77 ....kvdvvfhaAAlKhVPlveen 96 
                                           ++d++f+ A +    l e++
  gi|330506624|ref|YP_004383052.1|  86 fgegRIDILFNNAGVGLSGLFEQQ 109
                                       111156666666666666666555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.4e-05      0.03       1      67 [.      21      99 ..      21     103 .. 0.64
   2 ?   -3.2   0.0       3.4   7.5e+03      34      50 ..     241     258 ..     229     264 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                                      HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHH.T.........T.ESEEEETTTC.HHHHHHHHHTTTSSEEEEEESS CS
                        ADH_zinc_N  1 gvGlaavqlAkalGa.eviavdsseeklelakk.l.........G.adevinykea.dlverikeltggegvdvvfecv 66
                                      g+Gla++++  a+Ga +vi +d+++ekl+  +  l         G +  v  +++  dl ++ +++  ++ +d+ f+ +
  gi|330506624|ref|YP_004383052.1| 21 GIGLALCEAMLASGAnKVILADINKEKLDRERArLeveypgrvlGlMCDVTSEESVkDLIAKSAAFG-EGRIDILFNNA 98
                                      8***************************755443433334333343333333344445555555555.34677777766 PP

                                      C CS
                        ADH_zinc_N 67 G 67
                                      G
  gi|330506624|ref|YP_004383052.1| 99 G 99
                                      6 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.4
                                       TESEEEETTTC.HHHHHH CS
                        ADH_zinc_N  34 Gadevinykea.dlveri 50 
                                       Ga+ ++n+k a  +++++
  gi|330506624|ref|YP_004383052.1| 241 GATNCFNPKAAeGMDAYL 258
                                       888888887766666555 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 ?   11.5   0.0   4.9e-05      0.11       1      66 [.      14      82 ..      14      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.9e-05
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk.....viegDvtdkdkleealeg 66
                                      vvtGga  +G al+++++  + +++v  +D+++++  +e+  +++v+       + +Dvt+++++++ + +
  gi|330506624|ref|YP_004383052.1| 14 VVTGGASGIGLALCEAMLASG-ANKVILADINKEKLDRER-ARLEVEYpgrvlGLMCDVTSEESVKDLIAK 82
                                      8********************.699*****9887766554.445555445666899******999987765 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 ?    7.6   0.0   0.00096       2.2       2      74 ..      15      83 ..      14      86 .. 0.76
   2 ?    2.0   0.0     0.049   1.1e+02     146     171 ..     155     180 ..     152     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00096
                                      EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH CS
                     GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev 74
                                      +TG+a  iG  l+e +l+ g + +++ + +++    ++++ + + ++e+ +++    +D+t ++s+++l+a+ 
  gi|330506624|ref|YP_004383052.1| 15 VTGGASGIGLALCEAMLASGANKVILADINKE----KLDRERARLEVEYPGRVLGLMCDVTSEESVKDLIAKS 83
                                      9*******************998887655444....3333333334566788999999999999999999875 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.049
                                       -----SHHHHHHHHHHHHHHHHHHHH CS
                     GDP_Man_Dehyd 146 pfyPrsPYaaaKlyadwivvnyreay 171
                                       p+  +s Y+a+K++ + ++ + r +y
  gi|330506624|ref|YP_004383052.1| 155 PMAQQSMYSATKAALNGLTLALRYEY 180
                                       78889**********99999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1831.84
//
Query:       gi|330506625|ref|YP_004383053.1|  [L=289]
Description: hypothetical protein MCON_0375 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-40  136.7   0.0    1.1e-39  136.4   0.0    1.0  1  ADC       Acetoacetate decarboxylase (ADC)


Domain annotation for each model (and alignments):
>> ADC  Acetoacetate decarboxylase (ADC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.4   0.0   6.2e-44   1.1e-39      17     233 ..      23     255 ..       7     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 6.2e-44
                                       EEEEEEEEEEEE-HHHHHTTSBTTEEECS..TSEEEEEEEEEEEECTTTCEEEEEEEEEE.EEETTEEEEEEEEEEE CS
                               ADC  17 ynaealtvsyrtdpeaaaallPepLelae..rplvavyfaeypdssfgggqYneagivvp.vryggkegayilvlwv 90 
                                       +  e+l+++++tdp+ a+++lP+ Lel +  +p v+ yf+++++++f++ +Y+eagi++  +ry+  +g+y+  l +
  gi|330506625|ref|YP_004383053.1|  23 NEEEGLYIFWETDPKVARRVLPPQLELIDpeHPQVYSYFVNIREPTFAP-WYMEAGIGILgARYKEHTGLYFCNLQL 98 
                                       3899*******************************************98.********97366************** PP

                                       S...SHHHHHHHHHHTT--EEE-EEEEEE.ETTEEEEEEEETTEEEEEEEEEEEEEE-HHHHHHHHHTS........ CS
                               ADC  91 d...keaalaaGRElwGfPKklAditltr.egdtlggtverggkrlaeltvelkerapddeealpslka........ 155
                                       +   + ++l++GRE +G+PKk+++  + + ++d +++ ve++g+r++e+++e+++++ + +ea+  +          
  gi|330506625|ref|YP_004383053.1|  99 SgpgAQMGLLSGREMSGLPKKMCEKIVVErNDDIAHVVVEAKGRRIFEAEIEIGSYNEPIMEAGFTDLVpgasadgy 175
                                       ***********************9887777*********************************98777788999**7 PP

                                       .EEEEEEEEE-.TTSTSEEEEEEEEEEEEEEEEEEEEEEE.EEEEE-SSTTCCGGGSCCSEEEEEEEEEEEEEEEEE CS
                               ADC 156 .ptfllkiips.vdggkadvtelvryelsdtrvgeawtGp.aslelepsaddpladlpvlevlsayyikadltvggg 229
                                        + f ++i  +  d    ++++l  y++ +++  +++ +   s+++eps ddp+++l v ++l+a+y  +++ v+g+
  gi|330506625|ref|YP_004383053.1| 176 cFLFKYDICSGkDDNVILQNATLLGYDSVTDYR-SWEAASiKSISMEPSLDDPWSELVVIKPLGAAYSINSNWVRGM 251
                                       777888888886666666699999999999988.888888889999*************************999999 PP

                                       EEEE CS
                               ADC 230 evle 233
                                        vl+
  gi|330506625|ref|YP_004383053.1| 252 HVLA 255
                                       8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2134.42
//
Query:       gi|330506626|ref|YP_004383054.1|  [L=647]
Description: NADH oxidase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-66  223.6   0.0    5.2e-66  223.2   0.0    1.1  1  Oxidored_FMN   NADH:flavin oxidoreductase / NADH oxidase fami
    1.1e-19   70.9   4.5      3e-19   69.4   4.5    1.7  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.2e-11   43.8   2.9      4e-06   27.0   0.3    3.3  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    4.5e-11   43.2   3.5    1.4e-05   25.6   0.2    2.6  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    5.7e-08   31.9   3.4    8.1e-06   24.8   0.4    2.3  2  HI0933_like    HI0933-like protein
    1.6e-07   30.9   0.1     0.0056   16.0   0.0    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    5.6e-07   29.0   2.2      6e-05   22.3   0.2    2.4  2  GIDA           Glucose inhibited division protein A
    5.1e-06   26.1   4.2    2.1e-05   24.1   0.8    2.2  2  FAD_oxidored   FAD dependent oxidoreductase
    6.6e-06   25.5   4.5    0.00043   19.5   0.2    2.8  3  FAD_binding_2  FAD binding domain
    7.8e-06   25.4   3.6     0.0021   17.4   0.3    2.2  2  FAD_binding_3  FAD binding domain
    4.7e-05   22.6   0.0    7.6e-05   22.0   0.0    1.3  1  Dus            Dihydrouridine synthase (Dus)
      0.001   19.5   1.0       0.23   11.9   0.1    2.6  2  NAD_binding_7  Putative NAD(P)-binding
      0.003   16.9   5.1       0.45    9.8   0.5    2.4  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
     0.0032   16.7   4.1      0.068   12.4   0.6    2.4  2  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.013   15.4   4.0        1.5    8.7   0.4    2.3  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.016   14.8   9.0      0.026   14.1   0.2    3.0  4  DAO            FAD dependent oxidoreductase
      0.052   14.0   0.2        5.2    7.6   0.0    3.1  3  XdhC_C         XdhC Rossmann domain
      0.068   12.2   1.8       0.16   11.0   0.2    2.2  2  Lycopene_cycl  Lycopene cyclase protein
       0.14   11.5   0.4       0.46    9.8   0.0    2.0  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
       0.38   11.0   2.3         40    4.5   0.0    3.4  3  TrkA_N         TrkA-N domain
          1    9.4   3.4        1.3    9.0   0.2    2.3  2  NAD_binding_9  FAD-NAD(P)-binding


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 !  223.2   0.0   6.1e-69   5.2e-66       2     340 ..       5     338 ..       4     340 .. 0.87

  Alignments for each domain:
  == domain 1  score: 223.2 bits;  conditional E-value: 6.1e-69
                                       CCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEES.SCCC-SCTTSEE-SSGG CS
                      Oxidored_FMN   2 LFkPikignmtLknRivmapmtrlraldkgnvledlaaeyysqraeipvtliiteaafv.npksggfdnapgiwdee 77 
                                       LF    ig  ++knR+vm pm  + a + g+ ++d  ++yy+ ra+++v+li +e + v n  + ++  + +  +  
  gi|330506626|ref|YP_004383054.1|   5 LFSTGRIGRIEIKNRVVMTPMGTVIAAPGGG-VNDDIIAYYEARAKGGVGLIESELCRVlNGAGAAMTCQLAARNLA 80 
                                       6777789**************6666666664.5558999****************99873556669*********** PP

                                       GHHHHHHHHHHHHHTT-EEEEEEE--GGGS..SCSTCEC..SS.ESSSSSTTT-.S...CS-EE--HHHHHHHHHHH CS
                      Oxidored_FMN  78 qieewrklteavhengskvvvqlwhlGreakseyladqevdspsdpvaldaqeeesaeevykkeltkeeikqliqef 154
                                       ++++++ l++ vh++g k+++ql+h G++  s    ++  +++s   a++ +   +a e  +++l+ eei+++  +f
  gi|330506626|ref|YP_004383054.1|  81 DVAGLARLVDVVHKYGTKIFIQLHHPGGQGSSAIGGEPI-VAAS---AVKSP---TAYET-PHALQVEEIAKIESAF 149
                                       *****************************9554444443.5555...33333...34445.89************** PP

                                       HHHHHHHHHTT-SEEEEEE-CTSHHHHHH-TTT----STTSSSHHHHHHHHHHHHHHHHHHH-SSS.EEEEEECE-- CS
                      Oxidored_FMN 155 veAAkraieAgfDgVeihganGYLlnqFlspksnkrtDeygGslenRarFllevvdaVkeavgeer.vgyRlSpedv 230
                                          A   + Ag+DgV  hga+GYL+n Flsp+ nkrtD ygGslenR+rFll++++ ++e+ g ++ +g+RlS+e+ 
  gi|330506626|ref|YP_004383054.1| 150 ISGALFTKMAGADGVLLHGAHGYLINSFLSPYLNKRTDDYGGSLENRMRFLLDIIRGIREQCGGDFpIGVRLSVEEF 226
                                       ***************************************************************************** PP

                                       STTS--HHHH.HHHHHHHCHCCEEEEEEE.....TT-SSSSSTTS-TTTTHHHCCTTHHHHHHCCCHSSEEEE-SS- CS
                      Oxidored_FMN 231 vekgldfaet.aqkivllkelekrlkdgk.....klalvhaaeprkrgagsvrteqekntefvkevwkkplitvgri 301
                                        +k+ +  e     +++lke +++++d++     +  +   +ep  ++ g +r      +  +k++++ p+i+v +i
  gi|330506626|ref|YP_004383054.1| 227 LGKEGNDLEEsCRICEVLKEAGVDFIDVSctipgSPEVCACIEPGTYEQGWKRYM----AAEIKKHVNIPIIAVCNI 299
                                       *99888887769999***********98722222335556777777776666666....899*************** PP

                                       -SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTC CS
                      Oxidored_FMN 302 adeekaaeivaegeadLvamgRefladpdlveklkkglp 340
                                       +++++a+ei+ eg  d ++++R  ladp++ +k++ g +
  gi|330506626|ref|YP_004383054.1| 300 KEPDVAEEILVEGCCDFIGVARGHLADPEWCNKAQAGKA 338
                                       **********************************99865 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 !   69.4   4.5   3.5e-22     3e-19       2     245 ..     385     610 ..     384     620 .. 0.83

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 3.5e-22
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvki 78 
                                        vvv+GgGpAG++aal l   g+ v+l+ +    l+g+  ++ + +g ++ ++ +         g++    ++ +++
  gi|330506626|ref|YP_004383054.1| 385 TVVVVGGGPAGIEAALLLDSRGFHVVLF-DPAKRLGGTLNIADKGVGKEKITRLV--------DGLIAQVSASDIEL 452
                                       69**************************.77777777666655555555544433........34333333244555 PP

                                       EESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  79 dpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGv 155
                                        +g+ + ++ek      + +    +++A G+ +  ++ipG     gk+v t +++   k +l+  ++++ G+G++G+
  gi|330506626|ref|YP_004383054.1| 453 RMGE-EATVEK-----VKALSPCGIFVACGAIASMPPIPGI---DGKNVVTAEDVLIGKAQLKG-DCIILGSGMTGL 519
                                       4555.444432.....23677789*****************...67778899999999988888.************ PP

                                       HHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                       Pyr_redox_2 156 ElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngekle.vvledgeeidadlv 231
                                       E+A +  k+g+++t+v+ + ++ ++++ ++   ++++l + G + +lg+++ ei ++g  le v ++++  ++ +++
  gi|330506626|ref|YP_004383054.1| 520 ETAEVVLKAGHRTTIVDMLHEIGQGVPIMVLIDIKRRLSEYGPAYMLGHKALEIAEDGVVLErVADGEKVFVNGETI 596
                                       ***************************9999999*************************888777777777****** PP

                                       EE-S-EEES-HHCS CS
                                       xxxxxxxxxxxxxx RF
                       Pyr_redox_2 232 vvavGvrpstelle 245
                                       ++a Gv+p++e l+
  gi|330506626|ref|YP_004383054.1| 597 ILALGVQPRKEVLK 610
                                       *********99884 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 ?   -0.6   0.0       1.9   1.6e+03      19      38 ..      94     113 ..      66     132 .. 0.72
   2 !   27.0   0.3   4.7e-09     4e-06       1      35 [.     388     422 ..     388     440 .. 0.92
   3 !   15.1   0.1   2.3e-05      0.02       1      32 [.     511     542 ..     511     574 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.9
                                       TEEEEEE-SSSSSSGGG-EE CS
                     NAD_binding_8  19 gfdvlllekrdrlGGraasy 38 
                                       ++   ++ + +++GG+ +s+
  gi|330506626|ref|YP_004383054.1|  94 KYGTKIFIQLHHPGGQGSSA 113
                                       44445555667777777765 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 4.7e-09
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35 
                                       +vG+G +G  aA lL  +gf+v+l++ + rlGG +
  gi|330506626|ref|YP_004383054.1| 388 VVGGGPAGIEAALLLDSRGFHVVLFDPAKRLGGTL 422
                                       8********************************76 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2.3e-05
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32 
                                       I+G+G++Gl +A    kag++ +++++ + +G
  gi|330506626|ref|YP_004383054.1| 511 ILGSGMTGLETAEVVLKAGHRTTIVDMLHEIG 542
                                       89****************************98 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   3.8e-06    0.0033       2      40 ..     386     427 ..     385     462 .. 0.87
   2 !   25.6   0.2   1.6e-08   1.4e-05       3      71 ..     510     578 ..     508     586 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.8e-06
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS...TTSSH CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll...rllDe 40 
                                       vvvvGgG  g+E+A  l   g +V +++ +++l    +  D+
  gi|330506626|ref|YP_004383054.1| 386 VVVVGGGPAGIEAALLLDSRGFHVVLFDPAKRLGgtlNIADK 427
                                       9******************************99954445555 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 1.6e-08
                                       EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox   3 vvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsed 71 
                                       +++G+G +glE A++  + g+++t+v++  ++ ++ + ++   ++++l++ g   +l++k+ ei +++ 
  gi|330506626|ref|YP_004383054.1| 510 IILGSGMTGLETAEVVLKAGHRTTIVDMLHEIGQGVPIMVLIDIKRRLSEYGPAYMLGHKALEIAEDGV 578
                                       79**************************************************************96653 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.4   9.4e-09   8.1e-06       2      44 ..     385     429 ..     384     447 .. 0.87
   2 !    7.6   0.2    0.0015       1.3       2      37 ..     508     543 ..     507     547 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 9.4e-09
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHC..GG CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilis..Gg 44 
                                       +v+v+GgG+AG+ aA+ + +rg +V+l++ ak+lg  + i+  G 
  gi|330506626|ref|YP_004383054.1| 385 TVVVVGGGPAGIEAALLLDSRGFHVVLFDPAKRLGGTLNIAdkGV 429
                                       69*********************************9999983344 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0015
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37 
                                       d i++G G  Gl +A+ + k+g+r+++++  +++g+
  gi|330506626|ref|YP_004383054.1| 508 DCIILGSGMTGLETAEVVLKAGHRTTIVDMLHEIGQ 543
                                       689**************************9999987 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00012       0.1       1      25 [.     387     410 ..     387     419 .. 0.86
   2 !   16.0   0.0   6.5e-06    0.0056     128     276 ..     471     611 ..     455     620 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledyl 25 
                                       +++G+GPaG++aa+ l   g+ +++
  gi|330506626|ref|YP_004383054.1| 387 VVVGGGPAGIEAALLLDSRGF-HVV 410
                                       79***************9999.444 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 6.5e-06
                       Pyr_redox_3 128 viiAtGefdkPnklnipGeeklvkhyskvkefhkya.gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekee 203
                                       +++A G   +  ++ ipG + + ++++++  + k + + ++++ G + ++ ++A  + ++g++ t+v+  +ei +  
  gi|330506626|ref|YP_004383054.1| 471 IFVACGA--IASMPPIPGIDGKNVVTAEDVLIGKAQlKGDCIILGSGMTGLETAEVVLKAGHRTTIVDMLHEIGQG- 544
                                       6777887..777888888886666666665555555599********************************99997. PP

                       Pyr_redox_3 204 sdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevk.ddvvlatGykpdlsflkk 276
                                         + + +  di+ rl e+        +  +++ ei e+ + +  + +dg+kv v+ + ++la+G +p  ++lk+
  gi|330506626|ref|YP_004383054.1| 545 --VPIMVLIDIKRRLSEYGP----AYMLGHKALEIAEDGV-VLERVADGEKVFVNgETIILALGVQPRKEVLKA 611
                                       ..688999*********865....3445557888888655.555678888888861556677******999985 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2     7e-08     6e-05       1      32 [.     385     416 ..     385     454 .. 0.77
   2 !    6.2   0.2    0.0053       4.6       1      28 [.     508     535 ..     508     549 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 7e-08
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkl 32 
                                       +v+V+GgG AG+eAAl +  +G++v+L+ +  
  gi|330506626|ref|YP_004383054.1| 385 TVVVVGGGPAGIEAALLLDSRGFHVVLFDPAK 416
                                       59*************************94433 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0053
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi 28 
                                       d+i++G G+ G+e A  + ++G++++++
  gi|330506626|ref|YP_004383054.1| 508 DCIILGSGMTGLETAEVVLKAGHRTTIV 535
                                       79***********************998 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.8   2.4e-08   2.1e-05       2      38 ..     386     422 ..     385     455 .. 0.93
   2 ?    3.1   0.1     0.059        50       1      35 [.     508     542 ..     508     553 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.4e-08
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38 
                                       vvVvGGgpaG+ AA+    +G  v+L ++ ++lGG+l
  gi|330506626|ref|YP_004383054.1| 386 VVVVGGGPAGIEAALLLDSRGFHVVLFDPAKRLGGTL 422
                                       9**********************************87 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.059
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG 35 
                                       D ++ G+g+ G+  A    +aG ++ +v+    +G
  gi|330506626|ref|YP_004383054.1| 508 DCIILGSGMTGLETAEVVLKAGHRTTIVDMLHEIG 542
                                       899*************************9877776 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2     5e-07   0.00043       2      41 ..     386     425 ..     385     429 .. 0.94
   2 !    6.6   0.1    0.0041       3.5       1      33 [.     508     540 ..     508     544 .. 0.91
   3 ?   -1.2   0.0      0.98   8.4e+02     176     236 ..     577     638 ..     555     643 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5e-07
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG- CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggataws 41 
                                       v+V+G+G AG  AAl +  +G  v++ + +++ gg++ ++
  gi|330506626|ref|YP_004383054.1| 386 VVVVGGGPAGIEAALLLDSRGFHVVLFDPAKRLGGTLNIA 425
                                       9**********************************99887 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0041
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                       D i+ GsG+ GL  A    +aG+++++v+  +e
  gi|330506626|ref|YP_004383054.1| 508 DCIILGSGMTGLETAEVVLKAGHRTTIVDMLHE 540
                                       88**************************97665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.98
                                       EEEEEETTTTCEEEEEESEEEE-----GG...........GSSSBSSGTT-S-HHHHHHHCT CS
                     FAD_binding_2 176 GavvenpesgrevrirakavvlatgGfgr.allkellgaaaeaettnapavtGdglalalra 236
                                       G+v+e  ++g++v ++   ++la g  +r + lk +++a ++a++++ +   G+ l+++++a
  gi|330506626|ref|YP_004383054.1| 577 GVVLERVADGEKVFVNGETIILALGVQPRkEVLKAFRDAFPQAHIIGDANRGGRILEATQEA 638
                                       88888888999997666688888888888888888888889988888888888877777766 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   2.4e-06    0.0021       3      31 ..     385     413 ..     384     419 .. 0.92
   2 !    8.8   0.3   0.00098      0.84       3      33 ..     508     538 ..     506     584 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.4e-06
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlve 31 
                                       +V++VG+GpaG+ +allL ++G  vvl +
  gi|330506626|ref|YP_004383054.1| 385 TVVVVGGGPAGIEAALLLDSRGFHVVLFD 413
                                       699*********************99876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00098
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                       d +I G+G +Gl +a +  +aG r+++v+  
  gi|330506626|ref|YP_004383054.1| 508 DCIILGSGMTGLETAEVVLKAGHRTTIVDML 538
                                       568************************9965 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   8.9e-08   7.6e-05      98     232 ..     188     339 ..     180     370 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.9e-08
                                       EEGGGGGGSHHHHHHHHHHHHCCSS..S-EEEEEESESS.....TTTC.HHHHHHHHHHCT-SEEEEESS....... CS
                               Dus  98 gaGaaLlrkpdlvaqivkavvkave..iPvtvkirigid.....deeenalelakiveaaGaqaltvHgR....... 160
                                       ++G +L +  + + +i++ ++++ +  +P+ v+ ++        ++ e+++++++ +++aG++++ v +        
  gi|330506626|ref|YP_004383054.1| 188 DYGGSLENRMRFLLDIIRGIREQCGgdFPIGVRLSVEEFlgkegNDLEESCRICEVLKEAGVDFIDVSCTipgspev 264
                                       5666777777777778888888777664444444432223333778899****************999999999997 PP

                                       ...ECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHHHHHHHHS CS
                               Dus 161 ...traqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfaestavktg 232
                                           +   ye+  +    +e+k++v+ip+ia  +Ik+++ a++il e  +d + ++rg l +P   ++ +a k +
  gi|330506626|ref|YP_004383054.1| 265 cacIEPGTYEQGWKRYMAAEIKKHVNIPIIAVCNIKEPDVAEEILVEGCCDFIGVARGHLADPEWCNKAQAGKAQ 339
                                       76655555555333334689***************************9****************99854444443 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00027      0.23       6      55 ..     382     429 ..     379     467 .. 0.76
   2 ?    5.7   0.1     0.023        20       9      37 ..     508     536 ..     504     592 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeel 55 
                                       +g++v+vvGgG+ + + +  l + g +v++ +p+  + l +++++a++ +
  gi|330506626|ref|YP_004383054.1| 382 QGRTVVVVGGGPAGIEAALLLDSRGFHVVLFDPA--KRLGGTLNIADKGV 429
                                       799******************************9..55666666666655 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.023
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvva 37 
                                        +++ G G  +++ ++ +l+ag + t+v+
  gi|330506626|ref|YP_004383054.1| 508 DCIILGSGMTGLETAEVVLKAGHRTTIVD 536
                                       699************************97 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.4     0.001      0.89      30      61 ..     385     416 ..     380     461 .. 0.89
   2 !    9.8   0.5   0.00053      0.45      17      62 ..     497     540 ..     490     554 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.001
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61 
                                       +v+v+GgG aG++A+    + g +V+++D  +
  gi|330506626|ref|YP_004383054.1| 385 TVVVVGGGPAGIEAALLLDSRGFHVVLFDPAK 416
                                       69************************999755 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00053
                                       EETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C  17 gtlaGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrpa 62 
                                        +l+G+ +   ++  +++G G+ Gl+ +++  + g ++t++D+ ++
  gi|330506626|ref|YP_004383054.1| 497 DVLIGKAQ--LKGDCIILGSGMTGLETAEVVLKAGHRTTIVDMLHE 540
                                       57888888..899*****************************8665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.6   7.9e-05     0.068      19      57 ..     385     422 ..     378     507 .. 0.80
   2 ?    5.2   0.2     0.013        11      17      56 ..     506     544 ..     500     547 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-05
                                       EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                              Thi4  19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57 
                                        vv+vG+G++G+ aa  l  + +++v++++    +GG  
  gi|330506626|ref|YP_004383054.1| 385 TVVVVGGGPAGIEAALLLDSR-GFHVVLFDPAKRLGGTL 422
                                       59******************9.*******9999888864 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.013
                                       EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4  17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56 
                                       + D +i G+G +GL +a ++ k+ + +++i++    +G G
  gi|330506626|ref|YP_004383054.1| 506 KGDCIILGSGMTGLETAEVVLKA-GHRTTIVDMLHEIGQG 544
                                       5799****************999.9999998877666665 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 ?    7.6   0.2    0.0038       3.3       1      32 [.     385     416 ..     385     465 .. 0.83
   2 ?    8.7   0.4    0.0017       1.5       4      32 ..     511     539 ..     509     549 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0038
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdise 32 
                                       +v v+G G  G + a ++ s+g++Vvl+d ++
  gi|330506626|ref|YP_004383054.1| 385 TVVVVGGGPAGIEAALLLDSRGFHVVLFDPAK 416
                                       699**************************965 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0017
                                       EE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                           3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdise 32 
                                       ++G+G+ G + a+v+++ag+++++vd+ +
  gi|330506626|ref|YP_004383054.1| 511 ILGSGMTGLETAEVVLKAGHRTTIVDMLH 539
                                       89***********************9855 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       2.8   2.4e+03      13      31 ..      40      59 ..      33     160 .. 0.63
   2 ?   14.1   0.2     3e-05     0.026       2      36 ..     386     421 ..     385     427 .. 0.94
   3 ?    5.3   0.5     0.014        12       1      35 [.     508     544 ..     508     545 .. 0.91
   4 ?   -2.9   0.0       4.6   3.9e+03     160     205 ..     561     605 ..     550     618 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.8
                                      HHHHHHHHT.T.EEEEESSSS CS
                               DAO 13 stAyeLarr.g.Vtllekgdi 31
                                       +Ay+ ar+ g V l+e++  
  gi|330506626|ref|YP_004383054.1| 40 IIAYYEARAkGgVGLIESE-L 59
                                      5777777664478888877.3 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3e-05
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36 
                                       vv++GGG +G+ +A+ L  rg  V+l++ ++++g g+
  gi|330506626|ref|YP_004383054.1| 386 VVVVGGGPAGIEAALLLDSRGfhVVLFDPAKRLG-GT 421
                                       9****************999*********99999.76 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.014
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35 
                                       d +i G+G++Gl tA    ++g  +t++++ +++g+g
  gi|330506626|ref|YP_004383054.1| 508 DCIILGSGMTGLETAEVVLKAGhrTTIVDMLHEIGQG 544
                                       779***************99999******98888876 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 4.6
                                       T-EEEESECEEEEEEEETCEEEEEEECTEEE..EEEEEEEE--GGGHH CS
                               DAO 160 Gveilegtevtgleeedgkvwgverttpgen..daadavVnaaGawsd 205
                                       G    +g+++ ++ e+   ++ +er+++ge+  +  +++++a G++ +
  gi|330506626|ref|YP_004383054.1| 561 GPAYMLGHKALEIAED---GVVLERVADGEKvfVNGETIILALGVQPR 605
                                       5555667777787543...33333444455533355779999998865 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.1   1.8e+03      45      76 ..     314     349 ..     278     360 .. 0.72
   2 ?    7.6   0.0    0.0061       5.2       1      32 [.     386     417 ..     386     466 .. 0.89
   3 ?    2.4   0.0      0.24   2.1e+02       2      31 ..     510     539 ..     509     638 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.1
                                       -EEEE--S-HHHHHHHHHHHSSS--S....EEEESS CS
                            XdhC_C  45 tavvvlthdhklDaealeaalrkkaa....yigllG 76 
                                       + ++ + ++h  D e++++a ++ka+    +ig+l 
  gi|330506626|ref|YP_004383054.1| 314 CDFIGVARGHLADPEWCNKAQAGKAQtirkCIGCLS 349
                                       557788999**********99866443334777765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0061
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GG CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpree 32 
                                       +v++G+g+ + + a l+ + gf+v+++dp ++
  gi|330506626|ref|YP_004383054.1| 386 VVVVGGGPAGIEAALLLDSRGFHVVLFDPAKR 417
                                       689*************************9876 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.24
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-G CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpre 31 
                                       +i+G g  + + a+++ ++g r+t+vd   
  gi|330506626|ref|YP_004383054.1| 510 IILGSGMTGLETAEVVLKAGHRTTIVDMLH 539
                                       799***********************9755 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00019      0.16       2      36 ..     386     418 ..     385     426 .. 0.92
   2 ?   -0.2   0.1      0.48   4.1e+02       1      30 [.     508     535 ..     508     542 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       vvv+G+GpAg+  A  l     g +vvl ++++ l
  gi|330506626|ref|YP_004383054.1| 386 VVVVGGGPAGIEAALLL--DSRGFHVVLFDPAKRL 418
                                       8****************..999*******998765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.48
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvli 30 
                                       D ++ G+G  gl  A+ +   k+g + +++
  gi|330506626|ref|YP_004383054.1| 508 DCIILGSGMTGLETAEVV--LKAGHRTTIV 535
                                       89*************999..4555444444 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 ?    9.8   0.0   0.00054      0.46      28      73 ..     375     420 ..     354     472 .. 0.74
   2 ?   -2.3   0.1       2.9   2.5e+03      40      66 ..     510     536 ..     498     541 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00054
                                       CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73 
                                       + + ++ +g+tv ++G G  G ++a +l + g++v+ +d+ k+   
  gi|330506626|ref|YP_004383054.1| 375 ENPKYNGQGRTVVVVGGGPAGIEAALLLDSRGFHVVLFDPAKRLGG 420
                                       455566789*******************************987544 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.9
                                       EEES-SHHHHHHHHHHHHTT-EEEEES CS
                      2-Hacid_dh_C  40 GiiGlGrIGqavakrlkafgmkviayd 66 
                                        i+G G  G ++a+++ + g + +++d
  gi|330506626|ref|YP_004383054.1| 510 IILGSGMTGLETAEVVLKAGHRTTIVD 536
                                       599***********9999998888777 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         6   5.1e+03      30      65 ..     301     340 ..     280     343 .. 0.67
   2 ?    4.5   0.0     0.046        40       1      30 [.     386     415 ..     386     424 .. 0.86
   3 ?    4.2   0.2      0.06        51       2      29 ..     510     537 ..     509     545 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6
                                       SHHHHHHHHHTT.SE...EEES-TTSHHHHHHTTGGGESE CS
                            TrkA_N  30 deerveelreeg.le...vvvgdatdeevLeeagiekada 65 
                                       +++++ee+  eg ++   v  g+ +d+e   +a++ ka++
  gi|330506626|ref|YP_004383054.1| 301 EPDVAEEILVEGcCDfigVARGHLADPEWCNKAQAGKAQT 340
                                       4566666666665223347778888888888888888876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.046
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESS CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkd 30 
                                       ++++G G  G + a  L ++g +vv+ d  
  gi|330506626|ref|YP_004383054.1| 386 VVVVGGGPAGIEAALLLDSRGFHVVLFDPA 415
                                       79*****************77458888865 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.06
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEES CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidk 29 
                                       ii+G G +G + ae + + g+ + +++d 
  gi|330506626|ref|YP_004383054.1| 510 IILGSGMTGLETAEVVLKaGH-RTTIVDM 537
                                       9*****************566.79**996 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2    0.0015       1.3       1      39 [.     387     420 ..     387     428 .. 0.78
   2 ?    0.4   0.3      0.68   5.8e+02       2      38 ..     511     543 ..     510     547 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gag 39 
                                       ++vG+Gp+G+ ++  L +     + +++ lfdp++  g g
  gi|330506626|ref|YP_004383054.1| 387 VVVGGGPAGIEAALLLDS-----RGFHVVLFDPAKRlG-G 420
                                       69********99875544.....58********76625.4 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.68
                     NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdp.sepga 38 
                                       i G G++Gl ++e +l+       ++ t++d  +e+g+
  gi|330506626|ref|YP_004383054.1| 511 ILGSGMTGLETAEVVLKAG-----HRTTIVDMlHEIGQ 543
                                       88***********999994.....55566776666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); 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:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 4032.79
//
Query:       gi|330506627|ref|YP_004383055.1|  [L=148]
Description: hypothetical protein MCON_0377 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0046   16.7   0.2      0.012   15.4   0.2    1.7  1  HTH_10           HTH DNA binding domain
  ------ inclusion threshold ------
      0.019   14.5   0.0      0.033   13.7   0.0    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
      0.047   13.5   0.1      0.092   12.6   0.1    1.5  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.052   13.8   0.0       0.32   11.3   0.0    2.0  1  SAM_DrpA         DNA processing protein A sterile alpha motif
      0.059   12.9   0.1       0.14   11.7   0.1    1.6  1  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
      0.081   13.0   0.1       0.13   12.3   0.1    1.3  1  HTH_29           Winged helix-turn helix
       0.09   12.7   0.0        2.5    8.1   0.0    2.1  2  RseC_MucC        Positive regulator of sigma(E), RseC/MucC
       0.12   12.4   0.0        0.2   11.7   0.0    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   5.4e-06     0.012      23      51 ..      19      47 ..      16      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.4e-06
                            HTH_10 23 rvtlkeLAkelGIskstlsehLrkaeskl 51
                                      r++ k++A  +GIs++++s+ L ka +k+
  gi|330506627|ref|YP_004383055.1| 19 RMSNKAIAVSFGISRQAVSKALLKADEKV 47
                                      677899********************997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.5e-05     0.033      16      38 ..      18      40 ..      15      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                            HTH_24 16 prisqreLAerlglSpstvnrrl 38
                                      +r+s++ +A   g+S+++v++ l
  gi|330506627|ref|YP_004383055.1| 18 ARMSNKAIAVSFGISRQAVSKAL 40
                                      8******************9976 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 ?   12.6   0.1   4.1e-05     0.092      15      35 ..      17      37 ..      15      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                     HTH_AsnC-type 15 daRisyaeLAervGlSestvl 35
                                       aR+s++++A   G+S+++v 
  gi|330506627|ref|YP_004383055.1| 17 RARMSNKAIAVSFGISRQAVS 37
                                      69*****************97 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 ?   11.3   0.0   0.00014      0.32       3      39 ..       9      55 ..       8      64 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                          SAM_DrpA  3 nFelykLKkAGLtNlnilnil.........dYqeknek.sLsLrdma 39
                                      +Fe +kL++A ++N+ i             +  +  ek ++ Lrdma
  gi|330506627|ref|YP_004383055.1|  9 QFEFWKLRRARMSNKAIAVSFgisrqavskALLKADEKvEIALRDMA 55
                                      7***************9765544455444433333332356666665 PP

>> NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   6.1e-05      0.14      11      35 ..      98     124 ..      96     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.1e-05
                   NADH-G_4Fe-4S_3  11 nHpldCltCdknGnC..eLQdlayelg 35 
                                       +H+ dC +Cd   +C   L d+a elg
  gi|330506627|ref|YP_004383055.1|  98 EHDGDCGSCDEYAKCieLLWDYAGELG 124
                                       7***********999433566666666 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   0.1     6e-05      0.13       8      48 ..      15      56 ..      13      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6e-05
                            HTH_29  8 laeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rr 48
                                      l+++ ++ + iA   g+sr+ v ++l   +e+ + al+d   
  gi|330506627|ref|YP_004383055.1| 15 LRRARMSNKAIAVSFGISRQAVSKALLKADEKVEIALRDmAT 56
                                      55555569************************9999988665 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 ?    2.9   0.0     0.045     1e+02      44      81 ..      37      74 ..      19      83 .. 0.84
   2 ?    8.1   0.0    0.0011       2.5       7      29 ..      91     114 ..      84     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.045
                         RseC_MucC 44 neigakvGdkVevgieeksllkaallvYllPllllilg 81
                                      +++ +k+++kVe+++++ +  + ++++ + P l+++lg
  gi|330506627|ref|YP_004383055.1| 37 SKALLKADEKVEIALRDMATANRIAIMKINPKLGVLLG 74
                                      455678999*********99999999999999998887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0011
                         RseC_MucC   7 gtaeVeierksaCgsCaakssC.k 29 
                                       + ++V +e+   CgsC++ ++C +
  gi|330506627|ref|YP_004383055.1|  91 HGLQVWYEHDGDCGSCDEYAKCiE 114
                                       5678999999************51 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 ?   11.7   0.0   8.8e-05       0.2      19      42 ..      17      40 ..       2      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.8e-05
                                      EEEHHHHHHHHHTTSSHHHHHHHH CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsril 42
                                      + +++++ +A   G++r+ vs++l
  gi|330506627|ref|YP_004383055.1| 17 RARMSNKAIAVSFGISRQAVSKAL 40
                                      468*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1041.08
//
Query:       gi|330506628|ref|YP_004383056.1|  [L=260]
Description: hypothetical protein MCON_0378 [Methanosaeta concilii GP6]
Scores for complete 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   16.4   0.1     0.0087   15.8   0.1    1.4  1  DUF1673   Protein of unknown function (DUF1673)
  ------ inclusion threshold ------
       0.15   10.9   0.1       0.21   10.5   0.1    1.2  1  STT3      Oligosaccharyl transferase STT3 subunit


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 !   15.8   0.1   9.7e-07    0.0087       2      19 ..       3      20 ..       2      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.7e-07
                           DUF1673  2 fietIrKlmGWCPnakal 19
                                      ++e I  +mGWCP ++  
  gi|330506628|ref|YP_004383056.1|  3 VSEIIEHWMGWCPKKQRA 20
                                      7899*********99865 PP

>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   2.4e-05      0.21     443     486 ..      76     121 ..      22     122 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.4e-05
                                       HHCT.TTTTHHH.TTHHHCHHHHHHHHHHHH.HHHHHHHHHHHHHC CS
                              STT3 443 tksnglkeslew.kantnrdsvvitwwdygh.ilaveadrpVtfdg 486
                                         + ++ e+ +w  +nt++d+ v  wwdy   i+ v+++  V++++
  gi|330506628|ref|YP_004383056.1|  76 LRDSKAVEGYQWmANNTESDATVLAWWDYADgITGVAHRQAVIAEA 121
                                       44667789*********************85255677777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1891.70
//
Query:       gi|330506629|ref|YP_004383057.1|  [L=71]
Description: heavy metal-associated domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-17   61.9   0.0    6.5e-17   61.7   0.0    1.1  1  HMA       Heavy-metal-associated 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 !   61.7   0.0   3.6e-21   6.5e-17       2      62 .]       9      69 ..       8      69 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 3.6e-21
                               HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                      +++sgm C+gC+a+ve++L +l+gV+s+ vdl+ kt+ Ve+d ++++  ++++a+e+agyk
  gi|330506629|ref|YP_004383057.1|  9 LKISGMACGGCSAAVERALFGLDGVSSARVDLGQKTAYVEYDSAKLSEQDFRRAVEAAGYK 69
                                      689******************************************99999**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 575.57
//
Query:       gi|330506630|ref|YP_004383058.1|  [L=53]
Description: hypothetical protein MCON_0380 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-06   28.0   0.0      2e-06   28.0   0.0    1.0  1  Flavin_Reduct  Flavin reductase like domain


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.1e-10     2e-06      98     138 ..       3      43 ..       1      48 [. 0.92

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.1e-10
                                       CCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTT CS
                     Flavin_Reduct  98 tgapallgalasleCqvvgsvelgdhelfigeVvavkvgdd 138
                                       + ap ++g+la+ eC++ +++   +  l+ig+Vv+ + +d+
  gi|330506630|ref|YP_004383058.1|   3 VRAPGVEGCLAWAECTLEEEIAGEKFVLVIGKVVHLEADDK 43 
                                       679*********************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 421.58
//
Query:       gi|330506631|ref|YP_004383059.1|  [L=45]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       159  (0.00886831); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); 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: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 337.23
//
Query:       gi|330506632|ref|YP_004383060.1|  [L=439]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-25   88.2   0.1    5.9e-25   87.4   0.1    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family
    3.8e-21   75.6   0.0    7.3e-21   74.7   0.0    1.5  1  DEDD_Tnp_IS110  Transposase
  ------ inclusion threshold ------
      0.036   14.4   1.0      0.088   13.1   0.1    2.1  2  Init_tRNA_PT    Rit1 DUSP-like domain


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.1   9.8e-29   5.9e-25       2      83 ..     271     352 ..     270     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 9.8e-29
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaaira 78 
                                       +++ s+pG+G++ aa+++ae+gd r f+sa+++a+y+G++p+++qS++k r g+i+k G++++Rr+L+e A a++r+
  gi|330506632|ref|YP_004383060.1| 271 KIILSVPGVGFISAATIIAEMGDYRDFPSADKMAKYFGIVPSVYQSAGKLRTGKITKTGSKHMRRILVEVAKAISRT 347
                                       6899***********************************************************************99 PP

                    Transposase_20  79 npelr 83 
                                       ++ +r
  gi|330506632|ref|YP_004383060.1| 348 KKNSR 352
                                       75554 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.0   1.2e-24   7.3e-21       1     153 [.      31     174 ..      31     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 1.2e-24
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G D++kd   a++i+++g +l +er++++++gl a+ ++   ++++ + +ve+tg ++++++++ le +++ ++ n
  gi|330506632|ref|YP_004383060.1|  31 CGADIHKDFLIATMISRSGLKL-QERFNMNQDGLLAFRSW-IINHRCQRLAVESTGGFWYPIFTI-LEGHVEFILAN 104
                                       79*************9999885.668**************.889****************88876.7899******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdqv 153
                                       ++++++++     ++KtD++D++ IA + +  + ++p++  +++y++Lr++tr+re+lv+ r++ kn++++ L   
  gi|330506632|ref|YP_004383060.1| 105 AYQIRNIE-----HKKTDKLDSERIAIYCL-NNLITPSRIYPKDYRDLRSITRARETLVNARSKIKNQIHQSLSTC 174
                                       *****995.....89***************.****************************************99765 PP

>> Init_tRNA_PT  Rit1 DUSP-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.3   7.5e+03      26      43 ..     155     174 ..     141     184 .. 0.47
   2 ?   13.1   0.1   1.5e-05     0.088      10      80 ..     326     400 ..     318     411 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                      Init_tRNA_PT  26 dfvrkrlsedkk..kkilva 43 
                                       + v++r++ +++  +++  +
  gi|330506632|ref|YP_004383060.1| 155 TLVNARSKIKNQihQSLSTC 174
                                       33333333322222333333 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.5e-05
                      Init_tRNA_PT  10 gKkgsknLrtalpkivdfvrkrlsedkk....kkilvacetGkdlsvgvaLailcklfddakls...eeqsesnitK 79 
                                        K+gsk++r +l ++ ++++++ ++++     ++il+ c + +   v++a  +lc ++   +l    e+ +e+++tK
  gi|330506632|ref|YP_004383060.1| 326 TKTGSKHMRRILVEVAKAISRTKKNSRLmrffQRILARCGKKNIATVALARKVLCIIY---HLLmnhENYQEPEVTK 399
                                       49*****************99966655599**99******999999999888888888...2222235666777777 PP

                      Init_tRNA_PT  80 d 80 
                                       +
  gi|330506632|ref|YP_004383060.1| 400 T 400
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.23s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3173.31
//
Query:       gi|330506633|ref|YP_004383061.1|  [L=365]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete 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   75.9   0.1    4.3e-21   74.6   0.1    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.3e-21   75.4   0.0    8.8e-21   74.4   0.0    1.4  1  OrfB_IS605      Probable transposase
    4.4e-09   35.7   0.8    1.2e-08   34.3   0.8    1.7  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.3   0.2      0.025   14.6   0.2    1.3  1  DZR             Double zinc ribbon
      0.045   12.6   0.1      0.067   12.0   0.1    1.2  1  Pestivirus_E2   Pestivirus envelope glycoprotein E2
      0.069   12.7   0.6       0.45   10.1   0.1    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
        0.1   12.8   0.4       0.23   11.6   0.4    1.5  1  FYVE            FYVE zinc finger
        0.8    9.3   3.9        2.5    7.7   2.0    2.6  2  RecR            RecR protein


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 !   74.6   0.1   1.9e-24   4.3e-21       1      68 [.     282     349 ..     282     350 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.9e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++ l +  +yka  +G  v++v+p++TSk Cs+Cg   +++ls+r+++C+ Cg+++drD+nAaiNil+
  gi|330506633|ref|YP_004383061.1| 282 WNMLVTLTSYKAASAGSVVVLVDPRNTSKMCSRCGTLIEKSLSDRVHNCTLCGLSMDRDWNAAINILR 349
                                       667777889*********************************************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   3.9e-24   8.8e-21       4     117 ..     157     268 ..     154     270 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 3.9e-24
                        OrfB_IS605   4 veveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       ve e+  lp+ k + ++giD+G++ +at ++++   ++ ++r++++++ +la+++++l++  k++  +kka + + r
  gi|330506633|ref|YP_004383061.1| 157 VETEDVpLPPWKDGAVVGIDVGLESFATFSNGE---TIANPRFFREEEHELARAQRKLSKAPKGTPDRKKALKVVER 230
                                       5544334999999********************...***************************************** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       +h++++++r +++h ++++l+++   ++ e+Ln+++m+
  gi|330506633|ref|YP_004383061.1| 231 VHERIANKRYEFAHRVSHNLVDRFGLIAFEDLNIKGMV 268
                                       *************************************7 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.8   5.2e-12   1.2e-08      15      47 .]       3      35 ..       2      35 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 5.2e-12
                    HTH_OrfB_IS605 15 eQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                       Q +k++rt++ +R+ YN+ La+rk+a+e+egk
  gi|330506633|ref|YP_004383061.1|  3 SQITKMERTLDLCRWTYNQTLAYRKNAWENEGK 35
                                      7*****************************998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   1.1e-05     0.025      10      44 ..     307     343 ..     303     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + +++Cs+Cgt +++  +   ++C  Cg ++d +++ 
  gi|330506633|ref|YP_004383061.1| 307 NTSKMCSRCGTLIEKSLSdrVHNCTLCGLSMDRDWNA 343
                                       6789********99777799************99986 PP

>> Pestivirus_E2  Pestivirus envelope glycoprotein E2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     3e-05     0.067     125     184 ..     274     334 ..     251     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                                       EEESS-CT--EEEEEEEE-SSS--EEEEEEE.EE-S-B---TT---EEEETTEEEEEEE-S CS
                     Pestivirus_E2 125 fqmvcpigwtgtvsctsfnmdtlattvvrty.rrskpfphrqgcitqknlgedlhncilgg 184
                                        + +  ++w   v+ ts++  +  + vv    r +  +  r g + +k l + +hnc l g
  gi|330506633|ref|YP_004383061.1| 274 AKSISDVAWNMLVTLTSYKAASAGSVVVLVDpRNTSKMCSRCGTLIEKSLSDRVHNCTLCG 334
                                       56678899***********99988888776526677899*******************988 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0002      0.45      11      31 ..     301     321 ..     297     326 .. 0.84
   2 ?    0.3   0.1      0.23   5.2e+02      22      28 ..     330     336 ..     328     340 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
                                       CHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon  11 lveDpergelvCtdCGlVled 31 
                                       +++Dp ++   C++CG+++e 
  gi|330506633|ref|YP_004383061.1| 301 VLVDPRNTSKMCSRCGTLIEK 321
                                       68999*9999*********96 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.23
                                       ESSSSBE CS
                      TF_Zn_Ribbon  22 CtdCGlV 28 
                                       Ct CGl 
  gi|330506633|ref|YP_004383061.1| 330 CTLCGLS 336
                                       *****85 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4    0.0001      0.23       5      33 ..     305     335 ..     302     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                       ...--SB-TTT--B-..-SSS--EE-TTT-- CS
                              FYVE   5 ddsevkkCeiCakkF..sllrrrhhCrlCGk 33 
                                       + +++k C+ C +    sl+ r h C lCG 
  gi|330506633|ref|YP_004383061.1| 305 PRNTSKMCSRCGTLIekSLSDRVHNCTLCGL 335
                                       567899*******9976789**********5 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.2     5e+03       6      16 ..      61      71 ..      61      72 .. 0.87
   2 ?    7.7   2.0    0.0011       2.5      13      34 ..     306     333 ..     301     340 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.2
                                      HHHHHHHHHH- CS
                              RecR  6 aeaLqeakekv 16
                                      a++Lq++ e+v
  gi|330506633|ref|YP_004383061.1| 61 AQTLQNVQERV 71
                                      7899**99987 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0011
                                       HHH-EE-TTT--EESSS......S-CCC CS
                              RecR  13 kekvrhCsrCgnlteed......lCaIC 34 
                                       +++ + CsrCg+l e+        C+ C
  gi|330506633|ref|YP_004383061.1| 306 RNTSKMCSRCGTLIEKSlsdrvhNCTLC 333
                                       667789*******887744454458888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2593.44
//
Query:       gi|330506634|ref|YP_004383062.1|  [L=132]
Description: hypothetical protein MCON_0384 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 937.09
//
Query:       gi|330506635|ref|YP_004383063.1|  [L=131]
Description: hypothetical protein MCON_0385 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 989.70
//
Query:       gi|330506636|ref|YP_004383064.1|  [L=80]
Description: hypothetical protein MCON_0386 [Methanosaeta concilii GP6]
Scores for complete 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   37.0   0.0    2.4e-09   36.7   0.0    1.1  1  Hfq       Hfq protein
  ------ inclusion threshold ------
      0.083   12.6   0.0       0.12   12.0   0.0    1.3  1  LSM       LSM domain
       0.15   11.9   0.0       0.26   11.1   0.0    1.4  1  YabP      YabP family


Domain annotation for each model (and alignments):
>> Hfq  Hfq protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   4.1e-13   2.4e-09      15      59 ..      24      69 ..      17      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 4.1e-13
                                      EEEEEETTS-E.EEEEEEEE-SSEEEEEETTEEEEEEGGGEEEEEE CS
                               Hfq 15 pvtifLvnGik.lkGviksfDnftvlLesdgkqqlvYKhaistivp 59
                                      +v i L++G + + G+i+sf ++ +lL++ +   lv+Khai+ti  
  gi|330506636|ref|YP_004383064.1| 24 RVLIRLTSGGQpVTGTIESFNSYEILLQTAKGELLVFKHAIATIEV 69
                                      6889999987769**************9999999**********75 PP

>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.1e-05      0.12       2      30 ..      16      45 ..      15      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                                      HHHHTTTSEEEEEETTS.EEEEEEEEEEET CS
                               LSM  2 flkklinkkvtvelkng.relrGtLkgfDq 30
                                      f+ kl++k+v+++l++g + + Gt+++f  
  gi|330506636|ref|YP_004383064.1| 16 FIPKLKGKRVLIRLTSGgQPVTGTIESFNS 45
                                      7789***********96599*******976 PP

>> YabP  YabP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.3e-05      0.26      19      38 ..      40      59 ..      36      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.3e-05
                              YabP 19 vlsfdeeeirletkkgkltI 38
                                      ++sf++ ei+l+t kg+l +
  gi|330506636|ref|YP_004383064.1| 40 IESFNSYEILLQTAKGELLV 59
                                      99***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 615.56
//
Query:       gi|330506637|ref|YP_004383065.1|  [L=448]
Description: Na+/solute symporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-33  114.2  35.6    7.7e-31  107.3  35.6    2.9  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.3  35.6   4.3e-35   7.7e-31       1     405 [.      20     405 ..      20     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 4.3e-35
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlrnagalTlpdylsk 77 
                                       + lag++ + ++l  +  a+ ++a+  +G+aG+++  Gl ++++ l  ++++lll +llae+ r +g  Tlp+++  
  gi|330506637|ref|YP_004383065.1|  20 FHLAGKNQGTIALTGTFCATIMGASTTIGMAGLGYSRGLPGSWWLLSGTIGMLLLSVLLAEKIRATGCSTLPQLVGS 96 
                                       789***********************************************************************999 PP

                               SSF  78 RfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlm 154
                                        ++++   +  +++ + +  +  ++v++++ + ++  ++G +++  +++  ++ +lYt+ GG ++v+ td+ q +++
  gi|330506637|ref|YP_004383065.1|  97 FWGERA--RAAASILIAISWIGVIAVQIIASGNILLAVFGGDISHYMVACTMVFVLYTAYGGKVSVIRTDMFQILII 171
                                       888888..555555555666789****************************************************** PP

                               SSF 155 lvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvagl..philvRflaak 229
                                       ++g + l   +l+++G l  +     + a           +    +  +++s+   lv G a l  p +   +++  
  gi|330506637|ref|YP_004383065.1| 172 IFGMIALFWQALKAAGPLPLIQLSFPTSAE----------M----NCWEVISM--ILVVGSAYLigPDMYSHIFSSR 232
                                       *************99987665444333222..........2....22333333..3334443333366666678888 PP

                               SSF 230 dakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaim 306
                                       ++k + ++ +++ ++li + +++ s+++f+  l             ++++a+p L+  ll + + Gl+ a+ lAa m
  gi|330506637|ref|YP_004383065.1| 233 SSKGAKASAFISAVLLIPLAFLITSLGIFSRYLYPT---------ITPEQAIPSLMAGLLSPAIVGLVAAALLAAFM 300
                                       889999999998888888888877788777766544.........4689**************************** PP

                               SSF 307 stltslllsassaftkDlYkkirrkasak......ekelvgvsriivlvvislaillavqeeqkgvlklvelafagl 377
                                       s+ ++ l+ a s++t D+Y ++ r+  ++      + ++++vsri+v+ +++ a++lav +++   +k   +a  ++
  gi|330506637|ref|YP_004383065.1| 301 SSADTCLMTATSILTFDIYGEVYRRVRSNadpnaiQDHMMKVSRIAVVAIGASALILAVSNPDI--IKTLLIAYTVF 375
                                       *******************9998876443222233778999***********999999988875..99999****** PP

                               SSF 378 asavlavillalfwkrv..neqGAlaglii 405
                                       +s  l  +l + + +r+  + +GAl+++  
  gi|330506637|ref|YP_004383065.1| 376 TSGLLMPVLAGFYKDRLglTCNGALSAIAG 405
                                       ****************644899***98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3070.93
//
Query:       gi|330506638|ref|YP_004383066.1|  [L=136]
Description: hypothetical protein MCON_0388 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1065.05
//
Query:       gi|330506639|ref|YP_004383067.1|  [L=193]
Description: hypothetical protein MCON_0389 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.13   12.2   2.4          5    7.2   0.1    2.3  2  OppC_N           N-terminal TM domain of oligopeptide transpo
        2.4    8.6   4.8        1.3    9.5   0.2    2.1  2  FeoB_associated  FeoB-associated Cys-rich membrane protein


Domain annotation for each model (and alignments):
>> 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 ?    4.9   0.2    0.0028        25      19      36 ..      14      31 ..      12      48 .. 0.83
   2 ?    7.2   0.1   0.00056         5      15      36 ..     159     180 ..     158     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0028
                            OppC_N 19 glvilllllliaifaPli 36
                                      gl++l++++ +a+f  ++
  gi|330506639|ref|YP_004383067.1| 14 GLALLIVIAGFAAFTWYL 31
                                      899999999999997555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00056
                            OppC_N  15 lAvvglvilllllliaifaPli 36 
                                       + +v++ ++l+ llia++  + 
  gi|330506639|ref|YP_004383067.1| 159 MIMVSMTLILVSLLIAAIITYT 180
                                       67*********88888776665 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.7     0.094   8.5e+02       7      18 ..      16      27 ..      15      33 .. 0.60
   2 ?    9.5   0.2   0.00015       1.3       3      23 ..     167     187 ..     165     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.094
                   FeoB_associated  7 liiaaavafvir 18
                                      ++++++++f+ +
  gi|330506639|ref|YP_004383067.1| 16 ALLIVIAGFAAF 27
                                      456666666643 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00015
                   FeoB_associated   3 iIVgliiaaavafvirrlikk 23 
                                       i+V l+iaa++ +  ++ +kk
  gi|330506639|ref|YP_004383067.1| 167 ILVSLLIAAIITYTTYKGRKK 187
                                       899**************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1342.11
//
Query:       gi|330506640|ref|YP_004383068.1|  [L=103]
Description: hypothetical protein MCON_0390 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00018   21.7   0.0    0.00023   21.3   0.0    1.3  1  DUF3303   Protein of unknown function (DUF3303)
  ------ inclusion threshold ------
      0.019   15.4   0.0      0.024   15.1   0.0    1.2  1  Mvb12     ESCRT-I subunit Mvb12


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 !   21.3   0.0   2.6e-08   0.00023      17      89 ..      22      89 ..       3      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.6e-08
                           DUF3303 17 aykaferflesGaledkpegfellgrvhapgegrgfaiveaddakalfkhfapWralfGiefeitPvltdeev 89
                                       +k+   +le  ++  +  + +++ +    +  +g++ive++ +++lf ++++W     i+f+ +Pvl++++v
  gi|330506640|ref|YP_004383068.1| 22 MAKLQLSLLEVARA--NLKSGKMIDWGSYCDASGGYCIVETN-ESELFDQILKWYPY--ISFDAKPVLSVDQV 89
                                      45566667777777..8888999*****************96.678***********..**********9987 PP

>> Mvb12  ESCRT-I subunit Mvb12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.7e-06     0.024      10      76 ..      11      82 ..       4      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-06
                                      SSTTS--..----------------HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHH...HHHHHS--XXX CS
                             Mvb12 10 lgedfPk..eklsklevpelkleelqptkemlepwykecdelvealekhdksgeeFdk...WYkekyLskkP 76
                                       ++ +P    +++kl++  l++++++ ++  +  w + cd    ++  + +++e Fd+   WY    +  kP
  gi|330506640|ref|YP_004383068.1| 11 NESLMPAdpAMMAKLQLSLLEVARANLKSGKMIDWGSYCDASGGYCIVETNESELFDQilkWYPYISFDAKP 82
                                      455677655699**************9999999************************655599766666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 768.33
//
Query:       gi|330506641|ref|YP_004383069.1|  [L=188]
Description: flavoredoxin [Methanosaeta concilii GP6]
Scores for complete 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-28   97.9   0.0    6.6e-28   97.7   0.0    1.0  1  Flavin_Reduct  Flavin reductase like domain


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.0   3.7e-32   6.6e-28       4     148 ..      12     166 ..       9     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 3.7e-32
                                       S-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...S CS
                     Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgp 80 
                                       ++ pv+vv t ++ ++p+ +t+ +   ++ +Pp++a+slr++ +t+ ++ e + f+++l se+  + ad f+ +sg 
  gi|330506641|ref|YP_004383069.1|  12 YPAPVCVVGTYDHAGKPNVMTAAWAGICCSSPPCIAVSLRKATYTYGNILERKAFTVSLPSEEYIHQADYFGMASG- 87 
                                       799*************************************************************************. PP

                                       CCCCCCCCCCCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTECTT..........BEEC CS
                     Flavin_Reduct  81 rtddksifagltwees.ptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddadee..........pLly 146
                                       r++dk+  + lt+ ++  + ap++++ + +leC +++sv++g h+ fige+++vk +++  ++          pLl+
  gi|330506641|ref|YP_004383069.1|  88 RDEDKFARTRLTPVKGeLVDAPFVKEFPLALECSLHSSVQIGLHTEFIGEILDVKAEESCVGPdglpdiekirPLLF 164
                                       *****8888999999888999*********************************99987333345666666666666 PP

                                       CC CS
                     Flavin_Reduct 147 wr 148
                                         
  gi|330506641|ref|YP_004383069.1| 165 SP 166
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1479.15
//
Query:       gi|330506642|ref|YP_004383070.1|  [L=169]
Description: NADH dehydrogenase/NAD(P)H nitroreductase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-30  104.5   0.3    1.9e-16   60.6   0.1    2.1  2  Nitroreductase  Nitroreductase family
    5.8e-16   58.7   0.1    3.3e-06   26.8   0.0    3.1  3  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.19   11.6   0.0    1.4  1  DUF1601         Protein of unknown function (DUF1601)


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 !   60.6   0.1   3.2e-20   1.9e-16       1      53 [.       7      59 ..       7      67 .. 0.94
   2 !   42.5   0.0   1.1e-14   6.8e-11      88     170 .]      70     148 ..      64     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 3.2e-20
                                      HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHH CS
                    Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelrykl 53
                                      i++RrSiRkF+++ +p+e  +++leaa+ aPsagn qpw+fv+++d+++++++
  gi|330506642|ref|YP_004383070.1|  7 IKTRRSIRKFKPQDIPREIYRELLEAAMLAPSAGNEQPWQFVAIDDRRILDQI 59
                                      899*****************************************999988876 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 1.1e-14
                                       HHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHH..HHHHHHT-S..SEE CS
                    Nitroreductase  88 agapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaae..evrkllglpdeeei 162
                                       +++p+ i++        + + er  ++ ++d++aa++n+lLaA+alGlg+++ g + ++++   +r+l+ lpde  +
  gi|330506642|ref|YP_004383070.1|  70 RQSPLAILV------CGDSRYERYPDFWVQDCSAAVENILLAAHALGLGAVWAGVYPMKDRieGFRRLFALPDEITP 140
                                       566666666......333344555566689***************************9998889*********9*** PP

                                       EEEEEEE- CS
                    Nitroreductase 163 vvliavGy 170
                                       ++lia+Gy
  gi|330506642|ref|YP_004383070.1| 141 FALIALGY 148
                                       *******9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   4.6e-06     0.028       2      28 ..       3      29 ..       2      30 .. 0.90
   2 !   26.8   0.0   5.6e-10   3.3e-06     159     189 ..      25      55 ..      22      78 .. 0.84
   3 !   17.1   0.0   5.2e-07    0.0031      88     149 ..      99     165 ..      94     169 .] 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-06
                                      HHHHHHH--B---B--S---HHHHHHH CS
                    TM1586_NiRdase  2 lyeaiekRhsvRkYkdealeeelleel 28
                                       +eai++R+s+Rk+k + ++ e+  el
  gi|330506642|ref|YP_004383070.1|  3 ALEAIKTRRSIRKFKPQDIPREIYREL 29
                                      579*****************9998776 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 5.6e-10
                                       HHHHHHHHHHTS--GGG----EEE.E-SSEE CS
                    TM1586_NiRdase 159 wfkeileaarlAPsAlNqqpwrfelkdddei 189
                                        ++e+leaa+lAPsA N+qpw+f   dd +i
  gi|330506642|ref|YP_004383070.1|  25 IYRELLEAAMLAPSAGNEQPWQFVAIDDRRI 55 
                                       57899*******************8888766 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 5.2e-07
                                       HHHHHHHHHHTT-EEEEES--SST................T-S-EEEEE-BS----.-----HHHHB CS
                    TM1586_NiRdase  88 geqlvLkltalGlgtcWvggtykk.....kkakvelkkgeklvivIalGyaktklveakrkpleelc 149
                                        e+++L + alGlg  W g    k      +  + l+++ + +++IalGy+++k  + kr + e + 
  gi|330506642|ref|YP_004383070.1|  99 VENILLAAHALGLGAVWAGVYPMKdriegFRRLFALPDEITPFALIALGYPNEKPAPSKRYKEERVH 165
                                       699****************98888444332234789999999*************999998877765 PP

>> DUF1601  Protein of unknown function (DUF1601)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.1e-05      0.19      18      33 ..       4      21 ..       3      22 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.1e-05
                           DUF1601 18 lvaIr..rnaerFNsQeI 33
                                      l+aI+  r+++ F++Q+I
  gi|330506642|ref|YP_004383070.1|  4 LEAIKtrRSIRKFKPQDI 21
                                      7899999**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1382.47
//
Query:       gi|330506643|ref|YP_004383071.1|  [L=533]
Description: methyl coenzyme M reductase system, component A2 [Methanosaeta concilii GP6]
Scores for complete 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-51  172.5   0.1    3.2e-27   95.7   0.0    2.5  2  ABC_tran     ABC transporter
    3.6e-05   23.3   5.9      0.098   12.1   0.1    3.5  3  SMC_N        RecF/RecN/SMC N terminal domain
    0.00029   20.8   0.9       0.79    9.6   0.1    2.6  2  RsgA_GTPase  RsgA GTPase
    0.00062   19.5   3.8       0.25   11.1   0.0    2.7  2  AAA_29       P-loop containing region of AAA domain
     0.0051   17.0   0.0          9    6.6   0.0    3.4  2  SbcCD_C      Putative exonuclease SbcCD, C subunit
     0.0064   16.3   3.6         14    5.4   0.0    3.9  4  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
  ------ inclusion threshold ------
      0.013   14.7   3.1        2.3    7.3   0.6    2.5  2  NB-ARC       NB-ARC domain
      0.016   15.6   1.0        1.3    9.4   0.3    2.8  2  AAA_16       AAA ATPase domain
      0.019   14.8   0.8        2.2    8.2   0.5    2.5  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.023   13.4   0.1        4.8    5.7   0.0    2.9  3  AAA_13       AAA domain
      0.026   14.2   1.4        6.6    6.4   0.0    2.7  2  AAA_30       AAA domain
       0.03   14.4   3.3       0.11   12.6   0.1    2.5  2  DUF87        Helicase HerA, central domain
      0.049   14.2   1.0        7.4    7.1   0.2    2.9  2  AAA_18       AAA domain
      0.089   12.4   0.2         17    5.0   0.0    2.4  2  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
      0.095   13.0   2.0         15    5.8   0.0    3.0  2  AAA_22       AAA domain
        0.2   11.8   3.1        3.6    7.7   0.0    3.4  5  MMR_HSR1     50S ribosome-binding GTPase
       0.21   12.1   0.1         13    6.2   0.1    2.3  2  AAA_23       AAA domain
       0.41   10.3   2.0         20    4.8   0.0    2.3  2  PRK          Phosphoribulokinase / Uridine kinase family


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   1.3e-23   1.3e-20       1     136 [.      20     199 ..      20     200 .. 0.74
   2 !   95.7   0.0   3.2e-30   3.2e-27       2     136 ..     304     458 ..     303     459 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1.3e-23
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEE................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx................................. RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGei................................. 42 
                                       l+nv+l ++ege v+i+G++G+GKS L+ +l g ++    +G++                                 
  gi|330506643|ref|YP_004383071.1|  20 LRNVNLVIEEGESVGILGRSGSGKSVLMHVLRGVESFqdISGSViyhvarcskchhveppshvgrsckcgstlepfd 96 
                                       78******************************998764589***888888888888888888888888888777777 PP

                                       .EETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH..........HHHTC...HHHHHHHSTTGGTTCBGEST CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx..........xxxxx...xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  43 .lldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren..........esdee...iekalsklglkelkdtvvks 104
                                         + + d+++  ++ + k+i+++ q    l  + +v  n          +       ++++l++++l++   +v+  
  gi|330506643|ref|YP_004383071.1|  97 aDFVSLDINDPLRRDVVKRIAIMLQRtFALYGDERVIVNvmraveetgdT--MSvhvAADLLDEVNLSHRLMHVA-- 169
                                       64444445555555666666666666333333333444467766655442..22224666666777666555555.. PP

                                       TSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 105 spssLSgGqkqrvalarallkkpkllllDEpt 136
                                         ++LSgG+kqrv+lar l+k p +ll+DEpt
  gi|330506643|ref|YP_004383071.1| 170 --RELSGGEKQRVVLARQLAKSPMILLADEPT 199
                                       ..*****************************9 PP

  == domain 2  score: 95.7 bits;  conditional E-value: 3.2e-30
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG......B-HHHCCHCEEEE-SS--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx......xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke......qeleslrkeigvlpqepqlf 71 
                                       ++vsl+++ege+ ++vG +G GK+tL k+++g l+pt G+i ++ g+++ +      + + ++ k ig+l+qe +l 
  gi|330506643|ref|YP_004383071.1| 304 DEVSLEVNEGEIFGLVGISGGGKTTLSKMISGILTPTGGSISVRvGDEWVDmtvlgsNGRGRATKYIGILHQEYTLY 380
                                       79***************************************88877777777888879******************* PP

                                       TTSBHHHH............HHHTCHHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  72 peltvren............esdeeiekalsklglkelkdtvvkssp.ssLSgGqkqrvalarallkkpkllllDEp 135
                                       p  +v en             +++++ + l+++g +e +++ v +++ ++LS+G++ rva+a++l+k+p++++lDEp
  gi|330506643|ref|YP_004383071.1| 381 PSRSVIENlteaiglslpfeLAERKAIHTLETVGFSEEQAEAVLEKMpHELSEGERHRVAMAQVLIKEPRIVVLDEP 457
                                       *******************888899**********9987777766666***************************** PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                       t
  gi|330506643|ref|YP_004383071.1| 458 T 458
                                       9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.035        35      27      44 ..      33      50 ..      19      61 .. 0.82
   2 !   12.1   0.1   9.8e-05     0.098     123     205 ..     152     238 ..     103     252 .. 0.72
   3 !    8.6   0.4    0.0011       1.1     135     206 ..     418     499 ..     262     509 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.035
                                      EEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnlldAi 44
                                        i+G+ GSGKs l+  +
  gi|330506643|ref|YP_004383071.1| 33 VGILGRSGSGKSVLMHVL 50
                                      5699********998765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 9.8e-05
                                       HHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SE CS
                                       xxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                             SMC_N 123 vsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQ 191
                                        ++ll ++++s        +LSgGek+ v l    A q +k   + l De    LD +  + v + +k++ ++  + 
  gi|330506643|ref|YP_004383071.1| 152 AADLLDEVNLSHRlmhvarELSGGEKQRVVL----ARQLAKSPMILLADEPTGTLDPATARVVHDSIKRAVNDfkMT 224
                                       44444444444444444448******96655....5555555556677********************998874467 PP

                                       EEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxx RF
                             SMC_N 192 fivislreemleka 205
                                       +i++s+ e+++ + 
  gi|330506643|ref|YP_004383071.1| 225 LIITSHWEDVMVEL 238
                                       89999988766544 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0011
                                       T...........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SS CS
                                       x...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                             SMC_N 135 e...........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislr 198
                                       e           +LS Ge+  va+a ++    +k   +++lDe    +D+    +v + + +++++    fi++s++
  gi|330506643|ref|YP_004383071.1| 418 EqaeavlekmphELSEGERHRVAMAQVL----IKEPRIVVLDEPTGTMDAITKIEVTNSILNAREElgETFIIVSHD 490
                                       3666666666669*******99999885....566679************99999999999888885678******* PP

                                       HHHCCC-.S CS
                                       xxxxxxx.x RF
                             SMC_N 199 eemleka.d 206
                                        ++++++ d
  gi|330506643|ref|YP_004383071.1| 491 MDFVKNVcD 499
                                       999998644 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0012       1.2      92     122 ..      22      53 ..       5      69 .. 0.77
   2 !    9.6   0.1   0.00079      0.79      80     131 ..     293     345 ..     265     351 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                                       HHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       +++ ++++ + + ++G SG GKS L+ +l++ 
  gi|330506643|ref|YP_004383071.1|  22 NVNLVIEEgESVGILGRSGSGKSVLMHVLRGV 53 
                                       55556666577889***************985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00079
                                       EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       + ++    ++++e++ ++++ ++  lvG SG GK+tL +++ + l+   g++s
  gi|330506643|ref|YP_004383071.1| 293 ISIDRGVVKAVDEVSLEVNEgEIFGLVGISGGGKTTLSKMISGILTPTGGSIS 345
                                       444444457788888888777999**************999887666666666 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   0.00025      0.25      19      39 ..      27      47 ..      19      52 .. 0.79
   2 !    8.6   0.4    0.0015       1.5      13      49 ..     304     340 ..     297     345 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                            AAA_29 19 idlkgatlltGpsGsGKSTll 39
                                      i++ +++ + G+sGsGKS l+
  gi|330506643|ref|YP_004383071.1| 27 IEEGESVGILGRSGSGKSVLM 47
                                      454447889*********997 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0015
                            AAA_29  13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49 
                                       d+ ++e+++ +++ l+G sG GK+Tl   i+ +L+p+
  gi|330506643|ref|YP_004383071.1| 304 DEVSLEVNEGEIFGLVGISGGGKTTLSKMISGILTPT 340
                                       55677788666999************99899999886 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.015        15      23      42 ..     162     181 ..     145     216 .. 0.70
   2 !    6.6   0.0    0.0091         9      56      78 ..     447     463 ..     403     473 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.015
                           SbcCD_C  23 ekelsrssgtlSGGekqfla 42 
                                       + +l + +++lSGGekq ++
  gi|330506643|ref|YP_004383071.1| 162 SHRLMHVARELSGGEKQRVV 181
                                       5568889999******8765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0091
                           SbcCD_C  56 saegrepalrlvfLDEAFsklDe 78 
                                       +       +r+v+LDE  +++D+
  gi|330506643|ref|YP_004383071.1| 447 K------EPRIVVLDEPTGTMDA 463
                                       3......59*************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 ?    5.4   0.0     0.014        14       3      24 ..      34      55 ..      32      67 .. 0.81
   2 ?    0.7   0.0      0.37   3.6e+02     249     297 ..     181     230 ..     164     234 .. 0.76
   3 ?    5.4   0.4     0.014        14       1      48 [.     315     356 ..     315     398 .. 0.74
   4 ?    2.0   0.0      0.15   1.5e+02     235     268 ..     429     459 ..     424     494 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.014
                            AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                      ++ G+ gsGKS L+  l+++ +
  gi|330506643|ref|YP_004383071.1| 34 GILGRSGSGKSVLMHVLRGVES 55
                                      799***********99998854 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.37
                            AAA_21 249 tallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTH 297
                                       ++  +++k++ +ll DEp   L+P+  r + + +k++ +  +  +i+t+H
  gi|330506643|ref|YP_004383071.1| 181 VLARQLAKSPMILLADEPTGTLDPATARVVHDSIKRAVNdFKMTLIITSH 230
                                       444455555577777*********777777799988888899999***99 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.014
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsl 48 
                                       + +l+G  g GK++L + ++++       ++++ + s ++g  +++  
  gi|330506643|ref|YP_004383071.1| 315 IFGLVGISGGGKTTLSKMISGIL------TPTGGSISVRVGDEWVDMT 356
                                       5789***************8885......5666666666665555544 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.15
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEn 268
                                       +elS+G ++  a++  l+  +   +++++DEp  
  gi|330506643|ref|YP_004383071.1| 429 HELSEGERHRVAMAQVLIKEP---RIVVLDEPTG 459
                                       789*****9999999999988...********75 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0029       2.9      22      38 ..      32      48 ..      22      63 .. 0.84
   2 ?    7.3   0.6    0.0023       2.3      13      40 ..     308     333 ..     297     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0029
                                      EEEEEESTTSSHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlak 38
                                       v++ G+ G+GK++l++
  gi|330506643|ref|YP_004383071.1| 32 SVGILGRSGSGKSVLMH 48
                                      589************96 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0023
                                       HCTTTSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC  13 lekdelqslvvalvGmgGvGKttlakqi 40 
                                       le +e +  + +lvG  G GKttl+k i
  gi|330506643|ref|YP_004383071.1| 308 LEVNEGE--IFGLVGISGGGKTTLSKMI 333
                                       4456666..99*************9987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.3    0.0013       1.3      23      63 ..      29      73 ..      13     225 .. 0.81
   2 ?    4.1   0.0     0.056        56      24      52 ..     313     341 ..     301     456 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                            AAA_16 23 rpelvllsGesGvGKsslvrellr.....alekdggiflrgkcdql 63
                                      ++e+v + G sG+GKs l+  l+       ++++ +i+  ++c ++
  gi|330506643|ref|YP_004383071.1| 29 EGESVGILGRSGSGKSVLMHVLRGvesfqDISGS-VIYHVARCSKC 73
                                      458999************9766533222233333.55566666665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.056
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdg 52 
                                       +e+  l+G sG GK++l +++   l+ +g
  gi|330506643|ref|YP_004383071.1| 313 GEIFGLVGISGGGKTTLSKMISGILTPTG 341
                                       3778899**********999988777774 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 ?    4.3   0.0     0.036        36       2      35 ..      33      66 ..      32      80 .. 0.79
   2 ?    8.2   0.5    0.0022       2.2       1      31 [.     315     345 ..     315     349 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.036
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKh 35
                                      +gi g+sgsGK  L++ l  + + ++++ ++i h
  gi|330506643|ref|YP_004383071.1| 33 VGILGRSGSGKSVLMHVLRGVESFQDISGSVIYH 66
                                      789************9887766666666666666 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0022
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvg 31 
                                       ++g+vg sg GKTtL + +  +l+  g +++
  gi|330506643|ref|YP_004383071.1| 315 IFGLVGISGGGKTTLSKMISGILTPTGGSIS 345
                                       689************9999889988887776 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.25   2.5e+02      21      41 ..      35      55 ..      34     102 .. 0.88
   2 ?    3.2   0.1     0.027        27      23      39 ..     320     336 ..     315     357 .. 0.86
   3 ?    5.7   0.0    0.0048       4.8     498     580 ..     429     500 ..     420     523 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.25
                            AAA_13 21 iYGwNGaGKTtLSrllrslel 41
                                      i G+ G+GK+ L  +lr +e+
  gi|330506643|ref|YP_004383071.1| 35 ILGRSGSGKSVLMHVLRGVES 55
                                      67999************9975 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.027
                            AAA_13  23 GwNGaGKTtLSrllrsl 39 
                                       G  G GKTtLS++++ +
  gi|330506643|ref|YP_004383071.1| 320 GISGGGKTTLSKMISGI 336
                                       7789**********975 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0048
                            AAA_13 498 etLSeGEktaIaflYFlkslkeddseigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleff 574
                                       ++LSeGE+  +a+          +  i++ +ivv+D P   +D+     v + i +    ++  + ++i  H ++f 
  gi|330506643|ref|YP_004383071.1| 429 HELSEGERHRVAMA---------QVLIKEPRIVVLDEPTGTMDAITKIEVTNSILNAR--EELGETFIIVSHDMDFV 494
                                       78999999888874.........2336699**************99999999998885..78899999********* PP

                            AAA_13 575 kevkkn 580
                                       k+v ++
  gi|330506643|ref|YP_004383071.1| 495 KNVCDR 500
                                       *98665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0067       6.6      16      41 ..      29      53 ..      21      72 .. 0.76
   2 ?    5.3   1.1     0.015        15      19      49 ..     314     344 ..     301     476 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0067
                            AAA_30 16 sgdrvavltGpAGtGKttalkalrea 41
                                      +g   + + G+ G+GK+ ++ +lr +
  gi|330506643|ref|YP_004383071.1| 29 EG-ESVGILGRSGSGKSVLMHVLRGV 53
                                      44.367789************99755 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrv 49 
                                        +  l+G  G GKtt+ k +  +++  gg++
  gi|330506643|ref|YP_004383071.1| 314 EIFGLVGISGGGKTTLSKMISGILTPTGGSI 344
                                       47789***************99999987443 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00011      0.11      24      43 ..      31      50 ..      12      53 .. 0.85
   2 ?    1.4   0.7      0.29   2.8e+02      26      43 ..     316     333 ..     298     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                             DUF87 24 rHlAilgsTGsGKSntvavL 43
                                      ++++ilg++GsGKS ++ vL
  gi|330506643|ref|YP_004383071.1| 31 ESVGILGRSGSGKSVLMHVL 50
                                      679**************998 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.29
                             DUF87  26 lAilgsTGsGKSntvavL 43 
                                       ++ +g +G GK+++ + +
  gi|330506643|ref|YP_004383071.1| 316 FGLVGISGGGKTTLSKMI 333
                                       899*********998876 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     0.047        47       1      25 [.      33      61 ..      33      76 .. 0.71
   2 ?    7.1   0.2    0.0074       7.4       3      20 ..     318     335 ..     317     390 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.047
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf....g 25
                                      +++ G +G+GK+ l + L+  + f    g
  gi|330506643|ref|YP_004383071.1| 33 VGILGRSGSGKSVLMHVLRGVESFqdisG 61
                                      6899***********99954434433344 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0074
                            AAA_18   3 ltGtpGvGKttlakeLsk 20 
                                       l G++G GKttl+k +s 
  gi|330506643|ref|YP_004383071.1| 318 LVGISGGGKTTLSKMISG 335
                                       89***********98865 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 ?    5.0   0.0     0.017        17      11      36 ..      27      52 ..      22      77 .. 0.81
   2 ?    4.7   0.0     0.021        21      11      50 ..     310     349 ..     299     455 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
                                      EBTT-EEEEEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 11 ivqGqrtlipgafgvGktvisqslsk 36
                                      i +G+ ++i+g +g Gk+v+++ l  
  gi|330506643|ref|YP_004383071.1| 27 IEEGESVGILGRSGSGKSVLMHVLRG 52
                                      6689****************987755 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.021
                                       EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  11 ivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiG 50 
                                       + +G+  +++g +g Gkt++s+++s   + +  +i v +G
  gi|330506643|ref|YP_004383071.1| 310 VNEGEIFGLVGISGGGKTTLSKMISGILTPTGGSISVRVG 349
                                       567888999***************9887655444444433 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.016        15      10      26 ..      35      51 ..      27      86 .. 0.71
   2 ?    5.0   0.6     0.027        27      10      29 ..     318     337 ..     310     457 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.016
                            AAA_22 10 vtGesGtGKTtllrrll 26
                                      + G sG+GK++l+  l+
  gi|330506643|ref|YP_004383071.1| 35 ILGRSGSGKSVLMHVLR 51
                                      78*********997665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.027
                            AAA_22  10 vtGesGtGKTtllrrlleql 29 
                                       ++G sG GKTtl +++   l
  gi|330506643|ref|YP_004383071.1| 318 LVGISGGGKTTLSKMISGIL 337
                                       89**********99987666 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0036       3.6       2      21 ..      33      52 ..      32      78 .. 0.86
   2 ?   -3.3   0.0       9.7   9.6e+03      65      88 ..     119     142 ..      98     169 .. 0.68
   3 ?   -1.1   0.0         2     2e+03      18      45 ..     185     213 ..     180     300 .. 0.72
   4 ?    2.2   0.2      0.18   1.8e+02       3      21 ..     317     335 ..     315     356 .. 0.83
   5 ?   -2.4   0.0       4.8   4.8e+03      45      45 ..     448     448 ..     395     500 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0036
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      v+i+Gr+ +GKS L+  l g
  gi|330506643|ref|YP_004383071.1| 33 VGILGRSGSGKSVLMHVLRG 52
                                      89*************99866 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.7
                                       HHHHHHHHHHCTSEEEEEEETTTT CS
                          MMR_HSR1  65 glgkaflaleeadlillvvdasee 88 
                                       +l+++f+   +  +i+ v++a ee
  gi|330506643|ref|YP_004383071.1| 119 MLQRTFALYGDERVIVNVMRAVEE 142
                                       566666666666777777776633 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2
                                       HHHTS.TEEESSSTTSSSSEEEEEEEETT CS
                          MMR_HSR1  18 altge.kaivsdkpgtTrdinegrvklkg 45 
                                       +l ++     +d+p  T+d+ ++rv ++ 
  gi|330506643|ref|YP_004383071.1| 185 QLAKSpMILLADEPTGTLDPATARVVHDS 213
                                       55566334557888888888888876332 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.18
                                       EEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltg 21 
                                       ++vG +  GK+tL + ++g
  gi|330506643|ref|YP_004383071.1| 317 GLVGISGGGKTTLSKMISG 335
                                       89***********998876 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 4.8
                                       T CS
                          MMR_HSR1  45 g 45 
                                       +
  gi|330506643|ref|YP_004383071.1| 448 E 448
                                       2 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.088        88      22      39 ..      33      50 ..       4      53 .. 0.79
   2 ?    6.2   0.1     0.013        13      19      45 ..     313     339 ..     300     385 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.088
                            AAA_23 22 tlItGpNGaGKTTildAi 39
                                      + I G  G+GK+ ++  +
  gi|330506643|ref|YP_004383071.1| 33 VGILGRSGSGKSVLMHVL 50
                                      679*********998655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.013
                            AAA_23  19 kgltlItGpNGaGKTTildAiklaLyg 45 
                                         ++ ++G  G GKTT+   i  +L+ 
  gi|330506643|ref|YP_004383071.1| 313 GEIFGLVGISGGGKTTLSKMISGILTP 339
                                       46999************9999998874 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0      0.02        20       2      24 ..      33      55 ..      32      85 .. 0.71
   2 ?    4.6   0.5     0.024        23       1      24 [.     315     338 ..     315     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.02
                               PRK  2 IgvagsSGaGkttvarklekifg 24
                                      +g+ g SG+Gk+ +++ l+ +  
  gi|330506643|ref|YP_004383071.1| 33 VGILGRSGSGKSVLMHVLRGVES 55
                                      699**********9998875543 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.024
                               PRK   1 vIgvagsSGaGkttvarklekifg 24 
                                       + g+ g SG Gktt+++ +  i+ 
  gi|330506643|ref|YP_004383071.1| 315 IFGLVGISGGGKTTLSKMISGILT 338
                                       56999*************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 3341.19
//
Query:       gi|330506644|ref|YP_004383072.1|  [L=507]
Description: putative methanogenesis marker protein 3 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0062   16.6   0.0      0.016   15.3   0.0    1.6  1  Inhibitor_I78  Peptidase inhibitor I78 family
  ------ inclusion threshold ------
      0.064   13.1   0.0       0.16   11.8   0.0    1.7  1  PASTA          PASTA domain
      0.079   13.0   0.1       0.67   10.0   0.0    2.3  2  Fer2_4         2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Inhibitor_I78  Peptidase inhibitor I78 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.6e-06     0.016      20      50 ..     290     318 ..     282     322 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-06
                     Inhibitor_I78  20 advlkrsnsdsvRvlkPGqvvtleynpaRln 50 
                                       a+v    + d v++ kPGq++t++  p R+ 
  gi|330506644|ref|YP_004383072.1| 290 ARV--IKGMDMVKLAKPGQMITFDVTPERIM 318
                                       334..568899******************85 PP

>> PASTA  PASTA domain
   #    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       6      59 ..     319     369 ..     318     370 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                                       TTTSBHHHHHHHHHHTT--CCCEEEECTCCGTTBEEEECS-TTSEECTTS-EEE CS
                             PASTA   6 vtGmsvdeAkatLkalGlkiktveetsddvpeGtVisQsPeaGtevskgskvtl 59 
                                       + G+ +++A+++ ++ G+   ++ +   + ++  V++Q P a  e++k +kv +
  gi|330506644|ref|YP_004383072.1| 319 LLGKFLEDARQEMEQRGIEAEVEGY---EGEDAVVVKQEPGATMEILKAKKVRI 369
                                       57999*************4444443...455555************99999976 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00011      0.67       6      31 ..       3      28 ..       1      51 [. 0.85
   2 ?   -0.3   0.0      0.19   1.1e+03      68      79 ..     191     202 ..     176     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
                            Fer2_4  6 ltfDGkevtvpeGdtvasAllangvd 31
                                      + +DGke++  +G  +a+Al+++g +
  gi|330506644|ref|YP_004383072.1|  3 VLVDGKEIELAAGACLADALQKAGSN 28
                                      679********************954 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.19
                            Fer2_4  68 stpvedGlkvet 79 
                                       + pve+G+++ t
  gi|330506644|ref|YP_004383072.1| 191 TLPVEEGMEIYT 202
                                       679******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 3959.22
//
Query:       gi|330506645|ref|YP_004383073.1|  [L=137]
Description: putative methanogenesis marker protein 6 [Methanosaeta concilii GP6]
Scores for complete sequence (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  140.7   0.0    1.4e-41  140.4   0.0    1.1  1  DUF2102      Uncharacterized protein conserved in archaea (DU
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.15   11.9   0.0    1.2  1  Sigma54_CBD  Sigma-54 factor, core binding domain


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 !  140.4   0.0   1.6e-45   1.4e-41       1     102 [.       6     108 ..       6     109 .. 0.98

  Alignments for each domain:
  == domain 1  score: 140.4 bits;  conditional E-value: 1.6e-45
                           DUF2102   1 lvvieseaevtpselvrkvyeleedvtiketCfGllvegeeeevekvveevrkldpnkifvkeRgfppgderrCRak 77 
                                       +++++se++++ps++++k+y +  d+ +ketCfG++++geee +ek++ee+r+ldp+ ifvk+Rgfppgd+rrCR++
  gi|330506645|ref|YP_004383073.1|   6 YLIMSSESNILPSDIAMKIYGSGYDILVKETCFGVIIHGEEEIIEKLLEEIRSLDPAGIFVKDRGFPPGDPRRCRGR 82 
                                       6899************************************************************************* PP

                           DUF2102  78 r.ggaRpGfhqlekEvelleliskaL 102
                                       r ggaRpGf+++e+E +ll++is+aL
  gi|330506645|ref|YP_004383073.1|  83 RgGGARPGFYMIESESKLLPMISRAL 108
                                       *99**********************9 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 ?   11.9   0.0   1.7e-05      0.15      57      81 ..      40      68 ..      10      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.7e-05
                       Sigma54_CBD 57 l....eeeeveavlkliqsldPaGvgArd 81
                                      +    eee +e++l+ i+sldPaG++ +d
  gi|330506645|ref|YP_004383073.1| 40 ViihgEEEIIEKLLEEIRSLDPAGIFVKD 68
                                      1566688999***************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 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:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1110.26
//
Query:       gi|330506646|ref|YP_004383074.1|  [L=145]
Description: putative methanogenesis marker protein 5 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-61  204.0   0.0    1.1e-60  203.9   0.0    1.0  1  DUF2112   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2112  Uncharacterized protein conserved in archaea (DUF2112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.9   0.0   5.9e-65   1.1e-60       1     143 []       2     144 ..       2     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 203.9 bits;  conditional E-value: 5.9e-65
                           DUF2112   1 mkvaviPdnsliladlverfgheplslakeikekvktaeldspplniteedpkkGlkyaavevPsGvrGRlsligpl 77 
                                       +kv+v+P++s+il+dlv+r+gh++l++ + +++  ++++l sppln+t+e+pkkGl+yaav+vPsG+rGR++ligp+
  gi|330506646|ref|YP_004383074.1|   2 AKVIVYPPTSMILSDLVDRMGHKALVVPEVVRKLATDNNLASPPLNVTSEEPKKGLRYAAVDVPSGIRGRMALIGPI 78 
                                       59*************************************************************************** PP

                           DUF2112  78 ieeaeaaiiveeadilfgcvGCartnelvkalirkkdiPileleyPkseeeaielvkkineFLksl 143
                                       ieeaeaaiiv+++ +l gc+GC+rtnelv+ lir+k++Pil+l+yP+++ ea+++v+ki++FL +l
  gi|330506646|ref|YP_004383074.1|  79 IEEAEAAIIVQDPGWLTGCAGCNRTNELVRLLIRTKGVPILDLSYPTNDAEARDFVQKIKNFLGDL 144
                                       ***************************************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1066.94
//
Query:       gi|330506647|ref|YP_004383075.1|  [L=408]
Description: putative methanogenesis marker protein 15 [Methanosaeta concilii GP6]
Scores for 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-63  215.4   4.4    1.4e-63  214.9   4.4    1.2  1  BcrAD_BadFG    BadF/BadG/BcrA/BcrD ATPase family
    2.2e-05   24.8   0.1     0.0002   21.8   0.1    2.4  1  FtsA           Cell division protein FtsA
     0.0012   18.7   0.0       0.63    9.7   0.0    2.5  2  Peptidase_M22  Glycoprotease family
     0.0079   15.9   0.1      0.019   14.7   0.1    1.6  1  FGGY_C         FGGY family of carbohydrate kinases, C-termina
  ------ inclusion threshold ------
      0.041   13.6   0.3        3.6    7.3   0.0    2.4  2  MafB19-deam    MafB19-like deaminase
      0.047   13.4   0.1        0.1   12.3   0.1    1.6  2  HGD-D          2-hydroxyglutaryl-CoA dehydratase, D-component
      0.058   13.0   0.2       0.87    9.1   0.2    2.3  1  FGGY_N         FGGY family of carbohydrate kinases, N-termina
       0.12   12.4   0.2        2.5    8.2   0.1    2.5  2  UPF0004        Uncharacterized protein family UPF0004
       0.94    9.2   6.4       0.19   11.5   1.0    2.4  3  Hydant_A_N     Hydantoinase/oxoprolinase N-terminal region


Domain annotation for each model (and alignments):
>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.9   4.4   6.9e-67   1.4e-63       2     266 ..     149     401 ..     148     402 .. 0.97

  Alignments for each domain:
  == domain 1  score: 214.9 bits;  conditional E-value: 6.9e-67
                                       EEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCTC CS
                       BcrAD_BadFG   2 GiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratlp 78 
                                       GiD+GsTttk v+m++++ + + ++ +++ l+s++         +a++eal++ag +++di+ +  ++tgyGr  ++
  gi|330506647|ref|YP_004383075.1| 149 GIDSGSTTTKSVVMRDNKVIGTGWVPTTEVLKSAE---------DAFQEALKAAGVNKEDIQAV--GVTGYGRFLVG 214
                                       9****************999999988888888665.........******************66..*********** PP

                                       TTBSEEE-..HHHHHHHHHHHH-TT--...EEEEEETTEEEEEEEETTEEEEEEEESS--TTSHHHHHHHHHHHT-- CS
                       BcrAD_BadFG  79 ekfekeiirseilvhgdGavalypgtr...tvldigGqdskgiqidkgkvenfqmndrcaageGrylgiiadelnmg 152
                                       ++++++ i++ei+v+++Gav+l++++r   tv+digG+d+k+i +++g++  f+m++ ca+ +Gr+l+++a++l++ 
  gi|330506647|ref|YP_004383075.1| 215 KHINAKLIQEEITVNSKGAVFLADAQRgpaTVIDIGGMDNKAISVQDGIPGGFTMGGICAGASGRFLELAARRLGVD 291
                                       ***************************************************************************** PP

                                       TTTHHHHHTT--.S-------SHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG CS
                       BcrAD_BadFG 153 lreldglaekat.kkarinstcavfaeaelrdalsggekaedIlaglhraialrvialisrsggvtdevtltGGvak 228
                                       + el+ la k++ +k ++ns+c vf  + l++ ls g k ed+   +++++a++v +++ ++ +v++ v+++GG++ 
  gi|330506647|ref|YP_004383075.1| 292 ITELGKLALKGDyRKVAMNSYCIVFGTQSLVNSLSMGNKPEDVAMAACHSVAEQVYEQQLQEVEVKEPVIMVGGTSL 368
                                       ************7779************************************************************* PP

                                       -HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHHHH CS
                       BcrAD_BadFG 229 neaavkelrklvkenygevkininpdsiytgalGAalf 266
                                        e++ k++     e+ ++vk+ ++p+++y ga+GAal+
  gi|330506647|ref|YP_004383075.1| 369 IEGLPKAM-----EELLQVKVTVPPYAQYIGAVGAALL 401
                                       ********.....9999*******************97 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   9.8e-08    0.0002       1     102 [.     148     393 ..     148     394 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9.8e-08
                                       EEEEE-SSSEEEEEEETTEEEEEEEES--HHHHHHHHHHHHT--HHHHHHHHHH........H--S--EEEEEHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxx RF
                              FtsA   1 alvDiGagktdvavaedgalvhlrvigvggngitkdiakalrtaveeAerikik........yGsalaekeigrkel 69 
                                       a++D G+++t+ +v++d++++ +  +  +   + k+++ a+++a+++A   k +        yG  l  k+i+ k +
  gi|330506647|ref|YP_004383075.1| 148 AGIDSGSTTTKSVVMRDNKVIGTGWV--PTTEVLKSAEDAFQEALKAAGVNKEDiqavgvtgYGRFLVGKHINAKLI 222
                                       79***************766666665..667899999********99999995222222222444444555555555 PP

                                       H............................................................................ CS
                                       x............................................................................ RF
                              FtsA  70 s............................................................................ 70 
                                       +                                                                            
  gi|330506647|ref|YP_004383075.1| 223 Qeeitvnskgavfladaqrgpatvidiggmdnkaisvqdgipggftmggicagasgrflelaarrlgvditelgkla 299
                                       47777899999999999999999999*************************************************** PP

                                       .................................................................GGGGSTTHHHHH CS
                                       .................................................................xxxxxxxxxxxx RF
                              FtsA  71 .................................................................ggsalpnleela 82 
                                                                                                        g+s +++l +++
  gi|330506647|ref|YP_004383075.1| 300 lkgdyrkvamnsycivfgtqslvnslsmgnkpedvamaachsvaeqvyeqqlqevevkepvimvgGTSLIEGLPKAM 376
                                       ***************************************************************************** PP

                                       HHHHT-..HHHT-GGGHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              FtsA  83 eralspkleevsdpeyasal 102
                                       e+ l+    +v  p ya  +
  gi|330506647|ref|YP_004383075.1| 377 EELLQV---KVTVPPYAQYI 393
                                       ***944...46666677655 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0034       6.8      32      57 ..     181     206 ..     163     208 .. 0.88
   2 !    9.7   0.0   0.00032      0.63     157     263 ..     294     394 ..     265     400 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0034
                                       HHHHHHHHHHHHHTSTGGGEEEEEEE CS
                     Peptidase_M22  32 rllplieealaeaglsledldaIavt 57 
                                           + +eal++ag+++ed++a+ vt
  gi|330506647|ref|YP_004383075.1| 181 SAEDAFQEALKAAGVNKEDIQAVGVT 206
                                       566789*****************999 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00032
                                       HHHHHHCTC..S.......EETTEEE.CHHHHHHHHHHST.THHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEE.EE CS
                     Peptidase_M22 157 kieklakeg..kkiefprplkgldfsfsGlktavlkelek.evedlaasfqeavvdhlvekteralklpkakel.vi 229
                                       ++ kla +g  +     ++ ++  ++  G+++ v ++    + ed+a++  ++v+++   + e+ l++ ++ke  ++
  gi|330506647|ref|YP_004383075.1| 294 ELGKLALKGdyR-----KVAMNSYCIVFGTQSLVNSLSMGnKPEDVAMAACHSVAEQ---VYEQQLQEVEVKEPvIM 362
                                       455666666322.....333444456667766666665333599*****99997777...66667777888886155 PP

                                       ESGGGGXHHHHHCHCCHHHHTTSEEEXXXHH.HHS CS
                     Peptidase_M22 230 lGGvaankrLrealeeeaeelglkliiPplk.yct 263
                                       +GG +  ++L +a+e   e l++k+ +Pp + y+ 
  gi|330506647|ref|YP_004383075.1| 363 VGGTSLIEGLPKAME---ELLQVKVTVPPYAqYIG 394
                                       666666666666555...448899****9444544 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 !   14.7   0.1   9.5e-06     0.019     111     193 ..     322     401 ..     309     403 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.5e-06
                            FGGY_C 111 itglsssttlahiarAaleavalqlrailealekdsgkpldrlavdGGgskndllmqllAdilgvpVerpkt.aeat 186
                                       + +ls++++++++a+Aa+ +va q+++  ++l++      ++++++GG s  + l + + ++l+v+V +p++ + ++
  gi|330506647|ref|YP_004383075.1| 322 VNSLSMGNKPEDVAMAACHSVAEQVYE--QQLQE--VEVKEPVIMVGGTSLIEGLPKAMEELLQVKVTVPPYaQYIG 394
                                       57899*****************99986..34422..234589******************************999** PP

                            FGGY_C 187 alGaAil 193
                                       a+GaA+l
  gi|330506647|ref|YP_004383075.1| 395 AVGAALL 401
                                       *****98 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0018       3.6      57     102 ..      60     103 ..      44     131 .. 0.80
   2 ?    3.9   0.0      0.02        41       9      66 ..     141     194 ..     137     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0018
                       MafB19-deam  57 alqqAakklkskrlddatlyvtlepCdmCagaivqaglkklvygag 102
                                       a+ +A+  +++  l da+++ t   C     ai++++++k +   +
  gi|330506647|ref|YP_004383075.1|  60 AIARAVRIVENPDLADAVVVMTCFRCAEA--AIIRSEIRKYIHENS 103
                                       89999999999999999998876666555..7*******9987766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.02
                       MafB19-deam   9 kalaevekatkikedkigavivkdkkviargsnekelnakataHaEiaalqqAakklk 66 
                                       ++++ + ++++ ++ +   v++ d+kvi++g        ++++ aE +a+q A k+ +
  gi|330506647|ref|YP_004383075.1| 141 EKQKGLTAGIDSGSTTTKSVVMRDNKVIGTGWVP---TTEVLKSAE-DAFQEALKAAG 194
                                       5566677888889999999************983...335666666.56666666655 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 ?   12.3   0.1   5.2e-05       0.1     263     320 ..      72     129 ..       9     132 .. 0.84
   2 ?   -3.2   0.0       2.8   5.7e+03     160     205 ..     339     377 ..     307     396 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.2e-05
                                       TT-SEEEEEEETT-HHHHHHHHHHHHHHH.HTT--EEEEEE-S-STTHHHHHHHHHHHH CS
                             HGD-D 263 ykvdgvifqtgggCrpasgyiglirrale.kegiPvlsletDqsdiregqlktRVeafl 320
                                       + +d+v+++t   C  a + +++ir+ ++ +  iPvls ++    + ++ l tR ea++
  gi|330506647|ref|YP_004383075.1|  72 DLADAVVVMTCFRCAEAAIIRSEIRKYIHeNSKIPVLSYSFTERTT-AETLLTRMEALV 129
                                       568*************************97777*******966664.899999999987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.8
                                       -HHHHHHHHHHHHHHHHHHT.STS-EEEEEES---TT--HHHHHHH CS
                             HGD-D 160 gkeeatealeelleeleerskseriRllltGipvellaaklmkale 205
                                           a + +e+ l+e+e     +++ +++ G+ +  +   l ka+e
  gi|330506647|ref|YP_004383075.1| 339 CHSVAEQVYEQQLQEVEV----KEPVIMVGGTSLIEG---LPKAME 377
                                       333444445555555544....455555555554444...444444 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 ?    9.1   0.2   0.00044      0.87      46      83 ..     176     213 ..     146     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00044
                                       HHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS-EE CS
                            FGGY_N  46 eeiwqalaeairkvleqagisekqikaIgisgqreglv 83 
                                        e++++  +a +++l++ag+++++i+a+g++g +  lv
  gi|330506647|ref|YP_004383075.1| 176 TEVLKSAEDAFQEALKAAGVNKEDIQAVGVTGYGRFLV 213
                                       58899999***********************9987665 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0013       2.5      27      66 ..      64     102 ..      56     130 .. 0.77
   2 ?    1.3   0.0      0.17   3.5e+02      43      76 ..     174     207 ..     161     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                                       SS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTS CS
                           UPF0004  27 gyelvedeeeAdvvlvnTCavrekaekkviqalrelkalk 66 
                                        +++ve+++ Ad+v+v TC   ++a   +++++r++ +++
  gi|330506647|ref|YP_004383075.1|  64 AVRIVENPDLADAVVVMTCFRCAEA-AIIRSEIRKYIHEN 102
                                       5788999************655554.45566666665554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.17
                                       EE--SSSSHHHHTHHHHHHHHTTST.--EEEEEE CS
                           UPF0004  43 nTCavrekaekkviqalrelkalkkpekkvvvlG 76 
                                        T  v ++ae+ + +al+++  +k++ ++v+v+G
  gi|330506647|ref|YP_004383075.1| 174 PTTEVLKSAEDAFQEALKAAGVNKEDIQAVGVTG 207
                                       5778999999999999999999999999999999 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 ?   -1.4   0.1      0.83   1.7e+03      42      96 ..      90     143 ..      87     145 .. 0.66
   2 ?   11.5   1.0   9.3e-05      0.19       3      60 ..     149     203 ..     147     207 .. 0.87
   3 ?   -1.8   0.0       1.1   2.2e+03     152     172 ..     333     353 ..     315     358 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.83
                        Hydant_A_N  42 aleevleesiprtskidvvrmGTTvatNa..llerkgervaLittkgfrdlleigrq 96 
                                       ++++ +++ i+++ski v+ ++ T  t a  ll r +   aL+tt ++r ll+ ++q
  gi|330506647|ref|YP_004383075.1|  90 IIRSEIRKYIHENSKIPVLSYSFTERTTAetLLTRME---ALVTTVKYRGLLAREKQ 143
                                       5666677778888888888888887775522444443...67777777777766655 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.3e-05
                        Hydant_A_N   3 gIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvv 60 
                                       gID G+T T  v+++++ +++ +  +++t  +v +   +a++e+l++++ ++++i++v
  gi|330506647|ref|YP_004383075.1| 149 GIDSGSTTTKSVVMRDN-KVIGTGWVPTT--EVLKSAEDAFQEALKAAGVNKEDIQAV 203
                                       9**************87.***********..888888888888888888888888876 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.1
                        Hydant_A_N 152 siavvllhSylnpehElrvae 172
                                        +a +  hS++    E++ +e
  gi|330506647|ref|YP_004383075.1| 333 DVAMAACHSVAEQVYEQQLQE 353
                                       467778888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 2917.92
//
Query:       gi|330506648|ref|YP_004383076.1|  [L=190]
Description: putative methanogenesis marker protein 17 [Methanosaeta concilii GP6]
Scores for complete 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-63  211.0   0.2    9.8e-63  210.8   0.2    1.0  1  DUF2113   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2113  Uncharacterized protein conserved in archaea (DUF2113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.8   0.2   5.5e-67   9.8e-63       1     185 []       9     188 ..       9     188 .. 0.99

  Alignments for each domain:
  == domain 1  score: 210.8 bits;  conditional E-value: 5.5e-67
                           DUF2113   1 fevectdeegaeaYeeiirdilqDlnllrsierlkvyidpeeplFiiavllrktsspiklgdvaeveedkeegkvki 77 
                                       +ev++ +e+ga++Y+eii+dilqDl+l+rsi+rl+vy+d+++p+F++++llr+  +p++++dv++v++    g ++i
  gi|330506648|ref|YP_004383076.1|   9 IEVTGGEEYGAKKYREIIMDILQDLGLIRSIGRLYVYVDISVPVFAVYGLLRSGIPPLTIKDVGDVMK--VGGGYQI 83 
                                       6899****************************************************************..******* PP

                           DUF2113  78 kiedEtylpelLkkLwekygrenveqpdRfeiiiesdedleeleelvVaDpkeelkkkvidaliriaPEGfrvrkea 154
                                       ki+dE+++++lLk Lw++ygre+veqp R  +ii+sd+++   ++l+V+D+++e+ ++++dal+r++PEGfr+r+++
  gi|330506648|ref|YP_004383076.1|  84 KINDEEHMADLLKALWKRYGRERVEQPARDIVIIASDSSP---ADLMVTDMEAEFLQDLTDALVRVVPEGFRNRRNI 157
                                       ************************************9988...********************************** PP

                           DUF2113 155 lednsfvfvAseetlkeewieeakelkeelk 185
                                       ++++sf+fvA+ee +k+e+i+e++e+++e++
  gi|330506648|ref|YP_004383076.1| 158 MTKDSFFFVAAEESIKPELISEIEEKIREME 188
                                       ***************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1423.57
//
Query:       gi|330506649|ref|YP_004383077.1|  [L=307]
Description: putative methanogenesis marker protein 7 [Methanosaeta concilii GP6]
Scores for complete 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-121  401.9   0.1   1.1e-120  401.7   0.1    1.0  1  MCR_C     Methyl-coenzyme M reductase operon protein C


Domain annotation for each model (and alignments):
>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.7   0.1  6.4e-125  1.1e-120       1     271 []       2     270 ..       2     270 .. 0.99

  Alignments for each domain:
  == domain 1  score: 401.7 bits;  conditional E-value: 6.4e-125
                             MCR_C   1 lepltyeGGvykhdellelieDlGGyilqknvialevvltllvPkedvelieelakellgklteaPlagteiavvsp 77 
                                       lep++++GG+ykhd++lel+eDlGGyilqknv+++e++l llvP+ed++++e l+++l+g+l++aPlagte+avv+p
  gi|330506649|ref|YP_004383077.1|   2 LEPVMFTGGLYKHDLVLELVEDLGGYILQKNVTQTEIILLLLVPSEDMNALEILSRDLRGELVRAPLAGTEVAVVTP 78 
                                       689************************************************************************** PP

                             MCR_C  78 tLarhhlPhsaCDvaeylrraGaktnmiGlarGvgkriaqikeeekrlinehDlavfvlGnfkdCikkkkeklfedi 154
                                       tLa+hhlPh aCD+aeylrr+G+ktnmiG+arGvg++iaqi+e+e++linehD+avf++Gnf+dCikk ke l+++i
  gi|330506649|ref|YP_004383077.1|  79 TLAIHHLPHVACDIAEYLRRHGSKTNMIGMARGVGREIAQINEYETALINEHDAAVFIFGNFEDCIKK-KEDLYRNI 154
                                       *******************************************************************9.99****** PP

                             MCR_C 155 evPvvvtggPeelkleevpgaeayvgglGriahrlrkeeeiealdelveeveevldkkreelakDpllvsparvkke 231
                                        vPv++tggP +++ ee+p+a  yv ++Gr+ahr+rk++ei +ld++ve+v++ ldk+re++akDpl++sp rv+++
  gi|330506649|ref|YP_004383077.1| 155 GVPVIITGGP-KIDPEELPYAFGYVPSIGRMAHRTRKATEIGSLDNIVEMVGRALDKTREAIAKDPLTTSPPRVMDA 230
                                       **********.****************************************************************** PP

                             MCR_C 232 ieeqveeieevlsPapitlqldglrvklpydeyaekieev 271
                                       ++eqv+e+e ++sP pi+l+l g+rvklpy  y++k+++v
  gi|330506649|ref|YP_004383077.1| 231 VREQVPEVEFSYSPLPIALNLTGVRVKLPYAGYRDKVAAV 270
                                       ************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2399.93
//
Query:       gi|330506650|ref|YP_004383078.1|  [L=177]
Description: hypothetical protein MCON_0400 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      112  (0.00624686); 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):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1457.21
//
Query:       gi|330506651|ref|YP_004383079.1|  [L=246]
Description: hypothetical protein MCON_0402 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.5   0.2      0.066   13.5   0.2    1.6  1  TerB_C    TerB-C domain
       0.11   12.1   0.2       0.11   12.1   0.2    1.6  2  NRBF2     Nuclear receptor-binding factor 2, autophagy regula


Domain annotation for each model (and alignments):
>> TerB_C  TerB-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   7.4e-06     0.066      14      46 ..      94     126 ..      89     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.4e-06
                            TerB_C  14 kkkislDlsrlaairketaavselLaeifeeee 46 
                                       ++ i+l l+++++++k  + ++++L +if   e
  gi|330506651|ref|YP_004383079.1|  94 ERNIDLLLDQIERLQKKNKTIRDILLQIFNASE 126
                                       5789*************************9888 PP

>> NRBF2  Nuclear receptor-binding factor 2, autophagy regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.2e-05      0.11      69     113 ..      71     115 ..      59     125 .. 0.88
   2 ?   -2.4   0.2      0.34     3e+03      80     114 ..     178     212 ..     175     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                             NRBF2  69 kgskapkDDktkleeqatkiadLkrlvelLlaenerLrkenkqLk 113
                                       +g+k++k+D +   + +  ++  +r ++lLl++ erL+k nk ++
  gi|330506651|ref|YP_004383079.1|  71 IGAKSTKEDYVEALNEHRGLETFERNIDLLLDQIERLQKKNKTIR 115
                                       68999****9998888899***********************987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.34
                             NRBF2  80 kleeqatkiadLkrlvelLlaenerLrkenkqLka 114
                                       ++ee+    ++  r+v   +++ne++     +L  
  gi|330506651|ref|YP_004383079.1| 178 IMEEKFNVYNEYIRFVKEATEDNEQILLKLDKLLL 212
                                       56777777777778888888888876655555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1332  (0.074293); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 2095.65
//
Query:       gi|330506652|ref|YP_004383080.1|  [L=551]
Description: von Willebrand factor, type A [Methanosaeta concilii GP6]
Scores for complete sequence (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   58.0   0.0    3.1e-15   56.9   0.0    1.5  1  VWA           von Willebrand factor type A domain
    4.6e-14   52.7   0.1    6.6e-14   52.2   0.1    1.2  1  SBP_bac_11    Bacterial extracellular solute-binding protein
    9.5e-10   39.1   0.0    2.1e-09   38.0   0.0    1.6  1  VWA_2         von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.039   13.5   0.0      0.067   12.7   0.0    1.4  1  Citrate_bind  ATP citrate lyase citrate-binding
       0.13   12.6   0.0         21    5.4   0.0    2.6  2  Beta-Casp     Beta-Casp 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 !   56.9   0.0   8.5e-19   3.1e-15       3     165 ..     379     535 ..     378     548 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 8.5e-19
                                       EEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHC..HHHHHHHHHHTGSGGGGS CS
                               VWA   3 vfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndys..skeellsalnnlkysggg 77 
                                       vfv D+Sgsm++e +++ k+ + +  + +    ++  +glv++s++v++  +++++   +++ +  a+  l ++gg 
  gi|330506652|ref|YP_004383080.1| 379 VFVADVSGSMDGEPLNNLKKSLLEGQKYIG---KDNLIGLVSYSDDVYINLPISRFDlnNRSYFVGAVGGL-QAGGA 451
                                       8*******************9999888888...6666******************999899*********7.55555 PP

                                       SC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.HTHHHHHHHHGCTEEEEEEEESSSHHHHHHHHHSS CS
                               VWA  78 ttntgkalkyaleklfkssagaRenakkviilltdGksndg.dpkeaaneakeqgikvfavGvgnadekelLnkias 153
                                       t+ t ++++ a++ l ++ a   ++ k  i +l+dG++n g ++++  + + e+gi ++++G+ nad k+ L++i+ 
  gi|330506652|ref|YP_004383080.1| 452 TA-TFDGIAVAMKMLEEQLAL-DPKLKPKIFVLSDGETNRGhSLNDIRKLVEESGIPIYTIGY-NADIKA-LEEISL 524
                                       55.**********99999999.557899999*********87888888888888********8.788999.999977 PP

                                       SSCHHCEEEESS CS
                               VWA 154 epgeghvftvtd 165
                                        ++    +++++
  gi|330506652|ref|YP_004383080.1| 525 VNE-AASINADT 535
                                       776.33333333 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.1   1.8e-17   6.6e-14       5     229 ..      96     343 ..      95     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.8e-17
                                       E-SSTHHHHHHHHHHH.HHH...H-..--EEEEESSHHHHHHHHHHH...-SEEEESSH.HHHHHHHHGGGGGGG-E CS
                        SBP_bac_11   5 aagslaaalrelaaaF.eah...tg..vkvevsaggsgklarqiadga.rpDvwipassawlellaaaglvqaesav 74 
                                       a+g++  +l+e+a +F  a+    g    v++++  sg+ a+ i++g+  pD++ p ++ w e+l+++g+ +    +
  gi|330506652|ref|YP_004383080.1|  96 AGGGTDGWLTEVARDFnNAKimiDGkqTSVRLRGIASGQGADYITSGKyLPDAYTPSNELWGEMLISRGVDARLVQK 172
                                       5788899*********6666555447799*************************************9976666788* PP

                                       EEEEEEEEEEESTT-.........TT---S.HHHHHHSS--EEEE--T-TTTTH....H.HHHHGGG--........ CS
                        SBP_bac_11  75 plassplviavpkgn.........pkkikg.wadLlkpglklavadPttspsGl....aalalleaaga........ 129
                                        la++   i+  k++         + ++++ ++++++++l++++++P +s++Gl     +l++++   a        
  gi|330506652|ref|YP_004383080.1| 173 RLAGNAAGILITKSKkaeleakygAVNVTTvIDSVANNELQMGYTNPFASSTGLnfliSTLQAID---Asnplsnka 246
                                       ***********99996666655543456664888999*****************55444444444...333466667 PP

                                       HHHHHHHHHTEEEEESSHHHHHHHHHTTT-SEEEEEHHHHH..HSTTSSEEE.E--TTT--...EEEEEEEE-TT-- CS
                        SBP_bac_11 130 qellkalekkvvklgessrqlltaveageadagivyeseakaaengdkleav.ylpeglnldpldypaavlkkaakr 205
                                        + ++++++++++ + ++ q+ +a+++g  da++   +      n ++++ +  +p g+  d   y+++ l+ + k 
  gi|330506652|ref|YP_004383080.1| 247 IAGFDRFQENIPVVAYTTLQMREAAKSGVLDAFVLEYQTYV---NTPDIRSYeFIPFGVRHDSPIYAIGKLSPE-KT 319
                                       7789*****************************97777666...588888886789999865567888888866.78 PP

                                       HHHHHHHHHTTSHHHHHHHHHTT- CS
                        SBP_bac_11 206 eaAraFlafLrspeaqailrkyGf 229
                                       +  ++F++f +++  q++++kyGf
  gi|330506652|ref|YP_004383080.1| 320 KILDEFIKFSQQENYQNLATKYGF 343
                                       8**********************9 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 !   38.0   0.0   5.9e-13   2.1e-09       2     107 .]     379     486 ..     378     486 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 5.9e-13
                             VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallkslp.gdrvglvtfsdgpevliplt....kdkakilnalrnleakg 73 
                                       vfv D+SgSm ++      l  +k+ + +  k +  ++ +glv++sd++++ +p +     +++ +  a+ +l+a g
  gi|330506652|ref|YP_004383080.1| 379 VFVADVSGSMDGE-----PLNNLKKSLLEGQKYIGkDNLIGLVSYSDDVYINLPISrfdlNNRSYFVGAVGGLQA-G 449
                                       8***********9.....8*************997377****************98777899************9.6 PP

                             VWA_2  74 ggtnlaaaLqlarkalkkrr...kgekrvivlitDge 107
                                       g+t + +++  a+k+l+++     + k  i++++Dge
  gi|330506652|ref|YP_004383080.1| 450 GATATFDGIAVAMKMLEEQLaldPKLKPKIFVLSDGE 486
                                       ****************977699999999*******96 PP

>> Citrate_bind  ATP citrate lyase citrate-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.9e-05     0.067     106     171 ..     450     519 ..     401     526 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                      Citrate_bind 106 nvaatfkgiiraleelksklk...ehkvkiyvrr.ggpnyqeglkamkelgeelglpikvfgpethitai 171
                                         +atf+gi  a++ l+++l    + k ki+v   g +n  ++l+ +++l ee g+pi+  g +++i a+
  gi|330506652|ref|YP_004383080.1| 450 GATATFDGIAVAMKMLEEQLAldpKLKPKIFVLSdGETNRGHSLNDIRKLVEESGIPIYTIGYNADIKAL 519
                                       5679******9999999998733367899***8736678899******************9999988776 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.015        53      22     101 ..     306     419 ..     280     422 .. 0.69
   2 ?    5.4   0.0    0.0059        21      48     102 ..     461     514 ..     439     516 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.015
                                       -EEEEE-HHHHHHHHHGGGGGG..................................E-SHH....HHHH..HH.... CS
                         Beta-Casp  22 lpiyldsplaskatevYkeyae..................................veakslewmeskkeeln.... 60 
                                        piy  ++l+ + t++ +e+ +                                  +               +    
  gi|330506652|ref|YP_004383080.1| 306 SPIYAIGKLSPEKTKILDEFIKfsqqenyqnlatkygfngldeyrsefvpasgdvlI---------------Qaqkl 367
                                       599999999999999988886655566666666666666665555555544444433...............04444 PP

                                       .....HS-SSEEEEE.S-TTSSSSHHHHHHHHHTT.....STTSEEEESS-- CS
                         Beta-Casp  61 .....sskgpkvila.ssgmlegGrsrellkklle.....dprntvilvgyq 101
                                            + +  +v +a  sg+++g +  +l k+lle      ++n++ lv+y+
  gi|330506652|ref|YP_004383080.1| 368 wkekkNANICAVFVAdVSGSMDGEPLNNLKKSLLEgqkyiGKDNLIGLVSYS 419
                                       43332223345666645999***9*999999999977766778888888887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0059
                                       H....HHH.H..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS--- CS
                         Beta-Casp  48 slewmesk.keelnsskgpkvilassgmlegGrsrellkklledprntvilvgyqa 102
                                        ++++e++ +  l+ + +pk+ + s+g  + G s + ++kl+e++   ++ +gy a
  gi|330506652|ref|YP_004383080.1| 461 AMKMLEEQlA--LDPKLKPKIFVLSDGETNRGHSLNDIRKLVEESGIPIYTIGYNA 514
                                       4566666654..566779***********************999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.24s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3891.99
//
Query:       gi|330506653|ref|YP_004383081.1|  [L=375]
Description: Toxic anion resistance protein [Methanosaeta concilii GP6]
Scores for complete 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-78  262.8  20.2      5e-78  262.5  20.2    1.1  1  TelA           Toxic anion resistance protein (TelA)
     0.0076   16.9   1.2     0.0076   16.9   1.2    2.2  2  PMC2NT         PMC2NT (NUC016) domain
  ------ inclusion threshold ------
      0.034   14.2   0.0         12    6.1   0.1    2.7  2  IGR            IGR protein motif
       0.11   12.6  22.8       0.35   11.1   7.0    3.6  3  Fib_alpha      Fibrinogen alpha/beta chain family
       0.16   11.7   9.1       0.39   10.4   0.9    3.9  4  RPW8           Arabidopsis broad-spectrum mildew resistance p
        0.9    9.6  17.9      0.054   13.6   4.6    2.6  3  UPF0242        Uncharacterised protein family (UPF0242) N-ter
        2.2    9.2   4.6        1.4    9.8   1.4    2.3  3  Cytochrom_C_2  Cytochrome C'
        2.7    8.2  10.8       0.23   11.6   5.4    2.1  2  Med2           Mediator complex subunit 2
        3.6    8.0  13.8      0.064   13.6   2.5    3.5  4  Syntaxin_2     Syntaxin-like protein
        6.8    7.2   6.3         22    5.5   0.2    3.6  4  MtrB           Tetrahydromethanopterin S-methyltransferase su


Domain annotation for each model (and alignments):
>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.5  20.2   2.8e-81     5e-78      14     330 ..      54     365 ..      43     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 262.5 bits;  conditional E-value: 2.8e-81
                              TelA  14 nsilqfGaeaqkkiakfsdrlLe......svktkdlgevgklLseLvkelkeldpdelkeekklgllplfkkaknki 84 
                                       +s+ +fGae++k+ a+ ++++L+      s + +d g v+k L eL++el++ldp+ ++ +k  g+l+   k+ +++
  gi|330506653|ref|YP_004383081.1|  54 KSVESFGAESMKRSAA-KNSILQatvgdlSKNGDDGGVVAKGLMELTRELEDLDPSLIDFTKT-GILG---KLFDPV 125
                                       599**********999.************999************************9966655.9888...9999** PP

                              TelA  85 eklfakYekaeeqidkIvkeLekgqdellkdnaaLdqlyeknleyfkeLekyiaaGekkleeldekllpeleakaea 161
                                       +++fa+Y++a + i +I+++L+kg++ l++dn++L+ +++++++  ++L k +++G +    +de +++++e+++++
  gi|330506653|ref|YP_004383081.1| 126 RNYFARYQRADSAIADIIVSLDKGRTILKNDNTTLEIEQQSLRDLTRKLMKEVQLGAL----MDESIERQIEEARAR 198
                                       **********************************************************....*************** PP

                              TelA 162 sgdpedaqalrdleealdrleqrvqDLelaravsiQtapqirlvqknnkeLiekiqsaittTiplwknqlvvalalk 238
                                        +dpe+++ +++  e+l++l+qr++DL+++  v++Q++++ ++v +nn+eL++++++a t+Ti+++++ ++va al+
  gi|330506653|ref|YP_004383081.1| 199 DEDPEKVKFVSE--EVLFPLRQRIMDLQQMIVVNQQGVMATEVVIRNNRELMRGVERAKTVTISALRTSVMVASALY 273
                                       ************..*************************************************************** PP

                              TelA 239 rqklaleaqkavndtTnellkknAemlkqqsieiakeaergivdietLkkafetlietidevdqiqeegrekrkeae 315
                                       +qk +l++++ +n+tTn+l++++++mlk+q ++i+k++ ++ v+ e Lk+af++++e++d+++ +++e++ k++e++
  gi|330506653|ref|YP_004383081.1| 274 NQKIVLKKIQMLNETTNDLITSTSRMLKNQGADIQKQSMQTNVSAEDLKTAFADVMEALDSINSYKQEALPKMRETI 350
                                       ***************************************************************************** PP

                              TelA 316 keLeeleeelkkkLl 330
                                       ++++el ++ +++++
  gi|330506653|ref|YP_004383081.1| 351 EQFRELAAKGEEQIQ 365
                                       ********9999986 PP

>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.1   5.6e+03      33      53 ..     164     184 ..     150     210 .. 0.54
   2 !   16.9   1.2   4.2e-06    0.0076      28      79 ..     284     335 ..     275     336 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.1
                            PMC2NT  33 serllslinsllklaasksei 53 
                                       ++ l +l+ +l+k ++     
  gi|330506653|ref|YP_004383081.1| 164 QQSLRDLTRKLMKEVQLGALM 184
                                       445555555554444433333 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.2e-06
                            PMC2NT  28 sldeqserllslinsllklaaskseisassklededdveekfksvvdvvDsl 79 
                                        l+e+++ l+++++++lk+++++ ++++ +++ +++d+++ f++v++++Ds+
  gi|330506653|ref|YP_004383081.1| 284 MLNETTNDLITSTSRMLKNQGADIQKQSMQTNVSAEDLKTAFADVMEALDSI 335
                                       689***********************999*********************97 PP

>> IGR  IGR protein motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.015        26      20      52 ..      26      59 ..       9      61 .. 0.79
   2 ?    6.1   0.1    0.0066        12      19      40 ..     287     308 ..     278     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.015
                               IGR 20 swekLfelsskqlkelGi.pvrqRRYiLrwreky 52
                                      +++k+ e++ ++  +l i +  ++RYiL+ +e +
  gi|330506653|ref|YP_004383081.1| 26 QLQKVAESNVAEILTLDIdELAKKRYILKSVESF 59
                                      47888888888888888989999*******9987 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0066
                               IGR  19 eswekLfelsskqlkelGipvr 40 
                                       e+ ++L++++s+ lk+ G +++
  gi|330506653|ref|YP_004383081.1| 287 ETTNDLITSTSRMLKNQGADIQ 308
                                       55899*************9987 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 ?    4.0   0.1     0.029        51     101     130 ..      21      50 ..       5      54 .. 0.75
   2 ?    5.2   3.4     0.012        22      34     123 ..     164     253 ..     148     261 .. 0.75
   3 ?   11.1   7.0   0.00019      0.35      30     123 ..     275     369 ..     266     372 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 101 esnirvLqnvlesneqkiqkLeqdidqker 130
                                        +++ +Lq+v esn+ +i  L  d  +k+r
  gi|330506653|ref|YP_004383081.1|  21 PEEVAQLQKVAESNVAEILTLDIDELAKKR 50 
                                       26899**************99988777765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.012
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHH CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnv 110
                                       +++l++l+++l +  +    ++e +++  +  r++ +  ++ + v +++   l+++i++l++ i+ + + + +   v
  gi|330506653|ref|YP_004383081.1| 164 QQSLRDLTRKLMKEVQLGALMDESIERQIEEARARDEDPEKVKFVSEEVLFPLRQRIMDLQQMIVVNQQGVMATEVV 240
                                       3566677777766666666666666655555555555555568888899999************************* PP

                                       HHHHHHHHHHHHH CS
                         Fib_alpha 111 lesneqkiqkLeq 123
                                       +++n++ +   e 
  gi|330506653|ref|YP_004383081.1| 241 IRNNRELMRGVER 253
                                       ****999987765 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00019
                                       CCCCCHHHCCCCCCCCCCCCHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnst.keaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.sni 104
                                       +k v k+++ l+++ +++  st +  ++   +i+++  +++ s++d ++++ ++ + l+  i+ +k++   ++ ++i
  gi|330506653|ref|YP_004383081.1| 275 QKIVLKKIQMLNETTNDLITSTsRMLKNQGADIQKQSMQTNVSAEDLKTAFADVMEALD-SINSYKQEALPKMrETI 350
                                       67788999999999888655550556888889999999999999999************.9*****99999999*** PP

                                       HHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 105 rvLqnvlesneqkiqkLeq 123
                                       ++ +++  + e++iq+Le+
  gi|330506653|ref|YP_004383081.1| 351 EQFRELAAKGEEQIQQLEK 369
                                       *****************97 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2      0.03        55      39      68 ..      12      41 ..       9      58 .. 0.85
   2 ?   -1.4   0.0      0.93   1.7e+03      97     113 ..      99     115 ..      96     123 .. 0.85
   3 ?   -0.3   0.1      0.44   7.8e+02      37      69 ..     268     301 ..     244     304 .. 0.65
   4 ?   10.4   0.9   0.00022      0.39      22      81 ..     306     366 ..     292     374 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.03
                              RPW8 39 stleritPvvkeieklnkeldrpreeieeL 68
                                      + +e+++Pv +e+ +l+k+ ++  +ei  L
  gi|330506653|ref|YP_004383081.1| 12 EVIEQVKPVPEEVAQLQKVAESNVAEILTL 41
                                      789***************999888777655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.93
                              RPW8  97 kkklkeLekslrkfvqv 113
                                       +++l++L+ sl +f ++
  gi|330506653|ref|YP_004383081.1|  99 TRELEDLDPSLIDFTKT 115
                                       799********999775 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.44
                              RPW8  37 LestleritPvvkeieklnkel.drpreeieeLk 69 
                                        +s l + + v+k+i++ln+   d  ++   +Lk
  gi|330506653|ref|YP_004383081.1| 268 VASALYNQKIVLKKIQMLNETTnDLITSTSRMLK 301
                                       4555666666788888888887666666666665 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00022
                              RPW8  22 eakkksldfksilkrLestleritPvvkeieklnkel.drpreeieeLkklLekaekLVek 81 
                                       + +k+s++++ + ++L+    ++   ++ i++ ++e   ++re ie++++l  k+e+ +++
  gi|330506653|ref|YP_004383081.1| 306 DIQKQSMQTNVSAEDLKTAFADVMEALDSINSYKQEAlPKMRETIEQFRELAAKGEEQIQQ 366
                                       67899*****************************9999*****************998876 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 ?   -2.4   0.1       2.4   4.3e+03     146     146 ..      48      48 ..      10      83 .. 0.45
   2 ?    5.0   1.4     0.013        24      84     164 ..     153     234 ..     127     239 .. 0.60
   3 ?   13.6   4.6     3e-05     0.054      85     176 ..     276     368 ..     247     371 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
                           UPF0242 146 e 146
                                       +
  gi|330506653|ref|YP_004383081.1|  48 K 48 
                                       1 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.013
                           UPF0242  84 lktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae...dfeelkleleeqLaekqellqeyqet 157
                                       lk+ + +le  q+  ++L ++l +  ++       +++++ + e++ +   d e++k  +ee L   ++++ ++q++
  gi|330506653|ref|YP_004383081.1| 153 LKNDNTTLEIEQQSLRDLTRKLMKEVQL---GALMDESIERQIEEARArdeDPEKVKFVSEEVLFPLRQRIMDLQQM 226
                                       3333445555555555555444332222...22222344444443332333999999999****9999999999999 PP

                           UPF0242 158 ie.eqrsv 164
                                       i+ +q+ v
  gi|330506653|ref|YP_004383081.1| 227 IVvNQQGV 234
                                       85255555 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 3e-05
                           UPF0242  85 ktkeealeelqeeeeeLkeeldak.eeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetiee 160
                                       k+  ++++ l+e +++L    + + +++ +  +++  q ++ +e+ +  f+++  +l++   +kqe l +++etie+
  gi|330506653|ref|YP_004383081.1| 276 KIVLKKIQMLNETTNDLITSTSRMlKNQGADIQKQSMQTNVSAEDLKTAFADVMEALDSINSYKQEALPKMRETIEQ 352
                                       44445666666666666666555413334445555555566666667789999999999999*************** PP

                           UPF0242 161 qrsvlekrqdqieqLe 176
                                        r+   k ++qi+qLe
  gi|330506653|ref|YP_004383081.1| 353 FRELAAKGEEQIQQLE 368
                                       ***************9 PP

>> Cytochrom_C_2  Cytochrome C'
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.5   4.5e+03      78     102 ..      15      39 ..      10      50 .. 0.69
   2 ?   -2.8   0.1       6.3   1.1e+04      51      68 ..      57      72 ..      26      83 .. 0.63
   3 ?    9.8   1.4   0.00078       1.4      17      93 ..     293     370 ..     269     374 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHHHHHHCTSHHHH CS
                     Cytochrom_C_2  78 akaaaleeaaaeLaaaakagdlaal 102
                                       ++++ + e++a+L+++a+++ ++ l
  gi|330506653|ref|YP_004383081.1|  15 EQVKPVPEEVAQLQKVAESNVAEIL 39 
                                       5666777889999999988665555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.3
                                      GGC-TTGSSSSS--B-TH CS
                     Cytochrom_C_2 51 alFpegsdkgektkakpe 68
                                      + F+++s k  +++ak++
  gi|330506653|ref|YP_004383081.1| 57 ESFGAESMK--RSAAKNS 72
                                      334444444..2444444 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00078
                                       HHHHHHHHTTSST--HHHHHHHHHHHHHHHCSGGGGC-TTGSS.....SSS--B-THHHHTHHHHHHHHHHHHHHHH CS
                     Cytochrom_C_2  17 mgklgamlkgeapydaeavaaaaealaalakklpalFpegsdk.....gektkakpeiWedkekfkakaaaleeaaa 88 
                                       + +   mlk++     + ++++  + +  a++l+++F++  ++     + k +a+p++ e  e+f++ aa+ ee+++
  gi|330506653|ref|YP_004383081.1| 293 ITSTSRMLKNQG----ADIQKQSMQTNVSAEDLKTAFADVMEAldsinSYKQEALPKMRETIEQFRELAAKGEEQIQ 365
                                       455556666666....78899999999999*******99999999999779************************** PP

                                       HHHHH CS
                     Cytochrom_C_2  89 eLaaa 93 
                                       +L++ 
  gi|330506653|ref|YP_004383081.1| 366 QLEKG 370
                                       *9875 PP

>> Med2  Mediator complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       2.6   4.6e+03      80      80 ..     182     182 ..     145     204 .. 0.52
   2 ?   11.6   5.4   0.00013      0.23       5      92 ..     284     370 ..     280     374 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.6
                              Med2  80 k 80 
                                        
  gi|330506653|ref|YP_004383081.1| 182 A 182
                                       2 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00013
                              Med2   5 kLtqclddiLkvsgemlvqeqlktiqldsnvvtGfnnqlqksLkekikkFhsiLDdleiklndaksyveqlveikke 81 
                                        L+++ +d++ + + ml ++q   iq++s  ++   ++l+   ++ +++ +si    +  l + ++ +eq+ e + +
  gi|330506653|ref|YP_004383081.1| 284 MLNETTNDLITSTSRML-KNQGADIQKQSMQTNVSAEDLKTAFADVMEALDSINSYKQEALPKMRETIEQFRELAAK 359
                                       589999****9999999.*********************************************************** PP

                              Med2  82 keeekekeeee 92 
                                        ee+ ++ e+ 
  gi|330506653|ref|YP_004383081.1| 360 GEEQIQQLEKG 370
                                       99998887765 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.8   3.3e+03      32      65 ..      14      47 ..       9      58 .. 0.59
   2 ?   -0.8   0.2       1.2   2.1e+03      20      50 ..     151     179 ..     137     197 .. 0.61
   3 ?   13.6   2.5   3.6e-05     0.064      32      89 ..     279     335 ..     255     350 .. 0.87
   4 ?   -0.4   0.1      0.84   1.5e+03      34      57 ..     345     368 ..     339     373 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.8
                        Syntaxin_2 32 reklhelieeinelikktnellkklsqldnsssd 65
                                       e+++ + ee+ +l k  ++++ ++ +ld  ++ 
  gi|330506653|ref|YP_004383081.1| 14 IEQVKPVPEEVAQLQKVAESNVAEILTLDIDELA 47
                                      4555555566666666666666666666555554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                        Syntaxin_2  20 kqLgtkkdteelreklhelieeinelikktn 50 
                                       + L++++ t e+ +  ++l++ +++l k+++
  gi|330506653|ref|YP_004383081.1| 151 TILKNDNTTLEIEQ--QSLRDLTRKLMKEVQ 179
                                       44544444333333..466666666666654 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 3.6e-05
                        Syntaxin_2  32 reklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkdfkealqeFqki 89 
                                        +k++ l e +n+li+ t++ lk+  ++++++s  q ++++e Lk+ f ++++ + +i
  gi|330506653|ref|YP_004383081.1| 279 LKKIQMLNETTNDLITSTSRMLKNQGADIQKQSM-QTNVSAEDLKTAFADVMEALDSI 335
                                       589************************9999976.9999**********999887665 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.84
                        Syntaxin_2  34 klhelieeinelikktnellkkls 57 
                                       k++e+ie+ +el+ k +e++++l+
  gi|330506653|ref|YP_004383081.1| 345 KMRETIEQFRELAAKGEEQIQQLE 368
                                       556777777777777777777776 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.013        22      24      47 ..      10      33 ..       5      45 .. 0.85
   2 ?   -3.3   0.0       6.8   1.2e+04      25      44 ..      89     108 ..      74     115 .. 0.66
   3 ?    2.2   0.1      0.13   2.4e+02      28      51 ..     272     295 ..     254     305 .. 0.80
   4 ?   -0.0   0.1      0.67   1.2e+03      24      56 ..     305     336 ..     296     354 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                              MtrB 24 edvvllsldpvleeidkLekiadd 47
                                      +d v+ +++pv ee+++L+k+a+ 
  gi|330506653|ref|YP_004383081.1| 10 KDEVIEQVKPVPEEVAQLQKVAES 33
                                      6778999**************986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.8
                              MtrB  25 dvvllsldpvleeidkLeki 44 
                                       +vv   l++++ e+++L+  
  gi|330506653|ref|YP_004383081.1|  89 GVVAKGLMELTRELEDLDPS 108
                                       47777777788888877755 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.13
                              MtrB  28 llsldpvleeidkLekiaddlvns 51 
                                       l++ + vl++i+ L+++++dl++s
  gi|330506653|ref|YP_004383081.1| 272 LYNQKIVLKKIQMLNETTNDLITS 295
                                       56778899*************987 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.67
                              MtrB  24 edvvllsldpvleeidkLekiaddlvnsLdpet 56 
                                       +d+   s++  +   ++L+++  d++++Ld  +
  gi|330506653|ref|YP_004383081.1| 305 ADIQKQSMQT-NVSAEDLKTAFADVMEALDSIN 336
                                       5555555543.3444556666666666665433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1603  (0.0894082); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 2622.53
//
Query:       gi|330506654|ref|YP_004383082.1|  [L=159]
Description: hypothetical protein MCON_0405 [Methanosaeta concilii GP6]
Scores for complete 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-52  175.9   0.0    5.9e-52  175.7   0.0    1.0  1  SPOUT_MTase      Predicted SPOUT methyltransferase
     0.0034   16.8   0.0      0.005   16.2   0.0    1.3  1  SPOUT_MTase_2    AF2226-like SPOUT RNA Methylase fused to THU
  ------ inclusion threshold ------
      0.064   13.4   0.3         11    6.3   0.0    2.3  2  CinA_KH          Damage-inducible protein CinA KH domain
       0.14   12.2   0.0       0.24   11.5   0.0    1.3  1  Leucyl-specific  Leucine-tRNA synthetase-specific domain


Domain annotation for each model (and alignments):
>> SPOUT_MTase  Predicted SPOUT methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.7   0.0   1.3e-55   5.9e-52       1     154 []       1     158 [.       1     158 [. 0.93

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 1.3e-55
                                       XEEEEEEES---H.HHHHHHHHHHHHHTTT-EEEEEEE.......---S-HHHHHHHHHHT--....T.T-EEEEE- CS
                       SPOUT_MTase   1 mkikiiavgklkekylkelieeYlkrlkkyakleiielk...kekksekeeekakekegerilkklkk.kayvilld 73 
                                       m ++iiavg+l+e+y+++++++Y++rl++ya+l+++e++   ke ++   e +a+e+eg++il+klk+ +  vi+ld
  gi|330506654|ref|YP_004383082.1|   1 MILRIIAVGRLRESYWQDAAADYIRRLRPYARLDMVEVAissKEAATPGAEIRAMEAEGAAILDKLKRhSGPVIVLD 77 
                                       6789**********************************64434444488889999********9999615679**** PP

                                       TTSEE--HHHHHHHHHHHHHHT-.-EEEEE--TT---GGGGGG-SEEEE--SS---HHHHHHHHHHHHHHHHHHHT- CS
                       SPOUT_MTase  74 erGkelsSeelakkleklaeegkselvfvIGGsdGlseevkkradeklslsklTfpHqlvrvvllEQiYRaftIlkg 150
                                        +G++l+S++la++l++l  eg+se++f+IGG+ Gls++v++rad  ls+s++TfpHql+rv+llEQiYR+f+I+++
  gi|330506654|ref|YP_004383082.1|  78 RTGDALNSQQLAERLQDLILEGRSEVAFIIGGPLGLSPAVLDRADLLLSFSPMTFPHQLMRVILLEQIYRSFRIMHH 154
                                       ***************************************************************************** PP

                                       -XXX CS
                       SPOUT_MTase 151 epYH 154
                                       epYH
  gi|330506654|ref|YP_004383082.1| 155 EPYH 158
                                       **** 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 !   16.2   0.0   1.1e-06     0.005      90     151 ..      67     130 ..      49     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-06
                     SPOUT_MTase_2  90 krrkkellivtdPeGeeis..evkeelaeal.rkakevvvlvGsReGiPkGlfrfadfvvDlaPg 151
                                       kr+   ++iv+d +G+ ++  +++e+l++ + + + ev+ ++G   G+   +++ ad+++ ++P 
  gi|330506654|ref|YP_004383082.1|  67 KRH-SGPVIVLDRTGDALNsqQLAERLQDLIlEGRSEVAFIIGGPLGLSPAVLDRADLLLSFSPM 130
                                       333.479*********985226899999987467889************************9995 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 ?    5.0   0.2    0.0059        26       9      60 ..      11      58 ..       3      69 .. 0.69
   2 ?    6.3   0.0    0.0024        11      13      32 ..      87     106 ..      83     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0059
                                      --HHHHHHHHGGGS-BSSSEEEEEEETTEEEEEEE...EEHHHHHHHHH... CS
                           CinA_KH  9 igESavaekladlidrenptlAiyakegevtvRltakaaneeeaealiapve 60
                                      + ES  +++ ad+i+    +l +ya+ + v+v ++ k a    ae ++ ++e
  gi|330506654|ref|YP_004383082.1| 11 LRESYWQDAAADYIR----RLRPYARLDMVEVAISSKEAATPGAEIRAMEAE 58
                                      677777888888887....5668************98777666665555444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0024
                                       HHHHHHGGGS-BSSSEEEEE CS
                           CinA_KH  13 avaekladlidrenptlAiy 32 
                                       ++ae+l+dli +++ ++A+ 
  gi|330506654|ref|YP_004383082.1|  87 QLAERLQDLILEGRSEVAFI 106
                                       89**************9986 PP

>> Leucyl-specific  Leucine-tRNA synthetase-specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.4e-05      0.24      22      47 ..      31      56 ..      23      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.4e-05
                   Leucyl-specific 22 irLeleeseLsleevkKmGAELRehe 47
                                      +rL++ e ++s +e++  GAE+R+ e
  gi|330506654|ref|YP_004383082.1| 31 ARLDMVEVAISSKEAATPGAEIRAME 56
                                      69*********************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1129.19
//
Query:       gi|330506655|ref|YP_004383083.1|  [L=218]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   0.1       0.05   13.7   0.1    1.5  1  DUF3568   Protein of unknown function (DUF3568)


Domain annotation for each model (and alignments):
>> DUF3568  Protein of unknown function (DUF3568)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.8e-06      0.05      13      84 ..       7      77 ..       2      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-06
                           DUF3568 13 illasCaalvagaa.agagtvayvnGelkaeyeanlkkvykAtlkaiedlnvlsvvekskdsssatieakaae 84
                                      i+l+  aal+ + a a  gt   ++G+ +  y+a+++++++ +   +  ln    ++k++ + +a+++a++ +
  gi|330506655|ref|YP_004383083.1|  7 ICLVLIAALLTSPAwASCGT-WIIRGNTEYHYDAEYENAVRSSTGHATALN-PDSKSKEDANDQADVNASQMD 77
                                      6677779*******777777.89**********************999999.99999999999****998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1611.15
//
Query:       gi|330506656|ref|YP_004383084.1|  [L=211]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1367  (0.0762452); expected 358.6 (0.02)
Passed bias filter:                      835  (0.0465726); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1472.71
//
Query:       gi|330506657|ref|YP_004383085.1|  [L=395]
Description: hypothetical protein MCON_0408 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2940.78
//
Query:       gi|330506658|ref|YP_004383086.1|  [L=480]
Description: (R)-citramalate synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-69  234.6   3.8    1.4e-69  234.6   3.8    2.1  3  HMGL-like   HMGL-like
      4e-32  110.9   2.5      4e-32  110.9   2.5    1.8  2  LeuA_dimer  LeuA allosteric (dimerisation) domain
  ------ inclusion threshold ------
       0.17   10.8   5.6      0.034   13.1   1.9    1.7  2  IMPDH       IMP dehydrogenase / GMP reductase 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 !  234.6   3.8   2.4e-73   1.4e-69      21     264 .]       2     239 ..       1     239 [. 0.98
   2 ?   -1.2   0.0       0.2   1.2e+03     117     152 ..     316     365 ..     296     375 .. 0.77
   3 ?   -3.3   0.1      0.86   5.2e+03      72      93 ..     434     452 ..     417     467 .. 0.54

  Alignments for each domain:
  == domain 1  score: 234.6 bits;  conditional E-value: 2.4e-73
                                       -HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEEE CS
                         HMGL-like  21 sveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagakrvhvfi 97 
                                        ++eklaia+ Ld +gvd+iE+g ++ se+++ ++++ia+++ ka+i+++vra   di+ a +    + +++vh+++
  gi|330506658|ref|YP_004383086.1|   2 GMDEKLAIAQGLDSLGVDVIEAGSAMTSEGERLAIKKIADSGFKAEICSYVRALTADIDTALA----CDVDSVHLVV 74 
                                       579************************************************************....********** PP

                                       ES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---H CS
                         HMGL-like  98 atselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGatriniaDtvGvltP 174
                                       ++s+lh+++klk dre v+++a++++++a+++g  vels edasr+d +fla ++ a +eaGa+r+++ DtvGvl P
  gi|330506658|ref|YP_004383086.1|  75 PVSDLHIQIKLKADRESVVRMAVDVTEYAKDHGLIVELSGEDASRADQDFLAGLYTAGIEAGADRLAFCDTVGVLVP 151
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT.-B- CS
                         HMGL-like 175 neaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelvaalealg.vdt 250
                                       ++aa+++s+l++ ++  +++s+HcHnd+G+A+ant+aA++aGa++  +tvnG+GeraGna+lee+v+ale l  +dt
  gi|330506658|ref|YP_004383086.1| 152 EVAADIFSRLSR-LE--APISIHCHNDFGMATANTVAALRAGASQAHVTVNGIGERAGNASLEEVVMALESLYqIDT 225
                                       *********975.67..8****************************************************9977*** PP

                                       ---HHHHHHHHHHH CS
                         HMGL-like 251 gldlqklrsiaalv 264
                                       g+  +++++++++v
  gi|330506658|ref|YP_004383086.1| 226 GIRCKDIYQLSRTV 239
                                       **********9987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHTT-E..............TTT-BTTTBS--HHHHHHHH CS
                         HMGL-like 117 kkaeeavkaarslgkd..............velsledasrtdleflaevv 152
                                       ++ +++v ++++lg++              ++ls++++++ +le+l+ v+
  gi|330506658|ref|YP_004383086.1| 316 QQLNQIVTRVKELGDKgkrvsdvdlqsiadTVLSIQMEPKVKLEELTVVA 365
                                       56677788888888877777777777777778888888888887777665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.86
                                       -SSHHHHHHHHH....TT-SEE CS
                         HMGL-like  72 rarekdikaavealkgagakrv 93 
                                       ++++ d k +++   gaga+++
  gi|330506658|ref|YP_004383086.1| 434 TMAMADRKITAR---GAGADII 452
                                       444444443333...3333333 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.2   7.1e+03     105     129 ..     193     217 ..     173     221 .. 0.54
   2 !  110.9   2.5   6.7e-36     4e-32       2     132 ..     335     466 ..     334     467 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.2
                                       GGEEEEEEEESSHHHHHHHHHHHHH CS
                        LeuA_dimer 105 gkkvsgvGvdsdiveASlkAlisal 129
                                       + +v+  G+ +    ASl+ ++ al
  gi|330506658|ref|YP_004383086.1| 193 QAHVTVNGIGERAGNASLEEVVMAL 217
                                       3334555555555566666665555 PP

  == domain 2  score: 110.9 bits;  conditional E-value: 6.7e-36
                                       XXXXXXXXXXXXXXXXXX.--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH..T CS
                        LeuA_dimer   2 vtdedlealvkdelleae.erlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv..d 75 
                                       v+d dl+++++++l  +   ++kle+l+v+ g++ ++ta+vk+ +  g+e+ ++++G+GpvdA++nA+r+a++   d
  gi|330506658|ref|YP_004383086.1| 335 VSDVDLQSIADTVLSIQMePKVKLEELTVVAGNTVTPTASVKILL-AGNERLEAGVGVGPVDAAINAIRRAISGvaD 410
                                       89************99877**************************.99999********************998899 PP

                                       -EEEEEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHH CS
                        LeuA_dimer  76 ikLldYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrl 132
                                       ++L++Y+v+a+t+gt+a++ev V++ + d+k ++++G+ +di++AS++A+i+++nrl
  gi|330506658|ref|YP_004383086.1| 411 VRLDEYHVDAVTGGTNALVEVWVTMAMADRK-ITARGAGADIIMASVEAVINGINRL 466
                                       9*************************77777.***********************98 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       0.4   2.4e+03     187     218 ..      15      46 ..       7      63 .. 0.62
   2 ?   13.1   1.9   5.8e-06     0.034     104     179 ..     320     394 ..     287     453 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.4
                                       SB---HHHHHHHHHHHHCTCT-EEEEES---S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 187 gvGvpqltAvaevaeaakkagvpviaDGGiky 218
                                       ++Gv  + A +++++  ++  ++ iaD G k 
  gi|330506658|ref|YP_004383086.1|  15 SLGVDVIEAGSAMTSEGERLAIKKIADSGFKA 46 
                                       55666666666666666666777777777665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.8e-06
                                       THHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 104 dalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsi 179
                                       +  +rvk+l ++g  v  vd      ++vl+   e k k+ee++v+aGn +t  +  +++ ag + +  G+G G +
  gi|330506658|ref|YP_004383086.1| 320 QIVTRVKELGDKGKRVSDVDLQ-SIADTVLSIQMEPKVKLEELTVVAGNTVTPTASVKILLAGNERLEAGVGVGPV 394
                                       5678889999999888888874.4555666666667777888*****************************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 3325.79
//
Query:       gi|330506659|ref|YP_004383087.1|  [L=599]
Description: acetolactate synthase, large subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-60  203.3   0.1    4.6e-60  202.1   0.1    1.6  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    3.9e-54  182.1   0.1    7.1e-54  181.3   0.1    1.4  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
    5.9e-50  169.0   0.0    2.1e-49  167.2   0.0    2.0  3  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
     0.0062   16.3   0.2      0.016   15.0   0.2    1.6  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 !  202.1   0.1     1e-63   4.6e-60       1     166 [.      20     183 ..      20     186 .. 0.98
   2 ?   -3.7   0.0       1.7   7.8e+03     117     145 ..     510     538 ..     505     540 .. 0.74

  Alignments for each domain:
  == domain 1  score: 202.1 bits;  conditional E-value: 1e-63
                                       EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHH CS
                      TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGat 77 
                                       mt+a+a+++ Lk++gv++vfg+pG+ +lpl+da+ +++ ir++l+rhEqgaa++Adgyaratgk+gv+++tsgpGat
  gi|330506659|ref|YP_004383087.1|  20 MTGAQAVLESLKREGVDVVFGLPGGVLLPLYDAIYKSD-IRHILVRHEQGAAHMADGYARATGKVGVCIATSGPGAT 95 
                                       89***********************************6.************************************** PP

                                       HCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--E CS
                      TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgP 154
                                       n++t++a+A+ d++P+++++g+++t l+g++++q e d++++  p+tk+++ ++s++e+p ++r+A+ +a +grpgP
  gi|330506659|ref|YP_004383087.1|  96 NLVTGIANAYMDSVPMVAITGQVNTWLIGKDAFQ-EADITGITLPITKHNYLIRSAKEIPGVFREAFYIARTGRPGP 171
                                       **********************************.****************************************** PP

                                       EEEEEEHHHCC- CS
                      TPP_enzyme_N 155 vylelpkdvlle 166
                                       v+++lp+dv  +
  gi|330506659|ref|YP_004383087.1| 172 VLIDLPRDVTVD 183
                                       ********9765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.7
                                       CHHHCCCSSEEEE-SSGGGHHHHHHHHHH CS
                      TPP_enzyme_N 117 lalfrpvtkyaervtspeelpealrrAir 145
                                       ++l++ +     r t+p+e++ ++r A++
  gi|330506659|ref|YP_004383087.1| 510 VKLAEAYGAVGLRATKPSEVEDVIRSALA 538
                                       55666666667788999999999999986 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 !  181.3   0.1   1.6e-57   7.1e-54       1     137 []     208     343 ..     208     343 .. 0.99

  Alignments for each domain:
  == domain 1  score: 181.3 bits;  conditional E-value: 1.6e-57
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealee 77 
                                       i+kaa++l +a+rpvi++Gggv+++ a++el ela+k+++Pv+ttlmg g++pedhpl+lgmlg+hg+k+an a++e
  gi|330506659|ref|YP_004383087.1| 208 IKKAAKALMEAERPVIYAGGGVRYASAHKELFELARKVNAPVTTTLMGVGCFPEDHPLSLGMLGMHGTKYANYAIQE 284
                                       79*************************************************************************** PP

                                       -SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  78 aDlvlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                       +Dl++a+Garfdd r+tg+ + fap+a+i+hid+dpae+gkn++vd+++vgd++++l+ L
  gi|330506659|ref|YP_004383087.1| 285 SDLLMAIGARFDD-RVTGKISSFAPHARIVHIDVDPAEVGKNVRVDIPVVGDARNALQGL 343
                                       *************.******************************************9976 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 ?   -4.1   0.0       2.8   1.3e+04     133     152 ..     151     175 ..     145     175 .. 0.72
   2 ?   -3.2   0.0       1.4   6.4e+03      45      77 ..     218     251 ..     206     254 .. 0.54
   3 !  167.2   0.0   4.7e-53   2.1e-49       2     152 ..     399     546 ..     398     547 .. 0.96

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHH.....CSSSEEEEE CS
                      TPP_enzyme_C 133 eeleealkeal.....ekkgpalie 152
                                       +e+  +++ea+      + gp+li+
  gi|330506659|ref|YP_004383087.1| 151 KEIPGVFREAFyiartGRPGPVLID 175
                                       6777777777777768888999987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.4
                                       TTSEEEEEEEHHHHHHTGGGHHHHHHT.T-SEEE CS
                      TPP_enzyme_C  45 pdrevvaivGDGgflmilqelatavrr.nlpitv 77 
                                        +r+v+   G   ++  + el   +r+ n+p+t+
  gi|330506659|ref|YP_004383087.1| 218 AERPVIYAGGGVRYASAHKELFELARKvNAPVTT 251
                                       3455555444444555577777777773446666 PP

  == domain 3  score: 167.2 bits;  conditional E-value: 4.7e-53
                                       SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvv 78 
                                       +G++++waa+++  k p+++++sgglgtmGyg+paAiGak+ +p+ +v+ ++GDG+flm+ qelatav +++p++v 
  gi|330506659|ref|YP_004383087.1| 399 VGQNQMWAAQFFVHKDPQRFISSGGLGTMGYGFPAAIGAKMGRPECTVIDVAGDGSFLMNSQELATAVVNDIPVKVA 475
                                       9***********999************************************************************** PP

                                       EEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  79 vlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpalie 152
                                       vlnN+++gm++++qe f++kr+s++   + +++df+klaea+Ga g+r +k+  +e+e++++ al++++p++ +
  gi|330506659|ref|YP_004383087.1| 476 VLNNGCLGMVRQWQELFFEKRYSATI-LGRTSPDFVKLAEAYGAVGLRATKP--SEVEDVIRSALATDRPCVMD 546
                                       **********************9965.579999***************7788..*****************988 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 !   15.0   0.2   3.6e-06     0.016      35      94 ..      55     116 ..      48     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-06
                                       TEE.EEEE-SSHHHHHHHHHH.HHCTT-EE.EEEEECCHHHHCCCCHHHHHHTT--EEEEEE CS
                             POR_N  35 vgdvevvqmesEigaisaviG.AaaaGara.aTaTSgqGllLmienlglaageelPvvivvv 94 
                                       + d++ + +  E ga+ ++ G A a+G  +   aTSg+G    +  +  a ++ +P+v +  
  gi|330506659|ref|YP_004383087.1|  55 KSDIRHILVRHEQGAAHMADGyARATGKVGvCIATSGPGATNLVTGIANAYMDSVPMVAITG 116
                                       45778899999**********7778898761579************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (599 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 4123.02
//
Query:       gi|330506660|ref|YP_004383088.1|  [L=163]
Description: acetolactate synthase, small subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-31  107.4   5.4    8.1e-30  102.9   4.2    2.2  2  ALS_ss_C         Small subunit of acetolactate synthase
    1.5e-16   60.0   1.8    6.9e-16   57.8   0.1    2.5  3  ACT_5            ACT domain
    6.2e-13   48.3   3.8    7.3e-12   44.8   0.2    2.5  2  ACT              ACT domain
      9e-07   29.4   0.8      9e-07   29.4   0.8    2.0  2  ACT_4            ACT domain
    1.3e-06   28.2   1.0      0.017   15.0   0.1    2.3  2  NIL              NIL domain
     0.0004   20.7   0.3       0.03   14.7   0.0    2.4  2  Saccharop_dh_N   LOR/SDH bifunctional enzyme conserved region
     0.0051   17.2   0.3        1.7    9.1   0.0    2.4  2  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
      0.015   15.2   3.4       0.16   11.8   0.6    2.0  2  SLS              Mitochondrial inner-membrane-bound regulator
      0.016   15.2   2.1        6.4    6.8   0.2    3.0  2  ACT_6            ACT domain
      0.025   14.3   1.3      0.084   12.6   0.4    1.9  2  DUF4423          Domain of unknown function (DUF4423)
       0.16   12.0   4.1        1.3    9.1   4.1    2.0  1  SBDS_C           SBDS protein C-terminal 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 ?    3.7   0.0     0.046        74      37      58 ..      46      67 ..      40      74 .. 0.82
   2 !  102.9   4.2     5e-33   8.1e-30       1      74 []      84     157 ..      84     157 .. 0.99

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.046
                                      EEEEEEE-HHHHHHHHHHS-GG CS
                          ALS_ss_C 37 liieltgteekidaliellkpf 58
                                      ++i + g+++ ++++i+ l+++
  gi|330506660|ref|YP_004383088.1| 46 MTISVQGDRDVLEQVIKQLSKL 67
                                      89*****************854 PP

  == domain 2  score: 102.9 bits;  conditional E-value: 5e-33
                                       EEEEEEEEE.-SCHHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHHHHHHHHHS-GGGEEEEEEEEEEEEEST CS
                          ALS_ss_C   1 RElaLiKVkaekeerseileiaeifrakivdvspdsliieltgteekidaliellkpfgilevvRtGrvAleRG 74 
                                       REla+iKV+++ e+rse+++i++ifraki+dvs+ s+iie+tg+eek++a+i+ll++fgi+e++RtG+v + RG
  gi|330506660|ref|YP_004383088.1|  84 RELAIIKVSVDRESRSEVMQIVNIFRAKIIDVSQRSMIIEVTGDEEKVEAIIQLLRQFGIKELARTGKVSMVRG 157
                                       9**********************************************************************998 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.1   4.3e-19   6.9e-16       2      62 .]      12      73 ..      11      73 .. 0.95
   2 ?   -1.7   0.0       1.6   2.6e+03      47      47 ..     102     102 ..      79     117 .. 0.54
   3 ?    0.9   0.1      0.25   4.1e+02      35      51 ..     119     136 ..     104     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 4.3e-19
                             ACT_5  2 apgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvelLsnQleKLidVlkV 62
                                      + gvL R+ ++++rr F+++sl++ +t++ +++r++++V++  + +e++++Ql+KLi+V++V
  gi|330506660|ref|YP_004383088.1| 12 KSGVLTRIAGLFSRRSFNIDSLSVGATDNPDYSRMTISVQGdRDVLEQVIKQLSKLINVIRV 73
                                      689**************************************77788*************998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.6
                             ACT_5  47 e 47 
                                        
  gi|330506660|ref|YP_004383088.1| 102 M 102
                                       1 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.25
                             ACT_5  35 rieltVes.ersvelLsn 51 
                                       ++ ++V++ e+ ve ++ 
  gi|330506660|ref|YP_004383088.1| 119 SMIIEVTGdEEKVEAIIQ 136
                                       577888888888888654 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.2   4.5e-15   7.3e-12       1      66 [.       3      68 ..       3      69 .. 0.97
   2 ?    4.4   0.3     0.019        31      28      64 ..     107     140 ..      99     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 4.5e-15
                                      EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66
                                      +++ v v+++ G+L r++g++++r +Nids++++ ++    +++++ + +d ++le+v+++l kl+
  gi|330506660|ref|YP_004383088.1|  3 HIIAVIVENKSGVLTRIAGLFSRRSFNIDSLSVGATDNPDYSRMTISVQGDRDVLEQVIKQLSKLI 68
                                      67889**********************************************************997 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.019
                                       EEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT  28 idsieqrssedkvagivfvvivvdeedleevlealkk 64 
                                       i ++ +  +     + +++ +++dee +e++++ l++
  gi|330506660|ref|YP_004383088.1| 107 IFRAKIIDVSQ---RSMIIEVTGDEEKVEAIIQLLRQ 140
                                       55555555555...78899**************9997 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.8   5.5e-10     9e-07       9      79 ..       5      74 ..       3      74 .. 0.87
   2 ?   -0.8   0.3       1.4   2.4e+03      22      39 ..     100     117 ..      87     141 .. 0.66

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 5.5e-10
                             ACT_4  9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisVe 79
                                      + v++e+++g+L++i+ ++s    ni s+++ ++++  + +++i+v+  d++ L++vi++L ++ +Vi+V+
  gi|330506660|ref|YP_004383088.1|  5 IAVIVENKSGVLTRIAGLFSRRSFNIDSLSVGATDNPDYSRMTISVQ-GDRDVLEQVIKQLSKLINVIRVS 74
                                      789******************************76544665555555.5999****************995 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.4
                             ACT_4  22 ditqviseekanivsvna 39 
                                       +++q+++  +a+i +v+ 
  gi|330506660|ref|YP_004383088.1| 100 EVMQIVNIFRAKIIDVSQ 117
                                       555555555555555554 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   8.1e-05      0.13      27      67 ..      27      67 ..       5      73 .. 0.83
   2 !   15.0   0.1     1e-05     0.017      28      69 ..     105     143 ..      89     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-05
                                      EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHHT CS
                               NIL 27 evnIlqGsveriqgtpfGqlvielsgsqesiaaalqylrkr 67
                                      ++nI + sv+  ++  + +++i+++g+++ ++++++ l+k 
  gi|330506660|ref|YP_004383088.1| 27 SFNIDSLSVGATDNPDYSRMTISVQGDRDVLEQVIKQLSKL 67
                                      6777777899999999*********************9987 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1e-05
                                       EEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHHTT- CS
                               NIL  28 vnIlqGsveriqgtpfGqlvielsgsqesiaaalqylrkrnv 69 
                                       vnI  +++    +  + +++ie++g++e+++a++q lr+ ++
  gi|330506660|ref|YP_004383088.1| 105 VNIFRAKII---DVSQRSMIIEVTGDEEKVEAIIQLLRQFGI 143
                                       677777776...666668********************9877 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 !   14.7   0.0   1.9e-05      0.03      29      71 ..      27      69 ..      12      85 .. 0.76
   2 ?    3.8   0.0     0.046        74      49      80 ..     122     153 ..     106     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                                      EEEEEEEEXXSSTT.SXEEEEEEEEESSHHHHHHHHHHHHHHHH CS
                    Saccharop_dh_N 29 sfevlefevGkkkk.dtSyaelevsaedeevLeeileeltelga 71
                                      sf++ +++vG++ + d S  +++v++ d++vLe+++++l++l +
  gi|330506660|ref|YP_004383088.1| 27 SFNIDSLSVGATDNpDYSRMTISVQG-DRDVLEQVIKQLSKLIN 69
                                      8*********9754367777777776.569*********99844 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.046
                                       EEEEESSHHHHHHHHHHHHHHHHHSC.CCCEEE CS
                    Saccharop_dh_N  49 levsaedeevLeeileeltelgaelv.eeedvk 80 
                                       +ev+  dee++e+i++ l ++g +   ++ +v+
  gi|330506660|ref|YP_004383088.1| 122 IEVT-GDEEKVEAIIQLLRQFGIKELaRTGKVS 153
                                       3444.467999**********998774555554 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0     0.001       1.7      29      70 ..      36      77 ..      33      87 .. 0.84
   2 !    6.0   0.0    0.0094        15      38      65 ..     119     148 ..     112     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.001
                   Acylphosphatase 29 GyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeve 70
                                      G + N +  +  i ++g+++ +e+++++l++    +rv+e++
  gi|330506660|ref|YP_004383088.1| 36 GATDNPDYSRMTISVQGDRDVLEQVIKQLSKLINVIRVSELD 77
                                      66777777899*******************988889998876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0094
                   Acylphosphatase  38 sVeivaegeeekvekfleelks.gppk.ar 65 
                                       s  i+++g+eekve++++ l++ g ++ ar
  gi|330506660|ref|YP_004383088.1| 119 SMIIEVTGDEEKVEAIIQLLRQfGIKElAR 148
                                       56699***************9975554455 PP

>> SLS  Mitochondrial inner-membrane-bound regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6   9.8e-05      0.16      60     129 ..      40     108 ..       4     112 .. 0.79
   2 ?    4.2   0.2      0.02        33      59      86 ..     113     140 ..     109     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.8e-05
                               SLS  60 elnrsenklritAtkstaeyieasineilknittetvd.lsellkl.skvdklkdl.lseelleelgrltntv 129
                                         + s+ ++++++++ + e++ +++ ++++ i++ ++d ++    + ++   + ++ +++e  +e++++ n +
  gi|330506660|ref|YP_004383088.1|  40 NPDYSRMTISVQGDRDVLEQVIKQLSKLINVIRVSELDpVE----SlERELAIIKVsVDRESRSEVMQIVNIF 108
                                       55667889******************************422....2344455566668999999999998876 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.02
                               SLS  59 ielnrsenklritAtkstaeyieasine 86 
                                       i++++ +  + +t++++++e+i + +++
  gi|330506660|ref|YP_004383088.1| 113 IDVSQRSMIIEVTGDEEKVEAIIQLLRQ 140
                                       889999999**************99987 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0051       8.3       5      65 ..       5      67 ..       4      73 .. 0.81
   2 ?    6.8   0.2    0.0039       6.4      17      63 ..      99     139 ..      94     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0051
                             ACT_6  5 itvtGpdrpGltasLtsvlae..fgvnilDieqavihgrlsLgllvsgpedalarlekaLlfl 65
                                      i v+ +++ G++ +++++ ++  f+++ l ++     +    ++ v+g+ d l+++ k+L++l
  gi|330506660|ref|YP_004383088.1|  5 IAVIVENKSGVLTRIAGLFSRrsFNIDSLSVGATDNPDYSRMTISVQGDRDVLEQVIKQLSKL 67
                                      6666778889999999998873355555888888888999999*****************986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0039
                             ACT_6  17 asLtsvlaefgvnilDieqavihgrlsLgllvsgpedalarlekaLl 63 
                                       +++++++  f+++i+D+ q       s ++ v+g+e++++++ + L+
  gi|330506660|ref|YP_004383088.1|  99 SEVMQIVNIFRAKIIDVSQR------SMIIEVTGDEEKVEAIIQLLR 139
                                       68999************996......456666666666666665555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   5.1e-05     0.084      75     152 ..      42     119 ..      35     124 .. 0.92
   2 ?    0.2   0.0      0.33   5.3e+02      51      70 ..     127     146 ..     121     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.1e-05
                           DUF4423  75 kyrqtekslttssevkseavrsyhkqmlelAiealervpkeeRdissltlaiskedyekikkeirefrkkilaiaee 151
                                        y + + s++++ +v  ++++++ k +    ++ l+ v+  eR++  + +++++e+  ++ + ++ fr ki+++++ 
  gi|330506660|ref|YP_004383088.1|  42 DYSRMTISVQGDRDVLEQVIKQLSKLINVIRVSELDPVESLERELAIIKVSVDRESRSEVMQIVNIFRAKIIDVSQR 118
                                       6888899999999************999999******************************************9986 PP

                           DUF4423 152 s 152
                                       s
  gi|330506660|ref|YP_004383088.1| 119 S 119
                                       5 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.33
                           DUF4423  51 saeevekalefLlklgllkk 70 
                                       ++e+ve+++++L + g+ + 
  gi|330506660|ref|YP_004383088.1| 127 DEEKVEAIIQLLRQFGIKEL 146
                                       57888888888888886554 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 ?    9.1   4.1   0.00077       1.3      29      89 ..      84     143 ..      44     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00077
                                       HHHHHTT----TTS-CCCCHHHHHHHHT.TTS--EE-EEEEEEEE-...CCCHHHHHHHHHH CS
                            SBDS_C  29 kalkelgtsvktnksaksQalevikaLi.qeipiqrarmrlritcptsikdkilklieqves 89 
                                       + l  ++  v++++ + s ++++++  + ++i++  + m +++t ++++ + i++l+ q   
  gi|330506660|ref|YP_004383088.1|  84 RELAIIK--VSVDRESRSEVMQIVNIFRaKIIDVSQRSMIIEVTGDEEKVEAIIQLLRQFGI 143
                                       4554455..5559999999********99*****************9999999999988744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1047  (0.058397); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1014.02
//
Query:       gi|330506661|ref|YP_004383089.1|  [L=331]
Description: ketol-acid reductoisomerase [Methanosaeta concilii GP6]
Scores for complete 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  241.0   0.2    5.9e-72  240.6   0.2    1.2  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    5.1e-62  208.4   0.6    7.2e-62  207.9   0.6    1.2  1  IlvC           Acetohydroxy acid isomeroreductase, catalytic 
    3.8e-07   29.6   0.0    6.3e-07   28.9   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    2.3e-05   24.6   0.0    5.4e-05   23.4   0.0    1.6  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    0.00068   20.2   0.1     0.0015   19.0   0.1    1.6  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.014   14.8   1.0      0.026   13.9   1.0    1.3  1  Microvir_H     Microvirus H protein (pilot protein)
      0.046   13.8   0.0      0.086   12.9   0.0    1.3  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi


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 !  240.6   0.2   2.3e-75   5.9e-72       2     165 .]      15     178 ..      14     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 240.6 bits;  conditional E-value: 2.3e-75
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevye 78 
                                       l++k+ia++G+G+qGhaq++nl+dsgl+v+ +   gs+ +k+A+++g++ ++va+a+++ad + il+PDe+q ++y+
  gi|330506661|ref|YP_004383089.1|  15 LSDKTIAIVGWGNQGHAQGENLKDSGLNVIAADIPGSRAWKRAEADGVKAMSVADAARAADYIQILLPDEYQGKIYR 91 
                                       899************************************************************************** PP

                                       HHTGGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHHH CS
                              IlvN  79 eeiepnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelalay 155
                                       +ei+pnl+eg++l f+hGfni++ +i+pp++vdvv+vAPkgpG+lvr++y+egkGvp+l+aveqd sg+ak +alay
  gi|330506661|ref|YP_004383089.1|  92 DEIAPNLEEGNVLGFSHGFNIRYFQIVPPENVDVVMVAPKGPGDLVRRTYQEGKGVPCLVAVEQDHSGEAKRKALAY 168
                                       ***************************************************************************** PP

                                       HHHTTHHHH- CS
                              IlvN 156 akgiGatraG 165
                                       akgiG+traG
  gi|330506661|ref|YP_004383089.1| 169 AKGIGGTRAG 178
                                       *********9 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.9   0.6   2.8e-65   7.2e-62       1     144 []     184     327 ..     184     327 .. 1.00

  Alignments for each domain:
  == domain 1  score: 207.9 bits;  conditional E-value: 2.8e-65
                                       HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHH CS
                              IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdl 77 
                                       F+eEtetDlfgEq+ LcGgv+e+++a+Fetlv+aGy+pe+Ayfe +helklivdliyegG+ +m++++S+taeyg++
  gi|330506661|ref|YP_004383089.1| 184 FTEETETDLFGEQVDLCGGVTEMIKAAFETLVDAGYQPEIAYFEACHELKLIVDLIYEGGFMRMWNNVSNTAEYGGM 260
                                       99*************************************************************************** PP

                                       HHHHHHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHTTSHHHHHHHHHHHTSHHHHHHHHHHHCHTT CS
                              IlvC  78 tagprviteevkeemkeileeiqsGefakevieenkagrpelkklrkeeaeheiekvgkklralmpw 144
                                       t+g+r+i+e+++eem +il+eiqsGefa+e+i+e +ag p  k+l+k e+eh+ie+vg++lra+mpw
  gi|330506661|ref|YP_004383089.1| 261 TRGHRIINEQSREEMLDILAEIQSGEFAREWILESQAGLPVKKSLEKMESEHPIEEVGAQLRAMMPW 327
                                       *****************************************************************98 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.5e-10   6.3e-07      27     101 ..       8      83 ..       3     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.5e-10
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S-- CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlpl 101
                                       ++   k ls+kt++i+G G+ G+a  + lk  g++via d   ++   ++e+ gv+ +s+ ++ + +D++ + lp 
  gi|330506661|ref|YP_004383089.1|   8 QDADLKALSDKTIAIVGWGNQGHAQGENLKDSGLNVIAADIPGSRAWkRAEADGVKAMSVADAARAADYIQILLPD 83 
                                       5666789*********************************9998665689999*******************9994 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 !   23.4   0.0   2.1e-08   5.4e-05       1      86 [.      19     104 ..      19     107 .. 0.95
   2 ?   -3.2   0.0       3.3   8.4e+03      31      60 ..     207     236 ..     203     243 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.1e-08
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHC CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegll 77 
                                       +i+++G G+ G+   +nl+++g +v++ +   +++ + +++  + a s++++++++d + ++++++ + +   ++++
  gi|330506661|ref|YP_004383089.1|  19 TIAIVGWGNQGHAQGENLKDSGLNVIAADIPGSRAWKRAEADGVKAMSVADAARAADYIQILLPDEYQGKIYRDEIA 95 
                                       59****************************99999999999999999*********************9999999** PP

                                       CC--TT-EE CS
                     NAD_binding_2  78 ealkkgdil 86 
                                       ++l++g++l
  gi|330506661|ref|YP_004383089.1|  96 PNLEEGNVL 104
                                       *****9985 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.3
                                       SHHHHHHHHHTTEEE-SSHHHHHHHCSEEE CS
                     NAD_binding_2  31 tkekveelvaegakaaesieelvasldvvi 60 
                                        k+++e+lv++g ++     e++++l++++
  gi|330506661|ref|YP_004383089.1| 207 IKAAFETLVDAGYQPEIAYFEACHELKLIV 236
                                       567788888888888777778888887776 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1     6e-07    0.0015       1      74 [.      19      86 ..      19     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6e-07
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedv 74
                                      +i+i+G Gn+g+a  ++l  +g    +++ a++   ++a + ae+ gvk+  ++ ++aa+ ad + + ++ e+ 
  gi|330506661|ref|YP_004383089.1| 19 TIAIVGWGNQGHAQGENLKDSG---LNVI-AADIPGSRAWKRAEADGVKA--MSVADAARAADYIQILLPDEYQ 86
                                      59********************...9**9.65777777777777777555..55*********99887776655 PP

>> Microvir_H  Microvirus H protein (pilot protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.0     1e-05     0.026      73     127 ..      10      67 ..       6      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                                       XXXXXXXXXXXXXXXXXXXXXX..XXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX- CS
                        Microvir_H  73 agtsavsdklldlvglggksaa..dkgkdtr.dylaaafpelnaweragadassagmv 127
                                       a   a+sdk + +vg g +  a  ++ kd+  + +aa +p   aw+ra ad   a  v
  gi|330506661|ref|YP_004383089.1|  10 ADLKALSDKTIAIVGWGNQGHAqgENLKDSGlNVIAADIPGSRAWKRAEADGVKAMSV 67 
                                       56789***********9776651155677642689999*************9877544 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.4e-05     0.086      21      81 ..      15      76 ..       8      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                                      -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHH.HHCTT-EE--HHHCTTT-SE CS
                     AdoHcyase_NAD 21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalq.aameGfevvtleevvkkadi 81
                                      l+ k++ ++G+G+ G    + lk  G  vi +++    a + a  +G + + + ++++ ad 
  gi|330506661|ref|YP_004383089.1| 15 LSDKTIAIVGWGNQGHAQGENLKDSGLNVIAADIPGSRAWKrAEADGVKAMSVADAARAADY 76
                                      7889******************************99999753889*********99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2373.66
//
Query:       gi|330506662|ref|YP_004383090.1|  [L=137]
Description: hypothetical protein MCON_0413 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-31  109.0   0.0    2.2e-31  108.2   0.0    1.4  2  DUF1829   Domain of unknown function DUF1829


Domain annotation for each model (and alignments):
>> DUF1829  Domain of unknown function DUF1829
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.55   9.9e+03      37      50 ..      21      34 ..      14      40 .. 0.65
   2 !  108.2   0.0   1.2e-35   2.2e-31       1      87 []      42     128 ..      42     128 .. 1.00

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.55
                           DUF1829 37 kalfaweDvkeare 50
                                      + ++aw D +  r 
  gi|330506662|ref|YP_004383090.1| 21 EDVVAWLDENGIRY 34
                                      56778888666665 PP

  == domain 2  score: 108.2 bits;  conditional E-value: 1.2e-35
                           DUF1829   1 GkSglthkFDfvipkskkqperlikvinnpnknavkkalfaweDvkeareensklyvilnDkekkisseiedaleey 77 
                                       GkSg++h FDfvipkskk+per++++in+p+++++ +++faw D++e+r+++s++y++ nD+e+ +ss+++dal++y
  gi|330506662|ref|YP_004383090.1|  42 GKSGYDHLFDFVIPKSKKRPERILQAINRPSRDEAGATAFAWIDTREVRASDSRAYALPNDSERLVSSSVMDALNSY 118
                                       9**************************************************************************** PP

                           DUF1829  78 dikvilwser 87 
                                       ++++ilws+r
  gi|330506662|ref|YP_004383090.1| 119 EVYPILWSKR 128
                                       ********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 953.72
//
Query:       gi|330506663|ref|YP_004383091.1|  [L=300]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-31  105.1   3.9    2.2e-06   27.3   0.1    6.3  6  TPR_1         Tetratricopeptide repeat
    7.1e-27   93.8   3.3      3e-09   37.4   1.6    4.1  4  TPR_16        Tetratricopeptide repeat
    1.2e-26   90.6   6.8    1.8e-05   24.5   0.0    6.3  6  TPR_2         Tetratricopeptide repeat
    1.5e-24   86.3  20.1    3.9e-09   36.9   0.5    4.1  4  TPR_19        Tetratricopeptide repeat
    8.4e-23   78.6   1.4    0.00041   20.3   0.0    6.4  6  TPR_8         Tetratricopeptide repeat
    1.6e-20   72.0  13.8    9.9e-06   26.0   0.4    6.2  6  TPR_14        Tetratricopeptide repeat
    6.7e-20   71.0   7.1    2.1e-11   43.8   0.5    4.4  4  TPR_9         Tetratricopeptide repeat
      2e-18   65.8   8.5    4.1e-07   29.6   0.1    6.0  6  TPR_11        TPR repeat
    4.9e-17   61.0   0.6    3.2e-05   24.0   0.1    4.7  4  TPR_17        Tetratricopeptide repeat
    6.9e-17   61.5   9.1    1.2e-06   28.8   1.3    5.0  5  TPR_12        Tetratricopeptide repeat
    4.4e-12   45.8   4.1       0.31   11.8   0.0    6.1  6  TPR_6         Tetratricopeptide repeat
    1.8e-10   40.9   0.3    0.00035   20.7   0.1    3.5  3  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
      1e-09   38.3   0.1      0.037   14.1   0.0    5.0  5  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
    2.7e-07   30.2   6.3       0.37   10.7   0.3    5.7  6  TPR_10        Tetratricopeptide repeat
      3e-07   30.6   3.7        0.4   10.7   0.2    4.0  3  DUF3856       Domain of Unknown Function (DUF3856)
    5.5e-07   28.9   2.1    0.00072   18.6   0.2    2.6  2  NARP1         NMDA receptor-regulated protein 1
    4.3e-06   27.2   3.1       0.36   11.3   2.7    3.9  3  BTAD          Bacterial transcriptional activator domain
    5.5e-05   22.9   7.2         20    5.5   0.0    5.9  6  TPR_7         Tetratricopeptide repeat
     0.0001   21.8   0.5       0.14   11.5   0.0    3.3  3  TPR_MalT      MalT-like TPR region
     0.0003   20.6   0.1          6    6.6   0.0    3.4  3  TOM20_plant   Plant specific mitochondrial import receptor su
    0.00038   20.7   6.5        1.3    9.4   0.4    4.0  4  TPR_20        Tetratricopeptide repeat
    0.00051   20.0   2.3      0.032   14.2   0.0    3.7  4  Wzy_C_2       Virulence factor membrane-bound polymerase, C-t
     0.0011   19.4  10.8        2.8    8.8   0.2    4.9  5  TPR_4         Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.011   15.0   7.3       0.12   11.5   7.1    2.3  2  TPR_15        Tetratricopeptide repeat
      0.035   14.4   1.8        3.2    8.0   0.3    2.8  2  TPR_5         Tetratrico peptide repeat
      0.035   13.6   1.6        1.8    8.1   0.1    3.7  4  SHNi-TPR      SHNi-TPR
      0.038   14.1   0.0      0.063   13.4   0.0    1.2  1  Helicase_C_2  Helicase C-terminal domain
      0.049   13.7   0.1        1.6    8.8   0.0    3.0  3  ANAPC5        Anaphase-promoting complex subunit 5
        0.1   13.1   0.0         27    5.4   0.0    2.9  2  DUF4810       Domain of unknown function (DUF4810)
       0.13   11.7   2.1         19    4.5   0.1    3.1  3  Coatomer_E    Coatomer epsilon subunit


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0042       2.5      15      32 ..      71      88 ..      50      90 .. 0.69
   2 ?    6.8   0.0      0.01       6.2       9      33 ..     103     127 ..      97     128 .. 0.77
   3 !   16.7   0.0   8.1e-06    0.0048      16      34 .]     168     186 ..     165     186 .. 0.92
   4 !   27.3   0.1   3.6e-09   2.2e-06       1      34 []     187     220 ..     187     220 .. 0.97
   5 !   27.0   0.0   4.5e-09   2.7e-06       2      34 .]     222     254 ..     221     254 .. 0.97
   6 !   15.0   0.1   2.7e-05     0.016       2      31 ..     256     285 ..     255     287 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0042
                                      T-HHHHHHHHHHHHHHST CS
                             TPR_1 15 gkydeAleyyekALelnP 32
                                      + +++Al+ y++A+  +P
  gi|330506663|ref|YP_004383091.1| 71 ESFEKALQIYDQAIATRP 88
                                      447777777777777666 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.01
                                       HHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   9 nayfklgkydeAleyyekALelnPn 33 
                                       +++ klg++deA+   +  ++ +P+
  gi|330506663|ref|YP_004383091.1| 103 LLLVKLGRFDEAISTLDSTIKSYPE 127
                                       57789********877766666665 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 8.1e-06
                                       -HHHHHHHHHHHHHHSTTH CS
                             TPR_1  16 kydeAleyyekALelnPnn 34 
                                        yd+ l+++++AL l+P++
  gi|330506663|ref|YP_004383091.1| 168 IYDQSLQAFQRALDLDPDD 186
                                       59***************96 PP

  == domain 4  score: 27.3 bits;  conditional E-value: 3.6e-09
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a+ ++++ay  l+++deAl++ +kA+e++P +
  gi|330506663|ref|YP_004383091.1| 187 AEAWRGRALAYSGLKDHDEALKASDKAVEIDPGY 220
                                       89******************************76 PP

  == domain 5  score: 27.0 bits;  conditional E-value: 4.5e-09
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +a+  +G +++++g+ +eAl + ++AL+++P+n
  gi|330506663|ref|YP_004383091.1| 222 QAWLDRGILLLEMGRTEEALFALDRALSIQPDN 254
                                       69*****************************98 PP

  == domain 6  score: 15.0 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                       +al  ++ a+  lg+y+eA++++ +A   +
  gi|330506663|ref|YP_004383091.1| 256 DALSIKAEALTVLGRYQEAEAAFYQAMDMD 285
                                       6888899*******************8776 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.66     4e+02      48      66 ..      71      89 ..      61      91 .. 0.60
   2 !   13.8   0.0   0.00011     0.068       5      43 ..     103     138 ..     100     141 .. 0.89
   3 !   37.4   1.6   4.9e-12     3e-09      13      66 ..     169     219 ..     167     220 .. 0.95
   4 !   35.5   1.5   1.9e-11   1.2e-08       1      60 [.     225     282 ..     225     288 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.66
                            TPR_16 48 grlaeAaalyraalraapd 66
                                        +++A++ y+ a++  p+
  gi|330506663|ref|YP_004383091.1| 71 ESFEKALQIYDQAIATRPG 89
                                      3455555555555555555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00011
                            TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAllllgda 43 
                                       ++++++g++d+A+  l+ ++k++   P++  A+  +g +
  gi|330506663|ref|YP_004383091.1| 103 LLLVKLGRFDEAISTLDSTIKSY---PENLKAWKIKGFS 138
                                       6899*******************...**99999888865 PP

  == domain 3  score: 37.4 bits;  conditional E-value: 4.9e-12
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       yd+ + a+++al++d   Pd+aeA+ ++++a+  +++++eA+ + ++a++ +p+
  gi|330506663|ref|YP_004383091.1| 169 YDQSLQAFQRALDLD---PDDAEAWRGRALAYSGLKDHDEALKASDKAVEIDPG 219
                                       99*************...************************999999999997 PP

  == domain 4  score: 35.5 bits;  conditional E-value: 1.9e-11
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyraa 60 
                                       l+++ ++l+ g+ ++A+ al++al  +   Pd+ +Al  +++a+ ++gr++eA+ a+y+a+
  gi|330506663|ref|YP_004383091.1| 225 LDRGILLLEMGRTEEALFALDRALSIQ---PDNLDALSIKAEALTVLGRYQEAEaAFYQAM 282
                                       68999**********************...************************7777664 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0011      0.68       4      32 ..      53      81 ..      53      84 .. 0.88
   2 ?    6.7   0.0     0.015         9      11      34 .]     105     128 ..     103     128 .. 0.85
   3 !   14.5   0.0   4.7e-05     0.028      15      34 .]     167     186 ..     164     186 .. 0.92
   4 !   23.1   0.2   8.3e-08   4.9e-05       1      33 [.     187     219 ..     187     220 .. 0.97
   5 !   24.5   0.0     3e-08   1.8e-05       2      34 .]     222     254 ..     221     254 .. 0.96
   6 !    9.9   0.2    0.0014      0.85       3      28 ..     257     282 ..     255     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                             TPR_2  4 lynlGlayyklgdyeeAleafekAleldP 32
                                      +   G+  + +g + +A e fekAl+++ 
  gi|330506663|ref|YP_004383091.1| 53 WIKEGYKQMWKGSFSQANESFEKALQIYD 81
                                      66788889999***************986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.015
                             TPR_2  11 yyklgdyeeAleafekAleldPnn 34 
                                       + klg+++eA+  ++  ++ +P+n
  gi|330506663|ref|YP_004383091.1| 105 LVKLGRFDEAISTLDSTIKSYPEN 128
                                       779********9999888888876 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 4.7e-05
                             TPR_2  15 gdyeeAleafekAleldPnn 34 
                                       g y++ l+af++Al ldP++
  gi|330506663|ref|YP_004383091.1| 167 GIYDQSLQAFQRALDLDPDD 186
                                       679***************97 PP

  == domain 4  score: 23.1 bits;  conditional E-value: 8.3e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       aea+  ++lay  l+d++eAl+a +kA+e+dP+
  gi|330506663|ref|YP_004383091.1| 187 AEAWRGRALAYSGLKDHDEALKASDKAVEIDPG 219
                                       89******************************7 PP

  == domain 5  score: 24.5 bits;  conditional E-value: 3e-08
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +a+  +G +++++g+ eeAl a+++Al++ P+n
  gi|330506663|ref|YP_004383091.1| 222 QAWLDRGILLLEMGRTEEALFALDRALSIQPDN 254
                                       599****************************98 PP

  == domain 6  score: 9.9 bits;  conditional E-value: 0.0014
                             TPR_2   3 alynlGlayyklgdyeeAleafekAl 28 
                                       al   ++a+  lg+y+eA++af +A 
  gi|330506663|ref|YP_004383091.1| 257 ALSIKAEALTVLGRYQEAEAAFYQAM 282
                                       77788999*************96665 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   5.5e-08   3.3e-05       3      58 ..      69     128 ..      68     135 .. 0.89
   2 !   25.9   1.2   1.8e-08     1e-05       7      57 ..     169     219 ..     166     224 .. 0.92
   3 !   36.9   0.5   6.6e-12   3.9e-09       5      60 ..     201     256 ..     199     262 .. 0.92
   4 !   31.1   2.6   4.2e-10   2.5e-07       1      55 [.     231     285 ..     231     291 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.5e-08
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllL....AeallalgqldeAealLdalpeedpdd 58 
                                       a++ ++ Al+++ qa++  p++ +a l+     + +l++lg++deA+ +Ld   +++p +
  gi|330506663|ref|YP_004383091.1|  69 ANESFEKALQIYDQAIATRPGDINATLNAtnkkILLLVKLGRFDEAISTLDSTIKSYPEN 128
                                       578899***************9999997777789******************99999984 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.8e-08
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       y++ l+++++al+ dp++aea+ + A a+  l++ deA ++ d++ e dp 
  gi|330506663|ref|YP_004383091.1| 169 YDQSLQAFQRALDLDPDDAEAWRGRALAYSGLKDHDEALKASDKAVEIDPG 219
                                       8999*************************************9999999987 PP

  == domain 3  score: 36.9 bits;  conditional E-value: 6.6e-12
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                       +d++eAl++  +a + dp+++ a+l+  ++ll++g+++eA  +Ld+++  +pd+ +
  gi|330506663|ref|YP_004383091.1| 201 KDHDEALKASDKAVEIDPGYGQAWLDRGILLLEMGRTEEALFALDRALSIQPDNLD 256
                                       69**************************************************9544 PP

  == domain 4  score: 31.1 bits;  conditional E-value: 4.2e-10
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55 
                                       ll++g+ +eAl +l +al+  p+n++a+   Aeal  lg+++eAea+  +++++d
  gi|330506663|ref|YP_004383091.1| 231 LLEMGRTEEALFALDRALSIQPDNLDALSIKAEALTVLGRYQEAEAAFYQAMDMD 285
                                       79********************************************997777776 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.034        21       7      28 ..      63      84 ..      60      90 .. 0.58
   2 ?    6.6   0.0     0.017        10      10      32 ..     104     126 ..     103     128 .. 0.79
   3 !    8.1   0.0    0.0058       3.5      17      34 .]     169     186 ..     167     186 .. 0.94
   4 !   20.2   0.1   7.4e-07   0.00044       2      32 ..     188     218 ..     187     220 .. 0.90
   5 !   20.3   0.0   6.9e-07   0.00041       2      34 .]     222     254 ..     221     254 .. 0.96
   6 !   10.8   0.2   0.00079      0.47       7      32 ..     261     286 ..     255     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.034
                                      HHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8  7 lgsiylklgdyeeAkeyyekal 28
                                      +gs  +  + +e+A + y +a+
  gi|330506663|ref|YP_004383091.1| 63 KGSFSQANESFEKALQIYDQAI 84
                                      4444455555666666666665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.017
                                       HHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8  10 iylklgdyeeAkeyyekaleldp 32 
                                       ++ klg+++eA++++   ++  p
  gi|330506663|ref|YP_004383091.1| 104 LLVKLGRFDEAISTLDSTIKSYP 126
                                       6889********99876666655 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0058
                                       HHHHHHHHHHHHHHHHH. CS
                             TPR_8  17 yeeAkeyyekaleldpdn 34 
                                       y+++ +++++al+ldpd+
  gi|330506663|ref|YP_004383091.1| 169 YDQSLQAFQRALDLDPDD 186
                                       899*************96 PP

  == domain 4  score: 20.2 bits;  conditional E-value: 7.4e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ea+   +++y+ l+d++eA ++  ka+e+dp
  gi|330506663|ref|YP_004383091.1| 188 EAWRGRALAYSGLKDHDEALKASDKAVEIDP 218
                                       6666789***********************9 PP

  == domain 5  score: 20.3 bits;  conditional E-value: 6.9e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +a++  g ++l++g+ eeA  ++ +al+++pdn
  gi|330506663|ref|YP_004383091.1| 222 QAWLDRGILLLEMGRTEEALFALDRALSIQPDN 254
                                       79*****************************97 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.00079
                                       HHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekaleldp 32 
                                       ++ ++  lg+y+eA++++ +a ++d 
  gi|330506663|ref|YP_004383091.1| 261 KAEALTVLGRYQEAEAAFYQAMDMDS 286
                                       66667779**************9996 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0     0.002       1.2      13      39 ..      69      95 ..      60      99 .. 0.84
   2 !   11.1   0.0   0.00097      0.58      10      39 ..     104     133 ..      95     138 .. 0.88
   3 !   17.5   1.5   8.9e-06    0.0053      17      42 ..     169     194 ..     166     196 .. 0.90
   4 !   17.5   0.6   8.5e-06    0.0051       1      39 [.     187     225 ..     187     225 .. 0.96
   5 !   26.0   0.4   1.7e-08   9.9e-06       2      38 ..     222     258 ..     221     263 .. 0.94
   6 ?    4.4   0.8      0.14        87       6      27 ..     260     281 ..     256     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.002
                            TPR_14 13 alGdpdeAiallrralalaPddaeawl 39
                                      a++ +++A++++++a+a+ P+d  a l
  gi|330506663|ref|YP_004383091.1| 69 ANESFEKALQIYDQAIATRPGDINATL 95
                                      67789****************987765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00097
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawl 39 
                                       +l  lG++deAi  l+  ++ +P+++ aw 
  gi|330506663|ref|YP_004383091.1| 104 LLVKLGRFDEAISTLDSTIKSYPENLKAWK 133
                                       6889************************96 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 8.9e-06
                            TPR_14  17 pdeAiallrralalaPddaeawllla 42 
                                       +d+++++++ral+l+Pddaeaw+  a
  gi|330506663|ref|YP_004383091.1| 169 YDQSLQAFQRALDLDPDDAEAWRGRA 194
                                       6999******************8765 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 8.5e-06
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +ea++ +a a+  l d+deA+++ ++a++ +P+  +awl
  gi|330506663|ref|YP_004383091.1| 187 AEAWRGRALAYSGLKDHDEALKASDKAVEIDPGYGQAWL 225
                                       58********************************99996 PP

  == domain 5  score: 26.0 bits;  conditional E-value: 1.7e-08
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       +a+l+++ +ll+ G+++eA+ +l+ral+ +Pd+++a+
  gi|330506663|ref|YP_004383091.1| 222 QAWLDRGILLLEMGRTEEALFALDRALSIQPDNLDAL 258
                                       59*******************************9986 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.14
                            TPR_14   6 alaeallalGdpdeAiallrra 27 
                                         aeal  lG+++eA+a++ +a
  gi|330506663|ref|YP_004383091.1| 260 IKAEALTVLGRYQEAEAAFYQA 281
                                       56899999*********99887 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00068      0.41       6      62 ..      68     128 ..      64     135 .. 0.87
   2 !   16.5   0.4   1.1e-05    0.0068      12      41 ..     170     199 ..     168     201 .. 0.89
   3 !   43.8   0.5   3.5e-14   2.1e-11       8      70 ..     200     262 ..     196     265 .. 0.95
   4 ?    1.2   0.2      0.69   4.1e+02      37      62 ..     263     288 ..     261     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00068
                             TPR_9   6 ireedweralavverllllaPddpeerrdRG....lllaqlGclsaAladLeaylalapda 62 
                                       + +e +e+al++++  ++  P d+   +       lll++lG++ +A+  L+  +   p++
  gi|330506663|ref|YP_004383091.1|  68 QANESFEKALQIYDQAIATRPGDINATLNATnkkiLLLVKLGRFDEAISTLDSTIKSYPEN 128
                                       57899*******************999987666669***************9999888876 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.1e-05
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaq 41 
                                       ++ l++ +r l l+Pdd+e +r R+l++  
  gi|330506663|ref|YP_004383091.1| 170 DQSLQAFQRALDLDPDDAEAWRGRALAYSG 199
                                       5668999********************965 PP

  == domain 3  score: 43.8 bits;  conditional E-value: 3.5e-14
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeaira 70 
                                        +d+++al++++  + ++P   + ++dRG+ll ++G++++Al++L+++l+++pd+ da  i+a
  gi|330506663|ref|YP_004383091.1| 200 LKDHDEALKASDKAVEIDPGYGQAWLDRGILLLEMGRTEEALFALDRALSIQPDNLDALSIKA 262
                                       689*******************************************************99987 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.69
                             TPR_9  37 lllaqlGclsaAladLeaylalapda 62 
                                        +l  lG++++A a++ ++++++ ++
  gi|330506663|ref|YP_004383091.1| 263 EALTVLGRYQEAEAAFYQAMDMDSER 288
                                       567779**********9999998765 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.3    0.0067         4       9      30 ..      72      93 ..      68      97 .. 0.86
   2 ?    4.2   0.0     0.059        35       4      19 ..     105     120 ..     103     132 .. 0.76
   3 !   29.6   0.1   6.9e-10   4.1e-07      10      39 ..     169     198 ..     166     201 .. 0.93
   4 !   12.3   0.0   0.00017     0.099       9      42 .]     202     235 ..     200     235 .. 0.94
   5 !   15.8   0.0   1.4e-05    0.0085       4      31 ..     231     258 ..     228     265 .. 0.90
   6 ?    0.4   0.1      0.89   5.3e+02       4      24 ..     265     285 ..     262     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0067
                            TPR_11  9 kyeeAieaYkkAlkldPdnaea 30
                                       +e+A++ Y +A++ +P + +a
  gi|330506663|ref|YP_004383091.1| 72 SFEKALQIYDQAIATRPGDINA 93
                                      68************99988776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.059
                            TPR_11   4 yyeqGkyeeAieaYkk 19 
                                       ++++G+++eAi  +  
  gi|330506663|ref|YP_004383091.1| 105 LVKLGRFDEAISTLDS 120
                                       789********87765 PP

  == domain 3  score: 29.6 bits;  conditional E-value: 6.9e-10
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       y+++++a+++Al+ldPd+aea+ +++lay 
  gi|330506663|ref|YP_004383091.1| 169 YDQSLQAFQRALDLDPDDAEAWRGRALAYS 198
                                       9***************************95 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00017
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       + +eA++a  kA+++dP +  a++ +G +++++G
  gi|330506663|ref|YP_004383091.1| 202 DHDEALKASDKAVEIDPGYGQAWLDRGILLLEMG 235
                                       689***************************9998 PP

  == domain 5  score: 15.8 bits;  conditional E-value: 1.4e-05
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeay 31 
                                       + e G+ eeA+ a+ +Al + Pdn +a+
  gi|330506663|ref|YP_004383091.1| 231 LLEMGRTEEALFALDRALSIQPDNLDAL 258
                                       6799********************9997 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 0.89
                            TPR_11   4 yyeqGkyeeAieaYkkAlkld 24 
                                       ++ +G+y eA +a+ +A + d
  gi|330506663|ref|YP_004383091.1| 265 LTVLGRYQEAEAAFYQAMDMD 285
                                       556899***988888887665 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       2.7   1.6e+03       2      32 ..      80     114 ..      79     116 .. 0.46
   2 !   24.0   0.1   5.4e-08   3.2e-05       2      33 ..     176     207 ..     175     208 .. 0.95
   3 !   17.7   0.0   5.3e-06    0.0032       4      33 ..     212     241 ..     211     242 .. 0.96
   4 !   13.3   0.1   0.00014     0.085       2      33 ..     244     275 ..     243     276 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.7
                            TPR_17   2 ylkaleldPnn....adaynnLAelllknGdlmtA 32 
                                       y +a++  P +     +a n +  ll k+G++++A
  gi|330506663|ref|YP_004383091.1|  80 YDQAIATRPGDinatLNATNKKILLLVKLGRFDEA 114
                                       56666666655222222223333344466666666 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 5.4e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +++al+ldP++a+a+  +A +++ ++d+++A+
  gi|330506663|ref|YP_004383091.1| 176 FQRALDLDPDDAEAWRGRALAYSGLKDHDEAL 207
                                       9*****************************97 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 5.3e-06
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtAr 33 
                                       ka+e+dP +  a+  ++ lll+ G++++A+
  gi|330506663|ref|YP_004383091.1| 212 KAVEIDPGYGQAWLDRGILLLEMGRTEEAL 241
                                       9***************************96 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00014
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + +al + P+n da+  +Ae+l  +G++++A+
  gi|330506663|ref|YP_004383091.1| 244 LDRALSIQPDNLDALSIKAEALTVLGRYQEAE 275
                                       579****************************8 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0    0.0005       0.3      10      75 ..      64     125 ..      60     127 .. 0.74
   2 ?    6.2   0.0     0.021        12       5      31 ..      97     123 ..      90     144 .. 0.73
   3 !   22.3   0.3     2e-07   0.00012      25      75 ..     168     217 ..     164     218 .. 0.89
   4 !   28.8   1.3   1.9e-09   1.2e-06       3      75 ..     187     251 ..     185     253 .. 0.92
   5 !   15.1   0.1   3.5e-05     0.021       8      38 ..     260     290 ..     254     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0005
                            TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +++ ++ + +++Al+++++a++ +   +G+ + +t+++ +    l+ +lgr++eA++ l  +++ +
  gi|330506663|ref|YP_004383091.1|  64 GSFSQANESFEKALQIYDQAIATR---PGDIN-ATLNATNKKILLLVKLGRFDEAISTLDSTIKSY 125
                                       666677888899999999998888...55433.67777777777788********99988777665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.021
                            TPR_12   5 alnnlaavlrrlgrydeAlellekale 31 
                                       a n+  ++l +lgr+deA++ l+  + 
  gi|330506663|ref|YP_004383091.1|  97 ATNKKILLLVKLGRFDEAISTLDSTIK 123
                                       555577778889999999988876655 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 2e-07
                            TPR_12  25 llekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +++++l++++r+l+   p+ a++ r+ + +y+ l++++eAl++  +a++i+
  gi|330506663|ref|YP_004383091.1| 168 IYDQSLQAFQRALDL-DPDDAEAWRGRALAYSGLKDHDEALKASDKAVEID 217
                                       688999999888754.6899***************************9986 PP

  == domain 4  score: 28.8 bits;  conditional E-value: 1.9e-09
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a a++ +a+++  l+++deAl+  +ka+ei      p    + ++  + g+l++++gr+eeAl +l +al i 
  gi|330506663|ref|YP_004383091.1| 187 AEAWRGRALAYSGLKDHDEALKASDKAVEID-----PG---YGQAWLDRGILLLEMGRTEEALFALDRALSIQ 251
                                       789999*************************.....53...6899*************************986 PP

  == domain 5  score: 15.1 bits;  conditional E-value: 3.5e-05
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllG 38 
                                         a++l+ lgry+eA++ + +a+++ ++ ++
  gi|330506663|ref|YP_004383091.1| 260 IKAEALTVLGRYQEAEAAFYQAMDMDSERYE 290
                                       47999*******************9955443 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.093        56      15      31 ..      72      88 ..      60      90 .. 0.74
   2 !   11.5   0.0   0.00063      0.38      10      32 ..     105     127 ..     102     128 .. 0.89
   3 ?    6.8   0.0      0.02        12      14      32 ..     167     185 ..     147     186 .. 0.85
   4 ?    6.2   0.0     0.032        19       6      31 ..     193     218 ..     188     220 .. 0.85
   5 !   11.8   0.0   0.00052      0.31       1      33 []     222     254 ..     222     254 .. 0.93
   6 ?   -0.0   0.4         3   1.8e+03       7      24 ..     262     279 ..     256     283 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.093
                                      HHHHHHHHHHHHHHH-T CS
                             TPR_6 15 dtdkAlealerlikeYP 31
                                        +kAl+++++ i   P
  gi|330506663|ref|YP_004383091.1| 72 SFEKALQIYDQAIATRP 88
                                      56789999999988887 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00063
                                       HHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  10 yrklgdtdkAlealerlikeYPd 32 
                                       + klg+ d+A+ +l++ ik+YP+
  gi|330506663|ref|YP_004383091.1| 105 LVKLGRFDEAISTLDSTIKSYPE 127
                                       56889*****************7 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHHH-TT CS
                             TPR_6  14 gdtdkAlealerlikeYPd 32 
                                       g +d++l+a++r ++  Pd
  gi|330506663|ref|YP_004383091.1| 167 GIYDQSLQAFQRALDLDPD 185
                                       579************9998 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                       +al+y  l+d+d+Al+a ++ ++  P
  gi|330506663|ref|YP_004383091.1| 193 RALAYSGLKDHDEALKASDKAVEIDP 218
                                       789999999********999998877 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 0.00052
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPdS 33 
                                       +A + ++ +++++g+t++Al al+r ++  Pd+
  gi|330506663|ref|YP_004383091.1| 222 QAWLDRGILLLEMGRTEEALFALDRALSIQPDN 254
                                       5888999**********************9995 PP

  == domain 6  score: -0.0 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAleale 24 
                                       a+++  lg++++A +a+ 
  gi|330506663|ref|YP_004383091.1| 262 AEALTVLGRYQEAEAAFY 279
                                       666666789999988875 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.2e-05     0.025       2      69 ..      70     142 ..      69     153 .. 0.82
   2 ?    1.4   0.0      0.64   3.8e+02      39      78 ..     169     209 ..     162     213 .. 0.68
   3 !   20.7   0.1   5.9e-07   0.00035      30      79 ..     228     278 ..     200     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.2e-05
                                       TT-HHHHHHHHHHHH.HHH--HHH....HHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHT CS
                            ANAPC3   2 qnnyknAiflaerllaaetesped....ayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkL 69 
                                       ++ +++A+ +++ + a+ + + ++    +  + l l ++g++++A+  l+++ k+++++l+++ +++ +l+ +
  gi|330506663|ref|YP_004383091.1|  70 NESFEKALQIYDQAIATRPGDINAtlnaTNKKILLLVKLGRFDEAISTLDSTiKSYPENLKAWKIKGFSLINI 142
                                       567888999999999877777666332245579**********************************999987 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.64
                                       HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  39 ykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       y++ ++ +++a +l++ + +++   A ++  Lk ++eA++a
  gi|330506663|ref|YP_004383091.1| 169 YDQSLQAFQRAlDLDPDDAEAWRGRALAYSGLKDHDEALKA 209
                                       66666666677777777777777777777777777777766 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 5.9e-07
                                       HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       +  l+++g+ ++A+  l++a  +++ +l ++ ++A++l  L++y+eA+aa+
  gi|330506663|ref|YP_004383091.1| 228 GILLLEMGRTEEALFALDRAlSIQPDNLDALSIKAEALTVLGRYQEAEAAF 278
                                       5678999*****************************************997 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 ?   -1.8   0.0       5.9   3.5e+03      17      34 ..      73      90 ..      70      94 .. 0.80
   2 ?    5.0   0.0     0.044        26      12      37 ..     106     131 ..     105     137 .. 0.92
   3 ?    3.0   0.0      0.18   1.1e+02      17      37 ..     169     189 ..     167     190 .. 0.90
   4 !   14.1   0.0   6.2e-05     0.037       8      37 ..     194     223 ..     193     225 .. 0.96
   5 !    9.3   0.0     0.002       1.2      18      41 ..     238     261 ..     232     265 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.9
                                      HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C 17 YseArryvdalLeiEPen 34
                                      +++A++  d+ ++  P+ 
  gi|330506663|ref|YP_004383091.1| 73 FEKALQIYDQAIATRPGD 90
                                      789999999999888876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.044
                                       HHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQa 37 
                                        klg+++eA   +d  ++  Pen  a
  gi|330506663|ref|YP_004383091.1| 106 VKLGRFDEAISTLDSTIKSYPENLKA 131
                                       69*********************877 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  17 YseArryvdalLeiEPenrQa 37 
                                       Y+++++  ++ L ++P+   a
  gi|330506663|ref|YP_004383091.1| 169 YDQSLQAFQRALDLDPDDAEA 189
                                       9***************98765 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 6.2e-05
                                       HHHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C   8 AlGhyklgeYseArryvdalLeiEPenrQa 37 
                                       Al++  l++++eA++  d   ei+P+  Qa
  gi|330506663|ref|YP_004383091.1| 194 ALAYSGLKDHDEALKASDKAVEIDPGYGQA 223
                                       99*************************998 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHHTTS-HHHHHHH CS
                        Fis1_TPR_C  18 seArryvdalLeiEPenrQaqsLk 41 
                                       +eA+  +d+ L+i+P+n  a+s k
  gi|330506663|ref|YP_004383091.1| 238 EEALFALDRALSIQPDNLDALSIK 261
                                       799999**************9876 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.036        22      18      32 ..      73      87 ..      64      87 .. 0.81
   2 ?   -0.7   0.0       2.5   1.5e+03      12      21 ..     105     114 ..     103     119 .. 0.83
   3 ?   -0.5   0.0       2.1   1.3e+03      25      37 ..     169     181 ..     167     187 .. 0.66
   4 !    7.2   0.1     0.008       4.8       9      31 ..     194     216 ..     193     216 .. 0.93
   5 ?    4.2   0.1     0.069        41       9      31 ..     228     250 ..     226     251 .. 0.89
   6 !   10.7   0.3   0.00061      0.37       9      31 ..     262     284 ..     255     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.036
                            TPR_10 18 ydeAealleealair 32
                                      +++A++++++a+a+r
  gi|330506663|ref|YP_004383091.1| 73 FEKALQIYDQAIATR 87
                                      788999999999986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.5
                            TPR_10  12 lrqrgrydeA 21 
                                       l ++gr+deA
  gi|330506663|ref|YP_004383091.1| 105 LVKLGRFDEA 114
                                       5679*****9 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.1
                            TPR_10  25 leealairrrllG 37 
                                       ++++l++ +r+l 
  gi|330506663|ref|YP_004383091.1| 169 YDQSLQAFQRALD 181
                                       6677777777765 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.008
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       a a++ ++++deA++  ++a++i
  gi|330506663|ref|YP_004383091.1| 194 ALAYSGLKDHDEALKASDKAVEI 216
                                       789************99999986 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.069
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       +++l ++gr +eA+  l++al+i
  gi|330506663|ref|YP_004383091.1| 228 GILLLEMGRTEEALFALDRALSI 250
                                       8999*********9999999987 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.00061
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       a al+ +gry+eAea + +a+++
  gi|330506663|ref|YP_004383091.1| 262 AEALTVLGRYQEAEAAFYQAMDM 284
                                       778999**************987 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0025       1.5      14      83 ..      55     123 ..      48     130 .. 0.77
   2 !   10.7   0.2   0.00067       0.4      46     120 ..     178     241 ..     173     254 .. 0.76
   3 !    8.7   0.1    0.0029       1.7     102     134 ..     257     289 ..     253     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHT-HHHHHHHHHHHHHHHTTS-TTS---.HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  14 seaekqleegayeeaaasyrkalevsrtipaeeafd.heGfdalchaglsealaklgrydealesadkalr 83 
                                        e+ kq+ +g++++a++s++kal++     a    d  + ++a     l   l+klgr+dea+++ d++++
  gi|330506663|ref|YP_004383091.1|  55 KEGYKQMWKGSFSQANESFEKALQIYDQAIATRPGDiNATLNATNKKIL--LLVKLGRFDEAISTLDSTIK 123
                                       68899*******************9755444444451455666666665..5899******9999988776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00067
                                       S---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHH CS
                           DUF3856  46 eafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdeal 120
                                        a+d +  da ++ g + a+ +l+++deal+++dka+       e++   G+ W+    +r+  l e+Gr++eal
  gi|330506663|ref|YP_004383091.1| 178 RALDLDPDDAEAWRGRALAYSGLKDHDEALKASDKAV-------EIDPGYGQAWL----DRGILLLEMGRTEEAL 241
                                       578899999**************************98.......45555555554....4566666666666665 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH-- CS
                           DUF3856 102 avfsravaleelGrkdealkafrmagemiaerk 134
                                       a+  +a al  lGr++ea  af +a +m +er 
  gi|330506663|ref|YP_004383091.1| 257 ALSIKAEALTVLGRYQEAEAAFYQAMDMDSERY 289
                                       566799**********************99984 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00077      0.46      12      76 ..      65     133 ..      58     182 .. 0.68
   2 !   18.6   0.2   1.2e-06   0.00072      11      72 ..     228     289 ..     219     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00077
                                       HHHHHHTHHHHHHHHHHH....HGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHH CS
                             NARP1  12 qiieeagkleeAlehLee....kekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYye 76 
                                       +  +  ++ e+Al+  ++       +i  +l+ +++k  ll+kLgr++eA +t+ + ++  pen k ++
  gi|330506663|ref|YP_004383091.1|  65 SFSQANESFEKALQIYDQaiatRPGDINATLNATNKKILLLVKLGRFDEAISTLDSTIKSYPENLKAWK 133
                                       5566778888888765542222667899999999******************************98665 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-C CS
                             NARP1  11 nqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpens 72 
                                         ++ e g++eeAl  L+++ +   D+l  + +kae l+ Lgr++eAea++ + +++ +e +
  gi|330506663|ref|YP_004383091.1| 228 GILLLEMGRTEEALFALDRALSIQPDNLDALSIKAEALTVLGRYQEAEAAFYQAMDMDSERY 289
                                       568899**********************************************9999988865 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0      0.01       6.1      18      95 ..      62     128 ..      48     134 .. 0.64
   2 ?    4.9   0.1     0.055        33      78     118 ..     169     209 ..     161     217 .. 0.87
   3 !   11.3   2.7    0.0006      0.36      32     124 ..     186     283 ..     176     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.01
                                       HTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                              BTAD  18 aagdpeeaaelleaAlalwrGpaladleagewleaererleelrlealealaeaelrlGraeealaelealvaehPl 94 
                                        +g + +a e++e+Al++++                     +  l a+ + + ++++lGr +ea+++l++ ++ +P 
  gi|330506663|ref|YP_004383091.1|  62 WKGSFSQANESFEKALQIYDQAIATR-----------PGDINATLNATNKKILLLVKLGRFDEAISTLDSTIKSYPE 127
                                       44444444444444444444333333...........1123456788888888899999999999999999999998 PP

                                       - CS
                              BTAD  95 r 95 
                                       +
  gi|330506663|ref|YP_004383091.1| 128 N 128
                                       7 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.055
                                       HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHH CS
                              BTAD  78 aeealaelealvaehPlrErlhrqlmrAlarsGrqaeALev 118
                                       +++ l+  +++++++P + +++r   +A+  + +  eAL++
  gi|330506663|ref|YP_004383091.1| 169 YDQSLQAFQRALDLDPDDAEAWRGRALAYSGLKDHDEALKA 209
                                       6788999999***************9999999999999987 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0006
                                       HHTT--SSTTG..GGTT...STTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHH CS
                              BTAD  32 AlalwrGpala..dlea...gewleaererleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlm 103
                                        ++ wrG+ala  +l++      + +++++++    +a  ++  ++l++Gr eeal  l+++++ +P + ++     
  gi|330506663|ref|YP_004383091.1| 186 DAEAWRGRALAysGLKDhdeALKASDKAVEIDPGYGQAWLDRGILLLEMGRTEEALFALDRALSIQPDNLDALSIKA 262
                                       5667888887622444433344445555555555666666777799******************************* PP

                                       HHHHHTT-HHHHHHHHHHHHH CS
                              BTAD 104 rAlarsGrqaeALevYerlrr 124
                                       +Al  +Gr +eA +++ ++++
  gi|330506663|ref|YP_004383091.1| 263 EALTVLGRYQEAEAAFYQAMD 283
                                       ***************998886 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.034        20      15      35 ..      73      91 ..      70      92 .. 0.87
   2 ?    4.8   0.0     0.056        34       9      22 ..     105     118 ..     103     124 .. 0.85
   3 ?    4.9   0.1     0.052        31      15      35 ..     169     187 ..     164     188 .. 0.86
   4 ?   -0.8   0.0       3.4     2e+03       6      20 ..     194     208 ..     190     217 .. 0.84
   5 ?    1.4   0.0      0.68     4e+02       5      25 ..     227     247 ..     223     258 .. 0.71
   6 ?    4.3   0.4     0.083        50      12      31 ..     268     287 ..     257     291 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.034
                             TPR_7 15 yeeAielyeqsLaltkdpeda 35
                                      +e+A+++y q  a++ +p+d+
  gi|330506663|ref|YP_004383091.1| 73 FEKALQIYDQ--AIATRPGDI 91
                                      79********..888888875 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.056
                             TPR_7   9 ysrlGdyeeAiely 22 
                                        ++lG+++eAi+ +
  gi|330506663|ref|YP_004383091.1| 105 LVKLGRFDEAISTL 118
                                       689********975 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.052
                             TPR_7  15 yeeAielyeqsLaltkdpeda 35 
                                       y++ ++ +++  al+ dp+da
  gi|330506663|ref|YP_004383091.1| 169 YDQSLQAFQR--ALDLDPDDA 187
                                       99********..999998887 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3.4
                             TPR_7   6 arlysrlGdyeeAie 20 
                                       a +ys l d++eA++
  gi|330506663|ref|YP_004383091.1| 194 ALAYSGLKDHDEALK 208
                                       668899999999975 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.68
                             TPR_7   5 LarlysrlGdyeeAielyeqs 25 
                                        + l  ++G++eeA+  + ++
  gi|330506663|ref|YP_004383091.1| 227 RGILLLEMGRTEEALFALDRA 247
                                       577889999***998666664 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.083
                             TPR_7  12 lGdyeeAielyeqsLaltkd 31 
                                       lG+y+eA+  + q++ ++++
  gi|330506663|ref|YP_004383091.1| 268 LGRYQEAEAAFYQAMDMDSE 287
                                       8*********9995555554 PP

>> TPR_MalT  MalT-like TPR region
   #    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      47     127 ..      57     141 ..      47     144 .. 0.79
   2 ?    1.2   0.0      0.32   1.9e+02      24      60 ..     176     211 ..     166     217 .. 0.73
   3 ?    5.1   0.6      0.02        12     118     187 ..     217     281 ..     204     299 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                          TPR_MalT  47 GeasllqGdleaAlqalqeaekl.....arqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqql 118
                                       G+ ++ +G + +A +++++a ++     a + + ++++l a+ + + +lv+ Gr++eA+ t    ++ ++e+  + +
  gi|330506663|ref|YP_004383091.1|  57 GYKQMWKGSFSQANESFEKALQIydqaiATRPGDINATLNATNKKILLLVKLGRFDEAISTLDSTIKSYPENLKA-W 132
                                       5666777777778777776655534444788999999******************************88887655.7 PP

                          TPR_MalT 119 plvgfllvl 127
                                        + gf l+ 
  gi|330506663|ref|YP_004383091.1| 133 KIKGFSLIN 141
                                       777777665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.32
                          TPR_MalT  24 ArqALallpeddllariaatavlGeasllqGdleaAl 60 
                                        ++AL+l p+d+  +r+ a+a  G    +++ l+a+ 
  gi|330506663|ref|YP_004383091.1| 176 FQRALDLDPDDAEAWRGRALAYSG-LKDHDEALKASD 211
                                       589999999999999999988888.444455555554 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.02
                          TPR_MalT 118 lplvgfllvlladllyEwndLeeAeqhlqeGielleqlepeaaldayvllarialaqGdleeAetlleka 187
                                        p +g +   ++ ll+E+++ eeA  +l++++ +  +      lda+ + a+   + G+ +eAe+++ +a
  gi|330506663|ref|YP_004383091.1| 217 DPGYGQAWLDRGILLLEMGRTEEALFALDRALSIQPDN-----LDALSIKAEALTVLGRYQEAEAAFYQA 281
                                       56666666678888888888888888888888777666.....444444444445567777777776666 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 ?    6.6   0.0      0.01         6      90     113 ..      67      90 ..      52     138 .. 0.86
   2 ?    4.5   0.0     0.045        27      87     115 ..     160     188 ..     143     223 .. 0.83
   3 ?    6.0   0.0     0.015       9.2      52      91 ..     238     277 ..     233     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHHHHHHHH-TT- CS
                       TOM20_plant  90 eeakenfekatqffqqavdedPdn 113
                                        +a+e feka q+++qa++  P++
  gi|330506663|ref|YP_004383091.1|  67 SQANESFEKALQIYDQAIATRPGD 90 
                                       689*****************9985 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.045
                                       --HHHHHHHHHHHHHHHHHHHHH-TT-HH CS
                       TOM20_plant  87 pdeeeakenfekatqffqqavdedPdndl 115
                                       ++++e    ++++ q fq+a d dPd+  
  gi|330506663|ref|YP_004383091.1| 160 SNTTELDGIYDQSLQAFQRALDLDPDDAE 188
                                       56778888899**************9754 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHH CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWcignaytsfafltpdeee 91 
                                       ++a+  l+ al i+P   dal + ++a t  +++ + e  
  gi|330506663|ref|YP_004383091.1| 238 EEALFALDRALSIQPDNLDALSIKAEALTVLGRYQEAEAA 277
                                       689999***********************99999765443 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.23   1.4e+02       8      49 ..      77     122 ..      71     131 .. 0.73
   2 !    9.4   0.4    0.0022       1.3       6      44 ..     171     209 ..     169     223 .. 0.88
   3 ?    5.2   0.1     0.046        27       4      45 ..     203     244 ..     201     248 .. 0.89
   4 !    8.1   0.8    0.0057       3.4       8      53 ..     241     286 ..     236     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.23
                            TPR_20   8 laeleaalaanpddldarldlAl....allaagryeeAleqLleil 49 
                                       l+  ++a+a++p d++a l+  +    +l++ gr +eA++ L + +
  gi|330506663|ref|YP_004383091.1|  77 LQIYDQAIATRPGDINATLNATNkkilLLVKLGRFDEAISTLDSTI 122
                                       566789999*****99999987522215667788888888776655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0022
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                       ++l+++++al  +pdd +a    Ala+   ++++eAl++
  gi|330506663|ref|YP_004383091.1| 171 QSLQAFQRALDLDPDDAEAWRGRALAYSGLKDHDEALKA 209
                                       6899********************************986 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.046
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleqL 45 
                                       +++ l++ ++a++ +p   +a ld   +ll+ gr eeAl +L
  gi|330506663|ref|YP_004383091.1| 203 HDEALKASDKAVEIDPGYGQAWLDRGILLLEMGRTEEALFAL 244
                                       5677889999****************************9766 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0057
                            TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                                       l +l++al  +pd+lda    A+al   gry+eA +++++ +  d+
  gi|330506663|ref|YP_004383091.1| 241 LFALDRALSIQPDNLDALSIKAEALTVLGRYQEAEAAFYQAMDMDS 286
                                       5689999***************************999988887665 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   5.4e-05     0.032     119     180 ..      66     132 ..      50     137 .. 0.83
   2 ?    0.6   0.1      0.78   4.7e+02     129     179 ..     172     223 ..     160     228 .. 0.61
   3 ?    1.9   0.1       0.3   1.8e+02     129     177 ..     206     255 ..     194     264 .. 0.69
   4 ?    0.3   0.1      0.97   5.8e+02     150     170 ..     262     282 ..     256     291 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-05
                           Wzy_C_2 119 lplspenlaaklalarklihlsPep.....avierlilslallGdedeAeqilararalfpeedakw 180
                                       +++  e  ++ l+ + ++i++ P+        +++ il+l+ lG+ deA  +l+  ++ +pe+ ++w
  gi|330506663|ref|YP_004383091.1|  66 FSQANESFEKALQIYDQAIATRPGDinatlNATNKKILLLVKLGRFDEAISTLDSTIKSYPENLKAW 132
                                       566777888899999999999997533222467899******************************* PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.78
                           Wzy_C_2 129 klalarklihlsPepavi.erlilslallGdedeAeqilararalfpeedak 179
                                        l++ ++++ l P  a   +  +l++ +l d+deA++  ++a  + p + ++
  gi|330506663|ref|YP_004383091.1| 172 SLQAFQRALDLDPDDAEAwRGRALAYSGLKDHDEALKASDKAVEIDPGYGQA 223
                                       4555555555555544331345777778888888887777776665555555 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.3
                           Wzy_C_2 129 klalarklihlsPe..pavierlilslallGdedeAeqilararalfpeed 177
                                        l+++ k+++  P+  +a + r il+l + G+++eA++ l+ra  + p++ 
  gi|330506663|ref|YP_004383091.1| 206 ALKASDKAVEIDPGygQAWLDRGILLLEM-GRTEEALFALDRALSIQPDNL 255
                                       55556666666664224556666666655.999999999999988777765 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.97
                           Wzy_C_2 150 ilslallGdedeAeqilarar 170
                                       +++l +lG+ +eAe    +a+
  gi|330506663|ref|YP_004383091.1| 262 AEALTVLGRYQEAEAAFYQAM 282
                                       78999********98877765 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.18   1.1e+02      10      24 ..     104     118 ..     102     120 .. 0.81
   2 ?    0.5   0.2       2.3   1.4e+03      16      23 ..     183     190 ..     183     193 .. 0.86
   3 ?    0.7   0.9         2   1.2e+03       2      21 ..     188     207 ..     187     208 .. 0.83
   4 !    8.1   0.7    0.0078       4.6       2      21 ..     222     241 ..     221     246 .. 0.88
   5 !    8.8   0.2    0.0047       2.8       3      23 ..     257     277 ..     255     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.18
                             TPR_4  10 allalGdldeArall 24 
                                       +l  lG++deA  +l
  gi|330506663|ref|YP_004383091.1| 104 LLVKLGRFDEAISTL 118
                                       67889******7776 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.3
                             TPR_4  16 dldeAral 23 
                                       d+d+A+a+
  gi|330506663|ref|YP_004383091.1| 183 DPDDAEAW 190
                                       89*****9 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 2
                             TPR_4   2 rallaLArallalGdldeAr 21 
                                        a  ++A a+  l d+deA+
  gi|330506663|ref|YP_004383091.1| 188 EAWRGRALAYSGLKDHDEAL 207
                                       57788999999999999996 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0078
                             TPR_4   2 rallaLArallalGdldeAr 21 
                                       +a l+++ +ll+ G+ +eA+
  gi|330506663|ref|YP_004383091.1| 222 QAWLDRGILLLEMGRTEEAL 241
                                       6899***************8 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0047
                             TPR_4   3 allaLArallalGdldeAral 23 
                                       al+  A+al  lG++ eA+a+
  gi|330506663|ref|YP_004383091.1| 257 ALSIKAEALTVLGRYQEAEAA 277
                                       67888**************96 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.19   1.2e+02     154     181 ..      65      92 ..      41     128 .. 0.66
   2 ?   11.5   7.1   0.00021      0.12     158     274 ..     165     281 ..      67     285 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.19
                            TPR_15 154 elyrqegqtdaAlrdyreAlalapdsse 181
                                       ++ +++   ++Al++y +A+a  p++ +
  gi|330506663|ref|YP_004383091.1|  65 SFSQANESFEKALQIYDQAIATRPGDIN 92 
                                       4555666667888888888888888643 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00021
                            TPR_15 158 qegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasL...wgplaaAlllLgrpk 231
                                         g  d++l+++++Al+l+pd++e+  +   ++  l+  +e   +lka  ++ e d+ +   w+  +  ll +gr++
  gi|330506663|ref|YP_004383091.1| 165 LDGIYDQSLQAFQRALDLDPDDAEAWRGRALAYSGLKDHDE---ALKASDKAVEIDPGYgqaWLDRGILLLEMGRTE 238
                                       4567799********************999999999*9997...8888888877777651115555889999***** PP

                            TPR_15 232 kALeylrkqakenrkdplwllaYADaleqagradeAwrlRrqv 274
                                       +AL  l + ++ ++++   l   A+al   gr +eA++  +q+
  gi|330506663|ref|YP_004383091.1| 239 EALFALDRALSIQPDNLDALSIKAEALTVLGRYQEAEAAFYQA 281
                                       ************************************9877776 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.095        57      55      97 ..      74     118 ..      69     133 .. 0.74
   2 ?    8.0   0.3    0.0053       3.2      48     108 ..     231     289 ..     220     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.095
                             TPR_5  55 eealaLLraeleapsdelddalaaf..laLvLsdlgrereavsiv 97 
                                       e+al++ ++ +++++ ++++ l+a+    L L++lgr  ea+s++
  gi|330506663|ref|YP_004383091.1|  74 EKALQIYDQAIATRPGDINATLNATnkKILLLVKLGRFDEAISTL 118
                                       677777777777777888888888722468899999999999875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0053
                             TPR_5  48 LRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgrereavsivllalaehlprY 108
                                       L  +G++eeal  L+  l+ ++d+ld+ l ++ a +L+ lgr +ea +   +a+     rY
  gi|330506663|ref|YP_004383091.1| 231 LLEMGRTEEALFALDRALSIQPDNLDA-L-SIKAEALTVLGRYQEAEAAFYQAMDMDSERY 289
                                       5679********************975.5.4677788889999999888888887777777 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0029       1.8      13      33 ..      62      82 ..      60      84 .. 0.89
   2 ?   -1.6   0.0       3.3     2e+03      16      22 ..     110     116 ..     109     122 .. 0.79
   3 ?    1.7   0.1       0.3   1.8e+02      17      30 ..     169     182 ..     166     182 .. 0.93
   4 ?   -2.1   0.0       4.6   2.7e+03      19      31 ..     239     251 ..     232     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0029
                          SHNi-TPR 13 EnenFpqAveDlrkaLeLreq 33
                                      + + F+qA e ++kaL+++ q
  gi|330506663|ref|YP_004383091.1| 62 WKGSFSQANESFEKALQIYDQ 82
                                      6677**************987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.3
                          SHNi-TPR  16 nFpqAve 22 
                                       +F++A++
  gi|330506663|ref|YP_004383091.1| 110 RFDEAIS 116
                                       9****97 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.3
                          SHNi-TPR  17 FpqAveDlrkaLeL 30 
                                       ++q ++ +++aL+L
  gi|330506663|ref|YP_004383091.1| 169 YDQSLQAFQRALDL 182
                                       89**********98 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 4.6
                          SHNi-TPR  19 qAveDlrkaLeLr 31 
                                       +A+  l++aL ++
  gi|330506663|ref|YP_004383091.1| 239 EALFALDRALSIQ 251
                                       56666899**998 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00011     0.063      13      83 ..      37     120 ..      29     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                      Helicase_C_2  13 lvffpSyklleevverlkeeleskkie.ifveekeesrekvleeyke.......k......kkkgaillavcrGkls 75 
                                       l+   S +++ee ++++ +e+ ++ ++  f +  +es+ek l+ y +       +        +++ill v  G++ 
  gi|330506663|ref|YP_004383091.1|  37 LCISASASTMEEDADHWIKEGYKQMWKgSFSQ-ANESFEKALQIYDQaiatrpgDinatlnATNKKILLLVKLGRFD 112
                                       677899**************976666526666.9*************887766515567779999************ PP

                      Helicase_C_2  76 EGidfsdd 83 
                                       E i   d 
  gi|330506663|ref|YP_004383091.1| 113 EAISTLDS 120
                                       *9976665 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.73   4.4e+02      19      69 ..      74     123 ..      59     129 .. 0.67
   2 ?    8.8   0.0    0.0027       1.6      36      78 ..     191     258 ..     162     274 .. 0.72
   3 ?   -1.3   0.0         4   2.4e+03      54      70 ..     268     284 ..     257     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.73
                            ANAPC5  19 dsLhryFDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleeair 69 
                                       ++  +++D ++ ++    + +++ a  +   l  ++g  +eA+++l  +i+
  gi|330506663|ref|YP_004383091.1|  74 EKALQIYDQAIATRPGDINATLN-ATNKKILLLVKLGRFDEAISTLDSTIK 123
                                       55555555555555555444443.334556677889999999999998887 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0027
                            ANAPC5  36 q.........................kksyqyalLnlaslhadfghneeAvkaleeairlArenkDks 78 
                                       +                            y  a L   +l  ++g  eeA+ al  a ++  +n D  
  gi|330506663|ref|YP_004383091.1| 191 RgralaysglkdhdealkasdkaveiDPGYGQAWLDRGILLLEMGRTEEALFALDRALSIQPDNLDAL 258
                                       35555566666666666666666666778999*************************99988887765 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4
                            ANAPC5  54 fghneeAvkaleeairl 70 
                                       +g ++eA +a+  a  +
  gi|330506663|ref|YP_004383091.1| 268 LGRYQEAEAAFYQAMDM 284
                                       68889999998888765 PP

>> DUF4810  Domain of unknown function (DUF4810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.045        27      53      77 ..     103     127 ..      52     130 .. 0.68
   2 ?    4.3   0.0     0.096        57      35      68 ..     208     244 ..     197     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.045
                           DUF4810  53 llylkegkkeeaieafekEkelfPE 77 
                                       ll++k g+ +eai+ +++  + +PE
  gi|330506663|ref|YP_004383091.1| 103 LLLVKLGRFDEAISTLDSTIKSYPE 127
                                       7999********************9 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.096
                           DUF4810  35 kaeakgkkvpPGl.yA..elGllylkegkkeeaieaf 68 
                                       ka++k  ++ PG+ +A  + G+l+l++g++eea  a+
  gi|330506663|ref|YP_004383091.1| 208 KASDKAVEIDPGYgQAwlDRGILLLEMGRTEEALFAL 244
                                       56677888999984233378************98766 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.058        35     178     230 ..      68     124 ..      44     132 .. 0.68
   2 ?    3.4   0.1     0.071        43     211     253 ..     231     273 ..     221     278 .. 0.82
   3 ?    4.5   0.1     0.032        19     202     237 ..     256     291 ..     252     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.058
                                       H-TTHHHHHHHHHHHH.HHH...S---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                        Coatomer_E 178 vggekiqdAyyifqel.sek...ykstplllngkAvvslllgryeeAeslLkeaLdk 230
                                       ++ e+++ A+ i+++  + +    + t    n k    ++lgr++eA s L +++++
  gi|330506663|ref|YP_004383091.1|  68 QANESFEKALQIYDQAiATRpgdINATLNATNKKILLLVKLGRFDEAISTLDSTIKS 124
                                       445777788888865413332225566667777888888888888888888877765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.071
                                       HHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HH CS
                        Coatomer_E 211 slllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdae 253
                                        l +gr eeA   L  aL  ++ + ++L+    a + lg+ +e
  gi|330506663|ref|YP_004383091.1| 231 LLEMGRTEEALFALDRALSIQPDNLDALSIKAEALTVLGRYQE 273
                                       6889***********************9877666666666555 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHH CS
                        Coatomer_E 202 lllngkAvvslllgryeeAeslLkeaLdkdakdeet 237
                                       + l  kA +   lgry+eAe    +a+d d++ +et
  gi|330506663|ref|YP_004383091.1| 256 DALSIKAEALTVLGRYQEAEAAFYQAMDMDSERYET 291
                                       5566788888899******************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 1890.67
//
Query:       gi|330506664|ref|YP_004383092.1|  [L=184]
Description: hypothetical protein MCON_0415 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1385.86
//
Query:       gi|330506665|ref|YP_004383093.1|  [L=1421]
Description: hypothetical protein MCON_0416 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.2   0.4       0.13   12.0   0.0    2.4  2  AAA_24    AAA domain
      0.025   14.9   0.1       0.13   12.6   0.0    2.3  2  AAA_22    AAA domain
      0.059   13.7   0.2       0.47   10.8   0.2    2.5  1  AAA_16    AAA ATPase domain
       0.07   13.5   1.5       0.59   10.6   0.5    2.9  3  HEAT_2    HEAT repeats
       0.15   12.4   0.0        6.1    7.2   0.0    2.6  2  AAA_19    AAA domain
       0.32   11.4   1.0        8.1    6.9   0.0    3.1  3  AAA       ATPase family associated with various cellular acti


Domain annotation for each model (and alignments):
>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.2e-05      0.13       5      32 ..      65     102 ..      62     158 .. 0.65
   2 ?   -0.0   0.1      0.21   6.1e+02      91     142 ..     957    1012 ..     953    1040 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.2e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..........gpkplfidte 32 
                                       ++i G++giGKT+ +k +          g+++l +d+ 
  gi|330506665|ref|YP_004383093.1|  65 VIILGEPGIGKTHAMKGAkkviegksdeGDRTLWLDLG 102
                                       789***************55555555555555555554 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.21
                            AAA_24   91 kaeskedkgdgkGygelaeefrrllkklqelrk....nvifiahektrkdedpege 142 
                                        k e ++ k   ++y+ +++e++++l  l +  +    n+ ++++ +  +d++   +
  gi|330506665|ref|YP_004383093.1|  957 KNEIIQQKLVKTAYQHAKKEIIQTLMSLIDDENqkfgNIFITSRIEDCWDDQLSAS 1012
                                        4344466677778**********999976655557999999999988888876444 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   4.2e-05      0.13       7     100 ..      64     155 ..      62     189 .. 0.80
   2 ?   -3.5   0.1       3.8   1.1e+04      52     103 ..     460     510 ..     434     533 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.2e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdllrellralglelkaerlsseell. 79 
                                       ++++ Ge+G+GKT+ ++  ++  +          e+++++  +l  s+s ++l r+l+++ +     +++++ +++ 
  gi|330506665|ref|YP_004383093.1|  64 CVIILGEPGIGKTHAMKGAKKVIE------GksdEGDRTLWLDLGRSGSEDKLIRDLFENETFASWQKGDNKLHIFl 134
                                       789*************99888763......12247*************99999999887644322224566666666 PP

                            AAA_22  80 ealeqalraravielliiDEa 100
                                       + l + + + ++i  l+iDE 
  gi|330506665|ref|YP_004383093.1| 135 DNLDEGILRVDTITSLLIDEL 155
                                       888888888888888888885 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.8
                            AAA_22  52 sskdllrellralglelkaerlsseellealeqalrarav.....ielliiDEaqhl 103
                                       ++ dl  ++ r +g   +      + l e+l  +++++ +     ++++ i Ea +l
  gi|330506665|ref|YP_004383093.1| 460 TLLDLDWDIRRMYGKLSH------SNLEEQLKPYISNKTKgeivrRVAISIAEACRL 510
                                       444444444444443222......222233333333333333335566666666666 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   0.2   0.00016      0.47      24      63 ..      62      93 ..      54     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                            AAA_16 24 pelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                       ++v++ Ge+G+GK+  ++ +++        +++gk d+ 
  gi|330506665|ref|YP_004383093.1| 62 FPCVIILGEPGIGKTHAMKGAKK--------VIEGKSDEG 93
                                      48**************9988887........455555554 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5    0.0002      0.59       4      77 ..     484     560 ..     481     566 .. 0.76
   2 ?   -0.6   0.0      0.61   1.8e+03      20      45 ..     965     990 ..     955     992 .. 0.66
   3 ?   -3.5   0.0       4.9   1.5e+04      21      40 ..    1160    1179 ..    1155    1183 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                            HEAT_2   4 LlqalendpdpevrraairaLg.rignpealpaLvell..ededpavRraaaeaLgaigdpealpaLkelldddddd 77 
                                       L  +++n    e+ r+++++++  ++ + +++aL +++  +++ +++R+ aa+aL  +gd+e+ + L+ l++ d  d
  gi|330506665|ref|YP_004383093.1| 484 LKPYISNKTKGEIVRRVAISIAeACRLQPLQDALANIAldQTQLMHIRAIAAHALCVVGDNETKAKLRPLATGDAGD 560
                                       556666666666555555555526788999******774445559*************************9998655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.61
                            HEAT_2  20 airaLgrignpealpaLvellededp 45 
                                        +++  + + +e++++L +l++de+ 
  gi|330506665|ref|YP_004383093.1| 965 LVKTAYQHAKKEIIQTLMSLIDDENQ 990
                                       44444466777888888888888875 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.9
                            HEAT_2   21 iraLgrignpealpaLvell 40  
                                        +  L ++g++ea +a+ +++
  gi|330506665|ref|YP_004383093.1| 1160 LNRLKQKGTQEACDAIKRIA 1179
                                        55566666666666665554 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     0.002       6.1      11      35 ..      63      87 ..      55     104 .. 0.82
   2 ?    2.0   0.0     0.079   2.4e+02      88     138 ..     485     544 ..     343     548 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.002
                            AAA_19 11 kvllvtaGpGtGKTrvlkhivallv 35
                                      +++++++ pG GKT+ +k++ ++++
  gi|330506665|ref|YP_004383093.1| 63 PCVIILGEPGIGKTHAMKGAKKVIE 87
                                      6899***********9998877655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.079
                            AAA_19  88 lelleeaeeekklqeeellivDEfqdvdelqyrLlkallgekkk...........lllvGDp 138
                                         ++ + +++ ++ ++ ++ + E+  +++lq +L +  l ++++           l++vGD+
  gi|330506665|ref|YP_004383093.1| 485 KPYISN-KTKGEIVRRVAISIAEACRLQPLQDALANIAL-DQTQlmhiraiaahaLCVVGDN 544
                                       333333.44445547778888888888888888877766.3333355777777779999997 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0027       8.1       1      73 [.      65     143 ..      65     181 .. 0.65
   2 ?   -4.0   0.1         6   1.8e+04      50      96 ..     421     459 ..     418     462 .. 0.66
   3 ?    1.6   0.1      0.12   3.6e+02      75     116 ..     967    1006 ..     956    1021 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0027
                                       EEEESSTTSSHHHHHHHHHHHH......THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.....TSEEEEEET CS
                               AAA   1 vllyGppGtGKTllakavakel......gvefleisgsellskyvgesekkirelfkeakeka.....kpsilfiDE 66 
                                       v++ G pG+GKT ++k   k +      g + l +++        g   k ir+lf++    +     ++  +f+D+
  gi|330506665|ref|YP_004383093.1|  65 VIILGEPGIGKTHAMKGAKKVIegksdeGDRTLWLDLG-----RSGSEDKLIRDLFENETFASwqkgdNKLHIFLDN 136
                                       6789*********9998877763322222333333333.....4457778888888874333356665567788888 PP

                                       GGGHHHH CS
                               AAA  67 idalaks 73 
                                       +d+ + +
  gi|330506665|ref|YP_004383093.1| 137 LDEGILR 143
                                       8876554 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 6
                                       HHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHT CS
                               AAA  50 fkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgv 96 
                                       fk++     p il+  E++ + +s+       + ++vn Ll++ +++
  gi|330506665|ref|YP_004383093.1| 421 FKRIMDVD-PEILLRSELEIMKESD-------RASLVNSLLRKYEEE 459
                                       56655554.6777777777664444.......888888888877765 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.12
                                        TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS.GGGST CS
                               AAA   75 sgseseeeervvnqLlteldgvkkkeskvivigatnr.pdkld 116 
                                        +++ +  +++++++L++ +d++++   k+  i +t r +d  d
  gi|330506665|ref|YP_004383093.1|  967 KTAYQHAKKEIIQTLMSLIDDENQ---KFGNIFITSRiEDCWD 1006
                                        4457788999************99...5777888887444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); 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:                         6  (0.000334653); expected 0.2 (1e-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 0.28s 00:00:01.20 Elapsed: 00:00:00.47
# Mc/sec: 9126.57
//
Query:       gi|330506666|ref|YP_004383094.1|  [L=139]
Description: pyridoxamine 5'-phosphate oxidase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-07   30.4   0.0    4.3e-07   30.0   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
       0.04   13.7   0.0       0.11   12.3   0.0    1.6  2  DUF447          Protein of unknown function (DUF447)


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 !   30.0   0.0   4.8e-11   4.3e-07       9      77 ..      10      81 ..       1      89 [. 0.82

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.8e-11
                                      HHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT....GSEEEEE CS
                    Putative_PNPOx  9 laeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde....lgrgvri 77
                                       ++++++ l+T+++dG ++v +++     ++ + ++a  a+ r+++nl+enp++  ++++ +    + +g+r+
  gi|330506666|ref|YP_004383094.1| 10 NRQPRLGILGTASKDGIVDVAVMGSLQMIDE-KTITAAFARGRTFANLQENPNAVYMIMNQGseilDWKGIRV 81
                                      34789*******************9988888.7888889999*************999999977775555555 PP

>> DUF447  Protein of unknown function (DUF447)
   #    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       4      52 ..      17      67 ..      16      75 .. 0.89
   2 ?   -1.3   0.0      0.18   1.6e+03     151     174 ..      94     117 ..      83     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                                      EEEEE-TT.-EEEEEEEEEE.SSSEEEEEEETTSHHHHHHHHHSEEEEEE- CS
                            DUF447  4 ivtTksek.rpnaaPiGviv.kgdkvvlrlfkgsrTleNllengelvinvt 52
                                      i++T s++    +a +G  +  ++k + + f + rT++Nl+en+++v  ++
  gi|330506666|ref|YP_004383094.1| 17 ILGTASKDgIVDVAVMGSLQmIDEKTITAAFARGRTFANLQENPNAVYMIM 67
                                      789999999999*****9987888899999***************998765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHH--HHHHHHHHHH CS
                            DUF447 151 eieylssvikktggerekealell 174
                                       ++e ++s + k+ ge+  e+++ +
  gi|330506666|ref|YP_004383094.1|  94 QLESYKSQVAKVVGEQAAEMVHVM 117
                                       678899999999999988888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1043.92
//
Query:       gi|330506667|ref|YP_004383095.1|  [L=673]
Description: DNA polymerase B [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.6e-20   70.9   0.2    6.1e-10   38.4   0.0    3.1  3  DNA_pol_B  DNA polymerase family B


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   3.4e-14   6.1e-10      23      87 ..     312     381 ..     302     384 .. 0.79
   2 !   15.8   0.0   2.4e-07    0.0042     117     205 ..     382     465 ..     379     475 .. 0.84
   3 !   13.9   0.0   9.3e-07     0.017     288     413 ..     524     639 ..     517     663 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 3.4e-14
                                       HHHTTBE-B-----.--SS......-.S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE-H CS
                         DNA_pol_B  23 akeegfilpdrtekkgkeee.....g.YqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlvas 87 
                                       a ++g+++p r+++ +++++     +   G++ ++P+ g+y+ +v  +DF SLYPsii+++Nl+++ l++ 
  gi|330506667|ref|YP_004383095.1| 312 ALRRGMVVPFRKSDVESARKitdlkAcDRGGMMFQPDPGVYE-QVHQIDFTSLYPSIIVKYNLSPESLDHP 381
                                       56778888865555444444666764489************8.5999********************9876 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.4e-07
                                       S---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHH CS
                         DNA_pol_B 117 vregllpklLkdllakRkaikkelkeekdefekalldkqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRem 193
                                       + +g l++++++ll+ R + k++ k  +++ e + +     +lK +  + +G+tG++n ++  +++ + +T+i Re 
  gi|330506667|ref|YP_004383095.1| 382 EVKGFLATVITSLLNLRIETKRRKK--TNP-EYRGI---DSVLKWMLVTCFGYTGYRNAKFGQIQVHERITAISREL 452
                                       5689****************99744..333.33444...56899999999*************************** PP

                                       HHHHHHHHHHT.. CS
                         DNA_pol_B 194 Lektkelvekk.a 205
                                       L+ +kel e++  
  gi|330506667|ref|YP_004383095.1| 453 LMDIKELAEDMdF 465
                                       *******998843 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 9.3e-07
                                       EEEESSTTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG- CS
                         DNA_pol_B 288 kvektskanklliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvleeleenkvplekfv 364
                                         +     +++ ++Gv   R d  ++ +++  ++ ell  + +++++l  + +  +++  +  ++l++ +v ++++ 
  gi|330506667|ref|YP_004383095.1| 524 LDK-----GRMKVRGVAARRGDTPRYLQRMQMDLFELLAGA-ANREELRLCKPRAEEVRRRYERDLMDARVAVRELA 594
                                       444.....789************************999988.889999999999999999999************** PP

                                       EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS CS
                         DNA_pol_B 365 lskelskepenyksknlphlevakrlkkrneeapevgdrisYvivekkk 413
                                       + ++ls++  ny+ +  +++++++ lk   ++ p +g ++ Yv+  + +
  gi|330506667|ref|YP_004383095.1| 595 VRRRLSRT--NYSRR-CAEASAVQALKIA-GRHPAPGMVVGYVVADAGR 639
                                       *******4..77544.4666666666555.5779999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (673 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 4740.91
//
Query:       gi|330506668|ref|YP_004383096.1|  [L=138]
Description: response regulator receiver domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   0.1    5.3e-30  103.9   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 !  103.9   0.1   2.9e-34   5.3e-30       1     111 [.       9     119 ..       9     120 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 2.9e-34
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT.TTSEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed.pelpvii 76 
                                       +li++D+p+++++ + +l++ g  +++ a++g+e+l+ l+++++dl+l+Di+mp+mdG+e++k+ir +  + +++i+
  gi|330506668|ref|YP_004383096.1|   9 ILIAEDNPVNQKVAQLMLQRLGH-RTDLAANGQEVLRALENQSCDLVLMDIQMPKMDGIEATKHIRSRWqQGPKIIA 84 
                                       8**********************.*****************************************999867899*** PP

                                       EESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  77 ltahseeedavealkagaddflsKpfdpeeLlkal 111
                                       +t+ + e  ++++++ag+ddf+ Kp++++eL +a+
  gi|330506668|ref|YP_004383096.1|  85 ITSFDPEFCREQCFSAGVDDFINKPIRMNELDAAI 119
                                       *******************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1059.90
//
Query:       gi|330506669|ref|YP_004383097.1|  [L=145]
Description: hypothetical protein MCON_0420 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-10   40.6   0.1    4.2e-10   39.9   0.1    1.3  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 !   39.9   0.1   2.3e-14   4.2e-10       2      75 ..       4      84 ..       3      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.3e-14
                   Acylphosphatase  2 rllvtG.rVQgvgFRkfvrrlAkelglkGyvrNlsdg.....sVeivaegeeekvekfleelksgppk.arvdevevee 73
                                      ++++ G +V+gvg+R+f++++A+ +g++G++ +++ g     +V + +eg++  +++f ++ +++ p  a+v++v +++
  gi|330506669|ref|YP_004383097.1|  4 KIEIIGpKVHGVGYRYFLMNQAMFMGVNGFAAQNQLGkngqqEVWVIIEGSKGPLDAFSTFAQTKRPDdAEVSDVIIKD 82
                                      5788899***********************8777665566889*********************88888******9987 PP

                   Acylphosphatase 74 le 75
                                       e
  gi|330506669|ref|YP_004383097.1| 83 FE 84
                                      65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1105.03
//
Query:       gi|330506670|ref|YP_004383098.1|  [L=257]
Description: exodeoxyribonuclease III [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-25   88.4   0.0    5.6e-25   88.2   0.0    1.0  1  Exo_endo_phos    Endonuclease/Exonuclease/phosphatase family
     0.0079   16.0   0.0      0.053   13.4   0.0    2.0  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 !   88.2   0.0   6.3e-29   5.6e-25       1     233 []       7     248 ..       7     248 .. 0.91

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 6.3e-29
                                       EEEEESTG.CHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHHTTCEEEEECCHECSSSTTSSEEE CS
                                       xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos   1 ltwNvngq.aspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllalggflgasstsptgggggggngga 76 
                                       l+wNvng  a +       ++   d+l + ++Dvl+LQE++  e +++++l  l g+  ++s     g+++g++g+a
  gi|330506670|ref|YP_004383098.1|   7 LSWNVNGLrAIY-------KKGFVDWLLKDRPDVLCLQEIKATEDQIPKELKGLPGYISFFSP----GARKGRDGVA 72 
                                       79*****85555.......677******************************99777777775....99******** PP

                                       EEECSTEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE...CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos  77 vlsrfpltslfrrtfiefndlvaalrreplaakleqlni...ashrdhdlvrdlqllalllqvealnadrgapviva 150
                                       ++ + +  sl++      +d   + +  + +  l+++++        ++l+ ++++++l+l++ +   ++g+ ++++
  gi|330506670|ref|YP_004383098.1|  73 LFTKIKTLSLEYSLGLPGFDDEQRAIVADYGDFLLFDVYfpnGKASKERLSYKMRFYDLFLDLMDRLVAEGRDIVIC 149
                                       *****************************************999999****************************** PP

                                       EE-SSSTSGGGBSCGHHHHHHCTTTH............H...........SSCESCETTTTTTTTTTTEB-BEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx............x...........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos 151 GDfNarpsdddsrvlrtrglalapap............v...........glyllgggptptyvtraggsrlDrila 204
                                       GD N+++ + d  ++ ++ +     p            +           g  + ++   + ++ r+ g+r+D+ ++
  gi|330506670|ref|YP_004383098.1| 150 GDVNTAHKEIDLARPKPNEKISGFLPeerawidrliehGfldtfrlfhpeGEKYSFWDMKTRARERNVGWRIDYFFV 226
                                       **************************8888776665551667778899***************************** PP

                                       ECHHHCCEEEEEEECCHHEEC.......TSSCSSSB CS
                                       xxxxxxxxxxxxxxxxxxxxx.......xxxxxxxx RF
                     Exo_endo_phos 205 spalalfrsgvlppplalvrr.......ealtlSDH 233
                                       s                 ++r       +++++SDH
  gi|330506670|ref|YP_004383098.1| 227 SL--------------GMRDRvksafilDDVYGSDH 248
                                       *7..............6666667777788999**** 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 !   13.4   0.0   5.9e-06     0.053       4     118 ..     108     251 ..     105     252 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.9e-06
                   Exo_endo_phos_2   4 isvYippsd...........elenlestlekllselkspkiiilGDfNakhplWgsedtds...........sarge 58 
                                       + vY p+ +             + +++ +++l+ e +  +i+i+GD+N  h++ +  + +            +a  +
  gi|330506670|ref|YP_004383098.1| 108 FDVYFPNGKaskerlsykmrFYDLFLDLMDRLVAEGR--DIVICGDVNTAHKEIDLARPKPnekisgflpeeRAWID 182
                                       6667766666666666544223334444444554444..9************9988544435567777554433334 PP

                   Exo_endo_phos_2  59 eLie..fleehslsllnllksgptfkssng.......sstiDltltsdnlals..kleleeedlgSDHrpi 118
                                        Lie  fl+++ l   ++  ++  f++ ++          iD +++s  ++++  +  + ++ +gSDH p+
  gi|330506670|ref|YP_004383098.1| 183 RLIEhgFLDTFRLF--HPEGEKYSFWDMKTrarernvGWRIDYFFVSLGMRDRvkSAFILDDVYGSDHCPV 251
                                       55432255555555..6666667777777667765556779999999888888777788889999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1806.46
//
Query:       gi|330506671|ref|YP_004383099.1|  [L=981]
Description: hypothetical protein MCON_0424 [Methanosaeta concilii GP6]
Scores for complete 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-52  177.0   0.0    7.3e-52  176.6   0.0    1.1  1  DUF1616          Protein of unknown function (DUF1616)
    1.6e-10   40.8   0.0     0.0012   18.8   0.0    4.2  4  Y_Y_Y            Y_Y_Y domain
    5.1e-07   29.4   1.5        1.2    9.0   0.1    4.7  4  PKD              PKD domain
    6.1e-06   26.9   5.3      0.051   14.3   0.1    4.9  5  Big_7            Bacterial Ig domain
    6.1e-06   26.5   0.1        5.1    7.6   0.0    4.7  5  DUF4399          Domain of unknown function (DUF4399)
       0.01   15.9   2.1       0.62   10.2   0.1    3.8  4  BiPBP_C          Penicillin-Binding Protein C-terminus Family
  ------ inclusion threshold ------
        4.2    7.1  11.0         24    4.7  11.0    2.0  1  DUF2157          Predicted membrane protein (DUF2157)


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 !  176.6   0.0   2.9e-55   7.3e-52       4     293 .]      14     296 ..      11     296 .. 0.93

  Alignments for each domain:
  == domain 1  score: 176.6 bits;  conditional E-value: 2.9e-55
                           DUF1616   4 lalllllailvpvlnetplRiv...lglplvLflPGYaliaaLFPekrdidgieRlaLSfglSiaivpliglvlnvt 77 
                                        +l++l ai++++l   pl+ +   l+l+lv+++PGY  +  LFP+ +d+d  +R++LS+g+S+ ++ li+l+l +t
  gi|330506671|ref|YP_004383099.1|  14 SILISLSAIALANLFAPPLKEAgsyLALALVILIPGYLAVLSLFPAAGDLDLNRRFLLSLGASLLLAGLISLILYLT 90 
                                       5678888999999999999987777**************************************************** PP

                           DUF1616  78 pwgirlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleek.sesrldkalnvlLvvsivlav 153
                                       p g+++++++++ls+++l+la+++++r+s++p+++rf +  ++ ++s +++ + +     ++ +l ++L++ +vla+
  gi|330506671|ref|YP_004383099.1|  91 PRGLQAASLATILSFLVLFLAALSYLRWSAIPRNRRFVIGAKRSYRSRRTSGRISsGFVSSRGPLLIALAAVLVLAG 167
                                       ***************************************999998888888877656667899************** PP

                           DUF1616 154 aalgyavva.....PkegekfTelyllgedgd.elvaenypteltagesqevivgieNhEheevnYtvvvllqevtd 224
                                        al++++++      ++ +++T+l++++++++ ++ +e+  t+l+ag++ e    i+NhE+ +vnY++++++++   
  gi|330506671|ref|YP_004383099.1| 168 LALAFYHYQpgmnfLSSPKGHTDLEVTWPKSElGDSSEGQYTTLAAGRDLEARARIDNHEGIPVNYSLRLAFDN--- 241
                                       *********4444435689*****************************************************96... PP

                           DUF1616 225 eeevevlerteldrrevtladnetweqelevepeatgenlrleflLYkdevpeeptteeayrslhlwVn 293
                                                +++  + ++ladnetwe++l + +e + +++rl++lL+k+      +++++++s hl V+
  gi|330506671|ref|YP_004383099.1| 242 ---------STIFVKGLRLADNETWESMLGFVLEGQPGQQRLDLLLFKE-----GDSTAPCKSEHLLVD 296
                                       .........68999***********************************.....************996 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 !   18.8   0.0   4.6e-07    0.0012       4      57 ..     544     596 ..     542     604 .. 0.84
   2 ?   -1.3   0.0      0.85   2.2e+03       7      22 ..     646     662 ..     643     694 .. 0.68
   3 ?    2.4   0.0     0.059   1.5e+02       5      50 ..     783     827 ..     781     835 .. 0.81
   4 !   13.5   0.1     2e-05     0.052       8      52 ..     885     928 ..     881     938 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.6e-07
                                       CCTTEEEEEEEETTE.SSEEEESSTS.EEEEES--SEEEEEEEEEEETTS-B-SS CS
                             Y_Y_Y   4 nperllYrYrlegid.keWveasdysqeasytnlppGdYtlkVkakdndgqwnyd 57 
                                       +++r+lYr+ l g + k+W+ +++   ++    lp+G+Y+++V+a+d + + ++ 
  gi|330506671|ref|YP_004383099.1| 544 DGDRILYRFLLNGEEmKNWSRSGSW--SFLTHYLPAGEYVITVQAMDGLHSPSDS 596
                                       589******9988888888888888..79999***************88776665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.85
                                       TEEEEEEEETTE.SSEE CS
                             Y_Y_Y   7 rllYrYrlegid.keWv 22 
                                        ++Yr+ l+g d   W+
  gi|330506671|ref|YP_004383099.1| 646 EISYRFLLDGQDmTGWM 662
                                       57888877777755565 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.059
                                       CTTEEEEEEEETTE.SSEEEESSTS.EEEEES--SEEEEEEEEEEET CS
                             Y_Y_Y   5 perllYrYrlegid.keWveasdysqeasytnlppGdYtlkVkakdn 50 
                                       ++ l+Y++ l+g d   W+++s+   +   +  ppG+ +++V a+d 
  gi|330506671|ref|YP_004383099.1| 783 GDELSYKFLLDGQDmTGWSSSSSW--TWDTSDAPPGTHRITVLARDG 827
                                       678999998888887777777777..788899999999999999985 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 2e-05
                                       EEEEEEEETTE.SSEEEESSTS.EEEEES--SEEEEEEEEEEETTS CS
                             Y_Y_Y   8 llYrYrlegid.keWveasdysqeasytnlppGdYtlkVkakdndg 52 
                                       +lY+++l g+d   W+e+++   + s + l++GdY+++V ++d   
  gi|330506671|ref|YP_004383099.1| 885 ILYKFQLGGKDmIRWSESNSW--SWSTRGLSAGDYQITVLVRDGRH 928
                                       89*****99995566666666..8*****************99655 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00064       1.6      21      66 ..     543     590 ..     536     594 .. 0.74
   2 ?    1.5   0.1       0.1   2.6e+02       9      59 ..     628     682 ..     623     693 .. 0.65
   3 !    9.0   0.1   0.00046       1.2      15      65 ..     773     827 ..     763     830 .. 0.76
   4 !    5.0   0.0    0.0085        22      19      66 ..     876     927 ..     862     932 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00064
                                       .-SS-SEEEEE--SS..--EEEEETTEEEEEE-SSEEEEEEEEEE-SS CS
                               PKD  21 pdganvtysWdfgdg..svvqvlseptvthtYlspGeYeVtvtasnav 66 
                                       pdg+++ y++ ++ +   +   + + ++  +Yl +GeY++tv a + +
  gi|330506671|ref|YP_004383099.1| 543 PDGDRILYRFLLNGEemKNWSRSGSWSFLTHYLPAGEYVITVQAMDGL 590
                                       7777788887777776444444445567889*************9976 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.1
                                       BSSEEEEEEEES...-SS-SEEEEE--SS.......--EEEEETTEEEEEE-SSEEEEEE CS
                               PKD   9 vpgatvaftaav..pdganvtysWdfgdg.......svvqvlseptvthtYlspGeYeVt 59 
                                       ++g  ++ ta+   pd ++++y++ ++ +       s+ +v+ ++ v+     +G++ +t
  gi|330506671|ref|YP_004383099.1| 628 PQGSLITWTASAadPDLDEISYRFLLDGQdmtgwmpSNSWVWNSSGVM-----AGDHKIT 682
                                       5566666677777799*******9988876555555444444444443.....5555555 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00046
                                       EEEEES...-SS-SEEEEE--SS--EEEEETTEEEEEE-S..SEEEEEEEEEE-S CS
                               PKD  15 aftaav..pdganvtysWdfgdgsvvqvlseptvthtYls..pGeYeVtvtasna 65 
                                       + ta+   pdg++++y + ++ ++ ++ +s+++ t   +   pG++ +tv+a + 
  gi|330506671|ref|YP_004383099.1| 773 NWTARAadPDGDELSYKFLLDGQDMTGWSSSSSWTWDTSDapPGTHRITVLARDG 827
                                       55677777*********9999986666666666555555569*********9886 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.0085
                                       ES...-SS-SEEEEE--SS--EEEEETTEEEEEE-S....SEEEEEEEEEE-SS CS
                               PKD  19 av..pdganvtysWdfgdgsvvqvlseptvthtYls....pGeYeVtvtasnav 66 
                                           pd +++ y +++g       +se++ + ++++    +G+Y++tv++ + +
  gi|330506671|ref|YP_004383099.1| 876 EAmdPDNDPILYKFQLGG-KDMIRWSESN-SWSWSTrglsAGDYQITVLVRDGR 927
                                       444577777777777777.4444444444.3344444555**********9986 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3       6.9   1.8e+04      31      58 ..     344     369 ..     323     378 .. 0.51
   2 ?    0.3   0.0      0.48   1.2e+03      36      70 .]     552     584 ..     538     584 .. 0.74
   3 ?    4.0   0.0     0.034        86      19      70 .]     633     683 ..     625     683 .. 0.74
   4 !   14.3   0.1     2e-05     0.051      33      70 .]     787     822 ..     760     822 .. 0.80
   5 !    6.3   0.0    0.0064        16      52      70 .]     903     921 ..     888     921 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.9
                                       EEEEEEEETTEE.EEEE-SSSEEEEEE- CS
                             Big_7  31 vskVefyvdgtlglgtdtsapysltwtt 58 
                                       v++V  ++  ++  ++ +s p s++  t
  gi|330506671|ref|YP_004383099.1| 344 VAQVSGSAASSS--SSAKSKPQSAATET 369
                                       333333333333..34444555555555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.48
                                       EEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  36 fyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                       f ++g++ + +  s   s+++ t  l+ag++ +tV
  gi|330506671|ref|YP_004383099.1| 552 FLLNGEE-MKNW-SRSGSWSFLTHYLPAGEYVITV 584
                                       5566666.5554.334455566666*********9 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.034
                                       EEEEEEEE-S..S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  19 vtisasAsdd..ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                       +t +asA d+  +++s   f +dg+  ++       s+ w+ + + ag h++tV
  gi|330506671|ref|YP_004383099.1| 633 ITWTASAADPdlDEISY-RFLLDGQD-MTGW-MPSNSWVWNSSGVMAGDHKITV 683
                                       67778888884444432.67899999.6444.5677999***99*********9 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 2e-05
                                       EEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  33 kVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                       + +f +dg+  ++   s+  s+tw+t++++ gth +tV
  gi|330506671|ref|YP_004383099.1| 787 SYKFLLDGQD-MTGW-SSSSSWTWDTSDAPPGTHRITV 822
                                       5579999999.8666.6799*****************9 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.0064
                                       EEEEEE--...SEEEEEEE CS
                             Big_7  52 ysltwtttaltagthtltV 70 
                                        s++w+t  l+ag +++tV
  gi|330506671|ref|YP_004383099.1| 903 NSWSWSTRGLSAGDYQITV 921
                                       589***************9 PP

>> DUF4399  Domain of unknown function (DUF4399)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         2   5.1e+03      24      39 ..     292     309 ..     265     315 .. 0.65
   2 !    5.6   0.0     0.008        20      58      78 ..     575     595 ..     570     605 .. 0.89
   3 ?    5.0   0.0     0.013        33      60      78 ..     676     694 ..     672     698 .. 0.89
   4 !    7.6   0.0     0.002       5.1      57      78 ..     812     833 ..     804     839 .. 0.88
   5 ?    1.2   0.0      0.18   4.7e+02      58      76 ..     912     930 ..     908     939 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2
                           DUF4399  24 hllvd..eeapeagepip 39 
                                       hllvd  +++ e +e+++
  gi|330506671|ref|YP_004383099.1| 292 HLLVDlvDDQSEDQEEME 309
                                       777777655555555555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.008
                           DUF4399  58 lppGkhtLqlqlgdaahvplk 78 
                                       lp+G++ +++q +d+ h p +
  gi|330506671|ref|YP_004383099.1| 575 LPAGEYVITVQAMDGLHSPSD 595
                                       89***************9987 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.013
                           DUF4399  60 pGkhtLqlqlgdaahvplk 78 
                                       +G+h++++q++d++h + +
  gi|330506671|ref|YP_004383099.1| 676 AGDHKITVQIMDGSHASQN 694
                                       7**************9865 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.002
                           DUF4399  57 elppGkhtLqlqlgdaahvplk 78 
                                       + ppG+h+++++  d++h p +
  gi|330506671|ref|YP_004383099.1| 812 DAPPGTHRITVLARDGKHAPTD 833
                                       679****************987 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.18
                           DUF4399  58 lppGkhtLqlqlgdaahvp 76 
                                       l++G++++++++ d++h +
  gi|330506671|ref|YP_004383099.1| 912 LSAGDYQITVLVRDGRHAS 930
                                       789**************87 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 ?   -0.8   0.0      0.63   1.6e+03      46      82 ..     550     589 ..     538     592 .. 0.83
   2 ?    1.4   0.1      0.13   3.2e+02      44      81 ..     642     687 ..     617     694 .. 0.76
   3 !   10.2   0.1   0.00024      0.62      44      83 ..     783     828 ..     756     832 .. 0.85
   4 ?   -0.5   0.0      0.51   1.3e+03      62      86 ..     903     930 ..     898     934 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.63
                           BiPBP_C  46 lrWlldgeplaetkrgrelawqp...epGrhrLtvvDaaG 82 
                                       +r+ll+ge +++ +r+ ++++       G++ +tv+  +G
  gi|330506671|ref|YP_004383099.1| 550 YRFLLNGEEMKNWSRSGSWSFLThylPAGEYVITVQAMDG 589
                                       6789999999999999998888778899*****9987777 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.13
                           BiPBP_C  44 a.....plrWlldgeplaetkrgrelawqp...epGrhrLtvvDaa 81 
                                       +     ++r+lldg+ ++   +++++ w +     G h++tv+  +
  gi|330506671|ref|YP_004383099.1| 642 PdldeiSYRFLLDGQDMTGWMPSNSWVWNSsgvMAGDHKITVQIMD 687
                                       345667899999**999999999999999999899******96444 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00024
                           BiPBP_C  44 a...plrWlldgeplaetkrgrelawqp...epGrhrLtvvDaaGr 83 
                                       +   ++++lldg+ ++  +++++++w+     pG+hr+tv+  +G+
  gi|330506671|ref|YP_004383099.1| 783 GdelSYKFLLDGQDMTGWSSSSSWTWDTsdaPPGTHRITVLARDGK 828
                                       14569999*******9999*******999999**********9998 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.51
                           BiPBP_C  62 relawqp...epGrhrLtvvDaaGrvdd 86 
                                       ++++w+    + G +++tv+  +Gr ++
  gi|330506671|ref|YP_004383099.1| 903 NSWSWSTrglSAGDYQITVLVRDGRHAS 930
                                       567777777899*******999999776 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  11.0    0.0093        24      35     118 ..      67     176 ..      52     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0093
                           DUF2157  35 leallvlGalllglGlilfvAanWqglsrlvkfllllvllllslllg.avlwrdr...................... 88 
                                       +++ll lGa ll++Gli+++ ++  +  +++ ++ +l+ l+l+l++  ++ w                         
  gi|330506671|ref|YP_004383099.1|  67 RRFLLSLGASLLLAGLISLILYLTPRGLQAASLATILSFLVLFLAALsYLRWSAIprnrrfvigakrsyrsrrtsgr 143
                                       799********************988888999999999998888888777777559999*************99999 PP

                           DUF2157  89 ........rvpprlgeallllaalllgaaialvgqifq 118
                                               r     g +l+ laa+l++a++al+ + +q
  gi|330506671|ref|YP_004383099.1| 144 issgfvssR-----GPLLIALAAVLVLAGLALAFYHYQ 176
                                       998554433.....668888999999999999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (981 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.93u 0.30s 00:00:01.23 Elapsed: 00:00:00.45
# Mc/sec: 6502.90
//
Query:       gi|330506672|ref|YP_004383100.1|  [L=350]
Description: glycosyl transferase, group 1 family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-30  105.2   0.0    3.7e-30  104.7   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
      2e-25   89.8   0.0      4e-25   88.8   0.0    1.5  2  Glyco_trans_1_4  Glycosyl transferases group 1
      2e-13   50.7   4.9    9.9e-12   45.2   4.0    2.5  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.4e-10   41.8   1.6      0.001   19.6   0.0    3.1  3  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.5e-09   38.1   0.0    2.7e-09   37.3   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.033   14.2   0.0    1.9  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   0.0   1.2e-33   3.7e-30      11     170 ..     173     326 ..     170     328 .. 0.94

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 1.2e-33
                                       TTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHH CS
                   Glycos_transf_1  11 knekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredle 87 
                                       k+ekk ++l+ grl ++Kg++ li+a+ +++k  + ++ lv++G+g ++ +l+++a  l +  + +f+g+++r++ +
  gi|330506672|ref|YP_004383100.1| 173 KREKKGYVLYAGRLLHYKGIESLIQAMSEVQK--KADLELVLVGDGYDRSRLEEMARRLDV--RARFTGRLDRSRFI 245
                                       789**************************976..6********************999888..999*********** PP

                                       HHHHCESEEEEEESS..BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHH CS
                   Glycos_transf_1  88 ellknadifvlpsis..EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelr 162
                                         l++a ++vlp ++  E+fGivllEAma+ +pv+a +++g+aev  +g    ++ ++   +l e i +l e+++lr
  gi|330506672|ref|YP_004383100.1| 246 DTLSHAEVLVLPTQNrlEAFGIVLLEAMACETPVLAFKTPGVAEVAGEGG--MIYSSP--GELGEMILELHESPNLR 318
                                       **********************************************9998..666555..99*************** PP

                                       HHHHHHHH CS
                   Glycos_transf_1 163 erlgenar 170
                                        +lg+++r
  gi|330506672|ref|YP_004383100.1| 319 MNLGRKGR 326
                                       ****9997 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 ?   -3.6   0.0       4.9   1.4e+04      66      80 ..     127     141 ..     119     149 .. 0.73
   2 !   88.8   0.0   1.3e-28     4e-25       3     132 ..     179     312 ..     177     314 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.9
                                       HHHHHHH-SEEEE-- CS
                   Glyco_trans_1_4  66 laellaaadvfvaPs 80 
                                       ++++l++a++++ ++
  gi|330506672|ref|YP_004383100.1| 127 IRPILDRAKIVISTT 141
                                       788888888888765 PP

  == domain 2  score: 88.8 bits;  conditional E-value: 1.3e-28
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.HEEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.dvrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaadv 75 
                                        +l+ Grl  ++kg++ l++a+ +++kk d++lv+vGdg  r ++lee+a++l+ r +ftG++  +   + l++a v
  gi|330506672|ref|YP_004383100.1| 179 YVLYAGRL-LHYKGIESLIQAMSEVQKKaDLELVLVGDGYdR-SRLEEMARRLDVRARFTGRLdrSRFIDTLSHAEV 253
                                       589*****.456**************9967*********955.5***999999999*******64459999****** PP

                                       EEE--....---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  76 fvaPs....egfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeailrLl 132
                                       +v+P+    e fg++llEama+++pv a++++g+aev ge g++ +  +p +l e il+L 
  gi|330506672|ref|YP_004383100.1| 254 LVLPTqnrlEAFGIVLLEAMACETPVLAFKTPGVAEVAGEGGMIYS--SPGELGEMILELH 312
                                       *****99888**************************88*9999998..8999999999886 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   4.0   3.3e-15   9.9e-12       2     169 ..      15     168 ..      14     169 .. 0.80
   2 ?   -2.2   0.0       1.2   3.6e+03       3      37 ..     191     225 ..     189     252 .. 0.67

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 3.3e-15
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHa 78 
                                       GGve hv eLa +La+rGh+Vtv ++ ++   +       r+p++       ++  ++  r       + + D+ H+
  gi|330506672|ref|YP_004383100.1|  15 GGVEYHVKELADGLAKRGHQVTVASSCGRWNNGFV-----RIPSID-----LFYVPIPIKR---P---NLEADIYHS 75 
                                       9***********************97766666555.....333333.....3322222221...1...2368***** PP

                    Glyco_transf_4  79 hspaalgaallalrrrlgiplVltvHglye.......krllkarlkplsrllralerrllrradrviavSeatadel 148
                                       h p +l+a +l  r     p+V+t+H+          ++l ++     + ++r++ r +l+ra+ vi ++++ a+  
  gi|330506672|ref|YP_004383100.1|  76 HVPSPLFAFVL--R--DSSPHVVTYHNDVVipgnlngHYLPRPVGAAVEGVNRKIIRPILDRAKIVISTTKSYAETS 148
                                       **999988865..5..588****************99999999999999*********************9999987 PP

                    Glyco_transf_4 149 rerygvppekitVipnGvDle 169
                                         + ++   k  ++pn+vD++
  gi|330506672|ref|YP_004383100.1| 149 PILKDYI-HKTKIVPNAVDVS 168
                                       7755555.78999******86 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                    Glyco_transf_4   3 GverhvleLaraLarrGheVtvvtpgddgpleeev 37 
                                       G+e  +  +++   ++  e ++v +g+d+   ee 
  gi|330506672|ref|YP_004383100.1| 191 GIESLIQAMSEVQKKADLELVLVGDGYDRSRLEEM 225
                                       78888888888888888888888888888888873 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.4e-06    0.0042       1      29 [.      15      43 ..      15      70 .. 0.79
   2 !   19.6   0.0   3.4e-07     0.001      74     143 ..      70     147 ..      66     164 .. 0.76
   3 ?    2.9   0.1     0.044   1.3e+02       2      48 ..     191     236 ..     190     288 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-06
                   Glyco_trans_4_4  1 gGigryvaelaraLaarGheVtvltpapa 29
                                      gG++ +v ela +La+rGh+Vtv  + ++
  gi|330506672|ref|YP_004383100.1| 15 GGVEYHVKELADGLAKRGHQVTVASSCGR 43
                                      8**********************986555 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 3.4e-07
                   Glyco_trans_4_4  74 pdvvhahsptaglaarlarrrrgiplvvtlh..........glllrrg.sgavrrlyralerrllrradavlvvsea 139
                                        d+ h+h p ++l+a ++r   + p+vvt+h          g+ l+r+ ++av  + r + r +l ra  v++++ +
  gi|330506672|ref|YP_004383100.1|  70 ADIYHSHVP-SPLFAFVLR--DSSPHVVTYHndvvipgnlnGHYLPRPvGAAVEGVNRKIIRPILDRAKIVISTTKS 143
                                       699999998.778787777..79********7776666544444555545566666699****************99 PP

                   Glyco_trans_4_4 140 eaee 143
                                        ae+
  gi|330506672|ref|YP_004383100.1| 144 YAET 147
                                       8886 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.044
                   Glyco_trans_4_4   2 GigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvp 48 
                                       Gi+  ++++++ + ++  e++++ +++++++ e++++++ v+  ++ 
  gi|330506672|ref|YP_004383100.1| 191 GIESLIQAMSEVQKKADLELVLVGDGYDRSRLEEMARRLDVRA-RFT 236
                                       889999999999999999*******999999988877666642.222 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 !   37.3   0.0   9.2e-13   2.7e-09       6      88 ..     260     340 ..     249     344 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 9.2e-13
                   Glyco_trans_1_2   6 srsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaeht 82 
                                       +r e +  +l+Ea+ac +++l+ +++g++e   +g  +++++++ el e i +l+++p +r  +++++r  v+++++
  gi|330506672|ref|YP_004383100.1| 260 NRLEAFGIVLLEAMACETPVLAFKTPGVAEVAGEG--GMIYSSPGELGEMILELHESPNLRMNLGRKGRMAVEEKYS 334
                                       45588999***********************9777..**************************************** PP

                   Glyco_trans_1_2  83 ydhrae 88 
                                       + ++++
  gi|330506672|ref|YP_004383100.1| 335 WPRALD 340
                                       *99876 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.1e-05     0.033      10      59 ..      18      68 ..      14     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                   Glyco_trans_4_2 10 svhtlrlakeLakrgyeVhvitp.kkgakdeleaegihvhrlkvdrkgple 59
                                      ++h+++la++Lakrg++V+v+++ +    ++ + + i +  +++++k p  
  gi|330506672|ref|YP_004383100.1| 18 EYHVKELADGLAKRGHQVTVASScGRWNNGFVRIPSIDLFYVPIPIKRPNL 68
                                      69********************95544477777777777777777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2598.01
//
Query:       gi|330506673|ref|YP_004383101.1|  [L=325]
Description: hypothetical protein MCON_0426 [Methanosaeta concilii GP6]
Scores for complete 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-44  151.1  37.3      6e-44  150.8  37.3    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 !  150.8  37.3   3.3e-48     6e-44       8     301 .]      15     311 ..       8     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 150.8 bits;  conditional E-value: 3.3e-48
                   LPG_synthase_TM   8 s.alllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfvnnv 83 
                                       s a+++++l + +d    ++++++++ w+llla++l+ ls++l +lr +ll + +g++i+++ ++r++l+++f+  +
  gi|330506673|ref|YP_004383101.1|  15 SlASIIFIL-YYTDADISWELISRVNGWFLLLAVALHVLSWILYSLRLKLLASMAGHQITFPLSFRCTLASNFLAAI 90 
                                       324444444.666**************************************************************** PP

                   LPG_synthase_TM  84 tPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalallllavla 160
                                       tP+++gGe++r+ +l+  +g+s+++a+a+v+ erlld ++++  ++++l+  g   + g   ++++ l++ll+++  
  gi|330506673|ref|YP_004383101.1|  91 TPSSAGGEPLRIKVLAD-DGMSYGAATAVVISERLLDSIFFLTSLAFFLMVSGFFAGFGL-KVGAIFLLFLLAFLAF 165
                                       *****************.*****************************9996666555433.2222222222222333 PP

                   LPG_synthase_TM 161 lllllllrrrlarlarvlkrlarllarfarklasakr......klvlasprrlllafllslliwllealtlylllra 231
                                       l  l+++++r arl  ++k+ ++ +a + +  +  +       +l+ +  r l++ + +++liw +++l+  +ll++
  gi|330506673|ref|YP_004383101.1| 166 LRQLIIRPKRVARLMEWIKKKTGNRAIVLTIEREIWLfrdagiQLAKETMRCLPVLVVMTALIWFSDFLVPSALLAG 242
                                       4445555555555555666655555555555555555******777777777************************* PP

                   LPG_synthase_TM 232 lgvdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                       +  d+s++l+++++ +l++v++lp++Pg +G++E ++  l++ + vs+a++l +++l+rlit+++ +++G
  gi|330506673|ref|YP_004383101.1| 243 MAQDPSILLSVTAQNILAIVSLLPLTPGASGIAELGMSYLYSTF-VSPALLLPLIVLWRLITYFFNIVVG 311
                                       ********************************************.**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2373.05
//
Query:       gi|330506674|ref|YP_004383102.1|  [L=559]
Description: protein export membrane protein [Methanosaeta concilii GP6]
Scores for complete 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-14   51.4  15.0    4.2e-12   45.8  15.0    2.2  1  SecD_SecF  Protein export membrane protein
    9.3e-06   25.0   0.4    2.7e-05   23.5   0.4    1.8  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 !   45.8  15.0   4.7e-16   4.2e-12      12     173 ..     357     542 ..     348     544 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.7e-16
                                       -EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HH.HHHHHHHHHHHHHHHHHHHHHHTT----HHHH CS
                         SecD_SecF  12 daekisvetvgpsvskelaekavlallialvliliyvalrFewr.valaaiialvhDviitvgvlsllgievdlatv 87 
                                       ++e++    v++ ++k+++ + v+a lial++++ +++ r++ r + l  + + ++ v i++gv sl + ++dla++
  gi|330506674|ref|YP_004383102.1| 357 NVEIVGSGQVSAALGKQFKIQMVIAGLIALLAVAGMIYYRYRERrIVLPMLFTSLSEVAIMLGVWSLAKWQLDLASL 433
                                       667777889********************************865167778888************************ PP

                                       HHHHHHTTSSSHHHHHHHHHHHHH........................HHH--SS-HHHHHHHHHHHHHHHHHHTTH CS
                         SecD_SecF  88 aalLtiiGYSvndtvvvfdrvren........................lrkkkratlkeiinlslnqtLtrtiltsl 140
                                       a+++++iG  v++ v+++d v                           +  k  at+ +i    l+  +   + + +
  gi|330506674|ref|YP_004383102.1| 434 AGIIMVIGTGVDQLVIITDEVIRGgeaapaasdrsikeraaeaadkagV-GKVAATTSKIYLSRLSRAFAIILGAAA 509
                                       *******************986655666666555544433332111111.111222222222223333333334555 PP

                                       HHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTT CS
                         SecD_SecF 141 ttllvvvallllggdslkdfalallvGlivgty 173
                                       tt+++++ ll +g ++l++fal++++G+++gt+
  gi|330506674|ref|YP_004383102.1| 510 TTIVAMLPLLYMGFGALTGFALIIIIGVVLGTL 542
                                       6999***************************97 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.4     3e-09   2.7e-05       3      25 ..      27      49 ..      27      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3e-09
                                      HHHC--EE-TTTS-EEEEEEEE- CS
                            Sec_GG  3 lftkGlNLGlDFtGGthielqfd 25
                                      l+ +Gl++GlD++GG+ ++l+ +
  gi|330506674|ref|YP_004383102.1| 27 LGAFGLKYGLDLQGGSYLQLKLQ 49
                                      6789****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 4112.61
//
Query:       gi|330506675|ref|YP_004383103.1|  [L=297]
Description: protein export membrane protein [Methanosaeta concilii GP6]
Scores for complete 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-25   87.6   9.6    9.6e-25   87.1   9.6    1.2  1  SecD_SecF   Protein export membrane protein
    1.6e-05   23.2   5.0    2.2e-05   22.8   5.0    1.1  1  Patched     Patched family
    2.8e-05   23.4   0.0    8.1e-05   22.0   0.0    1.9  1  Sec_GG      SecD/SecF GG Motif
  ------ inclusion threshold ------
       0.27   10.1  16.6      0.014   14.4  10.8    1.7  2  MMPL        MMPL family


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   9.6   2.1e-28   9.6e-25      15     186 ..     109     284 ..      96     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 2.1e-28
                                       EEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHH.HHHHHHHHHHHHHHTT----HHHHHHH CS
                         SecD_SecF  15 kisvetvgpsvskelaekavlallialvliliyvalrFewrvalaaiia.lvhDviitvgvlsllgievdlatvaal 90 
                                       + ++   gp +s+el+ +++  l ++++l++++v++ F++ + +  +++ ++ D++++++ + l+g++++l tvaal
  gi|330506675|ref|YP_004383103.1| 109 NAEIRHMGPIYSQELQAQVIRYLPLSFILMALVVFIVFRQAFVSLLVVLcALADILTAAASMNLTGVQLSLGTVAAL 185
                                       5677889********************************9988777666699************************* PP

                                       HHHTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHHHT....TTTHHHH CS
                         SecD_SecF  91 LtiiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslt..tllvvvallllgg....dslkdfa 161
                                       L++iGYSv+++++++ rv ++ + +++ ++k ++ ++l++  t + +++++  ++  ++ l+l  +    d+++d++
  gi|330506675|ref|YP_004383103.1| 186 LMLIGYSVDTDILLTMRVLKR-KGDTDDKIKGAMGTGLTMAGT-SAAAVISliLVSNLLHLVLP-SfsrmDVIADMS 259
                                       *******************99.777888888888888876555.33333331133334444443.24667******* PP

                                       HHHHHHTSTTTTTHHHHHHHHHHHH CS
                         SecD_SecF 162 lallvGlivgtyssifiasplllll 186
                                       ++l++Gl+++ ++++ ++++ l ++
  gi|330506675|ref|YP_004383103.1| 260 TVLIFGLAADLFNTWVTNAQGLRWY 284
                                       *****************99988877 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   5.0     5e-09   2.2e-05     654     775 ..     122     238 ..     107     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5e-09
                           Patched 654 tilpstiqnivlallcmfvvallfipelitvlvit.lsivsidigviGflslWgvdLDpismitiimsiGfsvdlsa 729
                                       ++++++i  + l++++m++v ++   + +++l+++ ++++ i +  +  + l gv+L   ++++++m iG+svd   
  gi|330506675|ref|YP_004383103.1| 122 ELQAQVIRYLPLSFILMALVVFIVFRQAFVSLLVVlCALADI-LTAAASMNLTGVQLSLGTVAALLMLIGYSVDTDI 197
                                       68889999999*******999987777766655550555555.677889**************************** PP

                           Patched 730 HiayafvrsekddakeRvvealealgwPvvqgalSTilgvlvLlfv 775
                                         + +  + ++ d++++++ a+      +  +++S  + + +L++v
  gi|330506675|ref|YP_004383103.1| 198 LLTMRVLKRKG-DTDDKIKGAMG---TGLTMAGTSAAAVI-SLILV 238
                                       ********999.9******9975...56777787765444.44444 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.8e-08   8.1e-05       6      25 ..      39      58 ..      37      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.8e-08
                                      C--EE-TTTS-EEEEEEEE- CS
                            Sec_GG  6 kGlNLGlDFtGGthielqfd 25
                                       ++NLG++FtGGt+ ++ + 
  gi|330506675|ref|YP_004383103.1| 39 SPVNLGIEFTGGTLATVPAT 58
                                      699***********999875 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.3      0.26   1.2e+03     168     184 ..      17      33 ..      11      41 .. 0.63
   2 ?   14.4  10.8   3.1e-06     0.014     150     289 ..     132     271 ..      98     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.26
                              MMPL 168 vaallplltvvvsllaa 184
                                       ++++++++ +++sl+++
  gi|330506675|ref|YP_004383103.1|  17 LIPIIVIILALISLGVT 33 
                                       34555555555555554 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.1e-06
                              MMPL 150 vvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRy 226
                                        +++++ +++ +iv+r     ll++l ++ ++l+a ++     +l g++ls  +++ + ++li+ ++D  +lL+ R 
  gi|330506675|ref|YP_004383103.1| 132 PLSFILMALVVFIVFRQAFVSLLVVLCALADILTAAAS----MNLTGVQLSLGTVA-ALLMLIGYSVDTDILLTMRV 203
                                       567899999*****************************....44556666654444.34456677777779999998 PP

                              MMPL 227 reelaagedr...eeaviravastgkvvtaaGltvaiamlgL...vvarlpvlaqvGvaialGvlvdvl 289
                                         + ++  d+   + +   ++a+t  + +++ l+++  +l L   +++r+ v+a + +++  G++ d++
  gi|330506675|ref|YP_004383103.1| 204 LKRKGDTDDKikgAMGTGLTMAGTSAAAVIS-LILVSNLLHLvlpSFSRMDVIADMSTVLIFGLAADLF 271
                                       6655555544100445556777777776666.6666666666233589999999999999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); 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:                         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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.61
# Mc/sec: 1460.20
//
Query:       gi|330506676|ref|YP_004383104.1|  [L=419]
Description: 3-hexulose-6-phosphate synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-42  144.4   0.5    2.9e-42  144.4   0.5    2.2  2  RraA-like      Aldolase/RraA
    1.2e-17   64.3   5.3    2.2e-17   63.4   5.3    1.5  1  OMPdecase      Orotidine 5'-phosphate decarboxylase / HUMPS f
    4.6e-07   29.2   3.1    4.6e-07   29.2   3.1    1.7  2  NanE           Putative N-acetylmannosamine-6-phosphate epime
      3e-06   27.0   4.7     0.0011   18.6   0.2    2.2  2  HMGL-like      HMGL-like
    3.9e-05   23.1   2.6    9.2e-05   21.8   0.5    2.3  2  TMP-TENI       Thiamine monophosphate synthase
     0.0001   21.9   2.5    0.00023   20.7   0.8    2.1  2  His_biosynth   Histidine biosynthesis protein
    0.00011   21.7   2.6       0.04   13.4   0.2    2.3  2  PEP_mutase     Phosphoenolpyruvate phosphomutase
      0.001   18.3   2.7     0.0012   18.1   0.7    2.1  1  PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
     0.0058   15.5   5.6      0.036   12.9   3.4    2.8  3  Trp_syntA      Tryptophan synthase alpha chain
     0.0064   15.9   5.4       0.01   15.2   5.4    1.3  1  NMO            Nitronate monooxygenase
  ------ inclusion threshold ------
      0.024   13.7   0.1       0.05   12.7   0.1    1.5  1  Dus            Dihydrouridine synthase (Dus)
      0.039   13.0   7.8       0.03   13.3   3.4    2.1  2  FMN_dh         FMN-dependent dehydrogenase
      0.044   13.0   2.3       0.13   11.4   2.3    1.8  1  IGPS           Indole-3-glycerol phosphate synthase
      0.084   12.0   2.5       0.13   11.4   1.0    2.1  2  DUF561         Protein of unknown function (DUF561)
       0.68    9.8   4.2       0.29   11.0   1.0    2.0  2  DUF3983        Protein of unknown function (DUF3983)


Domain annotation for each model (and alignments):
>> RraA-like  Aldolase/RraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.7       2.2   2.6e+03      58      58 ..     149     149 ..      36     191 .. 0.54
   2 !  144.4   0.5   2.4e-45   2.9e-42       2     150 .]     228     373 ..     227     373 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.2
                                       E CS
                         RraA-like  58 d 58 
                                        
  gi|330506676|ref|YP_004383104.1| 149 V 149
                                       1 PP

  == domain 2  score: 144.4 bits;  conditional E-value: 2.4e-45
                                       HHHHHHCEE-SSBSTB.TT.EE.S.EEEEEEEEEESS.BGHHHHHHHTS--TTEEEEEESTT.SSSSSECE-HHHHH CS
                         RraA-like   2 advsDalkklggrsggirpler.s.fvGpavTvkvveadnslvkealeeagpgdvlVvdgggdeslraallGgllat 76 
                                       +++sDa+++ g   +gi+pl + + +vG+a+Tv+++ +d+++  ea++ agpgdvlV+ +g+  +  a + Ggl + 
  gi|330506676|ref|YP_004383104.1| 228 SNISDAMHRKGA-MRGIHPLIPgKkIVGKAITVQTFAGDWAKPVEAIDLAGPGDVLVIYNGS--NSIAPW-GGLATL 300
                                       69******4444.446***66656799*******************************9888..448999.****** PP

                                       HHHHTTBSEEEEEEEES-HHHHTTSSSEEEEEEE-SSB-B-S.STSEESS-EEETTEEE-TTSEEEEETTEEEE CS
                         RraA-like  77 aakangvaGvvvdGavRDvaelreldfpvfargvtprkkpkkkgkgevnvpveiggvtvkpgdlivaDedGvvv 150
                                       ++k +g++GvvvdGavRD++e+r +d+p+f+  v+p++   k g ge+n ++ +gg+tv+pgd+iv+D++Gvvv
  gi|330506676|ref|YP_004383104.1| 301 SCKIRGIEGVVVDGAVRDLQEIRPMDYPLFSSDVVPNAGDPK-GMGEINSEIVCGGQTVRPGDYIVGDDSGVVV 373
                                       *************************************95555.******************************8 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   5.3   1.9e-20   2.2e-17       8     225 .]       2     197 ..       1     197 [. 0.90

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 1.9e-20
                                       -SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHHHHSTCH CS
                         OMPdecase   8 Dvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekqatagsa 81 
                                       D+ + ++ +++a+++    +++++ +++l++++g     ++ +++++k     +i++D+K++D G+ + ++a     
  gi|330506676|ref|YP_004383104.1|   2 DLLELDRSIQIAKEAVLgGADWIEAGTPLIKSEG-----MDSVREMKKALpgTKIVADMKTVDTGAMEVEMA----- 68 
                                       7778888899999999889***************.....*********9666********************..... PP

                                       HHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH..H..SHHHHHHHHHHHHHHHTTESE CS
                         OMPdecase  82 rikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe..k..gytqacveaarehkaedfvmG 154
                                        +k++adiv   a+ + ++v+ +++aa+k+g    ++ + ++ ++   + +  +  g+++ cv+   +++       
  gi|330506676|ref|YP_004383104.1|  69 -AKAGADIVALLAASDNSTVEDALRAARKYG--VQIMMDLLTVPDPVGRSRelEelGVDYICVHVGIDQQM------ 136
                                       .69***************************9..99***********9999976369************992...... PP

                                       EECCCHTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHHH CS
                         OMPdecase 155 fvaqetlnateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaery 225
                                          +++        d ++++++ ++    + ++g     + +++  +ga i+ivG +I+++++  e a+++
  gi|330506676|ref|YP_004383104.1| 137 --TGKDTI------DFLKQIVKEVKT-PVAAAGGMDAASAADAVA-SGAAIVIVGGSIVRSANVTESARKI 197
                                       ..344333......68899******8.999999999886666655.89*******************9986 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 !   29.2   3.1   3.8e-10   4.6e-07      51     184 ..      60     192 ..      21     199 .. 0.75
   2 ?   -2.4   0.0       1.9   2.3e+03     165     182 ..     305     322 ..     299     325 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 3.8e-10
                                       S-SHHHHHHHHTTT-SEEEEE--SS--T--HHHHHHHHHHH--EEEEE-SSHHHHH....HHHHTT-SEEE-TTTTS CS
                              NanE  51 tatlkdideLaaagadiialDatdrerpvtieelikkikekyqllmaDistleegl....vakklGvdivGttlsGy 123
                                       t    +++  a+agadi+al a++ +   t+e+ +++ ++ ++ +m D+ t+ + +      ++lGvd++   + G 
  gi|330506676|ref|YP_004383104.1|  60 TGA-MEVEMAAKAGADIVALLAASDN--STVEDALRAARKYGVQIMMDLLTVPDPVgrsrELEELGVDYICVHV-GI 132
                                       333.489999**********999876..6789**********99999*99998855222267899*****8765.54 PP

                                       STTS-.SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHH CS
                              NanE 124 tkeeekaepDfalvkalsea.glkviaeGrintPekakkaieiGvdavvvGsaitrleeiak 184
                                        + +   ++ ++++k+++++ +  v a G +++   a++a+ +G++ v+vG++i r +++++
  gi|330506676|ref|YP_004383104.1| 133 DQ-QMTGKDTIDFLKQIVKEvKTPVAAAGGMDAA-SAADAVASGAAIVIVGGSIVRSANVTE 192
                                       44.44445557788887665277799****9986.6778899****************9997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.9
                                       T--SEEEE-HHHH-HHHH CS
                              NanE 165 iGvdavvvGsaitrleei 182
                                        G++ vvv +a+  l+ei
  gi|330506676|ref|YP_004383104.1| 305 RGIEGVVVDGAVRDLQEI 322
                                       477778888887777776 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2     9e-07    0.0011      20     122 ..       4     105 ..       1     114 [. 0.87
   2 !   11.3   0.7   0.00015      0.18      14     101 ..     100     186 ..      96     236 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9e-07
                                       --HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEE CS
                         HMGL-like  20 lsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagakrvhvf 96 
                                       l++++ ++iak+ +  g d iE+g p    + +++vr+ +ka++ ++i+a ++ ++    + ve + +aga++v + 
  gi|330506676|ref|YP_004383104.1|   4 LELDRSIQIAKEAVLGGADWIEAGTPLIKSEGMDSVREMKKALPGTKIVADMKTVDTGA-MEVEMAAKAGADIVALL 79 
                                       678999*****************************************999988877664.34555677********* PP

                                       EES-HHHHHHHHSSTHHHHHHHHHHH CS
                         HMGL-like  97 iatselhlkaklkkdreevakkaeea 122
                                        a  +  ++  l+  r++ ++++ ++
  gi|330506676|ref|YP_004383104.1|  80 AASDNSTVEDALRAARKYGVQIMMDL 105
                                       99999999999999999888887766 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00015
                                       HTSSS---HHHHHHHHHHHHHHT-SEE--..TS..GGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH... CS
                         HMGL-like  14 qalkaalsveeklaiakaLdeagvdeiEv..gf..paaseddfevvraiakavkkarilalvrarekdikaavealk 86 
                                       q + + l+v++ +   ++L+e+gvd+i v  g+   + ++d ++++++i+k+vk++ + a   ++    + av+   
  gi|330506676|ref|YP_004383104.1| 100 QIMMDLLTVPDPVGRSRELEELGVDYICVhvGIdqQMTGKDTIDFLKQIVKEVKTP-VAAAGGMDAASAADAVA--- 172
                                       556666666666777799*********997754214679999***********998.44444444444444444... PP

                                       .TT-SEEEEEEES-H CS
                         HMGL-like  87 gagakrvhvfiatse 101
                                         ga++v v  ++  
  gi|330506676|ref|YP_004383104.1| 173 -SGAAIVIVGGSIVR 186
                                       .44444444433333 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.33     4e+02      13      44 ..      59      88 ..      49     106 .. 0.57
   2 !   21.8   0.5   7.7e-08   9.2e-05     111     178 ..     117     181 ..     111     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.33
                          TMP-TENI 13 eellevveealkggvtlvqlRekeldarelle 44
                                      ++ +  ve a+k+g+++v l + +  +++ +e
  gi|330506676|ref|YP_004383104.1| 59 DTGAMEVEMAAKAGADIVALLAAS--DNSTVE 88
                                      555667777777777777776643..333333 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 7.7e-08
                          TMP-TENI 111 eaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGitlenvaevleagadgvavv 178
                                       e+e+lg+dYi+v   +     ++     +++lk+++++++ Pv a GG++++++a+++++ga+ v v 
  gi|330506676|ref|YP_004383104.1| 117 ELEELGVDYICV---HVGIDQQMTGKDTIDFLKQIVKEVKTPVAAAGGMDAASAADAVASGAAIVIVG 181
                                       778889999986...33455566666789*********************************999875 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.36   4.3e+02      83     133 ..       8      61 ..       8      92 .. 0.70
   2 !   20.7   0.8   1.9e-07   0.00023      29     177 ..     109     242 ..      98     264 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.36
                                       SSHHHHHHHHHCT-SEEEESHHHHH-..THHHHHHHHHHCGGGEEEEEEEEE.C CS
                      His_biosynth  83 rsledveelleagadkviigtaavkn..pelikelaekfgsqkivvaiDarr.g 133
                                       rs++ ++e++  gad +  gt  +k+   + ++e+ ++ ++ kiv+   + + g
  gi|330506676|ref|YP_004383104.1|   8 RSIQIAKEAVLGGADWIEAGTPLIKSegMDSVREMKKALPGTKIVADMKTVDtG 61 
                                       567777888888999999999988873356699999999999999876655543 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.9e-07
                                       TSHHHHHHHHHHHT-SEEEE.EEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHH CS
                      His_biosynth  29 gdpvelakryeeegadelhv.vDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigta 104
                                        dpv   +++ee g+d+++v v +d  ++g++  +d +++i++ev+ pv   GG    + +++++ +ga  vi+g +
  gi|330506676|ref|YP_004383104.1| 109 PDPVGRSRELEELGVDYICVhVGIDQQMTGKD-TIDFLKQIVKEVKTPVAAAGGMDAAS-AADAVASGAAIVIVGGS 183
                                       6899999999999***9988688998887665.68999****************99888.899999*********** PP

                                       HHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS- CS
                      His_biosynth 105 avknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakkleelgageilltdidrdGtlsG 177
                                        v++ ++ +++ +   +     +iD+ +    a k   ee   ++v+l++ +++ +    +   ++r G + G
  gi|330506676|ref|YP_004383104.1| 184 IVRSANVTESARKI-RE-----SIDVAQA-STAPKMSLEE---EIVSLLRSVSSSN----ISDAMHRKGAMRG 242
                                       ***99888777664.44.....5776655.3333333333...3344443333333....3345555555555 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   5.9e-05     0.071     163     222 ..      66     131 ..      51     139 .. 0.79
   2 !   13.4   0.2   3.3e-05      0.04     161     227 ..     114     188 ..     110     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
                        PEP_mutase 163 raYaeAGAdgvfvpglqkdaeiaelvaav.dvplnvvp.lkgt.....lsvaelaelGvarislgnh 222
                                       ++ a+AGAd v    +++++++++ ++a  +  + +++ l  t        +el+elGv  i ++  
  gi|330506676|ref|YP_004383104.1|  66 EMAAKAGADIVALLAASDNSTVEDALRAArKYGVQIMMdLL-TvpdpvGRSRELEELGVDYICVHVG 131
                                       6789******************9999999666677777331.1233447899*********998765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.3e-05
                        PEP_mutase 161 RaraYaeAGAdgvfvpgl.......qkdae.iaelvaavdvplnvvplkgtlsvaelaelGvarislgnhllraa 227
                                       R r   e G d + v+ +       +++ + ++++v++v++p+ +  + ++ s a+  + G+a++++g +++r+a
  gi|330506676|ref|YP_004383104.1| 114 RSRELEELGVDYICVHVGidqqmtgKDTIDfLKQIVKEVKTPVAAAGGMDAASAADAVASGAAIVIVGGSIVRSA 188
                                       7788889999999999998998887777777899999999****9998778**********************99 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.7     1e-06    0.0012     148     261 ..     103     222 ..      89     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1e-06
                     PEP_hydrolase 148 ldllttayvfneeearamaeaGadvivahlGlttggsigaktalsleeavelvqe.........iadaakevnpdvi 215
                                       +dllt++       +r++ e G+d i++h+G+ ++ ++g++t   l++ v++v++          a+aa++v +   
  gi|330506676|ref|YP_004383104.1| 103 MDLLTVPD--PVGRSRELEELGVDYICVHVGIDQQ-MTGKDTIDFLKQIVKEVKTpvaaaggmdAASAADAVASGAA 176
                                       56666664..34567999*************9865.78999999999999999862211221114556677779999 PP

                     PEP_hydrolase 216 vlvhGGpiaepedaeyvlertkgvkGfigassleRlpvekaikett 261
                                       +++ GG i +  ++++  ++ ++    + as+  ++ +e+ i +  
  gi|330506676|ref|YP_004383104.1| 177 IVIVGGSIVRSANVTESARKIRESIDVAQASTAPKMSLEEEIVSLL 222
                                       9***************999999999999999999999999998765 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.15   1.8e+02      23      47 ..       6      30 ..       3      36 .. 0.90
   2 ?   -0.2   0.0       0.3   3.6e+02     119     154 ..      50      85 ..      30     103 .. 0.59
   3 !   12.9   3.4     3e-05     0.036     182     239 ..     137     193 ..      65     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.15
                                      HHHHHHHHHHHHHCT-SSEEEE--- CS
                         Trp_syntA 23 leqsleilkalekagadviElGlpf 47
                                      l++s++i k+   +gad iE G p 
  gi|330506676|ref|YP_004383104.1|  6 LDRSIQIAKEAVLGGADWIEAGTPL 30
                                      678999****************995 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.3
                                       EEETTSBCCCHHHH.HHHHHHTT-EEEEEE-TTS-HH CS
                         Trp_syntA 119 livpDlPleeaeel.veaakkkglelvflvapttsde 154
                                        iv+D+ + +   + ve+a k+g ++v l+a  ++++
  gi|330506676|ref|YP_004383104.1|  50 KIVADMKTVDTGAMeVEMAAKAGADIVALLAA-SDNS 85 
                                       45555555554444245555666666666655.4444 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 3e-05
                                       B-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHHHHHHHCTTTS CS
                         Trp_syntA 182 vaaevdelverlkkltavPvavGFGistkeqvkqvakvadGvivGSalvkkieeeaee 239
                                       + +++ ++++++ k  ++Pva   G+ +++ +++va++a+ vivG  +v+  +  +e+
  gi|330506676|ref|YP_004383104.1| 137 TGKDTIDFLKQIVKEVKTPVAAAGGMDAASAADAVASGAAIVIVGGSIVRSANV-TES 193
                                       455666778888888889*******************************98662.222 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   5.4   8.6e-06      0.01      73     225 ..      32     184 ..      21     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.6e-06
                               NMO  73 kkdaadraekykkeleeaalelnieegvrfyrkvevvldekvevvsfgfglpteevvarlkea...gvvliptiss. 145
                                       k + +d   ++kk l+++   + +++ ++    ve+ ++ ++++v + ++  +  v+++l +a   gv +++   + 
  gi|330506676|ref|YP_004383104.1|  32 KSEGMDSVREMKKALPGTKIVADMKTVDTGAMEVEMAAKAGADIVALLAASDNSTVEDALRAArkyGVQIMMDLLTv 108
                                       55667777888888888888888888888888999999999999999888888777777665422244444333331 PP

                               NMO 146 ...vkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgv 219
                                          v   r++e++G D + v  +    ++G      k+++  ++q+++ v+ Pv AaGG+      a a a GA+ v
  gi|330506676|ref|YP_004383104.1| 109 pdpVGRSRELEELGVDYICVHVGIDQQMTG------KDTIDFLKQIVKEVKTPVAAAGGMDA-ASAADAVASGAAIV 178
                                       1226789999999*9999995444444444......789********************855.555666799**999 PP

                               NMO 220 qigtrf 225
                                        +g   
  gi|330506676|ref|YP_004383104.1| 179 IVGGSI 184
                                       999765 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.2e-05      0.05     145     239 ..     116     207 ..     109     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.2e-05
                                       HHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTT CS
                               Dus 145 kiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPw 221
                                       + +e+ G++ + vH     q+ +g++ ++  k++ ++v++pv a G+   a++a+a+ +  Ga  v++g    +  +
  gi|330506676|ref|YP_004383104.1| 116 RELEELGVDYICVHVGID-QQMTGKDTIDFLKQIVKEVKTPVAAAGGMDAASAADAVAS--GAAIVIVGGSIVRSAN 189
                                       678999********9765.55678899999******************99999999865..5877888777777666 PP

                                       HHHHHHHHHHSC------ CS
                               Dus 222 lfaestavktgeaepapp 239
                                       + ++  +++++++  + +
  gi|330506676|ref|YP_004383104.1| 190 VTESARKIRESIDVAQAS 207
                                       665555665555444444 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   0.1     0.058        70      89     152 ..      51     116 ..      35     121 .. 0.70
   2 ?   13.3   3.4   2.5e-05      0.03     234     311 ..     119     192 ..     113     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.058
                                       S-EEEETT-SS-HHHHHHHHTT-EEEEEE-CSSHHHHHHHHHHHHHCTESEEE..EESSTSS---B CS
                            FMN_dh  89 ipfvlstvastsleevaaaaegplwfqlyvpkdrelteellkraeaagykalv..ltvDtpvlgkR 152
                                       i+  + tv + ++e  +aa+ g  ++ l   +d++++e+ l+ a++ g++ ++  ltv  pv   R
  gi|330506676|ref|YP_004383104.1|  51 IVADMKTVDTGAMEVEMAAKAGADIVALLAASDNSTVEDALRAARKYGVQIMMdlLTVPDPVGRSR 116
                                       555566666666665555566789999999999999999999999999999863345544444444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.5e-05
                                       HHTTESEEEE--GGG.TSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHH CS
                            FMN_dh 234 veaGvdgivvSNHGG.RqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaa 309
                                        e+Gvd i v  H G  q  +   tid L +iv++v+  ++v + gG    + ++ A+a GA +v++G  ++  +++
  gi|330506676|ref|YP_004383104.1| 119 EELGVDYICV--HVGiDQQMTGKDTIDFLKQIVKEVK--TPVAAAGGMD-AASAADAVASGAAIVIVGGSIVRSANV 190
                                       5778887777..544256677889************8..9*******75.56699**************99877665 PP

                                       HH CS
                            FMN_dh 310 gG 311
                                         
  gi|330506676|ref|YP_004383104.1| 191 TE 192
                                       44 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.3   0.00011      0.13     120     253 ..      61     196 ..       8     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                       SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEE...ESSHHHHHHHH.HTT-SEEEEESEETTTT CS
                              IGPS 120 deyqieearalgadaiLLivkvledeeleelaeaakslglevLvE...vhdeeeleral.klgakiiGvNnRnLktl 192
                                         +++e a ++gad++ L+++  +++++e+  +aa+++g++++++   v d    +r l +lg + i v    + + 
  gi|330506676|ref|YP_004383104.1|  61 GAMEVEMAAKAGADIVALLAAS-DNSTVEDALRAARKYGVQIMMDlltVPDPVGRSRELeELGVDYICVH-VGIDQQ 135
                                       5678999*********998765.77778888899999998886652226666667777778899988885.456666 PP

                                       EE-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHH CS
                              IGPS 193 evdlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekaire 253
                                        +  +t   L++ v++  + va  G  +++ + +  ++g+  ++vG s++r+++v+++ r+
  gi|330506676|ref|YP_004383104.1| 136 MTGKDTIDFLKQIVKEVKTPVAAAGGMDAASAADAVASGAAIVIVGGSIVRSANVTESARK 196
                                       77778888888888877899999999999999999999****************9998876 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.5   1.8e+03      75      88 ..      14      27 ..       9      58 .. 0.74
   2 ?   11.4   1.0   0.00011      0.13     173     233 ..     140     200 ..     101     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                            DUF561 75 leavkaGadlveiG 88
                                       eav+ Gad +e G
  gi|330506676|ref|YP_004383104.1| 14 KEAVLGGADWIEAG 27
                                      57888888888877 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00011
                            DUF561 173 stlastyeiskkvslPvicasGlsdvtvplalslgasGiGigsavsklndeeemvallsei 233
                                       +t+    +i+k+v+ Pv +a G+   ++  a++ ga+ + +g ++ +  + +e    ++e 
  gi|330506676|ref|YP_004383104.1| 140 DTIDFLKQIVKEVKTPVAAAGGMDAASAADAVASGAAIVIVGGSIVRSANVTESARKIRES 200
                                       46666779*********************************99999988887777666664 PP

>> DUF3983  Protein of unknown function (DUF3983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       3.7   4.5e+03       3       9 ..     195     201 ..     194     202 .. 0.86
   2 ?   11.0   1.0   0.00024      0.29       9      18 ..     382     391 ..     378     393 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.7
                           DUF3983   3 RKvRKAI 9  
                                       RK+R  I
  gi|330506676|ref|YP_004383104.1| 195 RKIRESI 201
                                       9***887 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00024
                           DUF3983   9 IARRAKdVEK 18 
                                       IARRAK+VEK
  gi|330506676|ref|YP_004383104.1| 382 IARRAKEVEK 391
                                       9********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); 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: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 2750.68
//
Query:       gi|330506677|ref|YP_004383105.1|  [L=299]
Description: diaminopimelate epimerase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-57  190.5   0.1      1e-33  116.1   0.0    2.1  2  DAP_epimerase  Diaminopimelate epimerase
    9.5e-05   21.6   0.0    0.00038   19.6   0.0    1.8  2  Pro_racemase   Proline racemase


Domain annotation for each model (and alignments):
>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1   0.0   1.1e-37     1e-33       1     119 [.      23     145 ..      23     147 .. 0.97
   2 !   72.6   0.1   3.3e-24     3e-20       1     120 [.     170     281 ..     170     282 .. 0.87

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 1.1e-37
                                       EEEECSSEEEEEEECCTTCSSHHH...HHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEETTTEEESTTHCCHH CS
                     DAP_epimerase   1 fakshGnpndvvvvddveaelvle...aelvaalcdreagpgadgvlfvkpsgeediklryfnrdgseaemCGnGvr 74 
                                       fak hGn+nd+++vd++  elv e   ++++ a c+r +g+gadgvlf   s+++d+ +r f  dgseaemCGnG+r
  gi|330506677|ref|YP_004383105.1|  23 FAKLHGNGNDFILVDEISRELVAEsakSRFAIACCRRSFGIGADGVLFLASSQRSDLGMRLFQPDGSEAEMCGNGIR 99 
                                       89*********************999999************************************************ PP

                                       HHHHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSS..EEEEEE--E CS
                     DAP_epimerase  75 vfaaylreggletkkevtvetlgGeleievkddgek..vkvdmGkas 119
                                       + a+y++e+g +  +++ vetl+G ++i+v++ +     +vdmG ++
  gi|330506677|ref|YP_004383105.1| 100 CLAKYAWESGYV-GQSFDVETLAGIIPIQVRERDGSfwARVDMGVPR 145
                                       **********77.*********************9999******987 PP

  == domain 2  score: 72.6 bits;  conditional E-value: 3.3e-24
                                       EEEECSSEEEEEEECCTTCSSHHHHHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEET.TTEEESTTHCC.HHH CS
                     DAP_epimerase   1 fakshGnpndvvvvddveaelvleaelvaalcdreagpgadgvlfvkpsgeediklryfnr.dgseaemCGnG.vrv 75 
                                       +a+++G+p++v++vdd++  ++ e  +++ + +   +p++ +v fvk    + +++r+f+r +++e+ +CG+G v+ 
  gi|330506677|ref|YP_004383105.1| 170 CAVNTGVPHAVIFVDDLDI-DIYE--AAPPIRHCSVFPEGANVDFVKL--GSSLQIRTFERgVEGETFSCGTGaVAS 241
                                       589***************5.5556..79*******************5..88999996665169*********8888 PP

                                       HHHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSSEEEEEE--EE CS
                     DAP_epimerase  76 faaylreggletkkevtvetlgGeleievkddgekvkvdmGkasl 120
                                       ++++ r g  +  +ev vet+gG+l i+ ++d++   ++ G+a+ 
  gi|330506677|ref|YP_004383105.1| 242 ASVARRMGL-V-GDEVLVETKGGPLIINFEKDKA---FMEGPAVT 281
                                       888877776.5.8*******************85...9***9986 PP

>> Pro_racemase  Proline racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   4.2e-08   0.00038      34     132 ..      44     139 ..      31     152 .. 0.81
   2 ?   -0.8   0.1     0.069   6.2e+02      80     116 ..     231     262 ..     226     284 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.2e-08
                                       HHH.HHHHHHHHSTTTS-TT-EEEEEE--SSTTSSEEEEEEESSSB-.SSTHHHHHHHHHHHHHTTSS-SEEEECEE CS
                      Pro_racemase  34 eedldalRralllePRGhdvmsgallvppkepdadlgvifletsgyl.pmcGsntigvvtvlletGlvevqepetkl 109
                                        ++  + R a+ +  R   +    +l+ ++++++dlg+ +++++g    mcG++  ++++ + e+G v        +
  gi|330506677|ref|YP_004383105.1|  44 VAESAKSRFAIACCRRSFGIGADGVLFLASSQRSDLGMRLFQPDGSEaEMCGNGIRCLAKYAWESGYVGQS-----F 115
                                       5555666677777777777777789999999************998626*******************865.....4 PP

                                       EEEETTEEEEEEEECTST.SEEEE CS
                      Pro_racemase 110 sletpaGlvevtaecrdg.kverv 132
                                        +et aG++ +++++rdg    rv
  gi|330506677|ref|YP_004383105.1| 116 DVETLAGIIPIQVRERDGsFWARV 139
                                       56***************9444555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.069
                                       -SSTHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTE CS
                      Pro_racemase  80 lpmcGsntigvvtvlletGlvevqepetklsletpaG 116
                                       + +cG ++++ + v+   Glv  +     + +et +G
  gi|330506677|ref|YP_004383105.1| 231 TFSCGTGAVASASVARRMGLVGDE-----VLVETKGG 262
                                       557999999999999999998643.....34455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2234.90
//
Query:       gi|330506678|ref|YP_004383106.1|  [L=146]
Description: hypothetical protein MCON_0431 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1111.58
//
Query:       gi|330506679|ref|YP_004383107.1|  [L=481]
Description: phosphoesterase, RecJ domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   54.6   0.5    3.7e-14   53.3   0.5    1.7  1  DHHA1     DHHA1 domain
     0.0039   17.4   0.1     0.0085   16.3   0.1    1.6  1  DHH       DHH family
  ------ inclusion threshold ------
      0.036   13.1   0.0        2.5    7.0   0.0    2.2  2  SelA      L-seryl-tRNA selenium transferase


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 !   53.3   0.5   6.2e-18   3.7e-14      54     137 ..     381     469 ..     344     470 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 6.2e-18
                                       HHHHHHHHHHHTHG.BT.TCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEH CS
                             DHHA1  54 galgiaadklkskl.kk.pvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGagipa 124
                                       +++gi+a++  ++   + p+ +f+ + eg   kvsar ++d    g+d++ +++  a+++gg GGGH+ AaGa+ip 
  gi|330506679|ref|YP_004383107.1| 381 TIIGIVAGMSFQMAdRSrPILAFAQNVEG-DLKVSARGTQDlvrsGLDLAHALSLSAQAVGGVGGGHNVAAGATIPL 456
                                       45666666666655555699999999999.*********************************************** PP

                                       CHHHHHHHHHHHH CS
                             DHHA1 125 ekleealealeea 137
                                       +  +e+le+++++
  gi|330506679|ref|YP_004383107.1| 457 QAKQEFLEKMDRI 469
                                       *********9986 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.4e-06    0.0085       2      68 ..      34     126 ..      33     168 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-06
                                       EEEE-ECSSSHHHHHH.HHHHHH................................CECS--TCGGCGCCHHCCCSEE CS
                                       xxxxxxxxxxxxxxxx.xxxxxx................................xxxxxxxxxxxxxxxxxxxxxx RF
                               DHH   2 ilivghknpDtDsigS.aialan................................llvDhneksqavegeakeeaed 45 
                                       il+  + + D+D++++ ai  a+                                +  D ++   ++   + e++ +
  gi|330506679|ref|YP_004383107.1|  34 ILV--VSHVDADGLTAaAIICAAldrhnidykplffrqldenaleevadqgadlvIFTDLGSGMIQE---ILERNLQ 105
                                       677..899********888888856666666665554444444444444444444455555444444...67***** PP

                                       EEEEE-S---SS---SS--EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  46 viiiDHHrlgeefetlapilfln 68 
                                        i+ DHH+++      +p+  +n
  gi|330506679|ref|YP_004383107.1| 106 AIVADHHKPKA--CPAQPLAHIN 126
                                       *********74..3333444444 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0   0.00042       2.5     153     188 ..      66     102 ..      48     110 .. 0.80
   2 ?    3.5   0.0    0.0047        28     159     191 ..     158     190 ..     148     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00042
                                       S-B---HHHHHHHHHH.HT--EEEEEES-B-S-GGGG CS
                              SelA 153 ftkevelaeLvelgke.kglpvleDlGsGllvdlsey 188
                                       f ++++++ L e++++  +l++++DlGsG++ ++ e 
  gi|330506679|ref|YP_004383107.1|  66 FFRQLDENALEEVADQgADLVIFTDLGSGMIQEILER 102
                                       677899999***9975389***********9987665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0047
                                       HHHHHHHHHHHT--EEEEEES-B-S-GGGGT-- CS
                              SelA 159 laeLvelgkekglpvleDlGsGllvdlseygls 191
                                       +++L++l+    +  l+D+ sG+l+ l++y l 
  gi|330506679|ref|YP_004383107.1| 158 NDDLAALAVVGAVGDLQDMASGQLIGLNRYILD 190
                                       579999999999******************885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3424.99
//
Query:       gi|330506680|ref|YP_004383108.1|  [L=140]
Description: hypothetical protein MCON_0433 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 949.80
//
Query:       gi|330506681|ref|YP_004383109.1|  [L=282]
Description: hypothetical protein MCON_0435 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-13   50.0   0.0    3.9e-06   26.7   0.0    2.1  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
    2.5e-10   40.2   0.0    9.1e-06   25.3   0.0    3.0  3  Sulfatase      Sulfatase
  ------ inclusion threshold ------
      0.018   14.4   0.0      0.037   13.4   0.0    1.6  1  Metalloenzyme  Metalloenzyme superfamily


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.5e-08   0.00015       3      65 ..      56     116 ..      54     119 .. 0.89
   2 !   26.7   0.0   6.6e-10   3.9e-06     168     236 ..     179     243 ..     139     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.5e-08
                                       EEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--S CS
                      Phosphodiest   3 vislDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivg 65 
                                       +i++D+l  dll +l   l+n ++L++ g+  +     +  +T p+ as+++Gl P++H+i++
  gi|330506681|ref|YP_004383109.1|  56 IIIVDSLGYDLLMHLLPCLKNTSRLIDDGILLR-A-KAVSNHTTPAIASILSGLVPEHHKIFD 116
                                       89**********99656999*************.5.555668889****************97 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 6.6e-10
                                       HCT..SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EE CS
                      Phosphodiest 168 kel..ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGmad 236
                                       +++  e p+ll+ y+ ++D++ H  G + + ++ a+  +D++igd+ e++de+     t +i+ +DH + +
  gi|330506681|ref|YP_004383109.1| 179 LQSlrEGPRLLVSYFIGIDKSVH-MGREWSGIRSAVLHIDRCIGDITEEADEK-----TLLIICGDHPIHA 243
                                       2334799****************.7788889**********************.....*********6665 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0022        13     280     309 .]       4      33 ..       1      33 [. 0.79
   2 !   25.3   0.0   1.5e-09   9.1e-06       2     100 ..      53     143 ..      52     153 .. 0.84
   3 !    6.5   0.0   0.00076       4.6     217     264 ..     212     268 ..     204     278 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0022
                                       EETTTSHCEEECSEEEGGGHHHHHHHHTTE CS
                         Sulfatase 280 wwpgekaprvseelvshiDlfptildlagi 309
                                          +  ++  se   s+ D++pt+++l+gi
  gi|330506681|ref|YP_004383109.1|   4 TTTESEPTTESERTFSQLDIAPTVARLLGI 33 
                                       555555567889999*************97 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1.5e-09
                                       EEEEEEESSE-TT.GSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHH CS
                         Sulfatase   2 nvvliladdlgag.dlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgggg 77 
                                       n  +i++d+lg++  ++l        +n +rl + g++++   ++  +++p+ a++l+g+ p+++++ ++     g 
  gi|330506681|ref|YP_004383109.1|  53 NAAIIIVDSLGYDlLMHLLPC----LKNTSRLIDDGILLRAKAVSN-HTTPAIASILSGLVPEHHKIFDKA----GA 120
                                       566899999977544444433....556688899********9995.*******************99999....99 PP

                                       CTTTS-HHHHHHHHTT-EEEEEE CS
                         Sulfatase  78 lpqteatLpellkeaGYntaaig 100
                                       ++ +  +Lpe+  +aG ++a+i 
  gi|330506681|ref|YP_004383109.1| 121 KASSILSLPEIASAAGLRSAVIM 143
                                       *****************998885 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.00076
                                       HHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCG..............HHTTSSSCT CS
                         Sulfatase 217 sveyvDdligrvlaaLeenglldntlvvftSDhgaslee..............sngplrggk 264
                                       +v  +D +ig++ +++     +++tl+++ +Dh  + ++              ++g+ +++k
  gi|330506681|ref|YP_004383109.1| 212 AVLHIDRCIGDITEEA-----DEKTLLIICGDHPIHAGPlkrssepyyvalilGRGRSKDNK 268
                                       5777899999999999.....************99997777666666666666555555555 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.3e-06     0.037     112     188 ..     167     242 ..     112     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-06
                                       TT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT.-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 112 pemkavevaekaldailsgkfdlvvvniknaDmvGHtg.dleatiaaieaaDeavkeildaieqvdgilvvtADHgn 187
                                       pe   +e +  +l+ + +g   l+v  +   D   H g + ++  +a+ ++D++++ i+++ +++  +l++++DH+ 
  gi|330506681|ref|YP_004383109.1| 167 PEEFDREACSMTLQSLREG-PRLLVSYFIGIDKSVHMGrEWSGIRSAVLHIDRCIGDITEEADEKT-LLIICGDHPI 241
                                       5555566666667777555.55677777788888887625677788999************98888.********86 PP

                                       - CS
                                       x RF
                     Metalloenzyme 188 a 188
                                        
  gi|330506681|ref|YP_004383109.1| 242 H 242
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1803.14
//
Query:       gi|330506682|ref|YP_004383110.1|  [L=80]
Description: hypothetical protein MCON_0438 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.1   0.0      0.086   12.5   0.0    1.4  1  Lambda_Kil  Bacteriophage lambda Kil protein


Domain annotation for each model (and alignments):
>> Lambda_Kil  Bacteriophage lambda Kil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.8e-06     0.086      16      33 ..      54      71 ..      47      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.8e-06
                        Lambda_Kil 16 rFlGDekMfleAvdayKk 33
                                       +l De+M +eAvd  +k
  gi|330506682|ref|YP_004383110.1| 54 AYLSDEGMAREAVDRIRK 71
                                      6899**********9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 630.33
//
Query:       gi|330506683|ref|YP_004383111.1|  [L=52]
Description: hypothetical protein MCON_0439 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 398.27
//
Query:       gi|330506684|ref|YP_004383112.1|  [L=155]
Description: hypothetical protein MCON_0440 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00088   19.2   0.1     0.0017   18.2   0.1    1.4  1  Cdc6_C          CDC6, C terminal winged helix domain
  ------ inclusion threshold ------
      0.035   14.3   0.1      0.067   13.4   0.1    1.4  1  PaaX            PaaX-like protein
      0.091   13.0   0.0       0.19   11.9   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind


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 !   18.2   0.1   2.9e-07    0.0017      13      73 ..      77     129 ..      71     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.9e-07
                                       SS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEE CS
                            Cdc6_C  13 keevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkis 73 
                                       ++++t++e+ e+Y++++++  +     ++vs +ls+++  g+le + ++    + ++r+i+
  gi|330506684|ref|YP_004383112.1|  77 NTWFTSQELRERYETVADDIKL-----STVSTYLSRMNRDGLLEKRGNRN---NRQYRLIE 129
                                       789**************99666.....99****************98733...34555555 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.1e-05     0.067      34      67 ..      95     128 ..      91     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                              PaaX  34 GiseslvRaalsRlakaGwlvrekegrrsfYrLs 67 
                                       +i+ s+v + lsR++++G+l +  + ++  YrL 
  gi|330506684|ref|YP_004383112.1|  95 DIKLSTVSTYLSRMNRDGLLEKRGNRNNRQYRLI 128
                                       67788999************999999999**996 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.2e-05      0.19      33      56 ..      95     118 ..      93     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                                       TS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress  33 nvspssVsemlkkLekdGyveyek 56 
                                       +++ s+Vs  l+++++dG++e  +
  gi|330506684|ref|YP_004383112.1|  95 DIKLSTVSTYLSRMNRDGLLEKRG 118
                                       5889***************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1177.87
//
Query:       gi|330506685|ref|YP_004383113.1|  [L=705]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-101  328.0  23.1    5.2e-08   32.4   0.1   18.1 18  TPR_1            Tetratricopeptide repeat
    7.4e-99  316.1  36.6    3.4e-07   29.9   0.3   18.7 19  TPR_2            Tetratricopeptide repeat
    2.2e-74  244.9  35.0    1.7e-09   37.2   0.1   18.6 19  TPR_11           TPR repeat
    2.6e-73  236.2  25.1      2e-05   24.4   0.0   17.8 18  TPR_8            Tetratricopeptide repeat
    3.5e-70  232.4  36.4    2.7e-09   37.5   0.4   12.2 14  TPR_16           Tetratricopeptide repeat
    1.1e-61  205.2  45.8    2.4e-08   34.3   0.6   12.2 12  TPR_19           Tetratricopeptide repeat
    3.3e-60  195.6  38.9    0.00012   22.5   0.3   17.7 18  TPR_14           Tetratricopeptide repeat
    2.2e-52  171.7  29.6    0.00056   20.1   0.0   19.3 19  TPR_17           Tetratricopeptide repeat
    2.9e-48  162.0  50.7    1.6e-08   34.7   0.3   14.1 15  TPR_12           Tetratricopeptide repeat
      5e-43  145.1  29.1      4e-06   26.9   0.0   11.1 13  TPR_9            Tetratricopeptide repeat
    3.2e-34  115.3  30.2     0.0039   17.7   0.2   15.7 15  TPR_6            Tetratricopeptide repeat
    2.1e-29   99.3  36.6     0.0063   16.5   0.2   14.8 14  TPR_7            Tetratricopeptide repeat
    2.5e-26   91.7  11.3      0.015   15.5   0.1    8.5  9  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    3.2e-17   61.8  38.0     0.0024   17.7   0.4   12.0 11  TPR_10           Tetratricopeptide repeat
    7.7e-16   58.1  22.0    1.5e-05   24.4   1.8    6.2  6  TPR_15           Tetratricopeptide repeat
      2e-15   56.7   8.3     0.0063   15.5   0.2    7.9 10  NARP1            NMDA receptor-regulated protein 1
    2.3e-15   57.3  23.0    5.5e-05   23.6   0.6    7.4  7  BTAD             Bacterial transcriptional activator domain
      3e-13   49.9  24.4     0.0022   18.3   0.4    8.7 10  TPR_20           Tetratricopeptide repeat
    1.5e-11   44.1  25.7      0.011   15.8   0.0   12.3 13  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    9.2e-11   41.3  43.3     0.0098   16.4   1.1   11.5 10  TPR_4            Tetratricopeptide repeat
    7.4e-08   32.2  10.6     0.0039   17.1   0.0    6.4  6  TPR_3            Tetratricopeptide repeat
    2.7e-07   30.0   0.0      0.017   14.1   0.0    3.9  4  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
    3.5e-07   30.4  11.7        1.5    8.9   0.0    8.2  7  DUF3856          Domain of Unknown Function (DUF3856)
    3.9e-07   30.0  20.4       0.02   14.6   1.5    7.6  7  TPR_21           Tetratricopeptide repeat-like domain
    1.2e-06   27.5   4.3      0.012   14.4   0.0    4.0  4  PknG_TPR         Protein kinase G tetratricopeptide repeat
    2.8e-06   27.0   6.0        1.1    8.6   0.3    5.1  5  Coatomer_E       Coatomer epsilon subunit
    2.8e-05   24.6   7.5         14    6.1   0.1    7.1  7  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    4.9e-05   23.3   6.8      0.037   13.9   0.4    5.4  6  Wzy_C_2          Virulence factor membrane-bound polymerase, 
    0.00042   20.3  20.0        8.8    6.5   0.1   10.1 10  MIT              MIT (microtubule interacting and transport) 
    0.00054   19.6   0.4       0.31   10.7   0.1    3.9  3  HrpB1_HrpK       Bacterial type III secretion protein (HrpB1_
     0.0013   18.5   0.8         11    5.8   0.0    5.5  4  TOM20_plant      Plant specific mitochondrial import receptor
  ------ inclusion threshold ------
       0.02   15.0   0.0          8    6.6   0.0    3.8  3  MAS20            MAS20 protein import receptor
      0.024   14.6   0.1        1.5    8.7   0.0    3.6  5  DUF4919          Domain of unknown function (DUF4919)
      0.026   13.9  10.0        5.4    6.3   0.1    5.8  7  SNAP             Soluble NSF attachment protein, SNAP


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.2   1.2e+03       3      22 ..      48      67 ..      46      77 .. 0.82
   2 !   12.1   0.0   0.00025      0.13       1      33 [.      80     112 ..      80     113 .. 0.96
   3 !   14.8   0.0   3.4e-05     0.018       2      34 .]     115     147 ..     114     147 .. 0.96
   4 !   23.7   0.7   5.4e-08   2.9e-05       3      34 .]     150     181 ..     149     181 .. 0.94
   5 ?    6.9   0.0     0.011       5.6       2      32 ..     183     213 ..     182     215 .. 0.89
   6 !   26.3   0.1   8.3e-09   4.4e-06       3      34 .]     218     249 ..     216     249 .. 0.95
   7 !   20.2   0.0   6.8e-07   0.00036       2      34 .]     251     283 ..     250     283 .. 0.95
   8 !   12.1   0.0   0.00024      0.13       6      34 .]     289     317 ..     285     317 .. 0.92
   9 !   22.4   0.0   1.5e-07   7.7e-05       2      34 .]     319     351 ..     318     351 .. 0.96
  10 !   17.0   0.1   7.3e-06    0.0038       1      32 [.     386     417 ..     386     419 .. 0.89
  11 !   20.1   0.0   7.4e-07   0.00039       2      34 .]     421     453 ..     420     453 .. 0.96
  12 !   20.2   0.1   6.7e-07   0.00036       1      32 [.     454     485 ..     454     486 .. 0.94
  13 !   16.4   0.0   1.1e-05     0.006       2      34 .]     488     520 ..     487     520 .. 0.93
  14 !   15.4   0.0   2.3e-05     0.012       3      34 .]     523     554 ..     521     554 .. 0.94
  15 !   23.8   0.0   5.1e-08   2.7e-05       2      27 ..     556     581 ..     555     587 .. 0.94
  16 !   25.4   0.0   1.6e-08   8.3e-06       1      34 []     589     622 ..     589     622 .. 0.97
  17 !   14.2   0.0   5.5e-05     0.029       3      34 .]     625     656 ..     623     656 .. 0.95
  18 !   32.4   0.1   9.9e-11   5.2e-08       3      34 .]     659     690 ..     658     690 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.2
                                      HHHHHHHHHHHTT-HHHHHH CS
                             TPR_1  3 alynlGnayfklgkydeAle 22
                                       + + ++ y ++g y  Ale
  gi|330506685|ref|YP_004383113.1| 48 FYLREAMNYSQNGSYPLALE 67
                                      57788888**********98 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+a+  +G ++f lg ++eA+   +++L+++ +
  gi|330506685|ref|YP_004383113.1|  80 AEAWLLKGRILFGLGYLQEAIRSLDQVLRIDQS 112
                                       89****************************975 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +a+  +G + ++ g+y  A  +++ AL+l+P n
  gi|330506685|ref|YP_004383113.1| 115 EAWSLKGEIMMETGRYRMAQLCFDSALRLDPGN 147
                                       79*****************************87 PP

  == domain 4  score: 23.7 bits;  conditional E-value: 5.4e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                        +++l++  + l++yd Al  y+kAL+l+ nn
  gi|330506685|ref|YP_004383113.1| 150 LYNRLAQSQLMLEDYDHALRSYKKALSLEANN 181
                                       59*************************98776 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       ++l+n G +++ l +y eAl  ++  Le n 
  gi|330506685|ref|YP_004383113.1| 183 EILFNQGDLFLTLARYPEALNSFNLLLEQNK 213
                                       679********************98888876 PP

  == domain 6  score: 26.3 bits;  conditional E-value: 8.3e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       al++++ +y++lg+ d A+e+y  +Le nP++
  gi|330506685|ref|YP_004383113.1| 218 ALKGRAECYRQLGQVDRAEEDYYTVLEKNPED 249
                                       899***************************86 PP

  == domain 7  score: 20.2 bits;  conditional E-value: 6.8e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +++ +lG++ +  ++y   l+++++AL++nP++
  gi|330506685|ref|YP_004383113.1| 251 ESWRGLGMVRYATEDYSSSLQAFDQALKINPHD 283
                                       6899***************************86 PP

  == domain 8  score: 12.1 bits;  conditional E-value: 0.00024
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   6 nlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++G +++  g++  Ale y+ AL l  +n
  gi|330506685|ref|YP_004383113.1| 289 GKGDLLLARGNFSSALESYSAALLLKKDN 317
                                       6899*******************998876 PP

  == domain 9  score: 22.4 bits;  conditional E-value: 1.5e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        aly++G+a+ +lg+ +eA ++y++ Lel+P+n
  gi|330506685|ref|YP_004383113.1| 319 SALYGKGLALSSLGREKEANKCYRRILELEPDN 351
                                       69*****************************98 PP

  == domain 10  score: 17.0 bits;  conditional E-value: 7.3e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+al +++ a + lg++d+Al+ ye+ L ++ 
  gi|330506685|ref|YP_004383113.1| 386 ARALLGMAKAQLDLGDLDQALQSYEELLGHDS 417
                                       79***********************9776665 PP

  == domain 11  score: 20.1 bits;  conditional E-value: 7.4e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        a+ ++G +++ + + d A+e +++AL ++P+n
  gi|330506685|ref|YP_004383113.1| 421 AAWIGRGEILLLQTNIDPAIESFNRALDIEPQN 453
                                       69*****************************97 PP

  == domain 12  score: 20.2 bits;  conditional E-value: 6.7e-07
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       ++al +l+ a++++g+++eA  yye A+  +P
  gi|330506685|ref|YP_004383113.1| 454 PDALMGLAEALHQKGRLEEARSYYEAAIAEEP 485
                                       589*************************9888 PP

  == domain 13  score: 16.4 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       + + +lGn++  +g+y + +  +e AL+ +P++
  gi|330506685|ref|YP_004383113.1| 488 RGYRGLGNILCAQGEYGQSIPLFESALSQEPSD 520
                                       67999*************************986 PP

  == domain 14  score: 15.4 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +l ++G+a+   g+   Al+++++ ++lnP++
  gi|330506685|ref|YP_004383113.1| 523 SLMGKGLALAATGNSSGALQCFNEIVSLNPED 554
                                       7899**************************86 PP

  == domain 15  score: 23.8 bits;  conditional E-value: 5.1e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekA 27 
                                        a+ n+G ++  lg+ydeA e  +kA
  gi|330506685|ref|YP_004383113.1| 556 AAWSNRGSIFAALGRYDEARESLQKA 581
                                       69***********************9 PP

  == domain 16  score: 25.4 bits;  conditional E-value: 1.6e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+++ynlG++y+ + ++++  +++e A +l P++
  gi|330506685|ref|YP_004383113.1| 589 ADIWYNLGQVYRLMDRHNQSRQAFENATRLSPDD 622
                                       799*****************************96 PP

  == domain 17  score: 14.2 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                        +  lG+a  + g+ + Al+  ++A+ l+P+n
  gi|330506685|ref|YP_004383113.1| 625 LWLELGLAQERTGEAKLALKSLQRAVVLDPKN 656
                                       6999**************************98 PP

  == domain 18  score: 32.4 bits;  conditional E-value: 9.9e-11
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a y l++a+  +g+++eAl+++e++Le+nP+n
  gi|330506685|ref|YP_004383113.1| 659 AQYSLALALAGQGRFQEALQAFERVLEINPKN 690
                                       779***************************98 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.29   1.5e+02       3      32 ..      48      77 ..      46      79 .. 0.89
   2 !   18.4   0.0     3e-06    0.0016       1      31 [.      80     110 ..      80     113 .. 0.95
   3 !   21.2   0.0   3.7e-07    0.0002       2      34 .]     115     147 ..     114     147 .. 0.97
   4 !   21.1   0.8   4.3e-07   0.00023       3      34 .]     150     181 ..     149     181 .. 0.93
   5 !   11.1   0.0   0.00066      0.35       2      33 ..     183     214 ..     182     215 .. 0.93
   6 !   15.8   0.1   2.1e-05     0.011       3      34 .]     218     249 ..     216     249 .. 0.93
   7 !   21.7   0.0   2.7e-07   0.00014       2      34 .]     251     283 ..     250     283 .. 0.95
   8 !   11.7   0.1   0.00044      0.23       7      34 .]     290     317 ..     287     317 .. 0.92
   9 !   21.9   0.0   2.3e-07   0.00012       3      34 .]     320     351 ..     318     351 .. 0.96
  10 ?   -0.1   0.0       2.6   1.4e+03       3      34 .]     354     385 ..     352     385 .. 0.83
  11 !   13.7   0.1   9.6e-05     0.051       1      30 [.     386     415 ..     386     419 .. 0.89
  12 !   18.5   0.0   2.9e-06    0.0015       2      34 .]     421     453 ..     420     453 .. 0.96
  13 !   23.4   0.4   7.3e-08   3.9e-05       1      32 [.     454     485 ..     454     486 .. 0.95
  14 !   15.3   0.0     3e-05     0.016       2      34 .]     488     520 ..     487     520 .. 0.93
  15 !   15.3   0.0   2.9e-05     0.016       3      34 .]     523     554 ..     521     554 .. 0.93
  16 !   21.7   0.1   2.6e-07   0.00014       2      27 ..     556     581 ..     555     585 .. 0.94
  17 !   24.0   0.0   4.8e-08   2.5e-05       1      34 []     589     622 ..     589     622 .. 0.97
  18 !   15.7   0.0   2.2e-05     0.012       3      34 .]     625     656 ..     623     656 .. 0.95
  19 !   29.9   0.3   6.4e-10   3.4e-07       3      34 .]     659     690 ..     657     690 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.29
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldP 32
                                       + + ++ y ++g y  Ale  + +le+d 
  gi|330506685|ref|YP_004383113.1| 48 FYLREAMNYSQNGSYPLALERINLSLEIDD 77
                                      68999***************9999999885 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       aea+   G++++ lg ++eA++ ++++l++d
  gi|330506685|ref|YP_004383113.1|  80 AEAWLLKGRILFGLGYLQEAIRSLDQVLRID 110
                                       89***************************98 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 3.7e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ea+   G++ ++ g+y  A  +f+ Al+ldP+n
  gi|330506685|ref|YP_004383113.1| 115 EAWSLKGEIMMETGRYRMAQLCFDSALRLDPGN 147
                                       79*****************************97 PP

  == domain 4  score: 21.1 bits;  conditional E-value: 4.3e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++++l+++ + l dy+ Al+ ++kAl+l+ nn
  gi|330506685|ref|YP_004383113.1| 150 LYNRLAQSQLMLEDYDHALRSYKKALSLEANN 181
                                       699************************98776 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.00066
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       e+l+n+G++ + l +y eAl+ f+  le +  
  gi|330506685|ref|YP_004383113.1| 183 EILFNQGDLFLTLARYPEALNSFNLLLEQNKS 214
                                       789************************99975 PP

  == domain 6  score: 15.8 bits;  conditional E-value: 2.1e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       al  ++++y++lg+ ++A+e++  +le +P++
  gi|330506685|ref|YP_004383113.1| 218 ALKGRAECYRQLGQVDRAEEDYYTVLEKNPED 249
                                       7889**************************86 PP

  == domain 7  score: 21.7 bits;  conditional E-value: 2.7e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       e +  lG++ y+  dy   l+af++Al+++P++
  gi|330506685|ref|YP_004383113.1| 251 ESWRGLGMVRYATEDYSSSLQAFDQALKINPHD 283
                                       789****************************86 PP

  == domain 8  score: 11.7 bits;  conditional E-value: 0.00044
                             TPR_2   7 lGlayyklgdyeeAleafekAleldPnn 34 
                                        G++++++g++  Ale + +Al l  +n
  gi|330506685|ref|YP_004383113.1| 290 KGDLLLARGNFSSALESYSAALLLKKDN 317
                                       6999******************998876 PP

  == domain 9  score: 21.9 bits;  conditional E-value: 2.3e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       aly  Gla+  lg+ +eA +++++ lel+P+n
  gi|330506685|ref|YP_004383113.1| 320 ALYGKGLALSSLGREKEANKCYRRILELEPDN 351
                                       89****************************98 PP

  == domain 10  score: -0.1 bits;  conditional E-value: 2.6
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       al  +++ ++++++  +A+e++   l  dP+n
  gi|330506685|ref|YP_004383113.1| 354 ALQKIADDLLERNESIQAAEHYGLILGQDPKN 385
                                       7788899999999999******8888777765 PP

  == domain 11  score: 13.7 bits;  conditional E-value: 9.6e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a+al  +++a + lgd+++Al+ +e+ l +
  gi|330506685|ref|YP_004383113.1| 386 ARALLGMAKAQLDLGDLDQALQSYEELLGH 415
                                       689999********************9855 PP

  == domain 12  score: 18.5 bits;  conditional E-value: 2.9e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        a+  +G++++ + + + A+e f++Al ++P+n
  gi|330506685|ref|YP_004383113.1| 421 AAWIGRGEILLLQTNIDPAIESFNRALDIEPQN 453
                                       69*****************************97 PP

  == domain 13  score: 23.4 bits;  conditional E-value: 7.3e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       ++al+ l++a+ ++g++eeA+ ++e+A++ +P
  gi|330506685|ref|YP_004383113.1| 454 PDALMGLAEALHQKGRLEEARSYYEAAIAEEP 485
                                       5899*************************998 PP

  == domain 14  score: 15.3 bits;  conditional E-value: 3e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +++  lG+++ ++g+y + + +fe Al+ +P +
  gi|330506685|ref|YP_004383113.1| 488 RGYRGLGNILCAQGEYGQSIPLFESALSQEPSD 520
                                       57999************************9975 PP

  == domain 15  score: 15.3 bits;  conditional E-value: 2.9e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                        l+  Gla+++ g+   Al++f++ ++l+P++
  gi|330506685|ref|YP_004383113.1| 523 SLMGKGLALAATGNSSGALQCFNEIVSLNPED 554
                                       67889*************************86 PP

  == domain 16  score: 21.7 bits;  conditional E-value: 2.6e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekA 27 
                                        a+ n+G + ++lg+y+eA+e ++kA
  gi|330506685|ref|YP_004383113.1| 556 AAWSNRGSIFAALGRYDEARESLQKA 581
                                       69***********************9 PP

  == domain 17  score: 24.0 bits;  conditional E-value: 4.8e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+++ynlG++y+ ++++++ ++afe A +l P++
  gi|330506685|ref|YP_004383113.1| 589 ADIWYNLGQVYRLMDRHNQSRQAFENATRLSPDD 622
                                       789*****************************97 PP

  == domain 18  score: 15.7 bits;  conditional E-value: 2.2e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++ +lGla ++ g+ + Al+ +++A+ ldP+n
  gi|330506685|ref|YP_004383113.1| 625 LWLELGLAQERTGEAKLALKSLQRAVVLDPKN 656
                                       799***************************97 PP

  == domain 19  score: 29.9 bits;  conditional E-value: 6.4e-10
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a y l+la++ +g+++eAl+afe++le++P+n
  gi|330506685|ref|YP_004383113.1| 659 AQYSLALALAGQGRFQEALQAFERVLEINPKN 690
                                       7899**************************97 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.039        21       4      42 .]      56      94 ..      55      94 .. 0.92
   2 !   17.8   0.0   3.8e-06     0.002       1      42 []      87     128 ..      87     128 .. 0.96
   3 !   10.8   0.0   0.00057       0.3       1      39 [.     121     159 ..     121     161 .. 0.90
   4 !   19.2   0.1   1.4e-06   0.00073       8      39 ..     162     193 ..     160     196 .. 0.92
   5 ?    2.1   0.0      0.29   1.6e+02       1      31 [.     189     219 ..     189     226 .. 0.80
   6 !   14.6   0.0   3.6e-05     0.019       4      39 ..     226     261 ..     223     263 .. 0.94
   7 !    9.4   0.0    0.0015      0.81       3      27 ..     259     283 ..     257     286 .. 0.88
   8 !   28.2   0.1     2e-09   1.1e-06       1      42 []     291     332 ..     291     332 .. 0.96
   9 !    8.7   0.1    0.0027       1.4       1      32 [.     325     356 ..     325     360 .. 0.87
  10 ?    6.6   0.1     0.011         6      12      42 .]     370     400 ..     359     400 .. 0.78
  11 !   11.0   0.1    0.0005      0.26       5      39 ..     397     431 ..     394     434 .. 0.89
  12 !   28.0   0.0   2.4e-09   1.3e-06       3      42 .]     429     468 ..     427     468 .. 0.89
  13 !    8.7   1.1    0.0027       1.4       2      22 ..     462     482 ..     461     486 .. 0.88
  14 !   16.1   0.0   1.3e-05    0.0067       1      42 []     494     535 ..     494     535 .. 0.97
  15 !   14.4   0.0   4.1e-05     0.022       1      42 []     528     569 ..     528     569 .. 0.96
  16 !   37.2   0.1   3.2e-12   1.7e-09       1      38 [.     562     599 ..     562     603 .. 0.96
  17 !   18.6   0.0   2.1e-06    0.0011       4      42 .]     599     637 ..     598     637 .. 0.91
  18 !   20.0   0.1   7.5e-07   0.00039       8      42 .]     637     671 ..     636     671 .. 0.92
  19 !   14.9   0.0     3e-05     0.016       7      30 ..     670     693 ..     668     697 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.039
                            TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      y + G y+ A+e+ +  l++d + aea++  G +++ +G
  gi|330506685|ref|YP_004383113.1| 56 YSQNGSYPLALERINLSLEIDDELAEAWLLKGRILFGLG 94
                                      55899***************************9999887 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.8e-06
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G++++ +G + eAi ++ + l++d++  ea++  G+++++ G
  gi|330506685|ref|YP_004383113.1|  87 GRILFGLGYLQEAIRSLDQVLRIDQSLDEAWSLKGEIMMETG 128
                                       8999********************************999887 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00057
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       G + +e G+y  A  ++  Al+ldP n ++y+ L++ ++
  gi|330506685|ref|YP_004383113.1| 121 GEIMMETGRYRMAQLCFDSALRLDPGNMTLYNRLAQSQL 159
                                       677789999999**********************99775 PP

  == domain 4  score: 19.2 bits;  conditional E-value: 1.4e-06
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                        +y+ A+ +YkkAl l  +n e+++n G++++
  gi|330506685|ref|YP_004383113.1| 162 EDYDHALRSYKKALSLEANNTEILFNQGDLFL 193
                                       58************************999886 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.29
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeay 31 
                                       Gd++  + +y+eA+++++  l+ + ++  a+
  gi|330506685|ref|YP_004383113.1| 189 GDLFLTLARYPEALNSFNLLLEQNKSDILAL 219
                                       666777779*********9999999988775 PP

  == domain 6  score: 14.6 bits;  conditional E-value: 3.6e-05
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       y+++G+ + A e+Y + l+ +P++ e + +LG + y
  gi|330506685|ref|YP_004383113.1| 226 YRQLGQVDRAEEDYYTVLEKNPEDFESWRGLGMVRY 261
                                       9*******************************8877 PP

  == domain 7  score: 9.4 bits;  conditional E-value: 0.0015
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdn 27 
                                       + y+  +y  +++a+ +Alk++P +
  gi|330506685|ref|YP_004383113.1| 259 VRYATEDYSSSLQAFDQALKINPHD 283
                                       679999*****************76 PP

  == domain 8  score: 28.2 bits;  conditional E-value: 2e-09
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       Gd++ ++G++  A+e+Y++Al l+ dn++a+y+ Gla+  +G
  gi|330506685|ref|YP_004383113.1| 291 GDLLLARGNFSSALESYSAALLLKKDNVSALYGKGLALSSLG 332
                                       99***********************************98777 PP

  == domain 9  score: 8.7 bits;  conditional E-value: 0.0027
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayy 32 
                                       G a+ ++G+ +eA ++Y++ l+l Pdn  a+ 
  gi|330506685|ref|YP_004383113.1| 325 GLALSSLGREKEANKCYRRILELEPDNIIALQ 356
                                       6778899999*****************98875 PP

  == domain 10  score: 6.6 bits;  conditional E-value: 0.011
                            TPR_11  12 eAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +A e+Y   l  dP+na+a++++++a++ +G
  gi|330506685|ref|YP_004383113.1| 370 QAAEHYGLILGQDPKNARALLGMAKAQLDLG 400
                                       566666666678***************9988 PP

  == domain 11  score: 11.0 bits;  conditional E-value: 0.0005
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                        ++G++++A+++Y++ l  d+++  a+ ++G++++
  gi|330506685|ref|YP_004383113.1| 397 LDLGDLDQALQSYEELLGHDSNSSAAWIGRGEILL 431
                                       589*******************9999999999876 PP

  == domain 12  score: 28.0 bits;  conditional E-value: 2.4e-09
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ++  q +++ Aie++++Al++ P+n++a+ +L++a++++G
  gi|330506685|ref|YP_004383113.1| 429 ILLLQTNIDPAIESFNRALDIEPQNPDALMGLAEALHQKG 468
                                       5555667888****************************98 PP

  == domain 13  score: 8.7 bits;  conditional E-value: 0.0027
                            TPR_11   2 dayyeqGkyeeAieaYkkAlk 22 
                                        a++++G++eeA   Y++A++
  gi|330506685|ref|YP_004383113.1| 462 EALHQKGRLEEARSYYEAAIA 482
                                       589****************98 PP

  == domain 14  score: 16.1 bits;  conditional E-value: 1.3e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+++++qG+y ++i  ++ Al   P++ e + + Gla+++ G
  gi|330506685|ref|YP_004383113.1| 494 GNILCAQGEYGQSIPLFESALSQEPSDTESLMGKGLALAATG 535
                                       9************************************99887 PP

  == domain 15  score: 14.4 bits;  conditional E-value: 4.1e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G a+ + G+  +A++++++ + l+P++  a++n+G +++++G
  gi|330506685|ref|YP_004383113.1| 528 GLALAATGNSSGALQCFNEIVSLNPEDSAAWSNRGSIFAALG 569
                                       7899999*******************************9998 PP

  == domain 16  score: 37.2 bits;  conditional E-value: 3.2e-12
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       G ++ ++G+y+eA e+++kA  +++++a+++ynLG++y
  gi|330506685|ref|YP_004383113.1| 562 GSIFAALGRYDEARESLQKAAGISSSSADIWYNLGQVY 599
                                       889**********************************9 PP

  == domain 17  score: 18.6 bits;  conditional E-value: 2.1e-06
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       y+   + +++ +a+++A +l+Pd++ ++++LGla+ + G
  gi|330506685|ref|YP_004383113.1| 599 YRLMDRHNQSRQAFENATRLSPDDPVLWLELGLAQERTG 637
                                       6666788999*************************9988 PP

  == domain 18  score: 20.0 bits;  conditional E-value: 7.5e-07
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+ + A++++++A+ ldP+n  a y L+la++ qG
  gi|330506685|ref|YP_004383113.1| 637 GEAKLALKSLQRAVVLDPKNEFAQYSLALALAGQG 671
                                       55667***************************998 PP

  == domain 19  score: 14.9 bits;  conditional E-value: 3e-05
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaea 30 
                                       qG++ eA++a+++ l+++P+n  a
  gi|330506685|ref|YP_004383113.1| 670 QGRFQEALQAFERVLEINPKNDLA 693
                                       8********************877 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       5.5   2.9e+03       2      31 ..      47      76 ..      46      78 .. 0.74
   2 !   20.9   0.0   5.1e-07   0.00027       1      32 [.      80     111 ..      80     113 .. 0.96
   3 !   13.1   0.0   0.00016     0.084       2      33 ..     115     146 ..     114     147 .. 0.95
   4 !   14.9   0.7   4.4e-05     0.023       3      34 .]     150     181 ..     149     181 .. 0.94
   5 ?    5.6   0.0     0.042        22       2      33 ..     183     214 ..     182     215 .. 0.91
   6 !    8.9   0.0    0.0035       1.8       8      33 ..     223     248 ..     221     249 .. 0.88
   7 !    9.6   0.0    0.0021       1.1       6      33 ..     255     282 ..     250     283 .. 0.88
   8 ?    7.4   0.1     0.011       5.7       6      34 .]     289     317 ..     284     317 .. 0.91
   9 !   19.9   0.1   1.1e-06   0.00057       2      34 .]     319     351 ..     318     351 .. 0.95
  10 !   12.9   0.1   0.00018     0.097       1      28 [.     386     413 ..     386     418 .. 0.92
  11 !   13.3   0.0   0.00014     0.072       3      34 .]     422     453 ..     420     453 .. 0.94
  12 !   19.7   0.1   1.3e-06   0.00067       2      32 ..     455     485 ..     454     486 .. 0.90
  13 ?    3.6   0.0      0.19        98       7      33 ..     493     519 ..     488     520 .. 0.89
  14 !    9.8   0.0    0.0019         1       2      34 .]     522     554 ..     521     554 .. 0.93
  15 !   20.7   0.0   5.8e-07   0.00031       3      31 ..     557     585 ..     555     588 .. 0.92
  16 !   24.4   0.0   3.8e-08     2e-05       1      34 []     589     622 ..     589     622 .. 0.97
  17 !    9.5   0.0    0.0023       1.2       3      34 .]     625     656 ..     624     656 .. 0.95
  18 !   20.1   0.0   9.1e-07   0.00048       4      34 .]     660     690 ..     659     690 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 5.5
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleld 31
                                      + y++ ++ y++ g y  A e ++  le+d
  gi|330506685|ref|YP_004383113.1| 47 DFYLREAMNYSQNGSYPLALERINLSLEID 76
                                      568888999999999977777666666665 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.1e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       aea++++g+i++ lg ++eA+ ++ ++l++d+
  gi|330506685|ref|YP_004383113.1|  80 AEAWLLKGRILFGLGYLQEAIRSLDQVLRIDQ 111
                                       79****************************97 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00016
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ea+ ++g i +++g+y +A+ ++  al+ldp 
  gi|330506685|ref|YP_004383113.1| 115 EAWSLKGEIMMETGRYRMAQLCFDSALRLDPG 146
                                       799***************************96 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +y++l++  l l+dy+ A  +y+kal+l+ +n
  gi|330506685|ref|YP_004383113.1| 150 LYNRLAQSQLMLEDYDHALRSYKKALSLEANN 181
                                       699*************************9886 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.042
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       e+++n g++ l+l +y eA  +++  le +++
  gi|330506685|ref|YP_004383113.1| 183 EILFNQGDLFLTLARYPEALNSFNLLLEQNKS 214
                                       789*********************99998775 PP

  == domain 6  score: 8.9 bits;  conditional E-value: 0.0035
                                       HHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyyekaleldpd 33 
                                       + +y++lg+ + A+e y  +le +p+
  gi|330506685|ref|YP_004383113.1| 223 AECYRQLGQVDRAEEDYYTVLEKNPE 248
                                       789**************999987765 PP

  == domain 7  score: 9.6 bits;  conditional E-value: 0.0021
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpd 33 
                                        lg++   ++dy ++ +++ +al+++p 
  gi|330506685|ref|YP_004383113.1| 255 GLGMVRYATEDYSSSLQAFDQALKINPH 282
                                       589999999******************7 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.011
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        +g+++l  g++ +A e+y  al l++dn
  gi|330506685|ref|YP_004383113.1| 289 GKGDLLLARGNFSSALESYSAALLLKKDN 317
                                       589**********************9986 PP

  == domain 9  score: 19.9 bits;  conditional E-value: 1.1e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +a+y +g+++++lg+ +eA ++y++ lel+pdn
  gi|330506685|ref|YP_004383113.1| 319 SALYGKGLALSSLGREKEANKCYRRILELEPDN 351
                                       689****************************97 PP

  == domain 10  score: 12.9 bits;  conditional E-value: 0.00018
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekal 28 
                                       a+a++ ++++ l+lgd+++A ++ye+ l
  gi|330506685|ref|YP_004383113.1| 386 ARALLGMAKAQLDLGDLDQALQSYEELL 413
                                       789999*******************987 PP

  == domain 11  score: 13.3 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+   g i+l + +++ A+e++++al+++p+n
  gi|330506685|ref|YP_004383113.1| 422 AWIGRGEILLLQTNIDPAIESFNRALDIEPQN 453
                                       89999*************************96 PP

  == domain 12  score: 19.7 bits;  conditional E-value: 1.3e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +a++ l+ +++++g++eeA +yye a+  +p
  gi|330506685|ref|YP_004383113.1| 455 DALMGLAEALHQKGRLEEARSYYEAAIAEEP 485
                                       68899*********************97665 PP

  == domain 13  score: 3.6 bits;  conditional E-value: 0.19
                                       HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                                       lg+i+  +g+y +++  +e al+ +p+
  gi|330506685|ref|YP_004383113.1| 493 LGNILCAQGEYGQSIPLFESALSQEPS 519
                                       78888899***************9987 PP

  == domain 14  score: 9.8 bits;  conditional E-value: 0.0019
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       e+++ +g+++  +g+   A +++++ ++l+p++
  gi|330506685|ref|YP_004383113.1| 522 ESLMGKGLALAATGNSSGALQCFNEIVSLNPED 554
                                       678899*************************86 PP

  == domain 15  score: 20.7 bits;  conditional E-value: 5.8e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a+ n gsi   lg+y+eA e+++ka  ++
  gi|330506685|ref|YP_004383113.1| 557 AWSNRGSIFAALGRYDEARESLQKAAGIS 585
                                       899**********************9887 PP

  == domain 16  score: 24.4 bits;  conditional E-value: 3.8e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+++ynlg++y+ + +++++ +++e a++l+pd+
  gi|330506685|ref|YP_004383113.1| 589 ADIWYNLGQVYRLMDRHNQSRQAFENATRLSPDD 622
                                       789*****************************96 PP

  == domain 17  score: 9.5 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +++ lg++ + +g+ + A +++++a+ ldp+n
  gi|330506685|ref|YP_004383113.1| 625 LWLELGLAQERTGEAKLALKSLQRAVVLDPKN 656
                                       5999**************************96 PP

  == domain 18  score: 20.1 bits;  conditional E-value: 9.1e-07
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        y l++++  +g+++eA +++e++le++p+n
  gi|330506685|ref|YP_004383113.1| 660 QYSLALALAGQGRFQEALQAFERVLEINPKN 690
                                       699**************************97 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.4e-05     0.013       2      62 ..      51     108 ..      50     114 .. 0.89
   2 !   15.8   0.1   3.2e-05     0.017       8      61 ..     125     175 ..     119     183 .. 0.91
   3 !   20.5   0.3   1.1e-06   0.00056       2      58 ..     187     241 ..     186     243 .. 0.92
   4 !   30.9   0.0   5.9e-10   3.1e-07       7      67 ..     226     283 ..     221     284 .. 0.95
   5 !   28.5   0.1   3.4e-09   1.8e-06       2      66 ..     289     350 ..     288     352 .. 0.92
   6 !   22.9   0.9   1.9e-07    0.0001       3      67 ..     358     419 ..     357     420 .. 0.95
   7 !   35.8   0.0   1.8e-11   9.4e-09       2      68 .]     391     454 ..     390     454 .. 0.95
   8 !   37.5   0.4   5.2e-12   2.7e-09      10      63 ..     433     483 ..     424     487 .. 0.88
   9 !   25.1   0.0     4e-08   2.1e-05       3      67 ..     493     554 ..     491     555 .. 0.92
  10 !   26.4   0.0   1.5e-08   7.9e-06      11      66 ..     535     587 ..     535     589 .. 0.92
  11 !   18.5   0.2   4.3e-06    0.0023       3      44 ..     561     599 ..     560     601 .. 0.92
  12 !   24.1   0.2   7.9e-08   4.2e-05       1      67 [.     593     656 ..     593     657 .. 0.88
  13 !   28.9   1.7   2.5e-09   1.3e-06       4      67 ..     630     690 ..     629     691 .. 0.91
  14 !   19.0   0.3   3.2e-06    0.0017       1      38 [.     661     695 ..     661     700 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.4e-05
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                        +a+ + ++g y+ A+++ +  l+ d    + aeA+ll+g++++ +g l+eA+  ++  lr
  gi|330506685|ref|YP_004383113.1|  51 REAMNYSQNGSYPLALERINLSLEID---DELAEAWLLKGRILFGLGYLQEAIRSLDQVLR 108
                                       6899999*******************...9***********************66666665 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.2e-05
                            TPR_16   8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       ++ g+y+ A+  ++ al++d   P +   ++ l+++ l + +++ A+  y++al
  gi|330506685|ref|YP_004383113.1| 125 METGRYRMAQLCFDSALRLD---PGNMTLYNRLAQSQLMLEDYDHALRSYKKAL 175
                                       5789****************...************************9999987 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 1.1e-06
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyr 58 
                                       ++++++l + +y++A++ ++ +l++++s+ +   Al ++++++ ++g +++A+ ++y 
  gi|330506685|ref|YP_004383113.1| 187 NQGDLFLTLARYPEALNSFNLLLEQNKSDIL---ALKGRAECYRQLGQVDRAEeDYYT 241
                                       89************************77777...*******************88875 PP

  == domain 4  score: 30.9 bits;  conditional E-value: 5.9e-10
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++++g+ d+A++ + ++l+++   P++ e++ +lg ++++  ++   +++++ al+  p +
  gi|330506685|ref|YP_004383113.1| 226 YRQLGQVDRAEEDYYTVLEKN---PEDFESWRGLGMVRYATEDYSSSLQAFDQALKINPHD 283
                                       889******************...*******************************999976 PP

  == domain 5  score: 28.5 bits;  conditional E-value: 3.4e-09
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                        +++++l++g++  A++ + aal +     d++ Al+++g+a+  +gr +eA   yr+ l+  pd
  gi|330506685|ref|YP_004383113.1| 289 GKGDLLLARGNFSSALESYSAALLLK---KDNVSALYGKGLALSSLGREKEANKCYRRILELEPD 350
                                       579***********************...***********************8888888877666 PP

  == domain 6  score: 22.9 bits;  conditional E-value: 1.9e-07
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                        a+++l++++  +Aa+ +   l +d   P +a+All+ + a l +g+l+ A++ y+++l++++++
  gi|330506685|ref|YP_004383113.1| 358 IADDLLERNESIQAAEHYGLILGQD---PKNARALLGMAKAQLDLGDLDQALQSYEELLGHDSNS 419
                                       699**********************...*********************************9986 PP

  == domain 7  score: 35.8 bits;  conditional E-value: 1.8e-11
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                        +a+a l++gd d+A+  +e++l  d   +   +A+ ++g+++l q + ++A++ +++al+  p++p
  gi|330506685|ref|YP_004383113.1| 391 GMAKAQLDLGDLDQALQSYEELLGHD---SNSSAAWIGRGEILLLQTNIDPAIESFNRALDIEPQNP 454
                                       5799**********************...88888****************************99997 PP

  == domain 8  score: 37.5 bits;  conditional E-value: 5.2e-12
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       + + d A++ +++al+     P++++Al++l++a+ ++grl+eA+ +y+aa+++
  gi|330506685|ref|YP_004383113.1| 433 QTNIDPAIESFNRALDIE---PQNPDALMGLAEALHQKGRLEEARSYYEAAIAE 483
                                       667788************...*****************************9976 PP

  == domain 9  score: 25.1 bits;  conditional E-value: 4e-08
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       l++++ ++g+y + ++++e al +    P + e+l+++g+a+++ g+  +A++ +++ +   p +
  gi|330506685|ref|YP_004383113.1| 493 LGNILCAQGEYGQSIPLFESALSQE---PSDTESLMGKGLALAATGNSSGALQCFNEIVSLNPED 554
                                       7899999******************...*************************999988777765 PP

  == domain 10  score: 26.4 bits;  conditional E-value: 1.5e-08
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       g+   A+  +++ + ++   P++ +A+ ++g +++++gr++eA++ +++a++ +++
  gi|330506685|ref|YP_004383113.1| 535 GNSSGALQCFNEIVSLN---PEDSAAWSNRGSIFAALGRYDEARESLQKAAGISSS 587
                                       67788************...************************999999988776 PP

  == domain 11  score: 18.5 bits;  conditional E-value: 4.3e-06
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaa 44 
                                       ++ +++++g+yd+A++ l+ a       +  a+ +++lg+++
  gi|330506685|ref|YP_004383113.1| 561 RGSIFAALGRYDEARESLQKAAGIS---SSSADIWYNLGQVY 599
                                       678899*******************...99999*******98 PP

  == domain 12  score: 24.1 bits;  conditional E-value: 7.9e-08
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++l++ ++   +  + + a+e a+++ p++P+    +l+lg+a  r g+ ++A+  +++a+  +p++
  gi|330506685|ref|YP_004383113.1| 593 YNLGQVYRLMDRHNQSRQAFENATRLSPDDPV---LWLELGLAQERTGEAKLALKSLQRAVVLDPKN 656
                                       5667777777788999***********88888...*******************9999999999987 PP

  == domain 13  score: 28.9 bits;  conditional E-value: 2.5e-09
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++a  r g+   A++ l++a+ +dp+  +   A++ l++a++ qgr++eA++++++ l+  p++
  gi|330506685|ref|YP_004383113.1| 630 GLAQERTGEAKLALKSLQRAVVLDPKNEF---AQYSLALALAGQGRFQEALQAFERVLEINPKN 690
                                       777888899999************77777...**************************999976 PP

  == domain 14  score: 19.0 bits;  conditional E-value: 3.2e-06
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAll 38 
                                       + la+a++ +g++++A+ a+e++l+ +   P +  A +
  gi|330506685|ref|YP_004383113.1| 661 YSLALALAGQGRFQEALQAFERVLEIN---PKNDLAKY 695
                                       679999999999999999999999999...77666666 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   1.2e-06   0.00063       3      67 ..      58     122 ..      57     123 .. 0.93
   2 !   11.7   0.2   0.00052      0.28       2      45 ..     125     168 ..     124     169 .. 0.94
   3 !   20.3   0.9   1.1e-06   0.00059       4      58 ..     161     215 ..     158     222 .. 0.92
   4 !   17.5   0.1   8.6e-06    0.0045       7      62 ..     198     254 ..     197     258 .. 0.88
   5 !   25.7   0.1   2.4e-08   1.2e-05       3      66 ..     262     323 ..     260     325 .. 0.92
   6 !   24.4   0.3   5.9e-08   3.1e-05       1      58 [.     294     351 ..     294     359 .. 0.93
   7 !   30.9   2.6   5.5e-10   2.9e-07       2      61 ..     363     422 ..     362     425 .. 0.90
   8 !   34.3   0.6   4.6e-11   2.4e-08       2      57 ..     431     486 ..     430     493 .. 0.90
   9 !   24.4   0.0   5.9e-08   3.1e-05       3      63 ..     499     559 ..     497     562 .. 0.95
  10 !   15.9   0.1   2.6e-05     0.014       3      46 ..     567     610 ..     565     612 .. 0.92
  11 !   18.2   0.9   5.2e-06    0.0028       6      66 ..     604     666 ..     600     668 .. 0.91
  12 !   18.6   0.1   3.7e-06     0.002       2      29 ..     668     695 ..     667     697 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.2e-06
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAk 67 
                                       ++g y  Al++    l+ d + aea+ll  ++l+ lg l+eA++ Ld++++ d+   +++sL++ 
  gi|330506685|ref|YP_004383113.1|  58 QNGSYPLALERINLSLEIDDELAEAWLLKGRILFGLGYLQEAIRSLDQVLRIDQSLDEAWSLKGE 122
                                       578899999999999****************************************9999999875 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00052
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAe 45 
                                       ++ g+y  A+  + +al  dp+n  +  +LA+ +l l ++d A 
  gi|330506685|ref|YP_004383113.1| 125 METGRYRMAQLCFDSALRLDPGNMTLYNRLAQSQLMLEDYDHAL 168
                                       67899999*********************************996 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 1.1e-06
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                        +dy+ Al+ +++al+ +++n e++ +  ++ l l ++ eA +  + l+e+++ d
  gi|330506685|ref|YP_004383113.1| 161 LEDYDHALRSYKKALSLEANNTEILFNQGDLFLTLARYPEALNSFNLLLEQNKSD 215
                                       58*************************************************9984 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 8.6e-06
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.arya 62 
                                       y eAl+ +  +l+++  +  a+ + Ae++ +lgq+d Ae+   +++e++p d + ++
  gi|330506685|ref|YP_004383113.1| 198 YPEALNSFNLLLEQNKSDILALKGRAECYRQLGQVDRAEEDYYTVLEKNPEDfESWR 254
                                       88999999999****************************988888888888766665 PP

  == domain 5  score: 25.7 bits;  conditional E-value: 2.4e-08
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66 
                                       a +dy + l+++ qal+ +p++    l+  ++lla g++  A +  +a+++ ++d  ++++L +
  gi|330506685|ref|YP_004383113.1| 262 ATEDYSSSLQAFDQALKINPHDIQTILGKGDLLLARGNFSSALESYSAALLLKKD--NVSALYG 323
                                       56799999***********************************************..7777765 PP

  == domain 6  score: 24.4 bits;  conditional E-value: 5.9e-08
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       lla+g++ +Al+ +++al  + +n  a+++   al +lg+ +eA ++  +++e +pd+
  gi|330506685|ref|YP_004383113.1| 294 LLARGNFSSALESYSAALLLKKDNVSALYGKGLALSSLGREKEANKCYRRILELEPDN 351
                                       79*******************************************************4 PP

  == domain 7  score: 30.9 bits;  conditional E-value: 5.5e-10
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       l+++   +A++++  +l +dpkna+a+l++A+a+l lg+ld+A +  ++l+ +d +++++
  gi|330506685|ref|YP_004383113.1| 363 LERNESIQAAEHYGLILGQDPKNARALLGMAKAQLDLGDLDQALQSYEELLGHDSNSSAA 422
                                       66777779*******************************************999997554 PP

  == domain 8  score: 34.3 bits;  conditional E-value: 4.6e-11
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       l + + + A++ + +al+ +p+n++a+++LAeal + g+l+eA+   +a+ +e+p 
  gi|330506685|ref|YP_004383113.1| 431 LLQTNIDPAIESFNRALDIEPQNPDALMGLAEALHQKGRLEEARSYYEAAIAEEPS 486
                                       56667788*************************************99999999886 PP

  == domain 9  score: 24.4 bits;  conditional E-value: 5.9e-08
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryas 63 
                                       a+g y + ++l+e+al+++p + e +++   al a+g+   A ++ +++   +p d++++s
  gi|330506685|ref|YP_004383113.1| 499 AQGEYGQSIPLFESALSQEPSDTESLMGKGLALAATGNSSGALQCFNEIVSLNPEDSAAWS 559
                                       89*****************************************************977664 PP

  == domain 10  score: 15.9 bits;  conditional E-value: 2.6e-05
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                       a g+y+eA + l++a   +  +a+++++L +++  + + ++ ++
  gi|330506685|ref|YP_004383113.1| 567 ALGRYDEARESLQKAAGISSSSADIWYNLGQVYRLMDRHNQSRQ 610
                                       569******************************99999998877 PP

  == domain 11  score: 18.2 bits;  conditional E-value: 5.2e-06
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd.d.aryasLlA 66 
                                       ++ +  +++e+a   +p+++ ++l L  a+  +g+ + A + L+++   dp+ + a+y+ +lA
  gi|330506685|ref|YP_004383113.1| 604 RHNQSRQAFENATRLSPDDPVLWLELGLAQERTGEAKLALKSLQRAVVLDPKnEfAQYSLALA 666
                                       66777899********************************************85699998887 PP

  == domain 12  score: 18.6 bits;  conditional E-value: 3.7e-06
                            TPR_19   2 laegdyaeAlalleqalqedpknaearl 29 
                                         +g+++eAl+++e++l+ +pkn+ a++
  gi|330506685|ref|YP_004383113.1| 668 AGQGRFQEALQAFERVLEINPKNDLAKY 695
                                       68*********************99987 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   3.6e-05     0.019       1      43 [.      80     122 ..      80     123 .. 0.93
   2 !   13.0   0.0   0.00028      0.15       2      43 ..     115     156 ..     114     157 .. 0.96
   3 !   11.1   0.1    0.0012      0.61       5      40 ..     152     187 ..     150     191 .. 0.88
   4 ?    4.3   0.0      0.17        89       9      43 ..     190     224 ..     188     225 .. 0.89
   5 !   16.4   0.0   2.2e-05     0.012       3      42 ..     218     257 ..     216     258 .. 0.92
   6 !    9.5   0.0    0.0036       1.9       2      39 ..     251     288 ..     250     293 .. 0.87
   7 !    8.8   0.0     0.006       3.2       8      39 ..     291     322 ..     286     327 .. 0.87
   8 !   12.6   0.0   0.00037       0.2       3      39 ..     320     356 ..     318     360 .. 0.87
   9 !    8.7   0.2    0.0067       3.6       3      43 ..     354     394 ..     352     395 .. 0.93
  10 !   18.7   0.4   4.2e-06    0.0022       2      43 ..     387     428 ..     386     429 .. 0.93
  11 !   16.7   0.1   1.8e-05    0.0095       2      43 ..     421     462 ..     420     463 .. 0.93
  12 !   18.9   0.9   3.5e-06    0.0018       1      36 [.     454     489 ..     454     493 .. 0.90
  13 !   12.5   0.0    0.0004      0.21       4      36 ..     490     522 ..     487     528 .. 0.89
  14 !   14.8   0.0   7.4e-05     0.039       8      39 ..     528     559 ..     522     564 .. 0.89
  15 !   17.8   0.3     8e-06    0.0042       3      43 ..     557     597 ..     556     598 .. 0.95
  16 !   21.2   0.1   6.2e-07   0.00033       2      42 ..     590     630 ..     589     633 .. 0.95
  17 !   18.3   0.2   5.4e-06    0.0028       3      42 ..     625     664 ..     623     664 .. 0.92
  18 !   22.5   0.3   2.4e-07   0.00012       3      37 ..     659     693 ..     658     695 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-05
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +ea+l+ +++l+ lG ++eAi+ l+++l+ + + +eaw l ++
  gi|330506685|ref|YP_004383113.1|  80 AEAWLLKGRILFGLGYLQEAIRSLDQVLRIDQSLDEAWSLKGE 122
                                       58*****************************999999987765 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00028
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       ea+ + +e++++ G+++ A  +++ al+l+P++ +++ +laq
  gi|330506685|ref|YP_004383113.1| 115 EAWSLKGEIMMETGRYRMAQLCFDSALRLDPGNMTLYNRLAQ 156
                                       79999***********************************98 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0012
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawll 40 
                                        +la+  l l+d+d A++ +++al+l  ++ e+++ 
  gi|330506685|ref|YP_004383113.1| 152 NRLAQSQLMLEDYDHALRSYKKALSLEANNTEILFN 187
                                       589999**********************99999876 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.17
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +++l+l ++ eA++ ++ +l+++ +d  a+   a+
  gi|330506685|ref|YP_004383113.1| 190 DLFLTLARYPEALNSFNLLLEQNKSDILALKGRAE 224
                                       6789999*******************999988776 PP

  == domain 5  score: 16.4 bits;  conditional E-value: 2.2e-05
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       al+ +ae +++lG+ d+A++ +  +l+++P+d e w+ l+
  gi|330506685|ref|YP_004383113.1| 218 ALKGRAECYRQLGQVDRAEEDYYTVLEKNPEDFESWRGLG 257
                                       56779999*************************9999885 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.0036
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       e ++ l+ + +a +d+  +++++++al+ +P d ++ l
  gi|330506685|ref|YP_004383113.1| 251 ESWRGLGMVRYATEDYSSSLQAFDQALKINPHDIQTIL 288
                                       679999*************************9987655 PP

  == domain 7  score: 8.8 bits;  conditional E-value: 0.006
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawl 39 
                                       +++lla+G++  A++ + +al l  d+  a++
  gi|330506685|ref|YP_004383113.1| 291 GDLLLARGNFSSALESYSAALLLKKDNVSALY 322
                                       6799*****************99999988875 PP

  == domain 8  score: 12.6 bits;  conditional E-value: 0.00037
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       al+  + al  lG+ +eA +++rr+l+l Pd+  a+ 
  gi|330506685|ref|YP_004383113.1| 320 ALYGKGLALSSLGREKEANKCYRRILELEPDNIIALQ 356
                                       67778899***********************987765 PP

  == domain 9  score: 8.7 bits;  conditional E-value: 0.0067
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       al+++a+ ll++ +  +A++++  +l ++P++a+a+l +a+
  gi|330506685|ref|YP_004383113.1| 354 ALQKIADDLLERNESIQAAEHYGLILGQDPKNARALLGMAK 394
                                       6788999999*****************************97 PP

  == domain 10  score: 18.7 bits;  conditional E-value: 4.2e-06
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +all +a+a l lGd+d+A++ ++++l ++ ++ +aw+  ++
  gi|330506685|ref|YP_004383113.1| 387 RALLGMAKAQLDLGDLDQALQSYEELLGHDSNSSAAWIGRGE 428
                                       7999*********************************98776 PP

  == domain 11  score: 16.7 bits;  conditional E-value: 1.8e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +a+  ++e+ll + + d Ai+ ++ral+  P++++a++ la+
  gi|330506685|ref|YP_004383113.1| 421 AAWIGRGEILLLQTNIDPAIESFNRALDIEPQNPDALMGLAE 462
                                       68899999999999**************************98 PP

  == domain 12  score: 18.9 bits;  conditional E-value: 3.5e-06
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddae 36 
                                       p+al+ laeal + G+++eA+ ++++a+a  P+ + 
  gi|330506685|ref|YP_004383113.1| 454 PDALMGLAEALHQKGRLEEARSYYEAAIAEEPSVRG 489
                                       6899***************************98665 PP

  == domain 13  score: 12.5 bits;  conditional E-value: 0.0004
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddae 36 
                                       ++ l+ +l a+G++ ++i l++ al++ P+d e
  gi|330506685|ref|YP_004383113.1| 490 YRGLGNILCAQGEYGQSIPLFESALSQEPSDTE 522
                                       778999***********************9976 PP

  == domain 14  score: 14.8 bits;  conditional E-value: 7.4e-05
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawl 39 
                                       + al+a G+  +A+++++++++l+P+d +aw 
  gi|330506685|ref|YP_004383113.1| 528 GLALAATGNSSGALQCFNEIVSLNPEDSAAWS 559
                                       6799**************************95 PP

  == domain 15  score: 17.8 bits;  conditional E-value: 8e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       a+  ++++++alG++deA++ l++a     ++a++w+ l+q
  gi|330506685|ref|YP_004383113.1| 557 AWSNRGSIFAALGRYDEARESLQKAAGISSSSADIWYNLGQ 597
                                       88999**********************************98 PP

  == domain 16  score: 21.2 bits;  conditional E-value: 6.2e-07
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       + ++ l+++++  +++ +++++++ a +l Pdd+++wl+l+
  gi|330506685|ref|YP_004383113.1| 590 DIWYNLGQVYRLMDRHNQSRQAFENATRLSPDDPVLWLELG 630
                                       679***********************************997 PP

  == domain 17  score: 18.3 bits;  conditional E-value: 5.4e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       ++l+l+ a ++ G+ + A++ l+ra+ l+P+++ a++ la
  gi|330506685|ref|YP_004383113.1| 625 LWLELGLAQERTGEAKLALKSLQRAVVLDPKNEFAQYSLA 664
                                       8*******************************98887665 PP

  == domain 18  score: 22.5 bits;  conditional E-value: 2.4e-07
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaea 37 
                                       a++ la al+ +G+++eA+++++r+l+ +P+++ a
  gi|330506685|ref|YP_004383113.1| 659 AQYSLALALAGQGRFQEALQAFERVLEINPKNDLA 693
                                       7899***************************9987 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.41   2.1e+02       5      31 ..      72      98 ..      71     101 .. 0.81
   2 ?    4.7   0.0     0.087        46       4      33 ..     105     134 ..     103     134 .. 0.92
   3 !   11.4   0.1   0.00064      0.34       1      30 [.     136     165 ..     136     169 .. 0.90
   4 !    9.9   0.3     0.002         1       2      32 ..     171     201 ..     170     203 .. 0.92
   5 !    9.2   0.0    0.0031       1.7       5      34 .]     208     237 ..     205     237 .. 0.93
   6 !    8.7   0.0    0.0046       2.4       2      28 ..     239     265 ..     238     271 .. 0.83
   7 ?    4.3   0.0      0.12        62       2      33 ..     273     304 ..     272     305 .. 0.90
   8 ?    6.1   0.1     0.031        16       2      32 ..     307     337 ..     306     337 .. 0.92
   9 !    7.9   0.0    0.0082       4.3       1      29 [.     340     368 ..     340     373 .. 0.76
  10 !   13.7   0.1   0.00012     0.062       8      34 .]     381     407 ..     378     407 .. 0.95
  11 ?    5.4   0.0     0.053        28       2      26 ..     409     433 ..     408     440 .. 0.90
  12 !   20.1   0.0   1.1e-06   0.00056       2      33 ..     443     474 ..     442     475 .. 0.96
  13 ?    2.6   0.0      0.42   2.2e+02      15      31 ..     489     505 ..     476     507 .. 0.79
  14 ?    7.4   0.0     0.012       6.3       1      34 []     509     542 ..     509     542 .. 0.94
  15 !   18.9   0.0   2.5e-06    0.0013       1      34 []     543     576 ..     543     576 .. 0.94
  16 !   13.2   0.0   0.00017     0.087       3      32 ..     579     611 ..     578     613 .. 0.78
  17 !   11.8   0.0   0.00047      0.25       2      33 ..     612     643 ..     611     644 .. 0.92
  18 !   10.7   0.1    0.0011      0.57       3      34 .]     647     678 ..     645     678 .. 0.95
  19 ?    3.8   0.0      0.17        88       2      13 ..     680     691 ..     679     696 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.41
                            TPR_17  5 aleldPnnadaynnLAelllknGdlmt 31
                                      +le+d   a+a+ +++++l  +G l++
  gi|330506685|ref|YP_004383113.1| 72 SLEIDDELAEAWLLKGRILFGLGYLQE 98
                                      68999999*********9977665555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.087
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtAr 33 
                                       ++l++d +  +a+ +++e++ + G++++A+
  gi|330506685|ref|YP_004383113.1| 105 QVLRIDQSLDEAWSLKGEIMMETGRYRMAQ 134
                                       6899999999******************97 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00064
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlm 30 
                                       ++  al+ldP n  +yn LA+ +l++ d++
  gi|330506685|ref|YP_004383113.1| 136 CFDSALRLDPGNMTLYNRLAQSQLMLEDYD 165
                                       67789********************99997 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.002
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       y+kal l+ nn + ++n + l+l + ++ +A
  gi|330506685|ref|YP_004383113.1| 171 YKKALSLEANNTEILFNQGDLFLTLARYPEA 201
                                       9*********************999888877 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0031
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmtArq 34 
                                        le+++++  a+  +Ae+++++G+ ++A++
  gi|330506685|ref|YP_004383113.1| 208 LLEQNKSDILALKGRAECYRQLGQVDRAEE 237
                                       5899************************96 PP

  == domain 6  score: 8.7 bits;  conditional E-value: 0.0046
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGd 28 
                                       y  +le++P +++++  L+ + +   d
  gi|330506685|ref|YP_004383113.1| 239 YYTVLEKNPEDFESWRGLGMVRYATED 265
                                       6679***************98776666 PP

  == domain 7  score: 4.3 bits;  conditional E-value: 0.12
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + +al+++P +      ++ lll +G++  A+
  gi|330506685|ref|YP_004383113.1| 273 FDQALKINPHDIQTILGKGDLLLARGNFSSAL 304
                                       889***********************987775 PP

  == domain 8  score: 6.1 bits;  conditional E-value: 0.031
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       y  al l ++n+ a++ ++ +l+++G+ ++A
  gi|330506685|ref|YP_004383113.1| 307 YSAALLLKKDNVSALYGKGLALSSLGREKEA 337
                                       67899999******************98887 PP

  == domain 9  score: 7.9 bits;  conditional E-value: 0.0082
                            TPR_17   1 lylkaleldPnnadaynnLAe.lllknGdl 29 
                                       +y++ lel+P+n  a++  A  ll +++++
  gi|330506685|ref|YP_004383113.1| 340 CYRRILELEPDNIIALQKIADdLL-ERNES 368
                                       8*****************998444.44444 PP

  == domain 10  score: 13.7 bits;  conditional E-value: 0.00012
                            TPR_17   8 ldPnnadaynnLAelllknGdlmtArq 34 
                                       +dP+na a+  +A+++l +Gdl++A+q
  gi|330506685|ref|YP_004383113.1| 381 QDPKNARALLGMAKAQLDLGDLDQALQ 407
                                       69***********************97 PP

  == domain 11  score: 5.4 bits;  conditional E-value: 0.053
                            TPR_17   2 ylkaleldPnnadaynnLAelllkn 26 
                                       y++ l +d n++ a+  ++e+ll +
  gi|330506685|ref|YP_004383113.1| 409 YEELLGHDSNSSAAWIGRGEILLLQ 433
                                       999999***************9865 PP

  == domain 12  score: 20.1 bits;  conditional E-value: 1.1e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + +al+++P n+da+  LAe+l+++G+l++Ar
  gi|330506685|ref|YP_004383113.1| 443 FNRALDIEPQNPDALMGLAEALHQKGRLEEAR 474
                                       789****************************8 PP

  == domain 13  score: 2.6 bits;  conditional E-value: 0.42
                            TPR_17  15 aynnLAelllknGdlmt 31 
                                        y  L+++l+ +G++++
  gi|330506685|ref|YP_004383113.1| 489 GYRGLGNILCAQGEYGQ 505
                                       57889********9987 PP

  == domain 14  score: 7.4 bits;  conditional E-value: 0.012
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       l++ al ++P++ +++  ++ +l+  G++  A+q
  gi|330506685|ref|YP_004383113.1| 509 LFESALSQEPSDTESLMGKGLALAATGNSSGALQ 542
                                       6899************************998876 PP

  == domain 15  score: 18.9 bits;  conditional E-value: 2.5e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       ++ + + l+P ++ a+ n++ +++ +G++++Ar+
  gi|330506685|ref|YP_004383113.1| 543 CFNEIVSLNPEDSAAWSNRGSIFAALGRYDEARE 576
                                       67888999************************96 PP

  == domain 16  score: 13.2 bits;  conditional E-value: 0.00017
                            TPR_17   3 lkaleldPnnadaynnLAelll...knGdlmtA 32 
                                       +ka+ +  ++ad ++nL+++++   + +++++A
  gi|330506685|ref|YP_004383113.1| 579 QKAAGISSSSADIWYNLGQVYRlmdRHNQSRQA 611
                                       6777788899***********966666666666 PP

  == domain 17  score: 11.8 bits;  conditional E-value: 0.00047
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +++a +l P++++++ +L+ ++++ G+ + A+
  gi|330506685|ref|YP_004383113.1| 612 FENATRLSPDDPVLWLELGLAQERTGEAKLAL 643
                                       899***********************999886 PP

  == domain 18  score: 10.7 bits;  conditional E-value: 0.0011
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       ++a+ ldP+n  a + LA +l+ +G++++A+q
  gi|330506685|ref|YP_004383113.1| 647 QRAVVLDPKNEFAQYSLALALAGQGRFQEALQ 678
                                       89999*************************97 PP

  == domain 19  score: 3.8 bits;  conditional E-value: 0.17
                            TPR_17   2 ylkaleldPnna 13 
                                       ++++le++P+n 
  gi|330506685|ref|YP_004383113.1| 680 FERVLEINPKND 691
                                       9*********95 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.33   1.7e+02      48      75 ..      49      76 ..      36      78 .. 0.81
   2 !   10.2   0.2    0.0014      0.73      11      76 ..      54     111 ..      46     112 .. 0.72
   3 !   11.0   0.1   0.00074      0.39       2      74 ..      79     143 ..      78     145 .. 0.81
   4 !   20.4   0.7   8.9e-07   0.00047       4      73 ..     115     176 ..     112     180 .. 0.92
   5 ?    6.4   0.0     0.021        11      47      73 ..     184     210 ..     178     214 .. 0.84
   6 !   23.4   0.1     1e-07   5.4e-05       5      74 ..     218     279 ..     214     282 .. 0.89
   7 !   16.4   0.4   1.6e-05    0.0083       4      74 ..     286     347 ..     283     350 .. 0.87
   8 !    9.0   0.5    0.0032       1.7       5      68 ..     320     375 ..     318     379 .. 0.85
   9 !   14.2   1.5   7.4e-05     0.039      28      72 ..     370     413 ..     365     415 .. 0.86
  10 !   19.9   0.5   1.3e-06   0.00066      26      74 ..     402     449 ..     386     452 .. 0.86
  11 !   15.0   1.1   4.3e-05     0.022       5      30 ..     456     481 ..     452     483 .. 0.83
  12 !   15.5   0.0     3e-05     0.016       6      72 ..     490     548 ..     486     553 .. 0.84
  13 !   34.7   0.3     3e-11   1.6e-08       3      74 ..     555     618 ..     553     621 .. 0.90
  14 !   20.0   0.4   1.2e-06   0.00064       3      72 ..     589     650 ..     587     655 .. 0.90
  15 !   19.1   2.1   2.3e-06    0.0012       6      75 ..     626     687 ..     621     689 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.33
                            TPR_12 48 lrnLgrlyralgryeeAlelleealaia 75
                                      +   ++ y++ g y  Ale+ + +l+i+
  gi|330506685|ref|YP_004383113.1| 49 YLREAMNYSQNGSYPLALERINLSLEID 76
                                      6667888999999999999999999886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0014
                            TPR_12  11 avlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       + + + g y  Ale  + +lei          ++a++    gr+++ lg ++eA++ l ++l+i++
  gi|330506685|ref|YP_004383113.1|  54 MNYSQNGSYPLALERINLSLEID-------D-ELAEAWLLKGRILFGLGYLQEAIRSLDQVLRIDQ 111
                                       55666666777777777776666.......2.4778888888888888888888888888888876 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00074
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +a a+   + +l+ lg ++eA++ l+++l+i ++l      ++a++l +  ++  ++gry+ A+  +  al++
  gi|330506685|ref|YP_004383113.1|  79 LAEAWLLKGRILFGLGYLQEAIRSLDQVLRIDQSL------DEAWSLKGEIMM--ETGRYRMAQLCFDSALRL 143
                                       67889899***********************9877......366776655555..799999999999998887 PP

  == domain 4  score: 20.4 bits;  conditional E-value: 8.9e-07
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                        a++  +++ ++ gry  A+ +++ al++      p +    t ++ L++ +++l++y+ Al+ +++al 
  gi|330506685|ref|YP_004383113.1| 115 EAWSLKGEIMMETGRYRMAQLCFDSALRLD-----PGN---MTLYNRLAQSQLMLEDYDHALRSYKKALS 176
                                       577789********************9999.....655...99*************************97 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.021
                            TPR_12  47 tlrnLgrlyralgryeeAlelleeala 73 
                                       +l+n g+l++ l ry eAl+ ++  l+
  gi|330506685|ref|YP_004383113.1| 184 ILFNQGDLFLTLARYPEALNSFNLLLE 210
                                       789999999999999999999986665 PP

  == domain 6  score: 23.4 bits;  conditional E-value: 1e-07
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       al  +a+++r+lg+ d A+e + ++le        ++p+  ++ r+Lg++ +a+++y   l+++ +al+i
  gi|330506685|ref|YP_004383113.1| 218 ALKGRAECYRQLGQVDRAEEDYYTVLE--------KNPEDFESWRGLGMVRYATEDYSSSLQAFDQALKI 279
                                       45579********************44........4556799**************************98 PP

  == domain 7  score: 16.4 bits;  conditional E-value: 1.6e-05
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       t+l   +++l+++g++  Ale + +al +      +d+   +++l++ g +++ lgr +eA + +++ l++
  gi|330506685|ref|YP_004383113.1| 286 TIL-GKGDLLLARGNFSSALESYSAALLLK-----KDN---VSALYGKGLALSSLGREKEANKCYRRILEL 347
                                       555.78889999999999999999998888.....776...99************************9986 PP

  == domain 8  score: 9.0 bits;  conditional E-value: 0.0032
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlell 68 
                                       al+  +++l  lgr  eA +++++ le+      pd+   +++l+ +++ ++++++  +A e++
  gi|330506685|ref|YP_004383113.1| 320 ALYGKGLALSSLGREKEANKCYRRILELE-----PDN---IIALQKIADDLLERNESIQAAEHY 375
                                       56688999999999999999999999999.....987...899999999999999999998887 PP

  == domain 9  score: 14.2 bits;  conditional E-value: 7.4e-05
                            TPR_12  28 kaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       +a e +  +lG + p  a++l +++ +++ lg++++Al+ +ee l
  gi|330506685|ref|YP_004383113.1| 370 QAAEHYGLILG-QDPKNARALLGMAKAQLDLGDLDQALQSYEELL 413
                                       56666655665.7899**************************976 PP

  == domain 10  score: 19.9 bits;  conditional E-value: 1.3e-06
                            TPR_12  26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       l++al+ +++llG+d+ + +++ ++ g++++++ + + A+e +++al+i
  gi|330506685|ref|YP_004383113.1| 402 LDQALQSYEELLGHDS-NSSAAWIGRGEILLLQTNIDPAIESFNRALDI 449
                                       677788888889***9.99****************************97 PP

  == domain 11  score: 15.0 bits;  conditional E-value: 4.3e-05
                            TPR_12   5 alnnlaavlrrlgrydeAlellekal 30 
                                       al  la++l++ gr++eA++++e+a+
  gi|330506685|ref|YP_004383113.1| 456 ALMGLAEALHQKGRLEEARSYYEAAI 481
                                       56689999999999999999999986 PP

  == domain 12  score: 15.5 bits;  conditional E-value: 3e-05
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       ++ l+++l+++g+y +++ l+e al +      p      ++l + g ++ a+g+   Al+ ++e +
  gi|330506685|ref|YP_004383113.1| 490 YRGLGNILCAQGEYGQSIPLFESALSQE-----PSD---TESLMGKGLALAATGNSSGALQCFNEIV 548
                                       667*********************8877.....543...4799999999999999999999999865 PP

  == domain 13  score: 34.7 bits;  conditional E-value: 3e-11
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       ++a++n++++ ++lgrydeA+e l+ka  i        +   a + +nLg++yr+++r+ + ++++e a+++
  gi|330506685|ref|YP_004383113.1| 555 SAAWSNRGSIFAALGRYDEARESLQKAAGIS-----S-S--SADIWYNLGQVYRLMDRHNQSRQAFENATRL 618
                                       57899**********************8888.....3.2..689***********************99987 PP

  == domain 14  score: 20.0 bits;  conditional E-value: 1.2e-06
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       a +++nl++v+r + r+ ++++ +e a ++      pd p        Lg +++++g+ + Al+ l++a+
  gi|330506685|ref|YP_004383113.1| 589 ADIWYNLGQVYRLMDRHNQSRQAFENATRLS-----PDDPV---LWLELGLAQERTGEAKLALKSLQRAV 650
                                       78999**********************7777.....98865...6999999999**************96 PP

  == domain 15  score: 19.1 bits;  conditional E-value: 2.3e-06
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       + +l+++  r g+   Al+ l++a+ +      p+++    +++ L+ ++  +gr++eAl+++e++l+i 
  gi|330506685|ref|YP_004383113.1| 626 WLELGLAQERTGEAKLALKSLQRAVVLD-----PKNE---FAQYSLALALAGQGRFQEALQAFERVLEIN 687
                                       5578889999999999999999994444.....8874...58999**********************996 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   6.9e-07   0.00036       5      60 ..      56     111 ..      54     120 .. 0.92
   2 ?    0.8   0.0         1   5.4e+02      34      64 ..     119     149 ..     115     160 .. 0.80
   3 !    7.7   0.1    0.0072       3.8       9      63 ..     162     216 ..     154     224 .. 0.91
   4 !   12.6   0.1   0.00022      0.12      10      62 ..     197     249 ..     189     249 .. 0.94
   5 !   21.5   0.1   3.5e-07   0.00019       4      64 ..     225     285 ..     223     288 .. 0.94
   6 !   16.9   0.0   9.7e-06    0.0051       5      65 ..     294     354 ..     291     357 .. 0.94
   7 ?    3.7   0.1      0.13        71      14      61 ..     371     418 ..     362     424 .. 0.78
   8 !   16.9   0.1     1e-05    0.0054       9      66 ..     400     457 ..     395     459 .. 0.95
   9 !   16.3   0.4   1.5e-05    0.0081       8      61 ..     433     486 ..     427     491 .. 0.91
  10 ?    5.3   0.2     0.042        22      37      61 ..     462     486 ..     460     525 .. 0.55
  11 !   26.9   0.0   7.5e-09     4e-06       6      61 ..     532     587 ..     527     592 .. 0.87
  12 !   24.8   0.3   3.5e-08   1.8e-05       9      62 ..     603     656 ..     595     660 .. 0.87
  13 !   13.4   0.1   0.00012     0.063      35      64 ..     663     692 ..     660     695 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.9e-07
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       + ++  ++ al+ +++ l ++ + +e ++  G++l+ lG l++A++ L++ l+++ 
  gi|330506685|ref|YP_004383113.1|  56 YSQNGSYPLALERINLSLEIDDELAEAWLLKGRILFGLGYLQEAIRSLDQVLRIDQ 111
                                       7799999******************************************9997765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1
                             TPR_9  34 dRGlllaqlGclsaAladLeaylalapdapd 64 
                                         G + ++ G+++ A  +++ +l+l+p + +
  gi|330506685|ref|YP_004383113.1| 119 LKGEIMMETGRYRMAQLCFDSALRLDPGNMT 149
                                       5688889999999999999999999996655 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0072
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       ed++ al+ +   l l  +  e ++  G l   l ++ +Al+ ++  l+++ ++ 
  gi|330506685|ref|YP_004383113.1| 162 EDYDHALRSYKKALSLEANNTEILFNQGDLFLTLARYPEALNSFNLLLEQNKSDI 216
                                       89*******************************************9999987665 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00022
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       ++++al   ++ll  +  d+  +  R+ ++ qlG++  A +d  + l+++p++
  gi|330506685|ref|YP_004383113.1| 197 RYPEALNSFNLLLEQNKSDILALKGRAECYRQLGQVDRAEEDYYTVLEKNPED 249
                                       7899*********************************************9986 PP

  == domain 5  score: 21.5 bits;  conditional E-value: 3.5e-07
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       ++ +  + +ra + +  +l  +P+d e +r  G++++  +++s  l++++++l ++p++ +
  gi|330506685|ref|YP_004383113.1| 225 CYRQLGQVDRAEEDYYTVLEKNPEDFESWRGLGMVRYATEDYSSSLQAFDQALKINPHDIQ 285
                                       68899999*************************************************9865 PP

  == domain 6  score: 16.9 bits;  conditional E-value: 9.7e-06
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       ++ + +++ al+ +   lll+ d ++ ++  Gl+l  lG+ ++A ++  + l+l+pd+  a
  gi|330506685|ref|YP_004383113.1| 294 LLARGNFSSALESYSAALLLKKDNVSALYGKGLALSSLGREKEANKCYRRILELEPDNIIA 354
                                       6788999*************************************************98776 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.13
                             TPR_9  14 alavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       a + + ++l  +P+ ++ ++  + ++  lG+l +Al+  e  l ++ +
  gi|330506685|ref|YP_004383113.1| 371 AAEHYGLILGQDPKNARALLGMAKAQLDLGDLDQALQSYEELLGHDSN 418
                                       5555566777799999999999999*************9999887765 PP

  == domain 8  score: 16.9 bits;  conditional E-value: 1e-05
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                                        d ++al+ +e ll  ++++   +  RG +l  + ++  A++ ++++l+++p++pda 
  gi|330506685|ref|YP_004383113.1| 400 GDLDQALQSYEELLGHDSNSSAAWIGRGEILLLQTNIDPAIESFNRALDIEPQNPDAL 457
                                       5899****************************************************96 PP

  == domain 9  score: 16.3 bits;  conditional E-value: 1.5e-05
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       + + + a++  +r l + P+ p+ ++  + +l+q G+l++A+   ea++a +p+
  gi|330506685|ref|YP_004383113.1| 433 QTNIDPAIESFNRALDIEPQNPDALMGLAEALHQKGRLEEARSYYEAAIAEEPS 486
                                       5667889999****************************************9995 PP

  == domain 10  score: 5.3 bits;  conditional E-value: 0.042
                             TPR_9  37 lllaqlGclsaAladLeaylalapd 61 
                                        +l+q G+l++A+   ea++a +p+
  gi|330506685|ref|YP_004383113.1| 462 EALHQKGRLEEARSYYEAAIAEEPS 486
                                       4555556666666666666655553 PP

  == domain 11  score: 26.9 bits;  conditional E-value: 7.5e-09
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       +   +++ al++ + ++ l+P+d   +  RG + a lG++ +A++ L+ ++ ++ +
  gi|330506685|ref|YP_004383113.1| 532 AATGNSSGALQCFNEIVSLNPEDSAAWSNRGSIFAALGRYDEARESLQKAAGISSS 587
                                       55667888****************************************99866655 PP

  == domain 12  score: 24.8 bits;  conditional E-value: 3.5e-08
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       +++ +  ++ e    l Pddp ++++ Gl++++ G  + Al+ L++++ l+p++
  gi|330506685|ref|YP_004383113.1| 603 DRHNQSRQAFENATRLSPDDPVLWLELGLAQERTGEAKLALKSLQRAVVLDPKN 656
                                       566666778899999***********************************9976 PP

  == domain 13  score: 13.4 bits;  conditional E-value: 0.00012
                             TPR_9  35 RGlllaqlGclsaAladLeaylalapdapd 64 
                                        +l+la +G++++Al+++e+ l+++p+++ 
  gi|330506685|ref|YP_004383113.1| 663 LALALAGQGRFQEALQAFERVLEINPKNDL 692
                                       69************************8765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       2.5   1.3e+03       1      28 [.      81     108 ..      81     110 .. 0.82
   2 ?    2.6   0.2      0.48   2.6e+02       5      28 ..     153     176 ..     153     181 .. 0.88
   3 ?    2.4   0.0      0.58   3.1e+02       3      29 ..     185     211 ..     183     212 .. 0.88
   4 !   11.1   0.1   0.00094      0.49       6      32 ..     222     248 ..     220     249 .. 0.93
   5 ?    5.3   0.0     0.069        36       6      32 ..     256     282 ..     253     283 .. 0.91
   6 !   11.3   0.0   0.00084      0.44       2      32 ..     320     350 ..     319     351 .. 0.95
   7 !   16.0   0.1   2.6e-05     0.014       2      27 ..     388     413 ..     387     419 .. 0.91
   8 ?    5.5   0.0     0.059        31       6      32 ..     426     452 ..     421     453 .. 0.87
   9 !   14.5   0.3   8.2e-05     0.043       1      31 [.     455     485 ..     455     486 .. 0.95
  10 ?   -0.9   0.0       6.3   3.3e+03       6      31 ..     493     518 ..     492     520 .. 0.83
  11 ?    6.6   0.0     0.025        13       2      32 ..     523     553 ..     522     554 .. 0.90
  12 ?    6.6   0.1     0.026        14       6      26 ..     561     581 ..     556     583 .. 0.85
  13 !   11.8   0.0   0.00057       0.3       3      32 ..     592     621 ..     590     622 .. 0.93
  14 !    8.2   0.0    0.0082       4.3       4      32 ..     627     655 ..     624     656 .. 0.89
  15 !   17.7   0.2   7.3e-06    0.0039       2      32 ..     659     689 ..     658     690 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                       +A ++ ++ ++ lg  ++A++ l+++++
  gi|330506685|ref|YP_004383113.1|  81 EAWLLKGRILFGLGYLQEAIRSLDQVLR 108
                                       5778888888888888999999999986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                       +la+s+++l d+d Al+ +++ ++
  gi|330506685|ref|YP_004383113.1| 153 RLAQSQLMLEDYDHALRSYKKALS 176
                                       79******88*********99876 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerlike 29 
                                       l++++ +++ l ++ +Al  ++ l+++
  gi|330506685|ref|YP_004383113.1| 185 LFNQGDLFLTLARYPEALNSFNLLLEQ 211
                                       99*******966*********999875 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00094
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                       +a++yr+lg+ d+A e +  ++++ P+
  gi|330506685|ref|YP_004383113.1| 222 RAECYRQLGQVDRAEEDYYTVLEKNPE 248
                                       69*****9***************9996 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.069
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                       l++ ++++ d++ +l+a+++ +k  P 
  gi|330506685|ref|YP_004383113.1| 256 LGMVRYATEDYSSSLQAFDQALKINPH 282
                                       89*****77*************99985 PP

  == domain 6  score: 11.3 bits;  conditional E-value: 0.00084
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       Aly  +l++ +lg+  +A + ++r+++  Pd
  gi|330506685|ref|YP_004383113.1| 320 ALYGKGLALSSLGREKEANKCYRRILELEPD 350
                                       9**********99***************999 PP

  == domain 7  score: 16.0 bits;  conditional E-value: 2.6e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerli 27 
                                       Al+ +a++++ lgd d+Al+ +e+l+
  gi|330506685|ref|YP_004383113.1| 388 ALLGMAKAQLDLGDLDQALQSYEELL 413
                                       9**********99***********98 PP

  == domain 8  score: 5.5 bits;  conditional E-value: 0.059
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                       +++ ++ +++ d A+e ++r ++  P+
  gi|330506685|ref|YP_004383113.1| 426 RGEILLLQTNIDPAIESFNRALDIEPQ 452
                                       789999999*************99887 PP

  == domain 9  score: 14.5 bits;  conditional E-value: 8.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                       dAl+ la+++ + g+ ++A+ ++e  i e P
  gi|330506685|ref|YP_004383113.1| 455 DALMGLAEALHQKGRLEEARSYYEAAIAEEP 485
                                       8***********88*************9988 PP

  == domain 10  score: -0.9 bits;  conditional E-value: 6.3
                                       HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                       l+  + ++g++ +++ ++e+ +++ P
  gi|330506685|ref|YP_004383113.1| 493 LGNILCAQGEYGQSIPLFESALSQEP 518
                                       566777889999*******9999988 PP

  == domain 11  score: 6.6 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       +l+  +l++ ++g+++ Al+ ++++++  P+
  gi|330506685|ref|YP_004383113.1| 523 SLMGKGLALAATGNSSGALQCFNEIVSLNPE 553
                                       788899*****99*************99886 PP

  == domain 12  score: 6.6 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerl 26 
                                       ++  + +lg++d+A+e l++ 
  gi|330506685|ref|YP_004383113.1| 561 RGSIFAALGRYDEARESLQKA 581
                                       677888999**********85 PP

  == domain 13  score: 11.8 bits;  conditional E-value: 0.00057
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPd 32 
                                        y+l++ yr ++++ ++++a+e+  +  Pd
  gi|330506685|ref|YP_004383113.1| 592 WYNLGQVYRLMDRHNQSRQAFENATRLSPD 621
                                       69**********************999998 PP

  == domain 14  score: 8.2 bits;  conditional E-value: 0.0082
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                                       + l+l+++++g++  Al+ l+r +   P+
  gi|330506685|ref|YP_004383113.1| 627 LELGLAQERTGEAKLALKSLQRAVVLDPK 655
                                       789******99***********9987776 PP

  == domain 15  score: 17.7 bits;  conditional E-value: 7.3e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       A+y lal++  +g+ ++Al+a+er+++  P+
  gi|330506685|ref|YP_004383113.1| 659 AQYSLALALAGQGRFQEALQAFERVLEINPK 689
                                       89*************************9997 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0027       1.4       1      33 [.      82     114 ..      82     116 .. 0.87
   2 ?    4.6   0.0     0.074        39       5      36 .]     120     149 ..     116     149 .. 0.85
   3 !    7.9   0.8    0.0063       3.3       2      29 ..     151     178 ..     150     183 .. 0.85
   4 ?    0.5   0.0       1.5   7.7e+02       2      23 ..     185     206 ..     184     215 .. 0.83
   5 ?    5.9   0.1     0.029        15       5      31 ..     222     246 ..     218     249 .. 0.77
   6 ?    4.0   0.0      0.11        61       6      31 ..     291     316 ..     286     317 .. 0.86
   7 ?    3.9   0.1      0.13        67       2      31 ..     321     350 ..     320     366 .. 0.86
   8 !   13.5   0.3    0.0001     0.055       1      27 [.     388     414 ..     388     421 .. 0.89
   9 !   16.5   0.2   1.2e-05    0.0063       1      34 [.     456     487 ..     456     489 .. 0.91
  10 !   13.6   0.0   9.7e-05     0.051       5      34 ..     493     520 ..     490     522 .. 0.90
  11 !   11.9   0.0   0.00034      0.18       1      28 [.     557     584 ..     557     590 .. 0.87
  12 ?    6.3   0.0     0.021        11       2      35 ..     592     623 ..     591     624 .. 0.94
  13 ?    4.2   0.0       0.1        54       2      33 ..     626     655 ..     625     657 .. 0.89
  14 !   10.1   0.1    0.0013      0.69       4      28 ..     662     686 ..     661     694 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0027
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       a+l  +r+ + lG+ +eAi+ + q+L+++ + +
  gi|330506685|ref|YP_004383113.1|  82 AWLLKGRILFGLGYLQEAIRSLDQVLRIDQSLD 114
                                       577889******************999988766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.074
                             TPR_7   5 LarlysrlGdyeeAielyeqsLaltkdpedae 36 
                                        +++  + G+y+ A  ++    al+ dp++++
  gi|330506685|ref|YP_004383113.1| 120 KGEIMMETGRYRMAQLCFDS--ALRLDPGNMT 149
                                       57777899************..*****99875 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0063
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLalt 29 
                                       +++La+ +  l dy+ A++ y+++L l+
  gi|330506685|ref|YP_004383113.1| 151 YNRLAQSQLMLEDYDHALRSYKKALSLE 178
                                       7899999999*************77664 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.5
                             TPR_7   2 LlnLarlysrlGdyeeAielye 23 
                                       L+n ++l+  l +y eA+  + 
  gi|330506685|ref|YP_004383113.1| 185 LFNQGDLFLTLARYPEALNSFN 206
                                       7899*************98775 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.029
                             TPR_7   5 LarlysrlGdyeeAielyeqsLaltkd 31 
                                        a++y++lG+ ++A+e y    +l+k 
  gi|330506685|ref|YP_004383113.1| 222 RAECYRQLGQVDRAEEDYYT--VLEKN 246
                                       699************98866..55555 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.11
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                       ++l  ++G+++ A+e y ++L l kd
  gi|330506685|ref|YP_004383113.1| 291 GDLLLARGNFSSALESYSAALLLKKD 316
                                       899999*************8888776 PP

  == domain 7  score: 3.9 bits;  conditional E-value: 0.13
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       L+  + + s+lG+ +eA ++y++ L+l+ d
  gi|330506685|ref|YP_004383113.1| 321 LYGKGLALSSLGREKEANKCYRRILELEPD 350
                                       66668899***************9998865 PP

  == domain 8  score: 13.5 bits;  conditional E-value: 0.0001
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLa 27 
                                       aLl +a ++ +lGd ++A++ ye++L+
  gi|330506685|ref|YP_004383113.1| 388 ALLGMAKAQLDLGDLDQALQSYEELLG 414
                                       7999********************664 PP

  == domain 9  score: 16.5 bits;  conditional E-value: 1.2e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       aL  La++ ++ G+ eeA ++ye+  a++++p++
  gi|330506685|ref|YP_004383113.1| 456 ALMGLAEALHQKGRLEEARSYYEA--AIAEEPSV 487
                                       5778********************..**999986 PP

  == domain 10  score: 13.6 bits;  conditional E-value: 9.7e-05
                             TPR_7   5 LarlysrlGdyeeAielyeqsLaltkdped 34 
                                       L+++ +++G+y + i l+e   al  +p+d
  gi|330506685|ref|YP_004383113.1| 493 LGNILCAQGEYGQSIPLFES--ALSQEPSD 520
                                       9*******************..88888876 PP

  == domain 11  score: 11.9 bits;  conditional E-value: 0.00034
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       a++n ++++ +lG+y+eA e ++++ ++
  gi|330506685|ref|YP_004383113.1| 557 AWSNRGSIFAALGRYDEARESLQKAAGI 584
                                       789******************9996655 PP

  == domain 12  score: 6.3 bits;  conditional E-value: 0.021
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       ++nL+++y+ + ++ +  + +e   a++ +p+d+
  gi|330506685|ref|YP_004383113.1| 592 WYNLGQVYRLMDRHNQSRQAFEN--ATRLSPDDP 623
                                       68*********************..***999986 PP

  == domain 13  score: 4.2 bits;  conditional E-value: 0.1
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       +l L+ +++r G+ + A++ +++  a+  dp 
  gi|330506685|ref|YP_004383113.1| 626 WLELGLAQERTGEAKLALKSLQR--AVVLDPK 655
                                       689********************..8888875 PP

  == domain 14  score: 10.1 bits;  conditional E-value: 0.0013
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLal 28 
                                        La +   +G+++eA++ +e++L++
  gi|330506685|ref|YP_004383113.1| 662 SLALALAGQGRFQEALQAFERVLEI 686
                                       68999999*************8887 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 !   11.2   0.0   0.00061      0.32      24      81 ..      45     105 ..      22     106 .. 0.87
   2 !   10.4   0.1    0.0011      0.58      24      81 ..     115     173 ..     109     174 .. 0.90
   3 !   11.1   0.5   0.00067      0.35       2      79 ..     127     205 ..     126     208 .. 0.83
   4 !    8.7   0.2    0.0038         2       4      54 ..     197     248 ..     194     275 .. 0.77
   5 ?    6.3   0.2     0.021        11       4      79 ..     265     341 ..     262     344 .. 0.86
   6 !   13.1   0.2   0.00016     0.083       6      81 ..     335     411 ..     331     412 .. 0.92
   7 !   13.8   0.0   9.7e-05     0.051      20      81 ..     415     479 ..     409     480 .. 0.86
   8 !   14.7   0.0   5.2e-05     0.028       2      81 ..     500     580 ..     499     581 .. 0.95
   9 !   15.5   0.1   2.9e-05     0.015      20      81 ..     620     682 ..     604     683 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00061
                                       HHHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  24 edayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++ ++l  A  + +ng y  A+e ++ + +++++  ++++l+++ l+ L+ ++eAi+ L+ 
  gi|330506685|ref|YP_004383113.1|  45 NSDFYLreAMNYSQNGSYPLALERINLSlEIDDELAEAWLLKGRILFGLGYLQEAIRSLDQ 105
                                       55555556888999************999****************************9975 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  24 edayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       e+  l+++ + ++g+y  A+  +++a +l++ ++     +Aq++l L+ y+ A++ ++k
  gi|330506685|ref|YP_004383113.1| 115 EAWSLKGEIMMETGRYRMAQLCFDSAlRLDPGNMTLYNRLAQSQLMLEDYDHALRSYKK 173
                                       55567799999*******************************************99877 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00067
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       +++y+ A ++++ +l  ++ +      lA++ + +++y+ A++ ++ka  l+ ++ ++++  +   l L +y eA++
  gi|330506685|ref|YP_004383113.1| 127 TGRYRMAQLCFDSALRLDPGNMTLYNRLAQSQLMLEDYDHALRSYKKAlSLEANNTEILFNQGDLFLTLARYPEALN 203
                                       6789999999999994444444444446********************999999999999999999999*****998 PP

                                       HH CS
                            ANAPC3  78 aL 79 
                                        +
  gi|330506685|ref|YP_004383113.1| 204 SF 205
                                       76 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0038
                                       -HHHHHHHHHHHH.HHH--HHHHHHH...HHHHHHTT-HHHHHHHHHCT.SHHHC CS
                            ANAPC3   4 nyknAiflaerllaaetespedayll...AlclylngqykrAyellrka.klnsk 54 
                                       +y +A+  +++ll    ++ +d+++l   A+c+ ++gq +rA e + +  ++n++
  gi|330506685|ref|YP_004383113.1| 197 RYPEALNSFNLLL---EQNKSDILALkgrAECYRQLGQVDRAEEDYYTVlEKNPE 248
                                       6888888899999...8888998888899*************8866665555555 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.021
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       +y + +  ++ +l+ ++++ + ++ ++  l+ +g++ +A+e ++ a  l++ +  ++y ++ +l  L++ +eA +++
  gi|330506685|ref|YP_004383113.1| 265 DYSSSLQAFDQALKINPHDIQTILGKGDLLLARGNFSSALESYSAAlLLKKDNVSALYGKGLALSSLGREKEANKCY 341
                                       5666666777788888888888888999******************99*********************99998776 PP

  == domain 6  score: 13.1 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3   6 knAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       k+A  ++ r+l+ e+++  ++   A  l+++++  +A e +    ++++k+ ++++ +A+++l+L+ +++A++ +e+
  gi|330506685|ref|YP_004383113.1| 335 KEANKCYRRILELEPDNIIALQKIADDLLERNESIQAAEHYGLIlGQDPKNARALLGMAKAQLDLGDLDQALQSYEE 411
                                       788899999999999999999999*********999999999999***************************99886 PP

  == domain 7  score: 13.8 bits;  conditional E-value: 9.7e-05
                                       H--HHHHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  20 tespedayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++s+++a +   ++ l+l+ + + A+e +++a +++++++ +++ +A++l + +++eeA++ +e+
  gi|330506685|ref|YP_004383113.1| 415 HDSNSSAAWIgrGEILLLQTNIDPAIESFNRAlDIEPQNPDALMGLAEALHQKGRLEEARSYYEA 479
                                       566777778667999********************************************998875 PP

  == domain 8  score: 14.7 bits;  conditional E-value: 5.2e-05
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       q+ y   i l+e +l++e+ + e+++ ++l+l  +g+   A++ +++   ln+++ +++   +    +L++y+eA+ 
  gi|330506685|ref|YP_004383113.1| 500 QGEYGQSIPLFESALSQEPSDTESLMGKGLALAATGNSSGALQCFNEIvSLNPEDSAAWSNRGSIFAALGRYDEARE 576
                                       56777889999****9************************************************************* PP

                                       HH-S CS
                            ANAPC3  78 aLek 81 
                                        L+k
  gi|330506685|ref|YP_004383113.1| 577 SLQK 580
                                       **98 PP

  == domain 9  score: 15.5 bits;  conditional E-value: 2.9e-05
                                       H--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  20 tespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +++p   + l+l+  ++g+ k A++ l++a  l++k++ + y +A +l  +++++eA++a+e+
  gi|330506685|ref|YP_004383113.1| 620 PDDPVLWLELGLAQERTGEAKLALKSLQRAvVLDPKNEFAQYSLALALAGQGRFQEALQAFER 682
                                       444444444699999*********************************************997 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.61   3.2e+02       9      31 ..      87     109 ..      87     113 .. 0.89
   2 ?    3.8   0.5       0.1        54       4      30 ..     150     176 ..     148     179 .. 0.84
   3 ?    5.7   0.3     0.028        15      12      30 ..     226     244 ..     223     245 .. 0.92
   4 ?   -0.2   0.0       1.9   9.9e+02       8      31 ..     256     279 ..     255     280 .. 0.92
   5 ?    2.6   0.1      0.25   1.3e+02       9      30 ..     325     346 ..     319     347 .. 0.90
   6 !    9.4   0.1    0.0018      0.94      22      40 ..     399     417 ..     386     419 .. 0.78
   7 !   15.7   1.3   1.9e-05    0.0098       4      30 ..     456     482 ..     455     483 .. 0.92
   8 !    8.0   0.0    0.0049       2.6       8      29 ..     493     514 ..     490     515 .. 0.93
   9 !    7.4   0.0    0.0079       4.2       7      29 ..     560     582 ..     559     585 .. 0.85
  10 ?    6.0   0.1     0.021        11       7      28 ..     594     615 ..     591     618 .. 0.93
  11 !   17.7   0.4   4.5e-06    0.0024       5      31 ..     660     686 ..     658     687 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.61
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       +++l+ +g ++eA + l+++l+i
  gi|330506685|ref|YP_004383113.1|  87 GRILFGLGYLQEAIRSLDQVLRI 109
                                       7899999*************998 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.1
                            TPR_10   4 slnNLanalrqrgrydeAealleeala 30 
                                        +n La     + +yd A++ +++al+
  gi|330506685|ref|YP_004383113.1| 150 LYNRLAQSQLMLEDYDHALRSYKKALS 176
                                       689999999999999999999999987 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.028
                            TPR_10  12 lrqrgrydeAealleeala 30 
                                       +rq+g+ d+Ae+++  +l+
  gi|330506685|ref|YP_004383113.1| 226 YRQLGQVDRAEEDYYTVLE 244
                                       9*************99986 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.9
                            TPR_10   8 LanalrqrgrydeAealleealai 31 
                                       L+++ +++ +y  +++ +++al i
  gi|330506685|ref|YP_004383113.1| 256 LGMVRYATEDYSSSLQAFDQALKI 279
                                       899999***************987 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.25
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       + al+++gr +eA + +++ l+
  gi|330506685|ref|YP_004383113.1| 325 GLALSSLGREKEANKCYRRILE 346
                                       789***************9987 PP

  == domain 6  score: 9.4 bits;  conditional E-value: 0.0018
                            TPR_10  22 ealleealairrrllGpdH 40 
                                       + +l++al+ +++llG+d+
  gi|330506685|ref|YP_004383113.1| 399 LGDLDQALQSYEELLGHDS 417
                                       56789***********996 PP

  == domain 7  score: 15.7 bits;  conditional E-value: 1.9e-05
                            TPR_10   4 slnNLanalrqrgrydeAealleeala 30 
                                       +l  La al+q gr++eA+ ++e a+a
  gi|330506685|ref|YP_004383113.1| 456 ALMGLAEALHQKGRLEEARSYYEAAIA 482
                                       6777*********************97 PP

  == domain 8  score: 8.0 bits;  conditional E-value: 0.0049
                            TPR_10   8 LanalrqrgrydeAealleeal 29 
                                       L+n+l+++g+y ++  l+e al
  gi|330506685|ref|YP_004383113.1| 493 LGNILCAQGEYGQSIPLFESAL 514
                                       9******************998 PP

  == domain 9  score: 7.4 bits;  conditional E-value: 0.0079
                            TPR_10   7 NLanalrqrgrydeAealleeal 29 
                                       N + +  ++grydeA++ l++a 
  gi|330506685|ref|YP_004383113.1| 560 NRGSIFAALGRYDEARESLQKAA 582
                                       66778899**********99996 PP

  == domain 10  score: 6.0 bits;  conditional E-value: 0.021
                            TPR_10   7 NLanalrqrgrydeAealleea 28 
                                       NL+ ++r + r++++++ +e a
  gi|330506685|ref|YP_004383113.1| 594 NLGQVYRLMDRHNQSRQAFENA 615
                                       9****************99976 PP

  == domain 11  score: 17.7 bits;  conditional E-value: 4.5e-06
                            TPR_10   5 lnNLanalrqrgrydeAealleealai 31 
                                       +  La al  +gr++eA++ +e++l+i
  gi|330506685|ref|YP_004383113.1| 660 QYSLALALAGQGRFQEALQAFERVLEI 686
                                       668**********************98 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   1.8   2.8e-08   1.5e-05     147     275 ..     115     243 ..      93     248 .. 0.84
   2 !   10.2   0.9   0.00058      0.31     154     246 ..     326     418 ..     293     425 .. 0.84
   3 !    8.9   0.0    0.0015       0.8     231     270 ..     437     476 ..     427     485 .. 0.86
   4 !   10.2   0.1   0.00058       0.3     144     232 ..     519     607 ..     496     617 .. 0.81
   5 !   13.5   0.5     6e-05     0.032     140     196 ..     616     673 ..     607     683 .. 0.77
   6 ?    0.3   0.0      0.64   3.4e+02     155     180 ..     666     691 ..     658     695 .. 0.54

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.8e-08
                            TPR_15 147 afllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrrae.LrellkawkaraesdasLwgplaa 222
                                         +++ +e+  ++g+   A  ++  Al+l+p++ +l ++l    + l+ ++  Lr++ ka+  + ++++++    + 
  gi|330506685|ref|YP_004383113.1| 115 EAWSLKGEIMMETGRYRMAQLCFDSALRLDPGNMTLYNRLAQSQLMLEDYDHaLRSYKKALSLE-ANNTEILFNQGD 190
                                       579************************************9988777777775466666666655.66666667789* PP

                            TPR_15 223 AlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAwrlRrqvw 275
                                         l+L r+ +AL+ ++  +++n++d+l l   A+   q g++d+A++  + v+
  gi|330506685|ref|YP_004383113.1| 191 LFLTLARYPEALNSFNLLLEQNKSDILALKGRAECYRQLGQVDRAEEDYYTVL 243
                                       *********************************************98666665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00058
                            TPR_15 154 elyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgplaaAlllLgrp 230
                                        + +  g++++A ++yr+ l+l+pd+  + +++   l+++++  ++ e      ++  ++a+  + +a A+l Lg+ 
  gi|330506685|ref|YP_004383113.1| 326 LALSSLGREKEANKCYRRILELEPDNIIALQKIADDLLERNESIQAAEHYGLILGQDPKNARALLGMAKAQLDLGDL 402
                                       5667889**************************999999999998888888888898999999999*********** PP

                            TPR_15 231 kkALeylrkqakenrk 246
                                       ++AL+ ++  +   ++
  gi|330506685|ref|YP_004383113.1| 403 DQALQSYEELLGHDSN 418
                                       *****99986655444 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0015
                            TPR_15 231 kkALeylrkqakenrkdplwllaYADaleqagradeAwrl 270
                                       + A e +++ ++ ++++p  l+  A+al q+gr +eA ++
  gi|330506685|ref|YP_004383113.1| 437 DPAIESFNRALDIEPQNPDALMGLAEALHQKGRLEEARSY 476
                                       568899999****************************987 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00058
                            TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapdsselra..allWlliDlgrraeLrellkawkaraesdasLwg 218
                                       ++   l+  + +  ++g++  Al+++ e ++l+p++s++ +  + +++ +  gr++e+re l++  + ++s+a++w 
  gi|330506685|ref|YP_004383113.1| 519 SDTESLMGKGLALAATGNSSGALQCFNEIVSLNPEDSAAWSnrGSIFAAL--GRYDEARESLQKAAGISSSSADIWY 593
                                       5556677777778899*********************9976226788877..*************9999******** PP

                            TPR_15 219 plaaAlllLgrpkk 232
                                        l+  + l+ r ++
  gi|330506685|ref|YP_004383113.1| 594 NLGQVYRLMDRHNQ 607
                                       **999999988765 PP

  == domain 5  score: 13.5 bits;  conditional E-value: 6e-05
                            TPR_15 140 eaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrr 196
                                        +++ +++  +l ++ +++++g+ + Al+ +++A++l+p+++ ++  l  +l   gr 
  gi|330506685|ref|YP_004383113.1| 616 TRLSpDDPVLWLELGLAQERTGEAKLALKSLQRAVVLDPKNEFAQYSLALALAGQGRF 673
                                       444458999*******************************887777766666655554 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 0.64
                            TPR_15 155 lyrqegqtdaAlrdyreAlalapdss 180
                                       +   +g+ ++Al++++++l+ +p+++
  gi|330506685|ref|YP_004383113.1| 666 ALAGQGRFQEALQAFERVLEINPKND 691
                                       33445555666666666666665543 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05    0.0075     199     257 ..      53     111 ..      41     116 .. 0.91
   2 ?    0.9   0.1       0.3   1.6e+02      43      98 ..     119     173 ..     115     182 .. 0.77
   3 ?    5.2   0.3     0.015       8.2      16      70 ..     160     214 ..     143     217 .. 0.82
   4 !   15.5   0.2   1.2e-05    0.0063       5     102 ..     183     279 ..     179     286 .. 0.77
   5 !   10.3   0.1   0.00043      0.23      11      78 ..     291     358 ..     282     381 .. 0.83
   6 ?   -1.0   0.0       1.2   6.4e+02      44      70 ..     392     418 ..     387     426 .. 0.85
   7 ?    1.6   0.0      0.19        98     208     252 ..     436     480 ..     430     484 .. 0.90
   8 ?    2.9   0.0     0.079        41     206     259 ..     501     554 ..     497     560 .. 0.89
   9 ?    4.9   0.0      0.02        10      16      87 ..     533     604 ..     520     684 .. 0.58
  10 ?    1.1   0.1      0.27   1.4e+02      18      72 ..     637     691 ..     625     702 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                             NARP1 199 AqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                       A+ y + gs+  Ale i+  +e +++l e +l K+ril   G l++A++ +++  ++D+
  gi|330506685|ref|YP_004383113.1|  53 AMNYSQNGSYPLALERINLSLEIDDELAEAWLLKGRILFGLGYLQEAIRSLDQVLRIDQ 111
                                       8899999*********************************************9877775 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.3
                                       HHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHH CS
                             NARP1  43 tkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalyde 98 
                                        k+e++++ gr+  A+  + + l+  p n++ y++l +++ +  ed ++ l  y++
  gi|330506685|ref|YP_004383113.1| 119 LKGEIMMETGRYRMAQLCFDSALRLDPGNMTLYNRLAQSQLML-EDYDHALRSYKK 173
                                       6899999999999999999999999999999999999987533.334555555554 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.015
                                       HHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT CS
                             NARP1  16 eagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpe 70 
                                         +++++Al   +++ +   ++ +++ ++++l l L r+ eA + ++ Lle+n+ 
  gi|330506685|ref|YP_004383113.1| 160 MLEDYDHALRSYKKALSLEANNTEILFNQGDLFLTLARYPEALNSFNLLLEQNKS 214
                                       35789999999999999999999*****************************975 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHH CS
                             NARP1   5 ellLyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyegleka 81 
                                       e+l  +  ++    ++ eAl+ ++   +q    +  ++ +ae + +Lg+ + Ae+ y + le+npe+ + ++gl  +
  gi|330506685|ref|YP_004383113.1| 183 EILFNQGDLFLTLARYPEALNSFNLLLEQNKSDILALKGRAECYRQLGQVDRAEEDYYTVLEKNPEDFESWRGLGMV 259
                                       5555566666666777888888887555554444556789**********************************999 PP

                                       T..SSS-HHHHHHHHHHTTTS CS
                             NARP1  82 kklskedeeallalydelaek 102
                                       +  ++ed ++ l+++d++ + 
  gi|330506685|ref|YP_004383113.1| 260 RY-ATEDYSSSLQAFDQALKI 279
                                       87.666677777888776655 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00043
                                       HHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHH CS
                             NARP1  11 nqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyegl 78 
                                         ++   g+  +Ale  +++     D+++ +  k+  l  Lgr++eA++ y+++le  p+n    +++
  gi|330506685|ref|YP_004383113.1| 291 GDLLLARGNFSSALESYSAALLLKKDNVSALYGKGLALSSLGREKEANKCYRRILELEPDNIIALQKI 358
                                       56677788899999999999989999***********************************8766655 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 1.2
                                       HHHHHHHTT-HHHHHHHHHHHHHH-TT CS
                             NARP1  44 kaelllkLgrkeeAeatyeaLlernpe 70 
                                       +a+ +l Lg+ ++A + ye+Ll + ++
  gi|330506685|ref|YP_004383113.1| 392 MAKAQLDLGDLDQALQSYEELLGHDSN 418
                                       6888999**************987665 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.19
                                       SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 208 rekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                        + A+e  ++a++ +p+  +  +  a+ l ++G l++A +  e a
  gi|330506685|ref|YP_004383113.1| 436 IDPAIESFNRALDIEPQNPDALMGLAEALHQKGRLEEARSYYEAA 480
                                       5689**********************************9887766 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.079
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                       g++ +++ + ++a++++p+ +e  + K+  l  +G+ ++A ++ +e  +l  +D
  gi|330506685|ref|YP_004383113.1| 501 GEYGQSIPLFESALSQEPSDTESLMGKGLALAATGNSSGALQCFNEIVSLNPED 554
                                       5667889999********************************999987776655 PP

  == domain 9  score: 4.9 bits;  conditional E-value: 0.02
                                       HHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS CS
                             NARP1  16 eagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklske 87 
                                        +g+   Al+ ++e  +   +  a   +++++  +Lgr++eA++ +++     + + + + +l ++ +l + 
  gi|330506685|ref|YP_004383113.1| 533 ATGNSSGALQCFNEIVSLNPEDSAAWSNRGSIFAALGRYDEARESLQKAAGISSSSADIWYNLGQVYRLMDR 604
                                       556666666666666665555556666666666666666666666665555555555544444444443333 PP

  == domain 10  score: 1.1 bits;  conditional E-value: 0.27
                                       THHHHHHHHHHHHGGG---HHHHHHHHHHH.HHHTT-HHHHHHHHHHHHHH-TT-C CS
                             NARP1  18 gkleeAlehLeekekqivDklavketkael.llkLgrkeeAeatyeaLlernpens 72 
                                       g+++ Al+ L+++   +  k ++ +    l l   gr++eA +++e+ le np n 
  gi|330506685|ref|YP_004383113.1| 637 GEAKLALKSLQRAV-VLDPKNEFAQYSLALaLAGQGRFQEALQAFERVLEINPKND 691
                                       55566666665532.22223444443333303345899**************9884 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.4      0.14        72      53     122 ..     105     174 ..      93     182 .. 0.84
   2 ?    4.8   0.1     0.069        36      59     122 ..     213     276 ..     175     280 .. 0.87
   3 !   13.8   1.0   0.00011     0.057      13     122 ..     291     412 ..     282     415 .. 0.87
   4 ?    7.2   0.2     0.012       6.2      78     122 ..     436     480 ..     423     484 .. 0.88
   5 !   10.3   0.0    0.0014      0.73      58     124 ..     483     549 ..     478     554 .. 0.87
   6 ?    4.0   0.0      0.12        61     108     135 ..     560     587 ..     556     591 .. 0.82
   7 !   23.6   0.6     1e-07   5.5e-05      71     123 ..     632     684 ..     606     687 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  53 ererleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       ++ r++++  ea     e  ++ Gr++ a+   +++++++P + +l+  l +    +++   AL+ Y+++
  gi|330506685|ref|YP_004383113.1| 105 QVLRIDQSLDEAWSLKGEIMMETGRYRMAQLCFDSALRLDPGNMTLYNRLAQSQLMLEDYDHALRSYKKA 174
                                       5556666666777788889999999999999999999999999999999999999999999999999986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.069
                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  59 elrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       ++ + al+ +ae   +lG+ ++a +++   ++++P + +++r l    +++++ +  L++++++
  gi|330506685|ref|YP_004383113.1| 213 KSDILALKGRAECYRQLGQVDRAEEDYYTVLEKNPEDFESWRGLGMVRYATEDYSSSLQAFDQA 276
                                       45688999999999**********************************************9987 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 0.00011
                                       HHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTT............STTHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                              BTAD  13 graalaagdpeeaaelleaAlalwrGpaladlea............gewleaererleelrlealealaeaelrlGr 77 
                                       g+ +la+g +  a+e+++aAl l ++ + a   +             + +  ++ +le + + al+++a+ +l+ ++
  gi|330506685|ref|YP_004383113.1| 291 GDLLLARGNFSSALESYSAALLLKKDNVSALYGKglalsslgrekeANKCYRRILELEPDNIIALQKIADDLLERNE 367
                                       66677888888888888888888777777666667777888888888889999999********************* PP

                                       HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  78 aeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                         +a++ +  ++ ++P + r+   + +A   +G+  +AL+ Ye+l
  gi|330506685|ref|YP_004383113.1| 368 SIQAAEHYGLILGQDPKNARALLGMAKAQLDLGDLDQALQSYEEL 412
                                       *******************************************97 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  78 aeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       ++ a++  +++++ +P + ++   l +Al++ Gr +eA  +Ye +
  gi|330506685|ref|YP_004383113.1| 436 IDPAIESFNRALDIEPQNPDALMGLAEALHQKGRLEEARSYYEAA 480
                                       6678899999********************************976 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  58 eelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       ee  ++ ++ l + + + G++ + ++  e++++++P + ++     +Ala++G+ + AL+ ++++++
  gi|330506685|ref|YP_004383113.1| 483 EEPSVRGYRGLGNILCAQGEYGQSIPLFESALSQEPSDTESLMGKGLALAATGNSSGALQCFNEIVS 549
                                       555666777778888999********************999999999***************99865 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.12
                                       HTT-HHHHHHHHHHHHHHHHHHHS---- CS
                              BTAD 108 rsGrqaeALevYerlrrlLaeeLgvepg 135
                                         G   +AL++Y+++r++L++  g++ +
  gi|330506685|ref|YP_004383113.1| 560 NRGSIFAALGRYDEARESLQKAAGISSS 587
                                       5677889*************99998765 PP

  == domain 7  score: 23.6 bits;  conditional E-value: 1e-07
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       a+ r G+a+ al+ l+++v ++P +E +   l +Ala +Gr +eAL+++er+ 
  gi|330506685|ref|YP_004383113.1| 632 AQERTGEAKLALKSLQRAVVLDPKNEFAQYSLALALAGQGRFQEALQAFERVL 684
                                       566899********************************************985 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       3.1   1.7e+03      14      43 ..     140     169 ..     137     183 .. 0.84
   2 ?    0.9   0.2       1.1     6e+02       8      54 ..     168     214 ..     162     237 .. 0.87
   3 ?   -1.0   0.0       4.3   2.2e+03      15      53 ..     209     247 ..     196     253 .. 0.80
   4 !    8.7   0.0     0.004       2.1       6      44 ..     268     306 ..     263     343 .. 0.91
   5 ?   -0.4   0.1       2.8   1.5e+03      15      44 ..     345     374 ..     332     381 .. 0.86
   6 ?    4.1   1.0      0.11        59      16      54 ..     380     418 ..     365     422 .. 0.90
   7 !   14.8   0.1   5.2e-05     0.027       5      41 ..     437     473 ..     433     476 .. 0.93
   8 !   10.8   0.0   0.00088      0.46      10      77 ..     509     574 ..     502     581 .. 0.87
   9 ?    4.2   0.1      0.11        56       4      47 ..     605     648 ..     602     651 .. 0.90
  10 !   18.3   0.4   4.1e-06    0.0022       6      54 ..     641     689 ..     637     696 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.1
                            TPR_20  14 alaanpddldarldlAlallaagryeeAle 43 
                                       al  +p ++ +   lA+ +l+ ++y+ Al 
  gi|330506685|ref|YP_004383113.1| 140 ALRLDPGNMTLYNRLAQSQLMLEDYDHALR 169
                                       677799999999999999999999999986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.1
                            TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                       l++ ++al  + ++ ++ ++  ++ l   ry eAl+ +  +l+++++
  gi|330506685|ref|YP_004383113.1| 168 LRSYKKALSLEANNTEILFNQGDLFLTLARYPEALNSFNLLLEQNKS 214
                                       677788899999999999*****************999999988876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 4.3
                            TPR_20  15 laanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                                       l++n++d+ a    A+ + + g+++ A e  +++l+++ 
  gi|330506685|ref|YP_004383113.1| 209 LEQNKSDILALKGRAECYRQLGQVDRAEEDYYTVLEKNP 247
                                       788888888888899999999999999888888888775 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.004
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                        +l+++++al+ np d+++ l   ++lla+g+   Ale 
  gi|330506685|ref|YP_004383113.1| 268 SSLQAFDQALKINPHDIQTILGKGDLLLARGNFSSALES 306
                                       6899*********************************96 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 2.8
                            TPR_20  15 laanpddldarldlAlallaagryeeAleq 44 
                                       l+ +pd++ a  + A+ ll++++  +A+e+
  gi|330506685|ref|YP_004383113.1| 345 LELEPDNIIALQKIADDLLERNESIQAAEH 374
                                       6779*****************999999886 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.11
                            TPR_20  16 aanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                        ++p++  a l +A+a+l  g+ ++Al+   e+l +d++
  gi|330506685|ref|YP_004383113.1| 380 GQDPKNARALLGMAKAQLDLGDLDQALQSYEELLGHDSN 418
                                       69**************************99999888876 PP

  == domain 7  score: 14.8 bits;  conditional E-value: 5.2e-05
                            TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeA 41 
                                       +p ++++ +al  +p++ da + lA+al+++gr eeA
  gi|330506685|ref|YP_004383113.1| 437 DPAIESFNRALDIEPQNPDALMGLAEALHQKGRLEEA 473
                                       689999******************************9 PP

  == domain 8  score: 10.8 bits;  conditional E-value: 0.00088
                            TPR_20  10 eleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllkifealgsqdpl 77 
                                        +e+al ++p+d +  +   lal+a g+   Al+ + ei++  ++ ed aa      if+alg  d++
  gi|330506685|ref|YP_004383113.1| 509 LFESALSQEPSDTESLMGKGLALAATGNSSGALQCFNEIVS--LNPEDSAAWSNRGSIFAALGRYDEA 574
                                       57999***********************************9..6677799999999999999998865 PP

  == domain 9  score: 4.2 bits;  conditional E-value: 0.11
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleqLle 47 
                                       ++++ +++e+a   +pdd  + l+l la+   g+ + Al+ L +
  gi|330506685|ref|YP_004383113.1| 605 HNQSRQAFENATRLSPDDPVLWLELGLAQERTGEAKLALKSLQR 648
                                       7888999********************************99965 PP

  == domain 10  score: 18.3 bits;  conditional E-value: 4.1e-06
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                         l++l++a+  +p++  a++ lAlal+ +gr +eAl+++ ++l+ + k
  gi|330506685|ref|YP_004383113.1| 641 LALKSLQRAVVLDPKNEFAQYSLALALAGQGRFQEALQAFERVLEINPK 689
                                       56899*********************************99999987765 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 ?    0.3   0.0       1.4   7.4e+02      13      42 ..      58      87 ..      51      89 .. 0.84
   2 ?    2.5   0.0       0.3   1.6e+02      14      44 ..      93     123 ..      90     126 .. 0.88
   3 ?    5.0   0.0     0.047        25      15      35 ..     128     148 ..     124     152 .. 0.93
   4 ?    6.0   0.2     0.024        13      12      36 ..     159     183 ..     150     186 .. 0.86
   5 ?    6.1   0.0     0.023        12      14      36 ..     263     285 ..     256     287 .. 0.88
   6 ?    6.2   0.0      0.02        11      14      35 ..     331     352 ..     318     365 .. 0.80
   7 ?    0.8   0.0         1   5.4e+02      10      35 ..     395     419 ..     391     422 .. 0.82
   8 ?    1.8   0.1      0.47   2.5e+02      24      38 ..     443     457 ..     437     467 .. 0.76
   9 ?    4.1   0.1      0.09        47       8      35 ..     461     488 ..     455     497 .. 0.81
  10 ?   -1.3   0.0       4.5   2.4e+03      14      34 ..     500     520 ..     498     524 .. 0.89
  11 ?   -0.9   0.1       3.5   1.8e+03      14      24 ..     568     578 ..     566     581 .. 0.83
  12 ?   -0.7   0.0       2.9   1.5e+03       7      37 ..     629     659 ..     629     661 .. 0.86
  13 !   15.8   0.0     2e-05     0.011       5      35 ..     661     691 ..     659     694 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.4
                                      HHT-HHHHHHHHHHHHHHTTS-HHHHHHHH CS
                        Fis1_TPR_C 13 klgeYseArryvdalLeiEPenrQaqsLke 42
                                        g Y  A++ ++  Lei+ e   a  Lk 
  gi|330506685|ref|YP_004383113.1| 58 QNGSYPLALERINLSLEIDDELAEAWLLKG 87
                                      5789***************99988888876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.3
                                       HT-HHHHHHHHHHHHHHTTS-HHHHHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaqsLkeli 44 
                                       lg  +eA r +d++L+i+ +   a sLk  i
  gi|330506685|ref|YP_004383113.1|  93 LGYLQEAIRSLDQVLRIDQSLDEAWSLKGEI 123
                                       677789******************9999876 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.047
                                       T-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenr 35 
                                       g+Y++A  + d  L+++P+n+
  gi|330506685|ref|YP_004383113.1| 128 GRYRMAQLCFDSALRLDPGNM 148
                                       89*****************97 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.024
                                       HHHT-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQ 36 
                                       + l +Y+ A+r  +  L++E +n  
  gi|330506685|ref|YP_004383113.1| 159 LMLEDYDHALRSYKKALSLEANNTE 183
                                       5689******************976 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.023
                                       HT-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQ 36 
                                         +Ys +++  d+ L+i P   Q
  gi|330506685|ref|YP_004383113.1| 263 TEDYSSSLQAFDQALKINPHDIQ 285
                                       679****************9877 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.02
                                       HT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenr 35 
                                       lg+ +eA ++ +++Le+EP+n 
  gi|330506685|ref|YP_004383113.1| 331 LGREKEANKCYRRILELEPDNI 352
                                       566689**************94 PP

  == domain 7  score: 0.8 bits;  conditional E-value: 1
                                       HHHHHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPenr 35 
                                       +++ lg+ ++A++  + lL ++ +n+
  gi|330506685|ref|YP_004383113.1| 395 AQLDLGDLDQALQSYEELLGHD-SNS 419
                                       67779**************998.555 PP

  == domain 8  score: 1.8 bits;  conditional E-value: 0.47
                                       HHHHHHHTTS-HHHH CS
                        Fis1_TPR_C  24 vdalLeiEPenrQaq 38 
                                        ++ L iEP+n  a+
  gi|330506685|ref|YP_004383113.1| 443 FNRALDIEPQNPDAL 457
                                       6789*******9986 PP

  == domain 9  score: 4.1 bits;  conditional E-value: 0.09
                                       HHHHHHHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C   8 AlGhyklgeYseArryvdalLeiEPenr 35 
                                       A +    g+ +eAr y +a ++ EP+ r
  gi|330506685|ref|YP_004383113.1| 461 AEALHQKGRLEEARSYYEAAIAEEPSVR 488
                                       5555666899***************977 PP

  == domain 10  score: -1.3 bits;  conditional E-value: 4.5
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                       +geY ++  + +  L+ EP+ 
  gi|330506685|ref|YP_004383113.1| 500 QGEYGQSIPLFESALSQEPSD 520
                                       599****************86 PP

  == domain 11  score: -0.9 bits;  conditional E-value: 3.5
                                       HT-HHHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArryv 24 
                                       lg+Y+eAr+ +
  gi|330506685|ref|YP_004383113.1| 568 LGRYDEARESL 578
                                       89******876 PP

  == domain 12  score: -0.7 bits;  conditional E-value: 2.9
                                       HHHHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C   7 lAlGhyklgeYseArryvdalLeiEPenrQa 37 
                                       l l++ + ge + A++ +++   ++P+n+ a
  gi|330506685|ref|YP_004383113.1| 629 LGLAQERTGEAKLALKSLQRAVVLDPKNEFA 659
                                       5688889999999**************9855 PP

  == domain 13  score: 15.8 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C   5 YylAlGhyklgeYseArryvdalLeiEPenr 35 
                                       Y lAl+ + +g+++eA++  +++Lei P+n 
  gi|330506685|ref|YP_004383113.1| 661 YSLALALAGQGRFQEALQAFERVLEINPKND 691
                                       89***************************97 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.57     3e+02       2      26 .]      81     105 ..      80     105 .. 0.87
   2 ?    2.8   0.3      0.45   2.4e+02       7      22 ..     222     237 ..     218     237 .. 0.91
   3 ?    0.2   0.0       3.2   1.7e+03       8      21 ..     291     304 ..     288     306 .. 0.80
   4 !   16.4   1.1   1.9e-05    0.0098       1      25 [.     386     410 ..     386     411 .. 0.92
   5 !   13.3   0.1   0.00019       0.1       3      21 ..     456     474 ..     454     478 .. 0.92
   6 ?    1.1   0.0       1.7   8.7e+02       7      23 ..     527     543 ..     522     546 .. 0.81
   7 !    9.8   0.0    0.0025       1.3       3      25 ..     557     579 ..     555     580 .. 0.85
   8 ?   -1.3   0.0       9.8   5.2e+03       5      25 ..     593     613 ..     591     614 .. 0.82
   9 ?   -0.7   0.1       6.3   3.3e+03       2      21 ..     624     643 ..     623     648 .. 0.80
  10 !   15.5   2.1   3.7e-05      0.02       3      26 .]     659     682 ..     658     682 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.57
                             TPR_4   2 rallaLArallalGdldeAraller 26 
                                        a l+ +r l+ lG l eA + l++
  gi|330506685|ref|YP_004383113.1|  81 EAWLLKGRILFGLGYLQEAIRSLDQ 105
                                       688999*************988876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.45
                             TPR_4   7 LArallalGdldeAra 22 
                                       +A+ + +lG+ d+A++
  gi|330506685|ref|YP_004383113.1| 222 RAECYRQLGQVDRAEE 237
                                       89************85 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 3.2
                             TPR_4   8 ArallalGdldeAr 21 
                                       + +lla+G++  A+
  gi|330506685|ref|YP_004383113.1| 291 GDLLLARGNFSSAL 304
                                       789*****997666 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 1.9e-05
                             TPR_4   1 arallaLArallalGdldeAralle 25 
                                       arall++A a+l+lGdld+A++  e
  gi|330506685|ref|YP_004383113.1| 386 ARALLGMAKAQLDLGDLDQALQSYE 410
                                       79*******************9776 PP

  == domain 5  score: 13.3 bits;  conditional E-value: 0.00019
                             TPR_4   3 allaLArallalGdldeAr 21 
                                       al +LA+al++ G+l+eAr
  gi|330506685|ref|YP_004383113.1| 456 ALMGLAEALHQKGRLEEAR 474
                                       8999**************9 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 1.7
                             TPR_4   7 LArallalGdldeAral 23 
                                        + al+a+G++  A++ 
  gi|330506685|ref|YP_004383113.1| 527 KGLALAATGNSSGALQC 543
                                       689*******9999875 PP

  == domain 7  score: 9.8 bits;  conditional E-value: 0.0025
                             TPR_4   3 allaLArallalGdldeAralle 25 
                                       a ++++   +alG++deAr+ l+
  gi|330506685|ref|YP_004383113.1| 557 AWSNRGSIFAALGRYDEARESLQ 579
                                       778888899**********9775 PP

  == domain 8  score: -1.3 bits;  conditional E-value: 9.8
                             TPR_4   5 laLArallalGdldeAralle 25 
                                       ++L++++ +  ++ + r+++e
  gi|330506685|ref|YP_004383113.1| 593 YNLGQVYRLMDRHNQSRQAFE 613
                                       89*****99999988887765 PP

  == domain 9  score: -0.7 bits;  conditional E-value: 6.3
                             TPR_4   2 rallaLArallalGdldeAr 21 
                                       ++ l L+ a+ ++G++  A+
  gi|330506685|ref|YP_004383113.1| 624 VLWLELGLAQERTGEAKLAL 643
                                       56788999******998776 PP

  == domain 10  score: 15.5 bits;  conditional E-value: 3.7e-05
                             TPR_4   3 allaLArallalGdldeAraller 26 
                                       a++ LA al+ +G++ eA++++er
  gi|330506685|ref|YP_004383113.1| 659 AQYSLALALAGQGRFQEALQAFER 682
                                       7999****************9997 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       6.3   3.3e+03      13      35 ..     160     180 ..     154     181 .. 0.70
   2 ?    0.4   0.0       1.3     7e+02       3      34 ..     252     281 ..     251     283 .. 0.83
   3 ?   -0.5   0.1       2.4   1.3e+03      10      26 ..     395     409 ..     390     413 .. 0.77
   4 !   17.1   0.0   7.5e-06    0.0039       1      27 [.     454     478 ..     454     484 .. 0.87
   5 ?    3.8   0.0      0.11        57      10      25 ..     564     579 ..     562     582 .. 0.84
   6 !   10.7   0.0   0.00076       0.4       5      25 ..     661     681 ..     661     687 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.3
                                       HTT-HHHHHHH..HHHHHHH-TT CS
                             TPR_3  13 nkkkyqeArelfsYallaildke 35 
                                       + ++y+ A+    Y+ +  l+++
  gi|330506685|ref|YP_004383113.1| 160 MLEDYDHALRS--YKKALSLEAN 180
                                       77899999988..7766666665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHTT-HHHHHHH..HHHHHHH-T CS
                             TPR_3   3 ylysyAaefynkkkyqeArelfsYallaildk 34 
                                       ++ +++ + y  ++y+  +++f+  ++ ++ +
  gi|330506685|ref|YP_004383113.1| 252 SWRGLGMVRYATEDYSSSLQAFD--QALKINP 281
                                       566889999********9***88..9998865 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.4
                                       HHHHTT-HHHHHHH..H CS
                             TPR_3  10 efynkkkyqeArelfsY 26 
                                       ++ + +++++A++   Y
  gi|330506685|ref|YP_004383113.1| 395 AQLDLGDLDQALQS--Y 409
                                       555679******98..4 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 7.5e-06
                                       HHHHHHHHHHHHHTT-HHHHHHH..HH CS
                             TPR_3   1 ldylysyAaefynkkkyqeArelfsYa 27 
                                       +d l+++A ++++k++++eAr +  Y+
  gi|330506685|ref|YP_004383113.1| 454 PDALMGLAEALHQKGRLEEARSY--YE 478
                                       588********************..54 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.11
                                       HHHHTT-HHHHHHH.. CS
                             TPR_3  10 efynkkkyqeArelfs 25 
                                        f   ++y+eAre ++
  gi|330506685|ref|YP_004383113.1| 564 IFAALGRYDEARESLQ 579
                                       68899*******9766 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.00076
                                       HHHHHHHHHTT-HHHHHHH.. CS
                             TPR_3   5 ysyAaefynkkkyqeArelfs 25 
                                       ys+A ++  ++++qeA+++f 
  gi|330506685|ref|YP_004383113.1| 661 YSLALALAGQGRFQEALQAFE 681
                                       9******************75 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.3e-05     0.017     195     290 ..      75     170 ..      49     182 .. 0.89
   2 ?    0.2   0.0      0.56     3e+02     219     290 ..     201     272 ..     176     276 .. 0.82
   3 !    9.3   0.0   0.00099      0.52     174     291 ..     459     578 ..     453     589 .. 0.87
   4 ?   -0.7   0.0         1   5.5e+02     263     292 ..     618     647 ..     587     683 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                                       HHTT-GGGHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHH CS
                             ChAPs 195 LkeeepevvillarvllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktW 271
                                       + +e  e+  l  r+l+      +a++ l + l+ +++  e  +l+ e +++  ++++A+ + ++a ++ P + + +
  gi|330506685|ref|YP_004383113.1|  75 IDDELAEAWLLKGRILFGLGYLQEAIRSLDQVLRIDQSLDEAWSLKGEIMMETGRYRMAQLCFDSALRLDPGNMTLY 151
                                       5566677777778888888888899999999999888889999********************************** PP

                                       HHHHHHHHHTT-HHHHHHH CS
                             ChAPs 272 alLvkvYikledienALlt 290
                                        +L+++ + led+++AL +
  gi|330506685|ref|YP_004383113.1| 152 NRLAQSQLMLEDYDHALRS 170
                                       ****************965 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.56
                                       HHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
                             ChAPs 219 avkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienALlt 290
                                       a++  n  le++++d   L+ +ae   +  + + A e      +  P +f+ W  L  v  + ed+++ L +
  gi|330506685|ref|YP_004383113.1| 201 ALNSFNLLLEQNKSDILALKGRAECYRQLGQVDRAEEDYYTVLEKNPEDFESWRGLGMVRYATEDYSSSLQA 272
                                       555556667777888777888888888888888888888889999**************9999999998865 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00099
                                       HHHHHHHHHT-HHHHHHHHHHHHTT-GGGHHH..HHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS CS
                             ChAPs 174 tllklvrltkrydralellekLkeeepevvil..larvllladeEvdavkllneeleeeekdaelLllqaefllskk 248
                                       +l + +++  r+++a++  e  ++eep v     l  +l ++ e  +++ l +++l++e++d+e L+ +   l    
  gi|330506685|ref|YP_004383113.1| 459 GLAEALHQKGRLEEARSYYEAAIAEEPSVRGYrgLGNILCAQGEYGQSIPLFESALSQEPSDTESLMGKGLALAATG 535
                                       566777777788888888888888888886543377888888888899***************************** PP

                                       --HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                             ChAPs 249 keelAlevakravksaPsefktWalLvkvYikledienALltL 291
                                       +++ Al++ ++ v++ P +++ W     ++ +l+ +++A  +L
  gi|330506685|ref|YP_004383113.1| 536 NSSGALQCFNEIVSLNPEDSAAWSNRGSIFAALGRYDEARESL 578
                                       *********************************9999986665 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1
                                       H-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                             ChAPs 263 saPsefktWalLvkvYikledienALltLN 292
                                       ++P +   W +L     + ++ + AL +L 
  gi|330506685|ref|YP_004383113.1| 618 LSPDDPVLWLELGLAQERTGEAKLALKSLQ 647
                                       444444444444444444444444444332 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.023        12      57     100 ..     150     193 ..     124     207 .. 0.83
   2 ?   -1.7   0.0       5.2   2.7e+03      96     126 ..     212     242 ..     192     248 .. 0.64
   3 !    8.9   0.0    0.0029       1.5      99     129 ..     317     347 ..     298     352 .. 0.91
   4 ?    1.8   0.0      0.43   2.3e+02      57      82 ..     388     413 ..     378     417 .. 0.84
   5 ?    2.0   0.0      0.37     2e+02      78     126 ..     436     480 ..     413     484 .. 0.73
   6 ?    4.8   0.1     0.051        27      81     127 ..     540     582 ..     521     588 .. 0.70
   7 ?    5.5   0.1     0.031        17     104     128 ..     661     685 ..     627     691 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHH CS
                           DUF3856  57 chaglsealaklgrydealesadkalryfnrrGeleqdeGklWi 100
                                        +  l+++ + l +yd+al+s +kal       e+  ++G l++
  gi|330506685|ref|YP_004383113.1| 150 LYNRLAQSQLMLEDYDHALRSYKKALSLEANNTEILFNQGDLFL 193
                                       5788999999999********99999887777777777776665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.2
                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  96 GklWiaavfsravaleelGrkdealkafrma 126
                                        k  i a+  ra ++ +lG+ d a + + ++
  gi|330506685|ref|YP_004383113.1| 212 NKSDILALKGRAECYRQLGQVDRAEEDYYTV 242
                                       3455667777777777777777777666655 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  99 WiaavfsravaleelGrkdealkafrmagem 129
                                        ++a++ ++ al++lGr++ea k +r + e+
  gi|330506685|ref|YP_004383113.1| 317 NVSALYGKGLALSSLGREKEANKCYRRILEL 347
                                       57899*********************98875 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.43
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  57 chaglsealaklgrydealesadkal 82 
                                       +  g+++a + lg+ d+al+s ++ l
  gi|330506685|ref|YP_004383113.1| 388 ALLGMAKAQLDLGDLDQALQSYEELL 413
                                       5568999*************988755 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  78 adkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       +d a++ fnr  ++e ++      a++  a al++ Gr +ea  +++ a
  gi|330506685|ref|YP_004383113.1| 436 IDPAIESFNRALDIEPQNP----DALMGLAEALHQKGRLEEARSYYEAA 480
                                       5667777777776666554....46778899999999999999998876 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.051
                                       HHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  81 alryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       al+ fn    l+ ++   W     +r+  ++ lGr+dea +++++a+
  gi|330506685|ref|YP_004383113.1| 540 ALQCFNEIVSLNPEDSAAW----SNRGSIFAALGRYDEARESLQKAA 582
                                       6666666666766666666....467777777777777777777665 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.031
                                       HHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmage 128
                                       +s a al++ Gr +eal+af+ + e
  gi|330506685|ref|YP_004383113.1| 661 YSLALALAGQGRFQEALQAFERVLE 685
                                       5566777777777777777776665 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   0.0      0.68   3.6e+02     125     174 ..      92     142 ..      78     150 .. 0.75
   2 ?    3.6   0.1     0.088        46     117     176 ..     152     212 ..     144     223 .. 0.75
   3 !    8.9   0.1    0.0022       1.2      90     177 ..     230     315 ..     216     329 .. 0.70
   4 !   14.6   1.5   3.7e-05      0.02      75     177 ..     385     485 ..     329     497 .. 0.75
   5 ?    5.4   0.1     0.024        13     150     174 ..     559     583 ..     529     599 .. 0.80
   6 ?    3.0   0.1      0.14        71     122     174 ..     564     617 ..     563     630 .. 0.73
   7 ?    2.3   0.9      0.22   1.2e+02      85     138 ..     632     682 ..     603     688 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.68
                            TPR_21 125 aekkydeAlktLeakkeeafa.alvaelrGDilvaqgkldeAraaYqaAla 174
                                         + ++eA++ L+++ +   +  ++  l+G+i++++g+   A+  ++ Al+
  gi|330506685|ref|YP_004383113.1|  92 GLGYLQEAIRSLDQVLRIDQSlDEAWSLKGEIMMETGRYRMAQLCFDSALR 142
                                       5566667777777765543331456679**************999999987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.088
                            TPR_21 117 lRLarvllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                        RLa+ +l  ++yd+Al+  +++ + ea + ++   +GD+++   +  eA + ++  l+++
  gi|330506685|ref|YP_004383113.1| 152 NRLAQSQLMLEDYDHALRSYKKALSlEANNTEILFNQGDLFLTLARYPEALNSFNLLLEQN 212
                                       59***************99876543266666666678888888888888877776666555 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0022
                            TPR_21  90 gdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeA 165
                                       g++++A++ +  vlek++++ +++     L  v  a+++y   l++ +++ + +  + +    +GD+l+a+g++  A
  gi|330506685|ref|YP_004383113.1| 230 GQVDRAEEDYYTVLEKNPED-FESWRG--LGMVRYATEDYSSSLQAFDQALKiNPHDIQTILGKGDLLLARGNFSSA 303
                                       56666666666666666555.443333..4456677777888888886664425566666667************** PP

                            TPR_21 166 raaYqaAlaale 177
                                        + Y+aAl  ++
  gi|330506685|ref|YP_004383113.1| 304 LESYSAALLLKK 315
                                       *******97655 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 3.7e-05
                            TPR_21  75 aalaaLllAkaaveagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLeakke.eafaalvae 150
                                        a+a L  Aka+ + gdl++A +++e++l + ++ + + + r    ++ll + ++d A++  +++ + e  +  +  
  gi|330506685|ref|YP_004383113.1| 385 NARALLGMAKAQLDLGDLDQALQSYEELLGHDSNSSAAWIGRG---EILLLQTNIDPAIESFNRALDiEPQNPDALM 458
                                       4788999***************************988888885...6788888888888887655441333333333 PP

                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaale 177
                                          ++l ++g+l+eAr+ Y+aA+a+  
  gi|330506685|ref|YP_004383113.1| 459 GLAEALHQKGRLEEARSYYEAAIAEEP 485
                                       3447999***************99865 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.024
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAla 174
                                         rG i++a g+ deAr+  q+A  
  gi|330506685|ref|YP_004383113.1| 559 SNRGSIFAALGRYDEARESLQKAAG 583
                                       569******************9975 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.14
                            TPR_21 122 vllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       + +a + ydeA + L+++   ++ +a +    G ++  +++ ++ r+a+++A +
  gi|330506685|ref|YP_004383113.1| 564 IFAALGRYDEARESLQKAAGiSSSSADIWYNLGQVYRLMDRHNQSRQAFENATR 617
                                       557788899999999765441344455555579999999999999999999976 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.22
                            TPR_21  85 aaveagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLea 138
                                       a+  +g+++ A ++L++++   ++   ++ a+  La  l+ ++ ++eAl++ e+
  gi|330506685|ref|YP_004383113.1| 632 AQERTGEAKLALKSLQRAVVLDPK---NEFAQYSLALALAGQGRFQEALQAFER 682
                                       444556666666666665555444...478999999999999999999998775 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 ?    4.7   0.0      0.02        10      94     169 ..      80     155 ..      57     181 .. 0.78
   2 ?    0.5   0.0      0.39     2e+02     106     165 ..     228     287 ..     193     340 .. 0.64
   3 !   14.4   0.0   2.2e-05     0.012      92     213 ..     384     505 ..     356     519 .. 0.78
   4 !    6.1   0.2    0.0076         4     107     222 ..     568     684 ..     563     699 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.02
                                       SHHHHHHHHHHHHCT-HHHHHHHHHHH...HHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHH CS
                          PknG_TPR  94 levpLaevrahldlGdveearelLdel...eeeveedWrldWyrglaeLlegdyeeAaaeFdevlaalpGEiaPkla 167
                                       +e  L + r+ + lG  +ea + Ld++   +++  e W l   +g   + +g+y+ A+ +Fd+ l++ pG ++    
  gi|330506685|ref|YP_004383113.1|  80 AEAWLLKGRILFGLGYLQEAIRSLDQVlriDQSLDEAWSL---KGEIMMETGRYRMAQLCFDSALRLDPGNMTLYNR 153
                                       5777888899************999852225667777777...599999******************9999875555 PP

                                       HH CS
                          PknG_TPR 168 LA 169
                                       LA
  gi|330506685|ref|YP_004383113.1| 154 LA 155
                                       55 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.39
                                       HCT-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHH CS
                          PknG_TPR 106 dlGdveearelLdeleeeveedWrldWyrglaeLlegdyeeAaaeFdevlaalpGEiaPk 165
                                       +lG+v++a+e   ++ e+++ed+      g+ + +++dy++  ++Fd+ l++ p +i   
  gi|330506685|ref|YP_004383113.1| 228 QLGQVDRAEEDYYTVLEKNPEDFESWRGLGMVRYATEDYSSSLQAFDQALKINPHDIQTI 287
                                       466777776666666666666655433457777777888888888887777777666555 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 2.2e-05
                                       C-SHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH---HHHHHH.HHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHH CS
                          PknG_TPR  92 eslevpLaevrahldlGdveearelLdeleeeveedWrldWy.rglaeLlegdyeeAaaeFdevlaalpGEiaPkla 167
                                       +++   L  ++a+ldlGd ++a +  +el  +  ++    W  rg   Ll+ + + A+++F++ l++ p      ++
  gi|330506685|ref|YP_004383113.1| 384 KNARALLGMAKAQLDLGDLDQALQSYEELLGHD-SNSSAAWIgRGEILLLQTNIDPAIESFNRALDIEPQNPDALMG 459
                                       4566778999*******************8755.55567776489999***************************** PP

                                       HHHHHHHHT---TT.-HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHH CS
                          PknG_TPR 168 LAataElagetdee.kyYrtVwrtdrgvvsAaFGlaRqlaaagdraa 213
                                       LA +    g+ +e+ +yY+     ++  v    Gl   l a+g+  +
  gi|330506685|ref|YP_004383113.1| 460 LAEALHQKGRLEEArSYYEAAIA-EEPSVRGYRGLGNILCAQGEYGQ 505
                                       **999999887765167776555.44556667788888888887655 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0076
                                       CT-HHHHHHHHHHHHHHH---HHHHHH.HHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT---.TT CS
                          PknG_TPR 107 lGdveearelLdeleeeveedWrldWy.rglaeLlegdyeeAaaeFdevlaalpGEiaPklaLAataElagetd.ee 181
                                       lG  +eare L++ +  +++   + Wy  g+   l+++ ++ +++F++  ++ p +    l L  + E++ge++ + 
  gi|330506685|ref|YP_004383113.1| 568 LGRYDEARESLQKAAGISSSSADI-WYnLGQVYRLMDRHNQSRQAFENATRLSPDDPVLWLELGLAQERTGEAKlAL 643
                                       788999999999998877777666.5526999999999999999999999999999999999999999999988444 PP

                                       -HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHTS- CS
                          PknG_TPR 182 kyYrtVwrtdrgvvsAaFGlaRqlaaagdraaAvaaLdeVp 222
                                       k  +     d     A + la +la +g+ ++A++a + V 
  gi|330506685|ref|YP_004383113.1| 644 KSLQRAVVLDPKNEFAQYSLALALAGQGRFQEALQAFERVL 684
                                       66666666777777899999999999999999999999885 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.3    0.0021       1.1     199     241 ..     146     188 ..     113     203 .. 0.81
   2 !    6.6   0.1    0.0084       4.4     182     237 ..     197     252 ..     190     278 .. 0.91
   3 !    7.7   0.0    0.0039       2.1     170     254 ..     386     473 ..     378     486 .. 0.85
   4 ?    2.9   0.0      0.12        62     184     251 ..     538     605 ..     527     625 .. 0.74
   5 ?   -2.6   0.0       5.4   2.8e+03     101     126 ..     656     681 ..     631     690 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0021
                                       --HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHH CS
                        Coatomer_E 199 stplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNl 241
                                        ++ l n  A  +l+l++y+ A  + k+aL  +a++ e L N 
  gi|330506685|ref|YP_004383113.1| 146 GNMTLYNRLAQSQLMLEDYDHALRSYKKALSLEANNTEILFNQ 188
                                       45667788999*****************************995 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0084
                                       HHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHH CS
                        Coatomer_E 182 kiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeet 237
                                       ++ +A+  f+ l e+ ks  l l+g+A +  +lg+ + Ae+   + L+k+++d e 
  gi|330506685|ref|YP_004383113.1| 197 RYPEALNSFNLLLEQNKSDILALKGRAECYRQLGQVDRAEEDYYTVLEKNPEDFES 252
                                       577899999999***************************************99886 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0039
                                       HHHHHHHHH-T...THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHH CS
                        Coatomer_E 170 Aqawvklavgg...ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvv 243
                                       A a++ +a++    + + +A+  ++el ++ ++ ++   g+  + ll+ + + A ++ + aLd +++++++L+ l  
  gi|330506685|ref|YP_004383113.1| 386 ARALLGMAKAQldlGDLDQALQSYEELLGHDSNSSAAWIGRGEILLLQTNIDPAIESFNRALDIEPQNPDALMGLAE 462
                                       55666666665444567889999******9888899999**********************************9999 PP

                                       HHHHTT--HHH CS
                        Coatomer_E 244 aaqhlgkdaev 254
                                       a ++ g+ +e+
  gi|330506685|ref|YP_004383113.1| 463 ALHQKGRLEEA 473
                                       99998887665 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-- CS
                        Coatomer_E 184 qdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkd 251
                                         A+  f+e+    ++ ++    +  +  +lgry+eA ++L++a    +  ++   Nl  +  ++++ 
  gi|330506685|ref|YP_004383113.1| 538 SGALQCFNEIVSLNPEDSAAWSNRGSIFAALGRYDEARESLQKAAGISSSSADIWYNLGQVYRLMDRH 605
                                       5677777777777777777777777778899*************999988888888886666666655 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 5.4
                                       -HHHHHHHHHHHHHTT-HHHHHHHHT CS
                        Coatomer_E 101 nevlrllaaivflkegdfddalkllk 126
                                       ne ++   a+ +  +g f++al++ +
  gi|330506685|ref|YP_004383113.1| 656 NEFAQYSLALALAGQGRFQEALQAFE 681
                                       44444444444444444444444433 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.11        57      73     123 ..      50     100 ..      43     116 .. 0.91
   2 ?   -0.6   0.0       3.2   1.7e+03      79     111 ..     124     156 ..     111     179 .. 0.79
   3 ?    1.6   0.1      0.68   3.6e+02      85     118 ..     198     231 ..     151     240 .. 0.64
   4 ?    0.1   0.0         2     1e+03      70     121 ..     285     336 ..     260     345 .. 0.72
   5 ?    5.9   0.2     0.032        17      52     121 ..     365     472 ..     360     485 .. 0.67
   6 ?    1.4   0.0      0.75   3.9e+02      68     121 ..     520     573 ..     511     581 .. 0.88
   7 ?    6.1   0.1     0.027        14      79     124 ..     633     678 ..     602     687 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.11
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  73 lekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       l++a ++ ++g y +a+e +n  ++ d+e aea  lk ++l  lgy +e+ 
  gi|330506685|ref|YP_004383113.1|  50 LREAMNYSQNGSYPLALERINLSLEIDDELAEAWLLKGRILFGLGYLQEAI 100
                                       667888899*************************************99975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.2
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHH CS
                   Alkyl_sulf_dimr  79 alkegdyrwaaellnhlvfadpenaeakelkad 111
                                        ++ g yr+a+   + ++  dp n +  + +a+
  gi|330506685|ref|YP_004383113.1| 124 MMETGRYRMAQLCFDSALRLDPGNMTLYNRLAQ 156
                                       578999*************99998655544444 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.68
                                       HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  85 yrwaaellnhlvfadpenaeakelkadaleqlgy 118
                                       y  a++  n l+++++++  a + +a++++qlg+
  gi|330506685|ref|YP_004383113.1| 198 YPEALNSFNLLLEQNKSDILALKGRAECYRQLGQ 231
                                       4556666667777777777777777777777776 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
                   Alkyl_sulf_dimr  70 ekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                                       +++l k    l++g++  a+e  + ++  +++n +a   k  al +lg+++e
  gi|330506685|ref|YP_004383113.1| 285 QTILGKGDLLLARGNFSSALESYSAALLLKKDNVSALYGKGLALSSLGREKE 336
                                       4555566666777888888888888888888888887777777777777766 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.032
                                       ---HHHHHHHHHHHTT....SHHHHHHHHHHHHHTT-HHHHHHHHHHHHH........................... CS
                   Alkyl_sulf_dimr  52 plppeekakrlvelmG....gaekvlekakealkegdyrwaaellnhlvf........................... 97 
                                       + +  ++a+++  ++G    +a ++l +ak++l+ gd+  a++  + l+                            
  gi|330506685|ref|YP_004383113.1| 365 RNESIQAAEHYGLILGqdpkNARALLGMAKAQLDLGDLDQALQSYEELLGhdsnssaawigrgeilllqtnidpaie 441
                                       55667778888888888887889999999999999999999999999999555555555555555555555555555 PP

                                       .......HSTT-HHHHHHHHHHHHHHHHH-S CS
                   Alkyl_sulf_dimr  98 .......adpenaeakelkadaleqlgyqae 121
                                               +p+n +a   +a+al q g+ +e
  gi|330506685|ref|YP_004383113.1| 442 sfnraldIEPQNPDALMGLAEALHQKGRLEE 472
                                       5544433455556666666666666666655 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.75
                                       SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
                   Alkyl_sulf_dimr  68 gaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                                       + e ++ k  + ++ g+   a++  n +v  +pe+++a + + +++ +lg+  e
  gi|330506685|ref|YP_004383113.1| 520 DTESLMGKGLALAATGNSSGALQCFNEIVSLNPEDSAAWSNRGSIFAALGRYDE 573
                                       6777888888889999999*********************99999999998776 PP

  == domain 7  score: 6.1 bits;  conditional E-value: 0.027
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  79 alkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                       + + g++++a++ l+ +v  dp+n+ a+  +a al   g+++e+ +
  gi|330506685|ref|YP_004383113.1| 633 QERTGEAKLALKSLQRAVVLDPKNEFAQYSLALALAGQGRFQEALQ 678
                                       556899**********************************999876 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.055        29     143     169 ..     148     174 ..     137     182 .. 0.82
   2 ?   -2.3   0.0       6.6   3.5e+03     152     170 ..     327     345 ..     325     351 .. 0.83
   3 ?    1.6   0.1      0.44   2.3e+02     123     170 ..     433     481 ..     427     484 .. 0.84
   4 ?    1.1   0.0      0.63   3.3e+02     151     181 ..     529     559 ..     500     566 .. 0.88
   5 ?   -2.2   0.0       6.1   3.2e+03     154     170 ..     566     582 ..     562     592 .. 0.87
   6 !   13.9   0.4   7.1e-05     0.037      78     177 ..     595     691 ..     581     700 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.055
                           Wzy_C_2 143 pavierlilslallGdedeAeqilara 169
                                        ++++rl++s+ +l d d A++ +++a
  gi|330506685|ref|YP_004383113.1| 148 MTLYNRLAQSQLMLEDYDHALRSYKKA 174
                                       37899****************998887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.6
                           Wzy_C_2 152 slallGdedeAeqilarar 170
                                       +l  lG+e+eA + ++r  
  gi|330506685|ref|YP_004383113.1| 327 ALSSLGREKEANKCYRRIL 345
                                       67789********999975 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.44
                           Wzy_C_2 123 penlaaklalarklihlsPe.pavierlilslallGdedeAeqilarar 170
                                       ++n+++ ++  ++++   P+ p  +  l+++l ++G+ +eA+ +++ a+
  gi|330506685|ref|YP_004383113.1| 433 QTNIDPAIESFNRALDIEPQnPDALMGLAEALHQKGRLEEARSYYEAAI 481
                                       678888888888888888863678889****************999876 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.63
                           Wzy_C_2 151 lslallGdedeAeqilararalfpeedakwv 181
                                       l+la++G  ++A+q   +   l pe+ a+w+
  gi|330506685|ref|YP_004383113.1| 529 LALAATGNSSGALQCFNEIVSLNPEDSAAWS 559
                                       6899**************************5 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 6.1
                           Wzy_C_2 154 allGdedeAeqilarar 170
                                       a+lG+ deA+  l++a 
  gi|330506685|ref|YP_004383113.1| 566 AALGRYDEARESLQKAA 582
                                       789******99999875 PP

  == domain 6  score: 13.9 bits;  conditional E-value: 7.1e-05
                           Wzy_C_2  78 leqlyltsepneaalrevtnpkvwkdrflfrayadllelgllplspenlaaklalarklihlsPepav.ierlilsl 153
                                       l q+y+  + + +++++ +n+     r+  ++ +  lelgl++     ++  l+  ++++ l P+  +  + l+l+l
  gi|330506685|ref|YP_004383113.1| 595 LGQVYRLMDRHNQSRQAFENAT----RLSPDDPVLWLELGLAQERTGEAKLALKSLQRAVVLDPKNEFaQYSLALAL 667
                                       5566666666666666655443....344467777899**************************98873579***** PP

                           Wzy_C_2 154 allGdedeAeqilararalfpeed 177
                                       a++G+ +eA+q  +r+  + p++d
  gi|330506685|ref|YP_004383113.1| 668 AGQGRFQEALQAFERVLEINPKND 691
                                       ***************998888776 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.9   1.5e+03       8      25 ..      50      67 ..      48      74 .. 0.88
   2 ?    4.4   0.1     0.074        39      18      32 ..     162     176 ..     153     177 .. 0.85
   3 ?    6.5   0.1     0.017       8.8      24      62 ..     195     237 ..     187     237 .. 0.85
   4 ?    4.0   0.0       0.1        53      23      52 ..     262     290 ..     259     297 .. 0.76
   5 ?    2.6   0.0      0.28   1.5e+02      17      31 ..     297     311 ..     293     313 .. 0.89
   6 ?    0.1   0.1       1.6   8.5e+02       4      29 ..     386     411 ..     384     414 .. 0.84
   7 ?    3.7   0.5      0.12        65      11      31 ..     461     481 ..     456     483 .. 0.85
   8 ?   -0.5   0.0       2.6   1.4e+03      27      48 ..     503     523 ..     494     528 .. 0.74
   9 ?   -0.3   0.0       2.2   1.2e+03      22      38 ..     566     582 ..     560     591 .. 0.75
  10 ?    0.2   0.1       1.5     8e+02      19      35 ..     672     681 ..     640     698 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.9
                               MIT  8 vkkAveeDnagnyeeAle 25
                                      +++A+++ ++g y+ Ale
  gi|330506685|ref|YP_004383113.1| 50 LREAMNYSQNGSYPLALE 67
                                      689*************98 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.074
                               MIT  18 gnyeeAlelYkeale 32 
                                       ++y+ Al+ Yk+al 
  gi|330506685|ref|YP_004383113.1| 162 EDYDHALRSYKKALS 176
                                       79***********96 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.017
                               MIT  24 lelYkealelLlqalkekneerrellrekieeYle.....Raee 62 
                                       l  Y eal+ ++++l  +n+++  +l+ ++e+Y +     Raee
  gi|330506685|ref|YP_004383113.1| 195 LARYPEALNSFNLLLE-QNKSDILALKGRAECYRQlgqvdRAEE 237
                                       56799**********6.788*************98777777775 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.1
                               MIT  23 AlelYkealelLlqalkekneerrellrek 52 
                                       A e Y+++l+ + qalk  n+ + +++  k
  gi|330506685|ref|YP_004383113.1| 262 ATEDYSSSLQAFDQALKI-NPHDIQTILGK 290
                                       7788*************4.55666666555 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.28
                               MIT  17 agnyeeAlelYkeal 31 
                                       +gn++ Ale Y+ al
  gi|330506685|ref|YP_004383113.1| 297 RGNFSSALESYSAAL 311
                                       79**********998 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 1.6
                               MIT   4 AlelvkkAveeDnagnyeeAlelYke 29 
                                       A +l+ +A  +   g+ + Al+ Y+e
  gi|330506685|ref|YP_004383113.1| 386 ARALLGMAKAQLDLGDLDQALQSYEE 411
                                       67788889888888**********86 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.12
                               MIT  11 AveeDnagnyeeAlelYkeal 31 
                                       A  + ++g  eeA ++Y+ a+
  gi|330506685|ref|YP_004383113.1| 461 AEALHQKGRLEEARSYYEAAI 481
                                       6777799************98 PP

  == domain 8  score: -0.5 bits;  conditional E-value: 2.6
                               MIT  27 YkealelLlqalkekneerrel 48 
                                       Y +++ l+  al+ +++++ e 
  gi|330506685|ref|YP_004383113.1| 503 YGQSIPLFESALS-QEPSDTES 523
                                       999999******9.34444444 PP

  == domain 9  score: -0.3 bits;  conditional E-value: 2.2
                               MIT  22 eAlelYkealelLlqal 38 
                                       +Al  Y ea e L++a 
  gi|330506685|ref|YP_004383113.1| 566 AALGRYDEARESLQKAA 582
                                       68888999988888876 PP

  == domain 10  score: 0.2 bits;  conditional E-value: 1.5
                               MIT  19 nyeeAlelYkealelLl 35 
                                               ++eal+ + 
  gi|330506685|ref|YP_004383113.1| 672 R-------FQEALQAFE 681
                                       2.......444444444 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.088        47      44      77 ..      79     112 ..      76     126 .. 0.83
   2 ?   -0.7   0.0         2     1e+03      32      68 ..     542     578 ..     517     589 .. 0.54
   3 !   10.7   0.1   0.00059      0.31      19      82 ..     628     694 ..     624     697 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.088
                        HrpB1_HrpK  44 vaeldllegvlliergrweeAlrlLreveaeasg 77 
                                       +ae+ ll g +l   g+++eA+r L +v    ++
  gi|330506685|ref|YP_004383113.1|  79 LAEAWLLKGRILFGLGYLQEAIRSLDQVLRIDQS 112
                                       57788999******************99866655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                        HrpB1_HrpK  32 llLdalrvLrPevaeldllegvlliergrweeAlrlL 68 
                                       +  +++  L Pe  ++    g +  + gr++eA+  L
  gi|330506685|ref|YP_004383113.1| 542 QCFNEIVSLNPEDSAAWSNRGSIFAALGRYDEARESL 578
                                       3334444455555555555555555666666666555 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00059
                        HrpB1_HrpK  19 slalasedtedaellLdalr...vLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyak 82 
                                        l+la+e+t +a+l L+ l+   vL P+++ ++   ++ l  +gr++eAl++++ v + +++ ++ak
  gi|330506685|ref|YP_004383113.1| 628 ELGLAQERTGEAKLALKSLQravVLDPKNEFAQYSLALALAGQGRFQEALQAFERVLEINPKNDLAK 694
                                       578888888888888887764558*********************************9999988887 PP

>> TOM20_plant  Plant specific mitochondrial import receptor subunit TOM20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.3   7.1e+02      96     113 ..     130     147 ..      93     181 .. 0.60
   2 ?   -2.0   0.0       4.8   2.5e+03      18      44 ..     277     303 ..     266     332 .. 0.61
   3 ?    5.8   0.0      0.02        11      51      98 ..     436     479 ..     429     492 .. 0.79
   4 ?    4.4   0.1     0.054        28      93     124 ..     670     701 ..     639     703 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHH-TT- CS
                       TOM20_plant  96 fekatqffqqavdedPdn 113
                                       +  a+ +f+ a   dP+n
  gi|330506685|ref|YP_004383113.1| 130 YRMAQLCFDSALRLDPGN 147
                                       344555555555555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.8
                                       HHH-TT-HHHHHHHHHHHHHHHHHS-H CS
                       TOM20_plant  18 ykknPldadnllrWggallelsqfqsv 44 
                                        k nP d + +l  g+ ll    f s 
  gi|330506685|ref|YP_004383113.1| 277 LKINPHDIQTILGKGDLLLARGNFSSA 303
                                       444555555555555555555555444 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHH CS
                       TOM20_plant  51 iqdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfek 98 
                                       i+ ai  ++ al i+P+  dal  +++a    ++l    eea++++e 
  gi|330506685|ref|YP_004383113.1| 436 IDPAIESFNRALDIEPQNPDALMGLAEALHQKGRL----EEARSYYEA 479
                                       77899******************999998777766....455555554 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.054
                                       HHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHH CS
                       TOM20_plant  93 kenfekatqffqqavdedPdndlyrkslelaa 124
                                       +  f+ a q f++  + +P+ndl + s+++++
  gi|330506685|ref|YP_004383113.1| 670 QGRFQEALQAFERVLEINPKNDLAKYSINVTS 701
                                       45799999999999999999999999988875 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.14        72      81     117 ..     120     156 ..     118     183 .. 0.92
   2 ?   -1.4   0.0       4.6   2.4e+03      80     104 ..     289     313 ..     260     319 .. 0.77
   3 ?    6.6   0.0     0.015         8      79     113 ..     424     458 ..     420     467 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.14
                             MAS20  81 lGEellaqgeeeeaaehlynAlkvcpqPqeLlqilqk 117
                                       +GE +++ g++++a +++  Al++ p    L + l +
  gi|330506685|ref|YP_004383113.1| 120 KGEIMMETGRYRMAQLCFDSALRLDPGNMTLYNRLAQ 156
                                       69*********************99999998877665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.6
                             MAS20  80 qlGEellaqgeeeeaaehlynAlkv 104
                                        +G+ lla+g+   a+e  + Al +
  gi|330506685|ref|YP_004383113.1| 289 GKGDLLLARGNFSSALESYSAALLL 313
                                       5788888888888888888877765 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.015
                             MAS20  79 vqlGEellaqgeeeeaaehlynAlkvcpqPqeLlq 113
                                       + +GE ll q + + a+e + +Al + pq  + l+
  gi|330506685|ref|YP_004383113.1| 424 IGRGEILLLQTNIDPAIESFNRALDIEPQNPDALM 458
                                       679***********************998655554 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       9.5     5e+03      73     112 ..     198     237 ..     192     258 .. 0.79
   2 ?   -1.7   0.0       4.5   2.4e+03      64      94 ..     257     287 ..     229     303 .. 0.75
   3 ?   -0.3   0.0       1.6   8.6e+02      62     112 ..     357     407 ..     334     414 .. 0.78
   4 ?    8.7   0.0    0.0028       1.5      71     115 ..     434     478 ..     419     482 .. 0.92
   5 ?   -0.7   0.0       2.2   1.1e+03      70     108 ..     500     538 ..     495     550 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 9.5
                           DUF4919  73 lkeiislaeealkknPfdlkqlnllayaykalgkkeeaki 112
                                       + e+++  + +l++n  d+ +l+  a  y++lg+ ++a++
  gi|330506685|ref|YP_004383113.1| 198 YPEALNSFNLLLEQNKSDILALKGRAECYRQLGQVDRAEE 237
                                       6677777788888888888888888999999988876654 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.5
                           DUF4919  64 dkkelseeelkeiislaeealkknPfdlkql 94 
                                           + +e++ + +++  +alk nP d++++
  gi|330506685|ref|YP_004383113.1| 257 GMVRYATEDYSSSLQAFDQALKINPHDIQTI 287
                                       5556778889999999999999999999876 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.6
                           DUF4919  62 kldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeaki 112
                                       k + + l+++e  ++ +    +l ++P + ++l  +a a   lg+ ++a +
  gi|330506685|ref|YP_004383113.1| 357 KIADDLLERNESIQAAEHYGLILGQDPKNARALLGMAKAQLDLGDLDQALQ 407
                                       5667777778888888888899****************9999999877654 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0028
                           DUF4919  71 eelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiysk 115
                                       ++++ +i+  ++al+ +P ++ +l+ la a++++g+ eea++y++
  gi|330506685|ref|YP_004383113.1| 434 TNIDPAIESFNRALDIEPQNPDALMGLAEALHQKGRLEEARSYYE 478
                                       6788999**********************************9986 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 2.2
                           DUF4919  70 eeelkeiislaeealkknPfdlkqlnllayaykalgkke 108
                                       + e+ + i l e+al+++P d + l+    a+ a g+++
  gi|330506685|ref|YP_004383113.1| 500 QGEYGQSIPLFESALSQEPSDTESLMGKGLALAATGNSS 538
                                       56788899999**************99988888888776 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.054        29     130     179 ..     156     206 ..     122     218 .. 0.67
   2 ?   -0.3   0.1       1.1   5.6e+02     101     178 ..     223     307 ..     196     322 .. 0.51
   3 ?    1.2   0.0      0.39     2e+02     152     186 ..     383     417 ..     367     433 .. 0.72
   4 ?    1.3   0.3      0.35   1.9e+02     127     143 ..     433     448 ..     385     488 .. 0.50
   5 ?   -0.0   0.1       0.9   4.8e+02     118     142 ..     458     481 ..     433     513 .. 0.79
   6 ?    1.4   0.0      0.32   1.7e+02     134     182 ..     567     616 ..     543     628 .. 0.56
   7 ?    6.3   0.1      0.01       5.4     162     195 ..     664     697 ..     633     700 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.054
                                       -HHHHHHHHHHHHHHHHHTT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                              SNAP 130 dlekAieaYekAaelyeqee.akalankcllkvAelsaelekyekAieiye 179
                                       + +  +e Y++A   y++    +a+ +++l +  +l  +l++y++A++ ++
  gi|330506685|ref|YP_004383113.1| 156 QSQLMLEDYDHALRSYKKALsLEANNTEILFNQGDLFLTLARYPEALNSFN 206
                                       334444555555555555543566666666666777777777777777776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHTT--......HHHHHHHHHHHHHHHHHTT.-HHHHHHHHHHHHHHHHHTT- CS
                              SNAP 101 ieiytekgrfrraAklkkeiaelyekelgd......lekAieaYekAaelyeqee.akalankcllkvAelsaelek 170
                                       +e+y + g+++ra + + ++ e   ++ +       ++ A+e Y    + ++q    + +  +  l   +l    ++
  gi|330506685|ref|YP_004383113.1| 223 AECYRQLGQVDRAEEDYYTVLEKNPEDFESwrglgmVRYATEDYSSSLQAFDQALkINPHDIQTILGKGDLLLARGN 299
                                       55555555555555555555554444442222222244444444444444444433333444444444444444444 PP

                                       HHHHHHHH CS
                              SNAP 171 yekAieiy 178
                                       ++ A+e y
  gi|330506685|ref|YP_004383113.1| 300 FSSALESY 307
                                       44444444 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTTS CS
                              SNAP 152 alankcllkvAelsaelekyekAieiyekvakksl 186
                                        +   +ll +A+ + +l+++++A++ ye++  +  
  gi|330506685|ref|YP_004383113.1| 383 PKNARALLGMAKAQLDLGDLDQALQSYEELLGHDS 417
                                       45556778888889999999999999999765554 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.35
                                       TT--HHHHHHHHHHHHH CS
                              SNAP 127 elgdlekAieaYekAae 143
                                       +  +++ Aie++++A +
  gi|330506685|ref|YP_004383113.1| 433 Q-TNIDPAIESFNRALD 448
                                       3.344444444444444 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 0.9
                                       HHHHHHHHHTT--HHHHHHHHHHHH CS
                              SNAP 118 keiaelyekelgdlekAieaYekAa 142
                                       + +ae + ++ g+le+A ++Ye A 
  gi|330506685|ref|YP_004383113.1| 458 MGLAEALHQK-GRLEEARSYYEAAI 481
                                       4567777777.77777777777774 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHHHHTT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              SNAP 134 AieaYekAaelyeqee.akalankcllkvAelsaelekyekAieiyekva 182
                                       A+  Y++A e  ++    ++++  ++ ++ +++  +++ +++ +++e+  
  gi|330506685|ref|YP_004383113.1| 567 ALGRYDEARESLQKAAgISSSSADIWYNLGQVYRLMDRHNQSRQAFENAT 616
                                       44444444444444443444444444444444444444444444444444 PP

  == domain 7  score: 6.3 bits;  conditional E-value: 0.01
                                       HHHHHHTT-HHHHHHHHHHHHHTTSS-TTTGGGH CS
                              SNAP 162 AelsaelekyekAieiyekvakkslennllkysv 195
                                       A   a ++++++A++++e+v +   +n l kys+
  gi|330506685|ref|YP_004383113.1| 664 ALALAGQGRFQEALQAFERVLEINPKNDLAKYSI 697
                                       55567788************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (705 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 1.10u 0.31s 00:00:01.41 Elapsed: 00:00:00.73
# Mc/sec: 2920.25
//
Query:       gi|330506686|ref|YP_004383114.1|  [L=120]
Description: hypothetical protein MCON_0442 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-39  135.2   0.0    1.6e-39  134.8   0.0    1.2  1  CTP-dep_RFKase  Domain of unknown function DUF120


Domain annotation for each model (and alignments):
>> CTP-dep_RFKase  Domain of unknown function DUF120
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.8   0.0   8.7e-44   1.6e-39       1     119 [.       5     117 ..       5     119 .. 0.96

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 8.7e-44
                                       EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEE CS
                    CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypaki 77 
                                       Vv Glg+G+yy+s++gy++qf +klgf p+pGTLN+klde+           ++i iegf++eer+fg++++y++k+
  gi|330506686|ref|YP_004383114.1|   5 VVGGLGQGQYYISRKGYRHQFIQKLGFVPFPGTLNIKLDEPFN------PGPHQILIEGFREEERSFGECRCYKIKL 75 
                                       899*************************************943......456789********************** PP

                                       CCEEEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEE CS
                    CTP-dep_RFKase  78 ekikaavvvperthyeedvlEiiapekLReklelkdgdevev 119
                                       +++++a+++p+r++y++d++Eii+p +LR++l+l+dgd ve+
  gi|330506686|ref|YP_004383114.1|  76 NGLEGAIIRPDRSSYPPDLVEIISPLRLRDELRLDDGDIVEL 117
                                       ****************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 888.94
//
Query:       gi|330506687|ref|YP_004383115.1|  [L=221]
Description: PHP domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-12   46.5   1.3    2.2e-12   46.5   1.3    1.5  2  PHP_C     PHP-associated
    5.9e-07   29.9   0.0    8.9e-07   29.3   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 ?   -3.5   0.0         1   9.2e+03       8      16 ..      22      30 ..      19      33 .. 0.74
   2 !   46.5   1.3   2.4e-16   2.2e-12       1      56 []     134     187 ..     134     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1
                             PHP_C  8 rrfAeklgl 16
                                      +r+A++++l
  gi|330506687|ref|YP_004383115.1| 22 LRAAARRDL 30
                                      578999887 PP

  == domain 2  score: 46.5 bits;  conditional E-value: 2.4e-16
                             PHP_C   1 geaNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleairegrt 56 
                                       g+aN rA+  A+++ lp+++GSD+H++++VG ++Te+e+  a   e +eai +grt
  gi|330506687|ref|YP_004383115.1| 134 GIANARALIGAKRRHLPAVAGSDSHFAATVGLGVTEIEAADA--FEAIEAIQAGRT 187
                                       579**********************************88877..8899******98 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0     1e-10   8.9e-07       1      74 [.       4      81 ..       4     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1e-10
                                      EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE............. CS
                                      xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                               PHP  1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse..... 73
                                      dlHvH++ s +  + +    ++++a+++ l+ + iTDh+ l g  +++k +++ +k ++ +i G+e++  +++      
  gi|330506687|ref|YP_004383115.1|  4 DLHVHSNCSdGR-DDV--RTILRAAARRDLDGLSITDHDTLRGSQQAMKIIQE-DKLDLILIPGAEVTTSEGHLlvlgi 78
                                      89*******666.677..9********************************65.557888999***6665555344444 PP

                                      ... CS
                                      ..x RF
                               PHP 74 ..k 74
                                         
  gi|330506687|ref|YP_004383115.1| 79 edL 81
                                      440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1606.91
//
Query:       gi|330506688|ref|YP_004383116.1|  [L=415]
Description: 3-isopropylmalate dehydratase large subunit 1 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.1e-102  344.4   0.0   1.2e-100  337.7   0.0    2.1  1  Aconitase  Aconitase family (aconitate hydratase)
  ------ inclusion threshold ------
      0.084   11.6   0.0       0.14   10.9   0.0    1.3  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 !  337.7   0.0  1.4e-104  1.2e-100      18     461 .]      29     406 ..       6     406 .. 0.92

  Alignments for each domain:
  == domain 1  score: 337.7 bits;  conditional E-value: 1.4e-104
                         Aconitase  18 pdrvllqdvtgvqalvdlaaareav.rrlggtlatidhlvpvdlvidhsvgaeealeknledefernkeryefLksa 93 
                                        d  +++d t+v a+  ++++++++ +++++ +   dh vp++          ++ +++l++e+++         +a
  gi|330506688|ref|YP_004383116.1|  29 IDYAMSHDGTSVLAIRSFREMGSEKvWDPDRVVVPYDHIVPAN----------NETAADLQREVRN---------WA 86 
                                       5888**************99987666*****************..........2234455555555.........77 PP

                         Aconitase  94 akafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipkvvgvk 170
                                        ++   ++++ g+G++Hqv +E+g+alpg+++vg DSH++++g++G++++GvG ++++++     l++++p+++g+k
  gi|330506688|ref|YP_004383116.1|  87 REQNISHFFDCGTGVCHQVFPEQGFALPGTLLVGADSHSCTYGAFGAFGTGVGATDMAEIYSAGRLWFRVPETIGIK 163
                                       77766689********************************************************************* PP

                         Aconitase 171 ltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdektleYLkat 247
                                       ++G+l + v+akD++l+vig l+++g++ k+vE++G+++e Ls+ +r+T++N+++E+GA+++++p+dekt e+L+  
  gi|330506688|ref|YP_004383116.1| 164 VEGRLAPFVSAKDIALQVIGDLGADGATYKAVEYIGPAIEGLSISGRMTLCNLGVEMGAKAAIVPPDEKTDEWLR-- 238
                                       ***************************************************************************.. PP

                         Aconitase 248 greeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavplselvkkefkeelekeaaekal 324
                                       gr+ ++     y++      + +d+d +y++ ++ d+++lep+va p+r++++ p+sel+                 
  gi|330506688|ref|YP_004383116.1| 239 GRARQP-----YTQ------VFSDPD-SYQQQYDYDIAELEPQVAAPFRVDNVRPVSELA----------------- 286
                                       998888.....333......447877.9****************************4444................. PP

                         Aconitase 325 eyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkayleaeGlleiLe 401
                                                    k+d+a+ig CTN+++ed++aaag+l+     g+kv++  +t+v P+S++v   + + G+ ++L 
  gi|330506688|ref|YP_004383116.1| 287 -----------GLKIDQAFIGTCTNGRLEDLEAAAGILK-----GKKVRA--RTLVIPASREVLLDALKRGIIQTLV 345
                                       ...........34599***********************.....******..************************* PP

                         Aconitase 402 kaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqgpntrayLaSPelvvaaAlaG 461
                                       +aG+ +  +gC++C+g   + l+ege++vs+sNRNF gR+g+++  yLaSP+ v+a+Al+G
  gi|330506688|ref|YP_004383116.1| 346 EAGAMIGPPGCGPCLGaHMGVLAEGEVCVSTSNRNFPGRMGKGGLVYLASPATVAASALQG 406
                                       ****************99*****************************************98 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   1.5e-05      0.14     298     357 ..     298     356 ..     275     378 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.5e-05
                            DUF521 298 cPhlsleElrelaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtC 357
                                       c    le+l++ a +lkgkk+   ++l++ +srev   a + g++++l +aG+ +    C
  gi|330506688|ref|YP_004383116.1| 298 CTNGRLEDLEAAAGILKGKKV-RARTLVIPASREVLLDALKRGIIQTLVEAGAMIGPPGC 356
                                       55567899********66666.6788999************************9977766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2929.92
//
Query:       gi|330506689|ref|YP_004383117.1|  [L=347]
Description: hypothetical protein MCON_0447 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.9   0.0      0.028   14.0   0.0    1.4  1  MTS       Methyltransferase small domain
      0.093   12.1   0.0       0.13   11.6   0.0    1.1  1  PrmA      Ribosomal protein L11 methyltransferase (PrmA)


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 ?   14.0   0.0   3.1e-06     0.028      29      79 ..     217     267 ..     209     281 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.1e-06
                                       CC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTT CS
                               MTS  29 ke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleank 79 
                                        + ++ +v+D  cG G lg+++a +  + ev+l dv   A++    nl+an+
  gi|330506689|ref|YP_004383117.1| 217 LQgKASRVVDGLCGPGTLGLMCALAGAK-EVVLNDVWLPAVQNVLLNLKANR 267
                                       3337778****************98888.9*******************996 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.5e-05      0.13     153     208 ..     210     267 ..     207     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.5e-05
                              PrmA 153 ealeklvkege..evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNk 208
                                       +++e+l+ +g+  +v+D  +G G L +  a+ gak+vv  D+   Av+    N++ N+
  gi|330506689|ref|YP_004383117.1| 210 RIIEQLMLQGKasRVVDGLCGPGTLGLMCALAGAKEVVLNDVWLPAVQNVLLNLKANR 267
                                       67888877776569***************************************99995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2683.49
//
Query:       gi|330506690|ref|YP_004383118.1|  [L=357]
Description: hypothetical protein MCON_0449 [Methanosaeta concilii GP6]
Scores for 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-39  136.9  34.4    1.3e-39  136.6  34.4    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 !  136.6  34.4   7.1e-44   1.3e-39       2     301 .]      20     329 ..      15     329 .. 0.91

  Alignments for each domain:
  == domain 1  score: 136.6 bits;  conditional E-value: 7.1e-44
                   LPG_synthase_TM   2 llglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayligl 78 
                                       ++gl +  l+    l+  + ++++++lrs+   +++la++lall vl +al+Wr++  + ++++++ + + +yl   
  gi|330506690|ref|YP_004383118.1|  20 AVGLFIYSLY----LYYAGYQDAIDTLRSAAISLFALAVVLALLGVLCDALAWRAIALKFNYKVPVKDIFLIYLSCG 92 
                                       2333333455....5555***************************999999******9******************* PP

                   LPG_synthase_TM  79 fvnnvtPgalg.Gevvrayllkr.kegvslskalasvvverlldllalvllgllallllggllaegaavllllalal 153
                                       f nn++P+++  Ge  r+y+l + + g +  ++ a+v + r++  + ++l ++++l++l    ++ + ++l+   a+
  gi|330506690|ref|YP_004383118.1|  93 FMNNLIPSGSFsGETTRVYFLEKlDGGCRIDQSSATVATTRIITAIPFFLGTAIGLAYLDLVTNAPP-WALATCYAI 168
                                       ***********************999********************************999877766.999999999 PP

                   LPG_synthase_TM 154 lllavlalllllllrrrlarlarvlkrlarllarfarklasakr............klvlasprrlllafllslliw 218
                                       +l+++l+ ++++ + ++  +l  + +++  +++r+       ++             l+++++r+l++++++ l+ w
  gi|330506690|ref|YP_004383118.1| 169 ALVLLLLNATFFGICFADNWLEIIAFSIIKHAERILHVHIDQNQcsrilgrfhhsmMLLAEHKRTLFISTFWALAGW 245
                                       999999988999999999999999999988888777655555559999********9******************** PP

                   LPG_synthase_TM 219 llealtlylllralgvdvslallllillaltlvgalpp.lPgGlGvrEaalalllallGvsaaealaaallyrlitl 294
                                       l+   ++ +++r++gv vs++++l+++ +++++++lp+ lPgG+G++++++ +l+ ++G++  +a+aa++l+rl++l
  gi|330506690|ref|YP_004383118.1| 246 LCMTTVAVVVFRSMGVIVSFWAVLAVYSVMIFLQMLPIfLPGGVGLVDIVMSTLFTAIGIPVHTAVAATILIRLVQL 322
                                       *********************************9999659************************************* PP

                   LPG_synthase_TM 295 ylllllG 301
                                       ++l+++G
  gi|330506690|ref|YP_004383118.1| 323 WMLTAIG 329
                                       *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2627.70
//
Query:       gi|330506691|ref|YP_004383119.1|  [L=59]
Description: hypothetical protein MCON_0450 [Methanosaeta concilii GP6]
Scores for complete 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   89.4   9.1    1.7e-25   89.3   9.1    1.0  1  DUF5350   Family of unknown function (DUF5350)
  ------ inclusion threshold ------
      0.016   14.9   1.0       0.42   10.3   0.0    2.0  2  DUF5548   Family of unknown function (DUF5548)


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 !   89.3   9.1   1.9e-29   1.7e-25       1      56 [.       1      56 [.       1      57 [. 0.98

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 1.9e-29
                           DUF5350  1 MGKTGsveWvkvKgrkgqirlVpkkegekkkpGPnQrfkssgkkrrikrrsakaiv 56
                                      MGKTGsveWvk+Kgrkgq+r+V+k+e+++kkpGP+Q++++sg++ +++rrs ka++
  gi|330506691|ref|YP_004383119.1|  1 MGKTGSVEWVKIKGRKGQVRQVTKAETTYKKPGPMQKYTASGSRVKKIRRSIKATQ 56
                                      ***************************************************99875 PP

>> DUF5548  Family of unknown function (DUF5548)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   4.7e-05      0.42      46      76 ..       7      38 ..       1      42 [. 0.81
   2 ?    4.5   0.2    0.0028        25     155     171 ..      41      57 ..      37      59 .] 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.7e-05
                           DUF5548 46 avwvhvrdgrgqln.lslatgrhkkpnphqnm 76
                                        wv++++ +gq+  ++ a   +kkp p q+ 
  gi|330506691|ref|YP_004383119.1|  7 VEWVKIKGRKGQVRqVTKAETTYKKPGPMQKY 38
                                      45**********953789999*******9975 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0028
                           DUF5548 155 rgqevrklqnsvkatri 171
                                        g  v+k++ s+kat+i
  gi|330506691|ref|YP_004383119.1|  41 SGSRVKKIRRSIKATQI 57 
                                       7999***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 454.87
//
Query:       gi|330506692|ref|YP_004383120.1|  [L=399]
Description: thiamine biosynthesis/tRNA modification protein ThiI [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-59  201.0   0.2      2e-59  200.5   0.2    1.2  1  ThiI           Thiamine biosynthesis protein (ThiI)
    1.4e-16   60.9   0.0    2.8e-16   59.9   0.0    1.5  1  THUMP          THUMP domain
      2e-07   30.8   0.1      0.012   15.2   0.0    2.9  3  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.017   13.9   0.0      0.034   13.0   0.0    1.5  1  tRNA_Me_trans  tRNA methyl transferase
      0.078   13.2   0.0       0.18   12.1   0.0    1.7  1  Multi_ubiq     Multiubiquitin


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 !  200.5   0.2   5.6e-63     2e-59       1     197 []     179     371 ..     179     371 .. 0.95

  Alignments for each domain:
  == domain 1  score: 200.5 bits;  conditional E-value: 5.6e-63
                              ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlk 77 
                                       g+qg+ la++SgGiDSpVaa+++++RGc v l+h++++p+   + i++ ++ +++lae+  + ++++++v+ k+ ++
  gi|330506692|ref|YP_004383120.1| 179 GSQGRMLAMISGGIDSPVAAWMMMRRGCTVSLLHFDSRPYA--DSIDQSKRCVQVLAEWTCGRKINFITVPIKKGIE 253
                                       79**********************************99986..567778899************************* PP

                              ThiI  78 eilekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiik 154
                                       +i+ + + + t++l++r m+riA +v e+ega  +vtG s+gqVaSqt eN+ + +a++ ++i  PLi++dK eii+
  gi|330506692|ref|YP_004383120.1| 254 KIQMHYP-RATCILCRRLMYRIAAQVMEKEGALGVVTGYSMGQVASQTAENILAEQAAIGVPIYHPLIAMDKSEIID 329
                                       ***9987.579****************************************************************** PP

                              ThiI 155 lAkeigtyeisiekedkCsvlakhPttkakleevekaeeklkl 197
                                       lA++igtye+++ + + C++++++P t+ak+ee+ +aee l+l
  gi|330506692|ref|YP_004383120.1| 330 LARKIGTYEVTMVT-KSCTAVPNKPMTRAKKEEILQAEEYLDL 371
                                       *********98765.68*******************9998875 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   7.9e-20   2.8e-16      23     142 ..      52     167 ..      37     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 7.9e-20
                                       EEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-......EEEEEEEES CS
                             THUMP  23 rivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeeke......tFaVrvkrr 93 
                                       ri+v +        + ++  + ++++g+++ +p+ + ++ +ledi +aa+e+  k +e   +      tFa+r +r 
  gi|330506692|ref|YP_004383120.1|  52 RIFVHTP-------DVRAAAIASQVFGVVSASPA-QSVPSNLEDISRAAVEVAAKTMERAMQsgaaiqTFAIRPRRF 120
                                       4444443.......334456688999********.*********************9999889*************9 PP

                                       SSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEE CS
                             THUMP  94 gkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisi 142
                                       g    f+s+ei ++vG+a++ +tg++V+l +P+  ++ve +++ +yi++
  gi|330506692|ref|YP_004383120.1| 121 GV--PFSSVEIGQKVGEAVRLATGASVNLRDPQMEIFVEARREGTYIFT 167
                                       99..9******************************************97 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.2e-06     0.012       2      44 ..     184     229 ..     183     257 .. 0.79
   2 !   12.5   0.0   2.1e-05     0.075     145     183 ..     306     346 ..     269     353 .. 0.81
   3 ?   -2.3   0.0      0.71   2.5e+03     156     176 ..     352     372 ..     347     386 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-06
                                       EEEE--SSHHHHHHHHHHHHH-SEEEEEEEE...SS-TTSHHHHHH CS
                              QueC   2 avvllSGGlDSttvlalakkegkevealtfd...Ygqrhkkeleaa 44 
                                        + ++SGG+DS +++++++++g  v +l+fd   Y    ++  +++
  gi|330506692|ref|YP_004383120.1| 184 MLAMISGGIDSPVAAWMMMRRGCTVSLLHFDsrpYADSIDQSKRCV 229
                                       5789**************************8444555555555555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.1e-05
                                       HHHHTS--EEE-TTTT--HHHHHHHHHHTT..HHHHH-B-S CS
                              QueC 145 nlgedkkieieaPlidlsKaeivklgkelg..vpleetlsC 183
                                       +   +  + i  Pli+++K+ei+ l+ ++g   ++  t sC
  gi|330506692|ref|YP_004383120.1| 306 AEQAAIGVPIYHPLIAMDKSEIIDLARKIGtyEVTMVTKSC 346
                                       3334567899********************76445667777 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.71
                                       -TTTT--HHHHHHHHHHTTHH CS
                              QueC 156 aPlidlsKaeivklgkelgvp 176
                                        P+++ +K+ei+++ + l+++
  gi|330506692|ref|YP_004383120.1| 352 KPMTRAKKEEILQAEEYLDLV 372
                                       688999999999988888743 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.4e-06     0.034       3      45 ..     184     228 ..     182     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.4e-06
                     tRNA_Me_trans   3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeeg..kec 45 
                                       +++ +SgG+DS vaa ++ ++g  v  +++     +d+ +  k+c
  gi|330506692|ref|YP_004383120.1| 184 MLAMISGGIDSPVAAWMMMRRGCTVSLLHFDSRPYADSIDqsKRC 228
                                       57789********************99999888776665533344 PP

>> Multi_ubiq  Multiubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.9e-05      0.18      19      68 ..     107     159 ..      93     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.9e-05
                        Multi_ubiq  19 GreivalAgpdpaddpvvleivty....gedgeirdgesVdLkakGverfvtrt 68 
                                       G+ i + A  +   + v + +v+     ge   ++ g sV+L+++ +e fv ++
  gi|330506692|ref|YP_004383120.1| 107 GAAIQTFAIRPR-RFGVPFSSVEIgqkvGEAVRLATGASVNLRDPQMEIFVEAR 159
                                       555555555554.555555555556688999********************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2803.84
//
Query:       gi|330506693|ref|YP_004383121.1|  [L=63]
Description: hypothetical protein MCON_0452 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-06   28.0   2.8      0.013   15.8   0.0    2.5  2  KGG       Stress-induced bacterial acidophilic repeat motif
     0.0069   16.8   6.3     0.0069   16.8   6.3    1.9  2  LEA_5     Small hydrophilic plant seed protein
  ------ inclusion threshold ------
       0.11   12.8   0.1       0.16   12.2   0.1    1.4  1  zf-H2C2   H2C2 zinc finger
       0.12   12.4   7.3       0.25   11.4   0.7    2.1  2  SASP      Small, acid-soluble spore proteins, alpha/beta type


Domain annotation for each model (and alignments):
>> KGG  Stress-induced bacterial acidophilic repeat motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.8     5e-05      0.22       9      17 ..      17      25 ..      17      25 .. 0.95
   2 !   15.8   0.0   2.9e-06     0.013       5      19 ..      33      47 ..      32      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5e-05
                               KGG  9 arEIGrKGG 17
                                      ++E+GrKGG
  gi|330506693|ref|YP_004383121.1| 17 VQEAGRKGG 25
                                      79******9 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.9e-06
                               KGG  5 DpEkarEIGrKGGqa 19
                                      ++E++  IG++GGq 
  gi|330506693|ref|YP_004383121.1| 33 GREFYEKIGHMGGQK 47
                                      79************6 PP

>> LEA_5  Small hydrophilic plant seed protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   3.0   0.00022      0.97      68      95 ..       6      35 ..       2      36 .. 0.75
   2 !   16.8   6.3   1.5e-06    0.0069      39      84 ..      19      63 .]      16      63 .] 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
                             LEA_5 68 rkeql..geegyqemgrkgglstidksgge 95
                                      r+e+   g+   qe grkgg+ t +  g e
  gi|330506693|ref|YP_004383121.1|  6 RREKKgkGRMTVQEAGRKGGMKTAETHGRE 35
                                      555541156789***********9998866 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.5e-06
                             LEA_5 39 egrsrggqtrkeqlgsegykelgskggetrkeqlgeegyqemgrkg 84
                                      e + +gg    e  g+e y+++g+ gg+  ke + eeg + +gr g
  gi|330506693|ref|YP_004383121.1| 19 EAGRKGGMKTAETHGREFYEKIGHMGGQKVKELI-EEGKKALGRSG 63
                                      7778999999999****************99966.89******987 PP

>> zf-H2C2  H2C2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.6e-05      0.16       4      17 ..      41      54 ..      39      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.6e-05
                           zf-H2C2  4 tHlGinkltallar 17
                                       H+G +k+++l+++
  gi|330506693|ref|YP_004383121.1| 41 GHMGGQKVKELIEE 54
                                      7***********98 PP

>> SASP  Small, acid-soluble spore proteins, alpha/beta type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.1    0.0044        20      30      47 ..       9      26 ..       3      31 .. 0.84
   2 ?   11.4   0.7   5.7e-05      0.25      39      60 .]      38      59 ..      27      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0044
                                      .....TSBHHHHHHHHHH CS
                              SASP 30 dgyngdltsrqaGsvGGe 47
                                      ++ +g +t ++aG+ GG+
  gi|330506693|ref|YP_004383121.1|  9 KKGKGRMTVQEAGRKGGM 26
                                      56789************7 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.7e-05
                                      HHHHHHHHHHHHHHHHHHHHTT CS
                              SASP 39 rqaGsvGGemvkklveqaeqqL 60
                                      ++ G++GG+ vk+l+e+ ++ L
  gi|330506693|ref|YP_004383121.1| 38 EKIGHMGGQKVKELIEEGKKAL 59
                                      678*************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.21s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 501.61
//
Query:       gi|330506694|ref|YP_004383122.1|  [L=170]
Description: hypothetical protein MCON_0453 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-40  135.8   0.0    8.2e-40  135.3   0.0    1.2  1  LigD_N    DNA polymerase Ligase (LigD)


Domain annotation for each model (and alignments):
>> LigD_N  DNA polymerase Ligase (LigD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.3   0.0   4.5e-44   8.2e-40       1     104 [.      41     151 ..      41     152 .. 0.98

  Alignments for each domain:
  == domain 1  score: 135.3 bits;  conditional E-value: 4.5e-44
                                       EEEESSSEEEEEEEEETTEEEEEEETT---SSTTSEEEEEEEEEE-GGGGGEEEEE-TTSTT-EEEEEEEEEEEEE. CS
                            LigD_N   1 qeHdaprlHYDlrLeidevlsswavpkglpedpnskrlAvetedhpleyadfegliekgeygaGsvliwDtGtyev. 76 
                                       qeH+ ++lHYD+rLe+d+vl+swavpkg++++p++krlAv+tedhp+eya+feg+i++geygaG+v iwD+G y++ 
  gi|330506694|ref|YP_004383122.1|  41 QEHHSRQLHYDFRLEVDGVLKSWAVPKGPSMNPKDKRLAVQTEDHPIEYASFEGTIPEGEYGAGTVAIWDRGIYQNl 117
                                       79*************************************************************************** PP

                                       ........-HHHHHHHTEEEEEEECSSSEEEEEE CS
                            LigD_N  77 ......eeklaealkkrkiklrLhGeklkgkyvl 104
                                             e +l++alk ++ ++ L+G++l+g ++l
  gi|330506694|ref|YP_004383122.1| 118 snkdgqEISLSQALKGGHASFWLKGKRLQGGFAL 151
                                       ****998899**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1334.22
//
Query:       gi|330506695|ref|YP_004383123.1|  [L=99]
Description: hypothetical protein MCON_0455 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00032   20.5   0.5    0.00041   20.1   0.5    1.1  1  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.25   11.8   4.4       0.33   11.4   4.4    1.2  1  FtsX          FtsX-like permease family


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 !   20.1   0.5   4.6e-08   0.00041     119     182 ..       2      71 ..       1      73 [. 0.92

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.6e-08
                      BPD_transp_1 119 ggllggavlleflgswpGlgtllleailgydyseis..........nggvlalviavlllnlvadilqrlldpr 182
                                       +g++   + l fl     lg +  +a++g+++s  +          +++ +a+ i vl++nl+ d l +++d +
  gi|330506695|ref|YP_004383123.1|   2 AGAILSLAGLGFLS----LGAQPPTAEWGSMLSDSQglifsapyliFIPGIAIMITVLAFNLLGDGLRDAIDSK 71 
                                       56777777788888....*****************************************************986 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.4   3.7e-05      0.33      29      83 ..       3      56 ..       1      61 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.7e-05
                              FtsX 29 tlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllalla 83
                                      +++ +++Glg+++l aq+  + ++s+++ ++  + ++   +++i ++++++++la
  gi|330506695|ref|YP_004383123.1|  3 GAILSLAGLGFLSLGAQPPTAEWGSMLS-DSQGLIFSAPYLIFIPGIAIMITVLA 56
                                      5678899**************9999987.55555566666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); 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 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 782.65
//
Query:       gi|330506696|ref|YP_004383124.1|  [L=214]
Description: hypothetical protein MCON_0456 [Methanosaeta concilii GP6]
Scores for complete sequence (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   35.3   0.0    2.2e-08   34.4   0.0    1.5  1  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
      0.068   12.9   0.0       0.11   12.2   0.0    1.3  1  CitX             Apo-citrate lyase phosphoribosyl-dephospho-C
        2.2    8.2   3.9    3.7e+02    1.1   0.0    4.5  5  YhdX             Uncharacterized YhdX-like


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 !   34.4   0.0   3.7e-12   2.2e-08       2      76 ..       4      84 ..       3      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3.7e-12
                   Acylphosphatase  2 rllvtG.rVQgvgFRkfvrrlAkelglkGy.vrNlsdg...sVeivaegeeekvekfleelksgppk.arvdeveveel 74
                                      ++++tG +V  vg+R+f+  +A++  ++ + + N++      V + a g+ee++++f+++++++ p+ ++v+++ +++ 
  gi|330506696|ref|YP_004383124.1|  4 KITITGpKVNDVGYRYFLLGIAMSNRIRMFeAHNMRSSegqAVLAFADGDEEAIKAFCAQIETERPArSEVSNIVFDDF 82
                                      799*************************99988876554589*********************88888******99886 PP

                   Acylphosphatase 75 ee 76
                                      + 
  gi|330506696|ref|YP_004383124.1| 83 QG 84
                                      65 PP

>> CitX  Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase
   #    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      63     104 ..      28      69 ..       3      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                              CitX  63 aeikilekevleektGpeaflvvdadaeevKklmielEeshp 104
                                       ++i++ e + +++++G +++ ++d d+e++K+ + ++E++ p
  gi|330506696|ref|YP_004383124.1|  28 NRIRMFEAHNMRSSEGQAVLAFADGDEEAIKAFCAQIETERP 69 
                                       56888999999***************************9977 PP

>> YhdX  Uncharacterized YhdX-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.75   4.5e+03      12      18 ..     128     134 ..     127     134 .. 0.88
   2 ?    1.1   0.0     0.062   3.7e+02      12      18 ..     138     144 ..     136     145 .. 0.91
   3 ?    1.1   0.0     0.062   3.7e+02      12      18 ..     148     154 ..     146     155 .. 0.91
   4 ?    1.1   0.0     0.062   3.7e+02      12      18 ..     158     164 ..     156     165 .. 0.91
   5 ?    1.1   0.0     0.062   3.7e+02      12      18 ..     168     174 ..     166     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.75
                              YhdX  12 IKvETDA 18 
                                       IK  TDA
  gi|330506696|ref|YP_004383124.1| 128 IKENTDA 134
                                       9999**9 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.062
                              YhdX  12 IKvETDA 18 
                                       IK+ TDA
  gi|330506696|ref|YP_004383124.1| 138 IKANTDA 144
                                       9*****9 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.062
                              YhdX  12 IKvETDA 18 
                                       IK+ TDA
  gi|330506696|ref|YP_004383124.1| 148 IKANTDA 154
                                       9*****9 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.062
                              YhdX  12 IKvETDA 18 
                                       IK+ TDA
  gi|330506696|ref|YP_004383124.1| 158 IKANTDA 164
                                       9*****9 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.062
                              YhdX  12 IKvETDA 18 
                                       IK+ TDA
  gi|330506696|ref|YP_004383124.1| 168 IKANTDA 174
                                       9*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1508.67
//
Query:       gi|330506697|ref|YP_004383125.1|  [L=421]
Description: putative methanogenesis marker 16 metalloprotein [Methanosaeta concilii GP6]
Scores for complete 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-110  368.4   0.0   3.2e-110  368.2   0.0    1.0  1  HcyBio    Homocysteine biosynthesis enzyme, sulfur-incorporat
    7.8e-07   28.9  10.0    2.4e-05   24.2   3.2    2.4  2  Fer4_6    4Fe-4S binding domain
    8.5e-07   28.5  11.2     0.0042   16.8   0.5    3.3  2  Fer4      4Fe-4S binding domain
    5.7e-06   26.3  10.9    1.2e-05   25.3  10.9    1.6  1  Fer4_10   4Fe-4S dicluster domain
      5e-05   23.2  12.4     0.0031   17.5   3.0    2.6  2  Fer4_2    4Fe-4S binding domain
      6e-05   23.1  10.0    0.00013   22.1  10.0    1.6  1  Fer4_9    4Fe-4S dicluster domain
    0.00016   22.2  11.6     0.0013   19.3  12.3    2.1  2  Fer4_7    4Fe-4S dicluster domain
     0.0023   18.3  14.5      0.058   13.9   2.6    2.6  2  Fer4_4    4Fe-4S binding domain
     0.0029   17.7  10.1      0.017   15.3  10.4    2.0  2  Fer4_21   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   15.6   3.3      0.034   14.3   2.2    1.9  2  Fer4_18   4Fe-4S dicluster domain
      0.038   14.9  10.8       0.84   10.6   3.7    2.5  2  Fer4_16   4Fe-4S double cluster binding domain
      0.085   13.0   3.7       0.22   11.7   3.7    1.7  1  Fer4_11   4Fe-4S dicluster domain
       0.16   12.4   9.0       0.26   11.8   0.2    2.4  2  Fer4_8    4Fe-4S dicluster domain
       0.52   11.2   6.5          2    9.3   0.2    2.4  2  Fer4_22   4Fe-4S dicluster domain
       0.99   10.2  14.7        8.2    7.2   0.1    4.2  4  Fer4_15   4Fe-4S single cluster 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 !  368.2   0.0  2.7e-113  3.2e-110       1     347 []      17     414 ..      17     414 .. 0.98

  Alignments for each domain:
  == domain 1  score: 368.2 bits;  conditional E-value: 2.7e-113
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx......xx RF
                            HcyBio   1 avVltaeelkklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaepkiki..ekvwLngvpayag......la 69 
                                       a+Vlt +e++++v+ekg +  +++vDVVtt+T+++ms+++a+l+++ a p+++i  +++ +ngvpay+g      l+
  gi|330506697|ref|YP_004383125.1|  17 ATVLTQQEISEMVEEKG-EIGLKDVDVVTTATRAIMSGTYAVLSFPLAAPGSFIraSSARINGVPAYPGpcpnerLG 92 
                                       89*************55.689*******************************998899******************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio  70 avdlylgataeseddkeeeeyGGghviedLvagkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnY 146
                                       ++dl++++ta+s    ++ +yGGgh++++Lv+gk+v +e+ a+++     + +e++i ld++++a+++++Rna++nY
  gi|330506697|ref|YP_004383125.1|  93 IIDLMVYGTAHSI---RQPDYGGGHLLRELVEGKDVLVEVLAENG-----DLLEKDICLDEIPYARIFSTRNAFKNY 161
                                       *************...4459*************************.....99************************* PP

                                       xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 147 naavNssee...tiytymgelkpnlgnatysgaGelsPllnDpelktigiGtrilLgGaeGyvigeGTqsspekkre 220
                                        a+vN++     ti++   e+ p++  at+sg+G+++P++nDp+l+tigiGtril++Ga+G+v+g+GT+s+p+++  
  gi|330506697|ref|YP_004383125.1| 162 VAFVNPKGLplkTIFS-RLEFPPHFAAATVSGCGQINPIKNDPHLETIGIGTRILINGAQGFVMGTGTRSMPTRP-- 235
                                       ******998888****.9*********************************************************.. PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 221 ngvplgpagtLavigdlkeMspeylrgafltsyGpelivgvgipiPvldeevleelavkdedielpvvDvserrrer 297
                                                +L  ++d+++M+pey+ g+f ts+Gpe+i ++++piPvl+e +l+++ ++d+di+l+++Dv++r    
  gi|330506697|ref|YP_004383125.1| 236 ---------NLLGMADMRHMDPEYM-GGFATSAGPECIGSWAVPIPVLNEYILRSILLQDRDIPLTIMDVNVR---- 298
                                       .........****************.***********************************************.... PP

                                       xxxxxxxxxxx.................................................................x RF
                            HcyBio 298 ktlgevsYael.................................................................G 309
                                       +++g+ +Y+++                                                                 G
  gi|330506697|ref|YP_004383125.1| 299 QKIGKSTYGDVwdsvdlevqfdperckgctrctaapacpmnaisiedgrvlrdktkcfncglcvsqcsggafqgrlG 375
                                       89*************************************************************************** PP

                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 310 kieiegkev.ktarlsslkrareiaeeLkewiekgeflL 347
                                       +i++ ++++ + +r+s+++ra+ +a++Lke i++g+f++
  gi|330506697|ref|YP_004383125.1| 376 AIRLGERTIpIQLRQSDRARAMGLAKRLKEEILNGSFRI 414
                                       *********999*************************85 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   3.2     2e-08   2.4e-05       2      24 .]     317     341 ..     316     341 .. 0.94
   2 !    8.5   0.6    0.0018       2.2       4      23 ..     350     369 ..     347     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2e-08
                            Fer4_6   2 veidpdkCigCgdCvrv..CPegai 24 
                                       v++dp++C gC +C+++  CP++ai
  gi|330506697|ref|YP_004383125.1| 317 VQFDPERCKGCTRCTAApaCPMNAI 341
                                       89************99999****98 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0018
                            Fer4_6   4 idpdkCigCgdCvrvCPega 23 
                                        d+ kC  Cg Cv+ C  ga
  gi|330506697|ref|YP_004383125.1| 350 RDKTKCFNCGLCVSQCSGGA 369
                                       58999***********8665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   4.6   4.3e-05     0.051       1      24 []     317     342 ..     317     342 .. 0.88
   2 !   16.8   0.5   3.5e-06    0.0042       4      22 ..     351     369 ..     348     371 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                                       EEEETTTSSS-THH..HHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaC..vevCPvgAIt 24 
                                       v++d+e+C gC +C  + +CP +AI+
  gi|330506697|ref|YP_004383125.1| 317 VQFDPERCKGCTRCtaAPACPMNAIS 342
                                       579***********66679*****95 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.5e-06
                                       ETTTSSS-THHHHHSTTTE CS
                              Fer4   4 deekCigCGaCvevCPvgA 22 
                                       d+ kC +CG+Cv+ C  gA
  gi|330506697|ref|YP_004383125.1| 351 DKTKCFNCGLCVSQCSGGA 369
                                       899************7777 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3  10.9   9.9e-09   1.2e-05       2      55 ..     317     365 ..     316     366 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 9.9e-09
                           Fer4_10   2 vvidddtCirCgkCvka..CPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       v++d+++C +C++C++a  CP+       +++  e+++v  +  kC +cg Cv++C
  gi|330506697|ref|YP_004383125.1| 317 VQFDPERCKGCTRCTAApaCPM-------NAISIEDGRVLRDKTKCFNCGLCVSQC 365
                                       6789************555***.......78888888888899************* 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   3.0   2.6e-06    0.0031       3      21 ..     317     337 ..     315     338 .. 0.87
   2 !   10.5   2.0   0.00045      0.54       3      20 ..     348     365 ..     346     366 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.6e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsa..CP 21 
                                       v++d++rC gC  C+ a  CP
  gi|330506697|ref|YP_004383125.1| 317 VQFDPERCKGCTRCTAApaCP 337
                                       79************96666*9 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00045
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                       v  d  +C +Cg Cvs C
  gi|330506697|ref|YP_004383125.1| 348 VLRDKTKCFNCGLCVSQC 365
                                       567888**********99 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1  10.0   1.1e-07   0.00013       1      50 [.     323     369 ..     323     373 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-07
                            Fer4_9   1 kCtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       +C gC++C++a  Cp+++++ ++++  +  +     +C+ Cg Cv  C  ga
  gi|330506697|ref|YP_004383125.1| 323 RCKGCTRCTAApaCPMNAISIEDGRVLRDKT-----KCFNCGLCVSQCSGGA 369
                                       5*******76555******999988877653.....6***********8775 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   4.4   0.00039      0.46      30      52 .]     316     340 ..     298     340 .. 0.85
   2 !   19.3  12.3   1.1e-06    0.0013       1      51 [.     323     368 ..     323     369 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                            Fer4_7  30 kveidpekClgCgaCva..vCPtga 52 
                                       +v++dpe+C gC++C a  +CP +a
  gi|330506697|ref|YP_004383125.1| 316 EVQFDPERCKGCTRCTAapACPMNA 340
                                       5799**********98877899986 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.1e-06
                            Fer4_7   1 rCigCgaCvaa..CpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       rC gC +C+aa  Cp++ai++++        +v  d +kC +Cg Cv+ C  g
  gi|330506697|ref|YP_004383125.1| 323 RCKGCTRCTAApaCPMNAISIEDG-------RVLRDKTKCFNCGLCVSQCSGG 368
                                       8*******95444********764.......78899**************766 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   4.3    0.0015       1.8       1      17 []     321     339 ..     321     339 .. 0.92
   2 !   13.9   2.6   4.9e-05     0.058       2      15 ..     353     366 ..     352     372 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                            Fer4_4   1 qerCigCgsCvaa..CPqg 17 
                                       +erC gC +C+aa  CP++
  gi|330506697|ref|YP_004383125.1| 321 PERCKGCTRCTAApaCPMN 339
                                       69**************985 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.9e-05
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                        +C++Cg Cv+ C+
  gi|330506697|ref|YP_004383125.1| 353 TKCFNCGLCVSQCS 366
                                       58***********7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3  10.4   1.4e-05     0.017       3      51 ..     319     365 ..     317     371 .. 0.84
   2 !   11.1   1.7   0.00027      0.32       4      24 ..     351     371 ..     348     379 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                           Fer4_21   3 idedkCigCgkClia..CedtshqaieidaktvlkvvedeCvGCnlCssvC 51 
                                       +d+++C gC++C+ a  C+   ++ai+i++ +vl   + +C  C lC+s C
  gi|330506697|ref|YP_004383125.1| 319 FDPERCKGCTRCTAApaCP---MNAISIEDGRVL-RDKTKCFNCGLCVSQC 365
                                       699*********9752277...8*****988875.56889**********9 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00027
                           Fer4_21   4 dedkCigCgkCliaCedtshq 24 
                                       d+ kC +Cg+C+  C+ ++ q
  gi|330506697|ref|YP_004383125.1| 351 DKTKCFNCGLCVSQCSGGAFQ 371
                                       6889***********987766 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.1   1.4e+03       3      17 ..     139     153 ..     137     165 .. 0.85
   2 ?   14.3   2.2   2.9e-05     0.034      37      96 ..     300     366 ..     277     374 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                           Fer4_18   3 edvcvyvcPyarvqs 17 
                                        d+c+   Pyar+ s
  gi|330506697|ref|YP_004383125.1| 139 KDICLDEIPYARIFS 153
                                       699*********987 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.9e-05
                           Fer4_18  37 iagrkkekkalkekeerkekgagdcidcescvk..vcPtg.idirkGl....qleciscllcidacd 96 
                                       ++g+++  ++  +++++ + +   c  c  c +   cP++ i i +G     + +c +c+lc+  c+
  gi|330506697|ref|YP_004383125.1| 300 KIGKSTYGDVWDSVDLEVQFDPERCKGCTRCTAapACPMNaISIEDGRvlrdKTKCFNCGLCVSQCS 366
                                       455555666666777777777788999999976336**8549*****72233458*********996 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.7    0.0007      0.84       1      20 [.     323     344 ..     323     354 .. 0.77
   2 ?    8.3   0.7    0.0037       4.4       1      20 [.     354     373 ..     354     393 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0007
                           Fer4_16   1 rCgtCgkCae..vCPtnaikek 20 
                                       rC++C++C+   +CP nai+ +
  gi|330506697|ref|YP_004383125.1| 323 RCKGCTRCTAapACPMNAISIE 344
                                       6*******75337******976 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0037
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C +Cg C++ C  +a++++
  gi|330506697|ref|YP_004383125.1| 354 KCFNCGLCVSQCSGGAFQGR 373
                                       599*********99998865 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.7   0.00019      0.22       2      54 ..     316     365 ..     315     370 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                           Fer4_11   2 ewlflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveac 54 
                                       e++f pe C+ C++   + ++p++ai  +  +G Vl d++++  ++  +v+ c
  gi|330506697|ref|YP_004383125.1| 316 EVQFDPERCKGCTRCTAAPACPMNAISIE--DGRVLRDKTKCF-NCGLCVSQC 365
                                       678**********************9865..6*********96.888888888 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   4.3      0.15   1.8e+02       3      17 ..     322     338 ..     320     352 .. 0.75
   2 ?   11.8   0.2   0.00021      0.26       3      16 ..     353     366 ..     351     409 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.15
                            Fer4_8   3 ekCieCgaCq..saCpv 17 
                                       e+C +C +C+   aCp+
  gi|330506697|ref|YP_004383125.1| 322 ERCKGCTRCTaaPACPM 338
                                       68999999995556984 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00021
                            Fer4_8   3 ekCieCgaCqsaCp 16 
                                        kC +Cg+C s+C 
  gi|330506697|ref|YP_004383125.1| 353 TKCFNCGLCVSQCS 366
                                       58***********4 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2    0.0016         2      72      91 ..     314     333 ..     292     340 .. 0.76
   2 ?    3.9   1.8     0.084     1e+02      79      93 ..     352     366 ..     343     369 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0016
                           Fer4_22  72 efkekfgesgCvGCgRCiea 91 
                                       +++ +f+ + C GC RC++a
  gi|330506697|ref|YP_004383125.1| 314 DLEVQFDPERCKGCTRCTAA 333
                                       56678999*********974 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.084
                           Fer4_22  79 esgCvGCgRCieacp 93 
                                       +++C  Cg C+++c 
  gi|330506697|ref|YP_004383125.1| 352 KTKCFNCGLCVSQCS 366
                                       566777777777775 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.75     9e+02      26      57 ..      13      48 ..       5      49 .. 0.64
   2 ?    6.3   2.2     0.013        16       1      17 [.     317     333 ..     317     335 .. 0.90
   3 ?    3.9   0.5     0.077        92      55      66 .]     332     343 ..     331     343 .. 0.91
   4 ?    7.2   0.1    0.0069       8.2       4      19 ..     351     366 ..     348     396 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.75
                           Fer4_15 26 edglasvllddgeiaeg.....evpddeeeaaqeAar 57
                                      + g+a+vl+ ++ei+e      e++ ++++ +  A r
  gi|330506697|ref|YP_004383125.1| 13 KSGKATVLT-QQEISEMveekgEIGLKDVDVVTTATR 48
                                      579998884.344433334444777777777777776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                           Fer4_15   1 VvvDrdaCigcglCvae 17 
                                       V +D ++C gc +C a+
  gi|330506697|ref|YP_004383125.1| 317 VQFDPERCKGCTRCTAA 333
                                       789***********975 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.077
                           Fer4_15  55 AaraCPvdAIrv 66 
                                       Aa aCP  AI++
  gi|330506697|ref|YP_004383125.1| 332 AAPACPMNAISI 343
                                       99********97 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0069
                           Fer4_15   4 DrdaCigcglCvaeap 19 
                                       D+++C  cglCv  ++
  gi|330506697|ref|YP_004383125.1| 351 DKTKCFNCGLCVSQCS 366
                                       9***********9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2735.40
//
Query:       gi|330506698|ref|YP_004383126.1|  [L=302]
Description: GMP synthase subunit B [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-32  111.0   0.0    4.9e-32  109.8   0.0    1.7  1  GMP_synt_C     GMP synthase C terminal domain
    7.1e-10   38.4   0.0    1.6e-06   27.5   0.0    2.3  2  NAD_synthase   NAD synthase
    1.7e-05   24.4   0.0    0.00018   21.1   0.0    2.0  2  QueC           Queuosine biosynthesis protein QueC
    0.00025   20.0   0.1      0.017   14.0   0.0    2.1  2  tRNA_Me_trans  tRNA methyl transferase
    0.00046   19.8   0.0     0.0018   17.9   0.0    2.0  1  ThiI           Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.015   15.0   0.0       0.02   14.5   0.0    1.2  1  Asn_synthase   Asparagine synthase
      0.086   12.6   0.0       0.35   10.6   0.0    1.8  2  ATP_bind_3     PP-loop family


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   0.0   1.9e-35   4.9e-32      11      92 .]     221     301 ..     210     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 1.9e-35
                                       GSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---TTT CS
                        GMP_synt_C  11 kiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditskPp 87 
                                       + wQafa++l + ++Gv+gd+R y+yvva+Rav+s+Damta+++elp++vL++is ri+ e++ v+rvvyd+t kPp
  gi|330506698|ref|YP_004383126.1| 221 SPWQAFAAILGM-ATGVKGDNRVYGYVVAVRAVTSRDAMTAEAMELPWQVLRRISGRITGEIPTVSRVVYDLTPKPP 296
                                       56********95.78************************************************************** PP

                                       S-S-- CS
                        GMP_synt_C  88 atiEw 92 
                                       +tiE+
  gi|330506698|ref|YP_004383126.1| 297 GTIEF 301
                                       ****7 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   6.1e-10   1.6e-06       8      74 ..       6      74 ..       2     106 .. 0.73
   2 !    8.7   0.0   0.00034      0.87     148     177 ..     155     184 ..     152     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 6.1e-10
                                      HHHHHHHHCTT...SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTS CS
                      NAD_synthase  8 flkeyvkkaga...kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgi 74
                                      f+++ +++ +      +++GlSGGvDSs+ a+la +alg ++ + +++ s    +++     +l ++lg+
  gi|330506698|ref|YP_004383126.1|  6 FIENAIAEIKRdikGRAIIGLSGGVDSSVCAMLAHRALG-DRLVPVYVDSGLMRQSESDRIEELFKDLGL 74
                                      56665554433222468*********************5.677788887777777777777777777765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00034
                                       BETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                      NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpP 177
                                       ++p+ +l+K ev++ a++l   +++ ++ P
  gi|330506698|ref|YP_004383126.1| 155 VEPLRDLYKDEVRQVARALSLSPEISERMP 184
                                       68***********************99988 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   6.9e-08   0.00018       1      60 [.      21      81 ..      21     101 .. 0.85
   2 ?    1.0   0.0     0.099   2.5e+02     122     175 ..     119     175 ..     109     181 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 6.9e-08
                                      EEEEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE CS
                              QueC  1 kavvllSGGlDSttvlalakke.gkevealtfdYgqrhkkeleaakkiakelgveehkild 60
                                      +a++ lSGG+DS+++++la+++ g+++  + +d g  +++e +  ++++k+lg+++ +  d
  gi|330506698|ref|YP_004383126.1| 21 RAIIGLSGGVDSSVCAMLAHRAlGDRLVPVYVDSGLMRQSESDRIEELFKDLGLVRVNAQD 81
                                      6999***************987369****************************96655544 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.099
                                       -S-STT--GGG..SHHHHHHHHHHHHHHHTS--.EEE-TTTT--HHHHHHHHHHTTH CS
                              QueC 122 needfsgYPDc..rdefvkalnkalnlgedkki.eieaPlidlsKaeivklgkelgv 175
                                       +  + + YPD   +d  +ka +++  l +  ++ +i+ Pl dl K e+ +++  l +
  gi|330506698|ref|YP_004383126.1| 119 CLIQGTIYPDRieSDGGIKAHHNVGGLPSRIEFkNIVEPLRDLYKDEVRQVARALSL 175
                                       55666777775213345666666655555555525999**********999988875 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   6.5e-06     0.017       4      23 ..      23      42 ..      20      71 .. 0.81
   2 !    3.9   0.0    0.0072        18     161     186 ..     151     176 ..     147     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.5e-06
                     tRNA_Me_trans  4 vvalSgGVDSsvaaallkeq 23
                                      +++lSgGVDSsv a+l +++
  gi|330506698|ref|YP_004383126.1| 23 IIGLSGGVDSSVCAMLAHRA 42
                                      799************99876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0072
                     tRNA_Me_trans 161 lekllfPlgeltKeevrkiAkeagla 186
                                        ++++ Pl +l K+evr++A++ +l+
  gi|330506698|ref|YP_004383126.1| 151 FKNIVEPLRDLYKDEVRQVARALSLS 176
                                       577888**************998876 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   6.9e-07    0.0018       3     116 ..      19     124 ..      17     186 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.9e-07
                              ThiI   3 qgkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdf.kevlk 77 
                                       +g+++  lSgG+DS V a l+ +  G r v v++++ ++  + + +++e+l + l           v v+  ++ l+
  gi|330506698|ref|YP_004383126.1|  19 KGRAIIGLSGGVDSSVCAMLAHRAlGDRLVPVYVDSGLM-RQSESDRIEELFKDLGL---------VRVNAqDRFLE 85 
                                       6899999***********888764599*******85555.55566777777665543.........33444044556 PP

                              ThiI  78 eilekvkekltivllkrkmlriAekvaeeegakalvtGe 116
                                        ++  v+++ + +++  +++r+ e+ a++ g ++l++G 
  gi|330506698|ref|YP_004383126.1|  86 ALKGVVDPEEKRMVVGETFIRVFEEEARRIGGDCLIQGT 124
                                       666666666677777889*******************96 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     8e-06      0.02      24      92 ..      26      91 ..      20     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8e-06
                      Asn_synthase 24 LSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdvi 92
                                      LSGG+DSS+ a+la r +  +l  + ++    + +e++  +e+ ++lg+     v  ++ +l+al+ v+
  gi|330506698|ref|YP_004383126.1| 26 LSGGVDSSVCAMLAHRALGDRLVPVYVDSGLMRQSESDRIEELFKDLGLVR---VNAQDRFLEALKGVV 91
                                      9***************99987777777775588888888888888888873...445555666666665 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00014      0.35       2      46 ..      22      63 ..      21      82 .. 0.77
   2 ?   -1.0   0.0       0.5   1.3e+03     135     158 ..     149     172 ..     134     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                                      EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHH CS
                        ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskee 46
                                      +++++SgG+DS +  +l+++    lg +lv ++vd gl  +s+++
  gi|330506698|ref|YP_004383126.1| 22 AIIGLSGGVDSSVCAMLAHRA---LGDRLVPVYVDSGLMRQSESD 63
                                      689********9988888877...455899999999987555443 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.5
                                       ETTCCEE-CCCT--HHHHHHHHHH CS
                        ATP_bind_3 135 iasirlvRPlLkvskeeleeylke 158
                                       i+ +++v Pl +++k+e++++++ 
  gi|330506698|ref|YP_004383126.1| 149 IEFKNIVEPLRDLYKDEVRQVARA 172
                                       56689999*********9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2421.10
//
Query:       gi|330506699|ref|YP_004383127.1|  [L=79]
Description: hypothetical protein MCON_0460 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-21   76.9   0.0    1.6e-21   76.8   0.0    1.0  1  DHNA      Dihydroneopterin aldolase


Domain annotation for each model (and alignments):
>> DHNA  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0     9e-26   1.6e-21      29     107 ..       2      78 ..       1      79 [] 0.97

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 9e-26
                                       TTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-STS-EE--TTTEEEEEEEEETTEEEEEEEEEETTTTEEEE CS
                              DHNA  29 esaeslekaieesielQPfvedvkvkidrekleekleefgYteLtgemldveitvkyeeaevkarleyieeldYplm 105
                                       ++a+slekaieesi+lQP+v++v+v+idr++l+e++  fgY eL+g+m+ + ++++ye+  ++arley++e  Yplm
  gi|330506699|ref|YP_004383127.1|   2 RTASSLEKAIEESISLQPYVRRVEVRIDRDMLSENV--FGYGELEGRMIWALVEIEYEGEVISARLEYDRERCYPLM 76 
                                       5899******************************99..*************************************** PP

                                       EE CS
                              DHNA 106 kv 107
                                       ++
  gi|330506699|ref|YP_004383127.1|  77 SL 78 
                                       87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 594.74
//
Query:       gi|330506700|ref|YP_004383128.1|  [L=223]
Description: CDP-diacylglycerol--serine O-phosphatidyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (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   48.5   1.3    1.1e-12   48.5   1.3    3.3  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
        0.2   10.6  16.5     0.0077   15.2  10.2    1.6  2  DUF3488          Domain of unknown function (DUF3488)
        8.3    6.8  12.9         20    5.5   0.2    3.4  3  Ost5             Oligosaccharyltransferase subunit 5


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 !   48.5   1.3   1.8e-16   1.1e-12       3      66 .]      10      75 ..       9      75 .. 0.92
   2 ?   -8.3  12.1         3   1.8e+04       6      13 ..     175     182 ..      79     216 .. 0.66

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1.8e-16
                                      HHHHHHHHHHHHHHHHHGGGS-H.....HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  3 PnaiTllrlllsvlailllltyyp...lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      P+++T+l+++l+++ail++  ++    l +a++l+++a+++D+lDG++AR++++   lG+ lDslaD
  gi|330506700|ref|YP_004383128.1| 10 PDLFTMLNIALGFAAILVICESQSldiLKVAVVLIILAAIADGLDGFVARKRGS-GPLGANLDSLAD 75
                                      99**************87755555****************************88.88*********9 PP

  == domain 2  score: -8.3 bits;  conditional E-value: 3
                                       HHHHHHHH CS
                   CDP-OH_P_transf   6 iTllrlll 13 
                                       +++l+++ 
  gi|330506700|ref|YP_004383128.1| 175 LSILGFFT 182
                                       33333333 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.4      0.16   9.7e+02      53      82 ..      15      47 ..       3      51 .. 0.42
   2 ?   15.2  10.2   1.3e-06    0.0077      12     131 ..      85     209 ..      76     221 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.16
                           DUF3488 53 llallav.allllsygt.llg.rdagvalLvll 82
                                      +l++++  a++l+  ++  l+ ++++v l++l+
  gi|330506700|ref|YP_004383128.1| 15 MLNIALGfAAILVICESqSLDiLKVAVVLIILA 47
                                      333333323333333322344355555555544 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.3e-06
                           DUF3488  12 allplalrlplwvl...llaalllvwrlllarrraplpsr..wlllllallavallllsygtllgrdagvalLvl.. 81 
                                        l+ +a  lp+ ++   ++++++ ++rl     r ++ ++   l  +l + a a+++ls   llgr ++   L+l  
  gi|330506700|ref|YP_004383128.1|  85 FLVVQAFSLPFLIWpaaIFFVICGALRL----ARFNISNKsdQLFEGLPIPA-AGMALSASVLLGRPGLAVTLMLil 156
                                       4555666666655533244445555554....23333332112323333333.666666666777666655555500 PP

                           DUF3488  82 .llalKllElrsrRDalvllllgffllats..flfsqsllfalylllalllll 131
                                        ll++  + + + RD +vl +lgff++a++  ++f+ + +++++ll al+++ 
  gi|330506700|ref|YP_004383128.1| 157 aLLMISSIPYPKIRDKRVLSILGFFTIAAAwaVFFQSNTIYTAILLGALIIMY 209
                                       055555566789**************998533566666666666555555443 PP

>> Ost5  Oligosaccharyltransferase subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2    0.0092        55      17      54 ..      13      50 ..       5      57 .. 0.73
   2 ?    5.5   0.2    0.0034        20      15      59 ..     100     144 ..      87     146 .. 0.89
   3 ?    3.5   2.4     0.015        87      13      68 ..     146     201 ..     145     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0092
                              Ost5 17 fvllligllltalfflyevtstkkkrslvkelllalvA 54
                                      f++l i+l ++a+ ++ e++s    +  v  ++la++A
  gi|330506700|ref|YP_004383128.1| 13 FTMLNIALGFAAILVICESQSLDILKVAVVLIILAAIA 50
                                      78899999999999999887754444455555555555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0034
                              Ost5  15 lafvllligllltalfflyevtstkkkrslvkelllalvASlflG 59 
                                        a+++++ g l +a f +++ + ++ +  ++  + +al AS++lG
  gi|330506700|ref|YP_004383128.1| 100 AAIFFVICGALRLARFNISNKSDQLFEGLPIPAAGMALSASVLLG 144
                                       589999999999****9999988888877**************99 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.015
                              Ost5  13 ptlafvllligllltalfflyevtstkkkrslvkelllalvASlflGfGvvfllla 68 
                                       p la++l+li  ll+ + + y     k+  s++ ++++a++ ++f+   +++++  
  gi|330506700|ref|YP_004383128.1| 146 PGLAVTLMLILALLMISSIPYPKIRDKRVLSILGFFTIAAAWAVFFQSNTIYTAIL 201
                                       66999999999999999999999998988889999999999888887777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1582.27
//
Query:       gi|330506701|ref|YP_004383129.1|  [L=221]
Description: phosphatidylserine decarboxylase-like protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   90.2   0.3    3.8e-22   78.8   0.1    2.1  2  PS_Dcarbxylase  Phosphatidylserine decarboxylase
      0.005   17.0   0.0       0.35   11.1   0.0    3.3  3  Peptidase_M23   Peptidase family M23
     0.0085   16.0   0.8        1.3    9.0   0.0    3.0  3  RnfC_N          RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.011   15.6   0.0        8.2    6.3   0.0    3.4  3  Biotin_lipoyl   Biotin-requiring enzyme
      0.024   14.7   0.0        2.3    8.3   0.0    2.3  2  Apocytochr_F_C  Apocytochrome F, C-terminal


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 !   10.0   0.0   0.00013      0.46       4      34 ..      39      67 ..      37      73 .. 0.85
   2 !   78.8   0.1   1.1e-25   3.8e-22      73     199 ..      72     190 ..      69     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
                    PS_Dcarbxylase  4 ffvrklkdgaRpidddpgaivsPaDgrilqi 34
                                      f++ +++d++R + +++g ++sPaDgri q 
  gi|330506701|ref|YP_004383129.1| 39 FMIFFHRDPDRLP-QSEG-MLSPADGRIIQA 67
                                      788999*****99.6666.*********987 PP

  == domain 2  score: 78.8 bits;  conditional E-value: 1.1e-25
                    PS_Dcarbxylase  73 vviyLspgdyHryhaPvsgkveerrhipGellsvnpsalkelrglftlneRvvlvie.wkGkvavvpvGatnvgsiv 148
                                       v+++++ gd+H++++P +g++ ++++ +G+ l   p++l+++    ++n+++ + i+ + G++ + ++ +t+v+ i 
  gi|330506701|ref|YP_004383129.1|  72 VTVFMGFGDVHVNRSPLDGTIISVEQRKGTHL---PAFLNRS----CQNQQNRIRIDtEDGEIQLCQITGTFVREII 141
                                       789***************************66...7788999....99999999***5489**************** PP

                    PS_Dcarbxylase 149 lnvlkgdelkkGeelGyFqfGStvvlvfeagkfieslvekgqkvkmGeklg 199
                                       ++v++gd++ +Ge++G+++fGS+v + ++ g  ++ +v  g++v++G++++
  gi|330506701|ref|YP_004383129.1| 142 CYVKPGDHVLRGERIGMIRFGSRVETTIPRG--YKLQVAIGDSVRAGKTVL 190
                                       *******************************..***************986 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   9.6e-05      0.35      18      73 ..      86     160 ..      49     179 .. 0.80
   2 ?    1.6   0.0     0.092   3.3e+02      46      69 ..     166     189 ..     158     198 .. 0.74
   3 ?   -2.2   0.0       1.4   4.9e+03      12      28 ..     199     215 ..     188     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.6e-05
                                       ESSSEEEEEEEEET.............TTEEEEEEEECTCEEEEEEEESEES......S-TTEEE-TTCEEEEEB CS
                     Peptidase_M23  18 AaadGtVvfagkke.............gyGnvviidhgdgystlyahlskis......vkegqkVkaGqvIGtvg 73 
                                       ++ dGt++ +++++             +  n ++id +dg ++l     ++       vk+g++V +G+ IG + 
  gi|330506701|ref|YP_004383129.1|  86 SPLDGTIISVEQRKgthlpaflnrscqNQQNRIRIDTEDGEIQLCQITGTFVreiicyVKPGDHVLRGERIGMIR 160
                                       6788888888775557788888888855599999999999666655555533355678**************874 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.092
                                       EEEEEEESEESS-TTEEE-TTCEE CS
                     Peptidase_M23  46 stlyahlskisvkegqkVkaGqvI 69 
                                       +t++    k++v  g+ V+aG+++
  gi|330506701|ref|YP_004383129.1| 166 ETTIPRGYKLQVAIGDSVRAGKTV 189
                                       555555567889999***999986 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.4
                                       TT-EEEESSSEEEEEEE CS
                     Peptidase_M23  12 kgtpVlAaadGtVvfag 28 
                                       +g pV + ++G+ v +g
  gi|330506701|ref|YP_004383129.1| 199 PGVPVASGSSGVLVSSG 215
                                       37799999999998877 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.091   3.3e+02      71      87 ..      86     102 ..      67     108 .. 0.77
   2 !    9.0   0.0   0.00037       1.3      43      60 ..     141     158 ..      98     169 .. 0.75
   3 ?    3.0   0.2     0.026        94      43      78 ..     174     212 ..     163     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.091
                            RnfC_N  71 asvsGtVkaiekrlvah 87 
                                       ++  Gt++++e+r+ +h
  gi|330506701|ref|YP_004383129.1|  86 SPLDGTIISVEQRKGTH 102
                                       8999********98776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00037
                            RnfC_N  43 kplvkvgdkVlkGqkiae 60 
                                        + vk gd+Vl+G++i+ 
  gi|330506701|ref|YP_004383129.1| 141 ICYVKPGDHVLRGERIGM 158
                                       4679************96 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.026
                            RnfC_N  43 kplvkvgdkVlkGqkiaea...egfvsapvhasvsGtVk 78 
                                       k+ v+ gd V+ G+ + +    +++  +pv + +sG  +
  gi|330506701|ref|YP_004383129.1| 174 KLQVAIGDSVRAGKTVLAIkcnSELPGVPVASGSSGVLV 212
                                       667999*******97654312145888999999999765 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       0.1   3.7e+02      47      64 ..      86     103 ..      82     105 .. 0.87
   2 ?    6.3   0.0    0.0023       8.2       9      33 ..     134     156 ..     126     170 .. 0.87
   3 ?    4.3   0.0    0.0097        35      16      36 ..     172     192 ..     154     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.1
                                       BSSSEEEEEESSTTTEEE CS
                     Biotin_lipoyl  47 apkaGvvkeilvkeGdtv 64 
                                       +p +G++ ++ + +G+ +
  gi|330506701|ref|YP_004383129.1|  86 SPLDGTIISVEQRKGTHL 103
                                       7899********999865 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0023
                                       EEEEEE.ECSESSSTTCEE-TTSEE CS
                     Biotin_lipoyl   9 GesveegvvevlvkvGdkVkagqvl 33 
                                       G++v+   +  +vk+Gd+V  g+ +
  gi|330506701|ref|YP_004383129.1| 134 GTFVR--EIICYVKPGDHVLRGERI 156
                                       88888..58899*******999876 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0097
                                       ECSESSSTTCEE-TTSEEEEE CS
                     Biotin_lipoyl  16 vvevlvkvGdkVkagqvlaev 36 
                                         +  v+ Gd+V ag +++ +
  gi|330506701|ref|YP_004383129.1| 172 GYKLQVAIGDSVRAGKTVLAI 192
                                       56788999*******999877 PP

>> Apocytochr_F_C  Apocytochrome F, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.011        38       6      58 ..      85     154 ..      80     159 .. 0.68
   2 ?    8.3   0.0   0.00065       2.3      33      60 ..     162     189 ..     155     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.011
                                       B-SSSEEEEEEEEEESS.............EEEEEEETSTSEEE-EEEESS..S-BS..--ST-EE-TT- CS
                    Apocytochr_F_C   6 kasaaGtiskiekeekg.............gtevtietedgeavvetipaG..peli..vsegqevkage 58 
                                       +++  Gti ++e+++               ++++ i+tedge    +i+     e+i  v+ g++v  ge
  gi|330506701|ref|YP_004383129.1|  85 RSPLDGTIISVEQRKGThlpaflnrscqnqQNRIRIDTEDGEIQLCQITGTfvREIIcyVKPGDHVLRGE 154
                                       678889999999887734555555566666999********98877775321145555577777776666 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00065
                                       SEEE-EEEESSS-BS--ST-EE-TT-BS CS
                    Apocytochr_F_C  33 geavvetipaGpelivsegqevkageal 60 
                                       g+ v++tip G +l v+ g++v+ag+++
  gi|330506701|ref|YP_004383129.1| 162 GSRVETTIPRGYKLQVAIGDSVRAGKTV 189
                                       778999******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1623.23
//
Query:       gi|330506702|ref|YP_004383130.1|  [L=258]
Description: hypothetical protein MCON_0463 [Methanosaeta concilii GP6]
Scores for complete 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  28.0    2.2e-09   37.2  28.0    1.1  1  Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
  ------ inclusion threshold ------
          1   10.1   3.5        1.9    9.3   2.8    2.0  1  NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21
        5.3    6.7   6.8       0.44   10.2   1.7    1.8  2  WTF              WTF protein


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 !   37.2  28.0   3.7e-13   2.2e-09      31     254 ..      10     237 ..       2     239 .. 0.67

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 3.7e-13
                   Exosortase_EpsH  31 vpllal.yllwdrwrralaasasll.gllllllglfl....lallgelsrvlllsalslvlillglvllllGlralr 101
                                       +++  l +l++   ++    s  +l g+ll+ +++++     +++  + ++ l+ a +l+++ ++++++       +
  gi|330506702|ref|YP_004383130.1|  10 LWISLLlLLVSSLTKK----SLIALsGWLLFGVFWLAqpghYLAINDYFNAILFTAAGLMCFYMAWIMTRRSGPSKA 82 
                                       2222220222222222....222223344443333334443355555556666666666666666666666677777 PP

                   Exosortase_EpsH 102 lllfpllll.llalPlpavlvaqlslpLqllvaavagfllsllgipvereG.nviqlptgqveVaeaCsGlrsllal 176
                                       +l+ + +     ++ +p + +++l+  L+ +++ +++ +l++l++pv + G n+++l+  +ve+  aC+       +
  gi|330506702|ref|YP_004383130.1|  83 QLWASYAAAvCGMVYFPFAEIEPLREALIGFTTLMTVQALQALSVPVVMPGwNIMTLNGRSVEIILACTA------I 153
                                       77776666657777777888899****************************7777778888*********......5 PP

                   Exosortase_EpsH 177 lalglllallfrrrlw.krklllllaavpiaflaNlvRilllvllayh..ygpeaaegllHeia...Gw.llfgval 246
                                        +++l+ +l++ +r++  r+++ l+++++ ++++NlvR+ + +++ ++  +g +++ +++H+++   G+ + ++++ 
  gi|330506702|ref|YP_004383130.1| 154 ESIALFSGLIISVRAPiGRRAAALVVSIISIYILNLVRNGFVIMAYGWswFGSASF-EVAHNLIakiGSvAALLLIS 229
                                       56677777777777777777*********************999987522688888.89996651114436666666 PP

                   Exosortase_EpsH 247 llllgllp 254
                                       +++++llp
  gi|330506702|ref|YP_004383130.1| 230 YMIFLLLP 237
                                       77777776 PP

>> NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.8   0.00031       1.9      19      65 ..      47      95 ..      44     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00031
                   NADH-u_ox-rdase 19 nfrpsDYvkaaaita.afplallaleklsPsvagka.mtlagligflgg 65
                                      ++  +DY +a+ +ta ++ + ++a+ + ++s  +ka ++++++ +++g 
  gi|330506702|ref|YP_004383130.1| 47 YLAINDYFNAILFTAaGLMCFYMAWIMTRRSGPSKAqLWASYAAAVCGM 95
                                      77889**********8888888888777755533346888888777773 PP

>> WTF  WTF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.3      0.34     2e+03     130     141 ..      62      73 ..      11      94 .. 0.72
   2 ?   10.2   1.7   7.4e-05      0.44      83     135 ..     176     233 ..     160     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.34
                               WTF 130 illtyfyetWtk 141
                                         l++fy  W+ 
  gi|330506702|ref|YP_004383130.1|  62 AGLMCFYMAWIM 73 
                                       236677777765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 7.4e-05
                               WTF  83 kllisvisisvlnvta..vCvlklkdaifGkveyslv...lgifcavcallfilltyf 135
                                        l++s+isi++ln++     ++ +  + fG + + ++   ++    v all+i+ + f
  gi|330506702|ref|YP_004383130.1| 176 ALVVSIISIYILNLVRngFVIMAYGWSWFGSASFEVAhnlIAKIGSVAALLLISYMIF 233
                                       489**********97667999*************998777555566888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1775.19
//
Query:       gi|330506703|ref|YP_004383131.1|  [L=1235]
Description: peptidase families S8 and S53 protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-50  172.1   4.6    4.5e-50  170.6   4.6    1.8  1  Peptidase_S8  Subtilase family
     0.0023   19.0   0.7     0.0023   19.0   0.7    4.2  4  PPC           Bacterial pre-peptidase C-terminal domain
  ------ inclusion threshold ------
      0.017   15.3   0.0      0.046   14.0   0.0    1.6  1  DUF4625       Domain of unknown function (DUF4625)
      0.023   15.3   0.0      0.049   14.3   0.0    1.5  1  Inhibitor_I9  Peptidase inhibitor I9


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.6   4.6   9.9e-54   4.5e-50       1     297 [.     165     477 ..     165     478 .. 0.80

  Alignments for each domain:
  == domain 1  score: 170.6 bits;  conditional E-value: 9.9e-54
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaan.a 76 
                                       g+g+ vav+D+G+d++hpdl  +                 +  a+ +   +++++dd +  + HGt +AGi+a++ a
  gi|330506703|ref|YP_004383131.1| 165 GRGINVAVIDSGIDKNHPDLIGK-----------------VI-AEKNFLANEITADD-L--LGHGTMIAGIIAGSgA 220
                                       89*****************9932.................33.33333444444444.2..34************99 PP

                                       .SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  77 peegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsiealainravnk 153
                                        + g  +g+apga+++ vkv+d++g      +++i++ie+a+++++dv+++slg + +l++t   i  +a+++a  +
  gi|330506703|ref|YP_004383131.1| 221 SSGGRYVGIAPGASLINVKVIDQNGDGRV--SDIIAGIEWAIYNGADVLSLSLG-GINLGETNPPIT-MAADNAA-D 292
                                       999999*******************9875..9**********************.*******99886.7999999.9 PP

                                       CT-EEEEE--SS-T-HH.....................EEE-TTCEECTTTS......................... CS
                                       xxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxx......................... RF
                      Peptidase_S8 154 kgvlvviSaGNngktgs.....................slqagspvgtpsts......................... 184
                                       +gv+v+++aGN++ t+                      +                                      
  gi|330506703|ref|YP_004383131.1| 293 QGVVVCVAAGNRNSTENenqlsgasssqlrgspvelsqT------------Eessgkdvyflfvpivfalppglids 357
                                       9************77776666666654444444433330............25555555566666666777777776 PP

                                       ....TTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHH..EEEE-SHHHCHHHHH CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                      Peptidase_S8 185 ....knvitvgayttegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglss..yqsmsGTSmAsPnaa 255
                                            nvit g+++ +g++a+fS +Gp+ d ++kpd+vapG++i+st++   +   +  +  y  +sGTS ++P aa
  gi|330506703|ref|YP_004383131.1| 358 pgdgVNVITLGSTDAAGHMASFSGSGPTRDDRIKPDVVAPGMDIISTVPAGLEGPEYV-DtyYARESGTSLSTPIAA 433
                                       65435*******************************************9999655444.448*************** PP

                                       HHHHHHHHHHTT--HHHHHHHHHCCS-EE........SSSSSST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                      Peptidase_S8 256 gaaAlllsalpkltpetvraallntAqdl..gkadniesfaqGa 297
                                       g aAlll++  +ltp+ ++ a+ + A  l      ++e + qG 
  gi|330506703|ref|YP_004383131.1| 434 GLAALLLQEWSNLTPAGIKGAMTRGAAKLnnTHGVAYEAYYQGT 477
                                       **************************999442233355555665 PP

>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.8         4   1.8e+04      33      54 ..     128     147 ..     118     150 .. 0.48
   2 !   19.0   0.7   5.2e-07    0.0023       3      70 .]     647     738 ..     645     738 .. 0.81
   3 ?    3.1   0.0     0.048   2.1e+02      54      70 .]     868     884 ..     817     884 .. 0.77
   4 ?   -0.8   0.0      0.78   3.5e+03      37      66 ..    1074    1113 ..    1022    1114 .. 0.44

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4
                                       TT..-SS-EE-STT-TTS-TTS CS
                               PPC  33 sngtsvaaydansapsgsdeyi 54 
                                       +n +sv+  ++n + ++sd yi
  gi|330506703|ref|YP_004383131.1| 128 DN-SSVDG-QDNDSDGPSDGYI 147
                                       33.33333.2222334455666 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 5.2e-07
                                       EEEEEEE-TT-E.EEEEES-TT..............................SEEEEE-TT..-SS-EE-STT-TTS CS
                               PPC   3 Dvysfevpagds.ltididggti............................dldLylldsngtsvaaydansapsgs 50 
                                       D+y+ ++p+g++ +++ +d+++                             +ldL+l  +  ++++a    + p gs
  gi|330506703|ref|YP_004383131.1| 647 DYYYLDLPVGSRgIEVRLDWNSEsdsidadrtdsnstafsstnasstdlgsSLDLFLISPT-SEYYA----GGPEGS 718
                                       9*****************9999988887777777777788888887777777777777777.66666....345567 PP

                                       -TTS-EE-SSSEEEEEEE.. CS
                               PPC  51 deyieftapqaGtYyvaVss 70 
                                       + ++ +  p  G + vaV+s
  gi|330506703|ref|YP_004383131.1| 719 SKRVAIESPPSGRWLVAVYS 738
                                       7999999***********96 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.048
                                       S-EE-SSSEEEEEEE.. CS
                               PPC  54 ieftapqaGtYyvaVss 70 
                                       +e+++pqaG + + V++
  gi|330506703|ref|YP_004383131.1| 868 VEVSNPQAGRWAINVYG 884
                                       78999**********96 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.78
                                        -SS-EE-ST.T-TT..S-TTS-EE-.......SSSEEEEE CS
                               PPC   37 svaaydans.apsg..sdeyiefta.......pqaGtYyv 66  
                                        +   ++a++ + sg  ++ + e+ a       +++GtY +
  gi|330506703|ref|YP_004383131.1| 1074 DPKEFQAPPaYISGfvNQTTMEVIAvgvnlsvTKPGTYRI 1113
                                        3444555554333355333333222233334488888865 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     1e-05     0.046      75     118 ..     567     611 ..     552     621 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                           DUF4625  75 kewsfeksy.dlsgskkeyelheeieiPadaeaGdYhlvirvtDa 118
                                        +w+  +   +   s++++ +  +i++P+da++GdY   + +tD 
  gi|330506703|ref|YP_004383131.1| 567 ADWVSLQALpEHISSNSQHVFAASIQVPEDADPGDYSGSLDITDS 611
                                       5566566665777888999***********************995 PP

>> Inhibitor_I9  Peptidase inhibitor I9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.1e-05     0.049      37      80 ..      67     109 ..      38     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                                       --EEEEEEESSSSSEEEEEE-GGGHHHHHTSTTEEEEEEEEEEE CS
                      Inhibitor_I9  37 akagilysYkilfnGfavklteeqaeklrkrpeVesVepDqsvr 80 
                                       +   ++ysY+ l+ G a++ ++ ++ ++++++ V +++ D + +
  gi|330506703|ref|YP_004383131.1|  67 DGFDVKYSYQ-LIPGLAGEASSTTIREMAESDRVSAIYFDDPAK 109
                                       567899****.9*************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 8050.19
//
Query:       gi|330506704|ref|YP_004383132.1|  [L=331]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   95.9   0.0    4.4e-27   95.5   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.017   15.2   0.0       0.04   14.0   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
       0.17   12.2   0.0       0.33   11.2   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 !   95.5   0.0   7.4e-31   4.4e-27       3     166 ..      34     200 ..      32     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 7.4e-31
                                       EESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCC CS
                                       xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet..vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklav 75 
                                       ++ gCnl C+fC++     +r++++ + +++++++e v+e++ ++   v+  i + gep+lypd+vel+ rl+ +  
  gi|330506704|ref|YP_004383132.1|  34 PSCGCNLSCPFCSVDAGpsSRSRVTDYQVDLDYLMEAVREIApFKEPgVECHIDSPGEPMLYPDIVELVGRLKGIG- 109
                                       677************99**************************55555***************************5. PP

                                       CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn..rghtfeevlealeklreagikrvvdriv 150
                                       +   +++ +ngt++dee+++ l e+g+dr++l+ +a+d+e    ++   +g +++ ++e+ e++++++i+   +  v
  gi|330506704|ref|YP_004383132.1| 110 EVSVVSMQSNGTRLDEEMIRSLEEAGLDRINLSMHALDPE-LAAYLAgrPGFDVQGLIETAENIAKSRID-LLIAPV 184
                                       888889**********************************.888887557777799**************.****** PP

                                       EBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeeleellel 166
                                        +pG nd+e+ +l+++
  gi|330506704|ref|YP_004383132.1| 185 YIPGINDQEIPKLIDF 200
                                       *************998 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.7e-06      0.04       7      94 ..      37     124 ..      33     145 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.7e-06
                           Fer4_14   7 gCnlsCkgCdnketwkselgkpqteelleqilk......dlkkseikiqglvltG.GePLhyenkkellklvkrlke 76 
                                       gCnlsC++C   +  +s++   + + +l+  ++       +k+  ++     +   GeP++y   +++++lv rlk 
  gi|330506704|ref|YP_004383132.1|  37 GCNLSCPFCSVDAGPSSRSRVTDYQVDLDYLMEavreiaPFKEPGVEC---HIDSpGEPMLY---PDIVELVGRLKG 107
                                       9********944444444433333333333333111111455555544...45555****99...************ PP

                           Fer4_14  77 eypekkiwletngtleie 94 
                                        ++   + +++ngt   +
  gi|330506704|ref|YP_004383132.1| 108 IGEVSVVSMQSNGTRL-D 124
                                       9977888899998854.3 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 ?   11.2   0.0   5.5e-05      0.33      14      99 ..      37     126 ..      31     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.5e-05
                           Fer4_12  14 gCnlsCkgCfnketwsfk...sgkeftkelleeiiedlkkesiegltl...lGGEPllpenaeallelvkevkeekp 84 
                                       gCnlsC++C   +  s +   +  +++ + l e++++++  + +g+     + GEP+l   +++++elv ++k  + 
  gi|330506704|ref|YP_004383132.1|  37 GCNLSCPFCSVDAGPSSRsrvTDYQVDLDYLMEAVREIAPFKEPGVEChidSPGEPML---YPDIVELVGRLKGIGE 110
                                       9********86555443322233344555555666666555555554433389*****...9***********9998 PP

                           Fer4_12  85 .ekdiwlytgytleel 99 
                                        + + + ++g+ l+e 
  gi|330506704|ref|YP_004383132.1| 111 vSVVSMQSNGTRLDEE 126
                                       7889999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2299.39
//
Query:       gi|330506705|ref|YP_004383133.1|  [L=221]
Description: HD domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-11   44.2   3.0    1.5e-10   41.3   0.8    2.1  2  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.8   8.4e-15   1.5e-10       2     122 .]      29     136 ..      28     136 .. 0.82
   2 !    3.1   0.1    0.0057     1e+02      54      89 ..     185     220 ..     165     221 .] 0.81

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 8.4e-15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHH.HHHCTCCHHHHHHHHHHHHHHHHHHHHH CS
                                HD   2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekk.eeefekflaHekvgaeilrevekrlgld 77 
                                       + H+l+V++ a+ ++  +g  +d  +lllaaLlHD  +g  ++ ++ + +  +++ +   +   + l+++ +++++ 
  gi|330506705|ref|YP_004383133.1|  29 FSHILRVYHNAKVIGLAEG--ADMPVLLLAALLHDALEGSKHSLGSLDaK--QDQDVRRREAVCQFLEKIDLPEEK- 100
                                       78*****************..*******************8885555431..333344556666666666666633. PP

                                       HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHHH CS
                                HD  78 ledvaklirehheswegkkrprglaerqlslearivklaDrlaam 122
                                          v  +i+ h++s  ++         + +le +i+++aDrl+am
  gi|330506705|ref|YP_004383133.1| 101 KAKVFYAIEVHRFSQGIE---------PETLEGKILQDADRLDAM 136
                                       788999*******99866.........****************98 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0057
                                       TCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC CS
                                HD  54 ekflaHekvgaeilrevekrlgldledvaklirehh 89 
                                        + + H+  g e+++++ ++l+ +l+d+ + i+eh+
  gi|330506705|ref|YP_004383133.1| 185 LESRMHTRRGKEMASRRNEVLRRYLKDLEEEIEEHS 220
                                       4456699**************999999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1744.89
//
Query:       gi|330506706|ref|YP_004383134.1|  [L=394]
Description: ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-13   52.0   0.2      2e-13   51.1   0.2    1.5  1  MacB_PCD         MacB-like periplasmic core domain
    4.8e-13   49.4   6.0    4.8e-13   49.4   6.0    2.9  3  FtsX             FtsX-like permease family
  ------ inclusion threshold ------
       0.14   12.0   0.0         14    5.6   0.0    2.2  2  ATS3             Embryo-specific protein 3, (ATS3)
        1.9    7.5  14.7        2.6    7.1  14.7    1.5  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.2   4.6e-17     2e-13       1     194 [.      28     236 ..      28     237 .. 0.71

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 4.6e-17
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdvealrr...evp.veavapvv 73 
                                       +ll+v +ia++v    + + +++g+++++ + i   ++l +vt+++ +g++    ++  l++   ++p v+av++ +
  gi|330506706|ref|YP_004383134.1|  28 TLLSVAAIALAVSISLVSIFMMDGFRDMLFDVII--EDLPHVTVTPKEGDDYI-YLYHSLSDriwDIPgVVAVSASL 101
                                       89************************77777655..55666666552233311.122123222456899****9998 PP

                          MacB_PCD  74 ....tvrgggsgeeevtvvgvdp.dyfkvfgl..klaeGrffteadlr.ggpnvvvigeelaerlf.pvGdtirl.. 139
                                           t ++ ++  e+v ++gvdp d+ +++ l  ++ +G       +  +  + v++g++l erl  + G+ti    
  gi|330506706|ref|YP_004383134.1| 102 gtsaTFTYKEN-VENVAMSGVDPeDFESIYHLeeYMIKGD-----LISvQSGKKVILGKKLSERLKvKMGQTIYAsf 172
                                       75432244432.34599***99735555888832234443.....333345556**********99*******99*9 PP

                          MacB_PCD 140 .....kpftVvGvledppgsgsalgddavylplttlqrrs.........itvrlkdgadleaaaaelek 194
                                             ++ V+G++++p g    + +d ++++l+t+++ +         + +rl d  +++aaa+ l++
  gi|330506706|ref|YP_004383134.1| 173 pdargTSLMVSGIFDPPVG----WPEDLAIVSLETARS-FlnegdvasnVDIRLGDIYQADAAARSLQD 236
                                       **99999*******54424....55889****998832.2356777777**************999986 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.33   1.5e+03      74      88 ..      32      46 ..      21      65 .. 0.63
   2 ?    0.7   0.4      0.16   7.3e+02      24      43 ..     261     281 ..     251     288 .. 0.59
   3 !   49.4   6.0   1.1e-16   4.8e-13       2      96 .]     290     388 ..     289     388 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.33
                              FtsX 74 vlllllallagllsi 88
                                      v ++ la+ ++l+si
  gi|330506706|ref|YP_004383134.1| 32 VAAIALAVSISLVSI 46
                                      333333333333333 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                              FtsX  24 eillitlvalviG.lglglla 43 
                                       e+ li l+ l+i+ +g+g+++
  gi|330506706|ref|YP_004383134.1| 261 ENNLIMLLILIIAsFGVGSVM 281
                                       445555555555556666555 PP

  == domain 3  score: 49.4 bits;  conditional E-value: 1.1e-16
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs.....selkisidlitvliii 73 
                                       +eig+l a+G+k+ +++ ++l+e+ l++l + ++G +lgl+++ +    l+ s+ +     + l++ i+l+++l+ii
  gi|330506706|ref|YP_004383134.1| 290 SEIGMLMAMGAKRQSIMNIFLIESGLLGLMGGAVGAVLGLALSLY-LGNLEFSMEApggqkITLPVVISLESFLVII 365
                                       7**********************************9999999666.444555566567788**************** PP

                              FtsX  74 vlllllallagllsiskilkkep 96 
                                       + ++ l ++ag ++++k+++ +p
  gi|330506706|ref|YP_004383134.1| 366 IAAIALSIIAGSYPAYKASRLDP 388
                                       ********************987 PP

>> ATS3  Embryo-specific protein 3, (ATS3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0032        14      80     119 ..      77     118 ..      57     123 .. 0.84
   2 ?    4.2   0.0    0.0085        38      25      55 ..     208     238 ..     197     261 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0032
                              ATS3  80 ylylkrsGtdg.W.iPetvkiyeegsksvtfyfnkalPenvW 119
                                       y+yl++s +d  W iP +v +  +  +s tf++++++ +   
  gi|330506706|ref|YP_004383134.1|  77 YIYLYHSLSDRiWdIPGVVAVSASLGTSATFTYKENVENVAM 118
                                       888888888864657********************9987655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0085
                              ATS3  25 aspaktrdqvsiafGdaysnevyaarlddpl 55 
                                        +  + + +v i++Gd y+ ++ a+ l+d  
  gi|330506706|ref|YP_004383134.1| 208 LNEGDVASNVDIRLGDIYQADAAARSLQDYG 238
                                       566677889****************997754 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 ?    7.1  14.7   0.00058       2.6     157     250 ..     258     373 ..      26     381 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00058
                   ABC2_membrane_3 157 snvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afgl 231
                                       + +++ l+ l+++i++++++ ++++ +v+Ek+s i +l+  +g ++ +++   ++ ++l++l   ++  +l  a++l
  gi|330506706|ref|YP_004383134.1| 258 ETFENNLIMLLILIIASFGVGSVMYLLVNEKTSEIGMLM-AMGAKRQSIMNIFLIESGLLGLMGGAVGAVLglALSL 333
                                       566677777777777777777799999*********887.999*****99999999999999998776665224444 PP

                   ABC2_membrane_3 232 .....................gipfgnlglllllfllfgl 250
                                                             i+ ++++++++  +  ++
  gi|330506706|ref|YP_004383134.1| 334 ylgnlefsmeapggqkitlpvVISLESFLVIIIAAIALSI 373
                                       6677999998888887766666666666666655554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2814.55
//
Query:       gi|330506707|ref|YP_004383135.1|  [L=386]
Description: ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-17   62.4   3.3    4.2e-17   62.4   3.3    3.0  3  FtsX      FtsX-like permease family
    1.8e-14   54.6   0.9    2.6e-14   54.0   0.9    1.2  1  MacB_PCD  MacB-like periplasmic core domain


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 ?    1.3   0.0     0.053   4.8e+02      26      44 ..      20      36 ..       7      62 .. 0.51
   2 ?    1.2   0.1     0.059   5.3e+02      59      78 ..     247     266 ..     215     279 .. 0.68
   3 !   62.4   3.3   4.6e-21   4.2e-17       2      96 .]     281     379 ..     280     379 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.053
                              FtsX 26 llitlvalviGlglgllaa 44
                                      + +++v l+++  + +l+ 
  gi|330506707|ref|YP_004383135.1| 20 FTVAAVTLAVA--IIVLFM 36
                                      22233333333..222222 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.059
                              FtsX  59 elkisidlitvliiivllll 78 
                                       e++  + +i +l+i++++ +
  gi|330506707|ref|YP_004383135.1| 247 ETQRVFAWIFYLLIFAIAGF 266
                                       55555556666666665544 PP

  == domain 3  score: 62.4 bits;  conditional E-value: 4.6e-21
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs....selkisidlitvliiiv 74 
                                       reigil a+G++++++l+++++e+l+++ +++++G +l++l aql++++  +  +     s ++is++++ ++ +++
  gi|330506707|ref|YP_004383135.1| 281 REIGILMAMGATRRSILKVFILESLILAPPSALMGGILAYLSAQLIMSYEIELPSEiymiSKMTISMKPEFFVWAVG 357
                                       9********************************************888866554436667***************** PP

                              FtsX  75 lllllallagllsiskilkkep 96 
                                       ++l +  +agl++++k+++++p
  gi|330506707|ref|YP_004383135.1| 358 IALTVNFVAGLYPAWKASRMDP 379
                                       ********************98 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.9   2.9e-18   2.6e-14       2     185 ..      19     217 ..      18     227 .. 0.70

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 2.9e-18
                          MacB_PCD   2 lltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdvealrr...evp.veavapvv. 73 
                                       l+tv +++++va +++++++++g+q+ +  +  ++   ++++p++ + + +   ++++++    + p veav++++ 
  gi|330506707|ref|YP_004383135.1|  19 LFTVAAVTLAVAIIVLFMGIMSGFQEEIITTTVENNPHIYIQPKE-DENYIY--LYRTVSNilwAYPgVEAVSARLa 92 
                                       68****************************965333324466653.222222..22222223445899******986 PP

                          MacB_PCD  74 ...tvrgggsgeeevtvvgvdp.dyfkvfgl..klaeGrffteadlrggpnvvvigeelaerlfpvGdtirl..... 139
                                          ++++ ++  ++++  gv+p d+ ++ ++  ++ +G   +++dl+++++++ ig +lae+l  +G++  +     
  gi|330506707|ref|YP_004383135.1|  93 gkgAAKYKDE-VRAISFLGVNPeDEDRMMDVrsDIISG---DFQDLERRKYAAFIGTGLAEKLK-IGQEDDFtltrg 164
                                       6653344442.234888997754999999998556889...5689999**************99.777655555999 PP

                          MacB_PCD 140 ...kpftVvGvledppgsgsalgddavylp...lttl.....qrrsitvrlkdgadl 185
                                           + +V+G +e+  g  +a +d+ +y+p   +++l      ++++ ++++d  ++
  gi|330506707|ref|YP_004383135.1| 165 nisLRIKVAGLFET--G--TAADDSLIYIPlmlAQDLiemgdVVSEVDAKVADIYQV 217
                                       99999*******44..5..4567999****666444444433255577777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2652.19
//
Query:       gi|330506708|ref|YP_004383136.1|  [L=262]
Description: hypothetical protein MCON_0469 [Methanosaeta concilii GP6]
Scores for complete 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   27.1   0.0      6e-06   26.6   0.0    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 !   26.6   0.0   3.3e-10     6e-06       2      94 ..       4      98 ..       3     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.3e-10
                           UPF0489  2 vivesHheaLeaiyraigskklpsdlslvHlDaHpDllipk.....kmsaddvfnallkileklaeelleelsidnwIl 75
                                      vi++sH+e+L +++r   ++k   +l +v +D+H D+         +++ +++f+    ++ + +e + + l+++n+  
  gi|330506708|ref|YP_004383136.1|  4 VIIDSHNEILLYWIREYCRHK--MPLVVVRIDRHHDMFS-DcprlpAKEGRNIFDYFDRMMPEIYEYAKRRLNEGNFTC 79
                                      79*************999999..99***********954.346465444444444422233555*************** PP

                           UPF0489 76 pavyaghisrvvwikpawa 94
                                      pa   g++  +  + p ++
  gi|330506708|ref|YP_004383136.1| 80 PAFHYGILGSLYHFDPRKE 98
                                      ********99999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1897.35
//
Query:       gi|330506709|ref|YP_004383137.1|  [L=99]
Description: hypothetical protein MCON_0470 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.37   10.9   0.0    1.7  2  DUF3288   Protein of unknown function (DUF3288)


Domain annotation for each model (and alignments):
>> DUF3288  Protein of unknown function (DUF3288)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.1e-05      0.37      47      78 ..       5      36 ..       2      46 .. 0.84
   2 ?   -0.0   0.0     0.051   9.1e+02      37      56 ..      32      50 ..      30      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.1e-05
                           DUF3288 47 qkdldkvlkkWqlteeeLfektreihaekkvy 78
                                       +dl + l   ++te+eLf+ t e+ + +++ 
  gi|330506709|ref|YP_004383137.1|  5 DEDLSSFLMDFGFTEDELFAVTYELDSYRSIP 36
                                      689********************998776655 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.051
                           DUF3288 37 YegFpGardiqkdldkvlkk 56
                                      Y+  pG   +++ l+++l++
  gi|330506709|ref|YP_004383137.1| 32 YRSIPGT-TVKRYLNRILQN 50
                                      7777885.588999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 722.89
//
Query:       gi|330506710|ref|YP_004383138.1|  [L=363]
Description: hypothetical protein MCON_0471 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.5e-112  376.4  25.7   1.8e-112  376.2  25.7    1.0  1  DUF1646          Protein of unknown function (DUF1646)
  ------ inclusion threshold ------
          2    8.4   7.7       0.95    9.4   2.7    2.6  2  Abhydrolase_9_N  Alpha/beta-hydrolase family N-terminus
        4.2    7.5  13.4       0.16   12.1   5.6    2.4  2  DUF3180          Protein of unknown function (DUF3180)


Domain annotation for each model (and alignments):
>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.2  25.7    3e-116  1.8e-112       4     347 .]      16     355 ..      13     355 .. 0.97

  Alignments for each domain:
  == domain 1  score: 376.2 bits;  conditional E-value: 3e-116
                           DUF1646   4 llvilvlvlilPlvvrkveenlelfllimgvaavtvsglfslelliealktplailevgaipigitqavllaGlvfe 80 
                                       l++i++lvl lP++ + ve+nle+fl+img  avt++  + ++l+  a  +p+          gi+ avl+aGl+f 
  gi|330506710|ref|YP_004383138.1|  16 LFAIFLLVLTLPFKIKVVEKNLEAFLFIMGATAVTITSKWGIDLITLAAGEPVEK--------GIVPAVLFAGLIFF 84 
                                       789*******************************************999999865........7************* PP

                           DUF1646  81 llkkklksllaevldklalkvfvfllivilGlassvisaivaavilaeivallplerkekvklvviasfaiGlGaal 157
                                       + k  ++  +    + ++l+vfv+++i++lG+ass+i+ai+a++ l+ei++l+p+er +k+k+v+ia+faiGlGa l
  gi|330506710|ref|YP_004383138.1|  85 YGKATINRAIRGLTNSVPLPVFVAVVIFVLGMASSLITAIIASLFLVEIANLMPMERSDKIKMVIIACFAIGLGAVL 161
                                       ***************************************************************************** PP

                           DUF1646 158 tPvGePlstiavskl.....nedflylidvlgeyiiiavlvlallaalslkrlskreelvevveyeeelkevlirav 229
                                       tP+GePlstiav+kl     n++f yl+d lg+ i+ +vl  al++a+++ r++ r   v+++  e  lkev+ira 
  gi|330506710|ref|YP_004383138.1| 162 TPLGEPLSTIAVTKLqgppyNASFWYLADQLGILIVLGVLGCALFGAFYVGRKAARV-EVQEIADEGGLKEVFIRAA 237
                                       **************96666569******************************98777.566677999********** PP

                           DUF1646 230 kvfvfilalellGegfkPlikayiaklkseilywvnlisavvdnatlaaaeisPelteeqirailmsllisGGlliP 306
                                       kv++f+ al llG+g++ li +y++k++  +l+wvn++sa++dnatl+aaeisP +++ qi a+l +llisGG+liP
  gi|330506710|ref|YP_004383138.1| 238 KVWLFVSALFLLGAGMEVLIFKYFTKIPDYVLFWVNMVSAILDNATLTAAEISPAMSQSQINAALYGLLISGGMLIP 314
                                       ***************************************************************************** PP

                           DUF1646 307 GniPnivsaGklkikskeWarvgvPlgiilliiyfivllvl 347
                                       GniPni+saGkl i+s+eWa++g+P+g++l  iyfi+++vl
  gi|330506710|ref|YP_004383138.1| 315 GNIPNIISAGKLGITSSEWAKLGIPMGLVLNAIYFILVFVL 355
                                       ***************************************97 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 ?    1.6   1.9      0.04   2.4e+02      59     121 ..      40     102 ..      30     131 .. 0.62
   2 ?    9.4   2.7   0.00016      0.95      37     117 ..      92     172 ..      75     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.04
                   Abhydrolase_9_N  59 valvvllvalvlaarwQrelralmgaeplgaaeyllvllvallvfalllllgrllralvrlla 121
                                        + ++ ++a+   ++w  +l +l   ep++   +++vl ++l++f    ++ r++r l++ + 
  gi|330506710|ref|YP_004383138.1|  40 FLFIMGATAVTITSKWGIDLITLAAGEPVEKGIVPAVLFAGLIFFYGKATINRAIRGLTNSVP 102
                                       455556666667777777778888888888888888888888888888888888887777665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00016
                   Abhydrolase_9_N  37 rllrlpepsrrvrrrlrlalavvalvvllvalvlaarwQrelralmgaeplgaaeyllvllvallvfalllllgrll 113
                                       r++r+ + s + +  + ++++v++++  l++++ a+    e+++lm +e+ +  +++ +++ a+ + a+l+ lg+ l
  gi|330506710|ref|YP_004383138.1|  92 RAIRGLTNSVPLPVFVAVVIFVLGMASSLITAIIASLFLVEIANLMPMERSDKIKMVIIACFAIGLGAVLTPLGEPL 168
                                       444466667777778889999999999999999999999********************************999988 PP

                   Abhydrolase_9_N 114 ralv 117
                                       + ++
  gi|330506710|ref|YP_004383138.1| 169 STIA 172
                                       7654 PP

>> DUF3180  Protein of unknown function (DUF3180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.6   2.7e-05      0.16      24     119 ..      66     161 ..      39     164 .. 0.77
   2 ?   -0.9   0.9      0.28   1.7e+03      43      81 ..     206     251 ..     186     258 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.7e-05
                           DUF3180  24 pplpwlaavvllvlavvelvlAlqvrrrirgrpgarqlepltaarllvlAkAsalvGAllaGvyaGllvyllragel 100
                                        p++  ++ ++l+ +++ ++   ++ r irg +++ +l   +a+ ++vl+ As+l+ A++a +++  ++ l++  + 
  gi|330506710|ref|YP_004383138.1|  66 EPVEKGIVPAVLFAGLIFFYGKATINRAIRGLTNSVPLPVFVAVVIFVLGMASSLITAIIASLFLVEIANLMPMERS 142
                                       45555556666667777777778999999999999*******************************99999999999 PP

                           DUF3180 101 paaaedllaavvavlaava 119
                                       +  +  ++a+++  l+av+
  gi|330506710|ref|YP_004383138.1| 143 DKIKMVIIACFAIGLGAVL 161
                                       9999888888888888875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.28
                           DUF3180  43 vlAlqvrrrirgr.....pgarqle..pltaarllvlAkAsalvGA 81 
                                       + A++v r+  +      +++  l+   ++aa+++++  A+ l+GA
  gi|330506710|ref|YP_004383138.1| 206 FGAFYVGRKAARVevqeiADEGGLKevFIRAAKVWLFVSALFLLGA 251
                                       3334443333222222221112222003455555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2483.97
//
Query:       gi|330506711|ref|YP_004383139.1|  [L=110]
Description: alkylhydroperoxidase-like protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-13   48.6   0.4    7.2e-13   48.4   0.4    1.2  1  CMD       Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
       0.03   14.1   1.0       0.37   10.7   0.1    2.6  2  IF2_N     Translation initiation factor IF-2, N-terminal regi
      0.085   13.1   0.4        0.2   11.9   0.3    1.7  2  CTU2      Cytoplasmic tRNA 2-thiolation protein 2
      0.098   12.5   1.2       0.46   10.3   0.1    2.1  2  GAGA      GAGA factor


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 !   48.4   0.4   1.6e-16   7.2e-13      18      71 ..      20      73 ..       5      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.6e-16
                                      SSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHH CS
                               CMD 18 eggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaaya 71
                                      ++ Ld ++ eLi++avsaa +c +C++ H+r A + Gv +++ia+++ +a   +
  gi|330506711|ref|YP_004383139.1| 20 QDMLDERTIELISIAVSAAIRCSHCMRLHIRTASKLGVPDDQIAAAVFMAGNLC 73
                                      556*******************************************99886665 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   8.2e-05      0.37      29      47 ..      14      31 ..       5      36 .. 0.88
   2 ?    1.5   0.1     0.059   2.7e+02      33      42 ..      79      88 ..      52      89 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.2e-05
                             IF2_N 29 GievkshsssLDeetaeli 47
                                      G+e k++++ LDe t+eli
  gi|330506711|ref|YP_004383139.1| 14 GKE-KTAQDMLDERTIELI 31
                                      99*.**************9 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.059
                             IF2_N 33 kshsssLDee 42
                                       s+ss LDee
  gi|330506711|ref|YP_004383139.1| 79 SSASSHLDEE 88
                                      5777777776 PP

>> CTU2  Cytoplasmic tRNA 2-thiolation protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.66     3e+03      42      52 ..      35      45 ..      11      48 .. 0.60
   2 ?   11.9   0.3   4.5e-05       0.2      25      57 ..      49     101 ..      39     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.66
                              CTU2 42 letsekCalCg 52
                                      ++++ +C+ C+
  gi|330506711|ref|YP_004383139.1| 35 VSAAIRCSHCM 45
                                      45566777775 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.5e-05
                              CTU2  25 vrTgeKLvknksseeae....................letsekCalCglpldd 57 
                                       +rT++KL+ ++++ +a+                     e+ e C++C+l++++
  gi|330506711|ref|YP_004383139.1|  49 IRTASKLGVPDDQIAAAvfmagnlctasvlssasshlDEEPEICPICQLASKS 101
                                       69********99877669*****************999999*******99944 PP

>> GAGA  GAGA factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.083   3.7e+02      32      44 ..      37      49 ..      33      57 .. 0.82
   2 ?   10.3   0.1    0.0001      0.46      20      32 ..      85      97 ..      64     104 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.083
                                      -EESSHHHHHHHH CS
                              GAGA 32 AviRqsRnLRRHL 44
                                      A iR s  +R H+
  gi|330506711|ref|YP_004383139.1| 37 AAIRCSHCMRLHI 49
                                      889****999996 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0001
                                      TTS--EE-TTT-- CS
                              GAGA 20 qsEqPAtCPiCqA 32
                                        E P  CPiCq 
  gi|330506711|ref|YP_004383139.1| 85 LDEEPEICPICQL 97
                                      4599*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 848.96
//
Query:       gi|330506712|ref|YP_004383140.1|  [L=982]
Description: excinuclease ABC subunit A [Methanosaeta concilii GP6]
Scores for 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  103.1   0.3    3.3e-29  101.1   0.2    2.1  2  UvrA_inter       UvrA interaction domain
    8.9e-28   96.8   0.0    4.9e-26   91.3   0.0    2.9  2  UvrA_DNA-bind    UvrA DNA-binding domain
    4.7e-21   75.7   0.1      2e-08   34.8   0.1    5.0  4  ABC_tran         ABC transporter
    1.3e-10   41.6   3.0      0.012   15.4   0.0    4.8  5  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.5e-10   40.2   0.0      0.066   12.6   0.0    4.1  4  SMC_N            RecF/RecN/SMC N terminal domain
    2.1e-08   34.7   0.0       0.02   15.3   0.0    3.7  3  AAA_16           AAA ATPase domain
    2.8e-08   33.4   0.2     0.0062   16.2   0.0    2.8  2  AAA_29           P-loop containing region of AAA domain
    2.1e-06   27.5   0.0       0.03   13.9   0.0    3.0  2  AAA_25           AAA domain
    3.4e-06   27.7   0.7      0.061   13.8   0.0    3.2  3  AAA_23           AAA domain
      6e-06   26.6   0.2       0.29   11.4   0.0    3.9  3  AAA_22           AAA domain
    1.4e-05   25.0   0.1       0.84    9.3   0.0    3.9  4  AAA_15           AAA ATPase domain
    6.2e-05   22.8   3.6      0.011   15.6   0.4    2.8  2  BCA_ABC_TP_C     Branched-chain amino acid ATP-binding casset
    7.9e-05   22.5   0.0       0.15   11.7   0.0    2.5  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0001   22.2   0.0       0.48   10.3   0.0    2.7  2  RsgA_GTPase      RsgA GTPase
    0.00014   21.9   0.0       0.84    9.7   0.0    3.1  2  AAA_14           AAA domain
    0.00018   22.1   0.1       0.34   11.4   0.0    3.0  2  AAA_18           AAA domain
     0.0002   21.6   0.0       0.82    9.8   0.0    2.9  2  AAA_33           AAA domain
    0.00029   20.8   1.1       0.93    9.4   0.0    3.2  2  APS_kinase       Adenylylsulphate kinase
    0.00033   20.6   0.1       0.13   12.1   0.0    2.9  2  ATPase_2         ATPase domain predominantly from Archaea
    0.00041   19.8   0.1       0.33   10.3   0.0    3.0  3  ATPase           KaiC
    0.00051   19.4   0.0       0.48    9.6   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00074   19.8   5.7      0.039   14.3   0.3    3.7  3  DnaJ_CXXCXGXG    DnaJ central domain
    0.00081   19.3   1.1        9.8    6.1   0.0    3.8  3  NTPase_1         NTPase
    0.00088   18.9   0.4       0.51    9.9   0.1    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00098   18.9   0.3        2.2    8.0   0.0    3.2  3  AAA_24           AAA domain
     0.0024   17.0   0.1        1.6    7.7   0.0    2.4  2  T2SSE            Type II/IV secretion system protein
     0.0032   17.4   0.1        1.8    8.4   0.0    2.8  3  NACHT            NACHT domain
     0.0087   16.4   0.0        4.5    7.7   0.0    3.1  2  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.011   15.4   0.5         13    5.5   0.0    3.4  3  AAA_30           AAA domain
      0.037   13.2   0.0         11    5.1   0.0    3.2  3  NB-ARC           NB-ARC domain
      0.044   14.0   0.1        5.1    7.3   0.0    2.9  2  AAA_28           AAA domain
      0.066   12.2   0.0         11    4.9   0.0    2.5  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.13   11.7   0.0         18    4.8   0.0    2.9  3  AAA_7            P-loop containing dynein motor region
       0.14   12.2   0.1         31    4.7   0.0    3.4  3  MMR_HSR1         50S ribosome-binding GTPase
       0.21   11.7   1.0         29    4.7   0.0    3.5  3  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.27   10.3   0.7         10    5.2   0.1    2.6  3  DAP3             Mitochondrial ribosomal death-associated pro
       0.61   10.1   9.5        6.2    6.9   0.4    3.8  4  Anti-TRAP        Tryptophan RNA-binding attenuator protein in


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 !  101.1   0.2   6.8e-32   3.3e-29       1     107 [.     130     252 ..     130     254 .. 0.82
   2 ?   -2.0   0.0       7.5   3.6e+03      80     107 ..     535     562 ..     525     564 .. 0.82

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 6.8e-32
                        UvrA_inter   1 QsveqIvdqilkl.................eegtkllilaPvvrerkgefkkllenlkkkGfvrvriDgeiydlded 60 
                                       Qs+e I+ +il+                  e+g +++ilaPv+r++kg++ +ll++l+ +G+ rvr++g+i ++de+
  gi|330506712|ref|YP_004383140.1| 130 QSPERIAVSILEEikgkepegtegtkemkgEDGGMITILAPVIRQKKGTYGQLLKDLNAEGYARVRLNGQIQRTDEE 206
                                       66677777777553333433333333333245567****************************************** PP

                        UvrA_inter  61 ieldknkkhsievvvDrlvvkkeersrlaesvetAlklgeglvivse 107
                                       ield++kkh+i+vv+Drl  ++ ++srl e++e+Alk +eglv+v +
  gi|330506712|ref|YP_004383140.1| 207 IELDRYKKHDIDVVIDRLDPRE-DKSRLVEAIEKALKKTEGLVYVLH 252
                                       *******************975.68*******************976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.5
                        UvrA_inter  80 vkkeersrlaesvetAlklgeglvivse 107
                                       +++++++rl e +++  +lg+ l++v++
  gi|330506712|ref|YP_004383140.1| 535 LHQRDNARLIETLKKLRDLGNTLIVVEH 562
                                       4566789**************9999986 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 ?    2.3   0.0      0.42     2e+02      78     108 ..      35      65 ..      24      67 .. 0.86
   2 !   91.3   0.0     1e-28   4.9e-26       1     110 []     303     413 ..     303     413 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.42
                                       .......---HHHHHHHHHH-------HHHH CS
                     UvrA_DNA-bind  78 krsyektfeGvipnlerryreteSeavreel 108
                                       + + +  f+ +  + +rry e+ S ++r+ l
  gi|330506712|ref|YP_004383140.1|  35 SGKSTLAFDTIYAEGQRRYVESLSAYARQFL 65 
                                       56777889999*****************966 PP

  == domain 2  score: 91.3 bits;  conditional E-value: 1e-28
                                       -S----.-----------GGG..TT-HHHHHHHHHHHTTTS------------S-THHHHH----............ CS
                     UvrA_DNA-bind   1 DpdlvvpdpslslaegAiapwsskkssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgee.kikveyksgg 76 
                                       Dp+l++pd+++ +a+gA+a +++  + ++ q l+ava+h+ +d+ tp+k+L++eq d+l+yGs+e+ +++++ k+g 
  gi|330506712|ref|YP_004383140.1| 303 DPELIIPDRDRCIADGAVALYRNIIDGWRGQHLAAVAKHFSFDIFTPIKDLTPEQYDALMYGSKEKiRMNMSMKNGD 379
                                       9**************************************************************98524455666699 PP

                                       ........---HHHHHHHHHH-------HHHHHH CS
                     UvrA_DNA-bind  77 rkrsyektfeGvipnlerryreteSeavreelek 110
                                         +s++ ++eG+ip+  r y +t Se+ reelek
  gi|330506712|ref|YP_004383140.1| 380 VYWSHNSQWEGLIPQSIRLYSQTASEYRREELEK 413
                                       99******************************97 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   2.7e-05     0.013       1      28 [.      14      41 ..      14      55 .. 0.91
   2 ?   -1.1   0.0       5.1   2.5e+03      24      48 ..     230     254 ..     229     285 .. 0.80
   3 !   15.9   0.0   2.9e-05     0.014      68     136 ..     458     532 ..     367     533 .. 0.73
   4 !   34.8   0.1   4.2e-11     2e-08       1     136 [.     637     873 ..     637     874 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.7e-05
                                      EEEEEEEEETTSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  1 lknvslklkegekvaivGenGaGKStLl 28
                                      lkn+++ l ++++++i+G +G+GKStL+
  gi|330506712|ref|YP_004383140.1| 14 LKNIDVLLPRDSLIVITGVSGSGKSTLA 41
                                      79************************95 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5.1
                                       HHHHHHHHTTSS--SEEEEEETTCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  24 KStLlkllagllkpteGeilldgkd 48 
                                       KS L++++ + lk+teG + +  ++
  gi|330506712|ref|YP_004383140.1| 230 KSRLVEAIEKALKKTEGLVYVLHEN 254
                                       99***************99665444 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 2.9e-05
                                       --S-TTSBHHHHHHHTC.HHHHHHHSTTGG...TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSS..EEEEESTT CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran  68 pqlfpeltvrenesdee.iekalsklglke...lkdtvvksspssLSgGqkqrvalarallkkpk..llllDEpt 136
                                        +l ++l+v+e e  ++ +++++s+lg  e   l   ++++++ sLSgG+ qr+ la  + ++ +  l++lDEp+
  gi|330506712|ref|YP_004383140.1| 458 MNLEEKLSVKEGEIARQvLKEIRSRLGFLEhvgLGYLTLSRNAGSLSGGEAQRIRLATQIGSNLTgvLYVLDEPS 532
                                       4455555555554444445555555555444445556666777****************99886555999***95 PP

  == domain 4  score: 34.8 bits;  conditional E-value: 4.2e-11
                                       EEEEEEEEETTSEEEEEESTTSSHHHHH.HHHTTSS--.......SEEEE................EETTCEGGGB- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.......xxxxx................xxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLl.kllagllkp.......teGei................lldgkdlkeqe 53 
                                       lk++++++  g +++++G +G+GKStL+  +l++ l +       t                     +d+ ++ +  
  gi|330506712|ref|YP_004383140.1| 637 LKEIDVDIPLGILTVVTGVSGSGKSTLIyDTLYRALMKriyhsseT---PgehdgirfdtevdkviVIDQSPIGR-- 708
                                       7899**********************98445665555422222332...12223333333333333222222222.. PP

                                       HHHCCHCEEEE-SS--S-TTSBHHHH................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                          ABC_tran  54 leslrkeigvlpqepqlfpeltvren................................................... 79 
                                                            t r+n                                                   
  gi|330506712|ref|YP_004383140.1| 709 ---------------------TPRSNpatytkvfdpirqayaqtkearirgyksgrfsfnvqggrceschgdgliki 764
                                       .....................2333333334444445555666666677788999********************** PP

                                       ....................................HHHTCHHHHHHHSTTGG.............TTCBGESTTSG CS
                                       ....................................xxxxxxxxxxxxxxxxx.............xxxxxxxxxxx RF
                          ABC_tran  80 ....................................esdeeiekalsklglke.............lkdtvvkssps 107
                                                                           + d  +e+a+++++++              l   ++++s +
  gi|330506712|ref|YP_004383140.1| 765 emnflpdvyieceeckgrrynqetlevkykgksiaeALDMTVEEAREHFENIPairskldtllgvgLGYIKLGQSST 841
                                       *****************99999999888888777775555577777777777777777777778778888888899* PP

                                       GS-HHHHHHHHHHHHHHHT...SSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxx...xxxxxxxxxx RF
                          ABC_tran 108 sLSgGqkqrvalarallkk...pkllllDEpt 136
                                       +LSgG+ qr++l r l+kk   ++++llDEpt
  gi|330506712|ref|YP_004383140.1| 842 TLSGGEAQRIKLTRELAKKgtgRTIYLLDEPT 873
                                       *****************9855579*******9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.13        61       1      15 [.      26      40 ..      26      47 .. 0.92
   2 ?   -1.3   0.1       3.2   1.5e+03     179     231 ..     194     257 ..     177     262 .. 0.75
   3 !   15.4   0.0   2.6e-05     0.012     116     295 ..     387     560 ..     367     567 .. 0.90
   4 ?    6.8   0.0     0.011       5.2       1      17 [.     649     665 ..     649     687 .. 0.94
   5 !   12.2   0.0   0.00024      0.12     254     298 ..     857     904 ..     843     909 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.13
                            AAA_21  1 lnvliGpNgsGKSnL 15
                                      l v++G  gsGKS+L
  gi|330506712|ref|YP_004383140.1| 26 LIVITGVSGSGKSTL 40
                                      579***********8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.2
                            AAA_21 179 akekrllqrlvrslklveielsdlgegeeliasvderlrer...........gvvflengdgqe 231
                                        ++++++qr   ++ l++ + +d++++++  +++ + +r +           g+v++ +++g e
  gi|330506712|ref|YP_004383140.1| 194 VRLNGQIQRTDEEIELDRYKKHDIDVVIDRLDPREDKSRLVeaiekalkkteGLVYVLHENGEE 257
                                       5677888889999999999999999999988888888888888888888888555555555554 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 2.6e-05
                            AAA_21 116 rgirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke........rigllnifadyfgfakekrl 184
                                       + +  + ++ +l++ + se+ +++ +k+   ++++a++ + l+++ +          + ++l+ +  + +f+++ + 
  gi|330506712|ref|YP_004383140.1| 387 QWEGLIPQSIRLYSQTASEYRREELEKFMRVLPCPACEGKRLKEKVLAVriqdlsivDVANLSVSECNEFFMNLEEK 463
                                       556677899999***********************************999999999999999999999999999999 PP

                            AAA_21 185 lqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparel...SdGtkrllalltallralkkg 258
                                       l+  ++++ ++ ++   ++                  ++++ g g+ + +r++   S G  + ++l+t + + l   
  gi|330506712|ref|YP_004383140.1| 464 LSVKEGEIARQVLKEIRSR----------------LGFLEHVGLGYLTLSRNAgslSGGEAQRIRLATQIGSNLTG- 523
                                       9999999999999998887................999999999999998888888****9999**********99. PP

                            AAA_21 259 sllliDEpEngLHPkllrrllellkelsrngaQvilt 295
                                        l+++DEp  gLH +  +rl+e lk+l++ g  +i++
  gi|330506712|ref|YP_004383140.1| 524 VLYVLDEPSIGLHQRDNARLIETLKKLRDLGNTLIVV 560
                                       9*************999*******9999988888875 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.011
                            AAA_21   1 lnvliGpNgsGKSnLLd 17 
                                       l+v++G  gsGKS+L++
  gi|330506712|ref|YP_004383140.1| 649 LTVVTGVSGSGKSTLIY 665
                                       79*************85 PP

  == domain 5  score: 12.2 bits;  conditional E-value: 0.00024
                            AAA_21 254 alkkg...sllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       ++kkg   +++l+DEp +gLH   +++l+ +l++l ++g  v++  H+
  gi|330506712|ref|YP_004383140.1| 857 LAKKGtgrTIYLLDEPTTGLHFDDVKKLIHVLDDLVSKGNTVVVIEHN 904
                                       45555667************************8888888888886555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0085       4.1       3      46 ..       2      46 ..       1      65 [. 0.74
   2 !   12.6   0.0   0.00014     0.066     135     211 ..     245     576 ..     137     581 .. 0.73
   3 ?    4.5   0.0     0.041        20      26      42 ..     649     665 ..     631     676 .. 0.81
   4 !   10.9   0.0   0.00045      0.22     135     211 ..     835     917 ..     699     923 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0085
                                      EEEEEESETTEECEEEEEET.TSSEEEEEESTTSSHHHH.HHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxx RF
                             SMC_N  3 krleienFksyagktvilpf.sksftaivGpNGSGKsnl.ldAilF 46
                                      k+++i++ +  + k++++ +  +s+ +i+G  GSGKs l +d i +
  gi|330506712|ref|YP_004383140.1|  2 KSIVIKGAREHNLKNIDVLLpRDSLIVITGVSGSGKSTLaFDTI-Y 46
                                      667777777776666665441567999**********9834555.5 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                                       T............................................................................ CS
                                       x............................................................................ RF
                             SMC_N 135 e............................................................................ 135
                                       e                                                                            
  gi|330506712|ref|YP_004383140.1| 245 Eglvyvlhengeervysarmacpvcglvfeelqprmfsfnspfgacescnglgfrmefdpeliipdrdrciadgava 321
                                       26666666666666666666666666666666666666666666666666666666666666666666666666666 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|330506712|ref|YP_004383140.1| 322 lyrniidgwrgqhlaavakhfsfdiftpikdltpeqydalmygskekirmnmsmkngdvywshnsqweglipqsirl 398
                                       66666666666666666666666666667777777777777777777777777777777777777777777777777 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|330506712|ref|YP_004383140.1| 399 ysqtaseyrreelekfmrvlpcpacegkrlkekvlavriqdlsivdvanlsvsecneffmnleeklsvkegeiarqv 475
                                       77777777777777777777777777777777777777777777777888888888888888888888888888888 PP

                                       ..........................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                       ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ..........................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                                                 +LSgGe + + la    i +     ly+lDe    L ++  +++ e lk+ 
  gi|330506712|ref|YP_004383140.1| 476 lkeirsrlgflehvglgyltlsrnagSLSGGEAQRIRLATQ--IGSNLTGVLYVLDEPSIGLHQRDNARLIETLKKL 550
                                       888888888888888888888888889*****987777665..67777889*************************9 PP

                                       CTT.SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 187 skn.aQfivislreemlekadklvgv 211
                                       ++    +iv+ ++e++++ ad+++ +
  gi|330506712|ref|YP_004383140.1| 551 RDLgNTLIVVEHDEDTIRSADHVLDI 576
                                       98768899************998766 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.041
                                       EEEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlld 42 
                                       +t+++G  GSGKs l+ 
  gi|330506712|ref|YP_004383140.1| 649 LTVVTGVSGSGKSTLIY 665
                                       799**********9875 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00045
                                       T......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC CS
                                       x......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N 135 e......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlek 204
                                       +      +LSgGe + + l   +A +    + +yllDe    L +  vkk+ ++l+   ++   ++vi ++ ++++ 
  gi|330506712|ref|YP_004383140.1| 835 KlgqsstTLSGGEAQRIKLTRELAKKG-TGRTIYLLDEPTTGLHFDDVKKLIHVLDDLVSKgNTVVVIEHNLDVIKS 910
                                       05555558*********9999999655.5678************************7755538999*********** PP

                                       -SCEEEE CS
                                       xxxxxxx RF
                             SMC_N 205 adklvgv 211
                                       ad l+ +
  gi|330506712|ref|YP_004383140.1| 911 ADYLIDM 917
                                       *999876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.2e-05      0.02      23      68 ..      23      71 ..      10     117 .. 0.77
   2 ?    0.9   0.0       1.1   5.3e+02      37      55 ..     230     248 ..     175     274 .. 0.70
   3 !   13.3   0.0   0.00017     0.081      27      54 ..     650     677 ..     639     708 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.2e-05
                            AAA_16 23 rpelvllsGesGvGKsslv.rellralekdggif..lrgkcdql..esaip 68
                                      r +l++++G sG+GKs+l+ ++++   e+++ ++  l++ ++q+  +++ p
  gi|330506712|ref|YP_004383140.1| 23 RDSLIVITGVSGSGKSTLAfDTIYA--EGQRRYVesLSAYARQFlgQMDKP 71
                                      44899**************766664..444456666888888886666665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.1
                            AAA_16  37 Ksslvrellralekdggif 55 
                                       Ks+lv+++ +al+k++g++
  gi|330506712|ref|YP_004383140.1| 230 KSRLVEAIEKALKKTEGLV 248
                                       6666666666666664333 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 0.00017
                            AAA_16  27 vllsGesGvGKsslv.rellralekdggi 54 
                                       ++++G sG+GKs+l+ ++l+ral k+ ++
  gi|330506712|ref|YP_004383140.1| 650 TVVTGVSGSGKSTLIyDTLYRALMKR-IY 677
                                       78*************99999988887.33 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 !   14.0   0.0   6.5e-05     0.031      22      38 ..      24      40 ..      11      47 .. 0.77
   2 !   16.2   0.0   1.3e-05    0.0062      23      39 ..     647     664 ..     635     675 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.5e-05
                            AAA_29 22 kgatlltGpsGsGKSTl 38
                                      ++ +++tG sGsGKSTl
  gi|330506712|ref|YP_004383140.1| 24 DSLIVITGVSGSGKSTL 40
                                      34789***********9 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.3e-05
                            AAA_29  23 g.atlltGpsGsGKSTll 39 
                                       g  t++tG sGsGKSTl+
  gi|330506712|ref|YP_004383140.1| 647 GiLTVVTGVSGSGKSTLI 664
                                       45899************8 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   6.2e-05      0.03      25      53 ..      16      44 ..       6      50 .. 0.85
   2 !   10.1   0.0   0.00092      0.45      29      55 ..     643     669 ..     617     685 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.2e-05
                            AAA_25 25 lvkgllpagelallaGapgtGKttlaldl 53
                                       ++ llp+++l++++G +g+GK+tla d 
  gi|330506712|ref|YP_004383140.1| 16 NIDVLLPRDSLIVITGVSGSGKSTLAFDT 44
                                      56779*********************986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00092
                            AAA_25  29 llpagelallaGapgtGKttlaldlal 55 
                                        +p+g l++++G +g+GK+tl +d  +
  gi|330506712|ref|YP_004383140.1| 643 DIPLGILTVVTGVSGSGKSTLIYDTLY 669
                                       479******************999765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   0.00013     0.061       1      35 [.       3      40 ..       3      44 .. 0.92
   2 ?   -0.4   0.0       2.9   1.4e+03     140     182 ..     199     244 ..      95     253 .. 0.65
   3 !   10.2   0.0    0.0016      0.77      20      47 ..     648     676 ..     627     827 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00013
                            AAA_23  1 kLkienfrsfrdqeidF...skgltlItGpNGaGKTTi 35
                                      ++ i++ r ++ ++id     + l +ItG  G+GK+T+
  gi|330506712|ref|YP_004383140.1|  3 SIVIKGAREHNLKNIDVllpRDSLIVITGVSGSGKSTL 40
                                      6889999999999999989999***************8 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.9
                            AAA_23 140 qer...feefelkdkkerleelekeleeledekkllekleqekeke 182
                                       q +   +e +++  kk  ++ +++ l+  ed+ +l+e+ e++++k 
  gi|330506712|ref|YP_004383140.1| 199 QIQrtdEEIELDRYKKHDIDVVIDRLDPREDKSRLVEAIEKALKKT 244
                                       2223322222233333345555555555555555555555544444 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0016
                            AAA_23  20 gltlItGpNGaGKTTil.dAiklaLyget 47 
                                        lt++tG  G+GK+T++ d +  aL  + 
  gi|330506712|ref|YP_004383140.1| 648 ILTVVTGVSGSGKSTLIyDTLYRALMKRI 676
                                       49**************9666666666654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0    0.0006      0.29       5      32 ..      24      51 ..      22     113 .. 0.74
   2 ?    1.2   0.0      0.87   4.2e+02      43      96 ..     165     250 ..     139     253 .. 0.74
   3 !    8.8   0.0    0.0039       1.9       8      23 ..     650     665 ..     647     732 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0006
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldee 32
                                      ++++v+tG sG+GK+tl+    +   ++
  gi|330506712|ref|YP_004383140.1| 24 DSLIVITGVSGSGKSTLAFDTIYAEGQR 51
                                      679*************986655555555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.87
                            AAA_22  43 vfvtlpsstsskdllrellralglelka.................................erlsseellealeqal 86 
                                       +++ +p+    k  + +ll++l+ e+ a                                 +r ++++l+ea+e+al
  gi|330506712|ref|YP_004383140.1| 165 ITILAPVIRQKKGTYGQLLKDLNAEGYArvrlngqiqrtdeeieldrykkhdidvvidrldPREDKSRLVEAIEKAL 241
                                       5555555566666677777777777777777777777777777777777888888888899999************* PP

                            AAA_22  87 raravielli 96 
                                       +++    + +
  gi|330506712|ref|YP_004383140.1| 242 KKTEG-LVYV 250
                                       99887.6665 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0039
                            AAA_22   8 lvvtGesGtGKTtllr 23 
                                       +vvtG sG+GK+tl+ 
  gi|330506712|ref|YP_004383140.1| 650 TVVTGVSGSGKSTLIY 665
                                       79***********974 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       4.4   2.1e+03      19      39 ..      19      40 ..       2      41 .. 0.77
   2 ?    5.7   0.0     0.022        11     321     357 ..     520     556 ..     498     566 .. 0.81
   3 ?    4.8   0.0      0.04        19      11      41 ..     637     665 ..     635     747 .. 0.80
   4 !    9.3   0.0    0.0017      0.84     319     361 ..     859     901 ..     847     908 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.4
                            AAA_15 19 idlsee.ltvliGkNnsGKSsi 39
                                      + l  + l v+ G  +sGKS++
  gi|330506712|ref|YP_004383140.1| 19 VLLPRDsLIVITGVSGSGKSTL 40
                                      444444499***********97 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.022
                            AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnkt 357
                                       + + v+++++EP + LH      li++lk+l + ++t
  gi|330506712|ref|YP_004383140.1| 520 NLTGVLYVLDEPSIGLHQRDNARLIETLKKLRDLGNT 556
                                       445699************************9888773 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.04
                            AAA_15  11 FRslkdveidlseeltvliGkNnsGKSsile 41 
                                        + ++ v+i+l   ltv+ G  +sGKS++++
  gi|330506712|ref|YP_004383140.1| 637 LKEID-VDIPLGI-LTVVTGVSGSGKSTLIY 665
                                       55555.7899999.**************874 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0017
                            AAA_15 319 ekeeknvilliEEPEahLHpqaqkvlikllkelandnktQvii 361
                                       +k +   i+l++EP + LH +  k li+ l +l+++++t v+i
  gi|330506712|ref|YP_004383140.1| 859 KKGTGRTIYLLDEPTTGLHFDDVKKLIHVLDDLVSKGNTVVVI 901
                                       4447788******************************954443 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 !   15.6   0.4   2.3e-05     0.011       2      16 ..     587     601 ..     587     601 .. 0.94
   2 !    7.5   0.2    0.0083         4       1      11 [.     927     937 ..     927     939 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-05
                      BCA_ABC_TP_C   2 vIAeGtPaEvrndPr 16 
                                       v AeGtP+E+ ++P+
  gi|330506712|ref|YP_004383140.1| 587 VVAEGTPEEIEANPK 601
                                       78************6 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0083
                      BCA_ABC_TP_C   1 rvIAeGtPaEv 11 
                                       rv A+GtP++v
  gi|330506712|ref|YP_004383140.1| 927 RVVATGTPEQV 937
                                       89********9 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0038       1.8       1      20 [.      27      46 ..      27      89 .. 0.70
   2 !   11.7   0.0   0.00032      0.15       1      20 [.     650     669 ..     650     683 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0038
                   Viral_helicase1  1 ivvhGvpGcGKStlirkllr 20
                                      iv+ Gv G+GKStl  + + 
  gi|330506712|ref|YP_004383140.1| 27 IVITGVSGSGKSTLAFDTIY 46
                                      79***********8765554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00032
                   Viral_helicase1   1 ivvhGvpGcGKStlirkllr 20 
                                       +vv Gv G+GKStli + l 
  gi|330506712|ref|YP_004383140.1| 650 TVVTGVSGSGKSTLIYDTLY 669
                                       69*************88775 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0     0.001      0.48      82     116 ..       6      41 ..       1      60 [. 0.81
   2 !    9.0   0.0    0.0025       1.2     100     117 ..     648     665 ..     616     687 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.001
                                       --TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHH CS
                       RsgA_GTPase  82 vsaktkegleelkellkd.ktsvlvGqSGvGKStLi 116
                                       ++  ++++l+++  ll   +++v+ G SG GKStL 
  gi|330506712|ref|YP_004383140.1|   6 IKGAREHNLKNIDVLLPRdSLIVITGVSGSGKSTLA 41 
                                       555667888999998876699*************95 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0025
                                       SEEEEECSTTSSHHHHHH CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLin 117
                                        ++v+ G SG GKStLi 
  gi|330506712|ref|YP_004383140.1| 648 ILTVVTGVSGSGKSTLIY 665
                                       6799************95 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0017      0.84       4      27 ..      26      49 ..      23      74 .. 0.84
   2 !    8.6   0.0    0.0037       1.8       5      40 ..     650     682 ..     647     726 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                            AAA_14  4 ilvitGaRrvGKTtllkqlikell 27
                                      ++vitG+  +GK+tl+++ i+ + 
  gi|330506712|ref|YP_004383140.1| 26 LIVITGVSGSGKSTLAFDTIYAEG 49
                                      79****************998765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0037
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldd 40 
                                        v+tG+  +GK+tl+++ +++ l    + +y + ++
  gi|330506712|ref|YP_004383140.1| 650 TVVTGVSGSGKSTLIYDTLYRAL---MKRIYHSSET 682
                                       69**************9999888...5566665555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00071      0.34       1      15 [.      27      41 ..      27      56 .. 0.95
   2 ?    7.2   0.0     0.014       6.8       2      15 ..     651     664 ..     651     704 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00071
                            AAA_18  1 IlltGtpGvGKttla 15
                                      I++tG++G+GK+tla
  gi|330506712|ref|YP_004383140.1| 27 IVITGVSGSGKSTLA 41
                                      99***********98 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.014
                            AAA_18   2 lltGtpGvGKttla 15 
                                       ++tG++G+GK+tl 
  gi|330506712|ref|YP_004383140.1| 651 VVTGVSGSGKSTLI 664
                                       59**********85 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0017      0.82       1      17 [.      26      42 ..      26     101 .. 0.83
   2 !    8.6   0.0     0.004         2       1      17 [.     649     665 ..     649     739 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0017
                            AAA_33  1 lvllvGlpGsGKstlae 17
                                      l+++ G++GsGKstla 
  gi|330506712|ref|YP_004383140.1| 26 LIVITGVSGSGKSTLAF 42
                                      78999**********95 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.004
                            AAA_33   1 lvllvGlpGsGKstlae 17 
                                       l+++ G++GsGKstl+ 
  gi|330506712|ref|YP_004383140.1| 649 LTVVTGVSGSGKSTLIY 665
                                       67899*********964 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0019      0.93       4      21 ..      26      43 ..      23      56 .. 0.85
   2 !    8.6   0.0    0.0034       1.6       4      38 ..     649     684 ..     646     697 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0019
                                      EEEEESSTTSSHHHHHHH CS
                        APS_kinase  4 vvwltGlsgsGKstiana 21
                                       + +tG+sgsGKst+a+ 
  gi|330506712|ref|YP_004383140.1| 26 LIVITGVSGSGKSTLAFD 43
                                      689************974 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0034
                                       EEEEESSTTSSHHHHHH.HHHHHHHHTT--EEEEEH CS
                        APS_kinase   4 vvwltGlsgsGKstian.alekkLvekgisvylLdG 38 
                                          +tG+sgsGKst+ + +l ++L+++ ++     G
  gi|330506712|ref|YP_004383140.1| 649 LTVVTGVSGSGKSTLIYdTLYRALMKRIYHSSETPG 684
                                       5578**********7652799999999887766555 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 !   12.1   0.0   0.00027      0.13       4      86 ..      10      87 ..       9     116 .. 0.66
   2 ?    5.2   0.0     0.035        17      22      51 ..     649     678 ..     633     716 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                          ATPase_2  4 RekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal 82
                                      Re  lk++  +l r  ++ ++i+G  gsGK++L    i    +   yv  ++a  ++++ ++d+   e ++ + l+ a+
  gi|330506712|ref|YP_004383140.1| 10 REHNLKNIDVLLPR--DSLIVITGVSGSGKSTLAFDTIYAEGQ-RRYVESLSAYARQFLGQMDKP--EVDSIDGLSPAI 83
                                      999*********99..99***************9999988744.345555666666666666665..555555555555 PP

                          ATPase_2 83 giav 86
                                      +i+ 
  gi|330506712|ref|YP_004383140.1| 84 SIEQ 87
                                      4433 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.035
                          ATPase_2  22 iyfiYGpegsGKtaLlkeiienledkdkyv 51 
                                         +++G  gsGK++L+   + + + k  y+
  gi|330506712|ref|YP_004383140.1| 649 LTVVTGVSGSGKSTLIYDTLYRALMKRIYH 678
                                       579*************98888776666555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00068      0.33      16      41 ..      21      46 ..      14      56 .. 0.86
   2 ?   -2.6   0.0       5.9   2.9e+03     194     226 ..     405     445 ..     395     448 .. 0.72
   3 ?    5.8   0.0     0.015       7.4      16      44 ..     644     672 ..     637     679 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00068
                            ATPase 16 ipegrvvlitGepGtGKtifalqFli 41
                                      +p+++ + itG++G+GK+++a   ++
  gi|330506712|ref|YP_004383140.1| 21 LPRDSLIVITGVSGSGKSTLAFDTIY 46
                                      699*****************976665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.9
                            ATPase 194 e.......elvRtleivkmRgtkhskkehpfeIte.egikv 226
                                       e       ++ R+l    + g++ + k++   I++ +++ v
  gi|330506712|ref|YP_004383140.1| 405 EyrreeleKFMRVLPCPACEGKRLKEKVLAVRIQDlSIVDV 445
                                       44555455788888888999999999999999999888877 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.015
                            ATPase  16 ipegrvvlitGepGtGKtifalqFlikga 44 
                                       ip g  + +tG++G+GK+++    l++ +
  gi|330506712|ref|YP_004383140.1| 644 IPLGILTVVTGVSGSGKSTLIYDTLYRAL 672
                                       7888899************9887777665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00099      0.48       2      25 ..      25      48 ..      24      71 .. 0.82
   2 !    7.2   0.0    0.0052       2.5       4      25 ..     650     671 ..     648     692 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00099
                           DUF2075  2 avvlVtGvaGtGKtvvllnllael 25
                                      +++++tGv+G+GK+ +++  +++ 
  gi|330506712|ref|YP_004383140.1| 25 SLIVITGVSGSGKSTLAFDTIYAE 48
                                      589**************9998875 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0052
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                        +VtGv+G+GK+ +    l+++
  gi|330506712|ref|YP_004383140.1| 650 TVVTGVSGSGKSTLIYDTLYRA 671
                                       69************99999987 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3      0.25   1.2e+02      42      52 ..     288     298 ..     253     305 .. 0.57
   2 ?    2.2   0.0       0.5   2.4e+02      17      24 ..     420     427 ..     404     455 .. 0.67
   3 !   14.3   0.3     8e-05     0.039      16      51 ..     752     783 ..     739     790 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.25
                     DnaJ_CXXCXGXG  42 stCpeCeGtGk 52 
                                         C++C+G G 
  gi|330506712|ref|YP_004383140.1| 288 GACESCNGLGF 298
                                       35666666554 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.5
                     DnaJ_CXXCXGXG  17 CktCkGsG 24 
                                       C++C+G+ 
  gi|330506712|ref|YP_004383140.1| 420 CPACEGKR 427
                                       55555554 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 8e-05
                     DnaJ_CXXCXGXG  16 tCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtG 51 
                                       +C++C+G G ++ e++ +      +  +C+eC+G+ 
  gi|330506712|ref|YP_004383140.1| 752 RCESCHGDGLIKIEMN-F---LPDVYIECEECKGRR 783
                                       6********7666653.4...4456689*****986 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0      0.02       9.8       2      17 ..      27      42 ..      26      52 .. 0.87
   2 ?    3.8   0.0     0.097        47      94     137 ..     213     256 ..     178     268 .. 0.81
   3 ?    5.6   0.0     0.028        13       3      18 ..     651     666 ..     649     677 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.02
                                      EEEE--TTSSHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvk 17
                                      ++iTG +G+GK+Tl  
  gi|330506712|ref|YP_004383140.1| 27 IVITGVSGSGKSTLAF 42
                                      79***********975 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.097
                                       HHH-E.EEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-- CS
                          NTPase_1  94 seadv.iviDEiGkmElkskkfkeaveevLksekpvlavihrrkd 137
                                       ++ d+ +viD   + E ks+ + ea+e++Lk+ + ++ v+h++ +
  gi|330506712|ref|YP_004383140.1| 213 KKHDIdVVIDRLDPREDKSR-LVEAIEKALKKTEGLVYVLHENGE 256
                                       55665478999999999886.6799****************9954 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.028
                                       EEE--TTSSHHHHHHH CS
                          NTPase_1   3 fiTGppGvGKtTlvkk 18 
                                       ++TG +G+GK+Tl+  
  gi|330506712|ref|YP_004383140.1| 651 VVTGVSGSGKSTLIYD 666
                                       79***********964 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0      0.01       4.9       3      23 ..      27      47 ..      25      55 .. 0.78
   2 !    9.9   0.1    0.0011      0.51       2      23 ..     649     670 ..     648     677 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
                                      EEEEESTTCCHHHHHHHHHCT CS
                              cobW  3 tvltGflGsGKTtLlnhllen 23
                                      +v+tG  GsGK+tL   ++  
  gi|330506712|ref|YP_004383140.1| 27 IVITGVSGSGKSTLAFDTIYA 47
                                      89************8877744 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                                       EEEEEESTTCCHHHHHHHHHCT CS
                              cobW   2 vtvltGflGsGKTtLlnhllen 23 
                                        tv+tG  GsGK+tL+  +l +
  gi|330506712|ref|YP_004383140.1| 649 LTVVTGVSGSGKSTLIYDTLYR 670
                                       589*************999844 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.011       5.3       5      20 ..      27      42 ..      24      51 .. 0.90
   2 ?   -1.0   0.0       2.4   1.2e+03     110     132 ..     542     564 ..     534     571 .. 0.79
   3 !    8.0   0.0    0.0045       2.2       6      44 ..     651     689 ..     647     747 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                            AAA_24  5 iliyGpsgiGKTtlak 20
                                      i+i+G sg+GK+tla 
  gi|330506712|ref|YP_004383140.1| 27 IVITGVSGSGKSTLAF 42
                                      89************96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.4
                            AAA_24 110 efrrllkklqelrknvifiahek 132
                                       +++++lkkl++l+++ i++ h +
  gi|330506712|ref|YP_004383140.1| 542 RLIETLKKLRDLGNTLIVVEHDE 564
                                       56788888999999999998865 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0045
                            AAA_24   6 liyGpsgiGKTtlakelgpkplfidtekGlksldadkfp 44 
                                       +++G sg+GK+tl++   +++l+  + +++     +++ 
  gi|330506712|ref|YP_004383140.1| 651 VVTGVSGSGKSTLIYDTLYRALMKRIYHSSETPGEHDGI 689
                                       899************998999987666666555555544 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 !    7.7   0.0    0.0034       1.6     126     147 ..      21      42 ..       2      52 .. 0.75
   2 !    6.7   0.0    0.0068       3.3     132     150 ..     650     668 ..     627     678 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0034
                             T2SSE 126 vrerglilvsGgTgsGKttlly 147
                                       + +  li+++G  gsGK+tl+ 
  gi|330506712|ref|YP_004383140.1|  21 LPRDSLIVITGVSGSGKSTLAF 42 
                                       446689*************974 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0068
                             T2SSE 132 ilvsGgTgsGKttllyall 150
                                        +v+G  gsGK+tl+y  l
  gi|330506712|ref|YP_004383140.1| 650 TVVTGVSGSGKSTLIYDTL 668
                                       68*************9776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0038       1.8       2      18 ..      26      42 ..      25      68 .. 0.86
   2 ?   -1.9   0.0       5.6   2.7e+03      16      45 ..     322     353 ..     320     362 .. 0.78
   3 ?    5.4   0.0     0.032        15       3      17 ..     650     664 ..     649     678 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0038
                                      CEEEEC-TTTCHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlq 18
                                      l++++G +GsGK+tL+ 
  gi|330506712|ref|YP_004383140.1| 26 LIVITGVSGSGKSTLAF 42
                                      799************85 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.6
                                       HHHHHHHHHCTS-SCCCC..-SEEEEEETTTT CS
                             NACHT  16 Llqklalawaegklpqga..fklvFflslrel 45 
                                       L + +++ w+ ++l ++a  f++ +f + ++l
  gi|330506712|ref|YP_004383140.1| 322 LYRNIIDGWRGQHLAAVAkhFSFDIFTPIKDL 353
                                       7789***********99966666667666665 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.032
                                       EEEEC-TTTCHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLl 17 
                                        +++G +GsGK+tL+
  gi|330506712|ref|YP_004383140.1| 650 TVVTGVSGSGKSTLI 664
                                       689**********97 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.066        32       1      17 [.      27      43 ..      27      68 .. 0.84
   2 !    7.7   0.0    0.0092       4.5       2      26 ..     651     676 ..     650     703 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.066
                      RNA_helicase  1 iwlyGpsgeGKStlake 17
                                      i+++G sg GKStla +
  gi|330506712|ref|YP_004383140.1| 27 IVITGVSGSGKSTLAFD 43
                                      789***********986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0092
                      RNA_helicase   2 wlyGpsgeGKStlake.Lakallkkl 26 
                                       +++G sg GKStl+++ L +al+k++
  gi|330506712|ref|YP_004383140.1| 651 VVTGVSGSGKSTLIYDtLYRALMKRI 676
                                       689**********9987999999888 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.03        14      17      34 ..      23      40 ..      17      63 .. 0.84
   2 ?    5.5   0.0     0.027        13      20      36 ..     649     665 ..     647     678 .. 0.84
   3 ?   -0.5   0.0       1.8   8.7e+02      68     135 ..     876     944 ..     851     954 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.03
                            AAA_30 17 gdrvavltGpAGtGKtta 34
                                      +d + v+tG+ G+GK+t+
  gi|330506712|ref|YP_004383140.1| 23 RDSLIVITGVSGSGKSTL 40
                                      56799***********97 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.027
                            AAA_30  20 vavltGpAGtGKttalk 36 
                                       ++v+tG+ G+GK+t++ 
  gi|330506712|ref|YP_004383140.1| 649 LTVVTGVSGSGKSTLIY 665
                                       689***********984 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.8
                            AAA_30  68 ieastiakllkrlkgrarlepgtllivDEagmvdtkqlaallkaaek...agakvilvGDerQlasVeaGg 135
                                       ++ + ++kl++ l++   +++g+ ++v E  +  +k+++ l++   +   ag +v+  G ++Q a V + +
  gi|330506712|ref|YP_004383140.1| 876 LHFDDVKKLIHVLDD--LVSKGNTVVVIEHNLDVIKSADYLIDMGPEggnAGGRVVATGTPEQVAEVMESH 944
                                       555566666666664..345556666667766666666666666555332578999999999988887654 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.024        11      22      38 ..      26      42 ..      14      53 .. 0.82
   2 ?    2.9   0.0      0.11        52      23      40 ..     650     667 ..     635     682 .. 0.76
   3 ?    0.4   0.0       0.6   2.9e+02      84     150 ..     876     944 ..     865     957 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.024
                                      EEEEEESTTSSHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlak 38
                                      ++ + G  G+GK+tla 
  gi|330506712|ref|YP_004383140.1| 26 LIVITGVSGSGKSTLAF 42
                                      6889***********85 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                                       EEEEESTTSSHHHHHHHH CS
                            NB-ARC  23 valvGmgGvGKttlakqi 40 
                                         + G  G+GK+tl+ + 
  gi|330506712|ref|YP_004383140.1| 650 TVVTGVSGSGKSTLIYDT 667
                                       4578*********98665 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.6
                                       SSS-STTSHHHHHHHHCCCTTEEEEEE...EE-SHHHH.....HHHHCHTTSEEEEEESBCCCCCCS-S- CS
                            NB-ARC  84 eekeeveslkrklvrlLltkrfllvlD...DVweeedwdkigvvlparenrlrvllTTRdeevanavsat 150
                                        ++++v++l + l  l  + ++++v+    DV ++ d+  i +     + + rv+ T   e+va+ ++ +
  gi|330506712|ref|YP_004383140.1| 876 LHFDDVKKLIHVLDDLVSKGNTVVVIEhnlDVIKSADY-LIDMGPEGGNAGGRVVATGTPEQVAEVMESH 944
                                       56666666666666666677999999888899999998.7999999999999999999999999998875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.011       5.1       2      16 ..      27      41 ..      26      88 .. 0.78
   2 ?    3.4   0.1      0.16        79       3      16 ..     651     664 ..     649     683 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                            AAA_28  2 ivitGgestGKTtll 16
                                      ivitG +++GK+tl+
  gi|330506712|ref|YP_004383140.1| 27 IVITGVSGSGKSTLA 41
                                      9*************8 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.16
                            AAA_28   3 vitGgestGKTtll 16 
                                       v+tG +++GK+tl+
  gi|330506712|ref|YP_004383140.1| 651 VVTGVSGSGKSTLI 664
                                       89**********98 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.031        15      28      46 ..      23      41 ..      10      53 .. 0.81
   2 ?    4.9   0.0     0.023        11      34      52 ..     652     671 ..     646     678 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.031
                                      -SEEEEEEE-TTSSHHHHH CS
                              MeaB 28 raqvvGltGvPGaGkstlv 46
                                      r   + +tGv G+Gkstl 
  gi|330506712|ref|YP_004383140.1| 23 RDSLIVITGVSGSGKSTLA 41
                                      566788***********85 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.023
                                       EEE-TTSSHHHHH.HHHHHH CS
                              MeaB  34 ltGvPGaGkstlv.ealgle 52 
                                       +tGv G+Gkstl+ + l   
  gi|330506712|ref|YP_004383140.1| 652 VTGVSGSGKSTLIyDTLYRA 671
                                       8**********993445555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0       0.1        48      27      55 ..      18      46 ..       5      63 .. 0.81
   2 ?    4.8   0.0     0.038        18      36      63 ..     650     678 ..     644     683 .. 0.82
   3 ?   -2.9   0.0       8.6   4.2e+03      42      88 ..     860     907 ..     858     916 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.1
                             AAA_7 27 elllknkkpvllvGptGtGKtviikdllk 55
                                      + ll ++  ++++G +G+GK++++ d++ 
  gi|330506712|ref|YP_004383140.1| 18 DVLLPRDSLIVITGVSGSGKSTLAFDTIY 46
                                      67888888999***********9988544 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.038
                             AAA_7  36 vllvGptGtGKtviikd.llkkldkekyl 63 
                                       ++++G +G+GK+++i d l ++l k+ y 
  gi|330506712|ref|YP_004383140.1| 650 TVVTGVSGSGKSTLIYDtLYRALMKRIYH 678
                                       5789*************888888776665 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 8.6
                             AAA_7  42 tGtGKtviikd.llkkldkekylsltinfsaqtsanqlqdiiesklek 88 
                                       +GtG+t+++ d  ++ l+ ++++ l+  +    s  ++  +ie +l+ 
  gi|330506712|ref|YP_004383140.1| 860 KGTGRTIYLLDePTTGLHFDDVKKLIHVLDDLVSKGNTVVVIEHNLDV 907
                                       689999988887888888888888888888888888888888877775 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.22   1.1e+02       2      15 ..      27      40 ..      26      55 .. 0.91
   2 ?   -1.6   0.0       5.8   2.8e+03      48      86 ..     525     563 ..     494     576 .. 0.61
   3 ?    4.7   0.0     0.063        31       3      20 ..     651     668 ..     650     712 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.22
                                      EEEEESTTSSHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStL 15
                                      ++i G + +GKStL
  gi|330506712|ref|YP_004383140.1| 27 IVITGVSGSGKSTL 40
                                      799**********9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.8
                                       EEEEECGGCSS.HHHHHHHHHHHHHHHHCTSEEEEEEETT CS
                          MMR_HSR1  48 ielvDtpGlie.gaseekglgkaflaleeadlillvvdas 86 
                                       ++++D p  i   ++++ +l +++++l++    l+vv+  
  gi|330506712|ref|YP_004383140.1| 525 LYVLDEPS-IGlHQRDNARLIETLKKLRDLGNTLIVVEHD 563
                                       56677776.4422344447777777777777777777644 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.063
                                       EEEESTTSSHHHHHHHHH CS
                          MMR_HSR1   3 aivGrpNvGKStLinalt 20 
                                       ++ G + +GKStLi   +
  gi|330506712|ref|YP_004383140.1| 651 VVTGVSGSGKSTLIYDTL 668
                                       689*********995433 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 ?    4.7   0.0      0.06        29       2      22 ..      27      47 ..      26      54 .. 0.78
   2 ?    0.7   0.0         1     5e+02      74     104 ..     214     244 ..      85     254 .. 0.82
   3 ?    2.2   0.1      0.37   1.8e+02       2      16 ..     650     664 ..     649     677 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.06
                                      EEEESSTTSSHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  2 aiastkGGvGKTtlaanLara 22
                                      +++ + +G+GK+tla   + a
  gi|330506712|ref|YP_004383140.1| 27 IVITGVSGSGKSTLAFDTIYA 47
                                      789999********9876655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1
                                       ..EEEEEEEEESS...-TTCHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  74 lkiagvvlnrvdgeneetllkealeelkqry 104
                                          + vv+ r d+++ + +l ea+e+ ++++
  gi|330506712|ref|YP_004383140.1| 214 KHDIDVVIDRLDPREDKSRLVEAIEKALKKT 244
                                       5667899999999999999999999998876 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.37
                                       EEEESSTTSSHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                              CbiA   2 aiastkGGvGKTtla 16 
                                       +++ + +G+GK+tl 
  gi|330506712|ref|YP_004383140.1| 650 TVVTGVSGSGKSTLI 664
                                       789999*******85 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.14        67      26      39 ..      27      40 ..      23      48 .. 0.87
   2 ?   -2.9   0.0       5.9   2.9e+03     249     276 ..     426     457 ..     371     476 .. 0.69
   3 ?    5.2   0.1     0.021        10      27      50 ..     651     674 ..     648     677 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.14
                                      EEEE-SSSSSTTTT CS
                              DAP3 26 lvltGekgsGKSvl 39
                                      +v+tG  gsGKS+l
  gi|330506712|ref|YP_004383140.1| 27 IVITGVSGSGKSTL 40
                                      69**********98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.9
                                       ................EEE-----GGGTHHHH CS
                              DAP3 249 krvaealk....gkvepieveglskeEarsll 276
                                       kr+ e++      ++++++v +ls +E ++++
  gi|330506712|ref|YP_004383140.1| 426 KRLKEKVLavriQDLSIVDVANLSVSECNEFF 457
                                       44444444466678889999999999888876 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.021
                                       EEE-SSSSSTTTTHHHHHHHGGGS CS
                              DAP3  27 vltGekgsGKSvlLlqalayAlek 50 
                                       v+tG  gsGKS+l+  +l  Al k
  gi|330506712|ref|YP_004383140.1| 651 VVTGVSGSGKSTLIYDTLYRALMK 674
                                       99************9999988876 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       2.7   1.3e+03      28      37 ..     261     270 ..     252     272 .. 0.76
   2 ?   -1.3   0.1       4.6   2.2e+03      12      20 ..     289     297 ..     288     305 .. 0.81
   3 ?    6.4   0.1     0.017       8.4      30      41 ..     417     428 ..     407     431 .. 0.83
   4 ?    6.9   0.4     0.013       6.2      12      40 ..     752     783 ..     750     786 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.7
                                       ....E-TTTT CS
                         Anti-TRAP  28 rasleCPkCs 37 
                                        a + CP C+
  gi|330506712|ref|YP_004383140.1| 261 SARMACPVCG 270
                                       6889*****6 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.6
                                       E-TTTTTTS CS
                         Anti-TRAP  12 kCdaCngsG 20 
                                       +C+ Cng G
  gi|330506712|ref|YP_004383140.1| 289 ACESCNGLG 297
                                       699999988 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.017
                                       ..E-TTTTTSSE CS
                         Anti-TRAP  30 sleCPkCsGkgl 41 
                                        l+CP+C+Gk l
  gi|330506712|ref|YP_004383140.1| 417 VLPCPACEGKRL 428
                                       69*******986 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.013
                                       E-TTTTTTSEETTE.........E-TTTTTSS CS
                         Anti-TRAP  12 kCdaCngsGkiepe...eprasleCPkCsGkg 40 
                                        C+ C+g G i+ e    p   +eC +C+G+ 
  gi|330506712|ref|YP_004383140.1| 752 RCESCHGDGLIKIEmnfLPDVYIECEECKGRR 783
                                       6********9998877879999********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (982 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); 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):              37  [number of targets reported over threshold]
# CPU time: 0.88u 0.27s 00:00:01.14 Elapsed: 00:00:00.43
# Mc/sec: 6932.11
//
Query:       gi|330506713|ref|YP_004383141.1|  [L=213]
Description: hypothetical protein MCON_0474 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); 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 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1443.01
//
Query:       gi|330506714|ref|YP_004383142.1|  [L=379]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.0    1.8e-33  116.1   0.0    1.3  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1   0.0     1e-37   1.8e-33       1     234 [.      51     309 ..      51     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 1e-37
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....................TS-BSBESSSB-HHHHHHH- CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..................aivevgadgeidvEklaalk 59 
                                       i++ +p+ ++i++alG  dk+v+ + +t+ +l      +                  + +e++++ +i +E++a l 
  gi|330506714|ref|YP_004383142.1|  51 IITRAPDEARIVIALGYGDKLVAGEQATKSCLCPMTFSNttegclecyeniidgrmpDLPEISTRYDIYFEEIARLE 127
                                       677789999*********************99999888899899999998888888888****************** PP

                                       -SEEEE-GGG...GGGHHHHHHHS-EEE----TTS...HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS- CS
                      Peripla_BP_2  60 PDlvilskglgltdedeellksgiptvivessntg...eslkeqiralgellgledeaeklvaeidsklaaaksaid 133
                                       PDl++  +     d++  ++k g+p+v+   + +    e++ ++ir+ ge+l+  d+a++l+a+ ++k+++++s ++
  gi|330506714|ref|YP_004383142.1| 128 PDLIFCGNLK---DAEAFEDKIGCPVVVLGGQGWNfgdEGYFDSIRVAGEALDARDQADELIAFAKGKVEMIESVTK 201
                                       *****99988...666667899********9999999**************************************** PP

                                       TT.-EEEEEEEETTE..EEEE-TTSTTTHHHHT.S--EES.TTT--......STT-EEE-HHHHHHH--SEEEEEEH CS
                      Peripla_BP_2 134 sekpkpvlvfggadeggyvvagsnsyigdllda.lgieni.aaesk......kseyeeisaEqilasdpdvifvsgr 202
                                       +++p+  + +++a +g+   +++  +++d++++  +++++ +a ++      +++  ++  Eqi a++pd if+s +
  gi|330506714|ref|YP_004383142.1| 202 EIDPDDRPKVYFASRGASNAFYDPKEGRDFTRTePKYDPLtIAGGNniaseiNGSTVNVALEQIIAWNPDFIFISNS 278
                                       **88888888888888888999999999998877777777666666777777************************* PP

                                       HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 203 aeadnktgleflkenpllaelpAvkngrVyal 234
                                         a n+tgl+f+k++p+la+++A+k+g+V+ +
  gi|330506714|ref|YP_004383142.1| 279 -NAGNNTGLDFIKNSPELASINAIKEGNVFNC 309
                                       .****************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2685.45
//
Query:       gi|330506715|ref|YP_004383143.1|  [L=281]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete 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   47.0   0.0    6.1e-12   46.1   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    4.5e-09   36.3   0.0    6.3e-09   35.8   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    1.4e-08   35.3   0.0    2.5e-08   34.5   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
      4e-06   27.5   0.0    1.3e-05   25.9   0.0    1.8  2  Methyltransf_12  Methyltransferase domain
    1.6e-05   24.5   0.0    2.5e-05   23.9   0.0    1.2  1  MTS              Methyltransferase small domain
    3.2e-05   23.4   0.0    4.6e-05   22.9   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.8e-05   22.6   0.0    7.9e-05   22.1   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    6.9e-05   22.0   0.0    0.00011   21.4   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00011   21.7   0.1    0.00017   21.1   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0002   21.2   0.0    0.00028   20.8   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    0.00023   20.9   0.0    0.00034   20.3   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00038   20.2   0.0    0.00056   19.7   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
    0.00061   18.9   0.0    0.00089   18.3   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
    0.00067   19.5   0.0      0.001   18.9   0.0    1.3  1  Met_10           Met-10+ like-protein
    0.00082   18.7   0.0     0.0013   18.1   0.0    1.3  1  GidB             rRNA small subunit methyltransferase G
     0.0011   18.6   0.0     0.0015   18.1   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0014   18.4   0.0     0.0021   17.9   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0035   16.7   0.0     0.0053   16.1   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0059   16.6   0.0      0.011   15.6   0.0    1.5  1  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
       0.13   11.7   0.2       0.28   10.6   0.0    1.6  2  SAM_MT           Putative SAM-dependent methyltransferase
       0.16   11.6   0.0       0.23   11.1   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.18   10.9   0.0       0.24   10.4   0.0    1.2  1  DREV             DREV 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 !   46.1   0.0   7.5e-15   6.1e-12       1      89 [.      66     151 ..      66     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 7.5e-15
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSS.STTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpf.edgsfDlvvssgalh 75 
                                       vLd+G+GtGrl++ +a+     +vt++D s++ml+  +e++++eg+ n++ +q++ e+l + e +  D+v+ss++l 
  gi|330506715|ref|YP_004383143.1|  66 VLDVGAGTGRLAIPMARIA--RSVTALDQSKGMLACLEENMAKEGIeNIRTIQKSWEELAEgEIELHDVVLSSNSLG 140
                                       9***************996..9************************************98647778999**998898 PP

                                       GSSHHHHHHHHHHH CS
                   Methyltransf_25  76 hlsdedlekalkei 89 
                                       +l+   l++ l+++
  gi|330506715|ref|YP_004383143.1| 141 VLN---LRESLAKM 151
                                       876...44445544 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   7.7e-12   6.3e-09       3      95 ..      62     149 ..      60     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 7.7e-12
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDli 78 
                                       ++ +vlD+G+GtG+l++ +a+ +++   v+ +D s+ ++   +en +k g++n++  q ++eel +  +e    D++
  gi|330506715|ref|YP_004383143.1|  62 SHETVLDVGAGTGRLAIPMARIARS---VTALDQSKGMLACLEENMAKEGIENIRTIQKSWEELAEGeIEL--HDVV 133
                                       5789****************65555...***********************************88765665..9999 PP

                   Methyltransf_31  79 lsnevl...naladpdkile 95 
                                       ls + l   n    + + l 
  gi|330506715|ref|YP_004383143.1| 134 LSSNSLgvlN----LRESLA 149
                                       9997774432....333333 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0     3e-11   2.5e-08       1      81 [.      67     148 ..      67     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 3e-11
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-T.T-EEEEEEES-CCC-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfed.nsfDlvvssevlhhve 75 
                                       LdvG+GtGrla ++a+ +++v+++D sk ml++ +e+  +eg+ +++ ++ + e+l   + +  D+v+ss++l  ++
  gi|330506715|ref|YP_004383143.1|  67 LDVGAGTGRLAIPMARIARSVTALDQSKGMLACLEENMAKEGIeNIRTIQKSWEELAEGEiELHDVVLSSNSLGVLN 143
                                       8**************999*************************************95555499********998885 PP

                                       CHHHHH CS
                   Methyltransf_11  76 dpekal 81 
                                        +++ l
  gi|330506715|ref|YP_004383143.1| 144 -LRESL 148
                                       .44444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.6e-08   1.3e-05       1      94 [.      67     156 ..      67     160 .. 0.82
   2 ?   -1.8   0.0       6.8   5.6e+03      63      78 ..     187     202 ..     165     211 .. 0.64

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.6e-08
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..ssfDlvvasnv 75 
                                       L++G+GtG+l+ ++++     ++t++D s+ +++  +e +ak++ +n   ++   ++l+   +g  +  D+v++sn 
  gi|330506715|ref|YP_004383143.1|  67 LDVGAGTGRLAIPMARI--ARSVTALDQSKGMLACLEENMAKEGIENIRTIQKSWEELA---EGeiELHDVVLSSNS 138
                                       8*************999..999***********77777777777666555555555554...44557********** PP

                   Methyltransf_12  76 lhhlkdirevldnirklLk 94 
                                       l +l ++re+l+++ ++ k
  gi|330506715|ref|YP_004383143.1| 139 LGVL-NLRESLAKMDSMAK 156
                                       ***8.89999988877765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.8
                   Methyltransf_12  63 ggssfDlvvasnvlhh 78 
                                        g+  D+ v+ n+l  
  gi|330506715|ref|YP_004383143.1| 187 FGGPADYLVIYNLLAD 202
                                       2368899999998865 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.1e-08   2.5e-05      32      89 ..      63     119 ..      53     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.1e-08
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-ST CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdv 89 
                                       +++vlD+G+G+G l++ +a+   +  vt++d+++  l++ +en++++++e +++++++ 
  gi|330506715|ref|YP_004383143.1|  63 HETVLDVGAGTGRLAIPMARIARS--VTALDQSKGMLACLEENMAKEGIEnIRTIQKSW 119
                                       568*****************8877..9**********************9866655543 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.6e-08   4.6e-05      46     133 ..      61     148 ..      42     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.6e-08
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-.T-EEEEE CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed.dsfDvvt 121
                                       ++ ++vlDv +Gtg la+ +++ +++   v+ lD ++ mL   e+ + +eg  ni+ +q + eeL + + +  Dvv 
  gi|330506715|ref|YP_004383143.1|  61 LSHETVLDVGAGTGRLAIPMARIARS---VTALDQSKGMLACLEENMAKEGIENIRTIQKSWEELAEGEiELHDVVL 134
                                       55679***************999885...899*********************************998878888875 PP

                                       E..ES-GGG-S-HH CS
                   Ubie_methyltran 122 v..sfGlrnvtDkl 133
                                          s G+ n+ + l
  gi|330506715|ref|YP_004383143.1| 135 SsnSLGVLNLRESL 148
                                       41156777766655 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   9.7e-08   7.9e-05      25     110 ..      57     144 ..      37     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.7e-08
                                       HCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE-...-GGG----S-EEE CS
                              TehB  25 avkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistaly...dineaklderydf 98 
                                       +  +++   vld+g g gr ++ ++ +   vta+d+ +  +a lee + ke ++ni+t      ++ e ++ e +d 
  gi|330506715|ref|YP_004383143.1|  57 TLGLLSHETVLDVGAGTGRLAIPMARIARSVTALDQSKGMLACLEENMAKEGIENIRTIQKsweELAEGEI-ELHDV 132
                                       556678889*************************************9999988888776550014555555.45788 PP

                                       EEEESSGGGS-G CS
                              TehB  99 ilstvvlmflea 110
                                       +ls+  l  l+ 
  gi|330506715|ref|YP_004383143.1| 133 VLSSNSLGVLNL 144
                                       888877776664 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.3e-07   0.00011      13      74 ..      45     108 ..      35     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.3e-07
                                       E--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..T CS
                            RrnaAD  13 lknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..k 74 
                                       +kn+  + + + +l l    tvl++g+G+G l  ++a +a++v++l + + +++ l++++    
  gi|330506715|ref|YP_004383143.1|  45 MKNPARATNQVATLGLLSHETVLDVGAGTGRLAIPMARIARSVTALDQSKGMLACLEENMAkeG 108
                                       566666777788888999***************************************9887333 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   2.1e-07   0.00017     161     231 ..      62     134 ..      53     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.1e-07
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk...eekadviv 231
                                       ++e+vlDvG+G+G Lai  a++ a++v+a+D  +  +   +eN+++ ++e+  +++ s e l+    e +dv++
  gi|330506715|ref|YP_004383143.1|  62 SHETVLDVGAGTGRLAIPMARI-ARSVTALDQSKGMLACLEENMAKEGIENIRTIQKSWEELAegeIELHDVVL 134
                                       679******************9.689*************************77787766665423334567776 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.4e-07   0.00028      11      93 ..      50     140 ..      36     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.4e-07
                   Methyltransf_23  11 dklerllpk.lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaa 77 
                                       ++++++++  l +   vLd+G+GtG+l+  +++   svt+ D+s  + + +e         ++++ qk+ +  + a+
  gi|330506715|ref|YP_004383143.1|  50 RATNQVATLgLLSHETVLDVGAGTGRLAIPMARIARSVTALDQSKGMLACLEenmakegieNIRTIQKSWE--ELAE 124
                                       4444444333566779****************************988887778888887776666666666..3333 PP

                   Methyltransf_23  78 epqgkfdlIvlrevle 93 
                                        + +  d++ ++++l+
  gi|330506715|ref|YP_004383143.1| 125 GEIELHDVVLSSNSLG 140
                                       3334666666666665 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.2e-07   0.00034      40     104 ..      61     123 ..      38     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.2e-07
                                       HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHH CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleal 104
                                       + +++vLD+ aG+G l++  + R a+++++++++k +++ l+en+++ ++e+ +++++++ +e +
  gi|330506715|ref|YP_004383143.1|  61 LSHETVLDVGAGTGRLAIP-MARIARSVTALDQSKGMLACLEENMAKEGIEN-IRTIQKSWEELA 123
                                       67899*************5.89***************************997.777776655554 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.8e-07   0.00056      46     141 ..      62     150 ..      42     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.8e-07
                   Methyltransf_16  46 sklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvkvevLdWgeeleedllekeev 121
                                       s+ +vl++G+GtG   + +a+     +v+  D+++ +l +l++n++ ++    +++++ + +W+ el e  +e +  
  gi|330506715|ref|YP_004383143.1|  62 SHETVLDVGAGTGRLAIPMARI--ARSVTALDQSKgMLACLEENMAKEG---IENIRTIQKSWE-ELAEGEIELH-- 130
                                       6789******************..999*99999988***********55...788999999**5.5767776665.. PP

                   Methyltransf_16 122 DlilaaDcvYledslelLvk 141
                                       D++l +  +   +  e L+k
  gi|330506715|ref|YP_004383143.1| 131 DVVLSSNSLGVLNLRESLAK 150
                                       99999976665555555554 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.1e-06   0.00089     203     263 ..      64     124 ..      51     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-06
                   tRNA_U5-meth_tr 203 gdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirlsaeelte 263
                                       + +l++  G G +++++ar  + v a + +k  ++    n+a++ i+n++ i+ s eel+e
  gi|330506715|ref|YP_004383143.1|  64 ETVLDVGAGTGRLAIPMARIARSVTALDQSKGMLACLEENMAKEGIENIRTIQKSWEELAE 124
                                       56789999**************************************************987 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.2e-06     0.001      99     164 ..      61     123 ..      31     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                                       -TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG-- CS
                            Met_10  99 eegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevi 164
                                          e+V+dv AG G +aip+a+   a+ v a d        l+en++   +e++ ++i++  +e++
  gi|330506715|ref|YP_004383143.1|  61 LSHETVLDVGAGTGRLAIPMAR--IARSVTALDQSKGMLACLEENMAKEGIENI-RTIQKSWEELA 123
                                       3579******************..88899******************9999874.57777666665 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.6e-06    0.0013      43     120 ..      59     134 ..      49     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-06
                                       GCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC..TTTTT-EE CS
                              GidB  43 ellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee..kqeeekyd 117
                                        ll+++   v+DvG+G G  +ip+a +    ++t l++++   a Lee +++ ++en++ +++  ee    e e  d
  gi|330506715|ref|YP_004383143.1|  59 GLLSHET--VLDVGAGTGRLAIPMARI--ARSVTALDQSKGMLACLEENMAKEGIENIRTIQKSWEElaEGEIELHD 131
                                       5556666..9*********9*999855..456789*******************************96555555666 PP

                                       EEE CS
                              GidB 118 vvt 120
                                       vv+
  gi|330506715|ref|YP_004383143.1| 132 VVL 134
                                       665 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.9e-06    0.0015       2      82 ..      64     140 ..      63     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.9e-06
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflS 78 
                                       +++lD+ +G+G  +i +a+  ++v a++ ++  lac ++N    g++ +i +++ +++el +  + e    d+v+ S
  gi|330506715|ref|YP_004383143.1|  64 ETVLDVGAGTGRLAIPMARIARSVTALDQSKGMLACLEENMAKEGIE-NIRTIQKSWEELAEG-EIEL--HDVVLSS 136
                                       679**************************************999885.699999999997765.4443..3777777 PP

                   Methyltransf_15  79 pPwG 82 
                                          G
  gi|330506715|ref|YP_004383143.1| 137 NSLG 140
                                       6555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.5e-06    0.0021      65     129 ..      54     115 ..      33     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-06
                                       HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEE CS
                              PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivv 129
                                        +  l l   + vL+vG+G+G l+  +ar+ ++++   +++++k + +  ++n+ k+++en+ ++
  gi|330506715|ref|YP_004383143.1|  54 QVATLGLLSHETVLDVGAGTGRLAIPMARIARSVT---ALDQSKGMLACLEENMAKEGIENIRTI 115
                                       455677889999******************99988...9*********************99765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.5e-06    0.0053      55     127 ..      55     128 ..      47     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.5e-06
                                       HTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...- CS
                              CMAS  55 leklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...k 127
                                       +  l+l   +t+Ld+G+G G l++ +++    +v +l  Sk   +  +++++++++e+ ++++   +e+l+e   +
  gi|330506715|ref|YP_004383143.1|  55 VATLGLLSHETVLDVGAGTGRLAIPMARI-ARSVTALDQSKGMLACLEENMAKEGIENIRTIQK-SWEELAEgeiE 128
                                       5678888999**************99987.889****************************986.69*99986553 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.4e-05     0.011      15      70 ..      63     115 ..      54     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                   Methyltransf_18  15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievr 70 
                                       +++v+D+G+  g l+i ++  ++a++v+a D ++g l+  +en++k+g+e+ i+++
  gi|330506715|ref|YP_004383143.1|  63 HETVLDVGAGTGRLAIPMA--RIARSVTALDQSKGMLACLEENMAKEGIEN-IRTI 115
                                       679***************9..68999**********************975.5554 PP

>> SAM_MT  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00034      0.28      72     116 ..      63     107 ..      29     133 .. 0.81
   2 ?   -2.8   0.0         4   3.3e+03      39      56 ..     173     190 ..     164     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                            SAM_MT  72 lptvlDaTaGlGrDafvlaslGckvtliErhpvvaaLLedglkRa 116
                                       + tvlD  aG Gr a+ +a +  +vt ++++  + a Le+ + + 
  gi|330506715|ref|YP_004383143.1|  63 HETVLDVGAGTGRLAIPMARIARSVTALDQSKGMLACLEENMAKE 107
                                       579*****************************9999999988765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4
                            SAM_MT  39 lvdfvsgaaahRrkfggg 56 
                                       ++df++g  + R++fgg 
  gi|330506715|ref|YP_004383143.1| 173 FADFLRGGKRARHHFGGP 190
                                       689**********99986 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00029      0.23       3      70 ..      57     121 ..      55     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                                       HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTC CS
                   Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDark 70 
                                       +L +  +et+lD+ a+ G     +a +   +  v+A+d++k  l  ++en+ + g++n+  ++    +
  gi|330506715|ref|YP_004383143.1|  57 TLGLLSHETVLDVGAGTGRLAIPMARI---ARSVTALDQSKGMLACLEENMAKEGIENIRTIQKSWEE 121
                                       6777789*********99988888888...889************************99988766555 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0003      0.24      95     134 ..      63     102 ..      51     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                              DREV  95 dkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkk 134
                                       ++++ld+GaG G ++  +a     v a + s+ m   l+ 
  gi|330506715|ref|YP_004383143.1|  63 HETVLDVGAGTGRLAIPMARIARSVTALDQSKGMLACLEE 102
                                       679******************************9887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2032.21
//
Query:       gi|330506716|ref|YP_004383144.1|  [L=260]
Description: hypothetical protein MCON_0479 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-33  116.6   1.1    1.5e-33  116.3   1.1    1.1  1  Band_7       SPFH domain / Band 7 family
     0.0014   18.4   0.1     0.0063   16.2   0.1    2.0  2  Band_7_1     SPFH domain-Band 7 family
  ------ inclusion threshold ------
      0.063   12.9   0.0      0.087   12.5   0.0    1.3  1  Maelstrom    piRNA pathway germ-plasm component
        0.1   11.5   0.0       0.17   10.8   0.0    1.4  1  Herpes_UL31  Herpesvirus UL31-like protein
       0.37   10.9   3.3         11    6.2   0.1    3.1  3  Arc_PepC     Archaeal Peptidase A24 C-terminal Domain


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 !  116.3   1.1   4.3e-37   1.5e-33       2     177 ..      23     192 ..      22     193 .. 0.99

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 4.3e-37
                            Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapkl 78 
                                       ++++ e++v++r Gk+++ ++pGl   +P+ +++++v++rv++ldv++ +tv++kD++ + +d++++y+v  da+++
  gi|330506716|ref|YP_004383144.1|  23 VVRQYERAVIFRLGKIKKERGPGLFALIPLADKMVRVDMRVRELDVPK-QTVISKDNVTLEVDAVIYYKV-MDASRA 97 
                                       799********************999**********************.*********************.****** PP

                            Band_7  79 vaaveresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaq 155
                                       + +v    ++ ++    +++ +lr ++++++l+++ls+r++l++++k+ l +    +G  v+ v+ +d+++p++  +
  gi|330506716|ref|YP_004383144.1|  98 IIEV----EDFEAATLLLAQTTLRDILGQNELDTILSDRDDLNKRIKEILDSTTGPWGMHVVMVTMRDVSLPENMLR 170
                                       ****....********************************************************************* PP

                            Band_7 156 alaakqaaeaeaqaeiaraeae 177
                                       a+a+ ++ae+e++a+i  ae+e
  gi|330506716|ref|YP_004383144.1| 171 AIARQAEAEREKRARIILAEGE 192
                                       *******************997 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.28     1e+03      18      44 ..      23      49 ..      17      53 .. 0.90
   2 !   16.2   0.1   1.8e-06    0.0063     143     209 ..     114     178 ..      78     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.28
                          Band_7_1 18 ivregqeavfvneGqiaDvfapGtytL 44
                                      +vr+  +av  + G+i    +pG + L
  gi|330506716|ref|YP_004383144.1| 23 VVRQYERAVIFRLGKIKKERGPGLFAL 49
                                      899*************99999999887 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.8e-06
                          Band_7_1 143 trlsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                       t+l d+l+++++  +   +  ++l +++ke l+++    G+++  ++++++slpe++ +a+ ++a++
  gi|330506716|ref|YP_004383144.1| 114 TTLRDILGQNELDTI--LSDRDDLNKRIKEILDSTTGPWGMHVVMVTMRDVSLPENMLRAIARQAEA 178
                                       556777777776654..577899***************************************99876 PP

>> Maelstrom  piRNA pathway germ-plasm component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.4e-05     0.087      66     139 ..     131     206 ..      90     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                                       -HHHHHHHHHHHHHHHH-SS..S-EEEEE-GGGHHHHHHHHHHH----HHHH-....EEEEEHHHHHHHHHHHHHHH CS
                         Maelstrom  66 dlkklveeilsflessseksneksliiltkeeeisvvksclknlaedvkfeee....vsvydiqelfldlkkevldv 138
                                       d ++l ++i + l+s+ +     + ++++++ ++s+ +++l+ +a++++ e e    ++  + ++  +++++++ d+
  gi|330506716|ref|YP_004383144.1| 131 DRDDLNKRIKEILDSTTGPW--GMHVVMVTMRDVSLPENMLRAIARQAEAEREkrarIILAEGEYQASKMMNQAADM 205
                                       55666666666666666544..9**********************99999888888899999999999999988876 PP

                                       T CS
                         Maelstrom 139 a 139
                                        
  gi|330506716|ref|YP_004383144.1| 206 Y 206
                                       5 PP

>> Herpes_UL31  Herpesvirus UL31-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.8e-05      0.17     113     192 ..      96     176 ..      65     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.8e-05
                                       CTCCCCHHHHHCCCCHHHHHHHHCCT-HHHHHHHHHHHCCTTSEEEEEEEETTCEEEEEEE.SSS-EEE-HHHHHHH CS
                       Herpes_UL31 113 skvvenkafylsllklsenlikksleQpelfyiyyvlkagvsdifpilfaedgklamyviF.kgsslHlseklirql 188
                                         ++e   f ++ l l++++++ +l+Q el  i     +++++i  il ++ g + m+v+  + +++ l+e+++r +
  gi|330506716|ref|YP_004383144.1|  96 RAIIEVEDFEAATLLLAQTTLRDILGQNELDTILSDRDDLNKRIKEILDSTTGPWGMHVVMvTMRDVSLPENMLRAI 172
                                       5688999999999999999***********9999999999********************9899***********99 PP

                                       HHHT CS
                       Herpes_UL31 189 ldnl 192
                                          +
  gi|330506716|ref|YP_004383144.1| 173 ARQA 176
                                       7665 PP

>> Arc_PepC  Archaeal Peptidase A24 C-terminal Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.047   1.7e+02      33      54 ..      63      84 ..      51     114 .. 0.73
   2 ?    6.2   0.1     0.003        11      39      68 ..     116     145 ..     110     149 .. 0.91
   3 ?    1.7   0.0     0.076   2.7e+02       3      82 ..     156     232 ..     154     254 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.047
                          Arc_PepC 33 LkEGdiladiilekeddevtvd 54
                                       +E d+++++++ k++  ++vd
  gi|330506716|ref|YP_004383144.1| 63 VRELDVPKQTVISKDNVTLEVD 84
                                      6899**********65444444 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.003
                          Arc_PepC  39 ladiilekeddevtvddksllkrlkealkt 68 
                                       l+di+ ++e d +  d+ +l kr+ke+l++
  gi|330506716|ref|YP_004383144.1| 116 LRDILGQNELDTILSDRDDLNKRIKEILDS 145
                                       899999********************9985 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.076
                          Arc_PepC   3 lvsitelkliskvikaltkeel.sdkkkve.eLkEGdiladiilekeddevtvddksllkrlkealktgdvskietk 77 
                                       +v++  ++l   ++ a+ +++  + +k+    L EG+  a++++++  d ++ d+ s l +l+e      +++i ++
  gi|330506716|ref|YP_004383144.1| 156 MVTMRDVSLPENMLRAIARQAEaEREKRARiILAEGEYQASKMMNQAAD-MYEDKPSAL-KLREYQT---LTEIAKE 227
                                       6777777777777777766543033333331489999999999999665.555555555.6777666...4444434 PP

                          Arc_PepC  78 gkvlv 82 
                                       +  +v
  gi|330506716|ref|YP_004383144.1| 228 KNLIV 232
                                       34433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1970.44
//
Query:       gi|330506717|ref|YP_004383145.1|  [L=376]
Description: iron chelate uptake ABC transporter permease [Methanosaeta concilii GP6]
Scores for 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-89  300.7  32.7    1.3e-89  300.3  32.7    1.1  1  FecCD     FecCD transport family
     0.0077   15.8  22.4      0.011   15.2  22.4    1.3  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 !  300.3  32.7   1.4e-93   1.3e-89       1     312 []      50     368 ..      50     368 .. 0.99

  Alignments for each domain:
  == domain 1  score: 300.3 bits;  conditional E-value: 1.4e-93
                             FecCD   1 llllllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNp 70 
                                       ll+ll+ l ++lg+ +is+ + ++all++        d+l + +v+++r+pr++ ++++G++L+++G+++Q+v++Np
  gi|330506717|ref|YP_004383145.1|  50 LLVLLTGLIITLGPLDISVLDSYSALLARFwpehfyvDELTSRVVWNIRFPRIMGGIMAGFGLGICGCVMQAVLKNP 126
                                       6788999999*****************9999********************************************** PP

                             FecCD  71 LadPsilGissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsa 146
                                       La+P +lGi++ga +g+ la++++ ++ ++ + ++  afl+al+ +l+++ la   kga+++ l+LaGiav+++++a
  gi|330506717|ref|YP_004383145.1| 127 LASPFTLGITAGAQFGISLAAVIGfSFLAGPYFIIGNAFLCALFCSLFIIGLA-AIKGATSENLVLAGIAVNYFFTA 202
                                       **********************9999999************************.*********************** PP

                             FecCD 147 ltsllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrll 223
                                       +++ll++++++e+l+ +++w +G+l+  sw++  +ll++++++++ll+    +l++++ gdetAks+Gvn er+r++
  gi|330506717|ref|YP_004383145.1| 203 ISQLLKYFATDEQLRLMTNWGMGDLAAFSWTNSRILLAIFVICIPLLMTKCWDLNIMTAGDETAKSIGVNAERTRIF 279
                                       ***************************************************************************** PP

                             FecCD 224 llllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtal 300
                                       ++++++ll+a++v+++G+i+FvGL++Ph+ar+++g dhr l+p+s++lGal+l+ ad ++ +l++pt +p+gi+t++
  gi|330506717|ref|YP_004383145.1| 280 IMVVSSLLVATIVSFMGTIAFVGLVAPHMARMVIGGDHRFLIPASGVLGALVLMSADAAGMNLIAPTIIPTGIMTSI 356
                                       ***************************************************************************** PP

                             FecCD 301 iGapffiylllr 312
                                       +G+pff+yl+++
  gi|330506717|ref|YP_004383145.1| 357 VGVPFFMYLMMK 368
                                       **********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 !   15.2  22.4   1.2e-06     0.011      31     256 ..     128     367 ..      96     369 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-06
                             ABC-3  31 qsllgdalsHaalpGvalayllgvn.......lllgailvgliaavalellkrktklked..taigivlsvflalgl 98 
                                       +s +  ++   a  G+ la ++g++       ++  a+l++l++++++  l++ +   ++  ++ gi +  f+    
  gi|330506717|ref|YP_004383145.1| 128 ASPFTLGITAGAQFGISLAAVIGFSflagpyfIIGNAFLCALFCSLFIIGLAAIKGATSEnlVLAGIAVNYFFTAIS 204
                                       4566666666777788888888888666666444458999*******999988776555522456999999986555 PP

                             ABC-3  99 vlvslikk.skvdl.dsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllll 173
                                        l+++  +  +  l +++ +G++++ s ++  ++++i ++++ ll+ +  +l ++t   e+Ak++g++ ++ ++ ++
  gi|330506717|ref|YP_004383145.1| 205 QLLKYFATdEQLRLmTNWGMGDLAAFSWTNSRILLAIFVICIPLLMTKCWDLNIMTAGDETAKSIGVNAERTRIFIM 281
                                       5555555445555416899********************************************************** PP

                             ABC-3 174 alialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvv....aGlllSyyldlatGavivlv 246
                                       ++ +l v++++ ++G i  +  l++P ++ + ++ + + l+  + +lg++ ++    aG+ l +   ++tG +  +v
  gi|330506717|ref|YP_004383145.1| 282 VVSSLLVATIVSFMGTIAFVG-LVAPHMARMVIGGDHRFLIPASGVLGALVLMsadaAGMNLIAPTIIPTGIMTSIV 357
                                       *****************9888.5899999999999999999888888876554122267777777777787777777 PP

                             ABC-3 247 atllfllall 256
                                        + +f+  ++
  gi|330506717|ref|YP_004383145.1| 358 GVPFFMYLMM 367
                                       7666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2665.55
//
Query:       gi|330506718|ref|YP_004383146.1|  [L=262]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-34  117.2   0.0    1.1e-33  116.7   0.0    1.2  1  ABC_tran      ABC transporter
    1.1e-09   38.6   0.1    1.1e-05   25.5   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.9e-07   29.7   0.5    5.9e-05   22.6   0.5    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
    1.8e-06   28.6   0.0      3e-06   27.9   0.0    1.3  1  AAA_23        AAA domain
      4e-06   26.5   0.0    8.3e-06   25.5   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
    5.5e-05   23.1   0.0    5.5e-05   23.1   0.0    1.2  1  AAA_15        AAA ATPase domain
    0.00025   21.5   0.0    0.00034   21.0   0.0    1.4  1  AAA_16        AAA ATPase domain
    0.00025   20.0   0.9       0.41    9.4   0.0    2.7  2  ABC_ATPase    Predicted ATPase of the ABC class
     0.0031   17.2   0.1       0.01   15.6   0.0    1.8  2  AAA_30        AAA domain
     0.0034   16.2   0.5      0.019   13.7   0.0    1.9  2  RNA12         RNA12 protein
     0.0037   16.6   0.0     0.0057   15.9   0.0    1.3  1  Zeta_toxin    Zeta toxin
     0.0037   17.2   0.1      0.015   15.2   0.0    1.8  2  Rad17         Rad17 P-loop domain
     0.0041   16.5   0.0      0.012   15.1   0.0    1.7  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0069   16.0   0.0      0.012   15.3   0.0    1.3  1  AAA_27        AAA domain
  ------ inclusion threshold ------
      0.011   16.0   0.7       0.13   12.5   0.0    2.1  2  AAA_22        AAA domain
      0.013   15.4   0.0      0.026   14.4   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
      0.017   15.3   0.0      0.053   13.7   0.0    1.8  2  AAA_33        AAA domain
      0.019   13.6   0.0          2    7.0   0.0    2.0  2  AAA_13        AAA domain
      0.026   13.7   0.7       0.26   10.4   0.0    2.0  2  NB-ARC        NB-ARC domain
       0.03   13.9   0.0      0.051   13.2   0.0    1.4  1  SRP54         SRP54-type protein, GTPase domain
      0.038   14.3   0.5       0.11   12.8   0.3    2.0  1  AAA_19        AAA domain
      0.038   13.4   0.4      0.057   12.8   0.4    1.2  1  HSM3_N        DNA mismatch repair protein HSM3, N terminal do
      0.065   12.4   0.0       0.18   10.9   0.0    1.7  2  DUF815        Protein of unknown function (DUF815)
      0.067   12.2   0.1       0.28   10.1   0.1    1.9  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.076   13.0   0.1        1.1    9.3   0.1    2.5  2  AAA_5         AAA domain (dynein-related subfamily)
       0.15   12.0   0.2       0.34   10.8   0.1    1.6  2  NACHT         NACHT domain
       0.15   12.1   0.1       0.63   10.1   0.0    2.1  2  AAA_14        AAA domain
       0.16   12.4   0.1       0.52   10.7   0.0    1.9  2  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 !  116.7   0.0   1.7e-36   1.1e-33       1     137 []      20     167 ..      20     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 1.7e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltv 76 
                                       l+nv++++ ++++v ivG+nG+GKStL+k++ + l p+ G+il+d kd+++ ++  + k ++++pq   ++fp+  v
  gi|330506718|ref|YP_004383146.1|  20 LQNVNFEIAPSKLVTIVGPNGSGKSTLIKCIDRILAPQGGSILIDRKDVTRMTRMDMAKYLSYVPQSsVRIFPTN-V 95 
                                       79*****************************************************************88899988.8 PP

                                       HHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        ++                +++++ ++l+ l+++ l+ ++     s+LSgGq+q+v +aral+++++++llDEpt+
  gi|330506718|ref|YP_004383146.1|  96 FDTilmgrrphigwlgseRDEDKVWEVLRLLDIERLAMSNF----SELSGGQQQKVLIARALVQEAEVMLLDEPTS 167
                                       888999999******88777777888888888888777777....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.6e-08   1.1e-05       2      24 ..      33      55 ..      32      89 .. 0.79
   2 !   11.0   0.0   0.00043      0.27     233     285 ..     135     188 ..     122     220 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.6e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                        ++GpNgsGKS+L++++d +  
  gi|330506718|ref|YP_004383146.1| 33 VTIVGPNGSGKSTLIKCIDRILA 55
                                      579***************99963 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00043
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkel 285
                                       +++elS G+++   ++ al + +    + l+DEp ++L+      ++  + +++k++
  gi|330506718|ref|YP_004383146.1| 135 NFSELSGGQQQKVLIARALVQEA---EVMLLDEPTSNLDIwhqlDVMNIIRDVVKKK 188
                                       67899*******77777777777...9***********9955544445555555444 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 !   22.6   0.5   9.3e-08   5.9e-05      24     189 ..      30     187 ..      16     214 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 9.3e-08
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsis 100
                                       +++  ivGpNGSGKs l+  i  +L  +          s li + k+  ++++ +++ +++   ++ +++   +++ 
  gi|330506718|ref|YP_004383146.1|  30 SKLVTIVGPNGSGKSTLIKCIDRILAPQGG--------SILIDR-KDVTRMTRMDMAKYLSYVPQS-SVRIFPTNVF 96 
                                       35788****************888886555........455555.333333333333333332222.2222223333 PP

                                       EEEETTSEEEEEETTEEE-H...HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtk...kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                        ++  + + ++   g+e  +    ev +ll  +++ ++   +LSgG+++     +l+A   v+ a ++llDe  ++L
  gi|330506718|ref|YP_004383146.1|  97 DTILMGRRPHIGWLGSERDEdkvWEVLRLLDIERLAMSnfsELSGGQQQK----VLIARALVQEAEVMLLDEPTSNL 169
                                       34444444333333333333002444444444444433333789998653....33344455888899999999999 PP

                                       -HHHHHHHHHHHHHHCTT CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N 172 Deknvkkvaellkekskn 189
                                       D  +   v ++++   k+
  gi|330506718|ref|YP_004383146.1| 170 DIWHQLDVMNIIRDVVKK 187
                                       999999999999865554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   4.7e-09     3e-06      11      43 ..      21      54 ..      13      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 4.7e-09
                            AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildAiklaL 43
                                      ++++++   ++l+ I+GpNG+GK+T++ +i  +L
  gi|330506718|ref|YP_004383146.1| 21 QNVNFEIaPSKLVTIVGPNGSGKSTLIKCIDRIL 54
                                      44455556669*******************7666 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.3e-08   8.3e-06      14      50 ..      22      58 ..      15      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.3e-08
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +  +ei ++  + ++Gp+GsGKSTl+  i  +L p+ 
  gi|330506718|ref|YP_004383146.1| 22 NVNFEIAPSKLVTIVGPNGSGKSTLIKCIDRILAPQG 58
                                      5678899999999********************9975 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   8.5e-08   5.5e-05      17      50 ..      25      57 ..      18     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 8.5e-08
                            AAA_15 17 veidlseeltvliGkNnsGKSsilealdlFlnnk 50
                                      +ei  s+ l +++G+N+sGKS++++ +d +l  +
  gi|330506718|ref|YP_004383146.1| 25 FEIAPSK-LVTIVGPNGSGKSTLIKCIDRILAPQ 57
                                      5666667.********************998865 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   5.4e-07   0.00034      25      63 ..      31      70 ..      18     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.4e-07
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                       lv ++G+ G+GKs+l++++ r l  +gg   +  k +  
  gi|330506718|ref|YP_004383146.1| 31 KLVTIVGPNGSGKSTLIKCIDRILAPQGGSIlIDRKDVTR 70
                                      7899******************999997444144333333 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00064      0.41     243     266 ..      29      52 ..      23      55 .. 0.91
   2 !    8.0   0.4    0.0017       1.1     323     376 ..     139     193 ..     131     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00064
                                       -SSEEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 243 pkGvtlIvGggfhGKsTLLeAlek 266
                                       p ++++IvG++  GKsTL++ +++
  gi|330506718|ref|YP_004383146.1|  29 PSKLVTIVGPNGSGKSTLIKCIDR 52 
                                       77899***************9975 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0017
                                       --HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHH...S-GGG--B--H CS
                        ABC_ATPase 323 ASGStsqAanimealeagakllLiDEDtsAtNlmirDermqel...vskekepitpl 376
                                        SG   q + i++al  +a+++L+DE ts   + ++ + m+ +   v  +k+ it++
  gi|330506718|ref|YP_004383146.1| 139 LSGGQQQKVLIARALVQEAEVMLLDEPTSNLDIWHQLDVMNIIrdvV--KKKEITAI 193
                                       599999**********************9888877666665331103..33335544 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   1.6e-05      0.01      18      50 ..      30      62 ..      23      78 .. 0.88
   2 ?   -1.8   0.1       3.4   2.2e+03      82     113 ..     150     182 ..     121     188 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvi 50
                                       ++++++Gp G+GK+t++k + ++++ +gg+++
  gi|330506718|ref|YP_004383146.1| 30 SKLVTIVGPNGSGKSTLIKCIDRILAPQGGSIL 62
                                      45899********************99987765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.4
                            AAA_30  82 grarlepgtllivDE.agmvdtkqlaallkaae 113
                                       +ra ++++++++ DE ++ +d+++  +++++++
  gi|330506718|ref|YP_004383146.1| 150 ARALVQEAEVMLLDEpTSNLDIWHQLDVMNIIR 182
                                       445566667777787445566666666666655 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   2.9e-05     0.019      16      59 ..      29      75 ..      16      85 .. 0.84
   2 ?    0.7   0.2      0.27   1.7e+02     307     373 ..     146     212 ..     113     250 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.9e-05
                             RNA12 16 vntFivvkGPrGSGkkeLv..ldrvlkdrkkvlvidCdelvk.arnd 59
                                      ++  +++ GP GSGk+ L+  +dr+l+ +   + id ++++  +r d
  gi|330506718|ref|YP_004383146.1| 29 PSKLVTIVGPNGSGKSTLIkcIDRILAPQGGSILIDRKDVTRmTRMD 75
                                      56789*************8778**************99998755555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.27
                             RNA12 307 eeiieqsaeeilkmflldseeakkakwtkeqaWklikklskkgsieynellleelfkgsaesalkaL 373
                                       + +i ++ ++  +++lld+  ++ + w++ ++ ++i+ + kk++i++ + l++  + +   + +  +
  gi|330506718|ref|YP_004383146.1| 146 KVLIARALVQEAEVMLLDEPTSNLDIWHQLDVMNIIRDVVKKKEITAIMALHDLNLASYYSDRIIMM 212
                                       4467777777777888888888889999999999999999999998888777766666555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     9e-06    0.0057      17      56 ..      31      70 ..      18     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9e-06
                        Zeta_toxin 17 klillgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56
                                      kl+ ++G  G+GKs+l++ +++ l++qg+ + +d+ d+ +
  gi|330506718|ref|YP_004383146.1| 31 KLVTIVGPNGSGKSTLIKCIDRILAPQGGSILIDRKDVTR 70
                                      7899******************************877655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.3e-05     0.015      35      72 ..      20      57 ..      15      97 .. 0.90
   2 ?   -0.4   0.1       1.4   9.3e+02     107     175 ..     134     199 ..     114     206 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.3e-05
                             Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLskelgik 72
                                      l+    e ++ +++ i GP G gkst +k + ++l+++
  gi|330506718|ref|YP_004383146.1| 20 LQNVNFEIAPSKLVTIVGPNGSGKSTLIKCIDRILAPQ 57
                                      566667889999*******************9999876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                             Rad17 107 esfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrds.dalrevirkylrssealplilvitei 175
                                         f+el   + + +k+      l  + +++l+++  ++  +     + ++ir +++ +e  + i+ + ++
  gi|330506718|ref|YP_004383146.1| 134 SNFSEL--SGGQQQKVL-IARALVQEAEVMLLDEPTSNLDIWHqLDVMNIIRDVVKKKEI-TAIMALHDL 199
                                       556666..333333333.345666677788888866766665435677899999888887.667766655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.8e-05     0.012      23      64 ..      31      72 ..      15      87 .. 0.80
   2 ?   -1.6   0.0       2.2   1.4e+03     119     142 ..     174     197 ..     135     248 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                      Mg_chelatase 23 HnlllvGppGsGKtmlakrlpsllpplseeealevakiasva 64
                                        + +vGp GsGK+ l+k++  +l+p   +  ++ + ++ ++
  gi|330506718|ref|YP_004383146.1| 31 KLVTIVGPNGSGKSTLIKCIDRILAPQGGSILIDRKDVTRMT 72
                                      55789********************98877777766666555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                      Mg_chelatase 119 krkvlevLRePledgevtisraka 142
                                       + +v++++R+ + ++e+t   a +
  gi|330506718|ref|YP_004383146.1| 174 QLDVMNIIRDVVKKKEITAIMALH 197
                                       345666666666666666554444 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   1.8e-05     0.012      18      50 ..      22      54 ..      12      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      +++f+ + ++l  i+GpN +GKst+++ i ++l
  gi|330506718|ref|YP_004383146.1| 22 NVNFEIAPSKLVTIVGPNGSGKSTLIKCIDRIL 54
                                      6889999*******************9998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0002      0.13       6      27 ..      31      52 ..      28      83 .. 0.84
   2 ?    1.8   0.3      0.41   2.6e+02      82     128 ..     144     195 ..     112     204 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                            AAA_22  6 gilvvtGesGtGKTtllrrlle 27
                                      ++++++G+ G+GK+tl++ + +
  gi|330506718|ref|YP_004383146.1| 31 KLVTIVGPNGSGKSTLIKCIDR 52
                                      5789*************97755 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.41
                            AAA_22  82 leqalrarav...ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                        ++ l ara     e++++DE    l+   + ++++ +r+ ++  +k ++ i++
  gi|330506718|ref|YP_004383146.1| 144 QQKVLIARALvqeAEVMLLDEPTSnLDiwhQLDVMNIIRDVVK--KKEITAIMA 195
                                       3333333333556679999999888988866999999999999..888887765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     4e-05     0.026      87     120 ..      17      51 ..       4      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4e-05
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       ++ l++++ +++  k++++vG+ G GKStLi+ ++
  gi|330506718|ref|YP_004383146.1|  17 SKILQNVNFEIAPsKLVTIVGPNGSGKSTLIKCID 51 
                                       456778888888879****************9886 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   8.3e-05     0.053       1      29 [.      32      64 ..      32     103 .. 0.73
   2 ?   -1.1   0.0       2.9   1.9e+03      16      91 ..     150     180 ..     120     205 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.3e-05
                            AAA_33  1 lvllvGlpGsGKstlaerl...lkklg.avlls 29
                                      lv +vG++GsGKstl++ +   l+++g  +l++
  gi|330506718|ref|YP_004383146.1| 32 LVTIVGPNGSGKSTLIKCIdriLAPQGgSILID 64
                                      7899***********874322255555455555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.9
                            AAA_33  16 aerllkklgavllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildat..nlsrrerarflk 90 
                                       a+ l+++  + ll++                                               +  nl+ +++ ++++
  gi|330506718|ref|YP_004383146.1| 150 ARALVQEAEVMLLDE-----------------------------------------------PtsNLDIWHQLDVMN 179
                                       333444444444444...............................................333444444444444 PP

                            AAA_33  91 l 91 
                                       +
  gi|330506718|ref|YP_004383146.1| 180 I 180
                                       4 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0031         2      21      39 ..      35      53 ..      24     119 .. 0.76
   2 ?    4.9   0.1     0.013       8.2     524     567 ..     154     196 ..     146     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0031
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      i G NG+GK+tL + ++ +
  gi|330506718|ref|YP_004383146.1| 35 IVGPNGSGKSTLIKCIDRI 53
                                      77**********9999876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.013
                            AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiL 567
                                       +++ ++  +D P S LD  ++  v++ i++++ kkk++  ++ L
  gi|330506718|ref|YP_004383146.1| 154 VQEAEVMLLDEPTSNLDIWHQLDVMNIIRDVV-KKKEITAIMAL 196
                                       5678999************************9.88888877655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00041      0.26      21      40 ..      31      50 ..      16      59 .. 0.85
   2 ?    1.7   0.2      0.18   1.2e+02      63     118 ..     114     177 ..      86     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00041
                                      EEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqi 40
                                       +v++vG  G+GK+tl+k i
  gi|330506718|ref|YP_004383146.1| 31 KLVTIVGPNGSGKSTLIKCI 50
                                      589*************9876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
                                       XHHHHHHHXXHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEE......EE-SHHHH CS
                            NB-ARC  63 dkseeiletilkeLslseddleekeeves...lkrklvrlLltkrfllvlD......DVweeedw 118
                                        ++ +++e +l+ L  +   +++++e       k  + r+L +   +++lD      D+w++ d 
  gi|330506718|ref|YP_004383146.1| 114 RDEDKVWE-VLRLLDIERLAMSNFSELSGgqqQKVLIARALVQEAEVMLLDeptsnlDIWHQLDV 177
                                       56667777.7777777777777777766565578889999***9999999966666667776552 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.9e-05     0.051       3      46 ..      32      75 ..      30      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.9e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHH CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAve 46
                                      ++ +vG++G+GK t +  + ++l  +g ++l+   D+ R+  ++
  gi|330506718|ref|YP_004383146.1| 32 LVTIVGPNGSGKSTLIKCIDRILAPQGGSILIDRKDVTRMTRMD 75
                                      6789*********************************9987665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   0.00018      0.11       7      62 ..      27      80 ..      21     204 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                            AAA_19  7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerl 62
                                       +++k++ ++++ G+GK++++k+i ++l  +gg     i    +t+   + +++ l
  gi|330506718|ref|YP_004383146.1| 27 IAPSKLVTIVGPNGSGKSTLIKCIDRILAPQGGS--ILIDRKDVTRMTRMDMAKYL 80
                                      568999******************9999888865..33334445555555555555 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 ?   12.8   0.4     9e-05     0.057      31     126 ..     138     233 ..     118     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-05
                            HSM3_N  31 nlstvaklkedakrllanikrllvenksedkldydlllelldklvkvssfedvlevysvddlvkalkseidslvvaa 107
                                       +ls  ++ k  + r l++   +++ ++++++ld    l++++ + +v++ +++ ++ +++dl  a   +   +++  
  gi|330506718|ref|YP_004383146.1| 138 ELSGGQQQKVLIARALVQEAEVMLLDEPTSNLDIWHQLDVMNIIRDVVKKKEITAIMALHDLNLASYYSDRIIMMNR 214
                                       455556666666777777777888889999**********************************99999999999** PP

                            HSM3_N 108 ckvieksyPkglfatseii 126
                                        k+i+   P+++ ++ +i 
  gi|330506718|ref|YP_004383146.1| 215 GKIIAAGDPQSVITEENIA 233
                                       ************9998886 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.18      49      97 ..      26      73 ..       7      90 .. 0.75
   2 ?   -3.6   0.0       7.6   4.9e+03      81      98 ..     122     139 ..     118     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                            DUF815 49 eglpannvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpk 97
                                      e +p++ v ++G  G+GKS+l+k + + +a +g   i ++++d++ + +
  gi|330506718|ref|YP_004383146.1| 26 EIAPSKLVTIVGPNGSGKSTLIKCIDRILAPQGGS-ILIDRKDVTRMTR 73
                                      4467888999**************99999988854.3467777766654 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.6
                            DUF815  81 gLrlievekedlkelpkl 98 
                                        Lrl+++e+  ++++++l
  gi|330506718|ref|YP_004383146.1| 122 VLRLLDIERLAMSNFSEL 139
                                       578888888877777766 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00044      0.28      14      58 ..      15      59 ..       5      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00044
                                      HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT- CS
                              MeaB 14 eakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGk 58
                                      ++ ++l+++  +   ++ v + G  G+Gkstl++ +   l+ +G 
  gi|330506718|ref|YP_004383146.1| 15 NSSKILQNVNFEIAPSKLVTIVGPNGSGKSTLIKCIDRILAPQGG 59
                                      578899999999999******************999888887775 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 ?    9.3   0.1    0.0017       1.1       3      24 ..      34      56 ..      32     166 .. 0.77
   2 ?    1.7   0.0      0.36   2.3e+02      19      53 ..     149     183 ..     143     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                                      EEE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5  3 lLvGppGtgKselaerlaaal.n 24
                                       +vGp G+gKs+l++ + + l  
  gi|330506718|ref|YP_004383146.1| 34 TIVGPNGSGKSTLIKCIDRILaP 56
                                      689***********999988852 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.36
                                       GGGGBS--EEEEE--TT--HHHHH--B--...... CS
                             AAA_5  19 laaalnreveyvqltrdtteedlkgrreikngtts 53 
                                       +a+al +e e+++l + t+  d+  +++++n  + 
  gi|330506718|ref|YP_004383146.1| 149 IARALVQEAEVMLLDEPTSNLDIWHQLDVMNIIRD 183
                                       78889999999999999999999999998754443 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00053      0.34       2      22 ..      32      52 ..      31      59 .. 0.84
   2 ?   -2.8   0.0       7.9     5e+03     112     135 ..     148     171 ..     135     197 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00053
                                      CEEEEC-TTTCHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklal 22
                                      lv + G++GsGK+tL++ + +
  gi|330506718|ref|YP_004383146.1| 32 LVTIVGPNGSGKSTLIKCIDR 52
                                      689************998755 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.9
                                       HHCTTTTT--EEEEEEECCCHHHH CS
                             NACHT 112 lirkkllpeasllltvrpralrdl 135
                                       li ++l++ea ++l   p++  d+
  gi|330506718|ref|YP_004383146.1| 148 LIARALVQEAEVMLLDEPTSNLDI 171
                                       555666666666655555555444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00099      0.63       3      27 ..      31      54 ..      29      92 .. 0.70
   2 ?   -1.4   0.0       3.4   2.2e+03      60      74 ..     153     166 ..     123     196 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00099
                            AAA_14  3 kilvitGaRrvGKTtllkqlikell 27
                                      k+++i+G+  +GK+tl+k + ++ l
  gi|330506718|ref|YP_004383146.1| 31 KLVTIVGPNGSGKSTLIKCI-DRIL 54
                                      789*************9644.4444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.4
                            AAA_14  60 lkeekktylflDEiq 74 
                                       l  ++ ++++lDE  
  gi|330506718|ref|YP_004383146.1| 153 LV-QEAEVMLLDEPT 166
                                       22.366778888854 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00081      0.52       2      23 ..      34      55 ..      33      91 .. 0.70
   2 ?   -1.7   0.0       5.9   3.8e+03      69     102 ..     176     210 ..     142     212 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00081
                      RNA_helicase  2 wlyGpsgeGKStlakeLakall 23
                                       ++Gp+g GKStl+k + + l+
  gi|330506718|ref|YP_004383146.1| 34 TIVGPNGSGKSTLIKCIDRILA 55
                                      689************9666555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.9
                      RNA_helicase  69 dlaelirlvsstpyplnmasleekg.tlftSkvvi 102
                                       d++++ir v  ++ ++   +l++ +  ++ S  +i
  gi|330506718|ref|YP_004383146.1| 176 DVMNIIRDVVKKKEITAIMALHDLNlASYYSDRII 210
                                       45555544444444444444444444555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 1897.52
//
Query:       gi|330506719|ref|YP_004383147.1|  [L=198]
Description: hypothetical protein MCON_0482 [Methanosaeta concilii GP6]
Scores for 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   66.9   0.0    2.6e-18   66.6   0.0    1.1  1  Flavin_Reduct  Flavin reductase like domain
    0.00035   20.4   0.0    0.00065   19.5   0.0    1.4  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 !   66.6   0.0   2.9e-22   2.6e-18       4     138 ..      12     146 ..       8     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 2.9e-22
                                       S-EE-EEEEE.EETTEEEEEEESSEEEEETTT.TEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS... CS
                     Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldP.plvafslrlpsstadalkeagefvinllsesqealadafsqksg 79 
                                       ++ pv+++tt   ++ +++a+ s ft++ l P   v  +   +++t+++++++gefv+n+ +   e+++  +++ ++
  gi|330506719|ref|YP_004383147.1|  12 LPLPVVLITTVSSQGIRNAAPWSNFTPI-LRPlEEVILASWIKRDTLENIRRTGEFVVNIPQMGMEDAIMICARSYP 87 
                                       678*******88899999*********9.89998888888889*******************************998 PP

                                       SCCCCCCCCCCCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTT CS
                     Flavin_Reduct  80 prtddksifagltwees.ptgapallgalasleCqvvgsvelgdhelfigeVvavkvgdd 138
                                         ++d++  agl++++s +++ap ++g+la+ eC + +++   +  l+ig+Vv+ +v++ 
  gi|330506719|ref|YP_004383147.1|  88 -PGVDEFLEAGLEPHPStKVKAPGIEGCLAWAECVLEEELVREKFVLIIGKVVHLEVDER 146
                                       .9***************99*******************999999***********99986 PP

>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   7.2e-08   0.00065       3     119 ..      17     147 ..      17     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.2e-08
                                       EEEEEE-TT.-EEEEEEE....EEESSSEEEEEEETTSHHHHHHHHHSEEEEEE....---HHHHHHHHHS---GGG CS
                            DUF447   3 vivtTksek.rpnaaPiG....vivkgdkvvlrlfkgsrTleNllengelvinv....tdDpllfakaalgdleesd 70 
                                       v++tT s++  +naaP      + +  ++v+l+ + +  TleN++++ge+v+n+    ++D++++    +    ++ 
  gi|330506719|ref|YP_004383147.1|  17 VLITTVSSQgIRNAAPWSnftpILRPLEEVILASWIKRDTLENIRRTGEFVVNIpqmgMEDAIMICARSYPPGVDEF 93 
                                       78999999999999996522225558999*************************44444699999888887666666 PP

                                       EEEETTTC.TT.....EETT-SEEEEEEEEEECTCECCEEEEEEEEEEEEETTB CS
                            DUF447  71 fdsetkpa.kia....vlksaeawveveveevegdsealelelepvkeeileer 119
                                       ++   +p  +++     ++++ aw+e+ +ee+  +++ + +  ++v+ e+ e++
  gi|330506719|ref|YP_004383147.1|  94 LEAGLEPHpSTKvkapGIEGCLAWAECVLEEELVREKFVLIIGKVVHLEVDERF 147
                                       66665544433333789************9999999999999999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1573.88
//
Query:       gi|330506720|ref|YP_004383148.1|  [L=249]
Description: carbon monoxide dehydrogenase accessory protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-16   58.1   0.0    1.4e-15   57.5   0.0    1.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    1.5e-08   34.8   0.0    2.2e-08   34.2   0.0    1.3  1  AAA_31           AAA domain
    1.7e-08   34.2   0.3    4.8e-07   29.5   0.0    2.6  2  ParA             NUBPL iron-transfer P-loop NTPase
    9.3e-08   31.6   2.7    4.7e-07   29.3   0.1    2.2  2  ArsA_ATPase      Anion-transporting ATPase
    3.1e-07   30.4   0.0    6.8e-07   29.3   0.0    1.6  1  APS_kinase       Adenylylsulphate kinase
      5e-07   29.4   0.0    0.00051   19.6   0.0    2.1  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
    1.2e-06   28.0   0.0     0.0011   18.4   0.0    2.1  2  MipZ             ATPase MipZ
    3.3e-06   26.8   3.1    0.00016   21.3   3.1    2.2  1  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
    3.1e-05   23.8   0.0     0.0026   17.6   0.0    2.3  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
    4.5e-05   23.7   0.4      0.032   14.5   0.0    2.5  2  TrkA_N           TrkA-N domain
     0.0001   21.9   0.0    0.00018   21.1   0.0    1.5  1  KTI12            Chromatin associated protein KTI12
    0.00011   22.4   0.1    0.00027   21.1   0.1    1.7  1  DUF87            Helicase HerA, central domain
    0.00017   21.0   0.0     0.0012   18.2   0.0    2.0  2  Zeta_toxin       Zeta toxin
    0.00017   21.3   0.0    0.00097   18.8   0.0    2.1  2  SRP54            SRP54-type protein, GTPase domain
    0.00057   19.7   0.1     0.0017   18.1   0.0    1.8  2  AAA_24           AAA domain
     0.0013   19.3   0.1     0.0034   17.9   0.0    1.8  1  AAA_18           AAA domain
     0.0013   18.3   0.2      0.079   12.5   0.0    2.2  2  GTP_EFTU         Elongation factor Tu GTP binding domain
     0.0014   19.1   0.1     0.0028   18.2   0.1    1.5  1  ABC_tran         ABC transporter
     0.0019   18.6   0.0     0.0094   16.3   0.0    2.1  2  RNA_helicase     RNA helicase
     0.0022   18.0   0.1      0.036   14.2   0.1    2.3  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0024   18.0   0.0     0.0059   16.8   0.0    1.6  1  AAA_33           AAA domain
     0.0086   15.7   1.8          1    8.9   0.3    2.7  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.011   15.1   0.2       0.02   14.3   0.2    1.6  1  ATPase           KaiC
      0.013   15.1   0.0      0.081   12.5   0.0    2.0  2  AAA_25           AAA domain
      0.017   15.0   0.0       0.06   13.3   0.0    1.9  1  FR47             FR47-like protein
      0.021   13.8   0.0      0.038   12.9   0.0    1.4  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.043   12.8   0.2      0.091   11.7   0.1    1.6  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.044   14.4   0.4       0.26   12.0   0.0    2.5  2  PglD_N           PglD N-terminal domain
      0.046   12.8   0.1      0.088   11.8   0.1    1.4  1  T2SSE            Type II/IV secretion system protein
      0.048   13.4   0.1        0.1   12.3   0.1    1.7  1  IstB_IS21        IstB-like ATP binding protein
       0.05   14.0   0.1      0.094   13.1   0.1    1.8  1  AAA_16           AAA ATPase domain
      0.052   13.8   0.1        0.1   12.9   0.1    1.6  1  AAA_22           AAA domain
      0.069   12.4   0.0        0.1   11.8   0.0    1.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.075   12.7   0.0       0.37   10.4   0.0    2.1  3  Thymidylate_kin  Thymidylate kinase
      0.082   12.8   0.0       0.21   11.5   0.0    1.8  2  NTPase_1         NTPase
      0.096   11.9   0.1       0.11   11.7   0.1    1.4  1  KAP_NTPase       KAP family P-loop domain
        0.1   12.5   0.1        1.7    8.5   0.1    2.2  2  RsgA_GTPase      RsgA GTPase
       0.12   12.4   0.0       0.16   12.0   0.0    1.3  1  ResIII           Type III restriction enzyme, res subunit
       0.15   11.7   0.1       0.44   10.2   0.0    1.9  2  SWI2_SNF2        SWI2/SNF2 ATPase


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 !   57.5   0.0   3.1e-18   1.4e-15       2     127 ..       3     232 ..       2     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 3.1e-18
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       +++ +kGG+GK+t++a Lar +a++g++Vl+vD+D    n   l++  ++++p                        
  gi|330506720|ref|YP_004383148.1|   3 IVICGKGGSGKSTISALLAREIAEKGNEVLVVDTDES--NFG-LYKQLGFEQPkdfmeslggkkalseklmkfirse 76 
                                       57889****************************9988..655.7788888888899999****************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|330506720|ref|YP_004383148.1|  77 qrerlqileeftvkdipeelvvgedkikliaigkihsfgegcacpmgalarefleklktngehvvvdtdagiehfgr 153
                                       ***************************************************************************** PP

                                       ..................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE CS
                                       ..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ..................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgvip 113
                                                         +++  ++ ++++++k     k+++++lnr d++  +++l +    l    +++v+g +p
  gi|330506720|ref|YP_004383148.1| 154 gveagcdkivvvidpsfeSVQL-SGKIAEMSEKI---GKPMFFILNRMDEN--SKELAD----LVD--KNKVIGTMP 218
                                       ****999999999999973333.44444444443...467*********99..554444....444..689****** PP

                                       --CCHCCCCHHTS- CS
                                       xxxxxxxxxxxxxx RF
                              CbiA 114 rdeavaeapargep 127
                                       +d++v +a  +ge 
  gi|330506720|ref|YP_004383148.1| 219 FDKDVFKACLKGEK 232
                                       ********999985 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   4.9e-11   2.2e-08       8     156 ..       6     175 ..       1     193 [. 0.62

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 4.9e-11
                            AAA_31   8 nqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt..glgiekne...........iektlyevlieeknike 71 
                                         KGG GK+T s  la  +a++g+ vL+vD D  +n     +lg+e+ +           ++++l++ +  +++ + 
  gi|330506720|ref|YP_004383148.1|   6 CGKGGSGKSTISALLAREIAEKGNEVLVVDTDE-SNFGLykQLGFEQPKdfmeslggkkaLSEKLMKFIR-SEQRER 80 
                                       56******************************7.455552245554333344444432223344444432.222222 PP

                            AAA_31  72 aiiktkvenldlipssidLaeaeielvelekk..........eeil.kellekvkdeYDyiiiDcpPsLglltenaL 137
                                       + i +++ +++ ip ++ + e +i+l+ + k             +l +e+lek+k +   +++D+   ++ + +   
  gi|330506720|ref|YP_004383148.1|  81 LQILEEF-TVKDIPEELVVGEDKIKLIAIGKIhsfgegcacpMGALaREFLEKLKTNGEHVVVDTDAGIEHFGRGVE 156
                                       2221222.222244444444444444444444444444555522254999***************999999999999 PP

                            AAA_31 138 vasdsviipvqaeayaleG 156
                                       +  d++++++++++ +++ 
  gi|330506720|ref|YP_004383148.1| 157 AGCDKIVVVIDPSFESVQL 175
                                       9999999999997766654 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0     1e-09   4.8e-07       7      55 ..       3      51 ..       1      80 [. 0.86
   2 ?    2.3   0.1      0.21        97     194     224 ..     201     232 ..     140     248 .. 0.61

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1e-09
                              ParA  7 avlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee 55
                                      +v+ gKGG GKSt+++ lA ++a+kg +v ++D+D   + + + lg e+
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAEKGNEVLVVDTDESNFGLYKQLGFEQ 51
                                      6899*******************************77777777776665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.21
                              ParA 194 geklaeel.gvpllgeipldpeireasdegkp 224
                                        ++la+ + + +++g++p+d+++ +a+ +g++
  gi|330506720|ref|YP_004383148.1| 201 SKELADLVdKNKVIGTMPFDKDVFKACLKGEK 232
                                       33333333123566666666666666666665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1     1e-09   4.7e-07       4      38 ..       3      37 ..       1      40 [. 0.95
   2 ?    2.4   0.3      0.16        72     155     230 ..     172     246 ..     161     249 .] 0.84

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1e-09
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      i++ GKGG GK+t+sa +a +++ekg++vl++ tD
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAEKGNEVLVVDTD 37
                                      7899******************************9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHH.HHHHHHHHHHHH CS
                       ArsA_ATPase 155 lvklkeklsplakqlvkllglggvsieealeeleetkeeikkveeiltdpertsfrlVvipEkl.slkEteRaikeL 230
                                        v+l +k+ ++++++ k + ++   ++e  +el + +++ k +  +  d++   f++ ++ Ek+ ++ E e  +++L
  gi|330506720|ref|YP_004383148.1| 172 SVQLSGKIAEMSEKIGKPMFFILNRMDENSKELADLVDKNKVIGTMPFDKDV--FKACLKGEKVpPIMEMEQIAEKL 246
                                       57888999**********99**9****99*****999999999888899998..99999999983488888877776 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.5e-09   6.8e-07       5      53 ..       3      51 ..       1      59 [. 0.93

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.5e-09
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSH CS
                        APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfse 53
                                      + + G  gsGKsti+  l++++ ekg +v ++d d+  +gL+k+Lgf++
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAEKGNEVLVVDTDESNFGLYKQLGFEQ 51
                                      7899*******************************************87 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   1.1e-06   0.00051      10      61 ..       8      58 ..       1      83 [. 0.76
   2 !    8.0   0.0    0.0037       1.7     106     181 ..     127     207 ..     100     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                          CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqregwara 61
                                      +GG G+++++a La+ + e g++vlv+D+  +n+  l+ ++ +eq + ++++
  gi|330506720|ref|YP_004383148.1|  8 KGGSGKSTISALLAREIAEKGNEVLVVDTDESNF-GLYKQLGFEQPKDFMES 58
                                      7****************************99995.45555555555555544 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0037
                          CBP_BcsQ 106 laalkelkeqyrwillDlpagasaltrellaladlvllvvepdanc.....hvrLhqqalpaaellLiNqfeaasql 177
                                        ++l++lk++ + +++D  ag ++  r + a +d+ + v+ p   +     ++    +++ +   +++N+++ +s+ 
  gi|330506720|ref|YP_004383148.1| 127 REFLEKLKTNGEHVVVDTDAGIEHFGRGVEAGCDKIVVVIDPSFESvqlsgKIAEMSEKIGKPMFFILNRMDENSKE 203
                                       567999***********************************988761111123333445566667788888888877 PP

                          CBP_BcsQ 178 qqDl 181
                                         Dl
  gi|330506720|ref|YP_004383148.1| 204 LADL 207
                                       7776 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.3e-06    0.0011       7      40 ..       6      39 ..       1     108 [. 0.88
   2 !    8.2   0.0     0.003       1.4      91     155 ..     128     192 ..     115     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-06
                                      -SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TT CS
                              MipZ  7 nekGGsGksttavhvavaLlkkGarvaaidldlr 40
                                        kGGsGkst++  +a  +++kG +v ++d d  
  gi|330506720|ref|YP_004383148.1|  6 CGKGGSGKSTISALLAREIAEKGNEVLVVDTDES 39
                                      469***************************9975 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.003
                                       HHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEESSHHHHCCCEEE-SSS--EEEE-HH CS
                              MipZ  91 elvadleaeldfividtPGsdsalsrlahsladtlvtPlndsfvdfdllgkvdpetlkvkrpsly 155
                                       e +++l+++ + +v+dt    ++  r + +  d +v  ++ sf  + l gk+   + k+ +p ++
  gi|330506720|ref|YP_004383148.1| 128 EFLEKLKTNGEHVVVDTDAGIEHFGRGVEAGCDKIVVVIDPSFESVQLSGKIAEMSEKIGKPMFF 192
                                       5678899999*************************************************999887 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   3.1   3.4e-07   0.00016       1      39 [.       1      39 [.       1     248 [. 0.51

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.4e-07
                         Fer4_NifH  1 rkiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPk 39
                                      +ki i GkGG+Gkst s+ l+  +ae+g+ vl+v  D  
  gi|330506720|ref|YP_004383148.1|  1 MKIVICGKGGSGKSTISALLAREIAEKGNEVLVVDTDES 39
                                      689*******************************98853 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.7e-06    0.0026       1      31 [.       7      37 ..       7      44 .. 0.94
   2 ?    4.0   0.0     0.082        38      86     119 ..     124     153 ..     119     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.7e-06
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlD 31
                                      G+  sGKST+++lL+ ++++kg+++++vD+D
  gi|330506720|ref|YP_004383148.1|  7 GKGGSGKSTISALLAREIAEKGNEVLVVDTD 37
                                      6778**************************9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.082
                            CLP1_P  86 elareveekleenkkakasgliIntpGwvkglga 119
                                       +lare+ ekl++    + ++++++t+  ++ +g+
  gi|330506720|ref|YP_004383148.1| 124 ALAREFLEKLKT----NGEHVVVDTDAGIEHFGR 153
                                       577777777666....589999999988887775 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   6.9e-05     0.032       1      41 [.       3      48 ..       3      51 .. 0.85
   2 ?    6.9   0.1     0.016       7.4       6      60 ..     122     179 ..     119     186 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.9e-05
                                      EEEES-SHHHHHHHHHHHHTT.....EEEEEEESSHHHHHHHHHTT CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLsegg.....kdvvvidkdeerveelreeg 41
                                      i+i+G G  G+s +  L +++     ++v+v+d+de+++  +++ g
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREiaekgNEVLVVDTDESNFGLYKQLG 48
                                      79**********9999999877999978********9877666655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.016
                                       -SHHHHHHHHHHHHTTEEEEEEESSH..HHHHHHHHTTSE..EEES-TTSHHHHHHTTG CS
                            TrkA_N   6 lGrvGrslaeeLseggkdvvvidkde..erveelreegle..vvvgdatdeevLeeagi 60 
                                       +G ++r+ +e+L+++g+  vv+d+d   e++ +  e g++  vvv d++ e+v  + +i
  gi|330506720|ref|YP_004383148.1| 122 MGALAREFLEKLKTNGE-HVVVDTDAgiEHFGRGVEAGCDkiVVVIDPSFESVQLSGKI 179
                                       8999**********995.9*****98444455555666555666677777776665555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.9e-07   0.00018       4      41 ..       3      40 ..       1      87 [. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.9e-07
                                      EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                             KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41
                                      +v++G   sGKst+++ La++++e++ +v v+d++  +
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAEKGNEVLVVDTDESN 40
                                      89*******************************88776 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   5.9e-07   0.00027      27      61 ..       4      37 ..       1      83 [. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.9e-07
                             DUF87 27 AilgsTGsGKSntvavLleellekkgatililDpH 61
                                       i g+ GsGKS+  a+L +e++ +kg ++l++D +
  gi|330506720|ref|YP_004383148.1|  4 VICGKGGSGKSTISALLAREIA-EKGNEVLVVDTD 37
                                      5899******************.**********76 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.6e-06    0.0012      19      53 ..       3      38 ..       1      58 [. 0.89
   2 ?    0.2   0.0      0.86     4e+02      31      52 ..     124     145 ..     122     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.6e-06
                        Zeta_toxin 19 illgGqpGAGKselaellkdele.rqgnvvrldpDd 53
                                      i++ G  G+GKs++++ll++e++ ++++v+++d+D+
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAeKGNEVLVVDTDE 38
                                      7899******************96666788899996 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.86
                        Zeta_toxin  31 elaellkdelerqgnvvrldpD 52 
                                       +la+++ ++l+++g+ v++d+D
  gi|330506720|ref|YP_004383148.1| 124 ALAREFLEKLKTNGEHVVVDTD 145
                                       6889999999999999999998 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.1e-06   0.00097       4      49 ..       3      48 ..       1      80 [. 0.91
   2 ?   -0.0   0.0       1.3   5.8e+02      76     100 ..     130     154 ..     110     203 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.1e-06
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHH CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLk 49
                                      i+++G  G+GK t  a La+ + ++g++vl+v +D    + ++QL 
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAEKGNEVLVVDTDESNFGLYKQLG 48
                                      899********************************99999999985 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.3
                                       HHHHHHTTSSEEEEEE.--SSTTHHH CS
                             SRP54  76 vekakeekidvvlvDT.aGrlqndke 100
                                       +ek k  + ++v+vDT aG  +  + 
  gi|330506720|ref|YP_004383148.1| 130 LEKLKT-NGEHVVVDTdAGIEHFGRG 154
                                       444444.4466777764554444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.7e-06    0.0017       4      35 ..       2      40 ..       1     118 [. 0.89
   2 ?   -1.0   0.0       2.6   1.2e+03      21      35 ..     135     148 ..     122     164 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.7e-06
                            AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtekGl 35
                                      ki+i G+ g+GK+t+ + l       g+++l++dt+++ 
  gi|330506720|ref|YP_004383148.1|  2 KIVICGKGGSGKSTISALLareiaekGNEVLVVDTDESN 40
                                      9**************99999****************975 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.6
                            AAA_24  21 elgpkplfidtekGl 35 
                                       ++  + +++dt++G 
  gi|330506720|ref|YP_004383148.1| 135 TN-GEHVVVDTDAGI 148
                                       22.555666666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   7.3e-06    0.0034       1      69 [.       3      74 ..       3     108 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7.3e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf....gvnlrdvakenglllevdpealdeskrldedkldklldaleenss 69
                                      I+++G+ G+GK+t++  L+++        v + d+   n  l+ +  ++ ++   +  +  ++l+++l++ ++
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREI-AekgnEVLVVDTDESNFGLYKQLGFEQPKDFMESLGGKKALSEKLMKFIR 74
                                      99****************8884.12344555555555555555555555555555555555555555555555 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 ?    3.7   0.0     0.082        38       5      29 ..       2      26 ..       1      46 [. 0.78
   2 !   12.5   0.0   0.00017     0.079      79     186 ..     147     238 ..     121     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.082
                                      EEEEEESTTSSHHHHHHHHHHHTTS CS
                          GTP_EFTU  5 nigiighvDhGKtTLtdrLlyktga 29
                                      +i+i+g   +GK+T++  L  +  +
  gi|330506720|ref|YP_004383148.1|  2 KIVICGKGGSGKSTISALLAREIAE 26
                                      689************9988755544 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00017
                                       SSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  79 GHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkee 155
                                       G + F + v++g   +D  v+v+d +    + + +++++  k g p+++++N mD+  +el  +v++ k  +     
  gi|330506720|ref|YP_004383148.1| 147 GIEHFGRGVEAG---CDKIVVVIDPSFESVQLSGKIAEMSEKIGKPMFFILNRMDENSKELADLVDKNK--V----- 213
                                       666666666655...899*******9999999999****************************999876..4..... PP

                                       HHHHHHHTTTTTEEEEEEBTTTTBTHHHHHH CS
                          GTP_EFTU 156 klekygekgekevpvvfgSalkgegvktlle 186
                                        +  ++++++     vf ++lkge+v +++e
  gi|330506720|ref|YP_004383148.1| 214 -IGTMPFDKD-----VFKACLKGEKVPPIME 238
                                       .455566665.....6666666666666665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1     6e-06    0.0028      13      48 ..       2      37 ..       1     109 [. 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6e-06
                                      EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilldgkd 48
                                      k++i G+ G+GKSt+ +lla++   +  e+l+ ++d
  gi|330506720|ref|YP_004383148.1|  2 KIVICGKGGSGKSTISALLAREIAEKGNEVLVVDTD 37
                                      689********************9998888665444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     2e-05    0.0094       1      65 [.       3      62 ..       3      83 .. 0.74
   2 ?   -0.8   0.0       4.3     2e+03      15      44 ..     122     151 ..     113     214 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdee 65
                                      i+++G+ g GKSt++  La++++     +k ++v +  ++++ +  Y++  +    Df+++  ++
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIA-----EKGNEVLVVDTDESNFGLYKQLGFEQPKDFMESLGGK 62
                                      799********************.....4557777777777777777777777777777766554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 4.3
                      RNA_helicase  15 akeLakallkklklkkkdsvysrnpeddfw 44 
                                       +  La+++l+klk++ ++ v+   +  +++
  gi|330506720|ref|YP_004383148.1| 122 MGALAREFLEKLKTNGEHVVVDTDAGIEHF 151
                                       556677777777655544333344444444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   7.8e-05     0.036       1     113 [.       2     195 ..       2     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.8e-05
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSST..TSSSSEEEEEEEETT.EE........................... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkp..gtTrdinegrvklkg.ke........................... 47 
                                       +++i G+  +GKSt+   l +e a+ +++     T + n+g +k  g ++                           
  gi|330506720|ref|YP_004383148.1|   2 KIVICGKGGSGKSTISALLAREIAEKGNEVlvVDTDESNFGLYKQLGfEQpkdfmeslggkkalseklmkfirseqr 78 
                                       589*************9999999999888755679999999888333222556777788888888888889999999 PP

                                       ............................................................EEEEEC.GGCSSHHHHH CS
                          MMR_HSR1  48 ............................................................ielvDt.pGliegasee 63 
                                                                                                    ++vDt +G ie     
  gi|330506720|ref|YP_004383148.1|  79 erlqileeftvkdipeelvvgedkikliaigkihsfgegcacpmgalarefleklktngeHVVVDTdAG-IE----- 149
                                       999999997777777777777777777777777777777777777777777666666666666666455.55..... PP

                                       HHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                          MMR_HSR1  64 kglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvln 113
                                         +g+ ++a   +d i++v+d s e   +l  +++e+ e+ +kp++++ln
  gi|330506720|ref|YP_004383148.1| 150 -HFGRGVEA--GCDKIVVVIDPSFE-SVQLSGKIAEMSEKIGKPMFFILN 195
                                       .45555554..48999999996644.335667788888778999999998 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-05    0.0059       2      72 ..       3      82 ..       3      96 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklg.....avllssdt....lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagr 71
                                      ++++G  GsGKst +  l+++ +     + ++++d+    l+++l  +++++  ++   ++ l + l +++r+ ++++ 
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAekgneVLVVDTDEsnfgLYKQLGFEQPKDFMESLGGKKALSEKLMKFIRSEQRERL 81
                                      689*************998887777877888888885555444444355555545555666666666677776666665 PP

                            AAA_33 72 n 72
                                      +
  gi|330506720|ref|YP_004383148.1| 82 Q 82
                                      5 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.033        15       3      36 ..       3      36 ..       1      46 [. 0.71
   2 !    8.9   0.3    0.0023         1      12     166 ..      61     214 ..      58     225 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.033
                                      EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS- CS
                              cobW  3 tvltGflGsGKTtLlnhllenraglklavivNef 36
                                      +v++G  GsGK+t+   l ++ a++   v+v + 
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAEKGNEVLVVDT 36
                                      799*********9766555665665555555554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0023
                                       CHHHHHHHHH...CT--SS-EEEEESS-SSCHCCCCCCHCCCT........EEEETTTTECCHCTT-HHHHHHHHHH CS
                              cobW  12 GKTtLlnhll...enraglklavivNefgevsiDaellretgve.......ivelenGciCctlredllkelealee 78 
                                       GK +L ++l+   + ++ ++l ++  ef   +i +el+  +++        i ++ +Gc C      + + le+l+ 
  gi|330506720|ref|YP_004383148.1|  61 GKKALSEKLMkfiRSEQRERLQIL-EEFTVKDIPEELVVGEDKIkliaigkIHSFGEGCACPM-GALAREFLEKLK- 134
                                       666666666666566666666654.57777788888886664334777788999999999987.333333334443. PP

                                       HHTT-SEEEEEE.CTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHC CS
                              cobW  79 reerldviliEt.tGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlld 154
                                          + +++++ t  G+ +             ++  d +v+v+D +  + + + +  ++ +++ +  +++ln +D  +
  gi|330506720|ref|YP_004383148.1| 135 --TNGEHVVVDTdAGIEHFGRG--------VEAGCDKIVVVIDPSFESVQLSGKIAEMSEKIGKPMFFILNRMDENS 201
                                       ..34588888873466554443........4899999******955577888899999999*************999 PP

                                       HC...HHHHHHHH CS
                              cobW 155 ee.allekleerl 166
                                       +e a+l   ++++
  gi|330506720|ref|YP_004383148.1| 202 KElADLVDKNKVI 214
                                       9877665555555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   4.3e-05      0.02      22      66 ..       3      46 ..       1     137 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-05
                            ATPase 22 vlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlren 66
                                      + i+G+ G+GK+++++  + + aek g++++ v ++e++  l+++
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAEK-GNEVLVVDTDESNFGLYKQ 46
                                      789************9988888777.************9666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00018     0.081      36      83 ..       3      40 ..       2      54 .. 0.81
   2 ?   -0.1   0.0       1.3     6e+02     123     150 ..     140     168 ..     121     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                            AAA_25 36 allaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdse 83
                                      ++++G +g+GK+t+   la ++a +G             Vl+v++++s+
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAeKGN-----------EVLVVDTDESN 40
                                      5799*******************5554...........56777776666 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                            AAA_25 123 gtl.ltadvdaleaaieevegvrlvviDp 150
                                         + ++a +++  + +e+ ++  +vviDp
  gi|330506720|ref|YP_004383148.1| 140 VVVdTDAGIEHFGRGVEAGCDKIVVVIDP 168
                                       33346777888888888888888999998 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   0.00013      0.06      43      79 ..      17      51 ..       8      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EE CS
                              FR47 43 vkalakeiaergktvllvvvasNtpsirlyeklGfek 79
                                       + la+eiae+g++vl  vv +++    ly++lGfe+
  gi|330506720|ref|YP_004383148.1| 17 SALLAREIAEKGNEVL--VVDTDESNFGLYKQLGFEQ 51
                                      45689*******9975..67899999*********97 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.2e-05     0.038      17      52 ..       2      37 ..       1      48 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.2e-05
                     TrwB_AAD_bind 17 hilivGttGsGKtqalekllrairargdraivlDlt 52
                                      +i+i G  GsGK++    l r+i ++g+ ++v+D+ 
  gi|330506720|ref|YP_004383148.1|  2 KIVICGKGGSGKSTISALLAREIAEKGNEVLVVDTD 37
                                      689*******************************85 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 ?   11.7   0.1    0.0002     0.091      32      68 ..       3      39 ..       1      42 [. 0.90
   2 ?   -3.5   0.0       8.7     4e+03      57      68 ..     158     169 ..     148     185 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                                      EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--- CS
                              MeaB 32 vGltGvPGaGkstlvealglelrrrGkrvavlavDPs 68
                                      + + G  G+Gkst+   l+ e++++G+ v v+  D s
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAEKGNEVLVVDTDES 39
                                      66899*************************9998865 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.7
                                       T--EEEEEE--- CS
                              MeaB  57 GkrvavlavDPs 68 
                                       G    v+ +DPs
  gi|330506720|ref|YP_004383148.1| 158 GCDKIVVVIDPS 169
                                       333334555555 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00056      0.26       1      36 [.       2      40 ..       2      71 .. 0.70
   2 ?   -1.3   0.0       7.8   3.6e+03      30      46 ..     197     216 ..     174     231 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00056
                            PglD_N  1 kivIiGaGGhgkvvadiieang...eyeiigflDdnkkt 36
                                      kivI G+GG gk  +  + a++   + +++ ++D ++++
  gi|330506720|ref|YP_004383148.1|  2 KIVICGKGGSGKSTISALLAREiaeKGNEVLVVDTDESN 40
                                      8***********998888777511145678888877643 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 7.8
                            PglD_N  30 lDdnkk...tevegypvlgk 46 
                                       +D+n+k   + v++ +v+g+
  gi|330506720|ref|YP_004383148.1| 197 MDENSKelaDLVDKNKVIGT 216
                                       45555422234455666664 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   0.1   0.00019     0.088     131     172 ..       2      42 ..       1      59 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                             T2SSE 131 lilvsGgTgsGKttllyallkeinksderivtvEDpvEiqle 172
                                        i++ G  gsGK+t+   l  ei+++  + v+v D+ E +  
  gi|330506720|ref|YP_004383148.1|   2 KIVICGKGGSGKSTISALLAREIAEK-GNEVLVVDTDESNFG 42 
                                       599**********************9.777888899998765 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 ?   12.3   0.1   0.00022       0.1      50      84 ..       3      37 ..       1      95 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                         IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvlfvrve 84
                                      iv++G  G GKs +++ l++e +++g +vl v ++
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAEKGNEVLVVDTD 37
                                      89***************************988765 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   0.1   0.00021     0.094      27      63 ..       3      39 ..       2     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00021
                            AAA_16 27 vllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      +++ G  G+GKs++   l+r++ ++g  +l  ++d++
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAEKGNEVLVVDTDES 39
                                      5789*********************644444444443 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   0.00022       0.1       8      56 ..       3      47 ..       2     135 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00022
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdl 56
                                      +v++G  G+GK+t  + l+++  e       + ev+ v+  +s+    k+l
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAEK------GNEVLVVDTDESNfgLYKQL 47
                                      79******************98543......66666666655553233333 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00022       0.1       4      84 ..       3      80 ..       2      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                           DUF2075  4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsef.kkae 81
                                      +++ G+ G+GK+ +   l+ e+   +e+ ++v+++   + +  l+++l  ++ +k++ e++ + +++ ++l +f ++++
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREI---AEKGNEVLVVDTDESNFGLYKQLGFEQ-PKDFMESLGGKKALSEKLMKFiRSEQ 77
                                      6899*****************9...888888888888888999*****9999.88888888888888888887764444 PP

                           DUF2075 82 ekk 84
                                      +++
  gi|330506720|ref|YP_004383148.1| 78 RER 80
                                      444 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00081      0.37       4      28 ..       8      34 ..       5      46 .. 0.77
   2 ?   -2.3   0.0       6.7   3.1e+03      14      29 ..     127     142 ..     120     153 .. 0.59
   3 ?   -2.3   0.0       6.6     3e+03     112     129 ..     184     200 ..     173     217 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00081
                                      STTSSHHHHHHHHHHHHHHTTE...EE CS
                   Thymidylate_kin  4 lDGaGKttqaellkerlkeegik..vv 28
                                        G+GK+t+++ll++ + e+g +  vv
  gi|330506720|ref|YP_004383148.1|  8 KGGSGKSTISALLAREIAEKGNEvlVV 34
                                      569******************884333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.7
                                       HHHHHHHHHTTE.EEE CS
                   Thymidylate_kin  14 ellkerlkeegikvvl 29 
                                       + + e+lk++g++vv+
  gi|330506720|ref|YP_004383148.1| 127 REFLEKLKTNGEHVVV 142
                                       3444555555555443 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.6
                                       GGTTSE-SEEEEEESSHH CS
                   Thymidylate_kin 112 edvllkPdltflldvdpe 129
                                       e+++ kP +++l  +d++
  gi|330506720|ref|YP_004383148.1| 184 EKIG-KPMFFILNRMDEN 200
                                       4443.4444444443332 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00046      0.21       1      37 [.       2      38 ..       2      92 .. 0.89
   2 ?   -2.1   0.0       6.9   3.2e+03      29      55 ..     174     199 ..     153     224 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00046
                                      EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEE CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfytee 37
                                      k++i G+ G+GK+T+   ++++++++g +v  + t e
  gi|330506720|ref|YP_004383148.1|  2 KIVICGKGGSGKSTISALLAREIAEKGNEVLVVDTDE 38
                                      689***********************99886665555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.9
                                       GEEEEEEEEE-------EEEEEET.T- CS
                          NTPase_1  29 kvgGfyteevreggrrigFkivdlasg 55 
                                       +++G ++e   + g+ + F +  + ++
  gi|330506720|ref|YP_004383148.1| 174 QLSGKIAEMSEKIGKPMFFILNRM-DE 199
                                       444444444444444444444444.33 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00023      0.11      23      60 ..       3      38 ..       1     167 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                        KAP_NTPase 23 vgLygkWGsGKssllnkledelkefakpvrflfaefna 60
                                      +++ gk GsGKs++ ++l +e+ e+   +++l+++ + 
  gi|330506720|ref|YP_004383148.1|  3 IVICGKGGSGKSTISALLAREIAEK--GNEVLVVDTDE 38
                                      7889999******************..89999998765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0036       1.7     102     130 ..       3      31 ..       1      37 [. 0.85
   2 ?    1.7   0.0      0.47   2.2e+02      19      63 ..     162     204 ..     149     225 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0036
                                       EEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpelelktgev 130
                                       +v++G+ G GKSt+   l+ e   k +ev
  gi|330506720|ref|YP_004383148.1|   3 IVICGKGGSGKSTISALLAREIAEKGNEV 31 
                                       699***********999998877766665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.47
                                       EEEEEESTTTT--HHHHHHHHHHHHHTT-EEE.EEEE-GGG--HHH CS
                       RsgA_GTPase  19 llivvslkepelslnlldrfLvlaeekgiepv.ivlnKiDlleeee 63 
                                       +++v  ++ p++++ +l+  ++++ ek  +p+  +ln++D  ++e 
  gi|330506720|ref|YP_004383148.1| 162 IVVV--ID-PSFESVQLSGKIAEMSEKIGKPMfFILNRMDENSKEL 204
                                       4444..34.7777777777777666555444315677777665554 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 ?   12.0   0.0   0.00034      0.16      29      82 ..       5      63 ..       1     144 [. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00034
                                      EEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH....HHHHHHH....HHGGGGTGG.. CS
                            ResIII 29 ikmaTGtGKTlvaaklierllkkgkeekflflvprk....slleqtl....eefkkflseay 82
                                      i    G+GK+ ++a l++++++kg+e   +++v++      l++q+     ++f++ l  ++
  gi|330506720|ref|YP_004383148.1|  5 ICGKGGSGKSTISALLAREIAEKGNE---VLVVDTDesnfGLYKQLGfeqpKDFMESLGGKK 63
                                      55667*****************9774...777777733444666665555545544444333 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00095      0.44      27      90 ..       9      73 ..       3     146 .. 0.74
   2 ?   -2.1   0.0       5.4   2.5e+03      52      73 ..     162     183 ..     155     217 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00095
                         SWI2_SNF2 27 qGSGKsltmvflakklleeelknpkvvvvtDRkd..LdkQls.ktfakageekpkqaesrkeLkell 90
                                       GSGKs  +++la++++e  + n  +vv tD ++  L kQl  ++ +++ e+   ++  +++L++ +
  gi|330506720|ref|YP_004383148.1|  9 GGSGKSTISALLAREIAE--KGNEVLVVDTDESNfgLYKQLGfEQPKDFMESLGGKKALSEKLMKFI 73
                                      6****************9..56777777788775446677641233333333333444445555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.4
                         SWI2_SNF2  52 vvvvtDRkdLdkQlsktfakag 73 
                                       +vvv+D +    Qls+++a+++
  gi|330506720|ref|YP_004383148.1| 162 IVVVIDPSFESVQLSGKIAEMS 183
                                       5555554433334443333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                       149  (0.00831056); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 1757.53
//
Query:       gi|330506721|ref|YP_004383149.1|  [L=536]
Description: ABC transporter substrate-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-76  257.8   2.8    2.1e-76  257.4   2.8    1.2  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.4   2.8   1.1e-80   2.1e-76       2     363 ..      94     440 ..      93     453 .. 0.90

  Alignments for each domain:
  == domain 1  score: 257.4 bits;  conditional E-value: 1.1e-80
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       +vpaLAes  ++++ +  y f LRk+v++ DG+++tA Dvvf++++++ +++++ ++        +kk+ea+dd+tv
  gi|330506721|ref|YP_004383149.1|  94 YVPALAES--WQMEGNDAYVFSLRKNVTWNDGEKFTANDVVFTIDYIKQHPYPWVNSEP------VKKAEALDDNTV 162
                                       79******..459*****************************************99665......69********** PP

                                       EEEESSETTTTTTHCHHHHHHHGC.CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTT.EEEEEE-TTSTTTSCSSSS CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiak.kaaekeddkdkdtnekpvgtGPYklkefkpgq.kivlernpdYwgggkpkld 153
                                       +++l++ +a+fl ++  + + +++   ++ ++ ++ + +++++gtGPYkl+++++ q +  +e+ + Y+  g+pk++
  gi|330506721|ref|YP_004383149.1| 163 KIYLNHSYAPFLDMVVGTLPILPEhIYKSVSNPAEFQDDKALIGTGPYKLVNYDKTQgTYLYEAYDGYY-LGAPKVK 238
                                       *********888888888887777434455666677888999*************995666999999*9.******* PP

                                       EEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHH CS
                         SBP_bac_5 154 riefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyA 230
                                       +++f  i +++ +aaal++G++ d++ +p++ +e+l++++ + +  ++p+ g+t +++N++k+p++d+++RqAl yA
  gi|330506721|ref|YP_004383149.1| 239 QLKFVKI-SNEMAAAALEKGDV-DAVVVPAETVEKLRKENFVVL--DGPRDGITKIMINHNKEPLSDTKLRQALYYA 311
                                       *******.999999999*****.7778********988887777..******************************* PP

                                       S-HHHHHHHCTTTSSEEESSS.STTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETT CS
                         SBP_bac_5 231 iDreeivkavlegyatpansl.lppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltlllasg 306
                                       iDr+++v+++l+gy++ a s  ++p s +++++ +p+  +ydp k  +l+ e Gy ++ g+++++ +++l+l+l   
  gi|330506721|ref|YP_004383149.1| 312 IDRQALVDVALRGYGIIASSGlFAPDSEWYNPDVEPY--KYDPIKTAELMSELGYAKD-GQYFSKGGEPLVLEL-LV 384
                                       ****************999999********9999997..89***************97.578877744444433.34 PP

                                       SHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTH CS
                         SBP_bac_5 307 spaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpd 363
                                       ++a +++ e+i qql+k+G+kv++++vd+ +t ++ v +++fd++l + g+  +dp+
  gi|330506721|ref|YP_004383149.1| 385 TAATERVGEMIRQQLEKAGFKVNLRSVDA-KTLDSLVGQWNFDLALNSHGGMGGDPE 440
                                       566789***********************.9**9****************9999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); 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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 4042.18
//
Query:       gi|330506722|ref|YP_004383150.1|  [L=181]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase-like protein [Methanosaeta concilii GP6]
Scores for complete 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   65.6   0.0    4.9e-18   65.4   0.0    1.0  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
    2.6e-10   40.1   0.0    3.8e-10   39.6   0.0    1.2  1  FdtA             WxcM-like, C-terminal
     0.0021   17.7   0.1       0.63    9.8   0.0    2.2  2  Cupin_2          Cupin domain


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 !   65.4   0.0   8.2e-22   4.9e-18       4     148 ..      29     171 ..      26     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 8.2e-22
                                       STTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEEE CS
                   dTDP_sugar_isom   4 iegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldva 80 
                                       iegv++ ++k f+DeRGf +e  + ++ + +   +++ q   s+s  g+++G H++++   q+  + +v+G v   +
  gi|330506722|ref|YP_004383150.1|  29 IEGVVIKDMKLFSDERGFLTELIRLDDEEMKA--SNIKQIIASYSYPGMIKGWHLHSK---QEDHLICVTGIVKVAL 100
                                       89********************9987766554..3589****************9855...7777789********* PP

                                       EE-BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEES.S---GG..GEEEE-TT-TTT CS
                   dTDP_sugar_isom  81 VDlRkgSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvt.eyyape..sergirwnDpel 148
                                        D R++Spt++   ++ + ++  r++yip+g+ hG   + ++  v+  +   +y+pe  +er +++ D+++
  gi|330506722|ref|YP_004383150.1| 101 YDYREDSPTYKFLNEIFMGEKCPRAVYIPPGVFHGTKNIGNDISVVIGMPsLFYDPEnvDERRVNPIDNDI 171
                                       ***************************************99988888887579***977899999999886 PP

>> FdtA  WxcM-like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   6.3e-14   3.8e-10       3     118 ..      32     158 ..      30     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 6.3e-14
                                       -EEEEEEEEEETTE...EEEEEEBTTTBSS--SEEEEEES--TTTEEEEEEESS--EEEEEEES-EEEEEE-SS-E. CS
                              FdtA   3 vklielpkikderg...nLsvieeekevpfeikrvyyvydvpegeerGeHahkkleqllialsGsvevllddgkkk. 75 
                                       v +++++ ++derg   +L+ ++ e+    +ik++  +y  p ++ +G H+h k+e  li+++G v+v l d ++  
  gi|330506722|ref|YP_004383150.1|  32 VVIKDMKLFSDERGfltELIRLDDEEMKASNIKQIIASYSYPGMI-KGWHLHSKQEDHLICVTGIVKVALYDYREDs 107
                                       66899*********55555566666778899***********999.************************9988763 PP

                                       ......EEEEE-STT.EEEEE-TT-EEEEE---TT.-EEEEEESS---GGG CS
                              FdtA  76 ......keilldsps.kglyipkmiWrelinfsed.avllvlasesydeed 118
                                             +ei++ ++   ++yip+++ + + n  +d +v++ + s  yd+e+
  gi|330506722|ref|YP_004383150.1| 108 ptykflNEIFMGEKCpRAVYIPPGVFHGTKNIGNDiSVVIGMPSLFYDPEN 158
                                       322223345554444489*****************99**********9986 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0019        11       7      34 ..      73     101 ..      71     109 .. 0.85
   2 !    9.8   0.0    0.0001      0.63      46      64 ..     125     143 ..     124     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0019
                                       TTEEEEEECSSSEEEEEEEEESEEEEE.E CS
                           Cupin_2   7 pGesapshrHpgedeffyVleGegelt.v 34 
                                       pG   ++h H+ ++  ++++ G +++  +
  gi|330506722|ref|YP_004383150.1|  73 PGMIKGWHLHSKQEDHLICVTGIVKVAlY 101
                                       677889*******9*******99998744 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0001
                                       EEEE-TT-EEEEEE-SSS- CS
                           Cupin_2  46 svyfpagtpHrfrNtgdep 64 
                                       +vy+p+g+ H+ +N g++ 
  gi|330506722|ref|YP_004383150.1| 125 AVYIPPGVFHGTKNIGNDI 143
                                       69**************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1349.07
//
Query:       gi|330506723|ref|YP_004383151.1|  [L=646]
Description: cation-transporting P-type ATPase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-47  160.0   1.2    1.2e-46  158.5   1.2    1.8  1  E1-E2_ATPase  E1-E2 ATPase
    1.6e-37  129.9   0.1    2.9e-37  129.0   0.1    1.4  1  Hydrolase     haloacid dehalogenase-like hydrolase
    0.00017   21.4   0.1      0.094   12.4   0.1    2.2  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.045   14.1   2.3        1.2    9.5   0.2    2.7  2  DUF1056       Protein of unknown function (DUF1056)
       0.14   12.5   0.0       0.49   10.8   0.0    2.0  1  HAD           haloacid dehalogenase-like hydrolase
       0.17   12.0   0.0       0.36   10.9   0.0    1.5  1  HAD_2         Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.5   1.2     4e-50   1.2e-46       2     179 ..     145     314 ..     144     316 .. 0.98

  Alignments for each domain:
  == domain 1  score: 158.5 bits;  conditional E-value: 4e-50
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvs 78 
                                       llp++++v+r+g+  ++  +e++ GD++l+++g+r+++Dg++v+g a+v ++a+TGEsl+vek++gd+vf+Gt    
  gi|330506723|ref|YP_004383151.1| 145 LLPDSVTVRREGRDLTVCLEEVRAGDMLLVRSGERIAVDGEVVSGVASVSQAAITGESLAVEKKAGDKVFAGTLLEV 221
                                       6899************************************************************************* PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHH CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralall 155
                                       g +++ Vt +g++t+lg+i +l+eea++ k+p+++ l++++k+++p++l++++l++             ++ra+++l
  gi|330506723|ref|YP_004383151.1| 222 GAIEVLVTGIGSETTLGQIRTLIEEAQAHKPPIERLLNRYAKIYMPTALIAGALLWWWS--------GDIMRAITML 290
                                       *************************************************9999998877........89******** PP

                                       HHHS-TTHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 156 vaaiPcaLplavplalalgarrla 179
                                       ++++Pc ++la+p+al+++++++a
  gi|330506723|ref|YP_004383151.1| 291 IVFCPCVIVLATPTALVAAIGNAA 314
                                       *********************998 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   0.1   9.5e-41   2.9e-37       1     210 []     332     550 ..     332     550 .. 0.94

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 9.5e-41
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHHHHHH...HHHHHETTTE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx. RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakarsgal...tgfatfigrg. 67 
                                       ++tv+fDk+GTLt g+p + ++ +  + +  + le +      sehp+g+a+v +ak r  +l   + f+ ++g g 
  gi|330506723|ref|YP_004383151.1| 332 VDTVIFDKTGTLTAGKPKLLQIEALGDNSQDELLEKAargekfSEHPLGRAMVDEAKSRDLDLvdpQFFEPLPGLGi 408
                                       68************************99999999999999*******************555546577888999999 PP

                                       .......HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHT CS
                                       .......xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 .......ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaa 133
                                              ++  g+   l+++   + +d +++ +s+++ g +v+ll   +r  ++f ++d+  ++pe   +v++L + 
  gi|330506723|ref|YP_004383151.1| 409 ranvdgqEIFLGRTSSLEREgiFVGQDIKERAESLEATGCSVILLaaGGRTEGLFVFEDE--LRPESHNVVQKLDEL 483
                                       98888889999999999999*************************6666***********..*************** PP

                                       TEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 134 gievvlltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                       g++vv++tgdn++  er+a+++G           + + + +  p+ kv++++eLq k+++va+VG gvnD +ala+A
  gi|330506723|ref|YP_004383151.1| 484 GLDVVIVTGDNRASTERVASRIG-----------VRElFFEKMPQEKVQIVKELQSKGRKVAFVGEGVNDGPALAQA 549
                                       ***********************...........777899999********************************** PP

                                       T CS
                                       x RF
                         Hydrolase 210 g 210
                                       +
  gi|330506723|ref|YP_004383151.1| 550 D 550
                                       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 !    6.6   0.0     0.002       5.8      15      55 ..     468     508 ..     464     513 .. 0.88
   2 !   12.4   0.1   3.1e-05     0.094     194     233 ..     521     560 ..     519     574 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.002
                                       ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                       Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                       ++ +++ ++++kl e g  vvi TG +  ++++v+  +g+ 
  gi|330506723|ref|YP_004383151.1| 468 ELRPESHNVVQKLDELGLDVVIVTGDNRASTERVASRIGVR 508
                                       56789999***********************9999988876 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.1e-05
                                       HHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-H CS
                       Hydrolase_3 194 klakelnisleeviafGDgeNDieMLeaaglgvAmgnase 233
                                       +++kel+ +  +v+ +G g ND + L +a++g+Amg a  
  gi|330506723|ref|YP_004383151.1| 521 QIVKELQSKGRKVAFVGEGVNDGPALAQADVGIAMGIAGT 560
                                       57899******************************97754 PP

>> DUF1056  Protein of unknown function (DUF1056)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00039       1.2      27      59 ..     102     134 ..      94     137 .. 0.86
   2 ?    3.4   0.1     0.033        98      35      53 ..     599     617 ..     589     621 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00039
                           DUF1056  27 tytaFlfnataGvlvisvvlflvGllsEvieek 59 
                                       t++a  ++  a   v++v l+l Gll E++ ++
  gi|330506723|ref|YP_004383151.1| 102 TMAAITIGEYAAAAVVAVLLLLGGLLEEFVAAR 134
                                       67888889999999****************986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.033
                           DUF1056  35 ataGvlvisvvlflvGlls 53 
                                        ++Gvl+++v+l + G+l+
  gi|330506723|ref|YP_004383151.1| 599 FSLGVLAVAVALTVPGILT 617
                                       579*************986 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00016      0.49      86     141 ..     469     514 ..     438     547 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                               HAD  86 ldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltge 141
                                       l+p+   ++++  + G  vv+v+g +r  +e+++ + g    + +       ++ +
  gi|330506723|ref|YP_004383151.1| 469 LRPESHNVVQKLDELGLDVVIVTGDNRASTERVASRIG----VRE------LFFEK 514
                                       5699999999999*************************....666......55555 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   0.0   0.00012      0.36      81     133 ..     470     522 ..     466     553 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                             HAD_2  81 ydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvek 133
                                        ++ ++++++L e g+ + ivT  +r+++e+  +++g+ ++F   + +e+v+ 
  gi|330506723|ref|YP_004383151.1| 470 RPESHNVVQKLDELGLDVVIVTGDNRASTERVASRIGVRELFFEKMPQEKVQI 522
                                       5778899********************************99977666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 4501.53
//
Query:       gi|330506724|ref|YP_004383152.1|  [L=355]
Description: hypothetical protein MCON_0488 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-17   63.1   0.0    1.8e-14   53.9   0.0    2.5  2  FmdE      FmdE, Molybdenum formylmethanofuran dehydrogenase o


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0004       7.1      10      88 ..      30     119 ..      26     153 .. 0.71
   2 !   53.9   0.0   9.8e-19   1.8e-14       1      88 [.     194     302 ..     194     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0004
                                       HHHHHHHHHHHHCC....-TTSSSEEEEES-S.........TCHHHHHHHHCS--TTTTSEEE...--SS-SEEEEE CS
                              FmdE  10 vlGyrmakaalkelgpkeeegdeelvaivetd.........sCldDAiqvltgctlGkgnliv...mdygkkaltfk 74 
                                       +lG ++a+ a++ lg +  +gd ++ a++            + +  +i    g ++G gnl+     ++    + f 
  gi|330506724|ref|YP_004383152.1|  30 ALGGKAAQKAMQDLGFE--KGDANVLALTDAGhaivdgqtsQAAIKGITNESGNSIGDGNLFRplrAHWKPLWFYFF 104
                                       6899**********985..4556666666666556666566777778888889999999998522134555556999 PP

                                       ETTT-EEEEEEE-.C CS
                              FmdE  75 krktgkavrlklk.e 88 
                                       +++tg+av l ++ e
  gi|330506724|ref|YP_004383152.1| 105 DKSTGEAVYLEANsE 119
                                       999999999999931 PP

  == domain 2  score: 53.9 bits;  conditional E-value: 9.8e-19
                                       HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--...SS-SEE... CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetdsCldDAiqvltgctlGkgnlivmd...ygkkal... 71 
                                       fH+HlCpg+++G+ +a+ + ++l++++ +  e + +i+  ++C+dD +q+ +++t+Gk  ++vm      kka+   
  gi|330506724|ref|YP_004383152.1| 194 FHDHLCPGVTSGLHIAEFVEEKLPITN-S-SESYKVIACPQWCKDDLFQMRWDATPGKSGMFVMAltdAEKKAVpnv 268
                                       9***********************963.3.58********************************8666677777655 PP

                                       .EEEET.....TT-EEEEEEE-...........C CS
                              FmdE  72 .tfkkr.....ktgkavrlklk...........e 88 
                                         ++ r     k+g+a+ l+++           +
  gi|330506724|ref|YP_004383152.1| 269 aGIYIRwndtaKEGDALVLAYNfsavdlpkwngP 302
                                       5555557888888888888888666555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2916.64
//
Query:       gi|330506725|ref|YP_004383153.1|  [L=327]
Description: daunorubicin resistance ATP-binding protein family [Methanosaeta concilii GP6]
Scores for complete 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   99.8   0.0    2.7e-28   99.2   0.0    1.3  1  ABC_tran      ABC transporter
    3.6e-12   46.7   0.0    2.6e-05   24.2   0.0    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    5.3e-10   39.9   0.0    1.1e-09   38.9   0.0    1.5  1  DUF4162       Domain of unknown function (DUF4162)
    0.00052   20.6   0.0      0.001   19.6   0.0    1.4  1  AAA_23        AAA domain
     0.0018   18.1   0.0       0.42   10.3   0.0    2.2  2  AAA_15        AAA ATPase domain
     0.0029   17.3   0.0     0.0062   16.3   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.018   14.6   0.0      0.038   13.6   0.0    1.5  1  SRP54         SRP54-type protein, GTPase domain
      0.034   14.6   0.0       0.17   12.3   0.0    2.1  1  AAA           ATPase family associated with various cellular 
      0.037   13.8   0.0      0.066   12.9   0.0    1.3  1  AAA_30        AAA domain
      0.038   13.4   0.0       0.34   10.3   0.0    2.1  2  SRPRB         Signal recognition particle receptor beta subun
      0.043   14.2   0.0       0.09   13.2   0.0    1.7  1  RNA_helicase  RNA helicase
      0.061   13.7   0.0        0.1   13.0   0.0    1.5  1  AAA_16        AAA ATPase domain
      0.062   13.6   0.0       0.11   12.8   0.0    1.6  1  AAA_22        AAA domain
      0.071   11.7   0.0        0.1   11.2   0.0    1.2  1  AAA_13        AAA domain
       0.08   12.9   0.0       0.14   12.0   0.0    1.4  1  NACHT         NACHT domain
        0.1   12.9   0.0       0.26   11.5   0.0    1.7  1  AAA_28        AAA domain
       0.13   11.7   0.0       0.22   11.0   0.0    1.3  1  AAA_7         P-loop containing dynein motor region
       0.16   12.2   0.0       0.32   11.2   0.0    1.4  1  Roc           Ras of Complex, Roc, domain of DAPkinase


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 !   99.2   0.0   2.7e-31   2.7e-28       1     136 [.      21     164 ..      21     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 2.7e-31
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ v+l +++ ++ a++G+nG+GK+tL+++l+ + +pt+G+  + g d  + + ++ r+ ig++pqe++++ +++ +
  gi|330506725|ref|YP_004383153.1|  21 LDGVDLRVEAARVFAFLGPNGSGKTTLMRILTTQIRPTSGQASIFGLDAIR-NGQEIRRIIGYVPQETSVWLDISGY 96 
                                       7899****************************************9888877.8999********************* PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en              ++++i++al+++g++e++d+ v    +s+SgG+ +r+++a+all  pk+l+lDEpt
  gi|330506725|ref|YP_004383153.1|  97 ENllvyskiygvpagMRQKRIQDALQSMGIEEMADRMV----KSYSGGMVRRLEIACALLVGPKILFLDEPT 164
                                       **************999999******************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.1e-07   0.00041       2      26 ..      34      60 ..      33      90 .. 0.66
   2 !   24.2   0.0   2.6e-08   2.6e-05     238     297 ..     138     195 ..     128     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.1e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl..d 26
                                       ++ GpNgsGK++L+++l    r    
  gi|330506725|ref|YP_004383153.1| 34 FAFLGPNGSGKTTLMRILTTQIRPtsG 60
                                      6799**************543333443 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 2.6e-08
                            AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTH 297
                                       S G+ r l ++ all  +   ++l++DEp  gL+P++ + ++  l++ +++ g+ v++ TH
  gi|330506725|ref|YP_004383153.1| 138 SGGMVRRLEIACALLVGP---KILFLDEPTIGLDPSARKAVWeNLISFKKEYGTTVFFNTH 195
                                       666666667777777666...9********************98999999999******** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   1.1e-12   1.1e-09       1      80 [.     219     307 ..     219     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.1e-12
                                       E-HHHHHTTS-SSEEEEE......-------..--.-EEEE-TTS-EEEEE--.-----------.----EEEEEEE CS
                           DUF4162   1 GtleeiKrsygknrieve......adaeelleepg.veeveeeggelelkled.eeaanellkal.tsgveirsFee 68 
                                       Gt +e+K+s+++++i+v       +++ +  +  + v+   +++++le+ +ed e++ + +l+ l ++gv+++++  
  gi|330506725|ref|YP_004383153.1| 219 GTASELKQSLRSEIIQVYpdgridGQVLKSIRDLAfVRGAINNNSHLEIVVEDsETKLPLILDVLrNEGVSLKRICT 295
                                       899***************8765433333333335557777888899*******9***********88********** PP

                                       E---HHHHHHHH CS
                           DUF4162  69 eePsLndIFiek 80 
                                        +P+L+d+F+++
  gi|330506725|ref|YP_004383153.1| 296 AKPTLDDVFLKY 307
                                       **********98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0     1e-06     0.001      19      40 ..      31      52 ..      13      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1e-06
                            AAA_23 19 kgltlItGpNGaGKTTildAik 40
                                        ++++ GpNG+GKTT+++ ++
  gi|330506725|ref|YP_004383153.1| 31 ARVFAFLGPNGSGKTTLMRILT 52
                                      4799**************9876 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   0.00042      0.42      25      43 ..      33      51 ..      19      63 .. 0.82
   2 ?    5.6   0.0     0.011        11     325     364 ..     156     195 ..     153     196 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00042
                            AAA_15 25 ltvliGkNnsGKSsileal 43
                                      +  + G+N+sGK++++++l
  gi|330506725|ref|YP_004383153.1| 33 VFAFLGPNGSGKTTLMRIL 51
                                      77899***********998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                            AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +il+++EP + L p+a k ++++l++  ++  t v++ TH
  gi|330506725|ref|YP_004383153.1| 156 KILFLDEPTIGLDPSARKAVWENLISFKKEYGTTVFFNTH 195
                                       79****************************9999999999 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   6.2e-06    0.0062      13      39 ..      22      48 ..      14      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.2e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      dg +++++ + ++ + Gp+GsGK+Tl+
  gi|330506725|ref|YP_004383153.1| 22 DGVDLRVEAARVFAFLGPNGSGKTTLM 48
                                      677888888889**************8 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.8e-05     0.038       3      43 ..      33      73 ..      31      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaa 43
                                      v++++G++G+GKTt +  L  +++    ++ +  +D  R +
  gi|330506725|ref|YP_004383153.1| 33 VFAFLGPNGSGKTTLMRILTTQIRPTSGQASIFGLDAIRNG 73
                                      889**********************9999999999999976 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017      0.17       3      25 ..      36      63 ..      34     165 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                                      EESSTTSSHHHHHHHHHHHH.....THE CS
                               AAA  3 lyGppGtGKTllakavakel.....gve 25
                                      + Gp G GKT+l++ + +++     +++
  gi|330506725|ref|YP_004383153.1| 36 FLGPNGSGKTTLMRILTTQIrptsgQAS 63
                                      78**************999733332233 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.7e-05     0.066      17      46 ..      30      60 ..      24      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.7e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa.g 46
                                       +rv +  Gp G+GKtt+++ l+  ++   g
  gi|330506725|ref|YP_004383153.1| 30 AARVFAFLGPNGSGKTTLMRILTTQIRPTsG 60
                                      56799999*************9777665534 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 ?   10.3   0.0   0.00034      0.34       4      33 ..      32      62 ..      29      80 .. 0.79
   2 ?    0.6   0.0      0.32   3.2e+02     119     144 ..     210     235 ..     182     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00034
                                      -EEEEE-STTSSHHHHHHHHHHS.S---B-- CS
                             SRPRB  4 pavllvGlsdsGKTslftrLttd.svkktvt 33
                                      + + ++G+  sGKT+l+  Ltt+   ++ ++
  gi|330506725|ref|YP_004383153.1| 32 RVFAFLGPNGSGKTTLMRILTTQiRPTSGQA 62
                                      67889**************999843344444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.32
                                       EE-TTSTT---HHHHHHHHHHHHHHH CS
                             SRPRB 119 CnKqelflakspklikdaLEkElnki 144
                                        nK  ++ + +++ +k++L +E+ ++
  gi|330506725|ref|YP_004383153.1| 210 INKGSIVKSGTASELKQSLRSEIIQV 235
                                       49999999999***********9887 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     9e-05      0.09       3      58 ..      36      93 ..      34     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9e-05
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvys..rnpeddfwdgYtgqevvvidDf 58
                                      + Gp+g GK+tl++ L++++  ++++ +   + +  ++ e     gY  qe  v+ D+
  gi|330506725|ref|YP_004383153.1| 36 FLGPNGSGKTTLMRILTTQIRPTSGQASIFGLDAirNGQEIRRIIGYVPQETSVWLDI 93
                                      78*****************997764333333222102333333455555555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0    0.0001       0.1      25      54 ..      32      61 ..      19     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggi 54
                                      ++  + G+ G+GK++l+r l ++++ + g 
  gi|330506725|ref|YP_004383153.1| 32 RVFAFLGPNGSGKTTLMRILTTQIRPTSGQ 61
                                      567789****************99988433 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   0.00011      0.11       5      30 ..      31      56 ..      27     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqld 30
                                      a++ +  G+ G+GKTtl+r l+ q  
  gi|330506725|ref|YP_004383153.1| 31 ARVFAFLGPNGSGKTTLMRILTTQIR 56
                                      6777889*************999864 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0001       0.1      21      59 ..      36      74 ..      27     107 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                            AAA_13 21 iYGwNGaGKTtLSrllrslelgetepkfangsi....eitnge 59
                                      + G NG+GKTtL r+l  +    + p   ++si    +i ng+
  gi|330506725|ref|YP_004383153.1| 36 FLGPNGSGKTTLMRILTTQ----IRPTSGQASIfgldAIRNGQ 74
                                      569*************996....33444444555556555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.14       1      24 [.      32      55 ..      32      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                      SCEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklalaw 24
                                      r+ +  G++GsGKTtL++ l +++
  gi|330506725|ref|YP_004383153.1| 32 RVFAFLGPNGSGKTTLMRILTTQI 55
                                      567889***********9988776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00026      0.26       2      22 ..      34      54 ..      33      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                            AAA_28  2 ivitGgestGKTtlleaLaar 22
                                      ++++G+ ++GKTtl++ L+ +
  gi|330506725|ref|YP_004383153.1| 34 FAFLGPNGSGKTTLMRILTTQ 54
                                      689**************9876 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00022      0.22      28      82 ..      26      80 ..      18      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                             AAA_7 28 lllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82
                                      l +++ + + + Gp G+GKt++++ l++++ +++ +  ++ + a  + +++++ii
  gi|330506725|ref|YP_004383153.1| 26 LRVEAARVFAFLGPNGSGKTTLMRILTTQIRPTSGQASIFGLDAIRNGQEIRRII 80
                                      5677888899***************999999999888888888877777777766 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00032      0.32       4      70 ..      36     100 ..      34     112 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00032
                                       EESSTTSSHHHHHHCHCT-CC.C-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEE.EE-SGGCTT CS
                               Roc   4 lvGdsgvGKtsllkrfvedkf.sekekstigvdfltkevtkikgvendkkvkkvklniW.DtaGqerfr 70 
                                       ++G +g+GKt+l++ ++++   ++ + s++g+d +++  ++i+ +     v   + ++W D++G e+  
  gi|330506725|ref|YP_004383153.1|  36 FLGPNGSGKTTLMRILTTQIRpTSGQASIFGLDAIRNG-QEIRRIIGY--V-PQETSVWlDISGYENLL 100
                                       79***********9999887724557889999998754.355543221..1.22456666777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 2555.55
//
Query:       gi|330506726|ref|YP_004383154.1|  [L=217]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-15   57.4   0.9    1.6e-15   57.1   0.9    1.1  1  ABC2_membrane    ABC-2 type transporter
    2.3e-05   23.7   0.2    2.8e-05   23.4   0.2    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 !   57.1   0.9   1.8e-19   1.6e-15       3     125 ..      10     133 ..       8     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.8e-19
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg.nsedglnr.....pgllffsvlflafsaltsvap 73 
                                        +a++  e+++  +d++ + ++r +qp+l++ vfgt+ g+++   ++gl +     pg+l  s++f++   + ++ +
  gi|330506726|ref|YP_004383154.1|  10 MFAMIELEIRRLRHDRTEI-YTRAVQPILWLGVFGTIMGRVNaIPTGGLPYidyitPGVLLQSTIFVS--VFYGLTI 83 
                                       5788888999999999888.9******************97752444443356799************..999999* PP

                     ABC2_membrane  74 vferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgl 125
                                       v+ere g+l+r+lv+p+ s  a v+++ +++ +++++qali++ ++ +l g 
  gi|330506726|ref|YP_004383154.1|  84 VWERETGILKRLLVAPT-SIYATVVGRSAASGVRAVVQALIIFPVAMLL-GG 133
                                       *****************.**************************99988.65 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 !   23.4   0.2   3.2e-09   2.8e-05     160     230 ..      60     132 ..      34     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.2e-09
                   ABC2_membrane_3 160 asflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllil..llafg 230
                                        +++ + ++l   if+++++ +  iv E+e++i++++lv++ s ++ ++++  ++++ +++q+l+i+  ++++g
  gi|330506726|ref|YP_004383154.1|  60 IDYITPgVLLQSTIFVSVFYGL-TIVWERETGILKRLLVAPTSIYATVVGRSAASGVRAVVQALIIFpvAMLLG 132
                                       4455551555555666666555.7****************************************9984335665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1498.70
//
Query:       gi|330506727|ref|YP_004383155.1|  [L=177]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-16   58.7   8.8    5.1e-16   58.7   8.8    1.6  2  ABC2_membrane    ABC-2 type transporter
    8.3e-07   28.4  17.1    9.7e-07   28.2  17.1    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
     0.0011   18.3  12.1     0.0014   18.0  12.1    1.1  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.12   12.2   4.8       0.13   12.1   0.2    2.8  3  CoxIIa           Cytochrome c oxidase subunit IIa family


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 !   58.7   8.8   1.1e-19   5.1e-16     130     209 ..      61     142 ..      43     143 .. 0.91
   2 ?   -2.5   0.4      0.61   2.7e+03     106     151 ..     155     167 ..     147     173 .. 0.36

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 1.1e-19
                     ABC2_membrane 130 f..flflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavea 204
                                       f  + ++l+l+l++  + ++++l+++++++ e ++ l++++++pl++ s +++pid+mp+ lq +a lnPltyav+a
  gi|330506727|ref|YP_004383155.1|  61 FyiAAAFLILFLVSGGFAAISILVASIMKTRERFMGLGQALIMPLFFASNALYPIDMMPSALQLFAVLNPLTYAVDA 137
                                       2337899********************************************************************** PP

                     ABC2_membrane 205 lrsnl 209
                                       +r+ +
  gi|330506727|ref|YP_004383155.1| 138 IRGLM 142
                                       **987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.61
                     ABC2_membrane 106 pvsllqalifllivyflvgldlsrfflflllllltalaasslglli 151
                                       +                                  +l++  + +++
  gi|330506727|ref|YP_004383155.1| 155 LA---------------------------------ILVFDMVVFAL 167
                                       22.................................22222222222 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2  17.1   2.2e-10   9.7e-07     238     344 ..      63     169 ..      41     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.2e-10
                   ABC2_membrane_3 238 lglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgll 314
                                       + +++l ++l +  ++a++ l+ s++k+ e  ++l  ++i++l++++ +l+p++ +psal+ ++ ++P+++  +++ 
  gi|330506727|ref|YP_004383155.1|  63 IAAAFLILFLVSGGFAAISILVASIMKTRERFMGLGQALIMPLFFASNALYPIDMMPSALQLFAVLNPLTYAVDAIR 139
                                       45567888888888888899********************************************************* PP

                   ABC2_membrane_3 315 rli.tgdplweillsliilalfavvylllal 344
                                        l+ +g+ l +il ++++ ++f  v+++la 
  gi|330506727|ref|YP_004383155.1| 140 GLMiSGE-LGNILVDVLAILVFDMVVFALAS 169
                                       **74666.99999777777777777777774 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 !   18.0  12.1   3.2e-07    0.0014     164     285 ..      63     174 ..      54     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.2e-07
                   ABC2_membrane_2 164 lvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllspt 239
                                       +++a+++l+l+   f+a+++l++s+++++++ + l  +l++ l ++ +++ly++ ++++  +        +  l+p 
  gi|330506727|ref|YP_004383155.1|  63 IAAAFLILFLVSgGFAAISILVASIMKTRERFMGLGQALIMPL-FFASNALYPIDMMPSALQL-------FAVLNPL 131
                                       556666666655989************9999999988887666.99***********996666.......8888888 PP

                   ABC2_membrane_2 240 sayntllneilagsdlnalgstatnllilllllavllvlgyvlFkr 285
                                        +   +++ +  +++   lg     +l++l+   v+++l+  +F++
  gi|330506727|ref|YP_004383155.1| 132 TYAVDAIRGLMISGE---LGNILVDVLAILVFDMVVFALASLSFRK 174
                                       877666666666664...89999*****************999987 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 ?   -2.2   0.0      0.86   3.8e+03       9      15 ..      67      73 ..      65      74 .. 0.71
   2 ?    0.9   0.2      0.09     4e+02       6      18 ..      75      87 ..      74      88 .. 0.85
   3 ?   12.1   0.2   2.9e-05      0.13       6      28 ..     145     167 ..     144     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.86
                                      HHHHHHH CS
                            CoxIIa  9 avivvLt 15
                                      ++i++L+
  gi|330506727|ref|YP_004383155.1| 67 FLILFLV 73
                                      6788886 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.09
                                      HHHHHHHHHHHHH CS
                            CoxIIa  6 GaLavivvLtatI 18
                                      G  a i +L+a I
  gi|330506727|ref|YP_004383155.1| 75 GGFAAISILVASI 87
                                      77899*****998 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                            CoxIIa   6 GaLavivvLtatILvFWfgvFyv 28 
                                       G L+ i+v ++ ILvF ++vF++
  gi|330506727|ref|YP_004383155.1| 145 GELGNILVDVLAILVFDMVVFAL 167
                                       77999****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1140.49
//
Query:       gi|330506728|ref|YP_004383156.1|  [L=327]
Description: 2-dehydropantoate 2-reductase [Methanosaeta concilii GP6]
Scores for complete 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-35  119.7   0.1    1.4e-34  118.9   0.1    1.4  1  ApbA_C        Ketopantoate reductase PanE/ApbA C terminal
    5.1e-21   74.9   0.0    1.1e-20   73.8   0.0    1.5  1  ApbA          Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.045   14.6   0.0       0.15   12.9   0.0    1.9  2  GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fol


Domain annotation for each model (and alignments):
>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.1   2.4e-38   1.4e-34       1     123 [.     201     322 ..     201     324 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 2.4e-38
                            ApbA_C   1 dirlarweKllinaainpltalldckngellespelralvrallkEalavaeaegvelseerleeaveavlektaan 77 
                                       d+++ +w+Kl in++inp++al+++kng +l s+ l   v+++++E +ava+++g+ ++++ + e v  v+ekt +n
  gi|330506728|ref|YP_004383156.1| 201 DFTRQQWNKLFINSVINPIAALARQKNGIIL-SEVLGGTVERVVREGVAVAQELGMDFDPDAVLELVLSVAEKTGEN 276
                                       68899**************************.999****************************************** PP

                            ApbA_C  78 rsSMlqDveagrktEidyinGavvklAeklgvetPvnellyellka 123
                                       + SMlqDv++++ tEid inG++v+lAe++ + +Pvn +ly+l+ka
  gi|330506728|ref|YP_004383156.1| 277 SCSMLQDVLKNKTTEIDSINGYIVRLAEEHSIAVPVNGALYSLIKA 322
                                       ********************************************97 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   1.8e-24   1.1e-20       1     149 [.      11     175 ..      11     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1.8e-24
                                       EEEES-SHHHHHHHHHHHH.HTHC......EEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCH..SCCCCS- CS
                              ApbA   1 iailGaGaiGsllaakLak.agad......vtlilrsrrlealkknGlrltseggeeilrppealsae..ekselep 68 
                                       i+i GaGaiGsl+++ L+  +  d      + l++r  ++e+++++Gl+++ ++g++ +++ + +++     +++ +
  gi|330506728|ref|YP_004383156.1|  11 ILIYGAGAIGSLMGYLLSDaHSSDgggvenMALLGRMGHMERISSEGLEVEAPDGKTLVYFGHLFTDLeeLGRSDFH 87 
                                       89***************99555559999999******************************9999998887788999 PP

                                       ESEEEE-SSGGGHHHHHHH.HGG.GECTC...EEEEEESSSSCHHHHHTTTSTTS..EEEEEEEE-EEEEEETTEEE CS
                              ApbA  69 idlvivtvKayqteealee.ikp.lldpn...tvvlllqNGlgheeelrealpkp..rvlggvtthgatregpgevh 138
                                        dlv+++vK+y++e+ ++e +++ lld +   +  lll NG+g+ e ++ ++p++  r++ g+t+ g++    g+++
  gi|330506728|ref|YP_004383156.1|  88 PDLVVICVKTYSLEKLCQElVQSgLLDGKlknALFLLLMNGMGNRELFESQVPQAsgRIIEGITSNGVKLAREGKIE 164
                                       *****************9965541555433337999****************88548******************** PP

                                       ECS--EEEEEE CS
                              ApbA 139 hagkgeikige 149
                                       ++gkg+++i++
  gi|330506728|ref|YP_004383156.1| 165 LKGKGTTVIEK 175
                                       ********986 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 ?   12.9   0.0   2.6e-05      0.15       2      86 ..      10     111 ..       9     114 .. 0.73
   2 ?   -2.9   0.0       1.9   1.1e+04      41      64 ..     268     293 ..     257     295 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                                       EEEEETTSHHHHHHHHHHHHTTTTE.....EEEEEECSSHHHHHHHHHHTTHE............EESSHHHHHTCT CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrle.....evvalldpdaeraeavaesfgve............aysdleelladp 61 
                                       +++i GaG igs  +  l ++ +       e +all +  +  +  +e ++ve             ++dleel +++
  gi|330506728|ref|YP_004383156.1|  10 NILIYGAGAIGSLMGYLLSDA-HSSdgggvENMALLGRMGHMERISSEGLEVEapdgktlvyfghLFTDLEELGRSD 85 
                                       789999999999988444444.33357889666666666666655555555554444444444778899******99 PP

                                       .TESEEEE-S-GGGHHHHHHHHHHTT CS
                      GFO_IDH_MocA  62 .eidavivatpngtheelakaaleag 86 
                                        ++d+v++++ +++ e+l++++++ g
  gi|330506728|ref|YP_004383156.1|  86 fHPDLVVICVKTYSLEKLCQELVQSG 111
                                       *************9999999999987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.9
                                       HHHHHTTHEEESSHHHHHTCT..TES CS
                      GFO_IDH_MocA  41 avaesfgveaysdleelladp..eid 64 
                                        vae++g +++s l+++l+++  eid
  gi|330506728|ref|YP_004383156.1| 268 SVAEKTGENSCSMLQDVLKNKttEID 293
                                       46888888888888888888755565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2511.62
//
Query:       gi|330506729|ref|YP_004383157.1|  [L=301]
Description: integral membrane protein [Methanosaeta concilii GP6]
Scores for 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-08   32.7  39.4    6.9e-07   29.5  11.9    2.9  3  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 !   29.5  11.9   3.8e-11   6.9e-07       6     136 ..       6     134 ..       2     135 .. 0.89
   2 !   14.8  11.3   1.4e-06     0.024       8     109 ..     158     263 ..     152     270 .. 0.87
   3 ?   -0.3   1.1     0.061   1.1e+03     122     136 ..     287     301 .]     283     301 .] 0.84

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.8e-11
                              EamA   6 lallaalfwaiyfvlskillrkv..spltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80 
                                       + +++a + a+++++ k  l ++  ++l+++fv  +i  ++ll++ ++ +  +    + + l+ l +g++  v+ + 
  gi|330506729|ref|YP_004383157.1|   6 FSIAGAACLAVTGIIDKFYLGRYvrNTLAYLFVLVVIQQVFLLPVFAYAGLEF---VYPQSLYALSIGVVQ-VILWA 78 
                                       5689999************9999899999999999999999999999999888...666667777777665.67789 PP

                              EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       +++ alk  + s+++  +++ Pvf+ +  ++llge+l+ ++++g +l +l++lli+
  gi|330506729|ref|YP_004383157.1|  79 AYLRALKVEETSRIAGQVYVFPVFVFLGEFFLLGETLQPSDYAGGALLVLAALLIS 134
                                       ******************************************************98 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.4e-06
                              EamA   8 llaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl....aklslkdwllllllgllgtvlafl 80 
                                        +  +f a+y ++sk+ll ++  ++l ++++l + +++l++++  e +        s   ++++l+l  l  +l+ +
  gi|330506729|ref|YP_004383157.1| 158 AVFWVFTAAYSLASKYLLDYMTEWHLIVWSSLGSLVAVLAFLARGEVRSevggYFRSGPRLISILFLNELFDFLGRG 234
                                       55568899*********************************9999999988744444444888899999******** PP

                              EamA  81 lffyalkktsasnaslitslePvftlils 109
                                        ++ a   +s++ +s +++l+P +tli+ 
  gi|330506729|ref|YP_004383157.1| 235 SLIFAYALGSVALVSSVSALQPFITLIYV 263
                                       *************************9964 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.061
                              EamA 122 llgivlillGvllil 136
                                       + ++vli++Gv+l++
  gi|330506729|ref|YP_004383157.1| 287 IGATVLIVAGVYLVS 301
                                       6689********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2205.06
//
Query:       gi|330506730|ref|YP_004383158.1|  [L=77]
Description: hypothetical protein MCON_0494, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-06   27.5   0.0    3.4e-06   27.4   0.0    1.1  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 !   27.4   0.0   1.9e-10   3.4e-06       2      66 ..       6      76 ..       5      77 .] 0.85

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.9e-10
                   Acylphosphatase  2 rllvtG.rVQgvgFRkfvrrlAkelglkGy.vrNlsdg...sVeivaegeeekvekfleelksgppk.arv 66
                                      +++  G +V+ vg+R f+ ++A++  l G  + N + +   +V +++eg+e  +++fl++++ +  + a+v
  gi|330506730|ref|YP_004383158.1|  6 KITLAGpKVHDVGYRVFLLKNAMNTALPGLsTYNWEADgrqQVIALVEGDEVRIKAFLKKIEMDRLElAQV 76
                                      57778889*********************9877755444999*******************9865555776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 585.00
//
Query:       gi|330506731|ref|YP_004383159.1|  [L=390]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete 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-22   77.1   0.1    2.6e-21   75.3   0.1    2.0  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.5e-07   30.1   0.5    4.5e-07   30.1   0.5    1.8  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.092   12.8   0.1       0.26   11.3   0.1    1.8  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.82    9.6   4.4        1.6    8.6   4.4    1.5  1  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
        1.1    9.3   3.2         23    5.1   0.0    2.3  2  DUF4337         Domain of unknown function (DUF4337)


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 !   75.3   0.1   7.4e-25   2.6e-21       1      67 [.     292     356 ..     292     357 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 7.4e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       f++lke+l+yka  +G+++++v+pa TS+tC++Cg+ + +  +g+ fkCp Cg + d+D+n+a Ni+
  gi|330506731|ref|YP_004383159.1| 292 FYQLKEFLSYKALAAGVPLVLVDPACTSQTCHQCGEHGIR--NGKSFKCPVCGWSGDADFNGAKNIA 356
                                       899*************************************..************************7 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2         1   3.7e+03      43      69 ..      97     123 ..      71     141 .. 0.66
   2 !   30.1   0.5   1.3e-10   4.5e-07      10     106 ..     165     259 ..     155     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                        OrfB_IS605  43 grrlksdykylakeiaelqsklkkskn 69 
                                       +  ++++ ++++++  e++ +l +s++
  gi|330506731|ref|YP_004383159.1|  97 SIDYDTRIFAFREKDEEISVTLLRSRQ 123
                                       455666677777777777777777765 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 1.3e-10
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn..ykkasrklarlhrkr 84 
                                       +++    +++g+DlGi ++a++++++     + g+ +k  +  +a  +a lq+k+ k ++  ++++++ ++rl+ k 
  gi|330506731|ref|YP_004383159.1| 165 PEQIHVDTVLGVDLGITDIAVTSEGQ----KFGGKTIKLIKNHYASMRAVLQQKAVKGTRssRRRCRELQQRLSGKE 237
                                       667777899****************9....78999999999***********9998888889*************** PP

                        OrfB_IS605  85 srrrkhllhklathliktlkev 106
                                       +r  +   h+++++++ + +e+
  gi|330506731|ref|YP_004383159.1| 238 ARYQRQINHEISKAIVTRAQEI 259
                                       ****************999987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   7.3e-05      0.26      57      95 ..     305     344 ..     247     355 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.3e-05
                                       TTT-EEE.EEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  57 legaeLe.ieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       ++g  L  ++    + +C++Cg+++  + k+++Cp Cg +
  gi|330506731|ref|YP_004383159.1| 305 AAGVPLVlVDPACTSQTCHQCGEHGIRNGKSFKCPVCGWS 344
                                       45555552334445679*****9998777789*****965 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.4   0.00046       1.6      17      40 .]     316     341 ..     309     341 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00046
                        zf-C3HC4_2  17 pCgHvfCqkCilrsLeekn..eCPlC 40 
                                       +C  ++C +C    +++++  +CP+C
  gi|330506731|ref|YP_004383159.1| 316 ACTSQTCHQCGEHGIRNGKsfKCPVC 341
                                       7999*********99998889***** PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.1     0.014        52      46     105 ..     198     261 ..     195     270 .. 0.76
   2 ?    5.1   0.0    0.0063        23      25      47 ..     275     297 ..     263     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.014
                           DUF4337  46 ksikehlaeleleqlelllkakaeelaaavdkkiakykkkiarykke.....kkeikkkAkelea 105
                                       k ik+h a++ +  l+ ++ ++++  +++ ++ +++++ k ary+++     +k+i ++A+e+ a
  gi|330506731|ref|YP_004383159.1| 198 KLIKNHYASM-RAVLQQKAVKGTRSSRRRCRELQQRLSGKEARYQRQinheiSKAIVTRAQEIPA 261
                                       5578888888.44444444444999999999***************9877777777778888765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0063
                           DUF4337  25 aqteailaqaeasdqWafYQAks 47 
                                       ++++a  ++ + ++ WafYQ k+
  gi|330506731|ref|YP_004383159.1| 275 VNQKAGKNHRRRVNGWAFYQLKE 297
                                       5677888899**********886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 2934.71
//
Query:       gi|330506732|ref|YP_004383160.1|  [L=112]
Description: hypothetical protein MCON_0496 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-07   31.0   0.5    3.3e-07   30.8   0.5    1.2  1  Rubrerythrin  Rubrerythrin
    1.7e-05   23.9   0.1      2e-05   23.7   0.1    1.0  1  Mn_catalase   Manganese containing catalase
     0.0001   22.1   0.2    0.00014   21.7   0.2    1.1  1  COQ7          Ubiquinone biosynthesis protein COQ7
    0.00078   19.8   0.2    0.00099   19.4   0.2    1.3  1  DUF2383       Domain of unknown function (DUF2383)
     0.0048   16.8   0.2     0.0059   16.5   0.2    1.2  1  Ferritin      Ferritin-like domain
     0.0069   16.5   0.1      0.011   15.9   0.1    1.3  1  TetR_C_35     Bacterial Tetracyclin repressor,  C-terminal do


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.5   1.1e-10   3.3e-07       4      66 ..      27      86 ..      24     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.1e-10
                                      HHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SS CS
                      Rubrerythrin  4 ekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevke 66
                                         +a+E +a  lY++ ae ++  +p ++e++ ++A eEr Ha+ + +ll+ l ++++ e ++
  gi|330506732|ref|YP_004383160.1| 27 RLDLAAEHEAVHLYMAHAEATD--NPLVKEVLIDIANEERVHAGEFSRLLQILTGDED-ELLA 86
                                      556799****************..*******************************999.3333 PP

>> Mn_catalase  Manganese containing catalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   6.6e-09     2e-05     135     203 ..      18      86 ..       8     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.6e-09
                       Mn_catalase 135 asGnliaDlranlaaEakarlqverlyeltddpgvrdmlsfLlaRelvHqlafekAleeleeeetkvvP 203
                                       +s +li  lr +laaE +a   ++   e td+p v++ l  +   e+vH  +f + l++l++ e++++ 
  gi|330506732|ref|YP_004383160.1|  18 TSEELIRALRLDLAAEHEAVHLYMAHAEATDNPLVKEVLIDIANEERVHAGEFSRLLQILTGDEDELLA 86 
                                       5679999********************************************************988875 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   4.7e-08   0.00014       4      57 ..      24      75 ..      21      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.7e-08
                              COQ7  4 rllRvdhaGElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellk 57
                                      r+lR d a E  Av++Y +++ +  +++p +k++l +++++E+ H   f++ll+
  gi|330506732|ref|YP_004383160.1| 24 RALRLDLAAEHEAVHLYMAHAEA--TDNPLVKEVLIDIANEERVHAGEFSRLLQ 75
                                      89*********************..79999*******************99986 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   3.3e-07   0.00099      10      63 ..      30      83 ..      21      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.3e-07
                                      HHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT----- CS
                           DUF2383 10 ietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiralggeped 63
                                      +++++ +++ y++ ae  ++p +k++l +ia+e + +a e++  ++ l g+ ++
  gi|330506732|ref|YP_004383160.1| 30 LAAEHEAVHLYMAHAEATDNPLVKEVLIDIANEERVHAGEFSRLLQILTGDEDE 83
                                      678899*****************************************9999876 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2     2e-06    0.0059       2      60 ..      24      79 ..      23     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS CS
                          Ferritin  2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGg 60
                                       aL+  la+e++a ++y+a+a   ++p  +++   + + a eer ha ++   ++ l g
  gi|330506732|ref|YP_004383160.1| 24 RALRLDLAAEHEAVHLYMAHAEATDNPLVKEV---LIDIANEERVHAGEFSRLLQILTG 79
                                      689999***************99999886665...************999887776665 PP

>> TetR_C_35  Bacterial Tetracyclin repressor,  C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   3.6e-06     0.011       5      60 ..      32      98 ..      29     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.6e-06
                         TetR_C_35  5 airaavrafle..eaaadpLvravltge.........akedLlpllTtdseplleaAsarlaevlae 60
                                      a ++av+ +++  ea+++pLv+ vl +          + + Ll++lT d + ll++ +++++e++ +
  gi|330506732|ref|YP_004383160.1| 32 AEHEAVHLYMAhaEATDNPLVKEVLIDIaneervhagEFSRLLQILTGDEDELLAQGAEEVDEMAGK 98
                                      55677777775115789********9886778888776778*******************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 882.18
//
Query:       gi|330506733|ref|YP_004383161.1|  [L=155]
Description: hypothetical protein MCON_0497 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       433  (0.0241508); 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:                         0  (0); expected 0.2 (1e-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 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1266.51
//
Query:       gi|330506734|ref|YP_004383162.1|  [L=168]
Description: transposase, OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1437.01
//
Query:       gi|330506735|ref|YP_004383163.1|  [L=293]
Description: hypothetical protein MCON_0500 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.1e-106  356.0   0.8   1.3e-106  355.8   0.8    1.0  1  SDH_sah        Serine dehydrogenase proteinase
    0.00016   21.6   0.3    0.00062   19.7   0.1    1.9  2  CLP_protease   Clp protease
     0.0075   15.6   0.0      0.011   15.1   0.0    1.3  1  ECH_1          Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.019   14.9   0.0      0.045   13.7   0.0    1.6  1  Peptidase_S49  Peptidase family S49


Domain annotation for each model (and alignments):
>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  355.8   0.8  2.8e-110  1.3e-106       4     275 ..      11     289 ..       8     293 .] 0.95

  Alignments for each domain:
  == domain 1  score: 355.8 bits;  conditional E-value: 2.8e-110
                           SDH_sah   4 sdplsslssllwfllflylllapqlkrkqlllarlkvlrkleekrksrvitmihrqesigflGipiykfitiedsee 80 
                                       +d +ssl+s  w+++f++l+l p l+r++l+++r++vl +l++ r+s+vit+ihrqe+i+flGip+ ++i+iedse+
  gi|330506735|ref|YP_004383163.1|  11 TDAFSSLLSNAWIIIFILLFLVPMLQRNYLQAERKRVLARLGKARGSQVITLIHRQETISFLGIPLARYIDIEDSEK 87 
                                       799************************************************************************** PP

                           SDH_sah  81 vlrairltpkdkpidliihtpGGlvlaatqiakalkehkaktrvivphyamsGGtlialaadeiildenavlGpvdp 157
                                       vlrair + kd pid+i+htpGGl+laatqia alk+h+ak +vivphyamsGGtlia+aad+ii+d++a lGpvdp
  gi|330506735|ref|YP_004383163.1|  88 VLRAIRRAQKDIPIDIILHTPGGLALAATQIAMALKSHPAKKTVIVPHYAMSGGTLIAFAADQIIMDQHAALGPVDP 164
                                       ***************************************************************************** PP

                           SDH_sah 158 qlgq....ypaasilkvvekkeakdiddktliladiakkaikqveefvyellkdky.deekakeiakklteGrwthd 229
                                       qlg+    ypa+s+l v ekk+ +++ddktl+ ++ a+ka+ q++e++ ++l  k  d  k   i +++ +G++thd
  gi|330506735|ref|YP_004383163.1| 165 QLGDaqgaYPATSLLAVAEKKKIDEMDDKTLVYVEEARKALAQMRELLQKILEGKCsDSSKLDVIINEFVSGKYTHD 241
                                       **7544449*******************************************88862567889999*********** PP

                           SDH_sah 230 ypltveelke.lGlevntnvpeevyellelyeqplgqrps.veyipvp 275
                                       +p+  e++k  lG  v+t+vpeevy l+ely+  +g+  + vey+p  
  gi|330506735|ref|YP_004383163.1| 242 HPFMAEDAKAlLGDCVQTDVPEEVYSLMELYRMEMGRSRPgVEYVPLV 289
                                       ********9835999********************876666*****75 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   1.4e-07   0.00062      33      98 ..      88     150 ..      55     173 .. 0.85
   2 ?   -0.3   0.0      0.19   8.6e+02     125     151 ..     198     224 ..     188     252 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEETHHHHHHHTS-T CS
                      CLP_protease  33 iiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticlGlaaSmgslllaagek 98 
                                       +   L ++   ++d +i +++++pGG   a++ I+ +++ + ++ ++i+   a+S g+l++ a+++
  gi|330506735|ref|YP_004383163.1|  88 V---LRAIRRAQKDIPIDIILHTPGGLALAATQIAMALKSHPAKKTVIVPHYAMSGGTLIAFAADQ 150
                                       4...445556688899***********************************************986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                      CLP_protease 125 ieieaeellkikerlneilakhtgqsl 151
                                       +e   + l +++e l++il+ ++  s 
  gi|330506735|ref|YP_004383163.1| 198 VEEARKALAQMRELLQKILEGKCSDSS 224
                                       566778899999999999998887654 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.4e-06     0.011      97     152 ..     135     190 ..     118     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-06
                                       SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHH CS
                             ECH_1  97 GaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeei 152
                                        +a+ GG ++a a+D +i++++a+ g    +lG   ga+    l     k+k  e+
  gi|330506735|ref|YP_004383163.1| 135 HYAMSGGTLIAFAADQIIMDQHAALGPVDPQLGDAQGAYPATSLLAVAEKKKIDEM 190
                                       589******************************99999987777766666666665 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     1e-05     0.045       9      40 ..     129     160 ..     121     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                                       EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                     Peptidase_S49   9 vvasaenvaaSggYylasaadkivanpstivg 40 
                                        ++++  +a Sgg ++a aad+i++++++  g
  gi|330506735|ref|YP_004383163.1| 129 KTVIVPHYAMSGGTLIAFAADQIIMDQHAALG 160
                                       4678889********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 2441.18
//
Query:       gi|330506736|ref|YP_004383164.1|  [L=131]
Description: pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein [Methanosaeta concilii GP6]
Scores for complete 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   55.9   0.0    4.3e-15   55.7   0.0    1.1  1  Putative_PNPOx   Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.083   13.5   0.0       0.13   12.9   0.0    1.3  1  Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase
       0.15   11.4   0.0         11    5.4   0.0    2.1  2  SPOUT_MTase_2    AF2226-like SPOUT RNA Methylase fused to THU


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 !   55.7   0.0   7.2e-19   4.3e-15       2      86 ..       2      86 ..       1      88 [. 0.95

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 7.2e-19
                                      HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEE CS
                    Putative_PNPOx  2 deelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGt 80
                                      ++ ++e l+++k v +AT++++G Pnv+ v+l +  +++++ +a n   ++++nleenp++++l ++ e+ ++++i+Gt
  gi|330506736|ref|YP_004383164.1|  2 PADVKETLEKQKPVPIATASKSGVPNVVFVGLLKIIDDETLMIADNFFYKTAQNLEENPKISVLCYNGETKKSFQIKGT 80
                                      56789**************************99988888**************************************** PP

                                      EEEESC CS
                    Putative_PNPOx 81 aelvsd 86
                                      +++ ++
  gi|330506736|ref|YP_004383164.1| 81 VTVSKE 86
                                      *99887 PP

>> Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.2e-05      0.13      19      99 ..      11      84 ..       3      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                                      GGGEEEEEEE-T.TS-EEEEEEE---B-TT...SS-.EEEEEETTSHHHHHHH.H--EEEEEEEETTTTEEEEEEEEEE CS
                   Pyridox_oxase_2 19 kstefqlaTvdeeegkPrvRtvvfRgfleekkeesdvltfttDvrseKvkqlessnaaveavfylketreQfRisGkaf 97
                                      k++ + +aT + ++g P+   vvf g l+  +  ++   +++D    K++q  ++n+++ ++ y  et++ f i+G+++
  gi|330506736|ref|YP_004383164.1| 11 KQKPVPIATAS-KSGVPN---VVFVGLLKIID--DE-TLMIADNFFYKTAQNLEENPKISVLCYNGETKKSFQIKGTVT 82
                                      56666666666.455565...56666666543..33.346789999999888889**********************99 PP

                                      EE CS
                   Pyridox_oxase_2 98 vi 99
                                      v 
  gi|330506736|ref|YP_004383164.1| 83 VS 84
                                      85 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 ?    5.4   0.0    0.0018        11     113     139 ..       4      30 ..       1      44 [. 0.88
   2 ?    4.4   0.0    0.0035        21      24      58 ..      69     103 ..      54     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0018
                     SPOUT_MTase_2 113 elaealrkakevvvlvGsReGiPkGlf 139
                                       +++e+l+k+k v +   s+ G+P+ +f
  gi|330506736|ref|YP_004383164.1|   4 DVKETLEKQKPVPIATASKSGVPNVVF 30 
                                       7899*******************9998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0035
                     SPOUT_MTase_2  24 GRavqafevkeliiapkekvdayelaeflrgvreG 58 
                                       G + ++f++k  +   ke vd  +++++++gv++ 
  gi|330506736|ref|YP_004383164.1|  69 GETKKSFQIKGTVTVSKEGVDYEAMKSWVHGVNNK 103
                                       566789**************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1028.42
//
Query:       gi|330506737|ref|YP_004383165.1|  [L=466]
Description: cobyrinic Acid a,c-diamide synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-41  141.7   0.0    3.4e-41  141.0   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    1.9e-16   60.5   0.1      4e-11   43.1   0.0    2.4  2  AAA_26         AAA domain
    1.4e-15   57.4   0.0    2.3e-15   56.8   0.0    1.4  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00084   19.2   0.0     0.0017   18.2   0.0    1.4  1  SNO            SNO glutamine amidotransferase family
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.051   13.5   0.0    1.8  2  MobB           Molybdopterin guanine dinucleotide synthesis p
      0.019   14.6   0.0      0.036   13.7   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 !  141.0   0.0   1.1e-44   3.4e-41       2     193 ..     260     449 ..     259     452 .. 0.92

  Alignments for each domain:
  == domain 1  score: 141.0 bits;  conditional E-value: 1.1e-44
                          GATase_3   2 iavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeagg 76 
                                       i+v++++a+++y+  +l+++e +++  v f+p++d sl+e +d ++++Gg+++i + +l+++++++ +i++a+e+++
  gi|330506737|ref|YP_004383165.1| 260 IGVAQDEAFNFYYrdNLELMELAGARIVPFSPVHDASLPE-VDGIYIGGGYPEIYARELSENQSFKSSIQKAHEKDI 335
                                       99************************************66.************************************ PP

                          GATase_3  77 pvlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel....aaegeevkGyEiHsGrt 149
                                       p++g+CGGl++LG+eie  +g+     + e+ gl++ + + + +++++ v+g++       ++ge + G+E+H+++ 
  gi|330506737|ref|YP_004383165.1| 336 PIFGECGGLMYLGREIEW-DGE-----RREMAGLIPGKARRGARRTVSYVHGHLAQasplGRAGEYIMGHEFHHSEM 406
                                       ***************964.566.....99************************77799998889************* PP

                          GATase_3 150 ilkekakpllkvkv..ggnng.ekdGavkksedgnvlGtYlHglfdn 193
                                         ++ka+  ++++   g+++  + dG++ +    n++++Y H++ ++
  gi|330506737|ref|YP_004383165.1| 407 LIDPKARVEYAIRLerGTGIAdGLDGIHIG----NLVASYSHIHSAS 449
                                       ************886444444899999977....*********9765 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     6e-06     0.018       2      36 ..      11      45 ..      10      55 .. 0.91
   2 !   43.1   0.0   1.3e-14     4e-11      85     194 ..      74     189 ..      62     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6e-06
                            AAA_26  2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36
                                      +i+++g + ++GKT++ +gL++al+ ++ kv+ fK
  gi|330506737|ref|YP_004383165.1| 11 RILLAGDRSSSGKTTIVAGLLSALRGRNLKVQPFK 45
                                      58999************************999887 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 1.3e-14
                            AAA_26  85 didlekivkelekdadivvVEGagglgvpitee.llnadiaknlgapvilVargglgtinqllltiealr.qknvrv 159
                                       + ++ +i  + ++ ad+ v+EG+ gl ++   +  ++a+iak+l++pvi+V+ +++ t   ++l   ++  +  v+ 
  gi|330506737|ref|YP_004383165.1|  74 EAAVREIYAHAAQGADVAVIEGVRGLYEGYEGDlGSTAQIAKMLRVPVIFVVDARSITRSCAALVKGYMDyDPAVQF 150
                                       455667755567789**************99998**********************9998888888888745699** PP

                            AAA_26 160 lGvilNkvrnp....envetlekksgipvlGvvPylpdl 194
                                       +GvilNkv ++    ++ +++e + +++v+G++  ++d+
  gi|330506737|ref|YP_004383165.1| 151 RGVILNKVGSArhadKATREIERYAKVEVVGTIRRNEDM 189
                                       *******98885554599***************998876 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   7.8e-19   2.3e-15       1     119 [.      12     190 ..      12     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 7.8e-19
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i++a+  + +GKTt++a+L+ al  r+l+V+++++  +    ++ +++   + +                       
  gi|330506737|ref|YP_004383165.1|  12 ILLAGDRSSSGKTTIVAGLLSALRGRNLKVQPFKVAMDYIDPSY-HTWITGRSCrnldgylmneaavreiyahaaqg 87 
                                       6789999***************************9999666663.333333333677777777888*********** PP

                                       ......................................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS...- CS
                                       ......................................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
                              CbiA  55 ......................................dlkrllellealgkkkall...lkiagvvlnrvdgenee 90 
                                                                             d+ ++ ++++al+k++ +    +++ gv+ln+v++ ++ 
  gi|330506737|ref|YP_004383165.1|  88 advaviegvrglyegyegdlgstaqiakmlrvpvifvvDARSITRSCAALVKGYMDYdpaVQFRGVILNKVGSARHA 164
                                       ******************************************************9999***************9988 PP

                                       TTCHHHHHHHHHHCTS-EEEEEE--CCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  91 tllkealeelkqrygvpvlgviprdeava 119
                                        +    +e++    +v+v+g i+r+e+  
  gi|330506737|ref|YP_004383165.1| 165 DKATREIERYA---KVEVVGTIRRNEDMH 190
                                       88888888887...**********99873 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   5.8e-07    0.0017      30      88 ..     296     354 ..     283     376 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.8e-07
                                       GGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB CS
                               SNO  30 dlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelene 88 
                                        l evd++ i GG     ++ + + + +++  +++++ + +++G C Gl++l +e+e +
  gi|330506737|ref|YP_004383165.1| 296 SLPEVDGIYIGGGYPEIYARELSENQSFKSSIQKAHEKDIPIFGECGGLMYLGREIEWD 354
                                       6889*********998888877777778888999*********************9876 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 ?   13.5   0.0   1.7e-05     0.051       7      40 ..      18      51 ..      12      57 .. 0.85
   2 ?   -3.0   0.0       2.1   6.2e+03      80      98 ..      76      95 ..      71      98 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                              MobB  7 ksgsGKTtLleklipelkarglrvgtiKhahhgf 40
                                      +s sGKTt++  l+++l+ r+l+v   K a + +
  gi|330506737|ref|YP_004383165.1| 18 RSSSGKTTIVAGLLSALRGRNLKVQPFKVAMDYI 51
                                      699*********************9999877655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.1
                              MobB 80 sleellarlse.vDlvlvEG 98
                                      +++e+ a+ ++ +D+ ++EG
  gi|330506737|ref|YP_004383165.1| 76 AVREIYAHAAQgADVAVIEG 95
                                      55666666644478888887 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05     0.036      79     136 ..     296     354 ..     266     361 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                                       HHHHSSEEEE--S-HHHHHHHHHHTTH.HHHHHHHHHTT-EEEEETHHHHTTSSB-GGG CS
                     Peptidase_S51  79 klleadviyvgGGntfrLlkllketgl.dkllreavqqglvyiGvSAGaivagesiett 136
                                        l e d+iy+gGG     +++l e++   + +++a ++ ++++G   G +  g++ie +
  gi|330506737|ref|YP_004383165.1| 296 SLPEVDGIYIGGGYPEIYARELSENQSfKSSIQKAHEKDIPIFGECGGLMYLGREIEWD 354
                                       4556******************99986256899999******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3256.48
//
Query:       gi|330506738|ref|YP_004383166.1|  [L=271]
Description: nitrogenase iron protein 1 [Methanosaeta concilii GP6]
Scores for complete 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-90  302.0   0.1    4.3e-90  301.8   0.1    1.0  1  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    1.3e-09   38.2   0.0    2.3e-09   37.4   0.0    1.5  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    1.7e-09   37.5   0.0    3.7e-09   36.4   0.0    1.5  1  ParA          NUBPL iron-transfer P-loop NTPase
    1.4e-08   34.8   0.1      3e-08   33.8   0.0    1.6  2  AAA_31        AAA domain
    6.5e-07   28.8   0.6    1.1e-06   28.1   0.3    1.5  2  ArsA_ATPase   Anion-transporting ATPase
    0.00031   20.1   0.1      0.005   16.2   0.0    2.2  2  MipZ          ATPase MipZ
     0.0013   17.8   0.3     0.0017   17.4   0.3    1.3  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
     0.0024   17.6   0.0     0.0045   16.7   0.0    1.4  1  AAA_24        AAA domain
     0.0043   17.3   0.0       0.97    9.7   0.0    2.6  3  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.012   15.4   0.2        4.4    7.0   0.0    2.2  2  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.013   15.2   0.1      0.027   14.1   0.1    1.5  2  SRP54         SRP54-type protein, GTPase domain
      0.016   15.3   0.1      0.035   14.2   0.1    1.5  2  DUF87         Helicase HerA, central domain
      0.023   14.2   0.7      0.054   13.1   0.0    1.9  3  AAA_25        AAA domain
      0.045   14.1   0.1       0.44   10.9   0.0    2.1  2  AAA_16        AAA ATPase domain
      0.082   12.6   0.2       0.13   12.0   0.2    1.2  1  IstB_IS21     IstB-like ATP binding protein
       0.18   11.0   0.1       0.27   10.4   0.1    1.2  1  NB-ARC        NB-ARC domain
       0.19   12.1   0.0       0.65   10.4   0.0    1.9  2  RNA_helicase  RNA helicase


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 !  301.8   0.1   4.1e-93   4.3e-90       2     268 ..       6     267 ..       5     270 .. 0.95

  Alignments for each domain:
  == domain 1  score: 301.8 bits;  conditional E-value: 4.1e-93
                         Fer4_NifH   2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkGy 78 
                                       ++aiyGkGGiGks t++n++aa ae g+kvl+vGCDPk+Ds  ++l g+ ++t++d++ + g   + k edvv++G+
  gi|330506738|ref|YP_004383166.1|   6 HVAIYGKGGIGKSCTASNIAAACAEEGHKVLMVGCDPKSDSS-ITLIGRRIPTMMDLILKGG---EFKEEDVVHQGF 78 
                                       79***************************************9.99999*********99888...59********** PP

                         Fer4_NifH  79 ggvkcvesGGPepGvGCaGrgvitaielleelg.ayddlDfvlyDvLGDvvCGGfalPiredkaqevyivtsgelma 154
                                       +gv+c+e GGPepGvGCaGrg+i ai++l + + a +++D+vlyDv GD+vCGGf++Pir++   + yi+tsge m 
  gi|330506738|ref|YP_004383166.1|  79 RGVRCIEVGGPEPGVGCAGRGIIVAIDFLRKVSkAMEEVDLVLYDVPGDIVCGGFSAPIRKGLVSQAYIITSGEYMP 155
                                       *****************************997626668*************************************** PP

                         Fer4_NifH 155 lyaanniakgiekyaksggvrlgGliinsrkv..ddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyap 229
                                       lyaanni+kg+ + +      l+G+i+nsr+   ++ere++++fa+el++++++++P++ iv++ e r  tvie ap
  gi|330506738|ref|YP_004383166.1| 156 LYAANNISKGLLRLN----TPLAGVICNSREAagEREREIVNQFAQELNSRMVAFIPKEPIVQQCERRTVTVIEGAP 228
                                       ***********9875....579********982346789************************************** PP

                         Fer4_NifH 230 eseqakeyrelarkilenkklviPkplsedeLeelleef 268
                                       +s++a  yr+lar+i++  +  iP+pls+++L el  + 
  gi|330506738|ref|YP_004383166.1| 229 DSKIAAVYRALAREIMSGGEARIPEPLSDERLRELSRDL 267
                                       **********************************98765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   2.2e-12   2.3e-09       3     120 ..       8     215 ..       6     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2.2e-12
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.....HTTEB-HHHH.................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxx.................... RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.....leglendiep.................... 54 
                                       ++ +kGG GK+ +a n+a+a a++g++Vl+v +Dp + ++ +     +        p                    
  gi|330506738|ref|YP_004383166.1|   8 AIYGKGGIGKSCTASNIAAACAEEGHKVLMVGCDPKSDSSITligrrI--------Ptmmdlilkggefkeedvvhq 76 
                                       5789********************************777653333330........235566666666666779999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|330506738|ref|YP_004383166.1|  77 gfrgvrcievggpepgvgcagrgiivaidflrkvskameevdlvlydvpgdivcggfsapirkglvsqayiitsgey 153
                                       ******************99999999999999999999999999999999999999999999999999999988777 PP

                                       ....CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCC CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ....dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavae 120
                                            +  +++ l +l ++      +agv+ n  +     ++++e + +  q+++ + +++ip+   v +
  gi|330506738|ref|YP_004383166.1| 154 mplyAANNISKGLLRLNTP------LAGVICNSREAA--GEREREIVNQFAQELNSRMVAFIPKEPIVQQ 215
                                       7777666666666666655......899999997666..8888999988888888888899998877655 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   3.5e-12   3.7e-09       9     245 ..       9     243 ..       3     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 3.5e-12
                              ParA   9 lSgKGGVGKStvavnlAlaLakkglkvgllDaD........iyGpsiprllgveeekpeqsekkliPveakgikvmS 77 
                                       + gKGG+GKS +a+n+A+a a++g+kv ++  D        ++G  ip+++++  +  e +e+ ++    +g++++ 
  gi|330506738|ref|YP_004383166.1|   9 IYGKGGIGKSCTASNIAAACAEEGHKVLMVGCDpksdssitLIGRRIPTMMDLILKGGEFKEEDVVHQGFRGVRCIE 85 
                                       469**************************98776666776678*********988877888878888888****999 PP

                              ParA  78 igfllesedeavvwrGpmkskaikqllkdve..wgelDyLiiDlPPG..tgDeqltvaqklplagaviVttpqeval 150
                                       +g            rG +++  i ++l++v+   +e+D+++ D+P     g  +  + + l +++a i+t+ + + l
  gi|330506738|ref|YP_004383166.1|  86 VGGPE--PGVGCAGRGIIVA--I-DFLRKVSkaMEEVDLVLYDVPGDivCGGFSAPIRKGL-VSQAYIITSGEYMPL 156
                                       99744..4777777777664..4.455555412689*********6422344455555555.78999********** PP

                              ParA 151 advkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvl 227
                                         ++   + + ++++++ Gv+ N    + ++        +++ ++++a+el+ ++++ ip +p ++++  +  ++++
  gi|330506738|ref|YP_004383166.1| 157 YAANNISKGLLRLNTPLAGVICNSREAAGER--------EREIVNQFAQELNSRMVAFIPKEPIVQQCERRTVTVIE 225
                                       ***********************87766654........334567889999*********99999888888889999 PP

                              ParA 228 kepeseaakaleeiaekv 245
                                        +p+s++a +++++a+++
  gi|330506738|ref|YP_004383166.1| 226 GAPDSKIAAVYRALAREI 243
                                       99************9998 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   2.8e-11     3e-08       9      48 ..      11      50 ..       4      79 .. 0.82
   2 ?   -3.1   0.1       5.9   6.3e+03     110     126 ..     109     125 ..     104     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.8e-11
                            AAA_31  9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattgl 48
                                       KGG+GK+ t+ n+aaa a++g+kvL+v +Dp + ++++l
  gi|330506738|ref|YP_004383166.1| 11 GKGGIGKSCTASNIAAACAEEGHKVLMVGCDPKSDSSITL 50
                                      5********************************9999854 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.9
                            AAA_31 110 llekvkdeYDyiiiDcp 126
                                       +++k  +e D+++ D+p
  gi|330506738|ref|YP_004383166.1| 109 KVSKAMEEVDLVLYDVP 125
                                       56677788999999998 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.3     1e-09   1.1e-06       2      40 ..       5      43 ..       4      49 .. 0.92
   2 ?   -3.4   0.0       4.1   4.3e+03     212     244 ..     148     180 ..     145     201 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1e-09
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDPA 40
                                      k + + GKGG+GK+  ++ +a+ ++e+g+kvl++  DP 
  gi|330506738|ref|YP_004383166.1|  5 KHVAIYGKGGIGKSCTASNIAAACAEEGHKVLMVGCDPK 43
                                      678899********************************5 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.1
                                       EEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                       ArsA_ATPase 212 VvipEklslkEteRaikeLkkygikvdavivNk 244
                                       ++  E ++l+  +   k L +++     vi N 
  gi|330506738|ref|YP_004383166.1| 148 ITSGEYMPLYAANNISKGLLRLNTPLAGVICNS 180
                                       566788888888888888888888888888775 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.8e-06     0.005       8      54 ..      11      57 ..       6      72 .. 0.89
   2 ?    1.4   0.0      0.15   1.6e+02      89     110 ..     106     127 ..      99     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.8e-06
                                      SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHH CS
                              MipZ  8 ekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraat 54
                                       kGG Gks ta  +a a +++G++v  +  d +  ++   ++ r  t
  gi|330506738|ref|YP_004383166.1| 11 GKGGIGKSCTASNIAAACAEEGHKVLMVGCDPKSDSSITLIGRRIPT 57
                                      59*****************************9999999988888765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHH-SEEEEE--SS CS
                              MipZ  89 leelvadleaeldfividtPGs 110
                                       + + v+++++e+d+++ d+PG 
  gi|330506738|ref|YP_004383166.1| 106 FLRKVSKAMEEVDLVLYDVPGD 127
                                       5566889999**********95 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   1.6e-06    0.0017      31      78 ..       6      52 ..       2     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilG 78
                                       v + G  G Gks + +++++  +++G++v ++  DP s  +  +++G
  gi|330506738|ref|YP_004383166.1|  6 HVAIYGKGGIGKSCTASNIAAACAEEGHKVLMVGCDPKSDSS-ITLIG 52
                                      68899*********************************9865.34555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.3e-06    0.0045       4      47 ..       6      56 ..       4      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.3e-06
                            AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie 47
                                       ++iyG+ giGK+ +a+++       g k+l++ ++  ++s     + +i+
  gi|330506738|ref|YP_004383166.1|  6 HVAIYGKGGIGKSCTASNIaaacaeeGHKVLMVGCDPKSDSSITLIGRRIP 56
                                      589********************************9866655555555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00092      0.97       6      70 ..       5      65 ..       2      82 .. 0.77
   2 ?   -0.3   0.0       1.1   1.2e+03      71      93 ..     184     205 ..     165     216 .. 0.77
   3 ?    4.6   0.0     0.034        36      37      81 ..     203     263 ..     188     270 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00092
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka 70
                                      ++++++G  G+GK+ ++ +++    e     e +++  v ++++s++s + + r++   ++l lk+
  gi|330506738|ref|YP_004383166.1|  5 KHVAIYGKGGIGKSCTASNIAAACAE-----EgHKVLMVGCDPKSDSSITLIGRRIPTMMDLILKG 65
                                      5789******************9733.....33677777888888888888888877777766665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                            AAA_22  71 erlsseellealeqalraravie 93 
                                       ++ +++e++++++q l++r+v +
  gi|330506738|ref|YP_004383166.1| 184 AGEREREIVNQFAQELNSRMV-A 205
                                       567899999999999999998.4 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.034
                            AAA_22  37 e.............erpevvfvtlpsstsskdllrellralglelka...erlsseellea 81 
                                       +             er++v  ++ + +++ + ++r+l+r++ ++++a   e+ls e+l+e+
  gi|330506738|ref|YP_004383166.1| 203 MvafipkepivqqcERRTVTVIEGAPDSKIAAVYRALAREIMSGGEAripEPLSDERLREL 263
                                       2444444555666666777788888888***************999988877777777765 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0073       7.7       1      36 [.       9      44 ..       9      47 .. 0.92
   2 ?    7.0   0.0    0.0042       4.4      66     102 ..      98     128 ..      95     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0073
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAa 36
                                      + G  G GK+   ++++  + ++g +v +v  DP +
  gi|330506738|ref|YP_004383166.1|  9 IYGKGGIGKSCTASNIAAACAEEGHKVLMVGCDPKS 44
                                      57999****************************966 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0042
                        ATP_bind_1  66 galvvaleflresldwldeelekeeddyllfDtPGQi 102
                                       ++++va++flr+   +  ee+     d++l+D+PG i
  gi|330506738|ref|YP_004383166.1|  98 RGIIVAIDFLRKVS-KAMEEV-----DLVLYDVPGDI 128
                                       58999***999875.566666.....*********76 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.6e-05     0.027       4      38 ..       7      41 ..       4      46 .. 0.94
   2 ?   -3.9   0.0       8.6   9.1e+03      78      92 ..     112     125 ..     106     126 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      +++ G  G+GK  t++ +aa + +eg+kvl+v +D
  gi|330506738|ref|YP_004383166.1|  7 VAIYGKGGIGKSCTASNIAAACAEEGHKVLMVGCD 41
                                      6789******************************9 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 8.6
                                       HHHHTTSSEEEEEE- CS
                             SRP54  78 kakeekidvvlvDTa 92 
                                       ka  e++d+vl D  
  gi|330506738|ref|YP_004383166.1| 112 KAM-EEVDLVLYDVP 125
                                       333.47899999965 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   0.1   3.4e-05     0.035      24      57 ..       5      37 ..       3      45 .. 0.87
   2 ?   -2.8   0.0         5   5.3e+03     118     133 ..     189     203 ..     174     265 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-05
                             DUF87 24 rHlAilgsTGsGKSntvavLleellekkgatili 57
                                      +H+Ai g+ G GKS t++ + +  + + g ++l+
  gi|330506738|ref|YP_004383166.1|  5 KHVAIYGKGGIGKSCTASNIAAACA-EEGHKVLM 37
                                      7******************999888.77777765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5
                             DUF87 118 rsvleealdqakakee 133
                                       r++++++ +++ + + 
  gi|330506738|ref|YP_004383166.1| 189 REIVNQFAQELNS-RM 203
                                       4444444443332.22 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.2e-05     0.054      36      64 ..       7      36 ..       5      48 .. 0.82
   2 ?   -3.3   0.1       5.2   5.5e+03     130     146 ..     104     120 ..     101     123 .. 0.77
   3 ?   -2.8   0.0       3.8     4e+03     118     136 ..     224     242 ..     194     247 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.2e-05
                            AAA_25 36 allaGapgtGKttlaldlalava.tGkpwl 64
                                      ++++G +g GK+  a+++a+a+a +G+++l
  gi|330506738|ref|YP_004383166.1|  7 VAIYGKGGIGKSCTASNIAAACAeEGHKVL 36
                                      579********************7777543 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.2
                            AAA_25 130 vdaleaaieevegvrlv 146
                                       +d l+++ +++e+v+lv
  gi|330506738|ref|YP_004383166.1| 104 IDFLRKVSKAMEEVDLV 120
                                       55588889999999998 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.8
                            AAA_25 118 akdrggtlltadvdaleaa 136
                                        +++ +++++a+++al+++
  gi|330506738|ref|YP_004383166.1| 224 IEGAPDSKIAAVYRALARE 242
                                       3334444555555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00042      0.44      25      63 ..       5      43 ..       1      79 [. 0.78
   2 ?    1.2   0.0      0.41   4.3e+02      48     105 ..     199     244 ..     166     269 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00042
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                        v ++G  G+GKs  +  ++ a  ++g  +l   cd  
  gi|330506738|ref|YP_004383166.1|  5 KHVAIYGKGGIGKSCTASNIAAACAEEGHKVLMVGCDPK 43
                                      6799*****************777777666676666665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.41
                            AAA_16  48 lekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeal 105
                                       l+ + + f           ip  +++q+++r + ++ ++ +++s+ ++ +r+  +e +
  gi|330506738|ref|YP_004383166.1| 199 LNSRMVAF-----------IPKEPIVQQCER-RTVTVIEGAPDSKIAAVYRALAREIM 244
                                       33332222...........333344445533.33333333434434444444333333 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 ?   12.0   0.2   0.00013      0.13      49      81 ..       6      38 ..       2      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                         IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlfv 81
                                       +++ G  G+GKs  a  ++ + +++g++vl v
  gi|330506738|ref|YP_004383166.1|  6 HVAIYGKGGIGKSCTASNIAAACAEEGHKVLMV 38
                                      689***************************866 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00026      0.27      22      43 ..       6      27 ..       1      36 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00026
                                      EEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 22 vvalvGmgGvGKttlakqilnk 43
                                       va++G+gG+GK+  a++i   
  gi|330506738|ref|YP_004383166.1|  6 HVAIYGKGGIGKSCTASNIAAA 27
                                      69***************99876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00062      0.65       2      26 ..       8      32 ..       7      63 .. 0.77
   2 ?   -2.4   0.0       6.1   6.4e+03      31      56 ..     200     225 ..     189     243 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00062
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                       +yG+ g+GKS +a ++a+a +++ 
  gi|330506738|ref|YP_004383166.1|  8 AIYGKGGIGKSCTASNIAAACAEEG 32
                                      69**************999988544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.1
                      RNA_helicase  31 kdsvysrnpeddfwdgYtgqevvvid 56 
                                       ++++++  p++ +++++++ +v+vi+
  gi|330506738|ref|YP_004383166.1| 200 NSRMVAFIPKEPIVQQCERRTVTVIE 225
                                       33333444455555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2136.62
//
Query:       gi|330506739|ref|YP_004383167.1|  [L=991]
Description: S-layer-related duplication domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-132  440.1   4.8    8.3e-82  274.1   1.8    2.3  2  S-layer   S-layer protein
  ------ inclusion threshold ------
      0.089   12.7   0.1        0.4   10.6   0.0    2.2  2  FlgD_ig   FlgD Ig-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 !  166.5   0.1   6.5e-53   5.8e-49       9     256 ..      62     299 ..      55     301 .. 0.95
   2 !  274.1   1.8   9.3e-86   8.3e-82       4     258 .]     339     602 ..     337     602 .. 0.95

  Alignments for each domain:
  == domain 1  score: 166.5 bits;  conditional E-value: 6.5e-53
                           S-layer   9 eltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfagydn 85 
                                       + tw a++F  fyyd+d++ + E+l ++  ++ +rt ++g+++Y ++p +k+f++++wgsYev+ ++++ Y+a y +
  gi|330506739|ref|YP_004383167.1|  62 DGTWRANDFGWFYYDLDEDAGGEELQVK--DVVGRTAKKGDITYLSRPWSKHFDYAPWGSYEVLALFGKLYLASYPD 136
                                       678************************9..789******************************************77 PP

                           S-layer  86 saetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissskad 162
                                       s+  +d+vs l++++L+++l ded+e+tl+ +++l L++gY+l++  i   +d v + L+k+++ v ++v+s     
  gi|330506739|ref|YP_004383167.1| 137 SS-FTDEVSSLAKGELREILRDEDTEYTLTYNTTLPLAQGYSLTLGGISEKNDVVNFALYKNEKRVYDSVVSI---G 209
                                       77.6999******************************************************************...* PP

                           S-layer 163 styvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddv.leieegdefgkmevksvseneiemenddsi 238
                                       +++vy+       dv++i vh+ +++ +++  ++ ++gifq sd++  ++ eg   g+m+ +++se+ +e++n  +i
  gi|330506739|ref|YP_004383167.1| 210 EDFVYKM-----GDVPVILVHLANAMGSEDGGFAEVNGIFQTSDSPiAKLVEGGILGNMKLEDLSEEGLEFRNAVDI 281
                                       *****84.....58*****************************998579**************************** PP

                           S-layer 239 tLsrdktieimddlkfkv 256
                                       +L+rd+++ +++ l + v
  gi|330506739|ref|YP_004383167.1| 282 NLKRDSSVFLTQYLLLVV 299
                                       *********999887766 PP

  == domain 2  score: 274.1 bits;  conditional E-value: 9.3e-86
                           S-layer   4 eeeseeltwtasnFsgfyydiddglssEsltlelesksdrtie...............egelvYsttpvekefefee 65 
                                       +++s +++w++ n+sgfy+d +d+l++E+l+l+  s++dr+++               +++++Y+t  ++kefef++
  gi|330506739|ref|YP_004383167.1| 339 YDSSVTARWKSLNYSGFYFDPEDMLGDETLVLY--SVQDRRVSppsnpvvyeenntafQKGFQYTTLLEPKEFEFKP 413
                                       57788999***********************99..55677777777777777777777******************* PP

                           S-layer  66 wgsYevigflaekYfagydnsa.etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvw 141
                                       wg Y vi+fl++++fagyd+s   t++++sll++e+L +vlide+ + ++++g+ ++L+egYe++i+  D+++d+++
  gi|330506739|ref|YP_004383167.1| 414 WGYYLVINFLGMQWFAGYDSSLaGTKASKSLLEKEYLGRVLIDEEYQGVAFVGN-YSLQEGYEIRIR--DLENDSIF 487
                                       ******************8888799****************************9.************..******** PP

                           S-layer 142 leLtkdgeevdskvissskadstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddv.leieegdef 217
                                       leL kdg++++ +v++s   +sty+yekdlgd+dd++ii+vhvd+vf++ ++ +++i++ifqisd++ +++eeg+ +
  gi|330506739|ref|YP_004383167.1| 488 LELLKDGASIEGSVVRS---NSTYIYEKDLGDVDDLPIIMVHVDNVFNNISKGFATIDAIFQISDQFiIHVEEGNGI 561
                                       *****************...********************************************99879******** PP

                           S-layer 218 gkmevksvseneiemenddsitLsrdktieimddlkfkvaD 258
                                       g+m++ +v+ + i+m ndd i+L+rd+t++++ +++++vaD
  gi|330506739|ref|YP_004383167.1| 562 GEMQIVNVDPRGIWMVNDDYINLNRDSTVSLAPMMNIRVAD 602
                                       ****************************************9 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.2     1e+04      18      38 ..      77      97 ..      73     102 .. 0.73
   2 ?   10.6   0.0   4.5e-05       0.4      10      52 ..     633     678 ..     628     691 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.2
                                      .ESSSEEEEEEEE-SS--EEE CS
                           FlgD_ig 18 lpeaadevtvtikDasGevVr 38
                                      l+e+a   ++++kD  G++ +
  gi|330506739|ref|YP_004383167.1| 77 LDEDAGGEELQVKDVVGRTAK 97
                                      788888888899988887655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 4.5e-05
                                       --EEEEEE....ESSSEEEEEEEE-SS--EEEEEEEEESSSEEEEE CS
                           FlgD_ig  10 geaplgve...lpeaadevtvtikDasGevVrtidlgaqsaGvvsf 52 
                                       +++p++++    ++ + evtv+i D+s+++V + d ++  +G+ +f
  gi|330506739|ref|YP_004383167.1| 633 SKTPASFTmieQAAEIREVTVEIVDSSNRTVFSRDITNFGQGSGEF 678
                                       556777776568888899*************999999988887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (991 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.43
# Mc/sec: 6874.45
//
Query:       gi|330506740|ref|YP_004383168.1|  [L=175]
Description: imidazoleglycerol-phosphate dehydratase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-29  101.3   0.1    6.7e-29  101.1   0.1    1.1  1  IGPD          Imidazoleglycerol-phosphate dehydratase
  ------ inclusion threshold ------
       0.13   12.8   0.2        2.1    8.9   0.0    2.3  2  Ribosomal_S9  Ribosomal protein S9/S16


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 !  101.1   0.1   7.5e-33   6.7e-29       1     144 []      30     166 ..      30     166 .. 0.96

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 7.5e-33
                                       ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEE CS
                              IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaeval 77 
                                       T+i++ld +L++l k ++fdl++k++gd    dHht+ed+gi+lG+a+++a   k+gi   gs ++p   ala +a+
  gi|330506740|ref|YP_004383168.1|  30 TEIELLDMILTSLGKGANFDLRIKARGDSVTGDHHTIEDTGITLGKAIAQAK--KSGI---GSSTVPSSTALAVAAV 101
                                       89************************************************97..8997...9*************** PP

                                       E--SS-EEE.--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                              IGPD  78 dlsgrpylv.leaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                        + ++ y   ++  +k+e+ g ++ e++ +f+++la + g+tl +++  g ++  ++ea+  a++ra+
  gi|330506740|ref|YP_004383168.1| 102 RFGETGYRGeFS--FKSESAGGMTLENFGHFLRALAYNGGFTLVISAE-GGDDMSKIEAMSTALGRAI 166
                                       *******88455..********************************98.9999*************96 PP

>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.029   2.6e+02      43      71 ..      39      67 ..      10     101 .. 0.73
   2 ?    8.9   0.0   0.00024       2.1      44      81 ..     132     169 ..      97     175 .] 0.85

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.029
                                      HHHTTTSSSEEEEEEEESS-HHHHHHHHH CS
                      Ribosomal_S9 43 lkltgllgkfdvfvkvkgGGlsgqaeAir 71
                                      l+ +g+  +fd ++k +g  ++g  + i+
  gi|330506740|ref|YP_004383168.1| 39 LTSLGKGANFDLRIKARGDSVTGDHHTIE 67
                                      44555555799999999999999988886 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00024
                                       HHTTTSSSEEEEEEEESS-HHHHHHHHHHHHHHHHHHH CS
                      Ribosomal_S9  44 kltgllgkfdvfvkvkgGGlsgqaeAirlgiaraLval 81 
                                       +++   g f   ++ +gG  ++++eA+++++ ra+ + 
  gi|330506740|ref|YP_004383168.1| 132 RALAYNGGFTLVISAEGGDDMSKIEAMSTALGRAIRRA 169
                                       4555566799999*********************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1311.85
//
Query:       gi|330506741|ref|YP_004383169.1|  [L=183]
Description: GNAT family acetyltransferase [Methanosaeta concilii GP6]
Scores for complete 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   96.3   0.1    2.8e-27   96.1   0.1    1.1  1  Acetyltransf_3  Acetyltransferase (GNAT) domain
    3.6e-08   33.7   0.1    4.6e-08   33.3   0.1    1.2  1  Acetyltransf_1  Acetyltransferase (GNAT) family
    4.2e-08   33.5   0.0    4.8e-08   33.3   0.0    1.1  1  Acetyltransf_4  Acetyltransferase (GNAT) domain
    5.3e-05   22.9   0.0    0.00019   21.1   0.0    1.8  2  Acetyltransf_8  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   0.1   6.2e-31   2.8e-27       1     138 []      11     150 ..      11     150 .. 0.93

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 6.2e-31
                    Acetyltransf_3   1 RLlLrplteeDlealfelrsdpevmrylpe.pltleeaeewlerawaeeseeegygwaivlkdtgv.iGsvglrdle 75 
                                       R+ Lr++ ++Dle+l++++sd  v++y++   ++ ee++++++     ++++eg  waiv+k++gv  Gs+g+++++
  gi|330506741|ref|YP_004383169.1|  11 RFALREIGAADLETLHSYWSDDVVTKYMNVsFKNIEETKQMVDLLNSLPERGEGRRWAIVDKKSGVvQGSCGYHNVK 87 
                                       788************************666689**********5444556666677********987********** PP

                    Acetyltransf_3  76 eedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                        e+++ae+gy l++ +wg+G  +e+++a+++++fee g +r++a +   N +S + l++lGf+
  gi|330506741|ref|YP_004383169.1|  88 AEHRRAEIGYELGRRYWGQGAIQEVMKAVINHCFEERGFNRIEAFVTVGNNRSLNTLKRLGFR 150
                                       **************************************************************6 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.1     1e-11   4.6e-08      34     117 .]      65     149 ..      32     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1e-11
                                       EEEE..EEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TESEEEEEEETTEHH CS
                    Acetyltransf_1  34 gllv..aeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gikkivlaveednda 107
                                       + ++   ++ g + G ++++ +    +++ + +++   + y+g+G+ ++ ++a++ +++ee g+++i++ v++ n++
  gi|330506741|ref|YP_004383169.1|  65 RRWAivDKKSGVVQGSCGYHNVKA--EHRRAEIGYELGRRYWGQGAIQEVMKAVINHCFEErGFNRIEAFVTVGNNR 139
                                       444433445577888888877777..5666666****************************888************* PP

                                       HHHHHHHTTE CS
                    Acetyltransf_1 108 airlYeklGF 117
                                       + + +++lGF
  gi|330506741|ref|YP_004383169.1| 140 SLNTLKRLGF 149
                                       *****88**9 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   1.1e-11   4.8e-08       2     154 ..      15     169 ..      14     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.1e-11
                    Acetyltransf_4   2 raateeDakeilaiyaeyvvntaitfeyevssveefek...fleal.d.sekeyvflvae.sdrivGyaylgqfkkr 72 
                                       r +  +D++ +    +++vv + ++     + +ee+++   +l++l +  e+++   v++ s+ ++G + + ++k+ 
  gi|330506741|ref|YP_004383169.1|  15 REIGAADLETLHSYWSDDVVTKYMNVS--FKNIEETKQmvdLLNSLpErGEGRRWAIVDKkSGVVQGSCGYHNVKA- 88 
                                       667778888888888777766544422..23333333300033333322555777778889**************9. PP

                    Acetyltransf_4  73 akdwkaelsvylaerdnnkeglgrelidale.qvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkng 148
                                        +   ae+ + l  r    +g ++e ++a++  ++ e ++++++a + + n  s + +k+lGF+ +g ++++   +g
  gi|330506741|ref|YP_004383169.1|  89 -EHRRAEIGYELG-RRYWGQGAIQEVMKAVInHCFEERGFNRIEAFVTVGNNRSLNTLKRLGFRPEGLLREYEFTQG 163
                                       .***********8.668888888887777663788**************************************9999 PP

                    Acetyltransf_4 149 rwiDmi 154
                                          D++
  gi|330506741|ref|YP_004383169.1| 164 SFHDQV 169
                                       998876 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.27   1.2e+03       4      26 ..      20      42 ..      18      59 .. 0.69
   2 !   21.1   0.0   4.3e-08   0.00019      90     141 ..     102     153 ..      77     156 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.27
                                      GGHHHHHHHCTSCCCHHHH---- CS
                    Acetyltransf_8  4 aDlellhrWmnrprvaewweeag 26
                                      aDle+lh+  +++ v ++++ + 
  gi|330506741|ref|YP_004383169.1| 20 ADLETLHSYWSDDVVTKYMNVSF 42
                                      78999998888887777766555 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 4.3e-08
                                       HHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                    Acetyltransf_8  90 eargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                                       ++ g+g ++++++a+++ +f++++ +r+ +   v N r+++ l+++Gf++e+
  gi|330506741|ref|YP_004383169.1| 102 RYWGQGAIQEVMKAVINHCFEERGFNRIEAFVTVGNNRSLNTLKRLGFRPEG 153
                                       6789*********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1453.91
//
Query:       gi|330506742|ref|YP_004383170.1|  [L=170]
Description: GNAT family acetyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (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   48.3   0.0    1.4e-12   48.0   0.0    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    3.1e-10   40.3   0.0    3.9e-10   40.0   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.8e-08   34.7   0.0    2.7e-08   34.1   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.7e-07   32.0   0.0      2e-07   31.8   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    3.3e-05   23.8   0.0    4.7e-05   23.3   0.0    1.3  1  FR47             FR47-like protein
    9.3e-05   22.4   0.0    0.00011   22.1   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0038   17.3   0.0     0.0075   16.4   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
     0.0096   15.5   0.0      0.014   15.0   0.0    1.2  1  GNAT_acetyltran  GNAT acetyltransferase
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.026   14.5   0.0    1.4  1  Acetyltransf_13  ESCO1/2 acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   6.9e-16   1.4e-12       1     145 [.       5     144 ..       5     154 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 6.9e-16
                    Acetyltransf_4   1 iraateeDakeilaiyaeyvvntaitfeyevssveefekflealdsekeyvflvaesdrivGyaylgqfkkr.akdw 76 
                                       i ++++eD ++ + iy e  +    tfe+  +++++ +   ++   + e  + v + d +++ a+l+ +  r  +++
  gi|330506742|ref|YP_004383170.1|   5 INIMKPEDWEQVRSIYLEGIITGNSTFEA--DALDWDKWNCAH---LREHRLVVRYGDSVIAWAALSPVSTRcIYSG 76 
                                       667899**********9999999999996..777776555555...5888899************************ PP

                    Acetyltransf_4  77 kaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcik 145
                                        aels+y+a  + + +g+g+ l++a++    e ++ +l   i+ +n++s  ++k++GF+ vg+ ++++k
  gi|330506742|ref|YP_004383170.1|  77 VAELSIYVA-AKHRGKGIGSTLLKAIISSTEEAGLWTLQGGIFPENTQSLSLLKKHGFKEVGRRERIGK 144
                                       ********9.79***************************************************999887 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0     2e-13   3.9e-10      21     117 .]      32     133 ..      13     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2e-13
                                       HHH...HHHH.HHSTTCEEEEEEETTEEEEEEEEEEEET..TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHH CS
                    Acetyltransf_1  21 eee...fees.fsleaegllvaeedgeliGfisllkipd..ekggvayieslaVspeyrgkGlGsaLlealeerare 91 
                                       e++   + ++      e+ lv+++++ +i+++ l+++     + gva++ s++V+ ++rgkG+Gs+Ll+a++   +e
  gi|330506742|ref|YP_004383170.1|  32 EADaldWDKWnCAHLREHRLVVRYGDSVIAWAALSPVSTrcIYSGVAEL-SIYVAAKHRGKGIGSTLLKAIISSTEE 107
                                       3333444444333334488889***************999855688888.***********************8888 PP

                                       TTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  92 egikkivlaveedndaairlYeklGF 117
                                        g+  +   +++ n+++  l++k+GF
  gi|330506742|ref|YP_004383170.1| 108 AGLWTLQGGIFPENTQSLSLLKKHGF 133
                                       8995545599999********88**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.4e-11   2.7e-08       6      76 .]      51     135 ..      45     135 .. 0.66

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.4e-11
                                       EEEEETTEEEEEEEEEEES.....TCTEE.....EEE-GGGTTSSHHHHHHHHTT.....SEEEEEEEEE......T CS
                    Acetyltransf_7   6 fVaeddgkivGfialslld.....aeitr.....laVdpeyrgkGiGraLleaae.....kgiileqlel......n 61 
                                       +V++ ++ ++  +als+++         +     ++V+ ++rgkGiG+ Ll+a++      g+  +  +l      +
  gi|330506742|ref|YP_004383170.1|  51 LVVRYGDSVIAWAALSPVStrciyS---GvaelsIYVAAKHRGKGIGSTLLKAIIssteeAGL--W--TLqggifpE 120
                                       6778888888888888888765441...145567******************83333333332..2..222333332 PP

                                       HHHHHHHHHHTTEEE CS
                    Acetyltransf_7  62 aekaikfYeklGFee 76 
                                       +++++++ +k+GF+e
  gi|330506742|ref|YP_004383170.1| 121 NTQSLSLLKKHGFKE 135
                                       237899*******96 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0     1e-10     2e-07      65     138 .]      59     134 ..       4     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1e-10
                    Acetyltransf_3  65 viGsvglrdleeedee......aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvlekl 135
                                       vi ++ l +++    +      ael++++a +++gkG+++  ++a++    ee gl +l   i +eN++S  +l+k 
  gi|330506742|ref|YP_004383170.1|  59 VIAWAALSPVST---RciysgvAELSIYVAAKHRGKGIGSTLLKAIISST-EEAGLWTLQGGIFPENTQSLSLLKKH 131
                                       455555554444...1345777****************************.8888********************** PP

                    Acetyltransf_3 136 Gfe 138
                                       Gf+
  gi|330506742|ref|YP_004383170.1| 132 GFK 134
                                       **7 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   2.4e-08   4.7e-05      18      85 ..      74     141 ..      52     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.4e-08
                                       E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EEEEEEEE CS
                              FR47  18 rkdggelgalqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfekieetew 85 
                                        + + el +++v  +hr++G gs l ka++    e+g  t+   + ++Nt+s +l++k Gf++   +e+
  gi|330506742|ref|YP_004383170.1|  74 YSGVAEL-SIYVAAKHRGKGIGSTLLKAIISSTEEAGLwTLQGGIFPENTQSLSLLKKHGFKEVGRRER 141
                                       5555555.589************************9962666789*****************9876666 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.5e-08   0.00011      57     113 ..      82     140 ..      32     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.5e-08
                   Acetyltransf_10  57 lfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavgeeq 113
                                       ++V+ ++rg+Gig+ Ll+a+++  e++g+ + +  +   + +  ++ +k+GFk+vg+ +
  gi|330506742|ref|YP_004383170.1|  82 IYVAAKHRGKGIGSTLLKAIISSTEEAGLWTlQGGIFPENtQSLSLLKKHGFKEVGRRE 140
                                       69**************************99999999888889*************8765 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 !   16.4   0.0   3.8e-06    0.0075      30      58 ..      82     110 ..      76     112 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.8e-06
                   Acetyltransf_CG  30 TeVpeelrGkGiAkkLvkaalddareegl 58 
                                       ++V  ++rGkGi++ L ka++  ++e+gl
  gi|330506742|ref|YP_004383170.1|  82 IYVAAKHRGKGIGSTLLKAIISSTEEAGL 110
                                       79********************9999886 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   6.9e-06     0.014     170     236 ..      66     135 ..      51     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.9e-06
                   GNAT_acetyltran 170 sgasSysvyekgieieidTkedyrrkgLAtivaaalileclkrglyPsWDaa...neaSvaLaekLGYef 236
                                       s +s+ ++y++ +e +i  + ++r+kg  + + +a+i+   + gl          n++S++L +k G++ 
  gi|330506742|ref|YP_004383170.1|  66 SPVSTRCIYSGVAELSIYVAAKHRGKGIGSTLLKAIISSTEEAGLWTLQGGIfpeNTQSLSLLKKHGFKE 135
                                       5567888**********************************99998877766888999999999999986 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.3e-05     0.026       9      32 ..      81     104 ..      73     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                   Acetyltransf_13   9 riWvssshRrkgiAtkLldaaren 32 
                                        i+v+++hR kgi ++Ll+a++++
  gi|330506742|ref|YP_004383170.1|  81 SIYVAAKHRGKGIGSTLLKAIISS 104
                                       59*****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1237.63
//
Query:       gi|330506743|ref|YP_004383171.1|  [L=162]
Description: GNAT family acetyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-17   61.4   0.0    8.8e-17   61.2   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    7.9e-14   51.9   0.0      1e-13   51.5   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.8e-13   49.6   0.0    5.4e-13   49.2   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.5e-05   24.9   0.0    2.4e-05   24.2   0.0    1.4  1  FR47             FR47-like protein
      3e-05   24.1   0.0    0.00058   19.9   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0017   19.0   0.0     0.0022   18.7   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.019   14.7   0.0      0.024   14.4   0.0    1.2  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
      0.077   13.1   0.0       0.12   12.6   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   3.9e-20   8.8e-17      28     126 ..      50     151 ..      23     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 3.9e-20
                   Acetyltransf_10  28 egealllvaeeggkivGviel.rdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnaspyavpf 100
                                        + +++l a + +ki+G ++  ++++  ++++l+V+p+y+g+Gig+ L++++ee++  +  +   +t  +s+  +++
  gi|330506743|ref|YP_004383171.1|  50 YETKVFLKAVCVDKIIGSVRAsQNSGtcQVGRLIVHPDYQGRGIGTLLMKRIEEAF-SCAERFeLFTSTKSTSNIRL 125
                                       467788999999*********55555*****************************8.455555578888888***** PP

                   Acetyltransf_10 101 YeklGFkavgeeqeenGirfvpMeke 126
                                       Y+++G++++ ee    ++r+v Mek+
  gi|330506743|ref|YP_004383171.1| 126 YRRMGYQELYEEDLSPNVRLVFMEKR 151
                                       ***********************985 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   4.5e-17     1e-13      14     117 .]      37     131 ..      16     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 4.5e-17
                                       HHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHH CS
                    Acetyltransf_1  14 ppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerar 90 
                                       pp  ++  e++ e+   e++ +l a   +++iG ++++++      ++ + +l V+p+y+g+G+G++L++ +ee a+
  gi|330506743|ref|YP_004383171.1|  37 PPLTQTLSEIQSEY---ETKVFLKAVCVDKIIGSVRASQNSG----TCQVGRLIVHPDYQGRGIGTLLMKRIEE-AF 105
                                       44444444445555...4442222333369**********99....9***************************.77 PP

                                       HTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  91 eegikkivlaveedndaairlYeklGF 117
                                       +  +++ +l ++   +  irlY+++G+
  gi|330506743|ref|YP_004383171.1| 106 SC-AERFELFTSTKSTSNIRLYRRMGY 131
                                       77.577899999999999****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 !   49.2   0.0   2.4e-16   5.4e-13      12      76 .]      62     133 ..      46     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.4e-16
                                       TEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHH.HTT..SEEEEE.EEEETHH..HHHHHHHHTTEEE CS
                    Acetyltransf_7  12 gkivGfialslld..aeitrlaVdpeyrgkGiGraLle.aae..kgiile.qlelnae..kaikfYeklGFee 76 
                                       +ki+G +++s ++  ++ +rl V+p+y+g+GiG+ L++ + e    +    +l ++++   +i++Y+++G++e
  gi|330506743|ref|YP_004383171.1|  62 DKIIGSVRASQNSgtCQVGRLIVHPDYQGRGIGTLLMKrI-EeaFSCAERfELFTSTKstSNIRLYRRMGYQE 133
                                       799*****999999888888*****************943.224334422333332223377*********86 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.1e-08   2.4e-05      22      81 ..      77     135 ..      56     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.1e-08
                                       SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEE CS
                              FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekie 81 
                                        ++g l v+p+ ++rG g++l k + ++ + ++    l + ++ t  irly ++G++++ 
  gi|330506743|ref|YP_004383171.1|  77 CQVGRLIVHPDYQGRGIGTLLMKRIEEAFSCAE-RFELFTSTKSTSNIRLYRRMGYQELY 135
                                       468999*******************99998765.5678899999*************984 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.6e-07   0.00058       6     126 ..       9     132 ..       5     134 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.6e-07
                                       -GGGHHHHHHHHHHHTT----H..........HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEE CS
                    Acetyltransf_9   6 teedldevlellkyaFqdeespl........eeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaa 74 
                                        + d +evl+l+k a+q e +           +   + +  +e + +l a + ++++g++++ + +         + 
  gi|330506743|ref|YP_004383171.1|   9 SPGDANEVLALQKLAYQSEAELNgdwtipplTQTLSEIQSEYETKVFLKAVCVDKIIGSVRASQNSG--------TC 77 
                                       5556666666666666666665555554433111222233333444444445555555555544333........34 PP

                                       EEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--....SSHHHHHTTT-E CS
                    Acetyltransf_9  75 gvtgVavapehrgrgvlskLlaraleemreegqplsllfP....ssipiYrrfGye 126
                                       +v+   v+p+++grg+ + L++r  e      +++ l +     s+i++Yrr+Gy+
  gi|330506743|ref|YP_004383171.1|  78 QVGRLIVHPDYQGRGIGTLLMKRIEEAFS-CAERFELFTStkstSNIRLYRRMGYQ 132
                                       789999**********9999999877533.4555555555555788*********7 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   9.7e-07    0.0022       7     137 ..       8     131 ..       3     132 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 9.7e-07
                    Acetyltransf_3   7 lteeDlealfel.....rsdpevm.ry.lpe.pltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdle 75 
                                       +++ D++++++l      s+ e++  + +p+ ++tl+e ++ +e+        + +  a++  d+ +iGsv+  + +
  gi|330506743|ref|YP_004383171.1|   8 ASPGDANEVLALqklayQSEAELNgDWtIPPlTQTLSEIQSEYET--------KVFLKAVC-VDK-IIGSVRASQNS 74 
                                       566677777543222213333333235533346666666666663........55777887.344.7****888666 PP

                    Acetyltransf_3  76 eedeeaelg.ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                       +    +++g ++++p+++g+G++t  ++ + e++     +er++  ++++ +  ir+++++G+
  gi|330506743|ref|YP_004383171.1|  75 GT---CQVGrLIVHPDYQGRGIGTLLMKRIEEAFSC---AERFELFTSTKSTSNIRLYRRMGY 131
                                       65...****5666699*************9999943...467888888888888888888886 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.1e-05     0.024       6      91 ..      18     106 ..      15     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                              PanZ   6 rltelsaqdkiDLakIy...pa.qsaealeaalteegalfaarFNdRlLgAvkveledkeaelsdlcVRevTRrRGV 78 
                                        l++l  q +  L+  +   p  q+ + ++    e + ++ a   d+ +g+v+  ++ ++ ++  l+V      RG+
  gi|330506743|ref|YP_004383171.1|  18 ALQKLAYQSEAELNGDWtipPLtQTLSEIQ-SEYETKVFLKAVCVDKIIGSVRASQNSGTCQVGRLIVHPDYQGRGI 93 
                                       677788888888888887754303334444.44556677889999******************************** PP

                              PanZ  79 gsyLleearrqaP 91 
                                       g  L++++ +   
  gi|330506743|ref|YP_004383171.1|  94 GTLLMKRIEEAFS 106
                                       *****99887664 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 ?   12.6   0.0   5.2e-05      0.12      20      49 ..      72     101 ..      49     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                   Acetyltransf_CG  20 rkegvldfthTeVpeelrGkGiAkkLvkaa 49 
                                       +++g+ ++   +V++ ++G+Gi+  L+k++
  gi|330506743|ref|YP_004383171.1|  72 QNSGTCQVGRLIVHPDYQGRGIGTLLMKRI 101
                                       666788888999***************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1212.02
//
Query:       gi|330506744|ref|YP_004383172.1|  [L=159]
Description: hypothetical protein MCON_0509 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-09   36.6   3.2    1.5e-08   35.0   3.2    1.9  1  PEMT         Phospholipid methyltransferase
      5e-05   22.9   1.0    7.3e-05   22.4   0.9    1.4  1  DUF1295      Protein of unknown function (DUF1295)
     0.0024   18.2   1.7     0.0075   16.7   1.7    1.9  1  ICMT         Isoprenylcysteine carboxyl methyltransferase (IC
  ------ inclusion threshold ------
       0.29   10.4   5.3       0.52    9.6   5.3    1.3  1  AgrB         Accessory gene regulator B
        1.6    7.9   6.8        2.6    7.2   6.9    1.3  1  Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)


Domain annotation for each model (and alignments):
>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   3.2   4.2e-12   1.5e-08      16     106 .]      52     143 ..      17     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 4.2e-12
                              PEMT  16 lvlssiealgefgtfygdfFlelmd...klvtsGiYrylnnPeyvgstlgf.lGlaLitgsaaglllallvllvyli 88 
                                       + +s + +l +  + +     +  d   kl t+G ++y+++P y +s+ +f +Gla++ +s   ++ a+l++ +++ 
  gi|330506744|ref|YP_004383172.1|  52 FFISCLMTLAIIVWSFKSL--PAADrgnKLCTTGAFKYVRHPLYAASLSVFdFGLAIYLNSHIFIFWAVLLHPIWQY 126
                                       5555666666666666655..3333557********************99989***********************9 PP

                              PEMT  89 alkfvEephlakiYgkre 106
                                       ++   Ee+++  i+g+++
  gi|330506744|ref|YP_004383172.1| 127 LVE-NEENMMIDIFGEEY 143
                                       999.***********976 PP

>> DUF1295  Protein of unknown function (DUF1295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.9     2e-08   7.3e-05     143     235 .]      65     150 ..      19     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2e-08
                           DUF1295 143 safkkdpan.kgk.vldsGLwrysRHPNYfgealiWwglflialealeglealaiagpllltlllvfvsgipllEkk 217
                                       ++fk+ pa+ +g+ ++++G ++y RHP Y +   +    ++i l++   + +++++ p++ +l+          E++
  gi|330506744|ref|YP_004383172.1|  65 WSFKSLPAAdRGNkLCTTGAFKYVRHPLYAASLSVFDFGLAIYLNSHIFIFWAVLLHPIWQYLV-------ENEENM 134
                                       899**997537877***************99987764445566676666779999999999985.......345777 PP

                           DUF1295 218 alkkykdkeeyreYqkkt 235
                                       +   ++  eey eYqkkt
  gi|330506744|ref|YP_004383172.1| 135 MIDIFG--EEYIEYQKKT 150
                                       777776..7777777776 PP

>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.7   2.1e-06    0.0075      20      92 ..      62     135 ..      44     137 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.1e-06
                              ICMT  20 Geiwttrvai..lpdhklvksglykylrHPnYllfvilelatllLlcnakltalvllalvalllf.vRikeEekaL 92 
                                         +w+ + +     + kl ++g +ky+rHP Y++ + +   +l++ +n     +++ a+ +  +    +++Ee+++
  gi|330506744|ref|YP_004383172.1|  62 IIVWSFKSLPaaDRGNKLCTTGAFKYVRHPLYAASLSVFDFGLAIYLNS--HIFIFWAVLLHPIWqYLVENEENMM 135
                                       44566665544467899****************9665554555555555..4455555555555545566777666 PP

>> AgrB  Accessory gene regulator B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.3   0.00015      0.52      79     180 ..      19     126 ..      19     128 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
                              AgrB  79 lilslliflllillakllslsls.....lllillliilliisliii..lllaPvdtpnkpisskekkkklki.lsii 147
                                       l++sl++++++i++ ++++l +      ll+ +++i +l++ +ii+  ++  P+  + +++ ++   k+ +  l   
  gi|330506744|ref|YP_004383172.1|  19 LLISLVLLFIAIWVNRQIDLPPLsnnqsLLNSAFFISCLMTLAIIVwsFKSLPAADRGNKLCTTGAFKYVRHpLYAA 95 
                                       589****************9999999984444444444444444441145678877777777777666666655555 PP

                              AgrB 148 vllil.liialllknekisnaillglllvavlql 180
                                       +l+++ + +a+ l n+    +i++++ll  ++q 
  gi|330506744|ref|YP_004383172.1|  96 SLSVFdFGLAIYL-NS--HIFIFWAVLLHPIWQY 126
                                       5555514444433.33..3467777777777876 PP

>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.9   0.00072       2.6      27     128 ..      21     129 ..      11     140 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00072
                                       XXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXXXXXXXXX CS
                       Herpes_LMP1  27 lallllllallfwlyivmsdwtgga.llvlysfallliiiiliifif.......rrdllcplgalcllllmitllli 95 
                                       ++l+ll++a+ +   i +   +    ll    f   l+ + +i++ f       r + lc  ga+  +   +    +
  gi|330506744|ref|YP_004383172.1|  21 ISLVLLFIAIWVNRQIDLPPLSNNQsLLNSAFFISCLMTLAIIVWSFkslpaadRGNKLCTTGAFKYVRHPLYAASL 97 
                                       33444444444444566666655440444333444455555555555223333356789999999888777666666 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Herpes_LMP1  96 alwnlhgqalylgivlfifgcllvlglwiylle 128
                                       ++++ +g a+yl   +fif ++l+  +w yl+e
  gi|330506744|ref|YP_004383172.1|  98 SVFD-FGLAIYLNSHIFIFWAVLLHPIWQYLVE 129
                                       7776.59************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1185.51
//
Query:       gi|330506745|ref|YP_004383173.1|  [L=127]
Description: hypothetical protein MCON_0511 [Methanosaeta concilii GP6]
Scores for 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   64.4   0.0    1.3e-17   64.1   0.0    1.0  1  DJ-1_PfpI  DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0     7e-22   1.3e-17       2     118 ..       5     126 ..       4     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 7e-22
                                       EEEEEEETTBEHHHHHHHHHHHHH.......TTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BH CS
                         DJ-1_PfpI   2 kvlvlladgvedvElivpvdvlkr.......agikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGr 71 
                                        v ++++d+ +d+E+++ ++ +++       + +++++v  ++ +v+++ G ++ +d +ld++++ +  +l+lpGG 
  gi|330506745|ref|YP_004383173.1|   5 EVHLFVFDNLSDWEASYAIAGINNpqfqkksGIYRIRSVAITRAPVVSTGGIRIQPDLALDELSQRDSAMLILPGGI 81 
                                       5889*******************88888887778******************************************* PP

                                       HHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE CS
                         DJ-1_PfpI  72 agperlrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrv 118
                                       a+ e      +++e+++ f+++  +vaaIC ++  La  g+l+ rr+
  gi|330506745|ref|YP_004383173.1|  82 AWDEGKN--REAIEVARVFLDSRVPVAAICGATAGLAHGGLLDCRRH 126
                                       *766554..47*******************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 889.79
//
Query:       gi|330506746|ref|YP_004383174.1|  [L=110]
Description: multidrug resistance protein, SMR family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-28   96.8   8.5    1.2e-27   96.4   8.5    1.2  1  Multi_Drug_Res   Small Multidrug Resistance protein
     0.0047   17.2   5.4     0.0047   17.2   5.4    2.1  2  Phage_holin_5_2  Phage holin family Hol44, in holin superfami
  ------ inclusion threshold ------
      0.028   14.6   6.9      0.037   14.3   6.9    1.2  1  UPF0060          Uncharacterised BCR, YnfA/UPF0060 family
       0.13   12.4  14.2       0.32   11.1  14.3    1.6  1  EamA             EamA-like transporter family
       0.14   12.5   4.3       0.24   11.7   4.4    1.4  1  YwiC             YwiC-like protein
       0.17   11.4   0.3       0.17   11.4   0.3    1.6  2  Mucin15          Cell-membrane associated Mucin15


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 !   96.4   8.5     4e-31   1.2e-27       1      93 []       1      94 [.       1      94 [. 0.99

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 4e-31
                                      XX-HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHH--.-----HHHHHHHHHHHHHHHHHHHHH CS
                    Multi_Drug_Res  1 mnwvllvlAillevvgailLklsegftkltpsllvivgygisfllLskalks.lpvsvAYavwsGiGtvlivlvgillf 78
                                      m+w++l+lAi+ ev+g+++Lk s+gftk  ps++v++gy+++f++Ls++lk  ++++v+Ya+wsG+G+ li+++g+l++
  gi|330506746|ref|YP_004383174.1|  1 MQWLFLFLAIIGEVIGTSALKASDGFTKIVPSIIVVAGYAVAFFFLSLTLKDnINIGVVYAIWSGVGVSLISVIGYLYY 79
                                      89************************************************988************************** PP

                                      --------HHHHHHH CS
                    Multi_Drug_Res 79 geslslkkliglali 93
                                      ++sl++  l+g+ali
  gi|330506746|ref|YP_004383174.1| 80 KQSLDIPALLGIALI 94
                                      *************98 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 !   17.2   5.4   1.6e-06    0.0047       4      74 ..       7      81 ..       4      82 .. 0.83
   2 ?    1.5   1.2      0.13   3.8e+02      23      39 ..      85     101 ..      84     109 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.6e-06
                   Phage_holin_5_2  4 ilyiiGeilKktekvkd.....kyIPlilgiiGiilgvvivfta..dfqaedilifgaiiqGilsggastglnQliKQ 74
                                      +l iiGe++  +  +k      k +P i+++ G +++   +f++    ++++i +  ai  G+ + ++s+ ++  +KQ
  gi|330506746|ref|YP_004383174.1|  7 FLAIIGEVIGTSA-LKAsdgftKIVPSIIVVAGYAVA--FFFLSltLKDNINIGVVYAIWSGVGVSLISVIGYLYYKQ 81
                                      6789999999886.44448999***************..444455455667888888****************99999 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                   Phage_holin_5_2  23 IPlilgiiGiilgvviv 39 
                                       IP +lgi  ii+gv+i+
  gi|330506746|ref|YP_004383174.1|  85 IPALLGIALIIIGVMII 101
                                       78888888888885443 PP

>> UPF0060  Uncharacterised BCR, YnfA/UPF0060 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   6.9   1.2e-05     0.037       8     102 ..       6     102 ..       1     107 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                           UPF0060   8 fllaalaeigGaylvwlwlreaksvl.....lalvaaillavygflatlqp.aafGrvyaayGGvfvvlallwglvv 78 
                                       ++la + e++G+      l+ + +++     + +va+ ++a + + +tl+   + G vya + Gv v l  + g++ 
  gi|330506746|ref|YP_004383174.1|   6 LFLAIIGEVIGTSA----LKASDGFTkivpsIIVVAGYAVAFFFLSLTLKDnINIGVVYAIWSGVGVSLISVIGYLY 78 
                                       45556666666533....33333322000003455666777777889999989***************99999**** PP

                           UPF0060  79 dgvkldlydwiGalialvGvlvil 102
                                        +  ld   ++G +  ++Gv++i 
  gi|330506746|ref|YP_004383174.1|  79 YKQSLDIPALLGIALIIIGVMIIN 102
                                       ********************9984 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  14.3   0.00011      0.32      64     136 ..      27     102 ..       3     103 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                              EamA  64 wlll.lllgllgtvlaf.llffyalkktsasnasli.tslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        +++  ++ + g ++af +l +++  +++ +++  i + + + ++ ++++l+++++l +  llgi+li++Gv++i+
  gi|330506746|ref|YP_004383174.1|  27 TKIVpSIIVVAGYAVAFfFLSLTLKDNINIGVVYAIwSGVGVSLISVIGYLYYKQSLDIPALLGIALIIIGVMIIN 102
                                       3444355555566666614445555589999988887899999******************************997 PP

>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   4.4     8e-05      0.24      24      98 ..      24      99 ..       3     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8e-05
                              YwiC 24 pvwahllllvawlvgYl.affplllllkarrrarylkplliYgavallllllalllqpallwwallflplvavavy 98
                                        ++ ++  + +++gY  aff+l l lk++ +  ++  ++   +v+l+ ++ +l+++++l ++all ++l+++ v+
  gi|330506746|ref|YP_004383174.1| 24 DGFTKIVPSIIVVAGYAvAFFFLSLTLKDNINIGVVYAIWSGVGVSLISVIGYLYYKQSLDIPALLGIALIIIGVM 99
                                      55666677788999**7255566677888888899999999999*************7777777777777777665 PP

>> Mucin15  Cell-membrane associated Mucin15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3      0.68     2e+03     220     234 ..       6      20 ..       5      22 .. 0.87
   2 ?   11.4   0.3   5.5e-05      0.17     211     240 ..      50      77 ..      43      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.68
                           Mucin15 220 vfGaiLGaiLGasLL 234
                                       +f ai+G ++G+s L
  gi|330506746|ref|YP_004383174.1|   6 LFLAIIGEVIGTSAL 20 
                                       588********9987 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.5e-05
                           Mucin15 211 qkenrntGvvfGaiLGaiLGasLLsLvGYl 240
                                        k+n n Gvv+    G  +G+sL+s++GYl
  gi|330506746|ref|YP_004383174.1|  50 LKDNINIGVVYAIWSG--VGVSLISVIGYL 77 
                                       699*******965555..6**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 769.22
//
Query:       gi|330506747|ref|YP_004383175.1|  [L=212]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-17   62.2   0.0    1.1e-16   61.3   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
      2e-16   60.2   0.0    4.1e-16   59.3   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    1.8e-15   57.3   0.0    3.3e-15   56.5   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    7.7e-15   55.0   0.1    9.5e-15   54.7   0.1    1.2  1  Methyltransf_31  Methyltransferase domain
    2.1e-14   54.1   0.1    4.3e-14   53.1   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    1.4e-08   34.4   0.0    1.7e-08   34.1   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    3.9e-08   33.0   0.1    5.5e-08   32.6   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.4e-07   31.3   0.0    1.9e-07   30.8   0.0    1.2  1  MTS              Methyltransferase small domain
    3.2e-07   30.3   0.0    4.4e-07   29.9   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    3.8e-05   23.1   0.1    5.4e-05   22.6   0.1    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00024   20.3   0.0    0.00031   19.9   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00084   19.0   0.0      0.001   18.7   0.0    1.1  1  NodS             Nodulation protein S (NodS)
      0.002   17.5   0.0     0.0029   16.9   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0064   16.5   0.0     0.0092   16.0   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
  ------ inclusion threshold ------
      0.014   14.5   0.0      0.025   13.6   0.0    1.4  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.026   13.6   0.1      0.045   12.9   0.0    1.4  2  DREV             DREV methyltransferase
      0.048   13.6   0.1      0.064   13.2   0.1    1.2  1  Methyltransf_18  Methyltransferase domain
      0.058   12.5   0.0      0.077   12.1   0.0    1.2  1  Fibrillarin      Fibrillarin
      0.097   12.5   0.1       0.28   11.0   0.0    1.8  2  Methyltransf_8   Hypothetical methyltransferase
       0.12   11.9   0.0       0.15   11.6   0.0    1.2  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas


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 !   61.3   0.0   1.2e-19   1.1e-16       1      96 [.      44     136 ..      44     136 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.2e-19
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       v+d+GcGtG l+l+l+  +   +vtgvD s++ml++ +e+++++++ nv+ v  d+++ +   g +Dlvvs+++lhh
  gi|330506747|ref|YP_004383175.1|  44 VMDFGCGTGLLALRLQPIV--RSVTGVDSSKGMLDIFNEKIAKQKVdNVSTVLVDLDKGDPLRGNYDLVVSNMTLHH 118
                                       89***************98..9*************************************9999********888*** PP

                                       SSHHHHHHHHHHHHHHEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpg 96 
                                       ++  ++  +l+++++v+ pg
  gi|330506747|ref|YP_004383175.1| 119 IK--EIGPLLAQLYEVIAPG 136
                                       97..899**********998 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.0   4.6e-19   4.1e-16      13     163 ..      28     180 ..      15     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 4.6e-19
                   Methyltransf_23  13 lerll.pk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......kakkaqkdqfdeqeaaepq 80 
                                       + r+  +   l  ++ v+d+GcGtG l+  l++ + svtgvD s  + +i        k ++   + +d ++ ++  
  gi|330506747|ref|YP_004383175.1|  28 IVRAIsEQidLTDDMDVMDFGCGTGLLALRLQPIVRSVTGVDSSKGMLDIFNekiakqKVDNVSTVLVDLDKGDPLR 104
                                       333331334478999**********99999999999********999999877776666666666666666888899 PP

                   Methyltransf_23  81 gkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhi.sffsarslkelle 156
                                       g +dl+v++++l+h++    ll+q+++ ++pg yl +s+ + +      +++        +++   f++ +l e++ 
  gi|330506747|ref|YP_004383175.1| 105 GNYDLVVSNMTLHHIKEIGPLLAQLYEVIAPGSYLCISDLDLDG---GQFHEDNT-----GVFhFGFDRAALQEDFL 173
                                       9**************************************97554...22222111.....22212355555555555 PP

                   Methyltransf_23 157 eaGlevv 163
                                       + G+++v
  gi|330506747|ref|YP_004383175.1| 174 KVGFDDV 180
                                       5555555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   3.7e-18   3.3e-15       2      96 .]      46     141 ..      45     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 3.7e-18
                                       EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCT.SS-TT-EEEEEEES-CCC-CC CS
                   Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaekl.pfednsfDlvvssevlhhved 76 
                                       d+GcGtG+la  l+  +++v+gvD sk ml++ +ek+ ++++ +v+ v  d+ k  p++   +Dlvvs+++lhh+++
  gi|330506747|ref|YP_004383175.1|  46 DFGCGTGLLALRLQPIVRSVTGVDSSKGMLDIFNEKIAKQKVdNVSTVLVDLDKGdPLRG-NYDLVVSNMTLHHIKE 121
                                       99************999**************************9999******9857766.99************** PP

                                       HHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  77 pekalkeiaRvLkpgGllvi 96 
                                          +l++++ v  pg +l+i
  gi|330506747|ref|YP_004383175.1| 122 IGPLLAQLYEVIAPGSYLCI 141
                                       ****************9976 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.1   1.1e-17   9.5e-15       2     125 ..      39     154 ..      38     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 1.1e-17
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDl 77 
                                       ++++ v+D GCGtG l+++l   +++   v+G+D s+ ++   +e+ +k+++dnv+    d  +  +  l   ++Dl
  gi|330506747|ref|YP_004383175.1|  39 TDDMDVMDFGCGTGLLALRLQPIVRS---VTGVDSSKGMLDIFNEKIAKQKVDNVSTVLVDLDKgDP--LR-GNYDL 109
                                       6899*****************98887...***********************************666..44.9**** PP

                   Methyltransf_31  78 ilsnevlnaladpdkileeiervlkpggilliedprllaelp.akveee 125
                                       ++sn +l+++++    l ++ +v+ pg++l+i+d +    l+ ++++e+
  gi|330506747|ref|YP_004383175.1| 110 VVSNMTLHHIKEIGPLLAQLYEVIAPGSYLCISDLD----LDgGQFHED 154
                                       **********************************99....444455444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.0   4.7e-17   4.3e-14       1      98 [.      45     138 ..      45     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 4.7e-17
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       +++GcGtG l+ +l +     ++tgvD s+ +++   ek+ak++ +n++ v ++ ld +d    + +Dlvv++ +lh
  gi|330506747|ref|YP_004383175.1|  45 MDFGCGTGLLALRLQPI--VRSVTGVDSSKGMLDIFNEKIAKQKVDNVSTVLVD-LDKGDPLR-GNYDLVVSNMTLH 117
                                       69************999..99999*********999999999886555444444.44444444.5************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                       h+k+i  +l++++++++pg +
  gi|330506747|ref|YP_004383175.1| 118 HIKEIGPLLAQLYEVIAPGSY 138
                                       ******************976 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.9e-11   1.7e-08      23     139 ..      33     147 ..      15     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.9e-11
                                       HHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG--.--S-EEE CS
                              TehB  23 veavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineak.lderydf 98 
                                        e +++ +   v+d+gcg g  +l l+ +   vt +d  +  +  ++e + k++++n+st l+d+++ + l  +yd+
  gi|330506747|ref|YP_004383175.1|  33 SEQIDLTDDMDVMDFGCGTGLLALRLQPIVRSVTGVDSSKGMLDIFNEKIAKQKVDNVSTVLVDLDKGDpLRGNYDL 109
                                       56667778889******************************************************99754999**** PP

                                       EEEESSGGGS-GGGHHHHHHHHHHTEEEEEEEEEEEEB--S CS
                              TehB  99 ilstvvlmfleaeripsiienmqectkvggynlivaamstd 139
                                       ++s + l  +  + i  +++++ e   +g y l ++ ++ d
  gi|330506747|ref|YP_004383175.1| 110 VVSNMTLHHI--KEIGPLLAQLYEVIAPGSY-LCISDLDLD 147
                                       ***9988766..57999***********999.555665554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   6.1e-11   5.5e-08     160     259 ..      38     142 ..      29     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 6.1e-11
                              PrmA 160 kege.evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleva..lseellkeekadvivaN 233
                                        +++  v+D+G+G+G+La+  + +  ++v++vD  +  +++ +e +++ kv++  +v   l +  + ++++d++v+N
  gi|330506747|ref|YP_004383175.1|  38 LTDDmDVMDFGCGTGLLALRLQPI-VRSVTGVDSSKGMLDIFNEKIAKQKVDNVSTVLvdLDKGDPLRGNYDLVVSN 113
                                       444349************987776.789*************************666641144444558********* PP

                              PrmA 234 ILaevlie...laedikklvkeggllilS 259
                                       +  + + e   l+ ++++++++g++l +S
  gi|330506747|ref|YP_004383175.1| 114 MTLHHIKEigpLLAQLYEVIAPGSYLCIS 142
                                       *99998873336779999999**999988 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.2e-10   1.9e-07      26     112 ..      35     121 ..      23     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.2e-10
                                       HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST.TS-EEE CS
                               MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve.ekkfdl 100
                                       +++ + + +v+D+GcG+G+l++ l+    +  vt vd ++  l++ +e ++++k++ v++v  d+ +  +  +++dl
  gi|330506747|ref|YP_004383175.1|  35 QIDLTDDMDVMDFGCGTGLLALRLQPIVRS--VTGVDSSKGMLDIFNEKIAKQKVDnVSTVLVDLDKGDPlRGNYDL 109
                                       555556778*************99988777..9************************9999999887665579**** PP

                                       EEE---STTTCH CS
                               MTS 101 ivsNPPfhagka 112
                                       +vsN  +h+ k+
  gi|330506747|ref|YP_004383175.1| 110 VVSNMTLHHIKE 121
                                       ****88887666 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   4.9e-10   4.4e-07      63     157 ..      30     121 ..      16     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 4.9e-10
                                       HHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGG CS
                              PCMT  63 alalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyee 139
                                        ++ e ++l++ + v++ G+G+G l+  l  +v++++   +++ +k + +  ++++ k++++nv++v  D  kG + 
  gi|330506747|ref|YP_004383175.1|  30 RAISEQIDLTDDMDVMDFGCGTGLLALRLQPIVRSVT---GVDSSKGMLDIFNEKIAKQKVDNVSTVLVDLDKGDPL 103
                                       56778999**************************988...************************************* PP

                                       G-SEEEEEESSBBSS--H CS
                              PCMT 140 kaPYdaihvgaaapeiPe 157
                                       +  Yd ++   + ++i e
  gi|330506747|ref|YP_004383175.1| 104 RGNYDLVVSNMTLHHIKE 121
                                       *****9987777666654 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1     6e-08   5.4e-05      48     150 ..      41     140 ..      22     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6e-08
                                       TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES CS
                   Ubie_methyltran  48 gakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsf 124
                                         +v+D  +Gtg la++l+  v++   v+++D ++ mL++ ++k+ ++ + n+  +  +  + +   + +D+v    
  gi|330506747|ref|YP_004383175.1|  41 DMDVMDFGCGTGLLALRLQPIVRS---VTGVDSSKGMLDIFNEKIAKQKVDNVSTVLVDLDKGDPLRGNYDLVVSNM 114
                                       4689****************9996...899**************************99999999999********** PP

                                       -GGG-S-HHHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 125 GlrnvtDklkaLkeayrvlkpGGrlv 150
                                        l  + ++   L ++y v+ pG  l 
  gi|330506747|ref|YP_004383175.1| 115 TLHHIKEIGPLLAQLYEVIAPGSYLC 140
                                       *********************98775 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.5e-07   0.00031      18      75 ..      28      87 ..      23     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.5e-07
                                      HHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TC CS
                            RrnaAD 18 vineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kd 75
                                      ++  I ++++l++++ v++ g G+G+l  +L  ++++v+ + + + ++ + ++k+   k 
  gi|330506747|ref|YP_004383175.1| 28 IVRAISEQIDLTDDMDVMDFGCGTGLLALRLQPIVRSVTGVDSSKGMLDIFNEKIAkqKV 87
                                      56678899*********************************************9984333 PP

>> NodS  Nodulation protein S (NodS)
   #    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      33     130 ..      27     130 ..       5     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                              NodS  33 qilrlslaqgsia...dalevGcaaGalterlapyckrltvvdvveeaiararerv..kesshiswivsdvqqfst. 103
                                       +i+r   +q +++   d+++ Gc +G l+ rl p+ +++t vd  +  ++  +e++  +++ ++s +  d+ + +  
  gi|330506747|ref|YP_004383175.1|  27 DIVRAISEQIDLTddmDVMDFGCGTGLLALRLQPIVRSVTGVDSSKGMLDIFNEKIakQKVDNVSTVLVDLDKGDPl 103
                                       566666666666511157788**********************9998877766666214567899999***999862 PP

                              NodS 104 dekfdlivvaevlyyiedvaelraavr 130
                                         ++dl+v    l++i+++  l a + 
  gi|330506747|ref|YP_004383175.1| 104 RGNYDLVVSNMTLHHIKEIGPLLAQLY 130
                                       679************999987766554 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.3e-06    0.0029      51     141 ..      29     120 ..      17     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.3e-06
                                       HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SS..S-EEEEES-GGG-- CS
                              CMAS  51 ldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldle..rkvevklldyedld 125
                                       ++ i e+++l + m ++d GcG G l+ r       +v g+  Sk      +++++++ ++   +v v+l +   l+
  gi|330506747|ref|YP_004383175.1|  29 VRAISEQIDLTDDMDVMDFGCGTGLLALRLQPI-VRSVTGVDSSKGMLDIFNEKIAKQKVDnvSTVLVDLDKGDPLR 104
                                       5678899*****************999886554.56899***********999998765550056667788888999 PP

                                       ---SEEEEES-GGGTS CS
                              CMAS 126 ekvdrvvsvgafehvg 141
                                       +++d vvs   + h++
  gi|330506747|ref|YP_004383175.1| 105 GNYDLVVSNMTLHHIK 120
                                       ********99888885 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     1e-05    0.0092      12      70 ..      28      81 ..      22     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                   Methyltransf_32 12 lvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekr 70
                                      +v+++ ++  + +++++v+D+G+G g L+ +l+        +v+g+d+++ + +  ++ 
  gi|330506747|ref|YP_004383175.1| 28 IVRAISEQ-IDLTDDMDVMDFGCGTGLLALRLQP----IVRSVTGVDSSKGMLDIFNEK 81
                                      44444444.678899*****************99....567999999998877665554 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.8e-05     0.025     200     254 ..      39      93 ..      19      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                   tRNA_U5-meth_tr 200 eskgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqii 254
                                       + + d++++ cG G ++l l   ++ v   + +k  ++     ia+ k+dnv+ +
  gi|330506747|ref|YP_004383175.1|  39 TDDMDVMDFGCGTGLLALRLQPIVRSVTGVDSSKGMLDIFNEKIAKQKVDNVSTV 93 
                                       34569***********************************************876 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     5e-05     0.045      94     201 ..      40     157 ..      27     164 .. 0.74
   2 ?   -3.5   0.0         5   4.5e+03      50      73 ..     182     205 ..     177     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5e-05
                              DREV  94 edkklldlGaGdGeitkrvaptfeevyatelsetmrd....rlkkkky.nvlsa.lelqetd...vkldlilclnll 161
                                       +d  ++d+G G G ++ r++p +  v   + s+ m d    ++ k+k  nv ++ ++l++ d    ++dl+++   l
  gi|330506747|ref|YP_004383175.1|  40 DDMDVMDFGCGTGLLALRLQPIVRSVTGVDSSKGMLDifneKIAKQKVdNVSTVlVDLDKGDplrGNYDLVVSNMTL 116
                                       5789******************************986222256666652443332356665532269****999999 PP

                              DREV 162 drcfdplklledirsalepngrv.ivalvlPvshyvetntg 201
                                           + + ll  ++++ +p +   i  l l   ++ e ntg
  gi|330506747|ref|YP_004383175.1| 117 HHIKEIGPLLAQLYEVIAPGSYLcISDLDLDGGQFHEDNTG 157
                                       99999999***999999995544044466666666666665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5
                              DREV  50 silslfmsktdinGllgrGsmfvl 73 
                                       si    m+k +i G ++r s+f++
  gi|330506747|ref|YP_004383175.1| 182 SINAAEMAKPSITGEMRRFSIFLM 205
                                       566667899999999999999986 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.2e-05     0.064      14      72 ..      40      95 ..      28     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.2e-05
                   Methyltransf_18 14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrls 72
                                      ++  v+D G+  g+l++ l  + ++++v+ +D ++g l+  +e+i+k+++++ ++++l 
  gi|330506747|ref|YP_004383175.1| 40 DDMDVMDFGCGTGLLALRL--QPIVRSVTGVDSSKGMLDIFNEKIAKQKVDN-VSTVLV 95
                                      34589**********9998..58*************************9965.555444 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.5e-05     0.077      46     126 ..      13      95 ..       3     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.5e-05
                                       EEE..-TTTSHHHHHHHTT-S.--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHH.HHHTTS CS
                       Fibrillarin  46 RvW..npfrsKlaaailkglk.elpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlreli.evakkR 118
                                         W  np rsKla  i++ ++ ++ +  +  v+ +G ++G  +  +  iv     v +v+ s+ +l  +  ++ak++
  gi|330506747|ref|YP_004383175.1|  13 AKWdeNPARSKLADDIVRAISeQIDLTDDMDVMDFGCGTGLLALRLQPIVR---SVTGVDSSKGMLDIFNeKIAKQK 86 
                                       5564479************962689***************99999888888...67777777766665553344333 PP

                                       .TTEEEEES CS
                       Fibrillarin 119 .knivPile 126
                                         n+  +l 
  gi|330506747|ref|YP_004383175.1|  87 vDNVSTVLV 95 
                                       256665555 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00031      0.28      46      93 ..       6      61 ..       3     101 .. 0.75
   2 ?   -1.5   0.0       2.1   1.9e+03      84     182 ..     166     181 ..     137     200 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                                      HHHHHHHCTSSS-HH.....HHHHHHHC...TS-TTS-EEEES-TT-HHHHH--S- CS
                    Methyltransf_8 46 kgfrsqvkkWPenPl.....dviirklk...kkkdnlvvadlGcGeakiaeavrek 93
                                      + f++   kW enP      d i+r +       d++ v+d+GcG   +a + +  
  gi|330506747|ref|YP_004383175.1|  6 RDFDKEAAKWDENPArsklaDDIVRAISeqiDLTDDMDVMDFGCGTGLLALRLQPI 61
                                      56889999*****9732223567777774444578999********9999766543 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                                       -HHHHH--S-..EEEEESS-SSTTEEES-TTS-S--TT-EEEEEEES---SS-HHHHHHHHHHHEEEEEEEEEEEEG CS
                    Methyltransf_8  84 akiaeavrekekvrsfdlvavnervvacdlakvPledesvdvavfclslmgtnladflkeanrvlkvGGllkvaevk 160
                                       a                                                                            
  gi|330506747|ref|YP_004383175.1| 166 AA--------------------------------------------------------------------------- 167
                                       33........................................................................... PP

                                       GG-S-HHHHHHHHHCTTEEEEE CS
                    Methyltransf_8 161 srfesvklfaraltklGfevks 182
                                               +++++ k+Gf+ ++
  gi|330506747|ref|YP_004383175.1| 168 --------LQEDFLKVGFDDVH 181
                                       ........44444455554443 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 ?   11.6   0.0   0.00017      0.15      52     136 ..      37     120 ..      25     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                   Methyltransf_PK  52 gkrevkvaldcGaGiGrvtknlLlkllskvDlvepvekflekakeelaeekkkvgkvyvvglqeftPeegrYdliWi 128
                                       + ++   ++d G+G G ++ + L ++++ v  v+  + +l+  +e++a++k    ++  v l++  P +g+Ydl+  
  gi|330506747|ref|YP_004383175.1|  37 DLTDDMDVMDFGCGTGLLALR-LQPIVRSVTGVDSSKGMLDIFNEKIAKQKVDNVSTVLVDLDKGDPLRGNYDLVVS 112
                                       5556667899******99877.689************************999999999*****************98 PP

                   Methyltransf_PK 129 qWcvghLt 136
                                          + h+ 
  gi|330506747|ref|YP_004383175.1| 113 NMTLHHIK 120
                                       88888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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):              20  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1536.98
//
Query:       gi|330506748|ref|YP_004383176.1|  [L=259]
Description: alpha/beta fold family hydrolase [Methanosaeta concilii GP6]
Scores for complete 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-22   78.3   0.0    2.8e-17   63.2   0.1    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    5.8e-14   53.2   0.0    6.6e-14   53.0   0.0    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
    5.1e-10   39.0   0.0      3e-08   33.2   0.0    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
     0.0035   17.5   0.0     0.0052   16.9   0.0    1.4  1  Thioesterase   Thioesterase domain
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.048   13.3   0.0    1.8  1  FSH1           Serine hydrolase (FSH1)
      0.018   14.8   0.4       0.11   12.1   0.4    2.0  1  PGAP1          PGAP1-like protein
      0.081   12.8   0.0      0.098   12.5   0.0    1.2  1  Palm_thioest   Palmitoyl protein thioesterase
      0.089   11.6   0.0        0.1   11.4   0.0    1.1  1  DUF1100        Alpha/beta hydrolase of unknown function (DUF1
       0.13   11.6   0.0       0.46    9.8   0.0    1.7  2  DUF915         Alpha/beta hydrolase of unknown function (DUF9
       0.23   11.2   0.0       0.59    9.9   0.0    1.6  2  Abhydrolase_2  Phospholipase/Carboxylesterase


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 !   63.2   0.1   1.6e-20   2.8e-17       2     110 ..      31     140 ..      30     183 .. 0.81
   2 !   13.1   0.0   3.2e-05     0.057     207     256 ..     194     243 ..     172     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.6e-20
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       +l++lhG++gs   + +  + + L+  +f +i++DlrG+g+S++++a      + a ++ d++++l  l++ ++ ++
  gi|330506748|ref|YP_004383176.1|  31 PLLLLHGGLGSIIDFNG--ILERLPS-QFSFIGIDLRGHGRSTTGSAR----LSYARYQSDVEAVLTYLNISSVSII 100
                                       89********9988888..******9.*******************76....66777999***************** PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESE........CSSC CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllga........idpa 110
                                       G+S GG ++  +aae +++V++lv+lga        ++ +
  gi|330506748|ref|YP_004383176.1| 101 GFSDGGIVGYRMAAEENSKVQKLVTLGAqwrlkeddPSFS 140
                                       ****************************777665322222 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.2e-05
                                       THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                     Abhydrolase_1 207 lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafleg 256
                                       ++ +++p l++ g++D l + ++  +l++l +++ l+ i+ agH ++ + 
  gi|330506748|ref|YP_004383176.1| 194 VQIIKCPLLIVRGDDDELLSLREAGELRSLVKGSGLLNIPFAGHEVHKDS 243
                                       56699****************************************99775 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   3.7e-17   6.6e-14       1     218 [.      32     248 ..      32     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 3.7e-17
                                       EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-..GGCS--HHHC.HHHHHHHCCTT..TTSEEEEEETC CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrs..dpppldledl.adlaalldelaagggpvvlvGHSl 74 
                                       +lllHG+ +s  ++    ++++l++++  + +Dl+GhGrs   ++ l+++++  d++a+l+ l      v ++G S 
  gi|330506748|ref|YP_004383176.1|  32 LLLLHGGLGSIIDFN--GILERLPSQFSFIGIDLRGHGRSttGSARLSYARYqSDVEAVLTYLN--ISSVSIIGFSD 104
                                       79***9777667776..999999***777*********77335555888886366699999996..9999******* PP

                                       HHHHHHHHHHCC.......EE.EEES-..----TTTS----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHHCCCCHC CS
                     Abhydrolase_6  75 GGalalaaapla.....lvvg.vlldppptalpagllaaalelllallallrllawlsreplprlfladedadaawr 145
                                       GG+++ +    a      v + v l +   ++++ + ++ +++l++l+a    + w+ + p++ ++++++ + ++++
  gi|330506748|ref|YP_004383176.1| 105 GGIVGYR---MAaeensKVQKlVTLGA---QWRLKEDDPSFSMLAGLTA----DMWMEMFPDSVRYYEKVNPNPDFN 171
                                       *******...666657866778*****...*******************....****9877777****99999**** PP

                                       HCCCGHHHHCCHHC..HTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH....STTEEETCE...SSS-HHHHSHH CS
                     Abhydrolase_6 146 arlarlaallaglg..llpaaawadlpvpllvl.ggeDplvprllerlla....qagarlpvvlpgaGHlphleepd 215
                                       a +  +  l++ lg   +p +a+  + +pll++ g++D+l+   l++++     + g +l   +p aGH +h ++pd
  gi|330506748|ref|YP_004383176.1| 172 ALVKKVVGLWTDLGptGYPGEAVQIIKCPLLIVrGDDDELLS--LREAGElrslVKGSGL-LNIPFAGHEVHKDSPD 245
                                       *******99997776577999*********999888888777..6666655446677777.99**********9*99 PP

                                       HHH CS
                     Abhydrolase_6 216 eva 218
                                        +a
  gi|330506748|ref|YP_004383176.1| 246 IFA 248
                                       887 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   1.7e-11     3e-08       7     135 ..      32     155 ..      26     176 .. 0.83
   2 ?    3.9   0.0     0.015        27     188     237 ..     195     242 ..     190     244 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.7e-11
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGh 83 
                                       ++l+HG   ++  ++ + e+L  q f+++++D rGhGrs    +   s+ +y  D++a+++ +      + + ++G 
  gi|330506748|ref|YP_004383176.1|  32 LLLLHGGLGSIIDFNGILERLPSQ-FSFIGIDLRGHGRSTTGSA-RLSYARYQSDVEAVLTYLN----ISSVSIIGF 102
                                       688999999999999999999765.**************85544.459***********98888....7789***** PP

                       Hydrolase_4  84 SmGGliallyllrypdkvaglilsaPalkikaklk.appllklllkllgkllp 135
                                       S GG++  ++++++ +kv++l+  ++  ++k++ + ++ l+ l++ +  +++p
  gi|330506748|ref|YP_004383176.1| 103 SDGGIVGYRMAAEENSKVQKLVTLGAQWRLKEDDPsFSMLAGLTADMWMEMFP 155
                                       ****************************9999865666666666665555555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.015
                       Hydrolase_4 188 akitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnE 237
                                       + i+ Pll++ G++D++ + +++ el   ++     l  +p + He++ +
  gi|330506748|ref|YP_004383176.1| 195 QIIKCPLLIVRGDDDELLSLREAGELRSLVK--GSGLLNIPFAGHEVHKD 242
                                       56889************99888866655555..45566666666666665 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.9e-06    0.0052       2     102 ..      31     128 ..      30     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-06
                                       EEEEE--TTCCSGGGHHHHHHCTTCEEEEEEECSTTST.SHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHH CS
                      Thioesterase   2 pLflfppagGsasvfrslasklsdpvvevlavqlpgre.rdepplesieelaaeyaealrqiqpegPyalfGhSlGg 77 
                                       pL l++++ Gs+  f+ + ++l+++  +++++ l+g++ +++  ++   +  ++ +ea+++      + ++G+S Gg
  gi|330506748|ref|YP_004383176.1|  31 PLLLLHGGLGSIIDFNGILERLPSQ-FSFIGIDLRGHGrSTTGSARLSYARYQSDVEAVLTYLNISSVSIIGFSDGG 106
                                       89**********************9.***********86444444444445566689999999999*********** PP

                                       HHHHHHHHHHHHCT-SEEEEEEESC CS
                      Thioesterase  78 llAfevArqLesqGlavkslflids 102
                                       ++ +++A++   + ++v+ l+  ++
  gi|330506748|ref|YP_004383176.1| 107 IVGYRMAAE---ENSKVQKLVTLGA 128
                                       *******85...3445555555555 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.7e-05     0.048      83     189 ..      78     226 ..      62     244 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                              FSH1  83 yegleesldavkdyikengpfdGiiGFSqGaalaallaslleellkea.........shpslkfailvsGfkleepk 150
                                       y +++  ++av  y++ +   + iiGFS G++++ ++a++ + + ++          ++++  f++l +G  ++  +
  gi|330506748|ref|YP_004383176.1|  78 YARYQSDVEAVLTYLNISS--VSIIGFSDGGIVGYRMAAEENSKVQKLvtlgaqwrlKEDDPSFSML-AGLTADMWM 151
                                       6667777888888887666..99***************99998887667888888884444444443.444443333 PP

                              FSH1 151 .....................................yeeyyeedkiqtptLhvlGelDtvvdeerseaLaeafkn 189
                                                                            y      + i++p L v G++D++ +  ++ +L   +k 
  gi|330506748|ref|YP_004383176.1| 152 emfpdsvryyekvnpnpdfnalvkkvvglwtdlgptgYPGEA-VQIIKCPLLIVRGDDDELLSLREAGELRSLVKG 226
                                       456666677666666666666655555555555443333333.455689999999999988887777666666655 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   6.4e-05      0.11      89     127 ..      93     128 ..      26     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.4e-05
                             PGAP1  89 eptsviliGHSmGGivaraaltlknyikqsvntiltlas 127
                                       +++sv +iG S GGiv   ++  +n   ++v++++tl++
  gi|330506748|ref|YP_004383176.1|  93 NISSVSIIGFSDGGIVGYRMAAEEN---SKVQKLVTLGA 128
                                       679**************98888888...78999999986 PP

>> Palm_thioest  Palmitoyl protein thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.4e-05     0.098      46     102 ..      76     129 ..      31     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.4e-05
                      Palm_thioest  46 sffgnlndqveavckklelangfhaiGfSQGglf.lRaliercddkknvrnlislggp 102
                                        ++   +  veav + l+  + + +iGfS Gg++  R  +e+    k v++l++lg++
  gi|330506748|ref|YP_004383176.1|  76 LSYARYQSDVEAVLTYLNI-SSVSIIGFSDGGIVgYRMAAEEN--SK-VQKLVTLGAQ 129
                                       4555556666667666544.789**********9447777775..44.*******987 PP

>> DUF1100  Alpha/beta hydrolase of unknown function (DUF1100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.7e-05       0.1     254     295 ..      88     129 ..      16     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.7e-05
                           DUF1100 254 dvpyvdhtrvgliGfrfGanvavrlaflesekvkavvalGav 295
                                        + y++   v++iGf  G+ v  r+a  e++kv+  v+lGa 
  gi|330506748|ref|YP_004383176.1|  88 VLTYLNISSVSIIGFSDGGIVGYRMAAEENSKVQKLVTLGAQ 129
                                       35799999********************************96 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 ?   -1.4   0.0      0.65   1.2e+03       9      35 ..      27      53 ..      23      62 .. 0.86
   2 ?    9.8   0.0   0.00025      0.46      91     144 ..      87     131 ..      73     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.65
                            DUF915  9 kkeiPtifihGyggtaeslnemvkqle 35
                                       +  P +++hG  g+   +n+++++l 
  gi|330506748|ref|YP_004383176.1| 27 PNGQPLLLLHGGLGSIIDFNGILERLP 53
                                      56789**********999999999985 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00025
                            DUF915  91 kvlseLkkkYnikkfnavGhSmGglaltsYleeyaddkslPqlkklvtiggpfn 144
                                       +vl++L    ni  + ++G+S Gg+  + Y ++ ++++   +++klvt+g+++ 
  gi|330506748|ref|YP_004383176.1|  87 AVLTYL----NISSVSIIGFSDGGI--VGYRMAAEENS---KVQKLVTLGAQWR 131
                                       555555....899**********96..67878888887...67*******9975 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.8     5e+03      12      24 ..      27      40 ..      22      46 .. 0.58
   2 ?    9.9   0.0   0.00033      0.59     102     138 ..      92     128 ..      73     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.8
                                      ---EEEEEE--.TT CS
                     Abhydrolase_2 12 kaqavviflHG.lG 24
                                      ++ + +++lHG lG
  gi|330506748|ref|YP_004383176.1| 27 PNGQPLLLLHGgLG 40
                                      55555666665244 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00033
                                       --GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES- CS
                     Abhydrolase_2 102 ipssriiigGFSqGaalalylaltlpkklggivafsg 138
                                       ++ s + i+GFS G++++   a  ++ k++  v ++ 
  gi|330506748|ref|YP_004383176.1|  92 LNISSVSIIGFSDGGIVGYRMAAEENSKVQKLVTLGA 128
                                       5678999***********9999999999988887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1826.34
//
Query:       gi|330506749|ref|YP_004383177.1|  [L=400]
Description: peptidase M28 [Methanosaeta concilii GP6]
Scores for complete 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-22   78.5   0.0    1.2e-21   77.4   0.0    1.6  2  Peptidase_M28  Peptidase family M28
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.33   10.9   0.0    1.6  1  SPOC           SPOC domain


Domain annotation for each model (and alignments):
>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.44   3.9e+03     138     163 ..      22      47 ..      17      75 .. 0.74
   2 !   77.4   0.0   1.3e-25   1.2e-21       1     193 [.     209     392 ..     209     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.44
                                       EEEEESSTT-STTHHHHTTT--EEEE CS
                     Peptidase_M28 138 pfdersgrgrsDhspflkagvpvldl 163
                                       p+ ++++ g+ D++ f ++ v +  +
  gi|330506749|ref|YP_004383177.1|  22 PNRRTGSLGNRDATDFFANTVRAYGY 47 
                                       66667777888888888888777666 PP

  == domain 2  score: 77.4 bits;  conditional E-value: 1.3e-25
                                       EEEEEESTTCESEEEEEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHH CS
                     Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllG 77 
                                       N+ia+l+ +a ++ ++++AH+D +    +p   GA DnAsg+ +lL  a++l +   r ++ + ++++++E+ +  G
  gi|330506749|ref|YP_004383177.1| 209 NIIARLNSNA-PRKVVITAHIDAYEG--SP---GASDNASGIIVLLLCAQMLSD--YRGENCIEIVALNGEDHYSAG 277
                                       9*********.9*************9..**...********************9..799**************9999 PP

                                       HH.HHHH.HHCCCTTEEEEEEECS-SSSS--EEEHHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHH CS
                     Peptidase_M28  78 Sk.afak.akpelkkiaavlnlDmvgsggkellfesgdkssselekelkalakpvgraaaedpfdersgrgrsDhsp 152
                                        +  + k   +e+ ki + +n+D vg +     + s  +   +lek+++++  ++++      + ++++ ++ Dh +
  gi|330506749|ref|YP_004383177.1| 278 GQmDYLKrYGTEMPKIMLAINIDDVGYKIGRTAY-SFYECPLSLEKKAEDVFLRFNS------LASGEQWFNGDHMI 347
                                       98346644555***************99887774.778889999*******999976......4566778999**** PP

                                       HHTTT--EEEE....CTSSS-TTTTSTTSSGGGB-HHHHHHHHHH CS
                     Peptidase_M28 153 flkagvpvldl....aetgfpevyHtprDtldnidkdtlariael 193
                                       f++++vp + +     ++ +++v Ht+ Dt+d id  +l ++ae 
  gi|330506749|ref|YP_004383177.1| 348 FAQNQVPSMAFtserMADLMKTVTHTSLDTPDLIDCYKLVEVAES 392
                                       ***********9998888889999***********9999888875 PP

>> SPOC  SPOC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.6e-05      0.33      84     118 ..     132     166 ..     127     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHHTTTEEEE.....EE-TTS-EEEEE-S CS
                              SPOC  84 faelvdYLksKqraGvvnlnksglnqngvlyifPp 118
                                        ++ +  L+s++ aG++   +++++q g ly fP+
  gi|330506749|ref|YP_004383177.1| 132 HQKIIALLESRKPAGIITATEKKPEQAGALYPFPL 166
                                       5678999***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.34s 00:00:01.02 Elapsed: 00:00:00.57
# Mc/sec: 2126.30
//
Query:       gi|330506750|ref|YP_004383178.1|  [L=249]
Description: short chain dehydrogenase/reductase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-60  203.1   0.0    5.6e-60  202.8   0.0    1.0  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    3.9e-51  173.3   0.0    4.9e-51  173.0   0.0    1.0  1  adh_short       short chain dehydrogenase
    4.2e-13   49.6   0.0    7.2e-13   48.8   0.0    1.3  1  KR              KR domain
     0.0048   16.6   0.0        0.3   10.7   0.0    2.2  2  ApbA            Ketopantoate reductase PanE/ApbA
      0.006   16.1   0.1      0.017   14.6   0.1    1.7  2  Epimerase       NAD dependent epimerase/dehydratase family
     0.0069   16.3   0.1      0.019   14.8   0.1    1.6  2  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.097   12.1   0.0       0.14   11.5   0.0    1.2  1  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.8   0.0   2.2e-63   5.6e-60       4     234 .]      15     247 ..      11     247 .. 0.96

  Alignments for each domain:
  == domain 1  score: 202.8 bits;  conditional E-value: 2.2e-63
                                       TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                        g+G+ iA++l ++Ga+vv++ ++ee+++ v +  + +g++v  +++DV+d+ +v++l++++ e+fg l+ +vnnag
  gi|330506750|ref|YP_004383178.1|  15 TGLGETIAEELFKRGARVVIAARHEEQARVVSDGLDPTGKRVyvCKTDVRDPRSVKNLIDTTLERFGALHLAVNNAG 91 
                                       79*************************999**99999999954699******************************* PP

                                       --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHH CS
                      adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtr 153
                                       i+ +    + + +  +++++++++l+++f ++k+ +p ++ +g g+ivn+ss  + +++++ + y+aaK+++++ltr
  gi|330506750|ref|YP_004383178.1|  92 ITGPGGITIPDYDICDWHDVIETDLTGVFFCLKYEIPaILSSGgGAIVNMSSGNGVVGLAGLAPYTAAKHGVIGLTR 168
                                       ****888999***************************9666667********************************* PP

                                       HHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEES CS
                      adh_short_C2 154 ylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvD 230
                                       ++A e+++kg R+Nav pg+++T+ +++ +  +e+l +++a++p+grl++ +eva +++fL+sd++++ tG    vD
  gi|330506750|ref|YP_004383178.1| 169 SAALEFADKGLRINAVGPGYVDTPKMRETP--KEILTQFAASHPMGRLAERREVAYLVAFLLSDQSTFSTGGFYPVD 243
                                       ***************************999..9******************************************** PP

                                       TTGG CS
                      adh_short_C2 231 gGlt 234
                                       gG+t
  gi|330506750|ref|YP_004383178.1| 244 GGYT 247
                                       ***8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.0   0.0   1.9e-54   4.9e-51       1     190 [.       6     197 ..       6     201 .. 0.96

  Alignments for each domain:
  == domain 1  score: 173.0 bits;  conditional E-value: 1.9e-54
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       kv++vtG+s G+G  ia+el k+Ga+vv+++r+ee+++ v + l  +g++++++++Dv+d ++v++l+++  +++g 
  gi|330506750|ref|YP_004383178.1|   6 KVAIVTGGSTGLGETIAEELFKRGARVVIAARHEEQARVVSDGLDPTGKRVYVCKTDVRDPRSVKNLIDTTLERFGA 82 
                                       89***********************************9999999999****************************** PP

                                       ESEEEE---S..S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                         adh_short  78 ldvLvnNAGi..tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAs 152
                                       l++ vnNAGi   g  ++ +++  +w +vie+ ltgvf + +  +pa+l++ +G+Ivn+sS +g v++ag+a+Y+A+
  gi|330506750|ref|YP_004383178.1|  83 LHLAVNNAGItgPGGITIPDYDICDWHDVIETDLTGVFFCLKYEIPAILSSGGGAIVNMSSGNGVVGLAGLAPYTAA 159
                                       **********554555788999******************************************************* PP

                                       HHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                         adh_short 153 KaavagltrslakelaptgirvnavaPGlvdTdmakel 190
                                       K++v+gltrs+a e+a++g r+nav PG+vdT+ ++e+
  gi|330506750|ref|YP_004383178.1| 160 KHGVIGLTRSAALEFADKGLRINAVGPGYVDTPKMRET 197
                                       ********************************987765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   2.8e-16   7.2e-13       4     154 ..       9     161 ..       7     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 2.8e-16
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       ++tGG  gLG ++a+ l ++gar +v+ +R+   +e+++   + l  +g +v v++ Dv d+ +v++l+++  ++++
  gi|330506750|ref|YP_004383178.1|   9 IVTGGSTGLGETIAEELFKRGAR-VVIAARH---EEQARVVSDGLDPTGKRVYVCKTDVRDPRSVKNLIDTTLERFG 81 
                                       8********************98.5667788...456666789********************************** PP

                                       ---EEEE--------..-TTT--HHHHHHHHTTTTHHHHH.HHHHTTT...S--SEEEEEEEHHHHH--TT-HHHHH CS
                                KR  81 pikGvihaAgvlrdk..lleemtaedleqvlapKvkGawn.Lhelled...esldffvlfSSiagllgsagqanYaa 151
                                       +++  ++ Ag++  +  ++ + +  d++ v++  ++G+   L+  ++    +    +v +SS  g++g ag a Y+a
  gi|330506750|ref|YP_004383178.1|  82 ALHLAVNNAGITGPGgiTIPDYDICDWHDVIETDLTGVFFcLKYEIPAilsSGGGAIVNMSSGNGVVGLAGLAPYTA 158
                                       ************9872255678888************9751554444455478899********************* PP

                                       HHH CS
                                KR 152 aNa 154
                                       a +
  gi|330506750|ref|YP_004383178.1| 159 AKH 161
                                       965 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00012       0.3       5      48 ..      13      59 ..       9      77 .. 0.80
   2 ?    3.7   0.0     0.017        44       6      54 ..     145     193 ..     142     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                                      S-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETT...C CS
                              ApbA  5 GaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseg...g 48
                                      G+ ++G ++a +L k ga v++ +r ++ ++++++Gl+ t+++    
  gi|330506750|ref|YP_004383178.1| 13 GSTGLGETIAEELFKRGARVVIAARHEEQARVVSDGLDPTGKRvyvC 59
                                      8889***********************8889******9888883333 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.017
                                       -SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETT.CEEEEEE CS
                              ApbA   6 aGaiGsllaakLakagadvtlilrsrrlealkknGlrltseg.geeilrp 54 
                                        G +G    a  ++a++ v+ ++rs+ + ++ ++Glr++ +g g +  ++
  gi|330506750|ref|YP_004383178.1| 145 NGVVGLAGLAPYTAAKHGVIGLTRSA-ALEFADKGLRINAVGpGYVDTPK 193
                                       566666666666779999********.666********999865444444 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   6.7e-06     0.017       2      63 ..       9      76 ..       8      93 .. 0.78
   2 ?   -1.3   0.0      0.48   1.2e+03     140     160 ..     154     174 ..     144     219 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.7e-06
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHHH CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfkee 63
                                      +VtG++  +G  ++++l ++g +v+  +r +++ +    + l        +++ d++d+ ++++l++++
  gi|330506750|ref|YP_004383178.1|  9 IVTGGSTGLGETIAEELFKRGARVVIAARHEEQAR-VVSDGLdptgkrvYVCKTDVRDPRSVKNLIDTT 76
                                      8**********************776666633333.33333368999999*************999975 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.48
                                       SHHHHHHHHHHHHHHHHHHHH CS
                         Epimerase 140 spYaaaKlageklveayaaqy 160
                                        pY aaK+ +  l++++a ++
  gi|330506750|ref|YP_004383178.1| 154 APYTAAKHGVIGLTRSAALEF 174
                                       467777766666666666555 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   7.5e-06     0.019       1      58 [.      12      73 ..      12      78 .. 0.84
   2 ?   -1.4   0.0      0.74   1.9e+03     130     180 ..     173     227 ..     141     231 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.5e-06
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH.....CTTTCEEEE--TT-CCHHHHHH CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaele.....aeeglevvegdvtdvedlaeal 58
                                      G++ + G  +++el +rg  +v++ +R++e++  ++       +++ v++ dv d+ ++++ +
  gi|330506750|ref|YP_004383178.1| 12 GGSTGLGETIAEELFKRG-ARVVIAARHEEQARVVSdgldpTGKRVYVCKTDVRDPRSVKNLI 73
                                      788899***********5.*************976644433447999**********999887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.74
                                       HHHHSSSEEEEEEE-CEE-ST..--SEEEEET..TSS----EEEHHHHHHHHHHH CS
                    NAD_binding_10 130 llrasgldwTivrpggLtdep..ttkyrvvek..gepfkggsisradVAdvlvav 180
                                       +  ++gl    v pg+    +  +t  +++++       g+  +r+ VA +++ +
  gi|330506750|ref|YP_004383178.1| 173 EFADKGLRINAVGPGYVDTPKmrETPKEILTQfaASHPMGRLAERREVAYLVAFL 227
                                       3445666666777777755433455555555421222234455777777665555 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.4e-05      0.14       2      73 ..      10      75 ..       9      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.4e-05
                                      EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHH CS
                     GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllae 73
                                      +TG++   G  +ae L ++g +v++  r++++ +   ++    dp   + +++ + k D++D +s+++l++ 
  gi|330506750|ref|YP_004383178.1| 10 VTGGSTGLGETIAEELFKRGARVVIAARHEEQAR--VVSDGL-DP---TGKRVYVCKTDVRDPRSVKNLIDT 75
                                      99999999***************88776666533..333332.45...4679*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 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:                        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: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1339.87
//
Query:       gi|330506751|ref|YP_004383179.1|  [L=73]
Description: hypothetical protein MCON_0518 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.094   12.7   0.0       0.12   12.3   0.0    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.6e-06      0.12      51      67 ..      22      39 ..       2      40 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.6e-06
                    OrfB_Zn_ribbon 51 n.CgfeadrDvnAaiNil 67
                                      + C  + d+D+n+a Ni+
  gi|330506751|ref|YP_004383179.1| 22 AgCRWSGDADFNGAKNIA 39
                                      4599*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       163  (0.00909142); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 533.78
//
Query:       gi|330506752|ref|YP_004383180.1|  [L=172]
Description: hypothetical protein MCON_0519 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1248.92
//
Query:       gi|330506753|ref|YP_004383181.1|  [L=80]
Description: hypothetical protein MCON_0520 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       736  (0.0410508); 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:                         0  (0); expected 0.2 (1e-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: 608.86
//
Query:       gi|330506754|ref|YP_004383182.1|  [L=327]
Description: peptide methionine sulfoxide reductase MsrB/MsrA [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-65  218.9   0.5    5.2e-65  218.3   0.5    1.3  1  PMSR      Peptide methionine sulfoxide reductase
    3.8e-48  162.5   0.0    6.7e-48  161.8   0.0    1.4  1  SelR      SelR domain
  ------ inclusion threshold ------
      0.094   12.6   0.0        2.9    7.8   0.0    2.9  3  Vsr       DNA mismatch endonuclease Vsr


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 !  218.3   0.5   8.7e-69   5.2e-65       2     151 ..     171     320 ..     170     322 .. 0.98

  Alignments for each domain:
  == domain 1  score: 218.3 bits;  conditional E-value: 8.7e-69
                                       EEEE-S-HHHHHHHHCTSTTEEEEEEEEESSS-SS--HHHHHTTTT--EEEEEEEEETTTS-HHHHHHHHHHTS-TT CS
                              PMSR   2 avlagGCFWgveklfeklkGvlstevGYagGktenptYeevcsgktghaEavevvydpekvsleellelffeihDpt 78 
                                       a++a+GCFWgve+ f++++Gvl+t+vGY+gG++++p+Y +vc+g+tghaEav+++ydp++vs++ell++f+++hDpt
  gi|330506754|ref|YP_004383182.1| 171 ATFAAGCFWGVEARFQQVRGVLETKVGYTGGTAPDPSYAQVCTGTTGHAEAVQIKYDPKVVSYRELLSIFWRMHDPT 247
                                       79*************************************************************************** PP

                                       -SSEETTEESGGG--EEEESSCCHHHHHHHHHHHHHTTHTTSSS---EEEEG-SEEE--CCCTTHHHH-TTS- CS
                              PMSR  79 qlnrqgnDvGtqYrsaiyytneeqkevaeevleelqkkkalkkkivteieplkefykaeeyHqqYleknpegy 151
                                       + nrqg D+GtqYrsai+y+neeq+ +aee++ee++++ a+ +k vt+i p++ef++aeeyHq+Y++k+ +  
  gi|330506754|ref|YP_004383182.1| 248 TPNRQGPDIGTQYRSAIFYHNEEQRIAAEESREEYDRSGAIARKAVTQIVPASEFFEAEEYHQDYFAKQGSVP 320
                                       ********************************************************************98765 PP

>> SelR  SelR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.8   0.0   1.1e-51   6.7e-48       2     121 .]      14     132 ..      13     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 161.8 bits;  conditional E-value: 1.1e-51
                                       HHCTSHCCHHHHHHHTT-SSTTSSSTSS--SSCEEEETTTS-EEEECCCCE-STTSSSEESS-STTTTEEEEEEECT CS
                              SelR   2 lkkkLtpeqyevlrekgterpftgeyekekekGvyecavcgepLfssetkfdsgcGwpsFaeaikeeavkekkdtsl 78 
                                        kkkLtp q++v+++ gte+pf++e++++k+ G+y+++ +gepLfss++kfdsg+GwpsF++++ke+++ e+ dts+
  gi|330506754|ref|YP_004383182.1|  14 SKKKLTPLQFHVTQQCGTEPPFQNEFWNNKRPGIYVDVLSGEPLFSSKDKFDSGTGWPSFTKPLKEDRIIENVDTSY 90 
                                       589************************************************************************** PP

                                       TSEEEEEEETTCECEEEEEECTSSSSS.SEEEEE-CCCEEEEE CS
                              SelR  79 gmertevvcakcdahlGhvFedgpkpttgkrycinsvslkfkp 121
                                       +m+r+ev+++++d+hlGhvF+dgp pt g+rycins+sl+f p
  gi|330506754|ref|YP_004383182.1|  91 NMRRVEVRSKDADSHLGHVFDDGPGPT-GLRYCINSASLRFIP 132
                                       *************************95.*************86 PP

>> Vsr  DNA mismatch endonuclease Vsr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.19   1.1e+03      34      45 ..     117     128 ..      82     135 .. 0.62
   2 ?    7.8   0.0   0.00048       2.9      50      67 ..     165     179 ..     150     184 .. 0.82
   3 ?   -0.0   0.0      0.14   8.2e+02      39      63 ..     242     267 ..     234     269 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.19
                                       TT--EEES-TTS CS
                               Vsr  34 lGlryRkndksl 45 
                                        Glry +n++sl
  gi|330506754|ref|YP_004383182.1| 117 TGLRYCINSASL 128
                                       688998888887 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00048
                                       SEEEGGGTEEEEEE-TTT CS
                               Vsr  50 DvvlkkykvvvFvhGcFW 67 
                                       D   ++y ++ F  GcFW
  gi|330506754|ref|YP_004383182.1| 165 D---PDYELATFAAGCFW 179
                                       4...79************ PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.14
                                       EES-TTSTT-..-SEEEGGGTEEEEEE CS
                               Vsr  39 RkndkslaGk..PDvvlkkykvvvFvh 63 
                                       R++d   + +  PD+   +y+ ++F h
  gi|330506754|ref|YP_004383182.1| 242 RMHDPTTPNRqgPDIG-TQYRSAIFYH 267
                                       5555555554448876.4799999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2262.41
//
Query:       gi|330506755|ref|YP_004383183.1|  [L=76]
Description: hypothetical protein MCON_0525 [Methanosaeta concilii GP6]
Scores for complete 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   36.2  12.9    5.2e-09   36.2  12.9    1.6  2  DUF1328        Protein of unknown function (DUF1328)
  ------ inclusion threshold ------
      0.016   14.2   1.6      0.018   14.0   1.6    1.0  1  CSG2           Ceramide synthase regulator
       0.75    9.6   4.8       0.81    9.5   4.8    1.0  1  FA_desaturase  Fatty acid desaturase
        1.3    8.2   9.2        1.2    8.3   9.2    1.1  1  CitMHS         Citrate transporter


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 !   36.2  12.9   1.2e-12   5.2e-09       1      38 [.      22      58 ..      22      59 .. 0.97
   2 ?   -2.4   0.0       1.3   5.7e+03      20      29 ..      64      73 ..      60      75 .. 0.60

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.2e-12
                           DUF1328  1 liFLviAliAgvLGFgGiagaaagiAkiLFfiFlvlfv 38
                                      ++F+ iAli gvLG++G ag +++iAk+L++ F++l++
  gi|330506755|ref|YP_004383183.1| 22 VVFFAIALILGVLGWRG-AGISMDIAKWLVIAFIILAI 58
                                      79***************.*******************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                           DUF1328 20 gaaagiAkiL 29
                                      g++++ A +L
  gi|330506755|ref|YP_004383183.1| 64 GGSINLATLL 73
                                      5566666555 PP

>> CSG2  Ceramide synthase regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.6   3.9e-06     0.018     339     393 ..       9      63 ..       2      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.9e-06
                              CSG2 339 lelnrkaspeylttvnlgiiifmgladwiceptqttivrWeviGYimlsvscivL 393
                                       + +++ +   yl+ v+++i +++g+  w     +  i +W vi +i+l++ ++v 
  gi|330506755|ref|YP_004383183.1|   9 MGVDKMVDLLYLAVVFFAIALILGVLGWRGAGISMDIAKWLVIAFIILAILSLVF 63 
                                       5577888889***************************************988765 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.8   0.00018      0.81     137     180 ..      18      63 ..       3      72 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00018
                     FA_desaturase 137 llawlllllawlglwlalllllglall....lwlvplllllfllalvl 180
                                       l++++++++  ++l+l++l++ g + +     wlv ++++l++l+lv+
  gi|330506755|ref|YP_004383183.1|  18 LYLAVVFFA--IALILGVLGWRGAGISmdiaKWLVIAFIILAILSLVF 63 
                                       334444444..788888888888888899999***********99997 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   9.2   0.00027       1.2     214     266 ..      21      64 ..       2      76 .] 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00027
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 214 svlllfaGvfllvgaleqtGilealadllgaggplvalalvlgliallsafis 266
                                        v++++++++l+v + ++ Gi+  +a++l      v   ++++++a+ls++++
  gi|330506755|ref|YP_004383183.1|  21 AVVFFAIALILGVLGWRGAGISMDIAKWL------V---IAFIILAILSLVFG 64 
                                       5899*************************......5...44666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1120  (0.0624686); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 559.61
//
Query:       gi|330506756|ref|YP_004383184.1|  [L=90]
Description: hypothetical protein MCON_0526 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00058   18.8   2.6     0.0006   18.8   2.6    1.0  1  DUF2079   Predicted membrane protein (DUF2079)


Domain annotation for each model (and alignments):
>> DUF2079  Predicted membrane protein (DUF2079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.6   3.3e-08    0.0006      82     153 ..       2      76 ..       1      87 [. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.3e-08
                           DUF2079  82 arer.lls.rrlalliallYllspvvinptl.fdFhpevlaiPllllalllalrrrkwllllvlilllllvredl 153
                                       ar+  l++  + +l+ ++  ll+ ++++ +l    hp+v ++Pl++ ++++++r ++++ +   + ++ lv  ++
  gi|330506756|ref|YP_004383184.1|   2 ARDMrLNNqAKVGLATVVCLLLQGYIFTYVLfVEPHPLVSILPLFPYLAYVYARGKRTWYFNKPLYWIGLVAMVT 76 
                                       66664444467788888899***********99*****************9********9987777776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 656.70
//
Query:       gi|330506757|ref|YP_004383185.1|  [L=645]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   54.8  49.1     0.0028   17.9   0.4   10.6 12  TPR_12       Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.026   14.4  41.2       0.61   10.0   1.2   11.9 14  TPR_10       Tetratricopeptide repeat
       0.14   11.5  18.7          1    8.8   0.6    5.3  5  HBM          Helical bimodular sensor domain
       0.17   11.8   0.4        2.1    8.3   0.1    2.5  2  Orexin       Prepro-orexin
        0.2   11.2   5.2       0.22   11.1   0.2    3.2  3  Arfaptin     Arfaptin-like domain
       0.86   10.6  41.0        2.3    9.3   0.3   10.6 12  TPR_14       Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.94   2.8e+03      18      28 ..       8      18 ..       3      23 .. 0.62
   2 !   10.2   0.4   0.00024      0.71      19      59 ..      53      91 ..      48      93 .. 0.83
   3 !    6.8   0.1    0.0028       8.4      19      61 ..     100     140 ..      93     161 .. 0.76
   4 ?   -0.7   0.0      0.58   1.7e+03      22      57 ..     150     183 ..     145     190 .. 0.59
   5 ?    2.1   0.0     0.081   2.4e+02      61      75 ..     198     212 ..     192     237 .. 0.63
   6 !   10.8   1.9   0.00016      0.48       3      36 ..     272     305 ..     246     310 .. 0.72
   7 !    9.8   2.4   0.00031      0.93       3      37 ..     272     306 ..     270     329 .. 0.92
   8 !    6.1   0.1    0.0046        14       5      41 ..     328     364 ..     319     370 .. 0.82
   9 !   15.3   1.9   6.1e-06     0.018       7      65 ..     377     432 ..     373     437 .. 0.90
  10 ?   -1.1   0.0      0.78   2.3e+03      14      36 ..     434     456 ..     430     469 .. 0.60
  11 !   17.9   0.4   9.3e-07    0.0028       5      48 ..     472     515 ..     467     518 .. 0.91
  12 !   12.7   0.9     4e-05      0.12       8      77 .]     521     588 ..     516     588 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.94
                            TPR_12 18 rydeAlellek 28
                                      +y++Al+ +e+
  gi|330506757|ref|YP_004383185.1|  8 EYEKALKTCER 18
                                      45556555554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00024
                            TPR_12 19 ydeAlellekaleiarrllGpdhpltattlrnLgrlyralg 59
                                      ++ A + ++++l+++++   p+h   a+++  Lg +y a+ 
  gi|330506757|ref|YP_004383185.1| 53 CEHAVQAYQRSLAVYTQENYPHH--RARVMKSLGYAYAARS 91
                                      567999*********77756999..***********98765 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0028
                            TPR_12  19 ydeAlellekaleiarrl.lGpdhpltattlrnLgrlyralgry 61 
                                       + +A+ + e++l++++rl + +d   +a+ +  L+ +yr+l ++
  gi|330506757|ref|YP_004383185.1| 100 LKQAINFWEESLAVYSRLsYPGD---YAILQDELSVAYRKLAEL 140
                                       789************99934444...799999999999887665 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.58
                            TPR_12  22 AlellekaleiarrllGpdhplt.attlrnLgrlyra 57 
                                       A++  + al i+ +l  +dhp++ a+   nLg +y+ 
  gi|330506757|ref|YP_004383185.1| 150 AIDAAKNALSIY-SL--KDHPQEfARGKTNLGSAYLT 183
                                       777777777777.45..66765424444555555555 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.081
                            TPR_12  61 yeeAlelleealaia 75 
                                        ++A++ +++al+++
  gi|330506757|ref|YP_004383185.1| 198 CKQAIASYQDALQVY 212
                                       445555555555544 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.00016
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrl 36 
                                       a+++nnl+++ ++l + +e+le+++ ale++r++
  gi|330506757|ref|YP_004383185.1| 272 AASQNNLGNAFLALAEEEESLENCQLALEAFRNA 305
                                       5567777777777777777777777777777665 PP

  == domain 7  score: 9.8 bits;  conditional E-value: 0.00031
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrll 37 
                                       a+++nnl+++ ++l + +e+le+++ ale++r++l
  gi|330506757|ref|YP_004383185.1| 272 AASQNNLGNAFLALAEEEESLENCQLALEAFRNAL 306
                                       788999***********************998875 PP

  == domain 8  score: 6.1 bits;  conditional E-value: 0.0046
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdh 41 
                                       a+  la++ + ++++ +A+   +kalei++r  +p+ 
  gi|330506757|ref|YP_004383185.1| 328 AHLALAQIQNPAENFLKAIGAARKALEIFNRDSNPEE 364
                                       5667999999999999999999999999988777665 PP

  == domain 9  score: 15.3 bits;  conditional E-value: 6.1e-06
                            TPR_12   7 nnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAl 65 
                                         la++++r++++  Ale +++ l+++++   ++++++a+++ +L+++y+ l ++e  +
  gi|330506757|ref|YP_004383185.1| 377 LTLADIEYRAENCLLALEACQERLAAFSQ---DKSLQYASCQKDLAITYSILADTEVSV 432
                                       479************************54...789***************999998765 PP

  == domain 10  score: -1.1 bits;  conditional E-value: 0.78
                            TPR_12  14 rrlgrydeAlellekaleiarrl 36 
                                       ++++++ +  e   +al i++++
  gi|330506757|ref|YP_004383185.1| 434 AKAEDCRKGAEAALEALSIYNES 456
                                       55666666666667777777333 PP

  == domain 11  score: 17.9 bits;  conditional E-value: 9.3e-07
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattl 48 
                                       a++ la+v+ + +++ +A++ +++a++i+++++ ++h++++ +l
  gi|330506757|ref|YP_004383185.1| 472 AYSALAEVEEKEENCRKAIDACQAAVRIYEASHPTEHADALKSL 515
                                       6779*********************************8888776 PP

  == domain 12  score: 12.7 bits;  conditional E-value: 4e-05
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                        la+v  +++++  A+e + ++le +++   p     a++lr+L+ +y    + e+ +e+ ++al++++k
  gi|330506757|ref|YP_004383185.1| 521 TLAEVTDKAENCRRAIEACSASLEHYQKDEAPRE--HAEILRDLAFAYVTISEVEDREEWVKRALRAYKK 588
                                       589999999******************9988865..9******************************986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.12   3.6e+02      24      36 ..       8      20 ..       3      20 .. 0.80
   2 ?    2.8   0.0     0.038   1.1e+02      11      36 ..      39      64 ..      35      75 .. 0.73
   3 ?   -0.3   0.0      0.37   1.1e+03       7      36 ..      82     111 ..      76     113 .. 0.62
   4 ?    0.8   0.0      0.16   4.9e+02      19      35 ..     101     117 ..      99     118 .. 0.82
   5 ?   -0.2   0.0      0.35     1e+03       5      41 ..     127     167 ..     124     168 .. 0.84
   6 ?   -2.4   0.0       1.7   5.1e+03       6      16 ..     175     185 ..     174     189 .. 0.76
   7 ?   -0.9   0.0      0.55   1.6e+03      26      37 ..     199     210 ..     190     215 .. 0.69
   8 ?    2.8   0.3     0.039   1.2e+02       5      19 ..     225     240 ..     222     262 .. 0.68
   9 ?   10.0   1.2    0.0002      0.61       2      37 ..     272     307 ..     272     315 .. 0.87
  10 ?    3.1   0.2     0.032        95       2      37 ..     319     354 ..     319     363 .. 0.85
  11 ?    0.3   0.0      0.23     7e+02       2      37 ..     412     448 ..     412     460 .. 0.61
  12 ?    6.0   0.4    0.0039        12      11      36 ..     472     497 ..     471     510 .. 0.79
  13 ?   -2.0   0.1       1.2   3.7e+03      19      37 ..     527     544 ..     526     547 .. 0.79
  14 ?    5.1   0.1    0.0072        22       2      35 ..     556     589 ..     555     589 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                            TPR_10 24 lleealairrrll 36
                                       +e+al +++r l
  gi|330506757|ref|YP_004383185.1|  8 EYEKALKTCERML 20
                                      46********976 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.038
                            TPR_10 11 alrqrgrydeAealleealairrrll 36
                                      ++ + ++ +  ++ +e+a+++++r l
  gi|330506757|ref|YP_004383185.1| 39 IYLEIFKKNNDLQSCEHAVQAYQRSL 64
                                      56666677777777888888888866 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.37
                            TPR_10   7 NLanalrqrgrydeAealleealairrrll 36 
                                        L+ a+ +r +  +  + l++a++ +++ l
  gi|330506757|ref|YP_004383185.1|  82 SLGYAYAARSDIFDQGESLKQAINFWEESL 111
                                       567777666655555555677888777765 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.16
                            TPR_10  19 deAealleealairrrl 35 
                                       ++A ++ ee+la++ rl
  gi|330506757|ref|YP_004383185.1| 101 KQAINFWEESLAVYSRL 117
                                       57999999999999775 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.35
                            TPR_10   5 lnNLanalrqrgrydeAealleealairrrllG....pdHP 41 
                                       +  L++a+r++ ++ + ++  + a+++ + +l      dHP
  gi|330506757|ref|YP_004383185.1| 127 QDELSVAYRKLAELGDGVNNSKMAIDAAKNALSiyslKDHP 167
                                       57899999999999999998889999999999888888888 PP

  == domain 6  score: -2.4 bits;  conditional E-value: 1.7
                            TPR_10   6 nNLanalrqrg 16 
                                       +NL+ a+  + 
  gi|330506757|ref|YP_004383185.1| 175 TNLGSAYLTLA 185
                                       69****97765 PP

  == domain 7  score: -0.9 bits;  conditional E-value: 0.55
                            TPR_10  26 eealairrrllG 37 
                                       ++a+a ++ +l 
  gi|330506757|ref|YP_004383185.1| 199 KQAIASYQDALQ 210
                                       567777776664 PP

  == domain 8  score: 2.8 bits;  conditional E-value: 0.039
                            TPR_10   5 lnNLanal.rqrgryd 19 
                                        nNLa+a+ +  g +d
  gi|330506757|ref|YP_004383185.1| 225 KNNLAIAYlSLAGAGD 240
                                       69******55555554 PP

  == domain 9  score: 10.0 bits;  conditional E-value: 0.0002
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllG 37 
                                       A+s+nNL+na  ++ + +e+++ ++ al++ r +l 
  gi|330506757|ref|YP_004383185.1| 272 AASQNNLGNAFLALAEEEESLENCQLALEAFRNALD 307
                                       89***************************9998886 PP

  == domain 10  score: 3.1 bits;  conditional E-value: 0.032
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllG 37 
                                       A+++n ++na+ ++ + +   + + +a+ + r++l+
  gi|330506757|ref|YP_004383185.1| 319 AATQNCIGNAHLALAQIQNPAENFLKAIGAARKALE 354
                                       899*********999999988888999999999997 PP

  == domain 11  score: 0.3 bits;  conditional E-value: 0.23
                            TPR_10   2 AsslnNLanalrqrgrydeAeal.leealairrrllG 37 
                                       As++ +La++++ + + + +++  +e++    +++l+
  gi|330506757|ref|YP_004383185.1| 412 ASCQKDLAITYSILADTEVSVEAkAEDCRKGAEAALE 448
                                       6777788888877666666665555555555555554 PP

  == domain 12  score: 6.0 bits;  conditional E-value: 0.0039
                            TPR_10  11 alrqrgrydeAealleealairrrll 36 
                                       a++++ + +e e+ +++a++++++++
  gi|330506757|ref|YP_004383185.1| 472 AYSALAEVEEKEENCRKAIDACQAAV 497
                                       78888888999999999998888875 PP

  == domain 13  score: -2.0 bits;  conditional E-value: 1.2
                            TPR_10  19 deAealleealairrrllG 37 
                                       d+Ae+  ++a++++ + l+
  gi|330506757|ref|YP_004383185.1| 527 DKAENC-RRAIEACSASLE 544
                                       678888.****99877665 PP

  == domain 14  score: 5.1 bits;  conditional E-value: 0.0072
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrl 35 
                                       A +l +La a+    + ++ e++ ++al++++++
  gi|330506757|ref|YP_004383185.1| 556 AEILRDLAFAYVTISEVEDREEWVKRALRAYKKA 589
                                       678999*************************986 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.4     0.024        73     191     215 ..      47      71 ..      44      96 .. 0.81
   2 ?    5.9   0.6    0.0025       7.4     183     212 ..     184     213 ..      80     217 .. 0.74
   3 ?    2.1   0.1     0.035     1e+02     175     215 ..     274     313 ..     233     323 .. 0.81
   4 ?    1.1   0.0     0.071   2.1e+02     159     198 ..     477     516 ..     470     521 .. 0.88
   5 ?    8.8   0.6   0.00034         1     130     224 ..     540     638 ..     520     642 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                               HBM 191 raalqqlesalskYRaaleqfkaav 215
                                       +++lq  e a+++Y ++l  + ++ 
  gi|330506757|ref|YP_004383185.1|  47 NNDLQSCEHAVQAYQRSLAVYTQEN 71 
                                       679999************9998865 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0025
                                       HHH-GG.GHHHHHHHHHHHHHHHHHHHHHH CS
                               HBM 183 rqalasdpraalqqlesalskYRaaleqfk 212
                                        +++a++p+++++  ++a+++Y +al+ + 
  gi|330506757|ref|YP_004383185.1| 184 LAQFADEPEDRMDSCKQAIASYQDALQVYD 213
                                       467999*********************996 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.035
                                       HHHHHHHHHHH-GG.GHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               HBM 175 alaeldqlrqalasdpraalqqlesalskYRaaleqfkaav 215
                                       ++++l++   ala+ +++ l++ + al+++R+al+ +++++
  gi|330506757|ref|YP_004383185.1| 274 SQNNLGNAFLALAE-EEESLENCQLALEAFRNALDLYPREQ 313
                                       45555555556665.67789999999999999999998775 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.071
                                       S--HHHHHHHHHHHHHHHHHHHHHHHH-GG.GHHHHHHHH CS
                               HBM 159 senedseqaavtaldaalaeldqlrqalasdpraalqqle 198
                                       +e e++e+   +a+da +a++   ++  + ++++al+ l+
  gi|330506757|ref|YP_004383185.1| 477 AEVEEKEENCRKAIDACQAAVRIYEASHPTEHADALKSLG 516
                                       5789999999*******************99999998775 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.00034
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH.HHS--HHHH...HHHHHHHHHHHHHHHHHHHH-GG.GHHHHHHHHHHHH CS
                               HBM 130 serlaqlqaiaelkrqvqlaryqvrgY.tfsenedse...qaavtaldaalaeldqlrqalasdpraalqqlesals 202
                                       s++l+ +q+ +  +++ +  r    +Y t+se ed e   + a++a  +a    + l+q+l+ + + + +++++ ++
  gi|330506757|ref|YP_004383185.1| 540 SASLEHYQKDEAPREHAEILRDLAFAYvTISEVEDREewvKRALRAYKKATRIFEGLAQELEAERDPEAAEMRNDVQ 616
                                       67777777777778888888888888834566677661114555555667777789999999*************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH CS
                               HBM 203 kYRaaleqfkaavaaieqarke 224
                                       + R+++++ k +++a+ + r e
  gi|330506757|ref|YP_004383185.1| 617 RCRRSMQSCKGILKASRKRRSE 638
                                       **************99998876 PP

>> Orexin  Prepro-orexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0007       2.1      23      50 ..     230     259 ..     222     267 .. 0.73
   2 ?    0.4   0.0      0.19   5.8e+02      20      66 ..     468     516 ..     462     520 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0007
                            Orexin  23 pallslg..vaaqslpdccrqktcscrlye 50 
                                        a lsl+  ++ +   +ccrq   scr   
  gi|330506757|ref|YP_004383185.1| 230 IAYLSLAgaGDERDKIECCRQSIQSCRDAL 259
                                       5666665115678889***********754 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.19
                            Orexin  20 llppallslgvaaqslpdccrqktcsc....rlyellhgaGnhaaGiltlG 66 
                                       ll  a  s  ++ +   + cr+   +c    r+ye  h + +ha  +  lG
  gi|330506757|ref|YP_004383185.1| 468 LLW-AAYSALAEVEEKEENCRKAIDACqaavRIYEASHPT-EHADALKSLG 516
                                       443.444555566666778887654443344999999975.7888887777 PP

>> Arfaptin  Arfaptin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   7.4e-05      0.22      26     125 ..      17     115 ..       9     118 .. 0.90
   2 ?   -0.6   0.0      0.27   8.1e+02      65      88 ..     270     293 ..     243     310 .. 0.72
   3 ?   -0.3   0.3      0.21   6.4e+02      62     106 ..     504     549 ..     474     627 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.4e-05
                                       ....CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..H-CCGHHHHHHHHHHHHH CS
                          Arfaptin  26 ervitvddeLeaklevlreiketykelvklaknlskallklsqtekelGdvfkdlskrekqealgeaftatgealrl 102
                                       er+ t + ++++  +++r+i + y+e+ k  ++l++    +   +++l+ + ++   +    ++ +++ ++  a + 
  gi|330506757|ref|YP_004383185.1|  17 ERMLTFEMDIAQESNIFRKIGDIYLEIFKKNNDLQSCEHAVQAYQRSLAVYTQENYPH-HRARVMKSLGYAYAARSD 92 
                                       679999999***************************************9888877775.55667999****9***** PP

                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                          Arfaptin 103 lakqgeallkalkrfiselntfv 125
                                       +  qge+l +a+++  ++l+++ 
  gi|330506757|ref|YP_004383185.1|  93 IFDQGESLKQAINFWEESLAVYS 115
                                       ********************996 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHHHHHH..H-CC CS
                          Arfaptin  65 klsqtekelGdvfkdlskrekqea 88 
                                         +  +++lG++f  l+++e + +
  gi|330506757|ref|YP_004383185.1| 270 AYAASQNNLGNAFLALAEEEESLE 293
                                       456789999999999999665543 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHHHHHH...H-CCGHHHHHHHHHHHHHHHHH CS
                          Arfaptin  62 allklsqtekelGdvfkdlsk.rekqealgeaftatgealrllakq 106
                                       + ++ + + k+lG +f  l++  +k e+  +a++a + +l   +k+
  gi|330506757|ref|YP_004383185.1| 504 HPTEHADALKSLGYSFITLAEvTDKAENCRRAIEACSASLEHYQKD 549
                                       4455666667788888777753577777777777777777666665 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.95   2.8e+03      16      28 ..       8      20 ..       3      27 .. 0.59
   2 ?   -0.8   0.0       1.3   3.8e+03      18      31 ..      54      67 ..      40      83 .. 0.76
   3 ?   -0.5   0.1       1.1   3.2e+03       3      29 ..      86     112 ..      77     140 .. 0.73
   4 ?   -2.2   0.0       3.7   1.1e+04      15      29 ..     145     159 ..     124     169 .. 0.59
   5 ?    2.8   0.1     0.092   2.7e+02      17      34 ..     198     220 ..     176     231 .. 0.60
   6 ?    7.9   0.7     0.002       6.1       2      35 ..     280     313 ..     279     321 .. 0.88
   7 ?    6.2   0.1    0.0076        23       2      33 ..     327     358 ..     326     365 .. 0.89
   8 ?    0.8   0.4      0.41   1.2e+03       4      38 ..     376     410 ..     373     415 .. 0.84
   9 ?   -1.9   0.1         3     9e+03      20      29 ..     443     451 ..     430     469 .. 0.48
  10 ?    9.3   0.3   0.00075       2.3       1      33 [.     470     502 ..     470     518 .. 0.86
  11 ?    1.3   0.3      0.27     8e+02       8      36 ..     523     551 ..     509     565 .. 0.70
  12 ?    3.6   0.3     0.051   1.5e+02       2      43 ..     557     598 ..     556     600 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.95
                            TPR_14 16 dpdeAiallrral 28
                                      ++++A++ ++r+l
  gi|330506757|ref|YP_004383185.1|  8 EYEKALKTCERML 20
                                      4555555555554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                            TPR_14 18 deAiallrralala 31
                                      + A+++++r la +
  gi|330506757|ref|YP_004383185.1| 54 EHAVQAYQRSLAVY 67
                                      45999999999955 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.1
                            TPR_14   3 allalaeallalGdpdeAiallrrala 29 
                                       a++a+ +++ + + +++Ai+  ++ la
  gi|330506757|ref|YP_004383185.1|  86 AYAARSDIFDQGESLKQAINFWEESLA 112
                                       456666666666777888888777776 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 3.7
                            TPR_14  15 GdpdeAiallrrala 29 
                                        + + Ai++++ al+
  gi|330506757|ref|YP_004383185.1| 145 NNSKMAIDAAKNALS 159
                                       344446666666666 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.092
                            TPR_14  17 pdeAiallrrala.....laPdd 34 
                                        ++Aia +++al+     ++Pd+
  gi|330506757|ref|YP_004383185.1| 198 CKQAIASYQDALQvydpgRFPDE 220
                                       3459*******996555556665 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.002
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPdda 35 
                                       +a lalae ++ l++ + A++++r al+l+P ++
  gi|330506757|ref|YP_004383185.1| 280 NAFLALAEEEESLENCQLALEAFRNALDLYPREQ 313
                                       5899**************************9764 PP

  == domain 7  score: 6.2 bits;  conditional E-value: 0.0076
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPd 33 
                                       +a+lala++   ++++ +Ai ++r+al+ +  
  gi|330506757|ref|YP_004383185.1| 327 NAHLALAQIQNPAENFLKAIGAARKALEIFNR 358
                                       5899***********************98765 PP

  == domain 8  score: 0.8 bits;  conditional E-value: 0.41
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       +l la++++++++   A+++++++la++ +d  ++
  gi|330506757|ref|YP_004383185.1| 376 YLTLADIEYRAENCLLALEACQERLAAFSQDKSLQ 410
                                       7889999999999999**********998887666 PP

  == domain 9  score: -1.9 bits;  conditional E-value: 3
                            TPR_14  20 Aiallrrala 29 
                                       A+a+l++ l+
  gi|330506757|ref|YP_004383185.1| 443 AEAALEA-LS 451
                                       3333333.23 PP

  == domain 10  score: 9.3 bits;  conditional E-value: 0.00075
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPd 33 
                                       ++a+ alae+++  ++ ++Ai+++++a++ + +
  gi|330506757|ref|YP_004383185.1| 470 WAAYSALAEVEEKEENCRKAIDACQAAVRIYEA 502
                                       68999***********************98754 PP

  == domain 11  score: 1.3 bits;  conditional E-value: 0.27
                            TPR_14   8 aeallalGdpdeAiallrralalaPddae 36 
                                       ae+   +++ ++Ai+++ + l+++ +d++
  gi|330506757|ref|YP_004383185.1| 523 AEVTDKAENCRRAIEACSASLEHYQKDEA 551
                                       44555566667899999999997766544 PP

  == domain 12  score: 3.6 bits;  conditional E-value: 0.051
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       e l++la a+ +  + ++ ++  +ral+++ +  ++   laq
  gi|330506757|ref|YP_004383185.1| 557 EILRDLAFAYVTISEVEDREEWVKRALRAYKKATRIFEGLAQ 598
                                       678899999999999999999999999999998888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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):               6  [number of targets reported over threshold]
# CPU time: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 4022.79
//
Query:       gi|330506758|ref|YP_004383186.1|  [L=167]
Description: hypothetical protein MCON_0528 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-08   33.7   0.1      8e-08   33.2   0.1    1.3  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola
  ------ inclusion threshold ------
      0.066   13.2   0.7       0.37   10.8   0.7    2.0  1  MetOD1         Metanogen output domain 1


Domain annotation for each model (and alignments):
>> ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.1   8.9e-12     8e-08      20     145 .]      32     165 ..      13     165 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 8.9e-12
                     ATC_hydrolase  20 igkeeakeiirkalerlgkergkklaekakakkdkadvekflalyseifekenalkfevlee.dkdeleidvtrCpy 95 
                                        g +ea e+ + +++ l k ++++++ ++      + ++++ a+ +   e     +f+++ + ++ ++ ++++rCp+
  gi|330506758|ref|YP_004383186.1|  32 RGFDEALELDEAVWQVLPKIQARAIKSMLMLDYGLDGLKEAIAA-RLALE-----EFDYELKeEESGFVVEIRRCPW 102
                                       45566666666555555566777776666655555555555554.33333.....355555557************* PP

                     ATC_hydrolase  96 ceawkkeGlp....elgkllC.eiDkavaeginpk........vklertktlaeGgdcCdfrf 145
                                       ++++++ G +    ++ +++C    +++a++++ k        +++er++ l +G   C+++f
  gi|330506758|ref|YP_004383186.1| 103 HDIMVRSGREslseKVSEVICqAENSVWAQEFSCKgvegegmeIRFERQERLCQGSNRCRLWF 165
                                       ******99765665888999*5555678888888888888999*****************998 PP

>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7   4.1e-05      0.37      81     149 ..      81     162 ..      73     167 .] 0.56

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.1e-05
                            MetOD1  81 nfgiktekkedeknvlleftnCpWg.......eea...rknPifCllcraivsrsftwt.....glkgsveqkktlg 142
                                       +f ++ +  e+e+ +++e+++CpW        +e+   + + ++C    ++  + f+       g+++++e++++l 
  gi|330506758|ref|YP_004383186.1|  81 EFDYELK--EEESGFVVEIRRCPWHdimvrsgRESlseKVSEVICQAENSVWAQEFSCKgvegeGMEIRFERQERLC 155
                                       4555555..89999**********72222111222111334455555555666655543111114455567777777 PP

                            MetOD1 143 ngdekCv 149
                                       +g+++C+
  gi|330506758|ref|YP_004383186.1| 156 QGSNRCR 162
                                       7777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1205.00
//
Query:       gi|330506759|ref|YP_004383187.1|  [L=140]
Description: hypothetical protein MCON_0529 [Methanosaeta concilii GP6]
Scores for complete 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   82.3   0.3    3.5e-23   81.4   0.3    1.5  1  Fer4_19   Divergent 4Fe-4S mono-cluster
    1.2e-17   63.9   0.4    2.3e-17   62.9   0.4    1.5  1  zf-CDGSH  Iron-binding zinc finger CDGSH type
  ------ inclusion threshold ------
      0.013   15.5   0.5       0.12   12.5   0.1    2.6  2  Fer4_6    4Fe-4S binding domain
      0.018   15.6   0.1      0.075   13.6   0.1    2.0  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.3   7.9e-27   3.5e-23       5      64 .]       8      67 ..       4      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 7.9e-27
                           Fer4_19  5 eitiednrelCihsgnCvkglpevFdpkrkpwikpdeasteeiievverCPSGALsyvek 64
                                       + + +n+e Cih+++Cv+glp+vF+ + +pwi+ ++as ++i++v++rCPSGALsy ek
  gi|330506759|ref|YP_004383187.1|  8 GLIVRWNPEKCIHAKECVNGLPQVFNHNSRPWINMQGASPAQIMKVIDRCPSGALSYQEK 67
                                      6789*****************************************************876 PP

>> zf-CDGSH  Iron-binding zinc finger CDGSH type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.4   5.1e-21   2.3e-17       1      47 [.      89     131 ..      89     132 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 5.1e-21
                          zf-CDGSH   1 nGPllVeGdvelvdadgesvelregrevvaLCrCgrSknkPfCDgsH 47 
                                       nGPllVeGd++l ++dg+++    g   +aLCrCg+S++kPfCDgsH
  gi|330506759|ref|YP_004383187.1|  89 NGPLLVEGDCRLFNSDGNEMAE--GA--FALCRCGASRKKPFCDGSH 131
                                       9*****************8763..33..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 ?   12.5   0.1   2.6e-05      0.12       1      16 [.      10      25 ..      10      26 .. 0.92
   2 ?   -0.4   0.0      0.33   1.5e+03      19      24 .]      57      62 ..      53      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                            Fer4_6  1 vveidpdkCigCgdCv 16
                                      +v+++p+kCi+  +Cv
  gi|330506759|ref|YP_004383187.1| 10 IVRWNPEKCIHAKECV 25
                                      699************8 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.33
                            Fer4_6 19 CPegai 24
                                      CP ga+
  gi|330506759|ref|YP_004383187.1| 57 CPSGAL 62
                                      999986 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 ?   13.6   0.1   1.7e-05     0.075       3      55 ..      15      61 ..      14      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                           Fer4_13  3 rdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPves 55
                                       ++Ci  + Cv+  P+vF  +       +  q  s+   a++++ +d CP  +
  gi|330506759|ref|YP_004383187.1| 15 PEKCIHAKECVNGLPQVFNHNSR---PWINMQGASP---AQIMKVIDRCPSGA 61
                                      689*****************986...4555555555...56888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1017.68
//
Query:       gi|330506760|ref|YP_004383188.1|  [L=145]
Description: large conductance mechanosensitive channel protein [Methanosaeta concilii GP6]
Scores for complete 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-39  133.0   2.3    7.7e-39  132.7   2.3    1.0  1  MscL             Large-conductance mechanosensitive channel, 
    1.6e-05   24.1   1.6    2.4e-05   23.6   1.6    1.3  1  zf-ribbon_3      zinc-ribbon domain
     0.0028   17.7   5.0     0.0047   17.0   5.0    1.3  1  UPF0547          Uncharacterised protein family UPF0547
  ------ inclusion threshold ------
      0.029   14.4   1.2      0.042   13.9   1.2    1.2  1  DZR              Double zinc ribbon
      0.057   13.6   0.0      0.083   13.1   0.0    1.3  1  UPF0239          Uncharacterised protein family (UPF0239)
       0.13   12.1   0.5       0.13   12.1   0.5    1.7  2  Gly-zipper_YMGG  YMGG-like Gly-zipper
        0.2   11.7   0.9        1.3    9.1   1.1    1.9  2  DUF2089          Protein of unknown function (DUF2089)


Domain annotation for each model (and alignments):
>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.7   2.3     3e-42   7.7e-39       2     114 ..       4     127 ..       3     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 3e-42
                              MscL   2 lkeFkefilrGnvidLAvgviiGaaftkiVtslvkdiimpliglllggvdfselkikl............kaeaavl 66 
                                       ++eFkef+++Gn +d+Avg+iiGaaf++iV+slv+diimp+ig+l+gg++f++++i+l            + +a ++
  gi|330506760|ref|YP_004383188.1|   4 ISEFKEFAVKGNAVDMAVGIIIGAAFGSIVNSLVNDIIMPPIGMLTGGINFADMFIALdgeayaslaeaqAVSAPTI 80 
                                       79*****************************************************************99977899** PP

                              MscL  67 kygafiqavinFliiafviFlivkainkkkkeeeeeeeaeekeeellt 114
                                       +yg fi+avi+F+i+af++F++v++in+ k++ +  + +++ke+ +++
  gi|330506760|ref|YP_004383188.1|  81 NYGLFINAVISFIIVAFAVFMLVRQINALKRQPAPLD-PTTKECPYCK 127
                                       ***************************9655544433.3334444443 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   1.6   9.2e-09   2.4e-05       2      22 ..     120     140 ..     119     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 9.2e-09
                       zf-ribbon_3   2 tvrCPnCGa.plssddnvCpyC 22 
                                       t++CP+C++ + + ++++C++C
  gi|330506760|ref|YP_004383188.1| 120 TKECPYCKEtI-AIGAIKCKHC 140
                                       799******55.********** PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   5.0   1.8e-06    0.0047       1      20 [.     121     140 ..     121     140 .. 0.99

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.8e-06
                           UPF0547   1 KvCPeCeakvPvaaqfCphC 20 
                                       K+CP C +++++ a +C hC
  gi|330506760|ref|YP_004383188.1| 121 KECPYCKETIAIGAIKCKHC 140
                                       99****************** PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.2   1.6e-05     0.042       1      23 [.     123     145 .]     112     145 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                               DZR   1 CpqCgeelppdarfCseCgtklk 23 
                                       Cp C+e +  +a+ C++C ++lk
  gi|330506760|ref|YP_004383188.1| 123 CPYCKETIAIGAIKCKHCTADLK 145
                                       88888888888888888888875 PP

>> UPF0239  Uncharacterised protein family (UPF0239)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.2e-05     0.083      20      48 ..      79     107 ..      65     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-05
                           UPF0239  20 llrYGLflGAifqlvCilAiillpsskse 48 
                                        + YGLf+ A+  ++ ++ ++++ + + +
  gi|330506760|ref|YP_004383188.1|  79 TINYGLFINAVISFIIVAFAVFMLVRQIN 107
                                       589**************999988766655 PP

>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5     5e-05      0.13       3      42 ..      11      52 ..      11      56 .. 0.81
   2 ?   -3.1   0.4       2.7   6.9e+03       8      11 ..     131     134 ..     130     135 .. 0.40

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5e-05
                                      ..XXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG  3 avrGAaiGAaaGAvvGaliG..sgggkGAaiGAaaGalaGga 42
                                      av+G a+  a+G ++Ga++G   +   + +i+  +G l+Gg+
  gi|330506760|ref|YP_004383188.1| 11 AVKGNAVDMAVGIIIGAAFGsiVNSLVNDIIMPPIGMLTGGI 52
                                      688888889999999999997766767888888888888885 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.7
                                       XXXX CS
                   Gly-zipper_YMGG   8 aiGA 11 
                                       aiGA
  gi|330506760|ref|YP_004383188.1| 131 AIGA 134
                                       3333 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.31     8e+02      39      67 ..      52      81 ..      46      91 .. 0.81
   2 ?    9.1   1.1    0.0005       1.3       1      21 [.     123     143 ..     123     145 .] 0.92

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.31
                           DUF2089 39 lefvelfikarGnl.kevekelgisYpTvr 67
                                      ++f  +fi   G+   +++++  +s pT+ 
  gi|330506760|ref|YP_004383188.1| 52 INFADMFIALDGEAyASLAEAQAVSAPTIN 81
                                      579999999999752678888889999886 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0005
                           DUF2089   1 CPvcgeelvvtrlkcescett 21 
                                       CP c+e++ +  +kc++c   
  gi|330506760|ref|YP_004383188.1| 123 CPYCKETIAIGAIKCKHCTAD 143
                                       ******************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1080  (0.0602376); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
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 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1052.70
//
Query:       gi|330506761|ref|YP_004383189.1|  [L=435]
Description: hypothetical protein MCON_0532 [Methanosaeta concilii GP6]
Scores for complete 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-47  160.5   5.9    4.4e-47  160.0   5.9    1.1  1  DUF21      Cyclin M transmembrane N-terminal domain
    1.2e-24   86.1   0.0    2.9e-24   84.9   0.0    1.7  1  CorC_HlyC  Transporter associated domain
    1.2e-08   35.3   0.2    5.3e-05   23.6   0.1    2.6  2  CBS        CBS domain


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.0   5.9   7.4e-51   4.4e-47       1     176 []       6     199 ..       6     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 160.0 bits;  conditional E-value: 7.4e-51
                             DUF21   1 liivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfve 77 
                                       lii++l+l+++ fs+aE+A+vs +++rl+++a++g+k+a+ +l+l++n +++Ls+++ g+tl  +l++a+++a++++
  gi|330506761|ref|YP_004383189.1|   6 LIILILILVNGAFSMAEMAVVSSRKARLRQMADSGDKGAAVALELISNSNQFLSAVQTGVTLMATLIGAFGGATLSD 82 
                                       6899**********************************************************************999 PP

                             DUF21  78 llae.............galavviatvivtllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwllskl 141
                                        la              +++a++++++ +t++ lv+gE++Pk++al ++e+ia+++a pl  +++++yPl+ llsk+
  gi|330506761|ref|YP_004383189.1|  83 ELAGyllglypalaqfsHGIALALVVLSITFVSLVIGELVPKRIALSNPERIASWSASPLNAFSKIVYPLILLLSKS 159
                                       99999************99********************************************************** PP

                             DUF21 142 lnlil.....esesepavseeelkklveeseeegvieeee 176
                                       ++++l     +s+ ep v+eee++ ++++++ +gvieeee
  gi|330506761|ref|YP_004383189.1| 160 TEFVLqalgvNSNAEPEVTEEEIRIMIDQGTMAGVIEEEE 199
                                       *************************************998 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.0   4.8e-28   2.9e-24       3      79 ..     350     428 ..     348     430 .. 0.93

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 4.8e-28
                                       ECTTEEEEETT-BHHHHHHHHTS.TTHHCT...-SBHHHHHHHHH-S---TT-EEEEEETTEEEEEEEEETTCEEEE CS
                         CorC_HlyC   3 ldegsylvdGslpldeleeelgl.elpeed...yeTlgGlllellgriPkegesvevdleglrftVlemdgrrIkkv 75 
                                       +++gs+lvdG++p d+++e l++ +lp+ed   y+T+gG+++++l+++P+ g+  +++++g+rf+V++md+rr++k+
  gi|330506761|ref|YP_004383189.1| 350 RSDGSWLVDGTMPADDFKETLDIdKLPDEDdgtYQTMGGFMMTHLEKVPTSGD--KFEWGGYRFEVMDMDERRVDKL 424
                                       79*********************77***74478********************..88888***************** PP

                                       EEEE CS
                         CorC_HlyC  76 rvek 79 
                                        v++
  gi|330506761|ref|YP_004383189.1| 425 LVTP 428
                                       **97 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00026       1.6       1      53 [.     214     269 ..     214     273 .. 0.85
   2 !   23.6   0.1   8.9e-09   5.3e-05       8      55 ..     285     332 ..     275     334 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00026
                                       HHHHSBS..SCEEEETTSBHHHHHHH.HHHHT.SSEEEEE.ETTTBEEEEEEHHHHHH CS
                               CBS   1 Vgdimtr..dvvtvppdttleealel.mrekg.vsrlPVV.dedgklvGivtlrDllr 53 
                                       V +imt+  ++v ++  +tl+e+ ++    +g ++ +PV   + ++++G++  +D+l+
  gi|330506761|ref|YP_004383189.1| 214 VNSIMTPrgKIVWLDIHDTLAEIQRKtV--SGpYTMFPVCsKKLDNVLGVIQSKDILN 269
                                       5679999999****************66..677*999**9644447**********97 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 8.9e-09
                                       SCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHH CS
                               CBS   8 dvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllral 55 
                                       ++++vp+++   ++le+++++g+ +l +V de+g + Giv l Dll+ l
  gi|330506761|ref|YP_004383189.1| 285 PPLFVPESMRALKVLEKFKQTGI-HLAIVlDEYGTVQGIVALVDLLEGL 332
                                       788***************99999.665555****999*********876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3292.04
//
Query:       gi|330506762|ref|YP_004383190.1|  [L=220]
Description: ExsB protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-69  232.6   0.0    3.6e-69  232.5   0.0    1.0  1  QueC           Queuosine biosynthesis protein QueC
     0.0002   21.2   0.0    0.00048   19.9   0.0    1.6  1  ATP_bind_3     PP-loop family
      0.003   17.2   0.0       0.01   15.4   0.0    2.1  2  ThiI           Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.018   14.7   0.0      0.024   14.3   0.0    1.2  1  Asn_synthase   Asparagine synthase
      0.041   13.0   0.0      0.054   12.6   0.0    1.2  1  NAD_synthase   NAD synthase
      0.076   11.8   0.0       0.13   11.1   0.0    1.3  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 !  232.5   0.0   1.2e-72   3.6e-69       1     207 [.       2     206 ..       2     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: 232.5 bits;  conditional E-value: 1.2e-72
                                       EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG----- CS
                              QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeei 77 
                                       kav++lSGGlDStt+l+  +++g+ v altf+Ygq+hkke+++a +i+++l+v  h+i+dl++l+++ g++ + +++
  gi|330506762|ref|YP_004383190.1|   2 KAVLILSGGLDSTTLLYKLLADGYLVDALTFNYGQKHKKEIDCAIAITSRLDV-PHQIIDLSTLAAFLGESALLGKK 77 
                                       79***************************************************.***********987666666667 PP

                                       ------...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH.HTS--E CS
                              QueC  78 evpkeeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg.edkkie 153
                                       evp+ +++ee +++t Vp+RN+i+ls+aa+yaea ++++++++++++d + YPDcr+efv+al+ a++lg  ++++e
  gi|330506762|ref|YP_004383190.1|  78 EVPSCHYTEEAARQTVVPNRNMIMLSVAAGYAEAHEITELFYAAHKNDQTIYPDCRPEFVEALKPAIRLGtAWNPVE 154
                                       8*********************************************************************8889*** PP

                                       EE-TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHH CS
                              QueC 154 ieaPlidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRkkgfe 207
                                       ++aP+++++Ka+iv++g +l+vp+e+t+sCY+g  ++ +C++C++C+ R+++f+
  gi|330506762|ref|YP_004383190.1| 155 LQAPFVHMTKADIVRMGLKLQVPYELTWSCYKG--KAMPCRTCPTCIEREEAFA 206
                                       *********************************..556**************97 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.6e-07   0.00048       3     155 ..       4     170 ..       2     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.6e-07
                                       EEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H........... CS
                        ATP_bind_3   3 lvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv........... 68 
                                       ++ +SgGlDS++Ll+ l       g  + a+++++g +   k+e +   ++ ++l+++++i ++++           
  gi|330506762|ref|YP_004383190.1|   4 VLILSGGLDSTTLLYKLLAD----GYLVDALTFNYGQK--HKKEIDCAIAITSRLDVPHQIIDLSTlaaflgesall 74 
                                       6679***********99998....45899999999965..5667778888999999999999998889999999999 PP

                                       ...HHCTTSTCCCHHHHH....HHHHH....HHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHH.H-S-SEE CS
                        ATP_bind_3  69 ...akkkgknleeaARel....RYevl....kealkkegievlllAhhadDqaEtfllrlargsglagl.agikeas 133
                                          +  + + +eeaAR+     R  ++    + ++++++i+ l  A h++Dq+   ++   r + +++l  +i+  +
  gi|330506762|ref|YP_004383190.1|  75 gkkEVPSCHYTEEAARQTvvpnRNMIMlsvaAGYAEAHEITELFYAAHKNDQT---IYPDCRPEFVEALkPAIRLGT 148
                                       8766667899999***96455465555111134567899999*********95...334444444433314566666 PP

                                       EETTCCEE-CCCT--HHHHHHH CS
                        ATP_bind_3 134 eiasirlvRPlLkvskeeleey 155
                                         + ++l  P+++++k+++ ++
  gi|330506762|ref|YP_004383190.1| 149 AWNPVELQAPFVHMTKADIVRM 170
                                       6666777777777777777665 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.4e-06      0.01       5      46 ..       2      42 ..       1     117 [. 0.81
   2 ?   -1.9   0.0      0.71   2.1e+03     142     159 ..     157     174 ..     148     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.4e-06
                              ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeai 46
                                      k++++lSgG+DS    y ll  G  v++++++ +  + +++i
  gi|330506762|ref|YP_004383190.1|  2 KAVLILSGGLDSTTLLYKLLADGYLVDALTFN-YGQKHKKEI 42
                                      6899***************************5.444444444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.71
                              ThiI 142 rPLigldKeeiiklAkei 159
                                        P + + K +i+++  ++
  gi|330506762|ref|YP_004383190.1| 157 APFVHMTKADIVRMGLKL 174
                                       699999999999987655 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.2e-06     0.024      22      80 ..       5      62 ..       2      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.2e-06
                      Asn_synthase 22 alLSGGlDSSliaa..laarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlt 80
                                      + LSGGlDS+++ +  la+ ++  ++ tF  g   k+ +e++ a ++  +l ++h+ + l+
  gi|330506762|ref|YP_004383190.1|  5 LILSGGLDSTTLLYklLADGYLV-DALTFNYGQ--KHKKEIDCAIAITSRLDVPHQIIDLS 62
                                      57********9987323444443.555666665..*******************9877665 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.8e-05     0.054      20      89 ..       2      69 ..       1     107 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                                      EEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHH CS
                      NAD_synthase 20 gvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpivrafe 89
                                      ++vl lSGG+DS++   l + + +   v al +   +++++++  a+a+  +l++  + id++   + + 
  gi|330506762|ref|YP_004383190.1|  2 KAVLILSGGLDSTTL--LYKLLADGYLVDALTFNYGQKHKKEIDCAIAITSRLDVPHQIIDLSTLAAFLG 69
                                      68999*******974..334444445599999*999*************************988766554 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.2e-05      0.13       2      70 ..       2      61 ..       1      64 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.2e-05
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdf 70
                                      k v  lSgG DS+  ++ l   gy v +++++  +++++         ++  a ++ ++l++p++++d+
  gi|330506762|ref|YP_004383190.1|  2 KAVLILSGGLDSTTLLYKLLADGYLVDALTFNYGQKHKK---------EIDCAIAITSRLDVPHQIIDL 61
                                      56788***********************99987776444.........444556777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1295.38
//
Query:       gi|330506763|ref|YP_004383191.1|  [L=100]
Description: hypothetical protein MCON_0534 [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.0    1.3e-11   44.4   0.0    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 !   44.4   0.0   7.1e-16   1.3e-11      11      68 ..      19      78 ..       8      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 7.1e-16
                                      HHHH.....TS---HHH..HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHH CS
                            DUF357 11 ekvkiapdeesplgeaa..eevlemaesYleDakyflekgdlvnAlasfsYaeGwLDaga 68
                                      e+vk +++ es  g+    e++le++ sYl+D+ +fl+++dl++A+ ++ +a++w++ g 
  gi|330506763|ref|YP_004383191.1| 19 ETVKWQEKAESLFGQLSgdERMLENISSYLSDSHHFLKQNDLIRAFEAVIWAWAWMEIGL 78
                                      456666677777777777899***********************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 616.16
//
Query:       gi|330506764|ref|YP_004383192.1|  [L=166]
Description: hypothetical protein MCON_0535 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1213.20
//
Query:       gi|330506765|ref|YP_004383193.1|  [L=471]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Methanosaeta concilii GP6]
Scores for complete 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-52  177.6   0.0      5e-52  177.0   0.0    1.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    3.4e-25   88.4   0.1    6.5e-25   87.5   0.1    1.5  1  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
    9.7e-17   61.3   0.1      3e-15   56.5   0.0    2.6  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    3.9e-10   39.4   0.1    5.8e-08   32.2   0.2    2.3  2  GIDA           Glucose inhibited division protein A
    1.1e-06   28.1   0.0    4.1e-06   26.3   0.0    1.9  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    2.3e-05   23.6   7.3    0.00016   20.9   2.3    2.8  2  FAD_binding_2  FAD binding domain
     0.0001   21.8   0.1    0.00017   21.1   0.1    1.4  1  FAD_oxidored   FAD dependent oxidoreductase
    0.00026   21.2   0.6       0.19   11.9   0.2    2.6  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.011   14.4   1.9       0.19   10.4   0.6    2.7  3  HI0933_like    HI0933-like protein
       0.02   14.5  11.5          2    7.9   1.3    3.5  4  DAO            FAD dependent oxidoreductase
      0.026   13.9   0.0        4.7    6.5   0.0    2.6  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      0.035   13.8   2.0       0.15   11.7   0.0    2.4  2  ApbA           Ketopantoate reductase PanE/ApbA
      0.053   13.4   0.2        1.4    8.8   0.0    2.5  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.11   12.8   1.0       0.39   11.1   0.0    2.3  3  UXS1_N         UDP-glucuronate decarboxylase N-terminal
        1.9    7.5   4.8         11    5.0   1.0    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 !  177.0   0.0   4.2e-55     5e-52       1     291 [.       7     321 ..       7     324 .. 0.87

  Alignments for each domain:
  == domain 1  score: 177.0 bits;  conditional E-value: 4.2e-55
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias................. 57 
                                       +d++viG+G+++l aa+ ++ ag +++lv+    +gtcln+gc++sk l + a+  + ++                 
  gi|330506765|ref|YP_004383193.1|   7 FDLIVIGSGAGALVAAQAAR-AGRNTALVDqgpMGGTCLNNGCIPSKMLIHPADMIRSIQeagavgvhariekidfp 82 
                                       589**********9987655.5*******999*************************999***********999999 PP

                                       .......HHHHCHHHHCCCCHCCT.CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEEC CS
                                       .......xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .......evvkklnqgielllgee.vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgkl 126
                                              +vv++ ++++e   ++   ++ +++++++ +e   +   +++++ + v+A+Gs++r ++i G++e +   
  gi|330506765|ref|YP_004383193.1|  83 rimnrvhKVVDEGRAQMEATIRSReNLTHYQKRAEFIDEYVLKAGSRTLTATQFVIASGSRSRVPPISGLEESG--- 156
                                       99999997777666665555553324444466678888777778899***********************5555... PP

                                       CSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 127 vrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklg 203
                                         ++d++  l+l + p++++++GgGyiG+E+  +++ +g evt++ + +rll + d+e+s++l+e + +   +v++g
  gi|330506765|ref|YP_004383193.1| 157 --YIDNVSLLNLREPPRSLIIIGGGYIGCEYGHFFSAMGTEVTILGRSPRLLCGEDPEISQRLHESFSR-YCRVVTG 230
                                       ..78************************************************99*************99.5****** PP

                                       CEEEEEEETTE....EEE.EEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE- CS
                                       xxxxxxxxxxx....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 204 tsvkeidgnge....kle.vvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyai 274
                                        +v  +++nge    +++ +++++ ++++ + v++a+G+r +++ll  e+ g+e+d++g+i vde+l+t+ +gi+a+
  gi|330506765|ref|YP_004383193.1| 231 YEVLSVERNGEkkvvSARgTKDGKIRQFEGEEVLLAAGRRSNSDLLRpERTGVEIDRQGWIRVDEYLQTSKKGIWAL 307
                                       **********97533222555555555************************************************** PP

                                       GGGCTECCSS--HHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 275 GDvaggkggpelaqaAv 291
                                       GD +   g+ +  ++A 
  gi|330506765|ref|YP_004383193.1| 308 GDAI---GKHMFRHTAN 321
                                       **99...6666666665 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 !   87.5   0.1   5.4e-28   6.5e-25       1     108 [.     348     456 ..     348     458 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 5.4e-28
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       +p +vf++p va vG+ e eAka g+++ vg+++++++++ +a+ae+ g+vK+v +++tg++lGa+i+Gp+a eliq
  gi|330506765|ref|YP_004383193.1| 348 VPYAVFSHPTVAGVGMKESEAKARGLKVLVGRARYTDSAKGVAMAEEYGLVKVVLEEETGRILGASIIGPEAPELIQ 424
                                       799************************************************************************** PP

                                       HHHHHHHTTS.BHHHHHTSBSSSSSTGGGGHC CS
                     Pyr_redox_dim  78 elavaikagl.tvedladtihihPtlsealke 108
                                       ++  +++ +    + +++   ihPt++e+l  
  gi|330506765|ref|YP_004383193.1| 425 QVVYLMNTDRqDLSTAMRSQVIHPTINEVLGR 456
                                       ******987725669************99865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.29   3.5e+02       2      20 ..       9      27 ..       8      39 .. 0.79
   2 !   56.5   0.0   2.5e-18     3e-15       2      74 ..     173     245 ..     172     253 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.29
                                      EEEECSSHHHHHHHHHHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalae 20
                                      ++v+G+G  +l +A+a+++
  gi|330506765|ref|YP_004383193.1|  9 LIVIGSGAGALVAAQAARA 27
                                      68*******9999988764 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 2.5e-18
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.ve 74 
                                       ++++GgGyig+E++ +++++g +Vt++ rs++ll ++D+e+s++l+e++++   +v+++ +v ++e ++++ v 
  gi|330506765|ref|YP_004383193.1| 173 LIIIGGGYIGCEYGHFFSAMGTEVTILGRSPRLLCGEDPEISQRLHESFSRY-CRVVTGYEVLSVERNGEKkVV 245
                                       79*************************************************9.*************99998554 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.2   4.8e-11   5.8e-08       1     154 [.       8     146 ..       8     162 .. 0.84
   2 ?    4.8   0.0      0.01        12       2      28 ..     173     199 ..     172     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 4.8e-11
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEEEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggiakgllvrEidalggliikaadkagiqfr 75 
                                       d+iViG G AG   A++aar+G +++L+   +  +t+++ +C ps   i  + + r i++  g ++  a   +i f 
  gi|330506765|ref|YP_004383193.1|   8 DLIVIGSG-AGALVAAQAARAGRNTALVdqGPMGGTCLNNGCIPSKMLIHPADMIRSIQEA-GAVGVHARIEKIDF- 81 
                                       689*****.9999999************888899**************************5.56666666777744. PP

                                       EESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-B CS
                              GIDA  76 ilNrskGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGtfl 152
                                              p +   r+    ++ ++++++++++ +nl+  ++++e ++        v+++  +t++a ++via+G+ +
  gi|330506765|ref|YP_004383193.1|  82 -------PRI-MNRVHKVVDEGRAQMEATIRSRENLTHYQKRAEFIDE------YVLKAGSRTLTATQFVIASGSRS 144
                                       .......223.33355557778899*********************66......99******************944 PP

                                       T- CS
                              GIDA 153 kg 154
                                       + 
  gi|330506765|ref|YP_004383193.1| 145 RV 146
                                       44 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.01
                                       EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLi 28 
                                       +i+iGgG  Gce     + +G +v+++
  gi|330506765|ref|YP_004383193.1| 173 LIIIGGGYIGCEYGHFFSAMGTEVTIL 199
                                       69*********************9987 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 !   26.3   0.0   3.4e-09   4.1e-06      97     302 ..     102     305 ..      10     308 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.4e-09
                       Pyr_redox_3  97 piklfeeVesvkked...egfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkya..gqkvv 168
                                        i+  e+ +  +k +   +++++++ ++t++A++ +iA G   + +++ i+G e+ +    +v+ + +++   + ++
  gi|330506765|ref|YP_004383193.1| 102 TIRSRENLTHYQKRAefiDEYVLKAGSRTLTATQFVIASGS--RSRVPPISGLEE-SGYIDNVSLL-NLRepPRSLI 174
                                       4555555555555431226799******************9..99*******994.4444444433.222136899* PP

                       Pyr_redox_3 169 ViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeey 245
                                       +iGg+  ++++   + ++g eVt++ r+  +   e        p i +rl+e  ++   +v++  ev +++++ e+ 
  gi|330506765|ref|YP_004383193.1| 175 IIGGGYIGCEYGHFFSAMGTEVTILGRSPRLLCGE-------DPEISQRLHESFSR-YCRVVTGYEVLSVERNGEKK 243
                                       ****************************9777765.......67788888887765.36666666666666666555 PP

                       Pyr_redox_3 246 kvk...tedgkkvev..kddvvlatGykpdlsflkk..slfeldedgrpvlteeteetnvpglf 302
                                        v+   t+dgk   +   ++v+la G +++ ++l+    ++e+d++g++ ++e   +t  +g++
  gi|330506765|ref|YP_004383193.1| 244 VVSargTKDGKIR-QfeGEEVLLAAGRRSNSDLLRPerTGVEIDRQGWIRVDEY-LQTSKKGIW 305
                                       5543336776543.3446788899**********998999*********99875.445566666 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   2.3   1.3e-07   0.00016       1      35 [.       8      40 ..       8      47 .. 0.90
   2 ?    4.4   0.0     0.014        17     139     207 ..     209     276 ..     195     289 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.3e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                      D+iViGsG++ L+AA  aa+aG+++a+v++++  g
  gi|330506765|ref|YP_004383193.1|  8 DLIVIGSGAGALVAAQ-AARAGRNTALVDQGPM-G 40
                                      89***********998.99***********985.4 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT.EEEEEEEEETTTTCEEEEEESEEEE-----GG.... CS
                     FAD_binding_2 139 tghallarlvesarkagvdfqerteadeLivedg.rvtGavvenpesgrevrirakavvlatgGfgr.all 207
                                       + +++  rl+es+ +  +++ + +e++++ ++++ +v+ a  +  ++g++++++   v+la+g  ++ +ll
  gi|330506765|ref|YP_004383193.1| 209 EDPEISQRLHESFSR-YCRVVTGYEVLSVERNGEkKVVSARGT--KDGKIRQFEGEEVLLAAGRRSNsDLL 276
                                       567788889999844.4999999*****999655799999999..******************99985444 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   1.4e-07   0.00017       1      47 [.       8      53 ..       8     157 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.4e-07
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdi 47
                                      D++V+G+g++ ++AA +AaraG++++Lv++ ++ G  l +g  ++ +
  gi|330506765|ref|YP_004383193.1|  8 DLIVIGSGAGALVAA-QAARAGRNTALVDQGPMGGTCLNNGCIPSKM 53
                                      99******9999988.899**********999755444444444433 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.2   0.00016      0.19       1      34 [.      11      42 ..      11      69 .. 0.79
   2 !    6.9   0.0     0.006       7.2       1      31 [.     175     205 ..     175     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGr 34
                                      ++G+G+++lvaA++++  g++  l+++++  GG 
  gi|330506765|ref|YP_004383193.1| 11 VIGSGAGALVAAQAARA-GRNTALVDQGPM-GGT 42
                                      8********99988775.999999999864.444 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.006
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       I+G+G  G+ + ++ +  g +v++l +++rl
  gi|330506765|ref|YP_004383193.1| 175 IIGGGYIGCEYGHFFSAMGTEVTILGRSPRL 205
                                       9************************999884 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00016      0.19       2      34 ..       8      39 ..       7      45 .. 0.83
   2 ?    2.3   0.0     0.047        56     123     166 ..     100     144 ..      59     157 .. 0.78
   3 ?   -2.7   0.0       1.5   1.8e+03     125     166 ..     226     271 ..     216     275 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                      d+iviG Ga G + A++aa++g++++l+++++ 
  gi|330506765|ref|YP_004383193.1|  8 DLIVIGSGA-GALVAAQAARAGRNTALVDQGPM 39
                                      89******6.666777888**********9865 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.047
                                       T-EEE-S--EEEEECETT..E.EEEEE.TTEEEEESEEEE----SS CS
                       HI0933_like 123 gvklrletevksvekeed..gkfrvktkseeeleadklvlAtGGlS 166
                                       + ++r ++++++ +k+++   ++ +k+ ++++l+a++ v+A+G+ S
  gi|330506765|ref|YP_004383193.1| 100 EATIRSRENLTHYQKRAEfiDEYVLKA-GSRTLTATQFVIASGSRS 144
                                       566677777777766555222356666.999************998 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.5
                                       EEE-S--EEEEECETTE.EEEEE.....TTEEEEESEEEE----SS CS
                       HI0933_like 125 klrletevksvekeedgkfrvkt.k...seeeleadklvlAtGGlS 166
                                       ++ +  ev sve++ ++k+  +  +   + +++e ++++lA G  S
  gi|330506765|ref|YP_004383193.1| 226 RVVTGYEVLSVERNGEKKVVSARgTkdgKIRQFEGEEVLLAAGRRS 271
                                       5666777888877776644333332233456899999999999887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.3    0.0017         2       1      42 [.       8      47 ..       8     125 .. 0.73
   2 ?   -1.8   0.0       1.5   1.8e+03     159     204 ..      99     144 ..      53     153 .. 0.70
   3 ?    6.9   0.7    0.0033       3.9       2      30 ..     173     203 ..     172     210 .. 0.87
   4 ?    5.1   0.1     0.012        14     161     207 ..     225     276 ..     207     344 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEE CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsg 42
                                      d+++iG+G +G+ +A ++ar+g  ++l+++g   g g+   n g
  gi|330506765|ref|YP_004383193.1|  8 DLIVIGSG-AGALVAAQAARAGrnTALVDQG-PMG-GTC-LNNG 47
                                      789*****.6999999999**99********.555.544.3334 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                                       TT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGH CS
                               DAO 159 lGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGaws 204
                                         ++i+ +++ t+ +++ + + +  + ++g++  +a++ V+a G  s
  gi|330506765|ref|YP_004383193.1|  99 MEATIRSRENLTHYQKRAEFIDEY-VLKAGSRtLTATQFVIASGSRS 144
                                       457777777777775543222222.3444555335688888888765 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0033
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                       ++iiGGG+iG+   ++ ++ g  Vt+l +++
  gi|330506765|ref|YP_004383193.1| 173 LIIIGGGYIGCEYGHFFSAMGteVTILGRSP 203
                                       68*********99999999999999998875 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.012
                                       -EEEESECEEEEEEEE.TCEEEEEEECT.EEEEEEEE.....EEE--GGGHH..HH CS
                               DAO 161 veilegtevtgleeed.gkvwgverttp.gendaada.....vVnaaGawsd..ll 207
                                       +++++g ev ++e+++ +kv+   r t+ g +   ++     v +aaG  s+  ll
  gi|330506765|ref|YP_004383193.1| 225 CRVVTGYEVLSVERNGeKKVVSA-RGTKdGKI---RQfegeeVLLAAGRRSNsdLL 276
                                       78999*******88653443333.54444664...4444466******88776444 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 ?    6.5   0.0    0.0039       4.7      38      70 ..     172     204 ..     162     229 .. 0.88
   2 ?    4.4   0.0     0.018        21      34      79 ..     297     342 ..     277     354 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0039
                                       EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                        + iiG G IG +  + ++a+g +v++  rs++
  gi|330506765|ref|YP_004383193.1| 172 SLIIIGGGYIGCEYGHFFSAMGTEVTILGRSPR 204
                                       678***********************9999876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.018
                                       GTTSEEEEES-S.HHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHT CS
                      2-Hacid_dh_C  34 lsgktvGiiGlG.rIGqavakrlkafgmkviaydrskkkeeeeeelg 79 
                                       l+ ++ Gi+ lG +IG+++ +  +  +++++a++    + e +e++ 
  gi|330506765|ref|YP_004383193.1| 297 LQTSKKGIWALGdAIGKHMFRHTANYEARIVAHNILLVQGE-AERKA 342
                                       778899******55********************9988776.33333 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.9      0.37   4.4e+02       3      31 ..      11      38 ..       9      48 .. 0.89
   2 ?   11.7   0.0   0.00012      0.15       2      32 ..     174     204 ..     173     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.37
                                      EES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  3 ilGaGaiGsllaakLakagadvtlilrsr 31
                                      ++G+Ga G l+aa+ a+ag++  l+++++
  gi|330506765|ref|YP_004383193.1| 11 VIGSGA-GALVAAQAARAGRNTALVDQGP 38
                                      89**99.**************99998765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00012
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCHH CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsrr 32 
                                        i+G G iG+ +++  ++ g +vt+++rs+r
  gi|330506765|ref|YP_004383193.1| 174 IIIGGGYIGCEYGHFFSAMGTEVTILGRSPR 204
                                       59**************************994 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.6       0.2   2.4e+02       4      30 ..      11      36 ..       8      49 .. 0.91
   2 ?    8.8   0.0    0.0011       1.4       4      49 ..     175     220 ..     172     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.2
                                      EE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdi 30
                                      viG+G  Ga +aa++a+ag ++ lvd 
  gi|330506765|ref|YP_004383193.1| 11 VIGSGA-GALVAAQAARAGRNTALVDQ 36
                                      999997.*****************996 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                                       EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCC CS
                           3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdiseealekalekiekslekl 49 
                                       +iG G +G +  + f + g eV+++ +s++ l     +i+++l++ 
  gi|330506765|ref|YP_004383193.1| 175 IIGGGYIGCEYGHFFSAMGTEVTILGRSPRLLCGEDPEISQRLHES 220
                                       9**************************9999888888888777665 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 ?   11.1   0.0   0.00033      0.39      37      59 ..      61      83 ..      57      92 .. 0.89
   2 ?   -2.3   0.0       4.9   5.9e+03      25      35 ..     179     189 ..     171     192 .. 0.75
   3 ?   -2.3   0.0       4.9   5.8e+03      38      48 ..     234     244 ..     228     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                            UXS1_N 37 mrsiqenGdvKvekkieelvaPl 59
                                      +rsiqe G v v+ +ie+++ P 
  gi|330506765|ref|YP_004383193.1| 61 IRSIQEAGAVGVHARIEKIDFPR 83
                                      5******************9985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.9
                            UXS1_N  25 aYvasvwGtfv 35 
                                        Y+ + +G f 
  gi|330506765|ref|YP_004383193.1| 179 GYIGCEYGHFF 189
                                       5*******985 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.9
                            UXS1_N  38 rsiqenGdvKv 48 
                                        s++ nG+ Kv
  gi|330506765|ref|YP_004383193.1| 234 LSVERNGEKKV 244
                                       58899999999 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.0    0.0091        11       1      34 [.       8      38 ..       8      44 .. 0.88
   2 ?   -2.6   0.0       1.9   2.2e+03      97     143 ..      91     144 ..      70     151 .. 0.55
   3 ?    2.8   0.0     0.042        50       2      38 ..     173     207 ..     172     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0091
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasp 34
                                      D++viG+G Ag ++Aa+   a++g +  l++ +p
  gi|330506765|ref|YP_004383193.1|  8 DLIVIGSG-AGALVAAQA--ARAGRNTALVDQGP 38
                                      9*******.788899999..89999999999887 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                     Lycopene_cycl  97 lvengvklleakves...veeeea....geslvvleggrkirarlvvdarglas 143
                                       +v++g+  +ea++ s    ++ ++     + +v  +g r++ a   v a+g  s
  gi|330506765|ref|YP_004383193.1|  91 VVDEGRAQMEATIRSrenLTHYQKraefIDEYVLKAGSRTLTATQFVIASGSRS 144
                                       445555555555543111222222100134567777777888888888888544 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.042
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsllf 38 
                                       +++iG+G  g+   +    +++g +v+++  sp ll 
  gi|330506765|ref|YP_004383193.1| 173 LIIIGGGYIGCEYGHFF--SAMGTEVTILGRSPRLLC 207
                                       79**************9..99********99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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):              15  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3080.21
//
Query:       gi|330506766|ref|YP_004383194.1|  [L=323]
Description: radical SAM domain family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-17   64.4   0.0    2.7e-17   63.7   0.0    1.3  1  Radical_SAM    Radical SAM superfamily
     0.0037   17.1   0.0     0.0065   16.3   0.0    1.3  1  DUF3463        Domain of unknown function (DUF3463)
  ------ inclusion threshold ------
       0.02   14.9   0.0        3.3    7.8   0.0    2.7  3  Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen r
      0.087   12.5   0.0         32    4.3   0.0    3.1  3  SSXT           SSXT protein (N-terminal region)
       0.15   11.7   0.1       0.25   11.0   0.1    1.3  1  PAR1           PAR1 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 !   63.7   0.0   7.5e-21   2.7e-17       6     164 ..      32     172 ..      29     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 7.5e-21
                                       EESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                        CnlrCsfC+ +     +++g ++++ ei + ++e+  + g+++      epll+ d+ ++l++++     g+ +++
  gi|330506766|ref|YP_004383194.1|  32 RCNLRCSFCQYW-----REPGGEMTKKEIFRMLDEA-SSFGIGVYNAWTVEPLLREDLPQILRHAKSQ---GLITSL 99 
                                       7***********.....69*****************.5999**************************8...****** PP

                                       EECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  83 etngtlpdeeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                                       +tng+l+    ++r +elg +d++s++++ + +    + + rg ++e +l++++++++ag + + +++v+    + e
  gi|330506766|ref|YP_004383194.1| 100 VTNGLLL----AKRADELGdLDYLSVSVDGIKSY---REL-RGVDLENILAGIRAAKKAGHE-ILINCVISSKNTGE 167
                                       ******8....66666666699***********8...777.89****************999.88888877655554 PP

                                       HHHHHH CS
                                       xxxxxx RF
                       Radical_SAM 159 eleell 164
                                        le+l+
  gi|330506766|ref|YP_004383194.1| 168 -LEDLV 172
                                       .67666 PP

>> DUF3463  Domain of unknown function (DUF3463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.8e-06    0.0065      20     128 ..     205     316 ..     196     321 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-06
                           DUF3463  20 erektkelfrkilelkkkkyklnesplyldflagkq.eykCtpWgnp.trnvlGwqkPCYlleegyaktfkelleet 94 
                                       +r++ +++++++++lk+++  +++s +yl+++   +  +kC +   +  +   G  + C + ++  a+  + l e  
  gi|330506766|ref|YP_004383194.1| 205 DRSEYEKAVHRLMDLKRSGAPIINSLTYLEMISSLKpGFKCHASDIIlHVAADGSIENCRVHTQSLANVKDGLAEAW 281
                                       6889999***************************7769***998765267889************************ PP

                           DUF3463  95 dwekyg.kgkdpkCanCmvhsgyEasavsdtvksl 128
                                       + ++ g ++  ++C  C    + E+s++ + v ++
  gi|330506766|ref|YP_004383194.1| 282 QASRIGrQEAVQSCPGCLFFGYAENSLLYEFVPEV 316
                                       ******6667899*************998877665 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 ?    4.4   0.0     0.011        38      52      85 ..     138     173 ..     116     183 .. 0.70
   2 ?    7.8   0.0   0.00092       3.3      31      82 ..     187     241 ..     179     267 .. 0.82
   3 ?   -1.4   0.0      0.65   2.3e+03      54      90 ..     247     283 ..     244     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.011
                     Nit_Regul_Hom  52 esaikiik..dlseeavlintvvdeekvekikeele 85 
                                       e+++  i+  + + + +lin+v+++++  ++++ ++
  gi|330506766|ref|YP_004383194.1| 138 ENILAGIRaaKKAGHEILINCVISSKNTGELEDLVH 173
                                       5555555511345677***********999998765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00092
                     Nit_Regul_Hom  31 lieYkGlsPqewkgflle..edpesaikiikdlsee.avlintvvdeekvekike 82 
                                       l+e +G+s + wk++ ++   + e+a++ + dl ++ a +in++   e+++++k 
  gi|330506766|ref|YP_004383194.1| 187 LHESRGISDSVWKDLGIRdrSEYEKAVHRLMDLKRSgAPIINSLTYLEMISSLKP 241
                                       7899***********9984468899999999998762458888888888887775 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.65
                     Nit_Regul_Hom  54 aikiikdlseeavlintvvdeekvekikeeleeklkd 90 
                                       a +ii +++ ++ + n+ v+++ + ++k+ l+e+ + 
  gi|330506766|ref|YP_004383194.1| 247 ASDIILHVAADGSIENCRVHTQSLANVKDGLAEAWQA 283
                                       5678999999999999999999999999999988765 PP

>> SSXT  SSXT protein (N-terminal region)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0099        35       3      18 ..      49      64 ..      47      67 .. 0.89
   2 ?   -1.0   0.0      0.39   1.4e+03      38      55 ..      95     112 ..      88     117 .. 0.75
   3 ?    4.3   0.0    0.0088        32      19      41 ..     155     177 ..     153     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0099
                              SSXT  3 evtteqIqklLDENsq 18
                                      e+t+++I ++LDE s+
  gi|330506766|ref|YP_004383194.1| 49 EMTKKEIFRMLDEASS 64
                                      799**********887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.39
                              SSXT  38 yqqiLhrNLvyLAtiADe 55 
                                         + L  N + LA+ ADe
  gi|330506766|ref|YP_004383194.1|  95 LITSLVTNGLLLAKRADE 112
                                       55667788899*****98 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0088
                              SSXT  19 LIqtIielqnkGraeecdqyqqi 41 
                                       LI+++i+  n G+ e++++  + 
  gi|330506766|ref|YP_004383194.1| 155 LINCVISSKNTGELEDLVHLAEE 177
                                       9***************9997765 PP

>> PAR1  PAR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   6.9e-05      0.25      36      96 ..     243     298 ..     233     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.9e-05
                              PAR1  36 ytcrtseveaeklkelietdecvkacGvdrksvGissdsllesqftkklcspaclnkcPni 96 
                                       ++c++s++       ++ +d  +++c v  +s+    d+l e+  ++++   + +++cP  
  gi|330506766|ref|YP_004383194.1| 243 FKCHASDII-----LHVAADGSIENCRVHTQSLANVKDGLAEAWQASRIGRQEAVQSCPGC 298
                                       566666665.....47899****************************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2347.38
//
Query:       gi|330506767|ref|YP_004383195.1|  [L=567]
Description: internalin-A [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-78  256.9 119.3    3.1e-10   40.1   0.8   11.6 12  LRR_4            Leucine Rich repeats (2 copies)
    8.5e-77  252.9 201.2    5.1e-10   39.0   6.0   11.5 16  LRR_8            Leucine rich repeat
      3e-30  101.7 103.3     0.0091   16.0   0.1   18.4 18  LRR_6            Leucine Rich repeat
    1.8e-14   53.6  38.2     0.0011   18.5   1.9    6.7  9  LRR_9            Leucine-rich repeat
  ------ inclusion threshold ------
       0.18   12.4  89.2        4.4    8.2   0.1   18.1 17  LRR_1            Leucine Rich Repeat
        3.8    8.5   4.8         10    7.1   0.2    3.8  5  bZIP_C           Basic leucine-zipper C terminal


Domain annotation for each model (and alignments):
>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   2.9   4.7e-10   1.4e-06       2      42 ..      81     119 ..      80     124 .. 0.90
   2 !   20.7   5.5   1.4e-07   0.00042       2      43 ..     124     163 ..     123     165 .. 0.87
   3 !   38.5   5.8   3.3e-13   9.9e-10       1      43 [.     166     207 ..     166     208 .. 0.94
   4 !   24.0   2.9   1.3e-08   3.8e-05       2      42 ..     211     248 ..     210     251 .. 0.89
   5 !   40.1   0.8     1e-13   3.1e-10       1      43 [.     252     293 ..     252     295 .. 0.96
   6 !   35.8   5.9   2.4e-12   7.3e-09       1      42 [.     296     335 ..     296     339 .. 0.91
   7 !   36.5  11.0   1.4e-12   4.3e-09       1      43 [.     339     380 ..     339     381 .. 0.94
   8 !   33.4  11.1   1.3e-11     4e-08       1      43 [.     361     402 ..     361     403 .. 0.95
   9 !   29.5   6.5   2.4e-10   7.1e-07       1      43 [.     383     424 ..     383     425 .. 0.96
  10 !   20.9   1.6   1.2e-07   0.00036       2      41 ..     406     444 ..     405     447 .. 0.85
  11 !   37.3   2.2   8.2e-13   2.5e-09       2      43 ..     450     490 ..     449     491 .. 0.95
  12 !   21.9   1.5   5.5e-08   0.00016       2      25 ..     494     517 ..     493     534 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 4.7e-10
                                       S--EEE--SS---E-S-HHH-TT--EEE-.-S-----GGGG CS
                             LRR_4   2 nLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdldeL 42 
                                       nLe+L+L+ N ++d ++l++l+ Lk L Ls+N +itd++ L
  gi|330506767|ref|YP_004383195.1|  81 NLENLSLRENEISDASSLSGLTGLKRLELSSN-QITDVS-L 119
                                       9****************************888.****95.3 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.4e-07
                                       S--EEE--SS---E-S-HHH-TT--EEE-..-S-----GGGGX CS
                             LRR_4   2 nLevLdLsnNqltdiplleklpnLkeLdL.sgNnlitdldeLk 43 
                                       nLe+L+L +N++t ++l + l+nL +L L +gN +i ++++L+
  gi|330506767|ref|YP_004383195.1| 124 NLETLSLWDNHITNVSLSG-LTNLDTL-LlWGN-KIINVSSLS 163
                                       9************887777.******9.55***.888988875 PP

  == domain 3  score: 38.5 bits;  conditional E-value: 3.3e-13
                                       SS--EEE--SS---E-S-HHH-TT--EEE-.-S-----GGGGX CS
                             LRR_4   1 pnLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdldeLk 43 
                                       +nL+ LdLs Nq+td ++l++l+nL+ LdL +Nn+itd+++L+
  gi|330506767|ref|YP_004383195.1| 166 TNLTDLDLSTNQITDASPLSGLTNLTDLDL-DNNQITDVSSLS 207
                                       7********66*******************.999*****9986 PP

  == domain 4  score: 24.0 bits;  conditional E-value: 1.3e-08
                                       S--EEE--SS---E-S-HHH-TT--EEE-.-S-----GGGG CS
                             LRR_4   2 nLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdldeL 42 
                                       nL +LdLs+N++t ++l + l+n   LdL+gN +itd++ L
  gi|330506767|ref|YP_004383195.1| 211 NLMNLDLSSNRITNVSLSG-LTNVVWLDLWGN-QITDVT-L 248
                                       8999*********887777.************.****95.4 PP

  == domain 5  score: 40.1 bits;  conditional E-value: 1e-13
                                       SS--EEE--SS---E-S-HHH-TT--EEE-.-S-----GGGGX CS
                             LRR_4   1 pnLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdldeLk 43 
                                       +nL+ Ld s Nq+ d+++l++l+nL++L+L g+n+itd+++L+
  gi|330506767|ref|YP_004383195.1| 252 TNLTWLDVSRNQIADVSSLSGLTNLTKLYL-GCNQITDVSSLS 293
                                       7*****************************.********9986 PP

  == domain 6  score: 35.8 bits;  conditional E-value: 2.4e-12
                                       SS--EEE--SS---E-S-HHH-TT--EEE-.-S-----GGGG CS
                             LRR_4   1 pnLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdldeL 42 
                                       +nL+ LdLs Nq+td ++l++l+nL++LdL +Nn+i+d++ L
  gi|330506767|ref|YP_004383195.1| 296 TNLTDLDLSTNQITDASPLSGLTNLTYLDL-DNNRINDVS-L 335
                                       7********66*******************.999**9995.4 PP

  == domain 7  score: 36.5 bits;  conditional E-value: 1.4e-12
                                       SS--EEE--SS---E-S-HHH-TT--EEE-.-S-----GGGGX CS
                             LRR_4   1 pnLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdldeLk 43 
                                       +nL+ L LsnNq+ d+++l++l+nLk LdL +Nn+i+d+++L+
  gi|330506767|ref|YP_004383195.1| 339 TNLTDLELSNNQINDVSSLSGLTNLKDLDL-SNNQINDISSLS 380
                                       7*****************************.666*****9986 PP

  == domain 8  score: 33.4 bits;  conditional E-value: 1.3e-11
                                       SS--EEE--SS---E-S-HHH-TT--EEE-.-S-----GGGGX CS
                             LRR_4   1 pnLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdldeLk 43 
                                       +nL+ LdLsnNq+ di++l++l+nL+ L Ls+N  it++++L+
  gi|330506767|ref|YP_004383195.1| 361 TNLKDLDLSNNQINDISSLSGLTNLTDLELSSN-EITNISSLS 402
                                       7*****************************888.999999987 PP

  == domain 9  score: 29.5 bits;  conditional E-value: 2.4e-10
                                       SS--EEE--SS---E-S-HHH-TT--EEE-.-S-----GGGGX CS
                             LRR_4   1 pnLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdldeLk 43 
                                       +nL+ L Ls+N +t i++l++l +L+ LdL +Nn+i d+++L+
  gi|330506767|ref|YP_004383195.1| 383 TNLTDLELSSNEITNISSLSSLASLRCLDL-DNNQIIDVSSLS 424
                                       7*****************************.999*****9986 PP

  == domain 10  score: 20.9 bits;  conditional E-value: 1.2e-07
                                       S--EEE--SS---E-S-HHH-TT--EEE-.-S-----GGG CS
                             LRR_4   2 nLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdlde 41 
                                       +L+ LdL nNq+ d+++l+ l++Lk L L +N   td ++
  gi|330506767|ref|YP_004383195.1| 406 SLRCLDLDNNQIIDVSSLSALTSLKWLRLCSN-HATDASS 444
                                       79***************999********9666.5556555 PP

  == domain 11  score: 37.3 bits;  conditional E-value: 8.2e-13
                                       S--EEE--SS---E-S-HHH-TT--EEE-.-S-----GGGGX CS
                             LRR_4   2 nLevLdLsnNqltdiplleklpnLkeLdLsgNnlitdldeLk 43 
                                       nL+ LdLs+Nq+td+++l++l nL  L+Ls+N +itd+++L+
  gi|330506767|ref|YP_004383195.1| 450 NLRWLDLSSNQITDVSPLSGLYNLGWLNLSSN-QITDVSPLS 490
                                       9****************************888.******997 PP

  == domain 12  score: 21.9 bits;  conditional E-value: 5.5e-08
                                       S--EEE--SS---E-S-HHH-TT- CS
                             LRR_4   2 nLevLdLsnNqltdiplleklpnL 25 
                                       nL+ LdLs+Nq+td+++l++l+nL
  gi|330506767|ref|YP_004383195.1| 494 NLTGLDLSSNQITDVSPLSNLTNL 517
                                       9****************9999998 PP

>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   2.0   1.8e-07   0.00054      24      61 .]      79     114 ..      67     114 .. 0.92
   2 !   28.6   6.8     3e-10   8.9e-07       2      61 .]      81     135 ..      80     135 .. 0.95
   3 !   19.6   3.4   1.9e-07   0.00057      18      61 .]     116     156 ..     114     156 .. 0.93
   4 !   29.0   8.1   2.2e-10   6.6e-07       2      61 .]     145     200 ..     144     200 .. 0.94
   5 !   33.0   7.5   1.2e-11   3.6e-08       1      61 []     188     243 ..     188     243 .. 0.95
   6 !   33.3   4.0     1e-11     3e-08       2      61 .]     211     264 ..     210     264 .. 0.95
   7 !   27.7   1.2   5.5e-10   1.6e-06      16      61 .]     243     286 ..     241     286 .. 0.94
   8 !   38.3   4.3   2.8e-13   8.3e-10       1      61 []     252     308 ..     252     308 .. 0.95
   9 !   39.0   6.0   1.7e-13   5.1e-10       1      61 []     274     330 ..     274     330 .. 0.95
  10 !   26.9   5.4   9.7e-10   2.9e-06      20      61 .]     313     351 ..     309     351 .. 0.92
  11 !   35.3  12.9   2.4e-12   7.2e-09       1      61 []     318     373 ..     318     373 .. 0.94
  12 !   28.4   7.2   3.4e-10     1e-06      19      59 ..     355     393 ..     352     393 .. 0.95
  13 !   28.6   6.1   2.9e-10   8.5e-07      19      61 .]     377     417 ..     374     417 .. 0.95
  14 !   23.5   2.2   1.1e-08   3.4e-05      16      61 .]     418     461 ..     418     461 .. 0.93
  15 !   28.2   1.9   3.9e-10   1.2e-06      21      61 .]     467     505 ..     462     505 .. 0.93
  16 !   25.3   4.6   3.3e-09   9.8e-06       2      59 ..     472     525 ..     472     527 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.8e-07
                                       -TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8  24 lsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                       + nL+ L+L++N+++  s  ++sgL+ L+ L Ls+N++
  gi|330506767|ref|YP_004383195.1|  79 CINLENLSLRENEISDAS--SLSGLTGLKRLELSSNQI 114
                                       679**************8..****************98 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 3e-10
                                       T-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8   2 nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                       nL++L+L+ N +++   ++ +gl++Lk L+Ls+N++t +   ++sgL++L+ L L +N++
  gi|330506767|ref|YP_004383195.1|  81 NLENLSLRENEISD--ASSLSGLTGLKRLELSSNQITDV---SLSGLANLETLSLWDNHI 135
                                       89**********96..6899*******************...6***************97 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 1.9e-07
                                       TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8  18 deaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                       d + +gl nL++L+L +N +t +   ++sgL++L+ L L gN++
  gi|330506767|ref|YP_004383195.1| 116 DVSLSGLANLETLSLWDNHITNV---SLSGLTNLDTLLLWGNKI 156
                                       67889******************...6***************97 PP

  == domain 4  score: 29.0 bits;  conditional E-value: 2.2e-10
                                       T-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8   2 nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                       nL +L L+ N++  ++ ++ +gl+nL+ LdLs N++t  s   +sgL++L+ LdL++N++
  gi|330506767|ref|YP_004383195.1| 145 NLDTLLLWGNKI--INVSSLSGLTNLTDLDLSTNQITDAS--PLSGLTNLTDLDLDNNQI 200
                                       99*********9..556799*******************9..8***************98 PP

  == domain 5  score: 33.0 bits;  conditional E-value: 1.2e-11
                                       TT-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8   1 pnLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                       +nLt LdL+nN++t++  ++ +gl nL+ LdLs+N++t +   ++sgL+++ +LdL gN++
  gi|330506767|ref|YP_004383195.1| 188 TNLTDLDLDNNQITDV--SSLSGLINLMNLDLSSNRITNV---SLSGLTNVVWLDLWGNQI 243
                                       59************98..5899******************...6***************97 PP

  == domain 6  score: 33.3 bits;  conditional E-value: 1e-11
                                       T-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8   2 nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                       nL++LdLs+Nr+t+++    +gl+n+ +LdL  N++t +   ++sgL++L++Ld+s+N++
  gi|330506767|ref|YP_004383195.1| 211 NLMNLDLSSNRITNVS---LSGLTNVVWLDLWGNQITDV---TLSGLTNLTWLDVSRNQI 264
                                       8*************96...78999***************...8***************98 PP

  == domain 7  score: 27.7 bits;  conditional E-value: 5.5e-10
                                       E-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8  16 lddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                       + d + +gl+nL++Ld s+N++  +s  ++sgL++L++L+L  N++
  gi|330506767|ref|YP_004383195.1| 243 ITDVTLSGLTNLTWLDVSRNQIADVS--SLSGLTNLTKLYLGCNQI 286
                                       778899*******************9..*************99987 PP

  == domain 8  score: 38.3 bits;  conditional E-value: 2.8e-13
                                       TT-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8   1 pnLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                       +nLt Ld+s+N++ ++  ++ +gl+nL+ L+L++N++t +s  ++sgL++L+ LdLs N++
  gi|330506767|ref|YP_004383195.1| 252 TNLTWLDVSRNQIADV--SSLSGLTNLTKLYLGCNQITDVS--SLSGLTNLTDLDLSTNQI 308
                                       59***********987..6899******************9..****************97 PP

  == domain 9  score: 39.0 bits;  conditional E-value: 1.7e-13
                                       TT-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8   1 pnLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                       +nLt+L+L +N++t++  ++ +gl+nL+ LdLs N++t  s   +sgL++L++LdL++Nr+
  gi|330506767|ref|YP_004383195.1| 274 TNLTKLYLGCNQITDV--SSLSGLTNLTDLDLSTNQITDAS--PLSGLTNLTYLDLDNNRI 330
                                       59************98..5899******************9..8***************98 PP

  == domain 10  score: 26.9 bits;  conditional E-value: 9.7e-10
                                       SSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8  20 aFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                         +gl+nL++LdL nN+++ +   ++s+L++L+ L Ls+N++
  gi|330506767|ref|YP_004383195.1| 313 PLSGLTNLTYLDLDNNRINDV---SLSDLTNLTDLELSNNQI 351
                                       5789***************99...6***************98 PP

  == domain 11  score: 35.3 bits;  conditional E-value: 2.4e-12
                                       TT-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8   1 pnLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                       +nLt+LdL+nNr++++   + ++l+nL+ L+LsnN+++ +s  ++sgL++L+ LdLs+N++
  gi|330506767|ref|YP_004383195.1| 318 TNLTYLDLDNNRINDV---SLSDLTNLTDLELSNNQINDVS--SLSGLTNLKDLDLSNNQI 373
                                       59**********9876...6899*****************9..****************98 PP

  == domain 12  score: 28.4 bits;  conditional E-value: 3.4e-10
                                       TSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS CS
                             LRR_8  19 eaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgN 59 
                                       ++ +gl+nLk LdLsnN+++ +s  ++sgL++L+ L Ls+N
  gi|330506767|ref|YP_004383195.1| 355 SSLSGLTNLKDLDLSNNQINDIS--SLSGLTNLTDLELSSN 393
                                       6889******************9..**************99 PP

  == domain 13  score: 28.6 bits;  conditional E-value: 2.9e-10
                                       TSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8  19 eaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                       ++ +gl+nL+ L+Ls+N++t +s  ++s+L+sLr LdL++N++
  gi|330506767|ref|YP_004383195.1| 377 SSLSGLTNLTDLELSSNEITNIS--SLSSLASLRCLDLDNNQI 417
                                       5789******************9..****************98 PP

  == domain 14  score: 23.5 bits;  conditional E-value: 1.1e-08
                                       E-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8  16 lddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                       +d ++ + l++Lk+L L +N  t  s  ++s+L +Lr+LdLs+N++
  gi|330506767|ref|YP_004383195.1| 418 IDVSSLSALTSLKWLRLCSNHATDAS--SLSSLVNLRWLDLSSNQI 461
                                       56788999************999998..****************98 PP

  == domain 15  score: 28.2 bits;  conditional E-value: 3.9e-10
                                       STT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                             LRR_8  21 FkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        +gl nL +L+Ls+N++t +s   +sgL++L+ LdLs+N++
  gi|330506767|ref|YP_004383195.1| 467 LSGLYNLGWLNLSSNQITDVS--PLSGLANLTGLDLSSNQI 505
                                       689*****************9..8***************98 PP

  == domain 16  score: 25.3 bits;  conditional E-value: 3.3e-09
                                       T-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS CS
                             LRR_8   2 nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgN 59 
                                       nL  L+Ls+N++t++++   +gl nL+ LdLs+N++t +s   +s+L++L ++dL++ 
  gi|330506767|ref|YP_004383195.1| 472 NLGWLNLSSNQITDVSP--LSGLANLTGLDLSSNQITDVS--PLSNLTNLIWMDLRSK 525
                                       6778*********9988..6789****************9..8999*99999999875 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1    0.0041        12       2      18 ..      79      95 ..      78      96 .. 0.91
   2 !   16.0   0.1   3.1e-06    0.0091       4      24 .]     103     123 ..     100     123 .. 0.91
   3 !    5.4   0.4    0.0076        23       4      22 ..     124     142 ..     122     143 .. 0.88
   4 !   11.4   0.7     9e-05      0.27       3      18 ..     166     181 ..     164     182 .. 0.91
   5 !   10.0   1.7   0.00026      0.78       3      18 ..     188     203 ..     186     204 .. 0.91
   6 !    9.5   1.0   0.00038       1.1       4      22 ..     211     229 ..     208     230 .. 0.86
   7 ?    1.8   0.1       0.1   3.1e+02       8      18 ..     236     246 ..     231     251 .. 0.87
   8 !    7.7   0.0    0.0014       4.1       3      18 ..     252     267 ..     250     268 .. 0.89
   9 !   11.4   0.2   8.7e-05      0.26       3      18 ..     274     289 ..     272     290 .. 0.91
  10 !   11.4   0.7     9e-05      0.27       3      18 ..     296     311 ..     294     312 .. 0.91
  11 !   11.7   0.9   6.9e-05      0.21       3      21 ..     318     336 ..     316     338 .. 0.89
  12 !   10.0   1.4   0.00026      0.77       3      18 ..     339     354 ..     337     355 .. 0.91
  13 !   10.5   1.8   0.00017      0.52       3      17 ..     361     375 ..     359     376 .. 0.92
  14 !    9.2   0.7   0.00046       1.4       3      17 ..     383     397 ..     381     398 .. 0.91
  15 !    6.5   0.3    0.0034        10       4      22 ..     406     425 ..     403     426 .. 0.79
  16 !   10.4   0.2   0.00019      0.57       4      18 ..     450     464 ..     447     465 .. 0.87
  17 !    7.8   0.1    0.0012       3.7       8      18 ..     476     486 ..     476     487 .. 0.93
  18 !   11.5   0.2   8.6e-05      0.26       4      18 ..     494     508 ..     491     509 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0041
                             LRR_6  2 nthLteLdLsgNdIgDe 18
                                      + +L+ L+L+ N+I+D+
  gi|330506767|ref|YP_004383195.1| 79 CINLENLSLRENEISDA 95
                                      779************96 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.1e-06
                             LRR_6   4 hLteLdLsgNdIgDeGaeaLa 24 
                                        L+ L+Ls+N+I+D+ ++ La
  gi|330506767|ref|YP_004383195.1| 103 GLKRLELSSNQITDVSLSGLA 123
                                       69**************99987 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0076
                             LRR_6   4 hLteLdLsgNdIgDeGaea 22 
                                       +L++L+L +N+I+++ ++ 
  gi|330506767|ref|YP_004383195.1| 124 NLETLSLWDNHITNVSLSG 142
                                       79************98875 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 9e-05
                             LRR_6   3 thLteLdLsgNdIgDe 18 
                                       t+Lt LdLs N+I+D+
  gi|330506767|ref|YP_004383195.1| 166 TNLTDLDLSTNQITDA 181
                                       89************96 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.00026
                             LRR_6   3 thLteLdLsgNdIgDe 18 
                                       t+Lt LdL  N+I+D+
  gi|330506767|ref|YP_004383195.1| 188 TNLTDLDLDNNQITDV 203
                                       89*************6 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.00038
                             LRR_6   4 hLteLdLsgNdIgDeGaea 22 
                                       +L  LdLs+N I+++ ++ 
  gi|330506767|ref|YP_004383195.1| 211 NLMNLDLSSNRITNVSLSG 229
                                       7889**********98875 PP

  == domain 7  score: 1.8 bits;  conditional E-value: 0.1
                             LRR_6   8 LdLsgNdIgDe 18 
                                       LdL gN+I+D+
  gi|330506767|ref|YP_004383195.1| 236 LDLWGNQITDV 246
                                       8999******6 PP

  == domain 8  score: 7.7 bits;  conditional E-value: 0.0014
                             LRR_6   3 thLteLdLsgNdIgDe 18 
                                       t+Lt Ld+s N+I D+
  gi|330506767|ref|YP_004383195.1| 252 TNLTWLDVSRNQIADV 267
                                       79999********996 PP

  == domain 9  score: 11.4 bits;  conditional E-value: 8.7e-05
                             LRR_6   3 thLteLdLsgNdIgDe 18 
                                       t+Lt+L L +N+I+D+
  gi|330506767|ref|YP_004383195.1| 274 TNLTKLYLGCNQITDV 289
                                       89*************6 PP

  == domain 10  score: 11.4 bits;  conditional E-value: 9e-05
                             LRR_6   3 thLteLdLsgNdIgDe 18 
                                       t+Lt LdLs N+I+D+
  gi|330506767|ref|YP_004383195.1| 296 TNLTDLDLSTNQITDA 311
                                       89************96 PP

  == domain 11  score: 11.7 bits;  conditional E-value: 6.9e-05
                             LRR_6   3 thLteLdLsgNdIgDeGae 21 
                                       t+Lt+LdL  N I+D+ ++
  gi|330506767|ref|YP_004383195.1| 318 TNLTYLDLDNNRINDVSLS 336
                                       89*************9887 PP

  == domain 12  score: 10.0 bits;  conditional E-value: 0.00026
                             LRR_6   3 thLteLdLsgNdIgDe 18 
                                       t+Lt L+Ls N+I+D+
  gi|330506767|ref|YP_004383195.1| 339 TNLTDLELSNNQINDV 354
                                       89************96 PP

  == domain 13  score: 10.5 bits;  conditional E-value: 0.00017
                             LRR_6   3 thLteLdLsgNdIgD 17 
                                       t+L+ LdLs N+I+D
  gi|330506767|ref|YP_004383195.1| 361 TNLKDLDLSNNQIND 375
                                       89***********98 PP

  == domain 14  score: 9.2 bits;  conditional E-value: 0.00046
                             LRR_6   3 thLteLdLsgNdIgD 17 
                                       t+Lt L+Ls+N+I++
  gi|330506767|ref|YP_004383195.1| 383 TNLTDLELSSNEITN 397
                                       89***********96 PP

  == domain 15  score: 6.5 bits;  conditional E-value: 0.0034
                             LRR_6   4 hLteLdLsgNd.IgDeGaea 22 
                                       +L+ LdL  N+ I+ + ++a
  gi|330506767|ref|YP_004383195.1| 406 SLRCLDLDNNQiIDVSSLSA 425
                                       8**********777666666 PP

  == domain 16  score: 10.4 bits;  conditional E-value: 0.00019
                             LRR_6   4 hLteLdLsgNdIgDe 18 
                                       +L+ LdLs+N+I+D+
  gi|330506767|ref|YP_004383195.1| 450 NLRWLDLSSNQITDV 464
                                       6777**********6 PP

  == domain 17  score: 7.8 bits;  conditional E-value: 0.0012
                             LRR_6   8 LdLsgNdIgDe 18 
                                       L+Ls+N+I+D+
  gi|330506767|ref|YP_004383195.1| 476 LNLSSNQITDV 486
                                       9*********6 PP

  == domain 18  score: 11.5 bits;  conditional E-value: 8.6e-05
                             LRR_6   4 hLteLdLsgNdIgDe 18 
                                       +Lt LdLs+N+I+D+
  gi|330506767|ref|YP_004383195.1| 494 NLTGLDLSSNQITDV 508
                                       7999**********6 PP

>> LRR_9  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.1    0.0062        19      89     117 ..      81     109 ..      53     121 .. 0.62
   2 !   10.4   0.7   0.00011      0.34      46     127 ..      84     158 ..      79     161 .. 0.83
   3 !   12.1   3.5   3.5e-05       0.1      41     126 ..     122     201 ..     105     204 .. 0.76
   4 !   10.3   5.2   0.00013      0.37      40     118 ..     142     218 ..     133     230 .. 0.84
   5 !    6.5   1.8    0.0018       5.3      47     102 ..     193     245 ..     185     291 .. 0.61
   6 !   15.7   1.1   2.6e-06    0.0078      25     123 ..     237     328 ..     230     331 .. 0.82
   7 !   16.9   3.9   1.1e-06    0.0034      46     116 ..     300     367 ..     293     369 .. 0.91
   8 !   18.5   1.9   3.6e-07    0.0011      47     119 ..     366     436 ..     365     446 .. 0.88
   9 !   13.4   0.2   1.3e-05      0.04      47     120 ..     454     522 ..     446     554 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0062
                             LRR_9  89 nleelvltnnelqeladldPlaslkklel 117
                                       nle+l l +ne+ + + l  l+ lk+lel
  gi|330506767|ref|YP_004383195.1|  81 NLENLSLRENEISDASSLSGLTGLKRLEL 109
                                       56666666666666666666666666654 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00011
                             LRR_9  46 tidlsdndirkldgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkklellsllk 122
                                        + l +n+i +  ++  l  lk l l++n+i+ ++      l nle+l l +n++++++    l  l +l++l l  
  gi|330506767|ref|YP_004383195.1|  84 NLSLRENEISDASSLSGLTGLKRLELSSNQITDVSL---SGLANLETLSLWDNHITNVS----LSGLTNLDTLLLWG 153
                                       567899*************************99974...46889**********99875....67777777777777 PP

                             LRR_9 123 npvtn 127
                                       n ++n
  gi|330506767|ref|YP_004383195.1| 154 NKIIN 158
                                       77765 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 3.5e-05
                             LRR_9  41 ldqfdtidlsdndirkldgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkklel 117
                                       l  ++t+ l dn i ++  +  l  l tlll  n+i++++      l nl+ l l+ n++++     Pl  l +l+ 
  gi|330506767|ref|YP_004383195.1| 122 LANLETLSLWDNHITNVS-LSGLTNLDTLLLWGNKIINVSSL--SGLTNLTDLDLSTNQITD---ASPLSGLTNLTD 192
                                       6678999999****9985.788999***********999864..468899999999998875...567777777777 PP

                             LRR_9 118 lsllknpvt 126
                                       l l +n +t
  gi|330506767|ref|YP_004383195.1| 193 LDLDNNQIT 201
                                       777777665 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00013
                             LRR_9  40 tldqfdtidlsdndirkldgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkkle 116
                                        l  +dt+ l  n+i ++ ++  l  l  l l+ n+i+  ++     l nl+ l l nn++++++ l  l++l +l+
  gi|330506767|ref|YP_004383195.1| 142 GLTNLDTLLLWGNKIINVSSLSGLTNLTDLDLSTNQITDASPL--SGLTNLTDLDLDNNQITDVSSLSGLINLMNLD 216
                                       4778999999***************************998874..4689****************999999999987 PP

                             LRR_9 117 ll 118
                                       l 
  gi|330506767|ref|YP_004383195.1| 217 LS 218
                                       64 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.0018
                             LRR_9  47 idlsdndirkldgfPllkrlktlllnnnrivria.egleevlPnleelvltnnelqe 102
                                       +dl++n+i ++ ++  l  l  l l++nri++++  gl     n+  l l +n++++
  gi|330506767|ref|YP_004383195.1| 193 LDLDNNQITDVSSLSGLINLMNLDLSSNRITNVSlSGL----TNVVWLDLWGNQITD 245
                                       67778888888888888888888888888877762233....333333444444443 PP

  == domain 6  score: 15.7 bits;  conditional E-value: 2.6e-06
                             LRR_9  25 dlrgykipvienlGatldqfdtidlsdndirkldgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelq 101
                                       dl g++i+ ++  G t   +  +d+s n+i ++ ++  l  l  l+l  n+i+ ++      l nl+ l l+ n+++
  gi|330506767|ref|YP_004383195.1| 237 DLWGNQITDVTLSGLT--NLTWLDVSRNQIADVSSLSGLTNLTKLYLGCNQITDVSSL--SGLTNLTDLDLSTNQIT 309
                                       6666666666665544..4666899*****************************9864..4689********99986 PP

                             LRR_9 102 eladldPlaslkklellsllkn 123
                                          d  Pl  l +l++l l +n
  gi|330506767|ref|YP_004383195.1| 310 ---DASPLSGLTNLTYLDLDNN 328
                                       ...5678999999999988666 PP

  == domain 7  score: 16.9 bits;  conditional E-value: 1.1e-06
                             LRR_9  46 tidlsdndirkldgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkkle 116
                                        +dls n+i +   +  l  l  l l+nnri  ++      l nl+ l l+nn++++++ l  l++lk+l+
  gi|330506767|ref|YP_004383195.1| 300 DLDLSTNQITDASPLSGLTNLTYLDLDNNRINDVSL---SDLTNLTDLELSNNQINDVSSLSGLTNLKDLD 367
                                       589****************************98873...4689*************************997 PP

  == domain 8  score: 18.5 bits;  conditional E-value: 3.6e-07
                             LRR_9  47 idlsdndirkldgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkklells 119
                                       +dls+n+i+++ ++  l  l  l l++n i++i+  l  +l +l++l l nn++ +++ l  l+slk l+l s
  gi|330506767|ref|YP_004383195.1| 366 LDLSNNQINDISSLSGLTNLTDLELSSNEITNISS-L-SSLASLRCLDLDNNQIIDVSSLSALTSLKWLRLCS 436
                                       699******************************86.3.67999***********9999999999998887654 PP

  == domain 9  score: 13.4 bits;  conditional E-value: 1.3e-05
                             LRR_9  47 idlsdndirkldgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkklellsl 120
                                       +dls n+i ++  +  l  l  l l++n+i+ +++     l nl+ l l++n++++   + Pl +l +l  + l
  gi|330506767|ref|YP_004383195.1| 454 LDLSSNQITDVSPLSGLYNLGWLNLSSNQITDVSPL--SGLANLTGLDLSSNQITD---VSPLSNLTNLIWMDL 522
                                       79*******************************985..4589**********9875...566777776666555 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.4         1     3e+03       1      14 [.      81      94 ..      81     101 .. 0.75
   2 ?    4.0   0.0     0.035   1.1e+02       2      15 ..     104     117 ..     103     123 .. 0.82
   3 ?    3.7   0.5     0.046   1.4e+02       1      18 [.     124     141 ..     124     163 .. 0.83
   4 ?    1.8   0.1       0.2   5.8e+02       1      16 [.     167     182 ..     167     187 .. 0.81
   5 ?    4.9   0.3     0.019        56       1      17 [.     189     205 ..     189     209 .. 0.82
   6 ?    2.7   0.7     0.099   2.9e+02       1      15 [.     211     225 ..     211     251 .. 0.79
   7 ?    3.3   0.0     0.062   1.9e+02       1      14 [.     253     266 ..     253     273 .. 0.78
   8 ?    3.8   0.1     0.041   1.2e+02       1      17 [.     275     291 ..     275     295 .. 0.82
   9 ?    1.8   0.1       0.2   5.8e+02       1      16 [.     297     312 ..     297     317 .. 0.81
  10 ?    7.1   0.6    0.0034        10       1      20 [.     319     338 ..     319     341 .. 0.77
  11 ?    3.0   0.4     0.075   2.2e+02       1      15 [.     340     354 ..     340     360 .. 0.77
  12 ?    7.2   1.3    0.0032       9.7       1      17 [.     362     378 ..     362     382 .. 0.80
  13 ?    2.1   0.8      0.15   4.4e+02       1      18 [.     384     401 ..     384     404 .. 0.82
  14 ?    4.6   2.2     0.023        69       1      19 [.     406     424 ..     406     448 .. 0.87
  15 ?    8.2   0.1    0.0015       4.4       1      17 [.     450     466 ..     450     471 .. 0.87
  16 ?    2.5   0.2      0.12   3.5e+02       4      17 ..     475     488 ..     472     492 .. 0.79
  17 ?    4.7   0.3     0.022        66       1      18 [.     494     511 ..     494     523 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1
                             LRR_1  1 nLrhLdLsnnpllg 14
                                      nL+ L L+ n +++
  gi|330506767|ref|YP_004383195.1| 81 NLENLSLRENEISD 94
                                      8999***9999853 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.035
                             LRR_1   2 LrhLdLsnnpllgl 15 
                                       L++L Ls+n++++ 
  gi|330506767|ref|YP_004383195.1| 104 LKRLELSSNQITDV 117
                                       9*********9765 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.046
                             LRR_1   1 nLrhLdLsnnpllglppn 18 
                                       nL++L L +n++++ + +
  gi|330506767|ref|YP_004383195.1| 124 NLETLSLWDNHITNVSLS 141
                                       8*********99655444 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.2
                             LRR_1   1 nLrhLdLsnnpllglp 16 
                                       nL+ LdLs n++++ +
  gi|330506767|ref|YP_004383195.1| 167 NLTDLDLSTNQITDAS 182
                                       8999******997655 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.019
                             LRR_1   1 nLrhLdLsnnpllglpp 17 
                                       nL+ LdL nn++++ ++
  gi|330506767|ref|YP_004383195.1| 189 NLTDLDLDNNQITDVSS 205
                                       899********976654 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.099
                             LRR_1   1 nLrhLdLsnnpllgl 15 
                                       nL  LdLs+n++++ 
  gi|330506767|ref|YP_004383195.1| 211 NLMNLDLSSNRITNV 225
                                       677899999998543 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.062
                             LRR_1   1 nLrhLdLsnnpllg 14 
                                       nL+ Ld+s+n++ +
  gi|330506767|ref|YP_004383195.1| 253 NLTWLDVSRNQIAD 266
                                       89********9843 PP

  == domain 8  score: 3.8 bits;  conditional E-value: 0.041
                             LRR_1   1 nLrhLdLsnnpllglpp 17 
                                       nL++L+L+ n++++ ++
  gi|330506767|ref|YP_004383195.1| 275 NLTKLYLGCNQITDVSS 291
                                       8**********976554 PP

  == domain 9  score: 1.8 bits;  conditional E-value: 0.2
                             LRR_1   1 nLrhLdLsnnpllglp 16 
                                       nL+ LdLs n++++ +
  gi|330506767|ref|YP_004383195.1| 297 NLTDLDLSTNQITDAS 312
                                       8999******997655 PP

  == domain 10  score: 7.1 bits;  conditional E-value: 0.0034
                             LRR_1   1 nLrhLdLsnnpllglppnsf 20 
                                       nL++LdL nn++ + + +++
  gi|330506767|ref|YP_004383195.1| 319 NLTYLDLDNNRINDVSLSDL 338
                                       8**********966666555 PP

  == domain 11  score: 3.0 bits;  conditional E-value: 0.075
                             LRR_1   1 nLrhLdLsnnpllgl 15 
                                       nL+ L Lsnn++ + 
  gi|330506767|ref|YP_004383195.1| 340 NLTDLELSNNQINDV 354
                                       8999******98443 PP

  == domain 12  score: 7.2 bits;  conditional E-value: 0.0032
                             LRR_1   1 nLrhLdLsnnpllglpp 17 
                                       nL+ LdLsnn++ ++++
  gi|330506767|ref|YP_004383195.1| 362 NLKDLDLSNNQINDISS 378
                                       8**********955544 PP

  == domain 13  score: 2.1 bits;  conditional E-value: 0.15
                             LRR_1   1 nLrhLdLsnnpllglppn 18 
                                       nL+ L Ls+n ++++++ 
  gi|330506767|ref|YP_004383195.1| 384 NLTDLELSSNEITNISSL 401
                                       8999*******9877664 PP

  == domain 14  score: 4.6 bits;  conditional E-value: 0.023
                             LRR_1   1 nLrhLdLsnnpllglppns 19 
                                       +Lr LdL nn++++ ++ s
  gi|330506767|ref|YP_004383195.1| 406 SLRCLDLDNNQIIDVSSLS 424
                                       69*********97766544 PP

  == domain 15  score: 8.2 bits;  conditional E-value: 0.0015
                             LRR_1   1 nLrhLdLsnnpllglpp 17 
                                       nLr LdLs+n++++ +p
  gi|330506767|ref|YP_004383195.1| 450 NLRWLDLSSNQITDVSP 466
                                       8**********988776 PP

  == domain 16  score: 2.5 bits;  conditional E-value: 0.12
                             LRR_1   4 hLdLsnnpllglpp 17 
                                        L+Ls+n++++ +p
  gi|330506767|ref|YP_004383195.1| 475 WLNLSSNQITDVSP 488
                                       69******988776 PP

  == domain 17  score: 4.7 bits;  conditional E-value: 0.022
                             LRR_1   1 nLrhLdLsnnpllglppn 18 
                                       nL+ LdLs+n++++ +p 
  gi|330506767|ref|YP_004383195.1| 494 NLTGLDLSSNQITDVSPL 511
                                       7999*******9877664 PP

>> bZIP_C  Basic leucine-zipper C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.7   5.2e+03      70     106 ..     173     207 ..     155     226 .. 0.53
   2 ?   -1.8   0.0         2   6.1e+03      71     106 ..     260     293 ..     251     313 .. 0.54
   3 ?    4.3   0.3     0.026        79      64     112 ..     340     386 ..     314     395 .. 0.72
   4 ?    7.1   0.2    0.0035        10      66     112 ..     364     408 ..     350     422 .. 0.75
   5 ?   -2.3   0.0       2.8   8.4e+03      75     105 ..     483     511 ..     456     529 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.7
                            bZIP_C  70 vlnnglpdissvelqekadlanaavaagkmgrtasLq 106
                                        + n + d+s+++  ++    +  ++++++ +++sL 
  gi|330506767|ref|YP_004383195.1| 173 LSTNQITDASPLSGLTNL--TDLDLDNNQITDVSSLS 207
                                       455555555555433322..23333445555555553 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2
                            bZIP_C  71 lnnglpdissvelqekadlanaavaagkmgrtasLq 106
                                       + n ++d+ss++  ++    +  +  +++ +++sL 
  gi|330506767|ref|YP_004383195.1| 260 SRNQIADVSSLSGLTNL--TKLYLGCNQITDVSSLS 293
                                       44555555555444433..23333445555555553 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.026
                            bZIP_C  64 taddlqvlnnglpdissvelqekadlanaavaagkmgrtasLqrvasLe 112
                                       + +dl+ +nn + d+ss++  ++   ++  ++++++++++sL   ++L 
  gi|330506767|ref|YP_004383195.1| 340 NLTDLELSNNQINDVSSLSGLTNL--KDLDLSNNQINDISSLSGLTNLT 386
                                       445678889999998888666644..45555667888888886666664 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0035
                            bZIP_C  66 ddlqvlnnglpdissvelqekadlanaavaagkmgrtasLqrvasLe 112
                                       +dl+ +nn + diss++  ++    + +++++++ +++sL + asL 
  gi|330506767|ref|YP_004383195.1| 364 KDLDLSNNQINDISSLSGLTNL--TDLELSSNEITNISSLSSLASLR 408
                                       568999*********9777744..56677788888888887777774 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 2.8
                            bZIP_C  75 lpdissvelqekadlanaavaagkmgrtasL 105
                                       + d+s+++  ++       ++++++ ++++L
  gi|330506767|ref|YP_004383195.1| 483 ITDVSPLSGLANL--TGLDLSSNQITDVSPL 511
                                       3333333222211..1222234444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3582.42
//
Query:       gi|330506768|ref|YP_004383196.1|  [L=280]
Description: phosphate binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-33  116.0   0.0      1e-32  114.0   0.0    1.7  1  PBP_like_2  PBP superfamily domain
    1.5e-18   66.6   0.0    2.1e-18   66.1   0.0    1.2  1  PBP_like    PBP superfamily domain
    2.7e-06   27.3   0.0      5e-05   23.2   0.0    2.0  1  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.0   1.7e-36     1e-32       9     282 .]      28     267 ..      23     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 1.7e-36
                        PBP_like_2   9 vgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangaggl 85 
                                        +++ ++Gs+t+ p+ +  a+ f+  + +++v+++++GSg gi  + +g  ++a+++r l   e  +++++    ++
  gi|330506768|ref|YP_004383196.1|  28 EQKVAISGSSTVMPLAEISAEEFNMLQDNYHVTVTAGGSGVGIVNVVEGRSAIAMTSRELHLVER-QRYETPT-EKF 102
                                       44689********************************************************9999.7777777.99* PP

                        PBP_like_2  86 iqvpvaigaialvvnkd...npln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqg 158
                                         + v+++ai+l+v+++    +++ ls+e+++ I+sg I+nW++ lg+p d+ I  + r +gsgt++ f + ++  +
  gi|330506768|ref|YP_004383196.1| 103 NVITVGYDAICLMVSPEvydFGVTdLSAEEVRRIYSGSISNWKE-LGGP-DEEIFAIGRRPGSGTRDSFDEIIMGSR 177
                                       ***************9967755558******************9.8888.**************************9 PP

                        PBP_like_2 159 pwtasgigasg..segvasavsn.ngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnpla 232
                                         ++ g++++   s++v++a+++ ++aigyv ++y    +g s                       kv+++     +
  gi|330506768|ref|YP_004383196.1| 178 EYETPGVSYEAaeSSEVKTAIRGsDNAIGYVGYSYIM--RGDS-----------------------KVISL-----D 224
                                       9999999977788********888**********999..3444.......................34444.....4 PP

                        PBP_like_2 233 wslqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyllsde 282
                                       + + p+ eni++g+yPl r +y+i+   +      +++akaF dy+ls e
  gi|330506768|ref|YP_004383196.1| 225 G-IPPTIENIKNGTYPLARELYFITLGRP------SPGAKAFTDYVLSPE 267
                                       4.9************************88......************976 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.0   3.5e-22   2.1e-18       1     175 [.      47     249 ..      47     263 .. 0.79

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 3.5e-22
                                       HHHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS..---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCC CS
                          PBP_like   1 aeelaeknpgvrvavanvGsggGlkalrageadiagshl..ldketeeynapalrkaldgievvlvnlarreqglvv 75 
                                       aee++  + +++v+v+  Gsg G+ ++ +g+  ia++++     e ++y++p+ +       + ++++ ++++ l+v
  gi|330506768|ref|YP_004383196.1|  47 AEEFNMLQDNYHVTVTAGGSGVGIVNVVEGRSAIAMTSRelHLVERQRYETPTEK-------FNVITVGYDAICLMV 116
                                       799***********************************96556688889999554.......778999999999999 PP

                                       HCCHHHS.................--BGGGC..-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSH CS
                          PBP_like  76 akgnpkk.................itnwkdl..adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearsh 133
                                        ++                     i+nwk+l  +d+++  ++R  GSGtrd fde + +   ++ + +g++ ea ++
  gi|330506768|ref|YP_004383196.1| 117 SPEVYDFgvtdlsaeevrriysgsISNWKELggPDEEIFAIGRRPGSGTRDSFDEIIMG--SREYETPGVSYEAAES 191
                                       999444145666667777788888*********************************55..68899*********** PP

                                       HHHHCCHCCETTCCE.................CCCGG-HCCCCCCECTTCE-EEEEEEE CS
                          PBP_like 134 lavaaaVaagradvg.................vgieavaeelkgldfvplaeerydlvv 175
                                       ++v++a++  + ++g                  gi ++ e++k+ +  pla+e y++ +
  gi|330506768|ref|YP_004383196.1| 192 SEVKTAIRGSDNAIGyvgysyimrgdskvislDGIPPTIENIKN-GTYPLARELYFITL 249
                                       ***************77777777666666443122222223322.22377777777655 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   8.3e-09     5e-05      11     229 ..      40     277 ..      31     278 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8.3e-09
                                       HHHHHH.HHHH.HHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEEEEEEEE CS
                        SBP_bac_11  11 aalrel.aaaF.eahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplassplviav 85 
                                        +l+e+ a++F + + + +v+v+aggsg  +  + +g+ + ++ +     +e+ + +  + + +  ++ +  ++++v
  gi|330506768|ref|YP_004383196.1|  40 MPLAEIsAEEFnMLQDNYHVTVTAGGSGVGIVNVVEGRSAIAMTSRELHLVERQRYETPTEKFNVITVGYDAICLMV 116
                                       44555439999777999********************9999999999888888888999998999999********* PP

                                       STT-T.................T---SHHHHHHSS--.EEEE--T-TTTTH..H.HHHHGGG--HHHHHHH.HHTEE CS
                        SBP_bac_11  86 pkgnp.................kkikgwadLlkpglk.lavadPttspsGl..aalalleaagaqellkal.ekkvv 141
                                        ++ +                  +i++w++L++p+ + +a+    + +sG+     +++  +       +    +v 
  gi|330506768|ref|YP_004383196.1| 117 SPEVYdfgvtdlsaeevrriysGSISNWKELGGPDEEiFAIGR--RPGSGTrdSFDEIIMGSR------EYeTPGVS 185
                                       ****433344444444444333467788888888774366665..344443224444443322......22023444 PP

                                       EEESSHHHHHHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--....EEEEE....EEE-TT--HHHHHHHH CS
                        SBP_bac_11 142 klgessrqlltaveageadagivyeseakaaengdkleavylpeglnl.dpldypaa....vlkkaakreaAraFla 213
                                        ++  s+ + ta++  + ++g v  s ++ ++ ++ +++  +p+++   +  +yp+a     ++ ++ +  A+aF +
  gi|330506768|ref|YP_004383196.1| 186 YEAAESSEVKTAIRGSDNAIGYVGYSYIM-RGDSKVISLDGIPPTIENiKNGTYPLArelyFITLGRPSPGAKAFTD 261
                                       45556688888888888888888888887.3444445444888888765655555551111455556678******* PP

                                       HTTSHHHHHHHHHTT- CS
                        SBP_bac_11 214 fLrspeaqailrkyGf 229
                                       +++spe+q+i+ ++Gf
  gi|330506768|ref|YP_004383196.1| 262 YVLSPEGQKIAIENGF 277
                                       ***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1886.25
//
Query:       gi|330506769|ref|YP_004383197.1|  [L=73]
Description: hypothetical protein MCON_0540 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.4   0.0      0.016   14.2   0.0    1.0  1  DUF2156    Uncharacterised conserved protein (DUF2156)
      0.028   14.0   0.0      0.031   13.8   0.0    1.1  1  AHJR-like  REase_AHJR-like
      0.032   14.7   0.0      0.038   14.5   0.0    1.1  1  NYN        NYN domain
      0.061   13.3   0.0      0.093   12.7   0.0    1.2  1  Slx4       Slx4 endonuclease
       0.13   10.6   0.0       0.15   10.5   0.0    1.0  1  IDH        Monomeric isocitrate dehydrogenase


Domain annotation for each model (and alignments):
>> DUF2156  Uncharacterised conserved protein (DUF2156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.6e-06     0.016     114     146 ..      26      58 ..      23      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-06
                                       GGHHHHHHHHHHHHCTECEEEEEGGGH-HHHHH CS
                           DUF2156 114 kfrnvRnainraeraGytveverisdlspella 146
                                       ++ + R  inr e +Gy+vev + + +spe++ 
  gi|330506769|ref|YP_004383197.1|  26 AMSQFRDLINRLEDDGYQVEVIPRNRMSPEEIR 58 
                                       5899********************999887765 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.6e-06     0.031       3      50 ..      20      66 ..      18      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.6e-06
                         AHJR-like  3 tstselererleslaeqyrekGyevllhPnredlPdfLksYrpDliar 50
                                      t++ ++   ++ +l++ +++ Gy+v + P +   P+ ++ +  D ia+
  gi|330506769|ref|YP_004383197.1| 20 TKQIKVAMSQFRDLINRLEDDGYQVEVIPRNRMSPEEIRAF-CDRIAT 66
                                      5667788899*************************999988.466665 PP

>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     1e-05     0.038     106     142 ..      28      63 ..      18      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                               NYN 106 gDFaplveklrergkrVevllaeeastsseLisaade 142
                                       + F +l+++l   g++Vev+  +++++++e ++ +d+
  gi|330506769|ref|YP_004383197.1|  28 SQFRDLINRLEDDGYQVEVIP-RNRMSPEEIRAFCDR 63 
                                       67******************9.668999999999997 PP

>> Slx4  Slx4 endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.6e-05     0.093      26      54 ..      30      63 ..      29      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                                      HHHHHHHHHHH-GGGG.....GS-HHHHHHHHHH CS
                              Slx4 26 LedltawLnteglglk.....evdpaelrewcds 54
                                      + dl+  L+++g +++     +++p+e+r++cd+
  gi|330506769|ref|YP_004383197.1| 30 FRDLINRLEDDGYQVEviprnRMSPEEIRAFCDR 63
                                      689********99998*****************6 PP

>> IDH  Monomeric isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.1e-05      0.15      71     115 ..       8      56 ..       2      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.1e-05
                                       STT-EEEE-----....B-HHHHHHHHHHHHTTT-------SS-SSHHH CS
                               IDH  71 kpeaniiklPnis....asvpqlkaaikeLqekGyklpdypeepktdee 115
                                       +++  i+k+P+i      +++q+++ i+ L+++Gy++   p++  + ee
  gi|330506769|ref|YP_004383197.1|   8 SAKIVILKVPDITkqikVAMSQFRDLINRLEDDGYQVEVIPRNRMSPEE 56 
                                       5567789***98722225678*****************99999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 557.58
//
Query:       gi|330506770|ref|YP_004383198.1|  [L=68]
Description: hypothetical protein MCON_0541 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0099   15.9   1.1      0.027   14.5   1.1    1.7  2  zinc_ribbon_6   Zinc-ribbon
  ------ inclusion threshold ------
      0.052   13.6   3.3       0.12   12.4   3.3    1.6  1  DZR             Double zinc ribbon
       0.11   12.4   4.2       0.17   11.8   3.6    1.6  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.27   11.2   3.1       0.66   10.0   3.1    1.7  1  zinc_ribbon_4   zinc-ribbon domain
       0.32   10.6   2.9       0.66    9.6   0.2    2.0  2  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.1   7.4e-06     0.027      26      53 ..      25      55 ..      18      57 .. 0.81
   2 ?    1.0   0.1      0.13   4.5e+02      30      38 ..      50      58 ..      46      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.4e-06
                     zinc_ribbon_6 26 kkvkilCnDCekksevkfhvlglk...CkeC 53
                                      ++++++C  C+k+++v+f+  g +   C+eC
  gi|330506770|ref|YP_004383198.1| 25 EMTDVTCSECGKQTQVPFKPDGSRpvyCSEC 55
                                      6789***************999763336666 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                     zinc_ribbon_6 30 ilCnDCekk 38
                                      ++C  C +k
  gi|330506770|ref|YP_004383198.1| 50 VYCSECYQK 58
                                      789999887 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   3.4e-05      0.12      12      40 ..      28      61 ..      21      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                               DZR 12 arfCseCgtklkavaa.....edrCpsCgekvdp 40
                                      + +CseCg++ + + +     +  C++C +k  p
  gi|330506770|ref|YP_004383198.1| 28 DVTCSECGKQTQVPFKpdgsrPVYCSECYQKHRP 61
                                      5689999999875555788889999999887554 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.6   4.8e-05      0.17      25      55 ..      25      58 ..      16      60 .. 0.85
   2 ?    4.5   0.6    0.0094        34      30      46 ..      51      67 ..      47      68 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
                    OrfB_Zn_ribbon 25 ayTSktCseCgsknke...alsgrtfkCpnCgfe 55
                                      + T  tCseCg++ +    ++ +r ++C++C  +
  gi|330506770|ref|YP_004383198.1| 25 EMTDVTCSECGKQTQVpfkPDGSRPVYCSECYQK 58
                                      45889*******99999999999********766 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0094
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrt 46
                                       CseC +k+++a+++r+
  gi|330506770|ref|YP_004383198.1| 51 YCSECYQKHRPAKTSRR 67
                                      6*******999666665 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.1   0.00018      0.66       3      33 ..      29      57 ..      26      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00018
                     zinc_ribbon_4  3 itCpsCkakyeiddeklpakgvkvrCskCgh 33
                                      +tC +C+++ +++ +  p++ + v Cs C +
  gi|330506770|ref|YP_004383198.1| 29 VTCSECGKQTQVPFK--PDGSRPVYCSECYQ 57
                                      89***********98..99999*******87 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00018      0.66       2      12 ..      28      38 ..      27      44 .. 0.81
   2 ?    1.5   0.2     0.062   2.2e+02       4      10 ..      51      57 ..      49      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00018
                            zf_UBZ  2 tylCerCgkei 12
                                       ++C++Cgk+ 
  gi|330506770|ref|YP_004383198.1| 28 DVTCSECGKQT 38
                                      589******85 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.062
                            zf_UBZ  4 lCerCgk 10
                                       C++C +
  gi|330506770|ref|YP_004383198.1| 51 YCSECYQ 57
                                      6****65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 526.77
//
Query:       gi|330506771|ref|YP_004383199.1|  [L=396]
Description: GTP-binding/TGS domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-29  100.5   0.0      1e-28   99.5   0.0    1.6  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    1.4e-21   76.7   0.0    3.1e-21   75.6   0.0    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
    4.4e-17   61.9   0.0    8.9e-17   60.9   0.0    1.5  1  TGS           TGS domain
    4.7e-15   55.5   0.0    4.6e-13   49.0   0.0    2.3  2  FeoB_N        Ferrous iron transport protein B
    6.6e-05   23.0   1.5      0.043   13.9   0.2    2.9  3  Dynamin_N     Dynamin family
    0.00023   21.1   0.3      0.043   13.7   0.4    2.6  2  RsgA_GTPase   RsgA GTPase
     0.0065   15.9   0.9      0.051   13.0   0.0    2.5  3  SRPRB         Signal recognition particle receptor beta subun
  ------ inclusion threshold ------
      0.012   15.0   0.6      0.019   14.3   0.0    1.6  2  AIG1          AIG1 family
      0.023   14.9   0.0      0.052   13.7   0.0    1.4  1  MnmE_helical  MnmE helical domain
      0.038   13.8   0.7      0.059   13.2   0.7    1.2  1  DUF724        Protein of unknown function (DUF724)
       0.11   11.1   0.1       0.16   10.5   0.1    1.1  1  DUF5357       Family of unknown function (DUF5357)
        1.9    8.8   6.7          8    6.8   6.7    2.0  1  ABC_tran_CTD  ABC transporter C-terminal domain
        2.6    8.2   6.2        5.9    7.1   0.5    2.3  2  bZIP_2        Basic region leucine zipper
        4.7    7.3   7.2         17    5.5   7.2    1.7  1  FlxA          FlxA-like protein


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.5   0.0   7.9e-32     1e-28       1     105 [.     212     318 ..     212     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 7.9e-32
                      MMR_HSR1_Xtn   1 kgGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldela 77 
                                       kgGi ++stv+lt+++e ++ +i++ y+i+na+v++red+++D l+d+++gnrvYip+l+++NK Dl      d+++
  gi|330506771|ref|YP_004383199.1| 212 KGGIIVRSTVPLTRMTEFEIAEIIRAYGIVNANVTVREDIDTDTLVDFLAGNRVYIPSLVAINKFDLRYGGIEDKIE 288
                                       69*****************************************************************8888888888 PP

                      MMR_HSR1_Xtn  78 re..pnsvviSaekelnldeLkekiweeLn 105
                                       ++  +++++iS+++  +l+eLk++i+e+L+
  gi|330506771|ref|YP_004383199.1| 289 EDlgRDYLPISCATTEGLEELKDHIYETLG 318
                                       865689*********************997 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.0   2.4e-24   3.1e-21       2     100 ..      95     194 ..      94     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 2.4e-24
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.ad 77 
                                       va+vG p vGKS+L+n ltg+k++v+++++tT++++ g +k+kg ei+++D+pG+i+ga ++kg g+++    + ad
  gi|330506771|ref|YP_004383199.1|  95 VALVGFPSVGKSSLLNYLTGSKSEVAAYQFTTLEVIPGVMKHKGAEIQILDMPGIIKGAARGKGRGREVITAARaAD 171
                                       9****************************************999*******************9999999888857* PP

                                       EEEEEEETTTTCSHHHHHHHHHH CS
                          MMR_HSR1  78 lillvvdaseeklkpldeeleel 100
                                       +ill+ d+ + +lk l++el e 
  gi|330506771|ref|YP_004383199.1| 172 MILLLGDVFNYNLKVLERELYEA 194
                                       *******8855666666666555 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   6.9e-20   8.9e-17       1      60 []     320     393 ..     320     393 .. 0.99

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 6.9e-20
                                       EEEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEEE CS
                               TGS   1 irvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIvt 60 
                                       ir+y+ P+G + d      l  g+tv+ ++ ++hr++++ f+yAlV+G       q  gldh+L+d dv++I+t
  gi|330506771|ref|YP_004383199.1| 320 IRIYLkPKGGKADleeplvLLDGSTVKSVCEHLHRDFVNLFRYALVWGksakfpgQSIGLDHELQDCDVLSIIT 393
                                       89**********************************************************************98 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   3.6e-16   4.6e-13       2      58 ..      94     150 ..      93     197 .. 0.82
   2 ?    4.2   0.0     0.022        28     109     156 .]     270     313 ..     262     313 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 3.6e-16
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----S CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiY 58 
                                       tvalvG p vGk++l+n ltg+k++v+ ++ +t e   g +k+kg e++i+D+PGi 
  gi|330506771|ref|YP_004383199.1|  94 TVALVGFPSVGKSSLLNYLTGSKSEVAAYQFTTLEVIPGVMKHKGAEIQILDMPGII 150
                                       79*****************************************************94 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.022
                                       EEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N 109 vlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellkai 156
                                       ++a+n++d  +  gi   ++k++e Lg + +++s +++eg+eel+++i
  gi|330506771|ref|YP_004383199.1| 270 LVAINKFDL-RYGGI---EDKIEEDLGRDYLPISCATTEGLEELKDHI 313
                                       556666653.33333...4789***********************986 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2       1.3   1.7e+03      60      90 ..      25      55 ..      15      73 .. 0.66
   2 !   13.9   0.2   3.4e-05     0.043       1      23 [.      95     117 ..      95     131 .. 0.83
   3 !    7.0   0.0    0.0044       5.7     101     135 ..     139     176 ..     128     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
                                      -EB--CHHHHHHHHHHHHHHHTSSSS--SS- CS
                         Dynamin_N 60 kkledfsevreeieketekiagankgiskkv 90
                                      k+ +++  ++e+i++ +e+i +++k+  ++ 
  gi|330506771|ref|YP_004383199.1| 25 KRKYKMATIEEQIKALEEEIFNTQKNKATEH 55
                                      5566777777777777777776555555443 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.4e-05
                                       EEEEEBTTTTHHHHHHHHHTS-- CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedi 23 
                                       +a+vG  S GKSS+ln L+g++ 
  gi|330506771|ref|YP_004383199.1|  95 VALVGFPSVGKSSLLNYLTGSKS 117
                                       799*****************985 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0044
                                       -SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEE CS
                         Dynamin_N 101 kgltlvDlPGldsvnkrdq...elvkeyikkadiilav 135
                                        ++ ++D+PG+++ ++r +   + v ++++ ad+il++
  gi|330506771|ref|YP_004383199.1| 139 AEIQILDMPGIIKGAARGKgrgREVITAARAADMILLL 176
                                       6799***********99998887777778888999886 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.4   3.3e-05     0.043      96     123 ..      89     116 ..      24     149 .. 0.77
   2 ?    4.8   0.0     0.018        23      28      99 ..     249     315 ..     217     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                                       HCTTSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallpel 123
                                       +  d t++lvG   vGKS+L+n l++++
  gi|330506771|ref|YP_004383199.1|  89 KSGDATVALVGFPSVGKSSLLNYLTGSK 116
                                       4456899*****************9973 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.018
                                       TT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  28 pelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd 99 
                                       +++++++l  fL+  ++  i+ ++++nK Dl           +  e+lg + l +s  t+egleelk+++ +
  gi|330506771|ref|YP_004383199.1| 249 EDIDTDTLVDFLAG-NRVYIPSLVAINKFDLRYGGI----EDKIEEDLGRDYLPISCATTEGLEELKDHIYE 315
                                       55666666666654.45568999********88877....44555678888999999999******998865 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 ?   -0.7   0.7      0.66   8.4e+02     121     150 ..      25      53 ..      17      74 .. 0.79
   2 !   13.0   0.0     4e-05     0.051       4      59 ..      93     149 ..      90     155 .. 0.80
   3 ?   -1.6   0.0       1.2   1.5e+03     112     140 ..     266     294 ..     253     313 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.66
                                       -TTSTT---HHHHHHHHHHHHHHHHHCHHH CS
                             SRPRB 121 KqelflakspklikdaLEkElnkiierrsk 150
                                       K    +a  ++ ik aLE+E+ + +++++ 
  gi|330506771|ref|YP_004383199.1|  25 KRKYKMATIEEQIK-ALEEEIFNTQKNKAT 53 
                                       66778888888997.899999888887765 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4e-05
                                       -EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT- CS
                             SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGh 59 
                                        +v lvG    GK sl++ Lt  + + +       ++   v ++kg +++++D+PG 
  gi|330506771|ref|YP_004383199.1|  93 ATVALVGFPSVGKSSLLNYLTGSKSEVAAYQFtTLEVIPGVMKHKGAEIQILDMPGI 149
                                       5799****************98755544444436666677789************95 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.2
                                       ---EEEEEE-TTSTT---HHHHHHHHHHH CS
                             SRPRB 112 avdiliACnKqelflakspklikdaLEkE 140
                                        ++ l+A nK +l     + +i + L ++
  gi|330506771|ref|YP_004383199.1| 266 YIPSLVAINKFDLRYGGIEDKIEEDLGRD 294
                                       577899******99999999999888665 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.4       5.4   6.9e+03     171     200 ..      34      63 ..      25      72 .. 0.55
   2 ?   14.3   0.0   1.5e-05     0.019       2      89 ..      94     175 ..      93     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 5.4
                                       HHHHHHHHHHHHHHHHHTTTT--B-HHHHH CS
                              AIG1 171 eeQvkellelveaivkenggkpytnelyek 200
                                       eeQ k l e + + +k++  +++  +++ k
  gi|330506771|ref|YP_004383199.1|  34 EEQIKALEEEIFNTQKNKATEHHLGKIKAK 63 
                                       455555555555555555555555555444 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.5e-05
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrcll 78 
                                       t+ lvG   +GkS+  N + g+k        q  t ++   + + +g +i++ D Pg++   ++ +   +e++    
  gi|330506771|ref|YP_004383199.1|  94 TVALVGFPSVGKSSLLNYLTGSKSEVAA--YQFTTLEVIPGVMKHKGAEIQILDMPGIIKGAARGKGRGREVIT--- 165
                                       788******************9864444..5777888999999******************9999999999985... PP

                                       HCTT-ESEEEE CS
                              AIG1  79 lseegihalll 89 
                                        ++   +++ll
  gi|330506771|ref|YP_004383199.1| 166 -AARAADMILL 175
                                       .3344444444 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.1e-05     0.052      46     130 ..      31     315 ..      26     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                      MnmE_helical  46 aeleaaiDFpeed.leelseeelaekleelkeelekllatakrgellreGik......................... 96 
                                       a +e +i   ee+  +  ++++ ++ l ++k+++ kl a+ + +++   G                           
  gi|330506771|ref|YP_004383199.1|  31 ATIEEQIKALEEEiFNTQKNKATEHHLGKIKAKIAKLRAQQELQKIKGGGGGrryyikksgdatvalvgfpsvgkss 107
                                       56666666667663444455578888999999999999999988877766558999999999999999999999999 PP

                                       ............................................................................. RF
                      MnmE_helical  97 ............................................................................. 96 
                                                                                                                    
  gi|330506771|ref|YP_004383199.1| 108 llnyltgsksevaayqfttlevipgvmkhkgaeiqildmpgiikgaargkgrgrevitaaraadmilllgdvfnynl 184
                                       99999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       ............................................................................. RF
                      MnmE_helical  97 ............................................................................. 96 
                                                                                                                    
  gi|330506771|ref|YP_004383199.1| 185 kvlerelyeagirldkqppnihitqerkggiivrstvpltrmtefeiaeiiraygivnanvtvredidtdtlvdfla 261
                                       9999999999999****************************************************999999999999 PP

                                       .......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      MnmE_helical  97 .......................DllkekeekeeeevlkiSaktgegieeLeeaike 130
                                                              D   + ee+   + l iS++t eg+eeL+++i e
  gi|330506771|ref|YP_004383199.1| 262 gnrvyipslvainkfdlryggieD---KIEEDLGRDYLPISCATTEGLEELKDHIYE 315
                                       999999999988888777775554...44466777788*****************87 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7   4.6e-05     0.059     101     150 ..      27      75 ..      21      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                            DUF724 101 kdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk 150
                                       k + + ++e++k+le++i + +++k+  e+++ +++ ki++l+ q++l k
  gi|330506771|ref|YP_004383199.1|  27 KYKMATIEEQIKALEEEIFNTQKNKA-TEHHLGKIKAKIAKLRAQQELQK 75 
                                       5567889************8888666.8****************999877 PP

>> DUF5357  Family of unknown function (DUF5357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00012      0.16     226     289 ..      31      90 ..      26      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                           DUF5357 226 leadkevkslgkqvldknlekveEkklWrvearvvnlksgYkldllsiWkGpssnakgyylkKs 289
                                        ++++++k l++++++++ +k +E++l +++a++ +l+ + +l+ +    G     + yy+kKs
  gi|330506771|ref|YP_004383199.1|  31 ATIEEQIKALEEEIFNTQKNKATEHHLGKIKAKIAKLRAQQELQKI--KGGG--GGRRYYIKKS 90 
                                       56899********************************887777643..3332..2456666666 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   6.7    0.0063         8       5      56 ..      25      70 ..      22      76 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0063
                      ABC_tran_CTD  5 keqreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleae 56
                                      k + +++++e++I aLEeei + ++  a +        l ++ a++++l+a+
  gi|330506771|ref|YP_004383199.1| 25 KRKYKMATIEEQIKALEEEIFNTQKNKATEHH------LGKIKAKIAKLRAQ 70
                                      78888999999999999999999987776553......44444444444443 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.5    0.0046       5.9      22      41 ..      25      44 ..      24      45 .. 0.94
   2 ?    3.7   0.8     0.051        65      25      50 ..      48      73 ..      47      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0046
                                      HHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2 22 kkkakeeeleervkeLeeeN 41
                                      k+k k++ +ee++k Leee+
  gi|330506771|ref|YP_004383199.1| 25 KRKYKMATIEEQIKALEEEI 44
                                      9*****************96 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.051
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2 25 akeeeleervkeLeeeNaqLrqkveq 50
                                      +k++ +e+ + + ++++a+Lr+++e 
  gi|330506771|ref|YP_004383199.1| 48 QKNKATEHHLGKIKAKIAKLRAQQEL 73
                                      78999***************999985 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   7.2     0.013        17      47      89 ..      26      68 ..      21      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                              FlxA 47 kkkqqqliqaQIqqlqaQIaqlqqqqaekaqekqqsekeeksk 89
                                      +k +  +i++QI++l+ +I   q+ +a +    + ++k +k +
  gi|330506771|ref|YP_004383199.1| 26 RKYKMATIEEQIKALEEEIFNTQKNKATEHHLGKIKAKIAKLR 68
                                      6778899999999999999999999999988777776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      783  (0.0436723); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 2695.68
//
Query:       gi|330506772|ref|YP_004383200.1|  [L=238]
Description: hypothetical protein MCON_0543 [Methanosaeta concilii GP6]
Scores for complete 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   27.0   0.0    5.1e-05   23.4   0.0    2.0  2  Cas_Cas4  Domain of unknown function DUF83
     0.0001   22.3   0.0    0.00024   21.1   0.0    1.6  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily
     0.0044   16.4   0.0     0.0055   16.1   0.0    1.2  1  Csa1      CRISPR-associated exonuclease Csa1


Domain annotation for each model (and alignments):
>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.042   2.5e+02       2      19 ..       7      24 ..       6      35 .. 0.84
   2 !   23.4   0.0   8.5e-09   5.1e-05      81     160 ..     148     227 ..      79     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.042
                          Cas_Cas4  2 gtkiqyyliCkrklwlis 19
                                      +++i+ yl C+r +++ s
  gi|330506772|ref|YP_004383200.1|  7 ISDISLYLRCPRLVYFDS 24
                                      6899**********9966 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 8.5e-09
                          Cas_Cas4  81 aaklQllyYlllLe.kkgveikeGvleypkekkreevelteelreelekaikeieeiissekppkvkkkkiCkkCay 156
                                        ++l l  Y llL  k++++++ G +eyp+    ++v +  +++ ++ ++ ++++ i + + p++++  + C++C  
  gi|330506772|ref|YP_004383200.1| 148 RDRLMLAGYSLLLGeKENIKVDWGQVEYPSLGMVRRVPVRSTDKARVLRIRDRVRLIKNGQLPDRPEG-SPCQSCHA 223
                                       347888999999998***************************************99999876666665.66*****9 PP

                          Cas_Cas4 157 aelC 160
                                       + +C
  gi|330506772|ref|YP_004383200.1| 224 QTMC 227
                                       9999 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 !   21.1   0.0     4e-08   0.00024       5     255 .]       8     228 ..       5     228 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4e-08
                          PDDEXK_1   5 srletfleCplrfflryllglreeeeleapdlGtlvHaaleefyewkkldkedleelleeaveelwpellleeeile 81 
                                       s ++ +l+Cp+  ++ +l +l++ ++ ++     l+ +++  + ++++l+++ +e+l + +ve  +  +l++ e+  
  gi|330506772|ref|YP_004383200.1|   8 SDISLYLRCPRLVYFDSLGKLPRFSSAKQ----ILMRSLALSLLQKDDLEGQLREALGRLEVELPLIYDLEPGEL-- 78 
                                       78999****************99777777....455555544444455666666666655555444444444444.. PP

                          PDDEXK_1  82 ssarlrylaeklkevleklverlaeeleakrgfrpvalelefggekvrLkGriDrvddkegelriiDyKtgsappks 158
                                            +   +++ e + ++v+ l+ +  +     p++ e+e  +ek+ L Gr+Dr+   +    ii   tg++p   
  gi|330506772|ref|YP_004383200.1|  79 -----QAALNEADEEIGSMVNGLKGWMDQLI---PFEAEVELYSEKLGLSGRLDRLAPGDT-PSII--RTGRPP--- 141
                                       .....77777778888888887777665554...55666555556777********86666.7776..599944... PP

                          PDDEXK_1 159 kelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkkmalteeeleallqeleelaeeilag 235
                                       ++  + +++l l+ Y l+l e+e+ k +   +++ y +         + v++++  +++ +++l +++++++ i++g
  gi|330506772|ref|YP_004383200.1| 142 ENGIWKRDRLMLAGYSLLLGEKENIKVD--WGQVEYPS--------LGMVRRVPVRSTDKARVL-RIRDRVRLIKNG 207
                                       44338999999********999433322..34444444........478888877777776666.57777899**** PP

                          PDDEXK_1 236 efparpskk.CeyCpyksvCr 255
                                       + p rp+   C++C  +  C+
  gi|330506772|ref|YP_004383200.1| 208 QLPDRPEGSpCQSCHAQTMCE 228
                                       *******889**********6 PP

>> Csa1  CRISPR-associated exonuclease Csa1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   9.2e-07    0.0055     159     273 ..     100     210 ..      63     230 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.2e-07
                              Csa1 159 aarviPvlvefkvdGsllGlsslvrvDafililplvvel....kvgsykeehelalaGYalalEsqleiPvDfGvli 231
                                       + + iP+ +e+++    lGls+++   a     p ++        g +k++ +l laGY+l l  +++i vD G + 
  gi|330506772|ref|YP_004383200.1| 100 MDQLIPFEAEVELYSEKLGLSGRLDRLA-PGDTPSIIRTgrppENGIWKRD-RLMLAGYSLLLGEKENIKVDWGQVE 174
                                       56789****************8887666.4455555543222235667666.**********************764 PP

                              Csa1 232 svtvngevklkaelvaisdslRkefleeRdraidivekesDP 273
                                       +  +       ++ v++  + + + l  Rdr+ +++++++ P
  gi|330506772|ref|YP_004383200.1| 175 YPSL-----GMVRRVPVRSTDKARVLRIRDRV-RLIKNGQLP 210
                                       4332.....33344444444455556666654.555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1729.67
//
Query:       gi|330506773|ref|YP_004383201.1|  [L=506]
Description: LysM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.046   13.8   0.0    1.9  1  LysM      LysM domain
      0.025   14.2   0.1       0.12   12.0   0.1    1.9  2  DUF4131   Domain of unknown function (DUF4131)
        1.9    8.4   4.1         23    4.9   0.3    2.7  2  ANTAR     ANTAR domain


Domain annotation for each model (and alignments):
>> LysM  LysM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.6e-06     0.046       1      44 []     260     308 ..     260     308 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.6e-06
                                       EEE-TT--HHHHHHHC......TCHHHHHHHHC.TCSSCGG--TTEEEEEE CS
                              LysM   1 YtVkkGDTLwsIAkry......gitveklleaN.nlsspdkifpGqkLkiP 44 
                                       +++++GD +w +A  y        t e+ +++N  ++  + ++pGq++ +P
  gi|330506773|ref|YP_004383201.1| 260 HKIRPGDRVWYLAEDYgysdrkRFT-EDVKKLNpAINFKT-LRPGQTINVP 308
                                       799*************999997666.89*****9888888.*******998 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.18   1.1e+03     118     128 ..     258     270 ..     249     279 .. 0.77
   2 ?   12.0   0.1   2.1e-05      0.12     118     145 ..     294     324 ..     280     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.18
                           DUF4131 118 e..glrpGdrlrl 128
                                       +  ++rpGdr++ 
  gi|330506773|ref|YP_004383201.1| 258 TahKIRPGDRVWY 270
                                       3459*******96 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.1e-05
                           DUF4131 118 e...glrpGdrlrltgrlkrprpatNpggFD 145
                                           +lrpG+++ + +++  p++ + p++FD
  gi|330506773|ref|YP_004383201.1| 294 InfkTLRPGQTINVPTKIGVPESLRPPYAFD 324
                                       14457************************** PP

>> ANTAR  ANTAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3    0.0038        23      33      52 ..     403     422 ..     392     422 .. 0.93
   2 ?    3.9   0.3    0.0078        47      26      43 ..     448     465 ..     443     470 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0038
                                       HHHHHHHCTTTS-HHHHHHH CS
                             ANTAR  33 rlLrklSmdsnvklrevAea 52 
                                       r+L+++S + n++   vA+a
  gi|330506773|ref|YP_004383201.1| 403 RWLQRTSDQLNRRPLAVAAA 422
                                       8****************986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0078
                                       --HHHHHHHHHHHHCTTT CS
                             ANTAR  26 lsedeAfrlLrklSmdsn 43 
                                        ++ +A r+L++ +++++
  gi|330506773|ref|YP_004383201.1| 448 FDAMDALRWLERDAQQRR 465
                                       57889***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3377.64
//
Query:       gi|330506774|ref|YP_004383202.1|  [L=242]
Description: hypothetical protein MCON_0545 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1644.58
//
Query:       gi|330506775|ref|YP_004383203.1|  [L=437]
Description: hypothetical protein MCON_0546 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.21s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 3123.00
//
Query:       gi|330506776|ref|YP_004383204.1|  [L=211]
Description: hypothetical protein MCON_0547 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1519.43
//
Query:       gi|330506777|ref|YP_004383205.1|  [L=777]
Description: hypothetical protein MCON_0548 [Methanosaeta concilii GP6]
Scores for 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  105.6   0.0    6.6e-30  104.5   0.0    1.6  2  Helicase_C_2  Helicase C-terminal domain
    2.5e-14   53.3   0.0    5.4e-14   52.2   0.0    1.7  1  DEAD_2        DEAD_2
    3.2e-07   30.5   0.0     0.0028   17.7   0.0    2.4  2  ResIII        Type III restriction enzyme, res subunit
    2.2e-05   24.2   0.0    5.7e-05   22.9   0.0    1.7  2  HBB           Helical and beta-bridge domain
    0.00037   20.9   0.3      0.012   16.0   0.0    2.9  3  AAA_16        AAA ATPase domain
    0.00065   19.5   0.1       0.51   10.1   0.0    2.5  2  DEAD          DEAD/DEAH box helicase
    0.00065   20.0   0.2       0.23   11.7   0.0    2.6  2  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.049   13.3   0.0        0.1   12.2   0.0    1.4  1  PAR1          PAR1 protein
       0.51   10.8   2.3         41    4.6   0.0    2.9  2  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 !  104.5   0.0   3.3e-33   6.6e-30       2     170 ..     509     682 ..     508     683 .. 0.90
   2 ?   -3.6   0.0       5.6   1.1e+04     149     167 ..     685     703 ..     684     704 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 3.3e-33
                      Helicase_C_2   2 lellevvpggvlvffpSyklleevverlkeeleskkieifvee.keesrekvleeyke.kkkkgaillavcrGklsE 76 
                                        +l+e+vpg+v vff+Sy ++++ +++  ++  + ++++ ve+ ++ +  ++l+ + +   + g +l +vc+Gkl E
  gi|330506777|ref|YP_004383205.1| 509 RSLIECVPGNVAVFFTSYPMMNNYRDVCLSSSRKVGKKLCVEPrSADQVPELLDLFFSlGARGGGVLTGVCGGKLAE 585
                                       6799***********************99999999999999997888999****99995599*************** PP

                      Helicase_C_2  77 GidfsddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDe 153
                                       Gid+++++l+ v +vglP+  +++ + e+   y  ++gk +++  +y+ +a+++  Qa+GR+iR + ++g+++++D+
  gi|330506777|ref|YP_004383205.1| 586 GIDYKGEALKGVAVVGLPLSAYDEIQKEINSYYTMKYGKIKGMLIAYTLPAINRGLQAAGRVIRAESERGVLLFCDR 662
                                       ********************99998877777777777776667789******************************* PP

                      Helicase_C_2 154 Rfakee...ireklpkwlre 170
                                       Rf  ++   +++ lp w+re
  gi|330506777|ref|YP_004383205.1| 663 RFGYDDlggVNQFLPGWVRE 682
                                       **986633367888888886 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.6
                      Helicase_C_2 149 vllDeRfakeeireklpkw 167
                                       +l+D R   e i+ek+ kw
  gi|330506777|ref|YP_004383205.1| 685 ILVDAREGGELIQEKIAKW 703
                                       89**************999 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   2.7e-17   5.4e-14       2     174 ..      62     271 ..      61     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2.7e-17
                                       EESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCH........ CS
                            DEAD_2   2 csRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeek........ 70 
                                       ++RT+sq++ +++e++++ s +  ++k ++  + +++++C  e   +    ++v + C +l++ +++          
  gi|330506777|ref|YP_004383205.1|  62 AVRTVSQIDIYIDEINRIWSKT--RHKPEIAYMVGKQRICPLEGEFR---AESVYAGCLRLREWTKNYVsskigkgn 133
                                       68****************7544..578899999*******7654444...4667788888776554333677999** PP

                                       ..................TTTTTT-SCC...CCHHHH.HHHHHHC---.CHHHHH........HHHHCT--HHHHHH CS
                            DEAD_2  71 ..................eekCsffenl...eelkkl.kkllleevvd.iedlve........lgeklklCPYylsr 116
                                                          + C+++ +     e++ + + +  ++++d +e l++        + + +++CPY ++ 
  gi|330506777|ref|YP_004383205.1| 134 aaiydphadsipeeepgyRTFCPYYLRSregFEINGSvHFRRSARALDvVEGLKKrvtapsglMDSCQGICPYEIMS 210
                                       *****************9999**9988854533333356666677777357888899999887777789******** PP

                                       HHHCCTSEEEEEHHHHTSCCCHHHHH...T..GCGCEEEECTCCCHHHHHHHCC-EEEECH CS
                            DEAD_2 117 elledadiiilpYqyLldekireslk...gislknsivilDEAhNiedvceeaasveisee 174
                                         +++ di+i+ Y+ L+++   + +    ++++++  +i+DEAhN+ d ++ ++s +++++
  gi|330506777|ref|YP_004383205.1| 211 LYAKNSDIVIMNYSHLFSPDFQDIIFqwlEMDSEKVTLIIDEAHNLGDAVRAMNSRHLTQR 271
                                       ********************99987667778999999*******************99986 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.4e-06    0.0028       3      45 ..      10      53 ..       9      99 .. 0.79
   2 !   10.2   0.0   0.00027      0.54     101     147 ..     213     259 ..     181     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
                                      EE-HHHHHHHHHHT......TTS.EEEEEESTTSTHHHHH.HHHH CS
                            ResIII  3 elreyQeeaienlleklkskrdk.rglikmaTGtGKTlva.akli 45
                                      +lr++Q ++++++ + ++ ++++  ++i ++TGtGKT ++ a+l+
  gi|330506777|ref|YP_004383205.1| 10 SLRPHQDRMLDAVYDVVS-RGNQgILMIDAPTGTGKTSCIsAALA 53
                                      59************9999.55551566**********99844444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00027
                                       ...-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS. CS
                            ResIII 101 stnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak 147
                                       ++n++i++++++ l ++  ++   +    ++++  +iiDEaH+lg++
  gi|330506777|ref|YP_004383205.1| 213 AKNSDIVIMNYSHLFSPDFQDIIFQWLEMDSEKVTLIIDEAHNLGDA 259
                                       57899999*****999998887778888888888**********984 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.6   7.1e+03      93     115 ..     230     252 ..     222     262 .. 0.76
   2 !   22.9   0.0   2.9e-08   5.7e-05     119     187 ..     419     491 ..     406     494 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHTS.TTTEEEEEE. CS
                               HBB  93 rlaefllawlssdeedYvrlvsk 115
                                       +++  + +wl++d+e+   ++ +
  gi|330506777|ref|YP_004383205.1| 230 DFQDIIFQWLEMDSEKVTLIIDE 252
                                       67778899999999987666655 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 2.9e-08
                                       .EECCCCS-TCCHH.HHHHHCHCCCCCCTS-SSHHHHHHH.HT......EEE.S..S.GGHCCCCCCCCCSHT CS
                               HBB 119 esLeavcldPskal.rflkerlssllmsgtltpleeysdi.iGle..aklkkfpspfpkEnlivlfatdVsTk 187
                                         Le   +dP+  + r   ++  +++ sgt +ple+y+   +G e  a+    p+pfpkEn++ l+a+  +T+
  gi|330506777|ref|YP_004383205.1| 419 VRLEVNNIDPAANIrRITDNVNATIMLSGTFSPLEAYELYcLGEEgrAEKLSLPNPFPKENRLLLVAKKATTQ 491
                                       5689999***865516778999***************9651566676677779***************99997 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   5.9e-06     0.012       7      55 ..      14      61 ..      11      84 .. 0.83
   2 ?    1.1   0.1      0.22   4.5e+02     123     158 ..     231     268 ..     215     279 .. 0.79
   3 ?   -3.8   0.0       7.2   1.4e+04      34      43 ..     412     421 ..     410     451 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.9e-06
                            AAA_16  7 eeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                      ++ ++L ++++ v++g  +++++  + G+GK+s + ++l a+ ++ +++
  gi|330506777|ref|YP_004383205.1| 14 HQDRMLDAVYDVVSRGNQGILMIDAPTGTGKTSCISAALAAAPGK-IVV 61
                                      566899999******************************888888.333 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.22
                            AAA_16 123 lkrll.allsrderplvlvlDdlqwadeaslql.laaL 158
                                       +++++ + l+ d++++ l++D+++ + +a +++  ++L
  gi|330506777|ref|YP_004383205.1| 231 FQDIIfQWLEMDSEKVTLIIDEAHNLGDAVRAMnSRHL 268
                                       677777888888889*********99997776644444 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 7.2
                            AAA_16  34 GvGKsslvre 43 
                                       GvGK +lvr 
  gi|330506777|ref|YP_004383205.1| 412 GVGKRKLVRL 421
                                       9999999975 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00025      0.51       4      36 ..      15      53 ..      12      92 .. 0.81
   2 !    6.9   0.0    0.0025         5      95     144 ..     213     267 ..     180     284 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                                      HHHHHHHHH......TTCEEEEEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  4 Qaeaiplil......gggdvlvaaeTGsGKTlaflipvl 36
                                      Q++++++++      ++g +++ a+TG+GKT + + ++ 
  gi|330506777|ref|YP_004383205.1| 15 QDRMLDAVYdvvsrgNQGILMIDAPTGTGKTSCISAALA 53
                                      5555555555555434456789***********998876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0025
                                       HTTCSEEEEEHHHHHH.HH.....HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHH CS
                                       xxxxxxxxxxxxxxxx.xx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  95 dngvdivvgtpgrldd.ll.....stgklnlsqvrflVlDEadrlldqgfsdfinr 144
                                        ++ div+++ + l++  +     +  +++ ++v +l++DEa++l d  +    ++
  gi|330506777|ref|YP_004383205.1| 213 AKNSDIVIMNYSHLFSpDFqdiifQWLEMDSEKV-TLIIDEAHNLGDAVRAMNSRH 267
                                       4667888888876666434343344344445555.69*********9844444443 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   0.00012      0.23       3      30 ..      29      56 ..      27      81 .. 0.84
   2 !    5.5   0.1    0.0099        20      92     104 ..     245     257 ..     231     280 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                            AAA_22  3 ktagilvvtGesGtGKTtllrrlleqld 30
                                      +++gil++ +++GtGKT ++   l  ++
  gi|330506777|ref|YP_004383205.1| 29 GNQGILMIDAPTGTGKTSCISAALAAAP 56
                                      589****************998877765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0099
                            AAA_22  92 ielliiDEaqhlr 104
                                       ++ liiDEa++l 
  gi|330506777|ref|YP_004383205.1| 245 KVTLIIDEAHNLG 257
                                       368*********4 PP

>> PAR1  PAR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.1e-05       0.1      78     116 ..     541     580 ..     534     595 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.1e-05
                              PAR1  78 sqftkklcs.paclnkcPnivdlyfnlaageGvflpelce 116
                                       +++ kklc  p+  ++ P+++dl+f+l a  G +l+ +c 
  gi|330506777|ref|YP_004383205.1| 541 RKVGKKLCVePRSADQVPELLDLFFSLGARGGGVLTGVCG 580
                                       567899**648999******************9****996 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.7     0.026        52       5      22 ..      38      55 ..      34      86 .. 0.74
   2 ?    4.6   0.0     0.021        41      26      78 ..     218     265 ..     205     320 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.026
                                      SSTTSSHHHHHHHHHHHH CS
                               AAA  5 GppGtGKTllakavakel 22
                                       p GtGKT++++a    +
  gi|330506777|ref|YP_004383205.1| 38 APTGTGKTSCISAALAAA 55
                                      699*******99988776 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.021
                                       EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCC CS
                               AAA  26 fleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgse 78 
                                       ++ ++ s l+      s++    +f+ ++  ++++ l+iDE+++l+ +    ++
  gi|330506777|ref|YP_004383205.1| 218 IVIMNYSHLF------SPDFQDIIFQWLEMDSEKVTLIIDEAHNLGDAVrAMNS 265
                                       5556666666......6666677888888887779**********988732223 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (777 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 5210.90
//
Query:       gi|330506778|ref|YP_004383206.1|  [L=114]
Description: hypothetical protein MCON_0549 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-46  155.7   0.0    3.8e-46  155.6   0.0    1.0  1  DUF555    Protein of unknown function (DUF555)
  ------ inclusion threshold ------
      0.052   12.9   0.9      0.084   12.2   0.9    1.2  1  zf-RanBP  Zn-finger in Ran binding protein and others


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 !  155.6   0.0   4.2e-50   3.8e-46       1     101 []       3     104 ..       3     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 155.6 bits;  conditional E-value: 4.2e-50
                            DUF555   1 dyevvleaawivrdvksvddAigiAiseagkrlnpe.ldfveievgetecPkcgeelesalvvadtalvglllemkv 76 
                                       +++v le+aw+vrdvk+ ddAig+Aiseagkrln++ +dfve+evg+++cP+c+e+l+++++va++alv+ll+e+k+
  gi|330506778|ref|YP_004383206.1|   3 NFNVLLEGAWLVRDVKTEDDAIGVAISEAGKRLNQRkMDFVEVEVGQWDCPECNEPLDGVFLVASMALVALLFEIKI 79 
                                       799********************************99**************************************** PP

                            DUF555  77 fnaeseEhaeriakseigkaledvP 101
                                       fnaeseEha riaks++gkal ++P
  gi|330506778|ref|YP_004383206.1|  80 FNAESEEHAGRIAKSTVGKALGTIP 104
                                       ************************9 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 ?   12.2   0.9   9.4e-06     0.084       3      11 ..      48      56 ..      47      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.4e-06
                                      SSEE-SSS- CS
                          zf-RanBP  3 gdWdCskCl 11
                                      g+WdC+ C+
  gi|330506778|ref|YP_004383206.1| 48 GQWDCPECN 56
                                      9*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 796.93
//
Query:       gi|330506779|ref|YP_004383207.1|  [L=1103]
Description: two-component hybrid sensor and regulator [Methanosaeta concilii GP6]
Scores for complete 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-38  129.7   0.1    1.3e-24   86.5   0.1    3.0  3  Response_reg    Response regulator receiver domain
    1.2e-30  106.3   0.2    2.3e-30  105.4   0.2    1.5  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    2.3e-20   72.4   1.1    1.6e-19   69.7   0.0    2.6  2  HisKA           His Kinase A (phospho-acceptor) domain
    4.1e-07   30.0   0.0      3e-06   27.2   0.0    2.4  1  PAS             PAS fold
    2.7e-06   27.6   0.0     0.0037   17.5   0.0    3.3  4  PAS_4           PAS fold
    1.4e-05   25.2   0.0    0.00013   22.2   0.0    2.6  1  PAS_9           PAS domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.025   14.4   0.0    1.6  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
      0.013   15.4   0.0      0.042   13.8   0.0    1.8  1  HATPase_c_5     GHKL domain
      0.067   13.2   0.0       0.23   11.5   0.0    1.9  1  PAS_8           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 ?   -2.9   0.0       3.9   7.7e+03      46      65 ..      80      99 ..      74     106 .. 0.83
   2 !   40.0   0.0   1.8e-13   3.5e-10       1     108 [.     837     951 ..     837     955 .. 0.84
   3 !   86.5   0.1   6.5e-28   1.3e-24       1     111 [.     984    1096 ..     984    1097 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.9
                                      EEEEESSCSSSEHHHHHHHH CS
                      Response_reg 46 lillDinmpgmdGlellkei 65
                                      + ++D+ +  ++G+ +l  +
  gi|330506779|ref|YP_004383207.1| 80 VAFTDLALIPINGMAALALL 99
                                      7899**********999877 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 1.8e-13
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH............HHHHESEEEEESSCSSSEHHHHHHHH CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealell............keekvdlillDinmpgmdGlellkei 65 
                                       vliv+ ++ vr+ l ++  + g+ e  + + ++ea+el+            k++++d+++lD  +p+m+Gl l+++i
  gi|330506779|ref|YP_004383207.1| 837 VLIVEGHRSVRDMLFRMAGSWGM-EAVALARAEEAIELMtrgtaisgtgqlKSNSFDCVILDTVLPDMEGLLLARRI 912
                                       8**********************.5666778999999996666666666656666********************** PP

                                       HHCTTTSEEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHH CS
                      Response_reg  66 reedpelpviiltahseeedavealkagaddflsKpfdpeeLl 108
                                       ++ +    v++++  +ee     + +   ++ l+Kp++p+ L+
  gi|330506779|ref|YP_004383207.1| 913 KDLSVASFVVMISHMGEEV----VKDDSLSGWLTKPVKPRLLK 951
                                       *************888744....44666789999999888776 PP

  == domain 3  score: 86.5 bits;  conditional E-value: 6.5e-28
                                        EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT...TTS CS
                      Response_reg    1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed...pel 72  
                                        +l+++D+p+++++   +l++ gy + ++a++g e+l  +k++++d+il+Di+mp+mdGle++++ire d   +++
  gi|330506779|ref|YP_004383207.1|  984 ILLAEDNPINQKVALIMLRHLGY-KADVASSGPEVLTSVKRKHYDVILMDIQMPDMDGLEATRHIREMDgsvSQP 1057
                                        89*********************.*********************************************99999* PP

                                        EEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg   73 pviiltahseeedavealkagaddflsKpfdpeeLlkal 111 
                                         +i++ta++ e d++e lkag++++ls p++  eL++al
  gi|330506779|ref|YP_004383207.1| 1058 HIIAMTAYALEGDREEFLKAGMNGYLSEPIQLGELKSAL 1096
                                        ***********************************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 !  105.4   0.2   1.2e-33   2.3e-30       1     109 [.     702     815 ..     702     818 .. 0.94

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 1.2e-33
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE...EE..TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTS CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveika...se..ddlvisveDnGiGipkedlkklfekfsq.ddstkrgg 71 
                                       gd++rLrqi+ nl++Na kf t++gei +++++   ++   +l+++v D+GiGi++e+l +lf+ f+q d+st+r +
  gi|330506779|ref|YP_004383207.1| 702 GDQIRLRQILVNLLGNATKF-TEKGEIVLSLSTtplDDgrIELHFRVMDTGIGISQENLSRLFQFFTQvDSSTTRHY 777
                                       79******************.***********8655225679999******************************** PP

                                       TSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  72 ggtGlGlsivkklvelmgGeiwvesepgrGttftftlp 109
                                       ggtGlGl+i+++lve+m+G+iwvese+g G+tf+ft++
  gi|330506779|ref|YP_004383207.1| 778 GGTGLGLAISRRLVEMMEGRIWVESEKGVGSTFHFTIR 815
                                       ***********************************985 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 ?    0.3   0.3      0.38   7.5e+02      41      56 ..     433     448 ..     393     452 .. 0.70
   2 !   69.7   0.0   8.1e-23   1.6e-19       1      66 [.     590     654 ..     590     655 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHHHHH CS
                             HisKA  41 letiesearrldhlve 56 
                                        + +++++rr+ ++++
  gi|330506779|ref|YP_004383207.1| 433 EAAMRDSERRMADIIN 448
                                       3456677779999998 PP

  == domain 2  score: 69.7 bits;  conditional E-value: 8.1e-23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       s++ fla+++HE+rtP++a+ g++ +L ++ +l +e++eyleti+ +++ l+++++++Ld+s+ie+
  gi|330506779|ref|YP_004383207.1| 590 SKSNFLANMSHEIRTPMNAVVGMTGLLLET-DLKPEQREYLETIRTGGNTLLAIINNILDYSKIEG 654
                                       799***********************9885.899******************************98 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   1.5e-09     3e-06       2      52 ..     442     492 ..     441     567 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBST CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldlihe 52 
                                       ++  i++ lpd++fv+++ g+++ +N+a+e +++ ++e++lgk  +++  +
  gi|330506779|ref|YP_004383207.1| 442 RMADIINFLPDATFVINKEGVVIAWNRAIEMMTQVKAEDILGKGEYEYSLP 492
                                       67789999***********************************98887655 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.9e-06    0.0037       4      45 ..     450     491 ..     448     511 .. 0.90
   2 !    5.8   0.0    0.0081        16      75     109 ..     537     571 ..     521     572 .. 0.87
   3 ?   -3.5   0.0       6.1   1.2e+04       6      25 ..     665     684 ..     665     691 .. 0.81
   4 ?   -1.7   0.0       1.7   3.4e+03      75      97 ..     723     743 ..     717     749 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.9e-06
                             PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellp 45 
                                       lpda++v++++g+v+++N+a++ + ++ +e++lGk  +e+  
  gi|330506779|ref|YP_004383207.1| 450 LPDATFVINKEGVVIAWNRAIEMMTQVKAEDILGKGEYEYSL 491
                                       79*********************************9888654 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0081
                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +g+  +++ ++  l d++G + g+++ +rDiT+++
  gi|330506779|ref|YP_004383207.1| 537 NGKLTYLQGSAAVLYDSEGNIYGAIESIRDITDQK 571
                                       77788888888999******************986 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.1
                             PAS_4   6 dalavldpdgrvlyaNaaaa 25 
                                       d+l ++ + + +++aNaa  
  gi|330506779|ref|YP_004383207.1| 665 DLLGCIEESMDMVAANAAEK 684
                                       56788999999*****9954 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.7
                             PAS_4  75 pgeerhyelrllPlrdesGevig 97 
                                       +++e +++l+ +Pl+d  G++  
  gi|330506779|ref|YP_004383207.1| 723 EKGEIVLSLSTTPLDD--GRIEL 743
                                       57788999******55..88654 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   6.5e-08   0.00013       1     104 []     451     569 ..     451     569 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.5e-08
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlf...............vtdpeanerlraaleqgrkker 62 
                                       pd+++++n++g ++ +N+a + +++ ++e++lgk   +                  + + + +   + l+ +++   
  gi|330506779|ref|YP_004383207.1| 451 PDATFVINKEGVVIAWNRAIEMMTQVKAEDILGKGEYEYSlpfykkrrpilidlvTNQDLDVKGCYEELKWHEDGSL 527
                                       68899999***777*********************777777778888888887776666666666666666666788 PP

                             PAS_9  63 evevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                       ++   + + ng+  + + +a+ ++d++g++ g+i  +rDit+
  gi|330506779|ref|YP_004383207.1| 528 AGVSFISNLNGKLTYLQGSAAVLYDSEGNIYGAIESIRDITD 569
                                       88888999999999999***********************96 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 ?   14.4   0.0   1.3e-05     0.025      34      79 ..     743     786 ..     705     827 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                       HATPase_c_3  34 geivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGlkl 79 
                                         +++ D G G+s+e+l + +++ t+  +  ++ + +G  G+Gl  
  gi|330506779|ref|YP_004383207.1| 743 LHFRVMDTGIGISQENLSRLFQFFTQVDS--STTRHYGGTGLGLAI 786
                                       6789******************9999998..58999**9**99544 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.1e-05     0.042       5      93 ..     706     806 ..     703     816 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                       HATPase_c_5   5 dlcvilgnlLdNAieacsk.........ieeekrfIrltvrekkksliisieNsyegek...kklesskskkeehGi 69 
                                        l  il nlL NA    +k         ++ ++  I+l++r  +  + is eN  +  +   +   s++++ +  G+
  gi|330506779|ref|YP_004383207.1| 706 RLRQILVNLLGNATKFTEKgeivlslstTPLDDGRIELHFRVMDTGIGISQENLSRLFQfftQVDSSTTRHYGGTGL 782
                                       577899***********99999999986444799*******************988866564666688899999*** PP

                       HATPase_c_5  70 Glksireivkkykgnlsieaedgl 93 
                                       Gl   r++v+  +g +++e e+g+
  gi|330506779|ref|YP_004383207.1| 783 GLAISRRLVEMMEGRIWVESEKGV 806
                                       *******************99984 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.23       5      42 ..     445     483 ..     441     497 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                             PAS_8   5 alfesspdgiavvd.lgdrivdvNqaalellGys.adlkg 42 
                                        +++ +pd+ +v++ +g  ++ +N+a ++++ ++ +d++g
  gi|330506779|ref|YP_004383207.1| 445 DIINFLPDATFVINkEGV-VIAWNRAIEMMTQVKaEDILG 483
                                       58999*********6666.*************88766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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):               9  [number of targets reported over threshold]
# CPU time: 0.87u 0.31s 00:00:01.18 Elapsed: 00:00:00.50
# Mc/sec: 6697.25
//
Query:       gi|330506780|ref|YP_004383208.1|  [L=237]
Description: hypothetical protein MCON_0551 [Methanosaeta concilii GP6]
Scores for complete 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-90  299.9   0.1    8.4e-90  299.7   0.1    1.0  1  PIN_5     PINc domain ribonuclease
  ------ inclusion threshold ------
       0.16   11.7   0.0        0.4   10.5   0.0    1.6  1  DUF5615   Domain of unknown function (DUF5615)


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 !  299.7   0.1   9.4e-94   8.4e-90       1     206 []       5     221 ..       5     221 .. 0.98

  Alignments for each domain:
  == domain 1  score: 299.7 bits;  conditional E-value: 9.4e-94
                             PIN_5   1 rfvlDTsaltdpevreklgeeeleeavkklldliaearlklgiscyip.psvykElkeflkreeveeeviakldtwl 76 
                                       rfvlDT+altd+ ++e+ g+++++e+++++ld i+e rl+lgiscyip psvy+E+k+f+++++++++++ k+dtwl
  gi|330506780|ref|YP_004383208.1|   5 RFVLDTTALTDSMAWESEGATDICEGMNAILDRISEGRLHLGISCYIPyPSVYNEIKDFARHNSCDSRILGKVDTWL 81 
                                       8**************************************************************************** PP

                             PIN_5  77 vkkspdryevkipaeilyeyveevrerinkGlrvaEeavreaaeeseklekee..........eeeevgelikklRe 143
                                       vkk+pdry+vk+p++i+yeyv+++r+rinkG++++Eeav+e+++++ +l++++          e+e+vg++i+k+Re
  gi|330506780|ref|YP_004383208.1|  82 VKKTPDRYKVKVPSKIFYEYVDYMRSRINKGMNISEEAVWESVSRCIALSESKgdlremrdeiEREVVGSIIRKFRE 158
                                       ***********************************************99644457888999999************* PP

                             PIN_5 144 kYrealRkGilDsaeDldvllLAkELdaavvssDeGikkwaeklGlrlveakkfpkvlkeylk 206
                                       kYr+alR+GilDsa+D+dvllLAkELdaavvs+D Gi++wae+lGlr++e+++fp ++key++
  gi|330506780|ref|YP_004383208.1| 159 KYRAALRYGILDSAPDIDVLLLAKELDAAVVSQDLGIQRWAEQLGLRFMESRSFPIMIKEYMN 221
                                       *************************************************************85 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.5e-05       0.4      32      57 ..     169     194 ..     145     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.5e-05
                           DUF5615  32 legasDeeileyAkeedriivTkDkD 57 
                                       l++a+D ++l +Ake d+++v++D  
  gi|330506780|ref|YP_004383208.1| 169 LDSAPDIDVLLLAKELDAAVVSQDLG 194
                                       6789********************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1680.58
//
Query:       gi|330506781|ref|YP_004383209.1|  [L=238]
Description: hypothetical protein MCON_0552 [Methanosaeta concilii GP6]
Scores for complete 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-81  271.1   0.1    7.2e-81  271.0   0.1    1.0  1  NRD1_2    NrpR regulatory domains NRD1 and 2


Domain annotation for each model (and alignments):
>> NRD1_2  NrpR regulatory domains NRD1 and 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.0   0.1     4e-85   7.2e-81       3     237 ..       6     232 ..       4     233 .. 0.99

  Alignments for each domain:
  == domain 1  score: 271.0 bits;  conditional E-value: 4e-85
                                       -HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE........EEEE CS
                            NRD1_2   3 fviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegekelevpegkvgia 79 
                                       f++++ie+l+++v+fdp+ +kGk+i+N+++++ke l+e+l ++ ++i+sgl+vs+++k++e + +        ++i+
  gi|330506781|ref|YP_004383209.1|   6 FTLARIENLMHQVSFDPAGMKGKIITNTTTVRKEALDETLAVFYDTINSGLAVSPMIKVIEGKGR--------IKIK 74 
                                       899**********************************************************9988........**** PP

                                       EE-CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEEEEEE CS
                            NRD1_2  80 tvCSitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkilAnlR 156
                                       t CS+t+ +v+lk+GIpv+pk GGl+e+ ++ep+rFt++++Y+ t++dP++v+++++l +++ +++tg+g+il+nl+
  gi|330506781|ref|YP_004383209.1|  75 TACSLTLCAVMLKHGIPVHPKGGGLVEVVEREPTRFTDMLMYWATTVDPIDVLTAQGLMNITGMMRTGNGRILGNLH 151
                                       ***************************************************************************** PP

                                       EEETTTHHHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEEEEEG CS
                            NRD1_2 157 eipvsarekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsglidi 233
                                       e p+ ar+k+e++le l +ag+ gvle+g+pn +vlgv+ve+++vg+++vgG+n++aa+ke +i+v  +++s+l+di
  gi|330506781|ref|YP_004383209.1| 152 EAPMLARDKIEDVLEALAQAGFAGVLELGQPNMNVLGVSVERDHVGLALVGGTNLMAAAKECQIDVMHESISDLTDI 228
                                       ***************************************************************************** PP

                                       GGSE CS
                            NRD1_2 234 selk 237
                                       selk
  gi|330506781|ref|YP_004383209.1| 229 SELK 232
                                       **98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 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:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1751.97
//
Query:       gi|330506782|ref|YP_004383210.1|  [L=577]
Description: PHP domain/helix-hairpin-helix motif protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-22   78.3   3.8    1.2e-21   76.9   1.4    2.9  3  HHH_8            Helix-hairpin-helix domain
    2.2e-21   75.8   0.0    4.7e-21   74.7   0.0    1.6  1  DNA_pol_B_thumb  DNA polymerase beta thumb
    3.8e-13   49.8   1.7    4.8e-07   30.3   0.1    3.2  3  HHH_5            Helix-hairpin-helix domain
    4.1e-08   33.7   0.0    2.2e-07   31.3   0.0    2.0  2  PHP              PHP domain
    1.3e-06   28.6   0.1    1.1e-05   25.6   0.0    2.2  2  DNA_pol_B_palm   DNA polymerase beta palm
    3.2e-05   23.6   2.4       0.14   12.1   0.2    3.8  3  HHH              Helix-hairpin-helix motif
      0.003   17.1   0.0     0.0085   15.6   0.0    1.8  1  RNase_P_p30      RNase P subunit p30
     0.0035   17.6   0.1        1.2    9.5   0.0    3.1  2  HHH_3            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.021   15.1   0.1        8.3    6.7   0.0    2.6  2  Cdd1             Pathogenicity locus
      0.037   13.9   0.0        1.6    8.6   0.0    2.6  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
      0.044   13.9   0.0       0.62   10.2   0.0    2.6  2  HHH_2            Helix-hairpin-helix motif
       0.13   12.4   0.0        2.4    8.3   0.0    2.6  2  DUF3701          Phage integrase protein
       0.14   11.9   0.2          1    9.2   0.0    2.6  2  PHP_C            PHP-associated


Domain annotation for each model (and alignments):
>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   1.4   8.5e-25   1.2e-21       1      67 [.       7      75 ..       7      76 .. 0.97
   2 ?   -0.2   0.0      0.93   1.3e+03      47      60 ..      93     108 ..      79     116 .. 0.70
   3 ?   -2.9   0.0       6.6   9.1e+03      34      57 ..     119     144 ..     117     153 .. 0.56

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 8.5e-25
                                      HHHHHHHHHHHHHHHHHCT--CCCHHHHHHHHCCCCC-SS-HHHH.TT.HCTTSTT--HHHHHHHHHHH CS
                             HHH_8  1 NkeiadaLeeladllelkgedpfrvraYrrAaraiealpeeitsl.ee.eltklpgiGkkiaakieeil 67
                                      N+eia +L ++a+llel+ e+ f++ aY+rAaraie+l+e+i+++ ++ +l+ +pg+Gk+ia+ki+e+l
  gi|330506782|ref|YP_004383210.1|  7 NREIAGILYQMAELLELHAENRFKIIAYSRAARAIESLTEDIEQVcRDgRLEGIPGVGKAIAEKIKEYL 75
                                      99********************************************556*******************9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.93
                                       T..HCTTSTT--HHHH CS
                             HHH_8  47 e..eltklpgiGkkia 60 
                                       +  el ++ g+G+k+ 
  gi|330506782|ref|YP_004383210.1|  93 GlaELLQISGLGPKTV 108
                                       3445999*****9985 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.6
                                       CCCC-SS-HHHHTTHCTTSTT--....H CS
                             HHH_8  34 aiealpeeitsleeeltklpgiG....k 57 
                                       ++++l+++ ++ +  +++lp +G    k
  gi|330506782|ref|YP_004383210.1| 119 NLDELEKAARE-HR-IRRLPRMGvvreK 144
                                       45555555555.43.7777777755554 PP

>> DNA_pol_B_thumb  DNA polymerase beta thumb
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.0   3.4e-24   4.7e-21       2      70 .]     258     319 ..     257     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 3.4e-24
                                       HHHHHS-HHHHHHHHHHHHCTTEEEETTEEE.......ETCCCEEEC-SSHHHHHHHCTS----GGGTT CS
                   DNA_pol_B_thumb   2 llyfTGsktFnrdlRrlakkkglkLnssglrdekgkaeddddgelvevetErdvfelLglpyipPeeRe 70 
                                       l+yfTGsk++n+++R+la ++g++L+++ l+       + ++g+++ +++E++v+++Lgl+yipPe+Re
  gi|330506782|ref|YP_004383210.1| 258 LQYFTGSKEHNVSMRQLALDRGYSLSEYSLT-------RLANGQDLFFDQEEEVYQALGLQYIPPELRE 319
                                       89*****************************.......9*****************************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 !   17.5   0.1   3.5e-06    0.0048      20      56 ..      39      76 ..      34      77 .. 0.87
   2 !   30.3   0.1   3.5e-10   4.8e-07       3      54 ..      96     149 ..      94     152 .. 0.90
   3 ?   -2.9   0.0       8.2   1.1e+04       6      29 ..     178     201 ..     173     219 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.5e-06
                                      TTT--SH.HHHHHS-HH.HHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5 20 saGiesv.edlaaadve.eLakipGiGkktAeriilelk 56
                                      +a ies+ ed+ + +++ +L  ipG+Gk  Ae+i++ l+
  gi|330506782|ref|YP_004383210.1| 39 RA-IESLtEDIEQVCRDgRLEGIPGVGKAIAEKIKEYLR 76
                                      55.7886599*****987*****************9887 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 3.5e-10
                                       HHHTSTT--HHHHHHHHTT.T--SHHHHHHS-HH.HHHTSTTS-HHHHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsa.Giesvedlaaadve.eLakipGiGkktAeriile 54 
                                       eLl++sG+Gpkt+  l+++  i+ +++l +a++e ++ ++p +G  + ++i+ +
  gi|330506782|ref|YP_004383210.1|  96 ELLQISGLGPKTVFMLHEKlDITNLDELEKAAREhRIRRLPRMGVVREKNILKS 149
                                       8******************55*******99987549************999876 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 8.2
                                       TSTT--HHHHHHHHTTT--SHHHH CS
                             HHH_5   6 svsGiGpktAlallsaGiesvedl 29 
                                       +++G+  +tA   ++   e+v d+
  gi|330506782|ref|YP_004383210.1| 178 GIEGLEHATAAGSYRRRKETVGDI 201
                                       667777777665555533344333 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.6   3.6e+03      79     125 ..      83     174 ..      49     197 .. 0.63
   2 !   31.3   0.0   1.6e-10   2.2e-07       1      74 [.     344     465 ..     344     507 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.6
                                       .....E....EHHHH.............................................HHHHHHHHH........ CS
                                       xxxxxxxxxxxxxxx.............................................xxxxxxxxxxxxxxxxx RF
                               PHP  79 hltllaknqeGyknl.............................................lkllskaylegfyrkpr 110
                                       h  lla + +G+ +l                                              k ++k+  ++++r +r
  gi|330506782|ref|YP_004383210.1|  83 HQDLLADTPQGLAELlqisglgpktvfmlheklditnldelekaarehrirrlprmgvvrEKNILKSIERYRKRSNR 159
                                       55566666666666655555555555555555555555555555555555555555555555555555555566666 PP

                                       ..HHHHHHS...... CS
                                       xxxxxxxxxxxxxxx RF
                               PHP 111 idkellekhsegLiv 125
                                       i  ++ e+  ++++ 
  gi|330506782|ref|YP_004383210.1| 160 ILYSTAESIVDEILT 174
                                       666665555455554 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 1.6e-10
                                       EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT............HHHHHHHHHHHHTTTTSEEEEEE CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP   1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlf............gyvefykaakkkykagikpiiGl 64 
                                       dlHvH+  s +  +++   el+++a++lg++ ia++Dh++              + +e++ +a+++  +gi++++G+
  gi|330506782|ref|YP_004383210.1| 344 DLHVHSIWSdGR-ASI--IELAQAARSLGYEYIALSDHSPSVgiaggigrekmeEKIEAVAEANDSL-EGITVLMGA 416
                                       89***9999433.555..9*********************99*********7665566666664444.8******** PP

                                       E................................................ CS
                                       xxxxxxxxx.......................................x RF
                               PHP  65 eayvaddse.......................................k 74 
                                       e++++ d+                                        +
  gi|330506782|ref|YP_004383210.1| 417 EVDIKADGSldypddllermdvvvasvhmaqqqkertitgrlisaienQ 465
                                       ****999987777766666666666666666665555555555555550 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   7.7e-09   1.1e-05      26      68 ..     184     228 ..     160     267 .. 0.72
   2 ?   -0.2   0.0      0.81   1.1e+03      43      74 ..     436     466 ..     414     474 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 7.7e-09
                                       EEEE-HHHHTT-SEESSEEEEEEBTTBSTT..SS--HHHHHHHHH CS
                    DNA_pol_B_palm  26 evivcGSYRRgaessGDvDvlitkkdakse..skklkklleklvk 68 
                                       +++++GSYRR +e+ GD+D+l t  + ++   +  +++l+e++++
  gi|330506782|ref|YP_004383210.1| 184 HATAAGSYRRRKETVGDIDILATAARPEEIvaAFVKMPLVEEVLA 228
                                       6799******************98776654212234455555554 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.81
                                       EEEEEEBTTBSTTSS--HHHHHHHHHHHHHTT CS
                    DNA_pol_B_palm  43 vDvlitkkdakseskklkklleklvkklkkkg 74 
                                       +Dv++   +++++ +k+++++ +l++++++++
  gi|330506782|ref|YP_004383210.1| 436 MDVVVASVHMAQQ-QKERTITGRLISAIENQN 466
                                       6999999998885.578999999999998876 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.2    0.0001      0.14      13      30 .]      57      74 ..      57      74 .. 0.93
   2 !    9.0   0.1   0.00095       1.3       6      23 ..      90     107 ..      85     108 .. 0.84
   3 ?   -2.7   0.0       4.8   6.6e+03      20      28 ..     230     238 ..     230     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                      HHTSTT-SHHHHHHHHHH CS
                               HHH 13 LlalPGVGpktAeaIlsy 30
                                      L+ +PGVG++ Ae+I +y
  gi|330506782|ref|YP_004383210.1| 57 LEGIPGVGKAIAEKIKEY 74
                                      788************998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00095
                                       HTSSHHHHHTSTT-SHHH CS
                               HHH   6 ipasreeLlalPGVGpkt 23 
                                        p  ++eLl+++G Gpkt
  gi|330506782|ref|YP_004383210.1|  90 TPQGLAELLQISGLGPKT 107
                                       567789***********9 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.8
                                       SHHHHHHHH CS
                               HHH  20 GpktAeaIl 28 
                                       Gp +A +I+
  gi|330506782|ref|YP_004383210.1| 230 GPTKASVIM 238
                                       9*****998 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 !   15.6   0.0   6.1e-06    0.0085      16     146 ..     358     506 ..     343     521 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.1e-06
                                       ...HHHHHHHHH-SEEEEEEEEEESS---HHHHH..........HHHHHHHH..HHSSEEEEEEES-H.HHHHHHHH CS
                       RNase_P_p30  16 s.rtiktlaelgytgvainftveaekekkpnase...pikeelkelkkelsglkllsRvtlvvsdpsklqrlskvrq 88 
                                         ++++ +++lgy+ +a++ +  +   +    +e   ++ e++ e +++l+g+++l + ++ ++   +l    ++  
  gi|330506782|ref|YP_004383210.1| 358 IiELAQAARSLGYEYIALSDHSPSVGIAGGIGREkmeEKIEAVAEANDSLEGITVLMGAEVDIKADGSLDYPDDLLE 434
                                       24789999**********9999965555544444667778889999999999***************9********* PP

                                       H--EEE..EE--SHH...HHH....HHHHT.T-SEEE-TTTT....SSS-S--.HHHHHHHHHHT-EEEEES CS
                       RNase_P_p30  89 kfdlla..vrPttek...alr....aacenldvDiisidlts....rlpfglk.hktiraAvergvafEiny 146
                                       ++d+++  v++  ++    ++     a+en +vDii +++      r p+ ++ h+ ++aA++ g+a+Ein 
  gi|330506782|ref|YP_004383210.1| 435 RMDVVVasVHMAQQQkerTITgrliSAIENQNVDIIGHPTGRiinqREPSDMDfHAVLEAAAKTGTALEINA 506
                                       ***9863344444331113222333789***********9878888*****9955677999999******85 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00084       1.2      16      47 ..      57      87 ..      52      89 .. 0.89
   2 ?    4.4   0.0     0.033        46      44      57 ..      95     108 ..      92     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00084
                             HHH_3 16 LqklpGlgpklAknIvayReknGpfksreeLl 47
                                      L+ +pG+g+++A++I +y    G+++s ++Ll
  gi|330506782|ref|YP_004383210.1| 57 LEGIPGVGKAIAEKIKEYL-RTGRIQSHQDLL 87
                                      8889**************7.689999999997 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.033
                             HHH_3  44 eeLlkvkglgpktf 57 
                                        eLl+++glgpkt+
  gi|330506782|ref|YP_004383210.1|  95 AELLQISGLGPKTV 108
                                       68999999999997 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.012        16       7      23 ..      56      72 ..      53      94 .. 0.77
   2 ?    6.7   0.0     0.006       8.3       3      39 ..      92     129 ..      90     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                              Cdd1  7 elqdiPniGkalaedlv 23
                                      +l+ iP++Gka+ae++ 
  gi|330506782|ref|YP_004383210.1| 56 RLEGIPGVGKAIAEKIK 72
                                      6899*********9976 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.006
                              Cdd1   3 kalkelqdiPniGkalaedlv.elGirsveelkgedpe 39 
                                       + l+el +i + G+++  +l+ +l+i++++el++   e
  gi|330506782|ref|YP_004383210.1|  92 QGLAELLQISGLGPKTVFMLHeKLDITNLDELEKAARE 129
                                       57899***************989*********987655 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.11   1.6e+02       3      16 ..      57      70 ..      56      87 .. 0.92
   2 ?    8.6   0.0    0.0012       1.6       2      31 ..      96     128 ..      95     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                   DNA_pol_lambd_f  3 FtkvyGVGpktAkk 16
                                      + ++ GVG ++A+k
  gi|330506782|ref|YP_004383210.1| 57 LEGIPGVGKAIAEK 70
                                      6799********98 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0012
                   DNA_pol_lambd_f   2 lFtkvyGVGpktAkkwyak.Girtledlra..k 31 
                                       +++++ G Gpkt  ++++k  i++l++l +   
  gi|330506782|ref|YP_004383210.1|  96 ELLQISGLGPKTVFMLHEKlDITNLDELEKaaR 128
                                       689*************************99652 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00045      0.62      37      60 ..      57      80 ..      46      83 .. 0.88
   2 ?    0.0   0.0      0.68   9.4e+02       7      33 ..      99     127 ..      93     132 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00045
                             HHH_2 37 LlevddiGeeiAqsivefFenekn 60
                                      L  ++++G+ iA++i+e++++ + 
  gi|330506782|ref|YP_004383210.1| 57 LEGIPGVGKAIAEKIKEYLRTGRI 80
                                      889***************998665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.68
                             HHH_2   7 GIrhVGektAklLakrFk..sldaLkkas 33 
                                        I   G kt   L ++ +  +ld+L+ka 
  gi|330506782|ref|YP_004383210.1|  99 QISGLGPKTVFMLHEKLDitNLDELEKAA 127
                                       34445555555555555444666666665 PP

>> DUF3701  Phage integrase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0018       2.4      33      71 ..      41      77 ..      31      97 .. 0.73
   2 ?    0.7   0.0      0.41   5.6e+02      31      67 ..     115     148 ..     102     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                           DUF3701 33 vktLaeLiarinrrgkrWwravprlGaakArrieafLaa 71
                                      ++ L e i+ + r g    + +p++G+a A++i+++L++
  gi|330506782|ref|YP_004383210.1| 41 IESLTEDIEQVCRDG--RLEGIPGVGKAIAEKIKEYLRT 77
                                      445554445554444..5799****************86 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.41
                           DUF3701  31 agvktLaeLiarinrrgkrWwravprlGaakArriea 67 
                                        ++++L+eL ++ +  +    r +pr+G  + ++i +
  gi|330506782|ref|YP_004383210.1| 115 LDITNLDELEKAAREHR---IRRLPRMGVVREKNILK 148
                                       47889999998888877...99999999998877754 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.3   5.9e+03      21      51 ..     189     217 ..     183     219 .. 0.54
   2 ?    9.2   0.0   0.00073         1       7      29 ..     517     539 ..     513     540 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.3
                             PHP_C  21 GSDAHrleeVGrayTefeepiatpdelleai 51 
                                       GS+  r e+VG   ++     a p+e+++a+
  gi|330506782|ref|YP_004383210.1| 189 GSYRRRKETVGDIDILA--TAARPEEIVAAF 217
                                       55555555555543333..333457777775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00073
                             PHP_C   7 ArrfAeklglpgtgGSDAHrlee 29 
                                        +r+A+++g+ +  +SDAH +++
  gi|330506782|ref|YP_004383210.1| 517 NARAAKEMGVQMSINSDAHDAGQ 539
                                       5799***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 3321.23
//
Query:       gi|330506783|ref|YP_004383211.1|  [L=425]
Description: adenylosuccinate synthetase [Methanosaeta concilii GP6]
Scores for 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  519.4   0.0   7.9e-156  519.2   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 !  519.2   0.0  4.4e-160  7.9e-156       2     419 .]       4     418 ..       3     418 .. 0.98

  Alignments for each domain:
  == domain 1  score: 519.2 bits;  conditional E-value: 4.4e-160
                                       EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHH CS
                   Adenylsucc_synt   2 vvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealle 78 
                                       ++ Gaq+GDEGKGk++Dllae++dv+vRfqGG+nAGHtvvv+gk+yklhl+pSG++  g + +iG+gvv++p +l +
  gi|330506783|ref|YP_004383211.1|   4 ILTGAQFGDEGKGKVIDLLAENYDVIVRFQGGDNAGHTVVVGGKTYKLHLVPSGAIF-GRRLLIGPGVVLNPRVLWN 79 
                                       789*****************************************************6.8899*************** PP

                                       HHTTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGSHHHH CS
                   Adenylsucc_synt  79 EieeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlldeeel 155
                                       Ei++le++g+++   +l i+ ++++++pyh++lD+l+e+a++ +kiGtT++GiG ay dkvar+ +++gdl d++ l
  gi|330506783|ref|YP_004383211.1|  80 EIQSLESEGIKV---DLGIDPKTTIIMPYHIELDSLREKART-EKIGTTNRGIGFAYVDKVAREEVQMGDLTDPALL 152
                                       **********88...8***********************986.9********************************* PP

                                       HHHHHHHHHHTHHHHHHT.....T-----HHHHHHHHHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTS CS
                   Adenylsucc_synt 156 eeklekllelknkllekldk..eeleveelleellkyaerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhG 230
                                       e+kl++++  k+k + ++    + ++++ +++e+l++ ++lk+ ++d+++++n a+ e+k+vL EGaqg++lD+ hG
  gi|330506783|ref|YP_004383211.1| 153 EAKLKEIAPGKEKAILDMGGdpTVVRYAPYIDEYLEIGKKLKSRIADVSREINIAILEEKSVLAEGAQGAFLDVIHG 229
                                       ********888888878766667778889************************************************ PP

                                       STTSS-SS--SHHHHHHHTT--GGGEEEEEEEEESSEEESSSS--TTB--SHHHHHHHHHTT-B-TTT--B-EEE-E CS
                   Adenylsucc_synt 231 tYPfvTsSnttaggaltglglapkkidevlgvvKAyttrvGeGpfptelkdevgeklrekGkEfgtttgrpRrcGwl 307
                                       t  fvTsS t+ag+a++ lg++p  +d+v+gv+KAy+trvGeGp+ptel d+ ge++rekG+E+gtttgr RrcGw+
  gi|330506783|ref|YP_004383211.1| 230 TQKFVTSSFTIAGSACANLGVGPVMVDNVVGVIKAYITRVGEGPMPTELVDSLGEQMREKGGEYGTTTGRARRCGWF 306
                                       ***************************************************************************** PP

                                       EHHHHHHHHHHHT-SEEEEE-GGGGTT-SEEEEEEEEEETTEEESS--S.....-GEEEEEEEEE--.S--TT---G CS
                   Adenylsucc_synt 308 DlvllryavrvngvtelaltklDvldgldeikvcvaYkldgkeldefpasleelekvepvyeelpgWkedisgvrsf 384
                                       D+vl  ++v +n++te+altklDvl+g++ ik+cv+Y+ldg++l + p+s+++l++++p+yee+pgW+edi++v+++
  gi|330506783|ref|YP_004383211.1| 307 DAVLGLKSVYLNSYTEMALTKLDVLTGINPIKICVGYDLDGDTLGYPPESTTDLARCKPIYEEVPGWTEDITEVKDY 383
                                       ***************************************************************************** PP

                                       GGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-EE CS
                   Adenylsucc_synt 385 edlpenakkyvefieellgvpvkiisvGpereqti 419
                                       +dlpena++yve +e+llgv+++ +svGp+reqti
  gi|330506783|ref|YP_004383211.1| 384 DDLPENARDYVEKLEDLLGVEISAVSVGPGREQTI 418
                                       *********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3000.24
//
Query:       gi|330506784|ref|YP_004383212.1|  [L=299]
Description: tetrahydromethanopterin:alpha-L-glutamate ligase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-25   90.0   0.0    1.8e-25   89.7   0.0    1.1  1  RimK            RimK-like ATP-grasp domain
    1.1e-11   44.5   0.0    1.6e-11   43.9   0.0    1.2  1  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
      2e-09   37.7   0.0    4.6e-09   36.5   0.0    1.6  1  ATP-grasp_3     ATP-grasp domain
    3.6e-06   26.4   0.0    9.1e-05   21.8   0.0    2.4  1  ATPgrasp_YheCD  YheC/D like ATP-grasp
    5.2e-05   23.6   0.0    0.00016   22.0   0.0    1.8  2  Rimk_N          RimK PreATP-grasp domain
     0.0072   15.6   0.0       0.19   10.9   0.0    2.1  2  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
  ------ inclusion threshold ------
       0.02   14.1   0.0      0.031   13.4   0.0    1.2  1  GSP_synth       Glutathionylspermidine synthase preATP-grasp


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.0   6.9e-29   1.8e-25       2     187 ..     101     289 ..     100     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 6.9e-29
                                       H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHH..HHHHHH..GGG CS
                              RimK   2 rdKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqkl..kqvlea..lke 74 
                                        +K+ + + L  a +++p+t  + +++ ae+ +  +k     v K ++g  G  ++l k  +++  +++ e    + 
  gi|330506784|ref|YP_004383212.1| 101 ANKYATSRRLHGASVPTPRTVATTSPKIAEEALYSFK---TAVSKPLFGYKGKDIILLKSSKQAdiESLREIveRRG 174
                                       6777777778888899999999999999988887775...5788*************98765541144444432334 PP

                                       --EEEEE--SS-S..EEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEE CS
                              RimK  75 ailvqeyieeaen..ediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGv 149
                                        + +qe+i+ + +  +diR +vvd+   +a+ r +  G++ snl rGg   +   + e+++lA++ a+a++++++Gv
  gi|330506784|ref|YP_004383212.1| 175 MVYLQEFINVTSGsaRDIRAFVVDGRLQGAIYRNAPPGEWISNLARGGRPTPCPKTRELEDLAVRSARAVGAIYCGV 251
                                       4589*****8877689************************************************************* PP

                                       EEEEETTEEEEEEEESS--SHHHHHHHT--HHHHHHHH CS
                              RimK 150 DllrakrgllvlEvnsspglekiektlgidiakkliea 187
                                       Dll++k+gl  +Evn  p  ++i   lgid+ + ++e 
  gi|330506784|ref|YP_004383212.1| 252 DLLESKDGLTTIEVNGTPSGKGIYDALGIDVTEAIAEH 289
                                       *******************************9999875 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 !   43.9   0.0   6.2e-15   1.6e-11      12     161 ..     117     265 ..     110     276 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 6.2e-15
                                       S--EEEES-HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT.-TTHHHHHHHHTTTTTS-EEEEE--GGG..GG-E CS
                         GSH-S_ATP  12 ipktlvskdkeeirafleeqgdvilKPldgkgGegvfrvkks.dpnlksilellteegkepviaqrylpei..keGD 85 
                                       +p+t+ +++ +  ++ l + ++++ KPl g+ G+ ++ +k+s +++++s+ e++ ++g   v +q++++    +  D
  gi|330506784|ref|YP_004383212.1| 117 TPRTVATTSPKIAEEALYSFKTAVSKPLFGYKGKDIILLKSSkQADIESLREIVERRGM--VYLQEFINVTsgSARD 191
                                       578888888888899999999******************998689********998887..899***9754114559 PP

                                       EEEEEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETTE..EEEEE CS
                         GSH-S_ATP  86 kRillvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigdk..ltEin 160
                                        R ++vdG+  g a+ R +  ge  snla ggr +  + t + + +a +   + ++ G ++ G+D++++k  lt i 
  gi|330506784|ref|YP_004383212.1| 192 IRAFVVDGRLQG-AIYRNAPPGEWISNLARGGRPTPCPKTRELEDLAVR---SARAVGAIYCGVDLLESKdgLTTIE 264
                                       9*********99.*********************999887777777654...55788*********98543466665 PP

                                       - CS
                         GSH-S_ATP 161 v 161
                                       v
  gi|330506784|ref|YP_004383212.1| 265 V 265
                                       5 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   1.8e-12   4.6e-09       1     156 [.     100     267 ..     100     272 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.8e-12
                                       HTSHHHHHHHHTTT.S---..........-EESS--SSSEEEEESS-------B--SS--TTE.............. CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvP......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve....... 64 
                                       a++K++t ++L+ a+v++P      +   aee+  + k+ v Kp  G  g+ + + +  ++a+  ie++        
  gi|330506784|ref|YP_004383212.1| 100 AANKYATSRRLHGASVPTPrtvattSPKIAEEALYSFKTAVSKPLFGYKGKDIILLKSSKQAD--IESLReiverrg 174
                                       69*****************87755444455566666******************999997776..444444568999 PP

                                       ..EEEE---SEEEEEE....EEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT-- CS
                       ATP-grasp_3  65 ..lvqefieGkplSvs....llsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevveklegla 135
                                          +qefi+ ++ S+     +++dg     +  n    e+  +++++ G  tp +  +++e+++la +  +++   a
  gi|330506784|ref|YP_004383212.1| 175 mvYLQEFINVTSGSARdiraFVVDGRLQGAIYRNAPPGEW-ISNLARGGRPTPCP--KTRELEDLAVRSARAV--GA 246
                                       9889*****9999996233356666555555555554444.33389999999988..999*************..45 PP

                                       EEEEEEEEESS.SEEEEEEES CS
                       ATP-grasp_3 136 GyvGvDlvlkdeepyviEvNP 156
                                        y GvDl+ +++++  iEvN 
  gi|330506784|ref|YP_004383212.1| 247 IYCGVDLLESKDGLTTIEVNG 267
                                       69******************6 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   3.5e-08   9.1e-05      29     167 ..     117     228 ..      98     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.5e-08
                    ATPgrasp_YheCD  29 LPetellesledleemlekyksvylKpanGskGkgilriekeekellllsrekkkkkkkrlaslselesllkkllkk 105
                                        P+t+  +s++  ee l  +k+ + Kp  G kGk+i+ +++                 ++ a++++l ++++   ++
  gi|330506784|ref|YP_004383212.1| 117 TPRTVATTSPKIAEEALYSFKTAVSKPLFGYKGKDIILLKS-----------------SKQADIESLREIVE---RR 173
                                       599**************************************.................22356677777766...44 PP

                    ATPgrasp_YheCD 106 krylvQqgidlatidgrpfDfRvlvqKngkgkWevtgiaaRiagkgsittnlsrGGtalple 167
                                         + +Q+ i++++  g   D+R++v    +g  ++ g++ R a++g+ ++nl+rGG+  p  
  gi|330506784|ref|YP_004383212.1| 174 GMVYLQEFINVTS--GSARDIRAFVV---DG--RLQGAIYRNAPPGEWISNLARGGRPTPCP 228
                                       45789******98..9999******9...44..4679*******************987765 PP

>> Rimk_N  RimK PreATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   6.1e-08   0.00016       1      94 []       1      97 [.       1      97 [. 0.97
   2 ?   -2.0   0.0       1.9   4.9e+03       5      27 ..     153     175 ..     151     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.1e-08
                            Rimk_N  1 mkiaiLsrnpelystrrLveaaekrghevevldplrcylkieaekpevyykgekleefdavipR.i...gasitfygta 75
                                      mk++i  ++++ ++ + L++   +r +++ +ld+++++  i + + +  + + +l ++da ++R +   ga  + ++ +
  gi|330506784|ref|YP_004383212.1|  1 MKVGIVVSDRDDWTAQALMASFSRRQMDATFLDFSELKSGIGK-RLDFSCGDVNLLDLDALVVRdLgrrGAVDVSFRFE 78
                                      9****************************************99.9*******************877778889****** PP

                            Rimk_N 76 vlrqFemmgvfvlneseAi 94
                                       l  + ++g+ v+n +eAi
  gi|330506784|ref|YP_004383212.1| 79 ALTALVELGISVINPPEAI 97
                                      ******************8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                            Rimk_N   5 iLsrnpelystrrLveaaekrgh 27 
                                       iL ++++    + L e +e+rg+
  gi|330506784|ref|YP_004383212.1| 153 ILLKSSKQADIESLREIVERRGM 175
                                       56666667788999999999997 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 !   10.9   0.0   7.5e-05      0.19       8      89 ..      89     165 ..      86     189 .. 0.80
   2 ?    2.6   0.0     0.026        67     223     267 ..     228     270 ..     223     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.5e-05
                       ATPgrasp_ST   8 rkyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvitered 84 
                                       + +Np +++   ++K  +++ ++ a +++p+++++ + +   ++l     ++++  v Kp  g  Gk+i+ +++ ++
  gi|330506784|ref|YP_004383212.1|  89 SVINPPEAISSAANKYATSRRLHGASVPTPRTVATTSPKIAEEAL----YSFKT-AVSKPLFGYKGKDIILLKSSKQ 160
                                       568999*************************88888776554444....44534.678**************99887 PP

                       ATPgrasp_ST  85 qdylk 89 
                                       +d+ +
  gi|330506784|ref|YP_004383212.1| 161 ADIES 165
                                       77654 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.026
                       ATPgrasp_ST 223 PnweevlelaakaaeklpglgylGwDivldeekgplllElNarpg 267
                                       P+ +e+ +la++ a   +g  y G+D+   +++ +  +E+N +p+
  gi|330506784|ref|YP_004383212.1| 228 PKTRELEDLAVRSAR-AVGAIYCGVDLLESKDG-LTTIEVNGTPS 270
                                       777788899999998.99999*****9666666.*******9975 PP

>> GSP_synth  Glutathionylspermidine synthase preATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.2e-05     0.031     289     360 ..     136     207 ..     120     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                         GSP_synth 289 gkkyvkKplfgREGanveiveegsevaeekege.ygeekviy.QeyaelpkfdgsypvlgswlvgdeaaGlgiR 360
                                        k+ v+Kplfg  G+ + +++  +++  e+  e  ++ +++y Qe++++ +  gs   + +++v+++  G   R
  gi|330506784|ref|YP_004383212.1| 136 FKTAVSKPLFGYKGKDIILLKSSKQADIESLREiVERRGMVYlQEFINVTS--GSARDIRAFVVDGRLQGAIYR 207
                                       5788****************8766665554444277789998799998876..888899999999998887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2260.83
//
Query:       gi|330506785|ref|YP_004383213.1|  [L=656]
Description: acetyl-coenzyme A synthetase [Methanosaeta concilii GP6]
Scores for complete 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-88  294.7   0.0    1.1e-87  294.4   0.0    1.1  1  AMP-binding     AMP-binding enzyme
    2.1e-22   79.9   1.4    2.7e-21   76.3   1.6    2.4  2  AMP-binding_C   AMP-binding enzyme C-terminal domain
    4.4e-14   52.1   5.6    4.4e-14   52.1   5.6    2.2  3  ACAS_N          Acetyl-coenzyme A synthetase N-terminus
  ------ inclusion threshold ------
       0.11   11.5   0.2       0.42    9.5   0.0    1.9  2  Glyco_hydro_14  Glycosyl hydrolase family 14
       0.11   12.7   0.0       0.21   11.8   0.0    1.4  1  DNA_pol_B_palm  DNA polymerase beta palm


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 !  294.4   0.0   3.1e-91   1.1e-87       2     422 ..      98     535 ..      97     536 .. 0.88

  Alignments for each domain:
  == domain 1  score: 294.4 bits;  conditional E-value: 3.1e-91
                                       HHHHHHST.TSEEEEE....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-E CS
                       AMP-binding   2 eeqaaktp.dkvalvd....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGav 73 
                                       +++a+ ++ +k a+++     g+ +++TY el++ vnr+A++L+++GvkkgdrV+i+lp+ pe+ va+la++k+Ga+
  gi|330506785|ref|YP_004383213.1|  98 DRHAKSWRrNKLAYIFvgepVGDVRKITYYELYRDVNRFANALQKMGVKKGDRVGIYLPMIPELPVAMLACAKLGAI 174
                                       57777777799999999999889****************************************************** PP

                                       EEEEETTS-HHHHHHHHHHHTESEEE.......ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCC CS
                       AMP-binding  74 vvplnptltaeelayiledseakvli.......atvdsel.leklleaaakleavklvivldadellkeeelkeeee 142
                                       +v++ ++++a +++  led+++kvli       +  + ++  ++++ea a le  ++v+v+++++ +++ ++  +  
  gi|330506785|ref|YP_004383213.1| 175 HVVVFSGFSAVAVRDRLEDCQPKVLItcdgsyrR-GKPIAtKPQADEAIAGLEYIEKVVVVKRNGQETAMQEGRDVW 250
                                       **************************99987652.345555667777888899999999999988766644444443 PP

                                       CSCTTS.......-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHH.HHHHHHHHHHHC.SCCTTT-EEEESS- CS
                       AMP-binding 143 seekae.......kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnl.vanvaslkletr.fklkeddvvlsilp 210
                                       ++   +       +  ++ + ++ d+++i+YT G  GkP G++++h+ + v  + + +     f++k++dv++++++
  gi|330506785|ref|YP_004383213.1| 251 WD---DfvagqpaTF-DTLPMDSADPLFILYTAGAGGKPRGIVHTHAGAsVGPAFTSS---WvFDIKDTDVYWCTAD 320
                                       33...2445677644.55589*************************666244444422...23778899******** PP

                                       TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-S CS
                       AMP-binding 211 lahifglilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslr 286
                                       + +i+g+++  +++l+ Gat v+++++++ +d ++++  ie+++v+vi+++P+++++++++g+     +++dls +r
  gi|330506785|ref|YP_004383213.1| 321 IGWITGHSYIAYGPLSLGATSVMYEGSPDyPDFGRWFSIIEEYGVSVIYTAPTAIRMFMNEGPNW--PQKYDLSTVR 395
                                       *****************************888****************************65333..4567****** PP

                                       EEEEESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE CS
                       AMP-binding 287 lvllggeplspellrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvp 360
                                       l+ ++ge+++p++  ++r+ +g+   ++++++ ++Et+  v+ +pl+    k+gs  +plpg  v++vDe+ g+p +
  gi|330506785|ref|YP_004383213.1| 396 LMGSVGEAMNPDAFIWWRKYVGGgaaPIMDTWFQSETCSQVI-APLPITPLKPGSPSFPLPGYNVRVVDEN-GQPSA 470
                                       **********************9******************9.7777777899*****************9.***** PP

                                       TTSEEEEEEEET..TS-SEBTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 361 dgeeGellvrgp..gvmkgYlkkpeataeafdse.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                        g +G + +  p  ++ +  +++p++ +e+++s  ++ + +GD +r+dedGy++ +gR +d++k+
  gi|330506785|ref|YP_004383213.1| 471 AGATGDIIITEPwpSMLREIYRDPAQYNETYWSTfPGKYFSGDKARVDEDGYIWALGRGDDVLKV 535
                                       ***********9778*****************845679*************************98 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.39   1.4e+03      42      67 ..      41      58 ..      19      65 .. 0.56
   2 !   76.3   1.6   7.6e-25   2.7e-21       1      76 []     544     622 ..     544     622 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.39
                                      HHHHHHHHHHHHT-TTTS-SEEEE-S CS
                     AMP-binding_C 42 leeeLkahvrkelgpyavpkkvvfvd 67
                                       e+eL+a++          ++v f d
  gi|330506785|ref|YP_004383213.1| 41 SEKELRAWCS--------ENYVQFWD 58
                                      2455555554........44555555 PP

  == domain 2  score: 76.3 bits;  conditional E-value: 7.6e-25
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.-.--.HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.s.ea.leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evE+   +hpaV+ aaVvG+pd+vkGe +v++ vl++g + +a l++++k +vrk+lgp+a p++vvfv+++p+++ 
  gi|330506785|ref|YP_004383213.1| 544 EVEASAEKHPAVKAAAVVGKPDKVKGESIVVYAVLNPGiEgDAnLQKDIKTFVRKTLGPIAIPSDVVFVEDIPRNKA 620
                                       8**********************************888633336********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|330506785|ref|YP_004383213.1| 621 GK 622
                                       *9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   5.6   1.2e-17   4.4e-14       2      55 .]      43      96 ..      42      96 .. 0.96
   2 ?   -3.4   0.0       2.6   9.5e+03      38      44 ..     350     357 ..     340     358 .. 0.68
   3 ?   -2.7   0.0       1.7   5.9e+03       3      18 ..     489     504 ..     487     514 .. 0.65

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.2e-17
                                      HHHHHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  2 kelykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                      kel ++  e++ +FW+e+a+   dW++p++ v+++ k+pf+kWF+GGk+Ni++N+
  gi|330506785|ref|YP_004383213.1| 43 KELRAWCSENYVQFWDEMARTyADWFEPYKDVVQW-KAPFAKWFTGGKINIAHNA 96
                                      68999***************98*************.******************7 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.6
                                       TC.T-EES CS
                            ACAS_N  38 gp.fikWF 44 
                                        p f +WF
  gi|330506785|ref|YP_004383213.1| 350 YPdFGRWF 357
                                       45599999 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.7
                                       HHHHHHHH-HHHHHHH CS
                            ACAS_N   3 elykeSiedpeaFWae 18 
                                       e+y+   + +e++W+ 
  gi|330506785|ref|YP_004383213.1| 489 EIYRDPAQYNETYWST 504
                                       5566666666777764 PP

>> Glyco_hydro_14  Glycosyl hydrolase family 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00012      0.42      99     147 ..      27      75 ..      22      79 .. 0.94
   2 ?   -1.2   0.1      0.21   7.6e+02      22      76 ..     231     292 ..     221     344 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
                    Glyco_hydro_14  99 skdelvfkdesGrankealsPllsgrtikeyselyasfaerfegykdvi 147
                                       s++ + + +e G++ ++ l    s+  ++ ++e+ +++a+ fe+ykdv+
  gi|330506785|ref|YP_004383213.1|  27 SSNVMAWMKEKGMKSEKELRAWCSENYVQFWDEMARTYADWFEPYKDVV 75 
                                       788999*****************************************98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.21
                    Glyco_hydro_14  22 lralkqnGveaitv...dvwwGlvekdGdqqfdf....syykelaqavkkaGlklvviisth 76 
                                       + ++k nG e+ +    dvww +     +  fd     s    ++     aG k   i+ th
  gi|330506785|ref|YP_004383213.1| 231 VVVVKRNGQETAMQegrDVWWDDFVAGQPATFDTlpmdSADPLFILYTAGAGGKPRGIVHTH 292
                                       567899999988844449***99988888888852221222235555555666666666665 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.7e-05      0.21      13      38 ..     186     211 ..     182     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.7e-05
                                       HHHHHHHHH-TT-EEEE-HHHHTT-S CS
                    DNA_pol_B_palm  13 lvkkaakeldpevevivcGSYRRgae 38 
                                       +v++ +++ +p+v +++ GSYRRg+ 
  gi|330506785|ref|YP_004383213.1| 186 AVRDRLEDCQPKVLITCDGSYRRGKP 211
                                       689999******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 4217.50
//
Query:       gi|330506786|ref|YP_004383214.1|  [L=661]
Description: acetyl-coenzyme A synthetase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-89  300.4   0.0      2e-89  300.1   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    9.3e-28   97.0   7.3    1.2e-27   96.6   4.3    2.7  3  AMP-binding_C  AMP-binding enzyme C-terminal domain
    5.7e-17   61.4   2.2    5.7e-17   61.4   2.2    2.1  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
  ------ inclusion threshold ------
       0.27   11.2   1.0       0.45   10.4   0.0    1.8  2  DUF3797        Domain of unknown function (DUF3797)


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.1   0.0   4.4e-93     2e-89       3     422 ..      99     539 ..      97     540 .. 0.90

  Alignments for each domain:
  == domain 1  score: 300.1 bits;  conditional E-value: 4.4e-93
                                       HHHHHST.TSEEEEE....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EE CS
                       AMP-binding   3 eqaaktp.dkvalvd....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavv 74 
                                       ++a+  + dkva+++     g+ + +TY++l+ +vn++A++L+ +Gv kgdrV+ +lp+ pe+ +++la++k+Ga++
  gi|330506786|ref|YP_004383214.1|  99 RHAKGAKkDKVAYHFigepVGDARDITYGQLYIEVNKMANALKGAGVVKGDRVVAYLPMIPELPITMLACAKIGAIH 175
                                       55655555*****9999*9889*********************88******************************** PP

                                       EEEETTS-HHHHHHHHHHHTESEEE.......ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCC CS
                       AMP-binding  75 vplnptltaeelayiledseakvli.......atvdsel.leklleaaakleavklvivldadellkeeelkeeees 143
                                         + +++++  l   ++d+eakv++       +  +     ++++ea+++ ++v++v+v+++ +++   ++  +   
  gi|330506786|ref|YP_004383214.1| 176 TIVFSGFSSGGLNSRVNDAEAKVVVtadgfyrR-GKPLPlKPNVDEAMKTAPSVQKVVVVKRTGVAVPMTEGRDV-Y 250
                                       *************************99887642.34556689999******************999986665555.3 PP

                                       SCTT.S...-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHH.HHHCSCCTTT-EEEESS-TTSC CS
                       AMP-binding 144 eeka.e...kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslk.letrfklkeddvvlsilplahi 214
                                       +++  +   +++e++ l+p+d ++i+YTSGTTGkPKG+ + h +++v+ +++ + +    ++++ddv+++++++ +i
  gi|330506786|ref|YP_004383214.1| 251 YDDFvKgqsEECETVMLDPEDRLFILYTSGTTGKPKGIEHAHgGYAVTPAQTTSwV---MDVHDDDVFWCTADCGWI 324
                                       333342567799999***************************77778887775431...457789************ PP

                                       HHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEE CS
                       AMP-binding 215 fglilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvll 290
                                       +g+++ ++++l+ Ga+ +l++++++ +d ++++  iek++vtv++++P++++++++ g++  ++k+++ls++r++ +
  gi|330506786|ref|YP_004383214.1| 325 TGHSYVVYGPLCLGASTILYEGSPDfPDLGRWWSIIEKYGVTVFYTAPTAIRMFMKTGEE--FVKKYNLSKVRILAS 399
                                       *************************88899**************************7544..467779********* PP

                                       ESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSE CS
                       AMP-binding 291 ggeplspellrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgee 364
                                       +gepl+pe+  +fr+  g    ++++++++TEt+++v+ +pl    +k+gsv +plpg    i De+  + vp g  
  gi|330506786|ref|YP_004383214.1| 400 VGEPLNPEAYMWFRKNIGSdraPIIDTWWQTETGCHVI-APLVMTPEKPGSVCFPLPGFNTDIFDED-ANSVPLGYG 474
                                       ****************999******************8.666666678******************9.9******** PP

                                       EEEEEEET..TS-SEBTT-HHHHHHHEEE.....TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 365 Gellvrgp..gvmkgYlkkpeataeafds.....egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       G ++ + p  ++ + +++++ + ++ +++     +++ +  GD +++d+dGy +i gR++d++k+
  gi|330506786|ref|YP_004383214.1| 475 GNIVQKTPwpSMLRAFFRDEVRYKKEYWDmywqvKPGTYLAGDKATRDKDGYWWIQGRIDDVLKV 539
                                       *******9778*****************999977457**************************98 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.9   1.3e+04      53      72 ..      43      62 ..      31      63 .. 0.71
   2 ?   -0.5   0.1      0.59   2.6e+03       2      18 ..     218     234 ..     217     247 .. 0.76
   3 !   96.6   4.3   2.7e-31   1.2e-27       1      76 []     548     626 ..     548     626 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.9
                                      HT-TTTS-SEEEE-S---B- CS
                     AMP-binding_C 53 elgpyavpkkvvfvdelpkt 72
                                      e+ ++   ++++f de+ kt
  gi|330506786|ref|YP_004383214.1| 43 EMRKWCSDNYIEFWDEMAKT 62
                                      55566444488899999988 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.59
                                       HHHHHHSSTTEEEEEEE CS
                     AMP-binding_C   2 vEsalvshpaVaeaaVv 18 
                                       v +a  + p V+ ++Vv
  gi|330506786|ref|YP_004383214.1| 218 VDEAMKTAPSVQKVVVV 234
                                       77899999********9 PP

  == domain 3  score: 96.6 bits;  conditional E-value: 2.7e-31
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE----.--..HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgs.ea..leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evEsa vshp+VaeaaVvG pdevkGe +vafV+l+dg+ e+  l++e+  hvrk lgp+a p+kv+fv+++pktrs
  gi|330506786|ref|YP_004383214.1| 548 EVESAAVSHPKVAEAAVVGQPDEVKGEKIVAFVILRDGVaESpeLAKEISVHVRKVLGPVAYPDKVYFVKDVPKTRS 624
                                       8***********************************99532257********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|330506786|ref|YP_004383214.1| 625 GK 626
                                       *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 !   61.4   2.2   1.3e-20   5.7e-17       3      55 .]      43      96 ..      41      96 .. 0.97
   2 ?   -3.1   0.3       1.8   7.9e+03       7      16 ..     518     527 ..     490     531 .. 0.59

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 1.3e-20
                                      HHHHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  3 elykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                      e+ k+  +++ +FW+e+ak   dW+ p++kvld+s +p++kWF+GGk+N++yN+
  gi|330506786|ref|YP_004383214.1| 43 EMRKWCSDNYIEFWDEMAKTyADWSVPYTKVLDDSGKPYYKWFTGGKINVAYNA 96
                                      7999***************98********************************7 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.8
                                       HHHH-HHHHH CS
                            ACAS_N   7 eSiedpeaFW 16 
                                       ++ +d +++W
  gi|330506786|ref|YP_004383214.1| 518 KATRDKDGYW 527
                                       3344444444 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0001      0.45      21      41 ..     188     208 ..     186     210 .. 0.94
   2 ?   -3.3   0.3       1.9   8.5e+03      34      46 ..     311     323 ..     309     323 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                           DUF3797  21 NnkvlNsegkviieddtfyre 41 
                                       N +v+  e+kv++  d fyr 
  gi|330506786|ref|YP_004383214.1| 188 NSRVNDAEAKVVVTADGFYRR 208
                                       99*****************96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.9
                           DUF3797  34 eddtfyreCkCgf 46 
                                       +dd f     Cg+
  gi|330506786|ref|YP_004383214.1| 311 DDDVFWCTADCGW 323
                                       7899999999*98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (661 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 4383.33
//
Query:       gi|330506787|ref|YP_004383215.1|  [L=662]
Description: acetyl-coenzyme A synthetase [Methanosaeta concilii GP6]
Scores for 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-93  311.7   0.0    7.8e-93  311.4   0.0    1.1  1  AMP-binding      AMP-binding enzyme
    5.6e-29  100.9   4.0    5.6e-29  100.9   4.0    2.3  3  AMP-binding_C    AMP-binding enzyme C-terminal domain
    4.4e-14   52.1   6.0    4.4e-14   52.1   6.0    2.1  2  ACAS_N           Acetyl-coenzyme A synthetase N-terminus
  ------ inclusion threshold ------
       0.15   11.4   0.0       0.26   10.6   0.0    1.3  1  DNA_pol3_finger  Bacterial DNA polymerase III alpha subunit f


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.4   0.0   1.7e-96   7.8e-93       3     422 ..     101     542 ..      99     543 .. 0.90

  Alignments for each domain:
  == domain 1  score: 311.4 bits;  conditional E-value: 1.7e-96
                                       HHHHHST.TSEEEEE.....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-E CS
                       AMP-binding   3 eqaaktp.dkvalvd.....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGav 73 
                                       ++a+  + dkva+++     ++  q++TY++l+++vn++A+gL+slGv kgdrV++++p+ p++ +a+lai+k+Ga+
  gi|330506787|ref|YP_004383215.1| 101 RHAQGAKkDKVAYIFvpeptDQPTQKITYAQLEKEVNKFANGLKSLGVVKGDRVMLYMPMIPQLPIAMLAIAKIGAI 177
                                       55655555************999****************************************************** PP

                                       EEEEETTS-HHHHHHHHHHHTESEEE.......ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCC CS
                       AMP-binding  74 vvplnptltaeelayiledseakvli.......atvdsel.leklleaaakleavklvivldadellkeeelkeeee 142
                                       +  + +++++  l   + d+eakv+i       +  +     ++++ea+a+ ++vk v+v ++ +++   ++ ++  
  gi|330506787|ref|YP_004383215.1| 178 HCIVFSGFSSGGLNSRIMDAEAKVVItvdgfyrR-GKPLPlKPNVDEATANTPSVKNVVVCKRTGVAVPMKEGKDIW 253
                                       **************************99888742.34556689999999999**********999998866666655 PP

                                       CSCTTS......-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHC.SCCTTT-EEEESS-T CS
                       AMP-binding 143 seekae......kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletr.fklkeddvvlsilpl 211
                                       ++   +      + +e e+ +++d ++i+YTSGTTGkPKG+ + h ++ v  +++l+     f++k++dv+++++++
  gi|330506787|ref|YP_004383215.1| 254 WD---DlvagksDACECEKMDSEDRLFILYTSGTTGKPKGIEHVHgGYQVGPAQTLH---WvFDVKDNDVWWCTADI 324
                                       55...13446677889999**************************555677767753...2478899********** PP

                                       TSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SE CS
                       AMP-binding 212 ahifglilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrl 287
                                        +i+g+++ ++++l+ Gat ++++++++ +d +++++ i++ kv+v++++P+++++l+++g+     k++d sslrl
  gi|330506787|ref|YP_004383215.1| 325 GWITGHSYIVYGPLVLGATSIMYEGSPDfPDLGRWYKIIQDNKVSVFYTAPTAVRMLMKAGDSW--AKKYDVSSLRL 399
                                       ****************************8889***************************86554..45679****** PP

                                       EEEESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEET CS
                       AMP-binding 288 vllggeplspellrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpd 361
                                       + ++gep++pe++ ++r++fg    ++++++++TEt+++++  pl+    k+gs+ +plpg  + ++Dee  +pvp 
  gi|330506787|ref|YP_004383215.1| 400 LGSVGEPINPEAWMWYRNTFGAgklPIMDTWWQTETGTFLV-SPLPITPLKPGSATFPLPGFNIDVLDEE-ANPVPL 474
                                       ****************************************9.6667777799*****************9.****** PP

                                       TSEEEEEEEET..TS-SEBTT-HHHHHHHEEE......TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 362 geeGellvrgp..gvmkgYlkkpeataeafds......egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       g  G ++   p  ++ + ++++pe+ ++ ++s      + + +  GD +  d+dGy++i gR++d++k+
  gi|330506787|ref|YP_004383215.1| 475 GSGGNIVSNTPwpSMLRAFYRDPERYQKEYWStywdirP-GTYLAGDKAMKDKDGYFFIQGRIDDVLKI 542
                                       *********99778*****************88998744.7**************************98 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.3   1.5e+04      31      50 ..     114     140 ..     105     148 .. 0.51
   2 ?   -1.8   0.1       1.4   6.3e+03       2      18 ..     221     237 ..     220     248 .. 0.78
   3 !  100.9   4.0   1.2e-32   5.6e-29       1      76 []     551     629 ..     551     629 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.3
                                       EEEEE---...---......HHHHHHHHH CS
                     AMP-binding_C  31 afVvlkdg...sea......leeeLkahv 50 
                                        f v+++    + +      le+e+++++
  gi|330506787|ref|YP_004383215.1| 114 IF-VPEPTdqpT-QkityaqLEKEVNKFA 140
                                       23.343222221.1354444666666554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                                       HHHHHHSSTTEEEEEEE CS
                     AMP-binding_C   2 vEsalvshpaVaeaaVv 18 
                                       v +a ++ p V++++V 
  gi|330506787|ref|YP_004383215.1| 221 VDEATANTPSVKNVVVC 237
                                       67889999******997 PP

  == domain 3  score: 100.9 bits;  conditional E-value: 1.2e-32
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evEsalvshp+VaeaaV+G+pdevkGe++vafV+l++g+e+   l++eL +hvr+ lgp+a p++v fv+++pktrs
  gi|330506787|ref|YP_004383215.1| 551 EVESALVSHPKVAEAAVIGKPDEVKGEVIVAFVILRTGQEEteeLKKELAKHVRTVLGPVAYPETVLFVKDVPKTRS 627
                                       8**********************************999533356********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|330506787|ref|YP_004383215.1| 628 GK 629
                                       *9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   6.0   9.8e-18   4.4e-14       2      55 .]      45      98 ..      44      98 .. 0.95
   2 ?   -2.7   0.0       1.3   5.7e+03       7      20 ..     492     505 ..     488     528 .. 0.60

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 9.8e-18
                                      HHHHHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  2 kelykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                      +e+  +  +++ +FW+e+ak   dW++p++++l++ k+p++kWF+GGk N+++Nc
  gi|330506787|ref|YP_004383215.1| 45 REMRLWCSANYIQFWGEMAKTyADWFEPWSSTLEW-KPPYAKWFVGGKCNVTHNC 98
                                      57888899999*********98*************.999**************** PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                       HHHH-HHHHHHHHH CS
                            ACAS_N   7 eSiedpeaFWaeqa 20 
                                          +dpe++ +e +
  gi|330506787|ref|YP_004383215.1| 492 AFYRDPERYQKEYW 505
                                       44455544333322 PP

>> DNA_pol3_finger  Bacterial DNA polymerase III alpha subunit finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.8e-05      0.26      74     146 ..     569     638 ..     561     645 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.8e-05
                                       SSHHHHHTTHHHHHHHHHTTSS----SSHHHTTTTTTTTT---BHHHHHHHHHHHH---HHHHHHHHHHHHH.- CS
                   DNA_pol3_finger  74 yRpgpvqggnvddyikrkngeekveyihpeleeiLketygvivyQEqvmqiaqvlagfslgeAdllrramgk.k 146
                                        +p  v+g+ +  ++  + g+e++e +++el++++++  g + y E v+ +    +++  +++ +++r + k k
  gi|330506787|ref|YP_004383215.1| 569 GKPDEVKGEVIVAFVILRTGQEETEELKKELAKHVRTVLGPVAYPETVLFV----KDVPKTRSGKIMRRVIKaK 638
                                       589999**************************************9988755....6677777777777776634 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4376.68
//
Query:       gi|330506788|ref|YP_004383216.1|  [L=672]
Description: acetyl-coenzyme A synthetase [Methanosaeta concilii GP6]
Scores for complete 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-94  316.1   0.0    4.3e-94  315.5   0.0    1.3  1  AMP-binding    AMP-binding enzyme
    1.7e-27   96.2   2.1    3.4e-27   95.2   1.8    1.7  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
    2.5e-17   62.5   2.5    2.5e-17   62.5   2.5    2.4  3  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 !  315.5   0.0   7.2e-98   4.3e-94       3     422 ..     108     551 ..     106     552 .. 0.91

  Alignments for each domain:
  == domain 1  score: 315.5 bits;  conditional E-value: 7.2e-98
                                       HHHHHST.TSEEEEE.....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-E CS
                       AMP-binding   3 eqaaktp.dkvalvd.....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGav 73 
                                       ++a+  + dkva+++     ++  q++TY++l+++vn++A+gL+slG+kkgdrV i++p+ p++ +a+la++k+G++
  gi|330506788|ref|YP_004383216.1| 108 RHAKGAKkDKVAYIWipeptDQPVQKITYGDLYKEVNKFANGLKSLGLKKGDRVSIYMPMIPQLPIAMLACAKLGVI 184
                                       56655555************999****************************************************** PP

                                       EEEEETTS-HHHHHHHHHHHTESEEE.......ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCC CS
                       AMP-binding  74 vvplnptltaeelayiledseakvli.......atvdsel.leklleaaakleavklvivldadellkeeelkeeee 142
                                       ++++ ++++++ l    +d++++++i       +  +     ++++eaa+  ++v+++iv+++++++ + ++  +  
  gi|330506788|ref|YP_004383216.1| 185 HSVVFSGFSSKGLMDRAADCGSRAIItvdgfyrR-GKPVPlKPNADEAAGGAPSVEKIIVYKRAGVDVSMKEGRDVW 260
                                       **************************99888742.34555578899999999***********99999877666665 PP

                                       CSCTTS...-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSC CS
                       AMP-binding 143 seekae...kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletr.fklkeddvvlsilplahi 214
                                       + +  +   +++e+++++p++ +yi+YTSGTTGkPKG+ + + +n+v  +++l+     f+lk+ddv+++++++ ++
  gi|330506788|ref|YP_004383216.1| 261 WHDLVKgqsEECEPVWVDPEHRLYILYTSGTTGKPKGIEHATgGNAVGPAQTLH---WvFDLKDDDVWWCTADIGWV 334
                                       55443267789999****************************9****9999974...3488999************* PP

                                       HHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEE CS
                       AMP-binding 215 fglilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvll 290
                                       +g+++ ++++l+ G+t  ++++ a+ +d +++++ i+++kvtv++++P+++++++++ga+    +++dlsslrl+ +
  gi|330506788|ref|YP_004383216.1| 335 TGHSYIVYAPLILGMTSLMYEGAADyPDFGRWWKNIQDHKVTVLYTAPTAVRMFMKQGAEW--PDKYDLSSLRLLGS 409
                                       *************************888****************************87665..5677********** PP

                                       ESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSE CS
                       AMP-binding 291 ggeplspellrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgee 364
                                       +gep++pe++ ++r++ g+   ++++++++TEt++++   pl+    k+gs+ +plpg ++ i+Dee g++vp g  
  gi|330506788|ref|YP_004383216.1| 410 VGEPINPEAWMWYREHIGRgelQIMDTWWQTETGTFLN-SPLPITPLKPGSCTFPLPGYDISILDEE-GNEVPLGSG 484
                                       *****************99******************8.6666666799*****************9.********* PP

                                       EEEEEEET..TS-SEBTT-HHHHHHHEEE......TCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 365 Gellvrgp..gvmkgYlkkpeataeafds......egr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                       G ++  +p  ++ + +++++e+  + +++      + r  +  GD + +d+dGy++i gR++d++ +
  gi|330506788|ref|YP_004383216.1| 485 GNIVALKPypSMLRAFWGDKERFMKEYWQfywdvpGRRgVYLAGDKAQRDKDGYFFIQGRIDDVLSV 551
                                       ****9999778*****************99999963344************************9865 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         3   1.8e+04      42      52 ..      47      57 ..      36      68 .. 0.74
   2 !   95.2   1.8   5.6e-31   3.4e-27       1      76 []     560     638 ..     560     638 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3
                                      HHHHHHHHHHH CS
                     AMP-binding_C 42 leeeLkahvrk 52
                                      +e+e +a++ +
  gi|330506788|ref|YP_004383216.1| 47 TEKEMRAWCSS 57
                                      67999999854 PP

  == domain 2  score: 95.2 bits;  conditional E-value: 5.6e-31
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evEsalv+hp++aeaaVvG+pdevkGe +vafV+l+ g+e+   l+++ +a+vrk+lgp+a+p +v+fv++lpktrs
  gi|330506788|ref|YP_004383216.1| 560 EVESALVAHPKIAEAAVVGKPDEVKGESIVAFVILRVGNEPspeLAKDAIAFVRKTLGPVAAPTEVHFVNDLPKTRS 636
                                       8**********************************867422347********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|330506788|ref|YP_004383216.1| 637 GK 638
                                       *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 !   62.5   2.5   4.1e-21   2.5e-17       5      55 .]      54     105 ..      49     105 .. 0.92
   2 ?   -3.5   0.0       1.8   1.1e+04      13      22 ..     364     373 ..     353     388 .. 0.61
   3 ?   -1.4   0.3      0.38   2.3e+03      14      27 ..     499     518 ..     493     541 .. 0.66

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 4.1e-21
                                       HHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N   5 ykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55 
                                       +  S e++ +FW+e+ak  +dW+k+++kv+d+s++p+++WF+GG++Ni+yN+
  gi|330506788|ref|YP_004383216.1|  54 WCSSDEHYLEFWDEMAKTyVDWHKTYTKVMDDSEMPYFHWFTGGEINITYNA 105
                                       44588999*********99********************************7 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.8
                                       HHHHHHHHCC CS
                            ACAS_N  13 eaFWaeqake 22 
                                        ++W+++ ++
  gi|330506788|ref|YP_004383216.1| 364 GRWWKNIQDH 373
                                       4677776655 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.38
                                       HHHHHHHC......CS--SB CS
                            ACAS_N  14 aFWaeqak......eldWek 27 
                                       aFW++  +      +++W+ 
  gi|330506788|ref|YP_004383216.1| 499 AFWGDKERfmkeywQFYWDV 518
                                       67776655433222366655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (672 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); 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:                         3  (0.000167327); expected 0.2 (1e-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: 4519.48
//
Query:       gi|330506789|ref|YP_004383217.1|  [L=437]
Description: hypothetical protein MCON_0563 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.9e-21   75.0   0.0    3.9e-20   72.9   0.0    2.0  2  Radical_SAM  Radical SAM superfamily
      1e-16   60.7   0.1    2.2e-16   59.7   0.1    1.5  1  UPF0004      Uncharacterized protein family UPF0004
    1.9e-05   24.6   0.0    3.7e-05   23.6   0.0    1.5  1  TRAM         TRAM domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.34     2e+03      74     105 ..      31      67 ..       7      70 .. 0.65
   2 !   72.9   0.0   6.5e-24   3.9e-20       1     167 []     153     325 ..     153     325 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.34
                                       C...CCTEEEEEEECSSCHG..HHHHHHHHHTT-SEE CS
                                       x...xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                       Radical_SAM  74 a...vpgiritvetngtlpd..eeklerllelgvdrv 105
                                           ++   + v t++++ +  +++l+rl++l+  r+
  gi|330506789|ref|YP_004383217.1|  31 PsglKEADMVIVNTCAVTERteRKILRRLRQLEGERL 67 
                                       4555555666666777776676888888888876655 PP

  == domain 2  score: 72.9 bits;  conditional E-value: 6.5e-24
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....TTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.....pdfvellerlak 72 
                                       v+v  gCn+ Cs+C++++    +gr +s++ve+++  v++l a  g+ e+ ++ ++  +      +d++ lle l +
  gi|330506789|ref|YP_004383217.1| 153 VNVADGCNGSCSYCIVSK---ARGRLKSRPVEDVVLAVERL-AQLGTAEIQISAQDTAAFgsdigSDLAGLLETLTE 225
                                       57899************8...8*******************.89999999999888888888888899999999999 PP

                                       TCCCTEEEEEEECSSCHG......HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxxxxxx......xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  73 lavpgiritvetngtlpd......eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagi 142
                                       +      + + +  + pd       + +e++        +++++++++de +l++m+r +t +e+ e++ ++r a  
  gi|330506789|ref|YP_004383217.1| 226 I---PGDFMLRVGMMNPDsarliqNRLIEAFQSPKiYRFLHIPVQSGSDE-ILQRMGRVYTSDEFFELVSAFRFA-Y 297
                                       9...4555555555555556888899999999977***************.************************.8 PP

                                       ET...EEEEEEEBTTTSHHHHHHHHHHH CS
                                       xx...xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 143 kr...vvdrivglpGendeeleellell 167
                                       ++   ++d+ivg+pGe+d+++ee ++l+
  gi|330506789|ref|YP_004383217.1| 298 PDisiITDIIVGFPGETDKDFEESMSLI 325
                                       999********************99876 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.1   3.6e-20   2.2e-16       1      87 [.       2      82 ..       2      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 3.6e-20
                                      XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHH CS
                           UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCma 79
                                      +++iet+GC+ N  +s+ la++L+++g+      +eAd+v+vnTCav+e++e+k++++lr+l+ ++     +vv+GC+a
  gi|330506789|ref|YP_004383217.1|  2 RFYIETFGCTSNFGNSQDLAEALREMGHIPSG-LKEADMVIVNTCAVTERTERKILRRLRQLEGER-----LVVAGCLA 74
                                      799************************97755.589***********************9999877.....9******* PP

                                      HS-HHHHH CS
                           UPF0004 80 qrekeell 87
                                       + +++++
  gi|330506789|ref|YP_004383217.1| 75 AAIPQSIQ 82
                                      99888775 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   6.2e-09   3.7e-05       1      60 [.     377     434 ..     377     435 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.2e-09
                                       XXXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEE CS
                              TRAM   1 rsyvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGe 60 
                                       r+y G+++  lv++ + ++ ++ +r  n+  +++pg+l  +G++ ++kI +++++yL G 
  gi|330506789|ref|YP_004383217.1| 377 RRYLGKVLHALVTECG-RDKTMKARSANYAGIVIPGALD-LGRWCQIKIMETTPYYLSGI 434
                                       689*************.*******************999.*****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 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:                        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 0.24s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2895.27
//
Query:       gi|330506790|ref|YP_004383218.1|  [L=346]
Description: hypothetical protein MCON_0564 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-39  136.5  30.5    1.4e-39  136.1  30.5    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 !  136.1  30.5     8e-44   1.4e-39       2     323 ..      15     332 ..      14     335 .. 0.91

  Alignments for each domain:
  == domain 1  score: 136.1 bits;  conditional E-value: 8e-44
                   AI-2E_transport   2 llilvllllllalypfiselllplliAlvlayllnpvvkfL.kkrgvkrvlavllvlllllvllvllvlllvpllia 77 
                                       +lil+l+++l+ + ++++ +l  ++++ v+ay+  p+ +++ k++++   +a+++v++ ++++l l  l ++    +
  gi|330506790|ref|YP_004383218.1|  15 ILILALAAVLMTACFAFP-FLDGIILGSVFAYVGRPIRDRFgKRKKLGSLVAAICVVVPIFLMLGLGSLEVA----T 86 
                                       578899999999999999.******************************************99999999999....9 PP

                   AI-2E_transport  78 qltqlvkslpayidslqnilnelpslleelenliqalkqslskilsnilssilns.llsllasllglilslvlvlll 153
                                       q++ l k+ +a+  +l  ++++    l+ +    + l + l++ +  i s  +++ +l++ + +  +i+++++++ +
  gi|330506790|ref|YP_004383218.1|  87 QIIALAKNQEALRYWLGYLMQQTATDLPSWA--RESLLSGLENAFGLIASLAASIpILQIGRMASLGIINFLISFPI 161
                                       9999999999999999999999999999995..67788888888888888886654778888888889********* PP

                   AI-2E_transport 154 lffllldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvgl 230
                                       ++f+lldge ++  +++llp++ ++ +++++ +++++lsg+++g+v ++++ ++++++++ ++ +p ++ la +v++
  gi|330506790|ref|YP_004383218.1| 162 CYFILLDGEGFVGSLISLLPDGEMRVLERYIDRIDRILSGIFIGTVYTSIVGSLIAAVIFFLFDIPRPIALASIVFI 238
                                       ***************************************************************************** PP

                   AI-2E_transport 231 anliPyiGavivlipiaiialltggikevliv.livvllvqliegnilePklmgkrlglhplvillsllaggklfGl 306
                                       a ++P++ ++ vl+p+a++ ++t g + +l++ +i+ +l+ l  + +++P++++ r +lhpl+++ls+++g+ ++G+
  gi|330506790|ref|YP_004383218.1| 239 AGMVPVLTSWAVLVPLAVYRYFTVGLEGALFFlVISSALIYLPSELFIRPYIISTRSSLHPLLVMLSFFGGALVAGI 315
                                       *************************6666655055666777778899****************************** PP

                   AI-2E_transport 307 vGlilavpltavikail 323
                                        G++la+ + ++i  i+
  gi|330506790|ref|YP_004383218.1| 316 GGFFLAPAVIGAISGIY 332
                                       *********99987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2408.95
//
Query:       gi|330506791|ref|YP_004383219.1|  [L=379]
Description: anthranilate phosphoribosyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-60  202.4   0.0    1.2e-59  202.0   0.0    1.2  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
      9e-13   47.9   0.1    2.3e-12   46.6   0.1    1.6  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
  ------ inclusion threshold ------
       0.19   12.0   1.1       0.47   10.7   1.1    1.6  1  Flagellin_IN     Flagellin hook IN motif


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 !  202.0   0.0     2e-63   1.2e-59       3     252 ..      91     348 ..      89     349 .. 0.91

  Alignments for each domain:
  == domain 1  score: 202.0 bits;  conditional E-value: 2e-63
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl 79 
                                       +l+D++gTG d  +tfNiStaa+iv+Aa  +++akhg r+++s++G+ D+Le+lg++++++ + v++++e +g+g+ 
  gi|330506791|ref|YP_004383219.1|  91 PLADNCGTGMDSIKTFNISTAASIVAAADKINMAKHGSRAITSSCGTVDMLEQLGIDVDCDVDLVKRSIEVAGIGIF 167
                                       689************************************************************************99 PP

                                       EHHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCS.TS.... CS
                   Glycos_transf_3  80 fapeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhg.dG.... 151
                                          + +      + +  ++ + Tv n+ G L npa + + + gvys e++ ++a ++ke+g +ra+v+hg +G    
  gi|330506791|ref|YP_004383219.1| 168 NGMSGKVHPSALSRILSQIRFGTVLNIAGSLANPALPAYGVRGVYSREMVLPIARAMKEIGYKRAFVIHGrSGddlr 244
                                       6666555556788999*****************************************************98854444 PP

                                       .HHHHHHHHHHHHHHHH.TTEEEEEEEEEGSSTSSSEEESHH..HHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHH CS
                   Glycos_transf_3 152 .ldevsllakttvaelk.dgeiteytlepedfglkraeleal..eggepkenaeilkavlegkksaakrdlvllnag 224
                                        +de+s+l+ t vael+ dg+i+ey+l++ d+gl++ + +al  +g+ ++e++++l +vl+g     +rd+v lna+
  gi|330506791|ref|YP_004383219.1| 245 gMDELSTLGRTDVAELDeDGRIREYALNACDLGLEKGDESALlnRGNIEEEAVRLL-RVLSGFDRGDRRDIVCLNAA 320
                                       49***************9*********************99833344445555555.67788888778********* PP

                                       HHHHHTTSSSSHHHHHHHHHHHHHTSHH CS
                   Glycos_transf_3 225 aalvlagkadslkegvakaeevidsGkA 252
                                        +l++ g+ ++l egv+ka ++idsG A
  gi|330506791|ref|YP_004383219.1| 321 PLLCITGRSEDLLEGVEKAGDIIDSGLA 348
                                       **************************98 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 !   46.6   0.1   3.8e-16   2.3e-12       6      59 ..      23      76 ..      21      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 3.8e-16
                                      HHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHH CS
                   Glycos_trans_3N  6 klrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAm 59
                                       l++g +Lt+ e+ +++++il++e +d q +AfL+A+ +kG taeEia+  eA+
  gi|330506791|ref|YP_004383219.1| 23 ELIKGRNLTRGEASDLFRQILNDEQPDLQQGAFLAAITAKGATAEEIAGIWEAI 76
                                      6899**********************************************9997 PP

>> Flagellin_IN  Flagellin hook IN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   7.8e-05      0.47      10      34 ..     101     125 ..      97     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.8e-05
                                       CS-EEEEECTTTBCHHHHHHHHHHC CS
                      Flagellin_IN  10 ketvtisvkagdtlddiadaINavs 34 
                                       + + t++++ ++++ ++ad+IN+++
  gi|330506791|ref|YP_004383219.1| 101 DSIKTFNISTAASIVAAADKINMAK 125
                                       45577*****************544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2618.46
//
Query:       gi|330506792|ref|YP_004383220.1|  [L=367]
Description: alcohol dehydrogenase, zinc-containing [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-28   97.5   0.2    6.8e-28   96.7   0.2    1.3  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    8.9e-08   32.2   0.0    1.4e-07   31.6   0.0    1.3  1  ADH_zinc_N    Zinc-binding dehydrogenase
     0.0039   18.2   0.0     0.0078   17.3   0.0    1.4  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
  ------ inclusion threshold ------
       0.13   12.9   3.0        2.4    8.8   0.6    2.4  2  IGFBP         Insulin-like growth factor binding protein


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   0.2   1.5e-31   6.8e-28       2     102 ..      25     128 ..      24     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 1.5e-31
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS....--TT-EEEE-SEEE-SSSHHHH CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkk....lkvGdrVvvepliscgeCaaCk 74 
                                       g +li+v+a+++Cg+D+++l++  +    +p ilGHE+vG +ee++++v+     l+ G+ V v p i+cg+C+aC 
  gi|330506792|ref|YP_004383220.1|  25 GGALIRVEACAVCGTDIKMLDQ-GHRDLCYPRILGHEVVGRIEEIDRKVQAdgrqLRAGELVQVWPGIACGHCHACF 100
                                       5689*****************9.7*************************999999********************** PP

                                       TT-GGG-TTBEETTTSS-SSSBSEEEEC CS
                             ADH_N  75 egeenlCeeakllgvsldGgfaeyvvvp 102
                                       +g++n C+++k++g+++dGgfaey+ +p
  gi|330506792|ref|YP_004383220.1| 101 RGADNRCRDMKIIGFNIDGGFAEYLALP 128
                                       ************************9887 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   3.1e-11   1.4e-07       1     125 [.     187     324 ..     187     329 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 3.1e-11
                                       HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEET.........TTC.HHHHHHHHHTTTSSEEEEEESS CS
                        ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadeviny.........kea.dlverikeltggegvdvvfecv 66 
                                       ++G +   lA + Ga e+  + + + +++  k+    +vi +         +   + +  i + t+g+gvdv++ ++
  gi|330506792|ref|YP_004383220.1| 187 PIGALHALLAEMRGAgEILLAERLPGRIREIKRHTSARVIGWfsgnreegqDPFeEAERTILSETDGRGVDVILTAT 263
                                       68999999**************************999***9999998776633334899999999************ PP

                                       CSHHHHHHHHHCEEEEEEEEECSCTSSEEE...EEHHHHHHTT-EEEEE-SSCHHHHHHHHH CS
                        ADH_zinc_N  67 GsgatleaalkllkpgGrlvvvGggkgeee...fdlrnlllkeksilGsllgslreefkeal 125
                                          +  ++ ++ll+pgGr+ ++ g++ ++    +dlr +++ e +i+G  ++s +++ + a 
  gi|330506792|ref|YP_004383220.1| 264 PEVKIDQRQMRLLAPGGRICIFSGPQPGDYegmIDLRSMHYLEQTITGAYGCS-SRQNRMAA 324
                                       *77888889**************9444433579********************.44444344 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.7e-06    0.0078      15     121 ..     244     353 ..     234     359 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
                                       H....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----...S-EEE-CHHHCTTT-EEEE--GGG...-. CS
                      ADH_zinc_N_2  15 e....aatggegvDvvldtvggealleaslkvlpggGrlvsiggpp..lsaallkpakkrkgrsvkyeflfsmkas. 84 
                                       e    ++t+g+gvDv+l ++   ++ ++ +++l++gGr++  +gp     +++ +++++    +  +        + 
  gi|330506792|ref|YP_004383220.1| 244 ErtilSETDGRGVDVILTATPEVKIDQRQMRLLAPGGRICIFSGPQpgDYEGMIDLRSMHYLEQTITGA------Yg 314
                                       144567899************888878888999888**9555544334333333333333222222222......13 PP

                                       ..-HHHHHHHHHHHHHHH--..--EEEEEEGGGHHHHHHH CS
                      ADH_zinc_N_2  85 .aqadileelaalieeGklr..pvvdrvfpleeaaeAhry 121
                                          ++  +  a l+e+G +r  + ++++ +l+++ +A+++
  gi|330506792|ref|YP_004383220.1| 315 cSSRQ-NRMAASLLESGGIRanWIITKRADLARISDAFEH 353
                                       32333.4567777777777655677777777777777776 PP

>> IGFBP  Insulin-like growth factor binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.021        95      14      32 ..      19      38 ..      11      46 .. 0.86
   2 ?    8.8   0.6   0.00055       2.4      27      44 ..      92     109 ..      80     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.021
                             IGFBP 14 aesCpagvelv.edgCgcCk 32
                                      +++Cp+g +l+  ++C+ C 
  gi|330506792|ref|YP_004383220.1| 19 RPRCPPGGALIrVEACAVCG 38
                                      589*9999999889999996 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00055
                             IGFBP  27 gCgcCkvCarqegesCgv 44 
                                       +Cg C+ C r+++++C  
  gi|330506792|ref|YP_004383220.1|  92 ACGHCHACFRGADNRCRD 109
                                       7***************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2799.02
//
Query:       gi|330506793|ref|YP_004383221.1|  [L=346]
Description: hypothetical protein MCON_0567 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2442.79
//
Query:       gi|330506794|ref|YP_004383222.1|  [L=245]
Description: hypothetical protein MCON_0569 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1783.08
//
Query:       gi|330506795|ref|YP_004383223.1|  [L=203]
Description: hypothetical protein MCON_0571 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1545.24
//
Query:       gi|330506796|ref|YP_004383224.1|  [L=421]
Description: Sep-tRNA:Cys-tRNA synthase [Methanosaeta concilii GP6]
Scores for complete 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  171.6   0.0    3.3e-50  170.9   0.0    1.3  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
      6e-13   48.5   0.0    9.4e-13   47.8   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    1.6e-08   34.2   0.0    2.4e-08   33.6   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
     0.0014   17.4   0.0     0.0022   16.8   0.0    1.2  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
  ------ inclusion threshold ------
      0.035   13.4   0.0      0.062   12.6   0.0    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.037   12.6   0.0      0.055   12.0   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
       0.14   11.4   0.0       0.15   11.3   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
       0.21   10.4   0.0       0.31    9.8   0.0    1.2  1  GDC-P            Glycine cleavage system P-protein


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 !  170.9   0.0   1.5e-53   3.3e-50      97     389 .]     120     403 ..     116     403 .. 0.95

  Alignments for each domain:
  == domain 1  score: 170.9 bits;  conditional E-value: 1.5e-53
                                       HHCC--CCEEEEEETC...HHHHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHH..HCCTCCCEEEEEECSSTTTT CS
                           SepSecS  97 krskakkviwvridek...SslkavelaGleialvekvlegDelitdvedveeii..ekkreevilavlstlsffap 168
                                       ++s  +k  +v++d +    s+ a+e+aGl++  v+  +e+D++i  +  + +i+   +k+++v+la+l++++++++
  gi|330506796|ref|YP_004383224.1| 120 MHSLCQKGDFVVMDGNahyTSVLAAERAGLNVEYVPSSKEPDYAISSEGYALAIEraYEKKGNVTLALLTYPDGNYG 196
                                       6777778888899888666888999**********************9987777655577999************** PP

                                       B----HHHHHHHHHCCT--EEEEGCCCCT-HHHHHHHHHHHHHTTC-EECCCHCHCCCEECCHCCCCESSCHCCCCC CS
                           SepSecS 169 rspDdvkeiakiCaeydvPhlvNgAYaiqsekyieklkkalkvGRvdvvvksldknllvpvGgaiiaasdesfikei 245
                                       +++D  ++ia +C++y+vP+l+NgAY++               GR++v  ++l+++++v++G++++aa ++ ++ + 
  gi|330506796|ref|YP_004383224.1| 197 NLAD-ARAIADVCHDYGVPLLLNGAYSV---------------GRMPVKARELGADIIVGSGHKSMAACGPVGVLGA 257
                                       ****.9**********************...............********************************** PP

                                       HCCCHCHCTSCHCCCCCCCHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC..............EEESSSTT- CS
                           SepSecS 246 skeypgrasaapskdvlisllllGskaykkllkeqkesfkllreklkklaeeve..............ekllevpeN 308
                                       s+ey+ ++ + + ++++++++llG++ ++++l+++++sf+ + e++ ++ ee e               ++++ p+N
  gi|330506796|ref|YP_004383224.1| 258 SEEYARIIFKPSATKKNKEVELLGCTVRGAPLITLMASFPTVVERVGRWPEELEnarwfssemekmdlVQVGDRPHN 334
                                       ******************************************************************9999******* PP

                                       SSEEEEE-CCCHCCCC...THHHHHHHHHHHTTECSSE.EE-SSTCECTTSSS-SSSEEEEEE-TT--HHHHHHHHH CS
                           SepSecS 309 pissaltletldeikk...karldlaseLfsrkvtGargvrasdsklTshlkeyhsrYlkiasaiGlkdedvdkvle 382
                                       ++++++ +e l++i++   ++r +l++e++ r v G++      ++lT        r +k+ s++Gl   +++ vl+
  gi|330506796|ref|YP_004383224.1| 335 HDLMFFLTERLYDISQtakGGRYFLYREMKDRGVCGIK------PGLT--------RQFKL-STYGLGRPELEVVLN 396
                                       **************9999899*****************......****........899**.*************** PP

                                       HHHHHHH CS
                           SepSecS 383 rldeile 389
                                       +l ei+e
  gi|330506796|ref|YP_004383224.1| 397 ALSEIIE 403
                                       ****986 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   4.2e-16   9.4e-13      62     221 ..     104     265 ..      97     294 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 4.2e-16
                                       GGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-.. CS
                       Aminotran_5  62 eeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekll.. 136
                                       +e+ +t+G+ e+  ++++sl    ++gd +v+  + h   +     +a+r g++v+++p  +e  + ++    +l  
  gi|330506796|ref|YP_004383224.1| 104 DEVRVTHGAREGKFAAMHSL---CQKGDFVVMDGNAHYTSV----LAAERAGLNVEYVPSSKEPDYAISSEGYALai 173
                                       57889***************...99***9999999998888....5566779******9999888886665555555 PP

                                       ......-TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT CS
                       Aminotran_5 137 ......nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtG 207
                                             + ++ l  +t      G++ +  +i+++++++g+ +l+ +a +vg +p++ ++lg+D+++ sghK +++ G
  gi|330506796|ref|YP_004383224.1| 174 erayekKGNVTLALLTYPDGNYGNLADARAIADVCHDYGVPLLLNGAYSVGRMPVKARELGADIIVGSGHKSMAACG 250
                                       88888778999999*********************************************************777777 PP

                                       .-EEEEEEHHHHHTS CS
                       Aminotran_5 208 .iGvlyvrkellekl 221
                                        +Gvl +++e+   +
  gi|330506796|ref|YP_004383224.1| 251 pVGVLGASEEYARII 265
                                       79**99999887666 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 !   33.6   0.0   1.1e-11   2.4e-08      69     240 ..     104     262 ..      91     271 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.1e-11
                                       EGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCT CS
                     Aminotran_1_2  69 aavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapeg 145
                                       ++v v+ Ga ++  a++  l +++gd ++++   +     +++ +g+ v ++p ++e+d+ +  e++  a+++a e+
  gi|330506796|ref|YP_004383224.1| 104 DEVRVTHGAREGKFAAMHSL-CQKGDFVVMDGNAHYTSVLAAERAGLNVEYVPSSKEPDYAISSEGYALAIERAYEK 179
                                       58999***************.8***************************************************9887 PP

                                       TETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSST CS
                     Aminotran_1_2 146 nkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKa 222
                                       +     + ++    P+G   +l++ ++++d+++ y++ l++  aY+++ +         +++ e  +++ivgs  K+
  gi|330506796|ref|YP_004383224.1| 180 KG---NVTLALLTYPDGNYGNLADARAIADVCHDYGVPLLLNGAYSVGRMP--------VKARELGADIIVGSGHKS 245
                                       77...66677777777777777777777777*****************997........555666668********* PP

                                       TSSGGG-EEEEEEEHHHH CS
                     Aminotran_1_2 223 fGlaGeRvGyilgnaavv 240
                                       +++ G  vG + ++++++
  gi|330506796|ref|YP_004383224.1| 246 MAACG-PVGVLGASEEYA 262
                                       *****.999998888765 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   9.6e-07    0.0022      87     248 ..     108     252 ..     104     314 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.6e-07
                                       ESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--E.B-TTS-BE---GGGGSHHHHHHHHHH CS
                          OKR_DC_1  87 vvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepe.rnalgiiggidlkefeeetlkekike 162
                                       v++G   +  + +++++++gd v++d N+H     a   +g +  y+ ++ +  + i+ + ++       ++++ ++
  gi|330506796|ref|YP_004383224.1| 108 VTHGAREGKFAAMHSLCQKGDFVVMDGNAHYTSVLAAERAGLNVEYVPSSkEPDYAISSEGYA-----LAIERAYEK 179
                                       678888899999*********************9*************9985677888877666.....344444444 PP

                                       STTTGSESEEEEESS.-TTSEEE-HHHHHHHHTTSESEEEEE-TT-TTGGGSGGGTTSSSSSSS-BTTBEEEEEEEH CS
                          OKR_DC_1 163 vpdakaprlavitns.TYdGvlynakeivdkleklsdrilfDeAwvgyeqfiplyadaskllaenendpgilvtqSv 238
                                       + +    +la++t +   +G l++a+ i d  + +++++l+  A+        ++++a +l+a+       + + S 
  gi|330506796|ref|YP_004383224.1| 180 KGN---VTLALLTYPdGNYGNLADARAIADVCHDYGVPLLLNGAYS----VGRMPVKARELGAD-------IIVGSG 242
                                       443...4457777763468***********************9986....46788999999999.......777888 PP

                                       CCCCS--TT- CS
                          OKR_DC_1 239 HKllaalsqa 248
                                       HK  aa    
  gi|330506796|ref|YP_004383224.1| 243 HKSMAACGPV 252
                                       9988886655 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 ?   12.6   0.0   2.8e-05     0.062      55     150 ..     120     224 ..      83     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                                       HHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B.-TTTSSB-GGGCGGG--TTE.......EEEE..EB-GG CS
                   DegT_DnrJ_EryC1  55 LralgvgpgdeVIvpsltFvatanavlelgakpvfvDv.dpdtynidpaaieaaitert.......kaIl..pVhly 121
                                       ++ l  ++gd V++  +   +++ a+ ++g+++ +v   ++ +y i+ +  + ai++          a l  p   y
  gi|330506796|ref|YP_004383224.1| 120 MHSL-CQKGDFVVMDGNAHYTSVLAAERAGLNVEYVPSsKEPDYAISSEGYALAIERAYekkgnvtLALLtyPDGNY 195
                                       4444.3569***************************7526789****998777777655554444433331144579 PP

                                       GB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1 122 GqvadmdalkaiaakhglkvieDaAhAlG 150
                                       G+ ad  a+ ++++++g++++   A ++G
  gi|330506796|ref|YP_004383224.1| 196 GNLADARAIADVCHDYGVPLLLNGAYSVG 224
                                       *********************99999988 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   2.4e-05     0.055     139     198 ..     184     244 ..     106     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                                       EEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTT CS
                   Cys_Met_Meta_PP 139 klvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp.llqrplklgaDivvhSaTK 198
                                        l +l  p     +++D ++ia+++++ gv++++  +++ + + +++ +lgaDi+v S+ K
  gi|330506796|ref|YP_004383224.1| 184 TLALLTYPDGNYGNLADARAIADVCHDYGVPLLLNGAYSVGrMPVKARELGADIIVGSGHK 244
                                       5555555555667899*************************999**************988 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.5e-05      0.15      53     205 ..     109     250 ..      35     406 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.5e-05
                                       ES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT..TBE-HHHHHHHS--S-TTS-E CS
                   Beta_elim_lyase  53 vpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea..Gkmdlekleaaikevgaheek 127
                                       ++  + +   ++  l+q+g+ v+++ +ah+   +   +ae ag ++  ++++++    ++ e  + ai++  a+e+k
  gi|330506796|ref|YP_004383224.1| 109 THGAREGKFAAMHSLCQKGDFVVMDGNAHY---TSVLAAERAGLNVEYVPSSKEpdYAISSEGYALAIER--AYEKK 180
                                       566666777788999999999999988885...4445556666666666666652255555666666666..65566 PP

                                       EEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS CS
                   Beta_elim_lyase 128 iklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanv 204
                                        ++ +   T     G+   l+  r++a+++++yg+pl+l gA  +     + ++++e   ++D+++ s+ K + a  
  gi|330506796|ref|YP_004383224.1| 181 GNVTLALLTYPD--GNYGNLADARAIADVCHDYGVPLLLNGAYSVG---RMPVKARE--LGADIIVGSGHKSMAA-C 249
                                       666666667776..99***********************9984432...22333333..3566777777666554.4 PP

                                       - CS
                   Beta_elim_lyase 205 G 205
                                       G
  gi|330506796|ref|YP_004383224.1| 250 G 250
                                       4 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 ?    9.8   0.0   0.00014      0.31     167     269 ..     138     251 ..     112     266 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHGGGT-EEEEE-GGG--S-................S-EEEEEEEES-.TTSB----HHHHHHHHHTT-E CS
                             GDC-P 167 tlevlktrakglgieivevdlteekvtd.............kekevagvlvqypn.teGriedlkelvekakkkksl 229
                                       +++vl     gl++e v +    +++ +             k+ +v+  l+ yp+   G++ d +++++ ++++ + 
  gi|330506796|ref|YP_004383224.1| 138 YTSVLAAERAGLNVEYVPSSKEPDYAISsegyalaierayeKKGNVTLALLTYPDgNYGNLADARAIADVCHDYGVP 214
                                       455666655566665555554444444445666666666668999999******8356******************9 PP

                                       EEEEE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG-- CS
                             GDC-P 230 vvvaadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGP 269
                                       + +        +     elgaDi+vGs+ +    ++  GP
  gi|330506796|ref|YP_004383224.1| 215 LLLNGAYSVGRMPVKARELGADIIVGSGHKS---MAACGP 251
                                       998875544445555679*********9873...555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3015.14
//
Query:       gi|330506797|ref|YP_004383225.1|  [L=304]
Description: glycerophosphoryl diester phosphodiesterase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-27   96.6   0.0    1.7e-24   87.0   0.0    2.1  1  GDPD      Glycerophosphoryl diester phosphodiesterase family
    3.5e-26   90.9   6.7    6.5e-26   90.1   6.7    1.4  1  zf-like   Cysteine-rich small domain
  ------ inclusion threshold ------
      0.037   14.3   0.0      0.066   13.5   0.0    1.4  1  CCDC117   Coiled-coil domain-containing protein 117
       0.17   12.4   0.1       0.42   11.1   0.1    1.7  1  GDPD_2    Glycerophosphoryl diester phosphodiesterase family


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.0   3.8e-28   1.7e-24       1     257 [.       7     211 ..       7     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 3.8e-28
                                       TTTTTTTSSTTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECCTTC CS
                              GDPD   1 HRGasgnlpEnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkiaken 77 
                                       HR a +   En+le +++A    ady+ +Dv+l++Dg++V++HD+++drttd++g   v+dl+  elk  +   ++n
  gi|330506797|ref|YP_004383225.1|   7 HRTARALAAENSLEGIRAAKRCLADYVHVDVRLSRDGKLVLMHDDSVDRTTDGKG--MVQDLNCIELKAIR---AGN 78 
                                       9******************************************************..*************9...444 PP

                                       CCCSCCCSSGCCB...BHHHHHHHHHHCCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHTT..STTCSCEEE CS
                              GDPD  78 kaqlsenrvrlefpfptleevlkkpqnvglnieikipmlseakeeeelqivkeilksvdeilkkvlkkadkrkvifs 154
                                                   +p+ptl+e+l+   + +l++++ +    e kee +        + v +++        k+k i++
  gi|330506797|ref|YP_004383225.1|  79 ------------EPVPTLAEALSL--AEELELGVVV----EMKEEGL-------EALVADVV-------PKKKSIIT 123
                                       ............478*******85..4444444444....4444444.......12334444.......34455666 PP

                                       ESTHHHHHHHHHTCTCTEEEEEEHHHHHHC-E.EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHHHHTT-EEEEB CS
                              GDPD 155 sfnpdilkllrekqpklpllflteggteaeadssleraakfakadallgevsavaeglgdpdlVkraksrglvvhvy 231
                                       s  +++l+ ++e ++ l++  ++ +   ++        a +a ada+ +e  +v+++     l k+a+++gl+v++ 
  gi|330506797|ref|YP_004383225.1| 124 SSYHASLREIKEISD-LKTGIIITSLPIKPVE-----LALWADADAIFPE--KVNPR-----LFKEAHQKGLEVYPG 187
                                       777889999999999.9999999988888888.....8999999999886..45555.....9*************9 PP

                                       SB-THSHHHHHHHHCCC-SEEEES-H CS
                              GDPD 232 tvnnedeeemkrlleagvdgvitDfp 257
                                        vn+   ++ ++ll++g dg++tD+p
  gi|330506797|ref|YP_004383225.1| 188 VVNTV--AQAAWLLRLGADGLVTDDP 211
                                       99999..*****************98 PP

>> zf-like  Cysteine-rich small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   6.7   1.5e-29   6.5e-26       6      80 ..     226     301 ..     222     303 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 1.5e-29
                           zf-like   6 snkeCeyyPCHktedenClfCyCPlYaledeelGefveteng.kvkdCskCllvHkkevadellkklkeileelkk 80 
                                        +++CeyyPCH+ e+++C++C+CPlY+++deelG+fv t+ g + ++C +C+lvH++ va++l ++++ ++eelk+
  gi|330506797|ref|YP_004383225.1| 226 GQSNCEYYPCHHFEGQDCTHCFCPLYPCRDEELGRFVRTKRGkRFWSCIDCKLVHRPIVAKYLAEHPESTTEELKA 301
                                       6789**************************************9***************************999986 PP

>> CCDC117  Coiled-coil domain-containing protein 117
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.5e-05     0.066      22      88 ..     104     175 ..      88     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                           CCDC117  22 e....dleadsvsrrPvLvlsDslkeglk..rgiddiltkkviesvsrssmELvlWkPleellsdklkdslqk 88 
                                       e     l ad v+++ +++ s s +  l+  ++i+d+ t  +i s+    +EL+lW   + ++++k    l k
  gi|330506797|ref|YP_004383225.1| 104 EegleALVADVVPKKKSIITS-SYHASLReiKEISDLKTGIIITSLPIKPVELALWADADAIFPEKVNPRLFK 175
                                       333435667888888887776.44455543389*********************************9887755 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   9.4e-05      0.42       6      29 ..     188     211 ..     183     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.4e-05
                            GDPD_2   6 ttddeavwrelvgaGVdgInTDdl 29 
                                       ++++ a+ + l+++G+dg+ TDd+
  gi|330506797|ref|YP_004383225.1| 188 VVNTVAQAAWLLRLGADGLVTDDP 211
                                       56888888889************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2194.55
//
Query:       gi|330506798|ref|YP_004383226.1|  [L=147]
Description: hypothetical protein MCON_0573 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1185.18
//
Query:       gi|330506799|ref|YP_004383227.1|  [L=607]
Description: metal-dependent phosphohydrolase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-11   44.0   0.2    5.9e-11   42.7   0.2    1.8  1  HD        HD domain
     0.0016   17.9   0.1     0.0049   16.4   0.1    1.7  2  HDOD      HDOD domain
  ------ inclusion threshold ------
      0.028   14.4   0.0      0.065   13.2   0.0    1.5  1  DUF758    Domain of unknown function (DUF758)


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 !   42.7   0.2   9.9e-15   5.9e-11       1      67 [.      71     147 ..      71     200 .. 0.69

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 9.9e-15
                                       HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHH...........HHHCTCCHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekk...........eeefekflaHekvgae 65 
                                       r+eHsl+++++a+r+ae+lg+  e++ +++la+LlHD+G+   ++a e             +   ++  +He+++  
  gi|330506799|ref|YP_004383227.1|  71 RFEHSLGTMHMAGRMAEHLGLsSEEVRKVRLAGLLHDLGHSALSHAVEGVlgrnpevqpllK--GKRASGHEEFTQD 145
                                       79****************************************88866554544444433220..2222233433333 PP

                                       HH CS
                                HD  66 il 67 
                                       i+
  gi|330506799|ref|YP_004383227.1| 146 II 147
                                       33 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   8.3e-07    0.0049      96     140 ..      72     118 ..      60     124 .. 0.88
   2 ?   -2.7   0.0      0.58   3.5e+03     119     146 ..     399     426 ..     390     438 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.3e-07
                                       HHHHHHHHHHHHHHHHHTT-S-H..HHHHHHHHTTTHHHHHHHHHSH CS
                              HDOD  96 wehslavAlvarelaeelgledp..eeaflaGLLhdiGklvllsllp 140
                                        ehsl +  +a ++ae+lgl+++   ++ laGLLhd+G  +l ++++
  gi|330506799|ref|YP_004383227.1|  72 FEHSLGTMHMAGRMAEHLGLSSEevRKVRLAGLLHDLGHSALSHAVE 118
                                       59****************998854699************99998765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.58
                                       HHHHHHHHTTTHHHHHHHHHSHHHHHHH CS
                              HDOD 119 eeaflaGLLhdiGklvllsllpeeleel 146
                                       e a+ aGL +++ + + +s+++++  e+
  gi|330506799|ref|YP_004383227.1| 399 ESALAAGLVKSLTRQIAISFFSDDRPEI 426
                                       7899999999999988888888876655 PP

>> DUF758  Domain of unknown function (DUF758)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.1e-05     0.065     114     170 ..     265     326 ..     240     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                            DUF758 114 adlLkecrellkqlverhLt....dkslgridhvfdflsdpefldalfspdse.yrellkki 170
                                       + +++++r++l++++e+ L+    d  + ri+ +f  + dp++l  ++++ ++  r+ll++i
  gi|330506799|ref|YP_004383227.1| 265 HPSVQSIRAMLLTALENALSrmneDDAKRRIELFFREYTDPDLLRFIWETGDDvSRDLLQRI 326
                                       56789999***********9333345578*******************99555599999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); 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: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 4684.44
//
Query:       gi|330506800|ref|YP_004383228.1|  [L=130]
Description: alpha-NAC-like protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-15   56.9   0.2      2e-15   56.5   0.2    1.2  1  NAC       NAC domain
     0.0029   17.8   0.1      0.031   14.5   0.0    2.0  2  ArlS_N    ArlS sensor 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 !   56.5   0.2   2.2e-19     2e-15       1      56 [.      16      74 ..      16      75 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.2e-19
                               NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeaee 56
                                      +kK++ +lk +g+   e++g+ eV+ir++d k++v++n++V   ++ g+ +y+++G+a e
  gi|330506800|ref|YP_004383228.1| 16 PKKMKGMLKSMGIdiDELEGVIEVVIRMPD-KEIVIQNASVAimDAHGQRSYQISGDATE 74
                                      7*****************************.***********99999**********987 PP

>> ArlS_N  ArlS sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.042   3.8e+02     100     119 ..      24      43 ..      17      45 .. 0.82
   2 !   14.5   0.0   3.5e-06     0.031      45      78 ..      47      80 ..      45     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.042
                            ArlS_N 100 grspiktgkfkGyvevvnpL 119
                                        ++ i+++++ G +evv ++
  gi|330506800|ref|YP_004383228.1|  24 KSMGIDIDELEGVIEVVIRM 43 
                                       567799**********9766 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.5e-06
                            ArlS_N 45 kinekdqtirildkdgkevlevsndspeikftvp 78
                                      +i+ ++ +++i+d++g++ +++s d +e++++ +
  gi|330506800|ref|YP_004383228.1| 47 EIVIQNASVAIMDAHGQRSYQISGDATERPLSGT 80
                                      7999********************9999976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 920.33
//
Query:       gi|330506801|ref|YP_004383229.1|  [L=203]
Description: hypothetical protein MCON_0578 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1403.29
//
Query:       gi|330506802|ref|YP_004383230.1|  [L=199]
Description: hypothetical protein MCON_0579 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1570.97
//
Query:       gi|330506803|ref|YP_004383231.1|  [L=220]
Description: hypothetical protein MCON_0581 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-29  102.2   0.0    4.8e-29  101.9   0.0    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.9   0.0   2.7e-33   4.8e-29       2     196 ..       9     198 ..       8     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 2.7e-33
                                       EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT.EEE-SEEEEEE.TTT.SEEEEEEE.. CS
                              PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg.relepprlyak.dsgsrdllvlqg.. 74 
                                       i G+pgiG+Vg++a+d+L + l++  +  ++s + +p     ++v+v++g  el+  +l+ + d  ++++ vl g  
  gi|330506803|ref|YP_004383231.1|   9 ICGLPGIGSVGKVAADYLSNALKCSGIKPFYSHS-FP-----SQVMVSDGlAELMHAELLRSqD--KENIFVLSGdt 77 
                                       89********************************.**.....*****************75545..79*******76 PP

                                       E-HSCHHH.HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT.....-CEEEEH CS
                              PAC2  75 repilqye.efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees.....eyggivg 145
                                          ++q++ ++a ++l+ +e+ gv+ v++L+++          + + k+ g atd+e ++ l +s     + g i+g
  gi|330506803|ref|YP_004383231.1|  78 QPLDVQGMyQLAGEILQAIESEGVTDVITLAAFV----G----DATAKILGSATDPESAAVLHDSgitllRSGAIGG 146
                                       5556666699************************....4....456699**********99965567889******* PP

                                       HHHHHHHHHHHTT-EEEEEEEEEEC.CC--HHHHHHHHHHHHHHHT---HCH CS
                              PAC2 146 itglLlsaakergipavgllaevph.ylpdPkaaaalleflskllglevdte 196
                                       ++glL ++a  +++ + +ll+ +++  l d +aa  ll+++ +l++l++d +
  gi|330506803|ref|YP_004383231.1| 147 MNGLLAGLAPLYNMRGFCLLGTSSGaDLIDIPAATNLLYAIRDLFKLDLDFS 198
                                       *************************6788999999**********9999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1654.34
//
Query:       gi|330506804|ref|YP_004383232.1|  [L=285]
Description: hypothetical protein MCON_0580 [Methanosaeta concilii GP6]
Scores for complete 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-36  123.5   0.1    4.7e-35  121.2   0.1    2.0  1  DUF89     Protein of unknown function DUF89
  ------ inclusion threshold ------
      0.095   12.6   0.1       0.46   10.3   0.0    1.9  2  DREPP     DREPP plasma membrane polypeptide


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 !  121.2   0.1   5.2e-39   4.7e-35       2     350 ..       4     278 ..       3     281 .. 0.87

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 5.2e-39
                                       HHTHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCTTCGHHH-HHHHT-BTTBSBHHHHHHHHHHHHHH CS
                             DUF89   2 leerlpciltqviddlekakdekeeelkkiieelselkeelqtdkpltpledeeekrswfnapwlfaecylyrrlle 78 
                                       + +++pc+l ++  ++++     ee++k+++eel +++    ++  +++l                + ++    +++
  gi|330506804|ref|YP_004383232.1|   4 ASNCYPCLLDRAKFECDMVFTR-EEDKKAAVEELLDFM--ACHKGGVPAL----------------MGTERELIIKR 61 
                                       6789*******99999995555.689999999999999..5566777777................78999999999 PP

                                       HHTHSGGGTTS-TTHHHHHHHHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHCG--CCCHTSHHCHHHHHHHH CS
                             DUF89  79 lfglskelknyDpFkeqKeesnksalkaveelakrleeledekelfkellkislwGNaiDlsllateediqkdqeee 155
                                         g      + Dp++e+Keesn+ a++++++  + +e+++d+   +++l++i+ + N + +++++  +d+ ++   +
  gi|330506804|ref|YP_004383232.1|  62 RSG------SSDPYRELKEESNQVARDLLPRAVEFYEQSPDK---IEALIRIASAANSMEFGVKG--HDFDNLTFGR 127
                                       999......*********************************...********************..8888888666 PP

                                       HHHHHHCTESEE-HHHHHHHHCTCHTSEEEEE--BTTHHHHHHHHHHHHHHHCTTTSEEEEEEBSS--TTTB-BHHH CS
                             DUF89 156 arkaleknilvddleklweklkkkkakrvdivlDNaGfElvfDlllaeeLlesglatkVvlhvkaiPwfvsDvtpeD 232
                                       + +++ ++ l  d+++l ++l  ++ +++++++DN+G E++fDl+++e+L+e  ++++Vv+  k+ P +++Dvt ++
  gi|330506804|ref|YP_004383232.1| 128 VFADTLQENLHADMAELKRRL--QSFGKILYLTDNCG-EVIFDLFVIEKLKE--MGKTVVVGSKSEP-IINDVTADE 198
                                       6666666666999********..**************.**************..*************.********* PP

                                       HHHHHHHHH-TTTSHHHHCHTTHHHHHHTSEEEEESSCGGSSS--CCGSS.SHHHHHHHHHC-SEEEEEHHHHHHHH CS
                             DUF89 233 fewlleqladsksfelsalgagldellkegklvlrgssfwttglsysemp.eapelyeelekadLvifKGdlNyrkL 308
                                       ++                        +++ +++ +g+    +g++++ ++ ea+ l+  ++   L+++KG++N++++
  gi|330506804|ref|YP_004383232.1| 199 LK-------------------S----FSDVDVIPTGNV---VGTALEHLSpEASVLL--FDPEWLILSKGMGNFETM 247
                                       **...................2....345888999988...999*****55555555..78899************* PP

                                       TTSCTTTTTSEHHHHTGTSS--EEEEEE--SHHHHHHH.STTT CS
                             DUF89 309 tgdrkwppttpfttalgfspvpvlaLrtvKadvvagll.egeg 350
                                       ++  +              + ++++++++K+++va+ + +++g
  gi|330506804|ref|YP_004383232.1| 248 SEFDQRL------------KGRLIYILRAKCEPVAAKMaVPRG 278
                                       7655544............578*************98866665 PP

>> DREPP  DREPP plasma membrane polypeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.13   1.1e+03      14      30 ..      21      37 ..      17      44 .. 0.81
   2 ?   10.3   0.0   5.1e-05      0.46      40      73 ..      72     105 ..      65     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.13
                             DREPP 14 kvFekngakkaaaaeav 30
                                       vF ++  kkaa  e++
  gi|330506804|ref|YP_004383232.1| 21 MVFTREEDKKAAVEELL 37
                                      79999999998887765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 5.1e-05
                             DREPP  40 inkeleekkteLqpkvveiyeaasaeikaLvker 73 
                                       +++e ++   +L p+ ve ye ++ +i aL++  
  gi|330506804|ref|YP_004383232.1|  72 LKEESNQVARDLLPRAVEFYEQSPDKIEALIRIA 105
                                       5666677788*********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2035.20
//
Query:       gi|330506805|ref|YP_004383233.1|  [L=281]
Description: histone deacetylase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-37  128.1   0.5      4e-36  125.1   0.5    1.8  2  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    1.4   0.0      0.01   1.8e+02       6      53 ..      21      68 ..      18      73 .. 0.83
   2 !  125.1   0.5   2.2e-40     4e-36      86     291 ..      70     259 ..      63     275 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.01
                                      HHHHHHHHHHHHT.THHHHCCE..EE-----HHHHTTTS-HHHHHHHHC CS
                                      xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  6 kRlsaileslaesvglldelel.liqpseatkeellkvHskeYlelles 53
                                      +R++   e+l es gl+d  e+ ++++++a  e ++k+H++ ++ ++e+
  gi|330506805|ref|YP_004383233.1| 21 ERIQPSFEKLMES-GLVDGIEVqVFRAKPAPMELVAKAHTEGHMANMET 68
                                      7888889999998.988887765788999999999*******9998874 PP

  == domain 2  score: 125.1 bits;  conditional E-value: 2.2e-40
                                       TCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE-SSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  86 ktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDvDvH 162
                                       +  ++a l++g+v++a++ v+ g++++af++   +gHHa ++ + GFC++N+vai+i +l++  +++r++i+DvD H
  gi|330506805|ref|YP_004383233.1|  70 QYRDVAILSAGSVMMAAEMVAAGQAESAFAFTGTAGHHASRGSCWGFCYFNDVAITILRLKE-MGFERFLIVDVDPH 145
                                       55678999*****************************************************9.99************ PP

                                       --HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 163 hGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvleefkP 239
                                       +G+Gt ++f++dpdv+++ +H        gtg+ +d      + +n  + l+ g ++e +l+++++ l  ++++f+ 
  gi|330506805|ref|YP_004383233.1| 146 FGDGTRDFFREDPDVFHINLHS-------GTGEEHDP-----QRNNYDIGLSFGADNERFLSALKSGL-VLARDFDF 209
                                       **********************.......89998888.....4699********************99.56799*** PP

                                       SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 240 dlilvsaGfDalkgdplgelnlsvegykeltkklaeladkvkkvvllleGGY 291
                                       ++  v  G D++++d +g++nl+ e y ++ + ++e   +   +v++l GG 
  gi|330506805|ref|YP_004383233.1| 210 QIAFVIFGHDSHQDD-YGGFNLTFEAYPRMAQIVKEAVGDK-GLVFVLSGGS 259
                                       ***********9765.799****************998754.8*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 00:00:00.40
# Mc/sec: 2127.57
//
Query:       gi|330506806|ref|YP_004383234.1|  [L=504]
Description: AMP phosphorylase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-13   50.6   0.3      8e-13   48.6   0.3    1.9  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    3.1e-12   46.1   0.0    9.1e-12   44.7   0.0    1.8  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
    7.8e-12   44.7   0.0    1.9e-11   43.5   0.0    1.7  1  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    0.00028   20.9   0.0    0.00059   19.8   0.0    1.5  1  Molydop_binding  Molydopterin dinucleotide binding domain
     0.0046   15.8   0.0     0.0072   15.2   0.0    1.2  1  DUF2254          Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.3   2.2e-16     8e-13       3     252 ..     157     384 ..     155     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 2.2e-16
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl 79 
                                       +++D+++ GG+  n   +S+   ++vAaaG+ ++k + r+++  +G+aD++e l   +e ++ e++++ e+vg +++
  gi|330506806|ref|YP_004383234.1| 157 PVMDKHSIGGVPGNK--VSLLIVPIVAAAGLLIPKTSSRAITGAGGTADLMEVL-APVEFSAAEIKEITEKVGGVIV 230
                                       689**********99..9**********************************99.5899*************98887 PP

                                       ..EHHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHH CS
                   Glycos_transf_3  80 ..fapeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGlde 154
                                         +a++  +a ++ +++  +l i            p   ++ l ++++k+ a ++++v+ +++v+ +  +++   d+
  gi|330506806|ref|YP_004383234.1| 231 wgGATNIAPADDKLIKAEYALSI-----------DP--YSQMLASIMAKKGAVGADAVVVDMPVGPGTKLPT--ADD 292
                                       34578888888888888888887...........55..5566899***************************..*** PP

                                       HHHHHHHHHHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHT CS
                   Glycos_transf_3 155 vsllakttvaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvla 230
                                        ++lak ++   +  g + e +++    +++r  + ale+   +e++ +l++   g++s   r+  l +ag +l + 
  gi|330506806|ref|YP_004383234.1| 293 GRTLAKDLIDLGDkLGIRVECAMTFGGSPVGRTIGPALEV---REALTLLENK-PGPNSL--REKSLSLAGILLEMG 363
                                       ************999*************************...9******999.777776..788899999998887 PP

                                       TSSSSHHHHHHHHHHHHHTSHH CS
                   Glycos_transf_3 231 gkadslkegvakaeevidsGkA 252
                                       g +    eg a aee+++sGkA
  gi|330506806|ref|YP_004383234.1| 364 G-VAGRGEGYAAAEEILSSGKA 384
                                       7.88899**************9 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   2.5e-15   9.1e-12       4      63 .]      89     148 ..      88     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.5e-15
                                       HHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N   4 ikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63 
                                       ik l+d+e+L++++ir ++++i++++++d+++aA  +A ++  +  eE++ l++Am+e g
  gi|330506806|ref|YP_004383234.1|  89 IKSLMDNEKLSEDQIRTIVQDIVDNNLSDIELAAYVTASYIHNMPSEEVVWLTKAMIETG 148
                                       899*****************************************************9976 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 !   43.5   0.0   5.2e-15   1.9e-11       1      74 [.     422     488 ..     422     489 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 5.2e-15
                                       EEEEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHHHHHHEEE CS
                            PYNP_C   1 yvseidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkklkkaiki 74 
                                       yv ++ ++++  +a+++GA       p d+++G+ +hkk+G++VkkGepl+ti +++ ++l++av ++k ++ i
  gi|330506806|ref|YP_004383234.1| 422 YVVAFYNKRLVELARMAGA-------PSDQKAGVIIHKKMGERVKKGEPLITICSSSDWELDSAVRDAKRSMPI 488
                                       567778899999999****.......*******************************************99887 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.7e-07   0.00059      31      78 ..      15      63 ..       8      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.7e-07
                                      EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEE.EEESSB-TTEEEEES CS
                   Molydop_binding 31 vveinpedAaalGikdGdlVevesrrGsvevra.kvtervrpGvvfmpf 78
                                       v++n  dA+++G++ Gd+V+v+ +  ++++    +t++v+pG + + +
  gi|330506806|ref|YP_004383234.1| 15 KVMLNIVDARERGLNPGDRVRVRAKGAATTALLdTTTQMVKPGEIGIFT 63
                                      79**********************9999999994555559**9987665 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     2e-06    0.0072     188     256 ..     408     481 ..     379     486 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-06
                           DUF2254 188 eeeeatpiraersGylqaidveaLvklae......ehdlvielevrpGdfvvkgeplakvwgeeddeelaeklre 256
                                         e+ + i a++ Gy+ a + ++Lv+la+      ++++ + +++++G+ v kgepl+++ + + d el  ++r+
  gi|330506806|ref|YP_004383234.1| 408 IGENCEEILAPAGGYVVAFYNKRLVELARmagapsDQKAGVIIHKKMGERVKKGEPLITICSSS-DWELDSAVRD 481
                                       567888999*******************744444467889********************9888.4555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3721.80
//
Query:       gi|330506807|ref|YP_004383235.1|  [L=311]
Description: hypothetical protein MCON_0584 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00031   21.0   0.0    0.00062   20.0   0.0    1.5  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.4e-08   0.00062      16      48 ..     115     157 ..     100     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.4e-08
                                       EEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH..........H CS
                      NTP_transf_2  16 kvvlfGSyarGtalkgSDiDllvvlpeevsre..........k 48 
                                       ++ ++GS+  G+  + SDiD++v++p + +            +
  gi|330506807|ref|YP_004383235.1| 115 EMGITGSRLIGLQAPASDIDFVVYGPMWWKARnivdrakregV 157
                                       77899*********************88554444444444442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2124.71
//
Query:       gi|330506808|ref|YP_004383236.1|  [L=190]
Description: Sua5/YciO/YrdC/YwlC family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-46  157.4   0.0    2.8e-46  157.3   0.0    1.0  1  Sua5_yciO_yrdC  Telomere recombination


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.3   0.0   1.6e-50   2.8e-46       5     179 .]      11     179 ..       7     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 1.6e-50
                                       TTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEE CS
                    Sua5_yciO_yrdC   5 kGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitll 81 
                                        Gg+v++ptetvYgL+++a +e+av r++ iK+rp + p+++ v+sle+l+++ae  v +  + +le ++PGp+ +l
  gi|330506808|ref|YP_004383236.1|  11 GGGVVVYPTETVYGLGANALDEQAVMRVFLIKKRPLSMPISLAVSSLEMLREVAE--VRDDDMDILEDLLPGPVSIL 85 
                                       69****************************************************8..9999999************* PP

                                       EE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---S CS
                    Sua5_yciO_yrdC  82 lkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeia 158
                                       l++ k+ +p+ +++g++ vG+r Pd++ a+++++++g p+++TSan+ g+p++ +a+ev++e++++v+l++dgg+++
  gi|330506808|ref|YP_004383236.1|  86 LRK-KSIVPDILTAGSSLVGIRFPDHESALRIIDKAG-PITSTSANRTGQPAPVSAKEVSKEIEDRVELVVDGGRCK 160
                                       **6.444****************************98.*************************************** PP

                                       SS---EEEETTSSTSSECEXX CS
                    Sua5_yciO_yrdC 159 vgvdstVvdltegkpkilRrG 179
                                         ++st +dl +   ki+R+G
  gi|330506808|ref|YP_004383236.1| 161 YCQPSTLLDLEN--RKIIRPG 179
                                       *********997..9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1496.39
//
Query:       gi|330506809|ref|YP_004383237.1|  [L=162]
Description: hypothetical protein MCON_0586 [Methanosaeta concilii GP6]
Scores for complete 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   24.7   1.3    2.9e-05   24.0   1.3    1.3  1  HTH_3     Helix-turn-helix
    2.3e-05   24.3   1.2      9e-05   22.4   1.3    1.9  2  HTH_19    Helix-turn-helix domain
    0.00025   21.3   0.1    0.00039   20.7   0.1    1.4  1  HTH_31    Helix-turn-helix domain
    0.00089   19.1   0.4      0.005   16.7   0.4    2.1  2  HTH_25    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.036   14.1   0.5      0.063   13.3   0.5    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 !   24.0   1.3   8.1e-09   2.9e-05       1      53 [.      82     134 ..      82     136 .. 0.97

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 8.1e-09
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsld 53 
                                       ++e+R+ lgl+ e+L +++  + + + +iE+ + +P  ++ kkl++ L+++l+
  gi|330506809|ref|YP_004383237.1|  82 IREAREGLGLTPEQLGARIKEKATLLKKIEREDISPEDDVRKKLERELKIKLT 134
                                       8***********************************************99987 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.3   2.5e-08     9e-05       1      56 [.      79     133 ..      79     140 .. 0.91
   2 ?   -1.4   0.0       0.7   2.5e+03      10      20 ..     148     158 ..     147     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.5e-08
                            HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidl 56 
                                       G++++eaRe lglt e+l  r++   + + +iE + +  p+ ++ +k+ ++l+i l
  gi|330506809|ref|YP_004383237.1|  79 GRKIREAREGLGLTPEQLGARIKEKATLLKKIEREDI-SPEDDVRKKLERELKIKL 133
                                       89*******************************9988.888888899988898876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.7
                            HTH_19  10 elgltqeelae 20 
                                        +glt+ ++a+
  gi|330506809|ref|YP_004383237.1| 148 GRGLTLGDIAN 158
                                       589*****996 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   1.1e-07   0.00039       1      52 [.      77     127 ..      77     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.1e-07
                            HTH_31   1 aLGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealar 52 
                                       ++G+  r++Re  GL+ e++++r+   ++ l ++E+  +  p  +v  +l r
  gi|330506809|ref|YP_004383237.1|  77 DFGRKIREAREGLGLTPEQLGARIKEKATLLKKIEREDI-SPEDDVRKKLER 127
                                       69************************************9.598877777766 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.4   1.4e-06     0.005       2      36 ..      82     116 ..      81     119 .. 0.95
   2 ?   -0.6   0.0      0.33   1.2e+03       9      18 ..     149     158 ..     147     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.4e-06
                                       HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25   2 LraaRearglsleevaketkIrkdylealEeddfd 36 
                                        r+aRe +gl+ e++ +++k ++ +l+++E++d++
  gi|330506809|ref|YP_004383237.1|  82 IREAREGLGLTPEQLGARIKEKATLLKKIEREDIS 116
                                       69*****************************9975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.33
                                       TT--HHHHHH CS
                            HTH_25   9 rglsleevak 18 
                                       rgl+l ++a+
  gi|330506809|ref|YP_004383237.1| 149 RGLTLGDIAN 158
                                       9*******98 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   1.7e-05     0.063      13      42 ..       4      41 ..       2      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                               DZR 13 rfCseCgtklkavaa........edrCpsCgekvdpea 42
                                      + C+ Cg++++  ++        +++C sC +  +pe+
  gi|330506809|ref|YP_004383237.1|  4 KQCEICGAEISGSPQkividrstMEVCKSCARFGKPED 41
                                      79*********9999***************98766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1172.57
//
Query:       gi|330506810|ref|YP_004383238.1|  [L=411]
Description: proteasome-activating nucleotidase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-42  145.3   0.0    2.6e-42  144.4   0.0    1.5  1  AAA              ATPase family associated with various cellul
    1.4e-12   47.2   0.1    3.5e-12   45.9   0.1    1.8  1  AAA_lid_3        AAA+ lid domain
    2.2e-11   43.5   0.1    5.4e-11   42.3   0.1    1.7  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    2.7e-06   27.9   1.4    0.00021   21.8   0.1    2.6  2  AAA_16           AAA ATPase domain
    2.8e-06   27.6   0.0      6e-06   26.5   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
    1.3e-05   25.3   0.2    0.00015   21.8   0.1    2.8  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00011   22.5   0.2      0.019   15.3   0.0    2.4  2  AAA_22           AAA domain
    0.00039   20.2   0.0      0.001   18.9   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00057   19.2   0.0     0.0012   18.1   0.0    1.5  1  TIP49            TIP49 P-loop domain
    0.00089   19.4   0.0      0.002   18.3   0.0    1.7  1  AAA_33           AAA domain
     0.0013   19.0   0.0      0.003   17.8   0.0    1.7  1  AAA_28           AAA domain
     0.0027   17.5   0.0     0.0061   16.3   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
     0.0028   17.5   0.0     0.0083   16.0   0.0    1.8  1  AAA_3            ATPase family associated with various cellul
     0.0031   17.3   0.3       0.01   15.6   0.3    1.8  1  AAA_30           AAA domain
     0.0031   16.7   0.0     0.0057   15.8   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
     0.0032   17.1   0.4      0.008   15.8   0.1    1.9  1  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
     0.0055   17.1   0.0     0.0099   16.3   0.0    1.4  1  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.013   14.9   0.5      0.037   13.4   0.0    1.9  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.013   15.4   0.2       0.11   12.4   0.1    2.2  2  NACHT            NACHT domain
      0.014   14.8   0.1      0.069   12.5   0.0    2.1  2  ATPase           KaiC
      0.016   15.7   0.1      0.068   13.7   0.0    2.1  2  AAA_18           AAA domain
      0.018   15.1   0.0      0.037   14.1   0.0    1.4  1  Torsin           Torsin
       0.02   14.7   0.5       0.16   11.7   0.0    2.1  2  AAA_11           AAA domain
      0.025   14.4   0.0      0.057   13.3   0.0    1.5  1  CPT              Chloramphenicol phosphotransferase-like prot
      0.031   13.8   0.0      0.051   13.1   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.038   14.0   0.0      0.073   13.1   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.051   13.3   0.0       0.17   11.6   0.0    1.8  2  Sigma54_activat  Sigma-54 interaction domain
      0.067   13.7   0.1       0.46   11.0   0.0    2.2  2  ABC_tran         ABC transporter
      0.077   11.9   0.0       0.24   10.2   0.0    1.8  2  AFG1_ATPase      AFG1-like ATPase
      0.087   12.7   0.1       0.27   11.1   0.0    1.9  1  NTPase_1         NTPase
      0.098   11.8   0.0       0.18   10.9   0.0    1.4  1  NB-ARC           NB-ARC domain
       0.11   12.6   0.0       0.24   11.4   0.0    1.5  1  AAA_14           AAA domain
       0.12   11.4   0.0        0.3   10.2   0.0    1.6  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.15   11.4   1.6       0.22   10.8   0.0    1.9  2  Zeta_toxin       Zeta toxin


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 !  144.4   0.0     5e-45   2.6e-42       1     132 []     188     321 ..     188     321 .. 0.96

  Alignments for each domain:
  == domain 1  score: 144.4 bits;  conditional E-value: 5e-45
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       vll+GppGtGKT+lakava++++++f+++ gse+++ky+ge+++ +relf+ ak+k+ p i++iDE+da++ +r   
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQSTEATFMRVVGSEFVQKYIGEGARLVRELFELAKSKS-PAIILIDELDAIGARRmdg 263
                                       79******************************************************9.****************987 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                        +s ++e +r++ q+l+e+dg++ + ++v +i+atnr d+ldpallr gRfdr+iei+l
  gi|330506810|ref|YP_004383238.1| 264 ATSGDREVQRTLMQILAEMDGFDAR-GEVKLIAATNRLDMLDPALLRpGRFDRVIEIPL 321
                                       7778889999**************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 !   45.9   0.1   6.7e-15   3.5e-12       1      44 [.     343     386 ..     343     387 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 6.7e-15
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                       dv+l  +Ae++eG SGADl+al  eA++ A+r+ ++++ ++dfe
  gi|330506810|ref|YP_004383238.1| 343 DVNLRLIAELSEGSSGADLKALSTEAGMYAIREERTTVYQSDFE 386
                                       9******************************************8 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.1     1e-13   5.4e-11       1      57 []      76     130 ..      76     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1e-13
                                       EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                    Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                       V+t+++vld+ +r+iVk+s++  +vvsl+  +  e++++g++V++++++++++ +LP
  gi|330506810|ref|YP_004383238.1|  76 VGTIVDVLDE-NRVIVKSSTGPRFVVSLSQFIE-EEIKVGAQVGLNQQSFAVMCVLP 130
                                       9*********.*********************9.66********************9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   3.9e-07   0.00021      24      57 ..     185     218 ..     155     237 .. 0.72
   2 ?    4.4   0.0     0.082        43     121     148 ..     231     257 ..     227     282 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.9e-07
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflr 57 
                                       p  vll+G++G+GK+ l+++++++ e++ + ++ 
  gi|330506810|ref|YP_004383238.1| 185 PKGVLLHGPPGTGKTILAKAVAQSTEATFMRVVG 218
                                       499*******************877666334444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.082
                            AAA_16 121 ellkrllallsrderplvlvlDdlqwad 148
                                       +l+++l++l+++ ++p ++++D+l+ + 
  gi|330506810|ref|YP_004383238.1| 231 RLVRELFELAKS-KSPAIILIDELDAIG 257
                                       567788899999.889*********543 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   1.1e-08     6e-06       6     104 ..     188     280 ..     184     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.1e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHH..HHHHHHTTT-HHHHTTSEEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlv..srligappgyvgaeegGivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a+  ++    +++r+  se+ +    + +   +rl+ +     + +   i+l+DE+d i
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQSTEA----TFMRVVGSEFVQ----KYIGegARLVRELFELAKSKSPAIILIDELDAI 256
                                       6889****************9985....999999999999....44441133333333444555566********** PP

                                       ------------HHHHHHHHHHHH CS
                             AAA_2  81 hpkessgadvSregVqrdLLqile 104
                                        +++  ga     +Vqr L+qil 
  gi|330506810|ref|YP_004383238.1| 257 GARRMDGATSGDREVQRTLMQILA 280
                                       **98999999999*********96 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   2.9e-07   0.00015       1     134 [.     187     307 ..     187     310 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.9e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                       +vlL GppGtgK+ la+ +a+ +++++  v ++++ ++    g r +      ++  +l  + ++++i+++DE++ +
  gi|330506810|ref|YP_004383238.1| 187 GVLLHGPPGTGKTILAKAVAQSTEATFMRVVGSEFVQKYIGEGARLV------RELFELA-KSKSPAIILIDELDAI 256
                                       59*****************************9997666555555555......4444444.5559999999999977 PP

                                       -.HHHHHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS--.-TT-TTHHH CS
                             AAA_5  78 e.sevlnsLlslleerrllleeggelvkaknddller..frviatanpldrslnelspal 134
                                         + + ++     e +r        ++ a+ d++  r  + +ia++n+ld     l+pal
  gi|330506810|ref|YP_004383238.1| 257 GaRRMDGATSGDREVQRT-----LMQILAEMDGFDARgeVKLIAATNRLD----MLDPAL 307
                                       633333333322222222.....222222222222333477777777777....566666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.5e-05     0.019       8      29 ..     188     209 ..     183     222 .. 0.87
   2 ?    5.7   0.0     0.033        17      52     104 ..     209     257 ..     206     297 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.5e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                       ++++G++GtGKT l++ ++++ 
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQST 209
                                       689**************99986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.033
                            AAA_22  52 sskdllrellralglelkaerlsseellealeqalraravielliiDEaqhlr 104
                                       + ++++r + +++ ++  +   +  +l++ l + +++++  ++++iDE + + 
  gi|330506810|ref|YP_004383238.1| 209 TEATFMRVVGSEFVQKYIG---EGARLVRELFELAKSKSP-AIILIDELDAIG 257
                                       5667777777777776666...888999999999999999.*********995 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 !   18.9   0.0   1.9e-06     0.001      34      71 ..     186     224 ..     180     261 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-06
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsg.Pvlek 71 
                                         vll+GpPG Gkt lak +a+  ++++    g   ++k
  gi|330506810|ref|YP_004383238.1| 186 KGVLLHGPPGTGKTILAKAVAQSTEATFMRVVGsEFVQK 224
                                       569********************9998755444044444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.3e-06    0.0012      51      90 ..     186     223 ..     182     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.3e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                       ++vLl Gp+gtGkt la a++++   +  f+ ++gse+ +
  gi|330506810|ref|YP_004383238.1| 186 KGVLLHGPPGTGKTILAKAVAQST--EATFMRVVGSEFVQ 223
                                       89*******************975..589*******9865 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   3.9e-06     0.002       2      28 ..     188     216 ..     188     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.9e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avll 28 
                                       vll+G+pG+GK+ la+ +++ +   + ++
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQSTEatFMRV 216
                                       799****************9988664444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.7e-06     0.003       2      40 ..     188     231 ..     187     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.7e-06
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileekla 40 
                                       + + G+++tGKT l++a a+      ++vv  E++ +++ e+++
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQSteatFMRVVgSEFVQKYIGEGAR 231
                                       6799***************5445558899999**9999988765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-05    0.0061      44      72 ..     182     210 ..     171     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveav 72 
                                       ie  ++++l Gp+G+GK+ la a+++++ 
  gi|330506810|ref|YP_004383238.1| 182 IEPPKGVLLHGPPGTGKTILAKAVAQSTE 210
                                       5666789*****************99765 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-05    0.0083       2      30 ..     188     216 ..     187     235 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll+g PG++kt+l+ka+a++ +++f r+
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQSTEATFMRV 216
                                       89*************************98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   1.9e-05      0.01      21      51 ..     188     218 ..     182     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-05
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrvig 51 
                                       ++l+Gp+GtGKt + ka+++  ea  +rv+g
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQSTEATFMRVVG 218
                                       6899*******************99989987 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-05    0.0057      51     116 ..     183     253 ..     136     256 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                            DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDDL 116
                                       +p + vLL G  GtGK  l ka+ ++++++ +r++  e  ++ + e  +lv++l    +++   i+++D L
  gi|330506810|ref|YP_004383238.1| 183 EPPKGVLLHGPPGTGKTILAKAVAQSTEATFMRVVgsEFVQKYIGEGARLVRELFelaKSKSPAIILIDEL 253
                                       67889*****************************9666778888888888876542226677788888877 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 !   15.8   0.1   1.5e-05     0.008       2      52 ..      76     125 ..      75     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                     Prot_ATP_OB_N   2 yGtflavnsqdgtadVlvggrrmrVavsPlvdaeeLrpGqeVlLnEalvvV 52 
                                       +Gt++ v ++ + +  ++ g r++V++s  ++ ee+++G++V Ln+++ +V
  gi|330506810|ref|YP_004383238.1|  76 VGTIVDVLDENRVIVKSSTGPRFVVSLSQFIE-EEIKVGAQVGLNQQSFAV 125
                                       6999999999999999****************.9***********998877 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.9e-05    0.0099       1      64 [.     188     242 ..     188     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkde 64 
                                       ++l+Gp+g+GK+ lak            ++++ +++r + ++f+++Y g+ + ++ ++ +  ++
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKA---------VAQSTEATFMRVVGSEFVQKYIGEGARLVRELFELAKS 242
                                       689**************.........34556788899999999999999988888887776655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       3.1   1.6e+03     117     143 ..      15      40 ..      13      45 .. 0.81
   2 ?   13.4   0.0     7e-05     0.037      25      43 ..     188     206 ..     180     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.1
                      Mg_chelatase 117 efkrkvlevLRePledgevtisrakak 143
                                       +f+r +l+ +R+ le+++++++ +k +
  gi|330506810|ref|YP_004383238.1|  15 DFSRYILDRMRQ-LEERNLALREQKDR 40 
                                       799********9.89888888776665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll GppG+GKt+lak+++
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVA 206
                                       89*************9975 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00021      0.11       3      23 ..     188     208 ..     186     215 .. 0.90
   2 ?    0.3   0.0       1.1   5.8e+02      71     112 ..     235     278 ..     219     286 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00021
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l+G++G GKT+L++ +a+ 
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQS 208
                                       79**************99985 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.1
                                       CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHH CS
                             NACHT  71 evwavllelperlLlilDglDelvtdlgq...kekqpvrtlLsel 112
                                       e   +l++ +  + +++D lD + +       ++ ++v++ L ++
  gi|330506810|ref|YP_004383238.1| 235 E-LFELAKSKSPAIILIDELDAIGARRMDgatSGDREVQRTLMQI 278
                                       4.45677888889999*****998866556666666666666555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013     0.069      13      37 ..     168     203 ..     151     213 .. 0.74
   2 ?   -1.1   0.0       1.8   9.7e+02     106     153 ..     231     281 ..     218     284 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                            ATPase  13 k...........gGipegrvvlitGepGtGKtifal 37 
                                       +            Gi   + vl+ G pGtGKti+a+
  gi|330506810|ref|YP_004383238.1| 168 ElplkrpdlftsVGIEPPKGVLLHGPPGTGKTILAK 203
                                       15555555555589999999**************97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                            ATPase 106 elieelaeaikeikakrvviDsitgl.ayeekeav..aReilrqlvrvlkk 153
                                        l++el e  k++    ++iD ++++ a++++ a+   Re  r+l+++l++
  gi|330506810|ref|YP_004383238.1| 231 RLVRELFELAKSKSPAIILIDELDAIgARRMDGATsgDREVQRTLMQILAE 281
                                       678888899999999999999999996655554442246666666666655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       5.6     3e+03      57      92 ..      26      61 ..      13      80 .. 0.66
   2 ?   13.7   0.0   0.00013     0.068       1      25 [.     188     219 ..     188     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 5.6
                            AAA_18 57 ldklldaleenssaleegknlvidghlaeleseaak 92
                                      + +  ++  +  +++ eg+  +i+ +  ++e ea+k
  gi|330506810|ref|YP_004383238.1| 26 QLEERNLALREQKDRVEGEKRLIENQKLKFEREARK 61
                                      333333333333367777777888888887777766 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00013
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.......g 25 
                                       +ll G+pG+GKt lak+++++++        +
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQSTEAtfmrvvgS 219
                                       7899**************99873335544442 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     7e-05     0.037      57      92 ..     189     227 ..     181     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7e-05
                                       EEEE-TTSSHHHHHHHHHH...HHSTTGGGSTTEEEEEH CS
                            Torsin  57 sfhGwtGtGknfvaeiiae...nlyrdGlrsdyvkkfva 92 
                                        +hG +GtGk  +a+ +a+   +++ + + s++v+k+++
  gi|330506810|ref|YP_004383238.1| 189 LLHGPPGTGKTILAKAVAQsteATFMRVVGSEFVQKYIG 227
                                       58**************99622267999999*******97 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.59   3.1e+02     150     185 ..      35      70 ..       8      92 .. 0.49
   2 ?   11.7   0.0    0.0003      0.16      19      38 ..     187     206 ..     170     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.59
                            AAA_11 150 eklkkskekskskleqerrklkkerkelskeleeae 185
                                       +++k   e +k+  e+++ k ++e+++l++ele+ +
  gi|330506810|ref|YP_004383238.1|  35 REQKDRVEGEKRLIENQKLKFEREARKLRSELERLR 70 
                                       222333333334444444444444444444444433 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0003
                            AAA_11  19 itliqGPPGtgKTktivell 38 
                                        +l++GPPGtgKT    ++ 
  gi|330506810|ref|YP_004383238.1| 187 GVLLHGPPGTGKTILAKAVA 206
                                       479**********5444443 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00011     0.057       4      40 ..     188     224 ..     186     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafvea 40 
                                       +lL+G + +GK+ la+a+ + ++++++ +   +fv++
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQSTEATFMRVVGSEFVQK 224
                                       89*************************9988888765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.7e-05     0.051      30      61 ..     182     213 ..     172     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.7e-05
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkek 61 
                                       ++  k vll Gp GtGKt+++k + ++ + + 
  gi|330506810|ref|YP_004383238.1| 182 IEPPKGVLLHGPPGTGKTILAKAVAQSTEATF 213
                                       556688*****************999888444 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00014     0.073      21      48 ..     187     216 ..     161     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                                       EEEEEESTTSSHHHHHHHHHHHTT--..-- CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakalgve..ev 48 
                                        +lL+G+ G+GKT l++++a++ + +  +v
  gi|330506810|ref|YP_004383238.1| 187 GVLLHGPPGTGKTILAKAVAQSTEATfmRV 216
                                       49*******************998775544 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00032      0.17      23      48 ..     186     211 ..     177     229 .. 0.83
   2 ?   -2.5   0.0         7   3.7e+03     133     143 ..     289     299 ..     269     310 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                                       S-EEEECSTTSSHHHHHHHHHHHSTT CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskr 48 
                                         vl++G  GtGK++la+a+ ++++ 
  gi|330506810|ref|YP_004383238.1| 186 KGVLLHGPPGTGKTILAKAVAQSTEA 211
                                       569****************9886654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7
                                       --EEEEEEESS CS
                   Sigma54_activat 133 vdvriiaatne 143
                                        +v++iaatn+
  gi|330506810|ref|YP_004383238.1| 289 GEVKLIAATNR 299
                                       46889999986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.8   1.5e+03      52      95 ..      23      69 ..       9     109 .. 0.72
   2 ?   11.0   0.0   0.00088      0.46       5      37 ..     179     211 ..     178     253 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.8
                                      B-HHHCCHCEEEE-SS--S-TTSBHHHH...HHHTCHHHHHHHSTTG CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
                          ABC_tran 52 qeleslrkeigvlpqepqlfpeltvren...esdeeiekalsklglk 95
                                      + ++  +++++  +q++++  e+++ en   + ++e+ k++s+l+  
  gi|330506810|ref|YP_004383238.1| 23 RMRQLEERNLALREQKDRVEGEKRLIENqklKFEREARKLRSELERL 69
                                      56677778888888888888888877777887777777777777654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00088
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkp 37 
                                       s+ +++ + v + G+ G+GK+ L+k++a+ ++ 
  gi|330506810|ref|YP_004383238.1| 179 SVGIEPPKGVLLHGPPGTGKTILAKAVAQSTEA 211
                                       6788899999****************9998775 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.4   1.8e+03     118     131 ..      35      48 ..      15      88 .. 0.55
   2 ?   10.2   0.0   0.00046      0.24      60     124 ..     183     253 ..     172     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.4
                       AFG1_ATPase 118 aivadrlaeearvl 131
                                        +  dr+ +e r++
  gi|330506810|ref|YP_004383238.1|  35 REQKDRVEGEKRLI 48 
                                       55555544444433 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00046
                       AFG1_ATPase  60 epvrglYlwGgvGrGKtylmdlffeslpvekkrrvhfhafm.......arvhdeltklrkekdplaivadrl 124
                                       ep++g+ l+G+ G GKt l     +s +  +  rv   +f+       ar+  el +l+k k p  i +d+l
  gi|330506810|ref|YP_004383238.1| 183 EPPKGVLLHGPPGTGKTILAKAVAQSTEA-TFMRVVGSEFVqkyigegARLVRELFELAKSKSPAIILIDEL 253
                                       79****************99888887776.666666555551112222345555666666666666666665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00052      0.27       2      55 ..     188     242 ..     187     260 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00052
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEE.EEEEE-------EEEEEET.T- CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf.yteevreggrrigFkivdlasg 55 
                                       v++ GppG+GKt l k v++  +   ++v G   ++++  +g r   ++ +la+ 
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQSTEATFMRVVGSeFVQKYIGEGARLVRELFELAKS 242
                                       6789******************999999999634667778888888887777655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00035      0.18      23      44 ..     188     209 ..     183     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       v l+G +G GKt+lak + ++ 
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQST 209
                                       679*************999883 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00046      0.24       5      76 ..     188     256 ..     185     292 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00046
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT l+k ++++       ++ +   +  +k + + ++l ++++e++k++   ++++DE   +
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQSTE---ATFMRVVGSEFVQKYIGEGARLVRELFELAKSKSPAIILIDELDAI 256
                                       7899**************98887...4444444444333444444467888888866668999*****8766 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 ?   10.2   0.0   0.00056       0.3     117     138 ..     188     209 ..     181     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00056
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                       v+++Gp+ tGkt+la+a a+ +
  gi|330506810|ref|YP_004383238.1| 188 VLLHGPPGTGKTILAKAVAQST 209
                                       899***************9976 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.4       2.3   1.2e+03     137     189 ..      34      85 ..      25      94 .. 0.62
   2 ?   10.8   0.0   0.00041      0.22      14      44 ..     183     211 ..     174     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.3
                        Zeta_toxin 137 rlgvldRyeeevaegRlvpke..ehdeafeglresvealeeekqldrvkikdrdg 189
                                         + +dR+e e    Rl++ +  ++++  ++lr+++e+l +   ++ +++   d+
  gi|330506810|ref|YP_004383238.1|  34 LREQKDRVEGE---KRLIENQklKFEREARKLRSELERLRVGPMIVGTIVDVLDE 85 
                                       33444444444...69997662257788899999999999888777666544444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00041
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqg 44 
                                       e Pk +ll G pG GK+ la+++++++e   
  gi|330506810|ref|YP_004383238.1| 183 EPPKGVLLHGPPGTGKTILAKAVAQSTE--A 211
                                       6799********************9984..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 2830.25
//
Query:       gi|330506811|ref|YP_004383239.1|  [L=158]
Description: hypothetical protein MCON_0588 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1136.11
//
Query:       gi|330506812|ref|YP_004383240.1|  [L=86]
Description: hypothetical protein MCON_0589 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 673.83
//
Query:       gi|330506813|ref|YP_004383241.1|  [L=74]
Description: hypothetical protein MCON_0590 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.065   13.3   0.0      0.075   13.1   0.0    1.1  1  COG2      COG (conserved oligomeric Golgi) complex component,


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 ?   13.1   0.0   4.2e-06     0.075      64     101 ..      32      69 ..      19      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.2e-06
                              COG2  64 Lvglqeeleevesplaaarkkvesvreklsereeeves 101
                                       L +++++l+ v++   a+ ++v++vr+  +++ ee+++
  gi|330506813|ref|YP_004383241.1|  32 LLDMRDDLKAVRKTSDATLDEVRAVRKTTDATLEEIKG 69 
                                       89*********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 597.47
//
Query:       gi|330506814|ref|YP_004383242.1|  [L=296]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete 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   81.9   0.3    7.4e-23   80.3   0.0    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.5e-07   30.9   0.5    2.5e-07   30.9   0.5    1.6  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.027   14.5   0.1       0.06   13.4   0.1    1.5  1  DZR             Double zinc ribbon
       0.05   13.6   0.0       0.13   12.3   0.0    1.8  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.14   12.1   0.6       0.26   11.2   0.6    1.4  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.57   10.3   4.0        8.6    6.5   0.1    2.2  2  DUF4337         Domain of unknown function (DUF4337)


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.4   4.1e+03       2       2 ..     133     133 ..     101     151 .. 0.63
   2 !   80.3   0.0   2.5e-26   7.4e-23       1      67 [.     198     262 ..     198     263 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.4
                    OrfB_Zn_ribbon   2 r 2  
                                       r
  gi|330506814|ref|YP_004383242.1| 133 R 133
                                       2 PP

  == domain 2  score: 80.3 bits;  conditional E-value: 2.5e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       f++lke+l+yka  +G+++++v+payTS+tC++Cg+ + +  +g+ fkCp Cg + d+D+n+a Ni+
  gi|330506814|ref|YP_004383242.1| 198 FYQLKEFLSYKALAAGVPLVLVDPAYTSQTCHQCGEHGIR--NGKSFKCPVCGWSGDADFNGAKNIA 262
                                       899*************************************..************************7 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.2   6.7e+03      51      70 ..      11      38 ..       8      47 .. 0.60
   2 !   30.9   0.5   8.5e-11   2.5e-07       7     106 ..      69     165 ..      60     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.2
                        OrfB_IS605 51 kylakeiaelqsklkkskn........y 70
                                      ++++++  e++ +l +s++        y
  gi|330506814|ref|YP_004383242.1| 11 FAFREKDEEVSVTLLRSRQriklvlgdY 38
                                      5677777788888877775333333334 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 8.5e-11
                        OrfB_IS605   7 evelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn..ykkasrklarlh 81 
                                       e  +++    +++g+DlGi ++a++++++     + g+ +k  +  +a  +a lq+k+ k ++  ++++++ ++rl+
  gi|330506814|ref|YP_004383242.1|  69 EA-PEQIHVDTVLGVDLGITDIAVTSEGQ----KFGGKTIKLIKNHYASMRAVLQQKAVKGTRssRRRCRELQQRLS 140
                                       33.667777899****************9....78999999999***********9998888889************ PP

                        OrfB_IS605  82 rkrsrrrkhllhklathliktlkev 106
                                        k +r  +   h+++++++ + +e+
  gi|330506814|ref|YP_004383242.1| 141 GKEARYQRQINHEISKAIVTRAQEI 165
                                       *******************999987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     2e-05      0.06      28      49 .]     225     248 ..     202     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                               DZR  28 edrCpsCgek.vdpearf.CpeCG 49 
                                       +++C +Cge  + ++++f Cp CG
  gi|330506814|ref|YP_004383242.1| 225 SQTCHQCGEHgIRNGKSFkCPVCG 248
                                       566777776666666666666666 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.4e-05      0.13      56      95 ..     210     250 ..     152     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
                                       TTTT-EEE.EEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  56 vlegaeLe.ieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       +++g  L  ++    + +C++Cg+++  + k+++Cp Cg +
  gi|330506814|ref|YP_004383242.1| 210 LAAGVPLVlVDPAYTSQTCHQCGEHGIRNGKSFKCPVCGWS 250
                                       455555553444556789*****9998777789*****965 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 ?   11.2   0.6   8.8e-05      0.26      25      43 ..     227     247 ..     219     250 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.8e-05
                                       E-HHHHHHHHH..TT-B-TTT CS
                        zf-C3HC4_3  25 lCeeCaekllk..rkkkCpiC 43 
                                       +C++C e+  +  ++ kCp+C
  gi|330506814|ref|YP_004383242.1| 227 TCHQCGEHGIRngKSFKCPVC 247
                                       8*******99999******** PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   1.2     0.011        34      46     105 ..     104     167 ..     101     176 .. 0.76
   2 ?    6.5   0.1    0.0029       8.6      25      47 ..     181     203 ..     169     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
                           DUF4337  46 ksikehlaeleleqlelllkakaeelaaavdkkiakykkkiarykke.....kkeikkkAkelea 105
                                       k ik+h a++ +  l+ ++ ++++  +++ ++ +++++ k ary+++     +k+i ++A+e+ a
  gi|330506814|ref|YP_004383242.1| 104 KLIKNHYASM-RAVLQQKAVKGTRSSRRRCRELQQRLSGKEARYQRQinheiSKAIVTRAQEIPA 167
                                       5578888888.44444444444999999999***************9877777777778888765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0029
                           DUF4337  25 aqteailaqaeasdqWafYQAks 47 
                                       ++++a  ++ ++++ WafYQ k+
  gi|330506814|ref|YP_004383242.1| 181 VNQKAGKNHRRKVNGWAFYQLKE 203
                                       567888899***********886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1884.68
//
Query:       gi|330506815|ref|YP_004383243.1|  [L=352]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete 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   75.4   0.0    4.8e-21   74.6   0.0    1.4  1  DUF772       Transposase domain (DUF772)
    1.5e-15   57.4   4.6      5e-15   55.7   4.6    1.9  1  DDE_Tnp_1    Transposase DDE domain
      3e-05   23.8   0.3    0.00012   21.8   0.3    1.9  1  DDE_Tnp_4    DDE superfamily endonuclease
    3.1e-05   24.2   0.4    5.3e-05   23.4   0.4    1.4  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
      0.052   13.9   0.1       0.12   12.8   0.1    1.6  1  EnY2         Transcription factor e(y)2


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 !   74.6   0.0   1.3e-24   4.8e-21       1      72 [.      51     122 ..      51     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.3e-24
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp+++ ++m+k+l+lq ++glSd ele+++ +++sfr flg     + +pd+st + fR+rl+e    e+l++e
  gi|330506815|ref|YP_004383243.1|  51 GRPNIDIVIMVKALVLQSWFGLSDPELERQVTDRISFRIFLGT---TEVIPDFSTVWLFRERLIEcgrYEDLWKE 122
                                       9*****************************************5...389****************9999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   4.6   1.4e-18     5e-15      20     214 .]     177     340 ..     133     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.4e-18
                         DDE_Tnp_1  20 k............................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkql 68 
                                       +                             ++ w +kg k+++gyk hi++dt+ +li ++++t+++ hds++    
  gi|330506815|ref|YP_004383243.1| 177 PdfdkdllnisnnivssnakpkrlddgpiNEGTWAKKGSKSFFGYKGHILIDTEYHLIRKIETTTASLHDSQVDLG- 252
                                       0555555555555555555556666666677889999**********************************99777. PP

                         DDE_Tnp_1  69 ldelrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnksk 145
                                       +++l++      +aD+GY++a++  + +                            ++k+ r++ l  ++++rnk  
  gi|330506815|ref|YP_004383243.1| 253 INGLPR------YADKGYSGAKTQGYDA---------------------------AMKKAARGHKLGIKDILRNK-- 294
                                       777887......*******888877777...........................89******************.. PP

                         DDE_Tnp_1 146 kekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                              +++r+R+qiEr F+ +kr  + +++++ + +r+ +++++  +++n+
  gi|330506815|ref|YP_004383243.1| 295 -----------------------RISRKRSQIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNI 340
                                       .......................******************999************************7 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   3.4e-08   0.00012      77     130 ..     257     313 ..     195     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.4e-08
                         DDE_Tnp_4  77 vilaDkgFklse..kl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgr 130
                                          aDkg+ +++   +   ++k  ++++l  ++  +n++i++ r  +Er+++ +k+ 
  gi|330506815|ref|YP_004383243.1| 257 PRYADKGYSGAKtqGYdAAMKKAARGHKLGIKDILRNKRISRKRSQIERCFAVMKRA 313
                                       3469*****99954333455555********************************65 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 !   23.4   0.4   1.5e-08   5.3e-05      74     124 ..     294     343 ..     265     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.5e-08
                       DDE_Tnp_1_6  74 kaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                       k+  +kR+ ++E+ fa +kr++++  + ++ ++++ ++f++  +++N+++l
  gi|330506815|ref|YP_004383243.1| 294 KRISRKRS-QIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNIEQL 343
                                       45556665.***************************************997 PP

>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.3e-05      0.12       5      31 ..     107     133 ..     106     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       HHHHHHTTHHHHHHHHHHHHHHHTTHH CS
                              EnY2   5 qqkLvesGererlkelLrerLeesGWr 31 
                                       +++L+e G +e+l + L+++L+e G+ 
  gi|330506815|ref|YP_004383243.1| 107 RERLIECGRYEDLWKELQNQLDEKGFA 133
                                       589**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2575.41
//
Query:       gi|330506816|ref|YP_004383244.1|  [L=128]
Description: transposase, IS605 family protein MITE [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.052   13.5   0.0      0.078   13.0   0.0    1.2  1  Mad3_BUB1_I  Mad3/BUB1 homology region 1


Domain annotation for each model (and alignments):
>> Mad3_BUB1_I  Mad3/BUB1 homology region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.4e-06     0.078      13      39 ..      19      45 ..      10      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.4e-06
                                      G....-THHHHHHHHHHHHHH-TT-T. CS
                       Mad3_BUB1_I 13 aeegdDpLelwlryikwieesypqssk 39
                                      aee+dD L+++ + ++wi+++ p + +
  gi|330506816|ref|YP_004383244.1| 19 AEEMDDTLKAFADACNWINQNTPAKLR 45
                                      289********************9443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1011.63
//
Query:       gi|330506817|ref|YP_004383245.1|  [L=55]
Description: transposase domain-containing protein, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-10   40.2   0.5    3.2e-10   39.8   0.5    1.1  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0025   17.2   3.6      0.027   13.9   3.3    2.2  1  zf-ribbon_3     zinc-ribbon domain
     0.0029   17.6   0.1     0.0035   17.3   0.1    1.1  1  DZR             Double zinc ribbon
     0.0091   16.1   0.2      0.013   15.6   0.2    1.3  1  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
       0.08   12.6   1.8        4.1    7.1   0.1    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
        0.1   12.9   2.5       0.28   11.5   2.5    1.7  1  zf-LITAF-like   LITAF-like zinc ribbon domain
       0.11   12.0   2.6        2.2    7.9   0.2    2.2  2  RecR            RecR protein
       0.22   11.3   4.0        3.2    7.6   0.8    2.2  1  zinc_ribbon_2   zinc-ribbon domain
       0.26   11.6   0.6       0.33   11.2   0.6    1.1  1  DUF2072         Zn-ribbon containing protein
        0.4   10.7   3.5        1.2    9.1   3.5    1.7  1  DUF1610         Domain of unknown function (DUF1610)
        1.1    9.3   4.6        1.2    9.2   0.7    2.1  2  Zn_Tnp_IS1595   Transposase 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 !   39.8   0.5     2e-13   3.2e-10      31      67 ..       2      38 ..       1      39 [. 0.97

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 2e-13
                    OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67
                                      Cs+Cg   ++als+ +++Cp+Cg++  rD+nAaiN+l
  gi|330506817|ref|YP_004383245.1|  2 CSRCGILIEKALSDSVHNCPHCGLSVSRDWNAAINML 38
                                      ***********************************86 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   3.3   1.7e-05     0.027       5      24 ..       2      25 ..       1      27 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                       zf-ribbon_3  5 CPnCG...ap.lssddnvCpyCGt 24
                                      C++CG   ++ ls+++ +Cp+CG 
  gi|330506817|ref|YP_004383245.1|  2 CSRCGiliEKaLSDSVHNCPHCGL 25
                                      8888855531369**********5 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.2e-06    0.0035      14      44 ..       1      33 [.       1      36 [. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.2e-06
                               DZR 14 fCseCgtklkavaa..edrCpsCgekvdpearf 44
                                      +Cs+Cg  ++++ +   ++Cp+Cg +v+ +++ 
  gi|330506817|ref|YP_004383245.1|  1 MCSRCGILIEKALSdsVHNCPHCGLSVSRDWNA 33
                                      5*******99877799*************9996 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   7.7e-06     0.013       8      38 ..       2      29 ..       1      31 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.7e-06
                       Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgsevrr 38
                                      C +Cg   e+  s  d   ++ CP+Cg  v r
  gi|330506817|ref|YP_004383245.1|  2 CSRCGILIEKALS--D--SVHnCPHCGLSVSR 29
                                      999**88886653..3..4555*****99988 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0025       4.1       5      14 ..       2      11 ..       1      16 [. 0.84
   2 ?    5.3   0.2    0.0089        14       4      13 ..      19      28 ..      16      32 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0025
                            zf_UBZ  5 CerCgkeipe 14
                                      C+rCg  i+ 
  gi|330506817|ref|YP_004383245.1|  2 CSRCGILIEK 11
                                      *****99986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0089
                            zf_UBZ  4 lCerCgkeip 13
                                       C+ Cg +++
  gi|330506817|ref|YP_004383245.1| 19 NCPHCGLSVS 28
                                      7*****9987 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 ?   11.5   2.5   0.00017      0.28      43      65 ..       5      26 ..       1      30 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                     zf-LITAF-like 43 cliPfcvdslkdvehyCpnCgal 65
                                      c i ++ + l d  h Cp+Cg  
  gi|330506817|ref|YP_004383245.1|  5 CGI-LIEKALSDSVHNCPHCGLS 26
                                      433.566899**********965 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0095        15      19      28 ..       2      11 ..       1      13 [. 0.81
   2 ?    7.9   0.2    0.0013       2.2      11      23 ..      12      24 ..      11      30 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0095
                                      -TTT--EESS CS
                              RecR 19 CsrCgnltee 28
                                      CsrCg l e+
  gi|330506817|ref|YP_004383245.1|  2 CSRCGILIEK 11
                                      *****98765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0013
                                      HHHHH-EE-TTT- CS
                              RecR 11 eakekvrhCsrCg 23
                                      ++ ++v+ C+ Cg
  gi|330506817|ref|YP_004383245.1| 12 ALSDSVHNCPHCG 24
                                      57899*******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 ?    7.6   0.8     0.002       3.2       2       6 ..      20      24 ..      19      30 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.002
                     zinc_ribbon_2  2 CpnCG 6 
                                      Cp+CG
  gi|330506817|ref|YP_004383245.1| 20 CPHCG 24
                                      88888 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6    0.0002      0.33       3      27 ..       1      25 [.       1      28 [. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                           DUF2072  3 kCtkCekvfedgskeilkGCpsCGg 27
                                      +C +C+ ++e + ++  + Cp+CG 
  gi|330506817|ref|YP_004383245.1|  1 MCSRCGILIEKALSDSVHNCPHCGL 25
                                      6***********************6 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.5   0.00075       1.2       1      23 [.       2      24 ..       2      24 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00075
                           DUF1610  1 CtSCGaelaprEravvFpCPNCG 23
                                      C+ CG+ +  +   +v+ CP CG
  gi|330506817|ref|YP_004383245.1|  2 CSRCGILIEKALSDSVHNCPHCG 24
                                      88899999888878********9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   5.0     0.033        54      19      25 ..      18      24 ..       1      25 [. 0.70
   2 ?    9.2   0.7   0.00073       1.2      19      27 ..      18      26 ..      10      34 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.033
                     Zn_Tnp_IS1595 19 fvCPhCg 25
                                      + CPhCg
  gi|330506817|ref|YP_004383245.1| 18 HNCPHCG 24
                                      4588887 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00073
                     Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                      + CPhCg +
  gi|330506817|ref|YP_004383245.1| 18 HNCPHCGLS 26
                                      56*****66 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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):              11  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 401.33
//
Query:       gi|330506818|ref|YP_004383246.1|  [L=425]
Description: integral membrane protein [Methanosaeta concilii GP6]
Scores for 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-56  188.9   4.7    8.6e-56  188.4   4.7    1.2  1  DUF21          Cyclin M transmembrane N-terminal domain
    8.4e-24   83.4   0.6    1.8e-23   82.4   0.6    1.6  1  CorC_HlyC      Transporter associated domain
    3.1e-13   50.0   1.7    8.1e-06   26.2   0.4    3.1  3  CBS            CBS domain
     0.0017   18.6   0.3     0.0042   17.3   0.3    1.6  1  HEPN_RES_NTD1  HEPN/RES N-terminal domain 1


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 !  188.4   4.7   1.9e-59   8.6e-56       5     175 ..      14     188 ..      10     190 .. 0.97

  Alignments for each domain:
  == domain 1  score: 188.4 bits;  conditional E-value: 1.9e-59
                             DUF21   5 lllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvellae 81 
                                       +ll++saffs++EtAl+sls++rl +l+e++ ++a+ ++kl+k+p+rlL t+l+gn+lvni +s++at+l+++++  
  gi|330506818|ref|YP_004383246.1|  14 FLLFASAFFSASETALMSLSKIRLIHLVEEKIRGASVVEKLRKDPSRLLGTILVGNNLVNISASSIATVLAIKYF-- 88 
                                       899************************************************************************.. PP

                             DUF21  82 galavviatvivtllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlil......esesep 152
                                       g+ +v iat ++t+l+l+fgEi+Pksla++++e++al++a+p++vl ++l+P+v+++s+++ ++l      ++++ p
  gi|330506818|ref|YP_004383246.1|  89 GDSGVGIATGVMTMLVLIFGEITPKSLAAQKSEQVALLVARPISVLAYILSPVVAVFSRVASIFLrlfgcrSNAKLP 165
                                       689********************************************************************99**** PP

                             DUF21 153 avseeelkklveeseeegvieee 175
                                        ++eeelk++v+++eeegvie  
  gi|330506818|ref|YP_004383246.1| 166 SITEEELKSMVNLGEEEGVIEDH 188
                                       ********************765 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   0.6     4e-27   1.8e-23       3      77 ..     339     411 ..     337     415 .. 0.94

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 4e-27
                                       ECTTEEEEETT-BHHHHHHHHTSTTHHCT-SBHHHHHHHHH-S---TT-EEEEEETTEEEEEEEEETTCEEEEEE CS
                         CorC_HlyC   3 ldegsylvdGslpldeleeelglelpeedyeTlgGlllellgriPkegesvevdleglrftVlemdgrrIkkvrv 77 
                                       ++eg+y+vdGs++++el+e++g+++++e ye++gG++++llgr+P++gesve+   + rf +++++++rIkk+rv
  gi|330506818|ref|YP_004383246.1| 339 IREGEYIVDGSTRIEELNELIGTDIESEHYESIGGFMIQLLGRLPRQGESVEYM--NTRFVIENVEKNRIKKIRV 411
                                       789**********************************************66666..******************9 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.8   7.9e+03      23      46 ..      37      65 ..      22      67 .. 0.62
   2 !   26.2   0.4   1.8e-09   8.1e-06       1      52 [.     204     258 ..     204     263 .. 0.85
   3 !   21.5   0.0   5.4e-08   0.00024      11      56 ..     277     322 ..     267     323 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.8
                                      HH.HHHHTSSEEEEE....ETTTBEEEEE CS
                               CBS 23 el.mrekgvsrlPVV....dedgklvGiv 46
                                       + ++e+++++  VV     +  +l+G +
  gi|330506818|ref|YP_004383246.1| 37 LIhLVEEKIRGASVVeklrKDPSRLLGTI 65
                                      44455677777778866653344577765 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 1.8e-09
                                       HHHHSBS..SCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHH CS
                               CBS   1 Vgdimtr..dvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDll 52 
                                       V+dim +  d++ ++ ++t e++++++r + +sr+PV  +  +++vGi+  +Dl+
  gi|330506818|ref|YP_004383246.1| 204 VKDIMVPrmDIIAININATYEDVIKIIRAEQFSRYPVYsNRIDNIVGILNVKDLV 258
                                       89998777799****************7666******9544447*********97 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 5.4e-08
                                       EEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHHH CS
                               CBS  11 tvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllrall 56 
                                       +  + ++ +e++ +m++++  ++ +V de+g   Givt++Dl++ ++
  gi|330506818|ref|YP_004383246.1| 277 YTFEFMNTSELFSEMKKRRT-HMAIVlDEYGGTAGIVTMEDLVEEIV 322
                                       55566777899****54445.554444****************9986 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 !   17.3   0.3   9.4e-07    0.0042      15      69 ..     310     361 ..     304     372 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.4e-07
                     HEPN_RES_NTD1  15 kkvvsleellefilegiekeYedaanelpydsreggylvgetydtedlleeviel 69 
                                          v++e+l+e i+ +i+ eY+ ++ne+    reg+y+v+ +   e+l +e+i++
  gi|330506818|ref|YP_004383246.1| 310 G-IVTMEDLVEEIVGEISDEYDMQTNEIETI-REGEYIVDGSTRIEEL-NELIGT 361
                                       3.789**********************9987.8*****9999555554.444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2848.24
//
Query:       gi|330506819|ref|YP_004383247.1|  [L=468]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-41  141.4   0.2    4.8e-41  140.9   0.2    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.8e-15   57.3   0.2    1.2e-09   38.6   0.0    3.5  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.6e-12   47.7   0.0    4.8e-12   46.1   0.0    1.8  1  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
    1.2e-09   38.2   0.1       0.17   11.5   0.1    3.3  3  DAO            FAD dependent oxidoreductase
    6.6e-06   25.1   0.0     0.0092   14.7   0.0    3.1  3  HI0933_like    HI0933-like protein
    9.6e-06   25.7   0.0       0.13   12.3   0.0    3.3  3  NAD_binding_9  FAD-NAD(P)-binding
    1.1e-05   24.8   0.1    8.4e-05   22.0   0.0    2.3  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
     0.0017   17.6   0.1       0.19   10.9   0.0    2.4  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
     0.0048   16.2   0.0       0.02   14.2   0.0    1.7  2  Amino_oxidase  Flavin containing amine oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.9   0.2   2.4e-44   4.8e-41       3     279 ..       5     300 ..       3     315 .. 0.87

  Alignments for each domain:
  == domain 1  score: 140.9 bits;  conditional E-value: 2.4e-44
                                       EEEE--SHHHHHHHHHHHH......HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...HHHHCHHHHCCCC CS
                                       xxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                       Pyr_redox_2   3 vvviGgGpAGlaaaltlaq......agakvtlvelegtclnggcllskallgvaedaeias...evvkklnqgiell 70 
                                        v+iGgG+ G+ ++++l++        +k++l+ +e+t     c l++al+g+ e  +++    e     +qg++++
  gi|330506819|ref|YP_004383247.1|   5 AVIIGGGISGIFVMKDLQEksiatkEDIKIVLLKREDTGWVSVCGLPYALRGWYEIDKVVInkpE--FFSEQGVDFR 79 
                                       69*****************999886699*****9999999999************9998888651..334569**** PP

                                       HCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCTTC.TTBEECCSECHHHHHHCCSS-T...S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                       Pyr_redox_2  71 lgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gipGvaenvgklvrtldsaealklkllp...k 143
                                       +++ev +i ++ k++kl     + +e+++yd+lv+AtG +p ++  i+    ++++ ++t+++a  ++ + +    k
  gi|330506819|ref|YP_004383247.1|  80 TKTEVERINTDDKTLKL-----KTGETLKYDYLVIATGRKPALPeMIEKSTMKNIFTLSTMEDAYSIEAAFKSgevK 151
                                       *****************.....5688******************88887777778888***************99** PP

                                       EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEE.EEEETTEEEE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx. RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvk.eidgngekle. 217
                                       +++v G G i++  Aaa+a    ++t++   + ll  +ld++++++l+e ++k+G+e+ l++++   ++++g +++ 
  gi|330506819|ref|YP_004383247.1| 152 NALVRGRGIIALQAAAAAAANRIKTTVLAGPPSLLpGGLDPDMGDMLKEWMQKQGIEFILENQPIsGLKEDGGRVRs 228
                                       *****************999999************99***********************99984144444446666 PP

                                       .EEETTSCE.EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.....BES.STTEEE-GGGC....T CS
                                       .xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxx.xxxxxxxxxxx....x RF
                       Pyr_redox_2 218 .vvledgee.idadlvvvavGvrpstelleeklglelderggivvdefl.....rtn.vpgiyaiGDva....g 279
                                        ++   ge+ i+a++vvva G+rp+ +l+ e++g+e+ ++ggi +d +l     + +  ++++a+GD++    g
  gi|330506819|ref|YP_004383247.1| 229 vLIGPRGEKeIPAEMVVVAMGMRPNVRLA-EEAGIEIGDTGGIITDNSLhaktkK-SyLKEVFALGDCIevidG 300
                                       6555554445*******************.*******************775433.559*********944443 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.069   1.4e+02       2      17 ..       5      20 ..       4      41 .. 0.80
   2 !   11.3   0.1   0.00019      0.38      50      78 ..      71      96 ..      62     101 .. 0.86
   3 !   38.6   0.0   5.8e-13   1.2e-09       2      77 ..     153     230 ..     152     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.069
                                      EEEECSSHHHHHHHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAga 17
                                      +v++GgG +g+ + + 
  gi|330506819|ref|YP_004383247.1|  5 AVIIGGGISGIFVMKD 20
                                      69********866555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00019
                                      HHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox 50 lekngievllntkveeiegsedgvesvkl 78
                                      ++++g++++++t+ve+i++++++   +kl
  gi|330506819|ref|YP_004383247.1| 71 FSEQGVDFRTKTEVERINTDDKT---LKL 96
                                      789****************9996...444 PP

  == domain 3  score: 38.6 bits;  conditional E-value: 5.8e-13
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedg.vesv 76 
                                       ++v G G i+l +A+a+a+ + k+tv+   + ll  +lD++++++l+e ++k+gie++l++++ +  +++ g v+sv
  gi|330506819|ref|YP_004383247.1| 153 ALVRGRGIIALQAAAAAAANRIKTTVLAGPPSLLpGGLDPDMGDMLKEWMQKQGIEFILENQPISGLKEDGGrVRSV 229
                                       6799*************************************************************999999999999 PP

                                       E CS
                         Pyr_redox  77 k 77 
                                        
  gi|330506819|ref|YP_004383247.1| 230 L 230
                                       6 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   2.4e-15   4.8e-12       9      95 ..     353     439 ..     349     452 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 2.4e-15
                                       SEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEEC.TTHHHHHHHHHHHH CS
                     Pyr_redox_dim   9 pevasvGlteeeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivG.pgageliqelavai 83 
                                       ++++svG+t e A +ag  ik+++ + +++++a++ +  +  ++Kl++da + k+lGa++++   ++++++e+avai
  gi|330506819|ref|YP_004383247.1| 353 LNFGSVGVTTEAAGRAG--IKTISGKATKLTKARYFPGaKPLTMKLIFDAFSMKLLGAQMISeVPVSDRVNEMAVAI 427
                                       678**************..*****************99999*********************656999********* PP

                                       HTTSBHHHHHTS CS
                     Pyr_redox_dim  84 kagltvedladt 95 
                                       +a + +edl +t
  gi|330506819|ref|YP_004383247.1| 428 RACVNAEDLRNT 439
                                       *******87765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   8.4e-05      0.17       2      33 ..       5      43 ..       4      47 .. 0.81
   2 !   11.3   0.0   9.5e-05      0.19     156     201 ..      71     112 ..      68     128 .. 0.78
   3 !   10.5   0.0   0.00016      0.32     152     205 ..     198     253 ..     188     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.4e-05
                                      EEEECTSHHHHHHHHHHHHTT........EEEEESSSSTT CS
                               DAO  2 vviiGGGiiGlstAyeLarrg........Vtllekgdiag 33
                                       viiGGGi G+++  +L+++         ++ll ++ + g
  gi|330506819|ref|YP_004383247.1|  5 AVIIGGGISGIFVMKDLQEKSiatkedikIVLLKRE-DTG 43
                                      59***************8765556678999999988.655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.5e-05
                                       HHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--G CS
                               DAO 156 aealGveilegtevtgleeedgkvwgverttpgendaadavVnaaG 201
                                       + ++Gv+++++tev+++ ++d+k  ++  +t ge+ ++d++V+a+G
  gi|330506819|ref|YP_004383247.1|  71 FSEQGVDFRTKTEVERI-NTDDKTLKL--KT-GETLKYDYLVIATG 112
                                       6789*************.555554555..44.777467*******9 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00016
                                       HHHHHHHTT-EEE.ESECEEEEEEEETCEEEEE...EECTEEE.EEEEEEEE--GGGHH CS
                               DAO 152 laraaealGveil.egtevtgleeedgkvwgve...rttpgen.daadavVnaaGawsd 205
                                       l + ++++G+e++ e+ ++ gl+e++g+v  v    r   ge+   a+ vV+a+G   +
  gi|330506819|ref|YP_004383247.1| 198 LKEWMQKQGIEFIlENQPISGLKEDGGRVRSVLigpR---GEKeIPAEMVVVAMGMRPN 253
                                       556699999976516789999*999899999966443...776345566******7654 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.053     1e+02       2      20 ..       4      22 ..       3      36 .. 0.82
   2 !   14.7   0.0   4.6e-06    0.0092     120     165 ..      72     114 ..      65     120 .. 0.83
   3 !    4.9   0.0    0.0044       8.7     113     163 ..     196     249 ..     192     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.053
                                      SEEEE--SHHHHHHHHHHH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaa 20
                                      + ++iGgG +G++    ++
  gi|330506819|ref|YP_004383247.1|  4 TAVIIGGGISGIFVMKDLQ 22
                                      579*********9866665 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.6e-06
                                       HHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 120 keagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                       +e+gv++r++tev++++++++  +++kt  +e+l+ d+lv+AtG +
  gi|330506819|ref|YP_004383247.1|  72 SEQGVDFRTKTEVERINTDDKT-LKLKT--GETLKYDYLVIATGRK 114
                                       689*************664444.66655..9*************65 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0044
                                       HHHHHHHHHHT-EEE-.S--EEEEECETTE.EEEEE...TTEEEEESEEEE--- CS
                       HI0933_like 113 dallkelkeagvklrl.etevksvekeedgkfrvkt..kseeeleadklvlAtG 163
                                       d+l++ ++++g+++ l ++ +++++++ +++ +v +  ++e+e+ a+ +v+A+G
  gi|330506819|ref|YP_004383247.1| 196 DMLKEWMQKQGIEFILeNQPISGLKEDGGRVRSVLIgpRGEKEIPAEMVVVAMG 249
                                       89***********87615679999887777777777667999**********99 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   6.3e-05      0.13       1      37 [.       6      43 ..       6      48 .. 0.89
   2 !    7.0   0.0    0.0027       5.3     121     155 ..      81     113 ..      71     114 .. 0.80
   3 ?    2.4   0.0      0.07   1.4e+02     112     155 ..     204     250 ..     192     251 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.3e-05
                     NAD_binding_9  1 aivGaGprGlavlerLlara.kkkspleitlfdpsepg 37
                                      +i+G+G++G+ v++ L +++ ++k++++i l  ++ +g
  gi|330506819|ref|YP_004383247.1|  6 VIIGGGISGIFVMKDLQEKSiATKEDIKIVLLKREDTG 43
                                      7*******************999999999998776665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0027
                     NAD_binding_9 121 raevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       ++ev++++++++  ++ l++g++l++d++v+A+G 
  gi|330506819|ref|YP_004383247.1|  81 KTEVERINTDDK--TLKLKTGETLKYDYLVIATGR 113
                                       567777776655..5889****************6 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.07
                     NAD_binding_9 112 pegvtvevhraevvdleeradgqavll...adgaslaadaVvLAlGh 155
                                       ++g+++ + ++ +  l+e++++++ +l   ++++++ a+ Vv+A+G+
  gi|330506819|ref|YP_004383247.1| 204 KQGIEFILENQPISGLKEDGGRVRSVLigpRGEKEIPAEMVVVAMGM 250
                                       456777777899999999999975444464566789*********96 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 ?   -0.8   0.2      0.37   7.4e+02       1      21 [.       6      26 ..       6      35 .. 0.86
   2 !   22.0   0.0   4.2e-08   8.4e-05      92     302 ..      72     289 ..      64     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.37
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagl 21
                                      +IiG+G  G+ +   l+++ +
  gi|330506819|ref|YP_004383247.1|  6 VIIGGGISGIFVMKDLQEKSI 26
                                      7*********99888888776 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 4.2e-08
                       Pyr_redox_3  92 ksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek.........lvkhyskvkef 159
                                       +++ ++ ++++eVe+++ +d++ +++t  et++ ++++iAtG+  kP ++++  ++              ys   +f
  gi|330506819|ref|YP_004383247.1|  72 SEQGVDFRTKTEVERINTDDKTLKLKT-GETLKYDYLVIATGR--KPALPEMIEKSTmkniftlstMEDAYSIEAAF 145
                                       56788999*****************98.579999********9..66666543333211111111123344444577 PP

                       Pyr_redox_3 160 hkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekik.vlfnaev 235
                                       +  + ++ +V G +  a  aA   +++  + tv+    ++          l pd+ + l+e ++++ i+ +l+n+ +
  gi|330506819|ref|YP_004383247.1| 146 KSGEVKNALVRGRGIIALQAAAAAAANRIKTTVLAGPPSLLP------GGLDPDMGDMLKEWMQKQGIEfILENQPI 216
                                       77778999************************9999886655......47*************99778825678899 PP

                       Pyr_redox_3 236 keikekeeey..kvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpv....lteeteetnvpglf 302
                                         +ke+  ++   +  ++g+k    + vv+a+G +p++++ +++++e+ ++g +     l+ +t+ + ++++f
  gi|330506819|ref|YP_004383247.1| 217 SGLKEDGGRVrsVLIGPRGEKEIPAEMVVVAMGMRPNVRLAEEAGIEIGDTGGIItdnsLHAKTKKSYLKEVF 289
                                       99**999888333458999998889999******************998887544011134455555555555 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.01        20     193     223 ..       4      36 ..       1      42 [. 0.79
   2 !   10.9   0.0   9.3e-05      0.19     117     182 ..      82     136 ..      71     169 .. 0.77
   3 ?   -3.6   0.0       2.3   4.6e+03     145     162 ..     237     254 ..     232     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.01
                       K_oxygenase 193 riaVvGsGqSaaeifedllrr..qkkvelklvt 223
                                       + +++G+G S+  +++dl ++  ++k ++k+v+
  gi|330506819|ref|YP_004383247.1|   4 TAVIIGGGISGIFVMKDLQEKsiATKEDIKIVL 36 
                                       6689***************99655567777764 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.3e-05
                       K_oxygenase 117 eeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseyl 182
                                       +eve+++ d++     l++++       e+l+   lv+++G +p++Pe++ek +  ++++  s++ 
  gi|330506819|ref|YP_004383247.1|  82 TEVERINTDDK----TLKLKT------GETLKYDYLVIATGRKPALPEMIEKST-MKNIFTLSTME 136
                                       45555555553....356654......67888899****************998.58888776654 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.3
                       K_oxygenase 145 eelearnlvlgvGtepki 162
                                       +e+ a+ +v+++G +p++
  gi|330506819|ref|YP_004383247.1| 237 KEIPAEMVVVAMGMRPNV 254
                                       677889999999999875 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   9.8e-06      0.02     220     261 ..      73     112 ..      65     125 .. 0.85
   2 ?   -1.1   0.0      0.43   8.5e+02     220     262 ..     205     250 ..     180     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.8e-06
                                       TTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S- CS
                     Amino_oxidase 220 lrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvp 261
                                       + g+d+r+ t+V +i++  d  t++l++ge++++D+ v+++ 
  gi|330506819|ref|YP_004383247.1|  73 EQGVDFRTKTEVERINT--DDKTLKLKTGETLKYDYLVIATG 112
                                       58***************..55566778*********999875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.43
                                       TTTEEEETSEEEEEEEEETTCEEEEETTSTEE...EESEEEE-S-H CS
                     Amino_oxidase 220 lrgldirlntrVkeikregdgvtvtledgevv...eaDaVvvTvpl 262
                                       ++   i+ n++ + +k +g+ v+  l   +     +a  Vvv++ +
  gi|330506819|ref|YP_004383247.1| 205 QGIEFILENQPISGLKEDGGRVRSVLIGPRGEkeiPAEMVVVAMGM 250
                                       555678899999999999999888888555555579*****99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3335.36
//
Query:       gi|330506820|ref|YP_004383248.1|  [L=364]
Description: transposase, Mutator family [Methanosaeta concilii GP6]
Scores for complete 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-101  338.2   0.2   6.2e-101  338.0   0.2    1.0  1  Transposase_mut  Transposase, Mutator family
    9.7e-10   38.7   0.0    1.6e-09   38.0   0.0    1.4  1  MULE             MULE transposase domain
  ------ inclusion threshold ------
      0.071   13.6   0.0       0.48   10.9   0.0    2.3  2  HTH_26           Cro/C1-type HTH DNA-binding domain
      0.084   12.8   0.9       0.31   11.0   0.1    2.4  3  HTH_12           Ribonuclease R winged-helix 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 !  338.0   0.2  1.4e-104  6.2e-101      22     380 ..       4     355 ..       1     356 [. 0.96

  Alignments for each domain:
  == domain 1  score: 338.0 bits;  conditional E-value: 1.4e-104
                   Transposase_mut  22 kddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspallerykR 98 
                                        +  lk++++ +l++++  e+  + ga  yers++r+ +RnG r+r+l+Tr+g+l+l+ P+ R+  F+  ++ery R
  gi|330506820|ref|YP_004383248.1|   4 PNSGLKQVITEFLNAVMLFEAYLQSGALPYERSPQRKAHRNGTRSRTLKTRVGELTLNKPQFREFPFESSVFERYCR 80 
                                       56789************************************************************************ PP

                   Transposase_mut  99 rekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkvR 175
                                        e+al  +++e y++Gvstrk+e+lve+++  + +S+sevS+++k lde+ve+f +R++e k   +l++Da+y kvR
  gi|330506820|ref|YP_004383248.1|  81 VEQALLMTIAESYIQGVSTRKMEELVENFGL-NRLSASEVSRLCKILDEKVEEFLKRPIEVK-IRYLLVDATYFKVR 155
                                       *******************************.77**************************99.************** PP

                   Transposase_mut 176 eegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaav 252
                                          + +++a l+ +gv  dG reiLg ++a+sE+   W ++++sLk+rGl+gvelv+sDahkG++ka++ +f +a++
  gi|330506820|ref|YP_004383248.1| 156 CGAQYKNRALLVVVGVREDGLREILGASIAESEDSGYWMTLFRSLKDRGLEGVELVISDAHKGIQKAVELSFVGASW 232
                                       ***************************************************************************** PP

                   Transposase_mut 253 QrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgk.kypkvaelldeaaedvlaflafpe 328
                                       Q Cr H +r +l+ +p k+++++a++lk    a+d e   ++l   +++l +  y  +ae++d+ + d+ ++ a+p+
  gi|330506820|ref|YP_004383248.1| 233 QYCRFHHSRAVLESIPNKDKQEIADKLKE---ASDDEIKMQEL---AKELRDrGYDPAAETIDRFRFDLWNYKAYPK 303
                                       ***************************95...66666555544...44444548*********************** PP

                   Transposase_mut 329 qirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                       +++++i++tN++Er+Nke++Rr+r vg FP ++s++rl g ++ + ++ew +
  gi|330506820|ref|YP_004383248.1| 304 AHWKRIRTTNIIERINKELKRRSRPVGAFPSDQSLMRLAGCIMININEEWVT 355
                                       **************************************************75 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   3.6e-13   1.6e-09       2      94 ..     145     240 ..     144     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 3.6e-13
                              MULE   2 vvlDgTyktnkyklp.....lltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekal 73 
                                       +++D+Ty + ++  +     ll vvgv + g   +l+  + ese++  +  l+++l+++    +  + +i+D +k++
  gi|330506820|ref|YP_004383248.1| 145 LLVDATYFKVRCGAQyknraLLVVVGVREDGLREILGASIAESEDSGYWMTLFRSLKDRGL--EGVELVISDAHKGI 219
                                       689999998887543333339999**********************************644..69************ PP

                              MULE  74 lnaleevfpeakhrlClfHia 94 
                                       ++a+e  f +a  + C fH  
  gi|330506820|ref|YP_004383248.1| 220 QKAVELSFVGASWQYCRFHHS 240
                                       *******************75 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 ?   10.9   0.0   0.00011      0.48      21      59 ..      96     135 ..      92     137 .. 0.89
   2 ?   -1.4   0.0      0.71   3.2e+03       8      19 ..     264     275 ..     260     292 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                            HTH_26  21 gisaatlsrlvkgk.pervsldtLdkiCdaLgctpgDLle 59 
                                       g+s  +++ lv +   +r+s+++ +++C++L+ ++++ l+
  gi|330506820|ref|YP_004383248.1|  96 GVSTRKMEELVENFgLNRLSASEVSRLCKILDEKVEEFLK 135
                                       77889999999996579****************9999875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.71
                            HTH_26   8 drgitkseLarg 19 
                                       d +i+ +eLa+ 
  gi|330506820|ref|YP_004383248.1| 264 DDEIKMQELAKE 275
                                       778999999863 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 ?   -2.1   0.0      0.84   3.8e+03      12      45 ..      95     129 ..      85     137 .. 0.60
   2 ?   11.0   0.1   6.8e-05      0.31      10      35 ..     263     288 ..     251     295 .. 0.80
   3 ?   -3.4   0.0       2.2   9.9e+03       5      15 ..     320     330 ..     316     331 .. 0.46

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.84
                            HTH_12  12 kpigakeiaeeLkkrg.ydigeravRyrLrkleer 45 
                                       + ++ ++++e +++ g   +++  v +  ++l+e+
  gi|330506820|ref|YP_004383248.1|  95 QGVSTRKMEELVENFGlNRLSASEVSRLCKILDEK 129
                                       55667777777766641446666666666777775 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6.8e-05
                            HTH_12  10 sdkpigakeiaeeLkkrgydigerav 35 
                                       sd+ i  +e+a+eL++rgyd  ++++
  gi|330506820|ref|YP_004383248.1| 263 SDDEIKMQELAKELRDRGYDPAAETI 288
                                       5778999*************999988 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.2
                            HTH_12   5 kilaesdkpig 15 
                                       k l+++++p+g
  gi|330506820|ref|YP_004383248.1| 320 KELKRRSRPVG 330
                                       33445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2381.97
//
Query:       gi|330506821|ref|YP_004383249.1|  [L=404]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete 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-141  469.5   0.0   4.6e-141  469.2   0.0    1.0  1  DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
    2.8e-06   27.5   0.0    8.9e-06   25.9   0.0    1.9  1  HTH_Tnp_Tc3_2    Transposase
    0.00039   20.5   0.0    0.00091   19.3   0.0    1.6  1  HTH_21           HTH-like domain
     0.0024   18.0   0.0     0.0038   17.3   0.0    1.3  1  GSH-S_N          Prokaryotic glutathione synthetase, N-termin
     0.0042   17.7   0.1      0.011   16.3   0.1    1.8  1  HTH_32           Homeodomain-like domain
  ------ inclusion threshold ------
      0.012   14.3   0.0       0.02   13.6   0.0    1.3  1  UPF0236          Uncharacterised protein family (UPF0236)
       0.02   14.5   0.3      0.073   12.7   0.1    2.0  3  HTH_33           Winged helix-turn helix
      0.031   14.2   0.4       0.11   12.4   0.1    2.1  2  HTH_12           Ribonuclease R winged-helix domain
      0.058   13.4   0.1       0.62   10.1   0.0    2.4  2  HTH_29           Winged helix-turn helix


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.2   0.0  2.3e-144  4.6e-141       1     308 []      91     398 ..      91     398 .. 1.00

  Alignments for each domain:
  == domain 1  score: 469.2 bits;  conditional E-value: 2.3e-144
                   DDE_Tnp_ISAZ013   1 dleelvepetrgdpesplrwttkslrklaeeLkeqghkvsaetvaelLkelgyslqsnrKtkegkkhpdrdaqFeki 77 
                                       dle+++e++t+gdp+s l+wt ks++++aeeL+++ghkvs++tv++lLke+gyslq+nrK+ egk+ p+rd+qF+++
  gi|330506821|ref|YP_004383249.1|  91 DLEKIMEESTAGDPMSLLKWTYKSTYAIAEELQSRGHKVSHDTVRRLLKESGYSLQANRKNLEGKSGPERDTQFRYV 167
                                       79*************************************************************************** PP

                   DDE_Tnp_ISAZ013  78 nekvkeaqeagqpvisvdtkkkeliGefkrsGkewrpkgepaevkdhdfvskeegkaipyGiydlaenegwvsvgtd 154
                                       +++++++ +ag+pvisvd+kkkel+G++k+sG++wr+kg+p+ v+++df+sk+ g+aipyG+yd+++neg+v++g++
  gi|330506821|ref|YP_004383249.1| 168 SSQAAKFIDAGDPVISVDAKKKELVGNYKNSGRTWRQKGQPELVNVYDFPSKAIGAAIPYGVYDPKRNEGVVNIGKS 244
                                       ***************************************************************************** PP

                   DDE_Tnp_ISAZ013 155 kdtaefavesirrwWqevgkarypkakrllitaDaggsnssrsrlwkkelqkladelgleiqvahfPpgtskwnkiE 231
                                       ++taefavesir+wW+ vgk+ry+ +k+lli+aD+ggsn+sr+r wk  lq+lade+g++i+v+hfPpgtskwnkiE
  gi|330506821|ref|YP_004383249.1| 245 HNTAEFAVESIRQWWNLVGKYRYAGCKNLLICADGGGSNGSRNRGWKFFLQQLADEIGITITVSHFPPGTSKWNKIE 321
                                       ***************************************************************************** PP

                   DDE_Tnp_ISAZ013 232 hRlfshitqnwrgrpltsvevvvnliaatttkkglkveaeldeksyetGikvskeemealeierdelhgewnytiap 308
                                       h++fs+i++nwrg+pl+s+e++++li++t+tkkgl++ea+ld+++yetGik+ +e+m++l+i+ +el++ wny+i+p
  gi|330506821|ref|YP_004383249.1| 322 HCMFSFISMNWRGKPLSSYETIIKLIGSTKTKKGLRIEARLDDRDYETGIKILDEDMARLKISVHELYPMWNYSIEP 398
                                       ***************************************************************************98 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.5e-09   8.9e-06      14      51 ..     113     150 ..      96     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.5e-09
                     HTH_Tnp_Tc3_2  14 itlreLanelkeeGksvsreTirrrLrkaglkkrkprk 51 
                                       ++  ++a+el+++G++vs+ T+rr L+++g++ +  rk
  gi|330506821|ref|YP_004383249.1| 113 KSTYAIAEELQSRGHKVSHDTVRRLLKESGYSLQANRK 150
                                       57779*****999******************9888777 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.5e-07   0.00091      26      59 ..     118     150 ..     116     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.5e-07
                            HTH_21  26 iwaeLrreggvrvnhkrVrRlMrelGLrgvqrrk 59 
                                       i+ eL+ +g+ +v+h +VrRl +e G+  + +rk
  gi|330506821|ref|YP_004383249.1| 118 IAEELQSRGH-KVSHDTVRRLLKESGYSLQANRK 150
                                       6789****99.5**************99888887 PP

>> GSH-S_N  Prokaryotic glutathione synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.9e-06    0.0038       8      60 ..     103     156 ..      96     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.9e-06
                           GSH-S_N   8 dplesikikkDttfalmleaqarghevfvleaadLslreg.katararkvevke 60 
                                       dp++ +k +  +t+a+++e q+rgh+v + ++++L  ++g +++a+ +++e k+
  gi|330506821|ref|YP_004383249.1| 103 DPMSLLKWTYKSTYAIAEELQSRGHKVSHDTVRRLLKESGySLQANRKNLEGKS 156
                                       9999***999*************************9987723455555555533 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   5.5e-06     0.011      20      73 .]      73     138 ..      51     138 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.5e-06
                            HTH_32  20 rprrgrpr..klsdevrariiallreep.........rWsprq...laarlaeregvkvShstvyriL 73 
                                       +p +gr+r     + +   + ++  ee+         +W+++    +a++l + +g kvSh tv+r+L
  gi|330506821|ref|YP_004383249.1|  73 KPGGGRKRvaDREPNLLNDLEKIM-EEStagdpmsllKWTYKStyaIAEEL-QSRGHKVSHDTVRRLL 138
                                       344557764435555666666666.433467779999997777777*****.888899********98 PP

>> UPF0236  Uncharacterised protein family (UPF0236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.9e-06      0.02     139     230 ..     119     216 ..     110     222 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.9e-06
                           UPF0236 139 aeklerivcqekvskeairqlvleigvalaaaekevkveikekrkvRvLyieaDg.lfvsrq......dgkkeeerl 208
                                       ae+l+++    kvs++++r+l  e g +l+a +k+ + + + +r+  + y+      f+         d kk+e   
  gi|330506821|ref|YP_004383249.1| 119 AEELQSR--GHKVSHDTVRRLLKESGYSLQANRKNLEGKSGPERDTQFRYVSSQAaKFIDAGdpvisvDAKKKELVG 193
                                       4555333..479***********************************999976531344433233322334444444 PP

                           UPF0236 209 lviheGrk.ekgsrleLvnrrdy 230
                                        +   Gr+ ++ ++ eLvn+ d+
  gi|330506821|ref|YP_004383249.1| 194 NYKNSGRTwRQKGQPELVNVYDF 216
                                       45666755356677778887665 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.4   2.9e+03      23      40 ..      97     114 ..      94     122 .. 0.83
   2 ?   12.7   0.1   3.7e-05     0.073      10      39 ..     118     146 ..     111     159 .. 0.85
   3 ?   -3.7   0.0       4.8   9.5e+03      13      26 ..     296     309 ..     295     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
                            HTH_33  23 svsgvyrlLkrlGfsyqk 40 
                                       ++s+ ++ +  l+++y++
  gi|330506821|ref|YP_004383249.1|  97 EESTAGDPMSLLKWTYKS 114
                                       6788888999999**997 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.7e-05
                            HTH_33  10 laqlieerfgvsysvsgvyrlLkrlGfsyq 39 
                                       +a+ ++ r g ++s+ +v+rlLk+ G+s q
  gi|330506821|ref|YP_004383249.1| 118 IAEELQSR-GHKVSHDTVRRLLKESGYSLQ 146
                                       66666666.999****************99 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.8
                            HTH_33  13 lieerfgvsysvsg 26 
                                        ++++ g++++vs+
  gi|330506821|ref|YP_004383249.1| 296 QLADEIGITITVSH 309
                                       5789999*999985 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.7e-05      0.11      17      40 ..     116     139 ..     107     149 .. 0.92
   2 ?   -2.9   0.0       3.5     7e+03      18      31 ..     357     370 ..     346     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.7e-05
                            HTH_12  17 keiaeeLkkrgydigeravRyrLr 40 
                                        +iaeeL+ rg +++  +vR+ L+
  gi|330506821|ref|YP_004383249.1| 116 YAIAEELQSRGHKVSHDTVRRLLK 139
                                       68*******************998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.5
                            HTH_12  18 eiaeeLkkrgydig 31 
                                       +i+  L +r+y+ g
  gi|330506821|ref|YP_004383249.1| 357 RIEARLDDRDYETG 370
                                       68888999998765 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00031      0.62       4      58 ..      27      82 ..      24      86 .. 0.78
   2 ?    0.2   0.0      0.39   7.8e+02      24      34 ..     129     139 ..     125     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00031
                            HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegG.laalld.rrrsgrprnrls 58
                                      a  +l+ G++ vs + +++g sr+t+++ +   e  + l+   + r+ +g +r+r+ 
  gi|330506821|ref|YP_004383249.1| 27 AAKALELGWGGVSKVSAITGFSRTTINKGIQELESNEdLKPPERlRK-PGGGRKRVA 82
                                      6678899999*****************98888776666888888554.676777654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.39
                            HTH_29  24 lsrrtvyrwlk 34 
                                       +s +tv+r lk
  gi|330506821|ref|YP_004383249.1| 129 VSHDTVRRLLK 139
                                       899*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2712.13
//
Query:       gi|330506822|ref|YP_004383250.1|  [L=521]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.7e-15   55.1   0.0      8e-14   51.8   0.0    2.1  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 !   51.8   0.0   4.5e-18     8e-14       5     214 .]     159     450 ..     155     450 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 4.5e-18
                         DDE_Tnp_1   5 evlivDattvrvpgtk.edarwgyk.ggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kg 77 
                                       e li+D t++   +    +  wgy+  g   + ++l ++ +++ +l+l ++++pg+ +d+ +lk l+ e+++    +
  gi|330506822|ref|YP_004383250.1| 159 ETLIFDITSLSSASRNiDWLEWGYNrDGLDLPQVNLGLVLSLHRHLPLYFKLFPGSISDVVTLKNLVAEVKALgiSK 235
                                       667777777776665578999****8888******************************************99**** PP

                         DDE_Tnp_1  78 klvlaDaGYasaelldtleekgvdyiirlkkntklyrk....gaeskrrgrlrkhdrnkiltksqkrrnk....... 143
                                       +l++ D+G+ s+++++++ + ++d+ii+l+  +++ +        +       k++ ++i++  +++          
  gi|330506822|ref|YP_004383250.1| 236 SLFILDRGFYSENNIKEMNDANIDFIIPLPFSVNVGKGliseTNREIESPANAKRFGGDIFYVLESEIQIgsvdayg 312
                                       *****************************777777766777745555677788999999999999988889999999 PP

                         DDE_Tnp_1 144 ......................................................................skkekgd 150
                                                                                                             ++++ g 
  gi|330506822|ref|YP_004383250.1| 313 yvlfnkkregletnsfynrlidiecaidgkefrnpidqfkrtagnferyfeytlegkkihlsrrvnaisqAVNRFGK 389
                                       999999999999999****************************************************8885555555 PP

                         DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                       ++++++  +++    ev  lyr R ++E  F +lk+ +    lr+ + +  +  l++ +++l l
  gi|330506822|ref|YP_004383250.1| 390 TILLSSSRRNW---DEVLSLYRERDEVEKKFDDLKNELEVMPLRVQKVETLQGLLFIFFISLIL 450
                                       55555555544...56779*************************************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 3620.97
//
Query:       gi|330506823|ref|YP_004383251.1|  [L=436]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete 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   27.8   0.6    2.7e-05   23.8   0.6    2.1  1  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
       0.14   12.7   4.6       0.18   12.3   2.2    2.4  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.15   12.2   0.7        7.5    6.8   0.1    2.4  2  Zn-ribbon_8      Zinc ribbon domain
       0.21   11.2   0.6         12    5.6   0.1    2.4  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.27   11.3   2.8        1.3    9.1   3.1    1.9  2  DZR              Double zinc ribbon
       0.66   10.0   2.5        7.3    6.7   0.3    2.6  2  YhfH             YhfH-like protein
        6.2    6.4   5.5         77    2.9   5.5    2.4  1  TF_Zn_Ribbon     TFIIB zinc-binding


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 !   23.8   0.6     1e-08   2.7e-05     111     259 ..     188     381 ..     146     393 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1e-08
                      DDE_Tnp_IS66 111 sRggevaealLag.....fkGvlvsDgyagYnklae....eqvthalCwaHlrRkfvdaeeakkksqaaaealar.. 176
                                       s  ++++e +L        + ++v+D y gY+++ +    ++v h++C+ Hl   +v+   +k   ++ +e l++  
  gi|330506823|ref|YP_004383251.1| 188 SKDADTIEGFLRRnldtqKQIFIVTDLYRGYSNVFKrvfgNKVIHQFCLLHLNKLIVNDFPRKT--SIEQELLKYkm 262
                                       55566666666655554445699**********9999***************999887776643..44444444442 PP

                      DDE_Tnp_IS66 177 igklya.............ierearea...........eae.........erlalrqeesrpllaelea.wleeql. 218
                                       ++ +++              e+ +r +           e           + + +r++es+ l+++ ++  l++ + 
  gi|330506823|ref|YP_004383251.1| 263 LNIFFNreleieflstlieEEKMMR-QrsnkeykswiaE-AkhlfydfvrRLELRRRRESKNLEQRTYHeALNNFKf 337
                                       4444445555555555543233332.1233344334331.0333333442555666777788877655504444448 PP

                      DDE_Tnp_IS66 219 ...kkvlpksklgkairyllkrweallrfledgrvpidNNaaER 259
                                          ++ +    ++k ++++ + w++l+ f    + p +NN +E+
  gi|330506823|ref|YP_004383251.1| 338 lkmQSDSFMISVRKRLDKIEELWPNLTAFYFTDNAPATNNPIEN 381
                                       777666677789*******************************9 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2     7e-05      0.18       8      51 ..      44     118 ..      43     123 .. 0.62
   2 ?   -1.0   0.0      0.99   2.5e+03      14      29 ..     284     299 ..     282     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7e-05
                   Zn_ribbon_recom   8 CgeCGspmtr......rkrkgkr.......hyYrCstyrrkgk..................k.Csnh...sireekl 49 
                                       C eCG+pm++      +    kr         Y C+++ ++ +                  + C+     ++++e++
  gi|330506823|ref|YP_004383251.1|  44 CPECGHPMSHngfntcQ----KRhlgganvGKYLCGACGKSTEedrdfwiklktdffgivtEiCTRLrlnHVSYEVI 116
                                       **********5543322....22355558889999988766655556666666666665531466544556666666 PP

                   Zn_ribbon_recom  50 ee 51 
                                       e+
  gi|330506823|ref|YP_004383251.1| 117 ES 118
                                       65 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.99
                   Zn_ribbon_recom  14 pmtrrkrkgkrhyYrC 29 
                                       +m r+++++++  ++ 
  gi|330506823|ref|YP_004383251.1| 284 KMMRQRSNKEYKSWIA 299
                                       7999999999988875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0029       7.5      26      35 ..      40      50 ..      25      53 .. 0.60
   2 ?    3.3   0.1     0.035        90       6      17 ..      72      83 ..      71      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                       Zn-ribbon_8 26 lta.CPeCgse 35
                                       ++ CPeCg++
  gi|330506823|ref|YP_004383251.1| 40 VPPlCPECGHP 50
                                      3444****986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.035
                       Zn-ribbon_8  6 YrCeeCghefev 17
                                      Y C +Cg+  e+
  gi|330506823|ref|YP_004383251.1| 72 YLCGACGKSTEE 83
                                      89*****99885 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0046        12       4      14 ..      43      53 ..      43      57 .. 0.86
   2 ?    3.5   0.1     0.021        54       2      15 ..      71      84 ..      70      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0046
                            zf_UBZ  4 lCerCgkeipe 14
                                      lC++Cg+++++
  gi|330506823|ref|YP_004383251.1| 43 LCPECGHPMSH 53
                                      6*******987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.021
                            zf_UBZ  2 tylCerCgkeipes 15
                                       ylC  Cgk+ +e+
  gi|330506823|ref|YP_004383251.1| 71 KYLCGACGKSTEED 84
                                      69*******97765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.9     0.002         5      30      46 ..      43      60 ..      26      63 .. 0.76
   2 ?    9.1   3.1   0.00049       1.3      15      43 ..      44      86 ..      41     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.002
                               DZR 30 rCpsCgek.vdpearfCp 46
                                       Cp+Cg++  ++++++C+
  gi|330506823|ref|YP_004383251.1| 43 LCPECGHPmSHNGFNTCQ 60
                                      688888886666777775 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00049
                               DZR 15 CseCgtklkavaa................edrCpsCgekvdpear 43
                                      C+eCg++++   +                ++ C +Cg++++++  
  gi|330506823|ref|YP_004383251.1| 44 CPECGHPMSH--NgfntcqkrhlgganvgKYLCGACGKSTEEDRD 86
                                      5556655552..123555555555556669999999998877665 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0028       7.3       7      24 ..      35      52 ..      31      61 .. 0.85
   2 ?    2.6   0.1     0.055   1.4e+02      15      26 ..      73      84 ..      67      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0028
                              YhfH  7 FfrnLPkKkCteCGkeie 24
                                      +fr++ +  C+eCG  + 
  gi|330506823|ref|YP_004383251.1| 35 IFRKIVPPLCPECGHPMS 52
                                      799999999*****9986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.055
                              YhfH 15 kCteCGkeieEq 26
                                       C  CGk  eE 
  gi|330506823|ref|YP_004383251.1| 73 LCGACGKSTEED 84
                                      6******99995 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   5.5      0.03        77       3      32 ..      44      84 ..      43      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.03
                                      ETTTTCEEC...........HEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon  3 CPnCgstnl...........veDpergelvCtdCGlVledn 32
                                      CP+Cg+++            +  ++ g ++C++CG   e++
  gi|330506823|ref|YP_004383251.1| 44 CPECGHPMShngfntcqkrhLGGANVGKYLCGACGKSTEED 84
                                      99999987458888888777777999999999999877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3211.49
//
Query:       gi|330506824|ref|YP_004383252.1|  [L=411]
Description: transposase, IS4 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-15   55.8   0.0    6.9e-15   55.1   0.0    1.3  1  DDE_5      DDE superfamily endonuclease
    1.5e-12   47.4   6.5    4.9e-11   42.4   6.4    2.3  1  DDE_Tnp_2  Archaeal putative transposase ISC1217
    9.9e-08   31.9   0.9    1.4e-07   31.4   0.9    1.2  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.034   14.1   0.1      0.084   12.8   0.1    1.6  1  SeqA       SeqA protein C-terminal domain
       0.12   11.4   0.3        0.2   10.7   0.3    1.3  1  Colicin_M  Colicin M


Domain annotation for each model (and alignments):
>> DDE_5  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   1.9e-18   6.9e-15       2     214 ..      18     222 ..      17     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1.9e-18
                             DDE_5   2 llealtradrrrglllylrgllldggrksvepmaarl...ehdg.shqalqrflsrspwddaklrrrlarlvl.pll 73 
                                       +++ +t+ + r+ ++ ++ +l  + + k+v ++  ++   + +  s+ ++  f+s+++wd+ ++ +r  +l +  l+
  gi|330506824|ref|YP_004383252.1|  18 FRDLFTKPSYRS-FRDLCGALSVCDKSKTVSNLCDTMadcSKGKkSRSSYNWFFSDANWDENEVAQRKVDLFIdSLC 93 
                                       889999999999.*****999999999***********995555599******************999999997777 PP

                             DDE_5  74 apeaav..laiDdTgfpkdGkasvgvarqycgalgkadncqvavslglatervsapldwrlylpeswaqdlsarrrr 148
                                        +e+    l+iDdT   k G ++ gv+++y++++   + ++ +v+  + ++  ++p +   y++             
  gi|330506824|ref|YP_004383252.1|  94 LKENDKllLIIDDTYNEKEGNQTDGVGKFYDHSKEAYIWGNNFVTSVVQSKGLFIPHKAKMYIK------------- 157
                                       77666679************************************99999999999999999999............. PP

                             DDE_5 149 agvpddvtaktkpeial.elldraraagvplqvvvaDagYgdaaalrqglrelglhyvvrvrsdral 214
                                        ++++   +ktk eia  e+++ ++  +  + ++v+D++  +++ +      lg ++v +++sd+++
  gi|330506824|ref|YP_004383252.1| 158 -NDDENENFKTKMEIAFeEIIKPLVVPKSIDLYIVFDSWWFSSDLF-SKCLKLGHNIVCQIKSDKKV 222
                                       .3456669********96677888888888889*******9*****.888889***********987 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   6.4   1.4e-14   4.9e-11     147     306 ..     147     340 ..      92     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.4e-14
                         DDE_Tnp_2 147 yiprkvaeilkerGeksefktkiellle.ileilkeefnva.avvfdsWyvnskl....lk..gnvvgelksnarv. 214
                                       +ip+k +  +k+  e+ +fktk+e++ e i++ l     +   +vfdsW+++s l    lk   n+v ++ks+++v 
  gi|330506824|ref|YP_004383252.1| 147 FIPHKAKMYIKNDDENENFKTKMEIAFEeIIKPLVVPKSIDlYIVFDSWWFSSDLfskcLKlgHNIVCQIKSDKKVg 223
                                       799999999***************98752777776655554279******997552222433369**********95 PP

                         DDE_Tnp_2 215 ve...................gerhvpvaelPeGeylveyl...dtvikllvldd..ykkdgrrylfstdlndtded 267
                                       ++                    +  v v    +  y  e     d+v ++++++    k+   +y+ st+  ++  +
  gi|330506824|ref|YP_004383252.1| 224 INkdmyfqvrdlanqiedkffIKTTVSVRGKKKTYYAFEKKviiDKVGEVKLVISkrKKDSTTKYIISTNGSLSLKE 300
                                       559****************999999999999999999886555688877776665115667789************* PP

                         DDE_Tnp_2 268 iittWenrWdievlirel.kalGledssflkrvrnkGfll 306
                                       i + +e rWdie  +re  + lG++d  +  +   + f+ 
  gi|330506824|ref|YP_004383252.1| 301 ILSIYEDRWDIETAHREAnQKLGFKDYQLRDKHSIERFIQ 340
                                       ****************983469998877766666666665 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.9     4e-11   1.4e-07      78     212 ..     188     346 ..     154     348 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4e-11
                         DDE_Tnp_1  78 klvlaDaGYasaelldtleekgvdyiirlkkntklyrk.....gaeskrrgrlrkhdrnkiltksqkrrnk...... 143
                                        +++ D++ +s +l+ ++ + g + + ++k+++k+ +         ++ ++++ k + + +++ + k++++      
  gi|330506824|ref|YP_004383252.1| 188 LYIVFDSWWFSSDLFSKCLKLGHNIVCQIKSDKKVGINkdmyfQVRDLANQIEDKFFIKTTVSVRGKKKTYyafekk 264
                                       5899*******************************99999**9888899**************************** PP

                         DDE_Tnp_1 144 ..............skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqll 206
                                                     + k + ++ y+ +tn  +ls +e+  +y  Rw iE+ +++  +k+g+   ++r++  +e+++ 
  gi|330506824|ref|YP_004383252.1| 265 viidkvgevklvisKRKKDSTTKYIISTNG-SLSLKEILSIYEDRWDIETAHREANQKLGFKDYQLRDKHSIERFIQ 340
                                       ************755555555555555555.899******************************************* PP

                         DDE_Tnp_1 207 llllal 212
                                       +++ ++
  gi|330506824|ref|YP_004383252.1| 341 MVFSVW 346
                                       998765 PP

>> SeqA  SeqA protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.4e-05     0.084      30      88 ..     237     300 ..     217     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                              SeqA  30 yradpeaFakatekvkGrtRvYfakdeetllasgks.....tkpkqipetpfWVitNnntarKr 88 
                                        +++++ F k+t +v+G++++Y+a +++ ++++  +     +k k+ ++t + + tN + + K+
  gi|330506824|ref|YP_004383252.1| 237 NQIEDKFFIKTTVSVRGKKKTYYAFEKKVIIDKVGEvklviSKRKKDSTTKYIISTNGSLSLKE 300
                                       466778899999*****************99887776888889999999999999998766665 PP

>> Colicin_M  Colicin M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   5.6e-05       0.2     155     233 ..     230     316 ..     209     322 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.6e-05
                         Colicin_M 155 ekindlkdiiksavvGettvst...ktsyatGddsvitriylGtitlki.......eGkltisasGsvsysGvvkay 221
                                        ++ dl + i+     +ttvs+   k +y++ +++vi    +G++ l i       + k  is++Gs+s + ++  y
  gi|330506824|ref|YP_004383252.1| 230 FQVRDLANQIEDKFFIKTTVSVrgkKKTYYAFEKKVIIDK-VGEVKLVIskrkkdsTTKYIISTNGSLSLKEILSIY 305
                                       4677777778777777888876333678999898888653.566666442222222678899*************** PP

                         Colicin_M 222 ddkydanasshr 233
                                       +d++d+++ +hr
  gi|330506824|ref|YP_004383252.1| 306 EDRWDIET-AHR 316
                                       *****986.466 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3175.86
//
Query:       gi|330506825|ref|YP_004383253.1|  [L=150]
Description: transposase IS200-like protein [Methanosaeta concilii GP6]
Scores for complete 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-29  100.0   0.0    1.1e-28   99.7   0.0    1.1  1  Y1_Tnp    Transposase IS200 like


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.0   6.2e-33   1.1e-28       2     121 .]      12     132 ..      11     132 .. 0.93

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 6.2e-33
                            Y1_Tnp   2 snlkyhivlvtkyRrkvltge.veerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgassr 77 
                                       +++ yh+v+ +kyRrk+l++    + +k +++ei e++ +++ ++ ++ DHvH++v + p++s+sk+++ +k+ ++r
  gi|330506825|ref|YP_004383253.1|  12 YKIRYHMVFSIKYRRKLLQDIdRINYIKFVCSEIGERYYFDFDAIGTDGDHVHIFVGAAPRYSPSKVMQIVKSITAR 88 
                                       7899*****************55566666779********************************************* PP

                            Y1_Tnp  78 linkefpelkkkklkkeslWqrgYfvstvgea.sletvkrYIenq 121
                                        ++k++pe+kk+ l+++++W++g +v tvg+   ++t+++Y+e+q
  gi|330506825|ref|YP_004383253.1|  89 EFFKKYPEVKKQ-LWGGEFWSDGGYVGTVGDGvMADTIRNYVETQ 132
                                       ********9988.56688************877**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1124.17
//
Query:       gi|330506826|ref|YP_004383254.1|  [L=271]
Description: Nitrogenase iron protein 2 [Methanosaeta concilii GP6]
Scores for 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-127  425.2   1.6   1.1e-127  425.1   1.6    1.0  1  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
    1.5e-10   41.2   0.0    2.7e-10   40.4   0.0    1.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    2.4e-08   34.1   0.8    5.9e-08   32.8   0.4    1.8  2  AAA_31           AAA domain
      1e-07   31.7   1.0    5.4e-06   26.0   0.2    2.3  2  ParA             NUBPL iron-transfer P-loop NTPase
    1.4e-05   24.5   0.1    2.7e-05   23.5   0.1    1.5  1  ArsA_ATPase      Anion-transporting ATPase
    0.00029   20.4   0.4       0.67    9.4   0.1    2.1  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
     0.0013   18.1   0.0     0.0025   17.2   0.0    1.4  1  MipZ             ATPase MipZ
     0.0022   17.0   0.0     0.0033   16.4   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0084   16.5   0.1      0.021   15.2   0.0    1.7  2  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.018   14.8   0.1    1.3  1  AAA_24           AAA domain
      0.052   13.2   0.4       0.11   12.1   0.4    1.5  1  SRP54            SRP54-type protein, GTPase domain
      0.057   13.1   0.0      0.078   12.7   0.0    1.2  1  Ku               Ku70/Ku80 beta-barrel domain
      0.076   13.3   0.0       0.13   12.5   0.0    1.3  1  c-SKI_SMAD_bind  c-SKI Smad4 binding domain
       0.14   12.2   0.2       0.27   11.3   0.1    1.6  2  DUF87            Helicase HerA, central domain
       0.15   12.4   0.1       0.37   11.1   0.0    1.7  2  AAA_22           AAA domain
       0.19   12.1   0.1       0.71   10.2   0.0    1.8  2  AAA_16           AAA ATPase 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 !  425.1   1.6    1e-130  1.1e-127       1     270 [.       2     269 ..       2     270 .. 0.99

  Alignments for each domain:
  == domain 1  score: 425.1 bits;  conditional E-value: 1e-130
                         Fer4_NifH   1 rkiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkG 77 
                                       r+iaiyGkGGiGkstt+qnl+aal++mgkk++++GCDPkaDs ++l++gk q++vldtlr++g     +++dv+k+G
  gi|330506826|ref|YP_004383254.1|   2 RQIAIYGKGGIGKSTTTQNLTAALSTMGKKIMQIGCDPKADSVKMLMNGKRQPSVLDTLRKEGE---GELDDVLKTG 75 
                                       79************************************************************96...679******* PP

                         Fer4_NifH  78 yggvkcvesGGPepGvGCaGrgvitaielleelgayd.dlDfvlyDvLGDvvCGGfalPiredkaqevyivtsgelm 153
                                       +gg++cvesGGPepGvGCaGrg+it+i lle+lgay+ dlD+v+yDvLGDvvCGGfa+Pire+kaqe+yiv+sge+m
  gi|330506826|ref|YP_004383254.1|  76 FGGIRCVESGGPEPGVGCAGRGIITSIGLLENLGAYTpDLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMM 152
                                       *************************************89************************************** PP

                         Fer4_NifH 154 alyaanniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyape 230
                                       alyaanni+kgi+k+a+sgg rlgG+i+nsr+vd+erel+++fae++g++++++vPrd+iv+++e++k+tvi+yap+
  gi|330506826|ref|YP_004383254.1| 153 ALYAANNICKGIQKFAESGGTRLGGIICNSRNVDRERELVSAFAEKIGSQMIQFVPRDNIVHQSEIHKQTVIQYAPD 229
                                       ***************************************************************************** PP

                         Fer4_NifH 231 seqakeyrelarkilenkklviPkplsedeLeelleefel 270
                                       s+qak y +la+++ en+ +viPkp++ +eLe++++e+++
  gi|330506826|ref|YP_004383254.1| 230 SDQAKAYLALAKAVDENQMFVIPKPMEYEELEQVMMEWGV 269
                                       ***********************************99875 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 !   40.4   0.0   2.5e-13   2.7e-10       4     126 ..       6     221 ..       4     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 2.5e-13
                                       EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                              CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                       + +kGG GK+t++ nL +al+  g+++  + +Dp a + +  +   ++++p                          
  gi|330506826|ref|YP_004383254.1|   6 IYGKGGIGKSTTTQNLTAALSTMGKKIMQIGCDPKADSVK--MLMNGKRQPsvldtlrkegegelddvlktgfggir 80 
                                       679********************************87776..444455555789*********************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|330506826|ref|YP_004383254.1|  81 cvesggpepgvgcagrgiitsigllenlgaytpdldyvfydvlgdvvcggfampiregkaqeiyivasgemmalyaa 157
                                       ********************************************************************999988888 PP

                                       .CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 .dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparge 126
                                        ++ ++++ +++ g++     ++ g++ n  + ++e +l + + e++    g + ++++prd  v +++ +++
  gi|330506826|ref|YP_004383254.1| 158 nNICKGIQKFAESGGT-----RLGGIICNSRNVDRERELVSAFAEKI----GSQMIQFVPRDNIVHQSEIHKQ 221
                                       8666666666666666.....899******99998788777777776....***********99988776665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.4   5.2e-11   5.9e-08       2      62 ..       2      59 ..       1      75 [. 0.77
   2 ?   -2.6   0.0       3.9   4.4e+03     142     169 ..     142     169 ..     139     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 5.2e-11
                            AAA_31  2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyev 62
                                      + Iai+  KGG+GK+Tt+ nl aal+++gkk++ + +Dp a +   l   + +++ +++++
  gi|330506826|ref|YP_004383254.1|  2 RQIAIY-GKGGIGKSTTTQNLTAALSTMGKKIMQIGCDPKADSVKMLM--NGKRQPSVLDT 59
                                      566665.5*******************************998877554..33444555555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.9
                            AAA_31 142 sviipvqaeayaleGleqllktieevkk 169
                                       ++ i+   e +al+ +++++k i+++ +
  gi|330506826|ref|YP_004383254.1| 142 EIYIVASGEMMALYAANNICKGIQKFAE 169
                                       5667777788889999999888888765 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 !   26.0   0.2   4.8e-09   5.4e-06      10      56 ..       7      53 ..       2      64 .. 0.87
   2 ?    4.3   0.0      0.02        23     192     245 ..     190     243 ..     139     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 4.8e-09
                              ParA 10 SgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveee 56
                                       gKGG+GKSt++ nl++aL+++g+k+  +  D    s+  l++ +++
  gi|330506826|ref|YP_004383254.1|  7 YGKGGIGKSTTTQNLTAALSTMGKKIMQIGCDPKADSVKMLMNGKRQ 53
                                      59************************999999999999988887664 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.02
                              ParA 192 gggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                                       + ++++ae++g +++  +p d+ ++++  +++++++ +p+s++aka+ ++a++v
  gi|330506826|ref|YP_004383254.1| 190 ELVSAFAEKIGSQMIQFVPRDNIVHQSEIHKQTVIQYAPDSDQAKAYLALAKAV 243
                                       55678999************99999999999999999***********999876 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   2.4e-08   2.7e-05       1      40 [.       1      41 [.       1      55 [. 0.90

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.4e-08
                                      -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-ST.T CS
                       ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDP.A 40
                                      ++ i + GKGG+GK+t    + + ls +gkk++ i  DP A
  gi|330506826|ref|YP_004383254.1|  1 MRQIAIYGKGGIGKSTTTQNLTAALSTMGKKIMQIGCDPkA 41
                                      788999*********************************44 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1    0.0006      0.67       1      40 [.       1      39 [.       1      53 [. 0.88
   2 !    9.4   0.0   0.00061      0.69     186     231 ..     196     241 ..     180     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0006
                          CBP_BcsQ  1 mkvlalqGvRGGvGttsllaaLawalhelgesvlviDlsp 40
                                      m+++a+ G +GG+G+++ +  L+ al ++g++++ i   p
  gi|330506826|ref|YP_004383254.1|  1 MRQIAIYG-KGGIGKSTTTQNLTAALSTMGKKIMQIGCDP 39
                                      78889998.8***********************9987655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00061
                          CBP_BcsQ 186 lqslrrllPlvihrDealaEalaakqPlgeyrpdslaaeevktLan 231
                                        ++  + + + + rD+ +  + ++kq + +y+pds  a++   La+
  gi|330506826|ref|YP_004383254.1| 196 AEKIGSQMIQFVPRDNIVHQSEIHKQTVIQYAPDSDQAKAYLALAK 241
                                       5555566668899**************************9999986 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.2e-06    0.0025       9      51 ..       9      51 ..       4      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-06
                                      STTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHH CS
                              MipZ  9 kGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenr 51
                                      kGG Gkstt+  +  aL+++G+++  i  d +  +++  ++ +
  gi|330506826|ref|YP_004383254.1|  9 KGGIGKSTTTQNLTAALSTMGKKIMQIGCDPKADSVKMLMNGK 51
                                      9*****************************9999998887755 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     3e-06    0.0033      31      69 ..       3      41 ..       1      73 [. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-06
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                      ++ + G  G Gkst++++l++ l   Gk++  +  DP +
  gi|330506826|ref|YP_004383254.1|  3 QIAIYGKGGIGKSTTTQNLTAALSTMGKKIMQIGCDPKA 41
                                      578999*******************************86 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-05     0.021       1      27 [.       4      30 ..       4      71 .. 0.76
   2 ?   -2.8   0.0       7.7   8.6e+03      27      42 ..     216     231 ..     191     243 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklk 27
                                      i +yG+ g+GKSt++++L++al++  k
  gi|330506826|ref|YP_004383254.1|  4 IAIYGKGGIGKSTTTQNLTAALSTMGK 30
                                      679*****************9995552 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.7
                      RNA_helicase  27 klkkkdsvysrnpedd 42 
                                        +++k++v+  +p++d
  gi|330506826|ref|YP_004383254.1| 216 SEIHKQTVIQYAPDSD 231
                                       3444455555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.6e-05     0.018       4      33 ..       3      39 ..       1      60 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                            AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtek 33
                                      +i+iyG+ giGK+t+  +l       g+k+  i ++ 
  gi|330506826|ref|YP_004383254.1|  3 QIAIYGKGGIGKSTTTQNLtaalstmGKKIMQIGCDP 39
                                      69**************999777766666666666665 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   0.4   9.7e-05      0.11       4      38 ..       4      38 ..       1      43 [. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.7e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      i++ G  G+GK tt+  L a l+++gkk++ + +D
  gi|330506826|ref|YP_004383254.1|  4 IAIYGKGGIGKSTTTQNLTAALSTMGKKIMQIGCD 38
                                      7899**************************99998 PP

>> Ku  Ku70/Ku80 beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     7e-05     0.078      78     135 ..     197     251 ..     151     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7e-05
                                Ku  78 dskglkllgFvplseilkeylsikssyfiyPddkdekgstkafsaLveamleskkvai 135
                                       ++ g + ++Fvp+++i+++    k++ + y+ d+d++   ka+ aL +a  e +++ i
  gi|330506826|ref|YP_004383254.1| 197 EKIGSQMIQFVPRDNIVHQSEIHKQTVIQYAPDSDQA---KAYLALAKAVDENQMFVI 251
                                       4778899********9998887777777777555555...6*********99998876 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 ?   12.5   0.0   0.00012      0.13      36      78 ..     204     246 ..     198     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                   c-SKI_SMAD_bind  36 llfspqkFvvHsHrskekrtchwGfdsanWraylllaeeeeke 78 
                                       + f p+  +vH+ + +++++ ++ +ds++ +ayl la+  +++
  gi|330506826|ref|YP_004383254.1| 204 IQFVPRDNIVHQSEIHKQTVIQYAPDSDQAKAYLALAKAVDEN 246
                                       5799*********************************764333 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00024      0.27      24      53 ..       2      30 ..       1      62 [. 0.86
   2 ?   -2.6   0.0       4.2   4.7e+03      85     107 ..     240     265 ..     209     266 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                             DUF87 24 rHlAilgsTGsGKSntvavLleellekkga 53
                                      r +Ai g+ G GKS+t+  L + l  ++g 
  gi|330506826|ref|YP_004383254.1|  2 RQIAIYGKGGIGKSTTTQNLTAALS-TMGK 30
                                      679*****************99998.4444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.2
                             DUF87  85 a...kdkelkinpwsldpeelldlle 107
                                       a   +++++ + p+ +++eel+++++
  gi|330506826|ref|YP_004383254.1| 240 AkavDENQMFVIPKPMEYEELEQVMM 265
                                       03345566666677788888877776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00033      0.37       8      32 ..       4      28 ..       2      72 .. 0.75
   2 ?   -2.0   0.0       3.6   4.1e+03      74      93 ..     187     205 ..     150     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldee 32
                                      ++++G  G+GK+t+ ++l+  l   
  gi|330506826|ref|YP_004383254.1|  4 IAIYGKGGIGKSTTTQNLTAALSTM 28
                                      78*****************998654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.6
                            AAA_22  74 sseellealeqalraravie 93 
                                       +++el++a+++ + +++  +
  gi|330506826|ref|YP_004383254.1| 187 RERELVSAFAEKIGSQMI-Q 205
                                       555555666655555554.3 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00063      0.71      27      52 ..       4      29 ..       2      74 .. 0.81
   2 ?   -1.0   0.0       1.8     2e+03      40      76 ..     191     227 ..     181     250 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00063
                            AAA_16 27 vllsGesGvGKsslvrellralekdg 52
                                      + ++G  G+GKs+  + l  al++ g
  gi|330506826|ref|YP_004383254.1|  4 IAIYGKGGIGKSTTTQNLTAALSTMG 29
                                      689**************998888764 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.8
                            AAA_16  40 lvrellralekdggiflrgkcdqlesaipysalaqal 76 
                                       lv ++++ +  + + f+  ++  ++s+i+ ++++q++
  gi|330506826|ref|YP_004383254.1| 191 LVSAFAEKIGSQMIQFVPRDNIVHQSEIHKQTVIQYA 227
                                       5566666666666666666666665554444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1975.00
//
Query:       gi|330506827|ref|YP_004383255.1|  [L=105]
Description: nitrogen regulatory protein P-II [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-30  105.8   1.9    1.7e-30  105.6   1.9    1.0  1  P-II       Nitrogen regulatory protein P-II
      0.007   16.6   0.4       0.04   14.1   0.4    2.0  1  CdAMP_rec  Cyclic-di-AMP receptor


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 !  105.6   1.9   1.9e-34   1.7e-30       1     102 []       4     101 ..       4     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 1.9e-34
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       i+a+irpe +++v + Le+ g+++lt +ev GrGkqk   ++  g+ ++++ lpk+++++vv+d++vek v++i ++
  gi|330506827|ref|YP_004383255.1|   4 IRAVIRPEAVDKVADSLETGGFTALTRIEVFGRGKQK---GIKVGNVVYDN-LPKTMIMLVVDDDSVEKSVKIIEDS 76 
                                       89***********************************...7889**99988.************************* PP

                                       H-SSSTTSEEEEEEEESEEEETTTT CS
                              P-II  78 aktgeiGDGkiFvlpveevirirtg 102
                                       a+tg+iGDGkiF++ v+e+++irtg
  gi|330506827|ref|YP_004383255.1|  77 ARTGNIGDGKIFISSVDEAYTIRTG 101
                                       ************************8 PP

>> CdAMP_rec  Cyclic-di-AMP receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.4   4.5e-06      0.04       1      66 [.       1      79 [.       1      93 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.5e-06
                                      EEEEEEEEEHHHHHHHHHHHHHTT-EE.EEEEEEE....TTT-SEE........EEEEEEEEGGGHHHHHHHHHHC--- CS
                         CdAMP_rec  1 mklviaivqdedanelvdalteknfka.tklattG....GflkeGn........ttlliGvedekvdevlsiikekckt 66
                                      mk++ a+++ e ++++ d+l   +f+a t++   G      +k Gn        t +++ v+d++v++ ++ii+++++t
  gi|330506827|ref|YP_004383255.1|  1 MKMIRAVIRPEAVDKVADSLETGGFTAlTRIEVFGrgkqKGIKVGNvvydnlpkTMIMLVVDDDSVEKSVKIIEDSART 79
                                      99**********************985489888773222236777755555555678999***************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 731.16
//
Query:       gi|330506828|ref|YP_004383256.1|  [L=124]
Description: nitrogen regulatory protein P-II [Methanosaeta concilii GP6]
Scores for complete 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-30  104.5   0.4    5.6e-30  104.0   0.4    1.2  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.4   3.1e-34   5.6e-30       1     102 []       4     116 ..       4     116 .. 0.94

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 3.1e-34
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTE...........EEEEEEEEEEEEEEEEEGGG CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrga...........eyevellpkvkleivvsded 66 
                                       ++aii+ +k+e++k+aLe +g++++t+ + +GrGkqkg +  +              e+ ++++pk++++++v+de 
  gi|330506828|ref|YP_004383256.1|   4 VIAIIQLNKMEATKDALEVIGISSFTAYKASGRGKQKGLQIPHPTPlderderderdEKRMKYIPKRMISVMVEDEF 80 
                                       78***********************************875544444888999**9999999**************** PP

                                       HHHHHHHHHHHH-SSSTTSEEEEEEEESEEEETTTT CS
                              P-II  67 vekvveaiikaaktgeiGDGkiFvlpveevirirtg 102
                                       v +vv +i+k+++tg++GDG+iFv+p+ee +rirtg
  gi|330506828|ref|YP_004383256.1|  81 VPAVVAVITKVNRTGNYGDGRIFVSPMEESVRIRTG 116
                                       ***********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 832.28
//
Query:       gi|330506829|ref|YP_004383257.1|  [L=516]
Description: nitrogenase molybdenum-iron protein alpha chain [Methanosaeta concilii GP6]
Scores for complete 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-129  431.7   0.0   2.8e-129  431.4   0.0    1.1  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


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 !  431.4   0.0  1.6e-133  2.8e-129       1     397 [.      45     497 ..      45     499 .. 0.97

  Alignments for each domain:
  == domain 1  score: 431.4 bits;  conditional E-value: 1.6e-133
                                       -HHHHHH.HHHTTBTTEEEEEES-HHHHHCCCCHHHCHHS.....S-H..S-EEEE--HHHHSSSSHHHHHHHHHHH CS
                    Oxidored_nitro   1 CaplGAa.lvllgikdalplvhGpqGCatyaralltrhfr.....epi..plastdltekdavfGgeekLkeaikei 69 
                                       Ca++G++ +v+++ikd+l+++hGp+GCa+++++++++  +     e +  +++std++e+d+vfG+e+kL+ ai+e+
  gi|330506829|ref|YP_004383257.1|  45 CAYAGSKgVVFGPIKDILHITHGPIGCAYFTWGTRRNLMSqdegrECYsgYCLSTDVKETDIVFGAEKKLATAIREA 121
                                       **************************************9977765444778************************** PP

                                       HHHC-TSEEEEEE-HHHHHTTTTHHHHHHHHHHHHTSSEEEEEE--TT.SSSHHHHHHHHHHHHHHHCTT-TT---S CS
                    Oxidored_nitro  70 vkrykpkaIgVittClteliGdDieavareaeeelgeipvipvstpgf.ggsqseGydaalealvrklvgkkgekep 145
                                       ++ +kp+ I V  tC+ +liGdDie+v+r+aee+l++ ++ipv+++g+ g+sqs+G+++a +al+++lvg ++e e+
  gi|330506829|ref|YP_004383257.1| 122 YAIFKPECISVFCTCPIGLIGDDIESVCRKAEEDLKI-KIIPVRCEGYrGVSQSAGHHIASNALMEHLVG-TEELEN 196
                                       ***********************************87.********************************.666666 PP

                                       S...EEEEEEETTCGHGHHHHHHHHHHHHTEEEEEEECTSB-HHHHGGGGG-SEEEEESHHCHHHHHHHHHHHH--- CS
                    Oxidored_nitro 146 r...kvnilgeynlgpgdlrelkelleklGlevnavftggtsleelraagraklnlvlcprsanyaaelleekfgvp 219
                                       +   +vn+ geyn+g gd++ +k+lle++G++++  ftg++s+ ++++a+rakln++lc+rs+ny+ +++eek+g+p
  gi|330506829|ref|YP_004383257.1| 197 PgpfDVNVFGEYNIG-GDYWVVKDLLERVGYRIVSPFTGDASFHDIAKAHRAKLNILLCHRSINYTNRMMEEKYGIP 272
                                       66*************.************************************************************* PP

                                       EEEEE-SSSHHHHHHHHHHHHHHHT....CHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEECSSHHHHHHHHHHH CS
                    Oxidored_nitro 220 yiklvspiGleatdaflrelakllg....kevaperiaeerarlldaladyheylagkrvaiygdpdrvvalarllk 292
                                       ++k v+  G+e+t ++lr++a++++    + +++++i ee+a++++ +  y+++lagkrv+i ++++r++++  +++
  gi|330506829|ref|YP_004383257.1| 273 WLK-VNYLGVEDTIKTLRDMAAFFDdpglTRRTEAVIDEEMAKIQPTIDMYRKRLAGKRVMILVGGSRAHHFRNMFE 348
                                       ***.*************************8899******************************************** PP

                                       HHT-EEEEEEESSS-HHHHH...................................................HHHHHS CS
                    Oxidored_nitro 293 elGmevvaagtetahrddee...................................................rlkael 318
                                        lGmevv+ag+e+ahrdd+e                                                   +l +++
  gi|330506829|ref|YP_004383257.1| 349 TLGMEVVVAGYEFAHRDDYEgrkiltsivhtgrskvledihyerdpnvvspydnealqkkkekiprlmdyeGLLPHM 425
                                       *******************999********************************************99999888889 PP

                                       .TT.SEEEES.CHHHHHHHHHHHT-SEEEE-CCHHHHHHHTT--EEE-TS-ECCTTTCS.S---SHHHHHHHHHHHH CS
                    Oxidored_nitro 319 eegepeviddadleeleelikelkpdlllggskeryiaeklgiplvrvgfPildrhgya.rgpyvGYeGalnllddi 394
                                       ++g + +idd++++e e+l++el++dl+++g+k++y+++k+        +P  ++h+y+ +gpy G+ G++++++di
  gi|330506829|ref|YP_004383257.1| 426 KDG-QIMIDDYSHQECERLVRELGVDLFCSGIKDKYVFQKM-------HIPSRQMHSYDySGPYTGFSGFVQFAKDI 494
                                       999.5************************************.......****************************9 PP

                                       HHH CS
                    Oxidored_nitro 395 ana 397
                                          
  gi|330506829|ref|YP_004383257.1| 495 DMS 497
                                       865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3575.77
//
Query:       gi|330506830|ref|YP_004383258.1|  [L=452]
Description: nitrogenase molybdenum-iron protein beta chain [Methanosaeta concilii GP6]
Scores for 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-121  405.5   0.0   2.3e-121  405.3   0.0    1.0  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


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 !  405.3   0.0  1.3e-125  2.3e-121       1     398 [.      23     435 ..      23     436 .. 0.97

  Alignments for each domain:
  == domain 1  score: 405.3 bits;  conditional E-value: 1.3e-125
                                       -HHHHHHHHHTTBTTEEEEEES-HHHHHCCCCHHHCHHSS-HS-EEEE--HHHHSSSSHHHHHHHHHHHHHHC-TSE CS
                    Oxidored_nitro   1 CaplGAalvllgikdalplvhGpqGCatyaralltrhfrepiplastdltekdavfGgeekLkeaikeivkrykpka 77 
                                       C+p+GA l+++gi++++p++hG+qGC++y r++l+rh+rep+  a++++te+++vfGg+++Lkea++++v+ y+p++
  gi|330506830|ref|YP_004383258.1|  23 CQPIGAILAYKGIHNCMPITHGSQGCSSYLRMVLARHYREPTLAATSSFTEDSVVFGGRNNLKEAVDNVVNIYHPDV 99 
                                       ***************************************************************************** PP

                                       EEEEE-HHHHHTTTTHHHHHHHHHHHHTS...SEEEEEE--TTSSSHHHHHHHHHHHHHHHCTT-TT---SSEEEEE CS
                    Oxidored_nitro  78 IgVittClteliGdDieavareaeeelge...ipvipvstpgfggsqseGydaalealvrklvgkkgekeprkvnil 151
                                        ++ ttC++e+iGdD+ ++++e++ee+     ++v+ +stp+++gs+++Gyd+a++a+v+ +  + ++  ++k+n++
  gi|330506830|ref|YP_004383258.1| 100 LAINTTCSSETIGDDVSSFMEEIKEEEFFdpnVRVVIASTPSYVGSHITGYDNAVKAIVQSF--ARRGSPNGKLNVI 174
                                       ***********************887654799******************************..46789999***** PP

                                       EETTCGHGHHHHHHHHHHHHTE...................EEEEEECTSB-HHHHGGGGG-SEEEEESHHCHHHHH CS
                    Oxidored_nitro 152 geynlgpgdlrelkelleklGl...................evnavftggtsleelraagraklnlvlcprsanyaa 209
                                       +++ ++pgd+re+k++l  +G+                       +++ggt++ +l++a++++++++l+++++++ a
  gi|330506830|ref|YP_004383258.1| 175 PGF-VEPGDIREIKRILGIMGVrhiifpdttdvfdapmspqSGGLFPPGGTTIPDLKDAANSRATIALGRTAGASGA 250
                                       ***.************************************9999999****************************** PP

                                       HHHHHHH---EEEEE-SSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEECSSHHHHH CS
                    Oxidored_nitro 210 elleekfgvpyiklvspiGleatdaflrelakllgkevaperiaeerarlldaladyheylagkrvaiygdpdrvva 286
                                        +l+ kf +p +  ++piG+++ daf+++++ l++ ++ p+ i+eer+rl+d + d+h++++gk  ai+gdpd+v +
  gi|330506830|ref|YP_004383258.1| 251 MVLKGKFQIPAVIGPMPIGIRNSDAFVMNVSSLMDVPI-PQGIEEERGRLVDMMTDAHPHFHGKSLAIFGDPDTVAG 326
                                       **************************************.************************************** PP

                                       HHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT.SEEEES.CHHHHHHHHHHHT-SEEEE-CCHHHHHHHTT--E CS
                    Oxidored_nitro 287 larllkelGmevvaagtetahrddeerlkaeleegepeviddadleeleelikelkpdlllggskeryiaeklgipl 363
                                       l++l  e+Gm++ +a+t+t+++++ee++    ++  +e +++ d + l++ ik+ ++d+l+++++++ ia++ +ipl
  gi|330506830|ref|YP_004383258.1| 327 LVSLAVEMGMNPTYALTGTPDKKFEEEVHSVSPD--CEAMIG-DTFLLHQKIKNNPVDMLVSNTYGKLIARAEDIPL 400
                                       *************************999886555..789999.899******************************* PP

                                       EE-TS-ECCTTTCSS---SHHHHHHHHHHHHHHHH CS
                    Oxidored_nitro 364 vrvgfPildrhgyargpyvGYeGalnllddianal 398
                                       vrvgfPi dr ++++ p++GY+Ga +l++ i na+
  gi|330506830|ref|YP_004383258.1| 401 VRVGFPITDRANLHYFPIIGYAGAARLVEMIGNAF 435
                                       *******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3200.07
//
Query:       gi|330506831|ref|YP_004383259.1|  [L=475]
Description: nitrogenase MoFe cofactor biosynthesis protein [Methanosaeta concilii GP6]
Scores for complete 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-120  402.3   0.0   2.2e-120  402.1   0.0    1.0  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


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 !  402.1   0.0  1.2e-124  2.2e-120       1     398 [.      41     436 ..      41     437 .. 0.97

  Alignments for each domain:
  == domain 1  score: 402.1 bits;  conditional E-value: 1.2e-124
                                       -HHHHHHHHHTTBTTEEEEEES-HHHHHCCCCHHHCHHSS-H...S-EEEE--HHHHSSSSHHHHHHHHHHHHHHC- CS
                    Oxidored_nitro   1 CaplGAalvllgikdalplvhGpqGCatyaralltrhfrepi...plastdltekdavfGgeekLkeaikeivkryk 74 
                                       C + GA++vl++++dal+lvhGp+GCa+y+++++++ ++ p    + +std++e d+v+Gge+kL++ai+ +++r++
  gi|330506831|ref|YP_004383259.1|  41 CVYSGARVVLNPLTDALHLVHGPIGCASYTWDIRGSSSSGPDlykNSFSTDMSELDVVYGGEKKLARAIRDLAERFH 117
                                       99*************************************7777788******************************* PP

                                       TSEEEEEE-HHHHHTTTTHHHHHHHHHHHHTSSEEEEEE--TTSSSHHHHHHHHHHHHHHHCTT-TT---SS...EE CS
                    Oxidored_nitro  75 pkaIgVittClteliGdDieavareaeeelgeipvipvstpgfggsqseGydaalealvrklvgkkgekepr...kv 148
                                       p aI+V++tC +++iGdD++av+r a++elg  pvipv+++gf+g+++eGy+aa++al++ + g ++e +p     +
  gi|330506831|ref|YP_004383259.1| 118 PPAIFVYSTCIVGIIGDDLKAVCRSATAELGL-PVIPVRSEGFRGNKNEGYKAACNALFELV-G-TKEYRPAipyAI 191
                                       ******************************87.***************************99.6.7778887899** PP

                                       EEEEETTCGHGHHHHHHHHHHHHTEEEEEEECTSB-HHHHGGGGG-SEEEEESHHCHHHHHHHHHHHH---EEEEE- CS
                    Oxidored_nitro 149 nilgeynlgpgdlrelkelleklGlevnavftggtsleelraagraklnlvlcprsanyaaelleekfgvpyiklvs 225
                                       n+lgeyn++ gdl+ +k l+e++G+ev+a+ftg+ +++e++++++a+lnlv+c+ s++y+a+++ee++g+py +  s
  gi|330506831|ref|YP_004383259.1| 192 NLLGEYNVA-GDLWAIKPLFEEMGIEVVATFTGDGRVAEIQRSHTARLNLVQCSGSMTYLAKKMEERYGIPYQH-IS 266
                                       *********.****************************************************************.99 PP

                                       SSSHHHHHHHHHHHHHHHT....CHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEECSS.HHHHHHHHHHHHHT-E CS
                    Oxidored_nitro 226 piGleatdaflrelakllg....kevaperiaeerarlldaladyheylagkrvaiygdp.drvvalarllkelGme 297
                                       ++Gl + +  lr  a+++      ++a+e i++e+ar++++++ y+++++gk++aiy+++  ++v+l+r+++elGme
  gi|330506831|ref|YP_004383259.1| 267 FFGLGDLASALRCAARFFAdqsmLAKAEEIIERETARVMPKIVYYRSRVQGKKAAIYMGGaAKAVSLVRAFEELGME 343
                                       *******************9999555599999999***********************9999*************** PP

                                       EEEEEESSS-HHHHHHHHHHS.TT.SEEEES.CHHHHHHHHHHHT-SEEEE-CCHHHHHHHTT--EEE-TS-ECCTT CS
                    Oxidored_nitro 298 vvaagtetahrddeerlkaeleegepeviddadleeleelikelkpdlllggskeryiaeklgiplvrvgfPildrh 374
                                       vv +gt+t++rdd+ ++++ +++g+ +++dda+  el+el+   k+dll++g+ker++a kl       g+ ++d +
  gi|330506831|ref|YP_004383259.1| 344 VVIIGTQTGDRDDYRKISCMVRDGT-VIVDDANPLELRELLAVQKADLLVAGVKERFLAYKL-------GIAFCDFN 412
                                       ************************6.9***********************************.......******** PP

                                       TCSS---SHHHHHHHHHHHHHHHH CS
                    Oxidored_nitro 375 gyargpyvGYeGalnllddianal 398
                                       +++++ + GY+G +n+++++   l
  gi|330506831|ref|YP_004383259.1| 413 HDRTTSFEGYDGLINFARELDASL 436
                                       *******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3323.53
//
Query:       gi|330506832|ref|YP_004383260.1|  [L=434]
Description: nitrogenase molybdenum-iron protein beta chain [Methanosaeta concilii GP6]
Scores for complete 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-123  411.2   0.0   4.2e-123  411.0   0.0    1.0  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


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 !  411.0   0.0  2.4e-127  4.2e-123       1     398 [.      14     428 ..      14     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 411.0 bits;  conditional E-value: 2.4e-127
                                       -HHHHHHHHHTTBTTEEEEEES-HHHHHCCCCHHHCHHSS-HS-EEEE--HHHHSSSSHHHHHHHHHHHHHHC-TSE CS
                    Oxidored_nitro   1 CaplGAalvllgikdalplvhGpqGCatyaralltrhfrepiplastdltekdavfGgeekLkeaikeivkrykpka 77 
                                       C p+G++l++ g+++++pl+hG+qGCaty+r++l++hfrep+++as++l+ek +v+Gg  +Lk ++ +++  y+pka
  gi|330506832|ref|YP_004383260.1|  14 CMPMGSVLAFRGVEGCMPLFHGSQGCATYMRLYLAHHFREPVDIASSALSEKGTVYGGSANLKMGLNNLIIGYSPKA 90 
                                       9**************************************************************************** PP

                                       EEEEE-HHHHHTTTTHHHHHHHHHHHHTS.SEEEEEE--TTSSSHHHHHHHHHHHHHHHCTT-TT---SSEEEEEEE CS
                    Oxidored_nitro  78 IgVittClteliGdDieavareaeeelge.ipvipvstpgfggsqseGydaalealvrklvgkkgekeprkvnilge 153
                                       IgV+ttCl+e+iGdDi ++++e+++e++  ip+ipvstp+++ s++eGy  al+alv+ l+   +++  +++n++ +
  gi|330506832|ref|YP_004383260.1|  91 IGVATTCLAETIGDDIVQIINEFRAEEKSnIPIIPVSTPSYSASHEEGYARALQALVQSLA--RRTEPGGRINLIIG 165
                                       ***********************87776679*****************************4..4456666******* PP

                                       TTCGHGHHHHHHHHHHHHTE....................EEEEEECTSB-HHHHGGGGG-SEEEEESHH.CHHHHH CS
                    Oxidored_nitro 154 ynlgpgdlrelkelleklGl....................evnavftggtsleelraagraklnlvlcpr.sanyaa 209
                                       ++++p+d+r lk+++ + G                     + + ++ ggt+le++ ++++++ +l ++ r  + +a+
  gi|330506832|ref|YP_004383260.1| 166 SFVSPADVRYLKNMIIDWGSadefilfpdisetldaprveNPPRITEGGTTLEDMVDTANSRCTLTIGGRfQSSSAG 242
                                       ***************************************999*************************99955559** PP

                                       HHHHHHH---EEEEE-SSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEECSSHHHHH CS
                    Oxidored_nitro 210 elleekfgvpyiklvspiGleatdaflrelakllgkevaperiaeerarlldaladyheylagkrvaiygdpdrvva 286
                                       e+le++f vp + l+ piGl++td f+  l++ +g++  per++++r+rlld lad+h+ylag rva+ygd d+v++
  gi|330506832|ref|YP_004383260.1| 243 EFLEREFRVPQTALPLPIGLKDTDLFVSMLEEQTGIAL-PERYEAQRGRLLDTLADVHKYLAGVRVAVYGDSDIVLG 318
                                       **************************************.************************************** PP

                                       HHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT.SEEEES.CHHHHHHHHHHHT-SEEEE-CCHHHHHHHTT--E CS
                    Oxidored_nitro 287 larllkelGmevvaagtetahrddeerlkaeleegepeviddadleeleelikelkpdlllggskeryiaeklgipl 363
                                       l+r+l+e G+ +++++t+ ++ ++e++++a  e+    ++ +ad+ ++++ i++ + dl+lg+s++r+i++k gipl
  gi|330506832|ref|YP_004383260.1| 319 LTRFLCEAGAIPAVVATGLRSTRFEAEIRAASED--ALILLGADFSQIHDKIRNARIDLMLGTSNGRQISKKEGIPL 393
                                       **************************99995555..49*************************************** PP

                                       EE-TS-ECCTTTCSS---SHHHHHHHHHHHHHHHH CS
                    Oxidored_nitro 364 vrvgfPildrhgyargpyvGYeGalnllddianal 398
                                       vrvg P +dr+g+ r++ vGYeGa +l+d i+nal
  gi|330506832|ref|YP_004383260.1| 394 VRVGLPNHDRVGATRQLLVGYEGATRLADAITNAL 428
                                       *********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3013.54
//
Query:       gi|330506833|ref|YP_004383261.1|  [L=279]
Description: molybdate ABC transporter substrate-binding protein [Methanosaeta concilii GP6]
Scores for complete 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  153.7   0.0    7.1e-45  153.5   0.0    1.0  1  SBP_bac_11  Bacterial extracellular solute-binding protein
    4.7e-10   39.9   0.2    2.3e-09   37.7   0.2    1.9  1  SBP_bac_1   Bacterial extracellular solute-binding protein
      2e-06   27.1   0.1    3.7e-06   26.2   0.1    1.4  1  PBP_like    PBP superfamily domain
    0.00018   21.0   0.1    0.00025   20.6   0.1    1.1  1  SBP_bac_6   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.024   14.2   0.1      0.092   12.3   0.0    1.9  3  OpuAC       Substrate binding domain of ABC-type glycine beta
       0.19   12.3   2.0       0.45   11.1   2.0    1.7  1  LPAM_1      Prokaryotic membrane lipoprotein lipid attachment


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 !  153.5   0.0   2.4e-48   7.1e-45       2     229 ..      29     258 ..      28     259 .. 0.98

  Alignments for each domain:
  == domain 1  score: 153.5 bits;  conditional E-value: 2.4e-48
                                       EEEE-SSTHHHHHHHHHHHHHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEE CS
                        SBP_bac_11   2 tvaaagslaaalrelaaaFeahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplas 78 
                                        v++a+sl+ a+ e+ + +e++tg++v++ + gs++l+ q+++ga +D++++a++++++++++++l++++s + +++
  gi|330506833|ref|YP_004383261.1|  29 IVFTAASLTGAFGEIGEIYENETGIHVAFNFDGSQALRTQLENGAYADLFASANTKQMNAVRESRLMNNSSVAIFTR 105
                                       599*****************************************************************9******** PP

                                       EEEEEEESTT-TT---SHHHHHHSS--EEEE--T-TTTTHH.HHHHGGG--.....HHHHHHHHHTEEEEESSHHHH CS
                        SBP_bac_11  79 splviavpkgnpkkikgwadLlkpglklavadPttspsGlaalalleaaga.....qellkalekkvvklgessrql 150
                                       ++l ++ pk+np+ki+++ dL++pg+k+++ + +  p+G++al++++++g      +++ + +  +v  +++++  +
  gi|330506833|ref|YP_004383261.1| 106 NKLSLIIPKDNPAKITNLSDLARPGVKIVMGT-KDVPVGDYALQIIARLGNdsaygPDYERDVLANVISQETNVNYV 181
                                       *******************************9.789*************9999999********************* PP

                                       HHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHHT CS
                        SBP_bac_11 151 ltaveageadagivyeseakaaengdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaqailrky 227
                                       +t v+ geadag++y s++  ++   k++ + +p+++n+  ++yp+++l  ++ +++ ++F++++ s+e++a+l+ky
  gi|330506833|ref|YP_004383261.1| 182 VTKVALGEADAGFAYISDIT-QDMTSKIDKIVIPDEYNI-IAEYPMGMLLESKYPAESQRFMDLVMSDEGRAVLEKY 256
                                       *******************9.67899************8.9************************************ PP

                                       T- CS
                        SBP_bac_11 228 Gf 229
                                       Gf
  gi|330506833|ref|YP_004383261.1| 257 GF 258
                                       *9 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.2   7.6e-13   2.3e-09       3     314 ..      35     250 ..      33     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 7.6e-13
                                       SHHHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHH CS
                         SBP_bac_1   3 sltegaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvk 79 
                                       slt   a+ ++  + +e  ++gi V +++ gs++l++    ++++G+ + D++a++n++    +++  l+  +++++
  gi|330506833|ref|YP_004383261.1|  35 SLTG--AFGEIG-EIYEN-ETGIHVAFNFDGSQALRT----QLENGAYA-DLFASANTKQMNAVRESRLMNNSSVAI 102
                                       5555..666666.55888.8**********9999999....******77.*****6666666788889999999999 PP

                                       HTTECTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCH CS
                         SBP_bac_1  80 aylapgvkdaadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkkpigga 156
                                           +      ++                     + ++i+              + ++l+++++k++  +k      
  gi|330506833|ref|YP_004383261.1| 103 FTRNKLSLIIPKD---------------------NPAKIT--------------NLSDLARPGVKIVMGTKDV---- 140
                                       8843332222222.....................556666..............**************99999.... PP

                                       CCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTT CS
                         SBP_bac_1 157 rggsasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaG 233
                                                + +al++++ lg                         +y+ +++ + l+++ +++++++ +++ ++ G
  gi|330506833|ref|YP_004383261.1| 141 -------PVGDYALQIIARLG----------------------NDSAYGPDYERDVLANVISQETNVNYVVTKVALG 188
                                       .......55566666666666......................3344555558889********************* PP

                                       SCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTS CS
                         SBP_bac_1 234 eaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldflls 310
                                       ea++++++ +++ + m +++ +  ++d  +                    +  y+++++  sk+p++ + F+d++ s
  gi|330506833|ref|YP_004383261.1| 189 EADAGFAYISDITQDMTSKIDKIVIPDEYNI-------------------IAEYPMGMLLESKYPAESQRFMDLVMS 246
                                       ***********87777777666666666666...................58999********************** PP

                                       HHHH CS
                         SBP_bac_1 311 peaq 314
                                       +e+ 
  gi|330506833|ref|YP_004383261.1| 247 DEGR 250
                                       *986 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   1.3e-09   3.7e-06      35     150 ..      73     195 ..      44     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.3e-09
                                       EEESS---.CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BGGGC-S-B-EEEEE-TTSHHHHHHH CS
                          PBP_like  35 agshlldk.eteeynapalrkaldgievvlvnlarreqglvvakgnpkkitnwkdladaplrlvnRetGSGtrdlfd 110
                                       a ++l+++  t++ na    +++++    ++ + r + +l++ k+np kitn++dla++++ +v+  ++    d+  
  gi|330506833|ref|YP_004383261.1|  73 AYADLFASaNTKQMNAVRESRLMNNS--SVAIFTRNKLSLIIPKDNPAKITNLSDLARPGVKIVMGTKDVPVGDYAL 147
                                       55666443166778888778777774..6788999****************************************** PP

                                       HHHC-CEECTE-SSTTSEEESSHHHH........HCCHCCETTCCECC CS
                          PBP_like 111 ellkkegiskssikgyaqearshlav........aaaVaagradvgvg 150
                                       + +++ g + +  ++y++ +  ++           + Va g+ad+g++
  gi|330506833|ref|YP_004383261.1| 148 QIIARLGNDSAYGPDYERDVLANVISqetnvnyvVTKVALGEADAGFA 195
                                       ******99996666666555544444555555559***********96 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   8.3e-08   0.00025      22     224 ..      76     267 ..      59     277 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 8.3e-08
                         SBP_bac_6  22 glfqpldpanlpnvnkdfaeeglkdpdgkyypygvgplvlavnkdrlkgrpvPksWaDLldPeykgkvalpgnngsd 98 
                                       +lf+   +an +++n  ++e+ l   +   ++++ + l+l++ kd  ++    +  +DL +P    k+++ +++   
  gi|330506833|ref|YP_004383261.1|  76 DLFA---SANTKQMN-AVRESRLMN-NSSVAIFTRNKLSLIIPKDNPAKI---TNLSDLARPGV--KIVMGTKDV-P 141
                                       5555...55555555.222333333.567778888888888888886555...89999999987..9*****999.8 PP

                         SBP_bac_6  99 lfealllalyk.dfgedgvkkllrnlkanlhpaq..mvkaagslesgepavsvvpyffadilpekkkgknlkvvwPe 172
                                          ++l ++++  ++++ + ++ r++ an+ + +   +  +++++ ge  ++ ++++ +di +     k  k+v+P 
  gi|330506833|ref|YP_004383261.1| 142 VGDYALQIIARlGNDSAYGPDYERDVLANVISQEtnVNYVVTKVALGE--ADAGFAYISDITQDMT-SKIDKIVIPD 215
                                       888888888886445777778888888887777774445679999999..************9997.5555889999 PP

                         SBP_bac_6 173 d..GalvspifmlvkkgkkkelakafidfllspevqailakaggvfPvvtnpav 224
                                       +    + +p+ ml+ ++  +++ ++f+d  +s+e++a+l+k g+ +Pv  +p  
  gi|330506833|ref|YP_004383261.1| 216 EynIIAEYPMGMLLESK-YPAESQRFMDLVMSDEGRAVLEKYGF-APVEREPMM 267
                                       95444558999999999.**************************.**9755544 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 ?   12.3   0.0   3.1e-05     0.092      23     119 ..      46     137 ..      40     153 .. 0.77
   2 ?   -1.7   0.0      0.57   1.7e+03      25      58 ..     175     196 ..     158     215 .. 0.56
   3 ?   -3.3   0.0       1.8   5.5e+03     137     158 ..     250     266 ..     244     277 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.1e-05
                                       HHHHT.TEEEEEEEEESHHHHHHHHHTTS.SSEEEEEEHHHHHHHHHHHHHHHHEEEEEEEESEEECEEEEEEHHHH CS
                             OpuAC  23 llekk.GykveltnlgstavlfaalasGd.iDvypeewtgtayeaykkaveekkglevlgplgagnteglavpkyva 97 
                                       + e+  G+ v  +n++++++l++ l++G  +D+++++ t ++ +  ++++ +   +    ++   n+  l++pk+  
  gi|330506833|ref|YP_004383261.1|  46 IYENEtGIHVA-FNFDGSQALRTQLENGAyADLFASANTKQMNAVRESRLMNNSSV----AIFTRNKLSLIIPKDNP 117
                                       55555566554.567777*********9857****999999775555555533333....5899***********97 PP

                                       HHHTTTBHHHHCTHHGGTEEEE CS
                             OpuAC  98 ekygiksisDLkkpaedlelga 119
                                          +i+ +sDL++p +++  g 
  gi|330506833|ref|YP_004383261.1| 118 A--KITNLSDLARPGVKIVMGT 137
                                       7..**********998655554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.57
                                       HHT.TEEEEEEEEESHHHHHHHHHTTSSSEEEEEE CS
                             OpuAC  25 ekk.GykveltnlgstavlfaalasGdiDvypeew 58 
                                       e + +y+v++++             G++D+   ++
  gi|330506833|ref|YP_004383261.1| 175 ETNvNYVVTKVA------------LGEADAGF-AY 196
                                       333344444444............44444444.44 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.8
                                       HHHHHHHT-TTCEEEGSCEEEE CS
                             OpuAC 137 egllkaYgldkvelvegseaam 158
                                       ++ l++Yg+      + + + m
  gi|330506833|ref|YP_004383261.1| 250 RAVLEKYGFA-----PVEREPM 266
                                       4556666662.....3333333 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 ?   11.1   2.0   0.00015      0.45       1      15 [.       1      16 [.       1      16 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                            LPAM_1  1 MKKi.llalgalllLs 15
                                      MKK+ ++a++a+l+Ls
  gi|330506833|ref|YP_004383261.1|  1 MKKSiFIAFFAALVLS 16
                                      ****666777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); 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:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2015.91
//
Query:       gi|330506834|ref|YP_004383262.1|  [L=297]
Description: molybdate ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-18   66.9  18.2    1.9e-18   66.9  18.2    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        3.6    7.9  12.7         22    5.4   0.4    3.5  3  DUF948        Bacterial protein of unknown function (DUF948)
        5.2    7.3   6.8        1.4    9.2   2.8    2.0  2  TMEM191C      TMEM191C family


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 ?   -1.5   3.5       0.3   1.8e+03      19      37 ..      44      62 ..      36     101 .. 0.57
   2 !   66.9  18.2   3.2e-22   1.9e-18       1     183 [.     100     291 ..      97     293 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.3
                      BPD_transp_1 19 llrpliivllslPsfvlai 37
                                      ll+++ i++ +lP+++l++
  gi|330506834|ref|YP_004383262.1| 44 LLLIIAITFIALPVVALFL 62
                                      3445555555555555433 PP

  == domain 2  score: 66.9 bits;  conditional E-value: 3.2e-22
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf...........vilsilghlilpviillllsaap 66 
                                       g+++++++a +++ ++++l + li+++  +P+ v +i l+++f           ++  ++ ++ l+vii+ ++ + p
  gi|330506834|ref|YP_004383262.1| 100 GTPIAYVSA-RFRYFGKELADSLIDLPVIMPPAVAGIALLMAFgrmgivghyldAFGISIAFTTLAVIIAQVFVSSP 175
                                       789999999.9999****************************************77778899999988888888888 PP

                      BPD_transp_1  67 yvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgsw.pGlgtlll 142
                                       + ++  r  ++ ++  l++aar+lG sr+ +f++v+lP a+  +++g+i+af+++lg++ ++ +++++ +G ++++ 
  gi|330506834|ref|YP_004383262.1| 176 FYIRQARTSFEDVDIALENAARTLGGSRIYTFFHVILPIAINGLVSGAIMAFARSLGEFGATIMFAGNfQGRTQTMP 252
                                       888888899999***********************************************988877743155555666 PP

                      BPD_transp_1 143 eailgydyseisnggvlalviavlllnlvadilqrlldprv 183
                                        ai   +       ++l ++i+++++++v+ +l++ l +rv
  gi|330506834|ref|YP_004383262.1| 253 LAIYTAMQGDLD--VSLCIAIILVAISFVVIFLVKTLTRRV 291
                                       666666555566..89*****************99999997 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 ?    5.4   0.4    0.0037        22       3      31 ..      45      73 ..      44      79 .. 0.86
   2 ?    3.8   0.2     0.012        69       6      39 ..     156     189 ..     153     200 .. 0.84
   3 ?    4.6   1.8    0.0064        38       1      22 [.     269     288 ..     269     293 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0037
                            DUF948  3 glIaAiAFvvLviflivvllklkktldea 31
                                      +lI+Ai+F++L ++   +   l  tl+++
  gi|330506834|ref|YP_004383262.1| 45 LLIIAITFIALPVVALFLRSPLDTTLQSL 73
                                      59*********999999988888888876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.012
                            DUF948   6 aAiAFvvLviflivvllklkktldeaaatieele 39 
                                       + iAF  L+++++ v+++    +++a+++ e++ 
  gi|330506834|ref|YP_004383262.1| 156 ISIAFTTLAVIIAQVFVSSPFYIRQARTSFEDVD 189
                                       689**************99888888888877765 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0064
                            DUF948   1 IAglIaAiAFvvLviflivvll 22 
                                       IA++++Ai+Fv  vifl+++l 
  gi|330506834|ref|YP_004383262.1| 269 IAIILVAISFV--VIFLVKTLT 288
                                       67777777776..577777775 PP

>> TMEM191C  TMEM191C family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.8   0.00023       1.4      52     107 ..      32      86 ..      19      96 .. 0.83
   2 ?   -1.4   0.1      0.43   2.6e+03      56      84 ..     258     286 ..     245     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00023
                          TMEM191C  52 alrlwalga.lqtllllPlgflalpllylvlvksdavraglpslssdaalrrlrytl 107
                                        lr +al a l +ll++ ++f+alp++ l l +   + + l+sl+   ++  lr +l
  gi|330506834|ref|YP_004383262.1|  32 RLREVALKAsLALLLIIAITFIALPVVALFLRS--PLDTTLQSLHDPVVMDALRLSL 86 
                                       5788888654899999**********9998875..5889999999999999999776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.43
                          TMEM191C  56 walgalqtllllPlgflalpllylvlvks 84 
                                          g l++ l + ++++a++++++ lvk+
  gi|330506834|ref|YP_004383262.1| 258 AMQGDLDVSLCIAIILVAISFVVIFLVKT 286
                                       55677888888889999999888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2156.77
//
Query:       gi|330506835|ref|YP_004383263.1|  [L=237]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-33  116.2   0.0    2.1e-33  115.8   0.0    1.1  1  ABC_tran     ABC transporter
    2.2e-08   34.3   0.4     0.0014   18.5   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00037   20.0   0.0       0.29   10.5   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0041   17.5   0.1     0.0061   17.0   0.1    1.6  1  AAA_16       AAA ATPase domain
      0.009   15.8   0.0      0.012   15.3   0.0    1.1  1  AAA_15       AAA ATPase domain
     0.0099   15.8   0.0      0.018   15.0   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.011   15.7   0.1       0.23   11.4   0.0    2.1  2  NACHT        NACHT domain
      0.016   15.5   0.1      0.059   13.6   0.1    1.9  1  AAA_22       AAA domain
      0.024   15.1   0.0      0.037   14.5   0.0    1.2  1  AAA_23       AAA domain
      0.024   14.4   0.0      0.044   13.5   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.034   13.7   0.0      0.064   12.8   0.0    1.4  1  AAA_7        P-loop containing dynein motor region
       0.06   12.9   0.0       0.12   11.9   0.0    1.6  1  AAA_25       AAA domain
      0.061   13.8   0.0       0.25   11.8   0.0    1.9  2  AAA          ATPase family associated with various cellular a
       0.11   12.3   0.2       0.19   11.6   0.2    1.3  1  Rop          Rop protein
       0.13   12.5   0.0       0.22   11.8   0.0    1.3  1  Roc          Ras of Complex, Roc, domain of DAPkinase
       0.15   11.8   0.1       0.41   10.4   0.1    1.6  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.21   10.3   0.0        9.9    4.8   0.0    2.2  2  ABC_ATPase   Predicted ATPase of the ABC class
       0.27   10.0   0.1       0.38    9.5   0.1    1.1  1  DLIC         Dynein light intermediate chain (DLIC)
       0.27   10.5   0.6       0.89    8.8   0.0    1.9  2  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 !  115.8   0.0   2.2e-36   2.1e-33       4     136 ..      17     162 ..      15     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 2.2e-36
                                       EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltv 76 
                                       v++ +kege++ +vG+nG+GK++Ll+l+agl +p+eG+i ldg++l +    ++     ++ig+++q   lfp+++v
  gi|330506835|ref|YP_004383263.1|  17 VKMMIKEGEILMLVGDNGCGKTSLLNLVAGLQDPDEGRIALDGRPLFDsglkIRVAPEGRNIGYVFQSYALFPHMSV 93 
                                       7899********************************************99999999999****************** PP

                                       HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++n             + ++++ + l+  gl ++++ ++     ++SgGq+qrvalaral+ +p+llllDEp 
  gi|330506835|ref|YP_004383263.1|  94 YDNvafglrtrrlsrrAIESRVMEHLKAAGLWDIRKARA----VEVSGGQRQRVALARALIIEPDLLLLDEPL 162
                                       ***********9988888888999999999999999998....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 !   18.5   0.0   1.5e-06    0.0014       2      25 ..      27      50 ..      26      77 .. 0.76
   2 !   14.0   0.1   3.6e-05     0.034     233     297 ..     131     193 ..     102     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                       +l+G+Ng+GK++LL +  +l++ 
  gi|330506835|ref|YP_004383263.1| 27 LMLVGDNGCGKTSLLNLVAGLQDP 50
                                      579******************974 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.6e-05
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQv..iltTH 297
                                        a e+S G+++  al+ al+  +   +lll+DEp + L+ + ++   + l ++ ++    v  i++TH
  gi|330506835|ref|YP_004383263.1| 131 RAVEVSGGQRQRVALARALIIEP---DLLLLDEPLSALDVRKQAAMRKELrERIHA--CHVpsIIVTH 193
                                       67899*******9*******999...9*************9998888666444444..5555566666 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00031      0.29      23      42 ..      23      42 ..       3      46 .. 0.72
   2 !    7.7   0.0    0.0023       2.2     136     198 ..     134     194 ..      71     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                                      TSSEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 23 sksftaivGpNGSGKsnlld 42
                                      + ++ ++vG NG+GK++ll+
  gi|330506835|ref|YP_004383263.1| 23 EGEILMLVGDNGCGKTSLLN 42
                                      4467899**********986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEE..EEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQf..ivislr 198
                                       + SgG+++ vala  + i+   p  l llDe  +aLD ++ +++ + l+e+ + + +  i+++++
  gi|330506835|ref|YP_004383263.1| 134 EVSGGQRQRVALARALIIE---P-DLLLLDEPLSALDVRKQAAMRKELRERIHACHVpsIIVTHD 194
                                       689***9999998776553...4.4899********************99887755433777765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   6.5e-06    0.0061      23      46 ..      23      46 ..      14     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.5e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellr 46
                                      ++e+++l+G+ G+GK+sl++ ++ 
  gi|330506835|ref|YP_004383263.1| 23 EGEILMLVGDNGCGKTSLLNLVAG 46
                                      5599***************99984 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.3e-05     0.012      20      42 ..      16      43 ..       3      52 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                            AAA_15 20 dlsee.....ltvliGkNnsGKSsilea 42
                                      +++       +  l+G N++GK+s+l++
  gi|330506835|ref|YP_004383263.1| 16 EVKMMikegeILMLVGDNGCGKTSLLNL 43
                                      433334445899*************986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.9e-05     0.018      93     124 ..      17      49 ..       5      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                                       HHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  93 lkellkd.ktsvlvGqSGvGKStLinallpele 124
                                       +k ++k+ ++ +lvG  G GK++L+n +++ ++
  gi|330506835|ref|YP_004383263.1|  17 VKMMIKEgEILMLVGDNGCGKTSLLNLVAGLQD 49 
                                       566777779*****************9988554 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   0.00024      0.23       3      20 ..      27      44 ..      25      52 .. 0.85
   2 ?    2.3   0.0      0.14   1.4e+02      35     123 ..      96     191 ..      90     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                                      EEEEC-TTTCHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkl 20
                                      ++l G++G+GKT Ll  +
  gi|330506835|ref|YP_004383263.1| 27 LMLVGDNGCGKTSLLNLV 44
                                      789***********9755 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                                       SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCSCCCEE..........EEEE-STT-SS-TCH.. CS
                             NACHT  35 klvFflslrelsrsgnarsladllfsqlpepaapvsevwavllelperlL..........lilDglDelvtdlgqke 101
                                        + F l+ r+lsr+  + ++ ++l + +++ +++ + v +   ++++ +L          l+l   De  + l+  +
  gi|330506835|ref|YP_004383263.1|  96 NVAFGLRTRRLSRRAIESRVMEHLKAAGLWDIRKARAVEVSGGQRQRVALaraliiepdlLLL---DEPLSALDVRK 169
                                       578889999999998778999999999999999998844444444444455554455553554...55555566666 PP

                                       .......HHHHHCTTTTT--EE CS
                             NACHT 102 kqpvrtlLselirkkllpeasl 123
                                       ++++r+ L+e i + ++p+  +
  gi|330506835|ref|YP_004383263.1| 170 QAAMRKELRERIHACHVPSIIV 191
                                       6888888888888866666544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   6.3e-05     0.059       4      33 ..      23      52 ..      19     198 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.3e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeea 33
                                      +  il+++G  G+GKT ll+ ++   d ++
  gi|330506835|ref|YP_004383263.1| 23 EGEILMLVGDNGCGKTSLLNLVAGLQDPDE 52
                                      6789***************99987765443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.9e-05     0.037      18      37 ..      23      42 ..       6      46 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-05
                            AAA_23 18 skgltlItGpNGaGKTTild 37
                                      +  +  ++G+NG+GKT++l+
  gi|330506835|ref|YP_004383263.1| 23 EGEILMLVGDNGCGKTSLLN 42
                                      5567789***********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 ?   13.5   0.0   4.6e-05     0.044      15      39 ..      17      41 ..      11      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.6e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                       +++i++ ++ +l+G++G GK++ll
  gi|330506835|ref|YP_004383263.1| 17 VKMMIKEGEILMLVGDNGCGKTSLL 41
                                      567788666**************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 ?   12.8   0.0   6.8e-05     0.064      26      52 ..      17      43 ..      12      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.8e-05
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikd 52
                                      +++++k++  ++lvG+ G+GKt++++ 
  gi|330506835|ref|YP_004383263.1| 17 VKMMIKEGEILMLVGDNGCGKTSLLNL 43
                                      6899******************99875 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   0.00013      0.12      26      50 ..      17      41 ..       5      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                            AAA_25 26 vkgllpagelallaGapgtGKttla 50
                                      vk ++ +ge+ +l+G+ g+GKt l+
  gi|330506835|ref|YP_004383263.1| 17 VKMMIKEGEILMLVGDNGCGKTSLL 41
                                      677899****************986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00027      0.25       1      20 [.      27      46 ..      27      84 .. 0.89
   2 ?   -0.3   0.0       1.4   1.3e+03      45      74 ..     138     168 ..     103     200 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                                      EEEESSTTSSHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavak 20
                                      ++l+G  G+GKT+l + va 
  gi|330506835|ref|YP_004383263.1| 27 LMLVGDNGCGKTSLLNLVAG 46
                                      589**************996 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHTS.TSEEEEEETGGGHHHHH CS
                               AAA  45 kirelfkeakeka.kpsilfiDEidalaksr 74 
                                         r+ ++ a++   +p  l++DE  +    r
  gi|330506835|ref|YP_004383263.1| 138 GQRQRVALARALIiEPDLLLLDEPLSALDVR 168
                                       4555555555555678888888854444444 PP

>> Rop  Rop protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2    0.0002      0.19       4      43 ..     140     179 ..     138     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                               Rop   4 QektALnmAkFIksQsLlLLeKLneLdlDeqAdlCErLHe 43 
                                        ++ AL  A  I    LlL e L +Ld+ +qA++  +L e
  gi|330506835|ref|YP_004383263.1| 140 RQRVALARALIIEPDLLLLDEPLSALDVRKQAAMRKELRE 179
                                       578899999999999999999*************999987 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 ?   11.8   0.0   0.00023      0.22       2      17 ..      27      42 ..      26      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                                      EEEESSTTSSHHHHHH CS
                               Roc  2 vvlvGdsgvGKtsllk 17
                                      ++lvGd+g GKtsll+
  gi|330506835|ref|YP_004383263.1| 27 LMLVGDNGCGKTSLLN 42
                                      79************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 ?   10.4   0.1   0.00043      0.41       3      22 ..      26      45 ..      24      49 .. 0.84
   2 ?   -2.1   0.0         3   2.9e+03     110     133 ..     114     137 ..     106     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00043
                         PduV-EutP  3 killiGkvgsGKttLtqalk 22
                                       ++l+G  g+GKt+L + + 
  gi|330506835|ref|YP_004383263.1| 26 ILMLVGDNGCGKTSLLNLVA 45
                                      58*************87665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3
                         PduV-EutP 110 aveelLksaGaekifevsavekeg 133
                                        v e Lk+aG   i +  ave +g
  gi|330506835|ref|YP_004383263.1| 114 RVMEHLKAAGLWDIRKARAVEVSG 137
                                       577899999999998888887665 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 ?    4.8   0.0      0.01       9.9     240     268 ..      19      47 ..      15      76 .. 0.82
   2 ?    3.4   0.0     0.028        27     322     353 ..     134     165 ..     126     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.01
                                       EEE-SS.EEEEEE-TTSSHHHHHHHHHHCC CS
                        ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAlekGv 268
                                       m i++G + ++vG +  GK+ LL+ l +G 
  gi|330506835|ref|YP_004383263.1|  19 MMIKEGeILMLVGDNGCGKTSLLN-LVAGL 47 
                                       88*********************8.44444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.028
                                       S--HHHHHHHHHHHHHHTT-SEEEEEGGGS-H CS
                        ABC_ATPase 322 dASGStsqAanimealeagakllLiDEDtsAt 353
                                       + SG   q +++++al ++ +llL+DE  sA 
  gi|330506835|ref|YP_004383263.1| 134 EVSGGQRQRVALARALIIEPDLLLLDEPLSAL 165
                                       569999999******************99996 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00041      0.38      26      55 ..      25      54 ..      15      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00041
                              DLIC 26 ksvlvlGedgsGkttliaklqGveeekkGr 55
                                        ++++G++g+Gkt+l+  + G++++  Gr
  gi|330506835|ref|YP_004383263.1| 25 EILMLVGDNGCGKTSLLNLVAGLQDPDEGR 54
                                      557889*******************99997 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00094      0.89      18      49 ..      26      57 ..      18      60 .. 0.81
   2 ?   -0.7   0.2      0.76   7.2e+02     133     157 ..     104     136 ..      94     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00094
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrl 49
                                      +++l+G  G+GK++l++l++   +++++ + l
  gi|330506835|ref|YP_004383263.1| 26 ILMLVGDNGCGKTSLLNLVAGLQDPDEGRIAL 57
                                      6789*************998776666665555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.76
                        Zeta_toxin 133 kelSrlgvldRyeeevae........gRlvpke 157
                                       ++lSr  +++R++e +++        +R v+++
  gi|330506835|ref|YP_004383263.1| 104 RRLSRRAIESRVMEHLKAaglwdirkARAVEVS 136
                                       679999999999999555567777656777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 1825.72
//
Query:       gi|330506836|ref|YP_004383264.1|  [L=606]
Description: S-layer-related duplication domain-containing protein, partial [Methanosaeta concilii GP6]
Scores for complete 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-128  425.6  14.3    2.3e-23   82.6   0.0    6.0  6  S-layer   S-layer protein
    2.1e-06   27.8   2.7       0.41   10.8   0.0    5.5  5  PrcB_C    PrcB C-terminal
     0.0002   20.1   1.6       0.37    9.4   0.1    3.9  4  GvpD      GvpD gas vesicle protein
     0.0005   20.1   0.0        2.2    8.4   0.0    4.2  4  DUF3876   Domain of unknown function, B. Theta Gene descripti
     0.0081   16.2   0.0        1.5    8.9   0.0    3.5  4  GUN4      GUN4-like
  ------ inclusion threshold ------
      0.094   12.3   0.4        9.8    5.7   0.1    2.9  3  DUF2140   Uncharacterized protein conserved in bacteria (DUF2


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 !   57.4   0.1   3.6e-19   1.1e-15     121     207 ..       2      85 ..       1      89 [. 0.94
   2 !   66.8   0.7   4.9e-22   1.5e-18     102     207 ..      88     191 ..      83     194 .. 0.93
   3 !   77.3   0.1   3.2e-25   9.6e-22     102     205 ..     193     293 ..     188     300 .. 0.92
   4 !   68.0   0.0   2.1e-22   6.3e-19     103     206 ..     299     399 ..     298     404 .. 0.95
   5 !   80.5   0.1   3.2e-26   9.6e-23     104     206 ..     405     504 ..     401     508 .. 0.96
   6 !   82.6   0.0   7.7e-27   2.3e-23     103     201 ..     509     604 ..     506     606 .] 0.95

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 3.6e-19
                           S-layer 121 eLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska.dstyvyekdlgdeddvviiavhvdevfrgtedslv 196
                                       eLe gYel +k+iD+dg++v+leL+kd e +ds++i + ++ d+++vy++   +++    i  ++++ fr++ ++l+
  gi|330506836|ref|YP_004383264.1|   2 ELEGGYELVVKSIDIDGNRVYLELYKDKEMIDSRIIVPANQvDDEFVYSRPGTSNE----IRAKLKNSFRSAYQNLA 74 
                                       79************************************9989*******9988877....9**************** PP

                           S-layer 197 viegifqisdd 207
                                       +i gi+q s+d
  gi|330506836|ref|YP_004383264.1|  75 TIVGIWQNSED 85 
                                       *******9955 PP

  == domain 2  score: 66.8 bits;  conditional E-value: 4.9e-22
                           S-layer 102 skvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska.dstyvyekdlgdeddv 177
                                        ++li++++  +l+s +s++LeegYel ik++D++gdk++leL kdg+ v ++vi + ++ d+ + y++   + +  
  gi|330506836|ref|YP_004383264.1|  88 DRILINKSQLIILSSKESIKLEEGYELFIKSMDIEGDKICLELDKDGKLVHEEVIIPPNDvDDIFHYSRAGTSHE-- 162
                                       589**************************************************99998889*******9888877.. PP

                           S-layer 178 viiavhvdevfrgtedslvviegifqis.dd 207
                                         i +h+++v+r+ +++lv+i+ i+q s d+
  gi|330506836|ref|YP_004383264.1| 163 --ILIHFKNVLRTPDQDLVTIDRIWQNSkDN 191
                                       ..99**********************99665 PP

  == domain 3  score: 77.3 bits;  conditional E-value: 3.2e-25
                           S-layer 102 skvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska.dstyvyekdlgdeddv 177
                                        ++li+++ + tl+s   leL+egYel i+  D++g+k++l++++dge +dsk i + ++ d+++vy++  +++   
  gi|330506836|ref|YP_004383264.1| 193 DRILINDSRSMTLSSQMPLELQEGYELAIRFADIEGNKAYLQFSRDGEVIDSKLIIPANEvDDNFVYSQAEASN--- 266
                                       689**************************************************99998888******9876664... PP

                           S-layer 178 viiavhvdevfrgtedslvviegifqis 205
                                         i+vh+++++rgt++sl++i+gi+q s
  gi|330506836|ref|YP_004383264.1| 267 -QIKVHFKNAYRGTDHSLAMIDGIWQTS 293
                                       .5************************98 PP

  == domain 4  score: 68.0 bits;  conditional E-value: 2.1e-22
                           S-layer 103 kvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska.dstyvyekdlgdeddvv 178
                                       ++li++ + +t++s   l LeegYelei+++D+dg++v++ L kdge v s+vi + ++ d+t++y+     ++   
  gi|330506836|ref|YP_004383264.1| 299 RILINDTQLRTVSSRFGLMLEEGYELEIQSMDLDGNRVYVVLVKDGEIVASQVIMPANEgDDTFIYSCPGTPQE--- 372
                                       79******************************************************8889******98877766... PP

                           S-layer 179 iiavhvdevfrgtedslvviegifqisd 206
                                        i v+++++frg++++l++ +g++q s+
  gi|330506836|ref|YP_004383264.1| 373 -IRVRFKNAFRGADQNLATADGLWQTSE 399
                                       .9***********************997 PP

  == domain 5  score: 80.5 bits;  conditional E-value: 3.2e-26
                           S-layer 104 vlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska.dstyvyekdlgdeddvvi 179
                                       +lid+  ++t++sg++l LeegY+l i++iD+dg+kv l L+kd+  +ds+vi + ++ d+t++y+    +++    
  gi|330506836|ref|YP_004383264.1| 405 ILIDDPRSRTMTSGTTLALEEGYKLAINSIDIDGNKVNLDLYKDEIVIDSQVIIPANEvDDTFIYSCPGTSQE---- 477
                                       89***************************************************998889*******9988877.... PP

                           S-layer 180 iavhvdevfrgtedslvviegifqisd 206
                                       i v+++++frg+++s+++++ ++q s+
  gi|330506836|ref|YP_004383264.1| 478 IRVRFKNAFRGADQSMATVDSLWQTSE 504
                                       9***********************996 PP

  == domain 6  score: 82.6 bits;  conditional E-value: 7.7e-27
                           S-layer 103 kvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska.dstyvyekdlgdeddvv 178
                                        +li++  ++t++sg+ l+LeegYel i +iD+dg+k +leL kdg  vds+vi+++++ d+t++y++   +++   
  gi|330506836|ref|YP_004383264.1| 509 PILINDTRSQTITSGTPLKLEEGYELIIPSIDIDGNKLYLELCKDGMMVDSQVITPENEvDDTFIYSRPETSQK--- 582
                                       69******************************************************999********9877765... PP

                           S-layer 179 iiavhvdevfrgtedslvviegi 201
                                        i+vh++++frg+e+slv+i+ i
  gi|330506836|ref|YP_004383264.1| 583 -IKVHFKNAFRGAEQSLVTIDSI 604
                                       .*******************998 PP

>> PrcB_C  PrcB C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.1    0.0071        21      13      34 ..       5      26 ..       3      39 .. 0.86
   2 ?    0.3   0.0      0.27     8e+02      13      34 ..     110     131 ..     107     144 .. 0.84
   3 !   10.8   0.0   0.00014      0.41       8      50 ..     315     353 ..     314     356 .. 0.84
   4 ?    4.7   0.1     0.011        33      13      40 ..     425     461 ..     423     475 .. 0.77
   5 ?   -0.2   0.0      0.37   1.1e+03      13      44 ..     530     557 ..     525     572 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0071
                            PrcB_C 13 gGYsievdkvyetenaiyvktt 34
                                      gGY + v+++  ++n++y+++ 
  gi|330506836|ref|YP_004383264.1|  5 GGYELVVKSIDIDGNRVYLELY 26
                                      9*****************9875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.27
                            PrcB_C  13 gGYsievdkvyetenaiyvktt 34 
                                       +GY + ++++  ++++i+++++
  gi|330506836|ref|YP_004383264.1| 110 EGYELFIKSMDIEGDKICLELD 131
                                       7*****************9986 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00014
                            PrcB_C   8 GeqptgGYsievdkvyetenaiyvkttllgPepgeevtqalty 50 
                                       G +  +GY +e++++ +++n++yv +     ++ge+v+  +  
  gi|330506836|ref|YP_004383264.1| 315 GLMLEEGYELEIQSMDLDGNRVYVVLV----KDGEIVASQVIM 353
                                       667789******************998....788888776655 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.011
                            PrcB_C  13 gGYsievdkvy.........etenaiyvkttllgPep 40 
                                       +GY++ ++++          + +++i+++ +++ P+ 
  gi|330506836|ref|YP_004383264.1| 425 EGYKLAINSIDidgnkvnldLYKDEIVIDSQVIIPAN 461
                                       6999999999988877888888889999999999943 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.37
                            PrcB_C  13 gGYsievdkvyetenaiyvkttllgPepgeev 44 
                                       +GY + + ++  ++n++y+++     ++g +v
  gi|330506836|ref|YP_004383264.1| 530 EGYELIIPSIDIDGNKLYLELC----KDGMMV 557
                                       7888888888888888887765....445555 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00012      0.37      63     150 ..      16     108 ..       7     117 .. 0.80
   2 ?    2.4   0.0     0.016        49      62     103 ..     225     267 ..     208     283 .. 0.80
   3 !    3.6   0.0     0.007        21      62      91 ..     435     465 ..     411     485 .. 0.75
   4 ?   -0.1   0.0     0.094   2.8e+02      64      90 ..     542     569 ..     523     586 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00012
                              GvpD  63 ld.ktalldllkdpleldldvdvPiekldlesllefvdeiaaiatkliialds....welvyeylaerydsPedikt 134
                                       +d +  +l+l+kd   +d  ++vP +++d e +++     ++i  kl  ++ s       ++    +  d+P+ i++
  gi|330506836|ref|YP_004383264.1|  16 IDgNRVYLELYKDKEMIDSRIIVPANQVDDEFVYSRPGTSNEIRAKLKNSFRSayqnLATIVGIWQNSEDNPDRILI 92 
                                       4556679***************************9999889999998887777211133344445567788888*** PP

                              GvpD 135 vkndlvvlaresgvrl 150
                                        k +l++l+ +++++l
  gi|330506836|ref|YP_004383264.1|  93 NKSQLIILSSKESIKL 108
                                       ************9998 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.016
                              GvpD  62 eld.ktalldllkdpleldldvdvPiekldlesllefvdeiaa 103
                                       +++ + a+l +++d+  +d + ++P +++d + +++  ++ ++
  gi|330506836|ref|YP_004383264.1| 225 DIEgNKAYLQFSRDGEVIDSKLIIPANEVDDNFVYSQAEASNQ 267
                                       5555789*******************88887777766655444 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.007
                              GvpD  62 eld.ktalldllkdpleldldvdvPiekldl 91 
                                       ++d +   ldl+kd + +d +v++P +++d 
  gi|330506836|ref|YP_004383264.1| 435 DIDgNKVNLDLYKDEIVIDSQVIIPANEVDD 465
                                       344556679****************987764 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.094
                              GvpD  64 d.ktalldllkdpleldldvdvPiekld 90 
                                       d +  +l+l kd++ +d +v+ P +++d
  gi|330506836|ref|YP_004383264.1| 542 DgNKLYLELCKDGMMVDSQVITPENEVD 569
                                       4455699***************987666 PP

>> DUF3876  Domain of unknown function, B. Theta Gene description (DUF3876)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00073       2.2       6      33 ..      69      96 ..      65     114 .. 0.82
   2 ?    0.9   0.0      0.16   4.8e+02       9      38 ..     177     206 ..     171     215 .. 0.82
   3 ?    0.4   0.0      0.23     7e+02       9      38 ..     282     311 ..     277     342 .. 0.76
   4 ?    3.5   0.0     0.025        76       8      35 ..     386     413 ..     382     432 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00073
                           DUF3876  6 eskeleklvGeWesvegkPdvllyeegk 33
                                      + ++l ++vG W+ +e +Pd +l ++++
  gi|330506836|ref|YP_004383264.1| 69 AYQNLATIVGIWQNSEDNPDRILINKSQ 96
                                      568999**************99988765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.16
                           DUF3876   9 eleklvGeWesvegkPdvllyeegkkykvt 38 
                                       +l ++   W+ ++ +Pd +l +++ + +++
  gi|330506836|ref|YP_004383264.1| 177 DLVTIDRIWQNSKDNPDRILINDSRSMTLS 206
                                       56666678************9999887765 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.23
                           DUF3876   9 eleklvGeWesvegkPdvllyeegkkykvt 38 
                                       +l ++ G W+ +   P  +l ++ +  +v+
  gi|330506836|ref|YP_004383264.1| 282 SLAMIDGIWQTSGMDPYRILINDTQLRTVS 311
                                       678899**********99998887766655 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.025
                           DUF3876   8 keleklvGeWesvegkPdvllyeegkky 35 
                                       ++l +  G W+ +e +Pd++l  +  + 
  gi|330506836|ref|YP_004383264.1| 386 QNLATADGLWQTSEVNPDLILIDDPRSR 413
                                       56677789************99876655 PP

>> GUN4  GUN4-like
   #    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      41      67 ..     161     187 ..     151     191 .. 0.84
   2 ?    0.8   0.0      0.16   4.9e+02      36      67 ..     261     292 ..     251     298 .. 0.86
   3 ?   -2.2   0.0       1.4     4e+03      44      66 ..     374     396 ..     361     398 .. 0.79
   4 ?    0.9   0.0      0.15   4.4e+02      41      67 ..     476     502 ..     459     504 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00049
                                       HHTS--HHHHHTS-HHHHHHHHHHHHH CS
                              GUN4  41 krgwlyfeevenfpvedlktidkLWvk 67 
                                       ++  ++f++v + p +dl tid++W++
  gi|330506836|ref|YP_004383264.1| 161 HEILIHFKNVLRTPDQDLVTIDRIWQN 187
                                       566789*******************86 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.16
                                       -HHHHHHTS--HHHHHTS-HHHHHHHHHHHHH CS
                              GUN4  36 geeavkrgwlyfeevenfpvedlktidkLWvk 67 
                                       + ea+++ +++f++  +   ++l++id +W++
  gi|330506836|ref|YP_004383264.1| 261 QAEASNQIKVHFKNAYRGTDHSLAMIDGIWQT 292
                                       5567788999999999999***********86 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.4
                                       S--HHHHHTS-HHHHHHHHHHHH CS
                              GUN4  44 wlyfeevenfpvedlktidkLWv 66 
                                        ++f++  + + ++l+t d LW+
  gi|330506836|ref|YP_004383264.1| 374 RVRFKNAFRGADQNLATADGLWQ 396
                                       567777777788999999***97 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.15
                                       HHTS--HHHHHTS-HHHHHHHHHHHHH CS
                              GUN4  41 krgwlyfeevenfpvedlktidkLWvk 67 
                                       ++  ++f++  + + ++++t+d+LW++
  gi|330506836|ref|YP_004383264.1| 476 QEIRVRFKNAFRGADQSMATVDSLWQT 502
                                       66778888888889999********85 PP

>> DUF2140  Uncharacterized protein conserved in bacteria (DUF2140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0033       9.8     132     185 ..      77     130 ..      73     132 .. 0.87
   2 ?    3.4   0.0     0.016        48     142     186 ..     402     446 ..     396     447 .. 0.87
   3 ?   -3.4   0.0         2   6.1e+03     145     185 ..     510     550 ..     507     551 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0033
                           DUF2140 132 LkyikksyklPewvkidpkkktilldlselklkeglkvkakkidLkndeiefel 185
                                         + ++s + P+ + i+ ++  il + +++kl+eg+++ +k++d++ d+i +el
  gi|330506836|ref|YP_004383264.1|  77 VGIWQNSEDNPDRILINKSQLIILSSKESIKLEEGYELFIKSMDIEGDKICLEL 130
                                       55667888999999999888888888899*********************9886 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.016
                           DUF2140 142 PewvkidpkkktilldlselklkeglkvkakkidLkndeiefely 186
                                       P+ + id  +++ + + ++l l+eg+k+ +++id+  ++++++ly
  gi|330506836|ref|YP_004383264.1| 402 PDLILIDDPRSRTMTSGTTLALEEGYKLAINSIDIDGNKVNLDLY 446
                                       77778887778888888999*********************9997 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2
                           DUF2140 145 vkidpkkktilldlselklkeglkvkakkidLkndeiefel 185
                                       + i+  +++ + + + lkl+eg+++ + +id+  +++ +el
  gi|330506836|ref|YP_004383264.1| 510 ILINDTRSQTITSGTPLKLEEGYELIIPSIDIDGNKLYLEL 550
                                       55666666666677789999999999999999999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.39
# Mc/sec: 4685.71
//
Query:       gi|330506837|ref|YP_004383265.1|  [L=272]
Description: imidazoleglycerol phosphate synthase, cyclase subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-76  256.8   0.3    1.8e-76  256.6   0.3    1.0  1  His_biosynth  Histidine biosynthesis protein
    3.3e-08   33.3   1.4    4.5e-05   23.0   0.3    2.3  2  NMO           Nitronate monooxygenase
    9.3e-08   31.7   0.4    0.00025   20.5   0.1    2.1  2  ThiG          Thiazole biosynthesis protein ThiG
    4.5e-07   29.3   0.0    6.2e-05   22.2   0.1    2.1  2  Dus           Dihydrouridine synthase (Dus)
    1.9e-05   24.1   0.3        0.1   11.9   0.1    2.3  2  TMP-TENI      Thiamine monophosphate synthase
    0.00051   19.1   0.5      0.019   14.0   0.2    2.1  2  IMPDH         IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.016   14.6   0.3       0.18   11.2   0.1    2.2  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
      0.055   12.3   0.1      0.085   11.7   0.1    1.4  1  Trp_syntA     Tryptophan synthase alpha chain


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.6   0.3   7.8e-80   1.8e-76       1     229 []       6     255 ..       6     255 .. 0.94

  Alignments for each domain:
  == domain 1  score: 256.6 bits;  conditional E-value: 7.8e-80
                                       EEEEEEEE..ETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSE CS
                      His_biosynth   1 riipalDl..kdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfip 75 
                                       +i+p+lD+   dG+   +vkG++f +l+ +gdpv++a+ry+++gadel+++D++a++egr+++ d+ +++a++v+ip
  gi|330506837|ref|YP_004383265.1|   6 KIVPCLDVkvVDGQPS-VVKGVKFVDLKRQGDPVQFARRYQDQGADELVFLDITASHEGRKTMVDVARRVADAVDIP 81 
                                       59*****955588743.46********************************************************** PP

                                       EEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE......C............. CS
                      His_biosynth  76 vqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr......g............. 133
                                       + vGGGI +l+ ++++l+agadkv i+taavknp+++ke++e+fgs++i+va+Darr      g             
  gi|330506837|ref|YP_004383265.1|  82 FAVGGGIGTLDGIKQILDAGADKVGINTAAVKNPDFVKEASEAFGSDRITVAVDARRntnivpGvnvyeledgakaw 158
                                       *********************************************************665555166777888899*9 PP

                                       EEEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHH CS
                      His_biosynth 134 ykvaikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelk 210
                                       ++++i+g+re +g+da+++ +k+e+ gage+l t++drdGt  G+dl+ltk+++eav+ipv+asGG+++++++ e++
  gi|330506837|ref|YP_004383265.1| 159 FELVIYGGREPVGVDAIDWCRKMESFGAGELLPTSMDRDGTNIGYDLPLTKAICEAVSIPVTASGGASTPQHILEAF 235
                                       ***************************************************************************** PP

                                       HTTC.SEEEESHHHHTTSS- CS
                      His_biosynth 211 segv.davivgsalyegelt 229
                                       +  + + ++++ +++ ge+t
  gi|330506837|ref|YP_004383265.1| 236 TVAKvEKALAAGMFHRGEYT 255
                                       77777************986 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.3     2e-08   4.5e-05     156     224 ..      48     110 ..      37     125 .. 0.80
   2 !    9.3   0.0    0.0003      0.67     182     212 ..     205     235 ..     169     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2e-08
                               NMO 156 GaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                       GaD l+     a  h+G +    k  + +  +v+davdiP    GGi +  g++ +L +GA  v i t+
  gi|330506837|ref|YP_004383265.1|  48 GADELVFLDITA-SHEG-R----KTMVDVARRVADAVDIPFAVGGGIGTLDGIKQILDAGADKVGINTA 110
                                       555555554444.3555.3....4478999***********************************9998 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0003
                               NMO 182 faLvpqvldavdiPviAaGGiidrrgvaaaL 212
                                       + L + + +av+iPv A GG  + + +  a+
  gi|330506837|ref|YP_004383265.1| 205 LPLTKAICEAVSIPVTASGGASTPQHILEAF 235
                                       678899**************98877776555 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   1.1e-07   0.00025     134     218 ..      38     122 ..      24     144 .. 0.80
   2 !    9.5   0.0   0.00024      0.53     136     194 ..     177     235 ..     159     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHTT-SEBEEBSSSTTS----S-HHHH.HHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHT CS
                              ThiG 134 lvlarrleevGcaavmPlaapiGsglGllnkeal.kiiieeakvPvivDAGigspsdaaqamelGadavllntavae 209
                                       + +arr ++ G+  ++ l     s +G +++  + + + + +++P  v  Gig+   + q ++ Gad v +nta  +
  gi|330506837|ref|YP_004383265.1|  38 VQFARRYQDQGADELVFLD-ITASHEGRKTMVDVaRRVADAVDIPFAVGGGIGTLDGIKQILDAGADKVGINTAAVK 113
                                       4478999999998888664.4568889988877625567777*********************************99 PP

                                       SSSHHHHHH CS
                              ThiG 210 akdpvamAr 218
                                         d v+ A+
  gi|330506837|ref|YP_004383265.1| 114 NPDFVKEAS 122
                                       999998774 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00024
                                       HHHHHHHTT-SEBEEBSS.STTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHH CS
                              ThiG 136 larrleevGcaavmPlaa.piGsglGllnkealkiiieeakvPvivDAGigspsdaaqam 194
                                        +r++e  G+  ++P +    G++ G   +   k i+e +++Pv    G  +p+++ +a+
  gi|330506837|ref|YP_004383265.1| 177 WCRKMESFGAGELLPTSMdRDGTNIGYDLPL-TKAICEAVSIPVTASGGASTPQHILEAF 235
                                       69*************9862579****98775.699********************99986 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   2.8e-08   6.2e-05     123     232 ..      19     128 ..       4     144 .. 0.82
   2 !    5.1   0.0    0.0047        11     174     202 ..     207     235 ..     179     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.8e-08
                                       S-EEEEEESESS.TTTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHH CS
                               Dus 123 iPvtvkirigid.deeenalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaeda 198
                                        P  vk   ++d + + + +++a++ +++Ga++l+    t+ ++ ++t   +  + v +av ip+ + G+I +++ +
  gi|330506837|ref|YP_004383265.1|  19 QPSVVKGVKFVDlKRQGDPVQFARRYQDQGADELVFLDITASHEGRKT-MVDVARRVADAVDIPFAVGGGIGTLDGI 94 
                                       66667766677777888999**************99888888777774.3456689********************* PP

                                       HHHHHHH--SEEEESCHHCCSTTHHHH.HHHHHHS CS
                               Dus 199 qaileetGadgvmigrgalgnPwlfae.stavktg 232
                                       ++il+  Gad v i  +a +nP +++e s+a+  +
  gi|330506837|ref|YP_004383265.1|  95 KQILDA-GADKVGINTAAVKNPDFVKEaSEAFGSD 128
                                       *****9.******************9866665554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0047
                                       HHHHHHHH-SS-EEEESS--SHHHHHHHH CS
                               Dus 174 aIkevkqavsipviaNGdIkdaedaqail 202
                                         k++++avsipv a G+  +++ + ++ 
  gi|330506837|ref|YP_004383265.1| 207 LTKAICEAVSIPVTASGGASTPQHILEAF 235
                                       5689**************99998887665 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   4.5e-05       0.1     110     176 ..      42     106 ..      36     111 .. 0.80
   2 !   10.2   0.0   0.00016      0.35     120     161 ..     184     227 ..     178     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.5e-05
                          TMP-TENI 110 eeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGi.tlenvaevleagadgva 176
                                       ++ +++gad +++  i  T+++++++   ++ ++++a+a+ iP+ + GGi tl+ ++++l+agad v 
  gi|330506837|ref|YP_004383265.1|  42 RRYQDQGADELVFLDI--TASHEGRK-TMVDVARRVADAVDIPFAVGGGIgTLDGIKQILDAGADKVG 106
                                       5667777777777777..77887774.4478899****************55789**********986 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00016
                          TMP-TENI 120 igvGpifpTdtKkdaeplgle..glkelaealeiPvvaiGGitl 161
                                       +g+G + pT+   d + +g +  + k+++ea++iPv a GG ++
  gi|330506837|ref|YP_004383265.1| 184 FGAGELLPTSMDRDGTNIGYDlpLTKAICEAVSIPVTASGGAST 227
                                       799********99998887652268****************754 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2   8.5e-06     0.019     112     174 ..      44     107 ..      31     120 .. 0.76
   2 ?    3.4   0.0     0.014        31     201     228 ..     210     237 ..     205     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.5e-06
                                       HHHTT-SEEE.EE-..STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-S CS
                                       xxxxxxxxxx.xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 112 lveagvdvlv.vds..ahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvGi 174
                                         ++g+d lv +d+  +h   ++++++ +++ ++v+    ++G + t +g+k++++agad v  Gi
  gi|330506837|ref|YP_004383265.1|  44 YQDQGADELVfLDItaSHEGRKTMVDVARRVADAVDIPFAVGGGIGTLDGIKQILDAGADKV--GI 107
                                       55667774443565115666788999999999999545679*******************65..54 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.014
                                       HHHCTCT-EEEEES---SHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 201 eaakkagvpviaDGGikysgdivkAlaa 228
                                       ++++   +pv a GG ++ ++i  A+++
  gi|330506837|ref|YP_004383265.1| 210 AICEAVSIPVTASGGASTPQHILEAFTV 237
                                       5688899****************99876 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   8.2e-05      0.18     127     167 ..      67     107 ..      65     112 .. 0.91
   2 ?    1.1   0.0       0.1   2.3e+02     131     158 ..     208     235 ..     202     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.2e-05
                                       GHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                      G3P_antiterm 127 vpkvikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                       + +v++++ ++++ip+  GG i t + ++++l+aGa+ v  
  gi|330506837|ref|YP_004383265.1|  67 MVDVARRVADAVDIPFAVGGGIGTLDGIKQILDAGADKVGI 107
                                       78999*******************************99865 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.1
                                       HCTSTTS...EEEEESS--SHHHHHHHC CS
                      G3P_antiterm 131 ikeikkelkipiiaGGLietkedveeal 158
                                       +k+i+++++ip+ a+G  +t +++ ea+
  gi|330506837|ref|YP_004383265.1| 208 TKAICEAVSIPVTASGGASTPQHILEAF 235
                                       68899***********999999988876 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.8e-05     0.085     185     232 ..      66     114 ..      40     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.8e-05
                                       THHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHH CS
                         Trp_syntA 185 evdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkk 232
                                       ++ ++ +r+ ++ + P avG Gi t + +kq+  ++ad v +  a vk+
  gi|330506837|ref|YP_004383265.1|  66 TMVDVARRVADAVDIPFAVGGGIGTLDGIKQILdAGADKVGINTAAVKN 114
                                       45567799999**********************9****99998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2152.54
//
Query:       gi|330506838|ref|YP_004383266.1|  [L=374]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-22   78.2   0.0    1.2e-21   77.2   0.0    1.5  1  OrfB_IS605      Probable transposase
    1.4e-21   76.2   0.1    3.5e-21   74.9   0.1    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.5e-19   68.5   2.3    5.3e-19   67.4   2.3    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.7   0.2       0.02   14.9   0.2    1.4  1  DZR             Double zinc ribbon
        1.7    8.3   4.7         16    5.1   0.1    3.1  3  RecR            RecR protein


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.0   3.3e-25   1.2e-21       3     117 ..     165     277 ..     163     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 3.3e-25
                        OrfB_IS605   3 pveveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        ve+e++ +p+ k ++ +g+D+G++ +at+++++   ++ ++r++++++k+la+ ++++++  k++  +kka r + 
  gi|330506838|ref|YP_004383266.1| 165 SVEIEDQlKPPWKDGSLVGVDVGLESFATLSNGE---TIANPRFFREEEKELARVQRKISKAPKGTPERKKALRMVE 238
                                       6899999666779999******************...**************************************** PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       r+h++++++r +++hk++++l+++   ++ e+L ++nm 
  gi|330506838|ref|YP_004383266.1| 239 RVHERIANKRYDFAHKVSRYLVNRFGLIAFEDLSIQNML 277
                                       *************************************97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.1   9.9e-25   3.5e-21       1      68 [.     291     358 ..     291     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 9.9e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++ l +  +yka  +G  v++v+p++TSk Cs+Cg  ++++ls+r+++C++Cg+++drD+nAaiNil+
  gi|330506838|ref|YP_004383266.1| 291 WNMLVTLTSYKAASAGSMVVLVDPRNTSKMCSRCGILVEKTLSNRVHNCTQCGLSLDRDWNAAINILR 358
                                       667777889*********************************************************97 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   2.3   1.5e-22   5.3e-19       1      47 []       1      46 [.       1      46 [. 0.99

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 1.5e-22
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkayk+r+yPT+ Q++k++rt++ +R+ YN+ La+rk+a+e+egk
  gi|330506838|ref|YP_004383266.1|  1 M-LKAYKFRIYPTKSQRTKMERTLDLCRWTYNQTLAYRKDAWEKEGK 46
                                      8.*******************************************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   5.6e-06      0.02      10      44 ..     316     352 ..     312     355 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.6e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + +++Cs+Cg  ++++ +   ++C +Cg ++d +++ 
  gi|330506838|ref|YP_004383266.1| 316 NTSKMCSRCGILVEKTLSnrVHNCTQCGLSLDRDWNA 352
                                       6789*********9877799************99986 PP

>> RecR  RecR protein
   #    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       5      16 ..      71      82 ..      69      84 .. 0.89
   2 ?    5.1   0.1    0.0046        16      13      28 ..     315     330 ..     310     332 .. 0.76
   3 ?    3.4   0.6     0.016        58      12      23 ..     332     343 ..     330     349 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.24
                                      HHHHHHHHHHH- CS
                              RecR  5 LaeaLqeakekv 16
                                      ++++Lq+a e+v
  gi|330506838|ref|YP_004383266.1| 71 FSQTLQNAQERV 82
                                      89*******998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0046
                                       HHH-EE-TTT--EESS CS
                              RecR  13 kekvrhCsrCgnltee 28 
                                       +++ + CsrCg l e+
  gi|330506838|ref|YP_004383266.1| 315 RNTSKMCSRCGILVEK 330
                                       667799*****99776 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.016
                                       HHHH-EE-TTT- CS
                              RecR  12 akekvrhCsrCg 23 
                                       + ++v+ C +Cg
  gi|330506838|ref|YP_004383266.1| 332 LSNRVHNCTQCG 343
                                       5689*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 2715.28
//
Query:       gi|330506839|ref|YP_004383267.1|  [L=177]
Description: ammonium transporter N-terminal protein, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-26   92.5  12.1    3.1e-26   92.0  12.1    1.2  1  Ammonium_transp  Ammonium Transporter Family
  ------ inclusion threshold ------
      0.066   13.0   0.1       0.11   12.2   0.1    1.3  1  Connexin         Connexin
        0.4   10.9  20.4          3    8.1  10.2    3.7  2  TrbC             TrbC/VIRB2 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 !   92.0  12.1   5.3e-30   3.1e-26       1     117 [.      49     170 ..      49     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 5.3e-30
                                       HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCB......SSSSSCE-TT CS
                   Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgksk......gvsgfignlg 71 
                                       a+ l+ a+lv+fmqagfa+l ag  r kn++n + k+ +d+ ++ l+y+++G++l+fg sk      +++++ig+ g
  gi|330506839|ref|YP_004383267.1|  49 AWTLIGAFLVFFMQAGFAFLGAGALRVKNTVNYFAKSYMDFSIGALAYWAVGFALMFGGSKlyagleDGNSIIGWSG 125
                                       799*******************************************************9965554456899999988 PP

                                       TTSCCGCCTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHH CS
                   Ammonium_transp  72 lsaagvqdetlldglfflfqlafaataitivsgavaerikfsayll 117
                                        +++g + +    ++f++fq++faata+tiv ga aer+k+ ayl+
  gi|330506839|ref|YP_004383267.1| 126 CFLSGNSYDVS-TMMFWMFQVVFAATAATIVAGACAERMKLQAYLM 170
                                       88777777555.6678****************************96 PP

>> Connexin  Connexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.9e-05      0.11      68      99 ..     133     164 ..     125     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                          Connexin  68 fpishvrfwvlqiilvstPsllylvyvlhkia 99 
                                         +s + fw++q+++ +t   ++ +  + +++
  gi|330506839|ref|YP_004383267.1| 133 YDVSTMMFWMFQVVFAATAATIVAGACAERMK 164
                                       5799*****************99998887765 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  10.2    0.0005         3       8      98 ..       4     113 ..       1     114 [. 0.79
   2 ?    3.4   2.5     0.014        86      62      98 ..     121     157 ..     118     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0005
                              TrbC   8 arrlllalalalvllllaspalAqaagg.....dpve..tvlqnivdfltgplakviatiaiivaGimlafgrls.. 75 
                                        + + +a+ ++++llll++ a+A +++g     d+v   +++ n+  +l g +  + +  +++++G++++  +    
  gi|330506839|ref|YP_004383267.1|   4 TKYTNIAASAFVLLLLLTTIAMAGDPNGsntytDDVAgmKLAVNFAWTLIGAFLVFFMQAGFAFLGAGALRVKNTvn 80 
                                       55667888999999999999999999999988855551245777888888878888888888888888777776688 PP

                              TrbC  76 ..........wrtlvmvviGiviifgAssivst 98 
                                                 +++l+++++G +++fg+s++ ++
  gi|330506839|ref|YP_004383267.1|  81 yfaksymdfsIGALAYWAVGFALMFGGSKLYAG 113
                                       9999999999999************99999775 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.014
                              TrbC  62 iivaGimlafgrlswrtlvmvviGiviifgAssivst 98 
                                       i ++G  l  +  ++ t++ + + +v++  A++iv++
  gi|330506839|ref|YP_004383267.1| 121 IGWSGCFLSGNSYDVSTMMFWMFQVVFAATAATIVAG 157
                                       667788888888889*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.56
# Mc/sec: 954.53
//
Query:       gi|330506840|ref|YP_004383268.1|  [L=314]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-23   81.4   0.0    6.3e-23   80.6   0.0    1.4  1  DUF772       Transposase domain (DUF772)
      3e-17   63.0   0.7    6.5e-17   61.9   0.7    1.6  1  DDE_Tnp_1    Transposase DDE domain
    4.6e-06   26.4   0.3    1.6e-05   24.6   0.0    1.9  2  DDE_Tnp_4    DDE superfamily endonuclease
    1.9e-05   24.7   0.1    4.9e-05   23.4   0.1    1.6  1  DDE_Tnp_1_3  Transposase DDE domain
  ------ inclusion threshold ------
      0.055   14.1   0.0       0.23   12.1   0.0    1.9  2  DUF3502      Domain of unknown function (DUF3502)
        0.1   12.4   0.1       0.29   11.0   0.1    1.8  1  DUF5315      Disordered region of unknown function (DUF5315)


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 !   80.6   0.0   2.1e-26   6.3e-23       1      72 [.      51     122 ..      51     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 2.1e-26
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp++++ +mlk l++q+ly+lSd++le+++ +++sfr flg     ++vpd +t+++fR+rl+e   ++++++e
  gi|330506840|ref|YP_004383268.1|  51 GRPNLDVIVMLKSLFIQQLYSLSDEQLEREIADRISFRVFLGT---TETVPDSTTIWKFRERLAEtgaDQKIWAE 122
                                       9*****************************************5...489****************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 !   61.9   0.7   2.2e-20   6.5e-17       9     213 ..     140     301 ..     132     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 2.2e-20
                         DDE_Tnp_1   9 vDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                        Dat+++    +                +d+ w +kg k+++gyklh a+d + gli ++++t++nvhds++  +  
  gi|330506840|ref|YP_004383268.1| 140 QDATFITSDPGHakadtprgdeaktrrsKDGAWAKKGTKSFFGYKLHDAMDEKFGLIRRIEVTAANVHDSQVDLA-- 214
                                       5777777555557777778888888888999***************************************98555.. PP

                         DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskk 146
                                       +     +g + +aD+GY++a++  + +                            +rk+ r+++l+ +++ rnk   
  gi|330506840|ref|YP_004383268.1| 215 E-----EGEVRYADKGYSGAKTKGYDA---------------------------AMRKATRGHPLSYKDEMRNK--- 256
                                       6.....9***********888877766...........................79******************... PP

                         DDE_Tnp_1 147 ekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllaln 213
                                                             +++++R+ +Er+ +++k +++ +++ + + +rv+ +++++ +++n
  gi|330506840|ref|YP_004383268.1| 257 ----------------------RISSKRSPVERFYAFIKCVCKAGHVAVTTVARVRVKMMITGIVFN 301
                                       ......................***************************************999988 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.38   1.1e+03      55      95 ..     116     151 ..     113     171 .. 0.63
   2 !   24.6   0.0   5.4e-09   1.6e-05      71     128 ..     211     273 ..     186     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.38
                         DDE_Tnp_4  55 Dkeilens.gllkalkeavkpgdvilaDkgFklsekllvpyk 95 
                                       D++i+++  + l+a+k  +k ++ i+ D+ F +s+    p +
  gi|330506840|ref|YP_004383268.1| 116 DQKIWAEMqRQLDAMK--LKVQKGIMQDATFITSD----PGH 151
                                       6777766546677766..45558889999998888....333 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 5.4e-09
                         DDE_Tnp_4  71 a..vkpgdvilaDkgFklse..kl.lvpykkkkkkqlseeevefnraiasarihvErvigrlk 128
                                           ++g+v  aDkg+ +++   +   + k +++++ls +++ +n++i+s r  vEr+ + +k
  gi|330506840|ref|YP_004383268.1| 211 VdlAEEGEVRYADKGYSGAKtkGYdAAMRKATRGHPLSYKDEMRNKRISSKRSPVERFYAFIK 273
                                       1445688999********99432223444449***************************9999 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 !   23.4   0.1   1.6e-08   4.9e-05      33     149 ..     173     280 ..     161     285 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.6e-08
                       DDE_Tnp_1_3  33 akrGkssmGWfyGfkLhliindk.GeilavkltpgnvdDrepveelakellgklfaDkgyiskklaeelleegieli 108
                                       a   k  +  f+G+kLh  +++k G i ++++t++nv+D +   +la+e  +  +aDkgy + k        + ++ 
  gi|330506840|ref|YP_004383268.1| 173 A---KKGTKSFFGYKLHDAMDEKfGLIRRIEVTAANVHDSQV--DLAEE-GEVRYADKGYSGAKTK----GYDAAMR 239
                                       3...4444559******9999883556679*********875..36666.4566******876532....2344455 PP

                       DDE_Tnp_1_3 109 tklrknmkkkllslldkllLrkrslietvndelknisqieh 149
                                         +r +  +   ++ +k + +krs +e  +  +k +++  h
  gi|330506840|ref|YP_004383268.1| 240 KATRGHPLSYKDEMRNKRISSKRSPVERFYAFIKCVCKAGH 280
                                       55555555555666666667777777777777776666655 PP

>> DUF3502  Domain of unknown function (DUF3502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.8e-05      0.23     100     127 ..     101     129 ..      81     131 .. 0.87
   2 ?   -0.9   0.0      0.79   2.4e+03      35      96 ..     237     299 ..     205     310 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.8e-05
                           DUF3502 100 etlpkfneklkaaGid.kviaelqkQlda 127
                                       +t+ kf+e+l + G d k+ ae+q+Qlda
  gi|330506840|ref|YP_004383268.1| 101 TTIWKFRERLAETGADqKIWAEMQRQLDA 129
                                       67889*********9758**********8 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.79
                           DUF3502  35 firyllegepedkwekvkefneeakaspalgF.tfDsspvkteiaalsnvveeykkaletGlv 96 
                                        +r+ ++g+p +  +++++   ++k sp+  F +f +   k+   a+++v    +k + tG+v
  gi|330506840|ref|YP_004383268.1| 237 AMRKATRGHPLSYKDEMRNKRISSKRSPVERFyAFIKCVCKAGHVAVTTVARVRVKMMITGIV 299
                                       344444555555555566665667777777762344444555566666666666666666655 PP

>> DUF5315  Disordered region of unknown function (DUF5315)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   9.8e-05      0.29      12      36 ..     115     141 ..     107     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.8e-05
                           DUF5315  12 rqDalWaeid.tLddVklsAeeg.kkt 36 
                                          ++Wae++ +Ld  kl  ++g +++
  gi|330506840|ref|YP_004383268.1| 115 ADQKIWAEMQrQLDAMKLKVQKGiMQD 141
                                       56799*************999985544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); 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:                         6  (0.000334653); expected 0.2 (1e-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 0.33s 00:00:01.00 Elapsed: 00:00:00.57
# Mc/sec: 1663.65
//
Query:       gi|330506841|ref|YP_004383269.1|  [L=270]
Description: ammonium transporter C-terminal protein, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-76  257.8  15.2    1.5e-76  257.6  15.2    1.0  1  Ammonium_transp  Ammonium Transporter Family
  ------ inclusion threshold ------
      0.022   14.0   0.2      0.032   13.5   0.2    1.2  1  PEP_hydrolase    Phosphoenolpyruvate hydrolase-like
       0.64    9.9   0.0       0.64    9.9   0.0    3.3  3  LapA_dom         Lipopolysaccharide assembly protein A domain
          6    6.6   9.4        3.3    7.5   6.5    2.1  2  PAP2             PAP2 superfamily


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 !  257.6  15.2   3.4e-80   1.5e-76     159     399 .]       1     240 [.       1     240 [. 0.97

  Alignments for each domain:
  == domain 1  score: 257.6 bits;  conditional E-value: 3.4e-80
                                       HHHHHHHHHHHHHS-STTTTG..TTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.HHHHHHHHHHH CS
                   Ammonium_transp 159 vggvagLaaalvlgkregrfe..gkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrararaavtTllAaaa 233
                                       +gg+++La++++lg+r+g+f+  g ++ai+gh++p++v+Gt++L fgWfgFN++s+l+a++ + +++av+T lA+aa
  gi|330506841|ref|YP_004383269.1|   1 MGGMVALAGIYLLGPRIGKFNkdGVPNAIPGHDVPMIVMGTFFLFFGWFGFNPASTLAATDLRISVIAVNTFLAGAA 77 
                                       59******************99999**************************************************** PP

                                       HHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTC-CTTHHHHH CS
                   Ammonium_transp 234 galtallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklkidDsldvvav 310
                                       ga  ++  + +k++k+++  ++nG+lAGlV+iTa+ca+v +w+A++iG+v+g+++++g+k+    lk+dD++++vav
  gi|330506841|ref|YP_004383269.1|  78 GATLVCYYTFFKTKKVDIALTCNGALAGLVGITASCAYVPTWAAVVIGVVSGFIVMYGIKFNDWVLKVDDPVGAVAV 154
                                       ***********************************************************9777789*********** PP

                                       HHHHHHHHHHHHHHHTSHHHCSSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB--HHHHHH CS
                   Ammonium_transp 311 HgvgGiwGllavgifaaekvvaskisggllsgegkqlvvqligilvilayafvvtlilllllklllgLrvseeeeev 387
                                       Hg  G+wGll+vgifa+     ++  +gl+ g+++q+++q+i ++v++++af++++il++++k+++gLrvs+eee +
  gi|330506841|ref|YP_004383269.1| 155 HGYNGLWGLLTVGIFADGT---YGGVSGLIVGNTSQIIAQIIDMVVVVVWAFGTGYILFYIIKKIVGLRVSPEEELT 228
                                       *****************98...4578889999999****************************************** PP

                                       SHHHHHHSSSSB CS
                   Ammonium_transp 388 glDvaehgetay 399
                                       glD+ ehg +ay
  gi|330506841|ref|YP_004383269.1| 229 GLDLGEHGYSAY 240
                                       ********9998 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   7.2e-06     0.032      50     123 ..      99     173 ..      71     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.2e-06
                     PEP_hydrolase  50 GrgslagllpygnaNeivvemakevlpvvketpvlaGvcatDpfrkleeflkelkelGfaGvqNfPtvgli.dge 123
                                        +g+lagl+ +  + + v   a+ v+ vv+   v+ G+  +D + k+++ +  +   G++G+    tvg++ dg+
  gi|330506841|ref|YP_004383269.1|  99 CNGALAGLVGITASCAYVPTWAAVVIGVVSGFIVMYGIKFNDWVLKVDDPVGAVAVHGYNGLWGLLTVGIFaDGT 173
                                       5799****************************************************************9863555 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00014      0.64      14      47 ..      59      92 ..      54      96 .. 0.90
   2 ?    1.9   0.3     0.043   1.9e+02      25      40 ..     120     135 ..     115     142 .. 0.83
   3 ?   -0.9   1.1      0.33   1.5e+03      19      35 ..     195     211 ..     188     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00014
                          LapA_dom 14 qvelpLsllllvafgiGallgwllslwsylrlrr 47
                                       ++l++s++ + +f++Ga  + l+++++ +++++
  gi|330506841|ref|YP_004383269.1| 59 ATDLRISVIAVNTFLAGAAGATLVCYYTFFKTKK 92
                                      45899**********************9999875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.043
                          LapA_dom  25 vafgiGallgwllslw 40 
                                       +a++iG++ g+++++ 
  gi|330506841|ref|YP_004383269.1| 120 AAVVIGVVSGFIVMYG 135
                                       6899999999999985 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.33
                          LapA_dom  19 LsllllvafgiGallgw 35 
                                        +++++ afg G +l +
  gi|330506841|ref|YP_004383269.1| 195 MVVVVVWAFGTGYILFY 211
                                       57999999999998865 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   6.5   0.00075       3.3      64     128 ..      75     137 ..      37     143 .. 0.89
   2 ?   -1.3   0.0      0.38   1.7e+03       5      18 ..     199     212 ..     180     234 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00075
                              PAP2  64 afalalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaalay 128
                                       ++a+a+l++++   k kk    +++++  +la lv+++  +++v ++ +v++G++ G+++ + ++
  gi|330506841|ref|YP_004383269.1|  75 GAAGATLVCYYTFFKTKK--VDIALTCNGALAGLVGITASCAYVPTWAAVVIGVVSGFIVMYGIK 137
                                       577888888888888888..4688888889999**************************998776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.38
                              PAP2   5 lllalalaalltsv 18 
                                       ++ a ++ ++l  +
  gi|330506841|ref|YP_004383269.1| 199 VVWAFGTGYILFYI 212
                                       22222222222223 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1910.06
//
Query:       gi|330506842|ref|YP_004383270.1|  [L=112]
Description: nitrogen regulatory protein P-II [Methanosaeta concilii GP6]
Scores for complete 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  137.7   1.4      2e-40  137.5   1.4    1.0  1  P-II       Nitrogen regulatory protein P-II
     0.0046   17.1   0.4      0.098   12.9   0.4    2.5  1  CdAMP_rec  Cyclic-di-AMP receptor


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 !  137.5   1.4   2.2e-44     2e-40       1     102 []       4     105 ..       4     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 137.5 bits;  conditional E-value: 2.2e-44
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       i+aiirp+k+eevk+aL++ag+++lt +e+kGrG+qkg t++ rg+ey+v++lpkvk+e+vv+d++ ++vve+i ka
  gi|330506842|ref|YP_004383270.1|   4 IQAIIRPSKVEEVKNALDEAGYTSLTSIEIKGRGRQKGITQIWRGEEYQVDMLPKVKVELVVPDDKEDEVVEIIRKA 80 
                                       89*************************************************************************** PP

                                       H-SSSTTSEEEEEEEESEEEETTTT CS
                              P-II  78 aktgeiGDGkiFvlpveevirirtg 102
                                       a tg+iGDGkiFvlpve++irirtg
  gi|330506842|ref|YP_004383270.1|  81 AYTGNIGDGKIFVLPVEKTIRIRTG 105
                                       ************************8 PP

>> CdAMP_rec  Cyclic-di-AMP receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.4   1.1e-05     0.098       1     108 [.       1     101 [.       1     102 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                                       EEEEEEEEEHHHHHHHHHHHHHTT-EE.EEEEEEETTT-SEEEEEEEEEEGGGHHHHHHHHHHC---EEEE-----T CS
                         CdAMP_rec   1 mklviaivqdedanelvdalteknfka.tklattGGflkeGnttlliGvedekvdevlsiikekcktreqlvasssp 76 
                                       mk++ ai++ + ++e+ +al e+++++ t +   G   ++G t +  G e+ +vd +        k + +lv +  +
  gi|330506842|ref|YP_004383270.1|   1 MKMIQAIIRPSKVEEVKNALDEAGYTSlTSIEIKGRGRQKGITQIWRG-EEYQVDMLP-------KVKVELVVPDDK 69 
                                       9***********************975277777777777887777776.667787654.......446678888888 PP

                                       TTTTTTT--SS--EEEEESEEEEEEE-SEEEE CS
                         CdAMP_rec  77 lgesadsyvpkpvevevGGatvfvldvekfvk 108
                                         e  ++  + +   ++G   +fvl+vek ++
  gi|330506842|ref|YP_004383270.1|  70 EDEVVEIIRKAAYTGNIGDGKIFVLPVEKTIR 101
                                       88888888888999999999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 852.53
//
Query:       gi|330506843|ref|YP_004383271.1|  [L=100]
Description: hypothetical protein MCON_0625 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 735.78
//
Query:       gi|330506844|ref|YP_004383272.1|  [L=209]
Description: hypothetical protein MCON_0626 [Methanosaeta concilii GP6]
Scores for complete 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   29.9  19.2    3.7e-07   29.4  19.2    1.2  1  MFS_1            Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.073   11.8   7.2       0.01   14.6   3.1    1.6  2  AftA_N           Arabinofuranosyltransferase N terminal
      0.098   12.4   0.5       0.17   11.6   0.4    1.4  1  TMEM174          Transmembrane protein 174


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4  19.2   6.2e-11   3.7e-07       4     178 ..      22     194 ..      17     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 6.2e-11
                             MFS_1   4 aaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       ++f    +++++++a ++ ++ + +g+s+++++  +++ a++++++ ++++r+s ++ rr+++++++++ ++++ll+
  gi|330506844|ref|YP_004383272.1|  22 ILFSLPSMSALAFIASSSyIYINGFGLSAQVYSYYYAINAIAMIFGPMLYMRVSRKCHRRSIIIVCFAAISASGLLI 98 
                                       455555555666666666677899*********************************99996666666666665888 PP

                             MFS_1  80 lfa..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       +f+   + w+l ++ + + +++ ++ + ga l+ +   + + g+a +l+s ++ +   +g+ +    + sl+W+ + 
  gi|330506844|ref|YP_004383272.1|  99 SFVggFQPWILTIVLLPATICGNCVRTPGANLMLEQQRE-DTGSAAALMSFSSIFIGSIGMTI----I-SLNWSNTI 169
                                       887565567788888899999999999999999987776.88888877777655555555444....4.588***** PP

                             MFS_1 155 yilaivsllafv.lfllllpeeppe 178
                                       ++l+i+ +l ++ + +l+l+ ++++
  gi|330506844|ref|YP_004383272.1| 170 LVLGIMNILIGLvCEALWLRISQKP 194
                                       *********9887878888877766 PP

>> AftA_N  Arabinofuranosyltransferase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   3.1   1.7e-06      0.01     231     296 ..      46     112 ..      18     124 .. 0.83
   2 ?   -1.7   0.1      0.15   9.2e+02     271     286 ..     167     182 ..     136     204 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-06
                            AftA_N 231 lGlsatlYtLytgvaalavvlvalvvavarvraerslkpllrllvigvisiliali.vwgPYllavl 296
                                        Glsa +Y+ y +++a+a+++  ++ + ++++ +r+  +++ +++i+++ +li  + ++ P++l+++
  gi|330506844|ref|YP_004383272.1|  46 FGLSAQVYSYYYAINAIAMIFGPMLYMRVSRKCHRRSIIIVCFAAISASGLLISFVgGFQPWILTIV 112
                                       59******************999888888788888899999************99845999999876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.15
                            AftA_N 271 lrllvigvisiliali 286
                                        ++lv+g++ ili l+
  gi|330506844|ref|YP_004383272.1| 167 NTILVLGIMNILIGLV 182
                                       3333444444444333 PP

>> TMEM174  Transmembrane protein 174
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   2.8e-05      0.17      20      53 ..     134     167 ..     124     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.8e-05
                           TMEM174  20 aqvsdddkagatlLfsGifLglvGitftvlgWik 53 
                                       +q  d   a a + fs if+g +G+t+  l W +
  gi|330506844|ref|YP_004383272.1| 134 QQREDTGSAAALMSFSSIFIGSIGMTIISLNWSN 167
                                       55567777888899******************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); 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):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1514.14
//
Query:       gi|330506845|ref|YP_004383273.1|  [L=82]
Description: hypothetical protein MCON_0627 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-07   31.7   0.9    1.8e-07   31.2   0.9    1.1  1  rve_2     Integrase core domain
    7.1e-06   25.7   0.0    9.2e-06   25.4   0.0    1.1  1  rve_3     Integrase core domain


Domain annotation for each model (and alignments):
>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.9     2e-11   1.8e-07       5      48 ..      25      73 ..      24      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2e-11
                             rve_2  5 gsLKtElvygetfktleeleaaiedYIew.YNnkRlk....glsPvqYr 48
                                      ++LK+E vy  +++t+e +   i ++Ie  YN+kRl+    + sPvq++
  gi|330506845|ref|YP_004383273.1| 25 KTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHsalnYRSPVQFE 73
                                      68*************************988*****988888*******8 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0     1e-09   9.2e-06      24      67 .]      25      69 ..      21      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1e-09
                             rve_3 24 gtlrdellneelfrslaearekleawred.YNteRPHssLgykTP 67
                                      +tl+ e ++ + ++++++a +++ +++e  YN++R Hs+L+y++P
  gi|330506845|ref|YP_004383273.1| 25 KTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHSALNYRSP 69
                                      79999999***********99999999866*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 590.02
//
Query:       gi|330506846|ref|YP_004383274.1|  [L=436]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete 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   27.8   0.6    2.7e-05   23.8   0.6    2.1  1  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
       0.14   12.7   4.6       0.18   12.3   2.2    2.4  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.15   12.2   0.7        7.5    6.8   0.1    2.4  2  Zn-ribbon_8      Zinc ribbon domain
       0.21   11.2   0.6         12    5.6   0.1    2.4  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.27   11.3   2.8        1.3    9.1   3.1    1.9  2  DZR              Double zinc ribbon
       0.66   10.0   2.5        7.3    6.7   0.3    2.6  2  YhfH             YhfH-like protein
        6.2    6.4   5.5         77    2.9   5.5    2.4  1  TF_Zn_Ribbon     TFIIB zinc-binding


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 !   23.8   0.6     1e-08   2.7e-05     111     259 ..     188     381 ..     146     393 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1e-08
                      DDE_Tnp_IS66 111 sRggevaealLag.....fkGvlvsDgyagYnklae....eqvthalCwaHlrRkfvdaeeakkksqaaaealar.. 176
                                       s  ++++e +L        + ++v+D y gY+++ +    ++v h++C+ Hl   +v+   +k   ++ +e l++  
  gi|330506846|ref|YP_004383274.1| 188 SKDADTIEGFLRRnldtqKQIFIVTDLYRGYSNVFKrvfgNKVIHQFCLLHLNKLIVNDFPRKT--SIEQELLKYkm 262
                                       55566666666655554445699**********9999***************999887776643..44444444442 PP

                      DDE_Tnp_IS66 177 igklya.............ierearea...........eae.........erlalrqeesrpllaelea.wleeql. 218
                                       ++ +++              e+ +r +           e           + + +r++es+ l+++ ++  l++ + 
  gi|330506846|ref|YP_004383274.1| 263 LNIFFNreleieflstlieEEKMMR-QrsnkeykswiaE-AkhlfydfvrRLELRRRRESKNLEQRTYHeALNNFKf 337
                                       4444445555555555543233332.1233344334331.0333333442555666777788877655504444448 PP

                      DDE_Tnp_IS66 219 ...kkvlpksklgkairyllkrweallrfledgrvpidNNaaER 259
                                          ++ +    ++k ++++ + w++l+ f    + p +NN +E+
  gi|330506846|ref|YP_004383274.1| 338 lkmQSDSFMISVRKRLDKIEELWPNLTAFYFTDNAPATNNPIEN 381
                                       777666677789*******************************9 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2     7e-05      0.18       8      51 ..      44     118 ..      43     123 .. 0.62
   2 ?   -1.0   0.0      0.99   2.5e+03      14      29 ..     284     299 ..     282     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7e-05
                   Zn_ribbon_recom   8 CgeCGspmtr......rkrkgkr.......hyYrCstyrrkgk..................k.Csnh...sireekl 49 
                                       C eCG+pm++      +    kr         Y C+++ ++ +                  + C+     ++++e++
  gi|330506846|ref|YP_004383274.1|  44 CPECGHPMSHngfntcQ----KRhlgganvGKYLCGACGKSTEedrdfwiklktdffgivtEiCTRLrlnHVSYEVI 116
                                       **********5543322....22355558889999988766655556666666666665531466544556666666 PP

                   Zn_ribbon_recom  50 ee 51 
                                       e+
  gi|330506846|ref|YP_004383274.1| 117 ES 118
                                       65 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.99
                   Zn_ribbon_recom  14 pmtrrkrkgkrhyYrC 29 
                                       +m r+++++++  ++ 
  gi|330506846|ref|YP_004383274.1| 284 KMMRQRSNKEYKSWIA 299
                                       7999999999988875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0029       7.5      26      35 ..      40      50 ..      25      53 .. 0.60
   2 ?    3.3   0.1     0.035        90       6      17 ..      72      83 ..      71      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                       Zn-ribbon_8 26 lta.CPeCgse 35
                                       ++ CPeCg++
  gi|330506846|ref|YP_004383274.1| 40 VPPlCPECGHP 50
                                      3444****986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.035
                       Zn-ribbon_8  6 YrCeeCghefev 17
                                      Y C +Cg+  e+
  gi|330506846|ref|YP_004383274.1| 72 YLCGACGKSTEE 83
                                      89*****99885 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0046        12       4      14 ..      43      53 ..      43      57 .. 0.86
   2 ?    3.5   0.1     0.021        54       2      15 ..      71      84 ..      70      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0046
                            zf_UBZ  4 lCerCgkeipe 14
                                      lC++Cg+++++
  gi|330506846|ref|YP_004383274.1| 43 LCPECGHPMSH 53
                                      6*******987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.021
                            zf_UBZ  2 tylCerCgkeipes 15
                                       ylC  Cgk+ +e+
  gi|330506846|ref|YP_004383274.1| 71 KYLCGACGKSTEED 84
                                      69*******97765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.9     0.002         5      30      46 ..      43      60 ..      26      63 .. 0.76
   2 ?    9.1   3.1   0.00049       1.3      15      43 ..      44      86 ..      41     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.002
                               DZR 30 rCpsCgek.vdpearfCp 46
                                       Cp+Cg++  ++++++C+
  gi|330506846|ref|YP_004383274.1| 43 LCPECGHPmSHNGFNTCQ 60
                                      688888886666777775 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00049
                               DZR 15 CseCgtklkavaa................edrCpsCgekvdpear 43
                                      C+eCg++++   +                ++ C +Cg++++++  
  gi|330506846|ref|YP_004383274.1| 44 CPECGHPMSH--NgfntcqkrhlgganvgKYLCGACGKSTEEDRD 86
                                      5556655552..123555555555556669999999998877665 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0028       7.3       7      24 ..      35      52 ..      31      61 .. 0.85
   2 ?    2.6   0.1     0.055   1.4e+02      15      26 ..      73      84 ..      67      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0028
                              YhfH  7 FfrnLPkKkCteCGkeie 24
                                      +fr++ +  C+eCG  + 
  gi|330506846|ref|YP_004383274.1| 35 IFRKIVPPLCPECGHPMS 52
                                      799999999*****9986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.055
                              YhfH 15 kCteCGkeieEq 26
                                       C  CGk  eE 
  gi|330506846|ref|YP_004383274.1| 73 LCGACGKSTEED 84
                                      6******99995 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   5.5      0.03        77       3      32 ..      44      84 ..      43      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.03
                                      ETTTTCEEC...........HEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon  3 CPnCgstnl...........veDpergelvCtdCGlVledn 32
                                      CP+Cg+++            +  ++ g ++C++CG   e++
  gi|330506846|ref|YP_004383274.1| 44 CPECGHPMShngfntcqkrhLGGANVGKYLCGACGKSTEED 84
                                      99999987458888888777777999999999999877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2952.51
//
Query:       gi|330506847|ref|YP_004383275.1|  [L=251]
Description: transposase IS3 family protein integrase [Methanosaeta concilii GP6]
Scores for complete 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   87.7   0.0    9.4e-25   87.1   0.0    1.2  1  rve            Integrase core domain
    7.8e-19   67.6   0.3    1.5e-18   66.7   0.3    1.5  1  HTH_21         HTH-like domain
    1.8e-05   24.4   0.0    5.3e-05   22.9   0.0    1.8  1  rve_3          Integrase core domain
  ------ inclusion threshold ------
      0.033   14.4   0.0      0.086   13.1   0.0    1.7  1  HTH_Tnp_Tc3_2  Transposase
      0.066   13.4   0.0       0.18   12.0   0.0    1.7  1  HTH_Tnp_1_2    Helix-turn-helix of insertion element transpos


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.0   2.6e-28   9.4e-25       5     115 ..     127     237 ..     124     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 2.6e-28
                               rve   5 gelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve..pervlsDngseyt 79 
                                       ++ w +D+t+v++      ++l+v++d +sr ++++ ls+++ ++++  +l +a++++ ++    ++++sD+g +y+
  gi|330506847|ref|YP_004383275.1| 127 NQAWASDITYVQLQHE--HIFLAVILDLYSRKCIGWELSRSIRSDLAMSALAKALKNRSKESleGLIHHSDQGVQYA 201
                                       899*********6655..5*****************************************8899************* PP

                               rve  80 skafrefladlgirvsftrpgrpqdnGkvErfhrtl 115
                                       sk++ + l+ ++i++s++r+g+p+dn+ +E+f++tl
  gi|330506847|ref|YP_004383275.1| 202 SKDYVDCLKAHDIQISMSRKGNPYDNAFAESFIKTL 237
                                       **********************************98 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.3   4.1e-22   1.5e-18       6      58 ..      49      99 ..      45     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 4.1e-22
                            HTH_21  6 llalireifeeskgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgvqrr 58
                                      l ++i+ei  e  + YGyrri+aeL+++g+ +vnhkrV RlMr+++L+++ ++
  gi|330506847|ref|YP_004383275.1| 49 LVNQIQEIALEF-PYYGYRRITAELQNRGY-AVNHKRVLRLMRQEKLLCYKKK 99
                                      7899********.9**************87.5*****************9544 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.5e-08   5.3e-05       1      26 [.     212     237 ..     212     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-08
                             rve_3   1 lgielsyiapgkPqqNglvEsfngtl 26 
                                       ++i++s+++ g P++N+++Esf++tl
  gi|330506847|ref|YP_004383275.1| 212 HDIQISMSRKGNPYDNAFAESFIKTL 237
                                       689*********************98 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.4e-05     0.086       3      56 ..      52     105 ..      50     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                     HTH_Tnp_Tc3_2   3 rIvrlvrkdPritlreLanelkeeGksvsreTirrrLrkaglkkrkprkkplLs 56 
                                       +I +++ + P+  +r++++el+++G  v ++ + r +r+++l  +k + kp+ +
  gi|330506847|ref|YP_004383275.1|  52 QIQEIALEFPYYGYRRITAELQNRGYAVNHKRVLRLMRQEKLLCYKKKFKPVTT 105
                                       68888889999**********************************999999755 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     5e-05      0.18      35      61 ..      21      48 ..      15      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5e-05
                                      HHTS-HHHHHHHH.H-HHHHHHHHHHHH CS
                       HTH_Tnp_1_2 35 evgvsrsTlykWk.kkkeFieyvnelae 61
                                       + vsrs +y+W+ + ++F+++ +e ++
  gi|330506847|ref|YP_004383275.1| 21 ALDVSRSGYYEWLkRSEKFTAENSESSD 48
                                      689*********9889999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1787.02
//
Query:       gi|330506848|ref|YP_004383276.1|  [L=109]
Description: IS3/IS66 family element, Orf1 protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.9e-11   41.8   0.1    1.6e-10   41.1   0.0    1.5  1  HTH_Tnp_1  Transposase
      0.002   17.8   0.0     0.0044   16.8   0.0    1.6  1  HTH_23     Homeodomain-like domain
     0.0046   17.0   0.0     0.0099   16.0   0.0    1.6  1  HTH_28     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.033   14.1   0.3      0.074   12.9   0.3    1.6  1  PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein k
      0.062   13.8   0.1       0.13   12.7   0.0    1.5  2  DUF4733    Domain of unknown function (DUF4733)


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   4.4e-14   1.6e-10       2      74 ..       3      75 ..       2      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 4.4e-14
                         HTH_Tnp_1  2 rrrrrwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyr...egeeaspaefeltaleeenrelkrel 74
                                      ++rrr+++ fK+++++e  e+gk+ +++Ar++g++p+   +W+++     e  +a   +    + +++++el+r+l
  gi|330506848|ref|YP_004383276.1|  3 KTRRRYDRDFKISVLAEL-EAGKPLAQIAREYGIHPSLPCRWKAELAenpE--KAFMGNGNKYKDQAKIAELERLL 75
                                      79***************9.*************************9975332..33333333344466777777765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.2e-06    0.0044       8      40 ..      14      46 ..       2      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                      +++l  l  G++ ++IAre+g++++  +rw+  
  gi|330506848|ref|YP_004383276.1| 14 ISVLAELEAGKPLAQIAREYGIHPSLPCRWKAE 46
                                      567888888***************987777765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.8e-06    0.0099       1      27 [.      12      38 ..      12      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
                            HTH_28  1 qRleiikllaaGhsvreaArelgisrr 27
                                      +++ ++ +l aG++ +++Are+gi+++
  gi|330506848|ref|YP_004383276.1| 12 FKISVLAELEAGKPLAQIAREYGIHPS 38
                                      7999********************997 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.1e-05     0.074       9      28 ..      67      86 ..      61      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                         PKcGMP_CC  9 RIRELEkrlaekdeEIqELr 28
                                      +I+ELE+ l + ++EI  L+
  gi|330506848|ref|YP_004383276.1| 67 KIAELERLLGQAHAEIDLLK 86
                                      9***************9888 PP

>> DUF4733  Domain of unknown function (DUF4733)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.7e-05      0.13      29      67 ..       4      42 ..       1      51 [. 0.88
   2 ?   -2.0   0.0       1.4     5e+03      32      32 ..      91      91 ..      64     106 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                           DUF4733 29 qplrpqravleelsaplelsqplsgllddyGilPkhPrp 67
                                        +r+ r +   + a le  +pl+++  +yGi+P  P +
  gi|330506848|ref|YP_004383276.1|  4 TRRRYDRDFKISVLAELEAGKPLAQIAREYGIHPSLPCR 42
                                      56899999999***********************99976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                           DUF4733 32 r 32
                                       
  gi|330506848|ref|YP_004383276.1| 91 M 91
                                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 789.39
//
Query:       gi|330506849|ref|YP_004383277.1|  [L=96]
Description: hypothetical protein MCON_0633 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-19   70.2   0.1    1.5e-19   70.1   0.1    1.0  1  Transposase_mut  Transposase, Mutator family
  ------ inclusion threshold ------
      0.032   14.4   0.0      0.037   14.2   0.0    1.2  1  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 !   70.1   0.1   1.7e-23   1.5e-19     299     380 ..       5      87 ..       1      88 [. 0.92

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.7e-23
                   Transposase_mut 299 leklgk.kypkvaelldeaaedvlaflafpeqirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaea 374
                                       +++l +  y  +ae++d+ + d+ ++ a+p++++++i++tN++Er+Nke++Rr+r vg FP ++s++rl g ++ + 
  gi|330506849|ref|YP_004383277.1|   5 AKELRDrGYDPAAETIDRFRFDLWNYKAYPKAHWKRIRTTNIIERINKELKRRSRPVGAFPSDQSLMRLAGCIMINI 81 
                                       5555555799999**************************************************************** PP

                   Transposase_mut 375 hdewke 380
                                       ++ew +
  gi|330506849|ref|YP_004383277.1|  82 NEEWVT 87 
                                       ****75 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.1e-06     0.037      88     124 ..      36      72 ..       6      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-06
                     DDE_Tnp_IS240  88 shvqvkylnnriEsdhrtlKkrlrptrgfkslksaak 124
                                        h+++    n+iE+ +++lK+r rp++ f s +s+ +
  gi|330506849|ref|YP_004383277.1|  36 AHWKRIRTTNIIERINKELKRRSRPVGAFPSDQSLMR 72 
                                       68888899*********************99888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 637.71
//
Query:       gi|330506850|ref|YP_004383278.1|  [L=79]
Description: hypothetical protein MCON_0634 [Methanosaeta concilii GP6]
Scores for complete 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-12   44.9   0.0    8.2e-12   44.7   0.0    1.0  1  Transposase_mut  Transposase, Mutator family


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 !   44.7   0.0   4.6e-16   8.2e-12     215     255 ..       3      43 ..       2      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 4.6e-16
                   Transposase_mut 215 avlesLknrGlkgvelvvsDahkGLvkaisavfpeaavQrC 255
                                       ++++sLk+rGl+gvelv+sDahkG++ka++ +f +a++Q  
  gi|330506850|ref|YP_004383278.1|   3 TLFRSLKDRGLEGVELVISDAHKGIQKAVELSFVGASWQIS 43 
                                       799************************************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 585.93
//
Query:       gi|330506851|ref|YP_004383279.1|  [L=193]
Description: hypothetical protein MCON_0635, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-50  172.0   0.0    1.9e-50  171.8   0.0    1.0  1  Transposase_mut  Transposase, Mutator family
  ------ inclusion threshold ------
      0.017   15.6   0.0      0.033   14.6   0.0    1.4  1  HTH_26           Cro/C1-type HTH DNA-binding domain
       0.11   11.9   0.2        9.5    5.6   0.0    2.7  3  mRNA_decap_C     mRNA-decapping enzyme C-terminus


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 !  171.8   0.0   3.1e-54   1.9e-50      22     213 ..       4     193 .]       1     193 [] 0.98

  Alignments for each domain:
  == domain 1  score: 171.8 bits;  conditional E-value: 3.1e-54
                   Transposase_mut  22 kddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspallerykR 98 
                                        +  lk++++ +l++++  e+  + ga  yers++r+ +RnG r+r+l+Tr+g+l+l+ P+ R+  F+  ++ery R
  gi|330506851|ref|YP_004383279.1|   4 PNSGLKQVITEFLNAVMLFEAYLQSGALPYERSPQRKAHRNGTRSRTLKTRVGELTLNKPQFREFPFESSVFERYCR 80 
                                       56789************************************************************************ PP

                   Transposase_mut  99 rekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkvR 175
                                        e+al  +++e y++Gvstrk+e+lv++++  + +S+sevS+++k lde+ve+f +R++e k   +l++Da+y kvR
  gi|330506851|ref|YP_004383279.1|  81 VEQALLMTIAESYIQGVSTRKMEELVKNFGL-NRLSASEVSRLCKILDEKVEEFLKRPIEVK-IRYLLVDATYFKVR 155
                                       *******************************.77**************************99.************** PP

                   Transposase_mut 176 eegrvvskavliaigvdadGsreiLglevadsEsekfW 213
                                          + +++a l+ +gv  dG reiLg ++a+sE+   W
  gi|330506851|ref|YP_004383279.1| 156 CGAQYKNRALLVVVGVREDGLREILGASIAESEDSGYW 193
                                       **********************************9999 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.5e-06     0.033      21      59 ..      96     135 ..      87     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-06
                            HTH_26  21 gisaatlsrlvkgk.pervsldtLdkiCdaLgctpgDLle 59 
                                       g+s  +++ lvk+   +r+s+++ +++C++L+ ++++ l+
  gi|330506851|ref|YP_004383279.1|  96 GVSTRKMEELVKNFgLNRLSASEVSRLCKILDEKVEEFLK 135
                                       78999*******9758*****************9999875 PP

>> mRNA_decap_C  mRNA-decapping enzyme C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0016       9.5      22      34 ..      14      28 ..      13      30 .. 0.78
   2 ?   -2.3   0.0      0.49   2.9e+03       3      11 ..      59      67 ..      58      67 .. 0.84
   3 ?    3.2   0.0    0.0093        56      24      40 ..      86     102 ..      83     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0016
                      mRNA_decap_C 22 sFLnt..IHeAYlqs 34
                                      +FLn+  ++eAYlqs
  gi|330506851|ref|YP_004383279.1| 14 EFLNAvmLFEAYLQS 28
                                      57876448******8 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.49
                      mRNA_decap_C  3 pLsksQLqd 11
                                      +L+k Q+++
  gi|330506851|ref|YP_004383279.1| 59 TLNKPQFRE 67
                                      599***986 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.0093
                      mRNA_decap_C  24 LntIHeAYlqslskdls 40 
                                       L tI e Y+q++s++++
  gi|330506851|ref|YP_004383279.1|  86 LMTIAESYIQGVSTRKM 102
                                       66899********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1440.99
//
Query:       gi|330506852|ref|YP_004383280.1|  [L=143]
Description: hypothetical protein MCON_0636 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-05   25.0   3.4    1.8e-05   24.8   3.4    1.1  1  UPF0158   Uncharacterised protein family (UPF0158)


Domain annotation for each model (and alignments):
>> UPF0158  Uncharacterised protein family (UPF0158)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   3.4     1e-09   1.8e-05      21     141 ..      21     135 ..       9     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1e-09
                           UPF0158  21 erdfylDrieGkvllidlekqqeeldklekeleeepdRyllipklsvyeskklmesFlnekvedidakekl...ldi 94 
                                        +  +l +++G +++ +  ++ +e+d+     e + d +++ip+    + + l ++ + e   +++ ++ l     i
  gi|330506852|ref|YP_004383280.1|  21 MNRAFLCLDNGEIIYRSEWDDPKEEDED----EFDCDHFIEIPHK---NDLDLGQTLVIE-FAEVHLQDDLdlvQRI 89 
                                       45579999*******9988888888888....889********74...556677777777.6777666543221566 PP

                           UPF0158  95 lqskkalenFlefiydfeaelekWqqfeqerlRirileWLrenelef 141
                                          + a++ F+e + d + +l+ W+ +e  r ++   eW+++ne+e 
  gi|330506852|ref|YP_004383280.1|  90 FSRRGAYRRFKELL-DERGLLQTWYDYEDIREKEALGEWVQDNEIEL 135
                                       66778999999866.668999***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1111.85
//
Query:       gi|330506853|ref|YP_004383281.1|  [L=181]
Description: 30S ribosomal protein S13p/S18e [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-39  133.2   1.6    8.7e-39  132.8   1.6    1.1  1  Ribosomal_S13  Ribosomal protein S13/S18


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.8   1.6   4.8e-43   8.7e-39       1     128 []      31     159 ..      31     159 .. 0.99

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 4.8e-43
                     Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdi 76 
                                       Ril+td+ gk++v++alt ikG+Grr aki  ++a+vd ++ +g l + ei+k++++ve+ a +  p w+ nr+ di
  gi|330506853|ref|YP_004383281.1|  31 RILNTDLAGKRQVHMALTGIKGVGRRCAKIFTERAGVDPNATLGLLPDAEIDKLKKVVEEDAINILPVWMvNRRGDI 107
                                       9******************************************************************9999****** PP

                     Ribosomal_S13  77 kdGkdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                       ++Gkd h +  dl+++lred++ +kk+rsy+GlRH+rGl+vRGQ+T++tgRt
  gi|330506853|ref|YP_004383281.1| 108 ETGKDIHIMGMDLNMTLREDLDLMKKMRSYKGLRHERGLRVRGQKTRSTGRT 159
                                       ***************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1330.49
//
Query:       gi|330506854|ref|YP_004383282.1|  [L=178]
Description: 30S ribosomal protein S4 [Methanosaeta concilii GP6]
Scores for complete 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   51.0   0.2    1.9e-13   49.9   0.2    1.7  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 !   49.9   0.2   1.1e-17   1.9e-13       1      47 [.     104     150 ..     104     151 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.1e-17
                                       EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCE CS
                                S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDv 47 
                                       rRL++ ++r+gla s ++Arq+I hG+++V G++v+ p+y V  g++
  gi|330506854|ref|YP_004383282.1| 104 RRLQTQVYRQGLANSLKQARQFIVHGHIQVSGRRVDVPGYLVPRGEE 150
                                       8*****************************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1278.04
//
Query:       gi|330506855|ref|YP_004383283.1|  [L=129]
Description: 30S ribosomal protein S11 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-46  156.6   3.2    3.6e-46  156.1   3.2    1.2  1  Ribosomal_S11  Ribosomal protein S11
  ------ inclusion threshold ------
      0.031   14.0   0.6      0.038   13.7   0.6    1.2  1  Pilus_CpaD     Pilus biogenesis CpaD protein (pilus_cpaD)


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.1   3.2     4e-50   3.6e-46       1     110 []       7     125 ..       7     125 .. 0.99

  Alignments for each domain:
  == domain 1  score: 156.1 bits;  conditional E-value: 4e-50
                     Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg...... 70 
                                       G+ahi++sfnntiititd++Gae+l+k++Gg++vka+r +ssPy+a+++a ++a++v+dkGi  v+vkv++      
  gi|330506855|ref|YP_004383283.1|   7 GIAHIFSSFNNTIITITDQTGAETLAKISGGMVVKAARdESSPYTAMQMAMQVADAVKDKGIVGVHVKVRApggnqq 83 
                                       9**************************************************************************** PP

                     Ribosomal_S11  71 ..pGpGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                         pGpG++aa+ralaraGl+igried tPiPhdg+++++++r
  gi|330506855|ref|YP_004383283.1|  84 rsPGPGAQAAIRALARAGLRIGRIEDATPIPHDGTKPRGGKR 125
                                       *************************************99887 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 ?   13.7   0.6   4.3e-06     0.038      68     122 ..      30      84 ..      22     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-06
                        Pilus_CpaD  68 yrregagaivisvpsgssneaaaaaaaaeiravlaaaGvpaseisvrayqaaape 122
                                         ++ +g +v+++ +++s++ +a+++a +++++++++G+ + +++vra  +++++
  gi|330506855|ref|YP_004383283.1|  30 TLAKISGGMVVKAARDESSPYTAMQMAMQVADAVKDKGIVGVHVKVRAPGGNQQR 84 
                                       566778999*************************************998777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 774.62
//
Query:       gi|330506856|ref|YP_004383284.1|  [L=264]
Description: DNA-directed RNA polymerase subunit D [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-21   77.4   0.0    1.8e-20   73.4   0.0    2.2  2  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    8.1e-12   44.4   0.0      1e-11   44.1   0.0    1.1  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain
    3.2e-08   33.6  22.5    9.5e-06   25.7  11.5    2.6  3  Fer4_9         4Fe-4S dicluster domain
    8.8e-08   31.7  15.1    9.6e-06   25.2   4.1    2.8  2  Fer4           4Fe-4S binding domain
    3.5e-05   24.0   2.1    6.6e-05   23.1   2.1    1.4  1  Fer4_18        4Fe-4S dicluster domain
    3.9e-05   23.7  10.2    3.9e-05   23.7  10.2    2.0  1  Fer4_10        4Fe-4S dicluster domain
    0.00013   21.8   3.7    0.00013   21.8   3.7    3.0  3  Fer4_6         4Fe-4S binding domain
    0.00094   19.1   4.2    0.00094   19.1   4.2    3.2  2  Fer4_2         4Fe-4S binding domain
      0.001   19.6  11.1      0.001   19.6  11.1    2.7  2  Fer4_7         4Fe-4S dicluster domain
     0.0011   19.8  12.7     0.0068   17.3   1.3    2.7  2  Fer4_16        4Fe-4S double cluster binding domain
     0.0017   19.2   3.6     0.0017   19.2   3.6    3.2  2  Fer4_3         4Fe-4S binding domain
      0.004   17.6  10.7          1    9.8   7.1    2.5  2  Fer4_8         4Fe-4S dicluster domain
     0.0062   17.0   2.7     0.0062   17.0   2.7    3.4  3  Fer4_4         4Fe-4S binding domain
  ------ inclusion threshold ------
      0.023   15.3   0.6      0.023   15.3   0.6    2.7  2  Fer4_17        4Fe-4S dicluster domain
      0.034   15.0   0.7      0.034   15.0   0.7    2.6  2  Fer4_22        4Fe-4S dicluster domain
        5.5    7.8  12.6       0.35   11.6   2.5    2.5  2  Fer4_15        4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.0   1.6e-23   1.8e-20       1     112 []      44     153 ..      44     153 .. 0.94
   2 ?    2.0   0.0      0.23   2.5e+02      53      72 ..     225     244 ..     187     264 .] 0.78

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 1.6e-23
                                       EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBESSSSCE CS
                     RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkledadve 77 
                                       +++++ntsvl DE +  r+g +plv +d+l+++   ++++    +g++ + v + L+++gpg v+++d+++ d+ v+
  gi|330506856|ref|YP_004383284.1|  44 INLYDNTSVLFDEQIGLRIGEVPLV-ADELDLFSQPEDCQ-CGGTGCPGCRVDFMLSKEGPGMVYSEDIQFTDPGVR 118
                                       6789*********************.5556669******4.3579******************************** PP

                                       ESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                     RNA_pol_A_bac  78 ivnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                       ++ ++i+++ L +g++l +e ++ k +Gkeh+k++
  gi|330506856|ref|YP_004383284.1| 119 PAFDKIPLVILGEGEKLVMEGYATKRVGKEHSKWQ 153
                                       **********************************6 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.23
                                       EEEEEEESSECEEGGGCBES CS
                     RNA_pol_A_bac  53 elkLnvkgpgevtagdlkle 72 
                                       ++ ++++g+g v a+dl+ +
  gi|330506856|ref|YP_004383284.1| 225 SFVVSIEGSGSVAAKDLVAR 244
                                       57889999999*****9974 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 !   44.1   0.0     9e-15     1e-11       3      66 ..      16     250 ..      14     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 9e-15
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................. RF
                         RNA_pol_L   3 llrgvdhtlgNaLRrillsevpgvaiea................................................. 30 
                                       ll+gv+++++N +Rr ++sevp +ai++                                                 
  gi|330506856|ref|YP_004383284.1|  16 LLSGVSAAFANGIRRACMSEVPILAIDEinlydntsvlfdeqiglrigevplvadeldlfsqpedcqcggtgcpgcr 92 
                                       789***********************************************999999999999999999999999999 PP

                                       ............................................................................. RF
                         RNA_pol_L  31 ............................................................................. 30 
                                                                                                                    
  gi|330506856|ref|YP_004383284.1|  93 vdfmlskegpgmvysediqftdpgvrpafdkiplvilgegeklvmegyatkrvgkehskwqagtlcgyknlpsitvs 169
                                       99999999999999999999999999888888888888888888888888888777777777777777777777777 PP

                                       .............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  31 .............................................pvvkvntdkdklilevetdgslkPeealkeAl 62 
                                                                                    + ++++   d ++ ++e  gs+ +++++++A+
  gi|330506856|ref|YP_004383284.1| 170 eacdgcgkcveacprdilvieegrakatnilecslcklcvgaceaAAIDLKPIHDSFVVSIEGSGSVAAKDLVARAV 246
                                       77777666666666666666666666665555555555555555533899999************************ PP

                                       xxxx RF
                         RNA_pol_L  63 kiLk 66 
                                       + +k
  gi|330506856|ref|YP_004383284.1| 247 DEIK 250
                                       9987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       1.6   1.8e+03      38      42 ..      87      91 ..      66     108 .. 0.68
   2 !   21.0   3.1   2.6e-07   0.00029      33      50 ..     154     186 ..     133     187 .. 0.71
   3 !   25.7  11.5   8.5e-09   9.5e-06       1      51 []     171     217 ..     171     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.6
                            Fer4_9 38 gCgaC 42
                                      gC  C
  gi|330506856|ref|YP_004383284.1| 87 GCPGC 91
                                      22222 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.6e-07
                            Fer4_9  33 e...............eaCigCgaCveaCpkga 50 
                                       +               eaC gCg+CveaCp+++
  gi|330506856|ref|YP_004383284.1| 154 AgtlcgyknlpsitvsEACDGCGKCVEACPRDI 186
                                       144555555566666689*************94 PP

  == domain 3  score: 25.7 bits;  conditional E-value: 8.5e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +C gCg+CveaCp ++ v ++++ ka +      +C  C+ Cv aC+  ai
  gi|330506856|ref|YP_004383284.1| 171 ACDGCGKCVEACPRDILVIEEGRAKATNIL----ECSLCKLCVGACEAAAI 217
                                       6*****************999999999865....5***********99876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   4.1   8.6e-09   9.6e-06       5      23 ..     169     187 ..     166     188 .. 0.89
   2 !   11.4   3.2    0.0002      0.23       7      23 ..     201     217 ..     198     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 8.6e-09
                                       TTTSSS-THHHHHSTTTEE CS
                              Fer4   5 eekCigCGaCvevCPvgAI 23 
                                        e C gCG+Cve+CP + +
  gi|330506856|ref|YP_004383284.1| 169 SEACDGCGKCVEACPRDIL 187
                                       589************9976 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0002
                                       TSSS-THHHHHSTTTEE CS
                              Fer4   7 kCigCGaCvevCPvgAI 23 
                                        C  C++Cv +C   AI
  gi|330506856|ref|YP_004383284.1| 201 ECSLCKLCVGACEAAAI 217
                                       6************9999 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   2.1   5.9e-08   6.6e-05      25      97 ..     136     214 ..     120     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.9e-08
                           Fer4_18  25 llvvydakrGekiagrkkekkalkekeerkekgagdcidcescvkvcPtgid.irkGlq.....leciscllcidac 95 
                                       ++  y +kr +k +++ ++ +    k++ + + +  c  c++cv+ cP +i  i +G       lec  c lc+ ac
  gi|330506856|ref|YP_004383284.1| 136 VMEGYATKRVGKEHSKWQAGTLCGYKNLPSITVSEACDGCGKCVEACPRDILvIEEGRAkatniLECSLCKLCVGAC 212
                                       455689999998888888888888999999999999*************9962556642223338************ PP

                           Fer4_18  96 dk 97 
                                       + 
  gi|330506856|ref|YP_004383284.1| 213 EA 214
                                       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 !   23.7  10.2   3.4e-08   3.9e-05       6      55 ..     169     212 ..     165     213 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.4e-08
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       ++ C +CgkCv+aCP        +  ++e+ a+ +++ +C  c  Cv aC
  gi|330506856|ref|YP_004383284.1| 169 SEACDGCGKCVEACPR------DILVIEEGRAKATNILECSLCKLCVGAC 212
                                       689*************......99999999******************** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.9       7.9   8.8e+03       9      13 ..      88      92 ..      88      92 .. 0.88
   2 !   21.8   3.7   1.2e-07   0.00013       7      22 ..     170     185 ..     168     189 .. 0.88
   3 ?    5.5   4.7     0.018        20       9      24 .]     202     217 ..     202     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.9
                            Fer4_6  9 CigCg 13
                                      C gC+
  gi|330506856|ref|YP_004383284.1| 88 CPGCR 92
                                      99996 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.2e-07
                            Fer4_6   7 dkCigCgdCvrvCPeg 22 
                                       ++C+gCg+Cv +CP +
  gi|330506856|ref|YP_004383284.1| 170 EACDGCGKCVEACPRD 185
                                       79************66 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.018
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       C  C  Cv +C ++ai
  gi|330506856|ref|YP_004383284.1| 202 CSLCKLCVGACEAAAI 217
                                       999*********9998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   4.2   8.4e-07   0.00094       7      21 ..     169     183 ..     166     184 .. 0.91
   2 ?    5.7   2.6     0.016        17      10      21 ..     202     213 ..     196     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.4e-07
                            Fer4_2   7 tdrCigCgaCvsaCP 21 
                                       +++C gCg+Cv aCP
  gi|330506856|ref|YP_004383284.1| 169 SEACDGCGKCVEACP 183
                                       799************ PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                            Fer4_2  10 CigCgaCvsaCP 21 
                                       C  C+ Cv aC 
  gi|330506856|ref|YP_004383284.1| 202 CSLCKLCVGACE 213
                                       999********5 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6  11.1   9.2e-07     0.001       1      51 [.     171     215 ..     171     216 .. 0.84
   2 !   12.0   0.8   0.00022      0.25       2      22 ..     202     222 ..     201     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.2e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       +C gCg+Cv+aCp + + ++e   +      + +  +C+ C+ Cv +C + 
  gi|330506856|ref|YP_004383284.1| 171 ACDGCGKCVEACPRDILVIEEGR-A-----KATNILECSLCKLCVGACEAA 215
                                       5******************8752.2.....2458899***********765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00022
                            Fer4_7   2 CigCgaCvaaCpvkaieldee 22 
                                       C  C+ Cv aC + ai+l++ 
  gi|330506856|ref|YP_004383284.1| 202 CSLCKLCVGACEAAAIDLKPI 222
                                       999*************99874 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 !   17.3   1.3   6.1e-06    0.0068       2      20 ..     172     190 ..     171     200 .. 0.79
   2 !   10.8   0.2   0.00065      0.73       2      20 ..     202     220 ..     201     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.1e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C +CgkC+e+CP + +  +
  gi|330506856|ref|YP_004383284.1| 172 CDGCGKCVEACPRDILVIE 190
                                       ************9987655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00065
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C  C+ C+ +C ++ai+ k
  gi|330506856|ref|YP_004383284.1| 202 CSLCKLCVGACEAAAIDLK 220
                                       99**************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 !   19.2   3.6   1.5e-06    0.0017       1      14 [.     172     185 ..     172     186 .. 0.93
   2 ?    0.9   5.6         1   1.2e+03       1      11 [.     202     212 ..     202     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.5e-06
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+gCg Cve+CP +
  gi|330506856|ref|YP_004383284.1| 172 CDGCGKCVEACPRD 185
                                       ************86 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C  C +Cv +C
  gi|330506856|ref|YP_004383284.1| 202 CSLCKLCVGAC 212
                                       999*****999 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   7.1   0.00093         1      44      65 .]     157     186 ..      80     186 .. 0.74
   2 !    9.1   0.1    0.0016       1.8      47      62 ..     198     213 ..     188     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00093
                            Fer4_8  44 e........eealwsCttcgaCtevCpvgi 65 
                                                 +  ++C +cg+C+e+Cp +i
  gi|330506856|ref|YP_004383284.1| 157 LcgyknlpsITVSEACDGCGKCVEACPRDI 186
                                       155555666778899************986 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0016
                            Fer4_8  47 alwsCttcgaCtevCp 62 
                                       ++ +C+ c+ C+ +C 
  gi|330506856|ref|YP_004383284.1| 198 NILECSLCKLCVGACE 213
                                       5666777777777775 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   4.1       5.3     6e+03       4      11 ..      81      92 ..      78      93 .. 0.68
   2 !   17.0   2.7   5.5e-06    0.0062       1      16 [.     169     184 ..     169     188 .. 0.91
   3 !    9.0   0.8     0.002       2.3       4      15 ..     202     213 ..     196     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.3
                            Fer4_4  4 C....igCgsCv 11
                                      C    +gC+ C+
  gi|330506856|ref|YP_004383284.1| 81 CqcggTGCPGCR 92
                                      6445579*9996 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5.5e-06
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       +e C gCg+Cv aCP 
  gi|330506856|ref|YP_004383284.1| 169 SEACDGCGKCVEACPR 184
                                       589************5 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.002
                            Fer4_4   4 CigCgsCvaaCP 15 
                                       C  C+ Cv aC+
  gi|330506856|ref|YP_004383284.1| 202 CSLCKLCVGACE 213
                                       999********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 ?   15.3   0.6     2e-05     0.023      41      60 ..     167     186 ..     135     187 .. 0.77
   2 ?   10.2   1.2   0.00076      0.85      37      57 ..     193     213 ..     188     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                           Fer4_17  41 ekaslCieCgeCerkCPqgl 60 
                                       ++ + C +Cg+C+++CP ++
  gi|330506856|ref|YP_004383284.1| 167 TVSEACDGCGKCVEACPRDI 186
                                       46789999********9886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00076
                           Fer4_17  37 aekeekaslCieCgeCerkCP 57 
                                         k +++ +C+ C++C+ +C 
  gi|330506856|ref|YP_004383284.1| 193 RAKATNILECSLCKLCVGACE 213
                                       45567999************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 ?   15.0   0.7   3.1e-05     0.034      60      96 .]     150     186 ..     135     186 .. 0.75
   2 ?    0.8   0.6      0.83   9.3e+02       3      17 ..     200     214 ..     194     225 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-05
                           Fer4_22  60 erlrqrllhklsefkekfgesgCvGCgRCieacpvki 96 
                                       ++++  +l  ++++ + + +++C GCg+C+eacp +i
  gi|330506856|ref|YP_004383284.1| 150 SKWQAGTLCGYKNLPSITVSEACDGCGKCVEACPRDI 186
                                       5555556666667777778899************976 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.83
                           Fer4_22   3 lsCgaCtlvCptCsC 17 
                                       l+C+ C+l+  +C  
  gi|330506856|ref|YP_004383284.1| 200 LECSLCKLCVGACEA 214
                                       556666666666654 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.5   0.00031      0.35       6      22 ..     170     186 ..     169     201 .. 0.71
   2 ?    1.3   2.6      0.53     6e+02       7      20 ..     201     214 ..     199     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                           Fer4_15   6 daCigcglCvaeapevf 22 
                                       +aC+gcg Cv+++p+ +
  gi|330506856|ref|YP_004383284.1| 170 EACDGCGKCVEACPRDI 186
                                       79***********8633 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.53
                           Fer4_15   7 aCigcglCvaeape 20 
                                       +C  c lCv +++ 
  gi|330506856|ref|YP_004383284.1| 201 ECSLCKLCVGACEA 214
                                       5*********9953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1943.28
//
Query:       gi|330506857|ref|YP_004383285.1|  [L=194]
Description: hypothetical protein MCON_0642 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1420.53
//
Query:       gi|330506858|ref|YP_004383286.1|  [L=102]
Description: hypothetical protein MCON_0643 [Methanosaeta concilii GP6]
Scores for complete 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   30.8   0.1    3.1e-07   30.0   0.1    1.4  1  Sigma70_r4_2     Sigma-70, region 4
    1.7e-06   28.0   0.2    3.8e-06   26.9   0.2    1.6  1  HTH_7            Helix-turn-helix domain of resolvase
    1.5e-05   24.6   0.0    2.6e-05   23.9   0.0    1.4  1  HTH_23           Homeodomain-like domain
    0.00036   20.5   0.0    0.00062   19.7   0.0    1.4  1  HTH_Mga          M protein trans-acting positive regulator (M
    0.00058   19.9   0.4     0.0016   18.5   0.1    1.8  2  HTH_22           HTH domain
     0.0015   18.3   0.1     0.0038   17.0   0.0    1.7  2  HTH_38           Helix-turn-helix domain
     0.0019   17.9   0.0     0.0047   16.7   0.0    1.6  2  HTH_30           PucR C-terminal helix-turn-helix domain
     0.0022   16.5   0.6     0.0026   16.3   0.6    1.0  1  FHIPEP           FHIPEP family
     0.0027   17.2   0.2     0.0058   16.1   0.0    1.6  1  Sigma70_r4       Sigma-70, region 4
     0.0036   16.8   0.2     0.0059   16.1   0.2    1.3  1  GerE             Bacterial regulatory proteins, luxR family
      0.004   16.7   0.6     0.0065   16.1   0.1    1.6  1  HTH_50           Helix-turn-helix domain
     0.0051   17.3   0.1     0.0088   16.5   0.1    1.4  1  SF3A3            Pre-mRNA-splicing factor SF3A3, of SF3a comp
     0.0094   16.2   0.6       0.02   15.2   0.6    1.5  1  NUMOD1           NUMOD1 domain
     0.0099   14.9   0.2       0.01   14.9   0.2    1.1  1  TnsD             Tn7-like transposition protein D
  ------ inclusion threshold ------
      0.012   15.7   0.0       0.02   15.0   0.0    1.4  1  HTH_28           Helix-turn-helix domain
      0.014   15.7   0.1      0.021   15.1   0.1    1.4  1  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
       0.02   15.3   0.1      0.028   14.9   0.1    1.3  1  HTH_40           Helix-turn-helix domain
      0.021   15.2   0.3       0.11   12.9   0.3    2.3  1  Recombinase      Recombinase
      0.021   14.7   0.0      0.036   14.0   0.0    1.4  1  HTH_36           Helix-turn-helix domain
      0.024   14.5   0.0      0.039   13.8   0.0    1.4  1  Phage_NinH       Phage NinH protein
       0.03   14.3   0.4      0.038   14.0   0.4    1.2  1  DUF2089          Protein of unknown function (DUF2089)
      0.031   14.2   0.3      0.057   13.4   0.1    1.6  1  HTH_11           HTH domain
      0.034   14.1   0.0        1.8    8.6   0.0    2.2  2  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.035   13.9   0.0      0.075   12.8   0.0    1.6  1  HTH_10           HTH DNA binding domain
      0.038   14.2   0.3      0.044   14.0   0.3    1.2  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.073   12.9   0.0       0.09   12.7   0.0    1.3  1  YdaS_antitoxin   Putative antitoxin of bacterial toxin-antito
      0.075   13.6   0.2       0.12   12.9   0.2    1.3  1  Mga              Mga helix-turn-helix domain
      0.079   13.3   0.1      0.098   13.0   0.1    1.4  1  HTH_Tnp_1        Transposase
      0.083   12.3   0.0       0.36   10.3   0.0    2.0  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
      0.091   12.3   0.1       0.25   10.9   0.0    1.7  2  HTH_24           Winged helix-turn-helix DNA-binding
       0.12   12.2   0.0       0.19   11.5   0.0    1.4  1  BrkDBD           Brinker DNA-binding domain
       0.12   12.4   0.0       0.21   11.7   0.0    1.5  1  HTH_3            Helix-turn-helix


Domain annotation for each model (and alignments):
>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   5.6e-10   3.1e-07      14      50 ..       3      38 ..       2      40 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5.6e-10
                                      HHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHH CS
                      Sigma70_r4_2 14 rqreifllryleglsykEIAellgisegtVksrlsRA 50
                                      + r+i+ l y+ ++syk +A++l+is +tVk++l++ 
  gi|330506858|ref|YP_004383286.1|  3 DVRRIVDL-YELHKSYKKVASELNISRNTVKKYLHQV 38
                                      5799999*.9*************************86 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 !   26.9   0.2   6.8e-09   3.8e-06      10      44 ..       3      37 ..       1      38 [. 0.92

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 6.8e-09
                                      HHGGGGSSTTTT--STTTSSSS---SSSS--SS-- CS
                             HTH_7 10 dinrvvkLleeGisiskIAkevnisRsTvYRylad 44
                                      d  r+v L+e   s +k+A e+nisR Tv++yl+ 
  gi|330506858|ref|YP_004383286.1|  3 DVRRIVDLYELHKSYKKVASELNISRNTVKKYLHQ 37
                                      5679999**************************96 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   4.6e-08   2.6e-05       9      46 ..       6      45 ..       2      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.6e-08
                            HTH_23  9 rillllaeGlsvreIAreLgvsrrTvyrwlkryr..eeGl 46
                                      ri+ l+   +s++++A eL++sr+Tv ++l+  +  +eGl
  gi|330506858|ref|YP_004383286.1|  6 RIVDLYELHKSYKKVASELNISRNTVKKYLHQVKdvQEGL 45
                                      789999999********************99863435665 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.1e-06   0.00062      22      46 ..      16      40 ..      11      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-06
                           HTH_Mga 22 tldelakeLglseltlqsdiseLne 46
                                      +++++a+eL++s+ t++++++++++
  gi|330506858|ref|YP_004383286.1| 16 SYKKVASELNISRNTVKKYLHQVKD 40
                                      699*******************996 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.8e-06    0.0016      38      62 ..      11      35 ..       8      36 .. 0.91
   2 ?   -1.1   0.0       3.7   2.1e+03      20      33 ..      63      76 ..      45      85 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.8e-06
                            HTH_22 38 FllkgavekvAekLgiSraTvYryL 62
                                      ++l ++ +kvA++L+iSr+Tv +yL
  gi|330506858|ref|YP_004383286.1| 11 YELHKSYKKVASELNISRNTVKKYL 35
                                      78999****************9998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.7
                            HTH_22 20 ltkeekieivraLd 33
                                      lt   +++i ++L+
  gi|330506858|ref|YP_004383286.1| 63 LTDLVRQKIHQYLE 76
                                      44445555555554 PP

>> HTH_38  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   6.7e-06    0.0038       9      42 ..       3      36 ..       1      37 [. 0.91
   2 ?   -1.9   0.0       5.1   2.9e+03       7      20 ..      65      78 ..      61      80 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.7e-06
                            HTH_38  9 eReeIerllaeGlslreIArrLgrspsTIsRElk 42
                                      + ++I +l++  +s++++A +L+ s++T+ + l+
  gi|330506858|ref|YP_004383286.1|  3 DVRRIVDLYELHKSYKKVASELNISRNTVKKYLH 36
                                      7899*************************98776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.1
                            HTH_38  7 leeReeIerllaeG 20
                                         R++I + l+ +
  gi|330506858|ref|YP_004383286.1| 65 DLVRQKIHQYLESN 78
                                      55589999988765 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 !   16.7   0.0   8.4e-06    0.0047      12      38 ..      14      40 ..       6      42 .. 0.89
   2 ?   -2.5   0.0       8.1   4.6e+03       6      44 ..      72      79 ..      69      83 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.4e-06
                                      TT-HHHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_30 12 ggnisatAkaLhvHrnTlryRLrriee 38
                                      + +++++A +L+++rnT+++ L+++++
  gi|330506858|ref|YP_004383286.1| 14 HKSYKKVASELNISRNTVKKYLHQVKD 40
                                      5799****************9999886 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.1
                                      HHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--T CS
                            HTH_30  6 raylenggnisatAkaLhvHrnTlryRLrrieellgldl 44
                                      ++yle++                               l
  gi|330506858|ref|YP_004383286.1| 72 HQYLESN-------------------------------L 79
                                      3555555...............................3 PP

>> FHIPEP  FHIPEP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   4.7e-06    0.0026     461     519 ..      12      71 ..       3      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.7e-06
                                       HHHHHHHHCHHHC.HCHHHHHHHHHHHHTTHHHHHHHHH.HHS-HHHHHHHHHHHHCTTX CS
                            FHIPEP 461 hlsevikrhaael.lgrqevkklldelkkeapklveelvpkllslgelqkvLqnLlkErv 519
                                       +l++  k+ a+el ++r+ vkk l+++k+ ++ l ee++pk+ ++ + ++vL  L+++++
  gi|330506858|ref|YP_004383286.1|  12 ELHKSYKKVASELnISRNTVKKYLHQVKDVQEGLAEEIIPKNRKIVQPSRVLTDLVRQKI 71 
                                       5778888999999899*****************************************998 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     1e-05    0.0058      10      43 ..       5      37 ..       3      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-05
                                      HHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4 10 revlelrfgeglTleEIgerlgiSrerVrqiekr 43
                                      r+++ l+ +++ +++ ++ +l+iSr +V+  +++
  gi|330506858|ref|YP_004383286.1|  5 RRIVDLYELHK-SYKKVASELNISRNTVKKYLHQ 37
                                      67777877888.*****************87776 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2     1e-05    0.0059      18      41 ..      15      38 ..      14      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-05
                                      S-HHHHHHHHTS-HHHHHHHHHHH CS
                              GerE 18 ksnkeIAeelniSekTVkvhksni 41
                                      ks k++A+elniS +TVk ++ ++
  gi|330506858|ref|YP_004383286.1| 15 KSYKKVASELNISRNTVKKYLHQV 38
                                      6889**************998765 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.2e-05    0.0065      16      46 ..       7      37 ..       3      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
                            HTH_50 16 ikkayekYpStRklAkrLGvShtaianklrk 46
                                      i ++ye ++S  k+A  L +S  ++ + l++
  gi|330506858|ref|YP_004383286.1|  7 IVDLYELHKSYKKVASELNISRNTVKKYLHQ 37
                                      7799********************9877776 PP

>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.6e-05    0.0088      10      58 ..       6      63 ..       3      84 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-05
                             SF3A3 10 kylDLnelyeeylnlk...eik.ldYlqYLesfdkf.....seipkkqkkskeYkeYl 58
                                      +++DL+el+++y +++   +i+  +  +YL++++++     +ei  k++k  + ++ l
  gi|330506858|ref|YP_004383286.1|  6 RIVDLYELHKSYKKVAselNISrNTVKKYLHQVKDVqeglaEEIIPKNRKIVQPSRVL 63
                                      78***********99965433147999******9998888844444444433333333 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.6   3.5e-05      0.02      18      37 .]      16      35 ..      14      35 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.5e-05
                            NUMOD1 18 SireAakyLgishntInkyl 37
                                      S+++ a  L+is+nt++kyl
  gi|330506858|ref|YP_004383286.1| 16 SYKKVASELNISRNTVKKYL 35
                                      8899999************8 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   1.8e-05      0.01     190     227 ..       6      42 ..       4      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                              TnsD 190 rlkeLveeeglslkeiAkelgvdiktVlryakklgllk 227
                                       r+  L+e   +s+k++A+el+++ +tV++y+ + ++ +
  gi|330506858|ref|YP_004383286.1|   6 RIVDLYE-LHKSYKKVASELNISRNTVKKYLHQVKDVQ 42 
                                       5666777.889********************9877665 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.6e-05      0.02       4      35 ..       6      37 ..       5      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-05
                            HTH_28  4 eiikllaaGhsvreaArelgisrrtvyrWikr 35
                                      +i+ l+  ++s++ +A el+isr tv++ +++
  gi|330506858|ref|YP_004383286.1|  6 RIVDLYELHKSYKKVASELNISRNTVKKYLHQ 37
                                      6788887788****************998875 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 ?   15.1   0.1   3.7e-05     0.021       8      47 ..      20      65 ..      15      87 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-05
                                      HHHTT-S-HHHHHHHHHHHHHHHHHHHH.......TS--TTT--HH CS
                   Phage_int_SAM_1  8 LikerglspnTlraYrrdLrrflkflae......rgkesleqltte 47
                                      + +e ++s+nT+  Y+++++++++ lae      r++ +  ++ t+
  gi|330506858|ref|YP_004383286.1| 20 VASELNISRNTVKKYLHQVKDVQEGLAEeiipknRKIVQPSRVLTD 65
                                      567889******************9999555444444455555555 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   0.1     5e-05     0.028       7      58 ..       9      72 ..       4      91 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5e-05
                            HTH_40  7 elleeglsieeIAkerglkesTIegHLaelieeg............eeidlerlvseeeekeIe 58
                                      +l+e  +s +++A e +++++T+ ++L +    +            + ++ +r++++  +++I+
  gi|330506858|ref|YP_004383286.1|  9 DLYELHKSYKKVASELNISRNTVKKYLHQVKDVQeglaeeiipknrKIVQPSRVLTDLVRQKIH 72
                                      7999***********************9976553223333333222222234444445555555 PP

>> Recombinase  Recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   0.00019      0.11       7      30 ..       4      27 ..       1     102 [] 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00019
                       Recombinase  7 vrrifelylegkslksiaryLnee 30
                                      vrri++ly   ks+k++a +Ln  
  gi|330506858|ref|YP_004383286.1|  4 VRRIVDLYELHKSYKKVASELNIS 27
                                      9*********************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 ?   14.0   0.0   6.4e-05     0.036      26      47 ..      15      36 ..       9      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.4e-05
                            HTH_36 26 psqetlakrlglsknTvsraik 47
                                       s++  a+ l++s+nTv +++ 
  gi|330506858|ref|YP_004383286.1| 15 KSYKKVASELNISRNTVKKYLH 36
                                      69******************96 PP

>> Phage_NinH  Phage NinH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     7e-05     0.039      21      42 ..      19      40 ..       2      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7e-05
                        Phage_NinH 21 EvARrlkcsRatvRkYvrDkea 42
                                       vA  l+ sR+tv+kY++  + 
  gi|330506858|ref|YP_004383286.1| 19 KVASELNISRNTVKKYLHQVKD 40
                                      6999************987665 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   6.8e-05     0.038      52     105 ..      17      72 ..       5      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.8e-05
                           DUF2089  52 lkevekelgisYpTvrnrldeileaLgyeeeee.eee.eeeerkeileklekgeis 105
                                        k+v++el+is +Tv++ l+++    +  +ee   ++ +  + +++l++l + +i+
  gi|330506858|ref|YP_004383286.1|  17 YKKVASELNISRNTVKKYLHQVKDVQEGLAEEIiPKNrKIVQPSRVLTDLVRQKIH 72 
                                       699****************9987655444443322222455678888888888775 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1    0.0001     0.057      18      40 ..      17      39 ..       5      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                            HTH_11 18 geeLAeeLnvSrrtvrrdIkaLe 40
                                       ++ A eLn+Sr tv +++ + +
  gi|330506858|ref|YP_004383286.1| 17 YKKVASELNISRNTVKKYLHQVK 39
                                      567799************98766 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0032       1.8      19      47 ..      12      40 ..       2      58 .. 0.85
   2 ?    3.9   0.0     0.093        52      39      52 ..      60      73 ..      55      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0032
                                      EEEHHHHHHHHHTTSSHHHHHHHHHHHHH CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkr 47
                                      el+ + +  As l+++r tv + l++ k+
  gi|330506858|ref|YP_004383286.1| 12 ELHKSYKKVASELNISRNTVKKYLHQVKD 40
                                      577788999***************99875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.093
                                      HHHHHHHHHTTSEE CS
                         HTH_Crp_2 39 srilseLkreglis 52
                                      sr+l++L r+++++
  gi|330506858|ref|YP_004383286.1| 60 SRVLTDLVRQKIHQ 73
                                      9**********998 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013     0.075      25      47 ..      16      38 ..      11      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                            HTH_10 25 tlkeLAkelGIskstlsehLrka 47
                                      + k++A el+Is++t++++L ++
  gi|330506858|ref|YP_004383286.1| 16 SYKKVASELNISRNTVKKYLHQV 38
                                      6789****************876 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   7.9e-05     0.044      26      79 ..       2      56 ..       1      78 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.9e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHH CS
                      Seryl_tRNA_N 26 advdelleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkel 79
                                      adv ++++l+e  ++ ++ + el+  rN++ k  ++ k+ +   aee+i + +++
  gi|330506858|ref|YP_004383286.1|  2 ADVRRIVDLYELHKSYKKVASELNISRNTVKKYLHQVKDVQeGLAEEIIPKNRKI 56
                                      6999**********************************98866666666665555 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   0.00016      0.09       8      44 ..      14      50 ..       7      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                    YdaS_antitoxin  8 vGgqkaLAealgvsqqaVsqWlkgkkqvpaervpeIe 44
                                        + k++A +l++s+ +V + l+  k v      eI 
  gi|330506858|ref|YP_004383286.1| 14 HKSYKKVASELNISRNTVKKYLHQVKDVQEGLAEEII 50
                                      56889******************99998887776665 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00022      0.12      29      65 ..      13      49 ..       9      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00022
                                      SEEEHHHHHHHCT--HHHHHHHHHHHHHHCHCCT-EE CS
                               Mga 29 eevsieelaqelyiSestlkrkikelnklLkefdlel 65
                                       ++s ++ a el iS+ t+k+ +++++ + +    e+
  gi|330506858|ref|YP_004383286.1| 13 LHKSYKKVASELNISRNTVKKYLHQVKDVQEGLAEEI 49
                                      578999********************98866666555 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00018     0.098      14      49 ..       6      43 ..       3      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00018
                         HTH_Tnp_1 14 riVreslepgksvsevArrhgvspnqLykWrrqyr...e 49
                                      riV ++ e  ks++ vA ++++s+n+  k   q++   e
  gi|330506858|ref|YP_004383286.1|  6 RIVDLY-ELHKSYKKVASELNISRNTVKKYLHQVKdvqE 43
                                      899999.*******************9999888874423 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00065      0.36      26      50 ..      14      37 ..       5      39 .. 0.88
   2 ?   -1.0   0.0       2.1   1.2e+03       5      20 ..      56      71 ..      55      78 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00065
                      HTH_Tnp_ISL3 26 esrsvkavArqlgvSwtTVwrildr 50
                                      +  s k vA +l++S +TV+ +l++
  gi|330506858|ref|YP_004383286.1| 14 HK-SYKKVASELNISRNTVKKYLHQ 37
                                      44.999**************99987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.1
                      HTH_Tnp_ISL3  5 warrrsriTlrleayi 20
                                      ++++ +  T + +++i
  gi|330506858|ref|YP_004383286.1| 56 IVQPSRVLTDLVRQKI 71
                                      5788888899888888 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   0.00044      0.25      19      38 ..      16      35 ..      14      36 .. 0.93
   2 ?   -2.4   0.0       6.7   3.7e+03       5      15 ..      68      78 ..      65      78 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00044
                            HTH_24 19 sqreLAerlglSpstvnrrl 38
                                      s++ +A +l++S++tv+++l
  gi|330506858|ref|YP_004383286.1| 16 SYKKVASELNISRNTVKKYL 35
                                      8999*************997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.7
                            HTH_24  5 drkILelLqkn 15
                                      + kI ++L+ n
  gi|330506858|ref|YP_004383286.1| 68 RQKIHQYLESN 78
                                      67888888766 PP

>> BrkDBD  Brinker DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00034      0.19      28      55 ..      17      44 ..       8      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00034
                                      HHHHHHHTTS-HHHHHHHHTTHHHHHHH CS
                            BrkDBD 28 yRAvAkkynisrknvekWlqveeqlqea 55
                                      y+ vA   nisr  v+k+l + ++ qe 
  gi|330506858|ref|YP_004383286.1| 17 YKKVASELNISRNTVKKYLHQVKDVQEG 44
                                      8899***************999998885 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00037      0.21       7      30 ..      12      35 ..       5      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00037
                                      HTTHHHHHHHHHHTSSHHHHHHHH CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisriE 30
                                      +l  s +++A +l++sr+t+ ++ 
  gi|330506858|ref|YP_004383286.1| 12 ELHKSYKKVASELNISRNTVKKYL 35
                                      577899****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1397  (0.0779185); expected 358.6 (0.02)
Passed bias filter:                      882  (0.049194); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 796.03
//
Query:       gi|330506859|ref|YP_004383287.1|  [L=250]
Description: hypothetical protein MCON_0644 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-14   52.6   0.0    6.7e-14   52.1   0.0    1.2  1  rve       Integrase core domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   3.7e-18   6.7e-14       2     117 ..       4     126 ..       3     128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 3.7e-18
                               rve   2 trpgelwqvDvt..vvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngs 76 
                                       +r g++ + D+   +++i++ ++k yl+v+v+ fs + +a  + ++ +   v++++ ++++  g v p+++ +D++ 
  gi|330506859|ref|YP_004383287.1|   4 PRVGQRAEFDWGevTLNIAEVWQKFYLAVFVLPFSLYRFARLYHRS-ARLEVIQAHIEFFREIGSV-PDAIFYDRMA 78 
                                       678999******9999******************************.99999999999********.********98 PP

                               rve  77 eytsk.......afrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                       +  ++       +f ef  ++g+++++++p++p+++G  E  ++++++
  gi|330506859|ref|YP_004383287.1|  79 AAYDSrkqqfndKFLEFSMHFGFQPCVCNPASPNEKGTDEESVGYVRR 126
                                       877667***************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2049.75
//
Query:       gi|330506860|ref|YP_004383288.1|  [L=305]
Description: transposase integrase [Methanosaeta concilii GP6]
Scores for complete 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   57.5   0.0    2.9e-15   56.5   0.0    1.4  1  rve           Integrase core domain
    5.5e-06   26.0   0.2    1.2e-05   24.9   0.2    1.6  1  HTH_23        Homeodomain-like domain
      6e-06   25.9   0.7    0.00015   21.5   0.2    3.1  2  rve_3         Integrase core domain
    1.9e-05   24.7   6.0    0.00012   22.2   0.7    3.4  3  HTH_21        HTH-like domain
    6.8e-05   22.8   0.0    0.00013   21.9   0.0    1.5  1  HTH_29        Winged helix-turn helix
    0.00046   20.3   0.3    0.00046   20.3   0.3    2.2  2  HTH_28        Helix-turn-helix domain
     0.0018   18.9   0.1     0.0048   17.5   0.1    1.8  1  HTH_32        Homeodomain-like domain
     0.0083   15.7   1.6        0.1   12.3   0.1    2.7  3  HTH_33        Winged helix-turn helix
     0.0098   15.3   0.1      0.024   14.0   0.1    1.7  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
  ------ inclusion threshold ------
      0.019   14.9   0.2      0.037   14.0   0.2    1.4  1  HTH_11        HTH domain
      0.022   14.7   0.1      0.049   13.5   0.1    1.6  2  PAX           'Paired box' domain
      0.073   12.5   0.5      0.096   12.1   0.5    1.2  1  RNase_E_G     Ribonuclease E/G family
       0.16   12.7   0.1       0.25   12.0   0.1    1.3  1  RPA_C         Replication protein A C terminal


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   2.1e-18   2.9e-15       3     115 ..     130     249 ..     128     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.1e-18
                               rve   3 rpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve.pervlsDngsey 78 
                                       ++ +  ++D+ + +  +  +++ ++v++dd+sr++la    +e+++++   ++++ v++f+++   ++++ D+gse+
  gi|330506860|ref|YP_004383288.1| 130 HSMSAGHIDWHEWD--G--TDVKVCVILDDASRMVLAGGEFTEINTENSMLIIDQLVDKFWWLCpLRELILDHGSEF 202
                                       56667788888777..3..3699**************9999997777777777777777777665899********* PP

                               rve  79 tsk..........afrefladlgirvsftrpgrpqdnGkvErfhrtl 115
                                        ++          +f++ l+++gi++ ++r+ +pq+nGk Erf++ +
  gi|330506860|ref|YP_004383288.1| 203 GAHrihddgswnsEFKDHLKKYGIKPILARAKHPQTNGKLERFFGEY 249
                                       ********************************************975 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2   8.9e-09   1.2e-05      10      49 ..      11      50 ..       4      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 8.9e-09
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryreeGlegl 49
                                      il+  ++G  ++eIAr   vs+r v++++k y+e G e++
  gi|330506860|ref|YP_004383288.1| 11 ILRQNRKGVATKEIARDVKVSQRRVQQIIKEYKETGQEPV 50
                                      77888889****************************9986 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.7   2.4e+03      27      53 ..      16      42 ..       8      45 .. 0.78
   2 !   21.5   0.2   1.1e-07   0.00015       2      63 ..     225     275 ..     224     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.7
                             rve_3 27 rdellneelfrslaearekleawredY 53
                                      r+ + ++e+ r+++  ++ +++ +++Y
  gi|330506860|ref|YP_004383288.1| 16 RKGVATKEIARDVKVSQRRVQQIIKEY 42
                                      666777788888888999999999998 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.1e-07
                             rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssLg 63 
                                       gi++ + + ++Pq+Ng+ E+f+g + ++    ++f          e+++++YN  RPH sL+
  gi|330506860|ref|YP_004383288.1| 225 GIKPILARAKHPQTNGKLERFFGEYVKHRPAFHSF----------EEFITWYND-RPHGSLN 275
                                       89999999***************998887777777..........********6.9****98 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.1      0.12   1.7e+02      28      49 ..      22      41 ..       5      43 .. 0.79
   2 !   22.2   0.7   8.5e-08   0.00012       4      53 ..      64     111 ..      61     122 .. 0.88
   3 ?   -1.1   0.0       1.6   2.2e+03      11      28 ..     192     209 ..     189     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.12
                            HTH_21 28 aeLrreggvrvnhkrVrRlMre 49
                                      +e+ r+  v+v+ +rV+ + +e
  gi|330506860|ref|YP_004383288.1| 22 KEIARD--VKVSQRRVQQIIKE 41
                                      455555..78*********998 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 8.5e-08
                            HTH_21   4 dallalireifeeskgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLr 53 
                                       +++ ++ir++++++  r G+r +   +r+++++ ++h+r++   + +GL 
  gi|330506860|ref|YP_004383288.1|  64 EKETEAIRAAHARY--RFGARMLETVIRKQFKICISHNRIHMYLKAAGLA 111
                                       567899******86..8*******************************94 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.6
                            HTH_21  11 reifeeskgrYGyrriwa 28 
                                       re+  ++    G+ ri+ 
  gi|330506860|ref|YP_004383288.1| 192 RELILDHGSEFGAHRIHD 209
                                       7888999999*****985 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   9.3e-08   0.00013       4      61 ..      11      67 ..      10      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 9.3e-08
                            HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrsgrprn.rlseeq 61
                                      +l+  ++Gv  +++iA+ + +s r v+ ++k + e+G +  l  +   grpr+     e+
  gi|330506860|ref|YP_004383288.1| 11 ILRQNRKGVA-TKEIARDVKVSQRRVQQIIKEYKETGQEPVLGeKV--GRPRKpFTEKET 67
                                      688999***8.*****************************998555..999985555554 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   3.3e-07   0.00046      11      52 .]      17      59 ..       8      60 .. 0.80
   2 ?   -1.8   0.1       2.6   3.6e+03      42      51 ..     113     122 ..     106     122 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.3e-07
                            HTH_28 11 aGhsvreaArelgisrrtvyrWikryeegGia.gLvprrrrpr 52
                                      +G++ +e+Ar + +s+r+v++ ik y e G +  L  + +rpr
  gi|330506860|ref|YP_004383288.1| 17 KGVATKEIARDVKVSQRRVQQIIKEYKETGQEpVLGEKVGRPR 59
                                      58999*************************9844444556665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                            HTH_28  42 agLvprrrrp 51 
                                       ++L++++rr+
  gi|330506860|ref|YP_004383288.1| 113 EDLKKQKRRK 122
                                       7889999986 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.5e-06    0.0048       2      72 ..      35     104 ..      34     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.5e-06
                            HTH_32   2 vsrwlkRyneeGle.gLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyri 72 
                                       v+  +k y+e+G e  L ++  r+r++ +++ + ++i+a   +  r+++r l   +++++ + +Sh  ++ +
  gi|330506860|ref|YP_004383288.1|  35 VQQIIKEYKETGQEpVLGEKVGRPRKP-FTEKETEAIRAAHARY-RFGARMLETVIRKQFKICISHNRIHMY 104
                                       678899******998999995555555.9999999999999455.***********8888999***999865 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.4   7.4e+03      21      32 ..      29      40 ..      27      42 .. 0.53
   2 !   12.3   0.1   7.3e-05       0.1       8      36 ..      82     110 ..      76     113 .. 0.92
   3 ?    1.6   0.0      0.16   2.2e+02      29      49 ..     219     239 ..     215     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.4
                            HTH_33 21 sysvsgvyrlLk 32
                                      ++s+++v ++ k
  gi|330506860|ref|YP_004383288.1| 29 KVSQRRVQQIIK 40
                                      555555555443 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.3e-05
                            HTH_33   8 arlaqlieerfgvsysvsgvyrlLkrlGf 36 
                                       + l+++i+++f + +s+ +++ +Lk +G+
  gi|330506860|ref|YP_004383288.1|  82 RMLETVIRKQFKICISHNRIHMYLKAAGL 110
                                       67899**********************97 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.16
                            HTH_33  29 rlLkrlGfsyqkPrprapkqd 49 
                                       + Lk+ G+ ++ +r ++p+ +
  gi|330506860|ref|YP_004383288.1| 219 DHLKKYGIKPILARAKHPQTN 239
                                       579**************9965 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.7e-05     0.024      18      51 ..       9      42 ..       8      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                      HTH_Tnp_ISL3 18 ayilelllesrsvkavArqlgvSwtTVwrildry 51
                                      +yil++ +++ + k++Ar++ vS ++V+ i+++y
  gi|330506860|ref|YP_004383288.1|  9 RYILRQNRKGVATKEIARDVKVSQRRVQQIIKEY 42
                                      68999999999********************987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   2.7e-05     0.037       4      49 ..       7      53 ..       4      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-05
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIese 49
                                      ++  +L+++r+ +  +e+A+  +vS r v++ Ik+ +e+g  p+ +e
  gi|330506860|ref|YP_004383288.1|  7 KVRYILRQNRKGVATKEIARDVKVSQRRVQQIIKEYKETGqEPVLGE 53
                                      66789******************************999997777665 PP

>> PAX  'Paired box' domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.6e-05     0.049      26      62 ..      11      47 ..       3      90 .. 0.84
   2 ?   -3.2   0.0       5.5   7.6e+03      76      98 ..     238     260 ..     224     261 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.6e-05
                               PAX 26 ivelahsgvrpcvisrqlrvshgcvskilgryqetgs 62
                                      i+   ++gv   +i+r ++vs+  v +i+  y+etg 
  gi|330506860|ref|YP_004383288.1| 11 ILRQNRKGVATKEIARDVKVSQRRVQQIIKEYKETGQ 47
                                      6677889****************************96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.5
                               PAX  76 atpevvkkieeykrenpsifawe 98 
                                       +  +++    ey ++ p++ ++e
  gi|330506860|ref|YP_004383288.1| 238 TNGKLERFFGEYVKHRPAFHSFE 260
                                       45556666677888888877766 PP

>> RNase_E_G  Ribonuclease E/G family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5     7e-05     0.096      39      78 ..       4      54 ..       1     138 [. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7e-05
                         RNase_E_G 39 kpeevGlIvRtaaegaseeelekdleelkkkweeileka...........k 78
                                      ++++v +I+R + +g+ ++e+++d++  ++++++i++++           k
  gi|330506860|ref|YP_004383288.1|  4 NKTKVRYILRQNRKGVATKEIARDVKVSQRRVQQIIKEYketgqepvlgeK 54
                                      5567789*******************************9443333333330 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00018      0.25      63      95 ..      14      46 ..       1      47 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                      XSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTT CS
                             RPA_C 63 eseeGvhvdeiaqklrlsvndvkqavdeLsneG 95
                                      ++ +Gv  +eia+ +++s + v+q+++e  + G
  gi|330506860|ref|YP_004383288.1| 14 QNRKGVATKEIARDVKVSQRRVQQIIKEYKETG 46
                                      4889**********************9988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.94
# Mc/sec: 978.87
//
Query:       gi|330506861|ref|YP_004383289.1|  [L=97]
Description: hypothetical protein MCON_0646 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       291  (0.0162307); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 760.53
//
Query:       gi|330506862|ref|YP_004383290.1|  [L=351]
Description: hypothetical protein MCON_0647 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2666.13
//
Query:       gi|330506863|ref|YP_004383291.1|  [L=339]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-40  139.5   0.0    1.5e-40  139.2   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 !  139.2   0.0   8.6e-45   1.5e-40       1     234 [.      43     279 ..      43     283 .. 0.93

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 8.6e-45
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                       ++sl+++v+e l+al+ ++++vg+d ++ +p   +++   ++   ++ ++d+E+++ l+PDlvi++++l   d+ +e
  gi|330506863|ref|YP_004383291.1|  43 VVSLGTGVAEYLYALDGEKSLVGRDSYSHFPPGLEEV---PIAGKSSYSPDLERIISLHPDLVIADTML-SDDDSKE 115
                                       89********************************985...68889999*********************.9999999 PP

                                       HHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE..EE CS
                      Peripla_BP_2  78 llksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggadeggyv 152
                                       l+ +gip++        ++  e ++ lg l g+e++a+++  +i +  ++++++i+s    ++p  vf ++++++y+
  gi|330506863|ref|YP_004383291.1| 116 LENAGIPVMLESLVDP-AKDNEVMEKLGALMGKEERAQEITDFIAGYQDMIQERIASVkpEDRPK-VFFEWAGKPYY 190
                                       *********9999988.8888899**********************************6433444.66667777999 PP

                                       EE-TTSTTTHHHHTS--EESTTT--..STT-EEE-HHHHHHH--SEEEEEEH.....HHHT-S--HHHHT-SHHHHT CS
                      Peripla_BP_2 153 vagsnsyigdlldalgieniaaesk..kseyeeisaEqilasdpdvifvsgr.....aeadnktgleflkenpllae 222
                                         ++++    l++ +g++nia++ +  +++y ++s+E++++ dpdvi+   +       ++ kt  ++++++p+la+
  gi|330506863|ref|YP_004383291.1| 191 TVSNGNPSDTLIRLAGGDNIAKDLGnsTHSYPTVSPEWVVEVDPDVIIQQRSsdkafTGNELKTLRDEIIARPELAD 267
                                       9999999999**************9************************99999***9******************* PP

                                       SHHHHTT-EEEE CS
                      Peripla_BP_2 223 lpAvkngrVyal 234
                                       ++Avk grVy +
  gi|330506863|ref|YP_004383291.1| 268 VKAVKDGRVYLV 279
                                       **********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2572.89
//
Query:       gi|330506864|ref|YP_004383292.1|  [L=208]
Description: precorrin-8X methylmutase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-58  196.7   0.8    3.5e-58  196.5   0.8    1.0  1  CbiC      Precorrin-8X methylmutase


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.5   0.8     2e-62   3.5e-58       1     196 []      17     204 ..      17     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 196.5 bits;  conditional E-value: 2e-62
                                       HHHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HH CS
                              CbiC   1 eIeaeSfaiideelgeeelseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitkk 77 
                                       +I ++S +ii e +g++   + e+++ +R+  at+d+++ae++rf +d ++agl+al ++a+i++D++mvk G+ kk
  gi|330506864|ref|YP_004383292.1|  17 DISRRSRKIISEIVGDR---TPEDRIRQRCAIATGDPSVAEIMRFVKDPISAGLRALDEKARIFVDINMVKDGVVKK 90 
                                       599************88...999***************************************************999 PP

                                       HHHTTC-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE--- CS
                              CbiC  78 rleklgnevlclladpevaelakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPv 154
                                        +++   +++ ++ +    +la+++gitr++a++ ++++el+g+iv+iGnAP+ALl+l++li++g vkpalvig+Pv
  gi|330506864|ref|YP_004383292.1|  91 GHQC---SITAMIGKG--DDLAEKDGITRTSAGVLAFQSELSGGIVMIGNAPSALLTLCDLIASGIVKPALVIGTPV 162
                                       8876...688888887..6799******************************************************* PP

                                       -SCCHHHHHHHHHCSSS-EEEESSS---HHHHHHHHHHHHHH CS
                              CbiC 155 GFvgaaesKealaesevpyitveGrkGGsavAaaivnaLlel 196
                                       GFv+aa sKe+l++++vp+i + G++GG+++A+a++n+++++
  gi|330506864|ref|YP_004383292.1| 163 GFVNAAASKERLRSLDVPSISIVGTRGGTPIAVAAMNEMINM 204
                                       **************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1713.01
//
Query:       gi|330506865|ref|YP_004383293.1|  [L=515]
Description: hypothetical protein MCON_0652 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-10   38.5   0.0    3.7e-08   33.2   0.0    2.4  2  Peptidase_C13  Peptidase C13 family
    2.6e-08   34.2   0.0    5.6e-08   33.0   0.0    1.6  2  Peptidase_C14  Caspase domain
  ------ inclusion threshold ------
       0.13   11.8   0.1       0.28   10.8   0.1    1.6  1  EF-hand_5      EF hand


Domain annotation for each model (and alignments):
>> Peptidase_C13  Peptidase C13 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.011        65       2      40 ..     232     269 ..     231     273 .. 0.89
   2 !   33.2   0.0   6.2e-12   3.7e-08     100     166 ..     296     361 ..     282     450 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.011
                                       EEEEEE---SG.GGHHHHHHHHHHHHHHHCTT--GGGEEE CS
                     Peptidase_C13   2 yavlvAGsngy.dnyrhqadvchayqllkkkglkdenivv 40 
                                       +av+v+G n+  d + ++++   +y +lk+ g++d +i  
  gi|330506865|ref|YP_004383293.1| 232 WAVIVCGFNDLpDTFDEDTE--GIYSILKSLGIDDSHIYF 269
                                       *******9997478999999..**************9975 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 6.2e-12
                                       -----TTSEEEEEEES-EETT.EEE-S...SSSEEEHHHHHHHHHHHHHCT--SEEEEEEESTTGGGGTTT CS
                     Peptidase_C13 100 vlksgkeDnvfiyltdhGapg.vlevp...eeddleakdLaeaLkkmhakkkykklviyleaceSgsmfee 166
                                         ksg +D+v+ ++++hG+ + +       ++ +++a dL + L++   k++     i++eac Sgs++ +
  gi|330506865|ref|YP_004383293.1| 296 AAKSGVNDKVLFFYSSHGGVDgL-VCStgtSGGTIYAGDLDNWLDRITCKEM----AIIVEACHSGSLIGK 361
                                       5689***************9954.444378899************9998888....************976 PP

>> Peptidase_C14  Caspase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       0.8   4.8e+03     110     150 ..     151     190 ..     144     207 .. 0.67
   2 !   33.0   0.0   9.3e-12   5.6e-08      22     169 ..     247     412 ..     232     470 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.8
                                       TTTHGGGTTS-EEEEEESES..SSBCBEEEEEEES-SSSHCCC CS
                     Peptidase_C14 110 gdklpslagkpktiiidaCr..gglldkgiekdtsptnkfeed 150
                                       g +  +++   k++++da     +++++ +++++++++ f+++
  gi|330506865|ref|YP_004383293.1| 151 GAHFAHPV---KLVVVDAVTrdQQVIETEWWPKVDSRQVFDKE 190
                                       55555554...77888854447788899999999988884333 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 9.3e-12
                                       HHHHHHHHHHHHHHTTEEEEEEEGGEES.........-CHHHHHHHHHHHHCHSGGTTESEEEEEEESEEET..... CS
                     Peptidase_C14  22 anDaermaklLvkrlgFevenililtdd.........ptgknirkalkwlvksadhspgDslvvhysGHGtrvpae. 88 
                                       + D e ++ +L k+lg + + i  l             t +n++ a++++++++    +D ++++ys+HG+ v++  
  gi|330506865|ref|YP_004383293.1| 247 DEDTEGIYSIL-KSLGIDDSHIYFLSPHtghtgvdalNTIENVQWAINEVAAKSG--VNDKVLFFYSSHGG-VDGLv 319
                                       78999999999.9***9999988777779*******99************97777..99************.45555 PP

                                       EEECTTCSSEEEHHHHHHTTSTTTHGGGTTS-EEEEEESES.SSBC.....................BEEEEEEES- CS
                     Peptidase_C14  89 civpvdvnsliqdddirdlfggdklpslagkpktiiidaCr.ggll.....................dkgiekdtsp 143
                                       c  +++ +++i   d+ + ++  ++++       ii+ aC+ g+l+                     +         
  gi|330506865|ref|YP_004383293.1| 320 CSTGTS-GGTIYAGDLDNWLDRITCKEM-----AIIVEACHsGSLIgkysdgtfvpaesdltadgetN--------- 381
                                       666666.888888888777755555555.....5*******999996666555555444444443332......... PP

                                       SSS.......HCCCHCHHHHHHCSHHCEEECTT CS
                     Peptidase_C14 144 tnk.......feedssskekkpekqslsklpse 169
                                         +        +++s+++ + p + + s   se
  gi|330506865|ref|YP_004383293.1| 382 --RviftsasTDSSSYPDIDGPDDPNPSDSGSE 412
                                       ..0443443322335555555555555544444 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   4.6e-05      0.28       8      20 ..     426     438 ..     425     441 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.6e-05
                                       H-SS-SSCE-HHH CS
                         EF-hand_5   8 iDlNgDGkIskeE 20 
                                       +D +gDG+Is+ E
  gi|330506865|ref|YP_004383293.1| 426 ADEDGDGRISFGE 438
                                       799*******988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 3552.05
//
Query:       gi|330506866|ref|YP_004383294.1|  [L=111]
Description: hypothetical protein MCON_0653 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 852.53
//
Query:       gi|330506867|ref|YP_004383295.1|  [L=342]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-29  103.4   0.0      2e-29  102.9   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9   0.0   1.1e-33     2e-29       1     233 [.      53     288 ..      53     290 .. 0.89

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 1.1e-33
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                       ++ l+ ++ e+ + l+a dkvvgv++++ + ++  ++  + +++g+++e+d+Ek+a+l PD+v++ k+   +  ++e
  gi|330506867|ref|YP_004383295.1|  53 VVLLTADNCELAVVLDARDKVVGVEKSAPGYAEIGEMFGKAANAGGSQEPDFEKIADLNPDVVLGYKSSLENGVADE 129
                                       78999********************99888777777777**************************9999899***** PP

                                       HHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE..EEE CS
                      Peripla_BP_2  78 llksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse.kpkpvlvfggadeggyvv 153
                                       l   gip+v+ e +   + +++ ++  g +lg+ed+a+++ a+++s ++ + ++++s+  +  + ++ ++ +   + 
  gi|330506867|ref|YP_004383295.1| 130 LKGMGIPFVVCECNRI-QTFEKDVELMGRILGKEDNAKEFLAFHNSIMDLIAERTRSIsSDQRTSLYLTGGG---TT 202
                                       **************97.******************************************5666666665555...9* PP

                                       E-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH......HHHT-S--HHHHT-SHHHHTSH CS
                      Peripla_BP_2 154 agsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr......aeadnktgleflkenpllaelp 224
                                       +g +++i ++l+a+g+++i +e +++++ ++++E++l +dp+vi+   +        +   +++e   ++p+l+ ++
  gi|330506867|ref|YP_004383295.1| 203 FGKDGGIEPYLSAVGAKSIGSELPGESSVTVDPEWVLDQDPQVIVHWITsskikpTPEPLIEVKESYSNDPVLNMTT 279
                                       *******************************************987777444554444445555555679******* PP

                                       HHHTT-EEE CS
                      Peripla_BP_2 225 AvkngrVya 233
                                       Avk grV  
  gi|330506867|ref|YP_004383295.1| 280 AVKDGRVHV 288
                                       ******965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2671.57
//
Query:       gi|330506868|ref|YP_004383296.1|  [L=450]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-25   89.8   0.0    3.3e-25   89.0   0.0    1.4  1  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
      0.014   14.7   0.3      0.021   14.1   0.3    1.3  1  DDE_Tnp_2    Archaeal putative transposase ISC1217
      0.019   13.3   0.0       0.03   12.6   0.0    1.2  1  DDE_Tnp_1_4  Transposase DDE domain group 1
      0.075   13.0   1.0        1.4    8.9   0.1    2.8  3  Tudor_FRX1   Fragile X mental retardation Tudor 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 !   89.0   0.0   7.3e-29   3.3e-25       2     212 ..     133     371 ..     132     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 7.3e-29
                         DDE_Tnp_1   2 skrevlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkq..lldelrprk 76 
                                       s+r+v i D+t +r +++ +d+++     k  +g+k+  ++++    + s+ i p n++d+k+lk   ++      k
  gi|330506868|ref|YP_004383296.1| 133 SFRDVMIQDSTIIRLHKSLADKWPATRSRKVAAGVKVAFLTSAIANSPKSISILPENTNDVKTLKIgpWV------K 203
                                       6899***************9999988899999********************************995555......7 PP

                         DDE_Tnp_1  77 gklvlaDaGYasaelldtleekgvdyiirlkkntklyrk.............gaeskrrgrlrkhdrnkiltksqkr 140
                                       + ++l D G+ +++l+ ++ e+g+++++rlk+n++ ++              + +++++ +l+k d    ++ + ++
  gi|330506868|ref|YP_004383296.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVgtnqvrntrgvdlNGKHLKDIKLEKSDDIFDVNVEVSF 280
                                       789************************************99777666666663444444444444444444444444 PP

                         DDE_Tnp_1 141 rnk...................skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrgl 198
                                       +++                    +++++++ y+tn++s+ l a+eva+ y+ Rw++E +Fk+lk+++ ld   ++++
  gi|330506868|ref|YP_004383296.1| 281 DRRsyrgeskkdnkifrlvaiyNTEAEEHHFYLTNISSDILNASEVAAVYSGRWEVELIFKELKSRYALDQITTKSP 357
                                       4447777777777799999999999**************************************************** PP

                         DDE_Tnp_1 199 nrveaqllllllal 212
                                        ++ea ++  +l+l
  gi|330506868|ref|YP_004383296.1| 358 YAIEALIWVSILTL 371
                                       *******9998876 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   4.6e-06     0.021     219     288 ..     274     346 ..     202     384 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                         DDE_Tnp_2 219 rhvpvaelPeGeylveyl.dtvikllvlddykkdgrrylfstdln...dtdediittWenrWdievlirelkal 288
                                        +v+v+ + + +y  e   d+ i  lv +   + +  +++ t++    + + ++ + +  rW++e +++elk+ 
  gi|330506868|ref|YP_004383296.1| 274 VNVEVS-FDRRSYRGESKkDNKIFRLVAIYNTEAEEHHFYLTNISsdiLNASEVAAVYSGRWEVELIFKELKSR 346
                                       445543.7777888887767777767777777888999**999973335799********************73 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.6e-06      0.03     217     368 ..     204     372 ..     197     399 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.6e-06
                       DDE_Tnp_1_4 217 kilvRgDSafarpellkwceergvdYviglaknsrlealiaelvekakteaaekkek................erey 277
                                       +i++  D +f + +l++ + e+g ++v +l++n++     ++ v +++  + + k+                 e+++
  gi|330506868|ref|YP_004383296.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVGTNQVRNTRGVDLNGKHLkdikleksddifdvnvEVSF 280
                                       578889999**********************999877766666666666666654436799999999**99999999 PP

                       DDE_Tnp_1_4 278 refayqaesWskerrVvakaerpaeglnlrfvvTsla..klspeelyeqlYcaRGemEnrIKeakldlaadrtsshs 352
                                        +  y+ es + ++   + a +++e  +++f +T+++   l+++e+   +Y  R e+E  +Ke k+  a+d++ ++s
  gi|330506868|ref|YP_004383296.1| 281 DRRSYRGESKKDNKIFRLVAIYNTEAEEHHFYLTNISsdILNASEVA-AVYSGRWEVELIFKELKSRYALDQITTKS 356
                                       99999999855444333334455556667999****99888999999.9*************************999 PP

                       DDE_Tnp_1_4 353 faaNqlrlllsalAyn 368
                                         a ++ +++s l   
  gi|330506868|ref|YP_004383296.1| 357 PYAIEALIWVSILTLL 372
                                       9999988888887654 PP

>> Tudor_FRX1  Fragile X mental retardation Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00031       1.4      17      36 ..      22      41 ..      18      44 .. 0.88
   2 ?    1.1   0.0     0.085   3.8e+02      18      31 ..     269     282 ..     257     291 .. 0.89
   3 ?   -2.6   0.0       1.2   5.4e+03      13      36 ..     313     337 ..     311     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00031
                        Tudor_FRX1 17 vkdvhedsltvaFennWqpe 36
                                       kd+ e++lt +Fe +W  +
  gi|330506868|ref|YP_004383296.1| 22 EKDIVEQELTRMFESKWIRD 41
                                      59***************765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.085
                        Tudor_FRX1  18 kdvhedsltvaFen 31 
                                        d+++ ++ v+F+ 
  gi|330506868|ref|YP_004383296.1| 269 DDIFDVNVEVSFDR 282
                                       59**********96 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.2
                        Tudor_FRX1  13 ykafvkdvhed.sltvaFennWqpe 36 
                                       +  +  d+++  ++ +++   W  e
  gi|330506868|ref|YP_004383296.1| 313 LTNISSDILNAsEVAAVYSGRWEVE 337
                                       5566778888526888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3242.15
//
Query:       gi|330506869|ref|YP_004383297.1|  [L=1251]
Description: cobaltochelatase, CobN subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
          0 1394.1   0.0          0 1393.9   0.0    1.0  1  CobN-Mg_chel   CobN/Magnesium Chelatase
  ------ inclusion threshold ------
      0.071   12.9   0.0        0.2   11.5   0.0    1.7  1  LexA_DNA_bind  LexA DNA binding domain


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 ! 1393.9   0.0         0         0       2    1088 ..     119    1231 ..     118    1232 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1393.9 bits;  conditional E-value: 0
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel    2 aYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilf 76  
                                        +Yl++gg++N knll y+ +++lg ++ ev +p++ p+egiyhpd   ++++l+ey ++   ++ke +pt+g++f
  gi|330506869|ref|YP_004383297.1|  119 RYLAYGGKDNSKNLLLYCLNQFLG-TSYEVGEPKRPPWEGIYHPDF-GYIATLDEYFRK---NYKEGRPTIGLWF 188 
                                        8**********************8.7889**************995.567777777755...89*********** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel   77 yrahllagntavidaliraleerglnvlpvfvssl...d...seaqealeelftkegeekvdalinttsfalvkg 145 
                                        y   ++a+n++++d+lir++e+r++nv+pvf +sl   +   + a+  ++++f+k+g++ +dali+t++f+l+++
  gi|330506869|ref|YP_004383297.1|  189 YSGFWQADNLRFVDSLIREIERRDANVIPVFLYSLkdvElgtKGAEWVIDNYFMKDGQPVIDALISTLMFSLTMK 263 
                                        ***********************************965266699999***************************9 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx. RF
                      CobN-Mg_chel  146 paeeeeeeaeeealkelnvPvlqailssqsreeWeessqGlspldlamsvalpEldGriepvvisfke...eee. 216 
                                        p++ee+    +  +++l+vPv++ail+++++eeW+es qGl+p+d++ms+a+pE+dG+++ v++++k+   +++ 
  gi|330506869|ref|YP_004383297.1|  264 PRDEEK-LFDKPFFERLGVPVIKAILTYNTEEEWRESFQGLNPMDVSMSIAMPEFDGMLIAVPVAAKKmteTDTl 337 
                                        975544.4556669*****************************************************99765558 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  217 eetevekyepipervervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeG 291 
                                        + ++++++epi+erv+++++l+ +wa+Lr+ +n+ek+vaii++nypp+++r+g+a gLd+p S++n+L+ l+ eG
  gi|330506869|ref|YP_004383297.1|  338 TGAKLTRFEPIDERVRKIVSLTLNWAKLRHISNQEKRVAIIFHNYPPRNDRIGTAFGLDSPVSVYNILRDLEGEG 412 
                                        9999*********************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  292 YdveelpesgdeLiellleggtndpew...eelkvgaaallpaeeYeewfeeLpeelreeveerWgeppgemvee 363 
                                        Y +e+lpesg+ Lie +++++tnd++w   e+++ +a++l+pae+Y++wfeeLp +++e+++  Wgeppg    e
  gi|330506869|ref|YP_004383297.1|  413 YGLESLPESGQVLIESMISRVTNDRRWsspEMMAEKAIDLVPAEQYRKWFEELPGAIQEKMVMSWGEPPG----E 483 
                                        ***999*********************88866766***********************************....5 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  364 eksgekklvipglqlGnvfvgvQPargyeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwl 438 
                                           ++++l+ipg++ Gn+f+g+QP+rg+ e+p+++yh+pdlp +h+Y+A+Y+W+r++f+ad v+H+GkHG+lEwl
  gi|330506869|ref|YP_004383297.1|  484 LFVHQGELIIPGISNGNIFIGLQPPRGFLENPEAIYHSPDLPIPHHYYAYYRWIRDVFRADLVMHIGKHGSLEWL 558 
                                        66679********************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  439 PGKqvglseecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeea 513 
                                        PGK+vglse+c+Pdi++ dlP++YpYi+nnpgEGtqAKRRsy++iidHl+P+m +a++y+e+a++e ++++Y +a
  gi|330506869|ref|YP_004383297.1|  559 PGKSVGLSESCFPDIAISDLPNIYPYIINNPGEGTQAKRRSYCCIIDHLIPVMHNADIYDEMAQIEVMLHDYTHA 633 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  514 esldperlkalreqilelveelnldkdlgleeakeeeeeefeellekldgyleelkeaqirdglhilGeapegeq 588 
                                        +s+dp++l+++r+ i+e+v e++ld+dl+++  +e++ ++f+++le+l+gyl+e++++qirdglhi+Ge+peg +
  gi|330506869|ref|YP_004383297.1|  634 ASEDPAKLPTQRKMIWEKVCEAKLDHDLETD--EETAFSDFDSFLERLHGYLHEIADTQIRDGLHIFGEPPEGSR 706 
                                        ****************************666..678899************************************ PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  589 lvdlvvailrleneegesltealaealgldlde...leeksekelrtagdalealeeeaeelveelleeeaeeee 660 
                                        l++++va++rl+n++ +sl+eal++  g+d+d+    + k  +  r+ g+++e+++e + +++++++e +++ ++
  gi|330506869|ref|YP_004383297.1|  707 LEEFLVALTRLKNGKVPSLREALVHLQGFDYDHlleCRGKLLDGERSGGHIIEEVHELSLKIMKRFHEAGFSVDD 781 
                                        *********************************766555566778999**************************9 PP

                                        xxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  661 aeaeeleeeeeeeee.................eteeEitallraLdGeyippgpsGdptrgraevLPTGrNfysv 718 
                                        + +  le   +++ +                 +t++E+t++l a  G+++ppgpsG+ptrg+a++LPTGrNfysv
  gi|330506869|ref|YP_004383297.1|  782 IPSVLLEIVGRTDPDveavlryigmtlvpniaSTTNELTNTLVACRGGFVPPGPSGAPTRGMADILPTGRNFYSV 856 
                                        999998888888777999*************8888**************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                      CobN-Mg_chel  719 DpraiPteaAwevGkklaeellerylqehgeyPekvglslwgtetmrteGediAqiLallGvrPvwdaa.grvvd 792 
                                        Dp aiP++aAw+vG + ae+ll+ryl+e+g+yPe+vg+++wgt  mrt+G+d+A+iL+l+GvrPvw+ + grv++
  gi|330506869|ref|YP_004383297.1|  857 DPLAIPSQAAWKVGIAQAEALLDRYLKEEGKYPENVGIIVWGTPIMRTKGDDVAEILYLMGVRPVWEPRsGRVTG 931 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                      CobN-Mg_chel  793 lelipleeLgRPRiDVtvriSGffRDafpnlielldkavelvaeldEpeedNfvrkhvleeeaeleeke....ea 863 
                                        lelipl+ L+RPRiDVt+riSGffRDafpn++ lld+avelva+l Ep+e+N++++hv ee ae + ++    +a
  gi|330506869|ref|YP_004383297.1|  932 LELIPLQDLNRPRIDVTLRISGFFRDAFPNIVTLLDEAVELVASLREPPESNYLARHVAEEIAEKVGQGidfeKA 1006
                                        **************************************************************9999966666466 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  864 eeratyRvFgskpGaYgagvqeliessnWedeedLaeaYlnwssyaYgkgaegeeaeeafearLkrvdvvvqnqd 938 
                                        +e+a yR+Fg +pGaYgagv ++i+s+nW+de+dLae+Y++w++yaYgk+++g + +e+f++rL ++d++v+n+d
  gi|330506869|ref|YP_004383297.1| 1007 KEEACYRIFGCRPGAYGAGVCDAIDSKNWKDEHDLAEIYITWGGYAYGKKNYGITVPEQFRRRLGQLDLTVKNED 1081
                                        6************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  939 srehdlldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvrtlkeeiarelrsrvlNPkWiegmmrhGy 1013
                                        sre+d+ld dd+y+f+GG++aav+s++g+ p++y+gdss+pe++k+r+  ee+++ +r+r+lNPkWie+m+rhGy
  gi|330506869|ref|YP_004383297.1| 1082 SREWDMLDGDDFYSFHGGMIAAVKSIKGELPKSYCGDSSDPERVKIRNTVEETKHIFRARILNPKWIESMKRHGY 1156
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 1014 kGafelaatvdnlfgwdatadvvddwvyeevaetYvlDeevrefleekNpwAlreiaerLlEaarrglWeaseet 1088
                                        kGa +++++vd  fgwdata+v +dw+yee+a++Y+lDe+++e+l++ Np+Al +i erLlEa++r++W+a++e+
  gi|330506869|ref|YP_004383297.1| 1157 KGAGDMSRMVDIAFGWDATAEVLEDWMYEELANRYALDEKMQEWLKDVNPHALLNISERLLEAIDRNMWNATDEM 1231
                                        ***********************************************************************9985 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.2e-05       0.2      22      55 ..     380     413 ..     374     420 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.2e-05
                                       HSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTS CS
                     LexA_DNA_bind  22 tgypPsireiaralglkSpsaveehLkaLerKGy 55 
                                       + ypP    i+ a+gl Sp +v + L+ Le  Gy
  gi|330506869|ref|YP_004383297.1| 380 HNYPPRNDRIGTAFGLDSPVSVYNILRDLEGEGY 413
                                       68****************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.82u 0.32s 00:00:01.13 Elapsed: 00:00:00.51
# Mc/sec: 7335.12
//
Query:       gi|330506870|ref|YP_004383298.1|  [L=322]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.9e-21   74.4   0.0    1.2e-20   74.1   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.0   6.9e-25   1.2e-20       1     233 [.      32     265 ..      32     268 .. 0.89

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 6.9e-25
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                       i+sl+p   e+    G  d++vg+d  + +p +  ++    v  g +++i+  ++++l+PD+v+   +  +++e e+
  gi|330506870|ref|YP_004383298.1|  32 IVSLTPIASELICIFGCIDRIVGRDDHSTFPPALGEK--PAVGSGVYRTISAKRVLDLDPDIVVTGRRV-PQEEFEK 105
                                       6777777788888788899999987665555555544..479999************************.9****** PP

                                       HHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE CS
                      Peripla_BP_2  78 llksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvva 154
                                       + ++gip+v+  +++++e l  ++  lg +l +e++  +lv ++++    ++++i s++ +  +++++  +  ++ +
  gi|330506870|ref|YP_004383298.1| 106 IGSAGIPVVVIGTGCELEALISNAWNLGRMLATEKKTGELVDFLERYANLIRDRIGSLNIESRPLVYNECAFRKYMT 182
                                       **********************************************************5555555555555559*** PP

                                       -TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH.....HHHT-S--HHHHT-SHHHHTSHHH CS
                      Peripla_BP_2 155 gsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr.....aeadnktgleflkenpllaelpAv 226
                                       +  +   + +  +g++nia  +   ++  +s E++   +pd+i+   +       +    + ++++++p+l++++A+
  gi|330506870|ref|YP_004383298.1| 183 KACTAADEGIALAGGANIAHGE-DLGRLAVSEEWLIGNNPDIIISQVSstspaTVEMLLSKRDEILSRPELKGTNAI 258
                                       ******************9998.*********************9999889987778888999************** PP

                                       HTT-EEE CS
                      Peripla_BP_2 227 kngrVya 233
                                       +ngrVy 
  gi|330506870|ref|YP_004383298.1| 259 RNGRVYI 265
                                       *****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2323.85
//
Query:       gi|330506871|ref|YP_004383299.1|  [L=339]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (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    1.5e-36  126.2   0.5    1.1  1  Peripla_BP_2  Periplasmic binding protein
     0.0003   20.2   0.3    0.00049   19.5   0.3    1.2  1  Rh5           Rh5 coiled-coil domain
  ------ inclusion threshold ------
       0.17   11.1   0.0       0.31   10.3   0.0    1.4  1  DUF2800       Protein of unknown function (DUF2800)


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 !  126.2   0.5   2.5e-40   1.5e-36       1     236 [.      52     287 ..      52     289 .. 0.94

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 2.5e-40
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                       i+s+++   ei   lG +d++vg+d ++ +p+  +++   +v++ ++ ++++E + + +PDlvi++++l   d+ ++
  gi|330506871|ref|YP_004383299.1|  52 IVSITSRASEIISVLGSEDRIVGRDSYSFFPSSLKDV---PVVAESSYSPNIELIHKIDPDLVIADSML-SEDDRKK 124
                                       89********************************985...6****************************.999**** PP

                                       HHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE CS
                      Peripla_BP_2  78 llksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvva 154
                                       ++++gip+++ +       ++  +  lg ll++e++a++l+++i++  + +k++++ +k +  + ++   +++y+ +
  gi|330506871|ref|YP_004383299.1| 125 IEAAGIPVIVETALDS-TTIEAFVSHLGILLDKEEQAQELINFIKKYQDIIKERTEDLKSEDKPAVYIEIGYPYSTM 200
                                       *******988777765.9****************************************666666666668888**** PP

                                       -TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH......HHHT-S--HHHHT-SHHHHTSHH CS
                      Peripla_BP_2 155 gsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr......aeadnktgleflkenpllaelpA 225
                                       +s + +  l+ a+g+ niaa++    y   ++E+i+++dpd+if + +       +++ k++ ++++++p+l++++A
  gi|330506871|ref|YP_004383299.1| 201 ASATTFHNLTIAAGGINIAADQ-PIKYPIMDPEWIVERDPDIIFSYATntaeenLTDKMKEIHDEILSRPELSDVKA 276
                                       **********************.9**************************999999999****************** PP

                                       HHTT-EEEE-H CS
                      Peripla_BP_2 226 vkngrVyalds 236
                                       vk+grVy l++
  gi|330506871|ref|YP_004383299.1| 277 VKEGRVYVLGN 287
                                       ********986 PP

>> Rh5  Rh5 coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   8.1e-08   0.00049      54     161 ..     158     265 ..     156     268 .. 0.97

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.1e-08
                               Rh5  54 kkkkeyvnClknkfkklkkkindikssikkelykiscynsnkcndavykkyaelykseinnklskiknsainkdkei 130
                                       ++ +e++n +k+ +  +k++++d ks+ k+ +y   +y+ + + +a +++++++    in  +++  +++i +   i
  gi|330506871|ref|YP_004383299.1| 158 EQAQELINFIKKYQDIIKERTEDLKSEDKPAVYIEIGYPYSTMASATTFHNLTIAAGGINIAADQPIKYPIMDPEWI 234
                                       567899999******************************************************************** PP

                               Rh5 131 lksikslinilkkelesknlidklkFlkkei 161
                                       ++   ++i     + +++nl dk+k +++ei
  gi|330506871|ref|YP_004383299.1| 235 VERDPDIIFSYATNTAEENLTDKMKEIHDEI 265
                                       ******************************9 PP

>> DUF2800  Protein of unknown function (DUF2800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   5.2e-05      0.31      65     111 ..     152     202 ..     116     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.2e-05
                           DUF2800  65 k..keeevteemeeavdeyvdfvlekieeak..kdalvlvEqrvdfskyvp 111
                                          ++ee  +e+++ +++y d+++e++e++k  +++ v +E   ++s+++ 
  gi|330506871|ref|YP_004383299.1| 152 IllDKEEQAQELINFIKKYQDIIKERTEDLKseDKPAVYIEIGYPYSTMAS 202
                                       26688999***********************98999*****9999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      921  (0.0513693); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2053.86
//
Query:       gi|330506872|ref|YP_004383300.1|  [L=336]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete 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-34  117.5   0.0    8.2e-34  117.2   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 !  117.2   0.0   4.6e-38   8.2e-34       1     236 [.      49     284 ..      49     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 4.6e-38
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                       ias+s+   ei  alGa dk+vg+d ++ +p +  ++    v++ ++ ++++E + +l+PDlvi++++l  +d+ ++
  gi|330506872|ref|YP_004383300.1|  49 IASISSRASEIICALGACDKIVGRDSYSFFPPALADV---QVVAESSYTPNIELIHKLDPDLVIADSML-SNDDRKK 121
                                       89********************************875...59999************************.******* PP

                                       HHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE..EE CS
                      Peripla_BP_2  78 llksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggadeggyv 152
                                       ++++gip+++ +++     + + +r +g ll++ d+ae+++ +i++    ++++++ +   +kp++ f ++ +  y+
  gi|330506872|ref|YP_004383300.1| 122 IESAGIPVIVETTWDS-KTVATPVRHIGVLLDKADRAEEIIGFIERYQGIIEERTAGLeeEDKPAVFFEWSRP--YY 195
                                       **************97.***************************99999999999999866777776666666..** PP

                                       EE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH......HHHT-S--HHHHT-SHHHHTS CS
                      Peripla_BP_2 153 vagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr......aeadnktgleflkenpllael 223
                                        +g+++ +  l+ a+g+ ni a++    y + ++E++++ dpd+i+ ++        +++  +  ++++++p+l ++
  gi|330506872|ref|YP_004383300.1| 196 SMGNGTLFHNLTVAAGGINIVADE-PVKYPTMDPEWLVEKDPDIIIRYDYstekgnLTDNMEKTRDEILSRPELGDV 271
                                       ********************9999.9************************99999867777777899********** PP

                                       HHHHTT-EEEE-H CS
                      Peripla_BP_2 224 pAvkngrVyalds 236
                                       +A+  grVy l++
  gi|330506872|ref|YP_004383300.1| 272 KAIVDGRVYILGN 284
                                       *********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2280.72
//
Query:       gi|330506873|ref|YP_004383301.1|  [L=139]
Description: hypothetical protein MCON_0664 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-31  106.9   0.0    5.5e-26   90.3   0.0    2.0  2  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 !   90.3   0.0   3.1e-30   5.5e-26       1      80 [.      12      92 ..      12      96 .. 0.93
   2 !   14.9   0.0   8.9e-07     0.016      78     103 .]     105     131 ..     101     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 3.1e-30
                           DUF2102  1 lvviese.aevtpselvrkvyeleedvtiketCfGllvegeeeevekvveevrkldpnkifvkeRgfppgderrCRakr 78
                                      +v++++e ++v+p ++ + +ye+++++ +ketCfG+++egee+++e++++e+r+ldp+ if+k+Rgf  gd+rrCR++ 
  gi|330506873|ref|YP_004383301.1| 12 YVILSPEcTDVLPCDVSTMIYESKHGIEVKETCFGAIIEGEEDAIESLIKEIRALDPAGIFIKDRGFLLGDPRRCRGDA 90
                                      67788773579*****************************************************************998 PP

                           DUF2102 79 gg 80
                                       g
  gi|330506873|ref|YP_004383301.1| 91 SG 92
                                      55 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 8.9e-07
                           DUF2102  78 r.ggaRpGfhqlekEvelleliskaLe 103
                                       r g+ RpG +++e+E ++l+lis+aLe
  gi|330506873|ref|YP_004383301.1| 105 RsGSVRPGSYMIEAESKMLPLISRALE 131
                                       55889********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 969.40
//
Query:       gi|330506874|ref|YP_004383302.1|  [L=406]
Description: adenosylcobinamide amidohydrolase [Methanosaeta concilii GP6]
Scores for complete 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-63  214.4   0.8      2e-63  214.0   0.8    1.2  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 !  214.0   0.8   1.1e-67     2e-63       2     192 .]      23     242 ..      22     242 .. 0.96

  Alignments for each domain:
  == domain 1  score: 214.0 bits;  conditional E-value: 1.1e-67
                              CbiZ   2 feeprrvlssavln.gGlre.lravlnhqvpegyered...........peeyleeyleelglppektvgllTaadm 65 
                                       + +p+rvls+++   gG+++ l +++nhq++e+++ ++           pe+y +e++++ +lp +++++l Taa+m
  gi|330506874|ref|YP_004383302.1|  23 LMTPHRVLSTCRSSaGGMHDdLMYLYNHQSCEPAGGHMnarmyrlavdsPEDYKREVADRHNLPFQRCATLGTAANM 99 
                                       679********975599*****************999988888888777799999999999**************** PP

                              CbiZ  66 enaaiaeeefedlevtavvTaGvesnavragd................edeeaekpGTINiivlinaaLtdaalvra 126
                                       +naai  e+f dlev++v+T+Gve+na+ragd                + e +++pGTIN ++++n++Lt++a+v a
  gi|330506874|ref|YP_004383302.1| 100 NNAAICIERFCDLEVVTVCTGGVEGNAGRAGDpatyyepqddsakgqiDLECERRPGTINAMIFLNRELTPGAMVTA 176
                                       ************************************************667899*********************** PP

                              CbiZ 127 litatEAKtaalqdlgvrsryseg.atGTgTDaiavaadkegeeeltyaGkhtklGeliaraVyeAv 192
                                       +itatEAKtaalq+l v s+yseg atGTgTD+iava++  g+ ++++aGkh+k+Geli+r++++Av
  gi|330506874|ref|YP_004383302.1| 177 VITATEAKTAALQELVVGSKYSEGlATGTGTDQIAVASKLGGK-AISFAGKHSKVGELIGRTMHDAV 242
                                       ***************************************9999.5*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3010.74
//
Query:       gi|330506875|ref|YP_004383303.1|  [L=567]
Description: nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-66  221.8   0.0    3.2e-41  141.4   0.0    2.0  2  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.0   1.8e-45   3.2e-41       1     257 [.       7     250 ..       7     253 .. 0.91
   2 !   78.5   0.0   2.8e-26     5e-22       1     211 [.     289     487 ..     289     506 .. 0.83

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 1.8e-45
                                       EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBS..SSHHHHHHHHBHSSSHHHHHHHHHHHHHT CS
                      CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgy..keeahfleaAeaglgetlallaalarkng 75 
                                       +vA+v +++ + ++++n+++ll+l +eAa++ga+Liv  El+ tgy   +++++ ++ e ++g+t++++  +a+++g
  gi|330506875|ref|YP_004383303.1|   7 KVALVHASISWKEKDKNIARLLALNREAAQNGARLIVNTELATTGYafLSRKEIAPLTESIPGPTTEAFGLIANEFG 83 
                                       79*******889**********************************996666666666799**************** PP

                                       EEEEEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SS.S-EEEETTEEEEEE CS
                      CN_hydrolase  76 iavvigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdg.ipvfdtpvgkiGaa 151
                                       ++++igl+e ++  g +  yn+a ll +++ ++++yrKl         p ++e     +g+  +pv++t++g +G+ 
  gi|330506875|ref|YP_004383303.1|  84 CYICIGLAEHDMRTGIF--YNSAALLGPTKGVAARYRKLS--------PAFRENLWAAKGNLpVPVVQTEFGALGMV 150
                                       **********8889999..*********************........88998888888999*************** PP

                                       EGGGGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHH...HHHHHHHHHTSEEEEEEBEEEHCETTEEEE-. CS
                      CN_hydrolase 152 iCyeigfpellralalkgaeilvnlserapvpksmgppqwel...lgraralengcfviaanqvggyeqlilwpvg. 224
                                       iC + +  + +r+ al+ga+il+  +         +pp +++     rar+leng++v+a+n++g+  +    ++g 
  gi|330506875|ref|YP_004383303.1| 151 ICADSYSYRPARIAALQGARILLVPA--------NWPPEHHNperFWRARSLENGIYVLACNRTGM--DKTMDCNGa 217
                                       ************************44........55555543222569******************..888888876 PP

                                       -EEEE-TTS-EEEECCSSSTEEEEEEEEHHHHH CS
                      CN_hydrolase 225 hSaiidpdGrilaglgeeeegvliaeidladvr 257
                                       +S+i++p+G+ +a+ +   +++++  ++l+ v+
  gi|330506875|ref|YP_004383303.1| 218 QSFIVNPQGETVAQMSSPDDTIIYGSLPLNGVT 250
                                       9**************99999********99876 PP

  == domain 2  score: 78.5 bits;  conditional E-value: 2.8e-26
                                       EEEEEEBB-....STTHHHHHHHHHHHHHHHHHHT...TESEEEEETTTTTBSSSHHHHHHHHB.HSSSHHHHHHHH CS
                      CN_hydrolase   1 rvAvvQlpq....kaadleanlqklleliaeAark...gadLivlPElfitgykeeahfleaAe.aglgetlallaa 69 
                                       ++A  Ql++    + ++++  + ++ +++a+Aar+    ++L+vlPEl+  g  + a++ e    +++g++++l+++
  gi|330506875|ref|YP_004383303.1| 289 TAATLQLCSeprnVVENTKRAIRLIDDALAKAAREkgtTINLVVLPELSTSGAIFGAEVAEICSeEIPGKVTDLFSQ 365
                                       589999999777766788888888888888899999999**************777777665446************ PP

                                       HHHHHTEEEEEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SS.S-EEEETT CS
                      CN_hydrolase  70 larkngiavvigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdg.ipvfdtpv 145
                                        a + +  +v+g++er    + l +yn+ vl+ +dg  vgkyr +hL        + + r   +pgdg ++ +d+p+
  gi|330506875|ref|YP_004383303.1| 366 KAGERDLFIVLGMAER----DELGFYNSSVLIGPDGI-VGKYRAVHL--------SWRDRNWASPGDGgFAAYDLPF 429
                                       ****************....77888***********9.7*******7........6889999999************ PP

                                       EEEEEEEGGGGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEB CS
                      CN_hydrolase 146 gkiGaaiCyeigfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanq 211
                                       ++iG++i  +  fpe++  la+ ga++l+          +++ +  +       l  ++ ++ anq
  gi|330506875|ref|YP_004383303.1| 430 ARIGMLIGHDLLFPEAADSLAKLGADVLCV-P-------ALWDDAKSRFIWEARLSEQMHLAVANQ 487
                                       ******************************.2.......355555554444455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 4244.52
//
Query:       gi|330506876|ref|YP_004383304.1|  [L=1282]
Description: cobaltochelatase, CobN subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
          0 1375.9   0.0          0 1375.6   0.0    1.1  1  CobN-Mg_chel   CobN/Magnesium Chelatase
  ------ inclusion threshold ------
      0.045   13.5   0.0       0.13   12.1   0.0    1.8  1  LexA_DNA_bind  LexA DNA binding domain


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 ! 1375.6   0.0         0         0       2    1088 ..     134    1254 ..     133    1255 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1375.6 bits;  conditional E-value: 0
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel    2 aYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilf 76  
                                        +Yl +gg++N+ +l+ yla+ ++g ++ e+++p++  +egiyhpd    f+++ + +e+++++    +ptvg++f
  gi|330506876|ref|YP_004383304.1|  134 QYLDYGGRKNFYSLILYLANYFIG-SNYEFSEPARPIWEGIYHPD----FDHVPTLKEYLQSKCVAGRPTVGLWF 203 
                                        8**********************8.77789*************99....4445444555556899********** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel   77 yrahllagntavidaliraleerglnvlpvfvssl...d...seaqealeelftkegeekvdalinttsfalvkg 145 
                                        y++ ++agnt +id li+++e++g+nv+pvf +++   +   + a+  +e+lf+k+g++ +d+li+t++f+l+ +
  gi|330506876|ref|YP_004383304.1|  204 YQSLWQAGNTLFIDRLIEEIERQGANVIPVFLHAAkdvErgtKGAEWVVENLFMKDGRPIIDVLISTLMFSLSIK 278 
                                        *********************************99865256689999**************************99 PP

                                        xxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  146 paeeeeeeaeeea.......lkelnvPvlqailssqsreeWeessqGlspldlamsvalpEldGriepvvisfke 213 
                                        p e++++ + +e        +k+lnvPvl+ai+++++ ++W+es qG sp+d++m +a+pE+dG++++v+++++e
  gi|330506876|ref|YP_004383304.1|  279 PWEGSDTGEGQEVarseewfIKRLNVPVLKAIVTYNTLADWNESLQGCSPMDISMGIAMPEFDGMLITVPVAARE 353 
                                        98888877776668999*********************************************************9 PP

                                        ...xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  214 ...eee.eetevekyepipervervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlL 284 
                                            ++ + ++v ++ep+per +++++l  +wa+Lr+ pn++kkvaii++nypp+++r+g+a gLd+p S++n++
  gi|330506876|ref|YP_004383304.1|  354 rtdIDPlTGARVIRFEPLPERTNKIVRLSLNWAKLRHIPNSQKKVAIIFHNYPPRDDRIGTAFGLDSPVSVLNIM 428 
                                        76433389999**************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  285 kalkeeGYdveelpesgdeLiellleggtndpew...eelkvgaaallpaeeYeewfeeLpeelreeveerWgep 356 
                                        ka+ ++GY++e  pe+g++Lie ++++ t d++w   eel+ +a++++++ +Y++wfe+Lp +++e+++ +Wge+
  gi|330506876|ref|YP_004383304.1|  429 KAMDDAGYTIERMPENGQALIEDVKSRLTLDRRWrspEELAKRAIDSVTEGDYKDWFEQLPVAVQEKMTSAWGEA 503 
                                        **********999*********************99977777********************************* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  357 pgemveeeksgekklvipglqlGnvfvgvQPargyeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvGk 431 
                                        pg    +   ++k+l+ipg+  Gn+f+g+QP+rg+ edp ++yh+pd p +h+Y+A+Y+W+r++f+ad v+H+Gk
  gi|330506876|ref|YP_004383304.1|  504 PG----KLFVHKKNLIIPGVINGNIFIGLQPPRGFLEDPAAIYHSPDHPIPHHYYAYYRWIRDVFRADLVMHIGK 574 
                                        **....5566789************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  432 HGtlEwlPGKqvglseecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeel 506 
                                        HG+lEwlPGK+vgls++c+Pdi++ dlP++YpYi+nnpgEGtqAKRRsy++iidHl+P+m +a+ y+e+aeLe +
  gi|330506876|ref|YP_004383304.1|  575 HGSLEWLPGKSVGLSDSCFPDIAISDLPNIYPYIINNPGEGTQAKRRSYCCIIDHLVPVMHNADAYDEMAELEVM 649 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  507 ideYeeaesldperlkalreqilelveelnldkdlgleeakeeeeeefeellekldgyleelkeaqirdglhilG 581 
                                        +++Y++a+s+dp++l+++++ i+++v e++ld+dl+ e  +ee+ ++f+++lekl++yl+e++++qirdglhilG
  gi|330506876|ref|YP_004383304.1|  650 LADYYQAASEDPSKLPTQKKMIWDKVCEAKLDHDLEIE--EEEAFSDFDKFLEKLHEYLHEMADTQIRDGLHILG 722 
                                        ***********************************666..577899***************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  582 eapegeqlvdlvvailrleneegesltealaealgldlde...leeksekelrtagdalealeeeaeelveelle 653 
                                        e+peg +l +++va++rl n++ +sl+++laea+g+d+d    ++ k  +  +t g+++++l++ a +lv+ l+e
  gi|330506876|ref|YP_004383304.1|  723 EPPEGSRLDEFLVALTRLANGQVPSLRQSLAEAMGYDYDYlldNRGKIVSGSKTCGQVIDDLNSLALRLVSGLHE 797 
                                        ****************************************665445555678999******************** PP

                                        xxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  654 eeaeeeeaeaeeleeeeeeeee.................eteeEitallraLdGeyippgpsGdptrgraevLPT 711 
                                        ++++  ++ + ++e   +++ +                 +t +E++a+l a dG++++pgpsG+ptrg+a++LPT
  gi|330506876|ref|YP_004383304.1|  798 QGFAVGTIPELVEEILGKRNPKiekvldyiattlapnidATVDELSAILCASDGGFVSPGPSGAPTRGMADILPT 872 
                                        **99999998888888888777899*************7666********************************* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  712 GrNfysvDpraiPteaAwevGkklaeellerylqehgeyPekvglslwgtetmrteGediAqiLallGvrPvwda 786 
                                        GrNfysvDp+aiP++aAw+vG + a++lleryl+++g yPe++g+++wg+ tmrt+G+diA++L l+GvrPvw++
  gi|330506876|ref|YP_004383304.1|  873 GRNFYSVDPQAIPSQAAWKVGVAQADALLERYLEDEGCYPESLGMVIWGSPTMRTKGDDIAEVLCLMGVRPVWEE 947 
                                        *************************************************************************** PP

                                        x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                      CobN-Mg_chel  787 a.grvvdlelipleeLgRPRiDVtvriSGffRDafpnlielldkavelvaeldEpeedNfvrkhvleeeaelee. 859 
                                        + grv+++elip+eeL+RPRiDV++riSGffRDafpn+++l+d+avelvae +Ep+e+Nf++khv ++ +e ++ 
  gi|330506876|ref|YP_004383304.1|  948 RsGRVTGIELIPMEELQRPRIDVMLRISGFFRDAFPNIVHLVDRAVELVAEQKEPPEQNFLAKHVSADISEKTAa 1022
                                        ***********************************************************************9996 PP

                                        ..xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  860 ..ke.eaeeratyRvFgskpGaYgagvqeliessnWedeedLaeaYlnwssyaYgkgaegeeaeeafearLkrvd 931 
                                           + +a+  a yR+Fg +pGaYgagv+++i+s+nW+de+dLae+Y++w++yaYg+++ g++ ++ f++rL+r+d
  gi|330506876|ref|YP_004383304.1| 1023 giDGeQAKTLACYRIFGCRPGAYGAGVSDAIDSKNWKDEKDLAEIYVKWGGYAYGRKNFGATVPDEFRRRLSRLD 1097
                                        66334777******************************************************************* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  932 vvvqnqdsrehdlldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvrtlkeeiarelrsrvlNPkWie 1006
                                        ++v+n+d+re+d+ld dd+y+++GG++aav++l+g+ p++y+gdss+p+++k+r+  ee+++ +r+r+lNPkWie
  gi|330506876|ref|YP_004383304.1| 1098 LTVKNEDTREYDMLDGDDFYSYHGGMIAAVKALKGELPRSYCGDSSDPDRVKTRSTVEETKHIFRARILNPKWIE 1172
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 1007 gmmrhGykGafelaatvdnlfgwdatadvvddwvyeevaetYvlDeevrefleekNpwAlreiaerLlEaarrgl 1081
                                        +m+rhGykGa +++++vd  fgwdata+v +dw+yee+a++Y+lD++++e+l++ Np+Al++iaerLlEa +rg+
  gi|330506876|ref|YP_004383304.1| 1173 SMKRHGYKGAGDISRMVDIAFGWDATAEVLEDWMYEELANKYALDKDMQEWLKKVNPHALQNIAERLLEAVERGM 1247
                                        *************************************************************************** PP

                                        xxxxxxx RF
                      CobN-Mg_chel 1082 Weaseet 1088
                                        W+a+ee+
  gi|330506876|ref|YP_004383304.1| 1248 WQATEEM 1254
                                        ***9985 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.4e-05      0.13      22      62 ..     403     444 ..     397     447 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.4e-05
                                       HSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTS.EE-GGG- CS
                     LexA_DNA_bind  22 tgypPsireiaralglkSpsaveehLkaLerKGy.ierdpgk 62 
                                       + ypP    i+ a+gl Sp +v + +ka+   Gy ier+p++
  gi|330506876|ref|YP_004383304.1| 403 HNYPPRDDRIGTAFGLDSPVSVLNIMKAMDDAGYtIERMPEN 444
                                       78*******************************878999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); 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: 0.89u 0.29s 00:00:01.18 Elapsed: 00:00:00.45
# Mc/sec: 8566.72
//
Query:       gi|330506877|ref|YP_004383305.1|  [L=364]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.7e-13   49.2   0.0      2e-12   47.8   0.0    1.6  2  Radical_SAM  Radical SAM superfamily
    4.9e-07   30.1   0.0    1.1e-06   28.9   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
    6.6e-06   26.3   0.0      2e-05   24.7   0.0    1.8  2  Fer4_14      4Fe-4S single cluster domain
     0.0094   16.4   0.1      0.025   15.1   0.1    1.7  1  SPASM        Iron-sulfur cluster-binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   4.5e-16     2e-12       2     151 ..      12     158 ..      11     162 .. 0.82
   2 ?   -2.2   0.0         1   4.7e+03      31      62 ..     238     269 ..     220     295 .. 0.60

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 4.5e-16
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       +vt  CnlrCs+C+ +   +++     ++ ++ ++ + e  ++  +  + ++ggepll+  ++e +  +  +    +
  gi|330506877|ref|YP_004383305.1|  12 SVTSDCNLRCSYCYAHGG-ESRASMGWVTARRAIDVMAEC-FD--GFKIQFTGGEPLLNLGLIERAVDYLDEMGLQV 84 
                                       68999***********74.555555555555555555555.55..999***********87777777777777779* PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH..HHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaadde..kvlklmn.rghtfeevlealeklreagikrvvdrivg 151
                                        + v tn+tl++ +++ rl +l    + ++l+ + +   +++     rg++ +  l+++ +lreagi+ v  ++v+
  gi|330506877|ref|YP_004383305.1|  85 PCQVQTNATLITSDVAGRLNDLK-IGIGVSLDGPPSVndRIRPFSSgRGGSAKSALNGIMALREAGIR-VGATCVL 158
                                       ***********************.99999999877655558888889*********************.7766665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHTTSEEEEEESSTGGGSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  31 veeileevkelkaekgvkevilgggepllypd 62 
                                       vee  e +   +++    +v++ gge ++ p 
  gi|330506877|ref|YP_004383305.1| 238 VEEGRERLHHCYFDACRSVVVMPGGEAFACPS 269
                                       33334444444334435555555666666555 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 !   28.9   0.0   2.5e-10   1.1e-06       5     122 ..       7     121 ..       4     137 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.5e-10
                           Fer4_12   5 GvrlslfvsgCnlsCkgCfnketwsfksgkeft.kelleeiiedlkkesiegltllGGEPllpenaeallelvkevk 80 
                                       G+ ++  +s+Cnl+C++C++    s  s   +t + +++ + +++     +++ ++GGEPll  n   + + v+++ 
  gi|330506877|ref|YP_004383305.1|   7 GLLALSVTSDCNLRCSYCYAHGGESRASMGWVTaRRAIDVM-AEC--FDGFKIQFTGGEPLL--NLGLIERAVDYLD 78 
                                       555666689**********9999877665555515555555.555..37799**********..***********99 PP

                           Fer4_12  81 eekpekdi.wlytgytleelskkekeellkeidvlvdGkfees 122
                                       e +++  + + ++ + +    + + ++l   i v +dG+ + +
  gi|330506877|ref|YP_004383305.1|  79 EMGLQVPCqVQTNATLITSDVAGRLNDLKIGIGVSLDGPPSVN 121
                                       9999544414444444444444477777777778888887755 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   4.6e-09     2e-05       5      92 ..      14      95 ..      11     116 .. 0.74
   2 ?   -3.5   0.0       2.4   1.1e+04      44      58 ..     251     264 ..     235     266 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.6e-09
                           Fer4_14  5 lsgCnlsCkgCd...nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeype 80
                                      +s Cnl C  C+      + + ++g + +++ + +++     + +k   + +tGGePL   n   + + v++l e + +
  gi|330506877|ref|YP_004383305.1| 14 TSDCNLRCSYCYahgG--ESRASMGWVTARRAI-DVM-AECFDGFK---IQFTGGEPL--LNLGLIERAVDYLDEMGLQ 83
                                      799*********6432..334455555555555.444.23346665...55*******..99***************** PP

                           Fer4_14 81 kkiwletngtle 92
                                      ++ +++tn+tl 
  gi|330506877|ref|YP_004383305.1| 84 VPCQVQTNATLI 95
                                      *********986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.4
                           Fer4_14  44 seikiqglvltGGeP 58 
                                       + + ++ +v+ GGe 
  gi|330506877|ref|YP_004383305.1| 251 DAC-RSVVVMPGGEA 264
                                       444.55688899985 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   5.7e-06     0.025       1      67 [.     248     309 ..     248     310 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.7e-06
                             SPASM   1 C.fapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnseeyqefrkskkfplielCrnC 67 
                                       C f   rs+++ + G+ + C    +  + el+lGni e ++++ + +   ++ r     + ++ Cr+C
  gi|330506877|ref|YP_004383305.1| 248 CyFDACRSVVVMPGGEAFAC---PSMLRPELRLGNIEEPDFAKRLIGRMVRARR---SVQDPQECRTC 309
                                       666667999***********...4668788************999999888888...33334679999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2742.89
//
Query:       gi|330506878|ref|YP_004383306.1|  [L=111]
Description: hypothetical protein MCON_0669 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0079   15.9   0.1      0.011   15.4   0.1    1.3  1  DHquinase_II  Dehydroquinase class II
  ------ inclusion threshold ------
       0.32   10.4   2.4       0.46    9.9   2.4    1.3  1  DUF4349       Domain of unknown function (DUF4349)


Domain annotation for each model (and alignments):
>> DHquinase_II  Dehydroquinase class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.3e-06     0.011       3      43 ..      29      70 ..      27      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-06
                                      EEEE-TTGGGTTTSTCCCC-SS-HHHHHHHHHHHHH.HTT-E CS
                      DHquinase_II  3 lvlnGpNlnllgkrepeiygsetledieeelkekae.elgve 43
                                      ++++G N   l  re +iyg+  ++ ++++l+e+ + elg e
  gi|330506878|ref|YP_004383306.1| 29 FIIKGINAGKLEFREGSIYGNPYIKVLRRQLEEYIAeELGKE 70
                                      59******************************9765145544 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.4   5.1e-05      0.46     106     144 ..      69     107 ..      53     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 5.1e-05
                           DUF4349 106 lallekaksvedlleiereLsevqaeieslegqlryLdn 144
                                       +++l+kak+  +l +i++e++ev+ ++ sl+ +  +L++
  gi|330506878|ref|YP_004383306.1|  69 KEYLNKAKNRTELRKIKKEIAEVECRLASLKLEKTALER 107
                                       689****************************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 789.14
//
Query:       gi|330506879|ref|YP_004383307.1|  [L=353]
Description: iron chelate uptake ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete 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-92  309.7  35.6    2.2e-92  309.4  35.6    1.0  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.4  35.6   1.2e-96   2.2e-92       4     312 .]      32     347 ..      24     347 .. 0.97

  Alignments for each domain:
  == domain 1  score: 309.4 bits;  conditional E-value: 1.2e-96
                             FecCD   4 lllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLad 73 
                                       ll  ++++lg++++s++ev+ a++++        +s +++iv+ lrl r+l+++l+G++La+aGa +Q++++NpLa+
  gi|330506879|ref|YP_004383307.1|  32 LLASMAVTLGSASLSIKEVYVAIMARFlpdyfesTSYANTIVWGLRLDRILMGILSGMGLAIAGAAMQGILKNPLAS 108
                                       455566899*************999989*99999999999************************************* PP

                             FecCD  74 PsilGissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsalts 149
                                         +lG+ss+a++ga+la++l+  +  +++ ++  af++ l+a++ v+ la k kg++p++liLaGia+ +l+sa+ts
  gi|330506879|ref|YP_004383307.1| 109 EFTLGVSSAAGFGAALAIVLGaGFVGGEYLVIGNAFIFTLIASFTVYGLA-KYKGITPETLILAGIAIMYLFSAMTS 184
                                       *********************9889999**********************.************************** PP

                             FecCD 150 llllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrlllll 226
                                       +l+++ ++e++++++fw++Gsl++ sw+k+ +++++l+++l++l++ + +++++  gdetAkslGvnver+r++ ++
  gi|330506879|ref|YP_004383307.1| 185 FLQYVGHAEQVQEVVFWMMGSLGKSSWEKAGIISAILAVCLPYLIIKSWDINAMGAGDETAKSLGVNVERTRVISMV 261
                                       ***************************************************************************** PP

                             FecCD 227 lvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGa 303
                                       lv+l+ta++++++G+igFvGL++Phi r+++g dhr llp sal+Gallll ad+lar++l+p+ lpvgi+t+++G+
  gi|330506879|ref|YP_004383307.1| 262 LVSLITASIICFTGTIGFVGLVAPHITRMVIGGDHRFLLPGSALVGALLLLGADTLARTILAPVILPVGIMTSFLGV 338
                                       ***************************************************************************** PP

                             FecCD 304 pffiylllr 312
                                       pff+yl+++
  gi|330506879|ref|YP_004383307.1| 339 PFFVYLFMK 347
                                       ******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2595.50
//
Query:       gi|330506880|ref|YP_004383308.1|  [L=260]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for 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    4.3e-33  114.7   0.0    1.2  1  ABC_tran      ABC transporter
      1e-10   41.9   1.2    0.00015   21.7   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.8e-05   24.3   0.5     0.0013   18.2   0.5    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
      3e-05   23.9   0.2    0.00041   20.2   0.0    2.0  2  AAA_15        AAA ATPase domain
    0.00015   22.2   0.0    0.00026   21.4   0.0    1.5  1  AAA_16        AAA ATPase domain
    0.00022   21.5   1.8     0.0047   17.2   1.8    2.1  1  AAA_22        AAA domain
    0.00077   19.2   0.1     0.0016   18.2   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
    0.00089   19.8   0.0     0.0016   19.0   0.0    1.3  1  AAA_23        AAA domain
     0.0017   17.1   0.1        0.5    8.9   0.0    2.0  2  AAA_13        AAA domain
     0.0049   16.3   0.1      0.032   13.6   0.0    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0082   15.9   0.0      0.013   15.2   0.0    1.5  1  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.012   16.0   0.4       0.13   12.7   0.4    2.1  1  AAA           ATPase family associated with various cellular 
      0.012   15.5   0.0      0.021   14.8   0.0    1.4  1  Rad17         Rad17 P-loop domain
      0.017   15.1   0.1          1    9.4   0.0    2.3  2  AAA_5         AAA domain (dynein-related subfamily)
      0.017   15.3   0.2       0.31   11.3   0.2    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.023   14.6   0.0      0.037   13.9   0.0    1.4  1  APS_kinase    Adenylylsulphate kinase
      0.025   14.0   0.7       0.81    9.1   0.2    2.1  2  TniB          Bacterial TniB protein
      0.029   13.6   0.4      0.075   12.2   0.1    1.7  2  NB-ARC        NB-ARC domain
      0.033   13.8   0.3        0.1   12.2   0.0    1.8  2  SRP54         SRP54-type protein, GTPase domain
      0.034   14.3   0.1      0.088   13.0   0.0    1.7  2  AAA_33        AAA domain
      0.034   14.1   0.0       0.84    9.5   0.0    2.0  2  ATPase_2      ATPase domain predominantly from Archaea
      0.049   13.4   0.0      0.083   12.6   0.0    1.4  1  AAA_24        AAA domain
      0.058   13.3   0.8       0.54   10.1   0.1    2.1  2  NTPase_1      NTPase
      0.059   12.1   0.2        1.9    7.2   0.0    2.0  2  ABC_ATPase    Predicted ATPase of the ABC class
       0.06   13.4   0.0        0.4   10.7   0.0    2.1  2  AAA_14        AAA domain
      0.064   13.6   0.2       0.13   12.6   0.2    1.6  1  AAA_19        AAA domain
      0.092   11.5   0.0       0.17   10.6   0.0    1.4  1  RNA12         RNA12 protein
        0.1   12.2   0.6        0.2   11.2   0.2    1.7  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.12   12.3   0.1       0.23   11.4   0.1    1.5  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.14   11.9   0.3       0.31   10.8   0.0    1.6  2  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.15   11.5   0.1       0.37   10.3   0.0    1.6  2  AAA_7         P-loop containing dynein motor region
       0.22   10.6   0.0       0.32   10.1   0.0    1.3  1  G-alpha       G-protein alpha subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.7   0.0   7.7e-36   4.3e-33       1     137 []      19     165 ..      19     165 .. 0.94

  Alignments for each domain:
  == domain 1  score: 114.7 bits;  conditional E-value: 7.7e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+n++l ++ +e++++vG+nG+GK+tL+k++ + lkp +G+il+dg+d+++ ++++l k++g++pq ++    +tv 
  gi|330506880|ref|YP_004383308.1|  19 LDNLNLVVEDSEVLGLVGPNGSGKTTLIKCMDKILKP-KGSILIDGRDIDTVSRTELAKRLGYVPQSSSTPLATTVF 94 
                                       79**********************************8.9****************************99999999** PP

                                       HH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       ++             sd++++k+++ lgl +l+   + ++ s+LSgGqkq+v +aral+++p++lllDEpt+
  gi|330506880|ref|YP_004383308.1|  95 DTvlmgrrphiswrVSDSDLDKVADILGLLHLEYLAM-RDFSQLSGGQKQKVLIARALAQEPEVLLLDEPTS 165
                                       99********999988888999999999999766666.777*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   2.7e-07   0.00015       3      22 ..      33      52 ..      31      81 .. 0.74
   2 !   19.4   0.1   1.4e-06   0.00077     220     285 ..     120     186 ..      81     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.7e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                      +l+GpNgsGK++L++++d +
  gi|330506880|ref|YP_004383308.1| 33 GLVGPNGSGKTTLIKCMDKI 52
                                      79**************9533 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.4e-06
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkel 285
                                        + +l+ ++   +++++lS G+k+   ++ al++ +    +ll+DEp ++L+     ++++++  l+ke+
  gi|330506880|ref|YP_004383308.1| 120 ILGLLHLEYLAMRDFSQLSGGQKQKVLIARALAQEP---EVLLLDEPTSSLDMkhqlEVMETISSLVKEK 186
                                       6677777788888999*********55555555555...9************955555555555555554 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 !   18.2   0.5   2.3e-06    0.0013      26     189 ..      31     185 ..      21     204 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.3e-06
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrr 102
                                       +  +vGpNGSGK+ l+  +  +L  + +  l   +  d +++  ++ +   ++v       +++ +  ++ v  ++ 
  gi|330506880|ref|YP_004383308.1|  31 VLGLVGPNGSGKTTLIKCMDKILKPKGS-ILIDGRDIDTVSR--TELAKRLGYVPQS----SST-PL-ATTVFDTVL 98 
                                       6679***************666664444.3333222233332..3333444444442....222.22.223333444 PP

                                       EETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingkevtk.kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                       + r  + ++++ +++  k +++  ll+ + + +    +LSgG+k+ v +a  +A    +   + llDe  + LD k+
  gi|330506880|ref|YP_004383308.1|  99 MGRRPHISWRVSDSDLDKvADILGLLHLEYLAMRdfsQLSGGQKQKVLIARALA----QEPEVLLLDEPTSSLDMKH 171
                                       55555678888888888879999999988886643339*****99776666555....33446799*********** PP

                                       HHHHHHHHHHHCTT CS
                                       xxxxxxxxxxxxxx RF
                             SMC_N 176 vkkvaellkekskn 189
                                         +v e + +  k+
  gi|330506880|ref|YP_004383308.1| 172 QLEVMETISSLVKE 185
                                       99999999887665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   7.3e-07   0.00041      25      72 ..      31      73 ..      19      79 .. 0.81
   2 ?    1.8   0.0      0.28   1.5e+02     322     356 ..     153     187 ..     127     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.3e-07
                            AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenis 72
                                      +  l+G+N+sGK+++++ +d++l+ k       i i+  d+++   ++
  gi|330506880|ref|YP_004383308.1| 31 VLGLVGPNGSGKTTLIKCMDKILKPK-----GSILIDGRDIDTVSRTE 73
                                      7779********************88.....67888888888776555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.28
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnk 356
                                       +++ +ll++EP  +L  ++q ++++++ +l++++k
  gi|330506880|ref|YP_004383308.1| 153 QEPEVLLLDEPTSSLDMKHQLEVMETISSLVKEKK 187
                                       567899*************************9985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.6e-07   0.00026      12      63 ..      18      68 ..      16     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.6e-07
                            AAA_16 12 LlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      +l+ l+ v +++ e++ l+G+ G+GK++l+++  + l+ +g i++ g+  + 
  gi|330506880|ref|YP_004383308.1| 18 ILDNLNLVVEDS-EVLGLVGPNGSGKTTLIKCMDKILKPKGSILIDGRDIDT 68
                                      566666666665.7899***********************999999998888 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.8   8.4e-06    0.0047       8     133 ..      32     199 ..      26     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.4e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee......................................erpevv... 43 
                                       l ++G+ G+GKTtl++ + + l+                                                  v   
  gi|330506880|ref|YP_004383308.1|  32 LGLVGPNGSGKTTLIKCMDKILKPK----GsilidgrdidtvsrtelakrlgyvpqssstplattvfdT----Vlmg 100
                                       5689****************99543....2445588888888777666666666666665555533220....2233 PP

                            AAA_22  44 ...fvtlpsstsskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lr...seeal 109
                                          ++   +s s  d   ++l  l+le  a   + ++l   + ++ l ara    +e+l++DE    l+   + e++
  gi|330506880|ref|YP_004383308.1| 101 rrpHISWRVSDSDLDKVADILGLLHLEYLA-MRDFSQLSgGQKQKVLIARALaqePEVLLLDEPTSsLDmkhQLEVM 176
                                       333344444444444444445555544444.7777888879999999999889999********999999766**** PP

                            AAA_22 110 eeLrsllnlsrkgvqliLvGtp.el 133
                                       e+++sl++  +k+++ +++ +  +l
  gi|330506880|ref|YP_004383308.1| 177 ETISSLVK--EKKISAVMALHDlNL 199
                                       ********..**9999987766555 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   2.8e-06    0.0016      23      50 ..      30      57 ..      18      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.8e-06
                            AAA_29 23 gatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++  l+Gp+GsGK+Tl+  +  +L p+ 
  gi|330506880|ref|YP_004383308.1| 30 EVLGLVGPNGSGKTTLIKCMDKILKPKG 57
                                      46669**************999999975 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.8e-06    0.0016      18      39 ..      28      49 ..      13      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.8e-06
                            AAA_23 18 skgltlItGpNGaGKTTildAi 39
                                      ++ +  ++GpNG+GKTT++ ++
  gi|330506880|ref|YP_004383308.1| 28 DSEVLGLVGPNGSGKTTLIKCM 49
                                      5567779************997 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0063       3.5      23      39 ..      36      52 ..      34      74 .. 0.87
   2 !    8.9   0.0   0.00089       0.5     526     564 ..     154     191 ..     146     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0063
                            AAA_13 23 GwNGaGKTtLSrllrsl 39
                                      G NG+GKTtL + ++++
  gi|330506880|ref|YP_004383308.1| 36 GPNGSGKTTLIKCMDKI 52
                                      99********9888775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00089
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQl 564
                                       + ++  +D P SSLD +++  v+  i s + k+kk++ +
  gi|330506880|ref|YP_004383308.1| 154 EPEVLLLDEPTSSLDMKHQLEVMETISSLV-KEKKISAV 191
                                       77899*******************999998.77777665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   5.7e-05     0.032      25      49 ..      32      56 ..      20      87 .. 0.83
   2 ?    0.3   0.0      0.69   3.9e+02      49      97 ..     167     216 ..     133     224 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.7e-05
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllppl 49
                                      l lvGp GsGKt l+k++ ++l p 
  gi|330506880|ref|YP_004383308.1| 32 LGLVGPNGSGKTTLIKCMDKILKPK 56
                                      5599*****************9874 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.69
                      Mg_chelatase  49 lseeealeva.kiasvagkkeeekllkrrpfraphhsaskaalvGggskp 97 
                                       l+++ +lev  +i+s++++k+ +++++   ++     + k a++ gg++ 
  gi|330506880|ref|YP_004383308.1| 167 LDMKHQLEVMeTISSLVKEKKISAVMALHDLNLASMFVDKLAILKGGKIY 216
                                       44455555431355555555556666666666666666666666666555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.4e-05     0.013      17      53 ..      28      70 ..      21     191 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaag......grviglA 53
                                      +  v  l+Gp G+GKtt++k + ++++ +g      +++  ++
  gi|330506880|ref|YP_004383308.1| 28 DSEVLGLVGPNGSGKTTLIKCMDKILKPKGsilidgRDIDTVS 70
                                      445999*******************999986666644444444 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   0.4   0.00023      0.13       3      35 ..      34      67 ..      32     194 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00023
                                      EESSTTSSHHHHHHHHHHHHTHE.EEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelgve.fleisgsell 35
                                      l+Gp G GKT+l+k + k l+ +  + i+g ++ 
  gi|330506880|ref|YP_004383308.1| 34 LVGPNGSGKTTLIKCMDKILKPKgSILIDGRDID 67
                                      89************99998863322333333333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.7e-05     0.021      42      78 ..      26      62 ..      16     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.7e-05
                             Rad17 42 srkkriLLisGPsGCgkstvvkvLskelgiklrewln 78
                                       +  ++L + GP G gk+t +k + k+l +k    ++
  gi|330506880|ref|YP_004383308.1| 26 VEDSEVLGLVGPNGSGKTTLIKCMDKILKPKGSILID 62
                                      44567999*******************9988665555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0018         1       4      23 ..      34      53 ..      31      68 .. 0.85
   2 ?    3.5   0.0      0.12        65      19      62 ..     147     185 ..     139     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                                      EE--SSSSHHHHHHHGGGGB CS
                             AAA_5  4 LvGppGtgKselaerlaaal 23
                                      LvGp G+gK++l++ + + l
  gi|330506880|ref|YP_004383308.1| 34 LVGPNGSGKTTLIKCMDKIL 53
                                      9************9998887 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
                                       GGGGBS--EEEEE--TT--HHHHH--B--.........------ CS
                             AAA_5  19 laaalnreveyvqltrdtteedlkgrreikngttslvdsplvra 62 
                                       +a+al +e e+ +l + t++ d+k ++e+++   slv+     +
  gi|330506880|ref|YP_004383308.1| 147 IARALAQEPEVLLLDEPTSSLDMKHQLEVMETISSLVK-----E 185
                                       78999999999999999999999999999655544444.....3 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00055      0.31      28      88 ..     132     179 ..     126     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00055
                           SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       r++++lSGG+kq++    +a ala    +       +++++LDE  s+lD + + +++e++
  gi|330506880|ref|YP_004383308.1| 132 RDFSQLSGGQKQKV---LIARALA----Q------EPEVLLLDEPTSSLDMKHQLEVMETI 179
                                       78899999999654...3443332....3......4789************9999999876 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.6e-05     0.037       4      54 ..      31      83 ..      28     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.6e-05
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT.--EEEEEHHHH.TTTTTTT--SSHH CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekg.isvylLdGdnv.RhgLnkdLgfsee 54
                                      v+ l G  gsGK+t+ + ++k L+ kg i +   d d+v R++L k Lg+  +
  gi|330506880|ref|YP_004383308.1| 31 VLGLVGPNGSGKTTLIKCMDKILKPKGsILIDGRDIDTVsRTELAKRLGYVPQ 83
                                      67789********************99566666777877899*******9765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.088        49      38      54 ..      32      48 ..      18      59 .. 0.84
   2 ?    9.1   0.2    0.0014      0.81     107     159 ..     142     192 ..     118     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.088
                              TniB 38 lllvGdsnnGKtmivek 54
                                      l lvG+   GKt++++ 
  gi|330506880|ref|YP_004383308.1| 32 LGLVGPNGSGKTTLIKC 48
                                      669***********985 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0014
                              TniB 107 leqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                       +++  ++   + +++vL++DE  + l   +++q e+++++ sL  e ki+ v+
  gi|330506880|ref|YP_004383308.1| 142 KQKVLIARALAQEPEVLLLDEPTSSL--DMKHQLEVMETISSLVKEKKISAVM 192
                                       44444555556789**********99..899*******************997 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00013     0.075      16      38 ..      27      47 ..      17      58 .. 0.82
   2 ?   -1.2   0.0       1.7   9.4e+02      81     110 ..     132     161 ..      83     192 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                      TTSCSEEEEEEESTTSSHHHHHH CS
                            NB-ARC 16 delqslvvalvGmgGvGKttlak 38
                                      ++++  v++lvG  G+GKttl+k
  gi|330506880|ref|YP_004383308.1| 27 EDSE--VLGLVGPNGSGKTTLIK 47
                                      5666..***************87 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                                       TTSSSS-STTSHHHHHHHHCCCTTEEEEEE CS
                            NB-ARC  81 ddleekeeveslkrklvrlLltkrfllvlD 110
                                        d ++ + +++ k  + r+L +   +l+lD
  gi|330506880|ref|YP_004383308.1| 132 RDFSQLSGGQKQKVLIARALAQEPEVLLLD 161
                                       344444444446667777777777777777 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00018       0.1       3      29 ..      31      57 ..      29      66 .. 0.83
   2 ?   -1.7   0.1       3.3   1.8e+03      78     121 ..     149     192 ..     139     204 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                      EEEEEESTTSSHHHHHHHHHHHHHHTT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkeg 29
                                      v+ lvG++G+GKTt +  + ++lk +g
  gi|330506880|ref|YP_004383308.1| 31 VLGLVGPNGSGKTTLIKCMDKILKPKG 57
                                      6679***********999988887665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.3
                                       HHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEE CS
                             SRP54  78 kakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvl 121
                                       +a +++ +v+l+D    +   k+ +e +++i++ vk++++  v+
  gi|330506880|ref|YP_004383308.1| 149 RALAQEPEVLLLDEPTSSLDMKHQLEVMETISSLVKEKKISAVM 192
                                       55566666777776666666677777777777777777766665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00016     0.088       4      29 ..      34      62 ..      31     126 .. 0.75
   2 ?   -1.5   0.0       4.5   2.5e+03      15      39 ..     147     171 ..     141     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                            AAA_33  4 lvGlpGsGKstlaerl...lkklgavlls 29
                                      lvG++GsGK+tl++ +   lk+ g +l++
  gi|330506880|ref|YP_004383308.1| 34 LVGPNGSGKTTLIKCMdkiLKPKGSILID 62
                                      89**********98664446666666655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.5
                            AAA_33  15 laerllkklgavllssdtlrrrlfg 39 
                                        a+ l+++  + ll+++t +  ++ 
  gi|330506880|ref|YP_004383308.1| 147 IARALAQEPEVLLLDEPTSSLDMKH 171
                                       5677888877999999986655554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0015      0.84      20      43 ..      29      52 ..      18     106 .. 0.83
   2 ?    2.9   0.0      0.16        89     144     204 ..     174     234 ..     136     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0015
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiien 43
                                      +e++ + Gp gsGKt+L+k + + 
  gi|330506880|ref|YP_004383308.1| 29 SEVLGLVGPNGSGKTTLIKCMDKI 52
                                      6677788***********976555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                          ATPase_2 144 eLlnliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkeg 204
                                       e ++ i sl kek++  v++l    l    v++ + l+g + y+  +++d  +a+n+ + +
  gi|330506880|ref|YP_004383308.1| 174 EVMETISSLVKEKKISAVMALHDLNLASMFVDKLAILKGGKIYAAGEPIDLLNAKNIRDVY 234
                                       6778999999***********99999999999************99999999999987765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00015     0.083       5      27 ..      32      53 ..      29     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                            AAA_24  5 iliyGpsgiGKTtlakelgpkpl 27
                                      + ++Gp+g+GKTtl+k + +k+l
  gi|330506880|ref|YP_004383308.1| 32 LGLVGPNGSGKTTLIKCM-DKIL 53
                                      5799**************.6654 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   0.00097      0.54       4      28 ..      34      58 ..      31      81 .. 0.80
   2 ?    1.7   0.1      0.38   2.1e+02      93     154 ..     151     217 ..     140     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00097
                                      EE--TTSSHHHHHHHHHHHH...GG CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkssgv 28
                                      + Gp G+GKtTl+k + + lk +g 
  gi|330506880|ref|YP_004383308.1| 34 LVGPNGSGKTTLIKCMDKILKPKGS 58
                                      78************99999998874 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.38
                                       H.HHH-EEEE--.-STTGGG-H.HHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE CS
                          NTPase_1  93 l.seadviviDE.iGkmElksk.kfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkvfe 154
                                       l +e++v+++DE   ++ +k + ++ e++  ++k ++   ++ +h  +  + +v+++   k++k++ 
  gi|330506880|ref|YP_004383308.1| 151 LaQEPEVLLLDEpTSSLDMKHQlEVMETISSLVKeKKISAVMALHDLNlASMFVDKLAILKGGKIYA 217
                                       3367788888884456777766468899999999677778999999888999999999999999985 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.06        33     247     270 ..      32      55 ..      26      76 .. 0.75
   2 ?    7.2   0.0    0.0034       1.9     323     370 ..     137     184 ..     132     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.06
                                       EEEEE-TTSSHHHHHHHHHHCCSE CS
                        ABC_ATPase 247 tlIvGggfhGKsTLLeAlekGvyn 270
                                         +vG++  GK+TL++ ++k   +
  gi|330506880|ref|YP_004383308.1|  32 LGLVGPNGSGKTTLIKCMDKILKP 55 
                                       5579************99876554 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0034
                                       --HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG CS
                        ABC_ATPase 323 ASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskek 370
                                        SG   q + i++al  + ++lL+DE ts   + ++ e m+ + s  k
  gi|330506880|ref|YP_004383308.1| 137 LSGGQKQKVLIARALAQEPEVLLLDEPTSSLDMKHQLEVMETISSLVK 184
                                       599999***********************9999888888887665444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00071       0.4       3      45 ..      30      70 ..      28      97 .. 0.75
   2 ?    0.2   0.0       1.3   7.2e+02      56      79 ..     147     169 ..     122     193 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00071
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkk 45
                                      ++l ++G+  +GKTtl+k ++++ l k++  + i+  d ++ +
  gi|330506880|ref|YP_004383308.1| 30 EVLGLVGPNGSGKTTLIK-CMDKIL-KPKGSILIDGRDIDTVS 70
                                      6899************85.556666.78888888877777644 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                            AAA_14  56 ileklkeekktylflDEiqevpew 79 
                                       i + l  ++ ++l+lDE   + ++
  gi|330506880|ref|YP_004383308.1| 147 IARALA-QEPEVLLLDEPTSSLDM 169
                                       223233.47889999997776443 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00023      0.13      10      51 ..      29      72 ..      23     196 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelggvkp..eeillvaft 51
                                      ++vl ++++ G+GKT+++k++ ++l+  g++    ++i  v+ t
  gi|330506880|ref|YP_004383308.1| 29 SEVLGLVGPNGSGKTTLIKCMDKILKPKGSILIdgRDIDTVSRT 72
                                      678999**************999999888764433444444444 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0003      0.17      23      74 ..      35      82 ..      24     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                             RNA12 23 kGPrGSGkkeLv..ldrvlkdrkkvlvidCdelvkarndaelisaaAsqlGYfP 74
                                       GP GSGk+ L+  +d++lk + + + id +++          +++A++lGY+P
  gi|330506880|ref|YP_004383308.1| 35 VGPNGSGKTTLIkcMDKILKPKGS-ILIDGRDIDT-----VSRTELAKRLGYVP 82
                                      6**********8779999988765.5689999854.....44457899999998 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 ?   11.2   0.2   0.00035       0.2       2      18 ..      31      47 ..      30      58 .. 0.88
   2 ?   -2.1   0.0       4.3   2.4e+03      69     116 ..     190     240 ..     174     241 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00035
                                      EEEEEESTTCCHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLln 18
                                      v++l+G+ GsGKTtL++
  gi|330506880|ref|YP_004383308.1| 31 VLGLVGPNGSGKTTLIK 47
                                      7899***********97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.3
                                       HHHHHHHHHHHHTT-SEEEEEECT..TTTHHHH.HTTSHHHHHCCCECEEE CS
                              cobW  69 llkelealeereerldviliEttG..laePapv.afteeelksdltldavv 116
                                       ++++l++l   +  +d + i ++G   a+  p+ +++++++++ + ++avv
  gi|330506880|ref|YP_004383308.1| 190 AVMALHDLNLASMFVDKLAILKGGkiYAAGEPIdLLNAKNIRDVYGVEAVV 240
                                       455666666666777888888888744444555666678888887777776 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   0.1   0.00041      0.23       1      27 [.      31      57 ..      31      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00041
                              MobB  1 vlgivgksgsGKTtLleklipelkarg 27
                                      vlg+vg +gsGKTtL++ + ++lk +g
  gi|330506880|ref|YP_004383308.1| 31 VLGLVGPNGSGKTTLIKCMDKILKPKG 57
                                      799*************99888887766 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00056      0.31       2      23 ..      35      56 ..      34      60 .. 0.88
   2 ?   -2.3   0.0       5.4     3e+03     195     212 ..     170     187 ..     141     202 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00056
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelr 23
                                      vGp GsGKtt+++ + +il+ +
  gi|330506880|ref|YP_004383308.1| 35 VGPNGSGKTTLIKCMDKILKPK 56
                                      8**************9998866 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.4
                        ATP_bind_1 195 ekykklaeaiaelleefa 212
                                       + + + +e+i++l++e +
  gi|330506880|ref|YP_004383308.1| 170 KHQLEVMETISSLVKEKK 187
                                       333344444444444444 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   0.00067      0.37      27      58 ..      23      54 ..      17      62 .. 0.80
   2 ?   -2.7   0.0       6.5   3.6e+03     100     126 ..     198     225 ..     170     228 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00067
                             AAA_7 27 elllknkkpvllvGptGtGKtviikdllkkld 58
                                      +l+++ +  + lvGp G+GKt++ik + k l+
  gi|330506880|ref|YP_004383308.1| 23 NLVVEDSEVLGLVGPNGSGKTTLIKCMDKILK 54
                                      566777777779************98777666 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.5
                             AAA_7 100 kklvvFvDDlnmpakek.ygaqppiell 126
                                       +   +FvD l + +  k y a +pi ll
  gi|330506880|ref|YP_004383308.1| 198 NLASMFVDKLAILKGGKiYAAGEPIDLL 225
                                       3345677777666543325666666665 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00057      0.32      27      51 ..      33      69 ..      26     211 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00057
                                      EEEESTTSSHHHHHHHHHHHCS--............- CS
                           G-alpha 27 lllGqseSGKsTilkqlkllykkg............f 51
                                       l+G ++SGK+T++k + ++ k++            +
  gi|330506880|ref|YP_004383308.1| 33 GLVGPNGSGKTTLIKCMDKILKPKgsilidgrdidtV 69
                                      589***************8887775665444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1675.51
//
Query:       gi|330506881|ref|YP_004383309.1|  [L=686]
Description: magnesium-chelatase subunit ChlD [Methanosaeta concilii GP6]
Scores for complete 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-22   76.7   0.1    3.2e-21   74.9   0.1    2.0  1  AAA_lid_2        AAA lid domain
    3.6e-15   56.5   0.1    2.7e-14   53.7   0.0    2.4  2  VWA_2            von Willebrand factor type A domain
    6.6e-11   42.8   0.0    3.8e-10   40.3   0.0    2.1  2  VWA              von Willebrand factor type A domain
    3.3e-10   40.1   0.0    4.3e-06   26.8   0.0    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
    1.9e-09   37.2   0.0    8.2e-07   28.6   0.0    2.8  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    7.4e-05   21.9   0.2      0.005   16.0   0.1    3.0  2  MCM              MCM P-loop domain
    0.00055   19.8   0.0     0.0018   18.1   0.0    2.0  1  Coilin_N         Coilin N-terminus
    0.00058   19.3   0.1     0.0013   18.1   0.1    1.5  1  VWA_CoxE         VWA domain containing CoxE-like protein
    0.00081   19.8   0.0    0.00081   19.8   0.0    2.4  1  AAA_16           AAA ATPase domain
     0.0016   18.5  17.8     0.0021   18.1  17.8    1.2  1  TFIIA            Transcription factor IIA, alpha/beta subunit
     0.0084   15.8   0.0       0.32   10.7   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.011   15.3  20.1      0.019   14.6  20.1    1.3  1  Spt20            Spt20 family
      0.033   14.3   0.1       0.13   12.4   0.1    2.0  1  Fer4_11          4Fe-4S dicluster domain
      0.034   14.4   0.0       0.17   12.2   0.0    2.2  1  AAA_22           AAA domain
      0.072   10.2   7.0       0.09    9.9   7.0    1.0  1  GREB1            Gene regulated by oestrogen in breast cancer
      0.078   12.8   0.0        3.8    7.4   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
      0.096   13.1  10.0       0.34   11.3  10.0    1.9  1  RNA_pol_Rpc4     RNA polymerase III RPC4
      0.097   13.1   0.1          1    9.8   0.0    2.7  1  AAA              ATPase family associated with various cellul
       0.21   11.8   5.4       0.44   10.7   5.4    1.6  1  CPSF100_C        Cleavage and polyadenylation factor 2 C-term
       0.23   11.6   7.3       0.36   11.0   7.3    1.3  1  DDHD             DDHD domain
       0.64   10.3  14.7          1    9.6  14.7    1.2  1  MMR1             Mitochondrial Myo2 receptor-related protein
       0.68    9.0  11.1        1.2    8.1  11.1    1.3  1  Roughex          Drosophila roughex protein
        1.3    9.4  13.9        2.9    8.3  13.9    1.6  1  CCDC53           Subunit CCDC53 of WASH complex
        1.5    7.5  13.5        2.1    7.0  13.5    1.2  1  Presenilin       Presenilin
        1.5    9.6  16.6       0.48   11.2  13.0    2.0  1  Hep_59           Hepatocellular carcinoma-associated antigen 
        1.5    8.2  12.8        2.5    7.5  12.8    1.3  1  SpoIIP           Stage II sporulation protein P (SpoIIP)
        1.9    6.8   4.2        2.5    6.4   4.2    1.1  1  SID-1_RNA_chan   dsRNA-gated channel SID-1
        2.7    8.0  12.1         21    5.2   0.0    2.5  2  Peptidase_S49_N  Peptidase family S49 N-terminal
        3.3    7.1   9.7        5.6    6.3   9.7    1.3  1  Endostatin       Collagenase NC10 and Endostatin
        3.8    6.8  10.8          6    6.2  10.8    1.2  1  DUF908           Domain of Unknown Function (DUF908)
        6.2    6.6  16.4         12    5.6  16.4    1.4  1  RR_TM4-6         Ryanodine Receptor TM 4-6
        6.9    5.6  12.1         11    5.0  12.1    1.2  1  SLC12            Solute carrier family 12
        7.2    5.2  10.5        9.9    4.7  10.5    1.1  1  Ndc1_Nup         Nucleoporin protein Ndc1-Nup
        8.8    5.2  19.5         14    4.5  19.5    1.2  1  DUF5427          Family of unknown function (DUF5427)
        9.3    6.3   8.7         17    5.5   8.7    1.4  1  Gti1_Pac2        Gti1/Pac2 family
        9.4    6.2   9.3         16    5.5   9.3    1.4  1  Neur_chan_memb   Neurotransmitter-gated ion-channel transmemb
        9.9    4.1  15.2         14    3.6  15.2    1.1  1  Hid1             High-temperature-induced dauer-formation pro


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 !   74.9   0.1   6.6e-24   3.2e-21       4      71 ..     270     337 ..     267     339 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 6.6e-24
                         AAA_lid_2   4 rahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegetteeive 71 
                                       +a+++i lgv ++Ra++++ r+A+++Aa+egr++ ++eDvk+a +l+LaHR+r +p+++++ +++++e
  gi|330506881|ref|YP_004383309.1| 270 IASTCIDLGVKTHRAEIVISRTAKTIAAFEGRTEANQEDVKKAMELALAHRMRSRPFEPPTLNKDKLE 337
                                       899*******************************************************9988888876 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   0.1       4.1     2e+03      73      91 ..     304     322 ..     229     355 .. 0.66
   2 !   53.7   0.0   5.5e-17   2.7e-14       1     106 [.     494     600 ..     494     601 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 4.1
                             VWA_2  73 gggtnlaaaLqlarkalkk 91 
                                       +++ ++ +a++la ++  +
  gi|330506881|ref|YP_004383309.1| 304 ANQEDVKKAMELALAHRMR 322
                                       4677777777777765543 PP

  == domain 2  score: 53.7 bits;  conditional E-value: 5.5e-17
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallk.slp.gdrvglvtfsd.gpevlipltkdkakilnalrnleakgg 74 
                                       l+fv+D+SgSm++     +r+e ak av +ll  s++ +d++g v+f++ ++e+++p++++ +  l++l++l + gg
  gi|330506881|ref|YP_004383309.1| 494 LLFVVDGSGSMGAM----QRMESAKGAVLSLLMeSYQkRDKIGMVAFRGtEAELILPPSSSVDLALSRLKELPT-GG 565
                                       69***********9....6*********8877746655***********88**********************7.7* PP

                             VWA_2  75 gtnlaaaLqlarkalkkrr...kgekrvivlitDg 106
                                       +t l a+L+   ++l+ +    + +k  +vl++Dg
  gi|330506881|ref|YP_004383309.1| 566 KTPLSAGLSRGLQLLQGEMrkdAETKLMMVLVSDG 600
                                       *************9987777888889999999999 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 ?   -0.8   0.0       3.4   1.6e+03     126     151 ..     199     224 ..     164     243 .. 0.77
   2 !   40.3   0.0   7.8e-13   3.8e-10       2     139 ..     494     633 ..     494     665 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.4
                                       HHHGCTEEEEEEEESSSHHHHHHHHH CS
                               VWA 126 eakeqgikvfavGvgnadekelLnki 151
                                        + + g++v +vG+ ++d + l+ k 
  gi|330506881|ref|YP_004383309.1| 199 LLDRFGLQVNVVGIEDVDQRMLIAKT 224
                                       5667899*******999998855444 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 7.8e-13
                                       EEEEEE-STTS.CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS.EEEEEETTSHCHHHHHHHHHHTGSGGGG CS
                               VWA   2 ivfvlDgSgsm.geenfekvkefikklveklevgpegtrvglvqfsse.vktefslndysskeellsalnnlkysgg 76 
                                       + fv+DgSgsm   +++e++k ++ +l+ + +  ++++++g+v f ++ ++ + + ++  s + +ls l++l   +g
  gi|330506881|ref|YP_004383309.1| 494 LLFVVDGSGSMgAMQRMESAKGAVLSLLMESY--QKRDKIGMVAFRGTeAELILPPSS--SVDLALSRLKEL--PTG 564
                                       57*********445788899999999888877..8**********9775888899998..669********8..666 PP

                                       SSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.......HTHHHHHHHHGCTEEEEEEEE CS
                               VWA  77 gttntgkalkyaleklfkssagaRenakkviilltdGksndg.......dpkeaaneakeqgikvfavGv 139
                                       g+t + ++l+ +l+ l+ ++++  +++k +++l++dG+ n g       ++ e +++ k+ g+ ++++  
  gi|330506881|ref|YP_004383309.1| 565 GKTPLSAGLSRGLQLLQGEMRK-DAETKLMMVLVSDGRANVGmggkikdELMEISERTKQLGVHTIVIDT 633
                                       6666**********99999888.5589************9988996666666666666666776666654 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    0.0009      0.44       2      39 ..      36      73 ..      35      88 .. 0.83
   2 !   26.8   0.0     9e-09   4.3e-06      30     138 .]     101     203 ..      91     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0009
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HH CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdttee 39
                                      vl+ G++Gt+Ks+ ++ la +l++ v++  ++ + +++
  gi|330506881|ref|YP_004383309.1| 36 VLIRGDKGTAKSTAVRALADLLEDIVVVEDCPFNCNPR 73
                                      8999******************8887777666665555 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 9e-09
                                       EE--TT--HHHHH--B--.............--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSE CS
                             AAA_5  30 vqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllleeggel 102
                                       + l+ + te+ ++g+++++    +g ++l++++l   a +  il++DEv+ ++++v+++Ll         +e  g  
  gi|330506881|ref|YP_004383309.1| 101 IDLPLGATEDRVVGSLNVEraikEGIRALEPGILA--AANRGILYIDEVNLLDDHVADVLLDSAAMGVNIVEREGVS 175
                                       556667899********999999***********9..55667******************66655555554444444 PP

                                       EE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5 103 vkaknddllerfrviatanpldrslnelspalrsRf 138
                                       v ++++     f +++t+np +    el p+l++Rf
  gi|330506881|ref|YP_004383309.1| 176 VAHPSK-----FILVGTMNPEE---GELRPQLLDRF 203
                                       444443.....*********99...77889999999 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     0.022        11       2      50 ..      11      61 ..      10      71 .. 0.86
   2 !   28.6   0.0   1.7e-09   8.2e-07      93     158 ..     125     190 ..     115     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.022
                      Mg_chelatase  2 lkdvkGqeeakraleiaaaGgH..nlllvGppGsGKtmlakrlpsllppls 50
                                      +++++Gqe+ k al + a+      +l+ G  G+ K+   ++l+ ll ++ 
  gi|330506881|ref|YP_004383309.1| 11 FTSIVGQEDMKFALILNAINPRigGVLIRGDKGTAKSTAVRALADLLEDIV 61
                                      5789***********99987542279*******************998765 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.7e-09
                      Mg_chelatase  93 ggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                       g +  +pG ++ a++G+L++DE+  ++ +v +vL +    g   ++r   +v +p++f lv +mNp
  gi|330506881|ref|YP_004383309.1| 125 GIRALEPGILAAANRGILYIDEVNLLDDHVADVLLDSAAMGVNIVEREGVSVAHPSKFILVGTMNP 190
                                       566789***********************************************************9 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      0.14        70      60      82 ..      36      58 ..       8      65 .. 0.76
   2 !   16.0   0.1     1e-05     0.005     101     178 ..     118     195 ..     106     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.14
                                      EEEEESSTSTHHHHHHHHHHHSS CS
                               MCM 60 vllvgdpgtaKsqlLkyveklap 82
                                      vl+ gd gtaKs+ ++++++l++
  gi|330506881|ref|YP_004383309.1| 36 VLIRGDKGTAKSTAVRALADLLE 58
                                      8999********99998887765 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1e-05
                                       EEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSS CS
                               MCM 101 vvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagr 177
                                       v r  ++g  +le G l  a++G+++iDe++  +++  ++l++        + + G+ +  +++  ++  +np++g+
  gi|330506881|ref|YP_004383309.1| 118 VERAIKEGIRALEPGILAAANRGILYIDEVNLLDDHVADVLLDSAAMGVNIVEREGVSVAHPSKFILVGTMNPEEGE 194
                                       55556666689******************************998888888889999999999999999999999987 PP

                                       C CS
                               MCM 178 y 178
                                        
  gi|330506881|ref|YP_004383309.1| 195 L 195
                                       5 PP

>> Coilin_N  Coilin N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.7e-06    0.0018      75     131 ..     263     387 ..     134     397 .. 0.51

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.7e-06
                          Coilin_N  75 V.......................................................................klegs 80 
                                                                                                               kle s
  gi|330506881|ref|YP_004383309.1| 263 SddllriiastcidlgvkthraeivisrtaktiaafegrteanqedvkkamelalahrmrsrpfepptlnkdKLEKS 339
                                       05555556666666666666666666666666666666666666666666666666666666666666663333322 PP

                          Coilin_N  81 etkleaqesededsresasksasttkqkkkkKrekkqeeqdeqkasqaakd 131
                                         ++++q + ++++++ +++++ +++q k+  ++kkqe+q e++ +q+++d
  gi|330506881|ref|YP_004383309.1| 340 --MEKQQ-QDQQQQKQQQQEQQPQEQQPKQPPQQKKQEQQPESSDQQEDSD 387
                                       ..22222.2333333333333444444444444444444444444443333 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 !   18.1   0.1   2.8e-06    0.0013       7     181 ..     431     622 ..     425     638 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.8e-06
                          VWA_CoxE   7 alllglarrrrrrkrrrrgrriDlrrtlranlrhgge..........lvelvrrkprerkprelvllvDvSgSmaay 73 
                                        l+l+   r  r++  ++g++i + +t+ra+    ++           +++  +++ +++++ l+++vD SgSm a 
  gi|330506881|ref|YP_004383309.1| 431 TLALQNSGRYLRQRMPKEGKDIAIDATIRAAAPYQKArsgpnaikvkSEDIREKERARKTSAMLLFVVDGSGSMGAM 507
                                       444444444479999999************9988877899999999777777777755666699*********9886 PP

                          VWA_CoxE  74 sai......flallhAllqqlprtevfaFdtrlvdlTral.rerDpaeaLarvsaaved.lgGgTrigaalaeflel 142
                                        ++      +l+ll    q+++++ ++aF    ++l   l   ++ + aL r++   e   gG T ++a+l   l+l
  gi|330506881|ref|YP_004383309.1| 508 QRMesakgaVLSLLMESYQKRDKIGMVAFRGTEAELI--LpPSSSVDLALSRLK---ELpTGGKTPLSAGLSRGLQL 579
                                       65422222256666666677779999***87666664..423367777888888...6669999****999988887 PP

                          VWA_CoxE 143 vt...rpaLsrravvvlvsDgl.ergdreellaelarlvrrar 181
                                        +   r++ + + ++vlvsDg  + g   ++++el ++++r  
  gi|330506881|ref|YP_004383309.1| 580 LQgemRKDAETKLMMVLVSDGRaNVGMGGKIKDELMEISERTK 622
                                       762224444778899*****74134555666666666666654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.7e-06   0.00081      20     155 ..      29     159 ..      18     171 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.7e-06
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy...salaqalareellrqlldeaesae 93 
                                         +r + vl++G++G+ Ks+ vr+l+  l +d +++++     +    p+    +   ++  ++   q+++++++  
  gi|330506881|ref|YP_004383309.1|  29 INPRIGGVLIRGDKGTAKSTAVRALA-DLLED-IVVVEDCPFNC---NPRnveEMCDLCF-DRSQRGQIKEASRK-- 97 
                                       4466689*******************.68888.77777777777...3333212233333.33555666555333.. PP

                            AAA_16  94 leawrekleeala.avpelagaea..srllellkrll.allsrderplvlvlDdlqwadeaslql.l 155
                                              ++  l+   + + g++   +++ e +++l    l+   r  +l +D++  +d++ +++ l
  gi|330506881|ref|YP_004383309.1|  98 ----TPVIDLPLGaTEDRVVGSLNveRAIKEGIRALEpGILAAANR-GILYIDEVNLLDDHVADVlL 159
                                       ....333333333211222233336577777777777766666344.89**********99999845 PP

>> TFIIA  Transcription factor IIA, alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1  17.8   4.4e-06    0.0021     198     257 ..     329     403 ..     237     514 .. 0.50

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.4e-06
                             TFIIA 198 q............qqqqqqqqqqqqqqqvqqqqqeesqqaqqasqe...qvagsqvessqtdgaedaleeespv... 256
                                       +            +qqq qqqq+qqqq    +qq ++qq++q++q+   +++++++++++++ +++a++ ++++   
  gi|330506881|ref|YP_004383309.1| 329 PtlnkdkleksmeKQQQDQQQQKQQQQ----EQQPQEQQPKQPPQQkkqEQQPESSDQQEDSDQAQAASPQEQIfei 401
                                       022233343222222222222233232....2222333333332221113333333333333333444444444332 PP

                             TFIIA 257 .l 257
                                         
  gi|330506881|ref|YP_004383309.1| 402 gA 403
                                       21 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.24   1.2e+02      24      44 ..      35      55 ..      19      76 .. 0.82
   2 !   10.7   0.0   0.00066      0.32      82     140 ..     127     187 ..      91     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.24
                                      -EEEECSTTSSHHHHHHHHHH CS
                   Sigma54_activat 24 svlitGesGtGKellaraihe 44
                                       vli+G++Gt K++  ra+ +
  gi|330506881|ref|YP_004383309.1| 35 GVLIRGDKGTAKSTAVRALAD 55
                                      69***********99998765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00066
                                       SS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHH..HHHHSEEESBTSSSEEE--EEEEEE CS
                   Sigma54_activat  82 ekekkGlfekadgGtlfLDeigelplelQekLlr..vlqegevervGsskeikvdvriiaa 140
                                       ++ + G + +a+ G+l++De++ l+ ++   Ll   ++  + ver G s  ++ ++ ++ +
  gi|330506881|ref|YP_004383309.1| 127 RALEPGILAAANRGILYIDEVNLLDDHVADVLLDsaAMGVNIVEREGVSVAHPSKFILVGT 187
                                       55567********************999999996224555667777777776666666655 PP

>> Spt20  Spt20 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6  20.1   3.9e-05     0.019     107     161 ..     341     395 ..     274     404 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-05
                             Spt20 107 qkqsqqnqqqqqqqqqqqqqqqqqqeqqqqqnekdsttteekekksksknnssks 161
                                       +kq+q +qqq+qqqq qq+q+qq ++  qq++++++ +++++++ s + +++s +
  gi|330506881|ref|YP_004383309.1| 341 EKQQQDQQQQKQQQQEQQPQEQQPKQPPQQKKQEQQPESSDQQEDSDQAQAASPQ 395
                                       2333333333333333333333322222222222222222222222222222222 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00026      0.13      50      86 ..      62      94 ..      47     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00026
                           Fer4_11 50 vveacPykivrkneetgkvekCdmcldrveaGllpac 86
                                      vve cP+++  +n e++    Cd+c+dr + G+    
  gi|330506881|ref|YP_004383309.1| 62 VVEDCPFNCNPRNVEEM----CDLCFDRSQRGQIKEA 94
                                      6899*****99998887....***********98765 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   0.00035      0.17       9     130 ..      37     187 ..      34     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00035
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............... 70 
                                       ++ G +Gt K+t +r l++ l         ++ vv  ++p  ++++++ ++    +++++ +               
  gi|330506881|ref|YP_004383309.1|  37 LIRGDKGTAKSTAVRALADLL---------EDIVVVEDCPFNCNPRNVEEMCDLCFDRSQRGqikeasrktpvidlp 104
                                       788******************.........999**999999998888766655556655555777************ PP

                            AAA_22  71 .............erlsseellealeqalraravielliiDEaqhlr.s..eealeeLrsllnl.......srkgvq 124
                                                     +   +e ++ale  + a+a +++l iDE+  l+ +  + +l    + +n+         ++ +
  gi|330506881|ref|YP_004383309.1| 105 lgatedrvvgslnVERAIKEGIRALEPGILAAANRGILYIDEVNLLDdHvaDVLLDSAAMGVNIveregvsVAHPSK 181
                                       **999999998887777888888888888888889***********7634455565556666667666667777888 PP

                            AAA_22 125 liLvGt 130
                                       +iLvGt
  gi|330506881|ref|YP_004383309.1| 182 FILVGT 187
                                       888887 PP

>> GREB1  Gene regulated by oestrogen in breast cancer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   7.0   0.00019      0.09    1181    1282 ..     327     427 ..     203     437 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00019
                             GREB1 1181 seeakspkasvtseeeeseeskekekeslsketesqlsleaseqkealdakasskssssssssssassPssscsl 1255
                                        +  + +  +  +s e+++++++++++++++++ ++q  + ++ q+++ +++ +s+ ++ +s +++a sP++++  
  gi|330506881|ref|YP_004383309.1|  327 EPPTLNKDKLEKSMEKQQQDQQQQKQQQQEQQPQEQQPK-QPPQQKKQEQQPESSDQQEDSDQAQAASPQEQIFE 400 
                                        111111111112222222222333333333333333333.34444444556677777888888999999999988 PP

                             GREB1 1256 akavkrPpivllskavydiltssdssg 1282
                                          a    + + +++   +i + + s++
  gi|330506881|ref|YP_004383309.1|  401 IGAPIDVRQINMPRKRDKIFRRKTSGR 427 
                                        888888888888888877777766655 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.22   1.1e+02       2      24 ..      36      58 ..      35      63 .. 0.91
   2 ?    7.4   0.0    0.0078       3.8      65     116 ..     141     194 ..     123     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.22
                             AAA_3  2 vllegvPGlaktllvkalakald 24
                                      vl++g  G+ak ++v+ala+ l+
  gi|330506881|ref|YP_004383309.1| 36 VLIRGDKGTAKSTAVRALADLLE 58
                                      7999***************9886 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0078
                             AAA_3  65 llladeinrappktqsalle..ameerqvtvegethklpepflvlatqnPieqe 116
                                       +l  de+n    ++   ll+  am  + v  eg + + p++f+++ t nP e e
  gi|330506881|ref|YP_004383309.1| 141 ILYIDEVNLLDDHVADVLLDsaAMGVNIVEREGVSVAHPSKFILVGTMNPEEGE 194
                                       7889***************855799999999*******************8754 PP

>> RNA_pol_Rpc4  RNA polymerase III RPC4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3  10.0    0.0007      0.34      19      96 ..     338     439 ..     323     441 .. 0.43

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0007
                      RNA_pol_Rpc4  19 kavsaaeddkseaesqsaekakaeeeskaekasgaeaeekkskkksskkkkkkkskalklkslpe............ 83 
                                       k+++++++d++++++q++e++ +e+++k++ ++++++++++s+  +++++++++++a       +            
  gi|330506881|ref|YP_004383309.1| 338 KSMEKQQQDQQQQKQQQQEQQPQEQQPKQPPQQKKQEQQPESS--DQQEDSDQAQAA-------Spqeqifeigapi 405
                                       2222222232333333222222222222222222222222211..111122222222.......1222444566677 PP

                      RNA_pol_Rpc4  84 .....................GviGkLlvhkSGk 96 
                                                             +i +L +  SG+
  gi|330506881|ref|YP_004383309.1| 406 dvrqinmprkrdkifrrktsgRRINTLALQNSGR 439
                                       7777777777777777777766777777777776 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    0.0021         1       1     129 [.      36     208 ..      36     210 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0021
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS........................................ CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk........................................ 37 
                                       vl+ G +Gt K+++++a+a  l+  ++  +++  ++                                         
  gi|330506881|ref|YP_004383309.1|  36 VLIRGDKGTAKSTAVRALADLLEDIVVVEDCPFNCNPrnveemcdlcfdrsqrgqikeasrktpvidlplgatedrv 112
                                       688899**************985333333333333222333334455555566666666666667777666666665 PP

                                       .STTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEE CS
                               AAA  38 .yvgesekkirelfkeakeka....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigat 109
                                           + e+ i+e +++++       +  il iDE+  l  +  +   +++   vn   +e   v +  sk+i++g+ 
  gi|330506881|ref|YP_004383309.1| 113 vGSLNVERAIKEGIRALEPGIlaaaNRGILYIDEVNLLDDHVADVLLDSAAMGVNIVEREGVSVAH-PSKFILVGTM 188
                                       5333345555555544433336664559*******9997777555555566666655555555555.6889999999 PP

                                       SS.GGGSTHHHHSTTSSEEEE CS
                               AAA 110 nr.pdkldpallrgRfdrkie 129
                                       n  + +l p+ll +Rf  +++
  gi|330506881|ref|YP_004383309.1| 189 NPeEGELRPQLL-DRFGLQVN 208
                                       988999999999.99987765 PP

>> CPSF100_C  Cleavage and polyadenylation factor 2 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   5.4   0.00092      0.44      34      79 ..     338     388 ..     260     422 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00092
                         CPSF100_C  34 a.....eeaeeeekeeeeeeeeeeeeeeeaskkqklaeksekeaseeesee 79 
                                       +     +++++++k++++e++ +e++ +++ +++k++++ e+++++e+s++
  gi|330506881|ref|YP_004383309.1| 338 KsmekqQQDQQQQKQQQQEQQPQEQQPKQPPQQKKQEQQPESSDQQEDSDQ 388
                                       022222222222222222222222222222222222111111111111111 PP

>> DDHD  DDHD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   7.3   0.00074      0.36      94     170 ..     295     404 ..     275     488 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00074
                              DDHD  94 ltsigaalkqkvsglvssls...............allnrslelaeeesaslaessksherasesskasqeskaaes 155
                                       ++ ++ +++ +++++ + ++               +l++  le ++e++++ ++++k+++++++ ++++ ++  +++
  gi|330506881|ref|YP_004383309.1| 295 IAAFEGRTEANQEDVKKAMElalahrmrsrpfeppTLNKDKLEKSMEKQQQDQQQQKQQQQEQQPQEQQPKQPPQQK 371
                                       33333333333333333333333333545544443133333333333333333333333333333333333333333 PP

                              DDHD 156 stasssaksskaee..................k 170
                                       +++++ ++s ++e+                   
  gi|330506881|ref|YP_004383309.1| 372 KQEQQPESSDQQEDsdqaqaaspqeqifeigaP 404
                                       333333322222221222333333333333330 PP

>> MMR1  Mitochondrial Myo2 receptor-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  14.7    0.0021         1      63     158 ..     293     393 ..     284     448 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0021
                              MMR1  63 kntenskkaseqeatgskqnnek..elnvekski.skltiketleql..reeksqqksksaekekqkr.svaakseq 133
                                       k++++ +  +e++++  k+  e      +  +++ ++   k++le+   ++++ qq++k++++e+q++ +++++  q
  gi|330506881|ref|YP_004383309.1| 293 KTIAAFEGRTEANQEDVKKAMELalAHRMRSRPFePPTLNKDKLEKSmeKQQQDQQQQKQQQQEQQPQeQQPKQPPQ 369
                                       44444444444444444444444445556666777777778888887322222233333333333322022333333 PP

                              MMR1 134 esekveeleksksereisetssaiS 158
                                       ++++++++ +s++++e s++++a S
  gi|330506881|ref|YP_004383309.1| 370 QKKQEQQP-ESSDQQEDSDQAQAAS 393
                                       32333333.3333333333333333 PP

>> Roughex  Drosophila roughex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  11.1    0.0026       1.2     211     344 ..     288     417 ..     254     432 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0026
                           Roughex 211 isrlrraslaranpqtddeeeevpqarslsvrrilfadgade..dgdedtdgsveekkddasepdlpdqnkeedkd. 284
                                       isr  ++ +a  + +t+ ++e+v +a +l++   + +   +     +++ + s+e++++d  +    +q++e++ + 
  gi|330506881|ref|YP_004383309.1| 288 ISRTAKT-IAAFEGRTEANQEDVKKAMELALAHRMRSRPFEPptLNKDKLEKSMEKQQQDQQQQK--QQQQEQQPQe 361
                                       4444444.477788888888888888887776555553322200223333445555555544433..3333333331 PP

                           Roughex 285 eqeqqaeqeeqaqqqaeeapvssdistalketnppaepivgernppeksiissltprkrt 344
                                       +q +q +q+++++qq+e +    d+  a+     p e i     p +   i    prkr 
  gi|330506881|ref|YP_004383309.1| 362 QQPKQPPQQKKQEQQPESSDQQEDSDQAQA--ASPQEQIFEIGAPIDVRQI--NMPRKRD 417
                                       344566777888888888888666666654..4578888877777665554..3577776 PP

>> CCDC53  Subunit CCDC53 of WASH complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  13.9     0.006       2.9      52     104 ..     338     392 ..     299     421 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.006
                            CCDC53  52 eveaeaaeastsddn..aarkgppppppsseaaaaaaqaeeasqaeesaeeeaee 104
                                       +  +++++ ++++++  +++++++++p++ +++++++q++e+s ++e++++++++
  gi|330506881|ref|YP_004383309.1| 338 KSMEKQQQDQQQQKQqqQEQQPQEQQPKQPPQQKKQEQQPESSDQQEDSDQAQAA 392
                                       2222222222222220022222222222222222222222222222222222222 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  13.5    0.0044       2.1     257     313 ..     335     391 ..     287     434 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0044
                        Presenilin 257 seeesseksaqsseseeeseeesseaessaeesseekeseessesseeeeeeeeeee 313
                                       + e+s ek++q +++++++++e++++e++++++ ++k++e++ ess+++e++++++ 
  gi|330506881|ref|YP_004383309.1| 335 KLEKSMEKQQQDQQQQKQQQQEQQPQEQQPKQPPQQKKQEQQPESSDQQEDSDQAQA 391
                                       111112222222222222222222222222222222222222222222222222221 PP

>> Hep_59  Hepatocellular carcinoma-associated antigen 59
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  13.0     0.001      0.48      20     100 ..     337     416 ..     298     419 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.001
                            Hep_59  20 eeeLakrkgkskqeqeeeeekeseassksedaede..lyevpehlkvsskkeeeealsnqmlggIpEVdLgieaklk 94 
                                       e++++k++++ +q+q++++++++ ++++++++ ++    + pe+  +  ++++++a+ ++ + +I E+  +i+++  
  gi|330506881|ref|YP_004383309.1| 337 EKSMEKQQQD-QQQQKQQQQEQQPQEQQPKQPPQQkkQEQQPESSDQ--QEDSDQAQAASPQEQIFEIGAPIDVRQI 410
                                       4444443322.222222222222222222222222212233333333..333333355667799***********99 PP

                            Hep_59  95 Nieete 100
                                       N+ + +
  gi|330506881|ref|YP_004383309.1| 411 NMPRKR 416
                                       987765 PP

>> SpoIIP  Stage II sporulation protein P (SpoIIP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  12.8    0.0051       2.5      17      77 ..     334     394 ..     303     428 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0051
                            SpoIIP  17 epteeapaeesekeekekeeeeeeekeeeeeeeikkeekeeekekeedseeeeekldkskp 77 
                                        + e++ +++++ ++++k++++e++++e++ ++  +++k+e++ +++d++e++ +++++ p
  gi|330506881|ref|YP_004383309.1| 334 DKLEKSMEKQQQDQQQQKQQQQEQQPQEQQPKQPPQQKKQEQQPESSDQQEDSDQAQAASP 394
                                       3444444455555555555555555555555555555444444444444444444444443 PP

>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.2    0.0052       2.5     146     224 ..     343     423 ..     270     434 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0052
                    SID-1_RNA_chan 146 vresseekrvkessssesaseslesvssavrsesessveeesdydtleeiesdknvirtkkvlvvsdls..rkdkrv 220
                                        +++++++++++++++++++++++  +++ ++++ +s+++++d d  + ++ +++++   + + v +++  rk  ++
  gi|330506881|ref|YP_004383309.1| 343 QQQDQQQQKQQQQEQQPQEQQPKQPPQQKKQEQQPESSDQQEDSDQAQAASPQEQIFEIGAPIDVRQINmpRKRDKI 419
                                       33355566666777778888888888888888888999999999999999999999999998988877755666666 PP

                    SID-1_RNA_chan 221 lekk 224
                                        ++k
  gi|330506881|ref|YP_004383309.1| 420 FRRK 423
                                       6665 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   8.9      0.16        78      44      90 ..     334     369 ..     284     401 .. 0.55
   2 ?    5.2   0.0     0.043        21      77     122 ..     475     520 ..     434     533 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.16
                   Peptidase_S49_N  44 tkLneeykelkeeleealldeeelkaaekkekkeekeekkaekkkak 90 
                                        kL+++ +++++            ++++k++++e++ ++++ k+  +
  gi|330506881|ref|YP_004383309.1| 334 DKLEKSMEKQQQ-----------DQQQQKQQQQEQQPQEQQPKQPPQ 369
                                       222222222222...........222222222222222222222111 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.043
                   Peptidase_S49_N  77 eekeekkaekkkakeeeekkrvfvldFkGdikAse.vesLreeitav 122
                                       + k+e+ +ek++a+ +++   +fv+d +G++ A + +es +  + ++
  gi|330506881|ref|YP_004383309.1| 475 KVKSEDIREKERAR-KTSAMLLFVVDGSGSMGAMQrMESAKGAVLSL 520
                                       33444444444444.567889**********9965144455444444 PP

>> Endostatin  Collagenase NC10 and Endostatin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   9.7     0.011       5.6      69     130 ..     317     388 ..     274     412 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                        Endostatin  69 s...........Pvvksskerlvllearrktksskesvkakekeaskeeleekaekkveesekslttarrask 130
                                                   P+++ +k ++++++++++++++k++++++++ +++++++++++kk+e++ +s+ +++ + +
  gi|330506881|ref|YP_004383309.1| 317 LahrmrsrpfepPTLNKDKLEKSMEKQQQDQQQQKQQQQEQQP-QEQQPKQPPQQKKQEQQPESSDQQEDSDQ 388
                                       0333344544546666666644444333333333333333332.22222222222222221111111111111 PP

>> DUF908  Domain of Unknown Function (DUF908)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  10.8     0.012         6     151     217 ..     342     402 ..     292     407 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                            DUF908 151 eeqkaesksskeeaseslissspstPtplrrssklgktssspsspaktstpskaaksqeglktfeip 217
                                       ++q+ ++++++++++++ ++++p+ P + ++++++      p+s+++++ +++a++++ + ++fei+
  gi|330506881|ref|YP_004383309.1| 342 KQQQDQQQQKQQQQEQQPQEQQPKQPPQQKKQEQQ------PESSDQQEDSDQAQAASPQEQIFEIG 402
                                       23333333333444444446677777666665544......55556667777777777777899996 PP

>> RR_TM4-6  Ryanodine Receptor TM 4-6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  16.4     0.024        12      72     158 ..     319     396 ..     280     412 .. 0.49

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.024
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX..........XXXXXXXXXXX CS
                          RR_TM4-6  72 Dlseteaeesptpelkkklaeeeeaeeekeeeeepeaeaeekadaengekeekekekeeeekeseeeeeekkkkkka 148
                                         + + + e+  p+l+k + e++++++++++++++++++ e++ +e++ k+  +++k+e++ es+ ++e +      
  gi|330506881|ref|YP_004383309.1| 319 HRMRSRPFEP--PTLNKDKLEKSMEKQQQDQQQQKQQQQ-EQQPQEQQPKQPPQQKKQEQQPESSDQQEDS------ 386
                                       3333334443..344444444444444444444433333.4444444444444444333333333333333...... PP

                                       XXXXXXXXXX CS
                          RR_TM4-6 149 kskkkeeaea 158
                                        +++ +++++
  gi|330506881|ref|YP_004383309.1| 387 DQAQAASPQE 396
                                       3333333333 PP

>> SLC12  Solute carrier family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  12.1     0.022        11     165     222 ..     319     393 ..     276     439 .. 0.37

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.022
                             SLC12 165 e.................ekskekeekekleekdsnlslseekkeeekekkkekkkkkekkeklkkkekslllke 222
                                       +                 eks+ek+++++ ++k++++++++++++ ++  +++k++++ +++++++++++   ++
  gi|330506881|ref|YP_004383309.1| 319 HrmrsrpfepptlnkdklEKSMEKQQQDQQQQKQQQQEQQPQEQQPKQPPQQKKQEQQPESSDQQEDSDQAQAAS 393
                                       022222333222222211222222222222222222222222222222222222222222222221122221222 PP

>> Ndc1_Nup  Nucleoporin protein Ndc1-Nup
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  10.5      0.02       9.9     348     413 ..     334     398 ..     298     507 .. 0.52

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.02
                          Ndc1_Nup 348 qrinergqpapkaapskapknkasapvkelprlsksplkkk..ddeifgn..sltaeaspkssssskegv 413
                                       ++++++++++++ ++++++++++++p++++p++   p+++k  +++   +  +++ ++ +++  s++e++
  gi|330506881|ref|YP_004383309.1| 334 DKLEKSMEKQQQDQQQQKQQQQEQQPQEQQPKQ---PPQQKkqEQQP--EssDQQEDSDQAQAASPQEQI 398
                                       455555552222222122222222222222222...22222211111..011122222222222222222 PP

>> DUF5427  Family of unknown function (DUF5427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  19.5     0.029        14      27     121 ..     300     391 ..     276     403 .. 0.43

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.029
                           DUF5427  27 kakkkdeediLaeLe.eLakke.srpaTPrvksn.kskkaspkkkksaeepakeekkkeeessedkrksvestrsle 100
                                         +++++ed+ + +e  La++  srp  P + ++ k +k+  +k+++ ++++k++ ++e++ +e++ k   +++++e
  gi|330506881|ref|YP_004383309.1| 300 GRTEANQEDVKKAMElALAHRMrSRPFEPPTLNKdKLEKSM-EKQQQDQQQQKQQ-QQEQQPQEQQPKQPPQQKKQE 374
                                       33344445999****99*99778***666444441333333.3222222222222.222222222211111111111 PP

                           DUF5427 101 asetpseeeseeqeaekkeee 121
                                       ++ ++s++    qe + ++++
  gi|330506881|ref|YP_004383309.1| 375 QQPESSDQ----QEDSDQAQA 391
                                       11111111....111111111 PP

>> Gti1_Pac2  Gti1/Pac2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   8.7     0.035        17      81     134 ..     338     388 ..     320     432 .. 0.47

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.035
                                       -----------------------------.................-------- CS
                         Gti1_Pac2  81 kkrakkkkkkkkkkskestkkeesksekasssssesseakessssseskaskss 134
                                       k+ +k++++++++k+++++++ ++++ k+ +++++++++ ess ++   +++++
  gi|330506881|ref|YP_004383309.1| 338 KSMEKQQQDQQQQKQQQQEQQPQEQQPKQPPQQKKQEQQPESSDQQ---EDSDQ 388
                                       2222222222222222222222222211111111111111111111...11111 PP

>> Neur_chan_memb  Neurotransmitter-gated ion-channel transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   9.3     0.033        16     111     182 ..     323     394 ..     281     434 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.033
                                       -----------.--------------------------------------SS---TTGGG--.....----- CS
                    Neur_chan_memb 111 rpsevkdnekklssgasseaeelilskskseskkaklseeqgsekastckckckegeeaspstqlskeelsp 182
                                        ++ +++  +k +  +s+e+++ +++++k++ ++++++e+q+++ ++++k ++++++  +++++ +++ +sp
  gi|330506881|ref|YP_004383309.1| 323 SRPFEPPTLNKDKLEKSMEKQQQDQQQQKQQQQEQQPQEQQPKQPPQQKKQEQQPESSDQQEDSDQAQAASP 394
                                       222222222222344444444444444444444444444444444444444444333333333333333333 PP

>> Hid1  High-temperature-induced dauer-formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6  15.2     0.029        14     595     686 ..     304     393 ..     267     401 .. 0.38

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.029
                              Hid1 595 ideeeeenssessrieesrsesrspslsevpelksslaitddeskaereksatessssqavsqlremsekarakesa 671
                                       +++e+ ++ +e   ++++rs   +p + ++ +l++s++++++++++  +k++++++++q ++ ++ +++k+++++++
  gi|330506881|ref|YP_004383309.1| 304 ANQEDVKKAMELALAHRMRSRPFEPPTLNKDKLEKSMEKQQQDQQQ--QKQQQQEQQPQEQQPKQPPQQKKQEQQPE 378
                                       2222222222222223323333333333333333333322222222..22222222222222233333333333333 PP

                              Hid1 672 esteesrqesatskk 686
                                       +s++++ +++a+ ++
  gi|330506881|ref|YP_004383309.1| 379 SSDQQEDSDQAQAAS 393
                                       333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2690  (0.150036); expected 358.6 (0.02)
Passed bias filter:                     1047  (0.058397); expected 358.6 (0.02)
Passed Vit filter:                       311  (0.0173462); 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):              37  [number of targets reported over threshold]
# CPU time: 1.18u 0.38s 00:00:01.56 Elapsed: 00:00:00.51
# Mc/sec: 4084.07
//
Query:       gi|330506882|ref|YP_004383310.1|  [L=286]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-31  109.5   0.0    2.7e-31  108.9   0.0    1.3  1  ABC_tran  ABC transporter
    2.4e-15   57.1   0.0    3.8e-08   33.5   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    3.6e-05   23.6   0.0       0.15   11.8   0.0    2.1  2  AAA_15    AAA ATPase domain
    0.00018   21.0   0.0    0.00034   20.1   0.0    1.5  1  SMC_N     RecF/RecN/SMC N terminal domain
     0.0018   18.8   0.6     0.0029   18.1   0.6    1.4  1  AAA_23    AAA domain
     0.0044   16.7   0.2      0.011   15.3   0.2    1.8  1  SRP54     SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.013   15.2   0.1      0.051   13.3   0.1    2.0  2  AAA_30    AAA domain
      0.043   14.1   0.0       0.06   13.6   0.0    1.3  1  AAA_28    AAA domain
       0.05   13.4   0.1      0.093   12.5   0.1    1.4  1  AAA_29    P-loop containing region of AAA domain
      0.062   13.2   0.0      0.099   12.6   0.0    1.4  1  Rad17     Rad17 P-loop domain
      0.063   13.8   0.0       0.12   13.0   0.0    1.5  1  AAA_18    AAA domain
      0.079   13.2   0.0       0.14   12.4   0.0    1.4  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
       0.18   10.4   0.0       0.69    8.5   0.1    1.7  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 !  108.9   0.0   1.9e-34   2.7e-31       5     136 ..      24     163 ..      20     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 1.9e-34
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                       sl++ +ge+ +++G+nGaGK+t +++l+ l+kpt+G+ l++g d+ + +l++++ e+g+++q+ +l+++lt++en  
  gi|330506882|ref|YP_004383310.1|  24 SLQVDPGELFGFLGPNGAGKTTTIRILTTLTKPTSGRALINGSDVVR-DLSKVKLEFGIVQQHLSLNKDLTIAENle 99 
                                       89********************************************9.9**************************** PP

                                       ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                  +++++i+++l+ ++l+e +d  +      +SgG+k+r ++aral+ +pkll+lDEpt
  gi|330506882|ref|YP_004383310.1| 100 lharlhhlpkaQRTKRISELLDYVELSEHADYLI----DDVSGGMKRRAMIARALIHRPKLLVLDEPT 163
                                       ********98888888999999999999777777....*****************************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 !   21.3   0.0   1.4e-07   0.00019       2      96 ..      33     113 ..      32     121 .. 0.89
   2 !   33.5   0.0   2.8e-11   3.8e-08     234     297 ..     133     193 ..     130     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.4e-07
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                        ++ GpNg+GK++ +++l  l              ++  + r  ++ +d   + +++++e+   ++q+   +  l++
  gi|330506882|ref|YP_004383310.1|  33 FGFLGPNGAGKTTTIRILTTL--------------TKPTSGRALINGSDVVRDLSKVKLEFG-IVQQHLSLNKDLTI 94 
                                       5789**************766..............7889999********************.************** PP

                            AAA_21  79 ersqv.eeklssvetlles 96 
                                        ++    ++l ++++ +++
  gi|330506882|ref|YP_004383310.1|  95 AENLElHARLHHLPKAQRT 113
                                       9999999998888888776 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 2.8e-11
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       ++++S G+kr  a+++  l  ++  +ll++DEp  gL+ +  r++++l+++ ++ g+ v+ltTH
  gi|330506882|ref|YP_004383310.1| 133 IDDVSGGMKRR-AMIARALIHRP--KLLVLDEPTVGLDAQTRRKVWDLIRKMNSDGTTVFLTTH 193
                                       689********.99999999888..7***********************777777********* PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00011      0.15      23      83 ..      31      98 ..      18     131 .. 0.74
   2 !   10.2   0.0   0.00032      0.44     288     364 ..     127     193 ..     105     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                            AAA_15 23 eeltvliGkNnsGKSsilealdlFlnnkekkn...........kkvikiekedleifeniseskdikIdvef 83
                                      e l  + G+N++GK++ +++l  + + +   +            +  k++ e+  ++++ s +kd+ I+ + 
  gi|330506882|ref|YP_004383310.1| 31 E-LFGFLGPNGAGKTTTIRILTTLTKPT---SgralingsdvvRDLSKVKLEFGIVQQHLSLNKDLTIAENL 98
                                      4.77799**************9999977...34457888888877777888888888888888888876555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00032
                            AAA_15 288 ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +  +  +++++ G++r   ++  +++           ++l+++EP + L  q  + +++l++++ +d+   v++tTH
  gi|330506882|ref|YP_004383310.1| 127 EHADYLIDDVSGGMKRRAMIARALIHRP---------KLLVLDEPTVGLDAQTRRKVWDLIRKMNSDGT-TVFLTTH 193
                                       6666677888888888887775555444.........66*************************99996.9****** PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.5e-07   0.00034      28     213 ..      34     209 ..       1     215 [. 0.66

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.5e-07
                                       EEEESTTSSHHHHHHHHHHHCTT..TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGer.sakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrv 103
                                         +GpNG+GK+  +  +  +L +  s ++l   + sd++    +k +++++ v+ +++ +++ +  e+ e+  + + 
  gi|330506882|ref|YP_004383310.1|  34 GFLGPNGAGKTTTIRIL-TTLTKPtSGRAL--INGSDVVRD-LSKVKLEFGIVQQHLSLNKDLTIAENLELHARLHH 106
                                       468********999866.566633022222..345666666.66666777777776665555544444444444444 PP

                                       ETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 104 krkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkva 180
                                         k +      ++  +  ++ el e+a+  ++  SgG k  +++a       +++  l +lDe    LD++ ++kv 
  gi|330506882|ref|YP_004383310.1| 107 LPKAQR----TKRISELLDYVELSEHADYLIDDVSGGMKRRAMIARA----LIHRPKLLVLDEPTVGLDAQTRRKVW 175
                                       444443....3334456788888888889999*****9876655433....23555699****************** PP

                                       HHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 181 ellkekskn.aQfivislreemlekadklvgvtk 213
                                       +l+++ +++ + ++ +++  e  e   + vg+ +
  gi|330506882|ref|YP_004383310.1| 176 DLIRKMNSDgTTVFLTTHYIEEAEALCERVGILH 209
                                       ****876655889999988777777777777666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.6   2.1e-06    0.0029      20      43 ..      31      54 ..      11     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.1e-06
                            AAA_23 20 gltlItGpNGaGKTTildAiklaL 43
                                       l+ + GpNGaGKTT ++ ++  +
  gi|330506882|ref|YP_004383310.1| 31 ELFGFLGPNGAGKTTTIRILTTLT 54
                                      599**************9988654 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   8.1e-06     0.011       6      41 ..      35      70 ..      31     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.1e-06
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSS CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDtfR 41
                                      ++G++GaGKTtt+  L  l k    ++l+   D+ R
  gi|330506882|ref|YP_004383310.1| 35 FLGPNGAGKTTTIRILTTLTKPTSGRALINGSDVVR 70
                                      79*********************999****999999 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   3.7e-05     0.051      20     106 ..      32     172 ..      22     194 .. 0.58
   2 ?   -2.7   0.0         3   4.1e+03      20      31 ..     252     263 ..     248     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-05
                            AAA_30  20 vavltGpAGtGKttalkalreaweaa.g.......................grviglAptgkaAkvLaeelgieast 72 
                                       +    Gp G+GKtt+++ l+ + +   g                       ++ + l    + A++L+         
  gi|330506882|ref|YP_004383310.1|  32 LFGFLGPNGAGKTTTIRILTTLTKPTsGralingsdvvrdlskvklefgivQQHLSLNKDLTIAENLEL-------- 100
                                       55678***************9999886744444444444444444444333333333333333333332........ PP

                            AAA_30  73 iakllkrlk............................................grarlepgtllivDEagmv.dtkq 104
                                              ++                                            +ra +++ +ll+ DE  +  d+++
  gi|330506882|ref|YP_004383310.1| 101 -------HArlhhlpkaqrtkriselldyvelsehadyliddvsggmkrramiARALIHRPKLLVLDEPTVGlDAQT 170
                                       .......2233333333334444444445568888888888888888888888667777778888888665434433 PP

                            AAA_30 105 la 106
                                        +
  gi|330506882|ref|YP_004383310.1| 171 RR 172
                                       33 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3
                            AAA_30  20 vavltGpAGtGK 31 
                                        ++++G +Gt K
  gi|330506882|ref|YP_004383310.1| 252 AQFVQGLPGTNK 263
                                       5899******88 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.4e-05      0.06       4      67 ..      35     107 ..      32     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.4e-05
                            AAA_28   4 itGgestGKTtlleaLaar.....gypvv..pEaareileeklakgedalpwv..edllafaervleeqleee 67 
                                       ++G+ ++GKTt+++ L+       g   +   +++r++ + kl++g  + + +  +dl   + + l+++l+ +
  gi|330506882|ref|YP_004383310.1|  35 FLGPNGAGKTTTIRILTTLtkptsGRALIngSDVVRDLSKVKLEFGIVQQHLSlnKDLTIAENLELHARLHHL 107
                                       78***************54456679999999999999999999887644443332455544555566666655 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 ?   12.5   0.1   6.7e-05     0.093      15      50 ..      23      58 ..      18      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.7e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +++++d+ + + + Gp+G+GK+T +  +++l  p++
  gi|330506882|ref|YP_004383310.1| 23 QSLQVDPGELFGFLGPNGAGKTTTIRILTTLTKPTS 58
                                      7788898889999**********9977777766665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.2e-05     0.099      33      70 ..      18      55 ..      11     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.2e-05
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                      + ++ ++L+  + ++    GP G gk+t++++L+    
  gi|330506882|ref|YP_004383310.1| 18 RVVDIQSLQVDPGELFGFLGPNGAGKTTTIRILTTLTK 55
                                      567888999999999999***************87554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.4e-05      0.12       4      92 ..      36     146 ..      34     197 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.4e-05
                            AAA_18   4 tGtpGvGKttlakeLskrlgf.......................gvnlrdvakenglllevdpealdeskrldedkl 57 
                                        G+ G+GKtt  + L  +++                        g++ +++  +++l + ++ e + + + l + ++
  gi|330506882|ref|YP_004383310.1|  36 LGPNGAGKTTTIRILTTLTKPtsgralingsdvvrdlskvklefGIVQQHLSLNKDLTIAENLELHARLHHLPKAQR 112
                                       69*************55542235556566545555555555555666666666666666666666666666666666 PP

                            AAA_18  58 dklldaleenssaleegknlvidghlaeleseaak 92 
                                        k +++l    + l e+ +++id++ + +   a++
  gi|330506882|ref|YP_004383310.1| 113 TKRISELLDYVE-LSEHADYLIDDVSGGMKRRAMI 146
                                       666666666555.7777888999998888777666 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 ?   12.4   0.0    0.0001      0.14      62      89 ..     152     179 ..     137     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                       ++++l++LDE   +lD+++++++ +l++
  gi|330506882|ref|YP_004383310.1| 152 HRPKLLVLDEPTVGLDAQTRRKVWDLIR 179
                                       6899********************9987 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0005      0.69      23      46 ..      37      60 ..      31      90 .. 0.84
   2 ?   -1.0   0.0      0.36     5e+02     526     570 ..     153     194 ..     147     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0005
                            AAA_13 23 GwNGaGKTtLSrllrslelgetep 46
                                      G NGaGKTt  r+l  l++     
  gi|330506882|ref|YP_004383310.1| 37 GPNGAGKTTTIRILTTLTKPTSGR 60
                                      99*************998755544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.36
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHn 570
                                         k  v+D P   LD++    v  li++     ++   +f+ TH 
  gi|330506882|ref|YP_004383310.1| 153 RPKLLVLDEPTVGLDAQTRRKVWDLIRKMN---SDGTTVFLTTHY 194
                                       567899*********************996...99999******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1942.61
//
Query:       gi|330506883|ref|YP_004383311.1|  [L=244]
Description: ABC transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-23   83.3  18.3    1.5e-23   83.3  18.3    1.8  2  ABC2_membrane    ABC-2 type transporter
    7.1e-08   31.9  26.2    7.1e-08   31.9  26.2    1.8  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
        7.1    5.8  26.3         20    4.4   0.2    2.5  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 !   83.3  18.3   2.5e-27   1.5e-23       6     201 ..       6     203 ..       3     212 .. 0.92
   2 ?   -1.7   2.0      0.27   1.6e+03     132     149 ..     219     236 ..     204     239 .. 0.56

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 2.5e-27
                     ABC2_membrane   6 llkreflqrwrdpslgllwrliqplllalvfgtvfgn.lg.nsedglnr..pgllffsvlflafsaltsvapvfere 78 
                                       +l+ ++ + +r +s +l++ l++pll+++ fg   g+ ++ n +++l++  pg+++ ++++++f+++++  +v    
  gi|330506883|ref|YP_004383311.1|   6 ILWADLVTLKRHWSRYLITTLMSPLLYLVAFGWGLGRsINlNGTSYLEFviPGIIALTAMTTSFNGASTRLNVDRLY 82 
                                       78999*******************************954466666665578*******************8888888 PP

                     ABC2_membrane  79 rgvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv.gldlsrfflflllllltalaasslgllisal 154
                                        +++++ l +p+  l++++++k+++ ++++l+ +++f+++++++   +++  +  fl+ lllt l++ +lg+l + l
  gi|330506883|ref|YP_004383311.1|  83 YKSFDECLMAPI-GLPSMLMGKAMIGVVRGLMSSFVFIAVAFLIApTIHI--GSPFLVGLLLTCLTFAFLGVLAALL 156
                                       999*********.**************************99998547888..79999******************** PP

                     ABC2_membrane 155 apsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltya 201
                                       a+s+ed++++asl+l+p+++l+G f++++++p+ l++  y++Plt+ 
  gi|330506883|ref|YP_004383311.1| 157 ARSHEDMATFASLILMPMTFLGGTFFSLSQVPSGLKYALYALPLTHS 203
                                       *********************************************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.27
                     ABC2_membrane 132 lflllllltalaasslgl 149
                                         ll+ll+++ a+++ g+
  gi|330506883|ref|YP_004383311.1| 219 TSLLILLVFFAAFLAGGM 236
                                       344444444444444444 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   1.3     0.091   5.4e+02       3     230 ..      21      41 ..      18      87 .. 0.54
   2 !   31.9  26.2   1.2e-11   7.1e-08     196     341 ..      90     233 ..      45     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.091
                   ABC2_membrane_3   3 fliitlllPiilvlllglifsnsveddentpiavvdednsslsqqlvealeaspsvelvyevdseeeakkalkngdi 79 
                                       +li+tl++P+++++ +g+                                                           
  gi|330506883|ref|YP_004383311.1|  21 YLITTLMSPLLYLVAFGWG---------------------------------------------------------- 39 
                                       3445555555555444443.......................................................... PP

                   ABC2_membrane_3  80 dgilvipkgfskdllkgesatvtvlinssnlnsskailnalnsllqqlnasalvlqseatstsaninvestqleeel 156
                                                                                                                    
  gi|330506883|ref|YP_004383311.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                   ABC2_membrane_3 157 snvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafg 230
                                                                                                               +g
  gi|330506883|ref|YP_004383311.1|  40 ------------------------------------------------------------------------LG 41 
                                       ........................................................................33 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1.2e-11
                   ABC2_membrane_3 196 lvsgvsplqywlskilgdflvyllqlllilllafglgipfg.nlgl.llllfllfglayialgyllsslfknsetaq 270
                                       l++++   +++++k  + ++ +l ++++++++af   i  + ++g+ +l+ +ll +l++++lg l   l +++e++ 
  gi|330506883|ref|YP_004383311.1|  90 LMAPIGLPSMLMGKAMIGVVRGLMSSFVFIAVAFL--IAPTiHIGSpFLVGLLLTCLTFAFLGVLAALLARSHEDMA 164
                                       67888889999********************9998..888889997577**************************** PP

                   ABC2_membrane_3 271 ilifivilllsgffgglfp.ledlpsalkwifsiiPffapglgllrlitgdplweillsliilalfavvyll 341
                                       ++++++++ ++ f+gg+f+ l+++ps+lk++++ +P+++ +l+l   +  +pl   ++sl+il++f++++l+
  gi|330506883|ref|YP_004383311.1| 165 TFASLILM-PMTFLGGTFFsLSQVPSGLKYALYALPLTHSSLFLRAAALDQPL--PWTSLLILLVFFAAFLA 233
                                       ********.77777777655************************999997744..689***********997 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2    0.0033        20     140     181 ..      30      69 ..      12      77 .. 0.78
   2 ?    4.2  20.8    0.0036        22     154     285 ..     125     241 ..      85     244 .] 0.67

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0033
                   ABC2_membrane_2 140 atvllalaiilalgivlaledllllvvasvlllllvvflalg 181
                                         +l+a+++ l+ +i+l++ ++l +v+  ++ l+++  ++ +
  gi|330506883|ref|YP_004383311.1|  30 LLYLVAFGWGLGRSINLNGTSYLEFVIPGIIALTAM--TTSF 69 
                                       45788**********************999999966..3333 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0036
                   ABC2_membrane_2 154 ivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqein 230
                                       i++++     ++v  +l+ l  +f+ lg+l + +ar s e +a   +l+++ + + ++  + +++ ++g ++     
  gi|330506883|ref|YP_004383311.1| 125 IAPTIHIGSPFLVGLLLTCL--TFAFLGVLAALLAR-SHEDMATFASLILMPMTFLGGTFFSLSQVPSGLKY----- 193
                                       22222222222222232233..66668888888888.**********************************9..... PP

                   ABC2_membrane_2 231 dflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkr 285
                                          ++  p  +  + l++    ++     + +t+llill+  a++l+ g+v+++r
  gi|330506883|ref|YP_004383311.1| 194 --ALYALPLTHSSLFLRAAALDQP-----LPWTSLLILLVFFAAFLAGGMVVLRR 241
                                       ..5555555555555555555554.....88*******************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1624.24
//
Query:       gi|330506884|ref|YP_004383312.1|  [L=46]
Description: hypothetical protein MCON_0675 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-09   37.5   0.5    1.4e-09   37.4   0.5    1.0  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.5   7.8e-14   1.4e-09     265     309 ..       1      45 [.       1      46 [] 0.96

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 7.8e-14
                             FecCD 265 lplsallGallllladllarlllsptelpvgivtaliGapffiyl 309
                                       +p+ +l+Gallll  d +ar++++p++ pv  +ta++Gap+f+yl
  gi|330506884|ref|YP_004383312.1|   1 MPAPGLFGALLLLGEDRVARTIMAPANFPVDTMTAFMGAPLFLYL 45 
                                       68889***************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       150  (0.00836633); expected 358.6 (0.02)
Passed bias filter:                      117  (0.00652574); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 352.06
//
Query:       gi|330506885|ref|YP_004383313.1|  [L=342]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-28  100.1   0.0    1.8e-28   99.7   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.0     1e-32   1.8e-28       1     235 [.      43     283 ..      43     285 .. 0.89

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 1e-32
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG....GGGH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskgl.gltdede 76 
                                       i++lsp+ +e+ +alG++d++ +v   + +p +  ++        +++++d+E++++l PDlvi+++g+  + +++ 
  gi|330506885|ref|YP_004383313.1|  43 IICLSPGAAEVIYALGESDRIIAVTDDCDMPPALLEK---ESIGKSSRNADLERIIELNPDLVIAKTGGlFPEEDEQ 116
                                       89*****************998876666555555433...344667899********************77777777 PP

                                       HHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE..E CS
                      Peripla_BP_2  77 ellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggadeggy 151
                                       +l + gip++ ++     + l  +i+ lg +lg+e+ a++++++i + ++++ +++ +    ++p ++f++    ++
  gi|330506885|ref|YP_004383313.1| 117 KLTDYGIPVLRYRLLHI-NALIPMIEDLGRILGEEEDARDMANDISGYYDSVLDRTGTMpdEDRPSVYFMSMGHFDW 192
                                       77889**********97.**************************************999988888888888888889 PP

                                       EEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH.........HHHT-S--HHHHT-SHH CS
                      Peripla_BP_2 152 vvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr.........aeadnktgleflkenpl 219
                                       + + ++++   +++ +g++niaa+  +     +++E++ ++dp+vi++s++           ++  ++  ++++ p+
  gi|330506885|ref|YP_004383313.1| 193 TGNRDSTGHVRIAE-AGGKNIAADL-QTKVPHVDMEWVIEEDPEVIVYSMTseqydgttpTIEEMEAKRMEIISLPG 267
                                       99999999999988.**********.*********************************966666666679****** PP

                                       HHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 220 laelpAvkngrVyald 235
                                       ++++ Avk+grVy +d
  gi|330506885|ref|YP_004383313.1| 268 FESIDAVKTGRVYITD 283
                                       *************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.53
# Mc/sec: 1958.39
//
Query:       gi|330506886|ref|YP_004383314.1|  [L=61]
Description: hypothetical protein MCON_0677 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 404.94
//
Query:       gi|330506887|ref|YP_004383315.1|  [L=77]
Description: copG family protein anti-toxin protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-08   32.7   0.3    8.7e-08   31.8   0.3    1.4  1  RHH_1     Ribbon-helix-helix protein, copG family
    5.5e-06   26.3   0.2    8.5e-06   25.6   0.2    1.3  1  RHH_3     Ribbon-helix-helix domain
  ------ inclusion threshold ------
      0.099   12.0   0.1       0.11   11.8   0.1    1.1  1  DUF5305   Family of unknown function (DUF5305)


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 !   31.8   0.3   1.4e-11   8.7e-08       3      39 .]       9      45 ..       9      45 .. 0.98

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.4e-11
                                      EEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHH CS
                             RHH_1  3 sirldeellerLdelarrrgrSrSelIReAlreyler 39
                                      s+rl++++++ L+ la +++r + ++IR A+++yle+
  gi|330506887|ref|YP_004383315.1|  9 SVRLPDDIARGLEDLASALDRPKTYIIRKAIEAYLEE 45
                                      8**********************************95 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.2   1.4e-09   8.5e-06       3      43 ..       6      46 ..       6      47 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.4e-09
                             RHH_3  3 trttvsidpelaekLkaLSekTrIprSklldeAiellLekY 43
                                      t+ +v++++++a  L++L  ++  p++ ++++Aie +Le+Y
  gi|330506887|ref|YP_004383315.1|  6 TSASVRLPDDIARGLEDLASALDRPKTYIIRKAIEAYLEEY 46
                                      5789************************************* PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.9e-05      0.11     145     190 ..      33      77 .]      22      77 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
                           DUF5305 145 ekyelelekilkeYdewIvkgslppdlgdekvievdsledLvdvai 190
                                          ++++e  l+eY+++ ++++ + d +d+ +++  ++++L+ +++
  gi|330506887|ref|YP_004383315.1|  33 YIIRKAIEAYLEEYADYFIALERMNDKDDR-IVSAGEMRELLGLQD 77 
                                       556789999******************999.**********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 589.17
//
Query:       gi|330506888|ref|YP_004383316.1|  [L=84]
Description: RelE/StbE family addiction module toxin [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-09   37.3   0.0    3.8e-09   37.0   0.0    1.1  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.18   11.8   0.0    1.3  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   4.2e-13   3.8e-09       1      90 []       5      82 ..       5      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 4.2e-13
                                      EEEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTC...CTTEEEEEECTEEEEEEEETSTT CS
                        ParE_toxin  1 vrltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrprrelg...lkglrririgdyriiYriddeel 76
                                      ++++ ++ +dl++++++i      akr+l+  e    +la +pa+g p    +    kgl+++ i+dyr+iY   +++ 
  gi|330506888|ref|YP_004383316.1|  5 IEYKSSVSRDLRHLDKNI------AKRILKDTE---GTLASDPAAGIP----LtgqFKGLLKLCIDDYRVIYSK-TGDG 69
                                      6789999***********......999999886...6889******99....5577889**************7.6889 PP

                                      EEEEEEEEEHHHHC CS
                        ParE_toxin 77 vvvilrvlhrsedy 90
                                      v+ ilr++ r + y
  gi|330506888|ref|YP_004383316.1| 70 VL-ILRIGPRNKVY 82
                                      **.*****998765 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     2e-05      0.18       4      83 ..       8      82 ..       5      84 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                   ParE-like_toxin  4 trrfkkalkklkek.lkadldkavkeiiedPelGeeKkGDLsgvfvykfklnkqltllaYeldekkrvlvlllvGtheN 81
                                      ++++++ l+ l ++  k+ l+++  ++++dP +G + +G  +g+     kl    +++ Y+ + + +   +l +G+++ 
  gi|330506888|ref|YP_004383316.1|  8 KSSVSRDLRHLDKNiAKRILKDTEGTLASDPAAGIPLTGQFKGLL----KLCIDDYRVIYSKTGDGV--LILRIGPRNK 80
                                      56889999******78888888889***************99995....667788999999888874..5999999998 PP

                   ParE-like_toxin 82 fY 83
                                       Y
  gi|330506888|ref|YP_004383316.1| 81 VY 82
                                      88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 575.91
//
Query:       gi|330506889|ref|YP_004383317.1|  [L=78]
Description: FeoA domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   65.3   1.2    4.9e-18   65.2   1.2    1.0  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   1.2   2.7e-22   4.9e-18       1      73 [.       3      75 ..       3      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 2.7e-22
                                      EEGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA  1 vpLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                      +p + l  G  + ++ +  +++ ++r+Lr mG+++G+r++vva  pf+gplv+ +++ ++ Lgr++Aq+++V+
  gi|330506889|ref|YP_004383317.1|  3 MPITSLRAGAVAQVTALLGQGGSFQRKLRTMGIREGKRLRVVAIHPFAGPLVLDIDGRQITLGRSIAQRVMVR 75
                                      79999*******************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 581.88
//
Query:       gi|330506890|ref|YP_004383318.1|  [L=568]
Description: GTP-binding domain/transporter gate domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-49  167.3   0.0    2.6e-49  166.8   0.0    1.3  1  FeoB_N     Ferrous iron transport protein B
      3e-26   91.9  20.6    6.5e-14   52.2   7.2    3.5  4  Gate       Nucleoside recognition
    1.2e-17   64.1   0.0    2.1e-17   63.3   0.0    1.4  1  MMR_HSR1   50S ribosome-binding GTPase
    1.3e-12   47.2   1.7    1.3e-12   47.2   1.7    2.6  2  FeoB_C     Ferrous iron transport protein B C terminus
     0.0022   17.5   0.0     0.0032   16.9   0.0    1.2  1  SRPRB      Signal recognition particle receptor beta subunit
  ------ inclusion threshold ------
       0.19   11.2   0.0       0.53    9.8   0.0    1.7  1  GTP_EFTU   Elongation factor Tu GTP binding domain


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   0.0   8.6e-53   2.6e-49       6     154 ..       1     147 [.       1     149 [. 0.98

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 8.6e-53
                                       EESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEE CS
                            FeoB_N   6 vGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdvv 82 
                                       +Gnpn+Gk+++f +ltga+   +N+pG+tv+ ++gk +++g+ ve++D PG+Ysl+++s  e+va ++l    +d++
  gi|330506890|ref|YP_004383318.1|   1 MGNPNIGKSVVFSRLTGAEVITSNYPGTTVDFSRGKARIQGEPVELIDAPGTYSLQPTSPVEEVAVEVLR--WADLI 75 
                                       6*******************************************************************96..799** PP

                                       EEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHH CS
                            FeoB_N  83 vnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellk 154
                                       vnvvd+tnlernL+Ltl+lle ++p++++lnm+dea+++g++idl+ L+++L+vpvv+t+a ++egi el++
  gi|330506890|ref|YP_004383318.1|  76 VNVVDSTNLERNLFLTLELLESKKPMIVVLNMWDEAKRSGVQIDLDGLEARLQVPVVATTALTGEGIAELVR 147
                                       *********************************************************************987 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.48   1.4e+03      25      55 ..     222     251 ..     184     278 .. 0.69
   2 !   47.9   0.4   4.5e-16   1.3e-12       3     111 ..     283     377 ..     281     378 .. 0.97
   3 ?   -1.6   0.1         1   3.1e+03      84     101 ..     380     397 ..     376     406 .. 0.74
   4 !   52.2   7.2   2.2e-17   6.5e-14       2     111 ..     440     537 ..     439     538 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.48
                              Gate  25 grigkllepvfaplgqeldwkatvslltgfa 55 
                                       g i+ l+ep+f     +l   ++ +l  g++
  gi|330506890|ref|YP_004383318.1| 222 GLISHLFEPLFELYR-PLAMSISSGLGPGML 251
                                       446666666666665.666666666666666 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 4.5e-16
                              Gate   3 kagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgf 79 
                                        ++p+i+ + +++++l++s++l r++ l + +f++lg  +++ a+++l++g++   ++v+ +  ++         + 
  gi|330506890|ref|YP_004383318.1| 283 MVLPYIVGFYLVLSILEDSGYLPRLATLSDNLFHRLG--MHGHAIIPLFLGLG---CNVPGALAIR---------TL 345
                                       689**********************************..**************...*********9.........** PP

                              Gate  80 dtpksalafllfvllytpcvatlavivrelgs 111
                                       +t+k++++   +++l++pc a  a+i++ lgs
  gi|330506890|ref|YP_004383318.1| 346 ETRKQRFISATLLGLAVPCTAKSAMIFGVLGS 377
                                       **************************999986 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1
                              Gate  84 salafllfvllytpcvat 101
                                       ++++fl+f +l+ + +a+
  gi|330506890|ref|YP_004383318.1| 380 QRYVFLVFATLALVYIAA 397
                                       688999999998887776 PP

  == domain 4  score: 52.2 bits;  conditional E-value: 2.2e-17
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfap.lgqeldwkatvslltgfaakevvvgtlgtlytsalgellq 77 
                                         a+p+++l+++l+++l+  +++++ig +++p++   l    +++a+++ll+gf+ k ++vg+l  l          
  gi|330506890|ref|YP_004383318.1| 440 SEAIPFLFLGVLLVNVLYTVGFIEWIGAIFAPFMEGwLN--IPGEAVAALLVGFFRKDLAVGMLLPL---------- 504
                                       679*******************************99566..***********************666.......... PP

                              Gate  78 gfdtpksalafllfvllytpcvatlavivrelgs 111
                                          + ++ +++ l+++ly+pcvat+av++relg 
  gi|330506890|ref|YP_004383318.1| 505 -GLSAQQMVVATLVLSLYFPCVATFAVLIRELGM 537
                                       .79999999**********************995 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.0   6.9e-21   2.1e-17       5     113 ..       1     106 [.       1     107 [. 0.82

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 6.9e-21
                                       EESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEE CS
                          MMR_HSR1   5 vGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adlil 80 
                                       +G+pN GKS ++++ltg+++i+s++pgtT d  +g+ +++g+++el+D pG ++  +    +++   ++ + adli+
  gi|330506890|ref|YP_004383318.1|   1 MGNPNIGKSVVFSRLTGAEVITSNYPGTTVDFSRGKARIQGEPVELIDAPGTYS-LQPTSPVEEVAVEVLRwADLIV 76 
                                       69*************************************************886.333445667777777779**** PP

                                       EEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                          MMR_HSR1  81 lvvdaseeklkpldeeleelleeakkplilvln 113
                                        vvd++ + l+++     ell e+kkp+i+vln
  gi|330506890|ref|YP_004383318.1|  77 NVVDST-N-LERNLFLTLELL-ESKKPMIVVLN 106
                                       ****54.4.655533334443.589******99 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 !   47.2   1.7   4.4e-16   1.3e-12       1      53 []     383     434 ..     383     434 .. 0.97
   2 ?   -1.8   0.4      0.84   2.5e+03       7      26 ..     546     564 ..     544     565 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 4.4e-16
                            FeoB_C   1 lfslYllgilvallvalllkkttlkgepspfvmELPpYrlPslknvliktweR 53 
                                       +f+++++  lv ++++l+l+++  kge++  ++E+PpYr+P l+ +l+ktw+R
  gi|330506890|ref|YP_004383318.1| 383 VFLVFATLALVYIAAGLILNRM-VKGESPEIFLEIPPYRRPELGMILKKTWMR 434
                                       6899999**************9.****************************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.84
                            FeoB_C   7 lgilvallvalllkkttlkg 26 
                                       ++++ all++  +++t l g
  gi|330506890|ref|YP_004383318.1| 546 IMLATALLAGGAMRWT-LSG 564
                                       7789999999999996.765 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-06    0.0032      10      99 ..       2      95 ..       1     106 [. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                                      -STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT-GCCSHHH.HHHHHHHGG...EEEEEEEE CS
                             SRPRB 10 GlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGheklrqkl.leklkakss...lkglvfvv 83
                                      G  + GK  +f rLt  +v ++        ++      +g+ ++liD PG  +l+    +e+ +a +    +  +v vv
  gi|330506890|ref|YP_004383318.1|  2 GNPNIGKSVVFSRLTGAEVITSNYPGtTVDFSRGKARIQGEPVELIDAPGTYSLQPTSpVEE-VAVEVlrwADLIVNVV 79
                                      78899**********9876554443324455554466799**************96541444.333331236789**** PP

                                      ETTS-HHHHHHHHHHH CS
                             SRPRB 84 DStidpkevkevAEll 99
                                      DSt  ++++  + Ell
  gi|330506890|ref|YP_004383318.1| 80 DSTNLERNLFLTLELL 95
                                      *********9999998 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00018      0.53      55     190 ..      29     151 ..      18     154 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00018
                                       CSSCEEEEEETTCSSEEEEEEEESSSGGG..HHHHHHH....HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEE CS
                          GTP_EFTU  55 TiksaaisleketkkylinliDtPGHvdF..skevirg....lrvlDgavlvvdaveGvepqteevlrlalkegvpi 125
                                       T++ +  +     +   + liD+PG  +   ++ v++     lr +D+ v vvd++   e     +   +l+ + p+
  gi|330506890|ref|YP_004383318.1|  29 TVDFSRGKAR--IQGEPVELIDAPGTYSLqpTSPVEEVavevLRWADLIVNVVDST-NLER-NLFLTLELLESKKPM 101
                                       4444444444..77888999999999875223333332323578888888888877.3333.33444455667778* PP

                                       EEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHH CS
                          GTP_EFTU 126 ivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealve 190
                                       iv++N  D++ ++ ++   + ++ +l                +vpvv + al+geg+ +l++ l++
  gi|330506890|ref|YP_004383318.1| 102 IVVLNMWDEAkRSGVQIDLDGLEARL----------------QVPVVATTALTGEGIAELVRRLDQ 151
                                       ********996666777777777777................589999999999999999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 4114.15
//
Query:       gi|330506891|ref|YP_004383319.1|  [L=695]
Description: PBS lyase HEAT domain-containing protein repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-14   53.9   3.7    2.5e-11   43.8   0.7    2.9  2  HEAT_2    HEAT repeats
    7.1e-09   35.5   2.3     0.0009   19.7   0.2    4.6  3  HEAT_PBS  PBS lyase HEAT-like repeat
    0.00021   21.2   2.2       0.72   10.3   0.0    4.3  5  HEAT      HEAT repeat


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.7   4.2e-15   2.5e-11       8      87 ..      66     144 ..      60     145 .. 0.90
   2 !   11.4   0.3   5.4e-05      0.32      17      87 ..     140     206 ..     135     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 4.2e-15
                            HEAT_2   8 lendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvReaAa 84 
                                       l ++ d+ +r++a+raLg++++p + + L+++l+d+ p vR++a+ aL+ +g+++a++ L+e+l ++++ + +  Aa
  gi|330506891|ref|YP_004383319.1|  66 LDRSLDHRIRYRAVRALGQLKDPLSEEVLIRALDDDYPIVRHMAVSALAGMGTDSAASKLEEMLGSKSNCL-KSMAA 141
                                       55677999*******************************************************98876655.88888 PP

                            HEAT_2  85 eaL 87 
                                       +aL
  gi|330506891|ref|YP_004383319.1| 142 RAL 144
                                       887 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.4e-05
                            HEAT_2  17 rraairaLgrignpea..lpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvReaAaeaL 87 
                                       +++a+++++   + ++  l++L++ll++ d++v +a+     +igd+ a+p+L+ +ld   + +vR+ Aa  L
  gi|330506891|ref|YP_004383319.1| 140 AARALIEIAGVPDSRLenLELLFKLLSSGDERVEKAIL----QIGDE-AIPFLLSRLDLG-STIVRQHAALVL 206
                                       456777777776664466****************8876....79997.*********876.577788888776 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 !   19.7   0.2   1.5e-07    0.0009       1      27 []      74     100 ..      74     100 .. 0.97
   2 !    9.7   0.0   0.00025       1.5       1      25 [.     105     129 ..     105     131 .. 0.93
   3 ?    2.2   0.1     0.068   4.1e+02       8      25 ..     175     191 ..     137     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-07
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       +R++A++aLgql+d+ + ++L++aL+d
  gi|330506891|ref|YP_004383319.1|  74 IRYRAVRALGQLKDPLSEEVLIRALDD 100
                                       6************************98 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                       vR+ A+ aL+ +g++ a+  L e L
  gi|330506891|ref|YP_004383319.1| 105 VRHMAVSALAGMGTDSAASKLEEML 129
                                       9*****************9999877 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.068
                                       HHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   8 aLgqlgdeeaipaLleaL 25 
                                       a+ q+gd eaip Ll  L
  gi|330506891|ref|YP_004383319.1| 175 AILQIGD-EAIPFLLSRL 191
                                       4446777.9999998766 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.011        67      13      27 ..      71      85 ..      60      87 .. 0.87
   2 !   10.3   0.0   0.00012      0.72       4      27 ..      93     116 ..      92     119 .. 0.90
   3 ?    3.2   0.0     0.022   1.3e+02       5      28 ..     125     148 ..     123     150 .. 0.91
   4 ?   -2.3   0.0       1.4   8.2e+03       2      16 ..     158     172 ..     158     172 .. 0.85
   5 ?   -2.8   0.0         2   1.2e+04       3      24 ..     185     206 ..     184     207 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.011
                                      SHHHHHHHHHHHHHH CS
                              HEAT 13 speVReaAakaLgal 27
                                      + ++R+ A++aLg+l
  gi|330506891|ref|YP_004383319.1| 71 DHRIRYRAVRALGQL 85
                                      5689*********98 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00012
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +l+++l D+ p VR +A+ aL+ +
  gi|330506891|ref|YP_004383319.1|  93 VLIRALDDDYPIVRHMAVSALAGM 116
                                       68999****************866 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.022
                                       HHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgala 28 
                                       l ++l ++s    ++Aa+aL ++a
  gi|330506891|ref|YP_004383319.1| 125 LEEMLGSKSNCLKSMAARALIEIA 148
                                       7899*****************998 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.4
                                       HHHHHHHHT-SSHHH CS
                              HEAT   2 lPlllkllsDpspeV 16 
                                       l ll klls+ + +V
  gi|330506891|ref|YP_004383319.1| 158 LELLFKLLSSGDERV 172
                                       67999****999887 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 2
                                       HHHHHHHT-.SSHHHHHHHHHHH CS
                              HEAT   3 PlllkllsD.pspeVReaAakaL 24 
                                       P+ll+ l D  s  VR+ Aa+ L
  gi|330506891|ref|YP_004383319.1| 185 PFLLSRL-DlGSTIVRQHAALVL 206
                                       6777776.446777898888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (695 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:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 4932.07
//
Query:       gi|330506892|ref|YP_004383320.1|  [L=286]
Description: sulfite reductase subunit beta [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-19   68.2   0.1    8.1e-19   67.7   0.1    1.2  1  NIR_SIR          Nitrite and sulphite reductase 4Fe-4S domain
      4e-16   58.1  16.2    4.1e-08   32.7   3.4    2.4  2  Fer4             4Fe-4S binding domain
    3.8e-14   52.3   0.1    6.3e-14   51.6   0.1    1.4  1  NIR_SIR_ferr     Nitrite/Sulfite reductase ferredoxin-like ha
      1e-12   47.5  18.9    1.1e-06   28.5   5.6    2.8  3  Fer4_6           4Fe-4S binding domain
    2.5e-12   46.1  12.4    9.3e-06   25.4   3.3    2.8  2  Fer4_2           4Fe-4S binding domain
    5.3e-12   45.7  24.5    1.1e-07   31.8  14.6    3.0  3  Fer4_10          4Fe-4S dicluster domain
    3.3e-10   40.4  29.7    2.5e-08   34.4  14.5    2.6  2  Fer4_7           4Fe-4S dicluster domain
    2.4e-08   34.0  12.5    5.7e-08   32.8  12.5    1.8  1  Fer4_9           4Fe-4S dicluster domain
    2.7e-08   33.8  13.9    0.00021   21.3   1.2    2.9  3  Fer4_21          4Fe-4S dicluster domain
    4.1e-07   30.0  18.1    0.00026   21.3   2.5    2.9  3  Fer4_4           4Fe-4S binding domain
    7.4e-07   29.5   9.5     0.0035   17.8   0.7    2.6  2  Fer4_8           4Fe-4S dicluster domain
      5e-06   27.0  11.5    0.00068   20.1   0.2    3.3  4  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
    1.1e-05   26.2  12.0      0.024   15.6   1.8    2.5  2  Fer4_16          4Fe-4S double cluster binding domain
    2.5e-05   24.9   9.1      0.037   14.8   0.3    3.1  3  Fer4_15          4Fe-4S single cluster domain
    0.00011   22.8  21.4      0.012   16.5   6.6    2.8  2  Fer4_3           4Fe-4S binding domain
    0.00019   22.2  13.5      0.099   13.5   2.4    3.0  3  Fer4_22          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.044   14.3  19.1      0.051   14.1   1.9    2.8  2  Fer4_17          4Fe-4S dicluster domain
        0.2   11.9  13.9       0.59   10.3   3.3    2.3  2  Fer4_18          4Fe-4S dicluster domain
        3.8    7.5  10.1       0.98    9.4   0.3    2.4  2  SCIFF            Six-cysteine peptide SCIFF


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 !   67.7   0.1   8.5e-22   8.1e-19       5     151 ..      96     284 ..      92     286 .] 0.97

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 8.5e-22
                                       CCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                           NIR_SIR   5 lrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei.. 79 
                                        rnv++c g+  c++a+ +t  la++i     +++  ++ P  +K+a+ gc   c + ++n igl+g + +++ +  
  gi|330506892|ref|YP_004383320.1|  96 FRNVVSCLGTDYCYKAVAETITLAREIG----DRFTGEKTPGPLKVAIGGCAFPCTRPQFNEIGLMGRVLPQIDLek 168
                                       59**************************....999************************************9999** PP

                                       ..................................................EEEEEE--B-SSSTC-TCEEEEEEEEE CS
                                       ..................................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  80 ..................................................gfnilvGGglgrthgakktsarlgfvp 106
                                                                                         g+ +lvGG+ +  + ++  +    +vp
  gi|330506892|ref|YP_004383320.1| 169 ctgcgkcvevckvgatkiveekaiidydkcvrcgrcvavcpeaakysaekGYIMLVGGRGSWPPHEGWVLC--DMVP 243
                                       ************************************************************99998887777..79** PP

                                       GGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR 107 eeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekv 151
                                        e +++++e i++vy+    + ++   R++++++ +G+e+F++ v
  gi|330506892|ref|YP_004383320.1| 244 RERIIPLIERILQVYK----EGAKPGMRMREFINSIGFEEFKRRV 284
                                       ****************....**********************988 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   3.4   4.4e-11   4.1e-08       1      22 [.     162     183 ..     162     185 .. 0.95
   2 !   31.0   5.0   1.5e-10   1.4e-07       2      22 ..     192     212 ..     191     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 4.4e-11
                                       EEEETTTSSS-THHHHHSTTTE CS
                              Fer4   1 vvideekCigCGaCvevCPvgA 22 
                                       ++id ekC+gCG+CvevC vgA
  gi|330506892|ref|YP_004383320.1| 162 PQIDLEKCTGCGKCVEVCKVGA 183
                                       68******************99 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.5e-10
                                       EEETTTSSS-THHHHHSTTTE CS
                              Fer4   2 videekCigCGaCvevCPvgA 22 
                                       +id++kC++CG+Cv vCP  A
  gi|330506892|ref|YP_004383320.1| 192 IIDYDKCVRCGRCVAVCPEAA 212
                                       7*****************987 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 !   51.6   0.1   6.7e-17   6.3e-14       2      69 .]      21      85 ..      20      85 .. 0.95

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 6.7e-17
                      NIR_SIR_ferr  2 kqkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLaea 69
                                      + +dgk  + + l v +G +ta+q +++ ++a kyg  ++++T rQ +++ g++ee+le+ l+eL+e+
  gi|330506892|ref|YP_004383320.1| 21 QRRDGK--FEIKLQVTGGLLTAQQVQRIGEVASKYG-SRVHFTVRQEVLILGIQEENLEPALAELKEV 85
                                      678988..79**************************.****************************995 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       8.3   7.9e+03       9      17 ..     102     110 ..      98     111 .. 0.64
   2 !   28.0   1.3   1.7e-09   1.6e-06       2      23 ..     162     183 ..     161     184 .. 0.93
   3 !   28.5   5.6   1.1e-09   1.1e-06       2      23 ..     191     212 ..     190     212 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.3
                            Fer4_6   9 CigCgdCvr 17 
                                       C+g + C++
  gi|330506892|ref|YP_004383320.1| 102 CLGTDYCYK 110
                                       666555776 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 1.7e-09
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       ++id +kC+gCg+Cv vC  ga
  gi|330506892|ref|YP_004383320.1| 162 PQIDLEKCTGCGKCVEVCKVGA 183
                                       789***************9998 PP

  == domain 3  score: 28.5 bits;  conditional E-value: 1.1e-09
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       + id+dkC+ Cg+Cv+vCPe+a
  gi|330506892|ref|YP_004383320.1| 191 AIIDYDKCVRCGRCVAVCPEAA 212
                                       679****************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 !   25.1   1.8   1.2e-08   1.2e-05       3      21 ..     162     180 ..     159     181 .. 0.91
   2 !   25.4   3.3   9.9e-09   9.3e-06       2      22 .]     190     210 ..     189     210 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.2e-08
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       +++d ++C+gCg+Cv +C 
  gi|330506892|ref|YP_004383320.1| 162 PQIDLEKCTGCGKCVEVCK 180
                                       89****************5 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 9.9e-09
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       ++ +d d+C++Cg Cv +CP+
  gi|330506892|ref|YP_004383320.1| 190 KAIIDYDKCVRCGRCVAVCPE 210
                                       5789****************5 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.6   1.5e+03       5      18 ..      98     111 ..      94     115 .. 0.70
   2 !   31.8  14.6   1.2e-10   1.1e-07       3      56 .]     163     209 ..     161     209 .. 0.83
   3 !   26.8   2.2   4.5e-09   4.2e-06       1      23 [.     190     212 ..     190     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.6
                           Fer4_10   5 dddtCirCgkCvka 18 
                                       +  +C++   C ka
  gi|330506892|ref|YP_004383320.1|  98 NVVSCLGTDYCYKA 111
                                       55677777777765 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.2e-10
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +id ++C++CgkCv++C       ++ + +  ee+  ++++kC +cg Cv++CP
  gi|330506892|ref|YP_004383320.1| 163 QIDLEKCTGCGKCVEVC-------KVGATKIVEEKAIIDYDKCVRCGRCVAVCP 209
                                       79***************.......4555555556666689*************9 PP

  == domain 3  score: 26.8 bits;  conditional E-value: 4.5e-09
                           Fer4_10   1 kvvidddtCirCgkCvkaCPadl 23 
                                       k++id d+C+rCg+Cv++CP  +
  gi|330506892|ref|YP_004383320.1| 190 KAIIDYDKCVRCGRCVAVCPEAA 212
                                       579*****************933 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   7.2   1.3e-06    0.0013      31      52 .]     154     183 ..     101     183 .. 0.54
   2 !   34.4  14.5   2.7e-11   2.5e-08       1      52 []     168     212 ..     168     212 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-06
                            Fer4_7  31 v........eidpekClgCgaCvavCPtga 52 
                                       +        +id ekC+gCg+Cv+vC +ga
  gi|330506892|ref|YP_004383320.1| 154 IglmgrvlpQIDLEKCTGCGKCVEVCKVGA 183
                                       1333333449*****************997 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 2.7e-11
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C+gCg+Cv++C+v+a ++ ee       k+ id++kC+ Cg+CvavCP  a
  gi|330506892|ref|YP_004383320.1| 168 KCTGCGKCVEVCKVGATKIVEE-------KAIIDYDKCVRCGRCVAVCPEAA 212
                                       7******************986.......689*****************875 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8  12.5     6e-11   5.7e-08       1      49 [.     168     211 ..     141     213 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 6e-11
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       kCtgCg+Cve+C+ g+++  + + ++ ++     +C+ Cg+Cv++Cp+ 
  gi|330506892|ref|YP_004383320.1| 168 KCTGCGKCVEVCKVGATKIVEEKAIIDYD-----KCVRCGRCVAVCPEA 211
                                       7********************99999995.....5************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 ?   -0.8   0.0       1.8   1.7e+03       7      20 ..     101     114 ..      98     123 .. 0.68
   2 !   18.7   2.6   1.5e-06    0.0015      13      53 ..     141     181 ..     137     189 .. 0.77
   3 !   21.3   1.2   2.3e-07   0.00021       1      22 [.     191     212 ..     191     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.8
                           Fer4_21   7 kCigCgkCliaCed 20 
                                       +C+g   C++a  +
  gi|330506892|ref|YP_004383320.1| 101 SCLGTDYCYKAVAE 114
                                       46666667666554 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.5e-06
                           Fer4_21  13 kCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                        C+  C     + i + ++   ++  ++C+GC  C++vC v
  gi|330506892|ref|YP_004383320.1| 141 GCAFPCTRPQFNEIGLMGRVLPQIDLEKCTGCGKCVEVCKV 181
                                       58888888888888887777777778999999999999987 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 2.3e-07
                           Fer4_21   1 AridedkCigCgkCliaCedts 22 
                                       A+id dkC+ Cg+C+ +C++++
  gi|330506892|ref|YP_004383320.1| 191 AIIDYDKCVRCGRCVAVCPEAA 212
                                       89*****************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 ?   -1.5   0.1       5.5   5.2e+03       4      12 ..     102     110 ..     101     111 .. 0.75
   2 !   17.2   3.6   5.4e-06    0.0051       2      16 ..     167     181 ..     166     182 .. 0.90
   3 !   21.3   2.5   2.7e-07   0.00026       1      15 [.     195     209 ..     195     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.5
                            Fer4_4   4 CigCgsCva 12 
                                       C+g + C+ 
  gi|330506892|ref|YP_004383320.1| 102 CLGTDYCYK 110
                                       888888985 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.4e-06
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e+C+gCg+Cv +C++
  gi|330506892|ref|YP_004383320.1| 167 EKCTGCGKCVEVCKV 181
                                       89***********97 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 2.7e-07
                            Fer4_4   1 qerCigCgsCvaaCP 15 
                                       +++C++Cg+Cva+CP
  gi|330506892|ref|YP_004383320.1| 195 YDKCVRCGRCVAVCP 209
                                       59************* PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.7   3.7e-06    0.0035      46      64 ..     164     182 ..     118     183 .. 0.85
   2 !   17.3   0.6   5.2e-06    0.0049       3      18 ..     196     211 ..     194     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.7e-06
                            Fer4_8  46 ealwsCttcgaCtevCpvg 64 
                                         l++Ct+cg+C+evC+vg
  gi|330506892|ref|YP_004383320.1| 164 IDLEKCTGCGKCVEVCKVG 182
                                       56899**********9986 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.2e-06
                            Fer4_8   3 ekCieCgaCqsaCpvl 18 
                                       +kC++Cg+C + Cp +
  gi|330506892|ref|YP_004383320.1| 196 DKCVRCGRCVAVCPEA 211
                                       7899999999999843 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 ?   -1.2   0.0       3.2     3e+03      16      34 ..      16      32 ..      13      44 .. 0.71
   2 ?   -2.3   0.1       7.2   6.8e+03       5      16 ..     101     112 ..     100     116 .. 0.81
   3 !   11.1   2.7   0.00047      0.44       1      16 [.     164     179 ..     164     181 .. 0.94
   4 !   20.1   0.2   7.3e-07   0.00068       1      30 [.     193     222 ..     193     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.2
                           Fer4_13 16 aPdvFeeddeggasvvaeq 34
                                       P vF++ d   ++ ++ q
  gi|330506892|ref|YP_004383320.1| 16 MPAVFQRRDG--KFEIKLQ 32
                                      6999*99974..6666555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.2
                           Fer4_13   5 tCiacgaCvela 16 
                                       +C + + C+++ 
  gi|330506892|ref|YP_004383320.1| 101 SCLGTDYCYKAV 112
                                       6999999*9875 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00047
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       +D ++C++cg+Cve++
  gi|330506892|ref|YP_004383320.1| 164 IDLEKCTGCGKCVEVC 179
                                       899************9 PP

  == domain 4  score: 20.1 bits;  conditional E-value: 7.3e-07
                           Fer4_13   1 VDrdtCiacgaCvelaPdvFeeddeggasv 30 
                                       +D d+C+ cg Cv+++P+  ++  e+g+  
  gi|330506892|ref|YP_004383320.1| 193 IDYDKCVRCGRCVAVCPEAAKYSAEKGYIM 222
                                       799****************99999998765 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.8   2.5e-05     0.024       1      20 [.     168     187 ..     168     196 .. 0.79
   2 !   15.3   2.9     3e-05     0.029       1      16 [.     197     212 ..     197     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++CgkC+evC ++a k  
  gi|330506892|ref|YP_004383320.1| 168 KCTGCGKCVEVCKVGATKIV 187
                                       5************9997654 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3e-05
                           Fer4_16   1 rCgtCgkCaevCPtna 16 
                                       +C++Cg+C+ vCP++a
  gi|330506892|ref|YP_004383320.1| 197 KCVRCGRCVAVCPEAA 212
                                       5************987 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 ?   -1.8   0.0       5.9   5.6e+03       8      25 ..     102     119 ..     100     129 .. 0.82
   2 !   14.2   1.0   5.8e-05     0.055       3      19 ..     164     180 ..     163     191 .. 0.82
   3 !   14.8   0.3   3.9e-05     0.037       3      22 ..     193     212 ..     192     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.9
                           Fer4_15   8 CigcglCvaeapevfeld 25 
                                       C g   C++++ e ++l+
  gi|330506892|ref|YP_004383320.1| 102 CLGTDYCYKAVAETITLA 119
                                       999999999999888876 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.8e-05
                           Fer4_15   3 vDrdaCigcglCvaeap 19 
                                       +D ++C+gcg Cv++++
  gi|330506892|ref|YP_004383320.1| 164 IDLEKCTGCGKCVEVCK 180
                                       89*************94 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 3.9e-05
                           Fer4_15   3 vDrdaCigcglCvaeapevf 22 
                                       +D d+C  cg+Cva++pe  
  gi|330506892|ref|YP_004383320.1| 193 IDYDKCVRCGRCVAVCPEAA 212
                                       9****************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 !   16.5   6.6   1.3e-05     0.012       1      15 []     169     183 ..     169     183 .. 0.98
   2 !   11.3   6.8   0.00056      0.53       1      13 [.     198     210 ..     198     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       CtgCg CvevC vgA
  gi|330506892|ref|YP_004383320.1| 169 CTGCGKCVEVCKVGA 183
                                       *************98 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00056
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+ Cg+Cv vCP+
  gi|330506892|ref|YP_004383320.1| 198 CVRCGRCVAVCPE 210
                                       99**********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 ?   -0.7   0.0       2.7   2.6e+03      34      51 ..      96     113 ..      82     127 .. 0.67
   2 !   13.0   3.1   0.00016      0.15      74      94 ..     161     181 ..     147     183 .. 0.86
   3 !   13.5   2.4    0.0001     0.099      71      94 ..     187     210 ..     183     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.7
                           Fer4_22  34 vrvwdsClleeftkvagg 51 
                                       +r++ sCl +++ + a  
  gi|330506892|ref|YP_004383320.1|  96 FRNVVSCLGTDYCYKAVA 113
                                       566667776666655544 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00016
                           Fer4_22  74 kekfgesgCvGCgRCieacpv 94 
                                         +++ ++C+GCg+C+e+c+v
  gi|330506892|ref|YP_004383320.1| 161 LPQIDLEKCTGCGKCVEVCKV 181
                                       5678999************97 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 0.0001
                           Fer4_22  71 sefkekfgesgCvGCgRCieacpv 94 
                                        e k+ ++  +Cv CgRC+++cp+
  gi|330506892|ref|YP_004383320.1| 187 VEEKAIIDYDKCVRCGRCVAVCPE 210
                                       55556678999***********97 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.4    0.0003      0.28      42      57 ..     165     180 ..     147     184 .. 0.77
   2 ?   14.1   1.9   5.4e-05     0.051      42      58 ..     194     210 ..     180     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                           Fer4_17  42 kaslCieCgeCerkCP 57 
                                         ++C++Cg+C+++C 
  gi|330506892|ref|YP_004383320.1| 165 DLEKCTGCGKCVEVCK 180
                                       5678999999999985 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.4e-05
                           Fer4_17  42 kaslCieCgeCerkCPq 58 
                                         ++C+ Cg+C+++CP+
  gi|330506892|ref|YP_004383320.1| 194 DYDKCVRCGRCVAVCPE 210
                                       5689************7 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   3.3     0.013        12      59      74 ..     167     182 ..     162     191 .. 0.85
   2 ?   10.3   3.3   0.00063      0.59      50      73 ..     187     210 ..     183     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                           Fer4_18  59 gdcidcescvkvcPtg 74 
                                        +c+ c++cv+vc +g
  gi|330506892|ref|YP_004383320.1| 167 EKCTGCGKCVEVCKVG 182
                                       57999********876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00063
                           Fer4_18  50 keerkekgagdcidcescvkvcPt 73 
                                       +ee++  +  +c+ c+ cv+vcP 
  gi|330506892|ref|YP_004383320.1| 187 VEEKAIIDYDKCVRCGRCVAVCPE 210
                                       56666677889************6 PP

>> SCIFF  Six-cysteine peptide SCIFF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   4.6      0.39   3.7e+02      15      28 ..     167     180 ..     160     185 .. 0.83
   2 ?    9.4   0.3     0.001      0.98       4      34 ..     185     215 ..     182     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.39
                             SCIFF  15 lkkggCgeCqtSCq 28 
                                        k +gCg+C   C+
  gi|330506892|ref|YP_004383320.1| 167 EKCTGCGKCVEVCK 180
                                       5779******9997 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.001
                             SCIFF   4 ktlskkslkktlkkggCgeCqtSCqSACKTS 34 
                                       k++++k + +  k   Cg C + C  A K S
  gi|330506892|ref|YP_004383320.1| 185 KIVEEKAIIDYDKCVRCGRCVAVCPEAAKYS 215
                                       789999999999****************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2187.76
//
Query:       gi|330506893|ref|YP_004383321.1|  [L=328]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete 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    2.9e-27   95.9   0.0    1.2  1  ABC_tran      ABC transporter
    6.3e-15   55.8   1.2    1.6e-09   38.1   0.2    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      0.002   17.9   0.0        1.3    8.6   0.0    2.1  2  AAA_15        AAA ATPase domain
     0.0055   17.1   0.2      0.013   15.9   0.2    1.6  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.013   15.8   0.0       0.04   14.2   0.0    1.8  1  AAA_22        AAA domain
      0.017   15.6   0.0      0.031   14.8   0.0    1.3  1  AAA_23        AAA domain
       0.13   12.1   0.0       0.26   11.0   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
       0.19   11.1   0.0        8.3    5.8   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
       0.22   10.9   0.4         19    4.6   0.1    2.2  2  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 !   95.9   0.0   1.4e-30   2.9e-27       2     136 ..      24     166 ..      23     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 1.4e-30
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +++s+++ ege+++++G+nG+GK+t +++l gl +p+eG+  l g +l    ++++++ +gv+p  ++l +el++ +
  gi|330506893|ref|YP_004383321.1|  24 DHISFQVTEGEIYGFLGPNGSGKTTTIRMLVGLAQPDEGSASLLGYHLPA-GINQAKRYMGVVPDVSNLYDELSALD 99 
                                       789*****************************************999999.99************************ PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e++ ++e++l+ +gl e ++++     s +S G+k+ + +a+al+ +p+ll+lDEpt
  gi|330506893|ref|YP_004383321.1| 100 NllfmaqlygvpheEQKPRAEQLLRDFGLYERRNDRF----SAFSRGMKRALTIAAALIHQPRLLFLDEPT 166
                                       ************9888888*****************9....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.9e-06    0.0077       2      24 ..      36      58 ..      35      76 .. 0.83
   2 !   38.1   0.2   7.8e-13   1.6e-09     233     298 ..     135     197 ..     113     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.9e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                       ++ GpNgsGK++ ++ l +la+
  gi|330506893|ref|YP_004383321.1| 36 YGFLGPNGSGKTTTIRMLVGLAQ 58
                                      5789****************986 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 7.8e-13
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                        ++ +S G+kr+l +++al+ ++   +ll++DEp +gL+ ++ r+l  l++ ls++g  ++ltTH 
  gi|330506893|ref|YP_004383321.1| 135 RFSAFSRGMKRALTIAAALIHQP---RLLFLDEPTTGLDAAAARSLRALISGLSDKGLTIFLTTHY 197
                                       56778***************999...***************************************6 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00066       1.3      28      48 ..      38      58 ..      24      94 .. 0.86
   2 !    7.2   0.0    0.0018       3.7     298     364 ..     140     196 ..     113     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00066
                            AAA_15 28 liGkNnsGKSsilealdlFln 48
                                      + G+N+sGK++ +++l  + +
  gi|330506893|ref|YP_004383321.1| 38 FLGPNGSGKTTTIRMLVGLAQ 58
                                      88*************977766 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0018
                            AAA_15 298 GsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       + G++r+l ++  +++  +          l+++EP + L   a ++l  l+  l++++   +++tTH
  gi|330506893|ref|YP_004383321.1| 140 SRGMKRALTIAAALIHQPRL---------LFLDEPTTGLDAAAARSLRALISGLSDKGL-TIFLTTH 196
                                       56788888887777776666.........*****************************8.9****** PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   6.7e-06     0.013      25     167 ..      34     189 ..      19     192 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.7e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggif.lrgkcdql..esaipy..........salaqalareellrqllde 88 
                                       e+  + G+ G+GK++ +r+l   ++ d+g + l g        +a +y          +  ++al++  +++ql   
  gi|330506893|ref|YP_004383321.1|  34 EIYGFLGPNGSGKTTTIRMLVGLAQPDEGSAsLLGYHLPAgiNQAKRYmgvvpdvsnlYDELSALDNLLFMAQLYGV 110
                                       566678***************98888843333444444443333344444422221112222444444444444444 PP

                            AAA_16  89 aesaeleawrekleealaavpelagaea.....srllellkrll.allsrderplvlvlDdlq.wadeaslqllaaL 158
                                       + + e+ + +e+l++ ++   e     +     s++ + +kr+l   ++  ++p +l+lD+    +d+a +  l+aL
  gi|330506893|ref|YP_004383321.1| 111 PHE-EQKPRAEQLLRDFG-LYE-----RrndrfSAFSRGMKRALtIAAALIHQPRLLFLDEPTtGLDAAAARSLRAL 180
                                       444.56666666666666.333.....233445999999999997666666779******65535555555556667 PP

                            AAA_16 159 lrlleskpl 167
                                        + l++k l
  gi|330506893|ref|YP_004383321.1| 181 ISGLSDKGL 189
                                       666666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     2e-05      0.04      11     127 ..      39     193 ..      32     204 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                            AAA_22  11 tGesGtGKTtllrrlleqldeeakaee...........erpevvfvtlpsst.....sskdllrellralglelka. 70 
                                        G+ G+GKTt++r+l+  ++ ++  +            + ++++ v + +s+     s  d l  +++ +g+++++ 
  gi|330506893|ref|YP_004383321.1|  39 LGPNGSGKTTTIRMLVGLAQPDEGSASllgyhlpaginQAKRYMGVVPDVSNlydelSALDNLLFMAQLYGVPHEEq 115
                                       59***************998777777788999998888444444444444443343344444455555555555555 PP

                            AAA_22  71 ................erlsseellealeqalrarav....ielliiDEaqh.lr..seealeeLrsllnlsrkgvq 124
                                                       ++++ +++ + + +al  +a+    ++ll +DE    l+   ++ l+ L s l   +kg++
  gi|330506893|ref|YP_004383321.1| 116 kpraeqllrdfglyerRNDRFSAFSRGMKRALTIAAAlihqPRLLFLDEPTTgLDaaAARSLRALISGLS--DKGLT 190
                                       5555555555555443344444444666666666666888888888888777774333555555544444..66666 PP

                            AAA_22 125 liL 127
                                       ++L
  gi|330506893|ref|YP_004383321.1| 191 IFL 193
                                       665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.6e-05     0.031      15      37 ..      26      51 ..      19      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                            AAA_23 15 idF...skgltlItGpNGaGKTTild 37
                                      i F   +  ++ + GpNG+GKTT ++
  gi|330506893|ref|YP_004383321.1| 26 ISFqvtEGEIYGFLGPNGSGKTTTIR 51
                                      667766678999***********987 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013      0.26      17      39 ..      28      50 ..      22      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                            AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                      +++++ +++ + Gp+GsGK+T +
  gi|330506893|ref|YP_004383321.1| 28 FQVTEGEIYGFLGPNGSGKTTTI 50
                                      45554448889**********77 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0041       8.3      28      41 ..      37      50 ..      23      56 .. 0.80
   2 ?    3.2   0.0     0.025        51     137     200 ..     139     196 ..     108     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0041
                                      EEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxx RF
                             SMC_N 28 aivGpNGSGKsnll 41
                                        +GpNGSGK+  +
  gi|330506893|ref|YP_004383321.1| 37 GFLGPNGSGKTTTI 50
                                      568*******9765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.025
                                       S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                             SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislree 200
                                       +S+G k     aL +A   +++  l +lDe    LD++  + +  l+   s++   ++ ++   +
  gi|330506893|ref|YP_004383321.1| 139 FSRGMKR----ALTIAAALIHQPRLLFLDEPTTGLDAAAARSLRALISGLSDKgLTIFLTT---H 196
                                       5555554....5666666677777899********************98886623333333...3 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1    0.0095        19      27      48 ..      38      59 ..      32      79 .. 0.87
   2 ?    4.3   0.0     0.012        23      11      52 ..     143     187 ..     140     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0095
                      Mg_chelatase 27 lvGppGsGKtmlakrlpsllpp 48
                                      ++Gp GsGKt  ++ l +l  p
  gi|330506893|ref|YP_004383321.1| 38 FLGPNGSGKTTTIRMLVGLAQP 59
                                      68***********999998655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.012
                      Mg_chelatase  11 akraleiaaaGgHn..lllvGppGsGKtm.lakrlpsllpplsee 52 
                                        kral+iaaa  H+  ll++  p +G     a+ l +l++ ls++
  gi|330506893|ref|YP_004383321.1| 143 MKRALTIAAALIHQprLLFLDEPTTGLDAaAARSLRALISGLSDK 187
                                       69*********996559*********7651556688888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2275.24
//
Query:       gi|330506894|ref|YP_004383322.1|  [L=243]
Description: ABC transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-27   93.8  15.2    9.6e-27   93.8  15.2    1.7  2  ABC2_membrane    ABC-2 type transporter
    8.2e-15   54.7  19.1      1e-14   54.4  19.1    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein
      5e-08   32.6  16.1    8.4e-08   31.8  16.1    1.3  1  ABC2_membrane_2  ABC-2 family transporter protein
    0.00086   18.9   9.5     0.0011   18.5   9.5    1.2  1  CcmB             CcmB 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 !   93.8  15.2   2.1e-30   9.6e-27       5     210 .]      12     209 ..       8     209 .. 0.93
   2 ?   -0.7   0.1      0.18   8.1e+02      53      64 ..     221     232 ..     213     240 .. 0.59

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 2.1e-30
                     ABC2_membrane   5 allkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedgl.nrpgllffsvlflafsaltsvapvfererg 80 
                                        +  +++++++  p  +  w +++pl ++l f +         d++   pgll+++++f + +a+ +v+++fe + g
  gi|330506894|ref|YP_004383322.1|  12 HIAIKDMRTYYLKPPAL-SWGMVFPLAWTLAFYLRSP-----GDFAeLVPGLLAMTIVFST-TAAEAVVINFELRLG 81 
                                       56678899999999999.9*************99999.....3666444************.9999999******** PP

                     ABC2_membrane  81 vlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllisalaps 157
                                       +ler+l +p+    +++l+kvl+ ++++l+ ++i+ + +++ ++l+++ ++ + ++++ +++++ss+g l+s+ ++ 
  gi|330506894|ref|YP_004383322.1|  82 TLERLLLAPI-GITSVLLGKVLGGFLFGLFTTAIVAAASILYMDLHPD-ILGLAIIAVPSLMVFSSMGALFSVSVKE 156
                                       **********.**************************555555****9.99999*********************** PP

                     ABC2_membrane 158 fedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnlf 210
                                       +  a++l +l  +++++l+G+++pi+++p  lq +a+l+Plty+v++lr+++f
  gi|330506894|ref|YP_004383322.1| 157 VFEAQTLLNLPRFLMVFLCGVVYPISALPDGLQLLARLLPLTYTVQGLRISFF 209
                                       ****************************99*******************9987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.18
                     ABC2_membrane  53 pgllffsvlfla 64 
                                       + ll+f++lfl 
  gi|330506894|ref|YP_004383322.1| 221 AALLVFMILFLL 232
                                       455555555555 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 !   54.4  19.1   2.3e-18     1e-14     158     341 ..      49     232 ..      35     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 2.3e-18
                   ABC2_membrane_3 158 nvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.afglgi 233
                                       ++a  + gl+++ ++f t +  av i +E + +++e++l++++  ++ +l+k+lg fl +l++++++ +  ++   +
  gi|330506894|ref|YP_004383322.1|  49 DFAELVPGLLAMTIVFSTTAAEAVVINFELRLGTLERLLLAPIGITSVLLGKVLGGFLFGLFTTAIVAAAsILY--M 123
                                       566677777777776666666666799**************************************999966888..8 PP

                   ABC2_membrane_3 234 pfg.nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffap 309
                                       +   +++ l +  ++ +++++++g+l+s+ +k   +aq+l+ +  +l+ +++g+++p+++lp++l+ +++++P+++ 
  gi|330506894|ref|YP_004383322.1| 124 DLHpDILGLAIIAVPSLMVFSSMGALFSVSVKEVFEAQTLLNLPRFLMVFLCGVVYPISALPDGLQLLARLLPLTYT 200
                                       8888999999************************************9****************************** PP

                   ABC2_membrane_3 310 glgllrlitgdplwe.illsliilalfavvyll 341
                                        +gl r+++ +++ + +++++++l++f +++ll
  gi|330506894|ref|YP_004383322.1| 201 VQGL-RISFFEHGDSlLWQDFAALLVFMILFLL 232
                                       ****.9996565555466************997 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8  16.1   1.9e-11   8.4e-08      77     285 ..      54     240 ..       7     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.9e-11
                   ABC2_membrane_2  77 vstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilal 152
                                       v++++a+ i++  +++ a +i+ E   gTl++lL  P+   ++llgK++gg++ gl+ +a+ + a+       il+ 
  gi|330506894|ref|YP_004383322.1|  54 VPGLLAMTIVFSTTAAEAVVINFELRLGTLERLLLAPIGITSVLLGKVLGGFLFGLFtTAIVAAAS-------ILYM 123
                                       88999*************************************************888777777777.......6678 PP

                   ABC2_membrane_2 153 givlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqei 229
                                         ++++  l +++v s+++     f ++g+l+S+ ++  + +a+  l l  +l+++  +v+y++++l+ g +     
  gi|330506894|ref|YP_004383322.1| 124 DLHPDILGLAIIAVPSLMV-----FSSMGALFSVSVK-EVFEAQTLLNLPRFLMVFLCGVVYPISALPDGLQL---- 190
                                       8888888887777777744.....46***********.9999999999999999***************9999.... PP

                   ABC2_membrane_2 230 ndflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkr 285
                                         + +ll+ t   + l+ ++++ +d     + +  +++ll+ ++ +l  ++ l+ r
  gi|330506894|ref|YP_004383322.1| 191 --LARLLPLTYTVQGLRISFFEHGD----SLLWQDFAALLVFMILFLLPAISLLHR 240
                                       ..55555555566666666666665....788999999999999988877766655 PP

>> CcmB  CcmB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   9.5   2.4e-07    0.0011      44     176 ..      50     178 ..      12     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-07
                              CcmB  44 lsriapgilWvaallaslLsldrlfaadfedGsLellllapvplellvlaKalAhwlltglplvllapllalllnle 120
                                       ++++ pg+l +++++++  +   + + +   G+Le lllap+ ++ ++l+K+l  +l+ +    ++a+   l ++l+
  gi|330506894|ref|YP_004383322.1|  50 FAELVPGLLAMTIVFSTTAAEAVVINFELRLGTLERLLLAPIGITSVLLGKVLGGFLFGLFTTAIVAAASILYMDLH 126
                                       678899***********99999999**************************************************** PP

                              CcmB 121 aaalgllaltLllGtpalsllgavgaAltvgLkrgglLlslLvlPliiPvlifave 176
                                         +lgl +    + +p+l + + +ga  +v++k      +lL lP ++ v++ +v 
  gi|330506894|ref|YP_004383322.1| 127 PDILGLAI----IAVPSLMVFSSMGALFSVSVKEVFEAQTLLNLPRFLMVFLCGVV 178
                                       *9999876....568******************99999999999999888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1808.68
//
Query:       gi|330506895|ref|YP_004383323.1|  [L=110]
Description: hypothetical protein MCON_0687 [Methanosaeta concilii GP6]
Scores for complete 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  105.3   0.5      2e-30  105.1   0.5    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 !  105.1   0.5   1.1e-34     2e-30       1     106 []       3     110 .]       3     110 .] 0.96

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 1.1e-34
                              CGGC   1 kiaiirCekvedvCpgvkClkalkerkgaFeeyeeevelvgfvtCggCpgkkvveklkelkkegvdvihlssCiktk 77 
                                       k+++irC+++ed+Cpg+ ++ +++e k aF+++  +ve+vgf++CggCpgk++v ++k+++++g+++i+++sCi++ 
  gi|330506895|ref|YP_004383323.1|   3 KVGVIRCQQTEDMCPGTMDFVVASEGKMAFADTG-PVEIVGFLSCGGCPGKRAVPRAKMMVDRGAEAIVIASCISKG 78 
                                       89*******************************9.**************************************9444 PP

                              CGGC  78 .kakkeCpeieeikeaieekl..gievvegth 106
                                         +  +Cp+ eeike i++k+  +++++e+th
  gi|330506895|ref|YP_004383323.1|  79 nPIGFPCPHFEEIKECIAKKIgpEVKIIEWTH 110
                                       48999****************88899*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 827.41
//
Query:       gi|330506896|ref|YP_004383324.1|  [L=216]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete 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   58.6   0.0    1.3e-15   57.8   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    2.9e-10   40.7   0.0    5.7e-10   39.8   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    2.6e-08   33.9   0.0    3.8e-08   33.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    5.8e-06   27.0   0.0    1.3e-05   25.8   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    4.8e-05   23.2   0.0    0.00019   21.2   0.0    2.0  1  Methyltransf_31  Methyltransferase domain
    6.8e-05   22.3   0.0     0.0001   21.7   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00094   18.8   0.0     0.0015   18.1   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
      0.064   12.2   0.0      0.083   11.8   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)


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 !   57.8   0.0   5.7e-19   1.3e-15       1      96 []      43     128 ..      43     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 5.7e-19
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       L+vG+GtGr+a++l       +gv+++++m k+a++++      +e++ a ae lpf+d+sfD+v++  ++++++dp
  gi|330506896|ref|YP_004383324.1|  43 LEVGAGTGRFAAPLG----IKIGVEPAQAMAKRARARG------IEVIYALAEALPFRDESFDFVLMVTTVCFLDDP 109
                                       89*************....779*********9997777......56699**************************** PP

                                       HHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                         a++e++R L pgG l+i
  gi|330506896|ref|YP_004383324.1| 110 LLACQEAKRTLVPGGSLII 128
                                       ****************996 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   2.5e-13   5.7e-10       2      97 .]      43     124 ..      43     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 2.5e-13
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhls 78 
                                       L++G+GtGr+++ l  +      +gv+++++m ++ar+r       +e++ + ae+lpf d+sfD+v+++ ++++l+
  gi|330506896|ref|YP_004383324.1|  43 LEVGAGTGRFAAPLGIK------IGVEPAQAMAKRARARG------IEVIYALAEALPFRDESFDFVLMVTTVCFLD 107
                                       89***********9866......7**************99......9**********************98899998 PP

                                       HHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                       d+    a++e++r L pgG
  gi|330506896|ref|YP_004383324.1| 108 DP--LLACQEAKRTLVPGG 124
                                       55..578***********9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   1.7e-11   3.8e-08      12     162 ..      28     173 ..      14     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.7e-11
                   Methyltransf_23  12 klerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkf 83 
                                       +++ l    +++g  L++G+GtG+++  l  +    +gv++  ++ ++a+              + ++  ++ +++f
  gi|330506896|ref|YP_004383324.1|  28 EIQALRSLIPSSGTGLEVGAGTGRFAAPLGIK----IGVEPAQAMAKRARargieV------IYALAEALPFRDESF 94 
                                       4444444467899**************99777....8****999999987654431......2222345567999** PP

                   Methyltransf_23  84 dlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGl 160
                                       d++ +  + + ++dp  + + +++ l pgG l++ ++++++++ r+++  +   +  +  +f sa+++  +l++ ++
  gi|330506896|ref|YP_004383324.1|  95 DFVLMVTTVCFLDDPLLACQEAKRTLVPGGSLIIGMIDRDSPAGRDYDRKKTTSKFYKFARFRSADEVMSWLKDLDF 171
                                       *****************************************999999998888877788899999999999999988 PP

                   Methyltransf_23 161 ev 162
                                        +
  gi|330506896|ref|YP_004383324.1| 172 YD 173
                                       65 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0     6e-09   1.3e-05       1      99 []      43     126 ..      43     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 6e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       Le+G+GtG+++++l  k      +gv++ +++ ++a+++  + +          a+ l  +d+  sfD v++  +++
  gi|330506896|ref|YP_004383324.1|  43 LEVGAGTGRFAAPLGIK------IGVEPAQAMAKRARARGIEVIY-------ALAEALPFRDE--SFDFVLMVTTVC 104
                                       8****************......**********666666666554.......44444444444..9*********** PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        l+d+  + +++++ L+pgG l
  gi|330506896|ref|YP_004383324.1| 105 FLDDPLLACQEAKRTLVPGGSL 126
                                       ********************76 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   8.6e-08   0.00019      32     113 ..      60     132 ..      38     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 8.6e-08
                   Methyltransf_31  32 vGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkileeiervlkpggill 108
                                       +G++        A+++a++     +e+  + +e+l+  + de+fD++l   +++ l dp  + +e++r l pgg l+
  gi|330506896|ref|YP_004383324.1|  60 IGVEP-------AQAMAKRARARGIEVIYALAEALP--FRDESFDFVLMVTTVCFLDDPLLACQEAKRTLVPGGSLI 127
                                       44444.......555555555568999*********..*************************************** PP

                   Methyltransf_31 109 iedpr 113
                                       i  ++
  gi|330506896|ref|YP_004383324.1| 128 IGMID 132
                                       *9888 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   4.5e-08    0.0001      88     151 ..      65     128 ..      46     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.5e-08
                                       HHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran  88 gekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                       +++ +k+     ie + a ae+Lpf d+sfD+v +   +  + D l a +ea r l pGG l++
  gi|330506896|ref|YP_004383324.1|  65 AQAMAKRARARGIEVIYALAEALPFRDESFDFVLMVTTVCFLDDPLLACQEAKRTLVPGGSLII 128
                                       455566666679************************************************9975 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.8e-07    0.0015       5      91 ..      30     109 ..      27     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.8e-07
                              MetW   5 eliaelikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvl 81 
                                       +++  li++  + l++G+G G +   l    +++  G+e  ++  +++ a+G++vi   ++  l  f+d+sfd+v++
  gi|330506896|ref|YP_004383324.1|  30 QALRSLIPSSGTGLEVGAGTGRFAAPL----GIK-IGVEPAQAMAKRARARGIEVIYALAE-AL-PFRDESFDFVLM 99 
                                       6778899***************99999....454.6********************97655.44.79********** PP

                              MetW  82 sqtlqatrnp 91 
                                         t+  + +p
  gi|330506896|ref|YP_004383324.1| 100 VTTVCFLDDP 109
                                       9998766655 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.7e-05     0.083     175     264 ..      85     175 ..      61     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                                       GGS-T.---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEEEEEE-BSS-TT-EE--SS-BTTBSS---EEBHHH CS
                    Methyltransf_9 175 eqlpe.leafdtvfsmGvlyhrrsPldhllqlkdqlvkgGelvletlvieGdenavlvPedryakmrnvyfiPsaaa 250
                                       e lp   e+fd v+ +  +     Pl   ++ k +lv gG l++  +  +         +++ +k      + sa  
  gi|330506896|ref|YP_004383324.1|  85 EALPFrDESFDFVLMVTTVCFLDDPLLACQEAKRTLVPGGSLIIGMIDRDSPAGRDYDRKKTTSKFYKFARFRSADE 161
                                       77887679***********************************987665555556666777778888888899**** PP

                                       HHHHHHHTT-EEEE CS
                    Methyltransf_9 251 lkvWlekvgfvdvr 264
                                       ++ Wl+  +f d+ 
  gi|330506896|ref|YP_004383324.1| 162 VMSWLKDLDFYDIL 175
                                       ***********984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1295.71
//
Query:       gi|330506897|ref|YP_004383325.1|  [L=284]
Description: methylase involved in ubiquinone/menaquinone biosynthesis [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-16   60.5   0.0    3.2e-15   56.6   0.0    2.3  2  Methyltransf_25  Methyltransferase domain
    1.5e-15   57.3   0.0    6.4e-15   55.3   0.0    1.8  2  Methyltransf_31  Methyltransferase domain
    2.2e-15   57.1   0.0    5.7e-15   55.7   0.0    1.7  2  Methyltransf_11  Methyltransferase domain
    1.8e-10   40.5   0.0    4.7e-10   39.2   0.0    1.6  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.1e-05   23.1   0.0      7e-05   22.6   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
     0.0008   19.2   0.0     0.0012   18.7   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0047   16.4   0.0      0.016   14.6   0.0    1.7  2  Methyltransf_4   Putative methyltransferase
  ------ inclusion threshold ------
      0.047   14.4   0.0       0.36   11.6   0.0    2.3  2  Methyltransf_12  Methyltransferase domain
      0.069   12.8   0.0       0.36   10.5   0.0    2.1  2  UPF0020          Putative RNA methylase family UPF0020
      0.079   12.5   0.0       0.11   12.0   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
      0.091   11.3   0.0       0.13   10.8   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
      0.099   13.7   0.0       0.43   11.6   0.0    2.1  2  Methyltransf_24  Methyltransferase domain
       0.14   11.7   0.0       0.22   11.1   0.0    1.3  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   2.3e-18   3.2e-15       2      97 .]      38     142 ..      38     142 .. 0.88
   2 ?    1.2   0.0      0.45   6.1e+02      24      76 ..     204     255 ..     192     264 .. 0.63

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 2.3e-18
                                       EEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       Ld++cG+G+++l+la++  +++ v g+Di +e l +a e a+++gl  ++ f+qgd+ ++pf+d+ fD v+++ +l 
  gi|330506897|ref|YP_004383325.1|  38 LDVACGNGDHSLWLARAAkPDGCVFGIDICKEGLVRAIESAKSAGLkgELAFLQGDVCSIPFPDHIFDWVWCADCLW 114
                                       8****************9659**********************999999***********************98854 PP

                                       .......GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 .......hlsdedlekalkeiarvLkpgG 97 
                                              +l   +   al+e+ rv++pgG
  gi|330506897|ref|YP_004383325.1| 115 pgprsqgFLG-MNPLPALEELVRVTRPGG 142
                                       3555544333.334569***********9 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.45
                                       EEEEESSHHHHHHHHHHHHHTTTTEEEEESBC.CGBSSSTT.TEEEEEEEST.GGG CS
                   Methyltransf_25  24 vtgvDiseemleaareraeeeglnvefvqgda.edlpfedg.sfDlvvssga.lhh 76 
                                           Di+  + ++a+  +   +l ++++ g a e+lp++++  f + +s ++   +
  gi|330506897|ref|YP_004383325.1| 204 TFVADIQGPLSDQAQDDL---QLCFQMLWGRAaEELPEKEReNFRVLCS-NCsADF 255
                                       556677777777777777...3666666666657788654416666555.553555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0   4.6e-18   6.4e-15       6     113 ..      36     150 ..      32     194 .. 0.87
   2 ?   -0.4   0.0      0.66   9.1e+02      64      91 ..     233     260 ..     206     274 .. 0.68

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 4.6e-18
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsn 81 
                                       r lD++CG+G+ ++ la+ + p++ v+GiDi +e + +A e a++ gl+ ++ F qgd+ +++  + d  fD + + 
  gi|330506897|ref|YP_004383325.1|  36 RGLDVACGNGDHSLWLARAAKPDGCVFGIDICKEGLVRAIESAKSAGLKgELAFLQGDVCSIP--FPDHIFDWVWCA 110
                                       569***************999******************************************..************ PP

                   Methyltransf_31  82 evl........naladpdkileeiervlkpggilliedpr 113
                                       + l         +  +p  +lee+ rv +pgg +++   +
  gi|330506897|ref|YP_004383325.1| 111 DCLwpgprsqgFLGMNPLPALEELVRVTRPGGTVALLFWS 150
                                       9998888888888888888999**********99875555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.66
                   Methyltransf_31  64 ee.leklledekfDlilsnevlnaladpd 91 
                                        e l+++ e+e+f +++sn+  + +a+++
  gi|330506897|ref|YP_004383325.1| 233 AEeLPEK-ERENFRVLCSNCSADFIAANQ 260
                                       3336663.667777777777765555554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   4.1e-18   5.7e-15       1      95 [.      38     145 ..      38     146 .. 0.90
   2 ?   -2.5   0.0         6   8.2e+03      73      87 ..     230     246 ..     201     259 .. 0.52

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 4.1e-18
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlh 72 
                                       Ldv+cG+G ++ +la+++   + v+g+D++ke l +a e a+ +gl  ++ f+++d+ ++pf+d+ fD v++  +l 
  gi|330506897|ref|YP_004383325.1|  38 LDVACGNGDHSLWLARAAkpdGCVFGIDICKEGLVRAIESAKSAGLkgELAFLQGDVCSIPFPDHIFDWVWCADCLW 114
                                       8**************8888999************99988888888888899***********************998 PP

                                       C-C........CHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  73 hve........dpekalkeiaRvLkpgGllv 95 
                                         +        +p  al+e++Rv +pgG+++
  gi|330506897|ref|YP_004383325.1| 115 PGPrsqgflgmNPLPALEELVRVTRPGGTVA 145
                                       87344455555*****************986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6
                                       C-..CCHHHHHHHHHHH CS
                   Methyltransf_11  73 hv..edpekalkeiaRv 87 
                                           e++ +  +e  Rv
  gi|330506897|ref|YP_004383325.1| 230 GRaaEELPEKERENFRV 246
                                       33333333333333333 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   3.4e-13   4.7e-10      47     156 ..      33     151 ..       6     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.4e-13
                                       -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEEE CS
                   Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvtv 122
                                       +g++ lDva+G gD ++ l+++++  g v ++Di ++ L  + + +k  g + ++ flq++   +pf d  fD v  
  gi|330506897|ref|YP_004383325.1|  33 PGSRGLDVACGNGDHSLWLARAAKPDGCVFGIDICKEGLVRAIESAKSAGLKgELAFLQGDVCSIPFPDHIFDWVWC 109
                                       68899*********************************************999*********************988 PP

                                       ES-G....GG-....S-HHHHHHHHHHHEEEEEEEEEEEE-- CS
                   Ubie_methyltran 123 sfGl....rnv....tDklkaLkeayrvlkpGGrlvvlefsk 156
                                       +  l    r       + l aL+e+ rv +pGG++  l  s 
  gi|330506897|ref|YP_004383325.1| 110 ADCLwpgpRSQgflgMNPLPALEELVRVTRPGGTVALLFWSS 151
                                       765511114431111245679**************9997775 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   5.1e-08     7e-05      26     110 ..      19     103 ..       4     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.1e-08
                             GCD14  26 taDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvc 102
                                        + +s  i  L l pGs+ ++   G g  s  +ar+ +P G +f ++  ++   +a+e  ++ +l++ +   + Dvc
  gi|330506897|ref|YP_004383325.1|  19 EPAVSSAISLLPLVPGSRGLDVACGNGDHSLWLARAAKPDGCVFGIDICKEGLVRAIESAKSAGLKGELAFLQGDVC 95 
                                       56678888999****************************************************************** PP

                             GCD14 103 keGfdeev 110
                                       +  f +++
  gi|330506897|ref|YP_004383325.1|  96 SIPFPDHI 103
                                       99997766 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.4e-07    0.0012      62     132 ..      22      93 ..       6      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.4e-07
                                       HHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES- CS
                              PCMT  62 valalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgD 132
                                       v+ a+ ll l +g+r L+v +G G ++  lar  +++g v +i+  ke   +a +  k  +l+ ++++  gD
  gi|330506897|ref|YP_004383325.1|  22 VSSAISLLPLVPGSRGLDVACGNGDHSLWLARAAKPDGCVFGIDICKEGLVRAIESAKSAGLKgELAFLQGD 93 
                                       5678899****************************************9999999999999888788888777 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   1.2e-05     0.016       6      51 ..      38      84 ..      34     104 .. 0.85
   2 ?   -1.4   0.0         1   1.4e+03      41      60 ..     232     251 ..     226     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                      EEET-TTSHHHHHHHH.HSTTSEEEEEES-HHHHHHHHHHHHHCTTS CS
                    Methyltransf_4  6 leiGcGkGeflvalAk.knPdknflGiEirvkvvakvlkkiealelk 51
                                      l++ cG+G++ + lA  ++Pd  ++Gi+i ++++ +++++++  +lk
  gi|330506897|ref|YP_004383325.1| 38 LDVACGNGDHSLWLARaAKPDGCVFGIDICKEGLVRAIESAKSAGLK 84
                                      79*************7368********************99998876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1
                                       HHHHHHHCTTSSEEEEES-C CS
                    Methyltransf_4  41 vlkkiealelkNlrilrgda 60 
                                       + ++  ++e +N+r+l+++ 
  gi|330506897|ref|YP_004383325.1| 232 AAEELPEKERENFRVLCSNC 251
                                       45566677999******997 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00026      0.36       1      97 [.      38     142 ..      38     144 .. 0.69
   2 ?   -0.3   0.0       1.3   1.8e+03       8      37 ..     230     259 ..     229     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrenn.nnnnvelealdlldldggssfDlvvasnv 75 
                                       L++ cG+G+ +  l+++  pd  + g+Di ++ +++a e  ++ + +   ++++ +++++   d  + fD v+++++
  gi|330506897|ref|YP_004383325.1|  38 LDVACGNGDHSLWLARAAkPDGCVFGIDICKEGLVRAIESAKSAGLKgELAFLQGDVCSIPFPD--HIFDWVWCADC 112
                                       8*************99998999999*********777776666665414455555555554333..68999999988 PP

                   Methyltransf_12  76 lhhl........kdirevldnirklLkpgG 97 
                                       l            ++  +l+++ ++ +pgG
  gi|330506897|ref|YP_004383325.1| 113 LWPGprsqgflgMNPLPALEELVRVTRPGG 142
                                       744445555555555556666666666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.3
                   Methyltransf_12   8 Gsllrallekl.pdieytgvDispsaiedak 37 
                                       G+ +++l ek  ++ +++++  s+++i +a 
  gi|330506897|ref|YP_004383325.1| 230 GRAAEELPEKErENFRVLCSNCSADFI-AAN 259
                                       556666666667899999999999999.443 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.1   1.6e+03      15      28 ..       9      22 ..       8      27 .. 0.81
   2 ?   10.5   0.0   0.00026      0.36      77     124 ..      59     106 ..      46     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                                      HHHHHHHHHTT--T CS
                           UPF0020 15 tLAaalvrlagwkp 28
                                      +LA+a++rl++   
  gi|330506897|ref|YP_004383325.1|  9 SLASAMHRLTEPAV 22
                                      59*******99866 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00026
                                       --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---E CS
                           UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdv 124
                                         ++g+D+ ++ + +a e a++ag++++ +f q d+++++ +++ +d 
  gi|330506897|ref|YP_004383325.1|  59 GCVFGIDICKEGLVRAIESAKSAGLKGELAFLQGDVCSIPFPDHIFDW 106
                                       4489**********************************9966666665 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.1e-05      0.11      12      55 ..      32      77 ..      24     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.1e-05
                              MetW 12 kpgsrvldlGcGdGellellkeekqvdg..rGleldeegvaecvak 55
                                       pgsr ld+ cG+G+   +l+   + dg   G+++ +eg++++++ 
  gi|330506897|ref|YP_004383325.1| 32 VPGSRGLDVACGNGDHSLWLARAAKPDGcvFGIDICKEGLVRAIES 77
                                      489************9999998887777336999999999998853 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 ?   10.8   0.0   9.2e-05      0.13     174     215 ..      96     144 ..      67     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.2e-05
                   Methyltransf_29 174 rlpyPsrsfdlihCsrCridwteedgil.......llevdRvlRpgGyf 215
                                        +p+P + fd + C+ C+ +  +++g l       l e+ Rv RpgG  
  gi|330506897|ref|YP_004383325.1|  96 SIPFPDHIFDWVWCADCLWPGPRSQGFLgmnplpaLEELVRVTRPGGTV 144
                                       58******************999999865455555789********964 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00031      0.43       2      75 ..      41     109 ..      40     146 .. 0.69
   2 ?   -1.8   0.0       4.5   6.3e+03      49      74 ..     223     248 ..     177     270 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                   Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfi 75 
                                        +G  +G  +lwl+ra++  g   ++ +d +++   +a + a++agl+  + ++++d  +    + +  +D++++
  gi|330506897|ref|YP_004383325.1|  41 ACG--NGDHSLWLARAAKPDG--CVFGIDICKEgLVRAIESAKSAGLKGELAFLQGDVCSI--PFPDHIFDWVWC 109
                                       689..*************999..6******9954444666677799999999999998665..333344666665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.5
                   Methyltransf_24  49 drvrlikadseealaslaagsiDllf 74 
                                         ++++ +++ e+l++ +++ + +l 
  gi|330506897|ref|YP_004383325.1| 223 LCFQMLWGRAAEELPEKERENFRVLC 248
                                       34555666666666666655666555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.22      30     100 ..      32     106 ..      14     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                                       CTCSEEEEET-TTSHHHHHHHHHT.TC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTT.STTS-EEE CS
                               MTS  30 elsgkvlDlGcGaGvlgaalakes.peaevtlvdvdarAlesakenleankle..vevvasdvlee.veekkfdl 100
                                           + lD++cG+G  +++la++  p+  v  +d+ ++ l  a e +++ +l+  + +++ dv +  ++++ fd+
  gi|330506897|ref|YP_004383325.1|  32 VPGSRGLDVACGNGDHSLWLARAAkPDGCVFGIDICKEGLVRAIESAKSAGLKgeLAFLQGDVCSIpFPDHIFDW 106
                                       456678**************9875166669999999888888888888888886677888888764134555665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 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:                        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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2160.12
//
Query:       gi|330506898|ref|YP_004383326.1|  [L=252]
Description: zinc/iron ZIP family permease [Methanosaeta concilii GP6]
Scores for complete 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-24   84.3  22.1    2.5e-20   73.0   5.5    2.4  2  Zip       ZIP Zinc transporter
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.27   11.2   0.0    1.5  1  SLATT_1   SMODS and SLOG-associating 2TM effector domain 1


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   8.9   2.3e-07    0.0021       5     100 ..      10      91 ..       4      99 .. 0.77
   2 !   73.0   5.5   2.8e-24   2.5e-20     174     330 ..      95     243 ..      89     249 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-07
                               Zip   5 ilaiiaililsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealealeesqleeehthplagll 81 
                                        l+++a l++++ +l++ +++p    +++ + lsl l fa+Gv+++ +f++L+  ++  l+           +a l+
  gi|330506898|ref|YP_004383326.1|  10 ALSLFAGLATGIGSLIS-YFIP----RPDMRYLSLSLGFAAGVMVYVGFVDLFCSSRIVLGF---------GYANLF 72 
                                       34444444444433333.3334....389999*************************99998.........79**** PP

                               Zip  82 vllGflllllveklltmiv 100
                                       +l+G++l++l+++l+ +i+
  gi|330506898|ref|YP_004383326.1|  73 FLMGLVLIYLLDHLIPHIH 91 
                                       ***************9985 PP

  == domain 2  score: 73.0 bits;  conditional E-value: 2.8e-24
                               Zip 174 edkeklaslkvraiilllglilHsfidGLAlG..vssssstgislfiAvllHelpeelglgaiLlkaglsrkkavll 248
                                       + ++++ +l   +i+ ++g+ +H++++G+ ++    ++   g+++ iA+ +H++pe+l+  ++L+ a  +r+k  l+
  gi|330506898|ref|YP_004383326.1|  95 QVDSQCDRLYRSGIMTTIGIAIHNLPEGMTVAlvSLADLRLGVPVAIAIAIHNIPEGLACSIPLYCATSDRRKSCLI 171
                                       577888999999********************9778999************************************** PP

                               Zip 249 nllfaltaplGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllG 325
                                       +++ ++t plG++++il   i     ++++ +   ++ aG+++  ++ el+p  ++n       + ++  ++gl++G
  gi|330506898|ref|YP_004383326.1| 172 SFAAGMTEPLGAVLAIL---ILYPFLNDWLLAAATSMVAGIMVFLSFDELIP--IANRY-----GGEHTTNIGLIAG 238
                                       *****************...666677899999999999**************..44444.....5678888888888 PP

                               Zip 326 falml 330
                                       f++m+
  gi|330506898|ref|YP_004383326.1| 239 FLVMM 243
                                       88886 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 ?   11.2   0.0     3e-05      0.27      19      81 ..     163     225 ..     160     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3e-05
                           SLATT_1  19 eneraakrwrlllillellalllaalrafgelsvdlvgvlaavaaallaWlelkqyeelaaaY 81 
                                       + +r++  ++ +  + e l+++la+l  ++ l+ +l++++++++a ++ +l + ++ + a +Y
  gi|330506898|ref|YP_004383326.1| 163 SDRRKSCLISFAAGMTEPLGAVLAILILYPFLNDWLLAAATSMVAGIMVFLSFDELIPIANRY 225
                                       56788888899999999*************99999*******************999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1780.35
//
Query:       gi|330506899|ref|YP_004383327.1|  [L=220]
Description: hypothetical protein MCON_0693 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-58  197.2   1.0    1.8e-58  197.0   1.0    1.1  1  DUF2202   Uncharacterized protein domain (DUF2202)


Domain annotation for each model (and alignments):
>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.0   1.0   9.9e-63   1.8e-58       1     160 [.      62     219 ..      62     220 .] 0.99

  Alignments for each domain:
  == domain 1  score: 197.0 bits;  conditional E-value: 9.9e-63
                           DUF2202   1 ekdsllymreeeklarDvYlelYdrwklqiflniakseqthtdavksllekYeledpvkederGkfedeelqelYnk 77 
                                       e d+ll+m eeekla DvY  l + w++++f+ni ++e th  avk+ll++Y+l+dp   +  G f +e+lq+lYn+
  gi|330506899|ref|YP_004383327.1|  62 EVDGLLFMIEEEKLAGDVYSALDEMWDMRVFENIGRAELTHQAAVKRLLDRYSLPDPRMGE--GEFANETLQDLYND 136
                                       6799*******************************************************99..************** PP

                           DUF2202  78 LvekgsksledaLkvgatiedldiaDlekalketdnkdikevYenllkGsrnhlRsfvrkleergkeYepqyiseee 154
                                       L++kgs+s+ daL++ga ie++di Dle+++ +td++di  vY nll+Gs+nhlR+fv++le++  eY+pqy+seee
  gi|330506899|ref|YP_004383327.1| 137 LLAKGSTSVSDALMAGAAIEEIDILDLEEYMAQTDKEDILLVYANLLRGSENHLRAFVNNLERQRVEYTPQYLSEEE 213
                                       ***************************************************************************** PP

                           DUF2202 155 fdeivs 160
                                       +  i++
  gi|330506899|ref|YP_004383327.1| 214 YRSIME 219
                                       ***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1619.74
//
Query:       gi|330506900|ref|YP_004383328.1|  [L=395]
Description: cation diffusion facilitator family transporter [Methanosaeta concilii GP6]
Scores for complete 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-32  111.0  12.5    7.2e-32  110.7  12.5    1.1  1  Cation_efflux  Cation efflux family
    5.1e-15   55.4   0.3    8.8e-15   54.6   0.3    1.4  1  ZT_dimer       Dimerisation domain of Zinc Transporter
    1.4e-11   44.5   0.0    2.3e-11   43.9   0.0    1.3  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
  ------ inclusion threshold ------
        2.6    7.8   6.6       0.14   12.0   0.7    1.9  2  Trp_oprn_chp   Tryptophan-associated transmembrane protein (T


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 !  110.7  12.5   1.6e-35   7.2e-32       3     199 .]       7     194 ..       5     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 1.6e-35
                     Cation_efflux   3 lsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllll 79 
                                       +sll+nl+l +++l++ +l++Slal ada+hs +d++++l l+l++k+s ++ +e fp G++++e+l+++  + ll+
  gi|330506900|ref|YP_004383328.1|   7 YSLLFNLALVAAKLTLSALSGSLALRADAIHSTVDVMASLALILGVKISERK-SESFPLGLYKVENLASIAISFLLF 82 
                                       799**********************************************665.699********************* PP

                     Cation_efflux  80 glavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvs 156
                                       ++a+ ++lea+        + ++ g++l  +++ + + +++  + +++g++++s++l a+ +++  D+lts  v ++
  gi|330506900|ref|YP_004383328.1|  83 LTAYEIVLEAVRGEA---LPINYQGWVLYAVAAIIPLPYLFGSFQIKVGERTGSPSLIADGVQHKADVLTSSLVFLA 156
                                       ***********9877...79********************************************************* PP

                     Cation_efflux 157 alvillfnlksgplaDpvaslligliilysalkllkeslseLl 199
                                       ++ + +  l+    +D +a+++i+l+i++ ++++l++ +++Ll
  gi|330506900|ref|YP_004383328.1| 157 LIAQSIS-LP----LDRIAAVIIALVIVKEGWGILVDGMRVLL 194
                                       ******6.66....9**************************97 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.3     2e-18   8.8e-15       2      78 ..     199     274 ..     198     275 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 2e-18
                                       ...HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                          ZT_dimer   2 deeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                       d +++++ir++i++ p+v+++++l +r+sG+++fv+ ++ +     +k+aH  ++++e rik+e+p+v +v iH+eP
  gi|330506900|ref|YP_004383328.1| 199 DAQTLKRIRALILEAPEVVSIKELVARNSGRYLFVQADLILR-LVDLKRAHLASERIESRIKRELPQVDRVQIHYEP 274
                                       67899************************************5.56******************************** 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 !   43.9   0.0   5.1e-15   2.3e-11       2      94 ..     290     386 ..     289     387 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 5.1e-15
                                       TSCB-STCCC-SEEEEEEESSSCEEEEEEE..E.GCCCTSSCSSTHHHHHHHHTT-SEEEESSS..CHHHHHHHCTT CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenr..veeaadaegggggklaqllaeegvdvvivgki..Gpralakleaa 74 
                                       g+r++ hFG++ yFa++e++ +e k+v ++   ++++d ++g+g k+aq+l   + dvv+  +   G+++  ++++a
  gi|330506900|ref|YP_004383328.1| 290 GGRLSRHFGESSYFALVEMDFEEMKLVRQEiiANPHKDLSKGKGLKVAQFLLGFKPDVVFSIEGleGKGPGYAFAEA 366
                                       6899*************************************************9999998866557*********** PP

                                       TSEEEES-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  75 gievykgaggtveealkevl 94 
                                       g+e +++ ++t+ee ++++l
  gi|330506900|ref|YP_004383328.1| 367 GVETVQTDAETLEELMADLL 386
                                       ***************99876 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 ?   -3.1   0.7       1.3   5.6e+03      75      88 ..      14      27 ..       3      54 .. 0.55
   2 ?   12.0   0.7   3.1e-05      0.14      36     105 ..     138     209 ..     123     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
                      Trp_oprn_chp 75 alagagaavaalsl 88
                                      al++a ++++als+
  gi|330506900|ref|YP_004383328.1| 14 ALVAAKLTLSALSG 27
                                      33333333333332 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.1e-05
                      Trp_oprn_chp  36 lsGadwapaltalAlvllAaav..Avlavrglgrrvvgvllalagagaavaalslltdpadaaraaaaaatg 105
                                       ++G +  + +   +lv lA ++    l + +++ ++++++++  g g++v ++++l+d++  a++ ++ +++
  gi|330506900|ref|YP_004383328.1| 138 ADGVQHKADVLTSSLVFLALIAqsISLPLDRIAAVIIALVIVKEGWGILVDGMRVLLDASVDAQTLKRIRAL 209
                                       566666666666677777766611556789****************************87766665544344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2893.46
//
Query:       gi|330506901|ref|YP_004383329.1|  [L=159]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   76.9   0.0    1.6e-21   76.4   0.0    1.3  1  Nitro_FeMo-Co    Dinitrogenase iron-molybdenum cofactor
  ------ inclusion threshold ------
      0.033   14.3   0.5      0.042   13.9   0.5    1.1  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
      0.067   12.8   0.3       0.26   10.8   0.2    1.8  2  PrpR_N           Propionate catabolism activator
       0.08   12.6   0.0      0.095   12.3   0.0    1.1  1  NIF3             NIF3 (NGG1p interacting factor 3)


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 !   76.4   0.0   3.6e-25   1.6e-21       3      94 ..      14     103 ..      12     104 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 3.6e-25
                                       SCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEE CS
                     Nitro_FeMo-Co   3 srvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievy 79 
                                         +d++FGr+p+F+i+++e+ ++  + n    + +a +g+g+++aq +a +g+ ++i+g++Gp+a++ l+aa+i+vy
  gi|330506901|ref|YP_004383329.1|  14 APMDPRFGRCPFFVIVDTESMSEISIANS---NVNATSGAGIQAAQEIARQGAAALITGNVGPNAMQTLSAANIDVY 87 
                                       6789*****************99999999...9******************************************** PP

                                       ES.-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  80 kg.aggtveealkevl 94 
                                       +   +g+v++++++++
  gi|330506901|ref|YP_004383329.1|  88 QYqGAGSVRDVVEKFK 103
                                       *99**********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 ?   13.9   0.5   9.3e-06     0.042      18      69 ..      43     104 ..      30     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.3e-06
                                       EEEEGGGCHHHHHHHHHHH...........HHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTT CS
                   Semialdhyde_dhC  18 tyqavSGaGkkgvreLlkq...........vaelqrsdeakpgvfgvpiagNlipyidkeedk 69 
                                        + a+SGaG ++ +e+++q            ++ q   +a+ +v++++ ag++   + k++ +
  gi|330506901|ref|YP_004383329.1|  43 NVNATSGAGIQAAQEIARQgaaalitgnvgPNAMQTLSAANIDVYQYQGAGSVRDVVEKFK-R 104
                                       5789****************99999999987888888899999999999999987777755.4 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1     0.091   4.1e+02      12      34 ..      46      68 ..      39      72 .. 0.82
   2 ?   10.8   0.2   5.9e-05      0.26      88     129 ..      75     116 ..      51     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.091
                            PrpR_N 12 gdleeavelakeleaegvdviiS 34
                                      ++  +++++a+e++++g+ ++i+
  gi|330506901|ref|YP_004383329.1| 46 ATSGAGIQAAQEIARQGAAALIT 68
                                      56678999999999999999997 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 5.9e-05
                            PrpR_N  88 tlselldldieiytinseeeaeaavkelkaegvevvvGdgvv 129
                                        ++ l   +i++y+++ + +++++v++ k+   + + G  v 
  gi|330506901|ref|YP_004383329.1|  75 AMQTLSAANIDVYQYQGAGSVRDVVEKFKRGELQKIAGASVP 116
                                       45666678**************************99998775 PP

>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.1e-05     0.095     174     219 ..      42      87 ..      22     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                              NIF3 174 kkvaicaGsGaslieeakakgaDlliTGelkhhealdakekgiavi 219
                                       ++v   +G+G +  +e++++ga +liTG +  ++++++ +++i v+
  gi|330506901|ref|YP_004383329.1|  42 SNVNATSGAGIQAAQEIARQGAAALITGNVGPNAMQTLSAANIDVY 87 
                                       578899************************9999999988888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1221.79
//
Query:       gi|330506902|ref|YP_004383330.1|  [L=119]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-22   78.7   0.0    3.7e-22   78.5   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 !   78.5   0.0   2.1e-26   3.7e-22       2      94 ..      14     101 ..      13     102 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 2.1e-26
                                       TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEE CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagiev 78 
                                       ++ ++qhFGrap+F++++++++e+ ++ n      +++ gg g + +++ +egv+v+ivg+ Gp+a++++++agi+v
  gi|330506902|ref|YP_004383330.1|  14 DEAICQHFGRAPTFTVVDLNDNEICVLPNV-----SEHMGGTGLPTETIFAEGVQVLIVGGLGPKAVMAFSEAGIDV 85 
                                       689*****************9999999999.....8899999*********************************** PP

                                       EES-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  79 ykgaggtveealkevl 94 
                                       ++ga gtv++a+++++
  gi|330506902|ref|YP_004383330.1|  86 FVGATGTVKDAIDDWR 101
                                       *************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 903.41
//
Query:       gi|330506903|ref|YP_004383331.1|  [L=287]
Description: iron sulfur cluster/nucleotide binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-17   62.8   0.0    4.8e-17   62.2   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.1e-15   57.7   0.2      3e-06   26.9   0.0    3.1  2  ParA         NUBPL iron-transfer P-loop NTPase
    9.6e-14   50.8  10.9    9.8e-07   28.6   1.8    2.5  2  Fer4_6       4Fe-4S binding domain
    3.6e-13   48.7  12.0    1.2e-06   28.1   2.6    2.5  2  Fer4         4Fe-4S binding domain
    4.3e-09   36.5   0.0     0.0024   17.8   0.0    2.1  2  AAA_31       AAA domain
    2.7e-07   31.1   9.7     0.0044   17.6   3.1    2.4  2  Fer4_7       4Fe-4S dicluster domain
    3.7e-07   30.2   9.3    7.9e-07   29.1   9.3    1.6  1  Fer4_21      4Fe-4S dicluster domain
    9.2e-07   28.6  11.8    0.00013   21.8   2.9    2.7  2  Fer4_2       4Fe-4S binding domain
    1.3e-06   28.4  11.5    1.9e-05   24.6  11.6    2.3  2  Fer4_10      4Fe-4S dicluster domain
      7e-06   26.9   8.7     0.0015   19.4   0.7    2.4  2  Fer4_16      4Fe-4S double cluster binding domain
    6.4e-05   23.0  14.2    0.00033   20.8  12.7    2.4  2  Fer4_9       4Fe-4S dicluster domain
     0.0019   17.6   0.0      0.047   13.0   0.0    2.1  2  MipZ         ATPase MipZ
      0.002   18.5  13.1      0.047   14.2   1.9    2.9  2  Fer4_4       4Fe-4S binding domain
     0.0022   18.4  10.8       0.11   13.0   1.1    2.5  2  Fer4_8       4Fe-4S dicluster domain
     0.0022   17.5   0.2       0.33   10.4   0.0    2.2  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
     0.0033   17.9  11.6       0.27   11.8   3.0    2.6  2  Fer4_17      4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   14.9   1.6      0.031   13.5   0.6    2.1  3  ArsA_ATPase  Anion-transporting ATPase
      0.056   13.0   0.4       0.25   10.9   0.2    1.9  2  AAA_25       AAA domain
      0.069   13.9   5.6        3.9    8.3   1.4    2.7  2  Fer4_15      4Fe-4S single cluster domain
      0.071   14.1  26.9      0.084   13.8   5.8    2.9  2  Fer4_3       4Fe-4S binding domain
        0.1   12.1   0.0       0.14   11.6   0.0    1.3  1  PhoH         PhoH-like protein
        0.2   12.5   9.7        3.1    8.7   1.4    2.4  2  Fer4_22      4Fe-4S dicluster domain
          1   10.0  12.7        3.3    8.3   2.3    2.7  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0   6.1e-20   4.8e-17       2     126 ..       4     257 ..       3     259 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 6.1e-20
                                       EEEESSTTSSHHHHHHHHHHHHHH.TT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   2 aiastkGGvGKTtlaanLaralar.rglrVllvDaDpqannlaileglendiep....................... 54 
                                       +ias+kGG+GKT ++++La++l   +  r++  D+D++ +n+++++ ++  +e+                       
  gi|330506903|ref|YP_004383331.1|   4 SIASGKGGTGKTLVSTSLAASLYSlGDGRIAIADCDVEEPNSHLFFPDRTLLEKescqvavpvideelcthcgkcse 80 
                                       79********************997889***************955555555555568999**************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|330506903|ref|YP_004383331.1|  81 vcayhalavlpgtvlifpelchgcgacsiicpekaisegsrsigeifharsggmdivwgelalgearttplikavkq 157
                                       ***************************************************************************** PP

                                       .........................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...- CS
                                       .........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 .........................................dlkrllellealgkkkalllkiagvvlnrvdgenee 90 
                                                                                dl+  l++l +++++         v++n+ +    +
  gi|330506903|ref|YP_004383331.1| 158 raqgdtvivdcppgtscsmvesvrgsdfcllvteptpfglyDLDIALKVLDKMKIP-------QAVLVNKSGVG--D 225
                                       ******************************************************99.......67*****9999..9 PP

                                       TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  91 tllkealeelkqrygvpvlgviprdeavaeaparge 126
                                       ++l+  lee     ++p+l +ip d ++ae++++ge
  gi|330506903|ref|YP_004383331.1| 226 RKLYHYLEEK----KIPLLMEIPLDRKIAEIYSQGE 257
                                       *******997....8*****************9986 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   3.9e-09     3e-06       6      52 ..       3      50 ..       1      78 [. 0.77
   2 !   24.8   0.1   1.7e-08   1.3e-05     111     243 ..     160     275 ..     124     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.9e-09
                              ParA  6 iavlSgKGGVGKStvavnlAlaLakkgl.kvgllDaDiyGpsiprllg 52
                                      + ++SgKGG GK+ v+++lA++L + g  ++++ D D+  p+   ++ 
  gi|330506903|ref|YP_004383331.1|  3 LSIASGKGGTGKTLVSTSLAASLYSLGDgRIAIADCDVEEPNSHLFFP 50
                                      789********************9887439********9998665554 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.7e-08
                              ParA 111 elDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekt 186
                                       + D +i+D+PPGt+    ++++++   + +++Vt p    l d   a+++++k+k++   +v N sg+         
  gi|330506903|ref|YP_004383331.1| 160 QGDTVIVDCPPGTS---CSMVESVrGSDFCLLVTEPTPFGLYDLDIALKVLDKMKIPQAVLV-NKSGVG-------- 224
                                       5699*********8...57777774456789**************************98776.555554........ PP

                              ParA 187 eifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiae 243
                                           + +  ++ ee ++pll eipld +i+e   +g+ +vl+ pe   ++ + e+a+
  gi|330506903|ref|YP_004383331.1| 225 ----DRKLYHYLEEKKIPLLMEIPLDRKIAEIYSQGEIFVLRMPE--WKERFVELAN 275
                                       ....34455778999**********************99999865..4455555554 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   1.8   1.3e-09   9.8e-07       1      24 []      64      87 ..      64      87 .. 0.94
   2 !   26.9   1.9   4.5e-09   3.5e-06       2      24 .]      94     116 ..      93     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.3e-09
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      v++id+++C++Cg+C  vC + a+
  gi|330506903|ref|YP_004383331.1| 64 VPVIDEELCTHCGKCSEVCAYHAL 87
                                      79******************9986 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 4.5e-09
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       v i p++C gCg+C ++CPe+ai
  gi|330506903|ref|YP_004383331.1|  94 VLIFPELCHGCGACSIICPEKAI 116
                                       6789*****************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   2.0   9.3e-09   7.3e-06       1      18 [.      65      82 ..      65      87 .. 0.92
   2 !   28.1   2.6   1.5e-09   1.2e-06       3      24 .]      96     117 ..      94     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 9.3e-09
                                      EEEETTTSSS-THHHHHS CS
                              Fer4  1 vvideekCigCGaCvevC 18
                                      +videe+C++CG+C evC
  gi|330506903|ref|YP_004383331.1| 65 PVIDEELCTHCGKCSEVC 82
                                      69**************** PP

  == domain 2  score: 28.1 bits;  conditional E-value: 1.5e-09
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                       i +e+C gCGaC  +CP  AI+
  gi|330506903|ref|YP_004383331.1|  96 IFPELCHGCGACSIICPEKAIS 117
                                       889*****************96 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.1e-06    0.0047       4      46 ..       3      46 ..       1      95 [. 0.76
   2 !   17.8   0.0   3.1e-06    0.0024     111     168 ..     152     211 ..     133     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.1e-06
                            AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgk.kvLlvDlDpQanatt 46
                                      ++ia  KGG GKT  s+ laa+l +lg  ++ + D+D  +  + 
  gi|330506903|ref|YP_004383331.1|  3 LSIASGKGGTGKTLVSTSLAASLYSLGDgRIAIADCDVEEPNSH 46
                                      589999*****************977643899999998776666 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.1e-06
                            AAA_31 111 lekvkde..YDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktieevk 168
                                       +++vk++   D +i+DcpP  ++ ++ ++  sd ++ +++++++ l+ l+  lk ++++k
  gi|330506903|ref|YP_004383331.1| 152 IKAVKQRaqGDTVIVDCPPGTSCSMVESVRGSDFCLLVTEPTPFGLYDLDIALKVLDKMK 211
                                       4444443337*************************************9999998888775 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   3.1   5.6e-06    0.0044      28      51 ..      62      85 ..      36      86 .. 0.75
   2 !   17.3   0.5   6.8e-06    0.0053       2      18 ..     101     117 ..      96     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.6e-06
                            Fer4_7 28 tekveidpekClgCgaCvavCPtg 51
                                      ++ ++id+e C++Cg+C +vC + 
  gi|330506903|ref|YP_004383331.1| 62 VAVPVIDEELCTHCGKCSEVCAYH 85
                                      356799***************765 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 6.8e-06
                            Fer4_7   2 CigCgaCvaaCpvkaie 18 
                                       C gCgaC   Cp kai+
  gi|330506903|ref|YP_004383331.1| 101 CHGCGACSIICPEKAIS 117
                                       99999999999999987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   9.3     1e-09   7.9e-07       2      57 ..      66     116 ..      65     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1e-09
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       +ide+ C +CgkC  +C    + a+ + + tv  +  + C GC  Cs++CP e++i
  gi|330506903|ref|YP_004383331.1|  66 VIDEELCTHCGKCSEVCA---YHALAVLPGTV-LIFPELCHGCGACSIICP-EKAI 116
                                       79***************9...89999998887.57899*************.6877 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   2.9   1.7e-07   0.00013       2      20 ..      64      82 ..      63      84 .. 0.93
   2 !   11.3   1.7   0.00039       0.3       7      22 .]      98     113 ..      93     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.7e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaC 20
                                      ++v+d++ C++Cg+C  +C
  gi|330506903|ref|YP_004383331.1| 64 VPVIDEELCTHCGKCSEVC 82
                                      799**************** PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00039
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                       ++ C gCgaC   CP+
  gi|330506903|ref|YP_004383331.1|  98 PELCHGCGACSIICPE 113
                                       789*******999**5 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6  11.6   2.5e-08   1.9e-05       3      56 .]      66     112 ..      64     112 .. 0.96
   2 !   16.3   1.7     1e-05    0.0081       4      24 ..      96     118 ..      93     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.5e-08
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       vid++ C++CgkC ++C a      + + a   ++v + +e C+gcgaC  +CP
  gi|330506903|ref|YP_004383331.1|  66 VIDEELCTHCGKCSEVC-A------YHALAVLPGTVLIFPELCHGCGACSIICP 112
                                       89***************.5......899*************************9 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1e-05
                           Fer4_10   4 idddtCirCgkCvkaCPadl..t 24 
                                       i ++ C +Cg+C   CP ++  +
  gi|330506903|ref|YP_004383331.1|  96 IFPELCHGCGACSIICPEKAisE 118
                                       66899*************66441 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   2.0   0.00068      0.53       2      17 ..      72      87 ..      71      92 .. 0.89
   2 !   19.4   0.7   1.9e-06    0.0015       2      22 ..     101     121 ..     100     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00068
                           Fer4_16  2 CgtCgkCaevCPtnai 17
                                      C+ CgkC evC  +a+
  gi|330506903|ref|YP_004383331.1| 72 CTHCGKCSEVCAYHAL 87
                                      ***********99987 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.9e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                       C++Cg+C  +CP++ai+e ++
  gi|330506903|ref|YP_004383331.1| 101 CHGCGACSIICPEKAISEGSR 121
                                       *****************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 !   12.6   4.6   0.00015      0.12      32      50 ..      68      86 ..      36      87 .. 0.75
   2 !   20.8  12.7   4.2e-07   0.00033       2      51 .]      72     116 ..      71     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                            Fer4_9 32 seeaCigCgaCveaCpkga 50
                                      +ee C++Cg+C e+C  +a
  gi|330506903|ref|YP_004383331.1| 68 DEELCTHCGKCSEVCAYHA 86
                                      2379***********9876 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 4.2e-07
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       Ct Cg+C e+C +++     ++  +  +      C+gCgaC  +Cp++ai
  gi|330506903|ref|YP_004383331.1|  72 CTHCGKCSEVCAYHALAVLPGTVLIFPE-----LCHGCGACSIICPEKAI 116
                                       *************999988888887763.....6*************987 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     6e-05     0.047       5      56 ..       5      57 ..       2      81 .. 0.84
   2 ?    2.4   0.0       0.1        80      95     138 ..     156     202 ..     142     215 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6e-05
                                      E--SSTTSSHHHHHHHHHHHHHTTT-.-EEEEE--TTT-HHHHHHHHHHHHHH CS
                              MipZ  5 lgnekGGsGksttavhvavaLlkkGa.rvaaidldlrqrtlarylenraatae 56
                                      ++  kGG+Gk+ ++  +a +L + G  r+a  d d+    ++ ++ +r+  ++
  gi|330506903|ref|YP_004383331.1|  5 IASGKGGTGKTLVSTSLAASLYSLGDgRIAIADCDVEEPNSHLFFPDRTLLEK 57
                                      6788*******************99659999**************99986544 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.1
                                       HHHHH-SEEEEE--.SS--HHHHHHHHT-S..EEEE.EEESSHHHHCC CS
                              MipZ  95 dleaeldfividtP.Gsdsalsrlahslad..tlvt.Plndsfvdfdl 138
                                       ++ a+ d +++d+P G+  +++ ++   +d   lvt P    + d+d+
  gi|330506903|ref|YP_004383331.1| 156 KQRAQGDTVIVDCPpGTSCSMVESVR-GSDfcLLVTePTPFGLYDLDI 202
                                       3456679******8254444444433.333124555455556666665 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   3.8    0.0043       3.4       2      14 ..      70      82 ..      69      84 .. 0.87
   2 !   14.2   1.9     6e-05     0.047       1      16 [.      98     113 ..      98     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0043
                            Fer4_4  2 erCigCgsCvaaC 14
                                      e C++Cg+C  +C
  gi|330506903|ref|YP_004383331.1| 70 ELCTHCGKCSEVC 82
                                      67*******9888 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6e-05
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       +e C gCg+C ++CP 
  gi|330506903|ref|YP_004383331.1|  98 PELCHGCGACSIICPE 113
                                       588************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 !   13.0   1.1   0.00014      0.11      49      63 ..      70      84 ..      41      86 .. 0.87
   2 !    9.4   2.7    0.0018       1.4      50      64 ..     100     114 ..      97     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                            Fer4_8 49 wsCttcgaCtevCpv 63
                                      + Ct+cg+C+evC  
  gi|330506903|ref|YP_004383331.1| 70 ELCTHCGKCSEVCAY 84
                                      579********9975 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0018
                            Fer4_8  50 sCttcgaCtevCpvg 64 
                                        C++cgaC+  Cp++
  gi|330506903|ref|YP_004383331.1| 100 LCHGCGACSIICPEK 114
                                       799999999999986 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00042      0.33       6      45 ..       7      47 ..       1     112 [. 0.84
   2 ?    5.4   0.0     0.014        11     190     246 ..     225     279 ..     205     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00042
                         Fer4_NifH  6 yGkGGiGksttsqnlsaalaemg.kkvlivGCDPkaDstrl 45
                                       GkGG Gk+  s+ l+a+l + g  ++ i  CD  +   +l
  gi|330506903|ref|YP_004383331.1|  7 SGKGGTGKTLVSTSLAASLYSLGdGRIAIADCDVEEPNSHL 47
                                      59********************9679*******77655544 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.014
                         Fer4_NifH 190 reliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkile 246
                                       +  + ++ ee ++++l  +P+d ++ +   + ++ +   pe++  + + ela++i e
  gi|330506903|ref|YP_004383331.1| 225 DRKLYHYLEEKKIPLLMEIPLDRKIAEIYSQGEIFVLRMPEWK--ERFVELANRIEE 279
                                       44567899999***********************999999999..9********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 !   11.8   3.0   0.00034      0.27      44      59 ..      70      85 ..      54      86 .. 0.88
   2 !   10.4   1.4   0.00095      0.74      44      58 ..      99     113 ..      96     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      +lC++Cg+C+++C ++
  gi|330506903|ref|YP_004383331.1| 70 ELCTHCGKCSEVCAYH 85
                                      68999****9999987 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00095
                           Fer4_17  44 slCieCgeCerkCPq 58 
                                       +lC++Cg C+  CP+
  gi|330506903|ref|YP_004383331.1|  99 ELCHGCGACSIICPE 113
                                       68999****999997 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6     4e-05     0.031       1      29 [.       1      29 [.       1      37 [. 0.83
   2 ?   -2.6   0.0       3.2   2.5e+03     122     136 ..     158     171 ..     149     184 .. 0.71
   3 ?   -1.2   0.0       1.2   9.2e+02     211     245 ..     188     222 ..     176     275 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                                      -EEEEEEESTTSSHHHHHHHHHHHHHHTT CS
                       ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekg 29
                                      +k+ + +GKGG GKt vs+++a+ l   g
  gi|330506903|ref|YP_004383331.1|  1 MKLSIASGKGGTGKTLVSTSLAASLYSLG 29
                                      5667889***************9986655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.2
                                       CSSSSEEEEESBSCC CS
                       ArsA_ATPase 122 eeeydvvvlDtaPTG 136
                                        ++ d+v++D +P G
  gi|330506903|ref|YP_004383331.1| 158 RAQGDTVIVDCPP-G 171
                                       5667999999988.4 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.2
                                       EEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE.E CS
                       ArsA_ATPase 211 lVvipEklslkEteRaikeLkkygikvdavivNk.l 245
                                       lV+ p    l++   a+k L k++i  +av+vNk  
  gi|330506903|ref|YP_004383331.1| 188 LVTEPTPFGLYDLDIALKVLDKMKIP-QAVLVNKsG 222
                                       67777788888888899999999987.678888843 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00032      0.25      34      58 ..       2      26 ..       1      41 [. 0.88
   2 ?   -0.5   0.0         1     8e+02     130     149 ..     148     167 ..     121     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                            AAA_25 34 elallaGapgtGKttlaldlalava 58
                                      +l++  G +gtGKt + ++la+++ 
  gi|330506903|ref|YP_004383331.1|  2 KLSIASGKGGTGKTLVSTSLAASLY 26
                                      58899*****************986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1
                            AAA_25 130 vdaleaaieevegvrlvviD 149
                                       +  l++a++++++ + v++D
  gi|330506903|ref|YP_004383331.1| 148 TTPLIKAVKQRAQGDTVIVD 167
                                       45689999999999999999 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   1.4     0.005       3.9       2      18 ..      66      82 ..      66      89 .. 0.91
   2 ?    6.8   0.2     0.014        11       6      20 ..      99     113 ..      94     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.005
                           Fer4_15  2 vvDrdaCigcglCvaea 18
                                      v+D+++C+ cg C +++
  gi|330506903|ref|YP_004383331.1| 66 VIDEELCTHCGKCSEVC 82
                                      69***********9998 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.014
                           Fer4_15   6 daCigcglCvaeape 20 
                                       ++C gcg+C   +pe
  gi|330506903|ref|YP_004383331.1|  99 ELCHGCGACSIICPE 113
                                       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 ?   13.8   5.8   0.00011     0.084       1      15 []      72      86 ..      72      86 .. 0.95
   2 ?   13.2   5.0   0.00017      0.13       1      15 []     101     115 ..     101     115 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct+Cg C evC ++A
  gi|330506903|ref|YP_004383331.1| 72 CTHCGKCSEVCAYHA 86
                                      ***********9987 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00017
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCgaC   CP++A
  gi|330506903|ref|YP_004383331.1| 101 CHGCGACSIICPEKA 115
                                       ************998 PP

>> PhoH  PhoH-like protein
   #    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      21      47 ..       3      29 ..       1      69 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                      EEEEE--TTSSTTHHHHHHHHHHHHTT CS
                              PhoH 21 ivfaiGpaGtGKtylavalavealkkk 47
                                      + +a G+ GtGKt+++++la+++++ +
  gi|330506903|ref|YP_004383331.1|  3 LSIASGKGGTGKTLVSTSLAASLYSLG 29
                                      77899***************9988765 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   1.4    0.0039       3.1      76      93 ..      66      83 ..      52      86 .. 0.78
   2 ?    7.9   1.6    0.0072       5.6      81      94 ..     100     113 ..      97     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0039
                           Fer4_22 76 kfgesgCvGCgRCieacp 93
                                       ++e+ C+ Cg+C+e+c 
  gi|330506903|ref|YP_004383331.1| 66 VIDEELCTHCGKCSEVCA 83
                                      458899999999999997 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0072
                           Fer4_22  81 gCvGCgRCieacpv 94 
                                        C GCg C+  cp+
  gi|330506903|ref|YP_004383331.1| 100 LCHGCGACSIICPE 113
                                       57788888777776 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.3    0.0042       3.3       1      16 [.      67      82 ..      67      85 .. 0.93
   2 ?    6.2   2.9      0.02        16       4      18 ..      99     113 ..      98     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0042
                           Fer4_13  1 VDrdtCiacgaCvela 16
                                      +D++ C+ cg+C e++
  gi|330506903|ref|YP_004383331.1| 67 IDEELCTHCGKCSEVC 82
                                      899***********99 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.02
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                       + C +cgaC  ++P+
  gi|330506903|ref|YP_004383331.1|  99 ELCHGCGACSIICPE 113
                                       56************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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 0.22s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2150.04
//
Query:       gi|330506904|ref|YP_004383332.1|  [L=284]
Description: iron sulfur cluster/nucleotide binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   0.0    2.7e-16   59.8   0.0    1.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
      1e-11   44.1  13.0    9.2e-07   28.4   2.5    2.8  2  Fer4         4Fe-4S binding domain
    2.7e-09   37.5   3.1     0.0018   18.8   0.2    2.5  2  Fer4_7       4Fe-4S dicluster domain
    4.7e-09   35.8  11.4    0.00012   21.9   1.8    2.8  2  Fer4_2       4Fe-4S binding domain
    2.6e-08   33.6   0.2     0.0065   16.0   0.0    2.7  2  ParA         NUBPL iron-transfer P-loop NTPase
    2.9e-08   33.4  11.8    0.00016   21.6   2.2    2.6  2  Fer4_6       4Fe-4S binding domain
    5.3e-07   30.5   2.7      0.013   16.4   0.2    2.4  2  Fer4_16      4Fe-4S double cluster binding domain
    5.9e-07   29.5  13.0    2.3e-06   27.6  13.0    2.1  1  Fer4_21      4Fe-4S dicluster domain
    6.8e-06   26.1   0.2       0.02   14.8   0.0    2.2  2  AAA_31       AAA domain
      2e-05   24.7  10.4     0.0013   18.9  11.6    2.4  3  Fer4_9       4Fe-4S dicluster domain
    4.3e-05   23.6  12.6      0.013   15.6   1.1    2.6  2  Fer4_10      4Fe-4S dicluster domain
    0.00017   21.5   0.4      0.044   13.7   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
     0.0025   17.7   0.8       0.35   10.6   0.0    2.8  2  AAA_26       AAA domain
     0.0031   17.9   0.0      0.008   16.6   0.0    1.7  1  AAA_16       AAA ATPase domain
     0.0031   18.2   6.5       0.29   11.9   0.2    2.6  2  Fer4_15      4Fe-4S single cluster domain
     0.0077   16.7  12.8        0.1   13.1   2.9    2.4  2  Fer4_8       4Fe-4S dicluster domain
     0.0087   16.5  16.6       0.17   12.5   4.6    2.7  2  Fer4_4       4Fe-4S binding domain
  ------ inclusion threshold ------
      0.011   15.4   0.5          2    8.0   0.0    2.4  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.012   15.1   0.5      0.024   14.2   0.0    1.7  2  GTP_EFTU     Elongation factor Tu GTP binding domain
      0.022   15.3  11.4       0.92   10.1   4.1    2.4  3  Fer4_17      4Fe-4S dicluster domain
      0.023   15.6  15.8       0.68   11.0   5.4    2.7  2  Fer4_3       4Fe-4S binding domain
      0.024   13.9   1.6      0.078   12.1   1.3    1.9  2  ArsA_ATPase  Anion-transporting ATPase
      0.026   14.1   0.1       0.25   10.9   0.0    2.1  2  AAA_25       AAA domain
      0.041   13.5   0.1        1.5    8.4   0.1    2.8  3  SRP54        SRP54-type protein, GTPase domain
      0.081   12.6   1.0       0.21   11.3   0.2    1.9  2  AAA_30       AAA domain
       0.13   12.0   0.3       0.58    9.9   0.0    2.0  2  RuvB_N       Holliday junction DNA helicase RuvB P-loop domai
       0.15   11.2   0.2         16    4.6   0.3    2.2  2  NB-ARC       NB-ARC domain
       0.28   11.8  12.6        2.5    8.7   4.5    2.7  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
        3.4    8.6  12.5        4.6    8.2   1.9    2.3  2  Fer4_22      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   4.4e-19   2.7e-16       1     124 [.       4     258 ..       4     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 4.4e-19
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       +ai+s+kGG+GKT++ a+La+ lar g+ V   D+D++a+ l+++ + e+ +++                       
  gi|330506904|ref|YP_004383332.1|   4 VAIVSGKGGTGKTSIIASLAA-LAR-GKAV-FADCDVDAPDLHLILQPEILERRefygikrafidkekciqcgicqd 77 
                                       69******************9.666.5655.67**********988888888889999******************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|330506904|ref|YP_004383332.1|  78 scrfgaiadfevetplcegcgvcqlvcpedavdmrdvqageayisqtrfgpmvhaelypgeeasgklvamvremard 154
                                       ***************************************************************************** PP

                                       ............................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS. CS
                                       ............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ............................................dlkrllellealgkkkalllkiagvvlnrvdge 87 
                                                                                   dl rll ++ ++g+k         v +n++d +
  gi|330506904|ref|YP_004383332.1| 155 laaeknldlilidgspgigcpviasltgvdlalvvteptvtgehDLVRLLDVADHFGIK-------TTVCINKYDLN 224
                                       ***********************************************************.......89********9 PP

                                       ..-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  88 neetllkealeelkqrygvpvlgviprdeavaeapar 124
                                           +    +eel+ + gv++ g +p+ ++v+ea  +
  gi|330506904|ref|YP_004383332.1| 225 P---EAARKIEELCGKRGVKIAGRLPYHTSVIEAMVK 258
                                       4...4455566666666****************9876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   2.5   1.5e-09   9.2e-07       2      23 ..      63      84 ..      62      85 .. 0.95
   2 !   20.5   3.0   4.8e-07   0.00029       7      23 ..      93     109 ..      87     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.5e-09
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                       id+ekCi CG+C + C +gAI
  gi|330506904|ref|YP_004383332.1| 63 FIDKEKCIQCGICQDSCRFGAI 84
                                      69*******************9 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 4.8e-07
                                       TSSS-THHHHHSTTTEE CS
                              Fer4   7 kCigCGaCvevCPvgAI 23 
                                       +C gCG C  vCP +A 
  gi|330506904|ref|YP_004383332.1|  93 LCEGCGVCQLVCPEDAV 109
                                       7**************96 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   2.9e-06    0.0018      26      52 .]      57      83 ..      33      84 .. 0.74
   2 !   18.7   0.3   3.2e-06     0.002       2      24 ..      94     116 ..      93     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.9e-06
                            Fer4_7 26 kgtekveidpekClgCgaCvavCPtga 52
                                       g++++ id ekC++Cg C++ C +ga
  gi|330506904|ref|YP_004383332.1| 57 YGIKRAFIDKEKCIQCGICQDSCRFGA 83
                                      3678899999*************9987 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 3.2e-06
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeen 24 
                                       C gCg C+ +Cp +a+++++++ 
  gi|330506904|ref|YP_004383332.1|  94 CEGCGVCQLVCPEDAVDMRDVQA 116
                                       999999**99*999999998753 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.8     2e-07   0.00012       2      20 ..      61      79 ..      60      80 .. 0.93
   2 !   18.2   2.4   3.1e-06    0.0019       3      22 .]      87     106 ..      85     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaC 20
                                      ++++d ++Ci+Cg+C+++C
  gi|330506904|ref|YP_004383332.1| 61 RAFIDKEKCIQCGICQDSC 79
                                      579**************** PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.1e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       ++v+t  C gCg C+ +CP+
  gi|330506904|ref|YP_004383332.1|  87 FEVETPLCEGCGVCQLVCPE 106
                                       6789999************5 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 !   16.0   0.0     1e-05    0.0065       6      47 ..       4      42 ..       2      59 .. 0.75
   2 !   14.5   0.1   2.9e-05     0.018      97     225 ..     145     262 ..     140     280 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                              ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsi 47
                                      +a++SgKGG GK+++ ++lA+ La +g++v   D D+  p++
  gi|330506904|ref|YP_004383332.1|  4 VAIVSGKGGTGKTSIIASLAA-LA-RGKAV-FADCDVDAPDL 42
                                      79*****************96.43.34443.45666666655 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.9e-05
                              ParA  97 skaikqllkdvew.gelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvve 172
                                        ++++++ +d +  ++lD+++iD  PG g   ++ +    ++ a++Vt p     +d  + ++++++  +k    ++
  gi|330506904|ref|YP_004383332.1| 145 VAMVREMARDLAAeKNLDLILIDGSPGIGCPVIASLTG--VDLALVVTEPTVTGEHDLVRLLDVADHFGIKTTVCIN 219
                                       5788888888877358*************988766555..5789***********************9999876665 PP

                              ParA 173 Nmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkpl 225
                                              p+           + e+l+ + gv++ g++p ++++ ea+ + + +
  gi|330506904|ref|YP_004383332.1| 220 KYD--LNPEA--------ARKIEELCGKRGVKIAGRLPYHTSVIEAMVKAQAV 262
                                       433..33332........34456666666777777777777766666666654 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   2.2   2.6e-07   0.00016       2      24 .]      62      84 ..      61      84 .. 0.94
   2 !   16.6   2.3   9.7e-06     0.006       3      23 ..      88     108 ..      87     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.6e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + id++kCi+Cg C + C +gai
  gi|330506904|ref|YP_004383332.1| 62 AFIDKEKCIQCGICQDSCRFGAI 84
                                      679*****************998 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9.7e-06
                            Fer4_6   3 eidpdkCigCgdCvrvCPega 23 
                                       e+   +C gCg C  vCPe+a
  gi|330506904|ref|YP_004383332.1|  88 EVETPLCEGCGVCQLVCPEDA 108
                                       567789*************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 !   14.0   0.3   0.00012     0.073       1      17 [.      68      84 ..      47      92 .. 0.67
   2 !   16.4   0.2   2.2e-05     0.013       2      20 ..      94     112 ..      93     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00012
                           Fer4_16  1 rCgtCgkCaevCPtnai 17
                                      +C++Cg C ++C  +ai
  gi|330506904|ref|YP_004383332.1| 68 KCIQCGICQDSCRFGAI 84
                                      35555555555555555 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.2e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C +Cg C  vCP++a++++
  gi|330506904|ref|YP_004383332.1|  94 CEGCGVCQLVCPEDAVDMR 112
                                       999**********999887 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6  13.0   3.8e-09   2.3e-06       1      59 []      62     111 ..      62     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.8e-09
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                       A+id++kCi+Cg C  +C+     ai       ++v +  C GC +C  vCP ed+++m
  gi|330506904|ref|YP_004383332.1|  62 AFIDKEKCIQCGICQDSCR---FGAIA-----DFEVETPLCEGCGVCQLVCP-EDAVDM 111
                                       89*****************...56665.....5789999*************.899988 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1    0.0016      0.96       4      31 ..       4      29 ..       1      42 [. 0.76
   2 !   14.8   0.0   3.2e-05      0.02     114     165 ..     157     208 ..     132     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0016
                            AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgk 31
                                      +ai+  KGG GKT     laa    +gk
  gi|330506904|ref|YP_004383332.1|  4 VAIVSGKGGTGKTSIIASLAALA--RGK 29
                                      899**********9999998753..344 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.2e-05
                            AAA_31 114 vkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktie 165
                                        +++ D+i+iD +P +g+ ++ +L+  d  +++++++    + l +ll+  +
  gi|330506904|ref|YP_004383332.1| 157 AEKNLDLILIDGSPGIGCPVIASLTGVDLALVVTEPTVTGEHDLVRLLDVAD 208
                                       57899*******************************9999888888887665 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   2.3   0.00012     0.073      35      51 .]      68      84 ..      47      85 .. 0.64
   2 !   18.9  11.6     2e-06    0.0013       1      50 [.      68     108 ..      68     109 .. 0.93
   3 !   14.2   1.8   5.9e-05     0.037       2      23 ..      94     115 ..      93     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                            Fer4_9 35 aCigCgaCveaCpkgai 51
                                      +Ci+Cg C + C  gai
  gi|330506904|ref|YP_004383332.1| 68 KCIQCGICQDSCRFGAI 84
                                      66666666666666554 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2e-06
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       kC++Cg C+++C +g++ + ++e+           C gCg C  +Cp++a
  gi|330506904|ref|YP_004383332.1|  68 KCIQCGICQDSCRFGAIADFEVETP---------LCEGCGVCQLVCPEDA 108
                                       7****************99999887.........5************997 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 5.9e-05
                            Fer4_9   2 CtgCgaCveaCpagvvvedaae 23 
                                       C gCg C+ +Cp ++v +++++
  gi|330506904|ref|YP_004383332.1|  94 CEGCGVCQLVCPEDAVDMRDVQ 115
                                       9999999999999999777665 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   4.4   0.00023      0.14       3      19 ..      63      79 ..      61      88 .. 0.90
   2 !   15.6   1.1     2e-05     0.013       7      27 ..      92     114 ..      86     129 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                           Fer4_10  3 vidddtCirCgkCvkaC 19
                                       id+++Ci+Cg C+++C
  gi|330506904|ref|YP_004383332.1| 63 FIDKEKCIQCGICQDSC 79
                                      699************** PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2e-05
                           Fer4_10   7 dtCirCgkCvkaCPadl..tsvg 27 
                                         C +Cg C+ +CP d+   +++
  gi|330506904|ref|YP_004383332.1|  92 PLCEGCGVCQLVCPEDAvdMRDV 114
                                       57*************76542222 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3     0.019        12     100     120 ..       3      23 ..       2      31 .. 0.87
   2 !   13.7   0.0   7.1e-05     0.044      16      77 ..     183     240 ..     160     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.019
                                       SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinall 120
                                       +++++ G+ G GK+++i +l+
  gi|330506904|ref|YP_004383332.1|   3 QVAIVSGKGGTGKTSIIASLA 23 
                                       57899************9997 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.1e-05
                                       --EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTS CS
                       RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgy 77 
                                       vd +l+v+  +   + ++ l r+L +a + gi+ ++++nK Dl  e+   ++++e   + g+
  gi|330506904|ref|YP_004383332.1| 183 VDLALVVTEPT--VTGEHDLVRLLDVADHFGIKTTVCINKYDLNPEAA--RKIEELCGKRGV 240
                                       66666665444..55677899**********************99988..555555555555 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.3     0.085        53       5      26 ..       6      27 ..       3      33 .. 0.77
   2 !   10.6   0.0   0.00057      0.35      94     195 ..     156     253 ..     114     256 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.085
                            AAA_26  5 vtgtdtgvGKTvvslgLvralk 26
                                      +++   g GKT++++ L++  +
  gi|330506904|ref|YP_004383332.1|  6 IVSGKGGTGKTSIIASLAALAR 27
                                      77777899**********7664 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00057
                            AAA_26  94 elekdadivvVEGagglgvpiteellnadiaknlgapvilVargglgtinqllltiealrqknvrvlGvilNkv.rn 169
                                       + ek+ d+++++G+ g+g p+++ l+ +d+a     p++    +g++ + +ll  ++++  k    + v +Nk   n
  gi|330506904|ref|YP_004383332.1| 156 AAEKNLDLILIDGSPGIGCPVIASLTGVDLALVVTEPTV----TGEHDLVRLLDVADHFGIK----TTVCINKYdLN 224
                                       456777999999999999999999999999977777776....5777788888888888643....56777773223 PP

                            AAA_26 170 p...envetlekksgipvlGvvPylpdle 195
                                       p   +++e+l+ k g+++ G++Py ++++
  gi|330506904|ref|YP_004383332.1| 225 PeaaRKIEELCGKRGVKIAGRLPYHTSVI 253
                                       323369******************99876 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   1.3e-05     0.008      27      63 ..       5      38 ..       2      71 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                       ++sG  G+GK+s++ +l+  ++++ ++f  ++cd  
  gi|330506904|ref|YP_004383332.1|  5 AIVSGKGGTGKTSIIASLAALARGK-AVF--ADCDVD 38
                                      68*****************655555.555..555554 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   1.9    0.0076       4.7       3      18 ..      64      79 ..      63      85 .. 0.90
   2 !   11.9   0.2   0.00047      0.29       2      20 ..      88     106 ..      87     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0076
                           Fer4_15  3 vDrdaCigcglCvaea 18
                                      +D+++Ci cg C + +
  gi|330506904|ref|YP_004383332.1| 64 IDKEKCIQCGICQDSC 79
                                      9***********9987 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00047
                           Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                       +v+  +C+gcg+C  ++pe
  gi|330506904|ref|YP_004383332.1|  88 EVETPLCEGCGVCQLVCPE 106
                                       578899***********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 !   13.1   2.9   0.00016       0.1       3      17 ..      67      81 ..      65      93 .. 0.82
   2 !    8.0   2.8    0.0063       3.9      50      63 ..      93     106 ..      88     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                            Fer4_8  3 ekCieCgaCqsaCpv 17
                                      ekCi+Cg Cq++C +
  gi|330506904|ref|YP_004383332.1| 67 EKCIQCGICQDSCRF 81
                                      79***********76 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0063
                            Fer4_8  50 sCttcgaCtevCpv 63 
                                        C +cg C+ vCp+
  gi|330506904|ref|YP_004383332.1|  93 LCEGCGVCQLVCPE 106
                                       58889999999987 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   4.6   0.00028      0.17       1      16 [.      66      81 ..      66      82 .. 0.90
   2 !   11.5   1.5   0.00057      0.35       4      16 ..      94     106 ..      91     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00028
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +e+Ci+Cg C ++C +
  gi|330506904|ref|YP_004383332.1| 66 KEKCIQCGICQDSCRF 81
                                      69************76 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00057
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C gCg+C  +CP 
  gi|330506904|ref|YP_004383332.1|  94 CEGCGVCQLVCPE 106
                                       99**********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 ?    5.4   0.2     0.021        13       2      26 ..       4      28 ..       3      33 .. 0.83
   2 ?    8.0   0.0    0.0032         2      80     161 ..     151     230 ..      93     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.021
                                      EEEEEESTTCCHHHHHHHHHCT--S CS
                              cobW  2 vtvltGflGsGKTtLlnhllenrag 26
                                      v +++G  G+GKT+++ +l + ++g
  gi|330506904|ref|YP_004383332.1|  4 VAIVSGKGGTGKTSIIASLAALARG 28
                                      7899************999866555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0032
                                       H.......TT-SEEEEEEC.TTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE CS
                              cobW  80 e.......erldviliEtt.GlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvln 148
                                               ++ld+ili  + G+ +P           s + +d  ++v + + + +++      + d++    ++ +n
  gi|330506904|ref|YP_004383332.1| 151 MardlaaeKNLDLILIDGSpGIGCPVIA--------SLTGVDLALVVTEPTVTGEHDLVRLLDVADHFGIKTTVCIN 219
                                       2333344469******97647****998........667777777777775544555555566789999999999** PP

                                       -HHHHCHC..HHH CS
                              cobW 149 KtDlldeeallek 161
                                       K+Dl +e+a   k
  gi|330506904|ref|YP_004383332.1| 220 KYDLNPEAAR--K 230
                                       ***9999833..3 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 ?   -1.9   0.1       3.4   2.1e+03       8      26 ..       7      25 ..       3      31 .. 0.76
   2 ?   14.2   0.0   3.8e-05     0.024      87     143 ..     176     232 ..     151     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.4
                                      EEESTTSSHHHHHHHHHHH CS
                          GTP_EFTU  8 iighvDhGKtTLtdrLlyk 26
                                      + g   +GKt+++ +L + 
  gi|330506904|ref|YP_004383332.1|  7 VSGKGGTGKTSIIASLAAL 25
                                      5566678999999999765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.8e-05
                                       HHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHH CS
                          GTP_EFTU  87 virglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiv 143
                                       vi++l  +D+a++v + +   e+   ++l +a   g+++ v+iNK D   +  ++i 
  gi|330506904|ref|YP_004383332.1| 176 VIASLTGVDLALVVTEPTVTGEHDLVRLLDVADHFGIKTTVCINKYDLNPEAARKIE 232
                                       8999**************999**************************9855555544 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.1    0.0015      0.92       1      21 [.      68      88 ..      68      94 .. 0.83
   2 ?    8.2   1.9    0.0058       3.6      45      59 ..      93     107 ..      85     109 .. 0.81
   3 ?    7.6   2.5     0.009       5.6      46      59 ..      94     107 ..      93     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0015
                           Fer4_17  1 rCiqCgyClpeCpsyeaydne 21
                                      +CiqCg C ++C ++++ d+e
  gi|330506904|ref|YP_004383332.1| 68 KCIQCGICQDSCRFGAIADFE 88
                                      6***********998887765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0058
                           Fer4_17  45 lCieCgeCerkCPqg 59 
                                       lC +Cg C+ +CP++
  gi|330506904|ref|YP_004383332.1|  93 LCEGCGVCQLVCPED 107
                                       688888888888876 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.009
                           Fer4_17  46 CieCgeCerkCPqg 59 
                                       C +Cg C+ +CP++
  gi|330506904|ref|YP_004383332.1|  94 CEGCGVCQLVCPED 107
                                       55555555555554 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   2.6     0.003       1.9       1      15 []      69      83 ..      69      83 .. 0.97
   2 ?   11.0   5.4    0.0011      0.68       1      15 []      94     108 ..      94     108 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.003
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C++Cg C ++C+ gA
  gi|330506904|ref|YP_004383332.1| 69 CIQCGICQDSCRFGA 83
                                      ************998 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0011
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gCg C  vCP++A
  gi|330506904|ref|YP_004383332.1|  94 CEGCGVCQLVCPEDA 108
                                       99**********998 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.3   0.00013     0.078       3      23 ..       4      24 ..       2      31 .. 0.87
   2 ?   -1.1   0.0       1.4   8.6e+02     104     134 ..     135     170 ..     119     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                      EEEEEESTTSSHHHHHHHHHH CS
                       ArsA_ATPase  3 vilvgGKGGVGKttvsaatav 23
                                      v +v+GKGG GKt++ a++a+
  gi|330506904|ref|YP_004383332.1|  4 VAIVSGKGGTGKTSIIASLAA 24
                                      6789**************996 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                                       STTHHHHHHHHHHHHHHH.....CSSSSEEEEESBS CS
                       ArsA_ATPase 104 lPGideilsfeellkyvk.....eeeydvvvlDtaP 134
                                        PG +    + ++++++      e++ d +++D +P
  gi|330506904|ref|YP_004383332.1| 135 YPGEEASGKLVAMVREMArdlaaEKNLDLILIDGSP 170
                                       477777777778888777777778888888888887 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   0.00041      0.25      35      64 ..       4      32 ..       2      51 .. 0.83
   2 ?    0.5   0.0      0.63   3.9e+02     127     149 ..     145     167 ..     127     169 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
                            AAA_25 35 lallaGapgtGKttlaldlalavatGkpwl 64
                                      +a++ G +gtGKt +  +la+ +a+Gk ++
  gi|330506904|ref|YP_004383332.1|  4 VAIVSGKGGTGKTSIIASLAA-LARGKAVF 32
                                      89****************985.67777665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.63
                            AAA_25 127 tadvdaleaaieevegvrlvviD 149
                                        a v+++++++ + ++++l+ iD
  gi|330506904|ref|YP_004383332.1| 145 VAMVREMARDLAAEKNLDLILID 167
                                       23445555555554446666665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0025       1.5       3      26 ..       4      27 ..       2      37 .. 0.85
   2 ?    1.5   0.0      0.32     2e+02      65      91 ..     142     168 ..     124     171 .. 0.69
   3 ?   -2.1   0.0       3.9   2.4e+03      92     112 ..     243     263 ..     240     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0025
                                      EEEEEESTTSSHHHHHHHHHHHHH CS
                             SRP54  3 villvGlqGaGKTttlaKLaallk 26
                                      v ++ G  G+GKT+ +a Laal +
  gi|330506904|ref|YP_004383332.1|  4 VAIVSGKGGTGKTSIIASLAALAR 27
                                      77899***************9876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.32
                                       TSCHHHHHHHHHHHHHHTTSSEEEEEE CS
                             SRP54  65 eadpaavakeavekakeekidvvlvDT 91 
                                       ++  a v + a + a e++ d++l+D 
  gi|330506904|ref|YP_004383332.1| 142 GKLVAMVREMARDLAAEKNLDLILIDG 168
                                       3344455556667789999*******6 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.9
                                       --SSTTHHHHHHHHHHHHHHH CS
                             SRP54  92 aGrlqndkelmeelkkikkvv 112
                                       aGrl ++++++e + k + vv
  gi|330506904|ref|YP_004383332.1| 243 AGRLPYHTSVIEAMVKAQAVV 263
                                       899999999999999988876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00034      0.21      19      43 ..       3      27 ..       2      36 .. 0.88
   2 ?   -0.9   0.0       1.9   1.2e+03      91     118 ..     186     213 ..     144     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                            AAA_30 19 rvavltGpAGtGKttalkalreawe 43
                                      +va++ G  GtGKt ++++l+++++
  gi|330506904|ref|YP_004383332.1|  3 QVAIVSGKGGTGKTSIIASLAALAR 27
                                      5899****************99876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                            AAA_30  91 llivDEagmvdtkqlaallkaaekagak 118
                                        l+v E  +++ ++l +ll+ a++ g+k
  gi|330506904|ref|YP_004383332.1| 186 ALVVTEPTVTGEHDLVRLLDVADHFGIK 213
                                       4788888999999999999988877765 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 ?   -0.7   0.0       1.7   1.1e+03      37      54 ..       6      23 ..       2      34 .. 0.76
   2 ?    9.9   0.0   0.00093      0.58      28      79 ..     156     204 ..     128     213 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.7
                            RuvB_N 37 llyGpPGlGkttlakiia 54
                                      +++G  G Gkt++ + +a
  gi|330506904|ref|YP_004383332.1|  6 IVSGKGGTGKTSIIASLA 23
                                      678999999999765554 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00093
                            RuvB_N  28 kreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaall 79 
                                       + e++ld +l+ G+PG+G   +a++   +l     + + P++  + dl+ ll
  gi|330506904|ref|YP_004383332.1| 156 AAEKNLDLILIDGSPGIGCPVIASLTGVDLAL---VVTEPTVTGEHDLVRLL 204
                                       45789*************98888877766654...34568888888888777 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.025        16      22      39 ..       4      21 ..       1      27 [. 0.82
   2 ?    4.5   0.0     0.027        17       4      38 ..     147     179 ..     145     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.025
                                      EEEEEESTTSSHHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlakq 39
                                      v  ++G+gG GKt ++++
  gi|330506904|ref|YP_004383332.1|  4 VAIVSGKGGTGKTSIIAS 21
                                      55689********99876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHH CS
                            NB-ARC   4 svekviekLlekdelqslvvalvGmgGvGKttlak 38 
                                       +v++++  L  +++l+  ++ + G +G+G  ++a+
  gi|330506904|ref|YP_004383332.1| 147 MVREMARDLAAEKNLD--LILIDGSPGIGCPVIAS 179
                                       88999999**999999..9***********99997 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 ?    8.7   4.5     0.004       2.5       1      16 [.      64      79 ..      64      80 .. 0.92
   2 ?    7.2   1.1     0.012       7.2       2      18 ..      90     106 ..      89     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.004
                           Fer4_13  1 VDrdtCiacgaCvela 16
                                      +D+++Ci cg+C + +
  gi|330506904|ref|YP_004383332.1| 64 IDKEKCIQCGICQDSC 79
                                      8***********9877 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                           Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                       +   C +cg+C  ++P+
  gi|330506904|ref|YP_004383332.1|  90 ETPLCEGCGVCQLVCPE 106
                                       6667************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 ?    5.3   3.2     0.059        36      77      93 ..      63      80 ..      50      84 .. 0.76
   2 ?    8.2   1.9    0.0074       4.6      77      94 ..      89     106 ..      83     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.059
                           Fer4_22 77 f.gesgCvGCgRCieacp 93
                                      f ++++C+ Cg C+++c 
  gi|330506904|ref|YP_004383332.1| 63 FiDKEKCIQCGICQDSCR 80
                                      347889999999999996 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0074
                           Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                       +++  C GCg C+ +cp+
  gi|330506904|ref|YP_004383332.1|  89 VETPLCEGCGVCQLVCPE 106
                                       567889999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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):              29  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1699.30
//
Query:       gi|330506905|ref|YP_004383333.1|  [L=202]
Description: hypothetical protein MCON_0699 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       350  (0.0195214); 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:                         0  (0); expected 0.2 (1e-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 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1471.77
//
Query:       gi|330506906|ref|YP_004383334.1|  [L=322]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-13   49.7   0.0    8.7e-13   49.0   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.021   14.9   0.0      0.042   13.9   0.0    1.4  1  DUF1272      Protein of unknown function (DUF1272)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   9.7e-17   8.7e-13       3     158 ..      25     185 ..      23     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 9.7e-17
                                       EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTT..SEEEEEE.SSTGGGSTTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx.xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekg..vkevilg.ggepllypdfvellerla 71 
                                       + + C++ C +C++++t     +rr ++      ++++++v e++ + g  ++++ ++  gep+l++++ e++++l+
  gi|330506906|ref|YP_004383334.1|  25 PAKICSYSCAYCQVGRTlqmsaERRSYYLPQQIFDQVAQKVAEAR-DLGltIDYLSFVpDGEPTLDSNLGEEIDMLK 100
                                       6789**************754444444444444455555555553.44433455544499***************** PP

                                       HTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH...HHHHHHTCTSHHHHHHHHHHHHHHTTSETE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  72 klavpgiritvetngtlpdeeklerllelgvdrvslgleaadde...kvlklmnrghtfeevlealeklreagikrv 145
                                        l   gi+i+v++n+ l+ +ek+++ l    d+vs+ ++++ d+   ++ +++ r   ++ +l++++ +++      
  gi|330506906|ref|YP_004383334.1| 101 TL---GIKIAVISNASLIWDEKVREDLF-KADWVSVKVDSLEDKawrRIDRPH-RSLRLDTILQGIKDFAREYSGIL 172
                                       **...*************9777777655.369************999999999.88999**********99988889 PP

                                       EEEEEEBTTTSHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 146 vdrivglpGende 158
                                        +  ++l G nd 
  gi|330506906|ref|YP_004383334.1| 173 ATESMLLAGINDC 185
                                       9999999999984 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.7e-06     0.042      14      33 ..      18      37 ..      14      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-06
                           DUF1272 14 dlppdseearicsyEctFCa 33
                                      +l  ++  a+icsy c++C+
  gi|330506906|ref|YP_004383334.1| 18 SLGINNIPAKICSYSCAYCQ 37
                                      56677889***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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 0.21s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2478.48
//
Query:       gi|330506907|ref|YP_004383335.1|  [L=286]
Description: metallo-beta-lactamase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-13   51.2   2.3    4.6e-13   49.6   2.3    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
    5.9e-08   32.5   0.1      1e-07   31.7   0.1    1.6  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.034   13.6   0.0      0.062   12.7   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
        0.1   12.5   0.1       0.16   11.9   0.1    1.3  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 !   49.6   2.3     1e-16   4.6e-13      17      98 ..      44     137 ..      38     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1e-16
                                       EEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHH CS
                       Lactamase_B  17 viLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasr 93 
                                        +L DtG ++e ++    l al+++p+++d ++l+H+H+DH+Ggl+g+ +++ +pv +va+ +   ++  + +   +
  gi|330506907|ref|YP_004383335.1|  44 KLLWDTGATPEVMLHN--LDALHIDPEEIDLICLSHGHYDHTGGLMGVLQRRRAPVPIVAHPDIFAPKLKVRPFLKY 118
                                       589***********96..8*************************************999999988888888887777 PP

                                       CCHH..............T CS
                       Lactamase_B  94 kgll..............l 98 
                                        g++              +
  gi|330506907|ref|YP_004383335.1| 119 IGAPftrdqleaaggimlP 137
                                       7765555555555555440 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   2.3e-11     1e-07      20     115 ..      58     152 ..      44     273 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.3e-11
                                       S--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH.HCCTTCGHHHCHTTTTEEEEEE-TTS CS
                     Lactamase_B_2  20 qPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla.vleanfvylaleeepavnvheldwge 94 
                                       ++   l  ++++id++ l+h+HyDH+ gl+ + ++r   +p++a++++ a +l+ + ++l    + + ++ +l++ +
  gi|330506907|ref|YP_004383335.1|  58 HNLDaLHIDPEEIDLICLSHGHYDHTGGLMGVLQRRRAPVPIVAHPDIFApKLKVR-PFLKYIGA-PFTRDQLEAAG 132
                                       34444567899***********************77666*****998876344444.55555555.56666666666 PP

                                       EEEECSTTEEEEEEEE-EE-- CS
                     Lactamase_B_2  95 sfelgdggleitatparhksg 115
                                        + l   g  +t+ p   ++g
  gi|330506907|ref|YP_004383335.1| 133 GIMLPCRG-PVTLAPGVMTTG 152
                                       66664333.455555555544 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.4e-05     0.062       4      57 ..      40      91 ..      37     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                     Lactamase_B_6  4 ldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallya 57
                                       +n+k+L D G + + v   + l+ l+   +++dli Lsh   +h G+++ +++
  gi|330506907|ref|YP_004383335.1| 40 SENMKLLWDTGATPE-VM-LHNLDALHIDPEEIDLICLSHGHYDHTGGLMGVLQ 91
                                      5899*********97.43.357888887889*****************976654 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.6e-05      0.16      30      50 ..      63      83 ..      21     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.6e-05
                     Lactamase_B_3 30 yeppaeeaDlvlisqaledHa 50
                                      + +++ee+Dl+++s+++ dH 
  gi|330506907|ref|YP_004383335.1| 63 LHIDPEEIDLICLSHGHYDHT 83
                                      44556***************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2037.68
//
Query:       gi|330506908|ref|YP_004383336.1|  [L=381]
Description: DOMON domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-50  169.9   1.5      5e-50  169.5   1.5    1.1  1  DUF2202   Uncharacterized protein domain (DUF2202)
    4.1e-25   88.4   0.0    6.4e-25   87.8   0.0    1.3  1  DOMON     DOMON domain


Domain annotation for each model (and alignments):
>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.5   1.5   5.6e-54     5e-50       1     160 [.     223     380 ..     223     381 .] 0.98

  Alignments for each domain:
  == domain 1  score: 169.5 bits;  conditional E-value: 5.6e-54
                           DUF2202   1 ekdsllymreeeklarDvYlelYdrwklqiflniakseqthtdavksllekYeledpvkederGkfedeelqelYnk 77 
                                       ekd+l++++eeek+arD+Y +lY++ +l+ifl++++se++h+d+ k +++kY+l  p+     G+fe+++lq+++++
  gi|330506908|ref|YP_004383336.1| 223 EKDGLIFIWEEEKAARDIYSSLYEKNNLTIFLDLTRSEESHMDQAKAVIDKYGLVLPADVP--GVFENQTLQDIHDR 297
                                       799***************************************************9997655..************** PP

                           DUF2202  78 LvekgsksledaLkvgatiedldiaDlekalketdnkdikevYenllkGsrnhlRsfvrkleergkeYepqyiseee 154
                                       L+++g +s e+aLkv+a +e+++i+Dle  l   +n+d+ ++Y++ll+Gsr+hlRs+v +l+e+g+eYep+++ ++e
  gi|330506908|ref|YP_004383336.1| 298 LLAEGLESDEQALKVAAEFEEISIMDLEAELAAAENEDVRTMYQGLLAGSRKHLRSYVADLKEQGIEYEPRHLLRSE 374
                                       ***************************************************************************** PP

                           DUF2202 155 fdeivs 160
                                       f+e v+
  gi|330506908|ref|YP_004383336.1| 375 FEETVR 380
                                       **9885 PP

>> DOMON  DOMON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.0   7.1e-29   6.4e-25       3     123 ..      65     182 ..      63     184 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 7.1e-29
                             DOMON   3 geykvswkvdgdgdeiefelsgkvntngyvaiGfsddgkMsnadvvvgwvdngrvyvqdyystggkgapriddt... 76 
                                       g++++sw+ d  +++++ +l+g +   g++a+Gf + ++M+++d+++++vd+g++ v d y+tg++g p+i+dt   
  gi|330506908|ref|YP_004383336.1|  65 GDMQISWRND--EEDLYLALNGST--LGWLALGFEPLEWMKDSDIILASVDKGTAVVLDEYCTGNYG-PHIEDTmlg 136
                                       6899***888..999******765..9****************************************.****9**** PP

                             DOMON  77 gsqditllsgseengvttlkfrRkldtcdpkqdnkidldttvyviwa 123
                                       g++di+  sgse+ g tt++ +R l+++d+  d+++ +++ v++iwa
  gi|330506908|ref|YP_004383336.1| 137 GTDDIQEFSGSESAGRTTIELKRSLQSSDR-FDKSFSPGQAVSIIWA 182
                                       *****************************9.***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2736.35
//
Query:       gi|330506909|ref|YP_004383337.1|  [L=219]
Description: hypothetical protein MCON_0706 [Methanosaeta concilii GP6]
Scores for complete 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   21.8   0.1    0.00029   20.6   0.1    1.6  1  HTH_IclR  IclR helix-turn-helix domain
    0.00024   21.0   0.0    0.00056   19.8   0.0    1.6  1  HTH_36    Helix-turn-helix domain
     0.0011   18.7   0.1     0.0041   16.8   0.0    2.0  2  HTH_DeoR  DeoR-like helix-turn-helix domain
     0.0012   18.7   2.0     0.0014   18.5   0.0    2.1  3  HTH_11    HTH domain
     0.0022   17.8   0.0     0.0095   15.8   0.0    2.0  2  MarR_2    MarR family
      0.004   16.8   0.1     0.0097   15.5   0.1    1.6  1  GntR      Bacterial regulatory proteins, gntR family
     0.0055   16.2   0.2      0.021   14.4   0.0    2.1  2  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.024   14.5   0.0    1.5  1  TrmB      Sugar-specific transcriptional regulator TrmB
      0.087   12.9   0.0       0.19   11.7   0.0    1.6  1  HTH_29    Winged helix-turn helix
       0.11   12.7   0.0       0.28   11.3   0.0    1.7  1  DprA_WH   DprA winged helix domain
       0.11   12.4   0.0       0.37   10.7   0.0    1.9  2  HTH_5     Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   1.8e-07   0.00029      17      50 ..      67     100 ..      62     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.8e-07
                                       SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       ++++l  lA+rtg +k+tv+  ++ L+ lG+ ++
  gi|330506909|ref|YP_004383337.1|  67 EPMSLDMLAERTGYSKTTVRSSMNLLESLGIARR 100
                                       78****************************9987 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.5e-07   0.00056      27      54 ..      70      97 ..      65      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.5e-07
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGy 54
                                      s + la+r+g sk Tv++  ++Le lG+
  gi|330506909|ref|YP_004383337.1| 70 SLDMLAERTGYSKTTVRSSMNLLESLGI 97
                                      7899**********************96 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.5e-06    0.0041      12      47 ..      66     101 ..      61     103 .. 0.91
   2 ?   -2.1   0.0         2   3.3e+03       7      20 ..     109     122 ..     105     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.5e-06
                          HTH_DeoR  12 qgklsveelvellgvSeaTiRRDLneLeeqglltRt 47 
                                       +  +s++ l+e+ g+S++T+R  +n Le  g+ +R+
  gi|330506909|ref|YP_004383337.1|  66 SEPMSLDMLAERTGYSKTTVRSSMNLLESLGIARRV 101
                                       566899**************************9996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
                          HTH_DeoR   7 ellkqqgklsveel 20 
                                       + +kq+++  v+++
  gi|330506909|ref|YP_004383337.1| 109 HNIKQHRYALVNDA 122
                                       67999999998876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   8.6e-07    0.0014      10      44 ..      63      97 ..      58     102 .. 0.88
   2 ?   -3.9   0.1       8.9   1.5e+04       5      15 ..     140     150 ..     139     152 .. 0.73
   3 ?   -3.2   0.0       5.4   8.8e+03      16      25 ..     205     214 ..     203     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.6e-07
                            HTH_11 10 leargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      + + +p+s + LAe+++ S++tvr  +  Le+lg+
  gi|330506909|ref|YP_004383337.1| 63 FLESEPMSLDMLAERTGYSKTTVRSSMNLLESLGI 97
                                      445667***************************95 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 8.9
                            HTH_11   5 ilelLleargp 15 
                                       il+ Ll+ r++
  gi|330506909|ref|YP_004383337.1| 140 ILQALLQVRDN 150
                                       78888887765 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5.4
                            HTH_11  16 isgeeLAeeL 25 
                                       ++++eL e L
  gi|330506909|ref|YP_004383337.1| 205 FTSKELIEIL 214
                                       6778887776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.8e-06    0.0095      16      59 ..      66     106 ..      61     106 .. 0.88
   2 ?   -1.9   0.0       1.9   3.1e+03      41      53 ..     201     213 ..     200     219 .] 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.8e-06
                                       CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSS CS
                            MarR_2  16 rrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeD 59 
                                        +p   ++   la+r+g+sk +v    + L++ G  +r+ +p D
  gi|330506909|ref|YP_004383337.1|  66 SEP---MSLDMLAERTGYSKTTVRSSMNLLESLGIARRVVDPQD 106
                                       444...89999****************************99887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.9
                                       HHHHHHHTTSEEE CS
                            MarR_2  41 ilkrLvaaGLver 53 
                                       ++ r+ ++ L+e 
  gi|330506909|ref|YP_004383337.1| 201 LISRFTSKELIEI 213
                                       5778999999985 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   5.9e-06    0.0097      22      56 ..      67     100 ..      57     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.9e-06
                                       SB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR  22 dkLPsereLaaefgVsrttvReALrrLeaeglver 56 
                                       +++ s   La++ g s+ttvR +++ Le+ g++ r
  gi|330506909|ref|YP_004383337.1|  67 EPM-SLDMLAERTGYSKTTVRSSMNLLESLGIARR 100
                                       677.8889***********************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 !   14.4   0.0   1.3e-05     0.021      23      46 ..      74      97 ..      67      99 .. 0.94
   2 ?   -2.3   0.0         2   3.3e+03       6      15 ..     208     217 ..     202     219 .] 0.60

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                            HTH_24 23 LAerlglSpstvnrrlkrLeeeGl 46
                                      LAer+g S++tv+  ++ Le+ G+
  gi|330506909|ref|YP_004383337.1| 74 LAERTGYSKTTVRSSMNLLESLGI 97
                                      9********************998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2
                            HTH_24   6 rkILelLqkn 15 
                                       ++++e+L+++
  gi|330506909|ref|YP_004383337.1| 208 KELIEILEEH 217
                                       4556666665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.5e-05     0.024      18      58 ..      64     104 ..      61     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                                       HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       l+++p++ d +ae++g ++++v ++++ Le+ G+ +r+   
  gi|330506909|ref|YP_004383337.1|  64 LESEPMSLDMLAERTGYSKTTVRSSMNLLESLGIARRVVDP 104
                                       799*******************************9998766 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.19      10      44 ..      67     104 ..      62     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                            HTH_29  10 eGvstvsqiAkllglsrrtvyrwlkrfeegGlaa....l 44 
                                       e +s   ++A+++g+s++tv+   ++ e  G+a      
  gi|330506909|ref|YP_004383337.1|  67 EPMS-LDMLAERTGYSKTTVRSSMNLLESLGIARrvvdP 104
                                       5566.899***********************98755444 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.28      21      50 ..      64      93 ..      61     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                           DprA_WH 21 LgpePvhvDqLvrrtglpaaevsaaLleLE 50
                                      L++eP+++D L++rtg +  +v +    LE
  gi|330506909|ref|YP_004383337.1| 64 LESEPMSLDMLAERTGYSKTTVRSSMNLLE 93
                                      789**************9999988877777 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.2   8.4e+03       6      13 ..       4      11 ..       4      13 .. 0.82
   2 ?   10.7   0.0   0.00023      0.37      10      45 ..      63      98 ..      61     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.2
                                      HHHHHHTT CS
                             HTH_5  6 kILklLae 13
                                      kIL++La 
  gi|330506909|ref|YP_004383337.1|  4 KILCFLAA 11
                                      79**9985 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00023
                                      HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5 10 lLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +L++++++   lae +g s+ tv+   + L+ +G+ 
  gi|330506909|ref|YP_004383337.1| 63 FLESEPMSLDMLAERTGYSKTTVRSSMNLLESLGIA 98
                                      578899****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1570.05
//
Query:       gi|330506910|ref|YP_004383338.1|  [L=151]
Description: heat shock protein Hsp20 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-14   53.7   0.4    2.5e-14   53.2   0.4    1.2  1  HSP20       Hsp20/alpha crystallin family
    1.9e-12   46.6   0.1    3.5e-12   45.7   0.1    1.5  1  ArsA_HSP20  HSP20-like domain found in ArsA
     0.0065   17.5   0.0       0.05   14.6   0.0    2.1  2  CS          CS domain
  ------ inclusion threshold ------
      0.031   14.7   0.0      0.061   13.7   0.0    1.6  1  PIH1_CS     PIH1 CS-like domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.4   5.7e-18   2.5e-14       3     101 ..      57     150 ..      55     151 .] 0.92

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 5.7e-18
                                       -SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETT CS
                             HSP20   3 keeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdG 79 
                                       ++ ++e    + +pg +k+ +++ v++++++++++      ++k+l++e ++r+ +r+++LP +v++++vkas+++G
  gi|330506910|ref|YP_004383338.1|  57 MDGKDELVALVSLPGRSKDMIDLRVTEDTLTISAKAA--AREGKYLHQEIENRNVEREIKLPLEVKPEQVKASFNNG 131
                                       677888888899*************************..9999********************************** PP

                                       EEEEEEEBSS--..-------- CS
                             HSP20  80 vLtvtvpkkepekkkkerkiqi 101
                                       +L+v++pk       ++++iq+
  gi|330506910|ref|YP_004383338.1| 132 ILEVHLPKLMVV---DSQRIQV 150
                                       ********9998...5677777 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 !   45.7   0.1   7.9e-16   3.5e-12       2      63 .]      61     137 ..      60     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 7.9e-16
                        ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkig................nfrRqitLPsvlarkevtsAkfedgvLeIr 62 
                                       de v  + LP+ +k+ idl+ ++d+LtI+++                n  R+i LP  ++ ++v +A+f++g Le++
  gi|330506910|ref|YP_004383338.1|  61 DELVALVSLPGRSKDMIDLRVTEDTLTISAKaaaregkylhqeienrNVEREIKLPLEVKPEQV-KASFNNGILEVH 136
                                       7788889*********************************************************.**********98 PP

                        ArsA_HSP20  63 F 63 
                                       +
  gi|330506910|ref|YP_004383338.1| 137 L 137
                                       5 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.27   1.2e+03      37      61 ..      27      48 ..       2      49 .. 0.71
   2 !   14.6   0.0   1.1e-05      0.05      14      76 .]      65     139 ..      58     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.27
                                      EEEEETSCEEEEECEBSS-BETTTE CS
                                CS 37 lkvkigkeklliegeLfgpIdpees 61
                                      ++++    k  i g+L + I  e+s
  gi|330506910|ref|YP_004383338.1| 27 ISIQA--AKK-ILGDLPSDISMEKS 48
                                      44443..223.46779999999998 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.1e-05
                                       EEEE-TTCTTTTTCEEEEEETTEEEEEETSCEEEEECE................BSS-BETTTEEEEEETTEEEEEE CS
                                CS  14 vtiyvkkvnikkkdvkvefkerslkvkigkeklliege................LfgpIdpeesswtieskkveitL 74 
                                         + +++  ++k+ ++++ +e++l+++   +    eg+                L  +++pe+ + ++ +  +e++L
  gi|330506910|ref|YP_004383338.1|  65 ALVSLPG--RSKDMIDLRVTEDTLTISA--KAAAREGKylhqeienrnvereikLPLEVKPEQVKASFNNGILEVHL 137
                                       5566666..5999999999999988887..345555556666678899999999*********************** PP

                                       EB CS
                                CS  75 kK 76 
                                        K
  gi|330506910|ref|YP_004383338.1| 138 PK 139
                                       98 PP

>> PIH1_CS  PIH1 CS-like domain
   #    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      31      87 ..      61     130 ..      43     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                           PIH1_CS  31 kelaieielPllksikevklrvgerrlel..............eskkakyfLslkLpYpvdedkveAkFvk 87 
                                       +el++ + lP+  s   ++lrv+e++l +              e ++ +   ++kLp +v+ ++v+A F++
  gi|330506910|ref|YP_004383338.1|  61 DELVALVSLPGR-SKDMIDLRVTEDTLTIsakaaaregkylhqEIENRNVEREIKLPLEVKPEQVKASFNN 130
                                       578888999996.999*************999999999988884455567778****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1106.58
//
Query:       gi|330506911|ref|YP_004383339.1|  [L=385]
Description: major facilitator family transporter [Methanosaeta concilii GP6]
Scores for complete 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-39  133.3  48.5    6.3e-20   71.4  13.4    2.0  2  MFS_1       Major Facilitator Superfamily
    3.5e-10   39.3  18.0    4.8e-07   29.0   0.4    2.1  2  Sugar_tr    Sugar (and other) transporter
    3.1e-08   32.9  16.4    2.7e-06   26.5  16.4    2.4  1  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
        0.1   11.0  17.1        1.3    7.3  12.8    2.6  2  MFS_3       Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4  13.4   1.4e-23   6.3e-20       3     241 ..       8     233 ..       6     242 .. 0.83
   2 !   64.8  35.6   1.4e-21   6.2e-18       2     167 ..     206     373 ..     205     383 .. 0.88

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.4e-23
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg.ll 77 
                                       ++ fl+ +++ i+ p+lpl++  +lg    ++gl+ ++   + +++ ++ G +sdr+Grr+ ++++g++++a g l+
  gi|330506911|ref|YP_004383339.1|   8 VVSFLNDISSEIIQPILPLFI-AQLGGGSMAVGLIGGVSDGLPSILKVLSGCWSDRLGRRKpLVVAGYAISAMGkLF 83 
                                       689***************655.889999999*******9999********************************555 PP

                             MFS_1  78 lllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWra 152
                                       l++  +s w  +++l  l   g g+  +   a+i++ + + +rgr++gl  a+ s+Ga++g +l+ ll    +g+++
  gi|330506911|ref|YP_004383339.1|  84 LPF--ASAWqHVFLLKTLERSGKGVRSAPRDAMISESTDQGHRGRGFGLHRAMDSAGAVVGSMLAYLLWqGGFGYPS 158
                                       555..777879**********************************************************999***** PP

                             MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltl 229
                                       + ++++i+s+ a++    ++++++++r+++  +       + +l++ ++  lk+     l+ia+l++ +g+++++++
  gi|330506911|ref|YP_004383339.1| 159 ILMLAGILSVAALL---PFYWVKESSRAPDCCTSS----IRLNLSS-LSPELKRF----LFIACLFA-LGNFSYMFF 222
                                       ************88...777777777777766666....6666666.44444444....55555555.466665555 PP

                             MFS_1 230 lplylqevlgls 241
                                       +   +q+++  s
  gi|330506911|ref|YP_004383339.1| 223 ILR-AQDHFSGS 233
                                       555.27777666 PP

  == domain 2  score: 64.8 bits;  conditional E-value: 1.4e-21
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigl..lltlyalgaavaslplGrlsdrfGrrrvlllglllfalgl 76 
                                       l++a+l al+ + +++++    ++++  s +++    l+ l+ l++a++++p+G +sdr+Gr+rvl+lg+ lfal++
  gi|330506911|ref|YP_004383339.1| 206 LFIACLFALGNFSYMFFIL-RAQDHFSGSMAVAAPllLYLLFNLVYALLAMPVGIWSDRVGRKRVLFLGYSLFALTA 281
                                       7889999999999999997.778887755554332347778***********************************5 PP

                             MFS_1  77 llllfa.sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWra 152
                                       + ++ a sslw l++l ++ Gl ++++  +  a+++d+ p   rg+ +g++++++++++i+  l++g++ s++g +a
  gi|330506911|ref|YP_004383339.1| 282 VGFA-AvSSLWGLIALFAMYGLVYALVDGSERAYVSDLCPAGLRGSSLGIYYGAVGVASIISSLVAGAIWSLWGAEA 357
                                       5555.34********************************************************************** PP

                             MFS_1 153 vfyilaivsllafv.l 167
                                       +f+  a++++la+v l
  gi|330506911|ref|YP_004383339.1| 358 SFLYGAAAAALAAVgL 373
                                       ************9842 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.4   1.1e-10   4.8e-07      64     196 ..      54     182 ..      51     182 .. 0.95
   2 !   14.2  11.6   3.3e-06     0.015     251     432 ..     201     375 ..     188     379 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.1e-10
                                       HHHHHHHHHTTHHHHHHH.HHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHH CS
                          Sugar_tr  64 lfagllgdrfGRkkslli.aavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgal 139
                                       +++g ++dr+GR+k l++ + +++  g +   +a    +++ +++ + l   g G+ s+     isE + + +Rg+ 
  gi|330506911|ref|YP_004383339.1|  54 VLSGCWSDRLGRRKPLVVaGYAISAMGKLFLPFAS---AWQHVFLLKTLERSGKGVRSAPRDAMISESTDQGHRGRG 127
                                       5789************9967789999999999999...9************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HH CS
                          Sugar_tr 140 vslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPr 196
                                        +l+  + ++G +v++++ + l + +   g++  l l+ +++++ l+ ++++ ES r
  gi|330506911|ref|YP_004383339.1| 128 FGLHRAMDSAGAVVGSMLAYLLWQGGF--GYPSILMLAGILSVAALLPFYWVKESSR 182
                                       **********************88887..8************************976 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.3e-06
                                       ...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHH CS
                          Sugar_tr 251 vrqrlligvvlqifqqltGinaimyysptifenlglsksllvtiivgvvnfvatfvaiflvdrfGRRtllllGaagm 327
                                        ++r+l ++ l ++ +++++++i+     +  ++ +  +ll  +++  v ++  + +   +dr+GR+++l+lG +  
  gi|330506911|ref|YP_004383339.1| 201 ELKRFLFIACLFALGNFSYMFFILRAQDHFSGSMAVAAPLLLYLLFNLVYALLAMPVGIWSDRVGRKRVLFLGYSLF 277
                                       67899999999999**********9999*********998888888888888888777889************9998 PP

                                       HHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 328 aicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisl 404
                                       a+ +v ++      v++      ++i+++a++  ++al  g+    +vs+l p ++R++ l i + +  +a+++ sl
  gi|330506911|ref|YP_004383339.1| 278 ALTAVGFA-----AVSS----LWGLIALFAMYGLVYALVDGSER-AYVSDLCPAGLRGSSLGIYYGAVGVASIISSL 344
                                       88887776.....5555....57899999*********999998.788***************99999999999998 PP

                                       HHHHHHCHHH...T-HHHHHHHHHHHHHHHH CS
                          Sugar_tr 405 lfpiiteaig...ggyvflvfaglavlfiif 432
                                       +   i +  g    + +++  a+la++++++
  gi|330506911|ref|YP_004383339.1| 345 VAGAIWSLWGaeaSFLYGAAAAALAAVGLLV 375
                                       8888887777444455555555555555554 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 !   26.5  16.4   6.1e-10   2.7e-06     133     384 ..     112     360 ..      11     361 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.1e-10
                        MFS_1_like 133 daatlkel..gedrkdyGrqrlfGsvGyaifafitGilidhysvnllpysallyvlaallvisllvvlilnetekes 207
                                       da++ + +  g++ + +G  r   s G  ++  ++ +l+ +  +   +y  +l+++ +l v++ll ++ ++e + ++
  gi|330506911|ref|YP_004383339.1| 112 DAMISESTdqGHRGRGFGLHRAMDSAGA-VVGSMLAYLLWQGGF---GYPSILMLAGILSVAALLPFYWVKESSRAP 184
                                       5555555543334444666666666663.333333444444344...377899************************ PP

                        MFS_1_like 208 klkvtkslqvllnilknpeviifllvalilgmswgiienFlflYL.kelgasntllGs.lvalgvvaeip.lfffa. 280
                                       ++    ++ +l  +  + + ++f++ ++ lg+++     ++f  L  +  +s++++ +  + l  + +++  ++ + 
  gi|330506911|ref|YP_004383339.1| 185 DCCTSSIRLNLSSLSPELKRFLFIACLFALGNFS-----YMFFILrAQDHFSGSMAVAaPLLLYLLFNLVyALLAMp 256
                                       *****99999999888888888888888888774.....55555545555555544330333333333331333331 PP

                        MFS_1_like 281 .eklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsg 356
                                          + +++G  ++l+++ ++++l+ ++ a+++++w ++ + +++g+ ++l+ ++   yvs++ p +l++   g++ g
  gi|330506911|ref|YP_004383339.1| 257 vGIWSDRVGRKRVLFLGYSLFALTAVGFAAVSSLWGLIALFAMYGLVYALVDGSERAYVSDLCPAGLRGSSLGIYYG 333
                                       146789*********************************************************************** PP

                        MFS_1_like 357 lyfglGralGsliGGllwdlksaiflFr 384
                                       + +g+ + + sl++G++w l +a   F 
  gi|330506911|ref|YP_004383339.1| 334 A-VGVASIISSLVAGAIWSLWGAEASFL 360
                                       9.9***************9999998886 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0022       9.8      39      92 ..      30      84 ..      21     121 .. 0.76
   2 ?    7.3  12.8    0.0003       1.3      59     178 ..     251     365 ..     246     379 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0022
                             MFS_3 39 disasplmvAlvq.aaatLPifllsilaGalaDnfdrRkvllav.qlllalvsvll 92
                                      ++    ++v l+  ++  LP  +l +l+G  +D + rRk l+++ +++ a++ ++l
  gi|330506911|ref|YP_004383339.1| 30 QLGGGSMAVGLIGgVSDGLPS-ILKVLSGCWSDRLGRRKPLVVAgYAISAMGKLFL 84
                                      555666778888537889997.5799*************88765155555555555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0003
                             MFS_3  59 fllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrr 135
                                        ll++++G+ +D + r++vl+ +++l al++v         + s w l+al  + g+  al d + +A v++l ++ 
  gi|330506911|ref|YP_004383339.1| 251 ALLAMPVGIWSDRVGRKRVLFLGYSLFALTAVGF-----AAVSSLWGLIALFAMYGLVYALVDGSERAYVSDLCPAG 322
                                       699**********************998777654.....455678999999999*******************9998 PP

                             MFS_3 136 dvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnals 178
                                          +   +    + +a  +   ++G + ++ Ga ++f   a +
  gi|330506911|ref|YP_004383339.1| 323 LRGSSLGIYYGAVGVASIISSLVAGAIWSLWGAEASFLYGAAA 365
                                       8888888887778888889999999999999999988654432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.22s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 2964.19
//
Query:       gi|330506912|ref|YP_004383340.1|  [L=70]
Description: hypothetical protein MCON_0709 [Methanosaeta concilii GP6]
Scores for complete 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-06   25.7   0.3    9.8e-06   25.5   0.3    1.1  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.3   5.5e-10   9.8e-06       2      58 .]       7      62 ..       6      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5.5e-10
                                      HCHHHHHHHTT-EEEEEETT.EEEEE-TTSS-EEEEE.S-SSS--CCCHHHHHHHCC- CS
                        HicA_toxin  2 reviklLeklGfevvrqkGS.HvrfkhpdkrgivtvppHpgkelkpgtlksIlkqaGl 58
                                      r +ik L++lG e    +G  H  +   ++ +i++ p H g++++  ++k Ilk+ G+
  gi|330506912|ref|YP_004383340.1|  7 RVLIKKLKNLGLEGPH-SGNkHPYMIIGETVIILPNP-HQGRDVDVRLIKTILKDVGI 62
                                      669**********998.6755******9999888888.99****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 515.21
//
Query:       gi|330506913|ref|YP_004383341.1|  [L=96]
Description: hypothetical protein MCON_0710 [Methanosaeta concilii GP6]
Scores for complete 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   18.5   0.0     0.0021   18.1   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.2e-07    0.0021       9      57 ..      32      80 ..      26      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-07
                   HicB_lk_antitox  9 edsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipe 57
                                      +d +y  +v  lpG++ +g+t+e   ++  e+ie ++   +++g +ip+
  gi|330506913|ref|YP_004383341.1| 32 KDGSYMATVAGLPGVIATGETIETCRDDLIEVIEEWVAIRLQRGFAIPA 80
                                      5778999********************************9999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 734.30
//
Query:       gi|330506914|ref|YP_004383342.1|  [L=341]
Description: hypothetical protein MCON_0712 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2392.64
//
Query:       gi|330506915|ref|YP_004383343.1|  [L=99]
Description: hypothetical protein MCON_0713 [Methanosaeta concilii GP6]
Scores for complete 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   17.6   0.1      0.004   17.2   0.1    1.2  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.2e-07     0.004       2      58 .]       7      64 ..       6      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-07
                                      HCHHHHHHHTT-EEEEEETTEEEEE-..TTSS-EEEEE.S-.SSS--CCCHHHHHHHCC- CS
                        HicA_toxin  2 reviklLeklGfevvrqkGSHvrfkh..pdkrgivtvppHp.gkelkpgtlksIlkqaGl 58
                                      +ev++ L++ Gf+  ++   H  +    ++k+++ t+  H+ ++e++p +l  ++k++G+
  gi|330506915|ref|YP_004383343.1|  7 DEVEAGLKRKGFQQSNN--KHKYYHLyiNGKKEAGTHVSHGkNQEIGPRLLGPMAKELGI 64
                                      79************986..344444465566666666667779*********99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 731.80
//
Query:       gi|330506916|ref|YP_004383344.1|  [L=598]
Description: hypothetical protein MCON_0714 [Methanosaeta concilii GP6]
Scores for complete sequence (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   81.0   0.0    1.7e-12   47.5   0.0    3.4  3  UvrD-helicase    UvrD/REP helicase N-terminal domain
    1.5e-16   61.0   0.0    6.3e-16   59.0   0.0    2.0  2  AAA_19           AAA domain
    5.2e-14   52.4   0.0    1.6e-12   47.4   0.0    2.1  2  UvrD_C           UvrD-like helicase C-terminal domain
    7.5e-11   42.2   0.0    0.00021   21.1   0.0    3.3  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    1.1e-07   31.6   0.1    8.4e-07   28.7   0.1    2.2  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    0.00098   18.9   0.0        0.3   10.8   0.0    2.4  2  AAA_30           AAA domain
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.25   10.9   0.0    1.5  1  AAA_12           AAA domain
       0.15   12.4   0.1        3.4    7.9   0.0    2.8  3  AAA_22           AAA 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 !   24.9   0.0   5.9e-09   1.3e-05       2      70 ..      10      78 ..       9     119 .. 0.90
   2 !   47.5   0.0   7.4e-16   1.7e-12     237     310 ..     186     269 ..     147     272 .. 0.74
   3 !    4.6   0.1    0.0085        19      63     100 ..     469     509 ..     403     512 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 5.9e-09
                                      SHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHH CS
                     UvrD-helicase  2 npeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealk 70
                                      +peq++ i s +  ++v A +GsGKT+v +e     i+    ++  i  + FTn A e + e i ++l 
  gi|330506916|ref|YP_004383344.1| 10 TPEQKAVIDSNSRITVVRACPGSGKTRVFVESLKMRIDSWTKKNAGIASISFTNVAQEQIAEGIGKHLP 78
                                      799*************************************999999**********9999998888665 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 7.4e-16
                                       HHHHHHHHH........CHHHHHHHHHHSSEEEESSGGG-BHHH.HHHHHHHHTTTTT.EEEEE-GGG--GGGGTB- CS
                     UvrD-helicase 237 hallellee........neelaealrerykeiliDEyQDTnkiQ.yrilkllasghee.lfmvGDpkQsIYgFRgAd 303
                                       h  +++  +        ++++ e + +r+++il+DE+QDTn     ++++ll s   e  ++vGDp+Q+I++F gA+
  gi|330506916|ref|YP_004383344.1| 186 HSDCQYISSlilchpefGKKVSELVTRRFPMILVDEFQDTNWFLgLALIELLRSPFLEsGLVVGDPDQAIFEFGGAN 262
                                       3333433334444477789999*******************86537899999888766799**************** PP

                                       THHHHHH CS
                     UvrD-helicase 304 ielflkk 310
                                       ++lf   
  gi|330506916|ref|YP_004383344.1| 263 PDLFKDI 269
                                       ***9865 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0085
                                       HHHHHHHHHCCHHCTT-H...HHHHHHHHCTTSEEEEHHHH CS
                     UvrD-helicase  63 eRieealkkaeqessdde...rlrlalqnlseanisTlHsf 100
                                        Ri   lk++++ +   +   +l+ + + +++a+i T+H++
  gi|330506916|ref|YP_004383344.1| 469 RRISDNLKQNLKGNVLRKmaeHLESSDSLIERATIKTIHQV 509
                                       566666666665555555666******************85 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   2.8e-19   6.3e-16       2     145 ..      13     258 ..      12     259 .. 0.88
   2 ?   -1.6   0.0       1.4   3.2e+03      68      76 ..     494     510 ..     470     587 .. 0.67

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 2.8e-19
                            AAA_19   2 reavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae......atTi 72 
                                       ++av ++++++ +v a pG+GKTrv ++ +++ ++  + k + i+ ++ft+ A ++++e +   g++      + T+
  gi|330506916|ref|YP_004383344.1|  13 QKAVIDSNSRITVVRACPGSGKTRVFVESLKMRIDSWTKKNAGIASISFTNVAQEQIAEGI---GKHlpyphfIGTL 86 
                                       567779*****************************************************99...4444488999999 PP

                            AAA_19  73 Hrlal........................................................................ 77 
                                        ++al                                                                        
  gi|330506916|ref|YP_004383344.1|  87 DAFALryvvrpfghlvglpkeghrlipspldeaieypeveidssgqkislfsirfadgplhkpnmkaktfrgqidie 163
                                       99999********************************************************************9999 PP

                            AAA_19  78 ..........................ldfddlltealelle...........eaeeekklqeee.llivDEfqdvd. 115
                                                                                            ++ ++ +++++ +++vDEfqd++ 
  gi|330506916|ref|YP_004383344.1| 164 pdytsnilkkkkaewrkrgrithsdcQ-------------YisslilchpefGKKVSELVTRRFpMILVDEFQDTNw 227
                                       999999988888887777765444321.............0223334456665567788889999***********9 PP

                            AAA_19 116 elqyrLlkallgek.kklllvGDpdQliyvf 145
                                        l  +L++ l  +  ++ l+vGDpdQ+i++f
  gi|330506916|ref|YP_004383344.1| 228 FLGLALIELLRSPFlESGLVVGDPDQAIFEF 258
                                       999999999998888889**********998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                            AAA_19  68 e........atTiHrla 76 
                                       +        ++TiH++ 
  gi|330506916|ref|YP_004383344.1| 494 SdslieratIKTIHQVK 510
                                       13334445588888874 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.025        55       3      81 ..     280     351 ..     278     361 .. 0.75
   2 !   47.4   0.0   7.4e-16   1.6e-12     236     347 ..     443     564 ..     377     566 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.025
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C   3 LekNyRStksLlkaankflenilnrralekekktvekgekivvleaeteeeEaekiaatikallekneklediavLv 79 
                                       L++ +R +k++  +a ++ +  ++    ++   ++ +g  i++    ++ +  +k+ a i +++   e+++++a++ 
  gi|330506916|ref|YP_004383344.1| 280 LNQTHRCPKKIAAIATALSDTGKQV---LPR-DNADQGSAIILVHDMEKIDRNKKVIANISKFC---EEEDQLAIIS 349
                                       7889999999999998888555555...223.56667777777777777778888888899999...7888888888 PP

                                       xx RF
                            UvrD_C  80 Rs 81 
                                       R 
  gi|330506916|ref|YP_004383344.1| 350 RR 351
                                       86 PP

  == domain 2  score: 47.4 bits;  conditional E-value: 7.4e-16
                                       x...xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 236 e...klenlreLy.sllkelekkeeeeeveeklneileiatLsesel..eeskkk.ekipiiTiHqAKGlEFdvVfl 305
                                            l ++r+L+ + + +l++++ + +++++l++ l+ + L+++ +  e+s++  e+ +i TiHq KG EF+ V++
  gi|330506916|ref|YP_004383344.1| 443 TwneWLLRIRKLIlDSALDLNCEFDKRRISDNLKQNLKGNVLRKMAEhlESSDSLiERATIKTIHQVKGDEFECVVI 519
                                       24446667777754778889999999999999********9998765114555559*****************9998 PP

                                       xx..xxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 306 ag..leegtfPsyrskk.......ekrleEEkRlfYVaiTRAkkrLfisys 347
                                       +    + ++                +  +EE+R+ +Va++RAkk L++  +
  gi|330506916|ref|YP_004383344.1| 520 LVpkPSPNNS------PcpsvewwPDGPSEERRVAFVAASRAKKTLILCIH 564
                                       7600222333......2444557788999******************9765 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00045         1       1      22 [.      24      45 ..      24      69 .. 0.83
   2 !    8.2   0.0    0.0008       1.8      62     141 ..     213     292 ..     186     347 .. 0.74
   3 !   21.1   0.0   9.3e-08   0.00021     183     233 ..     493     562 ..     443     563 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00045
                   Viral_helicase1  1 ivvhGvpGcGKStlirkllrts 22
                                      +vv ++pG+GK+++ ++ l+++
  gi|330506916|ref|YP_004383344.1| 24 TVVRACPGSGKTRVFVESLKMR 45
                                      699****************995 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0008
                   Viral_helicase1  62 kgkililDEylllha..Gyill.laalskaklvilfGDplQipfhsrnasfllahlpsslshrvgrrttyllpsdva 135
                                       ++  +++DE++  ++  G+ l  l++ + ++  +++GDp Q  f+       +++l++ ++++ g +   l++++++
  gi|330506916|ref|YP_004383344.1| 213 RFPMILVDEFQDTNWflGLALIeLLRSPFLESGLVVGDPDQAIFEF---GGANPDLFKDIENLPGAKSLPLNQTHRC 286
                                       588999****99987556666677888889999********98885...5689999999977777777777777777 PP

                   Viral_helicase1 136 eilsak 141
                                       +++ a 
  gi|330506916|ref|YP_004383344.1| 287 PKKIAA 292
                                       766665 PP

  == domain 3  score: 21.1 bits;  conditional E-value: 9.3e-08
                   Viral_helicase1 183 r........evttvhevqGltfdkVtlvllketdlelis...........esrenllvAlTRhrkslvil 233
                                       +         ++t h+v G +f+ V++++ k+++++  +           e+r + +vA +R++k+l+++
  gi|330506916|ref|YP_004383344.1| 493 SsdslieraTIKTIHQVKGDEFECVVILVPKPSPNNSPCpsvewwpdgpsEERRVAFVAASRAKKTLILC 562
                                       12333455779*************************998***********88***************987 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 !   28.7   0.1   3.7e-10   8.4e-07       3      52 .]     502     562 ..     500     562 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.7e-10
                          UvrD_C_2   3 yaltihkaQGsefpaVivfdpdlaaarmgel...........rrrlLYtavTRAreklilv 52 
                                       ++ tih+++G ef++V++  p  +    +              rr +++a++RA++ lil+
  gi|330506916|ref|YP_004383344.1| 502 TIKTIHQVKGDEFECVVILVPKPSPNNSPCPsvewwpdgpseERRVAFVAASRAKKTLILC 562
                                       677***************9999666655666999*************************96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00013       0.3      12      67 ..      15      74 ..      10      85 .. 0.80
   2 !    5.7   0.0    0.0048        11      85     172 ..     209     300 ..     150     321 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                            AAA_30 12 alltsgdrvavltGpAGtGKtta....lkalreaweaaggrviglAptgkaAkvLaeelg 67
                                      a++ s+ r++v+ + +G+GKt +    lk   + w++++  ++ ++ t+ a +++ae++g
  gi|330506916|ref|YP_004383344.1| 15 AVIDSNSRITVVRACPGSGKTRVfvesLKMRIDSWTKKNAGIASISFTNVAQEQIAEGIG 74
                                      55678899*************862222555677899998999999999999999998877 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0048
                            AAA_30  85 rlepg.tllivDEagmvdtkqlaallkaaekag.akvilvGDerQlasVeaGgvlrdlvea....agigtaeLtevv 155
                                        ++++  +++vDE   ++     al++ +++    + ++vGD++Q    e Gg+  dl+++     g+++  L++ +
  gi|330506916|ref|YP_004383344.1| 209 LVTRRfPMILVDEFQDTNWFLGLALIELLRSPFlESGLVVGDPDQA-IFEFGGANPDLFKDienlPGAKSLPLNQTH 284
                                       445556899999999999999999999999954488899*****84.345587766666555544788999****** PP

                            AAA_30 156 Rqkeseeraaalalreg 172
                                       R   ++++a+a al++ 
  gi|330506916|ref|YP_004383344.1| 285 RC-PKKIAAIATALSDT 300
                                       *9.56777777777654 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.25     128     194 ..     485     561 ..     467     565 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                            AAA_12 128 kkklkekeeekseke..........ievntvdgfQGrekdviilslVRsnekk.........eigflkderrlNVal 185
                                       +k+ +         +           +++t+ ++ G e +++++ + + ++++           g  +++r   Va 
  gi|330506916|ref|YP_004383344.1| 485 RKMAE---------HlessdslierATIKTIHQVKGDEFECVVILVPKPSPNNspcpsvewwPDGPSEERRVAFVAA 552
                                       22222.........244445555669******************999998777667766665455556666667*** PP

                            AAA_12 186 TRAksklii 194
                                       +RAk+ li+
  gi|330506916|ref|YP_004383344.1| 553 SRAKKTLIL 561
                                       *****9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0015       3.4       4      23 ..      20      39 ..      17      74 .. 0.78
   2 ?    0.5   0.0      0.29   6.5e+02      85     113 ..     209     238 ..     199     247 .. 0.71
   3 ?   -2.4   0.0       2.3   5.2e+03      91     112 ..     310     335 ..     264     348 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0015
                            AAA_22  4 tagilvvtGesGtGKTtllr 23
                                      + +i+vv +++G+GKT++  
  gi|330506916|ref|YP_004383344.1| 20 NSRITVVRACPGSGKTRVFV 39
                                      6789************9854 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.29
                            AAA_22  85 alraravielliiDEaqhlr...seealeeLr 113
                                        +  r+  +++++DE+q  +     +++e Lr
  gi|330506916|ref|YP_004383344.1| 209 LVT-RRF-PMILVDEFQDTNwflGLALIELLR 238
                                       344.444.59*******986555577777776 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.3
                            AAA_22  91 v...ielliiDEaqhlr.seealeeL 112
                                       +    +++++ ++++++ +++++ ++
  gi|330506916|ref|YP_004383344.1| 310 AdqgSAIILVHDMEKIDrNKKVIANI 335
                                       02233455555555554435555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); 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:                         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 0.21s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 4308.83
//
Query:       gi|330506917|ref|YP_004383345.1|  [L=613]
Description: hypothetical protein MCON_0715 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-32  113.8   0.4    2.5e-30  106.5   0.4    2.2  1  AAA_15       AAA ATPase domain
    7.3e-20   72.0  14.0    4.6e-11   43.1   9.4    3.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    3.6e-16   59.4   1.8    1.1e-09   38.0   0.2    2.3  2  DUF2813      Protein of unknown function (DUF2813)
    9.3e-12   45.9   0.2    2.1e-11   44.7   0.1    1.6  1  AAA_23       AAA domain
    1.2e-09   37.9   0.3    9.6e-09   35.0   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0021   17.8   0.0     0.0041   16.8   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.049   13.5   0.0    1.7  1  RsgA_GTPase  RsgA GTPase


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 !  106.5   0.4   9.6e-34   2.5e-30       1     369 []       1     342 [.       1     342 [. 0.60

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 9.6e-34
                            AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifen.iseskd 76 
                                       M+++ki++ NFR l++ e +ls+ l+v++G+Nn+GK+++l+al + l    +  ++ i + kedl+ + + +  +k+
  gi|330506917|ref|YP_004383345.1|   1 MYLSKISVHNFRNLESLEANLSPGLNVIVGENNVGKTNLLDALRVALGSAWNN-SEPIHLSKEDLHRSSDgNMIDKS 76 
                                       *******************************************9999966333.45566666776666441444566 PP

                            AAA_15  77 ikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekee 153
                                       i +d+ f          ++l ++e+ +               i + + k++++  + +++  +  +++++   +++ 
  gi|330506917|ref|YP_004383345.1|  77 IIVDLIF----------SELSEEEQAQFL------------EILNYNPKFPEKS-TASIHFEWSWNETNDRGYYRRW 130
                                       6666666..........222222222221............1122222222111.1111111222234444444444 PP

                            AAA_15 154 klekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkekileeal 230
                                         e ++ e++i  ++l+ l+                         l  a R++s+ +    ++ lg+l++       
  gi|330506917|ref|YP_004383345.1| 131 GGERSNSETSISEDILQMLSI-----------------------TLLGALRDASSGLAPGRQNRLGRLLRVSANAHD 184
                                       555555555555555555555.......................666777777777777777777777666655422 PP

                            AAA_15 231 qekleeelteklkeiqeklkeidkklaeelk..........kilkkkidkikkfnykgkkneeieik.......... 287
                                           + +l+e +++ +++l++  +  ++e+k                  ++k++ + +++++e +            
  gi|330506917|ref|YP_004383345.1| 185 ----KAQLEEVISKANNDLEQNPFVRSAEEKismalegasgP-------EFKQEAIIRSSEPEFDRIannlrlvlki 250
                                       ....22333333333333333222222222222212133330.......2223333333333222223444455555 PP

                            AAA_15 288 ........ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnk 356
                                                    +l  nG+G+++l+++++ + e+e     ++   +ll+EEPEahLHpq+q  li+ l++    ++
  gi|330506917|ref|YP_004383345.1| 251 sdldlatgKPITRELRSNGLGYNNLIYIATVLSELETV--AQAALPLLLVEEPEAHLHPQLQILLINFLLKRGAGSS 325
                                       566666544555689**********************9..9999***********************9987665555 PP

                            AAA_15 357 t....QviitTHSphii 369
                                            Qvi+t HSp i+
  gi|330506917|ref|YP_004383345.1| 326 EthgvQVIVTAHSPTIA 342
                                       55889*********996 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.3   3.4e-09   8.7e-06       1      24 [.      25      48 ..      25      57 .. 0.85
   2 !   43.1   9.4   1.8e-14   4.6e-11      87     301 ..      51     341 ..      48     343 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.4e-09
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                      lnv++G N++GK+nLLdal+++ +
  gi|330506917|ref|YP_004383345.1| 25 LNVIVGENNVGKTNLLDALRVALG 48
                                      7******************99865 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 1.8e-14
                            AAA_21  87 lssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrk 163
                                       + ++e+ ++s + l ++s+  + +++  ++ i++ +s++++++++ +   +++f++  t ++++ ws+++ +d +++
  gi|330506917|ref|YP_004383345.1|  51 WNNSEPIHLSKEDLHRSSDGNMIDKSIIVDLIFSELSEEEQAQFLEILNYNPKFPEKSTASIHFEWSWNETNDRGYY 127
                                       66789999********************************************************************* PP

                            AAA_21 164 erigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer..................... 219
                                       +r+g  +   ++    +++++l+  + + +++ +   + g +++l  +  +  +                       
  gi|330506917|ref|YP_004383345.1| 128 RRWGGERSNSETSISEDILQMLSITLLGALRDASSGLAPGRQNRLGRLLRVSANAHdkaqleeviskanndleqnpf 204
                                       *99999999999999999999999999999999999999877777666666655559999999************** PP

                            AAA_21 220 ............................................gvvflengdgqelparelSdGtkrl..lallta 250
                                                                                    +  l+   g++++    S G      ++++t 
  gi|330506917|ref|YP_004383345.1| 205 vrsaeekismalegasgpefkqeaiirssepefdriannlrlvlKISDLDLATGKPITRELRSNGLGYNnlIYIATV 281
                                       *******************************9999999999998444444444444444444555555540566666 PP

                            AAA_21 251 llralkkg....sllliDEpEngLHPkllrrllell.kelsr....ngaQviltTHSpll 301
                                       l ++   +    +lll++EpE++LHP+l+  l+ +l k+ +     +g+Qvi+t HSp++
  gi|330506917|ref|YP_004383345.1| 282 LSELETVAqaalPLLLVEEPEAHLHPQLQILLINFLlKRGAGssetHGVQVIVTAHSPTI 341
                                       66666666****************************955555566679**********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 !   38.0   0.2   4.4e-13   1.1e-09       1      90 [.       1      93 [.       1     123 [. 0.85
   2 !   20.6   0.1     9e-08   0.00023     278     358 ..     287     376 ..     243     387 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 4.4e-13
                           DUF2813  1 myLerieisGFRGinrLSlslee.ntvLiGENaWGKSSLldALsliln...vekelyqFtlkDFhvdeseeeeqekhlq 75
                                      myL +i +  FR ++ L  +l++ ++v++GEN  GK  LldAL ++l    +++e  + +++D h ++s+ +  +k++ 
  gi|330506917|ref|YP_004383345.1|  1 MYLSKISVHNFRNLESLEANLSPgLNVIVGENNVGKTNLLDALRVALGsawNNSEPIHLSKEDLH-RSSDGNMIDKSII 78
                                      9********************98579*********************8333578999********.55999999***** PP

                           DUF2813 76 lvltfkeeekeeeka 90
                                      + l+f+e ++ee+ +
  gi|330506917|ref|YP_004383345.1| 79 VDLIFSELSEEEQAQ 93
                                      ******988866543 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 9e-08
                           DUF2813 278 elkriarPilllEdpearLHPtmlaiaWell........ellPlQkiltTNSveLlsqvplesirrLvRe.sdrtqa 345
                                       ++ + a P+ll+E+pea+LHP+   ++ ++l        e+  +Q i+t  S  + s vp+e +r L R  s++ ++
  gi|330506917|ref|YP_004383345.1| 287 TVAQAALPLLLVEEPEAHLHPQLQILLINFLlkrgagssETHGVQVIVTAHSPTIASYVPIEILRVLHRDpSGKLRC 363
                                       3569999**************87666666553444444356789*********************9*9983579999 PP

                           DUF2813 346 yslerkslskedl 358
                                       + l++  l k + 
  gi|330506917|ref|YP_004383345.1| 364 MCLRECGLTKKEA 376
                                       9999999988774 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.1     8e-15   2.1e-11       1     100 [.       5     122 ..       5     217 .. 0.64

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 8e-15
                            AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese...gkvkay 74 
                                       k++++nfr ++  e ++s+gl++I+G+N  GKT +ldA++ aL+      ++++  ++ k+d + +s+    + k +
  gi|330506917|ref|YP_004383345.1|   5 KISVHNFRNLESLEANLSPGLNVIVGENNVGKTNLLDALRVALGS---AWNNSEPIHLSKEDLHRSSDgnmID-K-S 76 
                                       799*****************************************8...4555555666777777666633222.2.2 PP

                            AAA_23  75 ..veltfenkdgry..................trsiererelskkk 100
                                         v+l f+  ++++                  t si++e ++++++
  gi|330506917|ref|YP_004383345.1|  77 iiVDLIFSELSEEEqaqfleilnynpkfpeksTASIHFEWSWNETN 122
                                       3577777776666666666666555555554433333333333333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   3.8e-12   9.6e-09       1      53 [.       2      52 ..       2     110 .. 0.77
   2 ?    0.7   0.0      0.12     3e+02     142     201 ..     273     341 ..     168     356 .. 0.70

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 3.8e-12
                                      EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersa 53
                                      +l+++ ++nF+++  ++ + ++s+++++ivG+N  GK+nlldA++  LG + +
  gi|330506917|ref|YP_004383345.1|  2 YLSKISVHNFRNL--ESLEANLSPGLNVIVGENNVGKTNLLDALRVALGSAWN 52
                                      689**********..7*********************************7633 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHH...HHCCS--SEEEECTTTTTS-HHHHHHHHHHHH......HHCTTSEEEEE-SSHHH CS
                                       xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxx RF
                             SMC_N 142 ktLvalaLlfA...iqkvkpaplyllDeidaaLDeknvkkvaellk......eksknaQfivislreem 201
                                         L+ +a +++   + +    pl l+ e +a+L  +    + ++l       ++++ +Q+iv++++ ++
  gi|330506917|ref|YP_004383345.1| 273 NNLIYIATVLSeleTVAQAALPLLLVEEPEAHLHPQLQILLINFLLkrgagsSETHGVQVIVTAHSPTI 341
                                       456666666665444444556888888888888887777666665413333233445899999887665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.6e-06    0.0041       1      46 [.       3      47 ..       3      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.6e-06
                            AAA_29  1 LkrlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                      L+++++ N   ++  ++++++    +++G++ +GK+ llDA+ + L
  gi|330506917|ref|YP_004383345.1|  3 LSKISVHNFRNLESLEANLSPG-LNVIVGENNVGKTNLLDALRVAL 47
                                      6778888888888877888754.79*****************9877 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   1.9e-05     0.049      81     121 ..       5      45 ..       1      91 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                                       E--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  81 lvsaktkegleelkellkdktsvlvGqSGvGKStLinallp 121
                                       ++s+++ ++le+l+++l+  + v+vG+  vGK+ L++al+ 
  gi|330506917|ref|YP_004383345.1|   5 KISVHNFRNLESLEANLSPGLNVIVGENNVGKTNLLDALRV 45 
                                       67899999*****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 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:                        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):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 4210.85
//
Query:       gi|330506918|ref|YP_004383346.1|  [L=418]
Description: type I restriction-modification enzyme, S subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-26   92.9   0.0    6.3e-14   52.5   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 !   38.5   0.0   7.3e-14   1.3e-09       1     154 [.       7     164 ..       7     176 .. 0.81
   2 !   52.5   0.0   3.5e-18   6.3e-14      26     160 ..     231     379 ..     206     383 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 7.3e-14
                                       ETT-EEEEHHHHEEEEE-----TTGGTTT--EEEE-HH.HCCT.....EE-HHHHCCTT---B-TT-EEEE-S.SST CS
                       Methylase_S   1 pedwevvkLgdvfeikkgktpkkkelkengkypyirag.ilnn.....kvvkdglgykkkyilpkgdilissr.ati 70 
                                       p+ w++++L++v+e++k  + +    +++++ py++ + i ++         +++ +++k ++++gdil+++   + 
  gi|330506918|ref|YP_004383346.1|   7 PSSWKMISLDEVCELRKEAIHP----NKYPDLPYVGLEhIDSSnsilkRSGSSFEVNSSKSKFHSGDILYGKLrPYL 79 
                                       789************7777666....69*********9866667999855556777777788888888888655888 PP

                                       T-EEEESS-BEE-TTEEEEEESTTT--HHHHHHHHHHCHHHHHHH....CCSSTTT---HHHHCC-EEEE--HHHHH CS
                       Methylase_S  71 Gkvayrdkkyylnqsvivlipknkkkineflylylllklkklksl....svgstqpkltkenlkkikIplPpleeQk 143
                                        k  + d++  +++++ vl+ k+++   +fl +++ +   +++++    s+g ++p+ + + ++ +k+ lPpl+eQ 
  gi|330506918|ref|YP_004383346.1|  80 DKSVLVDFDGMCSTDILVLKTKESIV-PQFLVNIIHTS--QFINYavnsSKGLNHPRTSWSSISAFKFLLPPLPEQR 153
                                       8999999999***********96444.59999999744..3333333449*************************** PP

                                       HHHHHHHHHHH CS
                       Methylase_S 144 kIakiLsqldn 154
                                        Ia+ + ++ +
  gi|330506918|ref|YP_004383346.1| 154 AIARAMRAVQA 164
                                       *****998877 PP

  == domain 2  score: 52.5 bits;  conditional E-value: 3.5e-18
                                       GTTT--EEEE-HHHCCT.........EE-HHHHCCTT---B-TT-EEEE-SSSTT-EEEESS-B..EE-TTEEEEEE CS
                       Methylase_S  26 lkengkypyiragilnn.........kvvkdglgykkkyilpkgdilissratiGkvayrdkky..ylnqsvivlip 91 
                                       +   g+  + + +i n+         ++ +++ +++k +   +gd+l+s  a++G++ + + ++  +l+q+++ l++
  gi|330506918|ref|YP_004383346.1| 231 FSPAGVLVVRNFNIRNGrldlkfpsyTTEEEYSERVKRCEPTEGDVLFSREAPVGEACLVPPDVrlCLGQRMMLLRV 307
                                       5555555555555666666667777778899****************************9997444*********** PP

                                       STTT--HHHHHHHHH...HCHHHHHHHCCSSTTT---HHHHCC-EEEE--HHHHHHHHHHHHHHHH.HHHHHH CS
                       Methylase_S  92 knkkkineflylyll...lklkklkslsvgstqpkltkenlkkikIplPpleeQkkIakiLsqldn.tielek 160
                                        ++k++ +f +   +   ++ + ++++s g+t ++l+ +++k + Ip+ ++eeQk+I +iLs+ d+  ++le+
  gi|330506918|ref|YP_004383346.1| 308 DTSKLN-RFFLVQVFysnAIRSIMMAISSGVTAKHLNVADVKRLRIPFSSMEEQKQISDILSACDSkITALEH 379
                                       754444.66665555344566699999***************************************6666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3042.12
//
Query:       gi|330506919|ref|YP_004383347.1|  [L=546]
Description: N-6 DNA methylase [Methanosaeta concilii GP6]
Scores for complete 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-95  318.0   0.0    8.4e-95  317.6   0.0    1.1  1  N6_Mtase         N-6 DNA Methylase
    3.6e-26   92.4   0.0    8.9e-26   91.1   0.0    1.7  1  HsdM_N           HsdM N-terminal domain
    0.00088   19.0   0.0     0.0015   18.2   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
       0.08   12.7   0.0       0.17   11.7   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
       0.19   11.2   0.0       0.45    9.9   0.0    1.6  2  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 !  317.6   0.0   2.3e-98   8.4e-95       3     310 ..     191     508 ..     189     510 .. 0.94

  Alignments for each domain:
  == domain 1  score: 317.6 bits;  conditional E-value: 2.3e-98
                          N6_Mtase   3 kdllGdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkee..dgktke 77 
                                        d+lG++YEyllrkfae +g+s+Gef+TP+ev  li+el++p + +++yDpacGsggll++a    +++  d+  ++
  gi|330506919|ref|YP_004383347.1| 191 PDILGRAYEYLLRKFAEGQGQSAGEFYTPKEVGDLIAELIDPVPYSTIYDPACGSGGLLIKARLLYERRhpDERSRA 267
                                       79***********************************************************9987665567788888 PP

                          N6_Mtase  78 lsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfe...kdkkfdvvvaNppfnqkewkektlekde.. 149
                                         ++Gqe+n+ t+++akmN++lh+   +  + ++gdt+ kp f    + ++fd+vvaNp +nq++++++  e+d+  
  gi|330506919|ref|YP_004383347.1| 268 PRLWGQELNPVTFAMAKMNMFLHDYTDS--SFAIGDTFRKPGFGpegSLMQFDYVVANPMWNQDNYDDAFYENDSfn 342
                                       99*********************98888..6889*********999999************************9888 PP

                          N6_Mtase 150 rfreavapksnadlafllhiieslkpkGraavvlangvLfrg......gkegkIrkalvekdlveavialpeklFyn 220
                                       rf+ +++p+s+ad+ +++h+ +slk++Graavvl+ g+ +rg      ++e++Ir+a+ve+d +e+v+ lpe+lFyn
  gi|330506919|ref|YP_004383347.1| 343 RFNFGIPPRSSADWGWVQHMFASLKEGGRAAVVLDTGAVSRGsgsrssNREKAIRQAFVEADAIEGVVLLPENLFYN 419
                                       9999***********************************98534444478*************************** PP

                          N6_Mtase 221 tsiptcilvlkkekae.rkgkvlfidaseefkkkdrkknklteediekildtykekskevdkfskvveleeiaendy 296
                                       t++p++il+l+k+k+e r g++l+++as+ f k+ + kn+lt+e i+ ++++y+++ +  +k s+v++l+e++e dy
  gi|330506919|ref|YP_004383347.1| 420 TTAPGIILLLRKGKPEeRAGQILLVNASNYFVKE-KPKNALTPEGIAAVAEVYQKW-ETREKLSRVITLDEVREADY 494
                                       **************9989****************.8********************.9******************* PP

                          N6_Mtase 297 nlnvgryveteeee 310
                                       nl+++++ve +e e
  gi|330506919|ref|YP_004383347.1| 495 NLSPSQFVEINERE 508
                                       ********987766 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.0   2.5e-29   8.9e-26       1     136 [.      34     178 ..      34     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 2.5e-29
                                       HHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC................--...--------... CS
                            HsdM_N   1 lesklwkaadiLRgkvdaseykeyilgLlFlKrlddveeereeklleeyken.........al.eeleeklkskeaf 67 
                                       le +lw+aa+ +Rg+ da+++k++il+L+F Krl+dv+e++ ++ + ey+++         +l ++l+     +  f
  gi|330506919|ref|YP_004383347.1|  34 LETWLWDAACAIRGATDAPKFKDFILPLVFFKRLSDVFEDEFAAHVREYGDEelartiveeDLaHSLKTGSTPIIRF 110
                                       789**************************************88887887777776665532223444444445599* PP

                                       .S-CCCSHHHHHHS--HHHHHHHHHHCHHHHCT--STHHHHHHHS......S-----SSHHHHHHHHHH CS
                            HsdM_N  68 yipeelrWkelakkkdddelgenlnkafpaleelnkslkgvfmkddfnafalgeitkkspalLskviek 136
                                       y+p +++W+ ++++  d  lge++++ ++++++ln++l+gv++ +d+n+++ g+ ++ ++++L  +ie 
  gi|330506919|ref|YP_004383347.1| 111 YVPGDYNWRAIRNHGADGRLGEFVTESLREVARLNPDLQGVLDIKDYNERQSGQ-RTLDDDRLGALIEV 178
                                       **************55559***********************755777775555.79*********985 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   0.0   4.3e-07    0.0015      27      56 ..     233     262 ..     225     299 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.3e-07
                                       -TTS-EEETT-TTSHHHHHHHHHHTT--TT CS
                           UPF0020  27 kpgepllDPmCGsGtilIEaallganiapg 56 
                                        p ++++DP CGsG++lI a ll +++ p 
  gi|330506919|ref|YP_004383347.1| 233 VPYSTIYDPACGSGGLLIKARLLYERRHPD 262
                                       56689*******************999973 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.8e-05      0.17       6      95 ..     237     337 ..     235     377 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.8e-05
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkae.........vvGiDiseeaielArenaqklgldnveFeqgdieeleklled. 72 
                                       +++D++CG+G l++++  +l+++ +         + G + ++     A+ n   + ++  +F +gd + ++  + + 
  gi|330506919|ref|YP_004383347.1| 237 TIYDPACGSGGLLIKAR-LLYERRHpdersraprLWGQELNPVTFAMAKMNMFLHDYTDSSFAIGDTFRKPG-FGPe 311
                                       699************99.5555444445566778***********************************996.5667 PP

                   Methyltransf_31  73 ...ekfDlilsnevlnaladpdkile 95 
                                           +fD++++n   n  +  d+++e
  gi|330506919|ref|YP_004383347.1| 312 gslMQFDYVVANPMWNQDNYDDAFYE 337
                                       7999*******976655554444444 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00013      0.45      55      78 ..     236     259 ..     227     293 .. 0.71
   2 ?   -3.3   0.0       1.4   4.8e+03     116     155 ..     466     505 ..     462     519 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00013
                             AviRa  55 ltlyDpCCGgayLltvlgllhgkk 78 
                                        t+yDp CG++ Ll    ll++++
  gi|330506919|ref|YP_004383347.1| 236 STIYDPACGSGGLLIKARLLYERR 259
                                       48************9999998764 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                             AviRa 116 elaeeyekeshaealesaerleellakkgeekeievfkad 155
                                       ++ae y+k   +e+l+ +  l+e+ +++++  + + ++++
  gi|330506919|ref|YP_004383347.1| 466 AVAEVYQKWETREKLSRVITLDEVREADYNLSPSQFVEIN 505
                                       5677888888999999999999988888777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 4035.65
//
Query:       gi|330506920|ref|YP_004383348.1|  [L=486]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-18   65.4   0.0    3.3e-17   63.4   0.0    2.0  2  Radical_SAM  Radical SAM superfamily
    3.1e-14   53.1   0.2      6e-14   52.1   0.2    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 ?   -1.2   0.0      0.26   2.3e+03      32      60 ..      74     100 ..      47     137 .. 0.75
   2 !   63.4   0.0   3.7e-21   3.3e-17       1     163 [.     192     353 ..     192     357 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHTTSEEEEEESSTGGGS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  32 eeileevkelkaekgvkevilgggeplly 60 
                                       +e l++++++ +e  + + ++gg +p+l 
  gi|330506920|ref|YP_004383348.1|  74 QEALALARIA-KEA-GAQTVFGGYHPTLA 100
                                       4556666666.344.55555555556655 PP

  == domain 2  score: 63.4 bits;  conditional E-value: 3.7e-21
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla... 74 
                                       v+++rgC+++C+fC+++ +   +++ r+ ++e+++e ++ + +e+g++ +++  ++ +l+p+  e l +++  a   
  gi|330506920|ref|YP_004383348.1| 192 VETSRGCTQGCKFCSINLM--YGRHFRTFPIERVVEDIRDA-EEHGAGSIFFPDDNITLNPKRLERLCQAIIDAglt 265
                                       5789*************97..********************.9********************99999999999*** PP

                                       CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivg 151
                                       +  +++  +++g+  +++ ++++ e+g+d v lg+e+++++  l+ +++g+   +   a+++l++++i +++  i g
  gi|330506920|ref|YP_004383348.1| 266 HLRYKTQASASGIASSKRLVDKMGEAGFDGVFLGVESINKR-NLEFLGKGKMSNDAEIAVQYLHDNNIIVSTGLIGG 341
                                       9*************99*************************.*****99999999999***********65555556 PP

                                       BTTTSHHHHHHH CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 152 lpGendeeleel 163
                                        p   +e+l+e 
  gi|330506920|ref|YP_004383348.1| 342 NPDDDEEDLWEN 353
                                       666666777765 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.2   6.7e-18     6e-14      12     120 ..      21     128 ..      18     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 6.7e-18
                       B12-binding  12 lhplGlavlaaalrd.agfeVqll.ganvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvvv 86 
                                       l++lGla+laa++ d   ++V ++ g++ + e + +++++   d+vgl+a ++ q++++ +l++ +k++  ++ +v+
  gi|330506920|ref|YP_004383348.1|  21 LPNLGLASLAAHVDDlCTVHVADIhGLKDHREYVKKQVQDY--DLVGLTA-MSFQYQEALALARIAKEA--GAQTVF 92 
                                       799************43667765524444446666666655..*******.*****************9..669*** PP

                       B12-binding  87 GGahpsldpeetleak..lgiddvvvgegedaleal 120
                                       GG hp+l++ee+ + +    id++v+gege ++++l
  gi|330506920|ref|YP_004383348.1|  93 GGYHPTLAAEEIGQSDdsQLIDYIVRGEGEATFREL 128
                                       ***********99999*9999************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3392.04
//
Query:       gi|330506921|ref|YP_004383349.1|  [L=461]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   54.9   0.4    4.2e-14   53.3   0.3    1.9  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.046   13.7   0.0    1.8  2  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.3   4.7e-18   4.2e-14       3     161 ..     171     330 ..     169     336 .. 0.86
   2 ?   -1.8   0.0      0.38   3.4e+03      77     103 ..     377     401 ..     339     408 .. 0.60

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 4.7e-18
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                       +trgC+ +C+fC++p       ++ ++s+e+i++ + ++ +++g+++vi+   +   +++ ++++ +l  +   g+ 
  gi|330506921|ref|YP_004383349.1| 171 TTRGCPVGCKFCQTPV---FCNKPNIISLESIERVLAYY-KKMGINVVIIEDENFGCNRRHADEVVKLLDKY--GMV 241
                                       69*************9...8*******************.7*****************************84..444 PP

                                       EEEEECSSCHG...HHHHHHHHHTT.....-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEE CS
                                       xxxxxxxxxxx...xxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpd...eeklerllelg.....vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdr 148
                                         + + +  ++   ++++++  + g     +   ++g+e ++ e  l+ ++++++ e++le+l++l ++g+  + + 
  gi|330506921|ref|YP_004383349.1| 242 WGCMARADYLRkkiDDWADARMKNGkqvsgFAGAAIGIENLHQE-RLDEIKKKEGTEDILETLRMLQARGLGTIGYY 317
                                       44444444442446666665555559*9999*************.999999*********************99999 PP

                                       EEEBTTTSHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 149 ivglpGendeele 161
                                       ++g++  ++e l+
  gi|330506921|ref|YP_004383349.1| 318 MIGFEEDTKESLK 330
                                       9999999999876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.38
                                       TEEEEEEECSSCHGHHHHHHHHHTT-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvd 103
                                       g   +++ n++++ ++ ++++l++ + 
  gi|330506921|ref|YP_004383349.1| 377 GK--HLVWNHPHIKPDEMQEILDRSLR 401
                                       33..44445555555555555555444 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.2e-06     0.046      48     117 ..      73     135 ..      46     138 .. 0.78
   2 ?   -3.4   0.0         1   9.4e+03      23      40 ..     205     227 ..     200     237 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-06
                       B12-binding  48 raekpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedal 117
                                        +e  dvvglS+ + s+  ++ e++e++++++++  v++G  ++ +++ +       +d v vg++e+ l
  gi|330506921|ref|YP_004383349.1|  73 LQEGWDVVGLSF-YLSETHEAVEMAEAARSAGAG-EVWAGNYGALTTAVQ-----DRFDKVFVGYAEHQL 135
                                       45568*******.999999************998.999999884444444.....77799999****986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1
                       B12-binding  23 alrdagfeVqll.....ganven 40 
                                       + ++ g++V+++     g+n  +
  gi|330506921|ref|YP_004383349.1| 205 YYKKMGINVVIIedenfGCNRRH 227
                                       44444666666655544555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 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:                        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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3160.51
//
Query:       gi|330506922|ref|YP_004383350.1|  [L=102]
Description: hypothetical protein MCON_0720 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 772.38
//
Query:       gi|330506923|ref|YP_004383351.1|  [L=149]
Description: hypothetical protein MCON_0721 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-41  141.7   0.4    1.4e-41  141.5   0.4    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 !  141.5   0.4   7.7e-46   1.4e-41       7     143 ..       2     134 ..       1     135 [. 0.98

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 7.7e-46
                           DUF2240   7 aapfkkkrkdklsesdfvfalsldrkwlspdqakklldraeeegLlekkdgdlvpnfdvaeveiPlgFkpdeellke 83 
                                       a pfkk++k++l+ sdf+falsld+kw sp+++++ll +ae+eg+++ +++ ++++fd  +v++PlgFkp+     e
  gi|330506923|ref|YP_004383351.1|   2 ATPFKKRGKKSLKISDFIFALSLDLKWGSPEKVRALLREAEAEGMVKMDGEIVSAAFDIDAVDVPLGFKPS----TE 74 
                                       89*********************************************************************....89 PP

                           DUF2240  84 kstferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegvdvddliee 143
                                       + ++++ ++ i+++tg+++kev+a +n++q++lk+lv+++a++l++a++ g+dv+dl+++
  gi|330506923|ref|YP_004383351.1|  75 EAILDQGIRLITSQTGMSRKEVIALANDKQDSLKKLVEMDAVVLLLAREMGLDVHDLAAK 134
                                       *********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1195.18
//
Query:       gi|330506924|ref|YP_004383352.1|  [L=557]
Description: hypothetical protein MCON_0722 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00028   21.1   0.2        2.2    8.6   0.0    3.7  3  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
  ------ inclusion threshold ------
       0.04   14.0   0.0         39    4.3   0.0    3.4  3  DUF916       Bacterial protein of unknown function (DUF916)


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 !    6.8   0.0    0.0009       8.1      46      71 ..     108     133 ..     102     134 .. 0.92
   2 !    8.6   0.0   0.00025       2.2      30      76 ..     207     257 ..     185     259 .. 0.67
   3 ?    2.5   0.0      0.02   1.8e+02       2      21 ..     246     265 ..     245     305 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0009
                       NPCBM_assoc  46 slapGetveatvkVtppagaaaGdye 71 
                                        l pGe++e ++ + +p+++++G y+
  gi|330506924|ref|YP_004383352.1| 108 PLSPGEEAEIKIYIGIPPETKPGVYT 133
                                       799********************996 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00025
                       NPCBM_assoc  30 lPeGWtvvevs...pasaa...slapGetveatvkVtppagaaaGdyevtaka 76 
                                       +PeGW+vv ++   p s++    l pG+t e ++++   ++   +  +vt++a
  gi|330506924|ref|YP_004383352.1| 207 VPEGWSVVLMDddePMSMPydlPLNPGATHEIKLQI--QTDKPGSRENVTITA 257
                                       7*****887652226778895555666666555555..555555556666666 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.02
                       NPCBM_assoc   2 epGetvtltltvtndgtaaa 21 
                                       +pG++ ++t+t+t+ g++++
  gi|330506924|ref|YP_004383352.1| 246 KPGSRENVTITATSLGNRSM 265
                                       59*************98875 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 ?    1.2   0.0     0.041   3.6e+02      11      43 ..      51      83 ..      47      96 .. 0.85
   2 ?    4.3   0.0    0.0044        39      84     118 ..     104     138 ..      94     140 .. 0.86
   3 ?    4.2   0.0    0.0049        44      19      47 ..     226     257 ..     219     330 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.041
                            DUF916 11 qidkkksYFdLkvkpgqeqelevkikNssdkei 43
                                      q   +k+ Fd+ + pg  +e  +k+ N+ d++i
  gi|330506924|ref|YP_004383352.1| 51 QLAPDKERFDIVLHPGDGDERILKVMNNGDSTI 83
                                      77778889********************99985 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0044
                            DUF916  84 pkeitlpakesktvklkikmPkeefdGvilGGiyv 118
                                       p+   l ++e+ ++k+ i +P e   Gv+ G +y+
  gi|330506924|ref|YP_004383352.1| 104 PEDKPLSPGEEAEIKIYIGIPPETKPGVYTGFVYL 138
                                       5666799**********************998876 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.0049
                            DUF916  19 FdLkvkpgqeqelevkikNss...dkeitvei 47 
                                       +dL ++pg+++e++++i+ ++    +++t+++
  gi|330506924|ref|YP_004383352.1| 226 YDLPLNPGATHEIKLQIQTDKpgsRENVTITA 257
                                       89***************987532244444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.38
# Mc/sec: 4353.56
//
Query:       gi|330506925|ref|YP_004383353.1|  [L=1446]
Description: hypothetical protein MCON_0723 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-27   95.9   0.2    4.4e-27   95.3   0.2    1.2  1  Peptidase_C25  Peptidase family C25
    7.8e-06   26.1   0.1    3.7e-05   23.9   0.0    2.2  2  DUF11          Domain of unknown function DUF11
    0.00012   21.2   0.0    0.00022   20.4   0.0    1.3  1  GHL10          Glycosyl hydrolase-like 10
     0.0079   16.4   0.0        4.6    7.6   0.0    3.3  3  NPCBM_assoc    NPCBM-associated, NEW3 domain of alpha-galacto
  ------ inclusion threshold ------
      0.018   14.8   0.2      0.055   13.3   0.0    2.0  2  SH3_16         Bacterial dipeptidyl-peptidase Sh3 domain
      0.021   14.6   0.1      0.036   13.8   0.1    1.2  1  HGD-D          2-hydroxyglutaryl-CoA dehydratase, D-component


Domain annotation for each model (and alignments):
>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.3   0.2   1.5e-30   4.4e-27      63     377 ..     845    1153 ..     824    1154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 1.5e-30
                                        T.--SEEEEES-T.............TTS--EE-.....TTT-SEESHHHHS-T.....TSSS-SSEEEEE--SS CS
                     Peptidase_C25   63 s.klkYllLvGdtsivvkvkspitksdliptyqiakslgnestiptDdyyasldgnedsddltpdlavGRipvts 136 
                                        +  ++Yl+ vGd             + +i t  i+k+++  ++ ++ dy + +d      +++  +avGRi   s
  gi|330506925|ref|YP_004383353.1|  845 NlDPEYLMVVGDP----------GSIPFISTGLIQKLSEVMEYEVYRDYQIKPD-----LNNYSTVAVGRIMGLS 904 
                                        35689********..........677899999999999****************.....9*************** PP

                                        HHHHHHHHHHHHHHHCT--S-G....GGGEEEEEE--.........HHTHHHHHHHHHHHTSSGGGT-SEEEEE- CS
                     Peptidase_C25  137 aaeaaavvnKiiaYerntengsaagqwrnkvlliagdvvgeweaadgneiagttaettpseynvnklyadlaaye 211 
                                        + +a+++ ++++aY+r+      +g+w+n+ l+++                    +++p ++ +++++++  a  
  gi|330506925|ref|YP_004383353.1|  905 VYDASQLMARTMAYDRL------NGSWKNNGLVVSSP--------------ALSFPQAPVGIRIKEYLEE--AGL 957 
                                        ****************9......588***********..............4567999*********999..777 PP

                                        SS--.............TTTTHHHHH--SEEEEES-EETTEE.......TTTTEEHHHHHT---TT--EEEEEES CS
                     Peptidase_C25  212 aetetevpaanqpllttqnllkalnqGvlfvnytGHGsetaw.......adeslstndisaltntnklpiaitaa 279 
                                           +   ++ ++   t+q+  ++ln+G+++ ++ +HGse++w       +d  l+ +++++l+  +  + +++ a
  gi|330506925|ref|YP_004383353.1|  958 MVKD---LRHEE--ATYQQTISQLNNGQNIAHFDHHGSEDSWglsawsmTDSALTGSQVKELSLPP--QTTTASA 1025
                                        7777...33333..4789**************************9999999999**********98..99***** PP

                                        SSTT-TTSSS-.................-HHHHHHHSTTSSEEEEEEESS---SS--SHHHHHHHHHHHHHHH.. CS
                     Peptidase_C25  280 Cltgafdeetkr................sfgeklvlnangGavayigatrlgysgvndrlsraffealfadaart 338 
                                        C t++++    +                s++ +++   ++Gav+yig + l+y+  +d++ ++f+++l+  +  t
  gi|330506925|ref|YP_004383353.1| 1026 CVTTNLKGY--YlnvtgtrmyvpgnledSIALAFI---RAGAVNYIGGSALSYIFLSDDYYKSFYQSLIFRNS-T 1094
                                        ******444..346999999999998888888888...*******************************9998.6 PP

                                        .T-S-SS-HHHHHHH....................................EEEEE-TT-- CS
                     Peptidase_C25  339 lGealllaknelletgl.................aqsi..skgm.nkrt..fnllGDPalr 377 
                                        +G+a l a+n + ++                   +      ++m n+++   ++lGDP+++
  gi|330506925|ref|YP_004383353.1| 1095 VGQAQLDADNLFRLKSRgteslkpnsdydevlpaW--DisVHEMlNQTSymNVILGDPSFK 1153
                                        **********999887799*********9999753..235777878777545799***987 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         6   1.8e+04      14      48 ..     346     377 ..     338     395 .. 0.76
   2 !   23.9   0.0   1.2e-08   3.7e-05      13      77 ..     578     663 ..     562     666 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 6
                             DUF11  14 dtvtytltvtNtgpasangvvvtDtlPaglayvsv 48 
                                       d v y+l ++N  +a +    ++D++ +g ++v +
  gi|330506925|ref|YP_004383353.1| 346 DYVGYVLSTQNVKGAVS---YIEDLVGSGASGVVF 377
                                       46788888888877777...788888777777765 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.2e-08
                             DUF11  13 GdtvtytltvtNtgpasangvvvtDtlP.......aglayvsvsas...............qgtasaltsv.....g 62 
                                       G+ v+ + t+tN+g   + gv+++D+ P       a++ay +v  +               +g+            g
  gi|330506925|ref|YP_004383353.1| 578 GEVVRLNFTLTNSGDEVLRGVQLRDIFPmgrlirlASTAYGEVNVTdpysrkpvtetsaflNGS------LirwdfG 648
                                       899999**********************999999888888888888998888887554443222......2455559 PP

                             DUF11  63 sLeagesatlsftvr 77 
                                       +Le+gesa l+++v+
  gi|330506925|ref|YP_004383353.1| 649 RLEPGESASLNVEVE 663
                                       99*********9986 PP

>> GHL10  Glycosyl hydrolase-like 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   7.5e-08   0.00022     125     215 ..     189     283 ..     158     315 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.5e-08
                             GHL10 125 agerlwlnPliPevqdfitklvvevvkrYdvDgvqlDDyfylpesfGydlidvalYrqetkkealsnkeddl....w 197
                                        g+  ++ P+ Pev+d + + ++ ++  Y vDgv l  +    e+  y    ++++ q+t+ +   ++++      w
  gi|330506925|ref|YP_004383353.1| 189 GGNSSYYCPMNPEVKDRLYNQIEMLIDDYHVDGVVLYRFGFQDENHCYCDVCKEKFYQDTGIDISKVNANSYnrekW 265
                                       58899*******************************9997777777776666666666666454443333224555* PP

                             GHL10 198 idWRrdkisqlvkklnat 215
                                        +W++d++  +v    ++
  gi|330506925|ref|YP_004383353.1| 266 AEWKQDQLMDIVMDARNI 283
                                       ******999988776555 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 ?    4.3   0.0     0.016        47       3      33 ..     577     607 ..     576     615 .. 0.92
   2 ?   -1.3   0.0      0.87   2.6e+03      46      60 ..     649     663 ..     646     681 .. 0.71
   3 !    7.6   0.0    0.0016       4.6      10      46 ..     741     776 ..     736     790 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.016
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeG 33 
                                        Ge v+l++t+tn+g++ +++v+l+  +P G
  gi|330506925|ref|YP_004383353.1| 577 DGEVVRLNFTLTNSGDEVLRGVQLRDIFPMG 607
                                       69999*******************9888866 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.87
                       NPCBM_assoc  46 slapGetveatvkVt 60 
                                       +l+pGe+++ +v+V 
  gi|330506925|ref|YP_004383353.1| 649 RLEPGESASLNVEVE 663
                                       577777777777664 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0016
                       NPCBM_assoc  10 tltvtndgtaaatnvslslslPeGWtvvevspasaas 46 
                                       +l +tn +++ + +v++sl++P +W   ++++++a++
  gi|330506925|ref|YP_004383353.1| 741 RLKLTNITRDGLYDVRVSLQTPGNWL-FNIETDEART 776
                                       7899*********************9.6666666665 PP

>> SH3_16  Bacterial dipeptidyl-peptidase Sh3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.7   8.1e+03      41      48 .]      82      89 ..      82      89 .. 0.95
   2 ?   13.3   0.0   1.8e-05     0.055      20      46 ..     328     354 ..     326     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.7
                                      EEEEGGGG CS
                            SH3_16 41 GWlplsdL 48
                                      GW+++sdL
  gi|330506925|ref|YP_004383353.1| 82 GWIEESDL 89
                                      9******8 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.8e-05
                                       EEEEEEE.ETEEEEEETTT--EEEEEGG CS
                            SH3_16  20 lrvleea.dgwawVqlceDgYvGWlpls 46 
                                       +++ +++ +++++V+l  D+YvG++ ++
  gi|330506925|ref|YP_004383353.1| 328 VKLASREsTNPVYVRLN-DDYVGYVLST 354
                                       56677775779******.99*****886 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 ?   13.8   0.1   1.2e-05     0.036     239     300 ..     192     255 ..     189     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                                       HHHT--TT.SS.-HHHHHHHHHHHHHTT-SEEEEEEETT-HHHHHHHHHHHHHHH.HTT--EEEE CS
                             HGD-D 239 sgyykcpv.sp.kerrlewirdlideykvdgvifqtgggCrpasgyiglirrale.kegiPvlsl 300
                                       s yy cp+  + k+r  ++i+ lid+y+vdgv+++  g+ +    y    ++ +  ++gi +  +
  gi|330506925|ref|YP_004383353.1| 192 SSYY-CPMnPEvKDRLYNQIEMLIDDYHVDGVVLYRFGFQDENHCYCDVCKEKFYqDTGIDISKV 255
                                       5789.99955369**********************999998877777777777777777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.26s 00:00:01.07 Elapsed: 00:00:00.41
# Mc/sec: 10625.74
//
Query:       gi|330506926|ref|YP_004383354.1|  [L=303]
Description: family 2 glycosyl transferase [Methanosaeta concilii GP6]
Scores for 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   59.7   0.0    4.3e-16   59.2   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    2.3e-06   27.7   0.0    3.3e-06   27.2   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00033   21.1   0.0    0.00072   20.0   0.0    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.016   14.6   2.1      0.031   13.6   2.1    1.4  1  DUF4191          Domain of unknown function (DUF4191)
      0.045   13.5   0.8      0.062   13.0   0.8    1.1  1  Tetraspanin      Tetraspanin family
      0.071   13.5   0.0        0.1   12.9   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
       0.39   10.0   8.1        2.9    7.1   1.4    2.3  2  DUF1538          Protein of unknown function (DUF1538)


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 !   59.2   0.0   1.7e-19   4.3e-16       1     140 [.       7     135 ..       7     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.7e-19
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       ++ ipt Neek ++ +++   +      + i+vvD  StD+tve +++      + +v+ ++ + Gk+ al + + +
  gi|330506926|ref|YP_004383354.1|   7 CILIPTLNEEKSIQPVIREFQEL---GYDNILVVDGHSTDKTVEKARAS-----GAKVFIQS-GSGKGQALKEVFGH 74 
                                       699***************99888...77789999999************.....99******.66************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyf 140
                                        + +yil++D D ++ p +  +++e++ +++ad v+g+r  + ++   ++ n +   n ++++
  gi|330506926|ref|YP_004383354.1|  75 IKERYILLIDGDGTYLPRDAARIMEPILEGQADHVVGNRLENIQGGAIKRLNMFG--NKMINR 135
                                       ********************************************99999998763..333333 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 !   27.2   0.0   1.3e-09   3.3e-06       3     121 ..       5     110 ..       3     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.3e-09
                   Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksral 79 
                                       d+ +l+pt+nee+ +  v++++     + + + vv+  s+++t+e a++    + +++  v +++   gs gk +al
  gi|330506926|ref|YP_004383354.1|   5 DICILIPTLNEEKSIQPVIREFQEL--GYDNILVVDGHSTDKTVEKARA----S-GAK--VFIQS---GS-GKGQAL 68 
                                       6899******************995..44566777777999*9999987....4.434..44443...54.9***** PP

                   Glyco_tranf_2_3  80 nealravksdlvllvDdDtvvePdtlkrllqffltpkvgavg 121
                                       +e++ ++k +++ll+D+D    P+  +r+   +l  ++++v 
  gi|330506926|ref|YP_004383354.1|  69 KEVFGHIKERYILLIDGDGTYLPRDAARIMEPILEGQADHVV 110
                                       ******************877776666666655555555555 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.8e-07   0.00072       2      81 ..      14      86 ..      13      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.8e-07
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkel.pevkllhvdksyederrqvellkallaryaeadwvlvvD 79
                                      ne++ ++ +++   +lg+d+ilv+d +stD+t +  ++  ++v +    +s +      ++lk+++ +  +++++l +D
  gi|330506926|ref|YP_004383354.1| 14 NEEKSIQPVIREFQELGYDNILVVDGHSTDKTVEKARASgAKVFIQ--SGSGK-----GQALKEVFGH-IKERYILLID 84
                                      899999*****************************99962334433..33332.....3566777744.4677777777 PP

                   Glyco_tranf_2_4 80 aD 81
                                       D
  gi|330506926|ref|YP_004383354.1| 85 GD 86
                                      77 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.1   1.2e-05     0.031       8      69 ..     212     272 ..     208     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                           DUF4191   8 lkqiaqvfkltrkedkkllwlllaaflvvvvvfvvlglllgslilllilgillgllvalivl 69 
                                       lk i ++f++ + e++++ + l++ f++ +  +v + ++  +++l+ i  ++l +l+a++++
  gi|330506926|ref|YP_004383354.1| 212 LKIILTIFRMAKTENPMFYFGLMGSFVGLLGFLVGVYVA-RDWLLWRIEHVPLTILTAILII 272
                                       67799**********************987766666666.58*****999999999998875 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.8   2.4e-05     0.062       5      81 ..     228     298 ..     225     300 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin   5 lfffnllfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcigalkenkclllt 81 
                                       +f f l+   +g++ + vGv++      a +  l   + ++ +il+ +li+vG+ lf++g+ G ++a   + ++  +
  gi|330506926|ref|YP_004383354.1| 228 MFYFGLMGSFVGLLGFLVGVYV------ARDWLLWRIEHVPLTILTAILIIVGIQLFMIGMQGDMMASMHREMMREL 298
                                       7889999999************......445556778899999********************88877777766655 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.1e-05       0.1      21     106 ..      13      97 ..       9     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.1e-05
                                       CCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT CS
                      NTP_transf_3  21 lggkpllervldalraagvdevvvvggd..eevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacD 95 
                                       l+++  ++ v++ ++++g d+++vv g+  ++  + ++ +g++v+ ++  g g +++l+    ++ ++ ++l++ +D
  gi|330506926|ref|YP_004383354.1|  13 LNEEKSIQPVIREFQELGYDNILVVDGHstDKTVEKARASGAKVFIQS--GSGKGQALKEVFGHI-KERYILLIDGD 86 
                                       578888999****************999666677788999*******8..89999*********9.9********** PP

                                       -TT--HHHHHH CS
                      NTP_transf_3  96 mPlltpelver 106
                                         +l++++ + 
  gi|330506926|ref|YP_004383354.1|  87 GTYLPRDAARI 97 
                                       99999888764 PP

>> DUF1538  Protein of unknown function (DUF1538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.4    0.0011       2.9      10      44 ..     216     250 ..     212     254 .. 0.90
   2 ?    6.7   0.7    0.0015       3.8      18      55 ..     259     297 ..     253     303 .] 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0011
                           DUF1538  10 llvlklslkelaeillGlllvvlGlalFllGvelg 44 
                                       l+++++ ++e   +++Gl+  ++Gl  Fl+Gv ++
  gi|330506926|ref|YP_004383354.1| 216 LTIFRMAKTENPMFYFGLMGSFVGLLGFLVGVYVA 250
                                       678999999999********************876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0015
                           DUF1538  18 kelaeillGlllvvlGlalFllGvelgllp.lGeqvgsk 55 
                                       +++   +l ++l+++G+ lF++G++  ++  + +++ ++
  gi|330506926|ref|YP_004383354.1| 259 EHVPLTILTAILIIVGIQLFMIGMQGDMMAsMHREMMRE 297
                                       6667788999**************988774155555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2182.85
//
Query:       gi|330506927|ref|YP_004383355.1|  [L=439]
Description: phosphoglucomutase/phosphomannomutase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.9e-28   97.1   0.0    1.4e-27   96.1   0.0    1.5  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
      2e-18   66.9   0.0    3.9e-18   66.0   0.0    1.5  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    2.4e-17   63.2   0.0    3.8e-17   62.5   0.0    1.3  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    8.4e-09   35.5   0.0    2.1e-08   34.2   0.0    1.7  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 !   96.1   0.0   3.2e-31   1.4e-27       3     128 ..       5     124 ..       3     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 3.2e-31
                                       GBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-H CS
                         PGM_PMM_I   3 kfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllpt 79 
                                        f+++++Rg++g + lt++lv+++g+++++y +     ++v +GrDtR+s++ l++a++ g++++G++v  +g++p+
  gi|330506927|ref|YP_004383355.1|   5 VFRAYDVRGVYG-TDLTEQLVKRVGESFGSYAEG----GSVSLGRDTRISGPSLQKAFLDGVLSTGCQVNSFGIIPI 76 
                                       699*********.55*****************97....9************************************** PP

                                       HHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHH CS
                         PGM_PMM_I  80 PavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIe 128
                                        ++sf++ k +++a+ +i+aSHnppeyng+++ + +G+ +  + e+ I 
  gi|330506927|ref|YP_004383355.1|  77 AIISFITWKEELKAAAYISASHNPPEYNGVRFRTCDGYGLLYQ-ESSIM 124
                                       *****************************99988888776654.45555 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 !   66.0   0.0   8.8e-22   3.9e-18       5     103 .]     149     245 ..     148     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 8.8e-22
                                       HHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGG CS
                        PGM_PMM_II   5 ealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkke 81 
                                       e+++e v+ + + k++lk+v+d ++Ga+ +++ +  ++lg+++  ln + d+ fp++ p p+e e+l+ ++++ kk+
  gi|330506927|ref|YP_004383355.1| 149 ERYREYVQGKLNLKRPLKLVLDMGNGAACTMA-SFYQQLGFNPLILNGTTDGLFPGRGPAPNE-ESLRPACQMLKKK 223
                                       5556666666679***************9987.6899**************************.************* PP

                                       G-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  82 gadlglafDgDaDRlgvvderG 103
                                       +ad+g+ fD+DaDR +v+d++G
  gi|330506927|ref|YP_004383355.1| 224 EADFGVGFDPDADRGIVIDDKG 245
                                       ******************9987 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   8.5e-21   3.8e-17       2     111 ..     250     353 ..     249     356 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 8.5e-21
                                       HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETT CS
                       PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifld 78 
                                       +++++++++++  +   +++  v++ + +s++ler ++k gik+++ +vGd +v++++k+++avlG E Sgh+++++
  gi|330506927|ref|YP_004383355.1| 250 PEKVAIIITRARYK---PGD-LVISGFDCSMILERELEKDGIKVLRERVGDVFVANRVKNSKAVLGVERSGHFFLPE 322
                                       56788888887755...555.5******************************************************* PP

                                       TBSS--HHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                       PGM_PMM_III  79 eattkDGilaallvleilaetgkslselleell 111
                                       +++ +D   ++l+++ei++  g++ls+l+  ++
  gi|330506927|ref|YP_004383355.1| 323 FQYSDDPFAMSLALAEIVSS-GEKLSDLA-GMI 353
                                       ******************75.899**998.544 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 !   34.2   0.0   4.7e-12   2.1e-08      23      59 ..     379     421 ..     348     434 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 4.7e-12
                                       H......HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEES.SH CS
                        PGM_PMM_IV  23 a......sikeglkilledGrrlavRpSGTepllrvyvEak.sd 59 
                                              ++ +glki++e  ++l +RpS+Tep +r+y+E++  d
  gi|330506927|ref|YP_004383355.1| 379 SlaffepDTTDGLKITTESYSVL-IRPSNTEPIIRLYIETTrGD 421
                                       1334466899*************.***************97432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3079.61
//
Query:       gi|330506928|ref|YP_004383356.1|  [L=93]
Description: DNA-binding protein Alba [Methanosaeta concilii GP6]
Scores for complete 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   66.3   0.2      2e-18   66.0   0.2    1.2  1  Alba      Alba


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.2   1.1e-22     2e-18       2      64 ..       6      66 ..       5      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1.1e-22
                                      EEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEE CS
                              Alba  2 eiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvlt 64
                                      +i++++ +p+m+yv+++++++ nk   +V+lka+GraIs+Av++aei ++rf+++l   n + 
  gi|330506928|ref|YP_004383356.1|  6 VIFIGD-KPVMNYVLAVMTQF-NKPIASVILKARGRAISRAVDTAEITRNRFMPNLTVKNIII 66
                                      799***.**************.*******************************9977766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 722.32
//
Query:       gi|330506929|ref|YP_004383357.1|  [L=256]
Description: ribosomal RNA large subunit methyltransferase J [Methanosaeta concilii GP6]
Scores for complete 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-58  195.4   0.0      1e-57  195.1   0.0    1.1  1  FtsJ             FtsJ-like methyltransferase
    1.5e-05   24.8   0.3    2.7e-05   24.1   0.3    1.4  1  TRAM             TRAM domain
    0.00032   20.5   0.5       0.89    9.3   0.0    2.7  3  Methyltransf_31  Methyltransferase domain
     0.0012   18.8   0.0      0.012   15.4   0.0    2.1  1  Methyltransf_23  Methyltransferase domain
     0.0012   19.5   1.7        1.6    9.5   0.1    2.8  2  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.1   0.0   2.8e-61     1e-57       1     176 [.      18     190 ..      18     191 .. 0.98

  Alignments for each domain:
  == domain 1  score: 195.1 bits;  conditional E-value: 2.8e-61
                                       CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHH CS
                              FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetie 77 
                                       yr+RsayKLl+i+ekf+++k+g+ vvDlgaaPGgw qv+ +    +gk+v+vDl  ++p+pgv t+++dit  +t +
  gi|330506929|ref|YP_004383357.1|  18 YRARSAYKLLQINEKFHVIKKGDSVVDLGAAPGGWLQVAQKLS--GGKIVGVDLEGITPIPGVVTFRADITALSTVD 92 
                                       9**************************************7774..49****************************** PP

                                       HHCHCHHHSSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCEEE CS
                              FtsJ  78 kikealserkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfFek 154
                                       ++k+al++  +d+v++D ap+ sg +d d++++++L+++ale+a kll+p g+fv+k+f+g+ + ++l+++++ F  
  gi|330506929|ref|YP_004383357.1|  93 QVKDALGG-DADVVICDAAPNLSGAWDRDHAISIDLARSALEMAKKLLRPRGNFVVKVFQGDMFIDFLNDVRREFAV 168
                                       ******77.******************************************************************** PP

                                       EEEEE-SS--CCG-EEEEEEEE CS
                              FtsJ 155 vsvvkPkssrsesseeflvcrg 176
                                       v+ + P++sr+es+e+++v ++
  gi|330506929|ref|YP_004383357.1| 169 VHAHSPAASRKESAETYVVGKK 190
                                       *******************975 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.3   7.6e-09   2.7e-05       3      62 .]     197     252 ..     195     252 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 7.6e-09
                                       XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                         G  ++V +e ++ + g+g++ ++ g++++v+g +    +++ Vk++ v  +++++e++
  gi|330506929|ref|YP_004383357.1| 197 RKGDMLNVRIESVG-KSGDGVAMVE-GFAIIVRGSKL--KEELLVKVDAVLTNFAFAEIV 252
                                       679999********.**********.********744..8******************97 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1   0.00075       2.7       1      36 [.      36      69 ..      36      71 .. 0.86
   2 !    7.7   0.1    0.0008       2.9      61     112 ..      83     150 ..      77     164 .. 0.68
   3 !    9.3   0.0   0.00025      0.89      30      95 ..     121     186 ..     113     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00075
                   Methyltransf_31  1 ldkglrvlDlGCGtGeltfelaeelgpkaevvGiDi 36
                                      ++kg +v+DlG++ G  + ++  +  +++++vG+D 
  gi|330506929|ref|YP_004383357.1| 36 IKKGDSVVDLGAAPGGWLQVAQ-K-LSGGKIVGVDL 69
                                      57999**********9988888.3.4789******6 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0008
                   Methyltransf_31  61 gdieelekl..led...ekfDlilsnevl...........naladpdkileeiervlkpggilliedp 112
                                       +di++l++   ++d      D+++++++              +    ++le ++++l+p g +++  +
  gi|330506929|ref|YP_004383357.1|  83 ADITALSTVdqVKDalgGDADVVICDAAPnlsgawdrdhaISIDLARSALEMAKKLLRPRGNFVVKVF 150
                                       56666665433333666777888888666666667777666777777888888888888888887654 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00025
                   Methyltransf_31  30 evvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnevlnaladpdkile 95 
                                       + ++iD    a+e A++ ++  g   v++ qgd++  + +++  + f +++++++ +  +++++++ 
  gi|330506929|ref|YP_004383357.1| 121 HAISIDLARSALEMAKKLLRPRGNFVVKVFQGDMFIdFLNDVR-REFAVVHAHSPAASRKESAETYV 186
                                       6899****************99999*********987775555.89999999988766666666555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.4e-06     0.012      19     120 ..      35     150 ..      12     182 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.4e-06
                   Methyltransf_23  19 klraggrvLdiGcGtGillevl.rengfsvtgvDlspeaveiae.............kakkaqkdqfdeqeaaepqg 81 
                                         ++g +v+d+G++ G +l+v+ +  g +++gvDl  +    ++             +           q  +   g
  gi|330506929|ref|YP_004383357.1|  35 VIKKGDSVVDLGAAPGGWLQVAqKLSGGKIVGVDLEGI--TPIPgvvtfraditalsT-------VD--QVKDALGG 100
                                       368899****************666788*******543..322245554433321111.......11..22233445 PP

                   Methyltransf_23  82 kfdlIvlrevlehvpdpp...........ellrqiatllkpgGylllsep 120
                                         d++++    +    +            ++l ++++ll+p G++++ ++
  gi|330506929|ref|YP_004383357.1| 101 DADVVICDAAPNLSGAWDrdhaisidlarSALEMAKKLLRPRGNFVVKVF 150
                                       55555554443333333344445555555777777777777777777665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.2     0.001       3.7       1      29 [.      42      69 ..      42      72 .. 0.90
   2 !    9.5   0.1   0.00044       1.6      21      70 ..     119     171 ..     104     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.001
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEES CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDi 29
                                      v+dlG+ +G +++ ++k  g +k++gvD+
  gi|330506929|ref|YP_004383357.1| 42 VVDLGAAPGGWLQVAQKLSG-GKIVGVDL 69
                                      89*********999998876.*******8 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00044
                                       SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBC..CGBSSSTTTEEEEEE CS
                   Methyltransf_25  21 kakvtgvDiseemleaareraeeegl.nvefvqgda..edlpfedgsfDlvvs 70 
                                       + + + +D++ ++le a++ ++ +g   v++ qgd+  + l+   ++f +v++
  gi|330506929|ref|YP_004383357.1| 119 RDHAISIDLARSALEMAKKLLRPRGNfVVKVFQGDMfiDFLNDVRREFAVVHA 171
                                       578999***************9987789*******975557788888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2140.86
//
Query:       gi|330506930|ref|YP_004383358.1|  [L=122]
Description: hypothetical protein MCON_0730 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 929.00
//
Query:       gi|330506931|ref|YP_004383359.1|  [L=563]
Description: hypothetical protein MCON_0731 [Methanosaeta concilii GP6]
Scores for complete 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   1.8    8.4e-09   35.4   1.8    1.5  1  DDE_Tnp_1     Transposase DDE domain
  ------ inclusion threshold ------
       0.11   12.8   0.4          1    9.7   0.4    2.6  2  MADF_DNA_bdg  Alcohol dehydrogenase transcription factor Myb/


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 !   35.4   1.8   9.3e-13   8.4e-09      26     212 ..     208     487 ..     183     489 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 9.3e-13
                         DDE_Tnp_1  26 gykggk.ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYasaelldtleekg 99 
                                       gy+ ++ +++  +l i+v+ r +++ls  + +g++h + ++k ll++l ++  ++ +++ D+G  s+++++ ++e+g
  gi|330506931|ref|YP_004383359.1| 208 GYNPDRiRRRQANLAILVSKRDRYPLSHFVYNGSRHSISTVKNLLNRLSKMaiEPGTLIWDRGNVSKKHVQMVDESG 284
                                       888788899999************9999999********************************************** PP

                         DDE_Tnp_1 100 vdyiirlkkntklyrk.......gaeskrrgrlrkhdrnkiltksqkrrnk.......................... 143
                                       ++ i  ++k +k+ +        +++     r   +++  ++++++++++k                          
  gi|330506931|ref|YP_004383359.1| 285 WKLICGVPKTSKEAKEiigktkiPISPDSLVRSSHAGHIYAIKTENELFGKerstivyanrersvkdadarnealsv 361
                                       *******9999999889999999455555555566666666666666666666666668888888999999999*** PP

                         DDE_Tnp_1 144 .........................................................skkekgdvyyvtntnsells 163
                                                                                                +  ek+d+  + + ++ +l 
  gi|330506931|ref|YP_004383359.1| 362 igeslnelsqtgkdwsekrlhdriknivgqwsgfidasvrrkkdgpriewsydrqrlRSAEKYDGKWLILSTDYSLN 438
                                       *******************************************************99999999999999999999** PP

                         DDE_Tnp_1 164 aeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                       a   +++y  +  iE vF+ lk++   + +r+r   rv+a+l+ ++la+
  gi|330506931|ref|YP_004383359.1| 439 ANNAVNMYLEKDFIEKVFRVLKTHEEVEPVRHRLEHRVKAYLFVCMLAY 487
                                       ************************************************9 PP

>> MADF_DNA_bdg  Alcohol dehydrogenase transcription factor Myb/SANT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.28   2.5e+03       9      37 ..     264     293 ..     259     306 .. 0.70
   2 ?    9.7   0.4   0.00011         1       7      57 ..     337     393 ..     335     417 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.28
                      MADF_DNA_bdg   9 pvLwdrshpdyrnkek.rekaweeiaeeln 37 
                                       +++wdr + + ++++   e  w+ i+   +
  gi|330506931|ref|YP_004383359.1| 264 TLIWDRGNVSKKHVQMvDESGWKLICGVPK 293
                                       679***997777666636778988886655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00011
                      MADF_DNA_bdg   7 khpvLwdrshpdyrnkekrekaweeiaeelnekvd......veeckkkwknLRdryr 57 
                                       + ++ + ++ ++ ++ ++r++a++ i e+lne  +      +++++ ++kn+  + +
  gi|330506931|ref|YP_004383359.1| 337 RSTIVYANRERSVKDADARNEALSVIGESLNELSQtgkdwsEKRLHDRIKNIVGQWS 393
                                       56789*************************843333333324446667776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 4242.26
//
Query:       gi|330506932|ref|YP_004383360.1|  [L=124]
Description: hypothetical protein MCON_0732 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 901.84
//
Query:       gi|330506933|ref|YP_004383361.1|  [L=245]
Description: hypothetical protein MCON_0733 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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: 00:00:00.40
# Mc/sec: 1822.29
//
Query:       gi|330506934|ref|YP_004383362.1|  [L=713]
Description: hypothetical protein MCON_0735 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-06   28.1   0.0    1.8e-05   25.2   0.0    2.2  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 !   25.2   0.0     1e-09   1.8e-05      13     102 ..     121     214 ..     111     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1e-09
                    Transglut_core  13 dplekakaiyewvr......knveysaprrtpgsrd....aeavletgk.......GncedfaslfvallRalGipa 72 
                                       +  ++++ iy++++      k  +y+   ++p++ d    a+++l++g        G+c dfa l++al  ++G  +
  gi|330506934|ref|YP_004383362.1| 121 KTIDQIVSIYDYLKngdeskKGWGYV---SDPRGIDdfmfANQTLRNGErancvggGDCDDFAILMSALVESIGGTT 194
                                       44589999999999776666666666...55555556779******77778999999******************** PP

                    Transglut_core  73 RvvtgylsgeeekeqsvasedaHawvevyl 102
                                       R++   +           s + Ha++evyl
  gi|330506934|ref|YP_004383362.1| 195 RIILARNN----------STGGHAYTEVYL 214
                                       ***88765..........6799*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 4588.35
//
Query:       gi|330506935|ref|YP_004383363.1|  [L=258]
Description: hypothetical protein MCON_0736 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-07   31.5   0.0    3.9e-06   27.3   0.0    2.2  2  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 !   27.3   0.0   2.2e-10   3.9e-06      13     102 ..     121     214 ..     110     223 .. 0.81
   2 ?    2.3   0.0     0.012   2.2e+02      11      42 ..     219     249 ..     215     256 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.2e-10
                    Transglut_core  13 dplekakaiyewvr......knveysaprrtpgsrd....aeavletgk.......GncedfaslfvallRalGipa 72 
                                       +  ++++ iy++++      k  +y+   ++p++ d    a+++l++g        G+c dfa l++al  ++G  +
  gi|330506935|ref|YP_004383363.1| 121 KTIDQIVSIYDYLKngdeskKGWGYV---SDPRGIDdfmfANQTLRNGErancvggGDCDDFAILMSALVESIGGTT 194
                                       44589999999999777666666676...55555556779******77778999999******************** PP

                    Transglut_core  73 RvvtgylsgeeekeqsvasedaHawvevyl 102
                                       R++   +           s + Ha++evyl
  gi|330506935|ref|YP_004383363.1| 195 RIILARNN----------STGGHAYTEVYL 214
                                       ***88765..........6799*******9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.012
                    Transglut_core  11 akdplekakaiyewvrknveysaprrtpgsrd 42 
                                        +d+  +++ai +w++++ + + + +t+ + d
  gi|330506935|ref|YP_004383363.1| 219 NSDSGGQVEAIIDWLKEKLDAD-KIYTHIDTD 249
                                       5667799***********9999.555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1889.43
//
Query:       gi|330506936|ref|YP_004383364.1|  [L=183]
Description: hypothetical protein MCON_0737 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-16   60.8   0.6    3.8e-16   59.3   0.0    1.9  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 ?   -0.4   0.1     0.085   1.5e+03      47      60 ..      56      69 ..      20      79 .. 0.56
   2 !   59.3   0.0   2.1e-20   3.8e-16       2      84 ..      92     174 ..      91     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.085
                                      STTSSEEEEEEEEE CS
                     Inhibitor_I42 47 lvGaggthvwtfka 60
                                       vG   t++ +++a
  gi|330506936|ref|YP_004383364.1| 56 RVGQQTTSTTGIEA 69
                                      44444444444444 PP

  == domain 2  score: 59.3 bits;  conditional E-value: 2.1e-20
                                       EETT-EEEEEEEE-CCCT-EEEEEE--TTTEEE-TTTCECCECCE.STTSSEEEEEEEEESSSEEEEEEEEEE-TTS CS
                     Inhibitor_I42   2 vkvgetieieLpenpttGYsWtvdasdseglkllseeyipdesde.lvGaggthvwtfkalkpGettiefkyarpwe 77 
                                       +  ge++ i+ p+np+tG++W  ++ d+++l+l++ + ++d+ +  +vG++ ++++t++a+ pGet++ + + +pwe
  gi|330506936|ref|YP_004383364.1|  92 ATMGEEFNITIPSNPSTGFEWW-TEFDPQFLTLVGARSTQDNVSLeMVGVPENEIFTYRAVIPGETEVYLLLLQPWE 167
                                       578*******************.77789*******77777777777******************************* PP

                                       TSS--SC CS
                     Inhibitor_I42  78 kateaee 84 
                                       ++t+ae+
  gi|330506936|ref|YP_004383364.1| 168 NGTIAER 174
                                       **98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1394.75
//
Query:       gi|330506937|ref|YP_004383365.1|  [L=417]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete 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-26   90.2   0.1    1.4e-25   89.4   0.1    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family
    3.8e-21   75.6   0.0      7e-21   74.7   0.0    1.5  1  DEDD_Tnp_IS110  Transposase
  ------ inclusion threshold ------
      0.047   14.0   1.2      0.093   13.0   0.1    2.0  2  Init_tRNA_PT    Rit1 DUSP-like domain


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.1   2.4e-29   1.4e-25       2      83 ..     249     330 ..     248     336 .. 0.93

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 2.4e-29
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaaira 78 
                                       +++ s+pG+G++ aa+++ae+gd r f+sa+++a+y+G++p+++qS++k r g+i+k G++++Rr+L+eaA a++r+
  gi|330506937|ref|YP_004383365.1| 249 KIILSVPGVGFISAATIIAEMGDYRDFPSADKMAKYFGIVPSVYQSAGKLRTGKITKTGSKHMRRILVEAAKAISRT 325
                                       6899***********************************************************************99 PP

                    Transposase_20  79 npelr 83 
                                       ++ +r
  gi|330506937|ref|YP_004383365.1| 326 KKNSR 330
                                       75554 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.0   1.2e-24     7e-21       1     153 [.       9     152 ..       9     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 1.2e-24
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G D++kd   a++i+++g +l +er++++++gl a+ ++   ++++ + +ve+tg ++++++++ le +++ ++ n
  gi|330506937|ref|YP_004383365.1|   9 CGADIHKDFLIATMISRSGLKL-QERFNMNQDGLLAFRSW-IINHRCQRLAVESTGGFWYPIFTI-LEGHVEFILAN 82 
                                       79*************9999885.668**************.889****************88876.7899******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdqv 153
                                       ++++++++     ++KtD++D++ IA + +  + ++p++  +++y++Lr++tr+re+lv+ r++ kn++++ L   
  gi|330506937|ref|YP_004383365.1|  83 AYQIRNIE-----HKKTDKLDSERIAIYCL-NNLITPSRIYPKDYRDLRSITRARETLVNARSKIKNQIHQSLSAC 152
                                       *****995.....89***************.****************************************99765 PP

>> Init_tRNA_PT  Rit1 DUSP-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.2     7e+03      17      44 ..     124     153 ..     119     160 .. 0.50
   2 ?   13.0   0.1   1.6e-05     0.093      10      80 ..     304     378 ..     296     389 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                      Init_tRNA_PT  17 Lrtalpkivdfvrkrlsedkk..kkilvac 44 
                                       Lr++ +  ++ v++r++ +++  +++ ++c
  gi|330506937|ref|YP_004383365.1| 124 LRSITRARETLVNARSKIKNQihQSLSACC 153
                                       555544444444444433332334455554 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.6e-05
                      Init_tRNA_PT  10 gKkgsknLrtalpkivdfvrkrlsedkk....kkilvacetGkdlsvgvaLailcklfddakls...eeqsesnitK 79 
                                        K+gsk++r +l ++ ++++++ ++++     ++il+ c + +   v++a  +lc ++   +l    e+ +e+++tK
  gi|330506937|ref|YP_004383365.1| 304 TKTGSKHMRRILVEAAKAISRTKKNSRLmrffQRILARCGKKNIATVALARKVLCIIY---HLLmnhENYQEPEVTK 377
                                       49*****************99966655599**99******999999999888888888...2222235666777777 PP

                      Init_tRNA_PT  80 d 80 
                                       +
  gi|330506937|ref|YP_004383365.1| 378 T 378
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3125.83
//
Query:       gi|330506938|ref|YP_004383366.1|  [L=45]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       159  (0.00886831); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 320.29
//
Query:       gi|330506939|ref|YP_004383367.1|  [L=89]
Description: hypothetical protein MCON_0740 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.5   0.2       0.45   10.7   0.0    2.1  2  HR1       Hr1 repeat


Domain annotation for each model (and alignments):
>> HR1  Hr1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.012   2.1e+02      46      66 ..       5      25 ..       2      27 .. 0.85
   2 ?   10.7   0.0   2.5e-05      0.45       5      25 ..      30      50 ..      29      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.012
                               HR1 46 esnskielLreqLeelqasvq 66
                                      +s+ k++ ++e+L+++q +++
  gi|330506939|ref|YP_004383367.1|  5 KSSMKMKDINEALSDYQVQSL 25
                                      67889999********99875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 2.5e-05
                               HR1  5 lekklekElkireGAenllra 25
                                      le  +e+E+ i  GA++ll++
  gi|330506939|ref|YP_004383367.1| 30 LEGDIEIEMDISSGAQSLLSQ 50
                                      6778***************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 688.25
//
Query:       gi|330506940|ref|YP_004383368.1|  [L=414]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-22   79.0   0.0    5.1e-22   78.6   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
        0.5   10.6   4.5       0.93    9.7   4.5    1.5  1  Dockerin_1    Dockerin type I 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 !   78.6   0.0   5.6e-26   5.1e-22       5     236 ..     118     361 ..     114     363 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 5.6e-26
                                       SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....TS-BSBESSSB-HHHHHHH--SEEEE-GGG....GGGHHH CS
                      Peripla_BP_2   5 spsvteillalGatdkvvgvdtttsdpldadklee..aivevgadgeidvEklaalkPDlvilskgl.gltdedeel 78 
                                       s  ++e ++ l at+kvvgv+++    +     +e  + ++vg+ +  d+E+ + l+PDlvi+ +++    +++e+l
  gi|330506940|ref|YP_004383368.1| 118 SGLTAEAFKVLKATEKVVGVSNAIHEKTYF--FPEfaDLPSVGGWKIEDYEAAISLDPDLVISYEKWpPISEAEEKL 192
                                       6678899999***********987665544..55555******************************8888888888 PP

                                       HHHHS-EEE----TTSHHHHHHHHHHHHHTT-H...HHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE..E CS
                      Peripla_BP_2  79 lksgiptvivessntgeslkeqiralgellgle...deaeklvaeidsklaaaksaidse.kpkpvlvfggadeggy 151
                                       + +gip+v+ e++   + ++e++  l  +lg++   d++ ++ + +++ +++  + ++ +  p+  l  g++   ++
  gi|330506940|ref|YP_004383368.1| 193 DPAGIPVVVLEFTDP-NFVTEELVKLSYILGTNgaeDRYIQWRSGYERQIDDYVNNLSRDeRPSVFLETGFKGLNDV 268
                                       899**********99.6666666666666666544499999999999999999999999955555566666666777 PP

                                       EEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH.........HHHT-S--HHHHT-SHH CS
                      Peripla_BP_2 152 vvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr.........aeadnktgleflkenpl 219
                                          g++  ++ +l+  g++niaa+  +++y  ++ E+i +++p+v++ +            +++  +  e++ ++++
  gi|330506940|ref|YP_004383368.1| 269 GTYGEGAKGSLVLELTGGRNIAANM-SEAYPHVDSEWIITENPEVLMKYVYsseldwgwnSTDEPEALIEEISSRDG 344
                                       777777777777888*********9.********************98888889***99999999999********* PP

                                       HHTSHHHHTT-EEEE-H CS
                      Peripla_BP_2 220 laelpAvkngrVyalds 236
                                       ++++ Avkn rVy + +
  gi|330506940|ref|YP_004383368.1| 345 WESIDAVKNQRVYLISN 361
                                       *************9865 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.5    0.0001      0.93       5      53 ..      41      84 ..      37      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0001
                                      TSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHH CS
                        Dockerin_1  5 NgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallv 53
                                      N D +++  D+  +   +n     ++++  + aD N+DG++   D++++
  gi|330506940|ref|YP_004383368.1| 41 NLDDTIDQRDVDYVEGIIN-----GTQEYSELADANNDGNIGQEDIAQI 84
                                      889999999*999999999.....99*****************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 3072.07
//
Query:       gi|330506941|ref|YP_004383369.1|  [L=333]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-31  108.2   0.0    6.8e-31  107.7   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 !  107.7   0.0   3.8e-35   6.8e-31       2     234 ..      44     276 ..      44     279 .. 0.90

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 3.8e-35
                                       EE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHH CS
                      Peripla_BP_2   2 aslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedeel 78 
                                       +sls +  eil al++ +++vg++t++++p   +      v   +++++d+E + +l P lvi++++l   ++ + l
  gi|330506941|ref|YP_004383369.1|  44 VSLSAAASEILWALDEGKSMVGRSTSSNFPPMIES---LTVAGKHSNSPDLELIMELEPELVIADTML-SEEDRKVL 116
                                       7999***************************9985...457777889*********************.88888999 PP

                                       HHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE..EEE CS
                      Peripla_BP_2  79 lksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggadeggyvv 153
                                       ++ gi +v+ ++    +     i+ lg +lg+e++a +l+ ++++  + +k++i+     ++p++ f  + +++y  
  gi|330506941|ref|YP_004383369.1| 117 EEDGIAVVVERFIDP-NRTLLVIENLGRALGKEERASELAGQLKGYHDLIKERISGTnsEERPTVFFE-WLGKPYHS 191
                                       999******999998.6666679********************************9985555555555.5566**** PP

                                       E-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEE.EEEH....HHHT-S--HHHHT-SHHHHTSHH CS
                      Peripla_BP_2 154 agsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvif.vsgr....aeadnktgleflkenpllaelpA 225
                                       a++++    ++d +g+ niaa++ + +y ++s+E++ + dpdvi+ + g+     e++  +  ++++++p+l++  A
  gi|330506941|ref|YP_004383369.1| 192 ASNGTSYDNFIDFAGGVNIAANE-SVDYPDVSPEWVIEKDPDVILhILGSskdyTEEELEQWRDEIISRPELQNSRA 267
                                       **********************9.*******************97434446799999999999************** PP

                                       HHTT-EEEE CS
                      Peripla_BP_2 226 vkngrVyal 234
                                       vk+grVy l
  gi|330506941|ref|YP_004383369.1| 268 VKEGRVYVL 276
                                       *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 2748.41
//
Query:       gi|330506942|ref|YP_004383370.1|  [L=363]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-31  110.2   0.1    1.4e-31  109.9   0.1    1.1  1  Peripla_BP_2    Periplasmic binding protein
  ------ inclusion threshold ------
       0.17   10.6   0.1       0.39    9.4   0.0    1.6  2  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


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 !  109.9   0.1   1.6e-35   1.4e-31       1     234 [.      63     299 ..      63     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 1.6e-35
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESS.SB-HHHHHHH--SEEEE-GGG...GGGH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadg.eidvEklaalkPDlvilskglgltdede 76 
                                       i+sl+ +  ei  al+   ++vg++t + +p        +++evg+++ ++d+E +++l+PDlv++++++    + +
  gi|330506942|ref|YP_004383370.1|  63 IVSLAGGASEIICALDGGASLVGRSTNSDFPPYLA----TVAEVGKNSySPDIELILELDPDLVVADTMI-SDGDKK 134
                                       89**************************9999997....99999976559********************.888888 PP

                                       HHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT..-EEEE.EEEETTE..E CS
                      Peripla_BP_2  77 ellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse.kpkpvl.vfggadeggy 151
                                        l+++gip+++  +    +     ++ lg++lg+e++a++lv++i++  +++++ ++ +   + v+ vf ++++ +y
  gi|330506942|ref|YP_004383370.1| 135 TLEDAGIPVMEEKFIDP-SRTILVMENLGQVLGKEKRAQELVEFIKNYQDKIQNQVADLpE-EDVPrVFFEWYGTPY 209
                                       8999******9999988.45555579*********************************63.333325555666555 PP

                                       .EEE-TTSTTTHHHHTS--EESTTT--..STT-EEE-HHHHHHH--SEEEEEEH.....HHHT-S--HHHHT-SHHH CS
                      Peripla_BP_2 152 .vvagsnsyigdlldalgieniaaesk..kseyeeisaEqilasdpdvifvsgr.....aeadnktgleflkenpll 220
                                        +v++s+sy + ++  +g+ n+aa+ +  +++y ++s+E+++  dpdvi+ s        e++  +  ++++++p+l
  gi|330506942|ref|YP_004383370.1| 210 hTVSSSGSYQNFITF-AGGLNVAADLGneSNSYPDVSPEWVVQIDPDVILQSEPstknyTEDELAQLRDEIMSRPEL 285
                                       155555555555555.9999999999999***********************9999**9999999************ PP

                                       HTSHHHHTT-EEEE CS
                      Peripla_BP_2 221 aelpAvkngrVyal 234
                                       ++++Av+ grV+ +
  gi|330506942|ref|YP_004383370.1| 286 QSIKAVEDGRVFVM 299
                                       ***********987 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 ?    9.4   0.0   4.3e-05      0.39     211     264 ..     134     186 ..     105     195 .. 0.78
   2 ?   -3.0   0.0      0.26   2.3e+03     367     396 ..     206     236 ..     204     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 4.3e-05
                                       HHHHHH---EEEEE-SSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHH CS
                    Oxidored_nitro 211 lleekfgvpyiklvspiGleatdaflrelakllgkevaperiaeerarlldala 264
                                       +  e+ g+p+++ + +i    t   +++l+++lgke+  +++ e  ++++d+++
  gi|330506942|ref|YP_004383370.1| 134 KTLEDAGIPVME-EKFIDPSRTILVMENLGQVLGKEKRAQELVEFIKNYQDKIQ 186
                                       444556******.*********************88877777665555555554 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.26
                                       TS-ECCTTTCS.S---SHHHHHHHHHHHHHH CS
                    Oxidored_nitro 367 gfPildrhgya.rgpyvGYeGalnllddian 396
                                       g P++   +   ++ ++ ++G ln + d+ n
  gi|330506942|ref|YP_004383370.1| 206 GTPYHTVSSSGsYQNFITFAGGLNVAADLGN 236
                                       678887777777999999******9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2779.37
//
Query:       gi|330506943|ref|YP_004383371.1|  [L=173]
Description: hypothetical protein MCON_0744 [Methanosaeta concilii GP6]
Scores for complete 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   30.7   0.0    2.9e-07   30.3   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
          1    9.5   4.8        0.7   10.0   0.5    2.4  2  EGF_Tenascin  Tenascin EGF 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 !   30.3   0.0   3.2e-11   2.9e-07       1      88 [.      53     137 ..      53     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 3.2e-11
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                       i++++++ +e+  alG +d++v+v  ++ +p    +   + v  ++  ++  E ++alkPDlv+        d   +
  gi|330506943|ref|YP_004383371.1|  53 IVCVNSAAAELICALGCSDRIVAVTSACTMPPVLLE---KEVLGRSALSLEAEPIIALKPDLVVEGVPPLKEDVRQQ 126
                                       9******************************99976...5699999999999************9998878889999 PP

                                       HHHHHS-EEE- CS
                      Peripla_BP_2  78 llksgiptviv 88 
                                       l+++gip++ +
  gi|330506943|ref|YP_004383371.1| 127 LDEAGIPVLQY 137
                                       99******865 PP

>> EGF_Tenascin  Tenascin EGF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3     0.072   6.5e+02       6      14 ..      49      57 ..      46      59 .. 0.84
   2 ?   10.0   0.5   7.8e-05       0.7       2      17 ..      65      80 ..      64      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.072
                      EGF_Tenascin  6 CssRGvCvD 14
                                      C  R vCv+
  gi|330506943|ref|YP_004383371.1| 49 CPDRIVCVN 57
                                      88999**96 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 7.8e-05
                      EGF_Tenascin  2 CPLGCssRGvCvDGqC 17
                                      C LGCs R v v   C
  gi|330506943|ref|YP_004383371.1| 65 CALGCSDRIVAVTSAC 80
                                      9**********99888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1281.36
//
Query:       gi|330506944|ref|YP_004383372.1|  [L=360]
Description: iron chelate uptake ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete 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-91  306.4  38.1    2.3e-91  306.1  38.1    1.1  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.1  38.1   1.3e-95   2.3e-91       3     312 .]      38     354 ..      29     354 .. 0.97

  Alignments for each domain:
  == domain 1  score: 306.1 bits;  conditional E-value: 1.3e-95
                             FecCD   3 llllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLa 72 
                                       ++l  ++++lg+++i+p +v++++l++        +++ ++iv++lrl rv++a+++G++La+aGa +Q++++NpLa
  gi|330506944|ref|YP_004383372.1|  38 VALAGVAVTLGSAHITPFQVYSCILARFfpdyfqtTDFLDTIVWKLRLHRVILAIFAGMGLAIAGAAMQGILKNPLA 114
                                       456667899****************9999999999999999************************************ PP

                             FecCD  73 dPsilGissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsalt 148
                                       +P +lGi s+a++ga la++l+  +  +++ ++  af++ ++a+l v+ la k +g+sp++++LaGia+ +l+sa+t
  gi|330506944|ref|YP_004383372.1| 115 SPFTLGIASAASFGASLAIILGaGFIGGEYLIVGNAFIFTIMASLAVYGLA-KYRGISPETMVLAGIAIMYLFSAMT 190
                                       **********************88899999*********************.************************* PP

                             FecCD 149 sllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllll 225
                                       s+l+++ ++e++++++fw++Gsl++ sw+kv +++++++l+ l+l+ l+ +++ l  gdetAkslGvnve vr+  +
  gi|330506944|ref|YP_004383372.1| 191 SFLQYVGHAEQVHEVVFWMMGSLGRSSWDKVGIIALVTVLCSLILMRLSWDINTLGAGDETAKSLGVNVELVRVSGM 267
                                       ***************************************************************************** PP

                             FecCD 226 llvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliG 302
                                       +l+al+ta++++++G+igF+GL++Phi r++v+ dhr llp+s+l+Gallll ad++ar++++p+ lpvgi+ta++G
  gi|330506944|ref|YP_004383372.1| 268 MLAALITASVICFTGTIGFIGLVAPHITRMVVSGDHRFLLPASGLFGALLLLGADTVARTIMAPVILPVGIMTAFMG 344
                                       ***************************************************************************** PP

                             FecCD 303 apffiylllr 312
                                       +pff+yl+++
  gi|330506944|ref|YP_004383372.1| 345 VPFFLYLFMK 354
                                       *******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2456.35
//
Query:       gi|330506945|ref|YP_004383373.1|  [L=159]
Description: hypothetical protein MCON_0746 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-19   70.4   0.2      2e-19   70.0   0.2    1.2  1  LTD       Lamin Tail Domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.2   1.1e-23     2e-19       4     110 ..      17     124 ..      15     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 1.1e-23
                               LTD   4 aagdvvIsevmedgagnnan.........efvelyNtsskavdLsgwkledasge.....ytfpngtgtlaageyvv 66 
                                       a +dv I+e ++++a + ++         ef+elyN+++++vd sg++l+d+  +     y +pngt ++ +ge +v
  gi|330506945|ref|YP_004383373.1|  17 AGADVLINEMLANPATDWNDngqvggmddEFIELYNSGNESVDVSGYSLKDKVFRstpteYSIPNGT-VIGPGEFLV 92 
                                       5689**********655444899******************************99************.********* PP

                               LTD  67 vwsgsgttsasngskasssavwnnggdavaLydasgevvdsvgy 110
                                       ++ +++                 n+gda+ Lyd++g +vd+ +y
  gi|330506945|ref|YP_004383373.1|  93 IFVSESGV------------YQGNEGDAIMLYDPTGDLVDEKEY 124
                                       ****5322............33347***************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1261.21
//
Query:       gi|330506946|ref|YP_004383374.1|  [L=309]
Description: cobalt chelatase [Methanosaeta concilii GP6]
Scores for complete 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-73  247.0   0.0    3.6e-73  246.1   0.0    1.4  1  CbiK      Cobalt chelatase (CbiK)
    4.7e-07   30.1   0.1      9e-05   22.8   0.0    2.8  2  CbiX      CbiX


Domain annotation for each model (and alignments):
>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.1   0.0     4e-77   3.6e-73       2     260 ..      33     303 ..      32     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 246.1 bits;  conditional E-value: 4e-77
                                       EEEEEE---S-HHHHHHHHHHHHHHHHHC-TTSEEEEEES-HHHHHHHHHHH------HHHHHHHHHHCT--EEEEE CS
                              CbiK   2 aillvsFGtsykdarektiekiekkvaaefpdyevfraftSsiiikklkerdeievdtpeealeklkeegykevivq 78 
                                       aillv FGtsy++a++ ++e+ie+  ++efp+ ev+ aftS  i++kl +rd++++d p +al +l++egy +v+vq
  gi|330506946|ref|YP_004383374.1|  33 AILLVVFGTSYPEAQA-AYENIERVYREEFPQAEVRIAFTSDYIRRKLLDRDNVTIDNPLTALAHLNDEGYTDVVVQ 108
                                       9**************9.************************************************************ PP

                                       E--SCSSHHHHHHHHHHHHH.....GGGSSEEEEE--SCS......SHHHHHHHHHHHHTTS----T.......... CS
                              CbiK  79 plhiipGeeyeklkreVkkf.....kkkfekiklgrPlldykGvedsteDykevvealkdeierark.......... 140
                                       +lh+ipGee+ +l + V+++     k  f++++lg+Pll    + d+ +  + ++++++++ + +++          
  gi|330506946|ref|YP_004383374.1| 109 SLHVIPGEEFHDLANIVESVrgiegKFGFRNLVLGEPLLMN--FVDYRNVSRALASQFEQNTTGTERtphssprdag 183
                                       ***************997772222245699********984..4455555555555555544322211111111222 PP

                                       TEEEEEEE---SCHHHHHHHHHHHHHHHCT-S.EEEEETTSSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHCCC CS
                              CbiK 141 dealvfvgHGtehesnavyaeldkvlkekdfkqvvvgtvegyPeveevieelkkkgikevkliPlmlvAGdHaknDm 217
                                       + a++++gHGteh++n++y+++ ++l e + ++v++gtvegyP+ +ev+++l+++g+k+ +liP+m+vAGdHa nD+
  gi|330506946|ref|YP_004383374.1| 184 QMAVIYMGHGTEHSANSAYSQMANILAEDH-ENVFLGTVEGYPGYDEVLARLNESGVKKARLIPFMVVAGDHALNDL 259
                                       679***********************9975.99******************************************** PP

                                       CSSSTTSHHHHHHHT.T--EEE----GGGSHHHHHHHHHHHHHH CS
                              CbiK 218 asdeedswkealeaa.GikveiilkgLGeieeirsifikhikea 260
                                        ++e++swk++le++ G++++ +l g+Ge++ i +if+ h kea
  gi|330506946|ref|YP_004383374.1| 260 TGNESESWKSMLEKEgGFEIDYNLLGMGENDGIVEIFVGHTKEA 303
                                       ************998369***********************998 PP

>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.1    0.0053        47       2      33 ..      40      71 ..      40     146 .. 0.88
   2 !   22.8   0.0     1e-08     9e-05       1      74 [.     192     261 ..     192     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0053
                                      STSSCCHHHHHHHHHHHHHHHCCSCCCEECES CS
                              CbiX  2 GSrdpesneeveklaeelrekgpfkpvelgfl 33
                                      G++ pe++++ e++ + +re+ p+ +v+++f 
  gi|330506946|ref|YP_004383374.1| 40 GTSYPEAQAAYENIERVYREEFPQAEVRIAFT 71
                                      788999999**************9***99994 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1e-08
                                       -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHH CS
                              CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpe 74 
                                       HG+ ++++n++  ++a+ l e ++   v+lg +e   p ++e+l++l e+gvk+  ++P+++ aG h+ +D++ 
  gi|330506946|ref|YP_004383374.1| 192 HGT-EHSANSAYSQMANILAEDHE--NVFLGTVE-GYPGYDEVLARLNESGVKKARLIPFMVVAGDHALNDLTG 261
                                       788.8899*************777..99999988.77*********************************9954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2381.71
//
Query:       gi|330506947|ref|YP_004383375.1|  [L=86]
Description: hypothetical protein MCON_0748 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.9e-18   65.4   0.6    9.4e-18   65.1   0.6    1.1  1  DUF5320    Family of unknown function (DUF5320)
  ------ inclusion threshold ------
      0.021   15.2   0.2      0.026   15.0   0.2    1.1  1  ZapA       Cell division protein ZapA
      0.089   12.4   1.7       0.13   11.9   1.7    1.2  1  Trimer_CC  Trimerisation motif


Domain annotation for each model (and alignments):
>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.6   1.6e-21   9.4e-18       1      99 []       1      82 [.       1      82 [. 0.90

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 1.6e-21
                           DUF5320  1 MPrgdgtGpmGlGpmtGrglGyCagadapgyansagfGrgrggrglgrgfgrrrraggarlaaaetaeaskeeekelLe 79
                                      MP+gd tGp+++G++  r++Gy + + +      +  G+   g+g+grg+g+         +a++++++++eee+++Le
  gi|330506947|ref|YP_004383375.1|  1 MPWGDCTGPWWMGSRGNRAAGYYNPWCR------RAAGF---GMGYGRGYGY--------IPAEPFRQTTPEEERDYLE 62
                                      ***********************99887......56666...7799999999........3356788************ PP

                           DUF5320 80 eqaeaLeeeleaikkrlkel 99
                                      +  + Leeel+a+++++++l
  gi|330506947|ref|YP_004383375.1| 63 AVVRNLEEELKAVRAQIERL 82
                                      *****************986 PP

>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   4.3e-06     0.026      10      43 ..      49      82 ..      44      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-06
                              ZapA 10 ytlaceegeeeylreaaklvdekikeireaggnl 43
                                      ++ +++e+e++yl++++++++e++k++r++  +l
  gi|330506947|ref|YP_004383375.1| 49 FRQTTPEEERDYLEAVVRNLEEELKAVRAQIERL 82
                                      556799***********************98876 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.7   2.1e-05      0.13       6      39 ..      50      83 ..      47      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                                      XXXXXXXXXXXXXXX--HHHHHHHHHHHHHHHHH CS
                         Trimer_CC  6 rratpeasgtpssdavSRLEEelrkLqatVQelQ 39
                                      r++tpe  +   + +v  LEEel+  +a +  lQ
  gi|330506947|ref|YP_004383375.1| 50 RQTTPEEERDYLEAVVRNLEEELKAVRAQIERLQ 83
                                      678888887777777777************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1031  (0.0575046); expected 358.6 (0.02)
Passed bias filter:                      884  (0.0493056); expected 358.6 (0.02)
Passed Vit filter:                       136  (0.00758548); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 616.14
//
Query:       gi|330506948|ref|YP_004383376.1|  [L=133]
Description: hypothetical protein MCON_0749 [Methanosaeta concilii GP6]
Scores for complete 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   69.0   0.1    5.8e-19   68.5   0.1    1.3  1  DUF134        Protein of unknown function  DUF134
    3.9e-05   23.2   0.1    0.00011   21.8   0.0    1.7  2  Sigma70_r4_2  Sigma-70, region 4
  ------ inclusion threshold ------
      0.063   13.1   0.0       0.12   12.2   0.0    1.5  1  HTH_10        HTH 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 !   68.5   0.1   9.7e-23   5.8e-19      32      96 ..       3      67 ..       1      69 [. 0.96

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 9.7e-23
                            DUF134 32 kvaisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkkiakalveGraiilkGGeyk 96
                                       v i+l+elea+rlvd  dl qeeaa  mGis++++w+ l +ar+kia+alv G  + ++GG + 
  gi|330506948|ref|YP_004383376.1|  3 AVSITLEELEAVRLVDLLDLDQEEAAFYMGISRKAFWNDLMNARRKIAAALVYGMGLRIEGGSFA 67
                                      599***********************************************************985 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.8e-08   0.00011      17      54 .]      12      49 ..       7      49 .. 0.95
   2 ?   -2.1   0.0      0.53   3.2e+03      19      28 ..      95     104 ..      91     108 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.8e-08
                                      HHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2 17 eifllryleglsykEIAellgisegtVksrlsRArkkL 54
                                      e++ l +l +l+++E+A ++gis ++  + l+ Ar+k+
  gi|330506948|ref|YP_004383376.1| 12 EAVRLVDLLDLDQEEAAFYMGISRKAFWNDLMNARRKI 49
                                      899*********************************96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.53
                                       HHHHHTS--- CS
                      Sigma70_r4_2  19 fllrylegls 28 
                                       +l ++le+ls
  gi|330506948|ref|YP_004383376.1|  95 LLGSRLEHLS 104
                                       4445555555 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.1e-05      0.12      28      52 ..      26      50 ..      21      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                            HTH_10 28 eLAkelGIskstlsehLrkaeskli 52
                                      e A  +GIs+ ++++ L +a +k++
  gi|330506948|ref|YP_004383376.1| 26 EAAFYMGISRKAFWNDLMNARRKIA 50
                                      56789******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1005.32
//
Query:       gi|330506949|ref|YP_004383377.1|  [L=145]
Description: hypothetical protein MCON_0750 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1116.18
//
Query:       gi|330506950|ref|YP_004383378.1|  [L=296]
Description: ApbC/Nbp35 iron-sulfur cluster carrier protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-97  325.2   0.0      3e-97  324.9   0.0    1.0  1  ParA             NUBPL iron-transfer P-loop NTPase
    5.7e-14   52.3   0.0    1.7e-13   50.7   0.0    1.8  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    1.5e-09   38.0   0.4    3.7e-08   33.5   0.3    2.2  2  AAA_31           AAA domain
    3.1e-06   26.7   0.1    7.6e-06   25.4   0.1    1.7  1  MipZ             ATPase MipZ
    4.6e-06   26.3   0.1    0.00076   19.0   0.1    2.2  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
    0.00027   20.2   1.3     0.0018   17.5   0.9    2.4  3  ArsA_ATPase      Anion-transporting ATPase
     0.0008   19.3   0.0     0.0013   18.6   0.0    1.3  1  APS_kinase       Adenylylsulphate kinase
     0.0017   17.9   0.2      0.037   13.5   0.2    2.1  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
     0.0068   15.4   0.0      0.012   14.7   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.021   14.7   0.1    1.4  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.014   14.7   0.0      0.033   13.5   0.0    1.5  2  VirC1            VirC1 protein
      0.017   14.7   0.0      0.038   13.6   0.0    1.5  1  AAA_25           AAA domain
      0.021   14.7   0.4        2.8    7.7   0.3    2.3  2  AAA_26           AAA domain
       0.03   14.0   0.1      0.055   13.2   0.1    1.3  1  AAA_30           AAA domain
      0.045   13.4   0.4      0.096   12.3   0.4    1.4  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.085   11.0   0.0       0.12   10.6   0.0    1.1  1  FTHFS            Formate--tetrahydrofolate ligase
      0.095   13.0   0.1         18    5.7   0.0    2.7  2  PG_binding_2     Putative peptidoglycan binding domain
       0.11   12.4   0.5       0.23   11.4   0.2    1.7  2  NTPase_1         NTPase
       0.16   12.5   0.1       0.34   11.4   0.1    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 !  324.9   0.0  3.1e-100     3e-97       2     245 ..      44     286 ..      43     287 .. 0.97

  Alignments for each domain:
  == domain 1  score: 324.9 bits;  conditional E-value: 3.1e-100
                              ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSi 78 
                                       +  +ia++SgKGGVGKStv+vnlA+aL++ g+kvg+lD Di+Gp+ip+llg+e++k  +  ++l P +a gik++S+
  gi|330506950|ref|YP_004383378.1|  44 IGYKIAIASGKGGVGKSTVTVNLAAALRSLGYKVGILDGDITGPDIPKLLGIEDQKLVAGPSGLEPADAGGIKAISM 120
                                       5678****************************************************999999*************** PP

                              ParA  79 gfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvk 154
                                       ++ll+s+d++vvwrGpmk++a+kq++++v+wgelD+L++DlPPGt+De +++aq +  l+ga++Vttpqeval d +
  gi|330506950|ref|YP_004383378.1| 121 ALLLKSRDSPVVWRGPMKMAALKQFIEEVNWGELDFLLVDLPPGTSDEPISIAQLIpGLDGAIVVTTPQEVALLDSR 197
                                       ********************************************************7799***************** PP

                              ParA 155 kaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepe 231
                                       ka++mf  ++v++lG+veNmsg++cp+cg+++e+f++ggge++a+elgvp+lg+ipld+ei + +d gk+++ +  +
  gi|330506950|ref|YP_004383378.1| 198 KAVNMFLMMNVPMLGIVENMSGLICPHCGQRIEVFKTGGGEEAARELGVPFLGAIPLDTEIGSLGDMGKTFANS--K 272
                                       *********************************************************************77655..6 PP

                              ParA 232 seaakaleeiaekv 245
                                       ++aaka+eei++++
  gi|330506950|ref|YP_004383378.1| 273 TAAAKAFEEIVKSI 286
                                       999*******9987 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   1.8e-16   1.7e-13       1     122 [.      48     262 ..      48     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.8e-16
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       iaias+kGGvGK+t+++nLa+al   g++V  +D D  ++      +l + +++                       
  gi|330506950|ref|YP_004383378.1|  48 IAIASGKGGVGKSTVTVNLAAALRSLGYKVGILDGDITGPDIP---KLLGIEDQklvagpsglepadaggikaisma 121
                                       89***************************************98...44444444467******************** PP

                                       .........................................................................CCHC CS
                                       .........................................................................xxxx RF
                              CbiA  55 .........................................................................dlkr 58 
                                                                                                                d  +
  gi|330506950|ref|YP_004383378.1| 122 lllksrdspvvwrgpmkmaalkqfieevnwgeldfllvdlppgtsdepisiaqlipgldgaivvttpqevallDSRK 198
                                       *******************************************************************9999997777 PP

                                       CCHHHHHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHC.TS-EEEEEE--CCHCCCC CS
                                       xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                              CbiA  59 llellealgkkkall...lkiagvvlnrvdgeneetllkealeelkqry.gvpvlgviprdeavaeap 122
                                        ++++ ++   ++ l    ++ g++    + +  ++  k +  e+ +r  gvp+lg ip d+++  + 
  gi|330506950|ref|YP_004383378.1| 199 AVNMFLMMN--VPMLgivENMSGLICPHCGQR--IEVFKTGGGEEAARElGVPFLGAIPLDTEIGSLG 262
                                       777774444..345567799999999999988..8888887766665556***********9987665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.3     4e-11   3.7e-08       3      39 ..      47      83 ..      45      98 .. 0.94
   2 ?    2.6   0.0      0.12   1.1e+02     104     129 ..     139     165 ..     115     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 4e-11
                            AAA_31  3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlD 39
                                       Iaia  KGGvGK+T +vnlaaal +lg+kv + D D
  gi|330506950|ref|YP_004383378.1| 47 KIAIASGKGGVGKSTVTVNLAAALRSLGYKVGILDGD 83
                                      59*******************************9998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.12
                            AAA_31 104 eeilkellekvk.deYDyiiiDcpPsL 129
                                         +lk+++e+v+  e D+ ++D pP  
  gi|330506950|ref|YP_004383378.1| 139 MAALKQFIEEVNwGELDFLLVDLPPGT 165
                                       456899999998457**********64 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1     8e-09   7.6e-06       3     108 ..      48     162 ..      46     195 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8e-09
                                       EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHH..HHHHHHHHHHT--......----EEE-SS CS
                              MipZ   3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryl..enraataerkgls......Lplpealals 71 
                                       i ++  kGG Gkst++v +a aL + G +v+ +d d+    + + l  e+++ +a  +gl+      ++  ++  l 
  gi|330506950|ref|YP_004383378.1|  48 IAIASGKGGVGKSTVTVNLAAALRSLGYKVGILDGDITGPDIPKLLgiEDQKLVAGPSGLEpadaggIKAISMALLL 124
                                       789999****************************9998877777642245555555555552111111112222223 PP

                                       S-HHHHTTS-HHHHHHHHHHHHHHHH.HH-SEEEEE-- CS
                              MipZ  72 eaeeaeveeeeeaevaeleelvadle.aeldfividtP 108
                                       ++  + v     +++a+l++ +++++  eldf+++d P
  gi|330506950|ref|YP_004383378.1| 125 KSRDSPVVWRGPMKMAALKQFIEEVNwGELDFLLVDLP 162
                                       33344444444555677777777765246777777765 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   8.1e-07   0.00076       3      34 ..      48      80 ..      46      92 .. 0.86
   2 ?    5.2   0.0     0.013        12     189     247 ..     233     289 ..     183     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.1e-07
                         Fer4_NifH  3 iai.yGkGGiGksttsqnlsaalaemgkkvliv 34
                                      iai  GkGG+Gkst + nl+aal + g kv i+
  gi|330506950|ref|YP_004383378.1| 48 IAIaSGKGGVGKSTVTVNLAAALRSLGYKVGIL 80
                                      66635**********************999665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.013
                         Fer4_NifH 189 ereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilen 247
                                       +++  e+ a+elg++ l ++P+d ++       kt  + ++    ak ++e+ + il+ 
  gi|330506950|ref|YP_004383378.1| 233 KTGGGEEAARELGVPFLGAIPLDTEIGSLGDMGKTFANSKT--AAAKAFEEIVKSILDR 289
                                       555567889*****************988888888776544..45799*****999986 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.9   1.9e-06    0.0018       2      35 ..      47      80 ..      46      85 .. 0.88
   2 ?   -1.6   0.0       1.2   1.2e+03     110     134 ..     139     163 ..     136     167 .. 0.88
   3 ?   -1.0   0.0      0.85   8.1e+02     210     243 ..     183     216 ..     173     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.9e-06
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvlli 35
                                      k+ + +GKGGVGK+tv   +a+ l   g+kv ++
  gi|330506950|ref|YP_004383378.1| 47 KIAIASGKGGVGKSTVTVNLAAALRSLGYKVGIL 80
                                      667889**********************999776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHCSSSSEEEEESBS CS
                       ArsA_ATPase 110 ilsfeellkyvkeeeydvvvlDtaP 134
                                       ++++++++++v+  e d +++D +P
  gi|330506950|ref|YP_004383378.1| 139 MAALKQFIEEVNWGELDFLLVDLPP 163
                                       5789999999999*********999 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.85
                                       EEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                       ArsA_ATPase 210 rlVvipEklslkEteRaikeLkkygikvdavivN 243
                                       ++V++p +++l ++++a++ +  +++ +  ++ N
  gi|330506950|ref|YP_004383378.1| 183 IVVTTPQEVALLDSRKAVNMFLMMNVPMLGIVEN 216
                                       6899999***********9999999988877766 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.4e-06    0.0013       8      53 ..      52      97 ..      46     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                                      ESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSH CS
                        APS_kinase  8 tGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfse 53
                                      +G  g GKst++++l+ +L++ g++v +LdGd    ++ k Lg ++
  gi|330506950|ref|YP_004383378.1| 52 SGKGGVGKSTVTVNLAAALRSLGYKVGILDGDITGPDIPKLLGIED 97
                                      7999****************************98888888887765 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   3.9e-05     0.037       6      37 ..      50      81 ..      46      87 .. 0.88
   2 ?    2.2   0.0      0.11     1e+02     103     148 ..     140     189 ..     132     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-05
                          CBP_BcsQ  6 lqGvRGGvGttsllaaLawalhelgesvlviD 37
                                      +   +GGvG++++++ La al++lg++v ++D
  gi|330506950|ref|YP_004383378.1| 50 IASGKGGVGKSTVTVNLAAALRSLGYKVGILD 81
                                      55568***********************9888 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.11
                          CBP_BcsQ 103 eallaalkelk.eqyrwillDlpagasal...trellaladlvllvvepd 148
                                        al+++++e++ ++ +++l+Dlp g+s+      +l+   d  + v++p+
  gi|330506950|ref|YP_004383378.1| 140 AALKQFIEEVNwGELDFLLVDLPPGTSDEpisIAQLIPGLDGAIVVTTPQ 189
                                       567788888888999********988764111445555567777777765 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.012      35      66 ..      52      83 ..      27      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                      EE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 35 tGvPGaGkstlvealglelrrrGkrvavlavD 66
                                       G  G+Gkst++ +l++ lr+ G++v++l  D
  gi|330506950|ref|YP_004383378.1| 52 SGKGGVGKSTVTVNLAAALRSLGYKVGILDGD 83
                                      6999************************9765 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.2e-05     0.021       1      36 [.      53      88 ..      53      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqse 36
                                      G+  +GKST++ +L+  + + g+k+ ++D D+  ++
  gi|330506950|ref|YP_004383378.1| 53 GKGGVGKSTVTVNLAAALRSLGYKVGILDGDITGPD 88
                                      66789**************************97665 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.5e-05     0.033       4      40 ..      48      84 ..      46      89 .. 0.92
   2 ?   -3.5   0.0       5.6   5.2e+03      67      97 ..     137     167 ..     136     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-05
                             VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfeade 40
                                      i+++s kGG Gk+t  + l +al s g +v+++++d 
  gi|330506950|ref|YP_004383378.1| 48 IAIASGKGGVGKSTVTVNLAAALRSLGYKVGILDGDI 84
                                      7899******************************995 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.6
                             VirC1  67 delplleaayeeaegeGfdyaladtrgGsse 97 
                                       +++++l +  ee++    d+ l+d   G+s+
  gi|330506950|ref|YP_004383378.1| 137 MKMAALKQFIEEVNWGELDFLLVDLPPGTSD 167
                                       6789999999999999999999998888875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     4e-05     0.038      34      57 ..      47      70 ..      23      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                            AAA_25 34 elallaGapgtGKttlaldlalav 57
                                      ++a+  G +g+GK+t++++la+a+
  gi|330506950|ref|YP_004383378.1| 47 KIAIASGKGGVGKSTVTVNLAAAL 70
                                      568899***************986 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3     0.003       2.8       3      33 ..      48      78 ..      47      85 .. 0.90
   2 ?    4.7   0.0     0.025        23     121     194 ..     173     258 ..     118     261 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.003
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvg 33
                                      i +++   gvGK++v+  L++al++ g+kvg
  gi|330506950|ref|YP_004383378.1| 48 IAIASGKGGVGKSTVTVNLAAALRSLGYKVG 78
                                      67888999***************99999998 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.025
                            AAA_26 121 adiaknlgapvilVargglgtinqllltiealrqknvrvlGvilNk....vrnp....e.......nvetlekksgi 182
                                       a+++  l+   i+V+++++ ++ +   +++++   nv+ lG++ N     +  p    +         e++    g+
  gi|330506950|ref|YP_004383378.1| 173 AQLIPGLDGA-IVVTTPQEVALLDSRKAVNMFLMMNVPMLGIVENMsgliC--PhcgqRievfktgGGEEAARELGV 246
                                       5555555543.4555566666666666777888888999999988744332..334431333444444455555569 PP

                            AAA_26 183 pvlGvvPylpdl 194
                                       p lG++P ++++
  gi|330506950|ref|YP_004383378.1| 247 PFLGAIPLDTEI 258
                                       999999998876 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   5.9e-05     0.055       4      50 ..      32      78 ..      30      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.9e-05
                            AAA_30  4 aeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                      a+Q ++ ++l   g ++a++ G  G GK+t+   l++a+++ g++v 
  gi|330506950|ref|YP_004383378.1| 32 AQQNKINDRLSRIGYKIAIASGKGGVGKSTVTVNLAAALRSLGYKVG 78
                                      6788888899999999****************************996 PP

>> Desulfoferrod_N  Desulfoferrodoxin, 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     0.096       9      25 ..     222     238 ..     220     238 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                       -TTT--EEEECC--SS- CS
                   Desulfoferrod_N   9 CevCGniVeVleaGgGe 25 
                                       C +CG+ +eV + GgGe
  gi|330506950|ref|YP_004383378.1| 222 CPHCGQRIEVFKTGGGE 238
                                       9**************96 PP

>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00012      0.12      60      89 ..      48      77 ..      22      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                                      EESS--TT--SHHHHHHHHHHHHHHTT--E CS
                             FTHFS 60 taitPtplGeGKttttigLaqalnklgkka 89
                                       ai+  + G GK+t+t+ La al++lg k+
  gi|330506950|ref|YP_004383378.1| 48 IAIASGKGGVGKSTVTVNLAAALRSLGYKV 77
                                      58899999******************9886 PP

>> PG_binding_2  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.055        52      13      31 ..      29      47 ..      20      56 .. 0.77
   2 ?    5.7   0.0     0.019        18      16      36 ..      61      81 ..      54      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.055
                      PG_binding_2 13 laedvaeevqaaLsrLGyy 31
                                        ++ ++++++ Lsr Gy+
  gi|330506950|ref|YP_004383378.1| 29 DPKAQQNKINDRLSRIGYK 47
                                      55677899**********5 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.019
                      PG_binding_2 16 dvaeevqaaLsrLGyydgeag 36
                                      +v  +++aaL++LGy+ g  +
  gi|330506950|ref|YP_004383378.1| 61 TVTVNLAAALRSLGYKVGILD 81
                                      5667899********877665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00024      0.23       5      31 ..      52      78 ..      47      82 .. 0.91
   2 ?   -3.6   0.0       9.4   8.8e+03     115     134 ..     197     216 ..     190     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                                      E--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1  5 TGppGvGKtTlvkkvlellkssgvkvg 31
                                      +G+ GvGK+T+  +++ +l+s g+kvg
  gi|330506950|ref|YP_004383378.1| 52 SGKGGVGKSTVTVNLAAALRSLGYKVG 78
                                      7999********************995 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.4
                                       HHHHHHHHTTTSEEEEE--S CS
                          NTPase_1 115 keaveevLksekpvlavihr 134
                                       ++av+  L  ++p+l+++ +
  gi|330506950|ref|YP_004383378.1| 197 RKAVNMFLMMNVPMLGIVEN 216
                                       78888889999999988865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00036      0.34       5      27 ..      53      76 ..      50     100 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                            AAA_18  5 GtpGvGKttlakeLskrl.gfgvn 27
                                      G+ GvGK+t++ +L+  l  +g++
  gi|330506950|ref|YP_004383378.1| 53 GKGGVGKSTVTVNLAAALrSLGYK 76
                                      889***********9997333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2094.12
//
Query:       gi|330506951|ref|YP_004383379.1|  [L=94]
Description: transposase IS200-like protein, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-25   87.0   0.0    1.1e-24   86.9   0.0    1.0  1  Y1_Tnp    Transposase IS200 like


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.0   5.9e-29   1.1e-24      34     121 .]       5      91 ..       1      91 [. 0.95

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 5.9e-29
                            Y1_Tnp  34 iaekkevkilelelmpDHvHllvelppklsiskivkalkgassrlinkefpelkkkklkkeslWqrgYfvstvgeas 110
                                       ia++k++++++ e+mpDHvHl+v+++p  ++++i k +kg +++++++++pel+++ +  ++lW+++Y+v t+g+a+
  gi|330506951|ref|YP_004383379.1|   5 IAKQKGITLINQEIMPDHVHLFVTAHPIFAPANIAKIFKGITAKKLFEKHPELRDQLWD-GHLWNPSYYVGTCGDAT 80 
                                       899***************************************************99766.88*************** PP

                            Y1_Tnp 111 letvkrYIenq 121
                                       +++++rY+e q
  gi|330506951|ref|YP_004383379.1|  81 KDVIERYVEMQ 91 
                                       ********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 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:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 690.73
//
Query:       gi|330506952|ref|YP_004383380.1|  [L=91]
Description: hypothetical protein MCON_0755 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 684.88
//
Query:       gi|330506953|ref|YP_004383381.1|  [L=281]
Description: hypothetical protein MCON_0756 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1992.79
//
Query:       gi|330506954|ref|YP_004383382.1|  [L=430]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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  103.0   0.1    9.1e-29  101.0   0.0    1.9  2  Radical_SAM   Radical SAM superfamily
      7e-05   22.9   0.1      0.015   15.4   0.1    3.3  2  B12-binding   B12 binding domain
     0.0026   17.2   0.0      0.038   13.4   0.0    2.2  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   1.5e-32   9.1e-29       2     167 .]     154     323 ..     153     323 .. 0.94
   2 ?   -0.9   0.0      0.32   1.9e+03     117     140 ..     403     427 ..     396     429 .. 0.75

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 1.5e-32
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS........TTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly........pdfvellerl 70 
                                       ++ rgC + C+fC++p+    ++  rs+s+e+i++evke+ ++ gvk v ++gg+ +l           fve ++ l
  gi|330506954|ref|YP_004383382.1| 154 ETHRGCLGSCTFCQVPRF--FGRSIRSRSIENIVDEVKEM-KRLGVKRVAISGGTGSLFgyrnkinrEAFVEMIRSL 227
                                       6789*************8..********************.7***99999999999999999998888888888888 PP

                                       HHTCCCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  71 aklavpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr 144
                                       +++     +  ++++ +++d   e +le+ +++ + +v +gle+++d+ +l+ m++g t+e+ l+a+e+++++g+k+
  gi|330506954|ref|YP_004383382.1| 228 SQI---LGKRNLSVPDMRVDlvdETVLEAVRDYTIGWVFFGLESGSDR-ILRAMRKGVTVEDNLRAVELAKSLGVKV 300
                                       888...77778899999999999*************************.**************************** PP

                                       EEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 145 vvdrivglpGendeeleellell 167
                                         ++ivg pGe++e++ee+++++
  gi|330506954|ref|YP_004383382.1| 301 GGSFIVGYPGETREDFEETMSFV 323
                                       ********************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.32
                                       HHHHHT.CTSHHHHHHHHHHHHHHT CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 117 vlklmn.rghtfeevlealeklrea 140
                                       +l+  +  g ++++v+e+lek+r++
  gi|330506954|ref|YP_004383382.1| 403 YLDESRgQGRDIKRVIELLEKYRDV 427
                                       5555555788999999999999986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.5e-06     0.015      55     118 ..      41      98 ..       2     101 .. 0.66
   2 ?    0.4   0.0       0.1   6.1e+02      18      59 ..     225     266 ..     223     322 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-06
                       B12-binding  55 vglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetleak.lgiddvvvgegedale 118
                                       v+lS+ +t ql    ++ ++++++++   v vGG+ +sl pe++l +  +    vv geged ++
  gi|330506954|ref|YP_004383382.1|  41 VLLSLFSTLQL-LDPKIRDFVAERGN---VCVGGP-VSLCPEMVLGELnP--KAVVSGEGEDIVA 98 
                                       66666333333.34566666655544...99***7.7*********9544..6889*****9876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.1
                       B12-binding  18 avlaaalrdagfeVqllganvenedivaairaekpdvvglSa 59 
                                       ++l ++l +++ +V ++ ++  +e++++a+r+     v + +
  gi|330506954|ref|YP_004383382.1| 225 RSLSQILGKRNLSVPDMRVDLVDETVLEAVRDYTIGWVFFGL 266
                                       677888888888888888888889999999999888887733 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 !    9.3   0.0   0.00011      0.68      64     113 ..     175     227 ..     144     237 .. 0.72
   2 !   13.4   0.0   6.3e-06     0.038       2     107 ..     189     317 ..     188     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00011
                                       S.HHHHHHHHHHHHHHHHHHTBSEEEEEBCC...GBCTTTSGHHHHHHHHHHHH CS
                      AP_endonuc_2  64 r.reesvdalkraielaaaLGapllvlhpGt...agagpkgseeeawerlaesl 113
                                         r +s++++ ++++ +++LG++ + +  Gt   +g+++k ++e+ +  +++sl
  gi|330506954|ref|YP_004383382.1| 175 SiRSRSIENIVDEVKEMKRLGVKRVAISGGTgslFGYRNKINREA-FVEMIRSL 227
                                       257788**********************99776665566555553.33333333 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.3e-06
                                       HHHHHCT-SEEEEECCTCSHHHHC.......HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC............ CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvsel.......sdeelrelrkaldelglriaslslftrfgypded............ 59 
                                       ++ +++G++ v ++g ++  +  +       + e++r l ++l +++l ++ ++    ++ ++e             
  gi|330506954|ref|YP_004383382.1| 189 KEMKRLGVKRVAISGGTGSLFGYRnkinreaFVEMIRSLSQILGKRNLSVPDMRVDLVDETVLEAvrdytigwvffg 265
                                       6779999999999999999999999999999******************9999999999999999***********9 PP

                                       ........HTTCS...HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHH CS
                      AP_endonuc_2  60 ........erear...reesvdalkraielaaaLGapllvlhpGtagagpkgseeeawe 107
                                               +   r       v++  ra+ela+ LG+++   ++     +p++++e ++e
  gi|330506954|ref|YP_004383382.1| 266 lesgsdriL---RamrKGVTVEDNLRAVELAKSLGVKVGGSFIV---GYPGETRE-DFE 317
                                       986665551...054455689****************9777777...23333333.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2495.07
//
Query:       gi|330506955|ref|YP_004383383.1|  [L=559]
Description: methyl-coenzyme M reductase subunit alpha [Methanosaeta concilii GP6]
Scores for complete 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-145  480.9   0.2   1.3e-144  480.6   0.2    1.1  1  MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-ter
    1.8e-68  228.8   2.7    3.8e-68  227.8   2.7    1.6  1  MCR_alpha    Methyl-coenzyme M reductase alpha subunit, C-ter
  ------ inclusion threshold ------
       0.15   12.2   0.0       0.68   10.0   0.0    1.9  2  BofC_C       BofC C-terminal domain


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 !  480.6   0.2  2.1e-148  1.3e-144       1     270 []       7     276 ..       7     276 .. 0.99

  Alignments for each domain:
  == domain 1  score: 480.6 bits;  conditional E-value: 2.1e-148
                                       XX--HHHHHHH-S.S.-TT--B---S-S-GGGG-HHHHHHHHHHHHHHHHH-S----TTS....S--S-SS---EEE CS
                       MCR_alpha_N   1 eklflkalkkkfkke.dpeekktkfykfeGlkqserkrefveaakkiakkrgislynpdilhl.GvplGqrklmpyk 75 
                                       +klf+kal+kkf k+ d +++k ++ k+ G +q++rkref+e+akk++ krg++ ynp ++h+ G+plGqr+l+pyk
  gi|330506955|ref|YP_004383383.1|   7 KKLFVKALNKKFGKDfDLASQKVEY-KRLGPEQNARKREFMEYAKKLEGKRGMTGYNP-YVHAgGIPLGQRQLVPYK 81 
                                       689**********999999999999.********************************.77999************* PP

                                       BTTS--EEEGGGSSGGG-HHHHHHHHHHHTEEEEE-HHHHHHHHHTT-----HHHHHHHHHHHHHHTTT--SS-TT- CS
                       MCR_alpha_N  76 vsgtdvlvegddlhfvnnaalqqlwddirrtvivgldtahevlekrlGkevtPetineylevlnhalPGgavvqehm 152
                                       +s+t+++vegddlhfvnn+a+qq+wddirrt++vgld+ahevl+krlGkevtPetin+yle+lnha+PG+avvqehm
  gi|330506955|ref|YP_004383383.1|  82 LSSTEYVVEGDDLHFVNNPAMQQFWDDIRRTIVVGLDMAHEVLQKRLGKEVTPETINNYLEILNHAMPGAAVVQEHM 158
                                       ***************************************************************************** PP

                                       ----TTT-TT-EEEEEES-HHHHTTS-GGGB--HHHHS-HHHHHHHHHHH-S-EEEEEE--HHHHHHS-HHHHHHHH CS
                       MCR_alpha_N 153 vethPalvedcyvkvftGddeladeidkqflidinkefpeeqaeqlkkaiGkklyqvvriPtivsrtcdGgttsrws 229
                                       vethP+lv+dc v+vf+Gdd ladeid+q+ idink+fpe+qae+lk+aiGk+++q++++Ptiv+rtcdGgttsrws
  gi|330506955|ref|YP_004383383.1| 159 VETHPGLVDDCNVRVFSGDDALADEIDDQYKIDINKMFPEDQAETLKAAIGKTTWQAIHVPTIVVRTCDGGTTSRWS 235
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHT--SS-TTHHHHHHHHHTTSEEES---B- CS
                       MCR_alpha_N 230 amqigmsfisayklcaGeaavadlayaakhaeviemgellP 270
                                       amq++m+fi+ay++caGeaavadlayaakha+v++m+++lP
  gi|330506955|ref|YP_004383383.1| 236 AMQLCMTFIDAYNMCAGEAAVADLAYAAKHAAVLQMSDMLP 276
                                       ****************************************9 PP

>> MCR_alpha  Methyl-coenzyme M reductase alpha subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.8   2.7   6.4e-72   3.8e-68       1     127 []     324     450 ..     324     450 .. 1.00

  Alignments for each domain:
  == domain 1  score: 227.8 bits;  conditional E-value: 6.4e-72
                         MCR_alpha   1 dqiwlGsymsGGvGftqyataaytdnilddfvyygvdyvkdkygglakvkatlevvkdiatevtlyaleqyekyptl 77 
                                       dqiwlGsymsGGvGftqyataayt+++lddf+yygvdy +dk+gg+ak++at++v k++atevtly++eqye +ptl
  gi|330506955|ref|YP_004383383.1| 324 DQIWLGSYMSGGVGFTQYATAAYTNDVLDDFSYYGVDYANDKFGGFAKAPATIDVAKELATEVTLYGIEQYEAFPTL 400
                                       9**************************************************************************** PP

                         MCR_alpha  78 ledhfGGsqraavlaaaagistalatgnsnaGlngwylsmllhkeahsrl 127
                                       ledhfGGsqraavlaaa+gi++a+atg s+ Gl+gwylsmllhkea++rl
  gi|330506955|ref|YP_004383383.1| 401 LEDHFGGSQRAAVLAAASGITSAIATGHSQIGLAGWYLSMLLHKEAWGRL 450
                                       *************************************************8 PP

>> BofC_C  BofC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.39   2.3e+03      43      71 ..     118     146 ..     105     148 .. 0.79
   2 ?   10.0   0.0   0.00011      0.68      12      56 ..     162     207 ..     154     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.39
                                       TTS-HHHHHHHHH--S---HHHHHHHHHH CS
                            BofC_C  43 eklesslkeqLkkGIrveskeeyesvlet 71 
                                       ++  + l+++L k ++ e+ ++y ++l++
  gi|330506955|ref|YP_004383383.1| 118 DMAHEVLQKRLGKEVTPETINNYLEILNH 146
                                       55566778999999999999****99985 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00011
                                       -EEEETTTEEEEBSSS-STT-BS-------TTTS-HHHH.HHHHH- CS
                            BofC_C  12 YfGldedgtlslfeGepeeekviksffqidveklesslk.eqLkkG 56 
                                       + Gl +d ++ +f+G  +  + i + ++id++k+  +++ e Lk  
  gi|330506955|ref|YP_004383383.1| 162 HPGLVDDCNVRVFSGDDALADEIDDQYKIDINKMFPEDQaETLKAA 207
                                       569999***************************9776665778765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 4054.90
//
Query:       gi|330506956|ref|YP_004383384.1|  [L=255]
Description: methyl-coenzyme M reductase subunit gamma [Methanosaeta concilii GP6]
Scores for 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-110  365.9   0.0     9e-110  365.7   0.0    1.0  1  MCR_gamma  Methyl-coenzyme M reductase gamma subunit
  ------ inclusion threshold ------
       0.13   11.9   0.0        0.2   11.3   0.0    1.2  1  LdpA_C     Iron-Sulfur binding protein C terminal


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 !  365.7   0.0    1e-113    9e-110       1     246 []       5     253 ..       5     253 .. 0.99

  Alignments for each domain:
  == domain 1  score: 365.7 bits;  conditional E-value: 1e-113
                         MCR_gamma   1 aqyyPGeskvaenrrkfmdpeaeleklreisdedvvkilghraPGeeyksvhPPleemdepedpirelvePieGaka 77 
                                       +q+yPG+++v+ nrrk+m  + ++eklr+i++ dvv+++ghraPG++y s+hPPl+em ep++pir++v P+ Ga a
  gi|330506956|ref|YP_004383384.1|   5 PQFYPGSTSVGINRRKHM--SGNVEKLRDIPEADVVAVMGHRAPGADYSSTHPPLKEMGEPDCPIRQIVAPTAGAAA 79 
                                       7*****************..8899***************************************************** PP

                         MCR_gamma  78 GdrvryiqfadsmyfaPaqPyqrarlellryrgvdtGtlsGrqiievrerdlekiskelletelfdpartgirGatv 154
                                       Gdrvry q++dsmyfaP+ Py r+++ +++++g d+GtlsGrqiie+rerd+e+++k   ++e++d+a +++rG+tv
  gi|330506956|ref|YP_004383384.1|  80 GDRVRYSQWTDSMYFAPSIPYFRSYWGAINCKGCDPGTLSGRQIIEARERDIEDYTKAQYDSEMTDVALCSMRGCTV 156
                                       ***************************************************************************** PP

                         MCR_gamma 155 hGhslrldenGlmfdalqrlvldeedgevkyvkdqvgvpldkkvdvGkpldedelkkkttiyrldgval......rd 225
                                       hGhslrl+enG++fd+l+r+ l  +dg+v  vkdqvg+pldkkv++Gkp++e+e kk+tti+r dgv +      r+
  gi|330506956|ref|YP_004383384.1| 157 HGHSLRLEENGMQFDMLARTELG-SDGNVYGVKDQVGIPLDKKVNLGKPMSEAEAKKRTTIFRFDGVPMggkvgaRQ 232
                                       **********************8.9******************************************99999999** PP

                         MCR_gamma 226 dkevvevvkrihelrtklgfk 246
                                        +e++e++++++e r+k+g++
  gi|330506956|ref|YP_004383384.1| 233 FDEAIEMTHHMWERRSKWGYR 253
                                       *******************95 PP

>> LdpA_C  Iron-Sulfur binding protein C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.2e-05       0.2      63     102 ..     211     251 ..     196     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.2e-05
                            LdpA_C  63 lkcaliwqtdGrpmSGDigkgttraavklaqkvlaaklp.g 102
                                        k ++i++ dG pm G +g+    +a+++++++ + +   g
  gi|330506956|ref|YP_004383384.1| 211 KKRTTIFRFDGVPMGGKVGARQFDEAIEMTHHMWERRSKwG 251
                                       56789*************************99988765545 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1887.52
//
Query:       gi|330506957|ref|YP_004383385.1|  [L=167]
Description: methyl-coenzyme M reductase operon protein D [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-53  180.3   0.0    1.9e-53  180.1   0.0    1.0  1  MCR_D     Methyl-coenzyme M reductase operon protein D


Domain annotation for each model (and alignments):
>> MCR_D  Methyl-coenzyme M reductase operon protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.1   0.0   1.1e-57   1.9e-53       1     141 [.      11     150 ..      11     152 .. 0.99

  Alignments for each domain:
  == domain 1  score: 180.1 bits;  conditional E-value: 1.1e-57
                             MCR_D   1 dveifpeRlLkpetteklLnelvelegikrvvihGprLPkkvpygpakGkevehkerkvievkgeeveLkvkvGril 77 
                                       +vei+p+R+L p t++klLn ++e  gi+r++ihGp+LP+++pygp kG+++++++  +iev+g+ +eL vkvGr++
  gi|330506957|ref|YP_004383385.1|  11 QVEITPQRYLMPATAQKLLNAIYENGGITRIMIHGPNLPRTIPYGPGKGTPIDEHKDLLIEVAGQVFELGVKVGRVR 87 
                                       89*************************************************************************** PP

                             MCR_D  78 leledeeviekieeiceevlpfsyeikegkfirkkktvsDyakyGeeeadkrllGlvDpkskle 141
                                       lele+e++++ +e++ce++lpfs++ik+g+f+r+++t+sDyakyG+   dkrllGl+Dpk+++e
  gi|330506957|ref|YP_004383385.1|  88 LELESEKYMPGLEAACERALPFSFQIKRGRFFRNSPTLSDYAKYGDV-EDKRLLGLIDPKARKE 150
                                       ***********************************************.*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1246.15
//
Query:       gi|330506958|ref|YP_004383386.1|  [L=434]
Description: methyl-coenzyme M reductase subunit beta [Methanosaeta concilii GP6]
Scores for complete 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-135  450.5   9.2   2.2e-135  450.0   9.2    1.2  1  MCR_beta    Methyl-coenzyme M reductase beta subunit, C-termi
    4.2e-76  254.6   5.0    1.4e-75  253.0   1.4    2.3  2  MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-termi
  ------ inclusion threshold ------
        0.2   11.4   0.0       0.52   10.1   0.0    1.6  2  DUF1810     Protein of unknown function (DUF1810)


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 !  450.0   9.2  3.7e-139  2.2e-135       1     248 [.     186     433 ..     186     434 .] 0.99

  Alignments for each domain:
  == domain 1  score: 450.0 bits;  conditional E-value: 3.7e-139
                          MCR_beta   1 GyalrnikanhvvaitkknalnaaalssileqtavfemGdavGaferahllglayqGlnannlvydlvkengkegtv 77 
                                       G+alrn++anh+++itk+na+naaal+si+eq++ +emG+a+G fer++llg+ayqGlnann+vy+ vk+ngk+gt+
  gi|330506958|ref|YP_004383386.1| 186 GFALRNVMANHLAMITKRNAMNAAALASIYEQIGEMEMGNAMGIFERHQLLGMAYQGLNANNMVYETVKANGKTGTI 262
                                       8**************************************************************************** PP

                          MCR_beta  78 GtvveslveraiedkvikvekklpsgyklyetkdvalwnayaaaGllaavivnvgaaraaqavsstllyyndlleke 154
                                       Gtvv+s+v +a+edkvik+ kklpsgy +ye++dv++wnayaaaG+laa++vn+g+ r aqavsstlly+nd++eke
  gi|330506958|ref|YP_004383386.1| 263 GTVVQSIVGKALEDKVIKAGKKLPSGYVMYEANDVSKWNAYAAAGVLAATMVNCGSLRGAQAVSSTLLYFNDIIEKE 339
                                       ***************************************************************************** PP

                          MCR_beta 155 tglpGvdfGrveGtavGfsffshsiyGGGGpGifnGnhvvtrhskGfaipcvaaavaldaGtqlfspeatsglvgev 231
                                       t+lpG+dfGrv+GtavGfsffshsiyGGGGpG+fnGnhvvtrhs+GfaipcvaaavaldaGtq+f+pe+tsglvg +
  gi|330506958|ref|YP_004383386.1| 340 TALPGCDFGRVMGTAVGFSFFSHSIYGGGGPGVFNGNHVVTRHSRGFAIPCVAAAVALDAGTQMFTPEMTSGLVGAI 416
                                       ***************************************************************************** PP

                          MCR_beta 232 fgeidefreplkavaea 248
                                       +gei+efrep+  vaea
  gi|330506958|ref|YP_004383386.1| 417 YGEIKEFREPIVSVAEA 433
                                       **************986 PP

>> MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.0   1.4   2.3e-79   1.4e-75       1     182 []       3     184 ..       3     184 .. 1.00
   2 ?    2.7   0.1     0.014        85      47      78 ..     252     283 ..     245     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 253.0 bits;  conditional E-value: 2.3e-79
                        MCR_beta_N   1 DkidlyddkGkllesdvpleaisPlknpaikkivkdvkrtvavnlagiekalktgkvggkaskilGreldldivena 77 
                                       Dkidly+d+G ll+sdv+l+a+sPlkn+a++++++++krtvavnlag+e alktgkv+g  ++i+Grel++d+v+na
  gi|330506958|ref|YP_004383386.1|   3 DKIDLYSDRGVLLKSDVDLSAVSPLKNAAMQRLISLTKRTVAVNLAGVEGALKTGKVAGGRRQIKGRELNYDVVANA 79 
                                       9**************************************************************************** PP

                        MCR_beta_N  78 daiaekikelvqveedddtkvkllngGkqllvqvPskRleaaaeysvallataaavveaiidefdvdmfdasvvkaa 154
                                        a+aekik l+qv  +ddt+v+ l+gGkqllvqvP++R++aa+e+ v+l+ +a+a+vea+i++f+v++ +a++v+a 
  gi|330506958|ref|YP_004383386.1|  80 GALAEKIKTLLQVAPGDDTNVQILGGGKQLLVQVPTARVNAASEFVVGLTGAASATVEALIQQFKVGIVEAPMVHAS 156
                                       ***************************************************************************** PP

                        MCR_beta_N 155 vlGryPqtvdlaggnvasilsipqkneG 182
                                       v+G+yPqtv ++ggnvas+l+ipq++eG
  gi|330506958|ref|YP_004383386.1| 157 VWGEYPQTVGMNGGNVASVLNIPQNDEG 184
                                       ***************************9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.014
                        MCR_beta_N  47 giekalktgkvggkaskilGreldldivenad 78 
                                        +++  ktg++g+  ++i G+ l+ ++++  +
  gi|330506958|ref|YP_004383386.1| 252 TVKANGKTGTIGTVVQSIVGKALEDKVIKAGK 283
                                       6677779*****************99998655 PP

>> DUF1810  Protein of unknown function (DUF1810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   8.7e-05      0.52      32     109 ..     157     233 ..     140     248 .. 0.90
   2 ?   -3.2   0.0       1.2   6.9e+03      51      76 ..     292     317 ..     289     325 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.7e-05
                                       HHHHS--BTTS--SHHHHHTSB-SHHHHHHHHHSTTHHHHHHHHHHHHHH--S--HHHHS-TTHHHHHHHHHHHHHH CS
                           DUF1810  32 mWfvFPqlkglgksetaerYaiesleearaylahpvLgkrlreiteallaleeksaeeilGsidalKlrssmtLFae 108
                                       +W  +Pq  g++  + a+  +i + +e   +   +v+ ++l  it+  +a+++    +i  +i ++ +  +m +F++
  gi|330506958|ref|YP_004383386.1| 157 VWGEYPQTVGMNGGNVASVLNIPQNDEGLGFALRNVMANHLAMITKR-NAMNAAALASIYEQIGEMEMGNAMGIFER 232
                                       67789*************************************99986.66788899999999999999999999987 PP

                                       H CS
                           DUF1810 109 v 109
                                        
  gi|330506958|ref|YP_004383386.1| 233 H 233
                                       5 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                                       TSB-SHHHHHHHHHSTTHHHHHHHHH CS
                           DUF1810  51 YaiesleearaylahpvLgkrlreit 76 
                                       Y+ ++++  +ay a  vL + ++++ 
  gi|330506958|ref|YP_004383386.1| 292 YEANDVSKWNAYAAAGVLAATMVNCG 317
                                       77788888899999999999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3126.62
//
Query:       gi|330506959|ref|YP_004383387.1|  [L=766]
Description: DNA topoisomerase I [Methanosaeta concilii GP6]
Scores for complete 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-119  399.0   0.0   3.1e-119  398.7   0.0    1.1  1  Topoisom_bac    DNA topoisomerase
    1.4e-15   57.4   0.1    1.2e-14   54.4   0.0    2.4  2  Toprim          Toprim domain
    1.7e-15   56.5   0.9    1.7e-15   56.5   0.9    2.0  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
      9e-09   35.8   2.3      3e-08   34.1   2.3    2.0  1  HHH_5           Helix-hairpin-helix domain
    0.00067   19.9   0.2     0.0017   18.6   0.2    1.6  1  DUF4332         Domain of unknown function (DUF4332)
     0.0037   17.0   0.1     0.0097   15.7   0.1    1.7  1  HHH             Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.035   14.3   0.0    1.6  1  Cdd1            Pathogenicity locus
      0.025   14.9   0.0      0.083   13.3   0.0    1.9  1  IMS_HHH         IMS family HHH motif
       0.11   13.0   0.0         31    5.1   0.1    2.5  2  OAM_dimer       Dimerisation domain of d-ornithine 4,5-aminom
       0.21   11.2   0.4         32    4.2   0.1    2.7  2  PikAIV_N        Narbonolide/10-deoxymethynolide synthase PikA


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 !  398.7   0.0  1.7e-122  3.1e-119       2     412 ..     150     546 ..     149     547 .. 0.92

  Alignments for each domain:
  == domain 1  score: 398.7 bits;  conditional E-value: 1.7e-122
                      Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkg..kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkke 76 
                                       ++ +l++++eaR+++D+++G++l+r+++++  +  k++ls+GRVq+ptLaliv+Re+ei++Fvp++ywe+ a+l+++
  gi|330506959|ref|YP_004383387.1| 150 VDYDLAASGEARQIIDLVWGAALTRYISLTSGRlgKEFLSVGRVQSPTLALIVDREKEIQSFVPKPYWEIYADLERD 226
                                       57899***********************94444569*************************************8655 PP

                      Topoisom_bac  77 kkekekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqk 153
                                        +      +++++ri++k+e+++i+++l      ++s+++k + ++pp pfdtt++ ++as + g+sa+++++ia+ 
  gi|330506959|ref|YP_004383387.1| 227 LR-----VQHARGRIWEKDEVDSIVARL-GPVGIIRSIQTKPRVEKPPAPFDTTSFISAASGI-GFSAANAMRIAEW 296
                                       53.....589******************.5479*****************************8.************* PP

                      Topoisom_bac 154 LYekaglitYpRTdstrlsee.aelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpkl 229
                                       LY + g+i+YpRTd+t+++++ + ++ ++ +l+ +++ke+++    +   t+     ++  +++H++I+Pt+ ++k 
  gi|330506959|ref|YP_004383387.1| 297 LYVN-GFISYPRTDNTVYPPSiDLVALTRLFLKGEFSKEAEKLLGGKMVPTR-----GKRSTTDHPPIYPTAPVNK- 366
                                       ***7.****************7766777777777766666666666665554.....44566*********99986. PP

                      Topoisom_bac 230 kelsddekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkege 306
                                       +el+++++k+Yel+vrrf+a+l+++++++ t++k++++ e f+asg +++e+G++ +y+++k+ee+   lp+lkege
  gi|330506959|ref|YP_004383387.1| 367 SELKEEQWKIYELVVRRFFATLAESCVWDATSLKVDIGPEPFRASGARLVEPGWRYYYPYSKAEER--ILPALKEGE 441
                                       9***********************************************************999976..7******** PP

                      Topoisom_bac 307 evkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf. 382
                                       +++v + ++e+k+T+pp+ry +++Lik+m++ g+Gt++Tr++ii+kl+ r Yv+ +   ++pt+++ a+v++l+k+ 
  gi|330506959|ref|YP_004383387.1| 442 RLRVLGHSVEAKETQPPARYGQGKLIKLMDELGLGTKSTRHDIISKLYARAYVQGNP--MRPTNTAYAVVDTLQKYa 516
                                       ******************************************************966..9*************8898 PP

                      Topoisom_bac 383 kdlvspelTaeleekLdeIaegkadakevl 412
                                       +++++pe+T+ le+++ +I+e k++++ev+
  gi|330506959|ref|YP_004383387.1| 517 PTITKPEMTQTLEKDMTQISEQKIKEDEVI 546
                                       ****************************98 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   6.6e-18   1.2e-14       2     102 ..       3     134 ..       2     135 .. 0.87
   2 ?   -0.5   0.0      0.82   1.5e+03      14      54 ..     335     370 ..     332     389 .. 0.69

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 6.6e-18
                                       EEEESSHHHHHHHHHTHT................STEEEEEEESSSSEEEHS..........TTEEEEE........ CS
                            Toprim   2 lvivEgpsdaktiakalg................sgfqavtaslGhildlet..........efkpvye........ 44 
                                       l+i+E+  +ak ia++l+                 ++++v+ ++Ghi+ ++           +              
  gi|330506959|ref|YP_004383387.1|   3 LIIAEKHDAAKRIAQILSgnkprpyriggveafkFDDKVVMGLSGHIVGVDYppgynnwqkvD-----Ckeliraei 74 
                                       8********************************98899**************76666555551.....144555666 PP

                                       .ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTT.TEEEEEESS CS
                            Toprim  45 .eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellen.kigrvefse 102
                                        +++ + k+++al++l k+ad+i +atD DreGe i+ e+l+ +ke++++ +  rv+ s 
  gi|330506959|ref|YP_004383387.1|  75 vVRPINDKIVNALRSLGKEADRITVATDYDREGELIGVEALKIAKEANPRlREDRVRYSA 134
                                       69999999**********************************999888887777777765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.82
                                       HHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHH CS
                            Toprim  14 iakalgsgfqavtaslGhildletefkpvyeeiedkkkvlk 54 
                                       ++k+    ++++++++G+  + ++  +p+y   + +k+ lk
  gi|330506959|ref|YP_004383387.1| 335 AEKL---LGGKMVPTRGKRSTTDH--PPIYPTAPVNKSELK 370
                                       5666...44899***********9..888873333333333 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 !   56.5   0.9   9.6e-19   1.7e-15       1      38 [.     581     619 ..     581     620 .. 0.96
   2 ?   -1.4   0.1       1.2   2.2e+03       4       8 ..     652     656 ..     650     664 .. 0.68

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 9.6e-19
                                       -EE-SSS--EEEEEE-SSS.EEEEESST.T----EEB-G CS
                    zf-C4_Topoisom   1 vekCPkCggdLvlkrgkkG.kFvGCsnYPeCkftkklkk 38 
                                       v++C+kC+++L+++rg +G +F+GCs YPeC+ft +l++
  gi|330506959|ref|YP_004383387.1| 581 VGTCEKCNSELIIRRGHRGsRFIGCSGYPECRFTLPLPR 619
                                       589*********************************997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                                       -SSS- CS
                    zf-C4_Topoisom   4 CPkCg 8  
                                       CP C+
  gi|330506959|ref|YP_004383387.1| 652 CPHCN 656
                                       77775 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   2.3   1.7e-11     3e-08       4      56 ..     711     763 ..     709     764 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.7e-11
                                       HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                       L +++GiGpkt  +l+saGi++  +la a+++ La+ +G+++k+   ++ ++k
  gi|330506959|ref|YP_004383387.1| 711 LARLPGIGPKTLEKLASAGIKTSGELAGANAKSLAAKTGLSEKKIAAWKSAAK 763
                                       7789*********************************************9998 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   9.6e-07    0.0017       1      54 [.     715     763 ..     712     765 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.6e-07
                           DUF4332   1 pgigkeeaekLkkaGikttedLlelgktekgrkalaeklgisernvlklanlAd 54 
                                       pgig++  ekL++aGikt+ +L+ ++      k la+k+g+se+++ +++ +A+
  gi|330506959|ref|YP_004383387.1| 715 PGIGPKTLEKLASAGIKTSGELAGAN-----AKSLAAKTGLSEKKIAAWKSAAK 763
                                       7999******************9984.....346999************99985 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   5.4e-06    0.0097       7      29 ..     705     727 ..     702     728 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.4e-06
                                       TSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   7 pasreeLlalPGVGpktAeaIls 29 
                                       +a+ + L+ lPG+Gpkt e+ +s
  gi|330506959|ref|YP_004383387.1| 705 NADGDGLARLPGIGPKTLEKLAS 727
                                       79999************998876 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     2e-05     0.035       8      44 ..     711     747 ..     705     755 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                              Cdd1   8 lqdiPniGkalaedlvelGirsveelkgedpeelyek 44 
                                       l ++P+iG+++ e+l + Gi++  el+g ++++l +k
  gi|330506959|ref|YP_004383387.1| 711 LARLPGIGPKTLEKLASAGIKTSGELAGANAKSLAAK 747
                                       889****************************999876 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.6e-05     0.083      15      32 .]     713     730 ..     711     730 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-05
                           IMS_HHH  15 kipGiGgklgekLeklGi 32 
                                        +pGiG+k+ ekL++ Gi
  gi|330506959|ref|YP_004383387.1| 713 RLPGIGPKTLEKLASAGI 730
                                       69*************998 PP

>> OAM_dimer  Dimerisation domain of d-ornithine 4,5-aminomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0      0.02        35      17      49 ..     612     643 ..     607     645 .. 0.91
   2 ?    5.1   0.1     0.017        31      25      51 ..     734     760 ..     729     765 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.02
                                       EEEESS-SCHHHHHHHHHHHHCTTSEEEEEEEE CS
                         OAM_dimer  17 sftLPvpaeeeAeeAAlelakkmGledpeVvhk 49 
                                        ftLP+p ++ A     ++++k+G+  + +++k
  gi|330506959|ref|YP_004383387.1| 612 RFTLPLP-RSGAVVVTDKVCEKHGMFHIRIINK 643
                                       79*****.9******************999986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.017
                                       CHHHHHHHHHHHHCTTSEEEEEEEEEE CS
                         OAM_dimer  25 eeeAeeAAlelakkmGledpeVvhkee 51 
                                       +e A + A+ la+k+Gl++ ++++ ++
  gi|330506959|ref|YP_004383387.1| 734 GELAGANAKSLAAKTGLSEKKIAAWKS 760
                                       7899999**************998776 PP

>> PikAIV_N  Narbonolide/10-deoxymethynolide synthase PikA4 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.019        33       3      12 ..      80      89 ..      80      96 .. 0.89
   2 ?    4.2   0.1     0.018        32      13      21 ..     436     444 ..     436     445 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.019
                          PikAIV_N  3 deklVeALRa 12
                                      ++k+V ALR+
  gi|330506959|ref|YP_004383387.1| 80 NDKIVNALRS 89
                                      69*******6 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.018
                          PikAIV_N  13 SLkEnERLR 21 
                                       +LkE ERLR
  gi|330506959|ref|YP_004383387.1| 436 ALKEGERLR 444
                                       69******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (766 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 5210.49
//
Query:       gi|330506960|ref|YP_004383388.1|  [L=345]
Description: cell division protein pelota [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-26   93.4   0.0    1.5e-26   92.9   0.0    1.2  1  eRF1_1    eRF1 domain 1
    9.5e-22   77.6   0.2    3.8e-21   75.7   0.2    2.0  1  eRF1_3    eRF1 domain 3
    2.2e-07   31.3   0.0      8e-07   29.4   0.0    1.9  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 !   92.9   0.0   2.5e-30   1.5e-26       1     128 [.       1     125 [.       1     126 [. 0.94

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 2.5e-30
                                       HEEEEECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH........--CEEEEEEEEEEEEEEECT CS
                            eRF1_1   1 mkllkrdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqr.esstgsreservklkLtikvekvdfdk 76 
                                       m++lk+dl+++ +g + L+pe+ +dlwhl +l++ gd v a   rkv     +    + er++++L +k+e+v+f++
  gi|330506960|ref|YP_004383388.1|   1 MRVLKKDLRGE-EGEIALLPESLDDLWHLRHLVERGDLVFALSQRKVPAiADKARPEKMERKTVRLGVKIEDVEFHM 76 
                                       9*******965.9**********************************995566666679****************** PP

                                       TSSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                            eRF1_1  77 dagvlrisGkvieenehvklgafhtldlelkrpftiikeewdsfalerLkea 128
                                        ++ lr++G+++++ +   +g++htl++e++ +++i k++w    l r+++a
  gi|330506960|ref|YP_004383388.1|  77 YSNWLRLHGRIVSGMD---VGSYHTLNIEVGTDLSILKYHWRPDLLARIDDA 125
                                       ****************...9**********************9999999887 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.2   6.4e-25   3.8e-21       1     113 []     252     344 ..     252     344 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6.4e-25
                                       HHHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHH CS
                            eRF1_3   1 liqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelven 77 
                                       +++e+kl+ee+++e+a++ gka+YG+ ev+ka+++gA+e LLv++e+ r  d                  +++++++
  gi|330506960|ref|YP_004383388.1| 252 IAREAKLIEELFREIATG-GKAAYGIAEVQKAMNYGAIESLLVLDEFARRGD------------------VDDIMRQ 309
                                       689*************99.*****************************9852..................89***** PP

                                       HHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  78 veesgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                       v +s++kv+++sse+e G +l +++gG+aa+LR+k+
  gi|330506960|ref|YP_004383388.1| 310 VGNSRGKVIVFSSEFEPGDRL-ASLGGVAALLRFKI 344
                                       *********************.************97 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.3e-10     8e-07       3     131 ..     135     247 ..     133     249 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.3e-10
                                       EEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESE CS
                            eRF1_2   3 glivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkg 79 
                                        l +++egeAtigll++  +++ ++i +s   K   G+ +           + +f++ vaea+++a      +  + 
  gi|330506960|ref|YP_004383388.1| 135 VLALVEEGEATIGLLRQFGVQMAAEIRMSSG-K---GSGED---------TRASFMRGVAEAIDNA-----AGGGAD 193
                                       57789*********************99842.2...32333.........4579************.....677788 PP

                                       EEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC..CHHHH CS
                            eRF1_2  80 iilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlek..aaevl 131
                                       +ilagpgf+k+++ + +   +   +  i + d+s+ g+sg++evl+   +++vl
  gi|330506960|ref|YP_004383388.1| 194 VILAGPGFAKDDLKKVIDSSYPDLAGRIAMDDASSIGRSGFQEVLRRgaVKSVL 247
                                       9********************************************997666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2464.13
//
Query:       gi|330506961|ref|YP_004383389.1|  [L=264]
Description: hypothetical protein MCON_0768 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0027   17.5   0.0     0.0055   16.5   0.0    1.6  1  ATP_bind_3     PP-loop family
  ------ inclusion threshold ------
      0.072   13.1   0.0       0.11   12.5   0.0    1.3  1  NAD_binding_9  FAD-NAD(P)-binding


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 !   16.5   0.0   6.2e-07    0.0055       3     164 ..      44     210 ..      42     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.2e-07
                                       EEE--SCHHHHHHHHHHHHHCTTTTT.EEEEEEE.E-SSSTCHH.HHHHHHHHHHHHTT-EEEEEE--HHHCTTSTC CS
                        ATP_bind_3   3 lvAvSgGlDSmaLllllaklkkklgi.klvaihv.dhglreesk.eeaelvkelckklnikleiekvdvakkkgknl 76 
                                       ++A+ gG  S ++ +++++l  +    +l+++ + dhg  ++s+   ++ +   ++   +++   + +va++     
  gi|330506961|ref|YP_004383389.1|  44 ALAMDGGKGSAVMANIIKELFARRRDiDLALLILdDHGPGAKSAwIASQQLGLRVSIKALPVSLLNERVASDPAPDP 120
                                       67888888888888888887654443344444331566654333133344444444444555555555555555566 PP

                                       CCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEE....TTCCEE-CCCT--H CS
                        ATP_bind_3  77 eeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeasei....asirlvRPlLkvsk 149
                                          A ++R  +++ ++++ g++ ++++h  dD a  ++++   g+     +g +e ++       i  + Pl  +  
  gi|330506961|ref|YP_004383389.1| 121 ISFAQKMR--MMTGLAREMGANAIATGHDLDDMATEVFISYLEGNICGLQYGRQETRQEgyeqGMIPTIQPLRRIPG 195
                                       66777776..899******************************9999888998887766555344888999999999 PP

                                       HHHHHHHHHTT---B CS
                        ATP_bind_3 150 eeleeylkekkikwv 164
                                       +e++ y+ ++++ ++
  gi|330506961|ref|YP_004383389.1| 196 KEVRLYALQHGLCFA 210
                                       999999999988776 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.2e-05      0.11       6      64 ..      49     110 ..      48     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                     NAD_binding_9   6 GprGlavlerLlara...kkkspleitlfdpsepgagrvwrtdqseelllNvpasemslftd 64 
                                       G +G av+++++++    +++ +l + + d+++pga+++w ++q+  l++ ++a  +sl+ +
  gi|330506961|ref|YP_004383389.1|  49 GGKGSAVMANIIKELfarRRDIDLALLILDDHGPGAKSAWIASQQLGLRVSIKALPVSLLNE 110
                                       56788889999998886567777999999***************999999999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1894.19
//
Query:       gi|330506962|ref|YP_004383390.1|  [L=159]
Description: AsnC family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-14   53.3   0.2    4.4e-14   52.2   0.0    1.6  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    1.4e-08   34.2   0.2      3e-08   33.1   0.2    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.9e-07   30.9   0.0    5.1e-07   29.6   0.0    1.7  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    1.4e-06   28.1   0.1      1e-05   25.3   0.0    2.1  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    9.6e-06   25.6   0.0    1.9e-05   24.6   0.0    1.4  1  HTH_20          Helix-turn-helix domain
    0.00015   21.7   0.0    0.00031   20.6   0.0    1.5  1  MarR            MarR family
    0.00024   20.8   1.2     0.0051   16.5   0.1    2.8  3  HTH_38          Helix-turn-helix domain
    0.00073   19.4   0.0     0.0021   17.9   0.0    1.7  2  MarR_2          MarR family
     0.0022   17.9   0.0     0.0033   17.2   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.039   13.9   0.0    1.5  1  HTH_36          Helix-turn-helix domain
      0.022   14.9   2.2       0.16   12.1   0.8    2.2  2  Sigma70_r3      Sigma-70 region 3
       0.03   14.3   0.1      0.065   13.2   0.1    1.6  1  HTH_11          HTH domain
      0.031   14.0   0.2      0.055   13.2   0.2    1.5  1  DUF4423         Domain of unknown function (DUF4423)
       0.05   13.3   0.0        0.1   12.3   0.0    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.054   13.3   0.0       0.27   11.1   0.0    2.2  3  HTH_23          Homeodomain-like domain
      0.068   13.1   0.1       0.17   11.8   0.1    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.08   12.3   0.0       0.11   11.8   0.0    1.4  1  DUF1670         Protein of unknown function (DUF1670)
      0.099   12.8   0.0       0.18   12.0   0.0    1.4  1  HTH_34          Winged helix DNA-binding domain
       0.14   12.2   0.1       0.23   11.6   0.1    1.3  1  DUF2250         Uncharacterized protein conserved in archaea 
       0.15   12.1   0.0       0.65   10.1   0.0    2.1  2  HTH_29          Winged helix-turn helix
       0.15   12.1   0.1       0.31   11.1   0.1    1.5  1  Dimerisation    Dimerisation domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.6   4.8e+03      13      24 ..      27      38 ..      23      39 .. 0.73
   2 !   52.2   0.0   5.2e-17   4.4e-14       5      74 ..      70     137 ..      64     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.6
                                      HHHHHHHHHTST CS
                    AsnC_trans_reg 13 leefeealaelp 24
                                       ee++++++e++
  gi|330506962|ref|YP_004383390.1| 27 EEEVAREIKEME 38
                                      578888888875 PP

  == domain 2  score: 52.2 bits;  conditional E-value: 5.2e-17
                                       E-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   5 lepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       l++  +  +++++e++a++ eV+++  ++G +d+ + v+ ++++++  f+ ek+a l+gv++t t+++l+
  gi|330506962|ref|YP_004383390.1|  70 LQR--KTGYDAVAERIARFSEVESVRLISGGHDLSVTVRGKSMKDIAYFVAEKIAPLDGVQSTCTHFILK 137
                                       333..4589***********************************************************98 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.2   3.5e-11     3e-08       7      48 .]       3      44 ..       2      44 .. 0.98

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 3.5e-11
                            HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +ILe+L++n++ + +e+A  lg S   v r +k++e++G+I+
  gi|330506962|ref|YP_004383390.1|  3 EILEILYENAKATPSEIAALLGKSEEEVAREIKEMEDAGIIR 44
                                      7****************************************7 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0     6e-10   5.1e-07      23      66 ..      15      56 ..       6      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 6e-10
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHHHH CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisrgrririldleaLr 66
                                      t  e+A++lG + e v r+++e++++g+i++ + i++ ++e+L 
  gi|330506962|ref|YP_004383390.1| 15 TPSEIAALLGKSEEEVAREIKEMEDAGIIRK-Y-ITLINWEKLD 56
                                      778**************************95.4.********97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.2e-08     1e-05       7      42 .]       3      38 ..       2      38 .. 0.96
   2 ?    0.1   0.0      0.89   7.6e+02      32      40 ..      77      85 ..      76      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.2e-08
                     HTH_AsnC-type  7 kILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                       ILe+L e+a+++ +e+A+ +G Se++v+r ++ +e
  gi|330506962|ref|YP_004383390.1|  3 EILEILYENAKATPSEIAALLGKSEEEVAREIKEME 38
                                      59****************************999997 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.89
                     HTH_AsnC-type 32 stvlrRvrr 40
                                      ++v++R++r
  gi|330506962|ref|YP_004383390.1| 77 DAVAERIAR 85
                                      589****98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.2e-08   1.9e-05      15      55 ..       4      44 ..       3      46 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.2e-08
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      il  L +++ +t+se+a++l+ s  ++ + ++++e+ag+++
  gi|330506962|ref|YP_004383390.1|  4 ILEILYENAKATPSEIAALLGKSEEEVAREIKEMEDAGIIR 44
                                      9999***********************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.6e-07   0.00031       7      50 ..       3      46 ..       2      48 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.6e-07
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      +iL+ilye+  ++ se+a  lg s   v r ++++e++G i+++
  gi|330506962|ref|YP_004383390.1|  3 EILEILYENAKATPSEIAALLGKSEEEVAREIKEMEDAGIIRKY 46
                                      79***************************************987 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1     6e-06    0.0051      12      42 ..       4      35 ..       2      36 .. 0.90
   2 ?   -1.0   0.1       1.8   1.6e+03      15      32 ..      68      85 ..      64      85 .. 0.76
   3 ?    1.4   0.0      0.33   2.8e+02      19      27 ..     106     114 ..     104     116 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6e-06
                            HTH_38 12 eIerll.aeGlslreIArrLgrspsTIsRElk 42
                                       +e+l+ +++ + +eIA +Lg+s   ++RE+k
  gi|330506962|ref|YP_004383390.1|  4 ILEILYeNAKATPSEIAALLGKSEEEVAREIK 35
                                      5789996699********************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.8
                            HTH_38 15 rllaeGlslreIArrLgr 32
                                        l+++ ++ ++A r+ r
  gi|330506962|ref|YP_004383390.1| 68 VALQRKTGYDAVAERIAR 85
                                      567888889999999866 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.33
                            HTH_38  19 eGlslreIA 27 
                                       +G+s+++IA
  gi|330506962|ref|YP_004383390.1| 106 RGKSMKDIA 114
                                       79******9 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   2.5e-06    0.0021      10      53 ..       4      45 ..       2      48 .. 0.92
   2 ?   -2.6   0.0         6   5.2e+03      37      55 ..      78      96 ..      72     101 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-06
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +L  L+ +     t++e+a+ lg s   v r +k++++aG +++
  gi|330506962|ref|YP_004383390.1|  4 ILEILYENAK--ATPSEIAALLGKSEEEVAREIKEMEDAGIIRK 45
                                      7888999998..9****************************986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6
                                      HHHHHHHHHHHTTSEEEEE CS
                            MarR_2 37 avsrilkrLvaaGLverrp 55
                                      av  +++r+++   v+  +
  gi|330506962|ref|YP_004383390.1| 78 AVAERIARFSEVESVRLIS 96
                                      5666777777766666555 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 !   17.2   0.0   3.9e-06    0.0033       6      47 .]       3      45 ..       1      45 [. 0.95

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.9e-06
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      +IL +L e  +++ +e+a+ lg+s+  v +  k +++aG+++k
  gi|330506962|ref|YP_004383390.1|  3 EILEILYEnAKATPSEIAALLGKSEEEVAREIKEMEDAGIIRK 45
                                      89******889*****************************986 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.6e-05     0.039      29      55 .]      17      43 ..      10      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                            HTH_36 29 etlakrlglsknTvsraikeLeqlGyi 55
                                      + +a++lg+s++ v r ike e++G+i
  gi|330506962|ref|YP_004383390.1| 17 SEIAALLGKSEEEVAREIKEMEDAGII 43
                                      679**********************98 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   0.00018      0.16      20      39 ..      13      32 ..      10      40 .. 0.86
   2 ?    1.8   0.0      0.31   2.6e+02      10      32 ..      67      89 ..      62      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                      XXXHHHHHHHHTXXHHHHHH CS
                        Sigma70_r3 20 ePtpeEiAeeLglseekVre 39
                                       +tp EiA+ Lg see+V +
  gi|330506962|ref|YP_004383390.1| 13 KATPSEIAALLGKSEEEVAR 32
                                      58****************65 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.31
                                      HHHHHHHHSSXXXHHHHHHHHTX CS
                        Sigma70_r3 10 qreLeqelgrePtpeEiAeeLgl 32
                                      +  L++++g+++ +e iA + ++
  gi|330506962|ref|YP_004383390.1| 67 KVALQRKTGYDAVAERIARFSEV 89
                                      557999************98776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.6e-05     0.065       4      44 ..       3      42 ..       1      51 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.6e-05
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                       ile+L+e+ +  + +e+A  L+ S+  v r Ik++e++g+
  gi|330506962|ref|YP_004383390.1|  3 EILEILYENAK-ATPSEIAALLGKSEEEVAREIKEMEDAGI 42
                                      69********9.8**************************94 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   6.4e-05     0.055      33      83 ..      10      59 ..       1      74 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.4e-05
                           DUF4423 33 kdfkadpeelakrlrpkisaeevekalefLlklgllkkded.gkyrqteksl 83
                                      +++ka+p+e+a  l+   s+eev++ ++ ++++g+++k     ++++ ++s+
  gi|330506962|ref|YP_004383390.1| 10 ENAKATPSEIAALLG--KSEEEVAREIKEMEDAGIIRKYITlINWEKLDQSV 59
                                      45579**********..********************977666666666665 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 ?   12.3   0.0   0.00012       0.1       4      46 ..       3      45 ..       1      47 [. 0.95

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      +ile l +  k +  e+++llg Se+ + R ++e+e +g++++
  gi|330506962|ref|YP_004383390.1|  3 EILEILYENAKATPSEIAALLGKSEEEVAREIKEMEDAGIIRK 45
                                      89**************************************987 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00032      0.27       9      45 ..       6      41 ..       2      45 .. 0.78
   2 ?   -1.9   0.0       3.9   3.3e+03      17      24 ..     107     114 ..     101     114 .. 0.81
   3 ?   -3.1   0.0       8.8   7.5e+03      37      45 ..     135     143 ..     135     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                            HTH_23  9 rillllaeGlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      +il+  a +++++eIA++Lg s+  v r +k  +  G
  gi|330506962|ref|YP_004383390.1|  6 EILYENA-KATPSEIAALLGKSEEEVAREIKEMEDAG 41
                                      5555555.8*************999998888754455 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.9
                            HTH_23  17 GlsvreIA 24 
                                       G+s ++IA
  gi|330506962|ref|YP_004383390.1| 107 GKSMKDIA 114
                                       99****98 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 8.8
                            HTH_23  37 wlkryreeG 45 
                                       +lk y+e+G
  gi|330506962|ref|YP_004383390.1| 135 ILKSYKEHG 143
                                       688898888 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0002      0.17      15      54 ..       6      45 ..       2      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                        L ++ +at +eia  lg ++  v + ++++ed+G++++
  gi|330506962|ref|YP_004383390.1|  6 EILYENAKATPSEIAALLGKSEEEVAREIKEMEDAGIIRK 45
                                      567799******************************9976 PP

>> DUF1670  Protein of unknown function (DUF1670)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.11     104     139 ..      12      46 ..       4      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                           DUF1670 104 alltqsDlalllgvstrtvskqvkeyqeeegivlpt 139
                                       a  t s++a llg+s++ v +++ke+ e  gi+ ++
  gi|330506962|ref|YP_004383390.1|  12 AKATPSEIAALLGKSEEEVAREIKEM-EDAGIIRKY 46 
                                       5568899******************9.988888665 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00021      0.18       4      45 ..       3      44 ..       2      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                            HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                      ++l +L+++ +a+++e+ + l+ ++ + + ++k +e+ag i 
  gi|330506962|ref|YP_004383390.1|  3 EILEILYENAKATPSEIAALLGKSEEEVAREIKEMEDAGIIR 44
                                      699***********************************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 ?   11.6   0.1   0.00027      0.23      11      55 ..       2      46 ..       1      53 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                           DUF2250 11 lkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerv 55
                                      +++l++l +     +  ia  l ++ eev + +k++e++G++ ++
  gi|330506962|ref|YP_004383390.1|  2 HEILEILYENAKATPSEIAALLGKSEEEVAREIKEMEDAGIIRKY 46
                                      67778887777778899*************************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 ?   10.1   0.0   0.00076      0.65      13      41 ..      13      42 ..       3      56 .. 0.83
   2 ?   -1.7   0.0       3.6   3.1e+03      33      48 ..     136     150 ..     135     157 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00076
                            HTH_29 13 s.tvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      + t+s+iA+llg s+  v r +k +e  G+
  gi|330506962|ref|YP_004383390.1| 13 KaTPSEIAALLGKSEEEVAREIKEMEDAGI 42
                                      349********************9999886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.6
                            HTH_29  33 lkrfeegGlaalld.rr 48 
                                       lk + e+G  a+l  ++
  gi|330506962|ref|YP_004383390.1| 136 LKSYKEHG--AILTeQP 150
                                       79999999..3333355 PP

>> Dimerisation  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00037      0.31      10      34 ..       3      25 ..       3      34 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                      Dimerisation 10 glldiiakaggkplspsEiaskLpt 34
                                      ++l+i+++ +    +psEia+ L +
  gi|330506962|ref|YP_004383390.1|  3 EILEILYENA--KATPSEIAALLGK 25
                                      59*******6..89*******9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1135.43
//
Query:       gi|330506963|ref|YP_004383391.1|  [L=402]
Description: aminotransferase [Methanosaeta concilii GP6]
Scores for complete 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-65  220.6   0.0    3.8e-65  220.4   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0051   16.2   0.0     0.0095   15.3   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.044   14.4   0.3       0.07   13.7   0.3    1.2  1  Forkhead_N       Forkhead N-terminal region
      0.055   12.0   0.0       0.11   11.0   0.0    1.4  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 !  220.4   0.0   8.4e-69   3.8e-65       4     362 ..      48     394 ..      45     395 .. 0.94

  Alignments for each domain:
  == domain 1  score: 220.4 bits;  conditional E-value: 8.4e-69
                                       EESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHH CS
                     Aminotran_1_2   4 inLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagal 80 
                                       i Lg++e+++     t+ +v++a +   +   +++ y+ ++g pel+ea+++ ++r+ +++++ + +++ ++G +++
  gi|330506963|ref|YP_004383391.1|  48 ISLGVGEPDFV----TPWHVREACIY--SLELGNTHYTSNKGMPELREAICQEVSRDMGIDFDCNEEILITTGVSEA 118
                                       89*********....*********99..66667788***************************************** PP

                                       HHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS CS
                     Aminotran_1_2  81 iealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesp 157
                                        +++++++ lnpg+e +vp+p y  y++++ l+gg   ++p++ e++f++ +e++ + ++e      kt+ +l+  p
  gi|330506963|ref|YP_004383391.1| 119 VDLAFRAT-LNPGEEAVVPEPCYVAYTPDIILAGGVPKTVPTRLENEFRVQAEDVARRVTE------KTRSLLLSYP 188
                                       ********.****************************************************......9********* PP

                                       -TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEE CS
                     Aminotran_1_2 158 hNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyi 233
                                       +NPtG+++t+ +le+l+d++ ++ l++++De+Ya++ + + ++++  a++e   + +li+++lsK+ +++G+R+Gy+
  gi|330506963|ref|YP_004383391.1| 189 NNPTGAIMTRSDLEDLADVVVENDLIVISDEVYAELTYSK-SHIS-FAQLEGMKErTLILNGLSKSHAMTGWRIGYA 263
                                       **************************************94.5555.66666666669******************** PP

                                       EEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEE CS
                     Aminotran_1_2 234 lgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmfl 308
                                        g++a+v +++k+++      ++ +q a+++a++  ++   e+  mr ++  rr+ ++++L+++gl++++++++++ 
  gi|330506963|ref|YP_004383391.1| 264 MGDPALVGAMTKIHQYTMLcaPTMAQVAALEAMQSGKD---EMLHMRHEYDLRRRLFVSGLNRIGLDCFEPKGAFYA 337
                                       **************988886788888888888888875...9*********************************** PP

                                       EEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 309 ltdlsae..takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                       +  + +   + +e+++ Ll e++v+v+pg+ f+   +g+lR ++ ++++eel e++++
  gi|330506963|ref|YP_004383391.1| 338 FPSVQRFglSSEEFAERLLYEQKVAVVPGNVFGEsgEGFLRCSY-ATSREELIEALDR 394
                                       *999988999**********************************.8999998888876 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.1e-06    0.0095      46     144 ..     114     218 ..     103     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-06
                                       SHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-.TTTSSB-GGGCGGG--TTEEEEE...EB CS
                   DegT_DnrJ_EryC1  46 sGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvd.pdtynidpaaieaaitertkaIl...pV 118
                                         ++A+ la ra  ++pg+e +vp   +va    ++ +g +p  v    ++ + ++++++++ +te+t+  l   p 
  gi|330506963|ref|YP_004383391.1| 114 GVSEAVDLAFRA-TLNPGEEAVVPEPCYVAYTPDIILAGGVPKTVPTRlENEFRVQAEDVARRVTEKTRSLLlsyPN 189
                                       446789999998.4899***************************99863789****************999844445 PP

                                       -GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 119 hlyGqva...dmdalkaiaakhglkvieD 144
                                       +  G+++   d++ l ++  + +l+vi+D
  gi|330506963|ref|YP_004383391.1| 190 NPTGAIMtrsDLEDLADVVVENDLIVISD 218
                                       66776654448888888889999999998 PP

>> Forkhead_N  Forkhead N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   1.6e-05      0.07      47     108 ..     244     309 ..     220     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                       ...XXXXX..XXXXXXXXX.XXXXXX...XXXXXXXXXX.XXXXX..XXXXXXXXXXX..XXXXXXX CS
                        Forkhead_N  47 aamngmss.ssmtgmssgyasagspl...gmmgmssmss.slspsgtmgamgsapagsremgslspn 108
                                         +ng+s   +mtg   gy ++g p+    m +++++++  + ++++++a+ ++++g++em  + ++
  gi|330506963|ref|YP_004383391.1| 244 LILNGLSKsHAMTGWRIGY-AMGDPAlvgAMTKIHQYTMlCAPTMAQVAALEAMQSGKDEMLHMRHE 309
                                       4689**99799********.89999999989999****9999999999*********9999888776 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 ?   11.0   0.0   2.4e-05      0.11      73     176 ..     111     221 ..     103     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.4e-05
                                       ESSHHH.HHHHHHHTTS-TTEEEEEESTSSHH.HHHHHHHTHHHTTCEEEEEST..TSHHHHHHHCCTTEEEEEEES CS
                   Cys_Met_Meta_PP  73 vssGma.AiaaailallkaGdeivvsddlYgg.tqrllkkvlkklgievkfvdt..sdleelekaikentklvylEt 145
                                       +++G++ A+++a++a l+ G+e vv + +Y   t +++        + ++  +    ++e++++ ++e+t+ ++l  
  gi|330506963|ref|YP_004383391.1| 111 ITTGVSeAVDLAFRATLNPGEEAVVPEPCYVAyTPDIILAGGVPKTVPTRLENEfrVQAEDVARRVTEKTRSLLLSY 187
                                       5555544899999999999******99999653555544443334455555544337899***************** PP

                                       S-TTTT---...-HHHHHHHHHHTT-EEEEEGTT CS
                   Cys_Met_Meta_PP 146 ptnpllkvv...DiekiaklakkagvlvvvDntf 176
                                       p np+  ++   D+e++a+++ +++++v+ D ++
  gi|330506963|ref|YP_004383391.1| 188 PNNPTGAIMtrsDLEDLADVVVENDLIVISDEVY 221
                                       ****86653333****************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2896.06
//
Query:       gi|330506964|ref|YP_004383392.1|  [L=202]
Description: CDP-alcohol phosphatidyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-10   39.8   1.5    5.9e-10   39.8   1.5    2.3  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   1.5   3.3e-14   5.9e-10       2      66 .]      24      87 ..      23      87 .. 0.84
   2 ?    0.4   0.9     0.065   1.2e+03       8      19 ..     162     173 ..      92     192 .. 0.64

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 3.3e-14
                                      -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                       Pna Tl++l+ +++ ++  l++++l l+++++ ++++ D++DG +AR +nqvs+ G+++D ++D
  gi|330506964|ref|YP_004383392.1| 24 SPNAWTLISLVPALAGLV-ALVMHQLALGLAMFALSAFIDIVDGTVARVTNQVSDKGAYIDGVVD 87
                                      6**********8565554.44555578888888899*************************9988 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.065
                                       HHHHHHHHHHHH CS
                   CDP-OH_P_transf   8 llrlllsvlail 19 
                                       +++++l+++ i+
  gi|330506964|ref|YP_004383392.1| 162 YFGMFLGLFDIQ 173
                                       344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1481.71
//
Query:       gi|330506965|ref|YP_004383393.1|  [L=131]
Description: PIN domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-15   58.1   0.2    1.4e-15   57.9   0.2    1.0  1  PIN       PIN domain
     0.0012   18.6   0.1      0.003   17.3   0.1    1.7  1  DUF5615   Domain of unknown function (DUF5615)
  ------ inclusion threshold ------
       0.05   14.4   0.1      0.078   13.7   0.1    1.4  1  PIN_3     PIN domain
      0.083   12.9   0.2      0.096   12.7   0.2    1.1  1  YbhQ      Putative inner membrane protein YbhQ


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.2   3.1e-19   1.4e-15       1     120 [.       2     121 ..       2     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 3.1e-19
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTS..SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCH CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleel..eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpida 75 
                                       ++lDT++l++ll +++ka+++++ll e   e l +s+ ++  +  +l r +  ++   +  e++ll  +++++ i+ 
  gi|330506965|ref|YP_004383393.1|   2 YLLDTNILLELLLNQKKADEVERLLLETppEMLSVSEFTIDSIGVILIR-RIMHDIFLKAMEDMLLVGGIRLMRIGP 77 
                                       68*********************999999********************.8889999999999999*********** PP

                                       HHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  76 eiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                       e+  ++   +++ +l+  Da+ +A+A++++++++ +fD+df+r++
  gi|330506965|ref|YP_004383393.1|  78 EDMQRVVLASRRFKLDYDDAYQYALAEKYNLIIV-SFDSDFDRTE 121
                                       *******************************777.*******986 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   6.6e-07     0.003      35      63 ..      94     122 ..      78     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.6e-07
                           DUF5615  35 asDeeileyAkeedriivTkDkDFgelll 63 
                                        +D    ++A++ ++iiv++D+DF +  +
  gi|330506965|ref|YP_004383393.1|  94 YDDAYQYALAEKYNLIIVSFDSDFDRTER 122
                                       7899999*****************76544 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.7e-05     0.078       3     112 ..       3     112 ..       1     116 [. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                             PIN_3   3 vlDtnvlldallfdspaarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakvalerkava 79 
                                       +lDtn+ll+ ll++++a +  + +let +  l vs+ ++d +  +l r+   + f +  +d ++      l    + 
  gi|330506965|ref|YP_004383393.1|   3 LLDTNILLELLLNQKKADEVERLLLETPPEMLSVSEFTIDSIGVILIRRIMHDIFLKAMEDMLLVGGIR-L--MRIG 76 
                                       79**********888777777777788888889999999999988877766665555555553333332.3..4455 PP

                             PIN_3  80 pdaelrpllkcr....DpdDqkvlelAlaaradvlVT 112
                                       p+ ++r++l+ r    D dD+   +lA +    ++V+
  gi|330506965|ref|YP_004383393.1|  77 PEDMQRVVLASRrfklDYDDAYQYALAEKY-NLIIVS 112
                                       555555555555567999999888888765.555555 PP

>> YbhQ  Putative inner membrane protein YbhQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   2.1e-05     0.096      49     130 ..       6      87 ..       1      89 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                              YbhQ  49 avvlvamlllqrhpearlrevgdfleeltttyyfGaalialyllsrvlhnnlllalvGlvllaGpalvsllakekkr 125
                                       + +l+ +ll q++ ++  r + +   e+ +   f    i + l+ r++h+ +l a+  ++l+ G  l+ +   + +r
  gi|330506965|ref|YP_004383393.1|   6 TNILLELLLNQKKADEVERLLLETPPEMLSVSEFTIDSIGVILIRRIMHDIFLKAMEDMLLVGGIRLMRIGPEDMQR 82 
                                       668899999***99**********************************************99999998888888777 PP

                              YbhQ 126 rnlas 130
                                         las
  gi|330506965|ref|YP_004383393.1|  83 VVLAS 87 
                                       76665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1093.16
//
Query:       gi|330506966|ref|YP_004383394.1|  [L=68]
Description: hypothetical protein MCON_0776 [Methanosaeta concilii GP6]
Scores for complete 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   74.3   0.3      1e-20   74.2   0.3    1.0  1  DUF2281   Protein of unknown function (DUF2281)
  ------ inclusion threshold ------
      0.042   14.3   0.0       0.22   12.0   0.0    1.9  2  DUF2274   Protein of unknown function (DUF2274)
        0.1   12.3   0.0       0.14   11.9   0.0    1.3  1  FAM193_C  FAM193 family C-terminal


Domain annotation for each model (and alignments):
>> DUF2281  Protein of unknown function (DUF2281)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.3   1.7e-24     1e-20       1      64 []       3      62 ..       3      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 1.7e-24
                           DUF2281  1 eLyekiqeLPedlkqEvldFaefLleKyaakkkktlklrlaGilkglltmsdDfdepLEdqkey 64
                                      eL+e i+eLP+dl+qEv dFa+fL+eK+ +k k+++kl+++G+l+++    +D ++++E+q+++
  gi|330506966|ref|YP_004383394.1|  3 ELEEIIKELPPDLHQEVVDFARFLMEKRGPKRKGRMKLEWRGALQDM----KDEYTSVELQHKI 62
                                      799********************************************....***********95 PP

>> DUF2274  Protein of unknown function (DUF2274)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.7e-05      0.22      20      44 ..      10      34 ..       4      41 .. 0.88
   2 ?    0.5   0.0      0.14   8.3e+02       7      25 ..      44      62 ..      37      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                           DUF2274 20 elpaalhrdLaaYaellaretgeaa 44
                                      elp++lh++ +++a+ l +++g + 
  gi|330506966|ref|YP_004383394.1| 10 ELPPDLHQEVVDFARFLMEKRGPKR 34
                                      8*****************9999775 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.14
                           DUF2274  7 gplpddkpvkltvelpaal 25
                                      g+l+d k    +vel+ ++
  gi|330506966|ref|YP_004383394.1| 44 GALQDMKDEYTSVELQHKI 62
                                      6889999999999998776 PP

>> FAM193_C  FAM193 family C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.4e-05      0.14      19      46 ..      16      43 ..      13      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                          FAM193_C 19 erElEeFKRFCLdsakqtrkekvavNvk 46
                                       +E+  F RF ++   ++rk ++++ ++
  gi|330506966|ref|YP_004383394.1| 16 HQEVVDFARFLMEKRGPKRKGRMKLEWR 43
                                      6899*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 506.98
//
Query:       gi|330506967|ref|YP_004383395.1|  [L=481]
Description: ketoisovalerate oxidoreductase subunit [Methanosaeta concilii GP6]
Scores for complete 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-37  127.3   0.0    9.9e-37  126.7   0.0    1.3  1  POR           Pyruvate ferredoxin/flavodoxin oxidoreductase
    6.5e-23   81.2   0.0    1.1e-22   80.5   0.0    1.4  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.7   0.0   1.1e-40   9.9e-37       1     176 [.     307     469 ..     307     470 .. 0.91

  Alignments for each domain:
  == domain 1  score: 126.7 bits;  conditional E-value: 1.1e-40
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqGv+++g  la+aa+ +G  v+++++yg+e+rGg s++ v is   ++ s+ v+++d+lva++  +l+++++ +k
  gi|330506967|ref|YP_004383395.1| 307 GGQGVLSMGLALAQAAFGCGRFVSWYPDYGPEQRGGTSNCSVIISGV-PIGSPVVDHPDVLVAFNRPSLEKFAPTVK 382
                                       9********************************************98.8899999********************** PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT..S-HHHHHH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg..lplealee 152
                                       +gg+i+y+s      +    +e         gv+ + v+at+ia ++g  + aaNt+mlGal+++++  lp +a  +
  gi|330506967|ref|YP_004383395.1| 383 KGGVILYDS-LAGQFQA---PE---------GVKAISVPATEIAADKGA-SMAANTAMLGALMQAGKlgLPKDAYGD 445
                                       *********.3333333...33.........45679**********988.************7777733677***** PP

                                       HHHCCS-CH.HHHHHHHHHHHHHH CS
                               POR 153 aikkrfpkkkeviekNlkafragy 176
                                       a + +f+kk ++i kNl+ ++ag 
  gi|330506967|ref|YP_004383395.1| 446 AFRVTFAKKPKLIPKNLEIMEAGA 469
                                       **********************97 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   1.2e-26   1.1e-22       3     152 ..      64     221 ..      62     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 1.2e-26
                                       SHHHHHHHHHHTTSSSSEEECET.TTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEE CS
                      TPP_enzyme_C   3 Gcltlwaarllkvkrprsyltsg.glgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitv 77 
                                       Gc  +           + yl+sg + +++G++ ++A+G+++a+ d+ v+++ GDG+++ i l+e+++a++r+ ++ v
  gi|330506967|ref|YP_004383395.1|  64 GCAVF----------AYYYLDSGhVQAAHGRAPAIATGISRAEDDAIVISYQGDGDLASIgLNETIQAANRGEKLAV 130
                                       55555..........567888666999***************99********************************* PP

                                       EEEE-SBCCCHHHH...HHHHTCCTTTTSBB.....BS----HHHHHHHTTSEEE..EESSH.HHHH...HHHHHHH CS
                      TPP_enzyme_C  78 vvlnNegygmtggq...qepfggkrksgpagk....dlkpvdfaklaealGakga..rvekadveel...eealkea 142
                                       + +nN +ygmtggq   ++  g+ ++++p+g+    +++p++++++   l a+++  r + +d+e++   ++a+++a
  gi|330506967|ref|YP_004383395.1| 131 FFVNNTVYGMTGGQmapTTLIGEITSTTPQGRdpqeQGYPIHICEILDTLSAPVFieRASLSDIEHIrkaRRAVRRA 207
                                       ****************99999********999**988****************777977777777773336677777 PP

                                       H....CSSSEEEEE CS
                      TPP_enzyme_C 143 l....ekkgpalie 152
                                       l    +kkg a++e
  gi|330506967|ref|YP_004383395.1| 208 LevqrDKKGYAFVE 221
                                       78888889999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 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:                        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 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3312.68
//
Query:       gi|330506968|ref|YP_004383396.1|  [L=347]
Description: ketoisovalerate oxidoreductase subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-51  174.0   0.0      5e-51  173.7   0.0    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.1e-24   86.7   0.0    2.9e-24   85.3   0.0    1.7  2  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
      8e-07   29.0   0.0    1.4e-06   28.2   0.0    1.4  1  Transketolase_C  Transketolase, C-terminal domain
    0.00086   19.0   0.2     0.0016   18.1   0.2    1.5  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 !  173.7   0.0   1.1e-54     5e-51       2     208 ..      15     221 ..      14     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: 173.7 bits;  conditional E-value: 1.1e-54
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a++ag+d +++YPITP+sei++e++++ + ++    ++vq+esE +ai++v GAa+aG r++ a+Sg+G++L++e 
  gi|330506968|ref|YP_004383396.1|  15 GALYAGCDCFFGYPITPASEILQEASKFFPLVGR---KFVQAESEEAAINMVYGAATAGHRVLAASSGPGMSLKQEG 88 
                                       799******************************6...9*************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH......S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar......dtglivlasenvqeafdlalvAfnlAekvrvPv 149
                                       + ++ag++lP+viv++ Ra+p    +i ++qsD ++a        +  ivla+++vqe+ d++ ++f lA+k+r Pv
  gi|330506968|ref|YP_004383396.1|  89 ITYIAGAQLPCVIVDICRAGPGL-GNIGPEQSDYNQACkggghgCYHNIVLAPASVQEMCDFTRKGFDLAFKYRNPV 164
                                       ***********************.9************99**8877888***************************** PP

                                       EEEEEHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEES CS
                             POR_N 150 ivlfDgfllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtg 208
                                       i+l Dg+l+ h+ve++++p+e  + ++i++++  + r+e   +    i  +  + +++ 
  gi|330506968|ref|YP_004383396.1| 165 IILADGVLG-HMVEPLQFPQEA-IEHTIDTTWAVAGRAETRGNLVTSISLDFGDLEKHN 221
                                       *********.*********888.888999999888888875555544444444444444 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.9   8.6e+03      40      55 ..     181     196 ..     181     222 .. 0.65
   2 !   85.3   0.0   6.4e-28   2.9e-24       1     102 []     246     339 ..     246     339 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.9
                                       --HHHHHHHSTT-SEE CS
                           PFOR_II  40 FPeeelkellkkvkkv 55 
                                       FP+e++++ ++ + +v
  gi|330506968|ref|YP_004383396.1| 181 FPQEAIEHTIDTTWAV 196
                                       8888888877655444 PP

  == domain 2  score: 85.3 bits;  conditional E-value: 6.4e-28
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       A+vv+v +G++++ a+savd++R+egi++Gl+r++tl+PFP+e++++l+++  k++++++++     Gq+ ++++ a
  gi|330506968|ref|YP_004383396.1| 246 ADVVLVSYGISSRIARSAVDSARKEGIRAGLFRPITLYPFPTEQIAKLADRGCKFISVEMSN-----GQMRDDIRLA 317
                                       9*************************************************************.....********** PP

                                       TGGGTSEEEEEE--GGG----HHHH CS
                           PFOR_II  78 lkkskvkvvnfvaglgGrditvedi 102
                                         ++   +v++v + gG++i++++i
  gi|330506968|ref|YP_004383396.1| 318 SGCR---PVELVCRYGGNLINIDEI 339
                                       9887...**************9987 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   3.2e-10   1.4e-06       8      68 ..     244     304 ..     241     310 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.2e-10
                                       TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEE CS
                   Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvve 68 
                                       e  dv+lv+yG   + a  A++ ++kegi+a +  ++t+ p+ +e i++++ +  +++ ve
  gi|330506968|ref|YP_004383396.1| 244 EDADVVLVSYGISSRIARSAVDSARKEGIRAGLFRPITLYPFPTEQIAKLADRGCKFISVE 304
                                       678*************************************************999999887 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   3.6e-07    0.0016       5     100 ..      11     106 ..       9     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.6e-07
                                       HHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHH CS
                      TPP_enzyme_N   5 ealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatn 78 
                                       +++v aL a g +++fg+p +   ++l ++s+     g ++v+a +E++a+++  g a a +   v++++sgpG+  
  gi|330506968|ref|YP_004383396.1|  11 AVIVGALYA-GCDCFFGYPITPASEILQEASKFFplvGRKFVQAESEEAAINMVYGAATAGH--RVLAASSGPGMSL 84 
                                       678888888.*******************99998899****************988887764..689999*****99 PP

                                       CHHHHHHHHHHT--EEEEEEE- CS
                      TPP_enzyme_N  79 altalaeAkvdriPllvlsgdr 100
                                          ++   + +++P++++  +r
  gi|330506968|ref|YP_004383396.1|  85 KQEGITYIAGAQLPCVIVDICR 106
                                       8888888888888988876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.58
# Mc/sec: 1811.28
//
Query:       gi|330506969|ref|YP_004383397.1|  [L=633]
Description: acyl-coenzyme A synthetase [Methanosaeta concilii GP6]
Scores for complete sequence (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  251.4   0.0    1.6e-74  251.0   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    6.1e-25   88.0   0.5    1.2e-24   87.0   0.5    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    7.8e-08   32.8   9.2      2e-07   31.5   9.2    1.7  1  Fer4_7         4Fe-4S dicluster domain
    2.9e-06   27.3   8.8    1.8e-05   24.8   9.2    2.1  2  Fer4_9         4Fe-4S dicluster domain
    3.3e-06   26.7  15.5    0.00013   21.7   3.3    2.6  2  Fer4           4Fe-4S binding domain
    5.3e-06   26.5  10.2    4.1e-05   23.6  10.4    2.2  2  Fer4_10        4Fe-4S dicluster domain
    2.4e-05   24.1  13.9     0.0081   16.2   4.5    2.8  2  Fer4_2         4Fe-4S binding domain
    3.3e-05   23.9   9.8     0.0006   19.9  10.2    2.4  2  Fer4_21        4Fe-4S dicluster domain
    0.00014   22.2   4.5       0.16   12.4   0.2    2.6  2  Fer4_8         4Fe-4S dicluster domain
    0.00025   21.3  10.3       0.02   15.3   1.5    2.8  2  Fer4_4         4Fe-4S binding domain
    0.00054   20.5   6.9       0.11   13.0   0.1    2.9  3  Fer4_17        4Fe-4S dicluster domain
    0.00084   19.8   8.5      0.062   13.9   1.2    2.7  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
     0.0026   18.7  12.4      0.006   17.5   1.7    2.6  3  Fer4_16        4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.012   15.7   3.2      0.012   15.7   3.2    2.8  2  Fer4_6         4Fe-4S binding domain
      0.017   16.0   5.1        2.8    8.8   0.1    3.0  3  Fer4_22        4Fe-4S dicluster domain
       0.42   11.6  17.9        4.3    8.5   4.0    2.7  2  Fer4_3         4Fe-4S binding domain
        2.3    8.4   9.3    1.5e+02    2.6   9.7    2.4  2  Fer4_18        4Fe-4S dicluster 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 !  251.0   0.0   1.5e-77   1.6e-74       5     422 ..      43     459 ..      39     460 .. 0.86

  Alignments for each domain:
  == domain 1  score: 251.0 bits;  conditional E-value: 1.5e-77
                                       HHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEE CS
                       AMP-binding   5 aaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpln 78 
                                       aa+ pdk alv+   +ge +t++++el++ ++++A+ ++  G+kkgd+ ++ l+ ++e+ v ++++ k+Ga+++p  
  gi|330506969|ref|YP_004383397.1|  43 AAECPDKCALVWcndHGEAKTISFKELKKLSDKAANLFQGFGIKKGDTAMLTLKSRWEFWVCMVGLNKLGAIAIPST 119
                                       77899**********99************************************************************ PP

                                       TTS-HHHHHHHHHHHTESEEE....ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS... CS
                       AMP-binding  79 ptltaeelayiledseakvli....atvdselleklleaaakleavklvivldadellkeeelkeeeeseekae... 148
                                         l+a++  y +++++ k+++      v +e  ++++++a+  +++ ++ ++ + +l++e + +++ e e+++e   
  gi|330506969|ref|YP_004383397.1| 120 HMLKAKDFLYRIKKADLKLIVcigeNGVPAE-FDAAHREAG--DVPLVKALVGSRDLNREGWINFDLELERASEtfv 193
                                       *********************7664122222.233333333..4444555566667777777777776666553566 PP

                                       -TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EE.EESS-TTSCHHHHHHHHHH CS
                       AMP-binding 149 kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvv.lsilplahifglilellla 224
                                       +p+ ++++k+dd+++  +TSGTTG PK V + + + +  + ++k+   +++ edd + +++++  ++      +++ 
  gi|330506969|ref|YP_004383397.1| 194 RPKGNQATKNDDILLAYFTSGTTGYPKLVKHDQTYPLGHILTAKFW--QNV-EDDGLhYTVADTGWAKCAWGKIFGQ 267
                                       566778899************************9999999997632..334.44444488899999866559***** PP

                                       HHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHH CS
                       AMP-binding 225 llsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellr 301
                                        ++G++v +++ d ++d++++++ + k++vt+++++P++++ +++s+       ++d+s+l++++++gepl+p++ +
  gi|330506969|ref|YP_004383397.1| 268 WIAGSAVFVYDYD-RFDAGRMMDEMGKYGVTTFCAPPTIFRFMIKSDMS-----RYDFSRLKYAVTAGEPLNPSVYE 338
                                       *****99999966.669999*********************99996433.....45********************* PP

                                       HHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET.....T CS
                       AMP-binding 302 ffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp.....g 373
                                        f +++g +++egYG+TEt +++++   ++ ++k+gs Gkp +g ++ +v  +  + ++ geeGe+++r       g
  gi|330506969|ref|YP_004383397.1| 339 SFLETTGLRLMEGYGQTETVVCISNY--PWMEAKPGSMGKPAAGYDILLVGKN-DKICEVGEEGEIVIRTDkgkpvG 412
                                       ******99***************843..344458*****************99.99*************98777888 PP

                                       S-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 374 vmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       ++  Y+ +p++t+ ++   +++++TGD +++dedGy++++gR++d+ik+
  gi|330506969|ref|YP_004383397.1| 413 LFTDYHMDPDKTQNTWH--DDYYHTGDTAWRDEDGYFWFIGRTDDMIKS 459
                                       ***************97..57**************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.5   1.2e-27   1.2e-24       1      76 []     468     546 ..     468     546 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 1.2e-27
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..-.--HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..s.ealeeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evEsal+shpaV e+a+ Gvpd+++G++++a Vvl +g  + e+l++eL++hv+k  +py+ p+ v+fvdelpkt s
  gi|330506969|ref|YP_004383397.1| 468 EVESALMSHPAVLEVAITGVPDPIRGQVVKATVVLTQGfsPsEELKRELQDHVKKVTAPYKYPRIVEFVDELPKTIS 544
                                       8**********************************888753355********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|330506969|ref|YP_004383397.1| 545 GK 546
                                       *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 !   31.5   9.2   1.9e-10     2e-07       2      49 ..     567     614 ..     566     616 .. 0.97

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.9e-10
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                       C  C++Cv+aCp++++++  e n +g  +v ++ + C+gC aC  +CP
  gi|330506969|ref|YP_004383397.1| 567 CKACERCVEACPAGVLKMGSELNVRGYNYVLYSGDGCIGCAACYYTCP 614
                                       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 !   24.8   9.2   1.7e-08   1.8e-05       2      48 ..     567     615 ..     566     619 .. 0.75
   2 !   12.5   2.1   0.00012      0.13       2      27 ..     603     628 ..     602     632 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.7e-08
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase..eaCigCgaCveaCpk 48 
                                       C  C +CveaCpagv ++ +  + + ++   +  + CigC aC+  Cp+
  gi|330506969|ref|YP_004383397.1| 567 CKACERCVEACPAGVLKMGSELNVRGYNYVLYsgDGCIGCAACYYTCPE 615
                                       ***************976554443333222224489************7 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00012
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkar 27 
                                       C+gC aC + Cp  +++e ++++k +
  gi|330506969|ref|YP_004383397.1| 603 CIGCAACYYTCPEPLAIEVHVPQKEK 628
                                       ************99999999888765 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   3.3   1.2e-07   0.00013       1      23 [.     560     582 ..     560     583 .. 0.92
   2 !   10.0   4.4    0.0006      0.63       7      19 ..     602     614 ..     598     615 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.2e-07
                                       EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                       +vi+   C +C +Cve+CP g++
  gi|330506969|ref|YP_004383397.1| 560 PVINSLECKACERCVEACPAGVL 582
                                       689999**************987 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0006
                                       TSSS-THHHHHST CS
                              Fer4   7 kCigCGaCvevCP 19 
                                        CigC aC+  CP
  gi|330506969|ref|YP_004383397.1| 602 GCIGCAACYYTCP 614
                                       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 !   23.6  10.4   3.9e-08   4.1e-05       3      56 .]     561     614 ..     559     614 .. 0.82
   2 !   12.3   1.8   0.00013      0.14       5      22 ..     599     616 ..     595     632 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.9e-08
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       vi++  C  C++Cv+aCPa + ++g +    + + v    + C+gc aC+  CP
  gi|330506969|ref|YP_004383397.1| 561 VINSLECKACERCVEACPAGVLKMGSELNVRGYNYVLYSGDGCIGCAACYYTCP 614
                                       789999*************88666666666666666666788***********9 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00013
                           Fer4_10   5 dddtCirCgkCvkaCPad 22 
                                         d Ci+C++C   CP  
  gi|330506969|ref|YP_004383397.1| 599 SGDGCIGCAACYYTCPEP 616
                                       568899999999999984 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   4.5   7.7e-06    0.0081       1      22 []     558     579 ..     558     579 .. 0.93
   2 !   12.4   1.9   0.00012      0.13       8      22 .]     601     615 ..     595     615 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.7e-06
                            Fer4_2   1 apvvvdtdrCigCgaCvsaCPa 22 
                                       +++v+++  C +C+ Cv aCPa
  gi|330506969|ref|YP_004383397.1| 558 PYPVINSLECKACERCVEACPA 579
                                       5799**9**************8 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00012
                            Fer4_2   8 drCigCgaCvsaCPa 22 
                                       d CigC aC+  CP+
  gi|330506969|ref|YP_004383397.1| 601 DGCIGCAACYYTCPE 615
                                       67************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 !   13.4   2.3   5.9e-05     0.063      30      59 .]     555     584 ..     547     584 .. 0.75
   2 !   19.9  10.2   5.7e-07    0.0006       2      57 ..     561     619 ..     560     621 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.9e-05
                           Fer4_21  30 aktvlkvv.edeCvGCnlCssvCPvedciem 59 
                                       +++ ++v+ + eC +C+ C++ CP  ++++m
  gi|330506969|ref|YP_004383397.1| 555 KDKPYPVInSLECKACERCVEACPA-GVLKM 584
                                       455567762569************5.77776 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 5.7e-07
                           Fer4_21   2 ridedkCigCgkCliaCedtshqai...eidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       +i++ +C  C++C+ aC+ +  +     ++ + +++ +  d C+GC+ C+  CP   +i
  gi|330506969|ref|YP_004383397.1| 561 VINSLECKACERCVEACPAGVLKMGselNVRGYNYVLYSGDGCIGCAACYYTCPEPLAI 619
                                       688999************765554344367777888888***************66555 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   0.2   0.00015      0.16      50      65 .]     566     581 ..     535     581 .. 0.84
   2 !   10.7   0.6   0.00054      0.57       4      17 ..     602     615 ..     599     632 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                            Fer4_8  50 sCttcgaCtevCpvgi 65 
                                       +C +c++C+e+Cp g+
  gi|330506969|ref|YP_004383397.1| 566 ECKACERCVEACPAGV 581
                                       7************986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00054
                            Fer4_8   4 kCieCgaCqsaCpv 17 
                                        Ci+C aC  +Cp 
  gi|330506969|ref|YP_004383397.1| 602 GCIGCAACYYTCPE 615
                                       6***********93 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   1.8    0.0013       1.4       4      17 .]     567     580 ..     563     585 .. 0.89
   2 !   15.3   1.5   1.9e-05      0.02       3      15 ..     602     614 ..     600     626 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                            Fer4_4   4 CigCgsCvaaCPqg 17 
                                       C  C +Cv aCP g
  gi|330506969|ref|YP_004383397.1| 567 CKACERCVEACPAG 580
                                       999*********65 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.9e-05
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                        CigC +C+++CP
  gi|330506969|ref|YP_004383397.1| 602 GCIGCAACYYTCP 614
                                       6************ PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1         5   5.3e+03       7      26 ..      45      64 ..      43      81 .. 0.71
   2 !   13.0   0.1   0.00011      0.11      41      60 ..     562     581 ..     530     582 .. 0.68
   3 !   10.0   0.6   0.00091      0.96      45      59 ..     602     616 ..     592     618 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5
                           Fer4_17  7 yClpeCpsyeaydnepkkll 26
                                       C ++C   +++d  ++k++
  gi|330506969|ref|YP_004383397.1| 45 ECPDKCALVWCNDHGEAKTI 64
                                      48888888888877666554 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00011
                           Fer4_17  41 ekaslCieCgeCerkCPqgl 60 
                                        +  +C  C++C+++CP+g+
  gi|330506969|ref|YP_004383397.1| 562 INSLECKACERCVEACPAGV 581
                                       46679************986 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00091
                           Fer4_17  45 lCieCgeCerkCPqg 59 
                                        Ci+C  C + CP+ 
  gi|330506969|ref|YP_004383397.1| 602 GCIGCAACYYTCPEP 616
                                       699999999999985 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 !    9.2   1.1    0.0017       1.8       2      18 ..     563     579 ..     562     586 .. 0.89
   2 !   13.9   1.2   5.9e-05     0.062       4      18 ..     601     615 ..     600     627 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0017
                           Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                       +  +C ac+ Cve++P 
  gi|330506969|ref|YP_004383397.1| 563 NSLECKACERCVEACPA 579
                                       6669************5 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.9e-05
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                       d Ci+c+aC+ ++P+
  gi|330506969|ref|YP_004383397.1| 601 DGCIGCAACYYTCPE 615
                                       79************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 !   17.5   1.7   5.7e-06     0.006       2      22 ..     567     587 ..     566     597 .. 0.86
   2 ?    5.5   3.0     0.031        33      53      65 ..     602     614 ..     589     616 .. 0.71
   3 ?    5.1   3.5     0.041        43       2      14 ..     603     615 ..     602     632 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.7e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                       C+ C++C+e+CP++++k+ +e
  gi|330506969|ref|YP_004383397.1| 567 CKACERCVEACPAGVLKMGSE 587
                                       ****************98854 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.031
                           Fer4_16  53 aitgCdiCqdvCP 65 
                                        ++gC++C  +CP
  gi|330506969|ref|YP_004383397.1| 602 GCIGCAACYYTCP 614
                                       5666666666666 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.041
                           Fer4_16   2 CgtCgkCaevCPt 14 
                                       C++C +C  +CP+
  gi|330506969|ref|YP_004383397.1| 603 CIGCAACYYTCPE 615
                                       8999999999997 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   3.2   1.1e-05     0.012       9      24 .]     567     582 ..     560     582 .. 0.84
   2 ?   10.0   4.8   0.00072      0.76       9      21 ..     603     615 ..     601     619 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       C  C++Cv +CP+g++
  gi|330506969|ref|YP_004383397.1| 567 CKACERCVEACPAGVL 582
                                       *************986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00072
                            Fer4_6   9 CigCgdCvrvCPe 21 
                                       CigC +C+  CPe
  gi|330506969|ref|YP_004383397.1| 603 CIGCAACYYTCPE 615
                                       ************8 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.7   2.9e+03       6      66 ..      44     103 ..      41     107 .. 0.75
   2 ?    8.8   0.1    0.0026       2.8      75      95 ..     560     580 ..     532     581 .. 0.76
   3 ?    7.8   0.3    0.0055       5.8      81      94 ..     602     615 ..     592     631 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.7
                           Fer4_22   6 gaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrl 66 
                                       ++C   C+   C d  + ++ + ke +++   ++ l+++f   +g  ++  + k+r+++++
  gi|330506969|ref|YP_004383397.1|  44 AECPDKCALVWCNDHGEAKTISFKELKKLSDKAANLFQGFGIKKGD-TAMLTLKSRWEFWV 103
                                       5788899999999999999777788888888888888888877766.55556666666665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0026
                           Fer4_22  75 ekfgesgCvGCgRCieacpvk 95 
                                         +++  C  C RC+eacp++
  gi|330506969|ref|YP_004383397.1| 560 PVINSLECKACERCVEACPAG 580
                                       4567889***********986 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0055
                           Fer4_22  81 gCvGCgRCieacpv 94 
                                       gC+GC  C  +cp+
  gi|330506969|ref|YP_004383397.1| 602 GCIGCAACYYTCPE 615
                                       67777777777765 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   5.9    0.0052       5.5       1      14 [.     567     580 ..     567     581 .. 0.89
   2 ?    8.5   4.0    0.0041       4.3       1      12 [.     603     614 ..     603     617 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0052
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C  C++Cve+CP g
  gi|330506969|ref|YP_004383397.1| 567 CKACERCVEACPAG 580
                                       888*********66 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0041
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+gC aC   CP
  gi|330506969|ref|YP_004383397.1| 603 CIGCAACYYTCP 614
                                       ************ PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   9.7      0.14   1.5e+02      57      75 ..     563     581 ..     541     614 .. 0.68
   2 ?    2.5   1.0      0.16   1.6e+02      60      76 ..     602     618 ..     594     624 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.14
                           Fer4_18  57 gagdcidcescvkvcPtgi 75 
                                       ++ +c +ce cv+ cP g+
  gi|330506969|ref|YP_004383397.1| 563 NSLECKACERCVEACPAGV 581
                                       4569************997 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.16
                           Fer4_18  60 dcidcescvkvcPtgid 76 
                                        ci c +c   cP  + 
  gi|330506969|ref|YP_004383397.1| 602 GCIGCAACYYTCPEPLA 618
                                       59999999999997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4400.84
//
Query:       gi|330506970|ref|YP_004383398.1|  [L=189]
Description: hypothetical protein MCON_0781 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-16   57.5   0.1    2.2e-15   56.1   0.1    1.8  1  Cupin_2          Cupin domain
    4.3e-07   30.2   0.0    6.4e-07   29.6   0.0    1.2  1  HTH_31           Helix-turn-helix domain
      4e-06   26.8   0.0    7.1e-06   26.0   0.0    1.4  1  HTH_19           Helix-turn-helix domain
    0.00097   19.2   0.0     0.0017   18.4   0.0    1.4  1  HTH_3            Helix-turn-helix
     0.0026   17.7   0.0     0.0045   16.9   0.0    1.4  1  AraC_binding     AraC-like ligand binding domain
     0.0032   17.4   0.0     0.0044   16.9   0.0    1.3  1  MannoseP_isomer  Mannose-6-phosphate isomerase
     0.0065   16.1   0.0      0.011   15.3   0.0    1.3  1  Cupin_3          Protein of unknown function (DUF861)
  ------ inclusion threshold ------
       0.06   13.1   0.0       0.12   12.2   0.0    1.5  1  EutQ             Ethanolamine utilisation protein EutQ


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.1   9.7e-19   2.2e-15       4      70 ..     116     187 ..     113     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 9.7e-19
                                       EEETTEEEE......EECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   4 elppGesap......shrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       +++p  +++        +Hpg+ ef yVleG++++t++++ev+l++Gds++f+++  H ++  +d+p++ll v
  gi|330506970|ref|YP_004383398.1| 116 TIDPKKESQshpvhsLYSHPGQ-EFEYVLEGTLKITINENEVILNEGDSIFFDSTYDHVMEALSDKPVKLLAV 187
                                       555555444344443556****.***********************************************998 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   2.8e-10   6.4e-07       1      58 [.       9      65 ..       9      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.8e-10
                            HTH_31  1 aLGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldp 58
                                      ++G +Lr+lRe  ++s ee+Ae+l+v ++t++ +E G  +  + + l  +ar l++d 
  gi|330506970|ref|YP_004383398.1|  9 EIGTRLRELRELNRVSPEEMAEHLNVAVDTYNCYEDGMLD-IPASILIGIARRLNVDT 65
                                      589************************************8.77999999999999985 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   3.2e-09   7.1e-06       1      64 [.      11      73 ..      11      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.2e-09
                            HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqged 64
                                      G rL+e+Re +  + ee+ae+l +    ++ +E g   +++a+ l  ia+ l++d+  ll+ge+
  gi|330506970|ref|YP_004383398.1| 11 GTRLRELRELNRVSPEEMAEHLNVAVDTYNCYEDGML-DIPASILIGIARRLNVDTGLLLTGEE 73
                                      77*********************************66.788********************986 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   7.5e-07    0.0017       1      54 [.      14      67 ..      14      68 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.5e-07
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54
                                      l+elR+ +  s ee+Ae l+v + t++ +E G   +  ++l+ +a+ L+v++  
  gi|330506970|ref|YP_004383398.1| 14 LRELRELNRVSPEEMAEHLNVAVDTYNCYEDGMLDIPASILIGIARRLNVDTGL 67
                                      89******************************999***************9865 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 !   16.9   0.0     2e-06    0.0045      19      71 ..     132     184 ..     115     189 .] 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                                       ETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEE CS
                      AraC_binding  19 hvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgwey 71 
                                         h+  ++ yv+eGt ++++n++++ l++Gd +++     H +e+ s+++ ++
  gi|330506970|ref|YP_004383398.1| 132 YSHPGQEFEYVLEGTLKITINENEVILNEGDSIFFDSTYDHVMEALSDKPVKL 184
                                       5799999****************************999999999988888776 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     2e-06    0.0044      85     135 ..     137     187 ..      92     189 .] 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                   MannoseP_isomer  85 aehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkipleliev 135
                                        e   v++Gt k+t+++++++l+e +s++   +  h +e     p++l+ v
  gi|330506970|ref|YP_004383398.1| 137 QEFEYVLEGTLKITINENEVILNEGDSIFFDSTYDHVMEALSDKPVKLLAV 187
                                       4666799*********************************99999999876 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.1e-06     0.011      26      57 ..     137     167 ..     130     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.1e-06
                                       EEEEEEEECEEEEEETTTEEEEEETTEEEEE- CS
                           Cupin_3  26 dEfcyileGevkvtpeggetvelraGDlvvlp 57 
                                       +Ef y+leG  k+t  ++++v l +GD++++ 
  gi|330506970|ref|YP_004383398.1| 137 QEFEYVLEGTLKITI-NENEVILNEGDSIFFD 167
                                       89*************.9************995 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   5.3e-05      0.12      97     125 ..     138     166 ..     132     180 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.3e-05
                              EutQ  97 eidyvieGrldvlidGrkvvaeaGdvili 125
                                       e +yv+eG l++ i+ ++v+ + Gd i+ 
  gi|330506970|ref|YP_004383398.1| 138 EFEYVLEGTLKITINENEVILNEGDSIFF 166
                                       899**********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1429.98
//
Query:       gi|330506971|ref|YP_004383399.1|  [L=121]
Description: hypothetical protein MCON_0784 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.097   12.6   0.2       0.22   11.5   0.0    1.6  2  zinc_ribbon_4  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.2e-05      0.22       2      29 ..       3      30 ..       3      31 .. 0.93
   2 ?   -2.9   0.1      0.38   6.8e+03      11      17 ..      69      75 ..      68      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.2e-05
                     zinc_ribbon_4  2 kitCpsCkakyeiddeklpakgvkvrCs 29
                                      ki C++C+ + ei+d  l ++  ++ C+
  gi|330506971|ref|YP_004383399.1|  3 KIICKNCGVVNEISDGALDDGDDWLECT 30
                                      79****************9999999997 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.38
                     zinc_ribbon_4 11 kyeidde 17
                                      ky id+e
  gi|330506971|ref|YP_004383399.1| 69 KYDIDPE 75
                                      89**986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 888.09
//
Query:       gi|330506972|ref|YP_004383400.1|  [L=650]
Description: hypothetical protein MCON_0785 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (650 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2743  (0.152992); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                       366  (0.0204139); expected 17.9 (0.001)
Passed Fwd filter:                       139  (0.0077528); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 3.70u 0.40s 00:00:04.10 Elapsed: 00:00:00.94
# Mc/sec: 2081.73
//
Query:       gi|330506973|ref|YP_004383401.1|  [L=157]
Description: hypothetical protein MCON_0786 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1286.97
//
Query:       gi|330506974|ref|YP_004383402.1|  [L=297]
Description: hypothetical protein MCON_0787 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2238.43
//
Query:       gi|330506975|ref|YP_004383403.1|  [L=78]
Description: hypothetical protein MCON_0788 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       388  (0.0216409); 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:                         0  (0); expected 0.2 (1e-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: 594.92
//
Query:       gi|330506976|ref|YP_004383404.1|  [L=184]
Description: hypothetical protein MCON_0793 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1409.03
//
Query:       gi|330506977|ref|YP_004383405.1|  [L=449]
Description: hypothetical protein MCON_0794 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-28   99.4   0.0    3.7e-25   89.4   0.0    2.1  1  AAA_15    AAA ATPase domain
    1.2e-22   81.2   0.1    2.1e-22   80.3   0.1    1.4  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    6.1e-06   25.8   0.2    3.7e-05   23.3   0.0    2.0  2  SMC_N     RecF/RecN/SMC N terminal domain
    7.9e-05   23.0   0.0    0.00016   22.0   0.0    1.5  1  DUF3696   Protein of unknown function (DUF3696)
    0.00052   19.4   0.0     0.0025   17.1   0.0    1.8  2  DUF2813   Protein of unknown function (DUF2813)
    0.00069   20.2   0.0     0.0016   19.0   0.0    1.6  2  AAA_23    AAA domain
  ------ inclusion threshold ------
      0.055   13.2   0.0       0.14   11.9   0.0    1.6  1  AAA_29    P-loop containing region of 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 !   89.4   0.0   1.5e-28   3.7e-25       3     368 ..       5     375 ..       4     376 .. 0.70

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1.5e-28
                            AAA_15   3 IkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn........................ 54 
                                       I++i++k F+sl + ++i++ + lt+l G+N+sGKSsi++ l +++++ e                           
  gi|330506977|ref|YP_004383405.1|   5 ITRISVKGFKSLAEeCSIEVRP-LTILAGANSSGKSSIMQPLLIMKQTLEATYdpgpllldgpnvrftsvnqfmpkf 80 
                                       899*********999*******.************************994444799**************9999999 PP

                            AAA_15  55 .................kkvikiekedleifeniseskdikIdvefaekekakeyektlkskekkkadlllkkkesd 114
                                                        ++ i   +  le +++ s++ ++ I++ +                   + d+  + ++++
  gi|330506977|ref|YP_004383405.1|  81 nssggywispgllnefgVDLIHQFSLGLELENSMSFNESFIIKKSY-------------------EIDIGEISFQNE 138
                                       9988888888888887755666666667777777888888888888...................112222333334 PP

                            AAA_15 115 lkktikdkklklkknelsdekisvekkkskkelpkekeeklek.ekeelkid..kedlkklikkleeslkkeeelkn 188
                                         +ti   k+  +      ++  +  +   +  + +k+e ++k +k  ++ +  + +lk +  + e++++    l+ 
  gi|330506977|ref|YP_004383405.1| 139 YGNTILRPKMTHD----EMSSAFLLARRPGWTRNYFKNELNNKvPKLIIERNrfFLELKLITGDDEYITQ----LNR 207
                                       4444444444422....23333333344444444444444433023333333645555555554444443....335 PP

                            AAA_15 189 vlksaiiklllisakRnvsdedsek..kssllgklkekileealqekleeelteklkeiqeklkeidkklaeelk.. 261
                                        +++ai  l   +a R + + +++k  + + +  ++e +  +++ +++      + +  + +l  + + l+  +k  
  gi|330506977|ref|YP_004383405.1| 208 TFSNAILSLIHLPALRGNPERNYKKtsTGPRFPGTFEIYAASIIHNWQ-----ANRDPRLHALGAALEVLGLTWKvg 279
                                       777777778888888888775444400445555666666555544444.....333444444444444444445566 PP

                            AAA_15 262 .kilkkkidkikkfnykgkkneeieikddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLH 337
                                        + +++  +++  +   +kkn      +++ ++++++G+G++++l++++ +l ae +        ++ iE+PE+hLH
  gi|330506977|ref|YP_004383405.1| 280 aRAIDDVSFEVMVGRLIHKKNDD----SNDMVSIADVGFGLSQTLPVLVALLAAEPG-------QLVYIEQPEIHLH 345
                                       57777777887788888888888....******************************.......************* PP

                            AAA_15 338 pqaqkvlikllkelandnktQviitTHSphi 368
                                       p+aq+ +++ l+e+an +   v+++THS+ +
  gi|330506977|ref|YP_004383405.1| 346 PKAQMAMAQILAEAANCGV-RVVVETHSSML 375
                                       ******************7.********975 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.1   8.2e-26   2.1e-22       1     301 [.      27     375 ..      27     377 .. 0.81

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 8.2e-26
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarl..................drdvegltdelsggggirkipslldlydpeipfe 59 
                                       l++l G+N+sGKS++++ l +++++                  +++v++  +++ ++gg+++ p+ll++   +   +
  gi|330506977|ref|YP_004383405.1|  27 LTILAGANSSGKSSIMQPLLIMKQTleatydpgpllldgpnvrFTSVNQFMPKFNSSGGYWISPGLLNEFGVDLIHQ 103
                                       79**********************99999999999999888888888888888888888888888888888888888 PP

                            AAA_21  60 feieeflsqgvryryglrlersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepn 136
                                       f++ + l++++ ++ ++ +++s          + +e+ +   + +++ +++  +++  +  ++  +  ++ ++ + +
  gi|330506977|ref|YP_004383405.1| 104 FSLGLELENSMSFNESFIIKKSYE-------IDIGEISFQNEYGNTILRPKMTHDEMSSAFLLARRPGWTRNYFKNE 173
                                       888888888888888888888888.......6666666666666666666666666666666666667777777777 PP

                            AAA_21 137 dlqfgkaltditsrawsllllldglrke.rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasv 212
                                        + +++ l+  ++r++  l+l  g  ++ + ++  ++++ +   +++ l++  +r +k+    +++ g +e   as+
  gi|330506977|ref|YP_004383405.1| 174 LNNKVPKLIIERNRFFLELKLITGDDEYiTQLNRTFSNAILSLIHLPALRGNPERNYKKTSTGPRFPGTFEIYAASI 250
                                       77777777777777777777776666666666666666666666666666666666666666666666677777777 PP

                            AAA_21 213 derlrer....................................gvvflengdgqe.lparelSdGtkrllalltall 252
                                       ++ ++ +                                     +++ +n+d ++ +++++++ G  + l++l+all
  gi|330506977|ref|YP_004383405.1| 251 IHNWQANrdprlhalgaalevlgltwkvgaraiddvsfevmvgRLIHKKNDDSNDmVSIADVGFGLSQTLPVLVALL 327
                                       7777777************************************888888887776589******************* PP

                            AAA_21 253 ralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                       +a +   l+ i+ pE +LHPk++   +++l e+++ g+ v++ THS  l
  gi|330506977|ref|YP_004383405.1| 328 AAEPG-QLVYIEQPEIHLHPKAQMAMAQILAEAANCGVRVVVETHSSML 375
                                       *9999.****************************************543 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.5e-08   3.7e-05       2      44 ..       5      45 ..       4      51 .. 0.93
   2 ?   -0.2   0.0      0.22   5.6e+02     148     201 ..     321     375 ..     318     384 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.5e-08
                                      EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAi 44
                                      ++r+ +++Fks+a ++ ++++ + +t++ G+N SGKs++++ +
  gi|330506977|ref|YP_004383405.1|  5 ITRISVKGFKSLA-EECSIEVRP-LTILAGANSSGKSSIMQPL 45
                                      789*********8.99*****99.9**************9866 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.22
                                       HHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                             SMC_N 148 aLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreem 201
                                        +l+A+ +++p  l+++   + +L  k   ++a++l e+ +  + ++v ++++ +
  gi|330506977|ref|YP_004383405.1| 321 PVLVALLAAEPGQLVYIEQPEIHLHPKAQMAMAQILAEAANCgVRVVVETHSSML 375
                                       5789999999***************************999885677777776655 PP

>> DUF3696  Protein of unknown function (DUF3696)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   6.2e-08   0.00016       1      42 [.     388     427 ..     388     427 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.2e-08
                           DUF3696   1 ispndvalyfferdegkdsaidtevlsp.iddnGrisnWPeGF 42 
                                       +sp++v+l++f+r++   +   tev s  +d+ G + +WPe+F
  gi|330506977|ref|YP_004383405.1| 388 LSPDKVKLHWFKRRP---EDGVTEVSSAdLDKAGAFGDWPEDF 427
                                       58***********76...77788888999*************9 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   9.9e-07    0.0025       4      50 ..       6      53 ..       4      57 .. 0.85
   2 ?   -0.5   0.0      0.22   5.7e+02     287     304 ..     335     352 ..     328     380 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.9e-07
                           DUF2813  4 erieisGFRGi.nrLSlsleentvLiGENaWGKSSLldALslilnvek 50
                                       ri ++GF+ + +  S++++++t+L G N+ GKSS+++ L ++ ++ +
  gi|330506977|ref|YP_004383405.1|  6 TRISVKGFKSLaEECSIEVRPLTILAGANSSGKSSIMQPLLIMKQTLE 53
                                      699******983579***********************9987755555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.22
                           DUF2813 287 lllEdpearLHPtmlaia 304
                                       + +E+pe +LHP+    +
  gi|330506977|ref|YP_004383405.1| 335 VYIEQPEIHLHPKAQMAM 352
                                       679*********864443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   6.3e-07    0.0016       1      37 [.       7      43 ..       7      46 .. 0.93
   2 ?   -2.7   0.0       2.7   6.9e+03     115     115 ..     172     172 ..     110     215 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.3e-07
                            AAA_23  1 kLkienfrsf.rdqeidFskgltlItGpNGaGKTTild 37
                                      ++++++f+s+ ++ +i+   +lt++ G N +GK++i++
  gi|330506977|ref|YP_004383405.1|  7 RISVKGFKSLaEECSIEVR-PLTILAGANSSGKSSIMQ 43
                                      799*******77789**99.****************96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                            AAA_23 115 d 115
                                       +
  gi|330506977|ref|YP_004383405.1| 172 N 172
                                       2 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.4e-05      0.14      17      39 ..      20      42 ..       8      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.4e-05
                            AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                       +i+++  t+l+G++ sGKS+++
  gi|330506977|ref|YP_004383405.1| 20 CSIEVRPLTILAGANSSGKSSIM 42
                                      566666789************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3133.98
//
Query:       gi|330506978|ref|YP_004383406.1|  [L=176]
Description: hypothetical protein MCON_0795 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1297.89
//
Query:       gi|330506979|ref|YP_004383407.1|  [L=286]
Description: putative methanogenesis marker protein 8 [Methanosaeta concilii GP6]
Scores for complete 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-95  319.2   0.3    1.8e-95  319.0   0.3    1.0  1  DUF2099      Uncharacterized protein conserved in archaea (DU
     0.0046   17.1   0.2      0.011   15.9   0.2    1.6  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su


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 !  319.0   0.3     2e-99   1.8e-95       1     256 [.       4     259 ..       4     260 .. 0.99

  Alignments for each domain:
  == domain 1  score: 319.0 bits;  conditional E-value: 2e-99
                           DUF2099   1 HiiealgkarvvvkdgkvvevgepkikyCPlfkklrgikeitkeaikkniefrikefGlftkkRkleskedfvsfGa 77 
                                       H++e++g+ rv+v+dgkv+ ++ep+i++CPl ++l+gik  +ke++k+++e+++ e+G++ +kR+le +++ vsfGa
  gi|330506979|ref|YP_004383407.1|   4 HLLEMAGA-RVRVRDGKVEVLTEPAIRSCPLRQDLYGIKVESKETVKRVLEEHMAELGMYGPKRVLELEDKPVSFGA 79 
                                       99****98.******************************************************************** PP

                           DUF2099  78 sEilstalkeglidaavivcdgaGtvivtnpelvqglggrisGlveTePieevierieeeggivldketaeidqveG 154
                                       sEils+al+eglidaav+v++gaGtv++t+pe++q++g++++Glv+TePiee+++ +ee+g+i++d++ +++dqv G
  gi|330506979|ref|YP_004383407.1|  80 SEILSDALTEGLIDAAVLVSEGAGTVVATRPEVLQAIGAHMTGLVKTEPIEEIQSGLEERGCILIDRQ-GTVDQVLG 155
                                       *****************************************************************998.9******* PP

                           DUF2099 155 vkkAiekgykkiavtvae..aedakklrelekeegvkilifavhttgiskeeaeelveaaDlvtacAskeireivkk 229
                                       +++A+e+gy++iav++a   a+da++lre e++ g +++i+avhttgis++ea+ l+e +Dlv++cAs+++re+++ 
  gi|330506979|ref|YP_004383407.1| 156 FERAVEAGYSRIAVSLAGhrADDARALRERERALGARATILAVHTTGISENEAQVLAECCDLVWSCASRSVREVAGG 232
                                       ****************987799******************************************************* PP

                           DUF2099 230 kallqvgksvpvfaltekGkelilerl 256
                                       kal+q+g ++pvfalt +Gk+lil+r+
  gi|330506979|ref|YP_004383407.1| 233 KALMQIGIAIPVFALTPMGKRLILNRA 259
                                       *************************97 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 !   15.9   0.2   1.2e-06     0.011      22      66 ..      80     118 ..      79     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-06
                       FrhB_FdhB_N  22 tallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGs 66 
                                       +++l  +L eg+id+++ v ++        +++ t+ e+l+a G 
  gi|330506979|ref|YP_004383407.1|  80 SEILSDALTEGLIDAAVLVSEG------AGTVVATRPEVLQAIGA 118
                                       79******************99......34566666667777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1935.99
//
Query:       gi|330506980|ref|YP_004383408.1|  [L=428]
Description: histidinol dehydrogenase [Methanosaeta concilii GP6]
Scores for complete 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-165  551.1   0.1   1.9e-165  550.8   0.1    1.0  1  Histidinol_dh  Histidinol dehydrogenase


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  550.8   0.1  1.1e-169  1.9e-165       8     409 .]      24     424 ..      19     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 550.8 bits;  conditional E-value: 1.1e-169
                                       -HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC-- CS
                     Histidinol_dh   8 seeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaqke 84 
                                        ++v  +v+ei+ +v ++Gdeal++ytekF++++ l++lrv++eei+ +++ +d++l eal+ aa++i  fh++qke
  gi|330506980|ref|YP_004383408.1|  24 IQDVLPAVNEIIMEVGSKGDEALFKYTEKFEGAH-LDDLRVTQEEIDLSYDLVDDRLLEALSSAADHIFYFHNEQKE 99 
                                       678999*************************774.689*************************************** PP

                                       --EEEEEECTTEEEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SS.GG.--HHHHHHHHHC CS
                     Histidinol_dh  85 seeevketepgvvlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpq.dgkvnpavlaaakla 160
                                       ++ +++e +pgv +gqkv+p+++vG YvPgG+aaypS++lm+++pAkvA v++ivv+tPpq dg++np +laaa++a
  gi|330506980|ref|YP_004383408.1| 100 HDLWMSEASPGVLVGQKVVPLDSVGAYVPGGRAAYPSSALMTVIPAKVADVPRIVVCTPPQkDGSINPLTLAAADMA 176
                                       99*************************************************************************** PP

                                       T-SEEEE--HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHHHHH CS
                     Histidinol_dh 161 gvdeiykvGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvAaDL 237
                                       g+deiyk+GGaqAiaa+A Gt+si++vdkivGPGn+yV+aAK+l +g+v+iD++aGPsEvl++aD+tadp ++AaD+
  gi|330506980|ref|YP_004383408.1| 177 GADEIYKLGGAQAIAAMALGTDSIERVDKIVGPGNVYVTAAKMLTRGSVEIDFPAGPSEVLILADRTADPGVIAADM 253
                                       ***************************************************************************** PP

                                       HHHHTT-TT-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCCH-EEEE-SSHHHHHHHHHHH--SEEEEES CS
                     Histidinol_dh 238 lsqaEHdedaqavlvttseelaeaveeevekqleelprkeiaekslekqsaiilvedleeaielaneyApEHlelqv 314
                                       ++q EHd+++ +v+v+ ++ la+av+ee++ q++ + r++i+++sle+ sai+l++d++ea++++n++ApEHle+ +
  gi|330506980|ref|YP_004383408.1| 254 IAQGEHDPKSISVFVSLDDLLASAVAEELNIQAPGAARSDIVSESLEH-SAILLADDMDEALDFVNAFAPEHLEIIT 329
                                       ************************************************.**************************** PP

                                       TTHHHHGGG--S-SEEEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHHHHHHHH CS
                     Histidinol_dh 315 edpeellekiknaGaiflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkelaeavet 391
                                       ++p+++l++i+naG++flG+++p+++gDYa+GtnhvLPTsg+Ar++sgl+v++F+kk+++q +++e+l  l+e+++t
  gi|330506980|ref|YP_004383408.1| 330 REPMNVLRSIRNAGSVFLGKFTPVAAGDYASGTNHVLPTSGYARIFSGLNVDHFTKKMTLQMITDEGLLGLEETITT 406
                                       ***************************************************************************** PP

                                       HHHHTT-HHHHHHHHHHH CS
                     Histidinol_dh 392 lAeaEgLeaHaeavkvRl 409
                                       lAeaEgL aHae+v+ Rl
  gi|330506980|ref|YP_004383408.1| 407 LAEAEGLLAHAESVRRRL 424
                                       ***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3123.80
//
Query:       gi|330506981|ref|YP_004383409.1|  [L=556]
Description: DNA ligase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-56  191.4   0.0    2.1e-56  190.8   0.0    1.3  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
    2.3e-34  119.2   0.0    4.2e-33  115.1   0.0    2.5  2  DNA_ligase_A_N   DNA ligase N terminus
    6.3e-16   58.8   0.0    1.6e-15   57.4   0.0    1.8  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
    2.2e-08   34.6   0.0    3.8e-08   33.8   0.0    1.4  1  RNA_ligase       RNA ligase
     0.0065   16.3   0.0          7    6.4   0.0    3.1  3  mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.8   0.0   5.7e-60   2.1e-56       2     204 .]     227     419 ..     226     419 .. 0.96

  Alignments for each domain:
  == domain 1  score: 190.8 bits;  conditional E-value: 5.7e-60
                                       EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEE CS
                    DNA_ligase_A_M   2 mLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDG 78 
                                       mLA+  + i+  +++l ++a+ +E+KyDG+R+q+hk+g++v++fSRrl+d+t+++pe+v  ++e ++++   +ilDG
  gi|330506981|ref|YP_004383409.1| 227 MLAQVGEGISASMQEL-GSAA-IEWKYDGARVQIHKDGKRVRIFSRRLEDVTRSLPEIVRLAQEVRADK---AILDG 298
                                       9**************9.5666.9************************************9999999885...9**** PP

                                       EEEEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE CS
                    DNA_ligase_A_M  79 ElvavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvel 155
                                       E+va+ k+  ++l fq++ +r+++k++ve+++ke++l+lf+FD++yldg+s +d+pl  Rr+lLe i     d   l
  gi|330506981|ref|YP_004383409.1| 299 EVVAIGKD-SRPLAFQEILKRFRRKYNVEKQAKETPLHLFLFDLIYLDGQSTVDLPLTRRRELLEGIA----DPSIL 370
                                       ****9666.9*********************************************************9....66778 PP

                                       --EEEESSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 156 aeslevkdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                       a++   ++v+ +ee++++a+++g+EGl++Kn +s+Y pgkr+knwlK+K
  gi|330506981|ref|YP_004383409.1| 371 ADQVISDSVQRAEEIYHQALEKGHEGLILKNSMSVYAPGKRGKNWLKIK 419
                                       99**********************************************9 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.1   0.0   1.2e-36   4.2e-33       1     173 []       3     181 ..       3     181 .. 0.93
   2 !    5.4   0.1    0.0056        20      65     112 ..     177     233 ..     175     321 .. 0.72

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 1.2e-36
                                       BCHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT CS
                    DNA_ligase_A_N   1 pFaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealg 73 
                                       +F  +ael++++e   +  lek++++a+f+++++   +++l+ a  +    l+    + ++g+g+s+l++a+a+a+g
  gi|330506981|ref|YP_004383409.1|   3 SFLSFAELCQRVEG-VSGSLEKVDLVAAFLKNLD---DDELAVASGFimgdLFSPSMDLVMGVGPSILYEAMARACG 75 
                                       5899**********.45569**********8875...6689999988889955555569****************** PP

                                       --HHHHHHHHHHHS-HHHHHHHHHCCHHHH.....------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS- CS
                    DNA_ligase_A_N  74 lskkkikdalakvgDlgevaeevlskrstl.....akkspltieevnelLdklaaa.gkgsedekkkilkkllkras 144
                                        s++ i d+l+ +gD g va+++++k++++      k +pl+i+ev++ L  +a+a gkgs+d+k+k l+ l+++a+
  gi|330506981|ref|YP_004383409.1|  76 CSTERISDMLRATGDPGLVASAAVDKKKPIgfaafIKDEPLSIKEVYQRLVAVARAsGKGSQDAKVKNLQYLFSQAT 152
                                       *****************************9*****9******************999******************** PP

                                       HHHHHHHHHHHCT---SS--HHHHHHHHH CS
                    DNA_ligase_A_N 145 peEakyliriilkdlriglsektvldala 173
                                       p+Ea+y++r+  +d+rig++e+ v+da+a
  gi|330506981|ref|YP_004383409.1| 153 PLEAQYIARLAIEDMRIGIGEGGVRDAIA 181
                                       ***************************97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0056
                                       HHHHHHHHT--HHHHHHHHHHHS-HHHHHHHHHCCHHHH.....------BH....H CS
                    DNA_ligase_A_N  65 akalaealglskkkikdalakvgDlgevaeevlskrstl.....akksplti....e 112
                                       + a+a+a++ +  k++ a++ ++D+g va ++++          +++ ++ +    e
  gi|330506981|ref|YP_004383409.1| 177 RDAIAQAFSQDASKVERAYNLTNDIGLVAVNARKGTLADlsvliNHPIKMMLaqvgE 233
                                       6799*****99999*****99*******99988655442444443333333344442 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 !   57.4   0.0   4.6e-19   1.6e-15       2      99 .]     440     531 ..     439     531 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 4.6e-19
                                       GGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEESE CS
                    DNA_ligase_A_C   2 gglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfae 76 
                                       ++ +gs+ l++ d  + kl+ +g v+tG++d+ l+el++ ++el   ++ +    + e      ++P++++eV+++e
  gi|330506981|ref|YP_004383409.1| 440 ASFLGSYRLACLDeaTSKLQDIGWVATGLTDEALAELTELFRELILVQNGM----EVE------LKPAVIFEVAYEE 506
                                       6789*********99999************************999999999....333......89*********** PP

                                       EECTSSSTT..EECT-EEEEE-TTS CS
                    DNA_ligase_A_C  77 itasgkyka..slRfPrfkrlReDk 99 
                                       i++s++y++  +lRfPr++r+R+Dk
  gi|330506981|ref|YP_004383409.1| 507 IQKSQSYSSgyALRFPRLVRVRDDK 531
                                       ************************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   1.1e-11   3.8e-08       5     161 .]     247     419 ..     244     419 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.1e-11
                                       EEEE-SSEEEEEEEETT.EEEEETTCEB.....CTTTHHHHHHTHHHHHHHH..HHHHH..ECCEEEEEEEES.... CS
                        RNA_ligase   5 vtEKlDGtnfriylvke.vgvasRsqil.....pfgeekfkefkrwaaalrk..klkeklaneelilyGElig.... 69 
                                       ++ K DG++++i+++ + v+++sR+ +      p                 +  +l++  +  + il GE++     
  gi|330506981|ref|YP_004383409.1| 247 IEWKYDGARVQIHKDGKrVRIFSRRLEDvtrslP-----------------EivRLAQEVRADKAILDGEVVAigkd 306
                                       677************444******9888321111.................12245555555679********7776 PP

                                       .......SS........TTSS.........EEEEEEEEEEECTTBECE--HHHHHHHHHCCTB..EEEEE.SS..HH CS
                        RNA_ligase  70 ......hsi......kygglpk........efyvFdifdirdkeeqrylspdevealakglgtvpvlyegkfl..aa 124
                                             + i      ky+   +        ++++Fd++ ++  ++   l+  ++++l++g+   p + + +++    
  gi|330506981|ref|YP_004383409.1| 307 srplafQEIlkrfrrKYNV--EkqaketplHLFLFDLIYLD-GQSTVDLPLTRRRELLEGI-ADPSILADQVIsdSV 379
                                       5554443336666665555..034678889********997.55999999999999***77.444444444433444 PP

                                       HHHCCC..HHHHTC--EEEEEESSSSBE.TTE.BSEEEEE CS
                        RNA_ligase 125 eellell.lskgnkrEGlVikpeselyk.nkg.raifKvk 161
                                       + ++e++ +  ++  EGl++k+  ++y   k+ ++++K+k
  gi|330506981|ref|YP_004383409.1| 380 QRAEEIYhQALEKGHEGLILKNSMSVYApGKRgKNWLKIK 419
                                       44444444445669**************99999*****97 PP

>> mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0     0.002         7      20      80 ..     247     301 ..     240     311 .. 0.84
   2 !    4.3   0.0     0.009        32      88     119 ..     331     362 ..     323     373 .. 0.81
   3 ?    1.6   0.0     0.061   2.2e+02     159     195 .]     382     419 ..     372     419 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.002
                                       EEEEESSEEEEEEEEECTEEEEEEETTS-EEEESSST-BTTSSSSTCTSBGGSEEEEEEEE CS
                   mRNA_cap_enzyme  20 vseKaDGiRylmllteeeegvylidRenevyrvenlrfprekdkeklekvldetllDgElv 80 
                                       + +K DG R+ +  + +   v ++ R  e    +  +++r  +    e   d+++lDgE+v
  gi|330506981|ref|YP_004383409.1| 247 IEWKYDGARVQIHKDGK--RVRIFSRRLEDVTRSLPEIVRLAQ----EVRADKAILDGEVV 301
                                       67*******99887777..89*****99877777678888885....56799*******98 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.009
                                       EEEEEEEEEEEEEETTEEGTTSBHHHHHHHHH CS
                   mRNA_cap_enzyme  88 kkelryliyDivaingvtvaeeplskRleilk 119
                                        + l   ++D++ ++g++ ++ pl +R e+l+
  gi|330506981|ref|YP_004383409.1| 331 ETPLHLFLFDLIYLDGQSTVDLPLTRRRELLE 362
                                       34567789******************988876 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.061
                                       HHHCCCCCTTSTEEEEEEEESSSB--SE.EEEEEEEE- CS
                   mRNA_cap_enzyme 159 leekfikklshesDGLIfqpvkepyvag.rdsdllKwK 195
                                        ee   + l+    GLI++ + + y +g r ++ lK K
  gi|330506981|ref|YP_004383409.1| 382 AEEIYHQALEKGHEGLILKNSMSVYAPGkRGKNWLKIK 419
                                       5566678899999***************7778899987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 4082.29
//
Query:       gi|330506982|ref|YP_004383410.1|  [L=335]
Description: homoserine dehydrogenase [Methanosaeta concilii GP6]
Scores for complete 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  179.8   0.1    6.5e-53  179.2   0.1    1.3  1  Homoserine_dh    Homoserine dehydrogenase
    3.1e-11   44.0   0.1    5.1e-11   43.3   0.1    1.4  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
      0.007   17.1   0.4      0.024   15.3   0.2    2.0  2  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


Domain annotation for each model (and alignments):
>> Homoserine_dh  Homoserine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.2   0.1   1.1e-56   6.5e-53       1     173 []     152     323 ..     152     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: 179.2 bits;  conditional E-value: 1.1e-56
                                       --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHH CS
                     Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarla 77 
                                       P+i+ ++++l g++i  ++Gi+ngt+nyilt+m+eeg  ++++l+eaq++G+aeaDp+ DveG+D+a K++ila+ +
  gi|330506982|ref|YP_004383410.1| 152 PLISLVERTLVGNTILGVRGIFNGTCNYILTRMTEEGIPYAHALSEAQDMGIAEADPSYDVEGVDTAGKVLILANSL 228
                                       999**********************************99************************************** PP

                                       CTTT--GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEECEEEEEEEEEETTSGGGHSSST-EEEEEEESSSEEEEE CS
                     Homoserine_dh  78 fgleveledvevegiskltaedikeakeegkvlklvasavearVkpelvpkshplasvkgsenavlvetdrlgelvi 154
                                       f+++v+++dv+v+gi+ +t+e ++ ak++g+ +kl++ +  ++V+p+lvp ++pla v g+ n  +++td  g++++
  gi|330506982|ref|YP_004383410.1| 229 FNMNVKYSDVNVTGITGVTPEALALAKKRGYAIKLIGDVPALTVRPTLVPLDSPLA-VAGTLNSAAIYTDLSGTITV 304
                                       **************************************769***************.******************** PP

                                       EES-SSHHHHHHHHHHHHH CS
                     Homoserine_dh 155 qGpgaGaepTAsavlsDll 173
                                       +G gaG+ +TAsa+l D++
  gi|330506982|ref|YP_004383410.1| 305 SGLGAGSIETASAILTDII 323
                                       *****************97 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.1   8.5e-15   5.1e-11       1     116 [.      10     143 ..      10     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 8.5e-15
                                       --SHHHHHHHHHHHH---S.....SEEEEEEEEESS.EEE-TT.........HHHHHT--CB---HHHHHHHHS-EE CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqse.....ielelvavadrd.sllskd.........rkallasealtldlddliahldpdv 62 
                                       G+G +G +v++ l+r+++      ++l+lv v+d+  + ls+d            l++ ++  ++ ++ i+ +d d+
  gi|330506982|ref|YP_004383410.1|  10 GYGIVGHGVVDVLTRKREIlrdmgLNLMLVSVTDHTgTVLSEDgvdankilgERTLANVATSSMKGKEAINAIDSDL 86 
                                       99***************989**999999999999999999999******998777888889999999999999**** PP

                                       EEE-S--HHHHT.....THHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE- CS
                     NAD_binding_3  63 vVEcasseavae.....lvlkaLkagkdvvtankgaladealyeeLreaaeangakiyv 116
                                        +E+++ + v++     ++++aL++gk+vvt nkg l+  + y  L ++ae ng+ + +
  gi|330506982|ref|YP_004383410.1|  87 MIEVTPTNIVHGqpglgHMEAALASGKHVVTSNKGPLV--VSYGSLKKLAEDNGVMLKF 143
                                       ***********6444448********************..**************98776 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 !   15.3   0.2   4.1e-06     0.024      59     128 ..      56     126 ..      34     128 .. 0.82
   2 ?   -2.7   0.0       1.5     9e+03      62     104 ..     130     172 ..     126     174 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.1e-06
                                       HHHHHHHHHHTTSSSEEEESHHHHHHHHCHTT-SEEEE--S.SGGGHHHHHHHHHTTSEEEE--SHHHHHH CS
                   DXP_reductoisom  59 aeelkealkekelktevlvGeealkelaeeeeadvvvaaiv.GaaGLkptlaaikagkriaLANKEsLVva 128
                                       a+++  + + ++++t+ + G+ea++++ +   ++v  + iv G  GL    aa+ +gk+++ +NK  LVv+
  gi|330506982|ref|YP_004383410.1|  56 ANKILGERTLANVATSSMKGKEAINAIDSDLMIEVTPTNIVhGQPGLGHMEAALASGKHVVTSNKGPLVVS 126
                                       44444444457899999************99999998776559*************************985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                                       HHHHHHHTTSSSEEEESHHHHHHHHCHTT-SEEEE--SSGGGH CS
                   DXP_reductoisom  62 lkealkekelktevlvGeealkelaeeeeadvvvaaivGaaGL 104
                                       lk+  +++++  ++ +   +   l++  e  +v + i G+ G+
  gi|330506982|ref|YP_004383410.1| 130 LKKLAEDNGVMLKFEATVGGTMPLISLVERTLVGNTILGVRGI 172
                                       5555666666666666666777777777788888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 2452.23
//
Query:       gi|330506983|ref|YP_004383411.1|  [L=168]
Description: amino acid-binding ACT domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   18.1   0.1     0.0055   16.4   0.0    1.9  2  ACT             ACT domain
  ------ inclusion threshold ------
      0.022   15.1   0.0      0.048   14.1   0.0    1.6  1  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
        0.1   12.8   0.1       0.55   10.4   0.0    2.1  2  DUF2007         Putative prokaryotic signal transducing prote


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.2e-07    0.0055       6      63 ..       8      67 ..       4      70 .. 0.81
   2 ?   -1.4   0.0      0.35   2.1e+03      21      31 ..      66      76 ..      64      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.2e-07
                                      EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT..ECEEEEEEEEEEHHHHHHHHHHHH CS
                               ACT  6 gvpDrPGlLarvfgaladrgiNidsieqrssedk..vagivfvvivvdeedleevlealk 63
                                      +++D+PG L    + l+d+  Ni+s+ +++++ +  +   v +v++ d +++e+v ++l+
  gi|330506983|ref|YP_004383411.1|  8 ELQDVPGQLLLAMQPLSDNKANIISVVHHRDRKTprGMIPVRFVVEMDRSRIEAVQARLQ 67
                                      6799999999999*********************96666666666666666666666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.35
                                      HHHTTSEEEEE CS
                               ACT 21 ladrgiNidsi 31
                                      l + gi+++++
  gi|330506983|ref|YP_004383411.1| 66 LQESGISVVRA 76
                                      66778888765 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 ?   14.1   0.0     8e-06     0.048       3      74 ..      86     156 ..      84     168 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8e-06
                                       EEEEEEXXTTSSHHHHHHHHHHHTTXEEEEEEEEXXSS.TTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSC CS
                    Saccharop_dh_N   3 eveleGhliDsgilnkvldlileaggsfevlefevGkk.kkdtSyaelevsaedeevLeeileeltelgaelv 74 
                                       +v l Gh++Ds +   ++++i +  g  ev ++++     +++S+a l+++a+ ++++++ l+ l ++g e++
  gi|330506983|ref|YP_004383411.1|  86 SVVLVGHVLDSDL-GDTINRI-DSTGYAEVMDLSLTMPgVNEPSSAYLKIRATGKAEIQKALTILRNVGEEKK 156
                                       58899******95.6677777.5668899**999987526899*************************98865 PP

>> DUF2007  Putative prokaryotic signal transducing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   9.1e-05      0.55       9      32 ..      55      78 ..      48      94 .. 0.81
   2 ?   -0.4   0.0      0.23   1.4e+03      55      66 ..     140     151 ..     137     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.1e-05
                           DUF2007  9 dpveaelikslLeeagIeavvkde 32
                                      d+ ++e ++++L+e+gI +v ++e
  gi|330506983|ref|YP_004383411.1| 55 DRSRIEAVQARLQESGISVVRAGE 78
                                      7889**************998844 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.23
                           DUF2007  55 dleeAreileea 66 
                                         ++A +il+++
  gi|330506983|ref|YP_004383411.1| 140 EIQKALTILRNV 151
                                       5789*****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1356.69
//
Query:       gi|330506984|ref|YP_004383412.1|  [L=279]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for 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    1.9e-17   63.8   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
      1e-12   48.1   0.0    1.4e-12   47.6   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    4.9e-11   43.1   0.0    8.7e-11   42.3   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    3.3e-09   36.8   0.0    5.5e-09   36.1   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    4.4e-09   37.0   0.0    7.4e-09   36.3   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    5.1e-07   29.4   0.0    7.3e-07   28.9   0.0    1.3  1  MTS              Methyltransferase small domain
    1.9e-05   24.1   0.0    2.3e-05   23.8   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    5.9e-05   22.8   0.0    9.5e-05   22.1   0.0    1.3  1  NodS             Nodulation protein S (NodS)
    7.9e-05   22.4   0.0    0.00019   21.2   0.0    1.6  1  TPMT             Thiopurine S-methyltransferase (TPMT)
    0.00036   20.5   0.0    0.00057   19.9   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0034   16.8   0.0     0.0064   15.9   0.0    1.4  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.016   14.6   0.0    1.2  1  TehB             Tellurite resistance protein TehB
      0.077   11.9   0.0       0.11   11.4   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)


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 !   63.8   0.0   1.4e-20   1.9e-17       1      97 []      71     165 ..      71     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.4e-20
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhh 76 
                                       + d+GcG+G ++ +lak +  a+v+g+D+s+  +++are a+e gl +e+++++  d++ e+ +fDl++++++ ++ 
  gi|330506984|ref|YP_004383412.1|  71 IADFGCGPGLYANRLAKVG--ASVIGIDFSKCSIKHAREAAREVGLTIEYINQNYLDFETEH-RFDLILMIMCdFCA 144
                                       78**************995..*************************************9775.************** PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       ls+++++ +l++++++L pgG
  gi|330506984|ref|YP_004383412.1| 145 LSPSQRRIMLAKFHSMLLPGG 165
                                       ********************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0     1e-15   1.4e-12       3     113 ..      67     173 ..      65     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1e-15
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDl.. 77 
                                        ++r+ D GCG G ++ +la ++g  a v+GiD+s+ +i++Are a++ gl+ +e   ++  ++e+     +fDl  
  gi|330506984|ref|YP_004383412.1|  67 ADTRIADFGCGPGLYANRLA-KVG--ASVIGIDFSKCSIKHAREAAREVGLT-IEYINQNYLDFETE---HRFDLil 136
                                       6789****************.775..89***********************8.**********9954...89***55 PP

                   Methyltransf_31  78 ..ilsnevlnaladpdkile.eiervlkpggilliedpr 113
                                         +++  ++++ +++  i+  + ++ l pgg +l++ ++
  gi|330506984|ref|YP_004383412.1| 137 miMCD--FCALSPSQRRIMLaKFHSMLLPGGSVLLDVYS 173
                                       43333..445577776665459**********9998877 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   6.3e-14   8.7e-11       2      95 ..      73     168 ..      72     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 6.3e-14
                                       EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-...C CS
                   Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv...e 75 
                                       d+GcG G++a+ lak ga+v+g+D+sk  +k a+e+a+e gl++e++ ++  ++  e + fDl+++ ++ +      
  gi|330506984|ref|YP_004383412.1|  73 DFGCGPGLYANRLAKVGASVIGIDFSKCSIKHAREAAREVGLTIEYINQNYLDFETE-HRFDLILMIMCDFCAlspS 148
                                       89****************************************999999999985543.5******998543335877 PP

                                       CHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllv 95 
                                       +++  l++++ +L pgG ++
  gi|330506984|ref|YP_004383412.1| 149 QRRIMLAKFHSMLLPGGSVL 168
                                       89999************876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0     4e-12   5.5e-09      22     162 ..      67     253 ..      43     256 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 4e-12
                   Methyltransf_23  22 aggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..........kakkaqkdqfdeqeaaepqgkfdlIvl 88 
                                       a+ r+ d+GcG G  ++ l++ g+sv+g+D s   ++ a+          + ++++   f      e + +fdlI +
  gi|330506984|ref|YP_004383412.1|  67 ADTRIADFGCGPGLYANRLAKVGASVIGIDFSKCSIKHAReaarevgltiEYINQNYLDF------ETEHRFDLILM 137
                                       455888**************************9999999999999998885555555555......6669******* PP

                   Methyltransf_23  89 rev.lehvpd..ppellrqiatllkpgGylllseplasl.........................kedrllld..... 132
                                       +++ ++ + +      l++++++l pgG +ll ++ +s+                                      
  gi|330506984|ref|YP_004383412.1| 138 IMCdFCALSPsqRRIMLAKFHSMLLPGGSVLLDVYSQSAfkqrkeassygvnlldgfwsaekyyG------Flntfk 208
                                       **97888885235589*******************998865555555544444444444444431......044444 PP

                   Methyltransf_23 133 .............wlylvpag..rhisffsarslkelleeaGlev 162
                                                    ++ ++++    ++++f+ +sl + +e aG+ +
  gi|330506984|ref|YP_004383412.1| 209 yddamvvldkytiVESARKRTvyNWLQYFTPESLWREFEMAGFAD 253
                                       444444444444344445554556779999999999999999986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   5.3e-12   7.4e-09       2      98 ..      73     166 ..      72     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 5.3e-12
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas.nvlh 77 
                                       ++GcG G ++ +l++   +++++g+D+s+ +i++a+e  ++ +      +e+ +++ ld + ++ fDl++++ + ++
  gi|330506984|ref|YP_004383412.1|  73 DFGCGPGLYANRLAKV--GASVIGIDFSKCSIKHAREAAREVGL----TIEYINQNYLDFETEHRFDLILMImCDFC 143
                                       8***************..**************777777777665....6666666666666668******9977788 PP

                   Methyltransf_12  78 hl..kdirevldnirklLkpgGr 98 
                                       +l   ++r +l++++++L pgG 
  gi|330506984|ref|YP_004383412.1| 144 ALspSQRRIMLAKFHSMLLPGGS 166
                                       88899999*************96 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   5.3e-10   7.3e-07      16     103 ..      52     137 ..      39     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 5.3e-10
                                       --HHHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTT CS
                               MTS  16 lDkGsklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvlee 92 
                                       +D   + +++ ++  ++ +++D+GcG G+ +  lak   +  v  +d ++ +++ a+e +++ +l +e+++++ l+ 
  gi|330506984|ref|YP_004383412.1|  52 IDRSVEWIASRFSIGADTRIADFGCGPGLYANRLAKVGAS--VIGIDFSKCSIKHAREAAREVGLTIEYINQNYLDF 126
                                       5666667777777778899*****************8877..99********************************9 PP

                                       STTS-EEEEEE CS
                               MTS  93 veekkfdlivs 103
                                        +e++fdli++
  gi|330506984|ref|YP_004383412.1| 127 ETEHRFDLILM 137
                                       999******86 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.7e-08   2.3e-05      57     176 ..      62     181 ..      24     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.7e-08
                                       TTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---..--SEE CS
                              CMAS  57 klelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde..kvdrv 131
                                       + ++ +  ++ d GcG G  + r ++  +++v+g+ +Sk   k+a+++  e++l+   e   ++y d++   ++d +
  gi|330506984|ref|YP_004383412.1|  62 RFSIGADTRIADFGCGPGLYANRLAKV-GASVIGIDFSKCSIKHAREAAREVGLT--IEYINQNYLDFETehRFDLI 135
                                       55566667899*******999998887.***********************9964..5667799999998789**** PP

                                       EEES-.GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHH CS
                              CMAS 132 vsvga.fehvgkenydtffkklkkllkedGllllhtitslhkkela 176
                                         +   f ++  ++     +k++++l ++G +ll    +   k+++
  gi|330506984|ref|YP_004383412.1| 136 LMIMCdFCALSPSQRRIMLAKFHSMLLPGGSVLLDVYSQSAFKQRK 181
                                       988544889999999999*************999876665554444 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   6.9e-08   9.5e-05      46     142 ..      70     167 ..      51     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.9e-08
                              NodS  46 dalevGcaaGalterlapyckrltvvdvveeaiararervkess.hiswivsdvqqfstdekfdlivvaevlyyied 121
                                        + + Gc  G +++rla +  ++  +d  + +i++are  +e+   i +i ++   f+t+++fdli++    +    
  gi|330506984|ref|YP_004383412.1|  70 RIADFGCGPGLYANRLAKVGASVIGIDFSKCSIKHAREAAREVGlTIEYINQNYLDFETEHRFDLILMIMCDFCALS 146
                                       55678***********************************9985489*******************98877776666 PP

                              NodS 122 vaelraavrnlvsllapdgql 142
                                         + r  +  + s+l p+g +
  gi|330506984|ref|YP_004383412.1| 147 PSQRRIMLAKFHSMLLPGGSV 167
                                       666677777777777776665 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.4e-07   0.00019      45     113 ..      75     149 ..      70     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.4e-07
                                       T-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTT......SGGGGGEEEE--...........-TTT---SS CS
                              TPMT  45 lCGkaldlvwlAeqgrevvGvelselAvekffeeanl......epkvkelsgvkeysageiellcgdvFtlraee 113
                                       +CG +l +  lA+ g +v+G+++s+  ++++ e a +        + ++l++  e +++ i ++++d+ +l++++
  gi|330506984|ref|YP_004383412.1|  75 GCGPGLYANRLAKVGASVIGIDFSKCSIKHAREAAREvgltieYINQNYLDFETEHRFDLILMIMCDFCALSPSQ 149
                                       8***************************99765555565564333466777777799***********9998875 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   4.1e-07   0.00057      24      78 ..      66     116 ..      48     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.1e-07
                   Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78 
                                        ++++++D+G+G g  + +la      + +v+gid ++  +++a++ a+++g ++
  gi|330506984|ref|YP_004383412.1|  66 GADTRIADFGCGPGLYANRLAK----VGASVIGIDFSKCSIKHAREAAREVGLTI 116
                                       56789****************9....79**********************99544 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.7e-06    0.0064     161     230 ..      67     135 ..      53     143 .. 0.74
   2 ?   -3.7   0.0       4.5   6.2e+03      86     107 ..     218     239 ..     179     246 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.7e-06
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadvi 230
                                       +++++ D+G+G G+ a   ak+ga +v+++D  + ++k a+e a+  +++ +   ++  +  +e+++d+i
  gi|330506984|ref|YP_004383412.1|  67 ADTRIADFGCGPGLYANRLAKVGA-SVIGIDFSKCSIKHAREAAREVGLTIEYINQNYLDFETEHRFDLI 135
                                       567899*****************9.599**************9987666554422233344345666666 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.5
                              PrmA  86 kvkveeveeedWaeewkkyykP 107
                                       k+++ e + +  + +w +y+ P
  gi|330506984|ref|YP_004383412.1| 218 KYTIVESARKRTVYNWLQYFTP 239
                                       4444444445555677777777 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.2e-05     0.016      32     131 ..      69     168 ..      57     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                       -EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESS.GGG CS
                              TehB  32 gkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderydfilstvv.lmf 107
                                       +++ d+gcg g  +  l+ +g  v  +d  + si++ +e +    l+ i+    +  + + ++r+d+il  +  +  
  gi|330506984|ref|YP_004383412.1|  69 TRIADFGCGPGLYANRLAKVGASVIGIDFSKCSIKHAREAAREVGLT-IEYINQNYLDFETEHRFDLILMIMCdFCA 144
                                       6789**********************************999999898.88777777778888999999986543777 PP

                                       S-GGGHHHHHHHHHHTEEEEEEEE CS
                              TehB 108 leaeripsiienmqectkvggynl 131
                                       l + +   +++ ++ +  +gg  l
  gi|330506984|ref|YP_004383412.1| 145 LSPSQRRIMLAKFHSMLLPGGSVL 168
                                       888777777888888888887665 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     8e-05      0.11     115     150 ..      67     101 ..      38     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8e-05
                                       TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHH CS
                    Methyltransf_9 115 kgrtildvGcgnGyhlwrmvgegaklvvGidPself 150
                                        + +i+d Gcg G +  r++  ga +v+Gid s+  
  gi|330506984|ref|YP_004383412.1|  67 ADTRIADFGCGPGLYANRLAKVGA-SVIGIDFSKCS 101
                                       5789**************988877.689***88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2103.43
//
Query:       gi|330506985|ref|YP_004383413.1|  [L=133]
Description: hypothetical protein MCON_0802 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1051.28
//
Query:       gi|330506986|ref|YP_004383414.1|  [L=261]
Description: dihydrodipicolinate reductase [Methanosaeta concilii GP6]
Scores for complete 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-45  151.5   0.0    1.4e-44  151.0   0.0    1.2  1  DapB_C         Dihydrodipicolinate reductase, C-terminus
      2e-25   89.3   1.3    3.1e-25   88.7   1.3    1.3  1  DapB_N         Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.044   12.9   0.1      0.072   12.2   0.1    1.2  1  RmlD_sub_bind  RmlD substrate binding domain
       0.29   11.5   1.7          5    7.5   1.7    2.4  1  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 


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 !  151.0   0.0   3.2e-48   1.4e-44       1     121 []     123     258 ..     123     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 3.2e-48
                                       HHHHHHHHHHHHCCCSTTT.-EEEEEEEESTT--SSS-HHHHHHHHHHH....................-S-ETTCC CS
                            DapB_C   1 Gvnlllklveeaakllkea.ydveiiEkHhnkKaDaPSGTAlalaeaia....egke............arkkkeig 60 
                                       Gvnl+ klv++aa++lk+  +d+eiiE+Hhn+K+DaPSGTAla++eai+    e  +              + keig
  gi|330506986|ref|YP_004383414.1| 123 GVNLFWKLVADAAAALKGYdFDIEIIEAHHNQKKDAPSGTALATLEAIRrargE--SdlsevvygrngiMPRGKEIG 197
                                       9*****************99*****************************76650..145566666667745568*** PP

                                       CEEEETTT--CCCCEEEECTTEEEEEEEEEESCHHHHHHHHHHHHHH.HCTSSEESHHHHH CS
                            DapB_C  61 ihsvRgggvvgehevlfagegevieikhealsreiFaeGallaaewlakkkkglysmedvL 121
                                       +h+vR+g++vg+h+vl+ag ge++ei+h+a+sr+ Fa+Ga++aa w++++k+g+y+m dvL
  gi|330506986|ref|YP_004383414.1| 198 VHAVRAGDIVGDHTVLLAGPGERLEIRHQAHSRAAFASGAVRAATWVVGRKPGIYGMADVL 258
                                       ************************************************************8 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   1.3     7e-29   3.1e-25       2     124 .]       3     120 ..       2     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 7e-29
                                       EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEB..SSHHHHHHH..-SEEEE- CS
                            DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavt..ddleevlek..advliDF 74 
                                       ++a++Ga GrmG+ v++ + + e++elva++d+ +       ag+ l   + gv v+  ++le+vl++   dvliDF
  gi|330506986|ref|YP_004383414.1|   3 RIAITGALGRMGTLVIQEAARIEGMELVAGLDAVG-------AGKPL---QGGVLVKdaSQLEQVLKEtrPDVLIDF 69 
                                       8********************************99.......44433...45777776699*******99******* PP

                                       S-HHHHHHHHHHHHHTT-EEEE--SS--HHHHHHHHHHTTT.SEEEE-S-- CS
                            DapB_N  75 TtpeavlenlklalekgvklViGTTGlseeelaeleelakk.igvviapNf 124
                                       T  +a+++n+ +a++ gv+lV+GTTG+s+e+++e++e+ +  +++vi pNf
  gi|330506986|ref|YP_004383414.1|  70 TIAKAAVKNVCIAASLGVDLVVGTTGISSEQHSEMREAIEGnVAAVITPNF 120
                                       *************************************88877********8 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.6e-05     0.072       2      58 ..       3      69 ..       2      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                                      EEEEESTTSHHHHHHHHHCTT.TSEEEEEE-TT.........T--TTSHHHHHHHHHHH--SEEEE- CS
                     RmlD_sub_bind  2 kilvtGanGqlGseLakqlae.eglevlaltre.........eldltdaeavaellkeakpdvvvna 58
                                      +i +tGa G +G+ +++++a+ eg+e++a   +          + ++da++++++lke++pdv+++ 
  gi|330506986|ref|YP_004383414.1|  3 RIAITGALGRMGTLVIQEAARiEGMELVAGLDAvgagkplqgGVLVKDASQLEQVLKETRPDVLIDF 69
                                      899**********9999888879****9986667999999988999*****************9975 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 ?    7.5   1.7    0.0011         5       2      97 ..       3      96 ..       2     100 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0011
                                      EEEEES.TSHHHHHHHHHHHHHTTCEEEEEE-.TS-HHHHH..HHHHEETTTEC-SS-EEEE.TTEEEETTEEEEEE-- CS
                           Gp_dh_N  2 kvainG.fGRIGrlvlralleekelevvaind.ltdletla..yllkyDsvhgrfkgeveae.eealvvngkkikvlae 75
                                      ++ai G +GR+G lv++ +++ + +e+va  d ++  + l+   l+k  s   ++ +e + +   ++++ +  +k +  
  gi|330506986|ref|YP_004383414.1|  3 RIAITGaLGRMGTLVIQEAARIEGMELVAGLDaVGAGKPLQggVLVKDASQLEQVLKETRPDvLIDFTIAKAAVKNVCI 81
                                      89999977************99999999866644333333211444444444444444333322223333333333333 PP

                                      SSGGGS-CHHHTSSEEEE-SSS CS
                           Gp_dh_N 76 kdpeelpwkelgvdlVvestGv 97
                                      +       ++lgvdlVv +tG+
  gi|330506986|ref|YP_004383414.1| 82 A-------ASLGVDLVVGTTGI 96
                                      3.......36667777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1852.41
//
Query:       gi|330506987|ref|YP_004383415.1|  [L=291]
Description: dihydrodipicolinate synthase [Methanosaeta concilii GP6]
Scores for complete 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-95  317.9   0.0    4.3e-95  317.8   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.8   0.0   2.4e-99   4.3e-95       2     286 ..       2     284 ..       1     287 [. 0.97

  Alignments for each domain:
  == domain 1  score: 317.8 bits;  conditional E-value: 2.4e-99
                                       -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE-- CS
                             DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvG 78 
                                        sg+++a++tpf+ed  ld+e l++++e+l + g++g+v +GttGE+atl  ee++ ++eiave  +  +pviag+G
  gi|330506987|ref|YP_004383415.1|   2 YSGVLPAIITPFHEDKSLDEEGLKRNVEYLSKTGISGMVPCGTTGEAATLTFEEHKRVIEIAVE--NSTVPVIAGTG 76 
                                       589************************************************************9..689******** PP

                                       -SSHHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTST CS
                             DHDPS  79 snstseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaele 155
                                       sn+t+ea++l+ +a+eaGa+++l++tPYYnkp+ +g+ +hfk+++e+ d p++lYnvp+rtg dl+pe v++L+ ++
  gi|330506987|ref|YP_004383415.1|  77 SNNTREAVELTCHAAEAGAHAALLITPYYNKPNDRGMFEHFKTVAEKCDIPIVLYNVPKRTGIDLKPELVAKLSRIK 153
                                       ***************************************************************************** PP

                                       TEEEEEE-SS-CTHHHHHHCCC.STTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHH CS
                             DHDPS 156 nivgvKeavgdleevikikkev.gkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaae 231
                                       niv++Kea+g+l+++ +i++++ g+d+++++Gdd+l+l+a+ lGa+Gvisv +n+a+++  ++++a+ +Gdl++a++
  gi|330506987|ref|YP_004383415.1| 154 NIVAIKEASGSLSQLSQIIEQTwGSDFSVLCGDDDLTLPAMALGAKGVISVVANVAPRKTVAMVDAMMKGDLEKARS 230
                                       ***************999865439***************************************************** PP

                                       HHHHHHHHHHHCCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHH CS
                             DHDPS 232 lnekllplikilfaepnvilvktalellGlvveatlrkPltpleeeekeeleall 286
                                       l+ +l pl+ ++f e+n+i+vkta ++lGl  ++ lr Pl++++ ++++ l++ll
  gi|330506987|ref|YP_004383415.1| 231 LHYELAPLVRAMFLETNPIPVKTAHKYLGLAGGP-LRLPLGEMAADKEKMLKELL 284
                                       **********************************.************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2194.06
//
Query:       gi|330506988|ref|YP_004383416.1|  [L=58]
Description: hypothetical protein MCON_0805, partial [Methanosaeta concilii GP6]
Scores for complete 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-10   38.5   0.1    9.6e-10   38.4   0.1    1.0  1  Ribosomal_S17e  Ribosomal S17
  ------ inclusion threshold ------
      0.086   13.2   0.1       0.09   13.1   0.1    1.2  1  SWIRM           SWIRM domain


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 !   38.4   0.1   1.1e-13   9.6e-10      16      61 ..       3      48 ..       1      57 [. 0.89

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.1e-13
                                      HHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHHT CS
                    Ribosomal_S17e 16 iiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkri 61
                                      ++ +y s+++ dF++nk  ++e + i++k +rn+iaGy++++m++ 
  gi|330506988|ref|YP_004383416.1|  3 LLRTYESSFSPDFEQNKLRVSEYTDIKNKTIRNRIAGYISNVMRQR 48
                                      5679***************************************983 PP

>> SWIRM  SWIRM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     1e-05      0.09       8      46 ..       1      38 [.       1      58 [] 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                             SWIRM  8 pdslhpiEkellselfngkdktpeeYlkiRnkiialyre 46
                                      +d l   E    +++ ++ + +  eY +i+nk i+ +  
  gi|330506988|ref|YP_004383416.1|  1 MDLLRTYESSFSPDFEQN-KLRVSEYTDIKNKTIRNRIA 38
                                      577888998888888755.59***********9997764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 441.49
//
Query:       gi|330506989|ref|YP_004383417.1|  [L=445]
Description: phosphomethylpyrimidine kinase [Methanosaeta concilii GP6]
Scores for complete 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-84  281.9   0.1    4.8e-84  281.6   0.1    1.1  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    9.2e-32  109.9   0.0    1.5e-31  109.2   0.0    1.4  1  ThiP_synth    Thiamine-phosphate synthase
    4.5e-06   26.2   0.2    6.6e-06   25.6   0.2    1.3  1  PfkB          pfkB family carbohydrate kinase
  ------ inclusion threshold ------
      0.075   12.5   0.6       0.13   11.7   0.6    1.5  1  Carb_kinase   Carbohydrate kinase


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.6   0.1   1.1e-87   4.8e-84       1     246 []       8     247 ..       8     247 .. 0.99

  Alignments for each domain:
  == domain 1  score: 281.6 bits;  conditional E-value: 1.1e-87
                                       ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHH CS
                      Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiiev 77 
                                       Ds+GGAGiqAD+ktfs lg++g+s+ita+taqnt gv++v++l++e v+aqle+++ed++++ +K+Gml+sa+i+++
  gi|330506989|ref|YP_004383417.1|   8 DSGGGAGIQADIKTFSVLGLHGTSAITAITAQNTLGVQNVYALSPEEVRAQLESITEDFSIAWAKTGMLHSAQIVDT 84 
                                       9**************************************************************************** PP

                                       HHHHHHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHT CS
                      Phos_pyr_kin  78 vaeklkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllkl 154
                                       va+ l+  ++p+VlDPV+ a+ g +ll+++av+alke+L+pla v+tPN++EaeaL+g ++++ +++ +aa+ +++l
  gi|330506989|ref|YP_004383417.1|  85 VADHLQANDIPLVLDPVIEAEAGGRLLRPDAVSALKERLIPLAGVVTPNIFEAEALSGIRVRDMDSAAHAARGIMSL 161
                                       ***************************************************************************** PP

                                       T-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHH CS
                      Phos_pyr_kin 155 gakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvtea 231
                                       ga+aV++kGghl      +td+l+ +++ + l++eri+  ++hG GCt+s+a+++ la g s+e+A  +Ake+ ++a
  gi|330506989|ref|YP_004383417.1| 162 GAQAVIVKGGHL-----DCTDLLMVRNKSTLLPSERIP-GENHGIGCTFSAALTSFLALGCSIENAALNAKEFAKSA 232
                                       ***********8.....568******************.9************************************* PP

                                       HHCG-BSTSSS-B-- CS
                      Phos_pyr_kin 232 ikealelgkgagpvn 246
                                       ++ +l++gkg+gpvn
  gi|330506989|ref|YP_004383417.1| 233 LRGSLRVGKGVGPVN 247
                                       *************97 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.2   0.0   3.4e-35   1.5e-31       1     163 [.     264     427 ..     264     429 .. 0.92

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 3.4e-35
                                       HHHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC CS
                        ThiP_synth   1 eleralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkf 77 
                                       +le a++lle+++e+ +l+ + g+  a+a+p+A+++eDvaa++G ++++++rv+  g+ +fg+ s  a+v+laamk 
  gi|330506989|ref|YP_004383417.1| 264 DLEVAVDLLENSHELFDLMLKGGAGPAMAIPGARCPEDVAALEGGLTKIEERVCRFGGFRFGGRSDSASVILAAMKI 340
                                       5899************************************************************************* PP

                                       -TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCC..S.-ECEEEE--BCTB--EEEE CS
                        ThiP_synth  78 dpevraainirydekilealeelglkvvefdreeepeevgstmewgvaeaieel..e.vpdviydeGgvGkEpmiyv 151
                                       dp ++aai+++  +k l +++elgl +++  r +e  ++g+    g +e  e +  + +p +i+deG  GkEp +y+
  gi|330506989|ref|YP_004383417.1| 341 DPLAKAAIDLE--PKALLSCRELGLPIIDRARLDELAAIGQCHLKGEEELSEGEgsAlLPAAIWDEGVLGKEPRLYL 415
                                       *******9998..99***********************955555555555555554249****************** PP

                                       EESSHHHHHHHH CS
                        ThiP_synth 152 lgkdaeevvekv 163
                                       lg++a+ +ve +
  gi|330506989|ref|YP_004383417.1| 416 LGASASLLVELL 427
                                       ******999876 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.2   1.5e-09   6.6e-06     172     287 ..     109     230 ..      30     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.5e-09
                                       H.....HHHHHHHHH.CTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEE..TTEE CS
                              PfkB 172 q.....fkeallell.aladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvve..kdge 240
                                             +++al+e l +la +++pn  E+eal+g    d+++a++a+  + + ga+ v+v+ G   +      ++++
  gi|330506989|ref|YP_004383417.1| 109 RllrpdAVSALKERLiPLAGVVTPNIFEAEALSGIRVRDMDSAAHAARGIMSLGAQAVIVKGGHLDCTDLLmvRNKS 185
                                       1444455555555444************************************************9995444456666 PP

                                       EEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH CS
                              PfkB 241 lkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAa 287
                                          p+  ++ +    G G +f +++++ l+ g s+e a+  a ++A 
  gi|330506989|ref|YP_004383417.1| 186 TLLPS--ERIPGENHGIGCTFSAALTSFLALGCSIENAALNAKEFAK 230
                                       66666..4567888999999999999999999999999988877775 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   2.9e-05      0.13     120     217 ..     128     228 ..       1     241 [. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.9e-05
                                       EEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEEESTT....SEEEECTTEEEEE----GGG-STTHHHH CS
                       Carb_kinase 120 viLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvllkgek....dvivspegevlinstgssalakGGsGDv 192
                                        + TP++ E + L++  v   d+ +++ar +       v++kg +    d+++  + + ++++ +       G G +
  gi|330506989|ref|YP_004383417.1| 128 GVVTPNIFEAEALSGIRVRDMDSAAHAARGIMSLGAQAVIVKGGHldctDLLMVRN-KSTLLPSERIPGENHGIGCT 203
                                       489***************************99988888888887544435566655.5555555666666779999* PP

                                       HHHHHHHHHHCTSSHHHHHHHHHHH CS
                       Carb_kinase 193 LaGligalLaqneasyeaaiaaawl 217
                                        + ++ ++La   +  +aa++a + 
  gi|330506989|ref|YP_004383417.1| 204 FSAALTSFLALGCSIENAALNAKEF 228
                                       ********99999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3351.90
//
Query:       gi|330506990|ref|YP_004383418.1|  [L=183]
Description: hypothetical protein MCON_0807 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-07   31.8  12.9       0.39   10.6   0.1    5.0  5  Clathrin_H_link  Clathrin-H-link
      0.004   17.3   3.7       0.45   10.8   0.2    3.7  3  LPD22            Large polyvalent protein associated domain 2
     0.0077   15.7   0.0          3    7.5   0.0    3.4  4  Sigma70_r4       Sigma-70, region 4
  ------ inclusion threshold ------
      0.019   14.7   0.0         91    2.9   0.0    4.2  4  PHF12_MRG_bd     PHD finger protein 12 MRG binding domain
      0.032   14.3   1.4        3.1    7.9   0.0    3.8  4  TFIIB            Transcription factor TFIIB repeat
      0.071   13.4   0.4       0.22   11.8   0.1    1.9  2  P5CR_dimer       Pyrroline-5-carboxylate reductase dimerisati
       0.11   11.5   0.5       0.16   11.0   0.5    1.3  1  CRISPR_Cse1      CRISPR-associated protein Cse1 (CRISPR_cse1)
       0.11   12.2   3.5         17    5.2   0.1    4.1  4  PHP_C            PHP-associated
       0.14   12.2   0.2         15    5.7   0.1    2.4  2  EutK_C           Ethanolamine utilization protein EutK C-term


Domain annotation for each model (and alignments):
>> Clathrin_H_link  Clathrin-H-link
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00021      0.42      11      28 ..      11      28 ..       4      32 .. 0.92
   2 !    5.8   0.0    0.0063        13       6      30 ..      40      64 ..      33      68 .. 0.86
   3 ?    1.8   0.3      0.11   2.2e+02       9      31 ..      77      99 ..      74     112 .. 0.79
   4 !    8.9   0.1   0.00072       1.4       8      29 ..     110     131 ..     101     135 .. 0.88
   5 !   10.6   0.1    0.0002      0.39       6      30 ..     142     166 ..     139     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                   Clathrin_H_link 11 qqFeqllaqgnykeAakv 28
                                      ++F++ +++g ykeAak+
  gi|330506990|ref|YP_004383418.1| 11 RRFKEKMNAGAYKEAAKI 28
                                      79***************8 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0063
                   Clathrin_H_link  6 ddlyvqqFeqllaqgnykeAakvAa 30
                                      +d +   ++  +++g+y+ Aa++A 
  gi|330506990|ref|YP_004383418.1| 40 QDAVKSAYDANMKKGDYSLAAELAK 64
                                      577889999*************996 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.11
                   Clathrin_H_link  9 yvqqFeqllaqgnykeAakvAae 31
                                       +++F + + ++ y++Aa+ A e
  gi|330506990|ref|YP_004383418.1| 77 AQRSFYRKIDSEFYRAAAEYAKE 99
                                      67899999**********99966 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.00072
                   Clathrin_H_link   8 lyvqqFeqllaqgnykeAakvA 29 
                                         +q F++ ++ g +k+Aa++A
  gi|330506990|ref|YP_004383418.1| 110 AAIQAFNKSMSMGMVKNAAEIA 131
                                       5789*****************9 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.0002
                   Clathrin_H_link   6 ddlyvqqFeqllaqgnykeAakvAa 30 
                                       ++   ++Feq +++g y++A k+A 
  gi|330506990|ref|YP_004383418.1| 142 QEAAKKSFEQHMQAGLYRKALKIAQ 166
                                       5667899****************96 PP

>> LPD22  Large polyvalent protein associated domain 22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.13   2.6e+02      16      47 ..      20      52 ..       6      70 .. 0.73
   2 !   10.8   0.2   0.00023      0.45      20      47 ..      92     120 ..      75     156 .. 0.81
   3 ?    3.5   0.0      0.04        80      20      39 ..     160     179 ..     158     183 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.13
                             LPD22 16 DeaAralrlaeelGlppdvvern.leaferaae 47
                                       ++ +a ++  +lGlp ++ ++    a+++  +
  gi|330506990|ref|YP_004383418.1| 20 GAYKEAAKIKSDLGLPNSMLQDAvKSAYDANMK 52
                                      5556788999999*9999999885566655544 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00023
                             LPD22  20 ralrlaeelGlppdvvern.leaferaae 47 
                                        a ++a+e+Glp d+v++  ++af++  +
  gi|330506990|ref|YP_004383418.1|  92 AAAEYAKEFGLPEDMVRQAaIQAFNKSMS 120
                                       5789**************98899988763 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.04
                             LPD22  20 ralrlaeelGlppdvvernl 39 
                                       +al++a+++ lp ++v++  
  gi|330506990|ref|YP_004383418.1| 160 KALKIAQKYDLPEEMVAEAE 179
                                       689*************9865 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.5   6.9e+03      24      33 ..      60      69 ..      59      70 .. 0.84
   2 !    7.5   0.0    0.0015         3      25      47 ..      95     117 ..      91     117 .. 0.91
   3 ?    0.6   0.0       0.2     4e+02      23      34 ..     127     138 ..     119     139 .. 0.87
   4 ?    2.8   0.0     0.042        84      26      42 ..     164     180 ..     162     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.5
                                      HHHHHHHTS- CS
                        Sigma70_r4 24 eEIgerlgiS 33
                                      +E++++++++
  gi|330506990|ref|YP_004383418.1| 60 AELAKQYDLP 69
                                      6999999987 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0015
                                       HHHHHHTS-HHHHHHHHHHHHHH CS
                        Sigma70_r4  25 EIgerlgiSrerVrqiekrAlrk 47 
                                       E ++++g+++  Vrq   +A++k
  gi|330506990|ref|YP_004383418.1|  95 EYAKEFGLPEDMVRQAAIQAFNK 117
                                       5699***************9987 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.2
                                       HHHHHHHHTS-H CS
                        Sigma70_r4  23 leEIgerlgiSr 34 
                                        +EI++ ++++r
  gi|330506990|ref|YP_004383418.1| 127 AAEIADDFDLPR 138
                                       68*******998 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.042
                                       HHHHHTS-HHHHHHHHH CS
                        Sigma70_r4  26 IgerlgiSrerVrqiek 42 
                                       I++++++++e V   ek
  gi|330506990|ref|YP_004383418.1| 164 IAQKYDLPEEMVAEAEK 180
                                       9*********9977666 PP

>> PHF12_MRG_bd  PHD finger protein 12 MRG binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.046        91      22      29 ..      64      71 ..      62      76 .. 0.88
   2 ?    2.6   0.0     0.056   1.1e+02      21      30 ..      97     106 ..      91     111 .. 0.85
   3 ?    0.9   0.0      0.19   3.8e+02      23      31 ..     133     141 ..     124     145 .. 0.85
   4 ?    2.0   0.0     0.089   1.8e+02      22      30 ..     166     174 ..     165     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.046
                      PHF12_MRG_bd 22 kQFeLPkE 29
                                      kQ++LP++
  gi|330506990|ref|YP_004383418.1| 64 KQYDLPSD 71
                                      9*****97 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.056
                      PHF12_MRG_bd  21 PkQFeLPkEl 30 
                                       +k+F LP ++
  gi|330506990|ref|YP_004383418.1|  97 AKEFGLPEDM 106
                                       69******99 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.19
                      PHF12_MRG_bd  23 QFeLPkEle 31 
                                        F+LP+ ++
  gi|330506990|ref|YP_004383418.1| 133 DFDLPRPMK 141
                                       6****9886 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.089
                      PHF12_MRG_bd  22 kQFeLPkEl 30 
                                       + ++LP E+
  gi|330506990|ref|YP_004383418.1| 166 QKYDLPEEM 174
                                       679*****9 PP

>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.42   8.3e+02       6      23 ..      30      47 ..      26      55 .. 0.66
   2 ?    7.9   0.0    0.0015       3.1       5      32 ..      97     125 ..      94     126 .. 0.90
   3 ?    0.6   0.0       0.3     6e+02       4      27 ..     130     154 ..     128     159 .. 0.66
   4 ?    0.3   0.1      0.37   7.3e+02       3      20 ..     163     180 ..     162     183 .] 0.72

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.42
                                      HHTT--HHHHHHHHHHHH CS
                             TFIIB  6 daleLpekVadaAkelak 23
                                      + l+Lp+   ++A++ a 
  gi|330506990|ref|YP_004383418.1| 30 SDLGLPNSMLQDAVKSAY 47
                                      679999977777766443 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0015
                                       HHHTT--H.HHHHHHHHHHHHHTTSTTTT CS
                             TFIIB   5 adaleLpe.kVadaAkelaklaleekvlk 32 
                                       a++ +Lpe +V++aA ++++++++++++k
  gi|330506990|ref|YP_004383418.1|  97 AKEFGLPEdMVRQAAIQAFNKSMSMGMVK 125
                                       788999999***************99986 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.3
                                       HHHHTT--H.HHHHHHHHHHHHHTT CS
                             TFIIB   4 fadaleLpe.kVadaAkelaklale 27 
                                       +ad  +Lp  + ++aAk+ +++ ++
  gi|330506990|ref|YP_004383418.1| 130 IADDFDLPRpMKQEAAKKSFEQHMQ 154
                                       7888899995556666776666554 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.37
                                       HHHHHTT--HHHHHHHHH CS
                             TFIIB   3 rfadaleLpekVadaAke 20 
                                       ++a++ +Lpe+   +A++
  gi|330506990|ref|YP_004383418.1| 163 KIAQKYDLPEEMVAEAEK 180
                                       589999****65555554 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 ?   -1.0   0.0         1   2.1e+03      62      66 ..      39      43 ..       7      65 .. 0.59
   2 ?   11.8   0.1   0.00011      0.22      21      93 ..      89     161 ..      87     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1
                                      HHHHH CS
                        P5CR_dimer 62 lrdkv 66
                                      l+d+v
  gi|330506990|ref|YP_004383418.1| 39 LQDAV 43
                                      22222 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHCHSHHHHHHHH--TTSHHHHHHHHHHHTTHHHHHHHHH CS
                        P5CR_dimer  21 liealadagvklGlsreeArelaaqtvaGaaklllesepaelrdkvtspgGtTiaglkeleegglraavieav 93 
                                       +  a a+ + + Gl++++ r+ a+q++  ++++   +++ae+ d +  p+ + +++ k+  e++++a +++  
  gi|330506990|ref|YP_004383418.1|  89 FYRAAAEYAKEFGLPEDMVRQAAIQAFNKSMSMGMVKNAAEIADDFDLPRPMKQEAAKKSFEQHMQAGLYRKA 161
                                       6789999*********************999996534499999999999998888777655555555544433 PP

>> 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 ?   11.0   0.5   8.2e-05      0.16     373     439 ..      23     111 ..       7     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.2e-05
                                       HHHHHHHHHHH...HHHHHHHHHHHHHHHTSCSSHH.............HHHHHHHHHHHHHHHHHHHHHHHCCCCC CS
                       CRISPR_Cse1 373 eeaveaaeeva...ralrsavkaaakellkkgkkka.............gdasaaraafwaalegpfrellaalgpd 433
                                       +ea++ +++++   + l  avk+a++++ kkg+ +                 +aa+++f+ +++++f++  a+ +++
  gi|330506990|ref|YP_004383418.1|  23 KEAAKIKSDLGlpnSMLQDAVKSAYDANMKKGDYSLaaelakqydlpsdHRLEAAQRSFYRKIDSEFYRAAAEYAKE 99 
                                       5555555555566677888888888888888876658888888899888999*********************9999 PP

                                       S.......HCTH CS
                       CRISPR_Cse1 434 dd......aaea 439
                                       +       +++a
  gi|330506990|ref|YP_004383418.1| 100 FGlpedmvRQAA 111
                                       887644443333 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.14   2.7e+02       6      17 ..      58      69 ..      56      70 .. 0.90
   2 ?    2.7   0.1     0.053   1.1e+02       5      17 ..      91     103 ..      88     104 .. 0.89
   3 ?   -0.9   0.0      0.71   1.4e+03       6      18 ..     126     138 ..     124     138 .. 0.86
   4 ?    5.2   0.1    0.0087        17       5      17 ..     159     171 ..     158     172 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.14
                             PHP_C  6 rArrfAeklglp 17
                                       A+++A++++lp
  gi|330506990|ref|YP_004383418.1| 58 LAAELAKQYDLP 69
                                      699********9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.053
                             PHP_C   5 rrArrfAeklglp 17 
                                       r A+++A+++glp
  gi|330506990|ref|YP_004383418.1|  91 RAAAEYAKEFGLP 103
                                       679*********9 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.71
                             PHP_C   6 rArrfAeklglpg 18 
                                        A+++A+ ++lp+
  gi|330506990|ref|YP_004383418.1| 126 NAAEIADDFDLPR 138
                                       5999******995 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.0087
                             PHP_C   5 rrArrfAeklglp 17 
                                       r+A+++A+k++lp
  gi|330506990|ref|YP_004383418.1| 159 RKALKIAQKYDLP 171
                                       89**********9 PP

>> EutK_C  Ethanolamine utilization protein EutK C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.013        26      20      43 ..      93     116 ..      91     121 .. 0.90
   2 ?    5.7   0.1    0.0076        15      13      49 ..     118     160 ..     110     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.013
                            EutK_C  20 aGevaahfaWPLekarqvLeqLfs 43 
                                       a e a  f+ P +  rq+  q f 
  gi|330506990|ref|YP_004383418.1|  93 AAEYAKEFGLPEDMVRQAAIQAFN 116
                                       8899**************999986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0076
                            EutK_C  13 svrqGmt..aGevaahfaWP..L..ekarqvLeqLfsdGaLrk 49 
                                       s+  Gm   a e+a  f  P  +  e a++ +eq + +G  rk
  gi|330506990|ref|YP_004383418.1| 118 SMSMGMVknAAEIADDFDLPrpMkqEAAKKSFEQHMQAGLYRK 160
                                       6666774338999999998744333779***********9999 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:                      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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 1476.00
//
Query:       gi|330506991|ref|YP_004383419.1|  [L=149]
Description: hypothetical protein MCON_0808 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-45  152.6   0.2    5.9e-45  152.4   0.2    1.0  1  DUF61     Protein of unknown function DUF61
  ------ inclusion threshold ------
      0.095   12.8   0.1        1.8    8.7   0.0    2.1  2  OapA      Opacity-associated protein A LysM-like domain


Domain annotation for each model (and alignments):
>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   0.2   6.6e-49   5.9e-45       2     127 .]      13     138 ..      12     138 .. 0.99

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 6.6e-49
                                       S---SHHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSSSE. CS
                             DUF61   2 rilakeiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpelges 78 
                                       +il k+i+++n+hlP++r +L+elL++ekp i++kd++++++dk+el+ ++e +p+ lw++l+LP+l+em+p+ g++
  gi|330506991|ref|YP_004383419.1|  13 NILVKTIQTMNQHLPNRRLNLTELLAMEKPGIRGKDNTFFIMDKSELKLISESVPRFLWSRLRLPMLIEMSPDFGSG 89 
                                       5899************************************************************************* PP

                                       .EEEES-HHHHHHHHHHT--...-SSEEEHH.HHHHHHHH-ST...TEE CS
                             DUF61  79 vylvrgkaevkvvskilgkereeedelviykpevrelrrklptatqliF 127
                                       +++++g+aev++vskilgke+  ++++viy p+vrelrrklpt+tq++F
  gi|330506991|ref|YP_004383419.1|  90 GARIQGEAEVEMVSKILGKEKPLNKQIVIYLPDVRELRRKLPTTTQYAF 138
                                       ************************************************9 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 ?    8.7   0.0   0.00021       1.8       4      39 ..      13      50 ..      11      61 .. 0.86
   2 ?    1.9   0.0     0.026   2.4e+02      25      41 ..      97     113 ..      95     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00021
                              OapA  4 eyqvkkgktLaqvFRdnnLplsdvnalak..veGadkp 39
                                      +  vk+ +t+ q   ++ L+l+++ a+ k  + G+d++
  gi|330506991|ref|YP_004383419.1| 13 NILVKTIQTMNQHLPNRRLNLTELLAMEKpgIRGKDNT 50
                                      6679999********************98778888886 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.026
                              OapA  25 sdvnalakveGadkplS 41 
                                       ++v  ++k+ G++kpl 
  gi|330506991|ref|YP_004383419.1|  97 AEVEMVSKILGKEKPLN 113
                                       57999**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1234.40
//
Query:       gi|330506992|ref|YP_004383420.1|  [L=392]
Description: metal dependent phosphohydrolase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-11   42.4   3.2    1.8e-10   41.1   3.2    1.7  1  HD        HD domain
  ------ inclusion threshold ------
      0.094   12.2   0.0        0.2   11.1   0.0    1.5  1  HDOD      HDOD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   3.2     2e-14   1.8e-10       1     121 [.      43     154 ..      43     155 .. 0.69

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2e-14
                                       HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgl 76 
                                       r+eHsl+ +++a  l ++lg+ e+dr l+ +aaLlHD+G+gp ++a e + +   +fl  e +++  + + +++   
  gi|330506992|ref|YP_004383420.1|  43 RFEHSLGAYHMAFHLTDHLGLdEDDRLLVGAAALLHDVGHGPLSHATESALA---PFLRTEHESVIEILKKGELG-- 114
                                       79******************************************98888843...33334444443333333333.. PP

                                       HHHHHHHHHHTTCCHH.HHHHHHH...HHHCCTSCHHHHHHHHHHHHHH CS
                                HD  77 dledvaklirehhesw.egkkrpr...glaerqlslearivklaDrlaa 121
                                             ++  +h  +  +++   +   g ++ q+ + +++v+++D+l +
  gi|330506992|ref|YP_004383420.1| 115 ------EVLDRHGLKPtDIQ---SfihGQDKGQIVSGEIDVDRMDYLIR 154
                                       ......22233322220222...13448888888999999999998865 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.2e-05       0.2      96     148 ..      44      98 ..      36     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHHHHHHHHHHTT-S-HHHHHH..HHHTTTHHHHHHHHHSHHHHHHHHH CS
                              HDOD  96 wehslavAlvarelaeelgledpeeafl..aGLLhdiGklvllsllpeeleelle 148
                                        ehsl    +a +l ++lgl++ +++++  a+LLhd+G   l ++ +  l+ +l+
  gi|330506992|ref|YP_004383420.1|  44 FEHSLGAYHMAFHLTDHLGLDEDDRLLVgaAALLHDVGHGPLSHATESALAPFLR 98 
                                       58999999**************9999874478********999999998887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 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:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2925.02
//
Query:       gi|330506993|ref|YP_004383421.1|  [L=484]
Description: major facilitator family transporter [Methanosaeta concilii GP6]
Scores for 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-49  167.4  52.3      4e-49  167.4  52.3    2.4  2  MFS_1       Major Facilitator Superfamily
    2.8e-05   23.2  29.1    0.00083   18.3   3.0    3.4  3  MFS_1_like  MFS_1 like family
     0.0035   15.8  19.0       0.02   13.3   4.2    2.2  2  MFS_3       Transmembrane secretion effector
  ------ inclusion threshold ------
       0.51   10.5   3.5        3.2    7.9   0.0    3.1  2  Popeye      Popeye protein conserved region


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.4  52.3   8.9e-53     4e-49       2     352 ..      32     425 ..      31     426 .. 0.92
   2 ?   -2.1   0.6      0.32   1.4e+03     150     167 ..     458     475 ..     429     481 .. 0.61

  Alignments for each domain:
  == domain 1  score: 167.4 bits;  conditional E-value: 8.9e-53
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       l +++++ l+ s++++alp +++e++ +s +e ++++t+y ++   + l++G +++r+G  r+++lgl+lf +++l+
  gi|330506993|ref|YP_004383421.1|  32 LTGVLMAVLDGSVVSIALP-TITEHFRVSIAESQMIMTAYLVTITSLLLIFGKVAERVGKARLFMLGLALFTSSSLA 107
                                       5688999999*********.******************************************************666 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       + + s++  +l+++r++q+ g++++f+++aa+i   fpk+e+gra+g++++++++G+ilgp lgg+++++lgW+++f
  gi|330506993|ref|YP_004383421.1| 108 CGI-STSLeMLVLCRIFQATGGAMMFSISAAIIFLAFPKSEQGRAMGYIGSTVAIGSILGPTLGGFIVDLLGWSYIF 183
                                       665.78888******************************************************************** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeee........................................... 188
                                       +i+ +++++ ++l + +l+ e++++k  +   ++                                           
  gi|330506993|ref|YP_004383421.1| 184 LINVPIGIVQLLLSARYLRIEETRSKSLEV--DWiggltlialivsmmtflgqlsygfaptppilllalifvlsffg 258
                                       ************999999999888888744..33568**************************************** PP

                             MFS_1 189 ....kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgaila 261
                                           ++++++pl++ +++++ + +++   i+++lff+++ ++++l p+y+  v+g++ + ++gl++ ++ ++++++a
  gi|330506993|ref|YP_004383421.1| 259 fiinESRQKSPLLD-LSIFRYRMFVL-PSISMILFFVANLMITVLGPFYFEGVRGYT-ASQVGLIFLIVPAITVFGA 332
                                       **************.77777777665.99999999999999****************.8****************** PP

                             MFS_1 262 llagrlsdrlgrrrrlllallllllaalglallavt..ssavllllvlvliGfglgfvfpsllalasdlappeeagt 336
                                       +l+g++ dr + r    l++++++l+ ++l +la++  ++   ll+ +v++G+g++f++++ ++ +++++p ++   
  gi|330506993|ref|YP_004383421.1| 333 PLTGAVYDRHQFRYLAALGMSIMALSMIALGFLAMStaNDIRQLLICFVFMGLGAAFFQSPNNTELMRSLPVSKINI 409
                                       *********77777777777777777777777777755444445557888*************************** PP

                             MFS_1 337 asglfntagslggalg 352
                                       as+++ t+++lg+alg
  gi|330506993|ref|YP_004383421.1| 410 ASSFTATIRNLGMALG 425
                                       **************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.32
                             MFS_1 150 Wravfyilaivsllafvl 167
                                        + v++i+++++++++++
  gi|330506993|ref|YP_004383421.1| 458 ISRVMMIAGGLCIISAIV 475
                                       333455555555555442 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6  11.9   9.9e-06     0.044     272     384 ..      72     184 ..      24     185 .. 0.85
   2 ?    1.3   0.1     0.027   1.2e+02      28      96 ..     208     270 ..     206     280 .. 0.79
   3 !   18.3   3.0   1.8e-07   0.00083      14      86 ..     297     366 ..     283     396 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.9e-06
                        MFS_1_like 272 aeip.lfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksle 347
                                        +i+ l+++  k+ e++G  +l +++l +++   l  +i +++ ++++  ++++   ++++++ +  +  ++pks +
  gi|330506993|ref|YP_004383421.1|  72 VTITsLLLIFGKVAERVGKARLFMLGLALFTSSSLACGISTSLEMLVLCRIFQATGGAMMFSISAAIIFLAFPKSEQ 148
                                       33321556678999*************************************************************** PP

                        MFS_1_like 348 atgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                       ++ +g + ++ + +G+ lG  +GG++ dl +  ++F 
  gi|330506993|ref|YP_004383421.1| 149 GRAMGYIGST-VAIGSILGPTLGGFIVDLLGWSYIFL 184
                                       *****77766.99**************9988888875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.027
                        MFS_1_like  28 skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesk 96 
                                       sk l++  ig +tli+ ++s++   ++g l+  f+ + ++++l+l++ + +f   ++i   + rq ++ 
  gi|330506993|ref|YP_004383421.1| 208 SKSLEVDWIGGLTLIALIVSMM--TFLGQLSYGFAPTPPILLLALIFVLSFFG--FIIN--ESRQKSPL 270
                                       7789999999999999999987..59999999999999999999999888887..4444..55555555 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.8e-07
                        MFS_1_like  14 algsllPYltiylk.skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfip 86 
                                       ++  l P+   y++  +g++as++g+i li+p+++++++p++g++ Dr + r  +++l++ + a+++++l f+ 
  gi|330506993|ref|YP_004383421.1| 297 MITVLGPF---YFEgVRGYTASQVGLIFLIVPAITVFGAPLTGAVYDRHQFRY-LAALGMSIMALSMIALGFLA 366
                                       45566666...777679*******************************98765.56666666666666666665 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   6.9   0.00015      0.66      49     178 ..      65     189 ..      30     220 .. 0.81
   2 !   13.3   4.2   4.5e-06      0.02      62     169 ..     332     439 ..     315     453 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00015
                             MFS_3  49 lvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWq 125
                                       ++  a  + i  l ++ G +a+ + + ++++ + +l  ++s+   +++ l++     l+   ++ + G a++     
  gi|330506993|ref|YP_004383421.1|  65 MIMTAYLVTITSLLLIFGKVAERVGKARLFMLGLALFTSSSLACGISTSLEM-----LVLCRIFQATGGAMMFSISA 136
                                       5556666666777788999999999999999999999999988888877765.....4556667889******999* PP

                             MFS_3 126 AsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnals 178
                                       A++    ++++   A+      + i    GP lgG +v ++G  + f +n+  
  gi|330506993|ref|YP_004383421.1| 137 AIIFLAFPKSEQGRAMGYIGSTVAIGSILGPTLGGFIVDLLGWSYIFLINVPI 189
                                       *************************************************9844 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.5e-06
                             MFS_3  62 silaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvp 138
                                       + l+Ga+ D ++ R +   +++++al+ + l  la+    +   ll+  +++g+Gaa+ +   +  +   ++ ++++
  gi|330506993|ref|YP_004383421.1| 332 APLTGAVYDRHQFRYLAALGMSIMALSMIALGFLAMSTANDIRQLLICFVFMGLGAAFFQSPNNTELMRSLPVSKIN 408
                                       5579******************************************************999999999999******* PP

                             MFS_3 139 aAvaLnsvginiaRsvGPAlgGvlvaavGaa 169
                                        A   ++   n+  + G  l+G+lv++  a 
  gi|330506993|ref|YP_004383421.1| 409 IASSFTATIRNLGMALGVSLSGLLVSLQMAQ 439
                                       *************************986555 PP

>> Popeye  Popeye protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00072       3.2       4      82 ..     130     205 ..     128     211 .. 0.90
   2 ?    1.0   1.2     0.099   4.4e+02      11      40 ..     358     390 ..     352     393 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00072
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Popeye   4 llfhlanillllaflapsgvlgllvlrsllvlGflllalwawlvvCaldiflWnlllvlinlaqllyllyklrpvkf 80 
                                       ++f ++ ++++laf + ++   + ++ s++++G +l  + + ++   +d + W+ ++++   + ++ ll   r  ++
  gi|330506993|ref|YP_004383421.1| 130 MMFSISAAIIFLAFPKSEQGRAMGYIGSTVAIGSILGPTLGGFI---VDLLGWSYIFLINVPIGIVQLLLSARYLRI 203
                                       689999*************9*****************9999986...7**********9999999999999888777 PP

                                       xx RF
                            Popeye  81 ek 82 
                                       e+
  gi|330506993|ref|YP_004383421.1| 204 EE 205
                                       65 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.099
                                       xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
                            Popeye  11 illllaflapsgv...lgllvlrsllvlGflll 40 
                                        +++l+fla s+     +ll+++++++lG  ++
  gi|330506993|ref|YP_004383421.1| 358 SMIALGFLAMSTAndiRQLLICFVFMGLGAAFF 390
                                       4556666666555444899999***99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.38
# Mc/sec: 3832.46
//
Query:       gi|330506994|ref|YP_004383422.1|  [L=129]
Description: hypothetical protein MCON_0812 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.061   13.4   0.6      0.069   13.2   0.6    1.1  1  DUF2120   Uncharacterized protein conserved in archaea (DUF21
       0.13   12.6   1.9        2.3    8.6   0.6    2.4  2  GIY-YIG   GIY-YIG catalytic domain


Domain annotation for each model (and alignments):
>> DUF2120  Uncharacterized protein conserved in archaea (DUF2120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   7.7e-06     0.069      42     121 ..       7      88 ..       1     105 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.7e-06
                           DUF2120  42 eskleellekldaeevdleseeakkliekldesireveeieeevdafglerlkeslEalglev..eYklgkkddlav 116
                                       +++l++l +    e + le+    +++e  d  i+ + +i e+ da+ + +++  lE+l + +    k+ +k+++++
  gi|330506994|ref|YP_004383422.1|   7 RKMLKDLKKMTGIEMMVLENLTLLDIVEARDLAIKLERSIIEKKDAIRVLKVQARLEDLSVYCvkMEKVVRKGKTKI 83 
                                       56677777777777777777899999********************************9866521457888888777 PP

                           DUF2120 117 fvvlw 121
                                       +   +
  gi|330506994|ref|YP_004383422.1|  84 YTYWY 88 
                                       75433 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.012     1e+02      49      73 ..      27      51 ..      10      56 .. 0.86
   2 ?    8.6   0.6   0.00026       2.3      11      23 ..      97     108 ..      82     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.012
                                      EEEEEE----HHHHHHHHHHHHHHT CS
                           GIY-YIG 49 liileifptksealelEkklikkyk 73
                                      l+ l i + ++ a++lE+++i+k+ 
  gi|330506994|ref|YP_004383422.1| 27 LTLLDIVEARDLAIKLERSIIEKKD 51
                                      5567888999999********9975 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00026
                                       TT--EEEEEESSH CS
                           GIY-YIG  11 enkliYvGstknl 23 
                                       + k++Y+Gst+nl
  gi|330506994|ref|YP_004383422.1|  97 V-KNVYIGSTNNL 108
                                       3.446*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 935.39
//
Query:       gi|330506995|ref|YP_004383423.1|  [L=202]
Description: hypothetical protein MCON_0813 [Methanosaeta concilii GP6]
Scores for complete 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   18.3   0.0     0.0037   17.6   0.0    1.3  1  DDE_Tnp_IS1  IS1 transposase
  ------ inclusion threshold ------
       0.14   12.4   0.9         14    6.0   0.1    2.9  4  FAF          Fantastic Four meristem regulator


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS1  IS1 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.1e-07    0.0037      86     116 ..     107     137 ..     101     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.1e-07
                       DDE_Tnp_IS1  86 tqriernnltlrtrlkrlarkslsfsksvel 116
                                       t  +er nlt r+   r+ rk+lsfsk  e+
  gi|330506995|ref|YP_004383423.1| 107 TAYVERTNLTSRQMNGRMVRKTLSFSKEEEM 137
                                       6789***********************9886 PP

>> FAF  Fantastic Four meristem regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.39   3.5e+03       3      11 ..      29      36 ..      29      51 .. 0.68
   2 ?    6.0   0.1    0.0016        14      14      28 ..      71      85 ..      54      92 .. 0.83
   3 ?    3.6   0.0    0.0088        79      14      44 ..     111     141 ..     100     142 .. 0.82
   4 ?   -3.4   0.0       1.3   1.2e+04       5      12 ..     154     161 ..     154     169 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.39
                               FAF  3 PPPlpslsg 11
                                      PP+++s  g
  gi|330506995|ref|YP_004383423.1| 29 PPAISSD-G 36
                                      9999986.4 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0016
                               FAF 14 pwvllrshredGRLv 28
                                       ++++ +hr++GRL+
  gi|330506995|ref|YP_004383423.1| 71 RCLQVTKHRSGGRLI 85
                                      689999*******98 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.0088
                               FAF  14 pwvllrshredGRLvleevkvpsrheylrae 44 
                                       +++ l s++ +GR+v +  + ++++e+l+a+
  gi|330506995|ref|YP_004383423.1| 111 ERTNLTSRQMNGRMVRKTLSFSKEEEMLKAS 141
                                       5667889999*****9999999999999885 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 1.3
                               FAF   5 Plpslsgr 12 
                                       Pl+sl+++
  gi|330506995|ref|YP_004383423.1| 154 PLKSLREE 161
                                       88888633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1505.47
//
Query:       gi|330506996|ref|YP_004383424.1|  [L=81]
Description: hypothetical protein MCON_0815 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 608.10
//
Query:       gi|330506997|ref|YP_004383425.1|  [L=206]
Description: hypothetical protein MCON_0817 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       423  (0.0235931); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1541.45
//
Query:       gi|330506998|ref|YP_004383426.1|  [L=270]
Description: hypothetical protein MCON_0818 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2004.09
//
Query:       gi|330506999|ref|YP_004383427.1|  [L=434]
Description: phenylacetate-coenzyme A ligase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-32  111.4   0.0    3.9e-32  110.4   0.0    1.5  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    4.9e-16   58.4   0.2    1.4e-15   56.8   0.0    1.8  2  AMP-binding      AMP-binding enzyme
    0.00011   21.3   0.0     0.0024   17.0   0.0    2.1  2  LuxE             Acyl-protein synthetase, LuxE


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   0.0   6.6e-36   3.9e-32       1      96 []     336     432 ..     336     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 6.6e-36
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvke.gfsdelkelealekkiakklksklgvsvkvel 76 
                                       G+nvfPsq+e+vl++i+ev+++++i+v+r+g lD ++v+vE++e gfsd++ +l +le+k++k+lk +l++ +kv+l
  gi|330506999|ref|YP_004383427.1| 336 GINVFPSQVESVLMRIPEVGDHWEIIVDRKGPLDMMTVRVELTEsGFSDKIGDLMKLENKVSKELKGVLNIAAKVDL 412
                                       99******************************************99******************************* PP

                                       E-TT-S---------EEE-S CS
                   AMP-binding_C_2  77 vepgtlprsegKakrviDkR 96 
                                       vepgt+prs gKakrv+D+R
  gi|330506999|ref|YP_004383427.1| 413 VEPGTIPRSMGKAKRVTDNR 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 !   56.8   0.0   2.4e-19   1.4e-15     155     370 ..      80     287 ..      13     292 .. 0.73
   2 ?   -1.5   0.0      0.12     7e+02     410     423 .]     322     335 ..     303     335 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 2.4e-19
                                       S-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.HHHCSCCTTT-EE.EESS-TTSCHHHHHHHHHHHHTT- CS
                       AMP-binding 155 elkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk.letrfklkeddvv.lsilplahifglilelllallsGa 229
                                       ++ +++++    +SGTTGkP  V ++ + + +   sl+   t  +l++ddvv + +    +  gl    ++a   Ga
  gi|330506999|ref|YP_004383427.1|  80 SAPKNQVVRYHVSSGTTGKPTVVGYTRGDIETWSESLArALTSLGLSRDDVVqVGYGYGLFTGGL-GLHYGAERMGA 155
                                       4567788888889***************9955556665423346777899885666666666676.99999999999 PP

                                       EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHH CS
                       AMP-binding 230 tvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffr 304
                                       +v  + + ++ +     +el+++l+ t ia++P+ + +++e +++    ++ ++   l++ ++g+ep s e+ ++++
  gi|330506999|ref|YP_004383427.1| 156 AVLPVGTGNTeR----QIELMQDLGTTAIACTPSYFLHIMEvAEKMG--VSIRNDTQLKVGIFGAEPWSLETRKRIE 226
                                       888877776633....48***********************775555..33333345******************** PP

                                       HHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEE CS
                       AMP-binding 305 alfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvr 370
                                       a +g + +++YG +E +g ++  +++ + + +   G  +     ++vD++tgepv++ge+Gel++ 
  gi|330506999|ref|YP_004383427.1| 227 ANTGINAYDIYGTSEISGPLF-TECQAK-NGIHVWGDMF---LTEVVDPDTGEPVAEGEQGELVFT 287
                                       *******************98.554344.4555455554...569******************975 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.12
                                       EEEEEECCCEEEET CS
                       AMP-binding 410 leivgRkkdliklr 423
                                       ++i+gR++d++++r
  gi|330506999|ref|YP_004383427.1| 322 MRIMGRTDDMLIIR 335
                                       68********9985 PP

>> LuxE  Acyl-protein synthetase, LuxE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.014        84      37     128 ..      30     124 ..      14     133 .. 0.72
   2 !   17.0   0.0     4e-07    0.0024     267     359 ..     234     329 ..     224     340 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.014
                              LuxE  37 vnhykhneeyrkycqknkvddlvtegevddiPviPv....svfkaigtkllsvsedeikaklqssatsGlkstvlld 109
                                       +  y h+  yr+  +   + +  ++  ++d+  +P     ++     t + s+ ++++  +  ss+t+G ++ v   
  gi|330506999|ref|YP_004383427.1|  30 RYVYDHSAFYRQRFKEAGITPEDIK-TLADVAKLPFtkkaDLRDNYPTGMFSAPKNQVVRYHVSSGTTGKPTVVGYT 105
                                       5567777777776666666555444.456666655411113444556778899999999999*************** PP

                              LuxE 110 klsierllravarvmkevl 128
                                       +  ie    ++ar++  ++
  gi|330506999|ref|YP_004383427.1| 106 RGDIETWSESLARALTSLG 124
                                       *******999999987765 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 4e-07
                              LuxE 267 vdiygfteqvelntpdfkdelkrkrvysdviir...deetlkvvgdGkvGlleyvdalstsyPafvvltddlGviee 340
                                        diyg +e  +  +++++++ + ++v  d+++    d++t ++v++G  G l +      + P       dl v+++
  gi|330506999|ref|YP_004383427.1| 234 YDIYGTSEISGPLFTECQAK-NGIHVWGDMFLTevvDPDTGEPVAEGEQGELVFTTLHKFALPLIRYRIGDLSVMSN 309
                                       69999999888888888775.5799**999988888***************************999999******** PP

                              LuxE 341 slcegqkaGkl.vkvlrrvk 359
                                         ce++++  + +++++r++
  gi|330506999|ref|YP_004383427.1| 310 EVCECGRTHPRiMRIMGRTD 329
                                       ******98755268999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3257.45
//
Query:       gi|330507000|ref|YP_004383428.1|  [L=144]
Description: amino acid-binding ACT domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-15   55.4   0.1    6.2e-09   35.5   0.0    2.3  2  ACT       ACT domain
    1.4e-05   25.5   0.5      0.019   15.5   0.0    2.3  2  ACT_4     ACT domain
    0.00056   19.7   0.1      0.015   15.1   0.0    2.7  3  ACT_7     ACT domain
  ------ inclusion threshold ------
      0.037   14.0   0.0       0.17   11.9   0.0    2.0  2  ACT_6     ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   1.4e-12   6.2e-09       3      60 ..       7      61 ..       5      62 .. 0.86
   2 !   17.8   0.0   4.8e-07    0.0021       3      54 ..      73     120 ..      72     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.4e-12
                                      EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHH CS
                               ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevle 60
                                      ++++v++rPG  a+v+ +l+d+g+Ni+ +++++ +d     v+ +++ d+e   +vl+
  gi|330507000|ref|YP_004383428.1|  7 VSLFVENRPGRTAKVAKTLSDAGVNIRALTIAEAGD---FGVIRMVLDDAEKGYKVLK 61
                                      7889********************************...7777777777776666665 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 4.8e-07
                                       EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHH CS
                               ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeed 54 
                                       l v+++D+PG L ++ ++l+ + +N+d +  + +          +++   +d
  gi|330507000|ref|YP_004383428.1|  73 LAVEMKDQPGGLYEIVNTLGGNLVNVDYAYAFVTAK----AQRAMLILRVDD 120
                                       6699**************************999955....333333333333 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.3e-06     0.019       9      52 ..       7      48 ..       5      51 .. 0.84
   2 !    8.3   0.1   0.00079       3.5       9      65 ..      73     127 ..      63     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.3e-06
                             ACT_4  9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeiki 52
                                      +++ +e+r+g  a++++++s++++ni+++++ +  +  +  i++
  gi|330507000|ref|YP_004383428.1|  7 VSLFVENRPGRTAKVAKTLSDAGVNIRALTIAE--AGDFGVIRM 48
                                      67889*************************999..444666665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00079
                             ACT_4   9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrv 65 
                                       l ve++d++g L +i++++  + +n+    a  +   +  +  + + V d+++ ++v
  gi|330507000|ref|YP_004383428.1|  73 LAVEMKDQPGGLYEIVNTLGGNLVNVDYAYAFVTA--KAQRAMLILRVDDIAKARKV 127
                                       789***********************988887754..45566777777777766655 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.3e-06     0.015      20      45 ..      14      40 ..       6      62 .. 0.84
   2 ?    1.7   0.0     0.049   2.2e+02      19      63 ..      79     128 ..      66     130 .. 0.63
   3 ?   -1.3   0.0      0.44     2e+03      25      38 ..     122     135 ..     120     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-06
                                      S--HHHHHHHHHHTTT---EEEE.-SS CS
                             ACT_7 20 vtGivaklaspLaeagIsifqiS.tyr 45
                                       +G++ak+a+ L++ag++i +++  + 
  gi|330507000|ref|YP_004383428.1| 14 RPGRTAKVAKTLSDAGVNIRALTiAEA 40
                                      69*****************88875555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.049
                                       SS--HHHHHHHHHHTTT---.....EEEE-SS-EEEEEEGGGHHHHHHHH CS
                             ACT_7  19 dvtGivaklaspLaeagIsi.....fqiStyrtdyiLVpeedlekAveaL 63 
                                       d++G + ++++ L  + +++     f+++ ++  +++ + +d+ kA ++L
  gi|330507000|ref|YP_004383428.1|  79 DQPGGLYEIVNTLGGNLVNVdyayaFVTAKAQRAMLILRVDDIAKARKVL 128
                                       57888888888888888887333334444555555555555555555555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.44
                                       HHHHHHHHTTT--- CS
                             ACT_7  25 aklaspLaeagIsi 38 
                                       ak  ++L++ +I i
  gi|330507000|ref|YP_004383428.1| 122 AKARKVLSDKNIKI 135
                                       67778999999987 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.7e-05      0.17      10      40 ..      12      42 ..       6      62 .. 0.82
   2 ?   -1.5   0.0      0.57   2.6e+03      10      30 ..      78      98 ..      77      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.7e-05
                             ACT_6 10 pdrpGltasLtsvlaefgvnilDieqavihg 40
                                      ++rpG ta+++++l++ gvni  +  a  ++
  gi|330507000|ref|YP_004383428.1| 12 ENRPGRTAKVAKTLSDAGVNIRALTIAEAGD 42
                                      79*******************8877776666 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.57
                             ACT_6 10 pdrpGltasLtsvlaefgvni 30
                                      +d+pG + ++  +l  + vn+
  gi|330507000|ref|YP_004383428.1| 78 KDQPGGLYEIVNTLGGNLVNV 98
                                      599999999999987777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1079.55
//
Query:       gi|330507001|ref|YP_004383429.1|  [L=180]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1410.85
//
Query:       gi|330507002|ref|YP_004383430.1|  [L=202]
Description: hypothetical protein MCON_0822 [Methanosaeta concilii GP6]
Scores for complete 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   18.3   0.0     0.0037   17.6   0.0    1.3  1  DDE_Tnp_IS1  IS1 transposase
  ------ inclusion threshold ------
       0.14   12.4   0.9         14    6.0   0.1    2.9  4  FAF          Fantastic Four meristem regulator


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS1  IS1 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.1e-07    0.0037      86     116 ..     107     137 ..     101     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.1e-07
                       DDE_Tnp_IS1  86 tqriernnltlrtrlkrlarkslsfsksvel 116
                                       t  +er nlt r+   r+ rk+lsfsk  e+
  gi|330507002|ref|YP_004383430.1| 107 TAYVERTNLTSRQMNGRMVRKTLSFSKEEEM 137
                                       6789***********************9886 PP

>> FAF  Fantastic Four meristem regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.39   3.5e+03       3      11 ..      29      36 ..      29      51 .. 0.68
   2 ?    6.0   0.1    0.0016        14      14      28 ..      71      85 ..      54      92 .. 0.83
   3 ?    3.6   0.0    0.0088        79      14      44 ..     111     141 ..     100     142 .. 0.82
   4 ?   -3.4   0.0       1.3   1.2e+04       5      12 ..     154     161 ..     154     169 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.39
                               FAF  3 PPPlpslsg 11
                                      PP+++s  g
  gi|330507002|ref|YP_004383430.1| 29 PPAISSD-G 36
                                      9999986.4 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0016
                               FAF 14 pwvllrshredGRLv 28
                                       ++++ +hr++GRL+
  gi|330507002|ref|YP_004383430.1| 71 RCLQVTKHRSGGRLI 85
                                      689999*******98 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.0088
                               FAF  14 pwvllrshredGRLvleevkvpsrheylrae 44 
                                       +++ l s++ +GR+v +  + ++++e+l+a+
  gi|330507002|ref|YP_004383430.1| 111 ERTNLTSRQMNGRMVRKTLSFSKEEEMLKAS 141
                                       5667889999*****9999999999999885 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 1.3
                               FAF   5 Plpslsgr 12 
                                       Pl+sl+++
  gi|330507002|ref|YP_004383430.1| 154 PLKSLREE 161
                                       88888633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1462.33
//
Query:       gi|330507003|ref|YP_004383431.1|  [L=155]
Description: hypothetical protein MCON_0823 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.021   14.5   1.0      0.036   13.8   1.0    1.4  1  Zn_Tnp_IS1  InsA N-terminal domain
      0.032   14.0   0.1       0.05   13.4   0.1    1.4  1  HTH_23      Homeodomain-like domain
      0.036   14.5   0.1      0.069   13.6   0.1    1.5  1  LtuA        Late transcription unit A
       0.12   12.9   0.2       0.16   12.4   0.2    1.2  1  HTH_40      Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.0   8.1e-06     0.036      15      34 ..      28      47 ..      17      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.1e-06
                        Zn_Tnp_IS1 15 dVyRhGkstagHeRfrCrdC 34
                                      +++R G+  +g +R +C+ C
  gi|330507003|ref|YP_004383431.1| 28 NIVRYGRTSKGTQRLKCKTC 47
                                      58****************** PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.1e-05      0.05       6      41 ..      68     103 ..      63     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                            HTH_23   6 eRlrillllaeGlsvreIAreLgvsrrTvyrwlkry 41 
                                       e l+ l +lae+ s ++I r  g+ + T+  wl++ 
  gi|330507003|ref|YP_004383431.1|  68 EILECLAMLAERNSLAAIHRVKGIKEETIVDWLRKA 103
                                       5578899*************************9984 PP

>> LtuA  Late transcription unit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.5e-05     0.069      19      43 ..      34      60 ..      26      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                              LtuA 19 aakkGeqvmksrss..vWvGarGaiFY 43
                                       + kG q +k +    v+vG +G+iFY
  gi|330507003|ref|YP_004383431.1| 34 RTSKGTQRLKCKTCgrVFVGNKGTIFY 60
                                      5889***999876434*********** PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   3.6e-05      0.16       5      45 ..      72     112 ..      69     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.6e-05
                            HTH_40   5 tlelleeglsieeIAkerglkesTIegHLaelieegeeidl 45 
                                        l +l e  s+++I +  g+ke TI++ L ++  + eei++
  gi|330507003|ref|YP_004383431.1|  72 CLAMLAERNSLAAIHRVKGIKEETIVDWLRKASAHVEEIEA 112
                                       5789****************************999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1202.08
//
Query:       gi|330507004|ref|YP_004383432.1|  [L=98]
Description: hypothetical protein MCON_0825 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 814.02
//
Query:       gi|330507005|ref|YP_004383433.1|  [L=77]
Description: hypothetical protein MCON_0826 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   0.3      0.018   14.9   0.3    1.0  1  DUF3731       DNA-K related protein
      0.028   14.3   3.0       0.03   14.2   3.0    1.3  1  SprT-like     SprT-like family
      0.077   13.7   0.2       0.09   13.5   0.2    1.2  1  RNA_polI_A14  Yeast RNA polymerase I subunit RPA14


Domain annotation for each model (and alignments):
>> DUF3731  DNA-K related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.3     3e-06     0.018     152     212 ..      10      72 ..       3      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3e-06
                           DUF3731 152 sahkvvppeeveawlekllaldwkkkekaafaavqlarltgdrardlsee..lrekvlekLka 212
                                       s+ + ++++eve++le+ +++++ ++++    a+q+ar+++  a+d++++  l ++ +e Lk+
  gi|330507005|ref|YP_004383433.1|  10 SKGHDLNRHEVEHLLEHWIEHNQSHSTSFRERAAQVARVSELAAQDINRAaeLMDECTEMLKK 72 
                                       555668899**************************************9751156777777765 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   3.0   5.1e-06      0.03      70     104 ..      18      50 ..       4      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-06
                         SprT-like  70 HElcHlalfvisgvrnnpHGaeFkawaakvekala 104
                                       HE+ Hl+ + i++  n+ H  +F++ aa+v ++++
  gi|330507005|ref|YP_004383433.1|  18 HEVEHLLEHWIEH--NQSHSTSFRERAAQVARVSE 50 
                                       *************..***************88765 PP

>> RNA_polI_A14  Yeast RNA polymerase I subunit RPA14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   1.5e-05      0.09      10      56 ..      11      58 ..       6      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                      RNA_polI_A14 10 s.qhvskeevekfLteFIdekEssaselageesstkeaatglsvdtel 56
                                      + +++++ eve++L+++I+++ s ++++  ++++  ++++ ++ d + 
  gi|330507005|ref|YP_004383433.1| 11 KgHDLNRHEVEHLLEHWIEHNQSHSTSFRERAAQVARVSELAAQDINR 58
                                      347899****************98888888887776665444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1536  (0.0856713); expected 358.6 (0.02)
Passed bias filter:                      773  (0.0431145); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 560.02
//
Query:       gi|330507006|ref|YP_004383434.1|  [L=302]
Description: hypothetical protein MCON_0827 [Methanosaeta concilii GP6]
Scores for complete 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-45  153.3   0.0    8.7e-45  153.0   0.0    1.0  1  DUF2156   Uncharacterised conserved protein (DUF2156)


Domain annotation for each model (and alignments):
>> DUF2156  Uncharacterised conserved protein (DUF2156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.0   0.0   4.9e-49   8.7e-45       2     295 ..      23     291 ..      22     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 4.9e-49
                                       CCCCTSSGGGGHHHHHHCCHCCEEE.ECCTTEEEEEEEECTCEEEECS-EE.CCGHHHHHHHHHHHHHHCTSEEEEE CS
                           DUF2156   2 allersgsedslsnlalwrdksyyf.spsgdalvayrvkggvalalgdPvGdpeawpeaieeflelaaehgwrpafy 77 
                                       + +++++s+++++n+++w+ ++ y+ ++++d++++   +  + + + +P+G   + p++++e+l+la + + +  f+
  gi|330507006|ref|YP_004383434.1|  23 RRFPQRHSDNTFTNMVCWNYYANYRyAIVQDCVLLS-STIAGKTRYRPPIG--PRNPDLLHEVLALALKSDETRPFV 96 
                                       56788999*****************88888888877.7777889*******..99********************** PP

                                       EE-HHHHHHHHHCT....EEEECCCEEEEEEHHHH.HTTSGGGHHHHHHHHHHHHCTECEEEEEGGGH-HHHHHHHH CS
                           DUF2156  78 gvseelaellaelg....lsalrlgeeavvdledf.tLsGkkfrnvRnainraeraGytveverisdlspellaelk 149
                                        +++e++e++  ++    +++ r+++++v+ + d+  L Gk + ++R+++n++ ++ ++  ve+     +++++e+ 
  gi|330507006|ref|YP_004383434.1|  97 VLDQETLEWISGIYpelqFQPERMYFDYVYLANDLaHLPGKGYSTIRRQLNQFMKT-CSPLVEEL---GTDNIEEIN 169
                                       **********99999999**************************************.99999888...8******** PP

                                       HHHHHHHHHTT.......CHHHHCCCHHHHCHHHHTSEEEEEEE.TTEEEEEEEEEEECTTTEEEEEEEEE-TT.ST CS
                           DUF2156 150 eiseeWlkqke.......atEkgfslglfdelddldlrglvvrdeegrivAftsfeplngkdglsldlmRrdpdapn 219
                                       ++ e+W+++k+       a Ek +++ ++ + ++l+l g+++r  eg+i A+ +fe  n +d++ +++++  pd ++
  gi|330507006|ref|YP_004383434.1| 170 DFVEQWCEWKDcdsnpdlASEKDALCFALAHYRELELSGIAIRS-EGKIGAISLFEGQN-EDTALVHFEKGLPD-CK 243
                                       *********84457899***************************.***********999.8*************.** PP

                                       THHHHHHHHHHHHCHHTT-SEEEEEEE...............HHHHHHHHHHHHHTTTCHHHHHHHCT--CE.EEEE CS
                           DUF2156 220 GlmefliaelaeelkeegveyvsLgfaplaglgeregagllerllrllleflerdygfegLrrfKlkyqPew.eprY 295
                                       G++ +++ae+a+ l  ++++y++                            +e+d+g+eg r++K++y+P++ +++ 
  gi|330507006|ref|YP_004383434.1| 244 GIYRAINAETAKILA-KKYTYIN----------------------------RESDMGVEGIREAKMRYHPHHmVQVH 291
                                       **************9.99*****............................********************977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2315.00
//
Query:       gi|330507007|ref|YP_004383435.1|  [L=151]
Description: GNAT family acetyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (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   47.8   0.0    1.6e-12   47.5   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.9e-07   31.4   0.0      3e-07   30.8   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    5.5e-07   29.8   0.1    6.5e-07   29.6   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00021   21.2   0.0    0.00052   19.9   0.0    1.6  2  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   3.5e-16   1.6e-12      13     109 ..      36     136 ..      21     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 3.5e-16
                   Acetyltransf_10  13 fkefispealrerieegealllvaeeg..gkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekd 83 
                                       ++e+++p +l++ i +g+ l+ va +g  g+ vG++++ +dg    +i+ l+V  +++  G+g++++e+++e ++ +
  gi|330507007|ref|YP_004383435.1|  36 WREYMDPSHLNDLI-QGSFLFAVAVDGrsGRAVGMGRViSDGVsdgYIQDLVVLADWQNMGLGRMIIEKLIEGCRAR 111
                                       499***********.999999999988779********67666999******************************* PP

                   Acetyltransf_10  84 gikleltvnaspyavpfYeklGFkav 109
                                       +i+  + + a p  ++fY ++GF+++
  gi|330507007|ref|YP_004383435.1| 112 KIA-WVGLIAEPGKEDFYDSIGFRKM 136
                                       999.*******************986 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   6.7e-11     3e-07       5      76 .]      55     135 ..      49     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 6.7e-11
                                       EEEEEET..TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHHTTSEEEEE.EEEE...THHHHHHHHHHT CS
                    Acetyltransf_7   5 vfVaedd..gkivGfialslld...aeitrlaVdpeyrgkGiGraLleaaekgiile.qlel...naekaikfYekl 72 
                                       + Va d+  g+ vG+ ++  ++   ++i  l+V+ ++++ G+Gr ++e  ++g++    +++   +++  ++fY + 
  gi|330507007|ref|YP_004383435.1|  55 FAVAVDGrsGRAVGMGRVISDGvsdGYIQDLVVLADWQNMGLGRMIIEKLIEGCRARkIAWVgliAEPGKEDFYDSI 131
                                       456666677888999988888799899999******************645788733334444454446788***** PP

                                       TEEE CS
                    Acetyltransf_7  73 GFee 76 
                                       GF++
  gi|330507007|ref|YP_004383435.1| 132 GFRK 135
                                       **85 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   1.5e-10   6.5e-07      31     117 .]      50     133 ..      13     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.5e-10
                                       TTCEEEEEEET...TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETT CS
                    Acetyltransf_1  31 eaegllvaeed...geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveed 104
                                       + ++l+++  d   g+ +G+ ++  +       +yi +l+V  +++++GlG++ +e+l+e +r +   ki +     
  gi|330507007|ref|YP_004383435.1|  50 QGSFLFAVAVDgrsGRAVGMGRVISDGV---SDGYIQDLVVLADWQNMGLGRMIIEKLIEGCRAR---KIAWVGLIA 120
                                       3335666555546688*****9999999...99***************************99988...443322233 PP

                                       EHHHHHHHHHTTE CS
                    Acetyltransf_1 105 ndaairlYeklGF 117
                                         +   +Y   GF
  gi|330507007|ref|YP_004383435.1| 121 EPGKEDFYDSIGF 133
                                       4445666654665 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.74   3.3e+03      20      42 ..      50      73 ..      49      79 .. 0.66
   2 !   19.9   0.0   1.2e-07   0.00052      21      80 ..      79     136 ..      69     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.74
                                      TTSSEEEEEE-GGG.-SSSHHHHH CS
                              FR47 20 dggelgalqvlpeh.rrrGlgsrl 42
                                      +g++l+a+ v+    r  G+g+++
  gi|330507007|ref|YP_004383435.1| 50 QGSFLFAVAVDGRSgRAVGMGRVI 73
                                      567888988875431556777765 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.2e-07
                                       TSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  21 ggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                       +g++  l vl + +++Glg+ ++++l+++ ++r +  + ++++  +  + +y ++Gf+k+
  gi|330507007|ref|YP_004383435.1|  79 DGYIQDLVVLADWQNMGLGRMIIEKLIEGCRARKIAWVGLIAEPGK--EDFYDSIGFRKM 136
                                       599*****************************99876666655544..68*******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1189.27
//
Query:       gi|330507008|ref|YP_004383436.1|  [L=758]
Description: AAA family ATPase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-95  316.8   0.0    4.9e-47  159.7   0.0    2.4  2  AAA              ATPase family associated with various cellul
    2.5e-27   94.8   0.0    3.1e-26   91.4   0.2    2.6  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
      1e-24   86.1   2.9    4.8e-13   48.7   0.6    2.9  2  AAA_lid_3        AAA+ lid domain
    1.3e-15   58.2   0.4    3.7e-07   30.7   0.0    3.7  2  AAA_16           AAA ATPase domain
    1.8e-13   51.0   0.0    6.3e-07   29.7   0.0    2.5  2  AAA_2            AAA domain (Cdc48 subfamily)
    3.1e-13   49.3   0.3    7.3e-13   48.1   0.3    1.7  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    4.9e-13   49.1   0.0    3.8e-05   23.5   0.0    2.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.2e-12   47.4   0.2    0.00024   21.4   0.0    4.1  3  AAA_22           AAA domain
    5.1e-11   42.7   1.4    0.00027   20.9   0.0    4.0  2  AAA_5            AAA domain (dynein-related subfamily)
    7.3e-11   41.9   0.0    0.00043   19.6   0.0    2.8  2  TIP49            TIP49 P-loop domain
    8.2e-11   42.2   0.0    6.6e-05   23.1   0.0    2.6  2  AAA_33           AAA domain
    9.5e-11   41.9   0.0    2.9e-05   24.1   0.0    2.4  2  AAA_14           AAA domain
    1.6e-08   34.5   0.0     0.0054   16.5   0.0    3.1  3  IstB_IS21        IstB-like ATP binding protein
    4.3e-08   32.8   0.7     0.0061   16.0   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    5.6e-08   33.4   0.0      0.011   16.2   0.0    2.7  2  AAA_18           AAA domain
    1.3e-07   31.5   0.1      0.022   14.5   0.0    3.1  2  Sigma54_activat  Sigma-54 interaction domain
    1.3e-07   31.6   0.0     0.0092   15.7   0.0    2.7  2  AAA_24           AAA domain
    7.1e-07   29.3   0.2       0.11   12.3   0.0    3.8  4  NACHT            NACHT domain
    8.4e-07   29.4   0.0      0.062   13.7   0.0    2.5  2  RNA_helicase     RNA helicase
    1.2e-06   28.1   0.0      0.033   13.7   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
    1.9e-06   28.2   0.0      0.076   13.3   0.0    2.6  2  AAA_28           AAA domain
    3.2e-06   27.7   0.0      0.099   13.2   0.0    2.5  2  ABC_tran         ABC transporter
    3.4e-06   26.5   0.1      0.045   13.0   0.0    2.5  2  Zeta_toxin       Zeta toxin
      6e-06   26.3   0.0       0.19   11.7   0.0    2.8  3  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    8.8e-06   25.1   0.0      0.039   13.1   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    1.1e-05   25.5   0.1       0.71    9.7   0.0    3.7  3  ATPase_2         ATPase domain predominantly from Archaea
    1.2e-05   25.0   5.0       0.21   11.2   0.3    4.0  3  AAA_25           AAA domain
    2.3e-05   24.2   0.0       0.19   11.4   0.0    2.6  2  AAA_30           AAA domain
    2.6e-05   23.6   0.0       0.19   10.9   0.0    2.6  2  NB-ARC           NB-ARC domain
    2.6e-05   23.5   0.0       0.19   10.8   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    5.5e-05   23.0   0.0       0.47   10.3   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    0.00013   21.9   0.0       0.29   10.9   0.0    2.3  2  AAA_11           AAA domain
    0.00021   20.7   0.3       0.72    9.1   0.0    2.7  2  ATPase           KaiC
    0.00029   20.8   0.1        1.4    8.7   0.0    3.2  2  Bac_DnaA         Bacterial dnaA  protein
     0.0003   20.3   0.1       0.97    8.8   0.0    2.5  2  PhoH             PhoH-like protein
    0.00045   19.6   0.0       0.38   10.0   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00099   18.8   0.1         11    5.7   0.0    4.0  4  Guanylate_kin    Guanylate kinase
      0.001   19.4   0.0          2    8.7   0.0    2.6  2  AAA_19           AAA domain
     0.0011   18.5   0.0        2.7    7.4   0.0    3.0  2  TniB             Bacterial TniB protein
      0.002   18.3   0.0        2.6    8.1   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0022   18.4   0.0          2    8.8   0.0    2.7  2  AAA_17           AAA domain
     0.0026   16.7   0.0        1.1    8.0   0.0    2.4  2  AFG1_ATPase      AFG1-like ATPase
     0.0031   17.5   0.0          1    9.3   0.0    2.3  2  ResIII           Type III restriction enzyme, res subunit
     0.0032   17.4   0.0        1.9    8.3   0.0    2.7  2  NTPase_1         NTPase
     0.0064   16.4   0.0        3.5    7.5   0.0    2.5  2  CPT              Chloramphenicol phosphotransferase-like prot
     0.0097   15.9   0.1        3.6    7.7   0.0    2.7  2  Vps4_C           Vps4 C terminal oligomerisation domain
  ------ inclusion threshold ------
       0.01   16.1   0.3        2.8    8.2   0.0    2.3  2  Hydin_ADK        Hydin Adenylate kinase-like domain
       0.01   14.9   0.0        1.3    8.1   0.0    2.5  2  T2SSE            Type II/IV secretion system protein
      0.012   15.3   0.1        5.9    6.6   0.0    2.5  2  Cytidylate_kin   Cytidylate kinase
      0.013   15.3   0.0        5.3    6.7   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.019   14.2   0.0        1.4    8.1   0.0    2.7  3  KAP_NTPase       KAP family P-loop domain
      0.032   14.0   0.0         11    5.8   0.0    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.033   13.9   0.0         11    5.9   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
      0.042   14.0   0.0         13    5.9   0.0    3.0  3  SKI              Shikimate kinase
      0.059   12.5   0.0          3    6.9   0.0    2.4  2  MCM              MCM P-loop domain
      0.064   12.8   0.1         15    5.1   0.0    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.073   13.2   0.0        8.8    6.4   0.0    2.4  2  Torsin           Torsin
       0.18   11.2   0.1         13    5.1   0.0    2.4  2  IPT              Isopentenyl transferase
       0.18   12.3   0.0         15    6.0   0.0    2.4  2  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.7   0.0   1.6e-49   4.9e-47       1     131 [.     246     375 ..     246     376 .. 0.97
   2 !  154.9   0.0   4.6e-48   1.4e-45       1     131 [.     519     650 ..     519     651 .. 0.96

  Alignments for each domain:
  == domain 1  score: 159.7 bits;  conditional E-value: 1.6e-49
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+GppGtGKT+lakava+e++++f++i+g+e++sky gesek +r+lf+ea+++  p i+f+DE+d++a++r + 
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESDAYFISINGPEIMSKYYGESEKALRDLFEEAEKNT-PAIIFLDELDSIAPKRGDV 321
                                       79***************************************************9997.****************999 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLl+ +dg+k++++ vivig tnrp+ ld al+r gRfdr+ie++
  gi|330507008|ref|YP_004383436.1| 322 TGEVERRVVAQLLSLMDGLKERKN-VIVIGSTNRPEALDMALRRpGRFDREIELG 375
                                       *********************855.**************************9975 PP

  == domain 2  score: 154.9 bits;  conditional E-value: 4.6e-48
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..T CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..s 75 
                                       +llyGppGtGKT+lakava+e++++f++++gs llsk+ gesek+++e+f++a++ a psi+f+DE+dal++ r   
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEANFITVKGSALLSKWYGESEKRVEEIFRKARQVA-PSIIFLDELDALVPVRggA 594
                                       69******************************************************9.****************877 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        +e  ++er+vnqLl+e+dg+++ ++ v+vigatnrpd +dpallr gRfd+ i ++
  gi|330507008|ref|YP_004383436.1| 595 MGEPHVTERIVNQLLSEIDGLEELHG-VVVIGATNRPDIIDPALLRpGRFDELILVP 650
                                       7899*******************755.*************************99876 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.2     1e-28   3.1e-26       1      84 [.       8      91 ..       8      92 .. 0.98
   2 ?   -0.6   0.0       5.1   1.6e+03      20      64 ..     231     276 ..     231     278 .. 0.67

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 1e-28
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVt 79
                                      rL+++ea+q dvg+givr+  e me++g++p dvvei g+r T+a++++a+++d+g + Irmdg++R+nag siG+ V+
  gi|330507008|ref|YP_004383436.1|  8 RLKASEANQGDVGKGIVRMGDEFMERIGIRPLDVVEIIGSRPTAALAVSAYTQDQGIDMIRMDGLIRSNAGTSIGQYVE 86
                                      79***************************************************************************** PP

                                      EEEE- CS
                           CDC48_N 80 Vrkae 84
                                      V++a+
  gi|330507008|ref|YP_004383436.1| 87 VKRAT 91
                                      **986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 5.1
                                       -HHHHHHHTS-TTSEEEEEC...CCCEE.EEEEEBSTTSTTTTEEEE-H CS
                           CDC48_N  20 dpedmeelglepgdvveieg...krkTv.aivwpaepedegkgiIrmdg 64 
                                       +pe +++lg+ p + v ++g   + kT+ a+++++e +    + I ++g
  gi|330507008|ref|YP_004383436.1| 231 HPELFDRLGIDPPKGVLLHGppgTGKTMlAKAVANESD---AYFISING 276
                                       58999999999999999987522444443555555433...67888877 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   8.9e-12   2.7e-09       1      40 [.     398     437 ..     398     465 .. 0.87
   2 !   48.7   0.6   1.6e-15   4.8e-13       1      44 [.     673     718 ..     673     723 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 8.9e-12
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitm 40 
                                       dv l++ A +T G++GAD+aa+ reAa++Alrr +++i+ 
  gi|330507008|ref|YP_004383436.1| 398 DVVLEDYAIETYGFVGADIAAVSREAAMNALRRILPQIDL 437
                                       677899999************************8877754 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 1.6e-15
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik.e.itmedfe 44 
                                       d+d++eL e+T+ y+GAD+a+l+r+A++lAlr+++  + i++++f 
  gi|330507008|ref|YP_004383436.1| 673 DIDVEELLEQTDQYTGADIASLVRKAGRLALREDMAaTrISQKHFL 718
                                       89**********************************648*****95 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.2e-09   3.7e-07      16     139 ..     235     348 ..     232     350 .. 0.73
   2 !   22.6   0.1   3.7e-07   0.00011      16      62 ..     508     553 ..     503     624 .. 0.66

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.2e-09
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesa 92 
                                       ++r+  + p  vll+G++G+GK+ l++++++   +++++f++ +  +  ++  y    +al r +l+++ + +   +
  gi|330507008|ref|YP_004383436.1| 235 FDRLGIDPPKGVLLHGPPGTGKTMLAKAVAN---ESDAYFISINGPEI-MSKYYGESEKAL-R-DLFEEAEKN---T 302
                                       66666677799*******************6...6669**********.333333344444.4.555555444...4 PP

                            AAA_16  93 eleawrekleealaavpelagaeasrllellkrllallsrderplvl 139
                                        +  + ++l++ +   ++++g+ ++r+ ++l +l++ l++++  +++
  gi|330507008|ref|YP_004383436.1| 303 PAIIFLDELDSIAPKRGDVTGEVERRVVAQLLSLMDGLKERKN-VIV 348
                                       555666666666668889999999***********99999554.443 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 3.7e-07
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdq 62 
                                       ++r+  + p  +ll+G++G+GK+ l+++++++ e++ +i+++g +  
  gi|330507008|ref|YP_004383436.1| 508 FQRLGIDAPKGILLYGPPGTGKTMLAKAVANESEAN-FITVKGSALL 553
                                       5677778899********************988888.4444444433 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   2.1e-09   6.3e-07       6     105 ..     246     339 ..     241     346 .. 0.87
   2 !   18.7   0.0   4.7e-06    0.0014       6     101 ..     519     610 ..     515     616 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.1e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a+  ++     +i ++  e++     + + ++++  ++   +ae++   i++lDE+d i
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESDA----YFISINGPEIMS----KYYGESEKALRDLFEEAEKNTpaIIFLDELDSI 314
                                       6899******************96....************....88888888888888888888888********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk +  + +v r  V+  LL +++g
  gi|330507008|ref|YP_004383436.1| 315 APKrGDVTGEVERR-VVAQLLSLMDG 339
                                       **877777777765.77778899987 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 4.7e-06
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ill gp g+Gkt+laka+a+  ++    ++i++  s+ll     + + ++++  ++   +a +    i++lDE+d  
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEA----NFITVKGSALLS----KWYGESEKRVEEIFRKARQVApsIIFLDELDAL 587
                                       7999****************9985....************....89999999999999999998888********99 PP

                                       ---..---------HHHHHHHHH CS
                             AAA_2  81 hpk..essgadvSregVqrdLLq 101
                                        p   + +g+    e +++ LL 
  gi|330507008|ref|YP_004383436.1| 588 VPVrgGAMGEPHVTERIVNQLLS 610
                                       99776555555556666666665 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.3   2.4e-15   7.3e-13       8      63 ..     114     197 ..     103     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2.4e-15
                                       HHHHCCCTTEEE-TTEEE.....................EECCT..........CCCEEEEEEEECCCCSCEEECTS CS
                           CDC48_2   8 aylkrqFlgrpvtkGdlv.....................vfefk..........gqeiklvVvstePkgpvgitetT 53 
                                       + l+++F+grp+  Gd++                         +          ++eikl+Vvst+P g+v+ite T
  gi|330507008|ref|YP_004383436.1| 114 DVLTKVFNGRPLLRGDVIsttsvrkpptdsmgretmfeeI---FrgflgaqafgLGEIKLRVVSTSPGGIVKITEGT 187
                                       4899**************9999999988877777644443...05558889999*********************** PP

                                       CCEEESTTCC CS
                           CDC48_2  54 eielgtkpve 63 
                                        iel +++ve
  gi|330507008|ref|YP_004383436.1| 188 DIELLPQAVE 197
                                       *****99987 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.3e-07   3.8e-05      35      97 ..     245     315 ..     235     324 .. 0.74
   2 !   22.6   0.0   2.3e-07   6.9e-05      34      69 ..     517     552 ..     498     637 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.3e-07
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrls 97 
                                        vll+GpPG Gkt lak +a+e ++ + +  gP +      e ++ l  l+ + e++   ++f+de+  ++
  gi|330507008|ref|YP_004383436.1| 245 GVLLHGPPGTGKTMLAKAVANESDAYFISINGPEImskyygESEKALRDLFEEAEKNtpAIIFLDELDSIA 315
                                       69*******************************98332222233455555555554422588888877665 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 2.3e-07
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                         +llyGpPG Gkt lak +a+e ++++ +  g +l
  gi|330507008|ref|YP_004383436.1| 517 KGILLYGPPGTGKTMLAKAVANESEANFITVKGSAL 552
                                       569************************999888876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   7.9e-07   0.00024       8      62 ..     246     300 ..     241     304 .. 0.80
   2 ?    4.2   0.0      0.16        48      72     128 ..     285     349 ..     273     358 .. 0.73
   3 !   18.6   0.0   5.8e-06    0.0018       8      31 ..     519     542 ..     514     624 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.9e-07
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellr 62 
                                       ++++G++GtGKT+l++ ++++ d++  +  ++pe++ +++  s++ ++dl++e  +
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESDAYF-ISINGPEIMsKYYGESEKALRDLFEEAEK 300
                                       689******************97554.44468887778888888888888887655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.16
                            AAA_22  72 rlsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnl..srkgvqliLv 128
                                       + s+++l++++e+a +++ +  ++ +DE + +   +         +++ +L sl++   +rk   +i++
  gi|330507008|ref|YP_004383436.1| 285 GESEKALRDLFEEAEKNTPA--IIFLDELDSIApkRgdvtgeveRRVVAQLLSLMDGlkERK--NVIVI 349
                                       56888899999999999888..**********876245666777888888888888744333..44445 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 5.8e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqlde 31 
                                       ++++G++GtGKT+l++ ++++ ++
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEA 542
                                       89******************9742 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   2.7e-05    0.0082       1      79 [.     245     316 ..     245     365 .. 0.60
   2 !   20.9   0.0     9e-07   0.00027       2      77 ..     519     587 ..     518     640 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.7e-05
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK++la+ +a    + +  +++++ +++           g+ +     l ++a+  +++i++lDE++
  gi|330507008|ref|YP_004383436.1| 245 GVLLHGPPGTGKTMLAKAVANESDAYFISINGPEIMSKY------Y---GESEKALRDLFEEAEknTPAIIFLDELD 312
                                       59***************9998777766666666644432......2...3333444555555555566777777776 PP

                                       G--H CS
                             AAA_5  76 raes 79 
                                        + +
  gi|330507008|ref|YP_004383436.1| 313 SIAP 316
                                       6654 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 9e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEvera 77 
                                       +lL GppGtgK++la+ +a   ++++ +v +++      l+ ++   ++ +++v+ ++ +a +  ++i++lDE++ +
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEANFITVKGSA------LLSKWY--GESEKRVEEIFRKARQvAPSIIFLDELDAL 587
                                       89****************************999......788888..455566666665555599999999999865 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.2e-06   0.00067      51      97 ..     244     288 ..     241     298 .. 0.87
   2 !   19.6   0.0   1.4e-06   0.00043      50     107 ..     516     572 ..     510     576 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       ++vLl Gp+gtGkt la a+++e  +d  f++++g e+ s     +e
  gi|330507008|ref|YP_004383436.1| 244 KGVLLHGPPGTGKTMLAKAVANE--SDAYFISINGPEIMSKYYGESE 288
                                       89*******************99..5799*********998766665 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.4e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                             TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev.ltqalrksi 107
                                        +++Ll Gp+gtGkt la a+++e   +  f++++gs + s     +e  + + +rk+ 
  gi|330507008|ref|YP_004383436.1| 516 PKGILLYGPPGTGKTMLAKAVANES--EANFITVKGSALLSKWYGESEKrVEEIFRKAR 572
                                       589********************95..689*********99988888852667788875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.2e-07   6.6e-05       2      54 ..     246     301 ..     246     364 .. 0.82
   2 !   16.6   0.0   2.3e-05    0.0069       2      46 ..     519     565 ..     519     631 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.2e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdytr.vldr 54 
                                       vll+G+pG+GK+ la+ ++++ +  ++ ++ ++++++++g+ ++ ++d+ + ++++
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESDayFISINGPEIMSKYYGESEKALRDLFEeAEKN 301
                                       799****************999997778999****999998888877665533343 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.3e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                                       +ll G+pG+GK+ la+ ++++    ++++   +l+++ +g+ +++ +
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEanFITVKGSALLSKWYGESEKRVE 565
                                       6789***************9999889999999999988886555444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   9.6e-08   2.9e-05       5     110 ..     246     361 ..     243     376 .. 0.82
   2 !   15.3   0.0     5e-05     0.015       5      75 ..     519     586 ..     515     626 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 9.6e-08
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT+l+k +++e+      ++ in  +   k + ++ek l+ ++e+++++   ++flDE   +     
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESD---AYFISINGPEIMSKYYGESEKALRDLFEEAEKNTPAIIFLDELDSIapkrg 319
                                       7899***************9988...9999999999988888888777777777655669999************** PP

                            AAA_14  77 .......pewekalkslvd..egknldvivtGSnskllskeia 110
                                              +++   l sl+d  + ++ +viv GS +     ++a
  gi|330507008|ref|YP_004383436.1| 320 dvtgeveRRVVAQLLSLMDglK-ERKNVIVIGSTNRPEALDMA 361
                                       ******9999999999999643.5669******9876655555 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 5e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqe 75 
                                       +++ G+  +GKT+l+k +++e+     +++ ++      k + ++e +++e++++  ++   +++flDE   
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESE---ANFITVKGSALLSKWYGESEkRVEEIFRKA-RQVAPSIIFLDELDA 586
                                       7899***************9988...999999999988888777662555666665.444789******865 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 !   13.8   0.0   0.00012     0.036      47      70 ..     243     266 ..     233     275 .. 0.87
   2 ?   -1.3   0.0       5.2   1.6e+03      29      56 ..     324     352 ..     319     354 .. 0.75
   3 !   16.5   0.0   1.8e-05    0.0054      44      71 ..     513     540 ..     505     589 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00012
                         IstB_IS21  47 kenivllGpsGvGKshlaialgve 70 
                                        ++++l Gp+G+GK+ la a++ e
  gi|330507008|ref|YP_004383436.1| 243 PKGVLLHGPPGTGKTMLAKAVANE 266
                                       57899***************9976 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.2
                         IstB_IS21  29 sldkrkvkeLat.lsfiekkenivllGps 56 
                                       ++++r v++L + ++ +++++n++++G +
  gi|330507008|ref|YP_004383436.1| 324 EVERRVVAQLLSlMDGLKERKNVIVIGST 352
                                       67788888775515889999999999976 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.8e-05
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                                       i++ ++i+l Gp+G+GK+ la a++ e 
  gi|330507008|ref|YP_004383436.1| 513 IDAPKGILLYGPPGTGKTMLAKAVANES 540
                                       677789****************999875 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   5.4e-05     0.016      25      42 ..     246     263 ..     243     266 .. 0.90
   2 !   16.0   0.0     2e-05    0.0061      25      43 ..     519     537 ..     509     553 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.4e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +ll GppG+GKtmlak++
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAV 263
                                       79*************987 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKtmlak+++
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVA 537
                                       89*************9875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   0.00014     0.042       1      33 [.     246     296 ..     246     368 .. 0.61
   2 !   16.2   0.0   3.8e-05     0.011       1      38 [.     519     557 ..     519     611 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00014
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvak 33 
                                       +ll G+pG+GKt lak+++++  ++                    lrd++ 
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESdAYfisingpeimskyygesEKALRDLFE 296
                                       7899**************998756677666665555555555333333333 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.8e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gfgvnlrdvakengll 38 
                                       Ill G+pG+GKt lak+++++  ++ + ++  a  + ++
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESeANFITVKGSALLSKWY 557
                                       99****************877533333333333333333 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   7.3e-05     0.022      23      72 ..     244     285 ..     236     322 .. 0.72
   2 !   13.3   0.0   0.00017     0.051      20      60 ..     514     551 ..     501     589 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.3e-05
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHE CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFG 72 
                                         vl++G  GtGK++la+a+ ++s+   + f+++n  +i     +s+ +G
  gi|330507008|ref|YP_004383436.1| 244 KGVLLHGPPGTGKTMLAKAVANESD---AYFISINGPEI-----MSKYYG 285
                                       569****************998776...88999997665.....344444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00017
                                       TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTT CS
                   Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheaskrkekpfvavncaa 60 
                                       + +  +l+ G  GtGK++la+a+ ++s+   ++f++v  +a
  gi|330507008|ref|YP_004383436.1| 514 DAPKGILLYGPPGTGKTMLAKAVANESE---ANFITVKGSA 551
                                       556789*****************98887...6677776655 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   0.00022     0.067       5      76 ..     246     313 ..     243     325 .. 0.72
   2 !   15.7   0.0     3e-05    0.0092       4      42 ..     518     557 ..     515     597 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00022
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtide 76 
                                       +l+ Gp+g+GKT+lak    + ++ fi +++   ++  + +   es ++++d ++e +++ +   ++++D +d 
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVanESDAYFISING--PEIMSKYYG--ESEKALRDLFEEAEKNTP--AIIFLDELDS 313
                                       799**************99999999998887..233333332..366777777776654444..6677777665 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3e-05
                            AAA_24   4 kiliyGpsgiGKTtlakel..gpkplfidtekGlksldadk 42 
                                        il+yGp+g+GKT+lak    + ++ fi t kG++ l  + 
  gi|330507008|ref|YP_004383436.1| 518 GILLYGPPGTGKTMLAKAVanESEANFI-TVKGSALLSKWY 557
                                       699**************99743333333.334455555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00038      0.11       3      22 ..     246     265 ..     244     269 .. 0.90
   2 ?    0.4   0.0       1.7   5.3e+02      78     139 ..     299     362 ..     278     383 .. 0.63
   3 !   11.2   0.0   0.00087      0.26       3      23 ..     519     539 ..     517     546 .. 0.89
   4 ?   -1.1   0.0       5.3   1.6e+03      57      99 ..     552     593 ..     540     621 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00038
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       v+l+G++G GKT+L++ +a 
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVAN 265
                                       79**************9986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.7
                                       CSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEEEEECCCHHHHCTTS CS
                             NACHT  78 elperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasllltvrpralrdleeql 139
                                       e  + + + lD lD ++ + g    + +++v   L +l+ + l  +  ++++ ++++ + l   l
  gi|330507008|ref|YP_004383436.1| 299 EKNTPAIIFLDELDSIAPKRGDvtgEVERRVVAQLLSLMDG-LKERKNVIVIGSTNRPEALDMAL 362
                                       45556667799999999999889995555555555588888.44455555555555554455555 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00087
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++l G++G GKT+L++ +a +
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANE 539
                                       7899************99876 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 5.3
                                       HHCCCCTS--SSS-CCHHHHCCSCCCEE...EEEE-STT-SS-TCH CS
                             NACHT  57 llfsqlpepaapvsevwavllelperlL...lilDglDelvtdlgq 99 
                                       ll + + e++++v+e    + + ++++    + lD lD lv   g 
  gi|330507008|ref|YP_004383436.1| 552 LLSKWYGESEKRVEE----IFRKARQVApsiIFLDELDALVPVRGG 593
                                       667777788888888....444444443443557888888876655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00021     0.062       1      64 [.     246     300 ..     246     316 .. 0.73
   2 !   13.1   0.0   0.00031     0.093       1      26 [.     519     544 ..     519     567 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00021
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkde 64 
                                       ++l+Gp+g+GK++lak +          +++d +++  +  +++++Y g+      D+ +  ++
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAV---------ANESDAYFISINGPEIMSKYYGESEKALRDLFEEAEK 300
                                       689**************3.........2333444447788888888888888877777777666 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00031
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       i+lyGp+g+GK++lak +a++ + ++
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEANF 544
                                       789**************998876554 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   0.00042      0.13      34      58 ..     244     268 ..     234     293 .. 0.86
   2 !   13.7   0.0   0.00011     0.033      25      63 ..     508     545 ..     488     555 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00042
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                       k vll Gp GtGKt+++k + ++ d
  gi|330507008|ref|YP_004383436.1| 244 KGVLLHGPPGTGKTMLAKAVANESD 268
                                       789***************9999887 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00011
                             AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkldkekyl 63 
                                       + +l +++ k +ll+Gp GtGKt+++k + ++ +  +++
  gi|330507008|ref|YP_004383436.1| 508 FQRLGIDAPKGILLYGPPGTGKTMLAKAVANESE-ANFI 545
                                       55566788899*****************999887.4444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00025     0.076       2      41 ..     246     290 ..     245     314 .. 0.73
   2 !   12.2   0.0   0.00052      0.16       2      25 ..     519     545 ..     518     575 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00025
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileeklak 41 
                                       + + G+++tGKT l++a a++     +++  pE++ +++ e  + 
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANEsdayFISINgPEIMSKYYGESEKA 290
                                       6799***************76654344444788877777655544 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00052
                            AAA_28   2 ivitGgestGKTtlleaLaar...gyp 25 
                                       i + G+++tGKT l++a a++   ++ 
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANEseaNFI 545
                                       7899***************76533444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0    0.0008      0.24       8      67 ..     240     297 ..     237     352 .. 0.75
   2 !   13.2   0.0   0.00033     0.099      10      74 ..     515     578 ..     509     633 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0008
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                       + + + v + G+ G+GK+ L+k++a++++     i ++g ++ ++   +++k ++ l++e
  gi|330507008|ref|YP_004383436.1| 240 IDPPKGVLLHGPPGTGKTMLAKAVANESDA--YFISINGPEIMSKYYGESEKALRDLFEE 297
                                       566677899*****************9986..4566687777777777777777777777 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00033
                                       TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                          ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpel 74 
                                       + + + + G+ G+GK+ L+k++a++++  +  i+++g  l ++   +++k+++ ++ +  q+ p +
  gi|330507008|ref|YP_004383436.1| 515 APKGILLYGPPGTGKTMLAKAVANESE--ANFITVKGSALLSKWYGESEKRVEEIFRKaRQVAPSI 578
                                       55668899****************986..6889999999999899999999988888856666665 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   0.00085      0.26      15      49 ..     242     274 ..     234     287 .. 0.86
   2 !   13.0   0.0   0.00015     0.045      14      50 ..     514     548 ..     504     554 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00085
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                        Pk +ll G pG GK+ la+++++e   +  ++ +
  gi|330507008|ref|YP_004383436.1| 242 PPKGVLLHGPPGTGKTMLAKAVANES--DAYFISI 274
                                       5999********************98..5555555 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00015
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       + Pk ill G pG GK+ la+++++e   + n+++++
  gi|330507008|ref|YP_004383436.1| 514 DAPKGILLYGPPGTGKTMLAKAVANES--EANFITVK 548
                                       689***********************8..88888876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0    0.0009      0.27      20      51 ..     244     277 ..     221     298 .. 0.76
   2 ?   -1.5   0.0       7.8   2.4e+03      80     104 ..     481     505 ..     478     515 .. 0.70
   3 !   11.7   0.0   0.00062      0.19      19      46 ..     516     543 ..     490     552 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0009
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                       + +lL+G+ G+GKT+l++++a++ +    +++ P
  gi|330507008|ref|YP_004383436.1| 244 KGVLLHGPPGTGKTMLAKAVANESDAYfiSINGP 277
                                       459******************9987655556655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 7.8
                                       HHHCTTCCCCSTSCEEEEETGGGGC CS
                              TsaE  80 leelgleeyleeeavvlvEWpekle 104
                                       +e++g  e +++  v +vEWp + +
  gi|330507008|ref|YP_004383436.1| 481 WEDIGGLERVKDLMVEAVEWPLRNA 505
                                       56677667775557999***98844 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00062
                                       TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve 46 
                                        + ilL+G+ G+GKT+l++++a++ + +
  gi|330507008|ref|YP_004383436.1| 516 PKGILLYGPPGTGKTMLAKAVANESEAN 543
                                       346******************9987765 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0018      0.53      54     116 ..     244     311 ..     238     363 .. 0.64
   2 !   13.1   0.0   0.00013     0.039      21      82 ..     475     545 ..     458     585 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                            DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrl..ievekedlkelpklvellr...erperfilfvDDL 116
                                       + vLL G  GtGK  l ka+ ne  +  + +   e+  +   e +k ++ l    e+++  i+f+D L
  gi|330507008|ref|YP_004383436.1| 244 KGVLLHGPPGTGKTMLAKAVANESDAYFISIngPEIMSKYYGESEKALRDLFeeaEKNTPAIIFLDEL 311
                                       679*******************9988875552246666655555544444431113445578888876 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00013
                            DUF815  21 evdevklddLvgidkqkealve.......nteqfle.glpa.nnvLLwGarGtGKSslvkallneyaeegL 82 
                                       ev +v+++d+ g+++ k+ +ve       n+e f + g  a + +LL+G  GtGK  l ka+ ne +++ +
  gi|330507008|ref|YP_004383436.1| 475 EVPNVSWEDIGGLERVKDLMVEavewplrNAESFQRlGIDApKGILLYGPPGTGKTMLAKAVANESEANFI 545
                                       55677888888888888877642222222677776545444378********************9887763 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0041       1.2      23     121 ..     246     348 ..     233     350 .. 0.55
   2 !    9.7   0.0    0.0023      0.71      23      46 ..     519     542 ..     511     575 .. 0.84
   3 ?   -1.2   0.0         5   1.5e+03     110     136 ..     564     591 ..     552     630 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0041
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie......eeeekkklekal........gia 85 
                                       +++ Gp g GKt L k ++++++      +  i+  e+ ++++ e+ +      ee ek+     +        ++ 
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESDA----YFISINGPEIMSKYYGESEKalrdlfEEAEKN-----TpaiifldeLDS 313
                                       678999999999999999999843....22234455555555555522444443333333.....022334454333 PP

                          ATPase_2  86 vpkaeleeilkeksklvfkaielllekikkkgkkii 121
                                       +  +++  +  e  + v +++ +l++ +k+++  i+
  gi|330507008|ref|YP_004383436.1| 314 IAPKRG-DVTGEVERRVVAQLLSLMDGLKERKNVIV 348
                                       333334.34446666666777777777777644333 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0023
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienled 46 
                                       +++YGp g GKt L k +++++e 
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEA 542
                                       689**************9999854 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5
                          ATPase_2 110 lekikkkgkk...iiiiiDelqklidlgln 136
                                        e+i +k+++    ii++Del  l+   ++
  gi|330507008|ref|YP_004383436.1| 564 VEEIFRKARQvapSIIFLDELDALV--PVR 591
                                       567777777777679999**99998..333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0055       1.7      36      52 ..     246     262 ..     242     266 .. 0.87
   2 ?    4.6   0.0     0.068        21     128     184 ..     289     349 ..     261     352 .. 0.76
   3 !   11.2   0.3   0.00069      0.21      36      54 ..     519     537 ..     489     625 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0055
                            AAA_25  36 allaGapgtGKttlald 52 
                                       +ll G+pgtGKt+la  
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKA 262
                                       689***********965 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.068
                            AAA_25 128 advdaleaaieevegvrlvviDplsralgg..densnsd...vgalvealeriarrtgaavl 184
                                        ++++l +++e+ + ++ + +D l+++ +   d + + +   v++l++ ++ +++r++++v+
  gi|330507008|ref|YP_004383436.1| 289 KALRDLFEEAEK-NTPAIIFLDELDSIAPKrgDVTGEVErrvVAQLLSLMDGLKERKNVIVI 349
                                       567889999999.88***********999866666555444347777777777778877776 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00069
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pgtGKt+la  +a
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVA 537
                                       79***********996655 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    0.0018      0.55      21      40 ..     246     265 ..     234     275 .. 0.87
   2 !   11.4   0.0   0.00063      0.19      22      54 ..     520     552 ..     511     575 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0018
                            AAA_30  21 avltGpAGtGKttalkalre 40 
                                       ++l+Gp+GtGKt++ ka+++
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVAN 265
                                       6899**********999975 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00063
                            AAA_30  22 vltGpAGtGKttalkalreaweaaggrviglAp 54 
                                       +l Gp+GtGKt++ ka+++  ea+  +v g A 
  gi|330507008|ref|YP_004383436.1| 520 LLYGPPGTGKTMLAKAVANESEANFITVKGSAL 552
                                       688***************999999888888775 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00064      0.19      23      45 ..     246     268 ..     233     271 .. 0.87
   2 !    9.7   0.0    0.0015      0.45      23      44 ..     519     540 ..     495     548 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00064
                                       EEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                       v l+G +G GKt lak + n+sd
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESD 268
                                       789****************9976 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0015
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       + l+G +G GKt lak + n+s
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANES 540
                                       779****************994 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 !   10.3   0.0   0.00089      0.27     117     141 ..     246     270 ..     241     275 .. 0.90
   2 !   10.8   0.0   0.00062      0.19     117     137 ..     519     539 ..     514     543 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00089
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                       v+++Gp+ tGkt+la+a a+ ++ y
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESDAY 270
                                       789****************998876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00062
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       +++yGp+ tGkt+la+a a+ 
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANE 539
                                       899**************9986 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0016      0.47       2      30 ..     246     274 ..     245     282 .. 0.88
   2 !   10.2   0.0    0.0017      0.52       2      30 ..     519     547 ..     518     601 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0016
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll+g PG++kt+l+ka+a+  d+ f  i
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESDAYFISI 274
                                       89*****************9998877655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0017
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       +ll g PG++kt+l+ka+a+  +++f  +
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEANFITV 547
                                       7999****************999999766 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00097      0.29      20      40 ..     246     266 ..     223     303 .. 0.82
   2 !    8.6   0.0    0.0048       1.4      20      41 ..     519     540 ..     503     575 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00097
                            AAA_11  20 tliqGPPGtgKTktivellsq 40 
                                       +l++GPPGtgKT    ++ ++
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANE 266
                                       79**********776666665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0048
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                        l+ GPPGtgKT    ++ ++ 
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANES 540
                                       6899********8777776665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0037       1.1      15      38 ..     239     262 ..     232     348 .. 0.85
   2 !    9.1   0.0    0.0024      0.72      15      38 ..     512     535 ..     504     549 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0037
                            ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                       Gi   + vl+ G pGtGKt++a+ 
  gi|330507008|ref|YP_004383436.1| 239 GIDPPKGVLLHGPPGTGKTMLAKA 262
                                       67777889*************975 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0024
                            ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                       Gi   + +l++G pGtGKt++a+ 
  gi|330507008|ref|YP_004383436.1| 512 GIDAPKGILLYGPPGTGKTMLAKA 535
                                       77777889*************986 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0096       2.9      37     175 ..     246     386 ..     242     428 .. 0.61
   2 !    8.7   0.0    0.0045       1.4      37      65 ..     519     547 ..     513     569 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0096
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk 112
                                       ++++g+ G Gkt L ka++ne  + + +     +++ e +++     ++   + f e  +++  ++ +D++  +a k
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESDAYFIS-----INGPEIMSKYYGESEKALRDLFEEAEKNTpAIIFLDELDSIAPK 317
                                       799**************99976554443.....33333333333333333333344333333134445555555555 PP

                                       H.........HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHH CS
                          Bac_DnaA 113 e.........ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlail 175
                                                 ++  +l+ +++ l e ++ +v+ s   P++l+ +  r   rf++   +++  pd+e rl+i 
  gi|330507008|ref|YP_004383436.1| 318 RgdvtgeverRVVAQLLSLMDGLKERKNVIVIGSTNRPEALD-MALRRPGRFDRE--IELGVPDMEGRLEIF 386
                                       311111111124445666777777777777777777777774.455556677664..455557777777765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0045
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapel 65 
                                       +++yg+ G Gkt L ka++ne ++n+   
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEANFITV 547
                                       79*******************99987665 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    0.0038       1.2      22      40 ..     246     264 ..     240     269 .. 0.87
   2 !    8.8   0.0    0.0032      0.97      22      41 ..     519     538 ..     508     546 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0038
                                       EEEE--TTSSTTHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavala 40 
                                       v   Gp GtGKt+la a+a
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVA 264
                                       6778***********9998 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0032
                                       EEEE--TTSSTTHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalav 41 
                                       +   Gp GtGKt+la a+a 
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVAN 538
                                       5678***********99985 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0012      0.38       4      48 ..     246     283 ..     243     318 .. 0.74
   2 !    7.5   0.0    0.0068       2.1       4      25 ..     519     540 ..     516     577 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlr 48 
                                       vl +G +GtGKt+++ ++++e         a ++s N+p+++  +
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANES-------DAYFISINGPEIMSKY 283
                                       6889************999998.......6777777777766433 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0068
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       +l  G +GtGKt+++ ++++e 
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANES 540
                                       6789*************99998 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.053        16       4      30 ..     245     271 ..     243     279 .. 0.86
   2 ?   -1.2   0.0       4.4   1.3e+03      75      95 ..     280     300 ..     274     312 .. 0.77
   3 ?    5.7   0.0     0.036        11       3      30 ..     517     544 ..     515     551 .. 0.87
   4 ?    2.5   0.0      0.33     1e+02      76      96 ..     554     574 ..     547     583 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.053
                                       EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                        v l gp g+Gk +l ka+ +e   +f
  gi|330507008|ref|YP_004383436.1| 245 GVLLHGPPGTGKTMLAKAVANESDAYF 271
                                       68899**************99988887 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.4
                                       TTEEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                        +++yg+s +a +  +e++ +
  gi|330507008|ref|YP_004383436.1| 280 MSKYYGESEKALRDLFEEAEK 300
                                       6799**********9998865 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.036
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       + + l gp g+Gk +l ka+ +e + +f
  gi|330507008|ref|YP_004383436.1| 517 KGILLYGPPGTGKTMLAKAVANESEANF 544
                                       66899***************99988887 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.33
                                       TEEEEEEHHHHHHHHHTTSEE CS
                     Guanylate_kin  76 gnlygtsveaieevlekgkiv 96 
                                       ++ yg+s + +ee++ k+++v
  gi|330507008|ref|YP_004383436.1| 554 SKWYGESEKRVEEIFRKARQV 574
                                       678***************995 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.015       4.4      12      31 ..     245     264 ..     241     272 .. 0.82
   2 !    8.7   0.0    0.0066         2      12      34 ..     518     540 ..     510     592 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.015
                            AAA_19  12 vllvtaGpGtGKTrvlkhiv 31 
                                        +l+ ++pGtGKT + k++ 
  gi|330507008|ref|YP_004383436.1| 245 GVLLHGPPGTGKTMLAKAVA 264
                                       5899*********9877665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0066
                            AAA_19  12 vllvtaGpGtGKTrvlkhivall 34 
                                        +l+ ++pGtGKT + k++ ++ 
  gi|330507008|ref|YP_004383436.1| 518 GILLYGPPGTGKTMLAKAVANES 540
                                       5899*********9888776654 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0089       2.7      26      58 ..     234     266 ..     222     277 .. 0.83
   2 !    7.3   0.0     0.009       2.7      34      60 ..     515     541 ..     505     550 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0089
                              TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFarl 58 
                                       L+++   + ++ +ll+G++ +GKtm+++  a++
  gi|330507008|ref|YP_004383436.1| 234 LFDRLGIDPPKGVLLHGPPGTGKTMLAKAVANE 266
                                       566666667789**************9987766 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.009
                              TniB  34 rmpnlllvGdsnnGKtmivekFarlhp 60 
                                        ++ +ll+G++ +GKtm+++  a++ +
  gi|330507008|ref|YP_004383436.1| 515 APKGILLYGPPGTGKTMLAKAVANESE 541
                                       56789**************98887765 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 !    8.1   0.0    0.0087       2.6      24      80 ..     246     313 ..     242     318 .. 0.58
   2 ?    7.3   0.0     0.016       4.7      24      48 ..     519     543 ..     514     589 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0087
                                       EEEEEETT--HHHHHHCC--TTS-E.E--SSTTHHH.......H-HHHHHHHT...TTSEEEEEE-TT CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw.leifvverla.......klpldlleqa...kggtLylkdiad 80 
                                       v+l G++G+gk++ A++ +++s    ++i   e  +       k+  dl+e+a   ++++++l ++++
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESDAYfISINGPEIMSkyygeseKALRDLFEEAeknTPAIIFLDELDS 313
                                       99***************999875421222211111111111113446666665444566666666665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.016
                                       EEEEEETT--HHHHHHCC--TTS-E CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw 48 
                                       ++l G++G+gk++ A++ +++s+ +
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEAN 543
                                       799****************999874 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.029       8.8       2      25 ..     250     273 ..     249     318 .. 0.75
   2 !    8.8   0.0    0.0066         2       1      31 [.     522     554 ..     522     584 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.029
                                       E-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthls 25 
                                       G+PG GK+ +++ ++ + +  ++s
  gi|330507008|ref|YP_004383436.1| 250 GPPGTGKTMLAKAVANESDAYFIS 273
                                       9***********999988666655 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0066
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllr 31 
                                       +G+PG GK+ +++ ++ +   +f  +  + ll 
  gi|330507008|ref|YP_004383436.1| 522 YGPPGTGKTMLAKAVANESeaNFITVKGSALLS 554
                                       7***********999987622555555444444 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0037       1.1      60      79 ..     241     260 ..     228     269 .. 0.86
   2 ?    5.9   0.0     0.017       5.1      59      79 ..     513     533 ..     489     541 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0037
                       AFG1_ATPase  60 epvrglYlwGgvGrGKtylm 79 
                                        p++g+ l+G+ G GKt+l 
  gi|330507008|ref|YP_004383436.1| 241 DPPKGVLLHGPPGTGKTMLA 260
                                       79****************96 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.017
                       AFG1_ATPase  59 vepvrglYlwGgvGrGKtylm 79 
                                         +++g+ l+G+ G GKt+l 
  gi|330507008|ref|YP_004383436.1| 513 IDAPKGILLYGPPGTGKTMLA 533
                                       5699***************96 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.038        12      22      45 ..     241     264 ..     215     310 .. 0.83
   2 !    9.3   0.0    0.0034         1       4      77 ..     461     563 ..     458     584 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.038
                                       .TTSEEEEEESTTSTHHHHHHHHH CS
                            ResIII  22 krdkrglikmaTGtGKTlvaakli 45 
                                       +  k +l++ + GtGKT++a +++
  gi|330507008|ref|YP_004383436.1| 241 DPPKGVLLHGPPGTGKTMLAKAVA 264
                                       5678899***********996665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0034
                                       E-HHHHHHHHHHT.........................................TTSEEEEEESTTSTHHHHHHHHH CS
                            ResIII   4 lreyQeeaienlleklks...................................krdkrglikmaTGtGKTlvaakli 45 
                                       lre Q +a++++l ++ +                                   +  k +l+  + GtGKT++a +++
  gi|330507008|ref|YP_004383436.1| 461 LREIQPSAMREILVEVPNvswedigglervkdlmveavewplrnaesfqrlgiDAPKGILLYGPPGTGKTMLAKAVA 537
                                       77888888888885555566666667777777888888888888888888888999999************997777 PP

                                       HHH-S.....-EEEEESSHHHHHHHHHHGGGG CS
                            ResIII  46 erllkkgkeekflflvprkslleqtleefkkf 77 
                                        +   +      ++ v + +ll++++ e +k 
  gi|330507008|ref|YP_004383436.1| 538 NESEAN------FITVKGSALLSKWYGESEKR 563
                                       665553......34566777777777655555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.029       8.8       2      23 ..     246     267 ..     245     281 .. 0.83
   2 !    8.3   0.0    0.0064       1.9       2      32 ..     519     549 ..     518     564 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.029
                                       EEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                       v++ GppG+GKt l k v+++ 
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANES 267
                                       6789************999875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0064
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       +++ GppG+GKt l k v+++ + + ++v+G
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEANFITVKG 549
                                       6788****************99988888888 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.011       3.5       4      34 ..     246     276 ..     244     306 .. 0.84
   2 ?    6.0   0.0     0.032       9.6       4      39 ..     519     554 ..     517     579 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.011
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgv 34 
                                       +lL+G + +GK+ la+a+ + +d+ ++ ++ 
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESDAYFISING 276
                                       89*********************99998865 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.032
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafve 39 
                                       ilL G + +GK+ la+a+ + +++ ++ ++  a++ 
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEANFITVKGSALLS 554
                                       89***********************99987666655 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.075        23      20      44 ..     443     467 ..     434     476 .. 0.78
   2 ?    7.7   0.0     0.012       3.6      24      53 ..     707     736 ..     701     742 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.075
                            Vps4_C  20 psdklleP.pvtlkDflkalkkarpt 44 
                                       p +++l +  v+ +Df++al++ +p+
  gi|330507008|ref|YP_004383436.1| 443 P-KEILDRlIVQKSDFEAALREIQPS 467
                                       5.45555559**************99 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.012
                            Vps4_C  24 llePpvtlkDflkalkkarptVskeDLekh 53 
                                       + +  ++ k+fl+al++  p+V+++ ++ +
  gi|330507008|ref|YP_004383436.1| 707 MAATRISQKHFLAALEEIGPSVTADTMKYY 736
                                       55668999***************9988877 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 ?    8.2   0.0    0.0092       2.8       2      31 ..     246     275 ..     245     283 .. 0.92
   2 ?    5.8   0.1     0.048        14       2      30 ..     519     547 ..     518     552 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0092
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAlltiD 31 
                                       +++hG+P +GKt  a ++a + +a +++i 
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVANESDAYFISIN 275
                                       689******************999999986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.048
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       i++ G+P +GKt  a ++a + ea ++t+
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEANFITV 547
                                       7889********************99998 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.068        21     131     154 ..     245     268 ..     236     277 .. 0.84
   2 ?    8.1   0.0    0.0041       1.3     116     162 ..     503     546 ..     419     551 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.068
                             T2SSE 131 lilvsGgTgsGKttllyallkein 154
                                        +l+ G+ g+GKt l+ a+ +e +
  gi|330507008|ref|YP_004383436.1| 245 GVLLHGPPGTGKTMLAKAVANESD 268
                                       58999***********99988755 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0041
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivt 162
                                        + +++ r  + + + il+ G+ g+GKt l+ a+ +e ++   +++t
  gi|330507008|ref|YP_004383436.1| 503 RNAESFQRLGIDAPKGILLYGPPGTGKTMLAKAVANESEA---NFIT 546
                                       4556666777777899**************9998766443...4555 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.024       7.4       3      27 ..     248     272 ..     246     276 .. 0.88
   2 ?    6.6   0.0     0.019       5.9       3      27 ..     521     545 ..     519     550 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.024
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP g+GK  +a+a+a++ ++ ++
  gi|330507008|ref|YP_004383436.1| 248 LHGPPGTGKTMLAKAVANESDAYFI 272
                                       68****************9988776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.019
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP g+GK  +a+a+a++ +++++
  gi|330507008|ref|YP_004383436.1| 521 LYGPPGTGKTMLAKAVANESEANFI 545
                                       67*****************999987 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.017       5.3       2      70 ..     247     310 ..     246     313 .. 0.61
   2 ?    6.5   0.0     0.021       6.3       4      70 ..     522     583 ..     519     589 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.017
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                       + hG pG GK+ l + ++++s  + +++n p  e+ ++   ++++     +++++++        i++lDE
  gi|330507008|ref|YP_004383436.1| 247 LLHGPPGTGKTMLAKAVANESdaYFISINGP--EIMSKYYGESEKALRDLFEEAEKNT-----PAIIFLDE 310
                                       68******************88544444443..5555544444444344444444433.....23566665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.021
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                        G pG GK+ l + ++++s  ++ +++   +ll+++  +++++  + ++++ + +       i++lDE
  gi|330507008|ref|YP_004383436.1| 522 YGPPGTGKTMLAKAVANESeANFITVKG-SALLSKWYGESEKRVEEIFRKARQVA-----PSIIFLDE 583
                                       588***************9977766666.78999998777777666666554432.....25888888 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.6   1.7e+03      20      43 ..     243     266 ..     229     270 .. 0.80
   2 ?    8.1   0.0    0.0047       1.4     156     198 ..     286     327 ..     272     335 .. 0.78
   3 ?    2.6   0.0      0.22        66      23      63 ..     519     554 ..     513     597 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.6
                        KAP_NTPase  20 pivvgLygkWGsGKssllnklede 43 
                                       p  v L g+ G+GK+ l + + +e
  gi|330507008|ref|YP_004383436.1| 243 PKGVLLHGPPGTGKTMLAKAVANE 266
                                       5568899999*****999887665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0047
                        KAP_NTPase 156 eveelladmektLdalqkrlVvviDdLDrceteevlqlleavk 198
                                       e e+ l d++++ ++ +++ ++++D+LD++ +++   + e+ +
  gi|330507008|ref|YP_004383436.1| 286 ESEKALRDLFEEAEK-NTPAIIFLDELDSIAPKRGDVTGEVER 327
                                       555566677777666.****************99888777655 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.22
                        KAP_NTPase  23 vgLygkWGsGKssllnkledelkefakpvrflfaefnawsf 63 
                                       + Lyg+ G+GK+ l + + +e + +     f+ ++ +a+++
  gi|330507008|ref|YP_004383436.1| 519 ILLYGPPGTGKTMLAKAVANESEAN-----FITVKGSALLS 554
                                       789*********9999999888777.....66666666655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.039        12       2      28 ..     244     270 ..     243     273 .. 0.87
   2 ?    5.8   0.0     0.035        11       2      24 ..     517     539 ..     516     545 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.039
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkgeelkY 28 
                                       k +ll G+ g+GKt L++a+ +e+  Y
  gi|330507008|ref|YP_004383436.1| 244 KGVLLHGPPGTGKTMLAKAVANESDAY 270
                                       5699****************9987555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.035
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                       k ill G+ g+GKt L++a+ +e
  gi|330507008|ref|YP_004383436.1| 517 KGILLYGPPGTGKTMLAKAVANE 539
                                       6699***************9987 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.047        14      21      41 ..     243     262 ..     233     265 .. 0.75
   2 ?    5.9   0.0     0.035        11      18      41 ..     514     535 ..     497     538 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.047
                            AAA_29  21 lkgatlltGpsGsGKSTllDA 41 
                                       +kg +ll Gp G+GK+ l  A
  gi|330507008|ref|YP_004383436.1| 243 PKG-VLLHGPPGTGKTMLAKA 262
                                       356.9**********988655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.035
                            AAA_29  18 eidlkgatlltGpsGsGKSTllDA 41 
                                       +  +kg +ll Gp G+GK+ l  A
  gi|330507008|ref|YP_004383436.1| 514 DA-PKG-ILLYGPPGTGKTMLAKA 535
                                       33.466.9**********988655 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         8   2.4e+03      16      41 ..      62      87 ..      57     115 .. 0.77
   2 ?    4.3   0.0      0.13        39       1      22 [.     252     273 ..     252     300 .. 0.86
   3 ?    5.9   0.0     0.042        13       1      23 [.     525     547 ..     525     573 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 8
                                      HTSEEEEHHHHHHHHHTS-HHHHHHH CS
                               SKI 16 lglefiDlDeliekrtgksiaeifee 41
                                       g+++i +D li  ++g+si +++e 
  gi|330507008|ref|YP_004383436.1| 62 QGIDMIRMDGLIRSNAGTSIGQYVEV 87
                                      57788999*************99974 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.13
                                       TTSSHHHHHHHHHHHHTSEEEE CS
                               SKI   1 mGaGKstvGkllAkklglefiD 22 
                                       +G+GK+ ++k++A++ +  fi 
  gi|330507008|ref|YP_004383436.1| 252 PGTGKTMLAKAVANESDAYFIS 273
                                       69*************9999985 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.042
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ ++k++A++ + +fi +
  gi|330507008|ref|YP_004383436.1| 525 PGTGKTMLAKAVANESEANFITV 547
                                       69******************986 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.18        54      60      89 ..     246     274 ..     241     279 .. 0.81
   2 ?    6.9   0.0    0.0098         3      59      92 ..     518     550 ..     467     554 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.18
                                       EEEEESSTSTHHHHHHHHHHHSSSEEEEES CS
                               MCM  60 vllvgdpgtaKsqlLkyveklapravytsg 89 
                                       vll g pgt+K+ l k+v++  + a ++s+
  gi|330507008|ref|YP_004383436.1| 246 VLLHGPPGTGKTMLAKAVAN-ESDAYFISI 274
                                       89************999995.455566655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0098
                                       EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSS CS
                               MCM  59 nvllvgdpgtaKsqlLkyveklapravytsgkgs 92 
                                        +ll g pgt+K+ l k+v+ + ++a++++ kgs
  gi|330507008|ref|YP_004383436.1| 518 GILLYGPPGTGKTMLAKAVA-NESEANFITVKGS 550
                                       59*************99999.5566777777776 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.05        15       4      26 ..     247     269 ..     245     279 .. 0.83
   2 ?    4.9   0.0     0.057        17       4      26 ..     520     542 ..     518     547 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.05
                                       EEEESTTCCHHHHHHHHHCT--S CS
                              cobW   4 vltGflGsGKTtLlnhllenrag 26 
                                       +l G++G+GKT+L +++ ++++ 
  gi|330507008|ref|YP_004383436.1| 247 LLHGPPGTGKTMLAKAVANESDA 269
                                       689**********9998877655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.057
                                       EEEESTTCCHHHHHHHHHCT--S CS
                              cobW   4 vltGflGsGKTtLlnhllenrag 26 
                                       +l G++G+GKT+L +++ ++++ 
  gi|330507008|ref|YP_004383436.1| 520 LLYGPPGTGKTMLAKAVANESEA 542
                                       689**********9998876655 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.029       8.8      57      76 ..     247     266 ..     241     275 .. 0.88
   2 ?    4.0   0.0      0.16        50      53      76 ..     516     539 ..     482     547 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.029
                                       EEEE-TTSSHHHHHHHHHHH CS
                            Torsin  57 sfhGwtGtGknfvaeiiaen 76 
                                        +hG +GtGk  +a+ +a++
  gi|330507008|ref|YP_004383436.1| 247 LLHGPPGTGKTMLAKAVANE 266
                                       58*************99985 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.16
                                       -EEEEEEE-TTSSHHHHHHHHHHH CS
                            Torsin  53 pLvlsfhGwtGtGknfvaeiiaen 76 
                                       p  + ++G +GtGk  +a+ +a++
  gi|330507008|ref|YP_004383436.1| 516 PKGILLYGPPGTGKTMLAKAVANE 539
                                       3446689************99986 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.15        47       5      31 ..     247     273 ..     244     278 .. 0.88
   2 ?    5.1   0.0     0.042        13       5      30 ..     520     545 ..     517     548 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.15
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       l++G+ +tGKt  a ++a+e  a  i+
  gi|330507008|ref|YP_004383436.1| 247 LLHGPPGTGKTMLAKAVANESDAYFIS 273
                                       899***************998877766 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.042
                               IPT   5 lifGatttGKtaeaiklaketgapvi 30 
                                       l++G+ +tGKt  a ++a+e  a  i
  gi|330507008|ref|YP_004383436.1| 520 LLYGPPGTGKTMLAKAVANESEANFI 545
                                       89****************99887766 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.29        89      16      39 ..     241     263 ..     230     264 .. 0.80
   2 ?    6.0   0.0     0.048        15       5      39 ..     503     536 ..     502     537 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.29
                            AAA_23  16 dFskgltlItGpNGaGKTTildAi 39 
                                       d  kg+ l++Gp G+GKT +  A+
  gi|330507008|ref|YP_004383436.1| 241 DPPKGV-LLHGPPGTGKTMLAKAV 263
                                       555555.9**********999885 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.048
                            AAA_23   5 enfrsfrdqeidFskgltlItGpNGaGKTTildAi 39 
                                       +n  sf++  id  kg+ l++Gp G+GKT +  A+
  gi|330507008|ref|YP_004383436.1| 503 RNAESFQRLGIDAPKGI-LLYGPPGTGKTMLAKAV 536
                                       67789999999999999.***********999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (758 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        59  (0.00329076); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              59  [number of targets reported over threshold]
# CPU time: 0.80u 0.28s 00:00:01.08 Elapsed: 00:00:00.43
# Mc/sec: 5292.73
//
Query:       gi|330507009|ref|YP_004383437.1|  [L=38]
Description: hypothetical protein MCON_0831 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       147  (0.00819901); expected 358.6 (0.02)
Passed bias filter:                      135  (0.0075297); 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: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 292.30
//
Query:       gi|330507010|ref|YP_004383438.1|  [L=37]
Description: hypothetical protein MCON_0832 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.6   0.0      0.016   14.6   0.0    1.0  1  GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     9e-07     0.016     296     323 ..       4      31 ..       1      34 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9e-07
                                       GG--SS--SB--B-THHHHHHH----SS CS
                     GDP_Man_Dehyd 296 kyfrpgevdlllgdaskakeeLgWkpkv 323
                                       ++ rpg+ +  l+d+s a++eLg++p +
  gi|330507010|ref|YP_004383438.1|   4 EKPRPGDIQDSLADISAARNELGYEPGI 31 
                                       567**********************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       141  (0.00786435); expected 358.6 (0.02)
Passed bias filter:                      135  (0.0075297); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 272.15
//
Query:       gi|330507011|ref|YP_004383439.1|  [L=199]
Description: hypothetical protein MCON_0833 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-12   48.1   1.0    2.2e-12   47.2   0.1    1.8  2  Acylphosphatase  Acylphosphatase
     0.0004   19.4   1.8    0.00047   19.2   1.8    1.2  1  DUF812           Protein of unknown function (DUF812)
     0.0022   17.4   1.5     0.0031   16.9   1.4    1.4  1  DUF2353          Uncharacterized coiled-coil protein (DUF2353
     0.0049   16.9   0.3      0.016   15.3   0.3    1.9  1  TolA_bind_tri    TolA binding protein trimerisation
     0.0061   15.5   0.9     0.0067   15.4   0.9    1.3  1  Spc7             Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.015   15.3   4.0       0.11   12.6   2.5    2.6  2  DUF1664          Protein of unknown function (DUF1664)
      0.016   14.2   1.7      0.021   13.8   1.7    1.2  1  IFT57            Intra-flagellar transport protein 57
      0.021   14.2   2.1      0.024   14.1   1.5    1.4  1  DUF4618          Domain of unknown function (DUF4618)
      0.028   14.7   1.9       0.12   12.7   0.6    2.3  2  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.03   14.8   1.4      0.038   14.4   0.5    1.6  2  Fez1             Fez1
      0.042   13.8   0.8        4.7    7.2   0.2    2.5  2  BORCS8           BLOC-1-related complex sub-unit 8
      0.043   13.9   3.4       0.69   10.0   0.2    2.5  2  DUF2730          Protein of unknown function (DUF2730)
      0.044   13.7   0.2        0.1   12.5   0.2    1.6  1  DNA_ligase_OB    NAD-dependent DNA ligase OB-fold domain
      0.047   13.5   5.6      0.047   13.5   2.2    2.5  3  Phage_GP20       Phage minor structural protein GP20
      0.057   13.0   2.6      0.065   12.8   2.6    1.2  1  PEARLI-4         Arabidopsis phospholipase-like protein (PEAR
       0.06   13.6   4.8        1.2    9.4   0.7    3.1  3  KxDL             Uncharacterized conserved protein
       0.06   13.1   1.1      0.071   12.9   0.2    1.6  2  USP8_interact    USP8 interacting
      0.077   13.7   5.6       0.98   10.1   3.3    3.0  2  Cytochrom_B562   Cytochrome b562
      0.096   12.5   0.1        4.6    7.1   0.0    2.8  3  DASH_Duo1        DASH complex subunit Duo1
       0.11   11.3   1.2       0.14   10.9   0.7    1.4  1  Tektin           Tektin family
       0.11   11.8   3.7       0.04   13.3   0.9    1.7  2  GAS              Growth-arrest specific micro-tubule binding
       0.13   12.4   5.5       0.47   10.6   1.3    3.0  4  Vps51            Vps51/Vps67
       0.13   12.9   1.8       0.17   12.6   0.4    1.9  2  YabA             Initiation control protein YabA
       0.15   12.7   0.2       0.37   11.4   0.2    1.7  1  BST2             Bone marrow stromal antigen 2
       0.18   11.1   0.2       0.29   10.3   0.2    1.3  1  TMPIT            TMPIT-like protein
       0.21   11.3   0.6       0.89    9.3   0.1    2.2  3  Baculo_19        Baculovirus 19 kDa protein conserved region
       0.22   11.8   0.8        2.4    8.5   0.1    2.4  2  DUF948           Bacterial protein of unknown function (DUF94
       0.35   11.3   6.1       0.76   10.2   0.6    2.7  2  DUF3740          Sulfatase protein
        0.5   10.2   4.5       0.63    9.8   3.7    1.6  2  DUF724           Protein of unknown function (DUF724)
       0.54   10.5   4.3       0.35   11.1   1.5    2.2  2  XhlA             Haemolysin XhlA
       0.57   10.1   8.6       0.55   10.2   1.6    2.9  3  CsbD             CsbD-like
        5.3    7.6   7.1      2e+02    2.6   3.4    3.5  2  COMP             Cartilage oligomeric matrix protein


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 !   47.2   0.1   3.9e-15   2.2e-12       2      77 ..       4      85 ..       3      91 .. 0.92
   2 ?   -1.3   0.1       5.5   3.1e+03      50      52 ..     136     138 ..     114     170 .. 0.55

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 3.9e-15
                   Acylphosphatase  2 rllvtG.rVQgvgFRkfvrrlAkelglkGy.vrNlsdg...sVeivaegeeekvekfleelksgppk.arvdeveveel 74
                                      ++++tG +V++vg+R+f++  A + gl+G+ +rN+ +g   +V +++eg+ee++++f++  +s+ p+ + v+++ +e++
  gi|330507011|ref|YP_004383439.1|  4 KVTITGeNVHNVGYRYFLMTSAIDQGLDGFnARNTMKGneqQVVALIEGNEEAIAAFKKLAESQRPEhSLVSSIVFEDT 82
                                      789***99**************************9999999**********************77777********998 PP

                   Acylphosphatase 75 eee 77
                                      +++
  gi|330507011|ref|YP_004383439.1| 83 NSN 85
                                      876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.5
                   Acylphosphatase  50 vek 52 
                                       +++
  gi|330507011|ref|YP_004383439.1| 136 MKE 138
                                       222 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.8   8.3e-07   0.00047     317     406 ..      86     175 ..      22     189 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.3e-07
                            DUF812 317 kaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpd 393
                                        ++t e ++     +l++    + +++ +++e++ ++k+++ +ik+++  ++e+k   +e + ++k+ +k  +++p+
  gi|330507011|ref|YP_004383439.1|  86 VMKTGEYAQVCTAIQLNKAIPLLLDMRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRKNTDIIPQ 162
                                       45555555555555555555566788888999999999999999999999999999999999999999999999999 PP

                            DUF812 394 aeeniekLqalve 406
                                         e i+ + ++++
  gi|330507011|ref|YP_004383439.1| 163 IHEEIKGMREDIQ 175
                                       8888888777776 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.4   5.6e-06    0.0031      59     105 ..     103     157 ..      44     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.6e-06
                           DUF2353  59 e........kekekklsqlleesreenkalkleveeLrqklkeaqgDiklLReql 105
                                       +        +++ k++   ++e++   k++k +++e++  +ke++gD+k++R+++
  gi|330507011|ref|YP_004383439.1| 103 KaipllldmRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRKNT 157
                                       1455555556666777888888888888999999999999999999999998433 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 !   15.3   0.3   2.9e-05     0.016      18      58 ..     106     146 ..      98     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.9e-05
                     TolA_bind_tri  18 qlllelqqqlealqqelreLRGqiEelqyqleqleerQrdl 58 
                                        lll++   l++++ +++e++G+i e++ ++++++   +++
  gi|330507011|ref|YP_004383439.1| 106 PLLLDMRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEM 146
                                       6899*****************************99888876 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.9   1.2e-05    0.0067     201     264 ..     108     171 ..      39     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                              Spc7 201 Leelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgws 264
                                       L  +r++l+e k +++e k +++e++ +++e + +++e+k  ++ +++++    ++ ee kg++
  gi|330507011|ref|YP_004383439.1| 108 LLDMRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRKNTDIIPQIHEEIKGMR 171
                                       5568999999999999999999999999999999999999999999999888888888877765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.5   0.00019      0.11      67     106 ..     114     153 ..      93     175 .. 0.56
   2 ?    2.5   0.0      0.25   1.4e+02      76     111 ..     154     190 ..     149     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                           DUF1664  67 ridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                                       +++++   ++e+k  +ke+k +++e+++d++e++ d++ v
  gi|330507011|ref|YP_004383439.1| 114 DLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVV 153
                                       3334444444444444444444444444444444444444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.25
                           DUF1664  76 deqkeiskeikeevtevredlse.igedvesvkeave 111
                                        ++++i+ +i+ee++ +red++     +++ v++ ++
  gi|330507011|ref|YP_004383439.1| 154 RKNTDIIPQIHEEIKGMREDIQPgYAAQFRLVQADIR 190
                                       5677889999999999999987424455555555555 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.7   3.7e-05     0.021     276     349 ..     105     175 ..      80     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.7e-05
                             IFT57 276 lqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDgsplvkikkaltklkkEik 349
                                       +  + ++++ l+e+k ++k++++ ++e++ +++e++ +++++k +m+    + tD  p  +i + ++ ++++i+
  gi|330507011|ref|YP_004383439.1| 105 IPLLLDMRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVV-RKNTDIIP--QIHEEIKGMREDIQ 175
                                       5556678899************************************987.67799999..9**********996 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.5   4.2e-05     0.024     161     228 ..      88     155 ..      49     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-05
                           DUF4618 161 kkekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeepre 228
                                       k+ +  +  +  +l++    Ll++  + +++k  +++++  i+e++ +++e+k ++++++ +++ +r+
  gi|330507011|ref|YP_004383439.1|  88 KTGEYAQVCTAIQLNKAIPLLLDMRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRK 155
                                       44455555556666777788999999999999999999999999999999999999999999888876 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.8   9.9e+02      13      41 ..      37      65 ..      13      68 .. 0.77
   2 ?   12.7   0.6   0.00021      0.12      31      79 ..     124     172 ..     111     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.8
                           BLOC1_2 13 aeleatvedyklLeklNeaasekykklkd 41
                                      +++++  +++  L + Ne+a++ +kkl++
  gi|330507011|ref|YP_004383439.1| 37 NTMKGNEQQVVALIEGNEEAIAAFKKLAE 65
                                      56667777777777778888888887765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00021
                           BLOC1_2  31 aasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                       ++   +k++k  +++++ ++++++   + ++++ + i qi+++++ + e
  gi|330507011|ref|YP_004383439.1| 124 EMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRKNTDIIPQIHEEIKGMRE 172
                                       5667799*************************************99976 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       5.8   3.3e+03      38      67 ..      41      70 ..      34     104 .. 0.55
   2 ?   14.4   0.5   6.9e-05     0.038      34     105 ..     109     176 ..     100     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.8
                              Fez1 38 aqlrelrakleekeeeikeleesleektle 67
                                      ++ +++ a +e +ee+i  +++ +e++  e
  gi|330507011|ref|YP_004383439.1| 41 GNEQQVVALIEGNEEAIAAFKKLAESQRPE 70
                                      444444444444444444444444444433 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.9e-05
                              Fez1  34 valkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelse 105
                                       + ++ +l+e++ +++e    ike++  ++e + ++++++ +++  +++++++ +    ++ee+k++re+++ 
  gi|330507011|ref|YP_004383439.1| 109 LDMRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRKNTDIIPQ----IHEEIKGMREDIQP 176
                                       667888888888888888888888888888888888888888877777777666....88888999888765 PP

>> BORCS8  BLOC-1-related complex sub-unit 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.048        27      46      81 ..      34      69 ..      31      90 .. 0.83
   2 ?    7.2   0.2    0.0083       4.7      38      99 ..     102     163 ..     100     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.048
                            BORCS8 46 ekkkevkeleeelqgacydveyaisavksikesess 81
                                      + ++ +k  e+++   ++  e+ai+a k++ es+ +
  gi|330507011|ref|YP_004383439.1| 34 NARNTMKGNEQQVVALIEGNEEAIAAFKKLAESQRP 69
                                      67899999************************9954 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0083
                            BORCS8  38 rkalPelvekkkevkeleeelqgacydveyaisavksikesessfeniqelLknsiflkqql 99 
                                        ka+P l++ ++++ke++ ++++   d+++    +k++k   ++++  ++++++  ++  q+
  gi|330507011|ref|YP_004383439.1| 102 NKAIPLLLDMRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRKNTDIIPQI 163
                                       5899**************99999999999999999999887777766666666665555555 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.6    0.0014      0.79      61      89 ..     111     139 ..     101     140 .. 0.89
   2 ?   10.0   0.2    0.0012      0.69      64      95 ..     128     159 ..     127     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                           DUF2730  61 takdlekLkllladlrgelkaleaevrql 89 
                                        ++dl+++k ++++++g++k+++ +++++
  gi|330507011|ref|YP_004383439.1| 111 MRDDLKEMKGDMKEMKGDIKEMKGDMKEM 139
                                       5799******************9999876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0012
                           DUF2730  64 dlekLkllladlrgelkaleaevrqlshqvdL 95 
                                       d++++k ++++++g++k+++ +++ +++ +d+
  gi|330507011|ref|YP_004383439.1| 128 DIKEMKGDMKEMKGDMKEMKGDMKVVRKNTDI 159
                                       78889999999999999999999999998887 PP

>> DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00018       0.1      51      76 ..     147     172 ..     137     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     DNA_ligase_OB  51 igdtVvvekaGdvIPevvgvvlekre 76 
                                        gd+ vv+k  d+IP++ + ++ +re
  gi|330507011|ref|YP_004383439.1| 147 KGDMKVVRKNTDIIPQIHEEIKGMRE 172
                                       69*****************9999887 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 ?   -1.4   0.0       3.4   1.9e+03      83      97 ..      24      38 ..      21      56 .. 0.65
   2 ?   -0.2   0.1       1.4   8.1e+02      62      87 ..      82     107 ..      34     113 .. 0.49
   3 ?   13.5   2.2   8.3e-05     0.047      42      80 ..     113     151 ..     110     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.4
                        Phage_GP20 83 naielaLkeakakne 97
                                      +ai++ L++ +a+n+
  gi|330507011|ref|YP_004383439.1| 24 SAIDQGLDGFNARNT 38
                                      577777777777764 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                        Phage_GP20  62 qaknkkakaeyeakiadlkldnaiel 87 
                                       ++ n  +  ey++  ++++l++ai l
  gi|330507011|ref|YP_004383439.1|  82 TNSNVMKTGEYAQVCTAIQLNKAIPL 107
                                       33333445566666666666666665 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 8.3e-05
                        Phage_GP20  42 edLkkkakdneeLqkqieelqaknkkakaeyeakiadlk 80 
                                       +dLk++++d +e++ +i+e++ ++k+ k ++++   d+k
  gi|330507011|ref|YP_004383439.1| 113 DDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMK 151
                                       689999999999999999999999998877766555555 PP

>> PEARLI-4  Arabidopsis phospholipase-like protein (PEARLI 4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.6   0.00012     0.065     203     254 ..     109     160 ..      57     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                          PEARLI-4 203 llkkqEmekqekelaekEKeikevrekvtemaaklgelemkrarlekrlafl 254
                                       l  ++++++++ +++e+  +ike++  ++em++ + e++ +   + k+ +++
  gi|330507011|ref|YP_004383439.1| 109 LDMRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRKNTDII 160
                                       5567888888888888888888888888888888888876666666666555 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       8.4   4.7e+03      67      83 ..      53      69 ..      42      71 .. 0.59
   2 ?    8.5   0.3    0.0042       2.3      49      77 ..     107     135 ..      74     138 .. 0.55
   3 ?    9.4   0.7    0.0022       1.2      38      74 ..     124     160 ..     122     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8.4
                              KxDL 67 ifkkirslkaklakkyP 83
                                        + i ++k+ ++++ P
  gi|330507011|ref|YP_004383439.1| 53 NEEAIAAFKKLAESQRP 69
                                      44556666666666666 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0042
                              KxDL  49 rfkqgtkllkevkkdLesifkkirslkak 77 
                                        + +   +lke+k d++ ++  i+ +k  
  gi|330507011|ref|YP_004383439.1| 107 LLLDMRDDLKEMKGDMKEMKGDIKEMKGD 135
                                       44455556666666666666666666654 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0022
                              KxDL  38 lsqerlaklrarfkqgtkllkevkkdLesifkkirsl 74 
                                       +++   ++++ ++k+ + ++ke+k d++ ++k+++ +
  gi|330507011|ref|YP_004383439.1| 124 EMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRKNTDII 160
                                       556678899999999999*********9999998877 PP

>> USP8_interact  USP8 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       5.8   3.2e+03      20      37 ..      57      74 ..      36      96 .. 0.48
   2 ?   12.9   0.2   0.00013     0.071       2      59 ..     111     168 ..     110     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.8
                     USP8_interact 20 vaeqkqqlseqkrelell 37
                                      +a  k+  ++q+ e +l+
  gi|330507011|ref|YP_004383439.1| 57 IAAFKKLAESQRPEHSLV 74
                                      222333333333333333 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00013
                     USP8_interact   2 Lrelvqkqqqkiaelkkevaeqkqqlseqkrelellkeyiralrstnpvlraladqle 59 
                                       +r+ +++ +  ++e+k +++e+k  ++e k +++ +k  ++ +r+ +  +++++++++
  gi|330507011|ref|YP_004383439.1| 111 MRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRKNTDIIPQIHEEIK 168
                                       68888999999******************************************99885 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.6   9.1e+02      80      98 ..      53      71 ..      24      75 .. 0.62
   2 ?   10.1   3.3    0.0018      0.98      20      76 ..     113     168 ..      99     196 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.6
                    Cytochrom_B562 80 leeakaalkelkdlrkeyH 98
                                      +eea aa k+l + ++  H
  gi|330507011|ref|YP_004383439.1| 53 NEEAIAAFKKLAESQRPEH 71
                                      3455555555555555555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0018
                    Cytochrom_B562  20 ddaeelkkalkelraaaedakeatpsklekdseeqkdYqeGldklidqldkaealak 76 
                                       dd +e+k ++ke++   ++ k  +  ++++d +e+k+  +   k +d + ++++++k
  gi|330507011|ref|YP_004383439.1| 113 DDLKEMKGDMKEMKGDIKEMKGDMK-EMKGDMKEMKGDMKVVRKNTDIIPQIHEEIK 168
                                       5566666666666666666555555.5566555555555555555555555555544 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0083       4.6       8      39 ..     100     131 ..      98     134 .. 0.90
   2 ?    3.0   0.1      0.15        86      16      34 ..     129     147 ..     123     165 .. 0.57
   3 ?    0.9   0.0      0.69   3.8e+02       5      31 ..     149     175 ..     145     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0083
                         DASH_Duo1   8 qLrkinevienviesLkkaksniervketves 39 
                                       qL+k ++ + +++++Lk++k++++++k  +++
  gi|330507011|ref|YP_004383439.1| 100 QLNKAIPLLLDMRDDLKEMKGDMKEMKGDIKE 131
                                       799999*******************9988776 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.15
                         DASH_Duo1  16 ienviesLkkaksniervk 34 
                                       i+ +++++k++k++++++k
  gi|330507011|ref|YP_004383439.1| 129 IKEMKGDMKEMKGDMKEMK 147
                                       4444444455554444443 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.69
                         DASH_Duo1   5 EleqLrkinevienviesLkkaksnie 31 
                                       +++ +rk  ++i +++e++k ++++i+
  gi|330507011|ref|YP_004383439.1| 149 DMKVVRKNTDIIPQIHEEIKGMREDIQ 175
                                       567888888999999999999888876 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7   0.00025      0.14     255     299 ..     110     154 ..      78     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                            Tektin 255 etedaknkleeqlkkvleeiaeleknieeLekairdkeaplklaq 299
                                       +++d  ++++ + k+++ +i+e++ +++e++ +++++++ +k++ 
  gi|330507011|ref|YP_004383439.1| 110 DMRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVVR 154
                                       334444556667788888999999999999999999999999975 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 ?   -2.3   0.1       4.1   2.3e+03     150     168 ..      45      63 ..      34      77 .. 0.46
   2 ?   13.3   0.9   7.1e-05      0.04      39      98 ..     112     171 ..     107     195 .. 0.55

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.1
                               GAS 150 klkalqeelEkkeaqleev 168
                                       ++ al e  E++ a ++++
  gi|330507011|ref|YP_004383439.1|  45 QVVALIEGNEEAIAAFKKL 63 
                                       3333333333333333333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.1e-05
                               GAS  39 kkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkele 98 
                                       +   ++++ +++e++ + k++k  +k+ + +++e++ ++k  +k    + ++++++k + 
  gi|330507011|ref|YP_004383439.1| 112 RDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRKNTDIIPQIHEEIKGMR 171
                                       444444444444555555555555555555555544444444444444444444444444 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.3   0.00084      0.47      53      84 ..     108     139 ..     107     142 .. 0.91
   2 ?    8.0   1.2    0.0053         3      59      82 ..     128     151 ..     124     156 .. 0.86
   3 ?    1.6   0.4      0.54     3e+02      61      75 ..     144     158 ..     137     172 .. 0.61
   4 ?   -0.8   0.0         3   1.7e+03      56      68 ..     163     175 ..     152     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00084
                             Vps51  53 LisasdtIrkmksemdkldqklselkqaiski 84 
                                       L++  d++++mk++m++++  ++e+k  ++++
  gi|330507011|ref|YP_004383439.1| 108 LLDMRDDLKEMKGDMKEMKGDIKEMKGDMKEM 139
                                       78899*********************999887 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0053
                             Vps51  59 tIrkmksemdkldqklselkqais 82 
                                       +I++mk++m++++  ++e+k  ++
  gi|330507011|ref|YP_004383439.1| 128 DIKEMKGDMKEMKGDMKEMKGDMK 151
                                       69****************998776 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.54
                             Vps51  61 rkmksemdkldqkls 75 
                                       ++mk++m+ ++++++
  gi|330507011|ref|YP_004383439.1| 144 KEMKGDMKVVRKNTD 158
                                       455555555555554 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3
                             Vps51  56 asdtIrkmksemd 68 
                                       + ++I+ m+++++
  gi|330507011|ref|YP_004383439.1| 163 IHEEIKGMREDIQ 175
                                       4577888887764 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       6.5   3.6e+03      28      51 ..      43      66 ..      32      92 .. 0.64
   2 ?   12.6   0.4    0.0003      0.17       6      53 ..     111     161 ..     108     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.5
                                      HHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA 28 keelaelleenaeLeleneklrer 51
                                      ++++++l+e n+e  +  +kl e 
  gi|330507011|ref|YP_004383439.1| 43 EQQVVALIEGNEEAIAAFKKLAES 66
                                      556666666666655555555544 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0003
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...X CS
                              YabA   6 lfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl...e 53 
                                       + d l+e++ +++e++ +++e+k +++e+  + +e++ + + +r++     
  gi|330507011|ref|YP_004383439.1| 111 MRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRKNTdiiP 161
                                       567888999999999999999999999999999999998888888775552 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00066      0.37      48      86 ..     109     147 ..      93     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00066
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  48 vtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdae 86 
                                        +++++L+++k   ++++  ++e++g++k+++  +++ +
  gi|330507011|ref|YP_004383439.1| 109 LDMRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMK 147
                                       67899**************************99999876 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00052      0.29      22      82 ..     112     174 ..      98     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00052
                             TMPIT  22 kqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelkerkkvl 82 
                                       + +l+e++   ++++ +ik+ k ++ke+k ++k++k ++k  +++ +++ +++ee+k +++ +
  gi|330507011|ref|YP_004383439.1| 112 RDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKvvRKNTDIIPQIHEEIKGMREDI 174
                                       456677777777788888888888888888888887775555777778888888877766655 PP

>> Baculo_19  Baculovirus 19 kDa protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.4   2.5e+03      66      84 ..      37      55 ..      30      65 .. 0.65
   2 ?    9.3   0.1    0.0016      0.89      79     100 ..      79     100 ..      53     107 .. 0.82
   3 ?   -1.8   0.0       4.2   2.3e+03      70      88 ..     147     165 ..     142     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.4
                         Baculo_19 66 vfCakneqavvainrdtik 84
                                       +   neq+vva+ + + +
  gi|330507011|ref|YP_004383439.1| 37 NTMKGNEQQVVALIEGNEE 55
                                      3445788888887665544 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0016
                         Baculo_19  79 nrdtikdisetGiykivCtsvs 100
                                        +dt +++ +tG+y++vCt+++
  gi|330507011|ref|YP_004383439.1|  79 FEDTNSNVMKTGEYAQVCTAIQ 100
                                       46788999***********996 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.2
                         Baculo_19  70 kneqavvainrdtikdise 88 
                                       k++ +vv+ n+d i++i e
  gi|330507011|ref|YP_004383439.1| 147 KGDMKVVRKNTDIIPQIHE 165
                                       6788999999999999976 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.75   4.2e+02      31      61 ..      35      65 ..      25      88 .. 0.86
   2 ?    8.5   0.1    0.0042       2.4      18      65 ..     105     152 ..      95     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.75
                            DUF948 31 aaatieelekqvdpilkevedllakvnelle 61
                                      a++t+++ e+qv ++++  e+++a  ++l+e
  gi|330507011|ref|YP_004383439.1| 35 ARNTMKGNEQQVVALIEGNEEAIAAFKKLAE 65
                                      7899999999999999999999999988776 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0042
                            DUF948  18 ivvllklkktldeaaatieelekqvdpilkevedllakvnelledvne 65 
                                       i++ll +++ l+e++  ++e++ +++++  +++++   ++e+  d++ 
  gi|330507011|ref|YP_004383439.1| 105 IPLLLDMRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKV 152
                                       677888888888888888888888888888888888888887666554 PP

>> DUF3740  Sulfatase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.6    0.0014      0.76     112     140 ..      99     127 ..      84     131 .. 0.89
   2 ?    3.0   0.7      0.23   1.3e+02     128     139 ..     136     147 ..     127     157 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0014
                           DUF3740 112 lqiDkeIelLkdKiknLkevkghlrekrp 140
                                        q++k I lL d +++Lke+kg ++e + 
  gi|330507011|ref|YP_004383439.1|  99 IQLNKAIPLLLDMRDDLKEMKGDMKEMKG 127
                                       578899********************986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.23
                           DUF3740 128 Lkevkghlrekr 139
                                       +ke+kg ++e +
  gi|330507011|ref|YP_004383439.1| 136 MKEMKGDMKEMK 147
                                       344444444443 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.5     2e+03     131     150 ..      49      68 ..      31     100 .. 0.55
   2 ?    9.8   3.7    0.0011      0.63      90     146 ..     101     157 ..      57     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.5
                            DUF724 131 eidelekkilelerqlallk 150
                                        i+ +e++i+ +++ +++ +
  gi|330507011|ref|YP_004383439.1|  49 LIEGNEEAIAAFKKLAESQR 68 
                                       44444444443333333333 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0011
                            DUF724  90 lqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerql 146
                                       l + +  Ll ++d+ ++++  +k+++ +i+e + ++++++ +++e++  ++ ++++ 
  gi|330507011|ref|YP_004383439.1| 101 LNKAIPLLLDMRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRKNT 157
                                       5567888999********************999999999999999998887766655 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.5   0.00062      0.35       2      48 ..     111     157 ..     110     160 .. 0.86
   2 ?   -1.8   0.0       6.7   3.8e+03      37      46 ..     163     172 ..     152     175 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00062
                              XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleedlkklesnq 48 
                                       ++++l++++++ ++++ ++++ + ++ e++   k++  d+k   +n+
  gi|330507011|ref|YP_004383439.1| 111 MRDDLKEMKGDMKEMKGDIKEMKGDMKEMKGDMKEMKGDMKVVRKNT 157
                                       78999999999999999999999999999999999999988777775 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.7
                              XhlA  37 leedlkkles 46 
                                       ++e++k + +
  gi|330507011|ref|YP_004383439.1| 163 IHEEIKGMRE 172
                                       4444444333 PP

>> CsbD  CsbD-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.2   2.4e+03      30      39 ..      40      49 ..      34      57 .. 0.65
   2 ?   10.2   1.6   0.00098      0.55      24      49 ..     113     138 ..     112     139 .. 0.84
   3 ?    6.6   1.6     0.013       7.2       2      21 ..     131     150 ..     130     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.2
                              CsbD 30 eGkadqlkGk 39
                                      +G+++q+++ 
  gi|330507011|ref|YP_004383439.1| 40 KGNEQQVVAL 49
                                      5666666654 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00098
                              CsbD  24 dekleaeGkadqlkGkaqqkygdakd 49 
                                       d+ +e +G  ++ kG++++  gd k+
  gi|330507011|ref|YP_004383439.1| 113 DDLKEMKGDMKEMKGDIKEMKGDMKE 138
                                       78888899999999999999999887 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.013
                              CsbD   2 kikgkaeqvkGkvKeaaGka 21 
                                       ++kg ++++kG +Ke  G++
  gi|330507011|ref|YP_004383439.1| 131 EMKGDMKEMKGDMKEMKGDM 150
                                       57899999999999977765 PP

>> COMP  Cartilage oligomeric matrix protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   3.4      0.35     2e+02      10      28 ..     101     119 ..      98     158 .. 0.65
   2 ?    2.2   0.1      0.47   2.6e+02      15      31 ..     158     174 ..     154     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.35
                              COMP  10 LseltqllkeLreelrqQv 28 
                                       L+  + ll ++r++l+++ 
  gi|330507011|ref|YP_004383439.1| 101 LNKAIPLLLDMRDDLKEMK 119
                                       5555555666666665553 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.47
                              COMP  15 qllkeLreelrqQvkEi 31 
                                        ++  ++ee++ +++ i
  gi|330507011|ref|YP_004383439.1| 158 DIIPQIHEEIKGMREDI 174
                                       577789*****999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1175  (0.0655363); expected 358.6 (0.02)
Passed bias filter:                      738  (0.0411624); expected 358.6 (0.02)
Passed Vit filter:                       147  (0.00819901); 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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 1387.54
//
Query:       gi|330507012|ref|YP_004383440.1|  [L=104]
Description: hypothetical protein MCON_0834 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   13.8   0.0      0.075   12.8   0.0    1.6  1  SHOCT     Short C-terminal domain


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.2e-06     0.075       2      28 .]      58      84 ..      57      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-06
                             SHOCT  2 aLekLkeLyarGeIteEEFeakKakLL 28
                                      +L+ ++ L+ +G It  E+   K++LL
  gi|330507012|ref|YP_004383440.1| 58 KLQHYRYLLNSGSITNSEYASLKDQLL 84
                                      6888899*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 885.99
//
Query:       gi|330507013|ref|YP_004383441.1|  [L=380]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-23   82.3   0.2    2.9e-23   81.6   0.2    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    3.6e-22   78.8   0.0    8.4e-22   77.6   0.0    1.6  1  OrfB_IS605      Probable transposase
    8.2e-13   47.6   0.6    1.8e-12   46.5   0.6    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.058   12.9   1.4        1.9    8.1   0.1    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.059   13.0   1.4       0.13   12.0   1.4    1.5  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.087   12.9   0.2       0.15   12.1   0.2    1.4  1  DZR             Double zinc ribbon
       0.13   12.2   0.2       0.26   11.3   0.2    1.4  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type
       0.42   10.5   3.0        3.9    7.3   0.1    2.2  2  CortBP2         Cortactin-binding protein-2


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 !   81.6   0.2   1.3e-26   2.9e-23       1      68 [.     304     371 ..     304     372 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 1.3e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++kl++  +yka+++G+ ve+vnp+ TS+ Cs Cg++++++ls+r+++C+ Cg+++drD+nAaiNil+
  gi|330507013|ref|YP_004383441.1| 304 WNKLITTTSYKAEWAGKRVELVNPNGTSQICSGCGQVVQKDLSERVHRCSFCGLTLDRDHNAAINILR 371
                                       899***************************************************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   0.0   3.8e-25   8.4e-22       2     117 ..     178     290 ..     177     292 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 3.8e-25
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                       + veve+++p pk++  +g+D+G++ ++t+++++    + ++r++  ++ +lak++++l+   k++  + +a + + 
  gi|330507013|ref|YP_004383441.1| 178 FLVEVEPDEPLPKTGLSIGVDVGLKSFITLSNGE---QVDNPRFFVHEENALAKAQRKLSNAEKGTPERARALKVVH 251
                                       789*******************************...**************************************** PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       r+h++++++r+++++kl+ +l+k ++ ++ e+Ln+++m+
  gi|330507013|ref|YP_004383441.1| 252 RVHERITNKRDDFVQKLSISLVKSYDLIAFEDLNIKGMV 290
                                       **************************************8 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.6     8e-16   1.8e-12       1      47 []       1      46 [.       1      46 [. 0.97

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 8e-16
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lk  +yr+yPT+ Q++k+  +++ +R+ YN  +a r +aye+e k
  gi|330507013|ref|YP_004383441.1|  1 M-LKVLRYRIYPTKSQRTKMDDALELCRWTYNEVIAIRMNAYEQESK 46
                                      8.99***************************************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 ?    8.1   0.1   0.00085       1.9      13      32 ..     325     344 ..     319     349 .. 0.79
   2 ?    3.7   0.2      0.02        44      21      30 ..     351     360 ..     344     364 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00085
                                       EETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon  13 eDpergelvCtdCGlVledn 32 
                                       ++p+ +  +C+ CG V++ +
  gi|330507013|ref|YP_004383441.1| 325 VNPNGTSQICSGCGQVVQKD 344
                                       56666666*********876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.02
                                       EESSSSBEEE CS
                      TF_Zn_Ribbon  21 vCtdCGlVle 30 
                                       +C++CGl l+
  gi|330507013|ref|YP_004383441.1| 351 RCSFCGLTLD 360
                                       8*****9886 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.4   5.6e-05      0.13       2      29 ..     330     357 ..     330     358 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.6e-05
                     zf-NADH-PPase   2 thrFCgrCGaptepaeggwarvCpaCgl 29 
                                       t++ C+ CG+ +++   ++  +C+ Cgl
  gi|330507013|ref|YP_004383441.1| 330 TSQICSGCGQVVQKDLSERVHRCSFCGL 357
                                       6899**********************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   6.9e-05      0.15      12      44 ..     331     365 ..     324     368 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.9e-05
                               DZR  12 arfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       ++ Cs Cg+ +++  +   +rC+ Cg  +d +++ 
  gi|330507013|ref|YP_004383441.1| 331 SQICSGCGQVVQKDLSerVHRCSFCGLTLDRDHNA 365
                                       689********97766899*******999999986 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 ?   11.3   0.2   0.00011      0.26      18      44 ..     332     359 ..     321     366 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                          zf-C2HC5  18 pnClnCGkiiCakegls.kpCsfCgspl 44 
                                        +C  CG+++ +      ++CsfCg  l
  gi|330507013|ref|YP_004383441.1| 332 QICSGCGQVVQKDLSERvHRCSFCGLTL 359
                                       58*******977655547******9665 PP

>> CortBP2  Cortactin-binding protein-2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.4     0.029        65     152     188 ..      41      77 ..      36      80 .. 0.88
   2 ?    7.3   0.1    0.0017       3.9      92     141 ..     221     270 ..     215     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.029
                           CortBP2 152 qekaqkkklekelkkllekleeerkkqkqivllLvkE 188
                                       +e+++k+    + kkll  ++ee+ ++kq+ + +++E
  gi|330507013|ref|YP_004383441.1|  41 YEQESKSLSYYDTKKLLPGWKEEKPELKQVHSQVLQE 77 
                                       677777778889**********************998 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0017
                           CortBP2  92 kqreaqermleqLaaaekrhrkvleeLeeekrkheedtaqgddvtylLek 141
                                       +  +a  + +++L++aek   +  + L+   r he+ t++ dd++  L  
  gi|330507013|ref|YP_004383441.1| 221 HEENALAKAQRKLSNAEKGTPERARALKVVHRVHERITNKRDDFVQKLSI 270
                                       5667888999**********************************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2828.55
//
Query:       gi|330507014|ref|YP_004383442.1|  [L=136]
Description: transposase, IS200-like MITE [Methanosaeta concilii GP6]
Scores for complete 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-35  121.0   0.3    3.2e-35  120.8   0.3    1.0  1  Y1_Tnp    Transposase IS200 like


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.8   0.3   1.8e-39   3.2e-35       1     121 []      14     133 ..      14     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 1.8e-39
                            Y1_Tnp   1 vsnlkyhivlvtkyRrkvltgeveerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgassr 77 
                                       v+n++yh+v+ tkyRrkvl g+++e+l+ + + ia++k++++++ e+mpDHvHl+v+++p  ++++i k +kg +++
  gi|330507014|ref|YP_004383442.1|  14 VYNVYYHFVWSTKYRRKVLIGSIAEDLHWLHELIAKQKGITLINQEIMPDHVHLFVTAHPIFAPANIAKIFKGITAK 90 
                                       689************************************************************************** PP

                            Y1_Tnp  78 linkefpelkkkklkkeslWqrgYfvstvgeasletvkrYIenq 121
                                       ++++++pel+++ l  ++lW+++Y+v t+g+a++++++rY+e q
  gi|330507014|ref|YP_004383442.1|  91 KLFEKHPELRDQLLD-GHLWNPSYYVGTCGDATKDVIERYVEMQ 133
                                       **************9.77***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 936.53
//
Query:       gi|330507015|ref|YP_004383443.1|  [L=128]
Description: hypothetical protein MCON_0840 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-06   27.8   0.0    3.7e-06   27.2   0.0    1.3  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 !   27.2   0.0   2.1e-10   3.7e-06       3      84 ..       6      91 ..       4      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.1e-10
                   Acylphosphatase  3 llvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdg...sVeivaeg.eeekvekfleelksgppkarvdeveveeleee 77
                                      ++ +GrV gvg+R  +  lA+e+  +G ++ + d    sV + aeg ++++ e f +++  ++  ++ d+v+++ ++  
  gi|330507015|ref|YP_004383443.1|  6 AFLSGRVPGVGYRVKAITLADEMDPAGIIQDRLDKsvgSVLVIAEGkKKDESEWFTSAIAVKNALIHADNVDAQYSQGS 84
                                      5689**************************9877656699******5555588899999999999*******9999999 PP

                   Acylphosphatase 78 eefkdFe 84
                                      ++++ F+
  gi|330507015|ref|YP_004383443.1| 85 GQHSAFR 91
                                      9988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 932.00
//
Query:       gi|330507016|ref|YP_004383444.1|  [L=80]
Description: hypothetical protein MCON_0841 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 638.72
//
Query:       gi|330507017|ref|YP_004383445.1|  [L=304]
Description: hypothetical protein MCON_0842 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-11   42.8   0.0    1.5e-10   42.0   0.0    1.4  1  Methyltransf_24  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   8.6e-15   1.5e-10       2     106 .]     124     230 ..     123     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 8.6e-15
                   Methyltransf_24   2 EiGvysGvstlwllralrrnga.....grlvavdhdpgaeeaaalare..aglddrvrlikadseealasla.agsi 70 
                                       EiG  sG+stl+ ++a+ +n++      +l+a+++ p   +    +++  +gl++ v+   +d ++   +++   + 
  gi|330507017|ref|YP_004383445.1| 124 EIG--SGYSTLLAAQAVLKNEEegydnCELIAFEPYP---N--DTLKSgfHGLSKLVTAKIQDVPSC--RFNeLNKN 191
                                       9**..*****************99999999*******...4..456664566666666666666664..33344689 PP

                   Methyltransf_24  71 DllfiDgghaa...eavledleallprlapggvvlfdDi 106
                                       D+lfiD +h+    ++v+ ++ ++ p+l++g +v+++Di
  gi|330507017|ref|YP_004383445.1| 192 DILFIDSSHVLmigSDVQYEYLNIMPKLKKGVLVHIHDI 230
                                       **********55559***********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2542.81
//
Query:       gi|330507018|ref|YP_004383446.1|  [L=86]
Description: hypothetical protein MCON_0844 [Methanosaeta concilii GP6]
Scores for 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-06   27.4   0.0    3.7e-06   27.1   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   2.1e-10   3.7e-06       5      60 ..      18      73 ..      15      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.1e-10
                   HicB_lk_antitox  5 iekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipepss 60
                                      +e de + y   vPdlpG++ +g t+e+  ++  ++ie ++   +  g+ ip   s
  gi|330507018|ref|YP_004383446.1| 18 MEDDEPEPYYAHVPDLPGVWATGRTFEDCRKELVSVIEGWIALRLRFGDPIPPIDS 73
                                      67888899***********************************9999999996543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 633.88
//
Query:       gi|330507019|ref|YP_004383447.1|  [L=215]
Description: acylphosphatase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-20   73.1   0.2    4.7e-20   71.8   0.0    1.7  2  Acylphosphatase  Acylphosphatase
     0.0022   18.0   3.9     0.0041   17.2   3.9    1.4  1  DUF1664          Protein of unknown function (DUF1664)
     0.0028   16.5   0.8      0.051   12.4   0.5    2.0  2  Cas_Cas02710     CRISPR-associated protein (Cas_Cas02710)
  ------ inclusion threshold ------
      0.045   13.9   0.2       0.19   11.8   0.0    1.8  2  DUF1115          Protein of unknown function (DUF1115)
      0.096   12.1   8.0       0.14   11.6   8.0    1.2  1  DUF3552          Domain of unknown function (DUF3552)
       0.12   11.3   5.4       0.22   10.3   4.1    1.8  2  Spc7             Spc7 kinetochore protein
       0.53   10.8   9.8       0.48   10.9   7.9    1.8  2  DUF16            Protein of unknown function DUF16


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.0   1.8e-23   4.7e-20       2      85 .]       5      88 ..       4      88 .. 0.96
   2 ?   -2.6   0.0         3   7.6e+03      49      68 ..     177     198 ..     163     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 1.8e-23
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      +++  G VQ+vgFR  v ++A++lgl+G+v+Nl+  +V ivaegee+++++fl++++ +  ++rv++++v+++++++ef
  gi|330507019|ref|YP_004383447.1|  5 EIIAGGDVQRVGFRDAVWKIARNLGLSGTVQNLEPYDVSIVAEGEEDALKEFLKAINIQDGPIRVQKLKVNWSAATGEF 83
                                      677889****************************************************9999****************9 PP

                   Acylphosphatase 81 kdFei 85
                                        F+i
  gi|330507019|ref|YP_004383447.1| 84 LYFKI 88
                                      99987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3
                   Acylphosphatase  49 kvekfleelksgppk..arvde 68 
                                       +++ + ++l+++  k  ar+++
  gi|330507019|ref|YP_004383447.1| 177 EIRGMRSDLHENANKrlARIED 198
                                       4556666666644444577765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.9   1.6e-06    0.0041      24     120 ..     110     210 ..     104     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.6e-06
                           DUF1664  24 kGwklsd.lmfvTkrslsdave..svskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredls 97 
                                       +G+++ +  ++v k +l    e  s++k + + ++++ + ++++ ++ d + +k+d ++e++ e+ +e+  +r+dl+
  gi|330507019|ref|YP_004383447.1| 110 RGIEVGEqNLMVSKENLMVSKEnlSIGKMMLEKQDKMLEKQDKMIEKQDGMLEKQDRTIETQDETLDEIRGMRSDLH 186
                                       66666542588999998665551268899*********************************************985 PP

                           DUF1664  98 .eigedvesvkeavegleskleri 120
                                        + ++ +  +++ + +++ +++++
  gi|330507019|ref|YP_004383447.1| 187 eNANKRLARIEDDIVEIKRSIREL 210
                                       256777888888888888777776 PP

>> Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.018        47     254     276 ..      98     120 ..      35     125 .. 0.87
   2 !   12.4   0.5     2e-05     0.051     201     253 ..     139     194 ..     122     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.018
                                       TT-HHHHHHHHHHHHHHHHHHHH CS
                      Cas_Cas02710 254 eeryddAalrlYRalELlsqerl 276
                                        er+d+A+ +l R +E  +q+++
  gi|330507019|ref|YP_004383447.1|  98 GERFDVAVGLLHRGIEVGEQNLM 120
                                       69**************9999876 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2e-05
                                       GGGGGHHHHHHHHHHHHHHHHHHHHT-TT-HHH......HHHHHHHHHHHHHH.CT CS
                      Cas_Cas02710 201 vlnaerekleallevlralekilkekeaaleklrkf...vlalladLlanAerRaa 253
                                       +l+++ + le++ +++++ + +l+++++  e + +    ++ +  dL++nA++R a
  gi|330507019|ref|YP_004383447.1| 139 MLEKQDKMLEKQDKMIEKQDGMLEKQDRTIETQDETldeIRGMRSDLHENANKRLA 194
                                       7899*********************99999988877799***************87 PP

>> DUF1115  Protein of unknown function (DUF1115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.3e-05      0.19      14      55 ..      18      60 ..      11      63 .. 0.84
   2 ?   -0.4   0.1      0.43   1.1e+03      73      84 ..     148     159 ..      85     191 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.3e-05
                           DUF1115 14 rfkvdknAkqlsltGvvllg.pkfnlvvveGgekaikkYkklm 55
                                      r  v k A  l+l+G v    p+   +v+eG+e a+k++ k +
  gi|330507019|ref|YP_004383447.1| 18 RDAVWKIARNLGLSGTVQNLePYDVSIVAEGEEDALKEFLKAI 60
                                      67899**********66555555599*************8877 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.43
                           DUF1115  73 eekeaakekkee 84 
                                       e+++++ ek++ 
  gi|330507019|ref|YP_004383447.1| 148 EKQDKMIEKQDG 159
                                       222222222222 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   8.0   5.3e-05      0.14      85     142 ..     138     195 ..     113     200 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.3e-05
                           DUF3552  85 kRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrqeLer 142
                                         l++++++L+++++ +ek++  le++++ ++++ ++l+e +   ++l+e+ +++L r
  gi|330507019|ref|YP_004383447.1| 138 MMLEKQDKMLEKQDKMIEKQDGMLEKQDRTIETQDETLDEIRGMRSDLHENANKRLAR 195
                                       3345555555555555555555555555555555555555555555555555555555 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.13   3.3e+02       5      18 ..      50      63 ..      46      63 .. 0.82
   2 ?   10.3   4.1   8.7e-05      0.22     143     222 ..     132     207 ..      92     214 .. 0.44

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.13
                              Spc7  5 pisLqdFLnmtgIr 18
                                      +  L++FL+ ++I+
  gi|330507019|ref|YP_004383447.1| 50 EDALKEFLKAINIQ 63
                                      5579*********7 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.7e-05
                              Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekk 219
                                       +l+   + le+++++Lekq + +++    le++  ++e + e+l e    +  + ++  e++ ++la+++ +i e k
  gi|330507019|ref|YP_004383447.1| 132 NLSIGKMMLEKQDKMLEKQDKMIEKQDGMLEKQDRTIETQDETLDE----IRGMRSDLHENANKRLARIEDDIVEIK 204
                                       2222222333333333333333333333333333333333333333....222223333333333333333333333 PP

                              Spc7 220 kel 222
                                       + +
  gi|330507019|ref|YP_004383447.1| 205 RSI 207
                                       333 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.2   5.6e+03      50      68 ..      53      71 ..      33      83 .. 0.54
   2 ?   10.9   7.9   0.00019      0.48      33     103 ..     123     197 ..     116     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.2
                                      HHHHHHHHHHHHHHHHHHH CS
                             DUF16 50 inkleqkvekqgekikelk 68
                                      +++  ++++ q+  i+ +k
  gi|330507019|ref|YP_004383447.1| 53 LKEFLKAINIQDGPIRVQK 71
                                      3333444444444333333 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHH....HHHHHHHHHHHC CS
                             DUF16  33 kqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetlelilet....LqkinkRlDsie 103
                                       k++L  ++++++  +  ++k+ +  ekq++ i+++    ++q++ ++++detl+ i        ++ nkRl +ie
  gi|330507019|ref|YP_004383447.1| 123 KENLMVSKENLSIGKMMLEKQDKMLEKQDKMIEKQDGMLEKQDRTIETQDETLDEIRGMrsdlHENANKRLARIE 197
                                       5677777788888888999999999*******999999*********9999999886431111456789998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1130  (0.0630264); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1631.73
//
Query:       gi|330507020|ref|YP_004383448.1|  [L=61]
Description: hypothetical protein MCON_0849 [Methanosaeta concilii GP6]
Scores for 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   54.7   3.4    1.2e-14   54.5   3.4    1.0  1  DUF104          Protein of unknown function DUF104
     0.0014   18.5   1.1     0.0038   17.1   0.3    1.9  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.047   13.5   0.0      0.053   13.4   0.0    1.2  1  TrkA_C          TrkA-C domain


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   3.4     2e-18   1.2e-14       1      59 []       1      56 [.       1      57 [. 0.94

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 2e-18
                            DUF104  1 MskvIeavYEnGvLKPLekvdLkEGeevkikIeeakeilkklkgilkeadeeeleelle 59
                                      M+  I+a+YE++ LKP++++ LkEG ev+i++++  + +++++g++k + ++  +e++e
  gi|330507020|ref|YP_004383448.1|  1 MGIKIRARYEGNALKPFKEIGLKEGDEVEIVVKK--SAVDEFHGMMK-IPKKLADEIIE 56
                                      8999******************************..**********9.88888888776 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   6.4e-07    0.0038      17      40 ..      18      40 ..      15      45 .. 0.83
   2 ?    0.1   0.0      0.14   8.3e+02      11      18 ..      46      53 ..      42      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.4e-07
                                      HHCCEECTCEEEEEECTTCCCCCC CS
                    MazE_antitoxin 17 felgireGdevelevdgdkiilrp 40
                                      +e g++eGdeve++v++ + ++++
  gi|330507020|ref|YP_004383448.1| 18 KEIGLKEGDEVEIVVKK-SAVDEF 40
                                      567************98.777665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
                                      E-CCCHHH CS
                    MazE_antitoxin 11 iPkevrfe 18
                                      iPk +++e
  gi|330507020|ref|YP_004383448.1| 46 IPKKLADE 53
                                      99999987 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.9e-06     0.053      34      65 ..       8      40 ..       1      45 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.9e-06
                                      -T.-EEES--TT-B--TT-EEEEEEEHHHHHHH CS
                            TrkA_C 34 Rg.geliipsgdtvLeeGDvllvvgspsdlael 65
                                      R  g  + p  +  L+eGD++ +v+++s+++e+
  gi|330507020|ref|YP_004383448.1|  8 RYeGNALKPFKEIGLKEGDEVEIVVKKSAVDEF 40
                                      33789999***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 450.30
//
Query:       gi|330507021|ref|YP_004383449.1|  [L=153]
Description: hypothetical protein MCON_0850 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-12   47.6   0.0    2.6e-12   47.3   0.0    1.2  1  PIN          PIN domain
  ------ inclusion threshold ------
      0.069   13.2   0.0        0.1   12.7   0.0    1.2  1  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   2.9e-16   2.6e-12      24     121 ..      22     143 ..       2     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.9e-16
                                       HHHTS....SEEEEEHHHHHHHHHHHHS....................SCHCHHHHHHHHHHHHHHHTSEEEEBCHH CS
                               PIN  24 lleel....eelvtsalvlaEllyvlar....................rkskrekaaelvelllllsalkilpidae 76 
                                        l ++     + +ts+lvl E+ ++l+                     r++ ++++++l ++++l s++ i  +++ 
  gi|330507021|ref|YP_004383449.1|  22 FLKHVendeIKGFTSDLVLNEVFHKLMIadiaeiegiearnvaglikrRPDVIGELKRLWAEMELISNFGISVLSTT 98 
                                       444445547899***********************************99999************************* PP

                                       HHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  77 iaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                       ++ e  +++++y l+++Da ++At++++gi+  a++D+df+rv +
  gi|330507021|ref|YP_004383449.1|  99 AYPEFVRLSKEYMLTAADAAHLATMEANGIISMASNDRDFKRVPW 143
                                       ******************************************976 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.1e-05       0.1      17      75 ..      46     112 ..      42     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                       B12-binding  17 lavlaaalrdagfeVqllganven.edivaairaekpdv.....vglSalltsqleavkelvel..l 75 
                                       + ++a++ + +g+e +++   ++  +d++ +++++++++      g+S+l+t+ ++++ +l ++  l
  gi|330507021|ref|YP_004383449.1|  46 KLMIADIAEIEGIEARNVAGLIKRrPDVIGELKRLWAEMelisnFGISVLSTTAYPEFVRLSKEymL 112
                                       679*************995555555***************99999*************999998653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1215.04
//
Query:       gi|330507022|ref|YP_004383450.1|  [L=92]
Description: hypothetical protein MCON_0851 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.6   0.2       0.03   14.4   0.2    1.2  1  tRNA_lig_kinase  tRNA ligase kinase domain
      0.027   14.3   0.3      0.033   14.0   0.3    1.2  1  Dna2             DNA replication factor Dna2
      0.041   13.9   0.4      0.041   13.9   0.4    1.8  2  PspB             Phage shock protein B
       0.13   12.7   2.3       0.16   12.4   2.3    1.2  1  DUF1493          Protein of unknown function (DUF1493)


Domain annotation for each model (and alignments):
>> tRNA_lig_kinase  tRNA ligase kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   6.6e-06      0.03      40      82 ..      15      57 ..       3      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.6e-06
                                      S-HHHHHHHTTSSTT--EEEEES---SHHHHHHHHHHHHHHHH CS
                   tRNA_lig_kinase 40 kklvkealellkkdeskvvlvDrnnhqkreRkqlfeeidelke 82
                                      k+l k++lel+k++e k++l+Dr n++k    +++e+ + l++
  gi|330507022|ref|YP_004383450.1| 15 KDLRKKILELIKEEEDKLMLLDRSNKMKVFSDEIIETKEPLQK 57
                                      67889**********************9999999987666555 PP

>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   7.3e-06     0.033     131     187 ..      26      90 ..      10      92 .] 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.3e-06
                              Dna2 131 teeeakeeikekleeiekwakkyvkksnkakakvekkkekke........klsiskvldiEEniw 187
                                       +eee k ++ ++ ++++ +++++++++++ +++++k+  +k         ++si+++ld EE+ w
  gi|330507022|ref|YP_004383450.1|  26 KEEEDKLMLLDRSNKMKVFSDEIIETKEPLQKEERKRILDKYygsvkldrTISIEEILDLEEDTW 90 
                                       344445566677777777777777777766555555444444777777889************99 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.29   1.3e+03      34      53 ..      23      41 ..      15      43 .. 0.62
   2 ?   13.9   0.4   9.3e-06     0.041      31      72 ..      51      91 ..      46      92 .] 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.29
                              PspB 34 glsaedekrLeellekAekl 53
                                      +l +e+e++L  ll++++k+
  gi|330507022|ref|YP_004383450.1| 23 ELIKEEEDKL-MLLDRSNKM 41
                                      4556666666.466677777 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 9.3e-06
                              PspB 31 rskglsaedekrLeellekAekleeRietLEriLdaespnwR 72
                                      +++ l++e++kr+ + +  + kl++   ++E+iLd e+ +wR
  gi|330507022|ref|YP_004383450.1| 51 TKEPLQKEERKRILDKYYGSVKLDR-TISIEEILDLEEDTWR 91
                                      5677999999999999999999965.5579***********9 PP

>> DUF1493  Protein of unknown function (DUF1493)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.3   3.7e-05      0.16       2      60 ..      15      75 ..      14      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                           DUF1493  2 dsiekevlelireelgtklfk..gkeveltldtdldedlkldeddaedllekffkrfnVdr 60
                                      +++ k++leli+ee    +     +++++  d+ ++++  l++++ + +l+k+    + dr
  gi|330507022|ref|YP_004383450.1| 15 KDLRKKILELIKEEEDKLMLLdrSNKMKVFSDEIIETKEPLQKEERKRILDKYYGSVKLDR 75
                                      799********99876443323599****************************98777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 762.61
//
Query:       gi|330507023|ref|YP_004383451.1|  [L=116]
Description: hypothetical protein MCON_0852 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-12   47.3   0.0    3.2e-12   47.0   0.0    1.2  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   1.8e-16   3.2e-12      56     121 ..      47     111 ..       4     112 .. 0.72

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1.8e-16
                                       HHHHHHHHHHHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  56 aelvelllllsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                        e+++++l   ++k+l+   e+ +  ++  + y+llpnDa i+A ++++gi++iatfD+df+rva 
  gi|330507023|ref|YP_004383451.1|  47 LERLKSFLVEFRIKLLS-MPEDPDLLLKAVEAYRLLPNDAAIVAACQYYGIEKIATFDSDFNRVAS 111
                                       35556666677777777.89999999999999********************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 833.98
//
Query:       gi|330507024|ref|YP_004383452.1|  [L=84]
Description: hypothetical protein MCON_0853 [Methanosaeta concilii GP6]
Scores for 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-10   39.5   0.0    5.3e-10   39.5   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
     0.0011   18.9   0.0     0.0014   18.5   0.0    1.2  1  DUF1902          Domain of unknown function (DUF1902)
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.13   12.2   0.0    1.1  1  PHD_like         Antitoxin of toxin-antitoxin, RelE / RelB, T


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   8.8e-14   5.3e-10       1      49 [.       3      51 ..       3      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 8.8e-14
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegli 49
                                      + i+iekd+d  y     dlpGc s g+tleeai+n++eai   l++ +
  gi|330507024|ref|YP_004383452.1|  3 FKITIEKDDDGRYVAECLDLPGCLSEGETLEEAIENINEAIIGCLKSRL 51
                                      689**************************************99887644 PP

>> DUF1902  Domain of unknown function (DUF1902)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.4e-07    0.0014       3      49 ..       4      49 ..       2      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-07
                                      EEEEEEETTTTEEEEE-SSSTT---EESSHHHHHHHHHHHHHHHHHH CS
                           DUF1902  3 kvqvvwDeeAgVWvaesddipGlvteaetleeLlkkleamipdlLee 49
                                      k+ +  D++ g +vae+ d+pG   e etlee ++ ++ +i   L+ 
  gi|330507024|ref|YP_004383452.1|  4 KITIEKDDD-GRYVAECLDLPGCLSEGETLEEAIENINEAIIGCLKS 49
                                      666666655.889************************9999877765 PP

>> PHD_like  Antitoxin of toxin-antitoxin, RelE / RelB, TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.2e-05      0.13      56      98 ..       2      44 ..       1      53 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                                      T--EEEEEEEETTEEEEEECCGTEEEEESSHHHHHHHHHHHHH CS
                          PHD_like 56 klepeieeekdgevytltldelevyvegstkeeaaedLvedll 98
                                      k++++ie+++dg+     ld      eg+t+eea+e++ e ++
  gi|330507024|ref|YP_004383452.1|  2 KFKITIEKDDDGRYVAECLDLPGCLSEGETLEEAIENINEAII 44
                                      89************99999999***************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 626.57
//
Query:       gi|330507025|ref|YP_004383453.1|  [L=66]
Description: YcfA-like protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.1e-13   48.8   0.1    5.7e-13   48.7   0.1    1.0  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.1   3.2e-17   5.7e-13       6      57 ..       2      53 ..       1      54 [. 0.95

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 3.2e-17
                                      HHHHHTT-EEEEEETTEEEEE-TTSS-EEEEE.S-SSS--CCCHHHHHHHCC CS
                        HicA_toxin  6 klLeklGfevvrqkGSHvrfkhpdkrgivtvppHpgkelkpgtlksIlkqaG 57
                                      ++++++G++v   +GSH ++++++ + ++ +p+H+gk+l++g+lk+++ +a+
  gi|330507025|ref|YP_004383453.1|  2 AAFKRAGWVVNHIEGSHYIMVKEGSDVHLSIPVHKGKDLGIGLLKKLIAKAE 53
                                      699**********************99*******************998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 543.44
//
Query:       gi|330507026|ref|YP_004383454.1|  [L=66]
Description: hypothetical protein MCON_0855 [Methanosaeta concilii GP6]
Scores for complete 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   46.0   4.6    5.9e-12   45.8   4.6    1.0  1  DUF104          Protein of unknown function DUF104
  ------ inclusion threshold ------
        0.1   12.6   0.3       0.16   11.9   0.3    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   4.6   6.6e-16   5.9e-12       5      59 .]       3      54 ..       1      54 [. 0.96

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 6.6e-16
                            DUF104  5 IeavYEnGvLKPLekvdLkEGeevkikIeeakeilkklkgilkeadeeeleelle 59
                                      ++a+Y + vL+P +++dL+EGeev+++I++   i+k+++g++k +d+e+++e++e
  gi|330507026|ref|YP_004383454.1|  3 VKAIYKSHVLRPVGDLDLEEGEEVELEIKK--NIVKRTYGLIK-LDAESIDEIIE 54
                                      89****************************..********998.********987 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   1.8e-05      0.16      19      38 ..      18      36 ..      11      44 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
                                      CCEECTCEEEEEECTTCCCC CS
                    MazE_antitoxin 19 lgireGdevelevdgdkiil 38
                                      l+++eG evele++++ i+ 
  gi|330507026|ref|YP_004383454.1| 18 LDLEEGEEVELEIKKN-IVK 36
                                      79************95.554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 541.78
//
Query:       gi|330507027|ref|YP_004383455.1|  [L=439]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-25   88.3   0.1    5.9e-25   87.4   0.1    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family
    3.7e-20   72.4   0.0    7.3e-20   71.4   0.0    1.5  1  DEDD_Tnp_IS110  Transposase
  ------ inclusion threshold ------
      0.038   14.3   1.0      0.088   13.1   0.1    2.0  2  Init_tRNA_PT    Rit1 DUSP-like domain


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.1   9.8e-29   5.9e-25       2      83 ..     271     352 ..     270     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 9.8e-29
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaaira 78 
                                       +++ s+pG+G++ aa+++ae+gd r f+sa+++a+y+G++p+++qS++k r g+i+k G++++Rr+L+e A a++r+
  gi|330507027|ref|YP_004383455.1| 271 KIILSVPGVGFISAATIIAEMGDYRDFPSADKMAKYFGIVPSVYQSAGKLRTGKITKTGSKHMRRILVEVAKAISRT 347
                                       6899***********************************************************************99 PP

                    Transposase_20  79 npelr 83 
                                       ++ +r
  gi|330507027|ref|YP_004383455.1| 348 KKNSR 352
                                       75554 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   1.2e-23   7.3e-20       1     153 [.      31     174 ..      31     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.2e-23
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G D++ d   a++i+++g +l +er++++++gl a+ ++   ++++ + +ve+tg ++++++++ le +++ ++ n
  gi|330507027|ref|YP_004383455.1|  31 CGADIHRDFLIATMISRSGLKL-QERFNMNQDGLLAFRSW-IINHRCQRLAVESTGGFWYPIFTI-LEGHVEFILAN 104
                                       799************9999885.678**************.889****************88876.7899******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdqv 153
                                       ++++++++     ++KtD++D++ IA + +  + ++p++  +++y++Lr++tr+re+lv+ r++ kn++++ L   
  gi|330507027|ref|YP_004383455.1| 105 AYQIRNIE-----HKKTDKLDSERIAIYCL-NNLITPSRIYPKDYRDLRSITRARETLVNARSKIKNQIHQSLSTC 174
                                       *****995.....89***************.****************************************99765 PP

>> Init_tRNA_PT  Rit1 DUSP-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.3   7.5e+03      26      43 ..     155     174 ..     141     184 .. 0.47
   2 ?   13.1   0.1   1.5e-05     0.088      10      80 ..     326     400 ..     318     411 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                      Init_tRNA_PT  26 dfvrkrlsedkk..kkilva 43 
                                       + v++r++ +++  +++  +
  gi|330507027|ref|YP_004383455.1| 155 TLVNARSKIKNQihQSLSTC 174
                                       33333333322222333333 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.5e-05
                      Init_tRNA_PT  10 gKkgsknLrtalpkivdfvrkrlsedkk....kkilvacetGkdlsvgvaLailcklfddakls...eeqsesnitK 79 
                                        K+gsk++r +l ++ ++++++ ++++     ++il+ c + +   v++a  +lc ++   +l    e+ +e+++tK
  gi|330507027|ref|YP_004383455.1| 326 TKTGSKHMRRILVEVAKAISRTKKNSRLmrffQRILARCGKKNIATVALARKVLCIIY---HLLmnhENYQEPEVTK 399
                                       49*****************99966655599**99******999999999888888888...2222235666777777 PP

                      Init_tRNA_PT  80 d 80 
                                       +
  gi|330507027|ref|YP_004383455.1| 400 T 400
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3289.44
//
Query:       gi|330507028|ref|YP_004383456.1|  [L=65]
Description: hypothetical protein MCON_0857 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 464.71
//
Query:       gi|330507029|ref|YP_004383457.1|  [L=164]
Description: hypothetical protein MCON_0859 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1258.10
//
Query:       gi|330507030|ref|YP_004383458.1|  [L=102]
Description: hypothetical protein MCON_0860 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-12   45.5   0.2    5.8e-12   45.2   0.2    1.2  1  UPF0175   Uncharacterised protein family (UPF0175)
  ------ inclusion threshold ------
      0.065   13.0   0.0       0.12   12.1   0.0    1.5  1  HTH_psq   helix-turn-helix, Psq domain


Domain annotation for each model (and alignments):
>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.2   6.4e-16   5.8e-12      13      60 ..      35      82 ..      24      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 6.4e-16
                           UPF0175 13 eeelerelrialAvklYeegrlSlgkAaelaglsrveflelLarrgip 60
                                        e++  +r+++Av+lY+ +++S ++Aae+ag+s   f  +L +rgi 
  gi|330507030|ref|YP_004383458.1| 35 MIEVKPFIRLEMAVELYKSEKISMSRAAEIAGISIEGFKSFLESRGIK 82
                                      5589999***************************************97 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.3e-05      0.12       5      29 ..      44      68 ..      43      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.3e-05
                           HTH_psq  5 laaAleavvnGkmSirkAArkYgiP 29
                                      l+ A+e + ++k+S+++AA + gi+
  gi|330507030|ref|YP_004383458.1| 44 LEMAVELYKSEKISMSRAAEIAGIS 68
                                      678****************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 714.55
//
Query:       gi|330507031|ref|YP_004383459.1|  [L=84]
Description: hypothetical protein MCON_0861 [Methanosaeta concilii GP6]
Scores for complete 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   53.5   0.0    2.1e-14   53.2   0.0    1.1  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 !   53.2   0.0   1.1e-18   2.1e-14       2      60 ..      22      79 ..      21      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1.1e-18
                                      HHTTS-..EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHH CS
                       Epimerase_2  2 alkaeselelqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligle 60
                                      +++++  l++++++tGqH+++ m++++fe+le+++pd++l+++s++++++tgr+l  le
  gi|330507031|ref|YP_004383459.1| 22 ECQRR-GLDYSIIHTGQHYSYHMDRIFFEQLELPQPDHNLDVGSGNHGEQTGRILADLE 79
                                      56655.89***********************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 600.76
//
Query:       gi|330507032|ref|YP_004383460.1|  [L=318]
Description: glycosyl transferase, group 2 family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-21   74.4   0.0    1.2e-20   74.0   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    0.00025   21.0   0.0    0.00032   20.6   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0013   19.2   0.0       0.11   13.0   0.0    2.5  3  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.16   11.9   0.5        3.3    7.7   0.1    2.7  3  DUF1732          Domain of unknown function (DUF1732)
       0.68    9.3   4.0        1.4    8.3   0.7    2.3  2  DUF373           Domain of unknown function (DUF373)


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 !   74.0   0.0   3.4e-24   1.2e-20       3     123 ..       7     120 ..       5     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 3.4e-24
                                       EEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH-- CS
                   Glycos_transf_2   3 viptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraat 79 
                                        +p+yNee  +++++  +++      ++++vvDDgS+D t++i+e+l     +  v+r+e+n G+++al+  ++ a+
  gi|330507032|ref|YP_004383460.1|   7 AMPAYNEERSIAKMVLGCKKY----VDQVVVVDDGSSDATASIAEAL-----GAYVVRHEKNSGYGAALRSCFETAR 74 
                                       59*******************....**********************.....9************************ PP

                                       SS...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCC CS
                   Glycos_transf_2  80 gd...yilflDaDdepdpdwleklvealekdgadvvlgqrprifget 123
                                             ++++D+D ++d   +++l+++l++ g d+v+g+r+  + ++
  gi|330507032|ref|YP_004383460.1|  75 NLgaeKMVIIDSDGQHDASEIPELLDPLNN-GCDLVIGSRFCDGNGE 120
                                       98889*************************.********98766555 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 !   20.6   0.0   9.1e-08   0.00032       6     132 ..       6     122 ..       2     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.1e-08
                   Glyco_tranf_2_3   6 vlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                        + p++nee+ + +++    +     ++vvvv+d+s+++t++ ae+    l++    vv+ ++n g +++ r+ +e+
  gi|330507032|ref|YP_004383460.1|   6 AAMPAYNEERSIAKMVLGCKK---YVDQVVVVDDGSSDATASIAEA----LGA---YVVRHEKNSGYGAALRSCFET 72 
                                       567889998888888766666...48999*************9987....555...58899999************* PP

                   Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfll.nrstl 132
                                        r+   +  +++D+D   +   ++ ll  +   +++ v +++f++ n+++ 
  gi|330507032|ref|YP_004383460.1|  73 ARNLGAEKMVIIDSDGQHDASEIPELLDPL-NNGCDLVIGSRFCDgNGENI 122
                                       *****9***********************9.99**********99677665 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0     3e-05      0.11       2      49 ..      12      58 ..      11      66 .. 0.81
   2 ?    3.5   0.0     0.028     1e+02       6      33 ..      65      92 ..      63     109 .. 0.81
   3 ?   -3.2   0.0       3.5   1.2e+04      19      46 ..     160     188 ..     152     207 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhvd 49
                                      ne+  + +++   +++ +d+++v+d++s+D t+ i ++l ++ + h +
  gi|330507032|ref|YP_004383460.1| 12 NEERSIAKMVLGCKKY-VDQVVVVDDGSSDATASIAEALGAYVVRHEK 58
                                      7777777777777777.9********************9887666655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.028
                   Glyco_tranf_2_4  6 iLpeflahhlalgfdrilvydndstDgt 33
                                      +L ++ + +++lg+++++++d d + + 
  gi|330507032|ref|YP_004383460.1| 65 ALRSCFETARNLGAEKMVIIDSDGQHDA 92
                                      68899999**********9997655444 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.5
                   Glyco_tranf_2_4  19 fdrilvydndstDgtrailkelpe.vkll 46 
                                       ++ i++ d + + g+  +l++ ++ +++ 
  gi|330507032|ref|YP_004383460.1| 160 IESIYIKDSGMSAGSEVLLQAKDNdLSIK 188
                                       56677777777777777776654334433 PP

>> DUF1732  Domain of unknown function (DUF1732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   5.2e+03      59      77 ..      13      31 ..       7      31 .. 0.82
   2 ?    0.7   0.0      0.14   5.1e+02      55      78 ..     179     202 ..     176     205 .. 0.87
   3 ?    7.7   0.1   0.00093       3.3      62      79 ..     285     302 ..     279     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                           DUF1732 59 ndleitklvvelKseieki 77
                                      ++ +i+k+v+ +K+ ++++
  gi|330507032|ref|YP_004383460.1| 13 EERSIAKMVLGCKKYVDQV 31
                                      5678999999999999985 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                           DUF1732  55 gskandleitklvvelKseiekir 78 
                                        +k ndl+i+++ ++++  +e+  
  gi|330507032|ref|YP_004383460.1| 179 QAKDNDLSIKEVPIHCRYDVERAS 202
                                       6899****************9875 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00093
                           DUF1732  62 eitklvvelKseiekirE 79 
                                       +i+k+++e+K+eie+ir 
  gi|330507032|ref|YP_004383460.1| 285 SISKMMIEFKNEIEQIRK 302
                                       799*************96 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.046   1.6e+02      98     113 ..      28      43 ..      15      46 .. 0.84
   2 ?    8.3   0.7   0.00039       1.4     144     215 ..     214     298 ..     205     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.046
                            DUF373  98 adsaivVsDGaeDesv 113
                                       +d+++vV DG++D+++
  gi|330507032|ref|YP_004383460.1|  28 VDQVVVVDDGSSDATA 43 
                                       589**********875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00039
                            DUF373 144 lkkalkdpelrk..tiLvplGlllliyallll............lglpelalaiillllGlylllrGfgldelleel 206
                                       l k+l d elr+  + ++++G+ll  +++ +             l +    l+i+l+l+G +l + G+ l++ ++++
  gi|330507032|ref|YP_004383460.1| 214 LIKILHDMELRRplYYFTVPGILLAAVGVGMGldflrvfyhggsLAYGPTLLMILLTLVGSFLAMTGIILHS-ISKM 289
                                       56889999999866789***********99988999*****99988888999****************9998.6666 PP

                            DUF373 207 leklkesle 215
                                       + ++k+ +e
  gi|330507032|ref|YP_004383460.1| 290 MIEFKNEIE 298
                                       666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2289.02
//
Query:       gi|330507033|ref|YP_004383461.1|  [L=145]
Description: hypothetical protein MCON_0864 [Methanosaeta concilii GP6]
Scores for complete 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-42  143.8   0.0    3.3e-42  143.6   0.0    1.1  1  PDDEXK_3  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> PDDEXK_3  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   0.0   1.8e-46   3.3e-42       3     117 ..      27     141 ..      25     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 1.8e-46
                          PDDEXK_3   3 lteeiigaaieVhnelGegllEsvYekaLaveLkkrglkveeqvelpvvYkgkevgeeyrlDllveekvivElKave 79 
                                       l++eiigaaieVh++lG+gl EsvYe++L++eL  rg+++++qv+lp++Ykg ++++ yrlD+lv++ vivElKave
  gi|330507033|ref|YP_004383461.1|  27 LSREIIGAAIEVHRHLGPGLFESVYEECLCCELGLRGISFRRQVPLPLSYKGLNLDCGYRLDILVDDLVIVELKAVE 103
                                       789************************************************************************** PP

                          PDDEXK_3  80 elkeeheaqllnYlkltklklGlliNFnkkklkeeikr 117
                                       e++  heaqll+Ylkl +  lGlliNFn+++l+++i r
  gi|330507033|ref|YP_004383461.1| 104 EINFLHEAQLLTYLKLRNTWLGLLINFNVRMLRDGITR 141
                                       *********************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1132.81
//
Query:       gi|330507034|ref|YP_004383462.1|  [L=79]
Description: hypothetical protein MCON_0865 [Methanosaeta concilii GP6]
Scores for complete 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   52.4   1.7    5.7e-14   52.1   1.7    1.1  1  DUF2283   Protein of unknown function (DUF2283)


Domain annotation for each model (and alignments):
>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   1.7   3.2e-18   5.7e-14       1      49 []      22      71 ..      22      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 3.2e-18
                           DUF2283  1 kitYDpeaDalYIyl..segpveeseevdddiilDfDedGrlvGIEiLnAS 49
                                      +i+YD+eaD+lY+ +  +++ +e++e+ +d+ii  +D++G+l G++i  A+
  gi|330507034|ref|YP_004383462.1| 22 WIDYDEEADVLYVSFvyPPNAIEHEED-EDGIIRNYDKEGKLTGLTIIAAK 71
                                      89*************************.*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.18s 00:00:00.53 Elapsed: 00:00:00.33
# Mc/sec: 719.68
//
Query:       gi|330507035|ref|YP_004383463.1|  [L=110]
Description: hypothetical protein MCON_0866 [Methanosaeta concilii GP6]
Scores for complete 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   61.8   0.0      6e-17   61.5   0.0    1.1  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 !   61.5   0.0   3.4e-21     6e-17       2      70 ..      22      89 ..      21      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 3.4e-21
                                      HHTTS-..EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SE CS
                       Epimerase_2  2 alkaeselelqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDl 70
                                      +++++  l++++++tGqH++++m++++fe+le+++pd++l+++s++++++tgr+l  le v ++e+pD+
  gi|330507035|ref|YP_004383463.1| 22 ECQRR-GLDYSIIHTGQHYSYQMDRIFFEQLELPQPDHNLDVGSGNHGEQTGRILADLEGVPMAERPDI 89
                                      56555.89************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       189  (0.0105416); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 822.51
//
Query:       gi|330507036|ref|YP_004383464.1|  [L=164]
Description: hypothetical protein MCON_0867 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1289.95
//
Query:       gi|330507037|ref|YP_004383465.1|  [L=102]
Description: hypothetical protein MCON_0868 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-12   45.5   0.2    5.8e-12   45.2   0.2    1.2  1  UPF0175   Uncharacterised protein family (UPF0175)
  ------ inclusion threshold ------
      0.065   13.0   0.0       0.12   12.1   0.0    1.5  1  HTH_psq   helix-turn-helix, Psq domain


Domain annotation for each model (and alignments):
>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.2   6.4e-16   5.8e-12      13      60 ..      35      82 ..      24      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 6.4e-16
                           UPF0175 13 eeelerelrialAvklYeegrlSlgkAaelaglsrveflelLarrgip 60
                                        e++  +r+++Av+lY+ +++S ++Aae+ag+s   f  +L +rgi 
  gi|330507037|ref|YP_004383465.1| 35 MIEVKPFIRLEMAVELYKSEKISMSRAAEIAGISIEGFKSFLESRGIK 82
                                      5589999***************************************97 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.3e-05      0.12       5      29 ..      44      68 ..      43      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.3e-05
                           HTH_psq  5 laaAleavvnGkmSirkAArkYgiP 29
                                      l+ A+e + ++k+S+++AA + gi+
  gi|330507037|ref|YP_004383465.1| 44 LEMAVELYKSEKISMSRAAEIAGIS 68
                                      678****************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 768.81
//
Query:       gi|330507038|ref|YP_004383466.1|  [L=41]
Description: hypothetical protein MCON_0869 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      131  (0.0073066); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 338.16
//
Query:       gi|330507039|ref|YP_004383467.1|  [L=114]
Description: hypothetical protein MCON_0870 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00061   20.3   0.0    0.00072   20.1   0.0    1.1  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.024   14.9   0.0      0.033   14.5   0.0    1.3  1  PIN_9     PIN like domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     8e-08   0.00072      29     119 ..      15     100 ..       4     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8e-08
                                       SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT CS
                               PIN  29 eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehg 105
                                       ++ +++ l+l+E++ v++r       a++  ++l  l + + +  da + e+  +i  + + + +D +  A+A+e+g
  gi|330507039|ref|YP_004383467.1|  15 YANHIPLLALIETACVVSR----LSDAQRAGLALTFLGQNSRFYGDAYLMERSIRIGMRTKASGFDVVFMACAEETG 87 
                                       566899*************....7777777888888999999999******************************** PP

                                       -EEE.ESSTHHHHH CS
                               PIN 106 ikliatfDedfrrv 119
                                        +li t D+++++ 
  gi|330507039|ref|YP_004383467.1|  88 SILI-TDDRKMYDR 100
                                       ****.****98765 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.7e-06     0.033      70     115 ..      69     113 ..      49     114 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.7e-06
                             PIN_9  70 eaeeekaDdailelakeldaavlvTnDreLkkrllekgipvilLRq 115
                                       +++++  D + ++ a+e++  +l+T Dr++ +r+++ g++vi++R+
  gi|330507039|ref|YP_004383467.1|  69 RTKASGFDVVFMACAEETG-SILITDDRKMYDRANDYGLDVIFIRD 113
                                       3344556777778888888.6666********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 834.68
//
Query:       gi|330507040|ref|YP_004383468.1|  [L=61]
Description: hypothetical protein MCON_0871 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.3   0.1        3.1    7.7   0.0    2.0  2  Rop       Rop protein


Domain annotation for each model (and alignments):
>> Rop  Rop protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00017       3.1      36      54 ..       4      22 ..       1      25 [. 0.85
   2 ?    4.9   0.0    0.0013        24      23      54 ..      22      56 ..      21      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00017
                               Rop 36 dlCErLHedAeeLyrslsa 54
                                      d  Er+  dAe+L+ s++ 
  gi|330507040|ref|YP_004383468.1|  4 DCVERIYKDAEDLFLSVKL 22
                                      678***********99875 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0013
                               Rop 23 LeKLneLdlDeq.AdlCErLHedAe..eLyrslsa 54
                                      L K n+  lDe  A++ E+  edA+  e+ r++++
  gi|330507040|ref|YP_004383468.1| 22 LRKGNKVSLDEViAEIGEHVVEDADstEIIRKMRD 56
                                      5688999999954999*******984456666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:01.19
# Mc/sec: 155.38
//
Query:       gi|330507041|ref|YP_004383469.1|  [L=318]
Description: glycosyl transferase, group 2 family protein [Methanosaeta concilii GP6]
Scores for complete 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-22   77.8   0.0    1.1e-21   77.3   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    0.00035   20.5   0.0    0.00047   20.1   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00075   20.0   0.0       0.11   13.0   0.0    2.5  3  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.16   12.0   0.6        3.2    7.8   0.1    2.7  3  DUF1732          Domain of unknown function (DUF1732)
       0.61    9.5   4.0        1.3    8.4   0.7    2.3  2  DUF373           Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0   3.2e-25   1.1e-21       3     167 ..       7     161 ..       5     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 3.2e-25
                                       EEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH-- CS
                   Glycos_transf_2   3 viptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraat 79 
                                        +p+yNee  +++++  +++      ++++vvDDgS+D t++i+e+l     +  v+r+e+n G+++al+  ++aa+
  gi|330507041|ref|YP_004383469.1|   7 AMPAYNEERSIAKMVLGCKKY----VDQVVVVDDGSSDATASIAEAL-----GAYVVRHEKNSGYGAALRSCFEAAR 74 
                                       59*******************....**********************.....9************************ PP

                                       SS...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTT CS
                   Glycos_transf_2  80 gd...yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsf 153
                                             ++++D+D ++d   ++kl+++l++ g d+v+g+r+  + ++d    +k      ++    ++   + ++++
  gi|330507041|ref|YP_004383469.1|  75 NLgaeKMVIIDSDGQHDAAEIPKLLDPLNN-GCDLVIGSRFCDGNGKDIPAYRK---VGMKVLDVATNVAGGVSVTD 147
                                       98889*************************.*********98888887766665...46666666666666666666 PP

                                       CSTCCCEEEEHHHH CS
                   Glycos_transf_2 154 eigsaallrreale 167
                                         ++++++ r+a+e
  gi|330507041|ref|YP_004383469.1| 148 SQSGFRAYGRRAIE 161
                                       66666666666665 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 !   20.1   0.0   1.3e-07   0.00047       6     130 ..       6     120 ..       2     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.3e-07
                   Glyco_tranf_2_3   6 vlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                        + p++nee+ + +++    +     ++vvvv+d+s+++t++ ae+    l++    vv+ ++n g +++ r+ +ea
  gi|330507041|ref|YP_004383469.1|   6 AAMPAYNEERSIAKMVLGCKK---YVDQVVVVDDGSSDATASIAEA----LGA---YVVRHEKNSGYGAALRSCFEA 72 
                                       567889998888888766666...48999*************9987....555...588999999************ PP

                   Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfll.nrs 130
                                        r+   +  +++D+D   +   +++ll  +   +++ v +++f++ n++
  gi|330507041|ref|YP_004383469.1|  73 ARNLGAEKMVIIDSDGQHDAAEIPKLLDPL-NNGCDLVIGSRFCDgNGK 120
                                       ***99999*********99999*******9.999***999999986665 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   3.2e-05      0.11       2      49 ..      12      58 ..      11      65 .. 0.80
   2 ?    4.3   0.0     0.017        59       6      35 ..      65      94 ..      61     101 .. 0.83
   3 ?   -2.7   0.0       2.5   9.1e+03      19      48 ..     160     190 ..     152     209 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhvd 49
                                      ne+  + +++   +++ +d+++v+d++s+D t+ i ++l ++ + h +
  gi|330507041|ref|YP_004383469.1| 12 NEERSIAKMVLGCKKY-VDQVVVVDDGSSDATASIAEALGAYVVRHEK 58
                                      7777777777777777.9********************9887666655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.017
                   Glyco_tranf_2_4  6 iLpeflahhlalgfdrilvydndstDgtra 35
                                      +L ++ +++++lg+++++++d d + + ++
  gi|330507041|ref|YP_004383469.1| 65 ALRSCFEAARNLGAEKMVIIDSDGQHDAAE 94
                                      789999**************9876655555 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.5
                   Glyco_tranf_2_4  19 fdrilvydndstDgtrailkelpe.vkllhv 48 
                                       ++ i++ d + + g+  +l++ ++ +++ +v
  gi|330507041|ref|YP_004383469.1| 160 IESIYIKDSGMSAGSEVLLQAKDNdLSIKEV 190
                                       5677888877777777777766444444333 PP

>> DUF1732  Domain of unknown function (DUF1732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   5.2e+03      59      77 ..      13      31 ..       7      31 .. 0.82
   2 ?    0.7   0.0      0.14   5.1e+02      55      78 ..     179     202 ..     176     205 .. 0.87
   3 ?    7.8   0.1   0.00089       3.2      62      79 ..     285     302 ..     279     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                           DUF1732 59 ndleitklvvelKseieki 77
                                      ++ +i+k+v+ +K+ ++++
  gi|330507041|ref|YP_004383469.1| 13 EERSIAKMVLGCKKYVDQV 31
                                      5678999999999999985 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                           DUF1732  55 gskandleitklvvelKseiekir 78 
                                        +k ndl+i+++ ++++  +e+  
  gi|330507041|ref|YP_004383469.1| 179 QAKDNDLSIKEVPIHCRYDVERAS 202
                                       6899****************9875 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00089
                           DUF1732  62 eitklvvelKseiekirE 79 
                                       +i+k+++e+K+eie+ir 
  gi|330507041|ref|YP_004383469.1| 285 SISKMMIEFKNEIEQIRK 302
                                       799*************96 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.046   1.6e+02      98     113 ..      28      43 ..      15      46 .. 0.84
   2 ?    8.4   0.7   0.00035       1.3     144     216 ..     214     299 ..     205     306 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.046
                            DUF373  98 adsaivVsDGaeDesv 113
                                       +d+++vV DG++D+++
  gi|330507041|ref|YP_004383469.1|  28 VDQVVVVDDGSSDATA 43 
                                       589**********875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00035
                            DUF373 144 lkkalkdpelrk..tiLvplGlllliyallll............lglpelalaiillllGlylllrGfgldelleel 206
                                       l k+l d elr+  + ++++G+ll  +++ +             l +    l+i+l+l+G +l + G+ l++ ++++
  gi|330507041|ref|YP_004383469.1| 214 LIKILHDMELRRplYYFTVPGILLAAVGVGMGldflrvfyhggsLAYGPTLLMILLTLVGSFLAMTGIILHS-ISKM 289
                                       56889999999866789***********99988999*****99988888999****************9998.6677 PP

                            DUF373 207 leklkeslee 216
                                       + ++k+ +e+
  gi|330507041|ref|YP_004383469.1| 290 MIEFKNEIEQ 299
                                       7677766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2096.86
//
Query:       gi|330507042|ref|YP_004383470.1|  [L=145]
Description: hypothetical protein MCON_0873 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-43  145.6   0.0      9e-43  145.4   0.0    1.1  1  PDDEXK_3  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> PDDEXK_3  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.4   0.0     5e-47     9e-43       3     117 ..      27     141 ..      25     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 5e-47
                          PDDEXK_3   3 lteeiigaaieVhnelGegllEsvYekaLaveLkkrglkveeqvelpvvYkgkevgeeyrlDllveekvivElKave 79 
                                       l++eiigaaieVh++lG+gl EsvYe++L++eL  rg+++++qv+lp++Ykg ++++ yrlD+lve+ vivElKave
  gi|330507042|ref|YP_004383470.1|  27 LSREIIGAAIEVHRHLGPGLFESVYEECLCCELGLRGISFQRQVPLPLSYKGLNLDCGYRLDILVEDLVIVELKAVE 103
                                       789************************************************************************** PP

                          PDDEXK_3  80 elkeeheaqllnYlkltklklGlliNFnkkklkeeikr 117
                                       e++  heaqll+Ylkl +  lGlliNFn+++l+++i r
  gi|330507042|ref|YP_004383470.1| 104 EINFLHEAQLLTYLKLRNTWLGLLINFNVRMLRDGITR 141
                                       *********************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1049.49
//
Query:       gi|330507043|ref|YP_004383471.1|  [L=79]
Description: hypothetical protein MCON_0874 [Methanosaeta concilii GP6]
Scores for complete 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   52.4   1.7    5.7e-14   52.1   1.7    1.1  1  DUF2283   Protein of unknown function (DUF2283)


Domain annotation for each model (and alignments):
>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   1.7   3.2e-18   5.7e-14       1      49 []      22      71 ..      22      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 3.2e-18
                           DUF2283  1 kitYDpeaDalYIyl..segpveeseevdddiilDfDedGrlvGIEiLnAS 49
                                      +i+YD+eaD+lY+ +  +++ +e++e+ +d+ii  +D++G+l G++i  A+
  gi|330507043|ref|YP_004383471.1| 22 WIDYDEEADVLYVSFvyPPNAIEHEED-EDGIIRNYDKEGKLTGLTIIAAK 71
                                      89*************************.*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 604.82
//
Query:       gi|330507044|ref|YP_004383472.1|  [L=110]
Description: hypothetical protein MCON_0875 [Methanosaeta concilii GP6]
Scores for 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   64.1   0.0    1.3e-17   63.7   0.0    1.1  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 !   63.7   0.0   7.1e-22   1.3e-17       2      70 ..      22      89 ..      21      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 7.1e-22
                                      HHTTS-..EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SE CS
                       Epimerase_2  2 alkaeselelqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDl 70
                                      +++++  l++++++tGqH++++m++++fe+le+++pd++l+++s++++++tgr+l  le vl++ +pD+
  gi|330507044|ref|YP_004383472.1| 22 ECQRR-GLDYSIIHTGQHYSYQMDRIFFEQLELPQPDHNLDVGSGNHGEQTGRILADLEGVLMAKRPDI 89
                                      56555.89************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); 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 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 918.26
//
Query:       gi|330507045|ref|YP_004383473.1|  [L=156]
Description: hypothetical protein MCON_0876 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-16   59.9   2.7    3.8e-16   59.7   2.7    1.1  1  PIN       PIN domain
    1.5e-05   25.8   0.3    2.6e-05   24.9   0.3    1.5  1  PIN_3     PIN domain
    7.7e-05   23.3   0.2    0.00017   22.1   0.2    1.8  1  PIN_12    PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   2.7   6.4e-20   3.8e-16       1     116 [.       7     130 ..       7     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 6.4e-20
                                       EEE-HHHHHHHH...TTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHS...SCHCHHHHHHHHHHHHHHHTSEE CS
                               PIN   1 ivlDTsvliall...rgeekaeaarklleel.eelvtsalvlaEllyvlar...rkskrekaaelvelllllsalki 70 
                                       ++lD+sv+++++   +++ +a ++r++ ee   +l++sa+vl+E ++ l++    k+++++  +l+++++ l ++ +
  gi|330507045|ref|YP_004383473.1|   7 VCLDSSVVVKWFkveEESAEALKIRRWAEEGrIKLIISAIVLSESARALKKtgcDKEEIYEILDLFDAFISLCGVDV 83 
                                       69***********9999999999******99********************************************** PP

                                       EEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTH.H CS
                               PIN  71 lpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDed.f 116
                                       +p+   i + a+ +  +++l ++Da+++AtA  +  + +++ De+ f
  gi|330507045|ref|YP_004383473.1|  84 VPVELLIIKSAQSLVIEHNLYSADAIHVATATLTESDFFVSIDEHhF 130
                                       *************************************999*999844 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.3   4.4e-09   2.6e-05       1     112 [.       6     124 ..       6     128 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.4e-09
                             PIN_3   1 rvvlDtnvlldallfdsp..aarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakvaler 75 
                                       rv+lD++v++ ++ +++    a ki++ +e+g+i l++s+ +l E +r+l++ + +++   +  d+     + ++ +
  gi|330507045|ref|YP_004383473.1|   6 RVCLDSSVVVKWFKVEEEsaEALKIRRWAEEGRIKLIISAIVLSESARALKKTGCDKEEIYEILDL----FDAFISL 78 
                                       8*************999989999************************8886665555444444333....2222333 PP

                             PIN_3  76 ..........kavapdaelrpllkcrDpdDqkvlelAlaaradvlVT 112
                                                   ++  ++l++++++   +D+ ++++A  ++ d+ V+
  gi|330507045|ref|YP_004383473.1|  79 cgvdvvpvelLIIKSAQSLVIEHNLYS-ADAIHVATATLTESDFFVS 124
                                       333444444433333333444333333.4444444444444666666 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   2.9e-08   0.00017       1      52 [.       7      58 ..       7     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.9e-08
                            PIN_12  1 ifiDTnifldeffrlsee.ealkklleliesgkiklivpdivldEflknrekk 52
                                      +++D+++  + +f+ +ee ++  k+++  e+g+ikli+++ivl E  + ++k 
  gi|330507045|ref|YP_004383473.1|  7 VCLDSSVVVK-WFKVEEEsAEALKIRRWAEEGRIKLIISAIVLSESARALKKT 58
                                      89*******7.****9997888888999********************99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1167.04
//
Query:       gi|330507046|ref|YP_004383474.1|  [L=84]
Description: hypothetical protein MCON_0877 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.5   0.0       0.23   11.7   0.0    1.4  1  MLTD_N    MltD lipid attachment motif


Domain annotation for each model (and alignments):
>> MLTD_N  MltD lipid attachment motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.3e-05      0.23       1      20 [.       1      20 [.       1      22 [. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.3e-05
                            MLTD_N  1 MSpdyrkpsvkdALtRavqi 20
                                      MS +++k++v d L+ +v++
  gi|330507046|ref|YP_004383474.1|  1 MSDVIFKTKVDDFLAQRVKA 20
                                      9999**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 596.21
//
Query:       gi|330507047|ref|YP_004383475.1|  [L=77]
Description: hypothetical protein MCON_0878 [Methanosaeta concilii GP6]
Scores for complete 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   20.3   0.0    0.00048   20.2   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
      0.028   14.4   0.0      0.031   14.3   0.0    1.2  1  DUF1902          Domain of unknown function (DUF1902)
       0.03   14.0   0.1      0.053   13.2   0.1    1.4  1  GntR             Bacterial regulatory proteins, gntR family


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 !   20.2   0.0   8.1e-08   0.00048       3      57 ..       4      58 ..       2      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.1e-08
                   HicB_lk_antitox  3 iaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipe 57
                                      i iek ++ ay  +   lpG    g t+ e ++ a++++   +e+ ie+g+ +p 
  gi|330507047|ref|YP_004383475.1|  4 IKIEKLDEGAYLATSDVLPGLVAEGRTIAETMEIAQDVARKIIESYIEHGDPLPP 58
                                      789999999**999999**********************************9984 PP

>> DUF1902  Domain of unknown function (DUF1902)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.1e-06     0.031      13      42 ..      12      41 ..       2      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.1e-06
                                      TEEEEE-SSSTT---EESSHHHHHHHHHHH CS
                           DUF1902 13 gVWvaesddipGlvteaetleeLlkkleam 42
                                      g + a+sd +pGlv+e  t+ e ++  +++
  gi|330507047|ref|YP_004383475.1| 12 GAYLATSDVLPGLVAEGRTIAETMEIAQDV 41
                                      7789****************9988765555 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   8.8e-06     0.053       4      29 ..      36      61 ..      33      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.8e-06
                                      HHHHHHHHHHHTTSS-TTSB---HHH CS
                              GntR  4 qvyerLredIlsgelrpGdkLPsere 29
                                      ++++ + ++I++  +++Gd+LP+e++
  gi|330507047|ref|YP_004383475.1| 36 EIAQDVARKIIESYIEHGDPLPPEMA 61
                                      799*********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 621.95
//
Query:       gi|330507048|ref|YP_004383476.1|  [L=67]
Description: hypothetical protein MCON_0879 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-09   35.4   0.0    9.5e-09   35.4   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
       0.08   12.9   0.0      0.087   12.8   0.0    1.1  1  DUF1902          Domain of unknown function (DUF1902)


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   1.1e-12   9.5e-09       1      51 [.       3      53 ..       3      67 .] 0.86

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.1e-12
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhleglied 51
                                      + ++i ++ed    v  P lpGc s g t+eea++n+k+ai+  l+ l ++
  gi|330507048|ref|YP_004383476.1|  3 FKVIISNGEDGWLVVECPSLPGCVSQGRTVEEALENIKDAIQGCLDVLGDR 53
                                      6789999*************************************9987665 PP

>> DUF1902  Domain of unknown function (DUF1902)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.7e-06     0.087      12      47 ..      12      47 ..       4      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.7e-06
                                      TTEEEEE-SSSTT---EESSHHHHHHHHHHHHHHHH CS
                           DUF1902 12 AgVWvaesddipGlvteaetleeLlkkleamipdlL 47
                                       g  v e+  +pG v +  t+ee l+ ++++i+  L
  gi|330507048|ref|YP_004383476.1| 12 DGWLVVECPSLPGCVSQGRTVEEALENIKDAIQGCL 47
                                      5556899*************************9554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 565.69
//
Query:       gi|330507049|ref|YP_004383477.1|  [L=167]
Description: hypothetical protein MCON_0881 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.7   0.0      0.084   13.7   0.0    1.6  1  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.7e-06     0.084       5      52 ..      32      78 ..      29      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.7e-06
                      VAPB_antitox  5 IsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgilsee 52
                                      I+ +vY +L ++Kr g SF d I + l    + ++++l+++ +i +++
  gi|330507049|ref|YP_004383477.1| 32 ITNSVYAELMRAKRAGYSFPDRIFEQLP-VITIDRDDLKAFKDISTDS 78
                                      899******************9976554.3344466677666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1235.96
//
Query:       gi|330507050|ref|YP_004383478.1|  [L=98]
Description: hypothetical protein MCON_0882 [Methanosaeta concilii GP6]
Scores for complete 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   48.4   0.2    9.1e-13   47.7   0.2    1.5  1  UPF0175   Uncharacterised protein family (UPF0175)
  ------ inclusion threshold ------
      0.021   14.8   0.8      0.021   14.8   0.8    1.8  2  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.2     1e-16   9.1e-13      15      61 ..      33      79 ..      19      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1e-16
                           UPF0175 15 elerelrialAvklYeegrlSlgkAaelaglsrveflelLarrgipl 61
                                      +++  lri++A+ lY+ +++Sl kAae+agl   ef + La+r i l
  gi|330507050|ref|YP_004383478.1| 33 SMKPGLRIEIAIDLYRNEKVSLWKAAEIAGLCMEEFKDVLASRSIKL 79
                                      567889**************************************984 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 ?   14.8   0.8   2.3e-06     0.021      12      37 ..       6      32 ..       4      33 .. 0.94
   2 ?   -3.2   0.1       1.1   9.6e+03      29      37 ..      40      48 ..      40      49 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-06
                                      HHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1 12 erLdelarrrg.rSrSelIReAlreyl 37
                                      +++d+l r +  +Sr el+++Alr++l
  gi|330507050|ref|YP_004383478.1|  6 DEIDALMRTEIyKSREELLKDALRALL 32
                                      589*********************987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.1
                                      HHHHHHHHH CS
                             RHH_1 29 IReAlreyl 37
                                      I+ A+  y+
  gi|330507050|ref|YP_004383478.1| 40 IEIAIDLYR 48
                                      677887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 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:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 735.85
//
Query:       gi|330507051|ref|YP_004383479.1|  [L=77]
Description: hypothetical protein MCON_0883, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-17   61.7   0.0    6.3e-17   61.5   0.0    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 !   61.5   0.0   3.5e-21   6.3e-17     271     344 ..       2      69 ..       1      71 [. 0.94

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 3.5e-21
                                       HHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT-HHHHHHHHHHHCT-..--......--TT-SS-HHHHHHH CS
                       Epimerase_2 271 qeEapslgvpvvnlReeteRpegveagtnvlvgtdkeeIvaaleklledkkelekmanaknpYgdGkaserive 344
                                       qeE+++lgvp+v+lR++teRpe++e ++nvl+g+d+ ++v+++++++++       + +knp+gdG+a + iv+
  gi|330507051|ref|YP_004383479.1|   2 QEETCILGVPCVTLRDNTERPEALEVKSNVLAGADALRMVENAKRMMQQ------GNGWKNPFGDGRAGRIIVN 69 
                                       9**********************************************55......567889********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 583.89
//
Query:       gi|330507052|ref|YP_004383480.1|  [L=199]
Description: acylphosphatase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-18   66.3   0.3    2.5e-18   66.3   0.3    1.9  2  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
      0.025   14.5   0.7       0.63   10.0   0.1    2.5  3  Med10            Transcription factor subunit Med10 of Mediat
      0.031   14.5   1.3       0.19   12.0   1.2    2.2  1  DUF948           Bacterial protein of unknown function (DUF94
      0.083   12.9   0.9       0.46   10.5   0.6    1.9  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.094   12.9   0.4       0.13   12.4   0.4    1.2  1  SPT16            FACT complex subunit (SPT16/CDC68)
       0.19   11.8   3.7       0.83    9.7   3.1    2.1  1  DUF1664          Protein of unknown function (DUF1664)


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 !   66.3   0.3   8.2e-22   2.5e-18       2      83 ..       6      87 ..       5      89 .. 0.97
   2 ?   -1.2   0.1      0.94   2.8e+03      31      73 ..     139     181 ..     137     191 .. 0.60

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 8.2e-22
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      +++v+G+VQ vg+R+ v ++A+ +gl+G+v+N +dg+V+i +ege+ek++ f +++  ++  ++v+++e + ++++ ef
  gi|330507052|ref|YP_004383480.1|  6 TAIVSGKVQEVGYRARVIDIANAFGLRGMVENPKDGRVKIIVEGEDEKIKWFENAIVIKNALISVSSIEKSYSSANVEF 84
                                      689********************************************************************99999999 PP

                   Acylphosphatase 81 kdF 83
                                      ++F
  gi|330507052|ref|YP_004383480.1| 85 EKF 87
                                      988 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.94
                   Acylphosphatase  31 vrNlsdgsVeivaegeeekvekfleelksgppk.arvdevevee 73 
                                       vrN++d  + + +    +k ++++ e+k  + k  rv e ++ e
  gi|330507052|ref|YP_004383480.1| 139 VRNMNDR-LGGKMDQMLDKQDDLIIEVKDVNRKmDRVLETDIVE 181
                                       5666665.666666666666666666666444446666655555 PP

>> Med10  Transcription factor subunit Med10 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00021      0.63      74     110 ..     105     141 ..     103     152 .. 0.89
   2 ?    4.1   0.1     0.014        42      78     109 ..     134     165 ..     132     177 .. 0.85
   3 ?    2.1   0.1     0.058   1.7e+02       6      48 ..     152     192 ..     148     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Med10  74 iYtrefvelvrrkNqlmkGkmeafkkfrdvLaeelek 110
                                       +Y +e+v +v + N  + Gkm ++   +d L +e+++
  gi|330507052|ref|YP_004383480.1| 105 VYLKELVSAVNNMNDNLGGKMGQMLGKQDELLDEVRN 141
                                       8**********************99999999999876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Med10  78 efvelvrrkNqlmkGkmeafkkfrdvLaeele 109
                                       e++++vr+ N  + Gkm+++ + +d L  e++
  gi|330507052|ref|YP_004383480.1| 134 ELLDEVRNMNDRLGGKMDQMLDKQDDLIIEVK 165
                                       77899*************99998888877765 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.058
                                       HHHHHHHHHHHHHHS--TT.S-TTHHHHHHHHHHHHHHHHHHH CS
                             Med10   6 eviqsllelgvqvsdydenessqevlaqklktlvesLqelskt 48 
                                       +++++  +l + v+d++   + ++vl++++ +l ++++e++++
  gi|330507052|ref|YP_004383480.1| 152 QMLDKQDDLIIEVKDVNR--KMDRVLETDIVELKSDMAEVKSA 192
                                       556666778889999998..8999*********9999999865 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.2   6.4e-05      0.19      19      70 ..     127     174 ..      92     180 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.4e-05
                            DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekv 70 
                                        +l k  ++lde++++ + l+ ++d++l++ +dl+ +v++    vn+k+++v
  gi|330507052|ref|YP_004383480.1| 127 QMLGKQDELLDEVRNMNDRLGGKMDQMLDKQDDLIIEVKD----VNRKMDRV 174
                                       3444556667777777777777777777777777777766....77777766 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 ?    7.0   0.1    0.0019       5.5      52     107 ..      89     145 ..      61     148 .. 0.65
   2 ?   10.5   0.6   0.00015      0.46      31     108 ..     109     193 ..     100     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0019
                      Baculo_PEP_C  52 edlksllaeldtrldtll...tnLtdalnalqdtlrneLtnlnsiltnLlssvtNinst 107
                                       + +++   e dtrldt++   ++L +a+n+++d+l  ++  +  +  +Ll +v N+n  
  gi|330507052|ref|YP_004383480.1|  89 KLVTK--GETDTRLDTAAvylKELVSAVNNMNDNLGGKMGQMLGKQDELLDEVRNMNDR 145
                                       44444..4566677776511156666777777888888888888888888888888765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00015
                      Baculo_PEP_C  31 qilaqlatlldaietqLnalsedlksllaeldt.......rldtlltnLtdalnalqdtlrneLtnlnsiltnLlss 100
                                       +++++++++ d++ ++++++  +  +ll e+++       ++d++l++ +d + +++d  r+    l++++ +L s+
  gi|330507052|ref|YP_004383480.1| 109 ELVSAVNNMNDNLGGKMGQMLGKQDELLDEVRNmndrlggKMDQMLDKQDDLIIEVKDVNRKMDRVLETDIVELKSD 185
                                       455777888888888888888888888888887777666688888888888888888655555556899******** PP

                      Baculo_PEP_C 101 vtNinstL 108
                                       ++ ++s+L
  gi|330507052|ref|YP_004383480.1| 186 MAEVKSAL 193
                                       *9999998 PP

>> SPT16  FACT complex subunit (SPT16/CDC68)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   4.4e-05      0.13      26     126 ..      63     173 ..      59     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.4e-05
                             SPT16  26 iknv...skseegdytylrinFnvpgsavgkkeealfknpeaifikeltfrskdekk.....lqevfreikelkkkv 94 
                                       ikn+    +s e++y+   ++F   g+ v+k e+ +   + a+++kel    ++ +      + +++ +  el ++v
  gi|330507052|ref|YP_004383480.1|  63 IKNAlisVSSIEKSYSSANVEFEKFGKLVTKGETDTRLDTAAVYLKELVSAVNNMNDnlggkMGQMLGKQDELLDEV 139
                                       777755456778889*************99999777766999******98888877688888666666667777777 PP

                             SPT16  95 kkreae..kkekedlveqekLilskskrkprLkd 126
                                       ++ +++   k ++ l +q++Li++ +  + +++ 
  gi|330507052|ref|YP_004383480.1| 140 RNMNDRlgGKMDQMLDKQDDLIIEVKDVNRKMDR 173
                                       6665541134666677889997766666666655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.1   0.00028      0.83      50     108 ..     132     191 ..     105     196 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00028
                           DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtev.redlseigedvesvke 108
                                        +++ +++++  ++L  ++d++ +k+d+ +   k++++++++v + d+ e+++d+ +vk+
  gi|330507052|ref|YP_004383480.1| 132 QDELLDEVRNMNDRLGGKMDQMLDKQDDLIIEVKDVNRKMDRVlETDIVELKSDMAEVKS 191
                                       244445555555555555555555555555555555555554314455566666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1525.38
//
Query:       gi|330507053|ref|YP_004383481.1|  [L=172]
Description: membrane-bound metal-dependent hydrolase [Methanosaeta concilii GP6]
Scores for complete 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-13   48.4   8.9    8.5e-13   48.0   8.9    1.3  1  YdjM         LexA-binding, inner membrane-associated putative
     0.0025   17.8   0.1      0.004   17.2   0.1    1.2  1  Zn_dep_PLPC  Zinc dependent phospholipase C


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 !   48.0   8.9   9.4e-17   8.5e-13       5     127 ..       5     104 ..       1     154 [. 0.72

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 9.4e-17
                              YdjM   5 tHallGaalglalaallgaakeavllavavlgAllPD.iDhpsstlgrklgllskklaklvgHRgftHSllflalla 80 
                                       +H+ l++a++ ++            l++++lg++lPD iD p   l   +g  +         R+f H+llfl++l+
  gi|330507053|ref|YP_004383481.1|   5 AHVGLALATARLYSR--------LDLLFLALGSILPDiIDKPLGLLV--FGTPNM-------GRTFAHTLLFLLILG 64 
                                       444444444443333........6899**********99*4444443..333334.......9************99 PP

                              YdjM  81 lvlllllrlfgrsalrlglllllgvlsHlllDlltkyGvpllwPfsk 127
                                       ++ l l   + +s       l++gvl+Hl+lD++++++v llwP+ +
  gi|330507053|ref|YP_004383481.1|  65 AISLRLRDIRLAS-------LTWGVLVHLILDSMWSSPVILLWPLLG 104
                                       9887777777766.......************************975 PP

>> Zn_dep_PLPC  Zinc dependent phospholipase C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   4.5e-07     0.004      22     107 ..      18      92 ..       2      92 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.5e-07
                                       HHHTHHHHHHHHHGGGG.........-TT-GGG--BTTTTB-HHHHS....-HHHHHHHHHHHHHHHHHC.....T- CS
                       Zn_dep_PLPC  22 lklnkaalllGsvaPDl.......eylfnasshsykthtkagllged....hhweetgkfllllikklrelyksegs 87 
                                        +l++ +l lGs++PD+                         + +++    ++++  + +l l++ +lr       +
  gi|330507053|ref|YP_004383481.1|  18 SRLDLLFLALGSILPDIidkplglL----------------VFGTPNmgrtFAHTLLF-LLILGAISLRL-----RD 72 
                                       4688999**********44444331................22222244433333445.55555555556.....59 PP

                                       HHHHHHHHHHHHHHHHHHTS CS
                       Zn_dep_PLPC  88 lklaafllGvlsHyvaDvft 107
                                       ++la+   Gvl H++ D+ +
  gi|330507053|ref|YP_004383481.1|  73 IRLASLTWGVLVHLILDSMW 92 
                                       *****************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1259.33
//
Query:       gi|330507054|ref|YP_004383482.1|  [L=86]
Description: hypothetical protein MCON_0891 [Methanosaeta concilii GP6]
Scores for complete sequence (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   63.6   0.3    1.4e-17   63.5   0.3    1.0  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.029   14.2   0.0      0.039   13.9   0.0    1.2  1  TrmB      Sugar-specific transcriptional regulator TrmB
      0.047   13.2   0.0      0.067   12.8   0.0    1.3  1  HTH_47    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 !   63.5   0.3   2.3e-21   1.4e-17       1      76 [.       4      81 ..       4      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 2.3e-21
                            HTH_45  1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli...kkskekYvlTekGlelleklkeleela 76
                                      rRsk +Ii++IL+++ e++++ T+i+y++ +s+  ++ YL  L++++l+   + s   Y++T kGl + ++l+ l++l+
  gi|330507054|ref|YP_004383482.1|  4 RRSKDQIIVEILNIC-EKGENLTNIVYRSSISFASIKAYLAVLMKNDLLiyqDGSPRIYKTTPKGLAMRDRLEGLHKLM 81
                                      8**************.999*****************************7664447789**************9999876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.5e-06     0.039      19      66 ..      18      65 ..      11      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-06
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE-- CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravd 66
                                      +++  + + i  ++ ++ +++  +L  L++ +l   ++g+p++Y++++
  gi|330507054|ref|YP_004383482.1| 18 CEKGENLTNIVYRSSISFASIKAYLAVLMKNDLLIYQDGSPRIYKTTP 65
                                      567778899999*********************************987 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.1e-05     0.067      30      76 ..       5      51 ..       1      53 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                                      ---HHHHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-E CS
                            HTH_47 30 kqaemallwvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeagll 76
                                      +++ + ++++Ln++   ++L +i  r+ ++f+ ++a +  L +++ll
  gi|330507054|ref|YP_004383482.1|  5 RSKDQIIVEILNICEKGENLTNIVYRSSISFASIKAYLAVLMKNDLL 51
                                      56788999*************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 694.82
//
Query:       gi|330507055|ref|YP_004383483.1|  [L=97]
Description: hypothetical protein MCON_0892 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.55   10.3   6.1          4    7.6   0.8    2.2  2  Insulin_TMD  Insulin receptor trans-membrane segment


Domain annotation for each model (and alignments):
>> Insulin_TMD  Insulin receptor trans-membrane segment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4    0.0009        16      13      29 ..      36      52 ..      30      57 .. 0.85
   2 ?    7.6   0.8   0.00022         4      12      30 ..      69      87 ..      65      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0009
                       Insulin_TMD 13 nivkIvigPviciilll 29
                                      +++ I +++vic+i ll
  gi|330507055|ref|YP_004383483.1| 36 GVADISVVSVICLIALL 52
                                      6889999*******887 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00022
                       Insulin_TMD 12 snivkIvigPviciillll 30
                                      s ++ I i+P ++ ++l++
  gi|330507055|ref|YP_004383483.1| 69 STVLNIAIVPMVLTFFLIV 87
                                      67999*******9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1339  (0.0746835); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 759.35
//
Query:       gi|330507056|ref|YP_004383484.1|  [L=282]
Description: CAAX amino terminal protease family protein [Methanosaeta concilii GP6]
Scores for 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   52.7   9.0      4e-14   52.7   9.0    2.8  4  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.19   3.3e+03      66      89 ..      19      42 ..      11      45 .. 0.72
   2 ?   -1.7   1.1      0.22   3.9e+03      52      55 ..      79      82 ..      43     133 .. 0.63
   3 !   52.7   9.0   2.3e-18     4e-14       4      91 ..     153     242 ..     150     243 .. 0.91
   4 ?   -2.7   0.2      0.45   8.1e+03      57      73 ..     252     268 ..     244     274 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.19
                                      HHHHHHHHHHTT-HHHHHHHHHHH CS
                              CPBP 66 GlvlgylylktgsllaaillHall 89
                                       ++l+ + + +g+  aa+ +Hal+
  gi|330507056|ref|YP_004383484.1| 19 LILLAEILIFYGKAEAAMPIHALN 42
                                      456666667777799999999875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.22
                                      SGGG CS
                              CPBP 52 Hlpn 55
                                      Hl  
  gi|330507056|ref|YP_004383484.1| 79 HLTL 82
                                      3332 PP

  == domain 3  score: 52.7 bits;  conditional E-value: 2.3e-18
                                       THHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG..HHHHHHHHHHHHHHHHHHHHTT- CS
                              CPBP   4 lllvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn..gpsvllaalaGlvlgylylktgs 78 
                                        l+++l ++++++++EE++fR+ l++ lqer + +  ++++s++Fg++H  +  ++ +l+++laGl++g+l++ ++s
  gi|330507056|ref|YP_004383484.1| 153 MLILALTMIFFVGIVEEFVFRSSLQTVLQERIGLIGGLVLASVIFGFMHSGYhlTLELLYVSLAGLAFGVLFWLSKS 229
                                       5788999************************77799*************988544449******************* PP

                                       HHHHHHHHHHHHH CS
                              CPBP  79 llaaillHallnl 91 
                                       l ++ l+H+++n+
  gi|330507056|ref|YP_004383484.1| 230 LPIVSLAHGVTNI 242
                                       ***********97 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHHHHHH CS
                              CPBP  57 psvllaalaGlvlgyly 73 
                                       p +l+++++G ++ + +
  gi|330507056|ref|YP_004383484.1| 252 PEILPYLIIGPLFLFFF 268
                                       55566666665554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2232.04
//
Query:       gi|330507057|ref|YP_004383485.1|  [L=492]
Description: glycosyl transferase family protein [Methanosaeta concilii GP6]
Scores for complete 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-60  203.1   0.6    8.6e-60  202.6   0.6    1.2  1  Glyco_hydro_57   Glycosyl hydrolase family 57
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.23   11.4   0.0    1.4  1  Polysacc_deac_1  Polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.6   0.6   9.6e-64   8.6e-60       2     323 ..       6     296 ..       5     298 .. 0.96

  Alignments for each domain:
  == domain 1  score: 202.6 bits;  conditional E-value: 9.6e-64
                                       EEEEE-----TTS-..SSSSSHHHHHHHHHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-HHHHHHHHHHH CS
                    Glyco_hydro_57   2 fvfhqHqplykkpg..kgeytlpwvrehaaedYiklalilekfpkvhvtfeLsgsLiaqLeeylngekksylpatee 76 
                                       + f++Hqp++ k++   + y ++ v    ++ Y++ + ++ +f++v+                    +k+ylpa++ 
  gi|330507057|ref|YP_004383485.1|   6 LSFEVHQPIRLKKNffWDGYMNRQVVPDLWKYYFDCPENKRIFERVS--------------------DKCYLPANRA 62 
                                       6799******9888777889999999999******************....................********** PP

                                       HHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHH CS
                    Glyco_hydro_57  77 llelieeglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedi 153
                                       +le i++ + + +++k      +++++sg +le +q++  ++vl++f +l+++g vE+l ++yyH+l++l+ ds++ 
  gi|330507057|ref|YP_004383485.1|  63 ILEGIKKLQGSNRSFK------VSYSFSGVFLEECQRY-RPDVLDSFVDLVQTGMVEVLDQTYYHSLASLYDDSQEY 132
                                       *****9999999****......****************.************************************** PP

                                       HHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS.-EEEE CS
                    Glyco_hydro_57 154 eaqvkkarelyeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllknggiavff 230
                                       ++q+k++rel+ ++f  +P++f ++El++s++i++i   +G++ +ft+++      +   +p+++y+++n++ia+++
  gi|330507057|ref|YP_004383485.1| 133 IEQIKMHRELIWDIFALRPTTFENTELIYSDKIAQIADRMGYKAIFTEGVV-----A---DPNYVYRPPNTKIALLL 201
                                       ************************************************953.....4...689************** PP

                                       --CHH-TTTSGGG-................TTSB..........-TT---TTT-..-BB-TT-S---HHHHHHHHHH CS
                    Glyco_hydro_57 231 RdreLsddigFrys....eqypleavddfinwlkkvkkaksevvtialdgEnwg..hypetgkkeFleklyeeleen 301
                                       R+++L ddigFr+s    e ypl ++d+++ wl ++   ++++++i+ d+E++g  ++  tg+++F++ l+ ++ + 
  gi|330507057|ref|YP_004383485.1| 202 RNYQLTDDIGFRFSshnwEEYPL-TADKYASWLART---PGKCINIFCDYETFGehQWIDTGIFDFIRSLPNQVLRY 274
                                       ******************99***.**********99...************************************** PP

                                       HHHHHHHHHHHHHHHSS-EEEE CS
                    Glyco_hydro_57 302 glielvtpsefikklkpkglik 323
                                       + +++ tp e++++++p++ ++
  gi|330507057|ref|YP_004383485.1| 275 ENLQFATPCEVASTIPPERELS 296
                                       ****************998766 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.6e-05      0.23      53     123 ..     104     176 ..      60     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.6e-05
                                       HHHHTT.EEEEE--SS--EGGGSHHH.HHHHHHHHHHHHHHHHHS----EEE-GGGEE-HHHHHHHHHTT.EE CS
                   Polysacc_deac_1  53 emaasG.veignHtinhsnlkrlsee.evrreierakdalrkalgreprlfryPygsasatvlevarelgfay 123
                                        +++ G ve+   t+ hs  +    + e  ++i++ ++ + +++  +p++f    + +s+++ ++a ++g+++
  gi|330507057|ref|YP_004383485.1| 104 DLVQTGmVEVLDQTYYHSLASLYDDSqEYIEQIKMHRELIWDIFALRPTTFENTELIYSDKIAQIADRMGYKA 176
                                       67899*************885555444899*****************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3546.10
//
Query:       gi|330507058|ref|YP_004383486.1|  [L=621]
Description: glycogen debranching protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.1e-107  360.3   0.0   1.9e-107  359.5   0.0    1.3  2  GDE_C            Amylo-alpha-1,6-glucosidase
    4.5e-58  196.3   0.0    5.8e-58  195.9   0.0    1.1  1  GDE_N            Glycogen debranching enzyme N terminal
    2.1e-05   23.9   0.0    3.1e-05   23.3   0.0    1.1  1  DUF608           Glycosyl-hydrolase family 116, catalytic reg
     0.0093   14.7   0.0        5.8    5.5   0.0    2.8  3  Glyco_hydro_100  Alkaline and neutral invertase


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 ?   -4.1   0.0       1.3   5.8e+03     302     325 ..      15      38 ..      11      47 .. 0.68
   2 !  359.5   0.0  4.3e-111  1.9e-107       4     383 .]     267     613 ..     262     613 .. 0.93

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1.3
                             GDE_C 302 aYHqGtvWvwllgsyveallkfge 325
                                        Y qGt   wl++  + ++ + + 
  gi|330507058|ref|YP_004383486.1|  15 DYSQGTSREWLVANGLGSYASSTA 38 
                                       699999999988766655555444 PP

  == domain 2  score: 359.5 bits;  conditional E-value: 4.3e-111
                             GDE_C   4 dqflvrrkseslkeeekgvsliAGlpwFsdWGRDtfIaLsGllLvtgrfeeAreilltFaktlrhGliPNlldegqe 80 
                                       d+flv+r         + +sliAG++wF+dWGRD++IaL+G+lL+tgr+e Ar +l++Fa+++++G++PN l     
  gi|330507058|ref|YP_004383486.1| 267 DSFLVKR--------GNALSLIAGYHWFDDWGRDAMIALPGILLSTGRYEAARLVLSSFAGAMKDGVLPNDL---GA 332
                                       4455544........4789*****************************************************...45 PP

                             GDE_C  81 alyntvdaslwlieaiekYleyagdaeilrriypvlqeilqkyvqGtkykigldeedglisagerlnqlTWmDakvk 157
                                         yntvdaslw+++a ++Y++++gd ++l++ +p l +++++y +  +  +g d edgli+ g    +lTWmDa+v+
  gi|330507058|ref|YP_004383486.1| 333 RSYNTVDASLWFVQATSRYFDATGDLDFLAELWPKLLDVVERYSRPGD-DFGAD-EDGLINSGP---ALTWMDARVD 404
                                       67******************************************9777.78999.9********...********** PP

                             GDE_C 158 gepvtPRdGkaveinaLwyaaLkileelaekalgeakkssykelaekikesfekkFwdeaaaavakreilaDvlkss 234
                                       g+pvt R+Gk +einaLwy+aL+ +e+l++ al+    ++  ela+k+++s+ + Fw+      +++++l+Dv+++ 
  gi|330507058|ref|YP_004383486.1| 405 GRPVTSRTGKCCEINALWYSALRRTESLSR-ALDMPLDPKIPELADKVQKSYLR-FWN------SENGCLFDVIDH- 472
                                       ******************************.6665599**************99.***......9**********9. PP

                             GDE_C 235 eekdlslRpNflialslapellseekakkvlekaeeeLltplGlktLdpedpeYkgnYdgsedsrdaaYHqGtvWvw 311
                                         +d+s+RpN+++a  + p+ll +   + +le + ++Lltp+Gl+tL+p+dp+Y g+Y g+ ++rd  YHqGtvW+w
  gi|330507058|ref|YP_004383486.1| 473 --EDASIRPNQIFAAIV-PDLLPDVMRRSILEVVARDLLTPFGLRTLSPRDPRYAGRYAGEPKERDRSYHQGTVWPW 546
                                       ..89**********776.578888999************************************************** PP

                             GDE_C 312 llgsyveallkfgeklgkskea.leevkalLeglekhleeaglgslsElfdgdaellpkgciaQAWSvaellr 383
                                       l+g y+++ll++g + ++++e+ le +++lL+        +g+g+++E+fdgd +  p gci QAWSv+e+lr
  gi|330507058|ref|YP_004383486.1| 547 LIGPYIDLLLAVGGRSAETREKgLEALRPLLD------LAEGMGTIPEVFDGDLPQNPGGCISQAWSVGEVLR 613
                                       ************99755544444888888888......5679*****************************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 !  195.9   0.0   1.3e-61   5.8e-58       1     215 [.      22     225 ..      22     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 195.9 bits;  conditional E-value: 1.3e-61
                             GDE_N   1 REwllTNglGGYasgtvagantRryhGlLvaalnppsgRtlllskldeslevsgkvfeLstneypgeiepeGyeyLe 77 
                                       REwl++NglG+Yas+t  ++ntR yhGlLvaa++pp ++ lll++lde+l      f+L+ ++ypg i+p+G+ +L+
  gi|330507058|ref|YP_004383486.1|  22 REWLVANGLGSYASSTANCSNTRAYHGLLVAATEPPARKRLLLASLDEELGE----FRLANHQYPGAIYPQGFSHLQ 94 
                                       9*************************************************87....********************* PP

                             GDE_N  78 sFelepvptwtyrvgdvllekqivmpkgentvliaYrlenadepatLrlrpllafRdfheltkanellqksqeeglv 154
                                        F+ +p+p++ y++g ++lek++ m+++en ++i+Yr+++   +  +r++pl+++R+fh++ +  +l+q++   +++
  gi|330507058|ref|YP_004383486.1|  95 GFWTDPLPRFCYQMGTTTLEKTVSMVRNENSTIISYRIKG--YRGLIRIVPLIHDRSFHAAGDLPPLHQNT-WGKGT 168
                                       ****************************************..589******************88888877.43333 PP

                             GDE_N 155 eiqaseaepslrlqaskegefqeepvwyynveypeEaerGlddredlyspgyfevelkpge 215
                                       +     +++++++ ++  +++++++ +y n+ey+eE++rGl ++e+l+spg fe++++ ++
  gi|330507058|ref|YP_004383486.1| 169 T---ILSQTRFSIFSD-LARYIPQERVYSNFEYEEERRRGLGWKENLFSPGCFELDVSGEA 225
                                       2...335677788888.889***********************************998765 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 !   23.3   0.0     7e-09   3.1e-05      99     213 ..     339     461 ..     333     485 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 7e-09
                            DUF608  99 DlnlkfvLqvYRdyvitedkeflkemypkvkkvleklle....fDkdkdgliene...gfadqtYDa...wsvkGvs 165
                                       D  l fv    R + +t d +fl e++pk+  v+e+  +    f  d+dgli++      +d   D    +s +G  
  gi|330507058|ref|YP_004383486.1| 339 DASLWFVQATSRYFDATGDLDFLAELWPKLLDVVERYSRpgddFGADEDGLINSGpalTWMDARVDGrpvTSRTGKC 415
                                       66777999999***********************998755334778******9862223578888876667778888 PP

                            DUF608 166 aycgglwlaaLeaaiemaellgdkkdaeeykellekakkvyekkLwnG 213
                                         ++ lw++aL+ + ++++ l+   d  ++ el +k +k+y  ++wn 
  gi|330507058|ref|YP_004383486.1| 416 CEINALWYSALRRTESLSRALDMPLDP-KIPELADKVQKSYL-RFWNS 461
                                       9999*****************877666.69999999999999.99974 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 !    5.5   0.0    0.0013       5.8      96     138 ..     323     362 ..     305     368 .. 0.78
   2 ?   -0.2   0.0     0.069   3.1e+02     180     200 ..     412     432 ..     394     459 .. 0.84
   3 !    5.3   0.0    0.0015       6.7     346     369 ..     528     551 ..     480     615 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0013
                                       EEEEEEESSSSSGGG---HHHHHHHHHHHHHHHHHH---HHHH CS
                   Glyco_hydro_100  96 eeklkaDfGeraigRvapvDsslWWiillraYvkatgdlslae 138
                                       +  l  D G r+     +vD+slW++     Y  atgdl++ +
  gi|330507058|ref|YP_004383486.1| 323 DGVLPNDLGARSY---NTVDASLWFVQATSRYFDATGDLDFLA 362
                                       5567777777775...579*******************99865 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.069
                                       -BSBHHHHHHHHHHHHHHHHH CS
                   Glyco_hydro_100 180 ygapleiqaLlyaalrsakel 200
                                       +g+  ei+aL+y+alr +++l
  gi|330507058|ref|YP_004383486.1| 412 TGKCCEINALWYSALRRTESL 432
                                       57889***********99877 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0015
                                       TS-GGG-TTBTTBT-B-GGGHHHH CS
                   Glyco_hydro_100 346 GsDpkntpwsYhngGsWpvllWll 369
                                         +pk +  sYh g  Wp l+   
  gi|330507058|ref|YP_004383486.1| 528 AGEPKERDRSYHQGTVWPWLIGPY 551
                                       4589***************98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 4186.98
//
Query:       gi|330507059|ref|YP_004383487.1|  [L=533]
Description: cation transport protein [Methanosaeta concilii GP6]
Scores for complete 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-60  204.5  13.4      2e-32  112.3   6.2    3.0  2  TrkH      Cation transport protein
  ------ inclusion threshold ------
       0.36   10.6   0.1       0.36   10.6   0.1    2.5  3  PHBC_N    Poly-beta-hydroxybutyrate polymerase N terminal
       0.55   10.0   5.3       0.71    9.6   0.0    3.0  3  TMEM40    Transmembrane protein 40 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 !   93.6   0.6   1.6e-30   9.7e-27      12     250 ..      58     316 ..      48     338 .. 0.87
   2 !  112.3   6.2   3.4e-36     2e-32     319     491 ..     351     527 ..     343     533 .] 0.94

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 1.6e-30
                              TrkH  12 tialgavllfldkeskyplalkddfqivkaaeialsvdgtlklllesaslafldalfeavsgltttglsvivveesl 88 
                                       ++a g +l  l   s+ ++ l+++f  v   +ia+ + g+++ ++    +  +d lfe++s++tttg sv+++ ++l
  gi|330507059|ref|YP_004383487.1|  58 SLATGIALGRL--SSEEEPGLREAFALVALGWIAVAFFGAFPYVF--LGMSLIDGLFESMSAFTTTGSSVFTEINHL 130
                                       33333333333..55668999*********************884..555569************************ PP

                              TrkH  89 prsgltlraqlq..........................................qiGglgvvvlaylslptlgrgsa 123
                                       +++   +++ ++                                          ++Gg+g++ l +++lp+lg  + 
  gi|330507059|ref|YP_004383487.1| 131 GYWKM-NQTLADsslvaemqmqlvrmtgnsillrmrsgpddtimgllfwrsfaqWLGGMGIILLFVAILPRLGVAGR 206
                                       98854.344444467999*********************************************************** PP

                              TrkH 124 flylseaqkeelggkelrslselikilvvyyvgleilafvllvvliytakaysevvdstgvsplwwaffhsmSafnn 200
                                       +ly++e++++ ++ ++ +++++++++l+++y++l+++ ++ll           +++      p ++ f+h++S++ +
  gi|330507059|ref|YP_004383487.1| 207 QLYRAEVPGPDKESIK-PRIKQTARMLWMVYILLTLVEVALL---------LLAGM------PPFDSFCHAFSSMAT 267
                                       **********998766.99***********************.........999**......*************** PP

                              TrkH 201 lGfsltpnSlasfnknivillvaiifiilGnigFpillrviiaikkkilr 250
                                       +Gfs  + S++ +n+  +i +++++f +l + +F +++r+i    k  + 
  gi|330507059|ref|YP_004383487.1| 268 GGFSPRGLSIMAYNS-WIIDAIIVLFCFLAGANFALHYRMITSDRKALIS 316
                                       ***************.************************9877666555 PP

  == domain 2  score: 112.3 bits;  conditional E-value: 3.4e-36
                              TrkH 319 alFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkavskksi 394
                                       a Fq+vs +t+ GF+++d+ ++ +   ++l+l m ig+++gStag I+ +++  +f++  +e+ +  +pkav+++++
  gi|330507059|ref|YP_004383487.1| 351 AGFQVVSILTTtGFATADFNQWTATARITLLLLMIIGACAGSTAGAIKVVRLILIFKSAYRELIRTLHPKAVQSVRL 427
                                       67*************************************************************************** PP

                              TrkH 395 dgkhlerqllvdlwslflvlliilileglklsd..vqepdfsffdiLfevvSaygtvGLSlGa.knaslsaqlttis 468
                                       +   +++++l++   ++++++ii+ + +l l +    +p++++  +L +v+ ++g+vG+++G    + ++a++ +++
  gi|330507059|ref|YP_004383487.1| 428 GDMVVKEEILRASNIFVSMYIIIFAIASLLLAMisYSDPKMDMESVLSAVATTLGNVGPGFGVvGPMFSFADIHPAG 504
                                       ************************99998776511679************************66************* PP

                              TrkH 469 klvlialmirGrlrglpvlldra 491
                                       k++li+ m++Grl++++ ++++ 
  gi|330507059|ref|YP_004383487.1| 505 KMLLILCMWIGRLEVVTAMVLFL 527
                                       ********************997 PP

>> PHBC_N  Poly-beta-hydroxybutyrate polymerase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.68     4e+03       6      23 ..     106     123 ..     104     125 .. 0.86
   2 ?   10.6   0.1     6e-05      0.36       5      35 ..     254     285 ..     250     289 .. 0.88
   3 ?   -3.7   0.2       1.8   1.1e+04      24      31 ..     454     461 ..     453     462 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.68
                            PHBC_N   6 lDralhAalArlTgGlSP 23 
                                       +D +++ + A  T G S+
  gi|330507059|ref|YP_004383487.1| 106 IDGLFESMSAFTTTGSSV 123
                                       799999999*99999887 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 6e-05
                            PHBC_N   5 alDralhAalArlTgGlSPasla.lAylDWaa 35 
                                       ++D   hA    +TgG SP  l+ +Ay  W +
  gi|330507059|ref|YP_004383487.1| 254 PFDSFCHAFSSMATGGFSPRGLSiMAYNSWII 285
                                       6899*****************9549**99987 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 1.8
                            PHBC_N  24 aslalAyl 31 
                                       asl+lA++
  gi|330507059|ref|YP_004383487.1| 454 ASLLLAMI 461
                                       89***986 PP

>> TMEM40  Transmembrane protein 40 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.041   2.5e+02      64      97 ..     177     210 ..     171     213 .. 0.84
   2 ?   -2.0   0.2      0.49   2.9e+03      82      82 ..     317     317 ..     284     355 .. 0.51
   3 ?    9.6   0.0   0.00012      0.71      44      99 ..     439     495 ..     414     501 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.041
                            TMEM40  64 syhyyadwfmslgvglltfasletvgiyfglvyr 97 
                                        +  +a+w+  +g+ ll  a l  +g+    +yr
  gi|330507059|ref|YP_004383487.1| 177 FWRSFAQWLGGMGIILLFVAILPRLGVAGRQLYR 210
                                       56789*****************999998777777 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.49
                            TMEM40  82 f 82 
                                        
  gi|330507059|ref|YP_004383487.1| 317 D 317
                                       1 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00012
                            TMEM40  44 kddeffhfvllcfaigallvsyhyyadwfmslgvglltfa.sletvgiyfglvyrih 99 
                                         + f  + ++ fai +ll++   y+d  m +   l + a +l  vg  fg+v  + 
  gi|330507059|ref|YP_004383487.1| 439 ASNIFVSMYIIIFAIASLLLAMISYSDPKMDMESVLSAVAtTLGNVGPGFGVVGPMF 495
                                       45667888999*********************9999887736999***9*9996655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3903.54
//
Query:       gi|330507060|ref|YP_004383488.1|  [L=437]
Description: Trk system potassium uptake protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-51  173.7   3.5    7.9e-27   93.8   0.9    2.4  2  TrkA_N           TrkA-N domain
    5.9e-16   58.1   0.1    3.1e-08   33.3   0.0    2.7  2  TrkA_C           TrkA-C domain
    4.5e-11   43.1   1.5    4.9e-06   26.9   0.4    2.4  2  NAD_binding_7    Putative NAD(P)-binding
    1.7e-09   37.5   0.2    0.00037   20.2   0.1    2.5  2  ApbA             Ketopantoate reductase PanE/ApbA
    1.8e-09   37.8   1.2    0.00016   21.7   0.3    2.4  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      3e-08   33.8   0.1    0.00015   22.0   0.0    2.6  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    4.5e-08   33.4   1.8    3.4e-05   24.1   0.6    2.4  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    8.2e-08   31.8   2.7     0.0048   16.2   0.8    2.2  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    8.5e-07   29.5   1.0      0.065   13.8   0.1    2.8  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    4.7e-06   26.1   0.0     0.0024   17.2   0.0    2.3  2  FAD_binding_3    FAD binding domain
    2.7e-05   23.5   0.2     0.0013   18.0   0.0    2.3  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    6.4e-05   22.7   0.2       0.38   10.3   0.0    2.4  3  DAO              FAD dependent oxidoreductase
    6.8e-05   23.4   0.9      0.008   16.7   0.1    2.6  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    7.7e-05   22.3   1.0       0.27   10.8   0.1    2.9  3  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0001   22.2   1.3       0.17   11.8   0.1    2.4  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00019   21.1   0.6       0.29   10.7   0.1    2.3  2  DUF1188          Protein of unknown function (DUF1188)
     0.0006   19.3   1.1       0.32   10.4   0.2    2.2  2  Epimerase        NAD dependent epimerase/dehydratase family
     0.0011   18.6   1.9      0.037   13.6   0.4    2.3  2  NmrA             NmrA-like family
     0.0011   17.7   0.3       0.11   11.2   0.2    2.4  2  HI0933_like      HI0933-like protein
     0.0033   17.6   2.7       0.62   10.2   0.1    2.6  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0088   16.5   0.2        1.9    9.0   0.0    2.4  2  XdhC_C           XdhC Rossmann domain
  ------ inclusion threshold ------
      0.012   15.6   0.1       0.99    9.4   0.0    2.5  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.012   14.5   0.0       0.35    9.7   0.0    2.1  2  Trp_halogenase   Tryptophan halogenase
      0.013   14.6   0.0      0.025   13.7   0.0    1.4  1  GIDA             Glucose inhibited division protein A
      0.033   13.4   0.4        1.4    8.1   0.0    2.3  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
      0.052   12.6   0.2       0.56    9.2   0.0    2.1  2  Lycopene_cycl    Lycopene cyclase protein
      0.057   12.8   0.2       0.71    9.2   0.0    2.2  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


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 !   93.8   0.9   1.2e-29   7.9e-27       1     103 [.       3     103 ..       3     120 .. 0.90
   2 !   80.3   0.1   1.9e-25   1.3e-22       2     116 .]     226     341 ..     225     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 1.2e-29
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       i+i G+G+vG  +a eL +++ dv+vidkd++++++l++  ++v++g+a++  +L ea+i+kad+v+aatg+de+n+
  gi|330507060|ref|YP_004383488.1|   3 ILITGAGEVGFLIASELYADH-DVTVIDKDPDACARLQDMDVKVMQGNAANARLLSEADIKKADIVVAATGNDEVNV 78 
                                       789******************.7****************************************************** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehae 103
                                       +++ +a +l   +++iar+++pe+++
  gi|330507060|ref|YP_004383488.1|  79 ITCIIASHLGV-RQTIARVSNPEYID 103
                                       ******98777.79**********54 PP

  == domain 2  score: 80.3 bits;  conditional E-value: 1.9e-25
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT..SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg..levvvgdatdeevLeeagiekadaviaatgddean 76 
                                       +i+G G vG  la +L++ g+dv +i+kd +r++e++++   +++++gd++d ++L+e g+  +d+v a+tg d++n
  gi|330507060|ref|YP_004383488.1| 226 MIVGGGMVGFYLASRLEKMGMDVKLIEKDADRCAEIADKLsgTMILNGDGSDLALLQEEGAGAMDVVYAVTGLDDKN 302
                                       8*****************6668****************999899********************************* PP

                                       HHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  77 ilavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                       +l++ll+k+l    ki +r+++  +++l++ +g+d+++sp
  gi|330507060|ref|YP_004383488.1| 303 LLCSLLVKQLGA-TKILSRVNRNVYIKLFEMVGVDRAVSP 341
                                       ********9888.69***********************98 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.4e-07   9.6e-05      16      66 ..     164     213 ..     150     217 .. 0.83
   2 !   33.3   0.0   4.7e-11   3.1e-08       2      69 ..     370     435 ..     369     436 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.4e-07
                                       BHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHH CS
                            TrkA_C  16 tlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelr 66 
                                       ++  + l++ +++++ai R g++ ip + ++++ +D+l ++++  +l +l 
  gi|330507060|ref|YP_004383488.1| 164 PVENIVLPN-NCNLIAINRAGRIAIPKEGDEIRNDDHLMLLCDARSLPDLG 213
                                       566777999.*********************************99998875 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 4.7e-11
                                       EEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                       v +  ++g+++vGk+++   l++ + l   + R+g +i+p +d++  +GD+++v++ p++++++++l+
  gi|330507060|ref|YP_004383488.1| 370 VDFIAKPGAKIVGKSISK-ELPK-NSLAGMVIRDGAPIVPYEDFKVSAGDRVFVMSMPDAVSKVKKLF 435
                                       6677899*********99.9***.******************************************98 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.4   7.4e-09   4.9e-06       9      84 ..       2      86 ..       1     104 [. 0.69
   2 !   14.9   0.0   4.2e-05     0.028       7      69 ..     222     296 ..     217     319 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 7.4e-09
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapev..keele.......elvk..laeeel..ekdlegadlviaatddrel 74
                                      ++l+ G+Gev+   ++ l +   +vtv++++   +           + ++  +a+  l  e+d+++ad+v+aat ++e+
  gi|330507060|ref|YP_004383488.1|  2 RILITGAGEVGFLIASELYAD-HDVTVIDKDPdaC---ArlqdmdvKVMQgnAANARLlsEADIKKADIVVAATGNDEV 76
                                      79***********99998876.*******995442...333344332222223333336789***************** PP

                     NAD_binding_7 75 neriaeaaka 84
                                      n   +  a  
  gi|330507060|ref|YP_004383488.1| 77 NVITCIIASH 86
                                      9776666644 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.2e-05
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapev..keele....elvklaeee..l....ekdlegadlviaat 69 
                                       ++k ++vGgG v+   +++l + g +v+++ ++   ++e+     +++ l+ +   l    e+    +d+v+a+t
  gi|330507060|ref|YP_004383488.1| 222 TQKAMIVGGGMVGFYLASRLEKMGMDVKLIEKDAdrCAEIAdklsGTMILNGDGsdLallqEEGAGAMDVVYAVT 296
                                       6899*****************************644333332222111122211221222233344566666666 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   5.5e-07   0.00037       1      72 [.       3      67 ..       3     100 .. 0.78
   2 !   14.9   0.0   2.3e-05     0.015       2      38 ..     226     263 ..     225     269 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.5e-07
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEECEEECCHSCCCCS-ESEE CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrppealsaeekselepidlv 72
                                      i+i GaG +G l+a +L  a +dvt+i++++  +++l++ ++++ + +  + +l+ ++        +++++d+v
  gi|330507060|ref|YP_004383488.1|  3 ILITGAGEVGFLIASEL-YADHDVTVIDKDPdACARLQDMDVKVMQGNaANARLLSEA--------DIKKADIV 67
                                      89***************.78***********99999***9999998884333333333........44444554 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.3e-05
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHH CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkk 38 
                                        i+G G +G +la +L k g dv li +++ r++++ +
  gi|330507060|ref|YP_004383488.1| 226 MIVGGGMVGFYLASRLEKMGMDVKLIEKDAdRCAEIAD 263
                                       69****************************99998865 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.3   2.5e-07   0.00016      14      91 ..       2      79 ..       1     114 [. 0.73
   2 !   14.7   0.0   3.7e-05     0.025       6      61 ..     216     270 ..     211     303 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.5e-07
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHH....HHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS- CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakel....aeelkgeeiealkleelkellaeadvvisataseep 88
                                      ++l+ GaGe++ l+a+ L+a +  +v+v+  + +  ++l    ++ ++g+ ++a+ l+e +  +++ad+v++at+  e+
  gi|330507060|ref|YP_004383488.1|  2 RILITGAGEVGFLIASELYADH--DVTVIDKDPDACARLqdmdVKVMQGNAANARLLSEAD--IKKADIVVAATGNDEV 76
                                      79*****************764..79*****988776662222334588889999999988..***********99886 PP

                                      SB- CS
                      Shikimate_DH 89 ile 91
                                       + 
  gi|330507060|ref|YP_004383488.1| 77 NVI 79
                                      544 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.7e-05
                                       HHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET- CS
                      Shikimate_DH   6 kleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeei 61 
                                         es +++k++++G G+++  +a+ L + g++ v  +  + +r +e+a++l+g+ i
  gi|330507060|ref|YP_004383488.1| 216 LHESKTTQKAMIVGGGMVGFYLASRLEKMGMD-VKLIEKDADRCAEIADKLSGTMI 270
                                       55667899*******************99999.******************98855 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0     0.002       1.4       2      38 ..       6      41 ..       5      56 .. 0.85
   2 !   22.0   0.0   2.2e-07   0.00015       1      30 [.     227     256 ..     227     272 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.002
                                      E--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                     NAD_binding_8  2 vGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                       GaG  G ++A++L  + +dv++++k ++ + r+++ 
  gi|330507060|ref|YP_004383488.1|  6 TGAGEVGFLIASELYAD-HDVTVIDKDPDACARLQDM 41
                                      699**********9985.9**********99988765 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.2e-07
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                       IvG+G+ G ++A++L k g dv l+ek  +
  gi|330507060|ref|YP_004383488.1| 227 IVGGGMVGFYLASRLEKMGMDVKLIEKDAD 256
                                       9**************************876 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 !   24.1   0.6   5.1e-08   3.4e-05       1      79 [.       3      73 ..       3      88 .. 0.89
   2 !    8.2   0.0    0.0043       2.9       2      46 ..     226     267 ..     225     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.1e-08
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE-SS CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnlsp 78
                                      +li GaG vG  +a +l + +dv    tv+d++ + +++l    +  +++ ++ +a+n +  L+++ +k++d+vv +++
  gi|330507060|ref|YP_004383488.1|  3 ILITGAGEVGFLIASELYADHDV----TVIDKDPDACARL----QDMDVKVMQGNAANARL-LSEAdIKKADIVVAATG 72
                                      7999***************9986....*************....579*************9.88888********8887 PP

                                      G CS
                   Sacchrp_dh_NADP 79 p 79
                                      +
  gi|330507060|ref|YP_004383488.1| 73 N 73
                                      6 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0043
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTT CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalg 46 
                                       +i+G+G+vG  +a  l++ +    ++ +++++ ++++++a+k++g
  gi|330507060|ref|YP_004383488.1| 226 MIVGGGMVGFYLASRLEKMGM---DVKLIEKDADRCAEIADKLSG 267
                                       699***************985...6***************98765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.8   7.3e-06    0.0048      30      98 ..       2      70 ..       1      80 [. 0.87
   2 !   15.3   0.0   1.4e-05     0.009      29      74 ..     223     269 ..     208     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.3e-06
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHH.HHHH-SEEEE- CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellae.avkeadvvigt 98
                                      ++l+ G+G +G   ia     + +Vtv+D++p++  +l+++  k+++  +++++ll+e  +k+ad+v+ +
  gi|330507060|ref|YP_004383488.1|  2 RILITGAGEVGFL-IASELYADHDVTVIDKDPDACARLQDMDVKVMQGNAANARLLSEaDIKKADIVVAA 70
                                      68999******86.4455666789********************9999999999987626********87 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.4e-05
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCE CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakf 74 
                                        k +++GgG++G   ++   ++g +V++++++++r  ++ + l +++
  gi|330507060|ref|YP_004383488.1| 223 QKAMIVGGGMVGFYLASRLEKMGMDVKLIEKDADRCAEIADkLSGTM 269
                                       5899*******************************999988765554 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   9.8e-05     0.065       2      67 ..       3      69 ..       2      83 .. 0.73
   2 !   13.4   0.1   0.00013     0.086       4      49 ..     227     268 ..     224     299 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.8e-05
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHH.......HHH-SEEEE CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneea.......aeeadvvvl 67
                                      i i GaG++g+ +as l a     h+++v+ +++p+  + l++   vkv++++++ a       +++ad+vv 
  gi|330507060|ref|YP_004383488.1|  3 ILITGAGEVGFLIASELYAD----HDVTVI-DKDPDACARLQDM-DVKVMQGNAANArllseadIKKADIVVA 69
                                      5566***********99998....9***99.*****99999655.6777776665552222222345555555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00013
                                       EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-E CS
                     F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvk 49 
                                       i+G+G +g+ las+l + g    ++ ++ +++ ++ +e+a++l+ +
  gi|330507060|ref|YP_004383488.1| 227 IVGGGMVGFYLASRLEKMG---MDVKLI-EKDADRCAEIADKLSGT 268
                                       77*****************...****88.************99843 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0055       3.6       4      36 ..       3      34 ..       1      64 [. 0.92
   2 !   17.2   0.0   3.7e-06    0.0024       4      36 ..     225     257 ..     222     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0055
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                      +lI GaG +G++ a++L     +v++++k  ++
  gi|330507060|ref|YP_004383488.1|  3 ILITGAGEVGFLIASELYAD-HDVTVIDKDPDA 34
                                      79***************999.9******98765 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.7e-06
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrstt 36 
                                        +IVG+G +G+ la+ L + G +v l+ek +++
  gi|330507060|ref|YP_004383488.1| 225 AMIVGGGMVGFYLASRLEKMGMDVKLIEKDADR 257
                                       68***************************9876 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 ?    3.2   0.2     0.064        43     144     190 ..       2      43 ..       1      98 [. 0.61
   2 !   18.0   0.0     2e-06    0.0013     137     174 ..     217     254 ..     192     272 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.064
                                       EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaale 190
                                       ri++ G+G +G  +A++l  + ++vt+++  +  + r     l+++  
  gi|330507060|ref|YP_004383488.1|   2 RILITGAGEVGFLIASELY-ADHDVTVIDKDPDACaR-----LQDMDV 43 
                                       6888899999988888842.23478888888888732.....333322 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2e-06
                                       CCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 137 klkllpkrivvvGgGyiGvElAaalaklgkevtlvear 174
                                       ++ ++ +++++vGgG++G  lA+ l k+g +v l+e  
  gi|330507060|ref|YP_004383488.1| 217 HESKTTQKAMIVGGGMVGFYLASRLEKMGMDVKLIEKD 254
                                       44455599************************999864 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00057      0.38       2      33 ..       3      35 ..       2      39 .. 0.89
   2 ?   -3.1   0.0       6.9   4.5e+03     192     202 ..      63      73 ..      36     121 .. 0.51
   3 !   10.1   0.0   0.00065      0.43       3      31 ..     226     256 ..     224     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00057
                                      EEEECTSHHHHHHHHHHHHTT.EEEEESSSSTT CS
                               DAO  2 vviiGGGiiGlstAyeLarrg.Vtllekgdiag 33
                                      ++i G+G +G  +A eL + + Vt+++k+++a+
  gi|330507060|ref|YP_004383488.1|  3 ILITGAGEVGFLIASELYADHdVTVIDKDPDAC 35
                                      8999*************77667*******8875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.9
                                       EEEEEEE--GG CS
                               DAO 192 aadavVnaaGa 202
                                       +ad vV a+G 
  gi|330507060|ref|YP_004383488.1|  63 KADIVVAATGN 73 
                                       23445555553 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00065
                                       EEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                               DAO   3 viiGGGiiGlstAyeLarrg..Vtllekgdi 31 
                                        i+GGG++G   A  L + g  V l+ek+ +
  gi|330507060|ref|YP_004383488.1| 226 MIVGGGMVGFYLASRLEKMGmdVKLIEKDAD 256
                                       69**************8779********944 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.068        45       1      42 [.       2      43 ..       2      80 .. 0.82
   2 !   16.7   0.1   1.2e-05     0.008       1      31 [.     224     254 ..     224     270 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.068
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHH CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeea 42
                                      ++++ G+G +g   A++l +  ++Vtv++  +  + rl D ++
  gi|330507060|ref|YP_004383488.1|  2 RILITGAGEVGFLIASELYA-DHDVTVIDKDPDACaRLQDMDV 43
                                      689**************965.458*****99999977777664 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.2e-05
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvvers 31 
                                       k+++vGgG +g  lA+ l ++g +V+++e  
  gi|330507060|ref|YP_004383488.1| 224 KAMIVGGGMVGFYLASRLEKMGMDVKLIEKD 254
                                       578*************************975 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1    0.0004      0.27       1      48 [.       1      47 [.       1      68 [. 0.88
   2 ?   -1.5   0.0       2.4   1.6e+03     130     157 ..      77     103 ..      52     108 .. 0.70
   3 !    9.0   0.1    0.0015      0.97       2      41 ..     224     263 ..     223     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0004
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS-- CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiye 48
                                      m+i + G+G vG   a  l  + h+v+++D+d  + + l+  ++++++
  gi|330507060|ref|YP_004383488.1|  1 MRILITGAGEVGFLIASELY-ADHDVTVIDKDPDACARLQDMDVKVMQ 47
                                      89**********99998884.569*************99998888765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                                       HCHHHHHHHHCSS-TTCEEEEE------ CS
                    UDPG_MGDP_dh_N 130 elvkkileeaskkkgvdfdvvsnPEflr 157
                                       +++ +i++++     + +  vsnPE+++
  gi|330507060|ref|YP_004383488.1|  77 NVITCIIASHLGV-RQTIARVSNPEYID 103
                                       4566777766664.47888899999875 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0015
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCT CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklns 41 
                                       k  ++G G vG   a  l ++g++v ++ +d+ + +++  
  gi|330507060|ref|YP_004383488.1| 224 KAMIVGGGMVGFYLASRLEKMGMDVKLIEKDADRCAEIAD 263
                                       5679****************************99998865 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1    0.0016         1       2      61 ..       3      62 ..       2      82 .. 0.76
   2 !   11.8   0.1   0.00025      0.17       3      45 ..     226     268 ..     224     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0016
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTT.SS-HHHHC CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekg.klkeeeve 61
                                      + + GaG +G  ia+ +  a+++V+++d +++a ++ +++  k ++  +++   l+e++++
  gi|330507060|ref|YP_004383488.1|  3 ILITGAGEVGFLIASEL-YADHDVTVIDKDPDACARLQDMDVKVMQGNAANArLLSEADIK 62
                                      5688*********9875.689***************9998777666555544044555554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00025
                                       EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHH CS
                           3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseealekalekieks 45 
                                        ++G G++G  +a+ + + g++V+l++ ++++ ++ ++k++ +
  gi|330507060|ref|YP_004383488.1| 226 MIVGGGMVGFYLASRLEKMGMDVKLIEKDADRCAEIADKLSGT 268
                                       69******************************99999998874 PP

>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00043      0.29      45     106 ..       2      72 ..       1      81 [. 0.69
   2 !    8.6   0.1    0.0019       1.2      38     107 ..     218     298 ..     211     304 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                                       EEEEES-CCCHHHHHHHHCCCEEEEEEESSGGGGG.GSSST.......HHHHHH.HHTT.S---SEEEE--- CS
                           DUF1188  45 nvlviGaYltGaaiakkLskkeevtlvDiephlke.llekd.......vefkls.leev.ernadlviDltG 106
                                       ++l+ Ga  +G  ia++L ++++vt++D +p     l + d          +++ l+e+  ++ad+v+  tG
  gi|330507060|ref|YP_004383488.1|   2 RILITGAGEVGFLIASELYADHDVTVIDKDPDACArLQDMDvkvmqgnA-ANARlLSEAdIKKADIVVAATG 72 
                                       699***************************9765404444455555531.2222123333566777777776 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0019
                                       T--E..EEEEEES-CCCHHHHHHHHCCC.EEEEEEESSGG.GGGGSSST..........HHHHHHHHTTS---SEEE CS
                           DUF1188  38 eeeleeknvlviGaYltGaaiakkLskk.eevtlvDieph.lkellekd..........vefklsleevernadlvi 102
                                       e++  +++++++G  ++G ++a++L+k   +v l++ +    +e+ +k            ++ l  ee   ++d+v 
  gi|330507060|ref|YP_004383488.1| 218 ESKT-TQKAMIVGGGMVGFYLASRLEKMgMDVKLIEKDADrCAEIADKLsgtmilngdgSDLALLQEEGAGAMDVVY 293
                                       4444.799*******************999****9765431333333324445665666667766666677777777 PP

                                       E---T CS
                           DUF1188 103 DltGl 107
                                        +tGl
  gi|330507060|ref|YP_004383488.1| 294 AVTGL 298
                                       77776 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.2   0.00048      0.32       1      75 [.       3      72 ..       3      98 .. 0.85
   2 !    7.7   0.0    0.0032       2.1       2      69 ..     226     293 ..     225     302 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00048
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S-- CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavg 75
                                      il+tGa G +G  ++ +l + +++v+++d++++a ++ ++ d+++++++  ++  l ++ + +++d+v+ +   g
  gi|330507060|ref|YP_004383488.1|  3 ILITGA-GEVGFLIASELYA-DHDVTVIDKDPDACARLQDMDVKVMQGNAANARLLSEA-DIKKADIVVAA--TG 72
                                      89**99.***********97.79**********99999999999999999999988886.66689999877..33 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0032
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEE CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl....elveldltdrsalerlfkeeqpdavi 69 
                                       +++G+ G++G +l+ +l++ g +v  + ++  a++ a+++d+     + ++d  d + l++  +  ++d+v+
  gi|330507060|ref|YP_004383488.1| 226 MIVGG-GMVGFYLASRLEKMGMDVKLIEKD--ADRCAEIADKlsgtMILNGDGSDLALLQEEGAG-AMDVVY 293
                                       57777.***************999999998..444444444446778888888888888877664.666666 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.4   5.6e-05     0.037       3      83 ..       5      80 ..       3      91 .. 0.81
   2 ?    4.3   0.0     0.037        25       5      78 ..     228     302 ..     225     345 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.6e-05
                                      ESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHH.HTT-SEEEE---GGS-HHH CS
                              NmrA  3 viGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvea.lkgvdvvfsvtgfyskeie 80
                                      +  ++G+ G ++++  l a+h+v ++ +d+  ++ + l++  v++++g++ +  +l+ea +k++d v ++tg  ++e++
  gi|330507060|ref|YP_004383488.1|  5 I-TGAGEVG-FLIASELYADHDVTVIDKDP--DACARLQDMDVKVMQGNAANARLLSEAdIKKADIVVAATG--NDEVN 77
                                      4.4458887.55566677899999886666..6899*********************999************..88877 PP

                                      HHH CS
                              NmrA 81 dgk 83
                                        +
  gi|330507060|ref|YP_004383488.1| 78 VIT 80
                                      655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.037
                                       STTSHHHHHHHHHHHHHT-EEEEEES-S..-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-.SEEEE---GGS-H CS
                              NmrA   5 GaTGrqGksvvrallkaghkvralvRdt..kselakslkeaGvelvkgdlddkeslvealkgv.dvvfsvtgfyske 78 
                                        + G  G ++++ l k g +v+ + +d     e a++l  +G  +++gd  d ++l+e   g+ dvv++vtg+ +k+
  gi|330507060|ref|YP_004383488.1| 228 VGGGMVGFYLASRLEKMGMDVKLIEKDAdrCAEIADKL--SGTMILNGDGSDLALLQEEGAGAmDVVYAVTGLDDKN 302
                                       46699999999999**********99993334555555..699999**********998888758999999977554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.024        16       2      35 ..       2      34 ..       1      39 [. 0.87
   2 !   11.2   0.2   0.00016      0.11       2      33 ..     224     255 ..     223     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.024
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35
                                      ++++ G+G  G++ A ++  ++++V++++k + +
  gi|330507060|ref|YP_004383488.1|  2 RILITGAGEVGFLIASEL-YADHDVTVIDKDPDA 34
                                      58899************9.899*******98776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00016
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekak 33 
                                       + +++GgG  G++ A +++k g +V l+ek  
  gi|330507060|ref|YP_004383488.1| 224 KAMIVGGGMVGFYLASRLEKMGMDVKLIEKDA 255
                                       678**************************975 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 !   10.2   0.1   0.00094      0.62       4      96 ..       5     103 ..       2     120 .. 0.71
   2 !    7.1   0.2    0.0086       5.7       4      41 ..     227     264 ..     224     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00094
                                       EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHC........SEEEE-SSSHHHHHHH CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasl........dvvitmvkagkavdev 72 
                                       + G G+ G  +a++l  a+++v+v++ +++++ +l +  +k+++  ++ ++ l        d+v+   + +++v+ +
  gi|330507060|ref|YP_004383488.1|   5 ITGAGEVGFLIASELY-ADHDVTVIDKDPDACARLQDMDVKVMQGNAANARLLseadikkaDIVVAA-TGNDEVNVI 79 
                                       6799999999999986.79*******************95555544433333333366553555444.344667666 PP

                                       HHSHCCC--TT-EEEE-S---HHH CS
                     NAD_binding_2  73 iegllealkkgdilidgstssped 96 
                                       +  ++++l   +++  +s+ ++ d
  gi|330507060|ref|YP_004383488.1|  80 TCIIASHLGVRQTIARVSNPEYID 103
                                       666999999999999998877765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0086
                                       EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHT CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvae 41 
                                       ++G G+ G  +a++l+k g++v +++ +++++ e++++
  gi|330507060|ref|YP_004383488.1| 227 IVGGGMVGFYLASRLEKMGMDVKLIEKDADRCAEIADK 264
                                       6899****************************999886 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.036        24       2      54 ..       4      74 ..       3     115 .. 0.64
   2 !    9.0   0.0    0.0028       1.9       2      34 ..     226     258 ..     225     327 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.036
                                      EEE--STTHHHHHHHHHHHTEEEEEEES-G.GGG.......-GGG-TT-SE...................-EEEE--S- CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpre.efa.......tkerfpeade...................tavvvlthd 53
                                      +i Gag+v+  +a+ +  ++ +vtv+d+++ + a       +                            ++vv++t +
  gi|330507060|ref|YP_004383488.1|  4 LITGAGEVGFLIASEL-YADHDVTVIDKDPdACArlqdmdvK--------VmqgnaanarllseadikkaDIVVAATGN 73
                                      7899999998877765.57999********444444444330........13344444444444555654444444444 PP

                                      H CS
                            XdhC_C 54 h 54
                                       
  gi|330507060|ref|YP_004383488.1| 74 D 74
                                      3 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0028
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefa 34 
                                       +i+G+g v+  la+ ++++g++v +++++++  
  gi|330507060|ref|YP_004383488.1| 226 MIVGGGMVGFYLASRLEKMGMDVKLIEKDADRC 258
                                       69*************************999522 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.082        55       2      75 ..       3      69 ..       2      97 .. 0.78
   2 ?    9.4   0.0    0.0015      0.99       3      44 ..     226     267 ..     224     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.082
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivl 75
                                      i + GaG  G  +A  l    h+v+++ ++++ + ++++   +vk ++g + ++ l  ++d+++    adi+v 
  gi|330507060|ref|YP_004383488.1|  3 ILITGAGEVGFLIASELYAD-HDVTVIDKDPDACARLQDM--DVKVMQGNAANARLLSEADIKK----ADIVVA 69
                                      6789***********99876.59********999998764..6777788888888888888654....455554 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0015
                                       EEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSB CS
                    NAD_Gly3P_dh_N   3 avlGaGswGtalAkvlaenghevrlwvreeelieeineehen 44 
                                        ++G+G+ G  lA  l++ g +v+l+ ++++ + ei ++   
  gi|330507060|ref|YP_004383488.1| 226 MIVGGGMVGFYLASRLEKMGMDVKLIEKDADRCAEIADKLSG 267
                                       699*******************************99987665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.074        49       1      33 [.       2      30 ..       2      33 .. 0.87
   2 ?    9.7   0.0   0.00052      0.35       3      34 ..     226     254 ..     224     258 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.074
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                                      +i+i G+G  G+l A+ l   +    +vt++++
  gi|330507060|ref|YP_004383488.1|  2 RILITGAGEVGFLIASELYADH----DVTVIDK 30
                                      699*************998777....8888876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00052
                                       EEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase   3 vivGGGtaGwlaAaalakalkgklevtlvese 34 
                                       +ivGGG  G+  A+ l+k++   ++v+l+e++
  gi|330507060|ref|YP_004383488.1| 226 MIVGGGMVGFYLASRLEKMG---MDVKLIEKD 254
                                       7*******************...99*****97 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.7e-05     0.025       3      38 ..     226     261 ..     224     274 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
                                       EEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT-- CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLithkldtiael 38 
                                       +++GgG+ G+  A  + ++G++v+Li ++ d++ae+
  gi|330507060|ref|YP_004383488.1| 226 MIVGGGMVGFYLASRLEKMGMDVKLIEKDADRCAEI 261
                                       79*******************************997 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 ?    3.3   0.1      0.06        40     166     210 ..       2      45 ..       1      84 [. 0.77
   2 ?    8.1   0.0    0.0021       1.4     164     197 ..     222     255 ..     214     267 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.06
                       Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsysl 210
                                       ++++ G+++ ++ +A el++  ++Vtv++++    ++ +d+++++
  gi|330507060|ref|YP_004383488.1|   2 RILITGAGEVGFLIASELYAD-HDVTVIDKDPDACARLQDMDVKV 45 
                                       68999*************976.9******9998877776666655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0021
                       Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvvtrgs 197
                                       +qk +++Gg+  ++  A  l ++g++V+++ +++
  gi|330507060|ref|YP_004383488.1| 222 TQKAMIVGGGMVGFYLASRLEKMGMDVKLIEKDA 255
                                       6777777777777777777777777777777665 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.22   1.5e+02       2      35 ..       3      33 ..       2      74 .. 0.87
   2 ?    9.2   0.0   0.00085      0.56       3      34 ..     226     255 ..     225     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.22
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieasps 35
                                      +++ GaG  g ++A +l    ++  v++i+  p+
  gi|330507060|ref|YP_004383488.1|  3 ILITGAGEVGFLIASEL---YADHDVTVIDKDPD 33
                                      6899*************...66777788877665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00085
                     Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieasp 34 
                                       +++G+G  g  lA rl  +k+g+ v lie  +
  gi|330507060|ref|YP_004383488.1| 226 MIVGGGMVGFYLASRL--EKMGMDVKLIEKDA 255
                                       69**************..**********9765 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 ?    1.1   0.0      0.34   2.3e+02      38      81 ..       2      44 ..       1      75 [. 0.59
   2 ?    9.2   0.0    0.0011      0.71      35      70 ..     221     256 ..     209     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.34
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCE CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgve 81
                                      ++ i G+G++G  +a  l a + +v+++d+ +++ ++ +++ v+
  gi|330507060|ref|YP_004383488.1|  2 RILITGAGEVGFLIASELYA-DHDVTVIDKDPDACARLQDMDVK 44
                                      67899999999999987763.44444445444444433333333 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
                                       TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                       + ++  i+G G +G  +a rl+++gm+v  +++  +
  gi|330507060|ref|YP_004383488.1| 221 TTQKAMIVGGGMVGFYLASRLEKMGMDVKLIEKDAD 256
                                       568899*********************988876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 3104.81
//
Query:       gi|330507061|ref|YP_004383489.1|  [L=400]
Description: hypothetical protein MCON_0898 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-120  403.0   0.6   1.4e-120  402.8   0.6    1.0  1  DUF111    Protein of unknown function DUF111


Domain annotation for each model (and alignments):
>> DUF111  Protein of unknown function DUF111
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.8   0.6  7.8e-125  1.4e-120       1     372 [.       4     386 ..       4     387 .. 0.96

  Alignments for each domain:
  == domain 1  score: 402.8 bits;  conditional E-value: 7.8e-125
                            DUF111   1 lyldcssGisGDmllgALldlgadkeeleealeklgleeveleiekvkksgisatkvdveeeehehehrslaeieei 77 
                                       l++d+s+G++GDm++++Lldlgad++++++a+e++g+   +le+++++k +isat+++v++   +   +sl+e  +i
  gi|330507061|ref|YP_004383489.1|   4 LLFDPSAGAAGDMIMASLLDLGADEKRVRKAVESVGC---TLEVSRQEKGHISATRAQVIS---DRRYHSLEEAVSI 74 
                                       689********************************96...9******************87...6666799****** PP

                            DUF111  78 ieaaslsekvkekalaiferlaeAeakvhgvpleevhfhEvGavDaivdivgaalaldeLgvekvvasplalGsGtv 154
                                       ++++sl+ek+ +kala +++laeAe++vh+vp ++ hfhEvGa+Da++di g + a ++L+ +++++ p+++G+G v
  gi|330507061|ref|YP_004383489.1|  75 LKSSSLQEKALKKALAALDILAEAESRVHDVPKSRAHFHEVGALDALADIAGSCEAASSLKADRILSRPISVGGGYV 151
                                       ***************************************************************************** PP

                            DUF111 155 rcahGilPvPaPAvlellkelklkl..gevegElvTPTGaAilaalaeefg.slpamkvekiGyGaGkrdleeipnv 228
                                       + ahG lPvP PA le+l+++++    g+v+ El+TPTGaA+laal++ef  ++p ++ e++GyGaGk+dl ++pn+
  gi|330507061|ref|YP_004383489.1| 152 QSAHGLLPVPGPAALEILRAHNIPWmgGPVDDELLTPTGAALLAALVDEFVpRFPLIQAERVGYGAGKKDL-ATPNL 227
                                       ********************99998999***********************99******************.8**** PP

                            DUF111 229 lRvll.......eeeeeelekeevvvletniDDlspevlgyvlerLleaGAlDvfltpilmKKgRpavllsvlckee 298
                                       lR+l        + +  +++k++vv+letn+DD+++evlg+++e+L++aGAlDv+++p++mKKgR + ++++++++e
  gi|330507061|ref|YP_004383489.1| 228 LRALKarivsptRGAGMDHQKDRVVQLETNVDDVTGEVLGHLIEELMQAGALDVSVIPAVMKKGRSGNVIRAISSHE 304
                                       *****999998855667799********************************************************* PP

                            DUF111 299 daeeleellfretttlGvRese.verlvlereietvetelg....evrvKva...eevvkvkpEyedvkkiAeetgl 367
                                       d+++l+ +++ret++lGvR ++  +r+v+ere +tv+++l     +v++K++   ++ v+vk+Eyed+++iA+e g+
  gi|330507061|ref|YP_004383489.1| 305 DMSKLAGMIVRETGSLGVRVFPsLHRFVAEREERTVDLNLAgvtySVAIKISrmdGSLVNVKAEYEDCRRIAKEAGV 381
                                       **********************9****************998888999999998555******************** PP

                            DUF111 368 plkev 372
                                       pl+ v
  gi|330507061|ref|YP_004383489.1| 382 PLRMV 386
                                       **988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3161.73
//
Query:       gi|330507062|ref|YP_004383490.1|  [L=423]
Description: glutamate-1-semialdehyde-2,1-aminomutase [Methanosaeta concilii GP6]
Scores for complete 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-65  219.8   0.0    6.2e-65  219.4   0.0    1.0  1  Aminotran_3  Aminotransferase class-III
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.022   14.6   0.0    1.4  1  Rop-like     Rop-like
       0.14   12.2   0.0       0.31   11.1   0.0    1.5  1  HTH_16       Helix-turn-helix domain


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 !  219.4   0.0     1e-68   6.2e-65      11     375 ..      34     392 ..      26     413 .. 0.89

  Alignments for each domain:
  == domain 1  score: 219.4 bits;  conditional E-value: 1e-68
                                       EEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-.. CS
                       Aminotran_3  11 lvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgl 87 
                                       +   +a G yl+d dg+r++D   ++ +++lGh+hP++ +av++q++  ++     + +e  ++lae + +l p  +
  gi|330507062|ref|YP_004383490.1|  34 FYTARAIGPYLWDCDGNRFIDYCLAYGPMILGHRHPAIREAVSDQMDRGWLYG---TPSELEVRLAERVSSLYPS-M 106
                                       6678999******************************************9887...889999************9.* PP

                                       SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTB CS
                       Aminotran_3  88 dkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypd 164
                                       +++ ++ sG+eA+++A+++ar       +t +  ii+++g+fHG     l  +gs  +  tl  p + +v+r + + 
  gi|330507062|ref|YP_004383490.1| 107 ERLRFVSSGTEATMAAIRVARG------STGRDMIIKIEGGFHGAHDSVLVKAGS--GATTLGIPDSRGVPRDATKN 175
                                       **********************......***************************..67777777778888888888 PP

                                       GGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT..T CS
                       Aminotran_3 165 eevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGf..G 239
                                       ++++++n+        +le++ ++ +  +a +i+Ep+ g+ G + +++++l+++r l++k+dvlli+DEv tGf  +
  gi|330507062|ref|YP_004383490.1| 176 TIQVPYND------PAALEEVLERFSGRIACLIMEPVLGNIGPILPDKGYLQTARRLTEKNDVLLIFDEVITGFrlS 246
                                       99999999......455777777899************************************************877 PP

                                       TTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHHHTTH CS
                       Aminotran_3 240 rTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiieeekl 313
                                         G   A e +g++pDl+tl+K ++gG+p+ ++ ++a++m+++apg+   +++T+ G p   a+ la+l+++e+e+ 
  gi|330507062|ref|YP_004383490.1| 247 LGG---AQELFGIKPDLTTLGKIIGGGFPIGVFGGRADLMDQVAPGGaiyQAGTYNGSPASLAAGLATLDVMEKEDT 320
                                       888...9********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC...........HHHHHHHHHCTEE-E CS
                       Aminotran_3 314 lenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke...........keilkkakekGvlil 375
                                       +++ ++ g++++ +L+++ ++  +  +v g   m+ + ++ ++ ++             e++ ++++ G+ + 
  gi|330507062|ref|YP_004383490.1| 321 INKLNRSGESMRLALKDMVEDLGQDWSVVGIASMFKV-FFGPEPHNYaqalrcdrqgyFEFFRRMLDSGIFLT 392
                                       *****************99876444455555556666.55555545455666666666666666666666655 PP

>> Rop-like  Rop-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.6e-06     0.022       5      36 ..     316     347 ..     312     352 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTTTGG CS
                          Rop-like   5 eLkkevkKlnskAtqakmdLHDLaEdLPtnye 36 
                                       e +  + Kln+   +++  L D++EdL +++ 
  gi|330507062|ref|YP_004383490.1| 316 EKEDTINKLNRSGESMRLALKDMVEDLGQDWS 347
                                       557789*************************6 PP

>> HTH_16  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.2e-05      0.31      10      32 ..     182     204 ..     181     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.2e-05
                            HTH_16  10 GDeeAieeiLkhYegyIrklSlr 32 
                                       +D+ A+ee+L++++g I+ l + 
  gi|330507062|ref|YP_004383490.1| 182 NDPAALEEVLERFSGRIACLIME 204
                                       69****************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3222.85
//
Query:       gi|330507063|ref|YP_004383491.1|  [L=305]
Description: porphobilinogen deaminase [Methanosaeta concilii GP6]
Scores for complete 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-68  228.2   0.1    9.3e-68  227.7   0.1    1.2  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
      1e-08   35.5   0.2      2e-08   34.5   0.2    1.5  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.7   0.1     1e-71   9.3e-68       4     199 ..       2     201 ..       1     205 [. 0.94

  Alignments for each domain:
  == domain 1  score: 227.7 bits;  conditional E-value: 1e-71
                    Porphobil_deam   4 gtRkSkLAlaqaelvaeaLke.eeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKDlpt 79 
                                       gtR+S+LAl q+++v+e+Lk    ++++  +kt+GD  ldkpL+++ g g+F+ e++e++l+g+idlaVhS+KDlpt
  gi|330507063|ref|YP_004383491.1|   2 GTRGSPLALRQTQIVQERLKGlGIQTQLCRVKTSGDVFLDKPLHQLTGFGVFVAEIDERMLSGKIDLAVHSMKDLPT 78 
                                       9******************5566678*************************************************** PP

                    Porphobil_deam  80 elpeglelaavlkredprDvlvvks....sleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldeg 152
                                       + pe+l + avlkr++p Dvl++++    s+eel++ga+vgTsS+RR aql ++rpdl++ +lRGn++tRl+kl++g
  gi|330507063|ref|YP_004383491.1|  79 KRPEELIVSAVLKRDSPYDVLLCREksvkSIEELDQGARVGTSSMRRMAQLLRARPDLNILSLRGNLQTRLSKLERG 155
                                       **********************94445678*********************************************** PP

                    Porphobil_deam 153 eydaiiLAaAGLkRlgleerisevlspeellpavgQGalavevrked 199
                                       +ydai+LA+AGL+R+g++ +  + l+ e ++p++ QG++ v +++++
  gi|330507063|ref|YP_004383491.1| 156 DYDAIVLAEAGLERMGYHPDYVR-LDGERFVPSANQGTIIVVAKAGS 201
                                       ****************8887777.*****************999875 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 !   34.5   0.2   2.3e-12     2e-08       4      69 ..     219     286 ..     217     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2.3e-12
                                       HHHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S-EEEEEEEE.....-GGGHHHHHHHH CS
                   Porphobil_deamC   4 vlaERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglksaveeaeakg.....eleeaeelGkkl 69 
                                        + ER ++++ +GGC vP +v+a v+++e  +  + vls+dg++  + + e ++      l+ ae++G +l
  gi|330507063|ref|YP_004383491.1| 219 TMIERKIMETVGGGCVVPMAVHALVQKGE-ARVLAEVLSPDGKR--FVRLEERIslvqnHLAVAEDMGERL 286
                                       589***********************999.9***********88..7677666667777778888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2601.88
//
Query:       gi|330507064|ref|YP_004383492.1|  [L=501]
Description: uroporphyrinogen III synthase/methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-50  171.6   0.3    8.4e-50  169.7   0.1    2.1  2  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
      1e-46  159.2   0.3    1.3e-46  158.8   0.3    1.2  1  HEM4          Uroporphyrinogen-III synthase HemD


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 !  169.7   0.1   9.3e-54   8.4e-50       1     212 [.       5     214 ..       5     215 .. 0.92
   2 ?   -1.2   0.0      0.18   1.6e+03      92      94 ..     447     449 ..     398     481 .. 0.56

  Alignments for each domain:
  == domain 1  score: 169.7 bits;  conditional E-value: 9.3e-54
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       k+ylVG+GpGdpellT+++++ l +advvl d+ +  +++ld ++       + gk++ ++  ++eei++ l+e+++
  gi|330507064|ref|YP_004383492.1|   5 KVYLVGAGPGDPELLTIKGRKRLMEADVVLFDR-LLDSRMLDGVKG---ELIDVGKNAGRHKLKQEEINQLLIEKAK 77 
                                       79***************************9999.777777676664...5899999999****************** PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl......lpglak 148
                                       +gk Vv+l++GDP+++g+g+e++ a+r+   gi++ev+PGv+s+ aa+  +gip+t+++++++++      +pg  k
  gi|330507064|ref|YP_004383492.1|  78 EGKIVVRLKGGDPYLFGRGGEEAIACRD--WGIPFEVVPGVTSAIAAPELAGIPVTHRKVASALTivtgheEPG--K 150
                                       ***********************77777..7**************************************75555..5 PP

                      TP_methylase 149 eeereleallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                       +++ +++a++   +tlv+l+++++l+e   +L+ea + ++tp+a+ve++g++d+r++ gtl+++
  gi|330507064|ref|YP_004383492.1| 151 DSPLDWRAMAGLDGTLVVLMGVSRLEENTNRLIEAGKSPQTPAAMVEKGGWPDQRLISGTLGDI 214
                                       6999999999999**********************555577*********************97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.18
                      TP_methylase  92 vyg 94 
                                       v+ 
  gi|330507064|ref|YP_004383492.1| 447 VAA 449
                                       222 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.8   0.3   1.5e-50   1.3e-46       4     232 .]     259     479 ..     256     479 .. 0.89

  Alignments for each domain:
  == domain 1  score: 158.8 bits;  conditional E-value: 1.5e-50
                                       HHHHHHTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEESS CS
                              HEM4   4 aealearGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealkreeedvkalaslkvaavG 80 
                                       +++ e++G++pl +P+i  e+ + +++l + +      + ++++ftSan+v++   al  +++ ++ala +k++++G
  gi|330507064|ref|YP_004383492.1| 259 VDLAERYGFIPLSAPAIALERNPLPEDLLERIA-----AAECVAFTSANGVHI---ALG-NKAISRALAAKKIVSIG 326
                                       67889****************666666666665.....889************...554.799************** PP

                                       HHHHHHHHHTT---SEE-..SSSHHHHGGGS-.---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHH CS
                              HEM4  81 paTaraLeelglrvdlvpseegtaegLaeelaeslagkrvlllrgeiarddlaegLeergaevdevevYetvpaeee 157
                                       p+T++aL e+ ++ + +p+ ++++egL  +l+   + k++l+lr+ ++++ l +gL+e+g+ vd++++Y     ++ 
  gi|330507064|ref|YP_004383492.1| 327 PKTKQALNEYDIQSE-MPE-SYSSEGLERMLK--GRYKSILFLRSAQGSQYLSDGLREAGIVVDDIPLYGV--VNSS 397
                                       **************9.999.*******88787..45566********************************..3344 PP

                                       HHHHHHHHHT.T--SEEEESSHHHHHHHHHH-S-HH......HHHCTSEEEEESHHHHHHHHHTT---SEEETS--H CS
                              HEM4 158 peelkealka.gevdavvftSpstvrnllellkdeg......delkevkvaaiGptTaealkklglkvdvvaeepta 227
                                        ++l +++++ gevd+ +ftS+st+rnlle+++ +g      + l +++vaaiG+ Ta++l +lg+ vdv++e++t 
  gi|330507064|ref|YP_004383492.1| 398 DPRLDRLIERaGEVDIFAFTSSSTARNLLERARAMGreeqlrEALARATVAAIGKPTAQELSRLGVAVDVIPENFTF 474
                                       44555555444****************************************************************** PP

                                       HHHHH CS
                              HEM4 228 eglva 232
                                       e+++a
  gi|330507064|ref|YP_004383492.1| 475 EAMLA 479
                                       **985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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 0.25s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3691.60
//
Query:       gi|330507065|ref|YP_004383493.1|  [L=386]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   99.9   0.0    3.8e-28   99.0   0.0    1.5  2  Radical_SAM  Radical SAM superfamily
      7e-10   39.3   0.0    1.3e-09   38.5   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
    6.9e-09   36.1   0.5    1.8e-08   34.7   0.5    1.8  1  SPASM        Iron-sulfur cluster-binding domain
    7.2e-06   26.1   0.0    1.9e-05   24.8   0.0    1.7  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.0   0.0   8.5e-32   3.8e-28       2     166 ..      45     200 ..      44     201 .. 0.95
   2 ?   -3.3   0.0       2.2     1e+04      34      59 ..     236     262 ..     224     285 .. 0.55

  Alignments for each domain:
  == domain 1  score: 99.0 bits;  conditional E-value: 8.5e-32
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       + tr Cnl+Cs+C+        +   ++s+ee +++ + l a++ +  +il+ggepl+ ++f  +++++++    g+
  gi|330507065|ref|YP_004383493.1|  45 NLTRRCNLACSHCYMDA---IPKEDDEMSLEEGMRLTDDL-ARMKIPILILTGGEPLMSRNFFSIAFHAREA---GL 114
                                       579*************8...6*******************.8*****************************7...** PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                                       r++++tngtl+++e++++l+e+ + +v ++l++a +  + k  + ++ f++ l++l+++r+ag+k +  ri++ +  
  gi|330507065|ref|YP_004383493.1| 115 RTVISTNGTLITPEVARLLAEAKIRYVGVSLDSALPASHDKFRGVPGAFDRALQGLRNARDAGLK-TGLRITLTR-D 189
                                       *************************************666666699*******************.*******99.9 PP

                                       SHHHHHHHHHH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 156 ndeeleellel 166
                                       n++++ +ll+l
  gi|330507065|ref|YP_004383493.1| 190 NWQDVPALLNL 200
                                       99999998876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.2
                                       HHHHHHHHH.HHTTSEEEEEESSTGGG CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                       Radical_SAM  34 ileevkelk.aekgvkevilgggepll 59 
                                       +++++ e++ + k+++  il+ + p++
  gi|330507065|ref|YP_004383493.1| 236 VIRLLAEAAvELKDKNIEILTTDSPMD 262
                                       444444444233334444555554444 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 !   38.5   0.0   2.8e-13   1.3e-09      11     131 ..      46     157 ..      36     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 2.8e-13
                           Fer4_12  11 fvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekd 87 
                                       ++ +Cnl+C+ C+  ++  +k+ +e++ e   ++ +dl+  +i+ l+l+GGEPl+    + + +++ + +e+++  +
  gi|330507065|ref|YP_004383493.1|  46 LTRRCNLACSHCYMDAI--PKEDDEMSLEEGMRLTDDLARMKIPILILTGGEPLM---SRNFFSIAFHAREAGL-RT 116
                                       3789*********7666..7889999999999***********************...88999***********.69 PP

                           Fer4_12  88 iwlytgytleelskkekeellkeidv.lvdGkfeesledeslrfr 131
                                       +++++g+ +         +ll+e ++  v + ++ +l   + +fr
  gi|330507065|ref|YP_004383493.1| 117 VISTNGTLITPEV----ARLLAEAKIrYVGVSLDSALPASHDKFR 157
                                       ******9876543....4677777766677777777666666666 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.5   4.1e-12   1.8e-08       1      68 []     289     353 ..     289     361 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 4.1e-12
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIw...nseeyqefr..kskkfplielCrnCp 68 
                                       C a+ + + I+++GdV+pC     ++  ++++Gn+r+ s+++Iw     +e+ ++r  ks+   l   C +C+
  gi|330507065|ref|YP_004383493.1| 289 CSAGAKVANISYQGDVHPC-----HFMPQVVVGNVRDRSFQDIWidhPTPELLALRgiKSN---LKGACGSCN 353
                                       88889999***********.....46667***************65444466668854444...344577774 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   4.1e-09   1.9e-05       4      91 ..      46     124 ..      43     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.1e-09
                           Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeype 80 
                                        + +Cnl+C  C+  +   +e  + + ee + + ++dl   +i    l ltGGePL+    ++++ +  + +e +  
  gi|330507065|ref|YP_004383493.1|  46 LTRRCNLACSHCYMDA-IPKEDDEMSLEEGM-RLTDDLARMKI--PILILTGGEPLMS---RNFFSIAFHAREAG-- 113
                                       5789*********998.66666667777766.67767766666..569********76...77888888877777.. PP

                           Fer4_14  81 kkiwletngtl 91 
                                       ++  + tngtl
  gi|330507065|ref|YP_004383493.1| 114 LRTVISTNGTL 124
                                       77777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2902.82
//
Query:       gi|330507066|ref|YP_004383494.1|  [L=366]
Description: AAA ATPase family protein [Methanosaeta concilii GP6]
Scores for complete 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  118.7   0.1    4.3e-34  117.8   0.1    1.5  1  AAA              ATPase family associated with various cellul
    1.4e-08   34.4   0.1    2.8e-08   33.4   0.1    1.5  1  AAA_lid_3        AAA+ lid domain
    1.9e-05   24.9   0.0    3.7e-05   23.9   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
    5.3e-05   22.5   0.0     0.0093   15.2   0.0    2.2  2  DUF815           Protein of unknown function (DUF815)
    5.7e-05   23.1   0.0    9.2e-05   22.4   0.0    1.3  1  Bac_DnaA         Bacterial dnaA  protein
    0.00021   21.1   0.0     0.0013   18.5   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00022   20.5   0.1     0.0006   19.1   0.0    1.7  2  TIP49            TIP49 P-loop domain
    0.00085   19.7   0.1      0.034   14.5   0.0    2.4  2  AAA_16           AAA ATPase domain
     0.0015   18.0   0.0     0.0043   16.5   0.0    1.7  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0029   18.1   0.0     0.0068   16.9   0.0    1.6  1  AAA_18           AAA domain
     0.0042   17.1   0.1      0.015   15.3   0.1    2.1  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0095   16.1   0.0      0.022   14.9   0.0    1.7  2  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.024   14.4   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.014   15.7   0.8       0.28   11.4   0.1    2.4  2  AAA_22           AAA domain
      0.017   14.7   0.2       0.22   11.0   0.1    2.4  3  AAA_7            P-loop containing dynein motor region
      0.026   14.8   0.0      0.098   12.9   0.0    2.0  2  AAA_28           AAA domain
      0.054   13.2   0.1       0.12   12.1   0.1    1.5  1  AAA_24           AAA domain
      0.062   13.3   0.0       0.12   12.4   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.064   12.7   0.0       0.49    9.8   0.0    2.0  2  TniB             Bacterial TniB protein
      0.066   12.9   0.1       0.15   11.7   0.1    1.8  1  Sigma54_activat  Sigma-54 interaction domain
      0.082   11.8   0.0       0.13   11.2   0.0    1.2  1  Kinesin          Kinesin motor 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 !  117.8   0.1     5e-37   4.3e-34       1     131 [.     152     280 ..     152     281 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 5e-37
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       +l+yG  GtGKT++aka+  ++gv++l ++ ++l+ ++vge++++i+ l ++a+e+a p+i+fiDE+da+a +r  +
  gi|330507066|ref|YP_004383494.1| 152 ILFYGVSGTGKTMIAKALSAKAGVPMLAVKSTSLIGEFVGEGARQIHSLYEKAEEMA-PCIIFIDELDAIALDRrYQ 227
                                       69******************************************************9.****************999 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieie 131
                                       + +++ +++vn Llte+dg +++ + ++ i+atn+++ ld+ ++ +Rf+++ie++
  gi|330507066|ref|YP_004383494.1| 228 DLRGDVSEMVNSLLTEMDGISSRLG-ICTIAATNQIEVLDSSIR-SRFEEEIEFK 280
                                       999*******************988.******************.*******986 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.1   3.3e-11   2.8e-08       1      44 [.     304     347 ..     304     348 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.3e-11
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaa.lcreAallAlrrgikeitmedfe 44 
                                       dvdlke+A++T+G+SG Dl++ + + A ++Al +    i+++++e
  gi|330507066|ref|YP_004383494.1| 304 DVDLKEIARQTDGFSGRDLVEkVLKVALHHALMDECN-ISQKHIE 347
                                       9******************776*********966543.3566666 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   4.3e-08   3.7e-05       5     103 ..     151     244 ..     149     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.3e-08
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidK 79 
                                       +il+ g +g+Gkt++akal+    v    ++  +  ++l+     e + +   + +  y +aee    i+++DE+d 
  gi|330507066|ref|YP_004383494.1| 151 NILFYGVSGTGKTMIAKALSAKAGV----PMLAVKSTSLIG----EFVGEGARQIHSLYEKAEEMApcIIFIDELDA 219
                                       89*********************98....***********9....888889999999********9*********** PP

                                       ----...---------HHHHHHHHHHH CS
                             AAA_2  80 ihpk...essgadvSregVqrdLLqil 103
                                       i+     +  + dvS  + ++ LL  +
  gi|330507066|ref|YP_004383494.1| 220 IALDrryQDLRGDVS--EMVNSLLTEM 244
                                       *99777788888888..4556666555 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   1.1e-05    0.0093      25     129 ..     116     230 ..     100     239 .. 0.65
   2 ?    5.1   0.0     0.013        11     181     226 ..     268     313 ..     256     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                            DUF815  25 vklddLvgidkqkealventeqfle.....g.lpannvLLwGarGtGKSslvkallneyaeeg.....Lrli.evek 89 
                                       v++d++vg ++ k++++  +e++l+     g  + +n+L++G  GtGK  + kal +++           li e   
  gi|330507066|ref|YP_004383494.1| 116 VSFDEVVGQEEAKRKVKI-VEKYLSdperfGrWAPRNILFYGVSGTGKTMIAKALSAKAGVPMlavksTSLIgEFVG 191
                                       666777777777666543.233332111112134589******************9987776622222223334555 PP

                            DUF815  90 edlkelpklvellrerperfilfvDDLsFeeeeeeyksLk 129
                                       e  +++ +l+e+ + +   +i+f+D L   + +++y+ L+
  gi|330507066|ref|YP_004383494.1| 192 EGARQIHSLYEKAE-EMAPCIIFIDELDAIALDRRYQDLR 230
                                       55555555555544.3457999999999888888888887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.013
                            DUF815 181 sLsdRFGlwlgFykldqeeYleiveklakklglelekeeleeeAle 226
                                       s+  RF   + F+ +d++e l+i+ek a++l le+ + +l+e A +
  gi|330507066|ref|YP_004383494.1| 268 SIRSRFEEEIEFKLPDKDERLQILEKNASTLPLEMVDVDLKEIARQ 313
                                       6778************************999999888777766654 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   1.1e-07   9.2e-05      37     212 ..     152     329 ..     116     335 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.1e-07
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHT..T-HHHHHHHHT...T-SEEEEE-GGG CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrd..kkaeefkeklr...kvDvLliDDiqf 108
                                       +++yg +G Gkt + ka++ ++     + + + l +e F+ e ++ +++  +kaee+   +    ++D++ +D  ++
  gi|330507066|ref|YP_004383494.1| 152 ILFYGVSGTGKTMIAKALSAKAGVPMLAVKSTSLIGE-FVGEGARQIHSlyEKAEEMAPCIIfidELDAIALD-RRY 226
                                       799***********99999998888888887777765.77666666655444444444433311144444444.333 PP

                                       GTT-HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT-- CS
                          Bac_DnaA 109 lagkektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaekle 185
                                          + ++ e +  +++++ + + ++ +++  + +++e l++ +rsrfe  +  + + pd++ rl+il+k++++  le
  gi|330507066|ref|YP_004383494.1| 227 QDLRGDVSEMVNSLLTEMDGISSRLGICTIAATNQIEVLDSSIRSRFEEEI--EFKLPDKDERLQILEKNASTLPLE 301
                                       344445677777778888888999************************975..566799999**********99999 PP

                                       --TTHHHHHHHH--S.-HHHHHHHHHHH CS
                          Bac_DnaA 186 vpeevlefiaervtd.nvRelegalnrl 212
                                       + +  l+ ia++ +  + R+l   + ++
  gi|330507066|ref|YP_004383494.1| 302 MVDVDLKEIARQTDGfSGRDLVEKVLKV 329
                                       7777777788777643667776666665 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 !   18.5   0.0   1.5e-06    0.0013       5      97 ..     117     221 ..     115     279 .. 0.66
   2 ?   -2.7   0.0       5.2   4.4e+03       7      28 ..     315     336 ..     312     349 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                            RuvB_N   5 sleeyigqekvkeklkifieaak..kr..eealdhvllyGpPGlGkttlakiiakelgvkl.kitsgPvl.....ek 71 
                                       s++e +gqe+ k k+ki+ +     +r  + a   +l+yG  G Gkt +ak ++++ gv +  + s+  +     e 
  gi|330507066|ref|YP_004383494.1| 117 SFDEVVGQEEAKRKVKIVEKYLSdpERfgRWAPRNILFYGVSGTGKTMIAKALSAKAGVPMlAVKSTSLIgefvgEG 193
                                       58999***********9866433012311557899*********************999752333333332222356 PP

                            RuvB_N  72 agdlaalltnleekd..vlfideihrls 97 
                                       a+++ +l  + ee    ++fide+  ++
  gi|330507066|ref|YP_004383494.1| 194 ARQIHSLYEKAEEMApcIIFIDELDAIA 221
                                       7778888877776644589999987654 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.2
                            RuvB_N   7 eeyigqekvkeklkifieaakk 28 
                                       + + g++ v++ lk++++ a +
  gi|330507066|ref|YP_004383494.1| 315 DGFSGRDLVEKVLKVALHHALM 336
                                       6788888999999998887755 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   7.1e-07    0.0006      24      83 ..     119     180 ..      92     191 .. 0.77
   2 ?   -1.7   0.0       1.5   1.3e+03     274     289 ..     204     219 ..     195     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.1e-07
                                       XXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  24 eglvGqkkareaagvivelike....kklaGravLlaGpsgtGktalaiaiskelgedvpfval 83 
                                       + +vGq++a++ + ++ + + +    ++ a r +L+ G sgtGkt +a a+s + g  vp  a+
  gi|330507066|ref|YP_004383494.1| 119 DEVVGQEEAKRKVKIVEKYLSDperfGRWAPRNILFYGVSGTGKTMIAKALSAKAG--VPMLAV 180
                                       489*************99997632336778899******************99877..565555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                                       XXXXXXXXXXXXXXXX CS
                             TIP49 274 kaeivpGvlfiDevhm 289
                                         e+ p ++fiDe   
  gi|330507066|ref|YP_004383494.1| 204 AEEMAPCIIFIDELDA 219
                                       4578899999999765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     4e-05     0.034      23      46 ..     148     171 ..     128     185 .. 0.81
   2 ?    2.8   0.0      0.16   1.4e+02     125     146 ..     199     221 ..     179     253 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-05
                            AAA_16  23 rpelvllsGesGvGKsslvrellr 46 
                                        p+++l++G sG+GK+ ++++l  
  gi|330507066|ref|YP_004383494.1| 148 APRNILFYGVSGTGKTMIAKALSA 171
                                       469****************99875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.16
                            AAA_16 125 rllallsrderplvlvlDdlq..w 146
                                       +l +++++   p ++++D+l+   
  gi|330507066|ref|YP_004383494.1| 199 SLYEKAEE-MAPCIIFIDELDaiA 221
                                       44455555.458*********553 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.1e-06    0.0043       2      43 ..     118     170 ..     117     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.1e-06
                      Mg_chelatase   2 lkdvkGqeeakraleiaaa........Gg...HnlllvGppGsGKtmlakrlp 43 
                                       + +v+Gqeeakr ++i           G+    n+l++G +G+GKtm+ak+l+
  gi|330507066|ref|YP_004383494.1| 118 FDEVVGQEEAKRKVKIVEKylsdperfGRwapRNILFYGVSGTGKTMIAKALS 170
                                       6788888888888888643222222224422369****************996 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     8e-06    0.0068       1      44 [.     152     206 ..     152     255 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf...........gvnlrdvakenglllevdpe 44 
                                       Il  G++G+GKt +ak+Ls + g+           g+ +++ a++ ++l+e  +e
  gi|330507066|ref|YP_004383494.1| 152 ILFYGVSGTGKTMIAKALSAKAGVpmlavkstsliGEFVGEGARQIHSLYEKAEE 206
                                       8999***************998888888888888877777777777777776666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.8e-05     0.015       1      77 [.     151     220 ..     151     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       ++l  G +GtgK+++a+ l+a  + +++ v  t+      l+g+     g+ +++  +l+++a+   ++i+++DE++
  gi|330507066|ref|YP_004383494.1| 151 NILFYGVSGTGKTMIAKALSAKAGVPMLAVKSTS------LIGEFV---GEGARQIHSLYEKAEemAPCIIFIDELD 218
                                       57999********************999998877......444444...3444444888888887788999999988 PP

                                       G- CS
                             AAA_5  76 ra 77 
                                        +
  gi|330507066|ref|YP_004383494.1| 219 AI 220
                                       55 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.6e-05     0.022       2      46 ..     152     198 ..     152     261 .. 0.76
   2 ?   -3.1   0.0       9.1   7.8e+03      80     111 ..     318     349 ..     308     362 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                                       +l+ G++G+GK+  a+ l +k g  +  + s +l+   +g++ +++ 
  gi|330507066|ref|YP_004383494.1| 152 ILFYGVSGTGKTMIAKALSAKAGvpMLAVKSTSLIGEFVGEGARQIH 198
                                       6899******************9998999999999988886666554 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.1
                            AAA_33  80 lsrrerarflklarrlgvpvrivvvetdeetl 111
                                         r+  +++lk+a ++   +++ + +   e++
  gi|330507066|ref|YP_004383494.1| 318 SGRDLVEKVLKVALHHALMDECNISQKHIEEA 349
                                       55555566666666666555554444444444 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 ?   14.4   0.0   2.8e-05     0.024      48      76 ..     150     175 ..     130     238 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavragl 76 
                                        ni++ G sG+GK+ +a al+ +a    +
  gi|330507066|ref|YP_004383494.1| 150 RNILFYGVSGTGKTMIAKALSAKAG---V 175
                                       69******************98874...3 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00033      0.28       7      29 ..     151     173 ..     148     185 .. 0.85
   2 ?    2.2   0.0      0.23     2e+02      83     112 ..     201     240 ..     186     256 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00033
                            AAA_22   7 ilvvtGesGtGKTtllrrlleql 29 
                                        ++ +G sGtGKT+ ++ l  ++
  gi|330507066|ref|YP_004383494.1| 151 NILFYGVSGTGKTMIAKALSAKA 173
                                       6889*************998876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.23
                            AAA_22  83 eqalraravielliiDEaqhlr...s........eealeeL 112
                                       ++ +++ a + ++ iDE + +    +         e+++ L
  gi|330507066|ref|YP_004383494.1| 201 YEKAEEMA-PCIIFIDELDAIAldrRyqdlrgdvSEMVNSL 240
                                       44444444.599********865541434444555555555 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   0.00026      0.22      34      56 ..     150     172 ..     148     185 .. 0.87
   2 ?    0.4   0.0      0.47     4e+02     101     115 ..     209     223 ..     198     227 .. 0.84
   3 ?   -2.5   0.0       3.6     3e+03      74      98 ..     338     362 ..     324     364 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                             AAA_7  34 kpvllvGptGtGKtviikdllkk 56 
                                       +++l++G +GtGKt+i+k l  k
  gi|330507066|ref|YP_004383494.1| 150 RNILFYGVSGTGKTMIAKALSAK 172
                                       689**************987665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.47
                             AAA_7 101 klvvFvDDlnmpake 115
                                        +++F+D+l+  a +
  gi|330507066|ref|YP_004383494.1| 209 PCIIFIDELDAIALD 223
                                       69*******988877 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.6
                             AAA_7  74 sanqlqdiiesklekrrkgvygPpg 98 
                                       + n  q+ ie+ l + rk+   Pp 
  gi|330507066|ref|YP_004383494.1| 338 ECNISQKHIEEALPRARKHYRQPPT 362
                                       5677799999999999998888875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.9   2.4e+03      47      83 ..      44      77 ..      37      94 .. 0.62
   2 ?   12.9   0.0   0.00011     0.098       2      27 ..     152     178 ..     151     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.9
                            AAA_28 47 pwvedllafaervleeqleee.aaaaankvlfcDrgll 83
                                      p+v+d+  f+      ++e+   +  +++++++Dr l 
  gi|330507066|ref|YP_004383494.1| 44 PSVADARLFELY----AREQWyGEEVKPGCYLFDRRLY 77
                                      555455555443....3333312335799999999875 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00011
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvv 27 
                                       i + G ++tGKT +++aL+a+ g+p++
  gi|330507066|ref|YP_004383494.1| 152 ILFYGVSGTGKTMIAKALSAKaGVPML 178
                                       899****************98788765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00014      0.12       3      22 ..     150     169 ..     148     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                            AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                       ++il yG sg+GKT++ak l
  gi|330507066|ref|YP_004383494.1| 150 RNILFYGVSGTGKTMIAKAL 169
                                       689**************988 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.12      19      51 ..     149     183 ..     124     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        + il++G  G+GKT+++++l ++ gv   +vkS 
  gi|330507066|ref|YP_004383494.1| 149 PRNILFYGVSGTGKTMIAKALSAKAGVPmlAVKST 183
                                       4469***********************87899996 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00058      0.49      10      55 ..     121     169 ..     115     177 .. 0.76
   2 ?    0.2   0.0      0.48   4.1e+02     116     181 ..     205     275 ..     193     282 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00058
                              TniB  10 wigyprakeilerLeeLleypk...rkrmpnlllvGdsnnGKtmivekF 55 
                                        +g ++ak+ ++  e+ l+ p+   r  ++n+l++G s +GKtmi++  
  gi|330507066|ref|YP_004383494.1| 121 VVGQEEAKRKVKIVEKYLSDPErfgRWAPRNILFYGVSGTGKTMIAKAL 169
                                       566777777777788888887733234569***************9865 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.48
                              TniB 116 relkvrvLiiDEihnllagsark..qreflnalksLgnelk.i.pivlvGteealralr.tDpqlasRFep 181
                                       +e+ + ++ iDE++ +   ++ +  +  + +++ sL  e++ i +  ++ t +a++ ++  D+ + sRFe+
  gi|330507066|ref|YP_004383494.1| 205 EEMAPCIIFIDELDAIALDRRYQdlRGDVSEMVNSLLTEMDgIsSRLGICTIAATNQIEvLDSSIRSRFEE 275
                                       56777788899998876443332124466777777776665332456777777777776348888888886 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   0.1   0.00018      0.15      23      44 ..     150     171 ..     123     281 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                       S-EEEECSTTSSHHHHHHHHHH CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraihe 44 
                                        ++l  G sGtGK+++a+a+ +
  gi|330507066|ref|YP_004383494.1| 150 RNILFYGVSGTGKTMIAKALSA 171
                                       789***************9865 PP

>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.13      31     107 ..     100     180 ..      83     185 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                       EEEEECTTSCEEEEESEEEETTS-HHHHHHHHHHHHHHHHHTTSE.......EEEEEEESTTSSHHHHHTBCTTTSB CS
                           Kinesin  31 skkenkeeeekkfkFdkvfdeeatqeevyeetakplvesvleGyn.......atifaYGqtgsGKTyTmegkeeeee 100
                                        k e+k+e +k  ++d  fde + qee  +++  ++ve+ l+  +         i+ YG++g+GKT   +   ++++
  gi|330507066|ref|YP_004383494.1| 100 IKVEQKAEVKKGVSYDVSFDEVVGQEEAKRKV--KIVEKYLSDPErfgrwapRNILFYGVSGTGKTMIAKAL-SAKA 173
                                       45566677777888888888888888888887..88888887644111112257***********9766554.6677 PP

                                       SHHHHHH CS
                           Kinesin 101 Giipral 107
                                       G+ + a+
  gi|330507066|ref|YP_004383494.1| 174 GVPMLAV 180
                                       7766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 2575.99
//
Query:       gi|330507067|ref|YP_004383495.1|  [L=167]
Description: hypothetical protein MCON_0905 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0065   16.2   0.4      0.015   15.1   0.0    1.9  2  ACT       ACT domain
  ------ inclusion threshold ------
      0.074   13.1   0.1       0.21   11.7   0.0    1.8  2  HTH_29    Winged helix-turn helix


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.55     5e+03      49      64 ..      52      67 ..      50      69 .. 0.77
   2 !   15.1   0.0   1.7e-06     0.015      10      33 ..     105     128 ..     105     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.55
                                      EEEHHHHHHHHHHHHT CS
                               ACT 49 vvdeedleevlealkk 64
                                      +vd ++++++ +a+++
  gi|330507067|ref|YP_004383495.1| 52 EVDRRVVDTTAQAIRE 67
                                      5788888888888876 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.7e-06
                                       STTHHHHHHHHHHHTTSEEEEEEE CS
                               ACT  10 rPGlLarvfgaladrgiNidsieq 33 
                                       + GlL++v++a+a++g++i+ + +
  gi|330507067|ref|YP_004383495.1| 105 KTGLLGDVASAVARNGLSIRQAVS 128
                                       57******************9876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.3e-05      0.21      15      40 ..      44      69 ..      41      80 .. 0.89
   2 ?   -2.9   0.0       0.8   7.2e+03      16      25 ..     113     122 ..     107     127 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                            HTH_29 15 vsqiAkllglsrrtvyrwlkrfeegG 40
                                      ++qiAk l ++rr v+++  + +e++
  gi|330507067|ref|YP_004383495.1| 44 HAQIAKELEVDRRVVDTTAQAIREDE 69
                                      79****************99999987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.8
                            HTH_29  16 sqiAkllgls 25 
                                       + ++++ gls
  gi|330507067|ref|YP_004383495.1| 113 ASAVARNGLS 122
                                       5566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1274.99
//
Query:       gi|330507068|ref|YP_004383496.1|  [L=324]
Description: alanine dehydrogenase [Methanosaeta concilii GP6]
Scores for complete 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-111  371.0   0.0   4.4e-111  370.9   0.0    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
     0.0035   17.4   0.0     0.0054   16.8   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.9   0.0  4.9e-115  4.4e-111       6     316 ..       4     314 ..       1     316 [. 0.98

  Alignments for each domain:
  == domain 1  score: 370.9 bits;  conditional E-value: 4.9e-115
                                       E-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCCTS CS
                   OCD_Mu_crystall   6 ltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkksgl 82 
                                       lt++ev+++l +dd++ av+ af    +g+ ++pp+ +l  ++++g+l+ mpayl+g++l+gvK+vn+hp+n++ gl
  gi|330507068|ref|YP_004383496.1|   4 LTEEEVRSLLTIDDAIAAVQRAFLDHGNGRTQMPPKSYLYLPKHNGDLRCMPAYLEGQDLAGVKIVNVHPGNPQIGL 80 
                                       7899************************************************************************* PP

                                       SSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEEE CS
                   OCD_Mu_crystall  83 ptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikevri 159
                                       p+v+al++Ln+p+tG pla+m at+lt++RT+A++avaa++Lar+d++v+++iGaG+qa+tql+ l++ ++i++v +
  gi|330507068|ref|YP_004383496.1|  81 PSVMALLILNSPQTGEPLAVMGATYLTSMRTGAAGAVAARHLARQDSRVVGMIGAGTQARTQLQGLSRYFPIEQVMV 157
                                       ***************************************************************************** PP

                                       E-SSHHHHHHHHHHCCS..CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-HH CS
                   OCD_Mu_crystall 160 ydrdeeaaekfaenlqe.fefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLddd 235
                                       +d  e +a +f + +++ ++    a++ +eea e +di+vt+T++++p++ +ew++pG+hina+gada gk+eL+  
  gi|330507068|ref|YP_004383496.1| 158 FDSFEDQALAFKDDVSGfMKCSCIAVSGPEEACE-CDILVTTTPSRRPVVRDEWIQPGTHINAIGADAAGKQELEST 233
                                       *****************55**********99985.****************************************** PP

                                       HHHCCEEEESHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHHHHH CS
                   OCD_Mu_crystall 236 ilkradifvdseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaaklvye 312
                                       +lkra+i+vd+ aqa ++Ge++v++++g+++e+++ ae+ge+++Gkk+GRts+ eit+fds+Gl+++Dvaa + vye
  gi|330507068|ref|YP_004383496.1| 234 LLKRAKIVVDDIAQAVHSGEVNVPLSEGIIREKDIYAEIGEILTGKKTGRTSNDEITIFDSTGLGIQDVAAGHAVYE 310
                                       ***************************************************************************** PP

                                       HHCC CS
                   OCD_Mu_crystall 313 raee 316
                                       +a+ 
  gi|330507068|ref|YP_004383496.1| 311 KALR 314
                                       *986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.1e-07    0.0054       3      99 ..     118     215 ..     116     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.1e-07
                                       HHHHHS..TT-EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SE CS
                      Shikimate_DH   3 akkkleslkekkvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadv 78 
                                       a + l + +++ v +iGaG  a+  ++ L++   +++v+v+    ++a ++ ++++g     +   +  e   e+d+
  gi|330507068|ref|YP_004383496.1| 118 AARHLARQDSRVVGMIGAGTQARTQLQGLSRYfPIEQVMVFDSFEDQALAFKDDVSGFMKCSCIAVSGPEEACECDI 194
                                       66677777888899****************98799********************8874444444556778899*** PP

                                       EEE-SSSSS-SB-HHHHHCCH CS
                      Shikimate_DH  79 visataseepilekeeveeal 99 
                                       +++ t s+ p+++ e+++   
  gi|330507068|ref|YP_004383496.1| 195 LVTTTPSRRPVVRDEWIQPGT 215
                                       ***************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2384.47
//
Query:       gi|330507069|ref|YP_004383497.1|  [L=302]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.6e-23   81.4   0.4    1.4e-22   80.8   0.4    1.3  1  Radical_SAM  Radical SAM superfamily
    2.3e-06   27.7   2.5      3e-06   27.4   0.1    2.1  2  Fer4_14      4Fe-4S single cluster domain
    0.00026   21.3   0.1    0.00056   20.2   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 !   80.8   0.4   2.4e-26   1.4e-22       3     165 ..      47     226 ..      45     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 2.4e-26
                                       EESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet....vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlakl 73 
                                       v + Cn +C++C+r ++    +r+++++++l + e le v+++  +++  + + + g gepl++ +  e l++  ++
  gi|330507069|ref|YP_004383497.1|  47 VAPKCNIQCKYCIRDFDcvneSRPGVTSQVLKPKEALERVDQVLeKYHYiKVVAVAGPGEPLFNEETFETLRMVGEK 123
                                       6789***************************************988888788888899*******999999999999 PP

                                       CCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH................HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxx RF
                       Radical_SAM  74 avpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtf................eevleal 134
                                         p+i ++++tng+l+ ++k+++l++lgv  ++++l+a+d+  + +++   + +                 ++l+++
  gi|330507069|ref|YP_004383497.1| 124 Y-PNIILCLSTNGLLL-PDKIQELDRLGVCNITVTLNAIDPQ-IGQHI-YDYVNyegkryegleaatllcNQQLKGI 196
                                       7.**************.*************************.88888.55555788889***************** PP

                                       HHHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 135 eklreagikrvvdrivglpGendeeleelle 165
                                       e + ++  k v++++v++pG nd ++ ++++
  gi|330507069|ref|YP_004383497.1| 197 EEAVRLK-KIVKINTVIIPGINDLHIIDIAH 226
                                       ******5.55*************99999876 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 !   27.4   0.1     5e-10     3e-06       7      92 ..      50     138 ..      46     161 .. 0.74
   2 ?   -0.2   0.3      0.18   1.1e+03      11      28 ..     277     301 ..     271     302 .] 0.75

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5e-10
                           Fer4_14   7 gCnlsCkgCd......nketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlke 76 
                                       +Cn++Ck C       n++    +++  + +e le++ + l+k+++ i+ + + G GePL   n +e ++ ++++ e
  gi|330507069|ref|YP_004383497.1|  50 KCNIQCKYCIrdfdcvNESRPGVTSQVLKPKEALERVDQVLEKYHY-IKVVAVAGpGEPL--FN-EETFETLRMVGE 122
                                       8******887666555777666677777777777544443444444.7889*********..34.66677889**** PP

                           Fer4_14  77 eypekkiwletngtle 92 
                                       +yp++   l tng+l 
  gi|330507069|ref|YP_004383497.1| 123 KYPNIILCLSTNGLLL 138
                                       *************975 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.18
                           Fer4_14  11 sCk.......gCdnketwkselgkp 28 
                                       +C+       gCd +++++s+ +++
  gi|330507069|ref|YP_004383497.1| 277 QCRsdaigklGCDVQQEFESRTKEQ 301
                                       34477778889**999999998875 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   9.4e-08   0.00056      14     100 ..      50     142 ..      39     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.4e-08
                           Fer4_12  14 gCnlsCkgCfnketwsfk.......sgkeftkelleeiiedlkk.esiegltllG.GEPllpenaeallelvkevke 81 
                                        Cn++Ck+C+ ++  +++       s+   +ke+le++ + l+k ++i+ + + G GEPl    +e+  e ++ v e
  gi|330507069|ref|YP_004383497.1|  50 KCNIQCKYCI-RDFDCVNesrpgvtSQVLKPKEALERVDQVLEKyHYIKVVAVAGpGEPLF---NEETFETLRMVGE 122
                                       7*******98.555555533444423333369999999999998678899999999*****...5555667788999 PP

                           Fer4_12  82 ekp.ekdiwlytgytleels 100
                                       ++p    +++++g  l +  
  gi|330507069|ref|YP_004383497.1| 123 KYPnIILCLSTNGLLLPDKI 142
                                       99944567777787776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); 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:                         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 0.22s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2165.64
//
Query:       gi|330507070|ref|YP_004383498.1|  [L=104]
Description: SRP19 protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-20   73.1   0.1    3.4e-20   72.8   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 !   72.8   0.1   1.9e-24   3.4e-20       1      88 [.       8      88 ..       8     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 1.9e-24
                                      EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCC...EEEEEC-.......... CS
                             SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanp...GrVrvklkedgkevnek 76
                                      vi+P+Y+d+ ++r eGR v++e+a+++P+++ i +a  + gl+ ++e+ek++P+ w +p   Gr+ v +k         
  gi|330507070|ref|YP_004383498.1|  8 VIWPIYFDAARSRDEGRMVSREYAINEPNLDMIITASIKSGLKPEIEREKKHPKTWHKPeaaGRILVAKK--------- 77
                                      7********************************************************99999******96......... PP

                                      SS-CHHHHHHHH CS
                             SRP19 77 iknkkellkkia 88
                                        +k++ lkkia
  gi|330507070|ref|YP_004383498.1| 78 -GSKSATLKKIA 88
                                      .33333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 764.01
//
Query:       gi|330507071|ref|YP_004383499.1|  [L=210]
Description: PHP domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   37.1   0.0    5.3e-09   36.6   0.0    1.5  1  PHP          PHP domain
     0.0017   17.9   0.0     0.0034   16.9   0.0    1.7  1  RNase_P_p30  RNase P subunit p30


Domain annotation for each model (and alignments):
>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   5.9e-13   5.3e-09       1      74 [.       3      98 ..       3     201 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 5.9e-13
                                      EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT......HHHHHHHHHHHHTTTTSEEEEEEE........ CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlf......gyvefykaakkkykagikpiiGleayvaddse 73
                                      dlH+Ht++s   + + ++elv++a+ lg+ ai+iTDh+++       + v  +k++  +   +i+++ G+e++ ++ ++
  gi|330507071|ref|YP_004383499.1|  3 DLHTHTTFSDG-ELI-PSELVRRAEVLGYTAIGITDHADYTniehiiSCVSKAKYL--EGILDIRILPGVELTHVPPQK 77
                                      89*******55.234.6************************666444444444444..344789*******98888776 PP

                                      ..................... CS
                                      ....................x RF
                               PHP 74 ....................k 74
                                                          +
  gi|330507071|ref|YP_004383499.1| 78 iaqladlarnlgaeivvvhgE 98
                                      555555555555555555550 PP

>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.8e-07    0.0034      10     145 ..      12     144 ..       2     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.8e-07
                                       ........HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H.HHHHHH CS
                       RNase_P_p30  10 ddskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpsklqrlskv 86 
                                       d++  +s+++++++ lgyt++ i+ + ++ + +   +       + +  + + ++++l +v+l+   p+k+ +l+++
  gi|330507071|ref|YP_004383499.1|  12 DGELIPSELVRRAEVLGYTAIGITDHADYTNIEHIISCV----SKAKYLEGILDIRILPGVELTHVPPQKIAQLADL 84 
                                       4455567999*****************955544444333....34444555555***************99888888 PP

                                       HHH--..EEEEE--S......HHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEE CS
                       RNase_P_p30  87 rqkfd..llavrPtt......ekalraacenldvDiisidltsrlpfglkhktiraAvergvafEin 145
                                       ++     +++v++ +         +raa+e   vDi+ ++       +++ +++++A+++ v +Ei+
  gi|330507071|ref|YP_004383499.1|  85 ARNLGaeIVVVHGESpvepvrPGTNRAALEA-GVDILAHPG------FITLEEAEMARDNDVCLEIT 144
                                       8875444999876552222215677777765.*******99......6999**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 1680.95
//
Query:       gi|330507072|ref|YP_004383500.1|  [L=106]
Description: hypothetical protein MCON_0913 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-30  103.5   0.0      1e-29  103.3   0.0    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 !  103.3   0.0   5.7e-34     1e-29      18     120 ..       1     100 [.       1     101 [. 0.98

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 5.7e-34
                           DUF2209  18 mvcaaVslevsadriekveqvkilvvaseeepkledvvklieeaveelkeegtivaEkGelynepewlveailkkef 94 
                                       mvca  s++vs++ iekv++v+ lv + +e+ +l+ +++li++a   l   gtivaE+G+lyn + w++++il+++f
  gi|330507072|ref|YP_004383500.1|   1 MVCAVLSARVSPNFIEKVHSVR-LVPRIAEALDLNVIADLISDACLCL--PGTIVAEQGDLYNLEVWRAQSILGRDF 74 
                                       8*********************.9999******************999..9************************** PP

                           DUF2209  95 kyqeslgEreaielAHhvslsarkll 120
                                       ky+e+++Er aielAHh+sl+ r+l+
  gi|330507072|ref|YP_004383500.1|  75 KYPETIAERTAIELAHHISLAGRRLI 100
                                       ************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       179  (0.00998383); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 830.20
//
Query:       gi|330507073|ref|YP_004383501.1|  [L=415]
Description: GTP-binding protein HflX [Methanosaeta concilii GP6]
Scores for complete 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   74.3   0.0    1.2e-20   73.6   0.0    1.3  1  MMR_HSR1      50S ribosome-binding GTPase
    1.3e-17   64.2   0.0    3.8e-17   62.7   0.0    1.8  1  GTP-bdg_N     GTP-binding GTPase N-terminal
    1.3e-14   54.5   5.5    3.1e-14   53.3   5.5    1.6  1  GTP-bdg_M     GTP-binding GTPase Middle Region
    1.8e-09   37.3   0.0    3.7e-09   36.3   0.0    1.5  1  FeoB_N        Ferrous iron transport protein B
    2.3e-07   30.9   0.4       0.02   14.8   0.1    2.3  2  RsgA_GTPase   RsgA GTPase
    6.4e-05   22.9   0.0    0.00011   22.1   0.0    1.3  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0001   21.9   0.3     0.0049   16.4   0.3    2.4  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    0.00094   19.3   0.3     0.0032   17.6   0.1    1.9  3  Dynamin_N     Dynamin family
  ------ inclusion threshold ------
      0.026   14.3   0.1          6    6.6   0.1    3.1  3  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
      0.029   14.9   0.1      0.054   14.0   0.1    1.6  1  ABC_tran      ABC transporter
      0.053   13.1   1.4        7.4    6.1   0.2    2.3  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.058   13.2   0.2       0.23   11.2   0.0    1.9  2  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.068   12.5   0.0       0.12   11.7   0.0    1.2  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 !   73.6   0.0   9.1e-24   1.2e-20       2     114 .]     190     308 ..     189     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 9.1e-24
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHH....HH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkafla....le 74 
                                       +a++G++N+GKStL+n+ltg+++ ++d+p+tT+ ++++ ++++g++  l+Dt+G+i+  +  + l kaf++    + 
  gi|330507073|ref|YP_004383501.1| 190 IALAGYTNAGKSTLLNTLTGSVVNAQDQPFTTLSPTTRALEINGRRTMLTDTVGFID--DLPHFLIKAFQStlseIA 264
                                       89****************************************************887..444455555555332267 PP

                                       CTSEEEEEEETTTTCSHHHHHHHHHHHHH.....TTSEEEEEEES CS
                          MMR_HSR1  75 eadlillvvdaseeklkpldeeleellee.....akkplilvlnk 114
                                       +adl+llv d+s + l+ l+++l +  +       + p+i vlnk
  gi|330507073|ref|YP_004383501.1| 265 QADLVLLVADLS-DPLELLRRKLVASHKAlwdcqVTAPMITVLNK 308
                                       79********99.44444444444443334445578999999998 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 !   62.7   0.0   2.8e-20   3.8e-17       3      89 .]      23     104 ..      21     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 2.8e-20
                         GTP-bdg_N   3 sleEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkViD 79 
                                       ++ El+ La+++g++v++e+ q+r + d+++ iG+Gk+ee  +   +     +if + Lsp+q+ n+++e+  +V+D
  gi|330507073|ref|YP_004383501.1|  23 RMIELRGLANAVGYRVLQEIKQRR-ERDHRFQIGRGKIEEALSCHPK----KLIFYNPLSPTQVFNIRSEFPAQVLD 94 
                                       689******************997.7799***********8876655....69************************ PP

                         GTP-bdg_N  80 RtqLILdIFA 89 
                                       R +LIL+IFA
  gi|330507073|ref|YP_004383501.1|  95 RFNLILEIFA 104
                                       *********8 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   5.5   2.2e-17   3.1e-14       1      79 []     106     182 ..     106     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 2.2e-17
                                       H--SHHHHHHHHHHHHHHHHHHHCXXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.... CS
                         GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLeglgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelqrk 77 
                                       rA+t+eaklQVelA+l y  p++ + + +l++ g + g+rG+G ++ ++  + ir r+ak++ eL++v+   e +rk
  gi|330507073|ref|YP_004383501.1| 106 RASTREAKLQVELARLSYDAPQV-RSELALKKRGEQPGFRGAGAYE-QSMYHDIRGRMAKIRGELKEVEAMGEGRRK 180
                                       9**********************.44444444433456********.77789************************* PP

                                       .T CS
                         GTP-bdg_M  78 kR 79 
                                       +R
  gi|330507073|ref|YP_004383501.1| 181 RR 182
                                       98 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   2.7e-12   3.7e-09       3     154 ..     190     347 ..     188     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.7e-12
                                       EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSS CS
                            FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeep 79 
                                       +al+G  n+Gk+tl+n+ltg+  +    p +t   ++ +l+++g+++ ++D  G  +  ++   +    ++    ++
  gi|330507073|ref|YP_004383501.1| 190 IALAGYTNAGKSTLLNTLTGSVVNAQDQPFTTLSPTTRALEINGRRTMLTDTVGFIDDLPHFLIKAFQSTLSEIAQA 266
                                       89****************************************************98766666666666666667889 PP

                                       SEEEEEEEGGG....HHHHHHHHHHHH...HTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTH CS
                            FeoB_N  80 dvvvnvvdatn....lernLyLtlqll...elgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegi 149
                                       d+v+ v+d +     l+r+L+   + l   ++++p++ +ln++d +++   ++  +++++    p v +sa++++g 
  gi|330507073|ref|YP_004383501.1| 267 DLVLLVADLSDplelLRRKLVASHKALwdcQVTAPMITVLNKMDRLDEFDARMRFDQIKDLAPNP-VMVSAHSSQGQ 342
                                       9999999976433337899999877543336779***********************98766666.56899999999 PP

                                       HHHHH CS
                            FeoB_N 150 eellk 154
                                       e+l++
  gi|330507073|ref|YP_004383501.1| 343 ESLKE 347
                                       99987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.8e-05     0.025      87     125 ..     175     213 ..     148     249 .. 0.71
   2 !   14.8   0.1   1.4e-05      0.02      12      98 ..     262     350 ..     231     354 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                       HTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  87 kegleelkellkdktsvlvGqSGvGKStLinallpelel 125
                                       +eg ++ +++l  ++++l+G + +GKStL+n+l+++   
  gi|330507073|ref|YP_004383501.1| 175 GEGRRKRRRELGFDLIALAGYTNAGKSTLLNTLTGSVVN 213
                                       5666677778888899******************98533 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.4e-05
                                       TEES--EEEEEEESTTTT--HHHHHHHHHHHHHT....T-..EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE- CS
                       RsgA_GTPase  12 kvaNvdqllivvslkepelslnlldrfLvlaeek....gi..epvivlnKiDlleeeeeleelkeelealgyevllv 82 
                                       ++a  d +l+v  l++p   l+ll r Lv+ +++    ++  +++ vlnK+D l+e + ++   +++++l  ++++v
  gi|330507073|ref|YP_004383501.1| 262 EIAQADLVLLVADLSDP---LELLRRKLVASHKAlwdcQVtaPMITVLNKMDRLDEFD-ARMRFDQIKDLAPNPVMV 334
                                       38888888888888855...678899999876542222333255669***********.999999************ PP

                                       -TTTHTTHHHHHHHCT CS
                       RsgA_GTPase  83 saktkegleelkellk 98 
                                       sa++++g e+lke + 
  gi|330507073|ref|YP_004383501.1| 335 SAHSSQGQESLKECIY 350
                                       ***********99875 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 !   22.1   0.0   8.1e-08   0.00011      56     104 ..     300     353 ..     291     354 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.1e-08
                      MMR_HSR1_Xtn  56 ipclyvlNKiDlisl....eeldelare.pnsvviSaekelnldeLkekiweeL 104
                                        p+++vlNK+D++++      +d+++   pn v++Sa++  + ++Lke i+++L
  gi|330507073|ref|YP_004383501.1| 300 APMITVLNKMDRLDEfdarMRFDQIKDLaPNPVMVSAHSSQGQESLKECIYQHL 353
                                       699*********665111145666666359**********************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 !   16.4   0.3   3.5e-06    0.0049      40     147 ..     221     325 ..     188     355 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.5e-06
                                       HSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGG....GHHHHHHH....HHT-SEEEEEEETTTBST CS
                          GTP_EFTU  40 ervlDtlkeErergiTiksaaisleketkkylinliDtPGHvd....Fskevirg....lrvlDgavlvvdaveGve 108
                                       +    t++ E +   T+ + ++ +                  d    F  +  ++    ++++D+++lv d ++  e
  gi|330507073|ref|YP_004383501.1| 221 TLSPTTRALEINGRRTMLTDTVGFI-----------------DdlphFLIKAFQStlseIAQADLVLLVADLSDPLE 280
                                       3334444455555555555555554.................33333333332222223899***********9966 PP

                                       HHHHHHH...HHHHHTTTE..EEEEEESCGST.....HHHHHHHHHHHH CS
                          GTP_EFTU 109 pqteevl...rlalkegvp..iivfiNKmDrl.....kaelkeiveevk 147
                                          ++++   + +++ +v   +i+++NKmDrl     +    +  +++k
  gi|330507073|ref|YP_004383501.1| 281 LLRRKLVashKALWDCQVTapMITVLNKMDRLdefdaR----MRFDQIK 325
                                       655555411145555555555***********744333....4444444 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       7.7   1.1e+04      62      99 ..      49      79 ..      38      80 .. 0.52
   2 !   17.6   0.1   2.3e-06    0.0032       1      37 [.     190     226 ..     190     234 .. 0.91
   3 ?   -1.9   0.0       2.2   3.1e+03     120     143 ..     257     280 ..     226     309 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.7
                                      B--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETT CS
                         Dynamin_N 62 ledfsevreeieketekiagankgiskkvillkilsll 99
                                      +       + ++  + ki++a++   kk+i +++ls++
  gi|330507073|ref|YP_004383501.1| 49 D-------HRFQIGRGKIEEALSCHPKKLIFYNPLSPT 79
                                      3.......334444444555555555667777777665 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.3e-06
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EE CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrple 37 
                                       ia+ G +++GKS++ln L+g+ ++  ++  tT  p++
  gi|330507073|ref|YP_004383501.1| 190 IALAGYTNAGKSTLLNTLTGSVVNAQDQPFTTLSPTT 226
                                       7899********************9999999988875 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.2
                                       HHHHHHHSTTEEEEEEEETTS-CC CS
                         Dynamin_N 120 elvkeyikkadiilavtsanhdls 143
                                       + + + i +ad++l+v + +  l 
  gi|330507073|ref|YP_004383501.1| 257 QSTLSEIAQADLVLLVADLSDPLE 280
                                       566777888999999988887766 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 ?    2.1   0.0      0.11   1.4e+02     108     176 ..      25      91 ..      19      96 .. 0.81
   2 ?    6.6   0.1    0.0043         6       1      25 [.     194     218 ..     194     223 .. 0.90
   3 ?    1.1   0.0      0.22     3e+02     102     150 ..     233     286 ..     221     293 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.11
                            CLP1_P 108 IntpGwvkglgaellleliealepdvvvvldqeellnelkrdlplskvkvvklpkspgvvqrsreerre 176
                                       I   G+ + +g+++l+e+ +  e d+   +++ + ++ l+ + +  k+ + +  +  +v++  +e +++
  gi|330507073|ref|YP_004383501.1|  25 IELRGLANAVGYRVLQEIKQRRERDHRFQIGRGKIEEALSCHPK--KLIFYNPLSPTQVFNIRSEFPAQ 91 
                                       667799999**********************9888888877666..66666666667888877777765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0043
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkp 25 
                                       G +++GKSTl  +L   +++++ +p
  gi|330507073|ref|YP_004383501.1| 194 GYTNAGKSTLLNTLTGSVVNAQDQP 218
                                       779****************999877 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.22
                            CLP1_P 102 kasgliIntpGwvkglgaellle....liealepdvvvvldq.eellnelkrdl 150
                                       ++  ++ +t G++++l + l+++    l e+ ++d+v+++ + ++ l+ l+r+l
  gi|330507073|ref|YP_004383501.1| 233 GRRTMLTDTVGFIDDLPHFLIKAfqstLSEIAQADLVLLVADlSDPLELLRRKL 286
                                       56678899******9987665541222677888899999998888888887776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.9e-05     0.054      13      41 ..     189     217 ..     187     343 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.9e-05
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGe 41 
                                       ++a+ G + aGKStLl++l+g + +++++
  gi|330507073|ref|YP_004383501.1| 189 LIALAGYTNAGKSTLLNTLTGSVVNAQDQ 217
                                       689******************98776665 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2    0.0054       7.4       3      21 ..     190     208 ..     188     222 .. 0.80
   2 ?    6.0   0.1     0.006       8.3      88     162 ..     239     320 ..     220     334 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0054
                                       EEEEESTTCCHHHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhll 21 
                                       + l+G+  +GK+tLln+l+
  gi|330507073|ref|YP_004383501.1| 190 IALAGYTNAGKSTLLNTLT 208
                                       6799*************98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.006
                                       EEECTTTT..HHHHHTT.SHHHHHCCCECEEEEEEETTTH......CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC CS
                              cobW  88 iEttGlae..Papvaft.eeelksdltldavvavvDaknl.....eaeeekieekaedqlaaadllvlnKtDlldee 156
                                         t+G  +  P +++   +++l++ +++d v+ v D +        +   + + + + q++a  + vlnK+D lde 
  gi|330507073|ref|YP_004383501.1| 239 TDTVGFIDdlPHFLIKAfQSTLSEIAQADLVLLVADLSDPlellrRKLVASHKALWDCQVTAPMITVLNKMDRLDEF 315
                                       566664441144443335888999999999999999977778876555667778888999999999********998 PP

                                       ..HHHH CS
                              cobW 157 allekl 162
                                       +  +  
  gi|330507073|ref|YP_004383501.1| 316 DA-RMR 320
                                       44.333 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.72     1e+03       2      17 ..     193     208 ..     192     221 .. 0.82
   2 ?   11.2   0.0   0.00017      0.23     136     207 ..     276     352 ..     252     372 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.72
                        ATP_bind_1   2 vGpaGsGKttfvgals 17 
                                       +G   +GK+t+ ++l+
  gi|330507073|ref|YP_004383501.1| 193 AGYTNAGKSTLLNTLT 208
                                       688899*****99986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00017
                        ATP_bind_1 136 tdptkfisgllsals...amlrlelPhvvvlnkfDllkek.lekeleffedvealslllekee.ekykklaeaiael 207
                                       +dp +++ + l+a+      +++  P+++vlnk+D l+e  ++++++ ++d+     +   ++ + +++l+e+i + 
  gi|330507073|ref|YP_004383501.1| 276 SDPLELLRRKLVASHkalWDCQVTAPMITVLNKMDRLDEFdARMRFDQIKDLAPNPVMVSAHSsQGQESLKECIYQH 352
                                       5666666666665541113468999************9768999999999988777777666655566666666655 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.4e-05      0.12       3     131 ..     190     314 ..     189     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.4e-05
                                       EEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEE.EETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHH CS
                              AIG1   3 ivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksr.twdgkkinViDTPglfdlsvsadkiskeivrcll 78 
                                       i l G t +GkS+  N++ g+ +      +q+ t+ + + ++ + +g++    DT g +d      +++k  +  l+
  gi|330507073|ref|YP_004383501.1| 190 IALAGYTNAGKSTLLNTLTGSVVNAQ---DQPFTTLSPTTRAlEINGRRTMLTDTVGFIDDLP--HFLIKAFQSTLS 261
                                       6689****************987544...57777766666666***************99655..566776666544 PP

                                       HCTT-ESEEEEEEETT.B-SHHHHHHHHHHHHHHCGGGGGGEEEEEEEGGGGTT CS
                              AIG1  79 lseegihalllvlslg.rfteedekalktlkelFGekilkylivvftrkddled 131
                                         ++  + +llv +l+  ++   +k+++  k+l + +++  +i v+ + d l +
  gi|330507073|ref|YP_004383501.1| 262 EIAQ-ADLVLLVADLSdPLELLRRKLVASHKALWDCQVTAPMITVLNKMDRLDE 314
                                       4444.8**********889999************************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 2953.18
//
Query:       gi|330507074|ref|YP_004383502.1|  [L=251]
Description: hypothetical protein MCON_0915 [Methanosaeta concilii GP6]
Scores for complete 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   18.7   3.8       0.16   11.5   0.0    2.9  3  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 !   11.5   0.0   8.8e-06      0.16     124     189 ..      95     164 ..      17     167 .. 0.83
   2 !    5.2   1.6   0.00075        13     218     235 ..     178     196 ..     174     200 .. 0.91
   3 ?    0.4   0.0     0.021   3.7e+02     134     157 ..     209     233 ..     202     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.8e-06
                                       TTHHHHHHHHHHHHHHH.TT-EEEEEETTEEEEEC-ECT-EEEEEE-TT.S..SEEEEEEESSS..EEEEEE CS
                              ApbE 124 giaKGyavdrvaellka.giksalvnlGGdiralGpdgkpwrvgiedPr.a..ellavlslsdd..avaTSG 189
                                       ++  G ++  +++++ + g + a+v+ GGd+++l  dg p  vgi     +  +l+  +  +++  +++TS+
  gi|330507074|ref|YP_004383502.1|  95 ACVAGAIAGFAVQAMIDdGATYAIVDNGGDVCILN-DG-PILVGIYAGSsSirDLAFQIPARNKpfGICTSS 164
                                       556677888888888888**************999.64.9*****977741455555666665678888886 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.00075
                                       EEEEEESC.HHHHHHHHHH CS
                              ApbE 218 svtViads.alADalaTal 235
                                       ++tVi+d+ alADa+aTal
  gi|330507074|ref|YP_004383502.1| 178 AATVISDNlALADAAATAL 196
                                       79****999********97 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.021
                                       HHHHHHH.TT-EEEEEETTEEEEEC CS
                              ApbE 134 vaellka.giksalvnlGGdiralG 157
                                       +  ++++ gi++alv  G +++++G
  gi|330507074|ref|YP_004383502.1| 209 CFSAIERpGITGALVIRGQEMALWG 233
                                       55678999***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1699.72
//
Query:       gi|330507075|ref|YP_004383503.1|  [L=90]
Description: hypothetical protein MCON_0917 [Methanosaeta concilii GP6]
Scores for complete 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-37  127.0   1.8    3.2e-37  126.7   1.8    1.1  1  MC1       Non-histone chromosomal protein MC1


Domain annotation for each model (and alignments):
>> MC1  Non-histone chromosomal protein MC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.7   1.8   1.8e-41   3.2e-37       1      96 []       3      88 ..       3      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 126.7 bits;  conditional E-value: 1.8e-41
                               MC1  1 dkrnfalrdedGeeisvfsGkqPrqaaLkaarrletadseeeakeeeirLrekGtkkvhiyegkaeeeeaPddkpdWle 79
                                      ++rnfalrd++G+ei+vf+GkqPrqaaLkaa+r++++          irLre+Gtkkvhi+ g++ ++++P+ +p+W++
  gi|330507075|ref|YP_004383503.1|  3 ETRNFALRDKKGNEIGVFTGKQPRQAALKAANRGHKD----------IRLRERGTKKVHIFAGERVKVKKPKGAPAWMP 71
                                      68*********************************99..........******************************** PP

                               MC1 80 dkitkanvskqgiekle 96
                                      ++i+k++v+k g+ekl+
  gi|330507075|ref|YP_004383503.1| 72 NEIWKPKVKKIGVEKLD 88
                                      ***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 659.57
//
Query:       gi|330507076|ref|YP_004383504.1|  [L=220]
Description: hypothetical protein MCON_0918 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-43  147.1   0.0    4.9e-43  146.8   0.0    1.0  1  CofC          Guanylyl transferase CofC like
     0.0033   17.8   0.0     0.0039   17.6   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 !  146.8   0.0   5.4e-47   4.9e-43       2     208 ..       6     210 ..       5     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 146.8 bits;  conditional E-value: 5.4e-47
                              CofC   2 kviiPvsainsaktrlseilseeerkellkamlldvidalkrld.vlvvsedeevleyaldelgvevvkekekdlnt 77 
                                       +viiP++a +  ktrls+ l + er+ ++ aml dv  a+ +     ++s++e   e +l   +ve+++ +  +ln+
  gi|330507076|ref|YP_004383504.1|   6 HVIIPFKARE-GKTRLSSALKPAERRLFAFAMLRDVLAAVFGQGrTTILSRQEFRAE-EL-GIDVEILQSE-LELND 78 
                                       69******99.9****************************99665889998864332.23.4667788777.99999 PP

                              CofC  78 avekafeeiee....keviiipsdiPlikkedvkdllelekradvviaPargGGtnllllrksalevkyedfsflkh 150
                                       a++  + +  +    ++++i+++d+Pl+++++++ +l  ++  dvv+ P+rgGGtn++l+r   ++  y++ sf +h
  gi|330507076|ref|YP_004383504.1|  79 ALNSLISHQADldwpADILIVMADLPLLREKEIRGILSCQG--DVVLCPGRGGGTNMILIRSPKFRTCYHGLSFPEH 153
                                       999985433222233689*********************99..********************************** PP

                              CofC 151 leearkrglkvkiydsfylsvdinteedlgeillhGegtkakeylrklgfsvepeess 208
                                       +  ark  l+ ++++sf    di++++dl e+llh +g +ak+ l  +gfs++ +  s
  gi|330507076|ref|YP_004383504.1| 154 MAYARKACLNFSVFESFRAGCDIDEPQDLAEVLLHSDG-EAKKALEMMGFSLSESGRS 210
                                       ***********************************877.5788899999999877655 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 !   17.6   0.0   4.4e-07    0.0039      26     128 ..      36     145 ..      20     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.4e-07
                                       HHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HH CS
                      NTP_transf_3  26 llervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltpe 102
                                       +l+ vl+a+  +  ++ ++  ++e  +a+  + +v++++ e +    l sl +  + + +   +l++++D+Pll+++
  gi|330507076|ref|YP_004383504.1|  36 MLRDVLAAVFGQ--GRTTILSRQE-FRAEELGIDVEILQSELELNDALNSLISHQADLDWPADILIVMADLPLLREK 109
                                       666777777766..4666666665.44444567799999999999999999999999999999************** PP

                                       HHHHHHHCHHHHTSSEEEEESSSEE.............E CS
                      NTP_transf_3 103 lverllaaaaasgadvvvptyeger.............g 128
                                        ++ +l     +g+ v++p + g+               
  gi|330507076|ref|YP_004383504.1| 110 EIRGILSC---QGDVVLCPGRGGGTnmilirspkfrtcY 145
                                       *******7...4788899988887755555555444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1668.15
//
Query:       gi|330507077|ref|YP_004383505.1|  [L=246]
Description: F420-0:gamma-glutamyl ligase [Methanosaeta concilii GP6]
Scores for complete sequence (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  191.8   0.0    1.5e-56  191.5   0.0    1.0  1  F420_ligase  F420-0:Gamma-glutamyl ligase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.5   0.0   8.6e-61   1.5e-56       4     244 .]      16     221 ..      15     221 .. 0.98

  Alignments for each domain:
  == domain 1  score: 191.5 bits;  conditional E-value: 8.6e-61
                                       -----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H........ CS
                       F420_ligase   4 tplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfs 80 
                                       +p+ikegdd+ +++ + ++     +edgD++++++++vak+eg++ +l+d +ps++A+e a+ l ++dp        
  gi|330507077|ref|YP_004383505.1|  16 LPIIKEGDDIPTLIQSLFE-----IEDGDVICLASTIVAKSEGRMRHLDDYQPSSHAIEAARDL-GKDP-------- 78 
                                       79***********999988.....9***************************************.****........ PP

                                       ..........HHHHHHHHTEEEEEE-..S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHHHHHH CS
                       F420_ligase  81 liLkalakatrkvevvlsepsdevgn..qlidekytdevlvklGllgsnagidesnveegllkllPedpdksaeeik 155
                                                 r+v++v++e+sd++ +  +l++++       ++G++g+nagid+snv +++++llP dp +sa++++
  gi|330507077|ref|YP_004383505.1|  79 ----------RFVQAVFEESSDILIErpFLLTVT-------HFGHIGVNAGIDQSNVGDEMILLLPIDPCSSAQRLR 138
                                       ..........****************99999999.......**********************************99 PP

                                       HHHHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC-S CS
                       F420_ligase 156 kklkertgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladLvsGs 232
                                       ++l    g+d++V+i  +D++gr+++ + ++va+g+sg+ alrd+rg+ d +g++l +t++a++de++++a+L++G+
  gi|330507077|ref|YP_004383505.1| 139 QAL----GRDCAVII--TDTCGRPFRNGVAGVAVGWSGIAALRDWRGELDIHGRALSITQEAIADEIAAAANLLMGE 209
                                       998....89******..************************************************************ PP

                                       SSS---EEEEES CS
                       F420_ligase 233 adegtPvvlvrg 244
                                       a + tP+v++rg
  gi|330507077|ref|YP_004383505.1| 210 AGDLTPAVVFRG 221
                                       **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1617.54
//
Query:       gi|330507078|ref|YP_004383506.1|  [L=77]
Description: hypothetical protein MCON_0920 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 618.51
//
Query:       gi|330507079|ref|YP_004383507.1|  [L=209]
Description: translation initiation factor 2 subunit beta (eIF-2-beta) (aIF2-beta) [Methanosaeta concilii GP6]
Scores for complete 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-37  126.9   0.0    5.2e-37  126.3   0.0    1.2  1  eIF-5_eIF-2B  Domain found in IF2B/IF5
    5.5e-11   42.3   0.5      1e-10   41.4   0.5    1.4  1  TRAM          TRAM domain
  ------ inclusion threshold ------
       0.11   12.9   0.1        0.2   12.0   0.1    1.4  1  ZF-HD_dimer   ZF-HD protein dimerisation region
       0.24   11.8   2.2         18    5.8   0.1    2.9  3  S1            S1 RNA binding domain
       0.31   10.4   0.1       0.31   10.4   0.1    1.6  2  zf-RanBP      Zn-finger in Ran binding protein and others


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   0.0   1.4e-40   5.2e-37       4     117 .]      18     129 ..      16     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 1.4e-40
                                       CCSSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHH CS
                      eIF-5_eIF-2B   4 kedkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakklekll 80 
                                       ++++ker+ +p+++v +egk +tv++Nf  ia++Lnrdpeh++kyll+e+gt+g+i e++r i++gkf ++ + + +
  gi|330507079|ref|YP_004383507.1|  18 NRESKERFVIPSAKVFYEGK-TTVLENFGAIADTLNRDPEHLMKYLLQEMGTAGKI-EGQRGIFQGKFGETAIARQI 92 
                                       457899**************.***********************************.99****************** PP

                                       HHHHHHHTSTSSSTSTCEEECCSSSCEEEEESSSTCE CS
                      eIF-5_eIF-2B  81 dkyieeyVlCkeCkspetelekeerllvlkCkaCgak 117
                                       ++y eeyV+C+eC+ p+t+l+k++r+l+lkC+aCga+
  gi|330507079|ref|YP_004383507.1|  93 ESYFEEYVVCTECRLPDTHLIKSDRVLTLKCDACGAH 129
                                       ***********************************85 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.5   2.9e-14     1e-10       3      62 .]     147     202 ..     146     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 2.9e-14
                                       XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                       ++G+t+e  +e ++ ++g+gi+++d ++ +fvp + +  G++V +kI+k     +++e++
  gi|330507079|ref|YP_004383507.1| 147 EEGETYELRIESVG-NKGDGIAKVD-KYLIFVPSAIK--GEIVRAKIKKISGTLAFAEVV 202
                                       58************.**********.***********..*******************97 PP

>> ZF-HD_dimer  ZF-HD protein dimerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.7e-05       0.2      37      53 ..     120     136 ..     108     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.7e-05
                       ZF-HD_dimer  37 aLkCaaCgChrnFHrre 53 
                                       +LkC aCg hr   +r+
  gi|330507079|ref|YP_004383507.1| 120 TLKCDACGAHRPVRKRK 136
                                       79*********877765 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.92   3.3e+03       8      23 ..      34      49 ..      31      53 .. 0.84
   2 ?    4.9   0.1    0.0096        35      41      66 ..     137     162 ..     110     175 .. 0.84
   3 ?    5.8   0.1    0.0049        18       4      30 ..     181     206 ..     178     209 .] 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.92
                                      EEEEEEEEETTEEEEE CS
                                S1  8 veGeVtsvtkgGafVe 23
                                      +eG+ t ++++Ga+ +
  gi|330507079|ref|YP_004383507.1| 34 YEGKTTVLENFGAIAD 49
                                      78999999****9877 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0096
                                       CEESCHHHCEETTEEEEEEEEEEETT CS
                                S1  41 arvedpdevlkvGdevkvkvlkvdkd 66 
                                       a++ + ++v+ +G++++++++ v ++
  gi|330507079|ref|YP_004383507.1| 137 ATTAVQKDVIEEGETYELRIESVGNK 162
                                       6677889*************998665 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0049
                                       TTCEEEEEEEEEETTEEEEEETTTEEE CS
                                S1   4 kgevveGeVtsvtkgGafVelgngveg 30 
                                       kge+v +++++++   af e++ + +g
  gi|330507079|ref|YP_004383507.1| 181 KGEIVRAKIKKISGTLAFAEVV-ERKG 206
                                       9*************99999998.6655 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 ?   -2.7   0.3       1.1     4e+03       7      10 ..     102     105 ..     101     107 .. 0.77
   2 ?   10.4   0.1   8.8e-05      0.31      18      29 ..     120     131 ..     117     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.1
                                       -SSS CS
                          zf-RanBP   7 CskC 10 
                                       C+ C
  gi|330507079|ref|YP_004383507.1| 102 CTEC 105
                                       9999 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 8.8e-05
                                       SSB-TTT--BTS CS
                          zf-RanBP  18 stkCvaCqapkp 29 
                                       ++kC aC+a++p
  gi|330507079|ref|YP_004383507.1| 120 TLKCDACGAHRP 131
                                       58*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1702.08
//
Query:       gi|330507080|ref|YP_004383508.1|  [L=171]
Description: 50S ribosomal protein L16 [Methanosaeta concilii GP6]
Scores for complete 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-36  123.7   0.1    5.9e-36  123.4   0.1    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 !  123.4   0.1   3.3e-40   5.9e-36       3     132 .]      13     162 ..      10     162 .. 0.95

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 3.3e-40
                                       SSXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSX CS
                     Ribosomal_L16   3 rkkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwirv 67 
                                       +++y++++  y+ gv+ +k  ++++g+        + Lv++e++q++++aleaar+a+nryl k+ g+   +l++r 
  gi|330507080|ref|YP_004383508.1|  13 ERPYTRRK--YMGGVPgSKVVHYDMGNlqedyplkLTLVVMEPCQIRHTALEAARVAANRYLLKQMGRtnfHLKLRT 87 
                                       57999999..***********************9999**************************9999899******* PP

                                       XXXEEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE...TTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                     Ribosomal_L16  68 fphhpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei...kagvneeiakealrraasKlpiktkiv 132
                                       +phh+++++     ag+dR+++G+    Gk  g++arv++gq +f++    +    + akeal+ra +Klp++++i+
  gi|330507080|ref|YP_004383508.1|  88 YPHHVIRENkqatgAGADRVSSGMrmafGKAVGTAARVEAGQKLFTLgipPQ--YLNDAKEALTRAGHKLPTPIQII 162
                                       ***********************************************65444..67789**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1378.07
//
Query:       gi|330507081|ref|YP_004383509.1|  [L=413]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-60  203.9   0.9    3.1e-60  203.0   0.9    1.4  1  Asparaginase    Asparaginase, N-terminal
    1.5e-29  102.6   0.0    1.4e-28   99.4   0.0    2.2  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    3.2e-18   64.8   0.4      7e-18   63.7   0.4    1.6  1  GatD_N          GatD N-terminal domain


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.0   0.9   5.2e-64   3.1e-60       2     179 ..      75     257 ..      74     267 .. 0.96

  Alignments for each domain:
  == domain 1  score: 203.0 bits;  conditional E-value: 5.2e-64
                                       EEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.-S CS
                      Asparaginase   2 vlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.yd 77 
                                       v +l+tGGTias++d+++ga++ ++sa e+++a+pele+ia+++++++ +i S+nm  + w  la+ ++e++e+ ++
  gi|330507081|ref|YP_004383509.1|  75 VSILSTGGTIASKVDYRTGAVTSQFSAGEIITAIPELEEIANYRARVIYQILSENMRSDYWTALARSVAEEIERgAE 151
                                       88**********************************************************************766** PP

                                       EEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE..... CS
                      Asparaginase  78 gfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk..... 149
                                       g+V++hGTDT+ ytA+aLs+mlk+ ++pvvl+Gsqr++++++sD+ +N + A++va+s+  ia+v vv++g+     
  gi|330507081|ref|YP_004383509.1| 152 GVVITHGTDTMMYTAAALSFMLKT-PVPVVLVGSQRSSDRPSSDASMNAVCAATVATSD--IAEVSVVMHGTtnddy 225
                                       ************************.********************************87..**************** PP

                                       ..EEETTTEEE-BSSSSS-EEETTT--SEEEE CS
                      Asparaginase 150 ..llranrvtKvhtssldaFespnlgplaeve 179
                                         ++r++rv+K+hts++daF+++n  pl++v+
  gi|330507081|ref|YP_004383509.1| 226 ctIHRGTRVRKMHTSRRDAFQTINQHPLGRVD 257
                                       *****************************994 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       0.1     6e+02      20      65 ..     146     190 ..     111     223 .. 0.61
   2 !   99.4   0.0   2.3e-32   1.4e-28       3     113 ..     288     396 ..     286     397 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.1
                                       HHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEE.ESSSBS- CS
                    Asparaginase_C  20 lkkgakGvvlegtGvGnlpsallealkeakargivvvat.sqcpsgs 65 
                                       +++ga+Gvv+  +  + + +    al+ + ++ ++vv++ sq +s +
  gi|330507081|ref|YP_004383509.1| 146 IERGAEGVVITHGTDTMMYT--AAALSFMLKTPVPVVLVgSQRSSDR 190
                                       38889999998877766654..3344444444555443324444444 PP

  == domain 2  score: 99.4 bits;  conditional E-value: 2.3e-32
                                       EEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHH CS
                    Asparaginase_C   3 vvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkeler 79 
                                        ++k +pg ++++l ++++kg++GvvlegtG G++ s+++e + +ak+++i+vv+tsqc++g++ + +y++g+++ +
  gi|330507081|ref|YP_004383509.1| 288 SLVKYTPGSSPEILHYYIDKGYRGVVLEGTGLGHVASDWIEGIGRAKEENIPVVVTSQCLRGRICDRVYDTGRDMLD 364
                                       58999************************************************************************ PP

                                       HTEEE-TT--HHHHHHHHHHHCTT---HHHHHHH CS
                    Asparaginase_C  80 lgvisaddmtpeaarikLmlllgkgldpaevrkl 113
                                       +g+i+++dm pe a +kLm++l+++  p+ev +l
  gi|330507081|ref|YP_004383509.1| 365 AGAIEGGDMLPEVALVKLMWVLANN--PEEVVTL 396
                                       **********************986..6666655 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.4   1.2e-21     7e-18       1      55 []       1      51 [.       1      51 [. 0.97

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.2e-21
                                      --TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
                            GatD_N  1 ievGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                                      ++ GD++ ve++g++yeG+lmP+      d++v+KL+nGYNiG+k  e+ +i+l+
  gi|330507081|ref|YP_004383509.1|  1 MDLGDRVLVERNGISYEGVLMPSR---RADHVVIKLKNGYNIGLKARES-DIKLI 51
                                      689*********************...9*********************.99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        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 0.22s 00:00:00.71 Elapsed: 00:00:00.36
# Mc/sec: 3407.26
//
Query:       gi|330507082|ref|YP_004383510.1|  [L=386]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-23   81.5   0.5    9.7e-23   79.9   0.0    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.1e-07   30.2   0.7    4.1e-07   30.2   0.7    1.8  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.029   14.4   0.3      0.075   13.1   0.3    1.6  1  DZR             Double zinc ribbon
      0.069   13.2   0.0       0.19   11.8   0.0    1.8  1  HypA            Hydrogenase/urease nickel incorporation, meta
        1.2    9.3   4.6         16    5.6   0.1    2.3  2  DUF4337         Domain of unknown function (DUF4337)


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.5   8.8e+03       2      18 ..     223     239 ..     222     242 .. 0.73
   2 !   79.9   0.0   2.7e-26   9.7e-23       1      67 [.     288     352 ..     288     353 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.5
                    OrfB_Zn_ribbon   2 rklkeqleykakeyGik 18 
                                       r+l+++l+ k  +y ++
  gi|330507082|ref|YP_004383510.1| 223 RELQQRLSSKEARYQRQ 239
                                       57888888888877665 PP

  == domain 2  score: 79.9 bits;  conditional E-value: 2.7e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       f++lke+l+yka  +G+++++v+payTS+tC++Cg+ + +  +g+ fkCp Cg + d+D+n+a Ni+
  gi|330507082|ref|YP_004383510.1| 288 FYQLKEFLSYKALAAGVPLVQVDPAYTSQTCHQCGEHGIR--NGKSFKCPVCGWSGDADFNGAKNIA 352
                                       899*************************************..************************7 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2         1   3.7e+03      43      69 ..      93     119 ..      67     137 .. 0.66
   2 !   30.2   0.7   1.2e-10   4.1e-07      10     106 ..     161     255 ..     151     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                        OrfB_IS605  43 grrlksdykylakeiaelqsklkkskn 69 
                                       +  ++++ ++++++  e++ +l +s++
  gi|330507082|ref|YP_004383510.1|  93 SIDYDTRIFAFREKDEEISVTLLRSRQ 119
                                       455666677777777777777777765 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 1.2e-10
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn..ykkasrklarlhrkr 84 
                                       +++    +++g+DlGi ++a++++++     + g+ +k  +  +a  +a lq+k+ k ++  ++++++ ++rl+ k 
  gi|330507082|ref|YP_004383510.1| 161 PEQIHVDTVLGVDLGITDIAVTSEGQ----KFGGKTIKLIKNHYASMRAVLQQKAVKGTRssRRRCRELQQRLSSKE 233
                                       667777899****************9....78999999999***********99988888899************** PP

                        OrfB_IS605  85 srrrkhllhklathliktlkev 106
                                       +r  +   h+++++++ + +e+
  gi|330507082|ref|YP_004383510.1| 234 ARYQRQINHEISKAIVTRAQEI 255
                                       ****************999987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   2.1e-05     0.075      27      49 .]     314     338 ..     297     349 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                               DZR  27 aedrCpsCgek.vdpearf.CpeCG 49 
                                       ++++C +Cge  + ++++f Cp CG
  gi|330507082|ref|YP_004383510.1| 314 TSQTCHQCGEHgIRNGKSFkCPVCG 338
                                       3677777777766677777777776 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 ?   11.8   0.0   5.3e-05      0.19      64      95 ..     309     340 ..     242     351 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.3e-05
                                       EEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  64 ieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       ++    + +C++Cg+++  + k+++Cp Cg +
  gi|330507082|ref|YP_004383510.1| 309 VDPAYTSQTCHQCGEHGIRNGKSFKCPVCGWS 340
                                       556667889*****9998777789*****965 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.7     0.012        42      46     105 ..     194     257 ..     191     266 .. 0.75
   2 ?    5.6   0.1    0.0044        16      25      47 ..     271     293 ..     259     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.012
                           DUF4337  46 ksikehlaeleleqlelllkakaeelaaavdkkiakykkkiarykke.....kkeikkkAkelea 105
                                       k ik+h a++ +  l+ ++ ++++  +++ ++ +++++ k ary+++     +k+i ++A+e+ a
  gi|330507082|ref|YP_004383510.1| 194 KLIKNHYASM-RAVLQQKAVKGTRSSRRRCRELQQRLSSKEARYQRQinheiSKAIVTRAQEIPA 257
                                       5578888888.444444444449999999999*************99877777777778888765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0044
                           DUF4337  25 aqteailaqaeasdqWafYQAks 47 
                                       +++++  ++ ++++ WafYQ k+
  gi|330507082|ref|YP_004383510.1| 271 VNQKSGKNHRRKVNGWAFYQLKE 293
                                       5677778899**********886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1103  (0.0615204); expected 358.6 (0.02)
Passed bias filter:                      695  (0.038764); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2752.81
//
Query:       gi|330507083|ref|YP_004383511.1|  [L=272]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-21   75.7   0.0    4.2e-21   75.3   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    3.9e-21   75.6   0.0    8.4e-21   74.5   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    4.9e-20   72.0   0.0    8.8e-20   71.2   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    8.3e-15   55.3   0.0    1.3e-14   54.7   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    2.3e-13   50.3   0.0    3.5e-13   49.7   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    5.8e-12   45.4   0.0    1.1e-11   44.5   0.0    1.6  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    4.7e-08   32.8   0.0    7.5e-08   32.1   0.0    1.3  1  MTS              Methyltransferase small domain
    1.6e-05   24.4   0.0    1.9e-05   24.1   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    2.7e-05   24.0   0.0    3.9e-05   23.5   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0002   21.1   0.0    0.00028   20.6   0.0    1.3  1  NodS             Nodulation protein S (NodS)
    0.00021   20.7   0.0    0.00031   20.1   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain
    0.00031   19.9   0.0    0.00049   19.3   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00038   19.6   0.0    0.00062   18.9   0.0    1.2  1  DREV             DREV methyltransferase
    0.00063   19.3   0.0     0.0016   18.0   0.0    1.6  2  Methyltransf_4   Putative methyltransferase
  ------ inclusion threshold ------
      0.099   12.0   0.0       0.15   11.4   0.0    1.2  1  TehB             Tellurite resistance protein TehB
       0.13   11.2   0.0       0.26   10.2   0.0    1.5  2  Methyltransf_9   Protein of unknown function (DUF1698)


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   3.7e-24   4.2e-21       3     113 ..      31     137 ..      29     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 3.7e-24
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                        + r+lD+GCG G++t e+  +l p++ vvG+D s e++++A+++  +    n+eF+++d+ +l+  ++ ++fDlil
  gi|330507083|ref|YP_004383511.1|  31 GDERILDIGCGDGKITAEIS-RLVPRGSVVGLDSSLEMLNFAQSRFPDELWPNLEFQHQDARDLP--YH-DQFDLIL 103
                                       6789****************.99******************************************..88.8****** PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedpr 113
                                       s+++l+ + d   +l +i r lk++g++ ++   
  gi|330507083|ref|YP_004383511.1| 104 SFAALHWILDHRPVLAGIRRSLKSEGRVFMQFGG 137
                                       ****************************998655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   7.5e-24   8.4e-21       1      97 []      35     129 ..      35     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 7.5e-24
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       +Ld+GcG G++t+++++ +++++v+g+D s eml+ a++r+ +e + n+ef+++da+dlp++d +fDl++s+ alh+
  gi|330507083|ref|YP_004383511.1|  35 ILDIGCGDGKITAEISRLVPRGSVVGLDSSLEMLNFAQSRFPDELWpNLEFQHQDARDLPYHD-QFDLILSFAALHW 110
                                       8******************99********************886558**************98.*******877**9 PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       +   d++ +l+ i+r Lk +G
  gi|330507083|ref|YP_004383511.1| 111 IL--DHRPVLAGIRRSLKSEG 129
                                       76..6789**********998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.0   7.8e-23   8.8e-20       1      95 [.      36     132 ..      36     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 7.8e-23
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       Ld+GcG G++++++ + +  ++vvg+D s eml+ a+++ ++e   ++ef+++da++lp+ d +fDl++s+ +lh++
  gi|330507083|ref|YP_004383511.1|  36 LDIGCGDGKITAEISRLVprGSVVGLDSSLEMLNFAQSRFPDELWpNLEFQHQDARDLPYHD-QFDLILSFAALHWI 111
                                       8**************99999*********************9988*****************.************** PP

                                       CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                        d++ +l+ i+R Lk +G+++
  gi|330507083|ref|YP_004383511.1| 112 LDHRPVLAGIRRSLKSEGRVF 132
                                       ******************987 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.0   1.2e-17   1.3e-14       1      99 []      36     131 ..      36     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 1.2e-17
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L+iGcG+G +++++ +  p+ +++g+D s ++++ a+ ++ ++    + n+e++++d+ dl+  ++fDl++++ +lh
  gi|330507083|ref|YP_004383511.1|  36 LDIGCGDGKITAEISRLVPRGSVVGLDSSLEMLNFAQSRFPDEL---WPNLEFQHQDARDLPYHDQFDLILSFAALH 109
                                       8********************************99999998877...899999999999998889************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                       ++ d r vl+ ir+ Lk +Gr+
  gi|330507083|ref|YP_004383511.1| 110 WILDHRPVLAGIRRSLKSEGRV 131
                                       ********************85 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   3.1e-16   3.5e-13       8     163 ..      19     188 ..      12     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 3.1e-16
                   Methyltransf_23   8 elsdklerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae...kakkaqkdqfdeqeaae. 78 
                                       +++++l +++   r + r+LdiGcG+G  + ++++ +   sv+g D s e+ + a+    +  +++  f+ q+a++ 
  gi|330507083|ref|YP_004383511.1|  19 WAQELLSKIS--IRGDERILDIGCGDGKITAEISRLVPrgSVVGLDSSLEMLNFAQsrfPDELWPNLEFQHQDARDl 93 
                                       4555666666..78899**********7777776665559*************998888455555555544444444 PP

                   Methyltransf_23  79 .pqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl............kedrllldwlylvpag.r 141
                                          ++fdlI ++  l+++ d+  +l+ i++ lk +G+++ +  ++               e++     +y+  +g +
  gi|330507083|ref|YP_004383511.1|  94 pYHDQFDLILSFAALHWILDHRPVLAGIRRSLKSEGRVFMQFGGRGNaasvldlagemiDEEK-----WYPYFEGfQ 165
                                       4788**********************************9998554322334443322222222.....333333222 PP

                   Methyltransf_23 142 hi.sffsarslkelleeaGlevv 163
                                           f+  ++++ +l e+Gl+ v
  gi|330507083|ref|YP_004383511.1| 166 FPyGFYGPEEYRAWLDESGLRAV 188
                                       22578888999999999998766 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0     1e-14   1.1e-11      33     150 ..      17     132 ..      11     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1e-14
                                       HHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT CS
                   Ubie_methyltran  33 rlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaee 109
                                       + W + +    + +  +++lD+ +G g +++++s+ v  +g vv+lD + +mL+ ++ +  +e   n+ef + +a +
  gi|330507083|ref|YP_004383511.1|  17 QTWAQELLSKISIRGDERILDIGCGDGKITAEISRLV-PRGSVVGLDSSLEMLNFAQSRFPDELWPNLEFQHQDARD 92 
                                       67888777777788889*****************998.78************************************* PP

                                       -TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 110 LpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlv 150
                                       Lp++d  fD++     l  + D+  +L  ++r lk  Gr++
  gi|330507083|ref|YP_004383511.1|  93 LPYHD-QFDLILSFAALHWILDHRPVLAGIRRSLKSEGRVF 132
                                       **987.69*986555799********************997 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   6.7e-11   7.5e-08      23     103 ..      23     104 ..      17     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 6.7e-11
                                       HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-E CS
                               MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkf 98 
                                       Ll++++ + ++++lD+GcG G ++a++ +  p+ +v+ +d + + l++a+  + ++    +e+ ++d+ +   +++f
  gi|330507083|ref|YP_004383511.1|  23 LLSKISIRGDERILDIGCGDGKITAEISRLVPRGSVVGLDSSLEMLNFAQSRFPDELWPnLEFQHQDARDLPYHDQF 99 
                                       778888888899******************************************999988***********99**** PP

                                       EEEEE CS
                               MTS  99 dlivs 103
                                       dli+s
  gi|330507083|ref|YP_004383511.1| 100 DLILS 104
                                       ***98 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.7e-08   1.9e-05      44     140 ..      13     111 ..       6     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.7e-08
                                       HHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES CS
                              CMAS  44 eeAqlaKldlileklelkpGmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldlerkvevkll 119
                                        +Aq++  + +l k++++  +++LdiGcG G+++ +  +     +vvgl  S e  + a+ r+ ++ l  + e + +
  gi|330507083|ref|YP_004383511.1|  13 SSAQQTWAQELLSKISIRGDERILDIGCGDGKITAEISRLVpRGSVVGLDSSLEMLNFAQSRFPDE-LWPNLEFQHQ 88 
                                       579*****************************9987766542479******************875.577899**** PP

                                       -GGG---..--SEEEEES-GGGT CS
                              CMAS 120 dyedlde..kvdrvvsvgafehv 140
                                       d +dl+   ++d + s+ a+  +
  gi|330507083|ref|YP_004383511.1|  89 DARDLPYhdQFDLILSFAALHWI 111
                                       ****98666*******9998766 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   3.5e-08   3.9e-05      54     134 ..      11      91 ..       6     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.5e-08
                                       EEE--HHHHHHHHHHTT...--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEE CS
                              PCMT  54 atiSaphmvalalelle...lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvi 127
                                       + +Sa ++ a   ell+   ++  +r+L++G+G G  ta ++rlv + g vv+++ + e+ + a+ +   +   n+ 
  gi|330507083|ref|YP_004383511.1|  11 KSSSAQQTWAQ--ELLSkisIRGDERILDIGCGDGKITAEISRLVPR-GSVVGLDSSLEMLNFAQSRFPDELWPNLE 84 
                                       55566555554..44444449999*********************76.55***************999999999999 PP

                                       EEES-GG CS
                              PCMT 128 vvvgDGr 134
                                       +++ D r
  gi|330507083|ref|YP_004383511.1|  85 FQHQDAR 91 
                                       9988876 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.5e-07   0.00028      27     130 ..      15     122 ..       1     143 [. 0.76

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.5e-07
                              NodS  27 eqerlaqilrlslaqgsiadalevGcaaGalterlapyckrltvvdv..veeaiararervke..sshiswivsdvq 99 
                                        q+ +aq l   ++ +    +l++Gc  G +t +++ +  r +vv +    e ++ a+ r  +  ++++ +  +d +
  gi|330507083|ref|YP_004383511.1|  15 AQQTWAQELLSKISIRGDERILDIGCGDGKITAEISRLVPRGSVVGLdsSLEMLNFAQSRFPDelWPNLEFQHQDAR 91 
                                       455555544444444445679*********************999762145677888888754349*********** PP

                              NodS 100 qfstdekfdlivvaevlyyiedvaelraavr 130
                                        +  +++fdli+    l++i d   + a +r
  gi|330507083|ref|YP_004383511.1|  92 DLPYHDQFDLILSFAALHWILDHRPVLAGIR 122
                                       *******************999887776665 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.8e-07   0.00031      44     163 ..      13     132 ..       5     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.8e-07
                                       HTTHHHHHHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-H.HHHHHHHHHS-----TTEEEEES- CS
                    Methyltransf_2  44 qessslvakkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlp.eVveaAkehlsageeervefvgGd 119
                                       ++ ++  a+++l ++ ++g ++++D+G G G + ++i+++ P  +v+ +D + e  + A++++  ++ +++ef+  d
  gi|330507083|ref|YP_004383511.1|  13 SSAQQTWAQELLSKISIRGDERILDIGCGDGKITAEISRLVPRGSVVGLDSSlEMLNFAQSRFPDELWPNLEFQHQD 89 
                                       5667888999****************************************8758999******************** PP

                                       TTTS---...--SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEE CS
                    Methyltransf_2 120 ffkdslP...eaDaillkrvlhDwsdekcvklLkrvkkalpagGkvi 163
                                        +   lP   + D+il    lh w  ++ + +L+ ++++l+++G+v 
  gi|330507083|ref|YP_004383511.1|  90 AR--DLPyhdQFDLILSFAALH-WILDH-RPVLAGIRRSLKSEGRVF 132
                                       *9..788334455555556666.54444.568999999999999996 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.3e-07   0.00049      16      87 ..      17      92 ..       8     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.3e-07
                                      HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCG CS
                            RrnaAD 16 kkvineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhqDflk 87
                                      ++ ++e l+k+ ++ +  +l+ig G G  T+e+   +   +vv l +  +++++ q ++   + ++l+  hqD+ +
  gi|330507083|ref|YP_004383511.1| 17 QTWAQELLSKISIRGDERILDIGCGDGKITAEISRLVprGSVVGLDSSLEMLNFAQSRFPdeLWPNLEFQHQDARD 92
                                      778999*******************************9889999999999*******99877889******99876 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   5.5e-07   0.00062      91     186 ..      28     133 ..      14     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.5e-07
                              DREV  91 sdqedkklldlGaGdGeitkrvaptfee..vyatelsetmrdrlkkkky.nvlsalelqetdv.......kldlilc 157
                                       s + d+++ld+G GdG+it  ++  + +  v   + s +m +  + +   ++  +le+q+ d        ++dlil+
  gi|330507083|ref|YP_004383511.1|  28 SIRGDERILDIGCGDGKITAEISRLVPRgsVVGLDSSLEMLNFAQSRFPdELWPNLEFQHQDArdlpyhdQFDLILS 104
                                       556789*******************9877799999999999866654331455666766655322344448****** PP

                              DREV 158 lnlldrcfdplklledirsalepngrviv 186
                                       +  l    d   +l  ir  l+++grv +
  gi|330507083|ref|YP_004383511.1| 105 FAALHWILDHRPVLAGIRRSLKSEGRVFM 133
                                       **************************976 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.4e-06    0.0016       5      62 ..      35      92 ..      32     102 .. 0.93
   2 ?   -3.5   0.0       5.4   6.1e+03      28      47 ..     219     238 ..     215     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
                                      EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCC CS
                    Methyltransf_4  5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalk 62
                                      +l+iGcG G+++ +++   P  +++G++ + ++++ + ++  ++   Nl+  ++da +
  gi|330507083|ref|YP_004383511.1| 35 ILDIGCGDGKITAEISRLVPRGSVVGLDSSLEMLNFAQSRFPDELWPNLEFQHQDARD 92
                                      79***************************************************99944 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.4
                                       EEEEES-HHHHHHHHHHHHH CS
                    Methyltransf_4  28 flGiEirvkvvakvlkkiea 47 
                                        + +E+r++ +++v+++  +
  gi|330507083|ref|YP_004383511.1| 219 RVPVEMRSDFIHEVVDRYIQ 238
                                       56789999999999988655 PP

>> TehB  Tellurite resistance protein TehB
   #    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      20     107 ..      21     110 ..       3     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                       HHHHHHCCCS-S-EEEEES-TTSHHHHHHHHT..T-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S CS
                              TehB  20 sevveavkivkpgkvldlgcgqgrnslylsll..gydvtawdknensiafleeikekenlknistalydineaklde 94 
                                        e+++ + i    ++ld+gcg+g+ +  +s l     v  +d   + ++f ++    e   n++ +  d  ++  ++
  gi|330507083|ref|YP_004383511.1|  21 QELLSKISIRGDERILDIGCGDGKITAEISRLvpRGSVVGLDSSLEMLNFAQSRFPDELWPNLEFQHQDARDLPYHD 97 
                                       46777778888889**********99888866223479999**999*******999********************* PP

                                       -EEEEEEESSGGG CS
                              TehB  95 rydfilstvvlmf 107
                                       ++d+ils   l +
  gi|330507083|ref|YP_004383511.1|  98 QFDLILSFAALHW 110
                                       *******887765 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00023      0.26     105     217 ..      21     133 ..      12     159 .. 0.69
   2 ?   -2.7   0.0         2   2.2e+03     271     283 ..     198     210 ..     165     238 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                                       HHHGGGS.--TT-EEEEET-TTSHH...HHHHHHCT-SEEEEE---H..HHHHHHHHHHCCTTTTSSEEEE---GGG CS
                    Methyltransf_9 105 drvlphlsdlkgrtildvGcgnGyh...lwrmvgegaklvvGidPse..lfliqfeavrkllgedqrahllplgieq 176
                                       + +l  +s   + +ild+Gcg+G     + r+v +g  +vvG+d s   l + q +   +l  + + +h+      +
  gi|330507083|ref|YP_004383511.1|  21 QELLSKISIRGDERILDIGCGDGKItaeISRLVPRG--SVVGLDSSLemLNFAQSRFPDELWPNLEFQHQ---DARD 92 
                                       4577888888899**********8611156777766..58999976411333444444444443333333...4678 PP

                                       S-T---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEEE CS
                    Methyltransf_9 177 lpeleafdtvfsmGvlyhrrsPldhllqlkdqlvkgGelvl 217
                                       lp  + fd ++s   l+        l  ++ +l+++G + +
  gi|330507083|ref|YP_004383511.1|  93 LPYHDQFDLILSFAALHWILDHRPVLAGIRRSLKSEGRVFM 133
                                       88888888888888777665555567788888888887766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                                       --TTTB--BTTB- CS
                    Methyltransf_9 271 ttleeqrkteWle 283
                                       +  +    + W+e
  gi|330507083|ref|YP_004383511.1| 198 VQKDKAGLASWIE 210
                                       2222222233333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2151.71
//
Query:       gi|330507084|ref|YP_004383512.1|  [L=177]
Description: nucleoside-triphosphatase [Methanosaeta concilii GP6]
Scores for complete 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  158.6   0.0    1.8e-46  158.4   0.0    1.0  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.4   0.0     1e-50   1.8e-46       1     187 []       2     173 ..       2     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 158.4 bits;  conditional E-value: 1e-50
                                       EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTT CS
                        Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaLng 75 
                                       i f+T+NkgK+ e+++i++  +le k+l       ++E+q +t+ee+a    +++++  + p++ +D gL+++aL+g
  gi|330507084|ref|YP_004383512.1|   2 ISFITSNKGKYVEARAIID--GLEQKDL------GYTEIQaDTLEEVAVYGINEIMArLKEPAMLEDAGLFIEALGG 70 
                                       679**************95..6666777......5679**9*************88636888*************** PP

                                       TBGGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGG CS
                        Ham1p_like  76 lPGvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDp 152
                                       +PGvysa+++++      +++ +l+ +++  ++r+A f++v+++++p+ e+ ++f+G+veG+i +e+rg+ gfGyDp
  gi|330507084|ref|YP_004383512.1|  71 FPGVYSAYVQKTI-----GNEGILRLMDGI-SNRKAFFKSVVVYSEPGLEP-RMFQGIVEGQIGHEARGSSGFGYDP 140
                                       *********6544.....556666666533.47**************6666.9************************ PP

                                       GEEETT-SSBTTTS.CHHHHHHSHHHHHHHHHHHH CS
                        Ham1p_like 153 iFvpeegektfaelskeeknaiShRgkAlekllef 187
                                       iF++  gek++ae++ +ekn+iShR+ ++++l e+
  gi|330507084|ref|YP_004383512.1| 141 IFYV--GEKSLAEMELAEKNRISHRAASMRALDEW 173
                                       ****..599*********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1475.78
//
Query:       gi|330507085|ref|YP_004383513.1|  [L=87]
Description: hypothetical protein MCON_0929 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 679.65
//
Query:       gi|330507086|ref|YP_004383514.1|  [L=139]
Description: hypothetical protein MCON_0930 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-11   43.3   3.5    3.7e-11   42.6   3.5    1.3  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 !   42.6   3.5   2.1e-15   3.7e-11       5      37 .]      50      83 ..      49      83 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 2.1e-15
                           DUF1232  5 iagalaYlisPiDlIPD.fiPvlGflDDlavltl 37
                                      i++a+aY+i+P D+IP+  ++++G++DD++++++
  gi|330507086|ref|YP_004383514.1| 50 IIAAIAYFILPEDIIPEdKFGPVGYVDDIYLCAF 83
                                      89****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1091.60
//
Query:       gi|330507087|ref|YP_004383515.1|  [L=220]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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  128.9   4.5    1.1e-08   34.5   0.0    5.5  5  TPR_1       Tetratricopeptide repeat
    9.2e-36  119.1   4.6    5.4e-09   35.5   0.0    5.4  5  TPR_2       Tetratricopeptide repeat
    7.9e-34  115.1   6.8    4.9e-09   35.7   0.5    5.2  5  TPR_11      TPR repeat
    1.6e-27   93.4   1.3    3.1e-06   26.9   0.0    5.3  5  TPR_8       Tetratricopeptide repeat
    4.8e-23   79.8   7.4    1.3e-05   25.3   0.0    5.6  5  TPR_17      Tetratricopeptide repeat
    2.2e-21   76.2   5.6    8.8e-08   32.7   0.1    4.3  4  TPR_16      Tetratricopeptide repeat
    2.7e-19   68.2   2.5     0.0052   17.5   0.0    5.3  5  TPR_14      Tetratricopeptide repeat
    9.9e-16   58.0   6.0    0.00028   21.3   0.3    4.2  4  TPR_19      Tetratricopeptide repeat
    5.4e-15   55.5   9.4    9.5e-05   22.6   0.2    4.7  5  TPR_12      Tetratricopeptide repeat
    1.7e-13   50.5   0.2      0.001   19.2   0.1    3.2  3  TPR_9       Tetratricopeptide repeat
    1.7e-12   46.4   3.1     0.0039   17.1   0.0    4.8  4  TPR_7       Tetratricopeptide repeat
    8.9e-08   31.8   4.1      0.032   14.1   0.1    4.6  5  TPR_10      Tetratricopeptide repeat
    1.6e-06   28.3   1.0          3    8.7   0.0    4.5  4  TPR_6       Tetratricopeptide repeat
    2.1e-05   24.7   2.3     0.0043   17.2   0.1    3.1  3  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
    5.5e-05   22.5   1.3      0.097   11.9   0.2    3.3  2  TPR_15      Tetratricopeptide repeat
     0.0012   18.9   2.5       0.96    9.6   0.0    3.6  4  MIT         MIT (microtubule interacting and transport) domai
     0.0012   18.9   1.1         12    6.0   0.0    3.9  3  DUF3856     Domain of Unknown Function (DUF3856)
     0.0046   17.0   1.2       0.37   10.9   0.5    3.2  3  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
     0.0083   16.6   0.2       0.66   10.4   0.0    2.5  2  BTAD        Bacterial transcriptional activator domain
  ------ inclusion threshold ------
      0.029   14.2   0.2        3.4    7.4   0.0    2.8  3  DUF5113     Domain of unknown function (DUF5113)
       0.06   13.4   1.9        1.4    9.0   0.0    3.6  3  TPR_3       Tetratricopeptide repeat
      0.075   11.9   0.0         16    4.2   0.0    2.7  3  NARP1       NMDA receptor-regulated protein 1
       0.12   11.8   2.5         11    5.6   0.0    3.4  3  SHNi-TPR    SHNi-TPR


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   6.6e-08   5.1e-05       1      34 []      25      58 ..      25      58 .. 0.96
   2 !   34.5   0.0   1.4e-11   1.1e-08       2      34 .]      60      92 ..      59      92 .. 0.95
   3 !   17.5   0.1   3.3e-06    0.0026      10      32 ..     103     125 ..      93     127 .. 0.88
   4 !   17.8   0.0   2.7e-06    0.0021       2      32 ..     129     159 ..     128     161 .. 0.96
   5 !   33.9   0.0   2.3e-11   1.8e-08       3      34 .]     164     195 ..     162     195 .. 0.98

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.6e-08
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a+ +  lG   +++g  +eA   y++ALel+P n
  gi|330507087|ref|YP_004383515.1| 25 AEYWSSLGDQQLYNGSIEEAARSYDEALELDPGN 58
                                      789*****************************87 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 1.4e-11
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                      + ++++G+a+  lg+y++A++ +ekAL +n +n
  gi|330507087|ref|YP_004383515.1| 60 NLWNRKGYAFGILGRYEDAIASFEKALAINSTN 92
                                      68****************************987 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 3.3e-06
                                       HHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1  10 ayfklgkydeAleyyekALelnP 32 
                                       +y+ l ++deA+++++k+L ln 
  gi|330507087|ref|YP_004383515.1| 103 LYRGLDRHDEAIACFDKVLGLNA 125
                                       6999***************9985 PP

  == domain 4  score: 17.8 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       +a++++G+a+  +g++   l + + A +l+P
  gi|330507087|ref|YP_004383515.1| 129 EAWNGKGMALADKGDLSGSLVCLQMASKLDP 159
                                       8*****************************9 PP

  == domain 5  score: 33.9 bits;  conditional E-value: 2.3e-11
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a++n G++++++gky+eAle ++kAL l+Pnn
  gi|330507087|ref|YP_004383515.1| 164 AWNNEGVVLREQGKYQEALERFDKALLLDPNN 195
                                       9******************************8 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   6.7e-09   5.2e-06       1      34 []      25      58 ..      25      58 .. 0.97
   2 !   27.1   0.0   3.3e-09   2.5e-06       3      34 .]      61      92 ..      59      92 .. 0.94
   3 !   14.2   0.1   4.6e-05     0.036       2      31 ..      94     124 ..      93     127 .. 0.74
   4 !   14.0   0.0   5.4e-05     0.042       2      34 .]     129     161 ..     128     161 .. 0.95
   5 !   35.5   0.0     7e-12   5.4e-09       3      34 .]     164     195 ..     162     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6.7e-09
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      ae++  lG+  +++g  eeA++ +++AleldP+n
  gi|330507087|ref|YP_004383515.1| 25 AEYWSSLGDQQLYNGSIEEAARSYDEALELDPGN 58
                                      79******************************97 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 3.3e-09
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                                      ++++ G+a   lg+ye+A++ fekAl+++ +n
  gi|330507087|ref|YP_004383515.1| 61 LWNRKGYAFGILGRYEDAIASFEKALAINSTN 92
                                      8***************************9886 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 4.6e-05
                             TPR_2   2 ealynlGlayyk.lgdyeeAleafekAleld 31 
                                       eal++ Gla+y+ l++++eA+++f+k+l l+
  gi|330507087|ref|YP_004383515.1|  94 EALNWKGLALYRgLDRHDEAIACFDKVLGLN 124
                                       66777777766625666*********99776 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 5.4e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ea++  G+a++ +gd+   l +++ A +ldP n
  gi|330507087|ref|YP_004383515.1| 129 EAWNGKGMALADKGDLSGSLVCLQMASKLDPLN 161
                                       89*****************************65 PP

  == domain 5  score: 35.5 bits;  conditional E-value: 7e-12
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a++n G +++++g+y+eAle f+kAl ldPnn
  gi|330507087|ref|YP_004383515.1| 164 AWNNEGVVLREQGKYQEALERFDKALLLDPNN 195
                                       9******************************8 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.3     5e-09   3.9e-06       1      38 [.      32      69 ..      32      70 .. 0.91
   2 !   35.7   0.5   6.2e-12   4.9e-09       1      40 [.      66     105 ..      66     106 .. 0.94
   3 !   13.0   0.0   8.1e-05     0.063       9      42 .]     109     142 ..     107     142 .. 0.94
   4 !   20.0   0.0   5.2e-07   0.00041       2      37 ..     136     171 ..     135     172 .. 0.92
   5 !   26.6   0.3   4.4e-09   3.4e-06       3      34 ..     171     202 ..     169     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 5e-09
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                                      Gd     G +eeA  +Y +Al+ldP n+++++  G+a+
  gi|330507087|ref|YP_004383515.1| 32 GDQQLYNGSIEEAARSYDEALELDPGNVNLWNRKGYAF 69
                                      5666678****************************997 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 6.2e-12
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       G+a+  +G+ye+Ai++++kAl+++++n+ea+++ Gla+y+
  gi|330507087|ref|YP_004383515.1|  66 GYAFGILGRYEDAIASFEKALAINSTNVEALNWKGLALYR 105
                                       6777889*******************************96 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 8.1e-05
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       + +eAi+++ k l l+ ++ ea+++ G a++ +G
  gi|330507087|ref|YP_004383515.1| 109 RHDEAIACFDKVLGLNASDSEAWNGKGMALADKG 142
                                       679************************9999887 PP

  == domain 4  score: 20.0 bits;  conditional E-value: 5.2e-07
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                        a+ ++G++ +++ +++ A kldP n+ a++n G++
  gi|330507087|ref|YP_004383515.1| 136 MALADKGDLSGSLVCLQMASKLDPLNPGAWNNEGVV 171
                                       5899****************************8877 PP

  == domain 5  score: 26.6 bits;  conditional E-value: 4.4e-09
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynL 34 
                                       +++eqGky eA+e++ kAl ldP+n  a  n+
  gi|330507087|ref|YP_004383515.1| 171 VLREQGKYQEALERFDKALLLDPNNQAAQTNR 202
                                       799**********************9998887 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1     7e-05     0.055       1      33 [.      25      57 ..      25      58 .. 0.90
   2 !   26.9   0.0     4e-09   3.1e-06       2      33 ..      60      91 ..      59      92 .. 0.93
   3 !   19.8   0.0   7.6e-07   0.00059       2      33 ..      94     126 ..      93     127 .. 0.87
   4 !    8.6   0.0     0.003       2.3       2      32 ..     129     159 ..     128     159 .. 0.93
   5 !   19.0   0.0   1.4e-06    0.0011       3      34 .]     164     195 ..     162     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7e-05
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      ae++  lg+  l  g +eeA  +y +aleldp 
  gi|330507087|ref|YP_004383515.1| 25 AEYWSSLGDQQLYNGSIEEAARSYDEALELDPG 57
                                      67888899999999*****************96 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 4e-09
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                                       +++++g++   lg+ye A++++ekal ++ +
  gi|330507087|ref|YP_004383515.1| 60 NLWNRKGYAFGILGRYEDAIASFEKALAINST 91
                                      58**************************9976 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 7.6e-07
                                       CHHHHHH.HHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlg.siylklgdyeeAkeyyekaleldpd 33 
                                       ea++++g  +y+ l +++eA++++ k+l l+ +
  gi|330507087|ref|YP_004383515.1|  94 EALNWKGlALYRGLDRHDEAIACFDKVLGLNAS 126
                                       78999995566*******************976 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.003
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ea++ +g+++ ++gd+  +  +++ a +ldp
  gi|330507087|ref|YP_004383515.1| 129 EAWNGKGMALADKGDLSGSLVCLQMASKLDP 159
                                       89**************999999999999998 PP

  == domain 5  score: 19.0 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a++n g +++++g+y+eA e + kal ldp+n
  gi|330507087|ref|YP_004383515.1| 164 AWNNEGVVLREQGKYQEALERFDKALLLDPNN 195
                                       8*****************************97 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.6e-08   1.3e-05       2      33 ..      48      79 ..      47      80 .. 0.96
   2 !   16.4   0.1   1.1e-05    0.0088       2      33 ..      82     114 ..      81     115 .. 0.85
   3 !   11.6   0.0   0.00037      0.29       1      29 [.     116     144 ..     116     147 .. 0.93
   4 !   19.3   0.0   1.3e-06     0.001       3      34 .]     152     183 ..     150     183 .. 0.90
   5 !    7.4   0.1    0.0084       6.6       2      27 ..     185     210 ..     185     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.6e-08
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      y +aleldP n++++n +++++  +G++++A+
  gi|330507087|ref|YP_004383515.1| 48 YDEALELDPGNVNLWNRKGYAFGILGRYEDAI 79
                                      99****************************98 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.1e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelll.knGdlmtAr 33 
                                       ++kal+++ +n++a+n ++ +l+  + ++++A+
  gi|330507087|ref|YP_004383515.1|  82 FEKALAINSTNVEALNWKGLALYrGLDRHDEAI 114
                                       89******************7653777777776 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00037
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdl 29 
                                       ++ k+l l+ ++++a+n ++ +l+ +Gdl
  gi|330507087|ref|YP_004383515.1| 116 CFDKVLGLNASDSEAWNGKGMALADKGDL 144
                                       7899999********************96 PP

  == domain 4  score: 19.3 bits;  conditional E-value: 1.3e-06
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + a +ldP n+ a+nn +++l+++G++++A++
  gi|330507087|ref|YP_004383515.1| 152 QMASKLDPLNPGAWNNEGVVLREQGKYQEALE 183
                                       567799************************86 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0084
                            TPR_17   2 ylkaleldPnnadaynnLAelllknG 27 
                                       + kal ldPnn  a +n+ ++l   +
  gi|330507087|ref|YP_004383515.1| 185 FDKALLLDPNNQAAQTNRNNTLQDMN 210
                                       689*********99999999998766 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.1   1.1e-10   8.8e-08       3      63 ..      31      88 ..      29      92 .. 0.93
   2 !   25.6   0.1   1.8e-08   1.4e-05      11      58 ..      73     118 ..      72     120 .. 0.92
   3 !   19.9   0.0   1.1e-06   0.00085       7      54 ..     104     148 ..     103     162 .. 0.82
   4 !   18.1   0.1   4.1e-06    0.0032      25      65 ..     156     193 ..     150     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.1e-10
                            TPR_16  3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63
                                      l++  l++g  ++Aa+ +++al++d   P ++  ++ +g a+  +gr+++A+a +++al+ 
  gi|330507087|ref|YP_004383515.1| 31 LGDQQLYNGSIEEAARSYDEALELD---PGNVNLWNRKGYAFGILGRYEDAIASFEKALAI 88
                                      6777899******************...*****************************9976 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 1.8e-08
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrq.grlaeAaalyr 58 
                                       g+y+dA+a +e al+ +   + ++eAl+++g+a++r   r++eA+a ++
  gi|330507087|ref|YP_004383515.1|  73 GRYEDAIASFEKALAIN---STNVEALNWKGLALYRGlDRHDEAIACFD 118
                                       9****************...99*************666******98665 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 1.1e-06
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                                       ++ + + d+A+a ++ +l ++     + eA++++g a++ +g+l + +
  gi|330507087|ref|YP_004383515.1| 104 YRGLDRHDEAIACFDKVLGLN---ASDSEAWNGKGMALADKGDLSGSL 148
                                       5566789**************...55556**************98765 PP

  == domain 4  score: 18.1 bits;  conditional E-value: 4.1e-06
                            TPR_16  25 krdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       k+d   P+++ A+++ g+++ +qg ++eA++ +++al  +p
  gi|330507087|ref|YP_004383515.1| 156 KLD---PLNPGAWNNEGVVLREQGKYQEALERFDKALLLDP 193
                                       556...99999999999999999999999977766663444 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.7e-06    0.0052       2      42 ..      26      66 ..      25      69 .. 0.89
   2 !   14.0   0.0   9.1e-05     0.071       3      38 ..      61      96 ..      59     102 .. 0.85
   3 !   13.4   0.1   0.00014      0.11       9      38 ..     102     131 ..      94     138 .. 0.86
   4 ?    7.1   0.0     0.015        11      10      38 ..     137     165 ..     133     170 .. 0.92
   5 !   14.6   0.2   5.7e-05     0.044      10      39 ..     171     200 ..     168     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.7e-06
                            TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42
                                      e +  l++  l +G  +eA++ +++al+l+P++  +w + +
  gi|330507087|ref|YP_004383515.1| 26 EYWSSLGDQQLYNGSIEEAARSYDEALELDPGNVNLWNRKG 66
                                      66888999999***********************9997765 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 9.1e-05
                            TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeaw 38
                                      ++ + + a+  lG++++Aia +++ala + ++ ea+
  gi|330507087|ref|YP_004383515.1| 61 LWNRKGYAFGILGRYEDAIASFEKALAINSTNVEAL 96
                                      677778888899*****************9999886 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.00014
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeaw 38 
                                       ++++ l+++deAia+++++l l+ +d eaw
  gi|330507087|ref|YP_004383515.1| 102 ALYRGLDRHDEAIACFDKVLGLNASDSEAW 131
                                       4577799**********************9 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.015
                            TPR_14  10 allalGdpdeAiallrralalaPddaeaw 38 
                                       al+  Gd+ +++ +l+ a +l+P ++ aw
  gi|330507087|ref|YP_004383515.1| 137 ALADKGDLSGSLVCLQMASKLDPLNPGAW 165
                                       78999***********************9 PP

  == domain 5  score: 14.6 bits;  conditional E-value: 5.7e-05
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawl 39 
                                       +l+++G+++eA++ +++al l+P++++a++
  gi|330507087|ref|YP_004383515.1| 171 VLREQGKYQEALERFDKALLLDPNNQAAQT 200
                                       799***********************9986 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00036      0.28       2      29 ..      36      63 ..      35      68 .. 0.90
   2 !   11.3   0.0    0.0005      0.39       5      30 ..      73      98 ..      71     105 .. 0.89
   3 !   14.3   0.0   5.5e-05     0.043       6      59 ..     109     162 ..     102     166 .. 0.91
   4 !   21.3   0.3   3.6e-07   0.00028       1      29 [.     172     200 ..     172     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                            TPR_19  2 laegdyaeAlalleqalqedpknaearl 29
                                      l++g  +eA++ + +al+ dp+n +++ 
  gi|330507087|ref|YP_004383515.1| 36 LYNGSIEEAARSYDEALELDPGNVNLWN 63
                                      789********************99986 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0005
                            TPR_19  5 gdyaeAlalleqalqedpknaearll 30
                                      g+y++A+a +e+al+ +  n ea+ +
  gi|330507087|ref|YP_004383515.1| 73 GRYEDAIASFEKALAINSTNVEALNW 98
                                      89********************9875 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 5.5e-05
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                       +++eA+a + ++l  ++ ++ea+ +   al   g+l     +L+ + + dp ++
  gi|330507087|ref|YP_004383515.1| 109 RHDEAIACFDKVLGLNASDSEAWNGKGMALADKGDLSGSLVCLQMASKLDPLNP 162
                                       89********************************************99999765 PP

  == domain 4  score: 21.3 bits;  conditional E-value: 3.6e-07
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearl 29 
                                       l ++g+y+eAl+++ +al  dp+n++a+ 
  gi|330507087|ref|YP_004383515.1| 172 LREQGKYQEALERFDKALLLDPNNQAAQT 200
                                       679**********************9986 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   1.0    0.0011      0.88      37      75 ..      19      55 ..       2      56 .. 0.79
   2 !   22.6   0.2   1.2e-07   9.5e-05       5      72 ..      61     121 ..      59     122 .. 0.85
   3 !   12.3   0.1    0.0002      0.16       5      33 ..      95     124 ..      91     155 .. 0.80
   4 !   20.7   0.1   4.8e-07   0.00037       5      30 ..     164     189 ..     126     194 .. 0.67
   5 !   20.3   0.0   6.3e-07   0.00049       5      32 ..     164     191 ..     161     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                            TPR_12 37 lGpdhpltattlrnLgrlyralgryeeAlelleealaia 75
                                        ++h  ta++   Lg+ +++ g  eeA + + eal+++
  gi|330507087|ref|YP_004383515.1| 19 AAEEH--TAEYWSSLGDQQLYNGSIEEAARSYDEALELD 55
                                      33566..*****************************986 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.2e-07
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       ++n+ + +   lgry++A++ +ekal+i   +  ++   +a    +L+ + r l+r++eA++ + ++l
  gi|330507087|ref|YP_004383515.1|  61 LWNRKGYAFGILGRYEDAIASFEKALAIN--S--TNV--EALNWKGLALY-RGLDRHDEAIACFDKVL 121
                                       67778889999******************..2..444..78888888888.7999*********9987 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.0002
                            TPR_12   5 alnnlaavlrr.lgrydeAlellekaleia 33 
                                       aln  +++l+r l r+deA+++++k+l + 
  gi|330507087|ref|YP_004383515.1|  95 ALNWKGLALYRgLDRHDEAIACFDKVLGLN 124
                                       566678888666************998665 PP

  == domain 4  score: 20.7 bits;  conditional E-value: 4.8e-07
                            TPR_12   5 alnnlaavlrrlgrydeAlellekal 30 
                                       a+nn ++vlr++g+y+eAle ++kal
  gi|330507087|ref|YP_004383515.1| 164 AWNNEGVVLREQGKYQEALERFDKAL 189
                                       45555666666666666666666665 PP

  == domain 5  score: 20.3 bits;  conditional E-value: 6.3e-07
                            TPR_12   5 alnnlaavlrrlgrydeAlellekalei 32 
                                       a+nn ++vlr++g+y+eAle ++kal +
  gi|330507087|ref|YP_004383515.1| 164 AWNNEGVVLREQGKYQEALERFDKALLL 191
                                       6778888888888888888888888865 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.2e-05     0.017      11      60 ..      41      90 ..      36      97 .. 0.91
   2 !   17.3   0.0   5.2e-06     0.004       4      60 ..     103     159 ..     101     164 .. 0.92
   3 !   19.2   0.1   1.3e-06     0.001      17      66 ..     150     199 ..     148     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                             TPR_9 11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60
                                       e+a + ++  l l+P  + ++   G +   lG+++ A+a +e +la++ 
  gi|330507087|ref|YP_004383515.1| 41 IEEAARSYDEALELDPGNVNLWNRKGYAFGILGRYEDAIASFEKALAINS 90
                                      68999*****************************************9875 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.2e-06
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       ++   +++++a+a+ + +l l+  d e +   G++la  G+ls+ l +L+ +  l+p
  gi|330507087|ref|YP_004383515.1| 103 LYRGLDRHDEAIACFDKVLGLNASDSEAWNGKGMALADKGDLSGSLVCLQMASKLDP 159
                                       678889********************************************9999998 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 1.3e-06
                             TPR_9  17 vverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                                       ++++   l+P  p+ +   G++l ++G +++Al+ ++ +l l+p++++a 
  gi|330507087|ref|YP_004383515.1| 150 CLQMASKLDPLNPGAWNNEGVVLREQGKYQEALERFDKALLLDPNNQAAQ 199
                                       77888899************************************999886 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.046        36      16      35 ..      42      59 ..      25      60 .. 0.86
   2 !   12.1   0.0   0.00021      0.16      12      29 ..      72      89 ..      62      92 .. 0.88
   3 !    9.4   0.0    0.0015       1.2       8      33 ..     103     128 ..     102     130 .. 0.86
   4 !   17.1   0.0     5e-06    0.0039       2      34 ..     165     195 ..     164     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.046
                             TPR_7 16 eeAielyeqsLaltkdpeda 35
                                      eeA++ y +  al+ dp+++
  gi|330507087|ref|YP_004383515.1| 42 EEAARSYDE--ALELDPGNV 59
                                      89*******..888888875 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00021
                             TPR_7 12 lGdyeeAielyeqsLalt 29
                                      lG+ye+Ai  +e++La+ 
  gi|330507087|ref|YP_004383515.1| 72 LGRYEDAIASFEKALAIN 89
                                      8************99875 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0015
                             TPR_7   8 lysrlGdyeeAielyeqsLaltkdpe 33 
                                       ly+ l +++eAi ++ ++L+l  +++
  gi|330507087|ref|YP_004383515.1| 103 LYRGLDRHDEAIACFDKVLGLNASDS 128
                                       699999***********999987776 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 5e-06
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       ++n +++ +++G+y+eA+e + +  al  dp++
  gi|330507087|ref|YP_004383515.1| 165 WNNEGVVLREQGKYQEALERFDK--ALLLDPNN 195
                                       6677999****************..99999887 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.65   5.1e+02      18      30 ..      41      53 ..      36      55 .. 0.72
   2 !    7.8   0.0    0.0038         3      15      31 ..      72      88 ..      66      90 .. 0.90
   3 ?    6.4   0.0     0.011       8.7       5      29 ..      96     121 ..      93     124 .. 0.80
   4 ?   -3.0   0.0        10   7.8e+03       9      22 ..     135     148 ..     135     153 .. 0.78
   5 !   14.1   0.1   4.1e-05     0.032       9      29 ..     169     189 ..     166     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.65
                            TPR_10 18 ydeAealleeala 30
                                       +eA + ++eal+
  gi|330507087|ref|YP_004383515.1| 41 IEEAARSYDEALE 53
                                      5778888888886 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0038
                            TPR_10 15 rgrydeAealleealai 31
                                      +gry++A a +e+alai
  gi|330507087|ref|YP_004383515.1| 72 LGRYEDAIASFEKALAI 88
                                      7**************98 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.011
                            TPR_10   5 lnNLanal.rqrgrydeAealleeal 29 
                                       ln  + al r + r+deA a ++++l
  gi|330507087|ref|YP_004383515.1|  96 LNWKGLALyRGLDRHDEAIACFDKVL 121
                                       555566666************99998 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 10
                            TPR_10   9 analrqrgrydeAe 22 
                                       ++al + g++ +++
  gi|330507087|ref|YP_004383515.1| 135 GMALADKGDLSGSL 148
                                       78999999987765 PP

  == domain 5  score: 14.1 bits;  conditional E-value: 4.1e-05
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       +++lr++g+y+eA++ +++al
  gi|330507087|ref|YP_004383515.1| 169 GVVLREQGKYQEALERFDKAL 189
                                       89***************9998 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0         1   8.1e+02      14      32 ..      39      57 ..      28      58 .. 0.76
   2 ?    5.7   0.1     0.035        27       7      27 ..      45      86 ..      43      90 .. 0.74
   3 !    8.7   0.0    0.0039         3       5      27 ..      98     121 ..      94     124 .. 0.88
   4 !    8.6   0.0    0.0041       3.2       7      32 ..     169     194 ..     167     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1
                                      HHHHHHHHHHHHHHHH-TT CS
                             TPR_6 14 gdtdkAlealerlikeYPd 32
                                      g  ++A + +++ ++  P+
  gi|330507087|ref|YP_004383515.1| 39 GSIEEAARSYDEALELDPG 57
                                      5778999999999888775 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.035
                                      HHHHHHH.....................HHHHHHHHHHHHHH CS
                             TPR_6  7 alsyrkl.....................gdtdkAlealerli 27
                                      a+sy ++                     g++++A++ +e+ +
  gi|330507087|ref|YP_004383515.1| 45 ARSYDEAleldpgnvnlwnrkgyafgilGRYEDAIASFEKAL 86
                                      66666644666666666666777777779**********987 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0039
                                       HHHHHHHH.HHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrk.lgdtdkAlealerli 27 
                                       + +l++++ l+++d+A++ +++++
  gi|330507087|ref|YP_004383515.1|  98 WKGLALYRgLDRHDEAIACFDKVL 121
                                       6799999989***********997 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0041
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       +  +r++g++++Ale +++ +   P+
  gi|330507087|ref|YP_004383515.1| 169 GVVLREQGKYQEALERFDKALLLDPN 194
                                       6778999************9988887 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 !    8.7   0.2    0.0025       1.9      18      82 .]      18      85 ..       2      85 .. 0.82
   2 !   17.2   0.1   5.6e-06    0.0043       3      59 ..      73     131 ..      71     152 .. 0.89
   3 !    7.5   0.1    0.0062       4.8       5      81 ..     110     187 ..     108     200 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0025
                                      HHH--HHHHHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
                            ANAPC3 18 aetespedayl..lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLekl 82
                                      + +e + + y+  l+   + ng  ++A + +++a +l++ + + +  ++ +   L++ye+Aia +ek+
  gi|330507087|ref|YP_004383515.1| 18 SAAEEHTAEYWssLGDQQLYNGSIEEAARSYDEAlELDPGNVNLWNRKGYAFGILGRYEDAIASFEKA 85
                                      66788888888778999999*****************************9999***********9985 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.6e-06
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-.HHHHHHHHHCT.SHHHC-HHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngq.ykrAyellrka.klnskslgcr 59 
                                       ++y++Ai  +e++la ++ + e++ +++l+ly+  + +++A+  ++k  +ln ++ +++
  gi|330507087|ref|YP_004383515.1|  73 GRYEDAIASFEKALAINSTNVEALNWKGLALYRGLDrHDEAIACFDKVlGLNASDSEAW 131
                                       589***********999***************9877799*****999999999888776 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0062
                                       HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +++Ai +++++l  ++ ++e+   ++ +l   g+    +  l+ a kl++ ++g++   + +l +++ky+eA+  ++
  gi|330507087|ref|YP_004383515.1| 110 HDEAIACFDKVLGLNASDSEAWNGKGMALADKGDLSGSLVCLQMAsKLDPLNPGAWNNEGVVLREQGKYQEALERFD 186
                                       77777777777766666666666666666666666666666666666666666666666666666777777766555 PP

                                       S CS
                            ANAPC3  81 k 81 
                                       k
  gi|330507087|ref|YP_004383515.1| 187 K 187
                                       4 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.2   0.00012     0.097     130     184 ..       8      63 ..       1     129 [. 0.68
   2 !    6.4   0.1    0.0059       4.6     148     183 ..     164     199 ..     154     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                            TPR_15 130 aellksle.eeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselra 184
                                        +ll+  + + +a e  a +++ ++  ++ +g  ++A r y eAl+l+p++ +l +
  gi|330507087|ref|YP_004383515.1|   8 LALLAATSiPSAAEEHTAEYWSSLGDQQLYNGSIEEAARSYDEALELDPGNVNLWN 63 
                                       456666553555566999********************************999844 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0059
                            TPR_15 148 fllaraelyrqegqtdaAlrdyreAlalapdsselr 183
                                        +   + + r++g+ ++Al+ + +Al l+p++++++
  gi|330507087|ref|YP_004383515.1| 164 AWNNEGVVLREQGKYQEALERFDKALLLDPNNQAAQ 199
                                       5666677899*********************98776 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 ?    4.9   0.3     0.035        27      17      33 ..      38      54 ..      34      54 .. 0.87
   2 ?    1.7   0.0      0.34   2.6e+02      19      39 ..      74      87 ..      72      97 .. 0.60
   3 ?   -2.4   0.0       6.7   5.2e+03      27      39 ..     110     122 ..     107     134 .. 0.63
   4 !    9.6   0.0    0.0012      0.96      26      60 ..     177     212 ..     167     216 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.035
                               MIT 17 agnyeeAlelYkealel 33
                                      +g +eeA + Y ealel
  gi|330507087|ref|YP_004383515.1| 38 NGSIEEAARSYDEALEL 54
                                      68899*********996 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.34
                               MIT 19 nyeeAlelYkealelLlqalk 39
                                              Y++a+  + +al+
  gi|330507087|ref|YP_004383515.1| 74 R-------YEDAIASFEKALA 87
                                      4.......5566666665555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.7
                               MIT  27 YkealelLlqalk 39 
                                         ea+  + ++l 
  gi|330507087|ref|YP_004383515.1| 110 HDEAIACFDKVLG 122
                                       5678888888886 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0012
                               MIT  26 lYkealelLlqalk.ekneerrellrekieeYleRa 60 
                                       +Y+eale + +al    n +  ++ r+++ + ++R+
  gi|330507087|ref|YP_004383515.1| 177 KYQEALERFDKALLlDPNNQAAQTNRNNTLQDMNRI 212
                                       466777777777664444466666666666666665 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.015        12      14      38 ..      30      54 ..      21      57 .. 0.89
   2 ?    5.4   0.0     0.023        18     108     127 ..      67      86 ..      60     128 .. 0.73
   3 ?    2.7   0.0      0.16   1.2e+02     106     126 ..     168     188 ..     163     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.015
                                      HHHHHHHHHT-HHHHHHHHHHHHHH CS
                           DUF3856 14 seaekqleegayeeaaasyrkalev 38
                                      s +++ql +g+ eeaa+sy +ale+
  gi|330507087|ref|YP_004383515.1| 30 SLGDQQLYNGSIEEAARSYDEALEL 54
                                      7799******************996 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.023
                                       HHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 108 valeelGrkdealkafrmag 127
                                        a+  lGr+++a+ +f++a 
  gi|330507087|ref|YP_004383515.1|  67 YAFGILGRYEDAIASFEKAL 86 
                                       44444555555555554443 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.16
                                       HHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 106 ravaleelGrkdealkafrma 126
                                        +v l e G+++eal+ f +a
  gi|330507087|ref|YP_004383515.1| 168 EGVVLREQGKYQEALERFDKA 188
                                       567778888888888888766 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 ?    1.6   0.0      0.37   2.9e+02      18      34 ..      42      58 ..      37      61 .. 0.87
   2 ?    0.4   0.0      0.92   7.1e+02      14      38 ..      72      96 ..      71     102 .. 0.85
   3 !   10.9   0.5   0.00048      0.37      14      38 ..     175     199 ..     174     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.37
                                      HHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C 18 seArryvdalLeiEPen 34
                                      +eA r  d  Le++P+n
  gi|330507087|ref|YP_004383515.1| 42 EEAARSYDEALELDPGN 58
                                      688999999******99 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.92
                                      HT-HHHHHHHHHHHHHHTTS-HHHH CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPenrQaq 38
                                      lg+Y++A    +  L+i   n  a+
  gi|330507087|ref|YP_004383515.1| 72 LGRYEDAIASFEKALAINSTNVEAL 96
                                      799****999999999998887776 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00048
                                       HT-HHHHHHHHHHHHHHTTS-HHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaq 38 
                                       +g+Y+eA++  d  L ++P+n+ aq
  gi|330507087|ref|YP_004383515.1| 175 QGKYQEALERFDKALLLDPNNQAAQ 199
                                       589******************9888 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   0.00085      0.66      57     123 ..      20      86 ..      11      94 .. 0.89
   2 ?    3.7   0.0       0.1        78      71     121 ..     137     187 ..      92     192 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00085
                                       HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  57 leelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                        ee   e   +l + +l+ G +eea++ ++++++++P + +l+     A   +Gr ++A++ +e++ 
  gi|330507087|ref|YP_004383515.1|  20 AEEHTAEYWSSLGDQQLYNGSIEEAARSYDEALELDPGNVNLWNRKGYAFGILGRYEDAIASFEKAL 86 
                                       5666777778889999**********************************************99875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.1
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                       a++  G+ +  l  l+ + +++Pl+  ++      l+ +G+ +eALe++++
  gi|330507087|ref|YP_004383515.1| 137 ALADKGDLSGSLVCLQMASKLDPLNPGAWNNEGVVLREQGKYQEALERFDK 187
                                       555566666666667777777888888888888888888888888887765 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.9   2.2e+03       8      36 ..      25      53 ..      23      62 .. 0.77
   2 ?    3.7   0.0     0.061        47      11      37 ..      62      88 ..      48      99 .. 0.84
   3 ?    7.4   0.0    0.0044       3.4      10      36 ..     164     190 ..     160     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.9
                           DUF5113  8 andYanlayylnvegeyeeALeyldsale 36
                                      a+ + +l+ +  ++g+ eeA +  d+ale
  gi|330507087|ref|YP_004383515.1| 25 AEYWSSLGDQQLYNGSIEEAARSYDEALE 53
                                      55566777777888888888888888886 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.061
                           DUF5113 11 YanlayylnvegeyeeALeyldsaley 37
                                      +   +y+  + g+ye+A++ +++al +
  gi|330507087|ref|YP_004383515.1| 62 WNRKGYAFGILGRYEDAIASFEKALAI 88
                                      56678889999************9964 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0044
                           DUF5113  10 dYanlayylnvegeyeeALeyldsale 36 
                                       ++ n +  l  +g+y+eALe +d+al 
  gi|330507087|ref|YP_004383515.1| 164 AWNNEGVVLREQGKYQEALERFDKALL 190
                                       67888999999**************95 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1         1   7.9e+02      17      23 ..      48      54 ..      26      56 .. 0.67
   2 ?    0.4   0.0      0.85   6.6e+02      13      23 ..      71      81 ..      66      92 .. 0.71
   3 ?    9.0   0.0    0.0018       1.4      14      36 .]     175     195 ..     171     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1
                                      HHHHHHH CS
                             TPR_3 17 yqeArel 23
                                      y+eA+el
  gi|330507087|ref|YP_004383515.1| 48 YDEALEL 54
                                      6666666 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.85
                                      HTT-HHHHHHH CS
                             TPR_3 13 nkkkyqeArel 23
                                        ++y++A+  
  gi|330507087|ref|YP_004383515.1| 71 ILGRYEDAIAS 81
                                      679*****976 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0018
                                       TT-HHHHHHH..HHHHHHH-TT- CS
                             TPR_3  14 kkkyqeArelfsYallaildken 36 
                                       ++kyqeA+e f+   +  ld++n
  gi|330507087|ref|YP_004383515.1| 175 QGKYQEALERFD--KALLLDPNN 195
                                       9*********88..888888877 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.021        16     205     253 ..      38      86 ..      18      93 .. 0.85
   2 ?    3.7   0.0      0.03        24     203     256 ..     105     158 ..      90     161 .. 0.91
   3 ?   -0.3   0.0      0.49   3.8e+02      13      29 ..     171     187 ..     167     211 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.021
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeear 253
                                        gs e+A +  d+a+e +p  v+l+ +K+  +   G  ++A++  e+a 
  gi|330507087|ref|YP_004383515.1|  38 NGSIEEAARSYDEALELDPGNVNLWNRKGYAFGILGRYEDAIASFEKAL 86 
                                       46788999999******************99999999999999999885 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.03
                                       HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                         l + ++A+ + dk +  + +  e +  K+  l  +Gdl++   +++ a klD
  gi|330507087|ref|YP_004383515.1| 105 RGLDRHDEAIACFDKVLGLNASDSEAWNGKGMALADKGDLSGSLVCLQMASKLD 158
                                       55677889******************************************9999 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.49
                                       HHHHHTHHHHHHHHHHH CS
                             NARP1  13 iieeagkleeAlehLee 29 
                                       +++e+gk++eAle++++
  gi|330507087|ref|YP_004383515.1| 171 VLREQGKYQEALERFDK 187
                                       45555555555555544 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.64     5e+02      18      30 ..      42      54 ..      30      54 .. 0.81
   2 ?    5.6   0.0     0.014        11      16      30 ..      74      88 ..      73      96 .. 0.90
   3 ?    3.5   0.1     0.064        50      13      28 ..     174     189 ..     173     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.64
                          SHNi-TPR 18 pqAveDlrkaLeL 30
                                      ++A+  +++aLeL
  gi|330507087|ref|YP_004383515.1| 42 EEAARSYDEALEL 54
                                      68999999***98 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.014
                          SHNi-TPR 16 nFpqAveDlrkaLeL 30
                                      ++++A+  ++kaL++
  gi|330507087|ref|YP_004383515.1| 74 RYEDAIASFEKALAI 88
                                      9************98 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.064
                          SHNi-TPR  13 EnenFpqAveDlrkaL 28 
                                       E++++ +A+e ++kaL
  gi|330507087|ref|YP_004383515.1| 174 EQGKYQEALERFDKAL 189
                                       899***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1374.24
//
Query:       gi|330507088|ref|YP_004383516.1|  [L=166]
Description: hypothetical protein MCON_0932 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.14   11.0   0.0       0.17   10.7   0.0    1.1  1  NADase_NGA  Nicotine adenine dinucleotide glycohydrolase (NAD
       0.21   11.6   0.9       0.43   10.6   0.9    1.5  1  SNARE       SNARE domain


Domain annotation for each model (and alignments):
>> NADase_NGA  Nicotine adenine dinucleotide glycohydrolase (NADase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   1.9e-05      0.17      17     106 ..      25     114 ..      13     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.9e-05
                        NADase_NGA  17 vaialagamgssllansttyavsgkenkksdvk.yettkvmeanatsskednhvmhtldgsmstvweenspgggvge 92 
                                       + +a+ g  g   la  t  a+sg +n    vk y+t  vm    t     n   +   g+ +   +  sp gg+  
  gi|330507088|ref|YP_004383516.1|  25 IFMAIPGIKGEIPLAY-TPAAISGGQNDMLTVKnYDTGAVMTESYTDVEHLNRDTQVRTGAYANSADAASPRGGLEA 100
                                       5567777777777775.677999999999999779****************************************** PP

                        NADase_NGA  93 vlsykfaspmhigr 106
                                        +s ++    hi  
  gi|330507088|ref|YP_004383516.1| 101 SISSNVIGNAHIAW 114
                                       ***99999999975 PP

>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.9   4.8e-05      0.43      32      52 ..       9      29 ..       6      29 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.8e-05
                                      CTXXXXXXXXXXXXXXXXXXX CS
                             SNARE 32 ksnRklkciillilviillvv 52
                                      ++  +++++ l++lvii++++
  gi|330507088|ref|YP_004383516.1|  9 RNGDRWMWMKLICLVIIFMAI 29
                                      67779*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1229.34
//
Query:       gi|330507089|ref|YP_004383517.1|  [L=662]
Description: peptidase C1A, papain [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-42  145.1   4.8    4.8e-42  144.5   4.8    1.3  1  Peptidase_C1    Papain family cysteine protease
    1.1e-16   61.4   0.5      1e-06   29.4   0.1    3.4  4  DUF4114         Domain of unknown function (DUF4114)
  ------ inclusion threshold ------
      0.027   14.8   0.0        3.2    8.1   0.0    2.6  2  DUF4358         Domain of unknown function (DUF4358)
       0.13   11.0   2.3       0.98    8.1   0.6    2.1  2  Peptidase_C1_2  Peptidase C1-like family


Domain annotation for each model (and alignments):
>> Peptidase_C1  Papain family cysteine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.5   4.8   1.1e-45   4.8e-42       2     214 ..      70     274 ..      69     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 144.5 bits;  conditional E-value: 1.1e-45
                                       TSCEETTT.TTTG.SG---B-TSSBTHHHHHHHHHHHHHHHHHHS..SS---B-HHHHH..HHSTTTSTGGGBB-.H CS
                      Peptidase_C1   2 pesvDwre.kgga.vtpvkdqgsCGsCWafsavgaledrlaiktk..kklvslSeqelv..dCskeenegCnGGl.m 71 
                                       p+++Dwr+ +g+   tp+kdq +CGsC af++v+a+e+ l i ++  +   +lSe +l    C     + C  G+  
  gi|330507089|ref|YP_004383517.1|  70 PTQWDWRDvSGNDwTTPIKDQRQCGSCVAFATVAAIESNLEIFKRdpSLDPDLSEADLFfrGCG----DCCGRGWyF 142
                                       99******644448**************************999887777899*****9843343....456667615 PP

                                       HHHHHHHHHTEBEBTTTS--SSSCSSS-CGCGGGSEEBEESEEEEEESSBHHHHHHHHHHHSSEEEEEECCSHHHHT CS
                      Peptidase_C1  72 enafeyikkggivtekdypYkakeggkCkkkkkkekvakikgygkvkenseealkkalakngPvsvaidaseedfql 148
                                       + a+++++++g+ +e+++pY++ ++g+C  + k+  v+ki++ ++++++  ++ k++l ++gP+   ++++e df +
  gi|330507089|ref|YP_004383517.1| 143 TPALRFAQSSGVPDEACNPYQGDKTGSCPDRDKR--VVKIESWTTITNS--SQAKEWLSQRGPLIGGLSVYE-DFFY 214
                                       77********************999***998765..69*******9996..889******************.6*** PP

                                       EESSEESSTSCETSS-EEEEEEEEEEEETTEEEEEEE-SBTTTSTBTTEEEEESSSSTGGGTTSSE CS
                      Peptidase_C1 149 YksGvyketecsktelnhavlivGygvengkkyWivkNsWgtdwgekGYiriargknnecgiesea 214
                                       Y++Gvyk  +  +   +hav++vG++    k +Wi+kNsWg+ wge+G+++ia g   ecg+ s+ 
  gi|330507089|ref|YP_004383517.1| 215 YEKGVYKT-AYGGYMGDHAVCVVGFDDA--KGCWICKNSWGQGWGESGWFKIAYG---ECGMGSQF 274
                                       *******9.7788899*********987..78*********************98...79998775 PP

>> DUF4114  Domain of unknown function (DUF4114)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.3     1e+04      49      67 ..     223     241 ..     211     244 .. 0.76
   2 !   28.1   0.0   5.7e-10   2.6e-06       1      83 [.     337     402 ..     337     403 .. 0.82
   3 ?   -2.2   0.0       1.6   7.3e+03      27      49 ..     476     494 ..     460     524 .. 0.61
   4 !   29.4   0.1   2.3e-10     1e-06       4      84 ..     587     650 ..     578     651 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.3
                           DUF4114  49 qvalndtkstvvvlgfEDl 67 
                                         +++ +++ v v+gf+D 
  gi|330507089|ref|YP_004383517.1| 223 AYGGYMGDHAVCVVGFDDA 241
                                       5566667777999****96 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 5.7e-10
                           DUF4114   1 fpaGttigffLvangtnqellensssgiffSqeslNpdgedqngdrvhqvalndtkst.vvvlgfEDllrgsDkDFn 76 
                                       fpaGt++ f L +            ++if+S++ lN d  d+  ++++ ++      t ++ l +EDl   + kD+n
  gi|330507089|ref|YP_004383517.1| 337 FPAGTRLTFALKTSA----------GHIFYSDQLLNDDVCDH--VNKTGIG------TyKWQLNWEDLYGLGEKDYN 395
                                       899999999999998..........58***********8887..4444444......33578*****8666****** PP

                           DUF4114  77 Dlvfyve 83 
                                       D+ + +e
  gi|330507089|ref|YP_004383517.1| 396 DVSMEIE 402
                                       **99887 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.6
                           DUF4114  27 giffSqeslNpdgedqngdrvhq 49 
                                        ++++++  Npd  ++    v+ 
  gi|330507089|ref|YP_004383517.1| 476 YTYYTDQVKNPDFLSH----VRK 494
                                       6788888889986666....222 PP

  == domain 4  score: 29.4 bits;  conditional E-value: 2.3e-10
                           DUF4114   4 GttigffLvangtnqellensssgiffSqeslNpdgedqngdrvhqvalndtkstvvvlgfEDllrgsDkDFnDlvf 80 
                                       Gt++ f L +++          + +f++++ lN+dg+++       + l+ + s++  l +EDl   +D D+nDlv+
  gi|330507089|ref|YP_004383517.1| 587 GTRLIFALQTQD----------GAFFYTDSGLNEDGKSH------VLRLKLG-SNKCQLRWEDLYGLKDTDYNDLVV 646
                                       555555555555..........59***********9977......3333333.33689*****8666********** PP

                           DUF4114  81 yves 84 
                                        +++
  gi|330507089|ref|YP_004383517.1| 647 EIKM 650
                                       9986 PP

>> DUF4358  Domain of unknown function (DUF4358)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00071       3.2      18      80 ..     384     440 ..     380     445 .. 0.81
   2 ?    3.5   0.0     0.019        84      18      38 ..     631     651 ..     628     654 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00071
                           DUF4358  18 kklygldkddvedyvayvsassasadevlivkakdeedaeevkkaleerledqkksfedYlpe 80 
                                       ++lygl ++d+ d+ ++++ +sa+++++++ k  +      v ++l++r    k++f   +pe
  gi|330507089|ref|YP_004383517.1| 384 EDLYGLGEKDYNDVSMEIEIISATSEDLVMPK--E----GRVFATLKQRHAATKEEFRLSSPE 440
                                       789***********************998755..5....367888888888888877766666 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.019
                           DUF4358  18 kklygldkddvedyvayvsas 38 
                                       ++lygl+++d+ d v+++ ++
  gi|330507089|ref|YP_004383517.1| 631 EDLYGLKDTDYNDLVVEIKMD 651
                                       789*************99864 PP

>> Peptidase_C1_2  Peptidase C1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.014        65      55      80 ..      84     109 ..      66     143 .. 0.79
   2 ?    8.1   0.6   0.00022      0.98     353     397 ..     223     263 ..     212     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.014
                                       S-S--B--BSSTHHHHHHHHHHHHHH CS
                    Peptidase_C1_2  55 tdevtnqkqsGRCWlFaalnvlRlkl 80 
                                       t ++ +q+q G C  Fa++ ++  +l
  gi|330507089|ref|YP_004383517.1|  84 TTPIKDQRQCGSCVAFATVAAIESNL 109
                                       45899*************99987665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00022
                                       HTTS----EEEEEEEEEE-TTSSEEEEEEE-SBTTTSTBTTEEEE CS
                    Peptidase_C1_2 353 dygeslmtHamvltgvdvdddgkvtkwkvEnsWGedsGekGyfvm 397
                                       +yg  + +Ha+ ++g+d  ++g    w   nsWG+  Ge G+f +
  gi|330507089|ref|YP_004383517.1| 223 AYGGYMGDHAVCVVGFDD-AKG---CWICKNSWGQGWGESGWFKI 263
                                       57777889*******998.555...599**************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 4592.19
//
Query:       gi|330507090|ref|YP_004383518.1|  [L=163]
Description: hypothetical protein MCON_0934 [Methanosaeta concilii GP6]
Scores for complete 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-19   69.4   0.9    5.2e-17   62.6   0.2    2.0  2  DUF45      Protein of unknown function DUF45
    0.00077   19.3   0.2     0.0025   17.6   0.1    1.8  2  SprT-like  SprT-like family


Domain annotation for each model (and alignments):
>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0   0.00091       8.2       1      47 [.      13      58 ..      13      75 .. 0.79
   2 !   62.6   0.2   5.9e-21   5.2e-17     130     193 ..      77     142 ..      57     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00091
                             DUF45  1 knlrlrvepdgsvevsaPkgvseeeiedfvkkkakwiekklakleer 47
                                      k+++ r+   g++ev aP  +s++++++ ++k +  +ek++   ++ 
  gi|330507090|ref|YP_004383518.1| 13 KTIQARMVA-GKMEVLAPASISDAALRAHIEKLQIRLEKRIYPKDDL 58
                                      578888999.9*********************999999988666664 PP

  == domain 2  score: 62.6 bits;  conditional E-value: 5.9e-21
                             DUF45 130 kprsvsik.dmktrWGsc.sskgkirlnwrLvkappevidYVvvHElaHlleknHskrFwalvekl 193
                                       +++s++ + ++++r Gsc  ++++i ++ rL+ +p+ v dYV+vHElaHl+e+nH+krF alv+++
  gi|330507090|ref|YP_004383518.1|  77 SWNSIQYSsRQEHRRGSCnCAARTILISDRLASLPQWVEDYVIVHELAHLIEPNHGKRFKALVNRY 142
                                       666777651577899***999******************************************997 PP

>> SprT-like  SprT-like family
   #    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      33      57 ..      36      54 ..       9      59 .. 0.62
   2 !   17.6   0.1   2.8e-07    0.0025       6      98 ..      65     141 ..      60     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.28
                         SprT-like 33 aGranlkratvrhhasIeLseklld 57
                                      a ra++++       +I+L ++++ 
  gi|330507090|ref|YP_004383518.1| 36 ALRAHIEK------LQIRLEKRIYP 54
                                      33444444......77888887765 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.8e-07
                         SprT-like   6 kklddavfggqaaggvkiiwskrlnttaGranlkratvrhhasIeLseklldsrsedrllntLaHElcHlalfvisg 82 
                                       + l++ +f+g+ +   +i+ s+r +   G +n          +I +s +l    ++     +++HEl+Hl+      
  gi|330507090|ref|YP_004383518.1|  65 AALNERYFRGS-LSWNSIQYSSRQEHRRGSCNCAA------RTILISDRLASL-PQWVEDYVIVHELAHLIE---P- 129
                                       67999******.999999999**************......********9999.77777889*******986...4. PP

                         SprT-like  83 vrnnpHGaeFkawaak 98 
                                            HG++Fka+ ++
  gi|330507090|ref|YP_004383518.1| 130 ----NHGKRFKALVNR 141
                                       ....599999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.57
# Mc/sec: 860.04
//
Query:       gi|330507091|ref|YP_004383519.1|  [L=98]
Description: hypothetical protein MCON_0935 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0033   18.1   4.4     0.0044   17.7   4.4    1.2  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   4.4   2.4e-07    0.0044       2      71 ..       3      80 ..       2      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.4e-07
                          CxxCxxCC  2 CkeCgaCCkelkvklteedlerlkaaevaeeeeeskkiak.adgrCvfldeetk......lCkiYe...eRpkicrlfp 70
                                      Ck+Cg CC   +  +   + + + + + +++++ +  i k a++ C+++ ++++       C+i++    R + c+ f+
  gi|330507091|ref|YP_004383519.1|  3 CKRCGRCCL--HLDIFVVNPRSILPDGNMNKNDPEAMIHKpAGQMCPHFANKSGpeekiaTCTIHHlpcYRDTPCEKFE 79
                                      *********..555555556667777775666666666567999******9998999999****997777899998776 PP

                          CxxCxxCC 71 a 71
                                      +
  gi|330507091|ref|YP_004383519.1| 80 Q 80
                                      5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 714.57
//
Query:       gi|330507092|ref|YP_004383520.1|  [L=185]
Description: DJ-1/PfpI family protein [Methanosaeta concilii GP6]
Scores for complete 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-49  167.1   0.4    3.9e-49  166.6   0.0    1.4  2  DJ-1_PfpI  DJ-1/PfpI family
     0.0096   16.1   0.1        3.3    7.9   0.0    2.3  2  DUF2007    Putative prokaryotic signal transducing protein
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.027   14.1   0.0    1.4  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 !  166.6   0.0   6.5e-53   3.9e-49       1     164 [.       1     163 [.       1     164 [. 0.99
   2 ?   -2.5   0.1      0.64   3.8e+03      88     103 ..     169     184 ..     168     185 .] 0.75

  Alignments for each domain:
  == domain 1  score: 166.6 bits;  conditional E-value: 6.5e-53
                                       EEEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHHHH CS
                         DJ-1_PfpI   1 kkvlvlladgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGragperl 77 
                                       +k+lv ladg+e++E+i  +d+l+ragi+v++++++++ v+gs+G++v +d+sl+ +++++ D lvlpGG  g  +l
  gi|330507092|ref|YP_004383520.1|   1 MKILVTLADGFEEIEAINVIDILRRAGIDVVTAGLKDGLVEGSHGVRVMPDTSLGRINHKDLDGLVLPGGAPGFINL 77 
                                       69*************************************************************************** PP

                                       HTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEEEESSGGG CS
                         DJ-1_PfpI  78 renekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlvTsrgpga 154
                                        ++e+++++++e  +++k vaaIC +p +L++agvl+gr++T +p+ ++++  + a+++ +rvvvdgn++Tsr+pg+
  gi|330507092|ref|YP_004383520.1|  78 GKDERILNMIRELNQANKYVAAICGAPSVLIKAGVLQGRKATVHPSGEEEV-RSCAQFSSDRVVVDGNIITSRTPGT 153
                                       ***************************************************.999********************** PP

                                       HHHHHHHHHH CS
                         DJ-1_PfpI 155 aiefalelle 164
                                       a+efal+l+e
  gi|330507092|ref|YP_004383520.1| 154 AMEFALKLVE 163
                                       ********98 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.64
                                       HHHHHTT-EEEEETTT CS
                         DJ-1_PfpI  88 kefaekgklvaaICag 103
                                       k++ +++    aIC+g
  gi|330507092|ref|YP_004383520.1| 169 KKMEQAKAQTLAICKG 184
                                       5666777788999998 PP

>> DUF2007  Putative prokaryotic signal transducing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00055       3.3       9      50 ..      12      49 ..       1      52 [. 0.78
   2 !    6.0   0.0    0.0023        14      28      60 ..     140     175 ..     138     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00055
                           DUF2007  9 dpveaelikslLeeagIeavvkdeftssileGalgelpvril 50
                                       ++ea ++ ++L+ agI +v ++   + ++eG+ g   vr++
  gi|330507092|ref|YP_004383520.1| 12 EEIEAINVIDILRRAGIDVVTAGLK-DGLVEGSHG---VRVM 49
                                      57899***************99875.777999976...7776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0023
                           DUF2007  28 vvkdeftssileGalgelp...vrilVaeedleeAr 60 
                                       vv ++  +s+  G++ e++   v+++V ++ +e+A+
  gi|330507092|ref|YP_004383520.1| 140 VVDGNIITSRTPGTAMEFAlklVEVFVGKKKMEQAK 175
                                       666677788888996677777**************8 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 ?   14.1   0.0   4.5e-06     0.027      34      86 ..      51     105 ..      39     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.5e-06
                          GATase_3  34 deslg....edadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlq 86 
                                       d+slg    +d+d ++lpGg +    ++l +++++ + i+e+ +a++ v +iCG   
  gi|330507092|ref|YP_004383520.1|  51 DTSLGrinhKDLDGLVLPGGAPGF--INLGKDERILNMIRELNQANKYVAAICGAPS 105
                                       56666666688**********976..66677778********************755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1318.80
//
Query:       gi|330507093|ref|YP_004383521.1|  [L=160]
Description: TPR repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-44  147.6  12.8      4e-11   42.3   0.2    5.1  5  TPR_1          Tetratricopeptide repeat
    6.6e-37  122.7  10.8    6.4e-09   35.3   0.1    5.1  5  TPR_2          Tetratricopeptide repeat
    1.6e-35  120.5   9.8    6.6e-12   44.9   0.7    4.2  4  TPR_11         TPR repeat
    5.8e-33  110.3   3.3    6.4e-08   32.2   0.0    5.2  5  TPR_8          Tetratricopeptide repeat
    8.1e-31  104.2   7.4    5.7e-07   29.5   0.1    4.4  4  TPR_17         Tetratricopeptide repeat
    3.5e-27   94.8   2.9    6.7e-09   36.3   2.2    3.2  3  TPR_16         Tetratricopeptide repeat
    1.9e-21   74.9   3.2    9.3e-05   22.9   0.0    4.9  5  TPR_14         Tetratricopeptide repeat
    1.2e-18   67.2   9.2    1.1e-07   32.1   0.3    3.8  3  TPR_12         Tetratricopeptide repeat
    2.2e-18   64.9   1.9    8.9e-05   22.3   0.0    5.1  5  TPR_7          Tetratricopeptide repeat
    8.1e-17   61.5   2.0      1e-07   32.3   0.0    2.8  3  TPR_19         Tetratricopeptide repeat
    4.2e-16   58.9   4.7    2.1e-06   27.8   0.1    2.9  4  TPR_9          Tetratricopeptide repeat
    3.5e-12   46.1   1.1       0.31   11.8   0.0    5.2  5  TPR_6          Tetratricopeptide repeat
    3.8e-10   39.3  15.0    0.00044   20.0   0.1    4.4  5  TPR_10         Tetratricopeptide repeat
    8.4e-08   31.6   0.0     0.0017   17.3   0.0    2.2  2  NARP1          NMDA receptor-regulated protein 1
    6.5e-07   29.3   2.4      0.054   13.6   0.1    4.2  4  MIT            MIT (microtubule interacting and transport) do
    1.6e-06   28.2   0.7        1.4    9.8   0.0    5.3  5  TPR_4          Tetratricopeptide repeat
    2.6e-06   27.4   0.1        1.3    9.1   0.0    3.5  3  Fis1_TPR_C     Fis1 C-terminal tetratricopeptide repeat
    4.4e-06   26.4   1.5       0.18   11.3   0.0    3.1  3  EST1_DNA_bind  Est1 DNA/RNA binding domain
      2e-05   24.4   3.7      0.094   12.7   0.0    4.5  4  TPR_3          Tetratricopeptide repeat
     0.0002   21.5   0.6      0.034   14.4   0.0    2.8  3  ANAPC3         Anaphase-promoting complex, cyclosome, subunit
     0.0013   18.6   1.0        1.2    8.9   0.0    3.0  3  DUF5113        Domain of unknown function (DUF5113)
     0.0013   18.5   1.5          3    7.5   0.0    3.7  4  RPN7           26S proteasome subunit RPN7
     0.0041   16.9   0.3        1.7    8.3   0.0    3.1  3  TOM20_plant    Plant specific mitochondrial import receptor s
     0.0042   17.3   0.0         25    5.4   0.0    3.8  3  PPR            PPR repeat
     0.0072   16.8   0.3        5.9    7.3   0.0    2.5  2  BTAD           Bacterial transcriptional activator domain
  ------ inclusion threshold ------
      0.034   14.0   0.1        7.7    6.4   0.0    3.6  4  BPS            BPS (Between PH and SH2)
       0.14   12.0   0.1        9.6    6.1   0.0    2.3  2  Wzy_C_2        Virulence factor membrane-bound polymerase, C-
       0.16   12.8   3.2         58    5.2   0.1    4.2  3  NSF            Aromatic-di-Alanine (AdAR) 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 !   16.9   0.1   6.4e-06    0.0041      19      33 ..       2      16 ..       1      17 [. 0.94
   2 !   41.0   0.0   1.5e-13   9.5e-11       1      34 []      18      51 ..      18      51 .. 0.96
   3 !   42.3   0.2   6.2e-14     4e-11       3      34 .]      54      85 ..      53      85 .. 0.97
   4 !   40.1   0.2     3e-13   1.9e-10       1      34 []      86     119 ..      86     119 .. 0.97
   5 !   13.3   0.2   8.9e-05     0.057       1      30 [.     120     149 ..     120     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.4e-06
                                      HHHHHHHHHHHHSTT CS
                             TPR_1 19 eAleyyekALelnPn 33
                                      +A+++y++A+++nP+
  gi|330507093|ref|YP_004383521.1|  2 QAIQCYDEAIRINPD 16
                                      8*************8 PP

  == domain 2  score: 41.0 bits;  conditional E-value: 1.5e-13
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a a++n+G+ay+ +g++ eA+ + ++A+++nP++
  gi|330507093|ref|YP_004383521.1| 18 AMAWNNKGVAYHLQGNHSEAIRFLDEAIRINPDF 51
                                      679*****************************97 PP

  == domain 3  score: 42.3 bits;  conditional E-value: 6.2e-14
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                                      a++n+Gnay +lg++ eA+ +y+ A+ l+P++
  gi|330507093|ref|YP_004383521.1| 54 AWNNKGNAYANLGNFTEAIHCYDLAIGLDPDD 85
                                      9*****************************96 PP

  == domain 4  score: 40.1 bits;  conditional E-value: 3e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a++n+G a  ++g+y eA+ +y++A+++nP++
  gi|330507093|ref|YP_004383521.1|  86 ALAWNNKGRASGEQGNYTEAIRCYDEAIRINPDY 119
                                       68******************************97 PP

  == domain 5  score: 13.3 bits;  conditional E-value: 8.9e-05
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a a+yn+G a++  g+   A +++ +A el
  gi|330507093|ref|YP_004383521.1| 120 ALAWYNKGEALRATGDSVNADAAFARAREL 149
                                       78******************9999999776 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0    0.0003      0.19      19      33 ..       2      16 ..       2      17 .. 0.93
   2 !   31.9   0.0   1.2e-10   7.6e-08       1      33 [.      18      50 ..      18      51 .. 0.95
   3 !   33.1   0.1   4.9e-11   3.1e-08       3      34 .]      54      85 ..      52      85 .. 0.96
   4 !   35.3   0.1     1e-11   6.4e-09       1      34 []      86     119 ..      86     119 .. 0.96
   5 !   14.4   0.6   4.7e-05      0.03       1      30 [.     120     149 ..     120     151 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                             TPR_2 19 eAleafekAleldPn 33
                                      +A++++++A++++P+
  gi|330507093|ref|YP_004383521.1|  2 QAIQCYDEAIRINPD 16
                                      69************8 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1.2e-10
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPn 33
                                      a a++n G ay  +g++ eA++++++A++++P+
  gi|330507093|ref|YP_004383521.1| 18 AMAWNNKGVAYHLQGNHSEAIRFLDEAIRINPD 50
                                      569*****************************8 PP

  == domain 3  score: 33.1 bits;  conditional E-value: 4.9e-11
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                                      a++n G+ay++lg++ eA+++++ A+ ldP++
  gi|330507093|ref|YP_004383521.1| 54 AWNNKGNAYANLGNFTEAIHCYDLAIGLDPDD 85
                                      8*****************************97 PP

  == domain 4  score: 35.3 bits;  conditional E-value: 1e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a a++n G+a  ++g+y eA++++++A++++P++
  gi|330507093|ref|YP_004383521.1|  86 ALAWNNKGRASGEQGNYTEAIRCYDEAIRINPDY 119
                                       689*****************************96 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 4.7e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a a+yn G+a+++ gd   A +af +A el
  gi|330507093|ref|YP_004383521.1| 120 ALAWYNKGEALRATGDSVNADAAFARAREL 149
                                       689************************987 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.1   1.3e-11   8.2e-09      12      42 .]       2      32 ..       2      32 .. 0.98
   2 !   29.8   0.2   5.6e-10   3.6e-07       3      42 .]      27      66 ..      27      66 .. 0.98
   3 !   32.6   0.6   7.2e-11   4.6e-08       1      36 [.      59      94 ..      59      97 .. 0.96
   4 !   44.9   0.7     1e-14   6.6e-12       6      40 ..      98     132 ..      93     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.3e-11
                            TPR_11 12 eAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      +Ai++Y +A++++Pd a a++n G+ay+ qG
  gi|330507093|ref|YP_004383521.1|  2 QAIQCYDEAIRINPDLAMAWNNKGVAYHLQG 32
                                      7****************************99 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 5.6e-10
                            TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      ay+ qG+  eAi  + +A++++Pd+  a++n G+ay+++G
  gi|330507093|ref|YP_004383521.1| 27 AYHLQGNHSEAIRFLDEAIRINPDFGMAWNNKGNAYANLG 66
                                      79***********************************998 PP

  == domain 3  score: 32.6 bits;  conditional E-value: 7.2e-11
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36
                                      G+ay  +G+++eAi +Y  A+ ldPd+a a++n G 
  gi|330507093|ref|YP_004383521.1| 59 GNAYANLGNFTEAIHCYDLAIGLDPDDALAWNNKGR 94
                                      9********************************996 PP

  == domain 4  score: 44.9 bits;  conditional E-value: 1e-14
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       eqG+y+eAi +Y +A++++Pd+a a+yn G+a+ +
  gi|330507093|ref|YP_004383521.1|  98 EQGNYTEAIRCYDEAIRINPDYALAWYNKGEALRA 132
                                       8******************************9865 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0     0.002       1.3      19      33 ..       2      16 ..       2      17 .. 0.94
   2 !   25.8   0.0   1.2e-08   7.4e-06       3      33 ..      20      50 ..      18      51 .. 0.97
   3 !   32.2   0.0     1e-10   6.4e-08       3      34 .]      54      85 ..      54      85 .. 0.97
   4 !   28.6   0.1   1.5e-09   9.4e-07       3      34 .]      88     119 ..      86     119 .. 0.96
   5 !   11.1   0.0   0.00058      0.37       3      27 ..     122     146 ..     120     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.002
                                      HHHHHHHHHHHHHHH CS
                             TPR_8 19 eAkeyyekaleldpd 33
                                      +A+++y +a++++pd
  gi|330507093|ref|YP_004383521.1|  2 QAIQCYDEAIRINPD 16
                                      69************8 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 1.2e-08
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      a++n+g +y+ +g++ eA+ ++ +a++++pd
  gi|330507093|ref|YP_004383521.1| 20 AWNNKGVAYHLQGNHSEAIRFLDEAIRINPD 50
                                      8*****************************8 PP

  == domain 3  score: 32.2 bits;  conditional E-value: 1e-10
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      a++n+g++y +lg++ eA+ +y  a+ ldpd+
  gi|330507093|ref|YP_004383521.1| 54 AWNNKGNAYANLGNFTEAIHCYDLAIGLDPDD 85
                                      7*****************************96 PP

  == domain 4  score: 28.6 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a++n+g++  ++g+y eA+ +y +a++++pd+
  gi|330507093|ref|YP_004383521.1|  88 AWNNKGRASGEQGNYTEAIRCYDEAIRINPDY 119
                                       8*****************************85 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.00058
                                       HHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyeka 27 
                                       a+yn+g +++ +gd  +A +++ +a
  gi|330507093|ref|YP_004383521.1| 122 AWYNKGEALRATGDSVNADAAFARA 146
                                       8*******************99887 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   8.9e-10   5.7e-07       1      33 [.       6      38 ..       6      39 .. 0.96
   2 !   26.7   0.1   7.1e-09   4.5e-06       3      33 ..      42      72 ..      40      73 .. 0.93
   3 !   21.5   0.1   3.2e-07   0.00021       1      33 [.      74     106 ..      74     107 .. 0.93
   4 !   28.7   0.2   1.6e-09     1e-06       1      32 [.     108     139 ..     108     148 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 8.9e-10
                            TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      +y +a++++P+ a a+nn++++++ +G++ +A+
  gi|330507093|ref|YP_004383521.1|  6 CYDEAIRINPDLAMAWNNKGVAYHLQGNHSEAI 38
                                      8***************************99997 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 7.1e-09
                            TPR_17  3 lkaleldPnnadaynnLAelllknGdlmtAr 33
                                       +a++++P+   a+nn++++++++G++ +A+
  gi|330507093|ref|YP_004383521.1| 42 DEAIRINPDFGMAWNNKGNAYANLGNFTEAI 72
                                      79************************99996 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 3.2e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y  a+ ldP++a a+nn++++  ++G++ +A+
  gi|330507093|ref|YP_004383521.1|  74 CYDLAIGLDPDDALAWNNKGRASGEQGNYTEAI 106
                                       68889999**********************997 PP

  == domain 4  score: 28.7 bits;  conditional E-value: 1.6e-09
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y +a++++P++a a++n++e+l+  Gd+  A
  gi|330507093|ref|YP_004383521.1| 108 CYDEAIRINPDYALAWYNKGEALRATGDSVNA 139
                                       8**************************99765 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   4.2e-11   2.7e-08      15      66 ..       2      50 ..       1      50 [. 0.97
   2 !   23.2   0.0   1.2e-07   7.8e-05       2      43 ..      57      95 ..      56      96 .. 0.96
   3 !   36.3   2.2     1e-11   6.7e-09       3      62 ..      92     148 ..      91     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 4.2e-11
                            TPR_16 15 dAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66
                                      +A+  +++a++ +   Pd a A++++g+a+  qg++ eA+ ++++a+r  pd
  gi|330507093|ref|YP_004383521.1|  2 QAIQCYDEAIRIN---PDLAMAWNNKGVAYHLQGNHSEAIRFLDEAIRINPD 50
                                      89***********...********************************9996 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 1.2e-07
                            TPR_16  2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgda 43
                                      ++++a++++g++++A++ ++ a+ +d   Pd+a A++++g+a
  gi|330507093|ref|YP_004383521.1| 57 NKGNAYANLGNFTEAIHCYDLAIGLD---PDDALAWNNKGRA 95
                                      579***********************...***********97 PP

  == domain 3  score: 36.3 bits;  conditional E-value: 1e-11
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       ++ra  ++g+y++A++ +++a++ +   Pd a A++++g+a+ + g+   A a++++a +
  gi|330507093|ref|YP_004383521.1|  92 KGRASGEQGNYTEAIRCYDEAIRIN---PDYALAWYNKGEALRATGDSVNADAAFARARE 148
                                       5777789******************...********************999999999864 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0023       1.5      19      40 ..       2      23 ..       2      27 .. 0.89
   2 !   18.2   0.0   4.7e-06     0.003      10      39 ..      27      56 ..      24      60 .. 0.90
   3 !   21.5   0.0   4.2e-07   0.00027       8      43 ..      59      94 ..      54      95 .. 0.90
   4 !   22.9   0.0   1.4e-07   9.3e-05      13      43 ..      98     128 ..      92     129 .. 0.92
   5 ?    3.3   0.4      0.29   1.9e+02       3      30 ..     122     149 ..     122     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0023
                            TPR_14 19 eAiallrralalaPddaeawll 40
                                      +Ai+++++a++ +Pd a aw  
  gi|330507093|ref|YP_004383521.1|  2 QAIQCYDEAIRINPDLAMAWNN 23
                                      69*****************965 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 4.7e-06
                            TPR_14 10 allalGdpdeAiallrralalaPddaeawl 39
                                      a+  +G++ eAi+ l++a++ +Pd+  aw 
  gi|330507093|ref|YP_004383521.1| 27 AYHLQGNHSEAIRFLDEAIRINPDFGMAWN 56
                                      67889********************99995 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 4.2e-07
                            TPR_14  8 aeallalGdpdeAiallrralalaPddaeawlllaq 43
                                      + a+++lG++ eAi +++ a+ l+Pdda aw   ++
  gi|330507093|ref|YP_004383521.1| 59 GNAYANLGNFTEAIHCYDLAIGLDPDDALAWNNKGR 94
                                      789****************************87776 PP

  == domain 4  score: 22.9 bits;  conditional E-value: 1.4e-07
                            TPR_14  13 alGdpdeAiallrralalaPddaeawlllaq 43 
                                       ++G++ eAi+++++a++ +Pd a aw+  ++
  gi|330507093|ref|YP_004383521.1|  98 EQGNYTEAIRCYDEAIRINPDYALAWYNKGE 128
                                       68************************98876 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.29
                            TPR_14   3 allalaeallalGdpdeAiallrralal 30 
                                       a++  +eal+a Gd   A a++ ra +l
  gi|330507093|ref|YP_004383521.1| 122 AWYNKGEALRATGDSVNADAAFARAREL 149
                                       68888999*****988888888888664 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   2.2e-08   1.4e-05      22      74 ..       3      47 ..       1      50 [. 0.81
   2 !   32.1   0.3   1.7e-10   1.1e-07       4      75 ..      53     116 ..      50     118 .. 0.91
   3 !   26.5   1.2   9.3e-09     6e-06       3      74 ..      86     149 ..      84     152 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.2e-08
                            TPR_12 22 AlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74
                                      A++++++a++i      p   ++a + +n g +y+++g++ eA+++l ea++i
  gi|330507093|ref|YP_004383521.1|  3 AIQCYDEAIRIN-----P---DLAMAWNNKGVAYHLQGNHSEAIRFLDEAIRI 47
                                      566666665555.....5...59***************************998 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 1.7e-10
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                        a+nn +++++ lg+++eA+ +++ a+ +      pd    a + +n gr+  ++g+y eA++ + ea++i 
  gi|330507093|ref|YP_004383521.1|  53 MAWNNKGNAYANLGNFTEAIHCYDLAIGLD-----PD---DALAWNNKGRASGEQGNYTEAIRCYDEAIRIN 116
                                       5899**********************6666.....76...599**************************985 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 9.3e-09
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       a a+nn + +  ++g+y+eA++++++a++i      pd+   a + +n g+++ra+g+   A +++ +a ++
  gi|330507093|ref|YP_004383521.1|  86 ALAWNNKGRASGEQGNYTEAIRCYDEAIRIN-----PDY---ALAWYNKGEALRATGDSVNADAAFARAREL 149
                                       779999*********************9999.....985...99*************************987 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.51   3.2e+02      17      29 ..       2      12 ..       2      18 .. 0.70
   2 !   16.5   0.0   9.4e-06     0.006       1      29 [.      20      46 ..      20      52 .. 0.86
   3 !   22.3   0.0   1.4e-07   8.9e-05       1      34 [.      54      85 ..      54      87 .. 0.87
   4 !   17.3   0.0   5.3e-06    0.0034       1      29 [.      88     114 ..      88     119 .. 0.87
   5 ?    2.1   0.1      0.38   2.5e+02       1      24 [.     122     145 ..     122     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.51
                             TPR_7 17 eAielyeqsLalt 29
                                      +Ai++y +  a++
  gi|330507093|ref|YP_004383521.1|  2 QAIQCYDE--AIR 12
                                      79999999..544 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 9.4e-06
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLalt 29
                                      a++n +++y+ +G+++eAi+++ +  a++
  gi|330507093|ref|YP_004383521.1| 20 AWNNKGVAYHLQGNHSEAIRFLDE--AIR 46
                                      799*******************99..544 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 1.4e-07
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34
                                      a++n +++y +lG++ eAi +y    a+  dp+d
  gi|330507093|ref|YP_004383521.1| 54 AWNNKGNAYANLGNFTEAIHCYDL--AIGLDPDD 85
                                      799*********************..66666665 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 5.3e-06
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       a++n +r+  ++G+y eAi++y +  a++
  gi|330507093|ref|YP_004383521.1|  88 AWNNKGRASGEQGNYTEAIRCYDE--AIR 114
                                       789*********************..554 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.38
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeq 24 
                                       a++n +++ ++ Gd  +A   + +
  gi|330507093|ref|YP_004383521.1| 122 AWYNKGEALRATGDSVNADAAFAR 145
                                       68999********99888777766 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.6e-05     0.017       9      57 ..       2      50 ..       2      50 .. 0.97
   2 !   32.3   0.0   1.6e-10     1e-07       4      62 ..      31      89 ..      28      94 .. 0.95
   3 !   23.7   0.7   7.9e-08   5.1e-05       3      53 ..      98     148 ..      98     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-05
                            TPR_19  9 eAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57
                                      +A++ + +a+  +p+ a a+ +   a+  +g+  eA++ Ld++ + +pd
  gi|330507093|ref|YP_004383521.1|  2 QAIQCYDEAIRINPDLAMAWNNKGVAYHLQGNHSEAIRFLDEAIRINPD 50
                                      69999**************************************999998 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 1.6e-10
                            TPR_19  4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62
                                      +g++ eA+++l +a+  +p+ + a+ +  +a+ +lg+++eA+ + d +   dpdda ++
  gi|330507093|ref|YP_004383521.1| 31 QGNHSEAIRFLDEAIRINPDFGMAWNNKGNAYANLGNFTEAIHCYDLAIGLDPDDALAW 89
                                      9*****************************************************98876 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 7.9e-08
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       ++g+y+eA++ + +a+  +p++a a+++  eal a+g+   A a+ +++ e
  gi|330507093|ref|YP_004383521.1|  98 EQGNYTEAIRCYDEAIRINPDYALAWYNKGEALRATGDSVNADAAFARARE 148
                                       79************************************9999998888776 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.4e-06   0.00091      13      61 ..       2      50 ..       1      54 [. 0.96
   2 !   18.7   0.0   2.3e-06    0.0014      11      64 ..      34      87 ..      33      88 .. 0.94
   3 !   27.8   0.1   3.2e-09   2.1e-06       4      62 ..      61     119 ..      59     133 .. 0.93
   4 !   11.0   0.1   0.00058      0.37       9      55 ..     100     146 ..      97     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.4e-06
                             TPR_9 13 ralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61
                                      +a+++++  + ++Pd +  +   G++++ +G+ s+A++ L+ +++++pd
  gi|330507093|ref|YP_004383521.1|  2 QAIQCYDEAIRINPDLAMAWNNKGVAYHLQGNHSEAIRFLDEAIRINPD 50
                                      599******************************************9997 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.3e-06
                             TPR_9 11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64
                                      +++a++ ++  + ++Pd    +   G ++a lG++ +A+ + + ++ l+pd++ 
  gi|330507093|ref|YP_004383521.1| 34 HSEAIRFLDEAIRINPDFGMAWNNKGNAYANLGNFTEAIHCYDLAIGLDPDDAL 87
                                      6789999999*****************************************975 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 3.2e-09
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       ++++  ++ +a+ ++++ + l+Pdd+  +   G++  ++G++ +A+++ + +++++pd 
  gi|330507093|ref|YP_004383521.1|  61 AYANLGNFTEAIHCYDLAIGLDPDDALAWNNKGRASGEQGNYTEAIRCYDEAIRINPDY 119
                                       78999999************************************************975 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00058
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeay 55 
                                        ++ +a+++++  + ++Pd +  ++  G +l   G+   A a++ ++
  gi|330507093|ref|YP_004383521.1| 100 GNYTEAIRCYDEAIRINPDYALAWYNKGEALRATGDSVNADAAFARA 146
                                       56789************************999998877777776665 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.44   2.8e+02      18      32 ..       2      16 ..       1      17 [. 0.93
   2 !   11.6   0.0   0.00054      0.34       7      32 ..      25      50 ..      23      50 .. 0.93
   3 ?    5.1   0.0     0.067        43       7      32 ..      59      84 ..      57      85 .. 0.85
   4 !   11.8   0.0   0.00048      0.31       7      32 ..      93     118 ..      91     119 .. 0.89
   5 !    9.4   0.2    0.0028       1.8       2      27 ..     122     147 ..     121     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.44
                                      HHHHHHHHHHHH-TT CS
                             TPR_6 18 kAlealerlikeYPd 32
                                      +A++ +++ i+  Pd
  gi|330507093|ref|YP_004383521.1|  2 QAIQCYDEAIRINPD 16
                                      8**********9998 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00054
                                      HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  7 alsyrklgdtdkAlealerlikeYPd 32
                                      + +y  +g++++A++ l++ i+  Pd
  gi|330507093|ref|YP_004383521.1| 25 GVAYHLQGNHSEAIRFLDEAIRINPD 50
                                      889999****************9998 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.067
                                      HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  7 alsyrklgdtdkAlealerlikeYPd 32
                                      + +y +lg+ ++A+  ++  i   Pd
  gi|330507093|ref|YP_004383521.1| 59 GNAYANLGNFTEAIHCYDLAIGLDPD 84
                                      789***99******999988877776 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00048
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       +++  ++g++++A++ +++ i+  Pd
  gi|330507093|ref|YP_004383521.1|  93 GRASGEQGNYTEAIRCYDEAIRINPD 118
                                       67777899****************98 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerli 27 
                                       A y+ ++++r++gd+ +A +a+ r +
  gi|330507093|ref|YP_004383521.1| 122 AWYNKGEALRATGDSVNADAAFARAR 147
                                       89*********99*********9986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.5   2.2e+03      21      31 ..       3      13 ..       2      14 .. 0.66
   2 !   20.0   0.1   6.8e-07   0.00044       2      31 ..      18      47 ..      17      48 .. 0.94
   3 !   12.7   0.1   0.00014     0.092       6      29 ..      56      79 ..      53      81 .. 0.89
   4 !   15.1   0.3   2.4e-05     0.015       6      31 ..      90     115 ..      86     116 .. 0.94
   5 ?   -1.0   0.1       2.8   1.8e+03       9      30 ..     127     148 ..     124     154 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.5
                            TPR_10 21 Aealleealai 31
                                      A + ++ea++i
  gi|330507093|ref|YP_004383521.1|  3 AIQCYDEAIRI 13
                                      66677777765 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 6.8e-07
                            TPR_10  2 AsslnNLanalrqrgrydeAealleealai 31
                                      A++ nN ++a++ +g++ eA ++l+ea++i
  gi|330507093|ref|YP_004383521.1| 18 AMAWNNKGVAYHLQGNHSEAIRFLDEAIRI 47
                                      8888************************97 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00014
                            TPR_10  6 nNLanalrqrgrydeAealleeal 29
                                      nN +na+ ++g+++eA   ++ a+
  gi|330507093|ref|YP_004383521.1| 56 NNKGNAYANLGNFTEAIHCYDLAI 79
                                      999*************99988776 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 2.4e-05
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       nN ++a  ++g+y+eA + ++ea++i
  gi|330507093|ref|YP_004383521.1|  90 NNKGRASGEQGNYTEAIRCYDEAIRI 115
                                       999*********************97 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 2.8
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       + alr++g+   A a + +a +
  gi|330507093|ref|YP_004383521.1| 127 GEALRATGDSVNADAAFARARE 148
                                       6677777776666666666655 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.7e-06    0.0017     185     259 ..      13      85 ..       2      96 .. 0.87
   2 !   12.4   0.0   8.4e-05     0.054     205     255 ..      99     149 ..      93     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.7e-06
                                       ---SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 185 kepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                        +p  a+ w +  +A+h +  g+ ++A++++d+ai+ +p +   + +K++ +   G++++A+++ + a  lD  D
  gi|330507093|ref|YP_004383521.1|  13 INPDLAMAWNNKGVAYHLQ--GNHSEAIRFLDEAIRINPDFGMAWNNKGNAYANLGNFTEAIHCYDLAIGLDPDD 85 
                                       5666778888888888875..67889*********************************************9888 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 8.4e-05
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                        g++++A+++ d+ai+ +p     +++K++ l+ +Gd  +A ++  +ar+l
  gi|330507093|ref|YP_004383521.1|  99 QGNYTEAIRCYDEAIRINPDYALAWYNKGEALRATGDSVNADAAFARAREL 149
                                       57899********************************************98 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 ?    1.5   0.0      0.48   3.1e+02      22      32 ..       2      12 ..       1      13 [. 0.84
   2 ?    2.0   0.0      0.36   2.3e+02       9      31 ..      23      45 ..      16      47 .. 0.79
   3 !    9.0   0.1    0.0023       1.4      14      32 ..      62      80 ..      56      81 .. 0.86
   4 !   13.6   0.1   8.4e-05     0.054      12      32 ..      94     114 ..      84     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.48
                               MIT 22 eAlelYkeale 32
                                       A+++Y ea++
  gi|330507093|ref|YP_004383521.1|  2 QAIQCYDEAIR 12
                                      59999999996 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.36
                               MIT  9 kkAveeDnagnyeeAlelYkeal 31
                                      +k v +  +gn +eA++   ea+
  gi|330507093|ref|YP_004383521.1| 23 NKGVAYHLQGNHSEAIRFLDEAI 45
                                      6788888899*****99888887 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0023
                               MIT 14 eDnagnyeeAlelYkeale 32
                                      + n gn+ eA+++Y  a++
  gi|330507093|ref|YP_004383521.1| 62 YANLGNFTEAIHCYDLAIG 80
                                      6789************997 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 8.4e-05
                               MIT  12 veeDnagnyeeAlelYkeale 32 
                                         + ++gny eA+++Y ea++
  gi|330507093|ref|YP_004383521.1|  94 RASGEQGNYTEAIRCYDEAIR 114
                                       556689*************96 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0021       1.4       3      26 .]      20      43 ..      18      43 .. 0.85
   2 ?    2.6   0.0      0.45   2.9e+02       6      20 ..      57      71 ..      52      72 .. 0.84
   3 ?    0.5   0.1       2.1   1.4e+03      16      23 ..      82      89 ..      82      90 .. 0.93
   4 ?    2.4   0.0      0.53   3.4e+02       5      24 ..      90     109 ..      86     111 .. 0.78
   5 ?    6.5   0.2     0.024        16       2      23 ..     121     142 ..     120     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0021
                             TPR_4  3 allaLArallalGdldeAraller 26
                                      a  + + a++++G++ eA + l++
  gi|330507093|ref|YP_004383521.1| 20 AWNNKGVAYHLQGNHSEAIRFLDE 43
                                      5667899***********999986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.45
                             TPR_4  6 aLArallalGdldeA 20
                                      + + a++ lG++ eA
  gi|330507093|ref|YP_004383521.1| 57 NKGNAYANLGNFTEA 71
                                      6789********998 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 2.1
                             TPR_4 16 dldeAral 23
                                      d+d+A+a+
  gi|330507093|ref|YP_004383521.1| 82 DPDDALAW 89
                                      89****98 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.53
                             TPR_4   5 laLArallalGdldeArall 24 
                                        + +ra  ++G++ eA +  
  gi|330507093|ref|YP_004383521.1|  90 NNKGRASGEQGNYTEAIRCY 109
                                       567899999******98766 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.024
                             TPR_4   2 rallaLArallalGdldeAral 23 
                                        a ++ ++al a+Gd+  A a+
  gi|330507093|ref|YP_004383521.1| 121 LAWYNKGEALRATGDSVNADAA 142
                                       68999**********9777665 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0021       1.3       9      34 ..      26      51 ..      24      54 .. 0.89
   2 ?    5.9   0.0     0.021        14      10      34 ..      61      85 ..      59      88 .. 0.91
   3 !    8.2   0.0    0.0039       2.5      14      33 ..      99     118 ..      95     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0021
                                      HHHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  9 lGhyklgeYseArryvdalLeiEPen 34
                                      +++  +g++seA r++d  ++i P++
  gi|330507093|ref|YP_004383521.1| 26 VAYHLQGNHSEAIRFLDEAIRINPDF 51
                                      677778******************97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.021
                                      HHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C 10 GhyklgeYseArryvdalLeiEPen 34
                                      +++ lg+++eA  + d  + ++P+ 
  gi|330507093|ref|YP_004383521.1| 61 AYANLGNFTEAIHCYDLAIGLDPDD 85
                                      899**************99999985 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0039
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       +g+Y+eA r+ d  ++i P+
  gi|330507093|ref|YP_004383521.1|  99 QGNYTEAIRCYDEAIRINPD 118
                                       69*****************8 PP

>> EST1_DNA_bind  Est1 DNA/RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00035      0.23       1      36 [.       3      38 ..       3      38 .. 0.95
   2 !   11.3   0.0   0.00027      0.18       1      39 [.      37      75 ..      37      79 .. 0.96
   3 ?    3.7   0.0     0.056        36       1      15 [.     105     119 ..     105     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                                      HHHHHHHHHHH-TTBHHHHHHHHHHHHHTT-HHHHH CS
                     EST1_DNA_bind  1 AlrYYllAaellPsnGepyNQlgviaiysedkldav 36
                                      A+++Y++A+ + P++ ++ N  gv +  ++++ +a+
  gi|330507093|ref|YP_004383521.1|  3 AIQCYDEAIRINPDLAMAWNNKGVAYHLQGNHSEAI 38
                                      899***************************998886 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00027
                                      HHHHHHHHHHH-TTBHHHHHHHHHHHHHTT-HHHHHHHH CS
                     EST1_DNA_bind  1 AlrYYllAaellPsnGepyNQlgviaiysedkldavYyy 39
                                      A+r+ ++A+ + P++G++ N  g  + + ++ ++a+ +y
  gi|330507093|ref|YP_004383521.1| 37 AIRFLDEAIRINPDFGMAWNNKGNAYANLGNFTEAIHCY 75
                                      89*********************************9888 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHH-TTB CS
                     EST1_DNA_bind   1 AlrYYllAaellPsn 15 
                                       A+r+Y++A+ + P++
  gi|330507093|ref|YP_004383521.1| 105 AIRCYDEAIRINPDY 119
                                       89***********96 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.11        68       9      25 ..      26      42 ..      25      43 .. 0.87
   2 !   12.7   0.0   0.00015     0.094      10      36 .]      61      85 ..      59      85 .. 0.87
   3 ?    4.2   0.0     0.071        45      14      25 ..      99     110 ..      98     112 .. 0.87
   4 ?    1.4   0.0      0.53   3.4e+02       7      16 ..     119     128 ..     118     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.11
                                      HHHHHTT-HHHHHHH.. CS
                             TPR_3  9 aefynkkkyqeArelfs 25
                                       +++++++ +eA+ +++
  gi|330507093|ref|YP_004383521.1| 26 VAYHLQGNHSEAIRFLD 42
                                      589**********9866 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00015
                                      HHHHTT-HHHHHHH..HHHHHHH-TT- CS
                             TPR_3 10 efynkkkyqeArelfsYallaildken 36
                                      ++ n ++++eA++ ++  l+  ld+++
  gi|330507093|ref|YP_004383521.1| 61 AYANLGNFTEAIHCYD--LAIGLDPDD 85
                                      6899**********77..*99888876 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.071
                                       TT-HHHHHHH.. CS
                             TPR_3  14 kkkyqeArelfs 25 
                                       +++y+eA+  ++
  gi|330507093|ref|YP_004383521.1|  99 QGNYTEAIRCYD 110
                                       9*******8866 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.53
                                       HHHHHHHTT- CS
                             TPR_3   7 yAaefynkkk 16 
                                       yA + ynk++
  gi|330507093|ref|YP_004383521.1| 119 YALAWYNKGE 128
                                       9*******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 ?    4.4   0.0     0.067        43      30      50 ..      25      46 ..       2      54 .. 0.73
   2 !   14.4   0.0   5.2e-05     0.034      30      81 ..      59     111 ..      52     112 .. 0.95
   3 ?   -1.4   0.0       4.5   2.9e+03      29      42 ..     119     132 ..     116     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.067
                                      HHHHHHTT-HHHHHHHHHCT.S CS
                            ANAPC3 30 AlclylngqykrAyellrka.k 50
                                      + ++ l+g++ +A+++l++a +
  gi|330507093|ref|YP_004383521.1| 25 GVAYHLQGNHSEAIRFLDEAiR 46
                                      5678888888888888888744 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 5.2e-05
                                       HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       + ++ ++g++++A++ ++ a +l++ +  ++  +++++ ++++y eAi+++++
  gi|330507093|ref|YP_004383521.1|  59 GNAYANLGNFTEAIHCYDLAiGLDPDDALAWNNKGRASGEQGNYTEAIRCYDE 111
                                       67999********************************************9986 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.5
                                       HHHHHHHTT-HHHH CS
                            ANAPC3  29 lAlclylngqykrA 42 
                                       +Al+ y+ g+  rA
  gi|330507093|ref|YP_004383521.1| 119 YALAWYNKGEALRA 132
                                       67777777777776 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.012         8       8      37 ..      18      47 ..       7      64 .. 0.88
   2 ?    1.4   0.1      0.39   2.5e+02       6      28 ..      57      79 ..      52      92 .. 0.67
   3 !    8.9   0.0    0.0018       1.2      10      53 ..      88     130 ..      83     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                           DUF5113  8 andYanlayylnvegeyeeALeyldsaley 37
                                      a ++ n + ++  +g+++eA+++ld+a+++
  gi|330507093|ref|YP_004383521.1| 18 AMAWNNKGVAYHLQGNHSEAIRFLDEAIRI 47
                                      77889999*******************975 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.39
                           DUF5113  6 qiandYanlayylnvegeyeeAL 28
                                      ++ n+Yanl++++ +   y+ A+
  gi|330507093|ref|YP_004383521.1| 57 NKGNAYANLGNFTEAIHCYDLAI 79
                                      45567777777777777776665 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0018
                           DUF5113  10 dYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtl 53 
                                       ++ n + ++  +g+y+eA+++ d+a+++   +   +++k  + l
  gi|330507093|ref|YP_004383521.1|  88 AWNNKGRASGEQGNYTEAIRCYDEAIRINPDYALAWYNKG-EAL 130
                                       67788999999***************98878888888876.455 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.024        15      32      62 ..      14      44 ..       3      49 .. 0.87
   2 !    7.5   0.0    0.0047         3      36      60 ..      52      76 ..      46      80 .. 0.88
   3 ?    1.1   0.0      0.44   2.8e+02      48      63 ..      98     113 ..      84     117 .. 0.76
   4 ?    1.0   0.0      0.48   3.1e+02      34      64 ..     118     148 ..     114     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.024
                                      HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7 32 keeirrakldlaehYlkigdleeAlkaysri 62
                                        + ++a+++++  Y+  g+++eA++ + ++
  gi|330507093|ref|YP_004383521.1| 14 NPDLAMAWNNKGVAYHLQGNHSEAIRFLDEA 44
                                      56889**********************9995 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0047
                                      HHHHHHHHHHHHHCT-HHHHHHHHH CS
                              RPN7 36 rrakldlaehYlkigdleeAlkays 60
                                       +a++++++ Y++ g+++eA+ +y 
  gi|330507093|ref|YP_004383521.1| 52 GMAWNNKGNAYANLGNFTEAIHCYD 76
                                      6899*******************97 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.44
                                       HCT-HHHHHHHHHTCC CS
                              RPN7  48 kigdleeAlkaysrir 63 
                                       + g+++eA+++y +++
  gi|330507093|ref|YP_004383521.1|  98 EQGNYTEAIRCYDEAI 113
                                       569999******9953 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  34 eirrakldlaehYlkigdleeAlkaysrire 64 
                                       + + a+++++e    +gd  +A +a++r+re
  gi|330507093|ref|YP_004383521.1| 118 DYALAWYNKGEALRATGDSVNADAAFARARE 148
                                       56778999999999**************998 PP

>> TOM20_plant  Plant specific mitochondrial import receptor subunit TOM20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.82   5.2e+02      53      71 ..       2      20 ..       1      32 [. 0.76
   2 !    8.3   0.0    0.0027       1.7      52      86 ..      35      69 ..      29      88 .. 0.86
   3 ?    4.6   0.0     0.037        24      52     102 ..     103     149 ..      96     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.82
                                      HHHHHHHHHHHH-TT-HHH CS
                       TOM20_plant 53 daiskleeallidPkkhda 71
                                      +ai+ ++ea+ i+P    a
  gi|330507093|ref|YP_004383521.1|  2 QAIQCYDEAIRINPDLAMA 20
                                      6899999999999986655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0027
                                      HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH- CS
                       TOM20_plant 52 qdaiskleeallidPkkhdalWcignaytsfaflt 86
                                      ++ai  l+ea+ i+P    a    gnay   + +t
  gi|330507093|ref|YP_004383521.1| 35 SEAIRFLDEAIRINPDFGMAWNNKGNAYANLGNFT 69
                                      699***************999999****9887665 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHH CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqf 102
                                       ++ai  ++ea+ i+P    a +  g+a  +    t d+ +a   f +a ++
  gi|330507093|ref|YP_004383521.1| 103 TEAIRCYDEAIRINPDYALAWYNKGEALRA----TGDSVNADAAFARAREL 149
                                       68999**********999998888888755....55666666666666655 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.21   1.3e+02      12      28 ..      30      46 ..      27      48 .. 0.81
   2 ?    5.4   0.0     0.039        25       8      24 ..      60      76 ..      59      80 .. 0.91
   3 ?    3.7   0.0      0.14        87      12      28 ..      98     114 ..      94     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.21
                               PPR 12 knGkleeAlelfkeMke 28
                                        G+++eA+++++e ++
  gi|330507093|ref|YP_004383521.1| 30 LQGNHSEAIRFLDEAIR 46
                                      579*********99765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.039
                               PPR  8 sgycknGkleeAlelfk 24
                                      ++y+  G++ eA+ +++
  gi|330507093|ref|YP_004383521.1| 60 NAYANLGNFTEAIHCYD 76
                                      79**********99887 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.14
                               PPR  12 knGkleeAlelfkeMke 28 
                                         G++ eA+++++e ++
  gi|330507093|ref|YP_004383521.1|  98 EQGNYTEAIRCYDEAIR 114
                                       679**********9765 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0092       5.9      75     122 ..      31      78 ..       5      88 .. 0.89
   2 !    7.3   0.4    0.0095       6.1      11     121 ..      91     145 ..      81     159 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0092
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        G ++ea++ l+++++ +P    ++     A+a +G+  eA+  Y+ +
  gi|330507093|ref|YP_004383521.1|  31 QGNHSEAIRFLDEAIRINPDFGMAWNNKGNAYANLGNFTEAIHCYDLA 78 
                                       589****************************************99865 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0095
                                       HHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  11 aagraalaagdpeeaaelleaAlalwrGpaladleagewleaererleelrlealealaeaelrlGraeealaelea 87 
                                       ++gra+ ++g  +ea++++++A+++  + ala  ++ge l+a    +                              
  gi|330507093|ref|YP_004383521.1|  91 NKGRASGEQGNYTEAIRCYDEAIRINPDYALAWYNKGEALRATGDSV------------------------------ 137
                                       56666666666666777666666666666666666555555444433.............................. PP

                                       HHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  88 lvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                                                  A +++ r
  gi|330507093|ref|YP_004383521.1| 138 --------------------------NADAAFAR 145
                                       ..........................33333333 PP

>> BPS  BPS (Between PH and SH2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.99   6.3e+02      25      42 ..       8      25 ..       3      27 .. 0.83
   2 ?    6.4   0.0     0.012       7.7       9      43 ..      26      60 ..      21      65 .. 0.86
   3 ?   -0.6   0.0       1.8   1.2e+03      30      42 ..      81      93 ..      76      98 .. 0.80
   4 ?    2.3   0.0      0.24   1.5e+02      23      42 ..     108     127 ..      95     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.99
                               BPS 25 tEalsaaleegqaWRkks 42
                                       Ea  ++++ + aW  k 
  gi|330507093|ref|YP_004383521.1|  8 DEAIRINPDLAMAWNNKG 25
                                      69999999******8875 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.012
                               BPS  9 VaMDFSGqkgrvIeNptEalsaaleegqaWRkkss 43
                                      Va    G+++  I  + Ea  ++++ g aW  k +
  gi|330507093|ref|YP_004383521.1| 26 VAYHLQGNHSEAIRFLDEAIRINPDFGMAWNNKGN 60
                                      777778999999******************99986 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.8
                               BPS 30 aaleegqaWRkks 42
                                       ++++++aW  k 
  gi|330507093|ref|YP_004383521.1| 81 LDPDDALAWNNKG 93
                                      577899***8875 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.24
                               BPS  23 NptEalsaaleegqaWRkks 42 
                                          Ea  ++++ ++aW  k 
  gi|330507093|ref|YP_004383521.1| 108 CYDEAIRINPDYALAWYNKG 127
                                       5579999*********8774 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.015       9.6     130     180 ..       4      55 ..       1      63 [. 0.76
   2 ?    4.0   0.1     0.065        42     119     172 ..      95     149 ..      84     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                           Wzy_C_2 130 lalarklihlsPepav.ierlilslallGdedeAeqilararalfpeedakw 180
                                       ++ + ++i+  P  a+  ++  +++ l+G ++eA + l++a+ + p+   +w
  gi|330507093|ref|YP_004383521.1|   4 IQCYDEAIRINPDLAMaWNNKGVAYHLQGNHSEAIRFLDEAIRINPDFGMAW 55 
                                       55666666777766652467779******************99988877777 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.065
                           Wzy_C_2 119 lplspenlaaklalarklihlsPepav.ierlilslallGdedeAeqilararal 172
                                       ++ ++ n+ + +  + ++i+  P  a+  ++  ++l ++Gd   A+   arar l
  gi|330507093|ref|YP_004383521.1|  95 ASGEQGNYTEAIRCYDEAIRINPDYALaWYNKGEALRATGDSVNADAAFARAREL 149
                                       5567788888899999999999976542688899999999999999999999865 PP

>> NSF  Aromatic-di-Alanine (AdAR) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.091        58       1      10 [.       3      12 ..       3      13 .. 0.88
   2 ?    1.2   0.1       1.9   1.2e+03       4      12 .]      67      75 ..      67      78 .. 0.83
   3 ?    3.9   0.1      0.25   1.6e+02       1       9 [.     105     113 ..     101     115 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.091
                               NSF  1 AakhyekAae 10
                                      A+++y +A+ 
  gi|330507093|ref|YP_004383521.1|  3 AIQCYDEAIR 12
                                      9*******86 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.9
                               NSF  4 hyekAaeiy 12
                                      ++++A+++y
  gi|330507093|ref|YP_004383521.1| 67 NFTEAIHCY 75
                                      578899998 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.25
                               NSF   1 AakhyekAa 9  
                                       A+ +y +A+
  gi|330507093|ref|YP_004383521.1| 105 AIRCYDEAI 113
                                       566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1009.39
//
Query:       gi|330507094|ref|YP_004383522.1|  [L=615]
Description: hypothetical protein MCON_0940 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 4433.52
//
Query:       gi|330507095|ref|YP_004383523.1|  [L=391]
Description: hypothetical protein MCON_0941 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-80  270.3   0.0    3.1e-80  270.1   0.0    1.0  1  DUF111    Protein of unknown function DUF111


Domain annotation for each model (and alignments):
>> DUF111  Protein of unknown function DUF111
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.1   0.0   1.7e-84   3.1e-80      13     372 ..       1     374 [.       1     375 [. 0.92

  Alignments for each domain:
  == domain 1  score: 270.1 bits;  conditional E-value: 1.7e-84
                            DUF111  13 mllgALldlgadkeele...ealeklgl.eeveleiekvkksgisatkvdveeeehehehrs....laeieeiieaa 81 
                                       mll++L+dl  ++++le   +a+ +l+  + +++++ek  ++gisa+k+dv     e+  rs    +a+ ++++e++
  gi|330507095|ref|YP_004383523.1|   1 MLLSSLVDLIRSPATLEplaKAIGELPNcTAFSYKFEKNCSCGISAKKIDVVLM--EERFRSgivlVASARKLMEEL 75 
                                       99*******977665541116666655479*********************853..333333445599********* PP

                            DUF111  82 slsekvkekalaiferlaeAeakvhgvpleevhfhEvGavDaivdivgaalaldeLgv..ekvvasplalGsGtvrc 156
                                       +ls ++    ++++e l  A ++vh  + +++    v+++ ++++++g a++ld+ g+   +++a+p alGs  v +
  gi|330507095|ref|YP_004383523.1|  76 NLSREASGLVVSVLEDLIAAGERVHRHSFSSCR---VASLKTLFEVLGSAYILDKEGFleGTIYATPPALGSSAVGI 149
                                       **************************9999987...99*******************97667*************** PP

                            DUF111 157 ahGilPvPaPAvlellkelklkl..gevegElvTPTGaAilaalaeefg.slpamkvekiGyGaGkrdleeipnvlR 230
                                       +  ++  PaPA+le+l ++++     +v++El+T TGaA+la+la+ +   +pamk+ ++GyGaG+ dl+ +pnvlR
  gi|330507095|ref|YP_004383523.1| 150 DGIQIGGPAPATLEILCKHQMAYssLPVDSELTTSTGAALLANLADYIVdFYPAMKPIAVGYGAGTSDLNGRPNVLR 226
                                       *****************9999888889********************997899************************ PP

                            DUF111 231 vlleeeeeelekeevvvletniDDlspevlgyvlerLleaGAlDvfltpilmKKgRpavllsvlckeedaeeleell 307
                                       +l + e+ ++++e++++letniDDls+e++gyv++rL+++GA+Dvf+tp++ KK+Rp  ++sv++++++ +++ ++l
  gi|330507095|ref|YP_004383523.1| 227 ILEG-ESFRATRESIILLETNIDDLSGETVGYVMQRLFKEGAVDVFVTPAQGKKNRPVSIISVITDHSACDRMIRVL 302
                                       *995.7788899***************************************************************** PP

                            DUF111 308 fretttlGvReseverlvlereietvetelg....evrvKva...eevvkvkpEyedvkkiAeetglplkev 372
                                       ++et+tlGvR +ev r+v++re    +++++    evrvK++   ++++++kpEyed+kk+Ae  ++pl++v
  gi|330507095|ref|YP_004383523.1| 303 MEETGTLGVRVQEVPRVVADRERVPRQFSIQgkifEVRVKTSyvdGKIISIKPEYEDLKKMAECLNIPLNHV 374
                                       **********************9999988888899*******99777**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2740.33
//
Query:       gi|330507096|ref|YP_004383524.1|  [L=524]
Description: hypothetical protein MCON_0942 [Methanosaeta concilii GP6]
Scores for complete 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   0.3    1.2e-12   47.9   0.1    2.8  2  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
       0.15   12.2   1.7       0.86    9.7   0.1    2.4  2  DUF3826    Protein of unknown function (DUF3826)


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 ?   -1.0   0.0      0.13   1.1e+03       3      30 ..      35      62 ..      33      74 .. 0.75
   2 !   47.9   0.1   1.3e-16   1.2e-12      25     213 ..     192     464 ..     167     465 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.13
                         DDE_Tnp_1  3 krevlivDattvrvpgtkedarwgykgg 30
                                      k+ ++ vD+++vr+++ +++ +++ k++
  gi|330507096|ref|YP_004383524.1| 35 KYLGRNVDGQPVRMRSAPSEIKEKTKKK 62
                                      6777889*********996666655544 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 1.3e-16
                         DDE_Tnp_1  25 wgyk.ggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYasaelldtleek 98 
                                       +gy+  g   + +++ +++d   g+++ ++i+pg+ +d+ +l  +l+ ++++  ++ + ++D+G++s ++l +l ++
  gi|330507096|ref|YP_004383524.1| 192 YGYNrDGVDLPQINMSLIMDKDKGIPVMYDIFPGSISDVSTLSGTLKKIKAHgvQNYVAVMDRGFFSLGNLCELLDN 268
                                       4777555588999**************************************************************** PP

                         DDE_Tnp_1  99 gvdyiirlkkntklyrk....gaeskrrgrlrkhdrnkiltksqkrrnk............................ 143
                                       ++++++++k + + +++      ++  + ++  +++n+++  +  + n                             
  gi|330507096|ref|YP_004383524.1| 269 KISFVMAAKLQLNDLKQlmteAQKDIDDVKYLHKFNNEPIFAKPMTYNIdnmevrgyvyydpkleqnekqtllsrly 345
                                       ********999999999999855555666666666666666666666667777778888888888888888999999 PP

                         DDE_Tnp_1 144 ....................................................skkekgdvyyvtntnsellsaeeva 168
                                                                                           +++  g ++++++ +    +     
  gi|330507096|ref|YP_004383524.1| 346 direellkvrlkknsspqvafkekargfgnffewnvvdnrfdvsikqnavtqRMNKMGKYILFYSGDF---DWLNCL 419
                                       999999999999**************************************764444444444444444...444556 PP

                         DDE_Tnp_1 169 elyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllaln 213
                                        lyr R +iE +Fk lk+   ++ l++++   ++ +++  +l+l 
  gi|330507096|ref|YP_004383524.1| 420 SLYRERDEIEKSFKALKNEIDILPLNTHSEKTTRGFIFVAFLSLI 464
                                       9*************************************9999885 PP

>> DUF3826  Protein of unknown function (DUF3826)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2     0.045   4.1e+02      31      89 ..      31      86 ..      18      93 .. 0.69
   2 ?    9.7   0.1   9.5e-05      0.86     103     143 ..     312     352 ..     275     370 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.045
                                      HHHHHHHHHHHHHHHHHHHHHHH.CS--CHHHHHHHHHHHHHHHHHHHHHHTHHHHHHT CS
                           DUF3826 31 anqyrelndihnerdakikeikeginlatekkksklekaeiaksaklakvhkkllakLs 89
                                       ++ + l    + +++++++++++i+++t+kk+++++ + +        vh++ +++L+
  gi|330507096|ref|YP_004383524.1| 31 RHRSKYLGRNVDGQPVRMRSAPSEIKEKTKKKTAEVKSSFDY---GSILVHQSIMEELN 86
                                      555666666677888888889998877777777777665544...44456777777766 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 9.5e-05
                                       HCTTTHHHHHHHHHHHH-TT--HHHHHHHHHHHHHHHHHHT CS
                           DUF3826 103 kmTygvvavTlkgykeivpdLteeekaqIlkwLkeAReqAi 143
                                        mTy++ ++ + gy    p+L+++ek+++l+ L + Re+ +
  gi|330507096|ref|YP_004383524.1| 312 PMTYNIDNMEVRGYVYYDPKLEQNEKQTLLSRLYDIREELL 352
                                       5************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.58
# Mc/sec: 2730.03
//
Query:       gi|330507097|ref|YP_004383525.1|  [L=149]
Description: ABC transporter substrate-binding protein, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-11   44.8   0.0    1.6e-11   44.3   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   8.8e-16   1.6e-11      99     235 ..       6     149 .]       2     149 .] 0.85

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 8.8e-16
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE.........EEEE-TTSTTTHHHHT CS
                      Peripla_BP_2  99 eqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggade.......ggyvvagsnsyigdllda 166
                                       ++ir +ge++ +e+ a+++++ ++s +++++s+++      ++v ++  + +       g+ +  g ++  ++++++
  gi|330507097|ref|YP_004383525.1|   6 DEIRLVGEVFSREKDADDIASYLESQIDEIRSRTKDVpvE-EKVRMMQLGLSprareggGAGMAWGLDTIESYFIED 81 
                                       89***********************************742.33333333333579***9****************** PP

                                       .S--EESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTS...HHHHTT-EEEE- CS
                      Peripla_BP_2 167 .lgieniaaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflkenpllael...pAvkngrVyald 235
                                        ++++n+++   ++++  +   qil++dpdvi+  +    +    +++l + p +++l    A kngrVyal+
  gi|330507097|ref|YP_004383525.1|  82 tANAKNAYEG--TGAFVVVATGQILTMDPDVIVLPTA---QGYHPASELYTAPYYQNLqelSAMKNGRVYALP 149
                                       9******999..9************************...6666677777777765543339********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 932.72
//
Query:       gi|330507098|ref|YP_004383526.1|  [L=119]
Description: hypothetical protein MCON_0944 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 912.21
//
Query:       gi|330507099|ref|YP_004383527.1|  [L=360]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-19   70.2   0.0    3.3e-19   69.4   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   1.8e-23   3.3e-19      13     235 ..      25     293 ..      17     296 .. 0.80

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.8e-23
                                       HHTT-GGGEEEB-GGG--..GGGGGGT............TS............-BSBESSSB-HHHHHHH--SEEEE CS
                      Peripla_BP_2  13 lalGatdkvvgvdtttsd..pldadklee..........ai............vevgadgeidvEklaalkPDlvil 65 
                                       l lG++dk+vg++ t+ +  ++  ++  +          ++            +++++d  +++E++a+l PD+vil
  gi|330507099|ref|YP_004383527.1|  25 LVLGEEDKIVGIGSTCLPkiWNYTYESVKgepiiyqdgaNPvsllyphlrelpIVANGDAAPNFEAIAELEPDVVIL 101
                                       56788888888888875411444444333566666555511444555555555************************ PP

                                       -GGG...........GGGHHHHHHHS-EEE----TTS.......HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                      Peripla_BP_2  66 skgl........gltdedeellksgiptvivessntg.......eslkeqiralgellgledeaeklvaeidsklaa 127
                                        +g+          ++ ++ ++++ ip v+    n+        + + ++ir +g ++g+e+ea++l++ ++  ++ 
  gi|330507099|ref|YP_004383527.1| 102 RAGDcslryndeTAQKTISSFEALRIPLVVLYAHNFNeeqnkdiSTISDEIRIIGSVFGKEAEADELAEYLEVQVDL 178
                                       ********999888889999*********999999999*************************************** PP

                                       HHHTS-TT....-EEEEEEEETTE.......EEEE-TTSTTTHHHHT.S--EESTTT--STT-EEE-HHHHHHH--S CS
                      Peripla_BP_2 128 aksaidse...kpkpvlvfggade.....ggyvvagsnsyigdllda.lgieniaaeskkseyeeisaEqilasdpd 195
                                       + ++++     ++++vl++g +++     g+  v+g ++  +++++  + +en++ +   +++++++aEq+la dpd
  gi|330507099|ref|YP_004383527.1| 179 VSQRTEDVseeQKPKVLILGLSPSarkegGAGQVFGLDTIESYFIENlVHAENAYHD--PGYFKTLNAEQLLALDPD 253
                                       **9998777777777777777777788889999999999999999988889999888..8***************** PP

                                       EEEEEEHHHHT-S--HHHHT-SHHHHTS...HHHHTT-EEEE- CS
                      Peripla_BP_2 196 vifvsgraeadnktgleflkenpllael...pAvkngrVyald 235
                                       +i+  +    +    + +l e p +++l    Avk ++V al+
  gi|330507099|ref|YP_004383527.1| 254 AIVLCTA---SGYHPPRELYEAPYYQNLqemRAVKDRNVTALP 293
                                       *988777...666667777777765543333888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2711.68
//
Query:       gi|330507100|ref|YP_004383528.1|  [L=279]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete 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   40.6   0.0    6.7e-10   39.5   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.6e-07   31.9   0.0      3e-07   31.0   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    1.2e-06   28.5   0.0    1.7e-06   28.0   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.2e-06   28.3   0.0    3.8e-06   27.6   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    2.1e-05   24.1   0.0    3.4e-05   23.3   0.0    1.3  1  TehB             Tellurite resistance protein TehB
    5.9e-05   22.3   0.0    8.8e-05   21.7   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    7.7e-05   22.5   0.0    0.00018   21.3   0.0    1.6  2  Methyltransf_31  Methyltransferase domain
    0.00037   20.1   0.0    0.00055   19.5   0.0    1.2  1  MTS              Methyltransferase small domain
    0.00053   19.7   0.0     0.0012   18.6   0.0    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00091   18.6   0.0     0.0013   18.1   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G
     0.0021   17.9   0.0     0.0032   17.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0022   17.3   0.1     0.0063   15.9   0.0    1.7  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.003   16.7   0.0     0.0058   15.8   0.0    1.5  2  DREV             DREV methyltransferase
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.017   14.9   0.0    1.3  1  Met_10           Met-10+ like-protein
      0.017   14.6   0.0      0.024   14.1   0.0    1.2  1  SAM_MT           Putative SAM-dependent methyltransferase
      0.032   13.8   0.0      0.067   12.7   0.0    1.5  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
       0.12   11.7   0.0        0.2   11.0   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
       0.13   11.7   0.0       0.21   11.1   0.0    1.3  1  Methyltransf_4   Putative 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 !   39.5   0.0   6.8e-13   6.7e-10       1      89 [.      67     154 ..      67     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 6.8e-13
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTT...TEEEEEEEST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedg...sfDlvvssga 73 
                                       vLd+G+GtGrl++ +++    ++vt+v++s++mle  +  ++++++ n++++q+  ed++ + +   ++ lvv+s++
  gi|330507100|ref|YP_004383528.1|  67 VLDIGAGTGRLAIPFSRIA--SRVTAVEPSAQMLEVLNDDLKRHKIeNIDCIQKRWEDVEIPTDllmKYELVVASFS 141
                                       9***************985..*********************9999************987666666*******999 PP

                                       GGGSSHHHHHHHHHHH CS
                   Methyltransf_25  74 lhhlsdedlekalkei 89 
                                       l +l+   l++a++++
  gi|330507100|ref|YP_004383528.1| 142 LGFLD---LREAVSKM 154
                                       99876...44454444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0     3e-10     3e-07       1      80 [.      68     151 ..      68     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3e-10
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT...-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfedn...sfDlvvssevlhh 73 
                                       Ld+G+GtGrla ++ + ++rv++v++s++ml++ ++  ++ ++ ++++++ + e++ ++ +   ++ lvv+s++l +
  gi|330507100|ref|YP_004383528.1|  68 LDIGAGTGRLAIPFSRIASRVTAVEPSAQMLEVLNDDLKRHKIeNIDCIQKRWEDVEIPTDllmKYELVVASFSLGF 144
                                       8***************99*********************99999***********9988876779999999999999 PP

                                       -CCHHHH CS
                   Methyltransf_11  74 vedpeka 80 
                                       ++ +e++
  gi|330507100|ref|YP_004383528.1| 145 LDLREAV 151
                                       9644444 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.7e-09   1.7e-06      25      94 ..      66     144 ..      33     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.7e-09
                   Methyltransf_23  25 rvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqgkfdlIvlrevl 92 
                                        vLdiG+GtG+l+  +++    vt+v++s ++ e +          ++++ qk  +d +  ++   k++l+v++++l
  gi|330507100|ref|YP_004383528.1|  66 AVLDIGAGTGRLAIPFSRIASRVTAVEPSAQMLEVLNddlkrhkieNIDCIQKRWEDVEIPTDLLMKYELVVASFSL 142
                                       79********************************99777777777777777777777777777777********999 PP

                   Methyltransf_23  93 eh 94 
                                       + 
  gi|330507100|ref|YP_004383528.1| 143 GF 144
                                       85 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   3.8e-09   3.8e-06       1      89 [.      68     154 ..      68     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.8e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       L+iG+GtG+l+ ++ +    +++t+v++s++++e     l++++ +n ++++ + +d++   +   ++ lvvas+ l
  gi|330507100|ref|YP_004383528.1|  68 LDIGAGTGRLAIPFSRI--ASRVTAVEPSAQMLEVLNDDLKRHKIENIDCIQKRWEDVEIPTDLlMKYELVVASFSL 142
                                       8*************999..**************888888888888888888877777665544478*********** PP

                   Methyltransf_12  77 hhlkdirevldni 89 
                                         l d+re+++++
  gi|330507100|ref|YP_004383528.1| 143 GFL-DLREAVSKM 154
                                       998.666666554 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   3.4e-08   3.4e-05      27     120 ..      60     158 ..      46     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.4e-08
                                       CCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHH...HHHHTT-TTEEEEE--GGG.----S-EEEE CS
                              TehB  27 kivkpgkvldlgcgqgrnslylsllgydvtawdknensiaflee...ikekenlknistalydine.aklderydfi 99 
                                        + +p  vld+g g gr ++ +s +   vta++  ++ ++ l++    +++en++ i+ +  d++  ++l  +y+++
  gi|330507100|ref|YP_004383528.1|  60 ALSSPFAVLDIGAGTGRLAIPFSRIASRVTAVEPSAQMLEVLNDdlkRHKIENIDCIQKRWEDVEIpTDLLMKYELV 136
                                       5568999***********************************972223567999999999999985267999***** PP

                                       EEESSGGGS-.GGGHHHHHHHH CS
                              TehB 100 lstvvlmfle.aeripsiienm 120
                                       +++  l fl+ +e+++++ie  
  gi|330507100|ref|YP_004383528.1| 137 VASFSLGFLDlREAVSKMIEAS 158
                                       *********8568999999865 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   8.8e-08   8.8e-05      32      92 ..      65     127 ..      50     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 8.8e-08
                                       SEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHH CS
                            RrnaAD  32 ltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpe 92 
                                         vl+ig+G+G l  ++  +a  v+++E   +++++l++ l+  k e++  +++   + e+p 
  gi|330507100|ref|YP_004383528.1|  65 FAVLDIGAGTGRLAIPFSRIASRVTAVEPSAQMLEVLNDDLKrhKIENIDCIQKRWEDVEIPT 127
                                       57*************************************999666677777777666666665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.8e-07   0.00018       5      81 ..      65     139 ..      61     165 .. 0.78
   2 ?   -2.0   0.0       2.8   2.8e+03      57      91 ..     184     227 ..     174     258 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.8e-07
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled...ekfDli 78 
                                         vlD+G+GtG+l++ +  ++   ++v+ ++ s++++e+ +  +++++++n+   q  +e+ e  +      k+ l+
  gi|330507100|ref|YP_004383528.1|  65 FAVLDIGAGTGRLAIPFS-RI--ASRVTAVEPSAQMLEVLNDDLKRHKIENIDCIQKRWEDVE--IPTdllMKYELV 136
                                       679************999.54..468***********************************55..332233567776 PP

                   Methyltransf_31  79 lsn 81 
                                       ++ 
  gi|330507100|ref|YP_004383528.1| 137 VAS 139
                                       664 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                   Methyltransf_31  57 eFeqgdieeleklledekfDl...........ilsnevlnaladpd 91 
                                        F ++d ++++k+  d  f++           ++ +e l+ ++++d
  gi|330507100|ref|YP_004383528.1| 184 LFGKSDYQTMPKS--DIIFNVlyqmgiypnirVFRFEMLHRFTSLD 227
                                       5667777777754..5557776666666666666666666665554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.5e-07   0.00055      34      91 ..      66     125 ..      58     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.5e-07
                                       EEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-STTT CS
                               MTS  34 kvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevvasdvle 91 
                                        vlD+G+G+G l++ + +  ++  vt+v+ +a+ le+ +  l+++k+e    ++ +++dv  
  gi|330507100|ref|YP_004383528.1|  66 AVLDIGAGTGRLAIPFSRIASR--VTAVEPSAQMLEVLNDDLKRHKIEnidcIQKRWEDVEI 125
                                       49****************9888..9**********************997777777777754 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.2e-06    0.0012      41      94 ..      63     114 ..      52     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeeta 94 
                                           vLD+ aG+G l++   SR a+++++ve +++++++l+++l++ k+e+ ++
  gi|330507100|ref|YP_004383528.1|  63 SPFAVLDIGAGTGRLAI-PFSRIASRVTAVEPSAQMLEVLNDDLKRHKIEN-ID 114
                                       56679************.59****************************998.33 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.3e-06    0.0013      27     118 ..      40     129 ..      30     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHCHHHHHHHGGCS-CCC-...EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEE CS
                              GidB  27 peellerhlldslsvlellkekrd..kviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenve 101
                                         ++le   l s++ ++ +    +  +v+D+G+G G  +ip + +    ++t +e++ +  + L+   ++ k+en+ 
  gi|330507100|ref|YP_004383528.1|  40 YGRMLEEEDLQSIAPFRDIMALSSpfAVLDIGAGTGRLAIPFSRIA--SRVTAVEPSAQMLEVLNDDLKRHKIENID 114
                                       556666666777777766666655445*********9999987555..45789************************ PP

                                       EEES-CCCTTTTT-EEE CS
                              GidB 102 ivearaeekqeeekydv 118
                                        +++r e+   e + d+
  gi|330507100|ref|YP_004383528.1| 115 CIQKRWED--VEIPTDL 129
                                       ********..4444444 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.2e-06    0.0032      63     128 ..      53     115 ..      47     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.2e-06
                                       HHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEE CS
                              PCMT  63 alalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenviv 128
                                       a + + + l+    vL++G+G+G l+  ++r+  +++   ++e ++++ e  +  lk++++en+  
  gi|330507100|ref|YP_004383528.1|  53 APFRDIMALSSPFAVLDIGAGTGRLAIPFSRIASRVT---AVEPSAQMLEVLNDDLKRHKIENIDC 115
                                       56667888999999******************88777...9********************99865 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.5   1.5e+03      26      53 ..       2      29 ..       1      32 [. 0.84
   2 !   15.9   0.0   6.3e-06    0.0063      41     115 ..      57     128 ..      50     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.5
                                      HHHTTTHHHHHHHHHHH--S--TTEEEE CS
                   Ubie_methyltran 26 vlslgihrlWkkfveklvavkrgakvlD 53
                                      + sl+  ++Wk+ + k   + rg++ +D
  gi|330507100|ref|YP_004383528.1|  2 ITSLDWNEVWKERMAKSIESGRGRDCVD 29
                                      57999999****9999988888888777 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 6.3e-06
                                       HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T CS
                   Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfedd 115
                                       +++a  ++  vlD+ +Gtg la+ +s+ +    +v+ ++ +++mL+v ++ lk++   ni+ +q   e+++   d
  gi|330507100|ref|YP_004383528.1|  57 DIMALSSPFAVLDIGAGTGRLAIPFSRIAS---RVTAVEPSAQMLEVLNDDLKRHKIENIDCIQKRWEDVEIPTD 128
                                       788889999*****************9875...6889999***********************999888877665 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.9e-06    0.0058      94     165 ..      63     140 ..      42     165 .. 0.77
   2 ?   -3.3   0.0       3.7   3.7e+03     174     191 ..     236     253 ..     199     266 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.9e-06
                              DREV  94 edkklldlGaGdGeitkrvaptfeevyatelsetmr....drlkkkkynvlsale..lqetdvkldlilclnlldrc 164
                                        +  +ld+GaG G ++   +   ++v a e s +m     d lk++k + +  ++  +++ ++  dl++ ++l+   
  gi|330507100|ref|YP_004383528.1|  63 SPFAVLDIGAGTGRLAIPFSRIASRVTAVEPSAQMLevlnDDLKRHKIENIDCIQkrWEDVEIPTDLLMKYELVVAS 139
                                       56789****************************99722224567777777777666799998888888877776555 PP

                              DREV 165 f 165
                                       f
  gi|330507100|ref|YP_004383528.1| 140 F 140
                                       5 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.7
                              DREV 174 irsalepngrvivalvlP 191
                                         +al +  r ++  vlP
  gi|330507100|ref|YP_004383528.1| 236 KFNALSSTQRSVLKDVLP 253
                                       345666666777777766 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   1.7e-05     0.017     103     163 ..      66     123 ..      56     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                                       EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG- CS
                            Met_10 103 vVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrev 163
                                        V+d+ AG G +aip ++   a+rv a++   +  + l++ +k+ k+e++   i++  ++v
  gi|330507100|ref|YP_004383528.1|  66 AVLDIGAGTGRLAIPFSR--IASRVTAVEPSAQMLEVLNDDLKRHKIENI-DCIQKRWEDV 123
                                       599**************9..8999***********************985.4555555555 PP

>> SAM_MT  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.4e-05     0.024      73     119 ..      65     111 ..      31     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                            SAM_MT  73 ptvlDaTaGlGrDafvlaslGckvtliErhpvvaaLLedglkRakqd 119
                                         vlD  aG Gr a+ ++ +  +vt +E ++ +  +L+d lkR k +
  gi|330507100|ref|YP_004383528.1|  65 FAVLDIGAGTGRLAIPFSRIASRVTAVEPSAQMLEVLNDDLKRHKIE 111
                                       479****************************************8765 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 ?   12.7   0.0   6.7e-05     0.067      57     133 ..      65     143 ..      46     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.7e-05
                   Methyltransf_PK  57 kvaldcGaGiGrvtknlLlkllskvDlvepvekflekakeelaeekkkvgkvyvvglqeft.Pe..egrYdliWiqW 130
                                         +ld+GaG Gr++  +  +++s+v  vep +++le ++++l ++k +  ++++   ++   P     +Y+l+   +
  gi|330507100|ref|YP_004383528.1|  65 FAVLDIGAGTGRLAIPF-SRIASRVTAVEPSAQMLEVLNDDLKRHKIENIDCIQKRWEDVEiPTdlLMKYELVVASF 140
                                       5689*********9875.89**********************98444444444444444431333345666666655 PP

                   Methyltransf_PK 131 cvg 133
                                        +g
  gi|330507100|ref|YP_004383528.1| 141 SLG 143
                                       555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0002       0.2     164     232 ..      66     138 ..      57     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                              PrmA 164 evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk.....eekadviva 232
                                        vlD+G+G+G Lai  +++ a++v+av    + ++v ++ +++ k+e+   ++   e ++       k++++va
  gi|330507100|ref|YP_004383528.1|  66 AVLDIGAGTGRLAIPFSRI-ASRVTAVEPSAQMLEVLNDDLKRHKIENIDCIQKRWEDVEiptdlLMKYELVVA 138
                                       79****************9.689*************99999999999966565444443322233446666666 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00021      0.21       5      58 ..      67     118 ..      63     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                                       EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrg 58 
                                       vl+iG G G++ +  +       + ++E + ++++ +++  ++++++N+ ++++
  gi|330507100|ref|YP_004383528.1|  67 VLDIGAGTGRLAIPFSRIASR--VTAVEPSAQMLEVLNDDLKRHKIENIDCIQK 118
                                       89***********99998765..569*************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1972.33
//
Query:       gi|330507101|ref|YP_004383529.1|  [L=393]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete 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   76.8   0.0    2.7e-21   76.2   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.0   1.5e-25   2.7e-21      42     235 ..     114     327 ..      89     330 .. 0.88

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 1.5e-25
                                       -BSBESSSB-HHHHHHH--SEEEE-GGG...........GGGHHHHHHHS-EEE----TTS.....HHHHHHHHHHH CS
                      Peripla_BP_2  42 vevgadgeidvEklaalkPDlvilskgl........gltdedeellksgiptvivessntg.....eslkeqiralg 105
                                        ++ ++  +++E la lkPD++i+ +g+        g  ++++ ++++gip v+    nt      ++l e++r +g
  gi|330507101|ref|YP_004383529.1| 114 LVAKSGVAPNYEVLAGLKPDVIIVRAGDctfwkdkdGMKKAIDSIESLGIPLVVTYGPNTCekpslDKLSEELRIVG 190
                                       556666779***************9999999999999999***********887777777889************** PP

                                       HHTT-HHHHHHHHHHHHHHHHHHHHTS-TT....-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--.. CS
                      Peripla_BP_2 106 ellgledeaeklvaeidsklaaaksaidse...kpkpvlvfggadeggyvvagsnsyigdlldalgieniaaesk.. 177
                                       +++g+ed+a+kl+  ++s+++ ++++++ +    ++ +l+fg ++    + a+ + ++   ++   +eni  + +  
  gi|330507101|ref|YP_004383529.1| 191 QVFGKEDQADKLARYLESEVDTVRERTRDIpnsEKPSMLLFGLSPQTRGKGAAGDAWGLNTIESYFLENIVNARNaf 267
                                       ***************************99999988899999999998888888888888888888888887777778 PP

                                       ..STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTS...HHHHTT-EEEE- CS
                      Peripla_BP_2 178 ..kseyeeisaEqilasdpdvifvsgraeadnktgleflkenpllael...pAvkngrVyald 235
                                         + + e ++aE++la +pd+i+  +    +    + ++ e p +++l    A+kn+rV al+
  gi|330507101|ref|YP_004383529.1| 268 heQVSTEVVNAERVLAINPDAIVLPTD---FGYHPPREIYEAPYYQNLqelDAIKNKRVMALP 327
                                       779************************...9999999999999887654449*******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2590.23
//
Query:       gi|330507102|ref|YP_004383530.1|  [L=443]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete 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   78.7   0.1      1e-21   77.6   0.1    1.5  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.083   12.8   0.1       0.21   11.5   0.1    1.6  1  VbhA          Antitoxin VbhA
       0.22   11.1   4.3       0.33   10.5   0.6    2.5  2  EF-hand_5     EF hand
       0.55    9.9   2.3        1.5    8.5   0.4    2.5  2  EF-hand_1     EF hand


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   0.1   2.3e-25     1e-21      10     235 ..     107     375 ..     102     376 .. 0.83

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 2.3e-25
                                       HHHHHTT-GGGEEEB-GGG--GGGGGGT...........................TS-BSBESSSB-HHHHHHH--S CS
                      Peripla_BP_2  10 eillalGatdkvvgvdtttsdpldadklee.........................aivevgadgeidvEklaalkPD 61 
                                        + +a G+++k+vg++++t+  +  +                             ai+  g+ g  ++E++a   PD
  gi|330507102|ref|YP_004383530.1| 107 TTMYAFGDAEKIVGKGGCTKSGTTTRSFTYngksyshntpwciegilypkmlddeAIPFSGSIGKENYETIASTNPD 183
                                       567888888888888888888777776555677777777777777777777777788******************** PP

                                       EEEE-GGG..........GGGHHHHHHHS-EEE----TTS.....HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                      Peripla_BP_2  62 lvilskgl.......gltdedeellksgiptvivessntg.....eslkeqiralgellgledeaeklvaeidskla 126
                                       ++i+s+++          +++e  + +g+p+v+ ++         e ++++++ lg+++++ed+ae++++ +++ ++
  gi|330507102|ref|YP_004383530.1| 184 IIIVSTRQwgrdsgeTYLKSIETMRTLGVPVVVLNQVAKYdgdetEAVYTEVELLGKIFEKEDKAEEIINLLKEQVD 260
                                       **********988877888999999*********99987799*********************************** PP

                                       HHHHTS-TT...-EEEEEEEETTE...EEEE-TTSTTTHHHHTS--EESTTT--...STT-EEE-HHHHHHH--SEE CS
                      Peripla_BP_2 127 aaksaidse..kpkpvlvfggade.ggyvvagsnsyigdlldalgieniaaesk...kseyeeisaEqilasdpdvi 197
                                        +ks+++ +  ++k+ +++ +  + ++ +    + ++  +l+ + ieni  +++   +++++  saEq+l+ dpdvi
  gi|330507102|ref|YP_004383530.1| 261 FIKSRTADIpeDEKKSFLYLELSSySAGKGGVAYVDGENILEPILIENIVNAKNefkGEGRQLMSAEQLLTLDPDVI 337
                                       *********996666666666666688888888888899999999999988888898******************** PP

                                       EEEEH...HHHT-S--HHHHT-SHHH...HTSHHHHTT-EEEE- CS
                      Peripla_BP_2 198 fvsgr...aeadnktgleflkenpll...aelpAvkngrVyald 235
                                       +  +    +       +++l +n+ +   ++l A+k+++V +l+
  gi|330507102|ref|YP_004383530.1| 338 YLPTAqgvH------TPDELYNNESFkdlQDLRAIKERKVTGLP 375
                                       *****5554......45555555444000566999999998875 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.6e-05      0.21      19      41 ..      45      67 ..      44      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.6e-05
                              VbhA 19 psaetvadleayvrGeIdadElv 41
                                      +++e++a+ e y +GeI+++El 
  gi|330507102|ref|YP_004383530.1| 45 SDDELKAAEESYKKGEISTEELD 67
                                      699******************96 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.6   7.4e-05      0.33       9      23 ..      37      51 ..      36      52 .. 0.94
   2 ?    1.2   0.2     0.065   2.9e+02      14      22 ..      59      67 ..      57      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.4e-05
                                      -SS-SSCE-HHHHHH CS
                         EF-hand_5  9 DlNgDGkIskeELkt 23
                                      D++gD k+s +ELk+
  gi|330507102|ref|YP_004383530.1| 37 DTDGDNKVSDDELKA 51
                                      9************85 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.065
                                      SCE-HHHHH CS
                         EF-hand_5 14 GkIskeELk 22
                                      G Is eEL 
  gi|330507102|ref|YP_004383530.1| 59 GEISTEELD 67
                                      99*****95 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4   0.00034       1.5      10      24 ..      37      51 ..      36      52 .. 0.93
   2 ?   -0.1   0.1      0.19   8.4e+02      13      22 ..      57      66 ..      57      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00034
                                      TTTSSSEEEHHHHHH CS
                         EF-hand_1 10 DkDgdGkIdfeEfke 24
                                      D+Dgd k++ +E+k+
  gi|330507102|ref|YP_004383530.1| 37 DTDGDNKVSDDELKA 51
                                      9************97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.19
                                      SSSEEEHHHH CS
                         EF-hand_1 13 gdGkIdfeEf 22
                                      + G I+ eE+
  gi|330507102|ref|YP_004383530.1| 57 KKGEISTEEL 66
                                      579******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); 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: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3039.00
//
Query:       gi|330507103|ref|YP_004383531.1|  [L=278]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-30  104.1   0.0    1.2e-29  103.6   0.0    1.2  1  ABC_tran  ABC transporter
    6.8e-14   52.4   0.0    9.5e-09   35.5   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.4e-08   34.5   0.0    9.7e-08   31.7   0.0    2.0  1  SMC_N     RecF/RecN/SMC N terminal domain
    0.00047   20.6   0.0     0.0022   18.4   0.0    2.0  2  AAA       ATPase family associated with various cellular acti
    0.00068   20.2   0.4     0.0012   19.4   0.4    1.3  1  AAA_23    AAA domain
     0.0017   18.0   0.0       0.69    9.5   0.0    2.6  3  AAA_25    AAA domain
  ------ inclusion threshold ------
      0.021   14.9   0.0       0.43   10.6   0.0    2.2  2  AAA_14    AAA domain
       0.04   14.3   0.0      0.056   13.8   0.0    1.4  1  AAA_16    AAA ATPase domain
      0.051   13.3   0.0        2.7    7.6   0.0    2.1  2  AAA_15    AAA ATPase domain
      0.057   13.3   0.0      0.094   12.6   0.0    1.3  1  ATPase_2  ATPase domain predominantly from Archaea
       0.12   12.1   0.0       0.23   11.2   0.0    1.4  1  AAA_29    P-loop containing region of AAA domain
       0.14   12.4   0.0       0.29   11.4   0.0    1.5  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 !  103.6   0.0     8e-33   1.2e-29       1     137 []      17     166 ..      17     166 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 8e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltv 76 
                                       lk vs++++ege+ +++G+nG+GK+tL+k+ ++ lk   G+i++dgkd+k+ + e + k ++++pqe +  fp l +
  gi|330507103|ref|YP_004383531.1|  17 LKGVSFDVNEGELCGLFGPNGCGKTTLFKCCLNFLKSHLGSIRMDGKDVKDLRVEDMAKIVAYVPQEhKPPFPYL-A 92 
                                       799****************************************************************76677777.8 PP

                                       HHH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       re                  e++ ++++al+ lgl+el+d +     ++LSgGq+q++ +ara++++ +l++lDEpt
  gi|330507103|ref|YP_004383531.1|  93 REVvlmgrtprlngffgisrEDKMKAAEALDLLGLTELADYPY----NQLSGGQRQMILMARAIAQETPLMFLDEPT 165
                                       88899999**********9999999************999998....*****************************9 PP

                                       T CS
                                       x RF
                          ABC_tran 137 a 137
                                       +
  gi|330507103|ref|YP_004383531.1| 166 S 166
                                       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 !   14.8   0.0   1.3e-05     0.019       3      18 ..      31      46 ..      29      79 .. 0.79
   2 !   35.5   0.0   6.4e-12   9.5e-09     233     300 ..     134     198 ..     111     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                            AAA_21  3 vliGpNgsGKSnLLda 18
                                      +l GpNg+GK++L+++
  gi|330507103|ref|YP_004383531.1| 31 GLFGPNGCGKTTLFKC 46
                                      699***********96 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 6.4e-12
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                       p+++lS G+++++ ++ a+++   +++l ++DEp + L+ + + r++++++  +++g+ +++ +H+p 
  gi|330507103|ref|YP_004383531.1| 134 PYNQLSGGQRQMILMARAIAQ---ETPLMFLDEPTSALDFSNQIRIWRIMRMVAERGVTILACSHDPN 198
                                       899*********555555554...34****************************************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 !   31.7   0.0   6.5e-11   9.7e-08      28     204 ..      31     202 ..      18     218 .. 0.66

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 6.5e-11
                                       EEEESTTSSHHHHHHHHHHHCT.T.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLG.ersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsisrr 102
                                        + GpNG+GK+ l+   l  L  +  +  +  ++++dl  +       + a++  ++ +e k  ++  + ev+++ r
  gi|330507103|ref|YP_004383531.1|  31 GLFGPNGCGKTTLFKCCLNFLKsHLGSIRMDGKDVKDLRVE-------DMAKIVAYVPQEHKPpFPYLAREVVLMGR 100
                                       689***********987655540223334444555555444.......66666665544444457777777666666 PP

                                       EETTSEEEEEETTE.EE-HHHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingk.evtkkevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                         r +   + i ++ +++ +e  +ll  +++     ++LSgG+++++ +a       ++ +pl++lDe  +aLD++n
  gi|330507103|ref|YP_004383531.1| 101 TPRLNG-FFGISREdKMKAAEALDLLGLTELadyPYNQLSGGQRQMILMA----RAIAQETPLMFLDEPTSALDFSN 172
                                       655555.345544303444666666655554111679********98665....5556899**************** PP

                                       HHHHHHHHHHHCTT.SEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N 176 vkkvaellkekskn.aQfivislreemlek 204
                                         ++ ++++   ++ + ++  s++ ++++ 
  gi|330507103|ref|YP_004383531.1| 173 QIRIWRIMRMVAERgVTILACSHDPNHVSW 202
                                       *99999998766554777777787777665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.5e-06    0.0022       3      51 ..      32      82 ..      30      98 .. 0.79
   2 ?   -0.8   0.0       1.2   1.9e+03      14      66 ..     148     163 ..     128     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                                      EESSTTSSHHHHHHHHHHHHTHEE..EEEETTTCSSSSTTHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelgvef..leisgsellskyvgesekkirelfk 51
                                      l+Gp G+GKT+l k   + l++++  ++++g+++ +  v++++k ++ + +
  gi|330507103|ref|YP_004383531.1| 32 LFGPNGCGKTTLFKCCLNFLKSHLgsIRMDGKDVKDLRVEDMAKIVAYVPQ 82
                                      89******************9887669999999886666666665555554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                       HHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                               AAA  14 lakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDE 66 
                                       +a+a+a+e                                     +  +f+DE
  gi|330507103|ref|YP_004383531.1| 148 MARAIAQE-------------------------------------TPLMFLDE 163
                                       34444444.....................................35555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.4   8.1e-07    0.0012      12      39 ..      19      47 ..      10      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.1e-07
                            AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAi 39
                                      ++++d  +  l  ++GpNG+GKTT++ ++
  gi|330507103|ref|YP_004383531.1| 19 GVSFDVnEGELCGLFGPNGCGKTTLFKCC 47
                                      55566644468899************886 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   0.00046      0.69      31      49 ..      25      43 ..      16      48 .. 0.90
   2 !    5.6   0.0    0.0072        11       2      39 ..     155     192 ..     154     196 .. 0.93
   3 ?   -2.2   0.0       1.7   2.6e+03     110     139 ..     208     236 ..     199     243 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00046
                            AAA_25 31 pagelallaGapgtGKttl 49
                                       +gel+ l+G+ g+GKttl
  gi|330507103|ref|YP_004383531.1| 25 NEGELCGLFGPNGCGKTTL 43
                                      789***************8 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0072
                            AAA_25   2 aeplelsavsvadlaapppprrwlvkgllpagelalla 39 
                                       ++pl++ + ++++l+ + + r w +++++++ ++++la
  gi|330507103|ref|YP_004383531.1| 155 ETPLMFLDEPTSALDFSNQIRIWRIMRMVAERGVTILA 192
                                       68999********************************8 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.7
                            AAA_25 110 gv.eslpLfakdrggtlltadvdaleaaiee 139
                                        v ++++++++++ ++++t+d+  +++  ++
  gi|330507103|ref|YP_004383531.1| 208 VVmKDNRILKEGTSQSVITEDT--MDEIYQD 236
                                       3457899999999999999885..4444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00029      0.43       5      50 ..      30      72 ..      26      93 .. 0.65
   2 ?    2.0   0.0      0.13     2e+02      56      84 ..     147     175 ..     122     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                            AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe 50
                                      + + G+  +GKTtl k ++ + l  k++   i +d ++ k+l+ ++
  gi|330507103|ref|YP_004383531.1| 30 CGLFGPNGCGKTTLFKCCL-NFL--KSHLGSIRMDGKDVKDLRVED 72
                                      6789**********87776.444..466666666665555555332 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.13
                            AAA_14  56 ilek.lkeekktylflDEiqevpewekalk 84 
                                       ++++ +  +++ ++flDE   + ++++ ++
  gi|330507103|ref|YP_004383531.1| 147 LMARaIA-QETPLMFLDEPTSALDFSNQIR 175
                                       3444244.48999*****999999888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.7e-05     0.056      21      51 ..      26      54 ..      15     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.7e-05
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekd 51
                                      +g  el+ l G+ G+GK++l +++l+ l+ +
  gi|330507103|ref|YP_004383531.1| 26 EG--ELCGLFGPNGCGKTTLFKCCLNFLKSH 54
                                      33..78899****************766655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0018       2.7      25      49 ..      29      53 ..      17      84 .. 0.69
   2 ?    3.9   0.0     0.025        37     290     367 ..     131     198 ..      94     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0018
                            AAA_15 25 ltvliGkNnsGKSsilealdlFlnn 49
                                      l  l G+N++GK+++ +    Fl+ 
  gi|330507103|ref|YP_004383531.1| 29 LCGLFGPNGCGKTTLFKCCLNFLKS 53
                                      66688**********9976555553 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.025
                            AAA_15 290 eelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                        + p+n+ + G+++++l++  ++ a++         + +++EP   L  ++q  +++ ++ +a+ +   ++ ++H p
  gi|330507103|ref|YP_004383531.1| 131 ADYPYNQLSGGQRQMILMA--RAIAQET-------PLMFLDEPTSALDFSNQIRIWRIMRMVAERGV-TILACSHDP 197
                                       5678999999999998876..4444444.......88***************************997.899999998 PP

                            AAA_15 367 h 367
                                        
  gi|330507103|ref|YP_004383531.1| 198 N 198
                                       5 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.3e-05     0.094      25      46 ..      32      53 ..      22      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                          ATPase_2 25 iYGpegsGKtaLlkeiienled 46
                                      ++Gp g+GKt+L+k  ++ l++
  gi|330507103|ref|YP_004383531.1| 32 LFGPNGCGKTTLFKCCLNFLKS 53
                                      79************99887754 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.23      13      39 ..      18      44 ..       8      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      +g ++++++ + + l Gp+G GK+Tl+
  gi|330507103|ref|YP_004383531.1| 18 KGVSFDVNEGELCGLFGPNGCGKTTLF 44
                                      45667777555899***********97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.29      10      32 ..      32      54 ..      25      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                            AAA_22 10 vtGesGtGKTtllrrlleqldee 32
                                      ++G+ G+GKTtl +  l+ l+ +
  gi|330507103|ref|YP_004383531.1| 32 LFGPNGCGKTTLFKCCLNFLKSH 54
                                      89************999998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1950.59
//
Query:       gi|330507104|ref|YP_004383532.1|  [L=360]
Description: iron chelate uptake ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete 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-93  312.7  32.0    2.7e-93  312.4  32.0    1.0  1  FecCD            FecCD transport family
    1.1e-06   28.3  22.6    1.1e-06   28.3  22.6    2.4  2  ABC-3            ABC 3 transport family
  ------ inclusion threshold ------
       0.19   10.8   0.7       0.27   10.2   0.7    1.2  1  Potyvirid-P3     Protein P3 of Potyviral polyprotein
        3.1    7.7   9.7         50    3.8   9.7    2.5  1  Gly-zipper_OmpA  Glycine-zipper domain


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.4  32.0     6e-97   2.7e-93       1     311 [.      37     352 ..      36     353 .. 0.98

  Alignments for each domain:
  == domain 1  score: 312.4 bits;  conditional E-value: 6e-97
                             FecCD   1 llllllllslllgavkispsevfeallgka.........dsleaeivlelrlprvlaallvGaaLavaGallQtvtr 68 
                                       lll+++ +++++ga++is+ +v+ ++l++          ++l+++iv+elr+prvl+a++vG aLa+aGa++Q+ +r
  gi|330507104|ref|YP_004383532.1|  37 LLLITVGVAITFGAYSISIVDVYGIVLAHLspfgdlssvTKLHNTIVWELRIPRVLLAVAVGTALATAGAVFQGCFR 113
                                       68899999*******************999999***999999999******************************** PP

                             FecCD  69 NpLadPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsalls 145
                                       NpL++P+ilGissgaa+ga++++++   s+ + ++ l af+++ +a+++ ++lar rk++  ++liLaG+++++++s
  gi|330507104|ref|YP_004383532.1| 114 NPLVEPYILGISSGAAFGAAMGIVF---SSFFLSIQLSAFIFGSMAVAMAYFLARVRKETPIVTLILAGVIIGSIFS 187
                                       ***********************98...678889******************************************* PP

                             FecCD 146 altsllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrl 222
                                       a++s+l+++++++al++i+fwl+G +++a+w++v ll+++++ ++l++++l  kl++l++gd++A++lGvn+e++++
  gi|330507104|ref|YP_004383532.1| 188 AMVSILKYIATDAALREIVFWLMGGFYYATWNDVHLLVPIIIPSFLIMWALGWKLNILSMGDDEARALGVNPEKYKF 264
                                       ***************************************************************************** PP

                             FecCD 223 lllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivta 299
                                       +l+ l++l+t++av+ vG+i++vGL++Ph  r+++g+dhr+++p+sa+lG+  ll++d++ar+l+ ++e+pvgi+t+
  gi|330507104|ref|YP_004383532.1| 265 VLITLATLVTSLAVSTVGIIAWVGLMMPHATRMMLGPDHRYVIPASAMLGGSYLLVCDTMARTLT-SAEIPVGIITS 340
                                       ****************************************************************7.6********** PP

                             FecCD 300 liGapffiylll 311
                                       ++Gap+++yll+
  gi|330507104|ref|YP_004383532.1| 341 ILGAPYLFYLLR 352
                                       **********97 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2     0.095   4.3e+02     153     184 ..      16      46 ..      13      70 .. 0.61
   2 !   28.3  22.6   2.5e-10   1.1e-06      34     238 ..     124     331 ..      90     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.095
                             ABC-3 153 fdeelAkveglsvkllkllllalialavvval 184
                                       fd ++  +eg +v +l+ l+++l  ++v va+
  gi|330507104|ref|YP_004383532.1|  16 FDIAYGYSEGRKVLILSALFVLL-LITVGVAI 46 
                                       56666666666666666554433.34444444 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 2.5e-10
                             ABC-3  34 lgdalsHaalpGvala.yllgvnlllgai.lvgliaavalellkrktklkedtaigivlsvflalglvlvslikk.. 106
                                       ++ + +  a  G+++  ++l+++l++ ++  +++++a +l+ ++++t + + ++ g+++ ++++  + ++++i +  
  gi|330507104|ref|YP_004383532.1| 124 ISSGAAFGAAMGIVFSsFFLSIQLSAFIFgSMAVAMAYFLARVRKETPIVTLILAGVIIGSIFSAMVSILKYIATda 200
                                       6677777788898885377888866666623568889999************************9999999999655 PP

                             ABC-3 107 skvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvva 183
                                       +  ++  +L+G     + +d+ l++ i +  +l++  +  +l ++++  + A++ g++++ +k++l++l  l  ++a
  gi|330507104|ref|YP_004383532.1| 201 ALREIVFWLMGGFYYATWNDVHLLVPIIIPSFLIMWALGWKLNILSMGDDEARALGVNPEKYKFVLITLATLVTSLA 277
                                       5556666788999999****998887777777666666667999********************************* PP

                             ABC-3 184 lqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllSyyldla 238
                                       + +vG+i  + l+ +P at ++l+ + + ++  +++lg   +++  ++  +l  a
  gi|330507104|ref|YP_004383532.1| 278 VSTVGIIAWVGLM-MPHATRMMLGPDHRYVIPASAMLGGSYLLVCDTMARTLTSA 331
                                       *******999976.7*************999999999988877766666555555 PP

>> Potyvirid-P3  Protein P3 of Potyviral polyprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.7   6.1e-05      0.27     224     272 ..     151     198 ..     131     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.1e-05
                      Potyvirid-P3 224 ffktviagvayrirkiklrtPevvalvnallvvslLlsvmvvvqaylld 272
                                       +f  + + +ay++ ++ + tP +v+l+ a  +++ + s mv +  y+  
  gi|330507104|ref|YP_004383532.1| 151 IFGSMAVAMAYFLARVRKETP-IVTLILAGVIIGSIFSAMVSILKYIAT 198
                                       58889999*************.999999999999999988888888754 PP

>> Gly-zipper_OmpA  Glycine-zipper domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   9.7     0.011        50       5      39 ..      96     138 ..      94     141 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.011
                   Gly-zipper_OmpA   5 avGAalGAaaGAavGaitGsa.........GtGAaiGAasGava 39 
                                       avG+al A+aGA++ +   ++         ++GAa GAa+G+v+
  gi|330507104|ref|YP_004383532.1|  96 AVGTAL-ATAGAVFQGCFRNPlvepyilgiSSGAAFGAAMGIVF 138
                                       788888.8899996665545333333333379*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2328.26
//
Query:       gi|330507105|ref|YP_004383533.1|  [L=532]
Description: family 5 extracellular solute-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-76  255.5   0.2    8.9e-76  255.3   0.2    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.3   0.2     5e-80   8.9e-76       2     366 ..      91     439 ..      90     450 .. 0.89

  Alignments for each domain:
  == domain 1  score: 255.3 bits;  conditional E-value: 5e-80
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       +vpaLAes w+ +dD+  y f LRk+++++DG+p+tA Dvvf+++++++++++  + +l      +k++ea+ddytv
  gi|330507105|ref|YP_004383533.1|  91 YVPALAES-WQLEDDA--YVFDLRKNATWQDGEPFTANDVVFTIDYTKEHPYPLVSPKL------VKSAEALDDYTV 158
                                       79******.6988886..***********************************999776......59********** PP

                                       EEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGT.TTSE-BSSSEEEEEEETTT.EEEEEE-TTSTTTSCSSSS CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiakkaaekeddkdkdt.nekpvgtGPYklkefkpgq.kivlernpdYwgggkpkld 153
                                       +++l+  +a+f++++a   + ++++ +++ +++ ++  +e++ g GP+kl+++++ q +  +e+ +dY+  g+pk++
  gi|330507105|ref|YP_004383533.1| 159 KLYLNGSYAPFIEMVAGALPILPEHIYSNVANPAEFLeDEALTGMGPFKLVDYDRAQgTYLYEAYDDYY-LGAPKVK 234
                                       ***********************977777777766651566777***********995666*******9.******* PP

                                       EEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHH CS
                         SBP_bac_5 154 riefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyA 230
                                       +++f  + +++ +aaal++G++ d+a +pp+ +e l +a    +  ++   g+t l++N++k+pf+d+r+RqAl yA
  gi|330507105|ref|YP_004383533.1| 235 QLRFVKV-SNEMAAAALEKGDV-DAATVPPEKAEDLGVAGFDVL--RGSHDGITKLMVNHRKEPFSDARFRQALYYA 307
                                       *******.999999999*****.999999999999877766555..9****************************** PP

                                       S-HHHHHHHCTTTSSEEESSS.STTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETT CS
                         SBP_bac_5 231 iDreeivkavlegyatpansl.lppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltlllasg 306
                                       iDr+++v++vl+gy++ a    l++  +  +++ +++  +ydp+ A +lL+e Gy+++ g+++++++++l  + +  
  gi|330507105|ref|YP_004383533.1| 308 IDRQALVDTVLRGYGIIASPGlLAHDNDLCNPNVETY--DYDPARAGELLEELGYTKD-GQYFTKDGEPLE-MEMLV 380
                                       ***************8887777999999999888876..79***************97.689999955533.34455 PP

                                       SHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHH CS
                         SBP_bac_5 307 spaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnfl 366
                                       +++++++ e+i+qql++ G+kv+++++d+ +++++ v+++dfd++l + g+  +dp+   
  gi|330507105|ref|YP_004383533.1| 381 TATDERAGEMIKQQLEQTGFKVTLRSLDS-KARDSLVSEWDFDLALNSHGGMGADPEILS 439
                                       677899***********************.99999****************999998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 3215.05
//
Query:       gi|330507106|ref|YP_004383534.1|  [L=393]
Description: hypothetical protein MCON_0952 [Methanosaeta concilii GP6]
Scores for complete 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   0.0    3.2e-24   85.4   0.0    1.4  1  TrmO             tRNA-methyltransferase O
    3.2e-14   53.0   0.0    4.7e-14   52.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.1e-12   48.5   0.0    1.9e-12   47.7   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    8.7e-12   45.5   0.0    1.5e-11   44.8   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    3.1e-11   43.1   0.0    5.1e-11   42.4   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.1e-05   26.0   0.0    1.9e-05   25.3   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
      2e-05   24.5   0.0    3.4e-05   23.8   0.0    1.3  1  Methyltransf_8   Hypothetical methyltransferase
      3e-05   23.5   0.0    4.9e-05   22.8   0.0    1.2  1  TehB             Tellurite resistance protein TehB
  ------ inclusion threshold ------
      0.025   13.9   0.0       0.04   13.2   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
      0.027   14.0   0.0      0.042   13.4   0.0    1.3  1  MTS              Methyltransferase small domain
      0.036   13.8   0.0        0.1   12.3   0.0    1.6  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.16   12.1   0.0       0.39   10.8   0.0    1.7  1  FtsJ             FtsJ-like methyltransferase
       0.18   11.5   0.0       0.35   10.5   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
        0.2   11.2   0.0       0.35   10.4   0.0    1.3  1  DOT1             Histone methylation protein DOT1


Domain annotation for each model (and alignments):
>> TrmO  tRNA-methyltransferase O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0   2.5e-27   3.2e-24      20     117 ..     266     362 ..     253     363 .. 0.83

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 2.5e-27
                                       HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E.-TT-.SS.-E.EGGGS--S-SSS-EEEEEEEEEEEETTE CS
                              TrmO  20 peynseealegleefshlwllfvfhenaekklkakvr.pprlggn.ervGvfatRsphRpnpiglsvvklekvegnv 94 
                                       + +  +  l+g+ee+shl++l++ h+  e++ ++++r +p+ +++  + G+f+t sp Rpnp+ ++vv+l+  +gnv
  gi|330507106|ref|YP_004383534.1| 266 EGL--DGILDGIEEYSHLVILYWAHKVPEEG-RSLTRvHPMGREDiPEKGIFCTCSPARPNPVLMTVVHLKGRKGNV 339
                                       555..6789****************997777.55544255443334667**************************** PP

                                       EEEES----TT-EEEEEEE--HH CS
                              TrmO  95 levsgvDlldgtpvlDiKPYvpy 117
                                       lev g+D++dg+pv+DiKPYv++
  gi|330507106|ref|YP_004383534.1| 340 LEVLGLDAVDGSPVIDIKPYVKD 362
                                       ********************986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   3.7e-17   4.7e-14       7     120 ..      45     163 ..      39     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 3.7e-17
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsne 82 
                                       +lDlG+G G++++++ +++g+ ++ + +D +++ai   r +  + gl+n++ e++di   l+  ++d+++D+ +   
  gi|330507106|ref|YP_004383534.1|  45 FLDLGSGPGDYSIRASRLIGDTGRAYALDKNQDAIVDLRDKVVSEGLKNIKAEVCDISGpLP--VKDSCVDICFIST 119
                                       79************************************************************..9**********99 PP

                   Methyltransf_31  83 vl..naladpdki.leeiervlkpggilliedprllaelp....a 120
                                       vl    lad +++ + ei rvlkp+g+l+i +++  +++p     
  gi|330507106|ref|YP_004383534.1| 120 VLhsLNLADVESTlFSEIGRVLKPEGRLAIIECK-KEDQPcgppI 163
                                       9988444555554157******************.5554444441 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0   1.5e-15   1.9e-12       2      97 .]      46     145 ..      45     145 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.5e-15
                                       EEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG.BSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaed.lpfedgsfDlvvssgalh 75 
                                       LdlG G+G++++++++ +g  ++ +++D +++++   r ++ +egl n++ +++d++  lp +d+ +D++++s +lh
  gi|330507106|ref|YP_004383534.1|  46 LDLGSGPGDYSIRASRLIGdTGRAYALDKNQDAIVDLRDKVVSEGLkNIKAEVCDISGpLPVKDSCVDICFISTVLH 122
                                       9****************9779***********************************777*************988** PP

                                       GSSHHHHH.HHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedle.kalkeiarvLkpgG 97 
                                        l+ +d+e ++++ei rvLkp+G
  gi|330507106|ref|YP_004383534.1| 123 SLNLADVEsTLFSEIGRVLKPEG 145
                                       999999862589*********99 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   1.2e-14   1.5e-11       1      96 []      46     149 ..      46     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.2e-14
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCC.TSS-TT-EEEEEEES-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaek.lpfednsfDlvvssevlh 72 
                                       Ld+G+G G ++    +     +r +++D ++ ++   ++k++ egl +++  v+d++  lp++d+ +D++++s vlh
  gi|330507106|ref|YP_004383534.1|  46 LDLGSGPGDYSIRASRLIgdtGRAYALDKNQDAIVDLRDKVVSEGLkNIKAEVCDISGpLPVKDSCVDICFISTVLH 122
                                       8*******99999996666889***********************999999999999669***************** PP

                                       C-...CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  73 hv...edpekalkeiaRvLkpgGllvi 96 
                                        +   +  + +++ei RvLkp+G+l+i
  gi|330507106|ref|YP_004383534.1| 123 SLnlaDVESTLFSEIGRVLKPEGRLAI 149
                                       **9976778899************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 !   42.4   0.0     4e-14   5.1e-11      46     157 ..      40     155 ..      27     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 4e-14
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEE.EE--TTT-TTS-T-EEEEE CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinief.lqanaeeLpfeddsfDvvt 121
                                       +rg  +lD+ +G gD++++ s+ +g++g+   lD n++ +   ++k+  eg +ni+  ++  +  Lp +d   D+  
  gi|330507106|ref|YP_004383534.1|  40 QRGDCFLDLGSGPGDYSIRASRLIGDTGRAYALDKNQDAIVDLRDKVVSEGLKNIKAeVCDISGPLPVKDSCVDICF 116
                                       68999**************************************************9747777899***********9 PP

                                       EES-GG..G-S-HHHHH.HHHHHHEEEEEEEEEEEE--- CS
                   Ubie_methyltran 122 vsfGlr..nvtDklkaL.keayrvlkpGGrlvvlefskv 157
                                       +s  l   n++D + +L  e+ rvlkp Grl ++e  k 
  gi|330507106|ref|YP_004383534.1| 117 ISTVLHslNLADVESTLfSEIGRVLKPEGRLAIIECKKE 155
                                       99988655999*987764899**************9876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.5e-08   1.9e-05       1      99 []      46     147 ..      46     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.5e-08
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..ssfDlvvasn 74 
                                       L++G+G G+++ +  + +  + + +++D +++ai+d + k  +++    +n++ e++d++   +   s +D+ ++s 
  gi|330507106|ref|YP_004383534.1|  46 LDLGSGPGDYSIRASRLIgDTGRAYALDKNQDAIVDLRDKVVSEGL---KNIKAEVCDISGPLPVkdSCVDICFIST 119
                                       8*****************99999*****************999996...6799999998766665999********* PP

                   Methyltransf_12  75 vlhhl..kdir.evldnirklLkpgGrl 99 
                                       vlh l  +d++  ++++i ++Lkp+Grl
  gi|330507106|ref|YP_004383534.1| 120 VLHSLnlADVEsTLFSEIGRVLKPEGRL 147
                                       *******999967788**********97 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   2.6e-08   3.4e-05     106     199 ..      94     201 ..      75     223 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.6e-08
                                       TTEEES-T.TS-S--TT-EEEEEEES---SS-HHH....HHHHHHHHEEEEEEEEEEEEGGG-S..........-HH CS
                    Methyltransf_8 106 ervvacdl.akvPledesvdvavfclslmgtnlad....flkeanrvlkvGGllkvaevksrfe..........svk 167
                                        + ++cd+   +P++d+ vd+  +   l + nlad       e+ rvlk+ G l + e k   +          s +
  gi|330507106|ref|YP_004383534.1|  94 IKAEVCDIsGPLPVKDSCVDICFISTVLHSLNLADvestLFSEIGRVLKPEGRLAIIECKKEDQpcgppidmriSAE 170
                                       35678***668**********998877777776652222468****************9976444445555667889 PP

                                       HHHHHHHCTTEEEEEEE--STTEEEEEEEE-S CS
                    Methyltransf_8 168 lfaraltklGfevkskdlsnkqfvlfefkkve 199
                                        ++r +tk Gf   s      +  l++f+k++
  gi|330507106|ref|YP_004383534.1| 171 ELERTITKHGFRKLSLCDLG-YNYLIQFRKIP 201
                                       999999****9887765444.44577888876 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   3.8e-08   4.9e-05      34     158 ..      45     174 ..      38     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.8e-08
                                       EEEES-TTSHHHHHHHHTT-E...EEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG.---.-S-EEEE.EEESS CS
                              TehB  34 vldlgcgqgrnslylsllgyd...vtawdknensiafleeikekenlknistalydine.akl.derydfi.lstvv 104
                                        ldlg g g  s+  s l  d     a+dkn+++i  l++    e lkni++++ di   + + d   d+  +stv+
  gi|330507106|ref|YP_004383534.1|  45 FLDLGSGPGDYSIRASRLIGDtgrAYALDKNQDAIVDLRDKVVSEGLKNIKAEVCDISGpLPVkDSCVDICfISTVL 121
                                       59*******9999887654441224689*****************************86344514556875256665 PP

                                       GGGS-GGGHHHHHHHHHHTEEEEEEEEEEEEB--SSS--SS--S--B-TTHHHH CS
                              TehB 105 lmfleaeripsiienmqectkvggynlivaamstddvpctvpfsftfkegelke 158
                                         +  a+  +++ +++ +  k+ g   i+   + +d pc  p+ + +  +el +
  gi|330507106|ref|YP_004383534.1| 122 HSLNLADVESTLFSEIGRVLKPEGRLAIIE-CKKEDQPCGPPIDMRISAEELER 174
                                       5555566668899***********866665.67899******999999999976 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.2e-05      0.04      52     112 ..      31      93 ..      25     158 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-05
                                       HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHH..HHHHHTS-SSS CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqakla..kkrvdeldler 112
                                       dl+++ l+l+ G+  Ld+G G G   +ra +  +    +  l k+q + +  +++v +++l++
  gi|330507106|ref|YP_004383534.1|  31 DLVFGGLDLQRGDCFLDLGSGPGDYSIRASRLIGDTGRAYALDKNQDAIVdlRDKVVSEGLKN 93 
                                       789999****************************************99863355666666544 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.3e-05     0.042      31     142 ..      41     154 ..      31     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.3e-05
                                       TCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT..TSTTS-EEEEEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvle..eveekkfdlivs 103
                                       + +  lDlG+G G  ++ + +   ++    ++d++  A+   +  + +++l+ +++  +d+     v++  +d+   
  gi|330507106|ref|YP_004383534.1|  41 RGDCFLDLGSGPGDYSIRASRLIGDTGrAYALDKNQDAIVDLRDKVVSEGLKnIKAEVCDISGplPVKDSCVDICFI 117
                                       455689***************99988779*******************99999666666665511667889999999 PP

                                       ---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETT CS
                               MTS 104 NPPfhagkatelavaeeliaeAkeaLkegGeLliVanrk 142
                                          +h+ +    +v  +l+ e  ++Lk++G+L i+  +k
  gi|330507106|ref|YP_004383534.1| 118 STVLHSLNL--ADVESTLFSEIGRVLKPEGRLAIIECKK 154
                                       999999886..78999*****************997665 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 ?   12.3   0.0     8e-05       0.1      69     132 ..      37     100 ..      30     106 .. 0.94
   2 ?   -2.6   0.0       2.9   3.7e+03     154     174 ..     199     221 ..     197     230 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8e-05
                                       TT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT  69 lelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                       l+l++g+  L++GsG G  +   +rl+g++gr+ ++++ ++ + + + ++  ++l+n++  v D
  gi|330507106|ref|YP_004383534.1|  37 LDLQRGDCFLDLGSGPGDYSIRASRLIGDTGRAYALDKNQDAIVDLRDKVVSEGLKNIKAEVCD 100
                                       789*****************************************************99988877 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.9
                                       S--HHHHHTEE..EEEEEEEEES CS
                              PCMT 154 eiPealidQLk..eGGrlvvPvg 174
                                       +iPe+l+d Lk  +  +++ Pvg
  gi|330507106|ref|YP_004383534.1| 199 KIPEELTDLLKqkDASIVLHPVG 221
                                       79999999997224567777887 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0003      0.39      20      58 ..      40      84 ..      22     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                                      -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS......H CS
                              FtsJ 20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm......a 58
                                      ++g+ ++Dlg++PG +s  +++ +g +g+ +a+D ++       +
  gi|330507106|ref|YP_004383534.1| 40 QRGDCFLDLGSGPGDYSIRASRLIGDTGRAYALDKNQDaivdlrD 84
                                      477889******************999********8874553331 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 ?   10.5   0.0   0.00027      0.35       4      69 ..      37     102 ..      35     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00027
                                       H---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CT CS
                   Methyltr_RsmB-F   4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDar 69 
                                       L++q ++ +lDl ++PG      + l+ ++g+ +A+d+n+  +  + + +   g++n++    D++
  gi|330507106|ref|YP_004383534.1|  37 LDLQRGDCFLDLGSGPGDYSIRASRLIGDTGRAYALDKNQDAIVDLRDKVVSEGLKNIKAEVCDIS 102
                                       78999***********************************99999999998888888877666665 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00027      0.35      35      61 ..      34      60 ..      30      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                                      HHHTT--TT-EEEEES-TTSHHHHHHH CS
                              DOT1 35 ldkvnlkkedvFvDLGSGvGnvvlqaa 61
                                      +  ++l++ d+F+DLGSG G+  + a+
  gi|330507106|ref|YP_004383534.1| 34 FGGLDLQRGDCFLDLGSGPGDYSIRAS 60
                                      55689***************9988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.23s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2856.97
//
Query:       gi|330507107|ref|YP_004383535.1|  [L=264]
Description: tungsten formylmethanofuran dehydrogenase subunit E [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-31  108.5   0.0    3.5e-31  108.0   0.0    1.3  1  FmdE          FmdE, Molybdenum formylmethanofuran dehydrogena
  ------ inclusion threshold ------
      0.028   14.3   2.2       0.15   12.0   2.2    2.1  1  zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.0   0.0   3.9e-35   3.5e-31       1     131 [.      53     196 ..      53     197 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 3.9e-35
                                       HHSS--CHHHHHHHHHHHHHHCC....-TT..SSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEE CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeeg..deelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltfkk 75 
                                       +HGH+Cpg +lG++++ + l+ lg++  ++   e+l+a+vet++C++D++q++ gctlG+++l+++d+g+ a+tf  
  gi|330507107|ref|YP_004383535.1|  53 IHGHFCPGSALGVMASVHGLNLLGLDSISSdgLEDLMAVVETNACFADGVQAVSGCTLGNNALVYRDLGRLAVTFAI 129
                                       5************************98888999******************************************** PP

                                       TTT-EEEEEEE-...........CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHHHHHS.HHHHE CS
                              FmdE  76 rktgkavrlklk...........eelpelreklakgkakeekeeeeleeeleeaikkilnapeeelf 131
                                       r++ ++vr++++           +e+  l+ek++k+++  ++e+++++++ ++a+  ++++p +elf
  gi|330507107|ref|YP_004383535.1| 130 RGKETGVRIRVQpdfsssvakasPEFYPLMEKVIKNREGGAREKAAFRKAGRQAAFGVIQLPFDELF 196
                                       *9999999999999************************9999***********************99 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 ?   12.0   2.2   1.7e-05      0.15       4      19 ..     213     230 ..     210     243 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                      zf-dskA_traR   4 gs..CeeCGEpIpeaRlr 19 
                                       +s  C+ CGE+I+  + +
  gi|330507107|ref|YP_004383535.1| 213 ESivCSNCGEMIMATKTV 230
                                       4558*********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1888.47
//
Query:       gi|330507108|ref|YP_004383536.1|  [L=173]
Description: PadR family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-15   55.0   0.1    1.1e-14   54.1   0.1    1.5  1  PadR             Transcriptional regulator PadR-like family
     0.0074   16.5   0.1      0.085   13.1   0.0    2.4  2  PaaX             PaaX-like protein
      0.009   15.8   0.0      0.015   15.1   0.0    1.4  1  DUF4364          Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.013   16.3   0.9        3.8    8.4   1.3    2.3  2  DUF3349          Protein of unknown function (DUF3349)
      0.018   15.4   0.0      0.036   14.4   0.0    1.5  1  Penicillinase_R  Penicillinase repressor
      0.036   14.3   0.0      0.066   13.4   0.0    1.5  1  SgrR_N           Sugar transport-related sRNA regulator N-ter
      0.055   13.5   0.1       0.15   12.1   0.1    1.9  1  HTH_45           Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.1   4.3e-18   1.1e-14       1      74 [.      19      85 ..      19      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 4.3e-18
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      +L+++++++  Gy+iik++e+ s g  ++s Gs+Yp+Lk++e+eg+++++ e+      + yY lT+ G++ +a
  gi|330507108|ref|YP_004383536.1| 19 MLHIMKDGEASGYDIIKKVEAIS-G-KKPSTGSIYPLLKKMEREGWISGRAED-----GKTYYSLTEIGKEHVA 85
                                      69********************7.5.6***********************998.....699*********9875 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   3.3e-05     0.085      44      68 ..      54      78 ..      46      80 .. 0.91
   2 ?    0.3   0.0      0.32   8.1e+02      16      33 ..     125     142 ..     121     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.3e-05
                              PaaX 44 lsRlakaGwlvrekegrrsfYrLsd 68
                                      l  ++++Gw+ + +e  + +Y+L++
  gi|330507108|ref|YP_004383536.1| 54 LKKMEREGWISGRAEDGKTYYSLTE 78
                                      6789***********99*******8 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.32
                              PaaX  16 prggaiwlgsLirllael 33 
                                       +rg  +++++ i+lla+l
  gi|330507108|ref|YP_004383536.1| 125 HRGMRVPVKEQIELLAPL 142
                                       67889**********987 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   5.8e-06     0.015      39      88 ..      53     101 ..      49     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.8e-06
                           DUF4364  39 alseLvesglieeeekenktlykiTekGketlelfenripksirekidey 88 
                                        l++++ +g i+ + +++kt+y++Te Gke + ++ n++  ++ +k+ ++
  gi|330507108|ref|YP_004383536.1|  53 LLKKMEREGWISGRAEDGKTYYSLTEIGKEHVAQI-NEVKHDFIKKLHQS 101
                                       6899**************************99976.45555555555555 PP

>> DUF3349  Protein of unknown function (DUF3349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.013        34      52      91 ..      23      62 ..       3      65 .. 0.83
   2 ?    8.4   1.3    0.0015       3.8      27      86 ..     102     163 ..      82     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.013
                                      .SSS.BSHHHCHHHHHHHCTS---HHHHHHHHHHHHTTT- CS
                           DUF3349 52 eadeavdeedieelitkvteeepseedvarVaarLaaggw 91
                                       +d++ +  di + ++++  ++ps   +  + ++++++gw
  gi|330507108|ref|YP_004383536.1| 23 MKDGEASGYDIIKKVEAISGKKPSTGSIYPLLKKMEREGW 62
                                      4567889999****************************** PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0015
                                       HHHHCTT--HHHHHHHHHHHHHH--.SSS.BSH..HHCHHHHHHHCTS---HHHHHHHHHHH CS
                           DUF3349  27 lalLrrrLsdeevkevaeelvaeaaeadeavde..edieelitkvteeepseedvarVaarL 86 
                                       +al +++  d++v+++++++ + ++    +v+e  e ++ li++v+++  +++d +rV++ +
  gi|330507108|ref|YP_004383536.1| 102 IALASETFEDADVQDLMKDMHDLHRGMRVPVKEqiELLAPLIHQVADHLETDTDRERVRSVI 163
                                       577888999**********9999863444443311346789*****************9876 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.4e-05     0.036       8      92 ..      18     102 ..      15     123 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHS-EEHHHHHHT--GG..G---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXXXXXXX CS
                   Penicillinase_R   8 vmeilwekgeatvkevveeleee..kelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavasavkqlldk 82 
                                       +m ++ + gea+  ++++++e+   k+++  ++  ll+++++ g++s + e  ++ Ys + +  +    + +++ + 
  gi|330507108|ref|YP_004383536.1|  18 IMLHIMKDGEASGYDIIKKVEAIsgKKPSTGSIYPLLKKMEREGWISGRAEDGKTYYSLT-EIGKEHVAQINEVKHD 93 
                                       899****************9987335567777***************9888666645543.3333233344555555 PP

                                       XXXXXXXXXX CS
                   Penicillinase_R  83 lfegsvkelv 92 
                                       +++ ++++ +
  gi|330507108|ref|YP_004383536.1|  94 FIK-KLHQSI 102
                                       553.444444 PP

>> SgrR_N  Sugar transport-related sRNA regulator N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.6e-05     0.066      39     100 ..      53     114 ..      46     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                            SgrR_N  39 lLkkmqeegwleWqpevGRgkrsrLtfllepeelqeqlaeklleqgkiekalalldkdkaal 100
                                       lLkkm++egw++ ++e G    s  ++ +e+ + ++++ ++++++ +   ala    ++a +
  gi|330507108|ref|YP_004383536.1|  53 LLKKMEREGWISGRAEDGKTYYSLTEIGKEHVAQINEVKHDFIKKLHQSIALASETFEDADV 114
                                       8*******************999999999999999999999998766665555444444444 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.9e-05      0.15      39      73 ..      53      91 ..      12      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.9e-05
                            HTH_45 39 YLdmLvekgli....kkskekYvlTekGlelleklkele 73
                                       L+++  +g i    ++ k+ Y+lTe G+e + +++e++
  gi|330507108|ref|YP_004383536.1| 53 LLKKMEREGWIsgraEDGKTYYSLTEIGKEHVAQINEVK 91
                                      689999*****9998889999***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1330.64
//
Query:       gi|330507109|ref|YP_004383537.1|  [L=124]
Description: hypothetical protein MCON_0955, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1071.06
//
Query:       gi|330507110|ref|YP_004383538.1|  [L=201]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-31  109.6   0.0    1.5e-31  109.1   0.0    1.1  1  DDE_3     DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.063   13.5   0.0       0.12   12.5   0.0    1.5  1  rve_2     Integrase core domain
       0.11   12.3   0.3        2.3    8.1   0.0    2.5  3  rve_3     Integrase core domain


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.1   0.0   2.5e-35   1.5e-31      15     145 ..      10     171 ..       2     172 .. 0.96

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 2.5e-35
                             DDE_3  15 vrrrawakkGkrer.leeygrrgrvnligaldekgglaf.vtfeetlnaedfaeflerlletalqakkivlilDnas 89 
                                         +  ++ +Gk er ++ey+r+g++++i+++ +++g++  + + +t+n++df+ ++++++e+ l+  +++++ Dn++
  gi|330507110|ref|YP_004383538.1|  10 KHPGLPMAPGKVERrEFEYIRHGTQSFIVSFAVAKGKVDtISCGDTRNEDDFVSHIKEVVERSLSTSRWHFVADNLN 86 
                                       5666799********************************99************************************ PP

                             DDE_3  90 iHkseslrelveee.............................adrlellylPpySPelNpiEivwsklkrellkrr 137
                                       iHksesl+++v++                              +++++++y+P ++++ N++Ei++s+l+r+ll+r+
  gi|330507110|ref|YP_004383538.1|  87 IHKSESLVRYVADVsdldidlgikgrdgilksietresfladpSHSIVFHYTPIHASWMNQVEIWFSILVRKLLRRA 163
                                       ***************************************************************************** PP

                             DDE_3 138 sfksldeL 145
                                       sf s+ +L
  gi|330507110|ref|YP_004383538.1| 164 SFASINDL 171
                                       ****9998 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     2e-05      0.12       3      36 ..     151     184 ..     149     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
                             rve_2   3 fFgsLKtElvygetfktleeleaaiedYIewYNn 36 
                                        F +L ++l++ + f++++ l+a++  ++e++N+
  gi|330507110|ref|YP_004383538.1| 151 WFSILVRKLLRRASFASINDLNAKVLAFVEYFNK 184
                                       699999***************************7 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.041   2.4e+02       5      21 ..       7      23 ..       4      28 .. 0.88
   2 ?   -3.4   0.0       1.5   8.9e+03      19      33 ..      69      83 ..      67      93 .. 0.65
   3 ?    8.1   0.0   0.00038       2.3      24      55 ..     153     184 ..     131     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.041
                             rve_3  5 lsyiapgkPqqNglvEs 21
                                      l++ +pg P+  g+vE+
  gi|330507110|ref|YP_004383538.1|  7 LERKHPGLPMAPGKVER 23
                                      56789***********9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                             rve_3 19 vEsfngtlrdellne 33
                                      vE++  t r +++  
  gi|330507110|ref|YP_004383538.1| 69 VERSLSTSRWHFVAD 83
                                      677777766666554 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00038
                             rve_3  24 gtlrdellneelfrslaearekleawredYNt 55 
                                         l ++ll + +f s++++++k+ a++e++N+
  gi|330507110|ref|YP_004383538.1| 153 SILVRKLLRRASFASINDLNAKVLAFVEYFNK 184
                                       556678899999*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1553.76
//
Query:       gi|330507111|ref|YP_004383539.1|  [L=375]
Description: family 5 extracellular solute-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-69  234.1   1.7      3e-69  233.8   1.7    1.0  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.8   1.7   1.7e-73     3e-69       2     304 ..      75     366 ..      74     372 .. 0.89

  Alignments for each domain:
  == domain 1  score: 233.8 bits;  conditional E-value: 1.7e-73
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       +vpaLAe  w+  +D   y f+LRkgv++ DG+p+tA+Dv+f+f++++d++++   +s +      +k+ea+d++tv
  gi|330507111|ref|YP_004383539.1|  75 FVPALAET-WKYLPDENAYLFHLRKGVTWNDGEPFTADDVAFTFQYTKDHPYPLVDSSII------DKAEAIDENTV 144
                                       79******.799******************************************998886......8********** PP

                                       EEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-B.SSSEEEEEEETTTEEE.EEE-TTSTTTSCSSSS CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvg.tGPYklkefkpgqkiv.lernpdYwgggkpkld 153
                                       +++l+k +a+fl  +a  ++ ++ + + + +d+d++++ek  + tGP++l+++++ q +  +++n+dY+ +g p+++
  gi|330507111|ref|YP_004383539.1| 145 KIVLTKSYAPFLDQVAGAQPILPLHIYRNMSDPDDYKDEKALTgTGPFRLVDYDQTQGTYfYKANEDYY-QGSPRVK 220
                                       **********9999999999988878888888888877776555***********997664888****9.******* PP

                                       EEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHH CS
                         SBP_bac_5 154 riefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyA 230
                                       +++f  + +++ + a+l++G+i d+a++p++  e+l e++g ++  ++   ++  +a+N+kk+pf+d+r+R+A+ yA
  gi|330507111|ref|YP_004383539.1| 221 QLKFVKV-SNEMASASLKKGDI-DAASVPAETTEPL-EKEGFDI--KESHDTTMIMAINHKKEPFSDVRFRKAIYYA 292
                                       *******.999999999*****.8889999999997.4555555..4677777788********************* PP

                                       S-HHHHHHHCTTTSSEEESSS.STTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETC..EEEEEEEEE CS
                         SBP_bac_5 231 iDreeivkavlegyatpansl.lppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrek..klkltllla 304
                                       iDr+++v+++l+g + ++    lp+ +p+++++ +++   +dp+kA++lLke Gy ++ g++++++  +l++ ll++
  gi|330507111|ref|YP_004383539.1| 293 IDRQALVDIFLRGFGCAGCPGiLPSDHPWYNPDQEQY--SFDPAKAEELLKEMGYSKD-GQYFSKDgeRLEIELLVQ 366
                                       ***************9998888********9998886..79***************97.689999977666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2682.42
//
Query:       gi|330507112|ref|YP_004383540.1|  [L=463]
Description: MATE efflux family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-43  147.0  41.8    1.6e-26   92.9  14.4    2.6  3  MatE             MatE
    4.5e-06   25.5  17.8    4.5e-06   25.5  17.8    2.8  2  MurJ             Lipid II flippase MurJ
    4.3e-05   23.6  23.5    4.3e-05   23.6  23.5    4.7  5  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
       0.12   12.6   0.6       0.57   10.4   0.2    2.4  2  Holin_SPP1       SPP1 phage holin


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 !   92.9  14.4   3.6e-30   1.6e-26       1     161 []      24     184 ..      24     184 .. 0.99
   2 ?   -3.9   0.2       2.1   9.2e+03      51      60 ..     201     210 ..     197     222 .. 0.53
   3 !   64.8  14.2   1.6e-21   7.1e-18       2     161 .]     250     410 ..     249     410 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 3.6e-30
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+++  + + +++l+dt++vg+lg+  lAa+s++++++ ++  ++ ++++++++++++++G++n++++k+ +  +++
  gi|330507112|ref|YP_004383540.1|  24 PMIFGTISMIIFNLTDTFFVGQLGTGQLAAMSFTFPVVLFVNNLAHAVAIGASAVISHSIGEGNRNKVKRLTTDSIV 100
                                       99*************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       l+lll  +i+ ++ll +++++++++++ e++ ++++y+ i  lg++++++ +v +++ r+ag+tk+p++i+++++  
  gi|330507112|ref|YP_004383540.1| 101 LSLLLVGFIVPIGLLTINPLFHFLGASLEIITYIREYMVIWYLGLVFIVVPMVGTNAIRAAGDTKTPAFIMMFAAGA 177
                                       ***************************************************************************** PP

                              MatE 155 niplnyl 161
                                       ni+l+++
  gi|330507112|ref|YP_004383540.1| 178 NIILDPI 184
                                       ****986 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.1
                              MatE  51 alttlvgqal 60 
                                       a++t++++al
  gi|330507112|ref|YP_004383540.1| 201 AMATVIARAL 210
                                       4444444433 PP

  == domain 3  score: 64.8 bits;  conditional E-value: 1.6e-21
                              MatE   2 ialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglil 78 
                                        a ++++  l   ++t +v+ +gs+a+A+ +ia++  s+  +++++l++ + +++gq++Ga++f+r+k  +  +  +
  gi|330507112|ref|YP_004383540.1| 250 NAGAMIITPLAAGFITRIVATYGSDAVAGFGIATRMDSFALIVIMALASVVGPFIGQNWGAGKFDRIKSGTKFSYRF 326
                                       567888888999999************************************************************** PP

                              MatE  79 llllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.ll 154
                                       +l+ +li++++  ++     s+f++d+ev++++  yl+i+ +g+ ++++  ++++++   +k+  +++++l  + +l
  gi|330507112|ref|YP_004383540.1| 327 SLIWGLIMFIVFAFLGGTVGSIFSDDPEVISVTGLYLSIVPIGYGLYGIVAISTSAMSVLKKPIHAAILTLTQAfIL 403
                                       ***************************************************************************** PP

                              MatE 155 niplnyl 161
                                        ip++y+
  gi|330507112|ref|YP_004383540.1| 404 YIPMAYV 410
                                       *****97 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5  17.8     1e-09   4.5e-06     198     405 ..      16     224 ..      12     258 .. 0.78
   2 ?   -6.2  11.8         4   1.8e+04     252     403 ..     294     442 ..     257     459 .. 0.57

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1e-09
                              MurJ 198 kkflklllptllgvsvsqlnllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlL....PrlSrsakekd 270
                                       k+++ l +p+++g  + ++  l+dt++   l +g +++++++     +P+ lf++ ++ ++     + +S s  e++
  gi|330507112|ref|YP_004383540.1|  16 KTLIMLTIPMIFGTISMIIFNLTDTFFVGQLGTGQLAAMSFT-----FPVVLFVNNLAHAVAigasAVISHSIGEGN 87 
                                       567788888888888888888888888888888888777765.....666666665555443233389********* PP

                              MurJ 271 edevrdllsqairltllll.ipvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalvklllrvfY 346
                                        ++v++l+ ++i l+lll+ + v +gll      ++ lf     s e ++++ e + ++ lgL+++ +  + +++  
  gi|330507112|ref|YP_004383540.1|  88 RNKVKRLTTDSIVLSLLLVgFIVPIGLL-----TINPLFHFLGASLEIITYIREYMVIWYLGLVFIVVPMVGTNAIR 159
                                       ***********99987654144444444.....455566665678888999999999999***************** PP

                              MurJ 347 AredtktPvkislislvlnills......llllpplgvvglalatslsaliglvllyvllrkrlk 405
                                       A +dtktP++i ++++  ni+l+      +  +p+l+ +g a+at+++  + l++ +++l+   +
  gi|330507112|ref|YP_004383540.1| 160 AAGDTKTPAFIMMFAAGANIILDpilifgIGPVPRLEIAGAAMATVIARALTLIMSLYFLYYNER 224
                                       ***********************998777777899**************9999998888765544 PP

  == domain 2  score: -6.2 bits;  conditional E-value: 4
                              MurJ 252 vsistvlLPrlSrsakekdedevrdllsqairltllllipvsfgllvlskpivsllferGnFseedveataevLaay 328
                                       +++++v+ P + ++  ++  d +++ ++ + r++l+  + + +++++l+  + s++      ++e +  t+  L++ 
  gi|330507112|ref|YP_004383540.1| 294 MALASVVGPFIGQNWGAGKFDRIKSGTKFSYRFSLIWGLIMFIVFAFLGGTVGSIFS----DDPEVISVTGLYLSIV 366
                                       456666666666666666666666666666666666666666666666666555433....3444445555555544 PP

                              MurJ 329 algLipyalvklllrvfYAredtktPvkislislvlnills....llllpplgvvglalatslsaliglvllyvllr 401
                                        +g   y +v + ++   A    k+P+ +++++l    +l+    +++   +g+ g  la  +s+l++ +++++ l+
  gi|330507112|ref|YP_004383540.1| 367 PIGYGLYGIVAISTS---AMSVLKKPIHAAILTLTQAFILYipmaYVGSLLIGLWGVFLALPVSYLVSSIVAIYTLN 440
                                       444333333333333...45555555555555443333333333366666666666667777777777777777666 PP

                              MurJ 402 kr 403
                                       + 
  gi|330507112|ref|YP_004383540.1| 441 RI 442
                                       65 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   8.4         4   1.8e+04      30      86 ..      23      89 ..      18     134 .. 0.57
   2 !   23.6  23.5   9.6e-09   4.3e-05       2      91 ..     138     236 ..     137     301 .. 0.74
   3 ?   -7.0  12.0         4   1.8e+04      45     139 ..     233     340 ..     230     344 .. 0.55
   4 ?    2.2   2.9     0.038   1.7e+02      82     141 ..     321     380 ..     308     382 .. 0.59
   5 !    5.6  11.4    0.0034        15       2      90 ..     363     452 ..     362     459 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.7 bits;  conditional E-value: 4
                   Polysacc_synt_C 30 ialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllgikl...........e 86
                                      i++++  i++++  +   +++ ++g +G ++a+ +++ vv+++n  a    +g +            +
  gi|330507112|ref|YP_004383540.1| 23 IPMIFGTISMIIFNLTDTFFVGQLG-TGQLAAMSFTFPVVLFVNNLAHAVAIGASAvishsigegnrN 89
                                      5666666666666666667777777.888888888888888888666666666555455555655442 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 9.6e-09
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvavl 72 
                                       ++i  l+++f+++ +v+++ + + g +k+++ +++++a +++il  +li      p++ i Gaa+atv+a ++++++
  gi|330507112|ref|YP_004383540.1| 138 MVIWYLGLVFIVVPMVGTNAIRAAGDTKTPAFIMMFAAGANIILDPILIfgigpvPRLEIAGAAMATVIARALTLIM 214
                                       67778999*****************************************88888889999***********999999 PP

                   Polysacc_synt_C  73 nlyalr...rllgikl....ellrrl 91 
                                        ly+l+   r l +++    +    +
  gi|330507112|ref|YP_004383540.1| 215 SLYFLYyneRMLSFDIpslnS----I 236
                                       977775211555555543321....2 PP

  == domain 3  score: -7.0 bits;  conditional E-value: 4
                   Polysacc_synt_C  45 lnllliplfgi.......vGaaiatvlallvva.vlnlyalrrllgiklellrrllkpllaalvmgivvylllllll 113
                                       ln +l+ +++i        Ga+i t la  +++ ++  y      g+ +   +r+   +++ ++m+++   ++  ++
  gi|330507112|ref|YP_004383540.1| 233 LNSILVSWIQIlyiglpnAGAMIITPLAAGFITrIVATYGSDAVAGFGI--ATRM-DSFALIVIMALA--SVVGPFI 304
                                       6666776666666666888988888666666551444666666777777..3333.455555555555..2444444 PP

                   Polysacc_synt_C 114 glllla..........alalllavlvgalvYlllll 139
                                       g++++a           ++  ++++ g ++++++++
  gi|330507112|ref|YP_004383540.1| 305 GQNWGAgkfdriksgtKFSYRFSLIWGLIMFIVFAF 340
                                       444444445555777644444444455555554444 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.038
                   Polysacc_synt_C  82 gikl..ellrrllkpllaalvmgivvylllllllgllllaalalllavl.vgalvYlllllll 141
                                       ++++  +l+  l  ++++ +++g+ v  +++  +++++     l l+++ +g  +Y+++++ +
  gi|330507112|ref|YP_004383540.1| 321 KFSYrfSLIWGL-IMFIVFAFLGGTVGSIFSDDPEVISVT--GLYLSIVpIGYGLYGIVAIST 380
                                       444422333334.334444444444455666666666644..666666559999999998865 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.0034
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigal.vklilnllliplfgivGaaiatvlallvvavlnlyal 77 
                                       L+i+ ++  ++++  +++s +  l+++  a++ ++  a+ + + + ++   l+g+ G+ +a  +++lv++++ +y l
  gi|330507112|ref|YP_004383540.1| 363 LSIVPIGYGLYGIVAISTSAMSVLKKPIHAAILTLTQAFiLYIPMAYVGSLLIGLWGVFLALPVSYLVSSIVAIYTL 439
                                       6666677778889999999999999999888888876653788888888899************************* PP

                   Polysacc_synt_C  78 rrllgiklellrr 90 
                                       +r++ ++ + ++r
  gi|330507112|ref|YP_004383540.1| 440 NRIIMYREKTVKR 452
                                       ****999833444 PP

>> Holin_SPP1  SPP1 phage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.77   3.4e+03      11      41 ..     139     169 ..     132     179 .. 0.72
   2 ?   10.4   0.2   0.00013      0.57      11      57 ..     170     222 ..     168     225 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.77
                        Holin_SPP1  11 illllallnqlltilGknplpideealytai 41 
                                       ++  l+l+  ++ ++G n++    ++ + a+
  gi|330507112|ref|YP_004383540.1| 139 VIWYLGLVFIVVPMVGTNAIRAAGDTKTPAF 169
                                       5667899999999999999987766554444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00013
                        Holin_SPP1  11 illllallnqll...tilGknplpidee...alytaitlvftvataivawyKN 57 
                                       i++++a  n +l    i+G+ p+p  e    a+ t+i  ++t+++++++ y N
  gi|330507112|ref|YP_004383540.1| 170 IMMFAAGANIILdpiLIFGIGPVPRLEIagaAMATVIARALTLIMSLYFLYYN 222
                                       7888888899999989******998888888*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2804.41
//
Query:       gi|330507113|ref|YP_004383541.1|  [L=200]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-17   62.0   0.0    6.5e-17   61.7   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.5e-16   60.8   0.0    5.1e-16   59.1   0.0    1.8  2  Methyltransf_11  Methyltransferase domain
      9e-16   58.4   0.0    1.4e-15   57.8   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    4.9e-14   52.2   0.0    6.9e-14   51.7   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    6.5e-07   30.0   0.0      9e-07   29.6   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    3.4e-06   27.1   0.0      3e-05   24.0   0.0    2.0  1  Methyltransf_8   Hypothetical methyltransferase
    4.6e-05   22.9   0.0    0.00022   20.8   0.0    1.8  2  Methyltransf_4   Putative methyltransferase
    0.00013   21.8   0.0    0.00028   20.7   0.0    1.6  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00018   21.2   0.0     0.0013   18.5   0.0    1.9  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    0.00051   19.4   0.0    0.00081   18.7   0.0    1.4  1  Methyltransf_2   O-methyltransferase domain
    0.00078   18.9   0.0    0.00099   18.6   0.0    1.1  1  TehB             Tellurite resistance protein TehB
     0.0018   17.4   0.0     0.0023   17.1   0.0    1.2  1  Fibrillarin      Fibrillarin
     0.0024   17.7   0.0     0.0035   17.1   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)
     0.0031   17.4   0.0     0.0077   16.1   0.0    1.7  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
       0.01   15.2   0.0      0.022   14.0   0.0    1.5  2  CMAS             Mycolic acid cyclopropane synthetase
      0.021   14.2   0.0      0.029   13.8   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.033   13.8   0.0      0.049   13.2   0.0    1.3  1  MTS              Methyltransferase small domain
      0.037   13.6   0.0      0.069   12.7   0.0    1.4  1  DOT1             Histone methylation protein DOT1
       0.04   14.0   0.0      0.061   13.4   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   6.8e-20   6.5e-17       7     118 ..      45     168 ..      39     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 6.8e-20
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsne 82 
                                       +lD GCG+G++++++ e +g  ++v+ +D+ ++ i   +e+a +l l+n++  ++di++ l+  +ed ++D+ +   
  gi|330507113|ref|YP_004383541.1|  45 FLDMGCGSGDYAIRASEIVGNSGKVFALDRWQDGIDDLTEKAGSLRLNNLRAIAADITApLP--IEDGSIDVCFLAT 119
                                       79************************************************************..********99988 PP

                   Methyltransf_31  83 vlnaladpdkile....eiervlkpggilliedpr..........llael 118
                                       vl ++  ++++ +    ei rvlkpgg+++i +++          ++++ 
  gi|330507113|ref|YP_004383541.1| 120 VL-HIFKLADVEGvlfnEIRRVLKPGGRIVIINCKreiqpfgppvHMRQS 168
                                       88.44445544444445******************444444444433333 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       3.6   3.4e+03      72      84 ..      25      37 ..      22      38 .. 0.85
   2 !   59.1   0.0   5.4e-19   5.1e-16       1      96 []      46     149 ..      46     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.6
                                      CC-CCHHHHHHHH CS
                   Methyltransf_11 72 hhvedpekalkei 84
                                      ++++dpe++++e+
  gi|330507113|ref|YP_004383541.1| 25 FWIHDPEQVFSEL 37
                                      588*******996 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 5.4e-19
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCC.TSS-TT-EEEEEEES-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaek.lpfednsfDlvvssevlh 72 
                                       Ld+GcG+G +a    + +   ++v+++D ++  ++   eka   +l +++ + ad++  lp+ed+s+D++++  vlh
  gi|330507113|ref|YP_004383541.1|  46 LDMGCGSGDYAIRASEIVgnsGKVFALDRWQDGIDDLTEKAGSLRLnNLRAIAADITApLPIEDGSIDVCFLATVLH 122
                                       8**************7777889************99999999999999*********879***************** PP

                                       C-..CCHH.HHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  73 hv..edpe.kalkeiaRvLkpgGllvi 96 
                                        +  +d+e  +++ei+RvLkpgG++vi
  gi|330507113|ref|YP_004383541.1| 123 IFklADVEgVLFNEIRRVLKPGGRIVI 149
                                       **8855551678************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.0   1.5e-18   1.4e-15       2      97 .]      46     145 ..      45     145 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.5e-18
                                       EEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG.BSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaed.lpfedgsfDlvvssgalh 75 
                                       Ld+GcG+G++++++++ +g ++kv ++D  ++ ++   e+a + +l n++ + +d+++ lp edgs+D+++++ +lh
  gi|330507113|ref|YP_004383541.1|  46 LDMGCGSGDYAIRASEIVGnSGKVFALDRWQDGIDDLTEKAGSLRLnNLRAIAADITApLPIEDGSIDVCFLATVLH 122
                                       9****************9559********************998889*********888*************988** PP

                                       GSSHHHHHH.HHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlek.alkeiarvLkpgG 97 
                                       +++ +d+e  +++ei+rvLkpgG
  gi|330507113|ref|YP_004383541.1| 123 IFKLADVEGvLFNEIRRVLKPGG 145
                                       *****9997358**********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 !   51.7   0.0   7.3e-17   6.9e-14      40     157 ..      34     155 ..      23     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 7.3e-17
                                       HHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT.-TTS-T CS
                   Ubie_methyltran  40 eklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaee.Lpfedd 115
                                           + ++g  +lD+ +G+gD+a++ s+ vg++gkv  lD  ++ ++   +k+      n++ + a+  + Lp ed+
  gi|330507113|ref|YP_004383541.1|  34 FSELNLREGDCFLDMGCGSGDYAIRASEIVGNSGKVFALDRWQDGIDDLTEKAGSLRLNNLRAIAADITApLPIEDG 110
                                       45567899**********************************************99999*****9986544****** PP

                                       -EEEEEEE..S-GGG-S-HHHHH.HHHHHHEEEEEEEEEEEE--- CS
                   Ubie_methyltran 116 sfDvvtvs..fGlrnvtDklkaL.keayrvlkpGGrlvvlefskv 157
                                       s Dv  ++    +  ++D + +L +e++rvlkpGGr+v+++  + 
  gi|330507113|ref|YP_004383541.1| 111 SIDVCFLAtvLHIFKLADVEGVLfNEIRRVLKPGGRIVIINCKRE 155
                                       ***98766114566789*99998699*************997765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   9.5e-10     9e-07       1      99 []      46     147 ..      46     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 9.5e-10
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       L+ GcG+G+++ +  e      ++ ++D  ++ i+d  ek  + + nn   +  + +  l  ++ +s D+ +++ vl
  gi|330507113|ref|YP_004383541.1|  46 LDMGCGSGDYAIRASEIVgNSGKVFALDRWQDGIDDLTEKAGSLRLNNLRAIAADITAPLPIED-GSIDVCFLATVL 121
                                       89***********999988888899*********999999999998777777666666543333.6*********** PP

                   Methyltransf_12  77 hhl..kdir.evldnirklLkpgGrl 99 
                                       h +  +d++  ++++ir++LkpgGr+
  gi|330507113|ref|YP_004383541.1| 122 HIFklADVEgVLFNEIRRVLKPGGRI 147
                                       *****9***67778**********96 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   3.2e-08     3e-05     101     181 ..      89     184 ..      18     200 .] 0.63

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.2e-08
                                       SS-SSTTEEES-T.TS-S--TT-EEEEEEES---SS-HHH....HHHHHHHHEEEEEEEEEEEEGGG-S........ CS
                    Methyltransf_8 101 lvavnervvacdl.akvPledesvdvavfclslmgtnlad....flkeanrvlkvGGllkvaevksrfe........ 164
                                       l   n r +a d+ a +P+ed+s+dv  +   l   +lad      +e++rvlk+GG + + + k  ++        
  gi|330507113|ref|YP_004383541.1|  89 LRLNNLRAIAADItAPLPIEDGSIDVCFLATVLHIFKLADvegvLFNEIRRVLKPGGRIVIINCKREIQpfgppvhm 165
                                       3334668899***999**********998888777666652222579*************99988777644444433 PP

                                       ..-HHHHHHHHHCTTEEEE CS
                    Methyltransf_8 165 ..svklfaraltklGfevk 181
                                         s + ++  +++ Gfe +
  gi|330507113|ref|YP_004383541.1| 166 rqSPEELEGCINSYGFEKT 184
                                       3344445555555666555 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.3e-07   0.00022       4      70 ..      44     109 ..      41     118 .. 0.86
   2 ?   -0.3   0.0      0.69   6.5e+02      99     115 ..     133     149 ..     129     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.3e-07
                                       EEEEET-TTSHHHHHHHHHST.TSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-T CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkknP.dknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelled 70 
                                        +l++GcG+G+  ++ ++    + ++++++  +++++ + +k++ l+l+Nlr +  d +  l   +ed
  gi|330507113|ref|YP_004383541.1|  44 CFLDMGCGSGDYAIRASEIVGnSGKVFALDRWQDGIDDLTEKAGSLRLNNLRAIAADITAPL--PIED 109
                                       699**************987615699*******************************98777..3555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.69
                                       HHHHHHHHEEEEEEEEE CS
                    Methyltransf_4  99 llkelarvLkkgGvlel 115
                                       l +e+ rvLk+gG +++
  gi|330507113|ref|YP_004383541.1| 133 LFNEIRRVLKPGGRIVI 149
                                       568999*******9976 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0     3e-07   0.00028      68     132 ..      36     100 ..      23     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3e-07
                                       HTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT  68 llelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                        l+l++g+  L++G+GsG  +   +++vg++g+v +++r ++ +++ +++   l l+n+  + +D
  gi|330507113|ref|YP_004383541.1|  36 ELNLREGDCFLDMGCGSGDYAIRASEIVGNSGKVFALDRWQDGIDDLTEKAGSLRLNNLRAIAAD 100
                                       4789**********************************977655544444444444444433333 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 !   18.5   0.0   1.3e-06    0.0013       4      71 ..      37     104 ..      34     119 .. 0.93
   2 ?    0.7   0.0      0.38   3.6e+02     110     140 ..     123     153 ..     112     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                                       H---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCC CS
                   Methyltr_RsmB-F   4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarki 71 
                                       L+++e++ +lD+ ++ G      +e++ n+g+v+A+d+ +  ++ ++e    L ++n+  + aD++ +
  gi|330507113|ref|YP_004383541.1|  37 LNLREGDCFLDMGCGSGDYAIRASEIVGNSGKVFALDRWQDGIDDLTEKAGSLRLNNLRAIAADITAP 104
                                       899*************************************************************9875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHHHHCCCEEEEEEEEEEES- CS
                   Methyltr_RsmB-F 110 iaqlaklqkellsaaidllkkgGvlvYsTCs 140
                                       i +la  +  l++ +  +lk+gG +v   C 
  gi|330507113|ref|YP_004383541.1| 123 IFKLADVEGVLFNEIRRVLKPGGRIVIINCK 153
                                       667777777889999999********99996 PP

>> Methyltransf_2  O-methyltransferase 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   0.00081     112     175 ..      93     160 ..      20     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.5e-07
                                       TEEEEES-TTTS---....--SEEEEESSGGGS-HHHHHHHH.HHHHHH--TT-EEEEEE----TTS-- CS
                    Methyltransf_2 112 rvefvgGdffkdslP....eaDaillkrvlhDwsdekcvklL.krvkkalpagGkvivveavlgadpsg 175
                                       +++ ++ d+   +lP    + D+ +l+ vlh ++ +++  +L +++++ l++gG+++++++  + +p g
  gi|330507113|ref|YP_004383541.1|  93 NLRAIAADIT-APLPiedgSIDVCFLATVLHIFKLADVEGVLfNEIRRVLKPGGRIVIINCKREIQPFG 160
                                       5566666666.6777543345999**************9765388****************87777655 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06   0.00099      34     135 ..      45     152 ..      30     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                                       EEEES-TTSHHHHHHH.HTT-..EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG.----S.-EEE.EEEESS CS
                              TehB  34 vldlgcgqgrnslyls.llgy..dvtawdknensiafleeikekenlknistalydine.aklde.rydf.ilstvv 104
                                        ld+gcg+g  ++  s ++g   +v a+d+ ++ i  l e +    l+n+++   di + + +++   d   l+tv+
  gi|330507113|ref|YP_004383541.1|  45 FLDMGCGSGDYAIRASeIVGNsgKVFALDRWQDGIDDLTEKAGSLRLNNLRAIAADITApLPIEDgSIDVcFLATVL 121
                                       69*******88876552344322799*******************************87355654267862578888 PP

                                       GGGS-GGGHHHHHHHHHHTEEEEEEEEEEEE CS
                              TehB 105 lmfleaeripsiienmqectkvggynlivaa 135
                                        +f  a+    + +++++  k+gg  +i+  
  gi|330507113|ref|YP_004383541.1| 122 HIFKLADVEGVLFNEIRRVLKPGGRIVIINC 152
                                       8887777777788899********9999865 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.5e-06    0.0023      64     135 ..      35     108 ..      31     168 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.5e-06
                                       S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTT.S.TTEEEEES-TTSGGGGT CS
                       Fibrillarin  64 kelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakk.R.knivPileDArkPekYr 135
                                       +el +++g+  L +G +sG  +   s+ivg++g+v+a++  +  + +l+e a + R +n+  i +D + P   +
  gi|330507113|ref|YP_004383541.1|  35 SELNLREGDCFLDMGCGSGDYAIRASEIVGNSGKVFALDRWQDGIDDLTEKAGSlRlNNLRAIAADITAPLPIE 108
                                       678999*******************************************8765424368999999999997544 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.7e-06    0.0035      29     139 ..      45     149 ..      32     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.7e-06
                            DUF938  29 vLEiasGtGqHAvffApalpnl.kwqpsdqdeelresiaawadelalsnlkpPleldvtaevapvereappapasid 104
                                        L+++ G+G++A+   + + n  k  + d  +   + ++  a +l l+nl++ ++ d+ta+  p+e      + sid
  gi|330507113|ref|YP_004383541.1|  45 FLDMGCGSGDYAIRASEIVGNSgKVFALDRWQDGIDDLTEKAGSLRLNNLRA-IAADITAP-LPIE------DGSID 113
                                       6888999999999888887665366677877777788888888888999986.88899888.5555......89*** PP

                            DUF938 105 ailsinllHispwsaveg.lfagagellkkkavlvi 139
                                       + + + +lHi  +  veg lf+ + ++lk+++++vi
  gi|330507113|ref|YP_004383541.1| 114 VCFLATVLHIFKLADVEGvLFNEIRRVLKPGGRIVI 149
                                       *****************9679***********9987 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.1e-06    0.0077       8     117 ..      25     149 ..      18     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.1e-06
                   Methyltransf_23   8 elsdklerllpk..lraggrvLdiGcGtGillevlren.gfsvtgvDlspeaveiae...........kakkaqkdq 70 
                                       ++ +  e+++ +  lr+g   Ld+GcG+G  +  ++e  g s  ++ l++++ +i             +        
  gi|330507113|ref|YP_004383541.1|  25 FWIHDPEQVFSElnLREGDCFLDMGCGSGDYAIRASEIvGNSGKVFALDRWQDGIDDltekagslrlnN-------- 93 
                                       5666666666443379999**********8777776652666666666667777743333222222221........ PP

                   Methyltransf_23  71 fdeqeaae.............pqgkfdlIvlrevlehvp..dpp.ellrqiatllkpgGylll 117
                                                            ++g++d+  l  vl+ ++  d++  l++ i++ lkpgG++++
  gi|330507113|ref|YP_004383541.1|  94 -------LraiaaditaplpiEDGSIDVCFLATVLHIFKlaDVEgVLFNEIRRVLKPGGRIVI 149
                                       .......02233334445555677**************999988456799**********997 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.4e-05     0.022      54      82 ..      33      61 ..      28      74 .. 0.89
   2 ?   -3.1   0.0         4   3.8e+03     149     164 ..     134     149 ..     132     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                                      HHTTTT--TT-EEEEES-TTSHHHHHHHH CS
                              CMAS 54 ileklelkpGmtlLdiGcGWGslvrrave 82
                                      ++  l+l++G+  Ld+GcG G  ++ra e
  gi|330507113|ref|YP_004383541.1| 33 VFSELNLREGDCFLDMGCGSGDYAIRASE 61
                                      6889*******************999976 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4
                                       HHHHHHHS-TT-EEEE CS
                              CMAS 149 fkklkkllkedGllll 164
                                       f+++ ++lk++G++++
  gi|330507113|ref|YP_004383541.1| 134 FNEIRRVLKPGGRIVI 149
                                       8899999999999875 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.1e-05     0.029     159     257 ..      39     148 ..      31     152 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakL..gakkvvavDiDevAvkvake...NaelNkvea.klevalseellkeekadv 229
                                       ++eg+ +lD+G+GSG  ai a+ +  +  kv+a+D  +  ++   e    ++lN+++a   +++++  + + +++dv
  gi|330507113|ref|YP_004383541.1|  39 LREGDCFLDMGCGSGDYAIRASEIvgNSGKVFALDRWQDGIDDLTEkagSLRLNNLRAiAADITAPLPIED-GSIDV 114
                                       6788999************8888743456999*99655555433330114577877774444444444434.67777 PP

                              PrmA 230 i.vaNI.....Laevlielaedikklvkegglli 257
                                         +a +     La+v   l ++i +++k+gg+++
  gi|330507113|ref|YP_004383541.1| 115 CfLATVlhifkLADVEGVLFNEIRRVLKPGGRIV 148
                                       5223332224457777778888888888888876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.2e-05     0.049      29     139 ..      39     151 ..      31     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-05
                                       CCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST..TS-EEEE CS
                               MTS  29 kelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvleeve..ekkfdli 101
                                        ++ +  lD+GcG G  ++ + +   +   v ++d     ++  +e + + +l+ ++++a d+++ ++  ++++d+ 
  gi|330507113|ref|YP_004383541.1|  39 LREGDCFLDMGCGSGDYAIRASEIVGNSGkVFALDRWQDGIDDLTEKAGSLRLNnLRAIAADITAPLPieDGSIDVC 115
                                       4456668**************999887655************999999999998899******998655499***** PP

                                       EE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEE CS
                               MTS 102 vsNPPfhagkatelavaeeliaeAkeaLkegGeLliVa 139
                                            +h  k    +v   l++e +++Lk+gG+++i+ 
  gi|330507113|ref|YP_004383541.1| 116 FLATVLHIFKL--ADVEGVLFNEIRRVLKPGGRIVIIN 151
                                       **999999987..688999**************99875 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.4e-05     0.069      33      63 ..      32      62 ..      26      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.4e-05
                                      HHHHHTT--TT-EEEEES-TTSHHHHHHHHH CS
                              DOT1 33 evldkvnlkkedvFvDLGSGvGnvvlqaale 63
                                      +v++++nl++ d+F+D+G G G+  + a+  
  gi|330507113|ref|YP_004383541.1| 32 QVFSELNLREGDCFLDMGCGSGDYAIRASEI 62
                                      89*********************99988765 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.5e-05     0.061       2      77 ..      20     108 ..      19     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.5e-05
                                       CCCHHHHHHHHHHHHT-S-..TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEES.SSS.........HHH.TTEEE CS
                              FtsJ   2 rsRsayKLleidekfklfk..pgktvvDlgaaPGgwsqvllqrlgakgkvvavDl.qpm.........apl.pgvtt 65 
                                       r+Rs++ + +  + f+ ++  +g+ ++D g++ G ++  +++ +g++gkv+a+D  q +         +++ ++++ 
  gi|330507113|ref|YP_004383541.1|  20 RCRSSFWIHDPEQVFSELNlrEGDCFLDMGCGSGDYAIRASEIVGNSGKVFALDRwQDGiddltekagSLRlNNLRA 96 
                                       6777777776667776554449999********************9********96666998887765444699999 PP

                                       ECS-CCCSSHHH CS
                              FtsJ  66 iqgditdpetie 77 
                                       i +dit p  ie
  gi|330507113|ref|YP_004383541.1|  97 IAADITAPLPIE 108
                                       999999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1339.00
//
Query:       gi|330507114|ref|YP_004383542.1|  [L=165]
Description: PadR family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-14   53.6   0.2    2.9e-14   52.8   0.2    1.4  1  PadR         Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.012   15.4   0.2      0.016   14.9   0.2    1.3  1  DUF4364      Domain of unknown function (DUF4364)
      0.032   14.4   0.0      0.074   13.3   0.0    1.7  1  PaaX         PaaX-like protein
      0.047   13.6   0.1        0.2   11.6   0.2    2.0  3  Tautomerase  Tautomerase enzyme
      0.095   13.5   0.1         19    6.1   0.0    2.3  2  DUF3349      Protein of unknown function (DUF3349)


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.2     8e-18   2.9e-14       1      74 [.      10      76 ..      10      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 8e-18
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      +L++++ ++  Gy++ik++e+ + g +++s Gs+Yp+Lk++e+eg+v ++ e+      + yY lT++G++ +a
  gi|330507114|ref|YP_004383542.1| 10 MLHIIKGGEVSGYDLIKKVEAIT-G-EKPSTGSIYPLLKKMEREGWVLGRFED-----GKTYYSLTETGKEHIA 76
                                      699*******************5.6.7*************************9.....699*********9876 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   4.5e-06     0.016      39      91 ..      44      95 ..      40     131 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.5e-06
                           DUF4364 39 alseLvesglieeeekenktlykiTekGketlelfenripksirekideylke 91
                                       l++++ +g +  + +++kt+y++Te Gke + ++++    ++ +ki ++++ 
  gi|330507114|ref|YP_004383542.1| 44 LLKKMEREGWVLGRFEDGKTYYSLTETGKEHIAQIKEA-KHEFIKKIHQSIAL 95
                                      68999*********99****************998876.44455555555443 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.1e-05     0.074      39      70 .]      40      71 ..      11      71 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                              PaaX 39 lvRaalsRlakaGwlvrekegrrsfYrLsdkg 70
                                      ++   l  ++++Gw+ +  e  + +Y+L+++g
  gi|330507114|ref|YP_004383542.1| 40 SIYPLLKKMEREGWVLGRFEDGKTYYSLTETG 71
                                      55556899*********99999*******986 PP

>> Tautomerase  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.2     8e+03      38      53 ..      41      56 ..      31      56 .. 0.69
   2 ?   11.6   0.2   5.5e-05       0.2      13      57 ..      79     124 ..      76     127 .. 0.92
   3 ?   -2.2   0.0       1.2   4.2e+03      17      26 ..     131     140 ..     129     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.2
                                      -EEEEEEE-TTSEEET CS
                       Tautomerase 38 ivVvieEvpaenwgvg 53
                                      i+ ++  ++ e+w++g
  gi|330507114|ref|YP_004383542.1| 41 IYPLLKKMEREGWVLG 56
                                      5556677888888765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHHHHHHHHHHHTS.-GGG-EEEEEEE-TTSEEETTEEH CS
                       Tautomerase  13 aeqKaeLaervTealvealga.prsaivVvieEvpaenwgvggesv 57 
                                       +e K e++++++++++ a     +s+i+ + +E+ + + gv+  ++
  gi|330507114|ref|YP_004383542.1|  79 KEAKHEFIKKIHQSIALANETfEDSDIQALMNEMHDTHRGVHSQDI 124
                                       689***********************************99987766 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.2
                                       HHHHHHHHHH CS
                       Tautomerase  17 aeLaervTea 26 
                                       + L+++v e+
  gi|330507114|ref|YP_004383542.1| 131 ESLIREVAEL 140
                                       6788988886 PP

>> DUF3349  Protein of unknown function (DUF3349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0054        19      55      93 ..      17      55 ..       5      57 .. 0.87
   2 ?    5.2   0.3      0.01        37      28      81 ..      94     126 ..      70     142 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0054
                                      S.BSHHHCHHHHHHHCTS---HHHHHHHHHHHHTTT-GC CS
                           DUF3349 55 eavdeedieelitkvteeepseedvarVaarLaaggwpl 93
                                      ++v+  d+ + ++++t e+ps   +  + ++++++gw l
  gi|330507114|ref|YP_004383542.1| 17 GEVSGYDLIKKVEAITGEKPSTGSIYPLLKKMEREGWVL 55
                                      57788889999**************************76 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                                       HHHCTT--HHHHHHHHHHHHHH--.SSS.BSHHHCHHHHHHHCTS---HHHHHH CS
                           DUF3349  28 alLrrrLsdeevkevaeelvaeaaeadeavdeedieelitkvteeepseedvar 81 
                                       al +++  d +++++++e+ +++                     +  + +d+++
  gi|330507114|ref|YP_004383542.1|  94 ALANETFEDSDIQALMNEMHDTH---------------------RGVHSQDIEQ 126
                                       34444445555555555554444.....................2334444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1276  (0.0711696); expected 358.6 (0.02)
Passed bias filter:                      788  (0.0439511); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1208.42
//
Query:       gi|330507115|ref|YP_004383543.1|  [L=337]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-15   55.5   0.0    6.3e-15   55.0   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain
    1.2e-11   44.4   0.0      2e-11   43.7   0.0    1.4  1  Dimerisation2    Dimerisation domain
    1.2e-06   29.2   0.0    2.3e-06   28.2   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    2.4e-06   28.2   0.0    4.9e-06   27.2   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    2.3e-05   24.9   0.0      4e-05   24.2   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
      5e-05   23.1   0.0    8.3e-05   22.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    6.1e-05   22.9   0.0     0.0001   22.2   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0022   17.8   0.0     0.0034   17.1   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase
     0.0073   15.6   0.0      0.011   15.1   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0092   15.5   0.0      0.015   14.8   0.0    1.3  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   3.5e-18   6.3e-15      34     163 ..     134     269 ..     128     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 3.5e-18
                                       HHHHHHHHHHHTTHHH....HHHHHHHSS-.GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS CS
                    Methyltransf_2  34 eerakfnkglqesssl....vakkvleafd.leglkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehl 105
                                       +   +f + ++++ +      +++++     + ++++++D+GGG G +   +v+++Pt+++++fD   Vve A++++
  gi|330507115|ref|YP_004383543.1| 134 QKWSQFASWMANNERAgiaqQMSELISLQPeFASFRKMLDLGGGPGIFGISMVAKHPTMRGVIFDRKPVVEVAERFI 210
                                       555566666655443311112334444443699******************************************** PP

                                       .-----TTEEEEES-TTTS-----SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEE CS
                    Methyltransf_2 106 .sageeervefvgGdffkdslPeaDaillkrvlhDwsdekcvklLkrvkkalpagGkvi 163
                                        + g e+r+e+ +Gd+  d++ e+  ++ ++    ++ e+   ++k++++al++gG  +
  gi|330507115|ref|YP_004383543.1| 211 kEYGMEDRMEVLAGDYNLDPIGEGYDLIWASATLNFARENMDSVMKKIYEALNPGGLFV 269
                                       999*******************998889999999**********************755 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   1.1e-14     2e-11      11      89 ..      22      93 ..      12      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.1e-14
                     Dimerisation2 11 aSkaLftAceLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntelastyLvsssp 89
                                       +k + +  eL+vF+ L e  p+saeeva+e+  +++ t  +l+ ++a gL e++     ++lY+n+++a+++Lv++sp
  gi|330507115|ref|YP_004383543.1| 22 KAKLMMSGIELNVFNQLSE--PKSAEEVAKEIRGQSRNTMLFLNGLAACGLIEKH-----NGLYRNAPIAQAFLVEGSP 93
                                      6799*************99..********************************66.....47***************98 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.3e-09   2.3e-06       1      99 []     172     268 ..     172     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.3e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++G+G G +   + +k+p+ + +  D  p +   a++ +++++ ++  ++e+ a d   ++ g+ +Dl++as +l+
  gi|330507115|ref|YP_004383543.1| 172 LDLGGGPGIFGISMVAKHPTMRGVIFDRKPVVE-VAERFIKEYGMED--RMEVLAGDYNLDPIGEGYDLIWASATLN 245
                                       8****************9999999999988777.6666666666555..6666666654455558************ PP

                   Methyltransf_12  78 hl.kdirevldnirklLkpgGrl 99 
                                          +++++v+++i+++L+pgG +
  gi|330507115|ref|YP_004383543.1| 246 FArENMDSVMKKIYEALNPGGLF 268
                                       *********************75 PP

>> Methyltransf_25  Methyltransferase 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   4.9e-06       2      97 .]     172     266 ..     171     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.7e-09
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       LdlG G+G + + + ++ +  + + +D  +  +e a++ ++e g+  ++e++ gd  +l+   + +Dl+++s +l++
  gi|330507115|ref|YP_004383543.1| 172 LDLGGGPGIFGISMVAKHPTMRGVIFDRKP-VVEVAERFIKEYGMedRMEVLAGDY-NLDPIGEGYDLIWASATLNF 246
                                       9********99998888778999999*876.679******9999999********7.56666779******866775 PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                         +e+++ ++k+i+++L+pgG
  gi|330507115|ref|YP_004383543.1| 247 -ARENMDSVMKKIYEALNPGG 266
                                       .67999**************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.3e-08     4e-05       1      95 [.     172     269 ..     172     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.3e-08
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCT.SS-TT-EEEEEEES-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaekl.pfednsfDlvvssevlh 72 
                                       Ld+G G G++   +  +   +r v +D  k ++++a++ ++e g+  ++e++ +d   l p+ +  +Dl+++s +l+
  gi|330507115|ref|YP_004383543.1| 172 LDLGGGPGIFGISMVAKHptMRGVIFDR-KPVVEVAERFIKEYGMedRMEVLAGDYN-LdPIGE-GYDLIWASATLN 245
                                       8999999999887775554889999995.6677899999999999999999999999.648887.89********** PP

                                       C-.CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  73 hv.edpekalkeiaRvLkpgGllv 95 
                                       +  e++++++k+i+  L pgGl+v
  gi|330507115|ref|YP_004383543.1| 246 FArENMDSVMKKIYEALNPGGLFV 269
                                       *********************997 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   4.6e-08   8.3e-05       6     108 ..     170     269 ..     167     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.6e-08
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsn 81 
                                       ++lDlG G G +++ +     p  + v +D+++ ++e+A+   ++ g + ++e+ +gd +  +  +  e +Dli + 
  gi|330507115|ref|YP_004383543.1| 170 KMLDLGGGPGIFGISMV-AKHPTMRGVIFDRKP-VVEVAERFIKEYGMEdRMEVLAGDYNLDP--IG-EGYDLIWAS 241
                                       69***************.55777888889*998.69************99**********988..77.9******** PP

                   Methyltransf_31  82 evl.naladpdkileeiervlkpggill 108
                                       ++l  a  ++d+++++i ++l+pgg ++
  gi|330507115|ref|YP_004383543.1| 242 ATLnFARENMDSVMKKIYEALNPGGLFV 269
                                       ***778999*****************98 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   5.6e-08    0.0001       7     116 ..     153     269 ..     138     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.6e-08
                   Methyltransf_23   7 eelsdklerllpklraggrvLdiGcGtGillevl.rengf.svtgvDlspeaveiae...kakkaqkdqfdeqeaae 78 
                                       +++s+++    p+  +  + Ld+G G Gi+  ++ +++++   + +D  p+ ve ae   k + +++ ++      +
  gi|330507115|ref|YP_004383543.1| 153 QQMSELISLQ-PEFASFRKMLDLGGGPGIFGISMvAKHPTmRGVIFDRKPV-VEVAErfiKEYGMEDRME------V 221
                                       4555555533.446677899**********99997777778999****986.666655554444444444......3 PP

                   Methyltransf_23  79 pqg.........kfdlIvlrevlehvp.dppellrqiatllkpgGyll 116
                                        +g          +dlI ++ +l+  + ++ +++++i++ l+pgG+++
  gi|330507115|ref|YP_004383543.1| 222 LAGdynldpigeGYDLIWASATLNFAReNMDSVMKKIYEALNPGGLFV 269
                                       333445556667************99989****************986 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.9e-06    0.0034      40     111 ..     161     228 ..     141     263 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.9e-06
                   Methyltransf_16  40 lganelsklsvlELGsGtGlvGlavaellpeakviltDleellellkknielnknalkskvkvevLdWgeel 111
                                       l+ +  s +++l+LG G G++G+++ ++ p ++ ++ D++ ++e+ ++ i+     +++++  evL  + +l
  gi|330507115|ref|YP_004383543.1| 161 LQPEFASFRKMLDLGGGPGIFGISMVAKHPTMRGVIFDRKPVVEVAERFIKEY--GMEDRM--EVLAGDYNL 228
                                       5666678899*************999998*****************9999883..355544..444444455 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   5.9e-06     0.011      64     167 ..     169     273 ..     145     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.9e-06
                                       -EEEEES-TTSHHHHHHHHHH--EEEEEES-HHH.HHHHHHHHHTS-SSS-EEEEES-GG..G-----SEEEEES-G CS
                              CMAS  64 mtlLdiGcGWGslvrraverydvkvvglTlSkeq.aklakkrvdeldlerkvevklldye..dldekvdrvvsvgaf 137
                                        ++Ld+G G G   + +v++    + g+ + ++   ++a++ ++e ++e++ ev+  dy+   + e +d + +  a+
  gi|330507115|ref|YP_004383543.1| 169 RKMLDLGGGPGIFGISMVAK-HPTMRGVIFDRKPvVEVAERFIKEYGMEDRMEVLAGDYNldPIGEGYDLIWAS-AT 243
                                       589*****************.7899999998775167788889****************64357789*999875.56 PP

                                       GGTSGGGHHHHHHHHHHHS-TT-EEEEEEE CS
                              CMAS 138 ehvgkenydtffkklkkllkedGllllhti 167
                                         +  en d  +kk++++l+++Gl+++ + 
  gi|330507115|ref|YP_004383543.1| 244 LNFARENMDSVMKKIYEALNPGGLFVNLSE 273
                                       679**********************98665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   8.4e-06     0.015      31     101 ..     167     238 ..     155     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.4e-06
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdli 101
                                         +k+lDlG G G+ g+++ +++p+++ +++d +   +e+a++ +++ ++e  +ev+a d   +   + +dli
  gi|330507115|ref|YP_004383543.1| 167 SFRKMLDLGGGPGIFGISMVAKHPTMRGVIFDRK-PVVEVAERFIKEYGMEdrMEVLAGDYNLDPIGEGYDLI 238
                                       4678***********************9999986.579*****999999999999999998777666888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2496.01
//
Query:       gi|330507116|ref|YP_004383544.1|  [L=355]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-22   80.7   0.0    1.5e-22   80.4   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.018   14.5   0.0      0.029   13.9   0.0    1.2  1  CbiJ          Precorrin-6x reductase CbiJ/CobK


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.0   1.6e-26   1.5e-22      50     236 ..      89     290 ..      27     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 1.6e-26
                                       B-HHHHHHH--SEEEE-GGG.......GGGHHHHHHHS-EEE----TTS.....HHHHHHHHHHHHHTT-HHHHHHH CS
                      Peripla_BP_2  50 idvEklaalkPDlvilskgl....gltdedeellksgiptvivessntg.....eslkeqiralgellgledeaekl 117
                                       ++vE +a l PDlvi+  ++     +++  +   ++ ip+v+  +           ++e+ir lge++g++++ae++
  gi|330507116|ref|YP_004383544.1|  89 PNVEVVASLNPDLVIMRDQGadeeNTAKFLDAAKRLEIPVVVLKYADCYddisvGTIYEEIRLLGEVFGKQEKAEEI 165
                                       89******************66633333334445689*********9889*************************** PP

                                       HHHHHHHHHHHHHTS-TT...-EEEEEEEETTE........EEEE-TTSTTTHHHHT.S--EESTTT--STT-EEE- CS
                      Peripla_BP_2 118 vaeidsklaaaksaidse..kpkpvlvfggade......ggyvvagsnsyigdllda.lgieniaaeskkseyeeis 185
                                       va +++ ++ ++++++ +   +kp +++ ga++      g+ + +g+++  +++l++ ++++n+++   +++ e is
  gi|330507116|ref|YP_004383544.1| 166 VALMNEQVELIRERTKDIadEDKPRVLYFGAPSyakdrgGAGYAFGTDTIESAFLEDiINAKNAYD---GDNTELIS 239
                                       *******************96677777766777677777888888888888888877777777755...579***** PP

                                       HHHHHHH--SEEEEEEH...HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-H CS
                      Peripla_BP_2 186 aEqilasdpdvifvsgr...aeadnktgleflkenpllaelpAvkngrVyalds 236
                                       aE++l+ dpdvi+  +    +  +   + e++ +   ++el A k +rVy l +
  gi|330507116|ref|YP_004383544.1| 240 AERLLSIDPDVIILPTYsgyHPPSVMYNEEQFGK---VQELRALKDRRVYSLTA 290
                                       *****************55544444444444444...47779999999999876 PP

>> CbiJ  Precorrin-6x reductase CbiJ/CobK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.2e-06     0.029     164     218 ..      77     132 ..      64     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-06
                                       EEEE--SS--HHHHHHHHHHTT--EEEEES--SS.TTTHH.HHHHHHTT-EEEEE- CS
                              CbiJ 164 eiiamrGpfskelerallreykidvlVtKeSGgaGgteeK.leaArelgipvivik 218
                                       ++ a  Gp  ++ + +++   + d++++++ G++   ++K l+aA++l+ipv+v+k
  gi|330507116|ref|YP_004383544.1|  77 NVGAFGGPLGVAPNVEVVASLNPDLVIMRDQGADEENTAKfLDAAKRLEIPVVVLK 132
                                       5667789*************************98766666489***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2508.13
//
Query:       gi|330507117|ref|YP_004383545.1|  [L=56]
Description: hypothetical protein MCON_0963 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 427.08
//
Query:       gi|330507118|ref|YP_004383546.1|  [L=110]
Description: RelE/StbE family addiction module toxin [Methanosaeta concilii GP6]
Scores for complete sequence (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   38.8   0.2    1.7e-09   38.1   0.2    1.3  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
    2.7e-06   27.2   0.1    4.4e-06   26.6   0.1    1.4  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
    0.00079   19.7   0.0     0.0014   18.9   0.0    1.4  1  YafQ_toxin       Bacterial toxin of type II toxin-antitoxin s
  ------ inclusion threshold ------
      0.086   12.8   0.3       0.14   12.1   0.1    1.4  2  Ist1             Regulator of Vps4 activity in the MVB pathwa


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.2   3.8e-13   1.7e-09       9      90 .]      13      84 ..       6      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 3.8e-13
                                      HHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTCCTTEEEEEECTEEEEEEEETSTTEEEEEEEEEHH CS
                        ParE_toxin  9 kdlkkiadyiardgpaakrfldaleealellaenpalgrprrelglkglrririgdyriiYriddeelvvvilrvlhrs 87
                                      +++ k+ +         k ++d++  ++++++ np++g+p +  +lkg+r +++++++i Y+i d  + +v+l ++h+ 
  gi|330507118|ref|YP_004383546.1| 13 RQFIKLTRK-------NKALKDRFINKIDQILINPDMGEP-KSHRLKGVRAVHVDPFVIAYTIID--DCIVFLYLGHHN 81
                                      555555554.......8899999999**************.444477***************963..4555*******9 PP

                                      HHC CS
                        ParE_toxin 88 edy 90
                                      e+y
  gi|330507118|ref|YP_004383546.1| 82 EAY 84
                                      987 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   9.9e-10   4.4e-06       3      83 ..       7      84 ..       5      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 9.9e-10
                   ParE-like_toxin  3 qtrrfkkalkklkek...lkadldkavkeiiedPelGeeKkGDLsgvfvykfklnkqltllaYeldekkrvlvlllvGt 78
                                        ++f ++  kl +k   lk ++ +++++i+ +P +Ge+K   L+gv+ +++      + +aY++ ++ +  v l +G 
  gi|330507118|ref|YP_004383546.1|  7 RVPEFDRQFIKLTRKnkaLKDRFINKIDQILINPDMGEPKSHRLKGVRAVHV----DPFVIAYTIIDDCI--VFLYLGH 79
                                      567889999999766335678899999*********************9866....5789******9985..5899999 PP

                   ParE-like_toxin 79 heNfY 83
                                      h+  Y
  gi|330507118|ref|YP_004383546.1| 80 HNEAY 84
                                      99877 PP

>> YafQ_toxin  Bacterial toxin of type II toxin-antitoxin system, YafQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.2e-07    0.0014       8      86 ..      10      83 ..       5      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.2e-07
                                      HHHHHHHHHH.HTT--HHHHHHHHHHHHTT-S--GGG--EE-SSS-TTEEEEEEETTEEEEEEE-SSEEEEEEEE-HHH CS
                        YafQ_toxin  8 qfkkdlkrlk.krkkdleklkevlklLaegepLpekyrdHaLkgnwkgyrecHikpDllLiYrleddelvlvrlGsHse 85
                                      +f++++ +l  k+k  ++++ + ++ ++ +  +  + + H Lkg    +r +H+ p +++ Y++ dd +v++ lG H+e
  gi|330507118|ref|YP_004383546.1| 10 EFDRQFIKLTrKNKALKDRFINKIDQILINPDM-GEPKSHRLKG----VRAVHVDP-FVIAYTIIDDCIVFLYLGHHNE 82
                                      788888888834444444666666666666555.4678999995....9******9.********************98 PP

                                      H CS
                        YafQ_toxin 86 l 86
                                       
  gi|330507118|ref|YP_004383546.1| 83 A 83
                                      5 PP

>> Ist1  Regulator of Vps4 activity in the MVB pathway
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.2   5.2e+03     130     139 ..      23      32 ..      10      41 .. 0.49
   2 ?   12.1   0.1     3e-05      0.14      32      67 ..      74     109 ..      63     110 .] 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                                       .T--HHHHHH CS
                              Ist1 130 ngVnekvvkk 139
                                       +  ++++++k
  gi|330507118|ref|YP_004383546.1|  23 KALKDRFINK 32 
                                       1233333333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3e-05
                                       HHTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Ist1  32 lLengkeekArirveqliredillelleilelycel 67 
                                       +L  g++++A+ + e++++ d+++ell+ ++l+ ++
  gi|330507118|ref|YP_004383546.1|  74 FLYLGHHNEAYGKTEEILQKDRTIELLKEINLLYDY 109
                                       68889***********************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 814.46
//
Query:       gi|330507119|ref|YP_004383547.1|  [L=496]
Description: aromatic amino acid decarboxylase [Methanosaeta concilii GP6]
Scores for complete 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-66  222.3   0.0    9.7e-66  222.0   0.0    1.1  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    9.7e-10   38.2   0.0    1.2e-09   37.9   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    1.6e-07   30.7   0.0    2.2e-07   30.2   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    1.4e-05   24.5   0.0    2.5e-05   23.6   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
    2.2e-05   23.3   0.0    6.5e-05   21.8   0.0    1.6  2  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
  ------ inclusion threshold ------
      0.028   13.7   0.0      0.037   13.3   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.0   0.0   3.3e-69   9.7e-66      11     374 ..      64     427 ..      54     428 .. 0.89

  Alignments for each domain:
  == domain 1  score: 222.0 bits;  conditional E-value: 3.3e-69
                                       SHHSSHH.HHHHHHHHHHCTGGGS--TTSTTBHCSSH....HHHHHHHHHHHHHT-BTSSTTTSHHHHHHHHHHHHH CS
                     Pyridoxal_deC  11 aapekaesleqilediekilapgvttwhspefhkllpagnslisllgdlLadainkngftweesPaltelevvvldw 87 
                                       + p ++++ e+i ++  + + p     ++p+f  ++  +  ++++ ++l+++a   +     ++     +e+ vldw
  gi|330507119|ref|YP_004383547.1|  64 SPPVIPQTPEEIYQEFTQYILPYQIGNSHPRFWGWVAGTGTVMGMFAELISAATDAVS-GSFSYLSNNYVEMQVLDW 139
                                       45556666679999998877765555555********999********9988766554.333455556788999*** PP

                                       HHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHH.HHHHHHHHHHTTTS.HHHHHCCEEEEEETTS-HHHHHHHH CS
                     Pyridoxal_deC  88 laellglpeeflekegggvlqvgssestllallAar.tkvikemkekgkelkeaeildklvlytsdqahssvekaal 163
                                        + +lg p    ++ + g +++g s s+l++l  ar +k++  ++ kg+++ +    + + ly+s++ahss++ka +
  gi|330507119|ref|YP_004383547.1| 140 CKTMLGYP----AT-ASGLITSGCSASNLIGLAVARnAKAQFDLRSKGMRAAP----QLMTLYCSEEAHSSIQKAVE 207
                                       ********....66.99*************98655515677788888888554....7789**************** PP

                                       HHT-E...EEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEEE-TT CS
                     Pyridoxal_deC 164 vlgvk...lrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHvDAAy 237
                                       +lg++   lr +p++e++++  ++l++ai+ d e G+ p++vv  +Gtt++ga ddl+ l++ic+k++lwlHvD A+
  gi|330507119|ref|YP_004383547.1| 208 LLGFGsraLRRVPVNESMQIDLESLKEAIKTDREGGYHPICVVGVAGTTNTGAIDDLEALAEICSKEGLWLHVDGAF 284
                                       ****9999********************************************************************* PP

                                       GGGGGGSGGGGGGGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TT.....TTTS.EECC CS
                     Pyridoxal_deC 238 aGsaficpeirhllkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLehed.....sdva.adlg 308
                                       +  a i+p  +hl+ gieradS+++  hK++     +++++++d  +  ++++l ++YL h +      ++  + l 
  gi|330507119|ref|YP_004383547.1| 285 GAWAAIAPRSKHLVAGIERADSLAFDLHKWMYLSYPIGCVFIRDADEHRRTFSLTPTYLAHGEgerglTGIDvPWLS 361
                                       ************************************************************99888555444314468 PP

                                       CGSSSSSGHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEECSTTBSSEEEEEE CS
                     Pyridoxal_deC 309 tkaiplsrrvrilklwfvlralGveglqnqirksvelakyleklirkderfeivaevelglVcFrl 374
                                       ++  +lsr +++lk w+ ++  G+e + + i++ ++ a+yl++l++k  + e++  v l  VcFr+
  gi|330507119|ref|YP_004383547.1| 362 DYGFELSRGFQALKAWMTIKEQGTEKYGRLIQQNIDQAHYLASLVEKSPQLEMALPVSLNVVCFRY 427
                                       9****************************************************************8 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   4.1e-13   1.2e-09      74     233 ..     192     406 ..     103     475 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 4.1e-13
                                       EEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-T.TS-EEEEEEEESSBTTTTTB---HHH CS
                   Beta_elim_lyase  74 vivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevga.heekiklisltvTnntagGqvvslee 149
                                         ++e+ah   + +  +  +++  lr ++ +e  ++dle+l++aik + +  + +i ++ ++ T+nt  G    ++ 
  gi|330507119|ref|YP_004383547.1| 192 LYCSEEAHSSIQKAVELLGFGSRALRRVPVNESMQIDLESLKEAIKTDREgGYHPICVVGVAGTTNT--G---AIDD 263
                                       568888999999999999999999**********************9877878899**********9..6...5799 PP

                                       HHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHH...TTSSEEEEESSSTT..--SS-EEEEE-HH........ CS
                   Beta_elim_lyase 150 lrevaaiakkygiplhlDgARfanaakslgeivkemf...syvDsvtmslkKdl..lanvGgvlafrddel...... 215
                                       l+++a+i+ k+g+ lh+DgA  a aa  ++   k ++   + +Ds+ + l K +  + ++G v + + de       
  gi|330507119|ref|YP_004383547.1| 264 LEALAEICSKEGLWLHVDGAFGAWAA--IAPRSKHLVagiERADSLAFDLHKWMylSYPIGCVFIRDADEHrrtfsl 338
                                       99******************555555..55555665544488**********7522679998888777766899999 PP

                                       ....................................................HHHHHHHHHHHHT--- CS
                   Beta_elim_lyase 216 ..................................................edylaerveqrkylgggl 233
                                                                                            +++ + q+ yl++  
  gi|330507119|ref|YP_004383547.1| 339 tptylahgegergltgidvpwlsdygfelsrgfqalkawmtikeqgtekyGRLIQQNIDQAHYLASLV 406
                                       98888888888888888888888888888888888888888888888777677788888888877655 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   7.4e-11   2.2e-07      92     336 ..     192     449 ..     154     477 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 7.4e-11
                                       EEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-.......-TTEEEEEEESBETTTTEB--HHHH CS
                       Aminotran_5  92 vvteaehhanlvpwqelakrtgakvkvipldeegeldldelekll.......nektklvaithvsnvtGtiqpveei 161
                                       ++ + e h+ +  ++el  +    ++ +p++e  ++dl+ l++++          +  v   +  + tG i+++e++
  gi|330507119|ref|YP_004383547.1| 192 LYCSEEAHSSIQKAVELLGFGSRALRRVPVNESMQIDLESLKEAIktdreggY-HPICVVGVAGTTNTGAIDDLEAL 267
                                       6778899****9******9*99***********************65554422.23345555667889********* PP

                                       HHHHHHTT-EEEEE-TTTT.....TTS---HHHHT.ESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSE CS
                       Aminotran_5 162 gklakkkgalvlvDaaqav.....ghipidvkklg.vDflafsghK.llgPtGiGvlyvrkellekleplllggemv 231
                                       ++++ k+g +++vD+a ++     +  +  v+ ++ +D laf  hK ++    iG +++r+ + e  +++ l  +++
  gi|330507119|ref|YP_004383547.1| 268 AEICSKEGLWLHVDGAFGAwaaiaPRSKHLVAGIErADSLAFDLHKwMYLSYPIGCVFIRD-ADEHRRTFSLTPTYL 343
                                       **************9865411111455555665544899*********************9.888888999888888 PP

                                       EEEET.TEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHH...HHHHHHHHHHHHHHHCTSTTEEEES.-B CS
                       Aminotran_5 232 eevsl.eettfaeapskfeaGTpnvagiiglgaaleyleeigleai...ekhekelaeyllerlkslpgvrlygpdk 304
                                       ++ +   + t  + p+    G +   g+ +l+a + +  e+g e+     +++  +a+yl + ++++p+++++    
  gi|330507119|ref|YP_004383547.1| 344 AHGEGeRGLTGIDVPWLSDYGFELSRGFQALKAWMTIK-EQGTEKYgrlIQQNIDQAHYLASLVEKSPQLEMAL--- 416
                                       88888788888899999999988888888888776654.66666651114555567778888888888888866... PP

                                       -CTCBSEEEEEETTCSH.HHHHHHHHHT.TEEEE CS
                       Aminotran_5 305 aerrasivsfnfkgvha.edvatlLdee.gIavr 336
                                        + + ++v+f + + +  + +  lL+++ +++++
  gi|330507119|ref|YP_004383547.1| 417 -PVSLNVVCFRYIRSNMsDSMLDLLNKQiEVELQ 449
                                       .467788888875555514455566665555554 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   8.3e-09   2.5e-05     102     196 ..     198     290 ..     185     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8.3e-09
                                       S-THHHHHHHHTTSE...EEEEEBEETTTTEE-HHHHHHHHTTHHCTTE.TEEEEEEESS-TTT--B--HHHHHHHH CS
                     Aminotran_1_2 102 tyasyknilrlsgge...vvryplyseedfhldlealeealkeapegnk.ktkvilvesphNPtGtvatleelekll 174
                                        ++s++++++l g+    ++r+p++  e++++dle+l+ea+k++ eg   +++v+ v++  N tG++ +le l ++ 
  gi|330507119|ref|YP_004383547.1| 198 AHSSIQKAVELLGFGsraLRRVPVN--ESMQIDLESLKEAIKTDREGGYhPICVVGVAGTTN-TGAIDDLEALAEI- 270
                                       6889999999988754347788866..********************996777777777766.9*99999999999. PP

                                       HHHHHTTEEEEEEETTTTCBSS CS
                     Aminotran_1_2 175 dlakkynlllfvDeaYagfvfg 196
                                         + k +l+l vD a+++ +  
  gi|330507119|ref|YP_004383547.1| 271 --CSKEGLWLHVDGAFGAWAAI 290
                                       ..*************9987765 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 !   21.8   0.0   2.2e-08   6.5e-05     110     196 ..     198     286 ..     176     304 .. 0.83
   2 ?   -1.9   0.0      0.35   1.1e+03     261     293 ..     376     408 ..     371     422 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.2e-08
                                       ETCHHHHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHH..HCCTCCCEEEEEECSSTTTTB----HHHHHHHHHCC CS
                           SepSecS 110 dekSslkavelaGleialvekvlegDelitdvedveeii..ekkreevilavlstlsffaprspDdvkeiakiCaey 184
                                       ++ S  kavel G+  + + +v  ++++++d+e  +e+i  ++ ++  +++v+    +      Dd++++a+iC++ 
  gi|330507119|ref|YP_004383547.1| 198 AHSSIQKAVELLGFGSRALRRVPVNESMQIDLESLKEAIktDREGGYHPICVVGVAGTTNTGAIDDLEALAEICSKE 274
                                       4557779******************************99644555667889998877666666677*********** PP

                                       T--EEEEGCCCC CS
                           SepSecS 185 dvPhlvNgAYai 196
                                       ++ + v gA++ 
  gi|330507119|ref|YP_004383547.1| 275 GLWLHVDGAFGA 286
                                       *********985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.35
                                       CCCCHHHCCHHHCCHHHHHHHHHHHHHHHHHHH CS
                           SepSecS 261 vlisllllGskaykkllkeqkesfkllreklkk 293
                                       + +++  +G++ y++l++++ +  ++l  +++k
  gi|330507119|ref|YP_004383547.1| 376 AWMTIKEQGTEKYGRLIQQNIDQAHYLASLVEK 408
                                       5678999***********999999998887765 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.2e-05     0.037      95     195 ..     223     336 ..     218     459 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                                       TTSSB-GGGCGGG--TTE....EEEEEB-GGG.....B---HHHHHHHHHHCT-EEEEE-TT-TT-EETT...EECC CS
                   DegT_DnrJ_EryC1  95 dtynidpaaieaaitert....kaIlpVhlyG.....qvadmdalkaiaakhglkvieDaAhAlGatykg...kkvG 159
                                       ++++id +++++ai + +      I +V ++G     ++ d++al +i++k gl++  D A +  a ++    + v 
  gi|330507119|ref|YP_004383547.1| 223 ESMQIDLESLKEAIKTDReggyHPICVVGVAGttntgAIDDLEALAEICSKEGLWLHVDGAFGAWAAIAPrskHLVA 299
                                       6899**********99998998667777776511111567*******************987666655544446677 PP

                                       CSSSEEEEE-BTTSSS.-SSS-EEEEESTHHHHHHHH CS
                   DegT_DnrJ_EryC1 160 algdaavfSFyptKnl.ttGeGGavvtndeelaekar 195
                                        ++ a ++ F   K +      G v+ +d++ +++  
  gi|330507119|ref|YP_004383547.1| 300 GIERADSLAFDLHKWMyLSYPIGCVFIRDADEHRRTF 336
                                       7777777777777777656666777777766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3447.46
//
Query:       gi|330507120|ref|YP_004383548.1|  [L=231]
Description: riboflavin biosynthesis protein RibD C- domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-17   61.5   0.0      2e-16   60.4   0.0    1.5  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 !   60.4   0.0   1.1e-20     2e-16       1     198 [.       3     222 ..       3     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.1e-20
                                       -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHHHTT.G... CS
                            RibD_C   1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreaeadaea... 74 
                                       p vil  avSlDG+++    + +     + ++ +    +  da l G+ t+l+      v  ++++ a   + +   
  gi|330507120|ref|YP_004383548.1|   3 PRVILHNAVSLDGRIDGFPMDLQ-----QYYELISIWKE--DATLAGSHTFLQAAS---VAPPEDESAFVPP-Kmdp 68 
                                       679*************9998888.....45555554444..899999999999888...5555554332222.2367 PP

                                       ..SS-EEEEEETTS-S-TTSHHHHSS.S-EEE.EESSCSCHHHHHHCC.......E....SE-HHHHHHHHHHT.T- CS
                            RibD_C  75 ..rqpvrvVvdstlrvpldakvltdd.aptlv.atteeadkekveklk.......v....rvdlkelleeLker.gi 135
                                         +  + v++ds+ r++  + + t    +  v + +++++++++e lk       v    +vdl ++leeL  r  +
  gi|330507120|ref|YP_004383548.1|  69 gdKRAILVIPDSRGRIRTWHYLRTLPyWRHFVaLCSKSTPDDYLEYLKqrhidciVtgedHVDLRTALEELCSRyAV 145
                                       78*************99988866655544444156788999999999998876643899***************9** PP

                                       -EEEEEETHHHHHHHHHTTT-SEEEEEEESCE--T.TSBCSSSSST-SS.............EEEEEEEEEEETTEE CS
                            RibD_C 136 rsllveGGatLagsllraglvDelrlyiaPkllGg.agktlfdgegfka.............lklklvksealgegv 198
                                       r +   +G+tL+g llr+glv+e+ ++i+P l+Gg  + ++f   +++a             + l+l+k+e+l  +v
  gi|330507120|ref|YP_004383548.1| 146 RVVRADAGGTLNGLLLRQGLVNEVSVLIYPSLVGGeTTSSIFRAPDLPAaadgapgqgaegtISLQLMKTEKLKGDV 222
                                       ***********************************999999999999988899999998888888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.70
# Mc/sec: 998.28
//
Query:       gi|330507121|ref|YP_004383549.1|  [L=86]
Description: hypothetical protein MCON_0969 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 626.70
//
Query:       gi|330507122|ref|YP_004383550.1|  [L=684]
Description: stage II sporulation SpoIIE family protein [Methanosaeta concilii GP6]
Scores for 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  119.2   0.0    3.1e-34  118.6   0.0    1.3  1  SpoIIE    Stage II sporulation protein E (SpoIIE)
    1.6e-19   70.7   0.0    3.1e-19   69.7   0.0    1.5  1  dCache_1  Cache domain
    6.3e-06   26.5   0.2    1.7e-05   25.1   0.2    1.8  1  HAMP      HAMP domain
  ------ inclusion threshold ------
       0.25   11.6   0.6        4.7    7.5   0.2    2.5  2  DUF948    Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> SpoIIE  Stage II sporulation protein E (SpoIIE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   0.0   6.8e-38   3.1e-34       2     192 ..     496     683 ..     495     684 .] 0.91

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 6.8e-38
                                       TTEEEEEEEECSSSSHHHHHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHCHCTTSTT.TTCEEEEEEEETTTTEEEE CS
                            SpoIIE   2 dgrlalvvgDvvGhGleAalimgllrsalrelataglepaevlkrlnralardleeeerfaTavlavydpstgkley 78 
                                       d+++al+++ v G G++Aa+++ + r ++r+  + ++ p++ +++ln+++ ++++      ++++a +dps++ ley
  gi|330507122|ref|YP_004383550.1| 496 DDKIALAMAGVGGDGIQAAMLAIMSRALIRACPE-KMGPSNTISKLNSQI-SQYGRG-TNLACFYALLDPSNHILEY 569
                                       6899*************************99875.567************.999999.9****************** PP

                                       EEESSSSEEEEETTSTEEEEE--SS--TTTSSST-EEEEEEE--TTEEEEEESCCCCSSSHHHHHHCCCHHCHHHHC CS
                            SpoIIE  79 anaGhpppllvrpdggtklllastglplGilpeadyetaelelepgdtlllyTDGvtEardsdgelfgkerllalla 155
                                       +naG +pp++v+p gg +  l ++g++lG+l+ ++ e++ ++++pgd++++y+DGv+Ea+++dge fg+erl++l+ 
  gi|330507122|ref|YP_004383550.1| 570 VNAGFNPPFIVDP-GGMVDTLGGGGIALGMLDRLELEETCIPVQPGDVMVIYSDGVVEAENEDGEPFGLERLINLVI 645
                                       *************.*************************************************************** PP

                                       T.....HCCHHHHHHHHHHH..HTTSSSSS-EEEEEEEE CS
                            SpoIIE 156 saegesleelldalveelle..lgsgeleDDitllvlrv 192
                                       ++++ s+ee+l+   +e++     ++    D++++v+++
  gi|330507122|ref|YP_004383550.1| 646 NNRTLSAEEILWIAEKEIQGfsV-GSMNPVDLAMIVIKR 683
                                       ***********999999888532.233344667666665 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.0   6.9e-23   3.1e-19      64     248 ..     140     326 ..      38     327 .. 0.69

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 6.9e-23
                          dCache_1  64 lksilksnpdisgv.ylvdadGqviassdpssppnleg..tddpadrdwykealaggggkpvisdpyvdqtggkpvi 137
                                       ++s++++ + +  + y+ ++dG +++  +p+s  +l+    + + d++ y  a++++  k++++ py + + g+ ++
  gi|330507122|ref|YP_004383550.1| 140 MQSLHET-EPVLTLsYIGTEDGVLVT--WPYSTDSLKStaPFSYKDTPNYALAKSRK--KTIWTGPYENDE-GDRMM 210
                                       2222222.334445255567777765..666655777789999999999********..9*******8766.***** PP

                          dCache_1 138 tiavpiyddsgkfiGvlaadldldnlqdllsniklgetgyvfivdsdGniiahpdkdl........lgknlrdelka 206
                                       ti++p + + g+f G++++d++++++   ls ++ g +gy fi+d++G+i+a ++++           +nl+     
  gi|330507122|ref|YP_004383550.1| 211 TITTPFFRE-GEFAGIMGMDVSIESIFTDLSMMR-G-RGYPFIIDGTGLIVARSNNKPdeplniifGSENLS----- 279
                                       *******85.***********************8.5.5**************98843335777774333333..... PP

                          dCache_1 207 q......ealekalakiesgvssvklngeeylvayapiptglgWylvv 248
                                       +       a  k + k  sg+  v l+ ++ +vay+pi t  gW+l +
  gi|330507122|ref|YP_004383550.1| 280 EaaspevRAVAKKMLKGSSGSAIVALGRDDGYVAYSPITT-PGWILGI 326
                                       13344698888888999999999999997666******87.****976 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.2   3.8e-09   1.7e-05      10      52 ..     392     432 ..     383     433 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.8e-09
                                       HHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                              HAMP  10 LrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                       +  Lar a++i++Gd+d+r   ++  E+++La afN M+  L+
  gi|330507122|ref|YP_004383550.1| 392 IDSLARMAEKISRGDFDVR--ANTSGELADLAWAFNSMASDLK 432
                                       789****************..9*****************9886 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2     0.001       4.7       3      41 ..      16      54 ..      14      97 .. 0.81
   2 ?    1.6   0.0     0.075   3.3e+02       6      71 ..     370     439 ..     365     443 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.001
                            DUF948  3 glIaAiAFvvLviflivvllklkktldeaaatieelekq 41
                                      +++aA A++ L  + iv ll++ +  + +++ i++l   
  gi|330507122|ref|YP_004383550.1| 16 VILAAFALLPLFYVGIVSLLEMDQASRDVQENITQLSVS 54
                                      789******************************999843 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.075
                            DUF948   6 aAiAFvvLviflivvllklkktldeaaatieele....kqvdpilkevedllakvnelledvneklekvd 71 
                                       +Ai+++++    + + +++++ +d++a++ e++     +   +++ e++dl    n +++d+++  +++d
  gi|330507122|ref|YP_004383550.1| 370 FAITVIAVLGAGFLIGRRIEEDIDSLARMAEKISrgdfDVRANTSGELADLAWAFNSMASDLKHYAAALD 439
                                       3333334444444444577888999999999998777666678999999999999999999999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (684 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4464.21
//
Query:       gi|330507123|ref|YP_004383551.1|  [L=69]
Description: hypothetical protein MCON_0979 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-10   40.9   0.0      2e-10   40.9   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
    0.00019   21.3   0.0    0.00021   21.2   0.0    1.1  1  DUF1902          Domain of unknown function (DUF1902)
  ------ inclusion threshold ------
       0.18   12.0   0.0        0.2   11.8   0.0    1.2  1  DUF4119          Domain of unknown function, B. Theta Gene de


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 !   40.9   0.0   3.3e-14     2e-10       1      47 [.       3      49 ..       3      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3.3e-14
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhleg 47
                                      + +++ +ded  y  +vP+lpGc++ +++l++ ++ +keai+l+le+
  gi|330507123|ref|YP_004383551.1|  3 FEVVVRTDEDGYYVATVPELPGCHTQAKSLDDLMNRIKEAISLYLET 49
                                      678999***************************************98 PP

>> DUF1902  Domain of unknown function (DUF1902)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.6e-08   0.00021      10      57 ..      10      57 ..       3      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.6e-08
                                      TTTTEEEEE-SSSTT---EESSHHHHHHHHHHHHHHHHHHS----.-S CS
                           DUF1902 10 eeAgVWvaesddipGlvteaetleeLlkkleamipdlLeeNadsrakk 57
                                      +e g +va+  ++pG  t+a++l+ L+++++ +i   Le    s a+ 
  gi|330507123|ref|YP_004383551.1| 10 DEDGYYVATVPELPGCHTQAKSLDDLMNRIKEAISLYLETEGGSTAGS 57
                                      46699*****************************98888777666655 PP

>> DUF4119  Domain of unknown function, B. Theta Gene description (DUF4119)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.4e-05       0.2      59      85 ..      26      52 ..       7      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                           DUF4119 59 vkyskkLkdLakyiydkevlYvakhgG 85
                                      + + k+L dL + i++  +lY++++gG
  gi|330507123|ref|YP_004383551.1| 26 HTQAKSLDDLMNRIKEAISLYLETEGG 52
                                      5678*********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 523.79
//
Query:       gi|330507124|ref|YP_004383552.1|  [L=403]
Description: hypothetical protein MCON_0980 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-41  140.8   0.0    3.7e-41  139.9   0.0    1.5  1  DUF4277    Domain of unknown function (DUF4277)
    0.00045   19.9   0.0    0.00063   19.4   0.0    1.3  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
       0.11   13.1   0.1         13    6.5   0.0    2.9  3  DUF5395    Family of unknown function (DUF5395)


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   0.0   6.1e-45   3.7e-41       3     109 .]      10     116 ..       8     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 6.1e-45
                           DUF4277   3 vksldhlglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfpeffedkplerLlgegve 79 
                                       + sldhlglva+++d+lg++e+ide ipk++++k+s++ ++ka+++ngLgf +r+Ly+fp++fe+++lerL+++gv 
  gi|330507124|ref|YP_004383552.1|  10 TLSLDHLGLVAAIFDALGISEVIDESIPKTRNCKLSHSAIIKAMVINGLGFAERRLYIFPSYFENLALERLFNPGVV 86 
                                       679************************************************************************** PP

                           DUF4277  80 aehlnddrlgrtLDklyeagvtklfteial 109
                                       +e++n+d++grtLD++ ++g t+lf++ia+
  gi|330507124|ref|YP_004383552.1|  87 PEDFNEDVVGRTLDRINKFGSTALFNNIAM 116
                                       ****************************86 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.1e-07   0.00063       9     143 ..     131     277 ..     124     343 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-07
                         DDE_Tnp_1   9 vDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                       vD t++ v+g                  +d+rw        + + + +++++  g++l v+ ++gn++d k+l++++
  gi|330507124|ref|YP_004383552.1| 131 VDTTSFGVHGDYegldcnpameitlghpKDGRW------DLKQFIVSMVTNQC-GIPLFVQAHSGNKSDKKTLIETI 200
                                       666666666666666666554444444444444......55667788888888.9********************** PP

                         DDE_Tnp_1  70 delrpr....kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrn 142
                                       ++++ +     + ++ aD++ +s e+++ l      +i r++  +++ ++      +++++ +dr+ i++++ +  +
  gi|330507124|ref|YP_004383552.1| 201 QMFKSNldfsGKNYFAADSALFSSENIRLLG-DSTLWITRVPTTVREVKDLQRLDLEMKTCSDDRYSIFETEINYGG 276
                                       **********9*********99999999999.555599999888877777555568888888888888888777777 PP

                         DDE_Tnp_1 143 k 143
                                        
  gi|330507124|ref|YP_004383552.1| 277 I 277
                                       7 PP

>> DUF5395  Family of unknown function (DUF5395)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0021        13       4      41 ..     227     264 ..     225     274 .. 0.87
   2 ?   -1.9   0.0      0.95   5.7e+03      11      39 ..     279     306 ..     268     315 .. 0.61
   3 ?    3.1   0.0     0.025   1.5e+02      10      35 ..     330     355 ..     323     368 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0021
                           DUF5395   4 lrlvhdgekWiaeneelvvkgktleeLDenlakelkkr 41 
                                       +rl  d + Wi +  + v + k+l+ LD +++++  +r
  gi|330507124|ref|YP_004383552.1| 227 IRLLGDSTLWITRVPTTVREVKDLQRLDLEMKTCSDDR 264
                                       7889999***********************99986665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.95
                           DUF5395  11 ekWiaeneelvvkgktleeLDenlakelk 39 
                                       +kW++  +  ++++++ +  D+ + ke  
  gi|330507124|ref|YP_004383552.1| 279 QKWVVVDSR-EMHASKAKTFDRRIGKEFT 306
                                       578775432.4444555566666666555 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.025
                           DUF5395  10 gekWiaeneelvvkgktleeLDenla 35 
                                        ++Wi en +++ +g ++ e+ + + 
  gi|330507124|ref|YP_004383552.1| 330 ADRWISENPHFTLTGLSICEISKRID 355
                                       579************99999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2724.46
//
Query:       gi|330507125|ref|YP_004383553.1|  [L=109]
Description: IS3/IS66 family element, Orf1 protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.9e-11   41.8   0.1    1.6e-10   41.1   0.0    1.5  1  HTH_Tnp_1  Transposase
      0.002   17.8   0.0     0.0044   16.8   0.0    1.6  1  HTH_23     Homeodomain-like domain
     0.0046   17.0   0.0     0.0099   16.0   0.0    1.6  1  HTH_28     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.033   14.1   0.3      0.074   12.9   0.3    1.6  1  PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein k
      0.062   13.8   0.1       0.13   12.7   0.0    1.5  2  DUF4733    Domain of unknown function (DUF4733)


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   4.4e-14   1.6e-10       2      74 ..       3      75 ..       2      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 4.4e-14
                         HTH_Tnp_1  2 rrrrrwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyr...egeeaspaefeltaleeenrelkrel 74
                                      ++rrr+++ fK+++++e  e+gk+ +++Ar++g++p+   +W+++     e  +a   +    + +++++el+r+l
  gi|330507125|ref|YP_004383553.1|  3 KTRRRYDRDFKISVLAEL-EAGKPLAQIAREYGIHPSLPCRWKAELAenpE--KAFMGNGNKYKDQAKIAELERLL 75
                                      79***************9.*************************9975332..33333333344466777777765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.2e-06    0.0044       8      40 ..      14      46 ..       2      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                      +++l  l  G++ ++IAre+g++++  +rw+  
  gi|330507125|ref|YP_004383553.1| 14 ISVLAELEAGKPLAQIAREYGIHPSLPCRWKAE 46
                                      567888888***************987777765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.8e-06    0.0099       1      27 [.      12      38 ..      12      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
                            HTH_28  1 qRleiikllaaGhsvreaArelgisrr 27
                                      +++ ++ +l aG++ +++Are+gi+++
  gi|330507125|ref|YP_004383553.1| 12 FKISVLAELEAGKPLAQIAREYGIHPS 38
                                      7999********************997 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.1e-05     0.074       9      28 ..      67      86 ..      61      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                         PKcGMP_CC  9 RIRELEkrlaekdeEIqELr 28
                                      +I+ELE+ l + ++EI  L+
  gi|330507125|ref|YP_004383553.1| 67 KIAELERLLGQAHAEIDLLK 86
                                      9***************9888 PP

>> DUF4733  Domain of unknown function (DUF4733)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.7e-05      0.13      29      67 ..       4      42 ..       1      51 [. 0.88
   2 ?   -2.0   0.0       1.4     5e+03      32      32 ..      91      91 ..      64     106 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                           DUF4733 29 qplrpqravleelsaplelsqplsgllddyGilPkhPrp 67
                                        +r+ r +   + a le  +pl+++  +yGi+P  P +
  gi|330507125|ref|YP_004383553.1|  4 TRRRYDRDFKISVLAELEAGKPLAQIAREYGIHPSLPCR 42
                                      56899999999***********************99976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                           DUF4733 32 r 32
                                       
  gi|330507125|ref|YP_004383553.1| 91 M 91
                                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 824.40
//
Query:       gi|330507126|ref|YP_004383554.1|  [L=292]
Description: transposase IS3 family protein integrase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-25   89.8   0.0    2.2e-25   89.1   0.0    1.3  1  rve            Integrase core domain
    2.7e-19   69.1   0.3    1.9e-18   66.3   0.3    2.1  2  HTH_21         HTH-like domain
    3.8e-16   58.6   0.1    9.1e-16   57.4   0.1    1.7  1  rve_3          Integrase core domain
    4.7e-08   33.1   3.6    9.4e-08   32.1   2.4    2.1  2  rve_2          Integrase core domain
    0.00016   21.9   0.3    0.00028   21.1   0.3    1.4  1  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.027   14.6   0.1         12    6.1   0.0    2.4  2  GP3_package    DNA-packaging protein gp3
      0.041   14.1   0.0       0.11   12.7   0.0    1.7  1  HTH_Tnp_Tc3_2  Transposase
      0.049   13.8   0.1       0.17   12.0   0.0    1.9  2  HTH_Tnp_1_2    Helix-turn-helix of insertion element transpos


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.0   9.9e-29   2.2e-25       5     117 ..     127     239 ..     124     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 9.9e-29
                               rve   5 gelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve..pervlsDngseyt 79 
                                       ++ w +D+t+v++      ++l+v++d +sr ++++ ls+++ ++++  +l +a++++ ++    ++++sD+g +y+
  gi|330507126|ref|YP_004383554.1| 127 NQAWASDITYVQLQHE--HIFLAVILDLYSRKCIGWELSRSIRSDLAMSALAKALKNRSKESleGLIHHSDQGVQYA 201
                                       899*********6655..5*****************************************8899************* PP

                               rve  80 skafrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                       sk++ + l+ ++i++s++r+g+p+dn+ +E+f++tlk 
  gi|330507126|ref|YP_004383554.1| 202 SKDYVDCLKAHDIQISMSRKGNPYDNAFAESFIKTLKV 239
                                       ************************************95 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.3   8.5e-22   1.9e-18       6      58 ..      49      99 ..      45     101 .. 0.90
   2 ?   -0.0   0.0      0.45     1e+03      13      33 ..     257     277 ..     248     292 .] 0.66

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 8.5e-22
                            HTH_21  6 llalireifeeskgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgvqrr 58
                                      l ++i+ei  e  + YGyrri+aeL+++g+ +vnhkrV RlMr+++L+++ ++
  gi|330507126|ref|YP_004383554.1| 49 LVNQIQEIALEF-PYYGYRRITAELQNRGY-AVNHKRVLRLMRQEKLLCYKKK 99
                                      7899********.9**************87.5*****************9544 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.45
                            HTH_21  13 ifeeskgrYGyrriwaeLrre 33 
                                       i++    +Y ++r++ +L+ +
  gi|330507126|ref|YP_004383554.1| 257 ICNFIENVYNHKRLHSALNYR 277
                                       555445577788888888854 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1   4.1e-19   9.1e-16       1      67 []     212     279 ..     212     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 4.1e-19
                             rve_3   1 lgielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawred.YNteRPHssLgykTP 67 
                                       ++i++s+++ g P++N+++Esf++tl+ e ++ + ++++++a +++ +++e  YN++R Hs+L+y++P
  gi|330507126|ref|YP_004383554.1| 212 HDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHSALNYRSP 279
                                       689***************************************99999999866*************99 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.4     3e+03      21      33 ..     196     208 ..     184     209 .. 0.74
   2 !   32.1   2.4   4.2e-11   9.4e-08       1      48 [.     231     283 ..     231     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                             rve_2  21 eeleaaiedYIew 33 
                                       + ++ a +dY+++
  gi|330507126|ref|YP_004383554.1| 196 QGVQYASKDYVDC 208
                                       556788999*986 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 4.2e-11
                             rve_2   1 EsfFgsLKtElvygetfktleeleaaiedYIew.YNnkRlk....glsPvqYr 48 
                                       Esf ++LK+E vy  +++t+e +   i ++Ie  YN+kRl+    + sPvq++
  gi|330507126|ref|YP_004383554.1| 231 ESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHsalnYRSPVQFE 283
                                       9******************************988*****988888*******8 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   1.3e-07   0.00028       2     139 ..     128     271 ..     127     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                     DDE_Tnp_IS240   2 kswrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkek.lepeeivtDkasayasalke 76 
                                       ++w+ D Tyv+ + +  +l  ++D  +r  +++ +s     + a  +l kalk+ + ++ e ++    +  + a k 
  gi|330507126|ref|YP_004383554.1| 128 QAWASDITYVQLQHEHIFLAVILDLYSRkCIGWELSRSIRSDLAMSALAKALKNRSkESLEGLIHHSDQGVQYASKD 204
                                       68************************************999************998455555665555555555555 PP

                     DDE_Tnp_IS240  77 lkr...egelfdevshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktl.agfeavknlrkgh 139
                                         +     + + ++s+   +y n   Es  +tlK++  + +  ++++ a + + + +e v+n+++ h
  gi|330507126|ref|YP_004383554.1| 205 YVDclkAHDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNIcNFIENVYNHKRLH 271
                                       44411123556788899999***************************99877625679999999977 PP

>> GP3_package  DNA-packaging protein gp3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0053        12      49      78 ..      19      55 ..      15      63 .. 0.82
   2 ?    6.1   0.0    0.0052        12      51      90 ..     236     275 ..     199     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0053
                                      HHHHT--HHHHHHHGG..SHHH.......HHHHHHHH CS
                       GP3_package 49 alyLgisrstlkeyekrkrefs.......etierikq 78
                                      +l+L++srs  +e+ kr+++f        +++++i++
  gi|330507126|ref|YP_004383554.1| 19 CLALDVSRSGYYEWLKRSEKFTaensessDLVNQIQE 55
                                      899***************9998666666666666555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0052
                                       HHT--HHHHHHHGG..SHHHHHHHHHHHHHHHHHHHHHHT CS
                       GP3_package  51 yLgisrstlkeyekrkrefsetierikqivenqqiegala 90 
                                        L + + +l+eye+ +  f ++ + i+++ +++++  al 
  gi|330507126|ref|YP_004383554.1| 236 TLKVEEVYLNEYETFEDAFRNICNFIENVYNHKRLHSALN 275
                                       6889999*******999****************9999876 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.9e-05      0.11       3      56 ..      52     105 ..      50     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                     HTH_Tnp_Tc3_2   3 rIvrlvrkdPritlreLanelkeeGksvsreTirrrLrkaglkkrkprkkplLs 56 
                                       +I +++ + P+  +r++++el+++G  v ++ + r +r+++l  +k + kp+ +
  gi|330507126|ref|YP_004383554.1|  52 QIQEIALEFPYYGYRRITAELQNRGYAVNHKRVLRLMRQEKLLCYKKKFKPVTT 105
                                       68888889999**********************************999999755 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.7e-05      0.17      33      61 ..      19      48 ..      13      58 .. 0.83
   2 ?   -2.7   0.1       2.7   6.1e+03      55      72 ..     225     243 ..     224     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.7e-05
                                      HHHHTS-HHHHHHHH.H-HHHHHHHHHHHH CS
                       HTH_Tnp_1_2 33 aeevgvsrsTlykWk.kkkeFieyvnelae 61
                                      +  + vsrs +y+W+ + ++F+++ +e ++
  gi|330507126|ref|YP_004383554.1| 19 CLALDVSRSGYYEWLkRSEKFTAENSESSD 48
                                      56789*********9889999999888765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHT.THHHHH CS
                       HTH_Tnp_1_2  55 yvnelaeeflee.eraevy 72 
                                       y n  ae+f+++ +++evy
  gi|330507126|ref|YP_004383554.1| 225 YDNAFAESFIKTlKVEEVY 243
                                       7899999999873557777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2133.67
//
Query:       gi|330507127|ref|YP_004383555.1|  [L=283]
Description: transposase, IS116/IS110/IS902 family, partial [Methanosaeta concilii GP6]
Scores for complete 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-25   87.1   0.0    1.2e-24   86.4   0.0    1.3  1  Transposase_20  Transposase IS116/IS110/IS902 family


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4   0.0   6.7e-29   1.2e-24       3      86 ..     117     201 ..     115     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 6.7e-29
                    Transposase_20   3 lLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaairan 79 
                                       + +sipG G+v a+a+laeig+ + f++++qlaa++Gl+p+ +qS++k   g+i+k+G++++Rr+L++ A a++r++
  gi|330507127|ref|YP_004383555.1| 117 IAMSIPGTGFVSATAILAEIGNYTDFEKPEQLAAWCGLVPSLYQSAEKTILGGITKQGSKHIRRMLIQVAYAISRTK 193
                                       679*********************************************99************************998 PP

                    Transposase_20  80 .pelrayy 86 
                                        ++l++++
  gi|330507127|ref|YP_004383555.1| 194 dSKLKKFF 201
                                       89999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2182.28
//
Query:       gi|330507128|ref|YP_004383556.1|  [L=339]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete 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   87.3   0.0    1.1e-24   86.6   0.0    1.4  1  Transposase_20  Transposase IS116/IS110/IS902 family
    1.4e-13   51.0   0.0    3.3e-13   49.8   0.0    1.7  1  DEDD_Tnp_IS110  Transposase
  ------ inclusion threshold ------
       0.51   10.6   3.6          4    7.8   0.1    2.8  2  DUF4164         Domain of unknown function (DUF4164)


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.0   1.8e-28   1.1e-24       3      86 ..     173     257 ..     171     258 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 1.8e-28
                    Transposase_20   3 lLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaairan 79 
                                       + +sipG G+v a+a+laeig+ + fk+++qlaa++Gl+p+ +qS++k   g+i+k+G++++Rr+L++ A a++r++
  gi|330507128|ref|YP_004383556.1| 173 IAMSIPGTGFVSATAILAEIGNYTDFKKPEQLAAWCGLVPSLYQSAEKTILGGITKQGSKHIRRMLIQVAYAISRTK 249
                                       679*********************************************99************************998 PP

                    Transposase_20  80 .pelrayy 86 
                                        ++l++++
  gi|330507128|ref|YP_004383556.1| 250 dSKLKKFF 257
                                       89999885 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   5.5e-17   3.3e-13      87     154 ..      10      76 ..       1      77 [. 0.90

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 5.5e-17
                    DEDD_Tnp_IS110  87 lylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdqvf 154
                                        +  ++KtD  D+++IA+l +  g ++p++  +++ +eLr+ltr+re +vk++t++kn++++ Ld+ +
  gi|330507128|ref|YP_004383556.1|  10 KHTPGRKTDVSDSEWIAELCL-NGMIEPSRIFPKDDRELRRLTRAREGYVKQMTQEKNKIHQSLDSAC 76 
                                       456789***************.******************************************9876 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1   0.00068         4      32      64 ..      49      81 ..      41      84 .. 0.82
   2 ?    2.1   0.1      0.04   2.4e+02      11      33 ..     147     169 ..     140     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00068
                           DUF4164 32 rkrdeleaeiealgedrsRLaeeLdqaearaar 64
                                      r ++++e  +++++++++++ + Ld+a  ++a+
  gi|330507128|ref|YP_004383556.1| 49 RLTRAREGYVKQMTQEKNKIHQSLDSACIKLAS 81
                                      445788999*****************9888776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.04
                           DUF4164  11 trLeaaldsLEkavdrrleaerk 33 
                                       + +++ +d+L++ + +r++  ++
  gi|330507128|ref|YP_004383556.1| 147 KSIQERIDELDGEISARIQYRKN 169
                                       67888999999999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); 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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 2581.74
//
Query:       gi|330507129|ref|YP_004383557.1|  [L=158]
Description: transposase domain [Methanosaeta concilii GP6]
Scores for complete 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    2.5e-05   24.0   0.0    1.2  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 !   24.0   0.0   1.4e-09   2.5e-05     152     213 ..      14      76 ..       6      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.4e-09
                         DDE_Tnp_1 152 yyvtntnsellsaeevaelyrlRwqiErvFkwlkrk.fgldrlryrglnrveaqllllllaln 213
                                        +v+  n+++l+ e + ++y+ +  +E  F++lk+k f+   +++++ +r+ea  +++ l+l+
  gi|330507129|ref|YP_004383557.1|  14 RFVLASNDKTLEGELMLQYYKGQNAVEKGFRFLKDKsFRVAEVYLKKEERIEALSMIMVLSLL 76 
                                       578889999************************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1207.67
//
Query:       gi|330507130|ref|YP_004383558.1|  [L=292]
Description: transposase IS3 family protein integrase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-25   89.8   0.0    2.2e-25   89.1   0.0    1.3  1  rve            Integrase core domain
    2.7e-19   69.1   0.3    1.9e-18   66.3   0.3    2.1  2  HTH_21         HTH-like domain
    3.8e-16   58.6   0.1    9.1e-16   57.4   0.1    1.7  1  rve_3          Integrase core domain
    4.7e-08   33.1   3.6    9.4e-08   32.1   2.4    2.1  2  rve_2          Integrase core domain
    0.00016   21.9   0.3    0.00028   21.1   0.3    1.4  1  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.027   14.6   0.1         12    6.1   0.0    2.4  2  GP3_package    DNA-packaging protein gp3
      0.041   14.1   0.0       0.11   12.7   0.0    1.7  1  HTH_Tnp_Tc3_2  Transposase
      0.049   13.8   0.1       0.17   12.0   0.0    1.9  2  HTH_Tnp_1_2    Helix-turn-helix of insertion element transpos


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.0   9.9e-29   2.2e-25       5     117 ..     127     239 ..     124     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 9.9e-29
                               rve   5 gelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve..pervlsDngseyt 79 
                                       ++ w +D+t+v++      ++l+v++d +sr ++++ ls+++ ++++  +l +a++++ ++    ++++sD+g +y+
  gi|330507130|ref|YP_004383558.1| 127 NQAWASDITYVQLQHE--HIFLAVILDLYSRKCIGWELSRSIRSDLAMSALAKALKNRSKESleGLIHHSDQGVQYA 201
                                       899*********6655..5*****************************************8899************* PP

                               rve  80 skafrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                       sk++ + l+ ++i++s++r+g+p+dn+ +E+f++tlk 
  gi|330507130|ref|YP_004383558.1| 202 SKDYVDCLKAHDIQISMSRKGNPYDNAFAESFIKTLKV 239
                                       ************************************95 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.3   8.5e-22   1.9e-18       6      58 ..      49      99 ..      45     101 .. 0.90
   2 ?   -0.0   0.0      0.45     1e+03      13      33 ..     257     277 ..     248     292 .] 0.66

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 8.5e-22
                            HTH_21  6 llalireifeeskgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgvqrr 58
                                      l ++i+ei  e  + YGyrri+aeL+++g+ +vnhkrV RlMr+++L+++ ++
  gi|330507130|ref|YP_004383558.1| 49 LVNQIQEIALEF-PYYGYRRITAELQNRGY-AVNHKRVLRLMRQEKLLCYKKK 99
                                      7899********.9**************87.5*****************9544 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.45
                            HTH_21  13 ifeeskgrYGyrriwaeLrre 33 
                                       i++    +Y ++r++ +L+ +
  gi|330507130|ref|YP_004383558.1| 257 ICNFIENVYNHKRLHSALNYR 277
                                       555445577788888888854 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1   4.1e-19   9.1e-16       1      67 []     212     279 ..     212     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 4.1e-19
                             rve_3   1 lgielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawred.YNteRPHssLgykTP 67 
                                       ++i++s+++ g P++N+++Esf++tl+ e ++ + ++++++a +++ +++e  YN++R Hs+L+y++P
  gi|330507130|ref|YP_004383558.1| 212 HDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHSALNYRSP 279
                                       689***************************************99999999866*************99 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.4     3e+03      21      33 ..     196     208 ..     184     209 .. 0.74
   2 !   32.1   2.4   4.2e-11   9.4e-08       1      48 [.     231     283 ..     231     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                             rve_2  21 eeleaaiedYIew 33 
                                       + ++ a +dY+++
  gi|330507130|ref|YP_004383558.1| 196 QGVQYASKDYVDC 208
                                       556788999*986 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 4.2e-11
                             rve_2   1 EsfFgsLKtElvygetfktleeleaaiedYIew.YNnkRlk....glsPvqYr 48 
                                       Esf ++LK+E vy  +++t+e +   i ++Ie  YN+kRl+    + sPvq++
  gi|330507130|ref|YP_004383558.1| 231 ESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHsalnYRSPVQFE 283
                                       9******************************988*****988888*******8 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   1.3e-07   0.00028       2     139 ..     128     271 ..     127     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                     DDE_Tnp_IS240   2 kswrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkek.lepeeivtDkasayasalke 76 
                                       ++w+ D Tyv+ + +  +l  ++D  +r  +++ +s     + a  +l kalk+ + ++ e ++    +  + a k 
  gi|330507130|ref|YP_004383558.1| 128 QAWASDITYVQLQHEHIFLAVILDLYSRkCIGWELSRSIRSDLAMSALAKALKNRSkESLEGLIHHSDQGVQYASKD 204
                                       68************************************999************998455555665555555555555 PP

                     DDE_Tnp_IS240  77 lkr...egelfdevshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktl.agfeavknlrkgh 139
                                         +     + + ++s+   +y n   Es  +tlK++  + +  ++++ a + + + +e v+n+++ h
  gi|330507130|ref|YP_004383558.1| 205 YVDclkAHDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNIcNFIENVYNHKRLH 271
                                       44411123556788899999***************************99877625679999999977 PP

>> GP3_package  DNA-packaging protein gp3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0053        12      49      78 ..      19      55 ..      15      63 .. 0.82
   2 ?    6.1   0.0    0.0052        12      51      90 ..     236     275 ..     199     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0053
                                      HHHHT--HHHHHHHGG..SHHH.......HHHHHHHH CS
                       GP3_package 49 alyLgisrstlkeyekrkrefs.......etierikq 78
                                      +l+L++srs  +e+ kr+++f        +++++i++
  gi|330507130|ref|YP_004383558.1| 19 CLALDVSRSGYYEWLKRSEKFTaensessDLVNQIQE 55
                                      899***************9998666666666666555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0052
                                       HHT--HHHHHHHGG..SHHHHHHHHHHHHHHHHHHHHHHT CS
                       GP3_package  51 yLgisrstlkeyekrkrefsetierikqivenqqiegala 90 
                                        L + + +l+eye+ +  f ++ + i+++ +++++  al 
  gi|330507130|ref|YP_004383558.1| 236 TLKVEEVYLNEYETFEDAFRNICNFIENVYNHKRLHSALN 275
                                       6889999*******999****************9999876 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.9e-05      0.11       3      56 ..      52     105 ..      50     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                     HTH_Tnp_Tc3_2   3 rIvrlvrkdPritlreLanelkeeGksvsreTirrrLrkaglkkrkprkkplLs 56 
                                       +I +++ + P+  +r++++el+++G  v ++ + r +r+++l  +k + kp+ +
  gi|330507130|ref|YP_004383558.1|  52 QIQEIALEFPYYGYRRITAELQNRGYAVNHKRVLRLMRQEKLLCYKKKFKPVTT 105
                                       68888889999**********************************999999755 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.7e-05      0.17      33      61 ..      19      48 ..      13      58 .. 0.83
   2 ?   -2.7   0.1       2.7   6.1e+03      55      72 ..     225     243 ..     224     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.7e-05
                                      HHHHTS-HHHHHHHH.H-HHHHHHHHHHHH CS
                       HTH_Tnp_1_2 33 aeevgvsrsTlykWk.kkkeFieyvnelae 61
                                      +  + vsrs +y+W+ + ++F+++ +e ++
  gi|330507130|ref|YP_004383558.1| 19 CLALDVSRSGYYEWLkRSEKFTAENSESSD 48
                                      56789*********9889999999888765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHT.THHHHH CS
                       HTH_Tnp_1_2  55 yvnelaeeflee.eraevy 72 
                                       y n  ae+f+++ +++evy
  gi|330507130|ref|YP_004383558.1| 225 YDNAFAESFIKTlKVEEVY 243
                                       7899999999873557777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2152.36
//
Query:       gi|330507131|ref|YP_004383559.1|  [L=109]
Description: IS3/IS66 family element, Orf1 protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.9e-11   41.8   0.1    1.6e-10   41.1   0.0    1.5  1  HTH_Tnp_1  Transposase
      0.002   17.8   0.0     0.0044   16.8   0.0    1.6  1  HTH_23     Homeodomain-like domain
     0.0046   17.0   0.0     0.0099   16.0   0.0    1.6  1  HTH_28     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.033   14.1   0.3      0.074   12.9   0.3    1.6  1  PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein k
      0.062   13.8   0.1       0.13   12.7   0.0    1.5  2  DUF4733    Domain of unknown function (DUF4733)


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   4.4e-14   1.6e-10       2      74 ..       3      75 ..       2      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 4.4e-14
                         HTH_Tnp_1  2 rrrrrwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyr...egeeaspaefeltaleeenrelkrel 74
                                      ++rrr+++ fK+++++e  e+gk+ +++Ar++g++p+   +W+++     e  +a   +    + +++++el+r+l
  gi|330507131|ref|YP_004383559.1|  3 KTRRRYDRDFKISVLAEL-EAGKPLAQIAREYGIHPSLPCRWKAELAenpE--KAFMGNGNKYKDQAKIAELERLL 75
                                      79***************9.*************************9975332..33333333344466777777765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.2e-06    0.0044       8      40 ..      14      46 ..       2      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                      +++l  l  G++ ++IAre+g++++  +rw+  
  gi|330507131|ref|YP_004383559.1| 14 ISVLAELEAGKPLAQIAREYGIHPSLPCRWKAE 46
                                      567888888***************987777765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.8e-06    0.0099       1      27 [.      12      38 ..      12      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
                            HTH_28  1 qRleiikllaaGhsvreaArelgisrr 27
                                      +++ ++ +l aG++ +++Are+gi+++
  gi|330507131|ref|YP_004383559.1| 12 FKISVLAELEAGKPLAQIAREYGIHPS 38
                                      7999********************997 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.1e-05     0.074       9      28 ..      67      86 ..      61      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                         PKcGMP_CC  9 RIRELEkrlaekdeEIqELr 28
                                      +I+ELE+ l + ++EI  L+
  gi|330507131|ref|YP_004383559.1| 67 KIAELERLLGQAHAEIDLLK 86
                                      9***************9888 PP

>> DUF4733  Domain of unknown function (DUF4733)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.7e-05      0.13      29      67 ..       4      42 ..       1      51 [. 0.88
   2 ?   -2.0   0.0       1.4     5e+03      32      32 ..      91      91 ..      64     106 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                           DUF4733 29 qplrpqravleelsaplelsqplsgllddyGilPkhPrp 67
                                        +r+ r +   + a le  +pl+++  +yGi+P  P +
  gi|330507131|ref|YP_004383559.1|  4 TRRRYDRDFKISVLAELEAGKPLAQIAREYGIHPSLPCR 42
                                      56899999999***********************99976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                           DUF4733 32 r 32
                                       
  gi|330507131|ref|YP_004383559.1| 91 M 91
                                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 840.62
//
Query:       gi|330507132|ref|YP_004383560.1|  [L=171]
Description: hypothetical protein MCON_0988 [Methanosaeta concilii GP6]
Scores for complete 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-22   78.8   0.0    4.7e-22   78.5   0.0    1.1  1  DEDD_Tnp_IS110  Transposase


Domain annotation for each model (and alignments):
>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   2.6e-26   4.7e-22       1     148 [.      23     161 ..      23     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 2.6e-26
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +GiDv+k+   a+++ ++gk+  ++r++ + e+l ++ ++   + g+ +v++e+tg y+ ++v+ +le +i+++v n
  gi|330507132|ref|YP_004383560.1|  23 CGIDVHKRFLIATILCRDGKK-DTQRFSVTLEDLLKFRDW-VIENGCEQVAIESTGIYW-HPVHSVLEGKIDLIVAN 96 
                                       7*******************9.6779******9*999999.77899*************.56778899********* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlra 148
                                        +++k++      ++KtD  D+++IA+l +  g ++p++  +++ +eLr+ltr+re +vk++t++kn++++
  gi|330507132|ref|YP_004383560.1|  97 SYKIKHT-----PGRKTDVSDSEWIAELCL-NGMIEPSRIFPKDDRELRRLTRAREGYVKQMTQEKNKIHH 161
                                       ******9.....59****************.*************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1211.85
//
Query:       gi|330507133|ref|YP_004383561.1|  [L=88]
Description: hypothetical protein MCON_0989 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-16   60.1   0.0    1.7e-16   60.0   0.0    1.0  1  Transposase_mut  Transposase, Mutator family


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 !   60.0   0.0   9.7e-21   1.7e-16      20      95 ..       2      77 ..       1      86 [. 0.95

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 9.7e-21
                   Transposase_mut 20 sgkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspaller 95
                                      +++dd lk+ll+ +l+ +++ e+ ++ gae yer ++r++qRnG++er+l+Tr+g+lel+ P+ R+ sF+  ++ +
  gi|330507133|ref|YP_004383561.1|  2 KDQDDGLKKLLTWFLNLVMQLEAIQQSGAEPYERNDTRTTQRNGYKERSLKTRVGDLELKKPQFRDLSFKSCVFSE 77
                                      5789******************************************************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 671.41
//
Query:       gi|330507134|ref|YP_004383562.1|  [L=224]
Description: hypothetical protein MCON_0990 [Methanosaeta concilii GP6]
Scores for complete 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-47  161.3  10.2    2.5e-47  161.0  10.2    1.1  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 !  161.0  10.2   1.4e-51   2.5e-47       1     170 []      26     207 ..      26     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 161.0 bits;  conditional E-value: 1.4e-51
                           DUF1614   1 llgslinipvaelkske.elvevkvlgisykvpvleeeekktvvavNvGGaviPlllslylllrlavsllaallavl 76 
                                       +lgsl++ip++e+  ++ +   ++++ +s     + ++ +  ++avNvGG++iPl++s++l+lr ++s+++++l+v+
  gi|330507134|ref|YP_004383562.1|  26 ILGSLVDIPLMESPISAyPG--WYMTAMSQYPAAFPTTFHPLYLAVNVGGCIIPLVVSAHLILRGRASFFKSVLGVA 100
                                       689************77333..4444333333345555667************************************ PP

                           DUF1614  77 ivaavvyllarpvpgvGivvpllipplvaalaalllaeeea..aavaYisgvlGtLiGadllnl.........kkie 142
                                       +vaav+y++a+ +pg Giv+p++++pl+aa+++l+la+ ++  +++aYisg++GtLiGad+l+l         +   
  gi|330507134|ref|YP_004383562.1| 101 VVAAVTYYVAEAIPGEGIVLPFWLSPLLAAVMGLALARGYRrsPPLAYISGTIGTLIGADILSLltpgilpalSP-- 175
                                       *********************************9999999889*********************99866655533.. PP

                           DUF1614 143 klgap........vvsIGGaGtFdGifltgilavll 170
                                                    v+sIGGaG+FdGifltgi+avll
  gi|330507134|ref|YP_004383562.1| 176 ----LqllraqpvVLSIGGAGVFDGIFLTGIIAVLL 207
                                       ....1233334569********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1710.22
//
Query:       gi|330507135|ref|YP_004383563.1|  [L=397]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-25   88.5   0.1      5e-25   87.6   0.1    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family
      3e-20   72.7   0.0    5.9e-20   71.7   0.0    1.5  1  DEDD_Tnp_IS110  Transposase


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.1   5.5e-29     5e-25       2      83 ..     271     352 ..     270     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 5.5e-29
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaaira 78 
                                       +++ s+pG+G++ aa+++ae+gd r f+sa+++a+y+G++p+++qS++k r g+i+k G++++Rr+L+e A a++r+
  gi|330507135|ref|YP_004383563.1| 271 KIILSVPGVGFISAATIIAEMGDYRDFPSADKMAKYFGIVPSVYQSAGKLRTGKITKTGSKHMRRILVEVAKAISRT 347
                                       6899***********************************************************************99 PP

                    Transposase_20  79 npelr 83 
                                       ++ +r
  gi|330507135|ref|YP_004383563.1| 348 KKNSR 352
                                       75554 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   6.6e-24   5.9e-20       1     153 [.      31     174 ..      31     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 6.6e-24
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G D++ d   a++i+++g +l +er++++++gl a+ ++   ++++ + +ve+tg ++++++++ le +++ ++ n
  gi|330507135|ref|YP_004383563.1|  31 CGADIHRDFLIATMISRSGLKL-QERFNMNQDGLLAFRSW-IINHRCQRLAVESTGGFWYPIFTI-LEGHVEFILAN 104
                                       799************9999885.668**************.889****************88876.7899******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdqv 153
                                       ++++++++     ++KtD++D++ IA + +  + ++p++  +++y++Lr++tr+re+lv+ r++ kn++++ L   
  gi|330507135|ref|YP_004383563.1| 105 AYQIRNIE-----HKKTDKLDSERIAIYCL-NNLITPSRIYPKDYRDLRSITRARETLVNARSKIKNQIHQSLSTC 174
                                       *****995.....89***************.****************************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2840.22
//
Query:       gi|330507136|ref|YP_004383564.1|  [L=450]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-25   89.8   0.0    3.3e-25   89.0   0.0    1.4  1  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
      0.014   14.7   0.3      0.021   14.1   0.3    1.3  1  DDE_Tnp_2    Archaeal putative transposase ISC1217
      0.019   13.3   0.0       0.03   12.6   0.0    1.2  1  DDE_Tnp_1_4  Transposase DDE domain group 1
      0.075   13.0   1.0        1.4    8.9   0.1    2.8  3  Tudor_FRX1   Fragile X mental retardation Tudor 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 !   89.0   0.0   7.3e-29   3.3e-25       2     212 ..     133     371 ..     132     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 7.3e-29
                         DDE_Tnp_1   2 skrevlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkq..lldelrprk 76 
                                       s+r+v i D+t +r +++ +d+++     k  +g+k+  ++++    + s+ i p n++d+k+lk   ++      k
  gi|330507136|ref|YP_004383564.1| 133 SFRDVMIQDSTIIRLHKSLADKWPATRSRKVAAGVKVAFLTSAIANSPKSISILPENTNDVKTLKIgpWV------K 203
                                       6899***************9999988899999********************************995555......7 PP

                         DDE_Tnp_1  77 gklvlaDaGYasaelldtleekgvdyiirlkkntklyrk.............gaeskrrgrlrkhdrnkiltksqkr 140
                                       + ++l D G+ +++l+ ++ e+g+++++rlk+n++ ++              + +++++ +l+k d    ++ + ++
  gi|330507136|ref|YP_004383564.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVgtnqvrntrgvdlNGKHLKDIKLEKSDDIFDVNVEVSF 280
                                       789************************************99777666666663444444444444444444444444 PP

                         DDE_Tnp_1 141 rnk...................skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrgl 198
                                       +++                    +++++++ y+tn++s+ l a+eva+ y+ Rw++E +Fk+lk+++ ld   ++++
  gi|330507136|ref|YP_004383564.1| 281 DRRsyrgeskkdnkifrlvaiyNTEAEEHHFYLTNISSDILNASEVAAVYSGRWEVELIFKELKSRYALDQITTKSP 357
                                       4447777777777799999999999**************************************************** PP

                         DDE_Tnp_1 199 nrveaqllllllal 212
                                        ++ea ++  +l+l
  gi|330507136|ref|YP_004383564.1| 358 YAIEALIWVSILTL 371
                                       *******9998876 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   4.6e-06     0.021     219     288 ..     274     346 ..     202     384 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                         DDE_Tnp_2 219 rhvpvaelPeGeylveyl.dtvikllvlddykkdgrrylfstdln...dtdediittWenrWdievlirelkal 288
                                        +v+v+ + + +y  e   d+ i  lv +   + +  +++ t++    + + ++ + +  rW++e +++elk+ 
  gi|330507136|ref|YP_004383564.1| 274 VNVEVS-FDRRSYRGESKkDNKIFRLVAIYNTEAEEHHFYLTNISsdiLNASEVAAVYSGRWEVELIFKELKSR 346
                                       445543.7777888887767777767777777888999**999973335799********************73 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.6e-06      0.03     217     368 ..     204     372 ..     197     399 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.6e-06
                       DDE_Tnp_1_4 217 kilvRgDSafarpellkwceergvdYviglaknsrlealiaelvekakteaaekkek................erey 277
                                       +i++  D +f + +l++ + e+g ++v +l++n++     ++ v +++  + + k+                 e+++
  gi|330507136|ref|YP_004383564.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVGTNQVRNTRGVDLNGKHLkdikleksddifdvnvEVSF 280
                                       578889999**********************999877766666666666666654436799999999**99999999 PP

                       DDE_Tnp_1_4 278 refayqaesWskerrVvakaerpaeglnlrfvvTsla..klspeelyeqlYcaRGemEnrIKeakldlaadrtsshs 352
                                        +  y+ es + ++   + a +++e  +++f +T+++   l+++e+   +Y  R e+E  +Ke k+  a+d++ ++s
  gi|330507136|ref|YP_004383564.1| 281 DRRSYRGESKKDNKIFRLVAIYNTEAEEHHFYLTNISsdILNASEVA-AVYSGRWEVELIFKELKSRYALDQITTKS 356
                                       99999999855444333334455556667999****99888999999.9*************************999 PP

                       DDE_Tnp_1_4 353 faaNqlrlllsalAyn 368
                                         a ++ +++s l   
  gi|330507136|ref|YP_004383564.1| 357 PYAIEALIWVSILTLL 372
                                       9999988888887654 PP

>> Tudor_FRX1  Fragile X mental retardation Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00031       1.4      17      36 ..      22      41 ..      18      44 .. 0.88
   2 ?    1.1   0.0     0.085   3.8e+02      18      31 ..     269     282 ..     257     291 .. 0.89
   3 ?   -2.6   0.0       1.2   5.4e+03      13      36 ..     313     337 ..     311     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00031
                        Tudor_FRX1 17 vkdvhedsltvaFennWqpe 36
                                       kd+ e++lt +Fe +W  +
  gi|330507136|ref|YP_004383564.1| 22 EKDIVEQELTRMFESKWIRD 41
                                      59***************765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.085
                        Tudor_FRX1  18 kdvhedsltvaFen 31 
                                        d+++ ++ v+F+ 
  gi|330507136|ref|YP_004383564.1| 269 DDIFDVNVEVSFDR 282
                                       59**********96 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.2
                        Tudor_FRX1  13 ykafvkdvhed.sltvaFennWqpe 36 
                                       +  +  d+++  ++ +++   W  e
  gi|330507136|ref|YP_004383564.1| 313 LTNISSDILNAsEVAAVYSGRWEVE 337
                                       5566778888526888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3350.39
//
Query:       gi|330507137|ref|YP_004383565.1|  [L=51]
Description: hypothetical protein MCON_0993, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.20s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 438.74
//
Query:       gi|330507138|ref|YP_004383566.1|  [L=365]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-22   78.3   0.1      8e-22   76.9   0.1    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    5.2e-22   78.3   0.0    1.1e-21   77.2   0.0    1.5  1  OrfB_IS605      Probable transposase
    7.8e-09   34.9   1.0    2.1e-08   33.5   1.0    1.8  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0015   18.5   0.3     0.0026   17.8   0.3    1.3  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.057   12.9   0.5       0.45   10.1   0.1    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.12   12.1   0.8        0.2   11.4   0.8    1.4  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.17   11.8   0.3       0.17   11.8   0.3    2.0  2  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.23   10.9   0.9        1.2    8.6   0.9    2.1  1  zf-ribbon_3     zinc-ribbon domain
       0.41   10.2   4.9        5.7    6.6   0.1    2.8  3  RecR            RecR protein


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 !   76.9   0.1     4e-25     8e-22       1      68 [.     282     349 ..     282     350 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 4e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++ l +  +yka  +G  v++v+p++TSk Cs+Cg   +++ls+r+++C++Cg+++drD+nAaiNil+
  gi|330507138|ref|YP_004383566.1| 282 WNMLVTLTSYKAASAGSVVVLVDPRNTSKMCSRCGTLIEKSLSDRVHNCTQCGLSMDRDWNAAINILR 349
                                       667777889*********************************************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.0   5.7e-25   1.1e-21       4     117 ..     157     268 ..     154     270 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 5.7e-25
                        OrfB_IS605   4 veveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       ve e+  lp+ k + ++giD+G++ +at ++++   ++ ++r++++++++la+++++l++  k++  +kka + + r
  gi|330507138|ref|YP_004383566.1| 157 VETEDVpLPPWKDGAVVGIDVGLESFATFSNGE---TIANPRFFREEEQELARAQRKLSKAPKGTPDRKKALKVVER 230
                                       5544334999999********************...***************************************** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       +h++++++r +++h+++++l+++   ++ e+Ln+++m+
  gi|330507138|ref|YP_004383566.1| 231 VHERIANKRYEFAHQVSHNLVDRFGLIAFEDLNIKGMV 268
                                       *************************************7 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   1.0   1.1e-11   2.1e-08      15      47 .]       3      35 ..       2      35 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.1e-11
                    HTH_OrfB_IS605 15 eQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                       Q +k++rt++ +R+ YN+ La+rk+a+e+egk
  gi|330507138|ref|YP_004383566.1|  3 SQIAKMERTLDLCRWTYNQTLAYRKNAWENEGK 35
                                      69****************************998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.3   1.3e-06    0.0026      10      44 ..     307     343 ..     303     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + +++Cs+Cgt +++  +   ++C +Cg ++d +++ 
  gi|330507138|ref|YP_004383566.1| 307 NTSKMCSRCGTLIEKSLSdrVHNCTQCGLSMDRDWNA 343
                                       6789*********9777799************99986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00023      0.45      11      31 ..     301     321 ..     297     326 .. 0.84
   2 ?    0.5   0.1      0.23   4.5e+02      22      28 ..     330     336 ..     328     340 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00023
                                       CHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon  11 lveDpergelvCtdCGlVled 31 
                                       +++Dp ++   C++CG+++e 
  gi|330507138|ref|YP_004383566.1| 301 VLVDPRNTSKMCSRCGTLIEK 321
                                       68999*9999*********96 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.23
                                       ESSSSBE CS
                      TF_Zn_Ribbon  22 CtdCGlV 28 
                                       Ct CGl 
  gi|330507138|ref|YP_004383566.1| 330 CTQCGLS 336
                                       *****85 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8   9.8e-05       0.2       6      29 ..     312     335 ..     307     337 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.8e-05
                     zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCgl 29 
                                       C+rCG+  e++  ++   C +Cgl
  gi|330507138|ref|YP_004383566.1| 312 CSRCGTLIEKSLSDRVHNCTQCGL 335
                                       ***********************8 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.81   1.6e+03      37      45 ..     267     275 ..     265     278 .. 0.82
   2 ?   11.8   0.3   8.5e-05      0.17      10      38 ..     308     337 ..     304     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.81
                                       EE-CCCCTT CS
                              C1_1  37 lvHkkChek 45 
                                        vH++C+ k
  gi|330507138|ref|YP_004383566.1| 267 MVHNHCLAK 275
                                       59****876 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.5e-05
                                       S--B-TTT-SB--S.SSS-EEEETTT--EE CS
                              C1_1  10 qptfCkhCgeflwg.kekqglkCswCkllv 38 
                                        ++ C+ Cg ++++ ++ +   C++C+l++
  gi|330507138|ref|YP_004383566.1| 308 TSKMCSRCGTLIEKsLSDRVHNCTQCGLSM 337
                                       5789********999***********9976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.9   0.00061       1.2       5      24 ..     312     335 ..     309     337 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00061
                       zf-ribbon_3   5 CPnCGa.p...lssddnvCpyCGt 24 
                                       C++CG+ +   ls+++ +C+ CG 
  gi|330507138|ref|YP_004383566.1| 312 CSRCGTlIeksLSDRVHNCTQCGL 335
                                       999997555557899*******96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.5     5e+03       6      16 ..      61      71 ..      61      72 .. 0.87
   2 ?    6.6   0.1    0.0028       5.7      13      28 ..     306     321 ..     301     323 .. 0.77
   3 ?    5.4   0.3    0.0067        13      12      26 ..     323     337 ..     321     341 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.5
                                      HHHHHHHHHH- CS
                              RecR  6 aeaLqeakekv 16
                                      a++Lq++ e+v
  gi|330507138|ref|YP_004383566.1| 61 AQTLQNVQERV 71
                                      7899**99987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0028
                                       HHH-EE-TTT--EESS CS
                              RecR  13 kekvrhCsrCgnltee 28 
                                       +++ + CsrCg+l e+
  gi|330507138|ref|YP_004383566.1| 306 RNTSKMCSRCGTLIEK 321
                                       667799******9776 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0067
                                       HHHH-EE-TTT--EE CS
                              RecR  12 akekvrhCsrCgnlt 26 
                                       + ++v+ C +Cg   
  gi|330507138|ref|YP_004383566.1| 323 LSDRVHNCTQCGLSM 337
                                       679********9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2294.41
//
Query:       gi|330507139|ref|YP_004383567.1|  [L=906]
Description: type IIS restriction enzyme Eco57I (endonuclease Eco57I) [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-14   53.7   0.3    6.7e-14   52.3   0.3    1.7  1  Eco57I           Eco57I restriction-modification methylase
    2.7e-12   46.6   0.1    1.3e-06   27.9   0.0    3.3  2  N6_Mtase         N-6 DNA Methylase
    3.9e-11   43.1   0.0      1e-10   41.7   0.0    1.7  1  TaqI_C           TaqI-like C-terminal specificity domain
      2e-08   34.4   0.0    1.1e-05   25.4   0.0    2.5  1  HSDR_N           Type I restriction enzyme R protein N termin
    0.00022   20.9   0.0      0.072   12.8   0.0    2.9  2  UPF0020          Putative RNA methylase family UPF0020
    0.00075   19.5   0.0     0.0067   16.4   0.0    2.6  2  HSDR_N_2         Type I restriction enzyme R protein N termin
  ------ inclusion threshold ------
       0.17   11.7   0.0        2.2    8.1   0.0    2.3  2  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.3   2.6e-17   6.7e-14       3      99 ..     582     683 ..     577     686 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 2.6e-17
                            Eco57I   3 fdviiGNPPYqeseakkelkaleek......akdiyqkFvekalkle..dkylaliiparflasgkglkefrekllk 71 
                                       f+viiGNPPY  s  + +l+   +k      ++d y++F++++l+l+    + ++iip  +l + ++++++r++ll+
  gi|330507139|ref|YP_004383567.1| 582 FNVIIGNPPYLYSAGQVNLEYFTKKyklaqyQTDFYVYFIDRSLSLSnpGSMFSFIIPDSWL-NSEYFSKVRNHLLE 657
                                       9*********999977777666666778888****************8656789********.999*********** PP

                            Eco57I  72 dkklkklvefedskevFkdveikggilv 99 
                                       ++++k++  f     vF++v+i+++i +
  gi|330507139|ref|YP_004383567.1| 658 KHNIKSISIFDY--PVFDKVTIENSIFL 683
                                       *******99965..48********9976 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   5.1e-10   1.3e-06       4      68 ..     328     415 ..     326     422 .. 0.73
   2 !   13.1   0.0   1.6e-05     0.041     122     230 ..     578     684 ..     475     688 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5.1e-10
                          N6_Mtase   4 dllGdvYEyllrkfae.............eegksgGeffTPrevsklivell..........epksgesvyDpacGs 57 
                                       ++lG+vYE++l+k  +             e +k gG  +TP  ++  iv+ +           + ++ sv+DpacGs
  gi|330507139|ref|YP_004383567.1| 328 EILGQVYEQFLGKVIRltdghravvedkpEVKKAGGVKYTPAYIVDYIVKNTlwptleektpSDATKISVLDPACGS 404
                                       57888888888876431111111121221457889999***********98889***998765556668******** PP

                          N6_Mtase  58 ggllvqaekvl 68 
                                       g++l+ a ++l
  gi|330507139|ref|YP_004383567.1| 405 GSFLIVAYQHL 415
                                       *******9997 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.6e-05
                          N6_Mtase 122 kdkkfdvvvaNppfnqkewkektlekderfrea..vapksnadla.fllhiieslkpkGraavvlangvLfrggkeg 195
                                       +   f+v++ Npp+  +  + + +   e+f+++  +a+ ++  +  f+   ++  +p+   ++++++  L ++    
  gi|330507139|ref|YP_004383567.1| 578 QRGGFNVIIGNPPYLYS--AGQVNL--EYFTKKykLAQYQTDFYVyFIDRSLSLSNPGSMFSFIIPDSWLNSE-YFS 649
                                       67789*********999..444444..4444444477777777774666666666666667999999998766.567 PP

                          N6_Mtase 196 kIrkalvekdlveavialpeklFyntsiptcilvl 230
                                       k+r++l+ek++++++  +   +F +++i  +i+++
  gi|330507139|ref|YP_004383567.1| 650 KVRNHLLEKHNIKSISIFDYPVFDKVTIENSIFLV 684
                                       9***************************9999875 PP

>> TaqI_C  TaqI-like C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0     4e-14     1e-10       4     112 ..     795     902 ..     793     904 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 4e-14
                            TaqI_C   4 lkGkdikrysieikgnYldlikkklknekakelfeekpKilvrdisk.kldaaydekayyvlntlylliakdelevs 79 
                                       +kGk + r+ ++ ++ Y+++ ++  + ++  e+f  kpK+ +r+i + kl+ ++ e a+  +++ly++i +++   +
  gi|330507139|ref|YP_004383567.1| 795 IKGKHVDRFTFSSNDTYISYGPWLAEPRS-PEFFF-KPKLAIRKIIGtKLHGMLFEGAVALDQSLYIIISERDDIDE 869
                                       79*******************99887777.66776.7******9988799*******************99999899 PP

                            TaqI_C  80 lkyllgiLNSklikfyykkiystlrggysrlkr 112
                                       lk +lgiL S++ ++y+ + ys ++++y+ +++
  gi|330507139|ref|YP_004383567.1| 870 LKHILGILLSRICSWYLVNKYSIHDKLYPWFTK 902
                                       9*********************99999998776 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 !   25.4   0.0   4.4e-09   1.1e-05       2     192 ..      26     137 ..      25     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 4.4e-09
                                       SSHHHHHH.HHHHHHHHTT-EE...............----SHHHHHHHHHHHHHHHH-HHHHHHHHTT--HHHHHH CS
                            HSDR_N   2 lsEaeleqelidellrelGyqvlskkdveiegrrpevrkskaevaleknlreqlgalnikkltkrlalsdgnkefye 78 
                                       ++E ++++e++d+l+++lG++++++++    ++                                            
  gi|330507139|ref|YP_004383567.1|  26 YNETQVRREFVDPLFKALGWDIDNEQGFAEAYK-------------------------------------------- 58 
                                       79********************98886664442............................................ PP

                                       HHHTS-EEEETS-EEEEESS-SSSGGGS-EEEEE----S.SSS---EEEEEEETTEEEEEEEE--TT.-HHHHHHHH CS
                            HSDR_N  79 llkegkvkfkegrkknikLiDkknlenNrfqvvnQvtvt.gnqkrrpDivlfvnglplvviElKrpg.tieeAinQi 153
                                                                     +v+++  ++ g+++r pD++  ++g   +++E K+p+ +i+      
  gi|330507139|ref|YP_004383567.1|  59 ------------------------------DVIHEDAIRvGGTTRAPDYSFRIGGQRKFFLETKKPSvDIR------ 99 
                                       ..............................24455556668999*********************964532...... PP

                                       TSS---.---S.SSGGGGG-.....-EEEEE-SS-EEEEE--SSS CS
                            HSDR_N 154 kryrkeksdvs.ipqlfrYl.....qfgvisngketrfyaktkrr 192
                                        ++         + ql+rY+     ++ ++++++e+ +y+ t ++
  gi|330507139|ref|YP_004383567.1| 100 -EDI------HpAFQLRRYAwtaklPLSILTDFEEFSVYDCTVKP 137
                                       .222......239**************************998765 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   2.8e-05     0.072      31      94 ..     396     504 ..     390     516 .. 0.82
   2 ?    4.3   0.0     0.011        28     119     137 ..     579     597 ..     566     606 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                                       -EEETT-TTSHHHHHHHHHHTT--TTTT----SS........................................... CS
                           UPF0020  31 pllDPmCGsGtilIEaallganiapgllrefvle........................................... 64 
                                       + lDP CGsG++lI a +   +      re  ++                                           
  gi|330507139|ref|YP_004383567.1| 396 SVLDPACGSGSFLIVAYQHLLDWH----REWYVQnlvpllesglrpssiqirhmlpgiegaskgrkkerepelpvfq 468
                                       579***********9987777777....333333677799999999****************************999 PP

                                       .....HHHHHHHHHHHH--.EEEEES-HHHHHHHHH CS
                           UPF0020  65 .....lkaeaeeearaelk.lygsDldrrvvqgare 94 
                                             + +  e++r  l+ +yg+D+dr++v+ ++ 
  gi|330507139|ref|YP_004383567.1| 469 grggeWRLTTAERKRILLNnIYGVDIDRQAVEVTKL 504
                                       999986666666666444459******999998875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.011
                                       TS---EEEE---------- CS
                           UPF0020 119 egevdvivtnpPYGerlgs 137
                                       +g ++vi++npPY  + g+
  gi|330507139|ref|YP_004383567.1| 579 RGGFNVIIGNPPYLYSAGQ 597
                                       56799********999887 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 !   16.4   0.0   2.6e-06    0.0067       4     101 ..      30     138 ..      27     143 .. 0.75
   2 ?   -1.5   0.0      0.95   2.4e+03      12      40 ..     731     759 ..     729     762 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.6e-06
                          HSDR_N_2   4 wvRqklikyLveelgypk..........eliavekelqlgskkkraDivvykkdkkpllivecKapsvkise..evl 68 
                                        vR +++  L + lg +           +++  e  +++g++++ +D+ +     +   ++e K+psv i+e  +  
  gi|330507139|ref|YP_004383567.1|  30 QVRREFVDPLFKALGWDIdneqgfaeayKDVIHEDAIRVGGTTRAPDYSFRIGG-QRKFFLETKKPSVDIREdiHPA 105
                                       5666666666666655431111111122579999999999********998877.888899*********6633567 PP

                          HSDR_N_2  69 eqlksYlealkaeylvvtNglehivykvdkkkk 101
                                        ql +Y+ ++k ++ ++t+ +e+ vy++  k++
  gi|330507139|ref|YP_004383567.1| 106 FQLRRYAWTAKLPLSILTDFEEFSVYDCTVKPD 138
                                       8*************************9987765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.95
                          HSDR_N_2  12 yLveelgypkeliavekelqlgskkkraD 40 
                                       +++++++y+ e ++++++++ g    r+D
  gi|330507139|ref|YP_004383567.1| 731 KIIKKMEYDSEPLSQDFKINRGIHAYRTD 759
                                       68999*************99887666666 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00086       2.2       4      24 ..     394     414 ..     391     421 .. 0.86
   2 ?    0.7   0.0      0.16   4.2e+02      30      44 ..     488     502 ..     476     506 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00086
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaee 24 
                                       +++vlD++CG+G +++++++ 
  gi|330507139|ref|YP_004383567.1| 394 KISVLDPACGSGSFLIVAYQH 414
                                       689*************99974 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                   Methyltransf_31  30 evvGiDiseeaielA 44 
                                       +++G+Di+ +a+e+ 
  gi|330507139|ref|YP_004383567.1| 488 NIYGVDIDRQAVEVT 502
                                       49**********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (906 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.71u 0.26s 00:00:00.97 Elapsed: 00:00:00.44
# Mc/sec: 6225.59
//
Query:       gi|330507140|ref|YP_004383568.1|  [L=436]
Description: IS66 family element, transposase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-48  163.7   0.0    9.7e-48  163.1   0.0    1.3  1  DDE_Tnp_IS66   Transposase IS66 family
    3.2e-06   27.5   4.6    1.1e-05   25.7   4.6    2.0  1  zf-IS66        zinc-finger binding domain of transposase IS66
    0.00025   20.2   0.0    0.00033   19.8   0.0    1.1  1  Med1           Mediator of RNA polymerase II transcription su
     0.0016   18.7   0.0     0.0035   17.6   0.0    1.7  1  DDE_Tnp_IS240  DDE domain
     0.0021   18.0   0.6     0.0051   16.8   0.6    1.6  1  DZR            Double zinc ribbon
  ------ inclusion threshold ------
       0.26   11.1   2.6       0.72    9.7   2.6    1.7  1  DivIC          Septum formation initiator
        0.4   11.1   5.8        0.2   12.1   2.7    2.1  2  ZapB           Cell division protein ZapB
       0.74    9.9   4.8       0.31   11.1   2.1    1.8  2  MCC-bdg_PDZ    PDZ domain of MCC-2 bdg protein for Usher synd
        1.5    8.3   6.0        5.5    6.5   0.1    2.4  2  zf-ribbon_3    zinc-ribbon domain
        2.2    8.6   6.6        3.2    8.0   3.3    2.5  2  HALZ           Homeobox associated leucine zipper
        5.6    6.8   7.8        2.7    7.8   0.2    2.4  2  zinc_ribbon_2  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 !  163.1   0.0   5.9e-51   9.7e-48       2     280 ..     147     406 ..     146     408 .. 0.88

  Alignments for each domain:
  == domain 1  score: 163.1 bits;  conditional E-value: 5.9e-51
                      DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtl 77 
                                       + +g++++A++++ +y+d lP +++++ l+r  G++ls++t+ ++++ra+e+++p ++a+ ++++ ++++ +DET++
  gi|330507140|ref|YP_004383568.1| 147 GKFGNNVIAQATLMRYEDRLPHRKIQDTLKRIhGLALSPATIFDLTRRAGEAVRPEYDAILERIRGAPILYVDETGI 223
                                       57999************************************************************************ PP

                      DDE_Tnp_IS66  78 rvlkpgrgkgkksylWvyvtdkrkpavlfeyspsRggevaealLag.fkGvlvsDgyagYnklaeeqvthalCwaHl 153
                                               +g+k+++W++ t      ++f + +sRg++v  ++L+  f+G++v+Dg+++Y +++    +++ CwaHl
  gi|330507140|ref|YP_004383568.1| 224 H------VQGEKHWIWTFTTPS---ETFFVIRKSRGTNVLIEVLTRrFRGIIVCDGWKPYARFT---KNLQRCWAHL 288
                                       *......89***********88...9*****************9999****************5...899******* PP

                      DDE_Tnp_IS66 154 rRkfvdaeeakkksqaaaealarigklya.ierear.eaeaeerlalrqeesrpllaeleawleeqlkkvlpksklg 228
                                       +R+ +d++e+ +   +a    + ++ ly+ ++++++ e ++e r+++ q+ ++     l++w++        + k++
  gi|330507140|ref|YP_004383568.1| 289 LRESKDLSEKFG---EAVPLHEALKGLYEsLTKSLEcEPPPEVRMNIWQSAREV----LQHWIDR----EYLEVKVR 354
                                       ********9765...444444446666663344443332678888888885444....4455553....457789** PP

                      DDE_Tnp_IS66 229 kairyllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                       k+i ++ +  +  ++f+ +++v+ +NN+aERa+Rp v+ RK+ +++++ +G 
  gi|330507140|ref|YP_004383568.1| 355 KFIGKISNGFDYWFTFILNPGVETTNNRAERALRPHVVLRKILGTLRNRKGT 406
                                       ***********************************************99985 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 !   25.7   4.6   6.6e-09   1.1e-05       3      45 ..      89     132 ..      87     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.6e-09
                           zf-IS66   3 tCpcCGg.llkpigedrvreeldip.PakfrViehirpkyaCpcC 45 
                                        Cp+CG+ l  p   +    + +ip P+ ++V+e+ +  y CpcC
  gi|330507140|ref|YP_004383568.1|  89 RCPDCGAkLNLPFRFE-SKVIEEIPePQPVIVTEYKIAHYICPCC 132
                                       7******663366666.569999**999****************9 PP

>> Med1  Mediator of RNA polymerase II transcription subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     2e-07   0.00033      84     170 ..     246     347 ..     194     389 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2e-07
                              Med1  84 ereeAseiLlrdLr..........ltkkldeFaanLer.....LarlDklsgd..pklncfealegleesLqklsql 143
                                       ++++ +++L+++L+           +k  ++F++nL+r     L +   ls +    + ++eal+gl+esL+k  + 
  gi|330507140|ref|YP_004383568.1| 246 RKSRGTNVLIEVLTrrfrgiivcdGWKPYARFTKNLQRcwahlLRESKDLSEKfgEAVPLHEALKGLYESLTKSLEC 322
                                       378899*******************************9644444455556655999*****************9777 PP

                              Med1 144 esks....h.welekk......deeleelglcssvGkp 170
                                       e       + w++ ++      d             ++
  gi|330507140|ref|YP_004383568.1| 323 EPPPevrmNiWQSAREvlqhwiD-------------RE 347
                                       76555666677744444433331.............33 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.2e-06    0.0035       6      86 ..     218     291 ..     215     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.2e-06
                     DDE_Tnp_IS240   6 vDETyvkikGkwaYlyravDkegrildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkelkreg. 81 
                                       vDET + ++G++++++           f+++k R+t+  + +l++ ++        iv D+ + ya+  k+l+r   
  gi|330507140|ref|YP_004383568.1| 218 VDETGIHVQGEKHWIWTFTTPSET--FFVIRKSRGTNVLIEVLTRRFRGI------IVCDGWKPYARFTKNLQRCWa 286
                                       9***************98765554..48899*****************99......***************999543 PP

                     DDE_Tnp_IS240  82 elfde 86 
                                       +l++e
  gi|330507140|ref|YP_004383568.1| 287 HLLRE 291
                                       44444 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.6   3.1e-06    0.0051      10      47 ..      85     145 ..      80     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.1e-06
                               DZR  10 pdarfCseCgtklkavaa.......................edrCpsCgekvdpearfCpe 47 
                                         a  C++Cg+kl+ + +                       ++ Cp C ++v ++++ Cp+
  gi|330507140|ref|YP_004383568.1|  85 VTADRCPDCGAKLNLPFRfeskvieeipepqpvivteykiaHYICPCCRKEVVARDANCPH 145
                                       56788********97666999**************************************95 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.6   0.00044      0.72      19      51 ..       7      39 ..       4      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00044
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkdLk 51
                                      ++ql+++ + l  e++ lka+++eLea++++++
  gi|330507140|ref|YP_004383568.1|  7 IRQLREQNELLRLENEMLKARIRELEARLAKYE 39
                                      679999999999999999999999999998874 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.7   0.00012       0.2      20      54 ..       7      41 ..       5      56 .. 0.89
   2 ?   -1.3   0.1         2   3.2e+03      54      54 ..     345     345 ..     279     362 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                              ZapB 20 itlLqmeieeLkeeneelkeenreleeeneqlkee 54
                                      i++L++++e L+ ene lk ++rele+ + + ++ 
  gi|330507140|ref|YP_004383568.1|  7 IRQLREQNELLRLENEMLKARIRELEARLAKYENA 41
                                      899***********************888887655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                              ZapB  54 e 54 
                                       +
  gi|330507140|ref|YP_004383568.1| 345 D 345
                                       3 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 ?   11.1   2.1   0.00019      0.31       6      41 ..       7      41 ..       4      43 .. 0.93
   2 ?   -3.7   0.0         8   1.3e+04       7      21 ..     307     321 ..     305     321 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                       MCC-bdg_PDZ  6 IeeLkaqnelLsltleerkqqseeLsldlgkaEsna 41
                                      I +L+ qnelL+l  e  k++  eL  +l k+E na
  gi|330507140|ref|YP_004383568.1|  7 IRQLREQNELLRLENEMLKARIRELEARLAKYE-NA 41
                                      89*******************************.54 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8
                       MCC-bdg_PDZ   7 eeLkaqnelLsltle 21 
                                       e Lk   e L+++le
  gi|330507140|ref|YP_004383568.1| 307 EALKGLYESLTKSLE 321
                                       456666777777765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0034       5.5       4      25 ..      89      96 ..      82      98 .. 0.67
   2 ?    2.4   2.8      0.07   1.1e+02       2      21 ..     126     145 ..     125     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0034
                       zf-ribbon_3  4 rCPnCGaplssddnvCpyCGtk 25
                                      rCP CGa              k
  gi|330507140|ref|YP_004383568.1| 89 RCPDCGA--------------K 96
                                      5666665..............4 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.07
                       zf-ribbon_3   2 tvrCPnCGa.plssddnvCpy 21 
                                       ++ CP C + +  ++d +Cp+
  gi|330507140|ref|YP_004383568.1| 126 HYICPCCRKeV-VARDANCPH 145
                                       688****9977.888999998 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.3     0.002       3.2      17      42 ..      10      35 ..       8      36 .. 0.93
   2 ?    0.6   0.1      0.43     7e+02       8      19 ..     307     318 ..     306     322 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.002
                              HALZ 17 LksdydsLkkenekLkaelqeLkekl 42
                                      L+ +++ L+ ene Lka ++eL ++l
  gi|330507140|ref|YP_004383568.1| 10 LREQNELLRLENEMLKARIRELEARL 35
                                      8899*******************997 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.43
                              HALZ   8 dvLKasYdaLks 19 
                                       ++LK  Y++L+ 
  gi|330507140|ref|YP_004383568.1| 307 EALKGLYESLTK 318
                                       577888888874 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0016       2.7       1       9 [.      89      97 ..      89     100 .. 0.86
   2 ?    1.2   2.8       0.2   3.2e+02       2      18 ..     129     145 ..     128     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0016
                     zinc_ribbon_2  1 fCpnCGael 9 
                                      +Cp CGa+l
  gi|330507140|ref|YP_004383568.1| 89 RCPDCGAKL 97
                                      699999998 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.2
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpy 18 
                                       Cp C +e+  ++  Cp+
  gi|330507140|ref|YP_004383568.1| 129 CPCCRKEVVARDANCPH 145
                                       ********999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3064.33
//
Query:       gi|330507141|ref|YP_004383569.1|  [L=61]
Description: hypothetical protein MCON_0997 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   0.2       0.16   11.9   0.2    1.1  1  DUF2721     Protein of unknown function (DUF2721)
       0.18   11.8   0.1        0.2   11.6   0.1    1.0  1  RNA_capsid  Calicivirus putative RNA polymerase/capsid protei


Domain annotation for each model (and alignments):
>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   1.8e-05      0.16      24      58 ..       3      36 ..       1      41 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
                           DUF2721 24 riadrirqLedeleelaeeeeedeelakeiknlrr 58
                                      +++dr+  L+++l+e+ ++++ ++ l+++i++ +r
  gi|330507141|ref|YP_004383569.1|  3 SLVDRMLALHKQLQEARTPHD-ETALQRQIEVTDR 36
                                      799***********8888865.5*******98776 PP

>> RNA_capsid  Calicivirus putative RNA polymerase/capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.3e-05       0.2      38      62 ..      12      36 ..       5      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.3e-05
                        RNA_capsid 38 nkqLQqnsFkHDkemLqaQveatkq 62
                                       kqLQ++   HD+  Lq Q+e t +
  gi|330507141|ref|YP_004383569.1| 12 HKQLQEARTPHDETALQRQIEVTDR 36
                                      69*******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 463.51
//
Query:       gi|330507142|ref|YP_004383570.1|  [L=517]
Description: hypothetical protein MCON_0998 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-07   31.6   0.0    1.6e-05   24.5   0.0    2.5  2  Lactamase_B_2  Beta-lactamase superfamily domain
    6.8e-06   25.9   0.0    1.8e-05   24.6   0.0    1.7  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.2e-05   25.4   0.0    0.00013   22.0   0.0    2.4  2  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0031   17.4   0.0      0.022   14.6   0.0    2.3  3  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 !   24.5   0.0   3.7e-09   1.6e-05      30      71 ..      87     124 ..      76     142 .. 0.88
   2 !    4.3   0.0    0.0057        26      57     167 ..     164     271 ..     152     293 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.7e-09
                                       SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCC CS
                     Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavle 71 
                                        ++aVll+haH+DH+ ++ +lr+    ++p++a+++++ +++
  gi|330507142|ref|YP_004383570.1|  87 NVAAVLLSHAHMDHCGNIGMLRK----DIPIVASPETIVIMK 124
                                       589********************....599***999987665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0057
                                       EEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEE..CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE CS
                     Lactamase_B_2  57 klplyapkgvlavleanfvylaleeepavnvheldwgesfel..gdggleitatparhksgrrldrnagdtlGlrie 131
                                         +++++k+ +++l++ ++   ++ +++ ++++l++g+      +   +ei a+p+ h+           + +++++
  gi|330507142|ref|YP_004383570.1| 164 GRDFCCTKKPSEELTNFLS--RRPGQDGKRAKKLEPGTCSFYdnAAYPFEISAHPVDHSIFG--------ATAYILQ 230
                                       4567788888888887754..33333578888898888666667556689999999999988........999**** PP

                                       CTTEEEEEESS-S---......HHHHHHHCT-SEEEEE-S-S CS
                     Lactamase_B_2 132 gggkrvyyigDtgyip......eeigerlggadllllditay 167
                                        g+ +++y+gD            +  ++ ++a +l+ ++t+ 
  gi|330507142|ref|YP_004383570.1| 231 -GDTTIAYTGDFRLHGrngdatRDFVKKAKDASILITEGTRA 271
                                       .899*******9966555422244446666677777777765 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 !   24.6   0.0   3.9e-09   1.8e-05      11      42 ..     465     496 ..     463     498 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.9e-09
                             RMMBL  11 idfSgHadknellelirklkprnvilvHGeee 42 
                                       ++ SgHa +++l+ +i ++ p +++++H e +
  gi|330507142|ref|YP_004383570.1| 465 FHASGHASREDLKWVIDQVDPDYLVPIHTESR 496
                                       678**************************975 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0     3e-08   0.00013      34      76 ..      77     119 ..      13     156 .. 0.80
   2 ?    0.5   0.0      0.11   5.1e+02     138     162 ..     228     252 ..     209     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3e-08
                                       HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCE CS
                       Lactamase_B  34 elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgava 76 
                                       +l    ++ ++v av+l+H+H DH+G+ g l++  +++   + 
  gi|330507142|ref|YP_004383570.1|  77 DLSISQYPSLNVAAVLLSHAHMDHCGNIGMLRKDIPIVASPET 119
                                       56666788999********************998887765555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.11
                                       EEETTCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B 138 veygggkvlftGDallagetgridl 162
                                       +  g+ ++++tGD+ l g +g+ ++
  gi|330507142|ref|YP_004383570.1| 228 ILQGDTTIAYTGDFRLHGRNGDATR 252
                                       5668888999999988888887776 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 !   14.6   0.0     5e-06     0.022       7      77 ..      15     127 ..      13     173 .. 0.66
   2 ?   -3.1   0.0       1.4   6.2e+03      97     114 ..     225     241 ..     211     250 .. 0.75
   3 ?   -1.1   0.0      0.33   1.5e+03     144     163 .]     473     492 ..     469     492 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5e-06
                     Lactamase_B_3   7 hnsflletagarilvDPf..........kanlgyeppa....................................... 34 
                                        n + le +g+ +l+D +          +        +                                       
  gi|330507142|ref|YP_004383570.1|  15 GNKLYLEEGGKGVLLDFGknfgkygafyE--------Eflknrdtrgihdliyldlmpklniyrpdlipsdlsisqy 83 
                                       56667888888888887733333332220........2555556666666666666666666667777777777777 PP

                     Lactamase_B_3  35 ..eeaDlvlisqaledHahletlkqlaenvkvleegeslev.ggle 77 
                                          ++ +vl+s+a+ dH+    + +  +++++++++e++ + +g++
  gi|330507142|ref|YP_004383570.1|  84 psLNVAAVLLSHAHMDHCGNIGMLR--KDIPIVASPETIVImKGMQ 127
                                       779**************97655444..599*****99987633333 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                     Lactamase_B_3  97 ngflleqdgltiyhlGhl 114
                                       ++++l q++ ti++ G+ 
  gi|330507142|ref|YP_004383570.1| 225 TAYIL-QGDTTIAYTGDF 241
                                       56666.679999999996 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.33
                     Lactamase_B_3 144 qeealelakrLkpklvlPmh 163
                                       +e+ + ++ +++p++ +P+h
  gi|330507142|ref|YP_004383570.1| 473 REDLKWVIDQVDPDYLVPIH 492
                                       67888899**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3596.37
//
Query:       gi|330507143|ref|YP_004383571.1|  [L=88]
Description: hypothetical protein MCON_0999 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-15   55.7   0.0    6.1e-15   55.3   0.0    1.2  1  Mrr_cat    Restriction endonuclease
    1.2e-05   25.2   0.0    1.5e-05   24.9   0.0    1.1  1  Mrr_cat_2  Restriction endonuclease


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0   6.8e-19   6.1e-15      59     115 .]       4      61 ..       2      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 6.8e-19
                                       S-B-HHHHHHHHHHCTTS..SEEEEEESS-B-HHHHHHHHTT-.-EEEE-HHHHHHHH CS
                           Mrr_cat  59 nkvgvkeVqeligalkkrgadkgifvttsdftkaAreeaeeln.kieLldgdeLaell 115
                                       +++g+++Vq+++g+l++++a+kg+++tts+f+++A +++ +++ ki+L+dg++Lael+
  gi|330507143|ref|YP_004383571.1|   4 RTIGRQVVQAFAGSLEGHRARKGVLITTSQFSPDALDYVTRIEkKIVLIDGEKLAELM 61 
                                       589*************************************97658***********97 PP

>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.7e-09   1.5e-05      56     118 ..       4      65 ..       2      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.7e-09
                         Mrr_cat_2  56 ekiqkedidsFlsasgkkkftkrliisTtdkwsknaeealknqkipvkridledLeeseidws 118
                                       ++i ++ ++ F ++ + ++  k+++i Tt+++s +a + +   ++++ +id e+L+e++id+ 
  gi|330507143|ref|YP_004383571.1|   4 RTIGRQVVQAFAGSLEGHRARKGVLI-TTSQFSPDALDYVTRIEKKIVLIDGEKLAELMIDYG 65 
                                       5789999*******************.7778******************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 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:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 629.79
//
Query:       gi|330507144|ref|YP_004383572.1|  [L=74]
Description: hypothetical protein MCON_1000 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       351  (0.0195772); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 550.21
//
Query:       gi|330507145|ref|YP_004383573.1|  [L=98]
Description: RelE/StbE family addiction module toxin [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-08   33.2   0.4      7e-08   33.0   0.4    1.1  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
     0.0034   17.3   0.1     0.0056   16.6   0.1    1.5  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
  ------ inclusion threshold ------
      0.061   13.7   0.4        0.1   12.9   0.4    1.4  1  YafQ_toxin       Bacterial toxin of type II toxin-antitoxin s
       0.11   12.8   0.1       0.25   11.7   0.1    1.6  1  Pea-VEAacid      Pea-VEAacid family


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.4   1.6e-11     7e-08       4      87 ..       6      79 ..       3      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.6e-11
                                      EHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTC...CTTEEEEEECTEEEEEEEETSTTEEE CS
                        ParE_toxin  4 tprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrprrelg...lkglrririgdyriiYriddeelvvv 79
                                      tp++ +++ k+++         + +  +l ++++++++np +g p    +   l++ r  ++++y+i+Y +  ++ ++ 
  gi|330507145|ref|YP_004383573.1|  6 TPEFDEQFSKLIRK-------NRALEVRLLKKIRQILDNPSIGTP----KlhqLRHARGSHVDPYVIVYAVK-GDIIT- 71
                                      67777777788775.......667777888888888888888888....3345789999***********94.65666. PP

                                      EEEEEEHH CS
                        ParE_toxin 80 ilrvlhrs 87
                                      +l v h++
  gi|330507145|ref|YP_004383573.1| 72 FLYVDHHD 79
                                      ******97 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.3e-06    0.0056       4      47 ..       6      52 ..       3      86 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-06
                   ParE-like_toxin  4 trrfkkalkklkek...lkadldkavkeiiedPelGeeKkGDLsgvf 47
                                      t++f  + +kl +k   l+ +l k++++i+++P++G++K   L+  +
  gi|330507145|ref|YP_004383573.1|  6 TPEFDEQFSKLIRKnraLEVRLLKKIRQILDNPSIGTPKLHQLRHAR 52
                                      78888888888655344667899****************87776655 PP

>> YafQ_toxin  Bacterial toxin of type II toxin-antitoxin system, YafQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   2.3e-05       0.1       2      86 ..       2      81 ..       1      83 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                                      EEEEEHHHHHHHHHHHHTT--HH.HHHHHHHHHHTT-S--GGG--EE-SSS-TTEEEEEEETTEEEEEEE-SSEEEEEE CS
                        YafQ_toxin  2 kikptkqfkkdlkrlkkrkkdle.klkevlklLaegepLpekyrdHaLkgnwkgyrecHikpDllLiYrleddelvlvr 79
                                      +++ t +f+ ++ +l ++++ le +l + ++ ++++ ++    + H+L       r  H+ p  +++Y ++ d ++++ 
  gi|330507145|ref|YP_004383573.1|  2 EYDSTPEFDEQFSKLIRKNRALEvRLLKKIRQILDNPSI-GTPKLHQLR----HARGSHVDP-YVIVYAVKGDIITFLY 74
                                      567899999999999966665555555555666666666.456789998....57999**99.899************* PP

                                      EE-HHHH CS
                        YafQ_toxin 80 lGsHsel 86
                                      ++ H+ +
  gi|330507145|ref|YP_004383573.1| 75 VDHHDFV 81
                                      **99865 PP

>> Pea-VEAacid  Pea-VEAacid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   5.6e-05      0.25       6      13 ..      53      60 ..      51      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
                       Pea-VEAacid  6 GSHVDSYV 13
                                      GSHVD YV
  gi|330507145|ref|YP_004383573.1| 53 GSHVDPYV 60
                                      9******9 PP



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:                      487  (0.0271627); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 712.45
//
Query:       gi|330507146|ref|YP_004383574.1|  [L=58]
Description: hypothetical protein MCON_1002 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 445.74
//
Query:       gi|330507147|ref|YP_004383575.1|  [L=50]
Description: hypothetical protein MCON_1003 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 386.85
//
Query:       gi|330507148|ref|YP_004383576.1|  [L=52]
Description: hypothetical protein MCON_1004 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       132  (0.00736237); expected 358.6 (0.02)
Passed bias filter:                      112  (0.00624686); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 388.94
//
Query:       gi|330507149|ref|YP_004383577.1|  [L=318]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete 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-20   71.0   0.0    1.2e-19   70.1   0.0    1.4  1  DUF772       Transposase domain (DUF772)
      2e-15   57.0   5.4    6.9e-15   55.3   5.4    2.0  1  DDE_Tnp_1    Transposase DDE domain
    2.3e-05   24.1   0.4     0.0001   22.0   0.4    2.0  1  DDE_Tnp_4    DDE superfamily endonuclease
    2.6e-05   24.4   0.4    4.5e-05   23.7   0.4    1.4  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
      0.044   14.2   0.1        0.1   13.0   0.1    1.6  1  EnY2         Transcription factor e(y)2


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 !   70.1   0.0   3.2e-23   1.2e-19       3      72 ..      19      88 ..      17      89 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 3.2e-23
                            DUF772  3 payppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72
                                      p+++ ++m+k+l+lq ++glSd ele+++ +++sfr flg     + +pd+st + fR+rl+e    e+l++e
  gi|330507149|ref|YP_004383577.1| 19 PSIDIVIMVKALVLQSWFGLSDPELERQVTDRISFRIFLGT---TEVIPDFSTVWLFRERLIEcgrYEDLWKE 88
                                      9***************************************5...389****************9999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   5.4   1.9e-18   6.9e-15      20     214 .]     143     306 ..      99     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 1.9e-18
                         DDE_Tnp_1  20 k............................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkql 68 
                                       +                             ++ w +kg k+++gyk hi++dt+ +li ++++t+++ hds++    
  gi|330507149|ref|YP_004383577.1| 143 PdfdkdllnisnnivssnakpkrlddgpiNEGTWAKKGSKSFFGYKGHILIDTEYHLIRKIETTTASLHDSQVDLG- 218
                                       0555555555555555555666666666777889999**********************************99777. PP

                         DDE_Tnp_1  69 ldelrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnksk 145
                                       +++l++      +aD+GY++a++  + +                            ++k+ r++ l  ++++rnk  
  gi|330507149|ref|YP_004383577.1| 219 INGLPR------YADKGYSGAKTQGYDA---------------------------AMKKAARGHKLGIKDILRNK-- 260
                                       777887......*******888877777...........................89******************.. PP

                         DDE_Tnp_1 146 kekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                              +++r+R+qiEr F+ +kr  + +++++ + +r+ +++++  +++n+
  gi|330507149|ref|YP_004383577.1| 261 -----------------------RISRKRSQIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNI 306
                                       .......................******************999************************7 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.4   2.8e-08    0.0001      77     130 ..     223     279 ..     160     294 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.8e-08
                         DDE_Tnp_4  77 vilaDkgFklse..kl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgr 130
                                          aDkg+ +++   +   ++k  ++++l  ++  +n++i++ r  +Er+++ +k+ 
  gi|330507149|ref|YP_004383577.1| 223 PRYADKGYSGAKtqGYdAAMKKAARGHKLGIKDILRNKRISRKRSQIERCFAVMKRA 279
                                       3469*****99954333455555********************************65 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 !   23.7   0.4   1.3e-08   4.5e-05      74     124 ..     260     309 ..     231     310 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.3e-08
                       DDE_Tnp_1_6  74 kaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                       k+  +kR+ ++E+ fa +kr++++  + ++ ++++ ++f++  +++N+++l
  gi|330507149|ref|YP_004383577.1| 260 KRISRKRS-QIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNIEQL 309
                                       45556665.***************************************997 PP

>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.8e-05       0.1       5      31 ..      73      99 ..      72     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                                      HHHHHHTTHHHHHHHHHHHHHHHTTHH CS
                              EnY2  5 qqkLvesGererlkelLrerLeesGWr 31
                                      +++L+e G +e+l + L+++L+e G+ 
  gi|330507149|ref|YP_004383577.1| 73 RERLIECGRYEDLWKELQNQLDEKGFA 99
                                      589**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2409.63
//
Query:       gi|330507150|ref|YP_004383578.1|  [L=125]
Description: hypothetical protein MCON_1007 [Methanosaeta concilii GP6]
Scores for complete 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-20   71.6   0.5    6.2e-20   71.4   0.5    1.0  1  Transposase_mut  Transposase, Mutator family


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 !   71.4   0.5   3.4e-24   6.2e-20     261     380 ..       2     116 ..       1     117 [. 0.93

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 3.4e-24
                   Transposase_mut 261 rnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaedvlaflafpeqirrkikst 337
                                       r +l+++pkk++++va +lk    a + e   ++l+ +l+   k ++k a+++d+ + d+ ++ +fp+ ++++i++t
  gi|330507150|ref|YP_004383578.1|   2 RAVLKNIPKKEKKEVAYMLKD---AIEDEFKMQELAVILD--DKGFKKSADTIDSFRFDLWNYKSFPRSHWKRIRTT 73 
                                       8899*************9994...6677888888999998..56899****************************** PP

                   Transposase_mut 338 NllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                       N+lEr+Nke++Rr+rv g + n++s+lr+ + ++++ +++w++
  gi|330507150|ref|YP_004383578.1|  74 NVLERINKELKRRSRVAGAYSNDQSLLRVAVCIMMDINEDWIT 116
                                       *****************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 953.65
//
Query:       gi|330507151|ref|YP_004383579.1|  [L=258]
Description: hypothetical protein MCON_1008, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-77  259.6   0.1    5.1e-77  259.3   0.1    1.0  1  Transposase_mut  Transposase, Mutator family
    2.9e-06   27.6   0.0    4.7e-06   26.9   0.0    1.3  1  MULE             MULE transposase domain
  ------ inclusion threshold ------
      0.015   15.8   0.2        2.2    8.9   0.0    3.0  3  DUF5499          Family of unknown function (DUF5499)


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 !  259.3   0.1   8.5e-81   5.1e-77      21     260 ..      13     250 ..       2     256 .. 0.97

  Alignments for each domain:
  == domain 1  score: 259.3 bits;  conditional E-value: 8.5e-81
                   Transposase_mut  21 gkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspalleryk 97 
                                       + ++ +k+l+  +l+e+++ e++++++a  yer+++r+ +RnG r+rkl+T +g++el  P+ R+  F++a++er+ 
  gi|330507151|ref|YP_004383579.1|  13 DRKEGMKKLTAGFLNEVMQLEAENQIQARPYERTGKRRAHRNGTRSRKLKTIYGEIELDKPQIREFPFETAVFERFS 89 
                                       4568999********************************************************************** PP

                   Transposase_mut  98 RrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkv 174
                                       R e+ l  +v+e y +Gvstrkvek++ +++  k++S+sevS+i+k+ld+ v+ f +R++e +  p++f+Da y kv
  gi|330507151|ref|YP_004383579.1|  90 RVEDSLRVAVAESYFEGVSTRKVEKVFSKFGL-KNISASEVSRIAKKLDKLVKDFLNRPIEGS-IPYIFVDASYFKV 164
                                       *******************************9.88****************************.************* PP

                   Transposase_mut 175 ReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaa 251
                                       R +gr v+ka l+ ++++ dG+reiL+ +v+dsE+e+ W++ +esLk+rGlkgv+lv+sDahkG+++a++++f +a+
  gi|330507151|ref|YP_004383579.1| 165 RTDGRYVNKALLVVVAIHDDGYREILSATVDDSEDESCWENCFESLKARGLKGVKLVISDAHKGIQAAVQKSFLGAS 241
                                       ***************************************************************************** PP

                   Transposase_mut 252 vQrCrvHll 260
                                       +Q C v l 
  gi|330507151|ref|YP_004383579.1| 242 WQMCNVSLY 250
                                       *****9775 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   7.9e-10   4.7e-06      14      90 ..     172     246 ..     154     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 7.9e-10
                              MULE  14 klplltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlCl 90 
                                       +  ll vv+++d g   +l  ++ +se+e+++e  +++l+++    +  k +i+D +k+++ a+++ f +a  ++C 
  gi|330507151|ref|YP_004383579.1| 172 NKALLVVVAIHDDGYREILSATVDDSEDESCWENCFESLKARGL--KGVKLVISDAHKGIQAAVQKSFLGASWQMCN 246
                                       56789999********************************9644..69*************************9995 PP

>> DUF5499  Family of unknown function (DUF5499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.3   1.8e+03       9      26 ..      37      54 ..      32      70 .. 0.74
   2 ?    8.9   0.0   0.00037       2.2      25      64 ..     113     152 ..      95     165 .. 0.82
   3 ?    2.6   0.0     0.035   2.1e+02      29      54 ..     199     224 ..     180     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.3
                           DUF5499  9 dlkvrdydyfgkrkapdg 26
                                      +++ r y+  gkr+a   
  gi|330507151|ref|YP_004383579.1| 37 QIQARPYERTGKRRAHRN 54
                                      577899999999998644 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00037
                           DUF5499  25 dgvshkdmvenifrsdkwrrmkgidsevkdelnrqlrgev 64 
                                       + v  k  ++ni  s+  r  k +d  vkd lnr + g +
  gi|330507151|ref|YP_004383579.1| 113 EKVFSKFGLKNISASEVSRIAKKLDKLVKDFLNRPIEGSI 152
                                       4556677789************************999976 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.035
                           DUF5499  29 hkdmvenifrsdkwrrmkgidsevkd 54 
                                        +   en f s k r +kg+   + d
  gi|330507151|ref|YP_004383579.1| 199 DESCWENCFESLKARGLKGVKLVISD 224
                                       556779*************9877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1946.35
//
Query:       gi|330507152|ref|YP_004383580.1|  [L=353]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete 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   75.4   0.0    4.8e-21   74.6   0.0    1.4  1  DUF772       Transposase domain (DUF772)
    1.5e-15   57.4   4.6      5e-15   55.7   4.6    1.9  1  DDE_Tnp_1    Transposase DDE domain
      3e-05   23.8   0.3    0.00012   21.8   0.3    1.9  1  DDE_Tnp_4    DDE superfamily endonuclease
    3.1e-05   24.2   0.4    5.4e-05   23.4   0.4    1.4  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
      0.052   13.9   0.1       0.12   12.8   0.1    1.6  1  EnY2         Transcription factor e(y)2


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 !   74.6   0.0   1.3e-24   4.8e-21       1      72 [.      51     122 ..      51     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.3e-24
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp+++ ++m+k+l+lq ++glSd ele+++ +++sfr flg     + +pd+st + fR+rl+e    e+l++e
  gi|330507152|ref|YP_004383580.1|  51 GRPNIDIVIMVKALVLQSWFGLSDPELERQVTDRISFRIFLGT---TEVIPDFSTVWLFRERLIEcgrYEDLWKE 122
                                       9*****************************************5...389****************9999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   4.6   1.4e-18     5e-15      20     214 .]     177     340 ..     133     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.4e-18
                         DDE_Tnp_1  20 k............................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkql 68 
                                       +                             ++ w +kg k+++gyk hi++dt+ +li ++++t+++ hds++    
  gi|330507152|ref|YP_004383580.1| 177 PdfdkdllnisnnivssnakpkrlddgpiNEGTWAKKGSKSFFGYKGHILIDTEYHLIRKIETTTASLHDSQVDLG- 252
                                       0555555555555555555556666666677889999**********************************99777. PP

                         DDE_Tnp_1  69 ldelrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnksk 145
                                       +++l++      +aD+GY++a++  + +                            ++k+ r++ l  ++++rnk  
  gi|330507152|ref|YP_004383580.1| 253 INGLPR------YADKGYSGAKTQGYDA---------------------------AMKKAARGHKLGIKDILRNK-- 294
                                       777887......*******888877777...........................89******************.. PP

                         DDE_Tnp_1 146 kekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                              +++r+R+qiEr F+ +kr  + +++++ + +r+ +++++  +++n+
  gi|330507152|ref|YP_004383580.1| 295 -----------------------RISRKRSQIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNI 340
                                       .......................******************999************************7 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   3.4e-08   0.00012      77     130 ..     257     313 ..     195     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.4e-08
                         DDE_Tnp_4  77 vilaDkgFklse..kl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgr 130
                                          aDkg+ +++   +   ++k  ++++l  ++  +n++i++ r  +Er+++ +k+ 
  gi|330507152|ref|YP_004383580.1| 257 PRYADKGYSGAKtqGYdAAMKKAARGHKLGIKDILRNKRISRKRSQIERCFAVMKRA 313
                                       3469*****99954333455555********************************65 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 !   23.4   0.4   1.5e-08   5.4e-05      74     124 ..     294     343 ..     265     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.5e-08
                       DDE_Tnp_1_6  74 kaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                       k+  +kR+ ++E+ fa +kr++++  + ++ ++++ ++f++  +++N+++l
  gi|330507152|ref|YP_004383580.1| 294 KRISRKRS-QIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNIEQL 343
                                       45556665.***************************************997 PP

>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.3e-05      0.12       5      31 ..     107     133 ..     106     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       HHHHHHTTHHHHHHHHHHHHHHHTTHH CS
                              EnY2   5 qqkLvesGererlkelLrerLeesGWr 31 
                                       +++L+e G +e+l + L+++L+e G+ 
  gi|330507152|ref|YP_004383580.1| 107 RERLIECGRYEDLWKELQNQLDEKGFA 133
                                       589**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2697.96
//
Query:       gi|330507153|ref|YP_004383581.1|  [L=107]
Description: hypothetical protein MCON_1010 [Methanosaeta concilii GP6]
Scores for complete 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   22.2   0.0    0.00016   21.8   0.0    1.3  1  RHH_8            Ribbon-Helix-Helix transcriptional regulator
  ------ inclusion threshold ------
      0.036   13.1   0.0       0.04   12.9   0.0    1.1  1  DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
      0.043   13.8   0.4      0.094   12.7   0.4    1.7  1  RHH_1            Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.7e-08   0.00016      11      45 ..      14      48 ..       7      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.7e-08
                             RHH_8 11 gvvDLgqiDlLveeGfYsnRtDlirtairaqLakh 45
                                       + + +qi  L e G Y n +D++r air++L++ 
  gi|330507153|ref|YP_004383581.1| 14 APAEAAQIRELLEAGLYLNESDFVRDAIRHRLSEI 48
                                      5667789999**********************875 PP

>> DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.8e-06      0.04      92     134 ..      56      98 ..      31     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-06
                   DDE_Tnp_ISAZ013  92 isvdtkkkeliGefkrsGkewrpkgepaevkdhdfvskeegka 134
                                       + + t kke++G +k++G+ + ++       d+d+v k++g++
  gi|330507153|ref|YP_004383581.1|  56 VDFQTAKKEILGYYKARGEAYPDEAARDLELDFDLVMKATGEL 98 
                                       667899***************999999999********99986 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   1.6e-05     0.094       8      37 ..      15      45 ..       8      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1  8 eellerLdelarrrg.rSrSelIReAlreyl 37
                                        ++++++el +++   + S+++R+A+r++l
  gi|330507153|ref|YP_004383581.1| 15 PAEAAQIRELLEAGLyLNESDFVRDAIRHRL 45
                                      678999***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 833.24
//
Query:       gi|330507154|ref|YP_004383582.1|  [L=75]
Description: hypothetical protein MCON_1011 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-05   25.3   0.0    1.5e-05   25.1   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   8.3e-10   1.5e-05       1      57 [.       7      63 ..       7      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 8.3e-10
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipe 57
                                      y +++ ++++ ++   vP +pGc+ +g+t +ea  + +++ e+  ++  e+g+ +p+
  gi|330507154|ref|YP_004383582.1|  7 YTVILRPEDNGTFVAYVPAIPGCHAWGQTPQEAQMELTNVFEMIRDEYKEEGRMLPA 63
                                      88999999***************************************9999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 562.95
//
Query:       gi|330507155|ref|YP_004383583.1|  [L=71]
Description: YcfA family protein [Methanosaeta concilii GP6]
Scores for complete 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   68.7   0.2    3.9e-19   68.4   0.2    1.1  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.2   2.2e-23   3.9e-19       2      58 .]       6      61 ..       5      61 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 2.2e-23
                                      HCHHHHHHHTT-EEEEEETTEEEEE-TTSS-EEEEE.S-SSS--CCCHHHHHHHCC- CS
                        HicA_toxin  2 reviklLeklGfevvrqkGSHvrfkhpdkrgivtvppHpgkelkpgtlksIlkqaGl 58
                                      +++ k+ +klGf+vvrqkGSH r+khpd+r ++t+p H++ e++ ++l  Ilkq+++
  gi|330507155|ref|YP_004383583.1|  6 KDLQKAARKLGFRVVRQKGSHARWKHPDGR-ATTIPIHGNSEIGGWLLYEILKQLEI 61
                                      89***************************9.78*********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 540.75
//
Query:       gi|330507156|ref|YP_004383584.1|  [L=209]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.2   0.2        1.1    9.0   0.2    2.3  2  DUF3950   Domain of unknown function (DUF3950)


Domain annotation for each model (and alignments):
>> DUF3950  Domain of unknown function (DUF3950)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2   6.2e-05       1.1       7      23 ..      52      68 ..      51      74 .. 0.89
   2 ?    2.9   0.0    0.0052        93       9      23 ..     149     163 ..     146     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 6.2e-05
                           DUF3950  7 ealeseksqNFSAWVke 23
                                      ++++  +s+NF  W  +
  gi|330507156|ref|YP_004383584.1| 52 FSMKHSGSSNFAVWLLD 68
                                      69************876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0052
                           DUF3950   9 leseksqNFSAWVke 23 
                                       +e  + +NF  W  +
  gi|330507156|ref|YP_004383584.1| 149 MEHDGKRNFAIWLLD 163
                                       9999******99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1583.09
//
Query:       gi|330507157|ref|YP_004383585.1|  [L=50]
Description: hypothetical protein MCON_1015 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 431.69
//
Query:       gi|330507158|ref|YP_004383586.1|  [L=60]
Description: hypothetical protein MCON_1016 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       189  (0.0105416); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 477.34
//
Query:       gi|330507159|ref|YP_004383587.1|  [L=71]
Description: hypothetical protein MCON_1017 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 558.67
//
Query:       gi|330507160|ref|YP_004383588.1|  [L=259]
Description: hypothetical protein MCON_1018 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   12.1   0.0       0.32   11.2   0.0    1.5  1  RNase_Zc3h12a_2  Zc3h12a-like Ribonuclease NYN domain


Domain annotation for each model (and alignments):
>> RNase_Zc3h12a_2  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.8e-05      0.32      48      91 ..     101     146 ..      78     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.8e-05
                   RNase_Zc3h12a_2  48 dlvafqklidldfi..kfiteaenfkwfnvvadladrigavfvssa 91 
                                       d + f k  +++++   + t +++ kw+++++ +  rigav+    
  gi|330507160|ref|YP_004383588.1| 101 DYINFTKEAEFEYMpvSYQTGTYDQKWIEKLCVQNYRIGAVLTEMY 146
                                       6788999999999854568999*******************87544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1865.67
//
Query:       gi|330507161|ref|YP_004383589.1|  [L=524]
Description: hypothetical protein MCON_1020 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-15   56.6   0.3    7.3e-14   51.9   0.1    2.7  2  DDE_Tnp_1     Transposase DDE domain
  ------ inclusion threshold ------
      0.043   13.5   0.2       0.28   10.8   0.0    2.1  2  hGDE_central  Central domain of human glycogen debranching en


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 ?   -1.0   0.0      0.13   1.1e+03       3      30 ..      35      62 ..      33      75 .. 0.75
   2 !   51.9   0.1   8.1e-18   7.3e-14      24     213 ..     191     464 ..     167     465 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.13
                         DDE_Tnp_1  3 krevlivDattvrvpgtkedarwgykgg 30
                                      k+ ++ vD+++vr+++ +++ +++ k++
  gi|330507161|ref|YP_004383589.1| 35 KYLGRNVDGQPVRMRSAPSEIKEKTKKK 62
                                      6777889*********996666655544 PP

  == domain 2  score: 51.9 bits;  conditional E-value: 8.1e-18
                         DDE_Tnp_1  24 rwgyk.ggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYasaelldtlee 97 
                                        +gy+  g+  + +++ +++d   g+++ ++i+pg+ +d+ +l  +l+ ++++  ++ + ++D+G++s ++l +l +
  gi|330507161|ref|YP_004383589.1| 191 EYGYNrDGADLPQINMSLIMDKDKGIPVMYDIFPGSISDVSTLSGTLKKIKAHgvQNYVAVMDRGFFSLGNLCELLD 267
                                       45899899999****************************************************************** PP

                         DDE_Tnp_1  98 kgvdyiirlkkntklyrk....gaeskrrgrlrkhdrnkiltksqkrrnk........................... 143
                                       +++++++++k + + +++      ++  + ++  +++n+++  + ++ n                            
  gi|330507161|ref|YP_004383589.1| 268 NKISFVMAAKLQLNDLKQlmteAQKDIDDVKYLHKFNNEPIFAKPITYNIdnmevrgyvyydpkleqnekqtllsrl 344
                                       ***************9999999778888888888888888888888888899999999999999999999******* PP

                         DDE_Tnp_1 144 .....................................................skkekgdvyyvtntnsellsaeev 167
                                                                                            +++  g ++++++ +    +    
  gi|330507161|ref|YP_004383589.1| 345 ydireellkvrlkknsspqvafkekargfgnffewnvvdnrfdvsikqnavtqRMNKMGKYILFYSGDF---DWLNC 418
                                       ***************************************************764444444444444444...44455 PP

                         DDE_Tnp_1 168 aelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllaln 213
                                         lyr R +iE +Fk lk+   ++ l++++   ++ +++  +l+l 
  gi|330507161|ref|YP_004383589.1| 419 LSLYRERDEIEKSFKALKNEIDILPLNTHSEKTTRGFIFVAFLSLI 464
                                       69*************************************9999885 PP

>> hGDE_central  Central domain of human glycogen debranching enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.1e-05      0.28      93     166 ..      22      97 ..       4     120 .. 0.73
   2 ?    0.1   0.0     0.059   5.3e+02       3      34 ..     274     308 ..     273     406 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.1e-05
                                       .----SSEE----EEEE.E----EEEE.......ETT.TEEEEE--.S---SSEEEEEEEEETT--ST..HHHHHCS CS
                      hGDE_central  93 eykkdekfinGlpsklkeelkleevkvlkieevedee.eesvievefenfppGsvvvfetelsevdek..ldefaks 166
                                        y k++k i+  ++ l ++++ + v + +  ++ +e+ ++++ ev+ ++f  Gs++v+++ ++e++ +  l++   s
  gi|330507161|ref|YP_004383589.1|  22 YYDKEKKQIRHRSKYLGRNVDGQPVRMRSAPSEIKEKtKKKTAEVK-SSFDYGSILVLQSIMEELNLDryLENLLPS 97 
                                       567777788888888888999999999877777666669999****.************999976532234444333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.059
                                       HHHHHHHHHHHHHHHTT--S...EEEEEE.ETTEE CS
                      hGDE_central   3 ikakklLnklhkelakegfd...evhvdqleedii 34 
                                       ++ak  Ln+l++ + + + d     + ++ +++ i
  gi|330507161|ref|YP_004383589.1| 274 MAAKLQLNDLKQLMTEAQKDiddVKYLHKFNNEPI 308
                                       78999999999999877666444445565555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 00:00:00.44
# Mc/sec: 3580.98
//
Query:       gi|330507162|ref|YP_004383590.1|  [L=401]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 2871.68
//
Query:       gi|330507163|ref|YP_004383591.1|  [L=374]
Description: transposase, IS605 OrfB Family [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.0    2.2e-22   79.5   0.0    1.5  1  OrfB_IS605      Probable transposase
    7.9e-22   77.0   0.1    3.1e-21   75.0   0.1    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.5e-19   68.5   2.3    5.3e-19   67.4   2.3    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.8   0.2       0.02   14.9   0.2    1.4  1  DZR             Double zinc ribbon
       0.66    9.6   4.4         16    5.1   0.1    3.1  3  RecR            RecR protein


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.0   6.2e-26   2.2e-22       3     117 ..     165     277 ..     163     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 6.2e-26
                        OrfB_IS605   3 pveveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        ve+e++ +p+ k ++ +giD+G++ +at+++++   ++ ++r++++++ +la+ +++l++  k++  +kka r + 
  gi|330507163|ref|YP_004383591.1| 165 SVEIEDQlKPPWKDGSLVGIDVGLESFATLSNGE---TIANPRFFREEETELARVQRKLSKAPKGTPERKKALRMVE 238
                                       6899999666779999******************...**************************************** PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       r+h++++++r +++hk++++l+++   ++ e+L ++nm 
  gi|330507163|ref|YP_004383591.1| 239 RVHERITNKRCDFAHKVSRYLVNRFGLIAFEDLSIQNML 277
                                       *************************************97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   4.7e+03      19      32 ..     237     250 ..     231     259 .. 0.73
   2 !   75.0   0.1   8.8e-25   3.1e-21       1      68 [.     291     358 ..     291     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                    OrfB_Zn_ribbon  19 veevnpayTSktCs 32 
                                       ve v ++ T k+C 
  gi|330507163|ref|YP_004383591.1| 237 VERVHERITNKRCD 250
                                       67777777777774 PP

  == domain 2  score: 75.0 bits;  conditional E-value: 8.8e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++ l +  +yka  +G  v++v+p++TSk Cs+Cg  ++++ls+r+++C++Cg+++drD+nAaiNil+
  gi|330507163|ref|YP_004383591.1| 291 WNMLVTLTSYKAASAGSMVVLVDPRNTSKMCSRCGILVEKTLSDRVHNCTQCGLSLDRDWNAAINILR 358
                                       667777889*********************************************************97 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   2.3   1.5e-22   5.3e-19       1      47 []       1      46 [.       1      46 [. 0.99

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 1.5e-22
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkayk+r+yPT+ Q++k++rt++ +R+ YN+ La+rk+a+e+egk
  gi|330507163|ref|YP_004383591.1|  1 M-LKAYKFRIYPTKSQRTKMERTLDLCRWTYNQTLAYRKDAWEKEGK 46
                                      8.*******************************************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   5.6e-06      0.02      10      44 ..     316     352 ..     312     355 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.6e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + +++Cs+Cg  ++++ +   ++C +Cg ++d +++ 
  gi|330507163|ref|YP_004383591.1| 316 NTSKMCSRCGILVEKTLSdrVHNCTQCGLSLDRDWNA 352
                                       6789*********9877799************99986 PP

>> RecR  RecR protein
   #    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       5      16 ..      71      82 ..      69      84 .. 0.89
   2 ?    5.1   0.1    0.0045        16      13      28 ..     315     330 ..     310     332 .. 0.76
   3 ?    4.5   0.5     0.007        25      12      23 ..     332     343 ..     330     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.24
                                      HHHHHHHHHHH- CS
                              RecR  5 LaeaLqeakekv 16
                                      ++++Lq+a e+v
  gi|330507163|ref|YP_004383591.1| 71 FSQTLQNAQERV 82
                                      89*******998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0045
                                       HHH-EE-TTT--EESS CS
                              RecR  13 kekvrhCsrCgnltee 28 
                                       +++ + CsrCg l e+
  gi|330507163|ref|YP_004383591.1| 315 RNTSKMCSRCGILVEK 330
                                       667799*****99776 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.007
                                       HHHH-EE-TTT- CS
                              RecR  12 akekvrhCsrCg 23 
                                       + ++v+ C +Cg
  gi|330507163|ref|YP_004383591.1| 332 LSDRVHNCTQCG 343
                                       6799*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2445.44
//
Query:       gi|330507164|ref|YP_004383592.1|  [L=1080]
Description: carbamoyl-phosphate synthase, large subunit [Methanosaeta concilii GP6]
Scores for complete 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-105  349.1   0.3    7.8e-71  237.9   0.1    2.3  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.2e-40  138.6   0.0    2.9e-40  137.4   0.0    1.7  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    5.3e-19   68.2   2.2    1.5e-17   63.6   0.1    3.8  4  MGS              MGS-like domain
    1.2e-15   57.5   0.0    1.9e-06   27.6   0.0    2.4  2  ATP-grasp        ATP-grasp domain
    2.1e-14   53.4   0.1    6.2e-06   26.0   0.0    2.9  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    8.7e-13   48.3   0.0    2.9e-06   27.0   0.0    2.5  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    3.5e-11   43.4   0.2    0.00016   21.7   0.0    2.7  2  ATP-grasp_3      ATP-grasp domain
    5.9e-07   29.5   0.0      0.031   14.0   0.0    2.5  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    3.7e-05   23.3   0.0       0.26   10.7   0.0    2.7  2  ATP-grasp_5      ATP-grasp domain
    0.00024   20.8   0.0       0.36   10.4   0.0    3.5  3  RimK             RimK-like ATP-grasp domain
     0.0011   18.6   0.0        1.9    8.0   0.0    2.8  2  ATP-grasp_2      ATP-grasp domain
  ------ inclusion threshold ------
      0.013   15.3   0.0          1    9.3   0.0    3.1  2  HTH_23           Homeodomain-like domain
        0.1   12.0   0.0       0.56    9.6   0.0    2.1  2  Epimerase        NAD dependent epimerase/dehydratase family
       0.12   12.3   0.0        7.8    6.6   0.0    3.0  2  HHH              Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.9   0.1   6.1e-74   7.8e-71       1     210 [.     128     331 ..     128     332 .. 0.99
   2 !  109.2   0.0   1.5e-34   1.9e-31       1     210 [.     677     879 ..     677     880 .. 0.95

  Alignments for each domain:
  == domain 1  score: 237.9 bits;  conditional E-value: 6.1e-74
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D++ +k+a++k+++pv +s a+  +tl+eal++ +e+g P ++++a++lGG+G+++a+++eel +++  +l+ ++  
  gi|330507164|ref|YP_004383592.1| 128 DRDLFKQAMQKVGEPVPESRAV--NTLDEALEVMEELGLPLVVRPAYTLGGSGGGIAKTREELLQICDLGLKRSR-- 200
                                       9*******************99..**************************************************7.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                          +qvl+e+s+ g+ e+E+ev+rD+++++it+c++en++++  +t+++i+v P qtLtd+e q+lr+aa++++r++
  gi|330507164|ref|YP_004383592.1| 201 --ISQVLLEESVGGWTELEYEVMRDSNDTCITICNMENMDPMgiHTGESIVVTPIQTLTDHEIQMLRSAAINIIRAL 275
                                       ..99************************************************************************* PP

                                       T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 153 gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       +++g+++++f+++  ++ey viEvN+R+s++sala+kaTG++++ ++akia g++L+e
  gi|330507164|ref|YP_004383592.1| 276 KIEGGCNIQFAVK--DGEYRVIEVNPRVSRSSALASKATGYPIARVTAKIAIGMTLDE 331
                                       ************9..6****************************************97 PP

  == domain 2  score: 109.2 bits;  conditional E-value: 1.5e-34
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D+e++++++ ++n+p  ++ +a   +  ea ++a++igyPv++++++ lGG+ m ++++e+ l   +++a++ ++  
  gi|330507164|ref|YP_004383592.1| 677 DRERFNALMTRLNIPQPNAGIA--FSPAEAREVAAKIGYPVLVRPSYVLGGRAMEIVYDEKGLDVYMQEAVRVSR-- 749
                                       9**************9998888..8999**********************************************6.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                         ++ vl++ +l+   ei+v+ + D k+  i    +e + +   + +++  + P qtL     + +r    k++  +
  gi|330507164|ref|YP_004383592.1| 750 --EHPVLIDDFLQDAVEIDVDAVCDGKDVLIGA-IMEHIEEAgiHSGDSACMIPPQTLPGVVLEVVRDYVRKIALGL 823
                                       ..9************************987765.5777777678********************************* PP

                                       T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 153 gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       gv+g  +++ +++  ++  yv+E N+R s+  +  +kaTGl+l+k+aa +  g++L e
  gi|330507164|ref|YP_004383592.1| 824 GVIGIVNLQMAYK--DGTVYVLEANPRSSRTIPFVSKATGLPLAKIAANVMIGKSLAE 879
                                       ************9..6**************************************9986 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.4   0.0   2.3e-43   2.9e-40       3     122 .]     422     545 ..     420     545 .. 0.95

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 2.3e-43
                       CPSase_L_D3   3 lkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkk.....eldeellreakklGfsDk 74 
                                       l +ptd+R+fai+eal+rg s eei+++t i p+F++++ ++v++e+e++++k       +d+++lr+ak+ Gf+D+
  gi|330507164|ref|YP_004383592.1| 422 LVNPTDDRLFAIYEALKRGTSPEEISDITGIGPYFIYRIVNIVRMEEEIRRAKGtnensVMDADTLRRAKRTGFTDE 498
                                       789***********************************************998888888899999************ PP

                       CPSase_L_D3  75 qiaelleeeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                       qi ++++ +++ee+++lr++l+i p++k+vDtcAaeFea+tpY+Ys+Y
  gi|330507164|ref|YP_004383592.1| 499 QIGSMVG-RSREEIADLRRSLKIIPTFKMVDTCAAEFEATTPYYYSSY 545
                                       *****87.56677**********************************9 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.42   5.4e+02      51      75 ..      32      56 ..       6      67 .. 0.72
   2 ?   -0.6   0.1       1.2   1.6e+03      47      93 ..     278     327 ..     248     329 .. 0.72
   3 ?   -2.5   0.0       4.8   6.1e+03      51      71 ..     581     601 ..     566     611 .. 0.71
   4 !   63.6   0.1   1.2e-20   1.5e-17       5      95 .]     963    1045 ..     959    1045 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.42
                                      HHHHHHHTTSCCEEEEE--THHHHH CS
                               MGS 51 eildaikngeidlvintlypfkatv 75
                                      +  + +++++i++v ++ +p + ++
  gi|330507164|ref|YP_004383592.1| 32 QACKSLREEGIEVVLVNSNPATIMT 56
                                      7788999999999999999987665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                                       THCHHHHHHHHTTSCCEEEEE--THHHHHH...CHHHHHHHHHHHTTSHE CS
                               MGS  47 ggrveildaikngeidlvintlypfkatva...kdgykirraaenidIpl 93 
                                       +g ++i+ a+k+ge+ ++ +++   ++        gy i+r+  +i I++
  gi|330507164|ref|YP_004383592.1| 278 EGGCNIQFAVKDGEYRVIEVNPRVSRSSALaskATGYPIARVTAKIAIGM 327
                                       34457888889999998888887766665556678999999999999987 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.8
                                       HHHHHHHTTSCCEEEEE--TH CS
                               MGS  51 eildaikngeidlvintlypf 71 
                                       + + a+++++i++ i++ +p+
  gi|330507164|ref|YP_004383592.1| 581 HAVMALREQGIEAHIINNNPE 601
                                       556678888888555555554 PP

  == domain 4  score: 63.6 bits;  conditional E-value: 1.2e-20
                                        HHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHHCHH CS
                               MGS    5 lakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatvakdg 79  
                                         a+kl+++g +++AT  Ta++l+++gi+ +e v+k+  g +++    +ld +k ge++l+int++++++ +  dg
  gi|330507164|ref|YP_004383592.1|  963 AARKLVDAGLDIIATDNTAEYLSKSGIK-VERVQKIYNG-SPN----VLDYMKRGEVKLIINTPTTKQSVK--DG 1029
                                        69**************************.7777888888.899....*******************99886..** PP

                                        HHHHHHHHHTTSHEES CS
                               MGS   80 ykirraaenidIplpt 95  
                                        y+irr a+++++p++t
  gi|330507164|ref|YP_004383592.1| 1030 YQIRRSAVDYHVPYIT 1045
                                        **************98 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.5e-09   1.9e-06       2     161 ..     137     302 ..     136     310 .. 0.86
   2 !   27.4   0.0   1.7e-09   2.2e-06       3     160 ..     687     849 ..     685     852 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.5e-09
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE---- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpf 74 
                                       +k+g pvp+  av++ +e+ e++eelglp+vv+ +     G G  + + +e+l q+ +      +  +v++Ee v  
  gi|330507164|ref|YP_004383592.1| 137 QKVGEPVPESRAVNTLDEALEVMEELGLPLVVR-PAYTLGGSGGGIAKTREELLQICDLGlkrsRISQVLLEESVGG 212
                                       67889****************************.99999999999*******9999988777767789********* PP

                                       SEEEEEEEEEETTC-EEE--EEEEEEETTEEE...EEEECEE-SCHHH.HHHHHHHHHHHHHHTSSEEEEEEEEEET CS
                         ATP-grasp  75 ekElsvlvvrsaeGetafypvvetvqedgilr...lsvapaevsekaq.kkaeeiakkiveeLggvGvfavElFvle 147
                                        +El   v+r+ + +  ++  +e++   gi     ++v p +  ++++ +  ++ a +i+++L + G   + + v+ 
  gi|330507164|ref|YP_004383592.1| 213 WTELEYEVMRDSNDTCITICNMENMDPMGIHTgesIVVTPIQTLTDHEiQMLRSAAINIIRALKIEGGCNIQFAVK- 288
                                       *************999999999****9999853336788877766654044555566**************86666. PP

                                       TCTEEEEEEESS-- CS
                         ATP-grasp 148 dgellvnElapRpH 161
                                       dge  v E+ pR+ 
  gi|330507164|ref|YP_004383592.1| 289 DGEYRVIEVNPRVS 302
                                       ************85 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.7e-09
                                       TTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----S CS
                         ATP-grasp   3 klglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfe 75 
                                       +l++p p+  ++ s +e++e+a+++g+pv+v+ +     G+   +v +e+ l+  ++++    +e++v++ +f +  
  gi|330507164|ref|YP_004383592.1| 687 RLNIPQPNAGIAFSPAEAREVAAKIGYPVLVR-PSYVLGGRAMEIVYDEKGLDVYMQEAvrvsREHPVLIDDFLQDA 762
                                       5777888888888999****************.99999***********988777777777779************* PP

                                       EEEEEEEEEETTC-EEE--EEEEEEETTEE....EEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETT CS
                         ATP-grasp  76 kElsvlvvrsaeGetafypvvetvqedgil....rlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvled 148
                                       +E+ v +v + +  + + +++e+++e gi        + p++++   ++ ++++++ki+  Lg++G++ + + ++ d
  gi|330507164|ref|YP_004383592.1| 763 VEIDVDAVCDGKD-VLIGAIMEHIEEAGIHsgdsACMIPPQTLPGVVLEVVRDYVRKIALGLGVIGIVNLQMAYK-D 837
                                       ******9998776.88889999999887762221567778999999**************************999.* PP

                                       CTEEEEEEESS- CS
                         ATP-grasp 149 gellvnElapRp 160
                                       g+++v E  pR 
  gi|330507164|ref|YP_004383592.1| 838 GTVYVLEANPRS 849
                                       **********96 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.9e-08   2.5e-05      47     117 ..     262     333 ..     251     347 .. 0.78
   2 !   26.0   0.0   4.8e-09   6.2e-06      49     118 ..     812     882 ..     750     895 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.9e-08
                      ATPgrasp_Ter  47 eelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeve 117
                                       + l ++a +++++++++g  n+Q+  ++++++++E+NpR+s      s ++G  ++++ +k + g+  +e++
  gi|330507164|ref|YP_004383592.1| 262 QMLRSAAINIIRALKIEGGCNIQFAVKDGEYRVIEVNPRVSRSSAlASKATGYPIARVTAKIAIGMTLDEIR 333
                                       35668999********************************96555156677999999999999998544443 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 4.8e-09
                      ATPgrasp_Ter  49 lielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteevee 118
                                       + ++++++a  +g+ g+vn+Q+ +++++ ++LE NpR s ++  +s ++G+ l+++a++ + g++ +e   
  gi|330507164|ref|YP_004383592.1| 812 VRDYVRKIALGLGVIGIVNLQMAYKDGTVYVLEANPRSSRTIPfVSKATGLPLAKIAANVMIGKSLAEQGY 882
                                       457889999999******************************8357778**************85544443 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 !   27.0   0.0   2.3e-09   2.9e-06      26     174 ..     153     299 ..     139     303 .. 0.78
   2 !   18.4   0.0   9.2e-07    0.0012      28     174 ..     704     847 ..     694     865 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.3e-09
                                       HHHHHHHHHC-SSEEEEESSS..STTTTEEEESSGGGHHHHHHHHHTT-..SCEEEEE--.ESEEEEEEEEETSSCE CS
                   Dala_Dala_lig_C  26 ellekveeelgypvfVKpare..GSSvGvskveseeelkeaieeafkyd..ekvlvEeai.egreievavlgnekle 97 
                                       +   +v+eelg+p++V+pa +  GS  G++  +++eel +  +  +k+   ++vl Ee +    e+e  v+ + + +
  gi|330507164|ref|YP_004383592.1| 153 DEALEVMEELGLPLVVRPAYTlgGSGGGIA--KTREELLQICDLGLKRSriSQVLLEESVgGWTELEYEVMRDSNDT 227
                                       4567899***********964336666776..578999999998887762269*******7779********88888 PP

                                       EEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C  98 vsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                       + ++ ++   + +      ++++++ ++   +l++++ + ++ +a+++ +al+++G + + f ++ +ge  + EvN+
  gi|330507164|ref|YP_004383592.1| 228 CITICNMENMDPM----GIHTGESIVVTPIQTLTDHEIQMLRSAAINIIRALKIEGGCNIQFAVK-DGEYRVIEVNP 299
                                       8777766554432....23344445444445688888999***********************98.9*********6 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 9.2e-07
                                       HHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT..-SCEEEEE--.ESEEEEE.EEEETSSCEEEE CS
                   Dala_Dala_lig_C  28 lekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky..dekvlvEeai.egreiev.avlgneklevse 100
                                        ++v +++gypv+V+p+       ++ v  e+ l  +++ea++   ++ vl++ ++ ++ ei+v av +  ++ +  
  gi|330507164|ref|YP_004383592.1| 704 AREVAAKIGYPVLVRPSYVLGGRAMEIVYDEKGLDVYMQEAVRVsrEHPVLIDDFLqDAVEIDVdAVCDGKDVLIGA 780
                                       57899************9888889*****************97611677*******99******6788888899999 PP

                                       EEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C 101 vgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                       + e++ + g+       s+d+a +  p +l+  v e +++++ k+   l++ G++ + + ++ +g++++ E N+
  gi|330507164|ref|YP_004383592.1| 781 IMEHIEEAGIH------SGDSACMIPPQTLPGVVLEVVRDYVRKIALGLGVIGIVNLQMAYK-DGTVYVLEANP 847
                                       99999999986......578899999999****************99999999999998887.9*******996 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1     8e-07     0.001       6     158 ..     131     301 ..     126     304 .. 0.64
   2 !   21.7   0.0   1.3e-07   0.00016       9     157 ..     682     848 ..     675     852 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8e-07
                                       HHHHHHTTT.S---.........-EESS--.......SSSEEEEESS-------B--SS--TTE............. CS
                       ATP-grasp_3   6 ktykkLkeagvkvP.....tkleaeeleee.......ekklvvKprdGaggesvrvveekeeaeaaieeve...... 64 
                                        + +++++ g +vP     ++l +e    +         +lvv p++  gg++  +++ +ee+ ++++         
  gi|330507164|ref|YP_004383592.1| 131 LFKQAMQKVGEPVPesravNTL-DE----AlevmeelGLPLVVRPAYTLGGSGGGIAKTREELLQICDLGLkrsris 202
                                       5566777777888865553222.12....122233347789999999999999999998888776555332455644 PP

                                       ..EEEE---S.EEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEE...EES----HHHHHH...HHHHHHHTTST CS
                       ATP-grasp_3  65 ..lvqefieG.kplSvsllsdgekvlvlavnrqliekaekefvyaGn...vtpietelkeevv...elaeevvekle 132
                                         l+ e + G ++l  +++ d ++  +  +n + ++      + +G+   vtpi+t  ++e++   ++a +++++l 
  gi|330507164|ref|YP_004383592.1| 203 qvLLEESVGGwTELEYEVMRDSNDTCITICNMENMDPM---GIHTGEsivVTPIQTLTDHEIQmlrSAAINIIRAL- 275
                                       44555555554456666666666666666666666553...55666533368999877766651116777888888. PP

                                       T--EEEEEEEEESS.SEEEEEEESS- CS
                       ATP-grasp_3 133 glaGyvGvDlvlkdeepyviEvNPRl 158
                                       ++ G   + + +kd+e  viEvNPR+
  gi|330507164|ref|YP_004383592.1| 276 KIEGGCNIQFAVKDGEYRVIEVNPRV 301
                                       9999999******************8 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.3e-07
                                       HHHTTT.S---............-EESS--.SSSEEEEESS-------B--SS--TTE...............EEEE CS
                       ATP-grasp_3   9 kkLkeagvkvP........tkleaeeleee.ekklvvKprdGaggesvrvveekeeaeaaieeve........lvqe 68 
                                       ++L+ + +++P        + +ea e++ +  +++ v p++  gg ++ +v +++ ++  ++e          l+ +
  gi|330507164|ref|YP_004383592.1| 682 NALMTR-LNIPqpnagiafSPAEAREVAAKiGYPVLVRPSYVLGGRAMEIVYDEKGLDVYMQEAVrvsrehpvLIDD 757
                                       555555.4444447776665555555544459**************************9999988999********* PP

                                       ---.SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEE...EEES----HHHHHHHHHHHHHTTST...T--EEE CS
                       ATP-grasp_3  69 fie.GkplSvsllsdgekvlvlavnrqliekaekefvyaG...nvtpietelkeevvelaeevvekle...glaGyv 138
                                       f++   ++ v++++dg++vl+ a+ + + e      + +G   +++p + +l   v e++++ v+k+    g+ G+v
  gi|330507164|ref|YP_004383592.1| 758 FLQdAVEIDVDAVCDGKDVLIGAIMEHIEEA----GIHSGdsaCMIPPQ-TLPGVVLEVVRDYVRKIAlglGVIGIV 829
                                       *973679*********999999988766655....55556111555544.6799999*********98655666777 PP

                                       EEEEEESS.SEEEEEEESS CS
                       ATP-grasp_3 139 GvDlvlkdeepyviEvNPR 157
                                          + +kd+  yv+E NPR
  gi|330507164|ref|YP_004383592.1| 830 NLQMAYKDGTVYVLEANPR 848
                                       777789************* PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   2.4e-05     0.031       6     105 ..     132     227 ..     127     301 .. 0.83
   2 !   12.9   0.0   5.6e-05     0.072       8     106 ..     683     777 ..     677     794 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSS CS
                            GARS_A   6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagek 82 
                                        k+ ++k+g p +e +a++  +ea e++ee++ +  Vv+++   +g g  +ak++ee l++ +  l++ +     ++
  gi|330507164|ref|YP_004383592.1| 132 FKQAMQKVGEPVPESRAVNTLDEALEVMEELGLPL-VVRPAYTLGGSGGGIAKTREELLQICDLGLKRSRI----SQ 203
                                       6999*******************************.*****999*****************9999986555....59 PP

                                       EEEEE---S.EEEEEEEEECTTEE CS
                            GARS_A  83 vviEelleG.eEvsllalvdgktv 105
                                       v++Ee + G +E+   ++ d +++
  gi|330507164|ref|YP_004383592.1| 204 VLLEESVGGwTELEYEVMRDSNDT 227
                                       ******999668888888886654 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.6e-05
                                       HHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEE CS
                            GARS_A   8 dllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvv 84 
                                       +l+++ +ip ++     +p+ea+e+  + + ++  v+++ + +g+ + ++ +e+    +++e ++     + ++ v+
  gi|330507164|ref|YP_004383592.1| 683 ALMTRLNIPQPNAGIAFSPAEAREVAAKIGYPV-LVRPSYVLGGRAMEIVYDEKGLDVYMQEAVR----VSREHPVL 754
                                       79************999****************.99****************9988888888776....56789*** PP

                                       EEE---.SEEEEEEEEECTTEEE CS
                            GARS_A  85 iEelle.GeEvsllalvdgktvk 106
                                       i+++l+   E+ + a++dgk+v 
  gi|330507164|ref|YP_004383592.1| 755 IDDFLQdAVEIDVDAVCDGKDVL 777
                                       *****7368***********986 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00044      0.57      16      52 ..     133     169 ..     100     172 .. 0.91
   2 !   10.7   0.0    0.0002      0.26      16      51 ..     682     717 ..     674     721 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00044
                       ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvlK 52 
                                       k+ ++ +g pv+e+r +++ +ea+e++ee+g p v++
  gi|330507164|ref|YP_004383592.1| 133 KQAMQKVGEPVPESRAVNTLDEALEVMEELGLPLVVR 169
                                       566788999************************9986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0002
                       ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvl 51 
                                       ++l++ ++ip ++  +a s++ea e+a++igypv +
  gi|330507164|ref|YP_004383592.1| 682 NALMTRLNIPQPNAGIAFSPAEAREVAAKIGYPVLV 717
                                       689999***************************976 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0     0.007         9      10      85 ..     135     209 ..     126     305 .. 0.87
   2 !   10.4   0.0   0.00028      0.36       1      99 [.     675     776 ..     675     796 .. 0.83
   3 ?   -0.9   0.0      0.81     1e+03     126     157 ..     951     980 ..     942     991 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.007
                                       HHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.GGG--EEEEE--SS CS
                              RimK  10 lLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.lkeailvqeyieea 85 
                                        + k + +vp+++ ++  ++a +++e++  + P+vv+  ++  G +  +ak++++l q+ +  lk + + q  +ee+
  gi|330507164|ref|YP_004383592.1| 135 AMQKVGEPVPESRAVNTLDEALEVMEEL--GLPLVVRPAYTLGGSGGGIAKTREELLQICDLgLKRSRISQVLLEES 209
                                       5556666788888888999999999988..69***************************996688888877766665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00028
                                       HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.....G CS
                              RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.....l 72 
                                       a+d+ +  +l+ + +i+ pn+ +a ++ +a+++  ki  + Pv+v+ ++   G  + +  +e+ l   ++       
  gi|330507164|ref|YP_004383592.1| 675 AEDRERFNALMTRLNIPQPNAGIAFSPAEAREVAAKI--GYPVLVRPSYVLGGRAMEIVYDEKGLDVYMQEavrvsR 749
                                       578888899****************************..69********9999999999999999888865576645 PP

                                       GG--EEEEE--SS-SEEEEEEEETTEE CS
                              RimK  73 keailvqeyieeaenediRvlvvddev 99 
                                       ++ +l+ ++++ a + d+  +  +++v
  gi|330507164|ref|YP_004383592.1| 750 EHPVLIDDFLQDAVEIDVDAVCDGKDV 776
                                       566799999999999998776666555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.81
                                       ---HHHHHHHHHHHHHCT-SEEEEEEEEETTE CS
                              RimK 126 qlseeekelAikaakamelvvaGvDllrakrg 157
                                       ++++e  + A  a  a +lv aG+D++ +++ 
  gi|330507164|ref|YP_004383592.1| 951 SVKDE--DKAAAAVAARKLVDAGLDIIATDNT 980
                                       33444..44555666778999*****999875 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0015       1.9       8      62 ..     133     184 ..     106     197 .. 0.89
   2 !    7.5   0.0    0.0022       2.8       9      53 ..     683     726 ..     680     742 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0015
                                       HHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEE CS
                       ATP-grasp_2   8 keilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklv 62 
                                       k+ ++k g +vpe++ +++ +ea e++++lg    vv+     GG G  gG+  +
  gi|330507164|ref|YP_004383592.1| 133 KQAMQKVGEPVPESRAVNTLDEALEVMEELGLPL-VVRPAYTLGGSG--GGIAKT 184
                                       6788999************************998.999999999876..776554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0022
                                       HHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTC CS
                       ATP-grasp_2   9 eilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGR 53 
                                        ++ + +++ p++ +a+s+ ea+e+a+k+g  +  v+     GGR
  gi|330507164|ref|YP_004383592.1| 683 ALMTRLNIPQPNAGIAFSPAEAREVAAKIGYPV-LVRPSYVLGGR 726
                                       588999*************************99.66666666777 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00079         1       6      39 ..     428     462 ..     425     471 .. 0.90
   2 ?    2.2   0.0      0.13   1.7e+02      12      31 ..     488     508 ..     484     515 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00079
                            HTH_23   6 eRlrillllae.GlsvreIAreLgvsrrTvyrwlk 39 
                                       +Rl +++ +++ G s++eI+++ g+ +  +yr+++
  gi|330507164|ref|YP_004383592.1| 428 DRLFAIYEALKrGTSPEEISDITGIGPYFIYRIVN 462
                                       688899999988*********************86 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                            HTH_23  12 lllae.GlsvreIAreLgvsr 31 
                                       + +++ G + ++I  + g+sr
  gi|330507164|ref|YP_004383592.1| 488 RRAKRtGFTDEQIGSMVGRSR 508
                                       555557*************98 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00044      0.56       9      70 ..      28      88 ..      27     104 .. 0.84
   2 ?    0.9   0.0       0.2   2.6e+02       2      36 ..      86     121 ..      85     139 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00044
                                      HHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                         Epimerase  9 fiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavih 70
                                      f Gs+ +k l e+g+ev+ +++++ +  t   ++++ v+++ ++++ +++++++e+pd +i 
  gi|330507164|ref|YP_004383592.1| 28 FSGSQACKSLREEGIEVVLVNSNPATIMTD-PDTADKVYIEPLEPDIVAKIIEKERPDGIIA 88
                                      67*******************996655544.3334999********************9985 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.2
                                       EEETTTSHHHHHHHHHHHHCT....SEEEEEES-STTTT CS
                         Epimerase   2 lVtGatGfiGsalvkallekg....yevigldrlssasn 36 
                                       +++G+ G+ G +++ +l+e g    y+   +  l ++ +
  gi|330507164|ref|YP_004383592.1|  86 IIAGIGGQTGLNITSELAEMGilekYN---VEVLGTSVK 121
                                       699****************99865533...333333333 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.17   2.2e+02       3      16 ..     178     191 ..     177     197 .. 0.88
   2 ?    6.6   0.0    0.0061       7.8       9      27 ..     442     460 ..     441     463 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.17
                                       HHHHTSSHHHHHTS CS
                               HHH   3 eglipasreeLlal 16 
                                       +g i+ +reeLl++
  gi|330507164|ref|YP_004383592.1| 178 GGGIAKTREELLQI 191
                                       58899******987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0061
                                       SHHHHHTSTT-SHHHHHHH CS
                               HHH   9 sreeLlalPGVGpktAeaI 27 
                                       s+ee+ ++ G+Gp+   +I
  gi|330507164|ref|YP_004383592.1| 442 SPEEISDITGIGPYFIYRI 460
                                       89***********965555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1080 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); 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: 0.89u 0.28s 00:00:01.17 Elapsed: 00:00:00.47
# Mc/sec: 6966.30
//
Query:       gi|330507165|ref|YP_004383593.1|  [L=370]
Description: carbamoyl-phosphate synthase, small subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-41  142.0   0.0    2.8e-41  141.4   0.0    1.2  1  GATase           Glutamine amidotransferase class-I
    2.5e-37  127.5   0.0    3.5e-37  127.1   0.0    1.2  1  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    2.1e-10   40.8   0.1    2.1e-07   30.9   0.1    2.2  1  Peptidase_C26    Peptidase C26
  ------ inclusion threshold ------
      0.035   13.9   0.0      0.065   13.0   0.0    1.4  1  DJ-1_PfpI        DJ-1/PfpI family
       0.17   11.5   0.0        0.3   10.7   0.0    1.3  1  Peripla_BP_6     Periplasmic binding protein


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 !  141.4   0.0   7.8e-45   2.8e-41       2     178 ..     167     332 ..     166     342 .. 0.96

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 7.8e-45
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGI 77 
                                       +iD +  +++ ++++l  +++++ v+p +++++ i  ++ +pd++++s+Gpg+p+ +e++i+a++++++ ++Pi+GI
  gi|330507165|ref|YP_004383593.1| 167 VIDLG--IKRRILRSLSDRDFDLMVLPAHSTIQDI--EAAGPDALFLSNGPGDPErAEKAIQAVRHFAG-EMPIFGI 238
                                       78888..***********************99999..489*****************************.******* PP

                                       THHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEE CS
                            GATase  78 CLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeel 154
                                       CLG+Q++ +++g+++ k k ++hhgg+++++d       g++ ++i++++H+++v p++le +glevt  +++d+++
  gi|330507165|ref|YP_004383593.1| 239 CLGHQVISLALGAETFKLK-FGHHGGNQPVKD------LGKGIVYITSQNHNFAVVPSSLEGTGLEVTQLNASDGTV 308
                                       *******************.************......99999********************************** PP

                                       EEEEEETTTEEEESSBTTSTTSTT CS
                            GATase 155 meiiekknpfvgvQFHPEststpe 178
                                       ++i+ k+  +++vQ+HPE+ ++p+
  gi|330507165|ref|YP_004383593.1| 309 EGIQSKSLDVIAVQYHPEAYPGPH 332
                                       *********************998 PP

>> 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 !  127.1   0.0   9.9e-41   3.5e-37      14     127 ..       3     117 ..       1     118 [. 0.97

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 9.9e-41
                   CPSase_sm_chain  14 Gksfg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedvesekikvaglvvrelseepsnwr 89 
                                       G++fg  + ++GE+vf+T m+GY+e+ltDpsY+g++l++typl GnyGv+ +d++s+ ++ +++++re  ++p ++r
  gi|330507165|ref|YP_004383593.1|   3 GTGFGaPGVVAGELVFTTIMSGYEEALTDPSYHGEMLLFTYPLQGNYGVSGDDFQSDGMWPRAMICREHWDRPTHHR 79 
                                       8999955999******************************************************************* PP

                   CPSase_sm_chain  90 aeesLsewlkeekipgisgvDTRaLtkklrekgamkgv 127
                                        +++L+++l +e+ pg+++vDTR+Lt k+re+g++k++
  gi|330507165|ref|YP_004383593.1|  80 LNKTLNQFLLDEGRPGLCEVDTRMLTIKVREQGVLKAA 117
                                       **********************************9986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.1   5.9e-11   2.1e-07      83     216 .]     211     326 ..     204     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 5.9e-11
                     Peptidase_C26  83 eeeadpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsll 159
                                       +++ dpeR +  ++ +r+  + ++Pi+giC+G+q++  alG ++++ ++    + +h        ++ vk   ++++
  gi|330507165|ref|YP_004383593.1| 211 NGPGDPERAEKAIQAVRHF-AGEMPIFGICLGHQVISLALGAETFK-LK----FGHH------GGNQPVKDLGKGIV 275
                                       6677888888888887765.668******************98875.33....2333......34456654444444 PP

                     Peptidase_C26 160 aellgseeievnslHhqaike...laeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                       +   +         H++a+      +++l+v+   + Dg++E i+s++ +  v++vQ+HPE
  gi|330507165|ref|YP_004383593.1| 276 YITSQ--------NHNFAVVPsslEGTGLEVTQLNAsDGTVEGIQSKSLD--VIAVQYHPE 326
                                       44433........344444332225789999998777***********88..********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 ?   13.0   0.0   1.8e-05     0.065      48     108 ..     190     246 ..     156     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                                       EE-SEEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHH CS
                         DJ-1_PfpI  48 vtvdaslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLa 108
                                       +++  +++d++aa  Dal l  G   per    ek+++ v++fa  + +++ IC g q+ +
  gi|330507165|ref|YP_004383593.1| 190 LPAHSTIQDIEAAGPDALFLSNGPGDPER---AEKAIQAVRHFA-GEMPIFGICLGHQVIS 246
                                       55677899*************99775555...5589****9987.678*********9875 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   8.2e-05       0.3     181     234 ..     194     247 ..     191     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.2e-05
                                       HHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC-CHHHHHH CS
                      Peripla_BP_6 181 aqvlqikaagadavllagtgadlaallkaaaeaGldakrillvswsgseedlka 234
                                       + ++ i+aag+da++l+++++d   + ka++++   a+ +++++  ++ + +  
  gi|330507165|ref|YP_004383593.1| 194 STIQDIEAAGPDALFLSNGPGDPERAEKAIQAVRHFAGEMPIFGICLGHQVISL 247
                                       6799******************************99999999999887776543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2701.69
//
Query:       gi|330507166|ref|YP_004383594.1|  [L=114]
Description: hypothetical protein MCON_1027 [Methanosaeta concilii GP6]
Scores for complete 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   62.9   0.0    2.8e-17   62.7   0.0    1.1  1  DUF3467   Protein of unknown function (DUF3467)
  ------ inclusion threshold ------
      0.061   13.6   0.1      0.073   13.3   0.1    1.1  1  DUF3211   Protein of unknown function (DUF3211)
       0.33   10.6   2.2        2.3    7.9   0.1    2.5  3  BRK       BRK domain


Domain annotation for each model (and alignments):
>> DUF3467  Protein of unknown function (DUF3467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.0   4.8e-21   2.8e-17      15      90 ..       3      89 ..       1      90 [. 0.85

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 4.8e-21
                           DUF3467 15 lrie.vdesvaggsYsngaivmtspsEfiidF....lqlv.pgrpearvksr.....vvlspaaakqlvaaLqknldly 82
                                      +++e  ++s+++++Y++gai  +sp++f+i F    ++++  g ++  v +r     ++lsp aak+l+++L++++++y
  gi|330507166|ref|YP_004383594.1|  3 VSVEtTRSSEFKQIYAIGAIGGHSPYDFRIAFyndsPKIQrDGNKNITVMERkiemeIILSPLAAKELARWLEEHIKDY 81
                                      667767889***********************7777456656666666666677777********************** PP

                           DUF3467 83 etrfGeik 90
                                      e++fGeik
  gi|330507166|ref|YP_004383594.1| 82 EKKFGEIK 89
                                      *******9 PP

>> DUF3211  Protein of unknown function (DUF3211)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.2e-05     0.073      66     126 ..      28      88 ..      12      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                                       TEEEEEEEETTE....EEEEEEEEETTEEEEEEEES-HHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF3211  66 tevkyvfevskgeekgsGkieisveeekikleleyegelekliskllskrikkfeknldek 126
                                       ++ +++f+ ++ + ++ G+ +i+v e+ki++e+ +    +k + + l+++ik+ ek++ e+
  gi|330507166|ref|YP_004383594.1|  28 YDFRIAFYNDSPKIQRDGNKNITVMERKIEMEIILSPLAAKELARWLEEHIKDYEKKFGEI 88 
                                       556677777888899*******************************************997 PP

>> BRK  BRK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.029   1.7e+02       3      13 ..      45      55 ..      44      55 .. 0.85
   2 ?    7.9   0.1   0.00038       2.3      26      36 ..      67      77 ..      64      81 .. 0.93
   3 ?   -3.6   0.1       1.5   9.1e+03      19      24 ..     104     109 ..     104     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.029
                               BRK  3 gderVpVinrk 13
                                      g  +++V++rk
  gi|330507166|ref|YP_004383594.1| 45 GNKNITVMERK 55
                                      6789*****97 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00038
                               BRK 26 lkdLeeWLeen 36
                                      +k+L++WLee+
  gi|330507166|ref|YP_004383594.1| 67 AKELARWLEEH 77
                                      79********9 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.5
                               BRK  19 tGekAP 24 
                                       +Ge AP
  gi|330507166|ref|YP_004383594.1| 104 SGESAP 109
                                       699999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 923.88
//
Query:       gi|330507167|ref|YP_004383595.1|  [L=161]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-24   85.1   0.2      4e-11   42.2   0.0    4.2  4  TPR_1     Tetratricopeptide repeat
    4.3e-21   75.3   0.5    5.2e-11   43.0   0.0    2.9  3  TPR_16    Tetratricopeptide repeat
    6.2e-21   72.8   0.0    3.9e-09   35.9   0.0    4.2  4  TPR_2     Tetratricopeptide repeat
    5.9e-18   64.3   0.1    2.2e-07   30.5   0.2    4.2  4  TPR_11    TPR repeat
    7.7e-14   51.8   1.2    4.9e-05   23.5   0.0    3.9  3  TPR_12    Tetratricopeptide repeat
    3.6e-13   49.5   0.4    3.1e-06   27.2   0.6    3.0  3  TPR_9     Tetratricopeptide repeat
    2.7e-12   46.4   1.8    0.00014   22.4   0.1    4.2  4  TPR_14    Tetratricopeptide repeat
    2.3e-11   44.0   1.3    2.5e-05   24.7   0.5    3.2  3  TPR_19    Tetratricopeptide repeat
    6.6e-11   41.5   0.2    6.4e-06   26.0   0.0    4.4  5  TPR_8     Tetratricopeptide repeat
      1e-10   41.2   1.1    4.6e-05   23.5   0.1    3.4  3  TPR_17    Tetratricopeptide repeat
    1.4e-09   37.5   5.6      0.006   16.4   0.1    3.6  4  TPR_10    Tetratricopeptide repeat
    2.3e-08   33.5   0.2    0.00055   19.8   0.0    3.8  4  TPR_7     Tetratricopeptide repeat
    3.5e-08   33.6   0.4        1.2    9.9   0.0    3.9  4  TPR_6     Tetratricopeptide repeat
    1.7e-05   24.7   0.0       0.27   11.3   0.0    3.8  4  TPR_3     Tetratricopeptide repeat
    3.7e-05   23.9   0.8       0.55   11.0   0.0    3.3  3  TPR_4     Tetratricopeptide repeat
     0.0014   19.1   0.1       0.19   12.2   0.1    2.5  3  BTAD      Bacterial transcriptional activator domain
     0.0024   18.0   0.0        0.1   12.8   0.0    2.2  2  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
     0.0061   16.7   0.4         31    5.1   0.0    4.1  4  PPR       PPR repeat
     0.0089   16.1   0.1        1.2    9.2   0.0    2.8  2  DUF3856   Domain of Unknown Function (DUF3856)
  ------ inclusion threshold ------
      0.023   15.1   0.1       0.03   14.8   0.1    1.1  1  NIT       Nitrate and nitrite sensing


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 !   10.5   0.0   0.00047      0.42       7      32 ..      11      36 ..       6      38 .. 0.77
   2 !   42.2   0.0   4.5e-14     4e-11       1      34 []      39      72 ..      39      72 .. 0.97
   3 !   19.7   0.1   5.7e-07   0.00051       2      29 ..      74     101 ..      73     102 .. 0.95
   4 !    7.6   0.0    0.0038       3.4       8      25 ..     113     130 ..     113     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00047
                                      HHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1  7 lGnayfklgkydeAleyyekALelnP 32
                                      +G+ + +  ++++A+ey++ +   nP
  gi|330507167|ref|YP_004383595.1| 11 KGMDCVRRMDFEKAIEYFQIVTASNP 36
                                      677777889*********96665555 PP

  == domain 2  score: 42.2 bits;  conditional E-value: 4.5e-14
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      ++a++nlG+a++ lg+ deAle y++ + l+P+n
  gi|330507167|ref|YP_004383595.1| 39 PEAWNNLGVAFYGLGRIDEALESYDRSIALDPSN 72
                                      68******************************98 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 5.7e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALe 29 
                                       +al n++ ++++++++ eAle+y+ +Le
  gi|330507167|ref|YP_004383595.1|  74 DALRNRAFLLRNQKRLPEALEAYDTVLE 101
                                       6999*********************998 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0038
                                       HHHHHHTT-HHHHHHHHH CS
                             TPR_1   8 GnayfklgkydeAleyye 25 
                                       ++++  +g+++eAl +  
  gi|330507167|ref|YP_004383595.1| 113 AVVLTAMGRLEEALNCLY 130
                                       578999*********975 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   5.7e-14   5.2e-11      10      66 ..      18      71 ..      11      72 .. 0.93
   2 !   36.0   1.2     9e-12     8e-09       6      66 ..      48     105 ..      48     107 .. 0.93
   3 ?    0.1   0.0       1.5   1.3e+03      10      20 ..     119     129 ..     109     140 .. 0.60

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 5.7e-14
                            TPR_16 10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66
                                      + d+++A+++++++++++   Pd +eA+++lg+a++ +gr +eA++ y++ ++ +p+
  gi|330507167|ref|YP_004383595.1| 18 RMDFEKAIEYFQIVTASN---PDMPEAWNNLGVAFYGLGRIDEALESYDRSIALDPS 71
                                      559***************...*****************************9999997 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 9e-12
                            TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       a++ +g+ d+A++ +++ +++d   P + +Al +++ ++  q+rl+eA+++y+  l+ + d
  gi|330507167|ref|YP_004383595.1|  48 AFYGLGRIDEALESYDRSIALD---PSNLDALRNRAFLLRNQKRLPEALEAYDTVLEKGGD 105
                                       57999*****************...****************************99977655 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.5
                            TPR_16  10 agdyddAaaal 20 
                                        g+ ++A++ l
  gi|330507167|ref|YP_004383595.1| 119 MGRLEEALNCL 129
                                       34555555544 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0053       4.8      16      33 ..      20      37 ..       7      38 .. 0.83
   2 !   35.9   0.0   4.4e-12   3.9e-09       1      34 []      39      72 ..      39      72 .. 0.97
   3 !   18.8   0.1   1.4e-06    0.0012       2      29 ..      74     101 ..      73     105 .. 0.94
   4 ?    5.7   0.0     0.022        19       8      24 ..     113     129 ..     106     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0053
                             TPR_2 16 dyeeAleafekAleldPn 33
                                      d+e+A+e+f+ + + +P+
  gi|330507167|ref|YP_004383595.1| 20 DFEKAIEYFQIVTASNPD 37
                                      89*******988888876 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 4.4e-12
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      +ea++nlG a y lg+ +eAle ++++++ldP n
  gi|330507167|ref|YP_004383595.1| 39 PEAWNNLGVAFYGLGRIDEALESYDRSIALDPSN 72
                                      69******************************87 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 1.4e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                       +al n++ ++++++++ eAlea++ +le
  gi|330507167|ref|YP_004383595.1|  74 DALRNRAFLLRNQKRLPEALEAYDTVLE 101
                                       689**********************998 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.022
                             TPR_2   8 GlayyklgdyeeAleaf 24 
                                       + ++ ++g++eeAl+++
  gi|330507167|ref|YP_004383595.1| 113 AVVLTAMGRLEEALNCL 129
                                       778899********995 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   8.7e-08   7.8e-05       9      42 .]      20      53 ..      15      53 .. 0.96
   2 !   30.5   0.2   2.4e-10   2.2e-07       3      38 ..      48      83 ..      48      87 .. 0.92
   3 !    6.7   0.0    0.0063       5.6       4      22 ..      83     101 ..      82     102 .. 0.86
   4 ?    5.7   0.0     0.013        12       4      17 ..     116     129 ..     115     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 8.7e-08
                            TPR_11  9 kyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      ++e+Aie ++   + +Pd +ea++nLG+a+y +G
  gi|330507167|ref|YP_004383595.1| 20 DFEKAIEYFQIVTASNPDMPEAWNNLGVAFYGLG 53
                                      689****************************998 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 2.4e-10
                            TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                                      a+y +G+++eA+e+Y + ++ldP+n +a+ n+++++
  gi|330507167|ref|YP_004383595.1| 48 AFYGLGRIDEALESYDRSIALDPSNLDALRNRAFLL 83
                                      68999***************************9876 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0063
                            TPR_11   4 yyeqGkyeeAieaYkkAlk 22 
                                       ++ q +++eA+eaY + l+
  gi|330507167|ref|YP_004383595.1|  83 LRNQKRLPEALEAYDTVLE 101
                                       567899********99886 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.013
                            TPR_11   4 yyeqGkyeeAieaY 17 
                                       +++ G++eeA++++
  gi|330507167|ref|YP_004383595.1| 116 LTAMGRLEEALNCL 129
                                       6899*******985 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   5.5e-08   4.9e-05      17      76 ..      19      70 ..       4      71 .. 0.75
   2 !   13.7   0.1   6.6e-05     0.059       4      31 ..      74     101 ..      71     103 .. 0.92
   3 !   10.3   0.1   0.00072      0.65       9      31 ..     112     134 ..     105     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5.5e-08
                            TPR_12 17 grydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76
                                       +       +eka+e ++ +    +p+  ++ +nLg +++ lgr +eAle + +++a+++
  gi|330507167|ref|YP_004383595.1| 19 MD-------FEKAIEYFQIVT-ASNPDMPEAWNNLGVAFYGLGRIDEALESYDRSIALDP 70
                                      44.......555555554442.567889999************************99875 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.6e-05
                            TPR_12   4 talnnlaavlrrlgrydeAlellekale 31 
                                        al+n+a +lr ++r+ eAle ++++le
  gi|330507167|ref|YP_004383595.1|  74 DALRNRAFLLRNQKRLPEALEAYDTVLE 101
                                       57889*******************9997 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00072
                            TPR_12   9 laavlrrlgrydeAlellekale 31 
                                        a+vl+++gr++eAl +l  a+e
  gi|330507167|ref|YP_004383595.1| 112 TAVVLTAMGRLEEALNCLYLARE 134
                                       58999**********99988876 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   5.6e-09     5e-06       7      60 ..      17      70 ..      15      71 .. 0.96
   2 !   27.2   0.6   3.5e-09   3.1e-06      11      69 ..      55     113 ..      54     117 .. 0.93
   3 ?    2.2   0.0      0.23     2e+02      36      52 ..     113     129 ..     111     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5.6e-09
                             TPR_9  7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60
                                      r+ d+e+a+++ + + + +Pd pe +   G++ + lG++ +Al+  ++ +al+p
  gi|330507167|ref|YP_004383595.1| 17 RRMDFEKAIEYFQIVTASNPDMPEAWNNLGVAFYGLGRIDEALESYDRSIALDP 70
                                      788************************************************999 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 3.5e-09
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeair 69 
                                        ++al+ ++r ++l+P   + +r R++ll  + +l +Al++ ++ l++ +da d e  +
  gi|330507167|ref|YP_004383595.1|  55 IDEALESYDRSIALDPSNLDALRNRAFLLRNQKRLPEALEAYDTVLEKGGDAIDLESTA 113
                                       589*************************************************9999776 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.23
                             TPR_9  36 GlllaqlGclsaAladL 52 
                                       +++l  +G+l++Al++L
  gi|330507167|ref|YP_004383595.1| 113 AVVLTAMGRLEEALNCL 129
                                       78899999****99998 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   6.2e-05     0.056      14      42 ..      18      46 ..       9      48 .. 0.90
   2 !   22.4   0.1   1.6e-07   0.00014       2      44 .]      40      82 ..      40      82 .. 0.93
   3 !    8.5   0.3    0.0044         4       3      34 ..      75     106 ..      74     110 .. 0.87
   4 ?    4.3   0.1       0.1        93       8      27 ..     113     132 ..     109     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.2e-05
                            TPR_14 14 lGdpdeAiallrralalaPddaeawllla 42
                                      + d+++Ai++++ + a +Pd +eaw  l+
  gi|330507167|ref|YP_004383595.1| 18 RMDFEKAIEYFQIVTASNPDMPEAWNNLG 46
                                      5589*********************9887 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.6e-07
                            TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeawlllaql 44
                                      ea+  l+ a++ lG+ deA++ ++r +al+P++++a++  a+l
  gi|330507167|ref|YP_004383595.1| 40 EAWNNLGVAFYGLGRIDEALESYDRSIALDPSNLDALRNRAFL 82
                                      67888999*****************************998875 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0044
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPdd 34 
                                       al+ +a +l+++ ++ eA+++++ +l+++ d 
  gi|330507167|ref|YP_004383595.1|  75 ALRNRAFLLRNQKRLPEALEAYDTVLEKGGDA 106
                                       677789999******************99875 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.1
                            TPR_14   8 aeallalGdpdeAiallrra 27 
                                       a +l a G+++eA+++l  a
  gi|330507167|ref|YP_004383595.1| 113 AVVLTAMGRLEEALNCLYLA 132
                                       568999********988665 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   7.2e-08   6.5e-05       6      56 ..      20      70 ..      16      71 .. 0.93
   2 !   24.7   0.5   2.7e-08   2.5e-05       5      57 ..      53     105 ..      53     111 .. 0.95
   3 ?    5.3   0.1      0.03        27      32      48 ..     113     129 ..     106     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 7.2e-08
                            TPR_19  6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56
                                      d++ A+++++ + + +p+++ea+ +L  a + lg++deA +  d+  + dp
  gi|330507167|ref|YP_004383595.1| 20 DFEKAIEYFQIVTASNPDMPEAWNNLGVAFYGLGRIDEALESYDRSIALDP 70
                                      8999*************************************9999887776 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2.7e-08
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       g+ +eAl+ + + ++ dp n++a+ + A +l ++++l eA ++ d+++e+  d
  gi|330507167|ref|YP_004383595.1|  53 GRIDEALESYDRSIALDPSNLDALRNRAFLLRNQKRLPEALEAYDTVLEKGGD 105
                                       789*********************************************99887 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.03
                            TPR_19  32 AeallalgqldeAealL 48 
                                       A +l a+g+l+eA ++L
  gi|330507167|ref|YP_004383595.1| 113 AVVLTAMGRLEEALNCL 129
                                       78899********9998 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     0.067        60      16      25 ..      20      29 ..      19      37 .. 0.78
   2 !   26.0   0.0   7.1e-09   6.4e-06       2      34 .]      40      72 ..      39      72 .. 0.96
   3 ?    2.4   0.0      0.25   2.3e+02       6      29 ..      78     101 ..      73     101 .. 0.86
   4 ?    3.3   0.0      0.13   1.2e+02      10      24 ..     115     129 ..     113     134 .. 0.82
   5 ?   -2.2   0.0       7.7   6.9e+03       8      23 ..     132     147 ..     129     150 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.067
                                      -HHHHHHHHH CS
                             TPR_8 16 dyeeAkeyye 25
                                      d+e+A+ey++
  gi|330507167|ref|YP_004383595.1| 20 DFEKAIEYFQ 29
                                      799*****97 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 7.1e-09
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      ea++nlg +   lg+++eA e+y + + ldp+n
  gi|330507167|ref|YP_004383595.1| 40 EAWNNLGVAFYGLGRIDEALESYDRSIALDPSN 72
                                      89*****************************86 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.25
                                       HHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekale 29 
                                       n + ++++++++ eA e+y  +le
  gi|330507167|ref|YP_004383595.1|  78 NRAFLLRNQKRLPEALEAYDTVLE 101
                                       6788999************98886 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.13
                                       HHHHTT-HHHHHHHH CS
                             TPR_8  10 iylklgdyeeAkeyy 24 
                                       ++  +g++eeA  ++
  gi|330507167|ref|YP_004383595.1| 115 VLTAMGRLEEALNCL 129
                                       56789******9997 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 7.7
                                       HHHHHHTT-HHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkey 23 
                                       ++  l+l+++e  +e 
  gi|330507167|ref|YP_004383595.1| 132 AREKLSLKRLEDEIEM 147
                                       6666788888876665 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.2e-05     0.029       4      34 .]      23      60 ..      20      60 .. 0.76
   2 !   23.5   0.1   5.1e-08   4.6e-05       2      34 .]      62      94 ..      61      94 .. 0.95
   3 ?   -1.3   0.0       4.3   3.9e+03      21      32 ..     114     125 ..     111     134 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-05
                            TPR_17  4 kalel.......dPnnadaynnLAelllknGdlmtArq 34
                                      ka+e+       +P+ ++a+nnL+++++ +G+ ++A++
  gi|330507167|ref|YP_004383595.1| 23 KAIEYfqivtasNPDMPEAWNNLGVAFYGLGRIDEALE 60
                                      5555544443337888*******************985 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 5.1e-08
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtArq 34
                                      y ++++ldP+n da+ n+A ll+++++l +A++
  gi|330507167|ref|YP_004383595.1| 62 YDRSIALDPSNLDALRNRAFLLRNQKRLPEALE 94
                                      99*************************999975 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.3
                            TPR_17  21 elllknGdlmtA 32 
                                       ++l   G+l++A
  gi|330507167|ref|YP_004383595.1| 114 VVLTAMGRLEEA 125
                                       444455555555 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.9     8e+03      17      30 ..      20      26 ..      17      29 .. 0.52
   2 !   16.4   0.1   6.7e-06     0.006       6      30 ..      43      67 ..      41      68 .. 0.96
   3 !   13.4   0.2   5.8e-05     0.052       3      30 ..      74     101 ..      73     102 .. 0.92
   4 !    8.6   0.0    0.0019       1.7       9      25 ..     113     129 ..     113     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.9
                            TPR_10 17 rydeAealleeala 30
                                      +       +e+a++
  gi|330507167|ref|YP_004383595.1| 20 D-------FEKAIE 26
                                      4.......455554 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6.7e-06
                            TPR_10  6 nNLanalrqrgrydeAealleeala 30
                                      nNL++a + +gr deA++ +++++a
  gi|330507167|ref|YP_004383595.1| 43 NNLGVAFYGLGRIDEALESYDRSIA 67
                                      9*********************998 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 5.8e-05
                            TPR_10   3 sslnNLanalrqrgrydeAealleeala 30 
                                        +l N a +lr+++r+ eA++ ++ +l+
  gi|330507167|ref|YP_004383595.1|  74 DALRNRAFLLRNQKRLPEALEAYDTVLE 101
                                       7899*******************99987 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0019
                            TPR_10   9 analrqrgrydeAeall 25 
                                       a++l+++gr++eA++ l
  gi|330507167|ref|YP_004383595.1| 113 AVVLTAMGRLEEALNCL 129
                                       789***********986 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0071       6.4      14      29 ..      20      33 ..      13      37 .. 0.77
   2 !   19.8   0.0   6.2e-07   0.00055       1      34 [.      41      74 ..      41      76 .. 0.90
   3 ?   -0.5   0.0       1.9   1.7e+03       8      26 ..      82     100 ..      75     105 .. 0.73
   4 ?    1.4   0.0      0.47   4.2e+02       6      21 ..     113     128 ..     112     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0071
                             TPR_7 14 dyeeAielyeqsLalt 29
                                      d+e+Aie+++   +++
  gi|330507167|ref|YP_004383595.1| 20 DFEKAIEYFQI--VTA 33
                                      9********97..655 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 6.2e-07
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34
                                      a++nL++++  lG+ +eA+e y +s+al+ + +d
  gi|330507167|ref|YP_004383595.1| 41 AWNNLGVAFYGLGRIDEALESYDRSIALDPSNLD 74
                                      79**********************9998887766 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.9
                             TPR_7   8 lysrlGdyeeAielyeqsL 26 
                                       l +++ +  eA+e y  +L
  gi|330507167|ref|YP_004383595.1|  82 LLRNQKRLPEALEAYDTVL 100
                                       5667777889999998844 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.47
                             TPR_7   6 arlysrlGdyeeAiel 21 
                                       a++  ++G+ eeA+ +
  gi|330507167|ref|YP_004383595.1| 113 AVVLTAMGRLEEALNC 128
                                       6678899******988 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0014       1.2      11      32 ..      17      37 ..       8      37 .. 0.87
   2 !    9.3   0.0    0.0021       1.8       5      31 ..      44      70 ..      41      72 .. 0.88
   3 !    9.7   0.1    0.0015       1.4       1      29 [.      74     102 ..      74     102 .. 0.92
   4 ?   -1.0   0.0       4.1   3.6e+03      11      22 ..     117     128 ..     112     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0014
                                      HHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6 11 rklgdtdkAlealerlikeYPd 32
                                      r++ d +kA+e+++ +  + Pd
  gi|330507167|ref|YP_004383595.1| 17 RRM-DFEKAIEYFQIVTASNPD 37
                                      458.9*************9998 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0021
                                      HHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  5 klalsyrklgdtdkAlealerlikeYP 31
                                      +l+ +++ lg+ d+Ale ++r i   P
  gi|330507167|ref|YP_004383595.1| 44 NLGVAFYGLGRIDEALESYDRSIALDP 70
                                      699*****99*********99877666 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlike 29 
                                       dAl ++a ++r++++  +Alea++ ++++
  gi|330507167|ref|YP_004383595.1|  74 DALRNRAFLLRNQKRLPEALEAYDTVLEK 102
                                       688899*******************9986 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHHH CS
                             TPR_6  11 rklgdtdkAlea 22 
                                        ++g+ ++Al  
  gi|330507167|ref|YP_004383595.1| 117 TAMGRLEEALNC 128
                                       567888888875 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.043        39      16      25 ..      20      29 ..      20      35 .. 0.88
   2 !   11.3   0.0    0.0003      0.27       7      36 .]      45      72 ..      39      72 .. 0.86
   3 ?    4.2   0.0      0.05        45      13      25 ..      85      97 ..      80     102 .. 0.82
   4 ?   -1.4   0.0       2.8   2.5e+03      14      22 ..     119     127 ..     113     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.043
                                      -HHHHHHH.. CS
                             TPR_3 16 kyqeArelfs 25
                                      ++++A+e+f+
  gi|330507167|ref|YP_004383595.1| 20 DFEKAIEYFQ 29
                                      689*****99 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0003
                                      HHHHHHHTT-HHHHHHH..HHHHHHH-TT- CS
                             TPR_3  7 yAaefynkkkyqeArelfsYallaildken 36
                                      ++ +fy  ++++eA+e ++   + +ld+ n
  gi|330507167|ref|YP_004383595.1| 45 LGVAFYGLGRIDEALESYD--RSIALDPSN 72
                                      7899*************77..999999877 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.05
                                      HTT-HHHHHHH.. CS
                             TPR_3 13 nkkkyqeArelfs 25
                                      n+k++ eA+e+++
  gi|330507167|ref|YP_004383595.1| 85 NQKRLPEALEAYD 97
                                      89*********98 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.8
                                       TT-HHHHHH CS
                             TPR_3  14 kkkyqeAre 22 
                                       +++++eA++
  gi|330507167|ref|YP_004383595.1| 119 MGRLEEALN 127
                                       899999987 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00061      0.55       2      25 ..      40      63 ..      39      64 .. 0.85
   2 ?    3.9   0.2      0.12   1.1e+02       3      24 ..      75      96 ..      73      98 .. 0.89
   3 ?    6.0   0.0     0.026        24       8      22 ..     113     127 ..     110     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00061
                             TPR_4  2 rallaLArallalGdldeAralle 25
                                       a  +L+ a + lG+ deA++  +
  gi|330507167|ref|YP_004383595.1| 40 EAWNNLGVAFYGLGRIDEALESYD 63
                                      67789**************98665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.12
                             TPR_4  3 allaLArallalGdldeArall 24
                                      al ++A +l  + +l+eA+++ 
  gi|330507167|ref|YP_004383595.1| 75 ALRNRAFLLRNQKRLPEALEAY 96
                                      8999**************9976 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.026
                             TPR_4   8 ArallalGdldeAra 22 
                                       A +l a G+l+eA+ 
  gi|330507167|ref|YP_004383595.1| 113 AVVLTAMGRLEEALN 127
                                       89999********86 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00037      0.33      79     122 ..      22      65 ..      16      74 .. 0.89
   2 !   12.2   0.1   0.00021      0.19      74     134 ..      51     111 ..      41     121 .. 0.87
   3 ?    0.6   0.1      0.79   7.1e+02     106     126 ..     116     136 ..     108     153 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00037
                                       HHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  79 eealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       e+a+++ +  +a +P   +++  l  A + +Gr  eALe Y+r 
  gi|330507167|ref|YP_004383595.1|  22 EKAIEYFQIVTASNPDMPEAWNNLGVAFYGLGRIDEALESYDRS 65 
                                       678888999999999999***********************986 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00021
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS--- CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvep 134
                                        lGr++eal+ +++ +a++P + ++ r     l+ + r  eALe+Y+++ +   + +++e 
  gi|330507167|ref|YP_004383595.1|  51 GLGRIDEALESYDRSIALDPSNLDALRNRAFLLRNQKRLPEALEAYDTVLEKGGDAIDLES 111
                                       689*************************9999**************999888777777765 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.79
                                       HHHTT-HHHHHHHHHHHHHHH CS
                              BTAD 106 larsGrqaeALevYerlrrlL 126
                                       l ++Gr +eAL+    +r+ L
  gi|330507167|ref|YP_004383595.1| 116 LTAMGRLEEALNCLYLAREKL 136
                                       556677777776655555554 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00011       0.1       4      80 ..      20      97 ..      17      99 .. 0.93
   2 ?    4.6   0.1     0.043        39      42      79 ..      92     129 ..      82     132 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                      -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80
                                      ++++Ai ++  + a+++++pe+   l+ ++y +g+ ++A+e ++++  l++++l ++   A  l  +k++ eA+ a++
  gi|330507167|ref|YP_004383595.1| 20 DFEKAIEYFQIVTASNPDMPEAWNNLGVAFYGLGRIDEALESYDRSiALDPSNLDALRNRAFLLRNQKRLPEALEAYD 97
                                      6889999999999********************************************999999999999999999876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.043
                                       HHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3  42 AyellrkaklnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       A+e +++  +++ +   +  +A +l +++++eeA+++L
  gi|330507167|ref|YP_004383595.1|  92 ALEAYDTVLEKGGDAIDLESTAVVLTAMGRLEEALNCL 129
                                       55555555444555566677899999999999999987 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.15   1.3e+02      10      24 ..      15      29 ..      14      32 .. 0.90
   2 ?    5.1   0.0     0.035        31       2      24 ..      41      63 ..      40      67 .. 0.87
   3 ?   -0.1   0.0       1.6   1.4e+03      14      30 ..      87     103 ..      84     104 .. 0.83
   4 ?    2.7   0.0       0.2   1.8e+02      12      24 ..     118     130 ..     115     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.15
                               PPR 10 ycknGkleeAlelfk 24
                                      +++  ++e+A+e+f+
  gi|330507167|ref|YP_004383595.1| 15 CVRRMDFEKAIEYFQ 29
                                      788999*******96 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.035
                               PPR  2 tynslIsgycknGkleeAlelfk 24
                                      ++n l  ++   G+++eAle ++
  gi|330507167|ref|YP_004383595.1| 41 AWNNLGVAFYGLGRIDEALESYD 63
                                      69999999999********9776 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.6
                               PPR  14 GkleeAlelfkeMkekG 30 
                                        +l eAle ++  +ekG
  gi|330507167|ref|YP_004383595.1|  87 KRLPEALEAYDTVLEKG 103
                                       57889***999888887 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.2
                               PPR  12 knGkleeAlelfk 24 
                                         G+leeAl ++ 
  gi|330507167|ref|YP_004383595.1| 118 AMGRLEEALNCLY 130
                                       57*******9876 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0014       1.2      57      82 ..      41      66 ..       3     106 .. 0.64
   2 ?    4.1   0.0      0.05        44     105     133 ..     111     139 ..     104     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                                      HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 57 chaglsealaklgrydealesadkal 82
                                      ++  l  a+ +lgr deales d+++
  gi|330507167|ref|YP_004383595.1| 41 AWNNLGVAFYGLGRIDEALESYDRSI 66
                                      45566667777777777777766654 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.05
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHH- CS
                           DUF3856 105 sravaleelGrkdealkafrmagemiaer 133
                                       s av l  +Gr +eal+ +  a e ++ +
  gi|330507167|ref|YP_004383595.1| 111 STAVVLTAMGRLEEALNCLYLAREKLSLK 139
                                       6789999**********999999987655 PP

>> NIT  Nitrate and nitrite sensing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   3.3e-05      0.03      49     128 ..      55     140 ..      21     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.3e-05
                               NIT  49 larrldallral..d..qLpalRrqv.dtr.kldakeavaaYtdviaaLldladelaqgspdrelarqlralaalsr 119
                                       +++ l++ +r +  d  +L+alR+++   r +   +ea++aY++v++   d +d  +++   +++ r   al+ l  
  gi|330507167|ref|YP_004383595.1|  55 IDEALESYDRSIalDpsNLDALRNRAfLLRnQKRLPEALEAYDTVLEKGGDAIDLESTAVVLTAMGRLEEALNCLYL 131
                                       33333444444322367*********8855544577999*******9986666554445555999************ PP

                               NIT 120 akEalsqer 128
                                       a+E ls+ r
  gi|330507167|ref|YP_004383595.1| 132 AREKLSLKR 140
                                       *****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1228.27
//
Query:       gi|330507168|ref|YP_004383596.1|  [L=77]
Description: AsnC family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-10   40.8   0.1    1.9e-10   40.6   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    0.00071   19.6   0.5    0.00095   19.2   0.5    1.0  1  NapD            NapD protein


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.1   2.1e-14   1.9e-10       1      73 [.       5      73 ..       5      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.1e-14
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                      +++++epg     +++ ++l++++ + e+  v G+ d++++v v+ + +l+r +++ +++++gv++t+t + +
  gi|330507168|ref|YP_004383596.1|  5 IMINVEPGT---EKAVHDRLEKIKGICEVVPVYGERDFIAIVDVEGISDLNRAVMN-VREINGVTNTQTILGM 73
                                      789***999...********************************************.************9876 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.5   1.1e-07   0.00095       7      68 ..       6      68 ..       5      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.1e-07
                              NapD  7 vVqarperlaavkaalaalpg.vEvhasdeegklVvviEaesedeladtieaiealpgVlsas 68
                                       +++ p++ +av ++l++++g +Ev  + +e   + +++ e   +l +++ ++++++gV +++
  gi|330507168|ref|YP_004383596.1|  6 MINVEPGTEKAVHDRLEKIKGiCEVVPVYGERDFIAIVDVEGISDLNRAVMNVREINGVTNTQ 68
                                      699*****************988**************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 603.08
//
Query:       gi|330507169|ref|YP_004383597.1|  [L=402]
Description: major facilitator family transporter [Methanosaeta concilii GP6]
Scores for complete 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-59  199.0  43.7    1.7e-35  122.6  22.0    2.0  2  MFS_1          Major Facilitator Superfamily
    9.4e-18   64.2  14.2    2.2e-11   43.2   7.9    2.9  2  MFS_1_like     MFS_1 like family
    3.1e-10   39.5  27.4    1.7e-06   27.2   9.3    2.8  2  Sugar_tr       Sugar (and other) transporter
    5.3e-07   28.4  13.9    2.9e-06   26.0   1.8    2.6  2  MFS_3          Transmembrane secretion effector
    3.5e-06   26.8   1.9    3.5e-06   26.8   1.9    2.6  2  UNC-93         Ion channel regulatory protein UNC-93
  ------ inclusion threshold ------
      0.033   13.2  22.2      0.017   14.1   8.5    2.4  2  Nuc_H_symport  Nucleoside H+ symporter
      0.042   12.8  20.7      0.088   11.8   8.5    2.3  2  PUCC           PUCC protein
      0.057   13.7   6.2      0.053   13.8   2.1    2.9  2  UPF0060        Uncharacterised BCR, YnfA/UPF0060 family
        6.6    5.5  17.6        1.1    8.0   4.5    2.4  2  EcsB           Bacterial ABC transporter protein EcsB


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 !  122.6  22.0   8.4e-39   1.7e-35       1     225 [.      13     224 ..      13     231 .. 0.85
   2 !   79.3  18.8   1.2e-25   2.4e-22       4     184 ..     214     397 ..     211     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 8.4e-39
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.l 76 
                                       l+la+f++ l+++++ p++p  +  dlg+s + +g+++++y++ +++ ++p+Grlsdr+Gr+r++l+gl +fa+   
  gi|330507169|ref|YP_004383597.1|  13 LYLAVFVAVLGFTLVVPFFP-SYVMDLGASYTLLGFIISIYGASQLLVQVPIGRLSDRMGRKRLMLIGLMTFAVLpP 88 
                                       5799****************.66679*************************************************65 PP

                             MFS_1  77 llllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                       l++  a + ++ll+ r+l G+ga++++p+++ali d +    rg a+g+++a+f  + +lgp  gg+l+++ g +a+
  gi|330507169|ref|YP_004383597.1|  89 LYIY-AENAYTLLFIRALGGVGAAFVWPTAMALIIDQSRAHSRGAAMGFYNAAFYSALALGPFMGGALYDQMGLEAP 164
                                       5555.577779****************************************************************** PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg 225
                                       fy+ +++++ ++++  + + +++++   ++  e+     ++   p    l ++ +   + + ++++ + +sg
  gi|330507169|ref|YP_004383597.1| 165 FYFWTLLGIASIII--VTFKVPESRGIVPKADEQ----PQRREEP----LIAPGYA--ITFLACCAVILWSG 224
                                       ***********997..777777777777776666....3333333....3334433..44444444445554 PP

  == domain 2  score: 79.3 bits;  conditional E-value: 1.2e-25
                             MFS_1   4 aaflsalarsi.....lgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfal 74 
                                       +a+++ + +s       +++lp  +a++lg+s + igl++ +y+  +a++++ +Grl+dr Grr+ +++lg l+ ++
  gi|330507169|ref|YP_004383597.1| 214 LACCAVILWSGvvggfNITLLP-SYAKALGFSTTDIGLIYLVYGGITAISNIYFGRLADR-GRRKwLIFLGSLAGLI 288
                                       5555555555545553445555.89***********************************.8888677777777777 PP

                             MFS_1  75 glllllfa.sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgW 150
                                       + ++llf+ s+l  +l+l +  Glg g+  pa+aal+ad ++ ++rg  +g+++++   G+++gp+ +gl a+  g 
  gi|330507169|ref|YP_004383597.1| 289 S-FALLFIvSNLIQVLILFAGLGLGLGICSPAAAALVADTTNASRRGETYGIFNTARMSGVVVGPIMAGLAADMQGI 364
                                       7.444444388889*************************************************************** PP

                             MFS_1 151 ravfyilaivsllafvlfllllpeepperkrksp 184
                                        ++ y++++++l   + +++ ++e + ++ ++++
  gi|330507169|ref|YP_004383597.1| 365 DGALYAFTLIALAITL-GAVAIREAKEDSVNSRE 397
                                       **********999877.55666666666555554 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 !   43.2   7.9   1.1e-14   2.2e-11     230     384 ..      13     166 ..       2     167 .. 0.92
   2 !   23.0   0.4   1.5e-08   3.1e-05      24      86 ..     236     296 ..     220     400 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 1.1e-14
                        MFS_1_like 230 fllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfll 306
                                       + l++++    + ++  F+  Y  +lgas tllG ++ +  ++++ + +   +l +++G  +l++i+l+++++   l
  gi|330507169|ref|YP_004383597.1|  13 LYLAVFVAVLGFTLVVPFFPSYVMDLGASYTLLGFIISIYGASQLLVQVPIGRLSDRMGRKRLMLIGLMTFAVLPPL 89 
                                       55566666666678889************************************************************ PP

                        MFS_1_like 307 yaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                       y + ena  +l+i +L g+  + +w +a+  + +    + ++  +g+++++++++  alG ++GG+l+d+ ++   F
  gi|330507169|ref|YP_004383597.1|  90 YIYAENAYTLLFIRALGGVGAAFVWPTAMALIIDQSRAHSRGAAMGFYNAAFYSA-LALGPFMGGALYDQMGLEAPF 165
                                       **************************************************98885.89***********99988777 PP

                        MFS_1_like 384 r 384
                                       +
  gi|330507169|ref|YP_004383597.1| 166 Y 166
                                       6 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.5e-08
                        MFS_1_like  24 iylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfip 86 
                                        y k  g++  +ig+i+l+   ++ +s   +g laDr g+rk ++ l++l+ +++f+ llfi+
  gi|330507169|ref|YP_004383597.1| 236 SYAKALGFSTTDIGLIYLVYGGITAISNIYFGRLADR-GRRKWLIFLGSLAGLISFA-LLFIV 296
                                       588899******************************9.899****************.55566 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   9.3   8.6e-10   1.7e-06      38     194 ..      35     186 ..       7     201 .. 0.85
   2 !   17.8   9.6   6.2e-07    0.0012      43     166 ..     240     363 ..     193     390 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 8.6e-10
                                       HHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHH CS
                          Sugar_tr  38 ksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGi 114
                                       + +  +s +l+g+i si+ + +++ ++ +g l+dr+GRk  +li+ + f +   l + a+   + + l++ R l G+
  gi|330507169|ref|YP_004383597.1|  35 VMDLGASYTLLGFIISIYGASQLLVQVPIGRLSDRMGRKRLMLIGLMTFAVLPPLYIYAE---NAYTLLFIRALGGV 108
                                       44455577899*************************************************...88999999****** PP

                                       HHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG.GG CS
                          Sugar_tr 115 gvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill.lf 190
                                       g+ ++  ++  +i   + ++ Rga +++y+ a      ++ ++g +l +  +      ++++  ++ ++ +i++ + 
  gi|330507169|ref|YP_004383597.1| 109 GAAFVWPTAMALIIDQSRAHSRGAAMGFYNAAFYSALALGPFMGGALYDQMG---LEAPFYFWTLLGIASIIIVtFK 182
                                       *******************************999998888888877744444...7888888888888877777477 PP

                                       S--- CS
                          Sugar_tr 191 lPES 194
                                       +PES
  gi|330507169|ref|YP_004383597.1| 183 VPES 186
                                       9*99 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 6.2e-07
                                       H......HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHH CS
                          Sugar_tr  43 e...ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigv 116
                                       +   s++++gli  ++  + +i+ +++g l+dr  Rk+ +  +++  +i+ +l ++  +  +v +l++g   +G+g+
  gi|330507169|ref|YP_004383597.1| 240 AlgfSTTDIGLIYLVYGGITAISNIYFGRLADRGRRKWLIFLGSLAGLISFALLFIVSNLIQVLILFAG---LGLGL 313
                                       145588999999999999***************666666666777777776666666645455555555...9**** PP

                                       HHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS- CS
                          Sugar_tr 117 GlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsn 166
                                       G++s  +  +++  + ++ Rg   +++++a   G +v+ i+    +++++
  gi|330507169|ref|YP_004383597.1| 314 GICSPAAAALVADTTNASRRGETYGIFNTARMSGVVVGPIMAGLAADMQG 363
                                       *************************************9887666666665 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   1.8   1.5e-09   2.9e-06      58     187 ..      56     180 ..      12     206 .. 0.65
   2 !    6.9   4.7    0.0009       1.8      63     196 ..     264     395 ..     257     402 .] 0.67

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.5e-09
                             MFS_3  58 ifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkr 134
                                        +l+ ++ G l+D + r++++l++ +  a+   l     ++   + ++ll +  l g+Gaa+  P+  A + ++ ++
  gi|330507169|ref|YP_004383597.1|  56 QLLVQVPIGRLSDRMGRKRLMLIGLMTFAVLPPL-----YIYAENAYTLLFIRALGGVGAAFVWPTAMALIIDQSRA 127
                                       4566677777777777777777765444333222.....22234556677777777777777777777777777777 PP

                             MFS_3 135 rdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivall 187
                                       +   aA+      +  a + GP +gG l   +G  + f + +l  +a i++++
  gi|330507169|ref|YP_004383597.1| 128 HSRGAAMGFYNAAFYSALALGPFMGGALYDQMGLEAPFYFWTLLGIASIIIVT 180
                                       77777777777777777777777777777777777777766666555554443 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0009
                             MFS_3  63 ilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpa 139
                                       i  G laD   r+++++ + l  +++ +ll +++  +l++   +l+l   +g+G  + +Pa  A v +  +++   +
  gi|330507169|ref|YP_004383597.1| 264 IYFGRLADRGRRKWLIFLGSLAGLISFALLFIVS--NLIQ---VLILFAGLGLGLGICSPAAAALVADTTNASRRGE 335
                                       6778999987777777777666665555555443..3444...4555556788999999999999999998887777 PP

                             MFS_3 140 AvaLnsvginiaRsvGPAlgGvlvaav...Gaalafavnalsylalivallrwkrevrks 196
                                          +          vGP ++G+   +    Ga++af++ al+     va+ ++k +  +s
  gi|330507169|ref|YP_004383597.1| 336 TYGIFNTARMSGVVVGPIMAGLAADMQgidGALYAFTLIALAITLGAVAIREAKEDSVNS 395
                                       666544444444468899999876554222678888888888777777777777766655 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 !   26.8   1.9   1.8e-09   3.5e-06      39     141 ..      41     148 ..      32     157 .. 0.82
   2 ?    4.1   1.8     0.017        34      51     143 ..     260     353 ..     246     366 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.8e-09
                            UNC-93  39 GYyslaiiyavftvanlv....apsvvdlltakwalvigallyaifqlgFlll.nkyylyissallGvgaallwtgq 110
                                        Y+ l +i +++ ++ l+    +  + d ++ k +++ig +++a+ +  +++  n y l++  al Gvgaa++w   
  gi|330507169|ref|YP_004383597.1|  41 SYTLLGFIISIYGASQLLvqvpIGRLSDRMGRKRLMLIGLMTFAVLPPLYIYAeNAYTLLFIRALGGVGAAFVWPTA 117
                                       56666666666666666522123467888999*******************974778899***************** PP

                            UNC-93 111 GsyLsenstretiernssilwallksslliG 141
                                          ++ +s+ + ++   ++  a + s+l +G
  gi|330507169|ref|YP_004383597.1| 118 MALIIDQSRAHSRGAAMGFYNAAFYSALALG 148
                                       ***************9999999999998777 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.017
                            UNC-93  51 tvanlvapsvvdlltakwalvigal.lyaifqlgFlllnkyylyissallGvgaallwtgqGsyLsenstretiern 126
                                       +++n+    + d    kw++++g+l   ++f l F+  n + ++i  a lG+g  +   +    +   ++   +++ 
  gi|330507169|ref|YP_004383597.1| 260 AISNIYFGRLADRGRRKWLIFLGSLaGLISFALLFIVSNLIQVLILFAGLGLGLGICSPAAAALVADTTNASRRGET 336
                                       6788888888888899******98626899*********99999999999999998888887777777777777777 PP

                            UNC-93 127 ssilwallksslliGgi 143
                                        +i+ +   s +++G i
  gi|330507169|ref|YP_004383597.1| 337 YGIFNTARMSGVVVGPI 353
                                       77777777777777766 PP

>> Nuc_H_symport  Nucleoside H+ symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   8.5   8.5e-06     0.017     247     384 ..      47     178 ..      13     183 .. 0.80
   2 ?    4.5   5.7    0.0069        14      19     150 ..     228     364 ..     210     386 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.5e-06
                     Nuc_H_symport 247 illslsqvaeilfiLtlpfflkrfGikkvlllslvaaalrfalfaygaddepvgvvlllLslivyGvaydffyitay 323
                                        ++s+   + +l+ + ++++  r+G k+ +l++l+++a+   l++y  ++ ++ + +  L     Gv  +f + ta 
  gi|330507169|ref|YP_004383597.1|  47 FIISIYGASQLLVQVPIGRLSDRMGRKRLMLIGLMTFAVLPPLYIYA-ENAYTLLFIRAL----GGVGAAFVWPTAM 118
                                       5778888899999999******************************9.665555555555....79*******9999 PP

                     Nuc_H_symport 324 vfvdkevpkdirasaqGlflllvnGvGallgsilsgalvemftvdgvvdwqtlwlvfaama 384
                                         +  +   + r +a G+++         lg +++gal +++  +  + + tl  +++ ++
  gi|330507169|ref|YP_004383597.1| 119 ALIIDQSRAHSRGAAMGFYNAAFYSA-LALGPFMGGALYDQMGLEAPFYFWTLLGIASIII 178
                                       999999999*********99887654.4578888888888888888777777766655444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0069
                     Nuc_H_symport  19 GaWlvklfsylsktlfaaaeiglvysslgiaailspilvgiiaDkflsaervlavlhlig...avvlflaaqvtefe 92 
                                       G  ++ l sy   ++f++++igl+y   g    +s i  g +aD+    ++++ +  l+g     +lf+ ++  +  
  gi|330507169|ref|YP_004383597.1| 228 GFNITLLPSYAKALGFSTTDIGLIYLVYGGITAISNIYFGRLADRGR-RKWLIFLGSLAGlisFALLFIVSNLIQVL 303
                                       333455668999999**********99876666678889*****975.46666555554411055677777777777 PP

                     Nuc_H_symport  93 alflvl.LvyslaymPtlaltnsiafanlr.DvvtdfprirvlGt.vGfilaslaflllvv 150
                                        lf+ l L   +    + al+   + a  r +    f + r+ G  vG i+a+la  ++ +
  gi|330507169|ref|YP_004383597.1| 304 ILFAGLgLGLGICSPAAAALVADTTNASRRgETYGIFNTARMSGVvVGPIMAGLAADMQGI 364
                                       7776541333333333344444444443333666667777777752577777777655554 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.3    0.0014       2.8     271     364 ..      66     160 ..      26     181 .. 0.74
   2 ?   11.8   8.5   4.4e-05     0.088     276     364 ..     278     363 ..     233     386 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0014
                              PUCC 271 lkkarlaslgvllgllsflll..ilaallen.vallvagvlllGlasGlfavaaltlmldlaaeeraglalGaWGaa 344
                                       l+    +++ +l+gl++f +l  + +  +en  +ll+   +l G+++ ++  +a++l++d + +   g a+G + aa
  gi|330507169|ref|YP_004383597.1|  66 LSDRMGRKRLMLIGLMTFAVLppLYI-YAENaYTLLFI-RALGGVGAAFVWPTAMALIIDQSRAHSRGAAMGFYNAA 140
                                       33334456777888888887732233.33442444444.445589999999************************** PP

                              PUCC 345 Qaiaaglavllggalrdllk 364
                                          a +l+ ++ggal d + 
  gi|330507169|ref|YP_004383597.1| 141 FYSALALGPFMGGALYDQMG 160
                                       ***************99876 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4.4e-05
                              PUCC 276 laslgvllgllsflllilaallenvallvagvlllGlasGlfavaaltlmldlaaeeraglalGaWGaaQaiaagla 352
                                       l +lg l+gl+sf ll + + l +v +l+ag   lGl+ G+ + aa +l+ d++ + r g   G+   a      ++
  gi|330507169|ref|YP_004383597.1| 278 LIFLGSLAGLISFALLFIVSNLIQVLILFAG---LGLGLGICSPAAAALVADTTNASRRGETYGIFNTARMSGVVVG 351
                                       5567788888888888888888888888776...5888888888888888888888888888888877777777777 PP

                              PUCC 353 vllggalrdllk 364
                                        +++g ++d+  
  gi|330507169|ref|YP_004383597.1| 352 PIMAGLAADMQG 363
                                       777777766544 PP

>> UPF0060  Uncharacterised BCR, YnfA/UPF0060 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.56   1.1e+03      83     104 ..      32      53 ..       3      94 .. 0.65
   2 ?   13.8   2.1   2.6e-05     0.053      41     102 ..     233     294 ..     212     298 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.56
                           UPF0060  83 ldlydwiGalialvGvlvilya 104
                                       +     +Ga  +l+G ++ +y+
  gi|330507169|ref|YP_004383597.1|  32 PSYVMDLGASYTLLGFIISIYG 53 
                                       3333345666666666665554 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.6e-05
                           UPF0060  41 llavygflatlqpaafGrvyaayGGvfvvlallwglvvdgvkldlydwiGalialvGvlvil 102
                                       ll  y+  + + +++ G +y  yGG+  +  + +g++ d+ + + + ++G+l  l+  ++++
  gi|330507169|ref|YP_004383597.1| 233 LLPSYAKALGFSTTDIGLIYLVYGGITAISNIYFGRLADRGRRKWLIFLGSLAGLISFALLF 294
                                       44557777888999***************************************999887664 PP

>> EcsB  Bacterial ABC transporter protein EcsB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.5   0.00055       1.1     103     196 ..      13     108 ..       7     128 .. 0.80
   2 ?    3.0   5.2     0.019        38     112     200 ..     228     313 ..     137     325 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00055
                              EcsB 103 lllqllllllvllillPlllettglsiaelllllllllllkllnlllkweelrlqgkkkrridrlirlllnalllyl 179
                                       l l++++ +l + +++P++       +a++ ll +++ ++ +++ll+++   rl+++  r   +li l+  a+l  l
  gi|330507169|ref|YP_004383597.1|  13 LYLAVFVAVLGFTLVVPFFPSYVMDLGASYTLLGFIISIYGASQLLVQVPIGRLSDRMGRKRLMLIGLMTFAVLPPL 89 
                                       56889999************9999999999999999999999**************999999999999999999777 PP

                              EcsB 180 llalapllallli..llll 196
                                       ++++ ++  ll+i  l  +
  gi|330507169|ref|YP_004383597.1|  90 YIYAENAYTLLFIraLGGV 108
                                       7777766666665332222 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.019
                              EcsB 112 lvllillPlllettglsiaelllllllllllkl.lnlllkweelrlqgkkkrridrlirlllnalllylllalapll 187
                                        + + llP ++++ g+s +++ l++l++  + + +n+++ +   r + k   +i  ++  l+ ++ ++ll+++++l+
  gi|330507169|ref|YP_004383597.1| 228 GFNITLLPSYAKALGFSTTDIGLIYLVYGGITAiSNIYFGRLADRGRRK--WLI--FLGSLAGLISFALLFIVSNLI 300
                                       466889*******************999999886777777666664444..333..677777777777777777777 PP

                              EcsB 188 alllilllllvll 200
                                        +l++++ l + l
  gi|330507169|ref|YP_004383597.1| 301 QVLILFAGLGLGL 313
                                       7777655554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.37
# Mc/sec: 3254.80
//
Query:       gi|330507170|ref|YP_004383598.1|  [L=118]
Description: hypothetical protein MCON_1031 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 831.52
//
Query:       gi|330507171|ref|YP_004383599.1|  [L=3064]
Description: Cna B domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-83  274.5  26.5    9.5e-16   58.0   1.0    7.7  7  SdrD_B           SdrD B-like domain
    3.4e-36  123.4  29.6    1.2e-05   25.4   2.7    9.9  7  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    3.9e-30  104.0  20.4    0.00029   21.1   0.2    7.4  6  SpaA             Prealbumin-like fold domain
    4.4e-27   93.8  39.7        2.1    8.4   0.7   24.0 25  Y_Y_Y            Y_Y_Y domain
    5.6e-19   68.7 113.2      0.018   15.8   0.5   21.9 24  Big_7            Bacterial Ig domain
    1.4e-13   50.6  15.4      0.014   15.3   1.2    7.0  6  CarbopepD_reg_2  CarboxypepD_reg-like domain
    2.6e-12   46.9   0.1      0.039   14.1   0.0    6.0  5  DUF2012          Protein of unknown function (DUF2012)
    7.7e-11   42.2   0.0         87    3.6   0.0   12.3 13  DUF4399          Domain of unknown function (DUF4399)
    1.9e-08   34.0   2.7       0.49    9.8   0.0    6.2  6  Dioxygenase_C    Dioxygenase
     0.0011   19.0   2.9        1.4    9.0   0.0    5.5  6  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
  ------ inclusion threshold ------
       0.14   12.6  12.8    7.3e+02    0.7   0.0   11.0 11  Cadherin         Cadherin domain
       0.17   11.7  37.9       0.18   11.6   1.0    9.7 10  fn3_3            Polysaccharide lyase family 4, domain II


Domain annotation for each model (and alignments):
>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       8.8   1.3e+04      53      66 ..     150     163 ..     134     170 .. 0.78
   2 !   45.5   0.4     5e-15   7.5e-12       2      82 ..    1840    1918 ..    1839    1936 .. 0.87
   3 !   45.5   0.3   4.8e-15   7.1e-12       3      81 ..    1939    2015 ..    1937    2030 .. 0.88
   4 !   50.2   0.1   1.7e-16   2.6e-13       5      87 ..    2038    2120 ..    2034    2129 .. 0.85
   5 !   58.0   1.0   6.4e-19   9.5e-16       5      76 ..    2135    2205 ..    2131    2211 .. 0.92
   6 !   38.5   0.0   7.3e-13   1.1e-09       2      80 ..    2228    2310 ..    2227    2322 .. 0.86
   7 !   49.3   1.0   3.1e-16   4.7e-13       2      90 ..    2336    2425 ..    2335    2430 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.8
                            SdrD_B  53 tnltpGeYkVefta 66 
                                         l+pG+Y++++  
  gi|330507171|ref|YP_004383599.1| 150 AALEPGNYQIRVLV 163
                                       57899***999866 PP

  == domain 2  score: 45.5 bits;  conditional E-value: 5e-15
                            SdrD_B    2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakk 76  
                                        +i  +V+eD+n+nG+ d+ge + sg tV++++ ++++v +++T ++G+Y+F++l++G+Y+++ t p+g+++   +
  gi|330507171|ref|YP_004383599.1| 1840 NISGLVYEDKNGNGVSDSGE-ALSGWTVQITKPDQSQV-SVLTREDGTYSFQDLDAGSYTISETLPSGWVAAIPE 1912
                                        68899**************8.59*******88777777.9*****************************999988 PP

                            SdrD_B   77 aGsdda 82  
                                         Gs + 
  gi|330507171|ref|YP_004383599.1| 1913 GGSHNV 1918
                                        777654 PP

  == domain 3  score: 45.5 bits;  conditional E-value: 4.8e-15
                            SdrD_B    3 iGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakka 77  
                                        i  + ++D n+nG  d ge+g++g t++L +++g++++t tT+++G+YkF +l+pG+Y+V+ ++ ag+t ta  +
  gi|330507171|ref|YP_004383599.1| 1939 ISGRKFNDLNGNGAFD-GEPGMEGWTIEL-SRDGSLISTATTEKDGSYKFAELSPGSYTVSEVEQAGWTRTAPPE 2011
                                        666779********98.8***********.8899999*******************************9999988 PP

                            SdrD_B   78 Gsdd 81  
                                        Gs +
  gi|330507171|ref|YP_004383599.1| 2012 GSYT 2015
                                        8754 PP

  == domain 4  score: 50.2 bits;  conditional E-value: 1.7e-16
                            SdrD_B    5 dfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagy.tvtakkaG 78  
                                         + + D+n+nG++d+ge+g +gv ++L +++g+v++ ttT ++G+Y+F nl+pG+Y+++ +a +g+ ++ ++   
  gi|330507171|ref|YP_004383599.1| 2038 GTSFLDSNGNGVKDEGEPGRAGVAIQL-SRDGSVINATTTLEDGSYAFRNLSPGTYSISQVAAEGInQIAPEGPW 2111
                                        56699**********************.8899999*************************999999666666666 PP

                            SdrD_B   79 sddaldSda 87  
                                        + + +d+d+
  gi|330507171|ref|YP_004383599.1| 2112 TVELKDADV 2120
                                        666666666 PP

  == domain 5  score: 58.0 bits;  conditional E-value: 6.4e-19
                            SdrD_B    5 dfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakk 76  
                                           + D n+nG+qd++e+gi g +V+L  ++g+vva+ttTd++G Y+F+n+ pG+Y+++   p+g+++t++ 
  gi|330507171|ref|YP_004383599.1| 2135 GQKYYDINGNGLQDEDEPGIPGGEVSL-VENGKVVANTTTDENGLYSFENVLPGTYTINDPVPTGMVLTTSS 2205
                                        56689**********************.899***********************************998865 PP

  == domain 6  score: 38.5 bits;  conditional E-value: 7.3e-13
                            SdrD_B    2 siGdfVweDanknGiqdagekgisgvtVtLkdak..gevv..atttTdasGkYkFtnltpGeYkVeftapagytv 72  
                                        si  + +eD n + +++ gekg sg ++ L+ ++  g+ +   t tTd++G+YkF+ l pG+YkV+ t+ +g+t+
  gi|330507171|ref|YP_004383599.1| 2228 SISGMKYEDLNSDSTKNPGEKGLSGWEMVLTGSTwfGKPLptLTATTDNNGNYKFERLLPGTYKVSETSRTGWTQ 2302
                                        6777889***********************55443366555479*****************************99 PP

                            SdrD_B   73 takkaGsd 80  
                                        ta   Gs 
  gi|330507171|ref|YP_004383599.1| 2303 TAPAGGSH 2310
                                        99887765 PP

  == domain 7  score: 49.3 bits;  conditional E-value: 3.1e-16
                            SdrD_B    2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakk 76  
                                        si  + ++D n+nG+ d ge+g+ g +++L  a g v++  tT+a+G+Y+Ft++++G+Y+V+ ++  g+ ++a  
  gi|330507171|ref|YP_004383599.1| 2336 SISGVKYNDINGNGVRDPGEPGMGGWKINLEPAGGGVIKVATTEADGSYSFTDVASGTYTVREIHQPGWDQKAPA 2410
                                        5667779********************************************************999999777766 PP

                            SdrD_B   77 aGs.ddaldSdadpa 90  
                                        +G+   +ldS  +++
  gi|330507171|ref|YP_004383599.1| 2411 SGTyTVTLDSSTTSV 2425
                                        666145678876655 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.9   4.3e+03      11      43 ..    1803    1835 ..    1798    1838 .. 0.80
   2 !   25.1   0.1     1e-08   1.5e-05       7      64 ..    1854    1910 ..    1840    1931 .. 0.76
   3 !   22.9   0.1   5.2e-08   7.7e-05      13      79 ..    1958    2028 ..    1950    2029 .. 0.80
   4 !   22.4   0.1   7.5e-08   0.00011      14      53 ..    2049    2095 ..    2036    2118 .. 0.81
   5 !   25.4   2.7   8.3e-09   1.2e-05       8      79 ..    2148    2219 ..    2145    2222 .. 0.84
   6 !   16.7   0.1   4.3e-06    0.0065      29      63 ..    2269    2303 ..    2243    2316 .. 0.82
   7 !   21.8   0.6   1.1e-07   0.00016       6      53 ..    2350    2397 ..    2345    2425 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.9
                   CarboxypepD_reg   11 gapiagatVtvtnadtgtvastttdadGafrlr 43  
                                        +++  +++V v++ + + + +  ++ +G+f+l+
  gi|330507171|ref|YP_004383599.1| 1803 DRGENQVKVQVRDGQHSGEDGFDSEYSGYFTLA 1835
                                        5555678999999899999999********986 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1e-08
                   CarboxypepD_reg    7 tdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr 64  
                                        ++ sg++++g tV +t ++++++ s+ t +dG++++++l +g+y++  + p    a++
  gi|330507171|ref|YP_004383599.1| 1854 VSDSGEALSGWTVQIT-KPDQSQVSVLTREDGTYSFQDLDAGSYTISETLPSGWVAAI 1910
                                        45678899********.6999************************9876666555555 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 5.2e-08
                   CarboxypepD_reg   13 piagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr.....eevtltagqtttldi 79  
                                        +++g t++++  d++  +++tt++dG+++++ l pg+y+v    +   t+t       +v+lt+g+ +++++
  gi|330507171|ref|YP_004383599.1| 1958 GMEGWTIELS-RDGSLISTATTEKDGSYKFAELSPGSYTVSEVEQAGWTRTAppegsYTVELTDGDVADINF 2028
                                        47899999*9.59999***********************975444445555457776458899998888886 PP

  == domain 4  score: 22.4 bits;  conditional E-value: 7.5e-08
                   CarboxypepD_reg   14 i........agatVtvtnadtgtvastttdadGafrlrglppgtysvt 53  
                                        +        ag+++ ++  d+++   ttt +dG++++r+l pgtys+ 
  gi|330507171|ref|YP_004383599.1| 2049 VkdegepgrAGVAIQLS-RDGSVINATTTLEDGSYAFRNLSPGTYSIS 2095
                                        44444444599999999.4888899999******************96 PP

  == domain 5  score: 25.4 bits;  conditional E-value: 8.3e-09
                   CarboxypepD_reg    8 dasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtv.sapGyatatreevtltagqtttldi 79  
                                        d++  +i+g +V++  +++++va+tttd++G ++++++ pgty++     +G+  +t+++vt+t ++ +  ++
  gi|330507171|ref|YP_004383599.1| 2148 DEDEPGIPGGEVSLV-ENGKVVANTTTDENGLYSFENVLPGTYTINDpVPTGMVLTTSSTVTVTIKTVVVTNV 2219
                                        6777899*******9.477789***********************9767788888888999999888755454 PP

  == domain 6  score: 16.7 bits;  conditional E-value: 4.3e-06
                   CarboxypepD_reg   29 vastttdadGafrlrglppgtysvtvsapGyatat 63  
                                        + ++ttd++G+++++ l pgty+v  ++    t+t
  gi|330507171|ref|YP_004383599.1| 2269 TLTATTDNNGNYKFERLLPGTYKVSETSRTGWTQT 2303
                                        6799********************87766666665 PP

  == domain 7  score: 21.8 bits;  conditional E-value: 1.1e-07
                   CarboxypepD_reg    6 VtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvt 53  
                                        V+d+   ++ g ++ ++ a++g+ + +tt+adG++++++++ gty+v+
  gi|330507171|ref|YP_004383599.1| 2350 VRDPGEPGMGGWKINLEPAGGGVIKVATTEADGSYSFTDVASGTYTVR 2397
                                        899999999*************************************97 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.9e-06    0.0074       2      61 ..    1857    1901 ..    1836    1909 .. 0.78
   2 !   20.3   0.2   3.5e-07   0.00053       8      64 ..    1941    2002 ..    1934    2022 .. 0.71
   3 !   13.4   0.0   4.8e-05     0.072      28      80 ..    2058    2117 ..    2033    2119 .. 0.75
   4 !   20.4   2.0   3.3e-07    0.0005      28      79 ..    2151    2212 ..    2134    2214 .. 0.75
   5 !   21.1   0.2   1.9e-07   0.00029      11      62 ..    2234    2296 ..    2216    2303 .. 0.68
   6 !   19.4   0.1   6.5e-07   0.00097      28      78 ..    2360    2418 ..    2331    2422 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.9e-06
                                        CCCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEEEEE CS
                              SpaA    2 tgkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYllvEt 61  
                                        +g++L+G + +++k d               +   ++ t e+G+ +f +L++G+Y++ Et
  gi|330507171|ref|YP_004383599.1| 1857 SGEALSGWTVQITKPD---------------QSQVSVLTREDGTYSFQDLDAGSYTISET 1901
                                        4455555555555555...............67888999********************9 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 3.5e-07
                                        S-EEEEEETTTSCCCHCHHTT......TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-S CS
                              SpaA    8 GaeFtlykvdtttdgkdalea.....kktgtevttlttdenGkatfegLplGtYllvEtkaP 64  
                                        G +F  ++ + + dg+  +e+       +g+ + t+tt ++G  +f +L +G+Y++ E++  
  gi|330507171|ref|YP_004383599.1| 1941 GRKFNDLNGNGAFDGEPGMEGwtielSRDGSLISTATTEKDGSYKFAELSPGSYTVSEVEQA 2002
                                        55555555554455555555577777788999**************************9765 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 4.8e-05
                                        T.......TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEEE..-SSEEEEEECE CS
                              SpaA   28 a......kktgtevttlttdenGkatfegLplGtYllvEtkaPegYvl..dkepfevtvta 80  
                                        a        +g++++  tt e+G   f +L +GtY +  + a eg ++  ++ p++v++++
  gi|330507171|ref|YP_004383599.1| 2058 AgvaiqlSRDGSVINATTTLEDGSYAFRNLSPGTYSISQV-AAEGINQiaPEGPWTVELKD 2117
                                        14556655677888888999******************98.66676665788899999886 PP

  == domain 4  score: 20.4 bits;  conditional E-value: 3.3e-07
                                        T...........TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEEE.-SSEEEEEEC CS
                              SpaA   28 a..........kktgtevttlttdenGkatfegLplGtYllvEtkaPegYvl.dkepfevtvt 79  
                                        +           ++g++v++ ttdenG  +fe++ +GtY++    +P+g vl ++ +++vt++
  gi|330507171|ref|YP_004383599.1| 2151 EpgipggevslVENGKVVANTTTDENGLYSFENVLPGTYTINDP-VPTGMVLtTSSTVTVTIK 2212
                                        134444556777899***************************85.899999845556777775 PP

  == domain 5  score: 21.1 bits;  conditional E-value: 1.9e-07
                                        EEEEETT.TSCCCHCHHTT...........TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE CS
                              SpaA   11 Ftlykvd.tttdgkdalea..........kktgtevttlttdenGkatfegLplGtYllvEtk 62  
                                        ++ +++d t++ g++ l++            +   + t+ttd+nG+ +fe L +GtY++ Et+
  gi|330507171|ref|YP_004383599.1| 2234 YEDLNSDsTKNPGEKGLSGwemvltgstwFGKPLPTLTATTDNNGNYKFERLLPGTYKVSETS 2296
                                        44444444444444444445555544444333445589***********************96 PP

  == domain 6  score: 19.4 bits;  conditional E-value: 6.5e-07
                                        T.......TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEEE..-SSEEEEEE CS
                              SpaA   28 a......kktgtevttlttdenGkatfegLplGtYllvEtkaPegYvl..dkepfevtv 78  
                                        +       + g +++ +tt ++G  +f++++ GtY+++E+  P   ++   + +++vt+
  gi|330507171|ref|YP_004383599.1| 2360 GwkinlePAGGGVIKVATTEADGSYSFTDVASGTYTVREIHQPGWDQKapASGTYTVTL 2418
                                        244555566788999*************************9994444411444555555 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 !    6.9   0.0    0.0041       6.1      35      55 ..     151     171 ..     135     180 .. 0.80
   2 ?   -0.1   0.0      0.62   9.3e+02      39      65 ..     290     317 ..     285     318 .. 0.80
   3 ?   -1.1   0.0       1.3   1.9e+03      34      65 ..     383     415 ..     364     416 .. 0.75
   4 ?    4.5   0.0     0.023        34      37      65 ..     484     513 ..     462     514 .. 0.82
   5 ?    4.5   0.0     0.023        34      37      65 ..     582     611 ..     560     612 .. 0.82
   6 ?    3.1   0.0     0.061        91      38      65 ..     681     709 ..     659     710 .. 0.86
   7 ?    3.1   0.0     0.061        91      38      65 ..     779     807 ..     757     808 .. 0.86
   8 ?    3.1   0.0     0.061        91      38      65 ..     877     905 ..     855     906 .. 0.86
   9 ?    3.1   0.0     0.061        91      38      65 ..     975    1003 ..     953    1004 .. 0.86
  10 ?    5.3   0.0     0.013        19      36      65 ..    1071    1101 ..    1047    1102 .. 0.83
  11 ?    5.5   0.0     0.011        16      34      65 ..    1167    1199 ..    1147    1200 .. 0.80
  12 !    6.8   0.0    0.0042       6.3      25      65 ..    1254    1297 ..    1236    1298 .. 0.79
  13 ?    2.0   0.0      0.14     2e+02       6      57 ..    1336    1384 ..    1330    1392 .. 0.80
  14 ?   -0.5   0.0      0.83   1.2e+03       6      51 ..    1449    1491 ..    1443    1497 .. 0.81
  15 ?    3.4   0.0     0.051        77       9      51 ..    1571    1610 ..    1562    1618 .. 0.82
  16 ?   -0.5   0.0      0.82   1.2e+03      26      43 ..    1882    1898 ..    1868    1899 .. 0.78
  17 ?    3.7   0.0      0.04        59      22      43 ..    1973    1996 ..    1966    1997 .. 0.75
  18 ?    4.8   0.0     0.018        27      18      43 ..    2067    2094 ..    2063    2100 .. 0.80
  19 ?    4.5   0.1     0.023        34      23      43 ..    2172    2191 ..    2164    2192 .. 0.82
  20 ?    0.9   0.1      0.29   4.3e+02      24      43 ..    2274    2292 ..    2270    2293 .. 0.81
  21 ?    1.3   0.0      0.23   3.4e+02      25      43 ..    2379    2396 ..    2371    2397 .. 0.81
  22 ?    0.8   0.0      0.33   4.9e+02      37      50 ..    2499    2512 ..    2469    2529 .. 0.79
  23 !    8.1   0.4    0.0018       2.6       8      49 ..    2782    2829 ..    2778    2835 .. 0.92
  24 !    8.4   0.7    0.0014       2.1       7      49 ..    2886    2934 ..    2881    2941 .. 0.83
  25 ?    5.2   0.2     0.014        20       8      50 ..    2992    3040 ..    2986    3047 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0041
                                       S--SEEEEEEEEEEETTS-B- CS
                             Y_Y_Y  35 nlppGdYtlkVkakdndgqwn 55 
                                        l+pG+Y+++V ++d+  ++ 
  gi|330507171|ref|YP_004383599.1| 151 ALEPGNYQIRVLVRDPMHTSG 171
                                       69*************987765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.62
                                       EEEEEEEEEEETTS-B-SS-.EEEEEEE CS
                             Y_Y_Y  39 GdYtlkVkakdndgqwnydi.tslsfti 65 
                                       G+  ++V+a+dn+ + + d+ +  +f i
  gi|330507171|ref|YP_004383599.1| 290 GSHSIEVRARDNNHNPQGDSsQATQFAI 317
                                       67789********998888777766665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.3
                                       ES--SEEEEEEEEEEETTS-B-SS-.EEEEEEE CS
                             Y_Y_Y  34 tnlppGdYtlkVkakdndgqwnydi.tslsfti 65 
                                       t+   G+ t++++++dn+ + + d+ +  +f i
  gi|330507171|ref|YP_004383599.1| 383 TEQDIGSHTIEARTRDNNHNPQGDSsQATQFAI 415
                                       55566999**********998888777666665 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.023
                                       -SEEEEEEEEEEETTS-B-SS-.EEEEEEE CS
                             Y_Y_Y  37 ppGdYtlkVkakdndgqwnydi.tslsfti 65 
                                         G+  ++V+a+dn+ + + d+ ++++f++
  gi|330507171|ref|YP_004383599.1| 484 DIGSHSIEVRARDNNHNPEGDSsRTMDFVV 513
                                       568889****************9****998 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.023
                                       -SEEEEEEEEEEETTS-B-SS-.EEEEEEE CS
                             Y_Y_Y  37 ppGdYtlkVkakdndgqwnydi.tslsfti 65 
                                         G+  ++V+a+dn+ + + d+ ++++f++
  gi|330507171|ref|YP_004383599.1| 582 DIGSHSIEVRARDNNHNPEGDSsRTMDFVV 611
                                       568889****************9****998 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.061
                                       SEEEEEEEEEEETTS-B-SS-.EEEEEEE CS
                             Y_Y_Y  38 pGdYtlkVkakdndgqwnydi.tslsfti 65 
                                        G+  ++V+a+dn+ + + d+ ++ +f++
  gi|330507171|ref|YP_004383599.1| 681 IGSHIIEVRARDNNHNPEGDSsKTAEFVV 709
                                       58889************999999999987 PP

  == domain 7  score: 3.1 bits;  conditional E-value: 0.061
                                       SEEEEEEEEEEETTS-B-SS-.EEEEEEE CS
                             Y_Y_Y  38 pGdYtlkVkakdndgqwnydi.tslsfti 65 
                                        G+  ++V+a+dn+ + + d+ ++ +f++
  gi|330507171|ref|YP_004383599.1| 779 IGSHIIEVRARDNNHNPEGDSsKTAEFVV 807
                                       58889************999999999987 PP

  == domain 8  score: 3.1 bits;  conditional E-value: 0.061
                                       SEEEEEEEEEEETTS-B-SS-.EEEEEEE CS
                             Y_Y_Y  38 pGdYtlkVkakdndgqwnydi.tslsfti 65 
                                        G+  ++V+a+dn+ + + d+ ++ +f++
  gi|330507171|ref|YP_004383599.1| 877 IGSHIIEVRARDNNHNPEGDSsKTAEFVV 905
                                       58889************999999999987 PP

  == domain 9  score: 3.1 bits;  conditional E-value: 0.061
                                        SEEEEEEEEEEETTS-B-SS-.EEEEEEE CS
                             Y_Y_Y   38 pGdYtlkVkakdndgqwnydi.tslsfti 65  
                                         G+  ++V+a+dn+ + + d+ ++ +f++
  gi|330507171|ref|YP_004383599.1|  975 IGSHIIEVRARDNNHNPEGDSsKTAEFVV 1003
                                        58889************999999999987 PP

  == domain 10  score: 5.3 bits;  conditional E-value: 0.013
                                        --SEEEEEEEEEEETTS-B-SS-.EEEEEEE CS
                             Y_Y_Y   36 lppGdYtlkVkakdndgqwnydi.tslsfti 65  
                                           G+ t++V+a+dn+ + + d+ ++ +f++
  gi|330507171|ref|YP_004383599.1| 1071 QDIGSHTIEVRARDNNHNPEGDSsQTAEFVV 1101
                                        556999************9999999999987 PP

  == domain 11  score: 5.5 bits;  conditional E-value: 0.011
                                        ES--SEEEEEEEEEEETTS-B-SS-.EEEEEEE CS
                             Y_Y_Y   34 tnlppGdYtlkVkakdndgqwnydi.tslsfti 65  
                                        t+   G+ t++V+a+dn+ + + d+ ++ +f++
  gi|330507171|ref|YP_004383599.1| 1167 TEQDIGSHTIEVRARDNNHNPEGDSsQTAEFVV 1199
                                        55567999************9999999999987 PP

  == domain 12  score: 6.8 bits;  conditional E-value: 0.0042
                                        SSTS...EEEEES--SEEEEEEEEEEETTS-B-SS-.EEEEEEE CS
                             Y_Y_Y   25 sdysq..easytnlppGdYtlkVkakdndgqwnydi.tslsfti 65  
                                        + +s+  + + t+ + G+ t++V+a+dn+ + + d+ ++ +f++
  gi|330507171|ref|YP_004383599.1| 1254 FTSSPswTWTTTEQEIGSHTIEVRARDNNHNPEGDSsRTAEFVV 1297
                                        55555455555677789***************999999999987 PP

  == domain 13  score: 2.0 bits;  conditional E-value: 0.14
                                        TTEEEEEEEETTESSEEEESSTS.EEEEES--SEEEEEEEEEEETTS-B-SS CS
                             Y_Y_Y    6 erllYrYrlegidkeWveasdysqeasytnlppGdYtlkVkakdndgqwnyd 57  
                                        + ++Yr+     d   ++ +  +  + +t  ++G+  ++V++kd+  ++   
  gi|330507171|ref|YP_004383599.1| 1336 DTISYRF--LVNDTPVTDWQPEN-LFPWTATEAGTALITVQVKDDQHDEPAA 1384
                                        4455555..5799999******9.********************98877655 PP

  == domain 14  score: -0.5 bits;  conditional E-value: 0.83
                                        TTEEEEEEEETTESSEEEESSTS.EEEEES--SEEEEEEEEEEETT CS
                             Y_Y_Y    6 erllYrYrlegidkeWveasdysqeasytnlppGdYtlkVkakdnd 51  
                                        + ++Yr+     d   ++ ++ +  + +t   +G+  ++V++kd+ 
  gi|330507171|ref|YP_004383599.1| 1449 DTISYRF--LVNDTPVTDWQSEN-LFAWTATGAGTALVTVQVKDDQ 1491
                                        4455555..57999999*****9.***********99999999975 PP

  == domain 15  score: 3.4 bits;  conditional E-value: 0.051
                                        EEEEEEETTESSEEEESSTS.EEEEES--SEEEEEEEEEEETT CS
                             Y_Y_Y    9 lYrYrlegidkeWveasdysqeasytnlppGdYtlkVkakdnd 51  
                                        +Yr+     +   ++ ++ + ++ +t  ++G++ ++++a+d+ 
  gi|330507171|ref|YP_004383599.1| 1571 SYRF--LVNETAVTDWQAEN-KFIWTASEAGSFLITAQARDDQ 1610
                                        4444..45678889999999.*******************964 PP

  == domain 16  score: -0.5 bits;  conditional E-value: 0.82
                                        STS.EEEEES--SEEEEE CS
                             Y_Y_Y   26 dysqeasytnlppGdYtl 43  
                                        + + ++s+  l +G+Yt+
  gi|330507171|ref|YP_004383599.1| 1882 EDG-TYSFQDLDAGSYTI 1898
                                        344.99***********8 PP

  == domain 17  score: 3.7 bits;  conditional E-value: 0.04
                                        EEESSTS...EEEEES--SEEEEE CS
                             Y_Y_Y   22 veasdysq..easytnlppGdYtl 43  
                                        +++    +  ++++ +l+pG+Yt+
  gi|330507171|ref|YP_004383599.1| 1973 ISTATTEKdgSYKFAELSPGSYTV 1996
                                        55555555679***********96 PP

  == domain 18  score: 4.8 bits;  conditional E-value: 0.018
                                        ESSEEEESSTS...EEEEES--SEEEEE CS
                             Y_Y_Y   18 dkeWveasdysq..easytnlppGdYtl 43  
                                        d++ ++a+      ++ ++nl+pG+Y +
  gi|330507171|ref|YP_004383599.1| 2067 DGSVINATTTLEdgSYAFRNLSPGTYSI 2094
                                        6666666666557799**********87 PP

  == domain 19  score: 4.5 bits;  conditional E-value: 0.023
                                        EESSTS.EEEEES--SEEEEE CS
                             Y_Y_Y   23 easdysqeasytnlppGdYtl 43  
                                        ++++++  +s+ n  pG+Yt+
  gi|330507171|ref|YP_004383599.1| 2172 TTDENG-LYSFENVLPGTYTI 2191
                                        445566.9************8 PP

  == domain 20  score: 0.9 bits;  conditional E-value: 0.29
                                        ESSTS.EEEEES--SEEEEE CS
                             Y_Y_Y   24 asdysqeasytnlppGdYtl 43  
                                        +++++ ++++  l pG+Y++
  gi|330507171|ref|YP_004383599.1| 2274 TDNNG-NYKFERLLPGTYKV 2292
                                        45566.9***********86 PP

  == domain 21  score: 1.3 bits;  conditional E-value: 0.23
                                        SSTS.EEEEES--SEEEEE CS
                             Y_Y_Y   25 sdysqeasytnlppGdYtl 43  
                                         + + ++s+t   +G+Yt+
  gi|330507171|ref|YP_004383599.1| 2379 EADG-SYSFTDVASGTYTV 2396
                                        4556.99**********97 PP

  == domain 22  score: 0.8 bits;  conditional E-value: 0.33
                                        -SEEEEEEEEEEET CS
                             Y_Y_Y   37 ppGdYtlkVkakdn 50  
                                        p+G+Y+++V ++d 
  gi|330507171|ref|YP_004383599.1| 2499 PAGKYEVEVWIRDG 2512
                                        89********9995 PP

  == domain 23  score: 8.1 bits;  conditional E-value: 0.0018
                                        EEEEEEEETTE..SSEEEESSTS...EEEEES--S..EEEEEEEEEEE CS
                             Y_Y_Y    8 llYrYrlegid..keWveasdysq..easytnlpp..GdYtlkVkakd 49  
                                        llYr++l+g +  ++W+  +d s+  + ++  lp+  G Yt++V+++d
  gi|330507171|ref|YP_004383599.1| 2782 LLYRFWLKGPStgNSWKIVQDWSYknQWTWASLPSdgGAYTVYVYVRD 2829
                                        79********9999*******9999*********888*********99 PP

  == domain 24  score: 8.4 bits;  conditional E-value: 0.0014
                                        TEEEEEEEETTE..SSEEEESSTS...EEEEE..S--SEEEEEEEEEEE CS
                             Y_Y_Y    7 rllYrYrlegid..keWveasdysq..easyt..nlppGdYtlkVkakd 49  
                                         ++Yr++l+g +  + W+ a+d s   + +++  ++  G Yt++V+a+d
  gi|330507171|ref|YP_004383599.1| 2886 PIYYRFWLKGPStgNVWQIAQDWSLanQWTWSsmPNDGGAYTVYVYARD 2934
                                        589********98899*******999*66666115667*********99 PP

  == domain 25  score: 5.2 bits;  conditional E-value: 0.014
                                        EEEEEEEETTE..SSEEEESSTS.....EEEEES--SEEEEEEEEEEET CS
                             Y_Y_Y    8 llYrYrlegid..keWveasdysq....easytnlppGdYtlkVkakdn 50  
                                        l+Y ++l+g +  + W   ++ s     + s  +  +G+Y+++V+++d 
  gi|330507171|ref|YP_004383599.1| 2992 LYYQFWLKGPStgNVWRIVQSWSAknqwTWSSAPTDAGNYRVYVYVRDG 3040
                                        6777777777765666666655555646666678899*********995 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.067     1e+02      53      70 .]     144     161 ..      93     161 .. 0.88
   2 !    7.8   0.0    0.0038       5.7      14      70 .]     241     296 ..     234     296 .. 0.88
   3 !   14.4   0.2   3.4e-05      0.05      13      70 .]     338     394 ..     328     394 .. 0.87
   4 !   14.0   0.1   4.4e-05     0.065      13      70 .]     436     492 ..     426     492 .. 0.87
   5 !   13.5   0.1   6.2e-05     0.093      14      70 .]     535     590 ..     527     590 .. 0.89
   6 !    9.1   0.2    0.0015       2.2      14      70 .]     633     688 ..     625     688 .. 0.83
   7 !    8.8   0.2    0.0018       2.7      13      70 .]     730     786 ..     719     786 .. 0.82
   8 !    9.8   0.2   0.00091       1.4      13      70 .]     828     884 ..     817     884 .. 0.82
   9 !    8.8   0.2    0.0018       2.7      13      70 .]     926     982 ..     915     982 .. 0.82
  10 !   12.3   0.6   0.00015      0.23      13      70 .]    1024    1080 ..    1013    1080 .. 0.82
  11 !   14.9   0.1   2.4e-05     0.035      14      70 .]    1123    1178 ..    1117    1178 .. 0.89
  12 !   15.8   0.5   1.2e-05     0.018      14      70 .]    1221    1276 ..    1215    1276 .. 0.84
  13 ?    1.9   0.3      0.26     4e+02      16      70 .]    1321    1372 ..    1315    1372 .. 0.83
  14 ?    4.3   1.6     0.046        69      13      70 .]    1431    1485 ..    1418    1487 .. 0.79
  15 ?   -2.1   0.1       4.8   7.2e+03      16      65 ..    1553    1599 ..    1547    1610 .. 0.65
  16 ?   -2.9   1.5       8.5   1.3e+04       2      34 ..    1654    1685 ..    1654    1709 .. 0.72
  17 ?   -2.4   0.0       5.7   8.6e+03      51      68 ..    1885    1898 ..    1854    1899 .. 0.66
  18 ?   -0.9   0.1         2   2.9e+03      34      68 ..    1964    1996 ..    1963    2016 .. 0.72
  19 ?   -2.1   0.8       4.5   6.8e+03      34      68 ..    2159    2191 ..    2156    2209 .. 0.76
  20 ?   -2.6   0.7       6.6   9.9e+03       6      42 ..    2192    2227 ..    2188    2246 .. 0.55
  21 ?   -0.3   0.1       1.3   1.9e+03      45      68 ..    2377    2396 ..    2337    2422 .. 0.70
  22 ?    1.6   0.0      0.33     5e+02      44      70 .]    2481    2507 ..    2463    2507 .. 0.84
  23 ?   -2.1   0.3       4.7     7e+03      53      70 .]    2702    2719 ..    2687    2719 .. 0.80
  24 ?   -1.2   0.4       2.5   3.7e+03      17      70 .]    2976    3035 ..    2971    3035 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.067
                                       EEEEE--...SEEEEEEE CS
                             Big_7  53 sltwtttaltagthtltV 70 
                                       ++tw+t+al+ g+++++V
  gi|330507171|ref|YP_004383599.1| 144 TWTWNTAALEPGNYQIRV 161
                                       89**************98 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0038
                                       EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  14 vsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                       + g  vt+ a Asd+ +   +  f vdg+    td  ++ s+tw tt  + g+h++ V
  gi|330507171|ref|YP_004383599.1| 241 IAGAAVTFIAAASDPeNDPLEFMFLVDGQA--RTDFINNPSWTWMTTEQDIGSHSIEV 296
                                       5577899********999999999*****9..577777889***************98 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 3.4e-05
                                       -EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  13 tvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                       ++ g  vt++a Asd+ +   +  f vdg+    td  ++ s+twttt  + g+ht+ +
  gi|330507171|ref|YP_004383599.1| 338 QIAGAAVTFTAAASDPeNDPLEFMFLVDGQA--RTDFINNPSWTWTTTEQDIGSHTIEA 394
                                       567889**********999999999*****9..577777889**************986 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 4.4e-05
                                       -EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  13 tvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                       ++ g  vt++a Asd+ +   +  f vdg+    td  ++ s+twttt  + g+h++ V
  gi|330507171|ref|YP_004383599.1| 436 QIAGAAVTFTAAASDPeNDPLEFMFLVDGQA--RTDFINNPSWTWTTTEQDIGSHSIEV 492
                                       567889**********999999999*****9..577777889***************98 PP

  == domain 5  score: 13.5 bits;  conditional E-value: 6.2e-05
                                       EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  14 vsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                       + g  vt++a Asd+ +   +  f vdg+    td  ++ s+twttt  + g+h++ V
  gi|330507171|ref|YP_004383599.1| 535 IAGAAVTFTAAASDPeNDPLEFMFLVDGQA--RTDFINNPSWTWTTTEQDIGSHSIEV 590
                                       56789**********999999999*****9..577777889***************98 PP

  == domain 6  score: 9.1 bits;  conditional E-value: 0.0015
                                       EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  14 vsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                       + g+ vt++a Asd+ +   +  f +dg+   ++  s+  s+twttt+ + g+h + V
  gi|330507171|ref|YP_004383599.1| 633 IAGTAVTFTAAASDPeNDPLEFMFLLDGVA-QTEFISS-PSWTWTTTTESIGSHIIEV 688
                                       66889**********999999999******.7666554.4888888888999998877 PP

  == domain 7  score: 8.8 bits;  conditional E-value: 0.0018
                                       -EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  13 tvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                       ++ g  vt++a Asd+ +   +  f +dg+   ++  s+  s+twttt+ + g+h + V
  gi|330507171|ref|YP_004383599.1| 730 QIAGAAVTFTAAASDPeNDPLEFMFLLDGVA-QTEFISS-PSWTWTTTTESIGSHIIEV 786
                                       566789**********999999999******.7666554.4888888888999998877 PP

  == domain 8  score: 9.8 bits;  conditional E-value: 0.00091
                                       -EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  13 tvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                       ++ g  vt++a+Asd+ +   +  f +dg+   ++  s+  s+twttt+ + g+h + V
  gi|330507171|ref|YP_004383599.1| 828 QIAGAAVTFTADASDPeNDPLEFMFLLDGVA-QTEFISS-PSWTWTTTTESIGSHIIEV 884
                                       566789**********999999999******.7666554.4888888888999998877 PP

  == domain 9  score: 8.8 bits;  conditional E-value: 0.0018
                                       -EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  13 tvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                       ++ g  vt++a Asd+ +   +  f +dg+   ++  s+  s+twttt+ + g+h + V
  gi|330507171|ref|YP_004383599.1| 926 QIAGAAVTFTAAASDPeNDPLEFMFLLDGVA-QTEFISS-PSWTWTTTTESIGSHIIEV 982
                                       566789**********999999999******.7666554.4888888888999998877 PP

  == domain 10  score: 12.3 bits;  conditional E-value: 0.00015
                                        -EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7   13 tvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70  
                                        ++ g  vt++a Asd+ +   +  f +d++   ++ ts   s+twttt  + g+ht+ V
  gi|330507171|ref|YP_004383599.1| 1024 QIAGAAVTFTAAASDPeNDTLEFMFLLDDVA-QTEFTS-IPSWTWTTTEQDIGSHTIEV 1080
                                        566789**********766666667899999.777766.5599**************98 PP

  == domain 11  score: 14.9 bits;  conditional E-value: 2.4e-05
                                        EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7   14 vsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70  
                                        + g  vt++a Asd+ +   +  f vdg+    td  ++ s+twttt  + g+ht+ V
  gi|330507171|ref|YP_004383599.1| 1123 IAGAAVTFTAAASDPeNDPLEFMFLVDGQA--RTDFINNPSWTWTTTEQDIGSHTIEV 1178
                                        56789**********999999999*****9..577777889***************98 PP

  == domain 12  score: 15.8 bits;  conditional E-value: 1.2e-05
                                        EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7   14 vsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70  
                                        + g+ vt++a Asd+ +   +  f +d++   ++ ts+p s+twttt  + g+ht+ V
  gi|330507171|ref|YP_004383599.1| 1221 IAGTAVTFTAAASDPeNDTLEFMFLLDDVA-QTEFTSSP-SWTWTTTEQEIGSHTIEV 1276
                                        66889**********766666677899999.88877766.9***************98 PP

  == domain 13  score: 1.9 bits;  conditional E-value: 0.26
                                        TSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7   16 ggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70  
                                        g+ ++ +a+Asd+ +   +  f v++t+ + td +    + wt+t  +agt  +tV
  gi|330507171|ref|YP_004383599.1| 1321 GSRINWTATASDAeNDTISYRFLVNDTP-V-TDWQPENLFPWTAT--EAGTALITV 1372
                                        5678889******966667799******.7.67788999999998..799988887 PP

  == domain 14  score: 4.3 bits;  conditional E-value: 0.046
                                        -EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7   13 tvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70  
                                        +v g++v+ +a+Asd+ +   +  f v++t+ + td ++   ++wt+t   agt  +tV
  gi|330507171|ref|YP_004383599.1| 1431 QVLGSSVNWTATASDAeNDTISYRFLVNDTP-V-TDWQSENLFAWTAT--GAGTALVTV 1485
                                        455899**********9666678********.8.66678888999999..577777776 PP

  == domain 15  score: -2.1 bits;  conditional E-value: 4.8
                                        TSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEE CS
                             Big_7   16 ggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagt 65  
                                        g++v+ +a Asd+ +   +  f v+ t  + td +a   + wt++  +ag+
  gi|330507171|ref|YP_004383599.1| 1553 GSSVNWTAVASDPeDDPISYRFLVNETA-V-TDWQAENKFIWTAS--EAGS 1599
                                        5677777777777766667777777777.5.55566666667665..4444 PP

  == domain 16  score: -2.9 bits;  conditional E-value: 8.5
                                        EEEEEE--TT--EB.TSEEEEEEEEE-S.S-EEEE CS
                             Big_7    2 tvtitsPangatvs.ggtvtisasAsdd.ggvskV 34  
                                        +v++t+Pan   ++ +++ t +a+ +    +v++V
  gi|330507171|ref|YP_004383599.1| 1654 QVNVTAPAN---ITdEENATAQANMTAEaENVTEV 1685
                                        689999987...55455666666666665567666 PP

  == domain 17  score: -2.4 bits;  conditional E-value: 5.7
                                        SEEEEEE--...SEEEEE CS
                             Big_7   51 pysltwtttaltagthtl 68  
                                        +    ++ ++l+ag++t+
  gi|330507171|ref|YP_004383599.1| 1885 T----YSFQDLDAGSYTI 1898
                                        3....3345678888888 PP

  == domain 18  score: -0.9 bits;  conditional E-value: 2
                                        EEEEETTEE.EEEE-SSSEEEEEE--...SEEEEE CS
                             Big_7   34 Vefyvdgtlglgtdtsapysltwtttaltagthtl 68  
                                        +e++ dg+l ++t t+     ++  + l+ g++t+
  gi|330507171|ref|YP_004383599.1| 1964 IELSRDGSL-ISTATT-EKDGSYKFAELSPGSYTV 1996
                                        788999999.766655.344444455577777776 PP

  == domain 19  score: -2.1 bits;  conditional E-value: 4.5
                                        EEEEETTEE...EEEE-SSSEEEEEE--...SEEEEE CS
                             Big_7   34 Vefyvdgtl.g.lgtdtsapysltwtttaltagthtl 68  
                                        V +  +g++ + ++td ++ ys++   +    gt+t+
  gi|330507171|ref|YP_004383599.1| 2159 VSLVENGKVvAnTTTDENGLYSFENVLP----GTYTI 2191
                                        6667788886678889999999976554....66665 PP

  == domain 20  score: -2.6 bits;  conditional E-value: 6.6
                                        EE--TT--EBTSEEEEEEEEE-SS-EEEEEEEETTEE CS
                             Big_7    6 tsPangatvsggtvtisasAsddggvskVefyvdgtl 42  
                                          P +   v +++ t++++      v++V f + g+ 
  gi|330507171|ref|YP_004383599.1| 2192 NDPVPTGMVLTTSSTVTVTIKTV-VVTNVNFGIRGSN 2227
                                        55555444443444444444333.5677777666665 PP

  == domain 21  score: -0.3 bits;  conditional E-value: 1.3
                                        EEE-SSSEEEEEE--...SEEEEE CS
                             Big_7   45 gtdtsapysltwtttaltagthtl 68  
                                        +t +++ ys+t     +++gt+t+
  gi|330507171|ref|YP_004383599.1| 2377 TTEADGSYSFTD----VASGTYTV 2396
                                        344445555553....34566665 PP

  == domain 22  score: 1.6 bits;  conditional E-value: 0.33
                                        EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7   44 lgtdtsapysltwtttaltagthtltV 70  
                                        l+t  s+   +tw+t  ++ag + + V
  gi|330507171|ref|YP_004383599.1| 2481 LDTGYSSRSVWTWNTLGYPAGKYEVEV 2507
                                        67888888999************9987 PP

  == domain 23  score: -2.1 bits;  conditional E-value: 4.7
                                        EEEEE--...SEEEEEEE CS
                             Big_7   53 sltwtttaltagthtltV 70  
                                        ++tw tt ++agt  ++V
  gi|330507171|ref|YP_004383599.1| 2702 TWTWPTTPADAGTSEIKV 2719
                                        6777777789***99998 PP

  == domain 24  score: -1.2 bits;  conditional E-value: 2.5
                                        SEEEEEEEEE-S.S-EEEEEEEETTEE......EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7   17 gtvtisasAsdd.ggvskVefyvdgtl.g....lgtdtsapysltwtttaltagthtltV 70  
                                        ++v+ +a+Asd+       +f++ g + g    + ++ sa  ++tw+ +  +ag++ + V
  gi|330507171|ref|YP_004383599.1| 2976 TPVKWTATASDAdKDPLYYQFWLKGPStGnvwrIVQSWSAKNQWTWSSAPTDAGNYRVYV 3035
                                        567778888888777777888888776556667555556777777777777899998866 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 !   12.6   0.1   7.1e-05      0.11       6      48 ..    1855    1898 ..    1850    1901 .. 0.82
   2 ?    4.8   0.0     0.019        28      27      48 ..    1975    1996 ..    1961    2004 .. 0.91
   3 !    6.0   0.0    0.0079        12      14      48 ..    2057    2094 ..    2046    2104 .. 0.76
   4 !   15.3   1.2   9.7e-06     0.014       3      49 ..    2143    2192 ..    2141    2228 .. 0.73
   5 !    7.6   0.1    0.0024       3.7      26      48 ..    2270    2292 ..    2264    2303 .. 0.89
   6 !    7.8   0.1    0.0021       3.2      27      49 ..    2375    2397 ..    2370    2399 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-05
                   CarbopepD_reg_2    6 vdketkeplpgatVyvkg...tkkgtvTdenGnFelknlpagkytL 48  
                                        +d  ++e+l g tV++++   +++ + T e+G++++++l+ag yt+
  gi|330507171|ref|YP_004383599.1| 1855 SD--SGEALSGWTVQITKpdqSQVSVLTREDGTYSFQDLDAGSYTI 1898
                                        33..579*********77332467778*****************98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.019
                   CarbopepD_reg_2   27 gtvTdenGnFelknlpagkytL 48  
                                         ++T+++G++++ +l +g yt+
  gi|330507171|ref|YP_004383599.1| 1975 TATTEKDGSYKFAELSPGSYTV 1996
                                        578*****************97 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0079
                   CarbopepD_reg_2   14 lpgatVyvkgtk...kgtvTdenGnFelknlpagkytL 48  
                                         +g+ +++   +   + t+T e+G++ ++nl +g+y +
  gi|330507171|ref|YP_004383599.1| 2057 RAGVAIQLSRDGsviNATTTLEDGSYAFRNLSPGTYSI 2094
                                        5677777766543448899*****************76 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 9.7e-06
                   CarbopepD_reg_2    3 GtVvdketkeplpgatVyvkgtk...kgtvTdenGnFelknlpagkytLv 49  
                                        G+ +++e++  +pg  V++ +++   ++t+TdenG ++++n+ +g+yt++
  gi|330507171|ref|YP_004383599.1| 2143 GNGLQDEDEPGIPGGEVSLVENGkvvANTTTDENGLYSFENVLPGTYTIN 2192
                                        555667777899**999997765345899*******************96 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.0024
                   CarbopepD_reg_2   26 kgtvTdenGnFelknlpagkytL 48  
                                          ++Td nGn+++++l +g+y++
  gi|330507171|ref|YP_004383599.1| 2270 LTATTDNNGNYKFERLLPGTYKV 2292
                                        5689*****************87 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0021
                   CarbopepD_reg_2   27 gtvTdenGnFelknlpagkytLv 49  
                                         ++T+++G+++++++ +g+yt++
  gi|330507171|ref|YP_004383599.1| 2375 VATTEADGSYSFTDVASGTYTVR 2397
                                        579*****************985 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.6e-05     0.039       9      44 ..    1863    1898 ..    1855    1904 .. 0.82
   2 !    6.4   0.0    0.0062       9.2      22      45 ..    1974    1997 ..    1959    2005 .. 0.80
   3 !    7.5   0.0    0.0028       4.2      22      46 ..    2072    2096 ..    2056    2102 .. 0.77
   4 ?    2.5   0.0       0.1   1.5e+02       8      45 ..    2155    2192 ..    2149    2219 .. 0.81
   5 !    7.7   0.0    0.0024       3.6      24      45 ..    2376    2397 ..    2370    2405 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                           DUF2012    9 ntrvlLdsgqqrkfkalvrrDGsFifrdlpegsYlL 44  
                                        + +v + +  q ++++l+r+DG+++f+dl +gsY++
  gi|330507171|ref|YP_004383599.1| 1863 GWTVQITKPDQSQVSVLTREDGTYSFQDLDAGSYTI 1898
                                        55677766666789********************97 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0062
                           DUF2012   22 fkalvrrDGsFifrdlpegsYlLe 45  
                                         +a +++DGs+ f +l++gsY++ 
  gi|330507171|ref|YP_004383599.1| 1974 STATTEKDGSYKFAELSPGSYTVS 1997
                                        578899***************985 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0028
                           DUF2012   22 fkalvrrDGsFifrdlpegsYlLev 46  
                                         ++ + +DGs++fr+l++g+Y +  
  gi|330507171|ref|YP_004383599.1| 2072 NATTTLEDGSYAFRNLSPGTYSISQ 2096
                                        5677889**************9865 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.1
                           DUF2012    8 antrvlLdsgqqrkfkalvrrDGsFifrdlpegsYlLe 45  
                                        ++ +v+L ++ +   ++ + ++G ++f+++ +g+Y+++
  gi|330507171|ref|YP_004383599.1| 2155 PGGEVSLVENGKVVANTTTDENGLYSFENVLPGTYTIN 2192
                                        56778885555547889999***************985 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0024
                           DUF2012   24 alvrrDGsFifrdlpegsYlLe 45  
                                        a +++DGs++f+d+ +g+Y+++
  gi|330507171|ref|YP_004383599.1| 2376 ATTEADGSYSFTDVASGTYTVR 2397
                                        67899**************985 PP

>> DUF4399  Domain of unknown function (DUF4399)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.07     1e+02      55      79 ..     149     173 ..     142     183 .. 0.83
   2 ?    0.7   0.0      0.46   6.9e+02      56      80 ..     285     309 ..     279     318 .. 0.81
   3 ?    2.2   0.0      0.16   2.3e+02      54      80 ..     381     407 ..     376     416 .. 0.82
   4 ?    1.2   0.0      0.32   4.8e+02      54      84 ..     479     507 ..     475     514 .. 0.80
   5 ?    1.2   0.0      0.32   4.8e+02      54      84 ..     577     605 ..     573     612 .. 0.80
   6 ?   -0.4   0.0         1   1.5e+03      54      83 ..     675     702 ..     671     710 .. 0.79
   7 ?   -0.4   0.0         1   1.5e+03      54      83 ..     773     800 ..     769     808 .. 0.79
   8 ?   -0.4   0.0         1   1.5e+03      54      83 ..     871     898 ..     867     906 .. 0.79
   9 ?   -0.4   0.0         1   1.5e+03      54      83 ..     969     996 ..     965    1004 .. 0.79
  10 ?    3.2   0.0     0.079   1.2e+02      54      80 ..    1067    1093 ..    1063    1102 .. 0.80
  11 ?    3.2   0.0     0.077   1.1e+02      54      80 ..    1165    1191 ..    1160    1200 .. 0.81
  12 ?    3.6   0.0     0.059        87      54      80 ..    1263    1289 ..    1257    1298 .. 0.83
  13 ?   -2.3   0.0       4.1   6.1e+03      55      75 ..    2495    2515 ..    2492    2526 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.07
                           DUF4399  55 elelppGkhtLqlqlgdaahvplkp 79 
                                       +  l+pG++++++++ d +h++ + 
  gi|330507171|ref|YP_004383599.1| 149 TAALEPGNYQIRVLVRDPMHTSGDF 173
                                       6689****************98765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.46
                           DUF4399  56 lelppGkhtLqlqlgdaahvplkps 80 
                                        e   G+h +++   d++h+p + s
  gi|330507171|ref|YP_004383599.1| 285 TEQDIGSHSIEVRARDNNHNPQGDS 309
                                       56778****************8865 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.16
                           DUF4399  54 telelppGkhtLqlqlgdaahvplkps 80 
                                       t+ e   G+ht++    d++h+p + s
  gi|330507171|ref|YP_004383599.1| 381 TTTEQDIGSHTIEARTRDNNHNPQGDS 407
                                       6778889****************8865 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.32
                           DUF4399  54 telelppGkhtLqlqlgdaahvplkpsvlsk 84 
                                       t+ e   G+h +++   d++h+p + s  s+
  gi|330507171|ref|YP_004383599.1| 479 TTTEQDIGSHSIEVRARDNNHNPEGDS--SR 507
                                       6678889***************98855..54 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.32
                           DUF4399  54 telelppGkhtLqlqlgdaahvplkpsvlsk 84 
                                       t+ e   G+h +++   d++h+p + s  s+
  gi|330507171|ref|YP_004383599.1| 577 TTTEQDIGSHSIEVRARDNNHNPEGDS--SR 605
                                       6678889***************98855..54 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 1
                           DUF4399  54 telelppGkhtLqlqlgdaahvplkpsvls 83 
                                       t+ + + G+h +++   d++h+p + s  s
  gi|330507171|ref|YP_004383599.1| 675 TTTTESIGSHIIEVRARDNNHNPEGDS--S 702
                                       5667788****************8865..4 PP

  == domain 7  score: -0.4 bits;  conditional E-value: 1
                           DUF4399  54 telelppGkhtLqlqlgdaahvplkpsvls 83 
                                       t+ + + G+h +++   d++h+p + s  s
  gi|330507171|ref|YP_004383599.1| 773 TTTTESIGSHIIEVRARDNNHNPEGDS--S 800
                                       5667788****************8865..4 PP

  == domain 8  score: -0.4 bits;  conditional E-value: 1
                           DUF4399  54 telelppGkhtLqlqlgdaahvplkpsvls 83 
                                       t+ + + G+h +++   d++h+p + s  s
  gi|330507171|ref|YP_004383599.1| 871 TTTTESIGSHIIEVRARDNNHNPEGDS--S 898
                                       5667788****************8865..4 PP

  == domain 9  score: -0.4 bits;  conditional E-value: 1
                           DUF4399  54 telelppGkhtLqlqlgdaahvplkpsvls 83 
                                       t+ + + G+h +++   d++h+p + s  s
  gi|330507171|ref|YP_004383599.1| 969 TTTTESIGSHIIEVRARDNNHNPEGDS--S 996
                                       5667788****************8865..4 PP

  == domain 10  score: 3.2 bits;  conditional E-value: 0.079
                           DUF4399   54 telelppGkhtLqlqlgdaahvplkps 80  
                                        t+ e   G+ht+++   d++h+p + s
  gi|330507171|ref|YP_004383599.1| 1067 TTTEQDIGSHTIEVRARDNNHNPEGDS 1093
                                        6678889****************8865 PP

  == domain 11  score: 3.2 bits;  conditional E-value: 0.077
                           DUF4399   54 telelppGkhtLqlqlgdaahvplkps 80  
                                        t+ e   G+ht+++   d++h+p + s
  gi|330507171|ref|YP_004383599.1| 1165 TTTEQDIGSHTIEVRARDNNHNPEGDS 1191
                                        6778889****************8865 PP

  == domain 12  score: 3.6 bits;  conditional E-value: 0.059
                           DUF4399   54 telelppGkhtLqlqlgdaahvplkps 80  
                                        t+ e + G+ht+++   d++h+p + s
  gi|330507171|ref|YP_004383599.1| 1263 TTTEQEIGSHTIEVRARDNNHNPEGDS 1289
                                        6778999***************98754 PP

  == domain 13  score: -2.3 bits;  conditional E-value: 4.1
                           DUF4399   55 elelppGkhtLqlqlgdaahv 75  
                                        +l  p+Gk+++++ + d++h 
  gi|330507171|ref|YP_004383599.1| 2495 TLGYPAGKYEVEVWIRDGQHS 2515
                                        567789999999999999997 PP

>> Dioxygenase_C  Dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.088   1.3e+02      76     104 ..    1876    1904 ..    1865    1916 .. 0.85
   2 ?    4.2   0.0     0.018        26      75     100 ..    1973    1998 ..    1962    2009 .. 0.82
   3 ?    4.3   0.0     0.016        24      78     100 ..    2074    2096 ..    2060    2110 .. 0.78
   4 !    9.8   0.0   0.00033      0.49      77     110 ..    2170    2203 ..    2158    2208 .. 0.87
   5 !    5.5   0.0    0.0068        10      79     103 ..    2273    2297 ..    2267    2309 .. 0.86
   6 ?    0.6   0.0      0.22   3.3e+02      79     120 ..    2377    2411 ..    2366    2426 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.088
                                        EEEE--TTSEEEEEEE----EE--TTSHH CS
                     Dioxygenase_C   76 griltdeeGryrirtikPapYpipndGpt 104 
                                         ++lt e+G+y+++ +  ++Y i +  p 
  gi|330507171|ref|YP_004383599.1| 1876 VSVLTREDGTYSFQDLDAGSYTISETLPS 1904
                                        589*******************9986655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.018
                                        EEEEE--TTSEEEEEEE----EE--T CS
                     Dioxygenase_C   75 rgriltdeeGryrirtikPapYpipn 100 
                                          +  t+++G+y++  + P++Y + +
  gi|330507171|ref|YP_004383599.1| 1973 ISTATTEKDGSYKFAELSPGSYTVSE 1998
                                        556779****************9876 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.016
                                        EE--TTSEEEEEEE----EE--T CS
                     Dioxygenase_C   78 iltdeeGryrirtikPapYpipn 100 
                                        + t e+G+y +r + P++Y i +
  gi|330507171|ref|YP_004383599.1| 2074 TTTLEDGSYAFRNLSPGTYSISQ 2096
                                        56779***************998 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00033
                                        EEE--TTSEEEEEEE----EE--TTSHHHHHHHH CS
                     Dioxygenase_C   77 riltdeeGryrirtikPapYpipndGptgkllda 110 
                                        ++ tde+G y+++ + P++Y i++  ptg +l +
  gi|330507171|ref|YP_004383599.1| 2170 NTTTDENGLYSFENVLPGTYTINDPVPTGMVLTT 2203
                                        6789********************9999998865 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.0068
                                        E--TTSEEEEEEE----EE--TTSH CS
                     Dioxygenase_C   79 ltdeeGryrirtikPapYpipndGp 103 
                                         td++G+y+++ + P++Y++ +   
  gi|330507171|ref|YP_004383599.1| 2273 TTDNNGNYKFERLLPGTYKVSETSR 2297
                                        69*****************988554 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 0.22
                                        E--TTSEEEEEEE----EE--TTSHHHHHHHHTT---EE-SE CS
                     Dioxygenase_C   79 ltdeeGryrirtikPapYpipndGptgklldalgrhawRPaH 120 
                                         t+++G+y+++ +  ++Y +++       +++ g+++  Pa 
  gi|330507171|ref|YP_004383599.1| 2377 TTEADGSYSFTDVASGTYTVRE-------IHQPGWDQKAPAS 2411
                                        5899***************998.......6666666666665 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.5   3.7e+03       9      35 ..    1788    1815 ..    1786    1822 .. 0.73
   2 ?    2.8   0.0      0.08   1.2e+02      37      61 ..    1967    1991 ..    1955    2017 .. 0.86
   3 ?   -1.5   0.0       1.7   2.6e+03      29      60 ..    2058    2088 ..    2051    2106 .. 0.78
   4 !    9.0   0.0   0.00094       1.4      29      60 ..    2155    2185 ..    2141    2208 .. 0.85
   5 ?    1.0   0.0      0.28   4.2e+02      45      62 ..    2271    2288 ..    2268    2311 .. 0.85
   6 ?   -2.3   0.0       3.1   4.6e+03      33      59 ..    2363    2389 ..    2358    2397 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.5
                              bMG3    9 klgrdkllvwvt.sLdsgkPvagaeVrl 35  
                                         + +d  ++wvt s+d g+   +++Vr 
  gi|330507171|ref|YP_004383599.1| 1788 EWISDDTWAWVTsSIDRGENQVKVQVRD 1815
                                        6778999999983599999877777764 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.08
                              bMG3   37 dkkgevlaegtTDaqGvarfaalla 61  
                                        +++g ++ ++tT ++G ++fa+l++
  gi|330507171|ref|YP_004383599.1| 1967 SRDGSLISTATTEKDGSYKFAELSP 1991
                                        6899****************99854 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.7
                              bMG3   29 agaeVrlldkkgevlaegtTDaqGvarfaall 60  
                                        ag++++l +++g v+  +tT ++G + f +l+
  gi|330507171|ref|YP_004383599.1| 2058 AGVAIQL-SRDGSVINATTTLEDGSYAFRNLS 2088
                                        7888887.5789*************9999874 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.00094
                              bMG3   29 agaeVrlldkkgevlaegtTDaqGvarfaall 60  
                                        +g eV+l+ ++g+v+a++tTD++G+++f++ l
  gi|330507171|ref|YP_004383599.1| 2155 PGGEVSLV-ENGKVVANTTTDENGLYSFENVL 2185
                                        66677777.69*****************9865 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.28
                              bMG3   45 egtTDaqGvarfaallar 62  
                                        ++tTD++G ++f++ll+ 
  gi|330507171|ref|YP_004383599.1| 2271 TATTDNNGNYKFERLLPG 2288
                                        79***********98765 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 3.1
                              bMG3   33 VrlldkkgevlaegtTDaqGvarfaal 59  
                                        ++l  + g v+  +tT a+G ++f++ 
  gi|330507171|ref|YP_004383599.1| 2363 INLEPAGGGVIKVATTEADGSYSFTDV 2389
                                        5555567889999*********99875 PP

>> Cadherin  Cadherin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.5   2.2e+03      64      83 ..     289     307 ..     283     317 .. 0.67
   2 ?   -1.6   0.0       2.5   3.7e+03      64      82 ..     485     503 ..     479     513 .. 0.69
   3 ?   -1.6   0.0       2.5   3.7e+03      64      82 ..     583     601 ..     577     611 .. 0.69
   4 ?    0.7   0.0      0.49   7.3e+02      62      87 ..     679     704 ..     672     710 .. 0.73
   5 ?    0.7   0.0       0.5   7.4e+02      62      87 ..     777     802 ..     771     808 .. 0.73
   6 ?    0.7   0.0       0.5   7.4e+02      62      87 ..     875     900 ..     869     906 .. 0.73
   7 ?    0.7   0.0       0.5   7.4e+02      62      87 ..     973     998 ..     967    1004 .. 0.73
   8 ?   -0.2   0.0       0.9   1.4e+03      64      88 ..    1073    1097 ..    1067    1102 .. 0.69
   9 ?   -0.1   0.0      0.85   1.3e+03      64      88 ..    1171    1195 ..    1162    1200 .. 0.71
  10 ?   -0.0   0.0      0.83   1.2e+03      63      85 ..    1268    1290 ..    1226    1298 .. 0.79
  11 ?   -1.5   0.0       2.4   3.6e+03      41      77 ..    3004    3041 ..    2974    3048 .. 0.52

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.5
                                       SSEEEEEEEEEECTGCCEEE CS
                          Cadherin  64 qgeYeLtveatDesgsppls 83 
                                       +g+++++v+a+D++  +p+ 
  gi|330507171|ref|YP_004383599.1| 289 IGSHSIEVRARDNN-HNPQG 307
                                       48899999999994.33332 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.5
                                       SSEEEEEEEEEECTGCCEE CS
                          Cadherin  64 qgeYeLtveatDesgsppl 82 
                                       +g+++++v+a+D++++p  
  gi|330507171|ref|YP_004383599.1| 485 IGSHSIEVRARDNNHNPEG 503
                                       4789999999999554443 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.5
                                       SSEEEEEEEEEECTGCCEE CS
                          Cadherin  64 qgeYeLtveatDesgsppl 82 
                                       +g+++++v+a+D++++p  
  gi|330507171|ref|YP_004383599.1| 583 IGSHSIEVRARDNNHNPEG 601
                                       4789999999999554443 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.49
                                       TTSSEEEEEEEEEECTGCCEEEEEEE CS
                          Cadherin  62 EsqgeYeLtveatDesgspplssttt 87 
                                       Es+g++ ++v+a+D++++p  +s  t
  gi|330507171|ref|YP_004383599.1| 679 ESIGSHIIEVRARDNNHNPEGDSSKT 704
                                       88999999999999966665555444 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.5
                                       TTSSEEEEEEEEEECTGCCEEEEEEE CS
                          Cadherin  62 EsqgeYeLtveatDesgspplssttt 87 
                                       Es+g++ ++v+a+D++++p  +s  t
  gi|330507171|ref|YP_004383599.1| 777 ESIGSHIIEVRARDNNHNPEGDSSKT 802
                                       88999999999999966665555444 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 0.5
                                       TTSSEEEEEEEEEECTGCCEEEEEEE CS
                          Cadherin  62 EsqgeYeLtveatDesgspplssttt 87 
                                       Es+g++ ++v+a+D++++p  +s  t
  gi|330507171|ref|YP_004383599.1| 875 ESIGSHIIEVRARDNNHNPEGDSSKT 900
                                       88999999999999966665555444 PP

  == domain 7  score: 0.7 bits;  conditional E-value: 0.5
                                       TTSSEEEEEEEEEECTGCCEEEEEEE CS
                          Cadherin  62 EsqgeYeLtveatDesgspplssttt 87 
                                       Es+g++ ++v+a+D++++p  +s  t
  gi|330507171|ref|YP_004383599.1| 973 ESIGSHIIEVRARDNNHNPEGDSSKT 998
                                       88999999999999966665555444 PP

  == domain 8  score: -0.2 bits;  conditional E-value: 0.9
                                        SSEEEEEEEEEECTGCCEEEEEEEE CS
                          Cadherin   64 qgeYeLtveatDesgspplsstttv 88  
                                        +g+++++v+a+D++++p  +s  t 
  gi|330507171|ref|YP_004383599.1| 1073 IGSHTIEVRARDNNHNPEGDSSQTA 1097
                                        489999******9666665555554 PP

  == domain 9  score: -0.1 bits;  conditional E-value: 0.85
                                        SSEEEEEEEEEECTGCCEEEEEEEE CS
                          Cadherin   64 qgeYeLtveatDesgspplsstttv 88  
                                        +g+++++v+a+D++++p  +s  t 
  gi|330507171|ref|YP_004383599.1| 1171 IGSHTIEVRARDNNHNPEGDSSQTA 1195
                                        4899999*****9666665555554 PP

  == domain 10  score: -0.0 bits;  conditional E-value: 0.83
                                        TSSEEEEEEEEEECTGCCEEEEE CS
                          Cadherin   63 sqgeYeLtveatDesgspplsst 85  
                                        ++g+++++v+a+D++++p  +s 
  gi|330507171|ref|YP_004383599.1| 1268 EIGSHTIEVRARDNNHNPEGDSS 1290
                                        45899999999999555544443 PP

  == domain 11  score: -1.5 bits;  conditional E-value: 2.4
                                        TTSEEEETTTTE....EEESSTC-TTTSSEEEEEEEEEECT CS
                          Cadherin   41 ggkFridtetgd....lsttkpLdrEsqgeYeLtveatDes 77  
                                        g+ +ri ++        +  +p d    g+Y+++v+++D +
  gi|330507171|ref|YP_004383599.1| 3004 GNVWRIVQSWSAknqwTWSSAPTDA---GNYRVYVYVRDGK 3041
                                        6777775532222222555555566...8888999998884 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 ?   -1.8   0.0       1.8   2.7e+03      14      40 ..    1578    1603 ..    1559    1604 .. 0.77
   2 ?   -0.9   0.0      0.96   1.4e+03      31      49 ..    1880    1898 ..    1852    1908 .. 0.83
   3 ?    1.1   0.1      0.23   3.4e+02      29      49 ..    1976    1996 ..    1973    2006 .. 0.89
   4 ?    2.5   0.0     0.082   1.2e+02      29      50 ..    2074    2095 ..    2058    2108 .. 0.82
   5 ?   11.6   1.0   0.00012      0.18      29      69 ..    2171    2211 ..    2169    2217 .. 0.92
   6 ?    5.6   0.1    0.0093        14      29      49 ..    2272    2292 ..    2270    2302 .. 0.92
   7 ?    5.4   0.2      0.01        15      29      49 ..    2376    2396 ..    2375    2424 .. 0.83
   8 ?   -1.9   0.4         2     3e+03      45      55 ..    2819    2829 ..    2817    2833 .. 0.85
   9 ?   -0.8   0.2      0.92   1.4e+03      45      56 ..    2924    2935 ..    2889    2940 .. 0.87
  10 ?    4.7   0.8     0.018        27      22      55 ..    2991    3039 ..    2968    3044 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.8
                             fn3_3   14 s..vvsfqnetkayQYwteadssgsftip 40  
                                        +  v+++q e    ++  +a++ gsf i+
  gi|330507171|ref|YP_004383599.1| 1578 EtaVTDWQAE---NKFIWTASEAGSFLIT 1603
                                        24599****9...6777778889999885 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.96
                             fn3_3   31 adssgsftipnVkpGtYrl 49  
                                        + ++g++++++  +G+Y+ 
  gi|330507171|ref|YP_004383599.1| 1880 TREDGTYSFQDLDAGSYTI 1898
                                        6788*************96 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.23
                             fn3_3   29 teadssgsftipnVkpGtYrl 49  
                                        ++++++gs+++    pG+Y++
  gi|330507171|ref|YP_004383599.1| 1976 ATTEKDGSYKFAELSPGSYTV 1996
                                        678888*************98 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.082
                             fn3_3   29 teadssgsftipnVkpGtYrlt 50  
                                        t++ ++gs+++ n  pGtY+ +
  gi|330507171|ref|YP_004383599.1| 2074 TTTLEDGSYAFRNLSPGTYSIS 2095
                                        566678*************986 PP

  == domain 5  score: 11.6 bits;  conditional E-value: 0.00012
                             fn3_3   29 teadssgsftipnVkpGtYrltvYadglfgdykqdsvtVta 69  
                                        t++d++g ++++nV pGtY+    ++ +++ ++ ++vtVt 
  gi|330507171|ref|YP_004383599.1| 2171 TTTDENGLYSFENVLPGTYTINDPVPTGMVLTTSSTVTVTI 2211
                                        899*****************************999999985 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.0093
                             fn3_3   29 teadssgsftipnVkpGtYrl 49  
                                        +++d++g++++++  pGtY++
  gi|330507171|ref|YP_004383599.1| 2272 ATTDNNGNYKFERLLPGTYKV 2292
                                        78999**************97 PP

  == domain 7  score: 5.4 bits;  conditional E-value: 0.01
                             fn3_3   29 teadssgsftipnVkpGtYrl 49  
                                        ++++++gs+++++V  GtY++
  gi|330507171|ref|YP_004383599.1| 2376 ATTEADGSYSFTDVASGTYTV 2396
                                        567888*************98 PP

  == domain 8  score: -1.9 bits;  conditional E-value: 2
                             fn3_3   45 GtYrltvYadg 55  
                                        G Y+++vY+  
  gi|330507171|ref|YP_004383599.1| 2819 GAYTVYVYVRD 2829
                                        99******975 PP

  == domain 9  score: -0.8 bits;  conditional E-value: 0.92
                             fn3_3   45 GtYrltvYadgl 56  
                                        G Y+++vYa  +
  gi|330507171|ref|YP_004383599.1| 2924 GAYTVYVYARDG 2935
                                        99******9765 PP

  == domain 10  score: 4.7 bits;  conditional E-value: 0.018
                             fn3_3   22 tkayQYwteadssg...............sftipnVkpGtYrltvYadg 55  
                                        +  yQ+w +  s+g               ++++    +G+Yr++vY+  
  gi|330507171|ref|YP_004383599.1| 2991 PLYYQFWLKGPSTGnvwrivqswsaknqwTWSSAPTDAGNYRVYVYVRD 3039
                                        567999999988888999999999999889999999**********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (3064 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        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: 1.21u 0.31s 00:00:01.52 Elapsed: 00:00:00.49
# Mc/sec: 18662.37
//
Query:       gi|330507172|ref|YP_004383600.1|  [L=168]
Description: formaldehyde-activating enzyme [Methanosaeta concilii GP6]
Scores for complete 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-72  240.8   0.2    6.5e-72  240.7   0.2    1.0  1  Fae       Formaldehyde-activating enzyme (Fae)
  ------ inclusion threshold ------
      0.068   12.4   0.1       0.08   12.2   0.1    1.1  1  DUF4849   Putative glycoside hydrolase Family 18, chitinase_1


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 !  240.7   0.2   7.2e-76   6.5e-72       1     158 [.      10     167 ..      10     168 .] 0.99

  Alignments for each domain:
  == domain 1  score: 240.7 bits;  conditional E-value: 7.2e-76
                               Fae   1 vGEalvgegeevAhidliiGekdgpvgtAfanalanqskghtpllavlrpnllvkPatlmvnkvtiknekqaellfG 77 
                                       vGEalvgeg+evAhidl++G++d+pv++Af++ala++s+ghtpllavl+pnl+vkP+tlmvnkvtikn++qa ++fG
  gi|330507172|ref|YP_004383600.1|  10 VGEALVGEGPEVAHIDLVMGPRDSPVEKAFVRALASPSRGHTPLLAVLAPNLPVKPSTLMVNKVTIKNAQQAIMVFG 86 
                                       8**************************************************************************** PP

                               Fae  78 paQaavakavadaveegiipkeeaddlviivsvfidpeakdkkkiyeynyeAtklAikrAlkeePsidevleekdka 154
                                       p+Qaava+av+d+ve+g++p+e addl+iivsvf++++akdk+k+yeyny+Atk Ai+rA ++eP+  ++l++k++a
  gi|330507172|ref|YP_004383600.1|  87 PVQAAVARAVMDCVESGVLPEELADDLFIIVSVFVEWDAKDKDKVYEYNYQATKIAIERAANREPKPGDILAAKSTA 163
                                       ***************************************************************************** PP

                               Fae 155 khpf 158
                                       khpf
  gi|330507172|ref|YP_004383600.1| 164 KHPF 167
                                       ***9 PP

>> DUF4849  Putative glycoside hydrolase Family 18, chitinase_18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   8.9e-06      0.08     220     281 ..      90     150 ..      63     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.9e-06
                           DUF4849 220 adlalkllkaiaagevlvnevpadrfivavsleslddtdkktgyvdtkdnkmralagaArwi 281
                                       a +a++++++++ g vl++e   d fi++  + + d++dk + y  +++    a+  aA+  
  gi|330507172|ref|YP_004383600.1|  90 AAVARAVMDCVESG-VLPEELADDLFIIVSVFVEWDAKDKDKVYEYNYQATKIAIERAANRE 150
                                       67889999999999.99999999*********************999988888998888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1198.83
//
Query:       gi|330507173|ref|YP_004383601.1|  [L=188]
Description: GMP synthase subunit A [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-33  114.1   0.0    7.8e-33  113.8   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    4.1e-12   46.3   4.3    8.8e-12   45.2   1.0    2.4  2  Peptidase_C26  Peptidase C26
     0.0012   18.5   2.0      0.013   15.1   2.0    2.0  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8   0.0   1.3e-36   7.8e-33       2     187 ..      12     183 ..      11     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 1.3e-36
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEET CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGIC 78 
                                       +i+ny ++++ + ++++  +v++++  ++++ e i     ++dg+++ gGp    v+++     ++++ +iPiLGIC
  gi|330507173|ref|YP_004383601.1|  12 VINNYGQFNHLIRRSIR-DKVDCDLASNQTPPEDI-----DADGLILGGGPSLDRVGNCR---DYLLKLDIPILGIC 79 
                                       799**9**999988887.578********999999.....79**********99999876...5677799******* PP

                                       HHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEE CS
                            GATase  79 LGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelm 155
                                       LGmQ+++  fg++v   +  ++ +   +l d e ++l+g + +++++ +H + v     +p++++ +a+s   + ++
  gi|330507173|ref|YP_004383601.1|  80 LGMQIMGTTFGGQVTAGSIGGYAQVDVELID-EDDILKGFPAKFKTWASHADQVSL---LPSQFQRLATS-RICDIE 151
                                       ****************99999*******999.67*********************8...**********9.6789** PP

                                       EEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 156 eiiekknpfvgvQFHPEststpegpellfnfl 187
                                       ++ ++++p++gvQ+HPE+++t++g+ell nf+
  gi|330507173|ref|YP_004383601.1| 152 AMKHRNRPLYGVQWHPEVVHTEHGEELLDNFI 183
                                       *****************************984 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.76   4.5e+03      59      70 ..      47      58 ..      46      60 .. 0.83
   2 !   45.2   1.0   1.5e-15   8.8e-12     102     216 .]      69     168 ..      65     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.76
                     Peptidase_C26 59 ldgllltGgqdv 70
                                       dgl+l Gg+ +
  gi|330507173|ref|YP_004383601.1| 47 ADGLILGGGPSL 58
                                      59******9865 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 1.5e-15
                     Peptidase_C26 102 lergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavk.vekgsllaellgseeievnslHhqa 177
                                       l+ ++PilgiC+G+q++  ++GG++        g         +a + +v+ ++++ +l+ +    ++++   H   
  gi|330507173|ref|YP_004383601.1|  69 LKLDIPILGICLGMQIMGTTFGGQVTAGSIG--G---------YA-QVDVElIDEDDILKGFPA--KFKTWASHADQ 131
                                       6789*******************98654332..1.........22.233431668889988887..9********** PP

                     Peptidase_C26 178 ikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       ++ l ++++  A+++   iEa++++++  +++gvQwHPE
  gi|330507173|ref|YP_004383601.1| 132 VSLLPSQFQRLATSRICDIEAMKHRNR--PLYGVQWHPE 168
                                       **************************4..6********9 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   2.0   2.1e-06     0.013       2      93 ..       5      90 ..       4     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-06
                          GATase_3  2 iavirlpaisnytdldpLeaepevrvrfvplkdeslg...edadlvilpGgkdtiqdlallresgldeaikeaaeaggp 77
                                      +a++r   i+ny+ ++ L +++  +    +l  ++ +    dad +il+Gg +        r  + ++ + +    ++p
  gi|330507173|ref|YP_004383601.1|  5 VALMRVIVINNYGQFNHLIRRSIRDKVDCDLASNQTPpedIDADGLILGGGPSLD------RVGNCRDYLLK---LDIP 74
                                      78899999*****99999888766666666655555555546999******8644......44445555655...589* PP

                          GATase_3 78 vlgiCGGlqmLGeeie 93
                                      +lgiC G+q++G+++ 
  gi|330507173|ref|YP_004383601.1| 75 ILGICLGMQIMGTTFG 90
                                      ************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1435.22
//
Query:       gi|330507174|ref|YP_004383602.1|  [L=206]
Description: hypothetical protein MCON_1036 [Methanosaeta concilii GP6]
Scores for complete sequence (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   2.5      2e-12   47.6   0.5    2.1  2  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.5   1.1e-16     2e-12       1      84 [.      36     136 ..      36     137 .. 0.89
   2 ?    0.7   0.7     0.048   8.6e+02       5      48 ..     133     188 ..     131     198 .. 0.55

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.1e-16
                          CxxCxxCC   1 eCkeCgaCCk..elkvklteedlerlkaaevaeeeeeskkiak..................adgrCvfldeetklCk 57 
                                       +C +Cg+CC+  +++v + + +++r+ a+++ +  e ++  ++                  ++ rC+f+de   +C+
  gi|330507174|ref|YP_004383602.1|  36 QCLGCGQCCRgdDNSVVVFPFEVRRIMAKRELDWLEVAQPPEEgewdnngnfhtlewrlkkEGLRCRFYDEG--QCT 110
                                       6*********988999999*******9999988888888887799999************9999*******9..8** PP

                          CxxCxxCC  58 iYeeRpkicrlfpasekeellaraetC 84 
                                       iY +Rp+ cr++p+    e + r ++C
  gi|330507174|ref|YP_004383602.1| 111 IYGQRPLLCRTYPFY-LVEGELRCSEC 136
                                       **************4.66666666666 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.048
                          CxxCxxCC   5 CgaCCkelkvklteedlerlkaaevaeeeeeskkiak.............adgrCvf 48 
                                       C +C   l+++++e+  ++++ + + ++ +e  +++              ++g+C +
  gi|330507174|ref|YP_004383602.1| 133 CSECPG-LGMRINEDAAQEIAGQLILRHITEIVEAIAltkkyqdfqrggyKEGNCCI 188
                                       666655.77777777777777766655555444443344455555555554444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1574.35
//
Query:       gi|330507175|ref|YP_004383603.1|  [L=385]
Description: chaperone protein DnaJ [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-42  145.4   0.0    1.6e-42  145.0   0.0    1.2  1  DnaJ_C           DnaJ C terminal domain
    7.9e-28   96.4   2.1    1.3e-27   95.7   2.1    1.3  1  DnaJ             DnaJ domain
      3e-15   56.3  16.3    5.4e-15   55.5  16.3    1.4  1  DnaJ_CXXCXGXG    DnaJ central domain
    8.5e-05   22.4  17.9     0.0034   17.3   3.5    3.6  3  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
  ------ inclusion threshold ------
       0.79   10.0  22.7        4.3    7.6   0.7    4.4  4  DUF5351          Family of unknown function (DUF5351)
          3    7.8   8.3       0.69    9.9   0.8    2.6  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
        9.1    6.4   9.2         13    5.9   2.2    2.4  3  HypA             Hydrogenase/urease nickel incorporation, met
        9.2    6.4  11.2         65    3.7  11.2    2.1  1  DZR              Double zinc ribbon


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 !  145.0   0.0   7.3e-46   1.6e-42       2     148 .]     124     340 ..     123     340 .. 0.97

  Alignments for each domain:
  == domain 1  score: 145.0 bits;  conditional E-value: 7.3e-46
                                       EEEEEE-HHHHHH-.EEE.EEEE...................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                            DnaJ_C   2 eveleisleelykGktkkikikrnvi................................................... 27 
                                       +++++++le++ +G +++i++ r+++                                                   
  gi|330507175|ref|YP_004383603.1| 124 RYDIDLTLEQASRGLETTIEVPRTENcpkcqgsgakpgtspvtcstcrgsgqvtraqntpfgqmvtsstcpkcggrg 200
                                       799*********************99*************************************************** PP

                                       ...................TEEEEEE-TT--TT-EEEETT-SS.SS....S---EEEEEEE---SS-EEETTEEEEE CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  28 ...............kkekktlevkipaGikdgqkirlegeGd.eeg..gepGDlivtikvkphpvFkrkgndlyve 86 
                                                       ++ +++++kipaG++dgq+++l+g+Gd + g  g +GDl+v+i+ +ph+ F+r ++dl++e
  gi|330507175|ref|YP_004383603.1| 201 elitspcedcsgtgrARKARKINIKIPAGVEDGQHLKLRGQGDsA-GpkGVSGDLYVVINIQPHRLFQRLDSDLIME 276
                                       *************97555558**********************54.559**************************** PP

                                       EEEEHHHHHHTEEEEEE-SS-EEEEEE...--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  87 veislaeallGgklevptldgkvklki...tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                                        +is+++a+lG+ levptl+g++++k+   tq+g+v+r++gkGmp+l+ +++ Gdl+v+vk+++P
  gi|330507175|ref|YP_004383603.1| 277 TPISFTQAALGADLEVPTLNGRARIKVpagTQTGTVFRLRGKGMPRLH-GTGSGDLHVRVKINTP 340
                                       ***********************************************7.**************99 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   2.1   5.7e-31   1.3e-27       1      63 []       6      67 ..       6      67 .. 0.99

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 5.7e-31
                                      HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                              DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                      dyY++Lgvskdase++Ik aYrkla+k+HPD++ +dp aee+Fke++eAy vLsdp+kR++YD
  gi|330507175|ref|YP_004383603.1|  6 DYYDVLGVSKDASEKDIKTAYRKLAMKHHPDRS-DDPGAEEMFKELSEAYAVLSDPDKRQKYD 67
                                      8********************************.****************************9 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5  16.3   2.4e-18   5.4e-15       1      67 []     150     214 ..     150     214 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 2.4e-18
                     DnaJ_CXXCXGXG   1 CkkCkGsgakkgk.kktCktCkGsGvvreeqkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                                       C+kC+Gsgak+g+ + tC+tC+GsG+v++ q+t +g++v  ++stCp+C+G+G++i  +++C++C+G+g
  gi|330507175|ref|YP_004383603.1| 150 CPKCQGSGAKPGTsPVTCSTCRGSGQVTRAQNTpFGQMV--TSSTCPKCGGRGELI--TSPCEDCSGTG 214
                                       **********977799*********98888887799988..679************..778******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 !   13.3   5.6   2.7e-05     0.061      11      46 ..     148     180 ..     140     182 .. 0.87
   2 !   17.3   3.5   1.5e-06    0.0034      11      44 ..     165     204 ..     163     206 .. 0.86
   3 !    6.1   0.3    0.0047        11      11      25 ..     205     219 ..     201     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                                       EE-TTTTTTSEETTE......E-TTTTTSSEEE-HH CS
                         Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkglipTaq 46 
                                       ++C++C+gsG  +++   + + C  C G g +  aq
  gi|330507175|ref|YP_004383603.1| 148 ENCPKCQGSGAKPGT---SPVTCSTCRGSGQVTRAQ 180
                                       58*************...889********9887665 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.5e-06
                                       EE-TTTTTTSEETTE............E-TTTTTSSEEE- CS
                         Anti-TRAP  11 tkCdaCngsGkiepe......eprasleCPkCsGkglipT 44 
                                       ++C +C gsG++  +      +  +s  CPkC+G+g + T
  gi|330507175|ref|YP_004383603.1| 165 VTCSTCRGSGQVTRAqntpfgQMVTSSTCPKCGGRGELIT 204
                                       58*********9988776777777888*********9888 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0047
                                       EE-TTTTTTSEETTE CS
                         Anti-TRAP  11 tkCdaCngsGkiepe 25 
                                        +C+ C g+G++  +
  gi|330507175|ref|YP_004383603.1| 205 SPCEDCSGTGRARKA 219
                                       58*********9877 PP

>> DUF5351  Family of unknown function (DUF5351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.7    0.0019       4.3      17      28 ..     147     158 ..     146     159 .. 0.89
   2 ?    5.7   0.6    0.0077        17      19      28 ..     166     175 ..     164     176 .. 0.93
   3 ?    6.1   1.6    0.0055        12      17      28 ..     190     201 ..     189     202 .. 0.88
   4 ?    4.2   0.7     0.023        51      20      28 ..     207     215 ..     204     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0019
                           DUF5351  17 SETCesCeGtgk 28 
                                       +E C++C+G+g 
  gi|330507175|ref|YP_004383603.1| 147 TENCPKCQGSGA 158
                                       699*******96 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0077
                           DUF5351  19 TCesCeGtgk 28 
                                       TC  C G+g+
  gi|330507175|ref|YP_004383603.1| 166 TCSTCRGSGQ 175
                                       9*******97 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0055
                           DUF5351  17 SETCesCeGtgk 28 
                                       S TC++C G g+
  gi|330507175|ref|YP_004383603.1| 190 SSTCPKCGGRGE 201
                                       77*******996 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.023
                           DUF5351  20 CesCeGtgk 28 
                                       Ce C+Gtg 
  gi|330507175|ref|YP_004383603.1| 207 CEDCSGTGR 215
                                       *******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 ?    1.2   1.4      0.16   3.6e+02      30      53 ..     149     171 ..     139     181 .. 0.82
   2 ?    9.9   0.8   0.00031      0.69      26      52 ..     188     210 ..     184     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.16
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCg 53 
                                       +C++C   + + + +  ++C+ C 
  gi|330507175|ref|YP_004383603.1| 149 NCPKCQGSGAK-PGTSPVTCSTCR 171
                                       68899888888.788888888886 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00031
                    OrfB_Zn_ribbon  26 yTSktCseCgsknkealsgrtfkCpnC 52 
                                        TS+tC++Cg +++      t  C++C
  gi|330507175|ref|YP_004383603.1| 188 VTSSTCPKCGGRGEL----ITSPCEDC 210
                                       5**********9987....55555555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.7     0.017        38      66      96 ..     143     174 ..     128     183 .. 0.73
   2 ?    5.9   2.2    0.0057        13      71      97 ..     165     201 ..     160     208 .. 0.78
   3 ?    5.8   1.1    0.0058        13      70      98 ..     190     215 ..     174     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.017
                                       EE--EEEETTTS-EEECHHH.HHS-TTTSSS- CS
                              HypA  66 evpvkvrCreCgkefeleek.alrCpkCgsad 96 
                                       evp +  C +C+ ++ +  +  ++C +C +++
  gi|330507175|ref|YP_004383603.1| 143 EVPRTENCPKCQGSGAKPGTsPVTCSTCRGSG 174
                                       57777889999988886654477999998764 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0057
                                       EEETTTS-EEECHHH.HH.........S-TTTSSS-E CS
                              HypA  71 vrCreCgkefeleek.al.........rCpkCgsadv 97 
                                       v+C++C+ +++++++ ++         +CpkCg+++ 
  gi|330507175|ref|YP_004383603.1| 165 VTCSTCRGSGQVTRAqNTpfgqmvtssTCPKCGGRGE 201
                                       789***999997763233678899999******9764 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0058
                                       EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA  70 kvrCreCgkefeleekalrCpkCgsadve 98 
                                       + +C +Cg ++el ++   C++C++++ +
  gi|330507175|ref|YP_004383603.1| 190 SSTCPKCGGRGELITS--PCEDCSGTG-R 215
                                       678*******998754..799999864.4 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  11.2     0.029        65       1      48 [.     150     210 ..     138     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.029
                               DZR   1 CpqCgee.lppdar..fCseCgtklkavaa..........edrCpsCgekvdpearfCpeC 48 
                                       Cp+C+    +p+    +Cs+C+ + + + a          + +Cp+Cg   ++ ++ C  C
  gi|330507175|ref|YP_004383603.1| 150 CPKCQGSgAKPGTSpvTCSTCRGSGQVTRAqntpfgqmvtSSTCPKCGGRGELITSPCEDC 210
                                       8888766533333344999999886544446789999999999****99999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      698  (0.0389313); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 2639.74
//
Query:       gi|330507176|ref|YP_004383604.1|  [L=622]
Description: chaperone protein DnaK [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-223  743.9  13.2   8.6e-221  734.3  13.2    2.0  1  HSP70     Hsp70 protein
      8e-17   61.0   4.0      8e-17   61.0   4.0    2.6  2  MreB_Mbl  MreB/Mbl protein
    0.00016   21.5   0.0    0.00033   20.4   0.0    1.5  1  FGGY_C    FGGY family of carbohydrate kinases, C-terminal dom
  ------ inclusion threshold ------
        1.7    8.6   4.1        4.1    7.4   4.1    1.6  1  DUF45     Protein of unknown function DUF45
          3    8.1   9.1        4.7    7.5   9.1    1.2  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 !  734.3  13.2  2.4e-224  8.6e-221       1     599 []       4     579 ..       4     579 .. 0.98

  Alignments for each domain:
  == domain 1  score: 734.3 bits;  conditional E-value: 2.4e-224
                                       EEEEEEXSSEEEEEEEETTEEEEEXXTTSX....SSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXB CS
                             HSP70   1 viGiDLGttnsvvavmeggkievianeegn....rttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrk 72 
                                       +iGiDLGt ns+ av+ gg++++i  +eg+    ++ Ps+vaFtk+ + lvGe+Akrqavtnp+ tv+ +Kr +G++
  gi|330507176|ref|YP_004383604.1|   4 IIGIDLGTSNSAAAVLIGGRPTIIPSAEGTsiggKAFPSYVAFTKDgQVLVGEPAKRQAVTNPDGTVQGIKRKMGTD 80 
                                       69************************99863333789*********99****************************6 PP

                                       TTSHHHHHHHTTXSSEEEEETTSBEEEEEEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHH CS
                             HSP70  73 fsdpevqkeikelpykvvkkengkavveveaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqR 149
                                       ++              v            ++ ++++tpe+isa+vL+k+k++ae+yl ++v++avitvPaYfnd+qR
  gi|330507176|ref|YP_004383604.1|  81 YK--------------V------------RVFDKEYTPEDISAQVLRKIKTDAETYLADSVDKAVITVPAYFNDNQR 131
                                       65..............2............344789****************************************** PP

                                       HHHHHHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHH CS
                             HSP70 150 qatkdAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedf 226
                                       qatkdAg+iAGL+v+Ri+NepTAaala+Gldk   e++++v+DlGggt dv i+e+++Gvfev++T+gDt+lGG+d+
  gi|330507176|ref|YP_004383604.1| 132 QATKDAGTIAGLEVVRIINEPTAAALAFGLDKVG-EHKIMVFDLGGGTLDVTIMEIGEGVFEVLSTSGDTQLGGRDM 207
                                       *********************************9.****************************************** PP

                                       HHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTT.EEEEEEEEHHHHHHHH CS
                             HSP70 227 DealvehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqteinleietvdedg.kdlseklsRakfeelv 302
                                       D++l+++++++fk+++g+dl+ d++a+qrl+ea+e aK+eLSs+ qt++nl+++t+d++g k+ls+++ R+k+eelv
  gi|330507176|ref|YP_004383604.1| 208 DDRLTNYVLDRFKQESGVDLRGDSMAMQRLREAVEVAKIELSSVLQTNLNLPYITADASGpKHLSMTIARSKLEELV 284
                                       ***************************************************************************** PP

                                       HHHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCG CS
                             HSP70 303 edllertlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgee 379
                                       +d+ler+  p+ +alkd+kl+k++i +++lvGG tR+P+vqe vk+++gk+ +++v+p e+va+GAA+qagvl g  
  gi|330507176|ref|YP_004383604.1| 285 ADVLERCRGPMIQALKDSKLEKSDIGKIILVGGPTRMPMVQEFVKNFLGKDIERGVDPMECVAMGAAIQAGVLGG-- 359
                                       ***************************************************************************.. PP

                                       CSHCCEEEEBESS-EEEEETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEEC CS
                             HSP70 380 evkdllllDvtpLslgietlggvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldg 456
                                       evkdllllDvtpLslgietlg v+tkliernttipt+ksq+f+taadnqt+ve++vlqger +++dn +lg+f+l g
  gi|330507176|ref|YP_004383604.1| 360 EVKDLLLLDVTPLSLGIETLGSVTTKLIERNTTIPTRKSQIFTTAADNQTSVEVNVLQGERPMAQDNVSLGRFTLVG 436
                                       ***************************************************************************** PP

                                       ESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH CS
                             HSP70 457 ippaprGvpqieVtfdidanGiltvsakdketgkeeeitieaseglseeeiekmvkdaeesaeedkkkkeaieakne 533
                                       ippaprG pqieVtfdidanGi++vsakd +t+ke++iti+a ++ls+e+i+  +kdae++a++d k+ke+ie kn 
  gi|330507176|ref|YP_004383604.1| 437 IPPAPRGIPQIEVTFDIDANGIIHVSAKDLATKKEQRITITAPHKLSQEDIDAKIKDAERFAADDLKRKEEIEVKNA 513
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
                             HSP70 534 aeelvyslekkleeeaekvseaekekvesaieeLkeeleeeekeeieakteelkkvvekiaeklye 599
                                       ae+l+y  ek l+e+++ +++++kek+e+ai++Lk++ ++ e++ei+akte+l+++++++ +++y+
  gi|330507176|ref|YP_004383604.1| 514 AESLIYASEKMLKEAGDIATSEQKEKIEKAISDLKNAQTGGEISEIKAKTESLQNAIYELSAAMYQ 579
                                       ************************************************************999986 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   4.0   2.2e-20     8e-17      73     317 ..      95     352 ..       2     357 .. 0.67
   2 ?   -3.8   0.1       1.2   4.2e+03      90     125 ..     468     503 ..     459     514 .. 0.68

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 2.2e-20
                                       HHHHHHHHHHHHHHTSS-SS--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS-EEE CS
                          MreB_Mbl  73 vaeellkyfikkvkkkkslskprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveepsgnmv 149
                                       + +++l+++ +++++  + s ++ vi+vP   ++ +r+A k+a + aG + v +i+ep aAA+  gl+    +  mv
  gi|330507176|ref|YP_004383604.1|  95 ISAQVLRKIKTDAETYLADSVDKAVITVPAYFNDNQRQATKDAGTIAGLEVVRIINEPTAAALAFGLDKVGEHKIMV 171
                                       334445555555555545578899********************************************999999*** PP

                                       EEE-SS-EEEEEEETTEEE.....EEEEES-SHHHHHHHHHHHHHHHHSEE--.....H........HHHHHHHHHH CS
                          MreB_Mbl 150 vdiGggttevavislggiv.....tsksvrvaGdeldeaiikyirkkynlliG.....e........rtaekikiei 208
                                        d+Gggt +v+++ +g+ v     ts   +++G ++d+ +++y+  +++   G     +        + +e  kie+
  gi|330507176|ref|YP_004383604.1| 172 FDLGGGTLDVTIMEIGEGVfevlsTSGDTQLGGRDMDDRLTNYVLDRFKQESGvdlrgDsmamqrlrEAVEVAKIEL 248
                                       ***************975522222456689**************999987666221112111111101223334444 PP

                                       -BSS--HHHHEEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGG CS
                          MreB_Mbl 209 gsavkeeeeekmeikGrdlvtglpkevevsseevrealkepvsaiveavkevLektppeLaadivdrgivltGGgal 285
                                       +s+ +++ +        d       ++++  ++++e +++++++    + ++L++ + e  +di +  i+l+GG + 
  gi|330507176|ref|YP_004383604.1| 249 SSVLQTNLNL--PYITADASGPKHLSMTIARSKLEELVADVLERCRGPMIQALKDSKLE-KSDIGK--IILVGGPTR 320
                                       4444433332..22333433344446778888888888888888888899999998888.578864..99******* PP

                                       SBTHHHHHHHHHSS-EEE-SSTTTHHHHHHHH CS
                          MreB_Mbl 286 lkgldkllseetglpvkvaedpltcvakGtgk 317
                                       +  +++++++ +g  ++ + dp++cva G+++
  gi|330507176|ref|YP_004383604.1| 321 MPMVQEFVKNFLGKDIERGVDPMECVAMGAAI 352
                                       *****************************975 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.2
                                       -SS--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEE CS
                          MreB_Mbl  90 slskprvvicvPsgiteverrAvkeaakkaGarevl 125
                                       + +++r+ i+ P+++++ +  A ++ a++  a++ +
  gi|330507176|ref|YP_004383604.1| 468 TKKEQRITITAPHKLSQEDIDAKIKDAERFAADDLK 503
                                       456778888888888877777766666666666655 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 !   20.4   0.0   9.3e-08   0.00033     140     196 ..     297     356 ..     234     357 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 9.3e-08
                            FGGY_C 140 ealekd..sgkpldrlavdGGgskndllmqllAdilgvpVerpkt.aeatalGaAilAav 196
                                       +al+++  +++++ +++++GG ++ ++++++  + lg+++er  +  e++a+GaAi A+v
  gi|330507176|ref|YP_004383604.1| 297 QALKDSklEKSDIGKIILVGGPTRMPMVQEFVKNFLGKDIERGVDpMECVAMGAAIQAGV 356
                                       444333668899******************************8888************97 PP

>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.1    0.0012       4.1       6      77 ..     467     543 ..     464     592 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                             DUF45   6 rvepdgsvevsaPkgvseeeiedfvkkkakwiekklakleer.akeaekelesgesfpllGkkyrlkvekgk..... 76 
                                         +++++++++aP+++s+e+i++ +k  +++  + l++ ee   k+a ++l   ++ +l  +   + + ++k     
  gi|330507176|ref|YP_004383604.1| 467 ATKKEQRITITAPHKLSQEDIDAKIKDAERFAADDLKRKEEIeVKNAAESLIYASEKML-KEAGDIATSEQKekiek 542
                                       5677799**********************************854444444443333333.33334444433322333 PP

                             DUF45  77 e 77 
                                        
  gi|330507176|ref|YP_004383604.1| 543 A 543
                                       1 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 ?    7.5   9.1    0.0013       4.7      62     161 ..     481     589 ..     458     599 .. 0.47

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0013
                              Vfa1  62 akkkkeleeeiekvkkeyeekqkkkkekekkkkekd....kkdkdkkkekekdkkkekek.........eeekkkel 125
                                       + ++++++ +i++ ++   +  k+k+e e k+   +    +++k  k+  +  ++++kek         + ++  e+
  gi|330507176|ref|YP_004383604.1| 481 KLSQEDIDAKIKDAERFAADDLKRKEEIEVKNAA-EsliyASEKMLKEAGDIATSEQKEKiekaisdlkNAQTGGEI 556
                                       2233336777777766666666666655544422.134543333333333333333333322222221122222233 PP

                              Vfa1 126 kkaeeeleekeeprvkkykLhkefyqsRlerkrqae 161
                                       ++ +++   +e+ +++ y+L+  +yq+  +++++++
  gi|330507176|ref|YP_004383604.1| 557 SEIKAK---TESLQNAIYELSAAMYQKAAQDQQAQQ 589
                                       333333...45555556********99888865554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1244  (0.0693848); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 4083.32
//
Query:       gi|330507177|ref|YP_004383605.1|  [L=180]
Description: co-chaperone GrpE [Methanosaeta concilii GP6]
Scores for complete 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-36  123.5   6.0    1.1e-35  122.7   6.0    1.3  1  GrpE      GrpE
  ------ inclusion threshold ------
      0.032   14.2   0.4      0.054   13.4   0.4    1.5  1  LMP       LMP repeated region
       0.15   12.1   1.0       0.32   11.1   1.0    1.5  1  DUF1664   Protein of unknown function (DUF1664)


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 !  122.7   6.0   1.9e-39   1.1e-35       3     166 .]      19     172 ..      12     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 1.9e-39
                                       ....CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              GrpE   3 neeeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleral 79 
                                       +ee+e +++++++ele +l e++   +e  ++l+r +a+++nl kr  +eke+  k+a ek++++LLpvlD+le a 
  gi|330507177|ref|YP_004383605.1|  19 EEEDESSLTARIDELEGKLVEMQILSEERLDQLMRCRADLDNLMKRSVREKEDTVKYASEKLVQKLLPVLDSLEQAA 95 
                                       46788899999999999999999999999************************************************ PP

                                       HC..HHH-HHHHHHHHHHHHHHHHHHHHHTT-EE---TTSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEE CS
                              GrpE  80 ksakeneeekslleGvemtlkqllkiLekhgvekiepkgepFDpnlheavstveddekeegtvvevvqkGYklkdrv 156
                                       k+           eG +  + qll +L  +g+++ie++g++FDp  hea+++v++d+ ee+ v e++qkGY +++rv
  gi|330507177|ref|YP_004383605.1|  96 KH----------DEGQKVLHMQLLGVLFTEGLVPIEAVGKKFDPYRHEALFQVKKDDLEEDIVAEEIQKGYLFNSRV 162
                                       *8..........48999************************************************************ PP

                                       EE-EEEEEEE CS
                              GrpE 157 lRpAmVkVsk 166
                                       +R ++V V+k
  gi|330507177|ref|YP_004383605.1| 163 IRFSKVAVNK 172
                                       ********97 PP

>> LMP  LMP repeated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   9.1e-06     0.054      44      95 ..      21      76 ..       6     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.1e-06
                               LMP 44 sakssLdakvteitkkLekFnkdkeakFkeLeqtRkdieeFl.kdvknnp...nYa 95
                                        +ssL+a++ e++ kL + +   e + ++L + R d+++ +   v++++   +Ya
  gi|330507177|ref|YP_004383605.1| 21 EDESSLTARIDELEGKLVEMQILSEERLDQLMRCRADLDNLMkRSVREKEdtvKYA 76
                                      5579**************************************44444333455454 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.0   5.3e-05      0.32      61     116 ..      23      79 ..       7      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.3e-05
                           DUF1664  61 krhLssridrvdkkldeqkeiskeikeevtevredlsei.gedvesvkeaveglesk 116
                                          L++rid+++ kl e++ +s+e  +++++ r dl+++ ++ v++ +++v+   +k
  gi|330507177|ref|YP_004383605.1|  23 ESSLTARIDELEGKLVEMQILSEERLDQLMRCRADLDNLmKRSVREKEDTVKYASEK 79 
                                       5689********************************985156677666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1217.33
//
Query:       gi|330507178|ref|YP_004383606.1|  [L=546]
Description: thermosome subunit beta [Methanosaeta concilii GP6]
Scores for complete 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-164  547.0  15.3   4.2e-164  546.8  15.3    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 !  546.8  15.3  2.3e-168  4.2e-164       1     490 [.      35     521 ..      35     522 .. 0.97

  Alignments for each domain:
  == domain 1  score: 546.8 bits;  conditional E-value: 2.3e-168
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++v+ttlGPkGmdKml++  g+ ++TnDGatil+e++ie+P+ak++ve+a++qd+e+GDGTtt+vi+ag+Lle+a
  gi|330507178|ref|YP_004383606.1|  35 VAEAVRTTLGPKGMDKMLIDGSGDATITNDGATILREMDIENPVAKMIVEVAKAQDDEIGDGTTTAVIIAGKLLEKA 111
                                       689************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       e l++++vhpt+i++gy++a++ka e Lk++a+++s    d+e+Llk+arts+++k t+   ++ls++ vdA +++ 
  gi|330507178|ref|YP_004383606.1| 112 EALLEQDVHPTVIVQGYKQAAAKAQEVLKKMAIDVSG---DQEMLLKIARTSIRGKGTEMALDRLSQISVDAARAVV 185
                                       *******************************555554...68*******************************7776 PP

                                       CCSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHH CS
                        Cpn60_TCP1 155 enekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeele 231
                                         e++   ++ik+v+i gg++e+s++  G+vl+k+ +sp+mpk+++na+++ll+ +Le +k  t++++++++a++l 
  gi|330507178|ref|YP_004383606.1| 186 GFEGKDIEENIKMVHIPGGRIEESSINYGIVLEKERTSPQMPKSIKNARIMLLEGTLELKKLGTDAKITITEAKNLS 262
                                       6778888899******************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC CS
                        Cpn60_TCP1 232 klekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpee 308
                                       ++ + eek+++e++++ii++g+nvv+c+kgi   a+ +la +gila+rrvk++dl+ la atGa++v ++++l pe+
  gi|330507178|ref|YP_004383606.1| 263 SFKEGEEKIIKEQVDAIIATGANVVFCEKGIGVFAQGYLANRGILAARRVKREDLKMLALATGAKLVGDVMQLRPED 339
                                       ***************************************************************************** PP

                                       -EEEEEEEECCETTCC.EEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHH CS
                        Cpn60_TCP1 309 lGtakkveeekigsek.ttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelela 384
                                       lG+a  vee+++g+ek ++++e+++++++ +i+l g++d+ l+e+era++d+lnvv  +i+++k+vpGGGa e+ +a
  gi|330507178|ref|YP_004383606.1| 340 LGSAALVEERRVGKEKqMIFVEGCEKARAISIILHGVSDQLLEEMERALDDSLNVVMDVIRSGKIVPGGGAPEILVA 416
                                       *************96616669******************************************************** PP

                                       HHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEE CS
                        Cpn60_TCP1 385 kklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvD 461
                                       + l++ya++++g+eqlai+afa+A e+ip tLaeN+G+dp + la lra++ +g+  +g+d++sg++ d++++gvv+
  gi|330507178|ref|YP_004383606.1| 417 ENLRQYASTLEGREQLAIRAFADAVEAIPFTLAENSGFDPVDSLAALRANQGEGK-IYGLDIASGKPADMMAQGVVE 492
                                       *************************************************999999.********************* PP

                                       EHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 462 plkvkrqalksAteaastiLrideiikak 490
                                       plkvk+qa+ksA+eaa+++Lr+d++i ak
  gi|330507178|ref|YP_004383606.1| 493 PLKVKTQAIKSAAEAATMVLRVDDVIAAK 521
                                       **************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 3984.96
//
Query:       gi|330507179|ref|YP_004383607.1|  [L=248]
Description: phosphate ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-30  104.4   0.0    9.6e-30  103.9   0.0    1.3  1  ABC_tran         ABC transporter
    2.6e-12   47.2   0.0    1.3e-05   25.1   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.1e-07   30.6   0.0    3.5e-06   26.6   0.0    2.1  1  SMC_N            RecF/RecN/SMC N terminal domain
    1.2e-05   25.2   0.0    1.8e-05   24.6   0.0    1.3  1  AAA_15           AAA ATPase domain
    3.9e-05   23.7   0.0    6.2e-05   23.0   0.0    1.4  1  Rad17            Rad17 P-loop domain
    5.3e-05   23.2   0.0    0.00012   22.0   0.0    1.5  1  RsgA_GTPase      RsgA GTPase
    0.00023   21.4   0.0     0.0006   20.1   0.0    1.9  1  AAA_22           AAA domain
     0.0004   21.0   0.2    0.00068   20.2   0.1    1.8  1  AAA_23           AAA domain
    0.00096   18.9   0.0     0.0018   17.9   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
     0.0011   19.4   0.0     0.0019   18.6   0.0    1.6  1  AAA_16           AAA ATPase domain
     0.0079   16.7   0.0      0.021   15.4   0.0    1.7  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.013   14.2   0.0      0.024   13.3   0.0    1.4  2  AAA_13           AAA domain
      0.014   15.2   0.0       0.72    9.6   0.0    2.1  2  IstB_IS21        IstB-like ATP binding protein
      0.019   15.4   0.0       0.41   11.1   0.0    2.3  2  AAA              ATPase family associated with various cellul
      0.022   14.9   0.0      0.035   14.3   0.0    1.5  1  AAA_33           AAA domain
      0.022   14.5   0.0      0.037   13.7   0.0    1.4  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.035   13.7   0.0      0.098   12.2   0.0    1.7  2  AAA_25           AAA domain
      0.079   12.9   0.1       0.36   10.7   0.1    2.0  1  ATPase_2         ATPase domain predominantly from Archaea
      0.099   12.3   0.0        1.5    8.5   0.0    2.0  2  AAA_30           AAA domain
       0.12   11.6   0.0       0.17   11.1   0.0    1.4  1  NB-ARC           NB-ARC domain
       0.13   12.0   0.0       0.25   11.0   0.0    1.5  2  AAA_24           AAA domain
       0.14   12.6   0.1       0.51   10.7   0.1    2.1  2  RNA_helicase     RNA helicase
       0.16   11.7   0.0       0.26   11.0   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.18   10.6   0.0       0.38    9.5   0.0    1.4  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 !  103.9   0.0   1.3e-32   9.6e-30       1     136 [.      20     172 ..      20     173 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 1.3e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqepql 70 
                                       lk++slk+ e +++a++G++G+GKSt++++l ++ +       eG++ +d+ d+    ++  +lrk+ig+++q+p+ 
  gi|330507179|ref|YP_004383607.1|  20 LKDISLKIPEKQITALIGPSGCGKSTFIRCLNRMNDLvtsvrIEGKVFYDDMDIYGkdTDVVELRKRIGMVFQKPNP 96 
                                       79********************************998999999*******9999887789999************** PP

                                       -TTSBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       fp + +++n           + ++ +e+ l++  l e   +++++ +  LSgGq+qr+++ar+l+ +p+++l+DEp+
  gi|330507179|ref|YP_004383607.1|  97 FPMS-IYDNiaygprihgqkNVSKIVERSLKESALWEEVSERLDQPALGLSGGQQQRLCIARTLAMRPDVILFDEPC 172
                                       ****.9*********9986555555******************9999*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   6.5e-07   0.00048       1      25 [.      32      56 ..      32      94 .. 0.76
   2 !   25.1   0.0   1.8e-08   1.3e-05     220     295 ..     128     200 ..     103     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.5e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                      +++liGp g+GKS+++++l  + +l
  gi|330507179|ref|YP_004383607.1| 32 ITALIGPSGCGKSTFIRCLNRMNDL 56
                                      79*****************999665 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.8e-08
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP...kllrrllellkelsrngaQvi 293
                                          ++e + + + pa  lS G+++ l+++  l+ ++   +++l+DEp + L+P     +++l+e lke+ +   Q+i
  gi|330507179|ref|YP_004383607.1| 128 SALWEEVSERLDQPALGLSGGQQQRLCIARTLAMRP---DVILFDEPCSALDPistGKIESLMESLKEEYT---QII 198
                                       555666777788899999*******99999999988...9*************999999999999988866...998 PP

                            AAA_21 294 lt 295
                                       +t
  gi|330507179|ref|YP_004383607.1| 199 VT 200
                                       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 !   26.6   0.0   4.7e-09   3.5e-06      23     204 ..      29     208 ..      17     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4.7e-09
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHC.CCCC.C--BTTCSSTTEEEEEEEEEETTEESSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrsek.lsdl.ihkskekasvkkaeveitfdnedkklkiekeev 97 
                                       +k++ta++Gp G+GKs ++  +  +    ++  +  +  ++d+ i+ +++     + ++ ++f++++       +++
  gi|330507179|ref|YP_004383607.1|  29 EKQITALIGPSGCGKSTFIRCLNRMNDLVTSVRIEGKVfYDDMdIYGKDTDVVELRKRIGMVFQKPNPFPMSIYDNI 105
                                       6889*****************95443333333333333134443444677777778999*******99966667777 PP

                                       EEEEEEETTSEEEEEETTEEE-H....HHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  98 sisrrvkrkgeseykingkevtk....kevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                           r+  +++ +  + +++ ++    +evse l +  +    LSgG+++ + +a  +A+   +p  + l+De  +a
  gi|330507179|ref|YP_004383607.1| 106 AYGPRIHGQKNVSKIV-ERSLKEsalwEEVSERLDQPAL---GLSGGQQQRLCIARTLAM---RPD-VILFDEPCSA 174
                                       7777777666644333.3333330113666666666666...59******9999988876...454.679******* PP

                                       S-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkeksknaQfivislreemlek 204
                                       LD   + k+ +l+++ +++   i+++++ ++ ++
  gi|330507179|ref|YP_004383607.1| 175 LDPISTGKIESLMESLKEEYTQIIVTHNMQQAAR 208
                                       ***************9999666777777666554 PP

>> AAA_15  AAA ATPase 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   1.8e-05      13      95 ..      19     124 ..      18     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.5e-08
                            AAA_15  13 slkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn.kkvikiekedleifeniseskdikIdvef.... 83 
                                       +lkd+++++ e+ +t liG+ ++GKS++++ l+ + +  ++   + +++ ++ d+  ++ +  + + +I + f    
  gi|330507179|ref|YP_004383607.1|  19 ALKDISLKIPEKqITALIGPSGCGKSTFIRCLNRMNDLVTSVRiEGKVFYDDMDIYGKDTDVVELRKRIGMVFqkpn 95 
                                       5899999998888***********************98766659899999999999999999999999999996666 PP

                            AAA_15  84 .................aekekakeyekt 95 
                                                         +k+ +k+ e++
  gi|330507179|ref|YP_004383607.1|  96 pfpmsiydniaygprihGQKNVSKIVERS 124
                                       66666666666666554222344444444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   8.4e-08   6.2e-05      32      69 ..      17      54 ..      15      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8.4e-08
                             Rad17 32 kewlkadvLesrkkriLLisGPsGCgkstvvkvLskel 69
                                      k++lk  +L+  +k+i  + GPsGCgkst ++ L +  
  gi|330507179|ref|YP_004383607.1| 17 KQALKDISLKIPEKQITALIGPSGCGKSTFIRCLNRMN 54
                                      68999999*999*********************98764 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.6e-07   0.00012      86     127 ..      16      58 ..       4      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.6e-07
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                       +k++l++++ ++ + ++++l+G+SG GKSt+i  l+  ++l t
  gi|330507179|ref|YP_004383607.1|  16 EKQALKDISLKIPEkQITALIGPSGCGKSTFIRCLNRMNDLVT 58 
                                       5788899998888779*****************9998766554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   8.1e-07    0.0006       5      35 ..      30      60 ..      27     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.1e-07
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeaka 35
                                      ++i++++G+sG+GK+t +r l + +d + + 
  gi|330507179|ref|YP_004383607.1| 30 KQITALIGPSGCGKSTFIRCLNRMNDLVTSV 60
                                      799*******************999866554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   9.1e-07   0.00068      15      40 ..      23      51 ..       4     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.1e-07
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAik 40
                                      i +   +k +t+++Gp G+GK+T+++++ 
  gi|330507179|ref|YP_004383607.1| 23 ISLkipEKQITALIGPSGCGKSTFIRCLN 51
                                      55566799*******************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 !   17.9   0.0   2.5e-06    0.0018      16      39 ..      24      47 ..      12      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                      +++i +k++t l+GpsG GKST++
  gi|330507179|ref|YP_004383607.1| 24 SLKIPEKQITALIGPSGCGKSTFI 47
                                      56677777**************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.5e-06    0.0019      22      51 ..      28      59 ..      17     209 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.5e-06
                            AAA_16 22 grpelvllsGesGvGKsslvrellr..alekd 51
                                      ++ +++ l+G+sG+GKs+ +r+l r   l ++
  gi|330507179|ref|YP_004383607.1| 28 PEKQITALIGPSGCGKSTFIRCLNRmnDLVTS 59
                                      445899*****************975533333 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   2.8e-05     0.021       3      44 ..      35      79 ..      34      95 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.8e-05
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpe 44
                                      l G++G+GK+t+ + L++++ +   +++ ++v+++++  ++ d +
  gi|330507179|ref|YP_004383607.1| 35 LIGPSGCGKSTFIRCLNRMNDLvtsVRIEGKVFYDDMDIYGKDTD 79
                                      89****************986678777777777777776666665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         4     3e+03      23      40 ..      37      54 ..      35      85 .. 0.77
   2 ?   13.3   0.0   3.3e-05     0.024     527     572 ..     163     204 ..     155     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4
                            AAA_13 23 GwNGaGKTtLSrllrsle 40
                                      G  G GK+t+ r l+ ++
  gi|330507179|ref|YP_004383607.1| 37 GPSGCGKSTFIRCLNRMN 54
                                      667999999988888764 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.3e-05
                            AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnle 572
                                         ++ +D P S LD  s   + sl++s     +++ Q+++ THn++
  gi|330507179|ref|YP_004383607.1| 163 PDVILFDEPCSALDPISTGKIESLMESLK---EEYTQIIV-THNMQ 204
                                       679*************************7...*****865.***97 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 ?    9.6   0.0   0.00096      0.72      44     120 ..      27     108 ..      17     130 .. 0.69
   2 ?    3.6   0.0     0.064        48     101     151 ..     155     205 ..     144     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00096
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialg.....veavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilD 115
                                       i +k+  +l+GpsG GKs +   l      v  vr + +v++  ++   +   + +   ++    ++   + + i D
  gi|330507179|ref|YP_004383607.1|  27 IPEKQITALIGPSGCGKSTFIRCLNrmndlVTSVRIEGKVFYDDMDIYGKDTDVVELRKRIGMVFQKPNPFPMSIYD 103
                                       55788899**********99888862222234566667777777666666666666666666666666666666666 PP

                         IstB_IS21 116 dlgll 120
                                       ++++ 
  gi|330507179|ref|YP_004383607.1| 104 NIAYG 108
                                       66665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.064
                         IstB_IS21 101 ralkrllkvdllilDd..lgllpldqaeaellfeviekryerrsiiitsnlpf 151
                                        a +  +++d+++ D+   +l p++  + e l+e +++ y    ii+t n++ 
  gi|330507179|ref|YP_004383607.1| 155 IARTLAMRPDVILFDEpcSALDPISTGKIESLMESLKEEYT--QIIVTHNMQQ 205
                                       445556789******9555899**************99996..5999999865 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 ?   11.1   0.0   0.00055      0.41       3      35 ..      35      68 ..      33     102 .. 0.70
   2 ?    2.2   0.0      0.31   2.3e+02      47      66 ..     151     170 ..     105     208 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00055
                                      EESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelg.vefleisgsell 35
                                      l+Gp G+GK+++++ + +  + v+ ++i+g+ + 
  gi|330507179|ref|YP_004383607.1| 35 LIGPSGCGKSTFIRCLNRMNDlVTSVRIEGKVFY 68
                                      89************98777545666666666665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.31
                                       HHHHHHHHHTS.TSEEEEEET CS
                               AAA  47 relfkeakeka.kpsilfiDE 66 
                                       + l   a++ a +p ++++DE
  gi|330507179|ref|YP_004383607.1| 151 QRLC-IARTLAmRPDVILFDE 170
                                       3333.4566667799999999 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.7e-05     0.035       3      37 ..      34      71 ..      32     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.7e-05
                            AAA_33  3 llvGlpGsGKstlaerllkklg...avllssdtlrrrl 37
                                       l+G++G+GKst+++ l + ++    v+++  ++++ +
  gi|330507179|ref|YP_004383607.1| 34 ALIGPSGCGKSTFIRCLNRMNDlvtSVRIEGKVFYDDM 71
                                      589************99887776666777666666555 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     5e-05     0.037       3      51 ..      34      81 ..      32      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5e-05
                               PRK  3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflr.ldraekdlele 51
                                      ++ g+SG+Gk+t+ r l+ +     v+++ ieg++f   +d+  kd+ + 
  gi|330507179|ref|YP_004383607.1| 34 ALIGPSGCGKSTFIRCLNRMND--LVTSVRIEGKVFYDdMDIYGKDTDVV 81
                                      788************9987655..89999999999874266666666555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013     0.098      30      50 ..      27      47 ..      17      52 .. 0.90
   2 ?   -1.9   0.0       2.8   2.1e+03     112     147 ..     163     199 ..     132     211 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +p++ +++l+G++g+GK+t+ 
  gi|330507179|ref|YP_004383607.1| 27 IPEKQITALIGPSGCGKSTFI 47
                                      899****************96 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                            AAA_25 112 eslpLfak..drggtlltadvdaleaaieevegvrlvv 147
                                        ++ Lf++   + +++ t++++ l++ ++e e  + +v
  gi|330507179|ref|YP_004383607.1| 163 PDVILFDEpcSALDPISTGKIESLMESLKE-EYTQIIV 199
                                       455555442234455578888888888888.6566666 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00048      0.36      17      57 ..      29      71 ..      17     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00048
                          ATPase_2 17 repneiyfiYGpegsGKtaLlkeiienledkdk.....yviyyial 57
                                      +  ++i  + Gp g+GK+++++ + ++ +d+        +++y+++
  gi|330507179|ref|YP_004383607.1| 29 E--KQITALIGPSGCGKSTFIRCL-NRMNDLVTsvrieGKVFYDDM 71
                                      3..6888999**********9854.333333322344556666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0     0.002       1.5      18      40 ..      30      52 ..      17      61 .. 0.87
   2 ?    1.8   0.0      0.23   1.7e+02      89     133 ..     162     211 ..     119     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.002
                            AAA_30 18 drvavltGpAGtGKttalkalre 40
                                      +++++l Gp G GK+t ++ l++
  gi|330507179|ref|YP_004383607.1| 30 KQITALIGPSGCGKSTFIRCLNR 52
                                      57999*************98876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.23
                            AAA_30  89 g.tllivDEagmv....dtkqlaallkaaekagakvilvGDerQlasVea 133
                                       + ++++ DE   +    +t ++++l+++++++ +++i+    +Q a ++ 
  gi|330507179|ref|YP_004383607.1| 162 RpDVILFDEPCSAldpiSTGKIESLMESLKEEYTQIIVTHNMQQAARISD 211
                                       33788888876666777999999999999998899998888888777665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00022      0.17      16      76 ..      28     138 ..      16     213 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                                       TTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE.................................. CS
                            NB-ARC  16 delqslvvalvGmgGvGKttlakqilnksdeveg.rFdsvawv.................................. 57 
                                        e q  + al G  G+GK+t ++  ++  d v++ r ++ ++                                   
  gi|330507179|ref|YP_004383607.1|  28 PEKQ--ITALIGPSGCGKSTFIRCLNRMNDLVTSvRIEGKVFYddmdiygkdtdvvelrkrigmvfqkpnpfpmsiy 102
                                       4555..99**************9999998888776666666656666666666666666666666666666666666 PP

                                       .................EEESXXHHHHHHHXXHHHH CS
                            NB-ARC  58 .................vvsktdkseeiletilkeL 76 
                                                         v ++ k++ ++e++ ++L
  gi|330507179|ref|YP_004383607.1| 103 dniaygprihgqknvskIVERSLKESALWEEVSERL 138
                                       666666666666655555555555555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00034      0.25       3      22 ..      31      50 ..      29      71 .. 0.86
   2 ?   -3.3   0.0         8     6e+03      31      55 ..     168     193 ..     156     210 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                            AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                      +  +++Gpsg GK+t+++ l
  gi|330507179|ref|YP_004383607.1| 31 QITALIGPSGCGKSTFIRCL 50
                                      56789************988 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8
                            AAA_24  31 tekGlksldadkfpdiesw.edflde 55 
                                       +++   +ld++   +ies+ e +++e
  gi|330507179|ref|YP_004383607.1| 168 FDEPCSALDPISTGKIESLmESLKEE 193
                                       55555555555555555330222333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00069      0.51       3      19 ..      35      51 ..      33      81 .. 0.82
   2 ?   -2.1   0.0       6.5   4.9e+03      52      86 ..      65      99 ..      50     104 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00069
                      RNA_helicase  3 lyGpsgeGKStlakeLa 19
                                      l Gpsg+GKSt+++ L 
  gi|330507179|ref|YP_004383607.1| 35 LIGPSGCGKSTFIRCLN 51
                                      78**********98763 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.5
                      RNA_helicase 52 vvvidDfgqvkdeenpsdlaelirlvsstpyplnm 86
                                       v +dD+    ++++  +l   i++v  +p p +m
  gi|330507179|ref|YP_004383607.1| 65 KVFYDDMDIYGKDTDVVELRKRIGMVFQKPNPFPM 99
                                      56777777666553344777777777777777777 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00035      0.26       7      33 ..      39      59 ..      35      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                   Viral_helicase1  7 pGcGKStlirkllrts.liltvnrptae 33
                                       GcGKSt ir l r++ l        + 
  gi|330507179|ref|YP_004383607.1| 39 SGCGKSTFIRCLNRMNdL-------VTS 59
                                      5************99532.......233 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00051      0.38     251     285 ..      19      53 ..      17      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00051
                          PPV_E1_C 251 alkefLkgvPkknclvllGppntGkslfamslikf 285
                                       alk+   ++P k+   l+Gp+  Gks+f   l+++
  gi|330507179|ref|YP_004383607.1|  19 ALKDISLKIPEKQITALIGPSGCGKSTFIRCLNRM 53 
                                       678888899********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 1693.23
//
Query:       gi|330507180|ref|YP_004383608.1|  [L=217]
Description: phosphate transport system regulatory protein PhoU [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.5e-43  144.7  11.6    8.4e-22   77.4   3.8    2.1  2  PhoU        PhoU domain
     0.0015   18.0   0.9     0.0094   15.4   0.1    2.0  2  DUF4618     Domain of unknown function (DUF4618)
  ------ inclusion threshold ------
      0.089   12.5   1.0       0.12   12.1   1.0    1.3  1  Hema_stalk  Influenza C hemagglutinin stalk


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   3.8   1.4e-25   8.4e-22       2      88 ..      20     106 ..      19     107 .. 0.97
   2 !   72.4   1.0   5.1e-24   3.1e-20       1      88 [.     120     204 ..     120     205 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 1.4e-25
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERi 78 
                                       +++a+ v e++++++ al++ +++lare+i++d+e+d+l  +ie+ ++e+l  +qp+a+dlr+++++l+i  dlERi
  gi|330507180|ref|YP_004383608.1|  20 KDLADHVGEAIEKSVIALSDSNVDLAREIIKNDQEVDDLSIKIENLCMELLVLQQPMARDLRRIIGILKIGIDLERI 96 
                                       6899***********************************************99************************ PP

                                       HHHHHHHHHH CS
                              PhoU  79 gDhavniaer 88 
                                       gD av+ia+ 
  gi|330507180|ref|YP_004383608.1|  97 GDLAVDIARV 106
                                       ********96 PP

  == domain 2  score: 72.4 bits;  conditional E-value: 5.1e-24
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlER 77 
                                       + rmaei+++ml++++eal ++d ++ar++ + d eid l+ + +++ll+++  r ++   ++e +sll++ r+lER
  gi|330507180|ref|YP_004383608.1| 120 IPRMAEISRKMLRESMEALMNDDADTARQITKWDYEIDGLYVKARDKLLKIIIDRPEV---IKEGTSLLMVNRHLER 193
                                       579**********************************************999777777...779************* PP

                                       HHHHHHHHHHH CS
                              PhoU  78 igDhavniaer 88 
                                        gDh++ni+e 
  gi|330507180|ref|YP_004383608.1| 194 TGDHICNICET 204
                                       *********96 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.6e-06    0.0094     163     230 ..      16      84 ..       7      86 .. 0.91
   2 ?    1.0   0.1     0.038   2.3e+02     122     164 ..      96     136 ..      93     166 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-06
                           DUF4618 163 ekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqae.eprevi 230
                                       + l+k la ++ +a+++++ + + +n +l++ei k+ +++++l  +i++L  e+  Lq+ ++ + r +i
  gi|330507180|ref|YP_004383608.1|  16 KSLTKDLADHVGEAIEKSVIALSDSNVDLAREIIKNDQEVDDLSIKIENLCMELLVLQQPMArDLRRII 84 
                                       789999***************************************************997665999887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.038
                           DUF4618 122 Ianlvrqlqqlkdsqqdeldeleelikevleklskkiqkkkek 164
                                       I  l+ ++  ++++ ++e+ +le + ++  +++s+k+ +++ +
  gi|330507180|ref|YP_004383608.1|  96 IGDLAVDIARVAAQSHNEITKLEFIPRM--AEISRKMLRESME 136
                                       5667777777777777777777755443..3444444333333 PP

>> Hema_stalk  Influenza C hemagglutinin stalk
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.0     2e-05      0.12      37     132 ..      19     113 ..      10     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                        Hema_stalk  37 tkesaekgfekigndiqilrsstniaieklndrishdeqairdltleienarseallgelgiiral..lvgnisigl 111
                                       tk+ a++  e i + +  l s +n+    l   i +++q + dl+++ien   e l+ +  + r l  ++g + ig+
  gi|330507180|ref|YP_004383608.1|  19 TKDLADHVGEAIEKSVIAL-SDSNV---DLAREIIKNDQEVDDLSIKIENLCMELLVLQQPMARDLrrIIGILKIGI 91 
                                       5555555555555554333.34444...3566788999************************99986679*99**99 PP

                        Hema_stalk 112 q.eslwelaseitnragdlave 132
                                       + e + +la +i+  a +   e
  gi|330507180|ref|YP_004383608.1|  92 DlERIGDLAVDIARVAAQSHNE 113
                                       7588999999999888765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1508.69
//
Query:       gi|330507181|ref|YP_004383609.1|  [L=334]
Description: phosphate regulatory protein-like protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-22   78.8  10.9    1.2e-18   67.3   2.3    2.4  2  PhoU            PhoU domain
    0.00013   21.8   0.0    0.00039   20.3   0.0    1.9  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.023   14.2   4.5      0.039   13.5   4.5    1.3  1  PSY3            Shu complex component Psy3, DNA-binding descr
      0.039   12.5   0.1      0.055   12.0   0.1    1.2  1  Peptidase_C37   Southampton virus-type processing peptidase
       0.11   12.8   0.0        0.2   12.0   0.0    1.4  1  DrsE            DsrE/DsrF-like family
       0.12   12.1   1.1         17    5.2   0.1    2.6  2  DUF2299         Uncharacterized conserved protein (DUF2299)


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 !   67.3   2.3     4e-22   1.2e-18       1      88 [.     136     226 ..     136     227 .. 0.87
   2 !   16.3   1.6   3.3e-06    0.0099       4      88 ..     245     320 ..     242     321 .. 0.69

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 4e-22
                                       HHHHHHHHHHHHHHHHHHHHCT-H.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HGG-SHHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdt.elarevierddeidrlekeiersllealak..rqplaedlrellsllriard 74 
                                       lrr+  +v++m++d+ ++l +++  ela +vi+rdd++drl  +i+r+  e+l +   ++++++   +++++++a++
  gi|330507181|ref|YP_004383609.1| 136 LRRIRTVVKSMIHDSFTSLLNNNQdELAMDVIQRDDDVDRLNLLISRQFTEILRTgsVKQETQNPIHAFNYMQAASN 212
                                       6788999***********9999744***********************988887745333333677889******** PP

                                       HHHHHHHHHHHHHH CS
                              PhoU  75 lERigDhavniaer 88 
                                       lERi+Dha +ia++
  gi|330507181|ref|YP_004383609.1| 213 LERIADHAHRIAQI 226
                                       ************98 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.3e-06
                                       HHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HGG-SHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   4 maeiveemlddalealeekdtelarevierddeidrlekeiersllealak.rqplaedlrellsllriardlERig 79 
                                       m       +dda++ l + + + a+e+i++ +ei +   +i    ++  +  ++++   l++    l +a +lER+ 
  gi|330507181|ref|YP_004383609.1| 245 MEVQLCGFIDDAISYLLQTNSDKANEMIDLIREIQKSAARI---TVTSDSLgKSEM---LER----LVLAASLERMF 311
                                       5556667899**********9***99986655555555555...333333313333...333....5589******* PP

                                       HHHHHHHHH CS
                              PhoU  80 Dhavniaer 88 
                                       D++ ni e 
  gi|330507181|ref|YP_004383609.1| 312 DYIMNIGEL 320
                                       ******996 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.3e-07   0.00039       2      44 ..       9      52 ..       8      54 .. 0.88
   2 ?   -1.8   0.0       1.1   3.3e+03      15      28 ..      55      70 ..      53      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCHHS CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgd.kiilrplksl 44
                                      ++ ++ +v++Pk ++ ++gi +G+ v + + ++  + l+  +s+
  gi|330507181|ref|YP_004383609.1|  9 TGKSTFIVSLPKIWATKNGIAAGSIVYINQGDNgALTLSTDRSE 52
                                      78899***********************8888888888877766 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                      CHHHCCEEC..TCEEE CS
                    MazE_antitoxin 15 vrfelgire..Gdeve 28
                                      +r +l+i e  Gd+++
  gi|330507181|ref|YP_004383609.1| 55 LRVKLDIGEktGDDLI 70
                                      5557899999999986 PP

>> PSY3  Shu complex component Psy3, DNA-binding description
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   4.5   1.3e-05     0.039      23     165 ..     125     282 ..     110     293 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                              PSY3  23 lkknedenekkvelihlieksfklskikrkllvkv........reesedngsiliiDivsiwkqlle......sqae 85 
                                       l+++e ++ek +++i ++ ks+ +  ++  l ++         +   +d+   l+  i+  ++++l+      + ++
  gi|330507181|ref|YP_004383609.1| 125 LSSEELQSEKALRRIRTVVKSMIHDSFTSLLNNNQdelamdviQ--RDDDVDRLNLLISRQFTEILRtgsvkqETQN 199
                                       44555667788888888888865555555554333333433242..3333333333346677777767775545667 PP

                              PSY3  86 skksvsylnsls.ilnvdgLinfLeqlldspleALkrcqqedsldk..qLsgilidNlSylssepksklklLlkllk 159
                                         + ++y++ +s + ++ +  + ++q++ +   +L    +e+ +d   qL g + d +Syl + +++k+++++ l++
  gi|330507181|ref|YP_004383609.1| 200 PIHAFNYMQAASnLERIADHAHRIAQIAREYNCTLADDLKEELMDMevQLCGFIDDAISYLLQTNSDKANEMIDLIR 276
                                       778899999887245789999999999999999999766665555555***************************** PP

                              PSY3 160 klrktf 165
                                       +++k+ 
  gi|330507181|ref|YP_004383609.1| 277 EIQKSA 282
                                       ***975 PP

>> Peptidase_C37  Southampton virus-type processing peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.8e-05     0.055      64     143 ..     198     282 ..     172     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                                       XXXXXXXXXXXXXXXXXXX.X.XXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXX CS
                     Peptidase_C37  64 knrvsafkklaadnglgll.e.tarlGk..klkgvttieelksalkdvkiaecqivyrgakyslesdg.kgsvsvek 135
                                       +n + af+ + a ++l  + + + r+ +  +  ++t  ++lk+ l d++++ c  + ++  y l+++  k + +++ 
  gi|330507181|ref|YP_004383609.1| 198 QNPIHAFNYMQAASNLERIaDhAHRIAQiaREYNCTLADDLKEELMDMEVQLCGFIDDAISYLLQTNSdKANEMIDL 274
                                       67899999997766665441324566651145689999**************************9986267778887 PP

                                       ..XXXXXX CS
                     Peptidase_C37 136 vevkesql 143
                                       +++ ++ +
  gi|330507181|ref|YP_004383609.1| 275 IREIQKSA 282
                                       66544433 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.9e-05       0.2      17      87 ..     217     298 ..     197     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.9e-05
                                       HHHHHHHHHHHHTTT.............-EEE.EEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHH CS
                              DrsE  17 arealelalaaaalg.............hevs.vffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgq 79 
                                       a+ a+++a++a++++              ev    f++d++ +ll+   +n  + +++++l+++ ++  +++ v   
  gi|330507181|ref|YP_004383609.1| 217 ADHAHRIAQIAREYNctladdlkeelmdMEVQlCGFIDDAISYLLQ---TNSDKANEMIDLIREIQKSAARITVTSD 290
                                       56689999999999999999999999999999889***********...88888999**********99***99999 PP

                                       HHHHTT-- CS
                              DrsE  80 aakargld 87 
                                       ++ +  + 
  gi|330507181|ref|YP_004383609.1| 291 SLGKSEML 298
                                       98877665 PP

>> DUF2299  Uncharacterized conserved protein (DUF2299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0071        21      98     131 ..     114     146 ..     105     148 .. 0.88
   2 ?    5.2   0.1    0.0056        17      60      96 ..     218     254 ..     210     288 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0071
                                       S--.-EEEEEEEEEGGG--HHHHHHHHHHHHHHH CS
                           DUF2299  98 eelpqsiqvskeiykdgltknelldavkrvrnak 131
                                       e++ +++++++ + +++l+ ++ l  +++v+++ 
  gi|330507181|ref|YP_004383609.1| 114 ETI-NKVVIQDLLSSEELQSEKALRRIRTVVKSM 146
                                       446.89************************9986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0056
                                       HHHHHHHHS-HHHHHHHHHHHHHHHTTTT-EEEEE-T CS
                           DUF2299  60 ehkkalsslkeeerkeflselkrdLlrlcvdfqlipq 96 
                                       +h  ++ ++ +e +  +  +lk++L++++v+    ++
  gi|330507181|ref|YP_004383609.1| 218 DHAHRIAQIAREYNCTLADDLKEELMDMEVQLCGFID 254
                                       7999*************************98655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.36s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 1794.98
//
Query:       gi|330507182|ref|YP_004383610.1|  [L=151]
Description: methylated-DNA--protein-cysteine methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-28   97.5   0.0    5.4e-28   97.0   0.0    1.2  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   0.0     3e-32   5.4e-28       1      80 [.      65     143 ..      65     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 3e-32
                                       HHHHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHH CS
                     DNA_binding_1   1 afqqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLe 77 
                                       +fq+rV++++r I +Gk+ tYge+A l++ pk+araVg+a+a np+ailvPcHRVv+++g lgg+a+gle k+++L+
  gi|330507182|ref|YP_004383610.1|  65 DFQKRVYSVVRGIGRGKTLTYGEVAFLAQCPKGARAVGSAMATNPFAILVPCHRVVARKG-LGGFAWGLEVKERMLA 140
                                       59**********************************************************.**************** PP

                                       HTT CS
                     DNA_binding_1  78 aEg 80 
                                        E+
  gi|330507182|ref|YP_004383610.1| 141 LER 143
                                       995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 819.02
//
Query:       gi|330507183|ref|YP_004383611.1|  [L=176]
Description: phosphodiesterase [Methanosaeta concilii GP6]
Scores for complete 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-26   91.7   0.0    6.2e-26   91.6   0.0    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    0.00045   20.8   0.9     0.0012   19.4   0.9    1.7  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.0   6.9e-30   6.2e-26       1     164 [.       1     156 [.       1     157 [. 0.90

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 6.9e-30
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela.pvlaVrGNnDeevveedvlreaae 76 
                                       M ++i+SD H++++ ++ +l+ +++ gv +i++aGD+  +    +++++ l+ p++ V+GNnD    +  +++e+a+
  gi|330507183|ref|YP_004383611.1|   1 MLIGIMSDAHDRFQGVKDALRVFSSRGVFMILFAGDM--IGSGNCYTFEGLNiPIKLVYGNND--GDRVGLAKEFAR 73 
                                       99**********************************8..55557788888888**********..545678899999 PP

                     Metallophos_2  77 lgtdlp.eeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdg 152
                                       +g+++  +  e+e++g k++l+Hg+    ++ l +++ + ++  dv+v GH H+ ev+ +g +l+vnPG++ +  +g
  gi|330507183|ref|YP_004383611.1|  74 VGGEYLgDFGEVEVDGLKIALMHGT----EEPLVRAVLA-SQLYDVLVRGHNHIFEVSSHGRTLLVNPGEIWGHLTG 145
                                       999997799***************9....6777777776.56777*****************************999 PP

                     Metallophos_2 153 dpetyaildtde 164
                                          t+ai+dt++
  gi|330507183|ref|YP_004383611.1| 146 YS-TVAIFDTTS 156
                                       98.******987 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.9   1.4e-07    0.0012       3     123 ..       3      98 ..       1     143 [. 0.66

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.4e-07
                                       EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS.... CS
                       Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe.... 75 
                                       i +++D H      +++ ++++l+ + ++ ++ ++l+aGD +  g+  + ++ l        ip+ l+ GN +    
  gi|330507183|ref|YP_004383611.1|   3 IGIMSDAH-----DRFQGVKDALRVFSSR-GVFMILFAGDMIGSGNCYT-FEGL----N---IPIKLVYGNNDgdrv 65 
                                       889*****.....*************999.***************6666.4444....4...5899*******3333 PP

                                       CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE CS
                       Metallophos  76 gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg 123
                                       g            ++f+++   + + f+ + + +     lk+ l+hG 
  gi|330507183|ref|YP_004383611.1|  66 G----------LAKEFARVGGEYLGDFGEVEVDG-----LKIALMHGT 98 
                                       1..........23333444444444444444444.....355555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); 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 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1181.63
//
Query:       gi|330507184|ref|YP_004383612.1|  [L=72]
Description: hypothetical protein MCON_1047 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       540  (0.0301188); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 489.27
//
Query:       gi|330507185|ref|YP_004383613.1|  [L=165]
Description: hypothetical protein MCON_1048 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); 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:                         0  (0); expected 0.2 (1e-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: 1184.19
//
Query:       gi|330507186|ref|YP_004383614.1|  [L=888]
Description: hypothetical protein MCON_1050 [Methanosaeta concilii GP6]
Scores for complete 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-08   31.8   0.1       0.31   10.6   0.0    4.9  5  SH3_6      SH3 domain (SH3b1 type)
    6.7e-06   26.1   0.0    1.4e-05   25.0   0.0    1.4  1  Trypsin    Trypsin
    0.00024   22.0   0.2     0.0031   18.4   0.0    2.9  2  Trypsin_2  Trypsin-like peptidase domain
      0.005   16.6   5.2       0.86    9.5   0.1    5.6  7  PapC_C     PapC C-terminal domain


Domain annotation for each model (and alignments):
>> SH3_6  SH3 domain (SH3b1 type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.11   5.1e+02      23      43 ..     198     218 ..     195     223 .. 0.82
   2 !    6.3   0.0    0.0015       6.8      22      46 ..     299     323 ..     296     326 .. 0.90
   3 !   10.6   0.0   6.9e-05      0.31      20      46 ..     348     374 ..     345     377 .. 0.88
   4 !    7.0   0.0   0.00091       4.1      20      46 ..     399     425 ..     396     428 .. 0.88
   5 ?   -3.2   0.1       1.4   6.4e+03      38      53 .]     789     804 ..     787     804 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.11
                                       E-TT-EEEEEEE-TTSSEEEE CS
                             SH3_6  23 lkagtPVlilhaSkDgaWlfV 43 
                                       + +g+PV ++ + +++  +fV
  gi|330507186|ref|YP_004383614.1| 198 VEPGSPVSVASRGANNLDVFV 218
                                       89********99988776666 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0015
                                       EE-TT-EEEEEEE-TTSSEEEEE-S CS
                             SH3_6  22 alkagtPVlilhaSkDgaWlfVets 46 
                                       a+ +g+PV +  +S+++  +fV+ s
  gi|330507186|ref|YP_004383614.1| 299 AVDPGSPVSVVSRSANKLDVFVTGS 323
                                       799**************99999865 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 6.9e-05
                                       EEEE-TT-EEEEEEE-TTSSEEEEE-S CS
                             SH3_6  20 eSalkagtPVlilhaSkDgaWlfVets 46 
                                       + a+ +g+PV +  +S+D+  +fV+ s
  gi|330507186|ref|YP_004383614.1| 348 NNAVDPGSPVSVVSRSADKLDVFVTGS 374
                                       679****************99999866 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.00091
                                       EEEE-TT-EEEEEEE-TTSSEEEEE-S CS
                             SH3_6  20 eSalkagtPVlilhaSkDgaWlfVets 46 
                                       + a+ +g+PV +  + +D+  +fV+ s
  gi|330507186|ref|YP_004383614.1| 399 NNAVDPGSPVSVVSRGADKLDVFVTGS 425
                                       679****************99999866 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 1.4
                                       SSEEEEE-SS-EEEEE CS
                             SH3_6  38 gaWlfVetsfasGWve 53 
                                       + W+f   +  + Wv+
  gi|330507186|ref|YP_004383614.1| 789 QTWIFAVDEKGALWVR 804
                                       68***99999999996 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   3.1e-09   1.4e-05      26     196 ..       4     178 ..       2     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.1e-09
                                       EEEEEEEETTEEEEEGGGTTT..GGGEEEEESE.SBTTSCTTTEEEEEEEEEEEETTEBTTTT..TTTEEEEEESSS CS
                           Trypsin  26 lCgGslisenwvlTAaHCvsn..asdvkvvlge.hnlkksegkeqklkvekvivhpnynpstl..dnDiallklkep 97 
                                        C+++li+++ ++ AaHC+    + +++  l    n++ ++++ q + +++++v ++++        D+++ +l+++
  gi|330507186|ref|YP_004383614.1|   4 GCTATLIDSRHIVAAAHCFCYddTGSWQNNLFFyPNFNPNRTNTQSFAIDRAVVGTRVETGGEfqASDWGIGHLAKD 80 
                                       5*******************9897788885555599***************999999998884469*********** PP

                                       STSBSSBHCCBBCS...TTHTTSTTTEEEEEESSBSSTSS.BSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEEST CS
                           Trypsin  98 vklgdtvrpiclpa...assslpvgttclvsGwgrtkekg.ksdtlqevevpvvsretcksaykgkvtenmlcagak 170
                                       v+  ++   +c+ +   + +s+  g+  +  G+g+    g ++   +    p++ + +ck +   k+ +++l  +  
  gi|330507186|ref|YP_004383614.1|  81 VTDFPALPIACILTvpaNVNSSGYGRDLSFFGMGQAPPGGsSKMGCNVWWQPALVDPECKVY---KIDQDQLFFDC- 153
                                       99999999999888443222235555555666666555553233333333345555566663...48999999999. PP

                                       TSSSBCTTTTTTSEEEETTT...EEEEEE CS
                           Trypsin 171 eggkdacqGDSGGPlvcsdg...elvGiv 196
                                           ++  G+SG+P++ + g   +l+G++
  gi|330507186|ref|YP_004383614.1| 154 ----ATVGGNSGSPVLYKIGnnhFLAGVI 178
                                       ....9999*******99888788999987 PP

>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     7e-07    0.0031       1     141 [.       5     165 ..       5     171 .. 0.67
   2 ?   -0.4   0.0      0.42   1.9e+03      28     112 ..     633     730 ..     587     750 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7e-07
                         Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpak......vvaadp.......elDlAllkvss 64 
                                       +++ l++s++ i+ +aH++  +d+++  +   + +  ++++r+++ +      vv++         ++D  +  +  
  gi|330507186|ref|YP_004383614.1|   5 CTATLIDSRH-IVAAAHCFCYDDTGSW-QNNLFFYPNFNPNRTNTQSfaidraVVGTRVetggefqASDWGIGHL-A 78 
                                       58899*****.********99999999.6666666666666666666444444333333666677666*******.* PP

                         Trypsin_2  65 deraglpplplgpsealkggepvyvvGyp.......lggeksg.........svssGivsgvvesesaasgegesfl 125
                                       ++ +++p+lp+++   l +  +v   Gy+       +g+ ++g         +++   v   ++        + + l
  gi|330507186|ref|YP_004383614.1|  79 KDVTDFPALPIAC--ILTVPANVNSSGYGrdlsffgMGQAPPGgsskmgcnvWWQPALVDPECK----VYKIDQDQL 149
                                       **********999..3333336777777433333332333322444445666666666666666....555555566 PP

                         Trypsin_2 126 qtdaatspGsSGGplf 141
                                         d+at +G+SG+p++
  gi|330507186|ref|YP_004383614.1| 150 FFDCATVGGNSGSPVL 165
                                       78888888*******8 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.42
                         Trypsin_2  28 kaikkkveeagadgrevpakvvaadpel..DlAllkvssderaglpplplgpsealkggepvyvvGyp......... 93 
                                       ++ k +v ++ + g+ ++ +v +++ ++    + +++   ++   ++l ++   +++g ++++vvG           
  gi|330507186|ref|YP_004383614.1| 633 TNAKPQVVVTSEAGKLYTRAVSKSS-DSwnGWTTIDL---PAGVTEALDVDAAYDSEGNNQIFVVGDDgnlytrgri 705
                                       5556666666777777777777776.44467777777...6666677778887788888889999873223333332 PP

                         Trypsin_2  94 lggeksg...........svssGivsgvve 112
                                       +                  ++sG++++v+ 
  gi|330507186|ref|YP_004383614.1| 706 N-----KepdsawkgwekLTASGSIRKVTA 730
                                       0.....023333333333566666666655 PP

>> PapC_C  PapC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.052   2.3e+02      20      39 ..     206     229 ..     197     235 .. 0.70
   2 ?    0.7   0.0       0.1   4.6e+02      15      37 ..     252     278 ..     250     283 .. 0.80
   3 ?   -3.9   0.1       2.8   1.3e+04      22      37 ..     312     329 ..     307     331 .. 0.68
   4 ?   -0.1   0.0      0.19   8.3e+02      24      41 ..     467     486 ..     460     488 .. 0.70
   5 ?   -2.5   0.0         1   4.5e+03      23      42 ..     636     655 ..     628     657 .. 0.74
   6 !    9.5   0.1   0.00019      0.86      19      39 ..     682     703 ..     674     708 .. 0.82
   7 ?   -2.0   0.0      0.71   3.2e+03      23      40 ..     788     806 ..     782     811 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.052
                                       ETTSSS....-EEB-CCCEEEEEC CS
                            PapC_C  20 deengk....vgiVgqgGqvylrg 39 
                                        ++ g     v++Vg +G +y  +
  gi|330507186|ref|YP_004383614.1| 206 VASRGAnnldVFVVGKDGGIYTAA 229
                                       44444444779*********9876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.1
                                       T-EEEETTSSS....-EEB-CCCEEEE CS
                            PapC_C  15 GAevtdeengk....vgiVgqgGqvyl 37 
                                       G++v+  + g     +++Vg++G +y 
  gi|330507186|ref|YP_004383614.1| 252 GSSVSVTSRGAdwldIFVVGNDGGIYT 278
                                       67777777777788789*******996 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 2.8
                                       TSSS..-EEB-CCCEEEE CS
                            PapC_C  22 engk..vgiVgqgGqvyl 37 
                                       + +k  v++ g +G +y 
  gi|330507186|ref|YP_004383614.1| 312 SANKldVFVTGSDGGIYT 329
                                       355556899999999986 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.19
                                       SS..-EEB-CCCEEEEECE- CS
                            PapC_C  24 gk..vgiVgqgGqvylrglp 41 
                                       +k  +++Vg +G+v ++g +
  gi|330507186|ref|YP_004383614.1| 467 DKldIFVVGPDGKVQANGWE 486
                                       334579********988866 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 1
                                       SSS-EEB-CCCEEEEECE-S CS
                            PapC_C  23 ngkvgiVgqgGqvylrglpd 42 
                                       + +v +  + G++y r++++
  gi|330507186|ref|YP_004383614.1| 636 KPQVVVTSEAGKLYTRAVSK 655
                                       4457889999****999876 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.00019
                                       EETTSSS.-EEB-CCCEEEEEC CS
                            PapC_C  19 tdeengk.vgiVgqgGqvylrg 39 
                                       +d+e+++ +++Vg++G++y rg
  gi|330507186|ref|YP_004383614.1| 682 YDSEGNNqIFVVGDDGNLYTRG 703
                                       566666637***********98 PP

  == domain 7  score: -2.0 bits;  conditional E-value: 0.71
                                       SSS.-EEB-CCCEEEEECE CS
                            PapC_C  23 ngk.vgiVgqgGqvylrgl 40 
                                       ++  ++ V+++G +++r++
  gi|330507186|ref|YP_004383614.1| 788 EQTwIFAVDEKGALWVRAM 806
                                       3334678888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (888 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.24s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 6280.45
//
Query:       gi|330507187|ref|YP_004383615.1|  [L=274]
Description: F420-dependent methylenetetrahydromethanopterin dehydrogenase [Methanosaeta concilii GP6]
Scores for complete sequence (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  401.8   0.4   1.5e-120  401.6   0.4    1.0  1  MTD       methylene-5,6,7,8-tetrahydromethanopterin dehydroge
  ------ inclusion threshold ------
      0.087   12.5   0.1       0.87    9.2   0.1    2.3  3  DUF2529   Domain of unknown function (DUF2529)


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 !  401.6   0.4  1.7e-124  1.5e-120       1     274 []       2     272 ..       2     272 .. 0.99

  Alignments for each domain:
  == domain 1  score: 401.6 bits;  conditional E-value: 1.7e-124
                                       EEEEEEEES--HHHHHTTGGGSTTS--SSEEEEEEEEET--SHHHHHHHHHHHHHH--SEEEEE-S-TTSHHHHHHH CS
                               MTD   1 vkigiiklGnigtslvidlllDeradRedievrvvgsgaklkkeeveevveklkefdpdlvivisPnaaapgptkar 77 
                                       +kig++klGni+ts+ idl lDe+a+R+die+++++ g+k++++e +  +e+lk+++p+lv+++sPnaa++gpt+ar
  gi|330507187|ref|YP_004383615.1|   2 FKIGFVKLGNIATSTAIDLSLDEIAERTDIEFKIISFGPKMTEKEGK-GAEELKAWQPQLVVISSPNAATAGPTAAR 77 
                                       59*******************************************99.899************************** PP

                                       HHHHHSSS-EEEEEEGGGGGGH.HHHHHTT-EEEEETTS------TTT--HHHHHHHHHHHHHHHHHTTHHHHHHHH CS
                               MTD  78 ellsekdvpaivisDapgkkek.deleeeglGYiivkaDpliGarrefLDptemalfnadvlkvLaatGavRlvqee 153
                                       e++  +++p+i+isD+p+kke+ ++l++eg+GYii+++DpliGa+refLDp+emalfn+d+l+vLaa+Ga+Rlv+ee
  gi|330507187|ref|YP_004383615.1|  78 EAY--RGIPTIIISDGPSKKEArEALSAEGYGYIILPMDPLIGAKREFLDPAEMALFNSDALRVLAACGAIRLVEEE 152
                                       ***..***************999****************************************************** PP

                                       HHHHHHHHTTT-GGGS-EEEESGGGGGGSS--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT---HHHHHHHHHHHHH CS
                               MTD 154 ldkviekvkagkeielPkividaekaveaaefsnPYakakalaayeiaekvadidvkaCfmekelekyilivasahe 230
                                       ld++i+++ +g+ ++lP+i++++ek+ e+++fsnPYa+aka++a+++a++va+id++aCf+ kel+ ++l++a++he
  gi|330507187|ref|YP_004383615.1| 153 LDRTIASIISGQ-AKLPTILATPEKCAERMHFSNPYAQAKAMGALYMAQTVASIDAAACFRLKELKPIALTAAAGHE 228
                                       ***********9.9*************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHTT---B--B-TTSSB--BSSTTS--- CS
                               MTD 231 llraaakLadeaReieksndtvlRkphakdGkvlsktkllekPe 274
                                       ++raaa+LadeaRe+eksndtv+R+pha++G++++k +ll+kPe
  gi|330507187|ref|YP_004383615.1| 229 VMRAAARLADEARELEKSNDTVSRQPHARTGELMQKLSLLDKPE 272
                                       *******************************************8 PP

>> DUF2529  Domain of unknown function (DUF2529)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.048   4.3e+02      84     117 ..      38      70 ..      20     101 .. 0.73
   2 ?   -3.7   0.0       0.9   8.1e+03      47      69 ..     151     173 ..     149     177 .. 0.76
   3 ?    9.2   0.1   9.7e-05      0.87      25      79 ..     192     247 ..     183     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.048
                                       EES-S--HHHHHHHHHHHHHT--EEEEESS---T CS
                           DUF2529  84 fsresndkealklakkleekgievvavsskvkee 117
                                       f ++ ++ +  k a++l++++ ++v++ss ++++
  gi|330507187|ref|YP_004383615.1|  38 FGPKMTE-KEGKGAEELKAWQPQLVVISSPNAAT 70 
                                       5555555.45567888888888888888766554 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.9
                                       GGGGGGHHHHHCSTT--TTEEE- CS
                           DUF2529  47 geleaveaealegkeklpsvkkl 69 
                                       +el+  +a ++ g+ klp + + 
  gi|330507187|ref|YP_004383615.1| 151 EELDRTIASIISGQAKLPTILAT 173
                                       68888888888888888877655 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 9.7e-05
                                       HHHHHHHHHHHHTT--EEEEE-GGGGGGHHHHHCSTT--TTEEE--TT-.---TT- CS
                           DUF2529  25 edaarlLaqavigdgkvyikgfgeleaveaealegkeklpsvkkleeek.eltetD 79 
                                        ++a ++aq+v +  +      +el+ ++  a  g+e +  +++l +e+ el+++ 
  gi|330507187|ref|YP_004383615.1| 192 AMGALYMAQTVASIDAAACFRLKELKPIALTAAAGHEVMRAAARLADEArELEKSN 247
                                       579999***************************************99988877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2060.57
//
Query:       gi|330507188|ref|YP_004383616.1|  [L=252]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-31  109.7   0.0    2.3e-31  109.1   0.0    1.2  1  ABC_tran      ABC transporter
      8e-08   32.4   0.0     0.0032   17.3   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.8e-06   28.4   0.3    1.7e-05   25.3   0.3    2.1  1  AAA           ATPase family associated with various cellular 
     0.0001   22.3   0.0    0.00019   21.4   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
    0.00093   19.6   0.0     0.0013   19.2   0.0    1.3  1  AAA_16        AAA ATPase domain
     0.0012   19.2   0.0     0.0049   17.1   0.0    2.0  2  AAA_28        AAA domain
     0.0013   19.1   0.0      0.003   17.8   0.0    1.7  1  AAA_22        AAA domain
     0.0042   17.6   0.0     0.0072   16.9   0.0    1.3  1  AAA_23        AAA domain
     0.0054   16.7   0.0       0.03   14.3   0.0    1.9  2  ATPase_2      ATPase domain predominantly from Archaea
     0.0056   16.8   0.0      0.018   15.2   0.0    1.9  1  AAA_33        AAA domain
     0.0082   16.1   0.0      0.014   15.4   0.0    1.3  1  Rad17         Rad17 P-loop domain
     0.0083   15.9   0.0      0.041   13.6   0.0    1.8  2  AAA_15        AAA ATPase domain
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.036   13.8   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.022   14.5   0.0       0.17   11.6   0.0    2.0  2  AAA_30        AAA domain
      0.024   14.1   0.1      0.054   12.9   0.0    1.5  2  PhoH          PhoH-like protein
      0.026   14.0   0.0        4.9    6.5   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.031   14.2   0.1      0.089   12.7   0.0    1.8  2  NACHT         NACHT domain
      0.049   13.6   0.2       0.14   12.1   0.0    1.8  2  AAA_5         AAA domain (dynein-related subfamily)
       0.05   13.3   0.0        0.1   12.3   0.0    1.5  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.061   13.0   0.0       0.11   12.3   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein
      0.066   12.7   0.0       0.15   11.6   0.0    1.5  2  AAA_7         P-loop containing dynein motor region
      0.074   12.4   0.0       0.35   10.2   0.0    2.0  3  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.096   11.9   0.0       0.16   11.2   0.0    1.3  1  NB-ARC        NB-ARC domain
       0.18   11.8   0.0       0.31   11.0   0.0    1.3  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
        0.2   11.9   0.1       0.61   10.4   0.1    1.8  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 !  109.1   0.0   3.2e-34   2.3e-31       1     136 [.      23     162 ..      23     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 3.2e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++++l+++e++ v ++G++G+GK+tLl+++agl+ pt+G  ++dg+++        + e g+++qe +lfp  t+ 
  gi|330507188|ref|YP_004383616.1|  23 LHDINLTIEENQFVCFIGPSGCGKTTLLRIVAGLEAPTSGAATIDGEPIVG-----PSPERGMVFQEYSLFPWRTIL 94 
                                       789*********************************************999.....88999**************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +n             +++e+  ++l+ +gl++++++      ++LSgG+kqrva+aral+++pk ll+DEp+
  gi|330507188|ref|YP_004383616.1|  95 DNtvfglelkgidkaKREERGRQYLKMVGLEGFEKRYP----HELSGGMKQRVAIARALVNDPKALLMDEPF 162
                                       ************99988999**************9999....*****************************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 !   17.3   0.0   4.5e-06    0.0032       1      23 [.      35      57 ..      35     118 .. 0.74
   2 !   13.5   0.0   6.4e-05     0.046     230     298 ..     128     194 ..      91     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.5e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      + ++iGp g+GK++LL++  +l 
  gi|330507188|ref|YP_004383616.1| 35 FVCFIGPSGCGKTTLLRIVAGLE 57
                                      5789***************8883 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6.4e-05
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkelsrngaQviltTHS 298
                                        ++ ++elS G+k+  a++ al  ++   + ll DEp   L+      ++++ll++ +e+++    v+++THS
  gi|330507188|ref|YP_004383616.1| 128 EKRYPHELSGGMKQRVAIARALVNDP---KALLMDEPFGALDAqtrnTMQSELLRIWEEEKK---TVLFVTHS 194
                                       677899*********99999999999...67************9998899999999999988...*******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 !   25.3   0.3   2.3e-08   1.7e-05       1     111 [.      36     196 ..      36     223 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.3e-08
                                       EEEESSTTSSHHHHHHHHHHH......HTHE.............................................. CS
                               AAA   1 vllyGppGtGKTllakavake......lgve.............................................. 25 
                                       v+++Gp G+GKT+l + va        +                                                 
  gi|330507188|ref|YP_004383616.1|  36 VCFIGPSGCGKTTLLRIVAGLeaptsgA--Atidgepivgpspergmvfqeyslfpwrtildntvfglelkgidkak 110
                                       799****************985444330..13445555555556666666666666666666666555555555555 PP

                                       .......EEEEETTTCSSS...........STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHH CS
                               AAA  26 .......fleisgsellsk...........yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeee 83 
                                              +                      y  e +  +++ ++ a++   +p+ l++DE      ++       ++
  gi|330507188|ref|YP_004383616.1| 111 reergrqY----------LkmvglegfekrYPHELSGGMKQRVAIARALVnDPKALLMDEPFGALDAQ------TRN 171
                                       55555554..........04444444444699999999999998888877889*******76666777......799 PP

                                       HHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                               AAA  84 rvvnqLlteldgvkkkeskvivigatnr 111
                                       +++++Ll+ ++++kk    v++++ + +
  gi|330507188|ref|YP_004383616.1| 172 TMQSELLRIWEEEKKT---VLFVTHSVD 196
                                       9*************93...555544433 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.7e-07   0.00019      77     121 ..      10      55 ..       3      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.7e-07
                                       SEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  77 yevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       y+ ++ + k+ e+l++++  +++ ++++++G+SG GK+tL+  +++
  gi|330507188|ref|YP_004383616.1|  10 YKHFFADGKEMEALHDINLTIEEnQFVCFIGPSGCGKTTLLRIVAG 55 
                                       78899999999**********9989***************987765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.8e-06    0.0013       8     107 ..      19     145 ..      13     198 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.8e-06
                            AAA_16   8 eleqLlsalervrsgrpelvllsGesGvGKsslvrellr.alekdggiflrgkcdql...esa...ipy..salaqa 75 
                                       e+e+L+++  ++ ++  + v ++G+sG+GK++l+r ++  ++ ++g+ ++ g+       e++    +y   ++ ++
  gi|330507188|ref|YP_004383616.1|  19 EMEALHDINLTIEEN--QFVCFIGPSGCGKTTLLRIVAGlEAPTSGAATIDGEPIVGpspERGmvfQEYslFPWRTI 93 
                                       566666665555555..67999*************999534444466666666655533322244544432445555 PP

                            AAA_16  76 lareellrqlldeaesaeleawrekleeala.....................a 107
                                       l++ +++  +l   ++a++e+  ++ ++ ++                     +
  gi|330507188|ref|YP_004383616.1|  94 LDN-TVFGLELKGIDKAKREERGRQYLKMVGlegfekryphelsggmkqrvaI 145
                                       544.7777777776666666655555555555555555555555555544440 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   6.8e-06    0.0049       2      38 ..      36      84 ..      35     124 .. 0.70
   2 ?   -0.4   0.0       1.7   1.2e+03     134     160 ..     170     195 ..     139     206 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.8e-06
                            AAA_28  2 ivitGgestGKTtlleaLa.........ar..gypvv.pEaareileek 38
                                      ++++G++++GKTtll+  a         a+  g p+v p + r +++++
  gi|330507188|ref|YP_004383616.1| 36 VCFIGPSGCGKTTLLRIVAgleaptsgaATidGEPIVgPSPERGMVFQE 84
                                      89*************9999665554443225566666655555555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.7
                            AAA_28 134 reaiderlrealrelgipviivpsgdv 160
                                       r+ ++  l+ +++e    v+ v + +v
  gi|330507188|ref|YP_004383616.1| 170 RNTMQSELLRIWEEEKKTVLFV-THSV 195
                                       3333344444444433333333.3333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.2e-06     0.003       4      70 ..      32     107 ..      29     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.2e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.........erpevvfvtlpsstsskdllrellralglelka 70 
                                       + ++++ +G+sG+GKTtllr ++      + a++          + + + ++  s+  ++++l + +  l+l++ +
  gi|330507188|ref|YP_004383616.1|  32 ENQFVCFIGPSGCGKTTLLRIVAGLEAPTSGAATidgepivgpSPERGMVFQEYSLFPWRTILDNTVFGLELKGID 107
                                       678999**************99877655544444666666666444444555555556777777777766666666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     1e-05    0.0072      14      37 ..      25      51 ..       4      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1e-05
                            AAA_23 14 eidF...skgltlItGpNGaGKTTild 37
                                      +i++   ++ +++++Gp G+GKTT+l+
  gi|330507188|ref|YP_004383616.1| 25 DINLtieENQFVCFIGPSGCGKTTLLR 51
                                      3777888999***************97 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.1e-05      0.03       7      40 ..      22      53 ..      14      59 .. 0.75
   2 ?    0.0   0.0      0.94   6.7e+02     122     154 ..     156     186 ..     136     239 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-05
                          ATPase_2  7 elkeleeilerepneiyfiYGpegsGKtaLlkei 40
                                      +l +++  +e+  n+++   Gp g+GKt+Ll+ +
  gi|330507188|ref|YP_004383616.1| 22 ALHDINLTIEE--NQFVCFIGPSGCGKTTLLRIV 53
                                      56667666666..5555555***********965 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.94
                          ATPase_2 122 iiiDelqklidlglngaellvkeLlnliesltk 154
                                       +++De + + d + +  + + +eLl+++e+  k
  gi|330507188|ref|YP_004383616.1| 156 LLMDEPFGALDAQTR--NTMQSELLRIWEEEKK 186
                                       555666666544433..5555666666655222 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.4e-05     0.018       2      33 ..      36      94 ..      35     203 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklg....avllssdt.......................l 33
                                      v ++G++G+GK+tl++ ++  ++    a +++                          l
  gi|330507188|ref|YP_004383616.1| 36 VCFIGPSGCGKTTLLRIVAGLEAptsgAATIDGEPivgpspergmvfqeyslfpwrtiL 94
                                      789************98853222334544444333455556666666666666666651 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   1.9e-05     0.014      36      66 ..      24      54 ..      13      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                             Rad17 36 kadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                      +   L  ++++ +   GPsGCgk+t +++++
  gi|330507188|ref|YP_004383616.1| 24 HDINLTIEENQFVCFIGPSGCGKTTLLRIVA 54
                                      5555666777899999************987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   5.7e-05     0.041      15      42 ..      24      52 ..      22      56 .. 0.84
   2 ?   -0.3   0.0      0.96   6.9e+02     323     365 ..     152     194 ..     139     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.7e-05
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilea 42
                                       d+ + ++e+ + ++iG+ ++GK+++l++
  gi|330507188|ref|YP_004383616.1| 24 HDINLTIEENqFVCFIGPSGCGKTTLLRI 52
                                      56677777778***************986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.96
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +++ ll++EP   L  q  + +   l+++ +++k+ v++ THS
  gi|330507188|ref|YP_004383616.1| 152 DPKALLMDEPFGALDAQTRNTMQSELLRIWEEEKKTVLFVTHS 194
                                       6677888888888889999999999*********99******9 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     5e-05     0.036      16      39 ..      27      50 ..      19      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                       ++i++++++ ++GpsG GK+Tll
  gi|330507188|ref|YP_004383616.1| 27 NLTIEENQFVCFIGPSGCGKTTLL 50
                                      45566666999************8 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00024      0.17      14      41 ..      29      56 ..      24      77 .. 0.83
   2 ?    0.3   0.0      0.67   4.8e+02      34      68 ..     173     207 ..     168     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                            AAA_30 14 ltsgdrvavltGpAGtGKttalkalrea 41
                                      + +++++++  Gp G GKtt+l+ ++ +
  gi|330507188|ref|YP_004383616.1| 29 TIEENQFVCFIGPSGCGKTTLLRIVAGL 56
                                      55677899***************98765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.67
                            AAA_30  34 alkalreaweaaggrviglAptgkaAkvLaeelgi 68 
                                       + ++l ++we+++++v+ ++++   A  La+++ i
  gi|330507188|ref|YP_004383616.1| 173 MQSELLRIWEEEKKTVLFVTHSVDEAIYLADAIVI 207
                                       55678899**9999999999999999888877655 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   7.5e-05     0.054      15      43 ..      29      58 ..      19      65 .. 0.78
   2 ?   -3.1   0.0       6.1   4.4e+03     134     148 ..     171     185 ..     165     220 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                                      HHHH-SEEEEE--TTSSTT.HHHHHHHHHH CS
                              PhoH 15 alkkndivfaiGpaGtGKt.ylavalavea 43
                                      ++++n++v+ iGp+G+GKt +l +++++ea
  gi|330507188|ref|YP_004383616.1| 29 TIEENQFVCFIGPSGCGKTtLLRIVAGLEA 58
                                      5789**************824566666665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.1
                                       HHHHHHHTTB-TT-E CS
                              PhoH 134 eqmkmfltRlGensk 148
                                       ++m+  l R+ e+ k
  gi|330507188|ref|YP_004383616.1| 171 NTMQSELLRIWEEEK 185
                                       344444444433322 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.014        10      23      41 ..      32      50 ..      21      54 .. 0.84
   2 ?    6.5   0.0    0.0068       4.9     135     212 ..     133     209 ..      90     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.014
                                      TSSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 23 sksftaivGpNGSGKsnll 41
                                      +++f + +Gp G+GK+ ll
  gi|330507188|ref|YP_004383616.1| 32 ENQFVCFIGPSGCGKTTLL 50
                                      467999**********987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0068
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHH.HHH..HHCTTSEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvae.llk..eksknaQfivislreemlekadkl 208
                                       ++LSgG k+ va+a  +     +p++l l+De   aLD++ ++ + + ll+  e++k++ ++v+   +e +  ad++
  gi|330507188|ref|YP_004383616.1| 133 HELSGGMKQRVAIARAL---VNDPKAL-LMDEPFGALDAQTRNTMQSeLLRiwEEEKKTVLFVTHSVDEAIYLADAI 205
                                       489***99999988653...3566665.89*********99988754255555777777777777777777777777 PP

                                       EEEE CS
                                       xxxx RF
                             SMC_N 209 vgvt 212
                                       v ++
  gi|330507188|ref|YP_004383616.1| 206 VIMS 209
                                       7655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.089       3      21 ..      36      54 ..      34      62 .. 0.86
   2 ?   -1.7   0.0       3.3   2.4e+03     118     134 ..     201     217 ..     158     240 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                      v+  G++G+GKTtLl+ +a
  gi|330507188|ref|YP_004383616.1| 36 VCFIGPSGCGKTTLLRIVA 54
                                      8999***********8665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.3
                                       TT--EEEEEEECCCHHH CS
                             NACHT 118 lpeasllltvrpralrd 134
                                       l  a +++++rp++ +d
  gi|330507188|ref|YP_004383616.1| 201 LADAIVIMSARPGRIKD 217
                                       33444555555555555 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 ?   12.1   0.0    0.0002      0.14       2      20 ..      36      54 ..      35      61 .. 0.90
   2 ?   -2.1   0.0       4.9   3.5e+03      33      56 ..     169     192 ..     167     211 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                      EEEE--SSSSHHHHHHHGG CS
                             AAA_5  2 vlLvGppGtgKselaerla 20
                                      v+ +Gp+G+gK++l + +a
  gi|330507188|ref|YP_004383616.1| 36 VCFIGPSGCGKTTLLRIVA 54
                                      899***********99876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.9
                                       -TT--HHHHH--B--......... CS
                             AAA_5  33 trdtteedlkgrreikngttslvd 56 
                                       tr+t +++l+  +e +++t  +v 
  gi|330507188|ref|YP_004383616.1| 169 TRNTMQSELLRIWEEEKKTVLFVT 192
                                       677888888888885555544444 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015       0.1       4      24 ..      36      56 ..      33      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                         PduV-EutP  4 illiGkvgsGKttLtqalkge 24
                                      + +iG++g+GKttL + + g 
  gi|330507188|ref|YP_004383616.1| 36 VCFIGPSGCGKTTLLRIVAGL 56
                                      789***********9988775 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 ?   12.3   0.0   0.00015      0.11      34      64 ..      19      50 ..      11      66 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                         IstB_IS21 34 kvkeLatlsf.iekkenivllGpsGvGKshla 64
                                      ++++L   +  ie+++ ++++GpsG GK+ l 
  gi|330507188|ref|YP_004383616.1| 19 EMEALHDINLtIEENQFVCFIGPSGCGKTTLL 50
                                      55566555432899999***********9763 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   0.00021      0.15      26      51 ..      26      51 ..      18      61 .. 0.88
   2 ?   -3.5   0.0       8.6   6.2e+03     124     133 ..     176     185 ..     169     209 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                             AAA_7 26 lelllknkkpvllvGptGtGKtviik 51
                                      ++l +++++ v+++Gp+G+GKt++++
  gi|330507188|ref|YP_004383616.1| 26 INLTIEENQFVCFIGPSGCGKTTLLR 51
                                      5788999***************9875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.6
                             AAA_7 124 ellRqlldyg 133
                                       ellR + +++
  gi|330507188|ref|YP_004383616.1| 176 ELLRIWEEEK 185
                                       3444443332 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00049      0.35      22      55 ..      33      66 ..      17      82 .. 0.81
   2 ?   -1.4   0.0       1.8   1.3e+03     179     196 ..     129     146 ..     122     154 .. 0.85
   3 ?   -3.3   0.0       6.8   4.9e+03     137     160 ..     191     214 ..     176     234 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00049
                      Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsllpplseeeal 55
                                      +  + ++Gp+G+GKt l + +++l +p s + ++
  gi|330507188|ref|YP_004383616.1| 33 NQFVCFIGPSGCGKTTLLRIVAGLEAPTSGAATI 66
                                      556789**************99999888877666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                      Mg_chelatase 179 erYlsklsgplldRidlq 196
                                       +rY + lsg +  R+ + 
  gi|330507188|ref|YP_004383616.1| 129 KRYPHELSGGMKQRVAIA 146
                                       79999*********9886 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 6.8
                      Mg_chelatase 137 israkakvefparfqlvaamNpcp 160
                                       ++ +  ++ + a+  +++++ p +
  gi|330507188|ref|YP_004383616.1| 191 VTHSVDEAIYLADAIVIMSARPGR 214
                                       455556666777777777776655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.16      15      39 ..      30      52 ..      17      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                      TTTSCSEEEEEEESTTSSHHHHHHH CS
                            NB-ARC 15 kdelqslvvalvGmgGvGKttlakq 39
                                       +e q  +v + G  G+GKttl++ 
  gi|330507188|ref|YP_004383616.1| 30 IEENQ--FVCFIGPSGCGKTTLLRI 52
                                      56777..9**************875 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00044      0.31      10      40 ..      26      54 ..      15      62 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00044
                                      HHHHHHHCHTEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 10 lgkklakalgdvilLeGdLGaGKTtlvrgla 40
                                      +  ++ +  ++++++ G+ G+GKTtl r +a
  gi|330507188|ref|YP_004383616.1| 26 INLTIEE--NQFVCFIGPSGCGKTTLLRIVA 54
                                      3333333..788**************99765 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 ?   10.4   0.1   0.00085      0.61      61      84 ..     150     173 ..     127     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00085
                           SbcCD_C  61 epalrlvfLDEAFsklDeesiatl 84 
                                        ++++ +++DE F+ lD+++++t+
  gi|330507188|ref|YP_004383616.1| 150 VNDPKALLMDEPFGALDAQTRNTM 173
                                       467899**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 1841.65
//
Query:       gi|330507189|ref|YP_004383617.1|  [L=349]
Description: glycerol-1-phosphate dehydrogenase [Methanosaeta concilii GP6]
Scores for complete 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-68  230.4   0.1    4.4e-68  229.7   0.1    1.3  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    3.5e-20   72.2   2.8    1.4e-19   70.2   2.8    1.7  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    0.00024   20.4   0.1    0.00077   18.7   0.1    1.9  1  DHQ_synthase  3-dehydroquinate synthase
     0.0043   16.6   0.3      0.011   15.3   0.2    1.7  1  AIRC          AIR carboxylase
  ------ inclusion threshold ------
       0.15   12.4   0.0       0.26   11.6   0.0    1.3  1  DUF3362       Domain of unknown function (DUF3362)


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 !  229.7   0.1   1.2e-71   4.4e-68       2     250 .]      15     272 ..      14     272 .. 0.92

  Alignments for each domain:
  == domain 1  score: 229.7 bits;  conditional E-value: 1.2e-71
                          Fe-ADH_2   2 igegaleklgellkelelk.kvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketd 77 
                                       +g++a+ +l+++++ l+l+   l+v++ +t +++g+ + e l++ g +++++     +++leev +  +++re e+ 
  gi|330507189|ref|YP_004383617.1|  15 VGNEAILELPQICSYLHLEgPGLIVTGPHTDDVVGKTILELLNSGGFEPQTL--ICTASKLEEVDRAEARAREIEAG 89 
                                       68999***********997699***************************977..578999999999*********** PP

                          Fe-ADH_2  78 lvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrll 154
                                       ++++ GgG+ iDiak++s+++n+p++s+pTaaS+DG++s++asl+v+g+ +++ +a+ Pla++aD+ ++a+AP+rll
  gi|330507189|ref|YP_004383617.1|  90 FLIGAGGGRSIDIAKIASMRTNIPFLSLPTAASHDGICSSQASLTVNGEAVSL-PAQSPLAIVADTGIIARAPARLL 165
                                       ****************************************************9.*********************** PP

                          Fe-ADH_2 155 asGvGDllgkytaladwklan........evseplaklsaamvqeaaeklve..dkketealeellea.lalsgigi 220
                                       a+G+GD++++yta+ dw+la+        e++  l+ ++a+m++e a+ +    ++  + ++++l+++ +a+s++g+
  gi|330507189|ref|YP_004383617.1| 166 AAGCGDIISNYTAILDWQLAHrlrseefsEYASALSGMTAKMIVERASDIRPglEESAKIVVKALISSgVAMSIAGS 242
                                       *********************9999988888889**************9986443334445555554427******* PP

                          Fe-ADH_2 221 srpaSGsEHliSHaldmlalkqalHGeqVG 250
                                       srpaSGsEH+++H ++++a+++ lHGe +G
  gi|330507189|ref|YP_004383617.1| 243 SRPASGSEHKFAHSINRIAPRRGLHGELCG 272
                                       ***************************987 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   2.8   3.9e-23   1.4e-19       1     282 [.      10     279 ..      10     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 3.9e-23
                                       -SEEEEETTGGGGHHHHHTTT-...EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTT CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkklgak.ralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaal 76 
                                       P+ +  g+ a+ el++ ++ l ++   livt++ +  +  + +++le l++ g+e ++   +    +leev++a a+
  gi|330507189|ref|YP_004383617.1|  10 PRIVAVGNEAILELPQICSYLHLEgPGLIVTGPHT--DDVVGKTILELLNSGGFEPQT--LICTASKLEEVDRAEAR 82 
                                       677889*************998776899*****94..566888899999******993..456689*********** PP

                                       S-TT.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEE CS
                            Fe-ADH  77 areegadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegek 153
                                       are +a ++i+ GGG +iD+AK++++ ++                  +p+   PT a+ +  +++ a +t + e   
  gi|330507189|ref|YP_004383617.1|  83 AREIEAGFLIGAGGGRSIDIAKIASMRTN------------------IPFLSLPTAASHDGICSSQASLTVNGE--A 139
                                       *****************************..................***********************5555..4 PP

                                       EEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---.TTSSB--HHHHHHHHHHHHHHHHHHH CS
                            Fe-ADH 154 lsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanp.lsdalaleairliaknleravadged 229
                                         ++ p   P +++ D+ +++ +P+r++aa+ +D+++ +   +  + a+   s+ ++++a  l     + +v+ ++d
  gi|330507189|ref|YP_004383617.1| 140 --VSLPAQSPLAIVADTGIIARAPARLLAAGCGDIISNYTAILDWQLAHRlRSEEFSEYASALSGMTAKMIVERASD 214
                                       ..4445889****************************999887778888867888********99999999999998 PP

                                       H....HHHHHHHHHHHH.HHHHHHSS---.....HHHHHHHHHHC.CGGG....GGS-HHHHHHHHH CS
                            Fe-ADH 230 l....eareqmllastl.aglafsnaglg.....avHalahalgalfgip....hglanaillpavl 282
                                       +    e  ++++  +++ +g+a+s ag +       H +ah++  +   p    hg+++++     +
  gi|330507189|ref|YP_004383617.1| 215 IrpglEESAKIVVKALIsSGVAMSIAGSSrpasgSEHKFAHSINRIA--PrrglHGELCGLGTIMMM 279
                                       888996666666666666*****999999888889999999999943..244678888887554444 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   2.2e-07   0.00077      93     255 ..     145     316 ..      69     322 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-07
                                       ---SEEEEEGGGGGGS-HHHHHHHHHHHH.HHHHHT-HHHHHHHHHHHHHHHC.......TTTHHHHHHHH...... CS
                      DHQ_synthase  93 aqPkavlidlevLktLperelraGlaEvi.Kyalikdeelfelleenaeallk.......eeeeealeeli...... 155
                                         P a+++d+ +++  p+r l+aG++++i  y++i d +l ++l++++ +  +       +       ++i      
  gi|330507189|ref|YP_004383617.1| 145 QSPLAIVADTGIIARAPARLLAAGCGDIIsNYTAILDWQLAHRLRSEEFSEYAsalsgmtA-------KMIverasd 214
                                       5799***********************995699*************999998855555441.......444344444 PP

                                       .HHHHHHHHHHHHHCCTT........TTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-H CS
                      DHQ_synthase 156 .arsievkaevveeDeke........kglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkk 223
                                        +  +e  a++v +             + r +    H ++H i +++   + lHGe   +G ++ ++l         
  gi|330507189|ref|YP_004383617.1| 215 iRPGLEESAKIVVKALISsgvamsiaGSSRPASGSEHKFAHSINRIAPR-RGLHGELCGLGTIMMMYLH-------G 283
                                       433344444444444444000000114556667788**********988.9*************99988.......4 PP

                                       HHHHHHHHHHHHTT---STTTT..-HHHHHHHH CS
                      DHQ_synthase 224 eeverllkllkklglpvslkel.leveelleal 255
                                       ++ + +++ l+++g p+s ++  l++e+++eal
  gi|330507189|ref|YP_004383617.1| 284 KDWKMIREALAQVGAPTSADQIgLDAETVVEAL 316
                                       557789999999999999998877777777766 PP

>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   3.1e-06     0.011       4     112 ..      38     152 ..      37     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-06
                                       EEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEE.EEEESS--HHHHHHHHSSS- CS
                              AIRC   4 iimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviI.agAGgaahLpgvvaslttlP 79 
                                       i++G + D  v k + e+l++ g+e ++ ++ a +   e+ +  ++a+e +   +I ag G++ +++ + +  t++P
  gi|330507189|ref|YP_004383617.1|  38 IVTGPHTDDVVGKTILELLNSGGFEPQTLICTASKLE-EVDRAEARAREIEAGFLIgAGGGRSIDIAKIASMRTNIP 113
                                       89999****************************9975.5556666666666666662666669************** PP

                                       EEEEEE--STTCCHHHHHH......HHT--TTS--EE-S CS
                              AIRC  80 VigvPvkskalkgldsllS......ivqmPsgvpvatva 112
                                        ++ P+ +++    +s  S       v +P++ p+a va
  gi|330507189|ref|YP_004383617.1| 114 FLSLPTAASHDGICSSQASltvngeAVSLPAQSPLAIVA 152
                                       *******96654444444421222347888888888887 PP

>> DUF3362  Domain of unknown function (DUF3362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.2e-05      0.26      50      88 ..     277     318 ..     271     346 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.2e-05
                           DUF3362  50 llrYhdpknwpllreALkkmG...redLiGngkkhLiptfqp 88 
                                       ++ Y   k+w+++reAL ++G    +d iG + + ++ +  +
  gi|330507189|ref|YP_004383617.1| 277 MMMYLHGKDWKMIREALAQVGaptSADQIGLDAETVVEALVN 318
                                       5779999**************4444899**999988876544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2497.91
//
Query:       gi|330507190|ref|YP_004383618.1|  [L=149]
Description: hypothetical protein MCON_1057 [Methanosaeta concilii GP6]
Scores for complete 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-54  182.2   0.3    4.7e-54  182.1   0.3    1.0  1  UPF0179   Uncharacterised protein family (UPF0179)


Domain annotation for each model (and alignments):
>> UPF0179  Uncharacterised protein family (UPF0179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.1   0.3   2.6e-58   4.7e-54       1     140 []       7     147 ..       7     147 .. 0.99

  Alignments for each domain:
  == domain 1  score: 182.1 bits;  conditional E-value: 2.6e-58
                           UPF0179   1 kitLigkklAkeGteFiylgeaeeCekCklkkvClnLekgrkYrivevrekteheCavheegvvaveveeapieali 77 
                                       +itLig+klA+ G+eF+++g+++eCe+Ckl+++C+nLe+ r+Yr+ + r + +heC++he gv+avev+e+pi+a+ 
  gi|330507190|ref|YP_004383618.1|   7 QITLIGTKLASIGMEFTFMGPTPECESCKLRNTCINLEPRRRYRVLGTRGELVHECPIHEAGVRAVEVAESPIIAAF 83 
                                       59*************************************************************************** PP

                           UPF0179  78 eskkavegskitleseeCdevecesyelcepeglkegekvkivevlgeiee.ckkgrslkkvel 140
                                       +++ka+ gski +e+++Cd+++c++y++c+p glk+gek++ivev+ge++e c++g+ lk+ve+
  gi|330507190|ref|YP_004383618.1|  84 DARKAFPGSKIVFEAMKCDDYNCSMYDICHPIGLKDGEKCTIVEVVGEAPEdCPRGNILKLVEF 147
                                       *************************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1230.02
//
Query:       gi|330507191|ref|YP_004383619.1|  [L=333]
Description: 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase subunit CofG [Methanosaeta concilii GP6]
Scores for 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   50.5   0.1    8.5e-12   45.8   0.0    2.2  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   4.7e-16   8.5e-12       2     165 ..      13     181 ..      12     183 .. 0.83
   2 !    2.7   0.0    0.0079   1.4e+02     110     144 ..     199     233 ..     180     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.7e-16
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE......SSTGGGS............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxx............ RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilg......ggeplly............ 60 
                                       +vt+ C++rC +C++++   + + ++ +s     ++++e++ ++g+ e +++                         
  gi|330507191|ref|YP_004383619.1|  13 PVTNLCRNRCQYCSFRR---NLDEAHLISRSAAQQLLEEGR-DHGCSEALFTlgerpeE-----Vegfhlmlagegr 80 
                                       6899************8...8*******************6.99977666663444440.....3444444444444 PP

                                       TTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  61 pdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealekl 137
                                        d+  +l +l++la  +  +   tn++l++ee l++l +++   + l le+  + + ++   +g+++e +l+ + ++
  gi|330507191|ref|YP_004383619.1|  81 EDLLGYLVELCELA-IEHDLLPHTNAGLLSEEDLATLQPYN-ASMGLMLESCAKLDAHEQS-PGKNPELRLKHIARA 154
                                       55555555555554.7789**********************.*******************.*************** PP

                                       HHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 138 reagikrvvdrivglpGendeeleelle 165
                                        ++ i+  +++i+++ Ge+++++ + ++
  gi|330507191|ref|YP_004383619.1| 155 GRLHIP-FTTGILVGIGESWQDRIQSIQ 181
                                       ******.***************987766 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0079
                                       BSSSHH.HHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 110 eaadde.kvlklmnrghtfeevlealeklreagikr 144
                                       + +d++  +   +++++++e+++++++++re+ ++r
  gi|330507191|ref|YP_004383619.1| 199 QPFDPKpGTAMSTHPRPEREDLVRTVRLAREL-LPR 233
                                       4444443366677799***************9.886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2397.21
//
Query:       gi|330507192|ref|YP_004383620.1|  [L=59]
Description: hypothetical protein MCON_1059 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.0   1.2      0.048   12.9   1.2    1.0  1  MFS_Mycoplasma  Mycoplasma MFS transporter
       0.11   12.8   1.5       0.13   12.5   1.5    1.1  1  DUF4181         Domain of unknown function (DUF4181)
       0.27   11.4   0.1       0.27   11.4   0.1    2.0  2  Fun_ATP-synt_8  Fungal ATP synthase protein 8 (A6L)
       0.37   10.9   0.1       0.37   10.9   0.1    1.4  2  TssO            Type VI secretion system, TssO
       0.81    8.4   3.1       0.87    8.3   3.1    1.0  1  DUF2207         Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> MFS_Mycoplasma  Mycoplasma MFS transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.2   1.3e-05     0.048     179     220 ..       3      46 ..       1      55 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                    MFS_Mycoplasma 179 krflvtlfllgvvlvliailvvyfvg.lgtavglaf.vlIltFl 220
                                       k++l + +++g+vl++i++++++ +  +++  g  f ++Il F+
  gi|330507192|ref|YP_004383620.1|   3 KKYLEIGLSTGLVLLMIILILGAQMTlPTEERGSSFaIIILLFI 46 
                                       99******************966555156677888856677777 PP

>> DUF4181  Domain of unknown function (DUF4181)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.5   3.6e-05      0.13      32      72 ..       4      49 ..       1      54 [. 0.60

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
                           DUF4181 32 kkielilrv.lfiifiilsliiilsreyvdii....ilifvflvvl 72
                                      k+ e++l++ l+ ++iil+l   ++ ++ +      i+i +f+v++
  gi|330507192|ref|YP_004383620.1|  4 KYLEIGLSTgLVLLMIILILGAQMTLPTEERGssfaIIILLFIVAM 49
                                      899****999555555555555555555443333545555555554 PP

>> 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 ?   11.4   0.1   7.5e-05      0.27      13      34 ..      10      31 ..       5      34 .. 0.91
   2 ?    0.5   1.0       0.2   7.1e+02      17      28 ..      38      48 ..      36      52 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.5e-05
                                      HHHHHHHHHHHHHHHHHTHHHH CS
                    Fun_ATP-synt_8 13 ltfgfliltvllylfskyiLPr 34
                                      l++g+++l ++l+l ++  LP 
  gi|330507192|ref|YP_004383620.1| 10 LSTGLVLLMIILILGAQMTLPT 31
                                      789******************6 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.2
                                      HHHHHHHHHHHH CS
                    Fun_ATP-synt_8 17 fliltvllylfs 28
                                      f+i ++ll++++
  gi|330507192|ref|YP_004383620.1| 38 FAI-IILLFIVA 48
                                      443.44444444 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.7   6.3e+03      22      28 ..      15      21 ..       6      26 .. 0.54
   2 ?   10.9   0.1    0.0001      0.37       3      26 ..      31      54 ..      29      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                              TssO 22 lllfliv 28
                                      +ll++i+
  gi|330507192|ref|YP_004383620.1| 15 VLLMIIL 21
                                      2222222 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0001
                              TssO  3 kkErrsgflyflllFlvtvlllfl 26
                                      ++Er s+f   +llF+v++++++l
  gi|330507192|ref|YP_004383620.1| 31 TEERGSSFAIIILLFIVAMGIVGL 54
                                      58******************9985 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.1   0.00024      0.87     384     425 ..       8      52 ..       1      56 [. 0.60

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00024
                           DUF2207 384 salglgliilglilillallllvll...lvfllilllillliaii 425
                                       + l++gl++l++ilil+a ++l +    ++f+ i+ll+++ ++i+
  gi|330507192|ref|YP_004383620.1|   8 IGLSTGLVLLMIILILGAQMTLPTEergSSFAIIILLFIVAMGIV 52 
                                       456667777777777777777766677555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); 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:                         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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 427.13
//
Query:       gi|330507193|ref|YP_004383621.1|  [L=121]
Description: hypothetical protein MCON_1060 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-12   47.2   0.4    2.7e-12   46.8   0.4    1.2  1  SepF      Cell division protein SepF


Domain annotation for each model (and alignments):
>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.4   1.5e-16   2.7e-12       3      72 .]      40     111 ..      38     111 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.5e-16
                                       EEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTC..HHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-TT-EE CS
                              SepF   3 vveprsfedaqeiadalkegkiVilnledldk..eeakrivdflsgvvyaldGdiqkvgkkvflitPknvdi 72 
                                       v+e  ++e  +e+++++++g+iV+ ++ +l++  + + r++ +l+++v +++Gdi+ +g++ ++++Pk+++i
  gi|330507193|ref|YP_004383621.1|  40 VAEMGRIEVLPEVKQEIYNGNIVLADIAGLKRdkAALDRAIGELKKAVEDVSGDIAGIGDDLIVLVPKGIKI 111
                                       66777888899*********************778889********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 888.52
//
Query:       gi|330507194|ref|YP_004383622.1|  [L=189]
Description: zinc finger protein ZPR1-like protein [Methanosaeta concilii GP6]
Scores for 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-36  123.3   0.0    9.4e-36  123.1   0.0    1.0  1  zf-ZPR1   ZPR1 zinc-finger domain
  ------ inclusion threshold ------
       0.12   11.1   0.0       0.17   10.6   0.0    1.2  1  AtuA      Acyclic terpene utilisation family protein AtuA


Domain annotation for each model (and alignments):
>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.1   0.0     1e-39   9.4e-36       2     158 ..       8     162 ..       7     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 1e-39
                           zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetatv 78 
                                       +Cp C+ ++++    + +iPyf+e ++++ +Ce Cg++++++  ++++e+  +r tl ve+ edln +v++S+++t+
  gi|330507194|ref|YP_004383622.1|   8 NCPVCS-AQMQFSWETQDIPYFGEAMLIAGVCE-CGFRHSDTILLTQKEP--VRNTLVVETIEDLNVRVIRSSSGTI 80 
                                       8****6.7777777777****************.****************..************************* PP

                           zf-ZPR1  79 eipeleleippg.tlegrlttvEGlLeqikeele.keegdqaer..edeekekieeflekleeliegeepftlildD 151
                                       ++pel+++++pg ++++++++vEG+L++i+e +     + qa+   +++ +++ ee+le++  +++ge p+tli++D
  gi|330507194|ref|YP_004383622.1|  81 RVPELGVDVEPGyASDSYVSNVEGVLDRIEEIVCfA--TSQARAadNQDGARRGEEILESIALARKGEFPITLIIED 155
                                       *********************************642..3333333234799************************** PP

                           zf-ZPR1 152 pagnSfi 158
                                       p+gnS+i
  gi|330507194|ref|YP_004383622.1| 156 PLGNSAI 162
                                       *****99 PP

>> AtuA  Acyclic terpene utilisation family protein AtuA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   1.9e-05      0.17     169     204 ..      12      47 ..       5      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 1.9e-05
                              AtuA 169 apaawefgWkeddydelAgalvaGhllECgaqvtGG 204
                                         a ++f+W+++d+   ++a++++ + ECg   +  
  gi|330507194|ref|YP_004383622.1|  12 CSAQMQFSWETQDIPYFGEAMLIAGVCECGFRHSDT 47 
                                       445669***********************9766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1595.01
//
Query:       gi|330507195|ref|YP_004383623.1|  [L=297]
Description: LPPG:Fo 2-phospho-L-lactate transferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-44  152.1   0.0    2.1e-44  151.9   0.0    1.0  1  UPF0052   Uncharacterised protein family UPF0052


Domain annotation for each model (and alignments):
>> UPF0052  Uncharacterised protein family UPF0052
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.9   0.0   1.2e-48   2.1e-44       3     256 ..       3     263 ..       1     285 [. 0.88

  Alignments for each domain:
  == domain 1  score: 151.9 bits;  conditional E-value: 1.2e-48
                                       EEE-CHHHHHHHHHHCCSS..CEEEEEE-----SHHHHHHHHHHTS---HHHHHHHHHH...--S-C.......... CS
                           UPF0052   3 vlgGGtGlskllrglkevt..aeltavvtvaDdggssGelrrelgllaigDirnvlval...idder.......... 64 
                                       vl+GGtG++kllrglke+   +el++ v++a+d ++sG        ++ +Di++vl++l   id++r          
  gi|330507195|ref|YP_004383623.1|   3 VLSGGTGTPKLLRGLKELVlpQELSVAVNTAEDLWISG-------NYISPDIDSVLYTLadmIDEKRwwgikgdrtl 72 
                                       9*****************999*****************.......9*************776666668888888776 PP

                                       HHHHHCH-B-SS.....SSSSTT-BHHHHHHHHHHHHHS.-HHHHHHHHHHHTT-SSEEEES-SS--EEEEEETTS- CS
                           UPF0052  65 lleeLfqyRfkg.....dgdlaghslgnllLaalaeltg.sleeaiealskilkvrgrvlPatddpvelsaeledGe 135
                                       +++ L+   +++     d+d a h+++  lL+      g +l+  +ea++++l+v +rv+P+tdd v++++ + +G 
  gi|330507195|ref|YP_004383623.1|  73 THDFLLMMGVDEkltigDKDRAVHIFRSNLLRR-----GvKLSLTTEAIANALGVMQRVVPMTDDIVSTVIGTPEGM 144
                                       44445444333377888****************.....99************************************9 PP

                                       EEESTTTGGGG-S...-EEE.EEEESTT----HHHHHHHHH-SEEEE-SS-IIIIIHHHHTSCCHHHHHHH-SSEEE CS
                           UPF0052 136 eitgeskisearklkapikr.vflepegaeaapevleaikeAdlivlgpGslytSiiPiLlvpgiaealreskakkv 211
                                       +  ++ + s +++  +++++  f + e+a + ++ l+ +++ + +++gp++++tSi+PiL++ g+++ l  +k+k+v
  gi|330507195|ref|YP_004383623.1| 145 MHFQDFWASLKGR--PRVESvTFTGLEEALPCQGFLDLLEREETVIIGPSNPVTSIGPILALAGVRDRL--KKKKVV 217
                                       555*****77776..9****999999999****************************************..669*** PP

                                       EE--SB--TTTSTT-BHHHHHHHHHHCH-.....SS....S..-SEEEEE-S CS
                           UPF0052 212 lvsnimtqkGetdgfsvsdhvkaieravg.....kgvakay..vdavlvnts 256
                                       ++s++++      +++vs++++++++a g     +gva  +  vd ++v+ +
  gi|330507195|ref|YP_004383623.1| 218 AISPFVG------NKPVSGPAAKLMEARGvpasdEGVAALLgkVDIFVVDGK 263
                                       ******9......****************88776554444499999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2308.77
//
Query:       gi|330507196|ref|YP_004383624.1|  [L=319]
Description: putative methanogenesis marker protein 12 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.20s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2483.97
//
Query:       gi|330507197|ref|YP_004383625.1|  [L=81]
Description: hypothetical protein MCON_1064 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.2   0.1       0.12   12.9   0.1    1.1  1  DUF3245   Protein of unknown function (DUF3245)


Domain annotation for each model (and alignments):
>> DUF3245  Protein of unknown function (DUF3245)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.5e-06      0.12      27      57 ..      18      48 ..      10      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.5e-06
                           DUF3245 27 dekktdeelqkeedeiftavpetlGlGAklp 57
                                        k++ ++  kee+e+  a++e +GlG++l 
  gi|330507197|ref|YP_004383625.1| 18 YIKGEKAKVLKEEVEVAMARAEAAGLGSELI 48
                                      55677788899*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 604.36
//
Query:       gi|330507198|ref|YP_004383626.1|  [L=215]
Description: hypothetical protein MCON_1067 [Methanosaeta concilii GP6]
Scores for complete 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   0.7    1.4e-10   41.7   0.7    1.6  1  CxxCxxCC  Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
       0.11   12.3   1.4       0.21   11.4   1.4    1.6  1  DUF3109   Protein of unknown function (DUF3109)


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.7   1.6e-14   1.4e-10       1      76 [.      16     135 ..      16     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1.6e-14
                          CxxCxxCC   1 eCkeCgaCCk......................elkvklteedlerlkaaevaeeeeeskkiak.............. 41 
                                       +C++Cg CC+                      ++ ++lte+d++ ++    ++  ++  ++++              
  gi|330507198|ref|YP_004383626.1|  16 QCQRCGSCCHhkrplefddlipaeqiedfwrsSNLIYLTEKDVHAISNRTGMRPPDFVDTLYDysecyvkiedegrr 92 
                                       6*********999999999999999999999888899999999999888888888888888889************* PP

                          CxxCxxCC  42 ...........adgrCvfldeetklCkiYeeRpkicrlfpasekee 76 
                                                  +d  Cvf++e    C+iY+ Rp +crlfp+  +ee
  gi|330507198|ref|YP_004383626.1|  93 vildlpvlkskEDTTCVFYQEG---CSIYSVRPIACRLFPFRVEEE 135
                                       *******************998...****************84444 PP

>> DUF3109  Protein of unknown function (DUF3109)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.4   2.4e-05      0.21      99     133 ..     104     136 ..       3     159 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
                           DUF3109  99 gialCaiekayreg.kikfkKPisChlyPirvkkls 133
                                       + ++C +   y+eg +i   +Pi C+l+P rv++ +
  gi|330507198|ref|YP_004383626.1| 104 EDTTCVF---YQEGcSIYSVRPIACRLFPFRVEEET 136
                                       4555554...56662455789***********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1472.10
//
Query:       gi|330507199|ref|YP_004383627.1|  [L=311]
Description: tetrahydromethanopterin S-methyltransferase subunit H [Methanosaeta concilii GP6]
Scores for complete 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-121  405.1   0.6   1.8e-121  404.9   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 !  404.9   0.6  9.9e-126  1.8e-121       1     298 [.       6     300 ..       6     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 404.9 bits;  conditional E-value: 9.9e-126
                              MtrH   1 keqkvleiaGvkiGGqpGeyPtvlvgtifyakhkivedekkGifdkeaaealikkqeelsdktGnPalvqvvGetee 77 
                                       ++q+v++ +  k+GGqpGeyPt  +gt+fya+hkiv d ++G+fd +aae l+++q+e+s++tGn  ++q+v e++e
  gi|330507199|ref|YP_004383627.1|   6 RKQEVFDFGKFKLGGQPGEYPTCCIGTMFYARHKIVSDPEHGVFDVAAAERLWNTQVEMSEVTGNSCMNQIVAESNE 82 
                                       68*************************************************************************** PP

                              MtrH  78 aivkyidfvadvtdaPllidstsaevklaaakyatevGladrviynsinasiedaeiealkesdveaaivlafnpmd 154
                                       a+ k id+++ + d P+lids++ ev++ ++k+ate+G+adr+i+nsinasi  +e+ a+kesd+++aivl fn+ +
  gi|330507199|ref|YP_004383627.1|  83 AMAKEIDWFVGISDYPFLIDSSAPEVRAFGVKHATEIGVADRAIHNSINASITPEELAAVKESDLDSAIVLIFNAIE 159
                                       ***************************************************************************** PP

                              MtrH 155 ptvegklkileegegtaekgllelaeeaGiekplidvavtplgsgagaavkaslavkaklGlPvGsgihnvpsaWdw 231
                                         ++gk++++++++g+a+k l++ a+e+Gi++plid+a++plg+g+ga+++a +avka +GlPvG+g hn +saWdw
  gi|330507199|ref|YP_004383627.1| 160 KGTKGKMEMMNKAAGGAQKPLMDYAKECGITRPLIDTAAMPLGAGSGATYRACIAVKAMYGLPVGGGFHNGASAWDW 236
                                       ***************************************************************************** PP

                              MtrH 232 lrefkkkekekaaeyevadvganlvqvilgsdfvlyGPienakkvfPavamvdilikeaakelgvel 298
                                       ++++kk++ke+ a   + d+g+nlv+ i+g+d+ lyGPiena ++fPa amvdi+ +e a+elg+e+
  gi|330507199|ref|YP_004383627.1| 237 MKKWKKQHKEAFA---PVDIGSNLVAGIVGADYYLYGPIENAPMIFPAAAMVDIMKAESAQELGLEV 300
                                       **********999...99**********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2204.28
//
Query:       gi|330507200|ref|YP_004383628.1|  [L=85]
Description: tetrahydromethanopterin S-methyltransferase subunit G [Methanosaeta concilii GP6]
Scores for complete 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   91.4   0.2    2.7e-26   91.2   0.2    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 !   91.2   0.2   1.5e-30   2.7e-26       2      63 ..      13      74 ..      12      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 1.5e-30
                              MtrG  2 iPsvvvdpddfnevkkrLdeieekvefvnsEiaqriGkkvGRdiGilYGlviGliillvyil 63
                                      +P +vvdpd+ + v++rL++ieek+ef++sE ++r+Gk++GRd+G++YG+++Gli++l+y+l
  gi|330507200|ref|YP_004383628.1| 13 VPVAVVDPDQLRDVMARLEKIEEKIEFYSSEKYMRAGKSIGRDLGMAYGICAGLILVLAYVL 74
                                      8***********************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); 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: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 602.00
//
Query:       gi|330507201|ref|YP_004383629.1|  [L=75]
Description: tetrahydromethanopterin S-methyltransferase subunit F [Methanosaeta concilii GP6]
Scores for complete sequence (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   94.9   0.6    1.7e-27   94.6   0.6    1.1  1  MtrF      Tetrahydromethanopterin S-methyltransferase, F subu
  ------ inclusion threshold ------
        0.1   13.3   0.0       0.12   13.1   0.0    1.1  1  DUF5593   Domain of unknown function (DUF5593)


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 !   94.6   0.6   1.9e-31   1.7e-27       1      61 [.      10      70 ..      10      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 1.9e-31
                              MtrF  1 gvptvnkpnmkaiksvvedirYraqLiaReqkLdSGvsatgivGfaiGfvlAllLvvlPvl 61
                                      g+p+v++pnm +i+++ved+rY+ qL+aRe+kL+SGv++t  vGfaiGfvlA+++++ P++
  gi|330507201|ref|YP_004383629.1| 10 GLPAVIEPNMPMIDAIVEDVRYKGQLLARETKLSSGVMSTVSVGFAIGFVLAIVMMLGPFA 70
                                      689********************************************************86 PP

>> DUF5593  Domain of unknown function (DUF5593)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05      0.12      35      86 ..      17      68 ..      11      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                           DUF5593 35 aalaavrsaiaevvrsgepvsritpksdrviraepVlgpdgrvhgVqvWvGt 86
                                      +++  + +++++v+ +g+ ++r+t  s  v+ ++ V ++ g v ++ +  G+
  gi|330507201|ref|YP_004383629.1| 17 PNMPMIDAIVEDVRYKGQLLARETKLSSGVMSTVSVGFAIGFVLAIVMMLGP 68
                                      6678899**************************************9998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 589.06
//
Query:       gi|330507202|ref|YP_004383630.1|  [L=243]
Description: tetrahydromethanopterin S-methyltransferase subunit A [Methanosaeta concilii GP6]
Scores for complete 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-84  279.3   2.0    1.2e-83  278.9   2.0    1.1  1  MtrA      Tetrahydromethanopterin S-methyltransferase, subuni
  ------ inclusion threshold ------
      0.095   12.1   2.3       0.36   10.2   2.3    2.0  1  MtrF      Tetrahydromethanopterin S-methyltransferase, F subu


Domain annotation for each model (and alignments):
>> MtrA  Tetrahydromethanopterin S-methyltransferase, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.9   2.0   1.4e-87   1.2e-83       1     173 []       4     176 ..       4     176 .. 0.99

  Alignments for each domain:
  == domain 1  score: 278.9 bits;  conditional E-value: 1.4e-87
                                       -----TTSS-S--S-EE--TT-SEEEE-TT-SS-HHHHHHCT-SEEE----TTHHHHHHHHHHHT-TT--EEEEEE- CS
                              MtrA   1 kkepaegWPvvkGdyevGdaespvavvtlgshleeeavleaGaaiaGplktenlGiekvvanvisnpnirflivtGa 77 
                                       kk+p++ WP+++G+yevG++espvav+t+gshl+++ +++aGaa+aGp+kten+Giek+vanvisnpnirf++vtG+
  gi|330507202|ref|YP_004383630.1|   4 KKKPSDPWPTITGEYEVGNPESPVAVCTCGSHLHNADLIKAGAALAGPCKTENIGIEKMVANVISNPNIRFVLVTGM 80 
                                       89*************************************************************************** PP

                                       --TTT-HHHHHHHHHHH-B-TTSBBTT--SSS-B-SSS-HHHHHHHHHH-EEEEEET---HHHHHHHHHHHHHT--- CS
                              MtrA  78 evkGhitGqalkalhenGvdkekkivgakGaiPfienlteeaverfqeqvelvdlidtedvgaikakikelvakdpg 154
                                       evkGhitGqa++a++++G+dke++i+gakGaiPfi+nlt ea+er+++qve v +++ted+gai+ k+kel++kdpg
  gi|330507202|ref|YP_004383630.1|  81 EVKGHITGQAVEAFTQSGIDKEGRIIGAKGAIPFIQNLTPEAIERWKNQVEAVMMLNTEDIGAIAGKVKELASKDPG 157
                                       ***************************************************************************** PP

                                       --SS-------XXXXXXXX CS
                              MtrA 155 afeeeplvievkeeeeeee 173
                                       a++ ep+ ie+ke++eeee
  gi|330507202|ref|YP_004383630.1| 158 ALDVEPMAIEIKEGGEEEE 176
                                       ***************9985 PP

>> MtrF  Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.3   4.1e-05      0.36      31      57 ..     208     234 ..     190     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.1e-05
                              MtrF  31 qkLdSGvsatgivGfaiGfvlAllLvv 57 
                                       +kL++G+   +i G+a+G++++l++ +
  gi|330507202|ref|YP_004383630.1| 208 NKLQAGIYVGKIEGIALGMTVVLVIFG 234
                                       79******************9999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1907.85
//
Query:       gi|330507203|ref|YP_004383631.1|  [L=116]
Description: tetrahydromethanopterin S-methyltransferase subunit B [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-35  121.2   0.1    2.1e-35  121.0   0.1    1.0  1  MtrB       Tetrahydromethanopterin S-methyltransferase subuni
  ------ inclusion threshold ------
      0.029   13.7   1.1      0.036   13.5   0.2    1.6  2  MtrF       Tetrahydromethanopterin S-methyltransferase, F sub
      0.033   13.8   0.2      0.082   12.5   0.1    1.7  2  MotB_plug  Membrane MotB of proton-channel complex MotA/MotB


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 !  121.0   0.1   3.6e-39   2.1e-35       1      94 []       3      96 ..       3      96 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.0 bits;  conditional E-value: 3.6e-39
                              MtrB  1 lvkvlpelnlvldpetgvvaearedvvllsldpvleeidkLekiaddlvnsLdpetallesypgRektlviaGlltnlf 79
                                      +v+v pel+l++dp++gvv+e+r+dvvl+++dpv+e+i+k++k+addlvn+L p+++ll+sy++R k+++iaGl+tn++
  gi|330507203|ref|YP_004383631.1|  3 FVRVSPELGLIFDPMKGVVSEQRADVVLFTFDPVYERIEKMDKVADDLVNQLVPDNELLSSYARRGKASYIAGLYTNIW 81
                                      599**************************************************************************** PP

                              MtrB 80 yGfivglviaallal 94
                                       Gfi+glv++++l+l
  gi|330507203|ref|YP_004383631.1| 82 VGFIIGLVLSFVLLL 96
                                      ***********9975 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 ?   -2.4   0.0      0.55   3.3e+03       9      20 ..      39      50 ..      38      55 .. 0.81
   2 ?   13.5   0.2     6e-06     0.036      29      58 ..      66      98 ..      59     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.55
                              MtrF  9 nmkaiksvvedi 20
                                      +++++++v++d+
  gi|330507203|ref|YP_004383631.1| 39 RIEKMDKVADDL 50
                                      578899999986 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6e-06
                              MtrF 29 ReqkLd..SGvsatgivGfaiGfvlAllLvv.l 58
                                      R +k +  +G+ +   vGf+iG+vl ++L++ +
  gi|330507203|ref|YP_004383631.1| 66 RRGKASyiAGLYTNIWVGFIIGLVLSFVLLLsM 98
                                      555554448999999**************9855 PP

>> MotB_plug  Membrane MotB of proton-channel complex MotA/MotB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.33     2e+03      34      54 ..      28      50 ..      28      54 .. 0.59
   2 ?   12.5   0.1   1.4e-05     0.082      26      56 ..      85     115 ..      83     116 .] 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.33
                         MotB_plug 34 vlLfsmssvdek..kfqalaesl 54
                                      v+Lf++  v e   k++++a+ l
  gi|330507203|ref|YP_004383631.1| 28 VVLFTFDPVYERieKMDKVADDL 50
                                      67777766655333666666655 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.4e-05
                         MotB_plug  26 mtLLlaFFvlLfsmssvdekkfqalaeslre 56 
                                       ++ L   FvlL+sm+ ++ ++f+ + ++l +
  gi|330507203|ref|YP_004383631.1|  85 IIGLVLSFVLLLSMAFTNPATFEIVKKALGG 115
                                       5667778******************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 887.32
//
Query:       gi|330507204|ref|YP_004383632.1|  [L=275]
Description: tetrahydromethanopterin S-methyltransferase subunit C [Methanosaeta concilii GP6]
Scores for 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-104  347.8  25.7   3.6e-104  347.6  25.7    1.0  1  MtrC      Tetrahydromethanopterin S-methyltransferase, subuni
  ------ inclusion threshold ------
      0.027   14.1  33.6       0.44   10.1   2.4    3.0  3  TauE      Sulfite exporter TauE/SafE
       0.16   12.3   0.1       0.16   12.3   0.1    4.1  5  Ost5      Oligosaccharyltransferase subunit 5
       0.64    9.7   6.4        7.2    6.3   0.4    2.3  2  DUF697    Domain of unknown function (DUF697)


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 !  347.6  25.7  8.1e-108  3.6e-104       1     265 [.       1     271 [.       1     273 [. 0.99

  Alignments for each domain:
  == domain 1  score: 347.6 bits;  conditional E-value: 8.1e-108
                              MtrC   1 msaggggkeaeeaipekkllalgivggligiylasvl....epalgsllaalgaicaivwGadavrrvasYglGTGV 73 
                                       ms+gg++++a +a+++kkl ++g+vg+++giyl+s+l    +++++s+++a++ai+a+v+Ga++vrrv++Yg+GTGV
  gi|330507204|ref|YP_004383632.1|   1 MSVGGSAGGAPSAYEPKKLRMYGLVGSIVGIYLGSILnsalNTEVFSFIGAVAAIFAVVMGANSVRRVCAYGIGTGV 77 
                                       9************************************999999********************************** PP

                              MtrC  74 PSigmlalgmGivaalaglavgsalkl.lagpiialvvaliiglvvgvlakkvikmkipileksttelaaagalsii 149
                                       PSigmlalgmGi+a+++gl+v+++l   ++gpii+l++a ++g+++gv+a+kvik++ip++e++ ++l++agal+i+
  gi|330507204|ref|YP_004383632.1|  78 PSIGMLALGMGIIAVMFGLSVAETLGFgMLGPIITLIYAGVFGYIIGVIANKVIKFNIPVMEEGNADLSMAGALAIL 154
                                       *************************99************************************************** PP

                              MtrC 150 glsvaiagsfeikailskviatGliallfilaglailhPfNaclGPdEkqdRTLklalekgalaliivgivsletes 226
                                       g+s+ai+g++ +++i+++v++tG+ia++fi++glailhPfNa+lGPdEkqdRTL++a++ g la++++gi +l t++
  gi|330507204|ref|YP_004383632.1| 155 GWSFAISGTLGYDDIVNDVLMTGYIAIIFIAGGLAILHPFNANLGPDEKQDRTLVNAIMVGGLAMTATGIGALLTQG 231
                                       ***************************************************************************** PP

                              MtrC 227 aaa.lvviivgliiWlisfkkfvklvkrdaakvkgtgllP 265
                                       + a l++ii+g++iW+++fk+++klvkrda +v+gtgllP
  gi|330507204|ref|YP_004383632.1| 232 LGAgLLQIIIGFAIWYYFFKMYYKLVKRDASAVVGTGLLP 271
                                       98889**********************************9 PP

>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  23.3    0.0022       9.9      66     232 ..      20     185 ..       1     187 [. 0.61
   2 ?    7.6  14.8    0.0006       2.7      13     145 ..      81     225 ..      79     226 .. 0.73
   3 ?   10.1   2.4   9.9e-05      0.44      66     111 ..     211     256 ..     202     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0022
                              TauE  66 llllllgsliGallGallllllpsellkllfgvlllllallmll.rkkr..srakgrerrptaillvligglvGlls 139
                                        ++ l+gs++G++lG++l ++l++e++  ++g++ +++a+ m + + +r  +        ++ + ++++++++G+++
  gi|330507204|ref|YP_004383632.1|  20 RMYGLVGSIVGIYLGSILNSALNTEVF-SFIGAVAAIFAVVMGAnSVRRvcA----YGIGTGVPSIGMLALGMGIIA 91 
                                       4556789**************999996.666777777777775413332221....223333333444445588888 PP

                              TauE 140 GllGiGgGfllvpllllllglplkkavatslllilvislagalg.yal.....agavdwpllllllpgallGallGa 210
                                        ++G ++      +l + +  p+ +++ + ++  ++ ++a  ++ +        g+ d++++++l++ ++  a+ G+
  gi|330507204|ref|YP_004383632.1|  92 VMFGLSVAE----TLGFGMLGPIITLIYAGVFGYIIGVIANKVIkF-NipvmeEGNADLSMAGALAILGWSFAISGT 163
                                       888888776....333333446666665555555554444433322.145567999999999999999998888888 PP

                              TauE 211 rlarrlsertlrrlfallllvl 232
                                            + + +l   ++++++++
  gi|330507204|ref|YP_004383632.1| 164 LGYDDIVNDVLMTGYIAIIFIA 185
                                       7655555556666666666655 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0006
                              TauE  13 gllGiGggliavPlLll.l....lppavavatsllavvatslsgalah.........rrrgnvdwrlllllllgsli 75 
                                       g+l +G+g+iav + l  +    + +   ++t + a v+++++g++a+           +gn d++++  l++ +  
  gi|330507204|ref|YP_004383632.1|  81 GMLALGMGIIAVMFGLSvAetlgFGMLGPIITLIYAGVFGYIIGVIANkvikfnipvMEEGNADLSMAGALAILGWS 157
                                       5666677777776555422434447777899999999999999999986655555544479**************** PP

                              TauE  76 GallGallllllpsellkllfgvlllllallmllrkkr.srakgrerrptaillvligglvGllsGllGiG 145
                                        a+ G+l    + +++l + + +++ +++ l +l ++  + +    +++++ l+ +i +++Gl+ + +GiG
  gi|330507204|ref|YP_004383632.1| 158 FAISGTLGYDDIVNDVLMTGYIAIIFIAGGLAILHPFNaNLG--PDEKQDRTLVNAI-MVGGLAMTATGIG 225
                                       **********99999988888888888888887766642233..3444444444454.889**99999999 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 9.9e-05
                              TauE  66 llllllgsliGallGallllllpsellkllfgvlllllallmllrk 111
                                       +++++  ++ ++ +Gall + l + ll++++g+++ ++ + m+++ 
  gi|330507204|ref|YP_004383632.1| 211 AIMVGGLAMTATGIGALLTQGLGAGLLQIIIGFAIWYYFFKMYYKL 256
                                       455666678889999***************************7744 PP

>> Ost5  Oligosaccharyltransferase subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.2     0.081   3.6e+02      15      60 ..      22      62 ..      12      75 .. 0.48
   2 ?   -2.8   5.7       1.7   7.7e+03       6      65 ..      40      92 ..      35      99 .. 0.51
   3 ?   -0.4   1.0      0.32   1.4e+03      56      66 ..      83      93 ..      74     118 .. 0.69
   4 ?   12.3   0.1   3.5e-05      0.16      12      63 ..     176     227 ..     169     230 .. 0.92
   5 ?   -0.6   0.1      0.36   1.6e+03      18      33 ..     237     252 ..     233     270 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.081
                              Ost5 15 lafvllligllltalfflyevtstkkkrslvkelllalvASlflGf 60
                                      +++v  ++g+ l ++   +   s +++  +    ++a++ ++ +G 
  gi|330507204|ref|YP_004383632.1| 22 YGLVGSIVGIYLGSIL--N---SALNTEVFSFIGAVAAIFAVVMGA 62
                                      5555555555555555..1...222222233333333333333444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                              Ost5  6 pvppslqptlafvllligllltalfflyevtstkkkrslvkelllalvASlflGfGvvfl 65
                                       +++++++++++v+ + ++++ a   +      ++  +    + +  ++ l+lG+G++++
  gi|330507204|ref|YP_004383632.1| 40 ALNTEVFSFIGAVAAIFAVVMGANS-V------RRVCAYGIGTGVPSIGMLALGMGIIAV 92
                                      5555666666666666655555444.1......112223333444444556666666655 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.32
                              Ost5 56 lflGfGvvfll 66
                                      l+lG+G+++++
  gi|330507204|ref|YP_004383632.1| 83 LALGMGIIAVM 93
                                      45555555544 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 3.5e-05
                              Ost5  12 qptlafvllligllltalfflyevtstkkkrslvkelllalvASlflGfGvv 63 
                                         ++a+++++ gl+++  f  +    +k+ r+lv+ ++++ +A  + G+G++
  gi|330507204|ref|YP_004383632.1| 176 TGYIAIIFIAGGLAILHPFNANLGPDEKQDRTLVNAIMVGGLAMTATGIGAL 227
                                       579****************9999999999*********************97 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.36
                              Ost5  18 vllligllltalffly 33 
                                       + ++ig+++  +ff  
  gi|330507204|ref|YP_004383632.1| 237 LQIIIGFAIWYYFFKM 252
                                       5568888888888744 PP

>> DUF697  Domain of unknown function (DUF697)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.1    0.0018         8      57     136 ..      48     132 ..      41     149 .. 0.75
   2 ?    6.3   0.4    0.0016       7.2     107     135 ..     221     249 ..     204     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0018
                            DUF697  57 lirelaelYgielgyegaqrLar.svlknlaglGlvelgtdllkqllslnlatklsar....aaQGvvagllTarvG 128
                                        i  +a ++ + +g ++ +r+    +++ + ++G+++lg+ ++  +++l++a  l  +    ++  + ag++ +++G
  gi|330507204|ref|YP_004383632.1|  48 FIGAVAAIFAVVMGANSVRRVCAyGIGTGVPSIGMLALGMGIIAVMFGLSVAETLGFGmlgpIITLIYAGVFGYIIG 124
                                       5788999********99999965269***********************8887765440000455566888888888 PP

                            DUF697 129 lsaieylr 136
                                       + a ++++
  gi|330507204|ref|YP_004383632.1| 125 VIANKVIK 132
                                       87776665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0016
                            DUF697 107 atklsaraaQGvvagllTarvGlsaieyl 135
                                       at + a ++QG++agll  ++G ++  y+
  gi|330507204|ref|YP_004383632.1| 221 ATGIGALLTQGLGAGLLQIIIGFAIWYYF 249
                                       444556689**************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2053.66
//
Query:       gi|330507205|ref|YP_004383633.1|  [L=229]
Description: tetrahydromethanopterin S-methyltransferase subunit D [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-93  312.9  27.9    1.4e-93  312.6  27.9    1.1  1  MtrD      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrD  Tetrahydromethanopterin S-methyltransferase, subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.6  27.9   7.6e-98   1.4e-93       2     218 .]       8     215 ..       7     215 .. 0.98

  Alignments for each domain:
  == domain 1  score: 312.6 bits;  conditional E-value: 7.6e-98
                              MtrD   2 illliliviggvligvgvhfvPvGGapaamaqatGvgtGtaqlaaGagltGlltaaalaektdslllillsGavgam 78 
                                       i+++++iv+gg+l+gvgvhfvPvGGapaamaqatG+gtGt+qlaaG+gltGll+a++++++td+++l+l+sGavga+
  gi|330507205|ref|YP_004383633.1|   8 IVYILEIVVGGLLVGVGVHFVPVGGAPAAMAQATGIGTGTVQLAAGSGLTGLLAAGLMMSVTDNIWLVLASGAVGAG 84 
                                       899************************************************************************** PP

                              MtrD  79 lmlaitmlvgnliyvygvGvvaasakvekdpitgdkqekyvsqGteGhgiPtvsfvsGviGgllgGiGGalvyyall 155
                                       +m++ tml g++iy y+vGv+ +sakv++dpitg++q  y+++Gt GhgiPtv+fvsG+iGg++gG+GGa++yyal+
  gi|330507205|ref|YP_004383633.1|  85 IMVGSTMLTGSWIYAYAVGVPFVSAKVTYDPITGFSQPPYIAPGTVGHGIPTVCFVSGLIGGMMGGLGGAMIYYALY 161
                                       ***************************************************************************** PP

                              MtrD 156 ellkaalklaaaaavalaailavglflvnavlasynigGtieGfhdpkfkrlpkavvaslvas 218
                                        ++          ++al+a++a+g+f+vnav+as+ni+GtieGfhdpkfk++p a+ a+l+as
  gi|330507205|ref|YP_004383633.1| 162 LING---------NAALSAMFAIGIFMVNAVIASWNIQGTIEGFHDPKFKKWPFAFRACLIAS 215
                                       6655.........789*********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1635.46
//
Query:       gi|330507206|ref|YP_004383634.1|  [L=301]
Description: tetrahydromethanopterin S-methyltransferase subunit E [Methanosaeta concilii GP6]
Scores for complete 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-128  426.1   8.8   5.7e-128  425.9   8.8    1.0  1  MtrE             Tetrahydromethanopterin S-methyltransferase,
     0.0078   16.6   0.4       0.35   11.3   0.1    3.0  3  Phage_holin_3_1  Phage holin family (Lysis protein S)


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 !  425.9   8.8  6.4e-132  5.7e-128       1     271 []       6     278 ..       6     278 .. 0.99

  Alignments for each domain:
  == domain 1  score: 425.9 bits;  conditional E-value: 6.4e-132
                              MtrE   1 lGvlalmgalatiagaaedlesdvgsqsnpnsqvqLapqmgylhrifnkaisGePvaygllaavagavalvllsalk 77 
                                       +G++a+mgalat+aga+ed+esdvgsqsnpnsqvqLa+q+g++hri+nkaisGeP+a++l++a+a+ va++l++a++
  gi|330507206|ref|YP_004383634.1|   6 MGLIAAMGALATVAGASEDIESDVGSQSNPNSQVQLAAQVGNPHRIYNKAISGEPPANALWCATAAIVAYTLITAFQ 82 
                                       8**************************************************************************** PP

                              MtrE  78 lnvvlaivlgalvaalvhgvyavtaylGriasqakfkqpvyldvlkshlgaivahafiavfaivvlsylmtlvlk.. 152
                                       +++++a+v ga+vaal++gv+++++y+Gr++sqa+f+q++yld+++ ++++i+aha+i+ f+i+++sy+m+++l   
  gi|330507206|ref|YP_004383634.1|  83 MPALMALVAGASVAALFNGVFSMSSYFGRNSSQARFNQWIYLDIVRYTTPSIMAHAWITSFCIATISYIMVYMLPtp 159
                                       ************************************************************************99888 PP

                              MtrE 153 hpfplpllaliwGitvGaiGsstGdvhyGaereyqkkefGaGvpvaasGdivrkaeaGlrnsidnalfcakfggplt 229
                                       hpfp+p++aliwG++vGaiGss+Gd+hyG ere+q+++fG G++++ sG+ivrkaeaGlrnsidna+fc+kfggp+t
  gi|330507206|ref|YP_004383634.1| 160 HPFPMPIIALIWGLAVGAIGSSVGDIHYGGEREFQNRAFGCGLNTMLSGQIVRKAEAGLRNSIDNAWFCTKFGGPAT 236
                                       ***************************************************************************** PP

                              MtrE 230 GlafglivflelWrtivfekvtagwlavivgliivllliiln 271
                                       G++fgl+vfl++Wrt+vf++vt++ +a+++g++++l+ + +n
  gi|330507206|ref|YP_004383634.1| 237 GMGFGLTVFLDNWRTTVFDPVTQASYAILMGVFFILVEVSYN 278
                                       ***********************************9987765 PP

>> Phage_holin_3_1  Phage holin family (Lysis protein S)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   3.9e-05      0.35      21      80 ..      36      95 ..      23     111 .. 0.85
   2 ?    1.5   0.0     0.044     4e+02      24      61 ..     174     212 ..     165     226 .. 0.84
   3 ?   -1.2   0.0      0.31   2.8e+03      19      39 ..     259     279 ..     245     287 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.9e-05
                   Phage_holin_3_1 21 iiaavlAlviallrviYdgkswkkvlleallCgllalavrsllellglpaslavviggli 80
                                       +++ lA+ +     iY++    +  ++al C++ a+++  l++++++pa +a v+g+ +
  gi|330507206|ref|YP_004383634.1| 36 NSQVQLAAQVGNPHRIYNKAISGEPPANALWCATAAIVAYTLITAFQMPALMALVAGASV 95
                                      566778888888888999999999999****************************99987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.044
                   Phage_holin_3_1  24 avlAlviallrviYdgk.swkkvlleallCgllalavrs 61 
                                       av A+  ++  + Y+g+ +++++++ + l  +l+  ++ 
  gi|330507206|ref|YP_004383634.1| 174 AVGAIGSSVGDIHYGGErEFQNRAFGCGLNTMLSGQIVR 212
                                       5667888899999999999********999999987765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.31
                   Phage_holin_3_1  19 pqiiaavlAlviallrviYdg 39 
                                       +  +a+++ +++ l+ v Y+ 
  gi|330507206|ref|YP_004383634.1| 259 QASYAILMGVFFILVEVSYNH 279
                                       446677777888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2381.04
//
Query:       gi|330507207|ref|YP_004383635.1|  [L=178]
Description: hypothetical protein MCON_1076 [Methanosaeta concilii GP6]
Scores for complete 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-51  174.0   6.7    3.1e-51  173.8   6.7    1.0  1  CarS-like     CDP-archaeol synthase
    2.1e-05   24.5   0.5    2.1e-05   24.5   0.5    2.1  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 !  173.8   6.7   3.5e-55   3.1e-51       5     175 .]       4     178 .]       1     178 [] 0.90

  Alignments for each domain:
  == domain 1  score: 173.8 bits;  conditional E-value: 3.5e-55
                         CarS-like   5 ilksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsilaldss 81 
                                       ++ + +l+lpayv+n++a ++GGGtp+d+G+ + dG r +GdG+t+rGt+aG+++Gvl+gl+q  +  + +l +  +
  gi|330507207|ref|YP_004383635.1|   4 LIVAFWLMLPAYVPNNFAAIFGGGTPLDMGRVFQDGERTLGDGKTFRGTIAGTVCGVLMGLVQNQIAPFFGLPV--F 78 
                                       35679*************************************************************88877655..6 PP

                         CarS-like  82 gsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllayp......vkllpieliilivl 152
                                       g+  e++ + l l++Ga+lGd+v +f krrl+++rG p +++dq+dfv+ga ll+        +  ++  ++i++++
  gi|330507207|ref|YP_004383635.1|  79 GTGFEQLPILLGLSLGAMLGDIVAAFFKRRLRMKRGAPLVLIDQIDFVIGAWLLTMLiaplwfWHNFTPLIMIIVLI 155
                                       7777888888899**************************************9988432335558889999999999* PP

                         CarS-like 153 itlvlhlsaniiayklglkdvwy 175
                                       it++lh  +nii yk+g k  ++
  gi|330507207|ref|YP_004383635.1| 156 ITPILHRITNIIGYKIGAKREPW 178
                                       *****************998777 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.5   2.3e-09   2.1e-05     170     233 ..      46     112 ..      42     118 .. 0.86
   2 ?    0.9   0.6     0.036   3.2e+02     179     207 ..     129     156 ..     122     176 .. 0.42

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.3e-09
                                       --BHHHHHHHHHHHHHHHHHHHHHHHCTS...---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT-S CS
                      CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskal...alsllhllllslllslvavfGDLveSglKRafgiK 233
                                       +KT  G i+G+v+ v++gl+  ++++ +      + ++ l + l lsl a++GD+v+  +KR+++ K
  gi|330507207|ref|YP_004383635.1|  46 GKTFRGTIAGTVCGVLMGLVQNQIAPFFGlpvFGTGFEQLPILLGLSLGAMLGDIVAAFFKRRLRMK 112
                                       6******************988777765433366677888899999******************998 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.036
                                       HHHHHHHHHHHHHHHHHCTS---TTSHHH CS
                      CTP_transf_1 179 Glvaavvvglllalvlskalalsllhlll 207
                                       +++++++++ l  ++      ++++ l++
  gi|330507207|ref|YP_004383635.1| 129 AWLLTMLIAPLWFWHNFTP-LIMIIVLII 156
                                       3333333322222222222.122222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1233.55
//
Query:       gi|330507208|ref|YP_004383636.1|  [L=119]
Description: hypothetical protein MCON_1078 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 867.84
//
Query:       gi|330507209|ref|YP_004383637.1|  [L=239]
Description: hypothetical protein MCON_1080 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-09   35.7   0.0    1.5e-08   34.6   0.0    1.6  1  HTH_3     Helix-turn-helix
    6.7e-09   35.6   0.0    1.6e-08   34.5   0.0    1.6  1  HTH_19    Helix-turn-helix domain
    7.3e-07   29.4   0.0    1.6e-06   28.3   0.0    1.5  1  HTH_31    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.026   14.4   0.0       0.11   12.4   0.0    2.1  1  HTH_25    Helix-turn-helix domain
      0.033   13.8   0.0       0.13   11.8   0.0    2.0  2  HTH_24    Winged helix-turn-helix DNA-binding
      0.054   13.9   0.0       0.11   12.9   0.0    1.6  1  HTH_26    Cro/C1-type HTH DNA-binding domain
       0.11   12.5   0.0        4.1    7.4   0.0    2.8  3  MarR      MarR family
       0.12   12.3   0.3       0.57   10.1   0.1    2.3  2  HTH_5     Bacterial regulatory protein, arsR 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 !   34.6   0.0   6.5e-12   1.5e-08       1      48 [.      32      80 ..      32      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 6.5e-12
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklakaL 48
                                      l+++R   g++q++L+  l +s+s is++E+G + +P + ++ k+ +aL
  gi|330507209|ref|YP_004383637.1| 32 LRKWRRNFGITQTDLSNHLKISPSVISDYESGrRKSPGIMIVSKIIDAL 80
                                      89*******************************999*********9997 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0     7e-12   1.6e-08       1      48 [.      29      76 ..      29      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 7e-12
                            HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllki 48
                                      Ge L++ R+++g+tq +l+++l+is+s is +E+g+++ p+++ + ki
  gi|330507209|ref|YP_004383637.1| 29 GETLRKWRRNFGITQTDLSNHLKISPSVISDYESGRRKSPGIMIVSKI 76
                                      899********************************999***7777443 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   7.2e-10   1.6e-06       3      54 ..      29      80 ..      29      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 7.2e-10
                            HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54
                                      G++Lr +R+  G++q+++  +l +s+s +s++E+Grr  p    + ++ +al
  gi|330507209|ref|YP_004383637.1| 29 GETLRKWRRNFGITQTDLSNHLKISPSVISDYESGRRKSPGIMIVSKIIDAL 80
                                      899**********************************999888888887773 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.9e-05      0.11       2      33 ..      32      63 ..      31      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.9e-05
                                      HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT CS
                            HTH_25  2 LraaRearglsleevaketkIrkdylealEed 33
                                      Lr+ R+  g++  ++++ +kI+++++   E++
  gi|330507209|ref|YP_004383637.1| 32 LRKWRRNFGITQTDLSNHLKISPSVISDYESG 63
                                      999***********************988877 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 ?   11.8   0.0   5.9e-05      0.13      17      36 ..      40      59 ..      36      60 .. 0.89
   2 ?   -3.0   0.0       2.4   5.5e+03      19      27 ..     119     127 ..     117     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.9e-05
                            HTH_24 17 risqreLAerlglSpstvnr 36
                                      +i+q++L+ +l +Sps ++ 
  gi|330507209|ref|YP_004383637.1| 40 GITQTDLSNHLKISPSVISD 59
                                      8***************9886 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.4
                            HTH_24  19 sqreLAerl 27 
                                       + +++A++l
  gi|330507209|ref|YP_004383637.1| 119 PLNDIAKKL 127
                                       568999998 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.1e-05      0.11       2      50 ..      32      80 ..      31      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-05
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaL 50
                                      Lr++ +  git+++L+ ++ is + +s + +g+ +++ +   +ki daL
  gi|330507209|ref|YP_004383637.1| 32 LRKWRRNFGITQTDLSNHLKISPSVISDYESGRRKSPGIMIVSKIIDAL 80
                                      78888889************************98888888888887776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0018       4.1       7      35 ..      30      58 ..      24      60 .. 0.82
   2 ?   -1.7   0.0       1.3   2.9e+03      32      42 ..      71      81 ..      70      84 .. 0.84
   3 ?    1.6   0.0      0.12   2.6e+02      12      28 ..     112     128 ..     108     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHH CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvt 35
                                      ++Lr+ +++ ++++++L ++l++s+s ++
  gi|330507209|ref|YP_004383637.1| 30 ETLRKWRRNFGITQTDLSNHLKISPSVIS 58
                                      56777778889***************987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                                      HHHHHHHHHHH CS
                              MarR 32 stvtrvldrLe 42
                                      + v++++d+L 
  gi|330507209|ref|YP_004383637.1| 71 MIVSKIIDALL 81
                                      679*****997 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.12
                                       HHHSTTEEHHHHHHHHT CS
                              MarR  12 lyeqgplsvseLakklg 28 
                                       +++q+pl + ++akkl 
  gi|330507209|ref|YP_004383637.1| 112 CEYQEPLPLNDIAKKLD 128
                                       7899**********996 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 ?   10.1   0.1   0.00025      0.57      19      34 ..      44      59 ..      42      60 .. 0.90
   2 ?   -2.1   0.0       1.6   3.5e+03       9      26 ..     109     128 ..     108     129 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                                      HHHHHHHTS-HHHHHH CS
                             HTH_5 19 celaeelglsqstvSh 34
                                      ++l+++l++s+s +S 
  gi|330507209|ref|YP_004383637.1| 44 TDLSNHLKISPSVISD 59
                                      79************96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                                       HHHTT..SSEEHHHHHHHHT CS
                             HTH_5   9 klLae..gelcvcelaeelg 26 
                                       ++++e  ++l   ++a++l+
  gi|330507209|ref|YP_004383637.1| 109 CSVCEyqEPLPLNDIAKKLD 128
                                       67777766788899999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1697.53
//
Query:       gi|330507210|ref|YP_004383638.1|  [L=345]
Description: hydroxymethylglutaryl-CoA synthase [Methanosaeta concilii GP6]
Scores for complete 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   36.4   0.0    8.1e-09   35.5   0.0    1.5  1  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    3.8e-06   26.7   0.0    0.00019   21.2   0.0    2.4  3  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
  ------ inclusion threshold ------
      0.026   13.9   0.1      0.041   13.3   0.1    1.2  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 !   35.5   0.0   1.4e-12   8.1e-09       2      84 ..     219     301 ..     218     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.4e-12
                                       HHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB-..-THHHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEE CS
                     ACP_syn_III_C   2 ekagltpedidalvphqanlriidavakklglpeekvv..vnldeyGntsaasiplaLdeaveegklkpgdlvllvg 76 
                                       e+ + +ped d+ v+hq n ++   vak lg++++++     +  +Gnt +as ++ L+  ++    +pg+++ +++
  gi|330507210|ref|YP_004383638.1| 219 ERMKTRPEDYDYAVFHQPNGKFPVRVAKMLGFSKKQIEpgLVVPMIGNTYSASCLIGLAATLD--IARPGERIFVTS 293
                                       677889*****************************775115569*******************..99********** PP

                                       EETTTEEE CS
                     ACP_syn_III_C  77 fGaGltwg 84 
                                       fG G    
  gi|330507210|ref|YP_004383638.1| 294 FGSGAGSD 301
                                       ***97655 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 ?   -1.8   0.0      0.32   1.9e+03     128     161 ..      46      79 ..      37      82 .. 0.82
   2 ?    2.0   0.0     0.022   1.3e+02      66      82 ..     224     240 ..     204     249 .. 0.72
   3 !   21.2   0.0   3.2e-08   0.00019     139     206 ..     250     312 ..     242     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHHHHHHTGGGGHHHHHH---GGGH CS
                    HMG_CoA_synt_C 128 lekallkiakelfkkkvkpsllvptevGnmYtas 161
                                       l+   + ia e   +  + + + p+++G +Yt s
  gi|330507210|ref|YP_004383638.1|  46 LDEDAVTIAVEAARNALDRADVDPKRIGAIYTGS 79 
                                       56667788888888888889999999*****987 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.022
                                       -GGG-SEEEE--SSHHH CS
                    HMG_CoA_synt_C  66 tlddfdyvifhsPfckl 82 
                                         +d+dy +fh P  k+
  gi|330507210|ref|YP_004383638.1| 224 RPEDYDYAVFHQPNGKF 240
                                       45799********9886 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 3.2e-08
                                       HHHHHTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--S CS
                    HMG_CoA_synt_C 139 lfkkkvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvs 206
                                       + kk+++p l+vp  +Gn Y as    la+ l         g+ri + s+GsG  +  fs++v +  +
  gi|330507210|ref|YP_004383638.1| 250 FSKKQIEPGLVVPM-IGNTYSASCLIGLAATLD----IARPGERIFVTSFGSGAGSDAFSIKVLDRIE 312
                                       56889999999995.9****************3....34469*********************88765 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.8e-06     0.041      22     112 ..      49     139 ..      39     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.8e-06
                                       -HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHH CS
                        Thiolase_N  22 saeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqs 98 
                                        a+ ++ ea++++l++a vdp+ +  ++ G   +  + +     +  ++  + + ++   + +c  g +a+ ++ + 
  gi|330507210|ref|YP_004383638.1|  49 DAVTIAVEAARNALDRADVDPKRIGAIYTGSESHPYAVKPTGTIVGQAVCTSSSFTTADFEFACKAGTAAIQACLGL 125
                                       57788999**********************9888766555555555555555666888899**************** PP

                                       HHTTSHSEEEEEEE CS
                        Thiolase_N  99 iaageadvvvagGv 112
                                       + +  +d  +a+G+
  gi|330507210|ref|YP_004383638.1| 126 VGSDMIDLGLAIGA 139
                                       ************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2461.26
//
Query:       gi|330507211|ref|YP_004383639.1|  [L=387]
Description: thiolase [Methanosaeta concilii GP6]
Scores for complete sequence (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   90.6   3.2    1.6e-25   89.9   2.1    1.8  2  Thiolase_N       Thiolase, N-terminal domain
    9.8e-11   41.4   0.5    3.1e-10   39.8   0.5    1.9  1  Thiolase_C       Thiolase, C-terminal domain
    1.2e-07   31.6   9.7    2.1e-07   30.8   5.5    3.1  5  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
     0.0065   15.2   0.1      0.012   14.4   0.1    1.3  1  SpoVAD           Stage V sporulation protein AD (SpoVAD)
  ------ inclusion threshold ------
      0.031   14.1   3.0        1.9    8.4   1.5    2.6  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
       0.14   12.2   3.2          1    9.4   0.0    3.2  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   2.1   5.4e-29   1.6e-25       2     258 ..       5     224 ..       4     226 .. 0.91
   2 ?   -1.6   0.0      0.45   1.4e+03      19      46 ..     254     281 ..     241     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 5.4e-29
                                       EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-T.T CS
                        Thiolase_N   2 vivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipe.e 75 
                                        i++   t++g+      d s +++ aea+  ++e+a+++ e++d ++vGn+  + + +q  i   +a  ag+++ +
  gi|330507211|ref|YP_004383639.1|   5 SIIGVGCTKFGE----RWDSSLRDMIAEAGVLAIEDAEITGEQIDALYVGNMSGGrFIEQEhIGALIADCAGLSRlH 77 
                                       677888888888....88999********************************999777776888899999*98658 PP

                                       SEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT.TGGSSSSEEEEEHHHHHHTEETTT CS
                        Thiolase_N  76 vpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr.sglklgdekakdllipdgladafn 151
                                       vp+++v+ +c+Sg  a+ +a+ ++a+g +d+v+a GvE+m++++  +++d+  + +  + e   + + p        
  gi|330507211|ref|YP_004383639.1|  78 VPSTRVEAACASGGLALRQAVMAVASGYCDIVIAAGVEKMTDVSSGTAADALaAAADREWECFFGATFPA------- 147
                                       *********************************************9998876244455556667777777....... PP

                                       TSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHT CS
                        Thiolase_N 152 eehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLak 228
                                           ++ a++  ++y+ + ++ +++Avk+h++a  ++ a+ ++ ei                d+  rs+++a++L+ 
  gi|330507211|ref|YP_004383639.1| 148 --LYAMMAKMHMRRYGTTHDQMAQVAVKNHHHACMNPIAQ-YQMEI--------------GIDDVNRSSMVADPLHV 207
                                       ..889***********************************.*****..............789************** PP

                                       S-BSSSTTSS-BTTSB--BEEEEEEEEEEE CS
                        Thiolase_N 229 lkpaFkkeGtvtAgnasqisDGaaavllms 258
                                       l             ++s+isDGa+ v+l++
  gi|330507211|ref|YP_004383639.1| 208 L-------------DCSPISDGASVVVLAP 224
                                       *.............*************986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.45
                                       TTS-HHHHHHHHHHHHHHHHTS-GGGCC CS
                        Thiolase_N  19 kdlsaeeLlaealkallekagvdpeevd 46 
                                       +dl++ +   +a++++  +ag++p +vd
  gi|330507211|ref|YP_004383639.1| 254 RDLTTLDATVHAGRSAFRQAGIEPRQVD 281
                                       6778888888999999999999999998 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.5     1e-13   3.1e-10      24     114 ..     262     370 ..     244     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1e-13
                                       HHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-T CS
                        Thiolase_C  24 PayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPl 82 
                                        + a + +  +ag++ +++d+ E+++ F+   + ++++l++ +                    vN  GG  a GHP+
  gi|330507211|ref|YP_004383639.1| 262 TVHAGRSAFRQAGIEPRQVDVAEVHDCFTIAEILAIEDLGFVEkghggraaeegltaldgeVAVNTSGGLKACGHPV 338
                                       56788999*********************************999***************9889************** PP

                                       TTHHHHHHHHHHHHHHHCTTSEEEEEEEETTT CS
                        Thiolase_C  83 GasGaRivvtllselkkeggklgvaalCiggg 114
                                       Ga+G +++  ++ +l+ e g+  v  + ig +
  gi|330507211|ref|YP_004383639.1| 339 GATGIKQAYEIALQLRGEAGRRQVDEVEIGLA 370
                                       ***************99988877766666544 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.78   2.3e+03       2      17 ..       2      17 ..       1      38 [. 0.72
   2 ?    0.1   0.0      0.16   4.9e+02      92     126 ..      26      60 ..      16      69 .. 0.79
   3 !   30.8   5.5   7.1e-11   2.1e-07     164     222 ..      76     134 ..      62     143 .. 0.88
   4 ?   -2.7   0.0       1.2   3.5e+03     239     253 .]     214     228 ..     211     228 .. 0.88
   5 ?   -1.9   0.0      0.67     2e+03      95     113 ..     265     283 ..     260     292 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.78
                                      --EEEEEEEEEBTTBS CS
                     ketoacyl-synt  2 epvaivGmgarfPggn 17
                                      ++v i+G+g++  g +
  gi|330507211|ref|YP_004383639.1|  2 RSVSIIGVGCTKFGER 17
                                      7899*****9865555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHH CS
                     ketoacyl-synt  92 lleaawealedagltpeeldgsrvgvfiGvgagdy 126
                                         ea   a+eda++t e++d   vg++ G    ++
  gi|330507211|ref|YP_004383639.1|  26 IAEAGVLAIEDAEITGEQIDALYVGNMSGGRFIEQ 60 
                                       56778889***********9999999988765555 PP

  == domain 3  score: 30.8 bits;  conditional E-value: 7.1e-11
                                       --SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-T CS
                     ketoacyl-synt 164 lrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllsp 222
                                       l+ ps  v++AC+S+  a+ +av+++ sg +d+++a Gve ++  ++  + +a+++ ++
  gi|330507211|ref|YP_004383639.1|  76 LHVPSTRVEAACASGGLALRQAVMAVASGYCDIVIAAGVEKMTDVSSGTAADALAAAAD 134
                                       67799***************************************999999999985554 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.2
                                       B-EEEEEEEEECHHH CS
                     ketoacyl-synt 239 GEGvGavvLkrleda 253
                                       ++G+ +vvL + e+a
  gi|330507211|ref|YP_004383639.1| 214 SDGASVVVLAPTETA 228
                                       89*******999876 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 0.67
                                       HHHHHHHHHTS-HHTCTTG CS
                     ketoacyl-synt  95 aawealedagltpeeldgs 113
                                       a + a+++ag++p+++d  
  gi|330507211|ref|YP_004383639.1| 265 AGRSAFRQAGIEPRQVDVA 283
                                       67889********998755 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 !   14.4   0.1     4e-06     0.012      45     132 ..      16     113 ..      11     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4e-06
                                       SSHHHHHHHHHHHHHHHHHHHTT--GGG-SEEEEEES.....SGG.....GHHHHHHHHHH---EEEB--GGGHHHH CS
                            SpoVAD  45 ksfekaesklleeavkkalkkanlkkedidfllaGDL.....lnq.....lisssfaarelkiPflglygaCstsae 111
                                       + ++   + ++ ea   a++ a+++ e+id l  G++     ++q     li+   +   l++P   + +aC++   
  gi|330507211|ref|YP_004383639.1|  16 ERWDSSLRDMIAEAGVLAIEDAEITGEQIDALYVGNMsggrfIEQehigaLIADCAGLSRLHVPSTRVEAACASGGL 92 
                                       5799999***********************987665422222666333335666677899***************** PP

                                       HHHHHHHHHHTTS-SEEEEEE CS
                            SpoVAD 112 slalaallvdggfakrvlaat 132
                                       +l  a ++v +g+ + v+aa 
  gi|330507211|ref|YP_004383639.1|  93 ALRQAVMAVASGYCDIVIAAG 113
                                       ******************985 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.5   0.00062       1.9       3      40 ..      83     120 ..      82     135 .. 0.91
   2 ?    4.4   0.0     0.011        34      40      71 ..     201     231 ..     194     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00062
                                       EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGC CS
                       ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlski 40 
                                       ++aaC++   al +A  +++sg +  v+  g e+++++
  gi|330507211|ref|YP_004383639.1|  83 VEAACASGGLALRQAVMAVASGYCDIVIAAGVEKMTDV 120
                                       689*************************9**9998875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.011
                                       CS-TTTHHHHTTB-EEEEEEEEEEESSSSCEE CS
                       ACP_syn_III  40 ilDwkdrstavlfGDGAgAvvleaseeegari 71 
                                       + D+     +   +DGA  vvl ++e+ + r+
  gi|330507211|ref|YP_004383639.1| 201 VADPLHVLDCSPISDGASVVVLAPTETAR-RF 231
                                       56666666777889*********996443.44 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 ?   -1.4   0.3      0.77   2.3e+03      90     106 ..      85     101 ..      24     106 .. 0.58
   2 ?    9.4   0.0   0.00034         1      22      52 ..     258     288 ..     237     297 .. 0.79
   3 ?    1.5   0.0     0.097   2.9e+02      87     108 ..     334     355 ..     326     363 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.77
                                       -GGGHHHHHHHHHHHHH CS
                   Ketoacyl-synt_C  90 leaAaGvaelikvvlal 106
                                       + +A+G ++l ++v+a+
  gi|330507211|ref|YP_004383639.1|  85 AACASGGLALRQAVMAV 101
                                       34566666666666665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00034
                                       THHHHHHHHHHHHHHHT--GGGEEEEE-SS- CS
                   Ketoacyl-synt_C  22 ngeaqaraiekalaeagvdpedvdyveahgt 52 
                                         +a  +a ++a+++ag++p++vd+ e h+ 
  gi|330507211|ref|YP_004383639.1| 258 TLDATVHAGRSAFRQAGIEPRQVDVAEVHDC 288
                                       4567788899*******************86 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.097
                                       H-B-GGGHHHHHHHHHHHHHHH CS
                   Ketoacyl-synt_C  87 iGHleaAaGvaelikvvlalkh 108
                                        GH  +A G+ ++  ++l+l+ 
  gi|330507211|ref|YP_004383639.1| 334 CGHPVGATGIKQAYEIALQLRG 355
                                       7***************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 2844.96
//
Query:       gi|330507212|ref|YP_004383640.1|  [L=147]
Description: hypothetical protein MCON_1083 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-19   70.2   0.0    1.4e-19   69.8   0.0    1.2  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
      2e-10   40.3   3.1    3.5e-10   39.6   3.1    1.4  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.034   13.8   0.5      0.034   13.8   0.5    1.7  2  zf-CCHC_5      GAG-polyprotein viral zinc-finger
      0.058   13.1   0.6      0.088   12.5   0.6    1.2  1  TackOD1        Thaumarchaeal output domain 1
       0.13   12.2   0.0       0.17   11.8   0.0    1.1  1  FdhE           Protein involved in formate dehydrogenase form
       0.25   11.6   1.9       0.55   10.4   1.9    1.6  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0   4.8e-23   1.4e-19       3      65 .]      50     111 ..      48     111 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 4.8e-23
                                       EE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                     OB_aCoA_assoc   3 elsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                       +++g+Gt+ ++t++h a + f+  +Py +++++Ldeg++i++++v   + ev+iGmrVravfr
  gi|330507212|ref|YP_004383640.1|  50 AFKGTGTIITYTTIHNATDDFERLTPYNLAIIQLDEGPKITGQIVSSQE-EVKIGMRVRAVFR 111
                                       679******************************************9875.599*********7 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   3.1   1.2e-13   3.5e-10       3      34 ..      12      43 ..      10      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.2e-13
                           DUF35_N  3 aaaegrLvgqrCpdCGtvqfPPravCphCgsd 34
                                        +++ L+g++C  C  ++fPPr+ Cp+C+++
  gi|330507212|ref|YP_004383640.1| 12 IPQRYNLLGTHCNRCNEYFFPPRNLCPNCRRG 43
                                      689**************************976 PP

>> zf-CCHC_5  GAG-polyprotein viral zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3       1.6   4.9e+03       5       8 ..      23      26 ..      21      27 .. 0.79
   2 ?   13.8   0.5   1.1e-05     0.034       1      16 [.      33      48 ..      33      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                                      -TTT CS
                         zf-CCHC_5  5 CpRC 8 
                                      C RC
  gi|330507212|ref|YP_004383640.1| 23 CNRC 26
                                      8899 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.1e-05
                                      ---B-TTT-SSBS-TT CS
                         zf-CCHC_5  1 ppglCpRCkkgkHwar 16
                                      p +lCp C +g H  +
  gi|330507212|ref|YP_004383640.1| 33 PRNLCPNCRRGAHLES 48
                                      679**********865 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   2.9e-05     0.088      75      95 ..      22      42 ..      15      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                           TackOD1 75 lCpsCksghlnvrevCpkCkS 95
                                      +C++C+ + +  r+ Cp+C+ 
  gi|330507212|ref|YP_004383640.1| 22 HCNRCNEYFFPPRNLCPNCRR 42
                                      7******************74 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.6e-05      0.17     195     229 ..      21      55 ..      12      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-05
                                       EEETTT--EEE--TTS-TTT---SS-EEE------ CS
                              FdhE 195 lhCslCeteWhvvRvkCsnCeetkelaylsledek 229
                                        hC+ C+  +   R  C nC   ++l+ +++ ++ 
  gi|330507212|ref|YP_004383640.1|  21 THCNRCNEYFFPPRNLCPNCRRGAHLESHAFKGTG 55 
                                       59*************************99987765 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.9   0.00019      0.55       9      39 ..      14      40 ..      13      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00019
                     Auto_anti-p27  9 kGwtMLaetCpvCgvPLmrdrkggkvyCvaC 39
                                      + + +L+++C +C+   +  r   + +C++C
  gi|330507212|ref|YP_004383640.1| 14 QRYNLLGTHCNRCNEYFFPPR---N-LCPNC 40
                                      5689**********9999954...4.99999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1092.12
//
Query:       gi|330507213|ref|YP_004383641.1|  [L=354]
Description: hypothetical protein MCON_1085 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2726.13
//
Query:       gi|330507214|ref|YP_004383642.1|  [L=249]
Description: hypothetical protein MCON_1087 [Methanosaeta concilii GP6]
Scores for complete 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   17.8   0.1       0.44   11.0   0.1    2.6  2  Membrane_bind  Membrane binding


Domain annotation for each model (and alignments):
>> Membrane_bind  Membrane binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0036        65      16      66 ..      62     118 ..      48     123 .. 0.78
   2 !   11.0   0.1   2.4e-05      0.44      12      62 ..     147     197 ..     143     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0036
                                       EEEEE......EETT---EEEETTSS-EEEEE---SSTTSE.EEEEEEEEESST-SE CS
                     Membrane_bind  16 Yklti......kayqigpveivsgddyeeveivkltpkdsedivcqisvrdkatgay 66 
                                       Y+  i      ++++++  ++++ d   +++i  + + +s d v+++sv+d + g y
  gi|330507214|ref|YP_004383642.1|  62 YETEIkvpnkpNRFSVTARNVQNLDAGMKMGIWITKSFESHDGVVHLSVADIPPGMY 118
                                       555554455557888889999999999999999999999999999999999888777 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.4e-05
                                       T-TTEEEEEEETT---EEEETTSS-EEEEE---SSTTSE..EEEEEEEEESS CS
                     Membrane_bind  12 kegkYkltikayqigpveivsgddyeeveivkltpkdse.divcqisvrdka 62 
                                       ++g+Ykl i++ +i +++   + d +  + v +++k+++ +  +++sv++k+
  gi|330507214|ref|YP_004383642.1| 147 SSGSYKLVIDTTGIPESDYLIEGDGD-AKTVRIMSKEENrSSASDVSVAEKK 197
                                       6799**********966655444444.59*********999*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); 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 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1749.15
//
Query:       gi|330507215|ref|YP_004383643.1|  [L=355]
Description: hypothetical protein MCON_1089 [Methanosaeta concilii GP6]
Scores for complete 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-108  361.9   0.7     3e-108  361.7   0.7    1.0  1  DUF1616          Protein of unknown function (DUF1616)
  ------ inclusion threshold ------
       0.12   10.6   8.0       0.16   10.2   8.0    1.1  1  DUF2070          Predicted membrane protein (DUF2070)


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 !  361.7   0.7  3.3e-112    3e-108       3     293 .]      16     313 ..      14     313 .. 0.95

  Alignments for each domain:
  == domain 1  score: 361.7 bits;  conditional E-value: 3.3e-112
                           DUF1616   3 vlalllllailvpvlnetplRivlglplvLflPGYaliaaLFPekrdidgieRlaLSfglSiaivpliglvlnvtpw 79 
                                       v+++l++l++++ +l++ +lRi++gl++vLf+PGY+liaaLFP+k+d+dgieR+aLSfglSia+vpligl+ln+tpw
  gi|330507215|ref|YP_004383643.1|  16 VVLALAVLLFTLTPLSSLFLRIPIGLLMVLFVPGYVLIAALFPKKGDLDGIERIALSFGLSIAVVPLIGLGLNYTPW 92 
                                       566777777777889************************************************************** PP

                           DUF1616  80 girlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleek.sesrldkalnvlLvvsivlavaa 155
                                       girl p+++s+ +ftll+a+vA++rR +l++eerfs++lr++i slk+e + + ++  +dkal+++L++si+++++a
  gi|330507215|ref|YP_004383643.1|  93 GIRLIPVVLSIVAFTLLMAAVAYWRRISLSPEERFSLNLRQWIGSLKDEIRAEgERGWVDKALTIILILSIIASIVA 169
                                       ****************************************************988889******************* PP

                           DUF1616 156 lgyavvaPkegekfTelyllgedgdelvaenypteltagesqevivgieNhEheevnYtvvvllqev.......... 222
                                       l+y+vv+PkegekfTe+y+lg++g   +a +ypte+ ag++++vivg++NhE++ +nYt+++ll+++          
  gi|330507215|ref|YP_004383643.1| 170 LVYVVVTPKEGEKFTEFYILGPGG---KAYDYPTEVRAGNNSTVIVGVVNHEYRLTNYTMEILLNNTpavdiqlndt 243
                                       ************************...************************************************99 PP

                           DUF1616 223 ....tdeeevevlerteldrrevtladnetweqelevepeatgenlrleflLYkdevpeeptteeayrslhlwVn 293
                                           ++ e+ + +    + +++++l++n+tweq+l++ +++tg++++l+flLYk+      + +++yr+lhlwVn
  gi|330507215|ref|YP_004383643.1| 244 aialSTFEHDRSAPIIPIMSMNLSLQHNDTWEQPLTYVLDETGDRQKLQFLLYKE-----GNFTAPYRDLHLWVN 313
                                       9888333334445677999************************************.....**************7 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   8.0   1.8e-05      0.16      48     181 ..      12     182 ..       7     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 1.8e-05
                           DUF2070  48 alvaflltlpvlrilggrltykrslflalltelivviisllaillsall........qalvllalvlslalvfalrl 116
                                       +l+a++l l vl ++   lt   slfl + + l++v+++   +l++al+         + + l++ ls+a+v  + l
  gi|330507215|ref|YP_004383643.1|  12 LLAAVVLALAVLLFT---LTPLSSLFLRIPIGLLMVLFVPGYVLIAALFpkkgdldgIERIALSFGLSIAVVPLIGL 85 
                                       678889999999888...999999*********************99999988887777778888888888888888 PP

                           DUF2070 117 lvlvavsdesllkavlpaliqpllailllvly................................fspesflllllls 161
                                        + ++  + +l+ +vl  ++ +ll+++++++                                   ++   ++l+ls
  gi|330507215|ref|YP_004383643.1|  86 GLNYTPWGIRLIPVVLSIVAFTLLMAAVAYWRrislspeerfslnlrqwigslkdeiraegergWVDKALTIILILS 162
                                       88888888888888888888888888888888******************************884466667777777 PP

                           DUF2070 162 lifalavylfivvvdrplkr 181
                                       +i  +++++++vv  + +++
  gi|330507215|ref|YP_004383643.1| 163 IIASIVALVYVVVTPKEGEK 182
                                       77777777887777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2537.68
//
Query:       gi|330507216|ref|YP_004383644.1|  [L=144]
Description: hypothetical protein MCON_1090 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1157.01
//
Query:       gi|330507217|ref|YP_004383645.1|  [L=281]
Description: hypothetical protein MCON_1091 [Methanosaeta concilii GP6]
Scores for complete 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   0.1    2.9e-13   49.6   0.1    1.3  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    7.5e-09   35.5   0.1    1.7e-07   31.0   0.1    2.1  1  MafB19-deam      MafB19-like deaminase


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.1   3.2e-17   2.9e-13       6      99 ..     103     219 ..      99     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 3.2e-17
                                       HHHHHHHHHHHHHHTTTSCSEEEEEEE..TT..EEE..EEEESBHHCCTGTTB-HHHHHHHHHHHH.TSSCE..... CS
                   dCMP_cyt_deam_1   6 kllelalkaakeaqkcsnfkVGavivk..ng..eii..stgyngepaggsktiHAEvnAilkaakn.ggskl..... 70 
                                       ++++la++aa+e+ +++  +++a i++  n   +i+     +n+     ++t+HAE++Ai++a+   g  +l     
  gi|330507217|ref|YP_004383645.1| 103 RWMQLACLAARESVEEKGGPFAALILQidNCtdQILryWINHNQVTSALDPTAHAEIMAIRSACASlGVFDLgsirk 179
                                       79************************995331133311446677777788**************997766779**** PP

                                       ...........TTEEEEEEE--BHHHHHHHHHHT-SEEEE CS
                   dCMP_cyt_deam_1  71 ...........egatlyvtlePCsmCakaiiqsgikkvvv 99 
                                                    +++y + ePC+mC  ai +++i  + +
  gi|330507217|ref|YP_004383645.1| 180 desklaqpgdlSHCVIYSSAEPCPMCYAAICWANIPMLLF 219
                                       ********99999********************9987766 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1   1.9e-11   1.7e-07       4     106 ..     102     226 ..      99     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.9e-11
                       MafB19-deam   4 ekafrkalaevekatkikedkiga....vivkdkkvia..rgsnekelnakataHaEi...............aalq 59 
                                       +++++ a   +++ ++ k+ + +a    ++   ++++   +++n+     ++taHaEi                +++
  gi|330507217|ref|YP_004383645.1| 102 DRWMQLACLAARESVEEKGGPFAAlilqIDNCTDQILRywINHNQVTSALDPTAHAEImairsacaslgvfdlGSIR 178
                                       67888888889999999999999855444444566654227888888899********7777777777777777777 PP

                       MafB19-deam  60 qAakklksk.rlddatlyvtlepCdmCagaivqaglkklvygagnpks 106
                                       +   kl++   l+ +++y   epC+mC  ai  a+++ l+++a   ++
  gi|330507217|ref|YP_004383645.1| 179 KDESKLAQPgDLSHCVIYSSAEPCPMCYAAICWANIPMLLFAATRFDA 226
                                       77666665425899**************************99986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2279.60
//
Query:       gi|330507218|ref|YP_004383646.1|  [L=390]
Description: YVTN family beta-propeller repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.1     0.0095   15.2   0.0    4.3  4  Lactonase     Lactonase, 7-bladed beta-propeller
    2.8e-08   32.7   0.3     0.0032   16.1   0.1    2.7  2  Cytochrom_D1  Cytochrome D1 heme domain
    7.4e-07   29.3   1.3        1.2    9.3   0.0    4.8  5  Arylesterase  Arylesterase
    8.8e-07   28.8   0.1       0.32   10.5   0.0    4.1  5  SGL           SMP-30/Gluconolactonase/LRE-like region
    7.6e-05   22.6   0.5         21    5.4   0.0    5.3  5  NHL           NHL repeat
     0.0018   18.1   0.2        8.7    6.4   0.0    3.8  3  PD40          WD40-like Beta Propeller Repeat
  ------ inclusion threshold ------
        0.1   11.4   0.0       0.89    8.3   0.0    2.1  2  SBP56         56kDa selenium binding protein (SBP56)


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 !    4.1   0.0     0.009        23     269     318 ..      48      94 ..      19     101 .. 0.79
   2 !   12.1   0.0   3.3e-05     0.084     249     319 ..      72     138 ..      47     159 .. 0.81
   3 !   15.2   0.0   3.7e-06    0.0095     239     315 ..     191     261 ..     151     278 .. 0.69
   4 !   13.1   0.0   1.7e-05     0.043     249     324 ..     242     314 ..     238     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.009
                                       EEEEE-TTT--EEEEEEEE-SSS.--EEEE-TTSSEEEEEETTTTEEEEE CS
                         Lactonase 269 avfavdeadgtltlveevstegkfPRdfaldpsgklllvanqksdnvtvf 318
                                       +v ++d +   l+l+e+v++ g++  ++a+ +s + l+v + +sd+++v+
  gi|330507218|ref|YP_004383646.1|  48 TVAKIDGE--DLSLIETVEV-GDNAHSIAMVQSPNRLWVTCPDSDHIAVI 94 
                                       67778555..6********9.899***********************996 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.3e-05
                                       EEE-TTSSEEEEEETSSTEEEEEEE-TTT--EEEEEEEE-SSS.--EEEE-TTSSEEEEEETTTTEEEEEE CS
                         Lactonase 249 IrlspdgkflyvSnRgadsiavfavdeadgtltlveevstegkfPRdfaldpsgklllvanqksdnvtvfe 319
                                       I++ ++ + l+v    +d iav +     +t++l++++++eg++P  +a++p ++ ++v   ++++v +f+
  gi|330507218|ref|YP_004383646.1|  72 IAMVQSPNRLWVTCPDSDHIAVINP----STMELIDNIEIEGAQPTGIAVSPYDSRVYVTFSETGEVGIFN 138
                                       5566666677777777999999774....48************************************9995 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 3.7e-06
                                       SS-S---EEEEEE-TTSSEEEEEETSSTEEEEEEE-TTT--EEEEEEEE-SSS.--EEEE-TTSSEEEEEETTTTEE CS
                         Lactonase 239 gftgknsaaeIrlspdgkflyvSnRgadsiavfavdeadgtltlveevstegkfPRdfaldpsgklllvanqksdnv 315
                                       +f g++   +   spdg+ +y +n  +++i v +  ++d  l+ +e    +  +PR +a++p+g++l+ ++ +   +
  gi|330507218|ref|YP_004383646.1| 191 NFPGHA-IQDAIASPDGSTIYLANMDQNKIEVIRT-RDDFILAPME----TSLHPRGIAISPDGQYLFLGHYTATDA 261
                                       455553.33334699*******************9.5653444433....3457**************998776655 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 1.7e-05
                                       EEE-TTSSEEEEEETSSTEEEEEEE-TTT--EEEEEEEE-SSS.--EEEE-TTSSEEEEEETTTTEEEEEEEETTT CS
                         Lactonase 249 IrlspdgkflyvSnRgadsiavfavdeadgtltlveevstegkfPRdfaldpsgklllvanqksdnvtvferdaet 324
                                       I++spdg++l+  + +a    v  +  +dg++  +  +++   +PR ++++++g+ ++v + ++d +  + +  et
  gi|330507218|ref|YP_004383646.1| 242 IAISPDGQYLFLGHYTATDAYVDMIRLSDGQVVSTASIPS---NPRCIKVSSDGQRIFVTEHNEDALYAYDVSGET 314
                                       899*************888888888899999999999998...8*********************99999987766 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   8.3e-06     0.021       7     111 ..      81     186 ..      75     210 .. 0.86
   2 !   16.1   0.1   1.2e-06    0.0032      13     124 ..     215     330 ..     210     342 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.3e-06
                                       EEEEEGGGTEEEEEETTT-SEEEEEE-STTEEEEE.E-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE-SSEEEEE CS
                      Cytochrom_D1   7 fvvverdagkvalldgdskeilavletgyalHisr.vfasdgRyvyvigRDgkvtliDLwakeivaevkiGlnarsv 82 
                                         v+  d  ++a+++ ++ e + ++e ++a  ++  v+  d R   +++  g+v ++   + e +  +++G+n  s+
  gi|330507218|ref|YP_004383646.1|  81 LWVTCPDSDHIAVINPSTMELIDNIEIEGAQPTGIaVSPYDSRVYVTFSETGEVGIFNPQEMELISSIHVGGNPSSI 157
                                       56888999***********************66651566689988899***************************** PP

                                       EE--TTSEEEEEEEETTEEEEEETTT--E CS
                      Cytochrom_D1  83 avSqddryvivgnYlPgqlvildaetLel 111
                                            +  + v  Y+ + + ++da    l
  gi|330507218|ref|YP_004383646.1| 158 TFTPSGAKAYVVDYQEPAVYVIDAVRNAL 186
                                       ***9999999999**99999999966555 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.2e-06
                                       GGTEEEEEETTT-SEEEEEE-STTEE.EEEE-TT.SSEEEE...EETTSEEEEEESSSSSEEEEEE-SSEEEEEEE- CS
                      Cytochrom_D1  13 dagkvalldgdskeilavletgyalH.isrvfasdgRyvyv...igRDgkvtliDLwakeivaevkiGlnarsvavS 85 
                                       d+ k++++      ila +et   lH  +   ++dg y+++    + D+ v++i L   ++v +  i +n r ++vS
  gi|330507218|ref|YP_004383646.1| 215 DQNKIEVIRTRDDFILAPMETS--LHpRGIAISPDGQYLFLghyTATDAYVDMIRLSDGQVVSTASIPSNPRCIKVS 289
                                       6677777777777777777775..5624678899*****96444789****************************** PP

                                       -TTSEEEEEEEETTEEEEEE..TTT--EEEEEE--EE-SSS CS
                      Cytochrom_D1  86 qddryvivgnYlPgqlvild..aetLelvkvisargltvde 124
                                        d++ + v       l   d  +etL++  ++    +++++
  gi|330507218|ref|YP_004383646.1| 290 SDGQRIFVTEHNEDALYAYDvsGETLSPASHVDLNSVSGQQ 330
                                       *********999999988776589****9999888877744 PP

>> Arylesterase  Arylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.014        36      55      72 ..     111     128 ..      97     141 .. 0.86
   2 ?   -1.8   0.0       1.5   3.8e+03      60      76 ..     168     184 ..     155     189 .. 0.71
   3 ?    1.1   0.0      0.18   4.5e+02      62      84 ..     203     225 ..     195     227 .. 0.85
   4 !    8.4   0.0   0.00092       2.4      55      80 ..     238     263 ..     232     267 .. 0.89
   5 !    9.3   0.0   0.00049       1.2      44      83 ..     271     310 ..     264     313 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                      Arylesterase  55 sanGInidadkkyiyvad 72 
                                        ++GI +++ +  +yv+ 
  gi|330507218|ref|YP_004383646.1| 111 QPTGIAVSPYDSRVYVTF 128
                                       69**************85 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                      Arylesterase  60 nidadkkyiyvadilre 76 
                                       ++d ++  +yv d +r+
  gi|330507218|ref|YP_004383646.1| 168 VVDYQEPAVYVIDAVRN 184
                                       56777777888887776 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.18
                      Arylesterase  62 dadkkyiyvadilresihvmkkh 84 
                                       ++d   iy+a++ +++i v++ +
  gi|330507218|ref|YP_004383646.1| 203 SPDGSTIYLANMDQNKIEVIRTR 225
                                       89999***********9888765 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.00092
                      Arylesterase  55 sanGInidadkkyiyvadilresihv 80 
                                        + GI i++d +y++++  ++ + +v
  gi|330507218|ref|YP_004383646.1| 238 HPRGIAISPDGQYLFLGHYTATDAYV 263
                                       589*****************998886 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.00049
                      Arylesterase  44 sevkvvasglssanGInidadkkyiyvadilresihvmkk 83 
                                       ++v   as  s +  I++++d + i+v++  ++ ++++++
  gi|330507218|ref|YP_004383646.1| 271 GQVVSTASIPSNPRCIKVSSDGQRIFVTEHNEDALYAYDV 310
                                       56677788888999***********************998 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 !   10.1   0.0   0.00017      0.44     191     243 ..      75     127 ..      66     130 .. 0.89
   2 !   10.5   0.0   0.00013      0.32     185     242 ..     111     168 ..     105     172 .. 0.87
   3 ?    2.6   0.0     0.032        82     134     163 ..     196     224 ..     169     251 .. 0.66
   4 ?    2.2   0.0     0.044   1.1e+02     142     163 ..     203     224 ..     192     275 .. 0.64
   5 !    6.2   0.0    0.0027         7     125     174 ..     272     319 ..     241     340 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                               SGL 191 vDaeGnvwvAvwgggkvvrfdpd.GklieeiklpakrvtscaFgGpdlrtLyit 243
                                       v + +++wv++ +++++++++p   +li+ i++  +++t +a   p  +++y+t
  gi|330507218|ref|YP_004383646.1|  75 VQSPNRLWVTCPDSDHIAVINPStMELIDNIEIEGAQPTGIAV-SPYDSRVYVT 127
                                       566789*****************99*****************7.5666999998 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00013
                               SGL 185 epDGlavDa.eGnvwvAvwgggkvvrfdpd.GklieeiklpakrvtscaFgGpdlrtLyi 242
                                       +p G+av   + +v+v+  ++g+v  f+p+  +li  i++   +++s++F  p   + y+
  gi|330507218|ref|YP_004383646.1| 111 QPTGIAVSPyDSRVYVTFSETGEVGIFNPQeMELISSIHVG-GNPSSITF-TPSGAKAYV 168
                                       47899***99********************99*********.9*******.455566666 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.032
                               SGL 134 tipNGlawspdgktlYlaDsltrkiwaydv 163
                                       +i  ++a spdg+t+Yla+  ++ki ++  
  gi|330507218|ref|YP_004383646.1| 196 AIQDAIA-SPDGSTIYLANMDQNKIEVIRT 224
                                       5555554.8999999999999998887765 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.044
                               SGL 142 spdgktlYlaDsltrkiwaydv 163
                                       spdg+t+Yla+  ++ki ++  
  gi|330507218|ref|YP_004383646.1| 203 SPDGSTIYLANMDQNKIEVIRT 224
                                       5666666666666666655444 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.0027
                               SGL 125 klervlddltipNGlawspdgktlYlaDsltrkiwaydvdaeggklsnrr 174
                                       +++ +++  + p  + +s+dg+ +++++  ++ ++aydv+ e  +ls + 
  gi|330507218|ref|YP_004383646.1| 272 QVVSTASIPSNPRCIKVSSDGQRIFVTEHNEDALYAYDVSGE--TLSPAS 319
                                       55555555556667999**********************744..455544 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.15   3.9e+02       3      19 ..      68      85 ..      67      93 .. 0.83
   2 ?    3.9   0.0     0.024        61       3      27 ..     111     136 ..     110     137 .. 0.75
   3 ?   -2.2   0.0       2.1   5.4e+03       3      13 ..     153     164 ..     152     171 .. 0.65
   4 !    5.4   0.0    0.0083        21       3      15 ..     238     250 ..     237     251 .. 0.89
   5 ?    5.1   0.0      0.01        26       3      20 ..     282     300 ..     281     303 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.15
                                      SEEEEEEE.TTTEEEEEE CS
                               NHL  3 yPhGvavd.snGdiyVaD 19
                                      ++h++a++ s ++++V++
  gi|330507218|ref|YP_004383646.1| 68 NAHSIAMVqSPNRLWVTC 85
                                      57999999999*****97 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.024
                                       SEEEEEEE.TTTEEEEEECCCTEEEE CS
                               NHL   3 yPhGvavd.snGdiyVaDsenhrvqv 27 
                                       +P+G+av+  + ++yV+ se+  v +
  gi|330507218|ref|YP_004383646.1| 111 QPTGIAVSpYDSRVYVTFSETGEVGI 136
                                       8******9888888888666666655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.1
                                       SEEEEEEE.TTT CS
                               NHL   3 yPhGvavd.snG 13 
                                       +P++++ + s+ 
  gi|330507218|ref|YP_004383646.1| 153 NPSSITFTpSGA 164
                                       699999994444 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0083
                                       SEEEEEEETTTEE CS
                               NHL   3 yPhGvavdsnGdi 15 
                                       +P+G+a++++G+ 
  gi|330507218|ref|YP_004383646.1| 238 HPRGIAISPDGQY 250
                                       7**********96 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.01
                                       SEEEEEEE.TTTEEEEEEC CS
                               NHL   3 yPhGvavd.snGdiyVaDs 20 
                                       +P+++ v+ ++ +i+V++ 
  gi|330507218|ref|YP_004383646.1| 282 NPRCIKVSsDGQRIFVTEH 300
                                       7*******9999****984 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.012        31      16      24 ..     202     210 ..     190     210 .. 0.85
   2 !    6.4   0.0    0.0034       8.7      13      23 ..     241     251 ..     236     252 .. 0.89
   3 ?    2.4   0.0     0.061   1.6e+02      13      24 ..     285     296 ..     278     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.012
                                       E-TTSSEEE CS
                              PD40  16 fSPDGkrla 24 
                                        SPDG++++
  gi|330507218|ref|YP_004383646.1| 202 ASPDGSTIY 210
                                       5*******9 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0034
                                       EEEE-TTSSEE CS
                              PD40  13 aPsfSPDGkrl 23 
                                       ++++SPDG++l
  gi|330507218|ref|YP_004383646.1| 241 GIAISPDGQYL 251
                                       789******98 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.061
                                       EEEE-TTSSEEE CS
                              PD40  13 aPsfSPDGkrla 24 
                                       ++ +S DG+r+ 
  gi|330507218|ref|YP_004383646.1| 285 CIKVSSDGQRIF 296
                                       6779******96 PP

>> SBP56  56kDa selenium binding protein (SBP56)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.063   1.6e+02     308     353 ..     113     155 ..      86     228 .. 0.78
   2 ?    8.3   0.0   0.00035      0.89     356     385 ..     270     299 ..     237     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.063
                             SBP56 308 tDillslDDrflyvsnWltGdlrqydisdpkkPkltgqvrlGGiir 353
                                       t i++s  D  +yv+   tG++    i +p++ +l +++++GG  +
  gi|330507218|ref|YP_004383646.1| 113 TGIAVSPYDSRVYVTFSETGEVG---IFNPQEMELISSIHVGGNPS 155
                                       77888888888999999999986...55788899999999999655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00035
                             SBP56 356 ehpavkgrkleggPqmvelslDGkrlYvtn 385
                                       + ++v+  ++ + P+ +++s DG+r++vt+
  gi|330507218|ref|YP_004383646.1| 270 DGQVVSTASIPSNPRCIKVSSDGQRIFVTE 299
                                       56677888999*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 2873.04
//
Query:       gi|330507219|ref|YP_004383647.1|  [L=512]
Description: hypothetical protein MCON_1095 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.009   16.6   0.0      0.017   15.7   0.0    1.5  1  VWA_2     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.7e-07     0.017       1      71 [.     340     410 ..     340     438 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.7e-07
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallk.slp.gdrvglvtfsdgpevlipltkdkakilnalrnlea 71 
                                       l++vlD+S Sm+++    t+ ++a  a+ + ++ +   g  ++ ++fs++++ l+++t+d +++++ l +  a
  gi|330507219|ref|YP_004383647.1| 340 LLVVLDSSRSMEGPRK-GTKTHKATLAAFKACQfAHSmGAELAAINFSENYR-LASWTRDLNAVEDVLVEFLA 410
                                       689********99954.44444444444444442333488*********987.78999999999888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3778.88
//
Query:       gi|330507220|ref|YP_004383648.1|  [L=254]
Description: GXGXG motif protein [Methanosaeta concilii GP6]
Scores for complete 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-14   52.0  23.9    1.9e-11   43.9  15.5    2.5  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 !   20.4   1.2   1.7e-08   0.00031      89     159 ..      72     142 ..      62     144 .. 0.84
   2 !   43.9  15.5   1.1e-15   1.9e-11      41     160 ..     112     237 ..     112     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.7e-08
                                       B-S-SSTTTT--SEEEEESSB--SSTTTT-SS-EEEESEB-SSTTTT-EEEEEEE-S-B-SSBTTT--EEE CS
                             GXGXG  89 iivGnvvlygatgGklfirgkageRfavrnsgatavvegvgdhgceYmtGGvvvvLgktgrnfaaGmsgGi 159
                                       +i G     +a   +  ++ +ag+ ++   s  t++ e  gdh++e m GG++ +    g+++++ m+gG 
  gi|330507220|ref|YP_004383648.1|  72 VIWGHLSSIAAERSQQPLHLSAGNYAGLELSRGTIILEMGGDHVGERMKGGRIYLRQAAGDYLGQEMTGGG 142
                                       56666666666666666677899999999****************************************95 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 1.1e-15
                                       -TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--TT-SS-GGG...SB-...S-SSTTTT--SEEEEESSB-- CS
                             GXGXG  41 GqslgaflakGltleleGdandyvGkglsgGkivikpskeskfkaee...nii...vGnvvlygatgGklfirgkag 111
                                       G+ +g  + kG ++ l   a dy+G+ ++gG iv ++  + +f++ +    +i   +Gn +  g  gGk+  +g+ g
  gi|330507220|ref|YP_004383648.1| 112 GDHVGERM-KGGRIYLRQAAGDYLGQEMTGGGIVSRGAGNYAFRRMSgglGVIkgdCGNFLGLGCSGGKVVCQGSCG 187
                                       56677777.999***************************999887652225674445788999************** PP

                                       SSTTTT-SS-EEEESEB.-SSTTTT-EEEEEEE-S-B-SSBTTT--EEEE CS
                             GXGXG 112 eRfavrnsgatavvegv.gdhgceYmtGGvvvvLgktgrnfaaGmsgGia 160
                                       eR++  +s   + + g  gd+++  m GG++ v+g++gr  +  m+gG++
  gi|330507220|ref|YP_004383648.1| 188 ERAGWLMSSGSLRIHGDaGDYLGLLMKGGRITVFGRVGRRAGWRMKGGTI 237
                                       *******87777776666******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2075.28
//
Query:       gi|330507221|ref|YP_004383649.1|  [L=425]
Description: ATPase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-05   23.7   0.0    0.00019   21.3   0.0    2.0  2  AAA_3     ATPase family associated with various cellular acti


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 ?   -0.5   0.0      0.06   1.1e+03       3      30 ..      60      88 ..      58      94 .. 0.77
   2 !   21.3   0.0   1.1e-08   0.00019      67     129 ..     135     195 ..     130     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.06
                             AAA_3  3 llegvPGlaktllvkalaka.ldlefkri 30
                                      ll g  G  kt+lv+ l+++ l+l+f+ +
  gi|330507221|ref|YP_004383649.1| 60 LLYGGMGANKTTLVNLLGSSfLSLSFSEV 88
                                      77888899*******99764267777665 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.1e-08
                             AAA_3  67 ladeinrappktqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrf 129
                                       l +e+nr p   q  +le+++ r+++++g+ ++  ++ + l t nP e + typl ea ldr 
  gi|330507221|ref|YP_004383649.1| 135 LINEVNRFPGGKQNLFLEILQKRKISYAGQVYEPGDTCYYL-TMNP-EFSATYPLDEALLDRI 195
                                       679*****************************987776655.99*9.999************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3244.92
//
Query:       gi|330507222|ref|YP_004383650.1|  [L=106]
Description: hypothetical protein MCON_1098 [Methanosaeta concilii GP6]
Scores for complete 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-11   42.6   0.0    9.1e-11   42.4   0.0    1.1  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 !   42.4   0.0   5.1e-15   9.1e-11      91     167 .]       9      84 ..       2      84 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 5.1e-15
                                       HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  91 eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleellell 167
                                        e + r++++g+  +++g+e+++   +l+l++ g t+e+++++++ + e g+ +    ivg+pGen e+++ + +l+
  gi|330507222|ref|YP_004383650.1|   9 FETIFRMKRAGCVELAFGVESGSQA-ILDLLRNGITPEQIIRTFKQADEIGLVSDMLLIVGIPGENQEDIDMTKRLI 84 
                                       577889*******************.*************************99999**************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 734.28
//
Query:       gi|330507223|ref|YP_004383651.1|  [L=630]
Description: DNA gyrase subunit B [Methanosaeta concilii GP6]
Scores for complete 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-63  211.0   0.3    1.3e-62  210.4   0.3    1.3  1  DNA_gyraseB    DNA gyrase B
    8.7e-31  105.9   0.8    2.6e-30  104.4   0.3    2.1  2  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
    2.4e-23   82.8   0.1      6e-23   81.5   0.1    1.7  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    5.4e-18   65.1   0.0    1.3e-17   63.8   0.0    1.7  1  Toprim         Toprim domain
      0.002   18.0   0.1      0.011   15.5   0.0    2.2  2  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


Domain annotation for each model (and alignments):
>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.4   0.3   3.5e-66   1.3e-62       1     173 [.     221     389 ..     221     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 210.4 bits;  conditional E-value: 3.5e-66
                       DNA_gyraseB   1 GlkdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktln 77 
                                       G+ +fve+lnk+k+ l+++++++++ k  +   +vevalq+++sy+eni+s++N+i+t+eGGtH+ gf++alt+t+n
  gi|330507223|ref|YP_004383651.1| 221 GIISFVEYLNKNKEVLHEQPVYFSRSK--NG-TQVEVALQYNNSYAENIFSYANIINTREGGTHLMGFRAALTRTVN 294
                                       899**********************99..77.9******************************************** PP

                       DNA_gyraseB  78 eyakkkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakki 154
                                       +ya+++kl+k++  k+ ged+regl+av+svk+p+pqFeGQTK++Lgns++++ive++v+e l +++een+ +a++i
  gi|330507223|ref|YP_004383651.1| 295 DYARNNKLFKNEM-KLGGEDLREGLVAVISVKLPDPQFEGQTKTRLGNSSIRGIVESMVAEGLGEYFEENPLVATTI 370
                                       *********9987.*************************************************************** PP

                       DNA_gyraseB 155 lekaveaakareaarkare 173
                                       +eka+ea++areaarka+e
  gi|330507223|ref|YP_004383651.1| 371 VEKAAEAMRAREAARKAKE 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 ?   -2.1   0.0       1.3   4.7e+03      11      25 ..     355     370 ..     354     383 .. 0.75
   2 !  104.4   0.3   7.1e-34   2.6e-30       3      63 .]     559     619 ..     557     619 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                     DNA_gyraseB_C  11 GLGEm.npeqLweTTm 25 
                                       GLGE  +++ L  TT+
  gi|330507223|ref|YP_004383651.1| 355 GLGEYfEENPLVATTI 370
                                       9999724556888887 PP

  == domain 2  score: 104.4 bits;  conditional E-value: 7.1e-34
                     DNA_gyraseB_C   3 kveiqRfKGLGEmnpeqLweTTmdpetRrLlqvtiedaeeadelfstLmGkkvepRrefie 63 
                                       k  iqR+KGLGEmnpeqLweTTmdpe R +l+vt+eda ead++f++LmG++vepRrefie
  gi|330507223|ref|YP_004383651.1| 559 KPVIQRYKGLGEMNPEQLWETTMDPEGRIMLRVTLEDAVEADRIFTILMGDQVEPRREFIE 619
                                       778*********************************************************8 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.1   1.7e-26     6e-23       1     110 [.      32     174 ..      32     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 1.7e-26
                                       EHHHHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT..............GTCSTT CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkf..atkageieveikaseddlvisveDnGiGipkedlk..............klfekf 61 
                                       +d+ +L++++ ++vdN+v++   + ++ei+v+i+      ++s++D+G+Gip+++++              + ++kf
  gi|330507223|ref|YP_004383651.1|  32 TDSLGLHHLVYEVVDNSVDEalGGFCSEIDVTIN--P-GGSVSIRDDGRGIPVDNHPqfnrpaleivltvlHAGGKF 105
                                       5899****************54449*********..7.9******************************877777** PP

                                       CHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEE.....................EEETTTEEEEEEEEES CS
                         HATPase_c  62 sqddstkrggggtGlGlsivkklvelmgGeiwv.....................esepgrGttftftlpl 110
                                       +  +s+ ++gg +G+G+s+v++l+e m+ ++++                      s+++ Gtt+tf+++ 
  gi|330507223|ref|YP_004383651.1| 106 DH-ESYGVSGGLHGVGVSVVNALSEWMEVQVRRngriywqrfekgkvvsdleerGSSDHTGTTITFKPDT 174
                                       **.*************************99999999999*99999999988777666699******9986 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   3.8e-21   1.3e-17       1     101 [.     418     528 ..     418     530 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 3.8e-21
                                       EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH.....HHHHHHHHSEEEEE CS
                            Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildlet.efkpvye..eiedkkkvlka.....lkelakradeiila 69 
                                       e++ivEg+s+ +++++ +++ fqa+++++G+il++e  +++++++  ei++ + ++++     ++ ++ r+++++++
  gi|330507223|ref|YP_004383651.1| 418 EIYIVEGESAGGSAKQGRNRHFQAILPLRGKILNVERaRLDKILKnaEIRNMIVAFGTgvgddFDISKARYHKVVIM 494
                                       689**********************************888888887777777777777******************* PP

                                       CSSSHHHHHHHHHHHHHHT....HHHTTTEEEEEES CS
                            Toprim  70 tDpDreGeaiawellevlk....ellenkigrvefs 101
                                       tD+D++G++i+++ll++++    +l+++  g+v+++
  gi|330507223|ref|YP_004383651.1| 495 TDADVDGSHIRTLLLTFFYrymrPLIDA--GYVFIA 528
                                       *******************444444444..777666 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.1e-06     0.011       7      49 ..      41      83 ..      36     153 .. 0.81
   2 ?   -1.0   0.1       0.4   1.4e+03      49      83 ..     376     410 ..     372     413 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-06
                       HATPase_c_3  7 laelvdNsld....AdaenvkievnknrgktgeivieDdGkGmseee 49
                                      + e+vdNs+d    + + ++++++n      g+++i+DdG G++ ++
  gi|330507223|ref|YP_004383651.1| 41 VYEVVDNSVDealgGFCSEIDVTINPG----GSVSIRDDGRGIPVDN 83
                                      88********87767778899999995....7***********9774 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.4
                       HATPase_c_3  49 elknalrlatsskeakrkstslGkkGi.GlklAsls 83 
                                       e ++a + a+++ke +r ++ l++ G+ G klA +s
  gi|330507223|ref|YP_004383651.1| 376 EAMRAREAARKAKELTRRKNALSSGGLpG-KLADCS 410
                                       445566788888998899********977.999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (630 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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 0.24s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 4638.29
//
Query:       gi|330507224|ref|YP_004383652.1|  [L=797]
Description: DNA gyrase subunit A [Methanosaeta concilii GP6]
Scores for complete 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-160  532.2   0.1   1.1e-159  531.9   0.1    1.1  1  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
    4.5e-75  246.9  14.9      3e-14   52.2   0.2    6.6  6  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
  ------ inclusion threshold ------
       0.57   11.0   4.8        1.6    9.6   4.8    1.8  1  FliT           Flagellar protein FliT
        1.1    8.8   4.4        2.2    7.8   2.4    2.1  2  TPD52          Tumour protein D52 family


Domain annotation for each model (and alignments):
>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  531.9   0.1  2.5e-163  1.1e-159       1     425 [.      27     465 ..      27     466 .. 0.99

  Alignments for each domain:
  == domain 1  score: 531.9 bits;  conditional E-value: 2.5e-163
                     DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGn 76 
                                       Ra+P+vrDGlKPv+RriLyam+++ +++d+++kK+a++vG+v+gkYhPHGda++y+++vr+aq+f++++pl+d+qGn
  gi|330507224|ref|YP_004383652.1|  27 RALPDVRDGLKPVHRRILYAMYEQgMTHDQPYKKSARVVGDVMGKYHPHGDAAIYETMVRMAQTFSMRYPLIDGQGN 103
                                       9**************************************************************************** PP

                     DNA_topoisoIV  77 fGsildgdkdAaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipp 153
                                       fGsi dgd++Aa+RY+e+rLskia+e+l++i+k+tvd+++nyDgs kEP+vlp ++PnlL+nG++GIavGmat+ipp
  gi|330507224|ref|YP_004383652.1| 104 FGSI-DGDPAAAMRYTEVRLSKIAEEMLADIEKNTVDFVPNYDGSLKEPTVLPGKLPNLLLNGSTGIAVGMATNIPP 179
                                       ****.************************************************************************ PP

                     DNA_topoisoIV 154 hnlkeiidaliallkgeea...ellelvlgPdfptgggiigkeeikeayetgrGkikvrakveie...e.ktivitE 223
                                       hnl+e+  a+i+l+++++a   el+++ +gPdfptgg i+g+++i++ay tg+G+i ++ak eie   + ++i+ +E
  gi|330507224|ref|YP_004383652.1| 180 HNLNELAGAIIHLIDNPQAtvgELMHYLPGPDFPTGGYIVGRAGIESAYLTGKGSIIMQAKSEIEegaKsTRIIFSE 256
                                       *****************99*********************************************9999669****** PP

                     DNA_topoisoIV 224 lPigvntskliekieelvkkkkik.isdirdesdr.gvrivielkrgaseekvleklykktkLessisvnnlvlfdk 298
                                       lP++vn++klie ++e+vk ++++ isd+rdesd+ g+r+v+++k+g ++++vl++l+k+t+L++s+ +nn+vl+d+
  gi|330507224|ref|YP_004383652.1| 257 LPYQVNKAKLIEDMAEMVKGGRLEgISDLRDESDKeGIRMVVDIKTGFNANVVLNQLHKHTALQTSYGINNMVLVDG 333
                                       ********************************9988***************************************** PP

                     DNA_topoisoIV 299 kpkylslkeilkeflevrlevyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee..ls 373
                                        p++lslke l++++  r  v+err++++l+ +e+r++il gll+al++idevi +i++  + ++a++ Lie   ls
  gi|330507224|ref|YP_004383652.1| 334 MPRILSLKETLEQYIYYRSIVVERRTRFELDAAEKRAHILAGLLIALKNIDEVIRIIKAAPTPAEARDGLIEAflLS 410
                                       ***************************************************************************** PP

                     DNA_topoisoIV 374 eeqaeyllemrlrrLtkeeveklekeieelekeikelekllak...lkklikeel 425
                                       eeqa+++l+mrl+rLt +e+ek+ +e +elek i++l+++l++   + ++ik+el
  gi|330507224|ref|YP_004383652.1| 411 EEQAKAILDMRLQRLTGLEQEKIVSEAAELEKLIAHLRQILSSnleILSIIKDEL 465
                                       ******************************************9888778888776 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 !   39.2   0.3   7.5e-14   3.4e-10       4      46 ..     500     542 ..     498     544 .. 0.94
   2 !   42.4   0.0   7.8e-15   3.5e-11       1      48 []     547     597 ..     547     597 .. 0.98
   3 !   26.8   0.1     6e-10   2.7e-06       2      48 .]     603     646 ..     602     646 .. 0.96
   4 !   47.3   0.2   2.3e-16     1e-12       2      47 ..     650     695 ..     649     696 .. 0.96
   5 !   44.4   0.1   1.8e-15   8.2e-12       3      38 ..     703     738 ..     701     740 .. 0.95
   6 !   52.2   0.2   6.8e-18     3e-14       1      48 []     750     797 .]     750     797 .] 0.97

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 7.5e-14
                                       EEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEE CS
                     DNA_gyraseA_C   4 lliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlv 46 
                                       ++iTs Gy+kr p+++++ q+Rg++Gv+g  +k ++++++v  
  gi|330507224|ref|YP_004383652.1| 500 VTITSSGYIKRQPVNTYRMQRRGGRGVIGAETKTEEFVTDVST 542
                                       79************************************99975 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 7.8e-15
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS...ETTTTSSEEEEEEES CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgi...klkegdklvsvlvvs 48 
                                       d+ll++T++G++ +++++e+p++gR+a+G+ ++   +l++++++ ++++v+
  gi|330507224|ref|YP_004383652.1| 547 DYLLFFTDKGKAHWLKVYEVPALGRAARGKSIVnllQLEPDERIAGAIPVK 597
                                       8***********************************************995 PP

  == domain 3  score: 26.8 bits;  conditional E-value: 6e-10
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                       +++l+T+ G+++++pl  +++ ++g  G+k+++l +gd+lvs+ +++
  gi|330507224|ref|YP_004383652.1| 603 YIVLVTRSGNIVKMPLQAFSNPRKG--GIKAVNL-KGDSLVSAKLTN 646
                                       89***********************..*******.99*****99875 PP

  == domain 4  score: 47.3 bits;  conditional E-value: 2.3e-16
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                       ell++T+ G+++rf++ ++++++Rg++Gvk+i l+ gd+l+s+ v+
  gi|330507224|ref|YP_004383652.1| 650 ELLVATKFGKAIRFKEGDVRASNRGTMGVKAISLNMGDELISMDVI 695
                                       89*****************************************997 PP

  == domain 5  score: 44.4 bits;  conditional E-value: 1.8e-15
                                       EEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTT CS
                     DNA_gyraseA_C   3 llliTsnGyvkrfplselpeqgRgakGvkgiklkeg 38 
                                       ll++T++Gy+kr+ l+e+p+q+Rg+kGvk i+ ++g
  gi|330507224|ref|YP_004383652.1| 703 LLTVTNQGYGKRTELEEYPQQRRGGKGVKNIDARKG 738
                                       9******************************98876 PP

  == domain 6  score: 52.2 bits;  conditional E-value: 6.8e-18
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                       dell+ T+ G ++r+p+s++++qgR ++Gv++++ k+gd++ +++ ++
  gi|330507224|ref|YP_004383652.1| 750 DELLVTTRDGVIIRIPASDIRVQGRSTQGVRIMNVKPGDEVAAIARIN 797
                                       89*****************************************99876 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.8   0.00036       1.6      15      79 ..     416     479 ..     396     482 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHHHHHHCS--ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTHHHH CS
                              FliT  15 aleaerqqlverlreldaaplspaereekrellrrilandaeirallqprldelqkllgalrrqr 79 
                                       a ++ r q +  l+++     ++ae e++ + lr+il  + ei ++++ +l+el +++g+ rr++
  gi|330507224|ref|YP_004383652.1| 416 AILDMRLQRLTGLEQEK-IVSEAAELEKLIAHLRQILSSNLEILSIIKDELTELISKYGDERRTQ 479
                                       44444444444444444.6667777888888888*************************999987 PP

>> TPD52  Tumour protein D52 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.4    0.0005       2.2       9      56 ..     412     457 ..     406     469 .. 0.76
   2 ?   -0.3   0.0      0.16   7.3e+02     100     124 ..     647     671 ..     641     673 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0005
                             TPD52   9 tsedaaesvsaseptlteeereeLkseLakleeeivtLrqvLaakekh 56 
                                       ++++a  +++++   lt  e+e++ se a+le+ i+ Lrq+L++    
  gi|330507224|ref|YP_004383652.1| 412 EQAKAILDMRLQ--RLTGLEQEKIVSEAAELEKLIAHLRQILSSNLEI 457
                                       344444444444..6***************************997655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.16
                             TPD52 100 gqktsaalstvgsaisrklgdmrns 124
                                       g+k   + +++g+ai +k gd+r s
  gi|330507224|ref|YP_004383652.1| 647 GEKELLVATKFGKAIRFKEGDVRAS 671
                                       6777888999*************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (797 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 5278.12
//
Query:       gi|330507225|ref|YP_004383653.1|  [L=1141]
Description: dead/deah box helicase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-20   73.3   0.0    4.3e-20   72.2   0.0    1.6  1  DEAD        DEAD/DEAH box helicase
    2.6e-05   24.3   0.0    5.1e-05   23.3   0.0    1.4  1  ResIII      Type III restriction enzyme, res subunit
     0.0012   19.2   0.0     0.0074   16.6   0.0    2.2  1  Helicase_C  Helicase conserved C-terminal domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.0   7.2e-24   4.3e-20       4     170 ..     299     459 ..     296     465 .. 0.88

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 7.2e-24
                                       HHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   4 Qaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                       Q ea + ++ + +d++va +T +GKT ++ + +l+++      +  ++++v+P+r+L  q+ ++l   + +++++v+
  gi|330507225|ref|YP_004383653.1| 299 QIEAAQRAIdQSDDLVVALPTSAGKTRIAELCILRTL-----ASDLRIIYVTPLRALSAQVEQDLADTFLPLGISVS 370
                                       7777777774678*********************999.....6799******************************* PP

                                       EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  80 liiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdg 156
                                       +++g+   ++  ++  ++v+ivv+tp++ld  l+     +++v ++VlDE ++l  ++++  +++++++l + ++ g
  gi|330507225|ref|YP_004383653.1| 371 SLYGSAGIESSDADTLREVKIVVSTPEKLDFALRVDPTIIDNVGLIVLDEGHMLGPSEREVRYEALVQRLLRRSDAG 447
                                       ****88886555555499*************99877888*******************************8777776 PP

                                       TTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxx RF
                              DEAD 157 klqrqvivlSATlp 170
                                       +  r++++lSA +p
  gi|330507225|ref|YP_004383653.1| 448 S--RRIVCLSALFP 459
                                       6..78*****9665 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 !   23.3   0.0   8.6e-09   5.1e-05       3     147 ..     294     427 ..     282     457 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.6e-09
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       el + Q+ea ++ +     ++   ++++++T +GKT++a   i r l +    +++ + p ++l  q ++++++++ 
  gi|330507225|ref|YP_004383653.1| 294 ELWPSQIEAAQRAI-----DQSDDLVVALPTSAGKTRIAELCILRTLASDL--RIIYVTPLRALSAQVEQDLADTFL 363
                                       34444555555554.....7888****************888888888755..9***************99988777 PP

                                       G....GEEEESSS-B--........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS. CS
                            ResIII  80 eaykeigkkvsgdkkka.kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak 147
                                       +   +++  + + + ++  +    + ki+v+t ++ld ++       +    d+  +i+ DE H lg +
  gi|330507225|ref|YP_004383653.1| 364 PLGISVSSLYGSAGIESsDADTLREVKIVVSTPEKLDFAL-----RVDPTIIDNVGLIVLDEGHMLGPS 427
                                       7654433332222222233344568***************.....78899999999********99875 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 !   16.6   0.0   1.2e-06    0.0074      13     110 ..     549     687 ..     536     688 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-06
                                       TTTTSEEEEEESSHHHHHH.....HHHH...........................HHHT.........TSTEEEEST CS
                        Helicase_C  13 eeeggkilifvntidrlek.....vkll...........................lekk.........gikvavlhg 48 
                                         +g+++li+++ ++++ek     +                              l            ++ +a +hg
  gi|330507225|ref|YP_004383653.1| 549 VDQGKDVLIYCTMRRSVEKlgrviL--KcirqgmlkplrlmnqdiqdvmaagaewL--GpdhpavqclKYGIALHHG 621
                                       5666777777777776655543331..02233333444443444444444333330..03344455668999***** PP

                                       TSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSH.....HHHHHHHTTSSST CS
                        Helicase_C  49 elpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnv.....tsyiqriGRtgRa 110
                                        lp +  +e  +  +kg++++ ia+  +++G+++ +++++   +++rn      t++   iGR+gRa
  gi|330507225|ref|YP_004383653.1| 622 HLPRQFLNELEKLLRKGDIRLTIASPTLAQGLNL-SASVLLVPSIWRNRdiipaTEFANVIGRAGRA 687
                                       **********************************.6999999999988445666***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.28s 00:00:01.06 Elapsed: 00:00:00.44
# Mc/sec: 7758.25
//
Query:       gi|330507226|ref|YP_004383654.1|  [L=269]
Description: hypothetical protein MCON_1106 [Methanosaeta concilii GP6]
Scores for complete 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   55.8   0.0    7.4e-15   55.4   0.0    1.1  1  DUF1837   Domain of unknown function (DUF1837)


Domain annotation for each model (and alignments):
>> DUF1837  Domain of unknown function (DUF1837)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.0   4.1e-19   7.4e-15       6     154 ..      52     205 ..      50     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 4.1e-19
                           DUF1837   6 flfnniveyalsreeieklakeeyselseeeaakkfrk....dknlksGelGEllLylllehflkapkllsKmelkt 78 
                                        +f+++ ++ ls+    ++  +   el + ++a+++r+    +k+++sG+lGE+l   + e+ l+   +++++++k+
  gi|330507226|ref|YP_004383654.1|  52 NIFDELQNVLLSHYVAPEITAKRLAELGAPRTAELLREhlptTKTARSGDLGEILAIEFTERRLGFSVPIRRLRFKD 128
                                       688888888888888888888877777774555555445555*********************************** PP

                           DUF1837  79 ssnmevkgaDgvhikvdddgklqLwlGeSKlysdlksa.ideaveslkkflnedslnkelnlisnrldde.deelre 153
                                        +nm+  g D + i+ d +g l+++ GeSK y  l+   i+ea++ l++  +    ++   ++  rl d+ d +l++
  gi|330507226|ref|YP_004383654.1| 129 GRNMALRGDDLIAIDRDLKGSLKFLKGESKSYARLTPTvIKEAADALDRY-RGRPNRHSVLFVAERLRDKgDHDLAK 204
                                       **********************************9999899***999997.99999999999999999996555554 PP

                           DUF1837 154 a 154
                                       +
  gi|330507226|ref|YP_004383654.1| 205 D 205
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2145.27
//
Query:       gi|330507227|ref|YP_004383655.1|  [L=149]
Description: PIN domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   84.6   0.2    8.8e-24   84.3   0.2    1.1  1  PIN       PIN domain
      5e-06   27.1   1.2    6.7e-06   26.7   1.2    1.4  1  PIN_12    PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.2   9.9e-28   8.8e-24       1     122 []       2     144 ..       2     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 9.9e-28
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS......................SCHCHHHH CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar......................rkskreka 55 
                                       i++DT+++++++++ +++  ar+ +++  +lvts+ v+ El++v  r                      ++   ek+
  gi|330507227|ref|YP_004383655.1|   2 IFIDTNIFYNAFFDTKFSNSARRFIDQNHKLVTSSTVIHELIFVSVRnlceerygtknhasfkrflidnGYAPFEKE 78 
                                       79************************99************************************************* PP

                                       HHHHHHHHHHHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHHC CS
                               PIN  56 aelvelllllsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvakl 122
                                       +e   ++++++ ++++p   ++  +++e + +y+llp+Dalia+t+ ++gik+ia+fD+dfrrv++l
  gi|330507227|ref|YP_004383655.1|  79 IEAIFRFIDARCISLVP-INDDMNHWRETMIQYRLLPYDALIASTCYRNGIKKIASFDRDFRRVDFL 144
                                       *****************.77899*****************************************985 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   1.2   7.4e-10   6.7e-06       1      76 [.       2      73 ..       2     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 7.4e-10
                            PIN_12  1 ifiDTnifldeffrlseeealkklleliesgkiklivpdivldEflknrekkieeskklekalkslsklksakkkl 76
                                      ifiDTnif++ ff+++++++ +++   i++ + kl++++ v++E++    +++ e +  +k+++s++++  ++  +
  gi|330507227|ref|YP_004383655.1|  2 IFIDTNIFYNAFFDTKFSNSARRF---IDQ-NHKLVTSSTVIHELIFVSVRNLCEERYGTKNHASFKRFLIDNGYA 73
                                      9*****************888888...666.479**********98766555555523337777776666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1132.68
//
Query:       gi|330507228|ref|YP_004383656.1|  [L=63]
Description: hypothetical protein MCON_1109 [Methanosaeta concilii GP6]
Scores for complete 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   73.3   1.9    1.8e-20   73.1   1.9    1.0  1  DUF104    Protein of unknown function DUF104
  ------ inclusion threshold ------
      0.098   12.4   0.0       0.14   11.9   0.0    1.2  1  DUF22     Domain of unknown function DUF22


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   1.9     2e-24   1.8e-20       2      57 ..       4      57 ..       3      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 2e-24
                            DUF104  2 skvIeavYEnGvLKPLekvdLkEGeevkikIeeakeilkklkgilkeadeeeleel 57
                                      s++Ie+vYE+Gv+KP+e+v+L+EG+++kikIe+    l k++g++++a++e+leel
  gi|330507228|ref|YP_004383656.1|  4 SETIECVYEGGVFKPMEDVKLEEGTKLKIKIEK--VDLSKYYGMFGKASAERLEEL 57
                                      689******************************..9999****************7 PP

>> DUF22  Domain of unknown function DUF22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.5e-05      0.14      38      60 ..      19      41 ..      16      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.5e-05
                             DUF22 38 dedvevkkGevkkikikeielpe 60
                                       edv++++G   kiki++++l +
  gi|330507228|ref|YP_004383656.1| 19 MEDVKLEEGTKLKIKIEKVDLSK 41
                                      59******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.36s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 338.35
//
Query:       gi|330507229|ref|YP_004383657.1|  [L=583]
Description: indolepyruvate ferredoxin oxidoreductase subunit alpha [Methanosaeta concilii GP6]
Scores for complete 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-25   87.9   0.0    9.9e-25   87.1   0.0    1.4  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
    1.8e-13   50.8   0.3      4e-13   49.7   0.3    1.5  1  POR_N           Pyruvate flavodoxin/ferredoxin oxidoreductase
    1.2e-06   28.1   2.8    1.2e-06   28.1   2.8    2.6  2  Fer4            4Fe-4S binding domain
    1.7e-05   24.7   1.8    1.7e-05   24.7   1.8    2.8  3  Fer4_6          4Fe-4S binding domain
    0.00019   21.5  11.1      0.012   15.8   2.5    2.5  2  Fer4_21         4Fe-4S dicluster domain
    0.00026   20.9   9.6      0.005   16.9   1.1    2.8  2  Fer4_2          4Fe-4S binding domain
     0.0026   17.8   9.8      0.017   15.2   2.0    2.5  2  Fer4_10         4Fe-4S dicluster domain
       0.01   16.0  10.8      0.054   13.7  10.7    2.2  2  Fer4_9          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   16.2  10.5       0.56   10.8  10.5    2.6  1  Fer4_7          4Fe-4S dicluster domain
      0.018   14.7   0.2      0.051   13.2   0.1    1.8  2  TPP_enzyme_N    Thiamine pyrophosphate enzyme, N-terminal TPP
      0.027   15.4   1.7      0.027   15.4   1.7    2.4  2  Fer4_16         4Fe-4S double cluster binding domain
      0.046   14.0   0.0       0.23   11.8   0.0    2.1  2  PFOR_II         Pyruvate:ferredoxin oxidoreductase core domai
       0.23   10.7   0.1       0.37    9.9   0.1    1.2  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
        1.4    9.7  11.7       0.21   12.2   2.8    2.8  2  Fer4_4          4Fe-4S binding domain
        1.4    9.5  12.4       0.59   10.7   2.6    2.6  2  Fer4_17         4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.0   8.2e-28   9.9e-25       1     152 [.     368     510 ..     368     511 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 8.2e-28
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       diGc++l      ++ +p   ++     +mG g+++A+G++ a ++r+vv +vGD++f+++ ++ l  +v+++   t
  gi|330507229|ref|YP_004383657.1| 368 DIGCYSL------GAFPPLDRMD--SILCMGAGVSMAHGMEKAGEKRKVVGVVGDSTFFHSgITGLLDIVYNKGHST 436
                                       8999999......8888988888..799**************9999******************************* PP

                                       EEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpalie 152
                                       ++vl+N++++mtg+q +p +g++  g+    +  v+++ + +a+G++ + ++++++++  +ea+ke l+  +p+li+
  gi|330507229|ref|YP_004383657.1| 437 IIVLDNRTTAMTGHQDHPGTGRTIGGEP---TVAVSIEDIGRACGINrVRSIDPYQLDNAREAIKEELAALEPSLIV 510
                                       ********************98887766...99**************999******************9999*9995 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 !   49.7   0.3   3.3e-16     4e-13       2     175 ..      14     180 ..      13     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 3.3e-16
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a++agv + ++YP TPs+ei+e+la++ ++++          +E  a+++++GA++aGar++++    Gl  + + 
  gi|330507229|ref|YP_004383657.1|  14 GAYEAGVTIGTGYPGTPSTEILENLARYSPEVYC-----EWSPNEKVAFEVAAGASLAGARSIVTMKHVGLNVAADP 85 
                                       89****************************9996.....46779*****************************9999 PP

                                       HHHHHHTT--EEEEEEEEE-STTBE.EEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstgl.sirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfD 154
                                       l+  +   +      va   +++g+ s +++q   ++ar   + ++ +++ qea dl + A+ ++e++++P+i+ + 
  gi|330507229|ref|YP_004383657.1|  86 LMTLSYISVE--GGFVACVADDPGMhSSQNEQDTRNYARFARVPLFEPADSQEAKDLLMLALSVSEEFKTPAILRT- 159
                                       8877655443..33334445566651455666666889999999999*************************9987. PP

                                       HHHH.HEEEEEEC-SGG.GS- CS
                             POR_N 155 gfllshevekvelpdeedelk 175
                                        +++sh+++ vel ++e+ +k
  gi|330507229|ref|YP_004383657.1| 160 TTRVSHSRSLVELGEREQAKK 180
                                       57778*********9994443 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.5       0.1   1.2e+02       4      14 ..     530     540 ..     528     542 .. 0.83
   2 !   28.1   2.8   9.8e-10   1.2e-06       2      23 ..     556     577 ..     555     578 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                                       ETTTSSS-THH CS
                              Fer4   4 deekCigCGaC 14 
                                         e C +C +C
  gi|330507229|ref|YP_004383657.1| 530 LAEECRACELC 540
                                       5799******* PP

  == domain 2  score: 28.1 bits;  conditional E-value: 9.8e-10
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       +i++ +C gCG+C+++CP gAI
  gi|330507229|ref|YP_004383657.1| 556 KINQTLCAGCGLCEQICPAGAI 577
                                       79*******************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 ?   -2.9   0.4       7.3   8.7e+03       8      12 ..     345     349 ..     343     349 .. 0.83
   2 ?    0.1   1.5      0.85     1e+03       9      21 ..     534     547 ..     528     551 .. 0.71
   3 !   24.7   1.8   1.4e-08   1.7e-05       2      24 .]     555     577 ..     554     577 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.3
                            Fer4_6   8 kCigC 12 
                                       +C gC
  gi|330507229|ref|YP_004383657.1| 345 LCPGC 349
                                       8*999 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.85
                            Fer4_6   9 CigCgdCvrv.CPe 21 
                                       C  C+ C +  CP+
  gi|330507229|ref|YP_004383657.1| 534 CRACELCLSLgCPA 547
                                       77788885445885 PP

  == domain 3  score: 24.7 bits;  conditional E-value: 1.4e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       + i++ +C gCg C+ +CP+gai
  gi|330507229|ref|YP_004383657.1| 555 MKINQTLCAGCGLCEQICPAGAI 577
                                       679*******************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 !   10.6   1.4    0.0004      0.48      33      54 ..     526     548 ..     519     552 .. 0.79
   2 !   15.8   2.5   9.7e-06     0.012      33      57 ..     554     577 ..     547     579 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0004
                           Fer4_21  33 vlkvvedeCvGCnlCssv.CPve 54 
                                       + +++++eC +C+lC+s  CP  
  gi|330507229|ref|YP_004383657.1| 526 MRTILAEECRACELCLSLgCPAI 548
                                       457789*********88659965 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.7e-06
                           Fer4_21  33 vlkvvedeCvGCnlCssvCPvedci 57 
                                       v+k+ +  C GC lC ++CP  ++i
  gi|330507229|ref|YP_004383657.1| 554 VMKINQTLCAGCGLCEQICPA-GAI 577
                                       56888999************5.766 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   1.9    0.0033       3.9       8      22 .]     532     547 ..     527     547 .. 0.86
   2 !   16.9   1.1   4.2e-06     0.005       3      22 .]     555     574 ..     553     574 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0033
                            Fer4_2   8 drCigCgaCvsa.CPa 22 
                                       + C +C+ C+s  CPa
  gi|330507229|ref|YP_004383657.1| 532 EECRACELCLSLgCPA 547
                                       67********999**8 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.2e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       ++++   C gCg C + CPa
  gi|330507229|ref|YP_004383657.1| 555 MKINQTLCAGCGLCEQICPA 574
                                       7899999************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 !   12.7  10.6   8.5e-05       0.1       5      56 .]     530     573 ..     526     573 .. 0.91
   2 !   15.2   2.0   1.4e-05     0.017       2      21 ..     555     574 ..     554     582 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.5e-05
                           Fer4_10   5 dddtCirCgkCvka.CPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        ++ C  C+ C +  CPa         ++  +++ +++   C gcg C ++CP
  gi|330507229|ref|YP_004383657.1| 530 LAEECRACELCLSLgCPA---------IEGVDGVMKINQTLCAGCGLCEQICP 573
                                       5789*********88***.........999999999999*************9 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.4e-05
                           Fer4_10   2 vvidddtCirCgkCvkaCPa 21 
                                       ++i++  C +Cg C + CPa
  gi|330507229|ref|YP_004383657.1| 555 MKINQTLCAGCGLCEQICPA 574
                                       68999**************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 ?    3.3   1.8     0.077        92      34      47 ..     532     546 ..     509     550 .. 0.65
   2 !   13.7  10.7   4.5e-05     0.054       2      51 .]     534     577 ..     532     577 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.077
                            Fer4_9  34 eaCigCgaCv.eaCp 47 
                                       e+C  C+ C+   Cp
  gi|330507229|ref|YP_004383657.1| 532 EECRACELCLsLGCP 546
                                       569999999855777 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.5e-05
                            Fer4_9   2 CtgCgaCvea.CpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       C  C  C +  Cpa     + + + ++++++    C gCg C+++Cp gai
  gi|330507229|ref|YP_004383657.1| 534 CRACELCLSLgCPAI----EGVDGVMKINQT---LCAGCGLCEQICPAGAI 577
                                       777777744337764....444444444443...7*************987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  10.5   0.00047      0.56       2      52 .]     534     576 ..     475     576 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00047
                            Fer4_7   2 CigCgaCvaa.CpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       C  C+ C +  Cp  aie  +         ++i+++ C gCg C++ CP+ga
  gi|330507229|ref|YP_004383657.1| 534 CRACELCLSLgCP--AIEGVD-------GVMKINQTLCAGCGLCEQICPAGA 576
                                       6777777654477..566544.......36899*****************97 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   4.2e-05     0.051       2      87 ..       6      93 ..       5     166 .. 0.77
   2 ?   -1.7   0.0       1.6     2e+03      51      71 ..     392     412 ..     390     441 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                                      EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT..TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHH.HH CS
                      TPP_enzyme_N  2 tvaealvraLkalgvehvfgvpGsrilplldalseeq.girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGa.tn 78
                                      ++ ea++r   ++gv+   g+pG+ ++++l+ l++   ++ +  + +E +a   A g + a  +  v + ++g ++ + 
  gi|330507229|ref|YP_004383657.1|  6 SGNEAIARGAYEAGVTIGTGYPGTPSTEILENLARYSpEVYCEWSPNEKVAFEVAAGASLAGARSIVTMKHVGLNVaAD 84
                                      5789999*****************************888888899*****************99999999999865145 PP

                                      CHHHHHHHH CS
                      TPP_enzyme_N 79 altalaeAk 87
                                       l+ l   +
  gi|330507229|ref|YP_004383657.1| 85 PLMTLSYIS 93
                                      555555555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHTS-EEEEE- CS
                      TPP_enzyme_N  51 aafaAdgyaratgkpgvvlvt 71 
                                        + +A+g+ +a  k+ vv v 
  gi|330507229|ref|YP_004383657.1| 392 GVSMAHGMEKAGEKRKVVGVV 412
                                       678999999999887777554 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.3       2.5     3e+03       2      13 ..     534     546 ..     528     550 .. 0.77
   2 ?   15.4   1.7   2.2e-05     0.027       2      20 ..     562     580 ..     561     583 .] 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.5
                           Fer4_16   2 CgtCgkCaev.CP 13 
                                       C  C+ C++  CP
  gi|330507229|ref|YP_004383657.1| 534 CRACELCLSLgCP 546
                                       8888888874466 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.2e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C +Cg C ++CP++ai ++
  gi|330507229|ref|YP_004383657.1| 562 CAGCGLCEQICPAGAIVSR 580
                                       ****************876 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 ?   11.8   0.0   0.00019      0.23      21      60 ..     242     281 ..     232     292 .. 0.86
   2 ?   -2.1   0.0       4.1   4.9e+03      25      50 ..     473     498 ..     461     511 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                                       HHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE- CS
                           PFOR_II  21 elReegikvGllrlrtlrPFPeeelkellkkvkkvvvldr 60 
                                        +Re   ++ +l+l + +PFP + ++e++++v++++v++ 
  gi|330507229|ref|YP_004383657.1| 242 YAREVWPEASVLKLGFSYPFPDALIREFAQGVDRLLVVEE 281
                                       566666677799*************************985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                                       TT--EEEEEES--BS--HHHHHHHST CS
                           PFOR_II  25 egikvGllrlrtlrPFPeeelkellk 50 
                                        g   G+ r+r++ P+  ++ +e++k
  gi|330507229|ref|YP_004383657.1| 473 IGRACGINRVRSIDPYQLDNAREAIK 498
                                       57888999999999998888777764 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 ?    9.9   0.1   0.00031      0.37     119     173 ..     391     444 ..     383     458 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00031
                    DXP_synthase_N 119 aalGlavardlkgekkkvvaviGDgal.tgGmafealnnigelkkkllvilNdNem 173
                                       a++ +a+  +++gek+kvv v+GD+++  +G++  +l +i  +k +  +i+ dN+ 
  gi|330507229|ref|YP_004383657.1| 391 AGVSMAHGMEKAGEKRKVVGVVGDSTFfHSGIT--GLLDIVYNKGHSTIIVLDNRT 444
                                       444555667777899*********997245554..555665555555555556664 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.7      0.48   5.7e+02       2      15 ..     532     546 ..     531     551 .. 0.71
   2 ?   12.2   2.8   0.00017      0.21       3      17 .]     561     575 ..     559     575 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.48
                            Fer4_4   2 erCigCgsCvaa.CP 15 
                                       e C  C  C +  CP
  gi|330507229|ref|YP_004383657.1| 532 EECRACELCLSLgCP 546
                                       567777777665666 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00017
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                        C gCg C+ +CP g
  gi|330507229|ref|YP_004383657.1| 561 LCAGCGLCEQICPAG 575
                                       6************75 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   2.1     0.073        87      38      57 ..     526     546 ..     493     552 .. 0.72
   2 ?   10.7   2.6   0.00049      0.59      44      59 ..     560     575 ..     547     576 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.073
                           Fer4_17  38 ekeekaslCieCgeCe.rkCP 57 
                                       ++   a++C  C++C    CP
  gi|330507229|ref|YP_004383657.1| 526 MRTILAEECRACELCLsLGCP 546
                                       344578889999999856677 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00049
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                        lC++Cg+Ce+ CP+g
  gi|330507229|ref|YP_004383657.1| 560 TLCAGCGLCEQICPAG 575
                                       68***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 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:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.74u 0.35s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 3145.23
//
Query:       gi|330507230|ref|YP_004383658.1|  [L=220]
Description: indolepyruvate oxidoreductase subunit beta [Methanosaeta concilii GP6]
Scores for complete 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  135.0   0.0    3.5e-39  134.7   0.0    1.1  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.7   0.0     2e-43   3.5e-39       1     176 [.      41     217 ..      41     218 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.7 bits;  conditional E-value: 2e-43
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqG+++a++ila+aa+++Gy+v++n+++g+++rGg++++++r ++e+++p ++  +a++l al++ ++ ++++ l+
  gi|330507230|ref|YP_004383658.1|  41 GGQGILLASEILAQAAMIQGYQVKTNEVHGMAQRGGSVMAQIRYGEEVKSPLVSKKGAHILGALEKVEALRYWEFLR 117
                                       9*****************************************************************9999******* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH....T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl....gvrvygvdatkiakeiggneraaNtvmlGalaallglpleal 150
                                       p+g++ + s  + p ++   + +++e++e+l      r++ +da k+a e+g+ +raaN+++lG +++ l+lple++
  gi|330507230|ref|YP_004383658.1| 118 PDGLAAVSSQAIVPVTVSSGLARYPENAEELlaraFPRLVYIDAPKLAGELGD-SRAANIILLGTISRGLDLPLESW 193
                                       *****************************99*******************999.*********************** PP

                                       HHHHHCCS-CH.HHHHHHHHHHHHHH CS
                               POR 151 eeaikkrfpkkkeviekNlkafragy 176
                                       eeai   +++k  + ++Nl+af +g+
  gi|330507230|ref|YP_004383658.1| 194 EEAIGLCVREK--FRDLNLRAFSLGR 217
                                       *********95..9*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); 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: 00:00:00.45
# Mc/sec: 1468.00
//
Query:       gi|330507231|ref|YP_004383659.1|  [L=427]
Description: phenylacetate-coenzyme A ligase [Methanosaeta concilii GP6]
Scores for complete 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-19   68.4   0.0    1.1e-18   67.3   0.0    1.6  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    1.3e-14   53.7   0.0      2e-14   53.0   0.0    1.3  1  AMP-binding      AMP-binding enzyme
    6.4e-07   28.7   0.0    5.6e-05   22.4   0.0    2.1  2  LuxE             Acyl-protein synthetase, LuxE
     0.0074   15.2   0.0      0.013   14.4   0.0    1.3  1  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 !   67.3   0.0   2.5e-22   1.1e-18       1      96 []     339     425 ..     339     425 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 2.5e-22
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--EEEEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklgvsvkvelv 77 
                                       Gvn+fP+qie+ l  i++++++Yqi+v++e++ ++++v+vE+++g++            ++k+lk++lg+s+k +++
  gi|330507231|ref|YP_004383659.1| 339 GVNFFPKQIEQTLLGIPGIGNNYQIIVEEEDGVNSVRVNVEAEPGVTG---------YMVEKALKEALGFSPKGDVF 406
                                       9********************************************954.........5899**************** PP

                                       -TT-S---------EEE-S CS
                   AMP-binding_C_2  78 epgtlprsegKakrviDkR 96 
                                       + g lpr+egKakrv+ +R
  gi|330507231|ref|YP_004383659.1| 407 PLGGLPRQEGKAKRVFHNR 425
                                       ****************998 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   4.5e-18     2e-14     155     370 ..      83     289 ..      16     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 4.5e-18
                                       S-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH..HHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT- CS
                       AMP-binding 155 elkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk..letrfklkeddvvlsilplahifglilelllallsGa 229
                                        +  d+++ +  +SG+TG+P    ++ r+ + + a++   +++  ++k++d   +i pl+  f   ++++    + +
  gi|330507231|ref|YP_004383659.1|  83 CVPRDQIVEMHMSSGSTGTPVVMPYT-RSDLDQWAECMarCYRMAGAKPGDP-TQITPLFGLFNGGFGMYHGARAAG 157
                                       566788888999********544444.5555655555333443355667665.488999988888789999999888 PP

                                       EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHH CS
                       AMP-binding 230 tvvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffra 305
                                         v++ +      ++ ++l ++lk +v++gv +   +l+e   ++     +++l+ l++ ++g+e  s ++ +++++
  gi|330507231|ref|YP_004383659.1| 158 LFVIPAGPGN--TARQIRLARDLKTRVFTGVVSYGIRLMEvLAEE-----KESLPDLEIGIFGAEVFSDSMKKKISS 227
                                       8888887766..345689**********************65444.....4599*********************** PP

                                       HHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-T..TEEEEEE-TTTSCBEETTSEEEEEEE CS
                       AMP-binding 306 lfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplp..gvevkivDeetgepvpdgeeGellvr 370
                                        +   v+++YG+TE +gv t l  +++   + + G  ++     ++i+D++tgepv dgeeGel++ 
  gi|330507231|ref|YP_004383659.1| 228 GLDIDVFDIYGMTESGGVGT-LG-MDC---PAHDGIHIWedQYILEIIDPKTGEPVDDGEEGELVFT 289
                                       **99***************9.44.444...333466665337778999****************986 PP

>> LuxE  Acyl-protein synthetase, LuxE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.0    0.0038        17      12     128 ..       7     127 ..       3     139 .. 0.75
   2 !   22.4   0.0   1.2e-08   5.6e-05     259     353 ..     229     325 ..     214     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0038
                              LuxE  12 ldadPlel.seeekeklrkkflldelvnhykhneeyrkycqknkvddl..vtegevddiPviPvsvfka.igtklls 84 
                                       +  +P+e  s e+  ++  + l + + + y+ n  yr+    + v +    t  +v  +P    ++++      +  
  gi|330507231|ref|YP_004383659.1|   7 FHNEPMETaSRERITQIQSERLRAIVGHVYESNPIYRRLFDEKGVRPEdiRTAEDVVRLPFTGKDILREsYPLNMAC 83 
                                       67889987245555677777777777788*********999988865411445567788888888987614567889 PP

                              LuxE  85 vsedeikaklqssatsGlkstvlldklsierllravarvmkevl 128
                                       v  d+i     ss+++G +  +   +  +++   ++ar  +  +
  gi|330507231|ref|YP_004383659.1|  84 VPRDQIVEMHMSSGSTGTPVVMPYTRSDLDQWAECMARCYRMAG 127
                                       99999999999999999999998888888888888888776655 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.2e-08
                              LuxE 259 lnlsiddvvdiygfteqvelntpdfkd.elkrkrvysdviir...deetlkvvgdGkvGlleyvdalstsyPafvvl 331
                                       l++   dv diyg+te  ++ t  ++      +++  d +i    d++t ++v dG  G l + + + ++ P     
  gi|330507231|ref|YP_004383659.1| 229 LDI---DVFDIYGMTESGGVGTLGMDCpAHDGIHIWEDQYILeiiDPKTGEPVDDGEEGELVFTSLTREALPMIRFR 302
                                       443...799*******99988865554134679999999987788****************************9999 PP

                              LuxE 332 tddlG.vieeslcegqkaGklvk 353
                                       t dl  vi++  c+++++  ++ 
  gi|330507231|ref|YP_004383659.1| 303 TADLThVISRDRCKCGRTHIRLA 325
                                       9998559*********9988875 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     3e-06     0.013      73     109 ..      86     121 ..      80     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3e-06
                                       SSS-SEEEEECCEETTEEEEEEESHHHHHHHHHH.HH CS
                               GH3  73 sepiklfalsSGTtsgksKliPvteeslkelallvla 109
                                       +++i+++ +sSG+t g + ++P+t++ l+++a  +++
  gi|330507231|ref|YP_004383659.1|  86 RDQIVEMHMSSGST-GTPVVMPYTRSDLDQWAECMAR 121
                                       5899**********.***************9887443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.24s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2992.86
//
Query:       gi|330507232|ref|YP_004383660.1|  [L=370]
Description: hypothetical protein MCON_1113 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2634.36
//
Query:       gi|330507233|ref|YP_004383661.1|  [L=262]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (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  113.4   0.0    1.6e-32  112.9   0.0    1.2  1  ABC_tran      ABC transporter
    1.1e-10   41.8   0.2     0.0001   22.2   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    5.6e-06   25.9   1.2      8e-05   22.2   1.2    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    1.8e-05   25.2   0.1    4.6e-05   23.9   0.1    1.6  1  AAA_16        AAA ATPase domain
    2.1e-05   24.8   1.5    0.00021   21.6   1.5    2.0  1  AAA_22        AAA domain
    4.9e-05   23.0   0.1    9.2e-05   22.1   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00024   21.7   0.0    0.00047   20.7   0.0    1.4  1  AAA_23        AAA domain
    0.00028   20.7   0.7     0.0005   19.9   0.1    1.6  2  AAA_15        AAA ATPase domain
     0.0011   19.0   0.0     0.0016   18.4   0.0    1.4  1  Rad17         Rad17 P-loop domain
     0.0016   17.9   0.1      0.015   14.7   0.0    2.3  3  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0027   18.2   0.1       0.05   14.0   0.0    2.2  2  AAA           ATPase family associated with various cellular 
     0.0041   16.0   0.6        0.2   10.4   0.1    2.2  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.005   16.8   0.1       0.14   12.2   0.0    2.3  2  AAA_5         AAA domain (dynein-related subfamily)
     0.0086   15.9   0.3      0.041   13.8   0.0    2.1  2  DELLA         Transcriptional regulator DELLA protein N termi
  ------ inclusion threshold ------
      0.013   14.9   0.3      0.019   14.4   0.3    1.2  1  HSM3_N        DNA mismatch repair protein HSM3, N terminal do
      0.014   14.6   0.3        0.2   10.8   0.0    2.2  2  NB-ARC        NB-ARC domain
      0.015   15.0   0.0      0.022   14.5   0.0    1.5  1  AAA_30        AAA domain
      0.015   14.5   0.0      0.017   14.3   0.0    1.1  1  G-alpha       G-protein alpha subunit
      0.032   14.4   0.0      0.075   13.2   0.0    1.7  2  AAA_33        AAA domain
      0.041   13.5   0.0      0.074   12.7   0.0    1.4  1  SRP54         SRP54-type protein, GTPase domain
      0.056   13.4   0.2       0.38   10.6   0.0    2.1  2  NTPase_1      NTPase
      0.075   13.1   0.0       0.33   11.0   0.0    2.0  2  AAA_14        AAA domain
      0.085   12.4   0.0       0.16   11.5   0.0    1.4  1  AAA_7         P-loop containing dynein motor region
       0.09   13.1   0.5       0.23   11.8   0.5    1.8  1  AAA_19        AAA domain
        0.1   12.3   0.0       0.19   11.4   0.0    1.5  1  AAA_24        AAA domain
       0.11   12.7   0.1        1.7    9.0   0.1    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 !  112.9   0.0   2.3e-35   1.6e-32       1     137 []      19     165 ..      19     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 2.3e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ v++ +k +e++ +vG+nG+GK+tL+k++ + lkp +G+il++g+++++ +++++ ++ig++pq ++    +tv 
  gi|330507233|ref|YP_004383661.1|  19 LDGVNIIVKSSEILSLVGPNGSGKTTLIKCMDRILKP-KGSILMNGQEIERMSRQEVARQIGYVPQSSSTPLATTVF 94 
                                       6899********************************8.9****************************99999999** PP

                                       HH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       ++                + ++++++l++l l++l+ +      s+LSgGqkq+v +aral+++p +lllDEpt+
  gi|330507233|ref|YP_004383661.1|  95 DTvlmgrrphigwrvqdSDLDKVAEVLERLHLEDLAMRDF----SQLSGGQKQKVLIARALAQEPAVLLLDEPTS 165
                                       99**********9976555566888888888888877777....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.5e-07    0.0001       4      23 ..      34      53 ..      31      72 .. 0.82
   2 !   18.0   0.1     3e-06     0.002     220     282 ..     120     183 ..      62     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.5e-07
                            AAA_21  4 liGpNgsGKSnLLdaldlla 23
                                      l+GpNgsGK++L++++d + 
  gi|330507233|ref|YP_004383661.1| 34 LVGPNGSGKTTLIKCMDRIL 53
                                      9***************9884 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3e-06
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllell 282
                                        +  l+ +d   +++++lS G+k+   ++ al++ +   ++ll+DEp ++L+     ++++++  l+
  gi|330507233|ref|YP_004383661.1| 120 VLERLHLEDLAMRDFSQLSGGQKQKVLIARALAQEP---AVLLLDEPTSNLDMlhqlEVMETVSSLV 183
                                       556677777777889999*******55555555555...************9755555555555554 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 !   22.2   1.2   1.2e-07     8e-05      23     189 ..      28     185 ..      10     212 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.2e-07
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                       s+++ ++vGpNGSGK+ l+  +  +L  + +  +  ++++++  +   + + + ++v    + + +        +++
  gi|330507233|ref|YP_004383661.1|  28 SSEILSLVGPNGSGKTTLIKCMDRILKPKGSILMNGQEIERMSRQ---EVARQIGYVPQSSSTPLA--------TTV 93 
                                       4558899***************99999888878888888887555...566667777764322222........344 PP

                                       EEEEETTSE..EEEEETTEEE-H.HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxx..xxxxxxxxxxxx.xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkge..seykingkevtk.kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                         +v  + +    +++++++  k +ev e l+ +++ +    +LSgG+k+ v +a  +A    +  ++ llDe  ++
  gi|330507233|ref|YP_004383661.1|  94 FDTVLMGRRphIGWRVQDSDLDKvAEVLERLHLEDLAMRdfsQLSGGQKQKVLIARALA----QEPAVLLLDEPTSN 166
                                       4444444441145566666666556666666666665434449*****99776665554....5556789******* PP

                                       S-HHHHHHHHHHHHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkekskn 189
                                       LD  +  +v e + +  k+
  gi|330507233|ref|YP_004383661.1| 167 LDMLHQLEVMETVSSLVKE 185
                                       **99988888877765554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   6.6e-08   4.6e-05      24      88 ..      29      81 ..      17     168 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6.6e-08
                            AAA_16 24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88
                                      +e++ l+G+ G+GK++l+++  r l+ +g i+++g+  +    ++++         e+ rq++  
  gi|330507233|ref|YP_004383661.1| 29 SEILSLVGPNGSGKTTLIKCMDRILKPKGSILMNGQEIER---MSRQ---------EVARQIGYV 81
                                      4899************************999999999998...2222.........222333222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   1.5   3.1e-07   0.00021       5     136 ..      29     202 ..      25     203 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.1e-07
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...........erpevvfvtlpsstsskdllrellralglelka 70 
                                         il ++G+ G+GKTtl++ + + l+   ++ +           e ++++ + ++ss+  + l++ ++  +  ++  
  gi|330507233|ref|YP_004383661.1|  29 SEILSLVGPNGSGKTTLIKCMDRILKPKGSILMngqeiermsrqEVARQIGYVPQSSS--TPLATTVFDTVLMGRRP 103
                                       57899*******************9654444448888888866655555544444443..34444444444433333 PP

                            AAA_22  71 ..................erlsseell.ealeqalrarav...........ielliiDEaqh.lr...seealeeLr 113
                                                         erl +e+l  + + q +  ++            +++l++DE    l+   + e++e+++
  gi|330507233|ref|YP_004383661.1| 104 higwrvqdsdldkvaevlERLHLEDLAmRDFSQLSGGQKQkvliaralaqePAVLLLDEPTSnLDmlhQLEVMETVS 180
                                       5669999999999999996666666666666666666666666666669999*******9988988867******** PP

                            AAA_22 114 sllnlsrkgvqliLvGtp.elrkl 136
                                       sl++  +k+++ +++++  +l+ +
  gi|330507233|ref|YP_004383661.1| 181 SLVK--EKKISAVMAIHDlNLASR 202
                                       ****..*****9999887777665 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 !   22.1   0.1   1.3e-07   9.2e-05      13      55 ..      20      62 ..      13      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpakkvrfN 55
                                      dg  i ++ +++  l+Gp+GsGK+Tl+  +  +L p+ ++  N
  gi|330507233|ref|YP_004383661.1| 20 DGVNIIVKSSEILSLVGPNGSGKTTLIKCMDRILKPKGSILMN 62
                                      55677778788999********************999876665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   6.8e-07   0.00047      18      43 ..      28      53 ..      10      87 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.8e-07
                            AAA_23 18 skgltlItGpNGaGKTTildAiklaL 43
                                      s+ +  ++GpNG+GKTT++ ++  +L
  gi|330507233|ref|YP_004383661.1| 28 SSEILSLVGPNGSGKTTLIKCMDRIL 53
                                      6677789**************97776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   7.3e-07    0.0005      22      66 ..      29      67 ..       4      88 .. 0.80
   2 ?   -1.7   0.1       2.6   1.8e+03     322     356 ..     153     187 ..     141     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 7.3e-07
                            AAA_15 22 seeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedle 66
                                      se +  l+G+N+sGK+++++ +d +l+ k       i  + +++e
  gi|330507233|ref|YP_004383661.1| 29 SE-ILSLVGPNGSGKTTLIKCMDRILKPK-----GSILMNGQEIE 67
                                      33.999*********************88.....44555555555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnk 356
                                       +++++ll++EP  +L   +q +++++  +l++++k
  gi|330507233|ref|YP_004383661.1| 153 QEPAVLLLDEPTSNLDMLHQLEVMETVSSLVKEKK 187
                                       6789999****999999999999999999999875 PP

>> Rad17  Rad17 P-loop domain
   #    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      43     118 ..      27     102 ..      16     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-06
                             Rad17  43 rkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqksdfkgltekesrflsqiesfkeleLkdak 118
                                       +  +iL + GP G gk+t +k + ++l +k    +n+ ++   + q+   +     +s+  ++  +  +  L++ +
  gi|330507233|ref|YP_004383661.1|  27 KSSEILSLVGPNGSGKTTLIKCMDRILKPKGSILMNGQEIERMSRQEVARQIGYVPQSSSTPLATTVFDTVLMGRR 102
                                       44679*********************************99998887765554444444455554444344466655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.2e-05     0.015      23      49 ..      30      56 ..      12      92 .. 0.77
   2 ?    0.3   0.1      0.55   3.8e+02       1      61 [.     133     195 ..     133     211 .. 0.69
   3 ?   -2.2   0.0       3.2   2.2e+03      53      90 ..     223     260 ..     214     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                      Mg_chelatase 23 HnlllvGppGsGKtmlakrlpsllppl 49
                                        l lvGp GsGKt l+k++  +l p 
  gi|330507233|ref|YP_004383661.1| 30 EILSLVGPNGSGKTTLIKCMDRILKPK 56
                                      55789*******************874 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.55
                      Mg_chelatase   1 dlkdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlak..rlpsllpplseeealevakia 61 
                                       d++++ G +++k  +  a a +  +ll+  p s   ml +   ++++ + ++e+++  v +i+
  gi|330507233|ref|YP_004383661.1| 133 DFSQLSGGQKQKVLIARALAQEPAVLLLDEPTSNLDMLHQleVMETVSSLVKEKKISAVMAIH 195
                                       788888888999999999999999999999888888886521344444444444554555555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.2
                      Mg_chelatase  53 ealevakiasvagkkeeekllkrrpfraphhsaskaal 90 
                                         l+  +i+ v g ++   +   rp++ p +s ++aa+
  gi|330507233|ref|YP_004383661.1| 223 ALLNEVNISQVYGIEAMVMNAMGRPYVVPLRSLAEAAV 260
                                       55666777778888888888889999999999888875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   7.3e-05      0.05       3      52 ..      34      84 ..      32      99 .. 0.79
   2 ?    2.1   0.0      0.34   2.4e+02      47      66 ..     144     162 ..     111     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.3e-05
                                      EESSTTSSHHHHHHHHHHHHTHE.EEEEETTTCSSSSTTHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelgve.fleisgsellskyvgesekkirelfke 52
                                      l+Gp G GKT+l+k + + l+ +  + ++g e+  +  +e +++i  + ++
  gi|330507233|ref|YP_004383661.1| 34 LVGPNGSGKTTLIKCMDRILKPKgSILMNGQEIERMSRQEVARQIGYVPQS 84
                                      89*************999998542588888888888777777777666555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.34
                                       HHHHHHHHHTSTSEEEEEET CS
                               AAA  47 relfkeakekakpsilfiDE 66 
                                       + l+++a ++ +p +l++DE
  gi|330507233|ref|YP_004383661.1| 144 KVLIARALAQ-EPAVLLLDE 162
                                       3344444333.478888887 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 ?    4.0   0.0     0.026        18     245     265 ..      29      50 ..       9      55 .. 0.80
   2 !   10.4   0.1   0.00028       0.2     322     381 ..     136     195 ..     128     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.026
                                       S.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 245 G.vtlIvGggfhGKsTLLeAle 265
                                         +  +vG++  GK+TL++ ++
  gi|330507233|ref|YP_004383661.1|  29 SeILSLVGPNGSGKTTLIKCMD 50 
                                       348899************9886 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00028
                                       S--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHH CS
                        ABC_ATPase 322 dASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvr 381
                                       + SG   q + i++al  +  +lL+DE ts   ++++ e m+ + s  ke   + v  ++
  gi|330507233|ref|YP_004383661.1| 136 QLSGGQKQKVLIARALAQEPAVLLLDEPTSNLDMLHQLEVMETVSSLVKEKKISAVMAIH 195
                                       5699999*****************************999999887766665444444555 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 !   12.2   0.0    0.0002      0.14       4      34 ..      34      64 ..      31     105 .. 0.76
   2 ?    2.7   0.0      0.17   1.2e+02      19      94 ..     147     188 ..     131     247 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                                      EE--SSSSHHHHHHHGGGGBS--EEEEE--T CS
                             AAA_5  4 LvGppGtgKselaerlaaalnreveyvqltr 34
                                      LvGp G+gK++l++ + + l+ +  + ++ +
  gi|330507233|ref|YP_004383661.1| 34 LVGPNGSGKTTLIKCMDRILKPKGSILMNGQ 64
                                      9*****************9955544444443 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.17
                                       GGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HHHHHHHHHHHHSSEE CS
                             AAA_5  19 laaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrl 94 
                                       +a+al +e  + +l + t+  d++ ++e+                                  ++++ sl  e+++
  gi|330507233|ref|YP_004383661.1| 147 IARALAQEPAVLLLDEPTSNLDMLHQLEV----------------------------------METVSSLVKEKKI 188
                                       45555555555555555555555555555..................................4444444444433 PP

>> DELLA  Transcriptional regulator DELLA protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   5.9e-05     0.041       6      27 ..     104     125 ..     103     142 .. 0.84
   2 ?   -1.6   0.2       3.8   2.6e+03      21      40 ..     171     190 ..     165     194 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.9e-05
                             DELLA   6 vlGYkvrssdladVAqkLEqLe 27 
                                       ++G++v+ sdl +VA+ LE+L 
  gi|330507233|ref|YP_004383661.1| 104 HIGWRVQDSDLDKVAEVLERLH 125
                                       68******************96 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.8
                             DELLA  21 qkLEqLemvlgaaqedglsq 40 
                                       ++LE +e+v + ++e+++s 
  gi|330507233|ref|YP_004383661.1| 171 HQLEVMETVSSLVKEKKISA 190
                                       67888888877777777665 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 ?   14.4   0.3   2.7e-05     0.019      31     126 ..     136     231 ..     114     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-05
                            HSM3_N  31 nlstvaklkedakrllanikrllvenksedkldydlllelldklvkvssfedvlevysvddlvkalkseidslvvaa 107
                                       +ls  +k k  + r la+   +l+ ++++++ld    le+++ + ++++ + + +v +++dl  a + + + ++   
  gi|330507233|ref|YP_004383661.1| 136 QLSGGQKQKVLIARALAQEPAVLLLDEPTSNLDMLHQLEVMETVSSLVKEKKISAVMAIHDLNLASRFSDKLVMLKE 212
                                       56666667777888999999999********************************************99999999** PP

                            HSM3_N 108 ckvieksyPkglfatseii 126
                                        kv +   Pk+l+ + +i 
  gi|330507233|ref|YP_004383661.1| 213 GKVYAAGEPKALLNEVNIS 231
                                       ************9988875 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0003       0.2      21      38 ..      30      47 ..      22      56 .. 0.86
   2 ?    2.0   0.1      0.15     1e+02      65     111 ..     117     162 ..      63     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                                      EEEEEEESTTSSHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlak 38
                                       +++lvG  G+GKttl+k
  gi|330507233|ref|YP_004383661.1| 30 EILSLVGPNGSGKTTLIK 47
                                      49**************87 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                                       HHHHHHXXHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEEE CS
                            NB-ARC  65 seeiletilkeLslseddleekeeves...lkrklvrlLltkrfllvlDD 111
                                         e    +l++L+l++  +  +++       k  + r+L +   +l+lD 
  gi|330507233|ref|YP_004383661.1| 117 VAE----VLERLHLEDLAMRDFSQLSGgqkQKVLIARALAQEPAVLLLDE 162
                                       333....5556666655555555544444478889999999999999995 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.2e-05     0.022      14      46 ..      26      57 ..      20     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
                            AAA_30 14 ltsgdrvavltGpAGtGKttalkalreaweaag 46
                                      ++s+  +  l+Gp G+GKtt++k + ++++ +g
  gi|330507233|ref|YP_004383661.1| 26 VKSS-EILSLVGPNGSGKTTLIKCMDRILKPKG 57
                                      4555.48999***************99998887 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.4e-05     0.017      26      90 ..      32     113 ..      22     235 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
                                       EEEEESTTSSHHHHHHHHHHHCS--...--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT................. CS
                           G-alpha  26 llllGqseSGKsTilkqlkllykkg...fseeelatwraviqlnivrsiktilealesleselsesf.......... 89 
                                       l l+G ++SGK+T++k + ++ k++    ++   +++  + ++ + r+i  + +  +++  +   +           
  gi|330507233|ref|YP_004383661.1|  32 LSLVGPNGSGKTTLIKCMDRILKPKgsiLMNG--QEIERMSRQEVARQIGYVPQSSSTPLATTVFDTvlmgrrphig 106
                                       5699***************9998887884444..4455577777777777777766664333322224555555555 PP

                                       ......H CS
                           G-alpha  90 ......e 90 
                                             +
  gi|330507233|ref|YP_004383661.1| 107 wrvqdsD 113
                                       5555532 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00011     0.075       4      29 ..      34      62 ..      31     124 .. 0.71
   2 ?   -1.9   0.0       4.9   3.4e+03      16      33 ..     148     169 ..     144     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                            AAA_33  4 lvGlpGsGKstlaerl...lkklgavlls 29
                                      lvG++GsGK+tl++ +   lk+ g +l +
  gi|330507233|ref|YP_004383661.1| 34 LVGPNGSGKTTLIKCMdriLKPKGSILMN 62
                                      89**********98653335554433333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.9
                            AAA_33  16 aerllkklgavllssdt....l 33 
                                       a+ l+++ ++ ll+++t    +
  gi|330507233|ref|YP_004383661.1| 148 ARALAQEPAVLLLDEPTsnldM 169
                                       6667766667778888744441 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011     0.074       3      29 ..      31      57 ..      29      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                      EEEEEESTTSSHHHHHHHHHHHHHHTT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkeg 29
                                      ++ lvG++G+GKTt +  + ++lk +g
  gi|330507233|ref|YP_004383661.1| 31 ILSLVGPNGSGKTTLIKCMDRILKPKG 57
                                      6779***********998888887665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00056      0.38       4      29 ..      34      59 ..      31     111 .. 0.82
   2 ?    0.6   0.1      0.67   4.6e+02     113     154 ..     174     217 ..     142     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00056
                                      EE--TTSSHHHHHHHHHHHH...GGG CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkssgvk 29
                                      + Gp G+GKtTl+k + + lk +g  
  gi|330507233|ref|YP_004383661.1| 34 LVGPNGSGKTTLIKCMDRILKPKGSI 59
                                      78*************99999998754 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE CS
                          NTPase_1 113 kfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkvfe 154
                                       ++ e+v  ++k ++   ++ ih  +  +++ +++   k++kv+ 
  gi|330507233|ref|YP_004383661.1| 174 EVMETVSSLVKeKKISAVMAIHDLNlASRFSDKLVMLKEGKVYA 217
                                       56788888888666778899998888888999999888888885 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00048      0.33       2      45 ..      29      70 ..      28      97 .. 0.74
   2 ?   -0.5   0.0       1.6   1.1e+03      60      74 ..     151     164 ..     118     220 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00048
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkk 45
                                      ++il ++G+  +GKTtl+k  +++ l k++  + +n ++ +  +
  gi|330507233|ref|YP_004383661.1| 29 SEILSLVGPNGSGKTTLIKC-MDRIL-KPKGSILMNGQEIERMS 70
                                      57999************965.45555.67777777777766544 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                            AAA_14  60 lkeekktylflDEiq 74 
                                       l  ++  +l+lDE  
  gi|330507233|ref|YP_004383661.1| 151 LA-QEPAVLLLDEPT 164
                                       33.367778888854 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00023      0.16      27      61 ..      23      57 ..      10      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                             AAA_7 27 elllknkkpvllvGptGtGKtviikdllkkldkek 61
                                      + ++k++  + lvGp G+GKt++ik + + l+++ 
  gi|330507233|ref|YP_004383661.1| 23 NIIVKSSEILSLVGPNGSGKTTLIKCMDRILKPKG 57
                                      56788888899*************99888877655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   0.00033      0.23       9      40 ..      28      59 ..      22     199 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00033
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggv 40
                                      ++++l ++++ G+GKT+++k++ ++l+  g++
  gi|330507233|ref|YP_004383661.1| 28 SSEILSLVGPNGSGKTTLIKCMDRILKPKGSI 59
                                      56788999************998888877743 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00027      0.19       7      27 ..      34      53 ..      29      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                            AAA_24  7 iyGpsgiGKTtlakelgpkpl 27
                                      ++Gp+g+GKTtl+k + +++l
  gi|330507233|ref|YP_004383661.1| 34 LVGPNGSGKTTLIKCM-DRIL 53
                                      89************99.6654 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 ?    9.0   0.1    0.0024       1.7      27      86 ..     131     177 ..     117     181 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
                           SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatlle 86 
                                        r++++lSGG+kq+++   +a ala    +       +++++LDE  s+lD   + +++e
  gi|330507233|ref|YP_004383661.1| 131 MRDFSQLSGGQKQKVL---IARALA----Q------EPAVLLLDEPTSNLDMLHQLEVME 177
                                       6889999999996643...332322....2......367788888888888766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 1817.53
//
Query:       gi|330507234|ref|YP_004383662.1|  [L=335]
Description: small conductance mechanosensitive ion channel (MscS) family transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.8e-46  156.9   0.1    4.8e-46  156.9   0.1    1.6  2  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.044   14.0   4.6      0.068   13.4   4.6    1.3  1  EI24        Etoposide-induced protein 2.4 (EI24)


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 ?   -3.9   2.1      0.92   8.2e+03       3      15 ..      51      63 ..      39      72 .. 0.51
   2 !  156.9   0.1   5.3e-50   4.8e-46       7     206 .]     104     301 ..      98     301 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 0.92
                                      HHHHHHHHHHHHH CS
                        MS_channel  3 ilkiliivvgili 15
                                      i++i ii++ +++
  gi|330507234|ref|YP_004383662.1| 51 IISISIIIILTIL 63
                                      2222222222222 PP

  == domain 2  score: 156.9 bits;  conditional E-value: 5.3e-50
                                       HHHHHHHHHHHHTTT--...SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE- CS
                        MS_channel   7 liivvgilivlsllgvn...vsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedig 80 
                                        i+++g+l+++ l+        a+la++G++ la+g+a++d++sn+++Gi+l + kp++iGD+v++++  G+Vedi+
  gi|330507234|ref|YP_004383662.1| 104 AIYSIGFLMTILLIPSLnriAIAMLAGAGVATLAIGFAAQDSLSNIISGIFLAIFKPMRIGDYVDFKGEYGYVEDIT 180
                                       5666666666665554334378999**************************************************** PP

                                       SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EE CS
                        MS_channel  81 lrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkell 157
                                       lr t i+t+d+r +++Pn+ + ++ i+N+s +++++   v++g+ yssd   ++k+++++ e+++++p+vlk+k  +
  gi|330507234|ref|YP_004383662.1| 181 LRHTIICTWDQRRIIVPNKLMGSDFIVNWSIGNPETVWPVNFGIGYSSD---IDKARSIITEVAESHPHVLKEKGIN 254
                                       *************************************************...************************* PP

                                       EEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 158 vvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                       v+l e+gd ++n+++++++++   +  ++   +i++ +kk +++egiei
  gi|330507234|ref|YP_004383662.1| 255 VRLIELGDFAMNLRLTFYAPS--RGMAYDAGCDIREAVKKRFDAEGIEI 301
                                       *********************..8999********************97 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   4.6   7.6e-06     0.068      41     124 ..      44     131 ..      22     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.6e-06
                                       THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HH.....CCTTSHHHHHHHHHHHHHHHHHHHHHHHTT CS
                              EI24  41 llasllvllllllplwlfplvalllaapfygllaekvekrhl.....glvkslaeslkslllllllllvllplliPv 112
                                       ++ ++ +++++ ++++l+ l+a l+++++  ++ ++ve+++l     ++ +++++ l  ++++++ +l++++l+ P 
  gi|330507234|ref|YP_004383662.1|  44 VWYIISTIISISIIIILTILIARLVNGLLEKQIPKIVESSRLgkefdETSHAMTRRLIVAAIYSIGFLMTILLI-PS 119
                                       334777788888888889999********999999999988788888677777799999999999999888887.*9 PP

                                       HHH....HHHHH CS
                              EI24 113 vglilsplllsw 124
                                       ++ i++ +l + 
  gi|330507234|ref|YP_004383662.1| 120 LNRIAIAMLAGA 131
                                       998887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2157.05
//
Query:       gi|330507235|ref|YP_004383663.1|  [L=136]
Description: hypothetical protein MCON_1116 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-08   33.2   0.0    1.2e-07   32.5   0.0    1.4  1  Glyoxalase_6  Glyoxalase-like domain
    0.00067   19.8   0.0     0.0014   18.8   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 !   32.5   0.0   1.3e-11   1.2e-07       4      86 ..       9     105 ..       6     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.3e-11
                      Glyoxalase_6   4 ldaadpaalaaFwaaalgweveree................aaledpegvgpaaedaatllfqrvpe....paknrv 60 
                                       ++a++p+++a F+++++gw+ ++                  +      g +++ + +  l+f+r p     +  n +
  gi|330507235|ref|YP_004383663.1|   9 IQAENPERAASFYREVFGWQIDEWLipkvkikdenrywqvtT------GSEAEPGINGGLVFRRGPPpaegQSVNSF 79 
                                       7899*****************999999999999997654321......33333344568999999997766444579 PP

                      Glyoxalase_6  61 HldlavedldaevarlvalGArvlre 86 
                                          ++v+dld++++r++++G+rv  +
  gi|330507235|ref|YP_004383663.1|  80 ICTIEVPDLDEHIDRVIRAGGRVAVP 105
                                       9999******************9855 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 !   18.8   0.0   1.6e-07    0.0014       2      28 ..       4      30 ..       3     122 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-07
                                      EEEEEEEESHHHHHHHHHHHHHTSEEE CS
                        Glyoxalase  2 idhvallvgdleksldFYtkvLGfklv 28
                                      + h+ + + ++e++++FY++v+G+++ 
  gi|330507235|ref|YP_004383663.1|  4 VVHFEIQAENPERAASFYREVFGWQID 30
                                      579*********************963 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1130.00
//
Query:       gi|330507236|ref|YP_004383664.1|  [L=331]
Description: PA-phosphatase-like phosphoesterase [Methanosaeta concilii GP6]
Scores for complete 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   72.7   2.8    2.3e-20   72.7   2.8    2.3  3  PAP2      PAP2 superfamily
    2.8e-06   27.2   7.0    7.7e-06   25.7   7.0    1.8  1  PAP2_3    PAP2 superfamily
  ------ inclusion threshold ------
       0.14   11.5   4.2      0.046   13.2   1.1    1.7  2  DUF373    Domain of unknown function (DUF373)
        3.1    7.4  11.7        3.6    7.2   2.0    3.5  3  PetM      PetM family of cytochrome b6f complex subunit 7


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 !   72.7   2.8   5.2e-24   2.3e-20       3     125 ..      51     156 ..      49     163 .. 0.93
   2 ?   -3.1   0.3       1.3     6e+03     113     127 ..     178     192 ..     174     197 .. 0.57
   3 ?   -2.9   0.1       1.2   5.4e+03     114     128 ..     231     245 ..     230     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 5.2e-24
                              PAP2   3 lalllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkr 79 
                                       ++++l+l+++  l+s+lK ++  pRP++++++ + +++ ++           ++PSgH+++a++++ l a l+++++
  gi|330507236|ref|YP_004383664.1|  51 FRVGLMLVTSHGLNSALKIALHGPRPYWVDPNVQAWSTEPS----------FGMPSGHAQNAVSIWGLTAQLIHKRW 117
                                       67899********************************9654..........477*********************** PP

                              PAP2  80 kkiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaa 125
                                       +        l+++  ++l++lsR ylgvHfl Dvl+G+ +G++l+ 
  gi|330507236|ref|YP_004383664.1| 118 AY-------LLAAGTCLLIGLSRAYLGVHFLGDVLVGWGVGAVLLG 156
                                       **.......9*******************************99875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
                              PAP2 113 vlaGlliGialaala 127
                                       +l ++l ++a++al+
  gi|330507236|ref|YP_004383664.1| 178 ILLAALASFAIIALY 192
                                       455555555555544 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.2
                              PAP2 114 laGlliGialaalay 128
                                        aG+++Gi+ ++++ 
  gi|330507236|ref|YP_004383664.1| 231 AAGMMLGISSGYAIL 245
                                       589999999988775 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   7.0   1.7e-09   7.7e-06     114     187 ..      81     154 ..       2     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.7e-09
                            PAP2_3 114 vllrgtienglaafPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvDviaGvalalva 187
                                       +++++  +++   +PS H+  a+ +  ++++l +kr+  +la+  ++l+ ++  ++g H+l Dv++G+ +++v 
  gi|330507236|ref|YP_004383664.1|  81 PNVQAWSTEPSFGMPSGHAQNAVSIWGLTAQLIHKRWAYLLAAGTCLLIGLSRAYLGVHFLGDVLVGWGVGAVL 154
                                       3444444588999**********9999999******9*******************************999886 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.26   1.1e+03     205     235 ..     164     193 ..     115     248 .. 0.53
   2 ?   13.2   1.1     1e-05     0.046     151     201 ..     259     318 ..     233     325 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.26
                            DUF373 205 elleklkesleegritfvtyvvallllligi 235
                                        + ek+ ++  +g+i + +   +++++++++
  gi|330507236|ref|YP_004383664.1| 164 VMEEKIGRMNLKGQILLAALA-SFAIIALYL 193
                                       233455555555555444332.222222222 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1e-05
                            DUF373 151 pelrktiLvplGlllliyallll.........lglpelalaiillllGlylllrGfglde 201
                                        +l +++L+++G++l+ y+l            l++++++la + + lG+ l++ G+gl +
  gi|330507236|ref|YP_004383664.1| 259 RRLVRYLLGMIGVVLIWYGLKEAmqieaadwaLDYIRSMLAGLWVTLGAPLMFIGLGLAK 318
                                       57889***************999999*******************************987 PP

>> PetM  PetM family of cytochrome b6f complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   2.0   0.00081       3.6      14      25 ..     144     155 ..     143     155 .. 0.97
   2 ?   -1.7   0.5      0.51   2.3e+03      10      19 ..     188     197 ..     184     198 .. 0.78
   3 ?    5.2   0.1    0.0035        15      15      27 ..     235     247 ..     229     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00081
                              PetM  14 iLVGlAlGFlLL 25 
                                       +LVG+++G++LL
  gi|330507236|ref|YP_004383664.1| 144 VLVGWGVGAVLL 155
                                       8**********9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.51
                              PetM  10 cfvLiLVGlA 19 
                                        ++L L+GlA
  gi|330507236|ref|YP_004383664.1| 188 IIALYLLGLA 197
                                       5889999*99 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0035
                              PetM  15 LVGlAlGFlLLKi 27 
                                       ++G++ G+++LK 
  gi|330507236|ref|YP_004383664.1| 235 MLGISSGYAILKR 247
                                       68**********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2525.94
//
Query:       gi|330507237|ref|YP_004383665.1|  [L=150]
Description: hypothetical protein MCON_1118 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   15.7   0.5      0.029   14.8   0.5    1.6  1  ParD      Antitoxin ParD


Domain annotation for each model (and alignments):
>> ParD  Antitoxin ParD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.5   1.6e-06     0.029       6      39 ..       9      42 ..       6      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-06
                              ParD  6 IditpeqhqrlkAvAAlqGksikeYvLerlleep 39
                                      I+itpe + +l A A lq k++k+ + e +l+  
  gi|330507237|ref|YP_004383665.1|  9 IEITPEAYRALEAEAILQEKTLKKLASELILRGI 42
                                      9***********************9999999655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1207.57
//
Query:       gi|330507238|ref|YP_004383666.1|  [L=1345]
Description: hypothetical protein MCON_1119 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.3e-18   64.8   0.0      3e-17   62.8   0.0    2.1  2  TaqI_C     TaqI-like C-terminal specificity domain
      2e-15   57.2   0.0    5.4e-15   55.8   0.0    1.7  1  Eco57I     Eco57I restriction-modification methylase
    1.1e-11   44.6   0.0    1.3e-07   31.2   0.0    2.9  2  N6_Mtase   N-6 DNA Methylase
     0.0012   18.6   0.0      0.049   13.3   0.0    2.4  2  UPF0020    Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
       0.05   13.7   0.5        1.4    9.1   0.4    2.6  2  ssDNA_DBD  Non-canonical single-stranded DNA-binding domain


Domain annotation for each model (and alignments):
>> TaqI_C  TaqI-like C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   5.3e+03      24      63 ..     334     382 ..     324     385 .. 0.73
   2 !   62.8   0.0   8.3e-21     3e-17       1     120 []    1001    1159 ..    1001    1159 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                            TaqI_C  24 ikkklkneka.........kelfeekpKilvrdisk.kldaaydekayyv 63 
                                       +k++++++k+           ++e + + l+r i++ + ++ y ++++y+
  gi|330507238|ref|YP_004383666.1| 334 LKEEIAGKKDrgekilaiqSTYWE-SLRDLFRLINDgSEAFGYSKEEFYI 382
                                       566666666555556666577888.9999999999955669999999997 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 8.3e-21
                            TaqI_C    1 kpllkGkdikrysieikgnYldlikkklknek.................................a..kelfe.. 38  
                                        kp+l Gkdikry+   ++++l+li++++++ k                                 +  ++++e  
  gi|330507238|ref|YP_004383666.1| 1001 KPFLVGKDIKRYEPPASDQFLILIPNGWTRLKypesadvwskfredypaicshlspfaefgekryDkgEYWWElr 1075
                                        79******************************999******99999999999999888887766516799999** PP

                            TaqI_C   39 ........ekpKilvrdiskkldaaydekayyvlntlylliakdelevslkyllgiLNSklikfyykkiystlrg 105 
                                                e+pK+++++i++++++++d +++y++n++y++        s+ ++l++LNS+l+ +++ ++ ++l+g
  gi|330507238|ref|YP_004383666.1| 1076 pcdyydefENPKLFWPEIAGSARFTFDASKFYANNKAYIIS------DSDFFILALLNSSLLRIFIHSVCTDLQG 1144
                                        *****************************************......46799*********************** PP

                            TaqI_C  106 gysrlkrkeleklPi 120 
                                           +++   +e+ Pi
  gi|330507238|ref|YP_004383666.1| 1145 DSFNFSAAFVEQTPI 1159
                                        ******999999998 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   1.5e-18   5.4e-15       3     100 ..     792     895 ..     790     899 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 1.5e-18
                            Eco57I   3 fdviiGNPPYqeseakkelkaleek.......akdiyqkFvekalkle..dkylaliiparflasgkglkefrekll 70 
                                       fdv+iGNPPY ++e   e k   ++       a+d+y++F+e+++ l    ++ + i+ ++++ +++++k +r ++ 
  gi|330507238|ref|YP_004383666.1| 792 FDVVIGNPPYVRQEYLGEDKLYLQNeyrsyqsAADLYVYFIERGVLLLrpRGVFSYIVANKWM-KANYGKPLRVWMR 867
                                       9*************9888776555568999999************9998778999********.9**********97 PP

                            Eco57I  71 kdkklkklvefedskevFkdveikggilvf 100
                                       + ++l+++v+f d + vF++++++ +i+ +
  gi|330507238|ref|YP_004383666.1| 868 E-QSLEEIVDFGDLA-VFETATTYPCIIRI 895
                                       5.79***********.**********9866 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   3.5e-11   1.3e-07      21     106 ..     498     632 ..     491     647 .. 0.90
   2 !    9.8   0.0   0.00012      0.42     122     189 ..     788     855 ..     769     929 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 3.5e-11
                          N6_Mtase  21 egksgGeffTPrevsklivell.......................epksgesvyDpacGsggllvqaekvlkee... 71 
                                       e k +G f+TP+ ++k iv+ +                        +    +v+Dpa+Gsg +lv+a++++ +e   
  gi|330507238|ref|YP_004383666.1| 498 ERKATGSFYTPQYIVKYIVKNTleplikpmmeeasmdadlrtdllRKLLSIKVLDPAMGSGHFLVEATDYIAREiih 574
                                       67899**************9888999**********9999888775555567*******************999*** PP

                          N6_Mtase  72 .......................dgktkelsiyGqeknettyrLakmNlllhgieykk 106
                                                                +  +  iyG+++n+++++Lak+ l l+ ++ +k
  gi|330507238|ref|YP_004383666.1| 575 areiarqededsdavaendihwaRREVVRNCIYGVDLNPMAVELAKLSLWLKTVASNK 632
                                       ******************9999888888999********************9988775 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00012
                          N6_Mtase 122 kdkkfdvvvaNppfnqkew.kektlekderfreavapksnadla..fllhiieslkpkGraavvlangvLf 189
                                       +++ fdvv+ Npp+  +e+  e++l  ++ +r++   +s+adl   f+   +  l+p G  + ++an  + 
  gi|330507238|ref|YP_004383666.1| 788 EERGFDVVIGNPPYVRQEYlGEDKLYLQNEYRSY---QSAADLYvyFIERGVLLLRPRGVFSYIVANKWMK 855
                                       5788***************855555555545554...4555544448888888888888888888877764 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   1.4e-05     0.049      32      94 ..     550     621 ..     545     638 .. 0.75
   2 ?    2.4   0.0      0.03   1.1e+02     119     133 ..     789     803 ..     773     820 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                                       EEETT-TTSHHHHHHHHHHTT--TTTT----SS........HHHHHHHHHH..HH--EEEEES-HHHHHHHHH CS
                           UPF0020  32 llDPmCGsGtilIEaallganiapgllrefvle........lkaeaeeear..aelklygsDldrrvvqgare 94 
                                        lDP  GsG +l+Ea    a+ + +  re + +        + + ++ + r  ++  +yg+Dl++ +v+ a+ 
  gi|330507238|ref|YP_004383666.1| 550 VLDPAMGSGHFLVEATDYIAREI-IHAREIARQededsdavAENDIHWARRevVRNCIYGVDLNPMAVELAKL 621
                                       69*************97666655.467776666788888764444443333325555************9986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.03
                                       TS---EEEE------ CS
                           UPF0020 119 egevdvivtnpPYGe 133
                                       e  +dv+++npPY +
  gi|330507238|ref|YP_004383666.1| 789 ERGFDVVIGNPPYVR 803
                                       4469*********65 PP

>> ssDNA_DBD  Non-canonical single-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.4   0.00038       1.4      17      83 ..     288     355 ..     279     366 .. 0.78
   2 ?    1.3   0.0       0.1   3.7e+02      39      58 ..    1031    1050 ..    1028    1062 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00038
                                       HHHHT-GGGGGSTHHHHHHHHHHHHHH-HHHHHHHGGGCHHHHH--.-----HHCCCHHHHHHHCCTT CS
                         ssDNA_DBD  17 aselqlpelsqtkLaeNLlLLllKynESpkLseqfqleYqelleer.kqeyallqekkeelleelqke 83 
                                       ++e+ l e+++ +L     LL++ y+ES  L +  ++ Y+e++ +r k+e a  + + e++l +++++
  gi|330507238|ref|YP_004383666.1| 288 DQEQMLREVQENSLRLLYRLLFIFYAESRRLLKVDNRHYREMSLRRlKEEIAGKKDRGEKILAIQSTY 355
                                       5677788899999998899**********************976661555555555666677666555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
                                        HHHHH-HHHHHHHGGGCHHH CS
                         ssDNA_DBD   39 lKynESpkLseqfqleYqel 58  
                                        lKy ES++   +f  +Y  +
  gi|330507238|ref|YP_004383666.1| 1031 LKYPESADVWSKFREDYPAI 1050
                                        8****************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.86u 0.31s 00:00:01.17 Elapsed: 00:00:00.44
# Mc/sec: 9251.04
//
Query:       gi|330507239|ref|YP_004383667.1|  [L=147]
Description: hypothetical protein MCON_1120 [Methanosaeta concilii GP6]
Scores for 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-05   23.5   0.0     0.0001   22.8   0.0    1.4  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   5.8e-09    0.0001      65     118 ..      72     124 ..      59     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.8e-09
                                       HHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                               PIN  65 lsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrr 118
                                       l  ++i p d++i+e a+e+ +k +++p Dal++A A   g++ ++++D+++ +
  gi|330507239|ref|YP_004383667.1|  72 LCKIRIGP-DDKIYECALEYQRKSRITPKDALHLASANFIGADYFLSCDNRLLN 124
                                       55666666.999**************************************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1051.10
//
Query:       gi|330507240|ref|YP_004383668.1|  [L=70]
Description: hypothetical protein MCON_1121 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       382  (0.0213063); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 537.87
//
Query:       gi|330507241|ref|YP_004383669.1|  [L=168]
Description: hypothetical protein MCON_1122 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.7   0.1      0.052   13.9   0.1    1.4  1  Myb_DNA-bind_4  Myb/SANT-like DNA-binding domain


Domain annotation for each model (and alignments):
>> Myb_DNA-bind_4  Myb/SANT-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.9e-06     0.052      30      66 ..     120     160 ..     100     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-06
                                       SS--HHHHHHHHHH....HHHHC----HHHHHHHHHHHHHH CS
                    Myb_DNA-bind_4  30 kkrnkklWeevaea....maergykrspeqCkeKienLkkr 66 
                                       ++ nk  Weev+ +    m   g++++ e+C+eK+e+ +k+
  gi|330507241|ref|YP_004383669.1| 120 SSENKYSWEEVKLQlveiMDHLGVDVTWEECEEKLEKYMKK 160
                                       5678889****98833335668**************98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1159.37
//
Query:       gi|330507242|ref|YP_004383670.1|  [L=499]
Description: ribonuclease II family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-75  253.8   0.0    3.1e-75  253.5   0.0    1.1  1  RNB            RNB domain
    9.6e-15   54.3   0.7    3.6e-14   52.4   0.0    2.3  2  RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain
  ------ inclusion threshold ------
      0.017   15.5   0.3       0.59   10.5   0.1    2.9  2  S1             S1 RNA binding domain


Domain annotation for each model (and alignments):
>> RNB  RNB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.5   0.0   5.1e-79   3.1e-75       2     325 ..      57     388 ..      56     389 .. 0.96

  Alignments for each domain:
  == domain 1  score: 253.5 bits;  conditional E-value: 5.1e-79
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RNB   2 kdlrdllvitIdpedakdlDdAisieklpngnyelgVhIADvshyvkegspldkearkratsvyLpekvvpMLPqel 78 
                                       +dlr ll+ +Id++d++dlD+    e+l++g+ ++ V++ADv ++v+++s++d +a+  +tsvy + +++pMLP +l
  gi|330507242|ref|YP_004383670.1|  57 RDLRGLLWASIDNDDSEDLDQLTVAEPLDDGKARIRVAVADVDSLVHKDSAIDLDAQANTTSVYTAAQIFPMLPLKL 133
                                       79*************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxx RF
                               RNB  79 sedlcSLnpgedrlalsvlidvdekgevlsveiylsvIkskarltydevqdlleqkdekeekk.......taedLel 148
                                       s++l SLn ++drla++v ++v  +g++ + ++y++v++++a+l y++v+++le++      +        ae+L+l
  gi|330507242|ref|YP_004383670.1| 134 STNLTSLNLDQDRLAVVVDMTVAPDGSLVDSDVYRAVVHNHAKLAYNSVAAWLEGTGPMP--QavsamdgLAENLLL 208
                                       *****************************************************9887654..23569999******* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RNB 149 lyelakalrkkRlkkgalefdspeikllldedkgnrielkveeetkahslveelmllANelvArflseleipailri 225
                                         ++a+++++ R+k+gal++++ e+k  ++   ++  +l vee + a++++e++m++AN ++ r+l e++ p i r+
  gi|330507242|ref|YP_004383670.1| 209 QDKVAQNMKSLRHKEGALSLETIEAKPVFKG--ERLCDLLVEETNRAKQIIEDFMIAANGVTVRYLTERNMPSIRRV 283
                                       *****************************88..7899**************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx.....xxxxx RF
                               RNB 226 heepsnekledliklakklglklednsskknlqeslekleeee..aeqllselllrllkeakyssep.....vgHfg 295
                                        + p+  +++ ++++a+++ +kl+ n+s ++l+ +l+++++++   ++ ls  +++ll + +y  e      +gHfg
  gi|330507242|ref|YP_004383670.1| 284 VRVPK--RWDRIVQIAAQHAFKLPPNPSSRKLEIFLNMMKKKDplRFPDLSLAVIKLLGNGEYVAELpetepIGHFG 358
                                       *9998..9**************99999999*************9*******************955455566***** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RNB 296 LaleeYthfTSPirRYpDlvvhrllkalla 325
                                       La+++Y+h T+P rRYpDl+++rllka+++
  gi|330507242|ref|YP_004383670.1| 359 LAVKDYAHSTAPNRRYPDLITQRLLKAAIE 388
                                       **************************9986 PP

>> RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3      0.37   2.2e+03      39      48 ..      90      99 ..      79     101 .. 0.61
   2 !   52.4   0.0     6e-18   3.6e-14       1      58 [.     435     493 ..     435     494 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.37
                     RNase_II_C_S1 39 rvrVrLveAD 48
                                      r+rV ++++D
  gi|330507242|ref|YP_004383670.1| 90 RIRVAVADVD 99
                                      5555555555 PP

  == domain 2  score: 52.4 bits;  conditional E-value: 6e-18
                     RNase_II_C_S1   1 etFdAvVvdvddrggtVqladPaVeArv.eggaglplGervrVrLveADvatrrvrFep 58 
                                       e+F+A+V++ +++g++V+l d +Ve+++ ++++g+++G++v+V+L ++Dv  ++++F+ 
  gi|330507242|ref|YP_004383670.1| 435 ERFSAMVTGSSEKGTWVRLLDIPVEGMLkGKRKGIDVGDEVTVELISVDVNLGFIDFKQ 493
                                       89**************************99999************************86 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.9   1.1e+04      17      34 ..      86     104 ..      84     107 .. 0.65
   2 ?   10.5   0.1   9.8e-05      0.59       1      68 [.     430     487 ..     430     492 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.9
                                       TTEEEEEET.TTEEEEEEG CS
                                S1  17 kgGafVelg.ngvegfvpa 34 
                                       +g a++++  ++v+ +v++
  gi|330507242|ref|YP_004383670.1|  86 DGKARIRVAvADVDSLVHK 104
                                       5556666666677777775 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.8e-05
                                       HSTTTCEEEEEEEEEETTEEEEEET.TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTT CS
                                S1   1 kpekgevveGeVtsvtkgGafVelg.ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrr 68 
                                       +p++ge++++ Vt  +++G  V+l+  +veg++  +            + + vGdev v+++ vd++ +
  gi|330507242|ref|YP_004383670.1| 430 EPRIGERFSAMVTGSSEKGTWVRLLdIPVEGMLKGKR-----------KGIDVGDEVTVELISVDVNLG 487
                                       6899*********************999999987764...........456699999999999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3189.91
//
Query:       gi|330507243|ref|YP_004383671.1|  [L=110]
Description: TM2 domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0033   17.7   4.7     0.0047   17.2   4.7    1.2  1  TM2       TM2 domain


Domain annotation for each model (and alignments):
>> TM2  TM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   4.7   2.6e-07    0.0047       1      49 [.      28      75 ..      28      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.6e-07
                               TM2  1 rkksklvaylLwffLGglGvHRFYlGktgsGvlqlltfv.Gglgiwwlid 49
                                      +kk+ ++  l ++f  + G   +YlG + +G+l ll+ +  ++++++++d
  gi|330507243|ref|YP_004383671.1| 28 MKKNVGLITLISIF--IPGGGQIYLGEYLKGLLILLLAWlVLPWLYGIYD 75
                                      68999999999999..88999***************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 844.13
//
Query:       gi|330507244|ref|YP_004383672.1|  [L=274]
Description: hypothetical protein MCON_1125 [Methanosaeta concilii GP6]
Scores for complete 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   26.1   0.0    9.1e-06   25.3   0.0    1.4  1  Lon_C     Lon protease (S16) C-terminal proteolytic domain
     0.0054   16.6   0.0      0.014   15.3   0.0    1.6  1  ChlI      Subunit ChlI of Mg-chelatase


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 !   25.3   0.0     1e-09   9.1e-06     109     172 ..     150     213 ..     115     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1e-09
                                       GGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEGGG CS
                             Lon_C 109 GPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvilPken 172
                                       G saG + a   +++l ++ ++kd  +tG i   G +  iG + ek+ a + ag k  ++P+  
  gi|330507244|ref|YP_004383672.1| 150 GESAGAAAAILTIAALVDRDIKKDAVITGTINEDGSIGQIGSVLEKTKAVSDAGYKYFLIPEGQ 213
                                       89***********************************************************865 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.5e-06     0.014      64     119 ..     156     211 ..     149     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-06
                              ChlI  64 piAigilaaleqieaeeetlflGeLsldGslrpvkgvlpialaakkegikkvivpk 119
                                       + Ai  +aal + + +++ ++ G ++ dGs+ ++  vl+ + a++++g+k +++p+
  gi|330507244|ref|YP_004383672.1| 156 AAAILTIAALVDRDIKKDAVITGTINEDGSIGQIGSVLEKTKAVSDAGYKYFLIPE 211
                                       3455556999999******************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2153.56
//
Query:       gi|330507245|ref|YP_004383673.1|  [L=52]
Description: hypothetical protein MCON_1126 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       147  (0.00819901); expected 358.6 (0.02)
Passed bias filter:                      112  (0.00624686); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 401.91
//
Query:       gi|330507246|ref|YP_004383674.1|  [L=350]
Description: transposase, OrfB family [Methanosaeta concilii GP6]
Scores for complete 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   75.8   0.0    4.7e-21   74.5   0.0    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    9.1e-11   42.0   0.2    1.7e-10   41.1   0.2    1.5  1  OrfB_IS605      Probable transposase
     0.0011   18.4   6.4      0.016   14.7   3.3    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0057   16.6   3.4      0.013   15.5   3.4    1.6  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.083   12.9   0.5       0.19   11.8   0.5    1.5  1  DZR             Double zinc ribbon
       0.33   11.1   3.6         14    5.9   0.1    2.7  3  Zn-ribbon_8     Zinc ribbon domain
        0.4   10.5   2.4        4.5    7.1   0.1    2.3  2  zinc_ribbon_2   zinc-ribbon domain
       0.45   10.0   2.4       0.92    9.0   0.3    2.3  2  zf-ribbon_3     zinc-ribbon domain
       0.54   10.3   2.3         20    5.3   0.2    2.8  3  CpXC            CpXC protein
        2.1    8.2   4.1        7.3    6.4   0.3    2.4  2  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   2.6e-24   4.7e-21       1      67 [.     260     327 ..     260     329 .. 0.96

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 2.6e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       f+ l++++eykak +G++++ v+p++TS tC+ Cg+++k  ++++++f+C++Cgf   +D+ Aa+Ni+
  gi|330507246|ref|YP_004383674.1| 260 FGLLRTFVEYKAKVAGVPLVFVDPRNTSRTCPSCGHVSKAnRPTRDEFRCESCGFAGPADHIAAMNIA 327
                                       67799***********************************99*************************8 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.2   9.7e-14   1.7e-10       3     105 ..     136     228 ..     132     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 9.7e-14
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       +vev++ +++ +++ ++g+DlGi+ La+ ++++    + +g ++ ++ ++l   +a+lqsk  ks     a+r l++
  gi|330507246|ref|YP_004383674.1| 136 VVEVDE-ETPYDPKGTLGVDLGIKYLAVDSDGE----VHSGEQINQTRERLDSLKARLQSKGTKS-----AKRHLKK 202
                                       455554.77789999******************....************************6666.....8****** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlke 105
                                       l+ + +r+ +++ h +++h++ + k+
  gi|330507246|ref|YP_004383674.1| 203 LSGRTARFSRDVNHCISKHIVTKAKD 228
                                       ********************987654 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   4.8e-05     0.086      11      30 ..     279     298 ..     275     301 .. 0.84
   2 !   14.7   3.3   8.8e-06     0.016       2      26 ..     289     313 ..     288     314 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                                       CHEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon  11 lveDpergelvCtdCGlVle 30 
                                       + +Dp ++  +C++CG V  
  gi|330507246|ref|YP_004383674.1| 279 VFVDPRNTSRTCPSCGHVSK 298
                                       579**************986 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 8.8e-06
                                       EETTTTCEECHEETSTTCEEESSSS CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCG 26 
                                       +CP Cg+ +  + p r e++C++CG
  gi|330507246|ref|YP_004383674.1| 289 TCPSCGHVSKANRPTRDEFRCESCG 313
                                       8******999999***********9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   3.4     7e-06     0.013      19      44 ..     288     313 ..     283     315 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7e-06
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCr 44 
                                       ++CP Cg+  ka r ++   f+C++C+
  gi|330507246|ref|YP_004383674.1| 288 RTCPSCGHVsKANRPTR-DEFRCESCG 313
                                       89*****8877877776.********8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5    0.0001      0.19      10      37 ..     285     315 ..     277     323 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                               DZR  10 pdarfCseCgtklkavaa...edrCpsCgek 37 
                                       + +r+C+ Cg+  ka      e rC sCg +
  gi|330507246|ref|YP_004383674.1| 285 NTSRTCPSCGHVSKANRPtrdEFRCESCGFA 315
                                       5678888888876643336678888888865 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.1   9.2e+03      10      22 ..      12      24 ..      11      29 .. 0.68
   2 ?    5.9   0.1    0.0079        14      25      34 ..     286     295 ..     277     302 .. 0.68
   3 ?    5.3   0.2     0.012        21       5      12 ..     306     313 ..     306     320 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.1
                       Zn-ribbon_8 10 eCghefevlqsis 22
                                      +C++  e + +++
  gi|330507246|ref|YP_004383674.1| 12 ACNRIAETVFAMH 24
                                      7998888666666 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0079
                       Zn-ribbon_8  25 pltaCPeCgs 34 
                                          +CP+Cg+
  gi|330507246|ref|YP_004383674.1| 286 TSRTCPSCGH 295
                                       4556999997 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.012
                       Zn-ribbon_8   5 eYrCeeCg 12 
                                       e+rCe+Cg
  gi|330507246|ref|YP_004383674.1| 306 EFRCESCG 313
                                       8******9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0025       4.5      11      21 ..     285     295 ..     284     297 .. 0.80
   2 ?    2.9   0.2     0.052        94      12      21 ..     304     314 ..     298     316 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0025
                     zinc_ribbon_2  11 dnakFCpyCGt 21 
                                       ++++ Cp CG+
  gi|330507246|ref|YP_004383674.1| 285 NTSRTCPSCGH 295
                                       57788999998 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.052
                     zinc_ribbon_2  12 nakF.CpyCGt 21 
                                       ++ F C+ CG+
  gi|330507246|ref|YP_004383674.1| 304 RDEFrCESCGF 314
                                       56677888886 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3   0.00051      0.92       4      11 ..     289     296 ..     286     300 .. 0.73
   2 ?   -0.3   0.1      0.43   7.6e+02       4       9 ..     308     313 ..     305     314 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00051
                       zf-ribbon_3   4 rCPnCGap 11 
                                       +CP+CG++
  gi|330507246|ref|YP_004383674.1| 289 TCPSCGHV 296
                                       68888875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.43
                       zf-ribbon_3   4 rCPnCG 9  
                                       rC +CG
  gi|330507246|ref|YP_004383674.1| 308 RCESCG 313
                                       677776 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.6   2.8e+03      84     107 ..     197     226 ..     168     234 .. 0.63
   2 ?    5.3   0.2     0.011        20      37      53 ..     287     303 ..     280     306 .. 0.80
   3 ?    3.4   0.0     0.042        76       2      34 ..     308     340 ..     307     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.6
                              CpXC  84 k......egytlRlvidmaelaEkililea 107
                                       k      +g t R+  d ++ + k ++ +a
  gi|330507246|ref|YP_004383674.1| 197 KrhlkklSGRTARFSRDVNHCISKHIVTKA 226
                                       122333577777888888888888777765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.011
                              CpXC  37 eatCpkCgatakleapl 53 
                                       + tCp+Cg+  k++ p+
  gi|330507246|ref|YP_004383674.1| 287 SRTCPSCGHVSKANRPT 303
                                       56899999998888775 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.042
                              CpXC   2 tCpaCgkefeaeiwtsidadedpelkeklldgs 34 
                                       +C +Cg    a++   ++++ + e+ + +++g+
  gi|330507246|ref|YP_004383674.1| 308 RCESCGFAGPADHIAAMNIAFRAEVNQPIVAGK 340
                                       589999999999999999999999888888886 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.4     0.056     1e+02      17      22 ..     290     295 ..     289     299 .. 0.73
   2 ?    6.4   0.3    0.0041       7.3       1      10 [.     307     316 ..     307     318 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.056
                      Rubredoxin_2  17 CpsCgs 22 
                                       CpsCg+
  gi|330507246|ref|YP_004383674.1| 290 CPSCGH 295
                                       777775 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0041
                      Rubredoxin_2   1 YvCsqCGfes 10 
                                       ++C++CGf  
  gi|330507246|ref|YP_004383674.1| 307 FRCESCGFAG 316
                                       8******965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 2678.14
//
Query:       gi|330507247|ref|YP_004383675.1|  [L=201]
Description: NAD(P)H dehydrogenase (quinone) [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-33  114.7   0.0    4.9e-33  114.5   0.0    1.0  1  Flavodoxin_2  Flavodoxin-like fold
    4.8e-10   39.4   0.0    6.3e-10   39.0   0.0    1.2  1  FMN_red       NADPH-dependent FMN reductase
  ------ inclusion threshold ------
       0.16   12.1   0.1       0.34   11.1   0.1    1.5  1  zf-RING_13    RING/Ubox like zinc-binding domain


Domain annotation for each model (and alignments):
>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.5   0.0   8.2e-37   4.9e-33       1     170 [.       1     164 [.       1     194 [. 0.86

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 8.2e-37
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHCCHHHHTTC.HHHHHHH.HHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaaklayeekp.adveseq.iek 74 
                                       m++ +i ahp++ +sf++a+a a+++al  +g h v+ +dLy++ f+pvl    +       +++ +d    + + +
  gi|330507247|ref|YP_004383675.1|   1 MNVSLILAHPNQ-GSFNHAIAIAAINALDGNG-HSVRFHDLYRErFDPVLPYGEIP------KGAdIDSNLMKhCGE 69 
                                       8999********.6******************.******************97776......4444888888889** PP

                                       HHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSC.E..ETTCSSCCCCTTTTSEEEEEEEESS-GGGSSTTSSS- CS
                      Flavodoxin_2  75 llaadaivlqfPlwwfgvPailKgwiDrvltagfaf.y..teeggegrgggLkgkkalvivttGgpeesyqergleg 148
                                       + +ad i++++P ww + PailKgw+Drv ++g a+ +  ++ g++  +g+Lk +kalv +t++   +   er   g
  gi|330507247|ref|YP_004383675.1|  70 IVSADGIIIVHPNWWGMPPAILKGWVDRVIRPGVAYeFleGDSGEGVPRGLLKARKALVFNTSNTFPDR--EREAFG 144
                                       ************************************99986666645589999**********999776..455778 PP

                                       S-HHHHHHHHHHHHHHTT-EEE CS
                      Flavodoxin_2 149 aamdellpplrgilgfiGikdv 170
                                        ++++l+   + i+g++G++ +
  gi|330507247|ref|YP_004383675.1| 145 DPLQRLW--KDCIFGLCGVEEF 164
                                       8******..**********987 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   1.1e-13   6.3e-10       1     100 [.       1     100 [.       1     132 [. 0.90

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.1e-13
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--..---HCHGHTCGGSHHHHHHHHHHHH-SCE CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpcalcdkdlesegqtsddvaellekiaaadal 76 
                                       m++ +i + +++gs++ ++a +a +al  +g  v + dl      p +l+ ++ ++    + ++ +    i +ad++
  gi|330507247|ref|YP_004383675.1|   1 MNVSLILAHPNQGSFNHAIAIAAINALDGNGHSVRFHDLYRErFDP-VLPYGEIPKGADIDSNLMKHCGEIVSADGI 76 
                                       8999***********************999**********997777.8999999988888888888888999***** PP

                                       EEEEEECTTCE-HHHHHHHHCHT- CS
                           FMN_red  77 iivtPeYngsysgllKnalDrlsr 100
                                       iiv P ++g+++++lK   Dr+ r
  gi|330507247|ref|YP_004383675.1|  77 IIVHPNWWGMPPAILKGWVDRVIR 100
                                       *********************965 PP

>> zf-RING_13  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   5.7e-05      0.34      37      60 ..     154     177 ..     150     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.7e-05
                                       ESSSSS-SBGGGBSSSBTTTTSS- CS
                        zf-RING_13  37 slfancghdimyrstyctmcegsp 60 
                                        +f  cg + +yr tyc +   +p
  gi|330507247|ref|YP_004383675.1| 154 CIFGLCGVEEFYRKTYCVIATSTP 177
                                       57999*************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1446.42
//
Query:       gi|330507248|ref|YP_004383676.1|  [L=258]
Description: hypothetical protein MCON_1130 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-07   31.1   0.1    8.6e-07   28.9   0.1    2.0  2  HTH_20         Helix-turn-helix domain
      4e-06   26.6   0.0    1.7e-05   24.6   0.0    2.0  2  HTH_5          Bacterial regulatory protein, arsR family
     0.0072   16.2   0.3      0.011   15.5   0.3    1.3  1  Glyco_H_20C_C  Glycoside Hydrolase 20C C-terminal domain
  ------ inclusion threshold ------
       0.04   13.5   0.0      0.095   12.3   0.0    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
      0.059   13.2   0.7      0.084   12.7   0.7    1.2  1  SICA_alpha     SICA extracellular alpha 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 ?   -1.0   0.0      0.52   1.8e+03      26      35 ..     123     132 ..     121     148 .. 0.78
   2 !   28.9   0.1   2.4e-10   8.6e-07       4      60 ..     167     222 ..     164     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.52
                                       -HHHHHHHHT CS
                            HTH_20  26 taselaerld 35 
                                       ++se+a++ld
  gi|330507248|ref|YP_004383676.1| 123 CFSEVARLLD 132
                                       8899999996 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 2.4e-10
                                       HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20   4 aeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                       +e L+++ R+ il+aL  ae  t+s+lae+ +l+  +l +HL++L+  g + ++ e+
  gi|330507248|ref|YP_004383676.1| 167 LEPLSNKQRLQILKAL-FAETKTFSALAELTGLRGGNLLFHLQKLQNGGMILQRNER 222
                                       666999**********.**********************************999886 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         1   3.7e+03      16      27 ..     122     133 ..     121     134 .. 0.84
   2 !   24.6   0.0   4.6e-09   1.7e-05       2      45 ..     173     216 ..     172     216 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1
                                       EEHHHHHHHHTS CS
                             HTH_5  16 lcvcelaeelgl 27 
                                       +c++e a+ l++
  gi|330507248|ref|YP_004383676.1| 122 TCFSEVARLLDK 133
                                       79****999975 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 4.6e-09
                                       HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5   2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45 
                                       ++Rl+ILk+L  + ++++ lae +gl  +++  HL kL + G++
  gi|330507248|ref|YP_004383676.1| 173 KQRLQILKALFAETKTFSALAELTGLRGGNLLFHLQKLQNGGMI 216
                                       78************************************998875 PP

>> Glyco_H_20C_C  Glycoside Hydrolase 20C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   3.2e-06     0.011      13     103 ..      63     150 ..      53     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.2e-06
                     Glyco_H_20C_C  13 pgvkkknretanpsKylLYqDpLlglfdkqvagldlekhYeklaekleelaekskelnelfelykkLakvLalKael 89 
                                       +g+ +k+ +++n++K  L+ D+L + +d+  +g+  ++  +++++klee+ + ++++++  +  +++a++L + ++l
  gi|330507248|ref|YP_004383676.1|  63 EGKISKDCHMKNACKA-LFSDLLNSSLDQIKRGEVSADSINDAKSKLEEMRR-KSPYDQCKTCFSEVARLLDKQIDL 137
                                       5555678899999996.68*******************************99.9*********************** PP

                     Glyco_H_20C_C  90 girirkaYrakdre 103
                                          +r  Yr++d +
  gi|330507248|ref|YP_004383676.1| 138 MRSLR-VYRENDLT 150
                                       *9997.69999853 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 ?   12.3   0.0   2.7e-05     0.095       2      47 ..     172     216 ..     171     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                            HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       ++ +++IL++L +    + + LAe +gl  ++++ +l++L++ G I
  gi|330507248|ref|YP_004383676.1| 172 NKQRLQILKALFA-ETKTFSALAELTGLRGGNLLFHLQKLQNGGMI 216
                                       6788999999999.899*************************9988 PP

>> SICA_alpha  SICA extracellular alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   2.3e-05     0.084      27     137 ..      10     139 ..       4     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                        SICA_alpha  27 ekLkkelekmfeeLkkrLkk...qeskeiaklC.advkeevekkkkee.............ymkelCkalveilyfm 86 
                                       + +k++l+ m e++k+ +++   q+ ++i + C +d+ + +++  ++e             +mk+ Ckal+  l   
  gi|330507248|ref|YP_004383676.1|  10 NAIKSKLDIMHEDMKRFMERsnqQHLNSIVDGCrSDFFDVIRGYATDEiesslegkiskdcHMKNACKALFSDLLNS 86 
                                       578999999*****999998677888899999*6666666666666668999*******************988766 PP

                        SICA_alpha  87 sgvkkkrk...kktkkdekaeiekslkeaeaYlRCiVGavalseiygdhcklek 137
                                       s  + kr     ++ +d k + e +++ ++ Y +C    +   +++ ++ +l +
  gi|330507248|ref|YP_004383676.1|  87 SLDQIKRGevsADSINDAKSKLE-EMRRKSPYDQCKTCFSEVARLLDKQIDLMR 139
                                       65442333465555566666666.999999999998777777777777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1910.10
//
Query:       gi|330507249|ref|YP_004383677.1|  [L=79]
Description: hypothetical protein MCON_1131 [Methanosaeta concilii GP6]
Scores for complete 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-32  108.7   0.2    9.8e-32  108.6   0.2    1.0  1  MTH865         MTH865-like family
  ------ inclusion threshold ------
      0.047   13.5   0.1      0.051   13.4   0.1    1.0  1  PhageMin_Tail  Phage-related minor tail protein


Domain annotation for each model (and alignments):
>> MTH865  MTH865-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.6   0.2   1.1e-35   9.8e-32       1      69 [.       6      74 ..       6      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 1.1e-35
                                      HHHHHHHHHHTTSSSTTBHHHHHHHH-TTSS-----BTTB---TTTTGGGS-GGGSB-SHHHHHHHHHH CS
                            MTH865  1 elkeqivealegadFPikspeeLlaalPkGaettceagdvevtagelgkklkdsdFPyksaedladdiv 69
                                      e+++qiv+al++a+FPik+peeL+aalP+Ga+t+c+agdve+tag++gk lk+sdFP+k+a ++ad iv
  gi|330507249|ref|YP_004383677.1|  6 EIHAQIVGALKEAKFPIKTPEELMAALPQGAATKCKAGDVEITAGDAGKVLKASDFPFKDARQVADVIV 74
                                      79******************************************************************9 PP

>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.7e-06     0.051      18      84 ..       7      75 ..       1      78 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-06
                     PhageMin_Tail 18 l.aealeelasaG...vsteeilnll.egaaklataggaddleeaaeilstalnafglsaadaeeaaDvlaa 84
                                      + a+++++l+ a     + ee++++l +gaa+  +ag+   +e +a  ++++l+a   + +da ++aDv+++
  gi|330507249|ref|YP_004383677.1|  7 IhAQIVGALKEAKfpiKTPEELMAALpQGAATKCKAGD---VEITAGDAGKVLKASDFPFKDARQVADVIVK 75
                                      45788888888866668899999999666666666665...8999999***********88********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 590.99
//
Query:       gi|330507250|ref|YP_004383678.1|  [L=737]
Description: oligosaccharyl transferase STT3 subunit [Methanosaeta concilii GP6]
Scores for complete 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   72.5  37.7    1.3e-19   70.6  37.7    2.2  1  STT3           Oligosaccharyl transferase STT3 subunit
    1.1e-11   45.2  16.9    1.1e-11   45.2  16.9    3.7  3  PMT_2          Dolichyl-phosphate-mannose-protein mannosyltra
    1.3e-09   38.2   0.0      2e-09   37.6   0.0    1.3  1  AglB_L1        Archaeal glycosylation protein B long peripher
  ------ inclusion threshold ------
      0.032   12.8  40.6        0.1   11.2  40.1    1.8  1  DUF2339        Predicted membrane protein (DUF2339)
       0.12   12.2  45.1      0.042   13.7  15.9    3.5  3  7TMR-DISM_7TM  7TM diverse intracellular signalling
        2.2    8.2   6.4         23    4.8   1.8    2.8  3  60KD_IMP       60Kd inner membrane protein


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 !   70.6  37.7   4.2e-23   1.3e-19      33     485 ..      45     524 ..      35     525 .. 0.77

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 4.2e-23
                                       SCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHCCC.CHHHHHHCCHHCHHHHHHHHCCHHH CS
                              STT3  33 fDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygplivlLamlasaiinhsldvsirevclwlpal 109
                                        D+YY  R + +   n       ++ + wfd +  yP G  ++++pl   ++ ++   +   ++  +  ++ ++p +
  gi|330507250|ref|YP_004383678.1|  45 YDEYYHMRRILYGTSN-------FPDTLWFDTYLNYPHGFSITWPPLFDQISAALCIALGQHTKEGVEMTAAFVPVI 114
                                       6999999988888888.......8***************************9988888888888677777788999* PP

                                       HHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHHHHHHHHHHHHCCSTTCHHHHH CS
                              STT3 110 lgsLlaIpiyflvrelksdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllfvlffflkaiktksnkislavi 186
                                       +g L+ +++y+++rel++ + +llA ++ a+aP Yl  t+    D++ +e++++l+ l f++ a  + +++  +a++
  gi|330507250|ref|YP_004383678.1| 115 IGLLAMVVVYYIMRELFDHRIALLASFMTALAPYYLLYTMVAATDHHSLEVLFQLLSLLFMVLAFSRPDKRWLYASA 191
                                       ***************************************************************************** PP

                                       HHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTTS-CCHHHHHHHHHHHHHHH..CCCCCCCTTCHHHSTTTCHHC CS
                              STT3 187 aaliiflivlaWggyailiyallllfilalLiigrfelklkiavtfsviiaflviaiivllflgfqvvavseiigal 263
                                       a+++++ + ++W g  + + a +llf + ++    +++k ++ +   +++af++  i+vl+f +   ++ s ++ a+
  gi|330507250|ref|YP_004383678.1| 192 AGVALAALAYTWQGADVYFGA-YLLFAAFGMSLELRQEKPNLNIVSTLLVAFFLALILVLPFRNTPWMSPSFLGLAA 267
                                       **************9776665.5667777777777666666666666666666646777777766666678888888 PP

                                       CCCHHHHHHHHCCCHHC..CCCCCHHCC.CHHTT.HHHHTT--GGGHHHHH...HHHHHHHC............... CS
                              STT3 264 gifgllqlvafgsvvvlvaelkfyqfis.lfqpgilsevlgligevvtala...vlglialw............... 321
                                       ++++l++++a+ ++ +    ++ + f   +++ +i+s +l+ i    + l+    +g++ +w               
  gi|330507250|ref|YP_004383678.1| 268 IFVALAIMLALAHIIAK-RSISWKAFPLaILAIFIISLLLSKILGGFFGLEgliRTGMGYIWggemigkigeaepli 343
                                       99999999999998776.5555555554555555555555555333333330003344444477888999999**** PP

                                       ...............CCCCCTS---........--TTHHHHHHHHHS---S--CCHHHCCSSST.TTTCCCHH...H CS
                              STT3 322 ...............lgilyslldl........eyaklkikiiilvsvwlpvgllaltkglrfl.iftvPlgi...i 371
                                                      l il+sl +         +   +  +++ l+ +w + ++l+++   rfl i t+ +g+   i
  gi|330507250|ref|YP_004383678.1| 344 ydldtlsqvvfswlgLNILFSLAGAaaivvymrKEERRMQQSLLLLLIWAVFSILLTLGQGRFLyISTIFMGMlisI 420
                                       ************9997778888877888876644455666788999******************9988887776566 PP

                                       CHHCCHHCTCHHHHHHHHHHHHHCCC-SCHCCCCCHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHCT.T CS
                              STT3 372 fvgllleflavfvkiysvsqilfsgvvvillmltllpvlallaavkiskifstykdekeakikvaakavaptksngl 448
                                       +++  l  l+ f      + + ++ + +i ++l++lp+ +   + + +   +   d   + ++ ++++      + +
  gi|330507250|ref|YP_004383678.1| 421 LIFYALDRLKKFQEERG-AKLHRALAAAI-ILLLVLPTAIDAFNFASNSPPAIAGDWQDSLFWLKENS------DPT 489
                                       66666666666666555.44444444444.56666666666667777777788888777888875544......333 PP

                                       TTTHHHTTHHHCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              STT3 449 keslewkantnrdsvvitwwdyghilaveadrpVtfd 485
                                       +   +   +   +  v++wwdyg  + + ++rpV+++
  gi|330507250|ref|YP_004383678.1| 490 SHFADP--EEIPEYSVMSWWDYGNWILYLSERPVVAN 524
                                       333333..555667789*****************986 PP

>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2  16.9   3.6e-15   1.1e-11      20     154 ..     104     243 ..      82     257 .. 0.78
   2 ?   -4.8  11.0         6   1.8e+04      75     127 ..     266     320 ..     230     330 .. 0.57
   3 ?   -0.7   7.5      0.49   1.5e+03      76     127 ..     361     413 ..     342     458 .. 0.42

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 3.6e-15
                             PMT_2  20 selairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsa..lftpdaplvllwalalylllrale 94 
                                        e+ + +v++++g+l+++++y ++r+lf++r+alla++++a+ p+++ ++      + ++ vl+ +l+l++++ a  
  gi|330507250|ref|YP_004383678.1| 104 VEMTAAFVPVIIGLLAMVVVYYIMRELFDHRIALLASFMTALAPYYLLYTMvaATDHHSLEVLFQLLSLLFMVLAFS 180
                                       578999************************************9988887774355567899**************** PP

                             PMT_2  95 knklkywllagvlfGlgflsKytaallliaallyllis..arr.ilkekkpyl.alllalllfs 154
                                       ++  ++++++++ ++l+ l   +++  +  + +yll+   + +  l++ kp l ++   l++f+
  gi|330507250|ref|YP_004383678.1| 181 RPDKRWLYASAAGVALAALAYTWQGADVY-FGAYLLFAafGMSlELRQEKPNLnIVSTLLVAFF 243
                                       ***9*****************99987665.3444444444344467777776655544444443 PP

  == domain 2  score: -4.8 bits;  conditional E-value: 6
                             PMT_2  75 daplvllwalalylllraleknklkyw..llagvlfGlgflsKytaallliaall 127
                                        a++v+l ++++++ + a  + ++k++  +++++++   +lsK   +++++  l+
  gi|330507250|ref|YP_004383678.1| 266 AAIFVALAIMLALAHIIAKRSISWKAFplAILAIFIISLLLSKILGGFFGLEGLI 320
                                       3344444444444444444444455556677777777778888888888887766 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.49
                             PMT_2  76 aplvllwalalylllraleknklkywllagvlfGlgflsKytaa.llliaall 127
                                       +++ l+ a+a+ +++r  e++  + +ll+ +++++++l    ++ +l+i+ ++
  gi|330507250|ref|YP_004383678.1| 361 ILFSLAGAAAIVVYMRKEERRMQQSLLLLLIWAVFSILLTLGQGrFLYISTIF 413
                                       33333333333333333333333333333333333333211111011111111 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 !   37.6   0.0   6.8e-13     2e-09       1      92 []     645     733 ..     645     733 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 6.8e-13
                                       -EEEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTT.EEEEEE---SS......-SSSSEESS-EEEEETT.. CS
                           AglB_L1   1 GAtitGsaeagatvtasveletnqgrtftYrqeaeadedG.efeltvPYstegeedgetnssveaagpYevtagn.. 74 
                                       GA ++ ++  + + +a +++++n +r f Y ++a+   +G   e++vPYste      ++ +v+a+ pY v + +  
  gi|330507250|ref|YP_004383678.1| 645 GALLKIHTGRDGNGMALLNMTSNMDRRFVYLNQAT--WNGdALEVRVPYSTE------REHEVHATDPYMVFSVHgd 713
                                       566666666667778899****************6..555167*********......6899*********997667 PP

                                       ..EEEEE---HHHHHHT-EE CS
                           AglB_L1  75 ..vtaeveVpEeaVlsgetv 92 
                                         + + veV+Ee+Vl+g+t+
  gi|330507250|ref|YP_004383678.1| 714 dvKAQMVEVSEEDVLQGRTI 733
                                       778899***********997 PP

>> DUF2339  Predicted membrane protein (DUF2339)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  40.1   3.4e-05       0.1     171     420 ..     112     455 ..      88     482 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.4e-05
                           DUF2339 171 tfgiaalWgl.lnyapdlfastelflllfllly................lalalllallfvaarravdatlvfgapl 230
                                        ++i++l ++  +y +     + ++ll+ ++ +                +                +  +l+ ++ l
  gi|330507250|ref|YP_004383678.1| 112 PVIIGLLAMVvVYYIMRELFDHRIALLASFMTAlapyyllytmvaatdhH----------------SLEVLFQLLSL 172
                                       35555555556777777777777777777777733333333333333330................44555555555 PP

                           DUF2339 231 valvlqyalladl.....eygwalaala......................................laalylalaaw 264
                                       +++vl++ ++ +      + g+alaala                                      l a++lal  +
  gi|330507250|ref|YP_004383678.1| 173 LFMVLAFSRPDKRwlyasAAGVALAALAytwqgadvyfgayllfaafgmslelrqekpnlnivstlLVAFFLALILV 249
                                       55555544444444444444444444443333333332222222222233333333333333322247777777777 PP

                           DUF2339 265 larrkrekaralgeallllavvfltlAlplaleaa.......wltvalAlegaalawlaglrqkrrlarlfg..... 329
                                       l  r++   + ++ ++l la++f++lA++lal+         w +  lA+  ++++   +l  ++ l   fg     
  gi|330507250|ref|YP_004383678.1| 250 LPFRNT---PWMSPSFLGLAAIFVALAIMLALAHIiakrsisWKAFPLAILAIFII---SLLLSKILGGFFGlegli 320
                                       766655...34556788889999999999998887666666544444444444443...445566666666699999 PP

                           DUF2339 330 ......................................llalrlllaaalllalvllrl...alalsllvllpllll 365
                                                                             l  l  l++a  ++++v +r    ++++sll+ll+++++
  gi|330507250|ref|YP_004383678.1| 321 rtgmgyiwggemigkigeaepliydldtlsqvvfswlgLNILFSLAGA--AAIVVYMRKeerRMQQSLLLLLIWAVF 395
                                       999999999999999999999999999999888886643333334444..455555555788899999999999888 PP

                           DUF2339 366 llllkeke..lgalvwlllgyglpaaalalaawllrrre....dklarvleaaalllllll 420
                                        +ll++++     +  + +g+ ++++++++  +l ++ +    +kl r+l+aa +lll+l 
  gi|330507250|ref|YP_004383678.1| 396 SILLTLGQgrFLYISTIFMGMLISILIFYALDRL-KKFQeergAKLHRALAAAIILLLVLP 455
                                       8888877654222223445555555555444444.32225556555555555555554443 PP

>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   7.1     0.011        32      95     165 ..     109     178 ..      54     181 .. 0.56
   2 ?   13.7  15.9   1.4e-05     0.042      64     169 ..     201     306 ..     186     325 .. 0.79
   3 ?    5.8   6.1    0.0039        12      65     161 ..     355     448 ..     345     470 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.011
                     7TMR-DISM_7TM  95 rllklllllavllsllllllpllpyteslslaqllallvillllligikawrkgnkparyfliawllllig 165
                                        ++ ++++l+++++++ ++  l+ +  +  la+++++l+  +ll+++++a  ++     + l+++l+++++
  gi|330507250|ref|YP_004383678.1| 109 AFVPVIIGLLAMVVVYYIMRELFDHRIA-LLASFMTALAPYYLLYTMVAATDHHSLEVLFQLLSLLFMVLA 178
                                       4555555555555555555444433333.344466666666666666666666666666666666666665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.4e-05
                     7TMR-DISM_7TM  64 lnnkllyltlllllilfllFarsflelkk.kprllklllllavllsllllllpllpyteslslaqllallvilllll 139
                                       + ++   + ++  l lf++F +s lel++ kp l  +  ll++++++l+l+lp+  ++++++ ++ la++++ l+++
  gi|330507250|ref|YP_004383678.1| 201 YTWQGADVYFGAYL-LFAAFGMS-LELRQeKPNLNIVSTLLVAFFLALILVLPFRNTPWMSPSFLGLAAIFVALAIM 275
                                       55555666666666.8888****.6666668877777777777777*******************999999999999 PP

                     7TMR-DISM_7TM 140 igikawrkgnkparyfl.iawlllligvlid 169
                                       ++++ ++ +++ ++  + +a+l+++i +l+ 
  gi|330507250|ref|YP_004383678.1| 276 LALAHIIAKRSISWKAFpLAILAIFIISLLL 306
                                       999999888888877777********99993 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0039
                     7TMR-DISM_7TM  65 nnkllyltlllllilfll.Farsflelkkkprllklllllavllsllllllpllpyteslslaqllallvillllli 140
                                       ++  l ++++l+ +++++ ++r+  e  +  r+ + llll++++++ +ll   l +  +l+++++++ ++i +l++ 
  gi|330507250|ref|YP_004383678.1| 355 SWLGLNILFSLAGAAAIVvYMRK--EE-R--RMQQSLLLLLIWAVFSILL--TLGQGRFLYISTIFMGMLISILIFY 424
                                       55555666666665666667776..22.2..6666666666663333333..3334444444443333333333333 PP

                     7TMR-DISM_7TM 141 gikaw..rkgnkparyfl.iawll 161
                                       ++  +  ++ +++a++   +a ++
  gi|330507250|ref|YP_004383678.1| 425 ALDRLkkFQEERGAKLHRaLAAAI 448
                                       333335655555554433333333 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.8    0.0077        23      60     138 ..     100     177 ..      97     248 .. 0.68
   2 ?    4.6   0.1    0.0095        28      68     151 ..     263     410 ..     256     426 .. 0.58
   3 ?   -1.1   0.1      0.52   1.6e+03      73      91 ..     416     430 ..     409     467 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0077
                          60KD_IMP  60 kkegvnplaGclplLiqlpifialyrvlrslasfwikdLsapd...lpillavttflqqklskskkmqkmmlyvmpl 133
                                        kegv + a ++p++i l  ++ +y+++r+l +  i+ L++      p  l  t+++ +         +++  ++ l
  gi|330507250|ref|YP_004383678.1| 100 TKEGVEMTAAFVPVIIGLLAMVVVYYIMRELFDHRIALLASFMtalAPYYLLYTMVAATDHH----SLEVLFQLLSL 172
                                       5899**************************77444444444111121222222222111111....11222223333 PP

                          60KD_IMP 134 milff 138
                                       +++++
  gi|330507250|ref|YP_004383678.1| 173 LFMVL 177
                                       33333 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0095
                          60KD_IMP  68 aGclplLiqlpifialyrvlrsla................................................sfwik 96 
                                        G+  +++ l i++al +++ + +                                                +    
  gi|330507250|ref|YP_004383678.1| 263 LGLAAIFVALAIMLALAHIIAKRSiswkafplailaifiislllskilggffgleglirtgmgyiwggemigK---- 335
                                       5888999999999999999999668888888877776666666666666655555555555554444433331.... PP

                          60KD_IMP  97 dLsapd.........................lpillavttf.lqqklskskkmqkmmlyvmplmilffslsfpaglv 147
                                                                      l  l++++ + ++++   +++mq+ +l+++ + ++ ++l++  g  
  gi|330507250|ref|YP_004383678.1| 336 -----IgeaepliydldtlsqvvfswlglniLFSLAGAAAIvVYMRKE-ERRMQQSLLLLLIWAVFSILLTLGQGRF 406
                                       .....0344444444444456777878855533333333331334433.3344455545555555556666666666 PP

                          60KD_IMP 148 lYwl 151
                                       lY  
  gi|330507250|ref|YP_004383678.1| 407 LYIS 410
                                       6643 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.52
                          60KD_IMP  73 lLiqlpifialyrvlrsla 91 
                                       +Li + if+al     +l+
  gi|330507250|ref|YP_004383678.1| 416 MLISILIFYAL----DRLK 430
                                       56666666665....3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (737 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1023  (0.0570584); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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):               6  [number of targets reported over threshold]
# CPU time: 0.83u 0.32s 00:00:01.14 Elapsed: 00:00:00.47
# Mc/sec: 4734.13
//
Query:       gi|330507251|ref|YP_004383679.1|  [L=236]
Description: hypothetical protein MCON_1134 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1699.12
//
Query:       gi|330507252|ref|YP_004383680.1|  [L=393]
Description: hypothetical protein MCON_1135 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00053   20.2   1.8     0.0022   18.2   0.6    2.5  2  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
  ------ inclusion threshold ------
      0.017   15.4   0.8      0.068   13.5   0.3    2.3  2  DUF11        Domain of unknown function DUF11
       0.07   13.3   3.5         18    5.6   0.0    3.5  3  He_PIG       Putative Ig 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 ?   -1.6   0.0      0.55   3.3e+03      17      32 ..      55      70 ..      54      71 .. 0.85
   2 !   18.2   0.6   3.7e-07    0.0022       2      77 ..      79     153 ..      78     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.55
                       NPCBM_assoc 17 gtaaatnvslslslPe 32
                                      g++ a +v +sl++Pe
  gi|330507252|ref|YP_004383680.1| 55 GDSGALSVDVSLTGPE 70
                                      6788999******997 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.7e-07
                       NPCBM_assoc   2 epGetvtltltvtndg.taaatnvsls.lslPeGWtvvevspasaa.slapGetveatvkVtppagaaaGdyevtak 75 
                                       ++G++  + +tvtn+g t+a  +v ++ +++  +W       ++ +  +++G + + t++V+p  +a+aG+y+  ++
  gi|330507252|ref|YP_004383680.1|  79 TQGKELDFVVTVTNEGsTDADVEVCVKpMDCALDWF----GWTRSPmNIPAGGSRSQTLTVQPDINAVAGKYRFAVE 151
                                       79**************87787888776456777776....3333334899**********************99888 PP

                       NPCBM_assoc  76 ar 77 
                                       a+
  gi|330507252|ref|YP_004383680.1| 152 AS 153
                                       87 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.6   9.4e+03      33      51 ..      21      36 ..      18      66 .. 0.68
   2 ?   13.5   0.3   1.1e-05     0.068       7      36 ..      75     103 ..      71     178 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.6
                             DUF11 33 vvvtDtlPaglayvsvsas 51
                                      ++v+D   +g+++  vsa+
  gi|330507252|ref|YP_004383680.1| 21 ATVED---PGMELGDVSAT 36
                                      56777...77777777777 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.1e-05
                             DUF11   7 ksevrpGdtvtytltvtNtgpasangvvvt 36 
                                       ks  + G ++++++tvtN g ++a +v v+
  gi|330507252|ref|YP_004383680.1|  75 KSYTTQGKELDFVVTVTNEGSTDA-DVEVC 103
                                       556678******************.66654 PP

>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.6    0.0091        54      21      47 ..      56      93 ..      32      95 .. 0.67
   2 ?    5.6   0.0     0.003        18      23      46 ..     131     154 ..     127     155 .. 0.88
   3 ?   -1.5   0.0       0.5     3e+03      19      34 ..     200     215 ..     193     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0091
                            He_PIG 21 stGtitGtpdqtvap..........G.sytftVtatdg 47
                                       +G+++++++ t             G +++f Vt+t+ 
  gi|330507252|ref|YP_004383680.1| 56 DSGALSVDVSLTGPEseadksyttqGkELDFVVTVTNE 93
                                      567777775555333555556666688*********86 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.003
                            He_PIG  23 GtitGtpdqtvapGsytftVtatd 46 
                                        t+t++pd +  +G y f V a++
  gi|330507252|ref|YP_004383680.1| 131 QTLTVQPDINAVAGKYRFAVEASA 154
                                       589*******99*********987 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.5
                            He_PIG  19 dsstGtitGtpdqtva 34 
                                       ++ +  ++G++d  v+
  gi|330507252|ref|YP_004383680.1| 200 SNKDVIFSGSVDALVK 215
                                       578999****998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2770.30
//
Query:       gi|330507253|ref|YP_004383681.1|  [L=258]
Description: hypothetical protein MCON_1136 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1934.42
//
Query:       gi|330507254|ref|YP_004383682.1|  [L=260]
Description: hypothetical protein MCON_1137 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); 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:                         0  (0); expected 0.2 (1e-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 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1815.37
//
Query:       gi|330507255|ref|YP_004383683.1|  [L=66]
Description: hypothetical protein MCON_1138 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       144  (0.00803168); expected 358.6 (0.02)
Passed bias filter:                      136  (0.00758548); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 512.34
//
Query:       gi|330507256|ref|YP_004383684.1|  [L=240]
Description: hypothetical protein MCON_1139 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.3   0.3       0.25   11.0   0.0    1.8  2  Fels1     Fels-1 Prophage Protein-like


Domain annotation for each model (and alignments):
>> Fels1  Fels-1 Prophage Protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.4e-05      0.25      23      40 ..     123     140 ..     118     141 .. 0.92
   2 ?   -2.4   0.1      0.22   3.9e+03      23      29 ..     158     164 ..     157     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.4e-05
                             Fels1  23 erlCrdSggiSrklTkly 40 
                                       e+lC+++++i + lT++y
  gi|330507256|ref|YP_004383684.1| 123 EKLCVQNYRIGAVLTEMY 140
                                       9****************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.22
                             Fels1  23 erlCrdS 29 
                                        ++C+d+
  gi|330507256|ref|YP_004383684.1| 158 QNICVDN 164
                                       6799993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1802.63
//
Query:       gi|330507257|ref|YP_004383685.1|  [L=101]
Description: hypothetical protein MCON_1140 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 748.91
//
Query:       gi|330507258|ref|YP_004383686.1|  [L=240]
Description: hypothetical protein MCON_1141 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.3   0.3       0.25   11.0   0.0    1.8  2  Fels1     Fels-1 Prophage Protein-like


Domain annotation for each model (and alignments):
>> Fels1  Fels-1 Prophage Protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.4e-05      0.25      23      40 ..     123     140 ..     118     141 .. 0.92
   2 ?   -2.4   0.1      0.22   3.9e+03      23      29 ..     158     164 ..     157     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.4e-05
                             Fels1  23 erlCrdSggiSrklTkly 40 
                                       e+lC+++++i + lT++y
  gi|330507258|ref|YP_004383686.1| 123 EKLCVQNYRIGAVLTEMY 140
                                       9****************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.22
                             Fels1  23 erlCrdS 29 
                                        ++C+d+
  gi|330507258|ref|YP_004383686.1| 158 QNICVDN 164
                                       6799993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1668.69
//
Query:       gi|330507259|ref|YP_004383687.1|  [L=332]
Description: hypothetical protein MCON_1145 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-85  286.1   0.0    2.2e-85  285.7   0.0    1.1  1  NRD1_2    NrpR regulatory domains NRD1 and 2
      1e-21   76.6   0.3    2.1e-21   75.6   0.3    1.6  1  HTH_12    Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> NRD1_2  NrpR regulatory domains NRD1 and 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.7   0.0   2.5e-89   2.2e-85       1     237 [.      89     327 ..      89     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 285.7 bits;  conditional E-value: 2.5e-89
                                       ---HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE.......... CS
                            NRD1_2   1 vgfviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegek..elevpegk 75 
                                       +gfv+++iee++yk++fdp++g+G+Vi+N+s++dk d+ee+l++l +++++g+++s+rv il+eg+   +levp+g+
  gi|330507259|ref|YP_004383687.1|  89 IGFVNTRIEEYMYKSNFDPCSGQGQVIANTSIVDKADAEEVLDMLGRAFDQGYTISRRVLILDEGDAisTLEVPAGS 165
                                       79******************************************************************9******** PP

                                       EEEEEE-CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEE CS
                            NRD1_2  76 vgiatvCSitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkil 152
                                       +g+atvCSit+dg+L+k+GI v + ++Gl +i++k+p++Ft+lI+Y g+s+dP++vf+ +k+Tsv ++i+ g+g++l
  gi|330507259|ref|YP_004383687.1| 166 LGLATVCSITMDGILMKKGIAVLTSFAGLAKIKEKQPIEFTDLIAYAGSSLDPVKVFMGRKVTSVANAIRLGSGRVL 242
                                       ***************************************************************************** PP

                                       EEEEEEETTTHHHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEE CS
                            NRD1_2 153 AnlReipvsarekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsg 229
                                       An+Reipv+a  ++ e+le  ++ag+ g++++g p e++lg+pv  +k+gi++++G+n  +a++e+g ++++ ++s 
  gi|330507259|ref|YP_004383687.1| 243 ANVREIPVAAAGHALELLEASRSAGFGGLIKVGGPAEPILGCPVAAGKIGIAFYAGVNGTVAAEEMGARMKTLPISM 319
                                       ***************************************************************************** PP

                                       EEEGGGSE CS
                            NRD1_2 230 lidiselk 237
                                       l+d+s+++
  gi|330507259|ref|YP_004383687.1| 320 LVDYSRMT 327
                                       ******97 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.3   2.3e-25   2.1e-21       1      66 []      15      80 ..      15      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 2.3e-25
                            HTH_12  1 veILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGleeL 66
                                      +eIL++++ +  p+ga++i + L  rgyd+geravRy L++l+e g+tr++gy+gr +t  G  eL
  gi|330507259|ref|YP_004383687.1| 15 IEILRVIEGAGIPMGARAISDILCSRGYDLGERAVRYNLKILDELGFTRKKGYSGRVITSLGSREL 80
                                      79************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2456.06
//
Query:       gi|330507260|ref|YP_004383688.1|  [L=133]
Description: 30S ribosomal protein S6e [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-41  140.1   0.1      4e-41  139.9   0.1    1.0  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   0.1   2.2e-45     4e-41       1     124 [.       3     123 ..       3     124 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 2.2e-45
                                       -EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEE CS
                     Ribosomal_S6e   1 mklnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLls 77 
                                       +++++sdp++gk++++e+++  + +l+gk+ig++++gd+lG  ++gy +++tggsd++Gfpm+ ++++++r+++Lls
  gi|330507260|ref|YP_004383688.1|   3 FRVVVSDPKSGKAYQVELKDPGAGKLLGKHIGDKIEGDILG--MPGYSMQVTGGSDREGFPMRADLPGTKRRKILLS 77 
                                       689**************************************..********************************** PP

                                       TTSSSS-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--SS--TTTS CS
                     Ribosomal_S6e  78 kggvgyrprrkGerkrksvrGcivsadisqlnlvivkkgekdieglt 124
                                       + g+gy+p  +G++krks++G+ +s d+ q+n+++v++g+k++e+l+
  gi|330507260|ref|YP_004383688.1|  78 T-GTGYHPVAEGKKKRKSIHGRDISPDVGQINVKVVESGAKSLEELL 123
                                       *.*******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1023.49
//
Query:       gi|330507261|ref|YP_004383689.1|  [L=388]
Description: geranylgeranyl reductase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-12   47.6   0.0    2.4e-12   46.8   0.0    1.3  1  FAD_binding_3   FAD binding domain
    2.6e-05   24.0   4.8     0.0055   16.3   0.5    2.4  2  DAO             FAD dependent oxidoreductase
    0.00021   21.4   0.2    0.00094   19.4   0.2    2.1  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00035   19.8   0.0    0.00066   18.8   0.0    1.4  1  Lycopene_cycl   Lycopene cyclase protein
    0.00036   19.4   0.3    0.00062   18.6   0.3    1.4  1  HI0933_like     HI0933-like protein
    0.00037   19.8   0.0    0.00074   18.8   0.0    1.4  1  Thi4            Thi4 family
    0.00077   18.4   0.3       0.72    8.6   0.1    2.5  3  Trp_halogenase  Tryptophan halogenase
     0.0013   18.0   0.0     0.0024   17.2   0.0    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0018   17.7   1.6     0.0027   17.1   1.1    1.4  1  FAD_oxidored    FAD dependent oxidoreductase
     0.0033   16.5   4.3      0.018   14.2   0.7    2.4  3  FAD_binding_2   FAD binding domain
  ------ inclusion threshold ------
      0.023   13.8   0.4      0.037   13.1   0.4    1.3  1  GIDA            Glucose inhibited division protein A
       0.13   12.2   0.1       0.26   11.1   0.1    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   1.6e-15   2.4e-12       3     308 ..       6     295 ..       4     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.6e-15
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHH...HHHHTT-HHHHHHHSEECCCCEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtme...llrqlGledrilaegapnelmgeal 76 
                                       + ++VGaGpaG ++al+ ++   +vvl+++ s+     + +g+ ++  e   ll  +Gl d +++    ++ + + +
  gi|330507261|ref|YP_004383689.1|   6 QLAVVGAGPAGSTAALVAARE-LDVVLIDRKSEIGSPVQCGGFLPEAWEleaLLPRAGLPDALREIP--EHCILHRT 79 
                                       678******************.***********99999*****999988444599********9988..88766666 PP

                                       EEECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEE CS
                     FAD_binding_3  77 ynelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetv 153
                                       + +  ++  ++ + +    + +  v+    ++r L+++a+++g+++  +t+ + l + + + +  + ++       +
  gi|330507261|ref|YP_004383689.1|  80 QLQ--RIYSPSGKSK--EFAVAGRVIDRRAFDRHLASQAARAGARILPATRAT-LVEGGLELSGHYAGR-------L 144
                                       666..7766666666..344456788999**********************99.677777766666655.......8 PP

                                       EEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEE.CCTTEEEEEECCETEEEEEEE CS
                     FAD_binding_3 154 rakYlvGaDGgrStvrktlgiefegeetvyeagvldvlfdadlsdiveplvlils.aesrgvmviPlentlerfyvq 229
                                       r + ++GaDG  S+v + +g + ++ +   e ++ dv +d+d +    ++++  + a+ +   +iPl   + ++ v 
  gi|330507261|ref|YP_004383689.1| 145 RPQMIIGADGPSSIVSRYMGNPAQEVGICQEYEMTDVDIDSDAA----EMFFSARyAPGGYAWIIPLGPDRANVGVG 217
                                       9*********************9999989999999999999888....32333330333444999***999999999 PP

                                       EECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHH CS
                     FAD_binding_3 230 vearaekeersekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNt 306
                                       v+a++  ++r  ++ ++ v ++ +++ + +  +v   +   ++    ++ + +kg++ laGDAa  +  t G G+ +
  gi|330507261|ref|YP_004383689.1| 218 VRASYLSGQRLSDVLQRFVQDHPQASKKLASGEVLAVMRGLVPA-GGTVGSIQKGNMILAGDAAGHVLATSGGGIPL 293
                                       9****9******99999999888888777777776665555555.556789*************9999999999877 PP

                                       HH CS
                     FAD_binding_3 307 ai 308
                                       a+
  gi|330507261|ref|YP_004383689.1| 294 AV 295
                                       76 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.5   3.6e-06    0.0055       2      33 ..       7      39 ..       6      45 .. 0.89
   2 !    9.4   0.3   0.00048      0.72      96     204 ..      54     157 ..      41     303 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.6e-06
                                      EEEECTSHHHHHHHHHHHHTT.EEEEESSSSTT CS
                               DAO  2 vviiGGGiiGlstAyeLarrg.Vtllekgdiag 33
                                      ++++G+G +G+++A+ +ar+  V+l+++++++g
  gi|330507261|ref|YP_004383689.1|  7 LAVVGAGPAGSTAALVAARELdVVLIDRKSEIG 39
                                      68***************87746*******9998 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00048
                                       HHHHHHHHHHH..HHTTTTEE.EEEHHHHHHHSTTST.TTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESEC CS
                               DAO  96 lealdkllall..leagldae.lldaeevrelepalp.gllgalfypdtgqvdpakltaalaraaealGveilegte 168
                                       leal  +++l+  l   ++++ +l + +++++++  p g  + + + +  ++d +++ + la++a+++G++il  t+
  gi|330507261|ref|YP_004383689.1|  54 LEALLPRAGLPdaL-REIPEHcILHRTQLQRIYS--PsGKSKEFAVAG-RVIDRRAFDRHLASQAARAGARILPATR 126
                                       66665666666532.3345555899988999995..422223344444.778************************* PP

                                       EEEEEEEETCEEEEE..EECT.EEEEEEEEEEE--GGGH CS
                               DAO 169 vtgleeedgkvwgve..rttp.gendaadavVnaaGaws 204
                                       +t +e      +g+e       g+ +  + ++ a G+ s
  gi|330507261|ref|YP_004383689.1| 127 ATLVE------GGLElsG-HYaGRLRP-QMIIGADGPSS 157
                                       *9882......3443321.11143333.34777777776 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 !   19.4   0.2   6.3e-07   0.00094       1      32 [.       9      39 ..       9      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.3e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      +vGaG +G++aA  +a++ +dv+l+++ + +G
  gi|330507261|ref|YP_004383689.1|  9 VVGAGPAGSTAALVAARE-LDVVLIDRKSEIG 39
                                      8*********99999987.***********99 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.4e-07   0.00066       2     349 ..       7     361 ..       6     372 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.4e-07
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsdefedlga..............leecvehsWs 63 
                                       ++v+GaGpAg   Aa +  a+ +l vvli+   ++  p +      e  +l+a               e+c+ h+ +
  gi|330507261|ref|YP_004383689.1|   7 LAVVGAGPAGST-AALV--AARELDVVLIDRKSEIGSPVQCgGFLPEAWELEAllpraglpdalreiPEHCILHRTQ 80 
                                       79********76.5556..7999*******9888766665444444444444444555999998888899******* PP

                     Lycopene_cycl  64 gtivylddgkkillgraYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggr..kirarlvvda 138
                                         ++y + gk+++   a + + ++ + ++l+ + + +g++ l a+ +  +e         l+g    ++r ++++ a
  gi|330507261|ref|YP_004383689.1|  81 LQRIYSPSGKSKEFAVAGRVIDRRAFDRHLASQAARAGARILPATRATLVEGGL-----ELSGHYagRLRPQMIIGA 152
                                       ***********************************9999999998777776666.....566655558999999999 PP

                     Lycopene_cycl 139 rglaslkkarrlgl.QtfyGvevevdnppfdldk...mvlMDfrveqklkgltFlYalPldsdrllvE...eTelas 208
                                        g +s+  +r +g   +  G+  e +    d+d     ++  +r ++  +g+   +++Pl++dr+ v      ++ s
  gi|330507261|ref|YP_004383689.1| 153 DG-PSSIVSRYMGNpAQEVGICQEYEMTDVDIDSdaaEMFFSARYAP--GGY--AWIIPLGPDRANVGvgvRASYLS 224
                                       99.66664443332123345555555544444431002333444444..454..56799999998876222345555 PP

                     Lycopene_cycl 209 kpeLpadalkkrlaaylra.lglkvkevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaea 283
                                       ++ L+ d+l++ ++   +a + l+  ev    +g++P   gg +  +++   + +G aag v  + G  ++ ++ + 
  gi|330507261|ref|YP_004383689.1| 225 GQRLS-DVLQRFVQDHPQAsKKLASGEVLAVMRGLVPA--GGTVGSIQKGnMILAGDAAGHVLATSGGGIPLAVVAG 298
                                       55454.55666666555556888888888999999999..9999999887356789999999999999999888877 PP

                     Lycopene_cycl 284 pllasaiaaalresslsarawatlwprerkrqreffrllglalllkldiegrrrfldaFfrlpkel 349
                                       ++  ++  + l++ ++  ++   l+   +   re+ r+ ++  ++ + +   r + ++F  l++e 
  gi|330507261|ref|YP_004383689.1| 299 RIAGQSAIDHLQS-GTPLQEY--LSSIGQEFGRELDRSVQIRKMVDVAMRSDRLINALFAALSPEQ 361
                                       7666666666653.3333332..3333333445555555555555555555555555565555554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   4.1e-07   0.00062       2      43 ..       6      46 ..       5      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.1e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                      +++v+G+G+AG  aA+ a +r+ +V+l+++++++g+ ++  G
  gi|330507261|ref|YP_004383689.1|  6 QLAVVGAGPAGSTAALVA-ARELDVVLIDRKSEIGSPVQCGG 46
                                      579************998.789*************9777655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     5e-07   0.00074      20      63 ..       7      48 ..       2      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5e-07
                                      EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTT CS
                              Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGql 63
                                      +++vGaG++G taa + a++  l v++++r+  +G  +  GG l
  gi|330507261|ref|YP_004383689.1|  7 LAVVGAGPAGSTAALVAARE--LDVVLIDRKSEIGSPVQCGGFL 48
                                      689***********999998..**************99999976 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1   0.00048      0.72       2      37 ..       7      39 ..       6      58 .. 0.80
   2 ?   -2.5   0.0       1.2   1.7e+03     151     173 ..     101     123 ..      77     132 .. 0.76
   3 !    7.3   0.0    0.0012       1.8     251     369 ..     194     332 ..     178     363 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00048
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE.-SSS- CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlve.seeig 37
                                      + +vG+G+aG++aA + a+ l    +v l++ ++eig
  gi|330507261|ref|YP_004383689.1|  7 LAVVGAGPAGSTAALVAAREL----DVVLIDrKSEIG 39
                                      689************999999....788886244555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                                       E-HHHHHHHHHHHHHHCT-EEEE CS
                    Trp_halogenase 151 ldaalyakfLrrvaearGvtrve 173
                                       +d++ ++++L   a ++G +++ 
  gi|330507261|ref|YP_004383689.1| 101 IDRRAFDRHLASQAARAGARILP 123
                                       68889999999999998887664 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0012
                                       EEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHHCT--TTTS-EEEE---EE..............ES- CS
                    Trp_halogenase 251 ataekaGWtWkiPLqhrlgn.GyvyssahadddeAlaellaeldgkleaeprkirfttGr..............rkq 312
                                       a     G  W iPL     n G+ ++ ++++ ++  + l++ ++ +++a +   ++ +G                 +
  gi|330507261|ref|YP_004383689.1| 194 ARYAPGGYAWIIPLGPDRANvGVGVRASYLSGQRLSDVLQRFVQDHPQASK---KLASGEvlavmrglvpaggtVGS 267
                                       5556789*******9777777*********887777777776666655553...44445555566677888888899 PP

                                       SEETTEEE-CCCTEE--CCCS-HHHHHHH........HHHHHHHT--BTT--HHHHHHHHHHHHH CS
                    Trp_halogenase 313 awvknvvalGlasgfvePlestsihliqa........alrrLlallpdksdepaaiaefnrevar 369
                                       + + n+++ G+a+g v +  + +i l+ +        a+++L +  p + +     +ef re++r
  gi|330507261|ref|YP_004383689.1| 268 IQKGNMILAGDAAGHVLATSGGGIPLAVVagriagqsAIDHLQSGTPLQEYLSSIGQEFGRELDR 332
                                       999*********************99988666666666666666666666666666666666555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.6e-06    0.0024       2      32 ..       6      35 ..       5      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.6e-06
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvele 32
                                      +++v+G+GpAG +aal +a+ +++v+l++++
  gi|330507261|ref|YP_004383689.1|  6 QLAVVGAGPAGSTAALVAAR-ELDVVLIDRK 35
                                      579****************9.9******632 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.1   1.8e-06    0.0027       2      35 ..       7      39 ..       6      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.8e-06
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlG 35
                                      + VvG+gpaG +AA+ Aar+   v+L++++  +G
  gi|330507261|ref|YP_004383689.1|  7 LAVVGAGPAGSTAALVAARE-LDVVLIDRKSEIG 39
                                      68****************96.99******99998 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.7   1.2e-05     0.018       3      36 ..       8      40 ..       6      48 .. 0.86
   2 ?   -3.5   0.0       2.6   3.9e+03      76     113 ..     109     142 ..     103     151 .. 0.71
   3 ?    3.4   0.1     0.023        34     221     286 ..     208     275 ..     183     294 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                      EEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  3 iViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                       V+G+G AG +AAl  a + l+v++++ ++e g+
  gi|330507261|ref|YP_004383689.1|  8 AVVGAGPAGSTAAL-VAARELDVVLIDRKSEIGS 40
                                      7*************.7788999*****9999776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.6
                                       -S-HHHHHHHHHTHHHHHHHHHHTT----BCCTSSB-E CS
                     FAD_binding_2  76 ladqplveafveaapeavdeLeelgvpfsrtedgpvdv 113
                                       + + ++++a+++  p+ ++ L e g+ +s+    ++++
  gi|330507261|ref|YP_004383689.1| 109 HLASQAARAGARILPATRATLVEGGLELSG----HYAG 142
                                       447788888888888888888888888888....4443 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.023
                                       SGT.T-S-HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTB.B--THHHHTT-EEE-.TTSSBTH CS
                     FAD_binding_2 221 nap.avtGdglalalragaalnddrmeevqfhPtslvpirdgsgi.LitealrgeGgilvd.kdGrrFm 286
                                       ++  a+ G g ++ + +g +l d +  +vq hP++  ++++g+ + ++ ++l   Gg +   ++G+   
  gi|330507261|ref|YP_004383689.1| 208 GPDrANVGVGVRASYLSGQRLSDVLQRFVQDHPQASKKLASGEVLaVM-RGLVPAGGTVGSiQKGNMIL 275
                                       4556999******************************99999999555.66666666655557776655 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   2.5e-05     0.037       2      31 ..       7      35 ..       6      46 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                                      EEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLithk 31
                                      + V+G+G AG+ AAl aar  ++v+Li  k
  gi|330507261|ref|YP_004383689.1|  7 LAVVGAGPAGSTAALVAAR-ELDVVLIDRK 35
                                      57*************9998.6888888444 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   0.00018      0.26       2      33 ..       7      37 ..       6      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee 33
                                      +av+GaG  G+  aa++a+++l+Vvl+d+++e
  gi|330507261|ref|YP_004383689.1|  7 LAVVGAGPAGST-AALVAARELDVVLIDRKSE 37
                                      79********86.66777889*******9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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 0.26s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 2906.84
//
Query:       gi|330507262|ref|YP_004383690.1|  [L=631]
Description: Na+/solute symporter [Methanosaeta concilii GP6]
Scores for 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  102.1  33.1    3.8e-29  101.8  33.1    1.1  1  SSF       Sodium:solute symporter family
  ------ inclusion threshold ------
       0.32    9.9  31.2       0.57    9.1  31.2    1.4  1  Nramp     Natural resistance-associated macrophage protein


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8  33.1   4.3e-33   3.8e-29       1     406 []      35     425 ..      35     425 .. 0.83

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 4.3e-33
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlrnagalTlpdylsk 77 
                                       ++lagr+l+++ +gl++a+    a+ ++   G+  ++G++ +++ +   ++ l ++  + +r  n  alT p++++ 
  gi|330507262|ref|YP_004383690.1|  35 FWLAGRELGPISIGLAAASAWTTASALLLATGLFLLYGIGSIWIWVFPNIAGLAIIAAISGRIKNIPALTQPELMEI 111
                                       89***************************************999888888888889999****************** PP

                               SSF  78 RfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlm 154
                                       R++    +  +++ +++++i + +  d++g  + + + +G++   a+ ++a+++alY+ +GG++Avv+td+iq +l 
  gi|330507262|ref|YP_004383690.1| 112 RYDPMI-RAPVAIAVTIMMILFSV-TDFIGFKMVLGTFFGIEPIFAIAIMAVSVALYVGVGGFRAVVWTDMIQYIL- 185
                                       **8765.88899988888888876.59**********************************************765. PP

                               SSF 155 lvgalilliivllevG.gleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvRflaakd 230
                                       l+g+   + ++ +++G + ++ v+ +++ +  ++d     s   +   l al++ ++lv G +  +   +++ aa d
  gi|330507262|ref|YP_004383690.1| 186 LAGLA--AYVAHMALGlSANEGVSLIAASTMLGADWWDIFS---MGGILGALVFIVALVPGWVAEQDPWQKVWAARD 257
                                       55543..4455666776666666655555554555544333...33479999999********************** PP

                               SSF 231 akailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaims 307
                                        +++ +g+l + ++l+l++       l ai l  + p+    +  ++++ y +++   +p +l+Gll     Aa ms
  gi|330507262|ref|YP_004383690.1| 258 DRSAKRGLLLGATLLVLIYSF---CLLAAIGLSVIYPRP--GNEMEAEMLYLRIISDNVPGWLLGLLTIGFAAASMS 329
                                       ****************99998...789999999999985..455689*******************99999999*** PP

                               SSF 308 tltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlav 384
                                         ++   s++s +++Dl ++ +    a+ ke++ + ri++++++ ++ l+a++  +  +++ v +a+ + +   +  
  gi|330507262|ref|YP_004383690.1| 330 CTDTFATSGASCLSRDLIQRHLWPT-ATVKEMLILNRILIVIMVFISALIALNVDS--IMDAVIIATVIGTTSYFFP 403
                                       ****************998765544.455555555555555555555555555544..4555656665556666666 PP

                               SSF 385 illalfwkrvneqGAlagliiG 406
                                       i+ +l+wkr+++ GA+a+l++G
  gi|330507262|ref|YP_004383690.1| 404 IIGGLYWKRATKWGAMAALVAG 425
                                       789***************9988 PP

>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  31.2   6.3e-05      0.57      12     337 ..      72     394 ..      45     405 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 6.3e-05
                             Nramp  12 GykLlwvlllstllai.llqelsarLGlvTgkglaelirerlpkkvsillwilaelaiiatdlaeviGaAialnllf 87 
                                       G   +w+ ++ +++++ ++  +s r+  +   + +el++ r+++ +++ ++i++ +++i+++++++iG  ++l ++f
  gi|330507262|ref|YP_004383690.1|  72 GIGSIWIWVFPNIAGLaIIAAISGRIKNIPALTQPELMEIRYDPMIRAPVAIAVTIMMILFSVTDFIGFKMVLGTFF 148
                                       55667888887777641567789999999999999****************************************** PP

                             Nramp  88 gipllvgvlitavlvllllflekggyrklE..aliialvlvialsFiaelfl...vkpdwgevlkglvvPslpgkes 159
                                       gi  + ++ i+av v+l +    gg+r +    +i  ++l+ + +++a ++l   ++  ++ ++++++         
  gi|330507262|ref|YP_004383690.1| 149 GIEPIFAIAIMAVSVALYVG--VGGFRAVVwtDMIQYILLAGLAAYVAHMALglsANEGVSLIAASTM-LGAD-WWD 221
                                       ********************..6666665411334444444447888888762213333344444444.3333.479 PP

                             Nramp 160 lllavgilGatvmphnlflhsslvqerkitidrsekeealkyeriDtiialivaflinlailivaA..avly..sgg 232
                                       ++ + gilGa v + +l+      q+ ++++ + ++    + ++   ++++++  li ++ l++a   +v+y  +g+
  gi|330507262|ref|YP_004383690.1| 222 IFSMGGILGALVFIVALVPGWVAEQDPWQKVWAARD---DRSAKRGLLLGATLLVLIYSFCLLAAIglSVIYprPGN 295
                                       ***************999988888888866633444...59999999999988888877777766523677763333 PP

                             Nramp 233 kdvesledaaeaLepllGskaasvlFaigLlaaGlsStitgtlagqyvmegflglrislwlrrlitralafvpaliv 309
                                       + +e      ++++  +   +   l  ig  aa++s t t +++g+  ++  l ++  lw  + ++++l +  +liv
  gi|330507262|ref|YP_004383690.1| 296 E-MEAEMLYLRIISDNVP-GWLLGLLTIGFAAASMSCTDTFATSGASCLSRDL-IQRHLWPTATVKEMLILNRILIV 369
                                       3.3332333344555555.39999*************************9999.99999999*99*99999999999 PP

                             Nramp 310 illigaelelvkllvlsqvllslllPfa 337
                                       i+++ ++l    +l +  ++ ++++  +
  gi|330507262|ref|YP_004383690.1| 370 IMVFISALI---ALNVDSIMDAVIIATV 394
                                       999999888...5555555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 4515.76
//
Query:       gi|330507263|ref|YP_004383691.1|  [L=551]
Description: dihydroxy-acid dehydratase [Methanosaeta concilii GP6]
Scores for 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-208  692.2   1.0   4.6e-208  692.0   1.0    1.0  1  ILVD_EDD       Dehydratase family
  ------ inclusion threshold ------
      0.052   13.6   0.0        1.5    8.9   0.0    2.5  2  Inhibitor_I78  Peptidase inhibitor I78 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 !  692.0   1.0  5.1e-212  4.6e-208       1     516 [.      31     547 ..      31     548 .. 0.96

  Alignments for each domain:
  == domain 1  score: 692.0 bits;  conditional E-value: 5.1e-212
                          ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmlea 77 
                                       +p+ig++ns ++++p+h hl++l+eavk+g+ +aggvp+ef+tigv+Dgiamg++gmrysLpsReli d++e+m+e+
  gi|330507263|ref|YP_004383691.1|  31 RPFIGVVNSSNDFIPGHIHLDRLGEAVKAGILSAGGVPFEFQTIGVCDGIAMGHKGMRYSLPSRELIEDTIEIMAES 107
                                       7**************************************************************************** PP

                          ILVD_EDD  78 qllDalvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaa 152
                                       ++lD+lv+i++CDKivPg++maa rl++P+i+v+gGpm++g +   +ldl++vfe++++        e+l++le+ a
  gi|330507263|ref|YP_004383691.1| 108 HQLDGLVMIPTCDKIVPGHIMAAGRLDLPTIVVTGGPMMPGFACdkELDLINVFEEWQK------GGETLDALEDMA 178
                                       ****************************************7633247788877777765......46899******* PP

                          ILVD_EDD 153 cpgaGsCsgmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvl 229
                                       cpgaGsC+g++TAntmacl+ea+Glslpg+a+++a++a++ +la+ +g++i+elvek +++r+i+t ++++NAi v+
  gi|330507263|ref|YP_004383691.1| 179 CPGAGSCAGLFTANTMACLTEAMGLSLPGCATAHAVDARKIRLAKLSGMKIMELVEKGITARQIVTAASLDNAIRVD 255
                                       ***************************************************************************** PP

                          ILVD_EDD 230 lalGGStNavlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvl 306
                                       +a+GGStN+vlHl+AiA e+g++l++++fd+lsr++p+l++l+P g +++ dl+raGGvpav++ L+++  l+ d+l
  gi|330507263|ref|YP_004383691.1| 256 MAIGGSTNTVLHLMAIAAEFGLDLDIERFDQLSRETPHLVNLRPGGPHHIIDLERAGGVPAVMSALRSR--LDLDAL 330
                                       *******************************************************************66..****** PP

                          ILVD_EDD 307 tvtgktlaenleeaev....keqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseee 379
                                       tvtg+ ++enl++ +     ++++vi ++++p+++egg+a+L G+L+peG+vvK++av++++l+++gpA+v+dsee+
  gi|330507263|ref|YP_004383691.1| 331 TVTGQRVGENLDSFKLinplTNSRVISTISSPVHAEGGIAILFGSLSPEGSVVKQTAVSPSMLVHSGPAVVYDSEEA 407
                                       ***********984435677********************************************************* PP

                          ILVD_EDD 380 aveailkgkikagdvvviryeGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGp 456
                                        ++ i+ g++k+gdvvviryeGPkGgpGm+E+l+ptsa++g+g++++valitDGRfSG+++g++ighvsPEAa+gGp
  gi|330507263|ref|YP_004383691.1| 408 SMAGIVGGEVKPGDVVVIRYEGPKGGPGMREALAPTSAIAGAGMSESVALITDGRFSGGTRGPCIGHVSPEAAVGGP 484
                                       ***************************************************************************** PP

                          ILVD_EDD 457 ialvedGDiieidiekrtlelevseeelaaRraawkp..ekkvkt.rgllakyaklvssaseG 516
                                       ialv+ GD+i+i+i++r+l+l+v+ +el++Rr +w+    ++ +  +g+la+y+k+v+sas G
  gi|330507263|ref|YP_004383691.1| 485 IALVRPGDMISINIPARKLDLLVDPAELERRRGEWRMpdMPENAIkTGVLARYRKSVTSASMG 547
                                       ********************************99*98643333334***************99 PP

>> Inhibitor_I78  Peptidase inhibitor I78 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.031   2.8e+02      34      45 ..     417     428 ..     407     431 .. 0.91
   2 ?    8.9   0.0   0.00017       1.5      29      54 ..     483     508 ..     476     511 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.031
                     Inhibitor_I78  34 lkPGqvvtleyn 45 
                                       +kPG+vv + y+
  gi|330507263|ref|YP_004383691.1| 417 VKPGDVVVIRYE 428
                                       8******99996 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00017
                     Inhibitor_I78  29 dsvRvlkPGqvvtleynpaRlniive 54 
                                       +++ +++PG+++ ++  +++l + v+
  gi|330507263|ref|YP_004383691.1| 483 GPIALVRPGDMISINIPARKLDLLVD 508
                                       7899*****************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 4156.55
//
Query:       gi|330507264|ref|YP_004383692.1|  [L=181]
Description: 2'-5' RNA ligase [Methanosaeta concilii GP6]
Scores for complete 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-29  100.4   0.1    3.1e-15   56.1   0.1    2.1  2  LigT_PEase       LigT like Phosphoesterase
    1.8e-14   53.9   0.0    2.1e-14   53.7   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily


Domain annotation for each model (and alignments):
>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.1   3.4e-19   3.1e-15       1      87 []      10      89 ..      10      89 .. 0.93
   2 !   42.4   0.0   6.6e-15   5.9e-11      11      87 .]      96     173 ..      91     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 3.4e-19
                                      EE-CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEE CS
                        LigT_PEase  1 lgppeeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfps 79
                                      +++pee +e++  l+++++      gl++vrp+ +H+T++flg+v++ekv+++++ala +  +a+pf+ ++ g+g+fp 
  gi|330507264|ref|YP_004383692.1| 10 VDLPEEMREKVGPLQSKIA----TEGLRLVRPDLVHVTIKFLGDVPAEKVERVKKALAAV--RAAPFTARLVGLGAFPG 82
                                      6789999999999999999....99*********************************99..999************98 PP

                                      CCSCCEEE CS
                        LigT_PEase 80 rlrprviy 87
                                      r + rv++
  gi|330507264|ref|YP_004383692.1| 83 R-SVRVVW 89
                                      7.577776 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 6.6e-15
                                       HHHHHHHHHHHHCCTTEEET.SGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC.SCCE CS
                        LigT_PEase  11 larlaaeleralaklglkpv.rpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrl.rprv 85 
                                        ++l ae+e+a ++lg++p+ r f+pH+T++++g  ++ +  ell++++ + s +   +++v+++ l +s+l ++++
  gi|330507264|ref|YP_004383692.1|  96 FSQLSAEVEAATKSLGFPPEeRGFTPHVTIGRVGRPNAGTSRELLAKIG-LQSTVDLGSFTVEEFYLKKSTLtPGGP 171
                                       68999********************************999999998885.667777778****************** PP

                                       EE CS
                        LigT_PEase  86 iy 87 
                                       iy
  gi|330507264|ref|YP_004383692.1| 172 IY 173
                                       *9 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0   2.4e-18   2.1e-14      22     145 ..      36     161 ..      12     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2.4e-18
                   2_5_RNA_ligase2  22 prwppHitLlypfvededl.adlaellsrlaketepfevrldgfgvFehkks.vvylsvsdsealqalraallealp 96 
                                       + + +H+t++++++ +    ++++++l+++  +++pf++rl g+g F++++  vv+l    + ++++l a++++a +
  gi|330507264|ref|YP_004383692.1|  36 RPDLVHVTIKFLGDVPAEKvERVKKALAAV--RAAPFTARLVGLGAFPGRSVrVVWLGL--EGDFSQLSAEVEAATK 108
                                       44559*******999886546666666665..799**************9999******..9*************99 PP

                   2_5_RNA_ligase2  97 eagdkedsgeftPHlTiaqsadstsa..aelleklaqalpple...fevdeval 145
                                         g   ++++ftPH+Ti++  ++++   +ell+k+ +++ +++   f+v+e++l
  gi|330507264|ref|YP_004383692.1| 109 SLGFPPEERGFTPHVTIGRVGRPNAGtsRELLAKI-GLQSTVDlgsFTVEEFYL 161
                                       99999999**********9887777677*******.7777777777***99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1268.24
//
Query:       gi|330507265|ref|YP_004383693.1|  [L=437]
Description: CCA-adding enzyme [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-43  145.4   0.0    1.1e-42  144.8   0.0    1.3  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    1.5e-12   47.6   0.0    3.5e-12   46.5   0.0    1.6  1  NTP_transf_2     Nucleotidyltransferase domain
     0.0059   16.7   0.0      0.015   15.3   0.0    1.7  1  Polbeta          Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.041   14.1   0.0       0.18   11.9   0.0    1.9  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 !  144.8   0.0   2.6e-46   1.1e-42       1     113 []     139     249 ..     139     249 .. 0.98

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 2.6e-46
                                       HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEET CS
                   tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDP 77 
                                       d+v llK+flkgigvYGselk+ GfsGYl+Ellv+ y sf +vl+aa++w+p++v+dle + +  k +depl+v+DP
  gi|330507265|ref|YP_004383693.1| 139 DDVLLLKQFLKGIGVYGSELKTGGFSGYLVELLVILYRSFPDVLRAASHWRPDTVLDLEGEGK--KLHDEPLTVVDP 213
                                       89*******************************************************999998..889********* PP

                                       TEEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGGS CS
                   tRNA_NucTransf2  78 vDpkRNvaaalsleklaefilaareflkkpseefff 113
                                       vDp+RNvaaal+l+k+  f++a+r+fl++ps+efff
  gi|330507265|ref|YP_004383693.1| 214 VDPNRNVAAALTLDKMLLFSAASRSFLDRPSLEFFF 249
                                       ***********************************6 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   7.7e-16   3.5e-12       6      94 ..      27     125 ..      22     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 7.7e-16
                                       HHHHHHTT.TSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH........HHHEHHHHHHHHCCCEEECTTEEEE CS
                      NTP_transf_2   6 eelkelep.vakvvlfGSyarGtalkg.SDiDllvvlpeevsre........kkeegleklaeiikfleellglevd 72 
                                       e+l e+++ v ++ l+GS+ar+t+l + +D+D+++ +pe+++ +        + +e++e++ae+++++ ++ g evd
  gi|330507265|ref|YP_004383693.1|  27 ERLAEERGmVLQAMLVGSAARDTWLAQdHDLDIFLGVPENSDLSeamelarlVAPEHEERYAEHPYVHARVDGFEVD 103
                                       5566666679******************************9888********99999******************** PP

                                       EECEEECCCCTEEEEEECEEEH CS
                      NTP_transf_2  73 lvtrekledpllvksileerpl 94 
                                       lv+++ + d ++ ks+++++p+
  gi|330507265|ref|YP_004383693.1| 104 LVPCYLVDDASRLKSAVDRTPF 125
                                       ***************9999987 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.4e-06     0.015       2      53 ..      25      77 ..      24      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.4e-06
                                      STTTTHHHHHHHHSTTEEEEEE-S---.---EEEEEEEESS---HHHHHHHHH CS
                           Polbeta  2 kikeilekekeielaylFGSrakgkar.eeSDiDlavllkekldleeelelaa 53
                                      ki+ ++e++  +  a+l GS a+++   +++D+D+++ + e+ dl+e +ela 
  gi|330507265|ref|YP_004383693.1| 25 KIERLAEERGMVLQAMLVGSAARDTWLaQDHDLDIFLGVPENSDLSEAMELAR 77
                                      8999******************8886537*************99999999986 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.1e-05      0.18      11     135 ..       2     112 ..       1     119 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.1e-05
                             SMODS  11 lsnielsqttkdsissrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllvvvnevegd 87 
                                       ls++++s+++++ +    ++i ++++    e +  + + +lvGS ardT + +  d         d+++ v e+++ 
  gi|330507265|ref|YP_004383693.1|   2 LSQVRPSPKERERLRLISREIIAKIERLA-EERGMVLQAMLVGSAARDTWLAQDHD--------LDIFLGVPENSDL 69 
                                       78899999999999999999999999999.66678999*************95444........5666666664333 PP

                             SMODS  88 .epsdlleklkkalkktyksseirqdrqvvvvelneikidvvPavenkd 135
                                        e+ +l   +    +++        +++ v  +++++++d+vP+   +d
  gi|330507265|ref|YP_004383693.1|  70 sEAMELARLVAPEHEER------YAEHPYVHARVDGFEVDLVPCYLVDD 112
                                       03333322233333444......45599999999999999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 3394.22
//
Query:       gi|330507266|ref|YP_004383694.1|  [L=339]
Description: histone deacetylase family protein [Methanosaeta concilii GP6]
Scores for complete 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-86  288.7   0.0    8.4e-86  288.2   0.0    1.2  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.2   0.0   4.7e-90   8.4e-86       1     301 [.      22     302 ..      22     307 .. 0.93

  Alignments for each domain:
  == domain 1  score: 288.2 bits;  conditional E-value: 4.7e-90
                                       SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiaskll 77 
                                       hpe+++Rl ail+++++  gl d  e  i+p++at e+++ +H ++Y+++++ ++++ + +                
  gi|330507266|ref|YP_004383694.1|  22 HPERKERLTAILDRIESE-GL-DI-E-CITPKPATIEQVESIHGRRYIDQVKAICERGGGHL--------------- 79 
                                       89************9996.75.33.3.489*************************8877664............... PP

                                       SSSTHCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  78 dddtpvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrv 154
                                       d dt++s+++++aal+a+g++++avdav++g  + af+lvrPpgHHa++++ +GFC++Nnvaia++++q+   l++v
  gi|330507266|ref|YP_004383694.1|  80 DIDTILSKDSFDAALMAAGGAIAAVDAVIEG-HRGAFALVRPPGHHAMPNRGMGFCVFNNVAIAARHAQS-RDLEKV 154
                                       568***************************9.699***********************************.679*** PP

                                       EEEE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 155 ailDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilr 231
                                       +i+D+DvHhGnGt+++fysd +vl++S+H++++  yPgtg ++d+ge+ ++g+n+nvpl+ gtgde yl +++eil+
  gi|330507266|ref|YP_004383694.1| 155 LIVDWDVHHGNGTNAIFYSDRSVLYFSTHQFPH--YPGTGRMNDVGEDGAEGTNVNVPLPSGTGDEGYLMAYREILK 229
                                       ******************************777..****************************************** PP

                                       HHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-.G..EEEEE-S---H.HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxx.xxxxxxxx RF
                     Hist_deacetyl 232 pvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkv.k.kvvllleGGYnl.ealaravt 301
                                       p++ ef+Pd++lvsaG D +k+dplg++ l+++g++ +   ++e+ad + + +v ++leGGYnl +++++ v+
  gi|330507266|ref|YP_004383694.1| 230 PIAIEFSPDIVLVSAGQDPHKDDPLGGMGLTASGFAAIAGVVKEVADICsNgRVAAVLEGGYNLfAQAEAIVA 302
                                       *********************************************9999889***********9555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2018.76
//
Query:       gi|330507267|ref|YP_004383695.1|  [L=698]
Description: S-layer-related duplication domain-containing protein [Methanosaeta concilii GP6]
Scores for 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-182  602.5  33.5    2.7e-92  308.5  12.6    2.1  2  S-layer         S-layer protein
    2.4e-08   33.7   2.2      5e-08   32.7   2.2    1.6  1  PGF-CTERM       PGF-CTERM motif
    0.00029   21.1   7.9    0.00062   20.1   7.9    1.5  1  Alanine_zipper  Alanine-zipper, major outer membrane lipoprot
    0.00095   19.6   6.9       0.24   11.9   0.1    3.1  2  EF-hand_like    Phosphoinositide-specific phospholipase C, ef
     0.0014   18.6   9.2     0.0028   17.7   9.2    1.4  1  YscO-like       YscO-like protein
     0.0026   16.6   0.1        1.9    7.1   0.0    2.3  2  tRNA-synt_1g    tRNA synthetases class I (M)
  ------ inclusion threshold ------
      0.083   13.0   0.5       0.17   12.0   0.5    1.5  1  MCU             Mitochondrial calcium uniporter
       0.14   12.1   0.0         19    5.1   0.0    2.3  2  ELYS            Nuclear pore complex assembly
       0.18   11.0   8.9        0.3   10.3   8.9    1.2  1  ISG65-75        Invariant surface glycoprotein
       0.24   12.0   5.5       0.54   10.9   5.5    1.5  1  DUF883          Bacterial protein of unknown function (DUF883
        1.1    9.9   5.3        5.2    7.7   5.3    2.3  1  YtxH            YtxH-like protein
        3.5    8.1   7.6        5.9    7.3   7.6    1.3  1  DUF1771         Domain of unknown function (DUF1771)
        5.1    7.4  10.6         13    6.1   1.2    2.9  3  Binary_toxB     Clostridial binary toxin B/anthrax toxin PA C
        5.8    7.4   8.0         19    5.7   8.0    2.0  1  Dr_adhesin      Dr family adhesin


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 !  300.1  12.9   7.6e-93   9.8e-90       8     258 .]      37     300 ..      31     300 .. 0.96
   2 !  308.5  12.6   2.1e-95   2.7e-92       6     258 .]     325     590 ..     321     590 .. 0.96

  Alignments for each domain:
  == domain 1  score: 300.1 bits;  conditional E-value: 7.6e-93
                           S-layer   8 eeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfagy. 83 
                                        + twta++F+gfyyd+dd++++E+lt+++++ +++ +e +++vY+t+++  +f++e+wgsY+vigf+a+kYfagy 
  gi|330507267|ref|YP_004383695.1|  37 GTDTWTADDFAGFYYDLDDDIKTEELTATVTE-GNKLMEPDGVVYTTKVMADDFDYEAWGSYNVIGFMADKYFAGYi 112
                                       4557*************************987.*******************************************8 PP

                           S-layer  84 ..dnsa.......etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeev 151
                                            +       e+sdd+++lsde+L k+l+d+d+e+t++sg+ l +eegYel+i  iD+dg+kv+leL+kdg+ v
  gi|330507267|ref|YP_004383695.1| 113 dtP--DsvedvlfEESDDENVLSDEQLLKILMDNDDERTVTSGTPLAMEEGYELSIAAIDIDGNKVYLELSKDGAVV 187
                                       542..34578888899************************************************************* PP

                           S-layer 152 dskvissska.....dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevk 223
                                       dskvis+sk+     d+ty+y+kd+gd++dvvi+a h++++frg+e++l++i+g++q+sd++ +++e++e++km+++
  gi|330507267|ref|YP_004383695.1| 188 DSKVISPSKDgatmkDKTYYYKKDIGDSKDVVIVAAHFKNAFRGAEQNLATIDGLWQLSDNPRDVSENTEYDKMTIQ 264
                                       *******9999****************************************************************** PP

                           S-layer 224 svseneiemendds.itLsrdktieimddlkfkvaD 258
                                       +v+ ++i m+n+d+ itLs++k+i++m  +++++aD
  gi|330507267|ref|YP_004383695.1| 265 TVTADSIMMNNEDNdITLSKNKDITLMPGVSIRTAD 300
                                       ***********9988********************8 PP

  == domain 2  score: 308.5 bits;  conditional E-value: 2.1e-95
                           S-layer   6 eseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfag 82 
                                        ++++twta+nF+gfyydidd++++E+l++++++ +++ +e +++vY+t+++  +fe+e+wgsY+vigf+aekYfag
  gi|330507267|ref|YP_004383695.1| 325 ATDTFTWTADNFAGFYYDIDDNIKTEELVATISE-GNKLLEPDGVVYTTKVMADDFEYEPWGSYNVIGFMAEKYFAG 400
                                       6789***************************876.****************************************** PP

                           S-layer  83 y....dnsa.....etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgee 150
                                       y    d+ +     e+sdd+++lsde+L k+l+d+d+e+t++sg+ l +eegYel+i  iD+dg+kv+leL+kdg+ 
  gi|330507267|ref|YP_004383695.1| 401 YidtpDT-TddvlfEESDDENVLSDEQLLKILMDNDDERTVTSGTPLAMEEGYELSIAAIDIDGNKVYLELSKDGAV 476
                                       *976533.257898999************************************************************ PP

                           S-layer 151 vdskvissska.....dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmev 222
                                       vdskvis+sk+     d+ty+y+kd+gd++dvvi+a h++++frg+e++l++i+g++q+sd++ +++e++e++km++
  gi|330507267|ref|YP_004383695.1| 477 VDSKVISPSKDgatmkDKTYYYKKDIGDSKDVVIVAAHFKNAFRGAEQNLATIDGLWQLSDNPRDVSENTEYDKMTI 553
                                       ********9999***************************************************************** PP

                           S-layer 223 ksvseneiemendds.itLsrdktieimddlkfkvaD 258
                                       ++v+ ++i+m+ +d+ itLs++k+i++m  +++k+aD
  gi|330507267|ref|YP_004383695.1| 554 QTVTADSITMDIEDNdITLSKNKDISLMPGVSIKTAD 590
                                       ***********99888********************8 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   2.2   3.9e-11     5e-08       1      21 [.     674     694 ..     674     696 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 3.9e-11
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaR 21 
                                       tPGFG+++Al+GLLa+a+L+ 
  gi|330507267|ref|YP_004383695.1| 674 TPGFGSIFALTGLLAVAYLVL 694
                                       9******************85 PP

>> Alanine_zipper  Alanine-zipper, major outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   7.9   4.9e-07   0.00062       4      52 ..     622     670 ..     619     681 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.9e-07
                    Alanine_zipper   4 eelqakadqaeqdaaaaksaadeAkskAdeAaarAenAeaaAeeAqkaA 52 
                                        ++++ +++a++++++a+++ +eA++  +eA++ +++Aea AeeA++a+
  gi|330507267|ref|YP_004383695.1| 622 NDTEKVVEEAKEAVEEANKTVEEAEEVVEEAKEEVAEAEAHAEEAAEAT 670
                                       6788889999999999999999999999999999999999999998875 PP

>> EF-hand_like  Phosphoinositide-specific phospholipase C, efhand-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00018      0.24      11      84 ..     118     187 ..     112     189 .. 0.87
   2 !   11.0   0.0   0.00037      0.48      14      84 ..     411     477 ..     404     479 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                      EF-hand_like  11 ideifqeyskdgeklslkelveFLreeQkeedaseelalelIerYEpsetakkkkaltkdGFlmYL.lskdgsif 84 
                                       ++++  e s+d++ ls ++l + L+ +  e+  ++ + l + e YE s +a     + +dG  +YL lskdg ++
  gi|330507267|ref|YP_004383695.1| 118 VEDVLFEESDDENVLSDEQLLKILMDNDDERTVTSGTPLAMEEGYELSIAA-----IDIDGNKVYLeLSKDGAVV 187
                                       67777788***************************************9765.....7799999999558888876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00037
                      EF-hand_like  14 ifqeyskdgeklslkelveFLreeQkeedaseelalelIerYEpsetakkkkaltkdGFlmYL.lskdgsif 84 
                                       +  e s+d++ ls ++l + L+ +  e+  ++ + l + e YE s +a     + +dG  +YL lskdg ++
  gi|330507267|ref|YP_004383695.1| 411 VLFEESDDENVLSDEQLLKILMDNDDERTVTSGTPLAMEEGYELSIAA-----IDIDGNKVYLeLSKDGAVV 477
                                       455679**************************************9765.....7799999999558888876 PP

>> YscO-like  YscO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   9.2   2.2e-06    0.0028      54     130 ..     589     665 ..     583     673 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.2e-06
                                       HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         YscO-like  54 aKvaqlreeldkGttsdkikkmkryikvvkeelkqeekkvekQkekVkvAerkvEqareelakkrkeveklekhkee 130
                                       a  ++lr+ + k +t+++ + + + +  v   ++  ek ve+ ke+V++A++ vE+a+e + +++ ev   e h ee
  gi|330507267|ref|YP_004383695.1| 589 ADADELRYYIYKEATIEGEEEVAEEETAVVTPVNDTEKVVEEAKEAVEEANKTVEEAEEVVEEAKEEVAEAEAHAEE 665
                                       56689********************************************************************9987 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0015       1.9     313     358 ..     264     312 ..     253     325 .. 0.76
   2 !    7.0   0.0    0.0016         2     325     366 ..     569     610 ..     547     627 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0015
                                       S-EEEE--EEE---...-----------HHHHHHHH-HHHHHHHHHHHS CS
                      tRNA-synt_1g 313 kkvvaheyltvegk...KlSkSrgvvvkakealerldadllRYylaaea 358
                                       ++v+a + ++ +++    lSk + +  ++   + + dad lRYyl++e 
  gi|330507267|ref|YP_004383695.1| 264 QTVTADSIMMNNEDndiTLSKNKDITLMPGVSIRTADADELRYYLYKEI 312
                                       556666555444331225899999999******************9865 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0016
                                       -------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE CS
                      tRNA-synt_1g 325 gkKlSkSrgvvvkakealerldadllRYylaaeapekkDldf 366
                                       +  lSk + +  ++   +++ dad lRYy+++ea  + + + 
  gi|330507267|ref|YP_004383695.1| 569 DITLSKNKDISLMPGVSIKTADADELRYYIYKEATIEGEEEV 610
                                       456899999999*******************98776555544 PP

>> MCU  Mitochondrial calcium uniporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5   0.00013      0.17      26     109 ..     598     692 ..     546     695 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                       X..............XXXXXXXXXXXXXXXXX-SSSSSSTSSSSSHHHHHHHHHHHHH-SHHHHHHHHTCCCGGGCH CS
                               MCU  26 e..............eeakvllrvkqlvkalesalnveeeqlkkereleekleelreelepleekkeeidekAerrt 88 
                                                      ee++v++ v+ + k +e+a ++ ee++k ++e+ee  ee +ee+ ++e+   + +e+Ae+ +
  gi|330507267|ref|YP_004383695.1| 598 IykeatiegeeevaeEETAVVTPVNDTEKVVEEAKEAVEEANKTVEEAEEVVEEAKEEVAEAEA---HAEEAAEATA 671
                                       0444444444433333344444444444444444455566666666666666666666666666...6677777777 PP

                                       HHHGGGHHHHHHHHTHHHHHH CS
                               MCU  89 rrllwagLallavqlgilarL 109
                                       ++   +g +++ + l ++a+L
  gi|330507267|ref|YP_004383695.1| 672 NQTPGFGSIFALTGLLAVAYL 692
                                       777777777777777777776 PP

>> ELYS  Nuclear pore complex assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.021        27      54      97 ..     205     248 ..     191     273 .. 0.86
   2 ?    5.1   0.0     0.015        19      54      97 ..     495     538 ..     481     641 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.021
                              ELYS  54 llYlLlDldasseeselaedFaaafglprklvllvqglwlLDhg 97 
                                        +Y+ +D+ +s++   +a +F +af+  ++ +  ++glw L ++
  gi|330507267|ref|YP_004383695.1| 205 TYYYKKDIGDSKDVVIVAAHFKNAFRGAEQNLATIDGLWQLSDN 248
                                       69*****988777777***********************99765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.015
                              ELYS  54 llYlLlDldasseeselaedFaaafglprklvllvqglwlLDhg 97 
                                        +Y+ +D+ +s++   +a +F +af+  ++ +  ++glw L ++
  gi|330507267|ref|YP_004383695.1| 495 TYYYKKDIGDSKDVVIVAAHFKNAFRGAEQNLATIDGLWQLSDN 538
                                       69*****988777777************************9766 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   8.9   0.00023       0.3      64     127 ..     608     671 ..     591     678 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                          ISG65-75  64 ayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekae 127
                                       + ++++  +v   v++ e+++eeake  +  ++++e++++ +eeAk+++++a++ a++a+e+ +
  gi|330507267|ref|YP_004383695.1| 608 EEVAEEETAVVTPVNDTEKVVEEAKEAVEEANKTVEEAEEVVEEAKEEVAEAEAHAEEAAEATA 671
                                       4555555555566666677777777777777777777777777777777777777777766655 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 ?   10.9   5.5   0.00042      0.54      11      65 ..     621     674 ..     611     677 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00042
                            DUF883  11 ladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaa 65 
                                       ++d+e++++ea+ ea eea++  e++ee +e+a+e++++ae +++e a++ a+++
  gi|330507267|ref|YP_004383695.1| 621 VNDTEKVVEEAK-EAVEEANKTVEEAEEVVEEAKEEVAEAEAHAEEAAEATANQT 674
                                       689999996655.7888999999999************99999999999999887 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.3    0.0041       5.2      34      71 ..     624     660 ..     593     671 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0041
                              YtxH  34 addlkekakelleeakekakekaedlkekvkekadelk 71 
                                       ++++ e ake++eea+++ +e+ae+++e++ke++ e+ 
  gi|330507267|ref|YP_004383695.1| 624 TEKVVEEAKEAVEEANKT-VEEAEEVVEEAKEEVAEAE 660
                                       456666666666666555.5555555555555544433 PP

>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   7.6    0.0046       5.9      17      59 ..     626     670 ..     622     674 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0046
                           DUF1771  17 elfekAaeAyrrGd..gaaAkelseqGkehgekmeeanreAaeaI 59 
                                       +  e+A+eA ++ +   ++A e +e++ke  +++e+ ++eAaea 
  gi|330507267|ref|YP_004383695.1| 626 KVVEEAKEAVEEANktVEEAEEVVEEAKEEVAEAEAHAEEAAEAT 670
                                       6789*******99977799***********************985 PP

>> Binary_toxB  Clostridial binary toxin B/anthrax toxin PA Ca-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.2    0.0098        13       2      44 ..     170     212 ..     169     217 .. 0.89
   2 ?    6.1   1.2    0.0098        13       2      44 ..     460     502 ..     459     507 .. 0.89
   3 ?   -3.4   0.0       9.4   1.2e+04      53      69 ..     620     636 ..     612     640 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0098
                                       -SSSSSS-HHHHHH-EEEESEEEEE--TTHHHHHT---B---T CS
                       Binary_toxB   2 DsDdDgipdslEvnGYtldktllvPwvdklaekkgltkyvsdp 44 
                                       D D+  ++ +l  +G ++d+++++P +d  + k++   y+ d 
  gi|330507267|ref|YP_004383695.1| 170 DIDGNKVYLELSKDGAVVDSKVISPSKDGATMKDKTYYYKKDI 212
                                       99**************************999998888888775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0098
                                       -SSSSSS-HHHHHH-EEEESEEEEE--TTHHHHHT---B---T CS
                       Binary_toxB   2 DsDdDgipdslEvnGYtldktllvPwvdklaekkgltkyvsdp 44 
                                       D D+  ++ +l  +G ++d+++++P +d  + k++   y+ d 
  gi|330507267|ref|YP_004383695.1| 460 DIDGNKVYLELSKDGAVVDSKVISPSKDGATMKDKTYYYKKDI 502
                                       99**************************999998888888775 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 9.4
                                       SS-HHHHHHT-S-TTS- CS
                       Binary_toxB  53 PysDlekvsgkidknva 69 
                                       P  D ekv  ++ + v+
  gi|330507267|ref|YP_004383695.1| 620 PVNDTEKVVEEAKEAVE 636
                                       77899999888777775 PP

>> Dr_adhesin  Dr family adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   8.0     0.015        19       1      20 [.       1      20 [.       1      21 [. 0.93

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
                        Dr_adhesin  1 MKKLAIMaatSvltavsTaH 20
                                      MKKLA ++ tS+++   Ta 
  gi|330507267|ref|YP_004383695.1|  1 MKKLAAITFTSMVLLLATAM 20
                                      **************999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (698 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1738  (0.0969379); expected 358.6 (0.02)
Passed bias filter:                      817  (0.0455686); expected 358.6 (0.02)
Passed Vit filter:                       158  (0.00881254); 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):              14  [number of targets reported over threshold]
# CPU time: 0.86u 0.31s 00:00:01.17 Elapsed: 00:00:00.47
# Mc/sec: 4429.16
//
Query:       gi|330507268|ref|YP_004383696.1|  [L=341]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   64.0   0.0    6.8e-17   62.3   0.0    1.7  2  Radical_SAM     Radical SAM superfamily
  ------ inclusion threshold ------
      0.032   13.6   7.3       0.61    9.6   0.1    3.2  3  zf-ribbon_3     zinc-ribbon domain
      0.035   14.1   0.1      0.035   14.1   0.1    2.8  3  DZR             Double zinc ribbon
      0.059   13.6   0.9       0.11   12.8   0.0    1.8  2  Fer4_12         4Fe-4S single cluster domain
       0.17   11.8   0.1       0.17   11.8   0.1    2.3  3  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.78    9.3   4.9        3.5    7.2   0.1    3.0  3  TF_Zn_Ribbon    TFIIB zinc-binding
        1.3    9.2   6.0         12    6.1   0.0    3.6  4  Zn-ribbon_8     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 !   62.3   0.0   2.7e-20   6.8e-17       3     158 ..      85     233 ..      83     240 .. 0.94
   2 ?   -1.6   0.0       1.2   3.1e+03     123     145 ..     268     290 ..     254     300 .. 0.74

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.7e-20
                                       EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla 74 
                                        t gCn+rC +C++        +    +g ++++e++++ +    +++g+  v  +  ep+   +++ +++rla+  
  gi|330507268|ref|YP_004383696.1|  85 ATVGCNFRCLHCQNADIsqlphETGKLPGNYVPPEDVVAGA----VSRGCQSVAYTYTEPTIFFEYAYDVARLARA- 156
                                       689************99***9999999999*******9999....5566***************************. PP

                                       CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivg 151
                                        +++r+++++ng+    + ++++ +l  d ++++l+  d++ ++k +  +  ++ v+ ++ek+ +ag+  v +++++
  gi|330507268|ref|YP_004383696.1| 157 -SKLRNVFVSNGYIG-QDAADKIIPLL-DGINIDLKGDDEF-YRKVC--KAKLDPVKSNIEKFWRAGVW-VEVTTLV 226
                                       .9************9.*********98.*************.*****..499*****************.******* PP

                                       BTTTSHH CS
                                       xxxxxxx RF
                       Radical_SAM 152 lpGende 158
                                       +pG+nd+
  gi|330507268|ref|YP_004383696.1| 227 IPGYNDS 233
                                       *****97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                                       CTSHHHHHHHHHHHHHHTTSETE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 123 rghtfeevlealeklreagikrv 145
                                       ++ +++ +++al + reag+k v
  gi|330507268|ref|YP_004383696.1| 268 PPTGIKSIKRALNIGREAGLKYV 290
                                       55678899999999999999953 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2      0.78     2e+03      14      22 ..      19      27 ..      17      27 .. 0.74
   2 ?    9.6   0.1   0.00024      0.61      13      26 .]     298     311 ..     293     311 .. 0.83
   3 ?    6.9   0.4    0.0016       4.2       4      11 ..     328     336 ..     326     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.78
                       zf-ribbon_3 14 sddnvCpyC 22
                                      s+d++C  C
  gi|330507268|ref|YP_004383696.1| 19 SEDVNCSLC 27
                                      788999766 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00024
                       zf-ribbon_3  13 ssddnvCpyCGtkl 26 
                                       +s+ ++Cp CG +l
  gi|330507268|ref|YP_004383696.1| 298 ESESTICPDCGFVL 311
                                       57789******987 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0016
                       zf-ribbon_3   4 rCPnCGa.p 11 
                                       rCPnC+a +
  gi|330507268|ref|YP_004383696.1| 328 RCPNCKAaV 336
                                       8****9966 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   4.4       4.6   1.2e+04      28      34 ..      90      96 ..      13     104 .. 0.50
   2 ?   -3.6   0.0       4.8   1.2e+04      18      24 ..     199     205 ..     197     209 .. 0.57
   3 ?   14.1   0.1   1.4e-05     0.035      10      38 ..     299     336 ..     296     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.6
                               DZR 28 edrCpsC 34
                                      + rC +C
  gi|330507268|ref|YP_004383696.1| 90 NFRCLHC 96
                                      3345555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.8
                               DZR  18 Cgtklka 24 
                                       C++kl++
  gi|330507268|ref|YP_004383696.1| 199 CKAKLDP 205
                                       5555554 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 1.4e-05
                               DZR  10 pdarfCseCgtklkavaa.........edrCpsCgekv 38 
                                       +++  C++Cg  l +            e rCp+C+++v
  gi|330507268|ref|YP_004383696.1| 299 SESTICPDCGFVLIERRGyrvmkntvtEGRCPNCKAAV 336
                                       67889********966669****************986 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.2       5.7   1.5e+04      17      25 ..      22      30 ..      21      40 .. 0.65
   2 ?   12.8   0.0   4.2e-05      0.11       7     117 ..      81     190 ..      77     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 5.7
                           Fer4_12 17 lsCkgCfnk 25
                                      ++C+ C+++
  gi|330507268|ref|YP_004383696.1| 22 VNCSLCYQN 30
                                      578888754 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.2e-05
                           Fer4_12   7 rlslfvsgCnlsCkgCfnketwsfk.sgkeft..kelleeiiedlkkesiegltllGGEPllpenaeallelvkevk 80 
                                        +s+ + gCn++C  C n ++ +   +  + +      e +++ +  +  + + ++  EP      e  +++++  +
  gi|330507268|ref|YP_004383696.1|  81 AYSIATVGCNFRCLHCQNADISQLPhETGKLPgnYVPPEDVVAGAVSRGCQSVAYTYTEPTI--FFEYAYDVARLAR 155
                                       5788899************998654233333322333456666666889999999999**99..8889999999999 PP

                           Fer4_12  81 eekpekdiwlytgytleelskkekeellkeidvlvdG 117
                                       + k+  ++++++gy+ ++  + +  +ll+ i++ ++G
  gi|330507268|ref|YP_004383696.1| 156 ASKL-RNVFVSNGYIGQDAAD-KIIPLLDGINIDLKG 190
                                       9999.589999**99999986.588888888887776 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   1.1         7   1.8e+04      30      45 ..      23      37 ..      21      42 .. 0.64
   2 ?   -2.6   0.3       2.2   5.5e+03      46      57 ..      90      98 ..      84     102 .. 0.61
   3 ?   11.8   0.1   6.5e-05      0.17      28      54 ..     301     334 ..     280     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 7
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgr 45
                                      +Cs C ++ +  + g+
  gi|330507268|ref|YP_004383696.1| 23 NCSLCYQNCRI-RPGK 37
                                      68888877766.4444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.2
                    OrfB_Zn_ribbon 46 tfkCpnCgfead 57
                                      +f+C +C+   +
  gi|330507268|ref|YP_004383696.1| 90 NFRCLHCQ---N 98
                                      45666664...4 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 6.5e-05
                    OrfB_Zn_ribbon  28 SktCseCgsknke.......alsgrtfkCpnCgf 54 
                                       S+ C+ Cg ++ e       +++  + +CpnC++
  gi|330507268|ref|YP_004383696.1| 301 STICPDCGFVLIErrgyrvmKNTVTEGRCPNCKA 334
                                       99********999999999999999999****86 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.87   2.2e+03       1      17 [.      91     108 ..      91     111 .. 0.67
   2 ?    7.2   0.1    0.0014       3.5      18      29 ..     300     311 ..     298     316 .. 0.78
   3 ?    2.8   0.3     0.033        84       2       7 ..     328     333 ..     327     336 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.87
                                       EEETTTTCEEC.HEETST CS
                      TF_Zn_Ribbon   1 ykCPnCgstnl.veDper 17 
                                       ++C  C + ++  +++e+
  gi|330507268|ref|YP_004383696.1|  91 FRCLHCQNADIsQLPHET 108
                                       689999998843555555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0014
                                       TCEEESSSSBEE CS
                      TF_Zn_Ribbon  18 gelvCtdCGlVl 29 
                                         ++C+dCG Vl
  gi|330507268|ref|YP_004383696.1| 300 ESTICPDCGFVL 311
                                       5689*****998 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.033
                                       EETTTT CS
                      TF_Zn_Ribbon   2 kCPnCg 7  
                                       +CPnC+
  gi|330507268|ref|YP_004383696.1| 328 RCPNCK 333
                                       6****8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       1.9     5e+03      23      35 ..      18      30 ..       8      32 .. 0.60
   2 ?    0.2   0.1      0.33   8.4e+02       6      13 ..      91      98 ..      90     107 .. 0.82
   3 ?    6.1   0.0    0.0047        12      23      34 ..     298     309 ..     293     315 .. 0.69
   4 ?    3.3   0.1     0.036        93      27      36 ..     327     336 ..     317     339 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.9
                       Zn-ribbon_8 23 dapltaCPeCgse 35
                                      +++++ C  C ++
  gi|330507268|ref|YP_004383696.1| 18 ESEDVNCSLCYQN 30
                                      4444449888665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.33
                       Zn-ribbon_8  6 YrCeeCgh 13
                                      +rC  C++
  gi|330507268|ref|YP_004383696.1| 91 FRCLHCQN 98
                                      89999984 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0047
                       Zn-ribbon_8  23 dapltaCPeCgs 34 
                                       +++ t CP+Cg 
  gi|330507268|ref|YP_004383696.1| 298 ESESTICPDCGF 309
                                       555666****95 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.036
                       Zn-ribbon_8  27 taCPeCgsev 36 
                                         CP+C+++v
  gi|330507268|ref|YP_004383696.1| 327 GRCPNCKAAV 336
                                       35****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2423.30
//
Query:       gi|330507269|ref|YP_004383697.1|  [L=402]
Description: 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II [Methanosaeta concilii GP6]
Scores for complete 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-85  285.4   0.5    2.2e-85  285.1   0.5    1.1  1  DHBP_synthase    3,4-dihydroxy-2-butanone 4-phosphate synthas
    3.6e-73  244.5   0.0    8.8e-73  243.3   0.0    1.6  2  GTP_cyclohydro2  GTP cyclohydrolase II


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.1   0.5   2.4e-89   2.2e-85       1     192 []       7     198 ..       7     198 .. 0.99

  Alignments for each domain:
  == domain 1  score: 285.1 bits;  conditional E-value: 2.4e-89
                                       HHHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-SSTT-- CS
                     DHBP_synthase   1 eeaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveenedkhkt 77 
                                       eeai++++aG+f+i++Dde+renegdL++aAe+vtpe+++fm+r ++Glic+++t+er++eL++plm+++n+++++t
  gi|330507269|ref|YP_004383697.1|   7 EEAISDIRAGRFIIILDDENRENEGDLMMAAENVTPEAINFMARFGRGLICMPMTAERLRELDIPLMTSQNTESMGT 83 
                                       69*************************************************************************** PP

                                       -BB--EEESST-SSS-SHHHHHHHHHHHH-TT--GGGEEEEEEEEEEEE-TTGGGTS-SHHHHHHHHHHHTTS-SBE CS
                     DHBP_synthase  78 aftvsvdaaegttTGIsaaDRalTirkladpkakpedfrrPGhvfplrareggvleRrghTEaavdLarlaglkpaa 154
                                       aftvsvda+ +ttTGIsa DRa+T+++l+dp ++ +d+++PGh+fpl+a+eggvl+R+ghTEa+vdLarlagl+pa+
  gi|330507269|ref|YP_004383697.1|  84 AFTVSVDARINTTTGISAFDRATTVHALIDPVTRRNDIVTPGHLFPLQAKEGGVLRRTGHTEACVDLARLAGLQPAG 160
                                       ***************************************************************************** PP

                                       EEEEBB-TTSCB-BHHHHHHHHHHHT-EEEEHHHHHHH CS
                     DHBP_synthase 155 vicellnddgtmarrdeleefakkhglkiitiedliey 192
                                       vi+e++nddgtmar+++le+fa++hglk++tie+li+y
  gi|330507269|ref|YP_004383697.1| 161 VIVEIMNDDGTMARLPQLERFAQEHGLKMLTIESLIRY 198
                                       ************************************98 PP

>> GTP_cyclohydro2  GTP cyclohydrolase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.31   2.8e+03      66      89 ..       8      29 ..       5      93 .. 0.55
   2 !  243.3   0.0   9.8e-77   8.8e-73       4     163 .]     210     372 ..     207     372 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.31
                                      HHHHHHHHH-.EEEEEE--TTTTT CS
                   GTP_cyclohydro2 66 ealeliaeegrGvlvylrqegrgi 89
                                      ea+  i+ +gr  ++ l+ e+r+ 
  gi|330507269|ref|YP_004383697.1|  8 EAISDIR-AGR-FIIILDDENREN 29
                                      5555555.443.334444444332 PP

  == domain 2  score: 243.3 bits;  conditional E-value: 9.8e-77
                                       EEEEEEETTEEEEEEEE--.....EEEEEE-........EEEEEE--HHHHHS-B--TTTTTHHHHHHHHHHHH-.E CS
                   GTP_cyclohydro2   4 aeaklptrfgefrliayedkvdgkehlalvkgdi...pvlvRvHsecltgDvlgslrcdcgeqldealeliaeegrG 77 
                                       +e+++pt++g f++i+ye+ +dg+ h+alv gd+   + lvRvHsecltgDv+ s+rcdcgeql++al+li+++g+G
  gi|330507269|ref|YP_004383697.1| 210 SEVSMPTEYGLFTAIGYESVLDGQCHIALVAGDPtcpDALVRVHSECLTGDVFSSKRCDCGEQLRRALQLISKNGNG 286
                                       5899******************************999889*******************************99**** PP

                                       EEEEE--TTTTTHHHHHHHHHHHHHCT--HHHHHHHHT--S-----HHHHHHHHHTT--EEEEE-S-HHHHHHHCTT CS
                   GTP_cyclohydro2  78 vlvylrqegrgigllnklkayalqdeglDTveanlalglpadardygiaaqILkdlgvkkirLlTnnpekveaLegf 154
                                       vl+y+rqegrgigl+nkl+ayalqd g+DTvean++lg pad+rdygi+aqIL dlg+k+irLlTnnp+kv +Leg+
  gi|330507269|ref|YP_004383697.1| 287 VLLYMRQEGRGIGLANKLRAYALQDGGSDTVEANHRLGYPADLRDYGIGAQILVDLGIKQIRLLTNNPRKVIGLEGY 363
                                       ***************************************************************************** PP

                                       ....SEEEE CS
                   GTP_cyclohydro2 155 gievvervp 163
                                       g+e++ervp
  gi|330507269|ref|YP_004383697.1| 364 GLEIAERVP 372
                                       *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2818.05
//
Query:       gi|330507270|ref|YP_004383698.1|  [L=171]
Description: heat shock protein Hsp20 [Methanosaeta concilii GP6]
Scores for complete 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   75.3   1.0    4.5e-21   74.9   1.0    1.2  1  HSP20       Hsp20/alpha crystallin family
    2.1e-14   52.8   0.1    3.4e-14   52.2   0.1    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA
    7.9e-06   26.8   0.1    1.2e-05   26.3   0.1    1.2  1  CS          CS domain
  ------ inclusion threshold ------
      0.026   14.6   0.2          4    7.6   0.0    2.3  2  FKBP26_C    FKBP26_C-terminal


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 !   74.9   1.0     1e-24   4.5e-21       1     101 [.      71     170 ..      71     171 .] 0.93

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1e-24
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--....---TT----SS---EEEEEE--STTB-TTT-EEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgehe..eeeedekglikerssrkFsrkftLPenvdadkvkas 75 
                                       d++e+ee+  v++d+pg++k++++++v ++++ ++++++   e ++++++++er++  F+r++ LPe +++++ +a+
  gi|330507270|ref|YP_004383698.1|  71 DVHETEEALVVTMDMPGVEKQDINISVVEDELQISAQRKseAEVNEQDYHRRERTYTRFERRVLLPESIKTEEARAT 147
                                       67899**********************************877888999***************************** PP

                                       EETTEEEEEEEBSS--..-------- CS
                             HSP20  76 lkdGvLtvtvpkkepekkkkerkiqi 101
                                       l +GvL++t+pk +     + ++i+i
  gi|330507270|ref|YP_004383698.1| 148 LTNGVLQITLPKVSVL---TRKRIAI 170
                                       ************9886...5566666 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 !   52.2   0.1   7.5e-18   3.4e-14       4      63 .]      79     157 ..      76     157 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 7.5e-18
                        ArsA_HSP20   4 yvlkldLPfvdkeeidlsrsgdeLtIkig....................nfrRqitLPsvlarkevtsAkfedgvLe 60 
                                        v++ d+P+v+k++i++s ++deL I+++                    +f R++ LP++++ +e+ +A++ +gvL 
  gi|330507270|ref|YP_004383698.1|  79 LVVTMDMPGVEKQDINISVVEDELQISAQrkseaevneqdyhrrertytRFERRVLLPESIKTEEA-RATLTNGVLQ 154
                                       699***************************************************************.********** PP

                        ArsA_HSP20  61 IrF 63 
                                       I++
  gi|330507270|ref|YP_004383698.1| 155 ITL 157
                                       *96 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   2.6e-09   1.2e-05       6      76 .]      73     159 ..      70     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.6e-09
                                       EEETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECE................BSS-BETTTEEEE CS
                                CS   6 yQtldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliege................LfgpIdpeesswt 64 
                                       ++t++ +vvt  +++v  +k+d++++  e+ l ++  +k e ++ e +                L ++I++ee++ t
  gi|330507270|ref|YP_004383698.1|  73 HETEEALVVTMDMPGV--EKQDINISVVEDELQISAqRKsEAEVNEQDyhrrertytrferrvlLPESIKTEEARAT 147
                                       799************9..******************888677776666***************************** PP

                                       EETTEEEEEEEB CS
                                CS  65 ieskkveitLkK 76 
                                       +++  ++itL K
  gi|330507270|ref|YP_004383698.1| 148 LTNGVLQITLPK 159
                                       **********98 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0068        30       8      33 ..      80     105 ..      76     110 .. 0.88
   2 ?    7.6   0.0    0.0009         4      15      37 ..     138     160 ..     130     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0068
                                       HHHHH-TT--..--EEEEETTEEEEE CS
                          FKBP26_C   8 lIkryiPnidlekfkieiedktvtIe 33 
                                       ++ + +P +++++++i++ + +++I 
  gi|330507270|ref|YP_004383698.1|  80 VVTMDMPGVEKQDINISVVEDELQIS 105
                                       68899*************99999885 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0009
                                       T--..--EEEEETTEEEEE--TT CS
                          FKBP26_C  15 nidlekfkieiedktvtIelpee 37 
                                        i++e+++ ++++++++I+lp+ 
  gi|330507270|ref|YP_004383698.1| 138 SIKTEEARATLTNGVLQITLPKV 160
                                       5999*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 1272.89
//
Query:       gi|330507271|ref|YP_004383699.1|  [L=160]
Description: hypothetical protein MCON_1157 [Methanosaeta concilii GP6]
Scores for complete 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  156.0   0.0    4.5e-46  155.7   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
    2.3e-12   46.5   0.0    3.5e-12   45.9   0.0    1.3  1  RLI            Possible Fer4-like domain in RNase L inhibitor


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.7   0.0     5e-50   4.5e-46       1     127 []      37     158 ..      37     158 .. 0.95

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 5e-50
                                       EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHH CS
                     Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaal 77 
                                       ivlsp+++k+lsp+D+     +g+a++dcsWa++eev   ++   +er+LP+LvAaNpvn+gkp+kLs+vEAlaa+l
  gi|330507271|ref|YP_004383699.1|  37 IVLSPFSEKALSPEDKGA---RGLAALDCSWAHAEEVF-ARF-RLQERALPFLVAANPVNWGKPFKLSTVEALAAGL 108
                                       8**************665...9************9998.444.359******************************* PP

                                       HHTT-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHHH CS
                     Ribo_biogen_C  78 yilglkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkeyl 127
                                       +ilg+k++ae +lskf+wg+ Fleln+e+l+eYa+++ds+evv++q+ey+
  gi|330507271|ref|YP_004383699.1| 109 VILGEKSQAELILSKFNWGHVFLELNREPLSEYAAARDSAEVVRIQNEYM 158
                                       ************************************************97 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 !   45.9   0.0   3.9e-16   3.5e-12       5      31 ..       2      29 ..       1      33 [. 0.89

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 3.9e-16
                                      EES---------TTHHHHHTTSEEE.ES CS
                               RLI  5 ivdadqCdPKKCtgkkcarfcpvrl.vr 31
                                      i++a+qCdP+KC+gkk+arf++vrl ++
  gi|330507271|ref|YP_004383699.1|  2 IYHANQCDPRKCSGKKLARFNLVRLtHH 29
                                      9**********************99555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1196.40
//
Query:       gi|330507272|ref|YP_004383700.1|  [L=858]
Description: valyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete 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-128  428.7   0.2   4.4e-127  424.8   0.2    2.0  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    5.7e-36  123.8   0.0    1.4e-35  122.5   0.0    1.6  1  Anticodon_1    Anticodon-binding domain of tRNA
    1.2e-22   80.2   0.1    1.1e-13   50.7   0.0    3.3  3  tRNA-synt_1g   tRNA synthetases class I (M)
    2.5e-05   23.8   0.0       0.13   11.6   0.0    2.3  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
     0.0016   18.0   0.0     0.0082   15.7   0.0    2.0  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.8   0.2  1.2e-130  4.4e-127       4     600 ..      19     560 ..      16     562 .. 0.94

  Alignments for each domain:
  == domain 1  score: 424.8 bits;  conditional E-value: 1.2e-130
                       tRNA-synt_1   4 ekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakv 80 
                                         W+ + ++      e +k+++i+  +PPy tG+ HiG+al+    d+  rykrm+G++v +  GwD++Gl++e kv
  gi|330507272|ref|YP_004383700.1|  19 RSWDSSIYYFDW---ESKKPQYIIDTPPPYPTGNFHIGNALNWCYIDFAARYKRMRGYNVMFPQGWDCHGLPTEVKV 92 
                                       568777776665...7889********************************************************** PP

                       tRNA-synt_1  81 ekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliy 157
                                       e+   +++    +++ reefr  + +  +e +++ +k++ rlG s+D+++ey T+++e+   ++  fvr+++kg+iy
  gi|330507272|ref|YP_004383700.1|  93 EQLNHITK----NQVPREEFRRLCEKLTEEAIDRFHKSMGRLGLSIDWSNEYATMKPEYYVKTQTSFVRMYQKGQIY 165
                                       *9865555....69*************************************************************** PP

                       tRNA-synt_1 158 rgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitkekli 234
                                       r  ++vnw++++ ta++ +Evey   +++l +++f ++d+e    +iaT +Pe l + +avav+pe           
  gi|330507272|ref|YP_004383700.1| 166 REDHPVNWCPRCGTAIALAEVEYDSRTSTLNYMHFCAEDGEI---EIATSRPELLAACVAVAVHPE----------- 228
                                       ***********************************9888765...*********************........... PP

                       tRNA-synt_1 235 laeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynl 311
                                                           d+r+++ +g++v+ p+ n ++p++ad  vd+ +G+G V i    d++D +  +++ l
  gi|330507272|ref|YP_004383700.1| 229 --------------------DQRYQKYIGRTVKVPIFNYSVPVLADPAVDSSFGSGFVMICTFGDKQDVRWWMEHHL 285
                                       ....................9******************************************************** PP

                       tRNA-synt_1 312 evinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkela 388
                                       ++ +++d  g++   a+ ++gl+v+++++k++++l+e+g ++k+e+ e +v++c+r k+pi+  + +qWfvr+++l+
  gi|330507272|ref|YP_004383700.1| 286 PLRQAIDRGGRMMPIAGPYSGLTVEETKEKITQDLTEQGIIFKQEPLEQNVGLCWRCKTPIEILSEQQWFVRIDALE 362
                                       **************************************************************************996 PP

                       tRNA-synt_1 389 daalkavekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekka 464
                                         + k  e+++++p   + r ++w   ++ dWciSRqr+  ++ip+++ k+  e  v ee  ++             
  gi|330507272|ref|YP_004383700.1| 363 --IKKMAEEIEWIPAHMRVRLENWADSMEwDWCISRQRIFATPIPAWYCKNCHEALVAEE--SW--------LPLDP 427
                                       ..667788*****************99866**********************99999222..22........22223 PP

                       tRNA-synt_1 465 lekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslal 541
                                       + ++ k+k k++  e+  ++dvlD+W +S+ +  ++ g+p++  ++l+   p+++  +G Diir W    il + al
  gi|330507272|ref|YP_004383700.1| 428 NLTQPKKKCKCGSSEFIPEQDVLDTWMDSSISALAVAGWPDR--TDLR--MPTQLRPQGHDIIRTWAFYTILRTRAL 500
                                       33456677789999**************************98..7888..9************************** PP

                       tRNA-synt_1 542 tgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdin 600
                                        g +P+  +l++g+ + e+G+KmSKsl N i p++v ++ gadalR + +   + g+di 
  gi|330507272|ref|YP_004383700.1| 501 EGIRPWDAILINGMALGEDGHKMSKSLNNFIRPEEVFESNGADALRQWAAiGGSPGNDIP 560
                                       **********************************************99987888888875 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 !  122.5   0.0   3.8e-39   1.4e-35       1     148 [.     598     736 ..     598     741 .. 0.88

  Alignments for each domain:
  == domain 1  score: 122.5 bits;  conditional E-value: 3.8e-39
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       drw+ +el+ l+ ++tea+++++f++a++a+  f w+ l+d+y+elvk rly++++ +kraaq +l+++letl rl+
  gi|330507272|ref|YP_004383700.1| 598 DRWLSAELDLLITKTTEAMDRFQFDEALKAIRAFAWDVLADNYIELVKARLYGQDGPEKRAAQGTLFTALETLARLM 674
                                       9******************************************************977777**************** PP

                       Anticodon_1  78 aPfmPfitEelwqreeeelgkkesimlaewpekaeel...ekeleeeevellkeivkairklrselkikpssel 148
                                       aPf+Pf++Ee++    ++    +s+++++wp  a+ +          +   +ke+ +++r++++e++++ +s+l
  gi|330507272|ref|YP_004383700.1| 675 APFTPFLSEEIY----HT-LTGQSVHVQSWPV-AQGQpmdR------AGLAIKEVASTLRRYKAEKGVALNSPL 736
                                       ************....44.34568*******6.43333232......4456799***************99985 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   3.1e-17   1.1e-13       2     131 ..      38     182 ..      37     192 .. 0.79
   2 ?    2.5   0.3     0.014        49     168     239 ..     338     406 ..     312     415 .. 0.80
   3 !   22.6   0.0   1.1e-08   3.8e-05     307     373 ..     501     568 ..     481     576 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 3.1e-17
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTT.S-....HHH....HHHH CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekeg.vt....pee....lvek 69 
                                       ++ t+ pY++g+ H+G++l+    D  aRykr+rg++v+f  g D hG p+e+k e+ + +t    p+e    l+ek
  gi|330507272|ref|YP_004383700.1|  38 IIDTPPPYPTGNFHIGNALNWCYIDFAARYKRMRGYNVMFPQGWDCHGLPTEVKVEQLNhITknqvPREefrrLCEK 114
                                       789999***********************************************998754222111122223337888 PP

                                       HHHHHHHHHHH......TT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE- CS
                      tRNA-synt_1g  70 vheeikelfkk......lnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflp 131
                                        +ee  + f+k      l+i +++ + t + e +  +q  f ++++kg+iy+++  + +cp++++ ++
  gi|330507272|ref|YP_004383700.1| 115 LTEEAIDRFHKsmgrlgLSIDWSNEYATMKPEYYVKTQTSFVRMYQKGQIYREDHPVNWCPRCGTAIA 182
                                       7777666665434443345666677889999999999*************************998766 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.014
                                       .........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EETT CS
                      tRNA-synt_1g 168 ksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvPg 239
                                        +  +++  e+ +++++f +++++e  +k+   ee +  + +++  +++w ++   d++isr+  ++ p+P 
  gi|330507272|ref|YP_004383700.1| 338 LCWRCKTPIEILSEQQWFVRIDALE--IKKMA-EEIEWIPAHMRVRLENWADSMEWDWCISRQRIFATPIPA 406
                                       5777888888889999999999986..55655.44445788889999999999889*************994 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 1.1e-08
                                       TT----S-EEEE--.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHH CS
                      tRNA-synt_1g 307 aelklpkkvvahey.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfve 373
                                       ++++  +++  +++ l  +g+K+SkS ++++ ++e+ e+  ad+lR + a  ++  +D+ f+w+++++
  gi|330507272|ref|YP_004383700.1| 501 EGIRPWDAILINGMaLGEDGHKMSKSLNNFIRPEEVFESNGADALRQWAAIGGSPGNDIPFQWKEITA 568
                                       556666777777763456799*******************************************9875 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00013      0.48      22      91 ..      49     131 ..      45     174 .. 0.65
   2 !   11.6   0.0   3.6e-05      0.13     247     278 ..     516     547 ..     493     566 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                                       --BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEB......B--SHHHHHHHHHTTS-.......HHHHHHHHHHHHHH CS
                      tRNA-synt_1e  22 ashlGhaRslvafDilrrilqalgYdvqfvqnv......tDidDkiikrareeeks.......vkelaekfieefkk 85 
                                       + h+G+a +   +D  +r+ +++gY+v+f q        t++    +++ ++++         +++l+e+ i+ f+k
  gi|330507272|ref|YP_004383700.1|  49 NFHIGNALNWCYIDFAARYKRMRGYNVMFPQGWdchglpTEVKVEQLNHITKNQVPreefrrlCEKLTEEAIDRFHK 125
                                       57***************************886422222344444334433333332444444455556666666666 PP

                                       HHHHTT CS
                      tRNA-synt_1e  86 dleaLn 91 
                                        +  L+
  gi|330507272|ref|YP_004383700.1| 126 SMGRLG 131
                                       666655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.6e-05
                                       EEETTBE--TTTT---BHHHHHTTS-HHHHHH CS
                      tRNA-synt_1e 247 lkiegekmsksLknfitikdvlkkfdprqlRl 278
                                       l  +g+kmsksL+nfi+ ++v+++  + +lR 
  gi|330507272|ref|YP_004383700.1| 516 LGEDGHKMSKSLNNFIRPEEVFESNGADALRQ 547
                                       55689*****************9999999996 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.31   1.1e+03      19      46 ..     203     230 ..     196     241 .. 0.79
   2 !   15.7   0.0   2.3e-06    0.0082      86     143 ..     237     294 ..     231     321 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.31
                     tRNA-synt_1_2  19 seeklevfttrpdtlfGvtfvalapehp 46 
                                       ++ ++e+ t+rp+ l     va+ pe +
  gi|330507272|ref|YP_004383700.1| 203 EDGEIEIATSRPELLAACVAVAVHPEDQ 230
                                       34589**********9999999988876 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.3e-06
                     tRNA-synt_1_2  86 glkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpe 143
                                       g ++  Pi + ++p+     v +++g+g vm +   d++D +++ +++lp++q i   
  gi|330507272|ref|YP_004383700.1| 237 GRTVKVPIFNYSVPVLADPAVDSSFGSGFVMICTFGDKQDVRWWMEHHLPLRQAIDRG 294
                                       678889***********************************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (858 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 5493.33
//
Query:       gi|330507273|ref|YP_004383701.1|  [L=174]
Description: adenylyl cyclase CyaB [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-34  117.9   3.0    5.2e-34  117.7   3.0    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 !  117.7   3.0   2.9e-38   5.2e-34       1     179 []       1     163 [.       1     163 [. 0.90

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 2.9e-38
                                       EEEEEEEEEE-HHHHHHHHHHHHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEEEETTTEEEEEEEEECSSST. CS
                              CYTH   1 miEvEvKflvsaaeyedlelrlaelrakeettveqrdtYydtpdrdlartdeaLRiRraegdgeeltlKgpgvdge. 76 
                                       miEvEvK++ +    ed+++r+a l+a+  + ++  d Y+++p rd++++deaLRiR++ +dg+ lt+Kgp++d++ 
  gi|330507273|ref|YP_004383701.1|   1 MIEVEVKARAR----EDTKERIAALGATSIGVENHLDLYFNSPLRDFKKSDEALRIRIK-EDGARLTYKGPKLDQQt 72 
                                       89*******95....44456699**********************************88.99999**********87 PP

                                       ..EEEEEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEESSHH CS
                              CYTH  77 ..reevegevsreEyeeplsdaaeaaelldglglepvasvkklRrkyklegvevalDaveflegeevEiElevedee 151
                                         r+e+++ ++         d+ ++ ++l+ lg+++ a+v+k+R+ky + g  +alD+ve+l g+++E+E+++e+  
  gi|330507273|ref|YP_004383701.1|  73 ksRRELTIRID---------DPTQMRDILSLLGFVLSAEVRKRRTKYSYQGMVIALDEVEGL-GTFLEVEAQAEANW 139
                                       77777777777.........******************************************.**********9988 PP

                                       HHHHHHHHHHHHHHHTTEEGGGBSCSHH CS
                              CYTH 152 evkeaaekllallrelglssaskirrsy 179
                                       e ++ +   l++l++l l++   irrsy
  gi|330507273|ref|YP_004383701.1| 140 ENEKDRV--LSVLKRLELED--TIRRSY 163
                                       8666444..58888888887..688887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1344.69
//
Query:       gi|330507274|ref|YP_004383702.1|  [L=285]
Description: hypothetical protein MCON_1160 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-75  254.5  17.6    1.6e-75  254.2  17.6    1.1  1  SPP             Signal-peptide peptidase, presenilin aspartyl
    6.8e-05   22.5  18.0    0.00075   19.1  18.0    2.4  1  Peptidase_A22B  Signal peptide peptidase
  ------ inclusion threshold ------
        2.4    8.5  10.1       0.11   12.8   2.0    2.5  3  Cytochrom_B_C   Cytochrome b(C-terminal)/b6/petD
        5.9    5.5  19.4        5.7    5.6   0.0    3.2  2  Presenilin      Presenilin


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 !  254.2  17.6   3.7e-79   1.6e-75       3     283 .]       7     282 ..       5     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 254.2 bits;  conditional E-value: 3.7e-79
                               SPP   3 lfvvvqvlalllavplesaelqatedPtqvlnsvvyivlllvftlfvlivikkdkkliiskviyvivvavifyvflv 79 
                                       ++v vq+ al+++ ++ +++ + +edP   +n ++y++l+l+ft+ +l++ik +  + +++ i + ++++ifyv  +
  gi|330507274|ref|YP_004383702.1|   7 FLVAVQLIALAITPAISATDNRVFEDPASISNPIIYMLLILIFTAILLLAIKLKGDWLVRGFIQISIALTIFYVISA 83 
                                       6899**********************************************************************999 PP

                               SPP  80 llsivlvvaglvnlaslvvaialvvllyaypeWyvidlaGvilavGvsalfGislgvlpavvllialavydaisvyk 156
                                       ++++           +l++++a++ ll+ ypeWy++d+ G++++ Gv++l+G+s++v+p+++l+++lavydaisvyk
  gi|330507274|ref|YP_004383702.1|  84 IMPMW---------LALLPTLAVMLLLHYYPEWYILDAFGILVCAGVTSLLGVSMTVMPVIILMVILAVYDAISVYK 151
                                       99988.........34688999999**************************************************** PP

                               SPP 157 tkhmialaegvvdlklPillvvPetlaysfvee.....afeeaeeaearnvlfiGlGdavlPsilvvsaav.flesh 227
                                       t+hm+alaeg++ +k P+l+vvP++  ysf+ +     ++ + +++  r ++f+G+Gda++Psilv+sa+  +   +
  gi|330507274|ref|YP_004383702.1| 152 TRHMVALAEGAIKMKAPLLFVVPKSRDYSFRRKdavsiSMGNDKKKGDRGAYFLGMGDAIIPSILVISASWsYPPGD 228
                                       ******************************87522211233444445599******************997366666 PP

                               SPP 228 ilaglelavllalaGtlvGllvlsilvlrgrpaaGlPllnsGaiaGfligvlaagv 283
                                       il gl+l++l+a++Gt  G+++l+    r+rp+aGlP+lnsG+i Gfl g laag+
  gi|330507274|ref|YP_004383702.1| 229 IL-GLNLPALGAMLGTYAGFILLMT-TSRDRPQAGLPFLNSGSILGFLAGCLAAGI 282
                                       66.*********************9.9**************************997 PP

>> Peptidase_A22B  Signal peptide peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1  18.0   1.7e-07   0.00075      69     201 ..      65     218 ..       1     222 [. 0.65

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.7e-07
                                       XXXXXXXXXXXXXXX.XXXXXXXXXXXXX------S--XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX CS
                    Peptidase_A22B  69 lkkvelakvklefla.ielkaaeivalllsiviavlwllkrhwilndilglalailviellrlpslkv.galLLvgl 143
                                       ++ + + ++ l++++ i+  + + +all ++++++l    ++w + d++g+ ++  v +ll +    +   +L+v l
  gi|330507274|ref|YP_004383702.1|  65 VRGFIQISIALTIFYvISAIMPMWLALLPTLAVMLLLHYYPEWYILDAFGILVCAGVTSLLGVSMTVMpVIILMVIL 141
                                       334444444444442133333344455556666666667788*************9999999986554156777888 PP

                                       XXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXX...........XXXXXXXXXXXXX.............XXXXXX CS
                    Peptidase_A22B 144 flYDifwVFgtdvmvevAk...eldiPillklPq...........lsneieeaskfsi.............LGlGDi 193
                                        +YD   V+ t  mv++A+   ++++P+l+++P+                    + s+             LG+GD 
  gi|330507274|ref|YP_004383702.1| 142 AVYDAISVYKTRHMVALAEgaiKMKAPLLFVVPKsrdysfrrkdaV--------SISMgndkkkgdrgayfLGMGDA 210
                                       9******************99999*********9877544443330........333233333333333339***** PP

                                       XXXXXXXX CS
                    Peptidase_A22B 194 vlPGllia 201
                                       ++P +l+ 
  gi|330507274|ref|YP_004383702.1| 211 IIPSILVI 218
                                       ***99985 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.4      0.31   1.4e+03      63      81 ..      39      54 ..       3      80 .. 0.44
   2 ?   -1.3   1.4      0.59   2.7e+03      66      84 ..      73      91 ..      34     103 .. 0.48
   3 ?   12.8   2.0   2.4e-05      0.11      10      61 ..     102     155 ..      97     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.31
                                      HHHHHHHHHHHHHHHHHHH CS
                     Cytochrom_B_C 63 plakvllallvvsfvvLgy 81
                                      p+  +l   l++ f ++ +
  gi|330507274|ref|YP_004383702.1| 39 PIIYML---LILIFTAILL 54
                                      222222...2222222222 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.59
                                      HHHHHHHHHHHHHHHHHHT CS
                     Cytochrom_B_C 66 kvllallvvsfvvLgylGv 84
                                       +l ++ v+s+++ ++l+ 
  gi|330507274|ref|YP_004383702.1| 73 IALTIFYVISAIMPMWLAL 91
                                      2233334455555555554 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 2.4e-05
                                       T----GGGHHHHHHHHCS.SSHHHHHHHHHHHHHGGGC.HHHH---SSSSSTT- CS
                     Cytochrom_B_C  10 hIaPeWYflpfYaiLrai.pakllGvvamgaaivilfl.lpwldrskvksiryr 61 
                                       h +PeWY l ++ iL       llGv + ++ ++il++ l + d  +v ++r+ 
  gi|330507274|ref|YP_004383702.1| 102 HYYPEWYILDAFGILVCAgVTSLLGVSMTVMPVIILMViLAVYDAISVYKTRHM 155
                                       678************987578999998888877776651667787777766665 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.7  19.0         4   1.8e+04      59     116 ..      34      91 ..       3     163 .. 0.62
   2 ?    5.6   0.0    0.0013       5.7     316     368 ..     197     252 ..     173     267 .. 0.69

  Alignments for each domain:
  == domain 1  score: -6.7 bits;  conditional E-value: 4
                        Presenilin  59 nsllnalililvivvvtfllvlLykyrcykvikgwlilsslllLflvsglllaevlka 116
                                        s+ n +i +l+i++ t +l+l  k++   +++g++ +s +l +f+v  +++   l  
  gi|330507274|ref|YP_004383702.1|  34 ASISNPIIYMLLILIFTAILLLAIKLKGDWLVRGFIQISIALTIFYVISAIMPMWLAL 91 
                                       6888999999999999999999999999999999998888777776655554433332 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0013
                        Presenilin 316 eseergvkLGLGDFiFYSvLvgkAal...sgdlntvvacfvailiGLclTLllLai 368
                                       ++++++  LG+GD i  S+Lv  A+     gd+  + + +++ ++G  +  +lL +
  gi|330507274|ref|YP_004383702.1| 197 KGDRGAYFLGMGDAIIPSILVISASWsypPGDILGLNLPALGAMLGTYAGFILLMT 252
                                       23445788****************99333356666666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); 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:                        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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2038.20
//
Query:       gi|330507275|ref|YP_004383703.1|  [L=65]
Description: hypothetical protein MCON_1161 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00096   19.1   0.8     0.0015   18.5   0.8    1.4  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
     0.0036   16.8   1.9       0.86    9.2   0.1    2.2  2  RecR            RecR protein
      0.009   15.8   1.9      0.011   15.5   0.2    1.9  2  Cys_rich_KTR    Cysteine-rich KTR
  ------ inclusion threshold ------
      0.065   13.3   1.8       0.11   12.5   1.8    1.4  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.067   12.9   5.2       0.49   10.2   0.2    2.3  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.082   12.8   5.2       0.33   10.9   1.8    2.3  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
      0.084   11.4   0.0      0.089   11.3   0.0    1.0  1  Lon_2           Putative ATP-dependent Lon protease
      0.087   13.0   2.4       0.12   12.5   0.1    1.9  2  zf-Dof          Dof domain, zinc finger
        0.1   11.1   1.8       0.12   10.9   1.8    1.0  1  Terminase_GpA   Phage terminase large subunit (GpA)
       0.19   11.4   3.6       0.34   10.6   0.5    2.5  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
          1    9.2  11.6       0.26   11.0   3.9    2.2  2  zinc_ribbon_2   zinc-ribbon domain
        1.2    9.1   8.9        1.3    8.9   0.4    2.5  2  TFIIS_C         Transcription factor S-II (TFIIS)
        7.6    6.8   7.8        2.1    8.5   2.1    2.2  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like


Domain annotation for each model (and alignments):
>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.8   1.1e-06    0.0015      19      44 ..      14      52 ..       3      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                     Zn_Tnp_IS1595 19 fvCPhCgsr.kayrikt............rglfqCkeCr 44
                                      + CP+Cg++ ++  +++               + Ck C 
  gi|330507275|ref|YP_004383703.1| 14 PFCPKCGNEcEHKDLRRaldadewkkiviETIYYCKNCD 52
                                      55************************************5 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.4    0.0024       3.3      16      28 ..      13      25 ..       8      30 .. 0.84
   2 !    9.2   0.1   0.00062      0.86      13      25 ..      42      54 ..      39      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0024
                                      -EE-TTT--EESS CS
                              RecR 16 vrhCsrCgnltee 28
                                      + +C++Cgn +e+
  gi|330507275|ref|YP_004383703.1| 13 IPFCPKCGNECEH 25
                                      679******7775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00062
                                      HHH-EE-TTT--E CS
                              RecR 13 kekvrhCsrCgnl 25
                                       e++ +C++C n+
  gi|330507275|ref|YP_004383703.1| 42 IETIYYCKNCDNY 54
                                      58899*******9 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   7.9e-06     0.011      20      37 ..       6      23 ..       3      30 .. 0.88
   2 ?   -0.5   0.1      0.81   1.1e+03      28      33 ..      46      51 ..      37      55 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.9e-06
                      Cys_rich_KTR 20 dTvLknfpLfCPKCkqet 37
                                      + vL++f  fCPKC +e+
  gi|330507275|ref|YP_004383703.1|  6 HAVLEHFIPFCPKCGNEC 23
                                      789***********8875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.81
                      Cys_rich_KTR 28 LfCPKC 33
                                       +C  C
  gi|330507275|ref|YP_004383703.1| 46 YYCKNC 51
                                      478877 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.8   7.9e-05      0.11       2      22 ..      16      50 ..      15      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.9e-05
                    DNA_ligase_ZBD  2 CPvCGsavvRee........g......eaiyRCtn 22
                                      CP CG + ++++        +      e iy+C n
  gi|330507275|ref|YP_004383703.1| 16 CPKCGNECEHKDlrraldadEwkkiviETIYYCKN 50
                                      *********999899888761555666******88 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00036      0.49      18      30 ..      10      22 ..       6      25 .. 0.85
   2 ?    4.7   0.9     0.018        25      21      28 ..      45      52 ..      43      54 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00036
                     A2L_zn_ribbon 18 eqgylvCieCgas 30
                                      e+++ +C++Cg++
  gi|330507275|ref|YP_004383703.1| 10 EHFIPFCPKCGNE 22
                                      78899******86 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.018
                     A2L_zn_ribbon 21 ylvCieCg 28
                                      +++C++C 
  gi|330507275|ref|YP_004383703.1| 45 IYYCKNCD 52
                                      67777775 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 ?   10.9   1.8   0.00024      0.33       3       9 ..      15      21 ..      13      27 .. 0.89
   2 ?    3.4   0.1     0.052        71      22      28 ..      46      52 ..      32      54 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                                      BESTTTS CS
                    RNA_POL_M_15KD  3 FCpkCgN 9 
                                      FCpkCgN
  gi|330507275|ref|YP_004383703.1| 15 FCPKCGN 21
                                      ******9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.052
                                      EEESSSS CS
                    RNA_POL_M_15KD 22 feCrqCg 28
                                      + C +C+
  gi|330507275|ref|YP_004383703.1| 46 YYCKNCD 52
                                      6677775 PP

>> Lon_2  Putative ATP-dependent Lon protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.4e-05     0.089     141     183 ..       5      47 ..       1      54 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.4e-05
                             Lon_2 141 spfviedlkpiqlskvdleelkeaRkeftkeeWidlllrsvgl 183
                                       +  v+e++ p++++  +  e k+ R+++  +eW +++++++ +
  gi|330507275|ref|YP_004383703.1|   5 DHAVLEHFIPFCPKCGNECEHKDLRRALDADEWKKIVIETIYY 47 
                                       567899*********************************9976 PP

>> zf-Dof  Dof domain, zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.5      0.69   9.5e+02       6      10 ..      16      20 ..      13      27 .. 0.79
   2 ?   12.5   0.1     9e-05      0.12      29      41 ..      46      58 ..      41      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.69
                            zf-Dof  6 CprCe 10
                                      Cp+C 
  gi|330507275|ref|YP_004383703.1| 16 CPKCG 20
                                      99996 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9e-05
                            zf-Dof 29 yfCkaCrryWtkg 41
                                      y+Ck+C  yW +g
  gi|330507275|ref|YP_004383703.1| 46 YYCKNCDNYWSDG 58
                                      9*********987 PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.8   8.5e-05      0.12     195     239 ..      10      57 ..       5      62 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.5e-05
                     Terminase_GpA 195 rryyvpCphCgelqels.fer.lkwpege...aeekaryvCphcgsliee 239
                                       +++   Cp+Cg++ e +  +r l    +e      ++ y C++c+  +++
  gi|330507275|ref|YP_004383703.1|  10 EHFIPFCPKCGNECEHKdLRRaLDA--DEwkkIVIETIYYCKNCDNYWSD 57 
                                       588999*******996644442333..22334688999********9987 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5   0.00025      0.34       4      15 ..      14      25 ..      14      27 .. 0.80
   2 ?   -1.6   0.0       1.7   2.3e+03      17      22 ..      34      39 ..      31      40 .. 0.77
   3 ?    0.5   0.1      0.36     5e+02      23      29 ..      47      53 ..      43      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                     zf-NADH-PPase  4 rFCgrCGaptep 15
                                      +FC++CG ++e 
  gi|330507275|ref|YP_004383703.1| 14 PFCPKCGNECEH 25
                                      5******88776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
                     zf-NADH-PPase 17 eggwar 22
                                      +++w++
  gi|330507275|ref|YP_004383703.1| 34 ADEWKK 39
                                      78**97 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.36
                     zf-NADH-PPase 23 vCpaCgl 29
                                       C +C++
  gi|330507275|ref|YP_004383703.1| 47 YCKNCDN 53
                                      5999986 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.9   0.00019      0.26       1      10 [.      15      24 ..      15      27 .. 0.83
   2 ?    2.7   0.9     0.078   1.1e+02       1       5 [.      47      51 ..      47      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                     zinc_ribbon_2  1 fCpnCGaelq 10
                                      fCp+CG+e +
  gi|330507275|ref|YP_004383703.1| 15 FCPKCGNECE 24
                                      8999999975 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.078
                     zinc_ribbon_2  1 fCpnC 5 
                                      +C+nC
  gi|330507275|ref|YP_004383703.1| 47 YCKNC 51
                                      79999 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.9     0.043        59       3       9 ..      16      22 ..      15      31 .. 0.89
   2 ?    8.9   0.4   0.00093       1.3      27      38 ..      44      55 ..      33      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.043
                           TFIIS_C  3 CpkCgsr 9 
                                      CpkCg++
  gi|330507275|ref|YP_004383703.1| 16 CPKCGNE 22
                                      9999986 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00093
                           TFIIS_C 27 vfykCtkCghrW 38
                                      ++y C++C + W
  gi|330507275|ref|YP_004383703.1| 44 TIYYCKNCDNYW 55
                                      6899******99 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 ?    8.5   2.1    0.0016       2.1      25      32 ..      15      22 ..      10      44 .. 0.85
   2 ?    1.9   0.3      0.18   2.5e+02      23      31 ..      45      53 ..      37      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                      NOB1_Zn_bind 25 FCpkCGnk 32
                                      FCpkCGn+
  gi|330507275|ref|YP_004383703.1| 15 FCPKCGNE 22
                                      ******96 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.18
                      NOB1_Zn_bind 23 kkFCpkCGn 31
                                        +C++C n
  gi|330507275|ref|YP_004383703.1| 45 IYYCKNCDN 53
                                      568999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 500.50
//
Query:       gi|330507276|ref|YP_004383704.1|  [L=373]
Description: histone deacetylase family protein [Methanosaeta concilii GP6]
Scores for complete 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-77  259.0   0.0    9.3e-77  258.5   0.0    1.2  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.5   0.0   5.2e-81   9.3e-77       1     306 [.      19     307 ..      19     308 .. 0.94

  Alignments for each domain:
  == domain 1  score: 258.5 bits;  conditional E-value: 5.2e-81
                                       SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiaskll 77 
                                       hp np Rl    + ++e +gl+de  +  +p++a++e++l+vH++eYl +++  + +l                 l 
  gi|330507276|ref|YP_004383704.1|  19 HPFNPARLMLTFSLMEE-SGLIDEKVCRLEPRPASEEDILRVHTPEYLAAVKLEEPDLAF--------------GLG 80 
                                       899******55555555.5*******************************9843333222..............356 PP

                                       SSSTHCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  78 dddtpvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrv 154
                                       +ddtpv+ ++ + +++ +ga+++a+++++ +  ++    + ++ HHa ++ asGFC++ + a+ai++l++  +++rv
  gi|330507276|ref|YP_004383704.1|  81 SDDTPVFAGICESSRMLAGASIDAARRIIAE--DCSAFNIGGGLHHALPTVASGFCVFDDPALAIRVLRD--GFDRV 153
                                       899**************************99..78888889*****************************..999** PP

                                       EEEE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 155 ailDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilr 231
                                       +++D+D HhG+G++++fy dp+vlt+S+H+++  ++Pgtg +e++g g+gkg+++n+p++ ++gde+yl++f++i+ 
  gi|330507276|ref|YP_004383704.1| 154 LYIDIDGHHGDGVQQIFYTDPTVLTISMHESGLYLFPGTGFIEETGDGEGKGYSVNIPMPMYSGDEQYLRAFDQIVP 230
                                       ****************************************************************************9 PP

                                       HHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-.G..EEEEE-S---HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 232 pvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkv.k.kvvllleGGYnlealaravtavlsa 306
                                        ++e f+P++++ ++G+D++ +dpl +ln++ +gy+ l++++++la+++ + ++++l++GGYn+e +++a+t+vl++
  gi|330507276|ref|YP_004383704.1| 231 ILFEWFRPQAVVAQLGIDTHYSDPLTSLNVTLNGYTGLVRRIVDLARQHsGsRLLALGGGGYNMEVVPTAWTSVLHI 307
                                       99***********************************************989**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2855.52
//
Query:       gi|330507277|ref|YP_004383705.1|  [L=270]
Description: putative L-aspartate dehydrogenase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-32  112.4   0.2    1.9e-32  111.4   0.2    1.5  1  DUF108           Domain of unknown function DUF108
      1e-20   74.5   1.7    1.5e-20   74.0   1.7    1.3  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    2.6e-08   34.0   0.3    4.8e-08   33.2   0.2    1.5  2  DapB_N           Dihydrodipicolinate reductase, N-terminus
    5.3e-07   30.1   2.3    1.3e-06   28.9   2.3    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    1.6e-05   25.7   0.4    3.1e-05   24.8   0.4    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    0.00023   20.6   0.1    0.00035   20.0   0.1    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00059   20.1   1.2     0.0013   18.9   1.1    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0015   18.6   0.3     0.0029   17.7   0.3    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.041   14.3   0.4      0.072   13.5   0.4    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      0.049   13.0   2.2       0.36   10.1   2.2    2.1  1  ThiF             ThiF family
       0.13   12.3   1.0       0.28   11.3   1.0    1.5  1  AKAP7_RIRII_bdg  PKA-RI-RII subunit binding domain of A-kinas


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 !  111.4   0.2   1.2e-35   1.9e-32       2      89 .]     170     256 ..     169     256 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 1.2e-35
                                       SS-EEEEEEEHHHHHHHSTTS-CHHHHHHHHHH.CCGEEEEEEEETT-SSEEEEEEEEETTEEEEEEEEE-EETTEE CS
                            DUF108   2 teptvlFeGsareaikkfPknvNvaaalaLaalgfdrvkvelvadpnldkniheieveGsfgefslevenkpspenP 78 
                                       + pt +F+Gsa ea+++fP+nvNvaa+l Laa g ++v v+++adpn++ n+heieveG+fg+f ++ven+psp+nP
  gi|330507277|ref|YP_004383705.1| 170 SGPTQIFSGSAIEAVRAFPANVNVAATLYLAA-GEKEVLVKVFADPNIRVNRHEIEVEGDFGRFFTRVENVPSPRNP 245
                                       5799****************************.99****************************************** PP

                                       EEEHHHHHHHH CS
                            DUF108  79 ktsalaalsvi 89 
                                       kts+laals+i
  gi|330507277|ref|YP_004383705.1| 246 KTSYLAALSAI 256
                                       *********86 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   1.7   9.4e-24   1.5e-20       1     117 []       9     121 ..       9     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 9.4e-24
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHH CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvl 77 
                                       G+GaiG +++++++++    ++el av+d++++++ +  + l+ +++ +dl +l++    dvvVE+as++av  ++ 
  gi|330507277|ref|YP_004383705.1|   9 GCGAIGAEIAKAIDSGVV--DAELIAVCDHNPQTALALIESLQHKTKKADLAELVR--LSDVVVEAASQKAVPAVAR 81 
                                       9***************97..8**********66666666899999***********..******************* PP

                                       HHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                     NAD_binding_3  78 kaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                                       +aL+agk ++++++galad++l++e+ ++a+++  ++y++
  gi|330507277|ref|YP_004383705.1|  82 AALAAGKRLMIMSVGALADMDLFREIKSLAKSHCSQVYIP 121
                                       *********************************9999976 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.2   2.9e-11   4.8e-08       2     118 ..       4     117 ..       3     122 .. 0.81
   2 ?   -3.1   0.0         5   8.2e+03      47      72 ..     183     208 ..     173     222 .. 0.65

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.9e-11
                                       EEEEETTTSHHHHHHHHHHHH.STTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEB.SSHHHHHHH-SEEEE-S- CS
                            DapB_N   2 kvavvGasGrmGkevvkavee.aedlelvaavdrkeselegkdagellglgklgvavt.ddleevlekadvliDFTt 76 
                                       kv++vG+ G +G e++ka+++   d+el a+ d++++         l+ +++l+ +++ +dl+e+++ +dv+++  +
  gi|330507277|ref|YP_004383705.1|   4 KVGLVGC-GAIGAEIAKAIDSgVVDAELIAVCDHNPQ-------TALALIESLQHKTKkADLAELVRLSDVVVEAAS 72 
                                       9******.************9669***********93.......3445555666666559***************** PP

                                       HHHHHHHHHHHHHTT-EEEE--SS-..-HHHHHHHHHHTTT.SEE CS
                            DapB_N  77 peavlenlklalekgvklViGTTGl..seeelaeleelakk.igv 118
                                        +av +++++al++g++l i + G   + +   e+++lak+  + 
  gi|330507277|ref|YP_004383705.1|  73 QKAVPAVARAALAAGKRLMIMSVGAlaDMDLFREIKSLAKShCSQ 117
                                       ******************998888755555567777777665555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5
                                       HSSSS--S-BEBSSHHHHHHH-SEEE CS
                            DapB_N  47 llglgklgvavtddleevlekadvli 72 
                                       ++  ++ +v+v ++l  ++ + +vl+
  gi|330507277|ref|YP_004383705.1| 183 AVRAFPANVNVAATLYLAAGEKEVLV 208
                                       44555566666666666666666665 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 !   28.9   2.3   7.8e-10   1.3e-06       1      84 [.       4      85 ..       4      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 7.8e-10
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevls 79
                                      k+g++G+G +g+ +a+ ++ +g+ + e++ +++ np++a +l e+l+ k+++ d +e+++ +dvvv a   ++v++v++
  gi|330507277|ref|YP_004383705.1|  4 KVGLVGCGAIGAEIAK-AIDSGVVDAELIAVCDHNPQTALALIESLQHKTKKADLAELVRLSDVVVEAASQKAVPAVAR 81
                                      79*************9.999***777777799**********************************************9 PP

                                      HCGHH CS
                     F420_oxidored 80 elakd 84
                                      ++  +
  gi|330507277|ref|YP_004383705.1| 82 AA-LA 85
                                      88.33 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.4   1.9e-08   3.1e-05       1      90 [.       3      91 ..       3      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.9e-08
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngtheel 78
                                      l+v+++G+G ig + ++++     ++e++a++d +++ a a+ es++++   +dl+el++    d+v+ a   +   ++
  gi|330507277|ref|YP_004383705.1|  3 LKVGLVGCGAIGAEIAKAIDSGVVDAELIAVCDHNPQTALALIESLQHKtKKADLAELVR--LSDVVVEAASQKAVPAV 79
                                      689**********************************************8889999**99..77999989999999999 PP

                                      HHHHHHTT-EEE CS
                      GFO_IDH_MocA 79 akaaleagkhvl 90
                                      a+aal+agk ++
  gi|330507277|ref|YP_004383705.1| 80 ARAALAAGKRLM 91
                                      ******999776 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 !   20.0   0.1   2.2e-07   0.00035      38      98 ..       4      70 ..       2      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.2e-07
                                      EEEEES-SHHHHHHHHHHH..HTT-EEEEESSSHHHHH....CHHHHTCEECSHHHHHHH-SEEEE- CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk..afgmkviaydrskkkee....eeeelgvelvsleellaesDivslh 98
                                      +vG++G+G+IG ++ak +    +++++ia+  ++ +++    e  +++ ++++l el++ sD+v+ +
  gi|330507277|ref|YP_004383705.1|  4 KVGLVGCGAIGAEIAKAIDsgVVDAELIAVCDHNPQTAlaliESLQHKTKKADLAELVRLSDVVVEA 70
                                      79****************9767999999987776666678877777788999************865 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 !   18.9   1.1   8.2e-07    0.0013       1     101 [.       5      95 ..       5     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 8.2e-07
                                       EEEE--SHHHHHHHHHHHCTCCT-G.EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE- CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvda.eitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnl 76 
                                       v ++G+G++G  +a+ +     vda  i+v+d + + + al++          +l+ + ++a La+l++  d+vv +
  gi|330507277|ref|YP_004383705.1|   5 VGLVGCGAIGAEIAKAIDSG-VVDAeLIAVCDHNPQTALALIE----------SLQHKTKKADLAELVRLSDVVVEA 70 
                                       6789***********99886.5667588888888888666654..........45555555558889999******* PP

                                       SSGGGHHHHHHHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  77 sppissldvlkaCietgvhyvdtsi 101
                                       + +    +v++a++++g + +  s+
  gi|330507277|ref|YP_004383705.1|  71 ASQKAVPAVARAALAAGKRLMIMSV 95 
                                       *****************98876665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   1.8e-06    0.0029      14      96 ..       4      85 ..       2     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.8e-06
                                      EEEEES-SHHHHHHHHHHHCC..T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS.-S CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlak..gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatasee.pi 89
                                      kv l+G G ++ ++ak++ +    ++ ++v   + + a +l e+l+++    +k  +l el++ +dvv+ a + +  p 
  gi|330507277|ref|YP_004383705.1|  4 KVGLVGCGAIGAEIAKAIDSGvvDAELIAVCDHNPQTALALIESLQHK----TKKADLAELVRLSDVVVEAASQKAvPA 78
                                      799***************99855677899****************666....7788999999*******9988765244 PP

                                      B-HHHHH CS
                      Shikimate_DH 90 lekeeve 96
                                      + ++++ 
  gi|330507277|ref|YP_004383705.1| 79 VARAALA 85
                                      5555544 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   4.4e-05     0.072       1      92 [.       4      89 ..       4     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.4e-05
                                      EEEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGC.TT-SEEEE-SCHH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeel.kevdivflalpag 77
                                      kv++vG  G++G+e+++ +++   ++el++++ ++ +   +l e  +        k +++d +el +  d+v+ a++++
  gi|330507277|ref|YP_004383705.1|  4 KVGLVG-CGAIGAEIAKAIDSgVVDAELIAVCDHNPQTALALIESLQ-------HKTKKADLAELvRLSDVVVEAASQK 74
                                      79****.9*************9999********99977776666655.......333444444444999********** PP

                                      HHHHHHHHHHHTTSE CS
                    Semialdhyde_dh 78 vskelapklaeagvk 92
                                      +  ++a+++++ag +
  gi|330507277|ref|YP_004383705.1| 75 AVPAVARAALAAGKR 89
                                      ************985 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.2   0.00022      0.36      20      37 ..       4      21 ..       2     263 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                                      EEEEE--SHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                              ThiF 20 kvllvGaGglGsellknL 37
                                      kv lvG+G++G e++k++
  gi|330507277|ref|YP_004383705.1|  4 KVGLVGCGAIGAEIAKAI 21
                                      899************986 PP

>> AKAP7_RIRII_bdg  PKA-RI-RII subunit binding domain of A-kinase anchor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.0   0.00017      0.28       4      24 ..      56      76 ..      53      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                   AKAP7_RIRII_bdg  4 dDAELvrLSKRLVENAVLKAV 24
                                      d AELvrLS  +VE A  KAV
  gi|330507277|ref|YP_004383705.1| 56 DLAELVRLSDVVVEAASQKAV 76
                                      67******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1898.62
//
Query:       gi|330507278|ref|YP_004383706.1|  [L=282]
Description: nicotinate-nucleotide diphosphorylase (carboxylating) [Methanosaeta concilii GP6]
Scores for complete sequence (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  190.9   0.0    5.5e-56  189.0   0.0    1.7  2  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
    1.6e-20   72.9   0.0    3.8e-20   71.8   0.0    1.6  1  QRPTase_N       Quinolinate phosphoribosyl transferase, N-ter
     0.0023   17.8   0.1     0.0055   16.5   0.1    1.6  1  KDGP_aldolase   KDGP aldolase
  ------ inclusion threshold ------
       0.15   11.4   0.6        1.4    8.2   0.1    2.5  3  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family


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 ?   -0.7   0.0      0.23     1e+03      45      80 ..      52      88 ..      34      94 .. 0.78
   2 !  189.0   0.0   1.2e-59   5.5e-56       1     169 []     101     268 ..     101     268 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.23
                                      -TSSTTTSEEE-HH.HHHHHSSHHHHHHHHHHHHTTT CS
                         QRPTase_C 45 hrlgLsdmvlikdn.hiaaagsiveavksvreavdke 80
                                      +++gL++ +l  d   + a++ + e+v s+r+ ++ e
  gi|330507278|ref|YP_004383706.1| 52 QYFGLKSELLFDDGeFVPAMSTVLEVVGSARKILQSE 88
                                      6899999999998624567777999999999988765 PP

  == domain 2  score: 189.0 bits;  conditional E-value: 1.2e-59
                                       HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvreav 77 
                                       i tlt+++v  a ++  r+++TRkttPg+rl+ek+Av++GGgd+hr++Lsd++likdnhi+++g ++e +++++++ 
  gi|330507278|ref|YP_004383706.1| 101 ISTLTRECVLLAGGV--RVAATRKTTPGFRLFEKRAVYLGGGDTHRFNLSDAILIKDNHIMILG-LKECLRRAKDKS 174
                                       7899********998..9**********************************************.************ PP

                                       TTTSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT..SEEEEESS--TTTHHHHHCTT-SEE CS
                         QRPTase_C  78 dkevkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkr..vlievSGgvtlenveeyaksgvdvi 152
                                       ++++kieve+esle++  +++++adiim+Dn+++ ++++ v++lk+   r  v++e+SGg+tl+n+++y +sgvdvi
  gi|330507278|ref|YP_004383706.1| 175 SFTKKIEVEIESLEDMLIAAKEGADIIMFDNMDPAKIAEGVDVLKKEGLRerVILEASGGITLDNIKDYGRSGVDVI 251
                                       ********************************************88777777************************* PP

                                       EECHHCHTB----EEEE CS
                         QRPTase_C 153 svgalthsvkalDislk 169
                                       s+galt++++++D+sl+
  gi|330507278|ref|YP_004383706.1| 252 SLGALTKNARWIDLSLE 268
                                       ***************95 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.0   8.4e-24   3.8e-20      10      89 .]      21      99 ..      14      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 8.4e-24
                                      HHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHHHH CS
                         QRPTase_N 10 alipeekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLnllqrl 88
                                      +++++e +a + iiake+++++Gl++a e+f+++ gl+ ell++DGe v +  ++le+ G+ar++l+ ER++Ln++ r+
  gi|330507278|ref|YP_004383706.1| 21 STLIPELTACGIIIAKEDCIISGLAEAVEIFQYF-GLKSELLFDDGEFVPAMSTVLEVVGSARKILQSERLVLNFMARM 98
                                      4788999999************************.******************************************** PP

                                      H CS
                         QRPTase_N 89 S 89
                                      S
  gi|330507278|ref|YP_004383706.1| 99 S 99
                                      9 PP

>> KDGP_aldolase  KDGP aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.2e-06    0.0055     125     193 ..     172     242 ..     169     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-06
                                       CCHHHSS--EEEHHHHHHHH..HHCT--EEEE---TTTTTHHHHHHHHHHHHHCT-EEEEBSS--TTTHHH CS
                     KDGP_aldolase 125 pessqkekaivsvetaiall..kdmggssvkffpmeGlkrleelaavakaaakkgltlePtGGidldnfee 193
                                       ++ss ++k++v++e   ++l  ++ g++ + f  m+  k  e + ++ k   ++ ++le +GGi ldn++ 
  gi|330507278|ref|YP_004383706.1| 172 DKSSFTKKIEVEIESLEDMLiaAKEGADIIMFDNMDPAKIAEGVDVLKKEGLRERVILEASGGITLDNIKD 242
                                       56788999999999988876225679999***************************************985 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.15   6.5e+02      34      56 ..      63      86 ..      48     100 .. 0.81
   2 ?   -1.1   0.0      0.22     1e+03      21      35 ..     193     207 ..     179     214 .. 0.78
   3 ?    8.2   0.1   0.00032       1.4     165     194 ..     225     254 ..     209     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.15
                                      EBSSSSS-B-B-HHHHHHHGGG.E CS
                    Ribul_P_3_epim 34 mDghfvpNltigplvvealrkl.t 56
                                       Dg+fvp ++   +vv + rk+ +
  gi|330507278|ref|YP_004383706.1| 63 DDGEFVPAMSTVLEVVGSARKIlQ 86
                                      599999999999999999888743 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.22
                                       HHHTT-SEEEEEEEB CS
                    Ribul_P_3_epim  21 veeagadllHvDvmD 35 
                                       + ++gad++ +D mD
  gi|330507278|ref|YP_004383706.1| 193 AAKEGADIIMFDNMD 207
                                       457899999999999 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00032
                                       ---EEEEESS--TTTCHHHHHHT--EEEES CS
                    Ribul_P_3_epim 165 ldlkievDGGvkldnieqiaeagadvlVag 194
                                         + +e+ GG++ldni+   + g+dv+  g
  gi|330507278|ref|YP_004383706.1| 225 ERVILEASGGITLDNIKDYGRSGVDVISLG 254
                                       567899********************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2221.28
//
Query:       gi|330507279|ref|YP_004383707.1|  [L=400]
Description: hypothetical protein MCON_1165 [Methanosaeta concilii GP6]
Scores for 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-15   54.5   0.2    2.4e-11   43.3   0.1    2.5  2  TRAP_beta     Translocon-associated protein beta (TRAPB)
    3.4e-10   40.1   0.0    1.4e-09   38.1   0.0    2.1  3  DUF11         Domain of unknown function DUF11
    1.2e-05   25.5   0.3    0.00027   21.1   0.1    2.7  3  CARDB         CARDB
    4.4e-05   22.5   2.9    0.00011   21.2   0.2    2.4  3  BatD          Oxygen tolerance
  ------ inclusion threshold ------
      0.034   14.4   0.0        1.3    9.3   0.0    2.7  2  NPCBM_assoc   NPCBM-associated, NEW3 domain of alpha-galactos
      0.036   13.5   0.6       0.63    9.5   0.1    2.5  3  Peptidase_A4  Peptidase A4 family
      0.038   14.2   2.1        3.1    8.1   0.1    3.4  3  YDG           YDG domain
        5.9    7.3   6.4        4.9    7.6   0.7    2.2  2  BatA          Aerotolerance regulator N-terminal


Domain annotation for each model (and alignments):
>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.1   1.1e-14   2.4e-11      17     128 ..     148     255 ..     137     264 .. 0.88
   2 !    8.4   0.0   0.00059       1.3      41     102 ..     286     345 ..     282     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.1e-14
                         TRAP_beta  17 sarvlvkKkilnrllvegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvve 93 
                                       ++ ++v+K++ +   + g ++ v++ti+N G+ +A +++l Dd  p  +F+ v g   +  ++l+pg++ s ++++ 
  gi|330507279|ref|YP_004383707.1| 148 KPALTVQKSFDKSEMSVGDEVKVTVTIMNKGTGKAQNIKL-DDAPPLPEFSYVAGYPPKIKDTLDPGQSDSAVYMMN 223
                                       567999*****999999**********************9.55678889**************************** PP

                         TRAP_beta  94 pkksgsfngtaavvtYresekgaelqlalssepge 128
                                       + k+g +  +a  v+Y++s++   ++l  ssep+ 
  gi|330507279|ref|YP_004383707.1| 224 AIKEGTIRVSAIQVSYTDSKD---NVLLNSSEPFD 255
                                       ****************77666...66666666655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00059
                         TRAP_beta  41 ytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvvepkksgsfng 102
                                       ++i NvG+++A+ ++++ d  p+   e  +   + ++  ++pg +v++s+++  k sg++ +
  gi|330507279|ref|YP_004383707.1| 286 ISIENVGKAPATRIEAKGDIKPPVGLEASG--FERSFFEIPPGGEVNYSVMLSGKDSGNYTI 345
                                       788999999999999998888887766544..6778899*******************9976 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   6.4e-13   1.4e-09       1      82 [.     153     228 ..     153     251 .. 0.88
   2 ?   -2.5   0.0       2.9   6.6e+03      13      31 ..     279     297 ..     257     308 .. 0.71
   3 ?   -2.7   0.0       3.4   7.7e+03      10      22 ..     323     335 ..     312     345 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 6.4e-13
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlP.aglayvsvsasqgtasaltsv.gsLeagesatlsft 75 
                                       ++K++dkse+  Gd+v++t+t  N g+ +a+++++ D +P + ++yv +           ++  +L +g+s    + 
  gi|330507279|ref|YP_004383707.1| 153 VQKSFDKSEMSVGDEVKVTVTIMNKGTGKAQNIKLDDAPPlPEFSYVAGYPP--------KIkDTLDPGQSDSAVYM 221
                                       79***************************************99999999998........44478888888888877 PP

                             DUF11  76 vrvtrta 82 
                                       +++ +++
  gi|330507279|ref|YP_004383707.1| 222 MNAIKEG 228
                                       7776665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.9
                             DUF11  13 GdtvtytltvtNtgpasan 31 
                                       G+t   ++   N g a+a+
  gi|330507279|ref|YP_004383707.1| 279 GGTGMANISIENVGKAPAT 297
                                       5555556777777777775 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.4
                             DUF11  10 vrpGdtvtytltv 22 
                                       + pG++v+y + +
  gi|330507279|ref|YP_004383707.1| 323 IPPGGEVNYSVML 335
                                       5678888887765 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   1.2e-07   0.00027       1      40 [.     148     187 ..     148     190 .. 0.95
   2 ?   -3.5   0.0       5.5   1.2e+04      50      56 ..     228     234 ..     206     246 .. 0.48
   3 ?    1.3   0.0      0.19   4.2e+02      24      81 ..     285     346 ..     263     355 .. 0.58

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                                       S--EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEE CS
                             CARDB   1 tpDLtvtntlnpseafvgeentitvtvkNqGtaasgatkv 40 
                                       +p Ltv++++  se++vg+e+++tvt+ N+Gt++++++k+
  gi|330507279|ref|YP_004383707.1| 148 KPALTVQKSFDKSEMSVGDEVKVTVTIMNKGTGKAQNIKL 187
                                       589*********************************9986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.5
                                       EEEEESE CS
                             CARDB  50 gtvtvps 56 
                                       gt+ v++
  gi|330507279|ref|YP_004383707.1| 228 GTIRVSA 234
                                       2333332 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.19
                                       EEEEEE-SSS-EEEEEEEEEETTEEE.....EEEEESEE-CTEEEEEEEEEE-S-S-CEEEEE CS
                             CARDB  24 tvtvkNqGtaasgatkvalyldgelv.....gtvtvpsLaagesttvsftwtteategevtlt 81 
                                       +++++N G+a ++ ++++  +   +       + +  ++ +g++++ s+    +  +g++t+ 
  gi|330507279|ref|YP_004383707.1| 285 NISIENVGKAPATRIEAKGDIKPPVGleasgFERSFFEIPPGGEVNYSVMLSGK-DSGNYTIH 346
                                       567777777777766665444333322221111222455566666666666666.66666655 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   4.9e-08   0.00011     260     365 ..     148     245 ..     138     277 .. 0.83
   2 ?   -2.3   0.0      0.64   1.4e+03      76      92 ..     330     346 ..     327     357 .. 0.79
   3 ?    0.5   0.4     0.093   2.1e+02     427     450 ..     375     396 ..     342     399 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.9e-08
                              BatD 260 lPadFsgavgsfslsaslskdelkvgepltltvtisGtG.....NlkllqlPelnfpegfevYdpkpedntkktgng 331
                                       +Pa        ++++ s++k+e++vg+ + +tvti  +G     N+kl  +P+l++ + +  Y+pk +d+ ++ +  
  gi|330507279|ref|YP_004383707.1| 148 KPA--------LTVQKSFDKSEMSVGDEVKVTVTIMNKGtgkaqNIKLDDAPPLPEFSYVAGYPPKIKDTLDPGQ-- 214
                                       555........999*********************65554477889999999999999********999999876.. PP

                              BatD 332 lsGsrteeyalvPrkaGkytipaiefsyFDtatk 365
                                          s +  y++ + k+G++ + ai++sy D + +
  gi|330507279|ref|YP_004383707.1| 215 ---SDSAVYMMNAIKEGTIRVSAIQVSYTDSKDN 245
                                       ...4556688999999999999999999888766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.64
                              BatD  76 twtytLapkkeGtltIp 92 
                                        ++++L  k +G++tI 
  gi|330507279|ref|YP_004383707.1| 330 NYSVMLSGKDSGNYTIH 346
                                       59999999999999995 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.093
                              BatD 427 lfwlllllplllfvvllllwrkrr 450
                                         +llll+p++++  + +l+r+ r
  gi|330507279|ref|YP_004383707.1| 375 YEYLLLLIPIIII--AAWLYRRHR 396
                                       4468888888877..566666655 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 ?    9.3   0.0   0.00058       1.3       3      31 ..     164     192 ..     162     221 .. 0.86
   2 ?    2.0   0.0      0.11   2.5e+02       7      59 ..     282     335 ..     278     351 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00058
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslP 31 
                                        G++v++t+t+ n+gt  a+n++l+   P
  gi|330507279|ref|YP_004383707.1| 164 VGDEVKVTVTIMNKGTGKAQNIKLDDAPP 192
                                       69*********************975555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                       NPCBM_assoc   7 vtltltvtndgtaaatnvsls..lslPeGWtvvevspasaaslapGetveatvkV 59 
                                          ++++ n g+a+at+++ +  ++ P G +++ +  +s+ +++pG +v   v++
  gi|330507279|ref|YP_004383707.1| 282 GMANISIENVGKAPATRIEAKgdIKPPVGLEASGF-ERSFFEIPPGGEVNYSVML 335
                                       56688999999999999987522566888884444.4566688888877766655 PP

>> Peptidase_A4  Peptidase A4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       3.3   7.5e+03      85     102 ..      39      56 ..      37      57 .. 0.82
   2 ?    9.5   0.1   0.00028      0.63      86     114 ..     154     182 ..     145     187 .. 0.88
   3 ?    1.5   0.0     0.078   1.7e+02      92     121 ..     321     350 ..     308     369 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.3
                      Peptidase_A4  85 yavdfsglavsaGDsvtv 102
                                       + v+++++++  GD++ +
  gi|330507279|ref|YP_004383707.1|  39 DEVTYNDFTLGIGDRIDI 56 
                                       568899999*****9975 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00028
                      Peptidase_A4  86 avdfsglavsaGDsvtvtvtatsatsgtv 114
                                       + +f++ ++s GD+v+vtvt+ ++ +g++
  gi|330507279|ref|YP_004383707.1| 154 QKSFDKSEMSVGDEVKVTVTIMNKGTGKA 182
                                       56789999**************9998876 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.078
                      Peptidase_A4  92 lavsaGDsvtvtvtatsatsgtvtieNlst 121
                                       +++ +G +v  +v  ++++sg++ti  ++t
  gi|330507279|ref|YP_004383707.1| 321 FEIPPGGEVNYSVMLSGKDSGNYTIHLKTT 350
                                       899*********************975555 PP

>> YDG  YDG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.42   9.3e+02      32      68 ..      28      59 ..      21      63 .. 0.60
   2 ?    2.7   0.1     0.065   1.4e+02      38      75 ..     144     182 ..     130     190 .. 0.61
   3 ?    8.1   0.1    0.0014       3.1      63      84 ..     329     349 ..     325     350 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.42
                               YDG 32 gvvsgvvagdtvtvttgtasfddknvGtnktvtvsgl 68
                                      g v+g  a d+   +    +++d   G++  + +s++
  gi|330507279|ref|YP_004383707.1| 28 GAVQG--A-DDD--DDDEVTYNDFTLGIGDRIDISNY 59
                                      44455..1.222..23455888888888888887776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.065
                               YDG  38 vagdtvtvttgtasfddknv..GtnktvtvsgltlsGada 75 
                                        +gd+ ++ t   sfd  +   G++ +vtv+ ++ + ++a
  gi|330507279|ref|YP_004383707.1| 144 SSGDKPAL-TVQKSFDKSEMsvGDEVKVTVTIMNKGTGKA 182
                                       44588888.6667776665411777777766433333344 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0014
                               YDG  63 vtvsgltlsGadagNYtlaatt 84 
                                       v++s + lsG+d+gNYt++ +t
  gi|330507279|ref|YP_004383707.1| 329 VNYS-VMLSGKDSGNYTIHLKT 349
                                       5655.899*********96555 PP

>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.6     0.082   1.8e+02      58      75 ..       6      23 ..       3      24 .. 0.82
   2 ?    7.6   0.7    0.0022       4.9      12      32 ..     378     397 ..     368     400 .] 0.83

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.082
                              BatA 58 llllLrllalallvlalA 75
                                       l +Lrl++la+l+l l+
  gi|330507279|ref|YP_004383707.1|  6 HLDILRLVCLAVLILLLS 23
                                      56689*********9987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0022
                              BatA  12 allllplpiillyllkrrpqe 32 
                                       +lll+p+ ii+  +l rr +e
  gi|330507279|ref|YP_004383707.1| 378 LLLLIPI-IIIAAWLYRRHRE 397
                                       6889999.9999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2841.13
//
Query:       gi|330507280|ref|YP_004383708.1|  [L=369]
Description: hypothetical protein MCON_1167 [Methanosaeta concilii GP6]
Scores for 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  109.2   0.1    5.7e-31  108.3   0.0    1.5  2  Tubulin    Tubulin/FtsZ family, GTPase domain
    1.1e-05   24.9   0.1    2.1e-05   23.9   0.0    1.8  1  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 !  108.3   0.0   6.4e-35   5.7e-31       2     195 ..       4     185 ..       3     187 .. 0.88
   2 ?   -3.1   0.0      0.82   7.4e+03      90     113 ..     275     298 ..     247     308 .. 0.56

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 6.4e-35
                                       EEEEEEHHHHHHHHHHHHH...HHHCH......HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEE CS
                           Tubulin   2 iivigvGqcGnqignelwellakehgiqsdg..dslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnkl 76 
                                       ++++gvGqcGn+i++++ +    e ++   g  +++ ++  + +  + +  +vai+t  ++l+e++       +++l
  gi|330507280|ref|YP_004383708.1|   4 VLILGVGQCGNRILDAVNK----E-AMGG-GgaSKIAKYCLKPKFPSRV-ETVAINTAINDLKELRYT---TAKDRL 70 
                                       899****************....4.3321.1348999999885544444.555999987777777777...777999 PP

                                       E--CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEE CS
                           Tubulin  77 llgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtv 153
                                       ++     + +g+g++++vgk+a  ++++ i+ e+ek   ++  f+++s +GGTGS+++p+++  lk++yp+++vvtv
  gi|330507280|ref|YP_004383708.1|  71 HV----PNLHGMGANRNVGKQAFMDNRDSIMGEIEKRGDFDIAFVLTSTSGGTGSSFSPLLINELKRQYPNITVVTV 143
                                       99....7789******************************************************************* PP

                                       EEE--GG.G-HHHHHHHHHHHHHHHHT.-SEEEEEEHHHHHCC CS
                           Tubulin 154 vvlPsefsevvvepynailalkeliee.sdavividNdaLlki 195
                                        +lP+++ e+ ++ +na+++++el+e  +d +i+ dN+ ++++
  gi|330507280|ref|YP_004383708.1| 144 AILPFRE-EGSIYLQNAAFSMRELMELdADGIILADNQYMKRF 185
                                       *****99.******************88***********9986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.82
                                       T-HHHHHHHHHHTHHHHHHHHTT- CS
                           Tubulin  90 gypevgkeaaeeileeirkevekc 113
                                       +   +  + +    ++i kevek 
  gi|330507280|ref|YP_004383708.1| 275 AMVIIQGSREHLDVDQITKEVEKI 298
                                       444444444445556677777665 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.4e-09   2.1e-05     105     241 ..      67     190 ..      43     301 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.4e-09
                         Tubulin_2 105 leelrkapeseGAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllr 181
                                       +++l+++++ +G G +R vG+ a++ n ++i+ +++++ +              fV++S +GGTGS+       ll 
  gi|330507280|ref|YP_004383708.1|  67 KDRLHVPNL-HGMGANRNVGKQAFMDNRDSIMGEIEKRGDFDIA----------FVLTSTSGGTGSSFSP----LLI 128
                                       566777776.9************************987554333..........9***********9765....455 PP

                         Tubulin_2 182 kilkeekqkvkiiglvllPdvfplnkeggervkaNayaaLkELna.......lkdsdeetelevkyp 241
                                       ++lk++  ++ ++ +++lP       e+g  + +Na+ ++ EL         l d+++ +++++  +
  gi|330507280|ref|YP_004383708.1| 129 NELKRQYPNITVVTVAILPFR-----EEGSIYLQNAAFSMRELMEldadgiiLADNQYMKRFSGDIA 190
                                       666666666668899999985.....56899999998666655554448887666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2654.87
//
Query:       gi|330507281|ref|YP_004383709.1|  [L=296]
Description: GXGXG motif protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-08   33.5  14.3    1.7e-06   27.8   4.1    2.9  2  GXGXG     GXGXG motif
  ------ inclusion threshold ------
        8.6    4.8   6.4         12    4.4   0.2    2.2  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 !    9.1   2.8   9.8e-05      0.88     137     163 ..      82     108 ..      41     124 .. 0.70
   2 !   27.8   4.1   1.8e-10   1.7e-06      33     122 ..     175     251 ..     156     254 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 9.8e-05
                                       EEEEEEE-S-B-SSBTTT--EEEEEEE CS
                             GXGXG 137 tGGvvvvLgktgrnfaaGmsgGiayvl 163
                                         G +vv g++gr ++ +m +G++yv 
  gi|330507281|ref|YP_004383709.1|  82 GTGSIVVEGDVGRRMGISMLRGAIYVS 108
                                       4699*********************97 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 1.8e-10
                                       EEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--TT-SS-GGGSB-S-SSTTTT--SEEEEESSB CS
                             GXGXG  33 kiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpskeskfkaeeniivGnvvlygatgGklfirgk 109
                                       +ikl+G aG s g+ + +G ++ +eG a++ ++  l gG+i +++s+             + +   ++gG++fi+g+
  gi|330507281|ref|YP_004383709.1| 175 TIKLEGDAGMSTGILMRSG-QIIVEGCAQENTAVLLRGGRILVRGST------------KDFTGAEMRGGEVFIEGD 238
                                       5667777777777777444.566777777777777777777777776............356666788888888888 PP

                                       --SSTTTT-SS-E CS
                             GXGXG 110 ageRfavrnsgat 122
                                       ag+ ++ r++g +
  gi|330507281|ref|YP_004383709.1| 239 AGSFTCARMKGGV 251
                                       8888888888765 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.8    0.0038        34     195     228 ..      78     112 ..      50     119 .. 0.86
   2 ?    4.4   0.2    0.0013        12     182     227 ..     174     220 ..     172     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0038
                              FapA 195 GnIkfkGsViikGnVeegmkVka.sgditikGvve 228
                                       G I+ +Gs++++G+V   m ++   g i ++G v+
  gi|330507281|ref|YP_004383709.1|  78 GPIEGTGSIVVEGDVGRRMGISMlRGAIYVSGRVS 112
                                       77889**************9985478888888775 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0013
                              FapA 182 pvleikgdVdlstGnIkfkGsViikGnVeegmkVka.sgditikGvv 227
                                         ++++gd ++stG +   G +i++G  +e+  V   +g+i + G +
  gi|330507281|ref|YP_004383709.1| 174 KTIKLEGDAGMSTGILMRSGQIIVEGCAQENTAVLLrGGRILVRGST 220
                                       56899**********************99999997525688888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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: 00:00:00.40
# Mc/sec: 2229.41
//
Query:       gi|330507282|ref|YP_004383710.1|  [L=363]
Description: hypothetical protein MCON_1168 [Methanosaeta concilii GP6]
Scores for complete 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-121  404.7   4.4   4.4e-121  404.4   4.4    1.0  1  DUF373    Domain of unknown function (DUF373)
  ------ inclusion threshold ------
       0.89   10.0   7.2       0.21   12.0   0.4    2.3  2  MerC      MerC mercury resistance protein


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 !  404.4   4.4  4.9e-125  4.4e-121       5     334 ..       2     343 ..       1     344 [. 0.98

  Alignments for each domain:
  == domain 1  score: 404.4 bits;  conditional E-value: 4.9e-125
                            DUF373   5 lcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvgvea 81 
                                       lc+DrD+Dlgrk gv tPvvGrea++eaa kl+++dPeDSDvN++fg+ik+ de++a+g++ve+a ++Gd kvg+ +
  gi|330507282|ref|YP_004383710.1|   2 LCIDRDNDLGRKGGVITPVVGREANIEAALKLGMSDPEDSDVNTIFGGIKTFDEIAASGRNVEIASIAGDLKVGLIS 78 
                                       9**************************************************************************** PP

                            DUF373  82 drkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyllkkalkdpelrktiL 158
                                       d+kia+ql+++l++l++++++vVsDGaeDe++lpii sr+kv++v+rV+Vkqs+n+Estyyllk++++dp+l++t++
  gi|330507282|ref|YP_004383710.1|  79 DSKIASQLEDLLARLHPQGVVVVSDGAEDEAILPIITSRIKVEGVRRVLVKQSPNLESTYYLLKQLFTDPKLSHTLF 155
                                       ***************************************************************************** PP

                            DUF373 159 vplGlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvallllligi 235
                                       +p++l+ll++a+++l+g+p++a+++i++ +Glyll+rG+gld+++ee+ ++lk+sl++ +i f+ty++a++l++i++
  gi|330507282|ref|YP_004383710.1| 156 IPPALALLMFAFFSLIGYPSWAIVAITGSVGLYLLFRGLGLDDSMEEAKQTLKKSLYARKIAFITYILAAMLVVIAT 232
                                       ***************************************************************************** PP

                            DUF373 236 isgyislesvssasvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpflvlaiglvlyg 312
                                       ++g++ ++++ ++++ +g++tli++++y++++w+++a+l++ lgk++d+y+  e  + ar+++++f++la+glv+++
  gi|330507282|ref|YP_004383710.1| 233 VNGVAYFWQYFHEPTFPGYFTLIMIYLYESIWWYMAAALCVNLGKVMDMYM--EGIRDARTISYLFFILATGLVIWS 307
                                       ***************************************************..4457779***************** PP

                            DUF373 313 asaylls..............lsilalslvvgivva 334
                                       +s+++l+              ++ la+s +++i+++
  gi|330507282|ref|YP_004383710.1| 308 TSSFILAsnadlefgigmvesVQKLAISAIGAILIT 343
                                       *****999*************************997 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   2.4e-05      0.21      27     115 ..     140     234 ..     131     236 .. 0.83
   2 ?    1.0   1.6     0.063   5.6e+02      55     109 ..     283     343 ..     246     349 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                              MerC  27 llglsflasellhqvllilvvaigllalvvgyrrhrktsvlvlgalGllillvalflgteaeetl......lfgslw 97 
                                       ll ++f++ +l h ++++ ++a+ ++a+++         v + g +Gl +l+ +l l  ++ee++      l    +
  gi|330507282|ref|YP_004383710.1| 140 LLKQLFTDPKLSHTLFIPPALALLMFAFFSLIGYPSWAIVAITGSVGLYLLFRGLGLDDSMEEAKqtlkksLYARKI 216
                                       5566666677899999999**********99999999999*****************95455555666888899999 PP

                              MerC  98 qvltvlGaalLaiahvlN 115
                                       +++t++ aa+L+++  +N
  gi|330507282|ref|YP_004383710.1| 217 AFITYILAAMLVVIATVN 234
                                       999999999999988777 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.063
                              MerC  55 vvgyrrhrkts.vlvlgalGllillvalflg............teaeetllfgslwqvltvlGaalLa 109
                                       + g r  r  s +++++a+Gl+i  ++ f+                 e++        ++++Ga+l+ 
  gi|330507282|ref|YP_004383710.1| 283 MEGIRDARTISyLFFILATGLVIWSTSSFILasnadlefgigmV---ESV----QKLAISAIGAILIT 343
                                       44566666655145678888888888888875555555553221...222....22245556655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.39
# Mc/sec: 2818.20
//
Query:       gi|330507283|ref|YP_004383711.1|  [L=155]
Description: hypothetical protein MCON_1171 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1149.87
//
Query:       gi|330507284|ref|YP_004383712.1|  [L=427]
Description: thiamine biosynthesis protein ThiC [Methanosaeta concilii GP6]
Scores for complete 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-171  570.3   0.0   2.4e-171  570.1   0.0    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family
  ------ inclusion threshold ------
      0.041   13.2   0.0      0.055   12.7   0.0    1.2  1  EAP30         EAP30/Vps36 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 !  570.1   0.0  2.7e-175  2.4e-171       3     417 ..       4     420 ..       2     421 .. 0.99

  Alignments for each domain:
  == domain 1  score: 570.1 bits;  conditional E-value: 2.7e-175
                      ThiC_Rad_SAM   3 leaarkgiiteemeevaekenvepefvreevaeGrivipanknhkekpvaiGkglrtkvnaniGtsadasdieeEve 79 
                                       +++ar+g++teem+ vae+e+ +p+f+ +++a+Grivip+   + ++ v+iGkglrtkvna+iGts+d++d+e+Ev+
  gi|330507284|ref|YP_004383712.1|   4 IDDARAGRLTEEMKIVAEAEGKTPDFILRGIASGRIVIPRSPYRYTRSVGIGKGLRTKVNASIGTSSDIVDVEMEVA 80 
                                       689************************************************************************** PP

                      ThiC_Rad_SAM  80 KlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqalee...kekkveelteeellevieeqaedGvd 153
                                       K+++a++ gadt+m+Lstggd+ eir++++e+++++vg+vp+Yqa+ e   k+++ +++ e++l+++ eeqa+ G +
  gi|330507284|ref|YP_004383712.1|  81 KARTAEANGADTLMELSTGGDFLEIRRRVIEATTLSVGSVPLYQAFIEairKYGAGVDMPEDDLFRATEEQAKLGTN 157
                                       **********************************************999999999********************** PP

                      ThiC_Rad_SAM 154 fltiHagvtlellellkke.kRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsia 229
                                       f++iH+g++  ++e+l+++ +R+ g++SrgG++++ wml+n+kenply+efd+lleilke++vtlSlg+glR+G+++
  gi|330507284|ref|YP_004383712.1| 158 FMAIHTGINSICIERLRRQgGRFGGVCSRGGAFMIGWMLHNQKENPLYREFDYLLEILKEHEVTLSLGNGLRAGAVH 234
                                       ****************99878******************************************************** PP

                      ThiC_Rad_SAM 230 DatdeaqlaelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsa 306
                                       D+td+ q++eli+++el++ra++agvq++veGPGH+p+deieanv ++k++++e+Pfy+lGplvtDiapgYDhi++a
  gi|330507284|ref|YP_004383712.1| 235 DSTDRGQIQELIINSELADRAHAAGVQTIVEGPGHIPIDEIEANVLVMKRMTDEKPFYMLGPLVTDIAPGYDHIVAA 311
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 307 iGaalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfela 383
                                       iGa+l++a+Gad++CyvtpaEHl+lPd+edv+ G i+a+iaah++d++k+  + r++d ++ +aR+++ wekqf+la
  gi|330507284|ref|YP_004383712.1| 312 IGASLSSAYGADFICYVTPAEHLALPDVEDVRMGTITARIAAHIGDMIKN--NDRQKDLDMGRARRDMLWEKQFQLA 386
                                       *************************************************8..66799******************** PP

                      ThiC_Rad_SAM 384 ldpekareireeklpeeeeaCsmCgekCavkive 417
                                       +dpe+a+ +r++++p+++e+C+mCg++Ca+ki++
  gi|330507284|ref|YP_004383712.1| 387 IDPETAKLVRADRTPSDAEVCTMCGDFCALKIIK 420
                                       *******************************987 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.2e-06     0.055      83     166 ..      91     165 ..      54     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.2e-06
                             EAP30  83 lgfl.ellglgdfyyeLavqivevclatraengglisleelyalvnrarggvalvspdDllraiekllvlgsglsvl 158
                                          l el + gdf+ e+ ++++e+ +     + g ++l + +   +r++g+   +++dDl ra e   +lg +++++
  gi|330507284|ref|YP_004383712.1|  91 D-TLmELSTGGDFL-EIRRRVIEATT----LSVGSVPLYQAFIEAIRKYGAGVDMPEDDLFRATEEQAKLGTNFMAI 161
                                       2.335777788887.79999999998....56699***999999999995559************************ PP

                             EAP30 159 qvggkkvv 166
                                       ++g    +
  gi|330507284|ref|YP_004383712.1| 162 HTG----I 165
                                       954....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3208.56
//
Query:       gi|330507285|ref|YP_004383713.1|  [L=219]
Description: sulfite reductase, assimilatory-type [Methanosaeta concilii GP6]
Scores for 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  105.4   0.0    3.3e-30  104.7   0.0    1.4  1  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    1.3e-13   50.6   0.1    2.6e-13   49.6   0.0    1.5  2  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
  ------ inclusion threshold ------
       0.14   12.8   0.0       0.27   11.9   0.0    1.6  1  3HCDH         3-hydroxyacyl-CoA dehydrogenase, C-terminal dom


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 !  104.7   0.0   5.6e-34   3.3e-30       4     151 ..      86     217 ..      83     219 .] 0.96

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 5.6e-34
                                       SCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR   4 nlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekeig 80 
                                       ++r++++cpg+++c+    D+  +  +++    ++y+ ++lP KfK+ vsgc n c++  ++Digl+g+ k     g
  gi|330507285|ref|YP_004383713.1|  86 CVRSIKICPGTTFCKRGQQDAVGVGLKLD----EKYHGMQLPWKFKMGVSGCANSCAEPAVKDIGLIGTAK-----G 153
                                       89***************************....**************************************.....* PP

                                       EEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  81 fnilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekv 151
                                       +++lvGG+ g +++ ++ +a+   + ++ev++++++iv++yr     +  kk+Rl++++e++G+e F++++
  gi|330507285|ref|YP_004383713.1| 154 WRLLVGGSSGVKPRLGTLLAE--NLSDDEVFSCIDKIVNFYR-----DHAKKQRLGDFIEEIGFETFKKEI 217
                                       ********************5..677888*************.....88999*****************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 !   49.6   0.0   4.3e-17   2.6e-13       2      66 ..      12      75 ..      11      78 .. 0.96
   2 ?   -3.5   0.0       1.7     1e+04      25      38 ..     197     210 ..     194     213 .. 0.70

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 4.3e-17
                      NIR_SIR_ferr  2 kqkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeL 66
                                       q+d++++ ++  ++ +G+i+++ lr++ad+aeky    +++T+ Q + + g+++ed+++ +++L
  gi|330507285|ref|YP_004383713.1| 12 IQRDKETF-AIAPHIAGGIIDPAGLRRIADVAEKYHAKALKITSAQRIAIVGIDPEDIDNAWADL 75
                                      59999999.*****************************************************998 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.7
                      NIR_SIR_ferr  25 qlraladiaekygs 38 
                                        +++l d++e+ g+
  gi|330507285|ref|YP_004383713.1| 197 KKQRLGDFIEEIGF 210
                                       57788888888775 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.5e-05      0.27      13      43 ..      53      81 ..      30      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.5e-05
                                      HHHHHHHHTTSS-HHHHHHHHHHHHHHSSCH CS
                             3HCDH 13 neavrlveegvaspediDaamrlglGlpmGp 43
                                      + a r++  g ++pediD+a+ + lG+++G+
  gi|330507285|ref|YP_004383713.1| 53 TSAQRIAIVG-IDPEDIDNAWAD-LGMKTGA 81
                                      5688888999.************.****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1616.10
//
Query:       gi|330507286|ref|YP_004383714.1|  [L=97]
Description: hypothetical protein MCON_1173 [Methanosaeta concilii GP6]
Scores for complete 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   71.9   1.1    6.5e-20   71.5   1.1    1.2  1  ChaB      ChaB
  ------ inclusion threshold ------
      0.062   12.6   0.1      0.064   12.5   0.1    1.1  1  TAtT      TRAP transporter T-component


Domain annotation for each model (and alignments):
>> ChaB  ChaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   1.1   7.3e-24   6.5e-20       1      59 [.       9      70 ..       9      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 7.3e-24
                              ChaB  1 LPesvresLpehAqeifveafnsaleeYd...desdeerAhrvAwaavkekYekde.dgkWek 59
                                      LP+svr+ Lp++A++i+++afns++e+ +   ++ +e+++h+ Aw+avke+Yekd+ +g+W+k
  gi|330507286|ref|YP_004383714.1|  9 LPKSVRN-LPSRAKTIYMKAFNSCWEDLEiedETAREKASHESAWSAVKEQYEKDDeTGEWVK 70
                                      89***99.9*****************8857999*********************776****98 PP

>> TAtT  TRAP transporter T-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   7.2e-06     0.064      63     115 ..      13      63 ..       3      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.2e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHTSS-HHHHHHHHHT--GGG CS
                              TAtT  63 keaareRAkkLylrareyalraLetaydgltkalregeadeleaaLaklkked 115
                                        ++ ++RAk +y +a +  ++ Le ++++  ++ +  ++ ++ a+ ++++k+d
  gi|330507286|ref|YP_004383714.1|  13 VRNLPSRAKTIYMKAFNSCWEDLEIEDETAREKAS--HESAWSAVKEQYEKDD 63 
                                       57789*******************98777444444..4468999888998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 747.37
//
Query:       gi|330507287|ref|YP_004383715.1|  [L=278]
Description: hypothetical protein MCON_1174 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   13.5   0.0       0.11   12.4   0.0    1.5  1  GSAP-16   gamma-Secretase-activating protein C-term


Domain annotation for each model (and alignments):
>> GSAP-16  gamma-Secretase-activating protein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.1e-06      0.11      21      63 ..     162     204 ..     146     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.1e-06
                           GSAP-16  21 lelidelksseelalFhllerllealeelafPlPpgFhslftv 63 
                                       ++li    + +e+ lF++l+ +   ++e   P+PpgF++  t+
  gi|330507287|ref|YP_004383715.1| 162 AALIVMDINLDEYTLFNFLSYMNITVDESLTPIPPGFCTDTTA 204
                                       446666677899**************************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2180.35
//
Query:       gi|330507288|ref|YP_004383716.1|  [L=155]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-12   46.7   0.0    5.4e-12   46.1   0.0    1.2  1  LTD       Lamin Tail Domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0     3e-16   5.4e-12       4     108 ..      21     114 ..      19     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 3e-16
                               LTD   4 aagdvvIsevmedgagnnanefvelyNtsskavdLsgwkledasge.....ytfpngtgtlaageyvvvwsgsgtts 75 
                                       a ++vv++e+  ++++++a e++el+N+++++vd+s w+     g        +p gt +l+ag+ +v+  ++    
  gi|330507288|ref|YP_004383716.1|  21 AMASVVVNEIELNPPEGGA-EWIELFNSGNESVDISSWTAIITDGSwkgefSPVPLGT-ILPAGGFYVLDGQE---- 91 
                                       5689**********88887.*******************7777766566655566666.**********9994.... PP

                               LTD  76 asngskasssavwnn.ggdavaLydasgevvdsv 108
                                                  +wn  +g   +Ly asge+vd+ 
  gi|330507288|ref|YP_004383716.1|  92 -----------SWNHtDGGYCTLYSASGEEVDRT 114
                                       ...........46655777899*********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1152.94
//
Query:       gi|330507289|ref|YP_004383717.1|  [L=172]
Description: hypothetical protein MCON_1176 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-13   49.2   0.1    9.4e-13   48.5   0.1    1.3  1  LTD       Lamin Tail Domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.1   5.3e-17   9.4e-13       5     109 ..      38     128 ..      34     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 5.3e-17
                               LTD   5 agdvvIsevmedgagnnanefvelyNtsskavdLsgwkledasge..ytfpngtgtlaageyvvvwsgsgttsasng 79 
                                         dvvI+e+   ++ n++  +velyN+++++vdL+gw+++ + g    ++p    ++++ +  v   +++       
  gi|330507289|ref|YP_004383717.1|  38 ICDVVINEIELSAPHNET-VWVELYNAGDDPVDLTGWTVQIEDGAwkGIIPLQG-IIDPLGFKVAKGKDA------- 105
                                       569********9988777.9***********************77775555554.888888887777742....... PP

                               LTD  80 skasssavwnnggdavaLydasgevvdsvg 109
                                               +++g+ +v+Lyda ge +d+v 
  gi|330507289|ref|YP_004383717.1| 106 -------WATTGNGTVYLYDALGENMDRVY 128
                                       .......22335669************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1311.59
//
Query:       gi|330507290|ref|YP_004383718.1|  [L=528]
Description: CARDB domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-48  161.7   0.0    6.2e-10   39.2   0.0    4.1  4  CARDB      CARDB
    2.8e-05   23.6   0.0         16    4.9   0.0    4.1  4  TRAP_beta  Translocon-associated protein beta (TRAPB)
  ------ inclusion threshold ------
      0.011   16.0   0.0    1.3e+02    2.8   0.0    4.0  4  YkyB       YkyB-like protein


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 !   39.2   0.0   1.1e-13   6.5e-10       2     100 ..      29     132 ..      28     134 .. 0.86
   2 !   39.2   0.0     1e-13   6.2e-10       1     100 [.     157     261 ..     157     263 .. 0.86
   3 !   39.2   0.0     1e-13   6.2e-10       1     100 [.     286     390 ..     286     392 .. 0.86
   4 !   39.2   0.0     1e-13   6.2e-10       1     100 [.     415     519 ..     415     521 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.1e-13
                                       --EEE..EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-C..TEEEEEEEEEE-S CS
                             CARDB   2 pDLtv.tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaa..gesttvsftwtte 72 
                                       pDL v + +lnp+++++g+ +t+++ v+NqGt++sg ++v+    ++      +++v +L a  g+  t ++   + 
  gi|330507290|ref|YP_004383718.1|  29 PDLFVsEFSLNPETPVQGSPVTVRLGVYNQGTGSSGPFSVQWWPGENYRnlgCSWEVDGLVArgGKILTCTYDGYP- 104
                                       9****9999*********************************998888888989***9997621344444444455. PP

                                       -S-CEEEEEEEESTT-SS--SSCCCSEE CS
                             CARDB  73 ategevtltvvvDpdnevaEsnEtNNel 100
                                           ++  +v vD+++ vaEs+E+NN +
  gi|330507290|ref|YP_004383718.1| 105 SWYANINTKVLVDSGGVVAESDEANNIF 132
                                       599***********************86 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 1e-13
                                       S--EEE..EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-C..TEEEEEEEEEE- CS
                             CARDB   1 tpDLtv.tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaa..gesttvsftwtt 71 
                                       +pDL v + +lnp+++++g+ +t+++ v+NqGt++sg ++v+    ++      +++v +L a  g+  t ++   +
  gi|330507290|ref|YP_004383718.1| 157 SPDLFVsEFSLNPETPVQGSPVTVRLGVYNQGTGSSGPFSVQWWPGENYRnlgCSWEVDGLVArgGKILTCTYDGYP 233
                                       59****9999*********************************998888888989***9997621344444444455 PP

                                       S-S-CEEEEEEEESTT-SS--SSCCCSEE CS
                             CARDB  72 eategevtltvvvDpdnevaEsnEtNNel 100
                                            ++  +v vD+++ vaEs+E+NN +
  gi|330507290|ref|YP_004383718.1| 234 -SWYANINTKVLVDSGGVVAESDEANNIF 261
                                       .599***********************86 PP

  == domain 3  score: 39.2 bits;  conditional E-value: 1e-13
                                       S--EEE..EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-C..TEEEEEEEEEE- CS
                             CARDB   1 tpDLtv.tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaa..gesttvsftwtt 71 
                                       +pDL v + +lnp+++++g+ +t+++ v+NqGt++sg ++v+    ++      +++v +L a  g+  t ++   +
  gi|330507290|ref|YP_004383718.1| 286 SPDLFVsEFSLNPETPVQGSPVTVRLGVYNQGTGSSGPFSVQWWPGENYRnlgCSWEVDGLVArgGKILTCTYDGYP 362
                                       59****9999*********************************998888888989***9997621344444444455 PP

                                       S-S-CEEEEEEEESTT-SS--SSCCCSEE CS
                             CARDB  72 eategevtltvvvDpdnevaEsnEtNNel 100
                                            ++  +v vD+++ vaEs+E+NN +
  gi|330507290|ref|YP_004383718.1| 363 -SWYANINTKVLVDSGGVVAESDEANNIF 390
                                       .599***********************86 PP

  == domain 4  score: 39.2 bits;  conditional E-value: 1e-13
                                       S--EEE..EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-C..TEEEEEEEEEE- CS
                             CARDB   1 tpDLtv.tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaa..gesttvsftwtt 71 
                                       +pDL v + +lnp+++++g+ +t+++ v+NqGt++sg ++v+    ++      +++v +L a  g+  t ++   +
  gi|330507290|ref|YP_004383718.1| 415 SPDLFVsEFSLNPETPVQGSPVTVRLGVYNQGTGSSGPFSVQWWPGENYRnlgCSWEVDGLVArgGKILTCTYDGYP 491
                                       59****9999*********************************998888888989***9997621344444444455 PP

                                       S-S-CEEEEEEEESTT-SS--SSCCCSEE CS
                             CARDB  72 eategevtltvvvDpdnevaEsnEtNNel 100
                                            ++  +v vD+++ vaEs+E+NN +
  gi|330507290|ref|YP_004383718.1| 492 -SWYANINTKVLVDSGGVVAESDEANNIF 519
                                       .599***********************86 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 !    4.9   0.0    0.0026        16      28      49 ..      40      61 ..      16      68 .. 0.84
   2 !    4.4   0.0    0.0037        22      29      49 ..     170     190 ..     162     197 .. 0.89
   3 !    4.4   0.0    0.0037        22      29      49 ..     299     319 ..     291     326 .. 0.89
   4 !    4.4   0.0    0.0037        22      29      49 ..     428     448 ..     420     455 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0026
                         TRAP_beta 28 nrllvegedltveytiyNvGss 49
                                       + +v+g+ +tv++ +yN+G+ 
  gi|330507290|ref|YP_004383718.1| 40 PETPVQGSPVTVRLGVYNQGTG 61
                                      56789***************86 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0037
                         TRAP_beta  29 rllvegedltveytiyNvGss 49 
                                       + +v+g+ +tv++ +yN+G+ 
  gi|330507290|ref|YP_004383718.1| 170 ETPVQGSPVTVRLGVYNQGTG 190
                                       57899**************86 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0037
                         TRAP_beta  29 rllvegedltveytiyNvGss 49 
                                       + +v+g+ +tv++ +yN+G+ 
  gi|330507290|ref|YP_004383718.1| 299 ETPVQGSPVTVRLGVYNQGTG 319
                                       57899**************86 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.0037
                         TRAP_beta  29 rllvegedltveytiyNvGss 49 
                                       + +v+g+ +tv++ +yN+G+ 
  gi|330507290|ref|YP_004383718.1| 428 ETPVQGSPVTVRLGVYNQGTG 448
                                       57899**************86 PP

>> YkyB  YkyB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.021   1.3e+02      48      69 ..      35      56 ..      20      61 .. 0.87
   2 ?    2.3   0.0     0.031   1.8e+02      48      69 ..     164     185 ..     160     190 .. 0.92
   3 ?    2.3   0.0     0.031   1.8e+02      48      69 ..     293     314 ..     289     319 .. 0.92
   4 ?    2.3   0.0     0.031   1.8e+02      48      69 ..     422     443 ..     418     448 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.021
                              YkyB 48 hfsknPklsqqqsdvLvkvgdy 69
                                      +fs nP+   q s v v++g y
  gi|330507290|ref|YP_004383718.1| 35 EFSLNPETPVQGSPVTVRLGVY 56
                                      8******************998 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.031
                              YkyB  48 hfsknPklsqqqsdvLvkvgdy 69 
                                       +fs nP+   q s v v++g y
  gi|330507290|ref|YP_004383718.1| 164 EFSLNPETPVQGSPVTVRLGVY 185
                                       7******************998 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.031
                              YkyB  48 hfsknPklsqqqsdvLvkvgdy 69 
                                       +fs nP+   q s v v++g y
  gi|330507290|ref|YP_004383718.1| 293 EFSLNPETPVQGSPVTVRLGVY 314
                                       7******************998 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.031
                              YkyB  48 hfsknPklsqqqsdvLvkvgdy 69 
                                       +fs nP+   q s v v++g y
  gi|330507290|ref|YP_004383718.1| 422 EFSLNPETPVQGSPVTVRLGVY 443
                                       7******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       108  (0.00602376); expected 358.6 (0.02)
Passed bias filter:                       93  (0.00518713); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3974.72
//
Query:       gi|330507291|ref|YP_004383719.1|  [L=285]
Description: hypothetical protein MCON_1179 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.6   0.8       0.11   12.6   0.8    1.5  1  BAGE      B melanoma antigen family


Domain annotation for each model (and alignments):
>> BAGE  B melanoma antigen family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.8   6.3e-06      0.11       6      25 ..      26      46 ..      26      49 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-06
                              BAGE  6 vmLAASAQALE.AkLskeDLP 25
                                      ++LAASAQAL    +s ++ P
  gi|330507291|ref|YP_004383719.1| 26 LLLAASAQALPkSNYSWTEAP 46
                                      69********66666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2199.44
//
Query:       gi|330507292|ref|YP_004383720.1|  [L=560]
Description: arginyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-38  131.6   0.1    4.1e-38  131.2   0.1    1.1  1  tRNA-synt_1d     tRNA synthetases class I (R)
      4e-29  101.2   1.3      4e-29  101.2   1.3    2.3  3  DALR_1           DALR anticodon binding domain
    4.5e-12   46.4   0.0    1.7e-11   44.5   0.0    2.1  2  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
    7.8e-08   31.6   0.0    0.00029   19.9   0.0    2.1  2  tRNA-synt_1f     tRNA synthetases class I (K)
     0.0019   17.0   0.1       0.71    8.6   0.1    3.0  3  tRNA-synt_1g     tRNA synthetases class I (M)
  ------ inclusion threshold ------
      0.096   10.9   0.0       0.17   10.1   0.0    1.3  1  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
       0.11   11.1   0.0       0.18   10.4   0.0    1.2  1  SHMT             Serine hydroxymethyltransferase


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 !  131.2   0.1   1.6e-41   4.1e-38      15     349 .]     108     433 ..      94     433 .. 0.89

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 1.6e-41
                                       --SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTTS- CS
                      tRNA-synt_1d  15 ksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekllqe 91 
                                         r ++kv+v+++s n   ++hvGh+r  +iGd+++r+l  +G  v    +v D G+q  +++++l++ q +    +
  gi|330507292|ref|YP_004383720.1| 108 TGRMNEKVIVEHTSANPDGPLHVGHIRNSVIGDTLVRILRRAGCTVDAQYYVNDMGRQEAMVVVGLDHFQLDG---S 181
                                       457899**************************************************************99888...5 PP

                                       ----SCCCHHHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHCT---EC.--CC..C CS
                      tRNA-synt_1d  92 qelqdLeafykeakkdydeeeifaerarnyvvkLqsgdedirklwkllvditrtelqklydrldvtlie.rGes..l 165
                                       ++   +  +y  a+k+++ +  + e+a  +++  ++gd++++   +  v ++    +++ +r+++       es  +
  gi|330507292|ref|YP_004383720.1| 182 KPDHAIARVYIAANKEMESNPAIREEADRVIQLYEAGDPEVTAKVQSAVRYAIGGIEQTLQRMNICHDSyHWESefV 258
                                       67778889********************************9988888888888889999999999886665555548 PP

                                       CCCCHHHHHHHHHCTT-EEECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCC CS
                      tRNA-synt_1d 166 ykeslneivkelkkkglvkesdGalvvfldefgkrlgvvvqksDGgylytttDiaaakerkeelkadkvlyvidsrq 242
                                        + s+ eiv+ l+k glv  ++G l ++l+++g +  +v+++ +G+ ly t+D+a   +r +  + d+ + ++ +  
  gi|330507292|ref|YP_004383720.1| 259 RDGSVAEIVESLEKTGLVAWDEGSLQLDLNDYGFEKKMVLKRANGTSLYITRDLA--YHRWKSANSDRSVDILGADH 333
                                       889**************************************************97..6899999************* PP

                                       HHHHHHHHHHHHCTT.SSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCTS-CCC CS
                      tRNA-synt_1d 243 slhlqqiflilkkig.yvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkdkvlqad 318
                                       +l   q+ ++l  +g  +pe++  e  ++         +++trkG+ +  ++lLde  ++a++ ++ + +d   + +
  gi|330507292|ref|YP_004383720.1| 334 KLVSGQLRVALGLLGvREPEVVIFEFVSL------PTGSMSTRKGKFISADELLDEVEKQAMEEVRARRPD--ESPE 402
                                       ***************55677776655444......4569********************************..8999 PP

                                       CHCHHHHHHHHHHHHCCCCTS-TTS-EE--H CS
                      tRNA-synt_1d 319 elekvaeavgvgaikyaDlsknrindyifdw 349
                                        l++va  v+ ga++y  ++    +   fdw
  gi|330507292|ref|YP_004383720.1| 403 FLKEVARQVASGAVRYDVVKVSADKATTFDW 433
                                       9***************988776666666666 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   3.5e+03     100     117 ..     336     353 ..     334     355 .. 0.81
   2 ?   -3.0   0.0       3.1     8e+03      53      73 ..     392     412 ..     379     428 .. 0.62
   3 !  101.2   1.3   1.5e-32     4e-29       1     119 []     447     560 .]     447     560 .] 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHTT----S CS
                            DALR_1 100 vrqvLangLdlLGieape 117
                                       v+  L+ +L lLG++ pe
  gi|330507292|ref|YP_004383720.1| 336 VSGQLRVALGLLGVREPE 353
                                       5567899*******9987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
                                       HHHT-THHHHHHHHHHHHHHH CS
                            DALR_1  53 aeelephklaeylyeLaatfh 73 
                                       +++++p++  e+l+e+a ++ 
  gi|330507292|ref|YP_004383720.1| 392 VRARRPDESPEFLKEVARQVA 412
                                       334677777777777776654 PP

  == domain 3  score: 101.2 bits;  conditional E-value: 1.5e-32
                                       HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHH CS
                            DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYn 77 
                                       +qy+haR++silrk e++++     +++ll ++ e +L+k++aqf  v+ +aa el+ph la+y+ eLa++f+ fY+
  gi|330507292|ref|YP_004383720.1| 447 IQYSHARACSILRKGEQSEK----FQADLLVSDYEVALIKKIAQFDLVIDRAACELKPHHLATYARELAESFNLFYR 519
                                       7************9987663....33444589********************************************* PP

                                       HCTSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                            DALR_1  78 kervlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                         +vl+++ e + +aRLaL+ka+r+ L+++L+ LGi+a+e m
  gi|330507292|ref|YP_004383720.1| 520 YSPVLDASFELR-DARLALAKAARNALRTTLETLGISALETM 560
                                       *********988.***************************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 !   44.5   0.0   6.8e-15   1.7e-11       3      85 .]       9      89 ..       7      89 .. 0.82
   2 ?   -3.3   0.0       5.7   1.5e+04       5      30 ..      96     122 ..      94     125 .. 0.63

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 6.8e-15
                                      HHHHHHHHHHHHHSS-HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT.EEEEEEETT.E CS
                   Arg_tRNA_synt_N  3 lkeaiaealkkaagadleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei.iekvevagpGF 80
                                      ++ +++ al+++  +++ee   ++       ++D+a+ va++la  lkk+P  iA ei ++++ +   +ekve agp +
  gi|330507292|ref|YP_004383720.1|  9 VEGLLKSALDRCG-FAPEEGINSLGL-ELTPHADLASSVAFRLAPVLKKSPAAIAGEIHQAIPHEFRyVEKVELAGP-Y 84
                                      5667888888884.444443444443.5678**********************************888*********.* PP

                                      EEEEE CS
                   Arg_tRNA_synt_N 81 iNffL 85
                                      +Nff+
  gi|330507292|ref|YP_004383720.1| 85 LNFFM 89
                                      ***95 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.7
                                       HHHHHHHHHHHSS-HHHHGGG-E.-.S CS
                   Arg_tRNA_synt_N   5 eaiaealkkaagadleeeeivie.kpk 30 
                                       +++++al++ a  +  +e++++e +++
  gi|330507292|ref|YP_004383720.1|  96 AVLNQALADNAWTGRMNEKVIVEhTSA 122
                                       567888887775556677778883344 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 !    9.6   0.0   0.00016       0.4      22      71 ..     113     162 ..      96     167 .. 0.82
   2 !   19.9   0.0   1.1e-07   0.00029     203     319 ..     288     403 ..     249     415 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00016
                      tRNA-synt_1f  22 kdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdm 71 
                                       ++ +v  + + p G++H+G +r+ + +d ++r lr+ g +v+  ++++dm
  gi|330507292|ref|YP_004383720.1| 113 EKVIVEHTSANPDGPLHVGHIRNSVIGDTLVRILRRAGCTVDAQYYVNDM 162
                                       33444468999****************************99999999998 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.1e-07
                      tRNA-synt_1f 203 eecGeeeevdiregn.gKLqWkvdwa.mrWaalgVd..fEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYeli 274
                                       ++ G+e+++ ++ +n   L    d a  rW++ + d  +   G Dh      v+ + ++a  +lg+++Pe v++e++
  gi|330507292|ref|YP_004383720.1| 288 NDYGFEKKMVLKRANgTSLYITRDLAyHRWKSANSDrsVDILGADHKL----VSGQLRVAlGLLGVREPEVVIFEFV 360
                                       556666666666655445555566653478776654337889999999....666778899**************** PP

                      tRNA-synt_1f 275 llkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkl 319
                                       +l  g  ms  kG++++ +++l+ +e++ ++ + +r +P ++ ++
  gi|330507292|ref|YP_004383720.1| 361 SLPTG-SMSTRKGKFISADELLDEVEKQAMEEVRAR-RPDESPEF 403
                                       ***99.9********************999988888.88776665 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 !    8.6   0.1   0.00028      0.71      11      37 ..     125     151 ..     116     160 .. 0.88
   2 ?    2.0   0.0     0.028        71      73     116 ..     236     279 ..     216     297 .. 0.84
   3 ?    2.4   0.0     0.021        54     314     348 ..     353     387 ..     311     394 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00028
                                       SS---HHHHHHHHHHHHHHHHHHHTT- CS
                      tRNA-synt_1g  11 ngklHlGhllevisaDifaRykrlrge 37 
                                       +g+lH+Gh+++ +++D ++R  r  g 
  gi|330507292|ref|YP_004383720.1| 125 DGPLHVGHIRNSVIGDTLVRILRRAGC 151
                                       799********************9886 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.028
                                       HHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1g  73 eikelfkklnisfdkygrttseehkelvqeifkklkekgliyek 116
                                        i+++++++ni +d+y+  ++      v+ei++ l++ gl+   
  gi|330507292|ref|YP_004383720.1| 236 GIEQTLQRMNICHDSYHWESEFVRDGSVAEIVESLEKTGLVAWD 279
                                       578999********************************998755 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.021
                                       -EEEE--EEE--------------HHHHHHHH-HH CS
                      tRNA-synt_1g 314 kvvaheyltvegkKlSkSrgvvvkakealerldad 348
                                       +vv  e++ +  + +S+ +g ++ a+e+l++++++
  gi|330507292|ref|YP_004383720.1| 353 EVVIFEFVSLPTGSMSTRKGKFISADELLDEVEKQ 387
                                       577899***********************998865 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 ?   10.1   0.0   6.5e-05      0.17      30      65 ..     120     155 ..     104     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.5e-05
                       tRNA-synt_1  30 gPPyvtGslHiGhalaktlkdivirykrmkGkevly 65 
                                          +  G lH+Gh+ ++++ d+++r+ r  G +v+ 
  gi|330507292|ref|YP_004383720.1| 120 TSANPDGPLHVGHIRNSVIGDTLVRILRRAGCTVDA 155
                                       556778***********************9998875 PP

>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0     7e-05      0.18     318     361 ..     154     197 ..     146     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7e-05
                                       HTT-EEGGGS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE CS
                              SHMT 318 ekgyklvsgGtdnhlvlvdlrekgldGkraekvlekvnitankn 361
                                       +  y +   G ++ +v+v l + +ldG++ ++++ +v i+ank+
  gi|330507292|ref|YP_004383720.1| 154 DAQYYVNDMGRQEAMVVVGLDHFQLDGSKPDHAIARVYIAANKE 197
                                       567778888999*******************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                         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 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3894.75
//
Query:       gi|330507293|ref|YP_004383721.1|  [L=436]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-06   27.3   1.3      6e-05   22.7   1.3    2.1  1  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
      0.033   13.5   2.4       0.06   12.7   2.4    1.4  1  SF-assemblin     SF-assemblin/beta giardin
       0.15   12.2   0.9        7.5    6.8   0.1    2.4  2  Zn-ribbon_8      Zinc ribbon domain
       0.16   11.9   1.1        7.3    6.7   0.3    2.6  2  YhfH             YhfH-like protein
       0.22   11.6   2.9       0.78    9.8   2.8    1.8  1  DZR              Double zinc ribbon
        1.8    9.1   7.4       0.23   12.0   2.6    2.1  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
        3.1    7.4   4.8         38    3.9   4.8    2.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
        8.5    6.1   8.7        5.9    6.6   0.1    2.7  3  zf-NADH-PPase    NADH pyrophosphatase 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 !   22.7   1.3   2.7e-08     6e-05     103     259 ..     180     381 ..     146     392 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.7e-08
                      DDE_Tnp_IS66 103 avlfeyspsRggevaealLag.....fkGvlvsDgyagYnklae....eqvthalCwaHlrRkfvdaeeakkksqaa 170
                                       +++ e  +s  ++++e++L        + ++v+D y gY+ + +    ++v h++C+ Hl   +v+   +k   ++ 
  gi|330507293|ref|YP_004383721.1| 180 VIADELYDSKDADTIESFLRRnldtqKQIFIVTDLYRGYSDIFKrvfgNKVIHQFCLLHLNKLIVNDFPRKT--SIE 254
                                       666677788888999999888877655579***********9999****************99887777644..555 PP

                      DDE_Tnp_IS66 171 aealar..igklya...................ierearea...................eaeerlalrqeesrpll 207
                                       +e +++  ++ +y+                   +      +                    ++  l++r+e++    
  gi|330507293|ref|YP_004383721.1| 255 QELIKYrlLNIFYDrepeieflsclieeektmkQ------RsdkeykswikeaknafhkfVRDLELKRRRENKNLKQ 325
                                       5555555467777766666666666432222220......1222222222222222222211333333333333333 PP

                      DDE_Tnp_IS66 208 aeleawleeql....kkvlpksklgkairyllkrweallrfledgrvpidNNaaER 259
                                       +++++ l++ +    ++ +    ++k ++++ + w++l+ f    + p +NN +E+
  gi|330507293|ref|YP_004383721.1| 326 RDYYEALNNFKilkmQSDSFMISVRKRLAKIEELWPNLTAFYFVDNAPATNNPIEN 381
                                       33444444333766666666777999999*************************98 PP

>> SF-assemblin  SF-assemblin/beta giardin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.4   2.7e-05      0.06      19     106 ..     278     365 ..     271     398 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                      SF-assemblin  19 kelenEieqkrvdektrvklikeaiakleksvea.EvkkRaesdkdiqeefkkeikklqekikeevddlalelkkav 94 
                                         +e+E+  k+  +k+  + ikea +   k v   E k+R  ++k++++    e+++ ++  k + d   + ++k +
  gi|330507293|ref|YP_004383721.1| 278 CLIEEEKTMKQRSDKEYKSWIKEAKNAFHKFVRDlELKRR-RENKNLKQRDYYEALNNFKILKMQSDSFMISVRKRL 353
                                       5699****************************87255555.56899*9999999999999999999999******99 PP

                      SF-assemblin  95 eelnekinnvea 106
                                       ++++e   n+ a
  gi|330507293|ref|YP_004383721.1| 354 AKIEELWPNLTA 365
                                       999998877776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0033       7.5      26      35 ..      40      50 ..      25      53 .. 0.60
   2 ?    3.5   0.1     0.035        79       6      17 ..      72      83 ..      71      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0033
                       Zn-ribbon_8 26 lta.CPeCgse 35
                                       ++ CPeCg++
  gi|330507293|ref|YP_004383721.1| 40 VPPlCPECGHP 50
                                      3444****986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.035
                       Zn-ribbon_8  6 YrCeeCghefev 17
                                      Y C +Cg+  e+
  gi|330507293|ref|YP_004383721.1| 72 YLCGACGKSTEE 83
                                      99*****99886 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0032       7.3       7      24 ..      35      52 ..      31      61 .. 0.85
   2 ?    3.2   0.0     0.038        85      15      27 ..      73      85 ..      67      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0032
                              YhfH  7 FfrnLPkKkCteCGkeie 24
                                      +fr++ +  C+eCG  + 
  gi|330507293|ref|YP_004383721.1| 35 IFRKIVPPLCPECGHPMS 52
                                      799999999*****9986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.038
                              YhfH 15 kCteCGkeieEqa 27
                                       C  CGk  eE  
  gi|330507293|ref|YP_004383721.1| 73 LCGACGKSTEENR 85
                                      6*******99976 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.8   0.00035      0.78      15      44 ..      44      87 ..      31      89 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00035
                               DZR 15 CseCgtklkavaa................edrCpsCgekvdpearf 44
                                      C+eCg++++   +                ++ C +Cg++++++  f
  gi|330507293|ref|YP_004383721.1| 44 CPECGHPMSH--NgfntcqkrhlgganvgKYLCGACGKSTEENRDF 87
                                      6666666652..1235555666666666799999999998877655 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 ?   12.0   2.6    0.0001      0.23       8      51 ..      44     118 ..      43     123 .. 0.62
   2 ?   -3.5   0.2       7.3   1.6e+04      18      27 ..     319     329 ..     314     331 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                   Zn_ribbon_recom   8 CgeCGspmtr......rkrkgkr.......hyYrCstyrrkgk..................k.Csnh...sireekl 49 
                                       C eCG+pm++      +    kr         Y C+++ ++ +                  + C+     ++++e++
  gi|330507293|ref|YP_004383721.1|  44 CPECGHPMSHngfntcQ----KRhlgganvGKYLCGACGKSTEenrdfwvnlkadflgiitEiCTRLrlnHVSYEVI 116
                                       **********5543322....22355558888999988766555556666666666665531465544556666666 PP

                   Zn_ribbon_recom  50 ee 51 
                                       e+
  gi|330507293|ref|YP_004383721.1| 117 ES 118
                                       65 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.3
                   Zn_ribbon_recom  18 rkrk.gkrhyY 27 
                                        +++ ++r+yY
  gi|330507293|ref|YP_004383721.1| 319 ENKNlKQRDYY 329
                                       33447888898 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   4.8     0.017        38       3      32 ..      44      84 ..      43      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.017
                                      ETTTTCEEC...........HEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon  3 CPnCgstnl...........veDpergelvCtdCGlVledn 32
                                      CP+Cg+++            +  ++ g ++C++CG   e+n
  gi|330507293|ref|YP_004383721.1| 44 CPECGHPMShngfntcqkrhLGGANVGKYLCGACGKSTEEN 84
                                      9999998745888888887777799999******9888876 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0027       5.9       6      15 ..      44      53 ..      42      54 .. 0.82
   2 ?    5.0   0.1    0.0086        19       6      18 ..      74      86 ..      73      89 .. 0.86
   3 ?   -3.7   1.5       4.4   9.8e+03       3       6 ..     232     235 ..     232     235 .. 0.97

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0027
                     zf-NADH-PPase  6 CgrCGaptep 15
                                      C+ CG+p+  
  gi|330507293|ref|YP_004383721.1| 44 CPECGHPMSH 53
                                      999**99975 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0086
                     zf-NADH-PPase  6 CgrCGaptepaeg 18
                                      Cg CG  te +++
  gi|330507293|ref|YP_004383721.1| 74 CGACGKSTEENRD 86
                                      ********98875 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.4
                     zf-NADH-PPase   3 hrFC 6  
                                       h+FC
  gi|330507293|ref|YP_004383721.1| 232 HQFC 235
                                       9*** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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 0.24s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3000.41
//
Query:       gi|330507294|ref|YP_004383722.1|  [L=407]
Description: hypothetical protein MCON_1183 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-16   58.3   0.2    1.3e-15   57.6   0.2    1.4  1  DUF4139   Domain of unknown function (DUF4139)
  ------ inclusion threshold ------
      0.033   14.0   0.1      0.088   12.6   0.1    1.8  1  DUF4897   Domain of unknown function (DUF4897)
       0.11   12.7   0.2       0.23   11.6   0.2    1.6  1  Top6b_C   Type 2 DNA topoisomerase 6 subunit B C-terminal dom


Domain annotation for each model (and alignments):
>> DUF4139  Domain of unknown function (DUF4139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.2   2.2e-19   1.3e-15       2     204 ..     109     397 ..     108     401 .. 0.71

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 2.2e-19
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                           DUF4139   2 kvsyvvseag.WsPlYdlrldtakeevqltykAkvyQktgeDWknvnLtLstakpnrggsppelspwylrvvn.... 73 
                                        +sy+++ ag W+P Ydl+l ++   v l ++A v+++ geD knv+L+L  + p +   +p +++ +++ +     
  gi|330507294|ref|YP_004383722.1| 109 ALSYLMHSAGfWEPRYDLHLANDS--VLLNANAVVRNRGGEDLKNVRLKLVAGLPLA--VEPIYRSAQIQQAYaaea 181
                                       689****9998*********9887..9************************555544..344444444433224555 PP

                                       .........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                           DUF4139  74 .........................................evteggtsvtfeipkkvsipsdgeetkvt....... 102
                                                                                                            +       
  gi|330507294|ref|YP_004383722.1| 182 alneafdlaaapegsssgeletlyifelegrkdlamdkeigF---------------------------Plfqenvp 231
                                       566666666666655555555555555555555555555550...........................15555555 PP

                                       ...............................................................xxxxxxxxxxxxxx RF
                           DUF4139 103 ...............................................................Gvdpkikverkllk 116
                                                                                                      G   ++kv+rkl +
  gi|330507294|ref|YP_004383722.1| 232 lvrvytwnaylqeegpaveeiranntmknpwpsgtallyrnddyvstidmpytasgtnatlviGPSADLKVTRKLKD 308
                                       55555555555555555555555555555555555555666666666999*************99999999999887 PP

                                       xxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4139 117 kkksetgli..........gsqrrveyaytitvkNtksepvtlkvedqvPvSrdeeikveledaepskaevdkdtgi 183
                                        +  e ++            ++++++++y ++v+ + ++++tl+ +d++P+ + e i v     +p++ae +++   
  gi|330507294|ref|YP_004383722.1| 309 YNVTE-KIRaitsngrnhtVKETTETWTYHLKVESNLDRAATLEATDNLPQ-EAEMIDV-----TPKPAETTAT--S 376
                                       66553.222235887777789999**************************8.5688999.....4555555555..7 PP

                                       xxxxxxxxxxxxxxxxxxxxx RF
                           DUF4139 184 lewklklapgekkkiefsyev 204
                                       l+w l+l +++k+ i++sy+v
  gi|330507294|ref|YP_004383722.1| 377 LKWRLQLLARQKTAIDYSYRV 397
                                       9******************98 PP

>> DUF4897  Domain of unknown function (DUF4897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.5e-05     0.088     117     144 ..     353     380 ..     302     386 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                           DUF4897 117 vvslPkdaklisvePtPtkivenellWk 144
                                       + +lP++a++i+v+P+P++ ++  l W+
  gi|330507294|ref|YP_004383722.1| 353 TDNLPQEAEMIDVTPKPAETTATSLKWR 380
                                       4579***********************7 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 ?   11.6   0.2   3.8e-05      0.23      22      98 ..     325     400 ..     308     405 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.8e-05
                                       EEE--SSS-EEEEEEE---------EEE--EES-----------EEE-SSSEEE-EEE---TT-EEEE----SS-GG CS
                           Top6b_C  22 reveengdgvevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlkWelsvsageskvleYsvdseae 98 
                                       ++v+e  +  + +lkv+ + d+++++e ++ lp+e+e ++  +k  e      lkW+l++ a +++++ Ys    ++
  gi|330507294|ref|YP_004383722.1| 325 HTVKETTETWTYHLKVESNLDRAATLEATDNLPQEAEMIDVTPKPAETT-ATSLKWRLQLLARQKTAIDYSYRVVTT 400
                                       567777777899************************9999999888865.5689***************99766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.22s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2933.30
//
Query:       gi|330507295|ref|YP_004383723.1|  [L=89]
Description: hypothetical protein MCON_1184 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   15.0   3.0      0.014   14.8   3.0    1.1  1  DUF92     Integral membrane protein DUF92


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   3.0   7.9e-07     0.014     141     190 ..      23      71 ..       9      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.9e-07
                             DUF92 141 nGgVsllGllasllGalliallavlllllellillltlaGllGsllDSlL 190
                                       +Gg+s+ Gl  ++  +ll+ +++v++ l+   + + +l+G+ G l+DSlL
  gi|330507295|ref|YP_004383723.1|  23 SGGMSFQGLSLGARLSLLMPAIIVVISLFI-RTTVSLLSGFKGGLVDSLL 71 
                                       8*****************997755554443.5788999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 666.81
//
Query:       gi|330507296|ref|YP_004383724.1|  [L=91]
Description: hypothetical protein MCON_1185, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0042   15.9   0.0     0.0045   15.8   0.0    1.0  1  NPR2      Nitrogen permease regulator 2


Domain annotation for each model (and alignments):
>> NPR2  Nitrogen permease regulator 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.5e-07    0.0045      93     138 ..       9      60 ..       6      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-07
                              NPR2  93 fvidydesdttpYesvvkrlgrllrvlEeqnkfLskedkdvvffk......s 138
                                        vi ++ s +t Y+ +++r++  +++ E +n   s+ +    f++      +
  gi|330507296|ref|YP_004383724.1|   9 AVIAMSISGWTGYDRIIRRMTPSFQETEAHNMRCSEGQAVLAFNDgdevaiK 60 
                                       69999************************99998887774444445544331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 649.90
//
Query:       gi|330507297|ref|YP_004383725.1|  [L=60]
Description: hypothetical protein MCON_1187 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 417.55
//
Query:       gi|330507298|ref|YP_004383726.1|  [L=78]
Description: hypothetical protein MCON_1188 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.03   14.0   0.0      0.031   14.0   0.0    1.0  1  APP_E2    E2 domain of amyloid precursor protein


Domain annotation for each model (and alignments):
>> APP_E2  E2 domain of amyloid precursor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.7e-06     0.031      76     138 ..       7      71 ..       1      77 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-06
                            APP_E2  76 r..FqetvealEeeaaaerqqLvetHqqrveaalnekrrkalekylqalqeeppnaerilkaLkk 138
                                       +  Fqe +e+lE    ++r+ Lve+ ++r+  + +e+  + +++ l+a  + + ++  +   Lk 
  gi|330507298|ref|YP_004383726.1|   7 KpgFQELIETLEALPIEDREMLVEIINKRIIEQRRERLVADMKESLEACGRGEVHTGTVDDLLKD 71 
                                       444***************************99988888888888888888877777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.57
# Mc/sec: 414.37
//
Query:       gi|330507299|ref|YP_004383727.1|  [L=94]
Description: RelE/StbE family addiction module toxin [Methanosaeta concilii GP6]
Scores for complete sequence (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   38.5   0.0    1.2e-09   38.4   0.0    1.0  1  YafQ_toxin       Bacterial toxin of type II toxin-antitoxin s
      3e-05   24.5   0.0    3.2e-05   24.5   0.0    1.1  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
      0.003   17.5   0.0     0.0038   17.1   0.0    1.2  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.016   15.2   0.0    1.3  1  YoeB_toxin       YoeB-like toxin of bacterial type II toxin-a


Domain annotation for each model (and alignments):
>> YafQ_toxin  Bacterial toxin of type II toxin-antitoxin system, YafQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   2.6e-13   1.2e-09       5      86 ..       6      93 ..       2      94 .] 0.83

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 2.6e-13
                                      EEHHHHHHHHHHHHTT--HH.HHHHHHHHHHTT-S--GGG--EE-SSS-TTEEEEEEETT..EEEEEEE-SS....EEE CS
                        YafQ_toxin  5 ptkqfkkdlkrlkkrkkdle.klkevlklLaegepLpekyrdHaLkgnwkgyrecHikpD..llLiYrledd....elv 76
                                      + k+f++ lkr+ k++ d+  k++++l+lLae +p + + + H+Lkg+++ ++ c i  D  +l ++ ++ d     + 
  gi|330507299|ref|YP_004383727.1|  6 WAKAFRRALKRIVKQRPDILpKVEKALRLLAE-DPFHPELHSHKLKGQLERMWACSIDYDnrILFMFLKNPDsgadDVL 83
                                      6899********977766655******99986.58999********************983345555555547888*** PP

                                      EEEEE-HHHH CS
                        YafQ_toxin 77 lvrlGsHsel 86
                                      lv++G+H+e+
  gi|330507299|ref|YP_004383727.1| 84 LVSMGTHQEV 93
                                      ********97 PP

>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   7.1e-09   3.2e-05       1      78 [.       4      83 ..       4      94 .] 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7.1e-09
                                      EEEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEE.CTSTC..CTTEEEEEEC.TEEEEEEE.... CS
                        ParE_toxin  1 vrltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrp.rrelg..lkglrririg.dyriiYri.... 71
                                      +++++++++ lk+i++        +  +l ++e+al+llae+p + +   + l+  l++++ + i+ d ri++ +    
  gi|330507299|ref|YP_004383727.1|  4 LIWAKAFRRALKRIVKQ-------RPDILPKVEKALRLLAEDPFHPELhSHKLKgqLERMWACSIDyDNRILFMFlknp 75
                                      69*************95.......9***********************5555559*99*********999999876655 PP

                                      .ETSTTEE CS
                        ParE_toxin 72 .ddeelvv 78
                                        + ++v+
  gi|330507299|ref|YP_004383727.1| 76 dSGADDVL 83
                                      43333444 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   8.6e-07    0.0038       4      83 ..       7      94 .]       4      94 .] 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.6e-07
                   ParE-like_toxin  4 trrfkkalkklkek...lkadldkavkeiiedPelGe...eK.kGDLsgvfvykfklnkqltllaYeldek..krvlvl 73
                                       + f++alk++ ++      +++ka++ ++edP   e   +K kG L+ ++   + + ++   + +  +++  +  + l
  gi|330507299|ref|YP_004383727.1|  7 AKAFRRALKRIVKQrpdILPKVEKALRLLAEDPFHPElhsHKlKGQLERMWACSIDYDNRILFM-FLKNPDsgADDVLL 84
                                      5789******987744467899**********987652223359*************9875554.4444442466799* PP

                   ParE-like_toxin 74 llvGtheNfY 83
                                      +++Gth+  Y
  gi|330507299|ref|YP_004383727.1| 85 VSMGTHQEVY 94
                                      ******9988 PP

>> YoeB_toxin  YoeB-like toxin of bacterial type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   3.5e-06     0.016      17      67 ..      22      72 ..       4      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.5e-06
                                      HHHHHHHHHHHHHHHHSTTSSTT--EE-SGGGTTEEEEESSSSEEEEEEEE CS
                        YoeB_toxin 17 kkilkkineLikeikRdpfeGiGkPepLkedlsglwsRRideehRlvYlve 67
                                        il k+++ ++ ++ dpf+      +Lk++l+ +w+  id ++R+++++ 
  gi|330507299|ref|YP_004383727.1| 22 PDILPKVEKALRLLAEDPFHPELHSHKLKGQLERMWACSIDYDNRILFMFL 72
                                      5677889999999999******************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.55
# Mc/sec: 512.69
//
Query:       gi|330507300|ref|YP_004383728.1|  [L=408]
Description: hypothetical protein MCON_1190 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-14   53.8   2.3    4.6e-14   52.6   2.3    1.6  1  DUF4139   Domain of unknown function (DUF4139)
     0.0031   17.8   0.7      0.081   13.2   0.1    2.8  3  DUF11     Domain of unknown function DUF11
     0.0055   16.6   0.1      0.016   15.1   0.1    1.8  2  DUF4897   Domain of unknown function (DUF4897)
     0.0081   16.3   0.3       0.02   15.1   0.3    1.7  1  Top6b_C   Type 2 DNA topoisomerase 6 subunit B C-terminal dom


Domain annotation for each model (and alignments):
>> DUF4139  Domain of unknown function (DUF4139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   2.3     1e-17   4.6e-14       6     206 ..     114     400 ..     108     402 .. 0.71

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1e-17
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                           DUF4139   6 vvseagWsPlYdlrldtakeevqltykAkvyQktgeDWknvnLtLstakpnrggsppelspwylrvvn......... 73 
                                       ++s a+W+P Ydl+l++++  v ++ +A v+++ geD knv+L+L       +g  pe++ + + ++          
  gi|330507300|ref|YP_004383728.1| 114 MYSSATWKPIYDLHLSEDQ--VLVKSNAVVSNRGGEDLKNVRLKLV------AGLSPEVHAYPAAPRSagaadakma 182
                                       4689***********9998..9***********************9......4455555555544444555545677 PP

                                       ..........................................................xxxxxxxxxxxxxxxxxxx RF
                           DUF4139  74 ..........................................................evteggtsvtfeipkkvsi 92 
                                                                                                 +                  
  gi|330507300|ref|YP_004383728.1| 183 yameevayeaapdlpatgeletlyifelegrkdlamdkeigfplfekesplvriytwdA------------------ 241
                                       77777777777777766666666666666666666666666666554444444444440.................. PP

                                       xxxxxxxxxx.....................................................xxxxxxxxxxxxxx RF
                           DUF4139  93 psdgeetkvt.....................................................Gvdpkikverkllk 116
                                                                                                      G+  ++k+e kl +
  gi|330507300|ref|YP_004383728.1| 242 ---------SrqsegpadeevrinntlenpwpegkamlyrngeyvstiqmpytpagtnasivvGTSADLKLEKKLSD 309
                                       .........044444444444444566666666666666666666667777777777777777*********99998 PP

                                       xxxxx.xxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4139 117 kkkse.tgli........gsqrrveyaytitvkNtksepvtlkvedqvPvSrdeeikveledaepskaevdkdtgil 184
                                        +k e  + i         ++ r+ ++y +++k + +++++l+v+d vP+   e + +   +++p+++e++++  +l
  gi|330507300|ref|YP_004383728.1| 310 YNKTEeIKAIstpegnrtVKEIRQAWTYHLSIKSNLDRTADLEVTDTVPQ---EAVMI---SVSPEPDERTAT--TL 378
                                       6655436666899987767778899************************6...55555...346666666666..89 PP

                                       xxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4139 185 ewklklapgekkkiefsyevky 206
                                       +wkl++ p+++  i+++y+vk 
  gi|330507300|ref|YP_004383728.1| 379 KWKLEVMPRQEMSINYTYQVKT 400
                                       ********************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 ?    1.6   0.0     0.075   3.4e+02      21      40 ..     140     171 ..     135     208 .. 0.57
   2 ?   -2.8   0.0       1.8   8.2e+03      51      51 ..     275     275 ..     246     306 .. 0.48
   3 !   13.2   0.1   1.8e-05     0.081      15      82 ..     334     402 ..     318     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.075
                             DUF11  21 tvtNtgpasangvvvtDtl............P 40 
                                       +v+N+g+ ++++v+++ +             P
  gi|330507300|ref|YP_004383728.1| 140 VVSNRGGEDLKNVRLKLVAglspevhaypaaP 171
                                       699*******9999875445554444443332 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.8
                             DUF11  51 s 51 
                                        
  gi|330507300|ref|YP_004383728.1| 275 E 275
                                       1 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 1.8e-05
                             DUF11  15 tvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvrvtrta 82 
                                       + ty l  + +  ++a ++ vtDt+P+   ++svs   +  +++t+     ++ + ++  +++t +v++t 
  gi|330507300|ref|YP_004383728.1| 334 AWTYHLSIKSNLDRTA-DLEVTDTVPQEAVMISVSPE-PDERTATTLkwkLEVMPRQEMSINYTYQVKTTE 402
                                       5689999999999999.*******************9.444444444567899999999999999999886 PP

>> DUF4897  Domain of unknown function (DUF4897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.2   5.5e+03     115     138 ..      62      85 ..      52      93 .. 0.63
   2 !   15.1   0.1   3.5e-06     0.016     102     144 ..     340     381 ..     290     387 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                           DUF4897 115 elvvslPkdaklisvePtPtkive 138
                                       ++vv++P+ a++ sv    ++++ 
  gi|330507300|ref|YP_004383728.1|  62 KFVVNVPDKADFGSVLLSVSNATT 85 
                                       488888888887666555555554 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.5e-06
                           DUF4897 102 slgdiklnlagdselvvslPkdaklisvePtPtkivenellWk 144
                                       s+++ +l+ + d e++ ++P++a++isv P P ++++ +l Wk
  gi|330507300|ref|YP_004383728.1| 340 SIKS-NLDRTADLEVTDTVPQEAVMISVSPEPDERTATTLKWK 381
                                       4443.5667777778889************************8 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 !   15.1   0.3   4.4e-06      0.02      22     100 ..     326     403 ..     323     407 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.4e-06
                                       EEE--SSS-EEEEEEE---------EEE--EES-----------EEE-SSSEEE-EEE---TT-EEEE----SS-GG CS
                           Top6b_C  22 reveengdgvevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlkWelsvsageskvleYsvdseae 98 
                                       r+v+e  +  + +l++k + d+++++e+++++p+e+  +s +++  e      lkW+l+v + ++  ++Y+ + +++
  gi|330507300|ref|YP_004383728.1| 326 RTVKEIRQAWTYHLSIKSNLDRTADLEVTDTVPQEAVMISVSPEPDE-RTATTLKWKLEVMPRQEMSINYTYQVKTT 401
                                       7777776778899**********************998887776655.445689**************998776665 PP

                                       GS CS
                           Top6b_C  99 ee 100
                                       e 
  gi|330507300|ref|YP_004383728.1| 402 ES 403
                                       54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 2676.05
//
Query:       gi|330507301|ref|YP_004383729.1|  [L=139]
Description: heat shock protein Hsp20 [Methanosaeta concilii GP6]
Scores for complete 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   48.7   0.1    8.7e-13   48.3   0.1    1.2  1  HSP20       Hsp20/alpha crystallin family
    4.9e-11   42.0   0.1      7e-11   41.5   0.1    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA
  ------ inclusion threshold ------
      0.047   14.7   0.0      0.081   13.9   0.0    1.4  1  CS          CS domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.1   1.5e-16   8.7e-13      13     101 ..      55     138 ..      44     139 .] 0.93

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.5e-16
                                       EE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTEEEEEEEBSS CS
                             HSP20  13 ldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvLtvtvpkke 89 
                                       +++pg +k+ +++ v+++++ v ++      ++++l++e +s + +r+++LP +v++++v+a +kdG+L+v++pk  
  gi|330507301|ref|YP_004383729.1|  55 VALPGASKDMIDLRVTEDSLYVDAKAS--PREGRYLRQELNSISLKREIKLPAEVKPEQVRAMFKDGILEVHLPKLV 129
                                       679***********************9..88999*****************************************99 PP

                                       --..-------- CS
                             HSP20  90 pekkkkerkiqi 101
                                            + +k+q+
  gi|330507301|ref|YP_004383729.1| 130 VV---NAQKVQV 138
                                       98...5666766 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 !   41.5   0.1   1.2e-14     7e-11       8      63 .]      55     125 ..      38     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.2e-14
                        ArsA_HSP20   8 ldLPfvdkeeidlsrsgdeLtIkig................nfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                       ++LP+++k+ idl+ ++d L + ++                + +R+i LP  ++ ++v +A f+dg Le+++
  gi|330507301|ref|YP_004383729.1|  55 VALPGASKDMIDLRVTEDSLYVDAKaspregrylrqelnsiSLKREIKLPAEVKPEQV-RAMFKDGILEVHL 125
                                       89********************************************************.**********985 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.4e-05     0.081      16      76 .]      55     127 ..      47     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                                       EE-TTCTTTTTCEEEEEETTEEEEEETSCEEEEECE................BSS-BETTTEEEEEETTEEEEEEEB CS
                                CS  16 iyvkkvnikkkdvkvefkerslkvkigkeklliege................LfgpIdpeesswtieskkveitLkK 76 
                                       + ++++  +k+ ++++ +e+sl+v    +  + eg                 L ++++pe+ +  +++  +e++L K
  gi|330507301|ref|YP_004383729.1|  55 VALPGA--SKDMIDLRVTEDSLYVDA--KASPREGRylrqelnsislkreikLPAEVKPEQVRAMFKDGILEVHLPK 127
                                       456666..9999999******99998..3566677788888999*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1045.11
//
Query:       gi|330507302|ref|YP_004383730.1|  [L=447]
Description: dihydroorotase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-24   85.8   0.0    4.8e-24   85.3   0.0    1.2  1  Amidohydro_1  Amidohydrolase family
    2.1e-16   60.4   0.2      1e-08   35.1   0.1    2.3  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.0   5.3e-28   4.8e-24       1     343 [.      51     426 ..      51     427 .. 0.77

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 5.3e-28
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.....HHHHHHHHHHT CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.....giealleaaee 72 
                                       +vlPG IDaHvH++             +p+  ++e   sg ++   +G+ tv+d ++t+++     ++e  le a++
  gi|330507302|ref|YP_004383730.1|  51 LVLPGCIDAHVHFR-------------DPGPSYKEDWLSGSTASAAGGISTVIDQPNTDPRtldriSFEMKLERARA 114
                                       59***********9.............9*****************************99886555555555555555 PP

                                       SSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEE CS
                      Amidohydro_1  73 lplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpva 149
                                                 + ++d ++ +  + ++e+lk+  a             a+++ ++++ sd e+  +l e ++ +l  +
  gi|330507302|ref|YP_004383730.1| 115 ----------SSVVD-YCINGGPGKIEELKKAGA------------QAIGEIFCYEHSDPEIVRILAETRRLGLLAT 168
                                       ..........45666.9************99862............678899************************* PP

                                       EEETSSCHHHHHHHHHHTTTEEEETTTTSTCC..HHTTTHCCEE..EHCTCEEE.HHHHHHHHHHHHHHCEE..... CS
                      Amidohydro_1 150 iHaletkgevedaeaafgetiehgthlevaes..lglldeikli..lahgvhlt.pteaellkerlkeagva..... 216
                                       iHa + + ++e+a a   +   + + l ++ +  +++++++  +  + h++h++    ++l+ +   +  ++     
  gi|330507302|ref|YP_004383730.1| 169 IHAEDGSIIKEMAMALSSRQDPEVHSLARPVEaeVQAIEKVSGWsdRLHICHISsGQGLNLIERT--RQEWTreetv 243
                                       ***77777777777777644444334444433668888888888888888999885566666666..5555555554 PP

                                       ........HHHHHHHH.................................SEHHHHHHHHHHHHTSCEEEEEECT... CS
                      Amidohydro_1 217 ........hcpfsnsi.................................lrsgrealrkaldeGvkvglgtDga... 249
                                               h   +  +                                  + ++e+l++ l+ G + +l++D+a   
  gi|330507302|ref|YP_004383730.1| 244 aaepksaaH-NNA--NsrltcevtphhlllnvmdykkqgsllkmnpplrGKADSERLWEGLRTGSIDILASDHAphl 317
                                       677765542.233..1447899999999999999**************9999**********************9*9 PP

                                       ...........TSSCCG..GHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB-- CS
                      Amidohydro_1 250 ...........asgnsl..nlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdAD 313
                                                   +g  +  ++l  + +a+   r       +  l+l +++++  + +A+++gl+  +G+i+vGkdAD
  gi|330507302|ref|YP_004383730.1| 318 peekgediweaPAGVPGveTMLPLMLFAV---R-------RNLLRLDRLVDALATRPARIFGLA-GKGAIKVGKDAD 383
                                       99888888776444433556644455555...4.......788********************7.************ PP

                                       EEEECC....CT..........CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 314 lvvvdl....di..........laafvglkkdgnvkkvivkGkl 343
                                       lv+vd+     i           ++++g+k  + ++++i++G +
  gi|330507302|ref|YP_004383730.1| 384 LVIVDPkrvaEIradrlhsradWTPYEGMKAIF-PRMTIIRGSV 426
                                       ****99655422666677777655555555444.6666666655 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   4.6e-09   4.2e-05       3      49 ..      45      91 ..      43     100 .. 0.91
   2 !   35.1   0.1   1.2e-12     1e-08     405     472 ..     348     427 ..     328     428 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.6e-09
                      Amidohydro_3  3 iDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavr 49
                                      iDa+G+lvlPG +D+H H    g  + + +l++++++++ g+ t+++
  gi|330507302|ref|YP_004383730.1| 45 IDAQGMLVLPGCIDAHVHFRDPGPSYKEDWLSGSTASAAGGISTVID 91
                                      9**********************888999999999999999999986 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 1.2e-12
                      Amidohydro_3 405 deelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear............vrltvvd 468
                                       ++ l l  +++++ ++pA+++gl  + G ++vG+dADlv+ d +  +++ +++l++              +r+t+++
  gi|330507302|ref|YP_004383730.1| 348 RNLLRLDRLVDALATRPARIFGLAGK-GAIKVGKDADLVIVDpKRVAEIRADRLHSRAdwtpyegmkaifPRMTIIR 423
                                       567889999****************8.***************8777889988888888999**************** PP

                      Amidohydro_3 469 Grvv 472
                                       G vv
  gi|330507302|ref|YP_004383730.1| 424 GSVV 427
                                       *998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3285.69
//
Query:       gi|330507303|ref|YP_004383731.1|  [L=160]
Description: hypothetical protein MCON_1193 [Methanosaeta concilii GP6]
Scores for complete 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-71  237.4   0.0    5.9e-71  237.3   0.0    1.0  1  Adenosine_kin  Adenosine specific kinase


Domain annotation for each model (and alignments):
>> Adenosine_kin  Adenosine specific kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.3   0.0   3.3e-75   5.9e-71       1     154 []       6     159 ..       6     159 .. 1.00

  Alignments for each domain:
  == domain 1  score: 237.3 bits;  conditional E-value: 3.3e-75
                                       EEE---TTEEEEEEEESSTTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TTEE CS
                     Adenosine_kin   1 vkiekpeevnvilgqshfiktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigaghvf 77 
                                       vk+e+pe+ n++lgqshfikt edlyea++ ++pg+kfg+af+Easg++Lvr egnd elve+a+kn l +++gh+f
  gi|330507303|ref|YP_004383731.1|   6 VKMEIPEGSNLVLGQSHFIKTAEDLYEAMAGTAPGAKFGIAFSEASGDCLVRSEGNDLELVEAAKKNSLCLACGHTF 82 
                                       79*************************************************************************** PP

                                       EEEEEST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTTS- CS
                     Adenosine_kin  78 villknafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkigYk 154
                                       v+l++ afPinvlnaiks++ev+ if+Atanplev+vaet+ grg++gv+DGf p+g e++++++er+ llr++gYk
  gi|330507303|ref|YP_004383731.1|  83 VLLMNGAFPINVLNAIKSIQEVCGIFCATANPLEVVVAETDLGRGIMGVIDGFVPRGAENDQQVEERRLLLRRFGYK 159
                                       ****************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1269.09
//
Query:       gi|330507304|ref|YP_004383732.1|  [L=93]
Description: hypothetical protein MCON_1194 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        1.4    8.9   3.7        1.8    8.5   3.7    1.3  1  RseC_MucC  Positive regulator of sigma(E), RseC/MucC
        3.9    5.6   7.0        4.2    5.5   7.0    1.0  1  DUF2070    Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.7   0.00021       1.8      66     120 ..      24      79 ..      10      85 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00021
                         RseC_MucC  66 aallvYllPl.lllilgallgsallgssellaalgallglvlgflivrllskrlkk 120
                                       +a+++ ++ l + +  +++l  + +++s ++a+  a+l++++++l  r++ ++++k
  gi|330507304|ref|YP_004383732.1|  24 QAAIAAAFVLlIYIPYSYFLLRMSFTESIAMAVYSAVLFMAIYYLTSRFILRKTRK 79 
                                       444433333303333444444444466778999999************99998654 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   7.0   0.00047       4.2     117     181 ..      17      79 ..       3      86 .. 0.47

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.00047
                           DUF2070 117 lvlvavsdesllkavlpaliqpllailllvlyfspesfllllllslifalavylfivvvdrplkr 181
                                         + ++ ++ +  a ++ + +p++++ll + +  +es+++++ + ++f+++ yl  +++ r++++
  gi|330507304|ref|YP_004383732.1|  17 RQYALIQQAAIAAAFVLLIYIPYSYFLLRMSF--TESIAMAVYSAVLFMAIYYLTSRFILRKTRK 79 
                                       33333333333333333333333333333333..4455555555555555556666666666655 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:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 679.68
//
Query:       gi|330507305|ref|YP_004383733.1|  [L=341]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.42   10.4  34.2          1    9.2  11.0    2.8  3  DUF4013   Protein of unknown function (DUF4013)
        2.9    7.6  24.8      0.019   14.8  10.5    2.5  3  UPF0259   Uncharacterised protein family (UPF0259)


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 ?    9.2  11.0   0.00011         1      35     160 ..      43     191 ..      36     196 .. 0.67
   2 ?    8.8  17.9   0.00015       1.4      50     167 ..     177     291 ..     166     292 .. 0.61
   3 ?   -3.8   0.1       1.2     1e+04     101     108 ..     306     313 ..     297     324 .. 0.43

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00011
                           DUF4013  35 PefddwgkllvdGlkafvvslvYllipliialltllvalaslaagdsaa.gallvlall.................. 92 
                                        e +++gkl+ +G+ ++   l  l++p+i+     +++++ l+ ++  +   l+++  +                  
  gi|330507305|ref|YP_004383733.1|  43 NEMEEIGKLIGKGFGIWKKNLN-LCVPFIF-----SGFASILIVAAFFIaMFLAAMP-Flgedwthledledaevme 112
                                       5788999*******99999999.5599999.....2222222222222202222222.2467778888889999999 PP

                           DUF4013  93 ............glllalllvllllllfglllpvalarfartgslsaafnfkeilklikkkigkyiialilllvigi 157
                                                    +l+++l+++++l l+g ++ ++++ +ar+  ++   + +++++  +k ++++++  +++ ++ +
  gi|330507305|ref|YP_004383733.1| 113 glfagmdwqdflPILILFLGMIVVLSLVGSYFNAGAIGMARQALVEGKSRTSAMWSAGRKHFWNMFLLSLIMGLA-T 188
                                       999999****9955555556666666699999***********99999********8877765555555554443.2 PP

                           DUF4013 158 vls 160
                                       +++
  gi|330507305|ref|YP_004383733.1| 189 MAG 191
                                       222 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00015
                           DUF4013  50 afvvslvYlliplii...alltllvalaslaagdsaagallvlallglllalllvllllllfglllpvalarfartg 123
                                       +f++sl+++ + ++    +ll +++ l+ +++g+  ++ +l+++l g++l++l +l+    ++++l +a  +++ +g
  gi|330507305|ref|YP_004383733.1| 177 MFLLSLIMG-LATMAgliFLLPGMGQLTLALSGNLDNLEGLGMILAGFMLFILYALI----LSVILALAPYALVLEG 248
                                       566666666.33333233455556666666666666677777777777777774444....4444445555555555 PP

                           DUF4013 124 .....slsaafnfkeilklikkkigkyiialilllvigivlsllaillv 167
                                             ++a+++f +  k       +++i +++++++++vl+++++l++
  gi|330507305|ref|YP_004383733.1| 249 agpvqAIRAGIDFFRYNK------FDVLILWLVVMALSVVLQMIGSLIS 291
                                       100124555555555555......79********************985 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.2
                           DUF4013 101 vllllllf 108
                                        l++ll++
  gi|330507305|ref|YP_004383733.1| 306 SLVSLLVL 313
                                       22222222 PP

>> UPF0259  Uncharacterised protein family (UPF0259)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.4      0.42   3.8e+03     193     213 ..      65      86 ..      56      97 .. 0.46
   2 ?    3.3   1.0    0.0065        58      92     157 ..     137     200 ..     113     210 .. 0.79
   3 ?   14.8  10.5   2.1e-06     0.019     144     242 ..     219     316 ..     215     327 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.42
                           UPF0259 193 liaPavllWllvkllll.llis 213
                                       l +P +++ ++  l++  ++i+
  gi|330507305|ref|YP_004383733.1|  65 LCVPFIFSGFASILIVAaFFIA 86 
                                       4444444433333222112222 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0065
                           UPF0259  92 ssLignalLlgnlitliqlvsekk.rvsilnaiglsllllPklliLiflttlliqlGllllliPGii 157
                                        sL+g+ + +g++ +  q + e+k r s++ + g + +   +++ L  ++ l +  Gl++ l+PG+ 
  gi|330507305|ref|YP_004383733.1| 137 LSLVGSYFNAGAIGMARQALVEGKsRTSAMWSAGRKHFW--NMFLLSLIMGLATMAGLIF-LLPGMG 200
                                       579999999999988877666665266999999999888..99999999********976.569974 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 2.1e-06
                           UPF0259 144 iqlGllllliPGiivaillslsPiillkekksildsikasvnitfknikliaPavllWllvklllll..liskfsll 218
                                       i  G++l+++  +i++++l+l+P  l+ e  + +++i+a +   f++ k    +++lWl+v  l ++  +i ++  +
  gi|330507305|ref|YP_004383733.1| 219 ILAGFMLFILYALILSVILALAPYALVLEGAGPVQAIRAGIDF-FRYNKF--DVLILWLVVMALSVVlqMIGSLISS 292
                                       567**************************************97.666665..4577888776654440144555566 PP

                           UPF0259 219 skkiaflllnllsnlisailiiYl 242
                                        +++a+ ll+l++ l+s +++  l
  gi|330507305|ref|YP_004383733.1| 293 GNEVAYQLLSLATSLVSLLVLAPL 316
                                       789*********999999887533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2433.27
//
Query:       gi|330507306|ref|YP_004383734.1|  [L=416]
Description: hypothetical protein MCON_1197 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-35  119.9   0.1    8.9e-35  119.1   0.1    1.4  1  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
    0.00067   19.4   0.2     0.0041   16.9   0.0    2.1  2  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.017   15.4   0.1      0.039   14.2   0.1    1.5  1  DUF5403         Family of unknown function (DUF5403)
      0.074   12.3   0.0       0.24   10.6   0.0    1.8  2  DS              Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   0.1     2e-38   8.9e-35       3     100 .]      10     107 ..       8     107 .. 0.99

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 2e-38
                                       EEEEEEXXTTSSHHHHHHHHHHHTTXEEEEEEEEXXSSTTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSCCCCEE CS
                    Saccharop_dh_N   3 eveleGhliDsgilnkvldlileaggsfevlefevGkkkkdtSyaelevsaedeevLeeileeltelgaelveeedv 79 
                                       e+e++GhliDs++l+kvld+i+++gg+fe+++f++G kk+dtSy +++v +ed  +L++il el++lga++ve+ dv
  gi|330507306|ref|YP_004383734.1|  10 EIEMNGHLIDSQMLAKVLDKIMDMGGEFEIKNFRIGLKKNDTSYIQITVAGEDGYHLDRILLELHALGARMVEMVDV 86 
                                       89*************************************************************************** PP

                                       EECESSCTTB--TTB----SS CS
                    Saccharop_dh_N  80 klekaekdgvlpedFYsttnh 100
                                       k+e a++d+v+p++FYsttnh
  gi|330507306|ref|YP_004383734.1|  87 KTEIAPRDMVVPRGFYSTTNH 107
                                       ********************8 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.17   7.6e+02      12      66 ..     203     257 ..     188     263 .. 0.77
   2 !   16.9   0.0   9.1e-07    0.0041      67     137 .]     329     400 ..     310     400 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.17
                                       SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGG CS
                      TPP_enzyme_M  12 krpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglh 66 
                                        ++++++G      ga+  l+ l+++  i v+   ++  v + + +l+  +lg+ 
  gi|330507306|ref|YP_004383734.1| 203 GKIAVVCGPALVHTGAAPSLAWLIREGYIDVLLAGNAVAVHDIERQLFGTSLGMN 257
                                       3789999999999999999999999999999888888888888888887788875 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 9.1e-07
                                       SCHHHHHHHHH-SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC....--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  67 gskaanealeeaDlvlalGarfddirttgsepefapeakiihididpaeigkny....qvdlaivgdvketleaL 137
                                       +++a ++al+     ++lG+ ++ i +++  p f    k i idi+pa++ k        ++++v d++ +l +L
  gi|330507306|ref|YP_004383734.1| 329 AKYAMDKALQGVEMTIMLGTMLHSIAVGNLLPSFV---KTICIDINPATVTKLMdrgsAQAIGLVTDIGIFLPQL 400
                                       5678899*****************99998888887...67**********99984443366999***99999887 PP

>> DUF5403  Family of unknown function (DUF5403)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   8.8e-06     0.039      50      87 ..     118     154 ..     112     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.8e-06
                           DUF5403  50 ievetgrvdstvsleDPavlsieyGHlakegarwVpGi 87 
                                       +eve++++d  v+leD  ++    GH+ k++ r V G+
  gi|330507306|ref|YP_004383734.1| 118 VEVEHNHMDCLVVLEDGRAICTPIGHIKKGD-RVVIGT 154
                                       89**************************999.999987 PP

>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.3e-05      0.24      28      85 ..     199     255 ..     184     275 .. 0.79
   2 ?   -2.2   0.0      0.43   1.9e+03     149     165 ..     293     309 ..     264     317 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.3e-05
                                DS  28 kdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgkktylg 85 
                                       k+   +i + +  +l+ +G    +a+l++e+++dv+ +  +   +D+ + l   t lg
  gi|330507306|ref|YP_004383734.1| 199 KKAGGKIAVVCGPALVHTGAAPSLAWLIREGYIDVLLAGNAVAVHDIERQLFG-TSLG 255
                                       45556788888899****************************9***9888766.5555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.43
                                DS 149 eeSilywAykndipvfc 165
                                       + +i+y A k++ip   
  gi|330507306|ref|YP_004383734.1| 293 KGGIIYEAIKKGIPCIL 309
                                       56899999999999755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3009.60
//
Query:       gi|330507307|ref|YP_004383735.1|  [L=153]
Description: ectoine synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-55  185.9   0.0    9.7e-31  106.6   0.0    2.0  2  Ectoine_synth  Ectoine synthase
     0.0034   17.1   0.3        0.2   11.4   0.3    2.3  1  Cupin_2        Cupin domain


Domain annotation for each model (and alignments):
>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   1.1e-34   9.7e-31       1      72 [.       1      72 [.       1      83 [. 0.96
   2 !   77.8   0.0     9e-26   8.1e-22      74     125 ..      95     146 ..      82     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 1.1e-34
                                      -EEEEHHHHTTSTTEEEETTEEEEEEE-GGGSSSSEEEEEEE-TT--EEEE-TT-EEEEEEEE--EEEEETT CS
                     Ectoine_synth  1 mivrtleeiekterevksenweskRlllkddgmGfslhettikagtetelkYknHleavycieGegeveele 72
                                      mi+r+le++e+++r+v +enwes+Rlllk d mGfs+h+tti+ gtet+++YknHle+vycieGegeve l+
  gi|330507307|ref|YP_004383735.1|  1 MILRNLEDAERSDRRVVAENWESVRLLLKGDCMGFSFHITTIYPGTETHIWYKNHLESVYCIEGEGEVEVLD 72
                                      9*******************************************************************9875 PP

  == domain 2  score: 77.8 bits;  conditional E-value: 9e-26
                                       --EEEE-TTEEEEETTT-EEEEEESS-EEEEEEEES--XSSSTTTTBXXXXX CS
                     Ectoine_synth  74 gevyeikpgtlYlldkhdkHllrakkelrlvcvFnPpltGkevHdedgvypl 125
                                          y+i pgt+Y+ldk+d+H+lrak+ ++l+cvFnPpl+G+e+Hdedg+ypl
  gi|330507307|ref|YP_004383735.1|  95 CVIYRIAPGTIYVLDKNDRHILRAKTTMKLACVFNPPLNGREIHDEDGAYPL 146
                                       578***********************************************98 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.3   2.2e-05       0.2       4      37 ..      41      74 ..      38     128 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.2e-05
                                      EEETTE.EEEEECSSSEEEEEEEEESEEEEE.ECTE CS
                           Cupin_2  4 elppGe.sapshrHpgedeffyVleGegelt.vdge 37
                                      ++ pG+ ++ +    +  e +y++eGege++ +dg 
  gi|330507307|ref|YP_004383735.1| 41 TIYPGTeTHIWYK-NHL-ESVYCIEGEGEVEvLDGT 74
                                      6778775555555.333.78***********88864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1231.45
//
Query:       gi|330507308|ref|YP_004383736.1|  [L=450]
Description: diaminobutyrate--2-oxoglutarate aminotransferase [Methanosaeta concilii GP6]
Scores for complete 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-79  267.3   0.0    2.2e-79  267.0   0.0    1.0  1  Aminotran_3      Aminotransferase class-III
  ------ inclusion threshold ------
      0.047   13.0   0.0      0.074   12.3   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
       0.12   12.5   0.1       0.88    9.7   0.0    2.3  2  DUF1263          Protein of unknown function (DUF1263)


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 !  267.0   0.0   3.6e-83   2.2e-79       9     404 ..      34     425 ..      27     427 .. 0.89

  Alignments for each domain:
  == domain 1  score: 267.0 bits;  conditional E-value: 3.6e-83
                                       SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHH....HH CS
                       Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekl....lk 81 
                                       +++v tka+G+ ++d+ g++y+D++++  ++n Gh++P++ + + e +++  +v    l +e  +++ e      lk
  gi|330507308|ref|YP_004383736.1|  34 FPVVFTKAKGATIEDEKGREYIDFLAGAGALNYGHNNPAIKEKLLEYIESDKIVHSLDLVTEAKQAFIETFdsliLK 110
                                       5699*************************************999887765555555566666666666666552355 PP

                                       HCT-..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEE CS
                       Aminotran_3  82 lapkgldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevv 158
                                         +  + + f+  +G++Ave+A+K+ar+       t ++ ii+f+++fHG tlg++++tg+ +  ++ +g  l +++
  gi|330507308|ref|YP_004383736.1| 111 PRGMRYKMQFTGPTGTNAVEAAMKIARN------VTGRSTIISFTNGFHGVTLGSVAATGN-SYFRDACGIQLHGTT 180
                                       555555599*******************......9**************************.99999********** PP

                                       EE-TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TT CS
                       Aminotran_3 159 rlkypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvq 235
                                       +++++    + e+ ++++ l + l++ +    d+ aAvivE+iqgegG++va+ e+l+ l  +c+kh++lli+D +q
  gi|330507308|ref|YP_004383736.1| 181 FMPFDG--YMGEEVDTTEYLDKVLTD-RSSGLDQPAAVIVETIQGEGGINVATSEWLRSLERICRKHGILLIIDDIQ 254
                                       ****96..344555566666666666.57888999****************************************** PP

                                       TTTTTTSSSSGGGGCTS--SEEEE-GGGGT.TSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHH.HH CS
                       Aminotran_3 236 tGfGrTGklfAlehagvspDlmtlaKaltg.GlplsavlataevmqalapgshgsTfgGnplacavalavleii.ee 310
                                       +G GrTG++f  e+a +spD+++l+K+l++ G+p+s vl +  + ++++pg+h +Tf Gn la + a+a++e    +
  gi|330507308|ref|YP_004383736.1| 255 VGCGRTGTFFSFEEAKISPDIIILSKSLSSyGIPFSMVLMKPGI-DQWKPGEHNGTFRGNNLAFVTARAAIEEYwSD 330
                                       ****************************9757*******99987.6788**********************876267 PP

                                       TTHHHHHHHHHHHHHHHHHHHCTT-.TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETT..TEEEE CS
                       Aminotran_3 311 ekllenaqelgaalkegLeelqkky.evikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGd..nvirl 384
                                       + + ++++ +g+ ++e+  +l + +     + Rg+G++ a+++   + +    i + a ekG++i ++G   +v+++
  gi|330507308|ref|YP_004383736.1| 331 ASFSRKVRMKGEFVREHFDKLVDLDdTGTLSARGRGMVQALDCRTGEIAS--MISHVAFEKGLIIETSGAedQVLKF 405
                                       99*******************9999788999**************99966..899**************8889**** PP

                                       ---TT--HHHHHHHHHHHHH CS
                       Aminotran_3 385 lppliitdeeidelleilkk 404
                                       l pl+i+d+e+d++l+il++
  gi|330507308|ref|YP_004383736.1| 406 LAPLTISDHELDKGLSILEE 425
                                       ****************9987 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.2e-05     0.074      80     167 ..     164     251 ..      93     253 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                                       -HHHHSSTTHHHHCC--EEEEE-EBTT.............TBE.-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTT CS
                   Beta_elim_lyase  80 ahihfdetgaiaelagvklrdlknkea.............Gkm.dlekleaaikevgaheekiklisltvTnntagG 142
                                       ++ +f+ + +i              +               ++ + e l ++++++++  ++++++++++     gG
  gi|330507308|ref|YP_004383736.1| 164 GNSYFRDACGI--------------QLhgttfmpfdgymgEEVdTTEYLDKVLTDRSSGLDQPAAVIVETIQG-EGG 225
                                       44444444444..............333444444443332444145778888888777455555555554444.567 PP

                                       .B---HHHHHHHHHHHHHCT-EEEEE CS
                   Beta_elim_lyase 143 .qvvsleelrevaaiakkygiplhlD 167
                                        +v + e+lr +  i++k+gi l++D
  gi|330507308|ref|YP_004383736.1| 226 iNVATSEWLRSLERICRKHGILLIID 251
                                       3678899*****************99 PP

>> DUF1263  Protein of unknown function (DUF1263)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.28   1.7e+03      14      26 ..     128     141 ..     125     145 .. 0.70
   2 ?    9.7   0.0   0.00015      0.88       6      23 ..     282     299 ..     280     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.28
                           DUF1263  14 am.vrlkpgsdltg 26 
                                       a+ +++k   ++tg
  gi|330507308|ref|YP_004383736.1| 128 AVeAAMKIARNVTG 141
                                       45578888888887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00015
                           DUF1263   6 psSyndllamvrlkpgsd 23 
                                       +sSy++   mv +kpg+d
  gi|330507308|ref|YP_004383736.1| 282 LSSYGIPFSMVLMKPGID 299
                                       8***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3226.57
//
Query:       gi|330507309|ref|YP_004383737.1|  [L=176]
Description: L-2,4-diaminobutyric acid acetyltransferase [Methanosaeta concilii GP6]
Scores for complete 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   44.4   0.0    2.3e-11   43.9   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.9e-05   25.0   0.0    2.9e-05   24.4   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
      0.002   18.1   0.0     0.0028   17.6   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0034   18.0   0.0     0.0044   17.7   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.032   14.3   0.0      0.057   13.5   0.0    1.3  1  Tautomerase_2    Tautomerase enzyme
      0.058   13.5   0.0       0.22   11.6   0.0    1.9  1  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   7.8e-15   2.3e-11      28     114 ..      51     135 ..      27     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 7.8e-15
                                       HHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETT CS
                    Acetyltransf_1  28 fsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveed 104
                                        ++ a++++vaee+ge+++f+s++  pd + +v +i+++aV+ + r++G+++++l +++ r   + +++i+ +++++
  gi|330507309|ref|YP_004383737.1|  51 CRDFADTCVVAEEGGEIVAFLSGYRPPD-RWDVFFIWQIAVDVDSRNRGIAKRMLFDVLNRPSTRDCRYIETTISPS 126
                                       4557779999******************.779****************************************9**** PP

                                       EHHHHHHHHH CS
                    Acetyltransf_1 105 ndaairlYek 114
                                       n+a+ rl+ +
  gi|330507309|ref|YP_004383737.1| 127 NEASKRLF-R 135
                                       ******99.5 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   9.7e-09   2.9e-05       3      48 ..      56     107 ..      54     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 9.7e-09
                                       EEEEEEEETTEEEEEEEEEEES.....TCTEEEEE-GGGTTSSHHHHHH.HH CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld.....aeitrlaVdpeyrgkGiGraLl.ea 48 
                                       +++ Vae++g+iv f++ ++       + i+ +aVd + r++Gi++++l ++
  gi|330507309|ref|YP_004383737.1|  56 DTCVVAEEGGEIVAFLSGYRPPdrwdvFFIWQIAVDVDSRNRGIAKRMLfDV 107
                                       57999********9998888879888666666****************9443 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   9.5e-07    0.0028      32      97 ..      57     129 ..      49     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.5e-07
                   Acetyltransf_10  32 lllvaeeggkivGviel.rdgs.....hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnaspya 97 
                                       +++vaeegg+iv +++  r  +      i  ++Vd + r +Gi+k++l +v+++ ++++ +  e+t+  s++a
  gi|330507309|ref|YP_004383737.1|  57 TCVVAEEGGEIVAFLSGyRPPDrwdvfFIWQIAVDVDSRNRGIAKRMLFDVLNRPSTRDCRYiETTISPSNEA 129
                                       689***********955344446688899999**********************7777777779999888865 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.5e-06    0.0044      56     133 ..      58     135 ..       8     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-06
                    Acetyltransf_3  56 waivlkdtgv.iGsv.glrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSir 130
                                       +++  +++g+ + +  g+r+ +++d ++   + ++ +++++G+a+ ++  +l+   ++ + ++++ +i+++NeaS r
  gi|330507309|ref|YP_004383737.1|  58 CVVA-EEGGEiVAFLsGYRPPDRWDVFFIWQIAVDVDSRNRGIAKRMLFDVLNRP-STRDCRYIETTISPSNEASKR 132
                                       4453.3334447777688888888877777788888899****************.5666***************** PP

                    Acetyltransf_3 131 vle 133
                                       +++
  gi|330507309|ref|YP_004383737.1| 133 LFR 135
                                       997 PP

>> Tautomerase_2  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.9e-05     0.057      13      63 ..     102     148 ..      98     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                                       GEE--T.....TS-TT-EEEEEEEES---HHHHHHHHHHHHHHHHHHH--- CS
                     Tautomerase_2  13 elviddtylgieRsddlvvieitlsegRseeqKkaLyralaerlaaklgir 63 
                                       ++ +d   l+ + ++d+ +ie t+s   s+e+ k+L+r la++l a+++++
  gi|330507309|ref|YP_004383737.1| 102 RMLFDV--LNRPSTRDCRYIETTIS--PSNEASKRLFRGLAQELDAHCDVS 148
                                       666664..8899999******9999..799999***************997 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.5e-05      0.22      44     101 ..      58     110 ..      50     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.5e-05
                                       EEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHH CS
                    Acetyltransf_9  44 vlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaralee 101
                                       +++ae++ge+v+ l  ++     p  ++++  +  +av+ + r+rg+++++l  +l++
  gi|330507309|ref|YP_004383737.1|  58 CVVAEEGGEIVAFLSGYR-----PPDRWDVFFIWQIAVDVDSRNRGIAKRMLFDVLNR 110
                                       678888888888887776.....568999**********************9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 1021.28
//
Query:       gi|330507310|ref|YP_004383738.1|  [L=247]
Description: hypothetical protein MCON_1202 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   13.5   0.0       0.14   11.5   0.0    2.0  2  AroM      AroM protein


Domain annotation for each model (and alignments):
>> AroM  AroM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     8e-06      0.14     163     207 ..      64     107 ..      43     133 .. 0.91
   2 ?   -0.6   0.0      0.04   7.2e+02     164     203 ..     181     220 ..     159     235 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8e-06
                              AroM 163 eelaeaarelaeqgadlivldciGYteemkaavaealgkpVllar 207
                                       e l++aa+el +qg+  i  dc G+ + +++ +a++l++pV l+ 
  gi|330507310|ref|YP_004383738.1|  64 ELLHTAAEELVSQGVRAITGDC-GFLAIHQRSLAAVLDVPVFLSS 107
                                       67899*****************.*******************997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.04
                              AroM 164 elaeaarela.eqgadlivldciGYteemkaavaealgkpV 203
                                       +l+ a++ ++ eq++  i+l+c       + a+++a+++pV
  gi|330507310|ref|YP_004383738.1| 181 ALSVASEMVEeEQNVRAILLECSCLPPYAR-AIQKAIELPV 220
                                       444444444313556666666654443333.3455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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 0.22s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1722.31
//
Query:       gi|330507311|ref|YP_004383739.1|  [L=160]
Description: PUA domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   61.8   1.3    6.6e-17   61.2   1.3    1.3  1  PUA       PUA domain
    0.00019   21.6   0.0    0.00031   21.0   0.0    1.3  1  UPF0113   UPF0113 PUA domain
  ------ inclusion threshold ------
      0.042   14.1   0.0      0.094   13.0   0.0    1.5  1  FliO      Flagellar biosynthesis protein, FliO
       0.13   12.9   0.0          1   10.1   0.0    2.1  1  Pre-PUA   Pre-PUA-like domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   1.3   1.5e-20   6.6e-17       3      73 ..      80     150 ..      78     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1.5e-20
                                       EEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA   3 vvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveierv 73 
                                       vvvd gAv+++++ga+++ pG+v ++ ++ +gd V+iv e   +++a+G+a++ + e+ k +g+ ++ +++v
  gi|330507311|ref|YP_004383739.1|  80 VVVDSGAVRFVVNGADIMKPGIVTADPEIAPGDLVVIVEERhKKPLAIGRALVAGTEM-KGEGKAVKSLHHV 150
                                       8***************************************889***************.5667777666665 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.8e-08   0.00031       2      71 ..      80     151 ..      79     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.8e-08
                           UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenq.vvvVlnengeplGiGkirkdtk.aspgkivvknlaDiG 71 
                                       vvv+  a + ++ G d++k +i++ ++++  ++ vv+V    ++pl+iG++   +   + +++ vk l  +G
  gi|330507311|ref|YP_004383739.1|  80 VVVDSGAVRFVVNGADIMKPGIVTADPEIAPGDlVVIVEERHKKPLAIGRALVAGTeMKGEGKAVKSLHHVG 151
                                       6777777777788*************999966605555677799*******998855899999999887777 PP

>> FliO  Flagellar biosynthesis protein, FliO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.1e-05     0.094      19      50 ..      63      94 ..      55      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                              FliO 19 rrlkvvaslalgpkervvlVevgeellllGvt 50
                                      + + v++++ lgp +r+v+V+ g   +++ ++
  gi|330507311|ref|YP_004383739.1| 63 PFFTVLGAIDLGPSKRLVVVDSGAVRFVVNGA 94
                                      56789*****************9999998665 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00023         1       6      76 ..       2      64 ..       1      69 [. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00023
                           Pre-PUA  6 kvksntqlksSdrrkLraklleqfpslseeqleellpkkeevkvvklqgehvelyvvdgeplffqdregel 76
                                      k+ks+++lk+Sd+rk  a +    p l   + + +   k++++ +    e + l++v+g pl++ + ++++
  gi|330507311|ref|YP_004383739.1|  2 KIKSRHHLKGSDARKVVACIE---PFL---DDSSV-LRKASLERAVSD-EGLDLIFVNGRPLMMIVDDEPF 64
                                      79*************998885...445...11222.344555555445.6777777777777666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1120.43
//
Query:       gi|330507312|ref|YP_004383740.1|  [L=78]
Description: LSM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   75.2   0.2    2.6e-21   75.1   0.2    1.0  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.016   15.4   0.0      0.018   15.1   0.0    1.2  1  SM-ATX    Ataxin 2 SM domain
       0.12   12.1   0.1       0.29   10.8   0.0    1.6  2  Tudor_2   Jumonji domain-containing protein 2A Tudor 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 !   75.1   0.2   4.3e-25   2.6e-21       3      67 .]      15      78 .]      13      78 .] 0.97

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 4.3e-25
                                      HHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                               LSM  3 lkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                      l++++n  v+v+lk+gr++rG L+g+D +mNlv++++ee+ ++    r++g+v++RG+n+v+is+
  gi|330507312|ref|YP_004383740.1| 15 LNESLNGPVIVKLKDGRVFRGELQGYDIHMNLVMDKTEEVAEGA-VARNIGTVIVRGDNVVYISP 78
                                      8999**************************************99.******************96 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.1e-06     0.018      15      51 ..      22      56 ..      13      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-06
                                      EEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS CS
                            SM-ATX 15 evevtvknGevyeGifstvslekdfsvvLkmarkvkk 51
                                      +v v++k+G v++G +++++    +++v++ + +v++
  gi|330507312|ref|YP_004383740.1| 22 PVIVKLKDGRVFRGELQGYDI--HMNLVMDKTEEVAE 56
                                      699******************..**********9998 PP

>> Tudor_2  Jumonji domain-containing protein 2A Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.9e-05      0.29       4      23 ..      23      42 ..      22      44 .. 0.90
   2 ?   -2.6   0.1      0.75   4.5e+03       3       7 ..      65      69 ..      65      73 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.9e-05
                           Tudor_2  4 VivrwtDgryYnakvigvss 23
                                      Viv+ +Dgr+++++ +g + 
  gi|330507312|ref|YP_004383740.1| 23 VIVKLKDGRVFRGELQGYDI 42
                                      9*************999875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.75
                           Tudor_2  3 dVivr 7 
                                      +Vivr
  gi|330507312|ref|YP_004383740.1| 65 TVIVR 69
                                      69999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 576.71
//
Query:       gi|330507313|ref|YP_004383741.1|  [L=56]
Description: 50S ribosomal protein L37e [Methanosaeta concilii GP6]
Scores for complete 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   78.7   8.8    2.9e-22   78.5   8.8    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
     0.0022   17.9   2.3       0.14   12.1   0.6    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
     0.0094   16.1   2.0      0.021   15.0   2.0    1.6  1  zf-piccolo      Piccolo Zn-finger
  ------ inclusion threshold ------
      0.017   14.6   2.7       0.34   10.4   0.3    2.3  2  zn-ribbon_14    Zinc-ribbon
      0.018   15.0   0.9      0.025   14.6   0.9    1.2  1  DZR             Double zinc ribbon
        0.1   12.8   3.1       0.14   12.3   2.0    1.7  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.24   11.0   1.3       0.36   10.4   1.3    1.3  1  MraY_sig1       Phospho-N-acetylmuramoyl-pentapeptide-transfe
        0.3   10.8   4.6        5.1    6.9   0.5    2.2  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
        1.7    8.4   8.9        8.4    6.2   0.3    2.7  2  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   8.8   1.5e-25   2.9e-22       1      53 [.       2      54 ..       2      55 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 1.5e-25
                    Ribosomal_L37e  1 tkGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsaKa 53
                                      tkGt+s+Gkr +k +Hi+CrrCg+ s+++++k+C +cG+ +saklr+++W +Ka
  gi|330507313|ref|YP_004383741.1|  2 TKGTPSMGKR-HKSSHIRCRRCGSISFNFKRKVCVQCGFgNSAKLRSHKWMRKA 54
                                      8*********.999**************************************98 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.6     7e-05      0.14      19      32 ..       7      24 ..       2      31 .. 0.83
   2 !    6.0   0.0    0.0056        11       6      21 ..      33      49 ..      33      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7e-05
                    Zn_ribbon_SprT 19 si.rrhn...YrCrrCkg 32
                                      s  +rh+    rCrrC++
  gi|330507313|ref|YP_004383741.1|  7 SMgKRHKsshIRCRRCGS 24
                                      555899**********85 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0056
                    Zn_ribbon_SprT  6 rCtgCgreythhlsi.r 21
                                      +C++Cg    + l++ +
  gi|330507313|ref|YP_004383741.1| 33 VCVQCGFGNSAKLRShK 49
                                      7*****77777777755 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   2.0   1.1e-05     0.021      19      48 ..      15      50 ..       3      53 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                        zf-piccolo 19 nyntCteC.......kkqvCnlCGFnptphltekkeW 48
                                       +  C  C       k++vC++CGF  + +l + + W
  gi|330507313|ref|YP_004383741.1| 15 SHIRCRRCgsisfnfKRKVCVQCGFGNSAKLRS-HKW 50
                                      55555555444444489********99877665.445 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   0.00017      0.34       2      10 ..      18      26 ..      17      29 .. 0.89
   2 ?    4.4   0.1     0.014        27       3      13 ..      34      44 ..      32      45 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                      zn-ribbon_14  2 kCerCGylS 10
                                      +C+rCG +S
  gi|330507313|ref|YP_004383741.1| 18 RCRRCGSIS 26
                                      7*******9 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.014
                      zn-ribbon_14  3 CerCGylSSqk 13
                                      C +CG+  S k
  gi|330507313|ref|YP_004383741.1| 34 CVQCGFGNSAK 44
                                      *****976665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.9   1.3e-05     0.025      27      49 .]      15      38 ..       3      39 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                               DZR 27 aedrCpsCgek.vdpearfCpeCG 49
                                      +++rC +Cg+   + + ++C +CG
  gi|330507313|ref|YP_004383741.1| 15 SHIRCRRCGSIsFNFKRKVCVQCG 38
                                      3899******99999999*****9 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.5     0.014        28      22      40 .]       4      23 ..       4      23 .. 0.91
   2 ?   12.3   2.0   7.2e-05      0.14      18      40 .]      19      38 ..      15      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.014
                     Auto_anti-p27 22 gvPLmrdr.kggkvyCvaCd 40
                                      g+P m +r k+  + C +C+
  gi|330507313|ref|YP_004383741.1|  4 GTPSMGKRhKSSHIRCRRCG 23
                                      799***999999******96 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.2e-05
                     Auto_anti-p27 18 CpvCgvPLmrdrkggkvyCvaCd 40
                                      C +Cg++ +  +   +++Cv C+
  gi|330507313|ref|YP_004383741.1| 19 CRRCGSISFNFK---RKVCVQCG 38
                                      **********86...56*****6 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   0.00018      0.36       2       8 ..       3       9 ..       3       9 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                         MraY_sig1 2 kGTPTMG 8
                                     kGTP+MG
  gi|330507313|ref|YP_004383741.1| 3 KGTPSMG 9
                                     8*****9 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3    0.0054        11      24      30 ..      19      25 ..      18      27 .. 0.88
   2 ?    6.9   0.5    0.0025       5.1       2      11 ..      29      38 ..      28      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0054
                           zf-RRN7 24 CrrChtq 30
                                      CrrC+++
  gi|330507313|ref|YP_004383741.1| 19 CRRCGSI 25
                                      *****86 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0025
                           zf-RRN7  2 ekgppCgvCg 11
                                      +k+++C +Cg
  gi|330507313|ref|YP_004383741.1| 29 FKRKVCVQCG 38
                                      6899*****8 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3    0.0042       8.4       2      10 ..      18      26 ..      18      29 .. 0.76
   2 ?    5.0   3.2    0.0098        20       2       9 ..      33      40 ..      33      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0042
                      Rubredoxin_2  2 vCsqCGfes 10
                                      +C++CG+ s
  gi|330507313|ref|YP_004383741.1| 18 RCRRCGSIS 26
                                      788998765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0098
                      Rubredoxin_2  2 vCsqCGfe 9 
                                      vC qCGf 
  gi|330507313|ref|YP_004383741.1| 33 VCVQCGFG 40
                                      7*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 426.33
//
Query:       gi|330507314|ref|YP_004383742.1|  [L=469]
Description: amidophosphoribosyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (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   80.3   0.0    1.7e-21   76.8   0.0    2.3  2  GATase_6      Glutamine amidotransferase domain
    1.4e-20   73.4   0.0    2.6e-20   72.5   0.0    1.5  1  GATase_7      Glutamine amidotransferase domain
    2.2e-07   30.1   0.0    6.6e-06   25.2   0.0    2.2  2  GATase_4      Glutamine amidotransferases class-II
    7.5e-06   25.6   0.0    1.2e-05   24.8   0.0    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
        0.1   11.3   0.1        3.4    6.3   0.0    2.3  2  GATase_2      Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0   4.7e-25   1.7e-21       6     134 .]      66     201 ..      57     201 .. 0.84
   2 ?    0.4   0.0      0.19   6.9e+02      40      58 ..     219     237 ..     215     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 4.7e-25
                          GATase_6   6 laslvedevalaHvRlaivglaeeega.qPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevlla 79 
                                       +  l +++v+++HvR a++g +   ++ qP+  + +dg ++++hNG   n  +lre+l++ +g  f s+sDtev+++
  gi|330507314|ref|YP_004383742.1|  66 I-ALLRGHVGIGHVRYATSGRS-CIENsQPLlvKYKDGAIATAHNGNLVNSTQLREQLEE-AGDIFYSTSDTEVIAH 139
                                       4.355778*************9.66666***99999************************.9*99************ PP

                          GATase_6  80 ll......eelG..eevl.erlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                       l+       +l+  +++l ++++G ++ ++     +t+  +rd lg+kpl++++ +sg+++ase
  gi|330507314|ref|YP_004383742.1| 140 LFvkellhYDLPeaARALmRKIVGSYSLVFLW--GDTVLALRDPLGIKPLCIGEIDSGFMVASE 201
                                       99998866333355444449999998887665..4566666**********************8 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.19
                          GATase_6  40 grlllvhNGeiynykelre 58 
                                       g+l+++ NGe++ y+  r 
  gi|330507314|ref|YP_004383742.1| 219 GELIVIRNGEMKSYQLARS 237
                                       7899**********84444 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   7.4e-24   2.6e-20      11     121 ..      89     205 ..      77     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 7.4e-24
                          GATase_7  11 agaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea........ewgeealerlnGmf 78 
                                       +++QP++   +dg ++ ++nG ++N ++lre+Le++g  f ++sDtev+++l+ +        e  +++++++ G++
  gi|330507314|ref|YP_004383742.1|  89 ENSQPLLVkYKDGAIATAHNGNLVNSTQLREQLEEAGDIFYSTSDTEVIAHLFVKellhydlpEAARALMRKIVGSY 165
                                       689**998789*****************************************9999*******9************* PP

                          GATase_7  79 AfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkal 121
                                       +++ +  ++  +l+ RD+lGikPL +ge + +++++aSe  a+
  gi|330507314|ref|YP_004383742.1| 166 SLVFLWGDT--VLALRDPLGIKPLCIGEID-SGFMVASESVAI 205
                                       ****99999..******************6.79******9987 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.8e-09   6.6e-06      18     121 ..      26     120 ..       5     162 .. 0.69
   2 ?    2.6   0.0     0.015        52     236     258 ..     212     234 ..     191     244 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.8e-09
                          GATase_4  18 sftgfaarggltdahadGwGiafyegkaarvfkdpepsaesplaelvreyp...iksknvvaHiRkatqGevklent 91 
                                       s+ ++++rg++        Gi+ ++gk++r+       a   ++e+  + +   ++ ++ + H+R at G+   en+
  gi|330507314|ref|YP_004383742.1|  26 SLYALQHRGQE------AAGISVHDGKSIRTHR-----AMGLVSEVFDDAQialLRGHVGIGHVRYATSGRSCIENS 91 
                                       55555555554......3356666666665432.....2233444444433223789999***************** PP

                          GATase_4  92 hpFvRelwgrewifAHnGdlkeykpklegr 121
                                       +p   ++++  +  AHnG+l + + +l+++
  gi|330507314|ref|YP_004383742.1|  92 QPLLVKYKDGAIATAHNGNLVNST-QLREQ 120
                                       ********************7633.33233 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.015
                          GATase_4 236 tWkklepGellvfrdGalvatas 258
                                         ++++pGel+v+r+G+++  + 
  gi|330507314|ref|YP_004383742.1| 212 LVRDVKPGELIVIRNGEMKSYQL 234
                                       55789***********9987644 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   3.4e-09   1.2e-05      30     120 ..     281     378 ..     259     380 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.4e-09
                                       GEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...............EE----TTSEEEEE-SEESS CS
                      Pribosyltran  30 pdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.......rlledpagkkVliVDDildt 99 
                                        d+v +i+  G+++a  ++++ ++ +   + + ++ +++  ++ +++ e+       +  ++++g+k ++VDD +  
  gi|330507314|ref|YP_004383742.1| 281 ADTVTPIPDSGITLAVGYHQHSGISYRECLMKNRYIGRTFIMPDQNMRETavrlkmnTIRPNIEGHKLILVDDSIVR 357
                                       6899999999999999999999999886666666666666777888888889999999******************* PP

                                       SHHHHHHHHHHHCC-BSEEEE CS
                      Pribosyltran 100 GgTllaalelLkekgpeevri 120
                                       G+T +++++ ++++g++ev++
  gi|330507314|ref|YP_004383742.1| 358 GTTSRRIVNMVRKAGAQEVHV 378
                                       ******************985 PP

>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0   0.00095       3.4      23      82 ..      25      83 ..       5     124 .. 0.80
   2 ?    2.8   0.0     0.011        39     329     395 ..     162     225 ..     147     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00095
                                      HHHHHGGGGS-B-TTSSSBSEEEEEEE--HHHHHHHHHHTT-----GGG-EEEEEEE-SS CS
                          GATase_2 23 ealenleHRGavgadektGDGaGillqiPdeflrkeakekgielpeageyavgmlflpkd 82
                                        l  l+HRG  +a  +  DG  i ++    ++++++++++i l + g++++g++   ++
  gi|330507314|ref|YP_004383742.1| 25 YSLYALQHRGQEAAGISVHDGKSIRTHRAMGLVSEVFDDAQIALLR-GHVGIGHVRYATS 83
                                      4578899999999999999999999999999999999999999976.8999998765544 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.011
                                       -SSEEEEEE-SSEEEEEE-TT--S--EEEEETT--EEEESSTTSS---GGGEEEEEE--TT-EEEEE CS
                          GATase_2 329 DGPalivftdGkvvgavLDRnGLRPaRylvtkddlvvlasEvGvldleeeevvekgrlqPGrmllvd 395
                                        G  ++vf  G +v a  D  G++P  +   ++++ ++asE+  +d  + ++v+   ++PG+++++ 
  gi|330507314|ref|YP_004383742.1| 162 VGSYSLVFLWGDTVLALRDPLGIKPLCIGEIDSGF-MVASESVAIDTLNGKLVR--DVKPGELIVIR 225
                                       5777899999***************9887776665.579999888888888876..589****9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3581.56
//
Query:       gi|330507315|ref|YP_004383743.1|  [L=414]
Description: major facilitator family transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-29  101.5  91.1    7.1e-23   81.1  54.0    2.4  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.028   14.9   5.1      0.028   14.9   5.1    6.1  5  FtsX      FtsX-like permease family
      0.038   13.4   1.2        2.7    7.4   0.0    2.9  2  GPI2      Phosphatidylinositol N-acetylglucosaminyltransferas


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 !   81.1  54.0   1.2e-26   7.1e-23       5     329 ..      25     348 ..      14     350 .. 0.83
   2 !   34.2  29.0   2.2e-12   1.3e-08       3     177 ..     234     412 ..     232     414 .] 0.83

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 1.2e-26
                             MFS_1   5 aflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                       + +++++ ++  +++   a++++  +s+se+ l ++++ ++++va+++ G  ++++G+r++ +lg ++ +lg +ll+
  gi|330507315|ref|YP_004383743.1|  25 GSVYSWSVFVNPLTAHFaAMGQT--VSASEVLLPFSIFLFVFSVAMVFSGKYIEKYGPRKMAMLGGIICGLG-WLLA 98 
                                       33333333333333333345555..99*********************************************.8888 PP

                             MFS_1  81 .fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                        ++ss   l+    ++ Glg g+++   +a+ a+wfp+ +rg+a+gl  +gf+++a +++ ++ +l++++   ++f 
  gi|330507315|ref|YP_004383743.1|  99 sMSSSTSmLIPTYGIVGGLGVGIAYGCPVAVSARWFPD-KRGLAVGLTVLGFGFSAFFTANIATYLIEAFDVMSTFR 174
                                       786666656778999***********************.************************************99 PP

                             MFS_1 156 ilaivsllafv...lfllllpeepperkrkspkeeekgtgpaplvp..awkallkdpvlw.illialllfffgfsgl 226
                                       +++i++++ +    + l++ p+ +++ ++++p+++     +a+++     +++lk+  ++ ++l+ +++  +g++++
  gi|330507315|ref|YP_004383743.1| 175 FFGIAFIIIITlcsMPLVFPPAGYKPAGWNPPAPK----PGAAVTCefKREQMLKSTTFYgLWLCYFIGCVAGLMAI 247
                                       99999999966677777888999*********999....66666666767777777777645555555556666668 PP

                             MFS_1 227 ltllplylqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavl 302
                                        +  p+  qev  +  gl +++  ++++a+++ ++++++g l d++ +r++ +++++l+ la+l++  +av+  +++
  gi|330507315|ref|YP_004383743.1| 248 GISKPV-GQEVILIEsGLASML--VGFFAIFNGGGRPIFGTLTDKITPRNAAIVSFVLIGLASLMMWQMAVPGATTI 321
                                       888888.799999997767777..***************************************************** PP

                             MFS_1 303 lllvlvliGfglgfvfpsllalasdla 329
                                       ++++++++ ++lg   +++ +++++++
  gi|330507315|ref|YP_004383743.1| 322 YIVAFAILWMCLGGWLAIAPTATASFF 348
                                       *******99988887777777766665 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 2.2e-12
                             MFS_1   3 laaflsalarsilgpalplalaedlg.ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       l++f+ + a  +++ +    ++++   i    +++l++++a++ + + +++G l+d++ +r   +++++l +l++l+
  gi|330507315|ref|YP_004383743.1| 234 LCYFIGCVAGLMAIGISK-PVGQEVIlIESGLASMLVGFFAIFNGGGRPIFGTLTDKITPRNAAIVSFVLIGLASLM 309
                                       555555555555555555.3444433366778999***************************************888 PP

                             MFS_1  79 ll.fa.sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWr 151
                                       ++ +a ++ + + +v+ ++  ++ g+ ++++ +++a  f   + +r +g++ +++++Gai+gp l++++   s+++ 
  gi|330507315|ref|YP_004383743.1| 310 MWqMAvPGATtIYIVAFAILWMCLGGWLAIAPTATASFFGTCDYPRNYGVVFLAYGIGAIVGPQLAAAIKeMSGSYV 386
                                       888877887879**********************************************************77777** PP

                             MFS_1 152 avfyilaivsllafvlfllllpeepp 177
                                       +vf  +a++++l++v+++  l  ++p
  gi|330507315|ref|YP_004383743.1| 387 GVFPYVALLAALGIVIAFTMLKHPKP 412
                                       *************9974444444433 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   5.1   4.6e-06     0.028      26      94 ..      11      78 ..      10      80 .. 0.94
   2 ?   -1.6   3.1      0.64   3.8e+03      39      49 ..      93     103 ..      83     134 .. 0.55
   3 ?    3.3   5.3     0.019   1.1e+02      32      82 ..     144     193 ..     139     197 .. 0.83
   4 ?   -0.7  12.7      0.33     2e+03      31      88 ..     234     339 ..     219     346 .. 0.61
   5 ?   -0.1   3.8      0.22   1.3e+03      29      72 ..     360     403 ..     358     407 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.6e-06
                              FtsX 26 llitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagllsiskilkk 94
                                      +l+++++++i l lg+++++ ++   l+  f  ++  +++ + vl+ + ++l+++++a+++s   i k+
  gi|330507315|ref|YP_004383743.1| 11 WLFVILGTIIMLCLGSVYSWSVFVNPLTAHF-AAMGQTVSASEVLLPFSIFLFVFSVAMVFSGKYIEKY 78
                                      7899*********************999999.*****************************99888766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.64
                              FtsX  39 lgllaaqllsd 49 
                                       lg+l+a ++s+
  gi|330507315|ref|YP_004383743.1|  93 LGWLLASMSSS 103
                                       45555444332 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.019
                              FtsX  32 alviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllall 82 
                                        +v+G+g++++++  + ++l + ++  + ++ + +i+++iii l+ + +++
  gi|330507315|ref|YP_004383743.1| 144 LTVLGFGFSAFFTANIATYLIEAFD-VMSTFRFFGIAFIIIITLCSMPLVF 193
                                       5789999999999999999999988.8888999999999999888777765 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.33
                              FtsX  31 valviGlglgllaaqllsdvllss..........vf....................................s..se 59 
                                       ++++iG+++gl+a+ ++  v++++          ++                                    +  ++
  gi|330507315|ref|YP_004383743.1| 234 LCYFIGCVAGLMAIGISKPVGQEViliesglasmLVgffaifngggrpifgtltdkitprnaaivsfvliglAslMM 310
                                       45555555555555554444444422233333331133445555555555566666666666666555554414689 PP

                              FtsX  60 lkisidlitvliiivlllllallagllsi 88 
                                        ++ +++ t + i+++++l + l g+l+i
  gi|330507315|ref|YP_004383743.1| 311 WQMAVPGATTIYIVAFAILWMCLGGWLAI 339
                                       99999999999999999999999999987 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.22
                              FtsX  29 tlvalviGlglgllaaqllsdvllssvfsselkisidlitvlii 72 
                                       +++a+ iG ++g  +a ++  + +s+v+ +     +  + ++i+
  gi|330507315|ref|YP_004383743.1| 360 VFLAYGIGAIVGPQLAAAIKEMSGSYVGVFPYVALLAALGIVIA 403
                                       68899999999999999999999999864333333333333333 PP

>> GPI2  Phosphatidylinositol N-acetylglucosaminyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00045       2.7      49      93 ..      60     104 ..      41     241 .. 0.75
   2 ?    1.7   2.3     0.025   1.5e+02     206     265 ..     278     337 ..     260     349 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00045
                              GPI2  49 vcsviifvlvFvgiyqervspvsvvllssiltvlgwllwelwask 93 
                                       +++v+ +++vF g y e++ p+ +++l+ i++ lgwll ++ +s+
  gi|330507315|ref|YP_004383743.1|  60 FLFVFSVAMVFSGKYIEKYGPRKMAMLGGIICGLGWLLASMSSST 104
                                       467888999****************************99876654 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.025
                              GPI2 206 glfPvfrrslrhrswrlhvvltvllvllagagvgiilklllavvlllllalimgvcpwwl 265
                                       g  P+f     + + r  ++++++l+ la+++++++    ++ ++++++a++ +++  wl
  gi|330507315|ref|YP_004383743.1| 278 GGRPIFGTLTDKITPRNAAIVSFVLIGLASLMMWQMAVPGATTIYIVAFAILWMCLGGWL 337
                                       556777778888888889999999999999999988774445555544444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 2920.51
//
Query:       gi|330507316|ref|YP_004383744.1|  [L=189]
Description: hypothetical protein MCON_1210 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-14   52.2   8.8    1.4e-05   24.6   1.1    4.3  4  Hexapep     Bacterial transferase hexapeptide (six repeats)
      1e-09   38.0  11.5      0.038   13.7   0.1    4.7  4  Hexapep_2   Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
       0.12   12.7   1.3       0.78   10.1   1.0    2.2  1  Bactofilin  Polymer-forming cytoskeletal
       0.12   12.4   0.1       0.64   10.1   0.0    2.2  2  Gp138_N     Phage protein Gp138 N-terminal domain


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   4.7e-08   0.00021       3      34 ..      18      49 ..      16      51 .. 0.91
   2 !    6.5   0.1    0.0016       7.4      18      35 ..      55      72 ..      50      73 .. 0.76
   3 !   24.6   1.1   3.2e-09   1.4e-05       2      35 ..      79     112 ..      78     113 .. 0.94
   4 ?    3.1   0.0     0.019        84       3      17 ..     115     129 ..     113     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.7e-08
                                      EEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep  3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34
                                      +I+s ++++  a+i g+V +G++v+I++ v +
  gi|330507316|ref|YP_004383744.1| 18 QIHSSSYVDESATIIGDVRVGKDVYIAPSVSL 49
                                      79**************************8865 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0016
                                      TTEEE-TTEEEETTEEEE CS
                           Hexapep 18 gnVkIGdnvkIgagvvig 35
                                      ++++IGd + I   +v +
  gi|330507316|ref|YP_004383744.1| 55 SPIIIGDECNIQDSAVFH 72
                                      678999999998887765 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 3.2e-09
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       + +G+nv + ++avi+g++k Gd + +g ++v++
  gi|330507316|ref|YP_004383744.1|  79 IELGENVSVAHGAVIHGPIKMGDECFVGFNSVVH 112
                                       678*****************************97 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.019
                                       EEETTEEE-TTEEEE CS
                           Hexapep   3 vIGsnvlIgpfavig 17 
                                       ++G+++++g+ a + 
  gi|330507316|ref|YP_004383744.1| 115 TLGKKCFVGHLAAVI 129
                                       789******977664 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 !    5.2   0.0    0.0041        18      14      30 ..      29      47 ..      19      51 .. 0.68
   2 !   13.7   2.0   8.8e-06      0.04       1      32 [.      56      93 ..      56      94 .. 0.87
   3 !   13.7   0.1   8.5e-06     0.038       1      27 [.      96     123 ..      96     123 .. 0.89
   4 !   12.5   0.1   2.1e-05     0.093       4      26 ..     116     139 ..     113     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0041
                                      -EE.S.EEE-TT-EE-TT- CS
                         Hexapep_2 14 agi.G.vslGdncvvgaGv 30
                                      a+i G v +G+++ +++ v
  gi|330507316|ref|YP_004383744.1| 29 ATIiGdVRVGKDVYIAPSV 47
                                      3334559999999998766 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.8e-06
                                      .EEE-TT-EE-TT-EE....S..EEE-TT-EE-TT-EE CS
                         Hexapep_2  1 pviIGdnCliGanagi....G..vslGdncvvgaGvvi 32
                                      p+iIGd C+i  +a+     G  ++lG+n+ v+ G vi
  gi|330507316|ref|YP_004383744.1| 56 PIIIGDECNIQDSAVFhglkGssIELGENVSVAHGAVI 93
                                      89*************55456367************998 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 8.5e-06
                                       .EEE-TT-EE-TT-EE.SEEE-TT-EE- CS
                         Hexapep_2   1 pviIGdnCliGanagi.GvslGdncvvg 27 
                                       p++ Gd C++G n+++   +lG++c vg
  gi|330507316|ref|YP_004383744.1|  96 PIKMGDECFVGFNSVVhASTLGKKCFVG 123
                                       7899***********9878899999876 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 2.1e-05
                                       E-TT-EE-TT.-EESEEE-TT-EE CS
                         Hexapep_2   4 IGdnCliGan.agiGvslGdncvv 26 
                                        G+ C++G   a+iGv+l d++ v
  gi|330507316|ref|YP_004383744.1| 116 LGKKCFVGHLaAVIGVNLKDGSFV 139
                                       59******996779******9977 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.0   0.00017      0.78       2      83 ..      24     100 ..      23     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                        Bactofilin   2 ligegtkikGelevegdlridGkveGdieakgklvvgeggkvegnikaeevvvaGtvkGnveaeekvelkktakveG 78 
                                       +++e+++i G+++v +d+ i+ +v+ + ++++ +++g++ +++     +++v +G    ++e  e+v++++ a+++G
  gi|330507316|ref|YP_004383744.1|  24 YVDESATIIGDVRVGKDVYIAPSVSLRADEASPIIIGDECNIQ-----DSAVFHGLKGSSIELGENVSVAHGAVIHG 95 
                                       5788899999999999999988888888788888888888665.....66777787777888888888888888888 PP

                        Bactofilin  79 dikak 83 
                                        ik++
  gi|330507316|ref|YP_004383744.1|  96 PIKMG 100
                                       88764 PP

>> Gp138_N  Phage protein Gp138 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.36   1.6e+03      53      61 ..      55      63 ..      12      68 .. 0.61
   2 ?   10.1   0.0   0.00014      0.64      46      67 ..      88     109 ..      83     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.36
                           Gp138_N 53 fpvkaGdec 61
                                       p+  Gdec
  gi|330507316|ref|YP_004383744.1| 55 SPIIIGDEC 63
                                      355556666 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00014
                           Gp138_N  46 gggvtltfpvkaGdeclvvfse 67 
                                       + g+++  p+k Gdec+v f++
  gi|330507316|ref|YP_004383744.1|  88 AHGAVIHGPIKMGDECFVGFNS 109
                                       67899*************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1376.32
//
Query:       gi|330507317|ref|YP_004383745.1|  [L=342]
Description: aspartate-semialdehyde dehydrogenase [Methanosaeta concilii GP6]
Scores for complete 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-38  132.4   0.0      3e-38  131.8   0.0    1.3  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    1.3e-32  112.8   0.0    1.9e-32  112.2   0.0    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
  ------ inclusion threshold ------
      0.031   13.9   0.0      0.067   12.8   0.0    1.5  1  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
      0.068   13.3   0.0       0.11   12.6   0.0    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.072   13.3   0.3        2.3    8.4   0.0    2.3  2  MIase            Muconolactone delta-isomerase
      0.087   13.5   0.0       0.16   12.7   0.0    1.6  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
       0.12   12.2   0.0       0.19   11.6   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding


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 !  131.8   0.0   1.2e-41     3e-38       1     183 [.     158     322 ..     158     323 .. 0.94

  Alignments for each domain:
  == domain 1  score: 131.8 bits;  conditional E-value: 1.2e-41
                                       HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHH CS
                   Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetree 77 
                                       LkPL++  +++e+v++a++qavSGaG+                    +gv++++i+gN+ipyi++ee+k e+e +++
  gi|330507317|ref|YP_004383745.1| 158 LKPLMK--FGIESVHMASMQAVSGAGY--------------------EGVPSMAILGNVIPYIGGEEEKCETEPQKI 212
                                       8*****..56*****************....................6***************************** PP

                                       HHHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCS.......TTEEEEESSHCHH CS
                   Semialdhyde_dhC  78 lkavaetkkileftekvsatcvrVPvlrGhseavtiklk..lkdveveeveellaaa.......pevkvvvneeedr 145
                                       l+  + ++ i ++++ +sa+c+rVPv++Gh+ea+++k++  ++++ev++++  +          p+++++v++e+dr
  gi|330507317|ref|YP_004383745.1| 213 LGHFDGERIINANFS-ISASCHRVPVMDGHTEALWVKMRdnPTPEEVRQAMLDFDPGlddlptsPKKALIVKDEPDR 288
                                       **************8.***********************99**************99******************** PP

                                       SSHHHHTTC..SSSEEEEEEEEETTCTTEEEEEEEEETTT CS
                   Semialdhyde_dhC 146 Ptpaavagg..tnsvsVGRirkdemgdeglklvvvgDNll 183
                                       P+p++++ +  ++svsVGRir+         ++++g+N++
  gi|330507317|ref|YP_004383745.1| 289 PQPRLDRMRgnGMSVSVGRIRSGI------RFICMGHNTV 322
                                       ******97677**********865......4666666665 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 !  112.2   0.0   7.6e-36   1.9e-32       1     119 [.       5     128 ..       5     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 7.6e-36
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG......GGTTTECEBEEEGGGGGCTT-SEEE CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk......aleegkdlkvedvdeeelkevdivf 71 
                                       k++++GatG+vGq++++ L++hp++el+ l++s+rsaGkk++ea+k       ++++++++v +vd+ e+ ++divf
  gi|330507317|ref|YP_004383745.1|   5 KAGVLGATGAVGQRFIEGLKSHPWFELTSLAASERSAGKKYREAAKwrleseLPDDIAEMTVVNVDPREV-DADIVF 80 
                                       689***********************************************99999***************.9***** PP

                                       E-SCHHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGG CS
                    Semialdhyde_dh  72 lalpagvskelapklaeagvkviDlssdfRlkddavyvlpevnreaik 119
                                       +alpa  +++++p++a+ag+ v +++s +R+ +d+++ +pe n e+++
  gi|330507317|ref|YP_004383745.1|  81 SALPAADAMSVEPAFAAAGCAVASNTSSYRMVEDVPLLIPECNHEHLD 128
                                       *********************************************986 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 ?   12.8   0.0   2.6e-05     0.067      70     106 ..     226     262 ..     219     270 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                                       TTEEEEEEEESSSSEEEEEEEEEESSTS-HHHHHHHH CS
                           Gp_dh_C  70 gkldglAvrVPtpnvsvvdlvvelekevtveevnaal 106
                                         ++++  rVP+++++   l v+++++ t eev +a+
  gi|330507317|ref|YP_004383745.1| 226 FSISASCHRVPVMDGHTEALWVKMRDNPTPEEVRQAM 262
                                       56788899**************************998 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.4e-05      0.11       1      49 [.       4      50 ..       4      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSS CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellg 49
                                      ik +v+Ga+G +G++ ++ +++++ +el++   +++    gk+  e+++
  gi|330507317|ref|YP_004383745.1|  4 IKAGVLGATGAVGQRFIEGLKSHPWFELTSLAASER--SAGKKYREAAK 50
                                      6889*************************9988877..35555555544 PP

>> MIase  Muconolactone delta-isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00089       2.3      19      80 ..      30      92 ..      23      94 .. 0.86
   2 ?    2.4   0.1      0.07   1.8e+02      65      83 ..     150     168 ..     143     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00089
                             MIase 19 evaelkarekaraqelqrqGklvrlwrvvgeyanisifdvedndeLhe..lLssLPlfpymtie 80
                                      e+++l a+e+ + ++ +++ k++    +++ +a + +++v+   e+++  + s+LP ++ m++e
  gi|330507317|ref|YP_004383745.1| 30 ELTSLAASERSAGKKYREAAKWRLESELPDDIAEMTVVNVDP-REVDAdiVFSALPAADAMSVE 92
                                      66788999********************************65.55555457789*****99987 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.07
                             MIase  65 helLssLPlfpymtievtp 83 
                                        +++++LPl p+m+  +++
  gi|330507317|ref|YP_004383745.1| 150 TTIMFTLPLKPLMKFGIES 168
                                       6899*********988876 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.4e-05      0.16       3      47 ..       8      52 ..       6      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.4e-05
                                      EESTTSHHHHHHHHHHHHCTTTEEEEEEEE.SSTHHHHHHHHHHHT CS
                   DXP_reductoisom  3 iLGsTGSIGtqtLdvieenpdkfevvalaa.gsnvellaeqakefk 47
                                      +LG+TG +G+  ++ ++++p  fe+++laa +++  + ++ a++++
  gi|330507317|ref|YP_004383745.1|  8 VLGATGAVGQRFIEGLKSHP-WFELTSLAAsERSAGKKYREAAKWR 52
                                      9*******************.9********6666666666666665 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 ?   11.6   0.0   7.4e-05      0.19       1      73 [.      10      88 ..      10     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.4e-05
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHT........T-SEEEES---T CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealk........gadaVvsalggg 71
                                      GAtG vG++ ++ l ++  +e+t l+ ++ ++ +  +  ++    ++ + ++d+ae           +ad+V+sal + 
  gi|330507317|ref|YP_004383745.1| 10 GATGAVGQRFIEGLKSHPWFELTSLAASERSAGK--KYREAAKWRLESELPDDIAEMTVvnvdprevDADIVFSALPAA 86
                                      9*************************99999974..3345555666777788888877677888888999999999444 PP

                                      CC CS
                    NAD_binding_10 72 gk 73
                                      + 
  gi|330507317|ref|YP_004383745.1| 87 DA 88
                                      43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2598.87
//
Query:       gi|330507318|ref|YP_004383746.1|  [L=321]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   77.3   0.0    2.3e-21   76.9   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    2.6e-10   40.7   0.8    5.4e-10   39.7   0.8    1.5  1  SPASM        Iron-sulfur cluster-binding domain
      2e-08   34.6   0.0    4.5e-08   33.5   0.0    1.6  1  Fer4_12      4Fe-4S single cluster domain
    3.5e-06   27.2   0.3    8.7e-06   25.9   0.0    1.8  2  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.0   5.1e-25   2.3e-21       3     140 ..       8     137 ..       6     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 5.1e-25
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                        t +Cnl C++C  + +   e+++ +l+++e ++ v+++ a   +  +il+ggepll+pd+ ++++ ++ l   gir
  gi|330507318|ref|YP_004383746.1|   8 LTAACNLSCRYCRASAS--HEPDQGELDTDEAKRFVESI-APL-KPMLILSGGEPLLRPDLFQIIRLAVSL---GIR 77 
                                       6899***********97..********************.788.**************************9...*** PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklrea 140
                                       +++ +ngtl++   +e++++ gv rvs++l+ ad    +++ +++++fe+ ++++e+lr +
  gi|330507318|ref|YP_004383746.1|  78 VSLASNGTLITSGLAEEIADSGVSRVSISLDGADAA-MHDHGRGQGSFERSIKGIENLRGR 137
                                       ************************************.*********************976 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.8   1.2e-13   5.4e-10       1      68 []     232     291 ..     232     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1.2e-13
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIw.nseeyqefrkskkfplielCrnCp 68 
                                       C a++r +f++ +G+V+pC     +   +l++G++re+ + eIw ns+e+q++r+    +l   C +C+
  gi|330507318|ref|YP_004383746.1| 232 CLAGRRFVFVSRKGEVYPC----GYL--PLRVGSVREKNFIEIWeNSPELQALRE---GRLKGKCGRCE 291
                                       88999**************....233..7***************8888******3...33334477774 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0     1e-11   4.5e-08      12     101 ..       9      92 ..       2     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1e-11
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdi 88 
                                       ++ CnlsC++C + + +++++g+  t+e+ ++ +e++  + ++ l+l+GGEPll   +++l ++++   + ++  + 
  gi|330507318|ref|YP_004383746.1|   9 TAACNLSCRYCRASASHEPDQGELDTDEA-KRFVESI-APLKPMLILSGGEPLL---RPDLFQIIRLAVSLGI-RVS 79 
                                       678*******************9988777.6788888.89**************...9999999998888888.578 PP

                           Fer4_12  89 wlytgytleelsk 101
                                       ++++g+ +   ++
  gi|330507318|ref|YP_004383746.1|  80 LASNGTLITSGLA 92 
                                       8888887665554 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 !   25.9   0.0   1.9e-09   8.7e-06       5      96 ..       9      91 ..       6     110 .. 0.78
   2 ?   -4.7   1.8         4   1.8e+04       6      17 ..     288     301 ..     286     308 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.9e-09
                           Fer4_14  5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekki 83
                                      ++ CnlsC+ C  +++ + + g+ +t+e   + +++      k+  l l+GGePL+    ++l+++++  +  +  +++
  gi|330507318|ref|YP_004383746.1|  9 TAACNLSCRYCRASASHEPDQGELDTDEAK-RFVESIA--PLKPM-LILSGGEPLLR---PDLFQIIRLAVSLG--IRV 78
                                      689*********************999876.6664444..44445.9********55...99999999999988..9** PP

                           Fer4_14 84 wletngtleiele 96
                                       l +ngtl  +  
  gi|330507318|ref|YP_004383746.1| 79 SLASNGTLITSGL 91
                                      *****99976655 PP

  == domain 2  score: -4.7 bits;  conditional E-value: 4
                           Fer4_14   6 sgCnl..sCkgCdn 17 
                                       ++C++  sC gC  
  gi|330507318|ref|YP_004383746.1| 288 GRCEFsrSCGGCRA 301
                                       68887445999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2547.38
//
Query:       gi|330507319|ref|YP_004383747.1|  [L=154]
Description: hypothetical protein MCON_1213 [Methanosaeta concilii GP6]
Scores for complete 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   65.5   0.0    4.9e-18   65.1   0.0    1.2  1  AsnC_trans_reg2  AsnC-like ligand binding domain
    2.8e-06   27.1   0.0    1.7e-05   24.5   0.0    2.2  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.036   13.6   0.1        0.1   12.2   0.1    1.7  1  DDRGK            DDRGK 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 !   65.1   0.0   8.1e-22   4.9e-18       2      82 .]      62     141 ..      61     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 8.1e-22
                   AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeR..ewpynlyfmvharseeeveevlaeiaaatgledyevLp 76 
                                       lG +   l+a++v  e+ + +ae v++++ev+H+Y+R  e  yn++f+v+a+ ee+++evl+ei++ tg + + vLp
  gi|330507319|ref|YP_004383747.1|  62 LGRS-GILAALQVSPEEADGLAEFVNQYQEVSHNYLRpnESGYNMWFTVSAT-EERIQEVLEEIRKSTGRR-MLVLP 135
                                       6777.89******************************76689*******997.78***************9.***** PP

                   AsnC_trans_reg2  77 strefK 82 
                                       + r fK
  gi|330507319|ref|YP_004383747.1| 136 TGRIFK 141
                                       *****9 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   2.9e-09   1.7e-05       1      41 [.       1      44 [.       1      45 [. 0.96
   2 ?   -0.6   0.0       0.2   1.2e+03       8      14 ..      67      73 ..      66      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.9e-09
                     HTH_AsnC-type  1 LDeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrL 41
                                      +DeiD+++L++ q        ++++L+  + l e +v++R++ L
  gi|330507319|ref|YP_004383747.1|  1 MDEIDLRLLSLVQVGfplTPKPFEDLGGLLSLEEKEVIERLDGL 44
                                      9***************************************9866 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.2
                     HTH_AsnC-type  8 ILeaLqe 14
                                      IL+aLq 
  gi|330507319|ref|YP_004383747.1| 67 ILAALQV 73
                                      9****96 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.7e-05       0.1     117     177 ..      24      94 ..      21      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                                       HHHHHHH-S-HHHHHHHHHHHHHHSSS-...EEE-TT..--.....EEE---XXXXXXXXXXXXXXXXXXX CS
                             DDRGK 117 eelavkfklktqevierikeLeeqgslt...GvlDdr..Gk.....yiyitdeEleavakyikkkGrvsis 177
                                       e+l   ++l+ +evier++ L+++g +     +lD r  G+      + +++eE++ +a+++++   vs++
  gi|330507319|ref|YP_004383747.1|  24 EDLGGLLSLEEKEVIERLDGLQKEGLVRrigPILDLRrlGRsgilaALQVSPEEADGLAEFVNQYQEVSHN 94 
                                       899999******************97642216899876766333334789999999999999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 1266.62
//
Query:       gi|330507320|ref|YP_004383748.1|  [L=90]
Description: thioredoxin [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-20   73.0   0.0    1.7e-20   72.9   0.0    1.0  1  Thioredoxin    Thioredoxin
    1.3e-06   28.8   0.1    1.4e-05   25.4   0.1    1.9  1  Thioredoxin_2  Thioredoxin-like domain
    0.00046   20.5   0.0    0.00077   19.7   0.0    1.3  1  Thioredoxin_8  Thioredoxin-like
     0.0025   17.7   0.0     0.0034   17.3   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
     0.0053   16.8   0.0     0.0069   16.4   0.0    1.1  1  Thioredoxin_3  Thioredoxin domain
     0.0061   16.7   0.0     0.0085   16.3   0.0    1.5  1  Thioredoxin_7  Thioredoxin-like
     0.0077   15.9   0.0     0.0083   15.8   0.0    1.3  1  Redoxin        Redoxin
  ------ inclusion threshold ------
      0.044   13.6   0.0      0.051   13.4   0.0    1.2  1  TraF           F plasmid transfer operon protein
      0.048   13.4   0.1      0.067   13.0   0.1    1.4  1  Thioredoxin_9  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 !   72.9   0.0   8.6e-24   1.7e-20      19     102 ..       3      86 ..       1      87 [. 0.97

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 8.6e-24
                                       SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHH CS
                       Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegareke 95 
                                       k++l++FyA+wCg+Ck+  P +e+lae++kd   + k++vd + dla + ++  +Ptl+l ++g e+++  g ++++
  gi|330507320|ref|YP_004383748.1|   3 KPILMDFYADWCGPCKQQGPIFEALAEKMKDVADFKKINVDREGDLAMEKGIFVVPTLILERDGVEINRWMGLASEK 79 
                                       899************************************************************************** PP

                                       HHHHHHH CS
                       Thioredoxin  96 klaaflk 102
                                       +la+ ++
  gi|330507320|ref|YP_004383748.1|  80 ELADAIN 86 
                                       ***9997 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   7.3e-09   1.4e-05       6     108 ..       3      84 ..       1      85 [. 0.82

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 7.3e-09
                     Thioredoxin_2   6 kpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtP 82 
                                       kp+l++f++++C+ Ck+    ++ l    ++     +k+ +++k ++++++ + +              + g++ +P
  gi|330507320|ref|YP_004383748.1|   3 KPILMDFYADWCGPCKQQGPIFEAL---AEK-----MKDVADFKKINVDREGDLA-------------MEKGIFVVP 58 
                                       9****************77766666...555.....7777999999999999875.............455****** PP

                     Thioredoxin_2  83 tivfl.dgkeivarlpGyvpaeeleal 108
                                       t+++  dg  +++r+ G+ +++el+++
  gi|330507320|ref|YP_004383748.1|  59 TLILErDGV-EINRWMGLASEKELADA 84 
                                       *88651555.999**********9876 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.9e-07   0.00077       2      45 ..       3      46 ..       2      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.9e-07
                                      SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS CS
                     Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldk 45
                                      k +l+ f+a+wc pck+  p   +l ek+k+  +++ + v    
  gi|330507320|ref|YP_004383748.1|  3 KPILMDFYADWCGPCKQQGPIFEALAEKMKDVADFKKINVDREG 46
                                      7899*************************987777777776555 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.7e-06    0.0034      26      57 ..       3      33 ..       2      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
                                      SEEEEEEESTST-CCHHHHHHHHHHCHHHCCC CS
                          AhpC-TSA 26 kpvvlffypkdwcpvCttelpalaklyeefke 57
                                      kp++  fy+  wc +C+++ p +++l+e++k+
  gi|330507320|ref|YP_004383748.1|  3 KPILMDFYAD-WCGPCKQQGPIFEALAEKMKD 33
                                      6889999999.******************995 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.4e-06    0.0069      10      73 ..      14      83 ..       9      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.4e-06
                                      STTCHHHHHHHHHHCHCCT..CECEEECCTTHHHH.HHCT-SSSSEEECT....TCEEEESS---CCHHHH CS
                     Thioredoxin_3 10 CakCpklekavkeaaaekg..ikaevekvtdfeei.ekygVmsvPalvid....gkvvvsGkvpseeeirk 73
                                      C  C++   +++++a++++   +++ ++v    ++ ++ g+  vP+l+++    +  +++G + se+e++ 
  gi|330507320|ref|YP_004383748.1| 14 CGPCKQQGPIFEALAEKMKdvADFKKINVDREGDLaMEKGIFVVPTLILErdgvEINRWMG-LASEKELAD 83
                                      999999999999999999536777888889999999*************9998888999**.788887765 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.2e-06    0.0085      17      39 ..       2      24 ..       1      62 [. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.2e-06
                                      T--EEEEE--TT-HHHHHHHHHH CS
                     Thioredoxin_7 17 gkpvlvffgaswcftCqalerdf 39
                                       kp+l +f a+wc++C+ +   f
  gi|330507320|ref|YP_004383748.1|  2 TKPILMDFYADWCGPCKQQGPIF 24
                                      59**************9876555 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.2e-06    0.0083      29      60 ..       3      33 ..       1      66 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.2e-06
                                      SEEEEEEESTTT-HHHHHTHHHHHTHHHHHHC CS
                           Redoxin 29 kkvvvnfvpgafcPtCsaehpyleklaellke 60
                                      k++++ f++  +c++C+++ p +e lae+ k+
  gi|330507320|ref|YP_004383748.1|  3 KPILMDFYAD-WCGPCKQQGPIFEALAEKMKD 33
                                      7899999**9.***************999655 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.6e-05     0.051     133     199 ..       6      63 ..       2      85 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                              TraF 133 LlfFyrgkcpyceaqapilqafadkyg..levraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlv 199
                                       L+ Fy+  c+ c++q pi +a+a+k++   + + ++vd++ +  l+          + g+  +P+l+l 
  gi|330507320|ref|YP_004383748.1|   6 LMDFYADWCGPCKQQGPIFEALAEKMKdvADFKKINVDREGD--LAM---------EKGIFVVPTLILE 63 
                                       788**********************95337888999999888..443.........4477777777765 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   3.3e-05     0.067      49      73 ..      10      34 ..       5      82 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.3e-05
                                      --TT-HHHHHHHHHHHHHHHH-TTE CS
                     Thioredoxin_9 49 tedwCgDaavnvPvlakiaelnpni 73
                                       +dwCg + +  P+++++ae  +++
  gi|330507320|ref|YP_004383748.1| 10 YADWCGPCKQQGPIFEALAEKMKDV 34
                                      589****************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 670.52
//
Query:       gi|330507321|ref|YP_004383749.1|  [L=325]
Description: hypothetical protein MCON_1215 [Methanosaeta concilii GP6]
Scores for 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   24.2   0.5    6.1e-05   22.6   0.1    1.9  2  Lactamase_B_2  Beta-lactamase superfamily domain
      7e-05   22.7   0.0    0.00019   21.3   0.0    1.6  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
      0.003   17.5   0.1     0.0069   16.3   0.1    1.5  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.042   13.8   4.7       0.27   11.2   4.2    2.5  3  Lactamase_B    Metallo-beta-lactamase superfamily
      0.094   13.6   0.0       0.17   12.7   0.0    1.3  1  Vasculin       Vascular protein family Vasculin-like 1
       0.16   11.0   0.0       0.23   10.5   0.0    1.3  1  PDEase_II      cAMP phosphodiesterases class-II


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1     2e-08   6.1e-05      27     168 ..      46     159 ..      34     199 .. 0.83
   2 ?   -0.9   0.0      0.32   9.7e+02     178     200 ..     272     294 ..     262     301 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2e-08
                                       -..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTE CS
                     Lactamase_B_2  27 elppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggl 103
                                          + da l+thaH DH+ g   +    p   + +a+ ++++ le +  ++ ++       ++++ ges+ ++  ++
  gi|330507321|ref|YP_004383749.1|  46 ACTQPDAYLITHAHSDHY-GKSAMNS--P---RAVASVQTARALEIRYGREYMG-------RTFEVGESIMVD--EV 107
                                       456889************.7666666..4...3679999999999996655555.......56*********9..57 PP

                                       EEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SS CS
                     Lactamase_B_2 104 eitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditaye 168
                                       +i ++p  h+ g         ++++  e +g+rv+ +gD++ ++     +l  +d l+ ++++ +
  gi|330507321|ref|YP_004383749.1| 108 RINTHPTGHTIGS-------SAFSWQTE-TGERVLVTGDVKDYH-----HLPRCDYLVTEANYGD 159
                                       8***********9.......89999998.9**********9776.....4566777777776655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.32
                                       ---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 178 HltpeeaveaaadlgakrlvliH 200
                                       Hl+ ++ +++++++++++l++ H
  gi|330507321|ref|YP_004383749.1| 272 HLDFRGLMRMIEHISPRKLLVYH 294
                                       88889999999999999998888 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 !   21.3   0.0   6.2e-08   0.00019      11      58 ..     267     313 ..     265     316 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 6.2e-08
                             RMMBL  11 idfSgHadknellelirklkprnvilvHGeeeatsalarllkeeegid 58 
                                       i +S H d+++l+++i++++pr++ + H + e +s la +l ++ g d
  gi|330507321|ref|YP_004383749.1| 267 IQLSDHLDFRGLMRMIEHISPRKLLVYHPASERASLLAHYL-QQCGMD 313
                                       679*************************9999999999999.888866 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   2.3e-06    0.0069      35     108 ..      48     133 ..      29     159 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.3e-06
                     Lactamase_B_3  35 eeaDlvlisqaledHahletlkqlaenvkvlee...................geslevggleiravatshdavggse 92 
                                        ++D+ li++a++dH+   ++++  + v  +++                   ges+ v++++i++++t h+      
  gi|330507321|ref|YP_004383749.1|  48 TQPDAYLITHAHSDHYGKSAMNS-PRAVASVQTaraleirygreymgrtfevGESIMVDEVRINTHPTGHT------ 117
                                       789*****************999.77777777788888888888886666666667777777777777663...... PP

                     Lactamase_B_3  93 rgenngflleq.dglti 108
                                        g  ++f ++  +g ++
  gi|330507321|ref|YP_004383749.1| 118 IG-SSAFSWQTeTGERV 133
                                       22.24444433233333 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.7   5.1e+03     137     155 ..      26      44 ..      21      45 .. 0.79
   2 ?   11.2   4.2   9.2e-05      0.27      44     151 ..      49     139 ..      48     164 .. 0.74
   3 ?   -2.2   0.0       1.1   3.4e+03      90     129 ..     191     251 ..     166     256 .. 0.54

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                                       EEEETTCCEEEECTTTSSH CS
                       Lactamase_B 137 vveygggkvlftGDallag 155
                                       ++ ++ ++ lf+ D++ a+
  gi|330507321|ref|YP_004383749.1|  26 HLAIRFDSHLFSIDTSRAP 44 
                                       677788999******9875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.2e-05
                                       GEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTE CS
                       Lactamase_B  44 dvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggr 120
                                       ++da ++TH+H+DH+G  +    ++ + v   ++ +  + +e++++                  ++e ++ + ++++
  gi|330507321|ref|YP_004383749.1|  49 QPDAYLITHAHSDHYGKSAMNSPRAVASVQTARALEIRYGREYMGR------------------TFEVGESIMVDEV 107
                                       578889**********777666666666666666666666666644..................7888888888888 PP

                                       EEEEHECTTSTSCCEEEEEE.TTCCEEEECTT CS
                       Lactamase_B 121 ralyvtggpghghghgvvey.gggkvlftGDa 151
                                       r   ++ g++ g++ ++     g++vl+tGD+
  gi|330507321|ref|YP_004383749.1| 108 RINTHPTGHTIGSSAFSWQTeTGERVLVTGDV 139
                                       88888778887777777766678888888886 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.1
                                       HHHHCCHH.....................TTCHCGCCEEEEETTTEECCCTEEEEEHECTT CS
                       Lactamase_B  90 aasrkgll.....................lagvsadkpdvdeeeldgnaggrralyvtggp 129
                                        a+r  +l                          + +p +++++  +n+   ++ly+++g 
  gi|330507321|ref|YP_004383749.1| 191 KAQRAVALmramgykdeigmdekclaltqELMKEVAGPLTPINGSGFNVVTPWSLYQVPGR 251
                                       4444444444433333333333444444434445555666667777777777777777665 PP

>> Vasculin  Vascular protein family Vasculin-like 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.7e-05      0.17      14      41 ..     198     225 ..     194     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.7e-05
                          Vasculin  14 LlkemgwqeesendenylplTedElkEF 41 
                                       L+++mg+++e + de++l+lT++ +kE 
  gi|330507321|ref|YP_004383749.1| 198 LMRAMGYKDEIGMDEKCLALTQELMKEV 225
                                       99*********************99995 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   7.8e-05      0.23      83     106 ..      52      75 ..      45     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.8e-05
                                       EEE-S---GGGTHHHHHHGGGGGS CS
                         PDEase_II  83 sylItHsHLDHvsglvinSaefyk 106
                                        ylItH+H DH +   +nS+    
  gi|330507321|ref|YP_004383749.1|  52 AYLITHAHSDHYGKSAMNSPRAVA 75 
                                       6******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2371.90
//
Query:       gi|330507322|ref|YP_004383750.1|  [L=307]
Description: glycosyl transferase, group 2 family protein [Methanosaeta concilii GP6]
Scores for complete 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   83.4   0.0      2e-23   83.0   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
     0.0013   18.7   0.1     0.0028   17.6   0.0    1.6  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.032   14.6   0.1      0.056   13.9   0.1    1.4  1  G0-G1_switch_2   G0/G1 switch protein 2
      0.051   13.0   0.0      0.077   12.5   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
      0.089   12.8   1.2       0.18   11.7   0.8    1.7  2  RseC_MucC        Positive regulator of sigma(E), RseC/MucC
       0.14   12.6   0.0       0.23   12.0   0.0    1.3  1  Glyco_tranf_2_4  Glycosyl transferase family 2
       0.63    9.9   3.9       0.56   10.0   2.7    1.6  1  LapA_dom         Lipopolysaccharide assembly protein A domain
          2    7.8   6.9       0.41   10.1   2.0    2.0  2  DUF373           Domain of unknown function (DUF373)
        2.1    7.0   5.3        2.9    6.6   5.3    1.1  1  Transp_cyt_pur   Permease for cytosine/purines, uracil, thiam


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.0     1e-26     2e-23       2     125 ..       7     122 ..       6     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 1e-26
                                       EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH- CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraa 78 
                                       ++ p+yNee  +   + + ++      +++ivvDDgS D+t+e++  +     +  v+r+e n Gk++al +g++  
  gi|330507322|ref|YP_004383750.1|   7 AILPAYNEEVSIGSIVLRTRKF----ADRVIVVDDGSLDRTAEVAALA-----GAQVLRHEMNLGKGAALKTGFSLL 74 
                                       799*******************....*******************999.....9*********************** PP

                                       -SS.EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCC CS
                   Glycos_transf_2  79 tgd.yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetde 125
                                       +gd +i+++D D ++dp ++++lv+++ k++ad+v g+r+ ++ ++d+
  gi|330507322|ref|YP_004383750.1|  75 NGDaVIVTIDTDGQHDPADIPRLVRPILKGEADMVNGSRYLNGNKRDT 122
                                       ****************************************98877665 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.4e-06    0.0028       8     131 ..       9     122 ..       3     188 .. 0.75
   2 ?   -2.3   0.1       1.7   3.4e+03     155     177 ..     272     294 ..     264     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                   Glyco_tranf_2_3   8 Vptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealr 84 
                                        p++nee  +g+++  +      +++v+vv+d+s + t+eva         ++ +v++ ++nlg   k  al+ +++
  gi|330507322|ref|YP_004383750.1|   9 LPAYNEEVSIGSIVLRTR---KFADRVIVVDDGSLDRTAEVAAL-------AGAQVLRHEMNLG---KGAALKTGFS 72 
                                       566666555555443333...36799**************9842.......4668999999999...566889**** PP

                   Glyco_tranf_2_3  85 avksd.lvllvDdDtvvePdtlkrllqffltpkvgavgtpvfll.n.rst 131
                                         ++d +++ +D D   +P  ++rl++ +l  ++++v ++++l+ n r+t
  gi|330507322|ref|YP_004383750.1|  73 LLNGDaVIVTIDTDGQHDPADIPRLVRPILKGEADMVNGSRYLNgNkRDT 122
                                       ***663888889999999999********9999*******9997552444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                   Glyco_tranf_2_3 155 lgvltlnGsgslirrevlkeleg 177
                                       +++l+l+G  + i  +v+ e+++
  gi|330507322|ref|YP_004383750.1| 272 GSFLALTGMVLHILSRVMHEFKR 294
                                       56899999999999999999975 PP

>> G0-G1_switch_2  G0/G1 switch protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.8e-05     0.056      23      59 ..     265     301 ..     260     307 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                    G0-G1_switch_2  23 lvklYvlGsvLallGvviglvetvcspFssesrlree 59 
                                       ++ l +lGs Lal G+v+ ++  v++ F  e   + +
  gi|330507322|ref|YP_004383750.1| 265 MILLVLLGSFLALTGMVLHILSRVMHEFKRELMAQGR 301
                                       677889**********************987654444 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 ?   12.5   0.0   3.8e-05     0.077       3      92 ..       8      87 ..       6     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.8e-05
                   Glyco_tranf_2_2  3 viplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskae 81
                                      ++p +++e    i   vl+ +k+     ++ivvddgS + ++ ev ++  ++ l   ++e     +++aa   G+s  +
  gi|330507322|ref|YP_004383750.1|  8 ILPAYNEEVS--IGSIVLRTRKF---ADRVIVVDDGSLDRTA-EVAALAGAQVL---RHE--MNLGKGAALKTGFSLLN 75
                                      7788888888..999999999*9...789***********66.55555554444...444..578*************9 PP

                   Glyco_tranf_2_2 82 sd.lvlFlDaDc 92
                                      +d +++ +D+D 
  gi|330507322|ref|YP_004383750.1| 76 GDaVIVTIDTDG 87
                                      993456789885 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 ?   -3.2   0.0       3.8   7.5e+03      49      60 ..      74      85 ..      61      86 .. 0.75
   2 ?   11.7   0.8   9.3e-05      0.18      40     111 ..     198     277 ..     184     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.8
                         RseC_MucC 49 kvGdkVevgiee 60
                                        Gd V+v i++
  gi|330507322|ref|YP_004383750.1| 74 LNGDAVIVTIDT 85
                                      469999998875 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 9.3e-05
                         RseC_MucC  40 leveneigakvGdkVevgieeksllkaallvYllPllllilgall.gsall.......gssellaalgallglvlgf 108
                                       +++++e ++  G +V +++ +++ l+  l+ + +P l++ ++ +l g  +l         + +la+++ ll+l+ +f
  gi|330507322|ref|YP_004383750.1| 198 VNCSSENPVVHGLRVLINVLQDMQLRKPLICFTIPGLAMAAAGILmGLEFLqafahggSLQYGLALIMILLVLLGSF 274
                                       45577778899************************888876555404444478878765566666666666666666 PP

                         RseC_MucC 109 liv 111
                                       l +
  gi|330507322|ref|YP_004383750.1| 275 LAL 277
                                       655 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 ?   12.0   0.0   0.00012      0.23       1      48 [.      12      57 ..      12      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhv 48
                                      +ne+  +++ +   +++ +dr++v+d++s D+t+++  +l+ +++l++
  gi|330507322|ref|YP_004383750.1| 12 YNEEVSIGSIVLRTRKF-ADRVIVVDDGSLDRTAEVA-ALAGAQVLRH 57
                                      58999999999999999.***************9975.4455555555 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 ?   10.0   2.7   0.00028      0.56      14      58 ..     256     305 ..     243     307 .] 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00028
                          LapA_dom  14 qvelpLsllllvafgiGallgwllslwsyl.....rlrrelrrlkkkikk 58 
                                       ++++ L+l++++ +++G +l++  +++++l       +rel ++ +++k+
  gi|330507322|ref|YP_004383750.1| 256 SLQYGLALIMILLVLLGSFLALTGMVLHILsrvmhEFKRELMAQGRQNKE 305
                                       35999*********************988854445599999999999998 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.33   6.5e+02      98     112 ..      29      43 ..      20      48 .. 0.78
   2 ?   10.1   2.0    0.0002      0.41     146     214 ..     215     296 ..     209     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.33
                            DUF373  98 adsaivVsDGaeDes 112
                                       ad++ivV DG+ D +
  gi|330507322|ref|YP_004383750.1|  29 ADRVIVVDDGSLDRT 43 
                                       589*******98865 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0002
                            DUF373 146 kalkdpelrk..tiLvplGlllliyallll............lglpelalaiillllGlylllrGfgldelleelle 208
                                       ++l+d +lrk  + ++++Gl++   ++l+             l++    ++i+l+llG +l l G+ l+  l+++++
  gi|330507322|ref|YP_004383750.1| 215 NVLQDMQLRKplICFTIPGLAMAAAGILMGleflqafahggsLQYGLALIMILLVLLGSFLALTGMVLHI-LSRVMH 290
                                       5788888888556799************9999*******99988888888999999************97.778888 PP

                            DUF373 209 klkesl 214
                                       ++k+ l
  gi|330507322|ref|YP_004383750.1| 291 EFKREL 296
                                       777655 PP

>> Transp_cyt_pur  Permease for cytosine/purines, uracil, thiamine, allantoin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   5.3    0.0014       2.9      22      79 ..     228     288 ..     226     290 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0014
                    Transp_cyt_pur  22 nlnintwvigalglalgLnwwqsvl...viivgnligaifvallglaGakyGlpfpilsRa 79 
                                       ++ i+ ++++a g+ +gL + q+++   +   g  +++i+++llg + a +G+ ++ilsR+
  gi|330507322|ref|YP_004383750.1| 228 CFTIPGLAMAAAGILMGLEFLQAFAhggSLQYGLALIMILLVLLGSFLALTGMVLHILSRV 288
                                       7999********************955568999***************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2401.73
//
Query:       gi|330507323|ref|YP_004383751.1|  [L=364]
Description: glycosyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-29  102.7   0.0    2.6e-29  102.2   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    4.5e-19   69.2   0.0    7.5e-19   68.5   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    5.3e-07   29.4   0.5    7.8e-06   25.6   0.5    2.1  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    2.7e-05   24.2   0.0    4.3e-05   23.5   0.0    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
     0.0017   18.1   0.3      0.058   13.1   0.1    2.8  2  Glyco_tranf_2_5  Glycosyltransferase like family
     0.0021   18.5   0.0      0.011   16.2   0.0    2.0  2  Glyco_tranf_2_4  Glycosyl transferase family 2
     0.0027   17.3   0.0     0.0047   16.5   0.0    1.4  1  Glyco_transf_7C  N-terminal domain of galactosyltransferase
     0.0097   15.4   0.0      0.015   14.7   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 !  102.2   0.0   1.2e-32   2.6e-29       1     166 [.      13     177 ..      13     181 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 1.2e-32
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       s++i+ yN + +++ ++es+ +q  ++  eii vD++S+D++ +il+e    +p+vr+i++ en G++++ n+g+++
  gi|330507323|ref|YP_004383751.1|  13 SIIIVLYNSSRYIEPCIESIMRQ--DYPHEIIAVDNNSRDDSCQILKEK---YPHVRLIKNQENAGYGAGNNEGVKY 84 
                                       8**********************..999*********************...89*********************** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS....EEEECCHCCCCHCCCCCC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv....generlyfkerkrslkgn 150
                                       a+g+yi++l+ D+++++ wl++l+e+l ++++ +  +++  ++ge  +   + ++    ++   l  ++ + + k  
  gi|330507323|ref|YP_004383751.1|  85 ASGKYIVILNPDTIVEERWLRELIEPLRNEDKLITTPKILTYDGELINTCGAINHfsglTFTRGLGCPIDMPFCKTR 161
                                       *****************************************************99********************** PP

                                       STTCSTCCCEEEEHHH CS
                   Glycos_transf_2 151 lsfeigsaallrreal 166
                                       +s+++g+ +++rr+++
  gi|330507323|ref|YP_004383751.1| 162 VSGFSGCSFAIRRDLY 177
                                       *************976 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.0   3.3e-22   7.5e-19       5     214 ..      13     220 ..      11     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 3.3e-22
                   Glyco_tranf_2_3   5 avlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                       +++++ +n +++++ ++es+ +q+yp  e++ v+++s+++ ++ ++e   ++p+v  r++ n++n g +g+ +  ne
  gi|330507323|ref|YP_004383751.1|  13 SIIIVLYNSSRYIEPCIESIMRQDYPH-EIIAVDNNSRDDSCQILKE---KYPHV--RLIKNQENAG-YGAGN--NE 80 
                                       799********************9975.9999999999999999998...****6..89*9*99989.68877..** PP

                   Glyco_tranf_2_3  82 alravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaar...... 152
                                       +++ ++++++++++ Dt+ve + l+ l   + + + + ++tp+ l ++  l++  ga    ++h++ l ++      
  gi|330507323|ref|YP_004383751.1|  81 GVKYASGKYIVILNPDTIVEERWLRELIEPL-RNEDKLITTPKILTYDGELINTCGA----INHFSGLTFTrglgcp 152
                                       ******************************9.67779**************999999....6677777777677777 PP

                   Glyco_tranf_2_3 153 .....ralgvltlnGsgslirrevlkelegldplfllt.dDyelglrlrragfrtayvpgaavrevfp 214
                                               +v  ++G  ++irr+++  l+g+d +f +  dD++l+ r+  +gf++ y p+++v +  +
  gi|330507323|ref|YP_004383751.1| 153 idmpfCKTRVSGFSGCSFAIRRDLYLSLGGFDQRFFMYnDDADLSWRANLNGFKILYIPQSTVKHDYT 220
                                       87777667899999*******************555555***********************988744 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 !   25.6   0.5   3.5e-09   7.8e-06       1     199 [.      13     200 ..      13     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.5e-09
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGa 77 
                                       s++i l++s    yie  +  +  + d   e+i vd+ S ++  + ++    +  l+   ++  +  + +a  N G+
  gi|330507323|ref|YP_004383751.1|  13 SIIIVLYNSS--RYIEPCIESIMRQ-DYPHEIIAVDNNSRDDSCQILKEKYPHVRLIK--NQ--ENAGYGAGNNEGV 82 
                                       6899999876..47*********99.99**************8888887777766665..44..344678889**** PP

                   Glyco_tranf_2_2  78 skaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvv.dlnkedsevlkdvedltassrvledllaa 153
                                       ++a + +++ l+ D  +    +  +++    ++  + i ++ +l++  +l++    + +  +  +++++     + +
  gi|330507323|ref|YP_004383751.1|  83 KYASGKYIVILNPDTIVEERWLRELIE--PLRNEDKLITTPKILTYDgELINTCGAINHFSGLTFTRGLGCPIDMPF 157
                                       *****************9999999988..777778888888888775256666555555556666677766666888 PP

                   Glyco_tranf_2_2 154 kstlvkffapssssilinrraflevGGyDErfrGhgaEDfdlllRl 199
                                        +t v  f  s+ s+ i+r  +l +GG+D rf     +D dl  R 
  gi|330507323|ref|YP_004383751.1| 158 CKTRVSGF--SGCSFAIRRDLYLSLGGFDQRF-FMYNDDADLSWRA 200
                                       88888877..57899****************9.3445666666665 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.9e-08   4.3e-05       1     128 [.      89     219 ..      89     285 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.9e-08
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvp...... 71 
                                       +i++l  Dt + +  lre+++ l++ e +++++p + +  ++++ ++ a    ++h +   ++ +lg+++       
  gi|330507323|ref|YP_004383751.1|  89 YIVILNPDTIVEERWLRELIEPLRN-EDKLITTPKILTYDGELINTCGA----INHFSGLTFTRGLGCPIDmpfckt 160
                                       799*****************99975.66777777554434555555555....455555566666666555555666 PP

                   Glyco_trans_2_3  72 ....svGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspl 128
                                           + G  +++rr++  ++gg+d +++   +D d++ r+  +G+++ ++p+s vk    +
  gi|330507323|ref|YP_004383751.1| 161 rvsgFSGCSFAIRRDLYLSLGGFDQRFFMYNDDADLSWRANLNGFKILYIPQSTVKH--DY 219
                                       666699*********************************************995543..33 PP

>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   2.6e-05     0.058      32      84 ..      65     116 ..      13     117 .. 0.78
   2 ?   -1.0   0.0      0.54   1.2e+03     146     167 ..     193     213 ..     162     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                   Glyco_tranf_2_5  32 iiairnaksiaeaynkalsasdakykvYlhqDvliinkdfikdlleiFkkdkk 84 
                                       +i+ +++  + ++ n++++ ++ ky v l+ D+ i++++++++l+e +++++k
  gi|330507323|ref|YP_004383751.1|  65 LIKNQENAGYGAGNNEGVKYASGKYIVILNPDT-IVEERWLRELIEPLRNEDK 116
                                       34444558999*********************8.7999********9988776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.54
                   Glyco_tranf_2_5 146 qydvpwredlftgfhfYdvsqs 167
                                         d++wr + ++gf +  + qs
  gi|330507323|ref|YP_004383751.1| 193 DADLSWRAN-LNGFKILYIPQS 213
                                       357799999.899988777766 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 !   16.2   0.0   4.9e-06     0.011       2      52 ..      20      72 ..      19     107 .. 0.82
   2 ?   -0.6   0.0      0.86   1.9e+03      18      51 ..     182     213 ..     175     239 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.9e-06
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgf.drilvydndstDgtrailkel.pevkllhvdksy 52
                                      n   +++ +++ + + ++ ++i+ +dn+s+D++ +ilke  p+v+l++++++ 
  gi|330507323|ref|YP_004383751.1| 20 NSSRYIEPCIESIMRQDYpHEIIAVDNNSRDDSCQILKEKyPHVRLIKNQENA 72
                                      78899999*****9**99567****************885599**99998654 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.86
                   Glyco_tranf_2_4  18 gfd.rilvydndstDgtrailkelpevkllhvdks 51 
                                       gfd r+++y++d +  +  + ++l   k+l++++s
  gi|330507323|ref|YP_004383751.1| 182 GFDqRFFMYNDDAD-LS--WRANLNGFKILYIPQS 213
                                       47735666666665.33..3334444555555554 PP

>> Glyco_transf_7C  N-terminal domain of galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.1e-06    0.0047       5      71 ..     151     216 ..     147     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
                   Glyco_transf_7C   5 veidkfgyklpyekyfgGvlalrkedfekiNGfsntfwgWGgEDdelyaRlakkgleierpekgtgr 71 
                                       + id   +k + +++ g+ +a+r++ + +++Gf+++f+ +  +D +l  R   +g++i   +++t +
  gi|330507323|ref|YP_004383751.1| 151 CPIDMPFCKTRVSGFSGCSFAIRRDLYLSLGGFDQRFFMY-NDDADLSWRANLNGFKILYIPQSTVK 216
                                       6677777899999***************************.79**************9887777665 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 !   14.7   0.0   6.8e-06     0.015      24     149 ..      80     213 ..      61     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.8e-06
                   Glyco_transf_21  24 qaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaafl......ntl.agvlqa 93 
                                        ++++a  +++vi+  d++v++  L+el ++l+  + +l+t + + +    l ++  a  +      + +    +++
  gi|330507323|ref|YP_004383751.1|  80 EGVKYASGKYIVILNPDTIVEERWLRELIEPLRN-EDKLITTPKILTYDGELINTCGAINHfsgltfTRGlGCPIDM 155
                                       6788999**************************7.99*****99977777666666444442332112221333333 PP

                   Glyco_transf_21  94 kl..sglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspap 149
                                        +   +++   G s a+rr+   ++GGf +      +D+ l+++ + +G+k+   p+ 
  gi|330507323|ref|YP_004383751.1| 156 PFckTRVSGFSGCSFAIRRDLYLSLGGFDQRFFMYNDDADLSWRANLNGFKILYIPQS 213
                                       33333778899*****************998888999999999999999998777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2922.55
//
Query:       gi|330507324|ref|YP_004383752.1|  [L=507]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   3.7        0.4   11.0   0.6    3.2  3  DUF5438   Family of unknown function (DUF5438)


Domain annotation for each model (and alignments):
>> 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   0.0     0.076   1.4e+03      35      58 ..      17      40 ..      11      43 .. 0.81
   2 ?   11.0   0.6   2.2e-05       0.4       9      58 ..      74     126 ..      69     131 .. 0.87
   3 ?   -2.2   0.0       0.3   5.4e+03       6      13 ..     247     254 ..     243     266 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.076
                           DUF5438 35 ynlltiisttylsvsfrrvmsGfn 58
                                      y +   is  yl + f   + Gf 
  gi|330507324|ref|YP_004383752.1| 17 YLITFAISCCYLLLHFNSSIDGFA 40
                                      4444569*********99999995 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.2e-05
                           DUF5438   9 ftmtlkeinrsiiysttnsvisallmynlltiisttyls...vsfrrvmsGfn 58 
                                       ++m l e  r ++ys    +  a+l + l+  is +y+    vs   +m+Gf 
  gi|330507324|ref|YP_004383752.1|  74 LAMVLNENCRFLLYSPVQLIPYAVLFFVLMLKISNSYFLaslVSIAELMTGFT 126
                                       689********************************997423478899999997 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.3
                           DUF5438   6 phsftmtl 13 
                                       p sftm++
  gi|330507324|ref|YP_004383752.1| 247 PESFTMSV 254
                                       89999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 3506.35
//
Query:       gi|330507325|ref|YP_004383753.1|  [L=329]
Description: NAD dependent epimerase/dehydratase [Methanosaeta concilii GP6]
Scores for complete 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  234.1   0.0    3.2e-69  233.9   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    5.7e-52  176.6   0.0    6.7e-52  176.3   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.5e-21   75.4   0.0    4.7e-21   75.0   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.1e-14   54.2   0.0      4e-14   52.4   0.0    1.7  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.2e-11   43.4   0.1    6.1e-10   38.7   0.1    2.6  1  NAD_binding_4    Male sterility protein
      1e-09   38.5   0.0    2.1e-09   37.5   0.0    1.5  2  NAD_binding_10   NAD(P)H-binding
    2.6e-06   27.2   0.0    3.9e-06   26.6   0.0    1.2  1  NmrA             NmrA-like family
    7.2e-06   25.6   0.0     0.0066   15.9   0.0    2.8  3  adh_short        short chain dehydrogenase
    7.8e-06   25.2   0.0    1.1e-05   24.7   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding 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 !  233.9   0.0   1.6e-72   3.2e-69       1     332 []      11     313 ..      11     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: 233.9 bits;  conditional E-value: 1.6e-72
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG  GfiGs+l+e+L++ g +v g+ r++s  + g +e + +++     ++l++++gDl+D +++ +++++v  d
  gi|330507325|ref|YP_004383753.1|  11 LVTGAGGFIGSHLIERLIDLGADVKGFARYNSRNDWGLLEIIPSQK----LDSLQIISGDLQDYDAVFSAVRDV--D 81 
                                       9********************************9999999887533....468*******************99..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        +++L+    +++s+  P  t+e+n+l tl++L a+r+lg+e   +++++S+sEvYG++  vp++E++p++ +sPY+
  gi|330507325|ref|YP_004383753.1|  82 VIFHLGSLISIPYSYIRPRDTIENNILSTLNILTAARDLGVE---KVVHTSSSEVYGTALYVPIDEKHPLQGQSPYS 155
                                       ****************************************98...89****************************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                       a+K+ ad i+++++ +++l++ + + fn+++pr++++ +   i+++++++ +  qe+++lG l ++Rd+++vkD+v+
  gi|330507325|ref|YP_004383753.1| 156 ASKIGADKIAESFYCSFDLPVATIRPFNTYGPRQSARAI---IPTIITQAIE--QEKIKLGSLFPTRDYTFVKDTVN 227
                                       *********************************977644...5555665444..67899****************** PP

                                       HHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--S..S--SB- CS
                     GDP_Man_Dehyd 232 amwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrp..gevdll 306
                                       ++ +  ++++      + ge+ ++++ +e+++ +l ++i               ++++ +  d +++rp  +ev++l
  gi|330507325|ref|YP_004383753.1| 228 GFIRTAESKS------SIGEVINIGSNFEISMGDLAQRISSLL-----------NKDIMIMQDSSRVRPlkSEVKRL 287
                                       ****999887......69******************9987653...........345677788888888779***** PP

                                       -B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 307 lgdaskakeeLgWkpkvsfeelvrem 332
                                       + d++kak+ LgW+p+vs++e+++e+
  gi|330507325|ref|YP_004383753.1| 288 WCDNAKAKRLLGWEPQVSLDEGLKET 313
                                       ***********************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 !  176.3   0.0   3.4e-55   6.7e-52       1     241 []      10     246 ..      10     246 .. 0.96

  Alignments for each domain:
  == domain 1  score: 176.3 bits;  conditional E-value: 3.4e-55
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHHHT-SEEE CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerlfkeeqpdavi 69 
                                       +lVtGa GfiGs+l+++l + g +v g++r++s++ +++le +        +++ +dl d +a+  +++  ++d+++
  gi|330507325|ref|YP_004383753.1|  10 VLVTGAGGFIGSHLIERLIDLGADVKGFARYNSRNDWGLLEIIpsqkldslQIISGDLQDYDAVFSAVR--DVDVIF 84 
                                       79*****************************999999999988**************************..89**** PP

                                       E--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHH CS
                         Epimerase  70 hlAavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaK 146
                                       hl+   +++ s ++p d+ie+n+  tln+l aar+ gv+++++ sSsevYG    +p +e+    pl+ +spY+a+K
  gi|330507325|ref|YP_004383753.1|  85 HLGSLISIPYSYIRPRDTIENNILSTLNILTAARDLGVEKVVHTSSSEVYGTALYVPIDEKH---PLQGQSPYSASK 158
                                       **99***********************************************99999******...************ PP

                                       HHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHH CS
                         Epimerase 147 lageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeail 223
                                       + ++k++e++  +++l++ ++r+fn yGpr   ++ + +ip +i+++ e++ +++ lg++ + Rd+ +v+D +++++
  gi|330507325|ref|YP_004383753.1| 159 IGADKIAESFYCSFDLPVATIRPFNTYGPR---QSARAIIPTIITQAIEQE-KIK-LGSLFPTRDYTFVKDTVNGFI 230
                                       ******************************...99************9987.555.59******************* PP

                                       HHHHHHTT-STTEEEEES CS
                         Epimerase 224 lvlehvdagdkgeiyniG 241
                                       + +e  ++   ge++niG
  gi|330507325|ref|YP_004383753.1| 231 RTAESKSS--IGEVINIG 246
                                       *****444..599****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 !   75.0   0.0   2.4e-24   4.7e-21       1     222 [.      11     226 ..      11     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 2.4e-24
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrlee.lkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihla 74 
                                       +vtG++GF+G++l+++L++l+  +k    +  r++  lle + + + ++  +i gD++d d +  a+++vdv++hl 
  gi|330507325|ref|YP_004383753.1|  11 LVTGAGGFIGSHLIERLIDLGAdVKGFARYNSRNDWGLLEIIPSQKLDSlqIISGDLQDYDAVFSAVRDVDVIFHLG 87 
                                       69*******************867777778899999999998777777777************************** PP

                         3Beta_HSD  75 slvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesK 150
                                       sl+ +    ++     + n+  T n+l a+++ gv+++v+tSs ev g   l  +    dE+ +   + q++y+ sK
  gi|330507325|ref|YP_004383753.1|  88 SLISIPYsYIRPRDTIENNILSTLNILTAARDLGVEKVVHTSSSEVYGT-ALYVP---IDEKHP--LQGQSPYSASK 158
                                       **9997636666678889******************************9.33334...457655..56799****** PP

                         3Beta_HSD 151 alaEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgNva 222
                                         a+k+  ++         +l    +Rp   yG++++   + p++ + a  + +++k+g+   + d+++v   +
  gi|330507325|ref|YP_004383753.1| 159 IGADKIA-ESFY----CSFDLPVATIRPFNTYGPRQSarAIIPTIITQAIEQ-EKIKLGSLFPTRDYTFVKDTV 226
                                       9999864.4433....34489999**********975114556655554444.788888888888888887655 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0     2e-17     4e-14       1     128 [.      10     130 ..      10     139 .. 0.81
   2 ?   -0.9   0.0      0.35   7.1e+02     177     249 ..     193     266 ..     152     277 .. 0.71

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2e-17
                                       EEEETTTSHHHHHHHHHHHHHB-SE..E.EEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkk..i.illerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekale 74 
                                       vlvtGagG iGs+l++++++  +      +  +r++  l ei         ++kl+ ++  + gd++d + + +a++
  gi|330507325|ref|YP_004383753.1|  10 VLVTGAGGFIGSHLIERLIDLGADVkgFaRYNSRNDWGLLEII-------PSQKLD-SLQIISGDLQDYDAVFSAVR 78 
                                       8*******************96543002122334444444444.......344442.224567************** PP

                                       ..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                   Polysacc_synt_2  75 elkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                         +vdv+fh   l  +P     p ++i++N+l+t n+++aa + gv+kvv  S+
  gi|330507325|ref|YP_004383753.1|  79 --DVDVIFHLGSLISIPYSYIRPRDTIENNILSTLNILTAARDLGVEKVVHTSS 130
                                       ..************************************************9997 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.35
                                       SSHHHHHHHHHTTSSEEES-TT-EEEEE-HHHHHH.HHHHHHHH--SS-EEEE--.-EEEHHHHHHHH...... CS
                   Polysacc_synt_2 177 SviplFkkqikeggpvtvTdpemtRyfmtieeavq.LvlqalalakggeifvldmGepvkivdlakalielsgl 249
                                        +ip+   q  e++++ +     tR +  ++++v+ ++ +a ++++ ge+        +++ dla+++ +l ++
  gi|330507325|ref|YP_004383753.1| 193 AIIPTIITQAIEQEKIKLGSLFPTRDYTFVKDTVNgFIRTAESKSSIGEVINIGSNFEISMGDLAQRISSLLNK 266
                                       57777777777777777777777887777777776467777777888886544444455566888888777665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.1   3.1e-13   6.1e-10       1     208 [.      12     186 ..      12     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 3.1e-13
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TGa GF+G++L+e+L++  ++  +   +R +s         +      ++s+     ++ +++++GDl++ +    
  gi|330507325|ref|YP_004383753.1|  12 VTGAGGFIGSHLIERLIDLGAD--VKGFARYNSR------N-DWGLLEIIPSQK----LDSLQIISGDLQDYDA--- 72 
                                       7*******************96..4444554433......2.222222344444....689********99873... PP

                                       HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                          +   ++ vdvi+h +  +++ ++y +    ++ N+++t ++l+ a+ l     ++h S++ v+g+    v    
  gi|330507325|ref|YP_004383753.1|  73 ---VFSAVRDVDVIFHLGSLISIPYSYIRprdTIENNILSTLNILTAARDLGVE-KVVHTSSSEVYGTALY-V---- 140
                                       ...3344699***************99762236667*************99888.6777777666666662.2.... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                                    ++++  + +  Y+ sK  a+k+ ++   + +lpv+ +Rp + +g
  gi|330507325|ref|YP_004383753.1| 141 -----------PIDEKHPLQGQSPYSASKIGADKIAESFYCSFDLPVATIRPFNTYG 186
                                       ...........3445566666789**************999999*******977666 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 !   37.5   0.0   1.1e-12   2.1e-09       1     104 [.      14     136 ..      14     194 .. 0.78
   2 ?   -2.6   0.0       2.1   4.2e+03     138     182 ..     219     265 ..     217     267 .. 0.57

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.1e-12
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH....HHH...CTTTCEEEE--TT-CCHHHHHHTT-SEEEES-.. CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekla....ele...aeeglevvegdvtdvedlaealkgadaVvsal.. 68 
                                       GA G +G++l+++l++ g  +v+ ++R  ++ +    e+    + + l++++gd++d +++ +a++++d+++  +  
  gi|330507325|ref|YP_004383753.1|  14 GAGGFIGSHLIERLIDLG-ADVKGFARYNSRNDwgllEIIpsqKLDSLQIISGDLQDYDAVFSAVRDVDVIFHLGsl 89 
                                       9****************5.********999887666633233244899*********************99998888 PP

                                       ........--TCC.HHHH...HHHHHHHHHHCT--EEEEEEETTTTSG CS
                    NAD_binding_10  69 ........ggggk.deeg...aknivdaakeagvkRfvlvsaigvgde 104
                                                ++++ ++     + ni++aa+  gv+++v  s+  v+  
  gi|330507325|ref|YP_004383753.1|  90 isipysyiRPRDTiEN-NilsTLNILTAARDLGVEKVVHTSSSEVYGT 136
                                       8777776555555433.3599**********************99953 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.1
                                       EEEEEE-C..EE-ST--SEEEEETTSS----EEEHHHHHHHHHHHCT CS
                    NAD_binding_10 138 wTivrpgg..LtdepttkyrvvekgepfkggsisradVAdvlvavld 182
                                       +T+v+ +   +   +++k  ++e  +  ++ +is  d+A+ + ++l+
  gi|330507325|ref|YP_004383753.1| 219 YTFVKDTVngFIRTAESKSSIGEVINIGSNFEISMGDLAQRISSLLN 265
                                       55555443113444455555555555556678888888888777776 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0     2e-09   3.9e-06       1     101 [.      10     129 ..      10     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2e-09
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S......-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE- CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdt......kselakslkeaGvelvkgdlddkeslvealkgvdvvfsv 71 
                                       +lv+Ga G +G+++++ l++ g +v+   R          e + s k    ++++gdl+d++ + +a+++vdv+f  
  gi|330507325|ref|YP_004383753.1|  10 VLVTGAGGFIGSHLIERLIDLGADVKGFARYNsrndwgLLEIIPSQKLDSLQIISGDLQDYDAVFSAVRDVDVIFHL 86 
                                       79*************************9998878888866677777777789***********************98 PP

                                       --GG.............S-HHHHHHHHHHHHHHHS-SEEEEEE CS
                              NmrA  72 tgfy.............skeiedgkklvdAakeaGvkhfiySs 101
                                        ++              +++i    ++  Aa   Gv++++  s
  gi|330507325|ref|YP_004383753.1|  87 GSLIsipysyirprdtiENNILSTLNILTAARDLGVEKVVHTS 129
                                       8877788899***99999999999************9999765 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.3e-06    0.0066       1      72 [.       8      81 ..       8      90 .. 0.82
   2 !    6.3   0.0    0.0029       5.7     140     162 ..     145     167 ..     141     174 .. 0.86
   3 ?   -2.4   0.1       1.4   2.8e+03     125     137 ..     236     248 ..     224     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.3e-06
                                      SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHH.HHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHH CS
                         adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekle.evakelkee.gakalaiqvDvtdreevealvekav 72
                                      k vlvtGa++ IG  + ++l+  Ga+v  ++r +++    +++ + ++  +++ +i++D++d+++v  +v+++ 
  gi|330507325|ref|YP_004383753.1|  8 KKVLVTGAGGFIGSHLIERLIDLGADVKGFARYNSRNDwGLLEIIPSQkLDSLQIISGDLQDYDAVFSAVRDVD 81
                                      78*************************996666665551455556666678899************99999875 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0029
                                       TSB-TTBHHHHHHHHHHHHHHHH CS
                         adh_short 140 kvpvagvaaYsAsKaavagltrs 162
                                       k p+ g+++YsAsK + +++++s
  gi|330507325|ref|YP_004383753.1| 145 KHPLQGQSPYSASKIGADKIAES 167
                                       568899**********9998877 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.4
                                       HCTTEEEEEEEEG CS
                         adh_short 125 kqssGrIvnvsSv 137
                                       k+s G+++n++S+
  gi|330507325|ref|YP_004383753.1| 236 KSSIGEVINIGSN 248
                                       677899****996 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   5.5e-09   1.1e-05       2     234 ..       9     267 ..       8     296 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5.5e-09
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.......................T--TTSHHHHHHHHHHH--SEE CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre.......................eldltdaeavaellkeakpdvv 55 
                                       k+lvtGa+G +Gs+L+++l   g++v ++ r                        + dl+d +av +++++   dv+
  gi|330507325|ref|YP_004383753.1|   9 KVLVTGAGGFIGSHLIERLIDLGADVKGFARYnsrndwglleiipsqkldslqiiSGDLQDYDAVFSAVRD--VDVI 83 
                                       79***************************888899*******************99**************9..899* PP

                                       EE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHH CS
                     RmlD_sub_bind  56 vnaAAytavDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKla 131
                                        +++    +      ++   + n  ++ ++  aa+  g+ +++h S+  V+  +   p  e+++ + ++ Y ++K+ 
  gi|330507325|ref|YP_004383753.1|  84 FHLGSLISIPYSYIRPRDTIENNILSTLNILTAARDLGVeKVVHTSSSEVYGTALYVPIDEKHPLQGQSPYSASKIG 160
                                       **************************************9569*********999999999999999999******98 PP

                                       HHHHHHH....H-SSEEEEEE-SEESS..SSS-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHH.HHHHHCH CS
                     RmlD_sub_bind 132 GEqavla....agkkalivRtswvyge..kgknfvktmlrlakereelkvvaDqlgsPTsardlAevll.qllekaa 201
                                         +  ++        ++ +R    yg   + +  + t++  a e+e++k+       PT   +  + ++   +++a 
  gi|330507325|ref|YP_004383753.1| 161 ADKIAESfycsFDLPVATIRPFNTYGPrqSARAIIPTIITQAIEQEKIKLG---SLFPTRDYTFVKDTVnGFIRTAE 234
                                       777665543222224455666666655334455566666666666666654...34555544433333303333333 PP

                                       H.GGG-EEEE---BS-EEHHHHHHHHHHHHCHT CS
                     RmlD_sub_bind 202 eekelagvyHlanegetswlefArailkeagad 234
                                       +++++ +v  ++++ e+s  ++A+ i + +++d
  gi|330507325|ref|YP_004383753.1| 235 SKSSIGEVINIGSNFEISMGDLAQRISSLLNKD 267
                                       333446666666666666666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2494.89
//
Query:       gi|330507326|ref|YP_004383754.1|  [L=240]
Description: nucleotidyl transferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-44  152.0   0.0    2.3e-44  151.9   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
      5e-10   40.0   0.0    5.6e-10   39.8   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
       0.11   11.2   0.1       0.16   10.6   0.1    1.2  1  MSP1_C           Merozoite surface protein 1 (MSP1) C-terminu


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.9   0.0   3.8e-48   2.3e-44       1     246 [.       2     227 ..       2     229 .. 0.96

  Alignments for each domain:
  == domain 1  score: 151.9 bits;  conditional E-value: 3.8e-48
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kavILaGG GtRL P t   +k+l+p++++ +++++ +++l ++g++e i     + s+l+   +++gsk+g+++++
  gi|330507326|ref|YP_004383754.1|   2 KAVILAGGLGTRLKPYTTVFPKPLMPIGES-PILEIIVKQLKAKGFNE-ITLAVGHLSELIMAFFNNGSKYGLKIEY 76 
                                       79****************************.*****************.7777789********************* PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       + e+++ gtA+ + l ++ led++     lv++gD+l++ +++e++++++e+++  ++t+++ +++   ++Gv+e d
  gi|330507326|ref|YP_004383754.1|  77 SKEEKKLGTAGGLGLLKNKLEDDF-----LVMNGDVLTGLDFSEFLEFHKETGS--IATIALNRRHVDIDFGVVELD 146
                                       ********************9877.....9************************..********************* PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       e+++ +  +EKPk +    l+s+G+Y fn+++l+++         +  +i d+++++l+eg++   f+ ++  yW D
  gi|330507326|ref|YP_004383754.1| 147 ENRTLIGYIEKPKIDY---LVSMGVYAFNESILEYI------PSHEYLDIPDLMKRLLSEGEKVNGFIHDG--YWLD 212
                                       *************955...*****************......457889***********************..9*** PP

                                       XSSHHHHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleanekla 246
                                       +G +d++++ane+++
  gi|330507326|ref|YP_004383754.1| 213 IGRPDDYIKANEDIQ 227
                                       ************987 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   9.4e-14   5.6e-10       1     117 [.       3     126 ..       3     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 9.4e-14
                                       EEEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCTS-EEE-TT CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggd..eevlaal...arlgvrvveded 67 
                                       aviLAGG ++R++      +K+l+p+g+ p+le ++++l+a g++e+++++g+  e + a +    ++g+++ + ++
  gi|330507326|ref|YP_004383754.1|   3 AVILAGGLGTRLKPyttvfPKPLMPIGESPILEIIVKQLKAKGFNEITLAVGHlsELIMAFFnngSKYGLKIEYSKE 79 
                                       79**********9444689**********************************844444433443667888866654 PP

                                       S.S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSS CS
                      NTP_transf_3  68 p.gkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgad 117
                                       +   g++++l    +++  +d +lv+ +D+  lt     ++l+ ++++g+ 
  gi|330507326|ref|YP_004383754.1|  80 EkKLGTAGGLGLLKNKL--EDDFLVMNGDV--LTGLDFSEFLEFHKETGSI 126
                                       42689999987777766..799*******9..6777777777776655543 PP

>> MSP1_C  Merozoite surface protein 1 (MSP1) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   2.8e-05      0.16      47     138 ..      37     123 ..      34     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.8e-05
                            MSP1_C  47 likalteekvnalyleikklkellelsydryskyklklerlynkke.kiqqskrqikkltilkeklekrknslnnvf 122
                                       ++k+l+ +  n++ l + +l el+  ++++ sky lk+e  y k+e k+++       l +lk+kle     +n+  
  gi|330507326|ref|YP_004383754.1|  37 IVKQLKAKGFNEITLAVGHLSELIMAFFNNGSKYGLKIE--YSKEEkKLGTA----GGLGLLKNKLEDDFLVMNGDV 107
                                       4788999999****************************9..55554055544....579***************998 PP

                            MSP1_C 123 svlknyvaffnkkrea 138
                                           +++ f+  ++e+
  gi|330507326|ref|YP_004383754.1| 108 LTGLDFSEFLEFHKET 123
                                       8888999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 1999.18
//
Query:       gi|330507327|ref|YP_004383755.1|  [L=295]
Description: NAD dependent epimerase/dehydratase [Methanosaeta concilii GP6]
Scores for 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-52  177.5   0.0    3.7e-52  177.2   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    6.3e-50  170.4   0.1    5.3e-47  160.8   0.1    2.6  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    7.1e-23   81.0   0.3    7.7e-21   74.3   0.1    2.3  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    9.8e-20   70.8   0.0    5.3e-16   58.6   0.0    2.5  2  NAD_binding_4    Male sterility protein
    1.7e-19   70.0   0.0    2.2e-19   69.6   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    3.1e-18   65.9   0.0    1.5e-16   60.4   0.0    2.6  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    0.00054   19.9   0.0    0.00078   19.4   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.071   12.0   0.1        0.1   11.5   0.1    1.1  1  DUF2362          Uncharacterized conserved protein (DUF2362)
       0.18   11.2   0.2        2.9    7.3   0.1    2.3  2  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 !  177.2   0.0   1.8e-55   3.7e-52       1     241 []       8     224 ..       8     224 .. 0.96

  Alignments for each domain:
  == domain 1  score: 177.2 bits;  conditional E-value: 1.8e-55
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHH.T-SEEEE--S--- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkee.qpdavihlAavgg 76 
                                       +++tGa+Gf+G++lv+al+  g  v+ l+              +   ld+++++ ++  ++   ++d+++hlAa+++
  gi|330507327|ref|YP_004383755.1|   8 VIITGANGFVGRHLVNALNGMGSSVTLLKDI------------NGNSLDIRKKNLIKSSLDYLsDVDVIYHLAAIAS 72 
                                       68**************************999............56699******9999999889************* PP

                                       HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHH CS
                         Epimerase  77 vaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklv 153
                                       v+ s e+p d++e+n+ gtln+le +r +++++++++sS  vYGk++  p +e+     ++p++pY+++Kl ge+l+
  gi|330507327|ref|YP_004383755.1|  73 VNSSYENPHDTYETNVLGTLNILELCRLYDINKIVYASS-YVYGKPHYLPIDENH---MTNPTNPYSRSKLIGEELC 145
                                       **************************************9.********9988888...679**************** PP

                                       HHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHT CS
                         Epimerase 154 eayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvd 230
                                       ++y++++g+++i+lr+fn+yGp+   ++ + +ip +i+ i++g+   +++ d +++Rdf+y+ D+++a++++ e   
  gi|330507327|ref|YP_004383755.1| 146 KSYHDDFGIECIVLRPFNIYGPG---QRSDFLIPMIISCIKSGE---VIVRDPEPKRDFIYITDMIDAYIRAGEY-- 214
                                       ***********************...89999************9...8999***********************9.. PP

                                       T-STTEEEEES CS
                         Epimerase 231 agdkgeiyniG 241
                                          + +i+niG
  gi|330507327|ref|YP_004383755.1| 215 -EGDFDIFNIG 224
                                       .56688***99 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 !  160.8   0.1   2.6e-50   5.3e-47       1     332 []       9     288 ..       9     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: 160.8 bits;  conditional E-value: 2.6e-50
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH.T- CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev.qp 76 
                                       +iTG +Gf+G +l++ L   g  v+ +++ + +                        + D++ ++ +++ l+   ++
  gi|330507327|ref|YP_004383755.1|   9 IITGANGFVGRHLVNALNGMGSSVTLLKDINGN------------------------SLDIRKKNLIKSSLDYLsDV 61 
                                       59****************999999876533222........................23555555555554433378 PP

                                       SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHH CS
                     GDP_Man_Dehyd  77 devynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPY 153
                                       d +y+LAA   V+ s+e+P+ t+e+nvlGtl++Le++r + ++   +++ a +s vYGk+   p++E++ ++P++PY
  gi|330507327|ref|YP_004383755.1|  62 DVIYHLAAIASVNSSYENPHDTYETNVLGTLNILELCRLYDIN---KIVYA-SSYVYGKPHYLPIDENHMTNPTNPY 134
                                       ***************************************9875...56555.679********************** PP

                                       HHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                       + +Kl+ + ++++y++ +g+ +++ + fn ++p +  +f    i+ +++ i+ g+   +++ + ++kRd+ ++ D++
  gi|330507327|ref|YP_004383755.1| 135 SRSKLIGEELCKSYHDDFGIECIVLRPFNIYGPGQRSDFL---IPMIISCIKSGE---VIVRDPEPKRDFIYITDMI 205
                                       ***********************************99987...777788889998...5689*************** PP

                                       HHHHHHHHC.SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB- CS
                     GDP_Man_Dehyd 231 eamwlmlqq.dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdll 306
                                       +a+ ++ +  +  + ++i+ ge++sv+e++e+ ++ +g +                    +  + +  +r  e   +
  gi|330507327|ref|YP_004383755.1| 206 DAYIRAGEYeGDFDIFNIGYGESYSVKEIIEKIIKLHGSE--------------------TRVIYRGERRRNEIMDC 262
                                       *****998735568899*************9766666542....................234556788999***** PP

                                       -B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 307 lgdaskakeeLgWkpkvsfeelvrem 332
                                       +  ++kak  LgW+p ++++e++r m
  gi|330507327|ref|YP_004383755.1| 263 YSSTKKAKDILGWSPHINIDEGLRLM 288
                                       **********************9976 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 !   74.3   0.1   3.9e-24   7.7e-21       1     228 [.       9     211 ..       9     216 .. 0.78
   2 ?   -4.3   0.0       3.5   6.9e+03     138     151 ..     255     268 ..     252     272 .. 0.76

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 3.9e-24
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleea...legvdvvihla 74 
                                       ++tG+ GF+Gr+lv++L  +++   v  l   +++                 D+++k+ ++     l +vdv+ hla
  gi|330507327|ref|YP_004383755.1|   9 IITGANGFVGRHLVNALNGMGS--SVTLLKDINGN---------------SLDIRKKNLIKSSldyLSDVDVIYHLA 68 
                                       69***************99996..34333222222...............3455555555554111579******** PP

                         3Beta_HSD  75 slvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesK 150
                                       ++  v +   +    ++ nv GT n+le c+  +++++vY Ss+ v g+  +  +i   dE+  + ++++++y++sK
  gi|330507327|ref|YP_004383755.1|  69 AIASVNSsYENPHDTYETNVLGTLNILELCRLYDINKIVYASSY-VYGK-PHYLPI---DEN--HMTNPTNPYSRSK 138
                                       ******944456789****************************9.3333.344444...555..5677899****** PP

                         3Beta_HSD 151 alaEklvlkaNgrtlknggrlyTcaLRpagiyGegd..kllvpllkqlaklglalfkigdeevlsdrvYvgNvawah 225
                                        + E+l ++  +    +   +  + LRp  iyG+g+  ++l p++  ++k+g+ +++  d+e + d++Y   + +a+
  gi|330507327|ref|YP_004383755.1| 139 LIGEELCKSYHD----DF-GIECIVLRPFNIYGPGQrsDFLIPMIISCIKSGEVIVR--DPEPKRDFIYITDMIDAY 208
                                       *******99988....33.488899*********9622589***********66555..666677********9999 PP

                         3Beta_HSD 226 ilA 228
                                       i A
  gi|330507327|ref|YP_004383755.1| 209 IRA 211
                                       987 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 3.5
                         3Beta_HSD 138 yeslhqdaypesKa 151
                                       + +  +d+y+++K+
  gi|330507327|ref|YP_004383755.1| 255 RRNEIMDCYSSTKK 268
                                       56678999999998 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00026      0.52       1      16 [.      10      25 ..      10      35 .. 0.89
   2 !   58.6   0.0   2.7e-19   5.3e-16      85     243 ..      58     196 ..      37     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00026
                                      EE-TTSHHHHHHHHHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekL 16
                                      +TGa GF+G++L++ L
  gi|330507327|ref|YP_004383755.1| 10 ITGANGFVGRHLVNAL 25
                                      8************987 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 2.7e-19
                                       HHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H..... CS
                     NAD_binding_4  85 aeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegeke 158
                                        + vdvi+h aA  +++++y++    +++Nv+Gt ++lel++    +  +++ S+ yv+g+ +              
  gi|330507327|ref|YP_004383755.1|  58 LSDVDVIYHLAAIASVNSSYENphdTYETNVLGTLNILELCRLYDIN-KIVYASS-YVYGKPH-------------- 118
                                       478***************9987666899**************88888.9999996.5555554.............. PP

                                       .HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHHHHHH-EEE CS
                     NAD_binding_4 159 ekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwingsdlgirgllgliakgvlp 235
                                             +++++++ +n Y++sK ++E+l++++++  g+ ++++Rp +i+g       ++sd++i +++++i+ g + 
  gi|330507327|ref|YP_004383755.1| 119 --YLPIDENHMTNPTNPYSRSKLIGEELCKSYHDDFGIECIVLRPFNIYG-----PGQRSDFLIPMIISCIKSGEVI 188
                                       ..2346789999************************************76.....5678999************999 PP

                                       S-SB---T CS
                     NAD_binding_4 236 eilgdkea 243
                                          ++++ 
  gi|330507327|ref|YP_004383755.1| 189 VRDPEPKR 196
                                       77777654 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 !   69.6   0.0   1.1e-22   2.2e-19       2     166 ..       7     180 ..       6     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.1e-22
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...T--TTSHHHHHHHHHHH.--SEEEE------HHHHHHSHHHH CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre...eldltdaeavaellkea.kpdvvvnaAAytavDkaEseeeaa 74 
                                       ++++tGanG +G++L+++l+  g +v+ l+     +ld+++++ +++ l+   + dv++++AA   v    ++++  
  gi|330507327|ref|YP_004383755.1|   7 RVIITGANGFVGRHLVNALNGMGSSVTLLKDIngnSLDIRKKNLIKSSLDYLsDVDVIYHLAAIASVNSSYENPHDT 83 
                                       799********************999887332455**************9862579********************* PP

                                       HHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-S....SEEEEE CS
                     RmlD_sub_bind  75 yavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagk....kalivR 147
                                       y+ n+ ++ ++ e+++ +++  i + + yV+   +  p  e++ t+P n Y r+Kl GE+  +++++    +++++R
  gi|330507327|ref|YP_004383755.1|  84 YETNVLGTLNILELCRLYDINKIVYASSYVYGKPHYLPIDENHMTNPTNPYSRSKLIGEELCKSYHDdfgiECIVLR 160
                                       ********************99999999***999*****************************965533337899** PP

                                       E-SEESS.SSS-HHHHHHHH CS
                     RmlD_sub_bind 148 tswvyge.kgknfvktmlrl 166
                                          +yg  ++ +f+  m+  
  gi|330507327|ref|YP_004383755.1| 161 PFNIYGPgQRSDFLIPMIIS 180
                                       *****985778999888755 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   7.6e-20   1.5e-16      61     252 ..      43     247 ..       8     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 7.6e-20
                                       --TT-HHHHHHHTT...T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE........ CS
                   Polysacc_synt_2  61 gdvrdkerlekaleel.kvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt........ 128
                                        d+r+k+ +++ l+ l +vdv++h AA+  V    enp+++ +tNvlgt n++e +  ++++k+v+ S+        
  gi|330507327|ref|YP_004383755.1|  43 LDIRKKNLIKSSLDYLsDVDVIYHLAAIASVNSSYENPHDTYETNVLGTLNILELCRLYDINKIVYASSyvygkphy 119
                                       589999999999886438************************************************99756655555 PP

                                       .....GGGSS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTG...TTSSHHHHHHHHHTTSSEEES-T CS
                   Polysacc_synt_2 129 .....DKAvnPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlgS...rGSviplFkkqikeggpvtvTdp 197
                                                nPtn +  +K++ e l+ ++++       + +v R  N+ g    +  +ip+  + ik+g +v v dp
  gi|330507327|ref|YP_004383755.1| 120 lpideNHMTNPTNPYSRSKLIGEELCKSYHDDF---GIECIVLRPFNIYGPgqrSDFLIPMIISCIKSG-EVIVRDP 192
                                       555334679*******************99998...8999****99*99843225569********998.788**** PP

                                       T-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH......... CS
                   Polysacc_synt_2 198 emtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgleek 252
                                       e  R f+ i++ ++  + a+++  + +if    Ge+++++++ +++i+l g e++
  gi|330507327|ref|YP_004383755.1| 193 EPKRDFIYITDMIDAYIRAGEYEGDFDIFNIGYGESYSVKEIIEKIIKLHGSETR 247
                                       **************************************************98765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.9e-07   0.00078       1     132 [.      12     146 ..      12     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.9e-07
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC..HH CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk..de 75 
                                       GA+G vGr+lv+ l    g +vt+l        +++ +++l   ++d ++  d+  +l+ +  V s+  + ++  + 
  gi|330507327|ref|YP_004383755.1|  12 GANGFVGRHLVNALNGM-GSSVTLLKDINGNSLDIR-KKNLIKSSLDYLSDVDVIYHLAAIASVNSSYENPHDtyE- 85 
                                       9**********988777.69***9987544444586.69999999***********************66666342. PP

                                       HH....HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHH.HCCHHHHHHHHHHHHHHH CS
                    NAD_binding_10  76 eg....aknivdaakeagvkRfvlvsaigvgdevpgefgewnk.ellkaylaakraaeellr 132
                                        +    + ni++ ++  +++++v+ s+   g+ +  + +e  + +  ++y + k   eel +
  gi|330507327|ref|YP_004383755.1|  86 -TnvlgTLNILELCRLYDINKIVYASSYVYGKPHYLPIDENHMtNPTNPYSRSKLIGEELCK 146
                                       .33578*********************99997555444443331334566666666666555 PP

>> DUF2362  Uncharacterized conserved protein (DUF2362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.1e-05       0.1     378     423 ..      58     106 ..      56     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.1e-05
                           DUF2362 378 LsevhvvFHlvvddslksseins...rhpvilgLrniLkvasrhditti 423
                                       Ls+v+v++Hl +  s++ss  n     +  +lg  niL ++  +di++i
  gi|330507327|ref|YP_004383755.1|  58 LSDVDVIYHLAAIASVNSSYENPhdtYETNVLGTLNILELCRLYDINKI 106
                                       99***********9999955443222566799**************998 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0014       2.9       1      35 [.       6      41 ..       6      53 .. 0.83
   2 ?    1.3   0.0       0.1     2e+02      65     116 ..      48      95 ..      44     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0014
                                      SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHH CS
                         adh_short  1 kvvlvtGassGIGraiakelakeGakvvv.vdrsee 35
                                      k v++tGa + +Gr ++++l  +G +v++  d++ +
  gi|330507327|ref|YP_004383755.1|  6 KRVIITGANGFVGRHLVNALNGMGSSVTLlKDINGN 41
                                      679************************994555555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHH CS
                         adh_short  65 ealvekavkklgkldvLvnNAGitgsgpfselseeewervievNltgvfllt 116
                                       ++l++   + l  +dv+++ A+i+      + s e+  +++e+N+ g++++ 
  gi|330507327|ref|YP_004383755.1|  48 KNLIKSSLDYLSDVDVIYHLAAIA----SVNSSYENPHDTYETNVLGTLNIL 95 
                                       567777788889999999999994....344456667889999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2034.98
//
Query:       gi|330507328|ref|YP_004383756.1|  [L=147]
Description: capsular polysaccharide biosynthesis protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-22   79.2   0.1    8.1e-20   71.5   0.0    2.1  2  Alg14            Oligosaccharide biosynthesis protein Alg14 l
  ------ inclusion threshold ------
      0.022   14.8   0.0      0.029   14.4   0.0    1.2  1  Glyco_transf_4   Glycosyltransferase Family 4
      0.057   13.4   0.1      0.073   13.1   0.1    1.1  1  Glyco_trans_4_2  Glycosyl transferase 4-like
      0.069   13.2   0.0       0.15   12.1   0.0    1.7  1  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
       0.08   13.4   0.0      0.096   13.1   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Alg14  Oligosaccharide biosynthesis protein Alg14 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1    0.0026       9.2       2      37 ..       4      39 ..       3      51 .. 0.81
   2 !   71.5   0.0   2.3e-23   8.1e-20      76     173 ..      55     144 ..      46     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0026
                             Alg14  2 lvvlGSGGHTaEmlrllkklekeknikrtyvvssgD 37
                                       +v   GGH + ml l+++++ ++ i +ty    + 
  gi|330507328|ref|YP_004383756.1|  4 AIVCSHGGHLTQMLYLMDAFKGNDIIIITYDSKRTQ 39
                                      567778**************9999999999766655 PP

  == domain 2  score: 71.5 bits;  conditional E-value: 2.3e-23
                             Alg14  76 ifttllsllsaillvlrekrlpdvilvNGPgtcvpvvlaalllkllallkrskivyvEslarvktlSLsGklllpla 152
                                       ++ +l+++++ ++++ r +  pd+i+ NG   ++p +++ +l   l++    ki+++Es+arv++ SL+G+l++p+a
  gi|330507328|ref|YP_004383756.1|  55 PVRMLTAAITFLRVFSRYR--PDLIISNGSEIAIPALYIGRL---LGA----KIIFIESWARVNNPSLTGRLVYPIA 122
                                       5667888888888889999..**********99997776655...555....6************************ PP

                             Alg14 153 DrfvVqwpeLekky.kkaeyvg 173
                                       D f+Vqwp+L +ky kka + g
  gi|330507328|ref|YP_004383756.1| 123 DHFLVQWPQLISKYgKKAVFEG 144
                                       **************44444445 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     8e-06     0.029      16     101 ..      24     101 ..       9     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8e-06
                    Glyco_transf_4  16 arrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalr 92 
                                          G ++ ++t ++++ +e         ++    + +++ r+l+++  + r++ r++pD++ ++++  ++ al   r
  gi|330507328|ref|YP_004383756.1|  24 K--GNDIIIITYDSKRTQELD-----YKKYLVKNIGYNPVRMLTAAITFLRVFSRYRPDLIISNGSEIAIPALYIGR 93 
                                       4..668888887777776666.....334444456677899************************999988887777 PP

                    Glyco_transf_4  93 rrlgiplVl 101
                                       + lg+++++
  gi|330507328|ref|YP_004383756.1|  94 L-LGAKIIF 101
                                       6.9998886 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 ?   13.1   0.1     2e-05     0.073       1     102 [.       2      99 ..       2     109 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                   Glyco_trans_4_2   1 killlanlssvhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkg.pleylk.afklkklikkikP 75 
                                       ki+++  ++   t  l  + a +g ++ +it + ++ +el  +++ v++    + + p+  l+ a+++ +++ +  P
  gi|330507328|ref|YP_004383756.1|   2 KIAIVCSHGGHLTQMLYLMDAFKGNDIIIITYDSKRTQELDYKKYLVKN----IGYnPVRMLTaAITFLRVFSRYRP 74 
                                       678888877555555544444568********99966666665555555....5577*****8577*********** PP

                   Glyco_trans_4_2  76 Dvvhahyakpygllgslaarlsgvipv 102
                                       D+++    + +++ +  + rl+g  ++
  gi|330507328|ref|YP_004383756.1|  75 DLIISNG-SEIAIPALYIGRLLG-AKI 99 
                                       ***7554.334444444445455.555 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 ?   12.1   0.0   4.2e-05      0.15      59     120 ..      44     105 ..       5     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.2e-05
                                       TT..CHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHCCCCCHCCCTTHCCCCCHC CS
                   Glyco_transf_28  59 rrklspknlkeilkvlkavvkakkilkeakpdavvgtggyvslpaviaaplaripviihEqn 120
                                       +++l ++   ++ + l+a ++  +++ +++pd++++ g  +++pa++  +l+++++i+ E+ 
  gi|330507328|ref|YP_004383756.1|  44 KKYLVKNIGYNPVRMLTAAITFLRVFSRYRPDLIISNGSEIAIPALYIGRLLGAKIIFIESW 105
                                       4555555556778888889999*********************************9998875 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 ?   13.1   0.0   2.7e-05     0.096      53     101 ..      55     101 ..      35     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                   Glyco_trans_4_4  53 pladlaalralrrllrqrrerpdvvhahsptaglaarlarrrrgiplvv 101
                                       p+++l a+  + r++   r+rpd+++++++ ++++a+ + r  g+++++
  gi|330507328|ref|YP_004383756.1|  55 PVRMLTAAITFLRVF--SRYRPDLIISNGSEIAIPALYIGRLLGAKIIF 101
                                       6889999999*****..*************9999999988788888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1065.04
//
Query:       gi|330507329|ref|YP_004383757.1|  [L=154]
Description: glycosyl transferase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-09   36.9   0.0    6.5e-09   36.0   0.0    1.5  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
  ------ inclusion threshold ------
       0.12   11.7   0.0       0.16   11.3   0.0    1.2  1  Glyco_hydro_114  Glycoside-hydrolase family GH114


Domain annotation for each model (and alignments):
>> 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 !   36.0   0.0   7.2e-13   6.5e-09       1     118 [.       1     108 [.       1     144 [. 0.77

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 7.2e-13
                                       -EEEEE-..SSSHHHHHCCCTSHHHHHHHHHHHHCHHHCCT-EEC---STT-TTTTCEEEEEESSSSHHHHHHHH-E CS
                   Glyco_tran_28_C   1 tilVtGG..SqgaeaLnelvlselkllelksrelqvlhqtGkreleevkikveeltlkvevfefidkmaeaikaadL 75 
                                       +i+Vt+G   qg++ L+e     + ++e k     +++q G+ ++ + + ++ ++    +     ++  ++i++++ 
  gi|330507329|ref|YP_004383757.1|   1 MIFVTVGmhNQGFDRLIEKCDLLAGQIEDK-----MIIQKGSTSYCPRNAEYFDFA---S----NEEFLKLIRQSST 65 
                                       689999977777776666666666666665.....899999888888777766663...2....344666******* PP

                                       EEECS-CHHHHHHHHTT--EEEE--TT....S-HHHHHHHHHH CS
                   Glyco_tran_28_C  76 vIsRAGagtiaEllalgkplIlvplpeaaenhqdnNakeleka 118
                                       vI++ Gag+i+++l + k +I+vp  +++++  + N  +l+ +
  gi|330507329|ref|YP_004383757.1|  66 VITHDGAGSILNCLLNKKRTIVVPRLKEYNECRYDNKLDLALE 108
                                       *****************************99999998877654 PP

>> Glyco_hydro_114  Glycoside-hydrolase family GH114
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.8e-05      0.16     150     183 ..      31      99 ..      14     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.8e-05
                   Glyco_hydro_114 150 aiglknageliselvdafdfavnEeca...................................eyseCdt 183
                                       +i++k + +  ++ +++fdfa nEe                                     ey+eC  
  gi|330507329|ref|YP_004383757.1|  31 MIIQKGSTSYCPRNAEYFDFASNEEFLklirqsstvithdgagsilncllnkkrtivvprlkEYNECRY 99 
                                       7999***********************999999999999999999999999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1192.79
//
Query:       gi|330507330|ref|YP_004383758.1|  [L=391]
Description: glycosyl transferase group 1 family protein [Methanosaeta concilii GP6]
Scores for complete 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  124.9   0.0    4.1e-36  124.1   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    2.5e-24   86.2   0.0    6.6e-24   84.8   0.0    1.6  2  Glyco_trans_1_4  Glycosyl transferases group 1
    7.8e-15   55.3   0.1    1.8e-14   54.1   0.1    1.6  1  Glyco_transf_4   Glycosyltransferase Family 4
    2.2e-10   41.2   0.0    3.9e-10   40.4   0.0    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    4.2e-07   30.1   0.0    9.6e-07   28.9   0.0    1.7  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    1.8e-06   28.2   0.0    4.2e-06   27.1   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.076   13.7   0.2       0.15   12.8   0.2    1.4  1  Transthyretin    HIUase/Transthyretin family


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 !  124.1   0.0   1.6e-39   4.1e-36       5     159 ..     208     361 ..     204     373 .. 0.94

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 1.6e-39
                                       HHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECC CS
                   Glycos_transf_1   5 krkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgev 81 
                                        r+ l+++ekk+iil++g l+k+Kg+  li+a+ +l+ +  +++ ++i G+g+ ++el+k++++++l++ ++++g++
  gi|330507330|ref|YP_004383758.1| 208 CRRTLRLPEKKRIILTIGSLVKVKGHIDLIHAISELEGR-SKDILCIILGEGNLRNELQKEIKKCGLEEVIKLVGRK 283
                                       5778899*****************************998.************************************* PP

                                       HSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHS CS
                   Glycos_transf_1  82 sredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklled 158
                                       +re+l+ +++++difvlps +Eg ++v  EA+a+g+p +++++gg+++++++ e Gl+++ n+  +l +++ ++l+ 
  gi|330507330|ref|YP_004383758.1| 284 PREELPLWINACDIFVLPSLNEGNPTVMFEALACGIPFVSTDVGGVSDIITSKEYGLICECNDCMDLCNKMLDALNI 360
                                       ********************************************************************999999987 PP

                                       H CS
                   Glycos_transf_1 159 e 159
                                       +
  gi|330507330|ref|YP_004383758.1| 361 K 361
                                       6 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 ?   -2.7   0.0       2.8   7.2e+03      32      74 ..     133     183 ..     122     185 .. 0.44
   2 !   84.8   0.0   2.6e-27   6.6e-24       2     132 ..     219     358 ..     218     359 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.8
                                       EEEEEES--......-...HHHHHHHTT-T.TEEEE---.THHHHHHHH-S CS
                   Glyco_trans_1_4  32 vrlvivGdg......p.rpeeleelaagleerveftGfv.edlaellaaad 74 
                                       + l+i G g      p ++++ +e+++g+ ++      v + la+++++ d
  gi|330507330|ref|YP_004383758.1| 133 IPLIISGYGydlydlPfKNPQWRERIRGILNDSDCIITVsNRLADYIRKLD 183
                                       556666654222222232245555555433332222223224666666555 PP

  == domain 2  score: 84.8 bits;  conditional E-value: 2.6e-27
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaella 71 
                                       ++il++G+l  +vkg+  l++a+ +l  +  d+ ++i G+g+ r +el+++++  glee ++++G+   e+l+ +++
  gi|330507330|ref|YP_004383758.1| 219 RIILTIGSL-VKVKGHIDLIHAISELEGRskDILCIILGEGNlR-NELQKEIKkcGLEEVIKLVGRKprEELPLWIN 293
                                       689******.578**************66535**********66.6**9999779**999*****999889****** PP

                                       H-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLl 132
                                       a+d+fv+Ps  eg + ++ Ea+a+g+p V+tdvgg+++++  +e gl+++ +d  +l +++l+ l
  gi|330507330|ref|YP_004383758.1| 294 ACDIFVLPSlnEGNPTVMFEALACGIPFVSTDVGGVSDIItsKEYGLICECNDCMDLCNKMLDAL 358
                                       ****************************************98899*****9***99999998876 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.1   7.1e-18   1.8e-14      38     167 ..      71     196 ..      49     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 7.1e-18
                    Glyco_transf_4  38 elvvrvprvplpllkrllrs.laflrrlrrllkre..kpDvvHahspaalgaallalrrrlgiplVltvHglyekrl 111
                                       + v  vp +++p+++++++    ++r++ +++ +   +pD++H+h+ ++ g+++++l+ r++ipl+++  g +    
  gi|330507330|ref|YP_004383758.1|  71 VSVSTVPTFFIPIDYQYRHLgEKHYRKILNMIVQKkrEPDLIHSHFVWTSGYVGARLKERYHIPLIISGYGYDL--- 144
                                       3566666666666666665413455666555433346************************************3... PP

                    Glyco_transf_4 112 lkarlkplsrllralerrllrradrviavSeatadelrerygvppekitVipnGvD 167
                                         + l ++++ +r+  r +l+ +d++i+vS+ +ad++r+ ++v+  +++++p+G D
  gi|330507330|ref|YP_004383758.1| 145 --YDLPFKNPQWRERIRGILNDSDCIITVSNRLADYIRK-LDVN-TPVEILPTGYD 196
                                       ..34444444444456777********************.***9.9********99 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   1.5e-13   3.9e-10      61     160 .]      96     194 ..      51     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.5e-13
                   Glyco_trans_4_4  61 ralrrllrqrrerpdvvhahs.ptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvv 136
                                       r    ++ q+++ pd++h+h  +t+g+++++++ r +ipl+++ +g +l +  +++ + +r+  r +l+  d++++v
  gi|330507330|ref|YP_004383758.1|  96 RKILNMIVQKKREPDLIHSHFvWTSGYVGARLKERYHIPLIISGYGYDLYDL-PFKNPQWRERIRGILNDSDCIITV 171
                                       444444568999*********9***********999**********888766.67777777777************* PP

                   Glyco_trans_4_4 137 seaeaeelralgvpadrvvvvpng 160
                                       s+ +a+++r l v  + v+++p g
  gi|330507330|ref|YP_004383758.1| 172 SNRLADYIRKLDVN-TPVEILPTG 194
                                       ************97.788888876 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 !   28.9   0.0   3.7e-10   9.6e-07      62     138 ..      94     171 ..      33     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 3.7e-10
                   Glyco_trans_4_2  62 kafkl..kklikkikPDvvhahyakpygllgslaarlsgvipvvlsvwGldvlkfpkksklkklllklalkkatkvi 136
                                        ++k+  + + kk++PD++h h ++  g++g+ ++ +   ip+++s  G d ++ p+k++  +  ++  l+ ++++i
  gi|330507330|ref|YP_004383758.1|  94 HYRKIlnMIVQKKREPDLIHSHFVWTSGYVGARLKERYH-IPLIISGYGYDLYDLPFKNPQWRERIRGILNDSDCII 169
                                       3455522234599*********************99998.*******************999999999999999998 PP

                   Glyco_trans_4_2 137 st 138
                                       + 
  gi|330507330|ref|YP_004383758.1| 170 TV 171
                                       75 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.6e-09   4.2e-06       1      72 [.     297     370 ..     297     380 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.6e-09
                   Glyco_trans_1_2   1 ivLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaea 72 
                                       i++ ps +e++ +++fEa+acG++ +++d  g+ +++t ++ +++ e  d  +l  k+  +l+    r+ai  +
  gi|330507330|ref|YP_004383758.1| 297 IFVLPSLNEGNPTVMFEALACGIPFVSTDVGGVSDIITSKEYGLICEcnDCMDLCNKMLDALNIKWNRDAIQSH 370
                                       56789999*********************************999999877777777777777766666666555 PP

>> Transthyretin  HIUase/Transthyretin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   5.7e-05      0.15      91     108 ..     128     145 ..     112     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.7e-05
                                       TSEEEEEEEEETTEEEEE CS
                     Transthyretin  91 eehyhvPlllspfgYstY 108
                                       +e+yh+Pl++s +gY  Y
  gi|330507330|ref|YP_004383758.1| 128 KERYHIPLIISGYGYDLY 145
                                       599************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.40
# Mc/sec: 2915.17
//
Query:       gi|330507331|ref|YP_004383759.1|  [L=611]
Description: asparagine synthase [Methanosaeta concilii GP6]
Scores for complete 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-69  233.5   0.0    7.1e-69  233.1   0.0    1.1  1  Asn_synthase  Asparagine synthase
    2.8e-45  153.2   0.0    5.3e-45  152.3   0.0    1.5  1  GATase_7      Glutamine amidotransferase domain
    5.9e-43  146.3   0.0      1e-42  145.5   0.0    1.4  1  GATase_6      Glutamine amidotransferase domain
    9.3e-07   28.5   0.1    1.7e-06   27.7   0.1    1.3  1  DUF3700       Aluminium induced protein
  ------ inclusion threshold ------
       0.04   13.4   0.0      0.089   12.3   0.0    1.5  1  QueC          Queuosine biosynthesis protein QueC
       0.13   11.4   0.0       0.26   10.4   0.0    1.4  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 !  233.1   0.0   2.4e-72   7.1e-69       2     354 ..     239     601 ..     238     602 .. 0.88

  Alignments for each domain:
  == domain 1  score: 233.1 bits;  conditional E-value: 2.4e-72
                      Asn_synthase   2 lrelLedaVkrrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelv 78 
                                       +r+l+ d+V+ rl +dvpvG++LSGG+DSS+ia+l +r+   ++ktFs+ ++  + de++y   vae+ g+ +++++
  gi|330507331|ref|YP_004383759.1| 239 FRDLMVDSVDIRLISDVPVGTCLSGGIDSSAIACLINRKM--KIKTFSAVYNGYERDESRYISIVAEKTGMANYRVH 313
                                       79************************************99..7********88************************ PP

                      Asn_synthase  79 lteeelldalpdviyhleepfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaalsrsrefeklp.. 153
                                        t+e l + l ++i+ + epf ++s +++  + +lak  +v+vvL G+GaDEl +GY+yf    l+   +  +l+  
  gi|330507331|ref|YP_004383759.1| 314 PTAEKLREDLFKIIKLIGEPFPSASIYAQNCVQKLAKGNDVTVVLDGQGADELLAGYHYFLGFYLVDLLKTLRLKrf 390
                                       **********************************************************9988776654444444477 PP

                      Asn_synthase 154 .....larslrasllarklrklaellelaeardleelaelyrlkasdsae......aelegedelhrelyldlktll 219
                                               + ++ +++ +    + l+ +++++ + + + l+r+ ++ s        +++++ + l ++l ++lk+ l
  gi|330507331|ref|YP_004383759.1| 391 asecyNLIKGKEYMIGIQSSLYLLLPIFIREQIFLRESLLSREMMNGS-VatteyfKNFSDCRSLGQSLEFHLKYRL 466
                                       788775555555556666666666666666666666555544444333.1578889999****************** PP

                      Asn_synthase 220 pgdllrkDrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLRealegylPeeileRp.Kegfsapvgew 295
                                       +++l  +Dr sm +  E RvPflD+r++e++ +lp++  +r+g++K++LR a+ +++P+eil+R+ K g+  p ++w
  gi|330507331|ref|YP_004383759.1| 467 EQLLKWEDRNSMGNQTESRVPFLDYRIIEFISGLPDDFIIREGRTKALLRDAMIDIVPSEILKRRdKIGYETPDAYW 543
                                       ***9999********************************************************************** PP

                      Asn_synthase 296 klk.gelrelaeellsdsrlakeglldreaveelleeheagkrnesrqlwslllsleawl 354
                                        lk ++  +l+ + +       ++++d +++++ ++eh ++++n++r+lw+    leawl
  gi|330507331|ref|YP_004383759.1| 544 -LKtEDFEKLLSDWFLRGEPLCREYIDLKKLRHQIKEHIHKNKNHARNLWKAI-FLEAWL 601
                                       .98677777777777776666677****************************9.*****8 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.3   0.0   1.8e-48   5.3e-45       1     122 [.      42     163 ..      42     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 1.8e-48
                          GATase_7   1 hrrlsi.idseagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllalleaewgeealerlnG 76 
                                       h rlsi ++se+g+QPm+ ++++++ i++nGe+yN++ lreeLe  g++f++++Dtev+l  + + w e++le++nG
  gi|330507331|ref|YP_004383759.1|  42 HLRLSIiDLSENGHQPMS-DRQDKFFIIYNGEVYNFQALREELELLGYSFKSNTDTEVILYSYMQ-WKERCLEKFNG 116
                                       889**98889********.68899***********************************999986.*********** PP

                          GATase_7  77 mfAfaiwdeeekrlllaRDrlGikPLyygedk.gdallfaSelkall 122
                                       mfAfa++d+e+krl+laRDr+GikPLyy+ d+ ++ +lf+Se+  ll
  gi|330507331|ref|YP_004383759.1| 117 MFAFAVYDSESKRLFLARDRMGIKPLYYYFDEkNEVFLFSSEIPPLL 163
                                       *******************************98889******99886 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5   0.0   3.4e-46     1e-42       1     134 []      27     158 ..      27     158 .. 0.97

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 3.4e-46
                          GATase_6   1 pdasglaslvedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevl 77 
                                       pd++g+  +v++ev l+H Rl+i++l+ e+g+qP++ +++++ +++NGe+yn+++lreel+   g++f+s++Dtev+
  gi|330507331|ref|YP_004383759.1|  27 PDDEGI--YVDEEVSLGHLRLSIIDLS-ENGHQPMSDRQDKFFIIYNGEVYNFQALREELEL-LGYSFKSNTDTEVI 99 
                                       799***..******************9.**********************************.************** PP

                          GATase_6  78 lalleelGeevlerlrGmfafaiwdkrentlilardrlgvkplyyavd..esglafase 134
                                       l  + ++ e++le+++Gmfafa++d++ ++l+lardr+g+kplyy  d  ++ ++f+se
  gi|330507331|ref|YP_004383759.1| 100 LYSYMQWKERCLEKFNGMFAFAVYDSESKRLFLARDRMGIKPLYYYFDekNEVFLFSSE 158
                                       *********************************************99977888999998 PP

>> DUF3700  Aluminium induced protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   5.6e-10   1.7e-06      72     168 ..      60     153 ..      36     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 5.6e-10
                           DUF3700  72 avlddifClfqGslenlasLkkqyGL....sktanevllvieayrtLrdrgPypadqvvkdleGkfafvlydskakt 144
                                          d+ f +++G++ n   L+++  L     k+ ++  +++ +y   ++r        +++++G faf +yds++k 
  gi|330507331|ref|YP_004383759.1|  60 DRQDKFFIIYNGEVYNFQALREELELlgysFKSNTDTEVILYSYMQWKER-------CLEKFNGMFAFAVYDSESKR 129
                                       447999***************98765444447788899999999999887.......599***************** PP

                           DUF3700 145 vfvaldadgsvplyWGiaadgsvv 168
                                       +f+a+d+ g  ply+  +   +v 
  gi|330507331|ref|YP_004383759.1| 130 LFLARDRMGIKPLYYYFDEKNEVF 153
                                       **************9888777664 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     3e-05     0.089       5      56 ..     260     310 ..     258     322 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                                       E--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-E CS
                              QueC   5 llSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveeh 56 
                                        lSGG+DS+++++l +++  ++++ +  Y+  ++ e ++ + +a+++g+++ 
  gi|330507331|ref|YP_004383759.1| 260 CLSGGIDSSAIACLINRK-MKIKTFSAVYNGYERDESRYISIVAEKTGMANY 310
                                       69*******999988877.78************************9998654 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   8.6e-05      0.26      24      51 ..     260     287 ..     236     332 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.6e-05
                                       EE-SSHHHHHHHHHHHHHHTCGEEEEEE CS
                      NAD_synthase  24 GlSGGvDSslvaalavkalgkenvlall 51 
                                        lSGG+DSs +a+l  + +  + + a++
  gi|330507331|ref|YP_004383759.1| 260 CLSGGIDSSAIACLINRKMKIKTFSAVY 287
                                       39*************9999777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.25s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 4587.49
//
Query:       gi|330507332|ref|YP_004383760.1|  [L=439]
Description: hypothetical protein MCON_1228 [Methanosaeta concilii GP6]
Scores for complete 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   36.7   1.1    2.9e-08   33.8   0.7    2.1  2  Pectate_lyase_3  Pectate lyase superfamily protein
     0.0013   18.6   6.7     0.0013   18.6   6.7    3.2  3  Beta_helix       Right handed beta helix region
     0.0027   17.0   5.2      0.068   12.4   0.6    3.0  2  NosD             Periplasmic copper-binding protein (NosD)
  ------ inclusion threshold ------
      0.045   12.4   0.1       0.23   10.1   0.1    2.1  1  Adeno_E1B_55K    Adenovirus EB1 55K protein / large t-antigen


Domain annotation for each model (and alignments):
>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.7   6.4e-12   2.9e-08      14     200 ..      45     251 ..      37     265 .. 0.81
   2 ?    0.7   0.0     0.088   3.9e+02     130     187 ..     279     347 ..     270     373 .. 0.63

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 6.4e-12
                                       EEE-HHHHHHHH......HTSS-EEE-SEEEEESS-E..................EE-SSEEEEES-TTTEEEEE-T CS
                   Pectate_lyase_3  14 vtDdtaaiqkaiscasatttgavVYfPaGtYlvsspi..................ilksgvqLvGdgngrpvlkaaa 72 
                                        tDd+  i +ai   +  ++++ V ++ G Yl+s                       +++v+++G g g +vlk+++
  gi|330507332|ref|YP_004383760.1|  45 GTDDSRVITEAI---TFVPDNGNVLISNGEYLLSADTqfyldegdlnpfwicipiLGNKNVHIFGYGAGITVLKLKP 118
                                       49**********...99*************************************999******************88 PP

                                       T-SS--SEEES-TTT-..-EEEEEEEEEEE.GGGG-SS---SSEEE......ES-E.EEEEEEEEEES-SSEEE-SS CS
                   Pectate_lyase_3  73 afvgaglidgdpyvsggsealiatnnfyrq.irnlkiditavapga......tgih.wqtaqatslenvefemseas 141
                                           ++ + g p++   + a+  +  f+   + n+++d ++ +++       + i      ++ + +n ef++s ++
  gi|330507332|ref|YP_004383760.1| 119 ----NQFSVGHPVAMMLNRAISLDPGFTAFtVANMTFDGNRDNQEQwykdgaSLILtGSPRSGGNYYNLEFKNSYGT 191
                                       ....444444555433336788888888877***********77776774433333245778888************ PP

                                       S.---T.T---SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EE CS
                   Pectate_lyase_3 142 g.tkhq.gifiengsggflndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwgw 200
                                       g + ++ g  + + s + ++++v++  +  gi + + q+ +v++++f+ + tg  ++ ++++
  gi|330507332|ref|YP_004383760.1| 192 GlYLGNnG--MGSESHSSITNVVARDCSLEGILLdTAQDTVVSDCVFERCRTGLTIHGNNDY 251
                                       66333324..44455566899999999999999977999999*************9977665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.088
                                       EES-SSEEE-SSS---TT---SS--EEEEES-EEES-SS-SEEES...........-EEEEEES-EEE- CS
                   Pectate_lyase_3 130 lenvefemseasgtkhqgifiengsggflndlvfsglgdigiavg...........nqqftvrnitfnn 187
                                       l+   ++m++ +  +  g++i+++ g ++++++f+   + +  +g           + ++t++n++  +
  gi|330507332|ref|YP_004383760.1| 279 LQMSSVNMDCTASPNAYGLLIHSSIGVHIKESFFKSDRNKASSYGgasyidadidgPTAATLENCVLDG 347
                                       455566777777777778888888888888888888333333333344444445556666767666655 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 ?   -2.3   0.1      0.76   3.4e+03      84      84 ..      41      41 ..       8      86 .. 0.56
   2 !   18.6   6.7     3e-07    0.0013      11     100 ..     144     255 ..     133     328 .. 0.56
   3 ?    2.5   0.1     0.027   1.2e+02      33      68 ..     332     370 ..     287     436 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.76
                                      S CS
                        Beta_helix 84 n 84
                                       
  gi|330507332|ref|YP_004383760.1| 41 S 41
                                      1 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3e-07
                                       .EEESEEEES-.......SS-SEEE-SSS-.....EEES-EEES-SS-SEEE-TT.....-S-EEES-EEE---SEE CS
                        Beta_helix  11 vtiknntisns.......ggyGiylrgssn....vvienneiannsgsGiyilgs.....snntisnntisdnnggg 71 
                                       +t+ n+t++++       +++G  l  +++        n e+ n++g+G+y+ +      s++ i+n + +d+   g
  gi|330507332|ref|YP_004383760.1| 144 FTVANMTFDGNrdnqeqwYKDGASLILTGSprsgGNYYNLEFKNSYGTGLYLGNNgmgseSHSSITNVVARDCSLEG 220
                                       56777777777666666633333333333333444444466666777777777777777777777777777777777 PP

                                       E-TT--S--EEES-EEES-SS-SEE-TT.......- CS
                        Beta_helix  72 ialfgasnnlienneitdnggsGiylny.......s 100
                                       i l+ a+ ++++++ ++++++ G+++++       +
  gi|330507332|ref|YP_004383760.1| 221 ILLDTAQDTVVSDCVFERCRT-GLTIHGnndyqtrT 255
                                       777777777777777777766.77777423333330 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.027
                                       -......EEES-EEES-SS-SEEE-TT-S-EEES-EEE--- CS
                        Beta_helix  33 n.....vvienneiannsgsGiyilgssnntisnntisdnn 68 
                                             +++en+++ +  ++ +++lgs+ +t+++  ++ ++
  gi|330507332|ref|YP_004383760.1| 332 IdgptaATLENCVLDG--YYALHVLGSATATLRGGAVNASY 370
                                       2233334555555554..55555555555555554444444 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.5    0.0063        28     175     208 ..     148     182 ..     143     185 .. 0.80
   2 !   12.4   0.6   1.5e-05     0.068      46     137 ..     203     251 ..     180     269 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0063
                              NosD 175 nvkydgsn..nneWnttktsgtniiggpylgGNyWs 208
                                       n++ dg++  + +W +++ +   ++g p  gGNy++
  gi|330507332|ref|YP_004383760.1| 148 NMTFDGNRdnQEQWYKDG-ASLILTGSPRSGGNYYN 182
                                       4555555555999*9999.9999999********96 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.5e-05
                              NosD  46 ssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNt 122
                                       +s                                            ++ ++n ++++++  Gill++++++ +s+ +
  gi|330507332|ref|YP_004383760.1| 203 ES--------------------------------------------HSSITNVVARDCSLEGILLDTAQDTVVSDCV 235
                                       23............................................3355566666666666666666666666666 PP

                              NosD 123 isnnnkGiflens.ss 137
                                       + ++ +G+++ ++ ++
  gi|330507332|ref|YP_004383760.1| 236 FERCRTGLTIHGNnDY 251
                                       6666666666555334 PP

>> Adeno_E1B_55K  Adenovirus EB1 55K protein / large t-antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   5.2e-05      0.23     180     213 ..     218     251 ..      92     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.2e-05
                     Adeno_E1B_55K 180 ykgivsrsksklkvkkcvFekcvlgivseGkari 213
                                         gi   ++++  v+ cvFe+c  g++ +G+ + 
  gi|330507332|ref|YP_004383760.1| 218 LEGILLDTAQDTVVSDCVFERCRTGLTIHGNNDY 251
                                       467778889999*****************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3347.86
//
Query:       gi|330507333|ref|YP_004383761.1|  [L=423]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete 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   23.1   6.8    6.1e-05   23.1   6.8    4.0  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    0.00013   21.5  20.2    0.00013   21.5  20.2    2.2  2  Polysacc_synt    Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.038   13.3   0.0    1.7  1  LVIVD            LVIVD repeat
      0.094   12.3   3.9        4.1    7.0   0.3    2.7  2  DUF1449          Protein of unknown function (DUF1449)


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 ?   -2.1   3.8      0.82   3.7e+03      95     129 ..      35      68 ..       7      83 .. 0.47
   2 ?   -3.7  13.8       2.5   1.1e+04      51     138 ..      57     157 ..      27     162 .. 0.58
   3 ?   -4.4  11.5         4   1.8e+04      25     133 ..     161     277 ..     140     290 .. 0.63
   4 !   23.1   6.8   1.4e-08   6.1e-05       1      79 [.     341     419 ..     341     423 .] 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.82
                   Polysacc_synt_C  95 llaalvmgivvylllllllgllllaal.alllavlv 129
                                       +++a +m++ + +++ +++ ++l+a l +++la ++
  gi|330507333|ref|YP_004383761.1|  35 MAFANIMSAGC-GFFFWIIAARLYA-LeQVGLATAL 68 
                                       44444444443.3555555555555.2222222221 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.5
                   Polysacc_synt_C  51 plfgivGaaiatvlallvvavln.lyalrrllgikl......ellrrllkpllaalvmgiv.vylllllllglllla 119
                                       + +  vG a a + +l++va++  l + + ++++ +      ++ ++++++  a+++ g++ ++l++ +++++++++
  gi|330507333|ref|YP_004383761.1|  57 YALEQVGLATALISSLALVALFStLGFDSSIIRFLPledkgkVISTSFFVTTGASIIFGGIcILLMMIMTPSMPFWQ 133
                                       33455777777777777777777444444555555567677766666677777777777773333444444444444 PP

                   Polysacc_synt_C 120 ....al.alllavlvgalvYllll 138
                                           +l  +l+a+l  ++v ++ +
  gi|330507333|ref|YP_004383761.1| 134 dpgnSLaFILVAALNSIAVMGGYA 157
                                       778744466666666666666555 PP

  == domain 3  score: -4.4 bits;  conditional E-value: 4
                   Polysacc_synt_C  25 lgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrr.llgikl....ellrrll.... 92 
                                         +++ +++ +++ a+  +   ++l  ++g+ G+  a+ l++l++a++ l  ++  + +i++    e++r+ l    
  gi|330507333|ref|YP_004383761.1| 161 DRKADHYFLQNLLQAI-RIPALVPLA-FLGVFGIFGAIGLGYLTAALYSLTKIQLsICRIRPqadrEFIRKSLrfss 235
                                       5555555555555554.566666666.67888888899999999999998888764667777888844555543444 PP

                   Polysacc_synt_C  93 kpllaalvmgivvylllllllglllla.alalllavlvgalv 133
                                         +l++l+ ++ ++++  l+l+ll  a a    +a ++g lv
  gi|330507333|ref|YP_004383761.1| 236 LNYLSSLLYAAPTLMMPILVLSLLDEAeAAKYYIAFALGTLV 277
                                       777777777777665666666655555422555555555554 PP

  == domain 4  score: 23.1 bits;  conditional E-value: 1.4e-08
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyal 77 
                                       +L i+als ++ + ++++  i +   r+  ++k +++ +++ l+l+++++ ++gi+Ga +a++++++v+ +   + +
  gi|330507333|ref|YP_004383761.1| 341 LLKIIALSSFPVACYSLFIPIQNVRMRVESIVKLNALRCILLLGLSYVMVNRYGILGAGYAWMITYMVIVIWVGWVA 417
                                       589*****************************************************************999887766 PP

                   Polysacc_synt_C  78 rr 79 
                                        +
  gi|330507333|ref|YP_004383761.1| 418 LK 419
                                       55 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5  20.2   2.8e-08   0.00013       3     261 ..      30     284 ..      28     289 .. 0.75
   2 ?   -7.3   9.5         4   1.8e+04      82     189 ..     308     418 ..     273     423 .] 0.56

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.8e-08
                     Polysacc_synt   3 kgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslill 79 
                                       + +++ + +++++++ +f + ++ ar+   e++Gl +++++ + l  ++++lG++ +++r+   + + k +++++++
  gi|330507333|ref|YP_004383761.1|  30 RTSFFMAFANIMSAGCGFFFWIIAARLYALEQVGLATALISSLALVALFSTLGFDSSIIRFLPLEDKGKVISTSFFV 106
                                       56789999*******************************************************99988777777776 PP

                     Polysacc_synt  80 nvllvllvlvllfllllliaa....flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsr 152
                                        +  +++++  +++ll++i +    f ++p  ++l +il ++l    ++a + +  f + ++    +++++++ +++
  gi|330507333|ref|YP_004383761.1| 107 TTG-ASIIFGGICILLMMIMTpsmpFWQDPG-NSLAFILVAALN---SIAVMGGYAFVADRKADHYFLQNLLQAIRI 178
                                       655.566777777777777556665666664.444444444444...666666667788889999999********* PP

                     Polysacc_synt 153 vilvliavflfldivaavlgavlaalvggivslavlrkkf.rprfvilslklvrellsfsapltisslaillytyid 228
                                        +lv +a++++  i++a   + l++l+++++sl+ +     r r     ++ +r++l+fs    +ssl+    t + 
  gi|330507333|ref|YP_004383761.1| 179 PALVPLAFLGVFGIFGA---IGLGYLTAALYSLTKIQLSIcRIRPQAD-REFIRKSLRFSSLNYLSSLLYAAPTLMM 251
                                       *9999999887765544...4456666666666666633345555555.7*************************** PP

                     Polysacc_synt 229 si.llglllgaeavGiYnaayqllvaisgllapi 261
                                        i +l+ll +aea + Y  a  l +++ ++ +++
  gi|330507333|ref|YP_004383761.1| 252 PIlVLSLLDEAEA-AKYYIAFALGTLVLIIPSSF 284
                                       **67777777666.55555555555555544444 PP

  == domain 2  score: -7.3 bits;  conditional E-value: 4
                     Polysacc_synt  82 llvllvlvllfllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqv.veqlsrvilvl 157
                                        +++++l ++ +l+++  ++lgl +  ++  +  l +  l ++    ++lf   ++ +  + s v ++ l+ + l++
  gi|330507333|ref|YP_004383761.1| 308 ASLMIMLPAVLVLFFYGDQLLGLLRGEYVEGFGLLKIIALSSFPVACYSLFIPIQNVRMRVESIVkLNALRCILLLG 384
                                       44444444444455555455555555555555555555555555556666666666666555555255666666666 PP

                     Polysacc_synt 158 iavflfld..ivaavlgavlaalvggivslavlr 189
                                       +   +++   i++a+ + ++ ++v  i   +v  
  gi|330507333|ref|YP_004383761.1| 385 LSYVMVNRygILGAGYAWMITYMVIVIWVGWVAL 418
                                       6666666677777777777776666665555544 PP

>> LVIVD  LVIVD repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.5e-06     0.038       6      21 ..     149     164 ..     147     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.5e-06
                             LVIVD   6 dvavsGnYaYvAdqdn 21 
                                       ++av G+Ya+vAd++ 
  gi|330507333|ref|YP_004383761.1| 149 SIAVMGGYAFVADRKA 164
                                       8************975 PP

>> DUF1449  Protein of unknown function (DUF1449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3     0.002       9.1      92     150 ..      57     115 ..      35     118 .. 0.84
   2 ?    7.0   0.3   0.00092       4.1      60      87 ..     171     197 ..     136     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.002
                           DUF1449  92 asllgallpallaaaialllalplvrvlaallakilpkdetsavseeslvGrvavivlG 150
                                       ++l ++ l + l++ +al++ + ++ + ++++  + ++d  +++s++ +v   a i+ G
  gi|330507333|ref|YP_004383761.1|  57 YALEQVGLATALISSLALVALFSTLGFDSSIIRFLPLEDKGKVISTSFFVTTGASIIFG 115
                                       45566778899999999999999999999999888889******************998 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00092
                           DUF1449  60 gWLrvgrvPvLilLvlfLtlFglvGlvl 87 
                                       + L++ r+P+L+ L +fL +Fg++G + 
  gi|330507333|ref|YP_004383761.1| 171 NLLQAIRIPALVPL-AFLGVFGIFGAIG 197
                                       578999******98.69********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2965.94
//
Query:       gi|330507334|ref|YP_004383762.1|  [L=167]
Description: hypothetical protein MCON_1232 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1210.69
//
Query:       gi|330507335|ref|YP_004383763.1|  [L=233]
Description: glutamine amidotransferase class-I [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-15   57.9   0.0    1.4e-15   57.5   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
     0.0001   22.2   0.0    0.00019   21.3   0.0    1.5  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.016   15.0   0.0    1.2  1  DJ-1_PfpI      DJ-1/PfpI family
      0.034   13.7   0.0      0.048   13.2   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   3.2e-19   1.4e-15      40     176 ..      42     180 ..      21     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 3.2e-19
                                       HHSTSEEEEEEESSCTT.......TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEE CS
                            GATase  40 lknpdgilvsgGpgspg.......vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekekehhggtmrlgd 109
                                         ++d +lv gG  + +         ++ ++i++a+++k+ iLGICLG Ql+ + +g+ v+k++ + + g+     +
  gi|330507335|ref|YP_004383763.1|  42 DADFDLLLVLGGEMNIYqedlypwLAEEKRFIRRAMDSKKTILGICLGAQLISDILGGMVHKNR-YREIGWHEVKLN 117
                                       56899999999999999999999999999*********************************99.566665443333 PP

                                       TTT...CGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTS CS
                            GATase 110 det...allyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEstst 176
                                       + +   + ++g ++++++ ++H+++++    +p+g + +a +   + + ++   +n  vg+QFH Es+ +
  gi|330507335|ref|YP_004383763.1| 118 RAAfssSAFKGFPDRFTAFQWHGDTFD----LPRGATGLAST-AACANQAFEIGRN--VGLQFHLESSRQ 180
                                       344799*********************....68887776666.3345566666666..********9865 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   4.2e-08   0.00019      96     137 ..      71     112 ..      67     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.2e-08
                     Peptidase_C26  96 aLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsglt 137
                                         ir+a+++++ ilgiC+G ql+   lGG ++++ +++ g +
  gi|330507335|ref|YP_004383763.1|  71 RFIRRAMDSKKTILGICLGAQLISDILGGMVHKNRYREIGWH 112
                                       6799***************************99877655544 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.5e-06     0.016      58     108 ..      41      94 ..      21     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-06
                                       TCCG-SEEEE--BHHHHHHHHTSH...HHHHHHHHHHHTT-EEEEETTTHHHHH CS
                         DJ-1_PfpI  58 kaaeyDalvlpGGragperlrene...kvvelvkefaekgklvaaICagpqlLa 108
                                       k+a++D+l++ GG+ +  +    +   +   +++++++++k++  IC g+ql +
  gi|330507335|ref|YP_004383763.1|  41 KDADFDLLLVLGGEMNIYQEDLYPwlaEEKRFIRRAMDSKKTILGICLGAQLIS 94 
                                       4789*********998766666663224467*******************9876 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.1e-05     0.048      39      91 ..      43      96 ..      24     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                          GATase_3 39 edad.lvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGee 91
                                      +d d l++l+G  +  q+  +    + ++ i++a+ +++++lgiC G q+ ++ 
  gi|330507335|ref|YP_004383763.1| 43 ADFDlLLVLGGEMNIYQEDLYPWLAEEKRFIRRAMDSKKTILGICLGAQLISDI 96
                                      3445245677777888888888889999*********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1781.35
//
Query:       gi|330507336|ref|YP_004383764.1|  [L=145]
Description: hypothetical protein MCON_1234 [Methanosaeta concilii GP6]
Scores for complete 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-34  116.6   0.0    7.6e-34  116.4   0.0    1.0  1  UPF0146     Uncharacterised protein family (UPF0146)
  ------ inclusion threshold ------
       0.11   11.0   0.0       0.14   10.7   0.0    1.1  1  ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase cons


Domain annotation for each model (and alignments):
>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.0   8.4e-38   7.6e-34       3     127 ..      18     141 ..      16     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 8.4e-38
                                       HHHHHHHHHS-SSEEEEET-TT--HHHHHHHHHS-EEEEE-SS-S....STTEE---SSS--HHHHTTEEEEEEES- CS
                           UPF0146   3 elakkiaeenargkvvEvGiGrkldvaealakrgvdlvatDikekkakegvrivrDDvtdPnleiYkgadliYslRp 79 
                                       +la+ ia +n++g+vvEvG+G +++va+ l+  g+++++tD +e+    g+ + +DD++ P++eiY+ga liYs+Rp
  gi|330507336|ref|YP_004383764.1|  18 DLAEFIA-KNYPGRVVEVGVGHFPHVAQRLSDMGLEVILTDRVER-LLAGMMVEKDDIFAPRREIYQGAGLIYSIRP 92 
                                       5666666.9********************************9999.77899999*********************** PP

                                       -TTSHHHHHHHHHHHT-EEEEE-BTTB--.---TT-EEEEETTEEEEEE CS
                           UPF0146  80 PaelqsaildvakkvgAaliikpLlgedv.vvekelklvnykgalFyik 127
                                       P e+q a+ ++a +vgA++i++pL++e   ++    +lvny+ a Fy+ 
  gi|330507336|ref|YP_004383764.1|  93 PLEMQLAMGELAAAVGADVIVRPLQDEIAqLAGFGRRLVNYREARFYLF 141
                                       ***************************862456789***********85 PP

>> 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 ?   10.7   0.0   1.6e-05      0.14      68     131 ..      18      79 ..       6      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.6e-05
                                       HHHHHHH....CC--SEEEEE.SHHHHHHHHHCCTT-EEEEE----HHHHTTS-SSEEEEEEGGG CS
                        ADP_PFK_GK  68 elfeelvkaakklkkaelrmG.Gnagimanrlakegakvllgaklskklkellsekivvlgkpse 131
                                       +l e ++   k++++  +++G G  + +a+rl+ +g++v+l   +++ l+ ++ ek  +  + +e
  gi|330507336|ref|YP_004383764.1|  18 DLAEFIA---KNYPGRVVEVGvGHFPHVAQRLSDMGLEVILTDRVERLLAGMMVEKDDIFAPRRE 79 
                                       4444444...599999999999******************************9999776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1091.20
//
Query:       gi|330507337|ref|YP_004383765.1|  [L=360]
Description: cell division protein FtsZ [Methanosaeta concilii GP6]
Scores for complete 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-36  125.2   1.5    1.2e-35  123.6   1.5    1.8  1  Tubulin          Tubulin/FtsZ family, GTPase domain
    4.5e-28   97.4   0.0    1.4e-27   95.9   0.0    1.8  1  FtsZ_C           FtsZ family, C-terminal domain
     0.0045   16.9   0.0     0.0082   16.0   0.0    1.4  1  YjeF_N           YjeF-related protein N-terminus
  ------ inclusion threshold ------
      0.026   13.7  10.2       0.54    9.4   2.5    2.5  2  Tubulin_2        Tubulin like
      0.028   14.0   0.0       0.04   13.5   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.064   13.5   0.1       0.22   11.8   0.1    1.9  1  TrkA_N           TrkA-N domain
      0.095   12.0   0.1        0.2   11.0   0.1    1.5  1  ThiF             ThiF family
       0.14   11.5   1.5       0.17   11.1   0.1    1.8  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, 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 !  123.6   1.5   5.1e-39   1.2e-35       1     194 [.      22     179 ..      22     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 5.1e-39
                                       EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE CS
                           Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnkll 77 
                                       +i+++g+G++G++++n+l +      g+              g +++i    ai+td+q+l+ + a+      +k+l
  gi|330507337|ref|YP_004383765.1|  22 RILIVGCGGAGGNTINRLKR-----MGL-------------MG-AKTI----AINTDRQHLETVSAD------EKML 69 
                                       599***************99.....699.............77.5555....***************......**** PP

                                       --CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEE CS
                           Tubulin  78 lgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvv 154
                                       +g + +++ gagg+pevg++aae+ +  i++ ++++d+   +f++a++gGGTG+G +pv+++++++e  +alvv++v
  gi|330507337|ref|YP_004383765.1|  70 IGRKLTRGMGAGGDPEVGRKAAESARTDIEDLLRGADL---VFVLAGMGGGTGTGSAPVVARIARQE--GALVVAMV 141
                                       **************************************...**************************..******** PP

                                       EE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHC CS
                           Tubulin 155 vlPsefsevvvepynailalkelieesdavividNdaLlk 194
                                       ++P+++  +  ++  a+++l++l++++++ iv+dN++Ll+
  gi|330507337|ref|YP_004383765.1| 142 TTPFHM--ERKRIFIAEEGLENLRNYANTSIVMDNNRLLE 179
                                       ****99..899**************************987 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 !   95.9   0.0   6.1e-31   1.4e-27       1      95 []     229     323 ..     229     323 .. 0.98

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 6.1e-31
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       G   m vGe s ++  e+ +++a+++pLLdv+l+gAk+ l++i gg+d+tlkE+ ++a+ +++ +d+ anvi+Ga+i
  gi|330507337|ref|YP_004383765.1| 229 GASFMLVGEGSMKKSPENIVRSALNNPLLDVELRGAKACLLHIDGGPDMTLKEAASIASSLTQDLDPRANVIWGAKI 305
                                       7789************************************************************************* PP

                                       -TT--SEEEEEEEEES-X CS
                            FtsZ_C  78 deeledeirvtvvatglk 95 
                                       ++el++ ++ ++++tg+k
  gi|330507337|ref|YP_004383765.1| 306 KPELKGRVKLMAIITGVK 323
                                       ****************96 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 !   16.0   0.0   3.7e-06    0.0082       8     112 ..      90     199 ..      85     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.7e-06
                            YjeF_N   8 agravaevlrallgnspaekkvlvlvGsg..nnGgdglaaArhLaqegakVtvllleeeeklded...aeralellk 79 
                                       a++++   +++ll     +  v vl+G g     g + ++Ar  +qega V ++++++ +  ++    ae+ le+l+
  gi|330507337|ref|YP_004383765.1|  90 AAESARTDIEDLL---RGADLVFVLAGMGggTGTGSAPVVARIARQEGALVVAMVTTPFHMERKRifiAEEGLENLR 163
                                       4444444555566...77888999998885355588899***********999666665533332222677777777 PP

                            YjeF_N  80 kaggkvveekpeedleekls...apvdlviDAllGi 112
                                       ++ ++ +  ++   le++ +   +++  ++D+++G 
  gi|330507337|ref|YP_004383765.1| 164 NYANTSIVMDNNRLLERAPHlpfQEAFSLVDGITGE 199
                                       7777777766666666655589999********996 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.0   0.00054       1.2       1      19 [.      24      42 ..      24      62 .. 0.94
   2 ?    9.4   2.5   0.00024      0.54     116     183 ..      79     133 ..      63     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00054
                         Tubulin_2  1 lviGLGGtGgkvlaelrrr 19
                                      l++G+GG Gg+++++l+r+
  gi|330507337|ref|YP_004383765.1| 24 LIVGCGGAGGNTINRLKRM 42
                                      89***************98 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00024
                         Tubulin_2 116 GAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllrki 183
                                       GAG+ + vGR a  +  ++i + lr     +           vfV+ ++ GGTG G++  va + r++
  gi|330507337|ref|YP_004383765.1|  79 GAGGDPEVGRKAAESARTDIEDLLR----GAD---------LVFVLAGMGGGTGTGSAPVVARIARQE 133
                                       6666666666554333333333332....222.........4****************9999998875 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.8e-05      0.04       4      41 ..      24      65 ..      21     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                   Methyltransf_15  4 ilDlfsGaGGnviq.falv...fekviaieinleklacaqhN 41
                                      ++  ++GaGGn+i+ ++++   + k+iai++++++l+ +   
  gi|330507337|ref|YP_004383765.1| 24 LIVGCGGAGGNTINrLKRMglmGAKTIAINTDRQHLETVSAD 65
                                      55669*******963333355599************987655 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   0.1    0.0001      0.22       1      40 [.      23      65 ..      23      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                                      EEEES-SHHHHHHHHHHHHTT...EEEEEEESSHHHHHHHHHT CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLsegg...kdvvvidkdeerveelree 40
                                      i+i+G+G  G + +++L++ g    + ++i +d++++e+++++
  gi|330507337|ref|YP_004383765.1| 23 ILIVGCGGAGGNTINRLKRMGlmgAKTIAINTDRQHLETVSAD 65
                                      79*****************6669966*************9865 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1     9e-05       0.2      20      42 ..      22      44 ..      16      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9e-05
                                      EEEEE--SHHHHHHHHHHHHHTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 20 kvllvGaGglGsellknLalsGv 42
                                      ++l+vG+Gg G + +  L ++G+
  gi|330507337|ref|YP_004383765.1| 22 RILIVGCGGAGGNTINRLKRMGL 44
                                      89****************99997 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   7.7e-05      0.17      30      95 ..      22     108 ..      18     120 .. 0.82
   2 ?   -1.9   0.1      0.75   1.7e+03      12      32 ..     308     328 ..     299     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.7e-05
                                       EEEEESTSHHHHHHHHHHHHT...T-EEEEEESSHHHHHHHHH.....TTTCECEE..............HCHHHHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakgl...gakVtvlDvrparleqles.....lgakfvev..............lksqeel 84 
                                       ++l++G G aG + i+  k++   gak+ +++++ + le +++     +g+k ++                +s +  
  gi|330507337|ref|YP_004383765.1|  22 RILIVGCGGAGGNTINRLKRMglmGAKTIAINTDRQHLETVSAdekmlIGRK-LTRgmgaggdpevgrkaAESARTD 97 
                                       79****************99633379**************998556633333.444899999999999988888899 PP

                                       HHHHHHH-SEE CS
                       AlaDh_PNT_C  85 laeavkeadvv 95 
                                       +++ ++ ad+v
  gi|330507337|ref|YP_004383765.1|  98 IEDLLRGADLV 108
                                       99999999988 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.75
                                       GCTSEEETTCEETCB---EEE CS
                       AlaDh_PNT_C  12 ffggkgtlaGgvpgvepakvl 32 
                                         +g++ l++ ++gv+ a+vl
  gi|330507337|ref|YP_004383765.1| 308 ELKGRVKLMAIITGVKSAQVL 328
                                       468999999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2697.92
//
Query:       gi|330507338|ref|YP_004383766.1|  [L=419]
Description: UbiD family decarboxylase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-94  317.4   0.1    1.5e-94  317.2   0.1    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.2   0.1   8.1e-99   1.5e-94       1     406 []       7     380 ..       7     380 .. 0.93

  Alignments for each domain:
  == domain 1  score: 317.2 bits;  conditional E-value: 8.1e-99
                                       HHHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHH CS
                              UbiD   1 lealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeile 77 
                                       l++le  g + +++++v+p  E++e            +lF++v     + ++  n++gtr+ +a+alg+   e++++
  gi|330507338|ref|YP_004383766.1|   7 LDDLEGSGLMNHVRDPVSPVEEVTERSWGSG-----PILFDDVS----GHKCCLNILGTRDLLARALGIP-AEDMVR 73 
                                       5789***************998888776665.....99*****4....369*****************75.59**** PP

                                       HHHHHHHS..----EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEE CS
                              UbiD  78 klaellepkppippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmq 154
                                       +l+++  +    p ++v+     ++e+v    +++dLs+LP++t++pgDgGpyit+g+v++r   ++k n+ ++R++
  gi|330507338|ref|YP_004383766.1|  74 HLSQIGCQ---GPVREVDW--SSFMENV----SQPDLSRLPIMTYFPGDGGPYITSGVVVSRF--EDKINACVHRLM 139
                                       **999886...67999976..5688788....57***************************96..4589******** PP

                                       EEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SS CS
                              UbiD 155 vldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcet 231
                                       vl+k++l+ +++++++ ++ ++ a++kg +++ vavaiGvdP++++aA++++P+++ E+ +a+alrg+ vel+    
  gi|330507338|ref|YP_004383766.1| 140 VLGKDRLAARLVPGRHTHQLYEAALAKG-KEVAVAVAIGVDPLVLMAASTRVPPEM-EFCYAAALRGSHVELIAL-D 213
                                       ****************999999999999.8***********************776.9***************88.6 PP

                                       SSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHHHCHHHHH CS
                              UbiD 232 vdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkppeedallgkal 308
                                       +++ vp +A ivleG+i++ e+apEGPf+d+tG+ + vr+e pv+++t++++ ++piy+ +++    e+++l+g+++
  gi|330507338|ref|YP_004383766.1| 214 NGVLVP-HAQIVLEGYITT-ERAPEGPFVDITGTRDLVRQE-PVIRLTRMMMCNEPIYHGLLPAGG-EHKMLMGVPY 286
                                       69****.***********9.68*************999885.*****************8878888.9********* PP

                                       HHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHH CS
                              UbiD 309 ealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkev 385
                                       e+l+++ ++k v +vkdv l+e g+++++avv+i+k+++++a+++++a++++++  sl K+v+vvD d+d++d++++
  gi|330507338|ref|YP_004383766.1| 287 EPLIYREVSK-VAKVKDVMLTEGGCCYFHAVVQIEKETEEDARRAIDAAIKAHR--SL-KHVLVVDSDIDIHDPRDL 359
                                       ********77.678**************************************99..99.****************** PP

                                       HHHHHHC--CCCCEEEECCCE CS
                              UbiD 386 lwaiatrvdpdrDlviiegtr 406
                                       ++a+atr++ d+D+v+++++r
  gi|330507338|ref|YP_004383766.1| 360 EYALATRMRGDEDIVLYPNVR 380
                                       ****************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3098.05
//
Query:       gi|330507339|ref|YP_004383767.1|  [L=233]
Description: hypothetical protein MCON_1238 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-55  187.8  12.0    1.5e-55  187.8  12.0    1.7  2  DUF1614   Protein of unknown function (DUF1614)
     0.0041   17.2   1.8     0.0041   17.2   1.8    3.7  4  DUF4229   Protein of unknown function (DUF4229)


Domain annotation for each model (and alignments):
>> DUF1614  Protein of unknown function (DUF1614)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.19   1.7e+03      92     112 ..      10      31 ..       6      45 .. 0.64
   2 !  187.8  12.0   1.7e-59   1.5e-55       1     170 []      56     232 ..      56     232 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.19
                           DUF1614  92 vGivvpllipplvaalaa.lll 112
                                       vGi + l  + l+a++++ l+l
  gi|330507339|ref|YP_004383767.1|  10 VGILIMLGFAFLIAIVVSfLFL 31 
                                       6777777777777777774443 PP

  == domain 2  score: 187.8 bits;  conditional E-value: 1.7e-59
                           DUF1614   1 llgslinipvaelkskeel.ve..vkvlgisykvpvleeeekktvvavNvGGaviPlllslylllrlavsllaalla 74 
                                       l+gs+inip+++l+ ++++ +e  ++ +g+sy+vpv+++ +  t++a+NvGGa+iP l+s+ l++r++ s++ al +
  gi|330507339|ref|YP_004383767.1|  56 LVGSSINIPLTNLECSTPMvHErhIRAFGVSYHVPVVKSCN--TLLAINVGGALIPSLISMALIYRFPESIYYALSG 130
                                       79*************886644478***********999965..9************************99******* PP

                           DUF1614  75 vlivaavvyllarpvpgvGivvpllipplvaalaa.lllaeeea.....aavaYisgvlGtLiGadllnlkkieklg 145
                                       +++va++++++arpv+g+Giv+p+l+ppl+aalaa l++    a     + +aY++g+lGtL+Gad+lnl+ki++lg
  gi|330507339|ref|YP_004383767.1| 131 IVLVAIITNRVARPVRGLGIVTPALVPPLCAALAAiLMVYVLGAphdliFLIAYAAGTLGTLLGADILNLGKIRDLG 207
                                       ***********************************777776666888999*************************** PP

                           DUF1614 146 apvvsIGGaGtFdGifltgilavll 170
                                       apv+sIGGaGtFdG+fl+g++avll
  gi|330507339|ref|YP_004383767.1| 208 APVASIGGAGTFDGVFLSGLIAVLL 232
                                       ***********************98 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.8   4.6e-07    0.0041      23      58 ..       4      39 ..       2      48 .. 0.92
   2 ?   -1.9   0.1      0.41   3.7e+03      36      44 ..      49      57 ..      41      63 .. 0.53
   3 ?   -0.9   0.1       0.2   1.8e+03      29      49 ..      96     116 ..      81     121 .. 0.66
   4 ?   -1.2   4.9      0.24   2.2e+03       8      48 ..     131     171 ..     124     193 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.6e-07
                           DUF4229 23 rliglpvpllvaallAlvvalplSmvllkklRdrat 58
                                      rli  pv++l+++ +A+++a ++S+++l   R+++t
  gi|330507339|ref|YP_004383767.1|  4 RLIYSPVGILIMLGFAFLIAIVVSFLFLDLARTAFT 39
                                      688899***************************998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.41
                           DUF4229 36 llAlvvalp 44
                                      l+ l+++l+
  gi|330507339|ref|YP_004383767.1| 49 LFVLLASLV 57
                                      333333333 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.2
                           DUF4229  29 vpllvaallAlvvalplSmvl 49 
                                        +ll + + ++++  ++Sm l
  gi|330507339|ref|YP_004383767.1|  96 NTLLAINVGGALIPSLISMAL 116
                                       556666677788888888876 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.24
                           DUF4229   8 laLfvvltavillvarliglpvpllvaallAlvvalplSmv 48 
                                       ++L++++t  ++  +r +g+  p lv  l A+++a +  +v
  gi|330507339|ref|YP_004383767.1| 131 IVLVAIITNRVARPVRGLGIVTPALVPPLCAALAAILMVYV 171
                                       55555555544444444444445555555555555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 2007.41
//
Query:       gi|330507340|ref|YP_004383768.1|  [L=373]
Description: 3-dehydroquinate synthase [Methanosaeta concilii GP6]
Scores for complete 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-143  476.9   0.7   3.5e-143  476.8   0.7    1.0  1  DHQS      3-dehydroquinate synthase II
     0.0002   21.4   0.0       0.41   10.8   0.0    2.7  2  OapA      Opacity-associated protein A LysM-like domain
  ------ inclusion threshold ------
      0.063   13.5   0.3        9.2    6.5   0.1    3.2  3  TOBE_2    TOBE domain


Domain annotation for each model (and alignments):
>> DHQS  3-dehydroquinate synthase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.8   0.7  5.9e-147  3.5e-143       1     352 []       2     373 .]       2     373 .] 0.97

  Alignments for each domain:
  == domain 1  score: 476.8 bits;  conditional E-value: 5.9e-147
                              DHQS   1 kevwikadeeeweerkelvtaaleagvdavlveeedaekvkelgkikviakeed....davlvgkd........... 62 
                                       ke w++a +++wee k  +t+ale+g+++v+v++e++e+v+elg+i+v+ + ++    d++++g++           
  gi|330507340|ref|YP_004383768.1|   2 KEKWLMA-RGSWEEIKPQITTALESGFECVIVDRENVERVRELGNIQVACFGAEkgaeDILVIGRHgegdgsvplpk 77 
                                       788**66.59***************************************999555677999999999********** PP

                              DHQS  63 ......dleklkka.kkvaalveikskeeeeeaaeaakeadyvivelkdwtvIPlEnliAalqgeetkiiaavksae 132
                                             d++ +k+   ++aa+v i+ k++e++a+e++k++dy++v ++dw+vIPlEn+iA lqg+++kii++vks++
  gi|330507340|ref|YP_004383768.1|  78 dlnssmDYALAKTIsGNKAAYVVIAGKKYEQFAVEMGKHVDYLLVIGTDWKVIPLENMIAGLQGCQVKIISGVKSSD 154
                                       9988776666666678999********************************************************** PP

                              DHQS 133 eAklaletLEkGadgvllktedveeikelaelleeaeeekleLkeaevtkveevgmgdRvcvDtcslmkegeGmLvG 209
                                       eAklal tLE+Gadgvll+++d +eik++++++e++e+ +l+L +a+v++v++vgmgdRvcvDt+++m +geGmL+G
  gi|330507340|ref|YP_004383768.1| 155 EAKLALATLEQGADGVLLDSSDLSEIKRVMRAAEQSEKGRLDLIPARVVSVKPVGMGDRVCVDTANMMVPGEGMLIG 231
                                       ***************************************************************************** PP

                              DHQS 210 sssrglfLvhsEtlespYvasRPFRVNAGavhaYvlvpggkTkYLseLkaGdevlvvdkkGktreavvGRvKiEkRP 286
                                       s+++g+fLvhsE+++spYva+RPFRVNAGavhaY++v g+kT+YLseLk+Gdev++v+k+G +r+a+vGR+KiEkRP
  gi|330507340|ref|YP_004383768.1| 232 SQAKGFFLVHSESEDSPYVAARPFRVNAGAVHAYIRV-GEKTRYLSELKSGDEVTIVSKDGLSRSAIVGRAKIEKRP 307
                                       *************************************.*************************************** PP

                              DHQS 287 lllveaeaegkkvstilQnaetirlvtedgkaisvteLkeGdevlvyleekaRHfGikieEtiiEk 352
                                       ++l+eaea+g  +st+lQnaeti+lv++dg++ +vteLk+Gdevlv+lee+aRHfG+kieE+i+E+
  gi|330507340|ref|YP_004383768.1| 308 MILIEAEADGVLISTLLQNAETIKLVSSDGTPRPVTELKAGDEVLVHLEEAARHFGMKIEESIVER 373
                                       ****************************************************************97 PP

>> OapA  Opacity-associated protein A LysM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00062       3.7      24      53 ..     259     288 ..     252     321 .. 0.77
   2 !   10.8   0.0   6.8e-05      0.41      23      66 ..     325     368 ..     318     371 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00062
                              OapA  24 lsdvnalakveGadkplSnlksGqkvrikl 53 
                                          v+a  +v  + + lS+lksG++v+i  
  gi|330507340|ref|YP_004383768.1| 259 AGAVHAYIRVGEKTRYLSELKSGDEVTIVS 288
                                       566889999999999***********9853 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 6.8e-05
                              OapA  23 plsdvnalakveGadkplSnlksGqkvriklnaqgkvdelqlek 66 
                                       + ++  +l+  +G+ +p+ +lk+G++v ++l++  +   +++e+
  gi|330507340|ref|YP_004383768.1| 325 QNAETIKLVSSDGTPRPVTELKAGDEVLVHLEEAARHFGMKIEE 368
                                       55677889999***********************9999999987 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.082   4.9e+02      18      40 ..     197     219 ..     182     222 .. 0.77
   2 ?    6.5   0.1    0.0015       9.2      20      51 ..     259     290 ..     249     299 .. 0.86
   3 ?    1.4   0.0     0.059   3.5e+02      46      72 ..     332     359 ..     320     362 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.082
                            TOBE_2  18 glsGtVedveylGsstryvvela 40 
                                        ++++V++v   G   r+ v++a
  gi|330507340|ref|YP_004383768.1| 197 LIPARVVSVKPVGMGDRVCVDTA 219
                                       5699*********9999999987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0015
                            TOBE_2  20 sGtVedveylGsstryvvelaggqlvvvrqpn 51 
                                       +G V+  +  G+ try+ el +g +v+++  +
  gi|330507340|ref|YP_004383768.1| 259 AGAVHAYIRVGEKTRYLSELKSGDEVTIVSKD 290
                                       699999*******************9987765 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.059
                            TOBE_2  46 vvrqpnadr.dsalapGdtVelswdpdd 72 
                                       +v+ + ++r  + l++Gd+V ++++ ++
  gi|330507340|ref|YP_004383768.1| 332 LVSSDGTPRpVTELKAGDEVLVHLEEAA 359
                                       3444445554489999***999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3008.54
//
Query:       gi|330507341|ref|YP_004383769.1|  [L=214]
Description: 3-dehydroquinate dehydratase [Methanosaeta concilii GP6]
Scores for complete 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  161.2   0.1      5e-47  161.1   0.1    1.0  1  DHquinase_I  Type I 3-dehydroquinase
  ------ inclusion threshold ------
      0.033   14.0   2.3        2.1    8.2   0.2    2.6  2  HlyD_D4      Long alpha hairpin domain of cation efflux syste


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 !  161.1   0.1   5.6e-51     5e-47      17     227 ..      19     207 ..       6     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 161.1 bits;  conditional E-value: 5.6e-51
                                       HHHTTS-SEEEEEGGG-.TT.THHHHHHHHHHHHHHTTS-EEEE---GGGT-S.SSS-HHHHHHHHHHHHHCT-SEE CS
                       DHquinase_I  17 esgkekaDlvElRlDllketseaedvseeleelrstsdlpliftlrtkaeggrfkrkseeeylellrtaielgadyv 93 
                                       +++ ++aD++ElRlDl +e+      +++++ +r+ +++p+i+t r +aegg+f ++se e++ell +a e  ad+v
  gi|330507341|ref|YP_004383769.1|  19 KAA-SDADMIELRLDLATEP------IQTIKAIREATEKPIIATNRLQAEGGKF-QGSERERIELLVQASEY-ADLV 86 
                                       333.368********88665......56*******99*****************.9**************95.9*** PP

                                       EEEGG-.HHGHHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSHHHHHHHHHHHH CS
                       DHquinase_I  94 DvElteapeeskkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksieDvlrllslts 170
                                       D+El  a+    ++ i++    +  vIvS+hdf+g p  +el a+ e+m+  ga i+Kiav+++s +D l+ll++  
  gi|330507341|ref|YP_004383769.1|  87 DIELQ-AE--LREEFISQV---SRPVIVSFHDFQGMPGIDELAAIKERMKMAGAAIAKIAVTPRSLKDDLDLLEFLL 157
                                       ****4.33..334666665...7789*************************************************83 PP

                                       HHHHHT-SS-EEEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHHH CS
                       DHquinase_I 171 eakeekdeaplIamamGelGkiSRilgevfGspvtfasleeakasapGqltarelre 227
                                             ++ pl+ +amG+lG+  R +++++Gs++ ++ ++e+  +apGq++++el +
  gi|330507341|ref|YP_004383769.1| 158 -----AADLPLCLIAMGDLGRHLRAVAPLYGSALAYGYVRES--TAPGQMSLAELSS 207
                                       .....4579*****************************8888..**********986 PP

>> HlyD_D4  Long alpha hairpin domain of cation efflux system protein, CusB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2    0.0024        22      25      51 ..      20      46 ..      12      51 .. 0.79
   2 ?    8.2   0.2   0.00024       2.1      28      48 ..     121     141 ..     115     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0024
                                      -HHHHHHHHHHHHHCT--HHHHHHHHH CS
                           HlyD_D4 25 laslldaareRlrLaGMpdadIrrlea 51
                                      +as  d +  Rl La  p ++I++++ 
  gi|330507341|ref|YP_004383769.1| 20 AASDADMIELRLDLATEPIQTIKAIRE 46
                                      3788999****************9963 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHCT--HHHHHH CS
                           HlyD_D4  28 lldaareRlrLaGMpdadIrr 48 
                                       +l a++eR+++aG   a+I  
  gi|330507341|ref|YP_004383769.1| 121 ELAAIKERMKMAGAAIAKIAV 141
                                       5789*********99888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1644.78
//
Query:       gi|330507342|ref|YP_004383770.1|  [L=447]
Description: putative methanogenesis marker protein 10 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-08   35.0  13.1    2.8e-06   27.8   8.5    4.3  3  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   8.5   1.6e-10   2.8e-06      19     157 ..      32     185 ..      11     196 .. 0.79
   2 !    2.7   0.0    0.0084   1.5e+02      29     111 ..     231     316 ..     210     362 .. 0.77
   3 ?   -0.7   0.0      0.09   1.6e+03      21      72 ..     373     422 ..     346     444 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.6e-10
                                       T..................HHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       x..................xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  19 t..................vrregrgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlaklavp 76 
                                                             e  + ++s+++++ e+ +    ++     i g g+ +++pd+ +l+  l+   v 
  gi|330507342|ref|YP_004383770.1|  32 PlgckycpphkkgcdycsrAVVEIQPGFKSLDQLVFEASQQCiLSRPDSITIKGNGDASFHPDLLKLVQTLSNG-VV 107
                                       0444444444445555555557888888888888888876664455477777789******************8.58 PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglp 153
                                        i++ +++  +    + +  l e+g+ r+s+++ ++d+e  +++    + +e+ l +l+++ e+ ++  + +iv++p
  gi|330507342|ref|YP_004383770.1| 108 PIHLDYTSGKGFFKGDEAGPLIEAGLRRISFSVFSTDPE-LRRRYVNDKHPEAALSNLRTFCER-CD-LYAMIVLIP 181
                                       88888888888888*************************.77777788****************.**.********* PP

                                       TTSH CS
                                       xxxx RF
                       Radical_SAM 154 Gend 157
                                       G nd
  gi|330507342|ref|YP_004383770.1| 182 GIND 185
                                       ***9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0084
                                       HHHHHHHHHHHHHHHHTTSEEEEEE......SSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  29 lsveeileevkelkaekgvkevilg......ggepllypdfvellerlaklavpgiritvetngtlpdeeklerlle 99 
                                        sveei +++ e+  e+    vi +       g p++ ++  ++l rl ++   +++ t++t+ +     +l ++ e
  gi|330507342|ref|YP_004383770.1| 231 YSVEEIRRIATEIN-ERYDMRVIGTplwdpqTGAPFALAHHRKELNRLPAI---ERSATIITSSVAY--PFLSTIFE 301
                                       68999999999994.554444555568888888899999999999999998...8999999988884..44444444 PP

                                       TT...-SEEEEEEBS CS
                                       xx...xxxxxxxxxx RF
                       Radical_SAM 100 lg...vdrvslglea 111
                                            v++v+++ e+
  gi|330507342|ref|YP_004383770.1| 302 EIgedVNVVAVNKEI 316
                                       333446666666555 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.09
                                       HHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  21 rregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlak 72 
                                       ++e+  ++ + e i++ev++++   g + ++  +gge +  +  +++ ++++ 
  gi|330507342|ref|YP_004383770.1| 373 ESERSIYMTTEEVIAREVEAFS---GlICQINELGGEETESATVQKDRDNCSC 422
                                       5667778888899999999886...4466666666665555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3187.85
//
Query:       gi|330507343|ref|YP_004383771.1|  [L=111]
Description: hypothetical protein MCON_1243 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 827.83
//
Query:       gi|330507344|ref|YP_004383772.1|  [L=377]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   69.0   0.1    2.4e-17   63.8   0.0    2.2  2  Radical_SAM  Radical SAM superfamily
    3.9e-11   43.0   0.0    7.1e-11   42.2   0.0    1.4  1  B12-binding  B12 binding domain
  ------ inclusion threshold ------
      0.062   13.1   0.0       0.12   12.1   0.0    1.4  1  LPD30        Large polyvalent protein associated domain 30


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.019   1.1e+02      30      69 ..      43      82 ..      35      99 .. 0.82
   2 !   63.8   0.0   4.1e-21   2.4e-17       1     165 [.     144     311 ..     144     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.019
                                      HHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHH CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 30 sveeileevkelk.aekgvkevilgggepllypdfveller 69
                                      +  e+ +ev+ ++ a+    +++ gg +p++ p++v + + 
  gi|330507344|ref|YP_004383772.1| 43 QAGEVYQEVDTARkAKL-DAVFVAGGPHPSALPEEVLEHFD 82
                                      56789999999984444.88999999999999999988775 PP

  == domain 2  score: 63.8 bits;  conditional E-value: 4.1e-21
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS........TTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly........pdfveller 69 
                                       ++++rgC+ +C++C++p+    +++ r++++  +++ +++ k       + +++ + l+y         ++v++l++
  gi|330507344|ref|YP_004383772.1| 144 IEISRGCPWGCTYCQTPRL--FGRCMRHRTIPVVARFARRHK------DIRFTSPNSLAYgsdgrrprLEKVKALLE 212
                                       6899*************97..*****************9997......45555555555544444444777777777 PP

                                       HHHTCCCTEEEEEEECSSCHG...HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  70 laklavpgiritvetngtlpd...eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagi 142
                                       +  ++++ i +    ++++pd   +e le + ++    ++slg +++++  vlk ++rgh+++e+  a+e + ++g+
  gi|330507344|ref|YP_004383772.1| 213 ELSEQKKPIYFGTFPSEVRPDfvsDEALEIITKYCaNKTISLGGQSGSPA-VLKSIGRGHGRQEIESACEHILDHGL 288
                                       777766777777777777777*****************************.*************************9 PP

                                       ETEEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 143 krvvdrivglpGendeeleelle 165
                                        + vd i+glp e+ e+   +l+
  gi|330507344|ref|YP_004383772.1| 289 IPLVDLIFGLPMESAEDQHMTLD 311
                                       99**************9666666 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   1.2e-14   7.1e-11      54     121 .]      34      97 ..      21      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.2e-14
                       B12-binding  54 vvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleala 121
                                       + + S+  t q  +v + v+ +++++ ++  v+GG+hps++pee+le+   +d+vvvgege++l++l+
  gi|330507344|ref|YP_004383772.1|  34 IMLYSF-ATPQAGEVYQEVDTARKAKLDAVFVAGGPHPSALPEEVLEH---FDFVVVGEGEETLPELI 97 
                                       345566.8888888888888899999********************85...8*************985 PP

>> LPD30  Large polyvalent protein associated domain 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     2e-05      0.12      41      80 ..      51      91 ..      41     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                             LPD30 41 istggsaefDivFdn.GekskklPesilrgvqWkildeivs 80
                                      ++t++ a++D vF + G +   lPe +l + ++ +++e  +
  gi|330507344|ref|YP_004383772.1| 51 VDTARKAKLDAVFVAgGPHPSALPEEVLEHFDFVVVGEGEE 91
                                      578999*******761678899***********99998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); 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):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2814.76
//
Query:       gi|330507345|ref|YP_004383773.1|  [L=91]
Description: hypothetical protein MCON_1245 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 745.63
//
Query:       gi|330507346|ref|YP_004383774.1|  [L=76]
Description: hypothetical protein MCON_1247 [Methanosaeta concilii GP6]
Scores for complete 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   16.1   0.0     0.0067   16.0   0.0    1.0  1  DUF3786   Domain of unknown function (DUF3786)


Domain annotation for each model (and alignments):
>> DUF3786  Domain of unknown function (DUF3786)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.8e-07    0.0067      19      63 ..      23      67 ..       6      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.8e-07
                           DUF3786 19 ltlpflgreyrisypggeisdgedeeeddlnekilllnylleakg 63
                                      + +p+l ++y+++ ++ ++ + ++++ ++ + ++l+l+yl+  ++
  gi|330507346|ref|YP_004383774.1| 23 YAVPLLTETYEVDIDSRTVLSMSSGIPAEESIAVLILHYLMGMQK 67
                                      789**********************8899999********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 529.03
//
Query:       gi|330507347|ref|YP_004383775.1|  [L=405]
Description: hypothetical protein MCON_1249 [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.0    2.8e-08   34.2   0.0    1.6  1  DUF4263   Domain of unknown function (DUF4263)


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 !   34.2   0.0   1.6e-12   2.8e-08       4     141 ..     237     378 ..     234     394 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.6e-12
                           DUF4263   4 Ekkwqkffeknpwllypiisefpikev..dfk...........s.....DfllidslngnivlvEikkp..dknllt 60 
                                       E ++ +f+eknp +l  ++++ + ++v  + k           +     D+l+ ++ +g +++ ++k+p  dk  +t
  gi|330507347|ref|YP_004383775.1| 237 ETTIGDFLEKNPDFLRRAFRTLSCRDVlyQ-KelkwiegnpypEksikpDLLFERN-DGCFDIGDLKTPllDKGKIT 311
                                       78899**********777777777755431.234455554444145667*****99.************99888888 PP

                           DUF4263  61 kekkkgniapseelsgaisQikkylllldknkekgeeladlrntseleeglgikainpkgiliiGrreeleekekre 137
                                       k++++    ++++++++++Q+++y  +++   +k + +a        e++ gik  +pk ili+G++e++ ++e   
  gi|330507347|ref|YP_004383775.1| 312 KSDHR-RRRFTDDVNEGVAQLANYREYFS--FQKNRAYA--------ESKYGIKVSEPKLILIVGSYENVIQNE--- 374
                                       88877.99*****************9998..66666666........4566****************7776533... PP

                           DUF4263 138 sfel 141
                                         e+
  gi|330507347|ref|YP_004383775.1| 375 VNEA 378
                                       3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2536.76
//
Query:       gi|330507348|ref|YP_004383776.1|  [L=574]
Description: adenine deaminase [Methanosaeta concilii GP6]
Scores for complete 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-68  227.9   0.1    8.7e-68  226.9   0.1    1.5  1  Adenine_deam_C  Adenine deaminase C-terminal domain
    2.3e-27   96.2   0.0    1.5e-25   90.3   0.0    2.3  1  Amidohydro_1    Amidohydrolase family
    8.5e-11   42.0   0.0     0.0001   22.0   0.0    2.5  2  Amidohydro_3    Amidohydrolase family


Domain annotation for each model (and alignments):
>> Adenine_deam_C  Adenine deaminase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.9   0.1   1.5e-71   8.7e-68       1     168 [.     397     564 ..     397     565 .. 0.98

  Alignments for each domain:
  == domain 1  score: 226.9 bits;  conditional E-value: 1.5e-71
                                       .SS-EEEEEEEEEETTEEE-..-TTEEEEEEE--SSSS--EEEEEEESS--BSSEEEES--TTT--EEEEESSHHHH CS
                    Adenine_deam_C   1 qliTkelevelpvkdgvvvadlekdllkiavveRhgktgnvgvgfvkgfglkkgAiAssvahDshniivvGtndedm 77 
                                       q+iT++l +   +++g+vv+d+++d+lk+avveRh++tgnvg+g+v+gf l +gA+A+svahDshni+vvGt de+m
  gi|330507348|ref|YP_004383776.1| 397 QIITRSLPLFPLIREGKVVSDTDQDILKLAVVERHRATGNVGLGLVQGFRLVRGALATSVAHDSHNIVVVGTGDEEM 473
                                       689999999999***************************************************************** PP

                                       HHHHHHHHHTTSEEEEEETTEEEEEEE-TBTTTBBSS-HHHHHHHHHHHHHHHHTTS-TTTBSGGGGGSTT-TTSSS CS
                    Adenine_deam_C  78 alAvnrvielgGGivvvedgkvlaelpLpiaGlmSdepaeevaekleeleaalkelgvkledpfmtlsflalpviPe 154
                                       ++Av +v e+ GG+v+vedg+vla+lpLp+aGl+S+ +++evae ++e  +a+++lg++ledpfmtlsfl+lpviPe
  gi|330507348|ref|YP_004383776.1| 474 LAAVSAVTEMDGGLVAVEDGEVLASLPLPVAGLLSESHMQEVAEGIAECIDAAHKLGCTLEDPFMTLSFLSLPVIPE 550
                                       **************************************************88888********************** PP

                                       EEEETTSEEETTTT CS
                    Adenine_deam_C 155 lkltdkGlvdvkkf 168
                                       lkltd+Glvdv+ f
  gi|330507348|ref|YP_004383776.1| 551 LKLTDRGLVDVRVF 564
                                       ***********866 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.0   2.5e-29   1.5e-25       1     344 []      67     348 ..      67     348 .. 0.83

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 2.5e-29
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEE CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplgl 77 
                                       i+ PG+ID HvH+e+s++         + pe+a++++ +g++t + +++++++  g+    g++ +l++++++pl++
  gi|330507348|ref|YP_004383776.1|  67 ILAPGFIDGHVHIESSMV---------TVPEYARAVVPQGTTTVIADPHEIANVWGEE---GVRYILQSSRNVPLNV 131
                                       688***********9988.........******************************7...**************** PP

                                       EEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE. CS
                      Amidohydro_1  78 rilggkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHa. 152
                                        +++++++++++ +    a+    + g     +++++gv+  ++++  + + f d ++ + +++a   +   + Ha 
  gi|330507348|ref|YP_004383776.1| 132 FVMLPSCVPATDMETAGAALGPDALVG-----LFEEEGVIGlAEVMNCPGVIFRDPQIMKKIQLAG--GRLKDGHAp 201
                                       **********85555555666666666.....4678899999********************9886..778888888 PP

                                       .TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSEHH CS
                      Amidohydro_1 153 .letkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsg 228
                                        l+ +   +++ a++ +++e++t+ e  e+          l  g++++                      + + + +
  gi|330507348|ref|YP_004383776.1| 202 gLSGPDLSAYICAGIRSDHECTTLAEAEEK----------LFSGMFIMLR--------------------EGSAARN 248
                                       8**************************666..........9999999944....................2234445 PP

                                       HHHHHHHHHH.TSC.EEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTS CS
                      Amidohydro_1 229 realrkalde.Gvk.vglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkv 303
                                       + +l ++++  + + + +++D     + +++l+e+ + ++l++       + gl++  al+++++n+A+++gl+ ++
  gi|330507348|ref|YP_004383776.1| 249 LSDLLPLVTLkNSRqFLFVSD---DRHPADILREGHIDFMLRK-----AINEGLDPIVALQISSLNAARYFGLA-DL 316
                                       555555544433444899999...7888888899444443333.....23889********************7.** PP

                                       SSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 304 GsievGkdADlvvvdldilaafvglkkdgnvkkvivkGklv 344
                                       G+i++G++AD++v+            +   v++v+++G+lv
  gi|330507348|ref|YP_004383776.1| 317 GAIAPGYRADIAVL---------DGLDEPRVTHVFKDGRLV 348
                                       **************.........555666799999999887 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.4e-07     0.002       1      53 [.      59     107 ..      59     128 .. 0.81
   2 !   22.0   0.0   1.7e-08    0.0001     406     472 ..     292     348 ..     198     349 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.4e-07
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavrdqag 53 
                                       ++i ++  +++PGF+D H H     ++  +++ +++ar+   +g++t+++d  +
  gi|330507348|ref|YP_004383776.1|  59 QIISLEDQILAPGFIDGHVH-----IESsMVTVPEYARAVVPQGTTTVIADPHE 107
                                       6899****************.....66656888888888888999999988655 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.7e-08
                      Amidohydro_3 406 eelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaearvrltvvdGrvv 472
                                       e l+   al+  + ++A+ +gl d  G +++G++AD++vld     +d+p     rv ++ +dGr v
  gi|330507348|ref|YP_004383776.1| 292 EGLDPIVALQISSLNAARYFGLADL-GAIAPGYRADIAVLD----GLDEP-----RVTHVFKDGRLV 348
                                       5566666899999***********8.**************8....66777.....488888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.59
# Mc/sec: 2948.72
//
Query:       gi|330507349|ref|YP_004383777.1|  [L=737]
Description: AAA family ATPase [Methanosaeta concilii GP6]
Scores for complete 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  326.2   0.0      7e-50  168.9   0.0    2.6  2  AAA              ATPase family associated with various cellul
    1.6e-32  111.0   0.8    7.9e-17   60.8   0.2    2.8  2  AAA_lid_3        AAA+ lid domain
    1.4e-31  108.5   0.0    9.3e-31  105.9   0.0    2.5  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.8e-16   60.3   0.0    1.3e-07   31.5   0.0    3.6  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    4.6e-14   51.9   0.0    3.1e-13   49.3   0.1    2.2  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    8.8e-14   52.0   0.0    1.6e-06   28.4   0.0    3.0  3  AAA_2            AAA domain (Cdc48 subfamily)
    1.9e-13   51.2   0.0    2.5e-05   24.7   0.0    3.4  2  AAA_16           AAA ATPase domain
    1.3e-12   47.9   0.3    4.2e-05   23.6   0.0    4.0  2  AAA_5            AAA domain (dynein-related subfamily)
    7.5e-12   45.1   0.0    4.1e-05   23.0   0.0    2.7  3  TIP49            TIP49 P-loop domain
    4.8e-11   43.1   1.9     0.0081   16.4   0.0    4.6  5  AAA_22           AAA domain
      8e-10   38.9   0.0    0.00016   21.7   0.0    2.4  2  AAA_14           AAA domain
    2.5e-09   37.7   0.2     0.0043   17.6   0.0    2.9  2  AAA_18           AAA domain
    3.2e-09   37.1   0.0    0.00057   20.1   0.0    2.5  2  AAA_33           AAA domain
    1.2e-07   31.4   0.0     0.0089   15.4   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.3e-07   30.7   0.0       0.02   14.6   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    3.7e-07   29.9   0.6     0.0065   16.1   0.0    3.7  3  AAA_25           AAA domain
    4.4e-07   29.6   0.0       0.03   13.8   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    8.3e-07   28.9   0.1       0.14   11.8   0.0    3.5  2  Sigma54_activat  Sigma-54 interaction domain
    1.4e-06   27.7   0.1       0.04   13.2   0.0    2.7  2  Zeta_toxin       Zeta toxin
    2.1e-06   27.3   5.6       0.33   10.3   0.1    4.3  4  ATPase           KaiC
    2.1e-06   27.6   0.1        0.1   12.3   0.0    2.8  2  AAA_24           AAA domain
    2.5e-06   27.8   0.0      0.027   14.7   0.0    2.6  2  AAA_28           AAA domain
    3.6e-06   27.3   0.0       0.12   12.8   0.0    2.5  2  RNA_helicase     RNA helicase
    6.5e-06   25.4   0.2      0.057   12.5   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    1.5e-05   25.0   0.0       0.23   11.5   0.0    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    3.4e-05   24.3   0.0       0.54   10.7   0.0    3.4  2  AAA_17           AAA domain
    3.9e-05   24.2   0.0       0.22   12.0   0.0    2.5  2  ABC_tran         ABC transporter
    5.1e-05   23.1   0.0       0.26   11.2   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    5.6e-05   22.4   0.0       0.32   10.1   0.0    2.5  2  DUF815           Protein of unknown function (DUF815)
    5.7e-05   23.1   0.2       0.73    9.7   0.0    3.9  3  ATPase_2         ATPase domain predominantly from Archaea
    0.00011   22.3   0.0       0.25   11.5   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00015   21.2   0.2       0.56    9.6   0.0    2.9  3  IPT              Isopentenyl transferase
    0.00015   21.1   0.0       0.31   10.2   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00022   21.1   0.0       0.42   10.4   0.0    2.4  2  AAA_11           AAA domain
    0.00025   20.6   0.1       0.81    9.1   0.1    2.5  2  PhoH             PhoH-like protein
     0.0003   20.1   0.0       0.82    8.8   0.0    2.3  2  NB-ARC           NB-ARC domain
    0.00032   21.0   1.0        1.1    9.6   0.0    3.0  2  AAA_19           AAA domain
    0.00044   19.7   0.1        1.1    8.7   0.0    3.8  4  TniB             Bacterial TniB protein
    0.00059   19.6   0.7        1.4    8.6   0.0    2.7  2  AAA_30           AAA domain
    0.00059   19.7   0.0        1.8    8.4   0.0    2.8  2  Bac_DnaA         Bacterial dnaA  protein
    0.00089   19.2   0.3       0.69    9.8   0.0    3.2  3  NACHT            NACHT domain
     0.0014   18.8   0.0       0.45   10.6   0.0    2.6  2  Cytidylate_kin2  Cytidylate kinase-like family
     0.0016   18.1   0.0       0.46   10.1   0.0    2.5  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
     0.0016   18.4   0.0        2.5    8.0   0.0    2.8  3  Rad17            Rad17 P-loop domain
     0.0019   18.0   0.4        2.7    7.7   0.0    2.7  2  Cytidylate_kin   Cytidylate kinase
     0.0023   17.9   1.0        3.4    7.5   0.0    3.8  3  NTPase_1         NTPase
     0.0024   17.8   0.0        0.5   10.4   0.0    2.7  2  Vps4_C           Vps4 C terminal oligomerisation domain
     0.0045   17.1   0.0        5.3    7.1   0.0    2.8  2  SKI              Shikimate kinase
     0.0051   16.5   0.4         11    5.7   0.0    3.9  4  Guanylate_kin    Guanylate kinase
     0.0087   16.1   0.0        3.2    7.7   0.0    2.6  2  ResIII           Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.024   13.5   0.0        3.5    6.4   0.0    2.3  2  AFG1_ATPase      AFG1-like ATPase
      0.028   14.7   0.3        8.3    6.6   0.0    2.7  2  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.038   13.7   0.0        9.1    6.1   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
      0.045   12.8   0.0        1.8    7.5   0.0    2.4  2  T2SSE            Type II/IV secretion system protein
      0.065   12.3   0.0        6.8    5.7   0.0    3.0  3  MCM              MCM P-loop domain
      0.098   12.5   0.0        7.7    6.3   0.0    2.4  2  CPT              Chloramphenicol phosphotransferase-like prot
       0.18   11.5   0.0        4.7    6.9   0.0    2.2  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 !  168.9   0.0   2.2e-52     7e-50       1     131 [.     229     358 ..     229     359 .. 0.98
   2 !  154.8   0.0   4.9e-48   1.5e-45       1     130 [.     501     630 ..     501     632 .. 0.96

  Alignments for each domain:
  == domain 1  score: 168.9 bits;  conditional E-value: 2.2e-52
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vllyGppGtGKTl+akava+e+g++f++i g+e++sky gese+++re+f+ea+++a psi+fiDEid++a++r + 
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANESGANFISIAGPEIMSKYYGESEQRLREIFEEAQKSA-PSIIFIDEIDSIAPKRGEV 304
                                       79******************************************************9.****************999 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLl+++dg+k++ ++v+vigatnr++ +dpal+r gRfdr+ie++
  gi|330507349|ref|YP_004383777.1| 305 TGEVERRVVAQLLAMMDGLKER-GQVVVIGATNREEAIDPALRRpGRFDREIEVG 358
                                       *********************7.66***************************986 PP

  == domain 2  score: 154.8 bits;  conditional E-value: 4.9e-48
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       +llyGppGtGKT++a+ava+e++++f++i g+++lsk+vgesek ire+f++a++ + p i+f+DE+d++a+ r  +
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANETNANFISIRGPQMLSKWVGESEKAIREIFRKARQVS-PAIIFFDELDSIAPMRgMD 576
                                       69******************************************************9.****************888 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkiei 130
                                       +  ++ ervvnqLl+eldg++  ++ v+vi+atnrpd ldpallr gRfdr + +
  gi|330507349|ref|YP_004383777.1| 577 EGGRVMERVVNQLLAELDGLEALKD-VVVIAATNRPDILDPALLRsGRFDRMLLV 630
                                       8999******************755.************************98766 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0     3e-15   9.5e-13       1      42 [.     381     422 ..     381     427 .. 0.94
   2 !   60.8   0.2   2.5e-19   7.9e-17       1      43 [.     654     696 ..     654     698 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 3e-15
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmed 42 
                                       dv+l+ LA r++G++GAD  alc+eAa+ Alrr ++ +t ed
  gi|330507349|ref|YP_004383777.1| 381 DVNLEGLADRMHGFVGADVNALCKEAAMKALRRYLPDLTSED 422
                                       9********************************999888887 PP

  == domain 2  score: 60.8 bits;  conditional E-value: 2.5e-19
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                                       dv+l+eLAe+T+Gy+G Dl +lcreAa+lAlr+g++ ++m++ 
  gi|330507349|ref|YP_004383777.1| 654 DVSLEELAELTDGYVGSDLDNLCREAAMLALREGLDRVEMRHY 696
                                       9***************************************996 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   0.0     3e-33   9.3e-31       2      84 ..       9      91 ..       8      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 3e-33
                                      EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEE CS
                           CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtV 80
                                      L+Va+a+++d+ rgi+r+dp+++  l+l+pgd++eiegkr T+a+vw+a+++d+++++Ir+dg++R+nagv+iGdkV++
  gi|330507349|ref|YP_004383777.1|  9 LKVAKAYPNDSARGIARLDPNALLTLRLSPGDIIEIEGKRLTAAKVWRADRQDWSQDYIRIDGFIRQNAGVGIGDKVKI 87
                                      9******99********************************************************************** PP

                                      EEE- CS
                           CDC48_N 81 rkae 84
                                      rka+
  gi|330507349|ref|YP_004383777.1| 88 RKAK 91
                                      **96 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   4.1e-10   1.3e-07      34     103 ..     227     304 ..     219     352 .. 0.82
   2 !   23.2   0.0   1.5e-07   4.8e-05      35      69 ..     500     534 ..     489     573 .. 0.80
   3 ?    0.2   0.0       1.8   5.7e+02      24      43 ..     615     634 ..     588     649 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 4.1e-10
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsravee 102
                                         vllyGpPG Gkt +ak +a+e g+++ + +gP +      e ++ l  ++ + +++   ++fidei  ++++  e
  gi|330507349|ref|YP_004383777.1| 227 KGVLLYGPPGTGKTLIAKAVANESGANFISIAGPEImskyygESEQRLREIFEEAQKSapSIIFIDEIDSIAPKRGE 303
                                       569*******************************994433333456788999888765337*******999988777 PP

                            RuvB_N 103 v 103
                                       v
  gi|330507349|ref|YP_004383777.1| 304 V 304
                                       6 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 1.5e-07
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                        +llyGpPG Gkt +a+ +a+e ++++ +  gP +
  gi|330507349|ref|YP_004383777.1| 500 GILLYGPPGTGKTMIAQAVANETNANFISIRGPQM 534
                                       69*************************99999976 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.8
                            RuvB_N  24 eaakkreealdhvllyGpPG 43 
                                       + a  r+   d +ll+GpP 
  gi|330507349|ref|YP_004383777.1| 615 DPALLRSGRFDRMLLVGPPD 634
                                       55677888889999999985 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0         4   1.3e+03      18      30 ..      35      47 ..      29      60 .. 0.80
   2 !   49.3   0.1   9.8e-16   3.1e-13       3      63 ..     110     179 ..     109     180 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 4
                                      EE-TTEEEEECCT CS
                           CDC48_2 18 pvtkGdlvvfefk 30
                                       +++Gd++ +e k
  gi|330507349|ref|YP_004383777.1| 35 RLSPGDIIEIEGK 47
                                      589*****99876 PP

  == domain 2  score: 49.3 bits;  conditional E-value: 9.8e-16
                                       SCCCCH.HHHCCCTTEEE-TTEEEEECCT........CCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                           CDC48_2   3 dgdema.ylkrqFlgrpvtkGdlvvfefk........gqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                       +gde+a +++rq l+rpv++Gd+++++ +        + +++lvV++t P ++v++ e Tei l +kp++
  gi|330507349|ref|YP_004383777.1| 110 YGDEAAdMIRRQTLKRPVVAGDILPIMSSgthpfvgrMEPVPLVVTETHPDNVVVVCERTEIVLLEKPAK 179
                                       699*********************9999888888999*******************************97 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0     5e-09   1.6e-06       6     105 ..     229     322 ..     225     329 .. 0.86
   2 !   19.8   0.0   2.1e-06   0.00066       6     105 ..     501     595 ..     496     601 .. 0.77
   3 ?   -1.3   0.0       6.6   2.1e+03      76      95 ..     640     660 ..     639     663 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++aka+a+   +    ++i +   e++     + + ++++  ++   +a+++   i+++DEid i
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANESGA----NFISIAGPEIMS----KYYGESEQRLREIFEEAQKSApsIIFIDEIDSI 297
                                       6889******************96....************....77777777777777777777799********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk ++ + +v r  V+  LL +++g
  gi|330507349|ref|YP_004383777.1| 298 APKrGEVTGEVERR-VVAQLLAMMDG 322
                                       **988888888886.66678888886 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.1e-06
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ill gp g+Gkt++a+a+a+  ++    ++i +   ++l     + + ++++  ++   +a +    i+++DE+d i
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANETNA----NFISIRGPQMLS----KWVGESEKAIREIFRKARQVSpaIIFFDELDSI 569
                                       8999******************96....999998888888....55555555555555555555577********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +p  +  +     e V++ LL  l+g
  gi|330507349|ref|YP_004383777.1| 570 APMrGMDEGGRVMERVVNQLLAELDG 595
                                       **765556666678888888877776 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 6.6
                                       TGGG----.---------HHH CS
                             AAA_2  76 EidKihpk.essgadvSregV 95 
                                       Ei Kih++ + +g+dvS e+ 
  gi|330507349|ref|YP_004383777.1| 640 EILKIHASrTPKGEDVSLEEL 660
                                       899****99999*****9975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   7.9e-08   2.5e-05      24     139 ..     226     331 ..     198     332 .. 0.76
   2 !   21.6   0.0   7.3e-07   0.00023      24     138 ..     498     603 ..     490     606 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 7.9e-08
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.aesaeleawre 99 
                                       p  vll+G++G+GK+ ++++++++  ++   f++    +      +s +      e+ lr++ +e ++sa    + +
  gi|330507349|ref|YP_004383777.1| 226 PKGVLLYGPPGTGKTLIAKAVANESGAN---FISIAGPEI-----MSKYYGES--EQRLREIFEEaQKSAPSIIFID 292
                                       489*******************866666...999998888.....33322222..3555555555144555666667 PP

                            AAA_16 100 kleealaavpelagaeasrllellkrllallsrderplvl 139
                                       ++++ +   +e++g+ ++r+ ++l ++++ l+++++ +v+
  gi|330507349|ref|YP_004383777.1| 293 EIDSIAPKRGEVTGEVERRVVAQLLAMMDGLKERGQ-VVV 331
                                       77777779999999999***********99999777.665 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 7.3e-07
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                       p  +ll+G++G+GK+ ++++++++ +++   f++ +  q      +s ++    + + +r++ ++a++ +++     
  gi|330507349|ref|YP_004383777.1| 498 PKGILLYGPPGTGKTMIAQAVANETNAN---FISIRGPQM-----LSKWVGES-E-KAIREIFRKARQVSPAIIFFD 564
                                       4899******************987777...999999999.....44466665.3.788888888666555555554 PP

                            AAA_16 101 leealaavpelagaea.....srllellkrllallsrderplv 138
                                        +++   +++++g ++     +r+ ++l + l+ l+  ++ +v
  gi|330507349|ref|YP_004383777.1| 565 ELDS---IAPMRGMDEggrvmERVVNQLLAELDGLEALKD-VV 603
                                       4444...445555555555887777777777777776555.44 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 !   19.1   0.1   3.2e-06   0.00099       1      80 [.     228     300 ..     228     348 .. 0.66
   2 !   23.6   0.0   1.3e-07   4.2e-05       2     135 ..     501     619 ..     500     622 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.2e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ +a+ +a   ++++  +++++ +++     +          +  ++ ++a+   ++i+++DE++
  gi|330507349|ref|YP_004383777.1| 228 GVLLYGPPGTGKTLIAKAVANESGANFISIAGPEIMSKYYGESEQ---------RLREIFEEAQksAPSIIFIDEID 295
                                       59******************************9988765433333.........33677777776778899999999 PP

                                       G--HH CS
                             AAA_5  76 raese 80 
                                        + ++
  gi|330507349|ref|YP_004383777.1| 296 SIAPK 300
                                       88764 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 1.3e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       +lL GppGtgK+++a+ +a  +n+++  + +++      ++ ++    g+ +    ++ r+ar  +++i+++DE++ 
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANETNANFISIRGPQ------MLSKWV---GESEKAIREIFRKARqvSPAIIFFDELDS 568
                                       89**************************99998......555566...4444555677777777999*******995 PP

                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkakndd..llerfrviatanpldrslnelspalr 135
                                       + +      ++ ++e  + +e   ++  a+ d+  +l+++ via++n++d     l+pal+
  gi|330507349|ref|YP_004383777.1| 569 IAP------MRGMDEGGRVMERVVNQLLAELDGleALKDVVVIAATNRPD----ILDPALL 619
                                       553......34555555555555555555555443333388888888888....6666665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       9.9   3.1e+03     166     196 ..      31      61 ..      28      73 .. 0.79
   2 !   19.0   0.0   2.1e-06   0.00067      51      97 ..     227     271 ..     220     310 .. 0.87
   3 !   23.0   0.0   1.3e-07   4.1e-05      51     108 ..     499     555 ..     489     558 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.9
                                       HHHHT--TT-EEEEETTT--EEE-SSS-SS- CS
                             TIP49 166 llkekvkegDviviekesGkvkklGrseara 196
                                       ll+ +++ gD+i ie ++ +  k+ r++ + 
  gi|330507349|ref|YP_004383777.1|  31 LLTLRLSPGDIIEIEGKRLTAAKVWRADRQD 61 
                                       66778999*******9998888888877654 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 2.1e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       ++vLl Gp+gtGkt +a a+++e g    f++++g e+ s     +e
  gi|330507349|ref|YP_004383777.1| 227 KGVLLYGPPGTGKTLIAKAVANESG--ANFISIAGPEIMSKYYGESE 271
                                       89*********************88..78*********998666655 PP

  == domain 3  score: 23.0 bits;  conditional E-value: 1.3e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrksig 108
                                       +++Ll Gp+gtGkt +a a+++e +    f+++ g ++ s  v  +e ++ + +rk+ +
  gi|330507349|ref|YP_004383777.1| 499 KGILLYGPPGTGKTMIAQAVANETN--ANFISIRGPQMLSKWVGESEkAIREIFRKARQ 555
                                       89********************987..78**************99985788999*9865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00021     0.067       8      29 ..     229     250 ..     224     265 .. 0.84
   2 ?    7.5   0.0     0.015       4.8      73     135 ..     269     339 ..     260     341 .. 0.74
   3 ?   -0.0   0.1       3.1   9.6e+02      52     111 ..     383     445 ..     365     457 .. 0.76
   4 !   16.4   0.0   2.6e-05    0.0081       8      42 ..     501     526 ..     495     538 .. 0.81
   5 ?   -1.3   0.0         8   2.5e+03      82     105 ..     546     573 ..     536     605 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00021
                            AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                       ++++G++GtGKT+ ++ ++++ 
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANES 250
                                       689***************9986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.015
                            AAA_22  73 lsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnlsrkgvqliLvGtpelrk 135
                                        s+++l+e +e+a +++    ++ iDE++ +   +         +++ +L  +++  +   q++++G ++ ++
  gi|330507349|ref|YP_004383777.1| 269 ESEQRLREIFEEAQKSAPS--IIFIDEIDSIApkRgevtgeveRRVVAQLLAMMDGLKERGQVVVIGATNREE 339
                                       6777777777777777766..**********886245566677888888888888777788888888887665 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 3.1
                            AAA_22  52 sskdllrellralglelkaerlsseellealeqalrarav...ielliiDEaqhlrs...eealee 111
                                       +++ l+ ++  ++g + +a  l +e+ ++al+++l +      i+  iiD +q +     eeal+e
  gi|330507349|ref|YP_004383777.1| 383 NLEGLADRMHGFVGADVNA--LCKEAAMKALRRYLPDLTSedeIPQEIIDQMQVM-GadfEEALKE 445
                                       5666677777777888888..8999999999999999988999999999999999.6334444444 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 2.6e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpev 42 
                                       ++++G++GtGKT+ ++ ++++          ++ +
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANET---------NANF 526
                                       89*****************998.........4444 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 8
                            AAA_22  82 leqalrarav..ielliiDEaqhlr..s 105
                                       +++ +r+++   ++++  DE + +   +
  gi|330507349|ref|YP_004383777.1| 546 IREIFRKARQvsPAIIFFDELDSIApmR 573
                                       4555555555677999999999986441 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0     5e-07   0.00016       5     102 ..     229     336 ..     226     357 .. 0.78
   2 !   14.5   0.0   8.6e-05     0.027       5      76 ..     501     569 ..     498     604 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5e-07
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT ++k +++e+     +++ i+  +   k + ++e+ l++i+e+++++  +++f+DEi  +     
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANESG---ANFISIAGPEIMSKYYGESEQRLREIFEEAQKSAPSIIFIDEIDSIapkrg 302
                                       7899***************9999...99999999999998888777666666666566699*********9988888 PP

                            AAA_14  77 .......pewekalkslvd.egknldvivtGSns 102
                                              +++   l  ++d  +++++v+v G  +
  gi|330507349|ref|YP_004383777.1| 303 evtgeveRRVVAQLLAMMDgLKERGQVVVIGATN 336
                                       8888777666666666666433567888887765 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 8.6e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT++++ +++e      +++ i   +   k   ++ek +++i++k+++    ++f+DE   +
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANETN---ANFISIRGPQMLSKWVGESEKAIREIFRKARQVSPAIIFFDELDSI 569
                                       7899**********999998877...8999999999888887777777777777755557899*****9877 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.7e-05    0.0054       1      44 [.     229     270 ..     229     332 .. 0.82
   2 !   17.6   0.0   1.4e-05    0.0043       1      66 [.     501     595 ..     501     614 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44 
                                       +ll G+pG+GKt +ak+++++   g n +++a  + ++ ++ + 
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANES--GANFISIAGPEIMSKYYGES 270
                                       799***************9998..99999999888887776665 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.4e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvakenglllevdpe...........alde 48 
                                       Ill G+pG+GKt +a+++++++ ++                    +r+++++ + + +   +             de
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANETnANfisirgpqmlskwvgesEKAIREIFRKARQVSPAIIFfdeldsiapmrGMDE 577
                                       99****************99984336766666666666666544444444444444444333343444444444455 PP

                            AAA_18  49 skrldedkldklldalee 66 
                                         r+ e ++++ll +l++
  gi|330507349|ref|YP_004383777.1| 578 GGRVMERVVNQLLAELDG 595
                                       555555555555555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.8e-06   0.00057       2      81 ..     229     338 ..     229     362 .. 0.78
   2 !   14.6   0.0   8.8e-05     0.028       2      46 ..     501     547 ..     501     628 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.8e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       vll G+pG+GK+  a+ ++++ g  ++ ++ ++++++++g+ +q+++                              
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANESGanFISIAGPEIMSKYYGESEQRLReifeeaqksapsiifideidsiapkrgeVT 305
                                       7899*******************999999***********9888888777777777778888888877777666433 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatnls 81 
                                        +v+ r+ ++l ++ +   ++g+ v++ atn++
  gi|330507349|ref|YP_004383777.1| 306 GEVERRVVAQLLAMMDGLKERGQVVVIGATNRE 338
                                       446666666777777766666666777777776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 8.8e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                                       +ll G+pG+GK+  a+ +++++   ++ ++ ++++++ +g+ ++ ++
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANETNanFISIRGPQMLSKWVGESEKAIR 547
                                       6789***************9999888889999988888876665554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00015     0.048      25      43 ..     229     247 ..     225     304 .. 0.93
   2 !   15.4   0.0   2.8e-05    0.0089      25      43 ..     501     519 ..     494     530 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt++ak+++
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVA 247
                                       89*************9875 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.8e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKtm+a++++
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVA 519
                                       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 !   13.5   0.0   0.00014     0.044      47      71 ..     226     250 ..     213     294 .. 0.88
   2 !   14.6   0.0   6.5e-05      0.02      48      74 ..     499     525 ..     490     565 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00014
                         IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                        ++++l Gp+G+GK+ +a a++ e 
  gi|330507349|ref|YP_004383777.1| 226 PKGVLLYGPPGTGKTLIAKAVANES 250
                                       6789****************99876 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.5e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavra 74 
                                       ++i+l Gp+G+GK+ +a a++ e+ ++
  gi|330507349|ref|YP_004383777.1| 499 KGILLYGPPGTGKTMIAQAVANETNAN 525
                                       689*****************9987655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0091       2.9      36      51 ..     229     244 ..     223     252 .. 0.87
   2 ?    1.7   0.0      0.52   1.6e+02     129     176 ..     273     320 ..     253     337 .. 0.68
   3 !   16.1   0.0   2.1e-05    0.0065      12     146 ..     477     602 ..     470     605 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0091
                            AAA_25  36 allaGapgtGKttlal 51 
                                       +ll+G+pgtGKt +a 
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAK 244
                                       69**********9985 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.52
                            AAA_25 129 dvdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                        ++++ +++++   +  + iD ++++ +   +   +v +++v++l  + 
  gi|330507349|ref|YP_004383777.1| 273 RLREIFEEAQK-SAPSIIFIDEIDSIAPKRGEVTGEVeRRVVAQLLAMM 320
                                       56677888888.5599999999999999955555554455555444332 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 2.1e-05
                            AAA_25  12 vadlaapppprrwlvk.gllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelr 87 
                                       ++ +++p++++++  k g++p  + +ll+G+pgtGKt++a  +a ++    ++  ++ p+    ++   E +  e+ 
  gi|330507349|ref|YP_004383777.1| 477 IESIEWPIKQPEKFQKmGIRP-PKGILLYGPPGTGKTMIAQAVANETN--ANFISIRGPQMLSKWVGESEKAIREIF 550
                                       555667777777777756655.55589************987776655..466666677888888888888887888 PP

                            AAA_25  88 rRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlv 146
                                       r++r+v  a+      ++  l++    p++ +d gg + +++v++l a+++  e ++ v
  gi|330507349|ref|YP_004383777.1| 551 RKARQVSPAI-----IFFDELDSI--APMRGMDEGGRVMERVVNQLLAELDGLEALKDV 602
                                       8888777666.....555555443..566778888888889999999888887764433 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00019     0.058      30      58 ..     223     251 ..     214     296 .. 0.84
   2 !   13.8   0.0   9.7e-05      0.03      33      63 ..     498     527 ..     488     537 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00019
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkld 58 
                                       ++  k vll+Gp GtGKt+i+k + ++  
  gi|330507349|ref|YP_004383777.1| 223 IEPPKGVLLYGPPGTGKTLIAKAVANESG 251
                                       666789****************9888766 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 9.7e-05
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldkekyl 63 
                                        k +ll+Gp GtGKt+i++ + ++ +  +++
  gi|330507349|ref|YP_004383777.1| 498 PKGILLYGPPGTGKTMIAQAVANETN-ANFI 527
                                       6789****************999988.5554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00046      0.14      23      55 ..     227     256 ..     219     342 .. 0.84
   2 !   11.6   0.0   0.00053      0.17      20      47 ..     496     523 ..     479     537 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00046
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEE CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfva 55 
                                         vl+ G  GtGK+l+a+a+ ++s    ++f++
  gi|330507349|ref|YP_004383777.1| 227 KGVLLYGPPGTGKTLIAKAVANESG---ANFIS 256
                                       569****************998775...45555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00053
                                       TSSS-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheask 47 
                                       + +  +l+ G  GtGK+++a+a+ ++++
  gi|330507349|ref|YP_004383777.1| 496 RPPKGILLYGPPGTGKTMIAQAVANETN 523
                                       455789****************987655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00042      0.13      14      51 ..     224     259 ..     216     282 .. 0.89
   2 !   13.2   0.0   0.00013      0.04      14      51 ..     496     531 ..     486     536 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00042
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       e Pk +ll G pG GK+ +a+++++e   + n++ + +
  gi|330507349|ref|YP_004383777.1| 224 EPPKGVLLYGPPGTGKTLIAKAVANES--GANFISIAG 259
                                       67999*********************8..899998865 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00013
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       + Pk ill G pG GK+ +a+++++e+  + n++ + +
  gi|330507349|ref|YP_004383777.1| 496 RPPKGILLYGPPGTGKTMIAQAVANET--NANFISIRG 531
                                       56999*********************9..999998865 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1     0.001      0.33      11      38 ..     217     245 ..     215     262 .. 0.83
   2 ?    3.7   0.0      0.11        35     110     156 ..     273     328 ..     258     343 .. 0.63
   3 ?    2.8   0.1       0.2        62      57      80 ..     422     445 ..     418     482 .. 0.76
   4 !   10.0   0.1    0.0012      0.39      13      38 ..     492     517 ..     480     526 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.001
                            ATPase  11 il.kgGipegrvvlitGepGtGKtifalq 38 
                                       i+ k Gi   + vl++G pGtGKt++a+ 
  gi|330507349|ref|YP_004383777.1| 217 IFqKLGIEPPKGVLLYGPPGTGKTLIAKA 245
                                       555668888899**************985 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                            ATPase 110 elaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvl...kklgv 156
                                       +l+e+ +e +    + + iD i+++     e + +v R+ + ql+ ++   k++g+
  gi|330507349|ref|YP_004383777.1| 273 RLREIFEEAQKsapSIIFIDEIDSIapkRGEVTGEVERRVVAQLLAMMdglKERGQ 328
                                       4444444444333366677766666322566777889*******999943344444 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.2
                            ATPase  57 eepaedlrenakslGwdlekleee 80 
                                       +e +++++ +++ +G d+e+  +e
  gi|330507349|ref|YP_004383777.1| 422 DEIPQEIIDQMQVMGADFEEALKE 445
                                       7889***************98887 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0012
                            ATPase  13 kgGipegrvvlitGepGtGKtifalq 38 
                                       k Gi   + +l++G pGtGKt++a+ 
  gi|330507349|ref|YP_004383777.1| 492 KMGIRPPKGILLYGPPGTGKTMIAQA 517
                                       679999999*************9985 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      23 ..     229     249 ..     226     304 .. 0.69
   2 !   12.3   0.0   0.00033       0.1       5      22 ..     501     518 ..     498     531 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00036
                            AAA_24   5 iliyGpsgiGKTtlakel..g 23 
                                       +l+yGp+g+GKT +ak    +
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVanE 249
                                       89*************988441 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00033
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       il+yGp+g+GKT++a   
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAV 518
                                       89***********99877 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   8.4e-05     0.027       2      46 ..     229     278 ..     228     298 .. 0.69
   2 !   10.4   0.0    0.0019      0.59       2      23 ..     501     523 ..     500     560 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.4e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvv....pEaareileeklakgedal 46 
                                       + + G+++tGKT +++a a++ g + +    pE++ +++ e  ++ +++ 
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANEsGANFIsiagPEIMSKYYGESEQRLREIF 278
                                       6799***************8776665511256666665555544444433 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0019
                            AAA_28   2 ivitGgestGKTtlleaLaar.g 23 
                                       i + G+++tGKT +++a a++ +
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANEtN 523
                                       7899***************6543 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00064       0.2       1      26 [.     229     254 ..     229     296 .. 0.78
   2 !   12.8   0.0   0.00038      0.12       1      26 [.     501     526 ..     501     566 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00064
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       ++lyGp+g+GK+++ak +a++   ++
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANESGANF 254
                                       689**************887765444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00038
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       i+lyGp+g+GK+++a+ +a++   ++
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANETNANF 526
                                       789**************999877655 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    0.0007      0.22     117     137 ..     229     249 ..     223     252 .. 0.90
   2 !   12.5   0.0   0.00018     0.057     117     137 ..     501     521 ..     490     526 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0007
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v++yGp+ tGkt +a+a a+ 
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANE 249
                                       89***************9985 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00018
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       +++yGp+ tGkt++a+a a+ 
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANE 521
                                       89***************9985 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00072      0.23      19      59 ..     226     266 ..     201     277 .. 0.75
   2 !   10.8   0.0    0.0012      0.37      19      48 ..     498     529 ..     463     534 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00072
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEE CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeY 59 
                                        + +lL+G+ G+GKT +++++a++ g +  ++  P   ++++Y
  gi|330507349|ref|YP_004383777.1| 226 PKGVLLYGPPGTGKTLIAKAVANESGANfiSIAGP--EIMSKY 266
                                       4459********************99986666666..566655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0012
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..-- CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..ev 48 
                                        + ilL+G+ G+GKT++++++a++ + +  ++
  gi|330507349|ref|YP_004383777.1| 498 PKGILLYGPPGTGKTMIAQAVANETNANfiSI 529
                                       2359******************9987765555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0036       1.1       1      26 [.     232     257 ..     232     313 .. 0.79
   2 !   10.7   0.0    0.0017      0.54       1      48 [.     504     552 ..     504     592 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0036
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                       +G+PG GK+ +++ ++ + g  ++s 
  gi|330507349|ref|YP_004383777.1| 232 YGPPGTGKTLIAKAVANESGANFISI 257
                                       7******************9999985 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0017
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCT CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrk 48 
                                       +G+PG GK+ +++ ++ + +  ++s  G  + +    ++ +  r+ +rk
  gi|330507349|ref|YP_004383777.1| 504 YGPPGTGKTMIAQAVANETNANFISIrGPQMLSKWVGESEKAIREIFRK 552
                                       7******************999998766666655554444445555555 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       6      67 ..     221     280 ..     219     332 .. 0.76
   2 !   12.0   0.0   0.00069      0.22       7      99 ..     494     600 ..     491     609 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0042
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                       l +++ + v + G+ G+GK+ ++k++a+++   +  i + g ++ ++   +++++++ +++e
  gi|330507349|ref|YP_004383777.1| 221 LGIEPPKGVLLYGPPGTGKTLIAKAVANESG--ANFISIAGPEIMSKYYGESEQRLREIFEE 280
                                       6778888999****************99975..45566666666666666666666666665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00069
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx... RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren... 79 
                                        +++ + + + G+ G+GK+ +++++a++++  +  i ++g ++ ++   +++k i+ ++ +  q+ p +   ++   
  gi|330507349|ref|YP_004383777.1| 494 GIRPPKGILLYGPPGTGKTMIAQAVANETN--ANFISIRGPQMLSKWVGESEKAIREIFRKaRQVSPAIIFFDElds 568
                                       5666677899******************97..688889999999999999999999999997888888877666788 PP

                                       ............HHHTCHHHHHHHSTTGGTTC CS
                                       ............xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ............esdeeiekalsklglkelkd 99 
                                                    +++ ++++l++l+  e  +
  gi|330507349|ref|YP_004383777.1| 569 iapmrgmdeggrVMERVVNQLLAELDGLEALK 600
                                       88887777666666666666666666555555 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 !    9.5   0.0    0.0027      0.85       2      30 ..     229     257 ..     228     312 .. 0.84
   2 !   11.2   0.0   0.00082      0.26       2      31 ..     501     530 ..     500     612 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0027
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG++ktl++ka+a+  +++f  i
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANESGANFISI 257
                                       7999****************999998766 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00082
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       +ll g PG++kt++++a+a+  +++f  i+
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANETNANFISIR 530
                                       7999********************998775 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0012      0.39      52     115 ..     225     293 ..     216     341 .. 0.71
   2 !   10.1   0.0     0.001      0.32      51      83 ..     496     528 ..     445     615 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDD 115
                                       p + vLL+G  GtGK  + ka+ ne  ++ + +   e+  +   e ++ ++++    +++   i+f+D 
  gi|330507349|ref|YP_004383777.1| 225 PPKGVLLYGPPGTGKTLIAKAVANESGANFISIAgpEIMSKYYGESEQRLREIFeeaQKSAPSIIFIDE 293
                                       56789*******************999888666433565554444333333332011222335677765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.001
                            DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegLr 83 
                                       +p + +LL+G  GtGK  + +a+ ne++++ + 
  gi|330507349|ref|YP_004383777.1| 496 RPPKGILLYGPPGTGKTMIAQAVANETNANFIS 528
                                       57789*********************9998743 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 !    9.7   0.0    0.0023      0.73      15     119 ..     221     329 ..     215     333 .. 0.52
   2 ?    5.6   0.0     0.043        13      23      44 ..     501     522 ..     484     530 .. 0.80
   3 ?    2.2   0.0      0.46   1.4e+02     107     136 ..     543     576 ..     533     610 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0023
                          ATPase_2  15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie......eeeekkklekal... 82 
                                       l  ep + +++YGp g GKt + k +++++   ++     ia  e+ ++++ e+ +      e        +a    
  gi|330507349|ref|YP_004383777.1| 221 LGIEPPKGVLLYGPPGTGKTLIAKAVANES-GANF---ISIAGPEIMSKYYGESEQrlreifE--------EAQksa 285
                                       5567778899**********8888877777.3333...3344444555555544112222211........111222 PP

                          ATPase_2  83 ........giavpkaeleeilkeksklvfkaielllekikkkgkk 119
                                                 +    +  e+  e  + v +++ ++++ +k++g+ 
  gi|330507349|ref|YP_004383777.1| 286 psiifideI-DSIAPKRGEVTGEVERRVVAQLLAMMDGLKERGQV 329
                                       223344432.22222223455566666666666666677766654 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.043
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienl 44 
                                       +++YGp g GKt + + ++++ 
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANET 522
                                       789*********8887777765 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.46
                          ATPase_2 107 elllekikkkgkk...iiiiiDelqklidl.gln 136
                                       e+++++i +k+++    ii++Del  +  + g++
  gi|330507349|ref|YP_004383777.1| 543 EKAIREIFRKARQvspAIIFFDELDSIAPMrGMD 576
                                       567778888888888678899***9998653344 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0    0.0008      0.25      24      81 ..     229     297 ..     224     305 .. 0.66
   2 !    8.0   0.0    0.0094         3      24      48 ..     501     525 ..     496     575 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0008
                                       EEEEEETT--HHHHHHCC--TTS-E.E--SSTTHHHH-H.......HHHHHHT...TTSEEEEEE-TT- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw.leifvverlaklp.......ldlleqa...kggtLylkdiadl 81 
                                       v+l G++G+gk+l+A++ +++sg + ++i+  e  +k          +++e+a    + ++++ +i+++
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANESGANfISIAGPEIMSKYYgeseqrlREIFEEAqksAPSIIFIDEIDSI 297
                                       9*******************9987523333333333211222334466666654337778888888776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0094
                                       EEEEEETT--HHHHHHCC--TTS-E CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw 48 
                                       ++l G++G+gk+++A++ +++   +
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANETNAN 525
                                       799**************99876552 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.5   1.7e+03     135     156 ..     200     221 ..     195     222 .. 0.86
   2 !    8.2   0.1    0.0046       1.4       5      32 ..     230     257 ..     226     259 .. 0.92
   3 !    9.6   0.0    0.0018      0.56       5      38 ..     502     535 ..     499     557 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.5
                               IPT 135 akkRvrqmlrpeeegaslldEl 156
                                         +Rvr+m++   +++ +++ l
  gi|330507349|ref|YP_004383777.1| 200 EVQRVREMIELPMKHPEIFQKL 221
                                       679********99999998876 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0046
                               IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                       l++G+ +tGKt  a ++a+e ga  i++
  gi|330507349|ref|YP_004383777.1| 230 LLYGPPGTGKTLIAKAVANESGANFISI 257
                                       89*********************99875 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0018
                               IPT   5 lifGatttGKtaeaiklaketgapvivlDRvqcy 38 
                                       l++G+ +tGKt  a ++a+et a  i++   q  
  gi|330507349|ref|YP_004383777.1| 502 LLYGPPGTGKTMIAQAVANETNANFISIRGPQML 535
                                       89*********************99998666655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0     0.001      0.31       4      50 ..     229     269 ..     226     307 .. 0.67
   2 !    8.8   0.0    0.0027      0.85       4      25 ..     501     522 ..     498     558 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrea 50 
                                       vl  G +GtGKt+++ ++++e         a+++s  +p+++ +++ +
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANES-------GANFISIAGPEIMsKYYGE 269
                                       6789*************99998.......4555555554443134444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0027
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       +l  G +GtGKt+++ ++++e 
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANET 522
                                       6789**************9998 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0     0.006       1.9      19      39 ..     228     248 ..     214     287 .. 0.81
   2 !   10.4   0.0    0.0013      0.42      19      58 ..     500     535 ..     478     559 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.006
                            AAA_11  19 itliqGPPGtgKTktivells 39 
                                        +l+ GPPGtgKT    ++ +
  gi|330507349|ref|YP_004383777.1| 228 GVLLYGPPGTGKTLIAKAVAN 248
                                       4799*********76655555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0013
                            AAA_11  19 itliqGPPGtgKTktivellsqllsrrkseeeksakpriL 58 
                                         l+ GPPGtgKT    ++ ++ + +        ++p++L
  gi|330507349|ref|YP_004383777.1| 500 GILLYGPPGTGKTMIAQAVANETNAN----FISIRGPQML 535
                                       4699*********9999888888432....2333444443 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0026      0.81      22      41 ..     229     248 ..     220     254 .. 0.87
   2 !    8.7   0.0    0.0034       1.1      23      42 ..     502     521 ..     486     529 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0026
                                       EEEE--TTSSTTHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalav 41 
                                       v   Gp GtGKt++a a+a 
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVAN 248
                                       6789***********99985 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0034
                                       EEE--TTSSTTHHHHHHHHH CS
                              PhoH  23 faiGpaGtGKtylavalave 42 
                                          Gp GtGKt++a a+a e
  gi|330507349|ref|YP_004383777.1| 502 LLYGPPGTGKTMIAQAVANE 521
                                       678***********999865 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0026      0.82      22      44 ..     228     250 ..     213     270 .. 0.83
   2 !    8.8   0.0    0.0027      0.84      23      44 ..     501     522 ..     491     562 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
                                       EEEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnks 44 
                                        v l+G +G GKt +ak + n+s
  gi|330507349|ref|YP_004383777.1| 228 GVLLYGPPGTGKTLIAKAVANES 250
                                       4889***************9984 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0027
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       + l+G +G GKt +a+ + n+ 
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANET 522
                                       679***************9983 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.4    0.0074       2.3      11      32 ..     227     248 ..     222     298 .. 0.84
   2 !    9.6   0.0    0.0035       1.1      11      33 ..     499     521 ..     491     556 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0074
                            AAA_19  11 kvllvtaGpGtGKTrvlkhiva 32 
                                       k +l+ ++pGtGKT + k++ +
  gi|330507349|ref|YP_004383777.1| 227 KGVLLYGPPGTGKTLIAKAVAN 248
                                       56899*********99887765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0035
                            AAA_19  11 kvllvtaGpGtGKTrvlkhival 33 
                                       k +l+ ++pGtGKT + +++ ++
  gi|330507349|ref|YP_004383777.1| 499 KGILLYGPPGTGKTMIAQAVANE 521
                                       6689**********998877665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.036        11      34      58 ..     225     249 ..     208     257 .. 0.82
   2 ?   -0.6   0.0       2.3   7.3e+02     115     133 ..     281     299 ..     260     352 .. 0.65
   3 !    8.7   0.0    0.0034       1.1      35      60 ..     498     523 ..     473     530 .. 0.79
   4 ?   -1.6   0.0       4.9   1.5e+03     107     132 ..     545     570 ..     528     589 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.036
                              TniB  34 rmpnlllvGdsnnGKtmivekFarl 58 
                                        ++ +ll+G++ +GKt i++  a++
  gi|330507349|ref|YP_004383777.1| 225 PPKGVLLYGPPGTGKTLIAKAVANE 249
                                       56789*************9987765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.3
                              TniB 115 lrelkvrvLiiDEihnlla 133
                                        ++  + ++ iDEi+++  
  gi|330507349|ref|YP_004383777.1| 281 AQKSAPSIIFIDEIDSIAP 299
                                       3455678999****99863 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0034
                              TniB  35 mpnlllvGdsnnGKtmivekFarlhp 60 
                                       ++ +ll+G++ +GKtmi++  a++ +
  gi|330507349|ref|YP_004383777.1| 498 PKGILLYGPPGTGKTMIAQAVANETN 523
                                       3689**************98887665 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 4.9
                              TniB 107 leqqvlrllrelkvrvLiiDEihnll 132
                                       + +++ r  r++++ ++ +DE++++ 
  gi|330507349|ref|YP_004383777.1| 545 AIREIFRKARQVSPAIIFFDELDSIA 570
                                       44555666789999********9985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.2    0.0045       1.4      21      40 ..     229     248 ..     217     343 .. 0.83
   2 !    8.6   0.0    0.0044       1.4      22      42 ..     502     522 ..     485     531 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0045
                            AAA_30  21 avltGpAGtGKttalkalre 40 
                                       ++l Gp+GtGKt + ka+++
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVAN 248
                                       6789*********9999865 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0044
                            AAA_30  22 vltGpAGtGKttalkalreaw 42 
                                       +l Gp+GtGKt++ +a+++  
  gi|330507349|ref|YP_004383777.1| 502 LLYGPPGTGKTMIAQAVANET 522
                                       788**********99997655 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0056       1.8      37     190 ..     229     382 ..     224     412 .. 0.68
   2 !    8.2   0.0    0.0066       2.1      37      66 ..     501     530 ..     495     649 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0056
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagk 112
                                       +++yg+ G Gkt + ka++ne  +n+     + + + e +++     +++  e f e  + +  ++ iD+i  +a k
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANESGANF-----ISIAGPEIMSKYYGESEQRLREIFEEAQKsAPSIIFIDEIDSIAPK 300
                                       79**********99999998765554.....5677888888888877787788888877724468889999999988 PP

                                       H.........HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHH CS
                          Bac_DnaA 113 e.........ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkie 180
                                                 ++  +l+ +++ l e g+ vv+ +    ++++    r   rf++   +++  pd+e r++il+  i+
  gi|330507349|ref|YP_004383777.1| 301 RgevtgeverRVVAQLLAMMDGLKERGQVVVIGATNREEAIDPA-LRRPGRFDRE--IEVGVPDREGRIEILQ--IH 372
                                       62222211112334566677777777777777776666555443.3335677764..5666689999999986..44 PP

                                       HTT----TTH CS
                          Bac_DnaA 181 aeklevpeev 190
                                       ++++ v ++v
  gi|330507349|ref|YP_004383777.1| 373 MHSMPVADDV 382
                                       5555555554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0066
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelr 66 
                                       +++yg+ G Gkt + +a++ne+ +n+ + r
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANETNANFISIR 530
                                       79*******************999887665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.041        13       3      22 ..     229     248 ..     227     253 .. 0.89
   2 ?   -1.6   0.0       7.2   2.3e+03      62     108 ..     267     316 ..     261     347 .. 0.70
   3 !    9.8   0.0    0.0022      0.69       3      23 ..     501     521 ..     499     526 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.041
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       v+l G++G GKT  ++ +a 
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVAN 248
                                       799************99986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.2
                                       CTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............. CS
                             NACHT  62 lpepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtl 108
                                       + e++++ +e++++ ++ + ++ + +D +D ++ + g+     e++ v +l
  gi|330507349|ref|YP_004383777.1| 267 YGESEQRLREIFEEAQKSAPSIIF-IDEIDSIAPKRGEvtgeVERRVVAQL 316
                                       566777777777777777777766.58888888877776654444444444 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0022
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++l G++G GKT+ +q +a +
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANE 521
                                       7899************99976 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0014      0.45       8      53 ..     235     283 ..     231     333 .. 0.77
   2 ?    5.4   0.0     0.059        18       8      54 ..     507     554 ..     501     593 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0014
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevde..r 53 
                                        G+g++ i++a+A++ g +f++ + +e ++k  g se+ + e ++e  +
  gi|330507349|ref|YP_004383777.1| 235 PGTGKTLIAKAVANESGANFISIAGPEIMSKYYGESEQRLrEIFEEaqK 283
                                       59*************************************9666676421 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.059
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevders 54 
                                        G+g++ i++a+A++ + +f++ + +++++k  g se+ + e + +++
  gi|330507349|ref|YP_004383777.1| 507 PGTGKTMIAQAVANETNANFISIRGPQMLSKWVGESEKAIrEIFRKAR 554
                                       69*******************************999999955555544 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 ?    5.2   0.0     0.045        14      18      65 ..     230     283 ..     227     338 .. 0.74
   2 !   10.1   0.0    0.0015      0.46      18      78 ..     502     608 ..     498     618 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.045
                                       EEEESTTSSHHHHHHHHHHHSSTS.....S.EEEEEEESEEHHHHHHHHHHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd.....d.aiiyvgiGergnevaevleefpe 65 
                                       l+ g  g+Gkt i+++++++s ++        i     Ge ++ ++e++ee ++
  gi|330507349|ref|YP_004383777.1| 230 LLYGPPGTGKTLIAKAVANESGANfisiaGpEIMSKYYGESEQRLREIFEEAQK 283
                                       678999**************9777444442244444588888888888888877 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0015
                                       EEEESTTSSHHHHHHHHHHHSSTSSEEEEEE...........................................ESE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........................................xxx RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsddaiiyvg...........................................iGe 51 
                                       l+ g  g+Gkt+i+q++++++n++  i + g                                           + e
  gi|330507349|ref|YP_004383777.1| 502 LLYGPPGTGKTMIAQAVANETNAN-FISIRGpqmlskwvgesekaireifrkarqvspaiiffdeldsiapmrgMDE 577
                                       678999**************9888.4434446888888777777777777777777777777777777777777667 PP

                                       EHHHHHHHHHHCHH....SSGGGGEEEEEEE CS
                                       xxxxxxxxxxxxxx....xxxxxxxxxxxxx RF
                       ATP-synt_ab  52 rgnevaevleefpe....gtimkrtvlvant 78 
                                        g+ +++v++++       +++k +v++a+t
  gi|330507349|ref|YP_004383777.1| 578 GGRVMERVVNQLLAeldgLEALKDVVVIAAT 608
                                       7777777666666644323377777777766 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.021       6.7      48      79 ..     229     260 ..     218     288 .. 0.80
   2 ?   -0.1   0.0       2.4   7.5e+02     140     178 ..     261     297 ..     255     301 .. 0.78
   3 !    8.0   0.0     0.008       2.5      45     112 ..     498     566 ..     482     581 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.021
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnp 79 
                                       +L+ GP+G gk+ + k ++ e g +++    p
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANESGANFISIAGP 260
                                       6899******************9998876665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.4
                             Rad17 140 dlPnkfyrds.dalrevirkylrssealplilviteiesl 178
                                       ++ +k+y++s ++lre+  ++ +s  +   i+ i ei+s+
  gi|330507349|ref|YP_004383777.1| 261 EIMSKYYGESeQRLREIFEEAQKSAPS---IIFIDEIDSI 297
                                       567899999889999999998776655...7778888875 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.008
                             Rad17  45 kriLLisGPsGCgkstvvkvLskelgiklrewlnpvslke.pdnqksdfkgltekesrflsqiesfkel 112
                                        + +L+ GP+G gk+ + + ++ e   +++    p  l +     ++ ++ ++ k  +  + i  f el
  gi|330507349|ref|YP_004383777.1| 498 PKGILLYGPPGTGKTMIAQAVANETNANFISIRGPQMLSKwVGESEKAIREIFRKARQVSPAIIFFDEL 566
                                       4556889******************99999998887765414457777888888888888888888777 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1      0.01       3.2       4      28 ..     232     256 ..     229     259 .. 0.90
   2 !    7.7   0.0    0.0085       2.7       3      28 ..     503     528 ..     501     530 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.01
                                       E-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyld 28 
                                        GP g+GK  +a+a+a++ g+++++
  gi|330507349|ref|YP_004383777.1| 232 YGPPGTGKTLIAKAVANESGANFIS 256
                                       6*******************99986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0085
                                       EE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                       + GP g+GK  +a+a+a++ ++++++
  gi|330507349|ref|YP_004383777.1| 503 LYGPPGTGKTMIAQAVANETNANFIS 528
                                       67*******************99985 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.065        20       2      24 ..     229     251 ..     228     273 .. 0.81
   2 ?    1.4   0.1      0.83   2.6e+02      81     106 ..     270     296 ..     258     341 .. 0.77
   3 ?    7.5   0.0     0.011       3.4       2      32 ..     501     531 ..     500     544 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.065
                                       EEEE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellk 24 
                                       v++ GppG+GKt + k v+++  
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANESG 251
                                       6788********99999988754 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.83
                                       HHHHHHHHHHHHH.HHH-EEEE---ST CS
                          NTPase_1  81 feelalealrkal.seadviviDEiGk 106
                                        e+   e++++a+ s + +i iDEi +
  gi|330507349|ref|YP_004383777.1| 270 SEQRLREIFEEAQkSAPSIIFIDEIDS 296
                                       566777778888756667999***965 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.011
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       +++ GppG+GKt + + v+++ + + ++++G
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANETNANFISIRG 531
                                       6788****************99877777776 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 ?    4.4   0.0      0.12        38      17      45 ..     422     450 ..     414     459 .. 0.86
   2 !   10.4   0.0    0.0016       0.5      28      55 ..     690     717 ..     687     722 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.12
                            Vps4_C  17 mdipsdkllePpvtlkDflkalkkarptV 45 
                                        +ip++ + + +v   Df++alk+  p+ 
  gi|330507349|ref|YP_004383777.1| 422 DEIPQEIIDQMQVMGADFEEALKEIEPSA 450
                                       46998888999**************9995 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0016
                            Vps4_C  28 pvtlkDflkalkkarptVskeDLekhee 55 
                                        v++++  +alkk+rp+V +  L  +e+
  gi|330507349|ref|YP_004383777.1| 690 RVEMRHYREALKKVRPSVEEHMLSYYER 717
                                       589*****************99998875 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.017       5.3       1      23 [.     235     257 ..     235     285 .. 0.74
   2 ?    7.1   0.0     0.018       5.6       1      23 [.     507     529 ..     507     555 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.017
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ ++k++A++ g +fi +
  gi|330507349|ref|YP_004383777.1| 235 PGTGKTLIAKAVANESGANFISI 257
                                       69******************965 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.018
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ +++++A++ + +fi +
  gi|330507349|ref|YP_004383777.1| 507 PGTGKTMIAQAVANETNANFISI 529
                                       69******************965 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.19        59       4      30 ..     228     254 ..     226     262 .. 0.86
   2 ?    2.5   0.0      0.34   1.1e+02      74      95 ..     262     283 ..     252     301 .. 0.79
   3 ?    5.7   0.0     0.034        11       3      30 ..     499     526 ..     497     534 .. 0.87
   4 ?   -0.6   0.0       2.9   9.2e+02      76      96 ..     536     556 ..     529     564 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.19
                                       EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                        v l gp g+Gk  + ka+ +e   +f
  gi|330507349|ref|YP_004383777.1| 228 GVLLYGPPGTGKTLIAKAVANESGANF 254
                                       6899***************99998888 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.34
                                       ETTEEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  74 fsgnlygtsveaieevlekgki 95 
                                         +++yg+s +  +e++e++++
  gi|330507349|ref|YP_004383777.1| 262 IMSKYYGESEQRLREIFEEAQK 283
                                       6789**************9876 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.034
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       + + l gp g+Gk ++ +a+ +e + +f
  gi|330507349|ref|YP_004383777.1| 499 KGILLYGPPGTGKTMIAQAVANETNANF 526
                                       56899***************99998888 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.9
                                       TEEEEEEHHHHHHHHHTTSEE CS
                     Guanylate_kin  76 gnlygtsveaieevlekgkiv 96 
                                       ++  g+s +ai+e++ k+++v
  gi|330507349|ref|YP_004383777.1| 536 SKWVGESEKAIREIFRKARQV 556
                                       56789************9986 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.067        21      17      45 ..     219     247 ..     200     254 .. 0.78
   2 ?    7.7   0.0      0.01       3.2      12      49 ..     477     523 ..     469     531 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.067
                                       ......TTSEEEEEESTTSTHHHHHHHHH CS
                            ResIII  17 eklkskrdkrglikmaTGtGKTlvaakli 45 
                                       +kl ++  k +l+  + GtGKTl+a +++
  gi|330507349|ref|YP_004383777.1| 219 QKLGIEPPKGVLLYGPPGTGKTLIAKAVA 247
                                       45555778899999**********96655 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.01
                                       HHHHT...............TTSEEEEEESTTSTHHHHHHHHHHHH- CS
                            ResIII  12 ienlleklks.........krdkrglikmaTGtGKTlvaaklierll 49 
                                       ie+++  +k+         +  k +l+  + GtGKT++a +++ +  
  gi|330507349|ref|YP_004383777.1| 477 IESIEWPIKQpekfqkmgiRPPKGILLYGPPGTGKTMIAQAVANETN 523
                                       55555333334444446657778999*************88877655 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.042        13      58      78 ..     222     242 ..     200     250 .. 0.84
   2 ?    6.4   0.0     0.011       3.5      58      79 ..     494     515 ..     471     523 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.042
                       AFG1_ATPase  58 svepvrglYlwGgvGrGKtyl 78 
                                         ep++g+ l+G+ G GKt +
  gi|330507349|ref|YP_004383777.1| 222 GIEPPKGVLLYGPPGTGKTLI 242
                                       468****************76 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                       AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                         +p++g+ l+G+ G GKt++ 
  gi|330507349|ref|YP_004383777.1| 494 GIRPPKGILLYGPPGTGKTMIA 515
                                       4679****************85 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.077        24       2      30 ..     229     257 ..     228     289 .. 0.87
   2 ?    6.6   0.0     0.026       8.3       2      30 ..     501     529 ..     500     534 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.077
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       +++ G+P +GKt +a ++a + +a +++i
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANESGANFISI 257
                                       5789********************99998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.026
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       i++ G+P +GKt +a ++a + +a +++i
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANETNANFISI 529
                                       7889********************99998 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.074        23      21      38 ..     226     242 ..     217     248 .. 0.75
   2 ?    6.1   0.0     0.029       9.1      19      42 ..     495     518 ..     477     520 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.074
                            AAA_29  21 lkgatlltGpsGsGKSTl 38 
                                       +kg +ll Gp G+GK+ +
  gi|330507349|ref|YP_004383777.1| 226 PKG-VLLYGPPGTGKTLI 242
                                       356.9**********866 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.029
                            AAA_29  19 idlkgatlltGpsGsGKSTllDAi 42 
                                       i++   +ll Gp G+GK+ +  A+
  gi|330507349|ref|YP_004383777.1| 495 IRPPKGILLYGPPGTGKTMIAQAV 518
                                       4443349**********9886665 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 ?    2.6   0.0      0.18        57     130     152 ..     227     249 ..     173     258 .. 0.78
   2 ?    7.5   0.0    0.0058       1.8     120     156 ..     489     525 ..     427     531 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.18
                             T2SSE 130 glilvsGgTgsGKttllyallke 152
                                       + +l+ G+ g+GKt ++ a+ +e
  gi|330507349|ref|YP_004383777.1| 227 KGVLLYGPPGTGKTLIAKAVANE 249
                                       568999*********99998766 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0058
                             T2SSE 120 evlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                       ++ +  +r  + il+ G+ g+GKt ++ a+ +e n++
  gi|330507349|ref|YP_004383777.1| 489 KFQKMGIRPPKGILLYGPPGTGKTMIAQAVANETNAN 525
                                       444455555788*****************99998875 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.24        77      60      89 ..     229     257 ..     220     264 .. 0.83
   2 ?    5.7   0.0     0.022       6.8      51      90 ..     492     530 ..     482     536 .. 0.79
   3 ?   -0.9   0.0       2.3   7.1e+02       6      45 ..     573     612 ..     569     662 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.24
                                       EEEEESSTSTHHHHHHHHHHHSSSEEEEES CS
                               MCM  60 vllvgdpgtaKsqlLkyveklapravytsg 89 
                                       vll g pgt+K+ + k+v+ + + a+++s+
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVA-NESGANFISI 257
                                       89************99999.4556666665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.022
                                       SSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESS CS
                               MCM  51 ktklrgdinvllvgdpgtaKsqlLkyveklapravytsgk 90 
                                       k+ +r    +ll g pgt+K+ + ++v+ +  +a+++s++
  gi|330507349|ref|YP_004383777.1| 492 KMGIRPPKGILLYGPPGTGKTMIAQAVA-NETNANFISIR 530
                                       567888889****************999.55566677766 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.3
                                       HHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---E CS
                               MCM   6 kelakekdiieklvksiapsiyghedvkkaillqlfggvk 45 
                                       + + +  +++e++v+++  ++ g e+ k  ++++     +
  gi|330507349|ref|YP_004383777.1| 573 RGMDEGGRVMERVVNQLLAELDGLEALKDVVVIAATNRPD 612
                                       56777789999*****************999988765555 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.16        52       4      34 ..     229     259 ..     227     341 .. 0.84
   2 ?    6.3   0.0     0.025       7.7       4      33 ..     501     530 ..     499     568 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.16
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgv 34 
                                       +lL G + +GK+ +a+a+ + + + ++ ++ 
  gi|330507349|ref|YP_004383777.1| 229 VLLYGPPGTGKTLIAKAVANESGANFISIAG 259
                                       89****************9999999988875 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.025
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                       ilL G + +GK+ +a+a+ + +++ ++ + 
  gi|330507349|ref|YP_004383777.1| 501 ILLYGPPGTGKTMIAQAVANETNANFISIR 530
                                       89******************9999999876 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.41   1.3e+02       5      71 ..     233     294 ..     229     299 .. 0.66
   2 ?    6.9   0.0     0.015       4.7       4      70 ..     504     565 ..     501     570 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.41
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+ + + ++++s  ++ ++    e+ ++   +++++  + ++++++++       i+++DE+
  gi|330507349|ref|YP_004383777.1| 233 GPPGTGKTLIAKAVANESgANFISIAG-PEIMSKYYGESEQRLREIFEEAQKSA-----PSIIFIDEI 294
                                       78*******999999997755544444.45555555555555555555555544.....358888886 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.015
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                        G pG GK+ + + ++++   ++ ++r    +l++++ ++++   + ++++ +         i+++DE
  gi|330507349|ref|YP_004383777.1| 504 YGPPGTGKTMIAQAVANETnANFISIRG-PQMLSKWVGESEKAIREIFRKARQVS-----PAIIFFDE 565
                                       588***************9999999999.9******9887777777776555432.....35888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (737 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        57  (0.00317921); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              57  [number of targets reported over threshold]
# CPU time: 0.90u 0.32s 00:00:01.22 Elapsed: 00:00:00.50
# Mc/sec: 4405.02
//
Query:       gi|330507350|ref|YP_004383778.1|  [L=84]
Description: PRC-barrel domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-12   45.9   3.2    4.8e-12   45.8   3.2    1.0  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   3.2   2.7e-16   4.8e-12       1      77 [.       1      81 [.       1      83 [. 0.93

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 2.7e-16
                                      XEECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT..........-EEEEEGG.CEECCCTEEEETT CS
                               PRC  1 edefrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi.....gekevliPfdlavkigkdriivda 74
                                      ++ ++a ++ +ke++++dG+ lG +++++ +  +g+++ lvv+ + +l+      ++k+vliPf   v ++kd+i+vd+
  gi|330507350|ref|YP_004383778.1|  1 MGKVFAGSIGDKEIVNIDGTVLGDLENIIYEVMTGKLVDLVVKPNSGLDRskyreDGKFVLIPFS-SVVAVKDYIVVDE 78
                                      6678899999**********************************976555***************.************9 PP

                                      S-G CS
                               PRC 75 pke 77
                                      +++
  gi|330507350|ref|YP_004383778.1| 79 SRA 81
                                      875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 640.91
//
Query:       gi|330507351|ref|YP_004383779.1|  [L=172]
Description: peptidyl-prolyl cis-trans isomerase [Methanosaeta concilii GP6]
Scores for complete 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-53  178.8   0.1    1.1e-52  178.5   0.1    1.1  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.5   0.1   5.9e-57   1.1e-52       2     157 ..      25     169 ..      24     170 .. 0.94

  Alignments for each domain:
  == domain 1  score: 178.5 bits;  conditional E-value: 5.9e-57
                     Pro_isomerase   2 vdietsskGrivieLfadkaPktvenFlklvkegfYdgttFhRvikgfmvqgGdptgktsageqekkggesiraipd 78 
                                       v +ets +G+i+i+L++d  P+t +nFl lv++gfYdg++FhR+i+gfm+qgGdp+g++        gg   ++i+d
  gi|330507351|ref|YP_004383779.1|  25 VLLETS-MGNITIQLYSDM-PITTGNFLSLVEKGFYDGVIFHRIIDGFMIQGGDPEGTGM-------GG-PGYTIED 91 
                                       568996.**********99.**********************************999855.......33.2469*** PP

                     Pro_isomerase  79 EitsklkhkrGalamartgkepnsagsqFfItlkeaphldgkytvFGkVveGmdvvekiekvetde.erpkknvkiv 154
                                       E+t++ +++rG++ama++g  pn++gsqFfI+l ++++ld+k+ +FGkV+eGmdvv+ki+kvetd+ +rp ++v+iv
  gi|330507351|ref|YP_004383779.1|  92 EFTDNNRNDRGTIAMANAG--PNTGGSQFFINLVDNNFLDDKHPAFGKVIEGMDVVDKISKVETDSnDRPLEEVVIV 166
                                       ***999***********98..8******************************************************9 PP

                     Pro_isomerase 155 sae 157
                                       +a+
  gi|330507351|ref|YP_004383779.1| 167 RAG 169
                                       986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1270.92
//
Query:       gi|330507352|ref|YP_004383780.1|  [L=159]
Description: peptidyl-prolyl cis-trans isomerase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-53  181.8   0.1    1.1e-53  181.7   0.1    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 !  181.7   0.1   6.4e-58   1.1e-53       4     158 .]      14     157 ..      11     157 .. 0.94

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 6.4e-58
                     Pro_isomerase   4 ietsskGrivieLfadkaPktvenFlklvkegfYdgttFhRvikgfmvqgGdptgktsageqekkggesiraipdEi 80 
                                       ++ts +G+i+i+L++d  P+t++nF klv++gfYdg++FhR+i+gfm+qgGdptg+++       gg   +ai+dE+
  gi|330507352|ref|YP_004383780.1|  14 LATS-MGDITIQLYSDM-PITAGNFKKLVEKGFYDGVIFHRIIDGFMIQGGDPTGTGR-------GG-PGYAIKDEF 80 
                                       6895.**********99.*************************************965.......33.2469***** PP

                     Pro_isomerase  81 tsklkhkrGalamartgkepnsagsqFfItlkeaphldgkytvFGkVveGmdvvekiekvetde.erpkknvkivsa 156
                                       t++ k+ rG+++ma++g  pn++gsqFfI+l ++++ldgk+ +FGkV+eGmdvv+ki kv+t + +rp k+vki sa
  gi|330507352|ref|YP_004383780.1|  81 TPNSKNARGTISMANAG--PNTGGSQFFINLVDNNFLDGKHPAFGKVIEGMDVVDKIGKVQTGAmDRPAKEVKIMSA 155
                                       *999***********98..8*******************************************************99 PP

                     Pro_isomerase 157 ev 158
                                       +v
  gi|330507352|ref|YP_004383780.1| 156 KV 157
                                       86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1163.10
//
Query:       gi|330507353|ref|YP_004383781.1|  [L=142]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1002.78
//
Query:       gi|330507354|ref|YP_004383782.1|  [L=381]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-22   77.6   0.0    1.3e-21   76.3   0.0    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.4e-20   73.7   0.0    2.7e-20   72.8   0.0    1.4  1  OrfB_IS605      Probable transposase
    1.4e-18   66.1   3.6    2.6e-18   65.2   3.6    1.5  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0023   17.9   0.2      0.004   17.1   0.2    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.033   13.6   2.0       0.17   11.4   2.0    2.1  1  zf-ribbon_3     zinc-ribbon domain
       0.25   10.9   0.8        1.7    8.2   0.0    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.56    9.8   4.0         22    4.7   0.3    3.1  3  RecR            RecR protein


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 !   76.3   0.0   4.9e-25   1.3e-21       1      68 [.     291     358 ..     291     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 4.9e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++ l +  +yka  +G  v++v+p++TSk Cs+Cg  ++++ls+r+++Cp+Cg++ drD+nAaiNil+
  gi|330507354|ref|YP_004383782.1| 291 WNMLVTLTSYKAASAGSVVILVDPRNTSKMCSRCGILVEKTLSDRVHNCPHCGLSVDRDWNAAINILR 358
                                       667777889*********************************************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   0.0   1.1e-23   2.7e-20       3     117 ..     165     277 ..     163     279 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 1.1e-23
                        OrfB_IS605   3 pveveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        ve+e++ +p+ k ++ +g+D+G++ +at ++++   ++ ++r++++++k+l++ +++l++  k++  ++ as+ + 
  gi|330507354|ref|YP_004383782.1| 165 TVEMEDQpKPPWKDGSLVGVDVGLESFATFSNGE---KIANPRFFREEEKELTRVQRKLSKAPKGTLERRSASKVVE 238
                                       5788877566678999******************...**************************************** PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       r+h++++++r +++h+++++l+++   ++ e+L ++nm 
  gi|330507354|ref|YP_004383782.1| 239 RVHERIANKRYEFAHQVSRDLVNRFGLIAFEDLSIQNML 277
                                       *************************************97 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   3.6     1e-21   2.6e-18       1      47 []       1      46 [.       1      46 [. 0.99

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 1e-21
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkayk+r+yPT+ Q++k+++t++ +R+ YN+ La+rk+a+e+egk
  gi|330507354|ref|YP_004383782.1|  1 M-LKAYKFRIYPTKSQRTKMEQTLDLCRWTYNQTLAYRKNAWEKEGK 46
                                      8.*******************************************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   1.6e-06     0.004      10      44 ..     316     352 ..     312     355 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.6e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + +++Cs+Cg  ++++ +   ++Cp+Cg +vd +++ 
  gi|330507354|ref|YP_004383782.1| 316 NTSKMCSRCGILVEKTLSdrVHNCPHCGLSVDRDWNA 352
                                       6789*********9877799*************9996 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.0   6.5e-05      0.17       5      24 ..     321     344 ..     318     346 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.5e-05
                       zf-ribbon_3   5 CPnCG...ap.lssddnvCpyCGt 24 
                                       C++CG   ++ ls+++ +Cp+CG 
  gi|330507354|ref|YP_004383782.1| 321 CSRCGilvEKtLSDRVHNCPHCGL 344
                                       8888855532379**********5 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00067       1.7      10      31 ..     309     330 ..     306     335 .. 0.84
   2 ?    0.6   0.1      0.16   4.1e+02      22      27 ..     339     344 ..     337     349 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00067
                                       ECHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon  10 nlveDpergelvCtdCGlVled 31 
                                        +++Dp ++   C++CG ++e 
  gi|330507354|ref|YP_004383782.1| 309 VILVDPRNTSKMCSRCGILVEK 330
                                       5899*************99996 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.16
                                       ESSSSB CS
                      TF_Zn_Ribbon  22 CtdCGl 27 
                                       C+ CGl
  gi|330507354|ref|YP_004383782.1| 339 CPHCGL 344
                                       555555 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.42   1.1e+03       5      16 ..      71      82 ..      70      84 .. 0.89
   2 ?    3.7   3.5     0.018        47      13      34 ..     315     342 ..     310     342 .. 0.68
   3 ?    4.7   0.3    0.0087        22      12      23 ..     332     343 ..     330     349 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.42
                                      HHHHHHHHHHH- CS
                              RecR  5 LaeaLqeakekv 16
                                      ++++Lq+a e+v
  gi|330507354|ref|YP_004383782.1| 71 FSQTLQNAQERV 82
                                      899******998 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.018
                                       HHH-EE-TTT--EESSS......S-CCC CS
                              RecR  13 kekvrhCsrCgnlteed......lCaIC 34 
                                       +++ + CsrCg l e++       C+ C
  gi|330507354|ref|YP_004383782.1| 315 RNTSKMCSRCGILVEKTlsdrvhNCPHC 342
                                       666789*****99887744444447766 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0087
                                       HHHH-EE-TTT- CS
                              RecR  12 akekvrhCsrCg 23 
                                       + ++v+ C+ Cg
  gi|330507354|ref|YP_004383782.1| 332 LSDRVHNCPHCG 343
                                       6799*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2610.60
//
Query:       gi|330507355|ref|YP_004383783.1|  [L=143]
Description: hypothetical protein MCON_1260 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1055.83
//
Query:       gi|330507356|ref|YP_004383784.1|  [L=235]
Description: hypothetical protein MCON_1263 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1657.31
//
Query:       gi|330507357|ref|YP_004383785.1|  [L=192]
Description: hypothetical protein MCON_1266 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-07   30.6   0.0    5.4e-07   29.7   0.0    1.4  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 !   29.7   0.0     3e-11   5.4e-07       2     126 ..      26     149 ..      25     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 3e-11
                            DUF523   2 lvSaCLlgekvrydgkakksevleeelkelvkeelvpvCPEvaggLptPRepaelakrvlkkegedvtealekgaee 78 
                                       lv++CLl+   r +g +  s +  +        ++   CPE +  L+t R ++  + ++   + +++ ++l+   ++
  gi|330507357|ref|YP_004383785.1|  26 LVAHCLLNPLTRVKGLDTLS-FSPA--GP----TMQLPCPEALY-LGTERWAVTRN-QLDVPQFRQFCRSLIVHYAD 93 
                                       68999999999999999884.2221..22....23455***996.*******9997.56666668888888888999 PP

                            DUF523  79 aleelkeeeikga.ilkekSPSCGveki...Y....dgtfskklvegeGvfaallk 126
                                       +le+l++e++++  +  ++SPSCGv+++   Y      + ++++v+g+G+f++ l 
  gi|330507357|ref|YP_004383785.1|  94 LLEMLAKEGVRVRvVGVAGSPSCGVQTTsfgYaggrVHEAEHEHVPGRGIFMEELI 149
                                       999999999998615689**********97767665234566779*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1362.74
//
Query:       gi|330507358|ref|YP_004383786.1|  [L=146]
Description: hypothetical protein MCON_1267 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 1100.24
//
Query:       gi|330507359|ref|YP_004383787.1|  [L=381]
Description: hypothetical protein MCON_1268 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-77  257.8   0.0    6.1e-77  257.4   0.0    1.1  1  DUF1297   Domain of unknown function (DUF1297)
      6e-43  145.7   0.0    9.5e-43  145.1   0.0    1.3  1  DUF1246   Protein of unknown function (DUF1246)
  ------ inclusion threshold ------
       0.14   12.4   0.1         16    6.0   0.0    2.5  2  Kelch_6   Kelch motif


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 !  257.4   0.0     1e-80   6.1e-77       1     188 []     190     381 .]     190     381 .] 0.99

  Alignments for each domain:
  == domain 1  score: 257.4 bits;  conditional E-value: 1e-80
                                       HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT-. CS
                           DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelev. 76 
                                       e+ +k++ ll++++i+++ ++ a+ie+yv+G  fnl+yfysp+++++el+gid+R+e++ldg+ rlpa +ql+l++ 
  gi|330507359|ref|YP_004383787.1| 190 EYCQKADLLLRQNVIDQDGIELARIERYVIGPVFNLDYFYSPITKRIELIGIDWRFETSLDGHCRLPAPQQLTLNEq 266
                                       68899********************************************************************9988 PP

                                       ..---EEEEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT CS
                           DUF1297  77 ..epeyvvvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvyme 151
                                         +pey+v+G+++++lREsllek+f l+e +vea++++++pGiiGpFcLq++v+kdl+++++dv++Ri+ggtnv+m+
  gi|330507359|ref|YP_004383787.1| 267 qiNPEYTVCGHNSATLRESLLEKAFVLAEMYVEATQEYYKPGIIGPFCLQTCVDKDLNFYIYDVAPRIGGGTNVHMA 343
                                       889************************************************************************** PP

                                       .--CCHHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
                           DUF1297 152 .gspyskllfgeplsmGrrialEikeaiekdrleeivt 188
                                        g+py + l+++++s+Grr+a+E++ a+e+d+le+ivt
  gi|330507359|ref|YP_004383787.1| 344 vGHPYGNALWRTNMSTGRRLAREVRIALENDCLEQIVT 381
                                       *************************************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 !  145.1   0.0   1.6e-46   9.5e-43       1     121 [.      21     157 ..      21     158 .. 0.98

  Alignments for each domain:
  == domain 1  score: 145.1 bits;  conditional E-value: 1.6e-46
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT.............TT-SEEEE.S.S..TTSS--HHHHHH CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf.............kvidevivldkfkdilkeevqeklre 64 
                                       i+++aSHsal++++gA +e+f+tlavc++grek+Y k+             ++idev++l++f d+l+ e+q+ l+e
  gi|330507359|ref|YP_004383787.1|  21 IGMIASHSALDTADGAVEENFKTLAVCQEGREKPYIKYfraerdqkgnvitGMIDEVMMLKRFPDVLDPENQDILKE 97 
                                       89*************************************************************************** PP

                                       TTCEE--BTTHHHHC-HHHHH.C-SS-EES-TTHHHHHCSHHHHHHH..HHHTT-BB--B CS
                           DUF1246  65 enailvPhgsfveYvgiekie.elkvpifGnrkllrwEerrekkrky..LekAgiriPkk 121
                                       +n+++vP++sf++Y+gi+++e ++++p++G+r+llr+Eer +k+++y  LekAg+++P+ 
  gi|330507359|ref|YP_004383787.1|  98 KNTLFVPNRSFTSYCGIDAVEdQFTLPLLGSRNLLRSEERGDKRDYYwlLEKAGLPYPEP 157
                                       **********************************************99**********85 PP

>> Kelch_6  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.013        76      31      44 ..     227     240 ..     217     249 .. 0.84
   2 ?    6.0   0.0    0.0027        16      17      39 ..     334     361 ..     315     362 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.013
                           Kelch_6  31 wvydpetksWeqlp 44 
                                       ++y+p+tk++e ++
  gi|330507359|ref|YP_004383787.1| 227 YFYSPITKRIELIG 240
                                       89*********986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0027
                           Kelch_6  17 fGGytds.....spylnkvwvydpetks 39 
                                       +GG t+      +py n +w+ +++t++
  gi|330507359|ref|YP_004383787.1| 334 IGGGTNVhmavgHPYGNALWRTNMSTGR 361
                                       599999999****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2870.42
//
Query:       gi|330507360|ref|YP_004383788.1|  [L=164]
Description: 3-isopropylmalate dehydratase small subunit 2 [Methanosaeta concilii GP6]
Scores for complete 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-20   71.8   0.2    2.2e-19   70.1   0.3    1.7  2  Aconitase_C    Aconitase C-terminal domain
    0.00068   19.3   0.1     0.0044   16.7   0.1    2.0  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 ?    0.3   0.0     0.089     8e+02      16      57 ..       9      50 ..       5      52 .. 0.86
   2 !   70.1   0.3   2.5e-23   2.2e-19      72     123 ..      48      98 ..      37     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.089
                                      HSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTT CS
                       Aconitase_C 16 ksnvdtdlkipkqfegtianiglgnelveekrankttdlddg 57
                                       + +dtd++ip+  +   +  +l  +l+e++r++++ +++++
  gi|330507360|ref|YP_004383788.1|  9 MDDIDTDAIIPGRYLVMNDPRELAVHLFEGVRPKMASEVKES 50
                                      5778999999999999999999999*****999999988775 PP

  == domain 2  score: 70.1 bits;  conditional E-value: 2.5e-23
                                       TT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT- CS
                       Aconitase_C  72 egaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennlikngl 123
                                       ++++ vv++ +nfG+GSSRehA++al+  Gi av+a+SF+rIf +n+i+ gl
  gi|330507360|ref|YP_004383788.1|  48 KESDYVVAG-ENFGCGSSREHAPLALKGAGISAVVAKSFARIFFRNAINIGL 98 
                                       466777766.****************************************96 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.9e-07    0.0044      96     165 ..      80     150 ..       6     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.9e-07
                                       EEEEEE-HHHHHHHHHTT.-EEEE---TT--TT-EEEEETTTTEEEETT--EEEE---S-TCHHHHHHHTS CS
                     Aconitase_2_N  96 vlGgkiaPiFfntvedsG.alpieadvskletGdvieikpkegkikkeegevvsefklkpetlldevragg 165
                                       v+  + a iFf  + + G  l i  dv+++e Gd iei+ k g ik+ + +   + +  p+ l + v  gg
  gi|330507360|ref|YP_004383788.1|  80 VVAKSFARIFFRNAINIGlPLFICPDVDRIEDGDQIEIDMKGGVIKNITRKESYNTTPLPDFLREIVDVGG 150
                                       5666789999977666662688999*********************9666655555555777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1243.68
//
Query:       gi|330507361|ref|YP_004383789.1|  [L=374]
Description: 3-isopropylmalate dehydrogenase [Methanosaeta concilii GP6]
Scores for complete 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-99  330.9   0.0    1.1e-98  330.7   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 !  330.7   0.0    6e-103   1.1e-98       1     348 []       4     367 ..       4     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 330.7 bits;  conditional E-value: 6e-103
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CS.S CS
                            Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpk.e 76 
                                       k+++++gdgiGpe++++  kvl+aa++k++ +le+ ++ +G++ + +tge ++eetl+ +  ++++ lga+g p  +
  gi|330507361|ref|YP_004383789.1|   4 KVPVISGDGIGPEIIAEGQKVLEAAADKHNFSLEWIDYSIGAEHYLKTGELISEETLKELSGYRAIYLGAIGDPRvK 80 
                                       699************************************************************************77 PP

                                       SSSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET.......... CS
                            Iso_dh  77 kevrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg.......... 143
                                        +v  +  Ll++r  ld + nlrpvk++  ++v +plk+++++++d+v+vRe+t++ Y+g+ + +++          
  gi|330507361|ref|YP_004383789.1|  81 PGVLEKGVLLTMRFYLDQYINLRPVKLL--EGVWTPLKDKTPKDIDFVVVRENTEDFYIGIGSRAQKgkshadfqir 155
                                       77777778********************..89*****************************99888889******** PP

                                       .............TG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCC CS
                            Iso_dh 144 .............sifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaee 206
                                                    s  +ee a+++  +s+e+ +r++++af+lA+kr ++kv +vdKanvl+    +wr+++ +va+ 
  gi|330507361|ref|YP_004383789.1| 156 rnlynikfgldidS-DSEEIAYQIGEVSREGCQRVIKYAFDLARKR-HQKVSSVDKANVLSDIYgFWREVLLDVAK- 229
                                       **********9853.689****************************.9************98877***********. PP

                                       TTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCT CS
                            Iso_dh 207 eypdielehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdia 283
                                        yp+++++  +vD+++m  vk+p+ fdV+v++N+fGDi+ D+ a++ G+lGl+p+a+l+++++ +fE++HGsap++ 
  gi|330507361|ref|YP_004383789.1| 230 GYPEVKYDFNFVDAITMWFVKNPEWFDVVVAPNMFGDIITDLGAMIQGGLGLAPGANLNPEGTSMFEPIHGSAPKYK 306
                                       ***************************************************************************** PP

                                       TSS-S-THHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHH.TSCCHHHCTTSTCCCHHHHHHHHH CS
                            Iso_dh 284 gkdkaNpiavilSaalmLryslgleeaAdkiekAvekvlea.givTkDlageaakevstsefgdav 348
                                       g++++Np+a+i + al+L++ lg+ +aA++i +A+e++l + +i+T+Dl+g++    +tse+g ++
  gi|330507361|ref|YP_004383789.1| 307 GRNMVNPLATIWAGALLLEH-LGQPAAAEDIVSAIERNLFEgRIKTYDLGGSS----TTSEVGSEI 367
                                       ********************.*****************999799********9....999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2748.54
//
Query:       gi|330507362|ref|YP_004383790.1|  [L=78]
Description: DNA-directed RNA polymerase subunit H [Methanosaeta concilii GP6]
Scores for 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   94.3   0.0    3.3e-27   94.1   0.0    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.0   1.9e-31   3.3e-27       2      73 .]       5      76 ..       4      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 1.9e-31
                                      .-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                    RNA_pol_Rpb5_C  2 nitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                       + +He+vP+h +l++ee  ++lk+++i   qLPki+ sDp+a+++g+k Gd++kI+rks ta++++ YRlV
  gi|330507362|ref|YP_004383790.1|  5 AVKDHEMVPEHILLTPEEGLDVLKEFGIGAPQLPKIHISDPAAKEIGAKVGDIIKIIRKSTTAKHSTFYRLV 76
                                      5899*******************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 554.17
//
Query:       gi|330507363|ref|YP_004383791.1|  [L=496]
Description: DNA-directed RNA polymerase subunit B' [Methanosaeta concilii GP6]
Scores for complete 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-54  183.3   0.2    4.6e-54  183.0   0.2    1.1  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    4.2e-26   90.9   0.0    8.4e-26   89.9   0.0    1.5  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    1.3e-25   90.2   0.5    1.9e-25   89.6   0.5    1.2  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 !  183.0   0.2   7.7e-58   4.6e-54       2     202 ..      17     384 ..      16     385 .. 0.98

  Alignments for each domain:
  == domain 1  score: 183.0 bits;  conditional E-value: 7.7e-58
                                       TTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBXE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1   2 LvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltYs 78 
                                       Lv+ +++SFn+f+++ l+k+i+e + ie++ e+       ++k+++ir++kP+v+e+d+s +++yP++arlrnltY 
  gi|330507363|ref|YP_004383791.1|  17 LVHHHINSFNDFIDKGLQKVIDEVNIIETNIEN------TYVKLGNIRVEKPMVREADGSVERLYPNDARLRNLTYA 87 
                                       99*********************9999999886......69************************************ PP

                                       EEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1  79 aplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqek 155
                                       +p+ ++++ v      ++e+++ e +iG lP+Ml+sk c+ls++s +e++  +E+p+d+GGyF++nG+e+vi+ +e+
  gi|330507363|ref|YP_004383791.1|  88 SPIKLEMTIVE----GETEKDPVEADIGTLPIMLNSKVCNLSGLSADEMISFGEDPSDPGGYFVVNGSERVIMTLED 160
                                       *******9999....89999********************************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|330507363|ref|YP_004383791.1| 161 lapnkilveynqrydenievakvfsqrqgyrslvivergrrsilevsfpsvsgrlnfvtllrslgmetdmdivksvs 237
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|330507363|ref|YP_004383791.1| 238 dnpeiikfmlenleeaevstndealekigsrvaagqakeyqkkratyvldryllphigvdekdryakalflsrmaea 314
                                       ***************************************************************************** PP

                                       .......................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHH CS
                                       .......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1 156 .......................laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpit 202
                                                              l G+L+++lfrv++++l+rd+k +l++   +++dl++  +v+a+ +t
  gi|330507363|ref|YP_004383791.1| 315 cfelalarrneddkdhysnkrlkLSGDLMEDLFRVAFNRLTRDIKYQLERASMRNRDLNVVTTVRADVLT 384
                                       *****************************************************************99877 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 !   89.9   0.0   1.4e-29   8.4e-26       1      64 [.     405     465 ..     405     469 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 1.4e-29
                    RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLal 64 
                                       q+ldr+ ++++lshlrrv s+   ls+++ ++e+Rdlh+++wGriCp+eTPEG+ncGlvk++a+
  gi|330507363|ref|YP_004383791.1| 405 QLLDRTDYMATLSHLRRVISP---LSRSQPHFEARDLHATQWGRICPSETPEGPNCGLVKNFAQ 465
                                       89*******************...**************************************97 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 !   89.6   0.5   3.2e-29   1.9e-25      14     190 .]     164     337 ..     152     337 .. 0.87

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 3.2e-29
                                       SSE.............SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSS CS
                    RNA_pol_Rpb2_2  14 nki.............satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericyds 77 
                                       nki             +a+v s +  +r++v++++  +++l ++ +s+  + ++v +l+ lg+ +d +I+++++   
  gi|330507363|ref|YP_004383791.1| 164 NKIlveynqrydenieVAKVFSQRQGYRSLVIVERGRRSILEVSFPSVSGRLNFVTLLRSLGMETDMDIVKSVS--- 237
                                       44444444444444579999*****************************************************9... PP

                                       TTHHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH CS
                    RNA_pol_Rpb2_2  78 edsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenk 154
                                        d   + +++ e+ e++e+ t +eal++ig++va+++ +e + ++a  +l         +r+ l+ h+g++e+   +
  gi|330507363|ref|YP_004383791.1| 238 -DNPEIIKFMLENLEEAEVSTNDEALEKIGSRVAAGQAKEYQKKRATYVL---------DRYLLP-HIGVDEK---D 300
                                       .5666667777777778889999********9999999999999999998.........8*****.*******...5 PP

                                       ...HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                    RNA_pol_Rpb2_2 155 r.lkaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                       r +ka ++  m+++ ++l+l rr++DD+Dh+ nkR++
  gi|330507363|ref|YP_004383791.1| 301 RyAKALFLSRMAEACFELALARRNEDDKDHYSNKRLK 337
                                       669********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3551.58
//
Query:       gi|330507364|ref|YP_004383792.1|  [L=597]
Description: DNA-directed RNA polymerase subunit B' [Methanosaeta concilii GP6]
Scores for complete 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-124  413.7   0.0   9.4e-124  413.4   0.0    1.1  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    3.7e-29  101.0   0.3    1.6e-28   98.9   0.0    2.1  2  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    2.9e-19   69.1   0.0    5.4e-19   68.3   0.0    1.5  1  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    9.9e-10   38.8   5.2    2.9e-09   37.3   5.2    1.8  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
      0.032   14.1   0.3        8.1    6.5   0.0    2.6  2  Nudix_N_2       Nudix N-terminal
      0.035   13.8   0.2       0.62    9.8   0.0    2.7  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.085   13.0   1.3       0.16   12.2   1.3    1.4  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.11   12.5   0.2       0.22   11.6   0.2    1.4  1  DZR             Double zinc ribbon
       0.18   11.7   1.9       0.45   10.4   1.9    1.6  1  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
       0.31   10.8   2.2        3.9    7.3   0.3    2.3  2  zinc_ribbon_2   zinc-ribbon domain
       0.37   10.3   1.1         16    5.1   0.2    2.3  2  zf-ribbon_3     zinc-ribbon domain


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 !  413.4   0.0  5.8e-127  9.4e-124       2     390 .]     129     500 ..     128     500 .. 0.96

  Alignments for each domain:
  == domain 1  score: 413.4 bits;  conditional E-value: 5.8e-127
                                       HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SE CS
                    RNA_pol_Rpb2_6   2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalG 78 
                                       a l+p++eh+ spr+++ a m kq lg+ ++n+  r +++ + l+ +qk++v+t+ + +a++        ++e ++G
  gi|330507364|ref|YP_004383792.1| 129 AGLVPYPEHNASPRNTMGAGMVKQCLGMSTANMRLRPDTRGHYLNSPQKAIVRTK-TSKAIG--------FDERPAG 196
                                       7899***************************************************.999999........******* PP

                                       EEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-......-SS-GGGS-TT CS
                    RNA_pol_Rpb2_6  79 qnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv......seealkkLded 149
                                       qn+vVAv++yeGYniEDa+++n+ +++r++++s++++  e e r++++g+e+ ++ ++ v      ++ea+++Ld+d
  gi|330507364|ref|YP_004383792.1| 197 QNFVVAVLAYEGYNIEDALVMNRGSIQRGLARSHFFRVSEAEERKYPGGQEDKFEIPD-VevrgarGSEAYDQLDSD 272
                                       **************************************9***********88665555.4499*999********** PP

                                       SB--SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT- CS
                    RNA_pol_Rpb2_6 150 GivrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagv 226
                                       G+v+++a+v ++d+l+gk+  ++ ++ +e     ++fg + ++ ++ts++++s+e+gvVd v++       ++++++
  gi|330507364|ref|YP_004383792.1| 273 GLVNPNAYVGPNDVLIGKT--SPPRFLEE----PSEFGLTPQQRRETSVTMRSNEKGVVDMVIL-------TESSNG 336
                                       ******************8..78888744....457888888999*******************.......8999** PP

                                       -EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCS CS
                    RNA_pol_Rpb2_6 227 nklvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaal 303
                                       n+l+kv+ +++R +++GDKfasrhGqKGvv+li+pqeDmPf+e+Giv+D++lNP+++PSRmt+g++lE++ gk+++l
  gi|330507364|ref|YP_004383792.1| 337 NRLAKVKSRDQRIPELGDKFASRHGQKGVVGLIVPQEDMPFTESGIVPDLLLNPHAIPSRMTVGHVLEMIGGKVGSL 413
                                       ***************************************************************************** PP

                                       SSS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TT CS
                    RNA_pol_Rpb2_6 304 egkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpysll 380
                                       +g+++dat+F g++e e++ +L++ g++++G+e+ly+G tGe++ a+ fvGvi y+kL+h+v+ K+haRs+Gp+++l
  gi|330507364|ref|YP_004383792.1| 414 DGRFIDATAFLGENEPELRTALTKFGFSHTGREILYNGATGEQIMADLFVGVILYQKLYHMVTGKMHARSRGPVQVL 490
                                       ***************************************************************************** PP

                                       T--B-SCGGG CS
                    RNA_pol_Rpb2_6 381 tqQPlgGkaq 390
                                       t+QP++G+a+
  gi|330507364|ref|YP_004383792.1| 491 TRQPTEGRAR 500
                                       ********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 ?   -1.4   0.1       1.9   3.1e+03       6      22 ..      77      93 ..      74     101 .. 0.83
   2 !   98.9   0.0   9.7e-32   1.6e-28       1      86 [.     502     593 ..     502     594 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.9
                                      EHHHHHHHHHHTBHHHH CS
                    RNA_pol_Rpb2_7  6 GEMErdaliayGaaalL 22
                                      GEM  d l+a G  + L
  gi|330507364|ref|YP_004383792.1| 77 GEMKFDDLVAEGLVEYL 93
                                      9*********9987776 PP

  == domain 2  score: 98.9 bits;  conditional E-value: 9.7e-32
                                       BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHH CS
                    RNA_pol_Rpb2_7   1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafklL 71 
                                       GGlrfGEMErd+lia+Gaa  Lkerl+++SD+v+  vc++c+++a+ +       C+++  +++i +ve+++afklL
  gi|330507364|ref|YP_004383792.1| 502 GGLRFGEMERDVLIAHGAALALKERLVDESDKVTELVCSHCGMIAIHDrrrnadFCPTCGADTEIYPVEMSYAFKLL 578
                                       9*********************************************99*****9*********************** PP

                                       HHHHHHTTBEEEEES CS
                    RNA_pol_Rpb2_7  72 lqeLqslgialklll 86 
                                       l+e++slg+a++l+l
  gi|330507364|ref|YP_004383792.1| 579 LDEIKSLGVAPRLIL 593
                                       ***********9976 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   3.3e-22   5.4e-19       3      62 .]       1      60 [.       1      60 [. 0.99

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 3.3e-22
                                      CTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE-S CS
                    RNA_pol_Rpb2_4  3 vNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiVe 62
                                      +NG+++G+++dpk lve+lR+lR +g+is+++++++ e++ e+ ++tD+GR++RPli+Ve
  gi|330507364|ref|YP_004383792.1|  1 MNGEIVGYHDDPKTLVENLRRLRHSGSISSQTNVAYFEDTGEIFMNTDSGRARRPLIVVE 60
                                      6**********************************************************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 !   37.3   5.2   1.8e-12   2.9e-09       1      58 []      81     121 ..      81     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.8e-12
                                       HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEES-G CS
                    RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcEIhP 58 
                                       +ddL++eg+vEylDaeEEe+++Ia+ +ed++ +                 +TH+E++P
  gi|330507364|ref|YP_004383792.1|  81 FDDLVAEGLVEYLDAEEEENSLIAIWEEDITPE-----------------HTHLELDP 121
                                       9*****************************776.................56666666 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0049       8.1      16      31 ..     530     545 ..     521     546 .. 0.77
   2 ?    5.1   0.1     0.013        22       2      11 ..     556     565 ..     555     569 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0049
                                       TT-SS-EEEETTTTEE CS
                         Nudix_N_2  16 dgDnreRlvCpaCgti 31 
                                       + D+ + lvC++Cg+i
  gi|330507364|ref|YP_004383792.1| 530 ESDKVTELVCSHCGMI 545
                                       56666779******99 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.013
                                       B-TTT--B-E CS
                         Nudix_N_2   2 FCsqCGtpve 11 
                                       FC+ CG+ +e
  gi|330507364|ref|YP_004383792.1| 556 FCPTCGADTE 565
                                       9*****9876 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         5   8.1e+03      12      23 ..      55      66 ..      55      66 .. 0.82
   2 ?    0.5   0.1      0.29   4.8e+02      23      28 ..     538     543 ..     535     544 .. 0.61
   3 ?    9.8   0.0   0.00038      0.62       1      14 [.     552     565 ..     552     570 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5
                     zf-NADH-PPase 12 ptepaeggwarv 23
                                      p +++e+g+a+v
  gi|330507364|ref|YP_004383792.1| 55 PLIVVEDGRALV 66
                                      56789****986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.29
                     zf-NADH-PPase  23 vCpaCg 28 
                                       vC++Cg
  gi|330507364|ref|YP_004383792.1| 538 VCSHCG 543
                                       555554 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00038
                     zf-NADH-PPase   1 rthrFCgrCGapte 14 
                                       r+  FC++CGa te
  gi|330507364|ref|YP_004383792.1| 552 RNADFCPTCGADTE 565
                                       5778*******997 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 ?   12.2   1.3   9.5e-05      0.16      16      40 .]     537     561 ..     533     561 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.5e-05
                     Auto_anti-p27  16 etCpvCgvPLmrdrkggkvyCvaCd 40 
                                        +C+ Cg++   dr ++  +C++C+
  gi|330507364|ref|YP_004383792.1| 537 LVCSHCGMIAIHDRRRNADFCPTCG 561
                                       68************55566*****6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00014      0.22       1      22 [.     539     564 ..     530     572 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                               DZR   1 CpqCgee....lppdarfCseCgtkl 22 
                                       C++Cg       + +a fC++Cg++ 
  gi|330507364|ref|YP_004383792.1| 539 CSHCGMIaihdRRRNADFCPTCGADT 564
                                       88888655444777777999998875 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.9   0.00028      0.45       3      27 ..     538     560 ..     537     560 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00028
                                       B-TTT--BBEEEECTTEEEEE-TTT CS
                      zf-FPG_IleRS   3 pCpRCwryiervgqagrstyfCprC 27 
                                       +C +C+++  + +   r+  fCp+C
  gi|330507364|ref|YP_004383792.1| 538 VCSHCGMIAIHDRR--RNADFCPTC 560
                                       7*******999999..9******** PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.074   1.2e+02       2       6 ..     539     543 ..     533     544 .. 0.74
   2 ?    7.3   0.3    0.0024       3.9      12      21 ..     553     562 ..     551     563 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.074
                     zinc_ribbon_2   2 CpnCG 6  
                                       C++CG
  gi|330507364|ref|YP_004383792.1| 539 CSHCG 543
                                       66666 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0024
                     zinc_ribbon_2  12 nakFCpyCGt 21 
                                       na FCp CG+
  gi|330507364|ref|YP_004383792.1| 553 NADFCPTCGA 562
                                       7889999998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.031        51      18      24 ..     538     544 ..     533     545 .. 0.78
   2 ?    5.1   0.2    0.0096        16       4      10 ..     556     562 ..     553     564 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.031
                       zf-ribbon_3  18 vCpyCGt 24 
                                       vC +CG+
  gi|330507364|ref|YP_004383792.1| 538 VCSHCGM 544
                                       7899985 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0096
                       zf-ribbon_3   4 rCPnCGa 10 
                                       +CP CGa
  gi|330507364|ref|YP_004383792.1| 556 FCPTCGA 562
                                       5777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4036.18
//
Query:       gi|330507365|ref|YP_004383793.1|  [L=875]
Description: DNA-directed RNA polymerase subunit A' [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.5e-104  349.7   0.0   2.2e-104  349.1   0.0    1.3  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
      2e-68  229.8   0.2    3.3e-68  229.1   0.2    1.3  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    1.2e-32  113.0   0.0    2.3e-32  112.1   0.0    1.5  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
      1e-31  109.1   0.0    2.4e-31  107.9   0.0    1.7  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    1.1e-27   97.1   0.1    1.9e-27   96.4   0.1    1.3  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
       0.15   11.7   0.1       0.28   10.8   0.1    1.3  1  DUF1287         Domain of unknown function (DUF1287)


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.1   0.0  7.4e-108  2.2e-104       2     312 .]       5     309 ..       4     309 .. 0.93

  Alignments for each domain:
  == domain 1  score: 349.1 bits;  conditional E-value: 7.4e-108
                                       E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLak 78 
                                       k+i +i+fg++sp+e+rk+Svv++ +a+t++++  +P e+Gl+D+rlg+id  l+C+ Cg    eC+ghfGhi+L +
  gi|330507365|ref|YP_004383793.1|   5 KRIGKIRFGLISPQEFRKMSVVKIITADTYDDDG-FPIEMGLMDPRLGVIDPGLRCRSCGGRPGECPGHFGHIDLIA 80 
                                       899*****************************95.****************************************** PP

                                       EEE-HHHHHHHHHHCTTCETTTTEBSS-TTSH....HH.HHHHCSSSCC.CCHHHHHHHHCCS-BE-SSSSB-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1  79 Pvfhigffklilkilecvckecskllldeekkkllskl.kkrekleelk.krlkaieelckkinlcekCgavqpkle 153
                                       Pv+h+gf kli+k+l+ +c+ cs+l+l++++kk++ ++ ++ e+l ++  + ++++ +  +k ++c  Cg  +p+ e
  gi|330507365|ref|YP_004383793.1|  81 PVIHVGFAKLIRKVLRAICRDCSRLMLKDNEKKMYLEQiQELERLGQMTdDTVNKVFAEARKNKTCPYCG--APQQE 155
                                       *****************************999776554145555555545789999999999********..56666 PP

                                       EETTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 154 eegeklkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrs 230
                                        ++e+  + +++ ++     l+a+++++ +++++ded++v+g++++ +rPew+iltvlPVpP+++RPs++l++g+rs
  gi|330507365|ref|YP_004383793.1| 156 IKFERPLSYIEEGHK-----LTASDIRDRFEKVPDEDIQVMGMNPATARPEWMILTVLPVPPVTMRPSITLESGQRS 227
                                       667777777776666.....********************************************************* PP

                                       BECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 231 edDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGr 307
                                       edDlt+kl+dii++N+r+++++e+gap+ iie+ +elLQ+hv+t++dn +sg++pa+++s+rplk+lsqrLkGKeGr
  gi|330507365|ref|YP_004383793.1| 228 EDDLTHKLVDIIRINQRFQENREAGAPQPIIEDLWELLQYHVTTFLDNTVSGVPPARHRSGRPLKTLSQRLKGKEGR 304
                                       ***************************************************************************** PP

                                       CCCCT CS
                                       xxxxx RF
                    RNA_pol_Rpb1_1 308 fRgnL 312
                                       fRg+L
  gi|330507365|ref|YP_004383793.1| 305 FRGSL 309
                                       ***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 !  229.1   0.2   1.1e-71   3.3e-68       1     166 []     311     477 ..     311     477 .. 0.99

  Alignments for each domain:
  == domain 1  score: 229.1 bits;  conditional E-value: 1.1e-71
                                       SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT CS
                    RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkak 77 
                                       Gkrv++saR+vispdpnl++ evgvP+ +a+ l+vp i ++ n++ ++++v++gp+ +Pg +yv+r d+++ k++ k
  gi|330507365|ref|YP_004383793.1| 311 GKRVNFSARTVISPDPNLSIGEVGVPMDIAMELSVPMIANSRNMEIVKTFVRRGPDRHPGVNYVTRPDQRRVKVTDK 387
                                       9**************************************************************************99 PP

                                       -S.CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SS CS
                    RNA_pol_Rpb1_2  78 kr.klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqs 153
                                       +  ++a+++ +g+++ r++ dgd+vl+NRqPsLh++sim+hrvkv+++kt+rln +v+ +yNaDFDGDemn+h+pq+
  gi|330507365|ref|YP_004383793.1| 388 NCeEVAEQIDIGWKIDRQLADGDIVLFNRQPSLHRMSIMSHRVKVMPYKTFRLNPAVCPPYNADFDGDEMNMHVPQT 464
                                       9878************************************************************************* PP

                                       HHHHHHHHHCSBT CS
                    RNA_pol_Rpb1_2 154 eearaEaeelllv 166
                                       eearaEae l+ v
  gi|330507365|ref|YP_004383793.1| 465 EEARAEAEILMRV 477
                                       *********9975 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.0   7.6e-36   2.3e-32       1     156 [.     480     644 ..     480     645 .. 0.89

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 7.6e-36
                                       CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESS.SEBEEHHHHHHCCCH CS
                    RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkp.kelwtgkqtfsrilp 76 
                                       nilsp+ g P+ig ++D ++G++llT+ +  idr  a++ll+k +     t+++ p    + ++ wtgkq+fs+ilp
  gi|330507365|ref|YP_004383793.1| 480 NILSPRFGGPIIGGIHDYVTGSFLLTHGRKPIDRRGAMELLKKFDI----TELPAPEGELNgEPYWTGKQIFSLILP 552
                                       9*******************************************55....67889999999999************* PP

                                       C..CCCEEEE.....SSSS........STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHH CS
                    RNA_pol_Rpb1_3  77 n..einyerk.....neek........dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslq 138
                                       +  +  ++ k     n++         d +v+i++g+l  G+id k+vg + +g++ + ++key++  +++fld+++
  gi|330507365|ref|YP_004383793.1| 553 RglD--LNFKadfcyNCDVckneecenDAYVVIQDGQLKIGTIDAKAVG-AFKGKITDRIIKEYSPSVASEFLDRMT 626
                                       *663..444333444222255566777**********************.999************************ PP

                                       HHHHHHHHHHCEB-TGGG CS
                    RNA_pol_Rpb1_3 139 rlgfkyllqsgftigigD 156
                                       rl+ + ++++gf++gi+D
  gi|330507365|ref|YP_004383793.1| 627 RLALRGIMHAGFSFGIDD 644
                                       *****************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 !  107.9   0.0     8e-35   2.4e-31       2     108 .]     671     776 ..     670     776 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 8e-35
                                       HHHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEB CS
                    RNA_pol_Rpb1_4   2 eeaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnv 78 
                                       e+++  g+le+lpg++l+e++e++i++ l kard+agkia ++l  +Ns ++M+ sGa+Gs++n++q+a+c+Gqq+v
  gi|330507365|ref|YP_004383793.1| 671 EAYNA-GELEPLPGRTLDETLEMRIMQTLGKARDTAGKIAGRYLGLDNSGVVMAVSGARGSMLNLTQMAACVGQQSV 746
                                       56666.99*************************************66****************************** PP

                                       TTBSS--SSTSCSSTTSSSSESSTTTSSEE CS
                    RNA_pol_Rpb1_4  79 egkripkgfsgrtlphfkkidespesrGFv 108
                                       +g+ri +g+ grtlphf++ d ++e++GFv
  gi|330507365|ref|YP_004383793.1| 747 RGERIMRGYAGRTLPHFRRGDLGAEAHGFV 776
                                       *****************************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 !   96.4   0.1   6.3e-31   1.9e-27       1      66 [.     783     848 ..     783     868 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 6.3e-31
                                       B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                       GL+++efffh+ ggReGL+DtA++T++sGYlqRrlv+al+d+ vkyd+tv+++ g ivqf+ygedg
  gi|330507365|ref|YP_004383793.1| 783 GLNPTEFFFHAIGGREGLVDTAIRTSQSGYLQRRLVNALQDLEVKYDGTVKETRGMIVQFKYGEDG 848
                                       9****************************************************************8 PP

>> DUF1287  Domain of unknown function (DUF1287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   9.5e-05      0.28      79     131 ..     378     430 ..     357     438 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.5e-05
                           DUF1287  79 DfRRvknlevffkrkgasltvskdaedeyqpGdivvfkleekleHigivsdkr 131
                                       D RRvk  +   ++ ++++ +  +++++ + Gdiv+f+ + +l+ ++i+s++ 
  gi|330507365|ref|YP_004383793.1| 378 DQRRVKVTDKNCEEVAEQIDIGWKIDRQLADGDIVLFNRQPSLHRMSIMSHRV 430
                                       88*******************999999************99999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (875 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 5532.55
//
Query:       gi|330507366|ref|YP_004383794.1|  [L=379]
Description: DNA-directed RNA polymerase subunit A' [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-55  188.8   1.1    1.6e-55  188.5   1.1    1.1  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
     0.0036   17.2   0.2      0.011   15.7   0.2    1.8  1  NAC             NAC domain
  ------ inclusion threshold ------
      0.033   14.6   3.4        2.1    8.9   0.1    4.0  4  Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
       0.11   12.6   0.0       0.33   11.0   0.0    1.8  1  DUF496          Protein of unknown function (DUF496)
       0.18   12.0   0.4       0.32   11.2   0.3    1.7  1  MutS_III        MutS domain III
       0.21   10.6   0.9       0.41    9.7   0.9    1.3  1  FH2             Formin Homology 2 Domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.5   1.1   5.2e-59   1.6e-55      64     265 ..      51     326 ..       7     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: 188.5 bits;  conditional E-value: 5.2e-59
                                       GTSB--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5  64 edglvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakelek 140
                                       e + vep eavG++aaQSiGePgTQ+t++TFH+aGva+ nvtlG+prl ei+++ k+ +++++t++l++e+a++++ 
  gi|330507366|ref|YP_004383794.1|  51 EHSRVEPCEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKIPSTPTMTIKLTPEYAHDRDL 127
                                       33389************************************************************************ PP

                                       CHHHHHHHSE................................................................... CS
                                       xxxxxxxxxx................................................................... RF
                    RNA_pol_Rpb1_5 141 akkvkkaiek................................................................... 150
                                       a++v+ aie+                                                                   
  gi|330507366|ref|YP_004383794.1| 128 AREVAWAIESssilhlgsiatdlaemnviielnpgaleqrkitaeevaaklkeetgldvdqkenllvmapeepsyre 204
                                       *****99999999**************************************************************** PP

                                       ..............CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHH CS
                                       ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 151 ..............gikkikrilvkeaekgkeeekelvletegvnlsevlkveevvdageilsndiaeileilgiea 213
                                                     g+++ikr++++     ke  +e++l teg +l++v++ e+ vd ++i +n+i ei e+lgiea
  gi|330507366|ref|YP_004383794.1| 205 llqlvekikklslkGVEGIKRVVIR-----KEG-DEYILYTEGSSLKKVMQFEG-VDPTRIKTNNISEIGEVLGIEA 274
                                       ***8888888888888888888887.....222.56789***************.********************** PP

                                       HHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 214 arkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265
                                       ar+a+++e ++++++qg+sv+ rH++l++d+mt  ge+++++r+G+  ++ s
  gi|330507366|ref|YP_004383794.1| 275 ARNAIINEATDTLREQGLSVDVRHIMLVADIMTVDGELKQIGRHGVSGEKAS 326
                                       *********************************************9887765 PP

>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   3.6e-06     0.011       6      31 ..     210     235 ..     207     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-06
                               NAC   6 kalkklglkeipgieeVtirksdgkv 31 
                                       + +kkl lk ++gi++V+irk+++++
  gi|330507366|ref|YP_004383794.1| 210 EKIKKLSLKGVEGIKRVVIRKEGDEY 235
                                       569******************99665 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 ?   -1.6   0.1       1.3   3.8e+03      37      54 ..      21      39 ..       5      63 .. 0.60
   2 ?    8.9   0.1   0.00069       2.1      31      53 ..     168     190 ..     145     197 .. 0.89
   3 ?   -0.8   0.0      0.74   2.2e+03      41      65 ..     244     268 ..     242     270 .. 0.81
   4 ?    3.3   0.0     0.037   1.1e+02      39      68 ..     285     320 ..     280     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                                      HHHHHHHHT.-----GGGE CS
                    Ribosomal_L9_C 37 Iaealkkkl.gieidkkki 54
                                      I e ++++l g ei +++i
  gi|330507366|ref|YP_004383794.1| 21 IKESIQNELkGAEISSEEI 39
                                      4444444433444444444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00069
                                       ---HHHHHHHHHHHT-----GGG CS
                    Ribosomal_L9_C  31 sVtakdIaealkkklgieidkkk 53 
                                       ++ta+++a++lk+++g+++d+k+
  gi|330507366|ref|YP_004383794.1| 168 KITAEEVAAKLKEETGLDVDQKE 190
                                       59******************996 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.74
                                       HHHHT---.--GGGEE-TTT-SBSSE CS
                    Ribosomal_L9_C  41 lkkklgie.idkkkieleepiktlGe 65 
                                       lkk +++e +d  +i+  ++i ++Ge
  gi|330507366|ref|YP_004383794.1| 244 LKKVMQFEgVDPTRIKT-NNISEIGE 268
                                       77777888899999998.56999998 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.037
                                       HHHHHHT-----GGGEE-.......TTT-SBSSEEEE CS
                    Ribosomal_L9_C  39 ealkkklgieidkkkiel.......eepiktlGeyev 68 
                                       + l+++ g+++d ++i l       + ++k++G + v
  gi|330507366|ref|YP_004383794.1| 285 DTLREQ-GLSVDVRHIMLvadimtvDGELKQIGRHGV 320
                                       789999.**********98888876667999999877 PP

>> DUF496  Protein of unknown function (DUF496)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.33      25      67 ..       5      52 ..       1      60 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                            DUF496 25 ekkirdnqkrvlllenlleyike.....dmsieeikaiienmkddyed 67
                                      ek i++    v+l + ++e i++     ++s eei +i++++k+dye 
  gi|330507366|ref|YP_004383794.1|  5 EKEIQERLDGVELPQSIKESIQNelkgaEISSEEIDEIVSQVKADYEH 52
                                      67777788888888888888887222225799**************95 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00011      0.32      46      93 ..       3      52 ..       2     335 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                      S-HHHHHHHHHHHHHT..TT.HHHHHHHHTT--....-HHHHHHHHHTT--- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx RF
                          MutS_III 46 tdleeInaRldaVeeleneelreelrellrrlp....DleRllsrislgkak 93
                                      ++ +eI++Rld Ve    ++++e+++++l+  +     ++ ++s++++   +
  gi|330507366|ref|YP_004383794.1|  3 LSEKEIQERLDGVEL-P-QSIKESIQNELKGAEisseEIDEIVSQVKADYEH 52
                                      5789**********6.3.5569******997767788999999988875322 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.9   0.00014      0.41      90     144 ..     164     216 ..     162     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00014
                                       HHHHTS-HHHHHHHHHTTTTCCCTHHHHHHHHHHCGGHHHHHHHHCTCTSGTTB- CS
                               FH2  90 LkklkltaeeiveaileldeealdlellenLlkmaPtkeelkklkeykgevseLs 144
                                       L++ k+taee+ +++   +e+ ld+++ enLl maP++  + +l ++ +++++Ls
  gi|330507366|ref|YP_004383794.1| 164 LEQRKITAEEVAAKLK--EETGLDVDQKENLLVMAPEEPSYRELLQLVEKIKKLS 216
                                       5667899999999999..7788**********************99999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2675.20
//
Query:       gi|330507367|ref|YP_004383795.1|  [L=102]
Description: 50S ribosomal protein L30e [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-11   43.1   0.0    3.5e-11   42.7   0.0    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   1.9e-15   3.5e-11       3      94 ..       4      91 ..       3      92 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.9e-15
                                      HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECS CS
                    Ribosomal_L7Ae  3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvs 81
                                      + ++l+ + ++g+++lG ++++ a   g+akl++ A d++ +   +      ++ +v+ +++ + k+LG ++gk++ v+
  gi|330507367|ref|YP_004383795.1|  4 VDRALRSSIRTGNVMLGSNRTIEAGLGGQAKLIVYALDCPADVRMQ---LETMDLPVYGYQGMG-KDLGSACGKPFSVA 78
                                      567889999*******************************999988...445799*********.************** PP

                                      EEEEEESTTTHHH CS
                    Ribosomal_L7Ae 82 alaikdegdskdl 94
                                      alai+++gds+++
  gi|330507367|ref|YP_004383795.1| 79 ALAIIEPGDSEIM 91
                                      **********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 771.49
//
Query:       gi|330507368|ref|YP_004383796.1|  [L=143]
Description: NusA protein-like protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-21   74.4   5.6    2.5e-15   56.0   1.5    2.1  2  KH_2      KH domain
    4.6e-16   58.7   4.3    7.2e-16   58.0   1.8    2.1  2  KH_5      NusA-like KH domain
    1.5e-09   37.6   1.0    9.4e-05   22.2   0.1    2.2  2  KH_4      KH domain
    3.9e-05   23.4   1.6    0.00064   19.5   0.3    2.3  2  KH_1      KH domain


Domain annotation for each model (and alignments):
>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   1.5   5.7e-19   2.5e-15       2      65 ..      12      75 ..      11      78 .. 0.95
   2 !   20.7   0.2   5.9e-08   0.00026       2      56 ..      77     133 ..      76     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 5.7e-19
                                      HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC CS
                              KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk 65
                                      ++++l++++++  +++++++++++r+i+vi+++ +g +IG++Gsni++++k ++k+ie++e+++
  gi|330507368|ref|YP_004383796.1| 12 RYIALFESLTGGMARDCVVDEENERIIFVIKKGDMGAAIGRKGSNINRVKKSVGKQIEIVEYSE 75
                                      5789********************************************************9986 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 5.9e-08
                                       HHHHHHHHTECETEEEEEEECCS.CEEEEEEEESC.HHHHHTGGGHHHHHHHHHHHH CS
                              KH_2   2 ipeslaveikkagvskveIerta.nrviiviresq.pgivIGkgGsnikkigkelrk 56 
                                       ++e+l++ ++ a +++v + +++ +r+ +v+ +++ +gi+IG+ G+ni k +  +++
  gi|330507368|ref|YP_004383796.1|  77 VKEFLENLFQPAAIKNVMVVNKNsKRLAYVEVANKdKGIAIGRDGRNILKAKMLAQR 133
                                       5678888888888555555554449**999987654*************99999886 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   1.8   1.6e-19   7.2e-16       2      68 ..      34      94 ..      33      95 .. 0.97
   2 ?    0.9   0.0      0.11     5e+02      12      31 ..     111     125 ..     102     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.6e-19
                              KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVk 68
                                      +er+++++k+++     +Ga++g+kGs+i+ v++   g++i++ve+seD++ef +n+++Pa +++V 
  gi|330507368|ref|YP_004383796.1| 34 NERIIFVIKKGD-----MGAAIGRKGSNINRVKKSV-GKQIEIVEYSEDVKEFLENLFQPAAIKNVM 94
                                      689*********.....*******************.****************************97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.11
                              KH_5  12 hnpnvdpvGaivgkkGsrik 31 
                                       ++      G ++g+ G++i 
  gi|330507368|ref|YP_004383796.1| 111 KD-----KGIAIGRDGRNIL 125
                                       44.....7999******995 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   6.5e-06     0.029      22      52 ..      28      58 ..      16      61 .. 0.86
   2 !   22.2   0.1   2.1e-08   9.4e-05       2      51 ..      75     124 ..      74     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.5e-06
                              KH_4 22 eeeeeeeveielnvegedlGrvIGkrGrtld 52
                                      +  +ee+++i   +++ d+G  IG++G +++
  gi|330507368|ref|YP_004383796.1| 28 CVVDEENERIIFVIKKGDMGAAIGRKGSNIN 58
                                      55567789999999*************9986 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 2.1e-08
                              KH_4   2 elvedilkalvddpeeve.vteeeeeeeveielnvegedlGrvIGkrGrtl 51 
                                       e v+++l++l+ +p++++ v + ++++++   ++v+ +d+G+ IG++Gr++
  gi|330507368|ref|YP_004383796.1|  75 EDVKEFLENLF-QPAAIKnVMVVNKNSKRLAYVEVANKDKGIAIGRDGRNI 124
                                       679999***99.57766515555888899999*****************87 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   1.4e-07   0.00064       4      40 ..      39      76 ..      30      86 .. 0.86
   2 ?    2.8   0.0     0.023     1e+02       4      22 ..     106     124 ..     104     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-07
                                      EEEGGGHHHHHHTGGGHHHHHHHHHH.T-EEEEES.STT CS
                              KH_1  4 ilvPsslvgriIGkgGsnIkeIreet.gakIkvpk.sed 40
                                      + +++  +g+ IG++GsnI++ ++ + g +I +++ sed
  gi|330507368|ref|YP_004383796.1| 39 FVIKKGDMGAAIGRKGSNINRVKK-SvGKQIEIVEySED 76
                                      57888899****************.88*****9976665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.023
                                       EEEGGGHHHHHHTGGGHHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnI 22 
                                       ++v ++  g  IG+ G+nI
  gi|330507368|ref|YP_004383796.1| 106 VEVANKDKGIAIGRDGRNI 124
                                       67888889999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1096.39
//
Query:       gi|330507369|ref|YP_004383797.1|  [L=142]
Description: 30S ribosomal protein S23 (S12) [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-47  160.1   0.3    1.6e-47  159.8   0.3    1.1  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.8   0.3   8.8e-52   1.6e-47       1     113 [.      27     140 ..      27     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: 159.8 bits;  conditional E-value: 8.8e-52
                                       --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE- CS
                   Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGi 77 
                                       r+  ++k+k+d+l gap+ rG+vlekv++eak+PnsA+Rk+vr++Likng++vtaf+pg+ga+ f+dEhdevlv  i
  gi|330507369|ref|YP_004383797.1|  27 RRMSGSKMKADPLGGAPMGRGIVLEKVGIEAKQPNSAIRKAVRIQLIKNGRQVTAFAPGDGAIGFIDEHDEVLVDRI 103
                                       577889********************************************************************987 PP

                                       -......BTTSTTEEEEBETS---TSSSTTTTT---- CS
                   Ribosom_S12_S23  78 rrk.gkavkDlpGvrykvvkvagvslkalskykkekp 113
                                       +++ g++++D+pGvr+kv+ v++vsl++l++++kekp
  gi|330507369|ref|YP_004383797.1| 104 GGRqGRSMGDIPGVRFKVIAVNNVSLQELVRGRKEKP 140
                                       7666*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1120.95
//
Query:       gi|330507370|ref|YP_004383798.1|  [L=185]
Description: 30S ribosomal protein S7 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-39  134.0   7.6    3.9e-39  133.7   7.6    1.1  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.7   7.6   2.2e-43   3.9e-39      15     149 .]      42     185 .]      30     185 .] 0.95

  Alignments for each domain:
  == domain 1  score: 133.7 bits;  conditional E-value: 2.2e-43
                                       -SSTTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEE CS
                      Ribosomal_S7  15 dpkynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqv 87 
                                        +k ++++ve+l+nk+m+    +Gkk +A+ iv+ga+dii++ktk++pl+vl +A+ n+ Pr+ev ++++GG+t++ 
  gi|330507370|ref|YP_004383798.1|  42 FKKSEQHIVERLVNKMMRkeknTGKKLKAYAIVEGAFDIIAKKTKENPLTVLGQAIANAGPREEVVRLKYGGITVPK 118
                                       3468999**************9******************************************************* PP

                                       EEEE-HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                      Ribosomal_S7  88 pvevrpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                       +v+ +p+Rr+++Al++i+++a   +++k+k+++ +La+E+i+Aa+++  ++a++ ++ ++r+A+a+r
  gi|330507370|ref|YP_004383798.1| 119 AVDTAPQRRVDTALMFIAKGAhaaSFKKTKTAEAALADEIIAAANRDvkSYAINHKDSVERVAKAAR 185
                                       *******************9988899999*****************999****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1281.28
//
Query:       gi|330507371|ref|YP_004383799.1|  [L=201]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-18   67.0   0.0      3e-18   66.2   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    1.5e-15   57.6   0.0    2.4e-15   57.0   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    6.9e-09   35.8   0.0      9e-09   35.4   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.7e-08   35.1   0.0    2.4e-08   34.6   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    3.6e-06   26.8   0.0    4.4e-06   26.6   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.6e-05   23.7   0.0      4e-05   23.1   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0094   15.8   0.0      0.017   15.0   0.0    1.4  1  Methyltransf_8   Hypothetical methyltransferase
  ------ inclusion threshold ------
      0.046   13.3   0.0      0.069   12.7   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
       0.12   12.1   0.0       0.32   10.8   0.0    1.7  1  cIII             cIII protein family


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   1.5e-21     3e-18       1      96 []      32     124 ..      32     124 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 1.5e-21
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-..C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv..e 75 
                                       L++GcG G+ + a+ +   ++v++D+s  +l+l+++  ++++    ++ a+ae+lpf+++sfD v++++v  h+  +
  gi|330507371|ref|YP_004383799.1|  32 LELGCGDGKTLSAMPRS-WSIVALDISLPALRLCSRSHPQSD----LILANAERLPFKSESFDGVFAYHVAGHLflP 103
                                       89*************55.5**************988888876....6*****************************9 PP

                                       CHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllvi 96 
                                        ++++ +e+ RvLk gG+l++
  gi|330507371|ref|YP_004383799.1| 104 GRRALASEVSRVLKSGGKLFF 124
                                       ******************997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.0   1.2e-18   2.4e-15       1      97 []      31     120 ..      31     120 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 1.2e-18
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vL+lGcG G+++ a+ +     +++++Dis  +l+ + + +    ++ +++ ++ae+lpf+++sfD v++ ++  hl
  gi|330507371|ref|YP_004383799.1|  31 VLELGCGDGKTLSAMPRS---WSIVALDISLPALRLCSRSH----PQSDLILANAERLPFKSESFDGVFAYHVAGHL 100
                                       9**************988...7*****************99....899**********************7778887 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                         + ++++ +e++rvLk gG
  gi|330507371|ref|YP_004383799.1| 101 FLPGRRALASEVSRVLKSGG 120
                                       78999**************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   4.5e-12     9e-09      15     153 ..      20     163 ..       9     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 4.5e-12
                   Methyltransf_23  15 rllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.kakkaqkdqfdeqeaaepqgkfdlIvlre 90 
                                       r lp l++g rvL++GcG+G +l+ + ++ +s+++ D+s  a  + + + +++    ++++  ++++++fd + + +
  gi|330507371|ref|YP_004383799.1|  20 RNLPDLPEGTRVLELGCGDGKTLSAM-PRSWSIVALDISLPALRLCSrSHPQSDLILANAERLPFKSESFDGVFAYH 95 
                                       4456689999**************88.6778********99888876777777777777778888999********* PP

                   Methyltransf_23  91 vlehvp..dppellrqiatllkpgGylllseplasl...kedrllldwlylvpagrhisffsarslke 153
                                       v +h+      +l + + + lk gG l+++e++  +    e + +++ ++l+  g   ++f++++  e
  gi|330507371|ref|YP_004383799.1|  96 VAGHLFlpGRRALASEVSRVLKSGGKLFFREFGWLDmrmGEGQEVEEATFLRGSGIITHYFTESETSE 163
                                       ****973235689999***************7533344467777777777777654447777766655 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   1.2e-11   2.4e-08       1      99 []      32     122 ..      32     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.2e-11
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       Le+GcG+G +l+a+ ++   ++++++Dis  a+     +l +r+  + + +  +a+ l     + +sfD v+a +v 
  gi|330507371|ref|YP_004383799.1|  32 LELGCGDGKTLSAMPRS---WSIVALDISLPAL-----RLCSRSHPQSDLILANAERLP---FKsESFDGVFAYHVA 97 
                                       8*************999...*************.....666666544334444433333...3346*********** PP

                   Methyltransf_12  77 hhl..kdirevldnirklLkpgGrl 99 
                                        hl  + +r++ +++ ++Lk gG+l
  gi|330507371|ref|YP_004383799.1|  98 GHLflPGRRALASEVSRVLKSGGKL 122
                                       ****99999**************97 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   2.2e-09   4.4e-06       4     124 ..      28     139 ..      25     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.2e-09
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g+rvl+lGCG G+ + ++  +      +v +Dis  a++l+     +       +  +++e l+  ++ e+fD +++
  gi|330507371|ref|YP_004383799.1|  28 GTRVLELGCGDGKTLSAMP-R---SWSIVALDISLPALRLCSRSHPQSD-----LILANAERLP--FKSESFDGVFA 93 
                                       789***********99999.4...355**************99644444.....679*******..99********* PP

                   Methyltransf_31  81 nevl..naladpdkileeiervlkpggilliedprllaelpakvee 124
                                         v     l+   +   e++rvlk+gg l  +++ +l+   ++ +e
  gi|330507371|ref|YP_004383799.1|  94 YHVAghLFLPGRRALASEVSRVLKSGGKLFFREFGWLDMRMGEGQE 139
                                       ****6333333345556***************99944433333333 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     2e-08     4e-05      33     156 ..      13     129 ..      10     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2e-08
                                       HHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT CS
                   Ubie_methyltran  33 rlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaee 109
                                       rlW   v +l    +g++vl++ +G g      ++++ ++  +v lDi+   L+        ++  + +++ anae+
  gi|330507371|ref|YP_004383799.1|  13 RLWGGGVRNLPDLPEGTRVLELGCGDGKT----LSAMPRSWSIVALDISLPALRLC-----SRSHPQSDLILANAER 80 
                                       56666677777777899999999999865....34556678899999998888655.....456677899******* PP

                                       -TTS-T-EEEEEEES..-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE-- CS
                   Ubie_methyltran 110 LpfeddsfDvvtvsf..GlrnvtDklkaLkeayrvlkpGGrlvvlefsk 156
                                       Lpf+ +sfD v   +  G   ++ +     e+ rvlk GG+l+  ef  
  gi|330507371|ref|YP_004383799.1|  81 LPFKSESFDGVFAYHvaGHLFLPGRRALASEVSRVLKSGGKLFFREFGW 129
                                       *********875433226667888888889************9999875 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.5e-06     0.017      69     158 ..      24     126 ..      18     144 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.5e-06
                                       TS-TTS-EEEES-TT-HHHHH--S-..EEEEESS..........-SSTTEEES-TTS-S--TT-EEEEEEES-.... CS
                    Methyltransf_8  69 kkkdnlvvadlGcGeakiaeavrekekvrsfdlv..........avnervvacdlakvPledesvdvavfcls.... 131
                                         ++ + v +lGcG+ k  +a+ ++  + ++d+            ++++++  +  ++P + es d  vf       
  gi|330507371|ref|YP_004383799.1|  24 DLPEGTRVLELGCGDGKTLSAMPRSWSIVALDISlpalrlcsrsHPQSDLILANAERLPFKSESFDG-VFAYHvagh 99 
                                       556777899**********************98622121111112456677788899*********4.444440022 PP

                                       --SS-HHHHHHHHHHHEEEEEEEEEEE CS
                    Methyltransf_8 132 lmgtnladflkeanrvlkvGGllkvae 158
                                       l     +    e+ rvlk GG l+  e
  gi|330507371|ref|YP_004383799.1| 100 LFLPGRRALASEVSRVLKSGGKLFFRE 126
                                       5556778999***********998766 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.5e-05     0.069      12      37 ..      26      51 ..      20      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                              MetW 12 kpgsrvldlGcGdGellellkeekqv 37
                                      ++g+rvl+lGcGdG+ l+ +  +  +
  gi|330507371|ref|YP_004383799.1| 26 PEGTRVLELGCGDGKTLSAMPRSWSI 51
                                      7899***********99987665555 PP

>> cIII  cIII protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00016      0.32       5      31 ..     146     171 ..     145     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                              cIII   5 LaGsGvMSAYYPtESELskkiRrLIRA 31 
                                       L GsG++  Y+ tESE s  + rL+ A
  gi|330507371|ref|YP_004383799.1| 146 LRGSGIITHYF-TESETSELFCRLVPA 171
                                       77*****9776.***********9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1570.00
//
Query:       gi|330507372|ref|YP_004383800.1|  [L=395]
Description: lipoprotein-releasing system, ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-12   47.4   1.8      2e-12   47.4   1.8    3.1  3  FtsX         FtsX-like permease family
    9.7e-12   45.6   0.3    1.6e-11   44.9   0.3    1.3  1  MacB_PCD     MacB-like periplasmic core domain
  ------ inclusion threshold ------
          6    6.5   8.1        1.6    8.4   0.0    3.0  3  DUF4131      Domain of unknown function (DUF4131)


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   0.1      0.11   6.7e+02      17      38 ..      28      49 ..      24      69 .. 0.63
   2 ?    1.6   0.3     0.065   3.9e+02      67      91 ..     259     283 ..     226     287 .. 0.56
   3 !   47.4   1.8   3.4e-16     2e-12       2      96 .]     290     388 ..     289     388 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.11
                              FtsX 17 vlllllteillitlvalviGlg 38
                                      ++l +l  +l++++  ++++l+
  gi|330507372|ref|YP_004383800.1| 28 TFLSVLAVALAVSISIIFSSLI 49
                                      4444444444444444444444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.065
                              FtsX  67 itvliiivlllllallagllsiski 91 
                                         +  + +ll++++ ++g++si ++
  gi|330507372|ref|YP_004383800.1| 259 GFWTRLSILLFMVVAFFGVASIMNL 283
                                       3344444555555556678888776 PP

  == domain 3  score: 47.4 bits;  conditional E-value: 3.4e-16
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs....selkisidlitvliiiv 74 
                                       +eig+l a+G+++k+++ ++l e+ l++l+++++G +lgl+ +++l  v  ++  +    + l++ +++ ++l++ +
  gi|330507372|ref|YP_004383800.1| 290 KEIGMLMAMGARTKDIRNIFLAESSLLGLIGAAAGSLLGLAGIYYLGRVPFEVAAGgsviTTLPLILNPWDILLLNI 366
                                       8********************************************888887776657788***************** PP

                              FtsX  75 lllllallagllsiskilkkep 96 
                                       +++ l ++a+l++++k+++++p
  gi|330507372|ref|YP_004383800.1| 367 VVVALSMVAALYPARKASRIDP 388
                                       *******************997 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.3   2.7e-15   1.6e-11       1     180 [.      28     222 ..      28     233 .. 0.71

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.7e-15
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgk...gsgeslsdpdvealrrevp.veavapvv 73 
                                       ++l+vL++a++v   i++ sl++g q+ ++  ++  + l +v + +    +  +l  ++++++  ++p  ++ a+ +
  gi|330507372|ref|YP_004383800.1|  28 TFLSVLAVALAVSISIIFSSLINGQQQILTNLVE--EKLPHVVVEPregEDFIHLYNSLLDRIV-SQPgLRSTAASL 101
                                       8*************************88888777..4455665655224333334455555432.468888777765 PP

                          MacB_PCD  74 .....tvrgggsgeeevtvvgvdp.dyfkvfglklaeGrffteadlr..ggpnvvvigeelaerlf.pvGdtirl.. 139
                                            ++r ++  ++++ + g+dp d  k++++   +G++    d+   ++++ ++ig +la+ l  ++Gd++    
  gi|330507372|ref|YP_004383800.1| 102 stpatLSRKDK--TKNALLKGADPlDIDKIYKI---QGSL-VRGDFVsvQQDRNAAIGVKLADSLElKLGDKLLAtf 172
                                       56642223333..66699***997666667766...5864.5555553569999**********88*******8899 PP

                          MacB_PCD 140 .....kpftVvGvledppgsgsalgddavylplttlqrrs.........itvrlk 180
                                             ++tV++++++  g  + l+d  ++++l t++ ++         + ++l+
  gi|330507372|ref|YP_004383800.1| 173 prsrsTDLTVAAIFQT--G--TPLDDRVAFVSLDTAR-NFrdegdvinaVEISLN 222
                                       *999999******933..4..5689*******88873.22234555555555555 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00026       1.6      15      63 ..      14      59 ..       6      92 .. 0.82
   2 ?   -0.1   0.2      0.11   6.4e+02      28      45 ..     261     278 ..     228     286 .. 0.63
   3 ?    0.4   1.3     0.073   4.4e+02       9      61 ..     319     388 ..     311     394 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00026
                           DUF4131 15 llllllllllrrrprrrvllllllllllallgfalrapqpnandlsqll 63
                                      l+++l+ ++   r+rr+++l++l+++l++++ + ++++ ++++++ + l
  gi|330507372|ref|YP_004383800.1| 14 LTIALRHVI---RRRRQTFLSVLAVALAVSISIIFSSLINGQQQILTNL 59
                                      445555555...9********************9999999888876555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.11
                           DUF4131  28 prrrvllllllllllall 45 
                                       ++r  +ll++++++++++
  gi|330507372|ref|YP_004383800.1| 261 WTRLSILLFMVVAFFGVA 278
                                       445555555555555554 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.073
                           DUF4131   9 llalllllllllllllrr.................rprrrvllllllllllallgfalrapqpnandlsq 61 
                                       + a+++ ll l++++++                     + + +lll + ++al+++a+ +p + a+++++
  gi|330507372|ref|YP_004383800.1| 319 IGAAAGSLLGLAGIYYLGrvpfevaaggsvittlpLILNPWDILLLNIVVVALSMVAALYPARKASRIDP 388
                                       3334444444444444336777777777777666633333345555555555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2870.55
//
Query:       gi|330507373|ref|YP_004383801.1|  [L=385]
Description: ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-17   63.3   4.1    2.2e-17   63.3   4.1    3.0  3  FtsX             FtsX-like permease family
    7.7e-14   52.5   0.7    1.3e-13   51.7   0.7    1.4  1  MacB_PCD         MacB-like periplasmic core domain
  ------ inclusion threshold ------
       0.05   13.6   0.1       0.18   11.8   0.0    2.0  2  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial a
      0.066   12.3  12.2       0.16   11.0  12.2    1.7  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.053   2.4e+02      29      51 ..      21      46 ..      14      73 .. 0.50
   2 ?    0.4   0.7      0.21   9.4e+02      23      41 ..     252     270 ..     242     278 .. 0.56
   3 !   63.3   4.1   4.9e-21   2.2e-17       1      96 []     280     378 ..     280     378 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.053
                              FtsX 29 tlvalviGlgl...gllaaqllsdvl 51
                                      tl++ +i++++   +l +++ +s+ +
  gi|330507373|ref|YP_004383801.1| 21 TLISVAIAVAIiimSLGLTESVSSQI 46
                                      33333333222001333333333333 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.21
                              FtsX  23 teillitlvalviGlglgl 41 
                                       t il++ ++ l++++++++
  gi|330507373|ref|YP_004383801.1| 252 TNILFYMFILLISAFVIAN 270
                                       4444555555555544443 PP

  == domain 3  score: 63.3 bits;  conditional E-value: 4.9e-21
                              FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs...selkisidlitvliiiv 74 
                                       +reigil a+G+k++++l ++l+e++li+l+a ++G +lg++aa+++  + l++ ++     + i   ++ ++i+++
  gi|330507373|ref|YP_004383801.1| 280 RREIGILMAMGAKRRSILMIFLLENMLISLPAGILGAVLGYAAAWAITLLPLNVTSAaagEGIVIAARPEYFVIALA 356
                                       79********************************************999999998878889**************** PP

                              FtsX  75 lllllallagllsiskilkkep 96 
                                       ++l l  ++gl++++ +++ +p
  gi|330507373|ref|YP_004383801.1| 357 FALSLNFVSGLYPAYSAARLDP 378
                                       *****************99987 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.7   2.9e-17   1.3e-13       1     194 [.      18     226 ..      18     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 2.9e-17
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgk.gsgeslsdpdvealrr...evp.veavapv 72 
                                       +++t++++ai+va +i+ ++l+e++++++ ++  +     ++ +g+  s + +++  ++ l++   + p v av+p+
  gi|330507373|ref|YP_004383801.1|  18 TAFTLISVAIAVAIIIMSLGLTESVSSQIIENTVNKNP--HILIGPkESESYINM--YRSLSDqvgSYPgVLAVSPR 90 
                                       899****************************9886766..888876322222232..3334322445899******9 PP

                          MacB_PCD  73 v....tvrgggsgeeevtvvgvdpdyfk.vfgl.kl.aeGrffteadlrggpnvvvigeelaerlf.pvGdtirl.. 139
                                       +    ++r++++  ++v  vgvdp++ + + ++ +   +G   +++dlr +++++ +g ela++l  + G    l  
  gi|330507373|ref|YP_004383801.1|  91 LvgqgAARFQDN-VQSVEFVGVDPALEDrLMSVqEStISG---NFSDLRFNNRGAFLGVELARNLNiREGGDFYLyl 163
                                       755543344432.24489999**97766655554333668...5599**9**************8895566666678 PP

                          MacB_PCD 140 ....kpftVvGvledppgsgsalgddavylplttlqrrs........itvrlkdgadleaaaaelek 194
                                            +++ +G+l++     +  +++ vyl+l+t+q+          i v+l+d + + a+a++l++
  gi|330507373|ref|YP_004383801.1| 164 kndsLRLKMIGILQKD----TVKDETLVYLSLSTAQELVaegdvvseIGVKLADYTRAPAMAKKLND 226
                                       999988*******553....2235788****9988332244555566**********9999999876 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.3   5.9e+03      31      44 ..      51      65 ..      47      66 .. 0.79
   2 ?   11.8   0.0     4e-05      0.18      14      40 ..     146     172 ..     145     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
                                      ECTT.CCCCCCCHHS CS
                    MazE_antitoxin 31 vdgd.kiilrplksl 44
                                      v+++ +i++ p++s+
  gi|330507373|ref|YP_004383801.1| 51 VNKNpHILIGPKESE 65
                                      55667999*999875 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4e-05
                                       CCHHHCCEECTCEEEEEECTTCCCCCC CS
                    MazE_antitoxin  14 evrfelgireGdevelevdgdkiilrp 40 
                                       e+++ l+ireG +  l+ ++d++ l+ 
  gi|330507373|ref|YP_004383801.1| 146 ELARNLNIREGGDFYLYLKNDSLRLKM 172
                                       89*******************998875 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 ?   11.0  12.2   3.6e-05      0.16      60     226 ..     138     321 ..      16     374 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.6e-05
                   ABC2_membrane_3  60 lvyevdseeeakkalkngdidgilvipkgfskdll.......kgesatvtvli.nssnlnss............... 113
                                       +   +   e a+++   ++ d +l+++++ ++  +       + ++ t+++l+ ++++ +++               
  gi|330507373|ref|YP_004383801.1| 138 NRGAFLGVELARNLNIREGGDFYLYLKNDSLRLKMigilqkdTVKDETLVYLSlSTAQELVAegdvvseigvklady 214
                                       55555555555555555566666666666665444777776633333333333222222222444443333222222 PP

                   ABC2_membrane_3 114 ...kailnalnsllqqlnasalvlqseatstsaninvestqleeelsnvasflvgliliilifitasfiavsiveEk 187
                                          +a+++ ln+ ++ ++            + + ++ ++++++  +++v+++l+ +++++++ +++++++ ++v+ +
  gi|330507373|ref|YP_004383801.1| 215 traPAMAKKLNDASRYKA-----------TSWQDFS-REIARFVGNQGVTNILFYMFILLISAFVIANTTIMVVSKR 279
                                       222555555555333322...........2223333.33455*************9999999999999999999877 PP

                   ABC2_membrane_3 188 esrikelqlvsgvsplq....ywlskilgdflvyllqlllill 226
                                       ++ i  +++ +g ++ +    ++l ++l+++ +++l ++l  +
  gi|330507373|ref|YP_004383801.1| 280 RREIG-ILMAMGAKRRSilmiFLLENMLISLPAGILGAVLGYA 321
                                       77666.777999**99955555555555555555555444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2849.56
//
Query:       gi|330507374|ref|YP_004383802.1|  [L=258]
Description: lipoprotein-releasing system, ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-32  112.5   0.0      3e-32  112.0   0.0    1.2  1  ABC_tran        ABC transporter
    6.6e-10   38.8   1.2    1.2e-08   34.6   1.2    2.0  1  SMC_N           RecF/RecN/SMC N terminal domain
    3.6e-06   27.4   0.0    7.5e-06   26.4   0.0    1.5  1  AAA_16          AAA ATPase domain
    4.2e-06   26.8   0.0     0.0063   16.4   0.0    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    7.4e-06   25.6   0.1    1.5e-05   24.6   0.1    1.5  1  AAA_29          P-loop containing region of AAA domain
    0.00066   20.0   0.4     0.0047   17.2   0.4    2.1  1  AAA_22          AAA domain
      0.001   19.0   1.1     0.0016   18.3   0.2    1.7  2  RsgA_GTPase     RsgA GTPase
     0.0017   18.9   0.2     0.0044   17.6   0.0    1.6  2  AAA_23          AAA domain
     0.0028   17.4   0.0     0.0078   16.0   0.0    1.5  1  AAA_15          AAA ATPase domain
  ------ inclusion threshold ------
       0.01   15.4   0.2      0.088   12.4   0.1    2.1  2  AAA_25          AAA domain
      0.013   15.6   0.5       0.03   14.4   0.1    1.9  2  MMR_HSR1        50S ribosome-binding GTPase
      0.027   14.6   0.1       0.22   11.6   0.0    2.1  2  AAA_33          AAA domain
      0.028   14.0   0.6        0.4   10.2   0.1    2.2  2  cobW            CobW/HypB/UreG, nucleotide-binding domain
      0.035   13.8   0.2       0.66    9.7   0.0    2.1  2  IstB_IS21       IstB-like ATP binding protein
      0.035   14.0   0.1       0.22   11.4   0.0    2.1  2  NACHT           NACHT domain
      0.066   13.1   0.2        5.3    6.9   0.0    2.3  2  NTPase_1        NTPase
      0.069   13.2   0.1        3.9    7.5   0.0    2.2  2  MutS_V          MutS domain V
       0.08   12.3   0.6        8.8    5.6   0.1    2.2  2  ATPase          KaiC
      0.087   12.5   0.0       0.19   11.5   0.0    1.5  2  AAA_30          AAA domain
        0.1   12.1   0.1        1.2    8.6   0.0    2.1  2  AAA_7           P-loop containing dynein motor region
        0.1   11.7   0.1       0.21   10.7   0.1    1.5  1  NB-ARC          NB-ARC domain
       0.17   11.6   0.6       0.74    9.5   0.1    2.2  3  Cytidylate_kin  Cytidylate kinase
        0.2   11.3   0.3       0.42   10.3   0.0    1.6  2  AAA_24          AAA domain
       0.21   12.0   0.8         19    5.7   0.1    2.3  2  AAA             ATPase family associated with various cellula


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 !  112.0   0.0     4e-35     3e-32       1     136 [.      27     175 ..      27     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 4e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l+ vs+k+k+ge vaivG++G+GKStLl+++  l +p +G+i l+g d+++    ++ +  ++e+g+++q ++l pe
  gi|330507374|ref|YP_004383802.1|  27 LDGVSVKIKAGEFVAIVGPSGSGKSTLLNMIGLLDTPSSGHIFLKGIDVSRaspdERARLRNQELGFVFQYHHLIPE 103
                                       789************************************************9997777778899************* PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        t+ en             e+ ++ e++l+ +gl +    +++s+p++LSgGq qrva+aral+++p++++ DE t
  gi|330507374|ref|YP_004383802.1| 104 FTAVENvmmpmlianksktEAHKRGEELLRAVGLGD----RLHSRPNQLSGGQNQRVAVARALANNPSIVIGDELT 175
                                       **9999********9776666666788888888777....556667****************************77 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   1.2   1.6e-11   1.2e-08      23     212 ..      37     221 ..      22     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.6e-11
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevs 98 
                                         +f aivGp GSGKs ll+ i  +L + s+ ++  + ++    + +e+a++ + e+  +f+ +    + +  e+v 
  gi|330507374|ref|YP_004383802.1|  37 G-EFVAIVGPSGSGKSTLLNMI-GLLDTPSSGHIFLKGIDVSRASPDERARLRNQELGFVFQYHHLIpEFTAVENVM 111
                                       3.599*****************.677777776766655544444478999999999999999887763333444444 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                       +   +   ++s+ +  ++  +      l  + +  +++LSgG+ + va+a  +A    +  ++++ De+  +LD k 
  gi|330507374|ref|YP_004383802.1| 112 MP--MLIANKSKTEAHKRGEELLRAVGLGDRLHSRPNQLSGGQNQRVAVARALA----NNPSIVIGDELTGNLDTKS 182
                                       44..444444444444444444445555555566799***********998877....45679999*********** PP

                                       HHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 176 vkkvaellkekskn..aQfivislreemlekadklvgvt 212
                                        + + +ll+e +++    fi ++++ ++ ek d+++++ 
  gi|330507374|ref|YP_004383802.1| 183 SELIYNLLRELNQKinQTFILVTHDMTLAEKTDRILRIV 221
                                       *********988765255899**************9986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0     1e-08   7.5e-06       3     166 ..      18     198 ..      16     204 .. 0.59

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1e-08
                            AAA_16   3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd..ggiflrgkcdql....esaipy..sa 71 
                                       +G + e+++L  +  ++++g  e v ++G+sG+GKs+l++++   l +   g ifl+g  ++     e+a+ +  + 
  gi|330507374|ref|YP_004383802.1|  18 YGNGVEVRALDGVSVKIKAG--EFVAIVGPSGSGKSTLLNMIG-LLDTPssGHIFLKGIDVSRaspdERAR-LrnQE 90 
                                       56667787887777677777..79***************9999.555554534444443333333322222.13333 PP

                            AAA_16  72 laqalareellrqllde...........aesaeleawrekleeala.......avpelagaeasrllellkrll..a 128
                                       l  ++  ++l+ +  +            ++++e+    e+l++a++                 ++l    ++ +  a
  gi|330507374|ref|YP_004383802.1|  91 LGFVFQYHHLIPEFTAVenvmmpmlianKSKTEAHKRGEELLRAVGlgdrlhsRP--------NQLSGGQNQRVavA 159
                                       5555555677777766677777776433444444444444444444444333222........33333333333112 PP

                            AAA_16 129 llsrderplvlvlDdlq.wadeaslqllaaLlrllesk.p 166
                                       ++     p +++ D+l   +d+ s +l+++Llr+l++k +
  gi|330507374|ref|YP_004383802.1| 160 RALA-NNPSIVIGDELTgNLDTKSSELIYNLLRELNQKiN 198
                                       2222.457999999999999**************999655 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   8.4e-06    0.0063       1      22 [.      39      60 ..      39     104 .. 0.80
   2 !    8.9   0.0    0.0016       1.2     236     301 ..     147     210 ..     106     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.4e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      + +++Gp gsGKS+LL  + ll
  gi|330507374|ref|YP_004383802.1| 39 FVAIVGPSGSGKSTLLNMIGLL 60
                                      679**************99887 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTHSpll 301
                                       +lS G+ +  a++ al+  +   s+++ DE+  +L+ k  + ++ ll+el+++  Q  il+TH+ +l
  gi|330507374|ref|YP_004383802.1| 147 QLSGGQNQRVAVARALANNP---SIVIGDELTGNLDTKSSELIYNLLRELNQKINQTfILVTHDMTL 210
                                       56666655556666666666...99999*******************99999999999******887 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 !   24.6   0.1   2.1e-08   1.5e-05      12      49 ..      27      64 ..      23      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.1e-08
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                      +dg +++i+  +++ ++GpsGsGKSTll  i  l +p+
  gi|330507374|ref|YP_004383802.1| 27 LDGVSVKIKAGEFVAIVGPSGSGKSTLLNMIGLLDTPS 64
                                      578899999777****************7666665555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.4   6.3e-06    0.0047       5      30 ..      37      62 ..      33     222 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.3e-06
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqld 30
                                        +++++G+sG+GK+tll+++   ++
  gi|330507374|ref|YP_004383802.1| 37 GEFVAIVGPSGSGKSTLLNMIGLLDT 62
                                      56899*************99887764 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   2.2e-06    0.0016      94     119 ..      31      57 ..      15      68 .. 0.83
   2 ?   -2.1   0.0       4.2   3.1e+03      92     107 ..     157     172 ..     106     202 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.2e-06
                                       HHHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  94 kellkd.ktsvlvGqSGvGKStLinal 119
                                       + ++k  +++++vG+SG GKStL+n++
  gi|330507374|ref|YP_004383802.1|  31 SVKIKAgEFVAIVGPSGSGKSTLLNMI 57 
                                       5556555999***************87 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.2
                                       HHHHHCTTSEEEEECS CS
                       RsgA_GTPase  92 elkellkdktsvlvGq 107
                                       +++++l+++ s+++G 
  gi|330507374|ref|YP_004383802.1| 157 AVARALANNPSIVIGD 172
                                       3444455555555554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.9e-06    0.0044      21      40 ..      39      58 ..      24      62 .. 0.84
   2 ?   -1.7   0.0       4.6   3.4e+03     184     191 ..     189     196 ..     119     217 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.9e-06
                            AAA_23 21 ltlItGpNGaGKTTildAik 40
                                      +++I+Gp G+GK+T+l+ i 
  gi|330507374|ref|YP_004383802.1| 39 FVAIVGPSGSGKSTLLNMIG 58
                                      679*************9986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.6
                            AAA_23 184 eleeleee 191
                                        l el+++
  gi|330507374|ref|YP_004383802.1| 189 LLRELNQK 196
                                       12222222 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   0.0     1e-05    0.0078      17      65 ..      32      75 ..      25     134 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                            AAA_15 17 veidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedl 65
                                      v+i+  e +  ++G+ +sGKS++l+++ l+ + +    +  i+++  d+
  gi|330507374|ref|YP_004383802.1| 32 VKIKAGE-FVAIVGPSGSGKSTLLNMIGLLDTPS----SGHIFLKGIDV 75
                                      4566666.*******************9888877....33344444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00012     0.088      30      50 ..      34      54 ..      29      77 .. 0.90
   2 ?    0.6   0.0      0.47   3.5e+02     166     188 ..     184     206 ..     117     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      + age+++++G++g+GK+tl+
  gi|330507374|ref|YP_004383802.1| 34 IKAGEFVAIVGPSGSGKSTLL 54
                                      679****************97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.47
                            AAA_25 166 galvealeriarrtgaavllvhH 188
                                       + +++ l+++ ++ + +++lv H
  gi|330507374|ref|YP_004383802.1| 184 ELIYNLLRELNQKINQTFILVTH 206
                                       56778899999999999999999 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.1e-05      0.03       2      19 ..      40      57 ..      39      79 .. 0.92
   2 ?   -2.0   0.0       4.9   3.6e+03      29      38 ..     201     210 ..     177     232 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.1e-05
                                      EEEEESTTSSHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                      vaivG + +GKStL+n +
  gi|330507374|ref|YP_004383802.1| 40 VAIVGPSGSGKSTLLNMI 57
                                      8***************76 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.9
                                       STTSSSSEEE CS
                          MMR_HSR1  29 kpgtTrdine 38 
                                       +  +T d++ 
  gi|330507374|ref|YP_004383802.1| 201 FILVTHDMTL 210
                                       2233333333 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    0.0003      0.22       2      16 ..      40      54 ..      39      94 .. 0.92
   2 ?    0.8   0.0      0.65   4.9e+02      47      85 ..     178     216 ..     139     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                            AAA_33  2 vllvGlpGsGKstla 16
                                      v +vG++GsGKstl+
  gi|330507374|ref|YP_004383802.1| 40 VAIVGPSGSGKSTLL 54
                                      678**********97 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.65
                            AAA_33  47 dytrvldrlyqilnelarkalsagrnvildatnlsrrer 85 
                                         t+ ++ +y+ l+el +k  +  + v  d+t++++ +r
  gi|330507374|ref|YP_004383802.1| 178 LDTKSSELIYNLLRELNQKINQTFILVTHDMTLAEKTDR 216
                                       445667778888888887655555555558888877555 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 ?   10.2   0.1   0.00054       0.4       3      20 ..      40      57 ..      38      66 .. 0.88
   2 ?    2.0   0.0      0.18   1.4e+02      39      67 ..     204     231 ..     174     243 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00054
                                      EEEEESTTCCHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhl 20
                                      + ++G+ GsGK+tLln +
  gi|330507374|ref|YP_004383802.1| 40 VAIVGPSGSGKSTLLNMI 57
                                      5799***********976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.18
                                       CHCCCCCCHCCCT.EEEETTTTECCHCTT CS
                              cobW  39 vsiDaellretgveivelenGciCctlre 67 
                                       v +D +l ++t + i+ + +G+i c +r 
  gi|330507374|ref|YP_004383802.1| 204 VTHDMTLAEKT-DRILRIVDGKIVCEMRR 231
                                       56666666666.67999999999999764 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00088      0.66      44      68 ..      34      58 ..      21      67 .. 0.83
   2 ?    2.0   0.0       0.2   1.5e+02     106     153 ..     163     212 ..     145     219 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00088
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                      i++ e ++++GpsG GKs l   +g
  gi|330507374|ref|YP_004383802.1| 34 IKAGEFVAIVGPSGSGKSTLLNMIG 58
                                      788899************9977666 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.2
                         IstB_IS21 106 llkvdllilDdlgllpldqaeaellfevi...ekryerrsiiitsnlpfae 153
                                         +++++i D+l   +ld +++el+++++   +++ +++ i++t ++++ae
  gi|330507374|ref|YP_004383802.1| 163 ANNPSIVIGDELT-GNLDTKSSELIYNLLrelNQKINQTFILVTHDMTLAE 212
                                       3455777778874.5677777777777761115667778899998888776 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    0.0003      0.22       3      20 ..      40      57 ..      38      65 .. 0.90
   2 ?    0.1   0.0      0.89   6.7e+02      96     127 ..     177     206 ..     139     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                                      EEEEC-TTTCHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkl 20
                                      v++ G++GsGK+tLl  +
  gi|330507374|ref|YP_004383802.1| 40 VAIVGPSGSGKSTLLNMI 57
                                      89*************876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.89
                                       -TCH.........HHHHHCTTTTT--EEEEEE CS
                             NACHT  96 dlgqkekqpvrtlLselirkkllpeasllltv 127
                                        l+ k  + + +lL+el +k  + ++ +l+t 
  gi|330507374|ref|YP_004383802.1| 177 NLDTKSSELIYNLLRELNQK--INQTFILVTH 206
                                       44444444445555555555..5555555554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.007       5.3       2      19 ..      40      57 ..      39      75 .. 0.90
   2 ?    4.1   0.0     0.051        38      88     153 ..     158     226 ..     145     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.007
                                      EEEE--TTSSHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkv 19
                                      v+i Gp+G+GK+Tl++ +
  gi|330507374|ref|YP_004383802.1| 40 VAIVGPSGSGKSTLLNMI 57
                                      6899**********9865 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.051
                                       HHHHHHHHH-EEEE---.STTGGG-HHHHHHHHHHHT..TTSEEEEE--SS--SHHHHHHHT-TT-EEE CS
                          NTPase_1  88 alrkalseadviviDEi.GkmElkskkfkeaveevLk..sekpvlavihrrkdlalveeirerkdvkvf 153
                                       + r   +++ +++ DE  G++  ks +++  + + L+   ++ ++ v h  +  + +++i +  d+k++
  gi|330507374|ref|YP_004383802.1| 158 VARALANNPSIVIGDELtGNLDTKSSELIYNLLRELNqkINQTFILVTHDMTLAEKTDRILRIVDGKIV 226
                                       33444488899999**66**********99999999855567788888888766667777776666664 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.08        60       3      21 ..      42      60 ..      40      63 .. 0.88
   2 ?    7.5   0.0    0.0052       3.9      74     142 ..     162     229 ..     129     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.08
                                      EE-STTSSHHHHHHHHHHH CS
                            MutS_V  3 itGpnmaGkstylrqvali 21
                                      i Gp  +Gkst+l  ++l+
  gi|330507374|ref|YP_004383802.1| 42 IVGPSGSGKSTLLNMIGLL 60
                                      89***********999875 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0052
                                       T--TTSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEEE CS
                            MutS_V  74 natekslvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavke 142
                                        a++ s+vi DEl  G   +    + + +++ l +ki+ + ++ tH + l++ ++++ ++   ++ ++ 
  gi|330507374|ref|YP_004383802.1| 162 LANNPSIVIGDELT-GNLDTKSSELIYNLLRELNQKINQTFILVTHDMTLAEKTDRILRIVDGKIVCEM 229
                                       478899******96.555566778999*************************99999888877666654 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.012       8.8      16      35 ..      34      53 ..      21      66 .. 0.87
   2 ?    5.0   0.0     0.018        13     142     193 ..     184     233 ..     163     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.012
                            ATPase 16 ipegrvvlitGepGtGKtif 35
                                      i  g+ v i+G +G+GK+++
  gi|330507374|ref|YP_004383802.1| 34 IKAGEFVAIVGPSGSGKSTL 53
                                      788999***********987 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.018
                            ATPase 142 eilrqlvrvl.kklgvTailvsekssseeaaggygveefivdgvivLdlkeie 193
                                       e + +l+r+l +k+++T ilv+       a ++ ++   ivdg iv + ++++
  gi|330507374|ref|YP_004383802.1| 184 ELIYNLLRELnQKINQTFILVTHD--MTLAEKTDRILR-IVDGKIVCEMRRKD 233
                                       56778999998999********94..445667788999.9***9998877765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00025      0.19      19      41 ..      38      60 ..      30      93 .. 0.80
   2 ?   -2.9   0.0       6.1   4.5e+03       7      18 ..     155     166 ..     146     200 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                            AAA_30 19 rvavltGpAGtGKttalkalrea 41
                                       +++++Gp G+GK+t+l+ +  +
  gi|330507374|ref|YP_004383802.1| 38 EFVAIVGPSGSGKSTLLNMIGLL 60
                                      4899*************988655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.1
                            AAA_30   7 aaavealltsgd 18 
                                       + av+++l+++ 
  gi|330507374|ref|YP_004383802.1| 155 RVAVARALANNP 166
                                       444444443332 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0017       1.2      30      52 ..      34      56 ..      24      78 .. 0.82
   2 ?    1.2   0.0      0.31   2.3e+02      39      82 ..     175     218 ..     161     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                             AAA_7 30 lknkkpvllvGptGtGKtviikd 52
                                      +k++  v +vGp+G+GK+++++ 
  gi|330507374|ref|YP_004383802.1| 34 IKAGEFVAIVGPSGSGKSTLLNM 56
                                      67788899***********9886 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.31
                             AAA_7  39 vGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82 
                                       +G+  t  + +i +ll++l+++  ++ ++  + +t a+++ +i+
  gi|330507374|ref|YP_004383802.1| 175 TGNLDTKSSELIYNLLRELNQKINQTFILVTHDMTLAEKTDRIL 218
                                       455555567789999****9777777777777777788877776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00029      0.21      21      40 ..      38      57 ..      25      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                                      EEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqi 40
                                       +va+vG  G+GK+tl++ i
  gi|330507374|ref|YP_004383802.1| 38 EFVAIVGPSGSGKSTLLNMI 57
                                      489*************9866 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00099      0.74       1      17 [.      40      56 ..      40      60 .. 0.87
   2 ?   -1.6   0.0       2.4   1.8e+03     138     151 ..      78      91 ..      75     106 .. 0.79
   3 ?   -2.1   0.0       3.4   2.6e+03     186     208 ..     198     220 ..     176     222 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00099
                                      EEEE-STTSSHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvara 17
                                      +ai GP+gsGKs++  +
  gi|330507374|ref|YP_004383802.1| 40 VAIVGPSGSGKSTLLNM 56
                                      799**********9766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.4
                                       --HHHHHHHHHHHH CS
                    Cytidylate_kin 138 AsveeRakRRlkql 151
                                       As++eRa+ R+++l
  gi|330507374|ref|YP_004383802.1|  78 ASPDERARLRNQEL 91 
                                       99*****9999885 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.4
                                       TT-EEEETTTS-HHHHHHHHHHH CS
                    Cytidylate_kin 186 edaliidtskltieevvekilel 208
                                       +  +i+ t ++t++e  ++il+ 
  gi|330507374|ref|YP_004383802.1| 198 NQTFILVTHDMTLAEKTDRILRI 220
                                       45667777788888777777765 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   0.00056      0.42       5      22 ..      40      57 ..      37      70 .. 0.87
   2 ?   -3.1   0.0       7.3   5.4e+03     113     133 ..     188     209 ..     179     220 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00056
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++i+Gpsg+GK+tl++++
  gi|330507374|ref|YP_004383802.1| 40 VAIVGPSGSGKSTLLNMI 57
                                      78************9987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.3
                            AAA_24 113 rllkklqelrk.nvifiahekt 133
                                       +ll+ l++  + ++i++ h  t
  gi|330507374|ref|YP_004383802.1| 188 NLLRELNQKINqTFILVTHDMT 209
                                       3444443333357777777655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.042        31       2      18 ..      41      57 ..      40      66 .. 0.89
   2 ?    5.7   0.1     0.025        19      48     119 ..     154     215 ..     114     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.042
                                      EEESSTTSSHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakav 18
                                       ++Gp G GK++l + +
  gi|330507374|ref|YP_004383802.1| 41 AIVGPSGSGKSTLLNMI 57
                                      589*********98766 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.025
                                       HHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHH CS
                               AAA  48 elfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpal 119
                                       + ++ a++ a +psi++ DE+     ++       +++++  Ll+el++  +     ++i++t+++   ++  
  gi|330507374|ref|YP_004383802.1| 154 QRVAVARALAnNPSIVIGDELTGNLDTK-------SSELIYNLLRELNQKIN----QTFILVTHDMTLAEKTD 215
                                       3344444444559999999999888888.......78888888888888877....48999998876655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 1881.13
//
Query:       gi|330507375|ref|YP_004383803.1|  [L=183]
Description: hypothetical protein MCON_1289 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        3.1    8.2   4.5        5.7    7.3   4.1    1.6  2  Ly49      Ly49-like protein, N-terminal region


Domain annotation for each model (and alignments):
>> Ly49  Ly49-like protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.14   2.5e+03      16      28 ..      11      23 ..       9      27 .. 0.84
   2 ?    7.3   4.1   0.00032       5.7      52      95 ..      23      66 ..      13      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.14
                                      XXXXXXXXXXXXX CS
                              Ly49 16 lllLvtvavLvtk 28
                                      +llL++ avL+++
  gi|330507375|ref|YP_004383803.1| 11 VLLLMMTAVLAVS 23
                                      6899999999985 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00032
                                      XXXXXXXXXXXXXXXXXXXX..HHHHHHHHHHHHHHHHHHHTTT CS
                              Ly49 52 mqndinlkeelLrnkslecsilkdlleslkreqkrlysktktvl 95
                                        +d++l+  lL+n +l+ ++l+++  +l+ +q+  +s ++tv 
  gi|330507375|ref|YP_004383803.1| 23 SAQDNSLNATLLNNTTLNNTTLNNTTINLSANQTINVSANETVE 66
                                      5689*****************************99999999873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1492.80
//
Query:       gi|330507376|ref|YP_004383804.1|  [L=327]
Description: methenyltetrahydromethanopterin cyclohydrolase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.2e-122  407.7   0.0   3.6e-122  407.5   0.0    1.0  1  MCH            Cyclohydrolase (MCH)
  ------ inclusion threshold ------
        0.1   12.3   0.0       0.17   11.6   0.0    1.3  1  Peptidase_C28  Foot-and-mouth virus L-proteinase


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 !  407.5   0.0    4e-126  3.6e-122       2     311 .]       7     318 ..       6     318 .. 0.99

  Alignments for each domain:
  == domain 1  score: 407.5 bits;  conditional E-value: 4e-126
                                       HHHHHHHHHHHHHHTHHHHT-EEEE-TTS-EEEESSSSS---HHHHHHHHHHHTTT-EEEEEEEEEETTEEEEEEEE CS
                               MCH   2 vnelalelveellekaeelrieveelengatviDaGveaeGgleAGlllaeiclggLaevslelsevkgaklpavev 78 
                                       +ne+++e++ee+l++ +el+iev+eleng+ viDaGv+a+Gg+ AG++l+++c+++La+++l++ ++ g+ lp v+v
  gi|330507376|ref|YP_004383804.1|   7 INEMGFEVFEEMLDYGDELQIEVYELENGTVVIDAGVKAQGGIGAGIYLSRLCMSDLADIQLAPCDIGGILLPGVQV 83 
                                       8**************************************************************************** PP

                                       EESSHHHHHTTTTS--EEEEETTEEEEEESTTHHHHTS.HHHHHHHT-----S-EEEEEESSS---HHHHHHHHHHH CS
                               MCH  79 stdhPvlacLasqkAgWelsaekffalgsGPaRalaak.eelfeelgyedeadaavlvlesdklPdeevvekvaeec 154
                                       +td P+++c+asq+A W+++a+k+fa+gsGPaR la+k ++l+e++g+e+ +d +v+vles+klPde+v +++a++c
  gi|330507376|ref|YP_004383804.1|  84 ATDYPAVSCMASQCAMWQIKADKYFAMGSGPARVLAGKtRDLYEKIGFEEFSDIGVIVLESNKLPDEKVSASIAQKC 160
                                       **************************************9************************************** PP

                                       TS-GGGEEEEEE-SSSHHHHHHHHTTHHHHHHHHHHHTT--GGGEEEEEEEEE-----SSHHHHHHHHHHHHHHH-E CS
                               MCH 155 gvepenvtllvaptaSlaGsvqvaaRvvevalhkleelgfdlekivsavgtaPiapvakdelkamgrtndailYggr 231
                                       g++p+++ +++apt+S+aG vqv+aRvve++lhkl+++gfd+++i+s++g+aPi+p+++d++++mg++ndai+Ygg+
  gi|330507376|ref|YP_004383804.1| 161 GIDPADLRIAIAPTDSVAGLVQVSARVVETGLHKLFTMGFDINTIKSGWGRAPISPITGDATNCMGSSNDAIIYGGE 237
                                       ***************************************************************************** PP

                                       EEEEES....TTHHHHHHHSSGGGSTTTTS-HHHHHHHTTTTGGGS-GGGSS-SEEEEEETTT--EEEEE---HHHH CS
                               MCH 232 vhltve.aedeeaedlakklpssaskdygkpFaeifkeaeydfykidkalFspAevtvndletgktfkaGelneell 307
                                       +++t+  +++ee+++++k +pssas+d+g pF+++fk+a++df+k+d+++F+pA+v++n++++ +tf++G++++e+l
  gi|330507376|ref|YP_004383804.1| 238 TYYTLLyEDTEELQRYLKGMPSSASRDWGAPFYQTFKAAGFDFFKVDHNVFAPAKVVMNEIKSRRTFVCGKTDHEVL 314
                                       ****98688899***************************************************************** PP

                                       HHHT CS
                               MCH 308 aesf 311
                                       +esf
  gi|330507376|ref|YP_004383804.1| 315 MESF 318
                                       ***9 PP

>> Peptidase_C28  Foot-and-mouth virus L-proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     2e-05      0.17     110     179 ..      44     119 ..      17     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                     Peptidase_C28 110 llytgigtasrpsevcmvdgtdmcladfha.giflkg....qdhavfacvtsdg.wyaiddedfypwtpnpadvlv 179
                                           gig+    s +cm d +d+ la     gi+l g     d+  ++c++s+   + i  + ++     pa vl 
  gi|330507376|ref|YP_004383804.1|  44 KAQGGIGAGIYLSRLCMSDLADIQLAPCDIgGILLPGvqvaTDYPAVSCMASQCaMWQIKADKYFAMGSGPARVLA 119
                                       45679*********************98752699988322246778899999853678999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2366.99
//
Query:       gi|330507377|ref|YP_004383805.1|  [L=386]
Description: elongation factor Tu, domain 2 protein [Methanosaeta concilii GP6]
Scores for complete 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   44.5   1.5    3.8e-11   43.2   1.5    1.7  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00012   21.9   0.1    0.00023   21.0   0.1    1.5  1  GTP_EFTU_D4  Elongation factor Tu domain 4


Domain annotation for each model (and alignments):
>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   1.5   4.2e-15   3.8e-11       1      74 []     226     293 ..     226     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 4.2e-15
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                       Gtv+lg+v +Gtlkk de+++l+     k+    +++s++++ ed d a +g++ G+ ++++++ed + +G +lt
  gi|330507377|ref|YP_004383805.1| 226 GTVVLGSVAEGTLKKHDELMVLPgE---KT---AQVRSIQKHDEDFDVAGVGERTGIALKGVDVED-LDRGTILT 293
                                       9********************8844...55...*********************************.9***9986 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 !   21.0   0.1   2.6e-08   0.00023      17      73 ..     226     281 ..     209     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.6e-08
                                       CCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS CS
                       GTP_EFTU_D4  17 dpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegk 73 
                                         ++ G +v +G++k   +l+   G++  ++++iq++++  ++a  G++ +i+++g 
  gi|330507377|ref|YP_004383805.1| 226 GTVVLG-SVAEGTLKKHDELMVLPGEKTAQVRSIQKHDEDFDVAGVGERTGIALKGV 281
                                       457778.***********************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3027.84
//
Query:       gi|330507378|ref|YP_004383806.1|  [L=253]
Description: hypothetical protein MCON_1294 [Methanosaeta concilii GP6]
Scores for 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   47.9   0.0    1.5e-12   47.3   0.0    1.2  1  DUF364    Putative heavy-metal chelation


Domain annotation for each model (and alignments):
>> DUF364  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   8.5e-17   1.5e-12       4      98 ..     138     236 ..     135     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 8.5e-17
                            DUF364   4 dlleikkgkkVvvVGyfap.vlkklke..kgaeltvlelnpnlleeeegdl..pdeaaeellpeadvviitGstLvn 75 
                                       d l+ ++ + V++VG ++p +l+ l +    +++ v +l +  ++e+ g+       +ee+ +++++++itGst+vn
  gi|330507378|ref|YP_004383806.1| 138 DWLRDQEWEMVGLVG-LQPaILEALVKafGRERVMVSDLAE-AGSERCGVRvlDGLNSEEIFEQCQLILITGSTIVN 212
                                       66677788899****.7777888888633455666667666.4444444446799********************** PP

                            DUF364  76 gtlerllelak.kaaevvlvGPsa 98 
                                       gt+++ll++a  ++++vvl+G + 
  gi|330507378|ref|YP_004383806.1| 213 GTIDDLLDRAAeHDRRVVLFGVTI 236
                                       *******9987478999****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1867.05
//
Query:       gi|330507379|ref|YP_004383807.1|  [L=299]
Description: molybdate ABC transporter substrate-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-40  137.7   0.0    5.6e-40  137.5   0.0    1.1  1  SBP_bac_11      Bacterial extracellular solute-binding protei
    2.4e-05   23.9   0.0    0.00017   21.1   0.0    2.0  2  SBP_bac_6       Bacterial extracellular solute-binding protei
    5.5e-05   23.3   0.0    0.00099   19.1   0.0    2.2  1  SBP_bac_1       Bacterial extracellular solute-binding protei
    0.00044   20.1   0.0    0.00095   19.1   0.0    1.7  1  SBP_bac_8       Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.22   10.8   0.0    1.6  1  LysR_substrate  LysR substrate binding domain
       0.13   11.4   0.0        1.1    8.4   0.0    2.1  1  PBP_like        PBP superfamily domain


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 !  137.5   0.0   1.9e-43   5.6e-40       1     229 [.      47     277 ..      47     278 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.5 bits;  conditional E-value: 1.9e-43
                                       .EEEE-SSTHHHHHHHHHHHHHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEE CS
                        SBP_bac_11   1 ltvaaagslaaalrelaaaFeahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavpla 77 
                                       l ++++++++ a++e+a+ +e+ ++ +v++ + g  +l+ qi++ga +D++i+ ++ +++ l++ag++ +++ +++a
  gi|330507379|ref|YP_004383807.1|  47 LVIFCGAGFTGAMSEIAELYENSSNSQVRFNFDGLPALRVQIEEGAYADLLISPDQRYMDPLVDAGFIGEDTVEAFA 123
                                       67999************************************************************************ PP

                                       EEEEEEEESTT-TT---SHHHHHHSS--EEEE--T-TTTTHH.HHHHGGG--.....HHHHHHHHHTEEEEESSHHH CS
                        SBP_bac_11  78 ssplviavpkgnpkkikgwadLlkpglklavadPttspsGlaalalleaaga.....qellkalekkvvklgessrq 149
                                       s++++++ p +np++i+++ dL+ pg+k+++      p G++al++l+   +     +++ +a+  +vv l++ ++ 
  gi|330507379|ref|YP_004383807.1| 124 SNKVAVVLPVDNPANITTIRDLATPGTKIVMGIE-ELPIGDYALQVLDLMAKdpeygPAFKEAVLANVVSLETRVTG 199
                                       ********************************85.66***********876667778******************** PP

                                       HHHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHH CS
                        SBP_bac_11 150 lltaveageadagivyeseakaaengdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaqailrk 226
                                       +++ v+ geadag++  s++  ++ ++k++ + +peg+n+ +   +aavl++++++eaA+aF+++L s +aqail +
  gi|330507379|ref|YP_004383807.1| 200 IVSKVAMGEADAGFAFMSDVT-PQMRGKIRKISIPEGYNI-RGNCSAAVLSQSDNSEAAEAFIDLLISNDAQAILDE 274
                                       ********************9.6689*************9.99********************************** PP

                                       TT- CS
                        SBP_bac_11 227 yGf 229
                                       yGf
  gi|330507379|ref|YP_004383807.1| 275 YGF 277
                                       **9 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.095   2.8e+02       4      25 ..      94     115 ..      91     143 .. 0.82
   2 !   21.1   0.0   5.9e-08   0.00017     117     216 ..     180     278 ..     150     297 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.095
                         SBP_bac_6   4 pdlilsfdkdflekfieeglfq 25 
                                       +dl++s d+++++ ++++g++ 
  gi|330507379|ref|YP_004383807.1|  94 ADLLISPDQRYMDPLVDAGFIG 115
                                       8999**9999999999999986 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 5.9e-08
                         SBP_bac_6 117 kkllrnlkanlhpaq..mvkaagslesgepavsvvpyffadilpekkkgknlkvvwPedGalvspifmlvkkg.kkk 190
                                        ++++++ an+ + +   ++++ +++ ge  ++ +++f++d+ p+   gk  k+ +Pe   +   ++++v ++  ++
  gi|330507379|ref|YP_004383807.1| 180 PAFKEAVLANVVSLEtrVTGIVSKVAMGE--ADAGFAFMSDVTPQMR-GKIRKISIPEGYNIRGNCSAAVLSQsDNS 253
                                       578999999999999999999********..**************96.665666666666666666677777799** PP

                         SBP_bac_6 191 elakafidfllspevqailakaggvf 216
                                       e a+afid l s+++qail + g+ +
  gi|330507379|ref|YP_004383807.1| 254 EAAEAFIDLLISNDAQAILDEYGF-I 278
                                       *******************99998.4 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 !   19.1   0.0   3.3e-07   0.00099     206     315 .]     180     270 ..      54     270 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.3e-07
                                       HHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSE CS
                         SBP_bac_1 206 vanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpg 282
                                        a++++ l++++++++ ++  ++ ++ Gea++++++ ++      v p+   ++          ++ +P g +    
  gi|330507379|ref|YP_004383807.1| 180 PAFKEAVLANVVSLETRVTGIVSKVAMGEADAGFAFMSD------VTPQMRGKI---------RKISIPEGYNIR-- 239
                                       455677888889999999999999999999999888877......333333333.........444444444333.. PP

                                       EEEEEEEEEBTTCSTHHHHHHHHHHHTSHHHHH CS
                         SBP_bac_1 283 ilgayglaipkgsknpeaAkkFldfllspeaqa 315
                                         g+   a++++s+n eaA++F+d+l s++aqa
  gi|330507379|ref|YP_004383807.1| 240 --GNCSAAVLSQSDNSEAAEAFIDLLISNDAQA 270
                                       ..8888*************************96 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 !   19.1   0.0   3.2e-07   0.00095     176     261 ..     194     277 ..      92     281 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.2e-07
                                       -S...--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE--S--EEEEEEE.EEEBTTS-HHHHHHHHHHHHHTTSH CS
                         SBP_bac_8 176 dtg.adavsefanGevaftingswdiaaaqkagkklgaivpkqgsfaggkg.lavpknaknedlaAldFlkwltspe 250
                                       +t+ + +vs++a Ge+ +++++ +d++     + + ++ +p +g+ ++g+   av+++++n++ aA +F+  l s++
  gi|330507379|ref|YP_004383807.1| 194 ETRvTGIVSKVAMGEADAGFAFMSDVTPQMRGKIR-KISIP-EGYNIRGNCsAAVLSQSDNSE-AAEAFIDLLISND 267
                                       45445678899999999999999999998873333.45555.89*****96588*********.6************ PP

                                       HHHHHHHHH-- CS
                         SBP_bac_8 251 nqaalaektgy 261
                                       +qa l e +g+
  gi|330507379|ref|YP_004383807.1| 268 AQAILDE-YGF 277
                                       ***8766.555 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.4e-05      0.22     136     205 ..     197     264 ..     163     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.4e-05
                                       ESSHHHHHHHHHTTS-BEEEEGGGHHCCCHTTTEEEEEESST.TCEEEEEEEEETTCCCHHHHHHHHHHHH CS
                    LysR_substrate 136 vnsleallalvaaGlGiallprsavrdeladgrlvalplpep.plprelylvyrkgrelspavrafidflr 205
                                       v+ + + +a+ +a  G+a++++ + +    +g+++ + +pe  +++ + ++++ +++  s+a++afid+l 
  gi|330507379|ref|YP_004383807.1| 197 VTGIVSKVAMGEADAGFAFMSDVTPQM---RGKIRKISIPEGyNIRGNCSAAVLSQSDNSEAAEAFIDLLI 264
                                       56666778899999**********555...999*9999999779999*********************996 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00036       1.1      23     102 ..      80     158 ..      69     263 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00036
                                       HHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BGGGC-S-B-EEEEE CS
                          PBP_like  23 GlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkkitnwkdladaplrlvnR 99 
                                       Gl alr +  + a ++ll++ +++y  p +   + g++ ++  +a+ +  +v+  +np +it+++dla ++  +v+ 
  gi|330507379|ref|YP_004383807.1|  80 GLPALRVQIEEGAYADLLISPDQRYMDPLVDAGFIGED-TVEAFASNKVAVVLPVDNPANITTIRDLATPGTKIVMG 155
                                       55555555556677788888888888888888888865.66679999999*****************9999888875 PP

                                       -TT CS
                          PBP_like 100 etG 102
                                        + 
  gi|330507379|ref|YP_004383807.1| 156 IEE 158
                                       555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2192.63
//
Query:       gi|330507380|ref|YP_004383808.1|  [L=341]
Description: anthranilate phosphoribosyltransferase [Methanosaeta concilii GP6]
Scores for 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-98  328.5   2.5    4.1e-98  328.0   2.5    1.2  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    5.4e-16   58.2   0.7    1.4e-15   56.8   0.7    1.8  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.0   2.5  4.6e-102   4.1e-98       3     253 .]      72     321 ..      70     321 .. 0.99

  Alignments for each domain:
  == domain 1  score: 328.0 bits;  conditional E-value: 4.6e-102
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl 79 
                                        lvD++gTGGdg+nt+N+Staaaiv Aa+Gv+vakhgn ++ssk+Gsa vL+algv++  +p ev++l++evg+gf+
  gi|330507380|ref|YP_004383808.1|  72 TLVDTCGTGGDGSNTINVSTAAAIVTAACGVPVAKHGNYAISSKCGSANVLDALGVRISSDPAEVQSLIQEVGIGFM 148
                                       68*************************************************************************** PP

                                       EHHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHHH CS
                   Glycos_transf_3  80 fapeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldevs 156
                                       +ap +h+amk v pvrr+lgirTvfn+LGPL+npa +k+q++gvy+++l+ekla vl+ lg +ra+vv+g+G+de++
  gi|330507380|ref|YP_004383808.1| 149 LAPAFHPAMKRVGPVRRDLGIRTVFNILGPLTNPAGAKAQVMGVYDPSLCEKLACVLQILGAKRAMVVNGEGMDEIT 225
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSS CS
                   Glycos_transf_3 157 llakttvaelkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagka 233
                                        +++t v elkdg++++ytl+ped+g  +ae  +++gg p+ena+ l +vl+g++saa rd++++n gaa++++g +
  gi|330507380|ref|YP_004383808.1| 226 NTGETRVSELKDGSVKSYTLRPEDLGYPQAESADIAGGMPDENAKRLVEVLKGETSAA-RDIIVINSGAAVYVSGLV 301
                                       ********************************************************98.****************** PP

                                       SSHHHHHHHHHHHHHTSHHH CS
                   Glycos_transf_3 234 dslkegvakaeevidsGkAl 253
                                       +++k+g+  ae++idsG+Al
  gi|330507380|ref|YP_004383808.1| 302 STMKKGASMAEDAIDSGEAL 321
                                       ******************95 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.7   1.6e-19   1.4e-15       2      63 .]       2      62 ..       1      62 [. 0.98

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1.6e-19
                                      HHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N  2 diikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63
                                      ++++k+++g++L+ ee ++++++i++ +++da i+A L+Alr kGe++ Eia++a+ mres+
  gi|330507380|ref|YP_004383808.1|  2 SYLQKIMEGQDLSLEESEALMDEIFN-KASDAMIGAVLVALRRKGESVSEIAGFARKMRESA 62
                                      599**********************9.9********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.22s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2406.52
//
Query:       gi|330507381|ref|YP_004383809.1|  [L=213]
Description: N-(5'phosphoribosyl)anthranilate isomerase [Methanosaeta concilii GP6]
Scores for complete 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  125.2   0.0    3.1e-36  125.0   0.0    1.0  1  PRAI      N-(5'phosphoribosyl)anthranilate (PRA) isomerase
    0.00033   20.0   0.3    0.00072   18.9   0.3    1.5  1  TMP-TENI  Thiamine monophosphate synthase
  ------ inclusion threshold ------
      0.043   13.2   2.2       0.21   11.0   0.1    2.1  2  NMO       Nitronate monooxygenase
      0.075   12.0   1.2        3.7    6.5   0.8    2.3  2  FMN_dh    FMN-dependent dehydrogenase


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 !  125.0   0.0   6.8e-40   3.1e-36       1     193 [.       4     204 ..       4     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 125.0 bits;  conditional E-value: 6.8e-40
                                       TCE----SHHHHHHHHHHTSSEEEEE.--TTBTTB--HHHHHHHCCCS--E..EEEEESSS-HHHHHHHHHHCTECE CS
                              PRAI   1 akicgltrasdvkaavkagadelgli.faesskrevseeqaqellekvpak..lVGVfvNqpieevlriaqelgldv 74 
                                       +kicg+++ +d++ a +agad++g++ + + s++++s e+a+ l++kvp++   V+V    ++++ lr+a+  + dv
  gi|330507381|ref|YP_004383809.1|   4 VKICGIMSGDDLALALQAGADAVGFVvEIKDSRHCISAEEAADLIHKVPVYtkSVAVIHPCDLDDALRLADITRADV 80 
                                       69**********************97256789999**************77679*********************** PP

                                       EEE-CGG.-HHHHHHHHHHS-TTSEEEEEEE-S.SS--S-SSTT-.SEEEEE....SSS-SSSXXXXGGGGTTSXX. CS
                              PRAI  75 vQLHGdedeqeyeellktelpvikalkvaesvd.evkearradhv.dllllD....sgaGGtGelldwsliskllks 145
                                       +QLH + +++++++l++   +   +l+va  +d   ++a+r++ v d++llD       GGtG   dw++ +++ +s
  gi|330507381|ref|YP_004383809.1|  81 LQLHSSLPPSDVADLKS---RTGSKLVVAVAADdGGQQAERYERVaDAILLDsmveGRLGGTGRVHDWDKSAGIARS 154
                                       *******9999999988...444444444444447899******99******8887678***********9999999 PP

                                       ..TTEEEESSXXTTTHHHHHT.TXXSEEEEXGGGEEETEEXHHHHHHHHH CS
                              PRAI 146 ..lkviLAGGLtpeNvaeaiklegvlgvDvssGVEtnGvkDlekirkfvq 193
                                         ++viLAGGL+p+Nv  ai+  ++++vDvssG Et+G kD  k+r+fv+
  gi|330507381|ref|YP_004383809.1| 155 lqVPVILAGGLDPDNVLLAIERVRPYAVDVSSGTETAGRKDPFKVRAFVE 204
                                       99**********************************************98 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   1.6e-07   0.00072      62     169 ..      66     175 ..      13     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.6e-07
                          TMP-TENI  62 indrvdlalavgadgvHlgq..ddlpvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaep 136
                                       ++d ++la    ad + l       +va+++  +g++l++ + + +  + +e  +  ad i + ++ +       ++
  gi|330507381|ref|YP_004383809.1|  66 LDDALRLADITRADVLQLHSslPPSDVADLKSRTGSKLVVAVAADDGGQQAERYERVADAILLDSMVEGRLGGTGRV 142
                                       78899999988888887777446778999999***************9988888899******************** PP

                          TMP-TENI 137 lgleglkelaealeiPvvaiGGitlenvaevle 169
                                        ++++ + +a++l++Pv+  GG++++nv  ++e
  gi|330507381|ref|YP_004383809.1| 143 HDWDKSAGIARSLQVPVILAGGLDPDNVLLAIE 175
                                       ***************************977765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.4     0.028   1.3e+02     201     219 ..       8      26 ..       6      32 .. 0.93
   2 ?   11.0   0.1   4.6e-05      0.21      83     202 ..      44     165 ..      28     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.028
                               NMO 201 GiidrrgvaaaLalGAsgv 219
                                       Gi+ + ++a aL +GA +v
  gi|330507381|ref|YP_004383809.1|   8 GIMSGDDLALALQAGADAV 26 
                                       9****************99 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.6e-05
                               NMO  83 ykkeleeaalelnieegvr..fyrkvevvlde.kvevvsfgfglpteevvarlkeagvvliptissvkearkvearG 156
                                       +++ +++++++ +    ++  +    ++++d  +++v  ++  lp+ +v + +++ g  l++ +++ +  +++e+  
  gi|330507381|ref|YP_004383809.1|  44 AADLIHKVPVYTKSVAVIHpcDLDDALRLADItRADVLQLHSSLPPSDVADLKSRTGSKLVVAVAADDGGQQAERYE 120
                                       5555555555555544444564444455566559***************9999999999999998888777776433 PP

                               NMO 157 ..aDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGi 202
                                         aDa+ ++ + +G   Gt  v         + ++  +++Pvi aGG+
  gi|330507381|ref|YP_004383809.1| 121 rvADAILLDSMVEGRLGGTGRV---HDWDKSAGIARSLQVPVILAGGL 165
                                       44***********988884455...56666788999999********8 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.8   0.00083       3.7     279     298 ..       8      27 ..       3      30 .. 0.77
   2 ?    3.8   0.0    0.0053        24     203     235 ..     136     175 ..      67     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00083
                                       S--SHHHHHHHHHTT-SEEE CS
                            FMN_dh 279 GirrGsDvlkAlalGAdavl 298
                                       Gi++G D + Al  GAdav+
  gi|330507381|ref|YP_004383809.1|   8 GIMSGDDLALALQAGADAVG 27 
                                       78888888888888888876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0053
                                       -.......-HHHHHHHHHHHSSEEEEEEE-SHHHHHHHHH CS
                            FMN_dh 203 l.......twddikwlreqtklplvvKGvltaedakrave 235
                                       l       +wd+ + + + +++p+++ G l+++++ +a+e
  gi|330507381|ref|YP_004383809.1| 136 LggtgrvhDWDKSAGIARSLQVPVILAGGLDPDNVLLAIE 175
                                       244444459*************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1636.20
//
Query:       gi|330507382|ref|YP_004383810.1|  [L=484]
Description: anthranilate synthase component I [Methanosaeta concilii GP6]
Scores for complete 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-95  319.1   0.0    1.3e-93  313.3   0.0    2.6  3  Chorismate_bind  chorismate binding enzyme
    2.8e-30  105.4   0.2    6.8e-28   97.7   0.0    3.1  2  Anth_synt_I_N    Anthranilate synthase component I, N termina
  ------ inclusion threshold ------
       0.16   12.2   0.0       0.75   10.1   0.0    2.0  2  DUF5495          Family of unknown function (DUF5495)


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.016        97      40      92 ..      22      77 ..      11      85 .. 0.72
   2 ?   -1.2   0.0       0.2   1.2e+03     157     179 ..      95     117 ..      84     129 .. 0.83
   3 !  313.3   0.0   2.2e-97   1.3e-93       3     258 .]     221     472 ..     219     472 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.016
                                      HHHHHHHHHCTBSSSEEEEEEETT....EEEEEEESSEEEEEETTSEEEEECEEEEE CS
                   Chorismate_bind 40 plalyralrarnpapysflleled....sellgaSPElllkveggrrietepiaGTr 92
                                      pl+ly alr r   +    +e ++    ++++ga P  +++++ +r +e+e   G +
  gi|330507382|ref|YP_004383810.1| 22 PLSLYMALRDRRYPYLLESVEKSGqkarFSFVGADPSAMISIK-NRFLEMEFFSGGM 77
                                      7888888888765555555533334566999************.6699999888865 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.2
                                       EEEEEEESTT--HHHHHHHCSS- CS
                   Chorismate_bind 157 stiegelkedvslldllkalfPt 179
                                       s ++g++k++ +l+d+l+a +P 
  gi|330507382|ref|YP_004383810.1|  95 SVLQGSIKDGYDLFDVLRAAIPS 117
                                       67899**************9985 PP

  == domain 3  score: 313.3 bits;  conditional E-value: 2.2e-97
                                       CHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEET CS
                   Chorismate_bind   3 edYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkveg 79 
                                       e+Y++av+++ke+i +gd+++vvl+r++++e++   dp++ly +lr+ np+py++l+e++d  ++gaSPE+l+++  
  gi|330507382|ref|YP_004383810.1| 221 EEYKDAVSRAKEHIIDGDIFQVVLARSTRIECP---DPVKLYLKLRSINPSPYTYLFEFGDLAIVGASPETLFNTY- 293
                                       89*****************************77...7889************************************. PP

                                       TSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEE CS
                   Chorismate_bind  80 grrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlv 156
                                       +r ++++piaGT +rg+t  ed ++++ +l+deKeraEh+m+vdl rnd+++v+++g+v+v+++++v +ys+v+h+ 
  gi|330507382|ref|YP_004383810.1| 294 NRMLKVNPIAGTCPRGRTRSEDDRYARIMLNDEKERAEHVMLVDLGRNDVRSVCRSGTVQVEDFMSVLQYSHVQHIE 370
                                       66*************************************************************************** PP

                                       EEEEEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETTE CS
                   Chorismate_bind 157 stiegelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdke 233
                                       +t+ gel+e+++ +d+ +++fP+g+++GaPk rameiid+lE a+Rg+Y+G +gy++ dg+ ++a++IR+++vkd+ 
  gi|330507382|ref|YP_004383810.1| 371 TTVIGELREECDQFDAARSVFPAGTLSGAPKLRAMEIIDDLERAPRGIYGGGIGYFSIDGSSDFAIAIRSVLVKDGV 447
                                       ***************************************************************************** PP

                                       EEEEEEEEEETT--HHHHHHHHHHH CS
                   Chorismate_bind 234 lrlgaGaGIvadSdpeaEyeEtlaK 258
                                       ++++aGaGIvadSdpe+Ey+Et+ K
  gi|330507382|ref|YP_004383810.1| 448 ATVQAGAGIVADSDPEKEYQETERK 472
                                       **********************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 !   97.7   0.0   1.1e-31   6.8e-28       3     141 ..      20     177 ..      18     178 .. 0.91
   2 !    4.2   0.1    0.0075        45      84     103 ..     400     431 ..     253     451 .. 0.68

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 1.1e-31
                     Anth_synt_I_N   3 ltplsvylklaeeehkflLeSaeneggegrySfigldpflelkskngeveveg........................ 55 
                                       ++pls+y++l+++++++lLeS+e++g+++r+Sf+g+dp++ + +kn+ +e+e                         
  gi|330507382|ref|YP_004383810.1|  20 DAPLSLYMALRDRRYPYLLESVEKSGQKARFSFVGADPSAMISIKNRFLEMEFfsggmgpmterlsvcvdverkgsv 96 
                                       78*******************************************99999999999****************98888 PP

                     Anth_synt_I_N  56 pegeeleeeepldalrellerfrsaedseptelpfvgGlvGylgYDlvreieklpksakddln.lpdarlilydtli 131
                                        +g+ ++ ++++d+lr+ + + r a+ s++ ++ f+gG +G+l+YDlv+e  +l+   k +++ +pda++ l ++++
  gi|330507382|ref|YP_004383810.1|  97 LQGSIKDGYDLFDVLRAAIPSRRGAPNSFSRQV-FTGGGIGFLAYDLVKE--RLG---KGSTSqTPDAQFGLAESTF 167
                                       8888888888*************9988888888.*************765..577...444444************* PP

                     Anth_synt_I_N 132 vfDhkerrly 141
                                       +fDh+ r++y
  gi|330507382|ref|YP_004383810.1| 168 IFDHLDRKVY 177
                                       ********99 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0075
                     Anth_synt_I_N  84 e...........ptelp.fvgGlvGylgYDlv 103
                                                   +  ++ ++gG +Gy++ D  
  gi|330507382|ref|YP_004383810.1| 400 PklrameiiddlERAPRgIYGGGIGYFSIDGS 431
                                       04555555555444444689999999997765 PP

>> DUF5495  Family of unknown function (DUF5495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00013      0.75      22      68 ..     350     396 ..     336     408 .. 0.86
   2 ?   -1.3   0.0      0.45   2.7e+03       5      29 ..     407     431 ..     403     436 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                           DUF5495  22 gltqiegngfileyefsqwwlyanygelieyvdqfdsldaalgaanl 68 
                                       g  q+e    +l+y   q    +  gel e  dqfd+  + + a  l
  gi|330507382|ref|YP_004383810.1| 350 GTVQVEDFMSVLQYSHVQHIETTVIGELREECDQFDAARSVFPAGTL 396
                                       7789999999**************************98887777666 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.45
                           DUF5495   5 lindlrlagyevntngigltqiegn 29 
                                       +i+dl  a   +   gig   i+g 
  gi|330507382|ref|YP_004383810.1| 407 IIDDLERAPRGIYGGGIGYFSIDGS 431
                                       7999999999999******999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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 0.23s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 3861.57
//
Query:       gi|330507383|ref|YP_004383811.1|  [L=193]
Description: Anthranilate synthase component II [Methanosaeta concilii GP6]
Scores for complete 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-42  143.0   0.0    9.9e-42  142.9   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    2.8e-14   53.4   0.5    8.2e-13   48.6   0.5    2.1  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 !  142.9   0.0   1.1e-45   9.9e-42       2     187 ..       6     185 ..       5     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 142.9 bits;  conditional E-value: 1.1e-45
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT....TTTHHHHHHHHCT.STS- CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg....vegkieaikeare.nkiP 73 
                                       ++Dn+ds+++nlv+++  +  ++ v+ ++ s  e   ++ np gi++s+Gpg+p+    ++ ++e+i    +  k+P
  gi|330507383|ref|YP_004383811.1|   6 FVDNHDSFVWNLVDYVSVFYDNTIVRSNEISMAEV--ERLNPRGIVISPGPGHPAkardIGSCLEIIL---GhPKTP 77 
                                       69**************9998788888888888888..489***************8555555555554...3368** PP

                                       EEEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEET CS
                            GATase  74 iLGICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtaksed 150
                                       iLG+CLG+Q++ +++g+++ + +  + hg+t+++++d++++++g +n+++  ++H++++++   ++ ++e  a+s++
  gi|330507383|ref|YP_004383811.1|  78 ILGVCLGHQAMNLAYGGTISHTR--PLHGKTSQIEHDGRGIFRGVENPLQGGRYHSLAIEK---LSPEVEACARSAE 149
                                       *******************9887..9***********************************...9999*******99 PP

                                       TEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 151 deelmeiiekknpfvgvQFHPEststpegpellfnfl 187
                                       +  +m+i+++++p +g+QFHPEs++tp g+++++n +
  gi|330507383|ref|YP_004383811.1| 150 G-VVMAIRHRNRPHCGLQFHPESVLTPSGKRIIRNWV 185
                                       8.9******************************9975 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.5   9.2e-17   8.2e-13     104     216 .]      74     170 ..      53     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 9.2e-17
                     Peptidase_C26 104 rgvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaike 180
                                        ++Pilg+C+G+q +n a+GGt+            h       ++ +++ +  +++  +   +  +   +H+ ai++
  gi|330507383|ref|YP_004383811.1|  74 PKTPILGVCLGHQAMNLAYGGTISHTRPL------H------GKTSQIEHDGRGIFRGVE--NPLQGGRYHSLAIEK 136
                                       578*******************8765552......3......234455656666666554..699999********* PP

                     Peptidase_C26 181 laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       l++e++ +A+++ gv+ ai+++++  +  g+Q+HPE
  gi|330507383|ref|YP_004383811.1| 137 LSPEVEACARSAEGVVMAIRHRNR--PHCGLQFHPE 170
                                       ***********************4..69*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 1619.98
//
Query:       gi|330507384|ref|YP_004383812.1|  [L=243]
Description: indole-3-glycerol phosphate synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-60  204.6   0.0    1.6e-60  204.4   0.0    1.0  1  IGPS          Indole-3-glycerol phosphate synthase
     0.0013   17.9   0.1     0.0038   16.4   0.1    1.8  1  NanE          Putative N-acetylmannosamine-6-phosphate epimer
     0.0033   17.2   0.0     0.0054   16.5   0.0    1.3  1  QRPTase_C     Quinolinate phosphoribosyl transferase, C-termi
     0.0047   16.0   0.1      0.015   14.4   0.0    1.6  2  FMN_dh        FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.025   13.8   0.0    1.4  1  DHO_dh        Dihydroorotate dehydrogenase
      0.036   13.1   0.0      0.071   12.1   0.0    1.4  1  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.045   13.2   0.0      0.086   12.3   0.0    1.4  1  PcrB          PcrB family
      0.048   13.1   0.0       0.11   11.9   0.0    1.7  1  His_biosynth  Histidine biosynthesis protein
       0.14   11.0   0.0       0.38    9.5   0.0    1.8  2  Trp_syntA     Tryptophan synthase alpha chain


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 !  204.4   0.0     8e-64   1.6e-60      32     246 ..      26     235 ..       9     243 .] 0.89

  Alignments for each domain:
  == domain 1  score: 204.4 bits;  conditional E-value: 8e-64
                                       S-SS-HHHHCHCH..TTS-EEEEEE-SEETTTEESBSS--HHHHHHHHTTT.-SEEEEE--CCCC---CCHHHHHHH CS
                              IGPS  32 kpkrsfaeaLres..ekklaliaEvKkaSPskgliredfdpaeiAkkyeeagAsaiSVLteekyFqGsledLrevrq 106
                                       ++ r+++ + +e+  +  + +iaE+K +   + l +e  ++a +A++y+++gA aiSVLte+ +F+Gsle+ r++r+
  gi|330507384|ref|YP_004383812.1|  26 EERRDLVASAAEAkrNGLIPIIAEIKPKALGRTLAQE--EVATYARAYAQYGACAISVLTEPTHFKGSLENARTARR 100
                                       566677666666544667899******9877754444..6899*****************************99998 PP

                                       H-SS-EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEE CS
                              IGPS 107 avslpvlrKdFiideyqieearalgadaiLLivkvledeeleelaeaakslglevLvEvhdeeeleralklgakiiG 183
                                       a  lpvlrKdFi++e+q+     ++ad++LLi+++  d  l ++++aa++lg+e+LvEvh+e+e+eral+ +a+iiG
  gi|330507384|ref|YP_004383812.1| 101 A-GLPVLRKDFIFSEVQLS---EVQADLVLLIAAL--DIDLDRFVAAARDLGMEPLVEVHSEKEMERALSTEARIIG 171
                                       6.79**************9...79*******9875..55679*********************************** PP

                                       EESEETTTTEE-CHHHHHHCHCC-TT.SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TT CS
                              IGPS 184 vNnRnLktlevdlntteeLaklvpkd.vllvaeSGiktredveklkeegvnafLvGeslmrqed 246
                                       +NnRnLktlevdl+t+e+La+ +++  v+lvaeSG++++ed+ ++ ++g++a+LvG+ lm+ ++
  gi|330507384|ref|YP_004383812.1| 172 INNRNLKTLEVDLETFERLAPRARDAgVFLVAESGVHSPEDAVRMVRAGADALLVGTELMAGPE 235
                                       ************************778*********************************9876 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 !   16.4   0.1   1.9e-06    0.0038     140     176 ..     194     230 ..     133     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-06
                                       HHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHH CS
                              NanE 140 lseaglkviaeGrintPekakkaieiGvdavvvGsai 176
                                         +ag++++ae  +++Pe a ++++ G+da+ vG+ +
  gi|330507384|ref|YP_004383812.1| 194 ARDAGVFLVAESGVHSPEDAVRMVRAGADALLVGTEL 230
                                       4689******************************865 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 !   16.5   0.0   2.7e-06    0.0054      84     156 ..     150     228 ..     128     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-06
                                       EEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT......SEEEEESS--TTTHHHHHCTT-SEEEE CS
                         QRPTase_C  84 evevesleeleevleaeadiimLDnfsveelkkaveelkeknkr......vlievSGgvtlenveeyaksgvdvisv 154
                                        vev+s++e+e++l++ea ii + n + ++l+  +e+ ++ ++r      +l+  SG  + e+   + + g d++ v
  gi|330507384|ref|YP_004383812.1| 150 LVEVHSEKEMERALSTEARIIGINNRNLKTLEVDLETFERLAPRardagvFLVAESGVHSPEDAVRMVRAGADALLV 226
                                       6******************************9999999999998889998999999999999999999999999999 PP

                                       CH CS
                         QRPTase_C 155 ga 156
                                       g+
  gi|330507384|ref|YP_004383812.1| 227 GT 228
                                       87 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.58   1.2e+03      73      94 ..      87     108 ..      72     150 .. 0.77
   2 !   14.4   0.0   7.5e-06     0.015     224     307 ..     153     234 ..     150     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.58
                                       STTHHHHHHHHHHHHTS-EEEE CS
                            FMN_dh  73 hpdgelalaraaakagipfvls 94 
                                       h +g l+ ar+a++ag+p+   
  gi|330507384|ref|YP_004383812.1|  87 HFKGSLENARTARRAGLPVLRK 108
                                       6678889999999999987544 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.5e-06
                                       E-SHHHHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEES CS
                            FMN_dh 224 vltaedakraveaGvdgivvSNHGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllG 300
                                       v ++++++ra+   + +i + N   + l+    t++ L   ++ +g  + +++ +G+ + +D+++ +  GAda l+G
  gi|330507384|ref|YP_004383812.1| 153 VHSEKEMERALSTEARIIGINNRNLKTLEVDLETFERLAPRARDAG--VFLVAESGVHSPEDAVRMVRAGADALLVG 227
                                       6788899999999999999999555555555555555544444444..9999************************* PP

                                       HHHHHHH CS
                            FMN_dh 301 Rpflygl 307
                                         ++ g 
  gi|330507384|ref|YP_004383812.1| 228 TELMAGP 234
                                       9988875 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.3e-05     0.025     245     281 ..     199     234 ..     171     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                                       S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGT CS
                            DHO_dh 245 ipiIgvGGiesgeDalekieaGAslvqvytalvfegp 281
                                       + +++  G++s eDa+ +++aGA ++ v+t+l  +gp
  gi|330507384|ref|YP_004383812.1| 199 VFLVAESGVHSPEDAVRMVRAGADALLVGTEL-MAGP 234
                                       6678899************************9.5555 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.5e-05     0.071     199     244 ..     190     235 ..     183     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                                       HHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 199 vaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteE 244
                                        a  a++agv ++a  G+++ +d v+ + aGada+++G  l +  E
  gi|330507384|ref|YP_004383812.1| 190 LAPRARDAGVFLVAESGVHSPEDAVRMVRAGADALLVGTELMAGPE 235
                                       5678999*******************************86655555 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.3e-05     0.086     182     213 ..     200     232 ..     180     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                                       EEEEESS--SHHHHHHHHCC.SSEEEE-CHHHH CS
                              PcrB 182 rlivGGGirsaEkAkevvea.ADvivvGnvvee 213
                                        l+   G++s+E+A ++v+a AD+++vG+ +  
  gi|330507384|ref|YP_004383812.1| 200 FLVAESGVHSPEDAVRMVRAgADALLVGTELMA 232
                                       466678**********************97765 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.5e-05      0.11      74     114 ..     199     239 ..     153     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.5e-05
                                       SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHH CS
                      His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaavknpelike 114
                                       + +   +G+ s ed+ ++++agad + +gt+ +  pe + e
  gi|330507384|ref|YP_004383812.1| 199 VFLVAESGVHSPEDAVRMVRAGADALLVGTELMAGPERLGE 239
                                       5566789************************9999988766 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.91   1.8e+03     136     149 ..      36      49 ..      24      76 .. 0.46
   2 ?    9.5   0.0   0.00019      0.38     100     183 ..     131     215 ..     111     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.91
                                       HHHTT-EEEEEE-T CS
                         Trp_syntA 136 akkkglelvflvap 149
                                       a++k   l++++a 
  gi|330507384|ref|YP_004383812.1|  36 AEAKRNGLIPIIAE 49 
                                       22222333444433 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00019
                                       CCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH-.-S-EEEESTTC- CS
                         Trp_syntA 100 lsygeerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkevveqa.egfvYvvsraGv 175
                                       l    +rf+a++++ g++ l+ +   +e ++ l+++a+  g++   l +   + e++++++ +a ++ v++v+  Gv
  gi|330507384|ref|YP_004383812.1| 131 LDIDLDRFVAAARDLGMEPLVEVHSEKEMERALSTEARIIGINNRNLKTLEVDLETFERLAPRArDAGVFLVAESGV 207
                                       566789******************************************************98773578********* PP

                                       SSTTSSB- CS
                         Trp_syntA 176 Tgaenava 183
                                        + e+av 
  gi|330507384|ref|YP_004383812.1| 208 HSPEDAVR 215
                                       99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1739.27
//
Query:       gi|330507385|ref|YP_004383813.1|  [L=106]
Description: nucleotidyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-11   43.9   0.5    2.4e-11   43.8   0.5    1.2  1  NTP_transf_2  Nucleotidyltransferase domain
    3.2e-11   43.1   0.4    4.4e-11   42.7   0.4    1.2  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.019   15.2   0.0      0.032   14.4   0.0    1.4  1  SMODS         Second Messenger Oligonucleotide or Dinucleotid
       0.14   11.7   0.0       0.16   11.6   0.0    1.1  1  RlaP          RNA repair pathway DNA polymerase beta family


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.5   5.3e-15   2.4e-11       5      64 ..      13      69 ..       9     104 .. 0.68

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 5.3e-15
                                      HHHHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH......HHHEHHHHHHHHCCCEE CS
                      NTP_transf_2  5 leelkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsre......kkeegleklaeiikfle 64
                                      +++  + ++  + +++lfGS+arGt +++SDiDllvv+++e  r                    + + 
  gi|330507385|ref|YP_004383813.1| 13 IKRAVQSYGdqIQSITLFGSVARGTDRPDSDIDLLVVVDREDFRLrreligL-----------TFDIL 69
                                      5555555556899****************************65434444442...........33333 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.4   9.9e-15   4.4e-11       3      73 ..      13      85 ..      11     106 .] 0.71

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 9.9e-15
                                      TTTTHHHH.HHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH...SSSEEEEEETTTS- CS
                           Polbeta  3 ikeileke.keielaylFGSrakgkareeSDiDlavllkekldleeelelaaeledi..klgkkvDlvdlneap 73
                                      ik  ++++ ++i+ + lFGS+a+g+ r++SDiDl v+++++ d+  + el     di  ++g+++ + +l++ +
  gi|330507385|ref|YP_004383813.1| 13 IKRAVQSYgDQIQSITLFGSVARGTDRPDSDIDLLVVVDRE-DFRLRRELIGLTFDIllETGEDISVKVLSQDD 85
                                      78888888779******************************.66666666665555556677777777665432 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 ?   14.4   0.0   7.1e-06     0.032      25      74 ..       3      51 ..       2      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.1e-06
                             SMODS 25 ssrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeld 74
                                      ss+ +ai ++++   ++++++i++  l+GS ar+T  +p sd d+l+ +d
  gi|330507385|ref|YP_004383813.1|  3 SSKQNAIDEFIKRAVQSYGDQIQSITLFGSVARGTD-RPDSDIDLLVVVD 51
                                      57889******************************8.5555555555444 PP

>> RlaP  RNA repair pathway DNA polymerase beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.5e-05      0.16       4      45 ..       8      49 ..       5      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.5e-05
                              RlaP  4 riqeeLeeieeeeevkilyacesGSrawGfpspdsDyDvrfi 45
                                      +i+e +++  ++++ +i   ++ GS a G++ pdsD+D+  +
  gi|330507385|ref|YP_004383813.1|  8 AIDEFIKRAVQSYGDQIQSITLFGSVARGTDRPDSDIDLLVV 49
                                      567778888999999999********************8654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 826.13
//
Query:       gi|330507386|ref|YP_004383814.1|  [L=121]
Description: hypothetical protein MCON_1304 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   13.5   0.0       0.28   11.1   0.0    2.0  2  DUF1508   Domain of unknown function (DUF1508)
       0.11   12.4   0.1       0.18   11.7   0.1    1.3  1  DUF1425   Protein of unknown function (DUF1425)


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 ?   -0.5   0.0      0.13   1.1e+03       8      24 ..      11      26 ..      10      28 .. 0.71
   2 ?   11.1   0.0   3.1e-05      0.28       5      19 ..      61      75 ..      57      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.13
                                      EEEE-TTS-EEEE.EEEB CS
                           DUF1508  8 FrLkaaNgevIat.segY 24
                                      FrL +a  e+Ia+    Y
  gi|330507386|ref|YP_004383814.1| 11 FRLIDA--EIIADkKVSY 26
                                      777774..9999866666 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.1e-05
                                      EEEEEEE-TTS-EEE CS
                           DUF1508  5 efrFrLkaaNgevIa 19
                                      ++rF+L ++Ng+ ++
  gi|330507386|ref|YP_004383814.1| 61 KYRFHLIDKNGQMVF 75
                                      8***********986 PP

>> DUF1425  Protein of unknown function (DUF1425)
   #    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      37      55 ..      56      74 ..      48      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                                      S-EEEEEEEEEE-TTS-EE CS
                           DUF1425 37 kdltlqYrFyWyDkqGlev 55
                                       d++l+YrF  +Dk+G  v
  gi|330507386|ref|YP_004383814.1| 56 RDQRLKYRFHLIDKNGQMV 74
                                      689*************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1029.94
//
Query:       gi|330507387|ref|YP_004383815.1|  [L=99]
Description: hypothetical protein MCON_1305 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.14   11.5   0.0    1.1  1  Arena_ncap_C  Arenavirus nucleocapsid C-terminal domain


Domain annotation for each model (and alignments):
>> Arena_ncap_C  Arenavirus nucleocapsid C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.6e-06      0.14      95     150 ..       8      66 ..       3      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.6e-06
                                       -EEEESSHHHHHHHHHHTT-TTSEEEE-B-..-HHHHTTTHHHH.HHHHGGG---B-S- CS
                      Arena_ncap_C  95 mvitcqgsddirklldsqgrkdiklidvkl..tkedsrkyedkv.wdkygdlckmhtgv 150
                                       ++++++  dd + +++    ++i l+d+k+  ++++ r++e++   d ++ l k  +g 
  gi|330507387|ref|YP_004383815.1|   8 IIMSAKAVDDAQLIIKRSLEREISLLDMKMrlAENEIREFEERYgMDSHKFLSKFESGE 66 
                                       56789999*******************9863378999***9985379999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 809.95
//
Query:       gi|330507388|ref|YP_004383816.1|  [L=47]
Description: hypothetical protein MCON_1306 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-05   24.6   0.1    2.3e-05   24.5   0.1    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
      0.071   13.1   0.0      0.071   13.1   0.0    1.2  1  DUF2680          Protein of unknown function (DUF2680)


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 !   24.5   0.1   2.5e-09   2.3e-05      24      60 ..       2      38 ..       1      45 [. 0.90

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.5e-09
                   HicB_lk_antitox 24 fsagdtleeaianakeaielhlegliedgeeipepss 60
                                       sag+t ee  +  keaielhlegl ed   ip+p+ 
  gi|330507388|ref|YP_004383816.1|  2 VSAGETEEETAELMKEAIELHLEGLKEDRIPIPKPTI 38
                                      69*******************************9975 PP

>> DUF2680  Protein of unknown function (DUF2680)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.9e-06     0.071      28      54 ..       2      28 ..       1      43 [. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.9e-06
                           DUF2680 28 VeaGllTkeqgekikkniDkrlkylke 54
                                      V+aG+  +e +e +k+ i+ +l+ lke
  gi|330507388|ref|YP_004383816.1|  2 VSAGETEEETAELMKEAIELHLEGLKE 28
                                      99********************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 376.94
//
Query:       gi|330507389|ref|YP_004383817.1|  [L=38]
Description: hypothetical protein MCON_1307 [Methanosaeta concilii GP6]
Scores for complete 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   26.5   0.0    4.7e-06   26.5   0.0    1.1  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   2.6e-10   4.7e-06       2      24 ..       8      30 ..       7      38 .] 0.90

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.6e-10
                                      HCHHHHHHHTT-EEEEEETTEEE CS
                        HicA_toxin  2 reviklLeklGfevvrqkGSHvr 24
                                      r++ikl+e++G+++v++kGSH+ 
  gi|330507389|ref|YP_004383817.1|  8 RDAIKLIEADGWRLVNTKGSHRG 30
                                      9********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.22s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 316.41
//
Query:       gi|330507390|ref|YP_004383818.1|  [L=273]
Description: hypothetical protein MCON_1308 [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.0    2.6e-08   34.5   0.0    1.6  2  TIR_2     TIR domain
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.058   13.4   0.0    2.2  1  TIR-like  Predicted nucleotide-binding protein containing TIR


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 !   34.5   0.0   2.9e-12   2.6e-08       1     109 [.       9     122 ..       9     131 .. 0.83
   2 ?   -2.3   0.0      0.74   6.6e+03      68      75 ..     211     218 ..     176     257 .. 0.55

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2.9e-12
                             TIR_2   1 VFiSyssed.kewaeklaeaLeaa..girvwldrwdlkpgedweeeieeaiessdvvlvvlspaylesewcreelea 74 
                                       +FiS s+   k+ ae l++ L +    i++w+++ d+ +g +w ++++e++++ +  +++l+ + l+ +w   e+ a
  gi|330507390|ref|YP_004383818.1|   9 IFISWSGPRsKAMAEALKDWLPNViqSIDPWVSSSDIDAGMRWTPALAEELQQTQLGIICLTIENLSAPWLLFEAGA 85 
                                       8******76489*********555448***********************************************999 PP

                             TIR_2  75 ale.aaeegkkrlipvlle..p..ekpplaslqyidlskk 109
                                         + +    k+r+ p l+   p  +  pla++q++   k+
  gi|330507390|ref|YP_004383818.1|  86 LSKiI---DKTRVCPYLMGlePteVTGPLAQFQAVKAEKD 122
                                       99844...4678*******652222224899999987743 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.74
                             TIR_2  68 creeleaa 75 
                                       +++el  +
  gi|330507390|ref|YP_004383818.1| 211 VKNELAKY 218
                                       44443333 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 ?   13.4   0.0   6.5e-06     0.058       1      62 [.       8      73 ..       8     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.5e-06
                          TIR-like  1 kvFivhg..edeeaaeevkelLek.lg.lepiileeqvnkgktiiekleealksvdfaivlltpdD 62
                                      k+Fi  +  +++++ae++k++L + ++ ++p + ++++++g+    +l e+l++ + +i+ lt ++
  gi|330507390|ref|YP_004383818.1|  8 KIFISWSgpRSKAMAEALKDWLPNvIQsIDPWVSSSDIDAGMRWTPALAEELQQTQLGIICLTIEN 73
                                      79**9887***************97345********************************999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1999.89
//
Query:       gi|330507391|ref|YP_004383819.1|  [L=122]
Description: hypothetical protein MCON_1309 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-19   69.7   0.1    2.2e-19   69.6   0.1    1.0  1  Transposase_mut  Transposase, Mutator family
  ------ inclusion threshold ------
       0.03   14.3   0.5       0.19   11.7   0.3    2.3  2  HTH_12           Ribonuclease R winged-helix 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 !   69.6   0.1   2.4e-23   2.2e-19     265     380 ..       2     112 ..       1     113 [. 0.85

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 2.4e-23
                   Transposase_mut 265 akvpkkkadkvaealksiykaedaeearealeefleklgk.kypkvaelldeaaedvlaflafpeqirrkikstNll 340
                                       + +p k+++++a++lk       a   + +++e++++l +  y  +ae++d+ + d+ ++ a+p++++++i++tN++
  gi|330507391|ref|YP_004383819.1|   2 ESIPNKDKQEIADKLKE------ASYDEMKMQELAKELRDrGYDPAAETIDRFRFDLWNYKAYPKAHWKRIRTTNVI 72 
                                       56777777777777764......3333445556666666668*********************************** PP

                   Transposase_mut 341 ErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                       Er+Nke+ Rr+r vg FP ++s++rl g ++ + ++ew +
  gi|330507391|ref|YP_004383819.1|  73 ERINKELGRRSRPVGAFPSDQSLMRLAGCIMININEEWVT 112
                                       **************************************75 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   0.3   2.1e-05      0.19      12      35 ..      22      45 ..      10      52 .. 0.77
   2 ?   -2.6   0.0      0.64   5.7e+03       7      15 ..      79      87 ..      72      89 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
                            HTH_12 12 kpigakeiaeeLkkrgydigerav 35
                                      + +  +e+a+eL++rgyd  ++++
  gi|330507391|ref|YP_004383819.1| 22 DEMKMQELAKELRDRGYDPAAETI 45
                                      348889************999998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.64
                            HTH_12  7 laesdkpig 15
                                      l ++++p+g
  gi|330507391|ref|YP_004383819.1| 79 LGRRSRPVG 87
                                      445556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); 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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 888.55
//
Query:       gi|330507392|ref|YP_004383820.1|  [L=556]
Description: deoxyguanosinetriphosphate triphosphohydrolase [Methanosaeta concilii GP6]
Scores for complete 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-17   62.5   0.1    1.4e-16   60.8   0.1    1.9  1  HD        HD domain
    1.2e-12   48.2   0.7    7.3e-06   26.4   0.1    3.4  3  HD_assoc  Phosphohydrolase-associated domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.1   1.5e-20   1.4e-16       1     119 [.      84     241 ..      84     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 1.5e-20
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHH............HHH.....CTCCHHHH CS
                                HD   1 rleHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekk............eee.....fekflaHe 60 
                                       rl+H+leV+++ar + ++lg   +++l++++aL HDiG+ pfg+++e+             e +     +++f+ H 
  gi|330507392|ref|YP_004383820.1|  84 RLTHTLEVLQIARNISRYLG--LNEDLTEAIALGHDIGHTPFGHEGERVldqilsgkaeykE-LkyeinYTGFK-HN 156
                                       789*****************..*****************************99999887651.25667777766.** PP

                                       HHHHHHHHHHHHHHHHH.....HHHHHHHHHTTCCHHHHHHHH.................H....HHHCCTSCHHHH CS
                                HD  61 kvgaeilrevekrlgld.....ledvaklirehheswegkkrp.................r....glaerqlslear 111
                                       + + ++l e+ek  +       ++ v++ i++h++ +++++                   +      +e   +le +
  gi|330507392|ref|YP_004383820.1| 157 FNSLKVLDEIEKKYDNEsglnlTWQVLEGILKHTRIKRNNELWcdidrfllnlsnskfniKfenlLNYEYSVTLEGQ 233
                                       **********99995559*******************8655449999999988887665516678888899999999 PP

                                       HHHHHHHH CS
                                HD 112 ivklaDrl 119
                                       +v++aD +
  gi|330507392|ref|YP_004383820.1| 234 VVAIADEI 241
                                       99999986 PP

>> HD_assoc  Phosphohydrolase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.083   7.5e+02      33      55 ..     308     329 ..     297     341 .. 0.81
   2 !   16.9   0.0   7.5e-07    0.0067      12      58 ..     366     411 ..     357     418 .. 0.87
   3 !   26.4   0.1   8.2e-10   7.3e-06      71      92 .]     531     552 ..     505     552 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.083
                          HD_assoc  33 ekarriireLfealledperllp 55 
                                       +k + iir++ e+++ d + l+ 
  gi|330507392|ref|YP_004383820.1| 308 YKRNTIIRDIIEYFICDVT-LMS 329
                                       78899*********99988.665 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 7.5e-07
                          HD_assoc  12 aeLkkflfenvyrhpevqreeekarriireLfealledperllpeef 58 
                                       ++L +++ +++++++ev++   ka+ +i++Lf+a++++p+ ++ +  
  gi|330507392|ref|YP_004383820.1| 366 KKLDQYIKNRIVNSNEVNKFDGKANYVIKRLFKAYYSNPR-QMSKYA 411
                                       5678889999*****************************9.887665 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 8.2e-10
                          HD_assoc  71 aRvVcDyiAgmTDryalrlyar 92 
                                         v+cDyi+gmTD+ya ++y++
  gi|330507392|ref|YP_004383820.1| 531 LSVICDYISGMTDNYAEEEYQK 552
                                       569*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3821.60
//
Query:       gi|330507393|ref|YP_004383821.1|  [L=667]
Description: hypothetical protein MCON_1313 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-45  154.0   0.1    1.4e-44  151.2   0.0    2.4  2  DUF460          Protein of unknown function (DUF460)
     0.0011   19.2   0.4     0.0011   19.2   0.4    3.3  4  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
     0.0053   17.0   3.3      0.013   15.7   3.3    1.6  1  Fib_alpha       Fibrinogen alpha/beta chain family
     0.0061   17.1   1.7     0.0061   17.1   1.7    2.7  2  APG6_N          Apg6 coiled-coil region
     0.0074   16.6   1.1     0.0074   16.6   1.1    3.3  3  DUF641          Plant protein of unknown function (DUF641)
  ------ inclusion threshold ------
      0.013   14.8   0.2      0.013   14.8   0.2    1.6  2  HemX            HemX, putative uroporphyrinogen-III C-methylt
      0.023   15.1   0.5      0.072   13.5   0.5    1.8  1  LPP             Lipoprotein leucine-zipper
      0.042   13.4   0.1      0.088   12.3   0.1    1.5  1  DUF3000         Protein of unknown function (DUF3000)
      0.059   12.7   0.2       0.51    9.6   0.0    2.1  2  DNA_methylase   C-5 cytosine-specific DNA methylase
      0.078   13.5   0.4       0.18   12.3   0.4    1.6  1  NPV_P10         Nucleopolyhedrovirus P10 protein
       0.48    9.9   4.7       0.14   11.7   0.7    2.0  2  Exonuc_VII_L    Exonuclease VII, large subunit
          2    8.5   4.8       0.51   10.4   0.1    2.2  2  FlxA            FlxA-like protein
        2.2    7.6   9.4       0.12   11.7   3.0    1.9  2  DUF4407         Domain of unknown function (DUF4407)
        2.4    8.5   7.9       0.29   11.5   0.2    3.2  2  EccE            Putative type VII ESX secretion system transl
        4.3    6.9   9.0      0.071   12.7   0.9    2.1  2  Fzo_mitofusin   fzo-like conserved region


Domain annotation for each model (and alignments):
>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.3   1.6e+03      52      84 ..      29      58 ..      18      66 .. 0.74
   2 !  151.2   0.0   1.2e-47   1.4e-44       5     141 .]     215     344 ..     212     344 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                            DUF460 52 evlalkssreldreevieliselGkpvivAtDv 84
                                      +  al+    ++r+++i++i e  +p ivA D 
  gi|330507393|ref|YP_004383821.1| 29 DATALH--HMISRHKLIRMIRER-QPEIVAMDN 58
                                      554443..568999999999987.899999885 PP

  == domain 2  score: 151.2 bits;  conditional E-value: 1.2e-47
                            DUF460   5 kdvkvevesvekdkiefeplkkkrkkklivGiDPGittgiavldldgevlalkssreldreevieliselGkpvivA 81 
                                        d +++v+s+e+  ++++pl  +r+ ++ivG+DPG+ttgia+l+l+ge+++l ssr +++++vie+i++ G+++ivA
  gi|330507393|ref|YP_004383821.1| 215 VDAQLKVQSIERPALQYKPL-LHRRGYIIVGLDPGTTTGIAALNLRGELVDLISSRAMSSSDVIEWIAARGRSLIVA 290
                                       699*****************.9******************************************************* PP

                            DUF460  82 tDvspppetvkklarslkavlyvPeedlsveeKeelaeklsekekvkykddHeRDalaAA 141
                                       tDvsp+p +v+k++r+++avl++P  d++ eeK++l ++      v yk+dHeRDalaAA
  gi|330507393|ref|YP_004383821.1| 291 TDVSPTPGAVEKVKRAFNAVLFSPGADMAGEEKIALGRE------VGYKNDHERDALAAA 344
                                       ***************************************......99************9 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.93   1.1e+03      75     105 ..      19      52 ..       7      75 .. 0.68
   2 !   19.2   0.4   9.4e-07    0.0011      38      69 ..     147     178 ..     117     213 .. 0.83
   3 ?   -2.4   0.1       4.7   5.6e+03     114     123 ..     413     422 ..     364     457 .. 0.65
   4 ?   -2.4   0.1       4.7   5.6e+03      22      22 ..     534     534 ..     498     582 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.93
                           acVLRF1  75 ae...vvlgGdrslvaevledarlaplatlaree 105
                                       ++   vvl Gd ++++ + ++ +l ++ + +++e
  gi|330507393|ref|YP_004383821.1|  19 PSyslVVLEGDATALHHMISRHKLIRMIRERQPE 52 
                                       237779999***9999999887755444444433 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 9.4e-07
                           acVLRF1  38 aaGGwSqqRfaRrrenqadalleavaeaaarl 69 
                                        +GGwSq+R+ R++ + + a++++v++++++ 
  gi|330507393|ref|YP_004383821.1| 147 GRGGWSQNRYTRKIHGAVMAMAREVEKQLREA 178
                                       57************************999876 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.7
                           acVLRF1 114 ravLedavrr 123
                                        a L++ +++
  gi|330507393|ref|YP_004383821.1| 413 TAGLRQHIQQ 422
                                       4444444433 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 4.7
                           acVLRF1  22 e 22 
                                       e
  gi|330507393|ref|YP_004383821.1| 534 E 534
                                       2 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 !   15.7   3.3   1.1e-05     0.013      38     129 ..     414     504 ..     408     506 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                                       CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHH CS
                         Fib_alpha  38 ekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesn 114
                                       + l+++++++s++ k+ +++v e++ +l+ek +  ++  + + +++++   + ++ +++i    ++i  L+++l+s 
  gi|330507393|ref|YP_004383821.1| 414 AGLRQHIQQLSEQVKTLRTYVDELRAQLAEKDADLQKAIERLDRLKDKTS-REIKRDHEIRIRDKEIGRLRSILRSE 489
                                       5699********************************99999999999999.6667788999999************* PP

                                       HHHHHHHHHHHHHHH CS
                         Fib_alpha 115 eqkiqkLeqdidqke 129
                                       ++  +kL+  +++++
  gi|330507393|ref|YP_004383821.1| 490 RKYTKKLKRTVAARK 504
                                       *********999876 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.7   5.1e-06    0.0061      24     117 ..     337     481 ..     333     496 .. 0.76
   2 ?   -1.8   5.6       3.4   4.1e+03      61     120 ..     615     653 ..     603     662 .. 0.35

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.1e-06
                            APG6_N  24 erdaYeeflkklkkekkeeek...................................................qdeel 49 
                                       erda+ + l+ ++k+k++  +                                                    d ++
  gi|330507393|ref|YP_004383821.1| 337 ERDALAAALSAFRKYKNKFIQvekkapaevdpdeikalvvrgysienaiaefthpppaegrpaapaasgapaPDPDT 413
                                       56666666666666644443356666666666667777777777777777777777777777777777777788899 PP

                            APG6_N  50 eeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlellelee 117
                                       + l++ +++l+++ ++l +  +el ++ +e +a+l+++ e l++l+++  r++++ +e ++  +e   
  gi|330507393|ref|YP_004383821.1| 414 AGLRQHIQQLSEQVKTLRTYVDELRAQLAEKDADLQKAIERLDRLKDKTSREIKRDHEIRIRDKEIGR 481
                                       999*************************************************9999998877776655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.4
                            APG6_N  61 keeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeld 120
                                       +e+ e +++ +++  e e+le+  ++                     +++e ++ e++++
  gi|330507393|ref|YP_004383821.1| 615 RERWEVQQKARQARLEAEKLESLFQD---------------------YKVERMKEEKRKK 653
                                       12222222222222222222222222.....................3333333333222 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 !   16.6   1.1   6.2e-06    0.0074      71     124 ..     411     464 ..     398     468 .. 0.88
   2 ?    3.3   0.2     0.082        99      99     127 ..     470     498 ..     465     499 .. 0.90
   3 ?   -1.7   1.6       2.9   3.4e+03      82     114 ..     619     649 ..     592     661 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.2e-06
                            DUF641  71 aeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkk 124
                                       ++++ l+++iq++ + +kt+ + v++l+a+l +kd+++++  e+L++++ ++++
  gi|330507393|ref|YP_004383821.1| 411 PDTAGLRQHIQQLSEQVKTLRTYVDELRAQLAEKDADLQKAIERLDRLKDKTSR 464
                                       6788999***************************************99988765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.082
                            DUF641  99 aelkakdseieeLkekLeeaeksnkklek 127
                                        e++ +d+ei +L++ L++++k +kkl++
  gi|330507393|ref|YP_004383821.1| 470 HEIRIRDKEIGRLRSILRSERKYTKKLKR 498
                                       79999****************99999976 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.9
                            DUF641  82 eqrsllktyeitvkkleaelkakdseieeLkek 114
                                       e +++ +     ++kle+ +  +d ++e++ke+
  gi|330507393|ref|YP_004383821.1| 619 EVQQKARQARLEAEKLESLF--QDYKVERMKEE 649
                                       33333333333333333322..23333333332 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 ?   14.8   0.2   1.1e-05     0.013     169     238 ..     409     478 ..     406     492 .. 0.78
   2 ?   -4.8   2.1       9.8   1.2e+04      48      70 ..     621     643 ..     609     661 .. 0.33

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                              HemX 169 nqvDrdgiilrLeqLanqvdeLpladnelde..apsdadnaelsdslsdWkqnleksaksflshfirirrrd 238
                                       +++D  g+ ++++qL++qv++L+   +el +  a++dad +++ + l++ k   ++++k+  +h irir+++
  gi|330507393|ref|YP_004383821.1| 409 PDPDTAGLRQHIQQLSEQVKTLRTYVDELRAqlAEKDADLQKAIERLDRLKDKTSREIKR--DHEIRIRDKE 478
                                       689*******************99988888745667777777777777777777776654..6778888876 PP

  == domain 2  score: -4.8 bits;  conditional E-value: 9.8
                              HemX  48 eqqlaqveaekeqkqeleerlqq 70 
                                       +q++ q++ e+e+ + l ++++ 
  gi|330507393|ref|YP_004383821.1| 621 QQKARQARLEAEKLESLFQDYKV 643
                                       22222222222222222222221 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5     6e-05     0.072       2      35 ..     420     453 ..     419     457 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-05
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaake 35 
                                       +++Ls+qV++L + vd+l +++++  a++q+a e
  gi|330507393|ref|YP_004383821.1| 420 IQQLSEQVKTLRTYVDELRAQLAEKDADLQKAIE 453
                                       789*************************999865 PP

>> DUF3000  Protein of unknown function (DUF3000)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   7.4e-05     0.088      19      83 ..     505     572 ..     489     585 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.4e-05
                           DUF3000  19 peieleeipapqrlapysvAlgaevteeeeeeelatGrlilLhdpageeaWegtf...rlvayirael 83 
                                       +  ++ee++  +rl p+++  +  v +++e+ +la+G l+lL d +g  + + ++   r va i ae 
  gi|330507393|ref|YP_004383821.1| 505 KAERIEEVKGLRRLKPVAAFSKEAVLAAAERYSLAEGDLVLLEDSSGGGKSTAEMfreRGVAAIVAEG 572
                                       333799************999999*9999999************998765554332335566665554 PP

>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00043      0.51      94     118 ..      42      66 ..      39      75 .. 0.87
   2 ?    0.4   0.0      0.27   3.2e+02     210     275 ..     450     507 ..     377     565 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00043
                                       HHHHHHHH--SEEEEEEEGGGGGGC CS
                     DNA_methylase  94 iiriikekkPkvfllENVkgLlkhd 118
                                        ir+i+e++P+++ + NV++L ++ 
  gi|330507393|ref|YP_004383821.1|  42 LIRMIRERQPEIVAMDNVHELAQSH 66 
                                       79*******************9874 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.27
                                       SSSTT-EE--.......S---HHHTS--B--TTS...-B----S-STT--B-TTS---EEEETTEE CS
                     DNA_methylase 210 klvekeekikkttkaseegypkelsrnridkveelkglsatrrksgrgeklekelaeagklqknke 275
                                       k +e+  + k+  k+s+e+ ++ ++r r +++  l+++ ++ rk+ +      +l+++   +k++e
  gi|330507393|ref|YP_004383821.1| 450 KAIERLDRLKD--KTSREIKRDHEIRIRDKEIGRLRSILRSERKYTK------KLKRTVAARKKAE 507
                                       22222222221..1112222221111112223332222222222222......2222222222222 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   0.00015      0.18       9      56 ..     416     460 ..     414     487 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                        r+ i++++++V+ l + vd+++++l +     + L++  + L+ l++
  gi|330507393|ref|YP_004383821.1| 416 LRQHIQQLSEQVKTLRTYVDELRAQLAEK---DADLQKAIERLDRLKD 460
                                       5999*******************999773...3455555555555555 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   0.00012      0.14     157     251 ..     420     511 ..     334     546 .. 0.65
   2 ?   -0.9   0.2      0.82   9.7e+02     163     208 ..     623     642 ..     567     664 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                      Exonuc_VII_L 157 ekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq..lkkkrerleelkerlkekleekker 231
                                        +++++++++ ++ +++l+ +l+++++ l+++ +rld+l+++ +r++k+   ++ + +++ +l++ l+    ++++ 
  gi|330507393|ref|YP_004383821.1| 420 IQQLSEQVKTLRTYVDELRAQLAEKDADLQKAIERLDRLKDKTSREIKRDheIRIRDKEIGRLRSILR----SERKY 492
                                       22223344444455555555555556666666666666666666654444444445555555553332....22222 PP

                      Exonuc_VII_L 232 lkklkerlelleekkerlee 251
                                       +kklk+ +  +++k er+ee
  gi|330507393|ref|YP_004383821.1| 493 TKKLKRTV-AARKKAERIEE 511
                                       23332222.24444444443 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.82
                      Exonuc_VII_L 163 lleekkqrleklasrlkspeellerkrqrldeleerleralkkqlk 208
                                       + ++++ + ekl+s +                          + +k
  gi|330507393|ref|YP_004383821.1| 623 KARQARLEAEKLESLF--------------------------QDYK 642
                                       1111111111111111..........................1111 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00043      0.51      17      61 ..     411     455 ..     399     461 .. 0.68
   2 ?   -1.5   1.1       2.1   2.5e+03      30      52 ..     631     655 ..     613     663 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00043
                              FlxA  17 sqiasLqkQiknlqkqLkelses.deltkeekkkqqqliqaQIqql 61 
                                        ++a L++ i++l++q+k l +  del ++   ++   +q+ I+ l
  gi|330507393|ref|YP_004383821.1| 411 PDTAGLRQHIQQLSEQVKTLRTYvDELRAQ-LAEKDADLQKAIERL 455
                                       566667777777777777777775555555.666777777776655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                              FlxA  30 qkqLkelses..deltkeekkkqqq 52 
                                        ++L++l ++   e  keek+k++ 
  gi|330507393|ref|YP_004383821.1| 631 AEKLESLFQDykVERMKEEKRKKRM 655
                                       4666677676664444555555554 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.0    0.0001      0.12     131     224 ..     416     511 ..     386     537 .. 0.63
   2 ?   -1.4   0.5      0.96   1.1e+03     192     230 ..     611     649 ..     588     661 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                           DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..gtgttgvaGkgpaakekkaqldaaqaelaelkak 205
                                       l++ +++l +q++ l++ +d+++a+l+++ a++qk ++     +++t++   +  + + +++++ +++  l + ++ 
  gi|330507393|ref|YP_004383821.1| 416 LRQHIQQLSEQVKTLRTYVDELRAQLAEKDADLQKAIERLDrlKDKTSREIKRDHEIRIRDKEIGRLRSILRSERKY 492
                                       56666666666666666666666666666666666666433554444444455555555566666666655555555 PP

                           DUF4407 206 ldatarlaalraelaelea 224
                                        ++ +r+ a+r++++++e+
  gi|330507393|ref|YP_004383821.1| 493 TKKLKRTVAARKKAERIEE 511
                                       5555555555555555444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.96
                           DUF4407 192 ldaaqaelaelkakldatarlaalraelaeleaeraker 230
                                       l+aa+++++  ++ ++a+ + ++l++  ++ + er ke+
  gi|330507393|ref|YP_004383821.1| 611 LEAARERWEVQQKARQARLEAEKLESLFQDYKVERMKEE 649
                                       334444444444443322223333333333333333333 PP

>> EccE  Putative type VII ESX secretion system translocon, EccE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.99   1.2e+03      53      78 ..     107     132 ..     102     158 .. 0.78
   2 ?   11.5   0.2   0.00024      0.29      29      76 ..     157     204 ..     140     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.99
                              EccE  53 rarvleaeeldaalaalavglaaapa 78 
                                       r+r+le++e  a laa +vg+ ++++
  gi|330507393|ref|YP_004383821.1| 107 RTRPLEEAEASARLAARGVGAVVSAF 132
                                       67999999999999999998876665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00024
                              EccE  29 tegaaraaaaaarRlakaLreqGirarvleaeeldaalaalavglaaa 76 
                                       t +++ a++a+ar + k+Lre+G++ ++ ++e l  +++a +v++a +
  gi|330507393|ref|YP_004383821.1| 157 TRKIHGAVMAMAREVEKQLREAGLEYSLRTVEGLGGFTRAEFVVEATR 204
                                       567999*********************************999988654 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.9     6e-05     0.071      94     138 ..     418     462 ..     413     484 .. 0.87
   2 ?   -3.3   1.7       4.8   5.7e+03     100     140 ..     612     643 ..     607     660 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6e-05
                     Fzo_mitofusin  94 qvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkka 138
                                       q  q+ls+ ++ l++ vde +++l e+ ++l+k ie+l++++ k 
  gi|330507393|ref|YP_004383821.1| 418 QHIQQLSEQVKTLRTYVDELRAQLAEKDADLQKAIERLDRLKDKT 462
                                       66799**********************************998654 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.8
                     Fzo_mitofusin 100 sstfarlcqqvdetekeleeeikelekeiekleevqkkakl 140
                                       + + +r++ q +  ++ le+e         kle++ +  k+
  gi|330507393|ref|YP_004383821.1| 612 EAARERWEVQQKARQARLEAE---------KLESLFQDYKV 643
                                       555555555555555555544.........33333332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (667 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1908  (0.10642); expected 358.6 (0.02)
Passed bias filter:                      938  (0.0523175); expected 358.6 (0.02)
Passed Vit filter:                       133  (0.00741815); 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):              15  [number of targets reported over threshold]
# CPU time: 0.89u 0.33s 00:00:01.22 Elapsed: 00:00:00.50
# Mc/sec: 3995.56
//
Query:       gi|330507394|ref|YP_004383822.1|  [L=289]
Description: serine/threonine protein kinase RIO2 [Methanosaeta concilii GP6]
Scores for complete 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-41  139.7   0.0    1.1e-40  139.2   0.0    1.1  1  RIO1      RIO1 family
    3.7e-25   87.9   0.0    5.8e-24   84.1   0.1    2.6  3  Rio2_N    Rio2, N-terminal
    6.3e-06   26.3   3.3     0.0019   18.2   0.6    2.3  2  APH       Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.029   13.8   0.0      0.046   13.1   0.0    1.5  1  Pkinase   Protein kinase domain


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.0   2.5e-44   1.1e-40      11     180 ..     114     271 ..     103     279 .. 0.90

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 2.5e-44
                                       EEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE- CS
                              RIO1  11 kevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvmef 87 
                                       +++aiK+++ ++t+Fk++++ ++  k+    k +  +++ + l+a++Ef+ +++l+ + v++P+p+++ rh+l me+
  gi|330507394|ref|YP_004383822.1| 114 ASLAIKFHRQGRTSFKHVRRLRDHLKD----KPRVPWLYAASLAARREFAVMEKLYPK-VSIPRPVAISRHALAMEY 185
                                       489******************999999....679***********************9.****************** PP

                                       -EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHHHHH CS
                              RIO1  88 igedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnalefL 164
                                       +   g  + k+   +     ee ++ +l+e+ +++ +  +vH DLSe+N+++++ ++viID++Qav+++hp++ e+L
  gi|330507394|ref|YP_004383822.1| 186 VP--GPLLNKITLSD----PEEGLRLILQEVGRAL-DLDIVHSDLSEFNIMITDSGPVIIDWPQAVDAAHPHSDELL 255
                                       *9..66555555555....7889999*********.***************************************** PP

                                       HHHHHHHHHHHHTTC- CS
                              RIO1 165 erDveniikfFrrkgv 180
                                       +rD+ n+ +fFr k+ 
  gi|330507394|ref|YP_004383822.1| 256 KRDLGNVLRFFRSKYR 271
                                       ************8875 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.1   1.3e-27   5.8e-24       4      82 .]      11      89 ..       8      89 .. 0.98
   2 ?   -0.4   0.0      0.31   1.4e+03      66      79 ..     108     121 ..     102     123 .. 0.84
   3 ?   -0.9   0.0      0.45     2e+03      22      42 ..     183     204 ..     175     218 .. 0.75

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 1.3e-27
                            Rio2_N  4 LskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyLALktlvkr 82
                                      Ls+edf +L a+E+gmr he+Vpt  i+++++l++++ ++rl++l+++kl++r+ ++y GY++ +  yD LAL+ +v+r
  gi|330507394|ref|YP_004383822.1| 11 LSREDFSLLGAIETGMRTHEWVPTFIISKLAGLSASKSEYRLQHLFEKKLVVREAQHYLGYQINFDSYDLLALSDFVRR 89
                                      89************************************************************************99987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.31
                            Rio2_N  66 LtyeGyDyLALktl 79 
                                       L  +Gy  LA+k +
  gi|330507394|ref|YP_004383822.1| 108 LEAQGYASLAIKFH 121
                                       8899*******976 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.45
                            Rio2_N  22 hevVptelieeisrlk.eeevk 42 
                                        e+Vp  l+++i+  + ee+++
  gi|330507394|ref|YP_004383822.1| 183 MEYVPGPLLNKITLSDpEEGLR 204
                                       699*****99998766455555 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.2   0.00021      0.94      33     101 ..     150     213 ..     117     216 .. 0.76
   2 !   18.2   0.6   4.3e-07    0.0019     164     204 ..     214     252 ..     199     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00021
                                       -HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS...HHHHHHHHHHHHHHHHH CS
                               APH  33 aaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr...klsaaqlpellealgef 101
                                       a   +rre+a++  L    v++P+++a       i ++++++eyvpg  l      + ++ l+ +l+++g++
  gi|330507394|ref|YP_004383822.1| 150 ASLAARREFAVMEKLYPK-VSIPRPVA-------ISRHALAMEYVPGPLLNKitlSDPEEGLRLILQEVGRA 213
                                       456778999999999988.89******.......888999********999986655566666666666665 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 4.3e-07
                                       S-EEEE-SS-SGGGEEEC..TTEEEEE---.TT-EEEECCHH CS
                               APH 164 lptvllHgDlhpgNllvdpddgrvtGviDf.edaglgpplyD 204
                                       l+  ++H Dl+  N++++ d g+v  +iD+ + + +++p+ D
  gi|330507394|ref|YP_004383822.1| 214 LDLDIVHSDLSEFNIMIT-DSGPV--IIDWpQAVDAAHPHSD 252
                                       44679*************.88***..****666777777766 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     1e-05     0.046      72     145 ..     178     243 ..      94     260 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                                       EEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTS CS
                           Pkinase  72 elylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGla 145
                                       +  l +eyv+g  l+++     s +ee ++ i++++ ++l+      i+H Dl   Ni+i  +    i+D+  a
  gi|330507394|ref|YP_004383822.1| 178 RHALAMEYVPGPLLNKITL---SDPEEGLRLILQEVGRALD----LDIVHSDLSEFNIMIT-DSGPVIIDWPQA 243
                                       45689*****887777764...579999************7....69**************.555567787655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2039.80
//
Query:       gi|330507395|ref|YP_004383823.1|  [L=405]
Description: threo-isocitrate dehydrogenase [NAD] [Methanosaeta concilii GP6]
Scores for complete 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-70  237.6   0.0    3.1e-70  237.1   0.0    1.2  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.1   0.0   1.7e-74   3.1e-70       2     318 ..      45     353 ..      44     362 .. 0.91

  Alignments for each domain:
  == domain 1  score: 237.1 bits;  conditional E-value: 1.7e-74
                                       EEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHS...SSS-HHHHHHHHHSSEEEEEE---CS CS
                            Iso_dh   2 iallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetg...eplpeetleaikeadvvllgavgtpk 75 
                                       i ++ gdgiGp ++++a++vl+ + +++ ++ ++e + ++g +i+e     ++lpeetl+a+ke +v+l+g+++tpk
  gi|330507395|ref|YP_004383823.1|  45 IGVVGGDGIGPFITKEAVRVLEYILAEEIQSGKVELRWISGLTIEERVkvmKALPEETLAALKECHVILKGPLTTPK 121
                                       7899*********************9999888999999988888876545599************************ PP

                                       ....SSSSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GG CS
                            Iso_dh  76 ....ekevrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifte 148
                                             ++++    +++r+eldlfan+rpvkv e             +++d +  Re+t+g Y+   +  +    te
  gi|330507395|ref|YP_004383823.1| 122 kgdkWPNLESA--NVSMRRELDLFANVRPVKVPE-------------KGIDWIFYRENTEGEYVLGSSGFNV---TE 180
                                       64433444555..5*****************982.............3799************988777666...58 PP

                                       GEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHH CS
                            Iso_dh 149 evavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamq 224
                                       + avd k+++ ++ eri+r+afe+A+++g ++v +v+Kanv+k+++  + +i+ +va+ eyp+i++++ +vD +a++
  gi|330507395|ref|YP_004383823.1| 181 DLAVDFKVITSQGAERIVRLAFEYARNNGINRVSAVTKANVIKTTDgKFLEIARRVAA-EYPEIQFDDWFVDIMAAK 256
                                       9*********************************************99********99.****************** PP

                                       HHHSG..GGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-...S-THHHHHH CS
                            Iso_dh 225 lvksp..kqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdk...aNpiavilS 296
                                       lv +   + f Viv +Nl+GDil Deaa   G++G + Sa++g k+ a+fEa+HGsap++   +    a p +++ +
  gi|330507395|ref|YP_004383823.1| 257 LVDEKrrRDFKVIVLPNLYGDILTDEAAEFQGGVGTAGSANIG-KRYAMFEAIHGSAPRMVDEGRaqyADPASMMRA 332
                                       **988446677********************************.79************99866555559******** PP

                                       HHHHHHHTTT-HHHHHHHHHHH CS
                            Iso_dh 297 aalmLryslgleeaAdkiekAv 318
                                        ++mLr+ +   ++A+++e A+
  gi|330507395|ref|YP_004383823.1| 333 CVMMLRH-ISFIDQASRMEMAL 353
                                       *******.*********99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2958.60
//
Query:       gi|330507396|ref|YP_004383824.1|  [L=421]
Description: nucleotidyl transferase [Methanosaeta concilii GP6]
Scores for complete sequence (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  116.7   0.0    1.8e-33  116.2   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
      1e-10   40.9  11.6    0.00013   21.5   1.6    4.8  3  Hexapep          Bacterial transferase hexapeptide (six repea
    8.9e-05   20.8   0.4    0.00013   20.3   0.4    1.1  1  DUF4954          Domain of unknown function (DUF4954)
     0.0053   17.1   0.0       0.01   16.2   0.0    1.5  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
       0.26   11.1   8.3      0.084   12.6   0.6    3.2  2  Hexapep_2        Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.0     5e-37   1.8e-33       6     245 ..       9     250 ..       5     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 5e-37
                                       --S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEE.TTTHHHHHHHHTTSGGGT......SEE CS
                   NTP_transferase   6 aGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvlt.qehsflveeqlkegskfg......vev 75 
                                       +GGsGtRL+PLt +++k+lv   ++  +i   +  la++g+++ i+ +    +   + +++k+g+ f        + 
  gi|330507396|ref|YP_004383824.1|   9 VGGSGTRLYPLTLDQPKPLVELCDT-AIIANLFRVLASQGCRRFILGSKgASNTLNLSNYFKAGEGFFkrlgiaDHQ 84 
                                       5************************.*****************3333321344555667777777655677765456 PP

                                       EEEEESS--..BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEE.EEESS-CTTSE CS
                   NTP_transferase  76 lialepegk..gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfg.ivpveeateyG 149
                                        ++++p  +  g+Ad+++   ++++ +++   +lv++gD li+ +++ +v++++ ++   tv++  i p e  ++yG
  gi|330507396|ref|YP_004383824.1|  85 DFSYQPLYDdvGSADSLRYCMNYFDIKDD---LLVVSGDNLIDIDLSSIVQFHQLHKPVLTVALKeIAPGESISSYG 158
                                       67777776699**************9997...**************************666655427899999**** PP

                                       EEEECTTSBEEEEECS-S.SHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTT CS
                   NTP_transferase 150 vieadeegrverfvEKPk.eakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkd 225
                                       v+++de+ r+  fvEKPk + + s ++++  Y+f +ev + lak     ++ +d ++d++p+++e+g++ + f   +
  gi|330507396|ref|YP_004383824.1| 159 VARVDEDMRISGFVEKPKpGSEPSRMINTAFYLFSPEVREVLAK---MGDKARDIGGDLIPYLTENGYPVYGFPVAG 232
                                       *****************9434459******************76...89999************************* PP

                                       EE-EEEXSSHHHHHHHHHHH CS
                   NTP_transferase 226 aeyWsDvGtldslleanekl 245
                                         yW D+Gt++ l++a+++ 
  gi|330507396|ref|YP_004383824.1| 233 --YWIDIGTPERLHQAAMDC 250
                                       ..9*************9986 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   1.6   3.7e-08   0.00013      15      35 ..     288     308 ..     270     309 .. 0.90
   2 !   14.2   0.6   7.4e-06     0.026       8      33 ..     333     357 ..     308     359 .. 0.76
   3 !    7.1   0.1    0.0013       4.7       3      22 ..     370     389 ..     369     390 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.7e-08
                                       EEETTEEE-TTEEEETTEEEE CS
                           Hexapep  15 viggnVkIGdnvkIgagvvig 35 
                                       ++ gnV IG+n++I++gvvi 
  gi|330507396|ref|YP_004383824.1| 288 ILKGNVSIGRNCRIERGVVIE 308
                                       6889****************7 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 7.4e-06
                                       EEE-TTEEEETTEEE-TTEEEETTEE CS
                           Hexapep   8 vlIgpfaviggnVkIGdnvkIgagvv 33 
                                       ++I+  +vi + +++G+++++++++ 
  gi|330507396|ref|YP_004383824.1| 333 AHIM-HSVIINRAIVGRHCILEEHSA 357
                                       4555.78888**********999885 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0013
                                       EEETTEEE-TTEEEETTEEE CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkI 22 
                                       v+G+nv++ + +v++++V +
  gi|330507396|ref|YP_004383824.1| 370 VVGENVVLPSESVVAPGVRV 389
                                       899*************9987 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.4   3.5e-08   0.00013     190     257 ..     292     355 ..     276     361 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.5e-08
                           DUF4954 190 NvkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavisrcfvGqavklkkq 257
                                       Nv ig  + ie    +en  i     + + i ++V+++d++++s ++i ++++i+r++vG+ + l+++
  gi|330507396|ref|YP_004383824.1| 292 NVSIGRNCRIERGVVIENSHI----GHTSLIDRDVEIKDSMVMSFAHIMHSVIINRAIVGRHCILEEH 355
                                       9****************9766....57789*********************************99875 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 !   16.2   0.0   2.8e-06      0.01       6      96 ..      10     121 ..       5     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.8e-06
                                       ESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH.CHHHH..................HHTTC CS
                      NTP_transf_3   6 GGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggd.eevla..................alarl 58 
                                       GG ++R+      ++K+l++l+++ +++ +++ l+++g+++ ++  +  ++ l+                  + +++
  gi|330507396|ref|YP_004383824.1|  10 GGSGTRLypltlDQPKPLVELCDTAIIANLFRVLASQGCRRFILGSKGaSNTLNlsnyfkagegffkrlgiaDHQDF 86 
                                       9******7777678*************************99998876623333344555555555444443333455 PP

                                       TS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT- CS
                      NTP_transf_3  59 gvrvvededpgkgplaslaaalraaadadavlvlacDm 96 
                                        ++ ++d+    g + sl+  ++    +d +lv+++D 
  gi|330507396|ref|YP_004383824.1|  87 SYQPLYDD---VGSADSLRYCMNYFDIKDDLLVVSGDN 121
                                       56666665...688888888888887888888888885 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 ?   12.6   0.6   2.3e-05     0.084      17      33 ..     291     308 ..     283     309 .. 0.82
   2 ?    0.6   1.7      0.13   4.7e+02       6      26 ..     354     377 ..     344     389 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                                       S.EEE-TT-EE-TT-EE- CS
                         Hexapep_2  17 G.vslGdncvvgaGvvit 33 
                                       G vs+G+nc ++ Gvvi 
  gi|330507396|ref|YP_004383824.1| 291 GnVSIGRNCRIERGVVIE 308
                                       669*************95 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                                       TT-EE-TT-EE..SEE.E-TT-EE CS
                         Hexapep_2   6 dnCliGanagi..Gvs.lGdncvv 26 
                                       + + +G n g   Gv+ +G+n+v+
  gi|330507396|ref|YP_004383824.1| 354 EHSALGLNNGAegGVPvVGENVVL 377
                                       555566665533455424666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 2971.41
//
Query:       gi|330507397|ref|YP_004383825.1|  [L=78]
Description: hypothetical protein MCON_1318 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 564.67
//
Query:       gi|330507398|ref|YP_004383826.1|  [L=192]
Description: uracil DNA glycosylase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-46  157.6   0.0    2.9e-46  157.3   0.0    1.1  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.3   0.0   1.6e-50   2.9e-46       1     155 []      34     176 ..      34     183 .. 0.95

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 1.6e-50
                                       HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCC CS
                               UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaei 77 
                                       pg gp +a++++vGeaPg+eed +glpF+grag+ll+++lneaglkr     ++v+it+v+kcrpp+nr +p+++ei
  gi|330507398|ref|YP_004383826.1|  34 PGSGPSKAEIMLVGEAPGREEDLKGLPFVGRAGRLLDEALNEAGLKR-----EDVFITSVIKCRPPQNR-KPNKKEI 104
                                       799********************************************.....*****************.******* PP

                                       TCCHHHHHHHHHHHHSSEEEEESHHHHHH..HH.HHSCESCCCSCT.SEEEEES-SSTTTTTTTTSHHHHHHHHHHH CS
                               UDG  78 kacaplleeeiellkprlivllGktaakallge.klgklrgklleakirvlplphPsplnrnffksnpelkaeawed 153
                                       + c p+le+++++++pr+i+l+G+ta +a+lg   ++ lrg++l +  r+l+++hP++++rn     + l a+++ d
  gi|330507398|ref|YP_004383826.1| 105 ELCLPYLEDQMDAIRPRIICLMGNTAIQAVLGVvGVTVLRGRILSD--RFLVTYHPAAVLRN-----RNLMADFVSD 174
                                       *******************************77799**********..9*************.....7777776666 PP

                                       HH CS
                               UDG 154 Lk 155
                                       L+
  gi|330507398|ref|YP_004383826.1| 175 LR 176
                                       64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1485.09
//
Query:       gi|330507399|ref|YP_004383827.1|  [L=429]
Description: 3-isopropylmalate dehydratase large subunit 2 [Methanosaeta concilii GP6]
Scores for complete 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-93  314.3   1.5    8.8e-92  308.5   1.5    2.1  1  Aconitase  Aconitase family (aconitate hydratase)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.5   1.5   4.9e-96   8.8e-92       1     461 []      15     421 ..      15     421 .. 0.89

  Alignments for each domain:
  == domain 1  score: 308.5 bits;  conditional E-value: 4.9e-96
                         Aconitase   1 ekiwdahlvee..egiayv...pdrvllqdvtgvqalvdl.aaa..reavrrlggtlatidhlvpvdlvidhsvgae 69 
                                       eki+++ +++e   g ++v   +d  +++d+tg+ a++++ + a    +v+++ + +   dh+vp+d     s    
  gi|330507399|ref|YP_004383827.1|  15 EKILSRAANKEvkAG-EFVmanVDGAMIHDITGPLAVKGFyEIAgrDARVWDPTRIVLLFDHQVPAD-----SL--- 82 
                                       678776655443333.3333468***************99633321445699***************.....33... PP

                         Aconitase  70 ealeknledefernkeryefLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvG 146
                                              +      +e+  +L+++a++ +i  +++  G++Hqv++E+g +lpg++++gtDSHT+++g++G++a+GvG
  gi|330507399|ref|YP_004383827.1|  83 -------K--A---AENHIQLRKFAAEQDILNYDIFCGVCHQVMPEKGHVLPGNVILGTDSHTCTYGAFGAFATGVG 147
                                       .......2..2...2345568999999999999******************************************** PP

                         Aconitase 147 gieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNM 223
                                       ++++++v+++ +l++ +pk++++ ++G+l++ vt+kD vl +ig ++++g++  + Ef Ge++e++s+ +r+T++NM
  gi|330507399|ref|YP_004383827.1| 148 STDMASVFATGKLWFMVPKTLQIMIEGQLPSRVTSKDAVLRIIGDIGADGANYLACEFRGEAAERMSIPERMTVSNM 224
                                       ***************************************************************************** PP

                         Aconitase 224 aaEvGAttglfpvdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqda 300
                                       a+E+GA++g+fp d +t +YL+  gr +++   ea+   +a f ++ deda +++  e ++s+lep++a+p++++++
  gi|330507399|ref|YP_004383827.1| 225 AIEMGAKVGIFPADGTTKSYLE--GRVQDR---EAI---EAGF-VKGDEDAAFSR-REWNVSDLEPQIAMPHNVDNV 291
                                       **********************..996666...343...3335.789******98.59******************* PP

                         Aconitase 301 vplselvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvk 377
                                       +p+ ++v+                           ++++d++++gSCTN++ ed+++a ++++     +   ++gv+
  gi|330507399|ref|YP_004383827.1| 292 LPI-SQVP---------------------------QTRIDQVFLGSCTNGRFEDLQLASEMMK-----NEPLAKGVR 335
                                       ***.6665...........................23599***********************.....889999*** PP

                         Aconitase 378 tsvaPGSevvkayleaeGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqg.pntrayLaSPe 452
                                       ++v+P+S+    ++ ++Gl e +++aG+ v ++ C++C+g   + l +ge+++ +sNRNF gRqg p++  yL SP+
  gi|330507399|ref|YP_004383827.1| 336 MIVVPASRDEYMKCLRAGLVERFMEAGAMVESPCCGPCMGgSFGLLGAGERCLATSNRNFVGRQGsPQAFVYLSSPA 412
                                       ****************************************8889999*****************8577777****** PP

                         Aconitase 453 lvvaaAlaG 461
                                        + a+A++G
  gi|330507399|ref|YP_004383827.1| 413 TAGASAITG 421
                                       *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3206.04
//
Query:       gi|330507400|ref|YP_004383828.1|  [L=271]
Description: tRNA pseudouridine synthase A [Methanosaeta concilii GP6]
Scores for complete 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   91.1   0.0    2.2e-21   76.3   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 !   12.6   0.0   7.7e-06      0.14       4      76 ..       8      73 ..       6     102 .. 0.84
   2 !   76.3   0.0   1.2e-25   2.2e-21       1     108 []     126     224 ..     126     224 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.7e-06
                   PseudoU_synth_1  4 elvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvl.favgqgklspe 76
                                      +++G +++g f  qkq+++ tv +  ++a++++       ++ +++ +g++d++V a+++v+ f + + k++  
  gi|330507400|ref|YP_004383828.1|  8 AYLGDNYYG-F--QKQPDRVTVDSQVRRALAQIGV-----IHGDFCYAGRTDRGVSALGQVIdFWIDEDKIDLT 73
                                      599******.9..8999999999999999995554.....589*******************999988887765 PP

  == domain 2  score: 76.3 bits;  conditional E-value: 1.2e-25
                   PseudoU_synth_1   1 AakelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklsped 77 
                                       Aa +l+G+hdf++f    + k  tv+++ + +i+    e+++l  ++++++gFl+++VR +vg+  +vg g++++ +
  gi|330507400|ref|YP_004383828.1| 126 AADMLLGEHDFRNF---SSAKVGTVKRVEKLEIR----ERDGLFIFDIRADGFLWNMVRKIVGATEKVGSGQKDMRW 195
                                       899***********...5666789**********....88999********************************** PP

                   PseudoU_synth_1  78 vkellnakkrkkiavetapavglvlfhvrYd 108
                                       +k+ll  ++++   ++tapa+gl+l++v Yd
  gi|330507400|ref|YP_004383828.1| 196 FKDLLRPELNHG--APTAPAEGLILMEVGYD 224
                                       *********765..9***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1990.57
//
Query:       gi|330507401|ref|YP_004383829.1|  [L=144]
Description: flavodoxin domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-10   42.0   0.0    1.5e-10   41.5   0.0    1.2  1  Flavodoxin_1  Flavodoxin
    3.4e-09   37.1   0.0    3.7e-09   37.0   0.0    1.1  1  Flavodoxin_5  Flavodoxin domain
     0.0035   17.1   0.4      0.034   13.9   0.1    2.0  2  FMN_red       NADPH-dependent FMN reductase
  ------ inclusion threshold ------
      0.056   13.1   0.0      0.071   12.8   0.0    1.2  1  Flavodoxin_3  Flavodoxin 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 !   41.5   0.0   3.3e-14   1.5e-10       1     141 [.       6     133 ..       6     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 3.3e-14
                                       EEEETSSSHHHHHHHHHHHHHHH.TTTEEEEEEEEGTTSC.GGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHHHH CS
                      Flavodoxin_1   1 ilYgSetGnteklAkqlaeelge.hgfnadvvslsdydes.lseieeealllvvtsTfgnGdppengesffqdllel 75 
                                       i+Y++  G+t+k+A+++a +++  +    + v l+++ ++ l++i + + ++++ sT++   +   +          
  gi|330507401|ref|YP_004383829.1|   6 IIYATGMGRTKKMAEAIASGAMTiE---GTDVLLKEVYDAsLDDIADADAIVLGGSTYNYKLIK-SMD--------P 70 
                                       89********************733...34444444443449**************99988777.222........2 PP

                                       HCHHGCCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEESSSEEEETTST.HGHHHHHH CS
                      Flavodoxin_1  76 kgdeledgdlsgvrfavfglGdsayenFcaagkkldekleelGaerllkllegdednq.egqeeafr 141
                                       + +e  + dl+      +++G++++++  + + +l  +++  G++++ +++++ + +  e+ e++f+
  gi|330507401|ref|YP_004383829.1|  71 FLKEMVKLDLN--GKVGVAFGSHGWSG--EGVVTLIARMKSFGMRVVEPGTTAIQVPGkEDIEKCFH 133
                                       22222233344..45689*********..********************999999999999999997 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   8.3e-13   3.7e-09       2      83 ..       6      90 ..       5     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 8.3e-13
                      Flavodoxin_5  2 ilYsSrdGqTkkiaeriae.elreegelvdvedve.kesedlesydavvigasvyygkllpelakFvekh.reaLstkp 77
                                      i+Y++  G Tkk ae+ia  +++ eg++v +++v  ++ +d++++da+v+g+s y+ kl ++++ F+++  + +L+ k 
  gi|330507401|ref|YP_004383829.1|  6 IIYATGMGRTKKMAEAIASgAMTIEGTDVLLKEVYdASLDDIADADAIVLGGSTYNYKLIKSMDPFLKEMvKLDLNGKV 84
                                      9*****************8356666999999996525666***************************997667788877 PP

                      Flavodoxin_5 78 valfsv 83
                                       ++f  
  gi|330507401|ref|YP_004383829.1| 85 GVAFGS 90
                                      777665 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.038   1.7e+02       2      27 ..       3      26 ..       2      43 .. 0.78
   2 !   13.9   0.1   7.6e-06     0.034      66     140 ..      43     110 ..      32     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.038
                                      EEEEEES--STT-HHHHHHHHHHCCT CS
                           FMN_red  2 kilvisGSlrkgsntrklaewaaeal 27
                                      ki++i+++    ++t+k+ae++a+ +
  gi|330507401|ref|YP_004383829.1|  3 KIAIIYATGM--GRTKKMAEAIASGA 26
                                      8999999985..99*******99988 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.6e-06
                                       HHHHHHH-SCEEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT- CS
                           FMN_red  66 llekiaaadaliivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelga 140
                                        l+ ia+ada++++  +Yn+     +  +l  ++    k  l+gK++++++ +g+   g ++  + ++ +    +
  gi|330507401|ref|YP_004383829.1|  43 SLDDIADADAIVLGGSTYNYKLIKSMDPFLKEMV----KLDLNGKVGVAFGSHGWSGEGVVTLIARMKSFG---M 110
                                       56889*****************9999999*9999....************999986666555555555554...3 PP

>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.6e-05     0.071       2      65 ..       6      74 ..       5      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                      Flavodoxin_3  2 ilysSltGNTkkvAeaikealee.ekeivsikeakek....veeadvvfvGfwvdkgtadeealkflet 65
                                      i+y +  G Tkk+Aeai++ +   e + v +ke+ ++    +++ad +++G  ++  +  +++  fl++
  gi|330507401|ref|YP_004383829.1|  6 IIYATGMGRTKKMAEAIASGAMTiEGTDVLLKEVYDAslddIADADAIVLGGSTYNYKLIKSMDPFLKE 74
                                      99***************9977765445555555555557779999******999888888877777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1132.42
//
Query:       gi|330507402|ref|YP_004383830.1|  [L=217]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete 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   73.5   0.0    2.8e-20   72.8   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
      9e-18   64.5   0.0    1.1e-17   64.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    9.7e-18   64.6   0.0    1.5e-17   64.0   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.2e-12   48.0   0.0    1.4e-12   47.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      7e-12   46.0   0.0      1e-11   45.4   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    9.8e-11   41.4   0.0    1.1e-10   41.2   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    9.1e-10   38.3   0.0    1.1e-09   38.0   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    3.5e-07   30.2   0.0    5.3e-07   29.6   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    4.7e-05   22.9   0.0    6.7e-05   22.4   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00013   21.6   0.0    0.00019   21.1   0.0    1.2  1  NodS             Nodulation protein S (NodS)
     0.0011   18.9   0.0     0.0022   17.9   0.0    1.5  1  Methyltransf_18  Methyltransferase domain
     0.0027   16.8   0.0      0.004   16.2   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
     0.0039   16.3   0.0     0.0065   15.6   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0041   16.7   0.0      0.006   16.1   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0051   16.3   0.0     0.0096   15.4   0.0    1.6  1  Methyltransf_4   Putative methyltransferase
      0.008   15.9   0.0      0.012   15.4   0.0    1.2  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.031   13.4   0.0      0.046   12.8   0.0    1.6  1  DREV             DREV methyltransferase
      0.036   13.8   0.0        0.1   12.3   0.0    1.7  1  DUF938           Protein of unknown function (DUF938)
      0.099   12.3   0.0       0.13   11.9   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
       0.12   11.8   0.0        2.9    7.3   0.0    2.6  1  CheR             CheR methyltransferase, SAM binding domain
        1.2    9.9   2.6       0.92   10.3   0.6    1.7  2  Pal1             Pal1 cell morphology protein


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 !   72.8   0.0   3.2e-23   2.8e-20       2      97 .]      40     134 ..      39     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 3.2e-23
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       L++G+GtG+++la+a+r+  a+v+++Dis++ml++are+ + +g+ n++f++g + +++ +dg  D++vs+ a+hhl
  gi|330507402|ref|YP_004383830.1|  40 LEIGTGTGEFALAAARRC--ARVYAIDISPGMLQYAREKSQGQGIsNISFLVGGFLTYHHHDGPLDAIVSQIAMHHL 114
                                       89***************9..**************************************************999**** PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +d   + al +ia++L+pgG
  gi|330507402|ref|YP_004383830.1| 115 PDFWKQIALLNIASMLRPGG 134
                                       *999999************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   1.3e-20   1.1e-17       4     114 ..      36     150 ..      33     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 1.3e-20
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       + ++l++G+GtGe+++++a++    a+v+ iDis+ ++++Are++q +g++n++F +g + +     +d + D i+s
  gi|330507402|ref|YP_004383830.1|  36 HHSLLEIGTGTGEFALAAARR---CARVYAIDISPGMLQYAREKSQGQGISNISFLVGGFLTYH--HHDGPLDAIVS 107
                                       6689***************55...589***********************************88..569******** PP

                   Methyltransf_31  81 nevlnalad..pdkileeiervlkpggilliedpr.......l 114
                                       + ++++l+d  ++ +l +i + l+pgg+l+++d+         
  gi|330507402|ref|YP_004383830.1| 108 QIAMHHLPDfwKQIALLNIASMLRPGGRLCLRDIVysfdpgdY 150
                                       ********955577888****************9855555542 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   1.7e-20   1.5e-17       1      95 [.      40     137 ..      40     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 1.7e-20
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhved 76 
                                       L++G+GtG +a a a+r+arv+++D+s+ ml++a+ek++++g+ +++f+v+ + +    d+  D++vs+ ++hh++d
  gi|330507402|ref|YP_004383830.1|  40 LEIGTGTGEFALAAARRCARVYAIDISPGMLQYAREKSQGQGIsNISFLVGGFLTYHHHDGPLDAIVSQIAMHHLPD 116
                                       89*************************************************************************66 PP

                                       HHH..HHHHHHHHEEEEEEEE CS
                   Methyltransf_11  77 pek..alkeiaRvLkpgGllv 95 
                                         k  al +ia +L+pgG+l+
  gi|330507402|ref|YP_004383830.1| 117 FWKqiALLNIASMLRPGGRLC 137
                                       54323899**********997 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   1.6e-15   1.4e-12       4     125 ..      15     152 ..      10     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.6e-15
                   Methyltransf_23   4 qreeelsdklerllpk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae........kakkaqkdq 70 
                                       qr++ ++ ++e++l     ++  ++L+iG+GtG+++  ++++ + v+++D+sp + + a+        +        
  gi|330507402|ref|YP_004383830.1|  15 QRFRDIQGEIEEILSFleIKPHHSLLEIGTGTGEFALAAARRCARVYAIDISPGMLQYAReksqgqgiS-------- 83 
                                       55577777777776333279999**************9999988*********9888764333333330........ PP

                   Methyltransf_23  71 fdeqeaae.............pqgkfdlIvlrevlehvpd..ppellrqiatllkpgGylllseplasl......k 125
                                              +              +g  d Iv+   ++h+pd     +l +ia++l+pgG+l l+++  s        
  gi|330507402|ref|YP_004383830.1|  84 -------NisflvggfltyhhHDGPLDAIVSQIAMHHLPDfwKQIALLNIASMLRPGGRLCLRDIVYSFdpgdyeR 152
                                       .......23334444444444567***************987779******************9765545554433 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   1.2e-14     1e-11       1      99 []      40     136 ..      40     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.2e-14
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       LeiG+GtG+++ a +++   ++++++Disp +++ a+ek + ++  n +++    l  + +dg    D++v+  ++h
  gi|330507402|ref|YP_004383830.1|  40 LEIGTGTGEFALAAARR--CARVYAIDISPGMLQYAREKSQGQGISNISFLVGGFLTYHHHDG--PLDAIVSQIAMH 112
                                       8***********99999..********************************999999998887..9*********** PP

                   Methyltransf_12  78 hlkdir..evldnirklLkpgGrl 99 
                                       hl+d     +l ni+++L+pgGrl
  gi|330507402|ref|YP_004383830.1| 113 HLPDFWkqIALLNIASMLRPGGRL 136
                                       **7765226777**********97 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   1.3e-13   1.1e-10      45     214 ..      33     198 ..       3     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.3e-13
                                       S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEE CS
                   Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvt 121
                                        k+ +++l++ +Gtg++a++    +++  +v  +Di++ mL+ +++k + +g +ni fl++       +d+  D + 
  gi|330507402|ref|YP_004383830.1|  33 IKPHHSLLEIGTGTGEFALAA---ARRCARVYAIDISPGMLQYAREKSQGQGISNISFLVGGFLTYHHHDGPLDAIV 106
                                       5667799*********99865...5667799********************************************** PP

                                       EES-GGG-S-..HHHHHHHHHHHEEEEEEEEEEEE----SH.HHHHHHHHHHH.HHHHHHHHHHS-HHHHHHHHHHH CS
                   Ubie_methyltran 122 vsfGlrnvtD..klkaLkeayrvlkpGGrlvvlefskvelp.llsqayelyskevlPvlGkllakdldsyryLvesi 195
                                           +  ++D  k+ aL ++  +l+pGGrl   ++     p  ++   e +  + + ++G  +a+++ s+       
  gi|330507402|ref|YP_004383830.1| 107 SQIAMHHLPDfwKQIALLNIASMLRPGGRLCLRDIVYSFDPgDYERQIERFISKTMEKAGPGFAQSMTSHI-----N 178
                                       **********44466899***********988777655444268899999999999999999999976653.....3 PP

                                       HHS--HH.HHHHHHHHTTEE CS
                   Ubie_methyltran 196 rafPdqe.tlkeliedaGfk 214
                                       ++f  ++  ++ lie aGf 
  gi|330507402|ref|YP_004383830.1| 179 KEFSTMDwIMRGLIERAGFV 198
                                       45555552356777777775 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.3e-12   1.1e-09      51     211 ..      24     187 ..       9     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.3e-12
                                       HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEE..ES-GGG-- CS
                              CMAS  51 ldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevk..lldyedld 125
                                       ++ il  le+kp + lL+iG+G G+ +  a++r  ++v ++ +S    ++a+++ + +++++   +   +l y+  d
  gi|330507402|ref|YP_004383830.1|  24 IEEILSFLEIKPHHSLLEIGTGTGEFALAAARR-CARVYAIDISPGMLQYAREKSQGQGISNISFLVggFLTYHHHD 99 
                                       6789999**************************.9************************9988766433799***** PP

                                       ---SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTTCCCHHHHHHT...STTS---BHH CS
                              CMAS 126 ekvdrvvsvgafehvgkenydtffkklkkllkedGllllhtitslhkkelaerglklkfidkei...FPgGelpsie 199
                                       +++d++vs  a+ h+     +    ++ ++l+++G+l l+ i+        er+++ +fi+k +    Pg     ++
  gi|330507402|ref|YP_004383830.1| 100 GPLDAIVSQIAMHHLPDFWKQIALLNIASMLRPGGRLCLRDIVYSFDPGDYERQIE-RFISKTMekaGPGFAQSMTS 175
                                       ********999999976666666778999***************999999999999.9**98762225666777788 PP

                                       HHHHHHHHTT-E CS
                              CMAS 200 eieeeiseagft 211
                                       +i++e+s +++ 
  gi|330507402|ref|YP_004383830.1| 176 HINKEFSTMDWI 187
                                       888888888875 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   6.2e-10   5.3e-07      65     160 ..      27     119 ..      23     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 6.2e-10
                                       HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG- CS
                              PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeeka 141
                                       +l +le+k+  + Le+G+G+G  +   ar     +rv +i+ ++ + + a+++ + ++++n+++ vg   + +++  
  gi|330507402|ref|YP_004383830.1|  27 ILSFLEIKPHHSLLEIGTGTGEFALAAARRC---ARVYAIDISPGMLQYAREKSQGQGISNISFLVGGFLTYHHHDG 100
                                       6889*****************9988777655...5566*****************************7777777899 PP

                                       SEEEEEESSBBSS--HHHH CS
                              PCMT 142 PYdaihvgaaapeiPeali 160
                                       P dai+  +a +++P+ + 
  gi|330507402|ref|YP_004383830.1| 101 PLDAIVSQIAMHHLPDFWK 119
                                       ***************8663 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   7.9e-08   6.7e-05     159     247 ..      33     122 ..      24     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.9e-08
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klev..alseellkeekadviva 232
                                       +k+++++l +GtG+G  a+aaa+   ++v+a+Di +  ++ a+e  +  ++++ ++ v  +l+ +  ++++ d iv+
  gi|330507402|ref|YP_004383830.1|  33 IKPHHSLLEIGTGTGEFALAAARRC-ARVYAIDISPGMLQYAREKSQGQGISNiSFLVggFLTYHH-HDGPLDAIVS 107
                                       68899*****************975.58*************************6665532233333.4699****** PP

                              PrmA 233 NILaevlielaedik 247
                                        I  + l ++ ++i+
  gi|330507402|ref|YP_004383830.1| 108 QIAMHHLPDFWKQIA 122
                                       **9999999988764 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.2e-07   0.00019      45     143 ..      37     137 ..      21     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.2e-07
                              NodS  45 adalevGcaaGalterlapyckrltvvdvveeaiararervk..esshiswivsdvqqfs.tdekfdlivvaevlyy 118
                                        + le+G  +G ++   a  c r+  +d+ +  ++ are+ +    s+is++v     +   d   d iv    +++
  gi|330507402|ref|YP_004383830.1|  37 HSLLEIGTGTGEFALAAARRCARVYAIDISPGMLQYAREKSQgqGISNISFLVGGFLTYHhHDGPLDAIVSQIAMHH 113
                                       578*****************************9999988876115799999999877765156789*********** PP

                              NodS 119 iedvaelraavrnlvsllapdgqlv 143
                                       + d  + + a+ n+ s+l+p+g+l 
  gi|330507402|ref|YP_004383830.1| 114 LPDFWK-QIALLNIASMLRPGGRLC 137
                                       ***987.67999**********986 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.6e-06    0.0022      12      75 ..      33      93 ..      22     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.6e-06
                   Methyltransf_18 12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGl 75
                                      ++++++++ iGt  g  ++  +  +++ +v+a+Di++g l+ a+e+ + +g++ +i++ ++  l
  gi|330507402|ref|YP_004383830.1| 33 IKPHHSLLEIGTGTGEFAL--AAARRCARVYAIDISPGMLQYAREKSQGQGIS-NISFLVGGFL 93
                                      5667789999998887665..55689***********************9995.5777766555 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.7e-06     0.004     203     253 ..      37      87 ..      23      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.7e-06
                   tRNA_U5-meth_tr 203 gdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqi 253
                                       + lle+  G G+f+la ar+  +v a +i+   ++ a+   +   i n+++
  gi|330507402|ref|YP_004383830.1|  37 HSLLEIGTGTGEFALAAARRCARVYAIDISPGMLQYAREKSQGQGISNISF 87 
                                       579************************************999999999987 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   7.6e-06    0.0065      18      73 ..      23      78 ..      12      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.6e-06
                                      HHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT CS
                            RrnaAD 18 vineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls 73
                                       i+eIl+ l++++   +leig+G+G +    a r+  v ++ + + +++  ++k +
  gi|330507402|ref|YP_004383830.1| 23 EIEEILSFLEIKPHHSLLEIGTGTGEFALAAARRCARVYAIDISPGMLQYAREKSQ 78
                                      589*********************************************99999765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     7e-06     0.006      24     136 ..      28     137 ..      25     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7e-06
                                       HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST.TS-E CS
                               MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve.ekkf 98 
                                       l+ l+ + ++++l +G+G+G  ++a+a+++ +  v ++d++   l+ a+e  + ++++ ++++    l   + ++ +
  gi|330507402|ref|YP_004383830.1|  28 LSFLEIKPHHSLLEIGTGTGEFALAAARRCAR--VYAIDISPGMLQYAREKSQGQGISnISFLVGGFLTYHHhDGPL 102
                                       566777778899****************9998..9**********************99998888876654438999 PP

                                       EEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEE CS
                               MTS  99 dlivsNPPfhagkatelavaeeliaeAkeaLkegGeLl 136
                                       d+ivs   +h+  +  +++a   + + +++L++gG+L 
  gi|330507402|ref|YP_004383830.1| 103 DAIVSQIAMHHLPDFWKQIA---LLNIASMLRPGGRLC 137
                                       ***99888877776443333...344456788888876 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.1e-05    0.0096       4      60 ..      38      92 ..      35     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60
                                       +leiG+G Gef +a A + +   + +i+i+  +++++ +k + ++++N+  l g  
  gi|330507402|ref|YP_004383830.1| 38 SLLEIGTGTGEFALAAARRCAR--VYAIDISPGMLQYAREKSQGQGISNISFLVGGF 92
                                      579*********9988888775..6799**********************9998764 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.4e-05     0.012      98     142 ..      33      75 ..      18      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                                       --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHH CS
                            Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylke 142
                                       +++    +++  G G fa+++a+  +  rv+aid+ P   +y +e
  gi|330507402|ref|YP_004383830.1|  33 IKPHHSLLEIGTGTGEFALAAAR--RCARVYAIDISPGMLQYARE 75 
                                       667777888899***********..9999*********9999877 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.4e-05     0.046      95     133 ..      36      74 ..      15     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.4e-05
                              DREV  95 dkklldlGaGdGeitkrvaptfeevyatelsetmrdrlk 133
                                       ++ ll++G+G Ge +   a    +vya ++s  m +  +
  gi|330507402|ref|YP_004383830.1|  36 HHSLLEIGTGTGEFALAAARRCARVYAIDISPGMLQYAR 74 
                                       678****************************99987554 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012       0.1      24     138 ..      34     137 ..       6     143 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                            DUF938  24 kttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlkpPleldvtaevapvereappap 100
                                       k  + +LEi++GtG+ A   A     ++  + d  + + +  +   + +++sn+++ +    t +          ++
  gi|330507402|ref|YP_004383830.1|  34 KPHHSLLEIGTGTGEFALAAAR--RCARVYAIDISPGMLQYAREKSQGQGISNISFLVGGFLTYHH---------HD 99 
                                       33346***********975555..555667778888888888888888999998876654444442.........23 PP

                            DUF938 101 asidailsinllHisp.wsaveglfagagellkkkavlv 138
                                        ++dai+s   +H  p +   ++l++   ++l+++++l+
  gi|330507402|ref|YP_004383830.1| 100 GPLDAIVSQIAMHHLPdFWKQIALLNI-ASMLRPGGRLC 137
                                       456666654444444313344455543.34566666665 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00016      0.13      28     143 ..      23     137 ..      20     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                             GCD14  28 DisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvcke 104
                                       +i  i   Le+kp    +e GtG+g ++ a ar  a   ++++++      + are+ + +++s++  +    +  +
  gi|330507402|ref|YP_004383830.1|  23 EIEEILSFLEIKPHHSLLEIGTGTGEFALAAARRCA---RVYAIDISPGMLQYAREKSQGQGISNISFLVGGFLTYH 96 
                                       57779999**********************999876...99*********************988766666666666 PP

                             GCD14 105 GfdeevsgkvDavfL.DlPaPweaip..haakalkkeggrlC 143
                                         d  ++  v  + +  lP  w+ i   ++a++l + ggrlC
  gi|330507402|ref|YP_004383830.1|  97 HHDGPLDAIVSQIAMhHLPDFWKQIAllNIASML-RPGGRLC 137
                                       6666666666666542688888866521444444.7888888 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0034       2.9      11      93 ..      16      85 ..       9     166 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0034
                                      HHHHHHHCCH.HHHHHHHTSSSEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHHHHHTEEECCH CS
                              CheR 11 hfeelekevlepllakaknekrvriwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlekAkagvykeee 89
                                      +f+ ++ e+  + l+  + + + +++++g ++Ge  ++lA   ++   +      +++A+Di+  +l+ A++   + + 
  gi|330507402|ref|YP_004383830.1| 16 RFRDIQGEIE-EILSFLEIKPHHSLLEIGTGTGE--FALAA--AR---R----CARVYAIDISPGMLQYAREKS-QGQG 81
                                      5555555555.45555555555666666666665..22222..22...2....346899999999999998754.3334 PP

                                      HTTS CS
                              CheR 90 legl 93
                                      ++++
  gi|330507402|ref|YP_004383830.1| 82 ISNI 85
                                      4444 PP

>> Pal1  Pal1 cell morphology protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1         6   5.1e+03      22      34 ..       3      15 ..       2      18 .. 0.78
   2 ?   10.3   0.6    0.0011      0.92      12      28 ..      92     108 ..      86     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6
                              Pal1 22 fDAvtphrNknsk 34
                                      fDA++p   +n +
  gi|330507402|ref|YP_004383830.1|  3 FDAIAPSYDRNMQ 15
                                      9*****8777744 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0011
                              Pal1  12 fgglfHHdGPfDAvtph 28 
                                       f    HHdGP DA+ ++
  gi|330507402|ref|YP_004383830.1|  92 FLTYHHHDGPLDAIVSQ 108
                                       55678********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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):              21  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1526.93
//
Query:       gi|330507403|ref|YP_004383831.1|  [L=133]
Description: hypothetical protein MCON_1324 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.4    9.2  11.1        4.6    8.3  11.1    1.5  1  DUF4266   Domain of unknown function (DUF4266)


Domain annotation for each model (and alignments):
>> DUF4266  Domain of unknown function (DUF4266)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  11.1   0.00026       4.6      35      49 ..     118     132 ..     105     133 .] 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00026
                           DUF4266  35 aasgggGksGGGCGC 49 
                                       a++ ggG++GGGCGC
  gi|330507403|ref|YP_004383831.1| 118 ASTSGGGGGGGGCGC 132
                                       678999********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1021.28
//
Query:       gi|330507404|ref|YP_004383832.1|  [L=471]
Description: CO dehydrogenase/acetyl-CoA synthase complex subunit gamma [Methanosaeta concilii GP6]
Scores for complete 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-128  427.4   0.1   4.7e-128  427.2   0.1    1.0  1  CdhD      CO dehydrogenase/acetyl-CoA synthase delta subunit
    3.5e-13   49.0   2.5    7.9e-13   47.8   2.5    1.7  1  FeS       Putative Fe-S cluster
  ------ inclusion threshold ------
      0.078   13.0   1.2       0.16   12.0   1.2    1.5  1  YhfH      YhfH-like protein


Domain annotation for each model (and alignments):
>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.2   0.1  7.9e-132  4.7e-128       2     385 ..      70     463 ..      69     464 .. 0.96

  Alignments for each domain:
  == domain 1  score: 427.2 bits;  conditional E-value: 7.9e-132
                                       EEESSGCG-EEEE----SSTTTS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE....ETTEEEE--EEEEE-- CS
                              CdhD   2 vvlGaeekavkiGgeevLyrfeltffnptaiaidvsDelseellkalaerieevvddwakkrvgekltldaiairli 78 
                                       v +G+++k+vk+Gge+v+yr++ tffn++ +a+dv D+++e     l er+++++  w+k+++g+  ++++ia+r  
  gi|330507404|ref|YP_004383832.1|  70 VYVGVGDKQVKVGGEDVMYRHQMTFFNKPPFAFDVADNMEEA---KLIERVKKITT-WRKFYIGKWQGVEMIAVRSV 142
                                       789**********************************99985...7899*******.******************** PP

                                       SSST.HHHHHHHHHHHCC.--SEEEEE-SSHHHHHHHHTTTCCC--EEEEE-TTTHHHHHHHHHHTT--EEEE-.SS CS
                              CdhD  79 stdPakkfakavekvaka.vkvplvlggsdpevlkaalevvederpllyaAtkddykeiaelaleykvpvvllsind 154
                                       ++dP +kfa+ v++v+++  ++pl+l++++p+vlka+lev+  e+pl+yaAtkd++ke+a+la +ykvpv+l++  d
  gi|330507404|ref|YP_004383832.1| 143 TDDP-AKFAACVKTVMANgNGFPLILCSFNPAVLKAGLEVASKEKPLIYAATKDNWKEVAQLAYDYKVPVTLSVPFD 218
                                       ****.*********9865268******************************************************** PP

                                       HHHHHHHHHHHHCTT---EEEE---SH.....HHHHHHHHHHHHHHHHS.-TTS-S-BEEE---SSHHHHHHHHH.. CS
                              CdhD 155 leelkelarkllkagvkdivldPttaalGegleetidnvvriRraaikg.dkdlafPilslttnawlaresdeve.. 228
                                       l+ lk++a +++++g++d+vldP+ta+ G+ l++t++n++++Rraa+++  +d+a+P++ l++nawl+  +d v+  
  gi|330507404|ref|YP_004383832.1| 219 LDGLKSMAVTFAEMGLTDLVLDPGTAPNGKMLQQTLTNFINLRRAAVEEaQRDIAYPVMVLPINAWLTT-DDPVRaa 294
                                       ********************************************************************6.9999999 PP

                                       .........HHHTT-SEEEES---HHHHHHHHHHHHHHTS-SSS--B--SSEEEESS--TTS-EEEEESBHHHHHHH CS
                              CdhD 229 .........lvvrYadililrslekeellPvltlrqniYtDPrkPvavdpglyeigdrdensPvflttnfsLtyYtv 296
                                                +v+r + i+i +s+e ++++P ++lr+niYtDPr+Pv+v+pg+y++g+++ +sPvflttnf+LtyYtv
  gi|330507404|ref|YP_004383832.1| 295 ywesvltaaFVIRGGAIMIKHSTEPYSMMPDMHLRFNIYTDPRTPVQVKPGIYKVGNPGPESPVFLTTNFALTYYTV 371
                                       99999************************************************************************ PP

                                       HHHHHHTTS-EEEEEE-SSS--HHHHHHTTSSSHHHHHHHHHHTTHHHH.SSS-EEEE-GGGGGGHHHHHHHHT..S CS
                              CdhD 297 egdlesdkitayLLvldteGlgvevslaggqleaekvkdlieetgieek.vkhrflilPglvavlkgkiedltg..w 370
                                       e+d+ s++i ay+++++t+G+gv++s+aggql   k++d ++e+g++    k   ++lPg++a+ +g++edl+   +
  gi|330507404|ref|YP_004383832.1| 372 ESDVASNGIDAYIIAINTDGIGVQASVAGGQLSPVKIQDSFNEAGFDWAgQKYPAMVLPGMAAKFSGELEDLFAgkA 448
                                       ***********************************************98466789999**************96225 PP

                                       EEEE--SSGGGHHHH CS
                              CdhD 371 kvlvgprdsseivav 385
                                       k++vgp+ds++i+++
  gi|330507404|ref|YP_004383832.1| 449 KIMVGPEDSGRIIGW 463
                                       689*********998 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   2.5   1.3e-16   7.9e-13       1      33 []      13      45 ..      13      45 .. 0.99

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.3e-16
                               FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                      LP+tNC++CG+ +CmafA+ l++   ++e+C+p
  gi|330507404|ref|YP_004383832.1| 13 LPQTNCKKCGEETCMAFAAGLIARTRKVEECTP 45
                                      9******************************98 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.2   2.7e-05      0.16       3      22 ..       5      24 ..       4      27 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.7e-05
                              YhfH  3 kiveFfrnLPkKkCteCGke 22
                                      +++  +++LP+  C +CG+e
  gi|330507404|ref|YP_004383832.1|  5 SPLNLYKQLPQTNCKKCGEE 24
                                      67889*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3246.26
//
Query:       gi|330507405|ref|YP_004383833.1|  [L=450]
Description: CO dehydrogenase/acetyl-CoA synthase subunit delta [Methanosaeta concilii GP6]
Scores for complete 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-77  258.4   0.4    5.9e-73  245.8   0.0    3.1  3  CdhD         CO dehydrogenase/acetyl-CoA synthase delta subun
     0.0098   15.6   0.3       0.32   10.6   0.3    2.3  1  Pterin_bind  Pterin binding enzyme
  ------ inclusion threshold ------
      0.057   11.6   0.0      0.092   10.9   0.0    1.2  1  HSP70        Hsp70 protein


Domain annotation for each model (and alignments):
>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.8   0.0   9.8e-77   5.9e-73       1     228 [.     127     378 ..     127     379 .. 0.96
   2 !    5.3   0.0    0.0012         7     262     291 ..     378     405 ..     377     412 .. 0.84
   3 !    5.4   0.0    0.0011       6.3     350     380 ..     413     444 ..     406     449 .. 0.79

  Alignments for each domain:
  == domain 1  score: 245.8 bits;  conditional E-value: 9.8e-77
                                       EEEESS.......GCG-EEEE----SSTT.TS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE.......ETTE CS
                              CdhD   1 evvlGa.......eekavkiGgeevLyrf.eltffnptaiaidvsDelseellkalaerieevvdd...wakkrvge 66 
                                       ev+lGa       +++ vk+Gge+++  f ++ +++ ++i++dv+D++  + +ka+++++e+v ++   wakk+v+ 
  gi|330507405|ref|YP_004383833.1| 127 EVTLGAtkadggsRGHVVKLGGEKAMPFFpDAAMPHAPKITMDVFDMPI-GMAKAVKMHYEDVINSpgeWAKKAVRD 202
                                       677777777777799***********444699**************888.68*************9999******** PP

                                       EEE--EEEEE--SSST.......HHHHHHHHHHHCC--SEEEEE-S.....SHHHHHHHHTTTCCC--EEEEE-TT. CS
                              CdhD  67 kltldaiairlistdP......akkfakavekvakavkvplvlggs.....dpevlkaalevvederpllyaAtkd. 131
                                        +++d+++++listdP      a+ + k+ve+v++av+vp+++ggs     dp vl +a+ev+++er+l+++A+++ 
  gi|330507405|ref|YP_004383833.1| 203 -FGADMVTVHLISTDPllkdtsAQDAVKTVEEVLQAVDVPICIGGSgnpdkDPVVLSKAAEVAQGERVLIASANLNm 278
                                       .**************************************************************************** PP

                                       THHHHHHHHHHTT--EEEE-.SSHHHHHHHHHHHHC.TT-..--EEEE---SH.....HHHHHHHHHHHHHHHHS-T CS
                              CdhD 132 dykeiaelaleykvpvvllsindleelkelarkllk.agv..kdivldPttaalGegleetidnvvriRraaikgdk 205
                                       d+++i ++ +++++  +++++ +++++kel+rkl+k agv  ++iv+dPttaal +gl++++ n++riR+ a+kgd+
  gi|330507405|ref|YP_004383833.1| 279 DWEKIGKACVDNGHVCLAWTQLEINSQKELNRKLMKvAGVprESIVMDPTTAALAYGLDFAYSNMERIRLGALKGDD 355
                                       ************************************9999************************************* PP

                                       TS-S-BEEE---SSHHHHHHHHH CS
                              CdhD 206 dlafPilslttnawlaresdeve 228
                                       +l+fP++s+ttnaw++res++v+
  gi|330507405|ref|YP_004383833.1| 356 ELTFPMSSGTTNAWGVRESWMVR 378
                                       *********************95 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0012
                                       SS--B--SSEEEESS--TTS-EEEEES.BHH CS
                              CdhD 262 rkPvavdpglyeigdrdensPvflttn.fsL 291
                                       r+P + d ++   gdr  ++P++++ + +sL
  gi|330507405|ref|YP_004383833.1| 378 RSPNKDDSDW---GDRMLRGPIWEILTgYSL 405
                                       89********...***********9763565 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0011
                                       EEEE.-GGGGGGHHHHHHHHTSEEEE--SSGG CS
                              CdhD 350 flil.Pglvavlkgkiedltgwkvlvgprdss 380
                                       f+++ P++va l+++++ l+g   +  p+ + 
  gi|330507405|ref|YP_004383833.1| 413 FMMMhPTAVAYLHEITQSLMGRIEAKTPEANA 444
                                       89999**************9987666555444 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.3   5.3e-05      0.32      25     172 ..     194     328 ..     178     347 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHHT.T-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S.....-HHHHHHHHHT..T CS
                       Pterin_bind  25 aqarkmvee.GAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDtt.....kaevaeaAlka..g 93 
                                       ++a+k v++ GAd++ +   st P  +  +++++++ v +vl+     +dvpi+i  +     ++ v+++A ++  g
  gi|330507405|ref|YP_004383833.1| 194 EWAKKAVRDfGADMVTVHLISTDPLLKDTSAQDAVKTVEEVLQ----AVDVPICIGGSgnpdkDPVVLSKAAEVaqG 266
                                       6788877666********************************9....67999*997653333346677777777774 PP

                                       S.EEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHHHHHHHTT--GGGEEE CS
                       Pterin_bind  94 a.divNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearveaaeeaGvaperill 169
                                          ++ + ++ ++ +k+ + ++++g   v++++          +        e++++ e  ++ ++ aGv++e i++
  gi|330507405|ref|YP_004383833.1| 267 ErVLIASANLNMDWEKIGKACVDNGH--VCLAWT---------Q-------LEINSQKELNRKLMKVAGVPRESIVM 325
                                       43677888888877777777776663..333333.........1.......24555666666666667777777777 PP

                                       ETT CS
                       Pterin_bind 170 Dpg 172
                                       Dp 
  gi|330507405|ref|YP_004383833.1| 326 DPT 328
                                       765 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   1.5e-05     0.092     156     180 ..     313     337 ..     303     346 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.5e-05
                                       HHHTTXEEEEEEEHHHHHHHHHHTC CS
                             HSP70 156 gkiAGLnvlRivNepTAaalaYGld 180
                                        k+AG+    iv +pT aalaYGld
  gi|330507405|ref|YP_004383833.1| 313 MKVAGVPRESIVMDPTTAALAYGLD 337
                                       689*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3209.76
//
Query:       gi|330507406|ref|YP_004383834.1|  [L=252]
Description: nucleotide binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-17   62.1   0.1    6.3e-17   61.8   0.1    1.1  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    2.3e-14   53.7   0.0    4.3e-14   52.8   0.0    1.4  1  AAA_31        AAA domain
    9.3e-09   34.9   0.5    2.4e-08   33.6   0.5    1.7  1  ArsA_ATPase   Anion-transporting ATPase
    2.4e-07   30.5   0.0    4.2e-06   26.4   0.0    2.1  1  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
    4.8e-07   29.5   0.1    2.2e-05   24.1   0.1    2.7  1  ParA          NUBPL iron-transfer P-loop NTPase
    1.5e-06   27.9   0.3    3.3e-05   23.5   0.3    2.1  1  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    5.9e-05   22.9   0.0    8.6e-05   22.3   0.0    1.3  1  AAA_24        AAA domain
     0.0002   21.0   0.2      0.022   14.4   0.1    2.3  2  SRP54         SRP54-type protein, GTPase domain
    0.00058   19.6   0.0    0.00087   19.1   0.0    1.4  1  AAA_30        AAA domain
     0.0016   18.6   0.3     0.0051   16.9   0.2    1.7  2  DUF87         Helicase HerA, central domain
      0.002   17.2   0.0     0.0034   16.4   0.0    1.5  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
     0.0024   18.3   0.0     0.0038   17.6   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0042   17.0   0.3       0.81    9.6   0.0    2.4  2  NTPase_1      NTPase
     0.0047   17.2   0.0      0.013   15.8   0.0    1.8  1  AAA_22        AAA domain
     0.0047   16.8   0.1        4.8    7.0   0.1    2.8  3  AAA_26        AAA domain
     0.0059   17.0   0.7      0.009   16.4   0.7    1.6  1  AAA_19        AAA domain
      0.006   15.9   2.2       0.88    8.8   0.1    3.0  3  MipZ          ATPase MipZ
     0.0061   17.1   0.0     0.0095   16.5   0.0    1.6  1  ABC_tran      ABC transporter
      0.007   15.9   0.0      0.024   14.2   0.0    1.7  2  AAA_7         P-loop containing dynein motor region
     0.0071   16.9   0.0       0.12   13.0   0.0    2.3  2  AAA_18        AAA domain
  ------ inclusion threshold ------
      0.012   15.6   0.2      0.015   15.3   0.2    1.5  1  ResIII        Type III restriction enzyme, res subunit
      0.012   14.9   0.0       0.03   13.6   0.0    1.7  2  DUF2075       Uncharacterized conserved protein (DUF2075)
      0.025   14.6   0.0       0.12   12.4   0.0    2.0  2  AAA_14        AAA domain
      0.033   14.1   0.0      0.059   13.3   0.0    1.4  1  APS_kinase    Adenylylsulphate kinase
      0.036   13.3   0.0      0.053   12.8   0.0    1.2  1  KAP_NTPase    KAP family P-loop domain
      0.037   13.2   0.2      0.061   12.5   0.1    1.5  1  NB-ARC        NB-ARC domain
      0.041   13.5   0.0        0.3   10.6   0.0    2.3  2  AAA_25        AAA domain
      0.041   13.4   0.4       0.18   11.2   0.1    2.1  2  RecA          recA bacterial DNA recombination protein
      0.045   13.2   0.0        4.4    6.7   0.0    2.2  2  Pox_A32       Poxvirus A32 protein
      0.053   12.6   0.1       0.12   11.5   0.1    1.5  2  LpxK          Tetraacyldisaccharide-1-P 4'-kinase
      0.068   12.9   0.0       0.13   12.0   0.0    1.5  1  PRK           Phosphoribulokinase / Uridine kinase family
       0.08   13.3   0.0       0.76   10.2   0.0    2.3  2  RNA_helicase  RNA helicase
        0.1   11.5   0.1       0.19   10.6   0.0    1.4  2  DUF463        YcjX-like family, DUF463
       0.13   11.3   0.1       0.29   10.1   0.1    1.5  1  T2SSE         Type II/IV secretion system protein
        0.2   11.2   1.0          3    7.4   1.0    2.4  1  cobW          CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.1   1.2e-19   6.3e-17       2     127 ..       5     229 ..       4     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 1.2e-19
                                       EEEESSTTSSHHHHHHHHHHHHHH..TT--EEEEEEEESSCCCCHHTTEB-HHHH...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                              CbiA   2 aiastkGGvGKTtlaanLaralar..rglrVllvDaDpqannlaileglendiep...................... 54 
                                       +++ +kGG+GKT ++a L+r l++  +++r+l++DaDp+an++    g + ++                        
  gi|330507406|ref|YP_004383834.1|   5 IAITGKGGTGKTAVTAMLIRHLNNseKKFRILAIDADPDANLADA-LGAKVEKTVgdmrefmqdsrftsspdtdkqa 80 
                                       6789******************986679**************994.44444444456666***************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|330507406|ref|YP_004383834.1|  81 lfeakifeilleedgydllvmgkpegsgcycyvnnllraimdktakdydlividspaglehfsrkifpdlddlivvt 157
                                       ***************************************************************************** PP

                                       ........CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCH CS
                                       ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ........dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapa 123
                                               + +r+  +++++g k     k + vv+n++   ++++ + e+ + l    g+ v+g ip+de++a+ + 
  gi|330507406|ref|YP_004383834.1| 158 desrrgltTGERIRDIAREMGLK----YKDLYVVVNKITTGRRDKVI-ENATSL----GLTVIGTIPYDESLAKFDL 225
                                       ****9777777777777777777....789*********99766654.445555....**************99887 PP

                                       HTS- CS
                                       xxxx RF
                              CbiA 124 rgep 127
                                        g+p
  gi|330507406|ref|YP_004383834.1| 226 VGDP 229
                                       7765 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.0   8.3e-17   4.3e-14       2     156 ..       3     166 ..       2     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 8.3e-17
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkk..vLlvDlDpQanattglgiekneiektlyevl..ieeknikeaii 74 
                                       kvIai+  KGG GKT+ + +l   l +++kk  +L +D+Dp an++ +lg +   +ekt+ ++   +++++  +   
  gi|330507406|ref|YP_004383834.1|   3 KVIAIT-GKGGTGKTAVTAMLIRHLNNSEKKfrILAIDADPDANLADALGAK---VEKTVGDMRefMQDSRFTSSPD 75 
                                       899986.6*****************965554339****************75...5555555522134444444433 PP

                            AAA_31  75 ktkvenldlips...sidLaeaeielvelekk.........eeilkellekvkdeYDyiiiDcpPsLglltenaLva 139
                                          +++  l  +   +i L e   +l+ + k          ++ l+ +++k  ++YD+i+iD p  L+ + ++++  
  gi|330507406|ref|YP_004383834.1|  76 ---TDKQALFEAkifEILLEEDGYDLLVMGKPegsgcycyvNNLLRAIMDKTAKDYDLIVIDSPAGLEHFSRKIFPD 149
                                       ...334444444000455666666776666665678777777779******************************** PP

                            AAA_31 140 sdsviipvqaeayaleG 156
                                        d +i++++ + + l +
  gi|330507406|ref|YP_004383834.1| 150 LDDLIVVTDESRRGLTT 166
                                       ******99987766655 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.5   4.6e-11   2.4e-08       2     132 ..       3     135 ..       2     140 .. 0.66

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 4.6e-11
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-..EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHH CS
                       ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkk..vllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleea 76 
                                       kvi ++GKGG GKt+v a +  +l +++kk  +l i  DP  +l+D++  k++k++  ++e ++     ++ + +++
  gi|330507406|ref|YP_004383834.1|   3 KVIAITGKGGTGKTAVTAMLIRHLNNSEKKfrILAIDADPDANLADALGAKVEKTVGDMREFMQDSRFTSSPDTDKQ 79 
                                       799****************99888666655117888999**************999888887776666666655555 PP

                                       HCCHHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEES CS
                       ArsA_ATPase  77 kqevqkeeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDt 132
                                           +k  e ll+ ++ + ++  + +   +   +  + + +   ++++yd +v+D+
  gi|330507406|ref|YP_004383834.1|  80 ALFEAKIFEILLEEDGYDLLVMGKPEGSGCYCYVNNLLRAIMDKTAKDYDLIVIDS 135
                                       55555555555554443333222222224444444444444444467777777775 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   8.1e-09   4.2e-06       3     145 ..       4     157 ..       2     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 8.1e-09
                          CBP_BcsQ   3 vlalqGvRGGvGttsllaaLawalhelge..svlviDlspdnlLrlhFnvdieqregwaraeldgapwr......qa 71 
                                       v+a++G +GG+G+t+++a+L + l++ ++  ++l+iD+ pd  L+     ++e++ g +r  +++  +       ++
  gi|330507406|ref|YP_004383834.1|   4 VIAITG-KGGTGKTAVTAMLIRHLNNSEKkfRILAIDADPDANLADALGAKVEKTVGDMREFMQDSRFTsspdtdKQ 79 
                                       788888.8****************987653389**********9999999999999988877766655411111133 PP

                          CBP_BcsQ  72 aleyapgldll....PfGelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllv 144
                                       al  a+ +++l     +  l   + e   +++  ++ l a +++ +++y++i++D pag ++  r++    d  + v
  gi|330507406|ref|YP_004383834.1|  80 ALFEAKIFEILleedGYDLLVMGKPEGSGCYCYVNNLLRAIMDKTAKDYDLIVIDSPAGLEHFSRKIFPDLDDLIVV 156
                                       3333333444323333444555555555567888888999999999*****************99999988877776 PP

                          CBP_BcsQ 145 v 145
                                       +
  gi|330507406|ref|YP_004383834.1| 157 T 157
                                       5 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 !   24.1   0.1   4.2e-08   2.2e-05       6     244 ..       4     249 ..       1     251 [. 0.69

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.2e-08
                              ParA   6 iavlSgKGGVGKStvavnlAlaLakkglkvgll..D.......aDiyGpsiprllgveeekpeqsekkliPvea..k 71 
                                       ++ + gKGG GK+ v++ l  +L+++++k  +l  D       aD  G  + + +g  +e ++ s+ +  P +    
  gi|330507406|ref|YP_004383834.1|   4 VIAITGKGGTGKTAVTAMLIRHLNNSEKKFRILaiDadpdanlADALGAKVEKTVGDMREFMQDSRFTSSPDTDkqA 80 
                                       44568*******************99999999833311222222355666666666555555555555667766433 PP

                              ParA  72 gikvmSigfllesedeavvwrGp........mkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagav 140
                                         ++  +++lle++   ++  G          ++++++ ++ ++  ++ D+++iD P G    +  ++  l  ++ +
  gi|330507406|ref|YP_004383834.1|  81 LFEAKIFEILLEEDGYDLLVMGKpegsgcycYVNNLLRAIMDKT-AKDYDLIVIDSPAGLEHFSRKIFPDL--DDLI 154
                                       35667778899988777766653122222223445555555444.4789********99876666666655..799* PP

                              ParA 141 iVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeire 217
                                       +Vt   +  l+  ++  ++++++ +k   +   ++ +         +  +++++ + a++lg++++g+ip d+++++
  gi|330507406|ref|YP_004383834.1| 155 VVTDESRRGLTTGERIRDIAREMGLKYKDLYVVVNKI---------TTGRRDKVIENATSLGLTVIGTIPYDESLAK 222
                                       *********************9999986653222222.........2224566667888999999999999999999 PP

                              ParA 218 asdegkplvlkepeseaakaleeiaek 244
                                           g+pl+   ++s+a k++++++ k
  gi|330507406|ref|YP_004383834.1| 223 FDLVGDPLTGLPDDSPAVKEMANVVGK 249
                                       998999988888888888888888765 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 !   23.5   0.3   6.5e-08   3.3e-05       2     232 ..       4     238 ..       3     250 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.5e-08
                         Fer4_NifH   2 kiaiyGkGGiGksttsqnlsaalaemgkk..vlivGCDPkaDstrlllggkaqetvldt...lr..........ekg 63 
                                        iai GkGG Gk+  ++ l   l +  kk  +l +  DP a+ +   lg+k+++tv d+   ++          +k+
  gi|330507406|ref|YP_004383834.1|   4 VIAITGKGGTGKTAVTAMLIRHLNNSEKKfrILAIDADPDANLA-DALGAKVEKTVGDMrefMQdsrftsspdtDKQ 79 
                                       59*********************999986448999999999887.6899******9887322231111111111222 PP

                         Fer4_NifH  64 avedvkvedvvkkGyggvkcvesGGPepGvGCaGrgvitaielleelgayddlDfvlyDvLGDvvCGGfalPiredk 140
                                       a  + k+ +++ +   g + +  G Pe G GC  ++      ++++    +d+D+++ D         f+  i  d 
  gi|330507406|ref|YP_004383834.1|  80 ALFEAKIFEILLE-EDGYDLLVMGKPE-GSGCYCYVNNLLRAIMDKTA--KDYDLIVIDSPAG--LEHFSRKIFPD- 149
                                       2233344444444.4555555556555.89998887665556666654..6899999997554..46799999855. PP

                         Fer4_NifH 141 aqevyivtsgelmalyaanniakgiekyaksggvrlgG..liinsrkvddereliekfaeelgtkvlevvPrdeivr 215
                                        +++++vt+     l +  +i       a++ g++     +++n + ++ +r+ + + a++lg+ v+ ++P de + 
  gi|330507406|ref|YP_004383834.1| 150 LDDLIVVTDESRRGLTTGERIR----DIAREMGLKYKDlyVVVN-KITTGRRDKVIENATSLGLTVIGTIPYDESLA 221
                                       5789999999999999888764....445555555544115777.66788888888999999999999999999999 PP

                         Fer4_NifH 216 kaelrkktvieyapese 232
                                       k +l    ++   ++s+
  gi|330507406|ref|YP_004383834.1| 222 KFDLVGDPLTGLPDDSP 238
                                       88877666666555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.7e-07   8.6e-05       1      77 [.       1     139 [.       1     164 [. 0.87

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.7e-07
                            AAA_24   1 kklkiliyGpsgiGKTtlakel.........gpkplfidtekGlksldadkfpdie.swedfldevvel........ 59 
                                       +++ i+i+G+ g+GKT + ++l         + ++l id +   ++l ++ + ++e ++ d++++++          
  gi|330507406|ref|YP_004383834.1|   1 MGKVIAITGKGGTGKTAVTAMLirhlnnsekKFRILAIDADP-DANLADALGAKVEkTVGDMREFMQDSrftsspdt 76 
                                       5789*************************5555666666666.77888888888888888888888888899***** PP

                            AAA_24  60 .............................................aaeladyktlviDtidel 77 
                                                                                    ++  +dy+ +viD+   l
  gi|330507406|ref|YP_004383834.1|  77 dkqalfeakifeilleedgydllvmgkpegsgcycyvnnllraimDKTAKDYDLIVIDSPAGL 139
                                       *********************************************999999*******95444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   4.2e-05     0.022       2      38 ..       3      39 ..       2      47 .. 0.95
   2 ?    4.6   0.0     0.043        22      74     115 ..     118     160 ..     100     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.2e-05
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      +vi++ G  G+GKT  +a L ++l++++kk  + a D
  gi|330507406|ref|YP_004383834.1|  3 KVIAITGKGGTGKTAVTAMLIRHLNNSEKKFRILAID 39
                                      6899*******************************99 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.043
                                       HHHHHHHHTTSSEEEEEE.--SSTTHHHHHHHHHHHHHHHSSS CS
                             SRP54  74 eavekakeekidvvlvDT.aGrlqndkelmeelkkikkvvkpd 115
                                       +a+  + ++++d++++D+ aG  +  ++++ +l+++  v+++ 
  gi|330507406|ref|YP_004383834.1| 118 RAIMDKTAKDYDLIVIDSpAGLEHFSRKIFPDLDDLIVVTDES 160
                                       6778888999*******779*9999999999999988777655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.7e-06   0.00087      19      72 ..       3      56 ..       1     108 [. 0.89

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.7e-06
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieast 72
                                      +v ++tG  GtGKt + + l +++++++++  +lA  +   ++La++lg++ + 
  gi|330507406|ref|YP_004383834.1|  3 KVIAITGKGGTGKTAVTAMLIRHLNNSEKKFRILAIDADPDANLADALGAKVEK 56
                                      4789**********************************9999999999986654 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2     1e-05    0.0051      26      61 ..       5      41 ..       2      45 .. 0.94
   2 ?   -1.6   0.0       4.6   2.4e+03     169     225 ..      64     118 ..      42     120 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1e-05
                             DUF87 26 lAilgsTGsGKSntvavLleelle.kkgatililDpH 61
                                      +Ai g+ G+GK+  +a L++ l + +k+ +il +D++
  gi|330507406|ref|YP_004383834.1|  5 IAITGKGGTGKTAVTAMLIRHLNNsEKKFRILAIDAD 41
                                      79**********************99*********86 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.6
                             DUF87 169 ldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlvvsvilr 225
                                        ++ +++ +++ ++  +++ ++a+++e+l +e     + +++ + +  + +v+ +lr
  gi|330507406|ref|YP_004383834.1|  64 FMQDSRFTSSPDTD--KQALFEAKIFEILLEEDGYDLLVMGKPEGSGCYCYVNNLLR 118
                                       44445555555555..78888888888888877766666666555555555555555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.6e-06    0.0034      30      81 ..       3      54 ..       1     103 [. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.6e-06
                                      EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---------------- CS
                              MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDkl 81
                                      +v+ +tG  G+Gk  ++  l+ +l +  k+  +la+D     +    lG k+
  gi|330507406|ref|YP_004383834.1|  3 KVIAITGKGGTGKTAVTAMLIRHLNNSEKKFRILAIDADPDANLADALGAKV 54
                                      6899********************************9876666666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.4e-06    0.0038      26      94 ..       4      67 ..       1     135 [. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.4e-06
                            AAA_16 26 lvllsGesGvGKsslvrellralekd....ggiflrgkcdqlesaipysalaqalareellrqlldeaesael 94
                                      ++ ++G  G+GK+++  +l r+l+ +    +++++ ++ d +        la+al + ++ + ++d+ e  + 
  gi|330507406|ref|YP_004383834.1|  4 VIAITGKGGTGKTAVTAMLIRHLNNSekkfRILAIDADPDAN--------LADALGA-KVEKTVGDMREFMQD 67
                                      689********************9997755566677777777........8888855.777777777444444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0016      0.81       2      28 ..       5      31 ..       4      61 .. 0.93
   2 ?    5.4   0.0     0.029        15      83     135 ..     115     170 ..     108     204 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0016
                                      EEEE--TTSSHHHHHHHHHHHH...GG CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgv 28
                                      ++iTG+ G+GKt +   +++ l++s+ 
  gi|330507406|ref|YP_004383834.1|  5 IAITGKGGTGKTAVTAMLIRHLNNSEK 31
                                      89*******************988765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT...TTSEEEEE--SS CS
                          NTPase_1  83 elalealrkalseadviviDEiGkmElkskkfkeaveevLk...sekpvlavihrr 135
                                       +l  ++++k+ ++ d+iviD    +E +s+k+   +++++    +++  l++  r 
  gi|330507406|ref|YP_004383834.1| 115 NLLRAIMDKTAKDYDLIVIDSPAGLEHFSRKIFPDLDDLIVvtdESRRGLTTGERI 170
                                       45556667777999****************99988888653312444455554444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.5e-05     0.013       6      56 ..       3      49 ..       2     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl 56
                                      +++++tG  GtGKT + ++l + l++ +k    + +++ +++  + +++d 
  gi|330507406|ref|YP_004383834.1|  3 KVIAITGKGGTGKTAVTAMLIRHLNNSEK----KFRILAIDADPDANLADA 49
                                      689*********************87655....666666666666554444 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0093       4.8      11      31 ..      12      32 ..       3      36 .. 0.78
   2 ?   -1.3   0.0       3.2   1.6e+03      89     110 ..     118     139 ..     113     149 .. 0.79
   3 ?    6.5   0.0     0.013       6.6     162     195 ..     186     221 ..     159     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0093
                            AAA_26 11 gvGKTvvslgLvralkrkgvk 31
                                      g GKT+v+++L+r l++ + k
  gi|330507406|ref|YP_004383834.1| 12 GTGKTAVTAMLIRHLNNSEKK 32
                                      79************9776655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.2
                            AAA_26  89 ekivkelekdadivvVEGaggl 110
                                         i+++ +kd+d++v++   gl
  gi|330507406|ref|YP_004383834.1| 118 RAIMDKTAKDYDLIVIDSPAGL 139
                                       556688899*******987776 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.013
                            AAA_26 162 vilNkvrnp..envetlekksgipvlGvvPylpdle 195
                                       v++Nk++    ++v +  ++ g++v+G++Py+++l 
  gi|330507406|ref|YP_004383834.1| 186 VVVNKITTGrrDKVIENATSLGLTVIGTIPYDESLA 221
                                       89999765534455555555689*********9986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.7   1.8e-05     0.009      11      48 ..       3      38 ..       1     159 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.8e-05
                            AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggvkpeeillv 48
                                      kv+++t+  GtGKT v+ + +++l++ ++    +il++
  gi|330507406|ref|YP_004383834.1|  3 KVIAITGKGGTGKTAVTAMLIRHLNNSEKK--FRILAI 38
                                      899*********************999844..666654 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.07        36       7      38 ..       8      41 ..       3      58 .. 0.75
   2 !    8.8   0.1    0.0017      0.88      89     126 ..     117     154 ..     111     161 .. 0.81
   3 ?    1.8   0.0      0.23   1.2e+02     103     140 ..     186     227 ..     161     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.07
                                      -SSTTSSHHHHHHHHHHHHHTTT..--EEEEE-- CS
                              MipZ  7 nekGGsGksttavhvavaLlkkG..arvaaidld 38
                                        kGG+Gk++++  ++  L ++   +r+ aid d
  gi|330507406|ref|YP_004383834.1|  8 TGKGGTGKTAVTAMLIRHLNNSEkkFRILAIDAD 41
                                      569******9998888888765400556666655 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEE CS
                              MipZ  89 leelvadleaeldfividtPGsdsalsrlahsladtlv 126
                                       l+++++++++++d+ivid+P   ++ sr      d l+
  gi|330507406|ref|YP_004383834.1| 117 LRAIMDKTAKDYDLIVIDSPAGLEHFSRKIFPDLDDLI 154
                                       788999**************999999888776666665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.23
                                       EEEE..--SS--HHHHHHHHT-SEEEE..EEESSHHHHCCCE CS
                              MipZ 103 ivid..tPGsdsalsrlahsladtlvt..Plndsfvdfdllg 140
                                       +v++  t G+ ++++  a sl  t++   P ++s+  fdl+g
  gi|330507406|ref|YP_004383834.1| 186 VVVNkiTTGRRDKVIENATSLGLTVIGtiPYDESLAKFDLVG 227
                                       4443348899999********999995348899*******98 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.8e-05    0.0095      11      51 ..       2      42 ..       1     200 [. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-05
                                      TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51
                                      g+++ai+G+ G+GK+ + ++l+++l++ e + ++   d + 
  gi|330507406|ref|YP_004383834.1|  2 GKVIAITGKGGTGKTAVTAMLIRHLNNSEKKFRILAIDADP 42
                                      899**********************9999887665444443 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.7e-05     0.024      34      90 ..       3      58 ..       1      66 [. 0.85
   2 ?   -1.2   0.0       2.5   1.3e+03      34      59 ..      96     122 ..      85     131 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-05
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrr 90
                                      k + ++G+ GtGKt+++  l+++l++++ ++ ++ + a  +an l d + +k+ek  
  gi|330507406|ref|YP_004383834.1|  3 KVIAITGKGGTGKTAVTAMLIRHLNNSEKKFRILAIDADPDAN-LADALGAKVEKTV 58
                                      567899*******************999999999999888775.7788888888865 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.5
                             AAA_7  34 kpvllvG.ptGtGKtviikdllkkldk 59 
                                       + +l++G p+G+G  +++++ll+++ +
  gi|330507406|ref|YP_004383834.1|  96 YDLLVMGkPEGSGCYCYVNNLLRAIMD 122
                                       566666734677777777777776653 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00023      0.12       1      26 [.       5      35 ..       5     100 .. 0.77
   2 ?    1.8   0.0      0.66   3.4e+02      23      63 ..     163     202 ..     139     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00023
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.....gv 26
                                      I++tG+ G+GKt ++  L ++l++      +
  gi|330507406|ref|YP_004383834.1|  5 IAITGKGGTGKTAVTAMLIRHLNNsekkfRI 35
                                      89****************9999665555422 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.66
                            AAA_18  23 gf..gvnlrdvakenglllevdpealdeskrldedkldkllda 63 
                                       g+  g+++rd+a+e gl + +        +++ ++++dk++++
  gi|330507406|ref|YP_004383834.1| 163 GLttGERIRDIAREMGLKYKDLYV---VVNKITTGRRDKVIEN 202
                                       3466999**********9999888...6777777777766655 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2     3e-05     0.015      29      60 ..       7      38 ..       2     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-05
                                      EEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                            ResIII 29 ikmaTGtGKTlvaaklierllkkgkeekflfl 60
                                      i    GtGKT v a li++l +++k+ ++l +
  gi|330507406|ref|YP_004383834.1|  7 ITGKGGTGKTAVTAMLIRHLNNSEKKFRILAI 38
                                      56667*****************9886666544 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.9e-05      0.03       2      45 ..       3      45 ..       2      87 .. 0.67
   2 ?   -2.1   0.0       3.4   1.8e+03      84     212 ..     123     140 ..     110     146 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-05
                           DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl 45
                                      +v+ +tG+ GtGKt v   l+  l +++e++ +++++   p  +
  gi|330507406|ref|YP_004383834.1|  3 KVIAITGKGGTGKTAVTAMLIRHL-NNSEKKFRILAIDADPDAN 45
                                      6999****************9999.6666777766666555443 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.4
                           DUF2075  84 keepkedvvivDEAhrlltksdqaekqseenqlkelmkrakvvvalvDegQelntgeigteeelkklakklevelee 160
                                       k+                                                                           
  gi|330507406|ref|YP_004383834.1| 123 KT--------------------------------------------------------------------------- 124
                                       22........................................................................... PP

                           DUF2075 161 kvhLksqfRvaaseaviewvdalldgkkekakplssqenfdirvfddleelk 212
                                                                            +++d+ v+d+++ l+
  gi|330507406|ref|YP_004383834.1| 125 ------------------------------------AKDYDLIVIDSPAGLE 140
                                       ....................................4667777777777666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00024      0.12       2      49 ..       2      49 ..       1      95 [. 0.78
   2 ?   -0.3   0.0         2     1e+03      81     103 ..     115     138 ..     109     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49
                                      +k+++itG   +GKT +   li++l  +++++  +++d ++d++lad 
  gi|330507406|ref|YP_004383834.1|  2 GKVIAITGKGGTGKTAVTAMLIRHLNNSEKKFRILAIDADPDANLADA 49
                                      589*******************99995556666666666666555533 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2
                            AAA_14  81 kalkslvdeg.knldvivtGSnsk 103
                                       + l+ ++d++ k++d+iv  S ++
  gi|330507406|ref|YP_004383834.1| 115 NLLRAIMDKTaKDYDLIVIDSPAG 138
                                       568888887778888888888765 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00012     0.059       2      39 ..       2      39 ..       1      67 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                                      -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                        APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGd 39
                                      g v+ +tG  g+GK++++ +l ++L+++ ++  +L  d
  gi|330507406|ref|YP_004383834.1|  2 GKVIAITGKGGTGKTAVTAMLIRHLNNSEKKFRILAID 39
                                      7899**********************999888777544 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 ?   12.8   0.0    0.0001     0.053      22      59 ..       4      39 ..       2      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                        KAP_NTPase 22 vvgLygkWGsGKssllnkledelkefakpvrflfaefn 59
                                      v++++gk G+GK+++ ++l++ l++   +++f +  ++
  gi|330507406|ref|YP_004383834.1|  4 VIAITGKGGTGKTAVTAMLIRHLNNS--EKKFRILAID 39
                                      89************************..5555554443 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00012     0.061      22      55 ..       4      37 ..       1     102 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                      EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEE CS
                            NB-ARC 22 vvalvGmgGvGKttlakqilnksdevegrFdsva 55
                                      v+a+ G+gG GKt + +  ++++++ e++F ++a
  gi|330507406|ref|YP_004383834.1|  4 VIAITGKGGTGKTAVTAMLIRHLNNSEKKFRILA 37
                                      89**********************9999998765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00059       0.3      33      57 ..       2      26 ..       1     101 [. 0.84
   2 ?    0.1   0.0      0.98     5e+02     140     150 ..     125     135 ..     111     142 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00059
                            AAA_25 33 gelallaGapgtGKttlaldlalav 57
                                      g++++++G +gtGKt+++  l  ++
  gi|330507406|ref|YP_004383834.1|  2 GKVIAITGKGGTGKTAVTAMLIRHL 26
                                      899**************99887776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.98
                            AAA_25 140 vegvrlvviDp 150
                                       +++++l+viD+
  gi|330507406|ref|YP_004383834.1| 125 AKDYDLIVIDS 135
                                       2679******7 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00036      0.18      53     137 ..       2     101 ..       1     103 [. 0.75
   2 ?   -1.0   0.0         2     1e+03     131     143 ..     127     139 ..     116     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00036
                                       TSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHTT--GGG-............EEE--SSHH CS
                              RecA  53 GriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakklGvdidel............lvsqpdtGe 117
                                       G++i i G   +Gkt+++  +i + +++ +    +  +   d++ a +lG ++++             + s pdt +
  gi|330507406|ref|YP_004383834.1|   2 GKVIAITGKGGTGKTAVTAMLIRHLNNSEKKFRILAIDADPDANLADALGAKVEKTvgdmrefmqdsrFTSSPDTDK 78 
                                       99*****************9999998888877777777777888899998877653111122122222578999999 PP

                                       HHH...HHHHHHHTTT--SEEEE CS
                              RecA 118 qal...eiadalvrsgaidlivv 137
                                       qal   +i ++l++  + dl+v+
  gi|330507406|ref|YP_004383834.1|  79 QALfeaKIFEILLEEDGYDLLVM 101
                                       99866668999999999999886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2
                                       --SEEEEE-TTT- CS
                              RecA 131 aidlivvdsvaal 143
                                         dliv+ds a l
  gi|330507406|ref|YP_004383834.1| 127 DYDLIVIDSPAGL 139
                                       4699999999887 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.039        20      16      40 ..       5      29 ..       3      39 .. 0.80
   2 ?    6.7   0.0    0.0085       4.4       9      62 ..      91     149 ..      83     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.039
                           Pox_A32 16 lalvGgsGsGktvyLlsLlrtlvkk 40
                                      +a++G+ G Gkt+    L+r l + 
  gi|330507406|ref|YP_004383834.1|  5 IAITGKGGTGKTAVTAMLIRHLNNS 29
                                      79**********9999998888654 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0085
                           Pox_A32   9 LlkkpFrlalvGg.sGsGktvyLlsLlrtlvkk....ykhifLltpvknseYdkyvwPd 62 
                                       L ++ + l ++G+  GsG   y+ +Llr +++k    y  i +  p   +++ + ++Pd
  gi|330507406|ref|YP_004383834.1|  91 LEEDGYDLLVMGKpEGSGCYCYVNNLLRAIMDKtakdYDLIVIDSPAGLEHFSRKIFPD 149
                                       667789999999856*************9998722224455555556666677777776 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00023      0.12      46      71 ..      11      36 ..       4      37 .. 0.89
   2 ?   -3.3   0.0       7.2   3.7e+03     144     157 ..     125     138 ..     122     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                      S-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK 46 GGtGKTPlvialvkllqarglkvgvl 71
                                      GGtGKT ++++l+++l++++ k  +l
  gi|330507406|ref|YP_004383834.1| 11 GGTGKTAVTAMLIRHLNNSEKKFRIL 36
                                      9****************999888776 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.2
                                       --SEEEEEE..EHH CS
                              LpxK 144 ardleivvvdaerg 157
                                       a+d++++v+d+  g
  gi|330507406|ref|YP_004383834.1| 125 AKDYDLIVIDSPAG 138
                                       78999999997665 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00025      0.13       1      29 [.       4      32 ..       4      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvk 29
                                      vI+++g+ G Gkt+v++ l   +++ ++k
  gi|330507406|ref|YP_004383834.1|  4 VIAITGKGGTGKTAVTAMLIRHLNNSEKK 32
                                      8******************9999988777 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0015      0.76       1      31 [.       5      32 ..       5      74 .. 0.85
   2 ?    0.5   0.0       1.5   7.6e+02       2      30 ..      99     128 ..      98     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0015
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkk 31
                                      i ++G+ g+GK+ ++  L+++l ++   +kk
  gi|330507406|ref|YP_004383834.1|  5 IAITGKGGTGKTAVTAMLIRHLNNS---EKK 32
                                      5689******************944...344 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.5
                      RNA_helicase   2 wlyGps.geGKStlakeLakallkklklkk 30 
                                       ++ G++ g G   ++++L +a+++k  ++ 
  gi|330507406|ref|YP_004383834.1|  99 LVMGKPeGSGCYCYVNNLLRAIMDKTAKDY 128
                                       6789999999999*********99884443 PP

>> DUF463  YcjX-like family, DUF463
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00037      0.19       3      46 ..       5      48 ..       4      70 .. 0.83
   2 ?   -3.4   0.0       6.7   3.4e+03     248     265 ..     141     158 ..     139     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                            DUF463  3 lavTGLsraGKtvfitsLvnqLlaaekkarlplfeaaregrllg 46
                                      +a+TG  + GKt+  + L+++L ++ekk r+ + +a  + +l+ 
  gi|330507406|ref|YP_004383834.1|  5 IAITGKGGTGKTAVTAMLIRHLNNSEKKFRILAIDADPDANLAD 48
                                      89********************9888888877777776666655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.7
                            DUF463 248 pffrehFarldrqivLvD 265
                                       +f r+ F  ld  iv+ D
  gi|330507406|ref|YP_004383834.1| 141 HFSRKIFPDLDDLIVVTD 158
                                       799999*******99988 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00057      0.29     131     164 ..       4      39 ..       2      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00057
                             T2SSE 131 lilvsGgTgsGKttllyallkeinks..derivtvE 164
                                       +i ++G  g+GKt ++ +l+  +n+s  + ri+ + 
  gi|330507406|ref|YP_004383834.1|   4 VIAITGKGGTGKTAVTAMLIRHLNNSekKFRILAID 39 
                                       688*********************994344566554 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.0    0.0058         3       2      32 ..       4      36 ..       3     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0058
                                      EEEEEESTTCCHHHHHHHHH..CT--SS-EEEE CS
                              cobW  2 vtvltGflGsGKTtLlnhll..enraglklavi 32
                                      v+ +tG  G+GKT++   l+   n++++k  ++
  gi|330507406|ref|YP_004383834.1|  4 VIAITGKGGTGKTAVTAMLIrhLNNSEKKFRIL 36
                                      7889*********98877776644444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); 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: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 1577.60
//
Query:       gi|330507407|ref|YP_004383835.1|  [L=468]
Description: CO dehydrogenase/acetyl-CoA synthase complex subunit beta [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-56  189.7   0.0      5e-56  188.9   0.0    1.4  1  CdhC      CO dehydrogenase/acetyl-CoA synthase complex beta s


Domain annotation for each model (and alignments):
>> CdhC  CO dehydrogenase/acetyl-CoA synthase complex beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.9   0.0   2.8e-60     5e-56       1     155 []       4     158 ..       4     158 .. 0.99

  Alignments for each domain:
  == domain 1  score: 188.9 bits;  conditional E-value: 2.8e-60
                              CdhC   1 ipvevspafeGeriRkedlyvelggkktkafElvkvkeadevedgkieviGpdideveegsrlplailvevaGkkle 77 
                                       i +++sp++eGeriRk+dl+velgg k+++fEl  ++++de+edgk++viGpd+ e+ eg+++p++++++v G+k+e
  gi|330507407|ref|YP_004383835.1|   4 IKLDISPMYEGERIRKDDLWVELGGPKADGFELSLATPMDEIEDGKVTVIGPDLGETPEGTTMPFGMIFRVGGEKIE 80 
                                       6789*********************99************************************************** PP

                              CdhC  78 edlEpvlERriHeflnyieGvmHlgqRdiiwvRiskeavekGl.rlkhigevlyaklkeefeaivdkvevtlitdee 153
                                       +dlE+++ERr+H++l+yi G+mHl+qR++iw+Ri+k  ++kG+ ++k++   +++++k+e+ ++++k+++t++td++
  gi|330507407|ref|YP_004383835.1|  81 KDLESIIERRNHALLSYISGLMHLNQRYDIWMRIGKGLKKKGVtSWKEVYAPVIDLYKAEM-PFIEKMDITIVTDPA 156
                                       *******************************************99****************.**************9 PP

                              CdhC 154 kv 155
                                       kv
  gi|330507407|ref|YP_004383835.1| 157 KV 158
                                       97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3433.48
//
Query:       gi|330507408|ref|YP_004383836.1|  [L=187]
Description: CO dehydrogenase/acetyl-CoA synthase complex subunit epsilon [Methanosaeta concilii GP6]
Scores for complete sequence (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  126.2   0.0    1.3e-36  125.9   0.0    1.0  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha
    0.00033   20.4   0.0     0.0011   18.8   0.0    1.8  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.9   0.0   1.4e-40   1.3e-36       3     167 ..      13     181 ..      11     182 .. 0.94

  Alignments for each domain:
  == domain 1  score: 125.9 bits;  conditional E-value: 1.4e-40
                                       XXXXXXXXXXXXXXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEET.....HHHT CS
                             CO_dh   3 lekiPfdeaaianskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvata.....lkea 74 
                                       +++iPf+ a+i+++++a+   + kv+  +i+kakrPll+vG ++  + +++ k   + +  ++++ata     + ++
  gi|330507408|ref|YP_004383836.1|  13 KNPIPFEMAQIPGPEMAKTYLP-KVIGAIIRKAKRPLLVVGAELFDDPVMFDKMIEMGKMGIPIAATAhsvkgFVDR 88 
                                       5689******************.*********************************************888887777 PP

                                       T-G..GGSE..-HHHHHHHHHSTT--TTTSS---SEEEEES--HHHHHHHHHHHHHH-TT-EEEE-SSS--TTSSEE CS
                             CO_dh  75 glkdyekkn..klveltkllkdpepkgfdgegeydlvlfiGviyYyasqalsslkkftdkittiaidkyyhpdAdvs 149
                                       g    e+++   l+ lt++l  p++kg dg+g+yd+v+f+G+ y  a+ +ls lk+f   i+ ++id+yyh +Ad++
  gi|330507408|ref|YP_004383836.1|  89 GYL--ENVYqiGLHPLTNFLRFPDWKGLDGQGQYDVVIFLGIYYKFANGMLSTLKNFNRDIKRVSIDRYYHVNADMT 163
                                       776..77776689**************************************************************** PP

                                       E---GGGHHHHHHHHHHH CS
                             CO_dh 150 lanlskeeeeylemleel 167
                                       ++nl  +  +y   ++e+
  gi|330507408|ref|YP_004383836.1| 164 FGNLAFNPDDYHAAVDEV 181
                                       *****9999999988887 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 !   18.8   0.0   1.2e-07    0.0011       6     111 ..      39     154 ..      35     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-07
                                       HHHHH-SSEEEEE-CHHCHT.TGHHHHHHHHHHHT-EEEEEGGG.TTSS-TTSTTEEEESGGGS........CHHHH CS
                      TPP_enzyme_M   6 ellkaakrpvilvGggvars.gaseelrelaeklgiPvvttlmg.kgvipedhplylgmlglhg........skaan 72 
                                       +++++akrp+++vG +  ++    +++ e+  k+giP++ t +  kg++++    ++  +glh         + ++ 
  gi|330507408|ref|YP_004383836.1|  39 AIIRKAKRPLLVVGAELFDDpVMFDKMIEM-GKMGIPIAATAHSvKGFVDRGYLENVYQIGLHPltnflrfpDWKGL 114
                                       589*************98664566666664.58*****9998888***********99****987777777666666 PP

                                       HHHHH-SEEEEES-SSSTCCCTTTTT.TTTTT-EEEEEES CS
                      TPP_enzyme_M  73 ealeeaDlvlalGarfddirttgsep.efapeakiihidi 111
                                       +   + D+v++lG  +++ +   s   +f+++ k + id 
  gi|330507408|ref|YP_004383836.1| 115 DGQGQYDVVIFLGIYYKFANGMLSTLkNFNRDIKRVSIDR 154
                                       67788********998885444444436665546666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1370.30
//
Query:       gi|330507409|ref|YP_004383837.1|  [L=793]
Description: CO dehydrogenase/acetyl-CoA synthase complex subunit alpha [Methanosaeta concilii GP6]
Scores for complete 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-90  303.7   9.8    2.5e-77  260.7   0.0    2.1  2  Prismane         Prismane/CO dehydrogenase family
    4.1e-08   33.6   3.2     0.0014   19.1   0.6    3.1  2  Fer4_8           4Fe-4S dicluster domain
    9.8e-07   29.6   2.8      0.022   15.7   0.3    3.3  2  Fer4_16          4Fe-4S double cluster binding domain
    8.6e-05   23.0   6.4     0.0022   18.5   0.4    3.4  2  Fer4_17          4Fe-4S dicluster domain
    0.00017   21.6  12.2    0.00017   21.6  12.2    3.6  4  Fer4_10          4Fe-4S dicluster domain
    0.00043   20.5   8.0     0.0037   17.4   0.6    2.7  2  Fer4_18          4Fe-4S dicluster domain
    0.00078   20.0  11.8    0.00078   20.0  11.8    3.6  2  Fer4_7           4Fe-4S dicluster domain
     0.0019   18.3  21.8     0.0076   16.4   2.0    3.9  4  Fer4_9           4Fe-4S dicluster domain
     0.0096   16.0  12.2     0.0096   16.0  12.2    3.3  4  Fer4_21          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   16.2  12.5      0.037   14.9   2.4    2.9  3  Fer4_22          4Fe-4S dicluster domain
       0.23   11.2  10.1         13    5.6  10.4    2.6  2  Fer4_20          Dihydroprymidine dehydrogenase domain II, 4F
       0.29   11.0  27.0      0.025   14.4   3.4    3.9  3  Fer4             4Fe-4S binding domain
       0.84    9.9  26.2       0.48   10.6   3.4    4.0  3  Fer4_2           4Fe-4S binding domain
          2    9.1  20.8       0.56   10.8   5.8    3.7  2  Fer4_4           4Fe-4S binding domain
        8.4    6.7   8.7        3.1    8.1   1.3    2.8  2  c-SKI_SMAD_bind  c-SKI Smad4 binding domain


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   7.2   1.3e-14   1.6e-11       2      54 ..      54     106 ..      53     126 .. 0.91
   2 !  260.7   0.0   2.1e-80   2.5e-77     115     510 ..     130     678 ..     122     679 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.3e-14
                                       EE-SSTCT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane   2 fCrqCengpCritknkrGvCGkdadtavardlliavlkgaaahaahareladt 54 
                                        C +C++gpC++t+nk+G+CG+d+++a  + +l+avl+g++ah+ah+r+l++ 
  gi|330507409|ref|YP_004383837.1|  54 TCTLCTYGPCDLTGNKKGACGIDMAAACGKIVLVAVLMGTCAHTAHGRHLYHW 106
                                       7************************************************9543 PP

  == domain 2  score: 260.7 bits;  conditional E-value: 2.1e-80
                                       HHHHCCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHCCCCTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                          Prismane 115 rslkellpkglkglyaehaivlgyadeevveflaktlaglesdpldllskalrlGlldlkgmelldeantslfGtP. 190
                                       r++ +++pk+lk+     + +l+y +ee+v++la+t++g+e+  +d++sk+l+ G++d  g e++d ++t++++ P 
  gi|330507409|ref|YP_004383837.1| 130 RTILGIKPKSLKDF----GEALEYCEEEIVQLLAATHTGQEGYFMDFESKSLHGGMIDSLGKEICDMLQTVAYDMPr 202
                                       67778888888888....*********************************************************** PP

                                       ...--EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCCCCCCGCCCCCCHHHHHH.HHHCC......... CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx......... RF
                          Prismane 191 ...eppltevnlgvldkdkvnIlvsGHdladleelleqtegkglnvythgemLpghcctalk.lkyrh......... 254
                                           +pl+e+++g+ld++k +++  GH+la+ +e + ++e+++l ++++   + g+ccta + +++ +         
  gi|330507409|ref|YP_004383837.1| 203 gaaDAPLVEIGMGTLDQNKGVLIAYGHNLAAGAEAMIYAENNNLWDKVD---IGGVCCTAIDlTRITEtgresripp 276
                                       *99888************999999*************************...**********888888********* PP

                                       ....EEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-TTSEEE-.-CTTCH...... CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx...... RF
                          Prismane 255 ....lvgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktrlittsevakpgakhie.eeekad...... 320
                                            ++++G + + +k++++g++d ++vd++C++ ++ +  ++ ++++i+ +++++ g+ +   ++++a       
  gi|330507409|ref|YP_004383837.1| 277 nlgpKAKVAGAMGWWRKMVRAGIMDTVIVDEQCVFCDVLEDCQQRHIPVIASNDKIMLGLPDRTnDSADAIvedlvs 353
                                       **************************************999999*************99999883333331455677 PP

                                       ............HHHHHHHHHHHCCHCCTTCGG.-.......................................... CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxx.......................................... RF
                          Prismane 321 ............kdaseiiekAielakareekkve.......................................... 343
                                                   k+ + +i++A++++++re+ k e                                          
  gi|330507409|ref|YP_004383837.1| 354 fkmpgvaildpvKAGEVAIRTAVAVKPKREQYKKEslfteqqfkdtlatctecnqcafvcpphirisemisealkgn 430
                                       778888888899*****************997777899999999999999888888888888888777776666666 PP

                                       .................HHH.............................................HHTTSS-EEEEE CS
                                       .................xxx.............................................xxxxxxxxxxxx RF
                          Prismane 344 .................ida.............................................iksGtIkgvvlv 358
                                                          +                                             ++ G+I+gv+++
  gi|330507409|ref|YP_004383837.1| 431 lepfsstyevcvgcqrcE-QtcpqeipilklyeyanreyirnqkfkmragrgpvldteirkvgapLVLGQIPGVIAL 506
                                       666666666555555550.0555555555566666666666677777778888888888889999************ PP

                                       -B---TTCGCCHHHHHHHHCHHTTEEEEEECHHHHHC...CCTTTTEC...GHHHHSTHCEESEEEEESCCCHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 359 vGCdnakkgrdyytelakelikrdvlvltaGCakyal...nklglgti...eaaelagegiPrvLdvGsCvdnyriv 429
                                       vGC+n+++g++  +++ake++ r ++v+++GC+++++   ++++++ti   +   ++g +   + ++GsCv+n++i+
  gi|330507409|ref|YP_004383837.1| 507 VGCSNYPNGTKECYDIAKEFVDRGYIVVATGCMAMDMslyKDEDGKTIweqYEGAFDGRN---ICNIGSCVANAHIH 580
                                       ************************************9999*********9999999**99...************** PP

                                       HHHHHHHHHT.......TS.SGGGSSE...EEEECC-..-SHHHHHHHHHHHHTT-CEEECSS-TTTT-HHHHHHHH CS
                                       xxxxxxxxxx.......xx.xxxxxxx...xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 430 vialklaeal.......gv.dindLpl...aalalew..yeqKAvailltllalGinihlgptlpafgspnvlkvlv 493
                                       ++a+k+a ++       ++ di+d+++   +a+ ++w  y+qKA++i++++++lGi++++ p+  ++++ ++ ++  
  gi|330507409|ref|YP_004383837.1| 581 GAAIKVATIFahrneraNYdDIADYIMskvGACGVAWgaYSQKAASIATGVNRLGIPVVVQPSSVIYRRTFMGRTDK 657
                                       ****************9999*******999***************************************99988766 PP

                                       CH....HHHHHCEEEECHCHH CS
                                       xx....xxxxxxxxxxxxxxx RF
                          Prismane 494 ed....fedriggivtveedp 510
                                        +    ++++ g++ ++e++p
  gi|330507409|ref|YP_004383837.1| 658 PEdwmvIDAKNGNMQQIEPAP 678
                                       555666666666666666665 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.6   1.1e-06    0.0014      31      65 .]     381     417 ..     308     417 .. 0.77
   2 !   13.7   0.1   5.6e-05     0.067       4      17 ..     440     460 ..     431     513 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                            Fer4_8  31 eaaedvqeeqvlee..eealwsCttcgaCtevCpvgi 65 
                                       ++++++ e+  +e+  +++l +Ct+c++C+ vCp +i
  gi|330507409|ref|YP_004383837.1| 381 KREQYKKESLFTEQqfKDTLATCTECNQCAFVCPPHI 417
                                       33444555555444889*****************886 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.6e-05
                            Fer4_8   4 kCieCgaCqsaCp.......v 17 
                                        C++C++C+++Cp       +
  gi|330507409|ref|YP_004383837.1| 440 VCVGCQRCEQTCPqeipilkL 460
                                       477777777777655554442 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   1.8e-05     0.022      36      65 ..     386     414 ..     358     426 .. 0.66
   2 !   12.5   0.2   0.00019      0.22       2      16 ..     441     455 ..     431     487 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                           Fer4_16  36 aekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                       +++  ++e+++k++    +t C+ C+ vCP
  gi|330507409|ref|YP_004383837.1| 386 KKESLFTEQQFKDT-LATCTECNQCAFVCP 414
                                       44445555555555.555777777777776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00019
                           Fer4_16   2 CgtCgkCaevCPtna 16 
                                       C++C++C ++CP++ 
  gi|330507409|ref|YP_004383837.1| 441 CVGCQRCEQTCPQEI 455
                                       888888888888765 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.4   1.9e-06    0.0022      32      60 ..     389     417 ..     369     418 .. 0.75
   2 !   16.3   0.9   8.8e-06     0.011      41      60 ..     436     455 ..     420     456 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
                           Fer4_17  32 glleeaekeekaslCieCgeCerkCPqgl 60 
                                       +l++e++ +++  +C+eC++C+ +CP ++
  gi|330507409|ref|YP_004383837.1| 389 SLFTEQQFKDTLATCTECNQCAFVCPPHI 417
                                       456666667899**************987 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 8.8e-06
                           Fer4_17  41 ekaslCieCgeCerkCPqgl 60 
                                       ++ + C++C++Ce+ CPq++
  gi|330507409|ref|YP_004383837.1| 436 STYEVCVGCQRCEQTCPQEI 455
                                       56789*************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 ?   -0.8   0.4       1.4   1.7e+03       6      13 ..      52      59 ..      48      66 .. 0.77
   2 ?   -1.1   0.2       1.7   2.1e+03       3      16 ..     303     319 ..     297     327 .. 0.68
   3 !   21.6  12.2   1.5e-07   0.00017       7      56 .]     401     452 ..     396     452 .. 0.84
   4 !   14.2   2.1     3e-05     0.035       6      24 ..     438     462 ..     434     480 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                           Fer4_10  6 ddtCirCg 13
                                      ddtC+ C+
  gi|330507409|ref|YP_004383837.1| 52 DDTCTLCT 59
                                      68899997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                           Fer4_10   3 vidddtCirCg...kCv 16 
                                       vi d++C+ C    +C+
  gi|330507409|ref|YP_004383837.1| 303 VIVDEQCVFCDvleDCQ 319
                                       45566666665444444 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 1.5e-07
                           Fer4_10   7 dtCirCgkCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        tC++C++C  +CP ++  +++  ++ + + e+ +  +e C gc  C + CP
  gi|330507409|ref|YP_004383837.1| 401 ATCTECNQCAFVCPPHIriSEMISEALKGNLEPFSSTYEVCVGCQRCEQTCP 452
                                       69*************997555555666666778888***************9 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 3e-05
                           Fer4_10   6 ddtCirCgkCvkaCPadl......t 24 
                                        + C++C++C + CP+ +      +
  gi|330507409|ref|YP_004383837.1| 438 YEVCVGCQRCEQTCPQEIpilklyE 462
                                       578*************776665531 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.6   3.1e-06    0.0037      40      79 ..     382     421 ..     371     426 .. 0.80
   2 ?    5.8   1.6     0.013        16      59      78 ..     439     458 ..     424     464 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.1e-06
                           Fer4_18  40 rkkekkalkekeerkekgagdcidcescvkvcPtgidirk 79 
                                       r++ kk+   +e++ +++ + c++c++c  vcP +i i +
  gi|330507409|ref|YP_004383837.1| 382 REQYKKESLFTEQQFKDTLATCTECNQCAFVCPPHIRISE 421
                                       4455555666778889999*****************9965 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                           Fer4_18  59 gdcidcescvkvcPtgidir 78 
                                         c+ c+ c + cP +i i 
  gi|330507409|ref|YP_004383837.1| 439 EVCVGCQRCEQTCPQEIPIL 458
                                       56**************9886 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3     0.034        40      16      46 ..     287     320 ..     256     321 .. 0.83
   2 !   20.0  11.8   6.5e-07   0.00078       1      51 [.     402     454 ..     402     455 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.034
                            Fer4_7  16 aieldeeenekgtekveidpekClgCga...Cva 46 
                                       a+ ++ + + +g+++++i+ e+C++C++   C++
  gi|330507409|ref|YP_004383837.1| 287 AMGWWRKMVRAGIMDTVIVDEQCVFCDVledCQQ 320
                                       5556666677788999**********97777987 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 6.5e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaielde..eenekgt.ekveidpekClgCgaCvavCPtg 51 
                                       +C++C++C+ +Cp +  ++ e  +e  kg+ e     +e C+gC++C+++CP +
  gi|330507409|ref|YP_004383837.1| 402 TCTECNQCAFVCPPHI-RISEmiSEALKGNlEPFSSTYEVCVGCQRCEQTCPQE 454
                                       5************553.33330033344553445667899************86 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.5       5.1   6.1e+03      35      40 ..      54      59 ..      37      67 .. 0.66
   2 ?    0.5   0.1      0.57   6.9e+02      33      41 ..     301     314 ..     276     323 .. 0.64
   3 !   12.2   2.8   0.00013      0.15      33      49 ..     393     416 ..     370     418 .. 0.69
   4 !   16.4   2.0   6.3e-06    0.0076       2      31 ..     441     470 ..     440     509 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.1
                            Fer4_9 35 aCigCg 40
                                       C+ C 
  gi|330507409|ref|YP_004383837.1| 54 TCTLCT 59
                                      344443 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.57
                            Fer4_9  33 e.....eaCigCga 41 
                                       +     e+C++C  
  gi|330507409|ref|YP_004383837.1| 301 DtvivdEQCVFCDV 314
                                       03444469*99986 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00013
                            Fer4_9  33 e.......eaCigCgaCveaCpkg 49 
                                       e         C++C++C+ +Cp +
  gi|330507409|ref|YP_004383837.1| 393 EqqfkdtlATCTECNQCAFVCPPH 416
                                       1445567778***********987 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 6.3e-06
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraa 31 
                                       C+gC++C++ Cp+++ + +  e+ +r  ++
  gi|330507409|ref|YP_004383837.1| 441 CVGCQRCEQTCPQEIPILKLYEYANREYIR 470
                                       **************9999988888877665 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2       6.9   8.2e+03      40      45 ..      54      59 ..      46      65 .. 0.64
   2 ?   -0.2   0.2      0.92   1.1e+03      36      46 ..     304     314 ..     295     328 .. 0.76
   3 !    8.9   3.2    0.0014       1.7      38      52 ..     400     414 ..     389     423 .. 0.79
   4 !   16.0  12.2     8e-06    0.0096       6      53 ..     401     453 ..     398     457 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.9
                           Fer4_21 40 eCvGCn 45
                                      +C+ C+
  gi|330507409|ref|YP_004383837.1| 54 TCTLCT 59
                                      444443 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.92
                           Fer4_21  36 vvedeCvGCnl 46 
                                       +v+++Cv C++
  gi|330507409|ref|YP_004383837.1| 304 IVDEQCVFCDV 314
                                       45788888864 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0014
                           Fer4_21  38 edeCvGCnlCssvCP 52 
                                         +C+ Cn C+ vCP
  gi|330507409|ref|YP_004383837.1| 400 LATCTECNQCAFVCP 414
                                       468999999999999 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 8e-06
                           Fer4_21   6 dkCigCgkCliaCedtshqai....eidaktvl......kvvedeCvGCnlCssvCPv 53 
                                       ++C +C++C+ +C+   h  i    + +             + + CvGC+ C + CP 
  gi|330507409|ref|YP_004383837.1| 401 ATCTECNQCAFVCPP--HIRIsemiSEAL---KgnlepfSSTYEVCVGCQRCEQTCPQ 453
                                       68***********95..444432223222...122232266789*************4 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   2.6     0.021        26      79      94 ..     400     415 ..     365     417 .. 0.54
   2 ?    5.2   2.1     0.033        39       2      13 ..     403     414 ..     402     429 .. 0.90
   3 ?   14.9   2.4   3.1e-05     0.037      78      96 .]     437     455 ..     416     455 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.021
                           Fer4_22  79 esgCvGCgRCieacpv 94 
                                         +C+ C+ C  +cp 
  gi|330507409|ref|YP_004383837.1| 400 LATCTECNQCAFVCPP 415
                                       4556666666666664 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.033
                           Fer4_22   2 ClsCgaCtlvCp 13 
                                       C +C++C++vCp
  gi|330507409|ref|YP_004383837.1| 403 CTECNQCAFVCP 414
                                       9**********9 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 3.1e-05
                           Fer4_22  78 gesgCvGCgRCieacpvki 96 
                                         ++CvGC RC+++cp++i
  gi|330507409|ref|YP_004383837.1| 437 TYEVCVGCQRCEQTCPQEI 455
                                       5679************987 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  10.4     0.011        13      10      77 ..     389     453 ..     381     454 .. 0.73
   2 ?    2.7   2.5     0.086     1e+02      24      45 ..     441     460 ..     436     475 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.011
                                       ----HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-HHHHHHHS-G CS
                           Fer4_20  10 lglteeealeeAsRClqCkkapcvkgCPveidipefikkiaegnleeaakiiketnslpavcgrvCpq 77 
                                       + +te++ ++  + C +C  ++c   CP +i+i e+i++  +gnle   +   e     + c + Cpq
  gi|330507409|ref|YP_004383837.1| 389 SLFTEQQFKDTLATCTEC--NQCAFVCPPHIRISEMISEALKGNLEPFSS-TYEVCVGCQRCEQTCPQ 453
                                       45778888888899****..889********************9864333.33333444556666666 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.086
                                       ----TT-HHHHCSTT---HHHH CS
                           Fer4_20  24 ClqCkkapcvkgCPveidipef 45 
                                       C+ C  + c+++CP ei i + 
  gi|330507409|ref|YP_004383837.1| 441 CVGC--QRCEQTCPQEIPILKL 460
                                       9999..7899****99998665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.4       0.5   5.9e+02       2      11 ..     303     312 ..     302     314 .. 0.84
   2 ?   11.1   3.0   0.00023      0.27       7      19 ..     402     414 ..     400     417 .. 0.92
   3 ?   14.4   3.4   2.1e-05     0.025       5      21 ..     438     454 ..     437     457 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.5
                                       EEETTTSSS- CS
                              Fer4   2 videekCigC 11 
                                       vi  e C++C
  gi|330507409|ref|YP_004383837.1| 303 VIVDEQCVFC 312
                                       688999**** PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00023
                                       TSSS-THHHHHST CS
                              Fer4   7 kCigCGaCvevCP 19 
                                        C+ C++C+ vCP
  gi|330507409|ref|YP_004383837.1| 402 TCTECNQCAFVCP 414
                                       5************ PP

  == domain 3  score: 14.4 bits;  conditional E-value: 2.1e-05
                                       TTTSSS-THHHHHSTTT CS
                              Fer4   5 eekCigCGaCvevCPvg 21 
                                       +e C+gC +C++ CP +
  gi|330507409|ref|YP_004383837.1| 438 YEVCVGCQRCEQTCPQE 454
                                       689************87 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4      0.31   3.7e+02       8      16 ..      53      63 ..      48      66 .. 0.87
   2 ?   10.6   3.4    0.0004      0.48       8      21 ..     401     414 ..     396     415 .. 0.89
   3 ?   10.6   4.1   0.00041      0.49       8      22 .]     439     453 ..     436     453 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.31
                            Fer4_2  8 drCigC..gaC 16
                                      d+C+ C  g+C
  gi|330507409|ref|YP_004383837.1| 53 DTCTLCtyGPC 63
                                      79****88899 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0004
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                       ++C++C+ C  +CP
  gi|330507409|ref|YP_004383837.1| 401 ATCTECNQCAFVCP 414
                                       58***********9 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00041
                            Fer4_2   8 drCigCgaCvsaCPa 22 
                                       + C+gC  C + CP+
  gi|330507409|ref|YP_004383837.1| 439 EVCVGCQRCEQTCPQ 453
                                       79************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 ?    7.1   1.5    0.0072       8.6       3      15 ..     402     414 ..     400     425 .. 0.91
   2 ?   10.8   5.8   0.00047      0.56       2      16 ..     439     453 ..     438     454 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0072
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                       +C++C +C  +CP
  gi|330507409|ref|YP_004383837.1| 402 TCTECNQCAFVCP 414
                                       7********9999 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00047
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e C+gC +C+ +CPq
  gi|330507409|ref|YP_004383837.1| 439 EVCVGCQRCEQTCPQ 453
                                       78************8 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 ?    8.1   1.3    0.0026       3.1      11      41 ..     386     416 ..     381     427 .. 0.87
   2 ?    1.6   1.0      0.27   3.2e+02      21      40 ..     434     453 ..     425     472 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0026
                   c-SKI_SMAD_bind  11 kckGlfvpelyssseakCikCleCkllfspq 41 
                                       k + lf+ ++++++ a+C +C++C  +  p+
  gi|330507409|ref|YP_004383837.1| 386 KKESLFTEQQFKDTLATCTECNQCAFVCPPH 416
                                       5678999******************998886 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.27
                   c-SKI_SMAD_bind  21 yssseakCikCleCkllfsp 40 
                                       +ss+   C+ C++C+ +   
  gi|330507409|ref|YP_004383837.1| 434 FSSTYEVCVGCQRCEQTCPQ 453
                                       7888999*******987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (793 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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):              15  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.45
# Mc/sec: 5298.15
//
Query:       gi|330507410|ref|YP_004383838.1|  [L=305]
Description: cobalamin biosynthesis protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-85  287.1   1.4    1.4e-85  286.8   1.4    1.0  1  CobD_Cbib  CobD/Cbib protein


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.8   1.4     8e-90   1.4e-85       2     272 ..      13     284 ..      12     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: 286.8 bits;  conditional E-value: 8e-90
                         CobD_Cbib   2 llAlllDlllgdprrllhPvvligklisalekrlrkakkerlaGvllalllvllallvalllllla.laallglvle 77 
                                       llA+++D+l+g+p+ ++hPvv+ig+lis+l++r      ++++G+lla++++++++l+a ll+++a ++++l l++ 
  gi|330507410|ref|YP_004383838.1|  13 LLAVAFDILIGEPPVRVHPVVWIGRLISFLRARAG---PTKVQGILLAITVIAVSVLAAHLLVRAAhVMPVLPLLVG 86 
                                       89****************************99553...4689**********************88544444679** PP

                         CobD_Cbib  78 alllkltlalrsLleevrkvakalkgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPlfyflll 154
                                       a+llk+t+a+r+Lle+++++ + +++d+e+a++ +  +VgRdts+l+ ++ ++A++Es++EN +D++++P+fy++l+
  gi|330507410|ref|YP_004383838.1|  87 AYLLKSTFAIRCLLETSSNIGRMIDQDMEEAKKMLPALVGRDTSTLTTAQASSAVIESLSENYVDSILSPIFYYILF 163
                                       ************************99************************************************999 PP

                         CobD_Cbib 155 .....glpgalaykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllala......aalriarrdark 220
                                            gl +a+a+ka++T+Dsm+GYk++ ++++G+a ArlDDl+n+iPARl+++l+ala      +a+r a++++++
  gi|330507410|ref|YP_004383838.1| 164 apiglGLEAAIAFKAISTMDSMIGYKKPGLKELGYAGARLDDLANWIPARLSIILIALArprgarSAIREAFKYHSA 240
                                       777777788*************************************************877777778********** PP

                         CobD_Cbib 221 hpSpNsgwpeaalAgalgvrLggpnvY..lgkleekptlgdkkrpleaediera 272
                                       +pSpNsgwp+aa+Ag l++rL++p++Y  lg   e+p        +e++di ra
  gi|330507410|ref|YP_004383838.1| 241 TPSPNSGWPMAAAAGSLKIRLEKPGQYilLG---ENPN-------PETRDIFRA 284
                                       ***************************4333...3333.......255566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2209.07
//
Query:       gi|330507411|ref|YP_004383839.1|  [L=218]
Description: hypothetical protein MCON_1337 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.4   0.1       0.27   11.2   0.1    1.7  1  UCH_N     N-terminal of ubiquitin carboxyl-terminal hydrolase


Domain annotation for each model (and alignments):
>> UCH_N  N-terminal of ubiquitin carboxyl-terminal hydrolase 37
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   1.5e-05      0.27      42      85 ..      21      62 ..       3      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.5e-05
                             UCH_N 42 fnagkavktFqLnnNiksvvlrsygekqnrLhLtlkdnsflfid 85
                                      f  ++a+k F    ++ ++ ++s++e++n++ +++ +n +lfi 
  gi|330507411|ref|YP_004383839.1| 21 FGKEEAKKLFGW--DVAEILVNSSKEDENHILIIFNNNFMLFIR 62
                                      555555666654..799*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1672.45
//
Query:       gi|330507412|ref|YP_004383840.1|  [L=1286]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-132  431.7  90.6    1.4e-16   60.5   0.8   16.4 18  TPR_12        Tetratricopeptide repeat
    6.3e-79  256.9  76.9    1.3e-06   28.0   0.1   26.3 27  TPR_1         Tetratricopeptide repeat
    4.7e-76  244.9  97.4    7.7e-05   22.5   0.4   27.1 27  TPR_2         Tetratricopeptide repeat
    8.1e-71  229.0  94.2    7.6e-05   22.5   0.2   27.5 27  TPR_7         Tetratricopeptide repeat
    1.7e-54  180.3  97.7    4.7e-06   26.3   0.9   25.7 27  TPR_10        Tetratricopeptide repeat
    1.5e-47  162.4  20.7    1.3e-08   34.6   0.4   10.1 11  SNAP          Soluble NSF attachment protein, SNAP
    1.6e-46  159.3  53.9    2.1e-14   53.6   6.8    8.5  8  TPR_MalT      MalT-like TPR region
    1.3e-41  137.3  67.6      0.014   15.5   0.0   24.6 25  TPR_8         Tetratricopeptide repeat
    3.2e-34  117.3  80.3    0.00016   22.2   1.5   16.9 16  TPR_16        Tetratricopeptide repeat
    6.6e-29   99.3  43.9      0.015   14.9   0.0   20.2 22  TPR_11        TPR repeat
    6.1e-22   76.7  56.4      0.058   14.0   0.2   21.7 21  TPR_6         Tetratricopeptide repeat
    6.9e-20   71.5   6.7     0.0059   16.3   0.0   10.1 10  RPN7          26S proteasome subunit RPN7
    1.1e-19   69.4  83.0        0.3   12.0   0.0   23.6 24  TPR_14        Tetratricopeptide repeat
    1.7e-18   65.2  75.3      0.035   14.7   0.2   21.7 20  TPR_4         Tetratricopeptide repeat
    2.6e-16   59.9  75.9      0.055   14.0   0.0   17.5 19  TPR_19        Tetratricopeptide repeat
    2.7e-11   43.4  36.0       0.58   10.3   0.0   15.4 15  MIT           MIT (microtubule interacting and transport) dom
      9e-11   41.5  37.6    0.00085   18.6   0.0   11.6 13  TPR_15        Tetratricopeptide repeat
    5.6e-08   32.7  12.8      0.059   13.4   0.1    8.0  7  ANAPC5        Anaphase-promoting complex subunit 5
    2.4e-06   27.4  21.5         11    6.5   0.0   13.5 10  PPR           PPR repeat
    0.00012   21.8   7.7          5    6.8   0.1    7.5 10  DUF2225       Uncharacterized protein conserved in bacteria (
    0.00012   22.2  43.7         12    6.5   0.0   18.8 19  TPR_17        Tetratricopeptide repeat
    0.00031   20.4   5.0       0.47   10.0   0.0    6.0  6  Foie-gras_1   Foie gras liver health family 1
    0.00091   18.3  13.1          1    8.2   0.2    6.3  7  SRP68         RNA-binding signal recognition particle 68
     0.0011   19.0  20.4        6.1    7.0   0.0   10.6 10  TPR_3         Tetratricopeptide repeat
     0.0013   18.9  38.1      0.031   14.5   0.4   11.9 13  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
     0.0016   18.4   0.1       0.12   12.4   0.0    4.0  2  Tricorn_C1    Tricorn protease C1 domain
      0.003   17.7   0.2         65    3.8   0.0    6.5  5  PPR_2         PPR repeat family
     0.0045   17.3   0.3       0.62   10.4   0.2    4.7  3  RPN6_N        26S proteasome regulatory subunit RPN6 N-termin
      0.005   16.5   0.0         22    4.7   0.0    4.7  5  Ribosomal_S7  Ribosomal protein S7p/S5e
     0.0093   15.7  37.9        2.2    8.0   1.8   10.4 12  TPR_21        Tetratricopeptide repeat-like domain
  ------ inclusion threshold ------
      0.018   15.6   3.4         87    3.8   0.0    7.2  7  DUF4810       Domain of unknown function (DUF4810)
       0.06   13.4  19.4       0.39   10.8   0.1    7.7  7  DUF3856       Domain of Unknown Function (DUF3856)
       0.13   12.5   2.1        3.8    7.8   0.1    4.1  2  FliS          Flagellar protein FliS
       0.32   10.7   2.9         41    4.0   0.0    5.1  6  PPR_1         PPR repeat
       0.68    9.4  14.8        3.8    7.1   0.0    7.2  7  SHNi-TPR      SHNi-TPR


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   2.7   3.4e-08   1.7e-05       5      72 ..      75     140 ..      72     142 .. 0.93
   2 !   10.2   0.0    0.0014      0.71       5      32 ..     155     182 ..     151     186 .. 0.85
   3 !   32.1   0.5     2e-10     1e-07       4      71 ..     193     258 ..     190     261 .. 0.90
   4 !   43.1   1.6   7.4e-14   3.8e-11       2      77 .]     271     343 ..     270     343 .. 0.93
   5 !   39.5   0.8     1e-12   5.1e-10       3      76 ..     311     382 ..     308     383 .. 0.93
   6 !   17.3   0.3   8.4e-06    0.0043       2      48 ..     350     394 ..     349     395 .. 0.85
   7 !   40.4   0.3   5.1e-13   2.6e-10       3      73 ..     391     459 ..     389     463 .. 0.93
   8 !   31.0   0.1   4.5e-10   2.3e-07       4      76 ..     472     542 ..     469     543 .. 0.94
   9 !   41.7   1.6     2e-13     1e-10       2      76 ..     550     622 ..     549     623 .. 0.92
  10 !   35.7   1.5   1.5e-11   7.9e-09       3      76 ..     631     702 ..     629     703 .. 0.95
  11 !   52.2   1.2   1.1e-16   5.5e-14       2      73 ..     710     779 ..     709     782 .. 0.93
  12 !   60.5   0.8   2.8e-19   1.4e-16       2      76 ..     790     862 ..     789     863 .. 0.97
  13 !   40.7   0.0   4.3e-13   2.2e-10       5      76 ..     913     982 ..     910     983 .. 0.94
  14 !   32.6   0.0   1.4e-10   7.4e-08       7      75 ..     955    1021 ..     953    1023 .. 0.95
  15 !   11.3   0.0   0.00061      0.31      44      74 ..     990    1020 ..     987    1039 .. 0.61
  16 !   29.8   1.1     1e-09   5.3e-07      19      72 ..    1087    1138 ..    1070    1142 .. 0.90
  17 !   26.9   2.2   8.3e-09   4.2e-06       3      67 ..    1111    1173 ..    1109    1175 .. 0.94
  18 !    8.5   3.9    0.0048       2.4      14      75 ..    1162    1221 ..    1160    1223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.4e-08
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       a+ nl+ + ++l  ++ A+e++  a ++a+ l   d + +a++l  Lg ly + ++++ A + +e+al
  gi|330507412|ref|YP_004383840.1|  75 AWFNLGRLAHHLFFHQAAIEYYSNASDLAQIL--SDDDSLASILLCLGALYGEEEDWARACQCYEKAL 140
                                       6679*************************998..55567***************************98 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0014
                            TPR_12   5 alnnlaavlrrlgrydeAlellekalei 32 
                                       +l +l+ + r +g+y++A+ ++ + le+
  gi|330507412|ref|YP_004383840.1| 155 VLERLGRARRLQGEYHQAQICYSRILEV 182
                                       6778999999999999999999999987 PP

  == domain 3  score: 32.1 bits;  conditional E-value: 2e-10
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                        a +nla++++ +g++++A++l+++ l  ++ +  +d  ++a++l  L+ +y+++g+ + A+  l+ a
  gi|330507412|ref|YP_004383840.1| 193 EATSNLAELCQIQGDMEKAEKLYQTILKERELS--DDPVGAARALASLASIYSQTGNGKRAQISLQSA 258
                                       6778**********************9999766..77789*********************9888876 PP

  == domain 4  score: 43.1 bits;  conditional E-value: 7.4e-14
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       +a ++ +la+++++ gr+ eAlel+ ++l++ ++   + + l++ +l+ +g+++++ g++  A+++l++a+ai+++
  gi|330507412|ref|YP_004383840.1| 271 AAEMQCRLADIYFHEGRLKEALELYGRSLAALQKG--HPS-LASKALCRMGQCFLEDGNWTLAEDHLQRAIAIMKE 343
                                       5889999*************************855..667.899*****************************985 PP

  == domain 5  score: 39.5 bits;  conditional E-value: 1e-12
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       ++al +++++ ++ g+++ A+++l++a++i+++   +d+  +a++l  L+ +++++g++e Al+  +e+l+i+e
  gi|330507412|ref|YP_004383840.1| 311 SKALCRMGQCFLEDGNWTLAEDHLQRAIAIMKEH--KDSSSLARALVILAGVHHKQGQLEMALQCSRESLKIRE 382
                                       568889*************************776..88889*******************************98 PP

  == domain 6  score: 17.3 bits;  conditional E-value: 8.4e-06
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattl 48 
                                       +a+al+ la v++++g+++ Al++ +++l i++r+  +d  + a++l
  gi|330507412|ref|YP_004383840.1| 350 LARALVILAGVHHKQGQLEMALQCSRESLKIRERS--KDLSGSAEAL 394
                                       6889999*************************999..7666666665 PP

  == domain 7  score: 40.4 bits;  conditional E-value: 5.1e-13
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       a aln +a +++   ++ eA+e++++a +++ +   ++  ++a++l nLg +y++ g+++ Al+++ +a++
  gi|330507412|ref|YP_004383840.1| 391 AEALNCIARICCDCSDWPEAIECYQRAADLFMEM--GEVTAAAEALSNLGGVYHLKGDLDVALQMYSHAYN 459
                                       789999*************************776..77889***************************997 PP

  == domain 8  score: 31.0 bits;  conditional E-value: 4.5e-10
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        +++n+++v++ +g+++ A e+lek+++  + l  +d  ++a  +  Lg +y++ g++++A++ +e a +++e
  gi|330507412|ref|YP_004383840.1| 472 MVQSNIGLVYQSRGDLHLAGEFLEKSIATKEDL--GDQIGAAGNRLSLGLIYQLGGEWDQAQSCFEGAARAFE 542
                                       5789***********************999999..9******************************9998876 PP

  == domain 9  score: 41.7 bits;  conditional E-value: 2e-13
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +a+a nnl++++  +g++  A+ ++++ le++r l + d ++ a tl nL+ +y+++g+ e A+el++++++ ++
  gi|330507412|ref|YP_004383840.1| 550 LAAAENNLGNLYSDRGDLMHAILCYRQGLEARRVL-N-DGHGMAVTLGNLAGVYLQSGEEERAEELYQQSIDGFR 622
                                       58999***************************766.5.5559*****************************9887 PP

  == domain 10  score: 35.7 bits;  conditional E-value: 1.5e-11
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a++l+ la   +++g+++ Ale+++k+l+++  + G+d+   +++l  +  l++++gr++eAl ++ ++l++++
  gi|330507412|ref|YP_004383840.1| 631 ARSLYGLARSMAERGDLEGALECYRKCLDLQ--IVGGDSRSMIEALESMVNLLLRRGRWQEALTRYAQVLEALR 702
                                       77888**************************..7899**********************************987 PP

  == domain 11  score: 52.2 bits;  conditional E-value: 1.1e-16
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       va+++  l+++++ lg++deAle ++++l+i++ l  +d + ++ +++nLg +++++g++++Ale ++ +l+
  gi|330507412|ref|YP_004383840.1| 710 VAAVQCALGNLHADLGQWDEALEDYNESLAIMEGL--GDEYSVSVARNNLGNMCYRQGDWAAALENYRLSLE 779
                                       6888989**************************99..66668**************************9998 PP

  == domain 12  score: 60.5 bits;  conditional E-value: 2.8e-19
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        a++l+n+a +++++g++++Al+ + k+l ++++l  +d+++ a++l n+g ly+++g+ + A e++++al+i++
  gi|330507412|ref|YP_004383840.1| 790 EASVLSNVAGLCYKRGQWADALDSYSKSLSLFEKL--EDSAGIAQVLGNMGNLYHRQGERDLAAEHFQRALEIYR 862
                                       58899******************************..*************************************8 PP

  == domain 13  score: 40.7 bits;  conditional E-value: 4.3e-13
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +l+ la  ++  g+++eA++++++++e++ ++  ++ ++  ++l+n++ +y  +g++  A+ l+  al+i++
  gi|330507412|ref|YP_004383840.1| 913 VLSALAGSYTDSGQWAEAIACYKRSVERFDQT--GEVYNRGQVLFNMALVYKDMGDLNRARTLFDVALDIFQ 982
                                       6789****************************..77889******************************987 PP

  == domain 14  score: 32.6 bits;  conditional E-value: 1.4e-10
                            TPR_12    7 nnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75  
                                         n+a+v+  +g++  A++l++ al+i++ l  +  p++a++  nLg++  ++gr +eA+el+ +++ i+
  gi|330507412|ref|YP_004383840.1|  955 FNMALVYKDMGDLNRARTLFDVALDIFQDL--DALPCVASAKLNLGIISGQMGRSDEAIELFSQSIGIL 1021
                                        49****************************..99******************************98776 PP

  == domain 15  score: 11.3 bits;  conditional E-value: 0.00061
                            TPR_12   44 tattlrnLgrlyralgryeeAlelleealai 74  
                                        +a++  nLg++  ++gr +eA+el+ +++ i
  gi|330507412|ref|YP_004383840.1|  990 VASAKLNLGIISGQMGRSDEAIELFSQSIGI 1020
                                        4455555555555555555555555555444 PP

  == domain 16  score: 29.8 bits;  conditional E-value: 1e-09
                            TPR_12   19 ydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72  
                                        y eA +++ekal++ r+l    ++++a +   Lgrl +a+g+ye+Al++ ++al
  gi|330507412|ref|YP_004383840.1| 1087 YPEAKSCFEKALALSRKL--SLSYEEAKAISSLGRLALASGDYEDALRRMKQAL 1138
                                        99****************..8899*****************************8 PP

  == domain 17  score: 26.9 bits;  conditional E-value: 8.3e-09
                            TPR_12    3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlel 67  
                                        a+a + l+ + ++ g+y++Al+  ++al i+ rl  + ++++++++r++  l++a+++y+ A+e+
  gi|330507412|ref|YP_004383840.1| 1111 AKAISSLGRLALASGDYEDALRRMKQALVIFGRL--GASLDLIEVYRDMTLLFLAQDDYQRAEEM 1173
                                        778889***************************9..88*************************98 PP

  == domain 18  score: 8.5 bits;  conditional E-value: 0.0048
                            TPR_12   14 rrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75  
                                        +++ +y+ A+e+     ++a r+lG+  +l + +  +L+++  ++g+ eeA++ +  al++a
  gi|330507412|ref|YP_004383840.1| 1162 LAQDDYQRAEEMAMLRQRQA-RILGH-ADLSLLATVDLAECEARTGKKEEARADYAGALRLA 1221
                                        57999999999999998888.56665.6799************************9999986 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.2    0.0059         3       2      27 ..      74      99 ..      73     104 .. 0.91
   2 !    8.6   0.7    0.0033       1.7       2      28 ..     114     140 ..     113     141 .. 0.92
   3 !    9.3   0.0     0.002         1       3      30 ..     155     182 ..     153     183 .. 0.90
   4 !   12.5   0.1   0.00019     0.098       5      29 ..     196     220 ..     193     223 .. 0.91
   5 ?   -0.2   0.0         2     1e+03       1      16 [.     232     247 ..     232     254 .. 0.88
   6 !   15.0   0.4   3.2e-05     0.016       2      28 ..     273     299 ..     272     301 .. 0.90
   7 !   18.1   0.0   3.3e-06    0.0017       2      30 ..     312     340 ..     311     344 .. 0.94
   8 !    9.4   0.0    0.0019      0.97       1      31 [.     351     381 ..     351     384 .. 0.87
   9 !   15.8   0.1   1.8e-05    0.0093       1      30 [.     391     420 ..     391     421 .. 0.94
  10 !    9.2   0.0    0.0022       1.1       1      26 [.     431     456 ..     431     457 .. 0.92
  11 !    7.8   0.0     0.006       3.1       5      29 ..     475     499 ..     472     504 .. 0.89
  12 ?    5.2   0.0     0.038        19       6      25 ..     516     535 ..     515     537 .. 0.93
  13 !   20.0   0.3   8.3e-07   0.00042       1      29 [.     551     579 ..     551     582 .. 0.94
  14 !    9.9   0.0    0.0013      0.66       1      28 [.     591     618 ..     591     619 .. 0.92
  15 !   14.3   0.2   5.4e-05     0.027       1      30 [.     631     660 ..     631     661 .. 0.91
  16 ?   -1.3   0.0       4.5   2.3e+03       9      22 ..     679     692 ..     679     699 .. 0.79
  17 !   22.3   0.2   1.5e-07   7.8e-05       2      30 ..     712     740 ..     711     742 .. 0.91
  18 !   18.4   0.2   2.6e-06    0.0013       3      29 ..     753     779 ..     751     779 .. 0.92
  19 !   13.4   0.0   9.8e-05      0.05       2      32 ..     792     822 ..     791     824 .. 0.89
  20 !   28.0   0.1   2.5e-09   1.3e-06       1      31 [.     831     861 ..     831     864 .. 0.94
  21 !   12.7   0.0   0.00017     0.087       3      29 ..     913     939 ..     911     942 .. 0.88
  22 !    9.2   0.0    0.0021       1.1       3      30 ..     953     980 ..     951     984 .. 0.84
  23 !   12.1   0.0   0.00026      0.13       2      28 ..     992    1018 ..     991    1022 .. 0.90
  24 ?    6.8   0.1     0.012       6.1      17      31 ..    1087    1101 ..    1081    1104 .. 0.87
  25 ?    3.9   0.0     0.099        51       1      21 [.    1111    1131 ..    1111    1132 .. 0.91
  26 ?   -1.3   0.1       4.4   2.2e+03      11      22 ..    1161    1172 ..    1159    1173 .. 0.66
  27 ?   -0.5   0.3       2.4   1.2e+03       7      24 ..    1197    1214 ..    1196    1221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0059
                                      HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekA 27
                                      +a++nlG + ++l  ++ A+eyy+ A
  gi|330507412|ref|YP_004383840.1| 74 QAWFNLGRLAHHLFFHQAAIEYYSNA 99
                                      79*********************998 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0033
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekAL 28 
                                        +l  lG++y + +++  A ++yekAL
  gi|330507412|ref|YP_004383840.1| 114 SILLCLGALYGEEEDWARACQCYEKAL 140
                                       57889*********************9 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                       +l +lG a + +g+y +A  +y++ Le+
  gi|330507412|ref|YP_004383840.1| 155 VLERLGRARRLQGEYHQAQICYSRILEV 182
                                       56699*******************9995 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   5 ynlGnayfklgkydeAleyyekALe 29 
                                        nl+ +++ +g+ ++A++ y+  L+
  gi|330507412|ref|YP_004383840.1| 196 SNLAELCQIQGDMEKAEKLYQTILK 220
                                       69*******************9887 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHTT- CS
                             TPR_1   1 akalynlGnayfklgk 16 
                                       a+al  l+ +y + g+
  gi|330507412|ref|YP_004383840.1| 232 ARALASLASIYSQTGN 247
                                       799**********998 PP

  == domain 6  score: 15.0 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekAL 28 
                                       +  ++l+ +yf+ g+++eAle y + L
  gi|330507412|ref|YP_004383840.1| 273 EMQCRLADIYFHEGRLKEALELYGRSL 299
                                       6679*******************9988 PP

  == domain 7  score: 18.1 bits;  conditional E-value: 3.3e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                       kal+++G+++++ g++  A+++ ++A+ +
  gi|330507412|ref|YP_004383840.1| 312 KALCRMGQCFLEDGNWTLAEDHLQRAIAI 340
                                       8**************************87 PP

  == domain 8  score: 9.4 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                       a+al  l+ +++k+g+++ Al++ ++ L+++
  gi|330507412|ref|YP_004383840.1| 351 ARALVILAGVHHKQGQLEMALQCSRESLKIR 381
                                       678888999**************88888886 PP

  == domain 9  score: 15.8 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a+al+ ++ ++    ++ eA+e+y++A  l
  gi|330507412|ref|YP_004383840.1| 391 AEALNCIARICCDCSDWPEAIECYQRAADL 420
                                       89*************************765 PP

  == domain 10  score: 9.2 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyek 26 
                                       a+al nlG +y+ +g++d Al+ y+ 
  gi|330507412|ref|YP_004383840.1| 431 AEALSNLGGVYHLKGDLDVALQMYSH 456
                                       89****************99999975 PP

  == domain 11  score: 7.8 bits;  conditional E-value: 0.006
                                       HHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   5 ynlGnayfklgkydeAleyyekALe 29 
                                        n+G++y++ g++  A e+ ek + 
  gi|330507412|ref|YP_004383840.1| 475 SNIGLVYQSRGDLHLAGEFLEKSIA 499
                                       7*********************997 PP

  == domain 12  score: 5.2 bits;  conditional E-value: 0.038
                                       HHHHHHHHTT-HHHHHHHHH CS
                             TPR_1   6 nlGnayfklgkydeAleyye 25 
                                        lG++y+  g++d+A  ++e
  gi|330507412|ref|YP_004383840.1| 516 SLGLIYQLGGEWDQAQSCFE 535
                                       59**************9997 PP

  == domain 13  score: 20.0 bits;  conditional E-value: 8.3e-07
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALe 29 
                                       a a +nlGn+y   g++  A+ +y++ Le
  gi|330507412|ref|YP_004383840.1| 551 AAAENNLGNLYSDRGDLMHAILCYRQGLE 579
                                       6799**********************998 PP

  == domain 14  score: 9.9 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekAL 28 
                                       a +l nl+ +y++ g+ + A+e y++ +
  gi|330507412|ref|YP_004383840.1| 591 AVTLGNLAGVYLQSGEEERAEELYQQSI 618
                                       56899********************987 PP

  == domain 15  score: 14.3 bits;  conditional E-value: 5.4e-05
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a++ly+l+    + g+++ Ale+y+k+L l
  gi|330507412|ref|YP_004383840.1| 631 ARSLYGLARSMAERGDLEGALECYRKCLDL 660
                                       6789999999999***************98 PP

  == domain 16  score: -1.3 bits;  conditional E-value: 4.5
                                       HHHHHTT-HHHHHH CS
                             TPR_1   9 nayfklgkydeAle 22 
                                       n++++ g+++eAl 
  gi|330507412|ref|YP_004383840.1| 679 NLLLRRGRWQEALT 692
                                       678999******96 PP

  == domain 17  score: 22.3 bits;  conditional E-value: 1.5e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                        + + lGn++  lg++deAle+y++ L +
  gi|330507412|ref|YP_004383840.1| 712 AVQCALGNLHADLGQWDEALEDYNESLAI 740
                                       56789********************9986 PP

  == domain 18  score: 18.4 bits;  conditional E-value: 2.6e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALe 29 
                                       a +nlGn+++++g++  Ale y+  Le
  gi|330507412|ref|YP_004383840.1| 753 ARNNLGNMCYRQGDWAAALENYRLSLE 779
                                       789*******************98776 PP

  == domain 19  score: 13.4 bits;  conditional E-value: 9.8e-05
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                        +l n + +++k g++ +Al+ y+k L+l +
  gi|330507412|ref|YP_004383840.1| 792 SVLSNVAGLCYKRGQWADALDSYSKSLSLFE 822
                                       678899999******************9965 PP

  == domain 20  score: 28.0 bits;  conditional E-value: 2.5e-09
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                       a++l n+Gn+y+++g+ d A e++++ALe++
  gi|330507412|ref|YP_004383840.1| 831 AQVLGNMGNLYHRQGERDLAAEHFQRALEIY 861
                                       7899*************************97 PP

  == domain 21  score: 12.7 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALe 29 
                                       +l  l+  y   g++ eA+++y++ +e
  gi|330507412|ref|YP_004383840.1| 913 VLSALAGSYTDSGQWAEAIACYKRSVE 939
                                       67778889****************988 PP

  == domain 22  score: 9.2 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                       +l+n++++y  +g+++ A   ++ AL +
  gi|330507412|ref|YP_004383840.1| 953 VLFNMALVYKDMGDLNRARTLFDVALDI 980
                                       79****************9888766665 PP

  == domain 23  score: 12.1 bits;  conditional E-value: 0.00026
                                        HHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1    2 kalynlGnayfklgkydeAleyyekAL 28  
                                         a  nlG +  ++g+ deA+e +++ +
  gi|330507412|ref|YP_004383840.1|  992 SAKLNLGIISGQMGRSDEAIELFSQSI 1018
                                        6778*******************9987 PP

  == domain 24  score: 6.8 bits;  conditional E-value: 0.012
                                        HHHHHHHHHHHHHHS CS
                             TPR_1   17 ydeAleyyekALeln 31  
                                        y eA  ++ekAL l 
  gi|330507412|ref|YP_004383840.1| 1087 YPEAKSCFEKALALS 1101
                                        99**********996 PP

  == domain 25  score: 3.9 bits;  conditional E-value: 0.099
                                        HHHHHHHHHHHHHTT-HHHHH CS
                             TPR_1    1 akalynlGnayfklgkydeAl 21  
                                        aka   lG + +  g+y++Al
  gi|330507412|ref|YP_004383840.1| 1111 AKAISSLGRLALASGDYEDAL 1131
                                        688899**************8 PP

  == domain 26  score: -1.3 bits;  conditional E-value: 4.4
                                        HHHTT-HHHHHH CS
                             TPR_1   11 yfklgkydeAle 22  
                                        ++ + +y+ A+e
  gi|330507412|ref|YP_004383840.1| 1161 FLAQDDYQRAEE 1172
                                        666777777765 PP

  == domain 27  score: -0.5 bits;  conditional E-value: 2.4
                                        HHHHHHHTT-HHHHHHHH CS
                             TPR_1    7 lGnayfklgkydeAleyy 24  
                                        l+ +  + gk +eA ++y
  gi|330507412|ref|YP_004383840.1| 1197 LAECEARTGKKEEARADY 1214
                                        67888899*********9 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.5    0.0014      0.71       2      30 ..      74     102 ..      73     104 .. 0.91
   2 !   12.3   1.1   0.00029      0.15       2      28 ..     114     140 ..     113     142 .. 0.93
   3 !   11.0   0.0   0.00074      0.38       2      29 ..     154     181 ..     153     183 .. 0.92
   4 !    9.7   0.1     0.002         1       5      29 ..     196     220 ..     193     223 .. 0.90
   5 ?   -0.6   0.0       3.7   1.9e+03       1      25 [.     232     256 ..     232     259 .. 0.83
   6 !   15.1   1.0   3.5e-05     0.018       4      29 ..     275     300 ..     272     303 .. 0.90
   7 !   15.7   0.0   2.2e-05     0.011       2      33 ..     312     343 ..     311     344 .. 0.93
   8 ?    6.5   0.0     0.021        11       1      31 [.     351     381 ..     351     384 .. 0.89
   9 !   16.5   0.1   1.3e-05    0.0065       1      31 [.     391     421 ..     391     423 .. 0.95
  10 !    8.8   0.1    0.0038         2       1      27 [.     431     457 ..     431     460 .. 0.93
  11 ?    3.4   0.0      0.19        99       5      29 ..     475     499 ..     472     503 .. 0.90
  12 !    7.8   0.1    0.0079       4.1       7      33 ..     517     543 ..     515     544 .. 0.88
  13 ?    6.5   0.4      0.02        10       3      29 ..     553     579 ..     551     581 .. 0.90
  14 !    8.7   0.0     0.004       2.1       4      28 ..     594     618 ..     591     619 .. 0.90
  15 !   19.1   0.4   1.9e-06   0.00096       1      30 [.     631     660 ..     631     661 .. 0.94
  16 ?    5.9   0.1     0.031        16      10      29 ..     680     699 ..     679     702 .. 0.90
  17 !   22.0   0.2   2.2e-07   0.00011       2      31 ..     712     741 ..     711     744 .. 0.90
  18 !   15.4   0.2   2.9e-05     0.015       5      29 ..     755     779 ..     752     779 .. 0.91
  19 !   13.7   0.0   9.6e-05     0.049       2      32 ..     792     822 ..     791     824 .. 0.89
  20 !   22.5   0.4   1.5e-07   7.7e-05       1      32 [.     831     862 ..     831     864 .. 0.92
  21 !   15.2   0.0   3.3e-05     0.017       2      30 ..     912     940 ..     911     943 .. 0.91
  22 !   13.6   0.0   0.00011     0.055       3      31 ..     953     981 ..     951     984 .. 0.92
  23 ?    7.0   0.0     0.014       7.1       3      28 ..     993    1018 ..     991    1020 .. 0.88
  24 !    8.1   0.1    0.0061       3.1      17      32 ..    1087    1102 ..    1074    1104 .. 0.92
  25 !   12.2   0.1    0.0003      0.15       2      30 ..    1112    1140 ..    1111    1143 .. 0.89
  26 ?   -1.7   0.1       8.5   4.4e+03      12      22 ..    1162    1172 ..    1159    1173 .. 0.77
  27 !    8.3   0.5    0.0054       2.8       7      31 ..    1197    1221 ..    1193    1223 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0014
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAlel 30 
                                       +a++nlG+++ +l  ++ A+e++  A  l
  gi|330507412|ref|YP_004383840.1|  74 QAWFNLGRLAHHLFFHQAAIEYYSNASDL 102
                                       69*********************998665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00029
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAl 28 
                                        +l +lG +y +  d+++A +++ekAl
  gi|330507412|ref|YP_004383840.1| 114 SILLCLGALYGEEEDWARACQCYEKAL 140
                                       57899*********************9 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00074
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                       ++l +lG+a + +g+y +A  ++ + le
  gi|330507412|ref|YP_004383840.1| 154 QVLERLGRARRLQGEYHQAQICYSRILE 181
                                       6799********************9997 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.002
                             TPR_2   5 ynlGlayyklgdyeeAleafekAle 29 
                                        nl++++  +gd e+A+++++  l+
  gi|330507412|ref|YP_004383840.1| 196 SNLAELCQIQGDMEKAEKLYQTILK 220
                                       69*******************9998 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 3.7
                             TPR_2   1 aealynlGlayyklgdyeeAleafe 25 
                                       a+al  l+ +y + g+ ++A   ++
  gi|330507412|ref|YP_004383840.1| 232 ARALASLASIYSQTGNGKRAQISLQ 256
                                       689999**********988876665 PP

  == domain 6  score: 15.1 bits;  conditional E-value: 3.5e-05
                             TPR_2   4 lynlGlayyklgdyeeAleafekAle 29 
                                        ++l+++y++ g+++eAle++ ++l+
  gi|330507412|ref|YP_004383840.1| 275 QCRLADIYFHEGRLKEALELYGRSLA 300
                                       689*******************9996 PP

  == domain 7  score: 15.7 bits;  conditional E-value: 2.2e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +al+++G++ ++ g++  A++++++A+++  +
  gi|330507412|ref|YP_004383840.1| 312 KALCRMGQCFLEDGNWTLAEDHLQRAIAIMKE 343
                                       799*************************9876 PP

  == domain 8  score: 6.5 bits;  conditional E-value: 0.021
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       a+al  l+ ++ k+g++e Al++ +++l++ 
  gi|330507412|ref|YP_004383840.1| 351 ARALVILAGVHHKQGQLEMALQCSRESLKIR 381
                                       6789999****************99999875 PP

  == domain 9  score: 16.5 bits;  conditional E-value: 1.3e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       aeal+++++++    d+ eA+e++++A  l 
  gi|330507412|ref|YP_004383840.1| 391 AEALNCIARICCDCSDWPEAIECYQRAADLF 421
                                       79*************************9885 PP

  == domain 10  score: 8.8 bits;  conditional E-value: 0.0038
                             TPR_2   1 aealynlGlayyklgdyeeAleafekA 27 
                                       aeal nlG +y  +gd++ Al+ +  A
  gi|330507412|ref|YP_004383840.1| 431 AEALSNLGGVYHLKGDLDVALQMYSHA 457
                                       79********************99887 PP

  == domain 11  score: 3.4 bits;  conditional E-value: 0.19
                             TPR_2   5 ynlGlayyklgdyeeAleafekAle 29 
                                        n+Gl+y  +gd+  A e++ek+++
  gi|330507412|ref|YP_004383840.1| 475 SNIGLVYQSRGDLHLAGEFLEKSIA 499
                                       799******************9986 PP

  == domain 12  score: 7.8 bits;  conditional E-value: 0.0079
                             TPR_2   7 lGlayyklgdyeeAleafekAleldPn 33 
                                       lGl+y   g++++A  +fe A +  ++
  gi|330507412|ref|YP_004383840.1| 517 LGLIYQLGGEWDQAQSCFEGAARAFED 543
                                       8******************99887666 PP

  == domain 13  score: 6.5 bits;  conditional E-value: 0.02
                             TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                                       a +nlG++y  +gd+  A+ ++++ le
  gi|330507412|ref|YP_004383840.1| 553 AENNLGNLYSDRGDLMHAILCYRQGLE 579
                                       5589********************998 PP

  == domain 14  score: 8.7 bits;  conditional E-value: 0.004
                             TPR_2   4 lynlGlayyklgdyeeAleafekAl 28 
                                       l nl+ +y+++g+ e+A+e++++++
  gi|330507412|ref|YP_004383840.1| 594 LGNLAGVYLQSGEEERAEELYQQSI 618
                                       67999*****************987 PP

  == domain 15  score: 19.1 bits;  conditional E-value: 1.9e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a+ ly l+++ +++gd+e Ale+++k+l l
  gi|330507412|ref|YP_004383840.1| 631 ARSLYGLARSMAERGDLEGALECYRKCLDL 660
                                       6789************************98 PP

  == domain 16  score: 5.9 bits;  conditional E-value: 0.031
                             TPR_2  10 ayyklgdyeeAleafekAle 29 
                                       +++++g+++eAl  + ++le
  gi|330507412|ref|YP_004383840.1| 680 LLLRRGRWQEALTRYAQVLE 699
                                       789*************9998 PP

  == domain 17  score: 22.0 bits;  conditional E-value: 2.2e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                        + ++lG++++ lg+++eAle+++++l++ 
  gi|330507412|ref|YP_004383840.1| 712 AVQCALGNLHADLGQWDEALEDYNESLAIM 741
                                       67789**********************986 PP

  == domain 18  score: 15.4 bits;  conditional E-value: 2.9e-05
                             TPR_2   5 ynlGlayyklgdyeeAleafekAle 29 
                                       +nlG+ +y++gd++ Ale ++ +le
  gi|330507412|ref|YP_004383840.1| 755 NNLGNMCYRQGDWAAALENYRLSLE 779
                                       89******************98775 PP

  == domain 19  score: 13.7 bits;  conditional E-value: 9.6e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                        +l n + ++yk+g++++Al+ + k+l+l +
  gi|330507412|ref|YP_004383840.1| 792 SVLSNVAGLCYKRGQWADALDSYSKSLSLFE 822
                                       578899999*******************986 PP

  == domain 20  score: 22.5 bits;  conditional E-value: 1.5e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       a++l n+G++y ++g+ + A+e+f++Ale++ 
  gi|330507412|ref|YP_004383840.1| 831 AQVLGNMGNLYHRQGERDLAAEHFQRALEIYR 862
                                       56889************************985 PP

  == domain 21  score: 15.2 bits;  conditional E-value: 3.3e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAlel 30 
                                       e+l +l+ +y  +g+++eA++++++++e 
  gi|330507412|ref|YP_004383840.1| 912 EVLSALAGSYTDSGQWAEAIACYKRSVER 940
                                       78999********************9985 PP

  == domain 22  score: 13.6 bits;  conditional E-value: 0.00011
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                       +l+n++l+y  +gd+++A+ +f+ Al + 
  gi|330507412|ref|YP_004383840.1| 953 VLFNMALVYKDMGDLNRARTLFDVALDIF 981
                                       79************************986 PP

  == domain 23  score: 7.0 bits;  conditional E-value: 0.014
                             TPR_2    3 alynlGlayyklgdyeeAleafekAl 28  
                                        a  nlG +  ++g+ +eA+e+f +++
  gi|330507412|ref|YP_004383840.1|  993 AKLNLGIISGQMGRSDEAIELFSQSI 1018
                                        5679******************9875 PP

  == domain 24  score: 8.1 bits;  conditional E-value: 0.0061
                             TPR_2   17 yeeAleafekAleldP 32  
                                        y eA+ +fekAl+l  
  gi|330507412|ref|YP_004383840.1| 1087 YPEAKSCFEKALALSR 1102
                                        89***********975 PP

  == domain 25  score: 12.2 bits;  conditional E-value: 0.0003
                             TPR_2    2 ealynlGlayyklgdyeeAleafekAlel 30  
                                        +a   lG++++++gdye+Al+ +++Al +
  gi|330507412|ref|YP_004383840.1| 1112 KAISSLGRLALASGDYEDALRRMKQALVI 1140
                                        67778*********************966 PP

  == domain 26  score: -1.7 bits;  conditional E-value: 8.5
                             TPR_2   12 yklgdyeeAle 22  
                                        ++++dy++A+e
  gi|330507412|ref|YP_004383840.1| 1162 LAQDDYQRAEE 1172
                                        67899999976 PP

  == domain 27  score: 8.3 bits;  conditional E-value: 0.0054
                             TPR_2    7 lGlayyklgdyeeAleafekAleld 31  
                                        l+++ ++ g+ eeA++++  Al+l+
  gi|330507412|ref|YP_004383840.1| 1197 LAECEARTGKKEEARADYAGALRLA 1221
                                        8999******************996 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2      0.18        92       1      24 [.      75      98 ..      75     111 .. 0.84
   2 !   13.0   0.1   0.00016      0.08       5      29 ..     119     144 ..     116     150 .. 0.89
   3 !    9.9   0.1    0.0015      0.79       2      29 ..     156     184 ..     155     190 .. 0.83
   4 !   12.7   0.0    0.0002       0.1       3      26 ..     196     219 ..     194     228 .. 0.84
   5 ?    4.7   0.1      0.07        36       1      18 [.     234     251 ..     234     269 .. 0.88
   6 !   16.7   0.3   1.1e-05    0.0054       3      28 ..     276     302 ..     276     305 .. 0.91
   7 !   11.8   0.0   0.00038       0.2       1      30 [.     313     342 ..     313     348 .. 0.91
   8 ?    5.8   0.0     0.031        16       1      31 [.     353     383 ..     353     389 .. 0.87
   9 !   18.5   0.0   2.8e-06    0.0014       5      27 ..     397     419 ..     393     428 .. 0.83
  10 ?    4.0   0.0      0.12        63       1      22 [.     433     454 ..     433     458 .. 0.92
  11 !    9.8   0.0    0.0017      0.85       4      34 ..     476     506 ..     475     508 .. 0.94
  12 !   10.7   0.1   0.00087      0.45       4      27 ..     516     540 ..     515     548 .. 0.83
  13 !   10.7   0.1   0.00082      0.42       3      29 ..     555     579 ..     555     588 .. 0.89
  14 !   15.6   0.1   2.4e-05     0.012       1      33 [.     593     625 ..     593     628 .. 0.85
  15 !    8.2   0.2    0.0054       2.8       1      28 [.     633     660 ..     633     663 .. 0.89
  16 !   14.4   0.4   5.5e-05     0.028       2      32 ..     674     705 ..     673     708 .. 0.85
  17 !   18.4   0.2   2.9e-06    0.0015       3      34 ..     715     746 ..     715     748 .. 0.91
  18 !   15.4   0.1   2.7e-05     0.014       3      27 ..     755     779 ..     753     788 .. 0.89
  19 ?    6.3   0.0     0.021        11       2      30 ..     794     822 ..     793     828 .. 0.84
  20 !   22.5   0.2   1.5e-07   7.6e-05       2      32 ..     834     864 ..     833     869 .. 0.88
  21 !   16.7   0.0     1e-05    0.0053       2      26 ..     914     938 ..     913     947 .. 0.88
  22 ?    7.2   0.0     0.011       5.5       2      27 ..     954     979 ..     953     985 .. 0.87
  23 !    7.6   0.0    0.0084       4.3       3      28 ..     995    1020 ..     995    1025 .. 0.88
  24 ?    2.1   0.0      0.48   2.4e+02      15      30 ..    1087    1102 ..    1086    1107 .. 0.84
  25 !   11.1   0.1   0.00063      0.32       1      27 [.    1113    1139 ..    1113    1145 .. 0.90
  26 ?   -0.7   0.0       3.7   1.9e+03       6      20 ..    1158    1172 ..    1153    1173 .. 0.82
  27 ?   -1.0   0.1       4.6   2.3e+03      16      28 ..    1238    1248 ..    1237    1267 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.18
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeq 24
                                      a++nL+rl + l  ++ Aie+y  
  gi|330507412|ref|YP_004383840.1| 75 AWFNLGRLAHHLFFHQAAIEYYSN 98
                                      789*******************76 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00016
                             TPR_7   5 LarlysrlGdyeeAielyeqsL.alt 29 
                                       L+ ly ++ d+++A ++ye++L a++
  gi|330507412|ref|YP_004383840.1| 119 LGALYGEEEDWARACQCYEKALvAID 144
                                       899*****************998887 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0015
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsL.alt 29 
                                       L +L+r+++ +G+y +A  +y + L +l+
  gi|330507412|ref|YP_004383840.1| 156 LERLGRARRLQGEYHQAQICYSRILeVLD 184
                                       679******************99885544 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.0002
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsL 26 
                                       +nLa+l++ +Gd+e+A++ly+  L
  gi|330507412|ref|YP_004383840.1| 196 SNLAELCQIQGDMEKAEKLYQTIL 219
                                       7*******************9855 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.07
                             TPR_7   1 aLlnLarlysrlGdyeeA 18 
                                       aL  La++ys+ G+ ++A
  gi|330507412|ref|YP_004383840.1| 234 ALASLASIYSQTGNGKRA 251
                                       7999*********98888 PP

  == domain 6  score: 16.7 bits;  conditional E-value: 1.1e-05
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsL.al 28 
                                       ++La++y+ +G+ +eA+ely +sL al
  gi|330507412|ref|YP_004383840.1| 276 CRLADIYFHEGRLKEALELYGRSLaAL 302
                                       68**********************555 PP

  == domain 7  score: 11.8 bits;  conditional E-value: 0.00038
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       aL+++++++ ++G++  A++++++++a+ k
  gi|330507412|ref|YP_004383840.1| 313 ALCRMGQCFLEDGNWTLAEDHLQRAIAIMK 342
                                       89**********************888765 PP

  == domain 8  score: 5.8 bits;  conditional E-value: 0.031
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       aL+ La +++++G+ e A+++ ++sL ++++
  gi|330507412|ref|YP_004383840.1| 353 ALVILAGVHHKQGQLEMALQCSRESLKIRER 383
                                       6888*****************9999988864 PP

  == domain 9  score: 18.5 bits;  conditional E-value: 2.8e-06
                             TPR_7   5 LarlysrlGdyeeAielyeqsLa 27 
                                       +ar+++++ d+ eAie+y+++  
  gi|330507412|ref|YP_004383840.1| 397 IARICCDCSDWPEAIECYQRAAD 419
                                       8*******************654 PP

  == domain 10  score: 4.0 bits;  conditional E-value: 0.12
                             TPR_7   1 aLlnLarlysrlGdyeeAiely 22 
                                       aL+nL+ +y+  Gd + A++ y
  gi|330507412|ref|YP_004383840.1| 433 ALSNLGGVYHLKGDLDVALQMY 454
                                       79***************99998 PP

  == domain 11  score: 9.8 bits;  conditional E-value: 0.0017
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       n++ +y+++Gd   A e++e+s+a+ +d +d
  gi|330507412|ref|YP_004383840.1| 476 NIGLVYQSRGDLHLAGEFLEKSIATKEDLGD 506
                                       99*************************9987 PP

  == domain 12  score: 10.7 bits;  conditional E-value: 0.00087
                             TPR_7   4 nLarlysrlGdyeeAielyeqsL.a 27 
                                        L+ +y+  G++++A +++e +  a
  gi|330507412|ref|YP_004383840.1| 516 SLGLIYQLGGEWDQAQSCFEGAArA 540
                                       79******************97644 PP

  == domain 13  score: 10.7 bits;  conditional E-value: 0.00082
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLalt 29 
                                       +nL++lys++Gd   Ai +y+q  +l+
  gi|330507412|ref|YP_004383840.1| 555 NNLGNLYSDRGDLMHAILCYRQ--GLE 579
                                       7*********************..665 PP

  == domain 14  score: 15.6 bits;  conditional E-value: 2.4e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       +L nLa +y + G+ e+A+ely+qs+   ++ +
  gi|330507412|ref|YP_004383840.1| 593 TLGNLAGVYLQSGEEERAEELYQQSIDGFRELG 625
                                       799*********************986555555 PP

  == domain 15  score: 8.2 bits;  conditional E-value: 0.0054
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       +L+ Lar   ++Gd e A+e+y+++L l
  gi|330507412|ref|YP_004383840.1| 633 SLYGLARSMAERGDLEGALECYRKCLDL 660
                                       68889999999*************8754 PP

  == domain 16  score: 14.4 bits;  conditional E-value: 5.5e-05
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsL.altkdp 32 
                                       L  + +l  r+G+++eA++ y q+L al++++
  gi|330507412|ref|YP_004383840.1| 674 LESMVNLLLRRGRWQEALTRYAQVLeALRSRD 705
                                       66788999*****************8887654 PP

  == domain 17  score: 18.4 bits;  conditional E-value: 2.9e-06
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       ++L++l+ +lG+++eA+e y +sLa+ +  +d
  gi|330507412|ref|YP_004383840.1| 715 CALGNLHADLGQWDEALEDYNESLAIMEGLGD 746
                                       79***********************9987776 PP

  == domain 18  score: 15.4 bits;  conditional E-value: 2.7e-05
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLa 27 
                                       +nL++++ r+Gd++ A+e y+ sL+
  gi|330507412|ref|YP_004383840.1| 755 NNLGNMCYRQGDWAAALENYRLSLE 779
                                       8*********************996 PP

  == domain 19  score: 6.3 bits;  conditional E-value: 0.021
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       L+n a l+ ++G++++A++ y +sL l +
  gi|330507412|ref|YP_004383840.1| 794 LSNVAGLCYKRGQWADALDSYSKSLSLFE 822
                                       889999*****************996655 PP

  == domain 20  score: 22.5 bits;  conditional E-value: 1.5e-07
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       L n+++ly+r+G+++ A+e+++++L++ ++ 
  gi|330507412|ref|YP_004383840.1| 834 LGNMGNLYHRQGERDLAAEHFQRALEIYRRL 864
                                       89*********************99987665 PP

  == domain 21  score: 16.7 bits;  conditional E-value: 1e-05
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsL 26 
                                       L++La  y + G+++eAi +y++s 
  gi|330507412|ref|YP_004383840.1| 914 LSALAGSYTDSGQWAEAIACYKRSV 938
                                       89*********************65 PP

  == domain 22  score: 7.2 bits;  conditional E-value: 0.011
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLa 27 
                                       L+n+a +y ++Gd  +A +l+  +L 
  gi|330507412|ref|YP_004383840.1| 954 LFNMALVYKDMGDLNRARTLFDVALD 979
                                       89******************988665 PP

  == domain 23  score: 7.6 bits;  conditional E-value: 0.0084
                             TPR_7    3 lnLarlysrlGdyeeAielyeqsLal 28  
                                        lnL+ +  ++G+ +eAiel+ qs+++
  gi|330507412|ref|YP_004383840.1|  995 LNLGIISGQMGRSDEAIELFSQSIGI 1020
                                        69******************998765 PP

  == domain 24  score: 2.1 bits;  conditional E-value: 0.48
                             TPR_7   15 yeeAielyeqsLaltk 30  
                                        y eA +++e++Lal +
  gi|330507412|ref|YP_004383840.1| 1087 YPEAKSCFEKALALSR 1102
                                        77999*****999876 PP

  == domain 25  score: 11.1 bits;  conditional E-value: 0.00063
                             TPR_7    1 aLlnLarlysrlGdyeeAielyeqsLa 27  
                                        a++ L+rl  + Gdye+A++  +q+L+
  gi|330507412|ref|YP_004383840.1| 1113 AISSLGRLALASGDYEDALRRMKQALV 1139
                                        5789********************775 PP

  == domain 26  score: -0.7 bits;  conditional E-value: 3.7
                             TPR_7    6 arlysrlGdyeeAie 20  
                                          l+ ++ dy++A+e
  gi|330507412|ref|YP_004383840.1| 1158 TLLFLAQDDYQRAEE 1172
                                        56788999*****98 PP

  == domain 27  score: -1.0 bits;  conditional E-value: 4.6
                             TPR_7   16 eeAielyeqsLal 28  
                                        e+Aie++e+  + 
  gi|330507412|ref|YP_004383840.1| 1238 EKAIEFLEA--EA 1248
                                        89******9..54 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       6.1   3.1e+03       7      25 ..      78      96 ..      78     106 .. 0.90
   2 ?    5.9   0.2     0.023        12       1      29 [.     112     140 ..     112     142 .. 0.92
   3 ?   -1.6   0.1       5.6   2.9e+03       7      22 ..     158     173 ..     155     182 .. 0.79
   4 ?    6.8   0.1     0.012       6.2       4      30 ..     194     220 ..     191     223 .. 0.87
   5 ?    6.1   0.3     0.021        11       2      21 ..     232     251 ..     231     258 .. 0.91
   6 !   10.2   0.4    0.0011      0.54       7      34 ..     277     304 ..     272     306 .. 0.88
   7 ?    4.1   0.0     0.088        45      15      34 ..     324     343 ..     322     346 .. 0.90
   8 !   11.2   0.1   0.00053      0.27       2      34 ..     351     383 ..     350     385 .. 0.93
   9 ?    4.7   0.0     0.056        29       2      29 ..     391     418 ..     390     420 .. 0.93
  10 !   11.0   0.1   0.00061      0.31       2      30 ..     431     459 ..     430     469 .. 0.92
  11 !   12.8   0.0   0.00016     0.081       3      34 ..     472     503 ..     471     505 .. 0.93
  12 ?    0.6   0.1       1.1   5.6e+02       7      29 ..     516     538 ..     511     542 .. 0.87
  13 !   12.9   0.7   0.00015     0.077       6      40 ..     555     588 ..     550     590 .. 0.90
  14 !   17.7   0.1   4.6e-06    0.0024       2      34 ..     591     623 ..     590     626 .. 0.91
  15 !   10.1   0.1    0.0011      0.57       2      31 ..     631     660 ..     631     666 .. 0.93
  16 !    9.1   0.5    0.0024       1.2       5      32 ..     674     701 ..     671     703 .. 0.86
  17 !   18.3   0.2     3e-06    0.0015       1      33 [.     710     742 ..     710     744 .. 0.93
  18 !   15.4   0.4   2.5e-05     0.013       4      30 ..     753     779 ..     750     780 .. 0.91
  19 !    7.2   0.0    0.0094       4.8       2      34 ..     791     823 ..     791     826 .. 0.90
  20 !   26.3   0.9   9.2e-09   4.7e-06       2      35 ..     831     864 ..     830     868 .. 0.94
  21 !    9.9   0.0    0.0013      0.65       5      31 ..     914     940 ..     912     943 .. 0.92
  22 !    9.7   0.0    0.0015      0.77       7      31 ..     956     980 ..     956     984 .. 0.92
  23 !   11.7   0.0   0.00037      0.19       1      31 [.     990    1020 ..     990    1024 .. 0.90
  24 ?    1.4   0.0      0.62   3.2e+02      18      35 ..    1087    1104 ..    1086    1105 .. 0.90
  25 !    7.2   0.1    0.0091       4.6       4      29 ..    1113    1138 ..    1111    1143 .. 0.81
  26 ?   -2.1   0.2       7.6   3.9e+03      14      26 ..    1163    1174 ..    1160    1187 .. 0.74
  27 ?    1.6   0.4      0.55   2.8e+02      14      31 ..    1203    1220 ..    1196    1223 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.1
                            TPR_10  7 NLanalrqrgrydeAeall 25
                                      NL+++ ++++ +++A +++
  gi|330507412|ref|YP_004383840.1| 78 NLGRLAHHLFFHQAAIEYY 96
                                      9**************9998 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.023
                            TPR_10   1 tAsslnNLanalrqrgrydeAealleeal 29 
                                       +As+l  L++++ +  ++++A + +e+al
  gi|330507412|ref|YP_004383840.1| 112 LASILLCLGALYGEEEDWARACQCYEKAL 140
                                       5899999********************98 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5.6
                            TPR_10   7 NLanalrqrgrydeAe 22 
                                        L++a r +g+y++A 
  gi|330507412|ref|YP_004383840.1| 158 RLGRARRLQGEYHQAQ 173
                                       58999999****9996 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.012
                            TPR_10   4 slnNLanalrqrgrydeAealleeala 30 
                                       + +NLa + + +g+ ++Ae+l++  l 
  gi|330507412|ref|YP_004383840.1| 194 ATSNLAELCQIQGDMEKAEKLYQTILK 220
                                       568*******************98776 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.021
                            TPR_10   2 AsslnNLanalrqrgrydeA 21 
                                       A++l  La +++q+g++++A
  gi|330507412|ref|YP_004383840.1| 232 ARALASLASIYSQTGNGKRA 251
                                       899**************998 PP

  == domain 6  score: 10.2 bits;  conditional E-value: 0.0011
                            TPR_10   7 NLanalrqrgrydeAealleealairrr 34 
                                        La ++++ gr++eA++l+ ++la+ ++
  gi|330507412|ref|YP_004383840.1| 277 RLADIYFHEGRLKEALELYGRSLAALQK 304
                                       6999*******************98775 PP

  == domain 7  score: 4.1 bits;  conditional E-value: 0.088
                            TPR_10  15 rgrydeAealleealairrr 34 
                                        g+++ Ae++l++a+ai ++
  gi|330507412|ref|YP_004383840.1| 324 DGNWTLAEDHLQRAIAIMKE 343
                                       599999***********998 PP

  == domain 8  score: 11.2 bits;  conditional E-value: 0.00053
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrr 34 
                                       A++l  La +++++g+++ A++  +e+l ir+r
  gi|330507412|ref|YP_004383840.1| 351 ARALVILAGVHHKQGQLEMALQCSRESLKIRER 383
                                       788888*************************98 PP

  == domain 9  score: 4.7 bits;  conditional E-value: 0.056
                            TPR_10   2 AsslnNLanalrqrgrydeAealleeal 29 
                                       A +ln +a++ ++  ++ eA + +++a 
  gi|330507412|ref|YP_004383840.1| 391 AEALNCIARICCDCSDWPEAIECYQRAA 418
                                       889**********************996 PP

  == domain 10  score: 11.0 bits;  conditional E-value: 0.00061
                            TPR_10   2 AsslnNLanalrqrgrydeAealleeala 30 
                                       A +l+NL+ +++  g++d A++++ +a++
  gi|330507412|ref|YP_004383840.1| 431 AEALSNLGGVYHLKGDLDVALQMYSHAYN 459
                                       789********************988876 PP

  == domain 11  score: 12.8 bits;  conditional E-value: 0.00016
                            TPR_10   3 sslnNLanalrqrgrydeAealleealairrr 34 
                                       + ++N++ ++++rg+++ A ++le+++a+ + 
  gi|330507412|ref|YP_004383840.1| 472 MVQSNIGLVYQSRGDLHLAGEFLEKSIATKED 503
                                       679*************************9875 PP

  == domain 12  score: 0.6 bits;  conditional E-value: 1.1
                            TPR_10   7 NLanalrqrgrydeAealleeal 29 
                                        L+ +++  g++d+A   +e a 
  gi|330507412|ref|YP_004383840.1| 516 SLGLIYQLGGEWDQAQSCFEGAA 538
                                       69*************99998775 PP

  == domain 13  score: 12.9 bits;  conditional E-value: 0.00015
                            TPR_10   6 nNLanalrqrgrydeAealleealairrrllGpdH 40 
                                       nNL+n++++rg++  A   +++ l++ rr+l++ H
  gi|330507412|ref|YP_004383840.1| 555 NNLGNLYSDRGDLMHAILCYRQGLEA-RRVLNDGH 588
                                       9*************************.88888888 PP

  == domain 14  score: 17.7 bits;  conditional E-value: 4.6e-06
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrr 34 
                                       A +l NLa ++ q g+ ++Ae+l++++++  r+
  gi|330507412|ref|YP_004383840.1| 591 AVTLGNLAGVYLQSGEEERAEELYQQSIDGFRE 623
                                       789************************987665 PP

  == domain 15  score: 10.1 bits;  conditional E-value: 0.0011
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealai 31 
                                       A+sl  La+   +rg++++A++ ++++l++
  gi|330507412|ref|YP_004383840.1| 631 ARSLYGLARSMAERGDLEGALECYRKCLDL 660
                                       789999**********************87 PP

  == domain 16  score: 9.1 bits;  conditional E-value: 0.0024
                            TPR_10   5 lnNLanalrqrgrydeAealleealair 32 
                                       l  + n+l +rgr++eA+  + ++l++ 
  gi|330507412|ref|YP_004383840.1| 674 LESMVNLLLRRGRWQEALTRYAQVLEAL 701
                                       6667899******************975 PP

  == domain 17  score: 18.3 bits;  conditional E-value: 3e-06
                            TPR_10   1 tAsslnNLanalrqrgrydeAealleealairr 33 
                                       +A+ +  L+n++ ++g++deA++++ e+lai +
  gi|330507412|ref|YP_004383840.1| 710 VAAVQCALGNLHADLGQWDEALEDYNESLAIME 742
                                       5888999***********************976 PP

  == domain 18  score: 15.4 bits;  conditional E-value: 2.5e-05
                            TPR_10   4 slnNLanalrqrgrydeAealleeala 30 
                                       ++nNL+n+ +++g++++A++ ++ +l+
  gi|330507412|ref|YP_004383840.1| 753 ARNNLGNMCYRQGDWAAALENYRLSLE 779
                                       79******************9998775 PP

  == domain 19  score: 7.2 bits;  conditional E-value: 0.0094
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrr 34 
                                       As l+N a + ++rg++++A++ + ++l++ ++
  gi|330507412|ref|YP_004383840.1| 791 ASVLSNVAGLCYKRGQWADALDSYSKSLSLFEK 823
                                       789******************999999988776 PP

  == domain 20  score: 26.3 bits;  conditional E-value: 9.2e-09
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrl 35 
                                       A  l N++n+++++g++d A +++++al+i+rrl
  gi|330507412|ref|YP_004383840.1| 831 AQVLGNMGNLYHRQGERDLAAEHFQRALEIYRRL 864
                                       77899****************************8 PP

  == domain 21  score: 9.9 bits;  conditional E-value: 0.0013
                            TPR_10   5 lnNLanalrqrgrydeAealleealai 31 
                                       l+ La  +++ g+++eA a +++++++
  gi|330507412|ref|YP_004383840.1| 914 LSALAGSYTDSGQWAEAIACYKRSVER 940
                                       789********************9985 PP

  == domain 22  score: 9.7 bits;  conditional E-value: 0.0015
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N+a ++ ++g++++A+ l++ al+i
  gi|330507412|ref|YP_004383840.1| 956 NMALVYKDMGDLNRARTLFDVALDI 980
                                       99*******************9998 PP

  == domain 23  score: 11.7 bits;  conditional E-value: 0.00037
                            TPR_10    1 tAsslnNLanalrqrgrydeAealleealai 31  
                                        +As+  NL+++  q+gr deA +l+ +++ i
  gi|330507412|ref|YP_004383840.1|  990 VASAKLNLGIISGQMGRSDEAIELFSQSIGI 1020
                                        69999*******************9988866 PP

  == domain 24  score: 1.4 bits;  conditional E-value: 0.62
                            TPR_10   18 ydeAealleealairrrl 35  
                                        y eA   +e+ala+ r+l
  gi|330507412|ref|YP_004383840.1| 1087 YPEAKSCFEKALALSRKL 1104
                                        679999********9997 PP

  == domain 25  score: 7.2 bits;  conditional E-value: 0.0091
                            TPR_10    4 slnNLanalrqrgrydeAealleeal 29  
                                        + + L+++  + g+y++A++ +++al
  gi|330507412|ref|YP_004383840.1| 1113 AISSLGRLALASGDYEDALRRMKQAL 1138
                                        67888999999999999999998887 PP

  == domain 26  score: -2.1 bits;  conditional E-value: 7.6
                            TPR_10   14 qrgrydeAealle 26  
                                        ++ +y++Ae++  
  gi|330507412|ref|YP_004383840.1| 1163 AQDDYQRAEEM-A 1174
                                        68899999998.3 PP

  == domain 27  score: 1.6 bits;  conditional E-value: 0.55
                            TPR_10   14 qrgrydeAealleealai 31  
                                        ++g+ +eA+a++  al++
  gi|330507412|ref|YP_004383840.1| 1203 RTGKKEEARADYAGALRL 1220
                                        789*********999986 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1    0.0075       3.8      92     181 ..      91     179 ..      83     183 .. 0.74
   2 !   26.5   0.6   7.5e-09   3.8e-06      42     174 ..     199     330 ..     187     343 .. 0.87
   3 !   34.6   0.4   2.5e-11   1.3e-08      38     181 ..     314     457 ..     306     463 .. 0.87
   4 !   33.6   0.2   5.1e-11   2.6e-08      79     177 ..     391     493 ..     372     500 .. 0.78
   5 !   17.4   0.0   4.5e-06    0.0023      45     142 ..     481     578 ..     475     582 .. 0.90
   6 !   18.9   0.0   1.6e-06   0.00084      51     180 ..     607     736 ..     598     742 .. 0.90
   7 !    8.4   0.1    0.0025       1.3      86     178 ..     683     774 ..     666     794 .. 0.74
   8 !   27.5   0.2   3.9e-09     2e-06      51     179 ..     767     895 ..     758     908 .. 0.84
   9 !   25.7   0.0   1.4e-08   6.9e-06      82     180 ..     919    1016 ..     902    1019 .. 0.93
  10 !    8.3   0.1    0.0026       1.3      41     176 ..    1036    1172 ..    1029    1174 .. 0.84
  11 ?   -0.2   0.1         1   5.3e+02      59     105 ..    1195    1245 ..    1192    1275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0075
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT CS
                              SNAP  92 eAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsael 168
                                       +A+e +++A ++ +     +  A++   ++ ly +e +d+ +A+++YekA    ++ +   l  ++l+++      +
  gi|330507412|ref|YP_004383840.1|  91 AAIEYYSNASDLAQILSDDDSLASILLCLGALYGEE-EDWARACQCYEKALVAIDMAKRPRLLPQVLERLGRARRLQ 166
                                       455555555555444444455566677788888888.8999999999999888888888888888888888888888 PP

                                       T-HHHHHHHHHHH CS
                              SNAP 169 ekyekAieiyekv 181
                                       ++y++A   y+++
  gi|330507412|ref|YP_004383840.1| 167 GEYHQAQICYSRI 179
                                       8888888888776 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 7.5e-09
                                       HHHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                              SNAP  42 AnayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrfrraAklk 117
                                       A++ +++ ++e+A + ++ + + +e  +++  aa+a++  a++y+++ + ++A  +l++A +++++    + aA+++
  gi|330507412|ref|YP_004383840.1| 199 AELCQIQGDMEKAEKLYQTILKERELSDDPVGAARALASLASIYSQTgNGKRAQISLQSASHLLADLKDQSGAAEMQ 275
                                       666789999***********************************9998999************************** PP

                                       HHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHH CS
                              SNAP 118 keiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekA 174
                                         +a++y +e g+l++A+e Y +     ++    +la+k+l+++ +   e+++++ A
  gi|330507412|ref|YP_004383840.1| 276 CRLADIYFHE-GRLKEALELYGRSLAALQKG-HPSLASKALCRMGQCFLEDGNWTLA 330
                                       **********.************99988764.5677777777777777776666655 PP

  == domain 3  score: 34.6 bits;  conditional E-value: 2.5e-11
                                       HHHHHHHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHH.HHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHH CS
                              SNAP  38 yeqAAnayklakkweeAgeaflkaAecqeklkekdeaanayve.AakcykkvspeeAvealekAieiytekgrfrra 113
                                       +++ ++++  + +w+ A +  ++a ++ ++ k++++ a+a+v  A+   k+ + e A ++ +++ +i  ++  ++ +
  gi|330507412|ref|YP_004383840.1| 314 LCRMGQCFLEDGNWTLAEDHLQRAIAIMKEHKDSSSLARALVIlAGVHHKQGQLEMALQCSRESLKIRERSKDLSGS 390
                                       5666788888999999999999999999999999999998875266667777999********************** PP

                                       HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              SNAP 114 AklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiyekv 181
                                       A+  + ia ++ +  +d+++Aie+Y++Aa+l+ +++  ++a ++l ++  ++  +++++ A+++y++ 
  gi|330507412|ref|YP_004383840.1| 391 AEALNCIARICCDC-SDWPEAIECYQRAADLFMEMGEVTAAAEALSNLGGVYHLKGDLDVALQMYSHA 457
                                       **********9977.9******************9999999999999999999999999999999875 PP

  == domain 4  score: 33.6 bits;  conditional E-value: 5.1e-11
                                       HHHHHHHHHT.....-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT- CS
                              SNAP  79 veAakcykkv.....speeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeea 150
                                       +eA +c+ +      +  eA+e++++A+++++e+g ++ aA+   +++ +y  + gdl+ A+++Y +A + + q++ 
  gi|330507412|ref|YP_004383840.1| 391 AEALNCIARIccdcsDWPEAIECYQRAADLFMEMGEVTAAAEALSNLGGVYHLK-GDLDVALQMYSHAYNSFCQQGD 466
                                       5677776666554447779*********************************99.****************999988 PP

                                       HHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                              SNAP 151 kalankcllkvAelsaelekyekAiei 177
                                          a+ ++ ++  ++ + ++++ A e 
  gi|330507412|ref|YP_004383840.1| 467 RQGASMVQSNIGLVYQSRGDLHLAGEF 493
                                       877777777766666666666666555 PP

  == domain 5  score: 17.4 bits;  conditional E-value: 4.5e-06
                                       HHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              SNAP  45 yklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrfrraAklkkei 120
                                       y+ + +++ Age  +k  +++e+l+++  aa   +  + +y+   + ++A +++e A+  + ++g +r  A  ++++
  gi|330507412|ref|YP_004383840.1| 481 YQSRGDLHLAGEFLEKSIATKEDLGDQIGAAGNRLSLGLIYQLGgEWDQAQSCFEGAARAFEDNGDLRGLAAAENNL 557
                                       566667788999999999999999999999999999999999877999***************************** PP

                                       HHHHHHTT--HHHHHHHHHHHH CS
                              SNAP 121 aelyekelgdlekAieaYekAa 142
                                       ++ly +  gdl +Ai +Y++  
  gi|330507412|ref|YP_004383840.1| 558 GNLYSDR-GDLMHAILCYRQGL 578
                                       *****99.**********9975 PP

  == domain 6  score: 18.9 bits;  conditional E-value: 1.6e-06
                                       THHHHHHHHHHHHHHHH.TT-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              SNAP  51 weeAgeaflkaAecqek.lkekdeaanayveAakcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyek 126
                                        e+A e +++  +  ++  + + ea + y  A ++ ++ + e A e+++k+ ++ +  g  r   +  +++ +l+  
  gi|330507412|ref|YP_004383840.1| 607 EERAEELYQQSIDGFRElGDARGEARSLYGLARSMAERGDLEGALECYRKCLDLQIVGGDSRSMIEALESMVNLLLR 683
                                       5778888988888888845667788899999*********************************************9 PP

                                       TT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              SNAP 127 elgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiyek 180
                                         g++++A+  Y++  e  ++ +  ++   +++ + +l+a+l+++++A+e y++
  gi|330507412|ref|YP_004383840.1| 684 R-GRWQEALTRYAQVLEALRSRDDLSAVAAVQCALGNLHADLGQWDEALEDYNE 736
                                       9.*********************9999999999999**************9986 PP

  == domain 7  score: 8.4 bits;  conditional E-value: 0.0025
                                       HHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              SNAP  86 kkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvA 162
                                       ++ + +eA + + +  e + +++ ++  A  +  +++l  +  g++++A+e Y++   + e+ + + + + ++ ++ 
  gi|330507412|ref|YP_004383840.1| 683 RRGRWQEALTRYAQVLEALRSRDDLSAVAAVQCALGNLHADL-GQWDEALEDYNESLAIMEGLGDEYSVSVARNNLG 758
                                       555778899999999999999999999999999999988754.9999999999999888887666666666666666 PP

                                       HHHHHTT-HHHHHHHH CS
                              SNAP 163 elsaelekyekAieiy 178
                                       ++  +++++++A+e y
  gi|330507412|ref|YP_004383840.1| 759 NMCYRQGDWAAALENY 774
                                       6666666666666655 PP

  == domain 8  score: 27.5 bits;  conditional E-value: 3.9e-09
                                       THHHHHHHHHHHHHHHHTT-HHHHHHHHHH.HHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              SNAP  51 weeAgeaflkaAecqeklkekdeaanayve.AakcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyek 126
                                       w +A e +    e   k+++ ++ a+ + + A+ cyk+ + ++A ++++k+ +++ + +     A+   ++++ly  
  gi|330507412|ref|YP_004383840.1| 767 WAAALENYRLSLEGFGKAGDMESEASVLSNvAGLCYKRGQWADALDSYSKSLSLFEKLEDSAGIAQVLGNMGNLYHR 843
                                       5555555655555566666666666666654999******************************************* PP

                                       TT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                              SNAP 127 elgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiye 179
                                       + g+ + A e++++A e+y+  + +a a +++  + ++ a  ++ +  ie y+
  gi|330507412|ref|YP_004383840.1| 844 Q-GERDLAAEHFQRALEIYRRLKDQAGAAEMQASIDMIRAGRGEISPDIEEYK 895
                                       *.******************999999999999988888888887777777776 PP

  == domain 9  score: 25.7 bits;  conditional E-value: 1.4e-08
                                        HHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHH CS
                              SNAP   82 akcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalank 156 
                                        ++ + + + +eA++++++++e + + g + + ++  +++a +y++  gdl++A   ++ A +++++ +a     +
  gi|330507412|ref|YP_004383840.1|  919 GSYTDSGQWAEAIACYKRSVERFDQTGEVYNRGQVLFNMALVYKDM-GDLNRARTLFDVALDIFQDLDALPCVAS 992 
                                        5555667999*********************************977.**************************** PP

                                        HHHHHHHHHHHTT-HHHHHHHHHH CS
                              SNAP  157 cllkvAelsaelekyekAieiyek 180 
                                        ++l++  +s ++++ ++Aie++++
  gi|330507412|ref|YP_004383840.1|  993 AKLNLGIISGQMGRSDEAIELFSQ 1016
                                        **********************87 PP

  == domain 10  score: 8.3 bits;  conditional E-value: 0.0026
                                        HHHHHHHTT-THHHHHHHHHHHHHHHH.TT-HHHHHHHHHHHHH.HHHHT-HHHHHHHHHHHHHHHHHTT-HHHH CS
                              SNAP   41 AAnayklakkweeAgeaflkaAecqek.lkekdeaanayveAak.cykkvspeeAvealekAieiytekgrfrra 113 
                                        AA ++ +++  +  ++ +l  Ae+q + ++ +    + y   ++  +k     eA +++ekA ++  +     + 
  gi|330507412|ref|YP_004383840.1| 1036 AAALFNIQEGHSMQSRFYLSQAETQVSrTDYPPLKIQLYRAQGErFLKDMLYPEAKSCFEKALALSRKLSLSYEE 1110
                                        778899999999999999999999988666666667777544440455557779999*****9999999999999 PP

                                        HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHH CS
                              SNAP  114 AklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAie 176 
                                        Ak   +++ l     gd+e+A++  ++A  ++   +a+ +  +++ ++  l   +++y++A e
  gi|330507412|ref|YP_004383840.1| 1111 AKAISSLGRLALAS-GDYEDALRRMKQALVIFGRLGASLDLIEVYRDMTLLFLAQDDYQRAEE 1172
                                        *********99999.9*****************999999999999999999999999999976 PP

  == domain 11  score: -0.2 bits;  conditional E-value: 1
                                        HHHHHHHHHTT-HHHHHHHHHHHHHHHHHT...-HHHHHHH.HHHHHHHHH CS
                              SNAP   59 lkaAecqeklkekdeaanayveAakcykkv...speeAvea.lekAieiyt 105 
                                        +++Aec+ ++++k+ea   y+ A     k+    p++ +++  ekAie++ 
  gi|330507412|ref|YP_004383840.1| 1195 VDLAECEARTGKKEEARADYAGALRLAGKEgdrIPSSTIRQiSEKAIEFLE 1245
                                        5789****************9999988887665455555441467777765 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   1.7   5.1e-09   2.6e-06      38     186 ..      71     217 ..      58     227 .. 0.90
   2 !   53.6   6.8   4.1e-17   2.1e-14      40     187 ..     232     377 ..     221     400 .. 0.88
   3 !   25.1   0.1     2e-08     1e-05       8     110 ..     398     501 ..     389     513 .. 0.80
   4 !   27.7   1.2   3.1e-09   1.6e-06      44     186 ..     515     656 ..     510     662 .. 0.90
   5 !   27.7   5.3   3.3e-09   1.7e-06       8     182 ..     598     772 ..     597     775 .. 0.90
   6 !   14.7   1.1   2.8e-05     0.015      42     178 ..     753     888 ..     751     906 .. 0.76
   7 !   14.4   0.0   3.7e-05     0.019      29     198 ..     900    1068 ..     879    1082 .. 0.85
   8 !   11.4   2.2   0.00029      0.15     140     232 ..    1089    1181 ..    1073    1212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 5.1e-09
                          TPR_MalT  38 ariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqg 114
                                        +++a ++lG+ +++    +aA + ++ a++la+     +  +  ll+++ ++ +  +   A + ye+al  +++++
  gi|330507412|ref|YP_004383840.1|  71 NSVQAWFNLGRLAHHLFFHQAAIEYYSNASDLAQILSDDDSLASILLCLGALYGEEEDWARACQCYEKALVAIDMAK 147
                                       568999***************************88888888899999****************************** PP

                          TPR_MalT 115 lqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlepeaaldayvllarialaqGdleeAetllek 186
                                        ++l     +l  l++  + +++ ++A+ +  + +e+l+  +++ +++a+  la++++ qGd+e+Ae+l + 
  gi|330507412|ref|YP_004383840.1| 148 RPRLL--PQVLERLGRARRLQGEYHQAQICYSRILEVLDPRDKKGRMEATSNLAELCQIQGDMEKAEKLYQT 217
                                       **863..3333445999999************************************************9886 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 4.1e-17
                          TPR_MalT  40 iaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglq 116
                                       + a+a+l+ ++  +G+ ++A+ +lq+a++l+ + +    a+   +++a+i+++ GrL+eAle+y ++l+    q+++
  gi|330507412|ref|YP_004383840.1| 232 ARALASLASIYSQTGNGKRAQISLQSASHLLADLKDQSGAAEMQCRLADIYFHEGRLKEALELYGRSLAAL--QKGH 306
                                       557789999*********************99999999999999**********************99955..5566 PP

                          TPR_MalT 117 qlplvgfllvlladllyEwndLeeAeqhlqeGielleql.epeaaldayvllarialaqGdleeAetlleka 187
                                       +  +++ l++  ++ ++E ++ + Ae+hlq++i++ +++ ++   ++a+v+la +++ qG+le A++  ++ 
  gi|330507412|ref|YP_004383840.1| 307 PSLASKALCRM-GQCFLEDGNWTLAEDHLQRAIAIMKEHkDSSSLARALVILAGVHHKQGQLEMALQCSRES 377
                                       66788888777.**************************956677779******************9988775 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 2e-08
                          TPR_MalT   8 AllaiasgdaeralelArqALall.peddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallal 83 
                                       A ++  + d ++a+e  ++A +l+ +  ++ a + a+++lG++++l+Gdl+ Alq+++ a+    q++  + a +  
  gi|330507412|ref|YP_004383840.1| 398 ARICCDCSDWPEAIECYQRAADLFmEMGEVTAAAEALSNLGGVYHLKGDLDVALQMYSHAYNSFCQQGDRQGASMVQ 474
                                       677778888888888888888765155789999****************************8765666666555555 PP

                          TPR_MalT  84 lqqaeilvaqGrLheAletyeqalqla 110
                                         ++ +++ +G+Lh A e  e++++  
  gi|330507412|ref|YP_004383840.1| 475 SNIGLVYQSRGDLHLAGEFLEKSIATK 501
                                       56999***************9999854 PP

  == domain 4  score: 27.7 bits;  conditional E-value: 3.1e-09
                          TPR_MalT  44 avlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqqlpl 120
                                       ++lG +++l G+ ++A++ ++ a ++  + + l+  + a   +++++  +G+L  A+  y+q+l+ a++        
  gi|330507412|ref|YP_004383840.1| 515 LSLGLIYQLGGEWDQAQSCFEGAARAFEDNGDLRGLAAAENNLGNLYSDRGDLMHAILCYRQGLE-ARRVLND-GHG 589
                                       689*************************************************************9.4443333.356 PP

                          TPR_MalT 121 vgfllvlladllyEwndLeeAeqhlqeGielleql.epeaaldayvllarialaqGdleeAetllek 186
                                       + + l  la +++  ++ e+Ae+  q++i+  ++l + +  ++++  lar  + +Gdle+A++  +k
  gi|330507412|ref|YP_004383840.1| 590 MAVTLGNLAGVYLQSGEEERAEELYQQSIDGFRELgDARGEARSLYGLARSMAERGDLEGALECYRK 656
                                       77888999**********************999985779999*******************998877 PP

  == domain 5  score: 27.7 bits;  conditional E-value: 3.3e-09
                          TPR_MalT   8 AllaiasgdaeralelArqALallpeddllariaatavlGeasllqG..dleaAlqalqeaeklarqadslhvalla 82 
                                       A ++++sg+ era+el +q ++ ++e    ar+ a++++G a  +++  dle Al+ +++  +l    + ++ ++ a
  gi|330507412|ref|YP_004383840.1| 598 AGVYLQSGEEERAEELYQQSIDGFRELG-DARGEARSLYGLARSMAErgDLEGALECYRKCLDLQIVGGDSRSMIEA 673
                                       5688999**************9999876.89***********9886444**************************** PP

                          TPR_MalT  83 llqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlepea 159
                                       l + +++l  +Gr +eAl  y q l+  +  +   l +v  ++  l++l+ + ++ +eA +  +e++++ e l+ e 
  gi|330507412|ref|YP_004383840.1| 674 LESMVNLLLRRGRWQEALTRYAQVLEALRSRDD--LSAVAAVQCALGNLHADLGQWDEALEDYNESLAIMEGLGDEY 748
                                       **************************8876554..34555556669***************************9999 PP

                          TPR_MalT 160 ald.ayvllarialaqGdleeAet 182
                                       ++  a+  l   ++ qGd+ +A++
  gi|330507412|ref|YP_004383840.1| 749 SVSvARNNLGNMCYRQGDWAAALE 772
                                       997799**************9975 PP

  == domain 6  score: 14.7 bits;  conditional E-value: 2.8e-05
                          TPR_MalT  42 atavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqql 118
                                       a+ +lG     qGd +aAl+ ++   +   +a+ +   +  l  +a +  ++G+  +Al+ y ++l l ++ + + +
  gi|330507412|ref|YP_004383840.1| 753 ARNNLGNMCYRQGDWAAALENYRLSLEGFGKAGDMESEASVLSNVAGLCYKRGQWADALDSYSKSLSLFEKLEDS-A 828
                                       6678888888899999999999966655556666665555566678899999***************88765555.5 PP

                          TPR_MalT 119 plvgfllvlladllyEwndLeeAeqhlqeGielleql.epeaaldayvllarialaqGdle 178
                                        ++++l   +++l++ +++ + A++h q+++e+ ++l +++ a+++++ +  i++ +G+++
  gi|330507412|ref|YP_004383840.1| 829 GIAQVL-GNMGNLYHRQGERDLAAEHFQRALEIYRRLkDQAGAAEMQASIDMIRAGRGEIS 888
                                       777777.999**************************9444555567777777777777765 PP

  == domain 7  score: 14.4 bits;  conditional E-value: 3.7e-05
                          TPR_MalT   29 allpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAlety 103 
                                        +l ++ dl  ++ ++++l++ +   G+ ++A + ++  ++  +q + + +    l   a ++   G+L  A  ++
  gi|330507412|ref|YP_004383840.1|  900 ELEETGDLSGQGEVLSALAGSYTDSGQWAEAIACYKRSVERFDQTGEVYNRGQVLFNMALVYKDMGDLNRARTLF 974 
                                        55667788889999999999*************99987777777777766777777889999999********** PP

                          TPR_MalT  104 eqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlep.eaaldayvllarialaqGdl 177 
                                          al     q+l +lp v  +   l+ +   +++ +eA +   ++i +le l+      + y++ a   ++ G  
  gi|330507412|ref|YP_004383840.1|  975 DVALDIF--QDLDALPCVASAKLNLGIISGQMGRSDEAIELFSQSIGILEGLGAlPDLCEGYIAAALFNIQEGHS 1047
                                        ****965..56888999999999****************************966377889*************** PP

                          TPR_MalT  178 eeAetllekaeelaresnfhv 198 
                                         ++  +l +ae ++ +++++ 
  gi|330507412|ref|YP_004383840.1| 1048 MQSRFYLSQAETQVSRTDYPP 1068
                                        *************99999965 PP

  == domain 8  score: 11.4 bits;  conditional E-value: 0.00029
                          TPR_MalT  140 eAeqhlqeGielleql.epeaaldayvllarialaqGdleeAetllekaeelaresnfhvdwlanaeevrvrlwl 213 
                                        eA+ + +++++l+++l  +   ++a   l r+ala Gd e+A++ +++a     +   ++d ++  +++ ++ +l
  gi|330507412|ref|YP_004383840.1| 1089 EAKSCFEKALALSRKLsLSYEEAKAISSLGRLALASGDYEDALRRMKQALVIFGRLGASLDLIEVYRDMTLL-FL 1162
                                        7999***********977799999999***********************9999999999***999999985.79 PP

                          TPR_MalT  214 aqgdlaaaerwleaaelps 232 
                                        aq d ++ae+++   ++++
  gi|330507412|ref|YP_004383840.1| 1163 AQDDYQRAEEMAMLRQRQA 1181
                                        ********99654444433 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0015      0.74       2      31 ..      74     103 ..      73     105 .. 0.92
   2 ?    2.7   0.3      0.37   1.9e+02       7      28 ..     119     140 ..     113     140 .. 0.88
   3 ?    4.9   0.0     0.071        36       3      29 ..     155     181 ..     153     182 .. 0.88
   4 ?    7.1   0.2     0.014       7.2       6      29 ..     197     220 ..     194     223 .. 0.91
   5 ?    6.8   0.1     0.018       9.2       1      26 [.     232     257 ..     232     259 .. 0.88
   6 !   11.1   0.2   0.00075      0.38       1      27 [.     272     298 ..     272     301 .. 0.89
   7 ?   -0.4   0.0       3.7   1.9e+03       2      30 ..     312     340 ..     311     343 .. 0.89
   8 !   10.1   0.0    0.0015      0.77       1      32 [.     351     382 ..     351     384 .. 0.94
   9 ?    0.0   0.1       2.6   1.3e+03      19      30 ..     409     420 ..     409     421 .. 0.88
  10 ?    6.6   0.1      0.02        10       1      27 [.     431     457 ..     431     460 .. 0.92
  11 !    9.5   0.0    0.0024       1.2       6      29 ..     476     499 ..     473     503 .. 0.90
  12 ?    1.2   0.0       1.1   5.6e+02       6      29 ..     516     539 ..     513     544 .. 0.85
  13 !   10.2   0.0    0.0015      0.74       5      31 ..     555     581 ..     553     583 .. 0.93
  14 !    8.3   0.0    0.0059         3       4      28 ..     594     618 ..     591     619 .. 0.91
  15 !   12.1   0.2   0.00034      0.17       1      30 [.     631     660 ..     631     661 .. 0.93
  16 !    8.7   0.1    0.0043       2.2       3      29 ..     713     739 ..     711     740 .. 0.90
  17 ?    0.3   0.1       2.2   1.1e+03       4      29 ..     754     779 ..     752     779 .. 0.89
  18 ?   -1.8   0.1       9.9     5e+03       3      26 ..     800     823 ..     798     826 .. 0.81
  19 !   15.5   0.0   2.8e-05     0.014       1      31 [.     831     861 ..     831     863 .. 0.94
  20 ?    4.9   0.0     0.071        36       4      29 ..     914     939 ..     911     943 .. 0.86
  21 !   10.8   0.0   0.00092      0.47       2      30 ..     952     980 ..     951     983 .. 0.86
  22 !   10.1   0.0    0.0016       0.8       2      29 ..     992    1019 ..     991    1020 .. 0.89
  23 ?    5.7   0.2     0.039        20      19      33 ..    1089    1103 ..    1087    1104 .. 0.91
  24 ?    1.4   0.1      0.92   4.7e+02       3      23 ..    1113    1133 ..    1111    1138 .. 0.75
  25 ?    4.2   0.2      0.12        63       7      31 ..    1197    1221 ..    1195    1224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0015
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                       +a++nlg++ + l  +++A+eyy  a +l+
  gi|330507412|ref|YP_004383840.1|  74 QAWFNLGRLAHHLFFHQAAIEYYSNASDLA 103
                                       89*********************9998876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.37
                                       HHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekal 28 
                                       lg +y + +d   A ++yekal
  gi|330507412|ref|YP_004383840.1| 119 LGALYGEEEDWARACQCYEKAL 140
                                       788999999999*********7 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.071
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekale 29 
                                       ++ +lg++ + +g+y++A+ +y + le
  gi|330507412|ref|YP_004383840.1| 155 VLERLGRARRLQGEYHQAQICYSRILE 181
                                       67799*****************98876 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.014
                                       HHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekale 29 
                                       nl+ +++ +gd+e+A++ y+  l+
  gi|330507412|ref|YP_004383840.1| 197 NLAELCQIQGDMEKAEKLYQTILK 220
                                       899****************98776 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.018
                                       CCHHHHHHHHHHHTT-HHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyek 26 
                                       a+a+  l+siy+++g+ + A+ +++ 
  gi|330507412|ref|YP_004383840.1| 232 ARALASLASIYSQTGNGKRAQISLQS 257
                                       799*************9999988875 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.00075
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyeka 27 
                                       ae+ ++l++iy+  g+++eA e y + 
  gi|330507412|ref|YP_004383840.1| 272 AEMQCRLADIYFHEGRLKEALELYGRS 298
                                       6899******************99766 PP

  == domain 7  score: -0.4 bits;  conditional E-value: 3.7
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                       +a++++g++ l+ g+   A+  +++a+ +
  gi|330507412|ref|YP_004383840.1| 312 KALCRMGQCFLEDGNWTLAEDHLQRAIAI 340
                                       799***********999999999999865 PP

  == domain 8  score: 10.1 bits;  conditional E-value: 0.0015
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+a++ l+ +++k+g++e+A ++ ++ l++++
  gi|330507412|ref|YP_004383840.1| 351 ARALVILAGVHHKQGQLEMALQCSRESLKIRE 382
                                       79999************************986 PP

  == domain 9  score: 0.0 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHH CS
                             TPR_8  19 eAkeyyekalel 30 
                                       eA+e+y++a +l
  gi|330507412|ref|YP_004383840.1| 409 EAIECYQRAADL 420
                                       8*******9765 PP

  == domain 10  score: 6.6 bits;  conditional E-value: 0.02
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyeka 27 
                                       aea+ nlg +y+ +gd++ A + y +a
  gi|330507412|ref|YP_004383840.1| 431 AEALSNLGGVYHLKGDLDVALQMYSHA 457
                                       78999*****************99887 PP

  == domain 11  score: 9.5 bits;  conditional E-value: 0.0024
                                       HHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekale 29 
                                       n+g++y++ gd++ A e++ek + 
  gi|330507412|ref|YP_004383840.1| 476 NIGLVYQSRGDLHLAGEFLEKSIA 499
                                       89*******************986 PP

  == domain 12  score: 1.2 bits;  conditional E-value: 1.1
                                       HHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekale 29 
                                        lg+iy+  g+ ++A++++e a +
  gi|330507412|ref|YP_004383840.1| 516 SLGLIYQLGGEWDQAQSCFEGAAR 539
                                       699****************98866 PP

  == domain 13  score: 10.2 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleld 31 
                                       +nlg++y++ gd+  A+ +y++ le++
  gi|330507412|ref|YP_004383840.1| 555 NNLGNLYSDRGDLMHAILCYRQGLEAR 581
                                       69*********************9986 PP

  == domain 14  score: 8.3 bits;  conditional E-value: 0.0059
                                       HHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekal 28 
                                       + nl+ +yl+ g+ e A+e y++ +
  gi|330507412|ref|YP_004383840.1| 594 LGNLAGVYLQSGEEERAEELYQQSI 618
                                       679*******************988 PP

  == domain 15  score: 12.1 bits;  conditional E-value: 0.00034
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+++y l++   + gd+e A e+y+k+l+l
  gi|330507412|ref|YP_004383840.1| 631 ARSLYGLARSMAERGDLEGALECYRKCLDL 660
                                       789999999999****************98 PP

  == domain 16  score: 8.7 bits;  conditional E-value: 0.0043
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekale 29 
                                       + + lg+++ +lg+ +eA e y++ l 
  gi|330507412|ref|YP_004383840.1| 713 VQCALGNLHADLGQWDEALEDYNESLA 739
                                       6799*******************9986 PP

  == domain 17  score: 0.3 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekale 29 
                                        +nlg+ +  +gd  +A e y+  le
  gi|330507412|ref|YP_004383840.1| 754 RNNLGNMCYRQGDWAAALENYRLSLE 779
                                       689****************9998875 PP

  == domain 18  score: -1.8 bits;  conditional E-value: 9.9
                                       HHHHHHHHHHHTT-HHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyek 26 
                                       ++y+ g+  + l  y ++ + +ek
  gi|330507412|ref|YP_004383840.1| 800 LCYKRGQWADALDSYSKSLSLFEK 823
                                       688888888889999998888888 PP

  == domain 19  score: 15.5 bits;  conditional E-value: 2.8e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a+++ n+g++y+ +g+ + A e +++ale+ 
  gi|330507412|ref|YP_004383840.1| 831 AQVLGNMGNLYHRQGERDLAAEHFQRALEIY 861
                                       68999************************97 PP

  == domain 20  score: 4.9 bits;  conditional E-value: 0.071
                                       HHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekale 29 
                                       +  l+  y + g+  eA+++y++ +e
  gi|330507412|ref|YP_004383840.1| 914 LSALAGSYTDSGQWAEAIACYKRSVE 939
                                       567888999**************998 PP

  == domain 21  score: 10.8 bits;  conditional E-value: 0.00092
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                       ++++n++++y+++gd++ A   +  al++
  gi|330507412|ref|YP_004383840.1| 952 QVLFNMALVYKDMGDLNRARTLFDVALDI 980
                                       689****************9988766665 PP

  == domain 22  score: 10.1 bits;  conditional E-value: 0.0016
                                        CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8    2 eayynlgsiylklgdyeeAkeyyekale 29  
                                        +a +nlg i  ++g+ +eA+e + + + 
  gi|330507412|ref|YP_004383840.1|  992 SAKLNLGIISGQMGRSDEAIELFSQSIG 1019
                                        6789*******************99986 PP

  == domain 23  score: 5.7 bits;  conditional E-value: 0.039
                                        HHHHHHHHHHHHHHH CS
                             TPR_8   19 eAkeyyekaleldpd 33  
                                        eAk+++ekal l+++
  gi|330507412|ref|YP_004383840.1| 1089 EAKSCFEKALALSRK 1103
                                        8**********9986 PP

  == domain 24  score: 1.4 bits;  conditional E-value: 0.92
                                        HHHHHHHHHHHTT-HHHHHHH CS
                             TPR_8    3 ayynlgsiylklgdyeeAkey 23  
                                        a   lg++ l  gdye A   
  gi|330507412|ref|YP_004383840.1| 1113 AISSLGRLALASGDYEDALRR 1133
                                        556799**********99755 PP

  == domain 25  score: 4.2 bits;  conditional E-value: 0.12
                                        HHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8    7 lgsiylklgdyeeAkeyyekaleld 31  
                                        l+ +   +g++eeA + y  al+l+
  gi|330507412|ref|YP_004383840.1| 1197 LAECEARTGKKEEARADYAGALRLA 1221
                                        56666789*************9997 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2      0.13        67      33      57 ..      72      96 ..      58     103 .. 0.85
   2 ?    1.8   0.2      0.74   3.8e+02      23      50 ..     142     169 ..     119     183 .. 0.83
   3 !   13.2   0.1   0.00021      0.11      10      53 ..     205     251 ..     198     260 .. 0.92
   4 !   15.4   0.4   4.3e-05     0.022      24      61 ..     265     299 ..     254     307 .. 0.76
   5 !   18.4   0.2     5e-06    0.0026       2      61 ..     277     338 ..     276     341 .. 0.95
   6 !   10.9   0.0    0.0011      0.56       7      53 ..     321     370 ..     315     375 .. 0.82
   7 !   12.0   0.0   0.00049      0.25      12      57 ..     406     454 ..     405     462 .. 0.89
   8 !   10.4   1.0    0.0016      0.82       2      50 ..     516     567 ..     515     581 .. 0.86
   9 !   22.2   1.5   3.2e-07   0.00016       2      59 ..     596     656 ..     596     661 .. 0.93
  10 !   15.0   5.0   5.5e-05     0.028       4      61 ..     678     738 ..     676     741 .. 0.85
  11 !   17.4   0.7   9.9e-06    0.0051       1      61 [.     715     778 ..     715     784 .. 0.81
  12 !   12.8   0.8   0.00028      0.14       8      64 ..     802     861 ..     796     868 .. 0.91
  13 !   13.8   0.0   0.00013     0.068       2      64 ..     916     981 ..     915     985 .. 0.91
  14 ?    5.0   0.0     0.075        38       2      59 ..     956    1016 ..     955    1021 .. 0.87
  15 !   12.4   0.1   0.00038       0.2       3      25 ..    1117    1139 ..    1115    1154 .. 0.88
  16 ?    1.8   5.5      0.74   3.8e+02      33      64 ..    1190    1221 ..    1159    1224 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.13
                            TPR_16 33 aaeAllllgdaalrqgrlaeAaaly 57
                                       ++A+++lg++a ++  +++A+++y
  gi|330507412|ref|YP_004383840.1| 72 SVQAWFNLGRLAHHLFFHQAAIEYY 96
                                      68************98889888887 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.74
                            TPR_16  23 alkrdpssPdaaeAllllgdaalrqgrl 50 
                                       a+++++++ + ++ l  lg+a+  qg++
  gi|330507412|ref|YP_004383840.1| 142 AIDMAKRPRLLPQVLERLGRARRLQGEY 169
                                       5677888899999999999999999998 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00021
                            TPR_16  10 agdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeA 53 
                                       +gd ++A++++++ lk +  s d   aa+Al  l+ ++ + g+ ++A
  gi|330507412|ref|YP_004383840.1| 205 QGDMEKAEKLYQTILKERELSDDpvgAARALASLASIYSQTGNGKRA 251
                                       89****************88888999************999987776 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 4.3e-05
                            TPR_16  24 lkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       lk++   + aae++  l+d++++ grl+eA++ly + l
  gi|330507412|ref|YP_004383840.1| 265 LKDQ---SGAAEMQCRLADIYFHEGRLKEALELYGRSL 299
                                       4455...99**********************6554444 PP

  == domain 5  score: 18.4 bits;  conditional E-value: 5e-06
                            TPR_16   2 alaraalragdyddAaaal.eaalkrdpssPd.aaeAllllgdaalrqgrlaeAaalyraal 61 
                                        la++++  g+  +A++++ + + ++++++P  a  Al   g+++l+ g++++A++ +++a+
  gi|330507412|ref|YP_004383840.1| 277 RLADIYFHEGRLKEALELYgRSLAALQKGHPSlASKALCRMGQCFLEDGNWTLAEDHLQRAI 338
                                       699*****************************9*************************9997 PP

  == domain 6  score: 10.9 bits;  conditional E-value: 0.0011
                            TPR_16   7 alragdyddAaaaleaalk...rdpssPdaaeAllllgdaalrqgrlaeA 53 
                                       +l+ g+++ A+  l++a++    +++s+  a+Al  l+ ++ +qg l+ A
  gi|330507412|ref|YP_004383840.1| 321 FLEDGNWTLAEDHLQRAIAimkEHKDSSSLARALVILAGVHHKQGQLEMA 370
                                       7899*************962226666666****************99866 PP

  == domain 7  score: 12.0 bits;  conditional E-value: 0.00049
                            TPR_16  12 dyddAaaaleaalkrdpssPd......aaeAllllgdaalrqgrlaeAaaly 57 
                                       d+++A++ +++a +++    +      aaeAl +lg ++  +g+l+ A++ y
  gi|330507412|ref|YP_004383840.1| 406 DWPEAIECYQRAADLF---MEmgevtaAAEALSNLGGVYHLKGDLDVALQMY 454
                                       899*************...55666**********************998755 PP

  == domain 8  score: 10.4 bits;  conditional E-value: 0.0016
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrl 50 
                                        l++++   g++d+A+  +e a +++ +  d    a+A ++lg+++  +g+l
  gi|330507412|ref|YP_004383840.1| 516 SLGLIYQLGGEWDQAQSCFEGAARAFEDNGDlrgLAAAENNLGNLYSDRGDL 567
                                       56777777899***************88888*******************98 PP

  == domain 9  score: 22.2 bits;  conditional E-value: 3.2e-07
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeAaalyra 59 
                                       +la  +l++g+ ++A++++++ ++ +++  d    a++l++l+++ +++g+l++A++ yr+
  gi|330507412|ref|YP_004383840.1| 596 NLAGVYLQSGEEERAEELYQQSIDGFRELGDargEARSLYGLARSMAERGDLEGALECYRK 656
                                       5899**********************88888************************998876 PP

  == domain 10  score: 15.0 bits;  conditional E-value: 5.5e-05
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeAaalyraal 61 
                                        +++lr+g++++A+ ++ ++l++ +s  d    a+ + +lg++++ +g ++eA++ y++ l
  gi|330507412|ref|YP_004383840.1| 678 VNLLLRRGRWQEALTRYAQVLEALRSRDDlsaVAAVQCALGNLHADLGQWDEALEDYNESL 738
                                       5899*************998888754444777**********************7777755 PP

  == domain 11  score: 17.4 bits;  conditional E-value: 9.9e-06
                            TPR_16   1 lalaraalragdyddAaaal.eaalkrdpssPd..aaeAllllgdaalrqgrlaeAaalyraal 61 
                                       +al+++++++g++d+A++ + e +  + +   +     A+++lg++++rqg++a+A++ yr  l
  gi|330507412|ref|YP_004383840.1| 715 CALGNLHADLGQWDEALEDYnESLAIMEGLGDEysVSVARNNLGNMCYRQGDWAAALENYRLSL 778
                                       589*****************555555554444476888******************98887765 PP

  == domain 12  score: 12.8 bits;  conditional E-value: 0.00028
                            TPR_16   8 lragdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                       +++g+++dA+  +   l ++ +  d    a+ l + g+++ rqg+ ++Aa+ +++al+ +
  gi|330507412|ref|YP_004383840.1| 802 YKRGQWADALDSYSKSLSLFEKLEDsagIAQVLGNMGNLYHRQGERDLAAEHFQRALEIY 861
                                       789*****************888889999***************************9875 PP

  == domain 13  score: 13.8 bits;  conditional E-value: 0.00013
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                       ala ++ ++g++++A+a +++ ++r+  + +   + + l++ ++++   g+l +A+ l++ al+  
  gi|330507412|ref|YP_004383840.1| 916 ALAGSYTDSGQWAEAIACYKRSVERFDQTGEvynRGQVLFNMALVYKDMGDLNRARTLFDVALDIF 981
                                       7999**********************77777999999999999999999************99875 PP

  == domain 14  score: 5.0 bits;  conditional E-value: 0.075
                            TPR_16    2 alaraalragdyddAaaaleaalkrdpssPd......aaeAllllgdaalrqgrlaeAaalyra 59  
                                        ++a+ + + gd  +A+ +++ al+ +    d       a A l+lg +  + gr +eA++l+  
  gi|330507412|ref|YP_004383840.1|  956 NMALVYKDMGDLNRARTLFDVALDIF---QDldalpcVASAKLNLGIISGQMGRSDEAIELFSQ 1016
                                        6899999*****************99...77778999999999999999999999999998865 PP

  == domain 15  score: 12.4 bits;  conditional E-value: 0.00038
                            TPR_16    3 laraalragdyddAaaaleaalk 25  
                                        l+r+al++gdy+dA+++ ++al 
  gi|330507412|ref|YP_004383840.1| 1117 LGRLALASGDYEDALRRMKQALV 1139
                                        89****************99996 PP

  == domain 16  score: 1.8 bits;  conditional E-value: 0.74
                            TPR_16   33 aaeAllllgdaalrqgrlaeAaalyraalraa 64  
                                           A   l+++ +r g  +eA+a y+ alr a
  gi|330507412|ref|YP_004383840.1| 1190 SLLATVDLAECEARTGKKEEARADYAGALRLA 1221
                                        5567889******************9999876 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4       1.5   7.7e+02      13      38 ..      92     123 ..      89     126 .. 0.59
   2 ?    0.4   0.2         1   5.2e+02       4      21 ..     123     140 ..     120     141 .. 0.82
   3 ?   -0.9   0.1       2.7   1.4e+03       1      18 [.     160     177 ..     160     181 .. 0.85
   4 !    8.4   0.1    0.0032       1.7       2      21 ..     280     299 ..     279     301 .. 0.90
   5 ?   -1.0   0.0       2.8   1.4e+03       3      23 ..     320     340 ..     318     342 .. 0.86
   6 ?    2.1   0.0      0.31   1.6e+02       4      24 ..     361     381 ..     360     386 .. 0.84
   7 !   14.2   0.0   5.1e-05     0.026       2      42 .]     399     445 ..     398     445 .. 0.79
   8 ?    6.6   0.0     0.012       6.3       1      22 [.     558     579 ..     558     581 .. 0.95
   9 ?   -1.7   0.1       4.7   2.4e+03       3      21 ..     600     618 ..     600     626 .. 0.87
  10 !    9.7   0.0    0.0013      0.64       6      23 ..     643     660 ..     639     661 .. 0.89
  11 ?    6.0   0.0     0.019       9.7       2      22 ..     679     699 ..     679     700 .. 0.88
  12 !   14.9   0.0     3e-05     0.015       1      23 [.     718     740 ..     718     742 .. 0.94
  13 !   11.1   0.1   0.00047      0.24       1      18 [.     758     775 ..     758     779 .. 0.94
  14 !    8.0   0.0    0.0044       2.2       4      23 ..     801     820 ..     800     826 .. 0.90
  15 !    9.7   0.1    0.0013      0.68       1      23 [.     838     860 ..     838     862 .. 0.97
  16 !   12.2   0.0   0.00022      0.11       4      21 ..     921     938 ..     920     940 .. 0.90
  17 ?   -2.2   0.0       6.8   3.5e+03      30      42 .]     953     965 ..     951     965 .. 0.88
  18 ?   -1.3   0.0       3.5   1.8e+03       3      23 ..     960     980 ..     958     984 .. 0.85
  19 ?   -1.4   0.0       3.8   1.9e+03       6      21 ..    1003    1018 ..    1003    1020 .. 0.83
  20 ?   -2.5   0.0       8.2   4.2e+03      10      24 ..    1087    1101 ..    1087    1104 .. 0.83
  21 ?    3.2   0.0      0.14        73       5      22 ..    1122    1139 ..    1118    1140 .. 0.83
  22 ?   -1.9   0.1       5.3   2.7e+03       8      23 ..    1205    1220 ..    1203    1220 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.5
                            TPR_11  13 AieaYkkAlkl......dPdnaeayynLGlay 38 
                                       Aie Y++A +l      d + a+++++LG++y
  gi|330507412|ref|YP_004383840.1|  92 AIEYYSNASDLaqilsdDDSLASILLCLGALY 123
                                       56666666554222222667788888888887 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1
                            TPR_11   4 yyeqGkyeeAieaYkkAl 21 
                                       y e  ++  A ++Y+kAl
  gi|330507412|ref|YP_004383840.1| 123 YGEEEDWARACQCYEKAL 140
                                       556788999********8 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.7
                            TPR_11   1 GdayyeqGkyeeAieaYk 18 
                                       G+a + qG+y +A  +Y+
  gi|330507412|ref|YP_004383840.1| 160 GRARRLQGEYHQAQICYS 177
                                       89999******9977765 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0032
                            TPR_11   2 dayyeqGkyeeAieaYkkAl 21 
                                       d+y+  G+++eA+e Y + l
  gi|330507412|ref|YP_004383840.1| 280 DIYFHEGRLKEALELYGRSL 299
                                       9***************9866 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 2.8
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkl 23 
                                        + e G+++ A  ++++A+++
  gi|330507412|ref|YP_004383840.1| 320 CFLEDGNWTLAEDHLQRAIAI 340
                                       5778899999*********97 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.31
                            TPR_11   4 yyeqGkyeeAieaYkkAlkld 24 
                                        ++qG++e A+++ ++ lk++
  gi|330507412|ref|YP_004383840.1| 361 HHKQGQLEMALQCSRESLKIR 381
                                       689*********988888886 PP

  == domain 7  score: 14.2 bits;  conditional E-value: 5.1e-05
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkl......dPdnaeayynLGlayykqG 42 
                                       +++++  +++eAie+Y++A +l          aea++nLG +y+ +G
  gi|330507412|ref|YP_004383840.1| 399 RICCDCSDWPEAIECYQRAADLfmemgeVTAAAEALSNLGGVYHLKG 445
                                       6899999*************995555555678888888888888776 PP

  == domain 8  score: 6.6 bits;  conditional E-value: 0.012
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlk 22 
                                       G++y ++G++  Ai +Y++ l+
  gi|330507412|ref|YP_004383840.1| 558 GNLYSDRGDLMHAILCYRQGLE 579
                                       9******************986 PP

  == domain 9  score: -1.7 bits;  conditional E-value: 4.7
                            TPR_11   3 ayyeqGkyeeAieaYkkAl 21 
                                       +y + G+ e A e Y++ +
  gi|330507412|ref|YP_004383840.1| 600 VYLQSGEEERAEELYQQSI 618
                                       5899999999999999977 PP

  == domain 10  score: 9.7 bits;  conditional E-value: 0.0013
                            TPR_11   6 eqGkyeeAieaYkkAlkl 23 
                                       e+G++e+A+e+Y+k l+l
  gi|330507412|ref|YP_004383840.1| 643 ERGDLEGALECYRKCLDL 660
                                       89***********98876 PP

  == domain 11  score: 6.0 bits;  conditional E-value: 0.019
                            TPR_11   2 dayyeqGkyeeAieaYkkAlk 22 
                                       +++  +G++ eA+++Y + l+
  gi|330507412|ref|YP_004383840.1| 679 NLLLRRGRWQEALTRYAQVLE 699
                                       567889**********99886 PP

  == domain 12  score: 14.9 bits;  conditional E-value: 3e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                       G++  ++G+++eA+e+Y++ l++
  gi|330507412|ref|YP_004383840.1| 718 GNLHADLGQWDEALEDYNESLAI 740
                                       9999***************9987 PP

  == domain 13  score: 11.1 bits;  conditional E-value: 0.00047
                            TPR_11   1 GdayyeqGkyeeAieaYk 18 
                                       G+++y qG++ +A+e+Y+
  gi|330507412|ref|YP_004383840.1| 758 GNMCYRQGDWAAALENYR 775
                                       9****************7 PP

  == domain 14  score: 8.0 bits;  conditional E-value: 0.0044
                            TPR_11   4 yyeqGkyeeAieaYkkAlkl 23 
                                       +y++G++ +A+ +Y+k l l
  gi|330507412|ref|YP_004383840.1| 801 CYKRGQWADALDSYSKSLSL 820
                                       79**************9876 PP

  == domain 15  score: 9.7 bits;  conditional E-value: 0.0013
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                       G++y+ qG+ + A e++++Al++
  gi|330507412|ref|YP_004383840.1| 838 GNLYHRQGERDLAAEHFQRALEI 860
                                       9********************98 PP

  == domain 16  score: 12.2 bits;  conditional E-value: 0.00022
                            TPR_11   4 yyeqGkyeeAieaYkkAl 21 
                                       y++ G++ eAi++Yk+ +
  gi|330507412|ref|YP_004383840.1| 921 YTDSGQWAEAIACYKRSV 938
                                       99*************966 PP

  == domain 17  score: -2.2 bits;  conditional E-value: 6.8
                            TPR_11  30 ayynLGlayykqG 42 
                                       +++n++l+y  +G
  gi|330507412|ref|YP_004383840.1| 953 VLFNMALVYKDMG 965
                                       579******9998 PP

  == domain 18  score: -1.3 bits;  conditional E-value: 3.5
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkl 23 
                                       +y + G+++ A + +  Al++
  gi|330507412|ref|YP_004383840.1| 960 VYKDMGDLNRARTLFDVALDI 980
                                       7999*******9999888877 PP

  == domain 19  score: -1.4 bits;  conditional E-value: 3.8
                            TPR_11    6 eqGkyeeAieaYkkAl 21  
                                        + G+ +eAie +++ +
  gi|330507412|ref|YP_004383840.1| 1003 QMGRSDEAIELFSQSI 1018
                                        57999*****998865 PP

  == domain 20  score: -2.5 bits;  conditional E-value: 8.2
                            TPR_11   10 yeeAieaYkkAlkld 24  
                                        y+eA  +++kAl+l+
  gi|330507412|ref|YP_004383840.1| 1087 YPEAKSCFEKALALS 1101
                                        77888899****997 PP

  == domain 21  score: 3.2 bits;  conditional E-value: 0.14
                            TPR_11    5 yeqGkyeeAieaYkkAlk 22  
                                         + G+ye+A+ + k+Al 
  gi|330507412|ref|YP_004383840.1| 1122 LASGDYEDALRRMKQALV 1139
                                        689*********999996 PP

  == domain 22  score: -1.9 bits;  conditional E-value: 5.3
                            TPR_11    8 GkyeeAieaYkkAlkl 23  
                                        Gk eeA ++Y  Al+l
  gi|330507412|ref|YP_004383840.1| 1205 GKKEEARADYAGALRL 1220
                                        888*******999886 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.27   1.4e+02       6      26 ..     119     139 ..     116     141 .. 0.84
   2 ?    7.2   0.1     0.017       8.6       2      28 ..     155     181 ..     154     182 .. 0.89
   3 ?    5.6   0.1     0.058        30       8      29 ..     201     221 ..     196     223 .. 0.84
   4 ?    3.4   0.1      0.29   1.5e+02       5      25 ..     277     297 ..     277     300 .. 0.92
   5 ?    5.6   0.0     0.056        29       3      27 ..     314     338 ..     312     340 .. 0.88
   6 ?    0.9   0.0       1.8     9e+02      15      28 ..     406     419 ..     397     421 .. 0.87
   7 ?    1.5   0.1       1.2     6e+02       5      26 ..     416     437 ..     412     441 .. 0.84
   8 ?   -1.4   0.0       9.5   4.9e+03       5      25 ..     476     496 ..     476     499 .. 0.87
   9 ?    6.6   0.0     0.027        14       6      25 ..     517     536 ..     514     544 .. 0.84
  10 ?    0.9   0.0       1.8   9.3e+02       7      27 ..     598     618 ..     570     621 .. 0.82
  11 !   14.0   0.2   0.00011     0.058       2      28 ..     633     659 ..     632     661 .. 0.93
  12 ?    3.4   0.1      0.27   1.4e+02      10      28 ..     681     699 ..     669     702 .. 0.76
  13 ?    2.7   0.0      0.47   2.4e+02       6      24 ..     717     735 ..     716     739 .. 0.86
  14 ?    4.1   0.0      0.16        84       6      24 ..     757     775 ..     756     778 .. 0.78
  15 ?    4.9   0.0     0.092        47       7      25 ..     799     816 ..     798     821 .. 0.87
  16 ?    7.9   0.1      0.01       5.1       5      30 ..     836     861 ..     835     863 .. 0.94
  17 ?    4.6   0.0      0.11        58       9      31 ..     920     942 ..     910     944 .. 0.79
  18 !   13.5   0.0   0.00017     0.087       1      30 [.     952     981 ..     952     983 .. 0.91
  19 ?    2.1   0.0      0.71   3.6e+02       4      25 ..     995    1016 ..     992    1018 .. 0.84
  20 ?    2.0   0.3       0.8   4.1e+02       6      27 ..    1117    1138 ..    1098    1142 .. 0.70
  21 ?    1.6   0.2         1   5.3e+02       6      23 ..    1197    1214 ..    1193    1220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerl 26 
                                       l+ +y +  d+++A++ +e+ 
  gi|330507412|ref|YP_004383840.1| 119 LGALYGEEEDWARACQCYEKA 139
                                       577888856**********97 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                       +l +l++++r +g++ +A   + r+++
  gi|330507412|ref|YP_004383840.1| 155 VLERLGRARRLQGEYHQAQICYSRILE 181
                                       5669******************99875 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.058
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAlealerlike 29 
                                       l+++++ d +kA ++++ ++ke
  gi|330507412|ref|YP_004383840.1| 201 LCQIQG-DMEKAEKLYQTILKE 221
                                       678866.************997 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealer 25 
                                       +la  y+  g+  +Ale++ r
  gi|330507412|ref|YP_004383840.1| 277 RLADIYFHEGRLKEALELYGR 297
                                       79******99********976 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerli 27 
                                       l ++++++++ g+++ A + l+r i
  gi|330507412|ref|YP_004383840.1| 314 LCRMGQCFLEDGNWTLAEDHLQRAI 338
                                       559*******77***********98 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHH CS
                             TPR_6  15 dtdkAlealerlik 28 
                                       d+ +A+e ++r  +
  gi|330507412|ref|YP_004383840.1| 406 DWPEAIECYQRAAD 419
                                       799********877 PP

  == domain 7  score: 1.5 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerl 26 
                                       ++a ++ ++g+ ++A eal +l
  gi|330507412|ref|YP_004383840.1| 416 RAADLFMEMGEVTAAAEALSNL 437
                                       678999999*********9876 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 9.5
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealer 25 
                                       +++l y++ gd   A e le+
  gi|330507412|ref|YP_004383840.1| 476 NIGLVYQSRGDLHLAGEFLEK 496
                                       589*****88**999999987 PP

  == domain 9  score: 6.6 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealer 25 
                                       l+l y+ +g++d+A   +e 
  gi|330507412|ref|YP_004383840.1| 517 LGLIYQLGGEWDQAQSCFEG 536
                                       89*****99*******9985 PP

  == domain 10  score: 0.9 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerli 27 
                                       a  y++ g+ ++A e++++ i
  gi|330507412|ref|YP_004383840.1| 598 AGVYLQSGEEERAEELYQQSI 618
                                       44577757**********855 PP

  == domain 11  score: 14.0 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                       +ly la+s+ + gd + Ale ++++++
  gi|330507412|ref|YP_004383840.1| 633 SLYGLARSMAERGDLEGALECYRKCLD 659
                                       69*********99***********986 PP

  == domain 12  score: 3.4 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlealerlik 28 
                                       +++ g++++Al+ + ++++
  gi|330507412|ref|YP_004383840.1| 681 LLRRGRWQEALTRYAQVLE 699
                                       3444699999999998876 PP

  == domain 13  score: 2.7 bits;  conditional E-value: 0.47
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAleale 24 
                                       l+ ++  lg++d+Ale ++
  gi|330507412|ref|YP_004383840.1| 717 LGNLHADLGQWDEALEDYN 735
                                       678889999******9887 PP

  == domain 14  score: 4.1 bits;  conditional E-value: 0.16
                                       HH.HHHHHHHHHHHHHHHHH CS
                             TPR_6   6 la.lsyrklgdtdkAleale 24 
                                       l+ ++yr++ d+++Ale ++
  gi|330507412|ref|YP_004383840.1| 757 LGnMCYRQG-DWAAALENYR 775
                                       564677755.******9886 PP

  == domain 15  score: 4.9 bits;  conditional E-value: 0.092
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealer 25 
                                       +l+y+++ ++++Al+ + +
  gi|330507412|ref|YP_004383840.1| 799 GLCYKRG-QWADALDSYSK 816
                                       99***99.*******9976 PP

  == domain 16  score: 7.9 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6   5 klalsyrklgdtdkAlealerlikeY 30 
                                       +++ +y ++g+ d A e ++r ++ Y
  gi|330507412|ref|YP_004383840.1| 836 NMGNLYHRQGERDLAAEHFQRALEIY 861
                                       5899*******************988 PP

  == domain 17  score: 4.6 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   9 syrklgdtdkAlealerlikeYP 31 
                                       sy   g++++A++ ++r ++++ 
  gi|330507412|ref|YP_004383840.1| 920 SYTDSGQWAEAIACYKRSVERFD 942
                                       556548***********999986 PP

  == domain 18  score: 13.5 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeY 30 
                                       ++l+++al y+ +gd  +A+++++  ++ +
  gi|330507412|ref|YP_004383840.1| 952 QVLFNMALVYKDMGDLNRARTLFDVALDIF 981
                                       58*********************9998866 PP

  == domain 19  score: 2.1 bits;  conditional E-value: 0.71
                                        HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6    4 yklalsyrklgdtdkAlealer 25  
                                        ++l+    ++g++d+A+e++ +
  gi|330507412|ref|YP_004383840.1|  995 LNLGIISGQMGRSDEAIELFSQ 1016
                                        77888888999********976 PP

  == domain 20  score: 2.0 bits;  conditional E-value: 0.8
                                        HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6    6 lalsyrklgdtdkAlealerli 27  
                                        l+++ ++ gd+++Al+ +++ +
  gi|330507412|ref|YP_004383840.1| 1117 LGRLALASGDYEDALRRMKQAL 1138
                                        455555548******9998876 PP

  == domain 21  score: 1.6 bits;  conditional E-value: 1
                                        HHHHHHHHHHHHHHHHHH CS
                             TPR_6    6 lalsyrklgdtdkAleal 23  
                                        la++  ++g++++A++ +
  gi|330507412|ref|YP_004383840.1| 1197 LAECEARTGKKEEARADY 1214
                                        89*****99******977 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       9.1   4.7e+03      48      64 ..      85     101 ..      53     143 .. 0.54
   2 ?   -2.0   0.0       4.8   2.4e+03      49      64 ..     205     220 ..     191     269 .. 0.70
   3 !   13.7   0.3   7.6e-05     0.039      35     124 ..     271     362 ..     245     373 .. 0.77
   4 !   13.8   0.2   7.1e-05     0.037      13     110 ..     328     428 ..     324     432 .. 0.91
   5 ?    5.7   0.0     0.021        11      36     136 ..     431     534 ..     427     545 .. 0.81
   6 ?    4.3   0.0     0.058        30       8      62 ..     523     577 ..     518     594 .. 0.82
   7 ?   -2.1   0.0       5.2   2.6e+03      38      63 ..     593     618 ..     587     626 .. 0.84
   8 !   11.2   0.0   0.00043      0.22      42     136 ..     637     734 ..     622     741 .. 0.86
   9 !    7.2   0.0    0.0073       3.7      11     109 ..     726     854 ..     726     883 .. 0.70
  10 !   16.3   0.0   1.2e-05    0.0059      15     139 ..     890    1017 ..     878    1154 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.1
                                       HCT-HHHHHHHHHTCCC CS
                              RPN7  48 kigdleeAlkaysrire 64 
                                           ++ A+++ys + +
  gi|330507412|ref|YP_004383840.1|  85 HLFFHQAAIEYYSNASD 101
                                       44444444444444433 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.8
                                       CT-HHHHHHHHHTCCC CS
                              RPN7  49 igdleeAlkaysrire 64 
                                        gd+e+A k+y+ i++
  gi|330507412|ref|YP_004383840.1| 205 QGDMEKAEKLYQTILK 220
                                       5777777777776654 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 7.6e-05
                                       HHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHT...T-HHHHHHHHHHHHCSSS---. CS
                              RPN7  35 irrakldlaehYlkigdleeAlkaysrireyctslkhkidmllnlirvaiff...ndwdlvskylekakellekggd 108
                                        ++ + +la+ Y+  g l+eAl++y r +  + + +h      +l r++ +f   ++w l++ +l++a +++++ +d
  gi|330507412|ref|YP_004383840.1| 271 AAEMQCRLADIYFHEGRLKEALELYGRSLAALQK-GHPSLASKALCRMGQCFledGNWTLAEDHLQRAIAIMKEHKD 346
                                       3556779********************9887665.6666666777777766644489******************** PP

                                       HHHHHHHHHHHHHHHH CS
                              RPN7 109 werknrlkvyeGlall 124
                                        +  +r  v+ +  + 
  gi|330507412|ref|YP_004383840.1| 347 SSSLARALVILAGVHH 362
                                       **99998776555444 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 7.1e-05
                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHT...CCCC--SHHHHHHHHHHHHHHHHHT CS
                              RPN7  13 ekeleeLdaelkdakenlgkeeirrakldlaehYlkigdleeAlkaysr...ireyctslkhkidmllnlirvaiff 86 
                                       +   ++L++ +   ke   +++ +ra   la  ++k g+le Al++ ++   ire +  l+ +++ l ++ r++   
  gi|330507412|ref|YP_004383840.1| 328 TLAEDHLQRAIAIMKEHKDSSSLARALVILAGVHHKQGQLEMALQCSREslkIRERSKDLSGSAEALNCIARICCDC 404
                                       556689****************************************9977779************************ PP

                                       T-HHHHHHHHHHHHCSSS---.HH CS
                              RPN7  87 ndwdlvskylekakellekggdwe 110
                                        dw  + +  ++a +l  ++g+++
  gi|330507412|ref|YP_004383840.1| 405 SDWPEAIECYQRAADLFMEMGEVT 428
                                       *****9999999999988887765 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHH..HHHHHHHHHHHHHHH.TT-HHHHHHHHHHHHCSSS---.H CS
                              RPN7  36 rrakldlaehYlkigdleeAlkaysrireyctslk..hkidmllnlirvaif.fndwdlvskylekakellekggdw 109
                                       ++a  +l+  Y+  gdl+ Al++ys +++   + +  + ++m+ + i + +  ++d +l+ ++lek  ++ e+ gd+
  gi|330507412|ref|YP_004383840.1| 431 AEALSNLGGVYHLKGDLDVALQMYSHAYNSFCQQGdrQGASMVQSNIGLVYQsRGDLHLAGEFLEKSIATKEDLGDQ 507
                                       678889999*****************99998887622457788777777764368999********99999999998 PP

                                       HHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                              RPN7 110 erknrlkvyeGlallairkfkeAaell 136
                                          +  + + Gl++   +++ +A +++
  gi|330507412|ref|YP_004383840.1| 508 IGAAGNRLSLGLIYQLGGEWDQAQSCF 534
                                       777777777888888888888888877 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.058
                                       HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7   8 lrkknekeleeLdaelkdakenlgkeeirrakldlaehYlkigdleeAlkaysri 62 
                                       l  ++++  + ++   +  ++n+     ++a ++l++ Y + gdl  A+ +y++ 
  gi|330507412|ref|YP_004383840.1| 523 LGGEWDQAQSCFEGAARAFEDNGDLRGLAAAENNLGNLYSDRGDLMHAILCYRQG 577
                                       5566777777777777777777777888999*********************984 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 5.2
                                       HHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  38 akldlaehYlkigdleeAlkaysrir 63 
                                       +  +la  Yl+ g+ e A ++y++ +
  gi|330507412|ref|YP_004383840.1| 593 TLGNLAGVYLQSGEEERAEELYQQSI 618
                                       66789999**************9866 PP

  == domain 8  score: 11.2 bits;  conditional E-value: 0.00043
                                       HHHHHHHCT-HHHHHHHHHTCCCC--...SHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHCSSS---.HHHHHHH CS
                              RPN7  42 laehYlkigdleeAlkaysrireyct...slkhkidmllnlirvaiffndwdlvskylekakellekggdwerknrl 115
                                       la+  ++ gdle Al++y+++++  +    + + i+ l +++ + + ++ w+ + +  +++ e l + +d ++ + +
  gi|330507412|ref|YP_004383840.1| 637 LARSMAERGDLEGALECYRKCLDLQIvggDSRSMIEALESMVNLLLRRGRWQEALTRYAQVLEALRSRDDLSAVAAV 713
                                       66667889************99988722235567888899***************9999999999999********* PP

                                       HHHHHHHHHHTT-HHHHHHHH CS
                              RPN7 116 kvyeGlallairkfkeAaell 136
                                       +++ G +++  +++ eA e  
  gi|330507412|ref|YP_004383840.1| 714 QCALGNLHADLGQWDEALEDY 734
                                       *****************8865 PP

  == domain 9  score: 7.2 bits;  conditional E-value: 0.0073
                                       HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC...C--SHHHHHHHHHHHHHHHH CS
                              RPN7  11 knekeleeLdaelkdakenlgkeeirrakldlaehYlkigdleeAlkaysrire...yctslkhkidmllnlirvai 84 
                                       ++++ le+ ++ l   +  + + ++  a ++l++  ++ gd + Al++y+  +e   +   +++ +++l n+  +++
  gi|330507412|ref|YP_004383840.1| 726 QWDEALEDYNESLAIMEGLGDEYSVSVARNNLGNMCYRQGDWAAALENYRLSLEgfgKAGDMESEASVLSNVAGLCY 802
                                       57888888888888666666666899999999999999999999999999766533377778889999999999999 PP

                                       HTT-HHHHHHHHHHHHCSSS---............................H CS
                              RPN7  85 ffndwdlvskylekakellekggd...........................w 109
                                        +++w+ +    +k  +l ek +d                            
  gi|330507412|ref|YP_004383840.1| 803 KRGQWADALDSYSKSLSLFEKLEDsagiaqvlgnmgnlyhrqgerdlaaehF 854
                                       9999999999999999999999995555544333333333333333333220 PP

  == domain 10  score: 16.3 bits;  conditional E-value: 1.2e-05
                                        HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHTT-H CS
                              RPN7   15 eleeLdaelkdakenlgkeeirrakldlaehYlkigdleeAlkaysrireyctslkhkidmllnlirvaiffndw 89  
                                         +ee +++l++ +e++  +   +   +la  Y++ g+ +eA+++y+r +e   +++ + +    l  +a+ ++d+
  gi|330507412|ref|YP_004383840.1|  890 DIEEYKRQLEELEETGDLSGQGEVLSALAGSYTDSGQWAEAIACYKRSVERFDQTGEVYNRGQVLFNMALVYKDM 964 
                                        67889999999888888888889999*********************************9999999999998888 PP

                                        HHHHHHHHHHHCSSS---....HHHHHHHHHHHHHHHHHTT-HHHHHHHHCTS CS
                              RPN7   90 dlvskylekakellekggd...werknrlkvyeGlallairkfkeAaellldi 139 
                                        + +++        l+  +d       +  k   G+++ ++++  eA el+ ++
  gi|330507412|ref|YP_004383840.1|  965 GDLNRARTLFDVALDIFQDldaLPCVASAKLNLGIISGQMGRSDEAIELFSQS 1017
                                        77665444444444433332224444555666666666666666666666655 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       3.6   1.8e+03       2      29 ..      74     101 ..      73     111 .. 0.85
   2 ?    3.3   0.1      0.36   1.8e+02       4      29 ..     116     141 ..     113     149 .. 0.91
   3 ?    4.3   0.1      0.18        92       3      37 ..     155     190 ..     153     195 .. 0.84
   4 !    8.7   0.2    0.0069       3.5       2      43 ..     193     237 ..     192     239 .. 0.78
   5 ?    0.6   0.1       2.8   1.4e+03       2      27 ..     233     258 ..     231     269 .. 0.85
   6 !   10.6   0.2    0.0017      0.86       5      30 ..     276     301 ..     272     320 .. 0.74
   7 ?    5.9   0.0     0.052        27       4      40 ..     314     353 ..     311     357 .. 0.76
   8 ?    2.7   0.0      0.58   2.9e+02       2      31 ..     352     381 ..     351     387 .. 0.86
   9 ?    4.2   0.0      0.19        97       2      34 ..     392     424 ..     391     434 .. 0.76
  10 ?    0.5   0.0         3   1.5e+03       2      25 ..     432     455 ..     431     458 .. 0.87
  11 ?    4.3   0.3      0.17        89       5      42 ..     515     552 ..     511     554 .. 0.87
  12 ?    6.4   0.1     0.037        19       7      29 ..     597     619 ..     593     629 .. 0.89
  13 !   10.5   0.1    0.0018       0.9       3      30 ..     633     660 ..     631     667 .. 0.91
  14 ?    5.7   1.0     0.062        32       3      30 ..     673     700 ..     671     713 .. 0.79
  15 ?    7.3   0.1     0.019       9.6       6      29 ..     716     739 ..     710     744 .. 0.87
  16 ?    1.2   0.0       1.8   9.2e+02       7      29 ..     757     779 ..     753     786 .. 0.84
  17 ?    4.4   0.0      0.17        85       9      33 ..     799     823 ..     795     837 .. 0.79
  18 !    8.2   1.1    0.0097         5       7      38 ..     837     871 ..     831     877 .. 0.76
  19 !   12.0   0.0   0.00058       0.3       3      34 ..     913     944 ..     912     950 .. 0.86
  20 ?    2.4   0.0      0.73   3.7e+02       7      33 ..     957     983 ..     952    1000 .. 0.83
  21 ?    0.1   0.0       3.8     2e+03      13      27 ..    1003    1017 ..     991    1022 .. 0.83
  22 ?    5.7   0.2     0.064        33       5      31 ..    1115    1141 ..    1111    1147 .. 0.86
  23 ?   -0.6   0.2       6.7   3.4e+03       2      23 ..    1152    1173 ..    1151    1176 .. 0.86
  24 ?    1.0   0.5         2     1e+03       4      32 ..    1194    1222 ..    1192    1226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 3.6
                            TPR_14   2 eallalaeallalGdpdeAiallrrala 29 
                                       +a+  l+++  +l  +++Ai+++  a +
  gi|330507412|ref|YP_004383840.1|  74 QAWFNLGRLAHHLFFHQAAIEYYSNASD 101
                                       6899999999999999******998865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.36
                            TPR_14   4 llalaeallalGdpdeAiallrrala 29 
                                       ll+l++++ + +d+++A +++++al 
  gi|330507412|ref|YP_004383840.1| 116 LLCLGALYGEEEDWARACQCYEKALV 141
                                       799********************985 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.18
                            TPR_14   3 allalaeallalGdpdeAiallrrala.laPddaea 37 
                                       +l +l++a + +G++ +A  ++ r+l+ l+P d   
  gi|330507412|ref|YP_004383840.1| 155 VLERLGRARRLQGEYHQAQICYSRILEvLDPRDKKG 190
                                       56789********************99668988655 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0069
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaP...ddaeawlllaq 43 
                                       ea+  lae++  +Gd ++A++l++ +l+      d+  a ++la 
  gi|330507412|ref|YP_004383840.1| 193 EATSNLAELCQIQGDMEKAEKLYQTILKERElsdDPVGAARALAS 237
                                       667779**********************65433144567777775 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 2.8
                            TPR_14   2 eallalaeallalGdpdeAiallrra 27 
                                       +al+ la+++ + G+ ++A   l+ a
  gi|330507412|ref|YP_004383840.1| 233 RALASLASIYSQTGNGKRAQISLQSA 258
                                       79999**********99998777766 PP

  == domain 6  score: 10.6 bits;  conditional E-value: 0.0017
                            TPR_14   5 lalaeallalGdpdeAiallrralal 30 
                                        +la+++++ G+++eA++l+ r la+
  gi|330507412|ref|YP_004383840.1| 276 CRLADIYFHEGRLKEALELYGRSLAA 301
                                       589*******************9984 PP

  == domain 7  score: 5.9 bits;  conditional E-value: 0.052
                            TPR_14   4 llalaeallalGdpdeAiallrrala...laPddaeawll 40 
                                       l ++++ +l+ G++  A+++l+ra+a    + d+  + ++
  gi|330507412|ref|YP_004383840.1| 314 LCRMGQCFLEDGNWTLAEDHLQRAIAimkEHKDSSSLARA 353
                                       557899999****************955546666655555 PP

  == domain 8  score: 2.7 bits;  conditional E-value: 0.58
                            TPR_14   2 eallalaeallalGdpdeAiallrralala 31 
                                       +al  la ++  +G+++ A+++ r+ l+  
  gi|330507412|ref|YP_004383840.1| 352 RALVILAGVHHKQGQLEMALQCSRESLKIR 381
                                       68899****************999998865 PP

  == domain 9  score: 4.2 bits;  conditional E-value: 0.19
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPdd 34 
                                       eal ++a+++    d+ eAi++++ra +l+ + 
  gi|330507412|ref|YP_004383840.1| 392 EALNCIARICCDCSDWPEAIECYQRAADLFMEM 424
                                       677788888888899999999999998887655 PP

  == domain 10  score: 0.5 bits;  conditional E-value: 3
                            TPR_14   2 eallalaeallalGdpdeAiallr 25 
                                       eal  l+ ++   Gd+d A++++ 
  gi|330507412|ref|YP_004383840.1| 432 EALSNLGGVYHLKGDLDVALQMYS 455
                                       678889999*************96 PP

  == domain 11  score: 4.3 bits;  conditional E-value: 0.17
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       l l+ ++   G++d+A  +++ a +++ d+ +++ l a
  gi|330507412|ref|YP_004383840.1| 515 LSLGLIYQLGGEWDQAQSCFEGAARAFEDNGDLRGLAA 552
                                       6788899999*******************999887665 PP

  == domain 12  score: 6.4 bits;  conditional E-value: 0.037
                            TPR_14   7 laeallalGdpdeAiallrrala 29 
                                       la ++l++G+ ++A++l+++ ++
  gi|330507412|ref|YP_004383840.1| 597 LAGVYLQSGEEERAEELYQQSID 619
                                       899****************9876 PP

  == domain 13  score: 10.5 bits;  conditional E-value: 0.0018
                            TPR_14   3 allalaeallalGdpdeAiallrralal 30 
                                        l+ la+ ++++Gd+++A++++r++l+l
  gi|330507412|ref|YP_004383840.1| 633 SLYGLARSMAERGDLEGALECYRKCLDL 660
                                       6899********************9985 PP

  == domain 14  score: 5.7 bits;  conditional E-value: 0.062
                            TPR_14   3 allalaeallalGdpdeAiallrralal 30 
                                       al  ++ +ll++G+++eA++ + ++l++
  gi|330507412|ref|YP_004383840.1| 673 ALESMVNLLLRRGRWQEALTRYAQVLEA 700
                                       66678999****************9995 PP

  == domain 15  score: 7.3 bits;  conditional E-value: 0.019
                            TPR_14   6 alaeallalGdpdeAiallrrala 29 
                                       al+ +++ lG++deA++ +++ la
  gi|330507412|ref|YP_004383840.1| 716 ALGNLHADLGQWDEALEDYNESLA 739
                                       899**************9999887 PP

  == domain 16  score: 1.2 bits;  conditional E-value: 1.8
                            TPR_14   7 laeallalGdpdeAiallrrala 29 
                                       l+  ++++Gd+++A++ +r  l+
  gi|330507412|ref|YP_004383840.1| 757 LGNMCYRQGDWAAALENYRLSLE 779
                                       678899*********99987765 PP

  == domain 17  score: 4.4 bits;  conditional E-value: 0.17
                            TPR_14   9 eallalGdpdeAiallrralalaPd 33 
                                        +++ +G++++A++ + + l+l+ +
  gi|330507412|ref|YP_004383840.1| 799 GLCYKRGQWADALDSYSKSLSLFEK 823
                                       578899***************9863 PP

  == domain 18  score: 8.2 bits;  conditional E-value: 0.0097
                            TPR_14   7 laeallalGdpdeAiallrralala...Pddaeaw 38 
                                       ++ ++ ++G+ d A+++++ral+ +    d+a a 
  gi|330507412|ref|YP_004383840.1| 837 MGNLYHRQGERDLAAEHFQRALEIYrrlKDQAGAA 871
                                       67899*****************9652224555555 PP

  == domain 19  score: 12.0 bits;  conditional E-value: 0.00058
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPdd 34 
                                       +l ala  +  +G+++eAia+++r ++++ + 
  gi|330507412|ref|YP_004383840.1| 913 VLSALAGSYTDSGQWAEAIACYKRSVERFDQT 944
                                       6789**********************998665 PP

  == domain 20  score: 2.4 bits;  conditional E-value: 0.73
                            TPR_14   7 laeallalGdpdeAiallrralalaPd 33 
                                       +a ++   Gd+ +A++l++ al+ + d
  gi|330507412|ref|YP_004383840.1| 957 MALVYKDMGDLNRARTLFDVALDIFQD 983
                                       7899**************999987654 PP

  == domain 21  score: 0.1 bits;  conditional E-value: 3.8
                            TPR_14   13 alGdpdeAiallrra 27  
                                        + G+ deAi+l+ + 
  gi|330507412|ref|YP_004383840.1| 1003 QMGRSDEAIELFSQS 1017
                                        6799*******9876 PP

  == domain 22  score: 5.7 bits;  conditional E-value: 0.064
                            TPR_14    5 lalaeallalGdpdeAiallrralala 31  
                                          l+++ la+Gd+++A++  ++al  +
  gi|330507412|ref|YP_004383840.1| 1115 SSLGRLALASGDYEDALRRMKQALVIF 1141
                                        5699**************999999765 PP

  == domain 23  score: -0.6 bits;  conditional E-value: 6.7
                            TPR_14    2 eallalaeallalGdpdeAial 23  
                                        e+++++  ++la++d+++A+++
  gi|330507412|ref|YP_004383840.1| 1152 EVYRDMTLLFLAQDDYQRAEEM 1173
                                        5678888899*********998 PP

  == domain 24  score: 1.0 bits;  conditional E-value: 2
                            TPR_14    4 llalaeallalGdpdeAiallrralalaP 32  
                                        + +lae +++ G+ +eA+a +  al+la 
  gi|330507412|ref|YP_004383840.1| 1194 TVDLAECEARTGKKEEARADYAGALRLAG 1222
                                        67899999999999999999999998875 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.6         1   5.3e+02       2      21 ..     154     173 ..     153     173 .. 0.84
   2 ?    4.8   0.0      0.11        57       2      21 ..     193     212 ..     192     216 .. 0.89
   3 ?   -0.8   0.0       6.8   3.5e+03       1      20 [.     232     251 ..     232     252 .. 0.87
   4 ?    5.7   0.1     0.054        28       7      24 ..     278     295 ..     275     297 .. 0.89
   5 !    9.2   0.2    0.0042       2.1       1      25 [.     351     375 ..     351     376 .. 0.91
   6 ?    2.5   0.0      0.59     3e+02       1      23 [.     431     453 ..     431     454 .. 0.88
   7 ?    3.9   0.0      0.21   1.1e+02       4      24 ..     514     534 ..     514     535 .. 0.87
   8 ?   -1.1   0.1       8.5   4.4e+03       6      17 ..     556     567 ..     551     577 .. 0.76
   9 ?    5.8   0.1     0.054        27       1      26 []     591     616 ..     591     616 .. 0.91
  10 !   14.7   0.2   6.7e-05     0.035       1      25 [.     631     655 ..     631     656 .. 0.92
  11 ?    6.3   0.5     0.037        19       8      25 ..     678     695 ..     672     696 .. 0.81
  12 !    9.3   1.5     0.004         2       1      22 [.     711     732 ..     711     732 .. 0.91
  13 !    9.9   0.1    0.0026       1.3       2      22 ..     752     772 ..     751     772 .. 0.92
  14 ?   -0.5   0.0       5.4   2.8e+03       9      22 ..     799     812 ..     791     813 .. 0.80
  15 !    9.8   0.3    0.0026       1.3       1      26 []     831     856 ..     831     856 .. 0.91
  16 ?    1.4   0.0       1.4   7.1e+02       3      22 ..     913     932 ..     911     936 .. 0.86
  17 ?    2.0   0.0      0.89   4.5e+02       2      24 ..     952     974 ..     951     975 .. 0.89
  18 ?    1.1   0.0       1.6   8.4e+02       2      23 ..     992    1013 ..     991    1016 .. 0.84
  19 !    9.9   0.1    0.0025       1.3       6      24 ..    1116    1134 ..    1115    1136 .. 0.90
  20 ?    3.2   0.1      0.35   1.8e+02       3      22 ..    1193    1212 ..    1191    1212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 1
                             TPR_4   2 rallaLArallalGdldeAr 21 
                                       ++l  L+ra  ++G++ +A+
  gi|330507412|ref|YP_004383840.1| 154 QVLERLGRARRLQGEYHQAQ 173
                                       566679**********9996 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.11
                             TPR_4   2 rallaLArallalGdldeAr 21 
                                        a+++LA++++ +Gd + A+
  gi|330507412|ref|YP_004383840.1| 193 EATSNLAELCQIQGDMEKAE 212
                                       699************99887 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 6.8
                             TPR_4   1 arallaLArallalGdldeA 20 
                                       aral+ LA  + ++G+  +A
  gi|330507412|ref|YP_004383840.1| 232 ARALASLASIYSQTGNGKRA 251
                                       7999******9999998877 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.054
                             TPR_4   7 LArallalGdldeArall 24 
                                       LA  +++ G+l eA++l 
  gi|330507412|ref|YP_004383840.1| 278 LADIYFHEGRLKEALELY 295
                                       9**************996 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0042
                             TPR_4   1 arallaLArallalGdldeAralle 25 
                                       aral+ LA +++ +G+l+ A++  +
  gi|330507412|ref|YP_004383840.1| 351 ARALVILAGVHHKQGQLEMALQCSR 375
                                       79******************98755 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.59
                             TPR_4   1 arallaLArallalGdldeAral 23 
                                       a al++L+ ++++ Gdld A+++
  gi|330507412|ref|YP_004383840.1| 431 AEALSNLGGVYHLKGDLDVALQM 453
                                       579**************988775 PP

  == domain 7  score: 3.9 bits;  conditional E-value: 0.21
                             TPR_4   4 llaLArallalGdldeArall 24 
                                       +l L+  +++ G++d+A+  +
  gi|330507412|ref|YP_004383840.1| 514 RLSLGLIYQLGGEWDQAQSCF 534
                                       6789*************9766 PP

  == domain 8  score: -1.1 bits;  conditional E-value: 8.5
                             TPR_4   6 aLArallalGdl 17 
                                       +L+ ++ ++Gdl
  gi|330507412|ref|YP_004383840.1| 556 NLGNLYSDRGDL 567
                                       788888888885 PP

  == domain 9  score: 5.8 bits;  conditional E-value: 0.054
                             TPR_4   1 arallaLArallalGdldeAraller 26 
                                       a++l +LA ++l+ G+ ++A++l ++
  gi|330507412|ref|YP_004383840.1| 591 AVTLGNLAGVYLQSGEEERAEELYQQ 616
                                       57899*****************9876 PP

  == domain 10  score: 14.7 bits;  conditional E-value: 6.7e-05
                             TPR_4   1 arallaLArallalGdldeAralle 25 
                                       ar l++LAr ++++Gdl+ A++  +
  gi|330507412|ref|YP_004383840.1| 631 ARSLYGLARSMAERGDLEGALECYR 655
                                       6899*****************9887 PP

  == domain 11  score: 6.3 bits;  conditional E-value: 0.037
                             TPR_4   8 ArallalGdldeAralle 25 
                                         +ll++G++ eA++  +
  gi|330507412|ref|YP_004383840.1| 678 VNLLLRRGRWQEALTRYA 695
                                       578***********9765 PP

  == domain 12  score: 9.3 bits;  conditional E-value: 0.004
                             TPR_4   1 arallaLArallalGdldeAra 22 
                                       a+++ aL+ ++++lG++deA++
  gi|330507412|ref|YP_004383840.1| 711 AAVQCALGNLHADLGQWDEALE 732
                                       57899***************85 PP

  == domain 13  score: 9.9 bits;  conditional E-value: 0.0026
                             TPR_4   2 rallaLArallalGdldeAra 22 
                                       +a+ +L+  ++++Gd+++A++
  gi|330507412|ref|YP_004383840.1| 752 VARNNLGNMCYRQGDWAAALE 772
                                       6899***************85 PP

  == domain 14  score: -0.5 bits;  conditional E-value: 5.4
                             TPR_4   9 rallalGdldeAra 22 
                                        +++ +G++++A++
  gi|330507412|ref|YP_004383840.1| 799 GLCYKRGQWADALD 812
                                       57889*******85 PP

  == domain 15  score: 9.8 bits;  conditional E-value: 0.0026
                             TPR_4   1 arallaLArallalGdldeAraller 26 
                                       a++l +++ +++++G+ d A+++++r
  gi|330507412|ref|YP_004383840.1| 831 AQVLGNMGNLYHRQGERDLAAEHFQR 856
                                       578899****************9976 PP

  == domain 16  score: 1.4 bits;  conditional E-value: 1.4
                             TPR_4   3 allaLArallalGdldeAra 22 
                                       +l+aLA  + + G+++eA a
  gi|330507412|ref|YP_004383840.1| 913 VLSALAGSYTDSGQWAEAIA 932
                                       6899**************66 PP

  == domain 17  score: 2.0 bits;  conditional E-value: 0.89
                             TPR_4   2 rallaLArallalGdldeArall 24 
                                       ++l ++A ++ + Gdl +Ar+l+
  gi|330507412|ref|YP_004383840.1| 952 QVLFNMALVYKDMGDLNRARTLF 974
                                       57899***************997 PP

  == domain 18  score: 1.1 bits;  conditional E-value: 1.6
                             TPR_4    2 rallaLArallalGdldeAral 23  
                                         a l+L+    + G++deA +l
  gi|330507412|ref|YP_004383840.1|  992 SAKLNLGIISGQMGRSDEAIEL 1013
                                        678999999999*******766 PP

  == domain 19  score: 9.9 bits;  conditional E-value: 0.0025
                             TPR_4    6 aLArallalGdldeArall 24  
                                         L+r++la Gd+++A++ +
  gi|330507412|ref|YP_004383840.1| 1116 SLGRLALASGDYEDALRRM 1134
                                        59**************976 PP

  == domain 20  score: 3.2 bits;  conditional E-value: 0.35
                             TPR_4    3 allaLArallalGdldeAra 22  
                                        a+++LA+  +++G  +eAra
  gi|330507412|ref|YP_004383840.1| 1193 ATVDLAECEARTGKKEEARA 1212
                                        8999**************98 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       5.7   2.9e+03       7      28 ..      89     114 ..      89     119 .. 0.66
   2 !    9.7   0.4    0.0023       1.2       4      56 ..     166     223 ..     163     235 .. 0.78
   3 ?    7.4   1.6     0.012       6.4       4      53 ..     205     260 ..     205     272 .. 0.81
   4 !   12.6   1.4   0.00029      0.15       7      60 ..     255     308 ..     249     320 .. 0.83
   5 ?    7.4   0.2     0.012       6.1       2      46 ..     329     372 ..     321     380 .. 0.78
   6 ?    2.7   0.1      0.37   1.9e+02      25      50 ..     411     436 ..     391     443 .. 0.78
   7 ?   -1.0   0.0         5   2.6e+03       5      18 ..     445     458 ..     441     468 .. 0.88
   8 ?    3.0   0.1       0.3   1.5e+02       5      33 ..     525     552 ..     485     560 .. 0.75
   9 ?    7.5   0.1     0.012         6      25      51 ..     591     617 ..     563     629 .. 0.81
  10 ?    1.8   0.1       0.7   3.6e+02      23      48 ..     629     654 ..     621     661 .. 0.80
  11 !   11.3   1.4   0.00074      0.38       1      46 [.     681     732 ..     681     733 .. 0.76
  12 ?    2.2   0.3      0.51   2.6e+02       5      46 ..     732     772 ..     722     783 .. 0.67
  13 ?    3.9   0.1      0.15        77       3      46 ..     763     812 ..     761     817 .. 0.78
  14 !    9.1   0.8    0.0037       1.9       3      57 ..     803     863 ..     802     877 .. 0.78
  15 ?    7.2   0.0     0.014       7.3      21      57 ..     907     943 ..     895     950 .. 0.81
  16 !   14.0   0.0   0.00011     0.055       3      57 ..     923     983 ..     921     997 .. 0.88
  17 ?    0.1   0.0       2.3   1.2e+03       3      17 ..    1003    1017 ..    1003    1022 .. 0.80
  18 !    9.6   0.2    0.0025       1.3       1      18 [.    1121    1138 ..    1087    1156 .. 0.62
  19 ?    4.5   4.3     0.096        49       2      46 ..    1162    1212 ..    1161    1223 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5.7
                            TPR_19   7 yaeAlalleqalqe....dpknaear 28 
                                       +++A++++++a +     + +++ a 
  gi|330507412|ref|YP_004383840.1|  89 HQAAIEYYSNASDLaqilSDDDSLAS 114
                                       689*******9765445444455555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0023
                            TPR_19   4 egdyaeAlalleqalqe.....dpknaearllLAeallalgqldeAealLdalpeedp 56 
                                       +g y +A+  ++++l+      + +  ea  +LAe++  +g+ ++Ae+l +++++e  
  gi|330507412|ref|YP_004383840.1| 166 QGEYHQAQICYSRILEVldprdKKGRMEATSNLAELCQIQGDMEKAEKLYQTILKERE 223
                                       78888888888888877633324445566669**********************9876 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.012
                            TPR_19   4 egdyaeAlalleqalqe.....dpk.naearllLAeallalgqldeAealLdalpe 53 
                                       +gd + A +l++ +l+e     dp   a+a++ LA ++ ++g+ + A+  L+ +  
  gi|330507412|ref|YP_004383840.1| 205 QGDMEKAEKLYQTILKErelsdDPVgAARALASLASIYSQTGNGKRAQISLQSASH 260
                                       8999*********997766533443677888889**************99998765 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00029
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd.dar 60 
                                       +++A  ll+  l++  + ae + +LA++++  g+l+eA +l  + +++ ++ ++ 
  gi|330507412|ref|YP_004383840.1| 255 LQSASHLLAD-LKDQSGAAEMQCRLADIYFHEGRLKEALELYGRSLAALQKgHPS 308
                                       6777778888.688899999999******************99999999884454 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.012
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                       lae  +++A+a++++  +++   a+a+  LA ++ ++gql+ A +
  gi|330507412|ref|YP_004383840.1| 329 LAEDHLQRAIAIMKE-HKDSSSLARALVILAGVHHKQGQLEMALQ 372
                                       566677777777777.67777777777788**********99987 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.37
                            TPR_19  25 aearllLAeallalgqldeAealLda 50 
                                        e   + A++ +++g++++A ++L+ 
  gi|330507412|ref|YP_004383840.1| 411 IECYQRAADLFMEMGEVTAAAEALSN 436
                                       55566778888888888888888865 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 5
                            TPR_19   5 gdyaeAlalleqal 18 
                                       gd++ Al++++ a+
  gi|330507412|ref|YP_004383840.1| 445 GDLDVALQMYSHAY 458
                                       9*********9986 PP

  == domain 8  score: 3.0 bits;  conditional E-value: 0.3
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAe 33 
                                       g  ++A++ +e a  +  +n+++r  LA 
  gi|330507412|ref|YP_004383840.1| 525 GEWDQAQSCFEGAARAFEDNGDLRG-LAA 552
                                       4456666666666666666666666.444 PP

  == domain 9  score: 7.5 bits;  conditional E-value: 0.012
                            TPR_19  25 aearllLAeallalgqldeAealLdal 51 
                                       a  + +LA ++l++g+ + Ae+l ++ 
  gi|330507412|ref|YP_004383840.1| 591 AVTLGNLAGVYLQSGEEERAEELYQQS 617
                                       555669****************99875 PP

  == domain 10  score: 1.8 bits;  conditional E-value: 0.7
                            TPR_19  23 knaearllLAeallalgqldeAealL 48 
                                       + a+ +++LA+ + + g+l+ A ++ 
  gi|330507412|ref|YP_004383840.1| 629 GEARSLYGLARSMAERGDLEGALECY 654
                                       56777899999999999999999875 PP

  == domain 11  score: 11.3 bits;  conditional E-value: 0.00074
                            TPR_19   1 llaegdyaeAlalleqalqe......dpknaearllLAeallalgqldeAea 46 
                                       ll +g+ +eAl +++q+l++          a+++ +L +++  lgq+deA +
  gi|330507412|ref|YP_004383840.1| 681 LLRRGRWQEALTRYAQVLEAlrsrddLSAVAAVQCALGNLHADLGQWDEALE 732
                                       7899**************8854222233345555599************975 PP

  == domain 12  score: 2.2 bits;  conditional E-value: 0.51
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                       +dy e la++e + +e    + ar +L + ++ +g++++A +
  gi|330507412|ref|YP_004383840.1| 732 EDYNESLAIMEGLGDE-YSVSVARNNLGNMCYRQGDWAAALE 772
                                       3444444445553333.3377888899999999999999975 PP

  == domain 13  score: 3.9 bits;  conditional E-value: 0.15
                            TPR_19   3 aegdyaeAlalleqalqedpk......naearllLAeallalgqldeAea 46 
                                        +gd a+Al+ ++  l+   k       a ++ + A ++++ gq+++A +
  gi|330507412|ref|YP_004383840.1| 763 RQGDWAAALENYRLSLEGFGKagdmesEASVLSNVAGLCYKRGQWADALD 812
                                       69***********9999977766674344444466************986 PP

  == domain 14  score: 9.1 bits;  conditional E-value: 0.0037
                            TPR_19   3 aegdyaeA.......lalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       ++g+ a+A       l+l+e+ l+++++ a ++ ++ +++  +g+ d A +  ++++e ++ 
  gi|330507412|ref|YP_004383840.1| 803 KRGQWADAldsysksLSLFEK-LEDSAGIAQVLGNMGNLYHRQGERDLAAEHFQRALEIYRR 863
                                       689999994444444555555.588999999999********************99998776 PP

  == domain 15  score: 7.2 bits;  conditional E-value: 0.014
                            TPR_19  21 dpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                         +++e++ +LA  +  +gq++eA+a+ ++  e + +
  gi|330507412|ref|YP_004383840.1| 907 LSGQGEVLSALAGSYTDSGQWAEAIACYKRSVERFDQ 943
                                       4668999999*****************9998887766 PP

  == domain 16  score: 14.0 bits;  conditional E-value: 0.00011
                            TPR_19   3 aegdyaeAlalleqalqedpk......naearllLAeallalgqldeAealLdalpeedpd 57 
                                       ++g+ aeA+a +++  +   +       + ++ ++A ++  +g+l+ A+ l d +++ ++d
  gi|330507412|ref|YP_004383840.1| 923 DSGQWAEAIACYKRSVERFDQtgevynRGQVLFNMALVYKDMGDLNRARTLFDVALDIFQD 983
                                       689*****99999999887776666668888889*************************99 PP

  == domain 17  score: 0.1 bits;  conditional E-value: 2.3
                            TPR_19    3 aegdyaeAlalleqa 17  
                                        ++g+ +eA++l++q 
  gi|330507412|ref|YP_004383840.1| 1003 QMGRSDEAIELFSQS 1017
                                        578889999999885 PP

  == domain 18  score: 9.6 bits;  conditional E-value: 0.0025
                            TPR_19    1 llaegdyaeAlalleqal 18  
                                        +la+gdy++Al++++qal
  gi|330507412|ref|YP_004383840.1| 1121 ALASGDYEDALRRMKQAL 1138
                                        355566666666666554 PP

  == domain 19  score: 4.5 bits;  conditional E-value: 0.096
                            TPR_19    2 laegdyaeA..lalleq....alqedpknaearllLAeallalgqldeAea 46  
                                        la+ dy++A  +a+l+q    +l ++  ++ a  +LAe+   +g  +eA+a
  gi|330507412|ref|YP_004383840.1| 1162 LAQDDYQRAeeMAMLRQrqarILGHADLSLLATVDLAECEARTGKKEEARA 1212
                                        89*********99999966555555555888888***************97 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 ?    2.1   0.2      0.39     2e+02      21      37 ..      90     106 ..      89     116 .. 0.81
   2 ?    1.6   0.1      0.56   2.8e+02      16      34 ..     125     143 ..     111     150 .. 0.83
   3 ?    4.6   0.0     0.068        35      17      37 ..     285     305 ..     284     313 .. 0.89
   4 !   10.3   0.0    0.0011      0.58      19      37 ..     406     424 ..     405     437 .. 0.88
   5 ?    0.5   0.1       1.2   6.4e+02      17      34 ..     444     461 ..     440     464 .. 0.86
   6 ?    7.1   0.0     0.011       5.8       4      36 ..     591     623 ..     589     634 .. 0.88
   7 !    8.0   0.0    0.0057       2.9      11      33 ..     638     660 ..     629     684 .. 0.80
   8 ?   -0.3   0.0       2.3   1.2e+03      17      34 ..     684     701 ..     680     703 .. 0.85
   9 ?    1.4   0.0      0.65   3.3e+02      18      34 ..     725     741 ..     711     757 .. 0.86
  10 ?    3.3   0.0      0.17        89      17      39 ..     764     786 ..     763     797 .. 0.83
  11 ?    4.8   0.0     0.059        30      16      37 ..     803     824 ..     790     831 .. 0.89
  12 ?    5.9   0.0     0.027        14      17      36 ..     924     943 ..     916     947 .. 0.89
  13 ?   -2.3   0.0       9.8     5e+03       7      35 ..     954     982 ..     948     984 .. 0.84
  14 ?    1.5   0.0      0.62   3.2e+02      18      35 ..    1005    1022 ..     991    1026 .. 0.84
  15 ?    0.8   0.1         1   5.3e+02      14      34 ..    1121    1141 ..    1108    1146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.39
                               MIT  21 eeAlelYkealelLlqa 37 
                                       ++A+e+Y++a +l + +
  gi|330507412|ref|YP_004383840.1|  90 QAAIEYYSNASDLAQIL 106
                                       79********9986655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.56
                               MIT  16 nagnyeeAlelYkealelL 34 
                                       ++++++ A+++Y++al  +
  gi|330507412|ref|YP_004383840.1| 125 EEEDWARACQCYEKALVAI 143
                                       78999**********9665 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.068
                               MIT  17 agnyeeAlelYkealelLlqa 37 
                                       +g  +eAlelY  +l  L+++
  gi|330507412|ref|YP_004383840.1| 285 EGRLKEALELYGRSLAALQKG 305
                                       6899***********999986 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.0011
                               MIT  19 nyeeAlelYkealelLlqa 37 
                                       +++eA+e+Y+ a +l++++
  gi|330507412|ref|YP_004383840.1| 406 DWPEAIECYQRAADLFMEM 424
                                       689*************986 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 1.2
                               MIT  17 agnyeeAlelYkealelL 34 
                                       +g+ + Al++Y++a + +
  gi|330507412|ref|YP_004383840.1| 444 KGDLDVALQMYSHAYNSF 461
                                       689999********8766 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.011
                               MIT   4 AlelvkkAveeDnagnyeeAlelYkealelLlq 36 
                                       A+ l + A  + ++g+ e A elY+++++ + +
  gi|330507412|ref|YP_004383840.1| 591 AVTLGNLAGVYLQSGEEERAEELYQQSIDGFRE 623
                                       88999999999******************9876 PP

  == domain 7  score: 8.0 bits;  conditional E-value: 0.0057
                               MIT  11 AveeDnagnyeeAlelYkealel 33 
                                       A  + ++g+ e Ale+Y+++l+l
  gi|330507412|ref|YP_004383840.1| 638 ARSMAERGDLEGALECYRKCLDL 660
                                       6677899**************97 PP

  == domain 8  score: -0.3 bits;  conditional E-value: 2.3
                               MIT  17 agnyeeAlelYkealelL 34 
                                       +g ++eAl  Y + le L
  gi|330507412|ref|YP_004383840.1| 684 RGRWQEALTRYAQVLEAL 701
                                       7899*******9988877 PP

  == domain 9  score: 1.4 bits;  conditional E-value: 0.65
                               MIT  18 gnyeeAlelYkealelL 34 
                                       g+++eAle Y e+l ++
  gi|330507412|ref|YP_004383840.1| 725 GQWDEALEDYNESLAIM 741
                                       89***********9765 PP

  == domain 10  score: 3.3 bits;  conditional E-value: 0.17
                               MIT  17 agnyeeAlelYkealelLlqalk 39 
                                       +g++++Ale+Y+ +le + +a  
  gi|330507412|ref|YP_004383840.1| 764 QGDWAAALENYRLSLEGFGKAGD 786
                                       699*************9988765 PP

  == domain 11  score: 4.8 bits;  conditional E-value: 0.059
                               MIT  16 nagnyeeAlelYkealelLlqa 37 
                                       ++g++++Al+ Y+++l l+ ++
  gi|330507412|ref|YP_004383840.1| 803 KRGQWADALDSYSKSLSLFEKL 824
                                       6799**************9875 PP

  == domain 12  score: 5.9 bits;  conditional E-value: 0.027
                               MIT  17 agnyeeAlelYkealelLlq 36 
                                       +g+++eA+ +Yk ++e + q
  gi|330507412|ref|YP_004383840.1| 924 SGQWAEAIACYKRSVERFDQ 943
                                       799*************9976 PP

  == domain 13  score: -2.3 bits;  conditional E-value: 9.8
                               MIT   7 lvkkAveeDnagnyeeAlelYkealelLl 35 
                                       l+++A  +   g+   A  l+  al++++
  gi|330507412|ref|YP_004383840.1| 954 LFNMALVYKDMGDLNRARTLFDVALDIFQ 982
                                       6788988888899999*9***99999997 PP

  == domain 14  score: 1.5 bits;  conditional E-value: 0.62
                               MIT   18 gnyeeAlelYkealelLl 35  
                                        g  +eA+el+++++++L 
  gi|330507412|ref|YP_004383840.1| 1005 GRSDEAIELFSQSIGILE 1022
                                        7789**********9985 PP

  == domain 15  score: 0.8 bits;  conditional E-value: 1
                               MIT   14 eDnagnyeeAlelYkealelL 34  
                                        +  +g+ye+Al+  k+al ++
  gi|330507412|ref|YP_004383840.1| 1121 ALASGDYEDALRRMKQALVIF 1141
                                        56789*******999999766 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.5   2.6e+02      41      65 ..      90     114 ..      63     128 .. 0.76
   2 ?    1.9   0.1      0.21   1.1e+02      57     174 ..     106     141 ..      81     150 .. 0.58
   3 ?    2.8   0.4      0.11        55     110     174 ..     192     260 ..     184     272 .. 0.80
   4 ?    2.3   0.4      0.16        80     110     175 ..     232     301 ..     229     314 .. 0.78
   5 !    6.6   0.5    0.0077       3.9     127     182 ..     332     387 ..     268     391 .. 0.76
   6 ?    3.4   0.0     0.074        38     132     182 ..     377     427 ..     375     434 .. 0.86
   7 ?   -2.4   0.0       4.2   2.2e+03     142     174 ..     547     579 ..     516     582 .. 0.55
   8 !    6.7   0.0    0.0071       3.6     116     176 ..     601     661 ..     596     674 .. 0.86
   9 !    7.4   0.6    0.0044       2.2     123     174 ..     688     739 ..     666     743 .. 0.80
  10 !    8.1   0.2    0.0027       1.4      94     174 ..     771     859 ..     759     882 .. 0.71
  11 !   18.6   0.0   1.7e-06   0.00085     125     182 ..     890     947 ..     885     958 .. 0.91
  12 ?    0.2   0.4      0.67   3.5e+02     145     174 ..    1110    1139 ..    1086    1176 .. 0.69
  13 ?    2.6   1.1      0.12        63     107     178 ..    1154    1223 ..    1145    1228 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.5
                            TPR_15  41 skdteyWrtladLAwalqqedeark 65 
                                       +++ ey+ + +dLA+ l ++d+ + 
  gi|330507412|ref|YP_004383840.1|  90 QAAIEYYSNASDLAQILSDDDSLAS 114
                                       3455999999999999999988765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.21
                            TPR_15  57 lqqedearkAyrqLlasgkaraedyerliellydaepkeaarlaekgwrrfrsprlLssalellerakdydriaell 133
                                       l ++d+                                                                       
  gi|330507412|ref|YP_004383840.1| 106 LSDDDSL---------------------------------------------------------------------- 112
                                       3333322...................................................................... PP

                            TPR_15 134 ksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAla 174
                                                   a +ll +++ly +e ++++A ++y++Al+
  gi|330507412|ref|YP_004383840.1| 113 ------------ASILLCLGALYGEEEDWARACQCYEKALV 141
                                       ............44566666666666777777777777665 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.11
                            TPR_15 110 prlLssalellerakdydriaellksleeeeaae....qsaafllaraelyrqegqtdaAlrdyreAla 174
                                       ++  s+  el + ++d+++ ++l +++ +e +++    + a+ l+ +a++y+q+g+ ++A   ++ A  
  gi|330507412|ref|YP_004383840.1| 192 MEATSNLAELCQIQGDMEKAEKLYQTILKERELSddpvGAARALASLASIYSQTGNGKRAQISLQSASH 260
                                       5556667788888999999999999999888888444566789*****************999888855 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.16
                            TPR_15 110 prlLssalellerakdydriaellkslee.eeaae...qsaafllaraelyrqegqtdaAlrdyreAlal 175
                                        r L s   ++ ++++ +r +  l+s++  +++++   + a +  ++a +y  eg+ ++Al++y + la+
  gi|330507412|ref|YP_004383840.1| 232 ARALASLASIYSQTGNGKRAQISLQSASHlLADLKdqsGAAEMQCRLADIYFHEGRLKEALELYGRSLAA 301
                                       5788888999999999999999999988535555532266778899999999999999999999998865 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0077
                            TPR_15 127 driaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdssel 182
                                       d +++ ++ ++e ++ ++ a+ l+++a ++ ++gq + Al++ re l+    s++l
  gi|330507412|ref|YP_004383840.1| 332 DHLQRAIAIMKEHKDSSSLARALVILAGVHHKQGQLEMALQCSRESLKIRERSKDL 387
                                       344555555567788889999***************************99988876 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.074
                            TPR_15 132 llksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdssel 182
                                        lk  e+ +++++sa  l   a++  + +++ +A+++y++A +l+ +  e+
  gi|330507412|ref|YP_004383840.1| 377 SLKIRERSKDLSGSAEALNCIARICCDCSDWPEAIECYQRAADLFMEMGEV 427
                                       5666778899********************************998765555 PP

  == domain 7  score: -2.4 bits;  conditional E-value: 4.2
                            TPR_15 142 aeqsaafllaraelyrqegqtdaAlrdyreAla 174
                                       +++ aa    +++ly+++g+   A+ +yr++l+
  gi|330507412|ref|YP_004383840.1| 547 LRGLAAAENNLGNLYSDRGDLMHAILCYRQGLE 579
                                       444444444556777788888888888888776 PP

  == domain 8  score: 6.7 bits;  conditional E-value: 0.0071
                            TPR_15 116 alellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlala 176
                                       +l+++e+ ++ +  ++ +    e+ +a+++a+ l+ +a++  ++g+ + Al++yr+ l+l+
  gi|330507412|ref|YP_004383840.1| 601 YLQSGEEERAEELYQQSIDGFRELGDARGEARSLYGLARSMAERGDLEGALECYRKCLDLQ 661
                                       5677777777777788888889999*********************************986 PP

  == domain 9  score: 7.4 bits;  conditional E-value: 0.0044
                            TPR_15 123 akdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAla 174
                                       +++++r a++l+ l ++++++  aa+  a+++l+ + gq+d+Al+dy e la
  gi|330507412|ref|YP_004383840.1| 688 QEALTRYAQVLEALRSRDDLSAVAAVQCALGNLHADLGQWDEALEDYNESLA 739
                                       4455677888888889999*****************************9997 PP

  == domain 10  score: 8.1 bits;  conditional E-value: 0.0027
                            TPR_15  94 keaarlaekgwrrfrspr....lLssalellerakdy.driaellksle...eeeaaeqsaafllaraelyrqegqt 162
                                        e +rl+++g+ + ++++    +Ls+   l ++ +++ d++++  ksl+   ++e+ ++ a++l  +++ly ++g+ 
  gi|330507412|ref|YP_004383840.1| 771 LENYRLSLEGFGKAGDMEseasVLSNVAGLCYKRGQWaDALDSYSKSLSlfeKLEDSAGIAQVLGNMGNLYHRQGER 847
                                       56678888888887776522224666666666666662456666666552224555556678999999999999999 PP

                            TPR_15 163 daAlrdyreAla 174
                                       d A + +++Al+
  gi|330507412|ref|YP_004383840.1| 848 DLAAEHFQRALE 859
                                       999999999997 PP

  == domain 11  score: 18.6 bits;  conditional E-value: 1.7e-06
                            TPR_15 125 dydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdssel 182
                                       d+++ +++l++lee+ +++++  +l+a+a +y++ gq+++A+ +y++ +++++++ e+
  gi|330507412|ref|YP_004383840.1| 890 DIEEYKRQLEELEETGDLSGQGEVLSALAGSYTDSGQWAEAIACYKRSVERFDQTGEV 947
                                       6677899********************************************9987766 PP

  == domain 12  score: 0.2 bits;  conditional E-value: 0.67
                            TPR_15  145 saafllaraelyrqegqtdaAlrdyreAla 174 
                                        +a   + +++l+++ g+ ++Alr +++Al+
  gi|330507412|ref|YP_004383840.1| 1110 EAKAISSLGRLALASGDYEDALRRMKQALV 1139
                                        444444445555555555555555555554 PP

  == domain 13  score: 2.6 bits;  conditional E-value: 0.12
                            TPR_15  107 frsprlLssalellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapd 178 
                                        +r++ lL  a + ++ra+++  +++  +++   +++  s +  + +ae + ++g++++A  dy  Al+la++
  gi|330507412|ref|YP_004383840.1| 1154 YRDMTLLFLAQDDYQRAEEMAMLRQRQARILGHADL--SLLATVDLAECEARTGKKEEARADYAGALRLAGK 1223
                                        566666777777777777777666666665544444..34444568999*******************9876 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1     0.005       2.6      43      90 ..      75     122 ..      48     126 .. 0.90
   2 !   13.4   0.1   0.00012     0.059      10      89 ..     323     399 ..     320     403 .. 0.90
   3 ?    0.4   0.0       1.4     7e+02      45      90 ..     515     560 ..     401     564 .. 0.68
   4 ?    6.9   0.0     0.013       6.7      15      85 ..     688     755 ..     648     763 .. 0.78
   5 ?   -0.6   0.0       2.9   1.5e+03      46      82 ..     836     872 ..     805     880 .. 0.86
   6 ?    3.0   0.0       0.2     1e+02      40      69 ..     990    1019 ..     938    1022 .. 0.83
   7 ?   -0.3   0.1       2.2   1.1e+03      42      77 ..    1192    1227 ..    1161    1245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.005
                            ANAPC5  43 alLnlaslhadfghneeAvkaleeairlArenkDkscLalalawlarl 90 
                                       a +nl +l +++  +++A++  ++a  lA+  +D+ +La +l  l +l
  gi|330507412|ref|YP_004383840.1|  75 AWFNLGRLAHHLFFHQAAIEYYSNASDLAQILSDDDSLASILLCLGAL 122
                                       789************************************999877655 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00012
                            ANAPC5  10 rakdYqqaldsLhryFDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleeairlArenkDkscLalalaw 86 
                                       ++ +++ a d+L r   ++ ++++ss   s+  al+ la +h++ g+ e A++  +e+ ++   +kD s  a al+ 
  gi|330507412|ref|YP_004383840.1| 323 EDGNWTLAEDHLQRAIAIMKEHKDSS---SLARALVILAGVHHKQGQLEMALQCSRESLKIRERSKDLSGSAEALNC 396
                                       677899999*****************...********************************9999999987777776 PP

                            ANAPC5  87 lar 89 
                                       +ar
  gi|330507412|ref|YP_004383840.1| 397 IAR 399
                                       665 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.4
                            ANAPC5  45 LnlaslhadfghneeAvkaleeairlArenkDkscLalalawlarl 90 
                                       L+l  + +  g++++A + +e a r   +n+D   La a + l +l
  gi|330507412|ref|YP_004383840.1| 515 LSLGLIYQLGGEWDQAQSCFEGAARAFEDNGDLRGLAAAENNLGNL 560
                                       4555555555777888888888888888888888888777766666 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.013
                            ANAPC5  15 qqaldsLhryFDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleeairlArenkDkscLalala 85 
                                       q+al    +      s ++ s          +l +lhad+g+++eA++  +e+ ++    +D+ ++++a +
  gi|330507412|ref|YP_004383840.1| 688 QEALTRYAQVLEALRSRDDLS---AVAAVQCALGNLHADLGQWDEALEDYNESLAIMEGLGDEYSVSVARN 755
                                       555555555555555555555...33333456889*******************99999888888887765 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 2.9
                            ANAPC5  46 nlaslhadfghneeAvkaleeairlArenkDkscLal 82 
                                       n+ +l ++ g+++ A + ++ a ++ r  kD++  a 
  gi|330507412|ref|YP_004383840.1| 836 NMGNLYHRQGERDLAAEHFQRALEIYRRLKDQAGAAE 872
                                       778899999999***************9999987655 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.2
                            ANAPC5   40 yqyalLnlaslhadfghneeAvkaleeair 69  
                                          +a Lnl +++ ++g  +eA++ ++ +i 
  gi|330507412|ref|YP_004383840.1|  990 VASAKLNLGIISGQMGRSDEAIELFSQSIG 1019
                                        56789*****************99998885 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 2.2
                            ANAPC5   42 yalLnlaslhadfghneeAvkaleeairlArenkDk 77  
                                         a + la  +a+ g++eeA +    a rlA +++D 
  gi|330507412|ref|YP_004383840.1| 1192 LATVDLAECEARTGKKEEARADYAGALRLAGKEGDR 1227
                                        4778899999999***************99998885 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.33   1.7e+02      13      28 ..     205     220 ..     198     222 .. 0.85
   2 ?    6.5   0.0     0.022        11       8      24 ..     280     296 ..     277     299 .. 0.88
   3 ?    2.8   0.0      0.34   1.7e+02       4      25 ..     395     416 ..     392     419 .. 0.90
   4 ?    3.5   0.0      0.19        99       2      25 ..     593     616 ..     592     619 .. 0.86
   5 ?    1.8   0.1       0.7   3.6e+02       8      26 ..     639     657 ..     636     662 .. 0.82
   6 ?    2.6   0.0      0.39     2e+02       5      20 ..     676     691 ..     675     696 .. 0.93
   7 ?   -1.0   0.0       5.3   2.7e+03       9      21 ..     720     732 ..     716     732 .. 0.82
   8 ?   -0.8   0.0       4.7   2.4e+03       8      18 ..     779     789 ..     778     795 .. 0.80
   9 ?    2.4   0.0      0.45   2.3e+02       4      27 ..     915     938 ..     913     940 .. 0.85
  10 ?    3.7   0.0      0.17        85      11      24 ..    1002    1015 ..    1001    1018 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.33
                               PPR  13 nGkleeAlelfkeMke 28 
                                        G++e+A++l++ +++
  gi|330507412|ref|YP_004383840.1| 205 QGDMEKAEKLYQTILK 220
                                       69*********87665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.022
                               PPR   8 sgycknGkleeAlelfk 24 
                                       + y ++G+l+eAlel+ 
  gi|330507412|ref|YP_004383840.1| 280 DIYFHEGRLKEALELYG 296
                                       789************97 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.34
                               PPR   4 nslIsgycknGkleeAlelfke 25 
                                       n++ + +c + ++ eA+e++++
  gi|330507412|ref|YP_004383840.1| 395 NCIARICCDCSDWPEAIECYQR 416
                                       888999************9986 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.19
                               PPR   2 tynslIsgycknGkleeAlelfke 25 
                                       t   l  +y ++G+ e A+el+++
  gi|330507412|ref|YP_004383840.1| 593 TLGNLAGVYLQSGEEERAEELYQQ 616
                                       66678889*************985 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.7
                               PPR   8 sgycknGkleeAlelfkeM 26 
                                       ++ +  G+le Ale++++ 
  gi|330507412|ref|YP_004383840.1| 639 RSMAERGDLEGALECYRKC 657
                                       567889**********986 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.39
                               PPR   5 slIsgycknGkleeAl 20 
                                       s+++ + + G+++eAl
  gi|330507412|ref|YP_004383840.1| 676 SMVNLLLRRGRWQEAL 691
                                       79*************8 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 5.3
                               PPR   9 gycknGkleeAle 21 
                                        ++  G+++eAle
  gi|330507412|ref|YP_004383840.1| 720 LHADLGQWDEALE 732
                                       56789******97 PP

  == domain 8  score: -0.8 bits;  conditional E-value: 4.7
                               PPR   8 sgycknGklee 18 
                                        g++k+G++e 
  gi|330507412|ref|YP_004383840.1| 779 EGFGKAGDMES 789
                                       69*******96 PP

  == domain 9  score: 2.4 bits;  conditional E-value: 0.45
                               PPR   4 nslIsgycknGkleeAlelfkeMk 27 
                                       ++l  +y  +G++ eA+ ++k+ +
  gi|330507412|ref|YP_004383840.1| 915 SALAGSYTDSGQWAEAIACYKRSV 938
                                       578889**************9865 PP

  == domain 10  score: 3.7 bits;  conditional E-value: 0.17
                               PPR   11 cknGkleeAlelfk 24  
                                        ++ G+ +eA+elf 
  gi|330507412|ref|YP_004383840.1| 1002 GQMGRSDEAIELFS 1015
                                        589**********7 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.071        36     137     206 ..      85     154 ..      62     161 .. 0.87
   2 ?   -2.0   0.0       4.9   2.5e+03     167     199 ..     194     226 ..     169     239 .. 0.72
   3 ?    0.1   0.0         1   5.4e+02      87     153 ..     282     346 ..     252     399 .. 0.73
   4 ?   -2.4   0.0       6.1   3.2e+03     117     148 ..     430     461 ..     406     477 .. 0.56
   5 ?    0.9   0.0      0.64   3.3e+02      95     150 ..     569     623 ..     553     633 .. 0.77
   6 ?   -2.7   0.0       7.8     4e+03     142     185 ..     688     731 ..     647     741 .. 0.65
   7 ?   -0.2   0.0       1.4     7e+02     143     193 ..     769     819 ..     759     834 .. 0.87
   8 ?    0.7   0.0      0.71   3.7e+02      96     151 ..     810     864 ..     801     880 .. 0.75
   9 ?    2.5   0.0       0.2     1e+02      86     150 ..     920     983 ..     890     988 .. 0.76
  10 !    6.8   0.1    0.0097         5     127     192 ..    1073    1138 ..    1069    1156 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.071
                           DUF2225 137 eklflkkAlelykeayekesfpvegideatvlYLiaeLerrlgnkeealrwlskvigskkaskpskikdk 206
                                       ++ f + A+e+y +a    +  ++  + a++l+ ++ L    ++  +a++ ++k + + ++ k ++++ +
  gi|330507412|ref|YP_004383840.1|  85 HLFFHQAAIEYYSNASDLAQILSDDDSLASILLCLGALYGEEEDWARACQCYEKALVAIDMAKRPRLLPQ 154
                                       566889999**********************************************999999887776655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.9
                           DUF2225 167 vlYLiaeLerrlgnkeealrwlskvigskkask 199
                                        +  +aeL +  g+ e+a + ++ ++++++ s+
  gi|330507412|ref|YP_004383840.1| 194 ATSNLAELCQIQGDMEKAEKLYQTILKERELSD 226
                                       555579999999999999999999999999887 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1
                           DUF2225  87 fskertldeaiesYkLallcyelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelykeaye 153
                                       + +e  l+ea+e Y  +l   +  + + ++kA +  r++  + + ++ +  ++ l++A+ + ke   
  gi|330507412|ref|YP_004383840.1| 282 YFHEGRLKEALELYGRSLAALQKGHPSLASKALC--RMGQCFLEDGNWTLAEDHLQRAIAIMKEHKD 346
                                       4456679999999999999988888888888876..6677777888888888888888776665544 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 6.1
                           DUF2225 117 kAklalrlAWlyrdkedeekeklflkkAlely 148
                                        A  + +l+ +y +k+d ++ ++ + +A++ +
  gi|330507412|ref|YP_004383840.1| 430 AAEALSNLGGVYHLKGDLDVALQMYSHAYNSF 461
                                       33334444455555555555555555555554 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.64
                           DUF2225  95 eaiesYkLallcyelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelyke 150
                                       +ai  Y   l+   + +     +A+++ +lA +y ++++ee  ++++++ +++++e
  gi|330507412|ref|YP_004383840.1| 569 HAILCYRQGLEARRVLNDG-HGMAVTLGNLAGVYLQSGEEERAEELYQQSIDGFRE 623
                                       5555555555554444433.36899999*************************998 PP

  == domain 6  score: -2.7 bits;  conditional E-value: 7.8
                           DUF2225 142 kkAlelykeayekesfpvegideatvlYLiaeLerrlgnkeeal 185
                                       ++Al  y +++e  ++  +  + a v   +++L+  lg+ +eal
  gi|330507412|ref|YP_004383840.1| 688 QEALTRYAQVLEALRSRDDLSAVAAVQCALGNLHADLGQWDEAL 731
                                       45666666666666555555555555556666666666666555 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 1.4
                           DUF2225 143 kAlelykeayekesfpvegideatvlYLiaeLerrlgnkeealrwlskvig 193
                                        Ale y+ ++e   +  +  +ea+vl  +a L ++ g+  +al  +sk ++
  gi|330507412|ref|YP_004383840.1| 769 AALENYRLSLEGFGKAGDMESEASVLSNVAGLCYKRGQWADALDSYSKSLS 819
                                       699999999999999999999999*999**********9999999998765 PP

  == domain 8  score: 0.7 bits;  conditional E-value: 0.71
                           DUF2225  96 aiesYkLallcyelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelykea 151
                                       a+ sY  +l   e  +  ++ +A ++ +++ ly  +++ +   +  ++Ale+y++ 
  gi|330507412|ref|YP_004383840.1| 810 ALDSYSKSLSLFEKLE-DSAGIAQVLGNMGNLYHRQGERDLAAEHFQRALEIYRRL 864
                                       6666666665555443.345788888899999999999999999999999999875 PP

  == domain 9  score: 2.5 bits;  conditional E-value: 0.2
                           DUF2225  86 dfskertldeaiesYkLallcyelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelyke 150
                                       +++++ +  eai+ Yk +++  + +  +  + + ++ ++A +y+d +d +   ++   Al+++++
  gi|330507412|ref|YP_004383840.1| 920 SYTDSGQWAEAIACYKRSVERFDQTG-EVYNRGQVLFNMALVYKDMGDLNRARTLFDVALDIFQD 983
                                       56667777788888888887776554.45577888888888888888888888888888888875 PP

  == domain 10  score: 6.8 bits;  conditional E-value: 0.0097
                           DUF2225  127 lyrdkedeekeklflkkAlelykeayekesfpvegideatvlYLiaeLerrlgnkeealrwlskvi 192 
                                        lyr +++   ++ ++ +A  ++++a+   ++ +   +ea+ +  ++ L+   g++e+alr +++ +
  gi|330507412|ref|YP_004383840.1| 1073 LYRAQGERFLKDMLYPEAKSCFEKALALSRKLSLSYEEAKAISSLGRLALASGDYEDALRRMKQAL 1138
                                        8*******************************************************9999988754 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2       0.4     2e+02      11      24 ..      71      84 ..      71     134 .. 0.87
   2 ?   -0.7   0.0       4.9   2.5e+03      14      33 ..     154     173 ..     145     174 .. 0.87
   3 ?   -0.8   0.0       5.2   2.7e+03      18      33 ..     197     212 ..     176     213 .. 0.88
   4 ?   -0.4   0.0         4     2e+03      13      33 ..     232     252 ..     226     253 .. 0.86
   5 ?   -1.4   0.0       7.8     4e+03      17      34 .]     276     293 ..     272     293 .. 0.88
   6 ?    0.8   0.0       1.6   8.3e+02       9      33 ..     306     331 ..     299     332 .. 0.81
   7 ?    1.1   0.0       1.2   6.4e+02      13      34 .]     351     372 ..     334     372 .. 0.77
   8 ?   -0.4   0.0       3.8   1.9e+03      12      34 .]     390     412 ..     387     426 .. 0.85
   9 ?   -1.2   0.1       6.9   3.6e+03      13      30 ..     431     448 ..     430     452 .. 0.85
  10 ?    5.1   0.1     0.065        33      17      30 ..     555     568 ..     555     571 .. 0.90
  11 ?   -0.2   0.0       3.3   1.7e+03      14      34 .]     592     612 ..     588     612 .. 0.88
  12 ?    2.3   0.0      0.53   2.7e+02      13      34 .]     631     652 ..     613     652 .. 0.85
  13 ?    3.7   0.0      0.19        97      17      34 .]     715     732 ..     710     732 .. 0.88
  14 ?    4.7   0.1      0.09        46      13      34 .]     751     772 ..     749     772 .. 0.91
  15 ?    1.5   0.0      0.96   4.9e+02      13      29 ..     831     847 ..     824     859 .. 0.81
  16 ?    6.5   0.0     0.024        12      14      33 ..     952     971 ..     933     972 .. 0.89
  17 ?    1.7   0.1       0.8   4.1e+02       2      33 ..    1094    1131 ..    1093    1132 .. 0.69
  18 ?   -1.5   0.0       8.9   4.6e+03      18      34 .]    1156    1172 ..    1151    1172 .. 0.76
  19 ?   -1.0   0.0       5.9     3e+03      19      33 ..    1197    1211 ..    1195    1212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.4
                            TPR_17 11 nnadaynnLAelll 24
                                      n++ a++nL++l +
  gi|330507412|ref|YP_004383840.1| 71 NSVQAWFNLGRLAH 84
                                      68899999999865 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4.9
                            TPR_17  14 daynnLAelllknGdlmtAr 33 
                                        ++  L+++ + +G++ +A+
  gi|330507412|ref|YP_004383840.1| 154 QVLERLGRARRLQGEYHQAQ 173
                                       577789***********997 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 5.2
                            TPR_17  18 nLAelllknGdlmtAr 33 
                                       nLAel   +Gd ++A+
  gi|330507412|ref|YP_004383840.1| 197 NLAELCQIQGDMEKAE 212
                                       9**********99998 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 4
                            TPR_17  13 adaynnLAelllknGdlmtAr 33 
                                       a a+  LA ++++ G+ ++A+
  gi|330507412|ref|YP_004383840.1| 232 ARALASLASIYSQTGNGKRAQ 252
                                       568899******999988876 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 7.8
                            TPR_17  17 nnLAelllknGdlmtArq 34 
                                       + LA ++ + G+l++A++
  gi|330507412|ref|YP_004383840.1| 276 CRLADIYFHEGRLKEALE 293
                                       579************985 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 1.6
                            TPR_17   9 dPnn.adaynnLAelllknGdlmtAr 33 
                                       +P+  ++a++ +++++l+ G++  A+
  gi|330507412|ref|YP_004383840.1| 306 HPSLaSKALCRMGQCFLEDGNWTLAE 331
                                       6776699*************998776 PP

  == domain 7  score: 1.1 bits;  conditional E-value: 1.2
                            TPR_17  13 adaynnLAelllknGdlmtArq 34 
                                       a a+  LA +++k+G+l++A+q
  gi|330507412|ref|YP_004383840.1| 351 ARALVILAGVHHKQGQLEMALQ 372
                                       556666777777********97 PP

  == domain 8  score: -0.4 bits;  conditional E-value: 3.8
                            TPR_17  12 nadaynnLAelllknGdlmtArq 34 
                                       +a+a+n  A++ +   d+ +A++
  gi|330507412|ref|YP_004383840.1| 390 SAEALNCIARICCDCSDWPEAIE 412
                                       68999999999998888877764 PP

  == domain 9  score: -1.2 bits;  conditional E-value: 6.9
                            TPR_17  13 adaynnLAelllknGdlm 30 
                                       a+a+ nL+ +++ +Gdl+
  gi|330507412|ref|YP_004383840.1| 431 AEALSNLGGVYHLKGDLD 448
                                       789999999999999987 PP

  == domain 10  score: 5.1 bits;  conditional E-value: 0.065
                            TPR_17  17 nnLAelllknGdlm 30 
                                       nnL++l++ +Gdlm
  gi|330507412|ref|YP_004383840.1| 555 NNLGNLYSDRGDLM 568
                                       8***********98 PP

  == domain 11  score: -0.2 bits;  conditional E-value: 3.3
                            TPR_17  14 daynnLAelllknGdlmtArq 34 
                                       + + nLA ++l+ G+ ++A++
  gi|330507412|ref|YP_004383840.1| 592 VTLGNLAGVYLQSGEEERAEE 612
                                       56789*************986 PP

  == domain 12  score: 2.3 bits;  conditional E-value: 0.53
                            TPR_17  13 adaynnLAelllknGdlmtArq 34 
                                       a +++ LA+ ++++Gdl+ A++
  gi|330507412|ref|YP_004383840.1| 631 ARSLYGLARSMAERGDLEGALE 652
                                       7799*************99975 PP

  == domain 13  score: 3.7 bits;  conditional E-value: 0.19
                            TPR_17  17 nnLAelllknGdlmtArq 34 
                                       + L++l++ +G++++A++
  gi|330507412|ref|YP_004383840.1| 715 CALGNLHADLGQWDEALE 732
                                       78**************85 PP

  == domain 14  score: 4.7 bits;  conditional E-value: 0.09
                            TPR_17  13 adaynnLAelllknGdlmtArq 34 
                                       ++a nnL++  +++Gd++ A++
  gi|330507412|ref|YP_004383840.1| 751 SVARNNLGNMCYRQGDWAAALE 772
                                       6899*************99975 PP

  == domain 15  score: 1.5 bits;  conditional E-value: 0.96
                            TPR_17  13 adaynnLAelllknGdl 29 
                                       a ++ n+++l++++G+ 
  gi|330507412|ref|YP_004383840.1| 831 AQVLGNMGNLYHRQGER 847
                                       78999*******99964 PP

  == domain 16  score: 6.5 bits;  conditional E-value: 0.024
                            TPR_17  14 daynnLAelllknGdlmtAr 33 
                                        +++n+A +++  Gdl +Ar
  gi|330507412|ref|YP_004383840.1| 952 QVLFNMALVYKDMGDLNRAR 971
                                       699***************98 PP

  == domain 17  score: 1.7 bits;  conditional E-value: 0.8
                            TPR_17    2 ylkaleldPnn......adaynnLAelllknGdlmtAr 33  
                                        ++kal+l  +       a+a   L++l l  Gd+++A+
  gi|330507412|ref|YP_004383840.1| 1094 FEKALALSRKLslsyeeAKAISSLGRLALASGDYEDAL 1131
                                        5555555544435555577778899*********9996 PP

  == domain 18  score: -1.5 bits;  conditional E-value: 8.9
                            TPR_17   18 nLAelllknGdlmtArq 34  
                                         +  l+l + d+++A++
  gi|330507412|ref|YP_004383840.1| 1156 DMTLLFLAQDDYQRAEE 1172
                                        555678899******86 PP

  == domain 19  score: -1.0 bits;  conditional E-value: 5.9
                            TPR_17   19 LAelllknGdlmtAr 33  
                                        LAe+ ++ G++++Ar
  gi|330507412|ref|YP_004383840.1| 1197 LAECEARTGKKEEAR 1211
                                        9*************9 PP

>> Foie-gras_1  Foie gras liver health family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.81   4.1e+02     189     240 ..     271     321 ..     246     376 .. 0.76
   2 ?    1.1   0.0      0.48   2.5e+02     165     224 ..     406     465 ..     397     466 .. 0.90
   3 ?   -0.3   0.0       1.3   6.4e+02     171     215 ..     612     656 ..     605     662 .. 0.91
   4 ?    1.0   0.1      0.52   2.7e+02     166     211 ..     687     732 ..     671     740 .. 0.83
   5 ?    1.9   0.0      0.28   1.4e+02     166     214 ..     767     815 ..     754     865 .. 0.80
   6 !   10.0   0.0   0.00092      0.47     161     216 ..     922     977 ..     901     983 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.81
                       Foie-gras_1 189 aeelsleiAeeylrlgdwkkalellqpltlsyrkegWwsLleevlwalreca 240
                                       a+e++ ++A  y++ g+ k+alel+    + + + g +sL+++ l+   +c 
  gi|330507412|ref|YP_004383840.1| 271 AAEMQCRLADIYFHEGRLKEALELYGRSLAAL-QKGHPSLASKALCRMGQCF 321
                                       67778888888888888888888887654443.4455666666666555554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.48
                       Foie-gras_1 165 hskliidlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellqpltlsyrkeg 224
                                       ++ ++i+++++a   F + +    a+e   +++  y   gd + al++++ +++s+++ g
  gi|330507412|ref|YP_004383840.1| 406 DWPEAIECYQRAADLFMEMGEVTAAAEALSNLGGVYHLKGDLDVALQMYSHAYNSFCQQG 465
                                       677899999999999999999999999999999999999************999999975 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.3
                       Foie-gras_1 171 dlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellqp 215
                                       +l+++++  F++ +  R +++  + +A+   + gd + ale ++ 
  gi|330507412|ref|YP_004383840.1| 612 ELYQQSIDGFRELGDARGEARSLYGLARSMAERGDLEGALECYRK 656
                                       799*************************************99985 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.52
                       Foie-gras_1 166 skliidlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkale 211
                                       +++++  + ++le  ++r+    ++ ++  +++ + +lg+w++ale
  gi|330507412|ref|YP_004383840.1| 687 WQEALTRYAQVLEALRSRDDLSAVAAVQCALGNLHADLGQWDEALE 732
                                       5667777888888888888888999999999999999999999998 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.28
                       Foie-gras_1 166 skliidlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellq 214
                                       ++ +++ ++ +le F k +    ++++  ++A  +++ g+w++al+ ++
  gi|330507412|ref|YP_004383840.1| 767 WAAALENYRLSLEGFGKAGDMESEASVLSNVAGLCYKRGQWADALDSYS 815
                                       6667777777888888777777778888888888899999999888765 PP

  == domain 6  score: 10.0 bits;  conditional E-value: 0.00092
                       Foie-gras_1 161 kgvahskliidlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellqpl 216
                                       ++  +++++i+++++++e F + +    + ++ +++A  y ++gd + a +l++ +
  gi|330507412|ref|YP_004383840.1| 922 TDSGQWAEAIACYKRSVERFDQTGEVYNRGQVLFNMALVYKDMGDLNRARTLFDVA 977
                                       55667899********************************************9976 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 ?   -1.1   0.0       1.4   7.1e+02     129     149 ..     120     140 ..      94     164 .. 0.90
   2 !    7.2   0.6    0.0043       2.2     403     497 ..     267     370 ..     234     400 .. 0.76
   3 ?   -0.9   0.0       1.2   6.3e+02     136     161 ..     405     431 ..     398     438 .. 0.83
   4 !    8.2   0.2     0.002         1      97     159 ..     687     748 ..     675     760 .. 0.83
   5 ?    3.1   0.1     0.074        38     113     159 ..     782     828 ..     765     836 .. 0.70
   6 ?    1.5   0.0      0.22   1.1e+02     411     441 ..     914     944 ..     848     954 .. 0.71
   7 ?   -1.7   0.0       2.1   1.1e+03     129     159 ..    1118    1148 ..    1110    1157 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
                                       HHHHHHTT-HHHHHHHHHHHH CS
                             SRP68 129 GallfekqqWekalesyskar 149
                                       Gal  e+++W +a++ y+ka 
  gi|330507412|ref|YP_004383840.1| 120 GALYGEEEDWARACQCYEKAL 140
                                       888899999******999985 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0043
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXX CS
                             SRP68 403 kayfrAlrclyiarshalaskyaeAlALlkrAlelaeealeelsksdaksk.........peslevlleelqeLade 470
                                        +   A     +a+++  +++ +eAl L+ r+l  +++ +++l++++                 e +l+++ ++++e
  gi|330507412|ref|YP_004383840.1| 267 DQSGAAEMQCRLADIYFHEGRLKEALELYGRSLAALQKGHPSLASKALCRMgqcfledgnWTLAEDHLQRAIAIMKE 343
                                       555556666789*******************************9999833357999988866677778888889999 PP

                                       XXXXXXXXXXXXXX..XXXXX...... CS
                             SRP68 471 lkgelqrarAlveleelkkeeeslkks 497
                                        k +++ arAlv+l  ++ ++ +l+  
  gi|330507412|ref|YP_004383840.1| 344 HKDSSSLARALVILAGVHHKQGQLEMA 370
                                       9999999******99444444333332 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.2
                                       T-HHHHHHHHHHHHHHHHHHHHHH.TT CS
                             SRP68 136 qqWekalesyskaraiyeaLakvt.se 161
                                        +W +a+e y++a +++ ++++vt + 
  gi|330507412|ref|YP_004383840.1| 405 SDWPEAIECYQRAADLFMEMGEVTaAA 431
                                       69*******************999533 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHCS.-S--HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHH CS
                             SRP68  97 lAeeLvellseassgadertkLEarAYaallrGallfekqqWekalesyskaraiyeaLakvt 159
                                       + e L + ++   +   +r+ L a A  +   G+l+    qW++ale+y+++ ai e L+   
  gi|330507412|ref|YP_004383840.1| 687 WQEALTRYAQV-LEALRSRDDLSAVAAVQCALGNLHADLGQWDEALEDYNESLAIMEGLGDEY 748
                                       55666666644.6788899***************************************98765 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.074
                                       -HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHH CS
                             SRP68 113 dertkLEarAYaallrGallfekqqWekalesyskaraiyeaLakvt 159
                                        +   +E +A   +  + l   + qW +al+sysk+ +++e+L  ++
  gi|330507412|ref|YP_004383840.1| 782 GKAGDMESEASVLSNVAGLCYKRGQWADALDSYSKSLSLFEKLEDSA 828
                                       5555566666544444445567779******************9876 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.22
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             SRP68 411 clyiarshalaskyaeAlALlkrAlelaeea 441
                                         ++a s++ ++++aeA+A +kr+ e+ ++ 
  gi|330507412|ref|YP_004383840.1| 914 LSALAGSYTDSGQWAEAIACYKRSVERFDQT 944
                                       568999****************999988776 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 2.1
                                        HHHHHHTT-HHHHHHHHHHHHHHHHHHHHHH CS
                             SRP68  129 GallfekqqWekalesyskaraiyeaLakvt 159 
                                        G l++   ++e+al+++++a +i+  L+ + 
  gi|330507412|ref|YP_004383840.1| 1118 GRLALASGDYEDALRRMKQALVIFGRLGASL 1148
                                        88999999****************9998776 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       9.1   4.6e+03      18      25 ..      90      97 ..      90      99 .. 0.88
   2 ?    7.0   0.0     0.012       6.1       7      25 ..     198     216 ..     192     221 .. 0.83
   3 ?    0.5   0.1       1.2   6.3e+02      11      29 ..     282     299 ..     278     304 .. 0.70
   4 ?    5.6   0.1     0.031        16       5      25 ..     435     455 ..     432     459 .. 0.82
   5 ?   -1.9   0.0       6.9   3.6e+03       6      20 ..     516     530 ..     516     535 .. 0.89
   6 ?    1.7   0.0      0.51   2.6e+02       4      26 ..     634     654 ..     633     655 .. 0.92
   7 ?    0.6   0.0       1.1   5.9e+02      11      30 ..     761     778 ..     757     779 .. 0.89
   8 ?   -1.4   0.0         5   2.6e+03       8      25 ..     798     815 ..     794     823 .. 0.80
   9 ?    3.0   0.0      0.21   1.1e+02       8      32 ..     958     980 ..     954     983 .. 0.80
  10 ?    2.5   0.0       0.3   1.5e+02      13      28 ..    1003    1016 ..    1003    1019 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 9.1
                                      HHHHHH.. CS
                             TPR_3 18 qeArelfs 25
                                      q A+e++s
  gi|330507412|ref|YP_004383840.1| 90 QAAIEYYS 97
                                      78****88 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                                       HHHHHHHTT-HHHHHHH.. CS
                             TPR_3   7 yAaefynkkkyqeArelfs 25 
                                       +A  ++ +++ ++A+ l++
  gi|330507412|ref|YP_004383840.1| 198 LAELCQIQGDMEKAEKLYQ 216
                                       7888*************99 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.2
                                       HHHTT-HHHHHHH..HHHH CS
                             TPR_3  11 fynkkkyqeArelfsYall 29 
                                       ++  +++ eA+el+  + l
  gi|330507412|ref|YP_004383840.1| 282 YFHEGRLKEALELYG-RSL 299
                                       677899*******54.444 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.031
                                       HHHHHHHHHTT-HHHHHHH.. CS
                             TPR_3   5 ysyAaefynkkkyqeArelfs 25 
                                         ++ ++++k++++ A++ +s
  gi|330507412|ref|YP_004383840.1| 435 SNLGGVYHLKGDLDVALQMYS 455
                                       557779*************88 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 6.9
                                       HHHHHHHHTT-HHHH CS
                             TPR_3   6 syAaefynkkkyqeA 20 
                                       s++  +++ ++ ++A
  gi|330507412|ref|YP_004383840.1| 516 SLGLIYQLGGEWDQA 530
                                       78999********99 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.51
                                       HHHHHHHHHHTT-HHHHHHH..H CS
                             TPR_3   4 lysyAaefynkkkyqeArelfsY 26 
                                       ly++A +    ++++ A+e   Y
  gi|330507412|ref|YP_004383840.1| 634 LYGLARSMAERGDLEGALEC--Y 654
                                       9*****************99..6 PP

  == domain 7  score: 0.6 bits;  conditional E-value: 1.1
                                       HHHTT-HHHHHHH..HHHHH CS
                             TPR_3  11 fynkkkyqeArelfsYalla 30 
                                       +y +++   A+e   Y+l+ 
  gi|330507412|ref|YP_004383840.1| 761 CYRQGDWAAALEN--YRLSL 778
                                       9************..99985 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 5
                                       HHHHHHTT-HHHHHHH.. CS
                             TPR_3   8 AaefynkkkyqeArelfs 25 
                                       A  +y  ++  +A++ +s
  gi|330507412|ref|YP_004383840.1| 798 AGLCYKRGQWADALDSYS 815
                                       6679***********988 PP

  == domain 9  score: 3.0 bits;  conditional E-value: 0.21
                                       HHHHHHTT-HHHHHHH..HHHHHHH CS
                             TPR_3   8 AaefynkkkyqeArelfsYallail 32 
                                       A ++ ++++++ Ar lf+  ++  +
  gi|330507412|ref|YP_004383840.1| 958 ALVYKDMGDLNRARTLFD--VALDI 980
                                       5566689*********99..99766 PP

  == domain 10  score: 2.5 bits;  conditional E-value: 0.3
                                        HTT-HHHHHHH..HHH CS
                             TPR_3   13 nkkkyqeArelfsYal 28  
                                        ++++ +eA+elfs  +
  gi|330507412|ref|YP_004383840.1| 1003 QMGRSDEAIELFS--Q 1016
                                        68899******99..6 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1         2     1e+03       5      49 ..      96     139 ..      89     161 .. 0.76
   2 ?    2.6   0.1       0.3   1.5e+02       2      51 ..     166     221 ..     165     245 .. 0.76
   3 !    7.9   0.7    0.0069       3.6      16      81 ..     266     336 ..     251     337 .. 0.71
   4 ?    6.1   0.3     0.025        13       3      56 ..     286     345 ..     284     354 .. 0.71
   5 !   14.5   0.4     6e-05     0.031      22      81 ..     350     416 ..     336     417 .. 0.88
   6 ?   -0.1   0.0       2.2   1.1e+03      31      56 ..     479     504 ..     444     537 .. 0.61
   7 ?   -1.1   0.0       4.4   2.3e+03      27      49 ..     515     537 ..     509     545 .. 0.82
   8 ?    0.4   0.1       1.6     8e+02      29      49 ..     597     617 ..     582     657 .. 0.69
   9 ?    0.7   0.1       1.2   6.2e+02      22      52 ..     630     661 ..     607     697 .. 0.66
  10 ?    1.9   0.2      0.51   2.6e+02      34      76 ..     682     731 ..     643     737 .. 0.55
  11 ?   -0.1   0.1       2.2   1.1e+03      63      77 ..     798     812 ..     754     817 .. 0.53
  12 ?    2.9   0.0      0.25   1.3e+02      28      55 ..     916     944 ..     912     977 .. 0.64
  13 ?    2.4   0.1      0.36   1.8e+02       5      49 ..    1094    1137 ..    1086    1143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 2
                                       HHHHHHHHHHHH.HHH--HHHHHH.HHHHHHHTT-HHHHHHHHHCT CS
                            ANAPC3   5 yknAiflaerllaaetespedayl.lAlclylngqykrAyellrka 49 
                                       y nA  la  l   + +s+ +++l l+  + + +++ rA++ ++ka
  gi|330507412|ref|YP_004383840.1|  96 YSNASDLAQILS--DDDSLASILLcLGALYGEEEDWARACQCYEKA 139
                                       556666666666..666666666657999999999****9999987 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.3
                                       TT-HHHHHHHHHHHH......HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SH CS
                            ANAPC3   2 qnnyknAiflaerlla.....aetespedayllAlclylngqykrAyellrka.kl 51 
                                       q+ y+ A ++++r+l+      ++ + e++  lA+    +g+ ++A +l+++  k+
  gi|330507412|ref|YP_004383840.1| 166 QGEYHQAQICYSRILEvldprDKKGRMEATSNLAELCQIQGDMEKAEKLYQTIlKE 221
                                       678999*********55444577888888888999999999999999999888443 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0069
                                       H.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H.....HHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  16 laaetespedayllAlclylngqykrAyellrka.klnsksl.....gcrylfAqcllkLkkyeeAiaaLek 81 
                                          ++  +e    lA  +++ g+ k+A+el+ ++     k +     +++  ++qc l+ +++  A+++L++
  gi|330507412|ref|YP_004383840.1| 266 K-DQSGAAEMQCRLADIYFHEGRLKEALELYGRSlAALQKGHpslasKALCRMGQCFLEDGNWTLAEDHLQR 336
                                       4.5556666666799999999999999999999875444444366777777777888888999999988876 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.025
                                       T-HHHHHHHHHHHH.HHH--HHHHHHH.....HHHHHHTT-HHHHHHHHHCT.SHHHC-H CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayll.....AlclylngqykrAyellrka.klnsksl 56 
                                       +++k+A+ l+ r laa ++ + ++  +     ++c++++g+++ A + l++a  + ++++
  gi|330507412|ref|YP_004383840.1| 286 GRLKEALELYGRSLAALQKGHPSLASKalcrmGQCFLEDGNWTLAEDHLQRAiAIMKEHK 345
                                       57899999999999755444444332222334*****************99966655555 PP

  == domain 5  score: 14.5 bits;  conditional E-value: 6e-05
                                       -HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H......HHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  22 spedayllAlclylngqykrAyellrka.klnsksl......gcrylfAqcllkLkkyeeAiaaLek 81 
                                        + ++  lA ++ ++gq + A++  r++ k++++s+      +++ ++A+ + + + + eAi ++++
  gi|330507412|ref|YP_004383840.1| 350 LARALVILAGVHHKQGQLEMALQCSRESlKIRERSKdlsgsaEALNCIARICCDCSDWPEAIECYQR 416
                                       45568889***********************99999999999********************99876 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 2.2
                                       HHHHHTT-HHHHHHHHHCTSHHHC-H CS
                            ANAPC3  31 lclylngqykrAyellrkaklnsksl 56 
                                       l++ ++g+ + A e+l+k+   +++l
  gi|330507412|ref|YP_004383840.1| 479 LVYQSRGDLHLAGEFLEKSIATKEDL 504
                                       56666666666666666653333333 PP

  == domain 7  score: -1.1 bits;  conditional E-value: 4.4
                                       HHHHHHHHHTT-HHHHHHHHHCT CS
                            ANAPC3  27 yllAlclylngqykrAyellrka 49 
                                       + l+l + l g++++A+  ++ a
  gi|330507412|ref|YP_004383840.1| 515 LSLGLIYQLGGEWDQAQSCFEGA 537
                                       66899999999999999887765 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 1.6
                                       HHHHHHHTT-HHHHHHHHHCT CS
                            ANAPC3  29 lAlclylngqykrAyellrka 49 
                                       lA +++++g+ +rA el++++
  gi|330507412|ref|YP_004383840.1| 597 LAGVYLQSGEEERAEELYQQS 617
                                       577888888888888887776 PP

  == domain 9  score: 0.7 bits;  conditional E-value: 1.2
                                       -HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHH CS
                            ANAPC3  22 spedayllAlclylngqykrAyellrka.kln 52 
                                        + ++y lA ++ ++g+ + A+e +rk+ +l+
  gi|330507412|ref|YP_004383840.1| 630 EARSLYGLARSMAERGDLEGALECYRKClDLQ 661
                                       55677888999999999999999988885543 PP

  == domain 10  score: 1.9 bits;  conditional E-value: 0.51
                                       HHTT-HHHHHHHHHCT.SHHHC-HHHHHHHH.HHHH.....HTT-HHHHH CS
                            ANAPC3  34 ylngqykrAyellrka.klnskslgcrylfA.qcll.....kLkkyeeAi 76 
                                       +++g++++A++ + +  +   +      ++A qc+l     +L++++eA+
  gi|330507412|ref|YP_004383840.1| 682 LRRGRWQEALTRYAQVlEALRSRDDLSAVAAvQCALgnlhaDLGQWDEAL 731
                                       55555555554444443222222222222222333221112446666665 PP

  == domain 11  score: -0.1 bits;  conditional E-value: 2.2
                                       HHHHHHTT-HHHHHH CS
                            ANAPC3  63 AqcllkLkkyeeAia 77 
                                       A  ++k +++ +A++
  gi|330507412|ref|YP_004383840.1| 798 AGLCYKRGQWADALD 812
                                       344455555555544 PP

  == domain 12  score: 2.9 bits;  conditional E-value: 0.25
                                       HHHHHHHHTT-HHHHHHHHHCT.SHHHC- CS
                            ANAPC3  28 llAlclylngqykrAyellrka.klnsks 55 
                                       +lA ++  +gq+ +A+  ++++ +  +++
  gi|330507412|ref|YP_004383840.1| 916 ALAGSYTDSGQWAEAIACYKRSvERFDQT 944
                                       57888888899999988888875554444 PP

  == domain 13  score: 2.4 bits;  conditional E-value: 0.36
                                        HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                            ANAPC3    5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka 49  
                                        +++A+ l+ +l   + e ++++  l+   + +g+y+ A++  ++a
  gi|330507412|ref|YP_004383840.1| 1094 FEKALALSRKLS-LSYEEAKAISSLGRLALASGDYEDALRRMKQA 1137
                                        456777777777.88888888888888888888888888776665 PP

>> Tricorn_C1  Tricorn protease C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00024      0.12      29      65 ..     687     722 ..     682     726 .. 0.87
   2 ?    0.3   0.0       1.5   7.7e+02      27      48 ..     765     786 ..     760     795 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHGGGGG--SHHHHHHHHHHHHHTT--S-- CS
                        Tricorn_C1  29 WeavkerYepllprvatrdeladllsemlgeLntsHv 65 
                                       W+++++rY+++l+++++rd+l+ +   +++ L+  H+
  gi|330507412|ref|YP_004383840.1| 687 WQEALTRYAQVLEALRSRDDLSAV-AAVQCALGNLHA 722
                                       **********************97.567888888886 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHGGGGG--SHHH CS
                        Tricorn_C1  27 vDWeavkerYepllprvatrde 48 
                                        DW+a++e+Y+  l+   +  +
  gi|330507412|ref|YP_004383840.1| 765 GDWAAALENYRLSLEGFGKAGD 786
                                       5*********988887666655 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.13        65      12      31 ..     200     220 ..     195     227 .. 0.82
   2 ?    3.1   0.0      0.22   1.1e+02      11      26 ..     280     295 ..     278     297 .. 0.91
   3 ?   -0.1   0.0       2.1   1.1e+03      19      30 ..     414     425 ..     395     427 .. 0.84
   4 ?   -1.1   0.0       4.3   2.2e+03       8      23 ..     676     691 ..     675     696 .. 0.86
   5 ?   -0.4   0.0       2.7   1.4e+03      16      27 ..    1004    1015 ..    1000    1016 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.13
                             PPR_2  12 glck.kgkveeAfklfneMkk 31 
                                        lc+ +g++e+A kl++   k
  gi|330507412|ref|YP_004383840.1| 200 ELCQiQGDMEKAEKLYQTILK 220
                                       68999***********87665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.22
                             PPR_2  11 sglckkgkveeAfklf 26 
                                       + ++++g+++eA++l+
  gi|330507412|ref|YP_004383840.1| 280 DIYFHEGRLKEALELY 295
                                       579************9 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.1
                             PPR_2  19 veeAfklfneMk 30 
                                       ++ A +lf+eM 
  gi|330507412|ref|YP_004383840.1| 414 YQRAADLFMEMG 425
                                       678999999995 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 4.3
                             PPR_2   8 tlIsglckkgkveeAf 23 
                                       ++ + l+++g+++eA+
  gi|330507412|ref|YP_004383840.1| 676 SMVNLLLRRGRWQEAL 691
                                       58899**********8 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 2.7
                             PPR_2   16 kgkveeAfklfn 27  
                                         g+++eA++lf+
  gi|330507412|ref|YP_004383840.1| 1004 MGRSDEAIELFS 1015
                                        799********7 PP

>> RPN6_N  26S proteasome regulatory subunit RPN6 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.2    0.0012      0.62       7      54 ..     206     251 ..     163     269 .. 0.79
   2 ?   -2.1   0.0       9.2   4.7e+03       9      54 ..     687     730 ..     681     743 .. 0.69
   3 ?   -0.6   0.0       3.1   1.6e+03       7      63 ..     924     979 ..     918     986 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
                            RPN6_N   7 sdpkeaeelykeilskkskedeealreqeqalleLgelyrdqkkaeeL 54 
                                        d+++ae+ly++il++++ +d+       +al +L+++y+++++ +  
  gi|330507412|ref|YP_004383840.1| 206 GDMEKAEKLYQTILKERELSDD--PVGAARALASLASIYSQTGNGKRA 251
                                       3788999999999999986666..445668999999999998887654 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.2
                            RPN6_N   9 pkeaeelykeilskkskedeealreqeqalleLgelyrdqkkaeeL 54 
                                        +ea + y ++l+   ++d+  l +  +  ++Lg+l++d ++ +e 
  gi|330507412|ref|YP_004383840.1| 687 WQEALTRYAQVLEALRSRDD--LSAVAAVQCALGNLHADLGQWDEA 730
                                       67888999999988887666..555555556788888877776665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.1
                            RPN6_N   7 s.dpkeaeelykeilskkskedeealreqeqalleLgelyrdqkkaeeLaelikesrs 63 
                                       s + +ea++ yk+ +++  ++ e  + ++ q l++++ +y+d ++ +  + l+    +
  gi|330507412|ref|YP_004383840.1| 924 SgQWAEAIACYKRSVERFDQTGE--VYNRGQVLFNMALVYKDMGDLNRARTLFDVALD 979
                                       55788999999999998887776..8889999**********9998888887766555 PP

>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.8     3e+03       7      53 ..     219     265 ..     215     277 .. 0.83
   2 ?    3.1   0.0      0.13        65      16      56 ..     307     347 ..     296     389 .. 0.79
   3 ?    4.7   0.0     0.043        22      15      70 ..     666     721 ..     655     725 .. 0.90
   4 ?    1.1   0.0      0.54   2.8e+02      21      59 ..     832     870 ..     816     896 .. 0.77
   5 ?   -0.9   0.0       2.2   1.1e+03      30      62 ..    1201    1233 ..    1189    1248 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.8
                                       SCT------SSTTSBHHHHHHHHHSBTTBHHHHHHHHHHHHHHHHHH CS
                      Ribosomal_S7   7 akkrevlpdpkynselveklinklmkdGkkslAekivygaldiieek 53 
                                       +k+re+  dp+   + ++ l +   ++G+ ++A+  +++a +++++ 
  gi|330507412|ref|YP_004383840.1| 219 LKERELSDDPVGAARALASLASIYSQTGNGKRAQISLQSASHLLADL 265
                                       5789999999999999999*999999999999999998888777764 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.13
                                       SSTTSBHHHHHHHHHSBTTBHHHHHHHHHHHHHHHHHHHSS CS
                      Ribosomal_S7  16 pkynselveklinklmkdGkkslAekivygaldiieektkk 56 
                                       p   s+ + ++ ++ ++dG+ +lAe  +++a+ i++e +++
  gi|330507412|ref|YP_004383840.1| 307 PSLASKALCRMGQCFLEDGNWTLAEDHLQRAIAIMKEHKDS 347
                                       667788889999999*********************98543 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.043
                                       -SSTTSBHHHHHHHHHSBTTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS CS
                      Ribosomal_S7  15 dpkynselveklinklmkdGkkslAekivygaldiieektkkdplevleeAlenvk 70 
                                       d +   e +e ++n l+++G+ + A +   ++l+ ++++ +  ++  ++ Al n+ 
  gi|330507412|ref|YP_004383840.1| 666 DSRSMIEALESMVNLLLRRGRWQEALTRYAQVLEALRSRDDLSAVAAVQCALGNLH 721
                                       777888999******************************99999*99999999976 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.54
                                       BHHHHHHHHHSBTTBHHHHHHHHHHHHHHHHHHHSS-HH CS
                      Ribosomal_S7  21 elveklinklmkdGkkslAekivygaldiieektkkdpl 59 
                                       +++  + n   ++G++ lA + +++al+i ++ +++ + 
  gi|330507412|ref|YP_004383840.1| 832 QVLGNMGNLYHRQGERDLAAEHFQRALEIYRRLKDQAGA 870
                                       667777788899****************99986555443 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 2.2
                                        HSBTTBHHHHHHHHHHHHHHHHHHHSS-HHHHH CS
                      Ribosomal_S7   30 lmkdGkkslAekivygaldiieektkkdplevl 62  
                                          ++Gkk+ A+    gal +  ++ ++ p +++
  gi|330507412|ref|YP_004383840.1| 1201 EARTGKKEEARADYAGALRLAGKEGDRIPSSTI 1233
                                        5689**************999988655444333 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.78     4e+02     128     180 ..     135     187 ..     130     200 .. 0.88
   2 !    8.0   1.8    0.0042       2.2      89     179 ..     205     305 ..     198     318 .. 0.58
   3 ?    3.6   0.2     0.089        46      87     134 ..     322     372 ..     313     391 .. 0.79
   4 ?    1.6   0.1      0.39     2e+02     150     181 ..     435     467 ..     408     503 .. 0.81
   5 ?   -1.7   0.0         4     2e+03     145     176 ..     550     581 ..     528     599 .. 0.74
   6 ?   -1.1   0.0       2.6   1.3e+03     155     175 ..     600     620 ..     579     633 .. 0.78
   7 !    7.1   0.9     0.008       4.1      81     178 ..     636     743 ..     598     759 .. 0.69
   8 ?    4.6   0.5     0.046        23      95     178 ..     690     743 ..     681     795 .. 0.54
   9 !    7.8   0.3    0.0048       2.5     127     174 ..     812     859 ..     762     879 .. 0.89
  10 ?   -2.5   0.0       6.9   3.5e+03     156     179 ..     921     944 ..     886     959 .. 0.75
  11 ?   -1.2   0.1       2.7   1.4e+03     119     138 ..    1117    1136 ..    1083    1139 .. 0.75
  12 ?    2.9   0.2      0.15        79     113     172 ..    1191    1217 ..    1151    1234 .. 0.56

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.78
                            TPR_21 128 kydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaaleeka 180
                                        y++Al +++ +k+     +v e+ G +   qg+  +A+  Y++ l+ l++++
  gi|330507412|ref|YP_004383840.1| 135 CYEKALVAIDMAKRPRLLPQVLERLGRARRLQGEYHQAQICYSRILEVLDPRD 187
                                       58999**********************************99999888887765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0042
                            TPR_21  89 agdlaaAkaqLewvlekak...deelkalarlRLarvllaekk.......ydeAlktLeakkeeafaalvaelrGDi 155
                                       +gd+++A++ ++ +l++ +   d   +a a   La+++ ++++       ++ A ++L++ k+++ aa+++ +  Di
  gi|330507412|ref|YP_004383840.1| 205 QGDMEKAEKLYQTILKERElsdDPVGAARALASLASIYSQTGNgkraqisLQSASHLLADLKDQSGAAEMQCRLADI 281
                                       56666666666666655422112223333444566666666651111111334455556667777777777777888 PP

                            TPR_21 156 lvaqgkldeAraaYqaAlaaleek 179
                                       ++ +g+l+eA + Y ++laal+++
  gi|330507412|ref|YP_004383840.1| 282 YFHEGRLKEALELYGRSLAALQKG 305
                                       888888888888888888887776 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.089
                            TPR_21  87 veagdlaaAkaqLewvlekakd.eelkalar..lRLarvllaekkydeAlk 134
                                        e g++  A+ +L+++++  k+ ++ ++lar  + La v  ++++++ Al+
  gi|330507412|ref|YP_004383840.1| 322 LEDGNWTLAEDHLQRAIAIMKEhKDSSSLARalVILAGVHHKQGQLEMALQ 372
                                       678999999****99887543314455565522689*************97 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.39
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAlaaleeka.r 181
                                          G ++  +g+ld A + Y++A+++  ++  r
  gi|330507412|ref|YP_004383840.1| 435 SNLGGVYHLKGDLDVALQMYSHAYNSFCQQGdR 467
                                       556889999999999999999999988777653 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 4
                            TPR_21 145 aalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                        a++++  G++++ +g+l +A   Y+++l+a 
  gi|330507412|ref|YP_004383840.1| 550 LAAAENNLGNLYSDRGDLMHAILCYRQGLEAR 581
                                       56677778999999999999999999998876 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 2.6
                            TPR_21 155 ilvaqgkldeAraaYqaAlaa 175
                                       ++++ g+ + A + Yq++++ 
  gi|330507412|ref|YP_004383840.1| 600 VYLQSGEEERAEELYQQSIDG 620
                                       677777777888888777765 PP

  == domain 7  score: 7.1 bits;  conditional E-value: 0.008
                            TPR_21  81 llAkaaveagdlaaAkaqLewvle........kakdeelkalarlRLa..rvllaekkydeAlktLeakkeeafaal 147
                                        lA++++e+gdl+ A + +++ l+         +  e+l+++++l L   r + a   y++ l++L + ++ +  a+
  gi|330507412|ref|YP_004383840.1| 636 GLARSMAERGDLEGALECYRKCLDlqivggdsRSMIEALESMVNLLLRrgRWQEALTRYAQVLEALRSRDDLSAVAA 712
                                       47888888888888887666555422221111334477888888766511566777899999999**9999999*** PP

                            TPR_21 148 vaelrGDilvaqgkldeAraaYqaAlaalee 178
                                       v+   G++++  g+ deA + Y+++la +e 
  gi|330507412|ref|YP_004383840.1| 713 VQCALGNLHADLGQWDEALEDYNESLAIMEG 743
                                       ************************9987765 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.046
                            TPR_21  95 AkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqa 171
                                       A +                               y++ l++L + ++ +  a+v+   G++++  g+ deA + Y++
  gi|330507412|ref|YP_004383840.1| 690 ALT------------------------------RYAQVLEALRSRDDLSAVAAVQCALGNLHADLGQWDEALEDYNE 736
                                       333..............................44455555555555555555555555555555555555555555 PP

                            TPR_21 172 Alaalee 178
                                       +la +e 
  gi|330507412|ref|YP_004383840.1| 737 SLAIMEG 743
                                       5544433 PP

  == domain 9  score: 7.8 bits;  conditional E-value: 0.0048
                            TPR_21 127 kkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       + y + l++ e+ +++a  a+v    G+++ +qg++d A +++q+Al+
  gi|330507412|ref|YP_004383840.1| 812 DSYSKSLSLFEKLEDSAGIAQVLGNMGNLYHRQGERDLAAEHFQRALE 859
                                       6788888999999999999***************************97 PP

  == domain 10  score: -2.5 bits;  conditional E-value: 6.9
                            TPR_21 156 lvaqgkldeAraaYqaAlaaleek 179
                                       ++  g+ +eA a Y++++++ +++
  gi|330507412|ref|YP_004383840.1| 921 YTDSGQWAEAIACYKRSVERFDQT 944
                                       667888888999998888887776 PP

  == domain 11  score: -1.2 bits;  conditional E-value: 2.7
                            TPR_21  119 LarvllaekkydeAlktLea 138 
                                        L r+ la ++y++Al+++++
  gi|330507412|ref|YP_004383840.1| 1117 LGRLALASGDYEDALRRMKQ 1136
                                        56677777777777776655 PP

  == domain 12  score: 2.9 bits;  conditional E-value: 0.15
                            TPR_21  113 alarlRLarvllaekkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaA 172 
                                         la++ La+  + ++k +eA                                 ra Y  A
  gi|330507412|ref|YP_004383840.1| 1191 LLATVDLAECEARTGKKEEA---------------------------------RADYAGA 1217
                                        55555555555555555555.................................5555555 PP

>> DUF4810  Domain of unknown function (DUF4810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       3.4   1.7e+03      25      69 ..     211     256 ..     196     261 .. 0.66
   2 ?    0.4   0.0       1.9   9.8e+02      29      75 ..     494     541 ..     473     545 .. 0.73
   3 ?    1.0   0.1       1.3   6.5e+02      50      77 ..     596     623 ..     589     625 .. 0.86
   4 ?   -1.2   0.0       6.2   3.2e+03      47      70 ..     713     736 ..     687     742 .. 0.78
   5 ?    3.8   0.0      0.17        87      49      75 ..     835     861 ..     831     863 .. 0.87
   6 ?   -1.1   0.0       5.5   2.8e+03      19      69 ..     924     975 ..     915     982 .. 0.76
   7 ?    0.1   0.0       2.4   1.2e+03      50      70 ..     996    1016 ..     993    1018 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.4
                           DUF4810  25 qieklekiiekaeakgkkv.pPGlyAelGllylkegkkeeaieafe 69 
                                         + ++ i+++ e ++ +v +    A l+ +y+++g+ + a+  ++
  gi|330507412|ref|YP_004383840.1| 211 AEKLYQTILKERELSDDPVgAARALASLASIYSQTGNGKRAQISLQ 256
                                       4444555555555555555223357899999999999999887766 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.9
                           DUF4810  29 lekiiekaeakgkkv.pPGlyAelGllylkegkkeeaieafekEkelf 75 
                                       lek+i++ e+ g ++ + G +  lGl+y   g+ ++a++ fe   ++f
  gi|330507412|ref|YP_004383840.1| 494 LEKSIATKEDLGDQIgAAGNRLSLGLIYQLGGEWDQAQSCFEGAARAF 541
                                       666666666666555356888889999999999999999998666555 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.3
                           DUF4810  50 elGllylkegkkeeaieafekEkelfPE 77 
                                       +l+ +yl++g++e a e +++  + f E
  gi|330507412|ref|YP_004383840.1| 596 NLAGVYLQSGEEERAEELYQQSIDGFRE 623
                                       67789***************98887766 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 6.2
                           DUF4810  47 lyAelGllylkegkkeeaieafek 70 
                                       +++ lG l+++ g+ +ea e +++
  gi|330507412|ref|YP_004383840.1| 713 VQCALGNLHADLGQWDEALEDYNE 736
                                       677899999999999999887764 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.17
                           DUF4810  49 AelGllylkegkkeeaieafekEkelf 75 
                                        ++G ly ++g+++ a e+f++  e +
  gi|330507412|ref|YP_004383840.1| 835 GNMGNLYHRQGERDLAAEHFQRALEIY 861
                                       689*****************9866665 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 5.5
                           DUF4810  19 eeskekqieklekiiekaeakgkkvpPG.lyAelGllylkegkkeeaieafe 69 
                                       + + ++ i+ +++++e+ +++g+    G +  +++l+y ++g+ + a++ f+
  gi|330507412|ref|YP_004383840.1| 924 SGQWAEAIACYKRSVERFDQTGEVYNRGqVLFNMALVYKDMGDLNRARTLFD 975
                                       5566677788888888888888888888556789999999999999988886 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 2.4
                           DUF4810   50 elGllylkegkkeeaieafek 70  
                                        +lG++  ++g+++eaie f++
  gi|330507412|ref|YP_004383840.1|  996 NLGIISGQMGRSDEAIELFSQ 1016
                                        69***************9986 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.92   4.7e+02      56     105 ..     352     402 ..     311     433 .. 0.68
   2 ?   -1.1   0.0       3.5   1.8e+03      97     133 ..     668     704 ..     619     709 .. 0.64
   3 ?    1.3   0.3      0.62   3.2e+02      57      85 ..     713     741 ..     682     793 .. 0.71
   4 ?    1.5   0.3      0.54   2.8e+02      90      90 ..     746     746 ..     707     827 .. 0.52
   5 ?    2.4   0.2      0.29   1.5e+02      57     131 ..     793     862 ..     779     888 .. 0.75
   6 ?    4.0   0.1     0.094        48      45     125 ..     902     976 ..     892     985 .. 0.73
   7 ?   10.8   0.1   0.00076      0.39      14      89 ..    1076    1145 ..    1070    1151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.92
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TT.STHHHHHHHHHHH CS
                           DUF3856  56 lchaglsealaklgrydealesadkalryfnrrGele.qdeGklWiaavfs 105
                                        +   l++   k g+ + al+++ ++l+  +r  +l  ++e    ia ++ 
  gi|330507412|ref|YP_004383840.1| 352 RALVILAGVHHKQGQLEMALQCSRESLKIRERSKDLSgSAEALNCIARICC 402
                                       445679999999999999**9999999999999999724555556666655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH- CS
                           DUF3856  97 klWiaavfsravaleelGrkdealkafrmagemiaer 133
                                       +  i a+ s    l   Gr +eal  + ++ e +  r
  gi|330507412|ref|YP_004383840.1| 668 RSMIEALESMVNLLLRRGRWQEALTRYAQVLEALRSR 704
                                       3456666666666667777777777777777766555 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.62
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                           DUF3856  57 chaglsealaklgrydealesadkalryf 85 
                                       + ++l +  a lg++deale  +++l  +
  gi|330507412|ref|YP_004383840.1| 713 VQCALGNLHADLGQWDEALEDYNESLAIM 741
                                       45566666677777777777766666544 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.54
                                       - CS
                           DUF3856  90 e 90 
                                       +
  gi|330507412|ref|YP_004383840.1| 746 D 746
                                       1 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHH.HHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                           DUF3856  57 chaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavf.sravaleelGrkdealkafrmagemia 131
                                       + + +++   k g++ +al s  k+l  f++   le+  G   ia v+ + +  ++  G +d a ++f+ a e+  
  gi|330507412|ref|YP_004383840.1| 793 VLSNVAGLCYKRGQWADALDSYSKSLSLFEK---LEDSAG---IAQVLgNMGNLYHRQGERDLAAEHFQRALEIYR 862
                                       5566677778889999999999999999975...665555...554441667777888888989999988888754 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.094
                                       TS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                           DUF3856  45 eeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealk 121
                                       ee+ d  G    + ++l+++++  g++ ea+ + +++++ f++ Ge+ + +      ++f+ a  ++++G  + a  
  gi|330507412|ref|YP_004383840.1| 902 EETGDLSGQGE-VLSALAGSYTDSGQWAEAIACYKRSVERFDQTGEVYNRGQ-----VLFNMALVYKDMGDLNRART 972
                                       55566666544.45789*****************************987654.....45555555555555555555 PP

                                       HHHH CS
                           DUF3856 122 afrm 125
                                        f +
  gi|330507412|ref|YP_004383840.1| 973 LFDV 976
                                       5555 PP

  == domain 7  score: 10.8 bits;  conditional E-value: 0.00076
                                        HHHHHHHHHT-HHHHHHHHHHHHHHHTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH CS
                           DUF3856   14 seaekqleegayeeaaasyrkalevsrtipaeeafdheGfdalchaglsealaklgrydealesadkalryfnrr 88  
                                        +++e+ l++  y ea+  ++kal +sr ++      +e   a   ++l    +  g+y++al+  ++al  f r 
  gi|330507412|ref|YP_004383840.1| 1076 AQGERFLKDMLYPEAKSCFEKALALSRKLSL----SYEEAKA--ISSLGRLALASGDYEDALRRMKQALVIFGRL 1144
                                        699************************9875....4554444..46677777788*****************998 PP

                                        - CS
                           DUF3856   89 G 89  
                                        G
  gi|330507412|ref|YP_004383840.1| 1145 G 1145
                                        8 PP

>> FliS  Flagellar protein FliS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.6   8.4e+02      30      57 ..     316     343 ..     310     352 .. 0.83
   2 ?    7.8   0.1    0.0074       3.8      20      64 ..    1106    1150 ..    1100    1162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.6
                                       HHHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                              FliS  30 krakeaieekdiekkgeaiskaqdIise 57 
                                       ++ +  +e+++   +++++++a++I++e
  gi|330507412|ref|YP_004383840.1| 316 RMGQCFLEDGNWTLAEDHLQRAIAIMKE 343
                                       55666789999999***********987 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0074
                                        HHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHTCCT CS
                              FliS   20 mLydgalkflkrakeaieekdiekkgeaiskaqdIiseLrasLdl 64  
                                        + y++a    +  + a++++d+e++ + +++a  I+  L asLdl
  gi|330507412|ref|YP_004383840.1| 1106 LSYEEAKAISSLGRLALASGDYEDALRRMKQALVIFGRLGASLDL 1150
                                        67999999999999******************************8 PP

>> PPR_1  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.3   2.2e+03      21      29 ..     206     214 ..     205     216 .. 0.88
   2 ?    1.9   0.0      0.36   1.8e+02      19      30 ..     284     295 ..     280     297 .. 0.84
   3 ?   -2.4   0.1       7.9     4e+03      15      22 ..     459     466 ..     459     466 .. 0.89
   4 ?   -2.3   0.0       7.2   3.7e+03      15      24 ..     779     788 ..     778     789 .. 0.86
   5 ?   -2.1   0.0       6.4   3.3e+03      21      31 ..     965     975 ..     964     976 .. 0.91
   6 ?    4.0   0.0     0.081        41      20      32 ..    1004    1016 ..    1002    1016 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.3
                                       S-HHHHHHH CS
                             PPR_1  21 GrvdeAfel 29 
                                       G++++A++l
  gi|330507412|ref|YP_004383840.1| 206 GDMEKAEKL 214
                                       9*******9 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.36
                                       HTS-HHHHHHHH CS
                             PPR_1  19 kaGrvdeAfelf 30 
                                        +Gr++eA+el 
  gi|330507412|ref|YP_004383840.1| 284 HEGRLKEALELY 295
                                       58********95 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 7.9
                                       HHHHHTS- CS
                             PPR_1  15 dGlCkaGr 22 
                                       +++C++G+
  gi|330507412|ref|YP_004383840.1| 459 NSFCQQGD 466
                                       79****97 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 7.2
                                       HHHHHTS-HH CS
                             PPR_1  15 dGlCkaGrvd 24 
                                        G+ kaG+++
  gi|330507412|ref|YP_004383840.1| 779 EGFGKAGDME 788
                                       69******97 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 6.4
                                       S-HHHHHHHHH CS
                             PPR_1  21 GrvdeAfelfd 31 
                                       G++++A  lfd
  gi|330507412|ref|YP_004383840.1| 965 GDLNRARTLFD 975
                                       9*********8 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.081
                                        TS-HHHHHHHHHH CS
                             PPR_1   20 aGrvdeAfelfde 32  
                                         Gr deA+elf++
  gi|330507412|ref|YP_004383840.1| 1004 MGRSDEAIELFSQ 1016
                                        79*********86 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.3   2.2e+03       7      29 ..     278     300 ..     276     307 .. 0.71
   2 ?   -0.1   0.0       1.3   6.7e+02      21      34 ..     371     384 ..     354     387 .. 0.79
   3 ?   -0.0   0.0       1.2   6.2e+02      20      31 ..     650     661 ..     648     662 .. 0.84
   4 ?    7.1   0.0    0.0073       3.8      16      30 ..     726     740 ..     716     745 .. 0.86
   5 ?   -2.3   0.0       6.2   3.2e+03       8      29 ..     758     779 ..     756     779 .. 0.71
   6 ?    4.4   0.2     0.048        25      20      36 ..     850     866 ..     848     868 .. 0.90
   7 ?   -1.7   0.1       3.9     2e+03       6      34 ..    1076    1104 ..    1072    1105 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.3
                          SHNi-TPR   7 LGEislEnenFpqAveDlrkaLe 29 
                                       L++i +  ++ ++A+e + ++L+
  gi|330507412|ref|YP_004383840.1| 278 LADIYFHEGRLKEALELYGRSLA 300
                                       77777777777777777777775 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                          SHNi-TPR  21 veDlrkaLeLreql 34 
                                       ++  r++L++re  
  gi|330507412|ref|YP_004383840.1| 371 LQCSRESLKIRERS 384
                                       55579******976 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.2
                          SHNi-TPR  20 AveDlrkaLeLr 31 
                                       A+e +rk+L+L+
  gi|330507412|ref|YP_004383840.1| 650 ALECYRKCLDLQ 661
                                       56669******8 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0073
                          SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                       + ++A+eD++++L++
  gi|330507412|ref|YP_004383840.1| 726 QWDEALEDYNESLAI 740
                                       779**********98 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 6.2
                          SHNi-TPR   8 GEislEnenFpqAveDlrkaLe 29 
                                       G+++  ++    A+e++r +Le
  gi|330507412|ref|YP_004383840.1| 758 GNMCYRQGDWAAALENYRLSLE 779
                                       5555555556689*****9997 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.048
                          SHNi-TPR  20 AveDlrkaLeLreqllp 36 
                                       A+e +++aLe+++ l+ 
  gi|330507412|ref|YP_004383840.1| 850 AAEHFQRALEIYRRLKD 866
                                       8999*********9986 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 3.9
                          SHNi-TPR    6 lLGEislEnenFpqAveDlrkaLeLreql 34  
                                         +GE +l +  +p+A + ++kaL+L ++l
  gi|330507412|ref|YP_004383840.1| 1076 AQGERFLKDMLYPEAKSCFEKALALSRKL 1104
                                        5666666666699999999****997775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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):              35  [number of targets reported over threshold]
# CPU time: 1.34u 0.26s 00:00:01.60 Elapsed: 00:00:00.68
# Mc/sec: 5734.67
//
Query:       gi|330507413|ref|YP_004383841.1|  [L=128]
Description: 4Fe-4S ferredoxin, iron-sulfur binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-14   51.5  13.5    1.2e-07   31.3   2.8    2.2  2  Fer4             4Fe-4S binding domain
    3.2e-11   43.7   6.6    1.9e-05   25.2   0.2    2.2  2  Fer4_7           4Fe-4S dicluster domain
    1.6e-10   40.6  13.0    3.4e-05   23.7   2.6    2.2  2  Fer4_6           4Fe-4S binding domain
    3.9e-10   39.7  21.0    5.5e-07   29.7  12.7    2.0  2  Fer4_9           4Fe-4S dicluster domain
    4.7e-10   39.0  14.8    2.5e-05   24.1   2.7    2.3  2  Fer4_2           4Fe-4S binding domain
    1.8e-09   37.6   9.8    2.9e-09   36.9   9.8    1.3  1  Fer4_10          4Fe-4S dicluster domain
    3.2e-08   33.6   6.4      0.001   19.2   0.6    2.3  2  Fer4_21          4Fe-4S dicluster domain
    7.4e-08   32.3  16.8    0.00045   20.5   4.1    2.2  2  Fer4_4           4Fe-4S binding domain
    1.5e-07   32.2   9.2    0.00083   20.2   0.7    2.3  2  Fer4_16          4Fe-4S double cluster binding domain
    9.6e-07   29.3   3.8      0.018   15.5   0.6    2.2  2  Fer4_17          4Fe-4S dicluster domain
    4.8e-05   23.8  10.7     0.0038   17.7   1.2    2.5  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
    5.8e-05   23.7  20.7      0.016   16.1   5.8    2.2  2  Fer4_3           4Fe-4S binding domain
    0.00022   21.4  13.5      0.026   14.7  13.6    2.4  1  Fer4_18          4Fe-4S dicluster domain
    0.00042   20.7  14.2      0.071   13.6   3.0    2.2  2  Fer4_8           4Fe-4S dicluster domain
    0.00055   19.7   0.1    0.00078   19.2   0.1    1.2  1  NIL              NIL domain
  ------ inclusion threshold ------
      0.013   14.4   0.2      0.016   14.1   0.2    1.1  1  Trp_syntA        Tryptophan synthase alpha chain
      0.024   15.4  11.8       0.71   10.7   1.3    3.0  3  Fer4_15          4Fe-4S single cluster domain
      0.035   13.5   0.4        2.9    7.2   0.0    2.0  2  GMC_oxred_N      GMC oxidoreductase
      0.036   14.1   0.9       0.23   11.6   0.0    2.0  2  FeoC             FeoC like transcriptional regulator
      0.049   13.0   0.3       0.08   12.3   0.3    1.3  1  tify             tify domain
       0.17   12.1   3.6       0.35   11.0   3.4    1.5  1  DUF678           Protein of unknown function (DUF678)
       0.39   10.4   7.6        2.5    7.7   1.2    2.2  2  HCV_NS2          Hepatitis C virus non-structural protein NS2
        0.6   11.0  16.1        1.4    9.8   4.4    2.2  3  Fer4_22          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   2.8   1.5e-10   1.2e-07       2      22 ..      73      93 ..      72      95 .. 0.90
   2 !   26.0   3.2     7e-09   5.4e-06       2      24 .]     102     124 ..     101     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.5e-10
                                      EEETTTSSS-THHHHHSTTTE CS
                              Fer4  2 videekCigCGaCvevCPvgA 22
                                      + de+ C++CGaCv++CP+g 
  gi|330507413|ref|YP_004383841.1| 73 IRDESECVNCGACVSICPTGT 93
                                      679****************95 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 7e-09
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       v d  kCi CGaCv  CP  A++
  gi|330507413|ref|YP_004383841.1| 102 VADSGKCIQCGACVVGCPQRALK 124
                                       56999**************9985 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.2   2.4e-08   1.9e-05      35      51 ..      76      92 ..      43     105 .. 0.64
   2 !   20.9   2.1   5.1e-07    0.0004       1      19 [.     107     125 ..     107     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.4e-08
                            Fer4_7 35 pekClgCgaCvavCPtg 51
                                      +++C++CgaCv+ CPtg
  gi|330507413|ref|YP_004383841.1| 76 ESECVNCGACVSICPTG 92
                                      45566666666666665 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.1e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaiel 19 
                                       +Ci+CgaCv+ Cp++a++l
  gi|330507413|ref|YP_004383841.1| 107 KCIQCGACVVGCPQRALKL 125
                                       7*************99875 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   2.9   1.1e-07   8.6e-05       4      22 ..      74      92 ..      71      94 .. 0.88
   2 !   23.7   2.6   4.4e-08   3.4e-05       2      23 ..     101     122 ..     100     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-07
                            Fer4_6  4 idpdkCigCgdCvrvCPeg 22
                                       d++ C+ Cg+Cv++CP+g
  gi|330507413|ref|YP_004383841.1| 74 RDESECVNCGACVSICPTG 92
                                      58899************98 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 4.4e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       v+ d  kCi+Cg+Cv+ CP  a
  gi|330507413|ref|YP_004383841.1| 101 VVADSGKCIQCGACVVGCPQRA 122
                                       789****************665 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   1.2   2.7e-07   0.00021      33      49 ..      73      92 ..      46      94 .. 0.73
   2 !   29.7  12.7   7.1e-10   5.5e-07       1      50 [.      78     122 ..      78     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.7e-07
                            Fer4_9 33 e...eaCigCgaCveaCpkg 49
                                          ++C+ CgaCv +Cp+g
  gi|330507413|ref|YP_004383841.1| 73 IrdeSECVNCGACVSICPTG 92
                                      033367************97 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 7.1e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       +C++CgaCv+ Cp+g+++ ++ +  a        +Ci+CgaCv  Cp+ a
  gi|330507413|ref|YP_004383841.1|  78 ECVNCGACVSICPTGTFRFEDWRVVADSG-----KCIQCGACVVGCPQRA 122
                                       5****************988888888774.....5************986 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   4.5   4.5e-07   0.00035       5      22 .]      74      91 ..      71      91 .. 0.85
   2 !   24.1   2.7   3.2e-08   2.5e-05       1      22 []      99     120 ..      99     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.5e-07
                            Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                       d+  C++CgaCvs CP+
  gi|330507413|ref|YP_004383841.1| 74 RDESECVNCGACVSICPT 91
                                      57778************7 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 3.2e-08
                            Fer4_2   1 apvvvdtdrCigCgaCvsaCPa 22 
                                       ++vv+d+ +Ci+CgaCv  CP+
  gi|330507413|ref|YP_004383841.1|  99 WRVVADSGKCIQCGACVVGCPQ 120
                                       789******************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 !   36.9   9.8   3.8e-12   2.9e-09       2      56 .]      72     119 ..      71     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 3.8e-12
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       v++d++ C++Cg+Cv+ CP+         ++ e+ +v  +++kC++cgaCv  CP
  gi|330507413|ref|YP_004383841.1|  72 VIRDESECVNCGACVSICPT-------GTFRFEDWRVVADSGKCIQCGACVVGCP 119
                                       6789999*************.......9**************************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 !   19.2   0.6   1.3e-06     0.001      37      53 ..      75      91 ..      48      95 .. 0.77
   2 !   17.6   0.8   3.9e-06    0.0031       4      24 ..     104     124 ..     101     128 .] 0.84

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                           Fer4_21 37 vedeCvGCnlCssvCPv 53
                                       e+eCv C  C+s+CP+
  gi|330507413|ref|YP_004383841.1| 75 DESECVNCGACVSICPT 91
                                      26789999999999995 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.9e-06
                           Fer4_21   4 dedkCigCgkCliaCedtshq 24 
                                       d+ kCi+Cg C++ C++ + +
  gi|330507413|ref|YP_004383841.1| 104 DSGKCIQCGACVVGCPQRALK 124
                                       6789************98765 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   4.1   5.8e-07   0.00045       3      17 .]      78      92 ..      76      92 .. 0.91
   2 !   17.5   4.9   5.5e-06    0.0043       3      17 .]     107     121 ..     105     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.8e-07
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                       C++Cg+Cv++CP+g
  gi|330507413|ref|YP_004383841.1| 78 ECVNCGACVSICPTG 92
                                      6************86 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.5e-06
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                       +Ci+Cg+Cv  CPq+
  gi|330507413|ref|YP_004383841.1| 107 KCIQCGACVVGCPQR 121
                                       8************86 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.7   1.1e-06   0.00083       2      20 ..      79      97 ..      78     105 .. 0.85
   2 !   16.0   2.4   2.3e-05     0.018       1      18 [.     107     124 ..     107     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-06
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++Cg+C+++CPt+ ++ +
  gi|330507413|ref|YP_004383841.1| 79 CVNCGACVSICPTGTFRFE 97
                                      **************99877 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.3e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                       +C++Cg+C+  CP++a+k
  gi|330507413|ref|YP_004383841.1| 107 KCIQCGACVVGCPQRALK 124
                                       6***************97 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   3.4e-05     0.027      44      59 ..      77      92 ..      43      94 .. 0.84
   2 !   15.5   0.6   2.4e-05     0.018      44      58 ..     106     120 ..      96     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.4e-05
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      s+C++Cg C++ CP g
  gi|330507413|ref|YP_004383841.1| 77 SECVNCGACVSICPTG 92
                                      6899999999999975 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.4e-05
                           Fer4_17  44 slCieCgeCerkCPq 58 
                                       ++Ci+Cg C+  CPq
  gi|330507413|ref|YP_004383841.1| 106 GKCIQCGACVVGCPQ 120
                                       578888888888887 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.2   4.8e-06    0.0038       2      18 ..      75      91 ..      72      99 .. 0.88
   2 !   10.9   2.0   0.00067      0.52       2      18 ..     104     120 ..     102     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.8e-06
                           Fer4_13  2 DrdtCiacgaCvelaPd 18
                                      D+++C++cgaCv+++P 
  gi|330507413|ref|YP_004383841.1| 75 DESECVNCGACVSICPT 91
                                      889*************6 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00067
                           Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                       D  +Ci cgaCv  +P+
  gi|330507413|ref|YP_004383841.1| 104 DSGKCIQCGACVVGCPQ 120
                                       6789**********996 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   5.8   2.1e-05     0.016       1      14 [.      79      92 ..      79      93 .. 0.96
   2 !   13.7   6.9   0.00012     0.093       1      15 []     108     122 ..     108     122 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.1e-05
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C++CgaCv  CP+g
  gi|330507413|ref|YP_004383841.1| 79 CVNCGACVSICPTG 92
                                      ************98 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00012
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C++CgaCv+ CP +A
  gi|330507413|ref|YP_004383841.1| 108 CIQCGACVVGCPQRA 122
                                       ************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 !   14.7  13.6   3.3e-05     0.026      56      95 ..      74     118 ..      17     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-05
                           Fer4_18  56 kgagdcidcescvkvcPtgi....dirkGlql.eciscllcidac 95 
                                       +++++c++c++cv++cPtg     d r      +ci+c+ c+  c
  gi|330507413|ref|YP_004383841.1|  74 RDESECVNCGACVSICPTGTfrfeDWRVVADSgKCIQCGACVVGC 118
                                       5689**************9744456666554348********888 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   3.0   9.2e-05     0.071       4      17 ..      78      91 ..      75     107 .. 0.74
   2 !   12.6   3.4   0.00018      0.14       4      16 ..     107     119 ..      95     122 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.2e-05
                            Fer4_8  4 kCieCgaCqsaCpv 17
                                      +C++CgaC s Cp+
  gi|330507413|ref|YP_004383841.1| 78 ECVNCGACVSICPT 91
                                      67777777777774 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00018
                            Fer4_8   4 kCieCgaCqsaCp 16 
                                       kCi+CgaC   Cp
  gi|330507413|ref|YP_004383841.1| 107 KCIQCGACVVGCP 119
                                       5666666666665 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1     1e-06   0.00078      12      71 ..      12      65 ..       3      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1e-06
                                      -SS-HHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHHTT-EE CS
                               NIL 12 avePllshlvrqlglevnIlqGsveriqgtpfGqlvielsgsqesiaaalqylrkrnvdv 71
                                      ++ Pl+++++ +    vnI  +s+      + G +v+e++  +e+++++++ +++r+v+v
  gi|330507413|ref|YP_004383841.1| 12 VRHPLIASVILETEALVNIERASIN----AVSGEIVLEVP--PEKVQEVMEAFERRGVRV 65
                                      689*********************7....6699******7..99**************98 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2     2e-05     0.016     108     154 ..      30      76 ..      16      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                                       CHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HH CS
                         Trp_syntA 108 laelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsde 154
                                       ++++  + v g iv  +P+e+ +e++ea ++ g+++v+l  p ++de
  gi|330507413|ref|YP_004383841.1|  30 IERASINAVSGEIVLEVPPEKVQEVMEAFERRGVRVVPLEIPVIRDE 76 
                                       567777889999***************************99988876 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.3   9.9e+02      42      56 ..      40      58 ..      17      60 .. 0.68
   2 ?   10.7   1.3   0.00091      0.71       4      20 ..      75      91 ..      72     100 .. 0.81
   3 ?    9.6   1.5     0.002       1.5       1      20 [.     101     120 ..     101     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.3
                           Fer4_15 42 g....evpddeeeaaqeAa 56
                                      g    evp+++++++ eA 
  gi|330507413|ref|YP_004383841.1| 40 GeivlEVPPEKVQEVMEAF 58
                                      1344599999999999885 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00091
                           Fer4_15  4 DrdaCigcglCvaeape 20
                                      D+++C  cg+Cv  +p+
  gi|330507413|ref|YP_004383841.1| 75 DESECVNCGACVSICPT 91
                                      99*************75 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.002
                           Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                       Vv D  +Ci cg+Cv  +p+
  gi|330507413|ref|YP_004383841.1| 101 VVADSGKCIQCGACVVGCPQ 120
                                       678999**********9996 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0038       2.9     152     189 ..      50      92 ..      21      96 .. 0.85
   2 ?    5.0   0.2     0.017        13     165     189 ..      99     121 ..      94     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0038
                       GMC_oxred_N 152 lnkallkaaeelGlp.......vprdlngkhqcGvcllgvtcrtg 189
                                       +++ +++a e++G++       v rd +++ +cG c+    c+tg
  gi|330507413|ref|YP_004383841.1|  50 KVQEVMEAFERRGVRvvpleipVIRDESECVNCGACVSI--CPTG 92 
                                       56999**********999999999************998..8887 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.017
                       GMC_oxred_N 165 lpvprdlngkhqcGvcllgvtcrtg 189
                                       ++v+ d++++ qcG c++g  c++ 
  gi|330507413|ref|YP_004383841.1|  99 WRVVADSGKCIQCGACVVG--CPQR 121
                                       6799***************..9875 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00029      0.23       7      62 ..      25      84 ..      22      95 .. 0.80
   2 ?    0.2   1.3         1   8.1e+02      53      62 ..     104     113 ..      91     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                              FeoC  7 eyleergrvslkeLsrh..fkaspealeamLeqwvrkG.rvekvaatacc...sgsCkkCgg 62
                                      e+l + +r+s++  s +  +++ pe ++  +e  +r+G rv  ++        ++ C +Cg+
  gi|330507413|ref|YP_004383841.1| 25 EALVNIERASINAVSGEivLEVPPEKVQEVMEAFERRGvRVVPLEIP--VirdESECVNCGA 84
                                      56677789999999965338999***************555555555..4458*******95 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1
                              FeoC  53 csgsCkkCgg 62 
                                       +sg+C +Cg+
  gi|330507413|ref|YP_004383841.1| 104 DSGKCIQCGA 113
                                       4899*99985 PP

>> tify  tify domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3    0.0001      0.08      17      31 ..      43      56 ..      42      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                              tify 17 VfDdvpaeKAkaIml 31
                                      V + vp+eK++++m 
  gi|330507413|ref|YP_004383841.1| 43 VLE-VPPEKVQEVME 56
                                      556.**********5 PP

>> DUF678  Protein of unknown function (DUF678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.4   0.00046      0.35      18      64 ..      69     114 ..      53     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                            DUF678  18 t...vededdctTCSlCqSkLvkvsdvskvslsklkvavgkgntlrCaAC 64 
                                       +   + de +c+ C +C     ++      ++++ +v++  g+ ++C AC
  gi|330507413|ref|YP_004383841.1|  69 EipvIRDESECVNCGACV----SICPTGTFRFEDWRVVADSGKCIQCGAC 114
                                       155599***********5....5889999********************* PP

>> HCV_NS2  Hepatitis C virus non-structural protein NS2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.7    0.0077         6     164     191 ..      63      90 ..      49      93 .. 0.88
   2 ?    7.7   1.2    0.0031       2.5     166     191 ..      94     119 ..      91     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0077
                           HCV_NS2 164 vvfspmekkiirwgadtlaCGdivaGlP 191
                                       v + p e+ +ir+  + + CG +v+  P
  gi|330507413|ref|YP_004383841.1|  63 VRVVPLEIPVIRDESECVNCGACVSICP 90 
                                       6678999*****************9777 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0031
                           HCV_NS2 166 fspmekkiirwgadtlaCGdivaGlP 191
                                       f  ++ +++ ++ + + CG +v G P
  gi|330507413|ref|YP_004383841.1|  94 FRFEDWRVVADSGKCIQCGACVVGCP 119
                                       667899******************99 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.4    0.0018       1.4       1      14 [.      78      91 ..      50      93 .. 0.81
   2 ?    9.6   4.3    0.0021       1.7       1      15 [.      78      92 ..      78      98 .. 0.87
   3 ?    5.4   4.5     0.044        34       1      13 [.     107     119 ..     107     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0018
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C++CgaC  +Cpt
  gi|330507413|ref|YP_004383841.1| 78 ECVNCGACVSICPT 91
                                      46677777777766 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0021
                           Fer4_22  1 rClsCgaCtlvCptC 15
                                      +C++CgaC  +Cpt 
  gi|330507413|ref|YP_004383841.1| 78 ECVNCGACVSICPTG 92
                                      59***********95 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.044
                           Fer4_22   1 rClsCgaCtlvCp 13 
                                       +C++CgaC + Cp
  gi|330507413|ref|YP_004383841.1| 107 KCIQCGACVVGCP 119
                                       6999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:01.19
# Mc/sec: 324.14
//
Query:       gi|330507414|ref|YP_004383842.1|  [L=475]
Description: hypothetical protein MCON_1340 [Methanosaeta concilii GP6]
Scores for complete 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-131  438.3   0.0   2.1e-131  437.9   0.0    1.1  1  HcyBio    Homocysteine biosynthesis enzyme, sulfur-incorporat
    4.6e-26   91.0   4.5    4.3e-14   52.7   0.3    2.5  2  CBS       CBS domain
  ------ inclusion threshold ------
       0.21   10.9   0.3       0.41   10.0   0.3    1.4  1  tify      tify 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 !  437.9   0.0  3.4e-135  2.1e-131      10     347 .]       2     330 ..       1     330 [. 0.98

  Alignments for each domain:
  == domain 1  score: 437.9 bits;  conditional E-value: 3.4e-135
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio  10 kklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaepkikiekvwLngvpayaglaavdlylgataeseddke 86 
                                        +lv+e g++ a++evDVVttgTfg+m+ssg++lnlg+++p+iki +++Ln v+ay g+aavdl+lgat++sed  +
  gi|330507414|ref|YP_004383842.1|   2 PDLVDELGTAGAVREVDVVTTGTFGAMCSSGVFLNLGHSDPPIKIARAYLNRVEAYGGIAAVDLFLGATQPSED--R 76 
                                       689**********************************************************************4..3 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio  87 eeeyGGghviedLvagkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnYnaavNsseetiytymge 163
                                       + eyGG+hv+edLv gk++e+ea+++ +dcyp+ ++et+++l+d+n+a++vnpRnayq+Ynaa+Nss++t++tymg+
  gi|330507414|ref|YP_004383842.1|  77 GIEYGGAHVMEDLVIGKQIEVEAHGSPSDCYPQMDLETSLRLEDFNQATVVNPRNAYQRYNAATNSSDRTMHTYMGT 153
                                       45*************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 164 lkpnlgnatysgaGelsPllnDpelktigiGtrilLgGaeGyvigeGTqsspekkrengvplgpagtLavigdlkeM 240
                                       l p lgn++ysgaG lsPl nDp +++ig+Gtri+L+Ga+Gyvig GTq++pe+          ++tL+v+gdlk M
  gi|330507414|ref|YP_004383842.1| 154 LLPGLGNVHYSGAGVLSPLSNDPGFEYIGVGTRIFLAGAQGYVIGAGTQHNPENG---------FSTLMVTGDLKRM 221
                                       ***************************************************8877.........9************ PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                            HcyBio 241 speylrgafltsyGpelivgvgipiPvldeevleelavkdedielpvvDvserrrerktlgevsYael..Gkieieg 315
                                       ++++lr+a++++yGp+l++g+gipiP+l+e++++++av+d+di++pv D++++rr+++++ +vsY+el  G+i++ g
  gi|330507414|ref|YP_004383842.1| 222 NNSFLRAATFHKYGPSLYLGIGIPIPMLNERLAKSTAVRDSDITVPVQDYGIQRRDKPSVRMVSYEELksGTIDLGG 298
                                       ***************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 316 kevktarlsslkrareiaeeLkewiekgeflL 347
                                       kev +++lss+++are+a++Lke++e+geflL
  gi|330507414|ref|YP_004383842.1| 299 KEVSCSPLSSFQMAREVARTLKEQVERGEFLL 330
                                       ******************************97 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.3   7.2e-18   4.3e-14       1      55 [.     355     409 ..     355     411 .. 0.94
   2 !   39.7   0.4     8e-14   4.8e-10       2      56 ..     418     472 ..     417     473 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 7.2e-18
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       Vgd+m+rdvvtv +d ++e+a++l+++  +++lPVV  dg+l+Gi+t  D+ +a+
  gi|330507414|ref|YP_004383842.1| 355 VGDVMSRDVVTVFEDIPVEKAAKLIISGSFDHLPVVSRDGRLIGIITAWDISKAV 409
                                       89**********************87777*******99*************8887 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 8e-14
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllrall 56 
                                       ++imtr+v++v+ d+++e a++++ +++ +s+lPVVd ++k++G++t  +l r+l+
  gi|330507414|ref|YP_004383842.1| 418 AEIMTRRVHSVRLDEPIELAARTL-DTHsISALPVVDREHKVIGMITSNHLSRLLA 472
                                       79**********************.6666********************9988875 PP

>> tify  tify domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   6.9e-05      0.41      15      30 ..     364     379 ..     363     380 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.9e-05
                              tify  15 VvVfDdvpaeKAkaIm 30 
                                       V Vf+d+p eKA+ ++
  gi|330507414|ref|YP_004383842.1| 364 VTVFEDIPVEKAAKLI 379
                                       89**********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3290.19
//
Query:       gi|330507415|ref|YP_004383843.1|  [L=500]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-09   37.6   0.1    9.6e-09   35.8   0.0    2.0  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.095   12.7   0.0       0.26   11.3   0.0    1.7  1  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.3   1.2e+04     110     129 ..     175     193 ..     158     197 .. 0.52
   2 !   35.8   0.0   1.1e-12   9.6e-09       1     166 [.     217     400 ..     217     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                                       BSSSHHHHHHHHTCTSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 110 eaaddekvlklmnrghtfee 129
                                       e+  +e +++++ rg+++ e
  gi|330507415|ref|YP_004383843.1| 175 ESDFPEICRQII-RGENVPE 193
                                       344444445555.5555555 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 1.1e-12
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.........TTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.........pdfvelle 68 
                                       v+++rgC ++C fC+ +      + +r++++e+il+ v+ +  e g + +il++ +++ y         ++++el+ 
  gi|330507415|ref|YP_004383843.1| 217 VEIGRGCWRGCAFCSPT-----MRSVRHRPIENILKDVRVN-LECGQEDIILHSEDVFSYgskgtrpneKKMTELVT 287
                                       5799*************.....7******************.8999*******************988877777777 PP

                                       HHHHTC......CCTEEEEEEECSSCHGHHHHHHHHHTT..-SEEE..EEEBSSSHHHHHHHHTCTSHH........ CS
                                       xxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx..xxxxxxxxxxxxxxxxxxxxx........ RF
                       Radical_SAM  69 rlakla......vpgiritvetngtlpdeeklerllelg..vdrvs..lgleaaddekvlklmnrghtf........ 127
                                       + +kl       +     +v +n +l   + + +++  g   +++s  +g+e+++ + +lk++++++ +        
  gi|330507415|ref|YP_004383843.1| 288 EVKKLGpktmdfSHLSLASVHSNQGL--LREISKIVGIGsdQNHMSawIGIETGSCR-ILKMHMPQKALpgetenwp 361
                                       77777666666333333344444444..79999999999886665555899999999.9999986555579998888 PP

                                       HHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 128 eevlealeklreagikrvvdrivglpGendeeleellel 166
                                       + v ++ +++ e  + +v + ++glpGe+ e++  + el
  gi|330507415|ref|YP_004383843.1| 362 QIVEDCYRLFDEESWLPVASLVLGLPGETAEDVIRTTEL 400
                                       88888888888888888***************9999876 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.9e-05      0.26      75     120 ..     142     181 ..     129     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.9e-05
                       B12-binding  75 lkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                       +++ rp  +vv+GG +    ++e++ +k  +d++ +gege+ ++++
  gi|330507415|ref|YP_004383843.1| 142 IREHRP--RVVLGGNG----AWEVMGEKVDVDHIYLGEGESDFPEI 181
                                       566655..89****87....77778888999***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3538.53
//
Query:       gi|330507416|ref|YP_004383844.1|  [L=100]
Description: hypothetical protein MCON_1342 [Methanosaeta concilii GP6]
Scores for complete 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-29  100.0   0.2    7.7e-29   99.8   0.2    1.1  1  DUF2551        Protein of unknown function (DUF2551)
  ------ inclusion threshold ------
      0.052   13.7   0.0      0.069   13.3   0.0    1.1  1  FUR            Ferric uptake regulator family
        0.2   11.5   0.0       0.21   11.4   0.0    1.1  1  SEF14_adhesin  SEF14-like adhesin


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 !   99.8   0.2   1.3e-32   7.7e-29       1      83 []      12      93 ..      12      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 1.3e-32
                           DUF2551  1 LkkylerDksGiRrevLklfleakkltveeiyeklkek.fdvsykgvasmvGliasrlGIlkvkkeskgeknvYsLkee 78
                                      L++yl+rD  GiR++vLklfl+ + +t+e++++ l+++ fdvsy+gv++mvGl+++rlGIl++  +++g++nvYsLk +
  gi|330507416|ref|YP_004383844.1| 12 LRNYLKRDGVGIRKAVLKLFLSDGAYTTEDVFTYLAKEgFDVSYRGVSAMVGLMNTRLGILSI--DVSGDHNVYSLKGD 88
                                      89*************************************************************..*************9 PP

                           DUF2551 79 yadlv 83
                                      ++ +v
  gi|330507416|ref|YP_004383844.1| 89 HKGVV 93
                                      98876 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.2e-05     0.069      10      78 ..      24      89 ..      21      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSSSE CS
                               FUR 10 RekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelakkehh 78
                                      R+++l+++ +  ++ + e+v+  l +e+ ++s   V  ++ l++ +  + ++++++++++y l+   +h
  gi|330507416|ref|YP_004383844.1| 24 RKAVLKLFLSDGAY-TTEDVFTYLAKEGFDVSYRGVSAMVGLMNTRLGILSIDVSGDHNVYSLKG--DH 89
                                      99999999988887.679***************************99999************994..33 PP

>> SEF14_adhesin  SEF14-like adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.5e-05      0.21      58      86 ..      65      93 ..      29      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.5e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     SEF14_adhesin 58 agqklGtlsirltGshasvsvaGddasvs 86
                                         +lG lsi ++G h+  s+ Gd  +v 
  gi|330507416|ref|YP_004383844.1| 65 MNTRLGILSIDVSGDHNVYSLKGDHKGVV 93
                                      3468********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 737.13
//
Query:       gi|330507417|ref|YP_004383845.1|  [L=348]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      8e-09   36.1   0.4    1.9e-08   34.9   0.1    1.8  2  Radical_SAM  Radical SAM superfamily
    5.3e-08   33.0   0.0      9e-08   32.3   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain
    3.8e-05   24.0   0.0    6.6e-05   23.2   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 !   34.9   0.1   3.2e-12   1.9e-08       3     107 ..      33     138 ..      31     162 .. 0.84
   2 ?   -3.2   0.0       1.6   9.4e+03      13      37 ..     237     269 ..     236     276 .. 0.63

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 3.2e-12
                                       EESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.CC CS
                                       xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet..vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.vp 76 
                                       vt  C ++C +C+++e+  +++  ++ + +v e+++++ e++   g+ +  ++ggepll+ d+v +  r+ k++  +
  gi|330507417|ref|YP_004383845.1|  33 VTGRCERGCFYCPISEDrrGKDVAYADEQPVGELADILSEGR-AIGALGTGITGGEPLLRLDYVLDCIRALKEEfGS 108
                                       6889************96655555666666666666666664.6668899999*********************888 PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvsl 107
                                       + +i++ t g+lp++ +l+rl+++g+d + +
  gi|330507417|ref|YP_004383845.1| 109 EHHIHLYT-GILPNRSVLKRLVRAGLDEIRF 138
                                       88888877.78888***********998765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                                       TTSCCTT........HHHHHHHHHHHHHHHHHH CS
                                       xxxxxxx........xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  13 fCarpet........vrregrgrslsveeilee 37 
                                       +C+ +++         rr+    s+++++i ee
  gi|330507417|ref|YP_004383845.1| 237 YCPSRFKdavqlrerLRRRAERTSRPLDYITEE 269
                                       777777666666666566666666666666655 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   1.5e-11     9e-08       1      92 [.      31     121 ..      31     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.5e-11
                           Fer4_14   1 lfvrlsgCnlsCkgCd...nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrl 74 
                                       lfv +++C+  C  C    ++  ++  +  +q   +l +il   + + i + g  +tGGePL   + + +l+ ++ l
  gi|330507417|ref|YP_004383845.1|  31 LFV-TGRCERGCFYCPiseDRRGKDVAYADEQPVGELADIL--SEGRAIGALGTGITGGEPL--LRLDYVLDCIRAL 102
                                       688.9**********97776667788999999999999999..888999999**********..89*********** PP

                           Fer4_14  75 keey.pekkiwletngtle 92 
                                       kee+  e++i+l+t+ + +
  gi|330507417|ref|YP_004383845.1| 103 KEEFgSEHHIHLYTGILPN 121
                                       ****999*******98765 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 !   23.2   0.0   1.1e-08   6.6e-05       4      94 ..      25     118 ..      22     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.1e-08
                           Fer4_12   4 eGvrlslf.vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi...egltllGGEPllpenaeallelv 76 
                                       +G  l+lf +++C++ C +C   e ++ k     +++   e+ + l++ +     g  ++GGEPll    + +l+ +
  gi|330507417|ref|YP_004383845.1|  25 QGAGLVLFvTGRCERGCFYCPISEDRRGKDVAYADEQPVGELADILSEGRAigaLGTGITGGEPLL--RLDYVLDCI 99 
                                       4566788834569999999876666655555555677777777777664443447889********..********* PP

                           Fer4_12  77 kevkeekp.ekdiwlytgy 94 
                                       + +kee+  e  i lytg 
  gi|330507417|ref|YP_004383845.1| 100 RALKEEFGsEHHIHLYTGI 118
                                       *******9999999***96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 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:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2565.72
//
Query:       gi|330507418|ref|YP_004383846.1|  [L=594]
Description: indolepyruvate ferredoxin oxidoreductase subunit alpha [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-22   80.2   0.6    2.2e-22   79.5   0.6    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    9.8e-12   45.1   0.1    1.1e-10   41.7   0.1    2.1  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    3.1e-07   29.9  10.4    1.2e-05   25.0   2.5    2.9  2  Fer4          4Fe-4S binding domain
    0.00016   21.8  11.7    0.00047   20.3  11.7    1.9  1  Fer4_9        4Fe-4S dicluster domain
    0.00051   20.1  12.5       0.18   12.0  13.2    2.6  2  Fer4_21       4Fe-4S dicluster domain
    0.00096   19.1  16.6      0.012   15.6   2.2    3.2  3  Fer4_2        4Fe-4S binding domain
     0.0018   18.3   3.0     0.0018   18.3   3.0    3.4  3  Fer4_6        4Fe-4S binding domain
     0.0038   18.1  10.2      0.012   16.5   2.4    2.7  2  Fer4_16       4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.011   15.9  13.0      0.097   12.8  13.4    2.4  2  Fer4_10       4Fe-4S dicluster domain
       0.03   14.9  13.7      0.091   13.4   3.3    3.0  3  Fer4_7        4Fe-4S dicluster domain
       0.05   13.2   0.1       0.11   12.0   0.0    1.7  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
      0.058   13.9  13.3       0.67   10.6   2.9    2.9  2  Fer4_4        4Fe-4S binding domain
        1.5    9.4  13.7       0.65   10.6   2.8    2.7  3  Fer4_17       4Fe-4S dicluster domain
        3.1    8.6   8.9          5    7.9   1.3    2.7  2  Fer4_15       4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.6   1.7e-25   2.2e-22       1     152 [.     382     522 ..     382     523 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 1.7e-25
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       diGc+t+        +    +++  ++ +mG +++ A+G+ +  + + + a  GD++fl+  ++ l +a+++++ it
  gi|330507418|ref|YP_004383846.1| 382 DIGCYTM--------AVGMGTVD--TCLCMGASISLASGIRFGGETEGICASLGDSTFLHGgMTGLLNAAYNKARIT 448
                                       899***9........22445566..9****************766779***************************** PP

                                       EEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpalie 152
                                       v +l+N++++mtg+q++p +g + +g+    + +v++++la+alGa  + +v+++d+e + e +++a +  g +++ 
  gi|330507418|ref|YP_004383846.1| 449 VTILDNSTTAMTGHQPHPGTGVTATGEP---TAQVSLEELARALGAGlVETVDPYDLEGTMEGFQRAKDFPGLSVVI 522
                                       *********************9999987...9***************999*******************99999985 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 !   41.7   0.1   8.4e-14   1.1e-10       2     188 ..      14     194 ..      13     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 8.4e-14
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       + ++ag+  +a+YP TPssei+e l el  +  +   ++    +E  a ++++GA+++G r++ +    Gl  + + 
  gi|330507418|ref|YP_004383846.1|  14 GLLEAGIGLAAGYPGTPSSEIIEGLVELKGDLPL---HIEWSVNEKVALEVAAGASWTGCRSVATMKHVGLNVAADP 87 
                                       677899999******************9966665...899999******************************9998 PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEH CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfDg 155
                                       ++  a   + + + v+    p    s +++q    +a    +  l +++ qea d+a+ ++ l+ek+++Pv++    
  gi|330507418|ref|YP_004383846.1|  88 FMTLAYLGVGAGLLVICADDPFC-HSSQNEQDSRRFAQFASIPCLDPADPQEARDMAIYGLELSEKFNIPVMLR-PT 162
                                       88888777777666665444444.7888999889999999999****************************975.67 PP

                                       HHH.HEEEEEEC-SGG.GS-----SBXXXXXXX CS
                             POR_N 156 fllshevekvelpdeedelklikekleeyerke 188
                                       +++sh++ +ve+ ++   + +++++ ++  r  
  gi|330507418|ref|YP_004383846.1| 163 TRVSHARADVEVSQDR-PIPVERRFVKNPARRV 194
                                       8899********9887.8888888877666654 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   1.1    0.0011       1.4       5      16 ..     544     555 ..     540     556 .. 0.87
   2 !   25.0   2.5     9e-09   1.2e-05       5      23 ..     571     589 ..     567     590 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                                       TTTSSS-THHHH CS
                              Fer4   5 eekCigCGaCve 16 
                                        + C gC +Cve
  gi|330507418|ref|YP_004383846.1| 544 SDECQGCRICVE 555
                                       699********8 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 9e-09
                                       TTTSSS-THHHHHSTTTEE CS
                              Fer4   5 eekCigCGaCvevCPvgAI 23 
                                        ++C+gCG+C+++CP  AI
  gi|330507418|ref|YP_004383846.1| 571 NNLCTGCGICAQICPSSAI 589
                                       689*************999 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3  11.7   3.7e-07   0.00047       1      51 []     546     589 ..     546     589 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.7e-07
                            Fer4_9   1 kCtgCgaCvea.CpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +C gC+ Cve  Cpa  ++++ a+  +         C+gCg C+++Cp+ ai
  gi|330507418|ref|YP_004383846.1| 546 ECQGCRICVEYgCPAIEFEGEMAKINNL--------CTGCGICAQICPSSAI 589
                                       5*******6544****999988877765........************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 !    9.5   2.1   0.00084       1.1      36      53 ..     542     560 ..     525     563 .. 0.77
   2 !   12.0  13.2   0.00014      0.18      11      55 ..     547     587 ..     545     592 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00084
                           Fer4_21  36 vvedeCvGCnlCssv.CPv 53 
                                        v+deC GC +C++  CP 
  gi|330507418|ref|YP_004383846.1| 542 KVSDECQGCRICVEYgCPA 560
                                       579*********9855995 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00014
                           Fer4_21  11 CgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPved 55 
                                       C+ C i C + +  aie++++  ++ +++ C+GC +C+++CP   
  gi|330507418|ref|YP_004383846.1| 547 CQGCRI-CVEYGCPAIEFEGE--MAKINNLCTGCGICAQICPS-S 587
                                       555543.55566679*99865..45899**************5.4 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       4.8   6.2e+03       7      14 ..     354     361 ..     352     362 .. 0.78
   2 !   11.5   2.6    0.0002      0.26       3      22 .]     540     560 ..     538     560 .. 0.84
   3 !   15.6   2.2   9.7e-06     0.012       8      21 ..     572     585 ..     566     586 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.8
                            Fer4_2   7 tdrCigCg 14 
                                       ++ C gC+
  gi|330507418|ref|YP_004383846.1| 354 PALCPGCS 361
                                       56799995 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0002
                            Fer4_2   3 vvvdtdrCigCgaCvsa.CPa 22 
                                       ++ ++d C gC++Cv   CPa
  gi|330507418|ref|YP_004383846.1| 540 AFKVSDECQGCRICVEYgCPA 560
                                       5667889********888**8 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 9.7e-06
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                       + C+gCg+C + CP
  gi|330507418|ref|YP_004383846.1| 572 NLCTGCGICAQICP 585
                                       56************ PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2       1.4   1.8e+03       6      12 ..     354     360 ..     354     362 .. 0.82
   2 !    7.5   1.7    0.0036       4.6       9      21 ..     547     560 ..     541     565 .. 0.89
   3 !   18.3   3.0   1.4e-06    0.0018       6      24 .]     571     589 ..     567     589 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                            Fer4_6   6 pdkCigC 12 
                                       p +C gC
  gi|330507418|ref|YP_004383846.1| 354 PALCPGC 360
                                       679**** PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0036
                            Fer4_6   9 CigCgdCvrv.CPe 21 
                                       C gC+ Cv   CP+
  gi|330507418|ref|YP_004383846.1| 547 CQGCRICVEYgCPA 560
                                       *******9999*97 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.4e-06
                            Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                        ++C+gCg C+ +CP  ai
  gi|330507418|ref|YP_004383846.1| 571 NNLCTGCGICAQICPSSAI 589
                                       69*************9998 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.1     0.028        36      47      65 ..     540     559 ..     522     565 .. 0.73
   2 !   16.5   2.4   9.3e-06     0.012       2      20 ..     574     592 ..     573     594 .] 0.91

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.028
                           Fer4_16  47 kckkqeaitgCdiCqdv.CP 65 
                                       + k   ++ gC+iC++  CP
  gi|330507418|ref|YP_004383846.1| 540 AFKVSDECQGCRICVEYgCP 559
                                       44445789999999875466 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 9.3e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++Cg Ca++CP++ai e 
  gi|330507418|ref|YP_004383846.1| 574 CTGCGICAQICPSSAILEV 592
                                       ****************875 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  13.4   7.5e-05     0.097       6      56 .]     544     585 ..     539     585 .. 0.79
   2 ?   11.6   3.3   0.00018      0.23       6      21 ..     571     586 ..     566     592 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.5e-05
                           Fer4_10   6 ddtCirCgkCvka.CPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +d C +C+ Cv+  CPa       ++++ e ++       Ctgcg C+++CP
  gi|330507418|ref|YP_004383846.1| 544 SDECQGCRICVEYgCPA-------IEFEGEMAK---INNLCTGCGICAQICP 585
                                       789*********88***.......444444444...4558***********9 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00018
                           Fer4_10   6 ddtCirCgkCvkaCPa 21 
                                        + C++Cg C + CP+
  gi|330507418|ref|YP_004383846.1| 571 NNLCTGCGICAQICPS 586
                                       578************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 ?   -3.0   0.0       9.4   1.2e+04      11      19 ..     220     228 ..     219     233 .. 0.71
   2 ?    4.6   3.1     0.038        48      30      49 ..     539     559 ..     521     561 .. 0.71
   3 ?   13.4   3.3   7.1e-05     0.091       2      17 ..     574     589 ..     573     592 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.4
                            Fer4_7  11 aCpvkaiel 19 
                                        Cp++ ++l
  gi|330507418|ref|YP_004383846.1| 220 GCPWNRLTL 228
                                       588888776 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.038
                            Fer4_7  30 kveidpekClgCgaCva.vCP 49 
                                       ++  ++++C+gC+ Cv+  CP
  gi|330507418|ref|YP_004383846.1| 539 RAFKVSDECQGCRICVEyGCP 559
                                       455567888888888764566 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 7.1e-05
                            Fer4_7   2 CigCgaCvaaCpvkai 17 
                                       C+gCg C++ Cp++ai
  gi|330507418|ref|YP_004383846.1| 574 CTGCGICAQICPSSAI 589
                                       9999999999999887 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 ?   12.0   0.0   8.9e-05      0.11       4     106 ..       8     113 ..       5     168 .. 0.78
   2 ?   -3.1   0.0         4   5.1e+03      80     106 ..     434     460 ..     432     475 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.9e-05
                                       HHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHH CS
                      TPP_enzyme_N   4 aealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGat 77 
                                        +a+++ L ++g+  + g+pG+ + ++++ l e +    +++  +++E +a   A g +    + ++ + ++g +++
  gi|330507418|ref|YP_004383846.1|   8 NAAIAKGLLEAGIGLAAGYPGTPSSEIIEGLVELKgdlPLHIEWSVNEKVALEVAAGASWTGCRSVATMKHVGLNVA 84 
                                       6799*******************************9887888889************98887777777777787654 PP

                                       .HCHHHHHHHHHH.T--EEEEEEE--CCCHH CS
                      TPP_enzyme_N  78 .naltalaeAkvd.riPllvlsgdrptslrg 106
                                          ++ l  A++  +  llv+++d p  + +
  gi|330507418|ref|YP_004383846.1|  85 aDPFMTL--AYLGvGAGLLVICADDPFCHSS 113
                                       0344444..3333377777777777766666 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4
                                       HHHHHHHHHHT--EEEEEEE--CCCHH CS
                      TPP_enzyme_N  80 ltalaeAkvdriPllvlsgdrptslrg 106
                                       +t+l +A++++  + v   d++t+   
  gi|330507418|ref|YP_004383846.1| 434 MTGLLNAAYNKARITVTILDNSTTAMT 460
                                       788888888888888777777766555 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.8    0.0045       5.8       1      15 [.     544     559 ..     544     564 .. 0.91
   2 ?   10.6   2.9   0.00052      0.67       2      16 ..     572     586 ..     571     587 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0045
                            Fer4_4   1 qerCigCgsCvaa.CP 15 
                                       ++ C+gC+ Cv + CP
  gi|330507418|ref|YP_004383846.1| 544 SDECQGCRICVEYgCP 559
                                       589********99999 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00052
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + C+gCg C  +CP+
  gi|330507418|ref|YP_004383846.1| 572 NLCTGCGICAQICPS 586
                                       56************6 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   3.2      0.12   1.5e+02      42      57 ..     543     559 ..     526     561 .. 0.73
   2 ?    1.9   3.5      0.26   3.3e+02       1      15 [.     546     561 ..     546     569 .. 0.74
   3 ?   10.6   2.8   0.00051      0.65      43      58 ..     571     586 ..     562     589 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.12
                           Fer4_17  42 kaslCieCgeCe.rkCP 57 
                                       + ++C +C+ C+ + CP
  gi|330507418|ref|YP_004383846.1| 543 VSDECQGCRICVeYGCP 559
                                       56778888888766677 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.26
                           Fer4_17   1 rCiqCgyClp.eCpsy 15 
                                       +C++C+ C++  Cp  
  gi|330507418|ref|YP_004383846.1| 546 ECQGCRICVEyGCPAI 561
                                       5889999988667765 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00051
                           Fer4_17  43 aslCieCgeCerkCPq 58 
                                        +lC++Cg C++ CP+
  gi|330507418|ref|YP_004383846.1| 571 NNLCTGCGICAQICPS 586
                                       4778888888888886 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.2     0.063        81       6      17 ..     545     556 ..     544     569 .. 0.79
   2 ?    7.9   1.3    0.0039         5       6      20 ..     572     586 ..     571     591 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.063
                           Fer4_15   6 daCigcglCvae 17 
                                       d+C+gc  Cv+ 
  gi|330507418|ref|YP_004383846.1| 545 DECQGCRICVEY 556
                                       89********97 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0039
                           Fer4_15   6 daCigcglCvaeape 20 
                                       ++C+gcg C++ +p 
  gi|330507418|ref|YP_004383846.1| 572 NLCTGCGICAQICPS 586
                                       68***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4149.54
//
Query:       gi|330507419|ref|YP_004383847.1|  [L=195]
Description: indolepyruvate ferredoxin oxidoreductase subunit beta [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-35  120.5   0.0    9.4e-35  120.3   0.0    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   0.0   5.2e-39   9.4e-35       1     175 [.      14     190 ..      14     192 .. 0.96

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 5.2e-39
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqGv++++ ++++a + aG+ v +++++g+++rGg+++ h ri+ +  +p ++ g adll+al+++++ ++ + l 
  gi|330507419|ref|YP_004383847.1|  14 GGQGVILISDVIGRAGVLAGKPVRGAETHGMAQRGGSVINHTRIGCR-FSPLVAPGSADLLIALEPAEALRFGHFLS 89 
                                       9*********************************************9.7788888***********9999******* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH......T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl......gvrvygvdatkiakeiggneraaNtvmlGalaallglple 148
                                       p+g++++ +  + p +++  + +++ l++          rv+++dat++a+++g  + a+N+vmlGal++ + l++e
  gi|330507419|ref|YP_004383847.1|  90 PDGVALISNQPVLPVTVTTGRARYPSLDDLIeplcgqCQRVLALDATALARKAGT-AQAMNVVMLGALSQYIPLSEE 165
                                       *************************999877*****8899**********99777.********************* PP

                                       HHHHHHHCCS-CH.HHHHHHHHHHHHH CS
                               POR 149 aleeaikkrfpkkkeviekNlkafrag 175
                                       ++++a+ + +p k   +e+N++af +g
  gi|330507419|ref|YP_004383847.1| 166 HIIQALVEVVPPK--HLEANKRAFALG 190
                                       ***********95..8********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1121.97
//
Query:       gi|330507420|ref|YP_004383848.1|  [L=209]
Description: PBS lyase HEAT-like repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   65.9   4.9    1.8e-09   37.8   1.0    2.3  2  HEAT_2     HEAT repeats
    2.3e-07   30.5   0.2       0.22   11.9   0.0    3.9  4  HEAT       HEAT repeat
    4.6e-07   29.9   2.3     0.0047   17.5   0.5    3.9  4  HEAT_PBS   PBS lyase HEAT-like repeat
    2.2e-05   24.5   0.4       0.16   12.0   0.2    2.9  3  Cnd1       non-SMC mitotic condensation complex subunit 1
    4.3e-05   23.9   1.8        0.1   13.1   0.0    3.8  4  HEAT_EZ    HEAT-like repeat
  ------ inclusion threshold ------
      0.013   14.0   1.5       0.11   11.0   0.9    2.0  2  Adaptin_N  Adaptin N terminal region


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.3     5e-11   1.5e-07       1      67 [.      55     123 ..      55     124 .. 0.89
   2 !   37.8   1.0   6.1e-13   1.8e-09       3      78 ..     118     196 ..     116     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 5e-11
                            HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaig...dpealpaL 67 
                                       +++L++a  +d++  vr +ai+ L + +  e+l+aL+e+l+de+  v  +a  a++ +g   +++ ++aL
  gi|330507420|ref|YP_004383848.1|  55 IEKLIAAT-KDKHMLVRSNAIMLLSKRDISESLEALIEALKDEEYLVKSNAMVAIAGYGkqvSDRMIEAL 123
                                       57899999.9*********************************************999844446666666 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 6.1e-13
                            HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigd....pealpaLkelldddd 75 
                                        +++al +d+d++vr+ a++++g++++ +a++aL ++++d+ p  R +a  +L a+g+    pea p  ++   d +
  gi|330507420|ref|YP_004383848.1| 118 RMIEAL-EDADKDVRAGAAWVIGELKENRAVAALEKVAKDDYPLARIQAKASLIAMGRgpkkPEAQPPVAQTSEDST 193
                                       68999*.9************************************************944455999999999877776 PP

                            HEAT_2  76 ddv 78 
                                       ++ 
  gi|330507420|ref|YP_004383848.1| 194 EEG 196
                                       665 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0019       5.7       5      25 ..      58      78 ..      55      79 .. 0.84
   2 !    6.3   0.0    0.0047        14       2      24 ..      86     108 ..      86     114 .. 0.86
   3 !   11.9   0.0   7.3e-05      0.22       5      27 ..     119     141 ..     117     144 .. 0.89
   4 ?   -1.9   0.0         2     6e+03       5      25 ..     150     170 ..     147     174 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0019
                                      HHHHHT-SSHHHHHHHHHHHH CS
                              HEAT  5 llkllsDpspeVReaAakaLg 25
                                      l+ + +D+++ VR++A+  L 
  gi|330507420|ref|YP_004383848.1| 58 LIAATKDKHMLVRSNAIMLLS 78
                                      677789**********99885 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0047
                                       HHHHHHHHT-SSHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsDpspeVReaAakaL 24 
                                       l +l+++l+D++  V ++A  a+
  gi|330507420|ref|YP_004383848.1|  86 LEALIEALKDEEYLVKSNAMVAI 108
                                       5789*************997766 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 7.3e-05
                                       HHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgal 27 
                                       ++++l+D + +VR+ Aa+ +g+l
  gi|330507420|ref|YP_004383848.1| 119 MIEALEDADKDVRAGAAWVIGEL 141
                                       6899*****************98 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 2
                                       HHHHHT-SSHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLg 25 
                                       l k  +D+ p  R  A  +L 
  gi|330507420|ref|YP_004383848.1| 150 LEKVAKDDYPLARIQAKASLI 170
                                       556668888888877766665 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 ?   -1.2   0.0       1.6   4.8e+03      17      27 .]      54      64 ..      47      64 .. 0.78
   2 !    8.4   0.0    0.0013       3.9       1      27 []      69      95 ..      69      95 .. 0.82
   3 ?   -0.3   0.0      0.82   2.4e+03       4      27 .]     103     125 ..     100     125 .. 0.68
   4 !   17.5   0.5   1.6e-06    0.0047       1      27 []     130     156 ..     130     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                                      GHHHHHHHCTC CS
                          HEAT_PBS 17 aipaLleaLqd 27
                                      +i+ L++a +d
  gi|330507420|ref|YP_004383848.1| 54 SIEKLIAATKD 64
                                      79999999776 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0013
                                      HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLqd 27
                                      vR +A+  L +    e+++aL+eaL+d
  gi|330507420|ref|YP_004383848.1| 69 VRSNAIMLLSKRDISESLEALIEALKD 95
                                      677777777777779**********98 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.82
                                       HHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   4 aAakaLgqlgdeeaipaLleaLqd 27 
                                       +A+ a++  g  ++ ++ +eaL+d
  gi|330507420|ref|YP_004383848.1| 103 NAMVAIAGYGK-QVSDRMIEALED 125
                                       56666666666.777888899887 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR+ Aa+ +g+l+  +a++aL ++ +d
  gi|330507420|ref|YP_004383848.1| 130 VRAGAAWVIGELKENRAVAALEKVAKD 156
                                       8**********************9987 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.2   5.5e-05      0.16      23      82 ..      55     108 ..      51     111 .. 0.77
   2 !   11.8   0.0   6.1e-05      0.18      23      90 ..      86     146 ..      80     156 .. 0.78
   3 !    8.3   0.0   0.00074       2.2      23      89 ..     116     145 ..     111     169 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.5e-05
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaal 82 
                                       +e+L ++ kD+++ VR +a+++++k         ++ l+ l ++l+De+  V +na  a+
  gi|330507420|ref|YP_004383848.1|  55 IEKLIAATKDKHMLVRSNAIMLLSKR------DISESLEALIEALKDEEYLVKSNAMVAI 108
                                       57788888999999999999998873......3344677888888888888888887765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.1e-05
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisekse 90 
                                       +e L ++LkDe+  V+ +a++++a          k++ +++ ++leD ++ V+a a  ++ e++e+  
  gi|330507420|ref|YP_004383848.1|  86 LEALIEALKDEEYLVKSNAMVAIAG-------YGKQVSDRMIEALEDADKDVRAGAAWVIGELKENRA 146
                                       6778888999999999999998875.......455677899999999999999999999999988854 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00074
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteiseks 89 
                                       ++++ ++L+D d  VR  aa v+ +L                                     +e+ 
  gi|330507420|ref|YP_004383848.1| 116 SDRMIEALEDADKDVRAGAAWVIGEL-------------------------------------KENR 145
                                       44555556666666666666655555.....................................4443 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0088        26      30      54 ..      55      79 ..      44      79 .. 0.90
   2 ?    2.3   0.0     0.086   2.6e+02      27      52 ..      83     108 ..      81     111 .. 0.85
   3 !   13.1   0.0   3.5e-05       0.1      31      55 .]     117     141 ..     108     141 .. 0.77
   4 ?   -1.8   0.1       1.7     5e+03      29      40 ..     146     157 ..     144     174 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0088
                           HEAT_EZ 30 lpaLlalLnddsdeVRaaAagaLgn 54
                                      +  L+a+ +d++ +VR +A+  L++
  gi|330507420|ref|YP_004383848.1| 55 IEKLIAATKDKHMLVRSNAIMLLSK 79
                                      789*****************99985 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.086
                           HEAT_EZ  27 peilpaLlalLnddsdeVRaaAagaL 52 
                                       +e l aL+ +L+d++ +V+ +A  a+
  gi|330507420|ref|YP_004383848.1|  83 SESLEALIEALKDEEYLVKSNAMVAI 108
                                       566899*****999989999998886 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 3.5e-05
                           HEAT_EZ  31 paLlalLnddsdeVRaaAagaLgnl 55 
                                       + ++ +L+d +++VRa Aa+ +g l
  gi|330507420|ref|YP_004383848.1| 117 DRMIEALEDADKDVRAGAAWVIGEL 141
                                       456667777777**********986 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 1.7
                           HEAT_EZ  29 ilpaLlalLndd 40 
                                       +++aL +  +dd
  gi|330507420|ref|YP_004383848.1| 146 AVAALEKVAKDD 157
                                       344455444444 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.9   3.6e-05      0.11     108     179 ..      44     111 ..      41     125 .. 0.75
   2 ?    1.8   0.0     0.023        68     156     445 ..     118     144 ..     113     158 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.6e-05
                                       -CCCHHHHHHHHHHHHT-SSH...HHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHHHHHHHHHHH CS
                         Adaptin_N 108 vpelaedlapaikkllkdrsp...yvrkkAalailklykkdpdllrkqlveeikellsdkdpgvvlaAvalleei 179
                                       +p +++d+   i+kl+  ++     vr++A++ +      ++  +++  +e ++e+l+d++++v+++A  ++   
  gi|330507420|ref|YP_004383848.1|  44 MPAVLPDMSWSIEKLIAATKDkhmLVRSNAIMLL------SKRDISES-LEALIEALKDEEYLVKSNAMVAIAGY 111
                                       5778899999999999755544559999998654......44444566.99*****************9999755 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.023
                                       HHHHCTT-SSHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCHHHHHHCS-HHHHHHHHHHHCC---SSHHHH..HHH CS
                         Adaptin_N 156 eikellsdkdpgvvlaAvalleeikkndrlllkllpklvrrLcnllteldpwlqvkiiklltrlarqepeerskkel 232
                                       +++e+l+d d                                                                   
  gi|330507420|ref|YP_004383848.1| 118 RMIEALEDADKD----------------------------------------------------------------- 129
                                       444444444444................................................................. PP

                                       HHHHCGGCGCSSCHHHHHHHHHCCHCCCCSTHHHCCHHCHHHHHHSSCCTCHHHHHCHHHHHHHHXXTTTTTTTCCC CS
                         Adaptin_N 233 lesllnllqssnnaVlletvnlivelapknelivlavnaLvrllsskdenlryvaLrtllkivkkepkavqhldlki 309
                                                                                                                    
  gi|330507420|ref|YP_004383848.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       CSXXTTSXHHHHHHHHHHHCCCXXTTTHHHHHHHHHHHTTSSXXHHHHHHHHHHHHHHHHHSCCHHHHHHHHHHHHH CS
                         Adaptin_N 310 fllktdddvsirlkaldlllklvdesNvkeivkeLkkyvkevadedfksklvkaIgrlaekfatdaewvldvllell 386
                                                                                                                    
  gi|330507420|ref|YP_004383848.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       TTXXHHHHHHHHHHHHHHHHHSTTTSTTCHHHHCCTCCGXXSHHHHHHHHHHHHHTTTT CS
                         Adaptin_N 387 slsgesvkdeivevirdliqkvpelheeiiekLaellekieseearaaaiWllGeygel 445
                                                                                   +ra+a+W++Ge  e+
  gi|330507420|ref|YP_004383848.1| 130 --------------------------------------------VRAGAAWVIGELKEN 144
                                       ............................................566666666664443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1263  (0.0704445); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.26s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 1279.01
//
Query:       gi|330507421|ref|YP_004383849.1|  [L=78]
Description: hypothetical protein MCON_1348 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-22   77.8   0.1    6.4e-22   77.6   0.1    1.0  1  Dodecin   Dodecin


Domain annotation for each model (and alignments):
>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   0.1   3.5e-26   6.4e-22       1      63 [.       9      71 ..       9      72 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 3.5e-26
                                      EEEEEEEEEEESS-HHHHHHHHHHHHHHH-SSEEEEEEEEEEEEECTTCCEEEEEEEEEEEE- CS
                           Dodecin  1 VyKvielvGsSpkSwedAiqnAiaeAsktlrnirwveVketrahvedgkiaeYqvtlkvgFrl 63
                                      Vy  i+lvG+S++SwedA+q+Ai++A+++l n+r++eV+ ++ ++++g i eY+v++ ++F+ 
  gi|330507421|ref|YP_004383849.1|  9 VYNFIDLVGTSNESWEDAVQSAINTANRKLTNVRIAEVTRMDTRLREGGIMEYRVRVTLSFKH 71
                                      899**********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 557.24
//
Query:       gi|330507422|ref|YP_004383850.1|  [L=374]
Description: family 2 glycosyl transferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-23   83.3   0.0    2.5e-23   82.7   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    1.2e-07   31.8   0.0    1.9e-07   31.2   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    4.2e-05   24.0   0.0    0.00038   20.8   0.0    1.9  2  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.032   13.6   0.0      0.094   12.1   0.0    1.8  1  HOK_GEF          Hok/gef family
      0.085   12.9   7.2        3.6    7.7   2.7    2.6  2  CrgA             Cell division protein CrgA
      0.085   12.3   0.0       0.12   11.8   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
        1.4    8.3  11.9        1.3    8.4  10.0    1.8  2  DUF373           Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.0   9.7e-27   2.5e-23       1     168 [.       5     166 ..       5     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 9.7e-27
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglr 76 
                                       s +ipt Ne++t+++++ ++l+  +++     i+v D+StD t++i+ +      + +v+  +++ G+++a+  g++
  gi|330507422|ref|YP_004383850.1|   5 SLIIPTRNESQTIRQCIQRALEAfEKAGLEGEIIVADSSTDQTADIAASC-----GAKVVF-PQRLGYGNAYLLGFQ 75 
                                       78*********************98888888888999999**********.....777776.5588*********** PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTT CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsf 153
                                       +a gdyi+++D D+++dp+++ +++  le +++d+v+g+r + +  ++ ++  +r +  +++ + + +r    ++s+
  gi|330507422|ref|YP_004383850.1|  76 EAGGDYIFLMDGDLTYDPETILDMLPCLESGEYDLVMGSRLKGRIIPGAMPALHR-YVGNPILTWILNRLFSAGISD 151
                                       *************************************************999988.799999999999999999999 PP

                                       CSTCCCEEEEHHHHH CS
                   Glycos_transf_2 154 eigsaallrrealee 168
                                        +++ +++ r+al +
  gi|330507422|ref|YP_004383850.1| 152 AHCGLRGITRDALYK 166
                                       999999999999865 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   7.5e-11   1.9e-07       1     122 [.       2     113 ..       2     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 7.5e-11
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesll.aqeyprvevvvvv.desdaetlevaeelaaalpdvrvrvvvnarnlgstgk 75 
                                       pr +++++pt ne+++++ ++  +l a e   +e  ++v d s++ t++ a    a +++   +vv+++r lg   +
  gi|330507422|ref|YP_004383850.1|   2 PR-ISLIIPTRNESQTIRQCIQRALeAFEKAGLEGEIIVaDSSTDQTADIA----ASCGA---KVVFPQR-LG---Y 66 
                                       67.9*********************66677666665555477888888855....46766...5888888.55...6 PP

                   Glyco_tranf_2_3  76 sralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgt 122
                                        +a+  +++ + +d++ l+D+D   +P+t+  +l+ +++ +++ v +
  gi|330507422|ref|YP_004383850.1|  67 GNAYLLGFQEAGGDYIFLMDGDLTYDPETILDMLPCLESGEYDLVMG 113
                                       7888**************************99999998778877765 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 !   20.8   0.0   1.5e-07   0.00038      26     132 ..      20     124 ..      16     132 .. 0.86
   2 ?    1.7   0.0      0.11   2.9e+02      15      41 ..     125     151 ..     112     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.5e-07
                                       HHHHHHHHHCTT.-.CEEEEECSH.CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT-- CS
                      NTP_transf_3  26 llervldalraagv.devvvvggd.eevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPllt 100
                                        ++r+l+a+++ag+ +e++v+  + ++ ++ +a+ g++vv  +    g + + + + ++a + d+++++ +D+ + +
  gi|330507422|ref|YP_004383850.1|  20 CIQRALEAFEKAGLeGEIIVADSStDQTADIAASCGAKVVFPQ--RLGYGNAYLLGFQEA-GGDYIFLMDGDLTY-D 92 
                                       689**********945666664445889999999*******98..799***********9.9***********77.* PP

                                       HHHHHHHHHCHHHHTSSEEEEESSSEEEECCE CS
                      NTP_transf_3 101 pelverllaaaaasgadvvvptyegerghpll 132
                                       pe++  +l  +++ ++d v+ ++ ++r+ p +
  gi|330507422|ref|YP_004383850.1|  93 PETILDMLPCLESGEYDLVMGSRLKGRIIPGA 124
                                       *******************9999888876655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                                       THHHHCCCCCCHHHHHHHHHCTT.-CE CS
                      NTP_transf_3  15 dKallplggkpllervldalraagvde 41 
                                         al ++ g p+l ++l++l +ag+++
  gi|330507422|ref|YP_004383850.1| 125 MPALHRYVGNPILTWILNRLFSAGISD 151
                                       56899999************9999876 PP

>> HOK_GEF  Hok/gef family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.7e-05     0.094      19      38 ..     159     178 ..     157     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                           HOK_GEF  19 lvrkdLCElrirsGntEvaA 38 
                                       ++r+ L+ l++rsG++E+a 
  gi|330507422|ref|YP_004383850.1| 159 ITRDALYKLNLRSGGMEFAS 178
                                       79***************995 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.7    0.0014       3.6      38      81 ..     234     276 ..     221     280 .. 0.80
   2 ?    6.7   0.1     0.003       7.6      70      88 .]     306     328 ..     296     328 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0014
                              CrgA  38 mlglmllGllwlvvyYlageeipfmaelgawNlliGfgliivGl 81 
                                       +   +llGl+  vv+Y+ g++      lg   l+iG  ++++G+
  gi|330507422|ref|YP_004383850.1| 234 L-VALLLGLILAVVVYIEGGSRMHSLILGGLLLIIGYQMLLAGM 276
                                       3.44689************9666567799999999999999997 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.003
                              CrgA  70 lliGfgl....iivGllmttrWr 88 
                                       lliG++l    i++Gl++ +rWr
  gi|330507422|ref|YP_004383850.1| 306 LLIGLALlaagIVIGLVVLMRWR 328
                                       5677766222268899******9 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.8e-05      0.12       1     101 [.       5      98 ..       5     107 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyy.deeie.livvddgSsekfleevssiidlnllvylkdeddkayslaaarNr 75 
                                       s++ip r++ ++  i++ + +    +    +e  i+v d S++++++ + + + ++  v +++      + + a  +
  gi|330507422|ref|YP_004383850.1|   5 SLIIPTRNESQT--IRQCIQRALEAFeKAGLEgEIIVADSSTDQTAD-IAASCGAK--VVFPQR----LGYGNAYLL 72 
                                       789999999999..999997777776323333257888899999765.55555544..455666....67788899* PP

                   Glyco_tranf_2_2  76 GaskaesdlvlFlDaDcfissDkfek 101
                                       G+++a +d+++ +D+D  + ++ +  
  gi|330507422|ref|YP_004383850.1|  73 GFQEAGGDYIFLMDGDLTYDPETILD 98 
                                       ****************8777666555 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.62   1.6e+03      85     112 ..      17      47 ..      12      48 .. 0.67
   2 ?    8.4  10.0   0.00052       1.3     157     282 ..     228     361 ..     225     371 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.62
                            DUF373  85 iaeqldevlsklea...dsaivVsDGaeDes 112
                                       i++ +++ l+++e    ++ i+V D+++D++
  gi|330507422|ref|YP_004383850.1|  17 IRQCIQRALEAFEKaglEGEIIVADSSTDQT 47 
                                       555555555555543448899******9986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00052
                            DUF373 157 iLvplGlllliyallll........lglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyv 225
                                       +L ++Gl+ l+++l+l          ++ +l+l+ +ll++G  +ll G+ ++  +  +    ++s  ++ i+  + +
  gi|330507422|ref|YP_004383850.1| 228 FLLVPGLVALLLGLILAvvvyieggSRMHSLILGGLLLIIGYQMLLAGMHFRA-FGAAWGLSRSSGMKKLISYHS-L 302
                                       899*******9999998899999998899999**************9999998.444443333333333333332.2 PP

                            DUF373 226 .....vallllligiisgyislesvss.....asvssglltlilafiygavewlalailtaslgkii 282
                                            ++l+ll+ gi+ g++ l +++              +++    + a+ + +l+i t++ g +i
  gi|330507422|ref|YP_004383850.1| 303 ekellIGLALLAAGIVIGLVVLMRWRGagfgaL-------DAAQN-AMVAMILTILGIQTIFSGMFI 361
                                       344449***************999998544432.......32222.223333334444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2607.41
//
Query:       gi|330507423|ref|YP_004383851.1|  [L=371]
Description: glycosyl transferase, group 1 family protein [Methanosaeta concilii GP6]
Scores for complete 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  111.3   0.0    7.1e-32  110.3   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
    2.8e-25   89.3   0.0    6.4e-25   88.1   0.0    1.6  2  Glyco_trans_1_4  Glycosyl transferases group 1
    4.6e-21   75.6   0.1    2.5e-20   73.1   0.1    1.9  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.4e-14   54.9   0.1    3.9e-14   53.4   0.0    1.7  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.033   14.6   0.0    1.8  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 !  110.3   0.0     2e-35   7.1e-32      11     162 ..     193     344 ..     184     350 .. 0.89

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 2e-35
                                       TTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH.SSSH CS
                   Glycos_transf_1  11 knekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevs.redl 86 
                                          k   i++ grl  +K+++lli+a+   k +  p+v+  i+G+g+e ++l++l  +l+l++n++f g+++ ++d 
  gi|330507423|ref|YP_004383851.1| 193 PSPKSFDIVFAGRLAAHKNIHLLIQAVSIMKSE-IPDVRAAIIGDGPEMERLRSLTGKLGLEKNIEFCGFLEnYDDA 268
                                       55678899********************99876.******************************************* PP

                                       HHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET..TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHH CS
                   Glycos_transf_1  87 eellknadifvlpsisEgfGivllEAmaaglpviasn..aggpaevvkdgetGllvkpnnaealaeairklledeel 161
                                        +l+k++ +f+ ps++EgfG+++l A a+glpv+++   +  ++++v+++ tG++++p  +e+la+++  +l+++++
  gi|330507423|ref|YP_004383851.1| 269 LALMKSSRAFASPSTREGFGMAALDANACGLPVVTVEhrMNAVMDLVTEN-TGIICPPA-PEDLADGLLLALQESPR 343
                                       ************************************94344455666665.5******9.************99855 PP

                                       H CS
                   Glycos_transf_1 162 r 162
                                        
  gi|330507423|ref|YP_004383851.1| 344 M 344
                                       4 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.1   1.1e+04      54      69 ..      52      66 ..      24      69 .. 0.61
   2 !   88.1   0.0   1.8e-28   6.4e-25       3     133 ..     199     339 ..     197     340 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.1
                                      T.TEEEE---THHHHH CS
                   Glyco_trans_1_4 54 eerveftGfvedlael 69
                                      +e+v+f+G   + ++l
  gi|330507423|ref|YP_004383851.1| 52 REGVRFHGIC-EPRPL 66
                                      3679999977.55555 PP

  == domain 2  score: 88.1 bits;  conditional E-value: 1.8e-28
                                       EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---...THHHHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfv...edlaella 71 
                                       +i+f Grl+  +k+++ll++av  ++++  dvr  i+Gdgp + e+l++l+   gle+++ef+Gf+   +d  +l++
  gi|330507423|ref|YP_004383851.1| 199 DIVFAGRLA-AHKNIHLLIQAVSIMKSEipDVRAAIIGDGPeM-ERLRSLTGklGLEKNIEFCGFLenyDDALALMK 273
                                       79******5.55**************88855*********965.6999888559************99888****** PP

                                       H-SEEEE--..---SHHHHHHHHTT-EEEE-TG..GGTTT--.TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdv..ggiaevv.gengllvppgdpealaeailrLle 133
                                       +++ f  Ps  egfg+++l+a a+glpvV+ +    ++ ++v +++g+++pp  pe+la+ +l  l+
  gi|330507423|ref|YP_004383851.1| 274 SSRAFASPStrEGFGMAALDANACGLPVVTVEHrmNAVMDLVtENTGIICPP-APEDLADGLLLALQ 339
                                       **********99*******************872245677779999****97.5******9987665 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.1   7.1e-24   2.5e-20       2     167 ..      16     184 ..      15     187 .. 0.85
   2 ?   -0.0   0.0      0.22   7.7e+02      85     107 ..     288     309 ..     283     346 .. 0.81

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 7.1e-24
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvv.tpgddgpleeev.elvvrvprvplpllkrllrslaflrrlrrllkre..kpD 74 
                                       GG+e  ++e++r+La+rGh V+ +   +++g+ e e+  +   +++ p+pl+ + +rs+  + +++++l  +  k  
  gi|330507423|ref|YP_004383851.1|  16 GGAEKRIYEISRRLAARGHVVHCYgMKWWQGEDEIEReGVRFHGICEPRPLYVNGKRSIGEAAYFAARLLSHpsKEA 92 
                                       9***********************755555555555233444445578999999999**999999999999999889 PP

                    Glyco_transf_4  75 vvHahspaalgaallalrr...rlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadel 148
                                       vv ++++++l +  ++l+    +++ +l +t H  + k +++ +l+++  + r  e  ++r +dr +avS+ ta++l
  gi|330507423|ref|YP_004383851.1|  93 VVDCQNFPYLSCFSARLLNswrKKNQKLFITWHEVW-KDYWHEYLGKKGEIGRITELIAARLTDRNLAVSKRTARDL 168
                                       9999998887655444444566**************.9*************************************** PP

                    Glyco_transf_4 149 rerygvppekitVipnGvD 167
                                       ++ +g +   + V+pnG+D
  gi|330507423|ref|YP_004383851.1| 169 ES-LGARG--VQVVPNGID 184
                                       **.**766..********9 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.22
                    Glyco_transf_4  85 gaallalrrrlgiplVltvHgly 107
                                       g a+l + +  g+p+V+  H + 
  gi|330507423|ref|YP_004383851.1| 288 GMAALDANA-CGLPVVTVEHRMN 309
                                       445555554.9*********886 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 !   53.4   0.0   1.1e-17   3.9e-14       1     160 []      16     182 ..      16     182 .. 0.80
   2 ?   -1.8   0.0         1   3.7e+03      86     105 ..     289     313 ..     280     354 .. 0.62

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.1e-17
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrps..pladla.alralrrllrqrrerp 74 
                                       gG++++++e++r+LaarGh V+++  ++ +g++e+e++gvr h++  pr     + ++   a+  ++rll  +  + 
  gi|330507423|ref|YP_004383851.1|  16 GGAEKRIYEISRRLAARGHVVHCYGMKWWQGEDEIEREGVRFHGICEPRPLYvnGKRSIGeAAYFAARLL-SHPSKE 91 
                                       8******************************************996665553223333331333444454.456666 PP

                   Glyco_trans_4_4  75 dvvhahs.pt.aglaarlar..rrrgiplvvtlhgll...lrrgsgavrrlyralerrllrradavlvvseaeaeel 144
                                        vv +++ p+ + + arl+   r+++ +l++t+h+ +   ++++ g ++ + r  e  ++r  d+ l+vs   a++l
  gi|330507423|ref|YP_004383851.1|  92 AVVDCQNfPYlSCFSARLLNswRKKNQKLFITWHEVWkdyWHEYLGKKGEIGRITELIAARLTDRNLAVSKRTARDL 168
                                       69999996445889999996533559********8665557778999***9999999999***************** PP

                   Glyco_trans_4_4 145 ralgvpadrvvvvpng 160
                                       + lg++   v+vvpng
  gi|330507423|ref|YP_004383851.1| 169 ESLGAR--GVQVVPNG 182
                                       ******..68899**8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                   Glyco_trans_4_4  86 laarlarrrrgiplvvtlh......g 105
                                       +aa+ a  + g+p+v   h      +
  gi|330507423|ref|YP_004383851.1| 289 MAALDAN-ACGLPVVTVEHrmnavmD 313
                                       4444444.778888888885544441 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   9.3e-06     0.033       5      64 ..     281     342 ..     270     352 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.3e-06
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltdda..egleelftpgkevilfedleelaekiryllanpe 64 
                                       ps +e++ +  ++a acG +++t +    ++ +l+t+++ +i+   +e+la+ +  +l++  
  gi|330507423|ref|YP_004383851.1| 281 PSTREGFGMAALDANACGLPVVTVEHrmNAVMDLVTENTGIICPPAPEDLADGLLLALQESP 342
                                       78889******************97789**********9999999******99888887544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2574.52
//
Query:       gi|330507424|ref|YP_004383852.1|  [L=436]
Description: hypothetical protein MCON_1351 [Methanosaeta concilii GP6]
Scores for complete 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   69.8   0.0    8.5e-19   67.5   0.0    2.2  2  HATPase_c_4  Putative ATP-dependent DNA helicase recG C-termi
    7.5e-08   32.7   0.0    1.2e-07   32.1   0.0    1.3  1  AlbA_2       Putative DNA-binding domain


Domain annotation for each model (and alignments):
>> HATPase_c_4  Putative ATP-dependent DNA helicase recG C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.33   2.9e+03      34      78 ..      24      70 ..      13      75 .. 0.74
   2 !   67.5   0.0   9.4e-23   8.5e-19       1      88 []     261     345 ..     261     345 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.33
                       HATPase_c_4 34 grssaRNelLasllerlrl..meergsGiqrilealeeaglpepefr 78
                                      g+++  N lL +l  r+++   e + +G++ +l ++ +a+ ++ +f+
  gi|330507424|ref|YP_004383852.1| 24 GNEELENWLLHELSPRIHFqfFEVKVEGLSVVLLEIGRASRQPVQFK 70
                                      55666777888888887653379999999999999999888888886 PP

  == domain 2  score: 67.5 bits;  conditional E-value: 9.4e-23
                       HATPase_c_4   1 GakvqieifdDRleItspGglpggvtveskllegrssaRNelLasllerlrlmeergsGiqrilealeeaglpepef 77 
                                       Ga+ ++eif+DR+e+t+pG+ +  v++ + + + ++++RNe+La+l++r++++eergsG ++++ ++e ++lp+p +
  gi|330507424|ref|YP_004383852.1| 261 GASPMVEIFADRIEVTNPGKPL--VDTYR-FVDTPPRSRNEALAALMRRFGICEERGSGWDKVVFQTELYQLPAPLL 334
                                       78899****************9..66665.99********************************************* PP

                       HATPase_c_4  78 redgssftvtl 88 
                                       + ++++ +v+l
  gi|330507424|ref|YP_004383852.1| 335 EATSDHTRVVL 345
                                       ******99997 PP

>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   1.4e-11   1.2e-07      39     121 ..       2      84 ..       1      85 [. 0.94

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.4e-11
                            AlbA_2  39 iGVeD.dgkvvGv.ecsdqeedqlrlelksiikrfkpkvlpdiervelkgkkvlvvkvekskkkplyeneegvvyiR 113
                                       +GV+D +++++G+  + + ++  +++++++++ +++p++ +++++v+++g  v+++++ +++++p   + +g+ +iR
  gi|330507424|ref|YP_004383852.1|   2 WGVSDgNHSIIGTqFSPKTTKVGNEELENWLLHELSPRIHFQFFEVKVEGLSVVLLEIGRASRQP--VQFKGNEFIR 76 
                                       8************767788889999999*************************************..********** PP

                            AlbA_2 114 rggsskrl 121
                                       +g+ +krl
  gi|330507424|ref|YP_004383852.1|  77 VGSYKKRL 84 
                                       *****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 3213.00
//
Query:       gi|330507425|ref|YP_004383853.1|  [L=71]
Description: hypothetical protein MCON_1352 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 510.57
//
Query:       gi|330507426|ref|YP_004383854.1|  [L=331]
Description: hypothetical protein MCON_1354 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); 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:                         0  (0); expected 0.2 (1e-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 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2347.67
//
Query:       gi|330507427|ref|YP_004383855.1|  [L=344]
Description: hypothetical protein MCON_1355 [Methanosaeta concilii GP6]
Scores for complete 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   18.5   0.0     0.0015   18.0   0.0    1.2  1  MauJ      Methylamine utilization protein MauJ
  ------ inclusion threshold ------
      0.045   13.7   0.0       0.12   12.4   0.0    1.7  1  DUF4334   Domain of unknown function (DUF4334)


Domain annotation for each model (and alignments):
>> MauJ  Methylamine utilization protein MauJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.7e-07    0.0015      78     184 ..     116     225 ..      96     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-07
                              MauJ  78 GkLseiiyrveaasaqdaldaayadldarlarlalelGRgmaiaGWRvaDveheaR....WRcvPfRPsaleld.lp 149
                                       G L  i++ ++  + ++ald a++ +   l  + l+    ++i    v  + ++ R    +  +P+ P  l++d + 
  gi|330507427|ref|YP_004383855.1| 116 GLLRSIVMTIPEDNIDSALDIAHKTFIGILDAICLRKRIPIQIQRIEV--LTKKGRmqrsYTTMPYMPVELDVDdII 190
                                       789999999999999999999999999999999999877777765555..44444421236678********96367 PP

                              MauJ 150 alaaladdlkpllrLyqraRnatdpawRllaayai 184
                                       +++ +++ l+p l Ly++a n+ +p +Rll  + i
  gi|330507427|ref|YP_004383855.1| 191 TVNYIPQVLRPCLTLYREAINSCNPYYRLLCLFRI 225
                                       999**************************986655 PP

>> DUF4334  Domain of unknown function (DUF4334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05      0.12      18      37 ..       1      20 [.       1      26 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                                      EEESSSSEEEEEEEEETTEE CS
                           DUF4334 18 mvYDklPiiDhFRkVdddtv 37
                                      m Y  l i DhF+kVdd+tv
  gi|330507427|ref|YP_004383855.1|  1 MKYSPLGIKDHFKKVDDRTV 20
                                      6678888***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2736.15
//
Query:       gi|330507428|ref|YP_004383856.1|  [L=707]
Description: copper-translocating P-type ATPase [Methanosaeta concilii GP6]
Scores for complete 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-56  190.6   2.8    2.4e-56  190.1   0.9    2.2  2  E1-E2_ATPase  E1-E2 ATPase
    2.3e-43  148.9   0.7    7.5e-43  147.3   0.3    1.9  2  Hydrolase     haloacid dehalogenase-like hydrolase
    1.1e-05   25.3   0.1     0.0016   18.2   0.4    2.4  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
    0.00028   21.4   0.0    0.00093   19.6   0.0    1.9  1  HAD           haloacid dehalogenase-like hydrolase
     0.0074   15.5   0.0      0.023   13.9   0.0    1.7  1  Zip           ZIP Zinc transporter
  ------ inclusion threshold ------
      0.041   13.7   0.2       0.12   12.1   0.2    1.8  1  DUF5612       Domain of unknown function (DUF5612)
        9.1    5.6  11.0        2.3    7.5   7.4    1.7  2  TssN          Type VI secretion system, TssN


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         1   2.6e+03     112     147 ..      70     108 ..      61     119 .. 0.63
   2 !  190.1   0.9   9.4e-60   2.4e-56       2     180 ..     202     380 ..     201     381 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT...HH CS
                      E1-E2_ATPase 112 qkkldklgkvlvpvvlliallvflialllgksla...ea 147
                                       + + ++++  l++++ +++l  f++ l++++  +    +
  gi|330507428|ref|YP_004383856.1|  70 EDFKRRFIISLIITIPILLLSSFIQELFRFELQFpgsLY 108
                                       455567777777777777777777777776665554444 PP

  == domain 2  score: 190.1 bits;  conditional E-value: 9.4e-60
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvs 78 
                                       ++p++a++i+dg+++e++++ l+pGD vl+k+g+++p+Dg ++eg+++v+es+LTGEs+pv+k +gd v++G+++ +
  gi|330507428|ref|YP_004383856.1| 202 IMPSEAHLIKDGQTVEVKVESLKPGDRVLVKPGEKIPIDGTVIEGETSVNESMLTGESRPVRKRAGDDVIGGSINGE 278
                                       6899************************************************************************* PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHH CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralall 155
                                       g++ ++V ++g++t+l++i++lv++a+++k+++q  +d+ +++l++++l +++++f+++l   k+ a+a+ ra++++
  gi|330507428|ref|YP_004383856.1| 279 GSISIEVKKIGSETYLSQIIELVRQAQESKSRTQDLADNAARWLTIISLSVGAITFAAWLNFSKDSAFAIERAVTVM 355
                                       ***************************************************************************** PP

                                       HHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 156 vaaiPcaLplavplalalgarrlak 180
                                       v+++P aL+lavpl++a++++ +ak
  gi|330507428|ref|YP_004383856.1| 356 VISCPHALGLAVPLVVAVSTSLAAK 380
                                       ********************99998 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.59   1.5e+03       8      23 ..     239     254 ..     239     325 .. 0.80
   2 !  147.3   0.3   2.9e-46   7.5e-43       1     210 []     397     611 ..     397     611 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.59
                                       SBTTTBCHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                         Hydrolase   8 kdGTLttgepsvedvi 23 
                                       +dGT+++ge sv + +
  gi|330507428|ref|YP_004383856.1| 239 IDGTVIEGETSVNESM 254
                                       5999999998887755 PP

  == domain 2  score: 147.3 bits;  conditional E-value: 2.9e-46
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHH...HHHHHHHHHETTTE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx. RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakar...sgaltgfatfigrg. 67 
                                       i +vvfDk+GTLt+g+  v+d+i+ a l + ++l+++      seh i++ +++  k++    ++++gf  ++g+g 
  gi|330507428|ref|YP_004383856.1| 397 IQAVVFDKTGTLTEGRFGVTDIIPLAGLNETEVLRMAasleanSEHSIAAGIAEGSKEMgidLIPIQGFKSIPGKGi 473
                                       789***********************77777777777777777****************7777777*********** PP

                                       .......HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTE CS
                                       .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 .......ayaigkpewltaldippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagi 135
                                                ++ +p +l+++   +  ++++  + +qg+tv++l  ++r+++ +++ad   +++e +ea+++L++++i
  gi|330507428|ref|YP_004383856.1| 474 egqiqgrSWMVASPGYLREN-NIKLDDDRVNRLAEQGKTVVFLleEDRLVGAVALADV--IRKESREAIEELRSMNI 547
                                       99999999999999999999.66666788899999999999999999***********..***************** PP

                                       EEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHT.STGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 136 evvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLq.gkpeevamVGDgvnDaaalaaAg 210
                                       +  +ltgdn+  a+ +a+ lG           ++ +a+++p  k +air  q + +  vamVGDgvnDa+ala+A+
  gi|330507428|ref|YP_004383856.1| 548 NCMMLTGDNRFVARWVAEDLG----------LDDFFAEVLPHEKAQAIRNVQrEYI--VAMVGDGVNDAPALAQAD 611
                                       *********************..........5555****************95557..*****************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 ?    4.3   0.0     0.011        28      16      58 ..     531     573 ..     528     577 .. 0.92
   2 !   18.2   0.4   6.2e-07    0.0016     206     247 ..     594     635 ..     579     643 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.011
                                       --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                       Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                       i ++++eai++l++ +i+ +  TG +   ++ v+e+lgld ++
  gi|330507428|ref|YP_004383856.1| 531 IRKESREAIEELRSMNINCMMLTGDNRFVARWVAEDLGLDDFF 573
                                       7899**********************************99765 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 6.2e-07
                                       EEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GG CS
                       Hydrolase_3 206 viafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnn 247
                                       v+ +GDg ND + L +a++g+A+g +++ +++ Ad v   n+
  gi|330507428|ref|YP_004383856.1| 594 VAMVGDGVNDAPALAQADVGIAIGAGTDVAIESADIVLVRND 635
                                       5668********************************998776 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.6e-07   0.00093      82     187 ..     527     607 ..     496     608 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.6e-07
                               HAD  82 rpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaal 158
                                       +  +++ + +e++++ r+ ++ + +++g +r++++ +++ lg    l+        +++e       v  ++k++a+
  gi|330507428|ref|YP_004383856.1| 527 LADVIRKESREAIEELRSMNINCMMLTGDNRFVARWVAEDLG----LDD-------FFAE-------VLPHEKAQAI 585
                                       33345577788888888*************************....999.......8888.......7777888999 PP

                               HAD 159 rewlaaegegidleevvay.GDspsDlpll 187
                                       r    +++       +va  GD+++D p+l
  gi|330507428|ref|YP_004383856.1| 586 RN--VQRE------YIVAMvGDGVNDAPAL 607
                                       99..4444......366666*******998 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   8.9e-06     0.023     109     238 ..      12     372 ..       4     384 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.9e-06
                               Zip 109 ktpkkasssssesaakksvsndkveeseek.edhvaeadtdadskeelrngkqeksesekeqas............. 171
                                       + +++   +++  + +++++ +k+++  e  e+h+ + + ++d++++ ++g  e ++ e+ +               
  gi|330507428|ref|YP_004383856.1|  12 PKSPNRGMEHNIHGMHGTAKGHKTDDAGEMhENHQMGMARHPDKSSKRHRGRHEGHKTEDFKRRfiisliitipill 88 
                                       444444444555555555555555555444123334444444444555555544444444444499*********** PP

                               Zip 172 ............................................................................. 171
                                                                                                                    
  gi|330507428|ref|YP_004383856.1|  89 lssfiqelfrfelqfpgslyvvfllsslvyfyggypflkgffkevkdknigmmtliataisaayfyssavvfglmge 165
                                       ***************************************************************************** PP

                               Zip 172 ............................................................................. 171
                                                                                                                    
  gi|330507428|ref|YP_004383856.1| 166 tffwelatlidimlfghwiemrsilgasraleelvkimpseahlikdgqtvevkveslkpgdrvlvkpgekipidgt 242
                                       ***************************************************************************** PP

                               Zip 172 ...............................................................eeedkeklaslkvr 185
                                                                                                      e+++++++++ +++
  gi|330507428|ref|YP_004383856.1| 243 viegetsvnesmltgesrpvrkragddviggsingegsisievkkigsetylsqiielvrqaqESKSRTQDLADNAA 319
                                       ***************************************************************************** PP

                               Zip 186 aiilllglilHsfidGLAlGvssssstgislfiAvllHelpeelglgaiLlka 238
                                        ++ +++l++  ++    l +s++s+ +i   ++v++  +p++lgl ++L+ a
  gi|330507428|ref|YP_004383856.1| 320 RWLTIISLSVGAITFAAWLNFSKDSAFAIERAVTVMVISCPHALGLAVPLVVA 372
                                       **************999999******************************976 PP

>> DUF5612  Domain of unknown function (DUF5612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   4.8e-05      0.12      21      96 ..     215     295 ..     201     317 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.8e-05
                                       HHHHHHHHHHHHHHHHCT.SS-EEEEEEE--SHHHHHHHHHHGGGST...TEEEEEEESSB--.THHHHHHHHHHHT CS
                           DUF5612  21 vaqvalGaiseadrhnir.GerisvdtiplvGeeelaeaveavsrlp...rvkvlvlaGslmG.Gkiteavkklkee 92 
                                         +v + +++  dr  ++ Ge+i +d   + Ge+++ e++ + +  p   r+   v+ Gs+ G G+i+ +vkk+ +e
  gi|330507428|ref|YP_004383856.1| 215 TVEVKVESLKPGDRVLVKpGEKIPIDGTVIEGETSVNESMLTGESRPvrkRAGDDVIGGSINGeGSISIEVKKIGSE 291
                                       55677778888899888769******************99776554332389999******9989*********988 PP

                                       .T-E CS
                           DUF5612  93 kdii 96 
                                       + + 
  gi|330507428|ref|YP_004383856.1| 292 TYLS 295
                                       7664 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   7.4   0.00089       2.3      30     124 ..      73     169 ..      66     184 .. 0.75
   2 ?   -2.1   0.1      0.78     2e+03      99     133 ..     322     356 ..     312     371 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00089
                              TssN  30 kkkliiyiLlaglvlalpgllgf...lknefvpygyillqilylllGilhlylllkkffkelkekkilfeilltliv 103
                                       k+++ii +++++ +l l +++     ++ +f    y+++ + +l+  +     +lk ffke+k+k+i++ +l++  +
  gi|330507428|ref|YP_004383856.1|  73 KRRFIISLIITIPILLLSSFIQElfrFELQFPGSLYVVFLLSSLVYFYGGYP-FLKGFFKEVKDKNIGMMTLIATAI 148
                                       6789999999999999999987544666777766777666666666555444.788**********98888888888 PP

                              TssN 104 illglvlfvlvfnllselqyg 124
                                        +  ++   +vf l+ e+ + 
  gi|330507428|ref|YP_004383856.1| 149 SAAYFYSSAVVFGLMGETFFW 169
                                       888888888999999887743 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.78
                              TssN  99 ltlivillglvlfvlvfnllselqygvwaatsllv 133
                                       lt+i++ +g++ f  + n+ +++ +++  a +++v
  gi|330507428|ref|YP_004383856.1| 322 LTIISLSVGAITFAAWLNFSKDSAFAIERAVTVMV 356
                                       68899999999999999999998888755554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (707 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.26s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 4448.12
//
Query:       gi|330507429|ref|YP_004383857.1|  [L=496]
Description: hypothetical protein MCON_1357 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-33  112.6  64.7    8.6e-10   38.6   4.7    6.2  6  Pentapeptide_3  Pentapeptide repeats (9 copies)
    8.4e-05   22.7  20.8     0.0079   16.3   2.0    4.9  3  Pentapeptide_4  Pentapeptide repeats (9 copies)
    0.00096   19.1   3.1     0.0046   16.9   0.4    2.8  2  Ion_trans_2     Ion channel
  ------ inclusion threshold ------
      0.015   15.0  20.9       0.13   11.9   0.9    6.4  7  Pentapeptide    Pentapeptide repeats (8 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   9.9   1.9e-11   8.3e-08       2      47 ..      69     113 ..      68     114 .. 0.95
   2 !   38.6   4.7   1.9e-13   8.6e-10       1      47 [.     120     167 ..     120     168 .. 0.97
   3 !   14.6  11.7   6.2e-06     0.028       1      47 [.     164     211 ..     164     212 .. 0.93
   4 !   24.6   4.1   4.6e-09   2.1e-05       1      42 [.     218     259 ..     218     259 .. 0.93
   5 !   31.6   6.3   3.1e-11   1.4e-07       4      45 ..     254     296 ..     251     298 .. 0.94
   6 ?   -1.7   0.0      0.77   3.5e+03      30      39 ..     440     449 ..     436     451 .. 0.65

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.9e-11
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                       ++++  +a +F+g tF  +a+F ++ Fg+a+F+ga+F g++dF ++
  gi|330507429|ref|YP_004383857.1|  69 FNCTIPDA-SFEGITFAEDAFFWGSSFGNASFQGATFLGRADFANT 113
                                       68999999.**********************************998 PP

  == domain 2  score: 38.6 bits;  conditional E-value: 1.9e-13
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFg.sadFsgarFtgdvdFsga 47 
                                       F g++F+++a F ga F+++ sF+++ Fg +a+F ++rF g+vdF+ +
  gi|330507429|ref|YP_004383857.1| 120 FAGCTFYQPALFGGALFENDLSFEDTAFGlDASFHDVRFLGRVDFNYS 167
                                       89*******************************************976 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 6.2e-06
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFg.sadFsgarFtgdvdFsga 47 
                                       F+ + F+   +F  a Fs +a+Fs+ d++ ++dFs a+F+g ++F ++
  gi|330507429|ref|YP_004383857.1| 164 FNYSDFDSYSYFAAAEFSEDAFFSDVDLSaTSDFSAATFSGQANFIRS 211
                                       8999999999******************55***************776 PP

  == domain 4  score: 24.6 bits;  conditional E-value: 4.6e-09
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdv 42 
                                       F ++ Fsg+a+F +a+Fsg +sF +a+F ++a F  arF+ d+
  gi|330507429|ref|YP_004383857.1| 218 FGDVLFSGPAQFGMARFSGLTSFGGAVFaDEAGFGLARFS-DA 259
                                       66778***********************99*********9.75 PP

  == domain 5  score: 31.6 bits;  conditional E-value: 3.1e-11
                    Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFs 45 
                                       a+Fs+aa+F+ga+F++ a F  a+F + ++F+++rF+gd++F+
  gi|330507429|ref|YP_004383857.1| 254 ARFSDAAYFSGAHFQDLALFGLARFeDIVTFQDTRFDGDLNFK 296
                                       89***********************77***************7 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 0.77
                    Pentapeptide_3  30 sadFsgarFt 39 
                                       +a++++a F 
  gi|330507429|ref|YP_004383857.1| 440 RATLRNALFF 449
                                       5666666664 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.0   1.8e-06    0.0079       5      63 ..      70     125 ..      65     128 .. 0.68
   2 !    7.8  11.6    0.0008       3.6       2      63 ..      98     169 ..      92     220 .. 0.76
   3 ?    3.0   5.6     0.026   1.2e+02       8      56 ..     262     313 ..     175     334 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-06
                    Pentapeptide_4   5 rcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecn.lsdvdfaevdlkrasFsgcnl 63 
                                       +c+  ++ +++++F+e    d+ F ++ + n++F+ ++ l  +dfa+++++ asF gc++
  gi|330507429|ref|YP_004383857.1|  70 NCTIPDASFEGITFAE----DAFFWGSSFGNASFQGATfLGRADFANTSFRQASFAGCTF 125
                                       6777777777777777....5666666666666666552467777777777777777776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0008
                    Pentapeptide_4   2 eftrcsfnn.cklsnvnFsearlrdcnFtecrl.......snvnFdecnls.dvdfaevdlk.rasFsgcnl 63 
                                       +f+ ++f++ ++++n++F++a + +c+F ++ l       ++ +F+++ +  d++f +v++  r+ F  +++
  gi|330507429|ref|YP_004383857.1|  98 SFQGATFLGrADFANTSFRQASFAGCTFYQPALfggalfeNDLSFEDTAFGlDASFHDVRFLgRVDFNYSDF 169
                                       566666654478888888888888888888888999999888888888775567777777642445554444 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.026
                    Pentapeptide_4   8 fnncklsn.vnFsearlrd.cnFtecrl.snvnFdecnlsdvdfaevdlkra 56 
                                       f ++ + + + F  ar++d  +F+++r+  + nF++ ++ ++ f e++lk+ 
  gi|330507429|ref|YP_004383857.1| 262 FSGAHFQDlALFGLARFEDiVTFQDTRFdGDLNFKSGSITSLLFDEAELKEG 313
                                       3444444423344447777677777777777777777777777777777765 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.068     3e+02       9      33 ..     240     264 ..     234     267 .. 0.76
   2 !   16.9   0.4     1e-06    0.0046       5      78 ..     407     495 ..     402     496 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.068
                                       HHHHHHHT....T---HHHHHHHHH CS
                       Ion_trans_2   9 fgaviysleegwekwsfldalYfsf 33 
                                       fg ++++ e+g     f+da Yfs 
  gi|330507429|ref|YP_004383857.1| 240 FGGAVFADEAGFGLARFSDAAYFSG 264
                                       6667777766677889*******96 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1e-06
                                       HTCHHHHHHHHT....................T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHH CS
                       Ion_trans_2   5 lvlifgaviysl...............eeg.wekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlal 65 
                                       ++lifg v+ +                +++  e+ ++ +al+fs++ +++ G  d+ p++   r+ ++++++lG +l
  gi|330507429|ref|YP_004383857.1| 407 TILIFGLVFWIGdgirrsskplsgpveKDSiPERATLRNALFFSTMIFLSQGPIDFLPVGRH-RYYVMLEMILGWLL 482
                                       45555554444477777788888888844449999************************999.************** PP

                                       HHHHHHHHHHHHH CS
                       Ion_trans_2  66 falflavlgkvlt 78 
                                       +alfl +lgkv++
  gi|330507429|ref|YP_004383857.1| 483 LALFLVTLGKVMI 495
                                       *********9986 PP

>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2   0.00039       1.8      10      28 ..      86     104 ..      82     106 .. 0.62
   2 ?   11.9   0.9   2.9e-05      0.13       5      23 ..     107     125 ..     104     127 .. 0.51
   3 ?   -2.2   0.0      0.78   3.5e+03      20      28 ..     161     169 ..     151     170 .. 0.54
   4 ?    4.2   0.4    0.0078        35      15      35 ..     183     204 ..     182     204 .. 0.90
   5 ?   -0.8   0.0      0.27   1.2e+03       1      10 [.     206     215 ..     205     225 .. 0.48
   6 ?    0.2   0.1      0.13   5.9e+02       6      13 ..     260     267 ..     254     272 .. 0.57
   7 ?   -2.7   0.1       1.1     5e+03      31      36 ..     441     446 ..     439     449 .. 0.38

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00039
                                       CSCCEECCCESEEECT-B- CS
                      Pentapeptide  10 ganLsganlsgAnLtgAnl 28 
                                        a + g+++ +A+++gA++
  gi|330507429|ref|YP_004383857.1|  86 DAFFWGSSFGNASFQGATF 104
                                       4556666666666666666 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.9e-05
                                       T-B-CCSCCEECCCESEEE CS
                      Pentapeptide   5 gAnLsganLsganlsgAnL 23 
                                       +A++ ++++++a++ g+++
  gi|330507429|ref|YP_004383857.1| 107 RADFANTSFRQASFAGCTF 125
                                       4555555555555555555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.78
                                       SEEECT-B- CS
                      Pentapeptide  20 gAnLtgAnl 28 
                                       + +++++++
  gi|330507429|ref|YP_004383857.1| 161 RVDFNYSDF 169
                                       333333333 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.0078
                                       ECCCESEEECT-.B-TT-EECC CS
                      Pentapeptide  15 ganlsgAnLtgA.nlsgAdLsg 35 
                                       +a++s+ +L+ + ++s A +sg
  gi|330507429|ref|YP_004383857.1| 183 DAFFSDVDLSATsDFSAATFSG 204
                                       6999*******99999999987 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 0.27
                                       -B-TT-B-CC CS
                      Pentapeptide   1 AnLsgAnLsg 10 
                                       An+ + +L +
  gi|330507429|ref|YP_004383857.1| 206 ANFIRSRLNE 215
                                       3344444433 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.13
                                       -B-CCSCC CS
                      Pentapeptide   6 AnLsganL 13 
                                       A++sga++
  gi|330507429|ref|YP_004383857.1| 260 AYFSGAHF 267
                                       33333333 PP

  == domain 7  score: -2.7 bits;  conditional E-value: 1.1
                                       -EECCE CS
                      Pentapeptide  31 AdLsga 36 
                                       A L++a
  gi|330507429|ref|YP_004383857.1| 441 ATLRNA 446
                                       222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3270.20
//
Query:       gi|330507430|ref|YP_004383858.1|  [L=246]
Description: hypothetical protein MCON_1358 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-06   27.5   0.0    3.7e-06   27.0   0.0    1.3  1  DcrB      DcrB
    0.00093   19.4   0.3      0.011   15.9   0.3    2.1  1  PsbP      PsbP


Domain annotation for each model (and alignments):
>> DcrB  DcrB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   4.2e-10   3.7e-06      38     128 .]     117     206 ..      82     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.2e-10
                                       TTS-HHHHHHHHHHHHHHHSTT-EEEEEEEEEET.TEEEEEEEEEEEETTEEEEEEEEEE--SSSEEEEEEEE-CCC CS
                              DcrB  38 egetleeylerqlkqlrkrlkgfqlleekpatlgaglpaeelevtyrkkgkpvyqlqvlvevprrvLiftltspgef 114
                                       ++ tle y +  l  l++ ++++q+l+e+++t++ + pa+ + ++ +++g ++  l +   +++ + ift+ +p e 
  gi|330507430|ref|YP_004383858.1| 117 QDVTLEVYSQAALGVLNDIMPDLQILTESDITIN-EVPAHAIVYSLESEGVTFRVLEAWTVIDEYAYIFTYKAPDEV 192
                                       45689*****************************.9***************************************** PP

                                       HHHHHHHHHHHHCT CS
                              DcrB 115 teeqrahweailas 128
                                        ++ +++++ i++s
  gi|330507430|ref|YP_004383858.1| 193 YDQFAEDAADIIDS 206
                                       *******9999986 PP

>> PsbP  PsbP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   1.2e-06     0.011       6     155 ..      61     208 ..      58     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-06
                                       EEETTTTEEEEEETTEEEEE-TT...TEEEEEEESS-TTSEEEEEEEE-STT--CHHH--HHHHHHHHHHHCC..CH CS
                              PsbP   6 ytdeedgysflyPsgWqevkgae...gadvvFrdeiesdenvsVvispvskdksledlGspeevaerlvkqvl..as 77 
                                       y++ + g+++ yP++W+e + +    g  v F  + e   n +V    +++    e+l   ++v+ ++ +q+     
  gi|330507430|ref|YP_004383858.1|  61 YENYDYGFELIYPADWIEQEAEAndqGMIVGFLAPGEDVDNPTVYLL-LQN----EELPAGQDVTLEVYSQAAlgVL 132
                                       778889************7777677788889************9997.444....4666667777777666653322 PP

                                       CTSSEEEEEEEEEEEEET.TEEEEEEEEEEEETTEEEEEEEEEEEEETTEEEEEEEEEEHHHHCCCHHHHHHHHHC- CS
                              PsbP  78 sesgreaelidaeereaddgktyYeleytvkspdeqerhqlaavavsngkLYtltlqtpekrwekvekklekvvkSF 154
                                       ++   + +++  +   + ++ +   + y+++s++  + + l a +v ++  Y++t  +p++ +++  ++   +++SF
  gi|330507430|ref|YP_004383858.1| 133 NDIMPDLQILTESDI-TINEVPAHAIVYSLESEG-VTFRVLEAWTVIDEYAYIFTYKAPDEVYDQFAEDAADIIDSF 207
                                       333355667766665.556999**********99.8999999999999***************************** PP

                                       E CS
                              PsbP 155 r 155
                                       +
  gi|330507430|ref|YP_004383858.1| 208 D 208
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1648.90
//
Query:       gi|330507431|ref|YP_004383859.1|  [L=193]
Description: periplasmic copper-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-24   84.9   4.8    5.8e-24   84.7   4.8    1.1  1  NosD        Periplasmic copper-binding protein (NosD)
    7.1e-07   29.2  11.8    7.1e-07   29.2  11.8    1.5  1  Beta_helix  Right handed beta helix region


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   4.8   6.5e-28   5.8e-24     126     240 ..      63     181 ..      28     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 6.5e-28
                              NosD 126 nnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsnnneWnttkts..gtniiggp 200
                                        n+Gif+++ s+n i +N +++n  +Gi++ +++++nti+ N+F++n++ ++++   +n+W+ + ++   + + +g 
  gi|330507431|ref|YP_004383859.1|  63 GNAGIFIDS-SDNIILNNILYKN-RYGIYIEEGATNNTIHSNDFLENRVAANDTV--GNRWSMEMKEegLMGLLKGA 135
                                       589****99.6999999999999.*****999****************8888866..9****999775567899*** PP

                              NosD 201 ylgGNyWsdydg.....eDadgDGigDtpYeindgv.iDylplvnp 240
                                        + GN++sdyd      +D++ DG++D+p +i +g  iD++plv p
  gi|330507431|ref|YP_004383859.1| 136 KIIGNHYSDYDEpgegcNDTNSDGFCDEPRTIGNGPgIDEHPLVAP 181
                                       *********************************9999******987 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 !   29.2  11.8     8e-11   7.1e-07      65     142 ..      32     112 ..      24     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 8e-11
                                       E---SEEE-TT--S--EEES-EEES-SS-.....SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES CS
                        Beta_helix  65 sdnngggialfgasnnlienneitdnggs.....GiylnyssnntienNiidnnagsGividdsssnvtvtnNtitn 136
                                         n+++ + +  a+++ ie+ + t  gg+     Gi+++ ss+n+i nNi++ n+ +Gi+i+++++n+t++ N +  
  gi|330507431|ref|YP_004383859.1|  32 DANGSSSAITLRANGTRIEGFNLTGSGGCgcgnaGIFID-SSDNIILNNILYKNR-YGIYIEEGATNNTIHSNDFLE 106
                                       55665666666788999***9999996666666699886.9**************.*********999999999998 PP

                                       -SSEEE CS
                        Beta_helix 137 nkgaGi 142
                                       n+ a+ 
  gi|330507431|ref|YP_004383859.1| 107 NRVAAN 112
                                       885544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1310.08
//
Query:       gi|330507432|ref|YP_004383860.1|  [L=439]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-25   88.3   0.1    5.9e-25   87.4   0.1    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family
    3.7e-20   72.4   0.0    7.3e-20   71.4   0.0    1.5  1  DEDD_Tnp_IS110  Transposase
  ------ inclusion threshold ------
      0.038   14.3   1.0      0.088   13.1   0.1    2.0  2  Init_tRNA_PT    Rit1 DUSP-like domain


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.1   9.8e-29   5.9e-25       2      83 ..     271     352 ..     270     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 9.8e-29
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaaira 78 
                                       +++ s+pG+G++ aa+++ae+gd r f+sa+++a+y+G++p+++qS++k r g+i+k G++++Rr+L+e A a++r+
  gi|330507432|ref|YP_004383860.1| 271 KIILSVPGVGFISAATIIAEMGDYRDFPSADKMAKYFGIVPSVYQSAGKLRTGKITKTGSKHMRRILVEVAKAISRT 347
                                       6899***********************************************************************99 PP

                    Transposase_20  79 npelr 83 
                                       ++ +r
  gi|330507432|ref|YP_004383860.1| 348 KKNSR 352
                                       75554 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   1.2e-23   7.3e-20       1     153 [.      31     174 ..      31     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.2e-23
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G D++ d   a++i+++g +l +er++++++gl a+ ++   ++++ + +ve+tg ++++++++ le +++ ++ n
  gi|330507432|ref|YP_004383860.1|  31 CGADIHRDFLIATMISRSGLKL-QERFNMNQDGLLAFRSW-IINHRCQRLAVESTGGFWYPIFTI-LEGHVEFILAN 104
                                       799************9999885.678**************.889****************88876.7899******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdqv 153
                                       ++++++++     ++KtD++D++ IA + +  + ++p++  +++y++Lr++tr+re+lv+ r++ kn++++ L   
  gi|330507432|ref|YP_004383860.1| 105 AYQIRNIE-----HKKTDKLDSERIAIYCL-NNLITPSRIYPKDYRDLRSITRARETLVNARSKIKNQIHQSLSTC 174
                                       *****995.....89***************.****************************************99765 PP

>> Init_tRNA_PT  Rit1 DUSP-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.3   7.5e+03      26      43 ..     155     174 ..     141     184 .. 0.47
   2 ?   13.1   0.1   1.5e-05     0.088      10      80 ..     326     400 ..     318     411 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                      Init_tRNA_PT  26 dfvrkrlsedkk..kkilva 43 
                                       + v++r++ +++  +++  +
  gi|330507432|ref|YP_004383860.1| 155 TLVNARSKIKNQihQSLSTC 174
                                       33333333322222333333 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.5e-05
                      Init_tRNA_PT  10 gKkgsknLrtalpkivdfvrkrlsedkk....kkilvacetGkdlsvgvaLailcklfddakls...eeqsesnitK 79 
                                        K+gsk++r +l ++ ++++++ ++++     ++il+ c + +   v++a  +lc ++   +l    e+ +e+++tK
  gi|330507432|ref|YP_004383860.1| 326 TKTGSKHMRRILVEVAKAISRTKKNSRLmrffQRILARCGKKNIATVALARKVLCIIY---HLLmnhENYQEPEVTK 399
                                       49*****************99966655599**99******999999999888888888...2222235666777777 PP

                      Init_tRNA_PT  80 d 80 
                                       +
  gi|330507432|ref|YP_004383860.1| 400 T 400
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2869.81
//
Query:       gi|330507433|ref|YP_004383861.1|  [L=240]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-53  174.2   4.7    2.7e-09   36.4   0.0    7.1  7  TPR_1         Tetratricopeptide repeat
    2.5e-42  139.6  13.6    3.8e-07   29.7   0.1    7.1  7  TPR_2         Tetratricopeptide repeat
    1.3e-39  133.5   6.3    2.5e-07   30.2   0.0    6.4  6  TPR_11        TPR repeat
    7.2e-38  125.6   0.6      2e-06   27.6   0.0    7.0  7  TPR_8         Tetratricopeptide repeat
    1.8e-30  103.1   3.2    5.8e-07   29.5   0.0    7.5  7  TPR_17        Tetratricopeptide repeat
    1.9e-23   82.8  19.1    9.1e-10   39.0   0.1    4.6  4  TPR_16        Tetratricopeptide repeat
    1.8e-22   78.1  16.6     0.0019   18.8   0.1    6.9  7  TPR_14        Tetratricopeptide repeat
    4.7e-22   78.1  15.3    3.4e-08   33.6   0.2    5.5  4  TPR_12        Tetratricopeptide repeat
    4.9e-18   65.0   6.6    2.5e-07   30.8   0.1    3.9  4  TPR_9         Tetratricopeptide repeat
      7e-16   57.0   6.2       0.05   13.6   0.0    7.1  7  TPR_7         Tetratricopeptide repeat
    3.5e-15   56.3   7.7    1.7e-06   28.4   0.6    4.7  6  TPR_19        Tetratricopeptide repeat
    1.6e-13   50.0  22.9       0.34   10.8   0.0    7.1  7  TPR_10        Tetratricopeptide repeat
    5.7e-11   42.3   3.0        1.5    9.7   0.0    6.8  7  TPR_6         Tetratricopeptide repeat
    2.8e-08   33.9   3.4       0.81    9.8   0.1    5.5  5  DUF3856       Domain of Unknown Function (DUF3856)
    2.2e-07   30.9  22.9      0.089   13.5   0.3    6.9  7  TPR_4         Tetratricopeptide repeat
    1.6e-06   28.6  11.7     0.0005   20.5   1.0    3.4  3  BTAD          Bacterial transcriptional activator domain
    2.6e-06   27.5   1.9     0.0013   18.9   0.1    3.6  4  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    3.6e-05   22.9   0.1     0.0081   15.1   0.0    2.2  2  NARP1         NMDA receptor-regulated protein 1
    6.2e-05   22.4   4.0      0.001   18.3   0.5    3.4  3  TPR_15        Tetratricopeptide repeat
     0.0003   20.8   2.5       0.29   11.2   0.1    4.1  5  MIT           MIT (microtubule interacting and transport) dom
    0.00092   19.4   2.8          1    9.6   0.4    3.3  3  TPR_5         Tetratrico peptide repeat
     0.0012   18.2   0.3       0.16   11.1   0.1    2.3  2  FAT           FAT domain
  ------ inclusion threshold ------
       0.02   14.7   1.3         26    4.5   0.0    3.6  3  TOM20_plant   Plant specific mitochondrial import receptor su
       0.02   14.3   0.1        3.8    6.8   0.0    2.4  2  Coatomer_E    Coatomer epsilon subunit
      0.038   12.9   0.2       0.35    9.7   0.0    2.3  2  DUF5588       Family of unknown function (DUF5588)
      0.049   13.7   0.0        3.5    7.7   0.0    3.1  3  SRP_TPR_like  Putative TPR-like repeat
      0.088   13.2   2.3        7.8    6.9   0.0    3.6  3  TPR_20        Tetratricopeptide repeat
       0.11   12.4   0.9         23    4.9   0.1    2.9  2  Wzy_C_2       Virulence factor membrane-bound polymerase, C-t
        2.5    8.2   7.8         20    5.3   0.1    4.1  4  Exonuc_VII_S  Exonuclease VII small subunit
        3.7    7.7   7.1         31    4.7   0.0    4.0  2  ANAPC5        Anaphase-promoting complex subunit 5


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 !    9.8   0.0    0.0012      0.71       8      26 ..       9      27 ..       8      29 .. 0.91
   2 !   22.1   0.0   1.6e-07   9.3e-05       4      33 ..      38      67 ..      36      68 .. 0.95
   3 !   22.8   0.2   9.2e-08   5.5e-05       1      34 []      69     102 ..      69     102 .. 0.97
   4 !   29.6   0.0   6.7e-10     4e-07       2      32 ..     104     134 ..     103     134 .. 0.96
   5 !   36.4   0.0   4.6e-12   2.7e-09       2      32 ..     141     171 ..     141     173 .. 0.96
   6 !   32.8   0.0   6.5e-11   3.9e-08       4      34 .]     177     207 ..     174     207 .. 0.96
   7 !   15.6   0.1   1.7e-05      0.01       1      23 [.     208     230 ..     208     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                                      HHHHHHTT-HHHHHHHHHH CS
                             TPR_1  8 GnayfklgkydeAleyyek 26
                                      G  ++  g+y+eA+++ e+
  gi|330507433|ref|YP_004383861.1|  9 GESLYLRGDYEEAVAAWER 27
                                      77899***********998 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.6e-07
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  4 lynlGnayfklgkydeAleyyekALelnPn 33
                                      +y +G+a++klg+ +eA+ + ekAL+lnP+
  gi|330507433|ref|YP_004383861.1| 38 HYWKGVALRKLGRNEEAVCALEKALSLNPE 67
                                      899**************************7 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 9.2e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a+ n ++a+ +l +  +Al+ ++kAL ++P+n
  gi|330507433|ref|YP_004383861.1|  69 ADAWRNHAVALNQLDRGADALKSCQKALAIDPDN 102
                                       7999****************************98 PP

  == domain 4  score: 29.6 bits;  conditional E-value: 6.7e-10
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       +++  +G a++ lg+++eA+e y +A+elnP
  gi|330507433|ref|YP_004383861.1| 104 RTWIVRGFALHILGRFEEAVESYARAIELNP 134
                                       78999*************************9 PP

  == domain 5  score: 36.4 bits;  conditional E-value: 4.6e-12
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       +a++n+G+a+ +l +++eA+e ye+A+ ++P
  gi|330507433|ref|YP_004383861.1| 141 RAWNNRGAALDNLHRHEEAIESYEEAIMIDP 171
                                       69****************************9 PP

  == domain 6  score: 32.8 bits;  conditional E-value: 6.5e-11
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++n+G+ +  lg+ + A+ +++kA+e++P++
  gi|330507433|ref|YP_004383861.1| 177 WNNKGVSLSALGRQEAAVVCFRKAIEIDPEY 207
                                       *****************************86 PP

  == domain 7  score: 15.6 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHHHTT-HHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAley 23 
                                       a a++nl++ay++l + +eA+e+
  gi|330507433|ref|YP_004383861.1| 208 AVAWKNLAVAYRSLHRDQEAEEA 230
                                       78*******************97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   9.2e-05     0.055       8      27 ..       9      28 ..       8      30 .. 0.92
   2 !   22.1   0.0   1.7e-07    0.0001       4      33 ..      38      67 ..      38      68 .. 0.97
   3 !   14.0   0.2   7.1e-05     0.042       3      34 .]      71     102 ..      69     102 .. 0.81
   4 !   27.4   0.0   3.6e-09   2.2e-06       2      32 ..     104     134 ..     103     135 .. 0.95
   5 !   29.7   0.1   6.4e-10   3.8e-07       2      32 ..     141     171 ..     140     173 .. 0.95
   6 !   24.1   0.0   4.1e-08   2.4e-05       4      34 .]     177     207 ..     174     207 .. 0.95
   7 !   12.2   0.6   0.00026      0.16       2      27 ..     209     234 ..     208     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.2e-05
                             TPR_2  8 GlayyklgdyeeAleafekA 27
                                      G+++y +gdyeeA++a+e++
  gi|330507433|ref|YP_004383861.1|  9 GESLYLRGDYEEAVAAWERS 28
                                      899**************986 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.7e-07
                             TPR_2  4 lynlGlayyklgdyeeAleafekAleldPn 33
                                      +y+ G a++klg+ eeA+ a+ekAl+l+P+
  gi|330507433|ref|YP_004383861.1| 38 HYWKGVALRKLGRNEEAVCALEKALSLNPE 67
                                      89***************************7 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 7.1e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+ n + a+ +l++ ++Al+ ++kAl++dP+n
  gi|330507433|ref|YP_004383861.1|  71 AWRNHAVALNQLDRGADALKSCQKALAIDPDN 102
                                       5666666666788889**************98 PP

  == domain 4  score: 27.4 bits;  conditional E-value: 3.6e-09
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       + +  +G a+  lg++eeA+e + +A+el+P
  gi|330507433|ref|YP_004383861.1| 104 RTWIVRGFALHILGRFEEAVESYARAIELNP 134
                                       67999*************************9 PP

  == domain 5  score: 29.7 bits;  conditional E-value: 6.4e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       +a++n+G a+ +l ++eeA+e +e+A+ +dP
  gi|330507433|ref|YP_004383861.1| 141 RAWNNRGAALDNLHRHEEAIESYEEAIMIDP 171
                                       69****************************9 PP

  == domain 6  score: 24.1 bits;  conditional E-value: 4.1e-08
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++n G ++ +lg+ e A+ +f+kA+e+dP++
  gi|330507433|ref|YP_004383861.1| 177 WNNKGVSLSALGRQEAAVVCFRKAIEIDPEY 207
                                       9****************************85 PP

  == domain 7  score: 12.2 bits;  conditional E-value: 0.00026
                             TPR_2   2 ealynlGlayyklgdyeeAleafekA 27 
                                        a+ nl+ ay+ l + +eA+ea + A
  gi|330507433|ref|YP_004383861.1| 209 VAWKNLAVAYRSLHRDQEAEEAARIA 234
                                       69*******************98755 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00015     0.087       1      19 [.       9      27 ..       9      30 .. 0.90
   2 !   28.7   0.0   1.3e-09     8e-07       3      38 ..      44      79 ..      42      83 .. 0.91
   3 !   17.3   0.0   4.9e-06    0.0029      12      39 ..      87     114 ..      78     116 .. 0.88
   4 !   25.2   0.0   1.6e-08   9.8e-06       3      38 ..     112     150 ..     110     153 .. 0.82
   5 !   21.8   0.0   1.8e-07   0.00011       9      42 .]     155     188 ..     154     188 .. 0.92
   6 !   30.2   0.0   4.2e-10   2.5e-07       6      38 ..     186     218 ..     183     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                            TPR_11  1 GdayyeqGkyeeAieaYkk 19
                                      G  +y +G+yeeA++a+++
  gi|330507433|ref|YP_004383861.1|  9 GESLYLRGDYEEAVAAWER 27
                                      7789************987 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 1.3e-09
                            TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                                      a++++G++eeA+ a++kAl l+P++a+a+ n ++a+
  gi|330507433|ref|YP_004383861.1| 44 ALRKLGRNEEAVCALEKALSLNPESADAWRNHAVAL 79
                                      89****************************998887 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 4.9e-06
                            TPR_11  12 eAieaYkkAlkldPdnaeayynLGlayy 39 
                                       +A+++ +kAl++dPdn++ +  +G+a++
  gi|330507433|ref|YP_004383861.1|  87 DALKSCQKALAIDPDNPRTWIVRGFALH 114
                                       789999**************99999987 PP

  == domain 4  score: 25.2 bits;  conditional E-value: 1.6e-08
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnae...ayynLGlay 38 
                                       a++ +G++eeA+e+Y +A++l+P  ++   a++n+G+a+
  gi|330507433|ref|YP_004383861.1| 112 ALHILGRFEEAVESYARAIELNPLGPDgrrAWNNRGAAL 150
                                       7899******************97775444788888775 PP

  == domain 5  score: 21.8 bits;  conditional E-value: 1.8e-07
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       + eeAie+Y++A+ +dP +   ++n G+ + ++G
  gi|330507433|ref|YP_004383861.1| 155 RHEEAIESYEEAIMIDPFDIYPWNNKGVSLSALG 188
                                       579************************9988776 PP

  == domain 6  score: 30.2 bits;  conditional E-value: 4.2e-10
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       ++G+ e+A+ +++kA+++dP++a a+ nL++ay
  gi|330507433|ref|YP_004383861.1| 186 ALGRQEAAVVCFRKAIEIDPEYAVAWKNLAVAY 218
                                       68******************************9 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.26   1.5e+02      14      23 ..      15      24 ..       8      29 .. 0.81
   2 !   22.4   0.0   1.5e-07   9.2e-05       5      33 ..      39      67 ..      37      68 .. 0.95
   3 !   10.1   0.0    0.0014      0.81       1      34 []      69     102 ..      69     102 .. 0.91
   4 !   23.0   0.0   9.5e-08   5.7e-05       2      32 ..     104     134 ..     103     134 .. 0.95
   5 !   27.4   0.0   3.6e-09   2.2e-06       2      33 ..     141     172 ..     141     173 .. 0.96
   6 !   27.6   0.0   3.3e-09     2e-06       4      33 ..     177     206 ..     174     207 .. 0.96
   7 ?    3.2   0.0      0.22   1.3e+02       3      23 ..     210     230 ..     208     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.26
                                      TT-HHHHHHH CS
                             TPR_8 14 lgdyeeAkey 23
                                       gdyeeA+++
  gi|330507433|ref|YP_004383861.1| 15 RGDYEEAVAA 24
                                      59*****997 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.5e-07
                                      HHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  5 ynlgsiylklgdyeeAkeyyekaleldpd 33
                                      y++g +++klg+ eeA+ ++ekal+l+p+
  gi|330507433|ref|YP_004383861.1| 39 YWKGVALRKLGRNEEAVCALEKALSLNPE 67
                                      89**************************7 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0014
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+a+ n + ++ +l +   A ++++kal +dpdn
  gi|330507433|ref|YP_004383861.1|  69 ADAWRNHAVALNQLDRGADALKSCQKALAIDPDN 102
                                       5678889999999*******************97 PP

  == domain 4  score: 23.0 bits;  conditional E-value: 9.5e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       + +   g +++ lg++eeA+e+y +a+el+p
  gi|330507433|ref|YP_004383861.1| 104 RTWIVRGFALHILGRFEEAVESYARAIELNP 134
                                       789999************************9 PP

  == domain 5  score: 27.4 bits;  conditional E-value: 3.6e-09
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a++n g ++++l ++eeA+e+ye+a+ +dp 
  gi|330507433|ref|YP_004383861.1| 141 RAWNNRGAALDNLHRHEEAIESYEEAIMIDPF 172
                                       79****************************96 PP

  == domain 6  score: 27.6 bits;  conditional E-value: 3.3e-09
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++n+g  ++ lg+ e+A+ +++ka+e+dp+
  gi|330507433|ref|YP_004383861.1| 177 WNNKGVSLSALGRQEAAVVCFRKAIEIDPE 206
                                       9****************************8 PP

  == domain 7  score: 3.2 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHTT-HHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkey 23 
                                       a+ nl+ +y++l + +eA+e+
  gi|330507433|ref|YP_004383861.1| 210 AWKNLAVAYRSLHRDQEAEEA 230
                                       5669**************998 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.6   9.8e+02      21      33 ..      10      22 ..       9      23 .. 0.81
   2 ?    5.0   0.0     0.061        36      14      32 ..      36      54 ..      33      55 .. 0.91
   3 !   13.3   0.2   0.00014     0.085       2      26 ..      58      82 ..      57      90 .. 0.83
   4 !   20.7   0.0   6.1e-07   0.00037       2      34 .]      92     124 ..      91     124 .. 0.96
   5 !   10.8   0.2   0.00086      0.51       2      34 .]     126     161 ..     125     161 .. 0.80
   6 !   15.0   0.0   4.1e-05     0.024       2      32 ..     163     193 ..     162     194 .. 0.95
   7 !   29.5   0.0   9.6e-10   5.8e-07       1      34 []     196     229 ..     196     229 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.6
                            TPR_17 21 elllknGdlmtAr 33
                                      e l+ +Gd+++A+
  gi|330507433|ref|YP_004383861.1| 10 ESLYLRGDYEEAV 22
                                      678999****996 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.061
                            TPR_17 14 daynnLAelllknGdlmtA 32
                                      ++++ ++++l+k+G+ ++A
  gi|330507433|ref|YP_004383861.1| 36 EHHYWKGVALRKLGRNEEA 54
                                      789*************999 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 0.00014
                            TPR_17  2 ylkaleldPnnadaynnLAelllkn 26
                                      ++kal l+P +ada+ n A++l ++
  gi|330507433|ref|YP_004383861.1| 58 LEKALSLNPESADAWRNHAVALNQL 82
                                      69***************99888765 PP

  == domain 4  score: 20.7 bits;  conditional E-value: 6.1e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       ++kal++dP+n+  +  ++ +l+ +G++++A++
  gi|330507433|ref|YP_004383861.1|  92 CQKALAIDPDNPRTWIVRGFALHILGRFEEAVE 124
                                       79****************************975 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.00086
                            TPR_17   2 ylkaleld...PnnadaynnLAelllknGdlmtArq 34 
                                       y +a+el+   P+   a+nn++ +l +++++++A++
  gi|330507433|ref|YP_004383861.1| 126 YARAIELNplgPDGRRAWNNRGAALDNLHRHEEAIE 161
                                       77888888444444669*****************86 PP

  == domain 6  score: 15.0 bits;  conditional E-value: 4.1e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       y++a+ +dP + +++nn+++ l+ +G+ + A
  gi|330507433|ref|YP_004383861.1| 163 YEEAIMIDPFDIYPWNNKGVSLSALGRQEAA 193
                                       99*************************9988 PP

  == domain 7  score: 29.5 bits;  conditional E-value: 9.6e-10
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +++ka+e+dP +a+a+ nLA++++++++ ++A++
  gi|330507433|ref|YP_004383861.1| 196 CFRKAIEIDPEYAVAWKNLAVAYRSLHRDQEAEE 229
                                       79******************************86 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.7   2.1e-07   0.00013       6      59 ..      11      61 ..       7      62 .. 0.89
   2 !   31.1   1.3   4.5e-10   2.7e-07       4      68 .]      42     103 ..      39     103 .. 0.97
   3 !   39.0   0.1   1.5e-12   9.1e-10      11      67 ..     117     173 ..     116     174 .. 0.95
   4 !   11.5   2.8   0.00062      0.37       6      62 ..     183     236 ..     178     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.1e-07
                            TPR_16  6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyra 59
                                      +++ +gdy++A+aa+e+  k      +  e ++++g+a+ ++gr +eA+ al +a
  gi|330507433|ref|YP_004383861.1| 11 SLYLRGDYEEAVAAWERSEKGT----EGFEHHYWKGVALRKLGRNEEAVcALEKA 61
                                      56668************99999....599********************888765 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 4.5e-10
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       + a++++g+ ++A+ ale al ++   P+ a+A+ + ++a+ ++ r a+A+  +++al+ +pd+p
  gi|330507433|ref|YP_004383861.1|  42 GVALRKLGRNEEAVCALEKALSLN---PESADAWRNHAVALNQLDRGADALKSCQKALAIDPDNP 103
                                       56899*******************...************************************98 PP

  == domain 3  score: 39.0 bits;  conditional E-value: 1.5e-12
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       g++++A++ + +a++++p  Pd ++A++++g a+  + r++eA++ y++a+  +p++
  gi|330507433|ref|YP_004383861.1| 117 GRFEEAVESYARAIELNPLGPDGRRAWNNRGAALDNLHRHEEAIESYEEAIMIDPFD 173
                                       9************************************************99777765 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00062
                            TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       ++ ++g+ ++A+  ++ a++ d   P+ a A+ +l++a+  + r +eA+++ r a +
  gi|330507433|ref|YP_004383861.1| 183 SLSALGRQEAAVVCFRKAIEID---PEYAVAWKNLAVAYRSLHRDQEAEEAARIARD 236
                                       56677888999999********...************************99998865 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.16        95      10      27 ..      11      28 ..       9      34 .. 0.83
   2 !   17.4   0.2   9.2e-06    0.0055       8      42 ..      42      76 ..      35      78 .. 0.88
   3 !   18.0   0.0   6.2e-06    0.0037      10      42 ..      78     110 ..      75     112 .. 0.89
   4 !   14.4   0.1   8.6e-05     0.051       9      33 ..     111     135 ..     108     143 .. 0.80
   5 !   12.7   0.1    0.0003      0.18       2      32 ..     141     171 ..     140     179 .. 0.90
   6 !   18.8   0.1   3.3e-06    0.0019      11      43 ..     184     216 ..     180     217 .. 0.93
   7 ?    2.0   0.7      0.81   4.8e+02       7      28 ..     214     235 ..     214     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.16
                            TPR_14 10 allalGdpdeAiallrra 27
                                       l+ +Gd++eA+a+ +r 
  gi|330507433|ref|YP_004383861.1| 11 SLYLRGDYEEAVAAWERS 28
                                      67789*********9997 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 9.2e-06
                            TPR_14  8 aeallalGdpdeAiallrralalaPddaeawllla 42
                                      + al+ lG+ +eA+ +l++al+l+P++a+aw+  a
  gi|330507433|ref|YP_004383861.1| 42 GVALRKLGRNEEAVCALEKALSLNPESADAWRNHA 76
                                      67999**************************9765 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 6.2e-06
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawllla 42 
                                       al +l++ ++A++ +++ala +Pd++++w+  +
  gi|330507433|ref|YP_004383861.1|  78 ALNQLDRGADALKSCQKALAIDPDNPRTWIVRG 110
                                       788999999********************9876 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 8.6e-05
                            TPR_14   9 eallalGdpdeAiallrralalaPd 33 
                                        al  lG+++eA++ + ra++l+P 
  gi|330507433|ref|YP_004383861.1| 111 FALHILGRFEEAVESYARAIELNPL 135
                                       57889****************9984 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 0.0003
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaP 32 
                                       +a+  +++al +l +++eAi+ +++a+  +P
  gi|330507433|ref|YP_004383861.1| 141 RAWNNRGAALDNLHRHEEAIESYEEAIMIDP 171
                                       688889********************99888 PP

  == domain 6  score: 18.8 bits;  conditional E-value: 3.3e-06
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawlllaq 43 
                                       l alG+ ++A+ ++r+a++ +P+ a+aw  la 
  gi|330507433|ref|YP_004383861.1| 184 LSALGRQEAAVVCFRKAIEIDPEYAVAWKNLAV 216
                                       789***************************995 PP

  == domain 7  score: 2.0 bits;  conditional E-value: 0.81
                            TPR_14   7 laeallalGdpdeAiallrral 28 
                                       la a++ l + +eA++++r a 
  gi|330507433|ref|YP_004383861.1| 214 LAVAYRSLHRDQEAEEAARIAR 235
                                       5778888888888888887764 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.7   8.4e-06     0.005      10      66 ..       9      63 ..       6      67 .. 0.73
   2 !   27.9   0.8   3.5e-09   2.1e-06       2      74 ..      68     132 ..      67     133 .. 0.94
   3 !   33.6   0.2   5.7e-11   3.4e-08       8      74 ..     108     169 ..     101     171 .. 0.90
   4 !   18.8   0.3   2.4e-06    0.0014       6      69 ..     177     232 ..     176     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.4e-06
                            TPR_12 10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAle 66
                                      ++ l+ +g+y+eA +  e++    +    ++h++   +lr Lgr  +a   +e+Al+
  gi|330507433|ref|YP_004383861.1|  9 GESLYLRGDYEEAVAAWERSEKGTEGF--EHHYWKGVALRKLGRNEEAVCALEKALS 63
                                      778899999999999999999999887..8899986666666665555555555554 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 3.5e-09
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        a a++n a++l++l r ++Al+ ++kal+i      pd+p    t +  g +++ lgr+eeA+e + +a+++
  gi|330507433|ref|YP_004383861.1|  68 SADAWRNHAVALNQLDRGADALKSCQKALAID-----PDNPR---TWIVRGFALHILGRFEEAVESYARAIEL 132
                                       588999**************************.....**966...7************************996 PP

  == domain 3  score: 33.6 bits;  conditional E-value: 5.7e-11
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        ++ +l+ lgr++eA e + +a+e+      p  p+  ++ +n g +++ l r+eeA+e +eea+ i
  gi|330507433|ref|YP_004383861.1| 108 VRGFALHILGRFEEAVESYARAIELN-----PLGPDGRRAWNNRGAALDNLHRHEEAIESYEEAIMI 169
                                       57999*********************.....6677789**************************977 PP

  == domain 4  score: 18.8 bits;  conditional E-value: 2.4e-06
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelle 69 
                                       +nn ++ l +lgr + A  +++ka+ei      p+   +a +  nL+ +yr l r +eA+e+ +
  gi|330507433|ref|YP_004383861.1| 177 WNNKGVSLSALGRQEAAVVCFRKAIEID-----PE---YAVAWKNLAVAYRSLHRDQEAEEAAR 232
                                       6899************************.....87...5*********************9875 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       5.5   3.3e+03      40      51 ..      13      24 ..       9      27 .. 0.70
   2 !   26.6   0.5   7.9e-09   4.7e-06       9      61 ..      49     101 ..      41     102 .. 0.94
   3 !   30.8   0.1   4.1e-10   2.5e-07      10      66 ..      84     140 ..      81     144 .. 0.91
   4 !   19.5   0.0   1.3e-06    0.0008       9      62 ..     154     207 ..     147     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.5
                             TPR_9 40 aqlGclsaAlad 51
                                      + +G++++A+a+
  gi|330507433|ref|YP_004383861.1| 13 YLRGDYEEAVAA 24
                                      667888888876 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 7.9e-09
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                        ++e+a +++e  l l+P++++ +r  +++l ql++ + Al+  + +la++pd
  gi|330507433|ref|YP_004383861.1|  49 GRNEEAVCALEKALSLNPESADAWRNHAVALNQLDRGADALKSCQKALAIDPD 101
                                       689*************************************************8 PP

  == domain 3  score: 30.8 bits;  conditional E-value: 4.1e-10
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                                       + + al+ ++  l+++Pd p+ +  RG++l+ lG++++A++   ++++l+p  pd +
  gi|330507433|ref|YP_004383861.1|  84 RGADALKSCQKALAIDPDNPRTWIVRGFALHILGRFEEAVESYARAIELNPLGPDGR 140
                                       5578***********************************************777755 PP

  == domain 4  score: 19.5 bits;  conditional E-value: 1.3e-06
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       +++e+a++ +e  ++++P d++ +   G+ l  lG+ +aA+ ++  +++++p+ 
  gi|330507433|ref|YP_004383861.1| 154 HRHEEAIESYEEAIMIDPFDIYPWNNKGVSLSALGRQEAAVVCFRKAIEIDPEY 207
                                       689*************************************************54 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.17     1e+02       9      20 ..      13      23 ..      10      28 .. 0.77
   2 ?    6.4   0.0     0.017        10       6      32 ..      42      66 ..      41      70 .. 0.82
   3 ?    2.7   0.0      0.27   1.6e+02       7      31 ..      77     101 ..      71     104 .. 0.72
   4 !   10.7   0.0   0.00075      0.45      12      34 ..     116     136 ..     112     138 .. 0.87
   5 !   13.6   0.0   8.4e-05      0.05       1      34 [.     142     173 ..     142     175 .. 0.92
   6 !    8.3   0.0    0.0043       2.6       2      31 ..     177     204 ..     177     207 .. 0.84
   7 !    8.0   0.2    0.0052       3.1       1      20 [.     210     229 ..     210     233 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.17
                             TPR_7  9 ysrlGdyeeAie 20
                                      y r GdyeeA+ 
  gi|330507433|ref|YP_004383861.1| 13 YLR-GDYEEAVA 23
                                      555.******96 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.017
                             TPR_7  6 arlysrlGdyeeAielyeqsLaltkdp 32
                                      +++ ++lG+ eeA+  +e+  al   p
  gi|330507433|ref|YP_004383861.1| 42 GVALRKLGRNEEAVCALEK--ALSLNP 66
                                      7899**************9..665555 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.27
                             TPR_7   7 rlysrlGdyeeAielyeqsLaltkd 31 
                                       ++  +l + ++A++ ++++La++ d
  gi|330507433|ref|YP_004383861.1|  77 VALNQLDRGADALKSCQKALAIDPD 101
                                       55566777789*******6666655 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00075
                             TPR_7  12 lGdyeeAielyeqsLaltkdped 34 
                                       lG++eeA+e y +  a++  p++
  gi|330507433|ref|YP_004383861.1| 116 LGRFEEAVESYAR--AIELNPLG 136
                                       7************..88888776 PP

  == domain 5  score: 13.6 bits;  conditional E-value: 8.4e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       a++n + +  +l ++eeAie ye+  a+  dp+d
  gi|330507433|ref|YP_004383861.1| 142 AWNNRGAALDNLHRHEEAIESYEE--AIMIDPFD 173
                                       78999*******************..99999987 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0043
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       ++n ++  s+lG+ e A+ ++++  a++ d
  gi|330507433|ref|YP_004383861.1| 177 WNNKGVSLSALGRQEAAVVCFRK--AIEID 204
                                       5899999****************..55544 PP

  == domain 7  score: 8.0 bits;  conditional E-value: 0.0052
                             TPR_7   1 aLlnLarlysrlGdyeeAie 20 
                                       a+ nLa++y++l + +eA+e
  gi|330507433|ref|YP_004383861.1| 210 AWKNLAVAYRSLHRDQEAEE 229
                                       689********999999987 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.17        99       2      44 ..      13      54 ..      12      55 .. 0.76
   2 !   28.4   0.6   2.9e-09   1.7e-06       4      60 ..      48     104 ..      45     106 .. 0.94
   3 !   21.2   0.0   5.3e-07   0.00032       8      59 ..      86     137 ..      83     144 .. 0.91
   4 !    7.6   0.0    0.0089       5.3       5      56 ..     117     171 ..     113     177 .. 0.74
   5 ?    2.8   0.0      0.28   1.7e+02       6      45 ..     155     194 ..     153     198 .. 0.79
   6 !   18.0   0.3     5e-06     0.003       5      47 ..     188     230 ..     184     235 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.17
                            TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeA 44
                                      + +gdy+eA+a+ e+  ++  +  e  ++   al +lg+ +eA
  gi|330507433|ref|YP_004383861.1| 13 YLRGDYEEAVAAWERS-EKGTEGFEHHYWKGVALRKLGRNEEA 54
                                      6689999999999995.66666777777778888888888887 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 2.9e-09
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                        g+ +eA+ +le+al+ +p++a+a+ + A al +l + ++A + ++++++ dpd++r
  gi|330507433|ref|YP_004383861.1|  48 LGRNEEAVCALEKALSLNPESADAWRNHAVALNQLDRGADALKSCQKALAIDPDNPR 104
                                       588899************************************************987 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 5.3e-07
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                       a+Al+  ++al+ dp+n++ ++    al  lg+++eA +  +++ e +p  +
  gi|330507433|ref|YP_004383861.1|  86 ADALKSCQKALAIDPDNPRTWIVRGFALHILGRFEEAVESYARAIELNPLGP 137
                                       89******************************************99999755 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0089
                            TPR_19   5 gdyaeAlalleqalqedpk...naearllLAeallalgqldeAealLdalpeedp 56 
                                       g+++eA++ +++a++ +p      +a+ +   al +l + +eA++  +++   dp
  gi|330507433|ref|YP_004383861.1| 117 GRFEEAVESYARAIELNPLgpdGRRAWNNRGAALDNLHRHEEAIESYEEAIMIDP 171
                                       8999999999999999665222555555778999999999999888877766665 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.28
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAe 45 
                                       +++eA++ +e+a+  dp + + + +    l alg+ ++A 
  gi|330507433|ref|YP_004383861.1| 155 RHEEAIESYEEAIMIDPFDIYPWNNKGVSLSALGRQEAAV 194
                                       689*********9999988777777777777777777765 PP

  == domain 6  score: 18.0 bits;  conditional E-value: 5e-06
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47 
                                       g+ ++A+  +++a++ dp++a a+ +LA a+ +l + +eAe++
  gi|330507433|ref|YP_004383861.1| 188 GRQEAAVVCFRKAIEIDPEYAVAWKNLAVAYRSLHRDQEAEEA 230
                                       667899999*******************************986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.022        13      12      27 ..      12      27 ..       9      28 .. 0.75
   2 !    7.6   0.0     0.006       3.6       9      30 ..      42      63 ..      41      65 .. 0.92
   3 !    7.7   0.1    0.0055       3.3       9      31 ..      76      98 ..      73      98 .. 0.94
   4 !    9.0   0.1    0.0021       1.2       9      31 ..     110     132 ..     109     133 .. 0.91
   5 !    9.9   0.9    0.0011      0.66       6      29 ..     144     167 ..     141     167 .. 0.96
   6 !   10.8   0.0   0.00057      0.34       6      31 ..     178     203 ..     178     203 .. 0.96
   7 !   10.3   0.4   0.00084       0.5       7      25 ..     213     231 ..     213     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.022
                            TPR_10 12 lrqrgrydeAeallee 27
                                      l+ rg+y+eA+a  e+
  gi|330507433|ref|YP_004383861.1| 12 LYLRGDYEEAVAAWER 27
                                      7788999999887776 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.006
                            TPR_10  9 analrqrgrydeAealleeala 30
                                      ++alr++gr +eA+  le+al+
  gi|330507433|ref|YP_004383861.1| 42 GVALRKLGRNEEAVCALEKALS 63
                                      799***********999*9997 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0055
                            TPR_10  9 analrqrgrydeAealleealai 31
                                      a+al q+ r+++A++ +++alai
  gi|330507433|ref|YP_004383861.1| 76 AVALNQLDRGADALKSCQKALAI 98
                                      899******************97 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0021
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al+ +gr++eA++ + +a+++
  gi|330507433|ref|YP_004383861.1| 110 GFALHILGRFEEAVESYARAIEL 132
                                       678999**************985 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.0011
                            TPR_10   6 nNLanalrqrgrydeAealleeal 29 
                                       nN ++al ++ r++eA + +eea+
  gi|330507433|ref|YP_004383861.1| 144 NNRGAALDNLHRHEEAIESYEEAI 167
                                       9*********************97 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.00057
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       nN ++ l+++gr ++A+  +++a++i
  gi|330507433|ref|YP_004383861.1| 178 NNKGVSLSALGRQEAAVVCFRKAIEI 203
                                       899*********************97 PP

  == domain 7  score: 10.3 bits;  conditional E-value: 0.00084
                            TPR_10   7 NLanalrqrgrydeAeall 25 
                                       NLa+a+r++ r +eAe+ +
  gi|330507433|ref|YP_004383861.1| 213 NLAVAYRSLHRDQEAEEAA 231
                                       9***************965 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0072       4.3       7      25 ..       9      27 ..       8      27 .. 0.89
   2 !    9.7   0.0    0.0024       1.5       4      33 .]      39      68 ..      38      68 .. 0.95
   3 ?    0.7   0.0       1.7     1e+03       7      32 ..      76     101 ..      70     102 .. 0.76
   4 ?    6.1   0.0     0.033        19      13      31 ..     116     134 ..     110     135 .. 0.87
   5 ?    1.6   0.0      0.89   5.3e+02      15      27 ..     155     167 ..     145     167 .. 0.74
   6 ?    6.3   0.0     0.029        17       7      32 ..     181     206 ..     179     207 .. 0.89
   7 ?    2.3   0.1      0.52   3.1e+02       6      25 ..     214     236 ..     213     238 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0072
                                      HHHHHHHHHHHHHHHHHHH CS
                             TPR_6  7 alsyrklgdtdkAlealer 25
                                      ++s++  gd+++A++a+er
  gi|330507433|ref|YP_004383861.1|  9 GESLYLRGDYEEAVAAWER 27
                                      78999988********997 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0024
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6  4 yklalsyrklgdtdkAlealerlikeYPdS 33
                                      y+ + ++rklg+ ++A+ ale+ ++  P+S
  gi|330507433|ref|YP_004383861.1| 39 YWKGVALRKLGRNEEAVCALEKALSLNPES 68
                                      999******99***************9998 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       a ++ +l++ ++Al+  ++ +   Pd
  gi|330507433|ref|YP_004383861.1|  76 AVALNQLDRGADALKSCQKALAIDPD 101
                                       66666777788999999999999888 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHHHHHHH-T CS
                             TPR_6  13 lgdtdkAlealerlikeYP 31 
                                       lg+ ++A+e + r i+  P
  gi|330507433|ref|YP_004383861.1| 116 LGRFEEAVESYARAIELNP 134
                                       579************9887 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.89
                                       HHHHHHHHHHHHH CS
                             TPR_6  15 dtdkAlealerli 27 
                                       ++++A+e +e+ i
  gi|330507433|ref|YP_004383861.1| 155 RHEEAIESYEEAI 167
                                       789******9876 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + s+ +lg+ ++A+  +++ i+  P+
  gi|330507433|ref|YP_004383861.1| 181 GVSLSALGRQEAAVVCFRKAIEIDPE 206
                                       77888999*************99885 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.52
                                       HHHHHHHH...HHHHHHHHHHHH CS
                             TPR_6   6 lalsyrkl...gdtdkAlealer 25 
                                       la +yr+l   +++++A ++ ++
  gi|330507433|ref|YP_004383861.1| 214 LAVAYRSLhrdQEAEEAARIARD 236
                                       88999987666677788777766 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.021        12     104     127 ..      39      62 ..      26      70 .. 0.80
   2 ?    3.1   0.0      0.16        94     105     126 ..      74      95 ..      68     100 .. 0.83
   3 !    8.4   0.1    0.0037       2.2      90     129 ..      97     132 ..      76     135 .. 0.72
   4 !    9.8   0.1    0.0014      0.81      65     127 ..     113     167 ..     112     171 .. 0.76
   5 !    7.0   0.0    0.0094       5.6     105     129 ..     179     203 ..     174     213 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                                       HHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmag 127
                                       + ++val +lGr++ea+ a+++a 
  gi|330507433|ref|YP_004383861.1|  39 YWKGVALRKLGRNEEAVCALEKAL 62 
                                       668999999999999999988875 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.16
                                       HHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrma 126
                                       ++aval++l r ++alk+ ++a
  gi|330507433|ref|YP_004383861.1|  74 NHAVALNQLDRGADALKSCQKA 95 
                                       7899999999999999998887 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0037
                                       -TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  90 eleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                        ++ d+ + Wi     r+ al+ lGr +ea++++  a e+
  gi|330507433|ref|YP_004383861.1|  97 AIDPDNPRTWI----VRGFALHILGRFEEAVESYARAIEL 132
                                       46677777777....4999***************999886 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0014
                                       HHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  65 laklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       l  lgr++ea+es ++a++  n    l  d+ + W     +r++al++l r++ea+++++ a 
  gi|330507433|ref|YP_004383861.1| 113 LHILGRFEEAVESYARAIEL-N---PLGPDGRRAW----NNRGAALDNLHRHEEAIESYEEAI 167
                                       56688888888888888764.4...3555666666....69******************9875 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.0094
                                       HHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrmagem 129
                                       +++v+l+ lGr++ a+  fr+a e+
  gi|330507433|ref|YP_004383861.1| 179 NKGVSLSALGRQEAAVVCFRKAIEI 203
                                       799*******************997 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.3   0.00015     0.089       8      26 .]       9      27 ..       9      27 .. 0.93
   2 ?    6.0   0.0     0.038        23       3      21 ..      37      55 ..      36      60 .. 0.88
   3 ?    1.7   2.3      0.96   5.8e+02       3      21 ..      71      89 ..      69      89 .. 0.89
   4 !   12.1   0.0   0.00041      0.24       1      22 [.     103     124 ..     103     128 .. 0.89
   5 ?   -1.4   0.1       9.5   5.7e+03       3      20 ..     142     159 ..     141     165 .. 0.70
   6 ?    3.9   0.0      0.18   1.1e+02       8      25 ..     181     198 ..     177     199 .. 0.83
   7 ?    2.7   1.8      0.45   2.7e+02       9      25 ..     219     235 ..     219     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00015
                             TPR_4  8 ArallalGdldeAraller 26
                                      ++ l+++Gd++eA a++er
  gi|330507433|ref|YP_004383861.1|  9 GESLYLRGDYEEAVAAWER 27
                                      6889*************98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.038
                             TPR_4  3 allaLArallalGdldeAr 21
                                      ++++ + al  lG+ +eA 
  gi|330507433|ref|YP_004383861.1| 37 HHYWKGVALRKLGRNEEAV 55
                                      7999*************96 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.96
                             TPR_4  3 allaLArallalGdldeAr 21
                                      a  + A al +l + ++A+
  gi|330507433|ref|YP_004383861.1| 71 AWRNHAVALNQLDRGADAL 89
                                      67899************96 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00041
                             TPR_4   1 arallaLArallalGdldeAra 22 
                                       +r+ ++++ al+ lG+++eA +
  gi|330507433|ref|YP_004383861.1| 103 PRTWIVRGFALHILGRFEEAVE 124
                                       78999***************87 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 9.5
                             TPR_4   3 allaLArallalGdldeA 20 
                                       a  +++ al  l +++eA
  gi|330507433|ref|YP_004383861.1| 142 AWNNRGAALDNLHRHEEA 159
                                       556778888777788888 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.18
                             TPR_4   8 ArallalGdldeAralle 25 
                                       +  l alG+ ++A   ++
  gi|330507433|ref|YP_004383861.1| 181 GVSLSALGRQEAAVVCFR 198
                                       67899********87776 PP

  == domain 7  score: 2.7 bits;  conditional E-value: 0.45
                             TPR_4   9 rallalGdldeAralle 25 
                                       r l++  +++eA+++++
  gi|330507433|ref|YP_004383861.1| 219 RSLHRDQEAEEAARIAR 235
                                       6799999********98 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   1.0   8.3e-07    0.0005      68     121 ..      41      94 ..      14     102 .. 0.86
   2 !    7.7   0.2    0.0077       4.6      74     122 ..     115     166 ..     104     178 .. 0.83
   3 ?    6.8   0.4     0.014       8.5      73     118 ..     185     230 ..     179     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.3e-07
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  68 laeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                          a+ +lGr eea+  le++++++P   +++r +  Al +++r a+AL+  ++
  gi|330507433|ref|YP_004383861.1|  41 KGVALRKLGRNEEAVCALEKALSLNPESADAWRNHAVALNQLDRGADALKSCQK 94 
                                       5557889******************************************97665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0077
                                       HTT-HHHHHHHHHHHHHHSTT-H...HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrE...rlhrqlmrAlarsGrqaeALevYerl 122
                                        lGr eea++ ++++++++Pl     r++    +Al  + r +eA+e Ye++
  gi|330507433|ref|YP_004383861.1| 115 ILGRFEEAVESYARAIELNPLGPdgrRAWNNRGAALDNLHRHEEAIESYEEA 166
                                       589****************997612256677789***************987 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.014
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALev 118
                                       ++lGr e+a+   +++++ +P    +++ l  A++ + r +eA e+
  gi|330507433|ref|YP_004383861.1| 185 SALGRQEAAVVCFRKAIEIDPEYAVAWKNLAVAYRSLHRDQEAEEA 230
                                       689****************************************987 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   2.2e-06    0.0013      30      82 .]       9      61 ..       7      61 .. 0.95
   2 ?    7.1   0.0     0.011       6.4      12      78 ..      58     125 ..      56     129 .. 0.90
   3 ?    0.3   0.0       1.4   8.4e+02      69      81 ..     153     165 ..     147     169 .. 0.70
   4 ?   -1.1   0.1       3.9   2.3e+03      57      76 ..     209     228 ..     182     237 .. 0.48

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.2e-06
                                      HHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
                            ANAPC3 30 AlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLekl 82
                                      +++lyl+g+y++A    +++++  +  + +y ++ +l kL++ eeA+ aLek+
  gi|330507433|ref|YP_004383861.1|  9 GESLYLRGDYEEAVAAWERSEKGTEGFEHHYWKGVALRKLGRNEEAVCALEKA 61
                                      579*****************9999999***********************985 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.011
                                       HHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  12 aerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       +e++l+ ++es+++   +A +l ++ +   A++ ++ka  +++ +++ +++ + +l  L+++eeA+  
  gi|330507433|ref|YP_004383861.1|  58 LEKALSLNPESADAWRNHAVALNQLDRGADALKSCQKAlAIDPDNPRTWIVRGFALHILGRFEEAVES 125
                                       588888889999998889999999999999***********************************876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.4
                                       TT-HHHHHHHH-S CS
                            ANAPC3  69 LkkyeeAiaaLek 81 
                                       L+++eeAi  +e+
  gi|330507433|ref|YP_004383861.1| 153 LHRHEEAIESYEE 165
                                       6777777776665 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3.9
                                       HHHHHHHHHHHHTT-HHHHH CS
                            ANAPC3  57 gcrylfAqcllkLkkyeeAi 76 
                                        ++  +A ++  L++ +eA+
  gi|330507433|ref|YP_004383861.1| 209 VAWKNLAVAYRSLHRDQEAE 228
                                       33333333333344434443 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.4e-05    0.0081      18     131 ..      16     128 ..      11     133 .. 0.83
   2 !    5.7   0.1    0.0099       5.9      41      88 ..     177     224 ..     144     235 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                                       THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHH CS
                             NARP1  18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeealla 94 
                                       g++eeA++  e++ek  ++  + +  k+  l kLgr+eeA  ++e+ l+ npe+ + +++   a++  +  ++al++
  gi|330507433|ref|YP_004383861.1|  16 GDYEEAVAAWERSEK-GTEGFEHHYWKGVALRKLGRNEEAVCALEKALSLNPESADAWRNHAVALNQLDRGADALKS 91 
                                       788889888887765.5788899999**********************************99999655555666766 PP

                                       HHHH..TTTS-TT-SHHHHTHHHH--HHHHHHHHHHHHH CS
                             NARP1  95 lyde..laekyprsdaprRlpLdfleGeeFkelvdkYlr 131
                                       + +   +   +pr+ ++r ++L++l   +F+e+v++Y r
  gi|330507433|ref|YP_004383861.1|  92 CQKAlaIDPDNPRTWIVRGFALHILG--RFEEAVESYAR 128
                                       66651155788************994..89999999976 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0099
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS- CS
                             NARP1  41 ketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklsked 88 
                                        ++k+  l +Lgr+e A   +++ +e  pe    +++l  a +  + d
  gi|330507433|ref|YP_004383861.1| 177 WNNKGVSLSALGRQEAAVVCFRKAIEIDPEYAVAWKNLAVAYRSLHRD 224
                                       357888899999999999999999999999999999998888433322 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.66   3.9e+02      17      50 ..      11      43 ..       7      45 .. 0.78
   2 !   18.3   0.5   1.7e-06     0.001     156     243 ..      45     132 ..      38     143 .. 0.87
   3 ?    1.9   0.1      0.18   1.1e+02     156     178 ..     184     206 ..     149     230 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.66
                            TPR_15 17 llykqgdvkkAlevLkeaaqkaapskdteyWrtl 50
                                       ly +gd+++A ++  e  +k +   +  yW+ +
  gi|330507433|ref|YP_004383861.1| 11 SLYLRGDYEEAVAAW-ERSEKGTEGFEHHYWKGV 43
                                      689999999999999.556777677788999865 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.7e-06
                            TPR_15 156 yrqegqtdaAlrdyreAlalapdsselraallWlliDlgrrae.LrellkawkaraesdasLwgplaaAlllLgrpk 231
                                        r+ g++++A+ ++++Al+l+p+s+++  ++  +l+ l+r a  L++  ka+  +   +++ w + ++Al  Lgr +
  gi|330507433|ref|YP_004383861.1|  45 LRKLGRNEEAVCALEKALSLNPESADAWRNHAVALNQLDRGADaLKSCQKALAID-PDNPRTWIVRGFALHILGRFE 120
                                       6899*******************************99999987566666666544.999****************** PP

                            TPR_15 232 kALeylrkqake 243
                                       +A e + +  + 
  gi|330507433|ref|YP_004383861.1| 121 EAVESYARAIEL 132
                                       **9999887665 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.18
                            TPR_15 156 yrqegqtdaAlrdyreAlalapd 178
                                        ++ g+++aA+ ++r+A++ +p+
  gi|330507433|ref|YP_004383861.1| 184 LSALGRQEAAVVCFRKAIEIDPE 206
                                       45667778888888888777776 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 ?   -1.7   0.0       5.1     3e+03      18      26 ..      16      24 ..      15      28 .. 0.77
   2 ?   -2.2   0.0       7.4   4.4e+03      31      50 ..      55      73 ..      52      91 .. 0.61
   3 ?    5.9   0.0     0.022        13      18      33 ..     117     132 ..     115     133 .. 0.92
   4 !   11.2   0.1   0.00049      0.29      11      31 ..     147     167 ..     144     169 .. 0.89
   5 ?   -0.7   0.0       2.6   1.6e+03      12      32 ..     182     202 ..     179     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.1
                               MIT 18 gnyeeAlel 26
                                      g+yeeA+ +
  gi|330507433|ref|YP_004383861.1| 16 GDYEEAVAA 24
                                      899999865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.4
                               MIT 31 lelLlqalkekneerrellr 50
                                      +  L +al+  n+e+ +++r
  gi|330507433|ref|YP_004383861.1| 55 VCALEKALS-LNPESADAWR 73
                                      555556665.3444444444 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.022
                               MIT  18 gnyeeAlelYkealel 33 
                                       g +eeA+e Y  a+el
  gi|330507433|ref|YP_004383861.1| 117 GRFEEAVESYARAIEL 132
                                       789***********96 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00049
                               MIT  11 AveeDnagnyeeAlelYkeal 31 
                                        + +Dn +  eeA+e Y+ea+
  gi|330507433|ref|YP_004383861.1| 147 GAALDNLHRHEEAIESYEEAI 167
                                       5689****************8 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 2.6
                               MIT  12 veeDnagnyeeAlelYkeale 32 
                                       v +   g  e+A+ ++++a+e
  gi|330507433|ref|YP_004383861.1| 182 VSLSALGRQEAAVVCFRKAIE 202
                                       555566888999999999998 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.4    0.0017         1      47     102 ..      44      97 ..      15     105 .. 0.85
   2 ?    6.8   0.0     0.013       7.5       8      59 ..     110     161 ..     103     173 .. 0.84
   3 ?    1.3   0.0      0.66     4e+02      12      29 ..     185     202 ..     177     233 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0017
                             TPR_5  47 sLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgrereavsivllala 102
                                       +LR lG+ eea+  L++ l+ ++ e  da +   a++L +l+r ++a++   +ala
  gi|330507433|ref|YP_004383861.1|  44 ALRKLGRNEEAVCALEKALSLNP-ESADAWRN-HAVALNQLDRGADALKSCQKALA 97 
                                       79*************99988765.55677765.68999999999999999999987 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.013
                             TPR_5   8 agarDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeeala 59 
                                       + a    G+ ++av+ Y ra++    g   rra     ++L nl + eea++
  gi|330507433|ref|YP_004383861.1| 110 GFALHILGRFEEAVESYARAIELNPLGPDGRRAWNNRGAALDNLHRHEEAIE 161
                                       5566678999999999999999999999999999999999999999999976 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.66
                             TPR_5  12 DstGhedkavplYrraLa 29 
                                          G++++av  +r+a++
  gi|330507433|ref|YP_004383861.1| 185 SALGRQEAAVVCFRKAIE 202
                                       345666666666666654 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.021        13     251     333 ..      41     133 ..      19     135 .. 0.80
   2 !   11.1   0.1   0.00027      0.16     251     306 ..     180     228 ..     177     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.021
                                       CCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHHHHHSSSS................. CS
                               FAT 251 kGewqealqkldwseekieeilqsysaateidpswykawhtwalfnfevvskeeeqkeeee................ 311
                                       kG  +++l++       +ee++ +  +a +++p++++aw + a + ++  +     k+ ++                
  gi|330507433|ref|YP_004383861.1|  41 KGVALRKLGR-------NEEAVCALEKALSLNPESADAWRNHAVALNQLDRGADALKSCQKalaidpdnprtwivrg 110
                                       5666777777.......899999999999999999999999999999888888777666667778888887777777 PP

                                       .S-TCCHHHHCCT..CCHHHHTT CS
                               FAT 312 .pedlqeyvvpavkgflksisls 333
                                          ++    ++av+ + ++i l+
  gi|330507433|ref|YP_004383861.1| 111 fALHILGRFEEAVESYARAIELN 133
                                       76667777788888888888775 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00027
                                       CCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHHHHH CS
                               FAT 251 kGewqealqkldwseekieeilqsysaateidpswykawhtwalfnfevvskeeeq 306
                                       kG  ++al++       +e+++ ++++a eidp+ + aw ++a ++    +++e +
  gi|330507433|ref|YP_004383861.1| 180 KGVSLSALGR-------QEAAVVCFRKAIEIDPEYAVAWKNLAVAYRSLHRDQEAE 228
                                       6666777777.......899**************************9998888655 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 ?    3.2   0.1      0.11        63      52      71 ..      52      71 ..      46     102 .. 0.88
   2 ?    3.5   0.0     0.086        51      51      66 ..     156     171 ..     116     174 .. 0.84
   3 ?    4.5   0.0     0.044        26      97     126 ..     191     220 ..     182     238 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.11
                                      HHHHHHHHHHHHH-TT-HHH CS
                       TOM20_plant 52 qdaiskleeallidPkkhda 71
                                      ++a+  le+al ++P+  da
  gi|330507433|ref|YP_004383861.1| 52 EEAVCALEKALSLNPESADA 71
                                      589999*********99998 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.086
                                       HHHHHHHHHHHHHH-T CS
                       TOM20_plant  51 iqdaiskleeallidP 66 
                                        ++ai  +eea++idP
  gi|330507433|ref|YP_004383861.1| 156 HEEAIESYEEAIMIDP 171
                                       579************9 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHTH CS
                       TOM20_plant  97 ekatqffqqavdedPdndlyrkslelaaka 126
                                       e a  +f++a++ dP+  +  k l +a ++
  gi|330507433|ref|YP_004383861.1| 191 EAAVVCFRKAIEIDPEYAVAWKNLAVAYRS 220
                                       455666666666666666666666665543 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0064       3.8     209     255 ..      43      89 ..      26     103 .. 0.87
   2 ?    5.3   0.0     0.019        11     206     255 ..     179     228 ..     149     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0064
                                       HHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHH CS
                        Coatomer_E 209 vvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevs 255
                                       v+  +lgr eeA   L++aL  +++ +++  N  va ++l++ a++ 
  gi|330507433|ref|YP_004383861.1|  43 VALRKLGRNEEAVCALEKALSLNPESADAWRNHAVALNQLDRGADAL 89 
                                       55557899****************************99999887765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                                       HHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHH CS
                        Coatomer_E 206 gkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevs 255
                                        k v   +lgr e+A    ++a++ d++++ +  Nl va   l +d+e+ 
  gi|330507433|ref|YP_004383861.1| 179 NKGVSLSALGRQEAAVVCFRKAIEIDPEYAVAWKNLAVAYRSLHRDQEAE 228
                                       56666678999*****************************9999998876 PP

>> DUF5588  Family of unknown function (DUF5588)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.42   2.5e+02     141     172 ..      51      82 ..      42     102 .. 0.71
   2 ?    9.7   0.0   0.00058      0.35     135     173 ..     184     222 ..     140     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.42
                           DUF5588 141 lektilclqklislhpfnpwswgklaeaylsl 172
                                        e+++  l+k +sl p +  +w + a a  +l
  gi|330507433|ref|YP_004383861.1|  51 NEEAVCALEKALSLNPESADAWRNHAVALNQL 82 
                                       56777889999999999888888777765444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00058
                           DUF5588 135 csslqnlektilclqklislhpfnpwswgklaeaylslg 173
                                       +s+l   e +++c++k i + p    +w +la ay sl 
  gi|330507433|ref|YP_004383861.1| 184 LSALGRQEAAVVCFRKAIEIDPEYAVAWKNLAVAYRSLH 222
                                       588889999**************************9875 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 ?    3.0   0.0      0.16        96      15      42 ..      36      63 ..      16      73 .. 0.73
   2 ?    7.7   0.0    0.0058       3.5      16      64 ..      71     122 ..      57     131 .. 0.68
   3 ?   -2.2   0.0       6.8     4e+03      28      39 ..     154     165 ..     144     204 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.16
                      SRP_TPR_like 15 elkkfkvvaliklekyeeaLkllkkgsa 42
                                      e + +k val kl++ eea+ +l+k+ +
  gi|330507433|ref|YP_004383861.1| 36 EHHYWKGVALRKLGRNEEAVCALEKALS 63
                                      4445688888888888888888887654 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0058
                      SRP_TPR_like  16 lkkfkvvaliklekyeeaLkllkkgsalsed...vrfEkaYvlYklkkykka 64 
                                         + ++val +l++ ++aLk ++k+ a++ d   +   + ++l  l ++++a
  gi|330507433|ref|YP_004383861.1|  71 AWRNHAVALNQLDRGADALKSCQKALAIDPDnprTWIVRGFALHILGRFEEA 122
                                       345589******************9865433111455666666666666666 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 6.8
                      SRP_TPR_like  28 ekyeeaLkllkk 39 
                                        ++eea++  ++
  gi|330507433|ref|YP_004383861.1| 154 HRHEEAIESYEE 165
                                       555555444333 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.8     0.039        23       6      49 ..      53      96 ..      49     101 .. 0.85
   2 ?    6.9   0.0     0.013       7.8       7      44 ..      88     125 ..      85     134 .. 0.89
   3 ?    0.3   0.1       1.6   9.3e+02      76      83 ..     192     199 ..     153     232 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.039
                            TPR_20  6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleil 49
                                      + + +le+al  np+  da  + A al++  r ++Al+   + l
  gi|330507433|ref|YP_004383861.1| 53 EAVCALEKALSLNPESADAWRNHAVALNQLDRGADALKSCQKAL 96
                                      56779*******************************98765555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.013
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                        l++ ++ala +pd+  + +    al+  gr eeA+e 
  gi|330507433|ref|YP_004383861.1|  88 ALKSCQKALAIDPDNPRTWIVRGFALHILGRFEEAVES 125
                                       67889******************************997 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.6
                            TPR_20  76 plvakyRr 83 
                                       ++v+ +R+
  gi|330507433|ref|YP_004383861.1| 192 AAVVCFRK 199
                                       33333332 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.039        23     134     180 ..      59     106 ..      50     114 .. 0.85
   2 ?    4.9   0.1     0.038        23     134     170 ..     198     235 ..     182     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.039
                           Wzy_C_2 134 rklihlsPepa.vierlilslallGdedeAeqilararalfpeedakw 180
                                       +k++ l Pe a   ++++++l +l++ ++A++  ++a a+ p++  +w
  gi|330507433|ref|YP_004383861.1|  59 EKALSLNPESAdAWRNHAVALNQLDRGADALKSCQKALAIDPDNPRTW 106
                                       677788888653789************************999999999 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.038
                           Wzy_C_2 134 rklihlsPepavi.erlilslallGdedeAeqilarar 170
                                       rk+i+  Pe av  ++l++++  l +++eAe   + ar
  gi|330507433|ref|YP_004383861.1| 198 RKAIEIDPEYAVAwKNLAVAYRSLHRDQEAEEAARIAR 235
                                       7888999998885389**************99888776 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 ?   -1.7   0.1       5.4   3.2e+03      23      32 ..      19      28 ..      18      30 .. 0.65
   2 ?    5.3   0.1     0.033        20      25      43 ..      78      96 ..      77      97 .. 0.90
   3 ?    2.8   0.0      0.21   1.2e+02      23      35 ..     120     132 ..     118     133 .. 0.92
   4 ?    1.9   0.2      0.39   2.3e+02      23      33 ..     157     167 ..     157     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.4
                      Exonuc_VII_S 23 eeslklyeeG 32
                                      ee+++ +e+ 
  gi|330507433|ref|YP_004383861.1| 19 EEAVAAWERS 28
                                      6777777765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.033
                      Exonuc_VII_S 25 slklyeeGvkLlkeCekkL 43
                                      +l++  +G+  lk C+k L
  gi|330507433|ref|YP_004383861.1| 78 ALNQLDRGADALKSCQKAL 96
                                      678899***********98 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.21
                      Exonuc_VII_S  23 eeslklyeeGvkL 35 
                                       ee+++ y ++++L
  gi|330507433|ref|YP_004383861.1| 120 EEAVESYARAIEL 132
                                       99*********98 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.39
                      Exonuc_VII_S  23 eeslklyeeGv 33 
                                       ee+++ yee++
  gi|330507433|ref|YP_004383861.1| 157 EEAIESYEEAI 167
                                       89*******97 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.052        31      53      77 ..      47      71 ..      39      83 .. 0.89
   2 ?    2.0   2.0      0.36   2.2e+02      55      70 ..     154     169 ..     148     237 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.052
                            ANAPC5 53 dfghneeAvkaleeairlArenkDk 77
                                      ++g neeAv ale a +l  e++D 
  gi|330507433|ref|YP_004383861.1| 47 KLGRNEEAVCALEKALSLNPESADA 71
                                      689**************99999985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.36
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                       + +eeA+++ eeai++
  gi|330507433|ref|YP_004383861.1| 154 HRHEEAIESYEEAIMI 169
                                       5566666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1348.11
//
Query:       gi|330507434|ref|YP_004383862.1|  [L=170]
Description: hypothetical protein MCON_1365 [Methanosaeta concilii GP6]
Scores for complete sequence (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  148.8   0.0    1.5e-43  148.7   0.0    1.0  1  NTPase_1        NTPase
    5.3e-07   29.4   0.0    6.5e-07   29.1   0.0    1.2  1  DUF2478         Protein of unknown function (DUF2478)
    2.5e-05   24.3   0.3    4.5e-05   23.4   0.3    1.3  1  RsgA_GTPase     RsgA GTPase
    0.00014   21.0   0.8    0.00034   19.7   0.2    1.8  2  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
     0.0024   17.9   0.3     0.0041   17.2   0.3    1.6  1  MMR_HSR1        50S ribosome-binding GTPase
     0.0027   17.5   0.0     0.0053   16.5   0.0    1.6  1  AAA_24          AAA domain
     0.0099   16.3   0.4      0.013   15.9   0.4    1.6  1  AAA_16          AAA ATPase domain
  ------ inclusion threshold ------
       0.01   16.1   1.0       0.03   14.6   1.0    2.1  1  AAA_22          AAA domain
      0.019   14.9   0.6      0.071   13.0   0.3    1.9  2  NACHT           NACHT domain
      0.019   15.5   0.0      0.036   14.6   0.0    1.3  1  ABC_tran        ABC transporter
      0.028   15.0   0.1      0.057   14.0   0.1    1.6  1  AAA_18          AAA domain
       0.04   14.2   0.1      0.063   13.5   0.1    1.4  1  AAA_28          AAA domain
      0.048   13.6   0.0       0.06   13.3   0.0    1.4  1  Ploopntkinase3  P-loop Nucleotide Kinase3
      0.052   13.1   0.0      0.096   12.2   0.0    1.5  1  FeoB_N          Ferrous iron transport protein B
       0.09   12.4   0.2       0.29   10.7   0.1    1.8  2  cobW            CobW/HypB/UreG, nucleotide-binding domain
      0.096   12.4   1.8       0.59    9.8   1.9    2.1  1  AAA_30          AAA domain
       0.11   12.9   0.6       0.22   12.0   0.6    1.8  1  AAA             ATPase family associated with various cellula
       0.11   11.6   1.3       0.13   11.4   0.3    1.5  2  NB-ARC          NB-ARC domain
       0.12   12.1   0.2       0.23   11.2   0.2    1.4  1  AAA_29          P-loop containing region of AAA domain
       0.13   12.4   0.0       0.22   11.7   0.0    1.4  1  AAA_33          AAA domain
       0.28   11.5   1.9        4.8    7.5   0.7    2.4  2  AAA_19          AAA domain
       0.64    9.8   1.9        1.5    8.5   1.5    1.7  2  ATP_bind_1      Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.7   0.0   1.8e-46   1.5e-43       1     167 [.       4     163 ..       4     164 .. 0.98

  Alignments for each domain:
  == domain 1  score: 148.7 bits;  conditional E-value: 1.8e-46
                                       EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE- CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvvd 77 
                                       ++++TG+pGvGK+Tlv kv++      ++vgG+++++ r ++rr+gF++ dl++g  giLa ++   +p++gky v+
  gi|330507434|ref|YP_004383862.1|   4 RIAVTGSPGVGKSTLVAKVTSGT---KLRVGGVLARDRRYKDRRTGFELLDLSTGMVGILADES-GDGPQLGKYRVH 76 
                                       689*****************998...699***********************************.9*********** PP

                                       HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE CS
                          NTPase_1  78 vesfeelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdvkvfe 154
                                       +++++ ++++a+++al ++d+iv+DE+G+mEl+s++f  ave++++s kp+l+v+h+ ++++l ++ir +  ++v++
  gi|330507434|ref|YP_004383862.1|  77 LDDLDLIGAQAVENAL-GCDLIVVDEVGPMELSSHSFVLAVEKAIASPKPMLVVLHQWSNHRLAKKIRGS--FRVLT 150
                                       **************95.***************************************************98..***** PP

                                       --TTTTTTHHHHH CS
                          NTPase_1 155 vteenrdalleei 167
                                       vt+enrd+l++ei
  gi|330507434|ref|YP_004383862.1| 151 VTRENRDSLADEI 163
                                       ***********99 PP

>> DUF2478  Protein of unknown function (DUF2478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0     8e-10   6.5e-07      20     134 ..      20     134 ..       6     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 8e-10
                           DUF2478  20 aerlraeGlrvaGvvqenaeeaegkkcdmeledlatgeririsqdlgsgsq..gCrLdpeaLaea.aaaveralaeg 93 
                                       a+  + + lrv+Gv+ ++++ + ++++  el dl+tg +  +  + g g q    r++ + L  + a+ave+al  g
  gi|330507434|ref|YP_004383862.1|  20 AKVTSGTKLRVGGVLARDRRYK-DRRTGFELLDLSTGMVGILADESGDGPQlgKYRVHLDDLDLIgAQAVENAL--G 93 
                                       555667789******8888876.5678*******************9998833356777777765256889999..* PP

                           DUF2478  94 adlvivnkFGkqEaeGrGlreeiaaalaagiPvltaVsekl 134
                                       +dl++v   G  E + + +  ++++a+a+  P+l+++++  
  gi|330507434|ref|YP_004383862.1|  94 CDLIVVDEVGPMELSSHSFVLAVEKAIASPKPMLVVLHQWS 134
                                       ***********************************998755 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.3   5.5e-08   4.5e-05     103     157 ..       6      62 ..       3      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.5e-08
                                       EEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTT..EEEES CS
                       RsgA_GTPase 103 vlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaeg..glliD 157
                                       ++ G+ GvGKStL+ ++++ ++l++g v ++++r k   t  ell+l++g  g+l+D
  gi|330507434|ref|YP_004383862.1|   6 AVTGSPGVGKSTLVAKVTSGTKLRVGGVLARDRRYKDRRTGFELLDLSTGmvGILAD 62 
                                       678*******************************************99753355666 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   4.2e-07   0.00034      29      52 ..       2      25 ..       1      46 [. 0.85
   2 ?   -0.8   0.0      0.74   6.1e+02     117     131 ..      89     103 ..      84     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.2e-07
                                      SEEEEEEE-TTSSHHHHHHHHHHH CS
                              MeaB 29 aqvvGltGvPGaGkstlvealgle 52
                                      a ++ +tG+PG+Gkstlv +++  
  gi|330507434|ref|YP_004383862.1|  2 ALRIAVTGSPGVGKSTLVAKVTSG 25
                                      789*****************9864 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.74
                                       HHHTT-SEEEEEEES CS
                              MeaB 117 leaaGfDvvlietvG 131
                                        +a+G D ++++ vG
  gi|330507434|ref|YP_004383862.1|  89 ENALGCDLIVVDEVG 103
                                       5799*******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 !   17.2   0.3     5e-06    0.0041       1      31 [.       4      35 ..       4     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5e-06
                                      EEEEEESTTSSHHHHHHHHHTS.TEEESSSTT CS
                          MMR_HSR1  1 evaivGrpNvGKStLinaltge.kaivsdkpg 31
                                      ++a+ G p vGKStL+ + t   k +v+    
  gi|330507434|ref|YP_004383862.1|  4 RIAVTGSPGVGKSTLVAKVTSGtKLRVGGVLA 35
                                      69****************99764667765554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.4e-06    0.0053       1      74 [.       1     102 [.       1     119 [. 0.62

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.4e-06
                            AAA_24   1 kklkiliyGpsgiGKTtlakel.gpkplfi....................dtekGlksldadkfpdie...swedfl 53 
                                       ++l+i+++G++g+GK+tl+++    + l +                    d+  G+  + ad+  d +   ++   l
  gi|330507434|ref|YP_004383862.1|   1 MALRIAVTGSPGVGKSTLVAKVtSGTKLRVggvlardrrykdrrtgfellDLSTGMVGILADESGDGPqlgKYRVHL 77 
                                       5789****************997333333345555555555555555555555555444444444333333555555 PP

                            AAA_24  54 devvel....aaeladyktlviDti 74 
                                       d+++ +     ++  +++ +v+D +
  gi|330507434|ref|YP_004383862.1|  78 DDLDLIgaqaVENALGCDLIVVDEV 102
                                       5555556666566666777777766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   1.6e-05     0.013      27      51 ..       5      29 ..       2     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekd 51
                                      + ++G +GvGKs+lv ++    + +
  gi|330507434|ref|YP_004383862.1|  5 IAVTGSPGVGKSTLVAKVTSGTKLR 29
                                      679************9998533333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.0   3.7e-05      0.03       8      29 ..       5      26 ..       2     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleql 29
                                      ++vtG +G+GK+tl++++++  
  gi|330507434|ref|YP_004383862.1|  5 IAVTGSPGVGKSTLVAKVTSGT 26
                                      79***************99876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   8.8e-05     0.071       3      23 ..       5      25 ..       3      31 .. 0.87
   2 ?   -0.1   0.0      0.93   7.6e+02     100     139 ..     121     163 ..      77     168 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.8e-05
                                      EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklala 23
                                      ++++G +G+GK+tL++k+ + 
  gi|330507434|ref|YP_004383862.1|  5 IAVTGSPGVGKSTLVAKVTSG 25
                                      899**************9875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.93
                                       .........HHHHHCTTT...TT--EEEEEEECCCHHHHCTTS CS
                             NACHT 100 kekqpvrtlLselirkkl...lpeasllltvrpralrdleeql 139
                                       + ++p+ ++L+++ +  l   ++++  +ltv+ +++  l+  +
  gi|330507434|ref|YP_004383862.1| 121 ASPKPMLVVLHQWSNHRLakkIRGSFRVLTVTRENRDSLADEI 163
                                       4556666666666555441114556667777766666665555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.4e-05     0.036      13      51 ..       4      42 ..       2      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.4e-05
                                      EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51
                                      ++a++G+ G GKStL++ ++  +k   G +l +++  k+
  gi|330507434|ref|YP_004383862.1|  4 RIAVTGSPGVGKSTLVAKVTSGTKLRVGGVLARDRRYKD 42
                                      6899**************999999999999888777776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   7.1e-05     0.057       1      18 [.       5      22 ..       5      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.1e-05
                            AAA_18  1 IlltGtpGvGKttlakeL 18
                                      I++tG pGvGK+tl   +
  gi|330507434|ref|YP_004383862.1|  5 IAVTGSPGVGKSTLVAKV 22
                                      89***********98766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   7.7e-05     0.063       1      20 [.       4      23 ..       4      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-05
                            AAA_28  1 kivitGgestGKTtlleaLa 20
                                      +i++tG ++ GK+tl+++ +
  gi|330507434|ref|YP_004383862.1|  4 RIAVTGSPGVGKSTLVAKVT 23
                                      79*************99876 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.4e-05      0.06       6      29 ..       5      28 ..       1      91 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.4e-05
                    Ploopntkinase3  6 iylvGqPGaGkstlmaeltkgfdr 29
                                      i + G+PG Gkstl+a++t+g + 
  gi|330507434|ref|YP_004383862.1|  5 IAVTGSPGVGKSTLVAKVTSGTKL 28
                                      5688***************99765 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012     0.096       2      28 ..       4      31 ..       3      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                      EEEEEESTTSSHHHHHHHHH.TTSEEEE CS
                            FeoB_N  2 tvalvGnpnvGkttlfnalt.gakqkvg 28
                                      ++a+ G p vGk+tl+ ++t g+k +vg
  gi|330507434|ref|YP_004383862.1|  4 RIAVTGSPGVGKSTLVAKVTsGTKLRVG 31
                                      699**************99846777887 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00036      0.29       3      24 ..       5      26 ..       3      44 .. 0.81
   2 ?   -0.7   0.0       1.1   9.1e+02      93      99 ..     120     126 ..      79     166 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                                      EEEEESTTCCHHHHHHHHHCT- CS
                              cobW  3 tvltGflGsGKTtLlnhllenr 24
                                      + +tG++G GK+tL+ ++++ +
  gi|330507434|ref|YP_004383862.1|  5 IAVTGSPGVGKSTLVAKVTSGT 26
                                      679*************998554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                                       TTTHHHH CS
                              cobW  93 laePapv 99 
                                       +a+P+p+
  gi|330507434|ref|YP_004383862.1| 120 IASPKPM 126
                                       4444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.9   0.00072      0.59      22     100 ..       6     105 ..       2     121 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00072
                            AAA_30  22 vltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLa..eelgieastiakllkrlk.............. 81 
                                       ++tG +G GK+t++++++   + + gg   +lA   +  ++ +  e l++ +  +  l ++ +              
  gi|330507434|ref|YP_004383862.1|   6 AVTGSPGVGKSTLVAKVTSGTKLRvGG---VLARDRRYKDRRTgfELLDLSTGMVGILADESGdgpqlgkyrvhldd 79 
                                       689*************99888866552...44444444444221211122222222222222233333333334445 PP

                            AAA_30  82 ......grarlepg.tllivDEagmv 100
                                             ++++ + g +l++vDE+g +
  gi|330507434|ref|YP_004383862.1|  80 ldligaQAVENALGcDLIVVDEVGPM 105
                                       66666644445555678888887766 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   0.6   0.00027      0.22       3      25 ..       7      29 ..       5     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                                      EESSTTSSHHHHHHHHHHHHTHE CS
                               AAA  3 lyGppGtGKTllakavakelgve 25
                                      ++G pG+GK++l+  v + ++ +
  gi|330507434|ref|YP_004383862.1|  7 VTGSPGVGKSTLVAKVTSGTKLR 29
                                      79***********9999887655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00016      0.13      23      43 ..       5      25 ..       2      31 .. 0.87
   2 ?   -2.6   0.0       3.1   2.5e+03      64     100 ..     134     167 ..     126     169 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                      EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 23 valvGmgGvGKttlakqilnk 43
                                      +a+ G +GvGK+tl++++ + 
  gi|330507434|ref|YP_004383862.1|  5 IAVTGSPGVGKSTLVAKVTSG 25
                                      899**************9875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.1
                                       HHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHC CS
                            NB-ARC  64 kseeiletilkeLslseddleekeeveslkrklvrlL 100
                                       + +++ ++i   +      +   e+++sl++++ ++L
  gi|330507434|ref|YP_004383862.1| 134 SNHRLAKKIRGSFRVLTVTR---ENRDSLADEIAKAL 167
                                       45555555554443332222...22333556666666 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00028      0.23      26      39 ..       6      19 ..       2      24 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                            AAA_29 26 lltGpsGsGKSTll 39
                                       +tG  G+GKSTl+
  gi|330507434|ref|YP_004383862.1|  6 AVTGSPGVGKSTLV 19
                                      69***********8 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   0.00027      0.22       4      24 ..       7      27 ..       5      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                            AAA_33  4 lvGlpGsGKstlaerllkklg 24
                                      + G pG+GKstl+ ++   ++
  gi|330507434|ref|YP_004383862.1|  7 VTGSPGVGKSTLVAKVTSGTK 27
                                      78************9974444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.7    0.0059       4.8      13      31 ..       5      23 ..       2      36 .. 0.84
   2 ?    2.6   0.0      0.19   1.5e+02      93     125 ..      85     116 ..      69     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0059
                            AAA_19 13 llvtaGpGtGKTrvlkhiv 31
                                      ++vt+ pG GK++++ ++ 
  gi|330507434|ref|YP_004383862.1|  5 IAVTGSPGVGKSTLVAKVT 23
                                      689*********9987765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.19
                            AAA_19  93 eaeeekklqeeellivDEfqdvdelqyrLlkal 125
                                        ++ e+ l  ++l++vDE+  ++    +++ a+
  gi|330507434|ref|YP_004383862.1|  85 AQAVENAL-GCDLIVVDEVGPMELSSHSFVLAV 116
                                       45566777.888******988887666666555 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 ?    8.5   1.5    0.0018       1.5       1      21 [.       7      27 ..       7      32 .. 0.87
   2 ?   -1.3   0.0       1.9   1.5e+03      83     120 ..      85     122 ..      73     142 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                        ATP_bind_1  1 vvGpaGsGKttfvgalseile 21
                                      v+G +G+GK+t+v ++++ ++
  gi|330507434|ref|YP_004383862.1|  7 VTGSPGVGKSTLVAKVTSGTK 27
                                      89************9987665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                        ATP_bind_1  83 deeleke.eddyllfDtPGQielfthseslakiveeLes 120
                                       ++++e+    d++++D  G +el  hs +la + ++++s
  gi|330507434|ref|YP_004383862.1|  85 AQAVENAlGCDLIVVDEVGPMELSSHSFVLA-VEKAIAS 122
                                       4455555444888888888888888888888.5555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1036.84
//
Query:       gi|330507435|ref|YP_004383863.1|  [L=146]
Description: toprim domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-05   23.6   0.0     0.0001   22.5   0.0    1.6  1  Toprim    Toprim domain
    0.00019   21.9   0.0    0.00047   20.6   0.0    1.7  1  Toprim_4  Toprim domain
     0.0028   18.1   0.0     0.0039   17.6   0.0    1.3  1  Toprim_2  Toprim-like


Domain annotation for each model (and alignments):
>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.7e-08    0.0001       4      88 ..      42     105 ..      39     130 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.7e-08
                                       EESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHH CS
                            Toprim   4 ivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaia 80 
                                       ivEg +d  +++ + g ++ +++as+  +ldl++                      a+ + eiil+tD Dr G + a
  gi|330507435|ref|YP_004383863.1|  42 IVEGRRDELALRAL-GLTGPVIMASRRSALDLAE--------------------DAARSYREIILLTDWDRKGDEMA 97 
                                       55555555555554.4455555555555555555....................889******************** PP

                                       HHHHHHHT CS
                            Toprim  81 wellevlk 88 
                                         + ++l 
  gi|330507435|ref|YP_004383863.1|  98 RTIEQHLW 105
                                       99998887 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   7.9e-08   0.00047       3      76 ..      40     102 ..      38     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.9e-08
                          Toprim_4   3 iiiVEgyaDvlalekagiknvvav..lggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerlae 76 
                                       + iVEg+ D lal   g ++ v     ++al  l++++   + +          +e+il++d D  G+++a  + +
  gi|330507435|ref|YP_004383863.1|  40 ATIVEGRRDELALRALGLTGPVIMasRRSAL-DLAEDA--ARSY----------REIILLTDWDRKGDEMARTIEQ 102
                                       67****************9988641155777.555555..6777..........9****************98765 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   6.5e-07    0.0039       2      73 ..      42     115 ..      41     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.5e-07
                          Toprim_2   2 vfEgaiDalSlaqlgikektnvvalgGt.alteaalkllerypekkvvlalDnDkaGrkaakrlaellreag..... 72 
                                       ++Eg  D l+l +lg +     v +++  ++ + a +  ++y  ++++l +D D++G+++a+++ ++l + g     
  gi|330507435|ref|YP_004383863.1|  42 IVEGRRDELALRALGLT---GPVIMASRrSALDLAEDAARSY--REIILLTDWDRKGDEMARTIEQHLWSVGsrpdg 113
                                       78999999999999996...7777777745555666666666..99*******************999776655444 PP

                          Toprim_2  73 .v 73 
                                        +
  gi|330507435|ref|YP_004383863.1| 114 eI 115
                                       43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 978.54
//
Query:       gi|330507436|ref|YP_004383864.1|  [L=105]
Description: hypothetical protein MCON_1367 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-18   65.9   0.0      3e-18   65.7   0.0    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 !   65.7   0.0   1.7e-22     3e-18       2      76 ..      14      87 ..      13      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 1.7e-22
                                      EEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEEE CS
                            DUF167  2 vilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvri 76
                                      +i++ +v Pg+++ a++  + + +r+ l+ r++++p +G+AN++l++ La++lgv +s +e+++Geks +K++++
  gi|330507436|ref|YP_004383864.1| 14 CIIRFEVVPGSSRLAVP-SGFNPWRRSLEARLTEKPSRGRANRQLVEELARILGVDESGIEVIKGEKSGRKLLLV 87
                                      799**************.8899**************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 795.54
//
Query:       gi|330507437|ref|YP_004383865.1|  [L=450]
Description: phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase [Methanosaeta concilii GP6]
Scores for complete 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-85  285.6   0.0      6e-85  285.3   0.0    1.1  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme


Domain annotation for each model (and alignments):
>> AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.3   0.0   3.3e-89     6e-85       9     296 .]      70     381 ..      66     381 .. 0.92

  Alignments for each domain:
  == domain 1  score: 285.3 bits;  conditional E-value: 3.3e-89
                                       EEE-SGGGHHHHHHHHHC.T.B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...CSE...EEEEEEEEESSSSSTT CS
                   AICARFT_IMPCHas   9 tvvvdpadYeevleelkk.gevsletrkklaakaFahtaaYDaaiaeylskq...lpetlklslekkqkLrYGeNph 81 
                                       +v+ ++++  +vlee+++ g++s++tr  l a++  ++ + D +  + l+ +   lp+ ++ ++ek+q+LrYGeN+h
  gi|330507437|ref|YP_004383865.1|  70 AVLLHNSNCPSVLEEIRStGDLSQKTRDMLEARVLYRCLQKDIQRLASLQPEadgLPNYVASAYEKVQDLRYGENWH 146
                                       788999999*********99**********************999999977767777899999************** PP

                                       S-EEEEE-TTSTTHHH-EEEESS---HHHHHHHHHHHHHHCTS......E....EEEEEETTEEEEEEEESSHHHHH CS
                   AICARFT_IMPCHas  82 QkaalyeeeeeeglakaeqlqGkelsynNllDadaalelvkef......a....avaivKHanpcGvAvgetlaeAy 148
                                       Q+aaly++++  gl +a++l+G+e+synN++Da++ le++ ++      a      +ivKHanpcGvA g++l eAy
  gi|330507437|ref|YP_004383865.1| 147 QRAALYTNDQGLGLPAARKLNGREMSYNNMVDAETVLEMLIDLsdydgeAcnrpLSVIVKHANPCGVAYGTSLDEAY 223
                                       *******99999***************************997766676624566455******************** PP

                                       HHHHCCSHHHHTTEEEEECCEE-HHHHHHHTTS-ECEEEECEE-CCHHHCC.TTSSS-EEEE-SS..-......... CS
                   AICARFT_IMPCHas 149 ekAlaaDpvSaFGgiialnrevdaetaeeikkefleviiApsfeeealeil.kkkknlrvlelke..e......... 213
                                       + ++a+Dp SaFGg+i +nr+vd++ta+ i + f+ev++Ap++e+eal++l +kk n r+l++ +  +         
  gi|330507437|ref|YP_004383865.1| 224 RLSFATDPKSAFGGVIGFNRMVDVKTAQCIGDSFVEVLLAPGYEAEALRLLtEKKPNRRILDIGDllQrkselyrgy 300
                                       ***************************************************55569*******99661566788884 PP

                                       EEEEETTEEEEEE--G..TTCCCSEEECSC---HHHHHHHHHHHHHCCCS-SS-EEEEETTEEEEEE-SSSSHHHHH CS
                   AICARFT_IMPCHas 214 elrsvsgglLvqerdeakieeeelkvvtkkkpteeeledllfawkvvkhvkSNaivlakdgqtvgiGaGqmsRvdsa 290
                                         +++ gg+++q+ d+ +i+  e++vvt+++pt++e ++l+fawk++k+vkSNa v+++++qt+giG+Gq+sRvdsa
  gi|330507437|ref|YP_004383865.1| 301 YKKTIFGGMMLQDFDTGDIK--EWRVVTRRAPTDSEARALRFAWKIAKYVKSNALVYTTENQTIGIGSGQVSRVDSA 375
                                       55559**********97776..5****************************************************** PP

                                       HHHHHH CS
                   AICARFT_IMPCHas 291 rlAvek 296
                                       r+ +ek
  gi|330507437|ref|YP_004383865.1| 376 RFGAEK 381
                                       *99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); 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: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 3615.93
//
Query:       gi|330507438|ref|YP_004383866.1|  [L=473]
Description: periplasmic copper-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-44  150.4  28.9    9.4e-23   80.7   6.8    2.1  2  NosD             Periplasmic copper-binding protein (NosD)
    6.5e-32  110.6  19.3    1.8e-18   66.9  11.1    3.2  3  Beta_helix       Right handed beta helix region
    0.00021   21.2  22.7    0.00043   20.2   0.8    4.3  2  Pectate_lyase_3  Pectate lyase superfamily protein
    0.00022   20.7  12.3    0.00097   18.5   3.7    3.0  3  DUF1565          Protein of unknown function (DUF1565)


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 !   80.7   6.8   2.1e-26   9.4e-23      21     174 ..     118     271 ..      97     279 .. 0.93
   2 !   75.7  14.2     7e-25   3.1e-21     106     240 ..     278     403 ..     272     404 .. 0.88

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 2.1e-26
                              NosD  21 lensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsssnntle 96 
                                       + + ++  i+n +i   ++gi++ +++++t++++t+  +++G++l +  + +++++ + +++ +G+ +++s++ +++
  gi|330507438|ref|YP_004383866.1| 118 VVEGSDLAIKNSSIYGAQAGIYALDAEGITLQDSTLDGCDTGLFLHGGRGLNVSGCSIVNCKkYGLDIEQSREIVVK 194
                                       445578889******************************************************************** PP

                              NosD  97 nNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinns 173
                                       nN i++n+n Gill++ +  +  +N is++  G++l n+s n++++N+++ n  +Gil+++ s+ n+i++N +i+ns
  gi|330507438|ref|YP_004383866.1| 195 NNSIIRNSNIGILLREGKWAEMDDNLISECTFGLSLWNASFNQVRRNQLDHN-YYGILVTNWSSYNNITDNLLIDNS 270
                                       ****************************************************.***********************8 PP

                              NosD 174 e 174
                                        
  gi|330507438|ref|YP_004383866.1| 271 R 271
                                       5 PP

  == domain 2  score: 75.7 bits;  conditional E-value: 7e-25
                              NosD 106 yGillsdssn...ntisnNtisnnnkGiflens.ssntitgNriesnqkiGilllsssegntiynNyFinnsenvky 178
                                       +Gi ls ++n   n + +N++  n++G+ +++  + n +  N+ ++n k+Gi  ++++ +n+i++N+F  n++n++ 
  gi|330507438|ref|YP_004383866.1| 278 FGIGLSLQENschNMVIGNVARGNYNGLEISKGcQFNAVYANNAAEN-KHGIR-MNENRNNLIFGNNFQFNNINAYE 352
                                       466666555555599****************999*************.*****.**************999999999 PP

                              NosD 179 dgsnnneWnttktsgtniiggpylgGNyWsdydgeDadgDGigDtpYein...dgviDylplvnp 240
                                       ++s  n Wntt              GNy+sdy+geD+++DGigD+pY+++   +++ D++p ++p
  gi|330507438|ref|YP_004383866.1| 353 NQS-CNIWNTTL-------------GNYYSDYKGEDENKDGIGDVPYSLPgpeSSSSDRMPSIRP 403
                                       886.****9999.............**********************766443666899998876 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 !   56.8   1.1   5.1e-19   2.3e-15       3     137 ..      70     224 ..      68     227 .. 0.89
   2 !   66.9  11.1     4e-22   1.8e-18       2     138 ..     116     270 ..     115     282 .. 0.74
   3 !   14.2  18.3   6.7e-06      0.03      64     145 ..     275     351 ..     270     367 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 5.1e-19
                                       EEE-SS-E.EEESEEEES-.........................SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT CS
                        Beta_helix   3 isingssnvtiknntisns.........................ggyGiylrgssnvvienneiannsgsGiyilgs 54 
                                       ++++++++ ti++++i+++                         +++++ ++gs+   i+n+ i++  + Giy l +
  gi|330507438|ref|YP_004383866.1|  70 VVVKSDGV-TIDGFEIYGVgkdttakfeyymenreaargqrldmPNSAVVVEGSDL-AIKNSSIYG-AQAGIYALDA 143
                                       77777777.99999999999999999999999999999999998899999998887.999999999.9999999999 PP

                                       -S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES CS
                        Beta_helix  55 snntisnntisdnngggialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtn 131
                                       +++t++++t  ++  +g+ l g+ +  ++++ i +++++G+ +++s  ++++nN i  n++ Gi +++++ + ++ +
  gi|330507438|ref|YP_004383866.1| 144 EGITLQDSTLDGCD-TGLFLHGGRGLNVSGCSIVNCKKYGLDIEQSREIVVKNNSIIRNSNIGILLREGK-WAEMDD 218
                                       99999999999999.9999999999999999999999999999999999999999999999999999999.999999 PP

                                       -EEES- CS
                        Beta_helix 132 Ntitnn 137
                                       N i+ +
  gi|330507438|ref|YP_004383866.1| 219 NLISEC 224
                                       998765 PP

  == domain 2  score: 66.9 bits;  conditional E-value: 4e-22
                                       SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S CS
                        Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgas 78 
                                       +++++gs+   ikn+ i++  ++Giy+ ++++++++++++ +  ++G+ ++g+ + ++s+++i +++ +g+ ++++ 
  gi|330507438|ref|YP_004383866.1| 116 AVVVEGSDL-AIKNSSIYG-AQAGIYALDAEGITLQDSTLDG-CDTGLFLHGGRGLNVSGCSIVNCKKYGLDIEQSR 189
                                       567777777.9********.5*********************.********************************** PP

                                       --EEES-EEES-SS-SEE-TT......................-S--EEES-EEESTT--SEE---TT---EEES-E CS
                        Beta_helix  79 nnlienneitdnggsGiylny......................ssnntienNiidnnagsGividdsssnvtvtnNt 133
                                         +++nn i++n++ Gi l                        +s n++++N++d+n+ +Gi ++++ss +++t+N 
  gi|330507438|ref|YP_004383866.1| 190 EIVVKNNSIIRNSNIGILLREgkwaemddnlisectfglslwnASFNQVRRNQLDHNY-YGILVTNWSSYNNITDNL 265
                                       ************8886666652333333333333333333333666666666666666.666666666555566666 PP

                                       EES-S CS
                        Beta_helix 134 itnnk 138
                                       + +n+
  gi|330507438|ref|YP_004383866.1| 266 LIDNS 270
                                       66665 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 6.7e-06
                                       EE---SEEE-TT.--S--EEES-EEES-SS-SEE-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES-S CS
                        Beta_helix  64 isdnngggialf.gasnnlienneitdnggsGiyln.yssnntienNiidnnagsGividdsssnvtvtnNtitnnk 138
                                       i ++ g g+ l+ ++ +n++ +n  + n + G++++ +++ n +  N++ +n+ +Gi ++++  n+ +++N++  n+
  gi|330507438|ref|YP_004383866.1| 275 IDGF-GIGLSLQeNSCHNMVIGNVARGNYN-GLEISkGCQFNAVYANNAAENK-HGIRMNENR-NNLIFGNNFQFNN 347
                                       3444.4899999999*************98.*****88999************.*********.8889999998777 PP

                                       SEEEE-T CS
                        Beta_helix 139 gaGiavv 145
                                       ++    +
  gi|330507438|ref|YP_004383866.1| 348 IN---AY 351
                                       33...33 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 !   20.2   0.8   9.5e-08   0.00043     107     214 ..      71     183 ..      14     184 .. 0.63
   2 ?   -6.1  15.0         4   1.8e+04     147     213 ..     249     327 ..     186     380 .. 0.54

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.5e-08
                                       -SS---SSEEE.ES-EEEEEEEEEEE.S-SSEEE-SSS---TT---SS......--EEEEES-EEES-SS-SEEE.S CS
                   Pectate_lyase_3 107 kiditavapga.tgihwqtaqatsle.nvefemseasgtkhqgifien......gsggflndlvfsglgdigiav.g 174
                                       ++++++v+ ++ +   + ++++t+ + ++ +e++ea+   +q++ + n      gs   ++++ ++g  + gi    
  gi|330507438|ref|YP_004383866.1|  71 VVKSDGVTIDGfEI--YGVGKDTTAKfEYYMENREAA--RGQRLDMPNsavvveGSDLAIKNSSIYG-AQAGIYAlD 142
                                       34444443333211..223333332211123333333..4444444441111116666667777777.444444437 PP

                                       -EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSSE.EE CS
                   Pectate_lyase_3 175 nqqftvrnitfnnattgievlwgwgwtlknvkinnceg.Gi 214
                                        + +t+++ t  ++ tg  ++ g+g  +++++i nc++ G+
  gi|330507438|ref|YP_004383866.1| 143 AEGITLQDSTLDGCDTGLFLHGGRGLNVSGCSIVNCKKyGL 183
                                       ************************************99887 PP

  == domain 2  score: -6.1 bits;  conditional E-value: 4
                                       T---SS--E..EEEES-EEES.....-SS-SEEES-EEEEEES-EEE-....S--SEEE-TT-E.EEEEEEEEESSS CS
                   Pectate_lyase_3 147 gifiengsg..gflndlvfsg.....lgdigiavgnqqftvrnitfnn....attgievlwgwg.wtlknvkinnce 211
                                       gi++ n s+  ++ ++l +++     ++++gi ++ q+   +n+++ n    + +g e+++g +   + +++  + +
  gi|330507438|ref|YP_004383866.1| 249 GILVTNWSSynNITDNLLIDNsrgeiIDGFGIGLSLQENSCHNMVIGNvargNYNGLEISKGCQfNAVYANNAAENK 325
                                       55555544432222444444444444444444444455555555555544444444444443332222222222222 PP

                                       EE CS
                   Pectate_lyase_3 212 gG 213
                                        G
  gi|330507438|ref|YP_004383866.1| 326 HG 327
                                       22 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   3.7   2.2e-07   0.00097      18     194 ..      22     207 ..      18     209 .. 0.65
   2 !   15.4   1.4     2e-06    0.0091     101     192 ..     169     272 ..     158     289 .. 0.72
   3 ?   -2.0  13.2      0.41   1.8e+03     116     224 ..     248     359 ..     241     368 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-07
                           DUF1565  18 iTkAlllakageviqlapGtYseatgEtFPlvipegvnlvGneagKGlskslyagk.kvgp.lisgggddlsgvqnv 92 
                                       i  A+  a+ag++i++ pGtY   t ++    i eg+ +   +++  +  ++ ++   +    i g g+d+   +  
  gi|330507438|ref|YP_004383866.1|  22 IQSAINSAQAGDIIAVGPGTYISITIDRPLTLIGEGRPVLNATQQNPA-VVVKSDGvTIDGfEIYGVGKDTT-AK-F 95 
                                       678******************999988844467888888887777777.44444444333348999999977.55.4 PP

                           DUF1565  93 tivlaneatiaGvtitNpni...lkgtgvliesasakianNtitgniadGiev.........siyeaktgaggni.. 155
                                          ++n+   +G ++  pn    ++g  ++i+++s+  a+  i ++ a+Gi+                         
  gi|330507438|ref|YP_004383866.1|  96 EYYMENREAARGQRLDMPNSavvVEGSDLAIKNSSIYGAQAGIYALDAEGITLqdstldgcdTGL---------Flh 163
                                       5677888889*****99955233445555555555555555555555555555444444443222.........023 PP

                           DUF1565 156 ......isGnsil.feknGiaisgasaavenkienNiivkNli.Gvv 194
                                             +sG si   +k G++i+++++     ++nN i++N   G+ 
  gi|330507438|ref|YP_004383866.1| 164 ggrglnVSGCSIVnCKKYGLDIEQSREI---VVKNNSIIRNSNiGIL 207
                                       333333777775515666******9999...6899*88888654875 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2e-06
                           DUF1565 101 tiaGvtitNpnilkgtgvliesa.sakianNtitgniadGievsiyeaktgaggniisGnsil.............. 162
                                       ++ G  i N    k++g+ ie++  ++++nN i  n ++Gi  +  +   ++ +n is  +                
  gi|330507438|ref|YP_004383866.1| 169 NVSGCSIVNC---KKYGLDIEQSrEIVVKNNSIIRNSNIGILLREGK-WAEMDDNLISECTFGlslwnasfnqvrrn 241
                                       6788888888...88******999****************9997774.66666666554442222233333334444 PP

                           DUF1565 163 ...feknGiaisgasaavenkienNiivkNliG 192
                                           ++ Gi  ++ s   +n i +N+++ N +G
  gi|330507438|ref|YP_004383866.1| 242 qldHNYYGILVTNWSS--YNNITDNLLIDNSRG 272
                                       4337777887766554..59**********998 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.41
                           DUF1565 116 tgvliesa..sakianNtitgniadGiev...siyeaktgaggniisGnsilfeknGiaisgasaavenkienNiiv 187
                                       +g+l+++     +i +N + +n +  i         +++++ +n++ Gn  + ++nG+ is+  +   n +  N   
  gi|330507438|ref|YP_004383866.1| 248 YGILVTNWssYNNITDNLLIDNSRGEIIDgfgIGLSLQENSCHNMVIGNVARGNYNGLEISKGCQF--NAVYANNAA 322
                                       67777776323578888877654332222222233356789999999***********99987766..888777788 PP

                           DUF1565 188 kNliGvvanala..lDlGsgsegsaGnNi.fsnnaeaDin 224
                                       +N+ G+ +n     l +G++ +    nNi    n+ + i+
  gi|330507438|ref|YP_004383866.1| 323 ENKHGIRMNENRnnLIFGNNFQ---FNNInAYENQSCNIW 359
                                       9999987766652255566555...333312345555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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 0.26s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3423.27
//
Query:       gi|330507439|ref|YP_004383867.1|  [L=353]
Description: N2,N2-dimethylguanosine tRNA methyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-97  324.8   0.0    9.5e-97  324.5   0.0    1.0  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    0.00011   21.8   0.1    0.00057   19.5   0.1    1.9  2  MTS              Methyltransferase small domain
     0.0055   16.5   0.0     0.0072   16.1   0.0    1.4  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.027   13.9   0.1      0.039   13.4   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.027   15.2   0.0      0.063   14.0   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
      0.052   13.2   0.1       0.39   10.3   0.1    1.9  2  Cons_hypoth95    Conserved hypothetical protein 95
      0.054   13.2   1.3          1    9.2   0.1    2.4  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.11   12.3   0.0       0.17   11.6   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase


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 !  324.5   0.0  4.2e-100   9.5e-97      12     376 .]       9     349 ..       2     349 .. 0.93

  Alignments for each domain:
  == domain 1  score: 324.5 bits;  conditional E-value: 4.2e-100
                                       SS--TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHH CS
                               TRM  12 vtvskkeeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAve 88 
                                       +t+++ +  F+NP+++ nRD+ v++    ++l+       ++ldaLsasG+R++R a E +g+++v +ND+ ++Av+
  gi|330507439|ref|YP_004383867.1|   9 ITFEA-TGAFFNPRMQLNRDIGVAM---TKALGIS-----EYLDALSASGIRGMRVAAE-AGTEKVTLNDFDPRAVQ 75 
                                       44544.678****************...6667766.....89*****************.9**************** PP

                                       HHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHH CS
                               TRM  89 likeNvklneveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspe 165
                                       ++++Nv  n+ +  vv+ e++Anvl+  ++++f+++DlDPfGsp+p++ +a +s+++  +L +TaTDta+L+Ga+ +
  gi|330507439|ref|YP_004383867.1|  76 VMRRNVARNQLDC-VVS-EKNANVLM--HQEHFQAVDLDPFGSPSPYISAASRSARS--YLFITATDTAPLCGAHLK 146
                                       *****99988876.444.459*****..899********************999876..****************** PP

                                       HHHHHHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEE CS
                               TRM 166 kclrkYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhC 242
                                       +++rkY+av+l +++  E++ Rill++ are a+ +k  epll++++d+Yvr +++v +ga+ ++++l++lg++ hC
  gi|330507439|ref|YP_004383867.1| 147 SGIRKYMAVPLCTDYHREMGARILLGLAARELARLDKGTEPLLTHVTDHYVRTYLRVVKGAEAADRSLQSLGYLEHC 223
                                       ***************************************************************************** PP

                                       TTT--EEEE--GGG--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS--S CS
                               TRM 243 sgClseekvkglakfkaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeElldap 319
                                        +C s e+   l+ +   c hc +++ laGPlwlg+++d +++++ l + +      l  r kk+L+++ +E +d+p
  gi|330507439|ref|YP_004383867.1| 224 NSCGSFETLRLLHPV-GICRHCRSRTALAGPLWLGKIQDPDVITSALVAGD------LGPRAKKILSTCAKE-VDVP 292
                                       ***998888877776.89*************************99886555......47899**********.**** PP

                                       S-EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHHH CS
                               TRM 320 lyydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvevlr 376
                                       +yyd++ ++++l+++  + ++v+s lk+lg+++srtH+++ +ikTna+l ++ evlr
  gi|330507439|ref|YP_004383867.1| 293 MYYDHHCICEKLRITPGKIEDVISRLKSLGHQASRTHFTGLGIKTNATLPELEEVLR 349
                                       *****************************************************9986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   2.5e-07   0.00057      36     101 ..      42     107 ..      31     112 .. 0.87
   2 ?   -0.6   0.0      0.37   8.3e+02      14      30 ..     179     195 ..     177     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.5e-07
                                       EEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEE CS
                               MTS  36 lDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdli 101
                                       lD  +  G+ g+ +a+e  + +vtl d d rA+++ ++n+++n+l++ v ++++   +++++f+++
  gi|330507439|ref|YP_004383867.1|  42 LDALSASGIRGMRVAAEAGTEKVTLNDFDPRAVQVMRRNVARNQLDCVVSEKNANVLMHQEHFQAV 107
                                       566666789999**********************************99999999888888888776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.37
                                       TS--HHHHHHHHHCHCC CS
                               MTS  14 dklDkGsklLletlpke 30 
                                       ++lDkG++ Ll++++++
  gi|330507439|ref|YP_004383867.1| 179 ARLDKGTEPLLTHVTDH 195
                                       589*********99875 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.2e-06    0.0072     105     160 ..      42      97 ..       1     200 [. 0.69

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.2e-06
                                       EETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-G CS
                            Met_10 105 vdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDg 160
                                       +d +   G   + +a  +  ++v  +d +P++v+ +++n+++N+++ vv+  ++ +
  gi|330507439|ref|YP_004383867.1|  42 LDALSASGIRGMRVAAEAGTEKVTLNDFDPRAVQVMRRNVARNQLDCVVSEKNANV 97 
                                       5555555555566666678889************************9996544433 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.7e-05     0.039     172     215 ..      48      92 ..      35     110 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                              PrmA 172 SGiLai.aaakLgakkvvavDiDevAvkvakeNaelNkveaklev 215
                                       SGi  + +aa  g++kv+  D D+ Av+v ++N+++N+++  ++ 
  gi|330507439|ref|YP_004383867.1|  48 SGIRGMrVAAEAGTEKVTLNDFDPRAVQVMRRNVARNQLDCVVSE 92 
                                       666555357789*************************88765433 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.8e-05     0.063       6      68 ..      46     107 ..      42     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                                       -TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEE CS
                   Methyltransf_25   6 cGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlv 68 
                                         +G   +++a++ g +kvt  D+++++++ +r+++++++l++ + +++a+ l  + ++f +v
  gi|330507439|ref|YP_004383867.1|  46 SASGIRGMRVAAEAGTEKVTLNDFDPRAVQVMRRNVARNQLDCVVSEKNANVLMHQ-EHFQAV 107
                                       5567777788888889**********************999999999888877543.466655 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00018      0.39      40     121 ..      36     111 ..      16     113 .. 0.77
   2 ?    3.0   0.0     0.032        71      34      73 ..      96     135 ..      89     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                                       HCC-EEEETT-TTSHHHHH.HHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEE CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglE.AlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefd 115
                                       +  +++LD  + sG  g+  A+  g +k++l + d++av+++++n+++ +l+    ++ e++++ l ++    e+f+
  gi|330507439|ref|YP_004383867.1|  36 LGISEYLDALSASGIRGMRvAAEAGTEKVTLNDFDPRAVQVMRRNVARNQLDC---VVSEKNANVLMHQ----EHFQ 105
                                       66677899999999999863666799*********************999763...3333333333333....5788 PP

                                       EEEE-- CS
                     Cons_hypoth95 116 ivflDP 121
                                        v lDP
  gi|330507439|ref|YP_004383867.1| 106 AVDLDP 111
                                       888887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.032
                                       HHHCCC.HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES- CS
                     Cons_hypoth95  34 nilaae.iegarvLDlfaGsGalglEAlSRgakkavlvekd 73 
                                       n+l+++   +a  LD f Gs +  + A+SR a++ +++   
  gi|330507439|ref|YP_004383867.1|  96 NVLMHQeHFQAVDLDPF-GSPSPYISAASRSARSYLFITAT 135
                                       66665533344458888.99**************9999765 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00045         1      16      26 ..     222     232 ..     215     233 .. 0.90
   2 ?    2.4   0.2     0.057   1.3e+02      15      22 ..     239     246 ..     236     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00045
                      Rubredoxin_2  16 rCpsCgsWntl 26 
                                       +C+sCgs++tl
  gi|330507439|ref|YP_004383867.1| 222 HCNSCGSFETL 232
                                       8*********9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.057
                      Rubredoxin_2  15 GrCpsCgs 22 
                                       G C++C+s
  gi|330507439|ref|YP_004383867.1| 239 GICRHCRS 246
                                       77888875 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.6e-05      0.17      55      95 ..      46      88 ..      30     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.6e-05
                   Methyltransf_16 55 sGtGlvGlavaellpeakviltDlee.llellkknielnkn.a 95
                                      s +G+ G+ va+ ++  kv+l D +  +++++++n++ n+   
  gi|330507439|ref|YP_004383867.1| 46 SASGIRGMRVAAEAGTEKVTLNDFDPrAVQVMRRNVARNQLdC 88
                                      678*********************9879**********87333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2574.08
//
Query:       gi|330507440|ref|YP_004383868.1|  [L=223]
Description: NADPH-dependent F420 reductase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-17   64.2   0.1      3e-17   63.0   0.0    1.7  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0028   16.7   0.0     0.0043   16.1   0.0    1.3  1  PDH             Prephenate dehydrogenase
  ------ inclusion threshold ------
      0.016   15.7   0.0      0.028   14.9   0.0    1.4  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai


Domain annotation for each model (and alignments):
>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.0     5e-21     3e-17       1      97 []       2      99 ..       2      99 .. 0.96
   2 ?   -2.6   0.0       1.4   8.5e+03      77      92 ..     141     156 ..     127     167 .. 0.59

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 5e-21
                                      EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......-EEECECHHHHHHH-SEEEE-S-HH CS
                     F420_oxidored  1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......vkvtavdneeaaeeadvvvlavkpe 72
                                      ki+++ G+G++g ++a++l+ +    hei+++ sr+++ka+e a+++        ++ ++dn+ a++ ad v+l+v+pe
  gi|330507440|ref|YP_004383868.1|  2 KIALVgGTGDIGTGFALRLMCS----HEIIIG-SRKEDKARESASAIMqleganGNIWGTDNASAVAVADAVILCVPPE 75
                                      799**9**************99....9***88.************9999****999*********************** PP

                                      HHHHHHHHCGHHHHTTSEEEEESSS CS
                     F420_oxidored 73 dveevlselakdalkgklvisvlag 97
                                      ++++v  +l + +++++lvis +++
  gi|330507440|ref|YP_004383868.1| 76 HLKSVTYDL-STSFNHQLVISPVVP 99
                                      *********.999********9875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                                       HHHHCGHHHHTTSEEE CS
                     F420_oxidored  77 vlselakdalkgklvi 92 
                                       ++ +++++ lkg ++i
  gi|330507440|ref|YP_004383868.1| 141 AALQAKDRILKGDVLI 156
                                       3333344444444444 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.2e-07    0.0043       4      75 ..      17      94 ..      14      98 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.2e-07
                                      HHHHTT--SEEEEE-SSHHHHHHHHHT.TSSSEE.....ES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EE CS
                               PDH  4 alrrkgfkvtvigydideekaeaalel.glvdea.....tddieavkeadivvlavPvevilevlkelaphlkedali 75
                                      alr  + + ++ig  ++++++e a ++ +l+ ++     td+ +av  ad v+l+vP+e ++ v  +l+   +++++i
  gi|330507440|ref|YP_004383868.1| 17 ALRLMCSHEIIIGSRKEDKARESASAImQLEGANgniwgTDNASAVAVADAVILCVPPEHLKSVTYDLSTSFNHQLVI 94
                                      788888899999988888777777654244443311121334899*******************99999888887776 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 ?   14.9   0.0   4.7e-06     0.028       1      83 [.       2      81 ..       2      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.7e-06
                                      EEEEETTTSHHHHHH.HHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqel.lrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagv 78
                                      k+a+vG+tG +G+ + lrl+ +h     + + s+++++ ++ a+a  +le+ +     + ++ +++ +d v+l++p + 
  gi|330507440|ref|YP_004383868.1|  2 KIALVGGTGDIGTGFaLRLMCSHE----IIIGSRKEDKARESASAIMQLEGANGNIWGTDNASAVAVADAVILCVPPEH 76
                                      79*************788888886....55566666444444444445555555555556777779**********988 PP

                                      HHHHH CS
                    Semialdhyde_dh 79 skela 83
                                       k+++
  gi|330507440|ref|YP_004383868.1| 77 LKSVT 81
                                      77776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1782.69
//
Query:       gi|330507441|ref|YP_004383869.1|  [L=429]
Description: TraB family protein [Methanosaeta concilii GP6]
Scores for complete 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  106.8   0.0    2.5e-30  106.3   0.0    1.2  1  TraB       TraB family
  ------ inclusion threshold ------
       0.16   11.7   5.3       0.16   11.7   4.2    1.6  2  Claudin_2  PMP-22/EMP/MP20/Claudin tight junction
       0.19   10.4   4.8       0.67    8.7   4.9    1.6  1  DUF2207    Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.0   4.2e-34   2.5e-30      10     252 ..      34     247 ..      28     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 4.2e-34
                              TraB  10 ttsyLfGTiHvskksvyplspeveealeksdtvvvEldlsdd...tdeatqkelaklkllpdgktlsdllseelyar 83 
                                       +++ ++GT+Hvs+ks+ ++ +++ee   ++d v+vEl+ls++   t +++++e+   kll+ g++l  +l + l+a 
  gi|330507441|ref|YP_004383869.1|  34 HEITIVGTAHVSEKSALEVVRRIEE--TRPDIVAVELCLSRYkalTGQEEKSEIEIGKLLS-GGKLYVFLVQLLLAY 107
                                       4599*********************..8**************5555555555555566666.*************** PP

                              TraB  84 lqkalakrglplaaldkmkPwllalllslaelakkkagldpelvDrylaktakragkpvgglEtveeqlsllss.lp 159
                                       +q+++ + ++++      kP  ++++l++++  +++ g   +lvDr++ +t +r + ++g++ ++++  sl+++ l 
  gi|330507441|ref|YP_004383869.1| 108 MQQKIGQ-EMGV------KP--GSEMLAAIRA-AQSTGARVALVDRDVGITIQRFWSAMGFFDKIRLIGSLIQGaLW 174
                                       *******.9***......**..9999999996.6889999999***********************99999964465 PP

                              TraB 160 deeqlealeetldeleeakdlleelveaykegdlealeleaeaeeefpelkevlldeRnrrwaekieallkepgsvf 236
                                        ee++  +    d++  ++d +++++               e+++++p    vl+deR++++a+++ +l ++ g+v+
  gi|330507441|ref|YP_004383869.1| 175 GEEEEIDI----DNIT-QDDVVSQMIG--------------EFRKISPGAASVLVDERDAYLARNLLSLSRQ-GRVL 231
                                       55555555....4555.68899*****..............**************************97777.**** PP

                              TraB 237 vaVGagHlaGedgvla 252
                                       ++VGagH  G++ +l 
  gi|330507441|ref|YP_004383869.1| 232 AVVGAGHKEGIERHLS 247
                                       *********9998775 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 ?   11.7   4.2   2.7e-05      0.16      61     143 ..     241     319 ..     236     351 .. 0.83
   2 ?   -2.3   0.0      0.51   3.1e+03     105     130 ..     344     392 ..     323     410 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                         Claudin_2  61 vvltqasnpfekkeeeivsisatsllalarfvqvlliLslvlivlavvlgllallkqsvlllkaagilfllagvlgl 137
                                       +++++ snp+     e+ +++a+  + +++++ ++++L     +l+++++l+   ++s+ l++a +i f+++g l +
  gi|330507441|ref|YP_004383869.1| 241 GIERHLSNPEAIPAIESLNVKAKKKITFSQVFGAVVTLT----ILVMIALLVITAQSSRSLVLAFAIWFVITGTLSA 313
                                       678889999999999999999999999999999988888....44445555566677888999999*********** PP

                         Claudin_2 138 lavvvf 143
                                       l+v++ 
  gi|330507441|ref|YP_004383869.1| 314 LGVILA 319
                                       ***975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.51
                         Claudin_2 105 lavvlgllallkqsv.......................lllkaagilfl 130
                                        ++++g++ ++k +                         +l++a+   l
  gi|330507441|ref|YP_004383869.1| 344 AGWFAGMVEAWKIKPtvsdlkelpqaegfrqmmnnrlfKVLLVASLSNL 392
                                       4555555555554444444444444444444444444433334444444 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.9   0.00011      0.67     377     458 ..     263     379 ..     254     382 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00011
                           DUF2207 377 kkklkklsalglgliilglilillallllvll...............................lvfllilllillli 422
                                       kkk++ ++++g ++++ +l++i l+++++++                                +  ++ ++++  l 
  gi|330507441|ref|YP_004383869.1| 263 KKKITFSQVFGAVVTLTILVMIALLVITAQSSrslvlafaiwfvitgtlsalgvilarghplsVLTAFGIAWMTTLN 339
                                       55555555555555555555554444444444566555555555555555555556666778766666666666666 PP

                           DUF2207 423 aiivlllfsrllgrr....teeGaellakwkgFkkyLeDf 458
                                        ++++ +f+++++++    t    ++l +++gF+++++++
  gi|330507441|ref|YP_004383869.1| 340 PFVAAGWFAGMVEAWkikpTVSDLKELPQAEGFRQMMNNR 379
                                       7777777778999989988*****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3248.61
//
Query:       gi|330507442|ref|YP_004383870.1|  [L=366]
Description: peptidase M50 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-25   87.7   4.9    1.2e-11   44.9   0.5    2.4  2  CBS             CBS domain
    2.1e-11   43.6  14.5    2.8e-06   26.8   3.1    3.7  3  Peptidase_M50   Peptidase family M50
    7.9e-05   22.4   3.8    7.9e-05   22.4   3.8    2.4  3  Peptidase_M50B  Peptidase M50B-like
  ------ inclusion threshold ------
      0.074   13.4   0.1        2.1    8.7   0.0    2.5  2  GAF_2           GAF domain
      0.089   13.4   0.2          4    8.1   0.0    2.3  2  GAF             GAF domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.5   3.3e-15   1.2e-11       1      53 [.     244     295 ..     244     298 .. 0.88
   2 !   44.6   0.4     4e-15   1.4e-11       1      55 [.     306     359 ..     306     361 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 3.3e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       V dim++dv+tv+pd+tl ++ e m e++++++PV+ +d +++G+vtl+Dl r
  gi|330507442|ref|YP_004383870.1| 244 VMDIMSDDVHTVDPDMTLQDLKEHMFEEKHRGYPVMSGD-EVIGVVTLSDLQR 295
                                       569*********************646668******545.5*********976 PP

  == domain 2  score: 44.6 bits;  conditional E-value: 4e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+++mtr++ ++ p++  + a+ +m + +++rlPV+ +dg+lvGiv+++Dl+ra+
  gi|330507442|ref|YP_004383870.1| 306 VAEVMTRKLYVIGPSEEASAAMMMMNKMNIRRLPVM-SDGRLVGIVSREDLVRAI 359
                                       789**********************6666*******.8***************98 PP

>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.6     5e-07    0.0018       2      36 ..      63      97 ..      62     143 .. 0.83
   2 !   26.8   3.1   7.7e-10   2.8e-06     191     240 ..     147     194 ..     132     207 .. 0.73
   3 ?    3.1   0.1     0.013        46      96     109 ..     210     270 ..     198     342 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5e-07
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  2 filllgilvvvHElGHflvAklcgvkveefsigfG 36
                                      f l+l+ +v++HElGH ++A ++g+ ++++ + f 
  gi|330507442|ref|YP_004383870.1| 63 FSLVLFTCVALHELGHSYIALKNGIAIRSITLYFF 97
                                      889************************99877773 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 7.7e-10
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 191 flqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevan 240
                                       +l++l l++++L ++NLlP +++DGg+ll+a +      p  + ++++a+
  gi|330507442|ref|YP_004383870.1| 147 MLWMLGLLNIILMLFNLLPAFPMDGGRLLRAWFATQM--PYIKATQRAAS 194
                                       799***************************9876544..33333333333 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.013
                                       XXXXXXXXXXXXX...............................................- CS
                                       xxxxxxxxxxxxx...............................................x RF
                     Peptidase_M50  96 lanfilailvfvv...............................................p 109
                                        +nfil +++f+v                                                
  gi|330507442|ref|YP_004383870.1| 210 SFNFILLFVAFFVyvgaseeekatqisvslegtrvmdimsddvhtvdpdmtlqdlkehmfE 270
                                       47**********9777777666666666666666666666666666665555555555441 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.3       1.9   6.7e+03     187     192 ..      22      27 ..       7      38 .. 0.43
   2 !   22.4   3.8   2.2e-08   7.9e-05      24     109 ..      70     161 ..      54     169 .. 0.75
   3 ?    1.5   0.3     0.055     2e+02     104     138 ..     198     232 ..     171     254 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.9
                    Peptidase_M50B 187 vlwllv 192
                                       +l +++
  gi|330507442|ref|YP_004383870.1|  22 FLLVIL 27 
                                       221111 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 2.2e-08
                    Peptidase_M50B  24 vvffHElGHalaalLtGgrvkgielhsdesGvtvtrg.pgglg.qiltllaGYlgpallGlllills...asgka.r 94 
                                        v +HElGH  +al  G  + +i+l+   +Gv+ ++  p+ ++    +++aG+  + +lGl++ill+    +g++  
  gi|330507442|ref|YP_004383870.1|  70 CVALHELGHSYIALKNGIAIRSITLYFF-GGVSAMEEiPRNPRlELQMAFAGPAVSGILGLMGILLAtllDEGSPlG 145
                                       5889**********************96.6888888885554415679**************999994322344466 PP

                    Peptidase_M50B  95 lllv.llvllllvlll 109
                                       ++l+ l++l ++++l+
  gi|330507442|ref|YP_004383870.1| 146 IMLWmLGLLNIILMLF 161
                                       7888444444555554 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.055
                    Peptidase_M50B 104 llvllllvrnlfglvlllllgallllvlllaedel 138
                                       l++++++v  lf   ++ll++a+++ v   +e+++
  gi|330507442|ref|YP_004383870.1| 198 LFAIIMFVLGLFSFNFILLFVAFFVYVGASEEEKA 232
                                       44445555556666666666666666665555555 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00058       2.1      95     129 ..     275     310 ..     242     314 .. 0.76
   2 ?    1.8   0.0     0.074   2.7e+02      96     109 ..     338     351 ..     338     357 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00058
                                       EEEE-TTS---EEEEES.......--HHHHHHHHHH CS
                             GAF_2  95 avPlisegrvvGvlnlyankppa.fdeedlelLeel 129
                                       + P++s+++v+Gv++l+  ++ +  d +d +++e +
  gi|330507442|ref|YP_004383870.1| 275 GYPVMSGDEVIGVVTLSDLQRVPqVDHADTRVAEVM 310
                                       78****99********64444443788888887765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.074
                                       EEE-TTS---EEEE CS
                             GAF_2  96 vPlisegrvvGvln 109
                                       +P++s+gr+vG+++
  gi|330507442|ref|YP_004383870.1| 338 LPVMSDGRLVGIVS 351
                                       6**********986 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0011         4      92     126 ..     275     311 ..     246     317 .. 0.80
   2 ?    3.0   0.0     0.041   1.5e+02      79     106 ..     327     351 ..     309     354 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                                       EEEEEETTEEEEEEEEEE..SSSCSHHHHHHHHHHHH CS
                               GAF  92 vvPlvndgelwGllvlhn..psppftreelellqvla 126
                                       + P+++++e++G+++l +  + p+ + ++ ++++v+ 
  gi|330507442|ref|YP_004383870.1| 275 GYPVMSGDEVIGVVTLSDlqRVPQVDHADTRVAEVMT 311
                                       57****************6433366888777777765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.041
                                       HHHHHHTTESEEEEEEEEETTEEEEEEE CS
                               GAF  79 rdllenmgirsslvvPlvndgelwGllv 106
                                       ++ ++ m+ir    +P+++dg+l+G+++
  gi|330507442|ref|YP_004383870.1| 327 MMMMNKMNIR---RLPVMSDGRLVGIVS 351
                                       5566667777...89**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 2930.04
//
Query:       gi|330507443|ref|YP_004383871.1|  [L=201]
Description: class II aldolase/adducin family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-32  113.3   0.3    1.4e-32  113.2   0.3    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 !  113.2   0.3   7.7e-37   1.4e-32       1     181 [.       7     174 ..       7     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 7.7e-37
                                       HHHHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHH CS
                       Aldolase_II   1 eelaeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplH 77 
                                       +e+a+ +r++   gl++   GniS++ + +++++it++g  ++el+ + +v+v+l+  ++ e+ +  + +s+et +H
  gi|330507443|ref|YP_004383871.1|   7 QEIARFGRKVVSSGLTSSRFGNISIC-Q-DGRIFITATGSMLDELDSSTVVEVSLE--NPCEM-D--KIASIETCVH 76 
                                       6899*********************9.4.69**********************998..99987.3..4699****** PP

                                       HHHHHH-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEE CS
                       Aldolase_II  78 laiykarpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakav 154
                                       +aiy + +   a++HtHsp+av+ls++ + e ++p++ e+  +l  +evp+i+ +  gt+ l++a++ alk ++ a+
  gi|330507443|ref|YP_004383871.1|  77 RAIYLN-TGKMAIIHTHSPYAVVLSMV-EMEKVEPIDSEGVLFL--GEVPIIEGKL-GTDMLAKAASLALK-SHMAC 147
                                       *****6.899***************66.5688*********976..78****9999.*************8.779** PP

                                       EETTTEEEEEESSHHHHHHHHHHHHHH CS
                       Aldolase_II 155 llrnHGlltvGetleeAvalaetleea 181
                                       + r+HG++++G tl eA++ a ++e++
  gi|330507443|ref|YP_004383871.1| 148 IARGHGVFAAGGTLMEAYTAACMVEHS 174
                                       ***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 00:00:00.41
# Mc/sec: 1486.37
//
Query:       gi|330507444|ref|YP_004383872.1|  [L=510]
Description: peptidase S8 and S53, subtilisin [Methanosaeta concilii GP6]
Scores for complete 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  159.0   0.3    4.3e-46  157.5   0.0    1.7  2  Peptidase_S8  Subtilase family
  ------ inclusion threshold ------
      0.032   14.9   0.0      0.057   14.1   0.0    1.4  1  Inhibitor_I9  Peptidase inhibitor I9


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.11   9.5e+02     240     253 ..      99     122 ..      67     122 .. 0.63
   2 !  157.5   0.0   4.8e-50   4.3e-46       1     298 []     139     395 ..     139     395 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.11
                                       H..........EEEE-SHHHCHHH CS
                                       x..........xxxxxxxxxxxxx RF
                      Peptidase_S8 240 s..........yqsmsGTSmAsPn 253
                                       +          ++  s  Sm+sPn
  gi|330507444|ref|YP_004383872.1|  99 DgvrgvytdqkLTVLSAASMSSPN 122
                                       23345666677899999*****97 PP

  == domain 2  score: 157.5 bits;  conditional E-value: 4.8e-50
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanap 77 
                                       g+gv+va++DtG d +h  ls      rk+          ++ +d  + +t+ ++d ng    HGth+A+++a+   
  gi|330507444|ref|YP_004383872.1| 139 GEGVTVALIDTGADADHEALS------RKI----------VAFQDFVNNQTEPYDD-NG----HGTHCASLIAGD-- 192
                                       79*******************......677..........6666777777777776.47....************.. PP

                                       SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-S....EEEE-EESCETTCHHCHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  78 eegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvd....vinmslgestslpktgrsiealainra 150
                                             gvapga++  +kv+d +g      ++ ++a+++++ ++ +    +i+ s+g++   +  +   e  a++r+
  gi|330507444|ref|YP_004383872.1| 193 ---LGMGVAPGAELVVIKVMDRDGACY--LSDALKALDWCLDNRDRygikIISFSVGGEGPSDGASLLDE--ACDRM 262
                                       ...899**************9999554..59**********966557888*******5555555555556..9**** PP

                                       H.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 151 vnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgnivst 227
                                       v ++g  ++++aGN+g      ++ s++  p++++ vit+ga++  g i + SsrGp+  g++kpd+v  G++ v++
  gi|330507444|ref|YP_004383872.1| 263 V-EEGLTMCVAAGNSG------PSPSSIVMPGGAEKVITIGAIDRTGLIFEQSSRGPTLTGEIKPDLVTLGVD-VPS 331
                                       *.99************......8999***********************************************.888 PP

                                       CCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 228 wsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdlgkadniesfaqGaG 298
                                       +   s+n+     + s+sGTSmA P ++ga A+ll+a+p+l+p++++++ll+tA+ lg++  + ++ +G+G
  gi|330507444|ref|YP_004383872.1| 332 ALAGSKNG-----LSSVSGTSMAVPQVSGASAVLLEANPELQPADIKRLLLKTADELGQE--GKDNLYGYG 395
                                       88888777.....899*****************************************777..********9 PP

>> Inhibitor_I9  Peptidase inhibitor I9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.4e-06     0.057      29      79 ..      60     110 ..      22     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.4e-06
                                       HHHHTT...--EEEEEEESSSSSEEEEEE-GGGHHHHHTSTTEEEEEEEEEE CS
                      Inhibitor_I9  29 svlkge.dsakagilysYkilfnGfavklteeqaeklrkrpeVesVepDqsv 79 
                                         lkg+ +    ++++ +k ++ G a++++++ +ek++k+++V+ V+ Dq++
  gi|330507444|ref|YP_004383872.1|  60 DDLKGNlTGVGSSLEKRFK-VLPGSAMTVSSDNLEKIAKTDGVRGVYTDQKL 110
                                       3455555556889999999.89***************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 3720.95
//
Query:       gi|330507445|ref|YP_004383873.1|  [L=382]
Description: rhodanese domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.7e-22   79.3   0.0    8.6e-10   39.1   0.0    2.2  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   4.8e-14   8.6e-10       9     106 ..     132     231 ..     125     232 .. 0.67
   2 !   38.2   0.0   9.2e-14   1.7e-09      15      97 ..     269     347 ..     260     355 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 4.8e-14
                         Rhodanese   9 lekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr....aaa 81 
                                       l++ + +++D++p+       IpgA++++ d++ ++  + +p  e+   l e g+++++ +++y++ + +    +aa
  gi|330507445|ref|YP_004383873.1| 132 LDSSD-IIIDISPRST---EYIPGAISIPYDRFIDPAGRLEPIGEMARILGEAGVSENDSIIIYGECQPCgggpSAA 204
                                       45555.4*****8665...56*******5555555555555555555444444***********7754432101233 PP

                         Rhodanese  82 a..aallkklGyknvsvldGGfkawke 106
                                       +   ++lk lG+++v++ldGG+++w +
  gi|330507445|ref|YP_004383873.1| 205 TyvFWMLKFLGHEDVRLLDGGIDDWVA 231
                                       334457777**666***********87 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 9.2e-14
                         Rhodanese  15 allDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaallkklGy 91 
                                       +++D+R+  ++e+g+IpgA+n+   ++s  +  + +++  +ee+ + +++++++vvvy ++g +a+  +  l  lGy
  gi|330507445|ref|YP_004383873.1| 269 QIIDARTGRDFEAGSIPGAINI--PYTSVLDGKKIKDQSELEEIFS-DLQRERPVVVYTNTGVKASMIWLPLSLLGY 342
                                       5*********************..4444445555555555555555.69***************6666888888995 PP

                         Rhodanese  92 knvsvl 97 
                                        + +v+
  gi|330507445|ref|YP_004383873.1| 343 -DAKVY 347
                                       .55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        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 0.21s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3011.65
//
Query:       gi|330507446|ref|YP_004383874.1|  [L=509]
Description: periplasmic copper-binding protein NosD [Methanosaeta concilii GP6]
Scores for complete 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-45  153.1  44.0    3.9e-27   95.1  20.9    2.1  2  NosD        Periplasmic copper-binding protein (NosD)
    4.9e-29  101.2  44.5    9.4e-17   61.3  16.5    2.7  2  Beta_helix  Right handed beta helix region
    3.4e-07   29.8  27.4     0.0085   15.5   4.6    4.2  4  DUF1565     Protein of unknown function (DUF1565)


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 !   72.1  15.1   6.7e-24     4e-20      33     175 ..     102     252 ..      69     255 .. 0.88
   2 !   95.1  20.9   6.5e-31   3.9e-27      65     238 ..     233     404 ..     232     407 .. 0.93

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 6.7e-24
                              NosD  33 eisns.rdgilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsssnntlenNtisnnen.. 105
                                        i+ + rd+    ++s+++i+g  ++n+ yGi l+n  ++t+ +nt+ +++  Gial  s +n++++N++s n    
  gi|330507446|ref|YP_004383874.1| 102 VIQAGeRDACVNIEASDVSISGFLVRNGFYGIKLNNVRGCTVANNTVIRCTqPGIALLFSDGNIIQGNNASFNGLgg 178
                                       4444414555788999***********************************99********************8799 PP

                              NosD 106 ...yGillsdssnntisnNtis.nnnkGiflens.ssntitgNriesnqkiGilllsssegntiynNyFinnsen 175
                                          yGi+ls+s++n i +N++  n ++Gi l  s s+nti+gN +++n  +G+++++++++n i  N++  n+++
  gi|330507446|ref|YP_004383874.1| 179 egwYGIYLSNSNDNLILDNVAYgNGAYGINLFPScSNNTIRGNVLQGN-MYGLYMFTDCSNNIIEYNDLSRNTNS 252
                                       99**********************************************.********************999875 PP

  == domain 2  score: 95.1 bits;  conditional E-value: 6.5e-31
                              NosD  65 lensesntiedntlssne.sGialmsssnn.tlenNtisnnenyGillsdssnntisnNtis.nnnkGiflens.ss 137
                                       ++++++n+ie n ls+n+ sG+ l   + +  ++nN +++n  +G +l ds +n+is+N i  n  +G++++++ ++
  gi|330507446|ref|YP_004383874.1| 233 FTDCSNNIIEYNDLSRNTnSGLDLRFDCTDnLIRNNSMIENVVAGLTLLDSGYNSISGNLIEaNGRYGLQIQSNsNG 309
                                       6789*********************999555******************************99********97769* PP

                              NosD 138 ntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydg.. 212
                                       nti +N+i+++ ++Gi+ l+ss +n+iy+N    n +++++ g  +n+Wn +            lgGN Wsdy g  
  gi|330507446|ref|YP_004383874.1| 310 NTIIDNTISDS-QTGIF-LDSS-QNLIYRNKISYNVIQAEDRG--ENSWNASY----------PLGGNLWSDYHGsd 371
                                       ***********.*****.6665.9*****************99..9***9998..........799*********99 PP

                              NosD 213 .......eDadgDGigDtpYeindgviDylplv 238
                                              +    DG+gD pYei +++ D++p +
  gi|330507446|ref|YP_004383874.1| 372 dyqgpeqNVLGADGFGDLPYEIDSSSLDRYPIM 404
                                       999988655899*******************87 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3  16.5   1.6e-20   9.4e-17      25     146 ..     111     234 ..      90     237 .. 0.77
   2 !   45.6  20.0   1.1e-15   6.5e-12      29     139 ..     234     343 ..     232     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.6e-20
                                       SEEE-SSS-.EEES-EEES....-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-.... CS
                        Beta_helix  25 Giylrgssnvvienneian....nsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggs.... 93 
                                       ++ ++ s+   i+     +    n+++Gi ++++ ++t+ nnt+ ++++ gial  +++n+i++n+ + ng      
  gi|330507446|ref|YP_004383874.1| 111 CVNIEASDV-SIS-----GflvrNGFYGIKLNNVRGCTVANNTVIRCTQPGIALLFSDGNIIQGNNASFNGLGgegw 181
                                       233333332.444.....35555599999999999999999999999999999999999999999999994444455 PP

                                       .SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT CS
                        Beta_helix  94 .GiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvg 146
                                        Giyl++s++n i +N++++n+++Gi + +s+sn+t+++N++ +n+ +G++  +
  gi|330507446|ref|YP_004383874.1| 182 yGIYLSNSNDNLILDNVAYGNGAYGINLFPSCSNNTIRGNVLQGNM-YGLYMFT 234
                                       6999999999999999999999999999999999999999999999.9997655 PP

  == domain 2  score: 45.6 bits;  conditional E-value: 1.1e-15
                                       -SSS-.EEES-EEES-SS-SEEE-TT.-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-T.T-S-- CS
                        Beta_helix  29 rgssnvvienneiannsgsGiyilgs.snntisnntisdnngggialfgasnnlienneitdnggsGiyln.yssnn 103
                                        ++sn++ie n+++ n+ sG++++ + ++n i+nn+  +n   g+ l ++++n i++n i+ ng++G++++ +s+ n
  gi|330507446|ref|YP_004383874.1| 234 TDCSNNIIEYNDLSRNTNSGLDLRFDcTDNLIRNNSMIENVVAGLTLLDSGYNSISGNLIEANGRYGLQIQsNSNGN 310
                                       678999*********99999999999999****999988888*****************************66777* PP

                                       EEES-EEESTT--SEE---TT---EEES-EEES-SS CS
                        Beta_helix 104 tienNiidnnagsGividdsssnvtvtnNtitnnkg 139
                                       ti +N+i++ +  Gi++d+s+ n+ +  N+i+ n++
  gi|330507446|ref|YP_004383874.1| 311 TIIDNTISDSQ-TGIFLDSSQ-NL-IYRNKISYNVI 343
                                       ********999.*********.44.67777776663 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0   0.00081       4.8      20      40 ..      67      87 ..      63      97 .. 0.89
   2 !   15.5   4.6   1.4e-06    0.0085      95     194 ..     114     208 ..      88     212 .. 0.74
   3 !    7.9   8.8   0.00028       1.7     122     227 ..     208     305 ..     182     308 .. 0.56
   4 !   10.6   7.1   4.4e-05      0.26     116     196 ..     276     353 ..     265     370 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00081
                           DUF1565 20 kAlllakageviqlapGtYse 40
                                       A+ +a++g+++ +apGtY++
  gi|330507446|ref|YP_004383874.1| 67 AAINAAQPGDTLLVAPGTYEK 87
                                      59*****************97 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.4e-06
                           DUF1565  95 vlaneatiaGvtitNpnilkgtgvliesa.sakianNtitgniadGievsiyeaktgaggniisGnsilfekn...G 167
                                       + a+ ++i G+ ++N      +g+ ++++ + ++anNt+  +++ Gi            gnii Gn+  f+     G
  gi|330507446|ref|YP_004383874.1| 114 IEASDVSISGFLVRNG----FYGIKLNNVrGCTVANNTVIRCTQPGIALLFS------DGNIIQGNNASFNGLggeG 180
                                       4567899*********....469******9*****************98665......59*******9998654445 PP

                           DUF1565 168 iaisgasaavenkienNiivkNli.Gvv 194
                                             s++  n i +N+ + N   G++
  gi|330507446|ref|YP_004383874.1| 181 WYGIYLSNSNDNLILDNVAYGNGAyGIN 208
                                       5555566666677777777777545765 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00028
                           DUF1565 122 sasakianNtitgniadGievsiyeaktgaggniisGnsilfekn.GiaisgasaavenkienNiivkNliGvvana 197
                                       +  +  +nNti gn+ +G  +  y + t+  +nii  n +  ++n G++   + +   n i+nN +++N   vva +
  gi|330507446|ref|YP_004383874.1| 208 NLFPSCSNNTIRGNVLQGNMYGLY-MFTDCSNNIIEYNDLSRNTNsGLDLRFDCTD--NLIRNNSMIEN---VVAGL 278
                                       333445566666666666666555.3566666666666666655545555444333..77777777777...55555 PP

                           DUF1565 198 lalDlGsgsegsaGnNifsnnaeaDinisa 227
                                       + lD G +s    G N + +n++  ++i++
  gi|330507446|ref|YP_004383874.1| 279 TLLDSGYNSI--SG-NLIEANGRYGLQIQS 305
                                       5689999666..56.********9999843 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 4.4e-05
                           DUF1565 116 tgvliesa.sakianNtitgniadGievsiyeaktgaggniisGnsilfeknGiaisgasaa.venkienNiivkNl 190
                                        g+ + ++    i+ N i++n++ G++ +       ++gn+i  n+i + ++Gi  + +++  + nki  N+i    
  gi|330507446|ref|YP_004383874.1| 276 AGLTLLDSgYNSISGNLIEANGRYGLQIQSN-----SNGNTIIDNTISDSQTGIFLDSSQNLiYRNKISYNVIQAED 347
                                       455555554778999********99988766.....699***************99999998577********9988 PP

                           DUF1565 191 iGvvan 196
                                       +G ++ 
  gi|330507446|ref|YP_004383874.1| 348 RGENSW 353
                                       886554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.23s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3666.99
//
Query:       gi|330507447|ref|YP_004383875.1|  [L=195]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1499.93
//
Query:       gi|330507448|ref|YP_004383876.1|  [L=384]
Description: hypothetical protein MCON_1381 [Methanosaeta concilii GP6]
Scores for 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-08   33.4  15.5    5.7e-08   32.9  15.5    1.2  1  DsbD           Cytochrome C biogenesis protein transmembrane 
    6.8e-07   29.4  23.0    2.9e-06   27.3  13.2    2.2  2  DsbD_2         Cytochrome C biogenesis protein transmembrane 
     0.0014   18.8   0.0     0.0032   17.6   0.0    1.6  1  Glutaredoxin   Glutaredoxin
     0.0097   15.9   0.1      0.016   15.3   0.1    1.3  1  Thioredoxin_3  Thioredoxin domain


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9  15.5   1.3e-11   5.7e-08       4     207 ..     171     375 ..     168     381 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.3e-11
                              DsbD   4 aGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkevirr 80 
                                       +G+++ + PC++ ++    + i   s +  +      + ++  ++F  G+  ++ ++gl++  l +    +  + r+
  gi|330507448|ref|YP_004383876.1| 171 GGFVAGFNPCLFGILVFLAASIL--STSGKRR-----ELIMMVVFFSFGIFSMYFLFGLGMQRLLHSE-AIAATFRY 239
                                       89***********9865444443..2222222.....347888999***************9999987.89999999 PP

                              DsbD  81 vaglivillGlhflgvfkievleklkll.........lkikkk.aelsvlgalllGltFalgwsPCigPvlasvlal 147
                                       + +++ +  Gl+++  ++  +l++ k              ++  ++  +   +l+G +F+l+  PC+g +  ++l l
  gi|330507448|ref|YP_004383876.1| 240 ALTVLLLAAGLSQV--IDAILLKQGKASlfrtdwalqY-FQAGvEKGRFSSYFLAGALFSLVKIPCVGGLYLAILDL 313
                                       99999999999987..5655555555546777777742.3343034444566899********************** PP

                              DsbD 148 aaskeslakgallllvyvlGlaipfllvgllle..llkkklkslkkyska.veiaggvllvll 207
                                        + k     ga +l+++ lG  +p+++vg +l   +   ++  ++k  ++ ++  +g++l++l
  gi|330507448|ref|YP_004383876.1| 314 ISAKS-YFVGAAYLMFFNLGVILPIIVVGGFLAlgMSPDRVDRFRKDHRVgMRLFTGLMLLVL 375
                                       99988.89999*****************96654114456777777755542556666666655 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8  11.2    0.0027        12     120     198 ..     167     250 ..     156     251 .. 0.61
   2 !   27.3  13.2   6.6e-10   2.9e-06      54     177 ..     218     347 ..     209     377 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0027
                            DsbD_2 120 salllGllnGllpCgl.vysalllalasgsaleGalvm.la.FgLGTlpalllfglllgll..skklrkkllrlagv 191
                                       +  + G++ G+ pC + ++++l+++++s s  +  l+m ++ F+ G + + +lfgl +++l  s+++ ++++ ++ v
  gi|330507448|ref|YP_004383876.1| 167 AVTAGGFVAGFNPCLFgILVFLAASILSTSGKRRELIMmVVfFSFGIFSMYFLFGLGMQRLlhSEAIAATFRYALTV 243
                                       556779********776666666666666655444443133244444444456666666652255555555558888 PP

                            DsbD_2 192 llillgl 198
                                       ll+++gl
  gi|330507448|ref|YP_004383876.1| 244 LLLAAGL 250
                                       8888775 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 6.6e-10
                            DsbD_2  54 gllgsvlqlageleglrallgvllgllllllglklllkkkllklerlgkl.lsrllkklakkl..kslasalllGll 127
                                        l+g ++q   + e++ a++  +l +lll+ gl+ +  + llk ++++ +    +l+++++ +   +++s +l+G+l
  gi|330507448|ref|YP_004383876.1| 218 FLFGLGMQRLLHSEAIAATFRYALTVLLLAAGLSQVIDAILLKQGKASLFrTDWALQYFQAGVekGRFSSYFLAGAL 294
                                       5677777777888888888888888888888888888888777666554413334455555446578899******* PP

                            DsbD_2 128 nGll..pC.glvysalllalasgsaleGalvmlaFgLGTlpalllfglllgll 177
                                       ++l+  pC g +y+a+l  ++++s++ Ga+++++F LG +++++++g +l+l 
  gi|330507448|ref|YP_004383876.1| 295 FSLVkiPCvGGLYLAILDLISAKSYFVGAAYLMFFNLGVILPIIVVGGFLALG 347
                                       ***777**999****************************99999998887764 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.2e-07    0.0032       1      60 []      42     103 ..      42     103 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.2e-07
                                       EEEEESTSSHHHHHHHHHHHHTT..GGEEEEEGCCSHHHHHHHHHHH...TSSSSSEEEETTEEE CS
                      Glutaredoxin   1 vvlftkptCpyCkkakrlLkelg..vkfeeidvdkdeeireelkels...gvrtvPqvfidgkhv 60 
                                       v++  +p+Cp C++a r+L++ g  v     +v+    +++e  ++    + r +P + i+ +++
  gi|330507448|ref|YP_004383876.1|  42 VIIIISPGCPKCAAAERTLEKVGqtV---PLNVSSYYYYTDEGHRIIdqlNARDIPAIIIGTEVI 103
                                       788999****************9331...344444444444444444444778888888887765 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   3.5e-06     0.016       4      58 ..      43     101 ..      40     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.5e-06
                                       EE.ESSSSTTCHHHHHHHHHHCHCC..TCECEEECCTTHHHH.HHCT-SSSSEEECTTC CS
                     Thioredoxin_3   4 kv.lgpgCakCpklekavkeaaaek..gikaevekvtdfeei.ekygVmsvPalvidgk 58 
                                        + ++pgC+kC ++e+ ++++ ++   +++  ++ + +   i ++ + + +Pa++i  +
  gi|330507448|ref|YP_004383876.1|  43 IIiISPGCPKCAAAERTLEKVGQTVplNVSSYYYYTDEGHRIiDQLNARDIPAIIIGTE 101
                                       4449********9999999998887334555566666666667***********99755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2799.58
//
Query:       gi|330507449|ref|YP_004383877.1|  [L=394]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.1    1.9e-24   86.2   0.1    1.3  1  OrfB_IS605      Probable transposase
    8.6e-24   83.3   1.4    2.5e-23   81.8   0.6    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    3.5e-06   26.4   0.3    7.2e-06   25.4   0.3    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.018   15.1   0.1      0.046   13.7   0.1    1.7  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.055   13.0   1.5       0.63    9.6   0.0    2.5  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.068   12.6   5.1       0.87    9.1   5.1    2.4  1  zf-ribbon_3     zinc-ribbon domain
       0.52   10.3   3.7        1.3    9.0   3.7    1.7  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.59    9.8   6.5       0.36   10.4   1.5    2.8  3  RecR            RecR protein
        1.5    9.0   5.1        1.3    9.2   0.7    2.4  2  UPF0547         Uncharacterised protein family UPF0547


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 !   86.2   0.1   9.4e-28   1.9e-24       5     117 ..     165     274 ..     161     276 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 9.4e-28
                        OrfB_IS605   5 evevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlh 81 
                                       ++++++p p++++a+g+D+G+  +++ ++++   ++ ++r +k+   +la+ +++l++ + +s+nyk  + k+a+lh
  gi|330507449|ref|YP_004383877.1| 165 ANQEPQPLPETEEAVGLDVGLTSFVVDSVGN---EIENPRCAKQSADKLARLQRRLARAVRGSNNYKSLKGKIAKLH 238
                                       567889*************************...******************************************* PP

                        OrfB_IS605  82 rkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       ++++++r+++lhkl++  +++ + + ve+L+++++k
  gi|330507449|ref|YP_004383877.1| 239 KRINCQRDDFLHKLSRTYVNNFDIICVEDLDIKGLK 274
                                       *********************************998 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.91   1.8e+03      10      23 ..      37      50 ..      29      53 .. 0.77
   2 !   81.8   0.6   1.3e-26   2.5e-23       1      67 [.     291     357 ..     291     358 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.91
                    OrfB_Zn_ribbon 10 ykakeyGikveevn 23
                                      + ake+Gik+++ +
  gi|330507449|ref|YP_004383877.1| 37 NEAKEKGIKLKTYD 50
                                      4699*****99876 PP

  == domain 2  score: 81.8 bits;  conditional E-value: 1.3e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       ++k+  +l+yka+ +G+k+++v+p++T ++Cs Cgs+ +++ls r+++Cp Cgf++drD+nA++Nil
  gi|330507449|ref|YP_004383877.1| 291 WSKFVFMLSYKAQSAGRKLIKVDPRNTTQRCSACGSIAEKDLSVRVHECPYCGFSCDRDYNASRNIL 357
                                       99****************************************************************7 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.3   3.6e-09   7.2e-06       4      45 ..       2      43 ..       1      45 [. 0.92

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.6e-09
                    HTH_OrfB_IS605  4 kaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeee 45
                                       +yky + P++  + kla+ ++++R+ YN+ L+  +ea e++
  gi|330507449|ref|YP_004383877.1|  2 ISYKYPIFPNKITQWKLAENLDACRWLYNRLLQNLNEAKEKG 43
                                      58********************************99998776 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 ?   -3.5   0.0         5     1e+04      24      46 ..      53      75 ..      45      80 .. 0.76
   2 ?   13.7   0.1   2.3e-05     0.046      45     109 ..     293     360 ..     281     363 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5
                                      .EEEEEEEEEETTCT--HHHHHH CS
                              HypA 24 rkvtkvkvevGelsgvepeaLef 46
                                      + + ++k+e  +l++v  ++L++
  gi|330507449|ref|YP_004383877.1| 53 NMIPSLKLENPKLNQVYSKVLQM 75
                                      46778888888999998888886 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSSS.-EEEEESSSEEEEE CS
                              HypA  45 efafellaegtvlegaeLeieevpvkvrCreCgkefeleek..alrCpkCgsa.dveivsGeellvks 109
                                       +f+f l  + + + ++ ++++  + + rC+ Cg+  e++ +    +Cp Cg + d +  + +++l++ 
  gi|330507449|ref|YP_004383877.1| 293 KFVFMLSYKAQSAGRKLIKVDPRNTTQRCSACGSIAEKDLSvrVHECPYCGFScDRDYNASRNILISG 360
                                       56666667777777777899999**********9999776334669****965466677777766665 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00032      0.63      11      32 ..     310     331 ..     306     334 .. 0.83
   2 ?    1.1   0.9      0.14   2.8e+02       2       8 ..     338     344 ..     337     355 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00032
                                       CHEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon  11 lveDpergelvCtdCGlVledn 32 
                                       + +Dp +++ +C++CG++ e +
  gi|330507449|ref|YP_004383877.1| 310 IKVDPRNTTQRCSACGSIAEKD 331
                                       67899999*********98876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.14
                                       EETTTTC CS
                      TF_Zn_Ribbon   2 kCPnCgs 8  
                                        CP+Cg 
  gi|330507449|ref|YP_004383877.1| 338 ECPYCGF 344
                                       5999995 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   5.1   0.00044      0.87       2      23 ..     318     343 ..     317     345 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00044
                       zf-ribbon_3   2 tvrCPnCGaplssddnv....CpyCG 23 
                                       t+rC++CG+++++d +v    CpyCG
  gi|330507449|ref|YP_004383877.1| 318 TQRCSACGSIAEKDLSVrvheCPYCG 343
                                       78*******988887777777****9 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.7   0.00066       1.3       6      31 ..     320     343 ..     320     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00066
                    Zn_ribbon_SprT   6 rCtgCgreythhlsirrhnYrCrrCk 31 
                                       rC  Cg+  +  ls+r h   C++C+
  gi|330507449|ref|YP_004383877.1| 320 RCSACGSIAEKDLSVRVHE--CPYCG 343
                                       8******************..****8 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.83   1.6e+03       3      15 ..      30      42 ..      29      42 .. 0.87
   2 ?   10.4   1.5   0.00018      0.36      13      34 ..     315     342 ..     312     345 .. 0.83
   3 ?    4.0   0.6     0.018        36      15      29 ..     335     349 ..     330     350 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.83
                                      HHHHHHHHHHHHH CS
                              RecR  3 eeLaeaLqeakek 15
                                      ++L + L+eakek
  gi|330507449|ref|YP_004383877.1| 30 NRLLQNLNEAKEK 42
                                      5899*******96 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00018
                                       HHH-EE-TTT--EESSS......S-CCC CS
                              RecR  13 kekvrhCsrCgnlteed......lCaIC 34 
                                       +++ ++Cs Cg ++e+d       C+ C
  gi|330507449|ref|YP_004383877.1| 315 RNTTQRCSACGSIAEKDlsvrvhECPYC 342
                                       567899***********66665559999 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.018
                                       H-EE-TTT--EESSS CS
                              RecR  15 kvrhCsrCgnlteed 29 
                                       +v+ C+ Cg  +++d
  gi|330507449|ref|YP_004383877.1| 335 RVHECPYCGFSCDRD 349
                                       89*******999887 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3      0.26   5.2e+02      14      21 ..     318     325 ..     317     325 .. 0.90
   2 ?    9.2   0.7   0.00063       1.3      10      23 ..     332     345 ..     329     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.26
                           UPF0547  14 aqfCphCG 21 
                                       +q+C+ CG
  gi|330507449|ref|YP_004383877.1| 318 TQRCSACG 325
                                       699****9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00063
                           UPF0547  10 vPvaaqfCphCGyv 23 
                                       ++v + +Cp+CG++
  gi|330507449|ref|YP_004383877.1| 332 LSVRVHECPYCGFS 345
                                       667789******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2792.04
//
Query:       gi|330507450|ref|YP_004383878.1|  [L=395]
Description: bifunctional enzyme fae/hps [Methanosaeta concilii GP6]
Scores for complete sequence (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  236.6   0.1    1.9e-70  235.9   0.1    1.3  1  Fae              Formaldehyde-activating enzyme (Fae)
    6.1e-21   75.1   0.5      1e-20   74.3   0.3    1.5  2  OMPdecase        Orotidine 5'-phosphate decarboxylase / HUMPS
    0.00011   21.7   0.3    0.00032   20.1   0.3    1.8  1  Ribul_P_3_epim   Ribulose-phosphate 3 epimerase family
    0.00076   19.0   1.5      0.095   12.1   0.1    2.3  2  PcrB             PcrB family
     0.0027   17.2   0.0     0.0043   16.6   0.0    1.2  1  ATP-sulfurylase  ATP-sulfurylase
     0.0074   15.5   0.2      0.042   13.0   0.1    2.1  2  NanE             Putative N-acetylmannosamine-6-phosphate epi
  ------ inclusion threshold ------
       0.14   11.2   2.2       0.22   10.5   2.1    1.4  1  FMN_dh           FMN-dependent dehydrogenase


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 !  235.9   0.1   7.3e-74   1.9e-70       1     159 []       4     162 ..       4     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 235.9 bits;  conditional E-value: 7.3e-74
                               Fae   1 vGEalvgegeevAhidliiGekdgpvgtAfanalanqskghtpllavlrpnllvkPatlmvnkvtiknekqaellfG 77 
                                       vGEal+g+g+evAhidliiGek+gpvgtAfa+ l++ s+ghtpll v+rpnl+ kP+tl+v+kvt+kn++qa+++fG
  gi|330507450|ref|YP_004383878.1|   4 VGEALIGKGPEVAHIDLIIGEKEGPVGTAFASGLTQLSAGHTPLLGVIRPNLPPKPSTLIVPKVTVKNMDQAAQIFG 80 
                                       8**************************************************************************** PP

                               Fae  78 paQaavakavadaveegiipkeeaddlviivsvfidpeakdkkkiyeynyeAtklAikrAlkeePsidevleekdka 154
                                       paQ+avakavad+v+eg+ipk++a++l++ivsv+idp+a+d+++iy+yny AtklA++rA++++P+id+vl ek+++
  gi|330507450|ref|YP_004383878.1|  81 PAQTAVAKAVADSVAEGVIPKDRAEELLVIVSVYIDPKATDYDAIYRYNYGATKLAVARAMAGFPDIDKVLYEKERS 157
                                       ***************************************************************************** PP

                               Fae 155 khpfv 159
                                       +hp++
  gi|330507450|ref|YP_004383878.1| 158 THPIM 162
                                       **986 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       3.1   7.9e+03     117     147 ..      62      93 ..      57     105 .. 0.55
   2 !   74.3   0.3   3.9e-24     1e-20       2     224 ..     174     376 ..     173     377 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.1
                                       EEEESTSSGGHHHHHH.HSHHHHHHHHHHHHH CS
                         OMPdecase 117 lilaqmsskgnlmlqe.kgytqacveaarehk 147
                                       li+ +++ k+  + ++  g +q +v +a +++
  gi|330507450|ref|YP_004383878.1|  62 LIVPKVTVKNMDQAAQiFGPAQTAVAKAVADS 93 
                                       55555566655555554345555555444444 PP

  == domain 2  score: 74.3 bits;  conditional E-value: 3.9e-24
                                       EEEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHH CS
                         OMPdecase   2 nLclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekq 75 
                                        L++a D+ +  e+ +++  + +  ++ ++++++lv+  g     +++++++r+    + i++D+K+ D Gn + + 
  gi|330507450|ref|YP_004383878.1| 174 YLQVAFDLVDVAEVRRVLSALPDsDHILIEVGTPLVKMLG-----MSVVKEIRAIRpgAFIILDLKTLDTGNLEVRL 245
                                       69*********************99***************.....********99888******************* PP

                                       HHSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHH.SHHHHHHHHHHHHHHHTT CS
                         OMPdecase  76 atagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqek.gytqacveaarehkaedf 151
                                       a      +++ ad+v ++++a k++++  +++a+k+g     i+++++ ++ l++ ++  +  ++ve  r+   e  
  gi|330507450|ref|YP_004383878.1| 246 A------ADSTADAVVISGLAPKKTIELSINEARKTG--IYSIIDMLNVTDPLAVLKGlDVLPDVVELHRAIDME-- 312
                                       *......69***************************9..9*****************556666666666666633.. PP

                                       ESEEECCCHTHHHHHHTTCSCEEEH.HHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 152 vmGfvaqetlnateedaddfihltp.gigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                            a +  n    + +d++ l + g +l   ++++g++ + +e+++ +agadi++vGR+I++++d +  ae+
  gi|330507450|ref|YP_004383878.1| 313 ---KSAHAWQN----I-PDIKALAEeGRRL-LVAVAGGIRTD-TEGAALAAGADILVVGRAITRSRDIRDMAEQ 376
                                       ...34444444....4.6777776516666.*********87.66666779****************9998887 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 !   20.1   0.3   1.3e-07   0.00032     148     197 ..     316     364 ..     210     365 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.3e-07
                                       CHHHHHHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 148 evlekikkvrklidekeldlkievDGGvkldnieqiaeagadvlVagsav 197
                                       +  ++i ++++l++e ++ l + v GG+++d+  ++ +agad+lV+g+a+
  gi|330507450|ref|YP_004383878.1| 316 HAWQNIPDIKALAEE-GRRLLVAVAGGIRTDTEGAALAAGADILVVGRAI 364
                                       345677777777776.999*****************************98 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.1     0.003       7.6      23      77 ..     243     298 ..     228     304 .. 0.85
   2 !   12.1   0.1   3.7e-05     0.095     159     216 ..     311     369 ..     303     381 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.003
                                       HHHHHCTT-SEEEEECST.CHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSE CS
                              PcrB  23 veiviesgtDavmigGsq.svtldntvrllkkvsriklPivlepsnvegvvryaDa 77 
                                       v+ +++s +Dav+i+G   + t +  ++  +k   +++  +l ++++ +v +++D+
  gi|330507450|ref|YP_004383878.1| 243 VRLAADSTADAVVISGLApKKTIELSINEARKTGIYSIIDMLNVTDPLAVLKGLDV 298
                                       66789***********9989999999999999888888888999999999988886 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.7e-05
                                       EE-.TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCCSSEEEE-CHHHHHHH CS
                              PcrB 159 lEa.sGaledveevialkkklekarlivGGGirsaEkAkevveaADvivvGnvveekde 216
                                       +E  + a +++  ++al        + v GGir   + +  +  AD++vvG ++  + +
  gi|330507450|ref|YP_004383878.1| 311 MEKsAHAWQNIPDIKALAEEGRRLLVAVAGGIRTDTEGAALAAGADILVVGRAITRSRD 369
                                       5663446677888888988888889999*****99999999999**********98873 PP

>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.7e-06    0.0043      78     133 ..      96     154 ..      80     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                                       HHHS-GGGEEE-BB-SB---SCHHHHHHHHHHHHHTT-SEEEE-TTTT-STC....SS-T CS
                   ATP-sulfurylase  78 eeylpkdrvvlallplamryaGprEallhaiirknyGcthfivGrdhagvgd....fYgp 133
                                       e ++pkdr+   ll +   y  p+    +ai+r nyG+t++ v r +ag +d    +Y++
  gi|330507450|ref|YP_004383878.1|  96 EGVIPKDRAE-ELLVIVSVYIDPKATDYDAIYRYNYGATKLAVARAMAGFPDidkvLYEK 154
                                       4466666664.5566667899999999***********************9988887765 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 ?   -0.2   0.0      0.18   4.7e+02      33      61 ..      45      76 ..      38      81 .. 0.73
   2 !   13.0   0.1   1.6e-05     0.042     134     184 ..     321     372 ..     242     383 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.18
                                      S-EEEE-B---TTS---.BS-..SHHHHHHHH CS
                              NanE 33 lPiiGivkrdlpdsevr.ita..tlkdideLa 61
                                       P++G+++ +lp+++   i +  t+k++d+ a
  gi|330507450|ref|YP_004383878.1| 45 TPLLGVIRPNLPPKPSTlIVPkvTVKNMDQAA 76
                                      69**********99854155423566777655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHTT--..EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHH CS
                              NanE 134 falvkalseaglk..viaeGrintPekakkaieiGvdavvvGsaitrleeiak 184
                                       +  +kal e+g +  v + G i t  + + a+  G+d +vvG aitr ++i +
  gi|330507450|ref|YP_004383878.1| 321 IPDIKALAEEGRRllVAVAGGIRTDTEGA-ALAAGADILVVGRAITRSRDIRD 372
                                       44578999988774466789999988765.6789*************988743 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.1   8.5e-05      0.22     253     303 ..     313     364 ..     217     372 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.5e-05
                                       T---HHHCHHHHHHHH....SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 253 gapatidvLpeiveavgg..rievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                       ++  + + +p+i + +++  r+ v v gGir+ +    Ala GAd+ ++GR++
  gi|330507450|ref|YP_004383878.1| 313 KSAHAWQNIPDIKALAEEgrRLLVAVAGGIRTDTEG-AALAAGADILVVGRAI 364
                                       334445556666554443449***********9995.69************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2753.57
//
Query:       gi|330507451|ref|YP_004383879.1|  [L=521]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.7e-15   55.1   0.0      8e-14   51.8   0.0    2.1  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 !   51.8   0.0   4.5e-18     8e-14       5     214 .]     159     450 ..     155     450 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 4.5e-18
                         DDE_Tnp_1   5 evlivDattvrvpgtk.edarwgyk.ggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kg 77 
                                       e li+D t++   +    +  wgy+  g   + ++l ++ +++ +l+l ++++pg+ +d+ +lk l+ e+++    +
  gi|330507451|ref|YP_004383879.1| 159 ETLIFDITSLSSASRNiDWLEWGYNrDGLDLPQVNLGLVLSLHRHLPLYFKLFPGSISDVVTLKNLVAEVKALgiSK 235
                                       667777777776665578999****8888******************************************99**** PP

                         DDE_Tnp_1  78 klvlaDaGYasaelldtleekgvdyiirlkkntklyrk....gaeskrrgrlrkhdrnkiltksqkrrnk....... 143
                                       +l++ D+G+ s+++++++ + ++d+ii+l+  +++ +        +       k++ ++i++  +++          
  gi|330507451|ref|YP_004383879.1| 236 SLFILDRGFYSENNIKEMNDANIDFIIPLPFSVNVGKGliseTNREIESPANAKRFGGDIFYVLESEIQIgsvdayg 312
                                       *****************************777777766777745555677788999999999999988889999999 PP

                         DDE_Tnp_1 144 ......................................................................skkekgd 150
                                                                                                             ++++ g 
  gi|330507451|ref|YP_004383879.1| 313 yvlfnkkregletnsfynrlidiecaidgkefrnpidqfkrtagnferyfeytlegkkihlsrrvnaisqAVNRFGK 389
                                       999999999999999****************************************************8885555555 PP

                         DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                       ++++++  +++    ev  lyr R ++E  F +lk+ +    lr+ + +  +  l++ +++l l
  gi|330507451|ref|YP_004383879.1| 390 TILLSSSRRNW---DEVLSLYRERDEVEKKFDDLKNELEVMPLRVQKVETLQGLLFIFFISLIL 450
                                       55555555544...56779*************************************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); 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: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 3669.90
//
Query:       gi|330507452|ref|YP_004383880.1|  [L=352]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete 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   75.4   0.0    4.8e-21   74.6   0.0    1.4  1  DUF772       Transposase domain (DUF772)
    1.5e-15   57.4   4.6      5e-15   55.7   4.6    1.9  1  DDE_Tnp_1    Transposase DDE domain
      3e-05   23.8   0.3    0.00012   21.8   0.3    1.9  1  DDE_Tnp_4    DDE superfamily endonuclease
    3.1e-05   24.2   0.4    5.3e-05   23.4   0.4    1.4  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
      0.052   13.9   0.1       0.12   12.8   0.1    1.6  1  EnY2         Transcription factor e(y)2


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 !   74.6   0.0   1.3e-24   4.8e-21       1      72 [.      51     122 ..      51     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.3e-24
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp+++ ++m+k+l+lq ++glSd ele+++ +++sfr flg     + +pd+st + fR+rl+e    e+l++e
  gi|330507452|ref|YP_004383880.1|  51 GRPNIDIVIMVKALVLQSWFGLSDPELERQVTDRISFRIFLGT---TEVIPDFSTVWLFRERLIEcgrYEDLWKE 122
                                       9*****************************************5...389****************9999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   4.6   1.4e-18     5e-15      20     214 .]     177     340 ..     133     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.4e-18
                         DDE_Tnp_1  20 k............................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkql 68 
                                       +                             ++ w +kg k+++gyk hi++dt+ +li ++++t+++ hds++    
  gi|330507452|ref|YP_004383880.1| 177 PdfdkdllnisnnivssnakpkrlddgpiNEGTWAKKGSKSFFGYKGHILIDTEYHLIRKIETTTASLHDSQVDLG- 252
                                       0555555555555555555556666666677889999**********************************99777. PP

                         DDE_Tnp_1  69 ldelrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnksk 145
                                       +++l++      +aD+GY++a++  + +                            ++k+ r++ l  ++++rnk  
  gi|330507452|ref|YP_004383880.1| 253 INGLPR------YADKGYSGAKTQGYDA---------------------------AMKKAARGHKLGIKDILRNK-- 294
                                       777887......*******888877777...........................89******************.. PP

                         DDE_Tnp_1 146 kekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                              +++r+R+qiEr F+ +kr  + +++++ + +r+ +++++  +++n+
  gi|330507452|ref|YP_004383880.1| 295 -----------------------RISRKRSQIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNI 340
                                       .......................******************999************************7 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   3.4e-08   0.00012      77     130 ..     257     313 ..     195     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.4e-08
                         DDE_Tnp_4  77 vilaDkgFklse..kl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgr 130
                                          aDkg+ +++   +   ++k  ++++l  ++  +n++i++ r  +Er+++ +k+ 
  gi|330507452|ref|YP_004383880.1| 257 PRYADKGYSGAKtqGYdAAMKKAARGHKLGIKDILRNKRISRKRSQIERCFAVMKRA 313
                                       3469*****99954333455555********************************65 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 !   23.4   0.4   1.5e-08   5.3e-05      74     124 ..     294     343 ..     265     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.5e-08
                       DDE_Tnp_1_6  74 kaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                       k+  +kR+ ++E+ fa +kr++++  + ++ ++++ ++f++  +++N+++l
  gi|330507452|ref|YP_004383880.1| 294 KRISRKRS-QIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNIEQL 343
                                       45556665.***************************************997 PP

>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.3e-05      0.12       5      31 ..     107     133 ..     106     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       HHHHHHTTHHHHHHHHHHHHHHHTTHH CS
                              EnY2   5 qqkLvesGererlkelLrerLeesGWr 31 
                                       +++L+e G +e+l + L+++L+e G+ 
  gi|330507452|ref|YP_004383880.1| 107 RERLIECGRYEDLWKELQNQLDEKGFA 133
                                       589**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2826.91
//
Query:       gi|330507453|ref|YP_004383881.1|  [L=61]
Description: hypothetical protein MCON_1388 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0025   18.6   0.8     0.0029   18.3   0.8    1.2  1  VAPB_antitox  Putative antitoxin
     0.0056   16.8   0.2     0.0067   16.6   0.2    1.1  1  MatP_C        MatP C-terminal ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.8   3.3e-07    0.0029       1      48 [.       5      50 ..       5      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.3e-07
                      VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgi 48
                                      K I +++ v  +L++lK  g+ +s ++e+++e++kk +     ++ +i
  gi|330507453|ref|YP_004383881.1|  5 KRIPVTEAVWIELSELKSAGQTYSQLLEEMIEERKKARL--FRDMEKI 50
                                      7899****************************9997744..5555444 PP

>> MatP_C  MatP C-terminal ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   7.5e-07    0.0067      12      49 ..      12      47 ..       4      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.5e-07
                            MatP_C 12 avWqrLsklsqrrgsTLSetivqLieeaerkekyeeqv 49
                                      avW  Ls+l ++ g T S+ ++++iee+++ +++ + +
  gi|330507453|ref|YP_004383881.1| 12 AVWIELSEL-KSAGQTYSQLLEEMIEERKKARLF-RDM 47
                                      7*******9.789**************9776554.445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 432.14
//
Query:       gi|330507454|ref|YP_004383882.1|  [L=434]
Description: metalloenzyme domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-10   41.1   0.0    3.4e-10   39.7   0.0    1.6  2  Metalloenzyme    Metalloenzyme superfamily
    3.6e-09   36.7   0.1    1.3e-08   34.9   0.1    1.9  1  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
    5.8e-09   35.8   0.0    1.8e-08   34.2   0.0    1.7  2  Sulfatase        Sulfatase
    5.5e-05   22.3   0.0    0.00014   21.0   0.0    1.6  2  Alk_phosphatase  Alkaline phosphatase


Domain annotation for each model (and alignments):
>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.44     2e+03       4      15 ..      32      43 ..      30      58 .. 0.79
   2 !   39.7   0.0   7.5e-14   3.4e-10     121     218 ..     196     297 ..     181     321 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.44
                                      EEEEETTBB--- CS
                                      xxxxxxxxxxxx RF
                     Metalloenzyme  4 vlvvlDGlGeap 15
                                      v++v+DGlG + 
  gi|330507454|ref|YP_004383882.1| 32 VILVIDGLGSSY 43
                                      899******875 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 7.5e-14
                                       HHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                     Metalloenzyme 121 ekaldailsgkfdlvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdk. 196
                                         +++ +  gk  +++vn    D++GH+ +++++ + ++a+D  +++++ a+++++ +lvvtADHg      +    
  gi|330507454|ref|YP_004383882.1| 196 ADTVEHL-IGKPFIMLVNAGAVDSAGHNLNASGYLETVQALDGPLGRLVWACKKNNVLLVVTADHGMVFPDRE--Gk 269
                                       4455555.45455889**************************************************7532222..22 PP

                                       ...........-----EEEEEESTT--- CS
                                       ......xxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 197 ......qplTsHtlepVPilivgkglap 218
                                             +  T   +  VP+++ g+g+++
  gi|330507454|ref|YP_004383882.1| 270 gghsaeKYATRLEALRVPLVFQGPGIEE 297
                                       4566768888888888999999988776 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   2.8e-12   1.3e-08     156     238 ..     190     265 ..      31     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.8e-12
                                       HHHCHTHSHHHHHCT.SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES CS
                      Phosphodiest 156 wldaafakvvlekel.ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSD 231
                                       w  +a+ ++ +e+ l +kp  +lv+  ++D++gH++  + +  +++++ +D  +g+L+ a +++    ++ +++++D
  gi|330507454|ref|YP_004383882.1| 190 WALDAA-ADTVEH-LiGKPFIMLVNAGAVDSAGHNL--NASGYLETVQALDGPLGRLVWACKKN----NVLLVVTAD 258
                                       333333.334444.35*******************9..8999**********************....********* PP

                                       ---EEEH CS
                      Phosphodiest 232 HGmadvs 238
                                       HGm   +
  gi|330507454|ref|YP_004383882.1| 259 HGMVFPD 265
                                       ***8765 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.22     1e+03      31      64 ..      65      98 ..      31     120 .. 0.68
   2 !   34.2   0.0     4e-12   1.8e-08     208     309 .]     188     319 ..     150     319 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.22
                                      HHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHH CS
                         Sulfatase 31 rlaeeglrftnfysaaplcspsraalltgryphn 64
                                      +l+  g r  ++ +  p +++s + l tgr+ + 
  gi|330507454|ref|YP_004383882.1| 65 NLTGGGARAVDVRVPVPETTKSHSVLVTGRSEAD 98
                                      5677788888888999999999999999998776 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 4e-12
                                       H..................................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSS CS
                         Sulfatase 208 r..................................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhg 250
                                       +                                   +++ yl +v   D  +gr++ a     +++n+l+v+t+Dhg
  gi|330507454|ref|YP_004383882.1| 188 NawaldaaadtvehligkpfimlvnagavdsaghnLNASGYLETVQALDGPLGRLVWAC----KKNNVLLVVTADHG 260
                                       1445555555555566666666666666666666567788*******************....************** PP

                                       SCCCG..HHTTSSSCTTCSSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHHHTTE CS
                         Sulfatase 251 aslee..sngplrggkganayeggtrvPllvwwpgekaprvseelvshiDlfptildlagi 309
                                           +  ++g + ++k+ ++  + +rvPl+  +pg+ +  +  +  s +D++pt+l+l+++
  gi|330507454|ref|YP_004383882.1| 261 MVFPDreGKGGHSAEKY-ATRLEALRVPLVFQGPGIEEL-NLGGQWSEMDVAPTVLALLDV 319
                                       98755867788888888.********************9.9*****************985 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.36   1.6e+03       6     177 ..      33      57 ..      25      90 .. 0.63
   2 !   21.0   0.0   3.1e-08   0.00014     252     310 ..     206     263 ..     193     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.36
                                       EEEETT-SHHHHHHHHHHHCHCTCSSSTTS.TTGGG-SEEEEEESSECSTTSSGHHHHHHHHHHSSBTBTT-BSB-T CS
                   Alk_phosphatase   6 lligDGmgvstvtaaRslkeqakdklgeetllamdrfplvglsktyavdkqvtDSaataTAyacgvktyngaigvda 82 
                                       +l+ D                                                                        
  gi|330507454|ref|YP_004383882.1|  33 ILVID------------------------------------------------------------------------ 37 
                                       44444........................................................................ PP

                                       TST-B---HHHHHHHTT-EEEEEEEEETTSHHHHTTTTTBSSTTSSSHHHSTCCCHHTTS-SHHHHHHHCST-SEEE CS
                   Alk_phosphatase  83 aagkevksvleaAkkaGkstGlVtTtritdAtPaalvahvesRkwkedaavpaealeegkkdiaeqlikakkidvll 159
                                                                                                                    
  gi|330507454|ref|YP_004383882.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       EESCGGGSB..CSBCTSSTC CS
                   Alk_phosphatase 160 GGGrkeffp..aeyatdGer 177
                                       G G ++++p  + ya dG+ 
  gi|330507454|ref|YP_004383882.1|  38 GLGSSYVYPehNAYALDGSP 57 
                                       55555555544444555555 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 3.1e-08
                                       -EEEEEEETCHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHCHHCTTEEEEEEESSEESE CS
                   Alk_phosphatase 252 GFFLlVEGsrIDhaaHendavgalsEvvefdeAvkaalefakkeketlvvvTaDHshvf 310
                                        F +lV  + +D a+H+ +a g l+ v ++d  + + + + k +++ l+vvTaDH  vf
  gi|330507454|ref|YP_004383882.1| 206 PFIMLVNAGAVDSAGHNLNASGYLETVQALDGPLGRLVWACK-KNNVLLVVTADHGMVF 263
                                       58999*******************************998888.899*********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3103.07
//
Query:       gi|330507455|ref|YP_004383883.1|  [L=170]
Description: hypothetical protein MCON_1390 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-13   49.7   3.7    6.7e-13   48.9   3.7    1.5  1  DUF3795   Protein of unknown function (DUF3795)
  ------ inclusion threshold ------
        9.8    6.1  10.2        2.1    8.2   5.2    2.5  2  ZZ        Zinc finger, ZZ type


Domain annotation for each model (and alignments):
>> DUF3795  Protein of unknown function (DUF3795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   3.7   7.4e-17   6.7e-13       2      84 ..      34     137 ..      33     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 7.4e-17
                           DUF3795   2 iapCGldCeeCeayeakekeekkkkkk.......................eafeelllaleeikCeGCreeekkala 55 
                                       ++pCG+ C++C+   +  +e++++++k                       ++   l+++ + ++C GC++ +++   
  gi|330507455|ref|YP_004383883.1|  34 AGPCGILCGSCPLGGSIVAESASRTRKhitecdipnwapfvpggeaidwaAVDLGLAWMETYARCAGCENGGGPPD- 109
                                       589***********999998888888899*******************9888888999999************987. PP

                           DUF3795  56 eeCkirkCakekglefCaeCeef.pCeklk 84 
                                         C+ir Ca+ekg++ C +Cee+  C+k++
  gi|330507455|ref|YP_004383883.1| 110 --CTIRICAREKGYDLCSSCEELeGCTKFE 137
                                       ..*********************77*9986 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2      0.52   4.7e+03      30      34 ..      40      44 ..      40      48 .. 0.64
   2 ?    8.2   5.2   0.00024       2.1      22      35 ..     115     128 ..      92     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.52
                                      E-HHH CS
                                ZZ 30 LCqsC 34
                                      LC sC
  gi|330507455|ref|YP_004383883.1| 40 LCGSC 44
                                      56666 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00024
                                       ESSSSS-EE-HHHH CS
                                ZZ  22 clrcsdYDLCqsCf 35 
                                       c+r + YDLC+sC+
  gi|330507455|ref|YP_004383883.1| 115 CAREKGYDLCSSCE 128
                                       99999********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1242.26
//
Query:       gi|330507456|ref|YP_004383884.1|  [L=234]
Description: hypothetical protein MCON_1392 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-53  182.3   0.0    1.3e-53  182.0   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 !  182.0   0.0     7e-58   1.3e-53       2     204 ..      11     218 ..      10     219 .. 0.97

  Alignments for each domain:
  == domain 1  score: 182.0 bits;  conditional E-value: 7e-58
                            DUF169   2 LaealrlktePVavkfsdekpelpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfkelpeklks 78 
                                       L+ +l+ + ++V+v ++++++e+p++ + +e++ r+C m++ ar++g + ++ a+ ++C+gGa++lG+ e pe++++
  gi|330507456|ref|YP_004383884.1|  11 LKSSLGIRDNIVGVRLFKSEEEIPQDLKIVERPFRYCSMIQGARREGVSYLAHADYHQCKGGASGLGLLECPENIRT 87 
                                       7899**********************99888888******************************************* PP

                            DUF169  79 g......egylkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrlnv 149
                                       g      ++++++ e  + + +++pr+ +g++ + +vapL+k+   Pdvv+f++np q++r+vq+a++++gg r+++
  gi|330507456|ref|YP_004383884.1|  88 GalyfdkLHKCSTKESGAMIAANMPRILPGSTVASYVAPLDKMRVRPDVVIFVGNPLQARRIVQAAMFEKGG-RMSF 163
                                       *****9999999**********************************************************99.**** PP

                            DUF169 150 sfpgngaaCadivaypykegepniglgdpgarkfaklkddelafgiPyelleemv 204
                                       +++g+++ C d+++ py +ge n++lg+ g+ ++a+l+d+el++giPy+++e+++
  gi|330507456|ref|YP_004383884.1| 164 NTAGIQSFCVDATSSPYLKGEVNVSLGCDGSVRNAGLEDGELVVGIPYDMMEKIC 218
                                       ****************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1320.27
//
Query:       gi|330507457|ref|YP_004383885.1|  [L=318]
Description: hypothetical protein MCON_1393 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2262.18
//
Query:       gi|330507458|ref|YP_004383886.1|  [L=621]
Description: threonyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-49  167.7   0.0    2.7e-49  166.8   0.0    1.5  1  tRNA-Thr_ED     Archaea-specific editing domain of threonyl-t
    2.2e-16   60.3   0.9    4.4e-16   59.4   0.9    1.5  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    5.9e-16   58.4   0.1    1.3e-15   57.3   0.1    1.6  1  HGTP_anticodon  Anticodon binding domain


Domain annotation for each model (and alignments):
>> tRNA-Thr_ED  Archaea-specific editing domain of threonyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   0.0   4.5e-53   2.7e-49       1     137 []       1     137 [.       1     137 [. 0.97

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 4.5e-53
                                       -EEEEEEEEEEEEEEEEESSSS-...SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEE CS
                       tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeae..eeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvv 75 
                                       m+lLlih+d +e+eak+++ k ae  e++ k+grl+eal++FiavEk De+++++v+++ +k++++va +vka++++
  gi|330507458|ref|YP_004383886.1|   1 MQLLLIHSDFIEFEAKRPT-KLAEevEDSAKKGRLDEALCAFIAVEKFDEDDTDAVIAEGAKQVADVAGQVKAHRIM 76 
                                       9******************.77766999************************************************* PP

                                       EEE-STS-SSB--HHHHHHHHHHHHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE- CS
                       tRNA-Thr_ED  76 lypyaHLssslaspevakeilkkleeklkekglevkraPFGwykefeisckGhpLaelsrei 137
                                       +ypyaHLsssl++p +a++ilk + + l+++ +ev+raPFGwyk+f+isckGhpL+elsr+i
  gi|330507458|ref|YP_004383886.1|  77 IYPYAHLSSSLSTPATAVKILKGMADVLSQN-YEVMRAPFGWYKAFTISCKGHPLSELSRSI 137
                                       ****************************997.****************************97 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.9   7.4e-20   4.4e-16       3     178 ..     279     486 ..     277     487 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 7.4e-20
                                       EEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEE.EBTTTS.TBCTTTB-SEEEEEEEEEEES.GGGH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxx RF
                      tRNA-synt_2b   3 ledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtk.yRdEks.dsrGLlRvreFhqkdgyvfha.easl 76 
                                       +++ ++r++ L+  ++ +   ++ d  +  k LPlk++++++  +R+E++ ++ G+ R+r F++ d + ++    s+
  gi|330507458|ref|YP_004383886.1| 279 IDS-DKRKLFLRFAACFGQFLMGHDMSISYKSLPLKMIEMTRYsFRREQRgELVGIRRLRAFTMPDMHTMSRdMHSA 354
                                       444.469*******************888899*******99854******8999******************77999 PP

                                       HHHHHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETT............................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
                      tRNA-synt_2b  77 ddslrdlikaisriferlglefraiielmsaksadykdkkefeavses............................. 124
                                        +++r+   a   +++++gle+   +   +++  +yk+ +ef a                                 
  gi|330507458|ref|YP_004383886.1| 355 IEEFRKQYLASISVLKEVGLEVEDYEVAIRFTRDFYKENQEFIAGLVDiikkpvliemwderffyfvlkfefnfvdt 431
                                       *****9999999********994444444444456777777776544446777777777777777777777777777 PP

                                       TSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxx RF
                      tRNA-synt_2b 125 ltkgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileq 178
                                       ++k+  ++t+q +  + +er +++++de + ++++i+++ +  g +eR++ aile+
  gi|330507458|ref|YP_004383886.1| 432 MDKASALSTVQID-VENAERYDINYIDESGARRRPILLHCSpSGaIERVMYAILEK 486
                                       *************.999************************9999*********96 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.1   2.2e-19   1.3e-15       1      91 [.     507     596 ..     507     599 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 2.2e-19
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET... CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdr... 74 
                                       qv +ip++e   +++e a  la  L   g+r+++dd++e++gkkir+a + ++p++ v+G++el++g ++v  r   
  gi|330507458|ref|YP_004383886.1| 507 QVRIIPVAE---RHQERALALAGIL---GFRTDIDDRDETVGKKIRDAGREWVPYVAVIGDEELQSGRLAVTIRses 577
                                       89*******...9**********99...7****************************************99999989 PP

                                       ..TTCEEEEEETTHHHHHH CS
                    HGTP_anticodon  75 ..dtreqervsldelvekl 91 
                                         ++ ++ ++++del+e l
  gi|330507458|ref|YP_004383886.1| 578 tpKSPAKKSMTVDELKERL 596
                                       8888899********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4432.28
//
Query:       gi|330507459|ref|YP_004383887.1|  [L=450]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-25   89.8   0.0    3.3e-25   89.0   0.0    1.4  1  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
      0.014   14.7   0.3      0.021   14.1   0.3    1.3  1  DDE_Tnp_2    Archaeal putative transposase ISC1217
      0.019   13.3   0.0       0.03   12.6   0.0    1.2  1  DDE_Tnp_1_4  Transposase DDE domain group 1
      0.075   13.0   1.0        1.4    8.9   0.1    2.8  3  Tudor_FRX1   Fragile X mental retardation Tudor 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 !   89.0   0.0   7.3e-29   3.3e-25       2     212 ..     133     371 ..     132     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 7.3e-29
                         DDE_Tnp_1   2 skrevlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkq..lldelrprk 76 
                                       s+r+v i D+t +r +++ +d+++     k  +g+k+  ++++    + s+ i p n++d+k+lk   ++      k
  gi|330507459|ref|YP_004383887.1| 133 SFRDVMIQDSTIIRLHKSLADKWPATRSRKVAAGVKVAFLTSAIANSPKSISILPENTNDVKTLKIgpWV------K 203
                                       6899***************9999988899999********************************995555......7 PP

                         DDE_Tnp_1  77 gklvlaDaGYasaelldtleekgvdyiirlkkntklyrk.............gaeskrrgrlrkhdrnkiltksqkr 140
                                       + ++l D G+ +++l+ ++ e+g+++++rlk+n++ ++              + +++++ +l+k d    ++ + ++
  gi|330507459|ref|YP_004383887.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVgtnqvrntrgvdlNGKHLKDIKLEKSDDIFDVNVEVSF 280
                                       789************************************99777666666663444444444444444444444444 PP

                         DDE_Tnp_1 141 rnk...................skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrgl 198
                                       +++                    +++++++ y+tn++s+ l a+eva+ y+ Rw++E +Fk+lk+++ ld   ++++
  gi|330507459|ref|YP_004383887.1| 281 DRRsyrgeskkdnkifrlvaiyNTEAEEHHFYLTNISSDILNASEVAAVYSGRWEVELIFKELKSRYALDQITTKSP 357
                                       4447777777777799999999999**************************************************** PP

                         DDE_Tnp_1 199 nrveaqllllllal 212
                                        ++ea ++  +l+l
  gi|330507459|ref|YP_004383887.1| 358 YAIEALIWVSILTL 371
                                       *******9998876 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   4.6e-06     0.021     219     288 ..     274     346 ..     202     384 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                         DDE_Tnp_2 219 rhvpvaelPeGeylveyl.dtvikllvlddykkdgrrylfstdln...dtdediittWenrWdievlirelkal 288
                                        +v+v+ + + +y  e   d+ i  lv +   + +  +++ t++    + + ++ + +  rW++e +++elk+ 
  gi|330507459|ref|YP_004383887.1| 274 VNVEVS-FDRRSYRGESKkDNKIFRLVAIYNTEAEEHHFYLTNISsdiLNASEVAAVYSGRWEVELIFKELKSR 346
                                       445543.7777888887767777767777777888999**999973335799********************73 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.6e-06      0.03     217     368 ..     204     372 ..     197     399 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.6e-06
                       DDE_Tnp_1_4 217 kilvRgDSafarpellkwceergvdYviglaknsrlealiaelvekakteaaekkek................erey 277
                                       +i++  D +f + +l++ + e+g ++v +l++n++     ++ v +++  + + k+                 e+++
  gi|330507459|ref|YP_004383887.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVGTNQVRNTRGVDLNGKHLkdikleksddifdvnvEVSF 280
                                       578889999**********************999877766666666666666654436799999999**99999999 PP

                       DDE_Tnp_1_4 278 refayqaesWskerrVvakaerpaeglnlrfvvTsla..klspeelyeqlYcaRGemEnrIKeakldlaadrtsshs 352
                                        +  y+ es + ++   + a +++e  +++f +T+++   l+++e+   +Y  R e+E  +Ke k+  a+d++ ++s
  gi|330507459|ref|YP_004383887.1| 281 DRRSYRGESKKDNKIFRLVAIYNTEAEEHHFYLTNISsdILNASEVA-AVYSGRWEVELIFKELKSRYALDQITTKS 356
                                       99999999855444333334455556667999****99888999999.9*************************999 PP

                       DDE_Tnp_1_4 353 faaNqlrlllsalAyn 368
                                         a ++ +++s l   
  gi|330507459|ref|YP_004383887.1| 357 PYAIEALIWVSILTLL 372
                                       9999988888887654 PP

>> Tudor_FRX1  Fragile X mental retardation Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00031       1.4      17      36 ..      22      41 ..      18      44 .. 0.88
   2 ?    1.1   0.0     0.085   3.8e+02      18      31 ..     269     282 ..     257     291 .. 0.89
   3 ?   -2.6   0.0       1.2   5.4e+03      13      36 ..     313     337 ..     311     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00031
                        Tudor_FRX1 17 vkdvhedsltvaFennWqpe 36
                                       kd+ e++lt +Fe +W  +
  gi|330507459|ref|YP_004383887.1| 22 EKDIVEQELTRMFESKWIRD 41
                                      59***************765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.085
                        Tudor_FRX1  18 kdvhedsltvaFen 31 
                                        d+++ ++ v+F+ 
  gi|330507459|ref|YP_004383887.1| 269 DDIFDVNVEVSFDR 282
                                       59**********96 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.2
                        Tudor_FRX1  13 ykafvkdvhed.sltvaFennWqpe 36 
                                       +  +  d+++  ++ +++   W  e
  gi|330507459|ref|YP_004383887.1| 313 LTNISSDILNAsEVAAVYSGRWEVE 337
                                       5566778888526888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3389.97
//
Query:       gi|330507460|ref|YP_004383888.1|  [L=381]
Description: cell surface protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-45  154.1  99.2    1.6e-17   63.8  22.3    3.2  4  Beta_helix       Right handed beta helix region
    2.1e-41  141.8  59.1    1.5e-21   76.8  23.3    2.2  2  NosD             Periplasmic copper-binding protein (NosD)
    8.1e-06   25.8  25.0    1.5e-05   25.0  15.3    2.9  2  Pectate_lyase_3  Pectate lyase superfamily protein


Domain annotation for each model (and alignments):
>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8  22.3   2.8e-21   1.6e-17       4     119 ..      85     201 ..      82     203 .. 0.94
   2 !   63.1  26.2   4.5e-21   2.7e-17      36     157 ..     164     284 ..     164     285 .. 0.97
   3 !   40.8  15.7   3.3e-14     2e-10      62     156 ..     237     334 ..     237     335 .. 0.90
   4 !   27.7  11.0   3.5e-10   2.1e-06      94     156 ..     268     334 ..     265     365 .. 0.56

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 2.8e-21
                                       EE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S-- CS
                        Beta_helix   4 singssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnn 80 
                                        in ++  ++++++i+ + ++G+++ +++n +ienn i++   +Gi+++g+  n+i nn+i++n+  gi l+ ++ n
  gi|330507460|ref|YP_004383888.1|  85 TINADGA-KVSGFEIRTTRRTGVHVLSGGN-IIENNSISG-CLDGIRLEGAHSNIIANNSINNNT-NGITLYSSKEN 157
                                       5677777.**********************.*********.************************.*********** PP

                                       EEES-EEES-.....SS-SEE-TT-S--EEES-EEESTT--SEE CS
                        Beta_helix  81 lienneitdn.....ggsGiylnyssnntienNiidnnagsGiv 119
                                        i+n++i+dn     +++Gi+l yss n+i++N+++nn+   i+
  gi|330507460|ref|YP_004383888.1| 158 RIQNCDIRDNyineeSDCGIFLIYSSGNVIQDNQLRNNGDTSIS 201
                                       **********99999888********************987776 PP

  == domain 2  score: 63.1 bits;  conditional E-value: 4.5e-21
                                       EES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-T.T-S--EEES-EEE CS
                        Beta_helix  36 ienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiyln.yssnntienNiid 111
                                       i++n+i+  s+ Gi + +ss+n+i++n+ ++n+++ i l+ asnn i nn++++n+ +Gi+l+ +s+ n+i +N+++
  gi|330507460|ref|YP_004383888.1| 164 IRDNYINEESDCGIFLIYSSGNVIQDNQLRNNGDTSISLRSASNNSIINNTVIENDWYGISLSeSSNGNRIAYNNAS 240
                                       789************************************************************66777********* PP

                                       STT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E CS
                        Beta_helix 112 nnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNt 157
                                       nn  +Gi++d s  n+   +N++++n+ +Gi++ ++s+++ +++N 
  gi|330507460|ref|YP_004383888.1| 241 NNIDAGIYLDCSR-NNHLLGNRAVDNS-KGIYLSYDSNDNILEENY 284
                                       *************.************8.***************995 PP

  == domain 3  score: 40.8 bits;  conditional E-value: 3.3e-14
                                       -EEE---SEEE-TT--S--EEES-EEES-SS-SEE-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES- CS
                        Beta_helix  62 ntisdnngggialfgasnnlienneitdnggsGiyln.yssnntienNiidnnagsGividdsssnvtvtnNtitnn 137
                                       n+ s+n + gi+l+ + nn + +n+  dn++ Giyl+ +s++n++e+N+++ n+  G+++ + +sn+t+ +Nt+ +n
  gi|330507460|ref|YP_004383888.1| 237 NNASNNIDAGIYLDCSRNNHLLGNRAVDNSK-GIYLSyDSNDNILEENYLSQNG-KGLYLANHASNNTILGNTAQDN 311
                                       67788999*********************99.*****66999************.********************** PP

                                       SSEEEE-TT-SS.....--EEES- CS
                        Beta_helix 138 kgaGiavvgsss.....nvtvrnN 156
                                       + +Gi++++ss+      +++ nN
  gi|330507460|ref|YP_004383888.1| 312 G-YGIYLTFSSRwdlvyANHLINN 334
                                       7.********99766666666665 PP

  == domain 4  score: 27.7 bits;  conditional E-value: 3.5e-10
                                       SEE-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS.....--EEES- CS
                        Beta_helix  94 Giyln.yssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsss.....nvtvrnN 156
                                       Giyl+ +s++n++e+N+++ n+  G+++ + +sn+t+ +Nt+ +n+ +Gi++++ss+      +++ nN
  gi|330507460|ref|YP_004383888.1| 268 GIYLSyDSNDNILEENYLSQNG-KGLYLANHASNNTILGNTAQDNG-YGIYLTFSSRwdlvyANHLINN 334
                                       5555533555555555555555.55555555555555555555554.5555555555433333333333 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0  32.5   1.5e-23     9e-20      22     172 ..      86     242 ..      70     244 .. 0.90
   2 !   76.8  23.3   2.5e-25   1.5e-21      74     212 ..     236     361 ..     235     375 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 1.5e-23
                              NosD  22 ensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntle.. 96 
                                        n++g+++s+ ei+++r +  +  s +n i++n i+ +  Gi+le+++sn+i +n +++n++Gi+l+ss++n ++  
  gi|330507460|ref|YP_004383888.1|  86 INADGAKVSGFEIRTTRRTGVHVLSGGNIIENNSISGCLDGIRLEGAHSNIIANNSINNNTNGITLYSSKENRIQnc 162
                                       478999**************9*************************************************7766633 PP

                              NosD  97 ...nNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNyF 169
                                          +N i++ ++ Gi+l +ss+n i++N+   n ++ i+l+++s+n i +N++ +n+ +Gi l +ss+gn+i  N+ 
  gi|330507460|ref|YP_004383888.1| 163 dirDNYINEESDCGIFLIYSSGNVIQDNQLRnNGDTSISLRSASNNSIINNTVIENDWYGISLSESSNGNRIAYNNA 239
                                       333777777777******************98999***************************99999*****99998 PP

                              NosD 170 inn 172
                                        nn
  gi|330507460|ref|YP_004383888.1| 240 SNN 242
                                       565 PP

  == domain 2  score: 76.8 bits;  conditional E-value: 2.5e-25
                              NosD  74 edntlssnesGialmsssnntlenNtisnnenyGillsdssn.ntisnNtisnnnkGiflens.ssntitgNriesn 148
                                       ++n  ++ ++Gi+l+ s+nn l +N++ +n++ Gi+ls+ sn n +++N  s+n+kG++l n  s+nti gN+ ++n
  gi|330507460|ref|YP_004383888.1| 236 YNNASNNIDAGIYLDCSRNNHLLGNRAVDNSK-GIYLSYDSNdNILEENYLSQNGKGLYLANHaSNNTILGNTAQDN 311
                                       577888888***********999*********.**99976662667788888**********99************* PP

                              NosD 149 qkiGilllsssegntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydg 212
                                        ++Gi+l+ ss   ++y N +inn  n+++ g+ nn+W++ +            +GNy+sd  g
  gi|330507460|ref|YP_004383888.1| 312 -GYGIYLTFSSRWDLVYANHLINNGCNAYDRGE-NNRWDNGS------------QGNYYSDLGG 361
                                       .*****9999999*****************996.********............*******988 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 !   25.0  15.3   2.5e-09   1.5e-05      21     214 ..      35     247 ..      30     248 .. 0.73
   2 !    5.5   2.1    0.0022        13     143     210 ..     264     336 ..     252     340 .. 0.60

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.5e-09
                                       HHHHH......HTSS-EEE-SEEEEESS-EEE-SSEEEEES-..........TTTEEEEE-TT-SS--SEEES-TTT CS
                   Pectate_lyase_3  21 iqkaiscasatttgavVYfPaGtYlvsspiilksgvqLvGdg..........ngrpvlkaaaafvgaglidgdpyvs 87 
                                       +q ai       +g+++ + +G Y+ s  i  +  ++L G g          n+ ++    a++ g  + ++++++ 
  gi|330507460|ref|YP_004383888.1|  35 LQGAI---NRADSGDTIIVREGVYRESLNI--TRPIVLEGRGrplldgsaigNALTINADGAKVSGFEIRTTRRTG- 105
                                       77888...7778899999999999977776..9999**99996666666664333333333333555555555555. PP

                                       -.......-EEEEEEEEEEEGGGG-SS---S........SEEEES-EEEEEEEEEEES-SSEEE-SSS---TT---S CS
                   Pectate_lyase_3  88 ggs.....ealiatnnfyrqirnlkiditav........apgatgihwqtaqatslenvefemseasgtkhqgifie 151
                                         +      ++i++n+++ ++  +++             +++++gi   +++   ++n++++ +  ++++  gif+ 
  gi|330507460|ref|YP_004383888.1| 106 --VhvlsgGNIIENNSISGCLDGIRLEGAHSniiannsiNNNTNGITLYSSKENRIQNCDIRDNYINEESDCGIFLI 180
                                       ..03334566777777777766666663333335544447777****************9966666655667***** PP

                                       S--EEEEES-EEES-SS-SEEE.S.-EEEEEES-EEE-S--SEEE-TT-E.EEEE.EEEEESSSEEE CS
                   Pectate_lyase_3 152 ngsggflndlvfsglgdigiav.g.nqqftvrnitfnnattgievlwgwg.wtlk.nvkinncegGi 214
                                       ++sg++++d   +++gd+ i + + +++++++n +++n   gi+++++++   ++ n+  nn   Gi
  gi|330507460|ref|YP_004383888.1| 181 YSSGNVIQDNQLRNNGDTSISLrSaSNNSIINNTVIENDWYGISLSESSNgNRIAyNNASNNIDAGI 247
                                       *******99999999*******548*********************955547777477778888888 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0022
                                       ---TT---SS--EEEE...ES-EEES-SS-SEEES-EEEEEES-EEE-S--SEEE-T..T-EEEEEEEEE.ESS CS
                   Pectate_lyase_3 143 tkhqgifiengsggfl...ndlvfsglgdigiavgnqqftvrnitfnnattgievlw..gwgwtlknvki.nnc 210
                                       ++ +gi+++++s++ +   n l  +g g + ++ +  + t+  +t ++++ gi++     w+ +++n  i n+c
  gi|330507460|ref|YP_004383888.1| 264 DNSKGIYLSYDSNDNIleeNYLSQNGKGLYLAN-HASNNTILGNTAQDNGYGIYLTFssRWDLVYANHLInNGC 336
                                       5678*********77777444555554444444.4444455555555558888876512555666666553444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); 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:                         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 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2622.20
//
Query:       gi|330507461|ref|YP_004383889.1|  [L=210]
Description: hypothetical protein MCON_1400 [Methanosaeta concilii GP6]
Scores for complete 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-13   48.4   0.0    1.7e-12   47.6   0.0    1.4  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 !   47.6   0.0   9.3e-17   1.7e-12       2      78 ..       4      86 ..       3      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 9.3e-17
                   Acylphosphatase  2 rllvtG.rVQgvgFRkfvrrlAkelglkGy.vrNlsdg...sVeivaegeeekvekfleelksgppk.arvdeveveel 74
                                      ++++tG +V+ vg+R+++ ++A +l l+G+ v N+++g   sV +++  +++   +f e+ k++ p+ ar+d++  e++
  gi|330507461|ref|YP_004383889.1|  4 KITITGpKVHDVGYRPWLTEKAVDLALRGFeVYNDAEGdlqSVVALVDSDKRRATQFFEFAKAELPPlARIDDIRSEPY 82
                                      799***********************************999999*******************88888*********** PP

                   Acylphosphatase 75 eeee 78
                                      +ee 
  gi|330507461|ref|YP_004383889.1| 83 DEEI 86
                                      9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1451.56
//
Query:       gi|330507462|ref|YP_004383890.1|  [L=601]
Description: Radical SAM N-terminal domain-containing protein, partial [Methanosaeta concilii GP6]
Scores for complete 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-127  423.0   0.0   8.1e-127  422.6   0.0    1.2  1  Radical_SAM_N  Radical SAM N-terminal
    4.3e-31  108.3   0.0    7.9e-31  107.4   0.0    1.4  1  DUF3362        Domain of unknown function (DUF3362)
    4.5e-15   56.4   0.2    1.8e-14   54.5   0.1    2.0  2  Radical_SAM    Radical SAM superfamily


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 !  422.6   0.0  1.3e-130  8.1e-127       1     298 []       7     304 ..       7     304 .. 0.97

  Alignments for each domain:
  == domain 1  score: 422.6 bits;  conditional E-value: 1.3e-130
                     Radical_SAM_N   1 flpvsrkemeergwdelDvilvsgDaYvDhpsfgaaligrlLeaeGfrvgiiaqPdwksaedfkklGkPrlffgvsa 77 
                                       flp+s +e +++g++++D+ilvsgDaYvDhpsfg  l+gr+L ++G+ vgi+aqPdwk++ed+ +lG+Prlffg+++
  gi|330507462|ref|YP_004383890.1|   7 FLPISIQEAKNLGIEQFDIILVSGDAYVDHPSFGSGLLGRVLWDAGYAVGIVAQPDWKKDEDLLRLGRPRLFFGITS 83 
                                       9**************************************************************************** PP

                     Radical_SAM_N  78 GnlDsmvnkytaekklrsdDaytpggkagkRPdravivYsnlireaykdvpvvlGgiEaSLRriahYDywsdkvrrs 154
                                       Gn+Dsmvn++t + k+r++D y+pgg+   RPdra+i+Y+n++++++++vpvvlGgiEaSLRr+ahYDywsd+vr+s
  gi|330507462|ref|YP_004383890.1|  84 GNVDSMVNNFTPNLKRRRRDVYSPGGRL-LRPDRAAIIYANRVHSLFPNVPVVLGGIEASLRRFAHYDYWSDSVRQS 159
                                       **************************97.9*********************************************** PP

                     Radical_SAM_N 155 illdskadllvyGmgeraiveiakrlakgeeveelkdirgtavllkkea..kakekevielpsyeevkedkklyaea 229
                                       il+d+ adllvyGmge++i+e+a+rl++gee++++ d++gtav+ + ++  +a +++++ +p ++evk dk++ya+a
  gi|330507462|ref|YP_004383890.1| 160 ILADAPADLLVYGMGEKPILEVARRLNAGEEIAQIGDVPGTAVKEEVRRwrEAGRQDAVIIPGFAEVKGDKRKYAQA 236
                                       *******************************************87764433333489******************** PP

                     Radical_SAM_N 230 frlleeetnplnakalvqkhgdravvlnppalplsteelDevyelpyarkahpsykkkkipalemikfS 298
                                       f++ ++e++p++a+a+vq h +++v++nppalplst+elD++yelpy+rkahpsy ++ ipale ++fS
  gi|330507462|ref|YP_004383890.1| 237 FAAHYKEQDPYHARAVVQPHPKTVVIQNPPALPLSTAELDQIYELPYSRKAHPSY-REPIPALEPVRFS 304
                                       *******************************************************.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 !  107.4   0.0   1.3e-34   7.9e-31       1      86 [.     516     595 ..     516     600 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 1.3e-34
                           DUF3362   1 dqVqtFyPsPmatattmYhtgknpltkvkreeesvdvvrgekerrlhkAllrYhdpknwpllreALkkmGredLiGn 77 
                                       +qVq+F P+Pm+++t+mY+tg++p t      ++v+++rge e+r+++A+l+Y+dp n++l+re L++ Gr+dLiG+
  gi|330507462|ref|YP_004383890.1| 516 EQVQDFTPTPMTISTAMYYTGLDPFT-----LQPVHIPRGE-EKRIQRAMLQYRDPGNYDLVREGLERIGRKDLIGE 586
                                       7*************************.....99******87.689******************************** PP

                           DUF3362  78 gkkhLiptf 86 
                                       g+k+Lip +
  gi|330507462|ref|YP_004383890.1| 587 GEKCLIPSR 595
                                       *******86 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.43   2.6e+03      88     105 ..     201     218 ..     175     265 .. 0.69
   2 !   54.5   0.1   2.9e-18   1.8e-14       2     167 .]     306     508 ..     305     508 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.43
                                       CHGHHHHHHHHHTT.-SEE CS
                                       xxxxxxxxxxxxxx.xxxx RF
                       Radical_SAM  88 lpdeeklerllelg.vdrv 105
                                        + +e ++r +e+g  d v
  gi|330507462|ref|YP_004383890.1| 201 AV-KEEVRRWREAGrQDAV 218
                                       44.4444444444433322 PP

  == domain 2  score: 54.5 bits;  conditional E-value: 2.9e-18
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx................. RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggeplly................. 60 
                                       +  rgC + CsfCa +++  +++ ++s+s+ +i++e+++l++ +g ++ +  +gg p+++                 
  gi|330507462|ref|YP_004383890.1| 306 TSHRGCFGSCSFCALTHH--QGRIVQSRSISSIVREAERLAQMPGfKGIIQDVGG-PTANmyglvcprwkqgacpdr 379
                                       6779*************8..********************999997888888888.********************* PP

                                       .............TTHHHHHHHHHHTCCCTEEEEEEECSSCHG......HHHHHHHHHTT.-SEEEEEEBSSSHHHH CS
                                       .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                       Radical_SAM  61 .............pdfvellerlaklavpgiritvetngtlpd......eeklerllelg.vdrvslgleaaddekv 117
                                                    +  vell+rl+++  pg+r +++ +g+++d        +le l + +   ++ +  e+++   v
  gi|330507462|ref|YP_004383890.1| 380 lcsadcptlekdhSLQVELLRRLRAI--PGVRRVFVGSGIRHDlvmadrSGYLEDLCRHHvSGHLKIAPEHISRT-V 453
                                       **********8876677777777777..9**************99988866666666666677899999999998.9 PP

                                       HHHHT..CTSHHHHHHHHHHHHHHTTSET...EEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxx..xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 118 lklmn..rghtfeevlealeklreagikr...vvdrivglpGendeeleellell 167
                                        + m+  +++ ++++ e ++++ +a +++     + + g+pG + ++++el+e+l
  gi|330507462|ref|YP_004383890.1| 454 TECMHkpPRQVLDDFRERFRAASQAAGREqyiLPYLMSGHPGCTIADMVELAEYL 508
                                       998888888999*************99999999******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 4295.53
//
Query:       gi|330507463|ref|YP_004383891.1|  [L=314]
Description: hypothetical protein MCON_1403 [Methanosaeta concilii GP6]
Scores for complete 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   25.8   0.1    4.1e-05   23.2   0.1    2.2  1  Hpr_kinase_C  HPr Serine kinase C-terminal domain
    0.00093   18.0   0.0     0.0012   17.6   0.0    1.1  1  PEPCK_ATP     Phosphoenolpyruvate carboxykinase
     0.0052   16.9   0.0      0.012   15.8   0.0    1.6  1  AAA_33        AAA domain
  ------ inclusion threshold ------
        0.1   12.4   0.1       0.23   11.2   0.1    1.6  1  AAA_29        P-loop containing region of AAA domain
       0.15   12.3   0.0       0.29   11.3   0.0    1.5  1  AAA_28        AAA domain


Domain annotation for each model (and alignments):
>> Hpr_kinase_C  HPr Serine kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   1.1e-08   4.1e-05       7      50 ..     119     163 ..     113     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.1e-08
                                       EEEESEEEEETTEEEEEEESTCHHHHHHHHHHHTTT-.EEEEESS CS
                      Hpr_kinase_C   7 tsvhGvlvdvygvGvLitGesgvGKselaleLikrgh.rLvaDDa 50 
                                        svhG ++d+ g G+ i G sg GK+  +  L++    r+v+DD 
  gi|330507463|ref|YP_004383891.1| 119 YSVHGACLDMRGQGICILGGSGAGKTTHTYGLLRNPRmRVVSDDW 163
                                       589******************************987658999996 PP

>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.5e-07    0.0012     155     238 ..      76     162 ..      60     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.5e-07
                                       SS-EEEEETTTTEEEEES---THHHHHHHHHHHHHHHH.HTT-EEEEEEEEE-T.TS-EEEEEE-TTSSHHHHH... CS
                         PEPCK_ATP 155 setvvalnlekklvlilgteYaGEikKsifsvmnyllp.kkgvlsmhcsanvgekkgdvalfFGLSGtGKTtLs... 227
                                        e+ v+ n +++++ +++++Y G +k   +sv+  +l   +++ s+h ++    +++ +++ +G SG+GKTt +   
  gi|330507463|ref|YP_004383891.1|  76 GENQVLYNPQSRTAFLINMDYYGWVKSLALSVAGDILEdYHNIYSVHGACLDM-RGQGICI-LGGSGAGKTTHTygl 150
                                       578899***************************999997899*****988655.4545555.688*******88666 PP

                                       .-BTTB-EEESS CS
                         PEPCK_ATP 228 .adperkligdD 238
                                         +p+ +++ dD
  gi|330507463|ref|YP_004383891.1| 151 lRNPRMRVVSDD 162
                                       688999999998 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.3e-06     0.012       4      50 ..     135     185 ..     133     213 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.3e-06
                            AAA_33   4 lvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqq....sktdytr 50 
                                       + G +G+GK+t   +ll++  + ++s d ++ r+fg+d+      k+ y+r
  gi|330507463|ref|YP_004383891.1| 135 ILGGSGAGKTTHTYGLLRNPRMRVVSDDWFFGRIFGDDVLaygsEKNFYIR 185
                                       5699*************988899999999999****665422224444554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   6.5e-05      0.23      10      37 ..     119     145 ..     114     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.5e-05
                            AAA_29  10 gtfdghtieidlkgatlltGpsGsGKST 37 
                                       ++ +g  ++++ +g + + G sG+GK+T
  gi|330507463|ref|YP_004383891.1| 119 YSVHGACLDMRGQG-ICILGGSGAGKTT 145
                                       56666666666555.***********99 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.2e-05      0.29       2      27 ..     133     159 ..     132     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.2e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvv 27 
                                       i+i+Gg+++GKTt +  L ++  ++vv
  gi|330507463|ref|YP_004383891.1| 133 ICILGGSGAGKTTHTYGLLRNpRMRVV 159
                                       89***********99888776566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2131.39
//
Query:       gi|330507464|ref|YP_004383892.1|  [L=205]
Description: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [Methanosaeta concilii GP6]
Scores for complete sequence (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  149.0   0.3    1.5e-43  148.8   0.3    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)
  ------ inclusion threshold ------
       0.17   11.0   0.0       0.36    9.9   0.0    1.4  2  Sugar-bind  Putative sugar-binding domain


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.8   0.3   1.7e-47   1.5e-43       1     184 [.       4     196 ..       4     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 148.8 bits;  conditional E-value: 1.7e-47
                                       EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTT..S---EEEE-SSHHHHHHHHHHHHCTT...--EE CS
                        His_Phos_1   1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlag..epidaiysSplkRarqTaeliaealg...lpve 72 
                                       l+L+RHG++ wn+e+r+ g+td++L+ +G+e+A+ +++ ++g  + id++y+S lkRa++T+ +++++++   +pv+
  gi|330507464|ref|YP_004383892.1|   4 LVLLRHGQSLWNRERRFTGWTDIDLSFQGIEEARDAGRIMKGagITIDVAYTSLLKRAVRTMWIVLGEMDltrIPVI 80 
                                       79***************************************966777777*************************** PP

                                       E-GGGS----GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-B..S-BHHHHHHHHHHHHH.HHHHHTTTSE.EEEE CS
                        His_Phos_1  73 ldegLrEidfGdweglttaeiaeeypeeleawlrdpadvrppg..gEsledvaaRvaaale.elaarheget.vlvV 145
                                       +  +L+E+ +Gd+eg++ +e++e y +e  +++r+   +r+p    Esl+dv++R+ + ++ ++aa+ ++++ vlvV
  gi|330507464|ref|YP_004383892.1|  81 KSWRLNERAYGDFEGRSLDEAEELYGAEQVRRWRKGFLHRFPApsSESLKDVQERLLPLWQgQIAADLKKGRgVLVV 157
                                       **************************9999999988888888888****************888888887778**** PP

                                       E-HHHHHHHHHHHHT--GGGGGGB---TT-EEEEEE-SS CS
                        His_Phos_1 146 sHggvirallarllglpleelrrleldnaslsvlefdeg 184
                                       sHg +iral++++ +++ +++++le+++as    e+d++
  gi|330507464|ref|YP_004383892.1| 158 SHGNTIRALVKHIEEISDQNIEELEVHTASPILYELDGR 196
                                       ******************************988888876 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.28   2.5e+03     139     168 ..      20      49 ..      17      62 .. 0.76
   2 ?    9.9   0.0     4e-05      0.36      26      78 ..     124     177 ..     122     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.28
                                       HHHHHT-SEEEEE-EEHCCCCHHHCCTTS- CS
                        Sugar-bind 139 lelakkadvalvGiGsaseeaklvkrgflt 168
                                       ++ ++++d+ + Gi +a+++ +++k   +t
  gi|330507464|ref|YP_004383892.1|  20 FTGWTDIDLSFQGIEEARDAGRIMKGAGIT 49 
                                       677899999999999998888888777666 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 4e-05
                                       SSTSTTCHHHHHHHHHHHHHHHHH--TTE.EEEE-SSHHHHHHHHHTHHCCHTC CS
                        Sugar-bind  26 pddadeedvlealgraaaqllesllkdgd.vvgvgwGrtlsavaealtpkslrd 78 
                                       p+ ++ +dv+e+l ++    +   lk+g  v+ v++G+t++a+++++++ s ++
  gi|330507464|ref|YP_004383892.1| 124 PSSESLKDVQERLLPLWQGQIAADLKKGRgVLVVSHGNTIRALVKHIEEISDQN 177
                                       555666889999999999999999****99*****************9977666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1295.70
//
Query:       gi|330507465|ref|YP_004383893.1|  [L=94]
Description: peptidyl-prolyl cis-trans isomerase C [Methanosaeta concilii GP6]
Scores for complete 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   89.3   0.0    3.1e-25   88.9   0.0    1.2  1  Rotamase    PPIC-type PPIASE domain
    7.5e-25   87.7   0.0    1.1e-24   87.1   0.0    1.3  1  Rotamase_3  PPIC-type PPIASE domain
    5.2e-10   40.2   0.0    5.8e-10   40.1   0.0    1.0  1  Rotamase_2  PPIC-type PPIASE domain
  ------ inclusion threshold ------
       0.19   11.4   0.1       0.31   10.7   0.0    1.4  2  DUF2291     Predicted periplasmic lipoprotein (DUF2291)


Domain annotation for each model (and alignments):
>> Rotamase  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.0     7e-29   3.1e-25      17      95 ..      13      90 ..       2      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 7e-29
                                      HHHHHHHHHHCCTCCCHHHHHHHHCCC-.-CHHHCCTTEEECEETTTS-CCCHHHHCCS-CT-B-S-EEETTEEEEEEE CS
                          Rotamase 17 eakakaeeileqlksgedtFeelArkySddknsakngGdlgwvekgqlppefekaafslkkGeisepvetkfGfhiikl 95
                                      ++++ka e++e l sg+++F+++ArkyS +++s k+gGdlgw+ kg ++pefekaaf+ +kG+i++pv+++fG+h+i++
  gi|330507465|ref|YP_004383893.1| 13 KTEKKALEVKELLASGQESFAQMARKYS-QCPSGKSGGDLGWFGKGRMVPEFEKAAFEGEKGKIIGPVKSQFGYHLIRV 90
                                      56889***********************.************************************************98 PP

>> Rotamase_3  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.0   2.5e-28   1.1e-24      15     116 .]       4      94 .]       1      94 [] 0.89

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 2.5e-28
                        Rotamase_3  15 svkvshIlistkgkesrseeeakakadsllaalk.egadFaalAkeySdDpaskenGGelgwftkgqmvkeFedavf 90 
                                       +v+++hIl +t           ++ka ++ + l   +++Fa++A++yS+ p+ +++GG+lgwf kg+mv+eFe+a+f
  gi|330507465|ref|YP_004383893.1|   4 EVHAAHILCKT-----------EKKALEVKELLAsGQESFAQMARKYSQCPS-GKSGGDLGWFGKGRMVPEFEKAAF 68 
                                       56777777764...........56778888888868899**********886.************************ PP

                        Rotamase_3  91 slkkgeiskvvktdfGyHiikvtdkk 116
                                       + +kg+i+++vk++fGyH+i+v+dkk
  gi|330507465|ref|YP_004383893.1|  69 EGEKGKIIGPVKSQFGYHLIRVLDKK 94 
                                       ************************97 PP

>> Rotamase_2  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   1.3e-13   5.8e-10      27     108 ..       9      93 ..       2      94 .] 0.84

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.3e-13
                        Rotamase_2  27 lavvkdqvaaeaalalakagaekdfaalakgnskk.....aadlgifesasnlpeelakaafalkpgevsgpvetdn 98 
                                       ++  k++++a  +++l++ g +++fa++a+++s +      +dlg+f + + +p e++kaaf+ ++g++ gpv++++
  gi|330507465|ref|YP_004383893.1|   9 HILCKTEKKALEVKELLASG-QESFAQMARKYSQCpsgksGGDLGWFGKGRMVP-EFEKAAFEGEKGKIIGPVKSQF 83 
                                       55667888888899999999.69*********9995544455555***999887.********************** PP

                        Rotamase_2  99 gyyivkvtev 108
                                       gy++++v ++
  gi|330507465|ref|YP_004383893.1|  84 GYHLIRVLDK 93 
                                       *******886 PP

>> DUF2291  Predicted periplasmic lipoprotein (DUF2291)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     7e-05      0.31      36      75 ..       4      44 ..       1      50 [. 0.85
   2 ?   -2.7   0.0       0.9     4e+03     163     180 ..      60      77 ..      56      81 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7e-05
                                      HHHHHHHHHHHH--SEEHHHHHHHHHH-HHHHHHHHEB-.- CS
                           DUF2291 36 eiWdekllpaleekAvdlaellaalkadpeaagekygkr.v 75
                                      e+  +++l ++e+kA +++ella  ++++++++ ky++   
  gi|330507465|ref|YP_004383893.1|  4 EVHAAHILCKTEKKALEVKELLASGQESFAQMARKYSQCpS 44
                                      6677889999**************************98644 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.9
                                       HHHHHTTC--T-EEEEEE CS
                           DUF2291 163 lspldrealkGktveftG 180
                                       +++++++a +G++ +++G
  gi|330507465|ref|YP_004383893.1|  60 VPEFEKAAFEGEKGKIIG 77 
                                       567777777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 683.61
//
Query:       gi|330507466|ref|YP_004383894.1|  [L=228]
Description: cyclase family protein [Methanosaeta concilii GP6]
Scores for complete 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-18   64.7   0.0    1.3e-17   64.3   0.0    1.2  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 !   64.3   0.0   7.2e-22   1.3e-17       1     136 []      19     167 ..      19     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 7.2e-22
                           Cyclase   1 idLshplsedtpvwp..dp...................islsehtGTHlDapgHfae..ktidelpleelvgpavvl 54 
                                       +d+s+p++   p +p  +p                   +sl++htGTH+D p+H+ +    +d++p e++++pa v+
  gi|330507466|ref|YP_004383894.1|  19 YDISAPIEI-APNYPgdSPfsrqwmaglgkgsnyslsvLSLGSHTGTHIDFPSHILRdgFPLDSYPPERFITPAWVI 94 
                                       799999944.5777445226667789999999999999****************988766889************** PP

                           Cyclase  55 dvsakaaaedyeiitaedleaalakqgveikpgdivlirTgwskrl...edkeky..rnpglseeaaewlaekgvka 126
                                        v++     d   + a+ l++      v+i++g+++l++T  s  +    +++++  +   ls+ aae+ ++ g ++
  gi|330507466|ref|YP_004383894.1|  95 AVREI----DA--VPAQALQD------VNIQRGEAILFKTSNS--FqglMHNPTFqdEYVSLSPPAAELCVSLGASL 157
                                       **665....33..57888865......589**********765..3458555677655589**************** PP

                           Cyclase 127 vGvDtlsvDa 136
                                       vG+D +svD+
  gi|330507466|ref|YP_004383894.1| 158 VGIDYISVDR 167
                                       ********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); 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 0.21s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1713.16
//
Query:       gi|330507467|ref|YP_004383895.1|  [L=1090]
Description: multi-sensor hybrid histidine kinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-45  153.7   0.3    3.9e-15   55.8   0.0    4.6  4  PAS           PAS fold
    2.2e-39  133.9   0.8    5.7e-11   42.6   0.1    4.5  4  PAS_9         PAS domain
    3.9e-38  130.1   0.0    3.2e-13   49.9   0.0    4.4  4  PAS_4         PAS fold
    8.6e-31  106.8   0.0    1.6e-30  105.9   0.0    1.5  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    1.6e-27   95.9   0.4    3.5e-27   94.8   0.4    1.6  1  Response_reg  Response regulator receiver domain
    5.3e-26   90.1   0.0    3.9e-05   23.6   0.0    4.9  4  PAS_8         PAS domain
      3e-20   72.0   0.4    2.2e-19   69.2   0.0    2.7  3  HisKA         His Kinase A (phospho-acceptor) domain
    3.6e-18   65.6   0.2    6.4e-06   26.4   0.0    3.7  3  PAS_3         PAS fold
    3.9e-05   24.2   0.0      0.029   14.9   0.0    3.2  3  PAS_10        PAS domain
      7e-05   23.5   0.0    0.00021   21.9   0.0    1.9  1  GAF           GAF domain
    0.00046   20.5   0.0      0.015   15.6   0.0    2.9  2  GAF_2         GAF domain
      0.001   19.2   0.2       0.69   10.1   0.0    4.5  5  PAS_7         PAS fold
  ------ inclusion threshold ------
      0.027   14.3   0.0      0.057   13.2   0.0    1.5  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
       0.12   12.3   0.0        3.3    7.7   0.0    2.5  2  GRIP          GRIP domain
        6.2    6.5  10.3      0.081   12.6   1.5    2.4  3  Docking       Erythronolide synthase docking


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 !   18.5   0.0   1.3e-06    0.0015       2      35 ..       6      39 ..       4      48 .. 0.85
   2 !   32.3   0.1   6.5e-11   7.7e-08       1     113 []     320     434 ..     320     434 .. 0.87
   3 !   55.8   0.0   3.3e-18   3.9e-15       3     108 ..     458     560 ..     456     568 .. 0.89
   4 !   41.5   0.0   9.5e-14   1.1e-10       5     109 ..     583     686 ..     579     690 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                                      HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHS CS
                               PAS  2 dlraileslpdpifvvDedgrilyvNaaaeellG 35
                                      ++++ le l d+i++ D +g+ily N+aae++  
  gi|330507467|ref|YP_004383895.1|  6 MFQSTLEILEDGICICDPSGEILYSNPAAERMAR 39
                                      67777888***********************976 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 6.5e-11
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH...HHHHHHHHHHHHTT-ECC CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda...elaelleqlleqgeesra 74 
                                       e++r+++e++ + i+ vD +g i ++N+    ++G+++e++lg+++ + i+++        a + + +++  e+s++
  gi|330507467|ref|YP_004383895.1| 320 EKYRELVETSSSVIIRVDTSGAIRFINKFGLHFFGYNEEDILGRNVTETIFPPGGIgcnLKAIIGHIRENPEECSTH 396
                                       579*************************************************9887973333344556666666666 PP

                                       CCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  75 geisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                          +++  +g+ +++    + v ++ ge+ ++l++++di
  gi|330507467|ref|YP_004383895.1| 397 IAENIRS-NGELVWIAWAHRLVQNERGEVVEVLCIGNDI 434
                                       6777777.******************************8 PP

  == domain 3  score: 55.8 bits;  conditional E-value: 3.3e-18
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       l+++l+++ +pi+v+D + +i+ +N+a+e+l+G++++evlg+sl +l++ e++ +   ++ ++ ++ge+++a+ei +
  gi|330507467|ref|YP_004383895.1| 458 LDNLLSHANAPIIVWDPNFCITRFNHAFERLTGWRADEVLGRSLGILFPDESR-TESFAYIERTLSGESWNAVEIPI 533
                                       67899*******************************************98766.567777788889*********** PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEE CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflg 108
                                       + ++g+++ ++ + + ++d+ g++  ++ 
  gi|330507467|ref|YP_004383895.1| 534 CHQNGEVRTVLWNSANIYDEAGRR--VIA 560
                                       **********************95..443 PP

  == domain 4  score: 41.5 bits;  conditional E-value: 9.5e-14
                                       HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC CS
                               PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl 81 
                                       ++l++ +++++++D dgri+y+N+ ae+l ++++eevlg s+ d i ++++ + +e +++ ++++   +++    ++
  gi|330507467|ref|YP_004383895.1| 583 SLLDQVRNAVIATDFDGRIIYWNRFAESLYQWKAEEVLGASIKDTILPPEMKYNVEMVTKEILAKGYLECEYLVKRK 659
                                       689999***********************************************************999999988888 PP

                                       TTSSEEEEEEEEEEEEETTEEEEEEEEE CS
                               PAS  82 rdgrpihlevraspvrdaggeilgflgv 109
                                        dg+ +++    s++ d  ++++g++ v
  gi|330507467|ref|YP_004383895.1| 660 -DGSRFPASYIFSTICDNRQRRIGIISV 686
                                       .******999999999999999999876 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.8e-05     0.034       2      31 ..      16      44 ..      15     100 .. 0.75
   2 !   42.6   0.1   4.8e-14   5.7e-11       3     104 .]     331     436 ..     329     436 .. 0.91
   3 !   33.0   0.0   4.7e-11   5.6e-08       3     104 .]     468     570 ..     466     570 .. 0.90
   4 !   39.0   0.0   6.3e-13   7.5e-10       4     104 .]     592     692 ..     589     692 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-05
                             PAS_9  2 dgilidnpdgrilyaNeaalrllGyspeev 31
                                      dgi+i++p+g+ily N+aa+r+   s ee+
  gi|330507467|ref|YP_004383895.1| 16 DGICICDPSGEILYSNPAAERMA-RSLEEL 44
                                      8*********************5.454544 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 4.8e-14
                             PAS_9   3 gili.dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirknget 75 
                                       +++i ++++g i ++N+  l ++Gy++e++lg+++t+++ ++    ++l+a++  +r+   ++ +   ++ir+nge 
  gi|330507467|ref|YP_004383895.1| 331 SVIIrVDTSGAIRFINKFGLHFFGYNEEDILGRNVTETIFPPGGIGCNLKAIIGHIREnpeECSTHIAENIRSNGEL 407
                                       6778999***888**************************67777778888888888889*9999999********** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                       +w+    + v+++ ge+v +++i +Dite
  gi|330507467|ref|YP_004383895.1| 408 VWIAWAHRLVQNERGEVVEVLCIGNDITE 436
                                       **99999999******************8 PP

  == domain 3  score: 33.0 bits;  conditional E-value: 4.7e-11
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwv 78 
                                       +i++ +p++ i+++N a++rl+G  ++evlg+s+  lf +d+++ e ++ + ++++  +  +ve+ + + nge   v
  gi|330507467|ref|YP_004383895.1| 468 PIIVWDPNFCITRFNHAFERLTGWRADEVLGRSLGILF-PDESRTESFAYIERTLSGeSWNAVEIPICHQNGEVRTV 543
                                       677756********************************.8888888888888888777799999999********** PP

                             PAS_9  79 lltaspvkdd.dgelvgiivilrDite 104
                                       l + + ++d+ ++++++ i+  +Dite
  gi|330507467|ref|YP_004383895.1| 544 LWNSANIYDEaGRRVIATIAQGQDITE 570
                                       **********9999999*********8 PP

  == domain 4  score: 39.0 bits;  conditional E-value: 6.3e-13
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       ++ ++ dgri+y+N+ a+ l++ ++eevlg si+d++   + +++ e + + + ++     e e+   rk+g++f++
  gi|330507467|ref|YP_004383895.1| 592 VIATDFDGRIIYWNRFAESLYQWKAEEVLGASIKDTIlpPEMKYNVEMVTKEILAKG--YLECEYLVKRKDGSRFPA 666
                                       555789**************9999*************99777777777777777777..8***************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                          +s++ d+ ++ +gii++++D+te
  gi|330507467|ref|YP_004383895.1| 667 SYIFSTICDNRQRRIGIISVSTDLTE 692
                                       **********99*************8 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00021      0.26       4      34 ..      14      43 ..      11      48 .. 0.83
   2 !   33.5   0.0   3.4e-11   4.1e-08       2     110 .]     327     439 ..     326     439 .. 0.93
   3 !   49.9   0.0   2.7e-16   3.2e-13       1     109 [.     462     572 ..     462     573 .. 0.96
   4 !   29.9   0.0   4.5e-10   5.4e-07       1     109 [.     585     694 ..     585     695 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                             PAS_4  4 lpdalavldpdgrvlyaNaaaaelfgappee 34
                                      l d+++++dp g +ly N+aa++ ++++ ee
  gi|330507467|ref|YP_004383895.1| 14 LEDGICICDPSGEILYSNPAAER-MARSLEE 43
                                      789*****************988.5555555 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 3.4e-11
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlae.llpee.daarleralrrvlegeepiefleelll.. 74 
                                       + ++ +++ +d+ g ++++N+ + + fg+  e++lG+ + e ++p++  + +l +++ +  e  e +++++  +   
  gi|330507467|ref|YP_004383895.1| 327 ETSSSVIIRVDTSGAIRFINKFGLHFFGYNEEDILGRNVTEtIFPPGgIGCNLKAIIGHIRENPEECSTHIAENIrs 403
                                       77899999********************************7788888899999999999999999999888777788 PP

                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       +ge +++ +  + + +e+Gev+ vl+i+ DiTe +r
  gi|330507467|ref|YP_004383895.1| 404 NGELVWIAWAHRLVQNERGEVVEVLCIGNDITEKKR 439
                                       *********************************986 PP

  == domain 3  score: 49.9 bits;  conditional E-value: 2.7e-16
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..p 75 
                                       l++ +++++v+dp++ +++ N a+++l g++++e+lG++l  l+p+e++++  ++++r l+g e++  +e++ +  +
  gi|330507467|ref|YP_004383895.1| 462 LSHANAPIIVWDPNFCITRFNHAFERLTGWRADEVLGRSLGILFPDESRTESFAYIERTLSG-ESWNAVEIPIChqN 537
                                       57899*********************************************************.5888888888889* PP

                             PAS_4  76 geerhyelrllPlrdesGe.vigvlvisrDiTerr 109
                                       ge r+++++   + de G+ vi++++ ++DiTer+
  gi|330507467|ref|YP_004383895.1| 538 GEVRTVLWNSANIYDEAGRrVIATIAQGQDITERK 572
                                       *********************************97 PP

  == domain 4  score: 29.9 bits;  conditional E-value: 4.5e-10
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlae.llpeedaarleralrrvlegeepiefleelll.. 74 
                                       ld++  a+++ d dgr++y+N+ a++l+++ +ee+lG +  + +lp+e + ++e   ++ l+ +  + ++e+l+   
  gi|330507467|ref|YP_004383895.1| 585 LDQVRNAVIATDFDGRIIYWNRFAESLYQWKAEEVLGASIKDtILPPEMKYNVEMVTKEILAKG--YLECEYLVKrk 659
                                       789999****************9999***************77********************8..55555555544 PP

                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +g++ + +  ++ ++d + + ig++ +s+D+Ter+
  gi|330507467|ref|YP_004383895.1| 660 DGSRFPASYIFSTICDNRQRRIGIISVSTDLTERK 694
                                       66666666666***********************8 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   0.0   1.3e-33   1.6e-30       1     111 [.     825     939 ..     825     940 .. 0.89

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 1.3e-33
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE...EE.TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTST CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveika...se.ddlvisveDnGiGipkedlkklfekfsq.ddstkrggg 72 
                                       gd +rLrqi+ nl++Navkf t++g +++ ++a   ++  +++++v+D+GiGi+++ + +lf++fsq d+st+r++g
  gi|330507467|ref|YP_004383895.1| 825 GDMTRLRQILVNLLGNAVKF-TDKGFVRLDVSAlpvEDgHEIQFRVTDSGIGISQDRMSRLFQSFSQvDASTTRKYG 900
                                       6889***************9.75665555555466522699************************************ PP

                                       SSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                         HATPase_c  73 gtGlGlsivkklvelmgGeiwvesepgrGttftftlple 111
                                       gtGlGl+i+k l+elmgG iw es pg+G++f+ft++ e
  gi|330507467|ref|YP_004383895.1| 901 GTGLGLAICKHLAELMGGGIWAESVPGEGSSFYFTIQAE 939
                                       ***********************************9875 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.4   2.9e-30   3.5e-27       1     111 [.     970    1080 ..     970    1081 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 2.9e-30
                                        EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT.TTSEE CS
                      Response_reg    1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed.pelpv 74  
                                        +l+++D+ +++++  ++le+ gy + + a+dg+e+l+ l+++ +d++l+D++mp+mdGle+++ ir +  +++ +
  gi|330507467|ref|YP_004383895.1|  970 ILLAEDNLVNQKVAIRMLERLGY-TADIAADGQEVLAALESRPYDVVLMDVQMPEMDGLEATRSIRSTAcHQPYI 1043
                                        89*********************.*******************************************999***** PP

                                        EEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg   75 iiltahseeedavealkagaddflsKpfdpeeLlkal 111 
                                        i++tah+ + d++ +l+ag++d+++Kp+++eeL++al
  gi|330507467|ref|YP_004383895.1| 1044 IAMTAHAMKGDREVCLDAGMNDYIAKPVRIEELKAAL 1080
                                        *********************************9986 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   2.4e-06    0.0028       3      45 ..       7      45 ..       5      66 .. 0.80
   2 !   19.3   0.0   7.2e-07   0.00086       1      45 [.     320     365 ..     320     378 .. 0.87
   3 !   23.6   0.0   3.3e-08   3.9e-05       2      53 ..     457     509 ..     456     524 .. 0.87
   4 !   23.2   0.0   4.3e-08   5.2e-05       5      51 ..     583     631 ..     579     646 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-06
                             PAS_8  3 lralfesspdgiavvd.lgdrivdvNqaalellGysadlkgell 45
                                      +++ +e + dgi+++d  g+ i++ N+aa+++      +++el 
  gi|330507467|ref|YP_004383895.1|  7 FQSTLEILEDGICICDpSGE-ILYSNPAAERMAR----SLEELN 45
                                      78899***********8888.***********98....666554 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 7.2e-07
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgell 45 
                                       e++r l+e+s+  i+ vd  g  i+++N+  l+++Gy+ +d++g  +
  gi|330507467|ref|YP_004383895.1| 320 EKYRELVETSSSVIIRVDtSGA-IRFINKFGLHFFGYNeEDILGRNV 365
                                       79****************7777.***************999988766 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 3.3e-08
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlr 53 
                                       +l +l+ +++ +i+v+d +   i+  N a+++l+G++ ++++g  lg+l+p+  
  gi|330507467|ref|YP_004383895.1| 457 YLDNLLSHANAPIIVWDpNFC-ITRFNHAFERLTGWRaDEVLGRSLGILFPDES 509
                                       6778999**********8888.************************98877654 PP

  == domain 4  score: 23.2 bits;  conditional E-value: 4.3e-08
                             PAS_8   5 alfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellg.qllpv 51 
                                       +l+++++++++ +d +g+ i+++N+ a+ l+ ++ ++++g+ +  ++lp 
  gi|330507467|ref|YP_004383895.1| 583 SLLDQVRNAVIATDfDGR-IIYWNRFAESLYQWKaEEVLGASIKdTILPP 631
                                       79**********998888.***************9999999997644443 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       7.4   8.9e+03      23      48 ..     305     330 ..     300     335 .. 0.60
   2 ?   -1.6   0.1       2.4   2.8e+03      32      55 ..     439     462 ..     424     466 .. 0.72
   3 !   69.2   0.0   1.9e-22   2.2e-19       1      67 []     713     778 ..     713     778 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.4
                                       HHHHHHC..T-HSSCHHHHHHHHHHH CS
                             HisKA  23 naeaLkregklteelkeyletiesea 48 
                                       ++   k e +l+e+ ++y e +e ++
  gi|330507467|ref|YP_004383895.1| 305 FIGRFKAESALRESEEKYRELVETSS 330
                                       55555555566677777777766655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.4
                                       T-HSSCHHHHHHHHHHHHHHHHHH CS
                             HisKA  32 klteelkeyletiesearrldhlv 55 
                                       + +eelk+  +++++  + ld+l+
  gi|330507467|ref|YP_004383895.1| 439 RSSEELKRVAADLRETRDYLDNLL 462
                                       467777777777777777777665 PP

  == domain 3  score: 69.2 bits;  conditional E-value: 1.9e-22
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       ++++fla+++HE+rtP++a++g++++L ++ + +  +++y+eti+s+++ l+++++d+Ld+s+ie+g
  gi|330507467|ref|YP_004383895.1| 713 AKSEFLANMSHEIRTPMNAVIGFTSLLLNT-NIDSVQRDYIETIHSSGDSLLKVISDILDFSKIEGG 778
                                       589************************997.45699*****************************97 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.9e-06    0.0022       9      88 ..     350     430 ..     342     431 .. 0.85
   2 !   26.4   0.0   5.4e-09   6.4e-06       3      83 ..     480     558 ..     478     562 .. 0.90
   3 !   16.9   0.0   4.9e-06    0.0059       1      88 [.     601     686 ..     601     687 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-06
                             PAS_3   9 eeilGyspeellgkveswldlvhpeD.rervrealqeal.kkge.pyegeyRirrkdGeyrwveararvirdengkp 82 
                                        + +Gy +e++lg+  ++ + + p   +    +a+  ++ ++ e + ++    +r +Ge +w+ + +r +++e g++
  gi|330507467|ref|YP_004383895.1| 350 LHFFGYNEEDILGR--NVTETIFPPGgIGCNLKAIIGHIrENPEeCSTHIAENIRSNGELVWIAWAHRLVQNERGEV 424
                                       6789**********..9999999988777777777777766666366888*************************** PP

                             PAS_3  83 vrvigv 88 
                                       v+v+++
  gi|330507467|ref|YP_004383895.1| 425 VEVLCI 430
                                       **9986 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 5.4e-09
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepy.egeyRirrkdGeyrwveararvird 77 
                                         + ++e+++G++++e+lg+    l ++ p++ r + ++ +++ l +ge++  +e+ i++++Ge+r v +    i+d
  gi|330507467|ref|YP_004383895.1| 480 RFNHAFERLTGWRADEVLGR---SLGILFPDEsRTESFAYIERTL-SGESWnAVEIPICHQNGEVRTVLWNSANIYD 552
                                       6799****************...8888888888************.5555879************************ PP

                             PAS_3  78 engkpv 83 
                                       e g+ v
  gi|330507467|ref|YP_004383895.1| 553 EAGRRV 558
                                       ***965 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 4.9e-06
                             PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwveararvir 76 
                                       iiy+++  e ++ + +ee+lg   s++d + p +   +v+   +e+l+kg  +e+ey ++rkdG+ +  +   + i 
  gi|330507467|ref|YP_004383895.1| 601 IIYWNRFAESLYQWKAEEVLGA--SIKDTILPPEmKYNVEMVTKEILAKGY-LECEYLVKRKDGSRFPASYIFSTIC 674
                                       69********************..999998887736677777778887777.9************999999999998 PP

                             PAS_3  77 dengkpvrvigv 88 
                                       d+  + + +i+v
  gi|330507467|ref|YP_004383895.1| 675 DNRQRRIGIISV 686
                                       888888888765 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         3   3.5e+03      10      68 ..     331     392 ..     324     411 .. 0.70
   2 !   14.9   0.0   2.5e-05     0.029       1      74 [.     458     533 ..     458     558 .. 0.74
   3 ?    5.2   0.0     0.026        31       4      81 ..     584     664 ..     582     711 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3
                            PAS_10  10 ieltflDdnlqirrFtpaakklfklipadv.Grpladi.hpk.kavknveeviealrtgekd 68 
                                         ++ +D++  ir+ ++   ++f ++++d+ Gr++++   p+  +  n++ +i  +r++ ++
  gi|330507467|ref|YP_004383895.1| 331 SVIIRVDTSGAIRFINKFGLHFFGYNEEDIlGRNVTETiFPPgGIGCNLKAIIGHIRENPEE 392
                                       55777899999999999888889988888559999865245557777888888888776654 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.5e-05
                            PAS_10   1 lnnlLnstpieltflDdnlqirrFtpaakklfk.lipadvGrpladihpkkavknveeviealrtgek.devevvv 74 
                                       l+nlL++++  ++  D n +i+rF++a ++l   + ++ +Gr+l  + p+++ ++    ie+  +ge+ + ve+++
  gi|330507467|ref|YP_004383895.1| 458 LDNLLSHANAPIIVWDPNFCITRFNHAFERLTGwRADEVLGRSLGILFPDESRTESFAYIERTLSGESwNAVEIPI 533
                                       79*************************9988762566678****99999977777666666666666546666665 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.026
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfklipadv.Grpladi.hpkkavknveeviealrtgekdevevvvp.kn 77 
                                       lL+++  +++  D + +i+++++ a++l++ ++++v G +++d   p++ + nve v++++  +   e e+ v+ k+
  gi|330507467|ref|YP_004383895.1| 584 LLDQVRNAVIATDFDGRIIYWNRFAESLYQWKAEEVlGASIKDTiLPPEMKYNVEMVTKEILAKGYLECEYLVKrKD 660
                                       788999999999******************9987755****98626889999******9999998888887776555 PP

                            PAS_10  78 gkwv 81 
                                       g  +
  gi|330507467|ref|YP_004383895.1| 661 GSRF 664
                                       5554 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.7e-07   0.00021       3     114 ..     159     287 ..     157     304 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-07
                                       HHHHHHHHHHHHHHHTESEEEE...EEEEETTEEECEEEEECCEEEETTSHHHH...................HHHH CS
                               GAF   3 eelldtvveelrellgadrval...ylpdydGlhydipqasrwlfmkngrgicg...................qvla 57 
                                       + +l+  +e l+   ++dr+++   yl d++G ++ i+ + +w+   +g+ + +                   q+l+
  gi|330507467|ref|YP_004383895.1| 159 DVALNLSLEILGCSANVDRACIfehYL-DEEGRDQ-ISLGYEWISGNDGDARSAkirhpdlsyeayssipqwfQILS 233
                                       566666777777778889999945445.6777555.88888884444433311223333344444444445666666 PP

                                       HSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE...SSSCS CS
                               GAF  58 tgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhn...psppf 114
                                        g p+         r +++  r  le mg+rs++ vP++ +++ wG + + +   +++ +
  gi|330507467|ref|YP_004383895.1| 234 GGMPIWGR-----TRDLPPSARGPLETMGVRSFMIVPIFTTDRFWGFIGFEDyrlERD-W 287
                                       66666666.....222222356899***********************9999666555.5 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.3e-05     0.015      25     133 ..     182     302 ..     155     306 .. 0.66
   2 ?    1.2   0.0      0.34     4e+02      96     131 ..     531     564 ..     518     565 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                                       EEEE-TTS-..EEEE...EEEES-TTSTT-S-B--.....-TT.H.HHHHHHHTS-EEES-GGG-S-HHHHHHHHHT CS
                             GAF_2  25 illvdddgg..lrla...awgeaeeefgaaldrpl.....geg.l.vgealrtgrpvilndleedpdkkglpaghag 89 
                                        +++d++g+  + l     +g++++  +a++++p       ++ + + ++l  g p++   +++ p + + p++  g
  gi|330507467|ref|YP_004383895.1| 182 EHYLDEEGRdqISLGyewISGNDGDARSAKIRHPDlsyeaYSSiPqWFQILSGGMPIW-GRTRDLPPSARGPLETMG 257
                                       3445544442344447788888888888888884446677555587999999999*99.56999************* PP

                                       T--EEEEEE-TTS---EEEEES.......--HHHHHHHHHHHHHH CS
                             GAF_2  90 lrsflavPlisegrvvGvlnlyankppa.fdeedlelLeelaeqi 133
                                       +rsf++vP++  +r  G++++   + ++ ++++   +L ++a+ i
  gi|330507467|ref|YP_004383895.1| 258 VRSFMIVPIFTTDRFWGFIGFEDYRLERdWSWSVAFILMTMASAI 302
                                       *********9988*******9433333334444444444444444 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.34
                                       EEE-T.TS---EEEEES......--HHHHHHHHHHHH CS
                             GAF_2  96 vPlis.egrvvGvlnlyankppafdeedlelLeelae 131
                                       +P+++ +g+v  vl+   n  + +de+ ++++ ++a+
  gi|330507467|ref|YP_004383895.1| 531 IPICHqNGEVRTVLW---NSANIYDEAGRRVIATIAQ 564
                                       8**9999********...688889******9999986 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.12   1.4e+02       1      29 [.      11      39 ..      11      82 .. 0.86
   2 ?   -1.1   0.0       1.8   2.1e+03      38      38 ..     376     376 ..     326     442 .. 0.48
   3 ?   -3.5   0.0       9.8   1.2e+04       2      31 ..     463     492 ..     462     499 .. 0.81
   4 ?   -1.8   0.1       2.9   3.5e+03     104     115 .]     565     576 ..     559     576 .. 0.81
   5 !   10.1   0.0   0.00058      0.69       1      55 [.     585     638 ..     585     698 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.12
                             PAS_7  1 lenmsqGisvfDadlrLvawNrrylelld 29
                                      le +++Gi++ D +++++ +N    ++  
  gi|330507467|ref|YP_004383895.1| 11 LEILEDGICICDPSGEILYSNPAAERMAR 39
                                      567899***************99888765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                             PAS_7  38 g 38 
                                       g
  gi|330507467|ref|YP_004383895.1| 376 G 376
                                       2 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 9.8
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlp 31 
                                       ++ +  i+v D +  ++ +N+ + +l ++ 
  gi|330507467|ref|YP_004383895.1| 463 SHANAPIIVWDPNFCITRFNHAFERLTGWR 492
                                       5667779999999999999*9999998765 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 2.9
                             PAS_7 104 ytDiTerrraee 115
                                        +DiTer+ aee
  gi|330507467|ref|YP_004383895.1| 565 GQDITERKMAEE 576
                                       58******9986 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.00058
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefg 55 
                                       l++++++++  D d+r++ wNr   +l+++ +e v  g+++++ +     + +++
  gi|330507467|ref|YP_004383895.1| 585 LDQVRNAVIATDFDGRIIYWNRFAESLYQWKAEEV-LGASIKDTILPPEMKYNVE 638
                                       78999**************************9999.9999998886665555555 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 ?   13.2   0.0   4.8e-05     0.057       8      86 ..     835     913 ..     828     916 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.8e-05
                       HATPase_c_3   8 aelvdNsld.Adaenvkievn...knrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGlklA 80 
                                       + l+ N++   d   v + v+    ++g++ +++++D G G+s++ + + ++  ++     ++ +++G  G+G  lA
  gi|330507467|ref|YP_004383895.1| 835 VNLLGNAVKfTDKGFVRLDVSalpVEDGHEIQFRVTDSGIGISQDRMSRLFQSFSQVDA--STTRKYGGTGLG--LA 907
                                       555666665455555555555222233667899****************9985555555..38999*******..99 PP

                       HATPase_c_3  81 slslgk 86 
                                       +++ ++
  gi|330507467|ref|YP_004383895.1| 908 ICKHLA 913
                                       998765 PP

>> GRIP  GRIP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0028       3.3      21      40 ..     757     776 ..     748     777 .. 0.85
   2 ?    1.6   0.0      0.22   2.6e+02      13      39 ..     821     847 ..     819     847 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0028
                              GRIP  21 serkqLvpVlstlLkfspeE 40 
                                       s+ + L++V+s +L+fs+ E
  gi|330507467|ref|YP_004383895.1| 757 SSGDSLLKVISDILDFSKIE 776
                                       56678************987 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.22
                              GRIP  13 qFLeskeaserkqLvpVlstlLkfspe 39 
                                       ++L+ +    r+ Lv+ l+   kf+++
  gi|330507467|ref|YP_004383895.1| 821 RYLMGDMTRLRQILVNLLGNAVKFTDK 847
                                       799999999***************985 PP

>> Docking  Erythronolide synthase docking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       9.4   1.1e+04       3       8 ..     319     324 ..     318     324 .. 0.87
   2 ?   12.6   1.5   6.7e-05     0.081      10      21 ..     444     455 ..     444     456 .. 0.96
   3 ?   -1.3   0.3       1.5   1.7e+03      13      23 ..     696     706 ..     694     706 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 9.4
                           Docking   3 EeKLRd 8  
                                       EeK R+
  gi|330507467|ref|YP_004383895.1| 319 EEKYRE 324
                                       9****8 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.7e-05
                           Docking  10 LKRvTaDLrqtR 21 
                                       LKRv aDLr+tR
  gi|330507467|ref|YP_004383895.1| 444 LKRVAADLRETR 455
                                       9**********9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.5
                           Docking  13 vTaDLrqtRrR 23 
                                       v  DLr++++R
  gi|330507467|ref|YP_004383895.1| 696 VEQDLRDAKER 706
                                       5569****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1090 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.44
# Mc/sec: 7515.42
//
Query:       gi|330507468|ref|YP_004383896.1|  [L=323]
Description: replication factor C small subunit [Methanosaeta concilii GP6]
Scores for complete 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   79.2   0.1    6.2e-22   77.8   0.1    1.8  1  Rep_fac_C        Replication factor C C-terminal domain
    1.6e-15   57.7   0.0    3.4e-15   56.7   0.0    1.6  1  AAA              ATPase family associated with various cellul
    1.6e-14   54.0   0.0    1.2e-10   41.4   0.0    2.2  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    1.3e-08   34.8   0.0    9.3e-08   32.0   0.0    2.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.6e-06   27.5   0.8     0.0015   18.9   0.0    2.7  3  AAA_16           AAA ATPase domain
    4.8e-06   26.6   0.0    9.5e-06   25.7   0.0    1.5  1  Rad17            Rad17 P-loop domain
    0.00013   22.0   0.0    0.00027   21.0   0.0    1.5  1  AAA_14           AAA domain
    0.00023   20.6   0.0      0.085   12.2   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00033   20.7   0.0     0.0017   18.4   0.0    1.9  1  ResIII           Type III restriction enzyme, res subunit
    0.00044   20.5   0.0     0.0011   19.3   0.0    1.7  1  AAA_assoc_2      AAA C-terminal domain
    0.00068   19.5   0.0     0.0014   18.5   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
      0.002   17.4   0.0       0.02   14.1   0.0    2.1  2  TIP49            TIP49 P-loop domain
     0.0028   16.4   0.0      0.024   13.4   0.0    2.0  2  SNF2_N           SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.011   16.0   0.3        4.9    7.4   0.0    2.5  2  AAA_22           AAA domain
      0.011   15.4   0.0        4.6    6.9   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
      0.016   14.8   0.0       0.03   13.8   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
      0.016   14.3   0.0      0.027   13.6   0.0    1.3  1  MCM              MCM P-loop domain
      0.039   13.7   0.0       0.14   12.0   0.0    1.8  2  DNA_pol3_delta   DNA polymerase III, delta subunit
      0.085   12.6   0.0       0.37   10.5   0.0    2.0  2  IstB_IS21        IstB-like ATP binding protein
       0.14   12.1   0.1        1.7    8.7   0.1    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
       0.15   12.5   0.0       0.36   11.2   0.0    1.7  1  RNA_helicase     RNA helicase
       0.17   11.6   0.0       0.43   10.3   0.0    1.6  1  AAA_24           AAA domain


Domain annotation for each model (and alignments):
>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.1   7.7e-25   6.2e-22       2      87 ..     228     313 ..     227     314 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 7.7e-25
                                       -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-H CS
                         Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGase 78 
                                       +p+ei++ ++++ +gdf  a+++l++ll  kG+s++d++ q+hr + + +++ ++ ++++++++gei++r++eGa+e
  gi|330507468|ref|YP_004383896.1| 228 KPEEIKSFIKTAISGDFVGARAILDDLLLSKGLSGQDVVIQIHRAMLDLDDIADRDRVKLIDRIGEIDFRMTEGANE 304
                                       79**********9************************************99************************** PP

                                       HHHHHHHHH CS
                         Rep_fac_C  79 hlqlsalla 87 
                                       ++ql+alla
  gi|330507468|ref|YP_004383896.1| 305 RIQLEALLA 313
                                       *******98 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   4.1e-18   3.4e-15       1     129 [.      42     159 ..      42     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 4.1e-18
                                       EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHH CS
                               AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidala 71 
                                       +l++GppG+GKT++  +++ke+       +f+e+++s+ +   +    +k++++ + a   + + +++f+DE+dal+
  gi|330507468|ref|YP_004383896.1|  42 LLFSGPPGVGKTAASISIVKEIfgetwRNNFIELNASDER--GIDIIRHKVKDFARMAPLGEaDFKVIFLDEADALT 116
                                       69************9999999755444699**********..55555555555555553333335***********9 PP

                                       HHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEE CS
                               AAA  72 ksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkie 129
                                       ++            +++L + +++++    ++ +i+ +n+ +k+ +++  +R+ +  +
  gi|330507468|ref|YP_004383896.1| 117 NDA-----------QSALRRTMERYSA---TTRFILSCNYSSKIIEPIQ-SRCAVYRF 159
                                       888...........************9...589****************.9**98765 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 !   10.6   0.0   0.00042      0.35       1      47 [.      22      67 ..      22      78 .. 0.91
   2 !   41.4   0.0   1.5e-13   1.2e-10      84     163 .]      82     163 ..      70     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00042
                   DNA_pol3_delta2  1 gqeealkilskalksgrlahayLfeGdegigkkelalnlakallcee 47
                                      gq+e+++ l++ +k+ +l h +Lf+G+ g+gk ++   ++k+++ e 
  gi|330507468|ref|YP_004383896.1| 22 GQDEIVRRLKSYVKTRNLPH-LLFSGPPGVGKTAASISIVKEIFGET 67
                                      689999************99.8*********************9886 PP

  == domain 2  score: 41.4 bits;  conditional E-value: 1.5e-13
                   DNA_pol3_delta2  84 kldqirelieelsrkpre..skkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelk 158
                                        +d ir+  +++ r++    +  k+i +++a+ +t+ A+ al +t+E  s+ + fiL  + ++k++++i+SRc +++
  gi|330507468|ref|YP_004383896.1|  82 GIDIIRHKVKDFARMAPLgeADFKVIFLDEADALTNDAQSALRRTMERYSATTRFILSCNYSSKIIEPIQSRCAVYR 158
                                       68899977777776654313889****************************************************** PP

                   DNA_pol3_delta2 159 fspls 163
                                       f+pls
  gi|330507468|ref|YP_004383896.1| 159 FKPLS 163
                                       **985 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   1.1e-10   9.3e-08       2     111 ..      13     130 ..      12     137 .. 0.68

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.1e-10
                            RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvk......lkits....g.P 67 
                                       rP++l++ +gq+++  +lk ++++     ++l h+l++GpPG+Gkt+ +  i ke+  +      ++  +    g  
  gi|330507468|ref|YP_004383896.1|  13 RPERLDDIVGQDEIVRRLKSYVKT-----RNLPHLLFSGPPGVGKTAASISIVKEIFGEtwrnnfIELNAsderGiD 84 
                                       9******************99864.....5699**************998888886432111111111110111212 PP

                            RuvB_N  68 vle.kagdlaalltnleekd..vlfideihrlsraveevlysamedf 111
                                       ++  k +d+a  ++ l e d  v+f+de   l++ ++  l  +me +
  gi|330507468|ref|YP_004383896.1|  85 IIRhKVKDFA-RMAPLGEADfkVIFLDEADALTNDAQSALRRTMERY 130
                                       3441334444.445565554338899999999988888888888877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.9e-06    0.0015       3      40 ..      21      55 ..      19      73 .. 0.84
   2 ?    6.0   0.1     0.017        14     121     164 ..      88     132 ..      66     138 .. 0.69
   3 ?   -1.3   0.0         3   2.5e+03      87     106 ..     216     241 ..     172     313 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-06
                            AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKssl 40
                                      vG +e +++L+s++++ +    + +l+sG++GvGK++ 
  gi|330507468|ref|YP_004383896.1| 21 VGQDEIVRRLKSYVKTRN---LPHLLFSGPPGVGKTAA 55
                                      89************9554...489************85 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.017
                            AAA_16 121 ellkrllallsrder.plvlvlDdlqwadeaslqllaaLlrlles 164
                                       +++k++++ ++ +e    v++lD+++ +  + +++l+ ++++ ++
  gi|330507468|ref|YP_004383896.1|  88 HKVKDFARMAPLGEAdFKVIFLDEADALTNDAQSALRRTMERYSA 132
                                       444555533333333147*******************99987655 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3
                            AAA_16  87 de......aesaeleawrekleeala 106
                                       de      +++a++e+ + ++++a++
  gi|330507468|ref|YP_004383896.1| 216 DEetiyqiTSTAKPEEIKSFIKTAIS 241
                                       33444444333344444444444444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.2e-08   9.5e-06       6      78 ..       5      73 ..       3     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.2e-08
                             Rad17  6 nelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstv.vkvLskelgiklrewln 78
                                       e W+eky+Pe ++++    + ++ +k ++k+  L++     LL sGP+G gk+ + + ++  ++g   r++  
  gi|330507468|ref|YP_004383896.1|  5 EEIWIEKYRPERLDDIVGQDEIVRRLKSYVKTRNLPH-----LLFSGPPGVGKTAAsISIVKEIFGETWRNNFI 73
                                      689**************9*****************97.....5**********986366666677777776654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.4e-07   0.00027       5     126 ..      42     163 ..      38     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.4e-07
                            AAA_14   5 lvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqev.p 77 
                                       l+ +G+  vGKT     ++ke +  + +++++++n  der  ++    k+ ++ +   l e + +++flDE+  + +
  gi|330507468|ref|YP_004383896.1|  42 LLFSGPPGVGKTAASISIVKEIFgeTWRNNFIELNASDERGIDIIRH-KVKDFARMApLGEADFKVIFLDEADALtN 117
                                       5678999******9999999999998899*********999876655.355555554555567899******98736 PP

                            AAA_14  78 ewekalkslvdeg.knldvivtGSnskllskeiatslagrvaeielypls 126
                                       ++++al++ ++++    ++i++     + s++i +  + r a+++  pls
  gi|330507468|ref|YP_004383896.1| 118 DAQSALRRTMERYsATTRFILSC----NYSSKIIEPIQSRCAVYRFKPLS 163
                                       7**********994555666543....34445666777777777777776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0    0.0001     0.085       2      58 ..      17      76 ..      16      99 .. 0.78
   2 !    6.2   0.0    0.0071       5.8     108     135 ..     105     132 ..      94     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                      Mg_chelatase  2 lkdvkGqeeakrale..iaaaGgHnlllvGppGsGKtmla.krlpsllpplseeealeva 58
                                      l d++Gq+e  r l+  +      +ll+ GppG GKt    + +++++ +  +++ +e +
  gi|330507468|ref|YP_004383896.1| 17 LDDIVGQDEIVRRLKsyVKTRNLPHLLFSGPPGVGKTAASiSIVKEIFGETWRNNFIELN 76
                                      6789999998888873355556679***********986415667788888877777765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0071
                      Mg_chelatase 108 GvLfLDElpefkrkvlevLRePledgev 135
                                        v+fLDE+  +++++  +LR+ +e+ + 
  gi|330507468|ref|YP_004383896.1| 105 KVIFLDEADALTNDAQSALRRTMERYSA 132
                                       69*********************98764 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.1e-06    0.0017       8      78 ..      23      97 ..      20     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.1e-06
                                      HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH....HHHHHHHHHGGGGT CS
                            ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprk....slleqtleefkkfl 78
                                      Q e++++l++ +k ++  ++l+  + G+GKT  +++++++++ + ++++f+ l  +     +++    ++f++++
  gi|330507468|ref|YP_004383896.1| 23 QDEIVRRLKSYVKTRNLPHLLFSGPPGVGKTAASISIVKEIFGETWRNNFIELNASDergiDIIRHKVKDFARMA 97
                                      9999********978888******************************998775543333355555555555555 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 !   19.3   0.0   1.3e-06    0.0011       4      49 ..     179     218 ..     176     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-06
                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                       AAA_assoc_2   4 klkleddalealaeladGDaRkaLnlLElaaeaaeakegkieitle 49 
                                        l+++d  l+a+  +a+GD+Rka+n+L++aa   ++       ++e
  gi|330507468|ref|YP_004383896.1| 179 GLRVSDGGLSAIEYVAGGDMRKAINALQAAALLGDEV------DEE 218
                                       578899999*******************999887653......222 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 !   18.5   0.0   1.7e-06    0.0014       1      92 [.      41     133 ..      41     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-06
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkk..Gpvfanllladeinrap 75 
                                       h+l+ g PG++kt +  ++ k +  e  r  f  +l  sd  G++++++k k+f   +  G    ++++ de +  +
  gi|330507468|ref|YP_004383896.1|  41 HLLFSGPPGVGKTAASISIVKEIFGETWRNNFI-ELNASDERGIDIIRHKVKDFARMAplGEADFKVIFLDEADALT 116
                                       99***************************9997.79*****************9765333888889*********** PP

                             AAA_3  76 pktqsalleameerqvt 92 
                                         +qsal  +me    t
  gi|330507468|ref|YP_004383896.1| 117 NDAQSALRRTMERYSAT 133
                                       ***********987666 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.5e-05      0.02      42      87 ..      33      79 ..      13      97 .. 0.78
   2 ?    0.9   0.0      0.25     2e+02     281     315 ..     106     141 ..      88     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXX CS
                             TIP49 42 likekklaGravLlaGpsgtGktalaiaiskelgedv...pfvalsgse 87
                                       +k+++l    +L++Gp+g Gkta +i+i ke+  ++    f+ l++s+
  gi|330507468|ref|YP_004383896.1| 33 YVKTRNLP--HLLFSGPPGVGKTAASISIVKEIFGETwrnNFIELNASD 79
                                      56777776..79********************96443233688888886 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.25
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX CS
                             TIP49 281 vlfiDevhmlDiecfsylnraleselaPi.vilatn 315
                                       v+f+De+  l  ++ s l r++e   a    il+ n
  gi|330507468|ref|YP_004383896.1| 106 VIFLDEADALTNDAQSALRRTMERYSATTrFILSCN 141
                                       9**********************8766542566666 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.23   1.9e+02      60      77 ..      44      61 ..      29      77 .. 0.83
   2 !   13.4   0.0   2.9e-05     0.024     159     212 ..      85     139 ..      81     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.23
                                      E---TTS--HHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                            SNF2_N 60 LaDemGLGKTvqvlalil 77
                                      ++  +G+GKT  ++++++
  gi|330507468|ref|YP_004383896.1| 44 FSGPPGVGKTAASISIVK 61
                                      56679***********98 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.9e-05
                                       HHHHHT......TTS-S-S-SEEEES-GGGT--T.TSHHHHHHHH---S-EEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 159 vlsreaelqkkrsvlkqvewkrvvlDEghtlkns.tskaaeavskLstsnrwilt 212
                                       +++ +++ ++++ +l + + k + lDE+  l n  +s ++ +++++s+  r il+
  gi|330507468|ref|YP_004383896.1|  85 IIRHKVKDFARMAPLGEADFKVIFLDEADALTNDaQSALRRTMERYSATTRFILS 139
                                       56666666789999********************99******************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.015        12       7      21 ..      41      55 ..      36      90 .. 0.87
   2 ?    7.4   0.0     0.006       4.9      91     120 ..      99     131 ..      70     143 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                            AAA_22  7 ilvvtGesGtGKTtl 21
                                      +l+  G++G+GKT  
  gi|330507468|ref|YP_004383896.1| 41 HLLFSGPPGVGKTAA 55
                                      68899********75 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.006
                            AAA_22  91 v....ielliiDEaqhlrseealeeLrsllnlsr 120
                                             +++ +DEa+ l +++a + Lr+ ++  +
  gi|330507468|ref|YP_004383896.1|  99 LgeadFKVIFLDEADAL-TNDAQSALRRTMERYS 131
                                       2444446**********.9999999988887333 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0056       4.6      11      59 ..      26      78 ..      20      85 .. 0.78
   2 ?    6.0   0.0     0.011       8.6      90     119 ..     100     129 ..      93     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0056
                                      HHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHH..HSTTTTS-EEEEETT CS
                   Sigma54_activat 11 lleqikkvaktd..lsvlitGesGtGKellaraihe..askrkekpfvavnca 59
                                      +++++k+++kt+   ++l  G  G+GK+  + +i +    +  +++f+++n +
  gi|330507468|ref|YP_004383896.1| 26 IVRRLKSYVKTRnlPHLLFSGPPGVGKTAASISIVKeiFGETWRNNFIELNAS 78
                                      5666777776665568999**********999998855567788899999976 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
                                       HHTTTSEEEEETGGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat  90 ekadgGtlfLDeigelplelQekLlrvlqe 119
                                        +ad  ++fLDe   l+ ++Q+ L r +++
  gi|330507468|ref|YP_004383896.1| 100 GEADFKVIFLDEADALTNDAQSALRRTMER 129
                                       5788889*****************999987 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   3.7e-05      0.03      34      72 ..      40      78 ..      27     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.7e-05
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                       ++l+ Gp G+GKt+   +++k++  e++  ++i+++a+
  gi|330507468|ref|YP_004383896.1| 40 PHLLFSGPPGVGKTAASISIVKEIFGETWRNNFIELNAS 78
                                      489**********************9*********9986 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.3e-05     0.027      49     148 ..      31     130 ..      21     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                                       SSSSBBCSS-EEEEEESSTSTHHH....HHHHHHHHSSSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTT CS
                               MCM  49 edktklrgdinvllvgdpgtaKsq....lLkyveklapravytsgkgssaagLtaavvrdeetgefvleaGalvlad 121
                                       ++ +k+r   ++l+ g pg++K++    ++k++   + r++++  ++s + g+    ++ ++          l  ad
  gi|330507468|ref|YP_004383896.1|  31 KSYVKTRNLPHLLFSGPPGVGKTAasisIVKEIFGETWRNNFIELNASDERGIDIIRHKVKDFA----RMAPLGEAD 103
                                       5567889999************9544448899999999**************976644443333....3446889** PP

                                       TSEEEEESGGGSTCHHHHHHHHHHHHS CS
                               MCM 122 kGvcciDefdkmkeedrsalhEamEqq 148
                                         v+ +De d  +++ +sal   mE+ 
  gi|330507468|ref|YP_004383896.1| 104 FKVIFLDEADALTNDAQSALRRTMERY 130
                                       *************************86 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017      0.14      59     170 ..     105     206 ..      85     210 .. 0.91
   2 ?   -1.3   0.0         2   1.7e+03      12      49 ..     217     254 ..     215     277 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                       EEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHH CS
                    DNA_pol3_delta  59 rivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwi 135
                                       ++++l+ +      + l+ + + +L +++++++++t +il ++       k++  ++++  v ++k+l+ e + k i
  gi|330507468|ref|YP_004383896.1| 105 KVIFLDEA------DALTNDAQSALRRTMERYSATTRFILSCN----YSSKIIEPIQSRCAVYRFKPLSPEAVTKRI 171
                                       56666666......66899999*********************....55789************************* PP

                                       HHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                    DNA_pol3_delta 136 qkraqelglkiekealelLlelvennlsaikqele 170
                                       + +a+e+gl  ++  l+ + +  +++++ + ++l+
  gi|330507468|ref|YP_004383896.1| 172 KFIASEEGLRVSDGGLSAIEYVAGGDMRKAINALQ 206
                                       ******************************99998 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHTTTEEEEEEEE-STTS-HHH.HTTTS CS
                    DNA_pol3_delta  12 eeskdqilkqalkqgfedlnyikfdlnedwiddvleec 49 
                                       ee++ qi ++a+ ++++++  + ++++ + + ++l+++
  gi|330507468|ref|YP_004383896.1| 217 EETIYQITSTAKPEEIKSFIKTAISGDFVGARAILDDL 254
                                       67888999999999999999999999888888777765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00045      0.37      44     122 ..      36     117 ..      21     145 .. 0.66
   2 ?   -1.4   0.0       2.1   1.7e+03      19      45 ..     216     246 ..     199     255 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00045
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLve.elkrarrdgklaralkrllkv..dllilDdl 117
                                       +++   +++ Gp+GvGK+  +i++ +e   + ++  f+ +++  e  + + r++ k   +++ l ++  +++ lD+ 
  gi|330507468|ref|YP_004383896.1|  36 TRNLPHLLFSGPPGVGKTAASISIVKEIFGETWRNNFIELNASDErGIDIIRHKVKDFARMAPLGEAdfKVIFLDEA 112
                                       4444578999**************99999999999999876544313555555554444444444332256666666 PP

                         IstB_IS21 118 gllpl 122
                                         l+ 
  gi|330507468|ref|YP_004383896.1| 113 DALTN 117
                                       55554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                         IstB_IS21  19 ledidfraarsldkrkvkeL....atlsfie 45 
                                        e+  ++ +  ++++++k+     ++++f+ 
  gi|330507468|ref|YP_004383896.1| 216 DEETIYQITSTAKPEEIKSFiktaISGDFVG 246
                                       4444444444444443333211113444444 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   0.1    0.0021       1.7       1      89 [.      41     127 ..      41     136 .. 0.60
   2 ?   -3.2   0.0       9.2   7.5e+03      19      43 ..     207     234 ..     200     249 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0021
                                       EEEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEv 74 
                                       ++l  GppG+gK+  + ++ + +   +++ + + l++   e+ +   r+  + +   +  pl +a    ++++lDE 
  gi|330507468|ref|YP_004383896.1|  41 HLLFSGPPGVGKTAASISIVKEIfgeTWRNNFIELNA-SDERGIDIIRH--KVKDFARMAPLGEA--DFKVIFLDEA 112
                                       68999********988887777766644444444444.22333333333..33444444444433..4567777777 PP

                                       GG--HHHHHHHHHHH CS
                             AAA_5  75 eraesevlnsLlsll 89 
                                       + +  +++++L + +
  gi|330507468|ref|YP_004383896.1| 113 DALTNDAQSALRRTM 127
                                       777777777776555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.2
                                       GGGGB...S--EEEEE--TT--HHHHH- CS
                             AAA_5  19 laaal...nreveyvqltrdtteedlkg 43 
                                        aa+l    +e +++q+t+  ++e++k 
  gi|330507468|ref|YP_004383896.1| 207 AAALLgdeVDEETIYQITSTAKPEEIKS 234
                                       5555533333445666777666776665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00044      0.36       2      41 ..      43      79 ..      42      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00044
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnped 41
                                      +++Gp+g+GK+ ++ +++k++    +++++++++  n++d
  gi|330507468|ref|YP_004383896.1| 43 LFSGPPGVGKTAASISIVKEIF---GETWRNNFIELNASD 79
                                      799*************999999...566878877766555 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   0.00053      0.43       7      89 ..      44     127 ..      40     136 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                            AAA_24   7 iyGpsgiGKTtlakel.......gpkplfidtekGlks.ldadkfpdieswedfldevvelaaeladyktlviDtid 75 
                                         Gp+g+GKT    ++       + +  fi ++++  + +d ++        +++d++   +  +ad+k++++D +d
  gi|330507468|ref|YP_004383896.1|  44 FSGPPGVGKTAASISIvkeifgeTWRNNFIELNASDERgIDIIR-------HKVKDFARMAPLGEADFKVIFLDEAD 113
                                       5699******9888885555655333333344443322022222.......3455666666999************* PP

                            AAA_24  76 eleelclaevirqn 89 
                                        l + +   ++r  
  gi|330507468|ref|YP_004383896.1| 114 ALTNDAQSALRRTM 127
                                       **999988887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 2245.68
//
Query:       gi|330507469|ref|YP_004383897.1|  [L=1053]
Description: isoleucyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete 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-193  644.2   0.2     2e-193  643.9   0.2    1.1  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    1.6e-34  119.0   0.0    4.7e-34  117.5   0.0    1.8  2  Anticodon_1   Anticodon-binding domain of tRNA
    2.9e-26   92.1   1.0    1.8e-11   43.4   0.1    3.6  3  tRNA-synt_1g  tRNA synthetases class I (M)
    5.4e-06   26.0   0.0    6.9e-05   22.3   0.0    2.3  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    0.00017   20.6   0.0    0.00085   18.3   0.0    2.0  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 !  643.9   0.2  5.7e-197    2e-193       4     600 ..      20     633 ..      17     635 .. 0.95

  Alignments for each domain:
  == domain 1  score: 643.9 bits;  conditional E-value: 5.7e-197
                       tRNA-synt_1   4 ekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakv 80 
                                       + We +d ++k +e +   k+f +vdgPPy tG++H+G a++k++kd v ry++m+G+ev+ + GwD++Gl+ie kv
  gi|330507469|ref|YP_004383897.1|  20 SLWERADSYRKVRELRLGGKKFFFVDGPPYTTGRIHLGTAWNKVIKDAVLRYRSMNGFEVKDRAGWDMHGLPIEVKV 96 
                                       68*************************************************************************** PP

                       tRNA-synt_1  81 ekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliy 157
                                       e+ +g ++kk+ + +g+++f+++++e++ +++++++ q+k lG+++D+d++y+Tl++e+ ea ++++++ +++ l+ 
  gi|330507469|ref|YP_004383897.1|  97 EESFGFRNKKDIEAYGVDKFIQRCKEFALRQKDDMTAQFKILGAWMDWDDPYMTLKNEYLEAAWWTLKKAHEHNLLE 173
                                       ***************************************************************************** PP

                       tRNA-synt_1 158 rgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv....... 227
                                       rg+++vnw+++++ta+++ Evey d++d++i+v+fp+ ++e++++vi+TTtP+T+++++avavnp ++y+       
  gi|330507469|ref|YP_004383897.1| 174 RGSRVVNWCPRCQTAIADSEVEYWDETDYSIYVKFPVIGEENTYIVIWTTTPWTIPANVAVAVNPSFQYSrvrawkd 250
                                       **********************************************************************9999977 PP

                       tRNA-synt_1 228 itkeklilaeallkslvkke..sekkiledergkeLegkevelpl.......vnrkipiiaddyvdkeaGtGvVkia 295
                                        + e li+a+ l++s+++    +++++l+   +k+++++++e+pl       ++ +  + a d+v++e+ tG+V+ia
  gi|330507469|ref|YP_004383897.1| 251 GKSEILIMASELVDSVLRTGryQDYELLQGLSAKDMQKLKYEHPLldlvprqKEIEHGVYAADFVTAEN-TGCVHIA 326
                                       778899***********99876778********************99988777778889999***9986.******* PP

                       tRNA-synt_1 296 PahdedDyevgkkynlevinildedgtlteea.aefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkp 371
                                       P+h+ +Dye+g ++ le+ +++  dg++t ea +++ g++v++a+ +v+++l+e+ +ll + +  h +++c+r k+p
  gi|330507469|ref|YP_004383897.1| 327 PGHGLEDYELGLDHHLEIFCPVGGDGRYTAEAgEKYLGQYVKEADSNVIADLEERDKLLAQGRLAHRYGHCWRCKTP 403
                                       *****************************999789****************************************** PP

                       tRNA-synt_1 372 iiyrateqWfvrvkeladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvvree 447
                                       ii+ at+qWf r+++l+d++l+++++v+++p++ + +r+a+w+ n++dWciSRqr+WG ++p++   + + + v   
  gi|330507469|ref|YP_004383897.1| 404 IIFIATSQWFLRISDLRDKMLDEISRVKWYPEWaGSARFADWISNARDWCISRQRYWGIPLPIWTCPDCGHMEVIGT 480
                                       *********************************99***********************************8888555 PP

                       tRNA-synt_1 448 lkelvagreeeeaekkalekeakdkl...kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmll 521
                                        +el++    + +++++l++  +d +       g++ + +dv+DvWF+S+    +tl +p++ +ee+ + +pad+++
  gi|330507469|ref|YP_004383897.1| 481 ASELEE---RSGKKIADLHRPDVDAIvldCPCGGKMLRSPDVFDVWFDSAVASWATLRFPSH-EEEFGEWWPADFIT 553
                                       555554...7778888899988888877544568999************************9.9************* PP

                       tRNA-synt_1 522 eGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgr 597
                                       eG D++rgW+++ +  s+  +g++P+k+vl+hg+++d++GrKmSKs+gN+++p++v+++ gad+lR++++  +   +
  gi|330507469|ref|YP_004383897.1| 554 EGHDQTRGWFYSQLGASMVSFGRAPYKSVLMHGFTLDDQGRKMSKSIGNIVQPEEVVERFGADILRFYVLgANAPWE 630
                                       *********************************************************************96666666 PP

                       tRNA-synt_1 598 din 600
                                       d++
  gi|330507469|ref|YP_004383897.1| 631 DLH 633
                                       665 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.5   0.0   1.3e-37   4.7e-34       1     149 [.     683     834 ..     683     838 .. 0.91
   2 ?   -3.0   0.0       1.7   6.1e+03     121     143 ..     965     987 ..     937     995 .. 0.74

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 1.3e-37
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       drwils++n+l++e+t+ +e y+++++++++ +f+++dl++wy++lv+pr + e++++++  a+++++evl +l rl
  gi|330507469|ref|YP_004383897.1| 683 DRWILSRVNSLAEEITAEMEGYQLHRIVRSISDFILEDLSRWYIQLVRPRTWIEQDDPDKLaAYATIYEVLTKLARL 759
                                       9******************************************************999977799************* PP

                       Anticodon_1  77 laPfmPfitEelwqr......eeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpss 146
                                       +aPf+Pfi+E ++q+      e    +   s+++++w e ++   +  l ee+++l++e+ +a+ ++r++ + k ++
  gi|330507469|ref|YP_004383897.1| 760 MAPFTPFIAESIYQNlvrgldE----NARPSVHMCDWLEgDKGLIDVRL-EESMDLVREVSMAASNARQKGGRKLRW 831
                                       ***************9754432....4459********96665558888.99******************9999998 PP

                       Anticodon_1 147 elk 149
                                       +++
  gi|330507469|ref|YP_004383897.1| 832 PVS 834
                                       865 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                       Anticodon_1 121 eevellkeivkairklrselkik 143
                                       e+ ++++ei++ i+++r+el++ 
  gi|330507469|ref|YP_004383897.1| 965 EAEAYAREIIRRIQDMRKELDLR 987
                                       56678889999999999998775 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   2.2e-10     8e-07       8      59 ..      48      99 ..      43     197 .. 0.77
   2 !   16.9   0.0   5.8e-07    0.0021     168     238 ..     396     465 ..     358     475 .. 0.85
   3 !   43.4   0.1   5.1e-15   1.8e-11     244     374 ..     519     642 ..     509     652 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.2e-10
                                      B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT CS
                      tRNA-synt_1g  8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke 59
                                      pY++g++HlG + + ++ D++ Ry+ ++g ev   +g D+hG pie+k e++
  gi|330507469|ref|YP_004383897.1| 48 PYTTGRIHLGTAWNKVIKDAVLRYRSMNGFEVKDRAGWDMHGLPIEVKVEES 99
                                      8**********************************************98864 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 5.8e-07
                                       .........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 168 ksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                       ++  +++  ++  t+++f+++s++++k+ + i++ +   e   +    +w+++  +d++isr+  wGip+P
  gi|330507469|ref|YP_004383897.1| 396 HCWRCKTPIIFIATSQWFLRISDLRDKMLDEISRVKWYPEWAGSARFADWISN-ARDWCISRQRYWGIPLP 465
                                       6888888889999*****************995555445555667788***99.9**************99 PP

  == domain 3  score: 43.4 bits;  conditional E-value: 5.1e-15
                                       EE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEE..EGGGHH..HHHTHHHHHHHHTT----S-EE CS
                      tRNA-synt_1g 244 vlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfi..gkdiik..FHtifwPaillgaelklpkkvv 316
                                       v+ VW+d  +   +++   +    +ee++ e+W +        fi  g d ++  F + +  a + + +    k+v 
  gi|330507469|ref|YP_004383897.1| 519 VFDVWFDSAVASWATLRFPS----HEEEFGEWWPA-------DFIteGHDQTRgwFYSQL-GASMVSFGRAPYKSVL 583
                                       7889***9998888777776....689******44.......555225565543244444.3444556666778999 PP

                                       EE--.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHH CS
                      tRNA-synt_1g 317 ahey.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfver 374
                                        h++ l  +g+K+SkS g++v+++e++er+ ad+lR+y++ ++   +Dl+fswe + ++
  gi|330507469|ref|YP_004383897.1| 584 MHGFtLDDQGRKMSKSIGNIVQPEEVVERFGADILRFYVLGANAPWEDLHFSWEAVENT 642
                                       9999456789********************************************98765 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.072   2.6e+02      21      49 ..      52      80 ..      41      81 .. 0.89
   2 !   22.3   0.0   1.9e-08   6.9e-05     228     298 ..     569     641 ..     553     644 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.072
                                      S--BHHHHHHHHHHHHHHHHHHHTT-EEE CS
                      tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvq 49
                                        +hlG a + v+ D + r+  + g++v+
  gi|330507469|ref|YP_004383897.1| 52 GRIHLGTAWNKVIKDAVLRYRSMNGFEVK 80
                                      578***********************996 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.9e-08
                                       HHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-T.TS-EEE-HHHHHH CS
                      tRNA-synt_1e 228 qseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahy.rsqldfkeellee 298
                                        s+  f+  ++    +h   l  +g+kmsks++n+++ ++v+++f + +lR+++l a+   + l f+ e++e+
  gi|330507469|ref|YP_004383897.1| 569 ASMVSFGrAPYKSVLMHGFTLDDQGRKMSKSIGNIVQPEEVVERFGADILRFYVLGANApWEDLHFSWEAVEN 641
                                       56777775677788899999999*****************************998765314567777777765 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.22   8.1e+02      34      63 ..      51      80 ..      35      88 .. 0.83
   2 !   18.3   0.0   2.4e-07   0.00085     269     312 ..     583     626 ..     553     650 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.22
                      tRNA-synt_1f 34 SGliHiGnlrevltadlvaralrkrgeevr 63
                                       G+iH+G++ + +  d+v r  +  g ev+
  gi|330507469|ref|YP_004383897.1| 51 TGRIHLGTAWNKVIKDAVLRYRSMNGFEVK 80
                                      699******999999999998888888776 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.4e-07
                      tRNA-synt_1f 269 vvYelillkggekmssSkGnvltledwlevaepevlrflilrrk 312
                                       ++  + l+++g+kms+S Gn++ +e+++e    ++lrf++l ++
  gi|330507469|ref|YP_004383897.1| 583 LMHGFTLDDQGRKMSKSIGNIVQPEEVVERFGADILRFYVLGAN 626
                                       567788999999***************************98643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1053 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.81u 0.29s 00:00:01.10 Elapsed: 00:00:00.48
# Mc/sec: 6593.29
//
Query:       gi|330507470|ref|YP_004383898.1|  [L=158]
Description: hypothetical protein MCON_1411 [Methanosaeta concilii GP6]
Scores for complete sequence (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  134.9   0.1    1.4e-39  134.7   0.1    1.1  1  DNase-RNase  Bifunctional nuclease
  ------ inclusion threshold ------
       0.11   12.6   0.1       0.15   12.2   0.1    1.2  1  Lsr2         Lsr2


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.7   0.1   1.6e-43   1.4e-39       7     127 ..      24     143 ..      15     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 134.7 bits;  conditional E-value: 1.6e-43
                                       EETTTTEEEEEEEETTSSEEEEEE--HHHHHHHHHHHCT---SS--HHHHHHHHHHHTTEEEEEEEEEEEETTEEEE CS
                       DNase-RNase   7 ldassqspvvlLreeegrrvlpIwigaaeaqaialalegeeppRPlthDLlasllealgakvervvItdledgtfyA 83 
                                        d+s+ +pvvlL++e+gr ++pI++g +ea +i+ al+ge +pRP+thDL++s+le+l+a++++  I+dl+ g++yA
  gi|330507470|ref|YP_004383898.1|  24 SDESNPAPVVLLEDEKGR-IVPIFVGLSEAISIHHALSGELAPRPMTHDLFISTLESLSASITNALIDDLDGGIYYA 99 
                                       3444559**********9.********************************************************** PP

                                       EEEEEET---EEEEE-HHHHHHHHHHHT--EEEEHHHHHHH-EE CS
                       DNase-RNase  84 elvlrkeeeeleidaRpSDaiaLAlrtgapIyveeevleeasie 127
                                       +l++++++++ eidaRpSD++aLAlr++a+I v e+v+++asi+
  gi|330507470|ref|YP_004383898.1| 100 RLTIKSDSKKNEIDARPSDCLALALRAKASIEVRERVVADASIS 143
                                       *****98667*******************************997 PP

>> Lsr2  Lsr2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.7e-05      0.15       5      61 ..      84     140 ..      80     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                              Lsr2   5 vvvtlvDDldgseadetvefgldgveYeiDLseenaeklrdaLapyieaarrvggrk 61 
                                       ++  l+DDldg+     ++++ d ++ eiD + ++  +l    +  ie+  rv +++
  gi|330507470|ref|YP_004383898.1|  84 ITNALIDDLDGGIYYARLTIKSDSKKNEIDARPSDCLALALRAKASIEVRERVVADA 140
                                       56789****************************999999888888888888776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1025.21
//
Query:       gi|330507471|ref|YP_004383899.1|  [L=390]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete 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-22   78.0   0.0    1.3e-21   76.2   0.0    2.0  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    3.6e-07   30.4   0.5    3.6e-07   30.4   0.5    1.8  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.032   14.3   0.1      0.082   12.9   0.1    1.6  1  DZR             Double zinc ribbon
      0.064   13.3   0.0       0.18   11.8   0.0    1.8  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.096   13.0   0.1       0.21   11.9   0.1    1.5  1  C1_2            C1 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 !   76.2   0.0   3.7e-25   1.3e-21       2      67 ..     293     356 ..     292     357 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 3.7e-25
                    OrfB_Zn_ribbon   2 rklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       ++lke+l+yka  +G+++++v+pay+S+tC++Cg+ + +  +g+ fkCp Cg + d+D+n+a Ni+
  gi|330507471|ref|YP_004383899.1| 293 YQLKEFLSYKALAAGVPLVLVDPAYSSQTCHQCGEHGIR--NGKSFKCPVCGWSGDADFNGAKNIA 356
                                       589************************************..************************7 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2      0.78   2.8e+03      43      69 ..      97     123 ..      71     141 .. 0.68
   2 !   30.4   0.5     1e-10   3.6e-07       3     106 ..     159     259 ..     155     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.78
                        OrfB_IS605  43 grrlksdykylakeiaelqsklkkskn 69 
                                       +  ++++ ++l+++  e++ +l +s++
  gi|330507471|ref|YP_004383899.1|  97 SIDYDTRIFALREKDEEVSVTLLRSRQ 123
                                       456667777888888888888888875 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 1e-10
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn..ykkasrkl 77 
                                       +v+ e  +++    +++g+DlGi ++a++++++     + g+ +k  +  +a  +a lq+k+ k ++  ++++++ +
  gi|330507471|ref|YP_004383899.1| 159 QVKSEA-PEQIHVDTVLGVDLGITDIAVTSEGQ----KFGGKTIKLIKNHYASMRAVLQQKAVKGTRssRRRCRELQ 230
                                       444443.677778899****************9....78999999999***********9998888889******** PP

                        OrfB_IS605  78 arlhrkrsrrrkhllhklathliktlkev 106
                                       +rl+ k +r  +   h+++++++ + +e+
  gi|330507471|ref|YP_004383899.1| 231 QRLSGKEARYQRQINHEISKAIVTRAQEI 259
                                       ***********************999987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.3e-05     0.082      28      49 .]     319     342 ..     298     353 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                               DZR  28 edrCpsCgek.vdpearf.CpeCG 49 
                                       +++C +Cge  + ++++f Cp CG
  gi|330507471|ref|YP_004383899.1| 319 SQTCHQCGEHgIRNGKSFkCPVCG 342
                                       556666666655555555666665 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 ?   11.8   0.0     5e-05      0.18      50      95 ..     298     344 ..     246     355 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5e-05
                                       HHHCC.TTTT-EEE.EEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  50 llaegtvlegaeLe.ieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       +l+ + +++g  L  ++    + +C++Cg+++  + k+++Cp Cg +
  gi|330507471|ref|YP_004383899.1| 298 FLSYKALAAGVPLVlVDPAYSSQTCHQCGEHGIRNGKSFKCPVCGWS 344
                                       445555566666653344455679*****9998777789*****965 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.9e-05      0.21       6      39 ..     309     342 ..     308     348 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                              C1_2   6 pLtlskgedssesfnCsaCgrk..idgffYsCseCd 39 
                                       pL l+  ++ ++s +C+ Cg+    +g+ ++C+ C 
  gi|330507471|ref|YP_004383899.1| 309 PLVLV--DPAYSSQTCHQCGEHgiRNGKSFKCPVCG 342
                                       67777..89999**********8656666****9*6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      694  (0.0387082); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2690.23
//
Query:       gi|330507472|ref|YP_004383900.1|  [L=366]
Description: hypothetical protein MCON_1413 [Methanosaeta concilii GP6]
Scores for complete 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-118  395.6  28.6   2.8e-118  395.3  28.6    1.0  1  DUF1646          Protein of unknown function (DUF1646)
  ------ inclusion threshold ------
        6.5    7.5   7.0        1.1    9.9   0.1    3.0  3  DUF2645          Protein of unknown function (DUF2645)


Domain annotation for each model (and alignments):
>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.3  28.6  3.1e-122  2.8e-118       7     347 .]      23     359 ..      18     359 .. 0.97

  Alignments for each domain:
  == domain 1  score: 395.3 bits;  conditional E-value: 3.1e-122
                           DUF1646   7 ilvlvlilPlvvrkveenlelfllimgvaavtvsglfslelliealktplailevgaipigitqavllaGlvfellk 83 
                                       + + vli P++v+k+e+nle+fl++mgv +vt+ g++ + l+ ea+ +p++         gi+ avl+aG+ f++ +
  gi|330507472|ref|YP_004383900.1|  23 VALAVLIGPFTVKKIEHNLEAFLFVMGVLSVTIAGVWEMRLVEEAVMEPVVK--------GIVPAVLVAGMAFHYGR 91 
                                       5567999*****************************************9864........7**************** PP

                           DUF1646  84 kklksllaevldklalkvfvfllivilGlassvisaivaavilaeivallplerkekvklvviasfaiGlGaaltPv 160
                                       ++ +s +  vld++++k+++f++iv lGl+ssvi+ai+aa++l+e+v+++plerk+k++lv+i++faiGlGa ltP+
  gi|330507472|ref|YP_004383900.1|  92 SRAQSAMSYVLDNVSIKAVAFVMIVGLGLVSSVITAIIAALLLVELVNCMPLERKDKINLVIITCFAIGLGAVLTPL 168
                                       ***************************************************************************** PP

                           DUF1646 161 GePlstiavskl.....nedflylidvlgeyiiiavlvlallaalslkrlskreelvevveyeeelkevliravkvf 232
                                       GePlstia+skl     n++f++l++ l  y+i++vl+l++l++l+  +  +++e v +ve +e+l++v  ra kv+
  gi|330507472|ref|YP_004383900.1| 169 GEPLSTIAISKLqgppyNAGFFFLFEKLALYVIPGVLALGVLGVLFTGKA-TKQECVTMVEDTETLRDVGARAAKVY 244
                                       ***********955555699**************************9998.6677********************** PP

                           DUF1646 233 vfilalellGegfkPlikayiaklkseilywvnlisavvdnatlaaaeisPelteeqirailmsllisGGlliPGni 309
                                       vf++al llG+g+k +i++y++ ++se+lywvn++sa++dnatl+aaei+P+lt  qi a+lm+lli+GG+l+PGni
  gi|330507472|ref|YP_004383900.1| 245 VFVMALLLLGAGMKIIIDKYFTAIPSEVLYWVNMLSAILDNATLTAAEIAPSLTIGQITAALMGLLIAGGMLVPGNI 321
                                       ***************************************************************************** PP

                           DUF1646 310 PnivsaGklkikskeWarvgvPlgiilliiyfivllvl 347
                                       Pni++a kl i+skeWar+gvP+g++l+++yf+ ++++
  gi|330507472|ref|YP_004383900.1| 322 PNIIAANKLGITSKEWARLGVPVGLVLMLVYFVWIFYI 359
                                       ***********************************986 PP

>> DUF2645  Protein of unknown function (DUF2645)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.25   2.3e+03      55      90 ..      25      60 ..      16      63 .. 0.71
   2 ?   -1.1   0.6      0.34     3e+03      50      79 ..     125     154 ..      96     161 .. 0.53
   3 ?    9.9   0.1   0.00013       1.1      66      95 ..     332     361 ..     271     362 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.25
                           DUF2645 55 alllliPlllvlvkkklksaflvvialvillYiiWr 90
                                        +l+ P+ +  + + l+   +v+ +l + +  +W+
  gi|330507472|ref|YP_004383900.1| 25 LAVLIGPFTVKKIEHNLEAFLFVMGVLSVTIAGVWE 60
                                      445667887777777777777778888888888886 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.34
                           DUF2645  50 vaviaalllliPlllvlvkkklksaflvvi 79 
                                       +++i+a lll+ l+ ++  +++ +  lv+i
  gi|330507472|ref|YP_004383900.1| 125 ITAIIAALLLVELVNCMPLERKDKINLVII 154
                                       455555566666655444444443333333 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00013
                           DUF2645  66 lvkkklksaflvvialvillYiiWrFflRf 95 
                                       ++ k  +++ + v ++++l+Y++W F++ f
  gi|330507472|ref|YP_004383900.1| 332 ITSKEWARLGVPVGLVLMLVYFVWIFYIPF 361
                                       55677788889999999**********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); 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:                         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 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2657.76
//
Query:       gi|330507473|ref|YP_004383901.1|  [L=262]
Description: hypothetical protein MCON_1415 [Methanosaeta concilii GP6]
Scores for complete 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  112.0  16.6    4.7e-32  111.7  16.6    1.0  1  DUF1646          Protein of unknown function (DUF1646)
  ------ inclusion threshold ------
        1.7    8.7   0.0        1.7    8.7   0.0    2.7  3  FSAP_sig_propep  Frog skin active peptide family signal and p


Domain annotation for each model (and alignments):
>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.7  16.6   5.3e-36   4.7e-32       4     241 ..       9     242 ..       6     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 5.3e-36
                           DUF1646   4 llvilvlvlilPlvvrkveenlelfllimgvaavtvsglfslelliealktplailevgaipigitqavllaGlvfe 80 
                                       l+ i++ vl+ Pl+ +++e+nle+fll m++ av +s  + + ++ ea+++pl++        gi+++vllaGl+ +
  gi|330507473|ref|YP_004383901.1|   9 LIPIFLAVLLGPLLIKRIEQNLEMFLLLMSICAVAISRSWHIGIVEEAIQEPLVV--------GIVLTVLLAGLIAH 77 
                                       56688899999*****************************************975........7************* PP

                           DUF1646  81 llkkklksll.aevldklalkvfvfllivilGlassvisaivaavilaeivallplerkekvklvviasfaiGlGaa 156
                                       +++  +   + a  ld++++kv+ + ++++lGl +++i+ i++  +l+e v+ lpl rk+++k++++++++i lGaa
  gi|330507473|ref|YP_004383901.1|  78 YIRPDFLHNInAILLDRITMKVIFLEIVIVLGLLAAIITPILSFFMLVEAVNHLPLMRKTRAKITILGCLSISLGAA 154
                                       **9887665516779************************************************************** PP

                           DUF1646 157 ltPvGePlstiavsklnedf...lyl.idvlgeyiiiavlvlallaalslkrlskreelvevveyeeelkevlirav 229
                                       l  v    s+ia+++++ ++    +l  ++   yi+ ++l+l+l++++++++  +++   +    +   k++ i + 
  gi|330507473|ref|YP_004383901.1| 155 LALVDGSSSAIAITRMQGELpsaGFLpPELQSLYIFLSILALGLISMFFAEEN-MNSIRKQAHGRASAHKRIAIWSA 230
                                       ***************997753333552578889**************999877.55545555667888899****** PP

                           DUF1646 230 kvfvfilalell 241
                                       +v +f  al l+
  gi|330507473|ref|YP_004383901.1| 231 RVCMFAGALLLI 242
                                       *****9999775 PP

>> FSAP_sig_propep  Frog skin active peptide family signal and propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.5         2   1.8e+04      13      20 ..     144     151 ..     143     151 .. 0.86
   2 ?    8.7   0.0   0.00019       1.7      10      25 ..     193     208 ..     189     222 .. 0.86
   3 ?   -1.7   0.7      0.33     3e+03       7      13 ..     239     245 ..     238     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 2
                   FSAP_sig_propep  13 LGlVSlSl 20 
                                       LG  S+Sl
  gi|330507473|ref|YP_004383901.1| 144 LGCLSISL 151
                                       89999997 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00019
                   FSAP_sig_propep  10 vLFLGlVSlSlCEEek 25 
                                       +L LGl+S++++EE+ 
  gi|330507473|ref|YP_004383901.1| 193 ILALGLISMFFAEENM 208
                                       788**********985 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.33
                   FSAP_sig_propep   7 LLLvLFL 13 
                                       LLL++FL
  gi|330507473|ref|YP_004383901.1| 239 LLLIIFL 245
                                       9*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 2107.60
//
Query:       gi|330507474|ref|YP_004383902.1|  [L=368]
Description: hypothetical protein MCON_1416 [Methanosaeta concilii GP6]
Scores for complete 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-114  380.3  31.6   1.1e-113  380.1  31.6    1.0  1  DUF1646      Protein of unknown function (DUF1646)
  ------ inclusion threshold ------
      0.078   13.2   0.0       0.18   12.0   0.0    1.5  1  Thr_synth_N  Threonine synthase N terminus


Domain annotation for each model (and alignments):
>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.1  31.6  1.3e-117  1.1e-113       5     347 .]       2     360 ..       1     360 [. 0.93

  Alignments for each domain:
  == domain 1  score: 380.1 bits;  conditional E-value: 1.3e-117
                           DUF1646   5 lvilvlvlilPlvvrkveenlelfllimgvaavtvsgl..........fslelliealktplaile..vgaipigit 69 
                                       ++i+++vl+ P++v+k+e+nle+fl++mgv avt+ g           +  e + e+  +  +i+e  + ++  gi+
  gi|330507474|ref|YP_004383902.1|   2 FAIVLVVLVGPFMVKKIEHNLEAFLFVMGVLAVTIAGFesravleaigYNHEQIAEVGWNMKLIMEaaMEPVVKGIV 78 
                                       679999********************************8888888887666777776555545554234455569** PP

                           DUF1646  70 qavllaGlvfellkkklksllaevldklalkvfvfllivilGlassvisaivaavilaeivallplerkekvklvvi 146
                                        avl+aGl+f++ ++  +  +a+ ldk+++k++vfl++vilGlassvi+ai++a++l+e+v+++p++r++k++lv+i
  gi|330507474|ref|YP_004383902.1|  79 PAVLVAGLLFHYGRSYAQNAMAAILDKVSIKLVVFLMVVILGLASSVITAIISALLLVELVNCMPIDRQTKINLVII 155
                                       ***************************************************************************** PP

                           DUF1646 147 asfaiGlGaaltPvGePlstiavskl.....nedflylidvlgeyiiiavlvlallaalslkrlskreelvevveye 218
                                       a+f+iGlGa ltPvGePlstiav+kl     n++f++l++ l +yii++vl+++ la+ +  ++s++   v   e++
  gi|330507474|ref|YP_004383902.1| 156 ACFSIGLGAVLTPVGEPLSTIAVTKLqgapyNAGFFFLFNQLAIYIIPGVLAMGALAVAFTGKKSQEACHV-AAEET 231
                                       *************************955555689***********************99999997666555.46799 PP

                           DUF1646 219 eelkevliravkvfvfilalellGegfkPlikayiaklkseilywvnlisavvdnatlaaaeisPelteeqirailm 295
                                       e+l++v+ir+ kv++f++al llG g+k  i++y+  ++++ilywvn isa++dnat++aae+sP +   qi+a+lm
  gi|330507474|ref|YP_004383902.1| 232 ETLRDVVIRGAKVYLFVAALLLLGGGMKIAIDKYLLTVPPQILYWVNSISAILDNATMTAAELSPAMEITQIQAVLM 308
                                       ***************************************************************************** PP

                           DUF1646 296 sllisGGlliPGniPnivsaGklkikskeWarvgvPlgiilliiyfivllvl 347
                                       +lli+GG+liPGniPni+sa kl+i+sk+Wa++gvPlg++++++y++ ++++
  gi|330507474|ref|YP_004383902.1| 309 GLLIAGGMLIPGNIPNIISAQKLNISSKDWAKLGVPLGLVMMLVYYVWVFYI 360
                                       ************************************************9986 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 ?   12.0   0.0   2.1e-05      0.18      12      52 ..     300     340 ..     294     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                       Thr_synth_N  12 lsfeeallkGlAeDgGLyvPeeiPklsaeeleelrklsYae 52 
                                       ++  +a+l+Gl   gG+++P +iP++ +++  ++++ ++a+
  gi|330507474|ref|YP_004383902.1| 300 ITQIQAVLMGLLIAGGMLIPGNIPNIISAQKLNISSKDWAK 340
                                       56679********************9877666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       957  (0.0533772); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2719.17
//
Query:       gi|330507475|ref|YP_004383903.1|  [L=452]
Description: hypothetical protein MCON_1421 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-27   92.7   0.0    1.8e-26   91.6   0.0    1.6  1  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor
    3.4e-15   56.2   0.2    6.2e-12   45.8   0.0    3.2  3  CBS           CBS domain
    2.6e-10   40.2   1.5    4.5e-10   39.4   1.5    1.3  1  DUF1646       Protein of unknown function (DUF1646)
      3e-07   30.7   0.1    1.1e-06   28.9   0.0    1.9  2  Rrf2          Transcriptional regulator
  ------ inclusion threshold ------
       0.03   14.3   0.1      0.066   13.2   0.1    1.6  1  HTH_11        HTH domain
      0.065   13.1   0.1        0.2   11.6   0.1    1.9  1  MarR_2        MarR family


Domain annotation for each model (and alignments):
>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.0   5.9e-30   1.8e-26       1      75 [.     163     237 ..     163     241 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 5.9e-30
                      HrcA_DNA-bdg   1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealki 75 
                                       +Lt+vq++ l +L++l+r ++ravK++ei e+++rn+ t+R q+ sLkal+Lve+v+GP+GGY+ t++ay+al++
  gi|330507475|ref|YP_004383903.1| 163 DLTPVQRDTLSTLVNLHRTDSRAVKAKEIGELMDRNPETIRIQMRSLKALNLVESVTGPRGGYTATATAYDALSR 237
                                       69**********************************************************************987 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.3   3.7e+03       1      16 [.     191     206 ..     191     217 .. 0.76
   2 !    6.7   0.1    0.0032       9.6       7      54 ..     342     386 ..     331     389 .. 0.66
   3 !   45.8   0.0   2.1e-15   6.2e-12       1      56 [.     396     450 ..     396     451 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                                       HHHHSBSSCEEEETTS CS
                               CBS   1 Vgdimtrdvvtvppdt 16 
                                       +g++m r++ t++ ++
  gi|330507475|ref|YP_004383903.1| 191 IGELMDRNPETIRIQM 206
                                       5899999999998665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0032
                                       SSCEEEETTSBHHHHHHHHH.HHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   7 rdvvtvppdttleealelmr.ekgvsrlPVVdedgklvGivtlrDllra 54 
                                       r+ v ++p+ttl+ea ++++ + +  +l V d   +  G+v + D+++a
  gi|330507475|ref|YP_004383903.1| 342 RRAVRISPNTTLREASRILViNGAQEAL-VED---RSPGLVNMVDIAKA 386
                                       56689*************8635445444.422...34455555566655 PP

  == domain 3  score: 45.8 bits;  conditional E-value: 2.1e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V++imt+ ++t++ d+++ ea+++m ++g ++l VV ++g l Gi+t rDl++ l+
  gi|330507475|ref|YP_004383903.1| 396 VREIMTPGFLTINSDAPIFEAVRMMGKTGARQL-VVSDNGALWGIITPRDLMESLA 450
                                       89***********************888899**.**99**************9887 PP

>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   1.5   1.5e-13   4.5e-10      90     198 ..      48     157 ..      41     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.5e-13
                           DUF1646  90 laevldklalkvfvfllivilGlassvisaivaavilaeivallplerkekvklvviasfaiGlGaaltPvGePlst 166
                                       l + l++++l+v+++ +iv+lGl +  i+ i+  ++l  ++ +l+ +rk  +++vv++ ++ G+Ga lt vG P s 
  gi|330507475|ref|YP_004383903.1|  48 LGSALQEIPLNVLLATIIVMLGLLAIFITPILPLLVLCVVAFMLSFNRKATARFVVMGGLSTGFGA-LTTVGLPPSP 123
                                       5678899**********************************************************5.9********* PP

                           DUF1646 167 iavskln..edflylidvlgeyiiiavlvlalla 198
                                       i+  +l+  ++ + +++ l  y i  ++++++l+
  gi|330507475|ref|YP_004383903.1| 124 ITSLRLEgsASATNFLTNLDPYTIFVIAAIGILS 157
                                       **99997333445555666667666677776654 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   3.5e-10   1.1e-06      11      67 ..     172     227 ..     165     233 .. 0.91
   2 ?   -2.7   0.0       2.5   7.6e+03      48      82 ..     352     386 ..     331     387 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 3.5e-10
                                       HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEE CS
                              Rrf2  11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrL 67 
                                       l +l+ L + +++  v+++ei e ++ +p+ ++  ++ L+  +lv+sv G++GGy+ 
  gi|330507475|ref|YP_004383903.1| 172 LSTLVNLHRTDSRA-VKAKEIGELMDRNPETIRIQMRSLKALNLVESVTGPRGGYTA 227
                                       67889999988877.****************************************85 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                                       HHHHTTSEEEETTT-TCEEESSHCCCSBHHHHHHH CS
                              Rrf2  48 kLrkaglvksvrGkgGGyrLakppeeItlldvvra 82 
                                       +Lr+a  + ++ G++  ++  ++p  +++ d+ +a
  gi|330507475|ref|YP_004383903.1| 352 TLREASRILVINGAQEALVEDRSPGLVNMVDIAKA 386
                                       46666666666666666666666666777777666 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.2e-05     0.066       9      54 ..     178     225 ..     171     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                            HTH_11   9 Lleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GY 54 
                                       L ++++  + ++e+ e +++   t+r  +++L++l   +es+ g+  GY
  gi|330507475|ref|YP_004383903.1| 178 LHRTDSRaVKAKEIGELMDRNPETIRIQMRSLKALN-LVESVTGPrgGY 225
                                       44667777***************************9.9******99999 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   6.6e-05       0.2       3      58 ..     164     222 ..     162     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.6e-05
                                       --HHHHHH...HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                            MarR_2   3 ltpaqarv...LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58 
                                       ltp q++    L +L+r + r + ++e+ + ++  + ++    + L a  Lve ++gp+
  gi|330507475|ref|YP_004383903.1| 164 LTPVQRDTlstLVNLHRTDSRAVKAKEIGELMDRNPETIRIQMRSLKALNLVESVTGPR 222
                                       56555555000566777777799********************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3206.36
//
Query:       gi|330507476|ref|YP_004383904.1|  [L=366]
Description: hypothetical protein MCON_1422 [Methanosaeta concilii GP6]
Scores for 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-118  393.6  28.2   1.1e-117  393.3  28.2    1.0  1  DUF1646   Protein of unknown function (DUF1646)
  ------ inclusion threshold ------
        5.7    7.6   6.8        1.1    9.9   0.1    3.0  3  DUF2645   Protein of unknown function (DUF2645)


Domain annotation for each model (and alignments):
>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.3  28.2  1.2e-121  1.1e-117       7     347 .]      23     359 ..      18     359 .. 0.97

  Alignments for each domain:
  == domain 1  score: 393.3 bits;  conditional E-value: 1.2e-121
                           DUF1646   7 ilvlvlilPlvvrkveenlelfllimgvaavtvsglfslelliealktplailevgaipigitqavllaGlvfellk 83 
                                       + + vli P++v+k+e+nle+fl++mgv +vt+ g++ + l+ ea+ +p++         gi+ avl+aG+ f++ +
  gi|330507476|ref|YP_004383904.1|  23 VALAVLIGPFTVKKIEHNLEAFLFVMGVLSVTIAGVWEMRLVEEAVMEPVVK--------GIVPAVLVAGMAFHYGR 91 
                                       5567999*****************************************9864........7**************** PP

                           DUF1646  84 kklksllaevldklalkvfvfllivilGlassvisaivaavilaeivallplerkekvklvviasfaiGlGaaltPv 160
                                       ++ +s +  vld+ ++k+++f++iv lGl+ssvi+ai+aa++l+e+v+++plerk+k++lv+i++faiGlGa ltP+
  gi|330507476|ref|YP_004383904.1|  92 SRAQSAMSYVLDNTSIKAVAFVMIVGLGLISSVITAIIAALLLVELVNCMPLERKDKINLVIITCFAIGLGAVLTPL 168
                                       ***************************************************************************** PP

                           DUF1646 161 GePlstiavskl.....nedflylidvlgeyiiiavlvlallaalslkrlskreelvevveyeeelkevliravkvf 232
                                       GePlstia+skl     n++f++l++ l  y+i++vl+l++l++l+  +  ++++ v +ve +e+l++v  ra kv+
  gi|330507476|ref|YP_004383904.1| 169 GEPLSTIAISKLqgppyNAGFFFLFEKLALYVIPGVLALGVLGVLFTGKA-TKQKCVTMVEDTETLRDVGARAAKVY 244
                                       ***********955555699**************************9998.7778********************** PP

                           DUF1646 233 vfilalellGegfkPlikayiaklkseilywvnlisavvdnatlaaaeisPelteeqirailmsllisGGlliPGni 309
                                       vf++al llG+g+k +i++y++ ++se+lywvn++sa++dnatl+aaei+P+lt  qi a+lm+lli+GG+l+PGni
  gi|330507476|ref|YP_004383904.1| 245 VFVMALLLLGAGMKIIIDKYFTAIPSEVLYWVNMLSAILDNATLTAAEIAPSLTIGQITAALMGLLIAGGMLVPGNI 321
                                       ***************************************************************************** PP

                           DUF1646 310 PnivsaGklkikskeWarvgvPlgiilliiyfivllvl 347
                                       Pni++a kl i+skeWar+gvP+g++l+++yf+ ++++
  gi|330507476|ref|YP_004383904.1| 322 PNIIAANKLGITSKEWARLGVPVGLVLMLVYFVWIFYI 359
                                       ***********************************986 PP

>> DUF2645  Protein of unknown function (DUF2645)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.25   2.3e+03      55      90 ..      25      60 ..      16      63 .. 0.71
   2 ?   -1.1   0.6      0.33     3e+03      50      79 ..     125     154 ..      96     161 .. 0.52
   3 ?    9.9   0.1   0.00013       1.1      66      95 ..     332     361 ..     271     362 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.25
                           DUF2645 55 alllliPlllvlvkkklksaflvvialvillYiiWr 90
                                        +l+ P+ +  + + l+   +v+ +l + +  +W+
  gi|330507476|ref|YP_004383904.1| 25 LAVLIGPFTVKKIEHNLEAFLFVMGVLSVTIAGVWE 60
                                      445667887777777777777778888888888886 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.33
                           DUF2645  50 vaviaalllliPlllvlvkkklksaflvvi 79 
                                       +++i+a lll+ l+ ++  +++ +  lv+i
  gi|330507476|ref|YP_004383904.1| 125 ITAIIAALLLVELVNCMPLERKDKINLVII 154
                                       345555555555555444444433333333 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00013
                           DUF2645  66 lvkkklksaflvvialvillYiiWrFflRf 95 
                                       ++ k  +++ + v ++++l+Y++W F++ f
  gi|330507476|ref|YP_004383904.1| 332 ITSKEWARLGVPVGLVLMLVYFVWIFYIPF 361
                                       55677788889999999**********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2694.57
//
Query:       gi|330507477|ref|YP_004383905.1|  [L=347]
Description: transposase, OrfB family [Methanosaeta concilii GP6]
Scores for complete 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-19   67.9   1.2    2.4e-18   65.8   0.1    2.3  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.4e-07   31.8   0.1    2.2e-07   31.1   0.1    1.3  1  OrfB_IS605      Probable transposase


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 ?    0.2   0.1     0.078     7e+02      54      64 ..     203     213 ..     184     214 .. 0.68
   2 !   65.8   0.1   2.7e-22   2.4e-18       1      69 []     255     324 ..     255     324 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.078
                    OrfB_Zn_ribbon  54 feadrDvnAai 64 
                                       ++++rDvn +i
  gi|330507477|ref|YP_004383905.1| 203 ARFHRDVNHCI 213
                                       569****9876 PP

  == domain 2  score: 65.8 bits;  conditional E-value: 2.7e-22
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l++++ yka  +G++++ ++payTS++C+ C  +++  ++++++f C  Cgf+  +D+ Aa+Ni+ r
  gi|330507477|ref|YP_004383905.1| 255 FYQLRQYIDYKAAIAGVPLICIDPAYTSQECPICHLISRSnRPTRDEFSCVCCGFSGPADTIAARNIAAR 324
                                       899***********************************9999*************************976 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.1   2.5e-11   2.2e-07       4     103 ..     130     221 ..     127     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.5e-11
                        OrfB_IS605   4 veveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       v v+v+ ++k  +++++g+D Gi+n+a+ + ++     ++g ++ +   +  + +a lqs+  +s     a+r l++
  gi|330507477|ref|YP_004383905.1| 130 VVVDVPePKKSVPQNVLGVDHGIKNIAVDSSGE----EFSGEKIEKVRSKIDNLKADLQSCGTDS-----AKRHLKK 197
                                       5555553888899******************99....899*********************7777.....7899999 PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktl 103
                                       l+ k +r+ +++ h ++++l+ + 
  gi|330507477|ref|YP_004383905.1| 198 LSGKEARFHRDVNHCISKKLVAKA 221
                                       999999999999988888887543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2594.03
//
Query:       gi|330507478|ref|YP_004383906.1|  [L=251]
Description: hypothetical protein MCON_1425 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-31  109.0  20.5      4e-31  108.6  20.5    1.0  1  DUF1646          Protein of unknown function (DUF1646)
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.028   14.4   0.1    1.7  1  FSAP_sig_propep  Frog skin active peptide family signal and p


Domain annotation for each model (and alignments):
>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.6  20.5   4.5e-35     4e-31       3     245 ..       9     247 ..       7     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 4.5e-35
                           DUF1646   3 allvilvlvlilPlvvrkveenlelfllimgvaavtvsglfslelliealktplailevgaipigitqavllaGlvf 79 
                                        l++i++ vl+ Pl+ +++e+nle+fl+ +g  a+++s  + ++l+ ea+++p++i        gi++ vl+aGl++
  gi|330507478|ref|YP_004383906.1|   9 GLIAIFLAVLLGPLLIKRIERNLEAFLFLIGACAIVLSRSWHIDLVEEAVQEPVVI--------GILLSVLVAGLIV 77 
                                       6899999**********************************************975........7************ PP

                           DUF1646  80 ellkkklksllae.vldklalkvfvfllivilGlassvisaivaavilaeivallplerkekvklvviasfaiGlGa 155
                                       ++ + ++ + ++   ld +++kv+ + ++v+lGl++++i+ i+   +l+e v++l+l+r +++ ++ +++++i lGa
  gi|330507478|ref|YP_004383906.1|  78 HYRRPRFLQGINDiLLDGITMKVIFLEIVVVLGLSAAIITPIIPFFVLVEAVNCLSLPRGSRAIITALGCISIILGA 154
                                       ******99888751689************************************************************ PP

                           DUF1646 156 altPvGePlstiavsklnedf....lylidvlgeyiiiavlvlallaalslkrlskreelvevveyeeelkevlira 228
                                       al  v    s iav+k++ ++    +  +++   yi+ ++lvl+l+++++ +++ ++   ++  e     +++ i +
  gi|330507478|ref|YP_004383906.1| 155 ALPYVEGLSSEIAVTKMQGELpsagILPLELQSLYILLIILVLGLISIFFSEEK-VKAMEMQAFEGIAAHEKMAIWG 230
                                       *9666555568*****99876333356689999**************9998776.556677778888888899**** PP

                           DUF1646 229 vkvfvfilalellGegf 245
                                       v++f+f  al l+G +f
  gi|330507478|ref|YP_004383906.1| 231 VRLFMFAGALLLVGVAF 247
                                       **************998 PP

>> FSAP_sig_propep  Frog skin active peptide family signal and propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.2e-06     0.028       7      29 ..     191     213 ..     190     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-06
                   FSAP_sig_propep   7 LLLvLFLGlVSlSlCEEekrede 29 
                                       LL +L LGl+S+++ EE+ ++ e
  gi|330507478|ref|YP_004383906.1| 191 LLIILVLGLISIFFSEEKVKAME 213
                                       899************99876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2021.15
//
Query:       gi|330507479|ref|YP_004383907.1|  [L=89]
Description: hypothetical protein MCON_1427 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   11.6   0.6       0.23   11.5   0.6    1.1  1  Med26_M   Mediator complex subunit 26 middle domain


Domain annotation for each model (and alignments):
>> Med26_M  Mediator complex subunit 26 middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6   1.3e-05      0.23     109     151 ..      36      72 ..      20      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.3e-05
                           Med26_M 109 rsstyapkgsvpsPssrsqvldaqvpSPlplsqpvtsPvqakr 151
                                       + sty+p ++++ P   +      v SPlp+ +++++P+  k+
  gi|330507479|ref|YP_004383907.1|  36 KLSTYTPLNTISKPAVIT------VISPLPVINAIAPPSINKS 72 
                                       569**************9......99************97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       151  (0.00842211); expected 358.6 (0.02)
Passed bias filter:                      128  (0.00713927); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 654.57
//
Query:       gi|330507480|ref|YP_004383908.1|  [L=291]
Description: universal stress protein [Methanosaeta concilii GP6]
Scores for complete 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-38  130.5   0.3      4e-18   66.3   0.0    2.8  2  Usp          Universal stress protein family
  ------ inclusion threshold ------
      0.061   13.4   0.0        0.1   12.6   0.0    1.3  1  B12-binding  B12 binding domain
      0.063   13.1   0.0        3.1    7.6   0.0    2.7  3  RQC          RQC domain


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   6.7e-22     4e-18       1     138 [.       1     133 [.       1     136 [. 0.94
   2 !   60.9   0.1     3e-20   1.8e-16       2     141 .]     156     284 ..     155     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 6.7e-22
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       m++++l ++D+s++s+k+le   el   +  e++llhvi p ++ a  + +    +e+++   ++++ +     +  
  gi|330507480|ref|YP_004383908.1|   1 MFEKVLFPTDFSKYSQKVLECVKELPGVN--EVVLLHVIGPADPLAKVWNPGGRIDESKANLTEQSKIL---SSRGL 72 
                                       99**************************9..7*****************99999999999999999876...699** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVl 138
                                        +++++  + egd +++i +va+ee+ + iV+G+rg++ +++++lG+v+++vlr  +   l
  gi|330507480|ref|YP_004383908.1|  73 SVKTRTEAIMEGDISRVIQKVADEEESSVIVMGARGKGVVEGIFLGNVAKNVLRYGNTNIL 133
                                       *****************************************************98776666 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 3e-20
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       + rIl+++D s+ +++A+ +  +      +e+ l hv+   +   + +a  e+ +  l   ++el         e++
  gi|330507480|ref|YP_004383908.1| 156 FSRILCPTDLSKPAEEAIAFIKRTKGV--GEILLQHVVYRGETWREIEAQTEETTRKLNVIRDEL---------EEA 221
                                       679*************99998886555..689999999888777777777777777777777666.........678 PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        +kv++++ +g+paeei+ +ae+e+++li + s+g ++l++l +GS++  v++  + pVlv+r
  gi|330507480|ref|YP_004383908.1| 222 RIKVKIHTSVGNPAEEIISLAEKENVSLIAMSSHGTGWLKQLGVGSTTYDVAKIGDRPVLVIR 284
                                       9************************************************************98 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.7e-05       0.1       8      62 ..     202     257 ..     199     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                       B12-binding   8 vggdlhplGlavlaaalrdagfeVqllganven.edivaairaekpdvvglSallt 62 
                                       ++++  ++ l+v+ + l++a+++V++     ++ e+i++ +++e++ ++++S++ t
  gi|330507480|ref|YP_004383908.1| 202 AQTEETTRKLNVIRDELEEARIKVKIHTSVGNPaEEIISLAEKENVSLIAMSSHGT 257
                                       677889999****************884444446******************9744 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00052       3.1       5      22 ..       9      27 ..       8      38 .. 0.76
   2 ?   -2.2   0.0      0.59   3.5e+03      30      30 ..     112     112 ..      73     139 .. 0.59
   3 ?    2.2   0.0     0.024   1.4e+02       6      39 ..     164     197 ..     162     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00052
                                      EE-HHHHHHHHHHHHHT.T CS
                               RQC  5 vDvteeaqkilscvyrt.g 22
                                       D+++++qk+l+cv+++ g
  gi|330507480|ref|YP_004383908.1|  9 TDFSKYSQKVLECVKELpG 27
                                      59*************9952 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.59
                                       H CS
                               RQC  30 i 30 
                                       +
  gi|330507480|ref|YP_004383908.1| 112 V 112
                                       2 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.024
                                       E-HHHHHHHHHHHHHTTS-SBHHHHHHHHHT--- CS
                               RQC   6 DvteeaqkilscvyrtgqrfgaghivdvLrGskt 39 
                                       D ++ a+ ++ +++rt++   +     v+rG+  
  gi|330507480|ref|YP_004383908.1| 164 DLSKPAEEAIAFIKRTKGVGEILLQHVVYRGETW 197
                                       999*************755555544556677655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2002.27
//
Query:       gi|330507481|ref|YP_004383909.1|  [L=378]
Description: hypothetical protein MCON_1430 [Methanosaeta concilii GP6]
Scores for 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  382.6  32.8   2.6e-114  382.2  32.8    1.1  1  DUF1646   Protein of unknown function (DUF1646)


Domain annotation for each model (and alignments):
>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.2  32.8  1.5e-118  2.6e-114       4     347 .]      10     370 ..       8     370 .. 0.93

  Alignments for each domain:
  == domain 1  score: 382.2 bits;  conditional E-value: 1.5e-118
                           DUF1646   4 llvilvlvlilPlvvrkveenlelfllimgvaavtvsgl.....................fslelliealktplail 59 
                                       l+vi+++vl+ P++v+k+e+nle+fl++mgv avt+s                       + +e+++eal++p++  
  gi|330507481|ref|YP_004383909.1|  10 LFVIVLIVLLGPFLVKKIEHNLEAFLFVMGVLAVTISSFyskpdlmatlgytehqveligWNMEIVMEALEEPII-- 84 
                                       899***********************************9777788888777776555555555555555555543.. PP

                           DUF1646  60 evgaipigitqavllaGlvfellkkklksllaevldklalkvfvfllivilGlassvisaivaavilaeivallple 136
                                              gi+ avl+aG++f++ ++  ++ + +  + +++k++vfl++vilGl+ss+i+ai+a+++l+e+++++p +
  gi|330507481|ref|YP_004383909.1|  85 ------KGIVPAVLVAGILFHYGRSYAQMAMSKITKVIPIKIIVFLIVVILGLSSSIITAIIASLLLVELLNCMPFD 155
                                       ......48********************************************************************* PP

                           DUF1646 137 rkekvklvviasfaiGlGaaltPvGePlstiavskl.....nedflylidvlgeyiiiavlvlallaalslkrlskr 208
                                       r++k++lv+ia+f+iGlGa ltPvGePlstia++kl     n++f++l++ l +yii++ l+++lla+++  + +  
  gi|330507481|ref|YP_004383909.1| 156 RQTKINLVIIACFSIGLGAVLTPVGEPLSTIAITKLqgepyNAGFFFLFNQLAVYIIPGCLAFGLLAMFFTGKAKLS 232
                                       ***********************************955555689*****************************9888 PP

                           DUF1646 209 eelvevveyeeelkevliravkvfvfilalellGegfkPlikayiaklkseilywvnlisavvdnatlaaaeisPel 285
                                       e +v + e++  l+ev++ra kv++f++al llG+g+k +i++y+  ++++i+ywvn+isa++dnatl+aae+sP +
  gi|330507481|ref|YP_004383909.1| 233 ECMVAE-EEDGGLREVVVRAGKVYIFVMALLLLGSGMKVVIDKYLLGISPQIIYWVNMISAILDNATLTAAELSPAM 308
                                       866655.68999***************************************************************** PP

                           DUF1646 286 teeqirailmsllisGGlliPGniPnivsaGklkikskeWarvgvPlgiilliiyfivllvl 347
                                          qi+a+lm+ll+sGG+liPGniPni+saGkl i+skeWa++gvPlg+i ++iyf+ ++++
  gi|330507481|ref|YP_004383909.1| 309 DMVQIQAVLMGLLVSGGMLIPGNIPNIISAGKLGITSKEWAKLGVPLGLIAMLIYFVWIFYI 370
                                       ***********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2586.46
//
Query:       gi|330507482|ref|YP_004383910.1|  [L=287]
Description: universal stress protein [Methanosaeta concilii GP6]
Scores for complete 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-35  120.3   4.3    3.3e-17   63.3   0.2    2.1  2  Usp           Universal stress protein family
  ------ inclusion threshold ------
      0.033   14.4   0.1      0.068   13.4   0.1    1.5  1  DUF2316       Uncharacterized protein conserved in bacteria (
       0.23   11.7   1.6       0.43   10.8   0.5    1.9  2  Flagellin_IN  Flagellin hook IN motif


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.2   5.5e-21   3.3e-17       1     131 [.       1     125 [.       1     135 [. 0.96
   2 !   58.7   0.6   1.4e-19   8.6e-16       3     141 .]     153     280 ..     152     280 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 5.5e-21
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       m++++l+a+D+s+++kk++e   e+   +  e+ ll+vi+ ++ + v d+ +e ++ e++lee++++     +    
  gi|330507482|ref|YP_004383910.1|   1 MFEKVLIATDFSKHAKKVIECIGEMPGLK--EVLLLNVISRDPLARVWDPVSEIKDIEKKLEEEKNAI----KSPGV 71 
                                       99**************************8..7********************************9986....57999 PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHH CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlr 131
                                        + +  v v+eg++a +i++va ee+++l+ +G+rgrs +   llGS s++vlr
  gi|330507482|ref|YP_004383910.1|  72 TVNVKAVSVLEGEVASAINKVAMEENVSLVAMGARGRSLIMSTLLGSSSRNVLR 125
                                       999999**********************************************98 PP

  == domain 2  score: 58.7 bits;  conditional E-value: 1.4e-19
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                        rIl ++D s++s+ Al +   l     +e++ll+v++  + +++ +a+ + ++e+ e+ ++ l+          +g
  gi|330507482|ref|YP_004383910.1| 153 ARILFPTDLSQTSEVALSFLKSLKGI--GEIVLLNVVSKGETDEEIEANVALAKERIEEIAQNLK---------MAG 218
                                       59********************9776..79***********************999999999775.........68* PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        +v  +v++g+p e+i  +ae+ed++li + s g s++++  +GS++  v+++a+ pVl+ r
  gi|330507482|ref|YP_004383910.1| 219 MQVSSKVVVGQPTEVIRSEAEKEDVSLIAISSQGASAIKKGRIGSTAYDVANSASRPVLILR 280
                                       ***********************************************************987 PP

>> DUF2316  Uncharacterized protein conserved in bacteria (DUF2316)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.1e-05     0.068       3      41 ..     184     222 ..     182     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                           DUF2316   3 LnkeerkaTkkeLqanfelsgltveevaedLnlttekve 41 
                                       Ln   + +T +e++an +l++  +ee+a++L++   +v 
  gi|330507482|ref|YP_004383910.1| 184 LNVVSKGETDEEIEANVALAKERIEEIAQNLKMAGMQVS 222
                                       7888999*************************9988886 PP

>> Flagellin_IN  Flagellin hook IN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5   7.1e-05      0.43       9      40 ..      66      99 ..      61     102 .. 0.86
   2 ?   -2.3   0.0      0.86   5.2e+03       5      28 ..     185     212 ..     184     218 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.1e-05
                                      ECS-.EEEEECTTTBCHH.HHHHHHHHCCTTTEE CS
                      Flagellin_IN  9 gket.vtisvkagdtldd.iadaINavssktGVs 40
                                      +k + vt++vka + l+  +a+aIN+v+ + +Vs
  gi|330507482|ref|YP_004383910.1| 66 IKSPgVTVNVKAVSVLEGeVASAINKVAMEENVS 99
                                      45558***********999******999888886 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.86
                                       EETTECS-...EEEEECTT.TBCHHHHH CS
                      Flagellin_IN   5 nggggket...vtisvkag.dtlddiad 28 
                                       n+++++et   ++ +v+ +   +++ia+
  gi|330507482|ref|YP_004383910.1| 185 NVVSKGETdeeIEANVALAkERIEEIAQ 212
                                       6677777766766666655566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2047.80
//
Query:       gi|330507483|ref|YP_004383911.1|  [L=319]
Description: hypothetical protein MCON_1434 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.005   17.2   0.0     0.0083   16.5   0.0    1.4  1  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
      0.097   12.7   0.0       0.23   11.5   0.0    1.6  1  Radical_SAM_C  Radical_SAM C-terminal domain
       0.15   11.7   0.0       0.29   10.7   0.0    1.4  1  MtrA           Tetrahydromethanopterin S-methyltransferase, s


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 !   16.5   0.0   1.4e-06    0.0083       3     153 ..      36     187 ..      34     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-06
                                       EESEESS-.-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...C CS
                                       xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                       Radical_SAM   3 vtrgCnlr.CsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla...v 75 
                                        t gC+ + C+ C      +  + +++  + + +  +++ + e  + + i ++g  l+  ++   ++ ++ ++    
  gi|330507483|ref|YP_004383911.1|  36 RTVGCRWNrCTMCGYAG--EGAPASADDLIIQFESAMEKCSPEV-TVVKIYTSGSFLDSEEMPAGARIEILRRlenA 109
                                       688999888*****996..3666666666666666666665333.55555557766666555544444444443344 PP

                                       CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivg 151
                                          ++ +et +  ++++ +e+ l    + +++gle+a+d  +++++  +g  f+++++a e+ +  g+ +  + ++ 
  gi|330507483|ref|YP_004383911.1| 110 GIEKLIIETRPEYVNPDAVEECLSHLQTEFAMGLESANDL-IREHLIrKGFLFQDFVRASEMVHGQGGGVKAYLLLK 185
                                       677777777777777*********99**************.999887577778*********999998865555555 PP

                                       BT CS
                                       xx RF
                       Radical_SAM 152 lp 153
                                       +p
  gi|330507483|ref|YP_004383911.1| 186 PP 187
                                       55 PP

>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.9e-05      0.23       4      34 ..     212     242 ..     209     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.9e-05
                     Radical_SAM_C   4 vKlypllvikgTeLaelyksgeykplsleey 34 
                                       + l ++ v ++T  ++++++gey+p  l  +
  gi|330507483|ref|YP_004383911.1| 212 ISLNLCNVQRNTVVERMWEKGEYRPPWLWSA 242
                                       5566899*****************9866555 PP

>> MtrA  Tetrahydromethanopterin S-methyltransferase, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.9e-05      0.29      22      61 ..      78     116 ..      66     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.9e-05
                                       -SEEEE-TT-SS-HHHHHHCT-SEEE----TTHHHHHHHH CS
                              MtrA  22 spvavvtlgshleeeavleaGaaiaGplktenlGiekvva 61 
                                       + v + t gs l++e++  aGa i    + en Giek++ 
  gi|330507483|ref|YP_004383911.1|  78 TVVKIYTSGSFLDSEEM-PAGARIEILRRLENAGIEKLII 116
                                       4678999******9999.*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2406.20
//
Query:       gi|330507484|ref|YP_004383912.1|  [L=299]
Description: thioredoxin reductase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-36  124.8   0.9    4.4e-36  124.6   0.9    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.2e-21   77.2   0.6    8.8e-17   61.3   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      1e-07   31.4   4.7    2.3e-06   26.9   1.7    2.3  2  FAD_binding_2   FAD binding domain
      1e-05   25.1   1.3    1.7e-05   24.4   1.3    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    1.4e-05   25.5   1.3      0.026   15.1   0.0    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      2e-05   23.5   4.9    0.00022   20.1   1.2    2.8  3  HI0933_like     HI0933-like protein
    5.9e-05   22.4   0.4    5.9e-05   22.4   0.4    1.6  2  Thi4            Thi4 family
    0.00013   21.7   2.4     0.0024   17.5   2.0    2.1  2  DAO             FAD dependent oxidoreductase
    0.00034   20.0   0.5    0.00058   19.2   0.5    1.3  1  FAD_binding_3   FAD binding domain
     0.0011   18.1  13.1     0.0012   18.1   2.0    2.9  3  GIDA            Glucose inhibited division protein A
     0.0021   18.5   0.1      0.042   14.3   0.0    2.2  2  NAD_binding_7   Putative NAD(P)-binding
     0.0044   17.2   1.5     0.0044   17.2   1.5    2.4  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.025   13.6   0.3      0.063   12.3   0.3    1.7  2  Lycopene_cycl   Lycopene cyclase protein
      0.034   13.3   0.2        6.9    5.7   0.0    2.4  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.055   12.3   0.6       0.12   11.2   0.6    1.5  2  Trp_halogenase  Tryptophan halogenase
       0.13   12.0   1.0       0.14   11.9   0.0    1.5  2  ELFV_dehydrog   Glutamate/Leucine/Phenylalanine/Valine dehydr


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 !  124.6   0.9   3.9e-39   4.4e-36       1     294 []       2     287 ..       2     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 3.9e-39
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.........evvkklnqgie 68 
                                       +dvv++G+GpAGl+aa++ a+ g k++++   g + + +  +   ++++++++e +           + ++++++ +
  gi|330507484|ref|YP_004383912.1|   2 YDVVIVGAGPAGLTAAMYCARGGKKTLVL---GSIYGSQTAMGGLYENYPGFPEGINgielsermlAQAQRFGAENQ 75 
                                       69*******************99998888...778888899988888888888888888677665533334433333 PP

                                       CCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  69 lllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkri 145
                                       + l   v ki  + +++   k++ ++  +++ ++++lA+G+s r +g+pG++e + ++v+++ ++++    ++   +
  gi|330507484|ref|YP_004383912.1|  76 TEL---VEKI-VNLGDFFRLKTE-NW--QYESKTIILAMGASHRPIGVPGEKELTARGVSYCVHCDGALFRNKS--V 143
                                       222...3334.333566665544.44..8999************************************999988..* PP

                                       EEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEETTE..EEE.E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx..xxx.x RF
                       Pyr_redox_2 146 vvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidgnge..kle.v 218
                                       + vG G+ +     +la+++++v+l+   ++l+      ++  + e+++   + +  +g+++ ei+g++   ++e  
  gi|330507484|ref|YP_004383912.1| 144 ALVGYGNGAARAILYLANIASRVHLISPKEKLV------AEPVYLERIKSLtNYAATFGAQIAEIRGEEFveSVEfN 214
                                       ********************************9......888999999888899999************96666677 PP

                                       EETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 219 vledgeeidadlvvvavGvrpstelleeklglelderggivvdefl.rtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                       v ++ ++++++ v+v  G++p+ el+ e+lgl ++++g++++++   +t++pg++a+GD++   gg ++a +Av +G
  gi|330507484|ref|YP_004383912.1| 215 VGGTPRSLKVEGVFVEMGMKPNVELA-ENLGLDMTSGGFVKINRLNqETSMPGVFAAGDMT---GGRMQAATAVGAG 287
                                       8888888*******************.****************9884699***********...7777777777665 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   0.4   1.6e-05     0.018       1      27 [.       5      30 ..       5      48 .. 0.88
   2 !   61.3   0.0   7.9e-20   8.8e-17     100     305 .]      75     271 ..      61     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylil 27
                                      +I+GaGPaGl+aa+ + + g  + l+l
  gi|330507484|ref|YP_004383912.1|  5 VIVGAGPAGLTAAMYCARGGK-KTLVL 30
                                      7***************99998.56776 PP

  == domain 2  score: 61.3 bits;  conditional E-value: 7.9e-20
                       Pyr_redox_3 100 lfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek.lvk.hyskvk.efhkyagqkvvViGgk 173
                                       + e Ve++ + ++ f+++t++ +ye+k++i+A+G  ++P   ++pGe++ ++  +++ v+ + + ++++ v+ +G +
  gi|330507484|ref|YP_004383912.1|  75 QTELVEKIVNLGDFFRLKTENWQYESKTIILAMGASHRPI--GVPGEKElTARgVSYCVHcDGALFRNKSVALVGYG 149
                                       45779******************************77775..8****9742222333333378899*********** PP

                       Pyr_redox_3 174 nSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvkte 250
                                       n a+ a l l++  ++V+++ ++++            +p++ +r+++l +   + + f a++ ei+ +e    v+++
  gi|330507484|ref|YP_004383912.1| 150 NGAARAILYLANIASRVHLISPKEK---------LVAEPVYLERIKSLTN---YAATFGAQIAEIRGEEFVESVEFN 214
                                       ***********************84.........44579********976...89***********99888889988 PP

                       Pyr_redox_3 251 dgkkvev.kddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                        g + ++ k + v++ +G kp++++ ++ +++ ++ g+++++  ++et +pg+f aG
  gi|330507484|ref|YP_004383912.1| 215 VGGTPRSlKVEGVFVeMGMKPNVELAENLGLDMTSGGFVKINRLNQETSMPGVFAAG 271
                                       8766655566667776***************************************99 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   1.7   2.1e-09   2.3e-06       1      32 [.       3      34 ..       3      44 .. 0.86
   2 !    5.9   0.1    0.0052       5.8     386     413 ..     258     285 ..      97     289 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.1e-09
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                      Dv+++G+G AGL+AA+ +a+ G+k++v+    
  gi|330507484|ref|YP_004383912.1|  3 DVVIVGAGPAGLTAAMYCARGGKKTLVLGSIY 34
                                      9**************************97665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0052
                                       TTEEESSBTEEE-STCEESSSSTTS--T CS
                     FAD_binding_2 386 dadgqpipGLYAaGevaaggvhganrlg 413
                                        ++++  pG +AaG +++g ++ a + g
  gi|330507484|ref|YP_004383912.1| 258 LNQETSMPGVFAAGDMTGGRMQAATAVG 285
                                       5677899**********99999887655 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   1.3   1.5e-08   1.7e-05       1      28 [.       3      30 ..       3      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.5e-08
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLv 28
                                      Dvv+vG+gpaG++AA+ +ar G+k+l++
  gi|330507484|ref|YP_004383912.1|  3 DVVIVGAGPAGLTAAMYCARGGKKTLVL 30
                                      9************************987 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.3    0.0023       2.6       2      27 ..       4      29 ..       3      32 .. 0.90
   2 !   15.1   0.0   2.3e-05     0.026       2      78 ..     143     213 ..     142     219 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0023
                                      EEEECSSHHHHHHHHHHHHTTSEEEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtv 27
                                      vv+vG+G  gl +A + a+ gkk+ v
  gi|330507484|ref|YP_004383912.1|  4 VVIVGAGPAGLTAAMYCARGGKKTLV 29
                                      8****************999998765 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.3e-05
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvk 77 
                                       v+ vG G+ +  +  +la+++++V+++  ++kl       a+ +  e+++ + +    ++++++ei+g+e  vesv+
  gi|330507484|ref|YP_004383912.1| 143 VALVGYGNGAARAILYLANIASRVHLISPKEKLV------AEPVYLERIKSLtNYAATFGAQIAEIRGEEF-VESVE 212
                                       8899******************************......*********9999**************8887.99998 PP

                                       E CS
                         Pyr_redox  78 l 78 
                                       +
  gi|330507484|ref|YP_004383912.1| 213 F 213
                                       7 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.2     2e-07   0.00022       1      29 [.       2      30 ..       2      42 .. 0.92
   2 ?    3.5   0.0     0.021        23     127     165 ..      73     110 ..      50     124 .. 0.74
   3 ?   -0.7   0.1      0.39   4.4e+02     356     384 ..     248     273 ..     236     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2e-07
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlll 29
                                      +dv+++G+G+AGl aA+ +a+ gk++l+l
  gi|330507484|ref|YP_004383912.1|  2 YDVVIVGAGPAGLTAAMYCARGGKKTLVL 30
                                      59************************998 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.021
                                       E-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 127 rletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                       + +te+ +   + + +fr+kt ++ ++e+++++lA+G  
  gi|330507484|ref|YP_004383912.1|  73 ENQTELVEKIVNLGDFFRLKT-ENWQYESKTIILAMGAS 110
                                       3444444444677888*****.99***********9975 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.39
                                       EEEE.E-GGGB-TTT-BBTTSTTEEE-GGG CS
                       HI0933_like 356 TaGG.VdlkevssktmeskkvpgLffaGEv 384
                                       T GG V+++ ++++t     +pg+f aG +
  gi|330507484|ref|YP_004383912.1| 248 TSGGfVKINRLNQETS----MPGVFAAGDM 273
                                       6666589999998886....9*******87 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.4   5.2e-08   5.9e-05      19      49 ..       3      32 ..       1      46 [. 0.80
   2 ?   -4.3   1.4       7.6   8.5e+03      23      36 ..     284     298 ..     280     299 .] 0.76

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.2e-08
                                      EEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 19 DvvivGaGssGLtaayylakkpdlkvailer 49
                                      DvvivGaG++GLtaa y a+  + k+++l +
  gi|330507484|ref|YP_004383912.1|  3 DVVIVGAGPAGLTAAMYCARG-GKKTLVLGS 32
                                      9******************99.888888754 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 7.6
                                       E--S.HHHHHHHHHH CS
                              Thi4  23 vGaG.ssGLtaayyl 36 
                                       vGaG s+G++a +yl
  gi|330507484|ref|YP_004383912.1| 284 VGAGaSAGISALQYL 298
                                       788845799998887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   2.0   2.1e-06    0.0024       1      33 [.       3      35 ..       3      74 .. 0.73
   2 ?    3.0   0.0     0.054        60     150     227 ..      61     131 ..      48     206 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.1e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      dvvi+G+G +Gl++A++ ar g  +++l  + i g
  gi|330507484|ref|YP_004383912.1|  3 DVVIVGAGPAGLTAAMYCARGGkkTLVLG-S-IYG 35
                                      9*****************88779655553.3.455 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.054
                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HHHTTCTTTSEEEEEEEEE CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.llgllkeldlpispvrgqv 224
                                         ++++a++ G+e  ++  v+++ +  g+  ++ +t++    ++ +++++a+Ga  + +   ++  ++    +rg +
  gi|330507484|ref|YP_004383912.1|  61 ERMLAQAQRFGAENQTE-LVEKIVN-LGDFFRL-KTENwQY-ES-KTIILAMGASHRpIG--VPG-EKE-LTARGVS 128
                                       56777778888777776.6777744.2344555.4443333.34.88******9977432..111.122.4566666 PP

                                       EEE CS
                               DAO 225 lvl 227
                                       + +
  gi|330507484|ref|YP_004383912.1| 129 YCV 131
                                       666 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.5   5.1e-07   0.00058       2      30 ..       2      30 ..       1      37 [. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.1e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEE CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlv 30
                                      +dV+IVGaGpaGl++a+  ++ G +++++
  gi|330507484|ref|YP_004383912.1|  2 YDVVIVGAGPAGLTAAMYCARGGKKTLVL 30
                                      69*********************999987 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.0     1e-06    0.0012       1      28 [.       3      30 ..       3      86 .. 0.89
   2 ?   -0.9   0.1      0.58   6.6e+02       2      47 ..     143     188 ..     142     204 .. 0.83
   3 !    6.7   1.1     0.003       3.3     354     387 ..     263     297 ..     253     299 .] 0.76

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      dv+++G+G AG+ AA+ +ar G k+l +
  gi|330507484|ref|YP_004383912.1|  3 DVVIVGAGPAGLTAAMYCARGGKKTLVL 30
                                      79***********************987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.58
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-T CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggi 47 
                                       v  +G G     A l +a+   +v Li +k + +ae ++ + i+++
  gi|330507484|ref|YP_004383912.1| 143 VALVGYGNGAARAILYLANIASRVHLISPKEKLVAEPVYLERIKSL 188
                                       6778999999999999***********9999999999988887776 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.003
                                       SSBTEEE-CGGGTB-SHHH.HHHHHHHHHHHHHHH CS
                              GIDA 354 kvkgLflAGqinGteGYeE.aaaqGllAGinaark 387
                                       + +g+f+AG+++G   + + a++ G  AGi a ++
  gi|330507484|ref|YP_004383912.1| 263 SMPGVFAAGDMTGGRMQAAtAVGAGASAGISALQY 297
                                       489**********975444145599999*999775 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 ?    2.3   0.0      0.21   2.3e+02      10      36 ..       4      30 ..       2     106 .. 0.86
   2 !   14.3   0.0   3.7e-05     0.042       5      46 ..     138     183 ..     136     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.21
                     NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvv 36
                                      v++vG+G+ +++ +   ++ g+k  v+
  gi|330507484|ref|YP_004383912.1|  4 VVIVGAGPAGLTAAMYCARGGKKTLVL 30
                                      89*******999888888877777665 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.7e-05
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele.....e 46 
                                       +++k+v +vG G+ Aar +  l++   +v++++p+  + +      e
  gi|330507484|ref|YP_004383912.1| 138 FRNKSVALVGYGNGAARAILYLANIASRVHLISPKE-KLVAepvylE 183
                                       689********************************4.3333244442 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.5   3.9e-06    0.0044       1      25 [.       6      30 ..       6      43 .. 0.94
   2 ?   -2.4   0.6       5.1   5.8e+03       2       8 ..     284     290 ..     283     297 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.9e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlll 25
                                      IvGaG +Gl+aA ++a+ g++ l+l
  gi|330507484|ref|YP_004383912.1|  6 IVGAGPAGLTAAMYCARGGKKTLVL 30
                                      9*****************9999887 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.1
                                       E--SHHH CS
                     NAD_binding_8   2 vGaGlsG 8  
                                       vGaG+s+
  gi|330507484|ref|YP_004383912.1| 284 VGAGASA 290
                                       8999986 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   5.6e-05     0.063       1      30 [.       3      33 ..       3      45 .. 0.74
   2 ?   -2.4   0.0       1.6   1.8e+03     221     239 ..     188     206 ..     181     258 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.6e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarltea.kpglkvvli 30
                                      Dvv++GaGpAgl  A   ++  k+ l +++i
  gi|330507484|ref|YP_004383912.1|  3 DVVIVGAGPAGLTAAMYCARGgKKTLVLGSI 33
                                      9************999886541444555555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.6
                     Lycopene_cycl 221 laaylralglkvkevveeE 239
                                       l++y+++ g +++e+  eE
  gi|330507484|ref|YP_004383912.1| 188 LTNYAATFGAQIAEIRGEE 206
                                       4455555555555554444 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 ?    5.1   0.1    0.0091        10       2      22 ..       1      21 [.       1      31 [. 0.82
   2 ?    5.7   0.0    0.0062       6.9     133     219 ..      89     166 ..      62     178 .. 0.68
   3 ?   -3.4   0.0       3.7   4.1e+03     112     161 ..     192     236 ..     181     239 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0091
                       K_oxygenase  2 ilDligiGiGpsnLsLaille 22
                                      ++D++++G+Gp+ L+ a+  +
  gi|330507484|ref|YP_004383912.1|  1 MYDVVIVGAGPAGLTAAMYCA 21
                                      59************9988765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0062
                       K_oxygenase 133 ltveskdaegeeeelearnlvlgvGtepk...iPevlekle.gkervvHsseylerkeellakkriaVvGsGqSaae 205
                                       +++++     e+ ++e+++++l++G +     +P   e +  g + +vH + +l r+      k++a vG G  aa 
  gi|330507484|ref|YP_004383912.1|  89 FRLKT-----ENWQYESKTIILAMGASHRpigVPGEKELTArGVSYCVHCDGALFRN------KSVALVGYGNGAAR 154
                                       55554.....78999*********965321135544332222445666666666665......9************9 PP

                       K_oxygenase 206 ifedllrrqkkvel 219
                                        +  l++ ++   +
  gi|330507484|ref|YP_004383912.1| 155 AILYLANIAS--RV 166
                                       9998887655..34 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.7
                       K_oxygenase 112 qvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepk 161
                                          fg+++ e++ +e  e+  ++v      g+ ++l+ + + + +G +p+
  gi|330507484|ref|YP_004383912.1| 192 AATFGAQIAEIRGEEFVESVEFNV-----GGTPRSLKVEGVFVEMGMKPN 236
                                       467888888887777543333444.....356777777777777777775 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   0.00011      0.12       1      25 [.       3      27 ..       3      39 .. 0.88
   2 ?   -2.8   0.0       1.8   2.1e+03     102     156 ..      84     138 ..      66     141 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                      EEEEE--SHHHHHHHHHHHHHTTTS CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgk 25
                                      ++vivG+G+aG +aA+++a+ +k++
  gi|330507484|ref|YP_004383912.1|  3 DVVIVGAGPAGLTAAMYCARGGKKT 27
                                      69*****************998765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.8
                                       EHHHHHHHHHHTT--S-HHHHH-SCHHHHHTTB-SB-TT.S-B-S--EEEE-HHHH CS
                    Trp_halogenase 102 alhhywlkarargaaeeledysleavaakakkfsprekd.glsalsyAyhldaaly 156
                                       +l +++ + ++++++ e +++ l+  a ++   +p ek+ +++++sy  h d al+
  gi|330507484|ref|YP_004383912.1|  84 NLGDFF-RLKTENWQYESKTIILAMGASHRPIGVPGEKElTARGVSYCVHCDGALF 138
                                       333333.5555666666666666666666665566666666677777777777776 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.3       5.4     6e+03      35      59 ..       4      28 ..       3      42 .. 0.80
   2 ?   11.9   0.0   0.00012      0.14       2      95 ..     115     205 ..     115     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.4
                                      EEEE--SHHHHHHHHHHHHCT-EEE CS
                     ELFV_dehydrog 35 vaisGsGnvgsyaallltelgakvv 59
                                      v+i G G  g  aa  +++ g+k++
  gi|330507484|ref|YP_004383912.1|  4 VVIVGAGPAGLTAAMYCARGGKKTL 28
                                      7899999999999999988777654 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00012
                                       --TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE.-HH CS
                     ELFV_dehydrog   2 GsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGl.die 77 
                                       G+ +++e T++Gv y+v+     +++  +++k+va  G+Gn +  a+l l++   +v  +s ++  +++p  l  i+
  gi|330507484|ref|YP_004383912.1| 115 GVPGEKELTARGVSYCVH-----CDGALFRNKSVALVGYGNGAARAILYLANIASRVHLISPKEKLVAEPVYLeRIK 186
                                       67789999******9995.....5677799*******************************9999999999998889 PP

                                       HHHHHHHCSSS.STTHSHH CS
                     ELFV_dehydrog  78 ellelkeerks.vkeykks 95 
                                       +l+++++  ++ ++e+  +
  gi|330507484|ref|YP_004383912.1| 187 SLTNYAATFGAqIAEIRGE 205
                                       9999988877778887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); 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:                        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: 00:00:00.44
# Mc/sec: 2061.24
//
Query:       gi|330507485|ref|YP_004383913.1|  [L=778]
Description: hypothetical protein MCON_1437 [Methanosaeta concilii GP6]
Scores for complete sequence (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   50.9   0.0      4e-06   27.1   0.0    3.9  4  DUF11     Domain of unknown function DUF11
    5.9e-11   42.7   0.1    2.2e-10   40.8   0.1    2.0  1  LTD       Lamin Tail Domain
  ------ inclusion threshold ------
        0.1   12.9   0.4         28    5.1   0.0    3.9  4  CARDB     CARDB


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 ?   -2.3   0.0      0.94   5.6e+03      40      61 ..     180     201 ..     150     212 .. 0.79
   2 ?   -0.2   0.0      0.21   1.3e+03      30      51 ..     373     394 ..     369     427 .. 0.75
   3 !   27.1   0.0   6.6e-10     4e-06      13      91 .]     502     581 ..     490     583 .. 0.87
   4 !   17.9   0.0   4.6e-07    0.0028      16      81 ..     636     703 ..     624     707 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.94
                             DUF11  40 Paglayvsvsasqgtasaltsv 61 
                                       P g +++s+ +++g +sa++s+
  gi|330507485|ref|YP_004383913.1| 180 PVGGSFISHEHGSGDYSADSSF 201
                                       5677788888888888888876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.21
                             DUF11  30 angvvvtDtlPaglayvsvsas 51 
                                       a + v+ D +Pag +y   s +
  gi|330507485|ref|YP_004383913.1| 373 ARKNVILDYMPAGYSYSNDSVA 394
                                       5566899*********999888 PP

  == domain 3  score: 27.1 bits;  conditional E-value: 6.6e-10
                             DUF11  13 GdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatlsftvrvtrtaasga 86 
                                        d +++ +tv N g+++ + + v+Dt P+g++++ +s      +    ++s++ L  g s t+ ++ +v +++++  
  gi|330507485|ref|YP_004383913.1| 502 CDVLRFAVTVVNDGNRTFAPIYVRDTFPSGTRFIGSSVEpmeLARTYGNWSIPALGSGDSFTIDMQFKVITRKEN-- 576
                                       5899***********************************7764444556677*****************999997.. PP

                             DUF11  87 ltnva 91 
                                       +tn+a
  gi|330507485|ref|YP_004383913.1| 577 YTNRA 581
                                       77765 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 4.6e-07
                             DUF11  16 vtytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatlsftvrvtrt 81 
                                       v+y l++ Nt   +   + +t +lP+g++++ ++++   + ++ +++s++++ ag ++t+sf + + r+
  gi|330507485|ref|YP_004383913.1| 636 VSYRLILNNTADYTM-SANITALLPEGMSFINSTTAtleNDSGVVKWSIRRIDAGRRRTVSFMAGAERE 703
                                       789999999999999.*******************97776666777777*************9988876 PP

>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.1   3.8e-14   2.2e-10       3      71 ..      16      87 ..      15     126 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 3.8e-14
                               LTD  3 aaagdvvIsevmedgagnnan.efvelyNtsskavdLsgwkledasge...ytfpngtgtlaageyvvvwsgs 71
                                      +a+g+vvI+ev  d  +++a+ ++ve+yN+++++vd sgw +  + ++     + +gt +l +g+ ++ + g+
  gi|330507485|ref|YP_004383913.1| 16 SASGSVVINEVELDYIEDDAEiQWVEIYNNGEEEVDVSGWAIMSSDDRsrkEFIDEGT-ILSPGDFYLMYFGE 87
                                      899************999988**********************999888877777787.********999884 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.47   2.8e+03      25      48 ..      40      63 ..      25      79 .. 0.76
   2 ?   -1.8   0.1      0.65   3.9e+03      40      79 ..     286     329 ..     246     342 .. 0.61
   3 ?    5.1   0.0    0.0046        28      49      84 ..     548     583 ..     503     586 .. 0.77
   4 ?    2.7   0.0     0.025   1.5e+02      38      84 ..     667     712 ..     661     724 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.47
                                      EEEEE-SSS-EEEEEEEEEETTEE CS
                             CARDB 25 vtvkNqGtaasgatkvalyldgel 48
                                      v+++N+G+++   +  a++ +++ 
  gi|330507485|ref|YP_004383913.1| 40 VEIYNNGEEEVDVSGWAIMSSDDR 63
                                      589999999877777766666665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.65
                                       EEEEETTEEEEEEEE....SEE-CTEEEEEEEEEE-S-S-CEEE CS
                             CARDB  40 valyldgelvgtvtv....psLaagesttvsftwtteategevt 79 
                                       +++ l+ ++vg ++v     +L+ +e++   f++  ++t+ge++
  gi|330507485|ref|YP_004383913.1| 286 LKMKLSSDSVGRTNVeycsDKLKLSEEYLGGFHIEETITKGEYQ 329
                                       34445555555555555555566666666666655555666665 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0046
                                       EEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEE CS
                             CARDB  49 vgtvtvpsLaagesttvsftwtteategevtltvvv 84 
                                        g++++p+L +g+s t+++++++++ + ++t ++ +
  gi|330507485|ref|YP_004383913.1| 548 YGNWSIPALGSGDSFTIDMQFKVITRKENYTNRARA 583
                                       388999*****************9888888877765 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.025
                                       EEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEE CS
                             CARDB  38 tkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltvvv 84 
                                       +++a   +++ v ++++  ++ag  +tvsf   +e  eg  ++++ v
  gi|330507485|ref|YP_004383913.1| 667 STTATLENDSGVVKWSIRRIDAGRRRTVSFMAGAE-REGLFEVKALV 712
                                       56666777788889****************99999.88887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (778 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:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 5415.51
//
Query:       gi|330507486|ref|YP_004383914.1|  [L=89]
Description: hypothetical protein MCON_1438 [Methanosaeta concilii GP6]
Scores for complete 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   77.8   0.2    5.3e-22   77.6   0.2    1.1  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.045   14.2   0.0       0.24   11.9   0.0    2.0  2  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 !   77.6   0.2   5.9e-26   5.3e-22       1      73 [.       3      75 ..       3      79 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 5.9e-26
                            HTH_45  1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkele 73
                                      rR++le++++ILe++s ++a+kT+i+y+ nL++k++  YL+ L++kg++ k++++Y++T  G+e+l  lke+ 
  gi|330507486|ref|YP_004383914.1|  3 RRTRLEVLSSILEICSGEGASKTRIVYQINLNFKNAGVYLKWLTDKGYLVKEGKMYKITPAGKEMLLGLKEIC 75
                                      8*****************************************************************9999875 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 ?   11.9   0.0   2.6e-05      0.24      16      68 .]      19      64 ..       3      64 .. 0.86
   2 ?    0.1   0.0      0.13   1.2e+03      22      32 ..      72      82 ..      70      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      ++++++++++   n++  ++   lk Lt kG+++++g+        +++T++G
  gi|330507486|ref|YP_004383914.1| 19 GEGASKTRIVYQINLNFKNAGVYLKWLTDKGYLVKEGKM-------YKITPAG 64
                                      788999***************************777765.......9999998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.13
                            HTH_27 22 adlcgrlnved 32
                                      +++c  ln+e 
  gi|330507486|ref|YP_004383914.1| 72 KEICSILNIEE 82
                                      79******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 727.73
//
Query:       gi|330507487|ref|YP_004383915.1|  [L=151]
Description: hypothetical protein MCON_1439 [Methanosaeta concilii GP6]
Scores for complete 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    0.00077   19.3   0.0    1.7  1  MarR       MarR family
     0.0003   20.7   0.1    0.00097   19.1   0.0    1.9  2  HTH_Crp_2  Crp-like helix-turn-helix domain
     0.0009   19.7   0.0     0.0018   18.7   0.0    1.6  1  HTH_27     Winged helix DNA-binding domain
     0.0051   17.1   0.0      0.053   13.9   0.0    2.2  2  Rrf2       Transcriptional regulator
     0.0058   16.7   0.0      0.012   15.7   0.0    1.5  1  DUF2250    Uncharacterized protein conserved in archaea (DUF2
  ------ inclusion threshold ------
       0.03   14.2   0.1       0.28   11.1   0.0    2.2  2  MarR_2     MarR family
      0.033   14.2   0.6       0.24   11.5   0.0    2.5  2  HTH_20     Helix-turn-helix domain
      0.051   13.5   0.0       0.14   12.0   0.0    1.8  1  HTH_5      Bacterial regulatory protein, arsR family
      0.099   12.6   0.0       0.16   11.9   0.0    1.4  1  HTH_45     Winged helix-turn-helix
        0.1   12.5   0.0       0.18   11.7   0.0    1.4  1  TrmB       Sugar-specific transcriptional regulator TrmB
       0.14   11.8   2.1        8.6    6.0   0.0    3.2  4  HTH_24     Winged helix-turn-helix DNA-binding
       0.17   11.6   0.0       0.22   11.2   0.0    1.2  1  DUF4364    Domain of unknown function (DUF4364)


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 !   19.3   0.0   5.2e-07   0.00077      11      50 ..      20      59 ..      15      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.2e-07
                                      HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                       l+e++p++ +++ak++  + ++++ +l +Le++Gli ++
  gi|330507487|ref|YP_004383915.1| 20 ALSEMEPAYAAQIAKHIDSTFPHTSSILGELEEQGLIISR 59
                                      589**********************************776 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   6.5e-07   0.00097      25      62 ..      30      72 ..       8      74 .. 0.83
   2 ?   -1.4   0.0       1.6   2.4e+03      20      31 ..     116     127 ..      93     141 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.5e-07
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEE.E..TE.E.EEES-H CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis.r..gr.r.irildl 62
                                      +++A ++ +t  ++s il+eL+++gli  r  gr r ++++d+
  gi|330507487|ref|YP_004383915.1| 30 AQIAKHIDSTFPHTSSILGELEEQGLIIsRpeGRvRfLVLTDR 72
                                      69************************98754344345666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                                       EEHHHHHHHHHT CS
                         HTH_Crp_2  20 lpltqeelAsml 31 
                                       l   +++lA ++
  gi|330507487|ref|YP_004383915.1| 116 LGPLRRDLAKLM 127
                                       444566666654 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   1.2e-06    0.0018      15      68 .]      23      73 ..      10      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                            HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +++++ +a++++  + +  h+s++l +L+e+GL+    ++ ++r +++ lTd G
  gi|330507487|ref|YP_004383915.1| 23 EMEPAYAAQIAKHIDSTFPHTSSILGELEEQGLI---ISRPEGRVRFLVLTDRG 73
                                      677888999*************************...444489*********98 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   3.5e-05     0.053      14      58 ..      16      59 ..      14      63 .. 0.90
   2 ?    1.0   0.0      0.36   5.3e+02       9      42 ..      78     114 ..      69     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-05
                                      HHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 14 llyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      l++La+ e e p+ +++ia++ +   ++ + il +L+++gl+ s+
  gi|330507487|ref|YP_004383915.1| 16 LAVLALSEME-PAYAAQIAKHIDSTFPHTSSILGELEEQGLIISR 59
                                      6788888886.599****************************997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHSSTCC-...B-HHHHHHHHTS-HHHH CS
                              Rrf2   9 yalhallyLakeeeeep...vsseeiaerqnispsyl 42 
                                        al+ l +L ++++       +++e+a++ + s+ yl
  gi|330507487|ref|YP_004383915.1|  78 GALRELSDLLHKPDAMMqrlERLKELASSADGSKDYL 114
                                       5666666666666655433346778888888888876 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     8e-06     0.012      10      53 ..      15      57 ..       7      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8e-06
                           DUF2250 10 alkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLle 53
                                       l+vl+ l ++++ Ya +iak+++  + + +++l +Lee GL+ 
  gi|330507487|ref|YP_004383915.1| 15 SLAVLA-LSEMEPAYAAQIAKHIDSTFPHTSSILGELEEQGLII 57
                                      566664.789********************************84 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00019      0.28      13      56 ..      20      61 ..      12      65 .. 0.83
   2 ?    0.8   0.0      0.32   4.8e+02      31      47 ..      86     102 ..      66     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      aL   ++    ++++a++ + + + +s il +L+++GL+  rp 
  gi|330507487|ref|YP_004383915.1| 20 ALSEMEP--AYAAQIAKHIDSTFPHTSSILGELEEQGLIISRPE 61
                                      4555555..7899999999999*****************99875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.32
                                       HTSSHHHHHHHHHHHHH CS
                            MarR_2  31 lglsksavsrilkrLva 47 
                                       l +++ a+ ++l+rL +
  gi|330507487|ref|YP_004383915.1|  86 LLHKPDAMMQRLERLKE 102
                                       56788899999999976 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016      0.24      19      61 .]      21      63 ..       4      63 .. 0.92
   2 ?    0.1   0.1      0.58   8.6e+02      29      50 ..      82     102 ..      67     106 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                                      HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                      L++ e++ a+++a+ +d +    s  L +Lee gL+ ++ egr
  gi|330507487|ref|YP_004383915.1| 21 LSEMEPAYAAQIAKHIDSTFPHTSSILGELEEQGLIISRPEGR 63
                                      456699**********************************997 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.58
                                       HHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_20  29 elaerldlskntlsyHLrvLee 50 
                                       el ++l  ++  + ++L+ L e
  gi|330507487|ref|YP_004383915.1|  82 ELSDLL-HKPDAMMQRLERLKE 102
                                       344444.444458888888877 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 ?   12.0   0.0   9.6e-05      0.14       8      46 ..      18      57 ..      13      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.6e-05
                                      HHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  8 LklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      + +L+e +++++ ++a++++ + + +S  L  L+e+GL+ 
  gi|330507487|ref|YP_004383915.1| 18 VLALSEmEPAYAAQIAKHIDSTFPHTSSILGELEEQGLII 57
                                      789***999*****************************97 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.16      20      75 ..      27      86 ..      15      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                            HTH_45 20 akkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkeleel 75
                                      a   +i ++ + ++  +++ L  L e+gli    + +    vlT++G+++   l+el +l
  gi|330507487|ref|YP_004383915.1| 27 AYAAQIAKHIDSTFPHTSSILGELEEQGLIisrpEGRVRFLVLTDRGRQVAGALRELSDL 86
                                      55667888888899999************9887555667789*********999999876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.18      15      60 ..      19      64 ..       5      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                      laL + +pa a +ia++++   +   ++L +Le+ Gl+  +++ + 
  gi|330507487|ref|YP_004383915.1| 19 LALSEMEPAYAAQIAKHIDSTFPHTSSILGELEEQGLIISRPEGRV 64
                                      677799********************************99987655 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.2   4.7e+03      12      25 ..      10      23 ..       9      24 .. 0.80
   2 ?    6.0   0.0    0.0057       8.6      22      47 ..      31      56 ..      29      57 .. 0.88
   3 ?   -2.3   0.2       2.4   3.5e+03      36      42 ..      95     101 ..      92     103 .. 0.55
   4 ?    3.9   0.2     0.027        40       3      13 ..     140     150 ..     139     151 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.2
                            HTH_24 12 LqknprisqreLAe 25
                                      L+++p++    L+e
  gi|330507487|ref|YP_004383915.1| 10 LREKPSLAVLALSE 23
                                      78999998888887 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0057
                            HTH_24 22 eLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++A++++ + + ++  l +Lee+GlI
  gi|330507487|ref|YP_004383915.1| 31 QIAKHIDSTFPHTSSILGELEEQGLI 56
                                      788888888999999**********9 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.4
                            HTH_24  36 rrlkrLe 42 
                                       +rl+rL+
  gi|330507487|ref|YP_004383915.1|  95 QRLERLK 101
                                       4555554 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.027
                            HTH_24   3 etdrkILelLq 13 
                                       e+drkIL +L 
  gi|330507487|ref|YP_004383915.1| 140 ELDRKILAILS 150
                                       78*******97 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.22      33      72 ..      40      79 ..      30     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                           DUF4364 33 YfdlqqalseLvesglieeeekenktlykiTekGketlel 72
                                      + + +++l eL+e+gli ++ +    ++ +T++G++++  
  gi|330507487|ref|YP_004383915.1| 40 FPHTSSILGELEEQGLIISRPEGRVRFLVLTDRGRQVAGA 79
                                      5577899*************99**************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1268.29
//
Query:       gi|330507488|ref|YP_004383916.1|  [L=336]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.6   2.5        2.3    8.0   1.1    3.0  2  LppX_LprAFG  LppX_LprAFG lipoprotein
       0.23   12.0   2.6       0.54   10.9   2.6    1.7  1  LPAM_1       Prokaryotic membrane lipoprotein lipid attachmen


Domain annotation for each model (and alignments):
>> LppX_LprAFG  LppX_LprAFG lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.1   0.00026       2.3     109     139 ..     173     208 ..      46     222 .. 0.62
   2 ?    2.7   0.0     0.011        96     145     172 ..     233     282 ..     227     303 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00026
                                       C..TEEEEEEEEEEEETTEEEEEE...EEEE-HHHH CS
                       LppX_LprAFG 109 a..gvtdakaegreeidGtatvki...tGtvdadvv 139
                                          ++++a+++g+e+i+Gt ++k+    G  + d++
  gi|330507488|ref|YP_004383916.1| 173 EtfNISQAELAGSENINGTDAYKLriiNGAAESDAL 208
                                       23378999***************7555788777776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.011
                                       CG-SSS.EEEEEEEESS......................TT--EEEEEEE CS
                       LppX_LprAFG 145 slkedgtvpitlWiaed......................gelrlvrvvvd 172
                                       +l+e+g+++ t+Wi ++                       + ++++++++
  gi|330507488|ref|YP_004383916.1| 233 ELNETGRMEKTIWISKNtyipvkyesktsfkmtpiivagLDMNTSQMTMF 282
                                       57899*********999666666666666555555555544555555554 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 ?   10.9   2.6     6e-05      0.54       1      15 [.      16      30 ..      16      35 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6e-05
                            LPAM_1  1 MKKillalgalllLs 15
                                      MK+ ll++++l++L+
  gi|330507488|ref|YP_004383916.1| 16 MKRVLLVILILAALA 30
                                      ****88888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2338.18
//
Query:       gi|330507489|ref|YP_004383917.1|  [L=304]
Description: phosphoribosylaminoimidazole-succinocarboxamide synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-41  142.8   0.0      2e-41  142.3   0.0    1.2  1  SAICAR_synt   SAICAR synthetase
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.14   12.5   0.0    1.3  1  RNA_pol_Rpb4  RNA polymerase Rpb4


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 !  142.3   0.0   2.3e-45     2e-41       2     248 ..       6     259 ..       5     263 .. 0.88

  Alignments for each domain:
  == domain 1  score: 142.3 bits;  conditional E-value: 2.3e-45
                                       EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE.....-SSSE CS
                       SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklek..ipnhliksldpeqlegrs 76 
                                       l +GKv++ Y+l   d+l ++++D+is+fd v +++ip KG+ l +   +wfe  ++  i++h+++      l    
  gi|330507489|ref|YP_004383917.1|   6 LLKGKVKEAYDL--GDRLEFQFTDNISVFDKVIPSTIPFKGETLSREGVYWFERADEmgIRTHFLQY-----LPPAG 75 
                                       679********9..559***************************************778******66.....55667 PP

                                       EEEE-EEEESE..............EEEEEEE--HHH........HH......HH..T--TT-EEEEEEEEEEE--C CS
                       SAICAR_synt  77 mlvkklkmlpv..............EvvvRgyltGslwkeykks.gkvc..girlpeglkegeklpepiftpstKae 136
                                       ml+kk+++lp               E+++R y++Gsl+   k++       g +  + +k ge+lpep +++stK e
  gi|330507489|ref|YP_004383917.1|  76 MLCKKVDILPTnritpqsrnyliplEWICRWYVAGSLFDRVKAGeIAAQdlGFASGHVVKPGEELPEPFLEVSTKLE 152
                                       7777777777777777777777777************99998875333411555556689***************** PP

                                       CCT.S-EE-HHHHH.HTT.-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STTTE CS
                       SAICAR_synt 137 egehDeniseeevvealg.teeeaeeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpDss 212
                                       +   D  i +ee++++ g +++e+e+ +++ l++ e +++ +a+rg+i +D K E+ +d  d +++++D   t D  
  gi|330507489|ref|YP_004383917.1| 153 KT--DRLIAKEEALQISGlSPQEYEDARDIVLKIDEDINRSVASRGLIHADGKKELAFDM-DRQIMIVDVYGTADED 226
                                       95..9*********9999*****************************************5.9*************** PP

                                       EEEETTT.....GGGB-STHHHHTT-STHHHHHHHH CS
                       SAICAR_synt 213 RfwdaetyeegkeqeslDKqfvRdwleeveekwkek 248
                                       Rfwd ++y+eg+    l K++vR++ ++  +++k++
  gi|330507489|ref|YP_004383917.1| 227 RFWDRKRYDEGE-LVDLSKEYVRQYYRQ--TGYKDR 259
                                       *********886.5679********999..777765 PP

>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.6e-05      0.14      63     107 ..     142     188 ..      87     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHTTST..STHHHHHHHHHCSTSSHHHHHHHSTTGTTTS CS
                      RNA_pol_Rpb4  63 ekfnelvellksfe..LtkaEklqlvnlkPesavelktlieeleerf 107
                                       e f e+ ++l++++  + k E+lq+  l P++ ++++ ++ +++e +
  gi|330507489|ref|YP_004383917.1| 142 EPFLEVSTKLEKTDrlIAKEEALQISGLSPQEYEDARDIVLKIDEDI 188
                                       448899*********99********************9998888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        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 0.19s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2534.37
//
Query:       gi|330507490|ref|YP_004383918.1|  [L=545]
Description: thermosome subunit delta [Methanosaeta concilii GP6]
Scores for complete 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-184  612.1  21.2   7.4e-184  612.0  21.2    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.12   11.9   0.1       0.36   10.3   0.0    1.8  2  TrwC        TrwC relaxase


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  612.0  21.2  8.2e-188  7.4e-184       2     490 ..      38     524 ..      37     525 .. 0.99

  Alignments for each domain:
  == domain 1  score: 612.0 bits;  conditional E-value: 8.2e-188
                                       HHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   2 adivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeae 78 
                                       a +v+ttlGPkGmdKm v++ g+vv+TnDG+tilke++iehPaak++ve+a++qd evGDGTtt+v+LageLl++ae
  gi|330507490|ref|YP_004383918.1|  38 AGAVRTTLGPKGMDKMMVDNLGDVVITNDGVTILKEMDIEHPAAKMMVEIAKTQDAEVGDGTTTAVVLAGELLKQAE 114
                                       679************************************************************************** PP

                                       HHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCC CS
                        Cpn60_TCP1  79 kliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvkliee 155
                                        l+++++hpt+i  gy+ a++ka+e+L++i  ++s++ +d + L+k+a ts+++k + + +eel++l+v+Avk++ +
  gi|330507490|ref|YP_004383918.1| 115 GLLDQEIHPTVIAAGYRAAADKAMEILNKI--AVSVTVNDADFLKKIAITSMTGKGSGTAREELAALAVEAVKAVVD 189
                                       ****************************99..77777779********************************99999 PP

                                       CSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHH CS
                        Cpn60_TCP1 156 nekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeelek 232
                                       +++++d ++i v+k+ gg ++dselv+G+v+dk+ l+p+mpkk++ ak++ll+  +eiekte++++++++++++l++
  gi|330507490|ref|YP_004383918.1| 190 EDGSVDTDNITVEKKVGGGITDSELVHGMVIDKDRLHPNMPKKVTGAKIALLNAAIEIEKTEVDAKIEITSPDQLQA 266
                                       99*************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC- CS
                        Cpn60_TCP1 233 lekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeel 309
                                       ++++ee +l+ +++++ik+g+nvv+cqkgiddla+hflak+gi ++rrvkk+d+e+la+atG+++v+s+ dlt+++l
  gi|330507490|ref|YP_004383918.1| 267 FLDQEESMLKGMVDNVIKTGANVVFCQKGIDDLAQHFLAKEGIYTVRRVKKSDMEKLARATGGRVVTSIHDLTEKDL 343
                                       ***************************************************************************** PP

                                       EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHH CS
                        Cpn60_TCP1 310 GtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakk 386
                                       G a+ vee+kig+ek+t++ee++++k+++i+lrg t++v+de++ra edAl+vv  ++ed+ +vpGGGa e+ela +
  gi|330507490|ref|YP_004383918.1| 344 GRAGLVEERKIGDEKMTFVEECENPKSVSIILRGGTEHVVDELNRAMEDALRVVGVVVEDKMLVPGGGAPEVELALR 420
                                       ***************************************************************************** PP

                                       HHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEH CS
                        Cpn60_TCP1 387 lkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDpl 463
                                       l+eya +v g+eqlaieafa+++evipktLaeNaGld+i+ l  lr++h+kg k+ g+d+++g ++d+++ gvv+pl
  gi|330507490|ref|YP_004383918.1| 421 LREYAATVGGREQLAIEAFADSMEVIPKTLAENAGLDQIDSLVALRSQHEKGIKSSGLDMDTGVPVDMMKLGVVEPL 497
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 464 kvkrqalksAteaastiLrideiikak 490
                                       +vk+qa++sA+eaa +iLrid++i  k
  gi|330507490|ref|YP_004383918.1| 498 RVKTQAINSAAEAAVMILRIDDVIASK 524
                                       ************************876 PP

>> TrwC  TrwC relaxase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.25   2.2e+03     105     131 ..     125     151 ..     116     165 .. 0.78
   2 ?   10.3   0.0     4e-05      0.36      44     122 ..     315     402 ..     284     411 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.25
                              TrwC 105 aieaahdaAvkaalalleeeaaftRvg 131
                                        i+a  +aA+++a+++l + a+ + v+
  gi|330507490|ref|YP_004383918.1| 125 VIAAGYRAAADKAMEILNKIAVSVTVN 151
                                       46777899999****999987776665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 4e-05
                              TrwC  44 vteeqfeallegrhpd........tgerlgrakesaere.rkavagfDltfsaPKSvSllalvgdderraaieaahd 111
                                       v++ ++e+l + +  +        t++ lgra    er+  ++++ f   +  PKSvS++   g++++  ++ +a++
  gi|330507490|ref|YP_004383918.1| 315 VKKSDMEKLARATGGRvvtsihdlTEKDLGRAGLVEERKiGDEKMTFVEECENPKSVSIILRGGTEHVVDELNRAME 391
                                       55555555543333333346666699999998887777777777777777888******988777777677777777 PP

                              TrwC 112 aAvkaalalle 122
                                       +A + +   +e
  gi|330507490|ref|YP_004383918.1| 392 DALRVVGVVVE 402
                                       77665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3901.95
//
Query:       gi|330507491|ref|YP_004383919.1|  [L=239]
Description: creatininase [Methanosaeta concilii GP6]
Scores for complete 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-60  202.3   0.3    8.9e-60  202.1   0.3    1.0  1  Creatininase  Creatinine amidohydrolase


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.1   0.3     5e-64   8.9e-60       1     240 [.       5     227 ..       5     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 202.1 bits;  conditional E-value: 5e-64
                      Creatininase   1 eeltwpeveealkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTi 77 
                                       ee++wpe+ee lk ++++ilPvG+tE+HGphlp+ tDt++a + a+ va+k +  ++++P+++yGv+ + +gfpGTi
  gi|330507491|ref|YP_004383919.1|   5 EEMSWPEIEEGLKVTRTVILPVGATEEHGPHLPTITDTIQAMETARTVAQKRE--VFLAPPIHYGVCRSTRGFPGTI 79 
                                       69**********************************************99966..************999******* PP

                      Creatininase  78 slspetliavlrdileslarhGfrrivlvngHgg..nsaalkeaarelraehdaaavrvtaaekelaaalkleeaae 152
                                       +++++ l+++++++l s+ ++Gf+++++++gH g  +++alkea++ + +e  +  v+++  ++ +++         
  gi|330507491|ref|YP_004383919.1|  80 TVGHDALRSYVKEVLISFTDSGFENVLILTGHAGsqHMSALKEACQMALEER-EFRVSLVSLFDLIDP--------- 146
                                       *********************************999**********999988.666665555555555......... PP

                      Creatininase 153 aaeeseeee.gggHAgelEtSlmlalrpelVrmdraedpeeaklakegvstaedaeelspsGvlGdpskataekGea 228
                                           +++e+ ++gHAge+EtS+m+ +r++lV+    e++++ ++        +d+++l  +G++G+p+ at +kG+ 
  gi|330507491|ref|YP_004383919.1| 147 ----QAAETpHDGHAGEIETSMMMVIRKDLVKGLPEEHFPPRPR----FLIMKDVRHLMGNGIMGNPAPATIKKGQN 215
                                       ....445555**********************776555544433....46799999999****************** PP

                      Creatininase 229 lleaaveelael 240
                                       +l+ a+e l+e+
  gi|330507491|ref|YP_004383919.1| 216 FLAMAAEGLIEA 227
                                       *********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1717.70
//
Query:       gi|330507492|ref|YP_004383920.1|  [L=933]
Description: oligosaccharyl transferase STT3 subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-31  110.2  26.7    9.5e-30  103.9  26.7    2.2  1  STT3      Oligosaccharyl transferase STT3 subunit
    5.4e-27   93.9   0.4    9.8e-27   93.1   0.4    1.4  1  AglB_L1   Archaeal glycosylation protein B long peripheral do
    2.2e-06   28.0  12.3    2.2e-06   28.0  12.3    4.2  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9  26.7   1.6e-33   9.5e-30      11     478 ..      73     625 ..      62     628 .. 0.75

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 1.6e-33
                                       CCCCCHCC.CCCCCCT--S--SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHCCC.CHH CS
                              STT3  11 alvavasrdlFtdedglsylsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygplivlLamla 87 
                                       +  + ++  +Ftd +g+   se D +Y   l + ++ n         ++ wfd+ + +P G  +++gp+ ++   l+
  gi|330507492|ref|YP_004383920.1|  73 RTYYNWKL-VFTD-NGVVFSSETDAWYHMMLARGVVIN--------HQRLWFDPMTNFPNGTTLHFGPFHSWAIALV 139
                                       44555666.7877.577777*******87776666666........599***********************98999 PP

                                       HHHHCCHHC.HHHHHHH.HCCHHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CC.CCCTTSTT--STCCCCHH CS
                              STT3  88 saiinhsld.vsirevc.lwlpallgsLlaIpiyflvrelksdiaGllAAlllaiaPg.YlsrtvaGfyDtdmfeiv 161
                                       s+i+ +  + +++ +++  ++pa+lg Ll+ piyf+ rel+++ +Gl++Al++a+ Pg  +srt +Gf D+++ ei+
  gi|330507492|ref|YP_004383920.1| 140 SEILGLGNPsMHLVDTVgAIMPAVLGALLVFPIYFIGRELAGKNCGLISALIIAVIPGqVFSRTTLGFTDHHAAEIL 216
                                       99999988897777655389**************************************99***************** PP

                                       HHHHHHHHHHHHHHCCS...............TTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTTS- CS
                              STT3 162 lllfvlffflkaiktks...............nkislaviaaliiflivlaWggyailiyallllfilalLiigrfe 223
                                       l+ ++++f+l a+ ++                 +  ++++++l++ l++ aW+    l++ ++l+f++   i+  ++
  gi|330507492|ref|YP_004383920.1| 217 LSTIAMMFLLMALRSGRrmtfdslkddwskfkSPLIFSALSGLFLGLYIDAWSSG-FLFVGVILFFVFWQSIFDHMK 292
                                       ******************************************************9.9****************9999 PP

                                       CCHHHHHHHHHHHHHHH..CCCCCCCTTCHHHSTTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCC....CHHTT CS
                              STT3 224 lklkiavtfsviiaflviaiivllflgfqvvavseiigalgifgllqlvafgsvvvlvaelkfyqfis....lfqpg 296
                                        k     ++  +iaf+v  i +l+f++      +++  + ++++++ l+      v  a l+ y  ++      +pg
  gi|330507492|ref|YP_004383920.1| 293 GKSIDYLGIIAAIAFIVAIIPILPFVKPYY--GFNHYYYSLFQPTSLLIGAAAALVF-ALLSRYLNQKglkrYYYPG 366
                                       988888888888888885666666665443..4444444444444433322222222.2333333333222355555 PP

                                       .HHHHTT--.GGGHHHHHHHHHHHHC................................................... CS
                              STT3 297 ilsevlgli.gevvtalavlglialw................................................... 321
                                        +   + ++ g ++ a+  + ++                                                      
  gi|330507492|ref|YP_004383920.1| 367 SIAAATLIGtGILYIAIPQFTRP--Llaglsifqqktggaatigeasplfanvnnvltwfpgigwiegifsfhtnsm 441
                                       22222222123333333333333..2446777777777788889999999999999999999999999999999999 PP

                                       ................CCCCCTS-----TTHHHHH..HHHHS---S--CCHHHCCSSSTTTTCCCHHHCHHCCHHCT CS
                              STT3 322 ................lgilyslldleyaklkiki..iilvsvwlpvgllaltkglrfliftvPlgiifvglllefl 380
                                                       l  +++++++  ++++i++  +i++ ++l+     ++ g+  +++t+ l + ++ ++l+++
  gi|330507492|ref|YP_004383920.1| 442 ialllstftfalvallLLAFRNIWRQRPVDIAILSwsLIMLVMILAQNRFGYYYGVNVAVLTAFLVV-YILQKLGIE 517
                                       9999999999988888778888998888888887611344455556666777888888888877766.888888898 PP

                                       CHHHHHHH...HHHHHHCCC-SCHCCCCCHHHHHHHCCCHHHHHHHHCCHHHHHHHHH...HHHHH........HHH CS
                              STT3 381 avfvkiys...vsqilfsgvvvillmltllpvlallaavkiskifstykdekeakikv...aakav........apt 443
                                        + ++i      s++++s ++  + ++ ++ +l++l  +  s++++      e+++                  ++ 
  gi|330507492|ref|YP_004383920.1| 518 DMDLDIGNlkdPSRLVRS-NLKTIAAAIFIFALIILPSMSWSTVYARGASGPESDWLTsttW---LkdntpspgMEL 590
                                       888888886654444444.4445589999999999999999999999988888888774440...244555666677 PP

                                       HCT.TTTTHHHTTHHHCHHHHHHHHHHHHHHHHHH CS
                              STT3 444 ksnglkeslewkantnrdsvvitwwdyghilavea 478
                                        ++ ++ +    + + +   +++wwdygh++ v+ 
  gi|330507492|ref|YP_004383920.1| 591 YEKYQYPASGKYEYNDSAYGIMSWWDYGHLIEVVG 625
                                       77777777777667777889**********98875 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 !   93.1   0.4   1.6e-30   9.8e-27       1      92 []     840     931 ..     840     931 .. 0.99

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 1.6e-30
                                       -EEEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS......-SSSSEESS-EEEEETTEEE CS
                           AglB_L1   1 GAtitGsaeagatvtasveletnqgrtftYrqeaeadedGefeltvPYstegeedgetnssveaagpYevtagnvta 77 
                                       GA+++Gsa+ag+ v+as++++tnq+r+f+Yrq++++++dG+f l++PYsteg  +g t+++++a g+Y++ +gnv+ 
  gi|330507492|ref|YP_004383920.1| 840 GAVVKGSAPAGTPVMASIDIQTNQNRMFEYRQSNVSNSDGQFVLVLPYSTEGPISGGTQFDTKAGGNYTLYVGNVVY 916
                                       9**************************************************************************** PP

                                       EE---HHHHHHT-EE CS
                           AglB_L1  78 eveVpEeaVlsgetv 92 
                                        ++VpEe Vl+g+++
  gi|330507492|ref|YP_004383920.1| 917 GLRVPEEYVLAGASI 931
                                       ************987 PP

>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0  12.3   3.7e-10   2.2e-06       4     155 ..     130     310 ..     127     316 .. 0.76
   2 ?    0.3   0.4      0.12   7.2e+02     117     136 ..     335     354 ..     323     382 .. 0.51
   3 ?    1.0   8.5     0.073   4.4e+02      52     124 ..     444     517 ..     410     557 .. 0.63

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.7e-10
                             PMT_2   4 Pliawllalftklfgfs.......elairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsa... 70 
                                       P+++w +al+ +++g +       +++  +++a++g+l ++ +y++ r+l gk+ +l++al++av+p  v++ +   
  gi|330507492|ref|YP_004383920.1| 130 PFHSWAIALVSEILGLGnpsmhlvDTVGAIMPAVLGALLVFPIYFIGRELAGKNCGLISALIIAVIPGQVFSRTtlg 206
                                       999***********65401111224556678999*********************************8888877765 PP

                             PMT_2  71 lftpdaplvllwalalylllrale..........knklkyw.......llagvlfGlgflsKytaallliaallyll 130
                                          + a+ +ll ++a+ +ll+al           k+ ++ +       +l+g+++Gl +      +l++  +l++++
  gi|330507492|ref|YP_004383920.1| 207 FTDHHAAEILLSTIAMMFLLMALRsgrrmtfdslKDDWSKFksplifsALSGLFLGLYIDAWSSGFLFVGVILFFVF 283
                                       55668999***************966555555555555555999999999999999999999999999998888999 PP

                             PMT_2 131 is..arrilkekkpylalllalllfsp 155
                                       ++    ++  +++ yl+++ a++ +++
  gi|330507492|ref|YP_004383920.1| 284 WQsiFDHMKGKSIDYLGIIAAIAFIVA 310
                                       996444455557777744444444433 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.12
                             PMT_2 117 taallliaall.yllisarri 136
                                       t++l++ aa+l ++l+s r +
  gi|330507492|ref|YP_004383920.1| 335 TSLLIGAAAALvFALLS-RYL 354
                                       33333333333333333.222 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.073
                             PMT_2  52 allaalllavvplfvalsa.lftpdaplvllwalalylllraleknklkywllagvlfGlgflsKytaalllia 124
                                        ll+++  a+v+l++   + + +   + ++ ++++l +l++ l +n++ y++ + v++  +fl+ y    l+i 
  gi|330507492|ref|YP_004383920.1| 444 LLLSTFTFALVALLLLAFRnIWRQRPVDIAILSWSLIMLVMILAQNRFGYYYGVNVAVLTAFLVVYILQKLGIE 517
                                       233444444444444444444555678899999999999999************99999999988876666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (933 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.81u 0.30s 00:00:01.11 Elapsed: 00:00:01.11
# Mc/sec: 2538.77
//
Query:       gi|330507493|ref|YP_004383921.1|  [L=137]
Description: hypothetical protein MCON_1446 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.081   13.3   0.0       0.13   12.7   0.0    1.3  1  Bac_RepA_C  Replication initiator protein A C-terminal domain


Domain annotation for each model (and alignments):
>> Bac_RepA_C  Replication initiator protein A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.1e-06      0.13      57      92 ..      64      98 ..      47     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.1e-06
                        Bac_RepA_C 57 ktLrrffnslrisknkkvknvenYlmrtlknlFeeq 92
                                      +++ r + +lr  + ++vk+ve+Y++++l    +e+
  gi|330507493|ref|YP_004383921.1| 64 EVMDREILVLR-GDLETVKAVEKYMFEALDRKIAEW 98
                                      67999******.9*****************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 951.31
//
Query:       gi|330507494|ref|YP_004383922.1|  [L=115]
Description: queuosine biosynthesis protein QueD [Methanosaeta concilii GP6]
Scores for complete 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-33  113.3   0.0    6.9e-33  113.2   0.0    1.0  1  PTPS      6-pyruvoyl tetrahydropterin synthase


Domain annotation for each model (and alignments):
>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.2   0.0   3.8e-37   6.9e-33       5     118 ..       6     112 ..       2     115 .] 0.95

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 3.8e-37
                                       EEEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEECCCC-CCHHCCS.- CS
                              PTPS   5 efeFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkflnaddpeleellsp 81 
                                       ++eFdaaH l++++gkc+ +HGH+y+ve+ vege   e+g+v+df +lk+++ + l+elDh+ ln   + l+   +p
  gi|330507494|ref|YP_004383922.1|   6 TTEFDAAHSLPGYQGKCACMHGHTYQVEMVVEGE-VGEDGFVIDFYQLKKIIGATLQELDHSCLN---DTLP---NP 75 
                                       679*******************************.9****************************9...4555...4* PP

                                       -HHHHHHHHHHHHHHHHGCCCGCEEEEEEEEETTEEE CS
                              PTPS  82 TaEnlaklifeelkerlqekevklskvrvwEtpnswa 118
                                       TaE++a +i+e+lk+++++ ++kl+++++wE +n+w+
  gi|330507494|ref|YP_004383922.1|  76 TAESIALWIAERLKKEMETTSIKLYSLKLWEGKNKWV 112
                                       ***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 889.47
//
Query:       gi|330507495|ref|YP_004383923.1|  [L=56]
Description: hypothetical protein MCON_1448 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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: 0.34u 0.29s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 411.64
//
Query:       gi|330507496|ref|YP_004383924.1|  [L=265]
Description: diphthine synthase [Methanosaeta concilii GP6]
Scores for complete sequence (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   51.3   0.0    1.8e-13   50.9   0.0    1.3  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 !   50.9   0.0     1e-17   1.8e-13       1     167 [.       1     168 [.       1     221 [. 0.73

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 1e-17
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       +l++VG+G+ d  ++++++l+a+++ad+++++  ++++++   l++   l+ ++ +   pl +   e+    + +  
  gi|330507496|ref|YP_004383924.1|   1 MLHFVGLGLYDERDISLKGLEAVRAADCIYAEF-YTSRLMGTTLEKMEALYGRKIH---PLSRQEVEVDPS-WLEEG 72 
                                       699**************************8666.6666666555442122222232...333333333333.44444 PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl............ 142
                                       + kd+v+l++GD +v++t+  l   lra + gie++vi   s+++a+    g+  + +g ++++             
  gi|330507496|ref|YP_004383924.1|  73 RNKDIVFLSGGDAMVSTTHLDLR--LRAIKMGIETRVIHSSSIVTAVSGLCGLQNYRFGRSTTIPfpyvsrgrriip 147
                                       4468******************7..88888******************99999999999999888777765554432 PP

                      TP_methylase 143 lpglakeeereleallangdtlvll 167
                                       +++     + ++e+   n +t+++l
  gi|330507496|ref|YP_004383924.1| 148 QTP----YQVLRENQKRNLHTMLFL 168
                                       111....233333333346666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2036.06
//
Query:       gi|330507497|ref|YP_004383925.1|  [L=217]
Description: methyl-coenzyme M reductase operon protein C [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-10   38.1   1.4    6.2e-09   35.3   1.4    2.3  1  MCR_C     Methyl-coenzyme M reductase operon protein C
  ------ inclusion threshold ------
       0.13   12.8   0.7       0.46   11.0   0.1    2.2  2  MobC      Bacterial mobilisation protein (MobC)


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 !   35.3   1.4   6.9e-13   6.2e-09      72     172 ..      37     148 ..      19     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 6.9e-13
                             MCR_C  72 iavvsptLarhhlPhsaCDvaeylrraGaktnmiGlarGvgkria............qikeeekrlinehDlavfvl 136
                                       +  ++++  r+h+  ++C+++  lrr+G +t ++ l  G+g   +             ++e+e + i  h +avf l
  gi|330507497|ref|YP_004383925.1|  37 VIAIAMSPGRRHITKPVCEMTYGLRREGIQTSVLVLEAGTGVPESfpqgsrgygptfGLSEKEVEQIARHKIAVFHL 113
                                       556789999*************************9988877432211111111222258999999************ PP

                             MCR_C 137 GnfkdCikkkkeklfedievPvvvtggPeelkleev 172
                                       Gn ++ +  k +++++++++P vv++    ++le+ 
  gi|330507497|ref|YP_004383925.1| 114 GNVRSHVIFKAKEILSQVDIPAVVVAQC-PMDLEDF 148
                                       ******9999***********8888765.4777775 PP

>> MobC  Bacterial mobilisation protein (MobC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.26   2.3e+03      20      38 ..     113     131 ..     102     132 .. 0.63
   2 ?   11.0   0.1   5.1e-05      0.46      11      31 ..     189     211 ..     189     217 .] 0.68

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.26
                              MobC  20 sgqgsqavlaelkeelaei 38 
                                        g++  +v++ +ke+l+++
  gi|330507497|ref|YP_004383925.1| 113 LGNVRSHVIFKAKEILSQV 131
                                       4567777777777777765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.1e-05
                              MobC  11 lNQIAraaN..sgqgsqavlael 31 
                                       lNQ+A+++N   + +s+  + el
  gi|330507497|ref|YP_004383925.1| 189 LNQLAKVLNkhLAEISEREAREL 211
                                       8********55555555555555 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:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1714.67
//
Query:       gi|330507498|ref|YP_004383926.1|  [L=391]
Description: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [Methanosaeta concilii GP6]
Scores for complete 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-58  195.5   0.0    8.7e-58  195.0   0.0    1.3  1  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly
    2.5e-37  128.6   0.0    2.8e-37  128.4   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
  ------ inclusion threshold ------
      0.095   11.6   0.0       0.15   10.9   0.0    1.2  1  CitF           Citrate lyase, alpha subunit (CitF)


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 !  195.0   0.0   1.5e-61   8.7e-58       1     170 []      37     196 ..      37     196 .. 0.97

  Alignments for each domain:
  == domain 1  score: 195.0 bits;  conditional E-value: 1.5e-61
                                       HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTG CS
                      PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrra 77 
                                       A+ G++Gl+ tvp+g++pgSdvAnls+ Gydp++yytGR+plEA+++G++l++ d+afRcnlvt+  edgi+ d++a
  gi|330507498|ref|YP_004383926.1|  37 ARLGRSGLALTVPDGFPPGSDVANLSVVGYDPRRYYTGRAPLEAASMGVHLGESDIAFRCNLVTI--EDGIMRDYSA 111
                                       789**************************************************************..69******** PP

                                       GG-.-TTHHHHHHHT-EEE.TTEEEEEEE-STTEEEEEE--S-B--S--..SSTTS------BS.SGGGHHHHHHHH CS
                      PhosphMutase  78 gristeeakeLikalneeleegvevkfypgveyrhllvllsdkitdtdpphdkegkeikellplkseeaketaelln 154
                                       g+ist ea+eLi+a++  +    + ++y+gv+yrhllvl++ +   ++pphd+++++++++lp +    +e+ae+l 
  gi|330507498|ref|YP_004383926.1| 112 GHISTGEASELIEAIKPLMP---NERLYAGVSYRHLLVLQKGAGAVCTPPHDISDQPVADYLP-Q----GEDAEVLL 180
                                       *******************5...56**************88889*******************.6....9******* PP

                                       HHHHHHHHHHHHSHHH CS
                      PhosphMutase 155 elieksqeiLedhpvN 170
                                       el+e ++ +L+ hpvN
  gi|330507498|ref|YP_004383926.1| 181 ELMESAKSVLSGHPVN 196
                                       ***************9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4   0.0   4.7e-41   2.8e-37       2     243 ..       2     387 ..       1     391 [] 0.97

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 4.7e-41
                                       EEEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH........ CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                     Metalloenzyme   2 kvvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel........ 67 
                                       k+++++ DG+++ p  el++   ++vAk+P++d L+         + +g+a ++p++  ++s+v++l++        
  gi|330507498|ref|YP_004383926.1|   2 KLMVILGDGMADLPLGELQGktpLKVAKKPNMDLLARL-------GRSGLALTVPDGFPPGSDVANLSVvgydprry 71 
                                       78999**************99**************998.......89****************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|330507498|ref|YP_004383926.1|  72 ytgrapleaasmgvhlgesdiafrcnlvtiedgimrdysaghistgeaselieaikplmpnerlyagvsyrhllvlq 148
                                       ***************************************************************************** PP

                                       .................................................HHHHTT-----EEEEEEEE-S---SSHH CS
                                       .................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  68 .................................................lrisetvkfahvtffwnggrsgyfnple 95 
                                                                                        +ri+e +++a+ +++w++g  ++++++ 
  gi|330507498|ref|YP_004383926.1| 149 kgagavctpphdisdqpvadylpqgedaevllelmesaksvlsghpvnrKRIQENKRPANAIWLWGQGPGPSMPSFL 225
                                       ***************************************************************************** PP

                                       HHHT--EEEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HH CS
                                       xxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  96 ereeipsdtvitfdl....................qpemkavevaekaldailsgkfdlvvvniknaDmvGHtgdle 152
                                         +++ ++++ ++dl                    + ++++  +++ al+a+ s  +d+ +++++ +D+++H+gdle
  gi|330507498|ref|YP_004383926.1| 226 SLYGLTGAMISAVDLlrgiavyaglevievpgatgTIDTNYSGKVKGALEAL-SR-HDFAYLHVEAPDEASHEGDLE 300
                                       ****************************************************.54.9******************** PP

                                       HHHHHHHHHHH.HHHHHHTTS-TTTE..EEEEE-SSB--TTTSS........-----EEEEEESTT----S--S.SH CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                     Metalloenzyme 153 atiaaieaaDe.avkeildaieqvdg..ilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglapdkvke.ga 225
                                       ++i+aie +D+  v+ +++ +e++++   +++++DH ++ ++ +        H+++pVP++i+g+g++pd   + ++
  gi|330507498|ref|YP_004383926.1| 301 GKIRAIELLDQmVVGPVIEGLEKSGEdwRILLLPDHATPISIRT--------HSRDPVPFVIMGRGIEPDGLDRfDE 369
                                       ***********6789*******97643389**************........*****************999999** PP

                                       HHHTT-TTEEEEGGGHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 226 kfrekggLanvaatllnl 243
                                       +++e+gg ++v+at l  
  gi|330507498|ref|YP_004383926.1| 370 QSAEQGGYGRVDATALVR 387
                                       **************8865 PP

>> CitF  Citrate lyase, alpha subunit (CitF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.5e-05      0.15     331     372 ..      89     130 ..      84     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.5e-05
                              CitF 331 eidtkfnvnvltGsdGvirGasGGhcdtaaaaklsiivaplv 372
                                       e d  f  n++t  dG++r  s Gh  t  a++l   + pl+
  gi|330507498|ref|YP_004383926.1|  89 ESDIAFRCNLVTIEDGIMRDYSAGHISTGEASELIEAIKPLM 130
                                       67999****************************999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2645.54
//
Query:       gi|330507499|ref|YP_004383927.1|  [L=321]
Description: ADP-ribosylglycohydrolase superfamily [Methanosaeta concilii GP6]
Scores for complete sequence (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  208.9   0.9    1.4e-61  208.8   0.9    1.0  1  ADP_ribosyl_GH  ADP-ribosylglycohydrolase


Domain annotation for each model (and alignments):
>> ADP_ribosyl_GH  ADP-ribosylglycohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.8   0.9     8e-66   1.4e-61       1     291 []      14     293 ..      14     293 .. 0.97

  Alignments for each domain:
  == domain 1  score: 208.8 bits;  conditional E-value: 8e-66
                                       HHHHHHHHHHHHHGGGTT--HHHHHHHTSS--S.-----STTTTTS-TT---HHHHHHHHHHHTEET.TEE-HHHHH CS
                    ADP_ribosyl_GH   1 GallGaavGDAlGlpvefwsydeirrrygelge.tpdktgfghfglkpgewtddtqmalllleslleaggldpedla 76 
                                       G+llG+a+GDAlG+p+e+ + +ei+  +g+  +  p++ g+ h+gl++g++tddt+ +l l+esl+e+ g++++ + 
  gi|330507499|ref|YP_004383927.1|  14 GCLLGGAAGDALGMPTEGYTAGEIQSIFGRMVDmMPPPVGHFHAGLRAGQFTDDTEETLILAESLIEHSGFSADGFS 90 
                                       9*****************************998999999************************************** PP

                                       HHHHH.HHT......T--SS--HHHHHHHHHTTTT-...-S-B...---BTTTGGG-HHHHHHTSS-HHHHHHHHHH CS
                    ADP_ribosyl_GH  77 rrflaeWleep..gdteprgignttrealrnlksgepppeaganangsagngalmRaaplgllyagdpeeaaelaee 151
                                        +++  W  ++  +++   g+g +tr+a+ ++ +g+p++e+g +     ++g++mRaap+glly+ d++ +  +a  
  gi|330507499|ref|YP_004383927.1|  91 SKLAS-WGSSWclNERLWSGVGFATRSAIMSMIAGTPWQESGIS---IPTCGSAMRAAPIGLLYHSDLDLVRSYADL 163
                                       **888.88875579999**************************9...****************************** PP

                                       HHHTTB--HHHHHHHHHHHHHHHHHHTT--STHHHHHH..HHHHTTT-HHHHHHHGGGGG---HHH........HHH CS
                    ADP_ribosyl_GH 152 aarlTHnhpeavagaaayaaliaaalrgksleealdaaeeelavapaeeelaaalrkalaladsdkdvdvdaeeavd 228
                                       ++  TH+ p + aga+a+a  +a  l   ++e++l+ a  ++++   ++ela++l ++++l d  +      eea++
  gi|330507499|ref|YP_004383927.1| 164 QSLPTHSAPASRAGAVAVAVGVALCLIDLPKETILESA--ARQAGRVDRELAERLIWVQSLLDLPP------EEAMG 232
                                       *************************************9..888899999************99999......9**** PP

                                       HH--SSBHHHHHHHHHHHHHH.-SSHHHHHHHHHTS-SSHHHHHHHHHHHHHHHH-GGGS-HH CS
                    ADP_ribosyl_GH 229 elgsggyavealaaalyallhaaddfeeallaavnlGgDtdttgaiaGallGalyGleaiPee 291
                                       +++++  ++e++ +a+y++l++   +ee+l+aa+++GgDtd++++iaG+l+Ga yG+ +iP++
  gi|330507499|ref|YP_004383927.1| 233 RIRTSPLSKETVVSAFYCFLRF--RPEEGLIAAASGGGDTDSIASIAGNLFGAAYGTRWIPQR 293
                                       *********************6..5************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2446.34
//
Query:       gi|330507500|ref|YP_004383928.1|  [L=341]
Description: N-acetyl-gamma-glutamyl-phosphate reductase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-32  112.7   0.0    2.4e-32  111.9   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    3.6e-22   79.3   0.0      5e-22   78.9   0.0    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    0.00019   21.9   0.0    0.00047   20.7   0.0    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.095   13.5   0.0       0.16   12.8   0.0    1.3  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
       0.11   12.4   0.0       0.69    9.8   0.0    2.0  2  NAD_binding_10   NAD(P)H-binding


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 !  111.9   0.0   6.6e-36   2.4e-32       2     118 ..       4     135 ..       3     138 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 6.6e-36
                                       EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEE.GGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkved.vdeeelkevdivflalpag 77 
                                       v+i+G++Gy+G ellrlL++hpev++  ++s++   Gk+++ ++++l+++  l++e+   +e+ +++di+f+ +p+g
  gi|330507500|ref|YP_004383928.1|   4 VGIIGGSGYTGGELLRLLANHPEVDVKLVTSRKL-SGKPVSLVHPHLKSIYALNFEAlNAKEAAERCDIIFTGVPHG 79 
                                       9*********************************.**********************6666677************* PP

                                       HHHHHHHHHHHTTSEEEESSSTTTTST...............TSEBE-HHHHGGGG CS
                    Semialdhyde_dh  78 vskelapklaeagvkviDlssdfRlkd...............davyvlpevnreai 118
                                       ++++++p+l++ag++viDlssd+Rl                 da+++lpe+++e  
  gi|330507500|ref|YP_004383928.1|  80 TAMDWVPDLLDAGTRVIDLSSDYRLPVdvfektygmkhraprDAIFGLPELHSEVA 135
                                       *************************889***********************99865 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   1.4e-25     5e-22       1     184 []     154     312 ..     154     312 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 1.4e-25
                                       HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHH CS
                   Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetree 77 
                                       L+PL+ a g ++rv+ ++++++SGaG +                 +++  ++ +   N+ipy+ + ++++ pe+++e
  gi|330507500|ref|YP_004383928.1| 154 LAPLAHA-GLVDRVVYDSKSGISGAGIE-----------------PTETSHYPNMSQNVIPYKIT-THRHVPEIKQE 211
                                       89****9.*******************7.................99999***************.*********** PP

                                       HHHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES.......SSHHHHHHHHHHHHCSTTEEEEESSHCHHSS CS
                   Semialdhyde_dhC  78 lkavaetkkileftekvsatcvrVPvlrGhseavtiklk.......lkdveveeveellaaapevkvvvneeedrPt 147
                                       l+ +     +++ft+      + +P +rG+++++++ +k       ++++ v++++  ++++  ++v+  +   +P 
  gi|330507500|ref|YP_004383928.1| 212 LGLLSPG-IKVNFTP------HVIPSVRGILTTAHVFAKegaettlQDREAVARIYRDFYKD-APFVRMAD--VVPR 278
                                       ******5.6689999......78*******************99998999999999999999.*******8..**** PP

                                       HHHHTTCSSSEEEEEEEEETTCTTEEEEEEEEETTTT CS
                   Semialdhyde_dhC 148 paavaggtnsvsVGRirkdemgdeglklvvvgDNllk 184
                                       + av+g +n++++  ++  +  d+ +++v+++DNl+k
  gi|330507500|ref|YP_004383928.1| 279 LGAVRG-SNFCDIS-FEPEKGSDR-IVVVSAIDNLVK 312
                                       *****9.9******.***998887.**********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 !   20.7   0.0   1.3e-07   0.00047       2      94 ..       4      98 ..       3     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.3e-07
                                      EEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCC....HH..HHHHHHC-EEECECHHHHHHH-SEEEE-S-HHH CS
                     F420_oxidored  2 igii.GaGnmgealasgllaagaqpheivvansrnpek....ae..elaeelgvkvtavdneeaaeeadvvvlavkped 73
                                      +gii G+G  g  l++ l+++   + ++ +++sr+ +     +   +l++ +  + +a +++eaae++d+++  v+   
  gi|330507500|ref|YP_004383928.1|  4 VGIIgGSGYTGGELLRLLANHP--EVDVKLVTSRKLSGkpvsLVhpHLKSIYALNFEALNAKEAAERCDIIFTGVPHGT 80
                                      89**9***********888886..77888888887654221122225666777************************** PP

                                      HHHHHHHCGHHHHTTSEEEEE CS
                     F420_oxidored 74 veevlselakdalkgklvisv 94
                                      + + + +l   +++g+ vi+ 
  gi|330507500|ref|YP_004383928.1| 81 AMDWVPDL---LDAGTRVIDL 98
                                      99999999...8889999986 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 ?   12.8   0.0   4.4e-05      0.16       2      90 ..       3      96 ..       2      97 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.4e-05
                                      EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE..EESSHHHHHTCT...TESEEEE-S-GGG CS
                      GFO_IDH_MocA  2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgve..aysdleelladp...eidavivatpngt 74
                                       v+iiG+ G+ g + l  l +++++ +v  + +++ +       + +++     ++e+l a++   ++d+++ ++p gt
  gi|330507500|ref|YP_004383928.1|  3 DVGIIGGsGYTGGELL-RLLANHPEVDVKLVTSRKLSGKPVSLVHPHLKsiYALNFEALNAKEaaeRCDIIFTGVPHGT 80
                                      6999999677788888.55555589999888887776666554444444433333555555555549************ PP

                                      HHHHHHHHHHTT-EEE CS
                      GFO_IDH_MocA 75 heelakaaleagkhvl 90
                                       ++ + ++l ag  v+
  gi|330507500|ref|YP_004383928.1| 81 AMDWVPDLLDAGTRVI 96
                                      ************9987 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00019      0.69       1      68 [.       8      76 ..       8      97 .. 0.82
   2 ?   -0.2   0.0      0.22     8e+02      88     110 ..     296     316 ..     293     329 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00019
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH.CTTTCEEEE--TT-CCHHHHHHTT-SEEEES- CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaele.aeeglevvegdvtdvedlaealkgadaVvsal 68
                                      G++G +G +l++ l+++ +++v++++ ++ + + ++  +++l+ + +   ++   +ea + +d++++ +
  gi|330507500|ref|YP_004383928.1|  8 GGSGYTGGELLRLLANHPEVDVKLVTSRKLSGKPVSlVHPHLKSIYALNFEALNAKEAAERCDIIFTGV 76
                                      9***********999999******986654444343368****999999999999********999877 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.22
                                       CT--EEEEEEETTTTSGCGCHHH CS
                    NAD_binding_10  88 agvkRfvlvsaigvgdevpgefg 110
                                       +g  R+v+vsai+    v+g+ g
  gi|330507500|ref|YP_004383928.1| 296 KGSDRIVVVSAIDNL--VKGASG 316
                                       6889******99755..455544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2780.17
//
Query:       gi|330507501|ref|YP_004383929.1|  [L=160]
Description: CBS domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-33  112.4   4.7    5.3e-18   65.2   0.6    2.2  2  CBS       CBS domain
  ------ inclusion threshold ------
      0.085   12.8   0.1        2.9    7.8   0.0    2.2  2  MreC      rod shape-determining protein MreC


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 !   49.2   0.3   5.8e-17   5.2e-13       1      56 [.       3      57 ..       3      58 .. 0.92
   2 !   65.2   0.6   5.9e-22   5.3e-18       1      53 [.     100     151 ..     100     155 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 5.8e-17
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                      V+d+m+  +v+v  +++++ea++l++e+++s++PV+d  ++lvGiv+++Dllr+l+
  gi|330507501|ref|YP_004383929.1|  3 VRDVMNVMPVSVQASANVSEAARLLKENKISGMPVLD-GERLVGIVSESDLLRLLS 57
                                      89***9999****************8888*******6.556************985 PP

  == domain 2  score: 65.2 bits;  conditional E-value: 5.9e-22
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       V+d+m+r+++ + pd+++eea+ +m++++++rlPVV edg+lvGivt+ D+++
  gi|330507501|ref|YP_004383929.1| 100 VADVMSRNLHEIGPDDSIEEAASIMTRHRINRLPVV-EDGRLVGIVTRGDIIS 151
                                       89**********************************.9*************98 PP

>> MreC  rod shape-determining protein MreC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00032       2.9      25      41 ..      33      49 ..      28      52 .. 0.89
   2 ?    2.8   0.0     0.011        99      27      41 ..     132     146 ..     112     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00032
                                      TT-EEEETTEEEEEEEE CS
                              MreC 25 kgmpVvsgkglVGkVte 41
                                       gmpV++g+ lVG+V+e
  gi|330507501|ref|YP_004383929.1| 33 SGMPVLDGERLVGIVSE 49
                                      59******99*****97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.011
                                       -EEEETTEEEEEEEE CS
                              MreC  27 mpVvsgkglVGkVte 41 
                                        pVv++  lVG+Vt+
  gi|330507501|ref|YP_004383929.1| 132 LPVVEDGRLVGIVTR 146
                                       68999966*****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1241.45
//
Query:       gi|330507502|ref|YP_004383930.1|  [L=387]
Description: arginine biosynthesis bifunctional protein ArgJ [Methanosaeta concilii GP6]
Scores for complete 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-133  445.0   2.0     2e-133  444.8   2.0    1.0  1  ArgJ      ArgJ family
     0.0064   16.1   0.0      0.011   15.3   0.0    1.3  1  BID       BH3 interacting domain (BID)


Domain annotation for each model (and alignments):
>> ArgJ  ArgJ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.8   2.0  2.2e-137    2e-133       6     376 .]      16     387 .]      12     387 .] 0.96

  Alignments for each domain:
  == domain 1  score: 444.8 bits;  conditional E-value: 2.2e-137
                                       XXSSS..SXXEEEEEEEEEEEEEEEEEXXSSXXHHHHHHHHHHH.HHSEEEEEEEEEEXXXSXHHHHHHHHHHHHHH CS
                              ArgJ   6 aagikkkkkdlalivseepasaaavfTknkvkAapvkvsrevlkkkkgaravvvnsgnANavtgeqGledaeemaea 82 
                                       a+g+++ k  lali++  + +aa++fT+n+vkAap+ v+ e+l+k++ + ++++nsg+ANa+tg qG+eda+ ma++
  gi|330507502|ref|YP_004383930.1|  16 ACGVRAGKYGLALIAA--SGTAAGMFTTNRVKAAPLAVTAEHLAKGH-LDGIIANSGCANAYTGPQGVEDARMMASL 89 
                                       79***99*******99..6899*********************9776.***************************** PP

                                       HHHHHTSXGGGEEEEEEEESSXXXXHHHHHHHHHHX....X......HHHHHHHXSSXSSXXEEEEEEEETEEEEEE CS
                              ArgJ  83 vaealgikeeevlvasTGviGerlpmekieagieklvekle......eeaaeAimTTDtvpKlaavevelgkevtia 153
                                       +a  l+ +ee+++vasTGviG+ ++m+ i + +e++  +l+       ea +AimTTDt +K++ave    + +++a
  gi|330507502|ref|YP_004383930.1|  90 LAGFLKSDEERIAVASTGVIGRYMDMDIIGRLFEEARGRLRsdgeagLEAERAIMTTDTREKEVAVEH---QGLRVA 163
                                       *************************************99977778889******************98...59**** PP

                                       EEEEXSSSXXXXEE--EEEEEE-----HHHHHHHHHHHHHHTGGGB-SSS---SS-EEEEEE--TTTT.STTHHHHH CS
                              ArgJ 154 giaKGaGmihPnmaTmLafittDaavsaealqellkeavdksFnsisvDgdtSTnDtvlllAngaaeeeeedleefe 230
                                       gi KGaGmi+PnmaTmL+f++tDa+ s+e+l+++l +av++sFn+++vDgdtSTnD vll A+g+a   + ++e+f+
  gi|330507502|ref|YP_004383930.1| 164 GIVKGAGMIEPNMATMLCFLFTDADFSPEVLKSCLADAVRDSFNMLTVDGDTSTNDIVLLTATGRA---QGRIEDFQ 237
                                       *****************************************************************9...679***** PP

                                       HHHHHHHHHHHHHHHHTSTT-S-EEEEEEEEESSHHHHHHHHHHHHT-HHHHHHHHTT---HHHHHHHHHHSSS--- CS
                              ArgJ 231 ealtevlqeLakqivrDGEGatklveveVkgakseeeAkkvaksvanssLvKtAlfGeDanwGRilaavGyagaeld 307
                                       +al+ v+ +La+q++rDGEGa+k++e  V+ga++e++A+ +ak+va+ssLvKtA++G+D+nwGRi++avGy+gae++
  gi|330507502|ref|YP_004383930.1| 238 QALRYVCVDLARQMARDGEGASKFFETLVTGARNEADARLAAKAVAKSSLVKTAVYGADPNWGRIICAVGYSGAEMN 314
                                       ***************************************************************************** PP

                                       TTS-EE..TT....EEEEETTEE----HHHHHHHHH-SSEEEEEE--SSSEEEEEEEE---HHHHHHHTT-XX CS
                              ArgJ 308 pekvsvllge....vkvlekgepeevdeerakeilkeeeveievdlgegeeeatvwtcDLsyeYvkiNadYrt 376
                                       p+ v++ l++    v ++ kg+ +e   ++a+ei++ ee+ i++dlg g ++a+ ++cDL++eYv++Na+Y+t
  gi|330507502|ref|YP_004383930.1| 315 PDLVTLGLEGsglkVDLVWKGRIAEEVLDKAREIMSGEEIIINIDLGLGMGSARSFGCDLTHEYVNVNANYTT 387
                                       ******5554455599******7777899******************************************98 PP

>> BID  BH3 interacting domain (BID)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-06     0.011       8     143 ..      79     215 ..      73     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-06
                                       XXXXTHHHHHHHHHHHHHTSXSSSHHHHHHHGGG..XXXXXSXSSXS.XSSXXX-S-S---TTT-STTS-HCHHHHH CS
                               BID   8 glrderitnlLvfgFLqscsdseFheeLeaLgke..lpvkaeleedkddeLqtDGnrashlqagrleadsesqeevi 82 
                                       g++d r+   L+ gFL+s ++        ++g+   + +   l e+  + L  DG+     +   + +d+ ++e  +
  gi|330507502|ref|YP_004383930.1|  79 GVEDARMMASLLAGFLKSDEERIAVASTGVIGRYmdMDIIGRLFEEARGRLRSDGEAGLEAERAIMTTDTREKEVAV 155
                                       6788999999999****9999999999999998733455567789999********9999999999*********** PP

                                       HHHHHHHHHHHHHHHCCSSTTSHHHHHHHHHCHCCCCCCCCHHHHHHHHHHHCTS--SSHC CS
                               BID  83 rniarqLaqiGDeldksiqpklvneLaaqfvneslseedrrkkLaaaleqvmqtipkDlek 143
                                       ++   ++a i       i+p++   L   f++++ s e  +++La a+ +  + +  D + 
  gi|330507502|ref|YP_004383930.1| 156 EHQGLRVAGIVKG-AGMIEPNMATMLCFLFTDADFSPEVLKSCLADAVRDSFNMLTVDGDT 215
                                       *********9755.567*******************************9987666655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.54
# Mc/sec: 2155.57
//
Query:       gi|330507503|ref|YP_004383931.1|  [L=488]
Description: argininosuccinate lyase [Methanosaeta concilii GP6]
Scores for complete 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-59  200.9   0.0    4.5e-59  200.4   0.0    1.2  1  Lyase_1   Lyase
    4.1e-16   59.5   0.8      2e-15   57.3   0.0    2.7  3  ASL_C2    Argininosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.4   0.0     5e-63   4.5e-59      40     312 .]      43     292 ..      20     292 .. 0.95

  Alignments for each domain:
  == domain 1  score: 200.4 bits;  conditional E-value: 5e-63
                                       HHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHHHHHHTTHSSGIIIIITTT--HHHHHH CS
                           Lyase_1  40 akanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnevigellgekvepndkvhtgqSsnDqvp 116
                                        +++++ +e+a++ii+alde+ e g++        + e+ + a+++++  ++g          +  htg+S+nD v+
  gi|330507503|ref|YP_004383931.1|  43 KEMGQISEEVASKIIAALDEIEE-GSAL------GAGEDVHEAIEAAVIALVG-------PEGGRMHTGRSRNDEVA 105
                                       56788889999*********999.7777......6899********8888888.......899************** PP

                                       HHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Lyase_1 117 TalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrl 193
                                       T +r+al++ l + L++    +i++l++ a ++++ v +G+Th+q+A+P+tl++ l a+a+a  rd+ rlk++++r+
  gi|330507503|ref|YP_004383931.1| 106 TCIRIALRDDLLD-LMDGELSFIKTLVRLAANHRESVIPGFTHTQHAQPTTLAHHLLAHADAALRDLDRLKDAYRRV 181
                                       ***********77.9999999******************************************************** PP

                                       TCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                           Lyase_1 194 lvellgggtavgtglnadpefaelvakelakvtglpvkapnsfeavsdrDavvellgalkllatsLskfaeDlrlls 270
                                       ++++lg+++ + tg+++d+    + a+ l+ +++     +ns++avs+rD+v+e+l+al++ +++ s++ae+l+l s
  gi|330507503|ref|YP_004383931.1| 182 NKSPLGAAAFASTGFDIDRA---RTADLLG-FDS---LVENSMDAVSSRDFVLEVLAALSIAMVNCSRLAEELILWS 251
                                       ********************...99*****.999...9*************************************** PP

                                       STTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHHHH CS
                           Lyase_1 271 sgeaglvelslaesepGSSiMPgKvNPvqlElltgvagrvvG 312
                                       s+e+g+ el+  + +  SSiMP+K+NP+++El + + g v+G
  gi|330507503|ref|YP_004383931.1| 252 SSEFGYLELDNLYAT-TSSIMPQKKNPDTAELARAKTGSVIG 292
                                       **************9.9***********************98 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.63   5.7e+03      44      44 ..      57      57 ..      29      83 .. 0.50
   2 ?   -3.8   0.1         2   1.8e+04      21      30 ..     157     166 ..     156     179 .. 0.67
   3 !   57.3   0.0   2.3e-19     2e-15       1      69 []     355     428 ..     355     428 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.63
                                      H CS
                            ASL_C2 44 l 44
                                      +
  gi|330507503|ref|YP_004383931.1| 57 I 57
                                      1 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2
                                       HHHHHHHHHH CS
                            ASL_C2  21 AHeivgravr 30 
                                       AH++ ++a +
  gi|330507503|ref|YP_004383931.1| 157 AHHLLAHADA 166
                                       7777777644 PP

  == domain 3  score: 57.3 bits;  conditional E-value: 2.3e-19
                                       STTHHHHHHHHHHC.TS-HHHHHHHHHHHHHH.HHHTT--GGG--HHHHHHH-TT....--.GGGGGGSSHHHHTT CS
                            ASL_C2   1 FstATdlADyLvrk.GlpFReAHeivgravrl.aeekgkeleeltleelkeispl....le.edveeaLdpeasVa 69 
                                       FstAT+lAD Lvr  G+pFR+AH ivgr+++   e + ++l+e++le +   sp+    ++ + + +aLdp + Va
  gi|330507503|ref|YP_004383931.1| 355 FSTATELADSLVRItGMPFRTAHSIVGRIAAGkGEPTMRTLDEISLEIWG--SPAsergFSnDHLLRALDPVSNVA 428
                                       9************99*************8888134445558888888888..444446999999********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 2780.32
//
Query:       gi|330507504|ref|YP_004383932.1|  [L=299]
Description: NAD-dependent epimerase/dehydratase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-39  135.6   0.0    1.2e-38  133.4   0.0    1.8  1  GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
    9.9e-39  133.2   0.0    1.2e-38  133.0   0.0    1.1  1  Epimerase      NAD dependent epimerase/dehydratase family
    3.9e-08   32.6   0.0      1e-06   28.0   0.0    2.1  1  3Beta_HSD      3-beta hydroxysteroid dehydrogenase/isomerase 
    0.00035   19.8   0.1     0.0016   17.6   0.1    2.0  2  NAD_binding_4  Male sterility protein
    0.00042   19.5   0.1     0.0018   17.4   0.1    1.8  1  RmlD_sub_bind  RmlD substrate binding domain
  ------ inclusion threshold ------
      0.056   12.9   0.0      0.099   12.1   0.0    1.3  1  adh_short      short chain dehydrogenase
       0.11   12.3   0.1        0.2   11.5   0.1    1.3  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 !  133.4   0.0   4.5e-42   1.2e-38       1     331 [.       4     294 ..       4     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 133.4 bits;  conditional E-value: 4.5e-42
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+l+e Ll+ g +v ++++     +tg+ e+la      le++l+l++   +D s l     +++p+
  gi|330507504|ref|YP_004383932.1|   4 LVTGGAGFIGSNLVEDLLRAGEDVLVLDNM----HTGSAENLAG-----LEGRLELIQKSCNDLSTL-----DIHPQ 66 
                                       9***********************998754....5666677764.....4679**********8866.....689** PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                       ++y+L+  s  +    +P  + e+ + G + + e++r+ g     r++ aS+s +Y      p +E+  +     Y 
  gi|330507504|ref|YP_004383932.1|  67 KIYHLGIPSSSPMYKRNPYLVGEA-INGFISIYELARRSGS----RVVYASSSSLYNGIL-PPHREDMAIGVADYYT 137
                                       *************99999888887.*************985....99*********6664.79************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TT.SCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrget.fvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                        a+l+ + +++ y++ yg+  v  ++f  ++pr +++    + +t+++  +++gk++ l++G++ ++Rd+++v D+v
  gi|330507504|ref|YP_004383932.1| 138 EARLAMERMAELYQRLYGIASVGLRFFSVYGPREEAKkQYANMVTQFLWDMKAGKRP-LVYGDGTQTRDFTYVLDVV 213
                                       *********************************9864378899***********976.679**************** PP

                                       HHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       +am+l++ +d     +++tge +s +e++el +  +  ++e++                   +++++ +   v ++l
  gi|330507504|ref|YP_004383932.1| 214 RAMRLAMDSDYHGILNVGTGEAWSFNEVIELLNRMMDLSLEAQ-------------------YTENPIKN-YVLQTL 270
                                       ******************************9999998876543...................23333332.256778 PP

                                       B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeelvre 331
                                       +d++kak+ +g++ +++++e++ e
  gi|330507504|ref|YP_004383932.1| 271 ADTAKAKSTIGFRSRFGLKEGIGE 294
                                       999999999999999999999865 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.0   0.0   4.6e-42   1.2e-38       2     241 .]       4     231 ..       3     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 133.0 bits;  conditional E-value: 4.6e-42
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S. CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihlAa. 73 
                                       lVtG++GfiGs+lv+ ll++g +v++ld+  ++s++++   l    e     l ++s+ +    + +p+ ++hl+  
  gi|330507504|ref|YP_004383932.1|   4 LVTGGAGFIGSNLVEDLLRAGEDVLVLDNMHTGSAENLAG-LegrlE-----LIQKSCNDLSTLDIHPQKIYHLGIp 74 
                                       8*****************************7777665544.323334.....444444444444559*******885 PP

                                       ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHH CS
                         Epimerase  74 vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlage 150
                                        ++++   +++ +++ + ++g   + e ar++g  r++++sSs++Y    + p  e++    +     Y  a la+e
  gi|330507504|ref|YP_004383932.1|  75 SSSPMY--KRNPYLVGEAINGFISIYELARRSGS-RVVYASSSSLYNGILP-PHREDM---AIGVADYYTEARLAME 144
                                       555554..566688889*****************.***********98888.888888...8999************ PP

                                       HHHHHHHHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHH CS
                         Epimerase 151 klveayaaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvl 226
                                       +++e y++ yg+  + lr f++yGpr + +++ ++++++++  +++gk   +++gdgt+ Rdf yv Dv++a+ l++
  gi|330507504|ref|YP_004383932.1| 145 RMAELYQRLYGIASVGLRFFSVYGPReEAKKQYANMVTQFLWDMKAGK-RPLVYGDGTQTRDFTYVLDVVRAMRLAM 220
                                       **************************777777****************.**************************** PP

                                       HHHTT-STTEEEEES CS
                         Epimerase 227 ehvdagdkgeiyniG 241
                                       +     d  +i+n+G
  gi|330507504|ref|YP_004383932.1| 221 DS----DYHGILNVG 231
                                       *9....555688887 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 !   28.0   0.0     4e-10     1e-06       1     229 [.       4     220 ..       4     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 4e-10
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtGgaGF+G++lv+ L+r++e  +v vlD  +  +  + +   ++ ++i+   +d ++l+   ++++   hl ++ 
  gi|330507504|ref|YP_004383932.1|   4 LVTGGAGFIGSNLVEDLLRAGE--DVLVLDNMHTGSAENLAGLEGRLELIQKSCNDLSTLDIHPQKIY---HL-GIP 74 
                                       69*******************6..*******9999996666666777799999999999997776654...55.666 PP

                         3Beta_HSD  78 dvagkltedei.mkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                        +  +++++ +     ++G  ++ e ++++g  ++vY Ss +   +      il    ++ +     d y+e +   
  gi|330507504|ref|YP_004383932.1|  75 SSSPMYKRNPYlVGEAINGFISIYELARRSGS-RVVYASSSSLYNG------ILPP-HREDMAIGVADYYTEARLAM 143
                                       66666666654145689************995.579***9887666......4433.34456667889999998888 PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkql......aklglalfkigdeevlsdrvYvgNvawa 224
                                       E++        l +   +  + LR   +yG++++  ++ ++ +      +k g+  + +gd  ++ d++Yv  v+ a
  gi|330507504|ref|YP_004383932.1| 144 ERMAELYQR--LYG---IASVGLRFFSVYGPREEAKKQYANMVtqflwdMKAGKRPLVYGDGTQTRDFTYVLDVVRA 215
                                       887655444..443...58899*********987766555544111333478899999****************999 PP

                         3Beta_HSD 225 hilAa 229
                                         lA+
  gi|330507504|ref|YP_004383932.1| 216 MRLAM 220
                                       98885 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   6.4e-07    0.0016       1      33 [.       5      37 ..       5      58 .. 0.83
   2 ?   -0.1   0.0      0.16   4.2e+02     112     144 ..      91     122 ..      76     216 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.4e-07
                                      EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSS CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaks 33
                                      +TG+ GF+G+ L+e+LLr  ++v +   +++ s
  gi|330507504|ref|YP_004383932.1|  5 VTGGAGFIGSNLVEDLLRAGEDVLVLDNMHTGS 37
                                      7******************99865555555555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-T CS
                     NAD_binding_4 112 veGtrevlelakklkklkvllhvST.ayvngere 144
                                       ++G   + ela++  +   +++ S+ +  ng   
  gi|330507504|ref|YP_004383932.1|  91 INGFISIYELARRSGSR--VVYASSsSLYNGILP 122
                                       55666666666655444..333333244444333 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 !   17.4   0.1     7e-07    0.0018       1     164 [.       1     185 [.       1     241 [. 0.75

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7e-07
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.............T--TTSHHHHHHHHHHH--SEEEE------H CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre.............eldltdaeavaellkeakpdvvvnaAAytav 64 
                                       m  lvtG+ G +Gs+L++ l ++g +vl l++              +l+l +++  +    +++p+ +++++     
  gi|330507504|ref|YP_004383932.1|   1 MSTLVTGGAGFIGSNLVEDLLRAGEDVLVLDNMhtgsaenlaglegRLELIQKSCNDLSTLDIHPQKIYHLGIPSSS 77 
                                       778***************************8777888777777777777777777777779************9999 PP

                                       HHHHHSHHHH.HHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH.. CS
                     RmlD_sub_bind  65 DkaEseeeaa.yavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla.. 138
                                            ++ +  +a+n  +   + e+a++ g+ +++ S+   ++G    p +ed + +   +Y +++la+E++ +   
  gi|330507504|ref|YP_004383932.1|  78 PMYKRNPYLVgEAIN--GFISIYELARRSGSRVVYASSSSLYNGI-LPPHREDMAIGVADYYTEARLAMERMAELyq 151
                                       999888776515565..678899*********************9.5679*********************987733 PP

                                       ..H-SSEEEEEE-SEESS......SSS-HHHHHH CS
                     RmlD_sub_bind 139 ..agkkalivRtswvyge......kgknfvktml 164
                                         +g   + +R+  vyg       +  n+v+++l
  gi|330507504|ref|YP_004383932.1| 152 rlYGIASVGLRFFSVYGPreeakkQYANMVTQFL 185
                                       3344455558999999874443333345555555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.9e-05     0.099       4      44 ..       4      44 ..       2      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.9e-05
                                      EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHH CS
                         adh_short  4 lvtGassGIGraiakelakeGakvvvvdrseekleevakel 44
                                      lvtG+++ IG ++++ l+++G +v+v+d+     +e ++ l
  gi|330507504|ref|YP_004383932.1|  4 LVTGGAGFIGSNLVEDLLRAGEDVLVLDNMHTGSAENLAGL 44
                                      8***************************9988777666655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   7.9e-05       0.2       3      30 ..       3      30 ..       2      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.9e-05
                                      EEEETTTSHHHHHHHHHHHHHHS-EEEE CS
                                KR  3 ylitGGlGgLGlelarwlaekgarhlvl 30
                                       l+tGG+G +G  l++ l++ g+  lvl
  gi|330507504|ref|YP_004383932.1|  3 TLVTGGAGFIGSNLVEDLLRAGEDVLVL 30
                                      59**********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1994.88
//
Query:       gi|330507505|ref|YP_004383933.1|  [L=234]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete 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   71.4   0.0    1.3e-19   70.6   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    5.2e-19   68.5   0.0    6.7e-19   68.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    5.1e-18   65.5   0.0    7.6e-18   64.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    7.4e-17   61.9   0.0    1.4e-16   60.9   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    3.7e-14   52.8   0.0    5.2e-14   52.3   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
    8.8e-13   48.8   0.0    1.6e-12   48.0   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    2.3e-10   39.7   0.0    2.9e-10   39.3   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
    2.4e-08   33.6   0.0    3.1e-08   33.3   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.2e-06   26.5   0.0    1.1e-05   25.4   0.0    1.5  1  Methyltransf_8   Hypothetical methyltransferase
    2.1e-05   24.0   0.0    2.9e-05   23.5   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    2.2e-05   24.1   0.0    3.6e-05   23.4   0.0    1.3  1  MTS              Methyltransferase small domain
    4.2e-05   22.8   0.0    6.4e-05   22.2   0.0    1.3  1  DREV             DREV methyltransferase
      8e-05   22.1   0.0    0.00012   21.5   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    0.00021   20.8   0.0     0.0052   16.3   0.0    2.3  1  Methyltransf_4   Putative methyltransferase
    0.00025   20.7   0.0    0.00037   20.2   0.0    1.2  1  NodS             Nodulation protein S (NodS)
      0.002   17.7   0.0     0.0035   16.9   0.0    1.3  1  DOT1             Histone methylation protein DOT1
     0.0048   15.9   0.0     0.0087   15.0   0.0    1.4  1  Methyltransf_9   Protein of unknown function (DUF1698)
  ------ inclusion threshold ------
      0.022   14.1   0.0      0.032   13.6   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.036   13.5   0.0          2    7.9   0.0    2.1  2  CheR             CheR methyltransferase, SAM binding domain
      0.088   12.9   0.0       0.13   12.4   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
       0.12   11.5   0.0       0.15   11.2   0.0    1.3  1  NNMT_PNMT_TEMT   NNMT/PNMT/TEMT family


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 !   70.6   0.0   1.5e-22   1.3e-19       2      96 .]      32     123 ..      31     123 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 1.5e-22
                                       EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvssevlhhve 75 
                                       d+Gc  G +a  +a+++   +++gv++ ke+ ++a++++      +++ +ad+ ++ p++ +sfD+v +++vl+h+ 
  gi|330507505|ref|YP_004383933.1|  32 DLGCSDGEFALRIAQKAktLNIFGVEFLKEAAQRARSRG------IRVCQADLNEIlPLAAESFDVVHANQVLEHLS 102
                                       9*************887889******9999998886666......6679******55******************** PP

                                       CHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllvi 96 
                                       + ++++ke++R+LkpgG+ vi
  gi|330507505|ref|YP_004383933.1| 103 ETDRFIKEVHRILKPGGYAVI 123
                                       ******************986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   7.9e-22   6.7e-19       5     114 ..      28     130 ..      25     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 7.9e-22
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlils 80 
                                        +++DlGC  Ge+++++a++  +  +++G+++ +ea ++Ar++        ++++q+d +e l+  l+ e+fD++++
  gi|330507505|ref|YP_004383933.1|  28 AKIMDLGCSDGEFALRIAQK-AKTLNIFGVEFLKEAAQRARSR-------GIRVCQADLNEiLP--LAAESFDVVHA 94 
                                       689***************54.55678******99999999997.......889********999..8889******* PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedpr..l 114
                                       n+vl +l++ d +++e++r lkpgg+ +i++p+  +
  gi|330507505|ref|YP_004383933.1|  95 NQVLEHLSETDRFIKEVHRILKPGGYAVISTPNlaG 130
                                       ********************************9441 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   8.9e-21   7.6e-18      10     164 ..      15     195 ..       7     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 8.9e-21
                   Methyltransf_23  10 sdklerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae..kakkaqkdqfdeqeaae.pqg 81 
                                       ++ ++ l +  +++++++d+Gc +G+++  ++++ +  ++ gv+   ea ++a+  +++     q+d +e+ +  ++
  gi|330507505|ref|YP_004383933.1|  15 RKTVLDLIE-VNERAKIMDLGCSDGEFALRIAQKAKtlNIFGVEFLKEAAQRARsrGIRV---CQADLNEILPlAAE 87 
                                       555566665.68999****************8886667*********9999996442222...23333344442666 PP

                   Methyltransf_23  82 kfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl......................kedrllld.... 132
                                       +fd++++++vleh+    + ++ ++++lkpgGy+++s+p+                                     
  gi|330507505|ref|YP_004383933.1|  88 SFDVVHANQVLEHLSETDRFIKEVHRILKPGGYAVISTPNLAGlhnilslvfgkqpftahvsnevI------Vgnsl 158
                                       ***************************************876677777777666666665555441......04344 PP

                   Methyltransf_23 133 ......wlylvpagrhisffsarslkelleeaGlevve 164
                                              ++ + +  h++ f+ +sl+el+   G++v +
  gi|330507505|ref|YP_004383933.1| 159 dpkcgmLHASRGE-VHLRIFTPESLRELFSYHGFDVEQ 195
                                       3343323444444.999*****************9975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   1.7e-19   1.4e-16       1      97 []      30     119 ..      30     119 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.7e-19
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG.BSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaed.lpfedgsfDlvvssgalhh 76 
                                       ++dlGc  G+++l++a++ +  ++ gv++ +e+ ++ar+r       +++ q+d+++ lp++++sfD+v+++++l+h
  gi|330507505|ref|YP_004383933.1|  30 IMDLGCSDGEFALRIAQKAKTLNIFGVEFLKEAAQRARSRG------IRVCQADLNEiLPLAAESFDVVHANQVLEH 100
                                       89****************989*****************999......********8869************877*** PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       ls+   ++++ke++r+LkpgG
  gi|330507505|ref|YP_004383933.1| 101 LSET--DRFIKEVHRILKPGG 119
                                       *965..59************9 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.0     6e-17   5.2e-14       7     132 ..      18     147 ..      13     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 6e-17
                              MetW   7 iaeli..kpgsrvldlGcGdGel.lellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvv 80 
                                       +++li  +++++++dlGc dGe+ l++ ++ k ++  G+e  +e+ +++ ++G+ v q dl++ l   + +sfd+v 
  gi|330507505|ref|YP_004383933.1|  18 VLDLIevNERAKIMDLGCSDGEFaLRIAQKAKTLNIFGVEFLKEAAQRARSRGIRVCQADLNEILPL-AAESFDVVH 93 
                                       555551168899*********9769999*********************************998875.6789***** PP

                              MetW  81 lsqtlqatrnpkevldellri...grraivsfPnfGhWrvrlsllskGrmPvtda 132
                                        +q l  + ++++ ++e+ ri   g  a++s Pn+   +  lsl+  G+ P t +
  gi|330507505|ref|YP_004383933.1|  94 ANQVLEHLSETDRFIKEVHRIlkpGGYAVISTPNLAGLHNILSLV-FGKQPFTAH 147
                                       *****************9999555668*******98888888887.799998865 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   1.9e-15   1.6e-12       1      98 [.      31     120 ..      31     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1.9e-15
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       +++Gc +G+++ ++++k +++++ gv++ ++a ++a+ +  + +  +++ +e+  l ++      sfD+v+a++vl+
  gi|330507505|ref|YP_004383933.1|  31 MDLGCSDGEFALRIAQKAKTLNIFGVEFLKEAAQRARSRGIRVC--QADLNEILPLAAE------SFDVVHANQVLE 99 
                                       69*******************************66666555555..4556666666654......************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                       hl +++++++++++ LkpgG+
  gi|330507505|ref|YP_004383933.1| 100 HLSETDRFIKEVHRILKPGGY 120
                                       ********************6 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 !   39.3   0.0   3.5e-13   2.9e-10     109     222 ..      19     128 ..       9     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 3.5e-13
                   Methyltransf_29 109 ipliaaggkvrtvlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaLeRgvpailavlgtkrlpyPsrsfdli 185
                                       ++li+ +++  +++D+GC+   f+  +  ++  tl +   +  ++  q a  Rg++ + a l    lp  ++sfd++
  gi|330507505|ref|YP_004383933.1|  19 LDLIEVNER-AKIMDLGCSDGEFALRI-AQKAKTLNIFGVEFLKEAAQRARSRGIRVCQADLNE-ILPLAAESFDVV 92 
                                       555555444.4589*********7665.66789****9**********************9975.6*********** PP

                   Methyltransf_29 186 hCsrCridwteedgilllevdRvlRpgGyfvlsappv 222
                                       h  + + + +e+   ++ ev+R+l+pgGy v+s+p++
  gi|330507505|ref|YP_004383933.1|  93 HANQVLEHLSET-DRFIKEVHRILKPGGYAVISTPNL 128
                                       *99987666555.5789****************9976 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   3.6e-11   3.1e-08      36     150 ..      15     122 ..       1     139 [. 0.84

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 3.6e-11
                                       HHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--.TTT-T CS
                   Ubie_methyltran  36 kkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqan.aeeLp 111
                                       +k v +l  v + ak++D+ +  g++a+++++++++  ++ ++    + Lk++ ++++ +g   i+  qa+  e Lp
  gi|330507505|ref|YP_004383933.1|  15 RKTVLDLIEVNERAKIMDLGCSDGEFALRIAQKAKT-LNIFGV----EFLKEAAQRARSRG---IRVCQADlNEILP 83 
                                       5688999999********************998764.455554....579********999...556666625679* PP

                                       TS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 112 feddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlv 150
                                          +sfDvv     l  ++++++ +ke++r+lkpGG  v
  gi|330507505|ref|YP_004383933.1|  84 LAAESFDVVHANQVLEHLSETDRFIKEVHRILKPGGYAV 122
                                       ************************************865 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.3e-08   1.1e-05      70     156 ..      24     123 ..      13     127 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.3e-08
                                       S-TTS-EEEES-TT-HHHHH--S-.....EEEEES...S.....-SSTTEEES-T.TS-S--TT-EEEEEEES---. CS
                    Methyltransf_8  70 kkdnlvvadlGcGeakiaeavrek...ekvrsfdl...v.....avnervvacdl.akvPledesvdvavfclslm. 133
                                        ++   ++dlGc +   a ++ +k    ++  +++   +     + + rv   dl   +Pl+ es dv+     l  
  gi|330507505|ref|YP_004383933.1|  24 VNERAKIMDLGCSDGEFALRIAQKaktLNIFGVEFlkeAaqrarSRGIRVCQADLnEILPLAAESFDVVHANQVLEh 100
                                       567788*******9999866554410044544443221211111233467777995557*********887666641 PP

                                       SS-HHHHHHHHHHHEEEEEEEEE CS
                    Methyltransf_8 134 gtnladflkeanrvlkvGGllkv 156
                                         +   f+ke++r+lk+GG+  +
  gi|330507505|ref|YP_004383933.1| 101 LSETDRFIKEVHRILKPGGYAVI 123
                                       467889*************9876 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   3.4e-08   2.9e-05      49     220 ..      13     184 ..       6     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.4e-08
                                       HHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG- CS
                              CMAS  49 aKldlileklelkpGmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldlerkvevklldyedl 124
                                       + ++++l+ +e+++  +++d+Gc  G+ + r +++    +++g+ + ke a++a+ r  ++  ++ +e++ l     
  gi|330507505|ref|YP_004383933.1|  13 ENRKTVLDLIEVNERAKIMDLGCSDGEFALRIAQKAkTLNIFGVEFLKEAAQRARSRGIRVCQADLNEILPLA---- 85 
                                       567889999********************99998851579999999999999998887777766767766554.... PP

                                       ----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEE..EEE--HHHHHCTTCCC..HHHHHHTSTTS--.- CS
                              CMAS 125 dekvdrvvsvgafehvgkenydtffkklkkllkedGllllht..itslhkkelaerglkl..kfidkeiFPgGel.p 196
                                       +e +d v + +++eh+ +   d+f+k+++++lk++G  ++ t  +  lh+      g++   +++++e+  g  l p
  gi|330507505|ref|YP_004383933.1|  86 AESFDVVHANQVLEHLSE--TDRFIKEVHRILKPGGYAVISTpnLAGLHNILSLVFGKQPftAHVSNEVIVGNSLdP 160
                                       5699***********975..69**************99998733455555555545544356677777766666558 PP

                                       BHHHHHHHHHHTT-EEEEEEE-HH CS
                              CMAS 197 sieeieeeiseagftvvdveslra 220
                                       +  +++++  e+++++ + eslr 
  gi|330507505|ref|YP_004383933.1| 161 KCGMLHASRGEVHLRIFTPESLRE 184
                                       899999999999999999999986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   4.2e-08   3.6e-05      23     156 ..      18     142 ..       7     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.2e-08
                                       HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST..TS CS
                               MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve..ek 96 
                                        l+ ++ +++ k++DlGc  G  ++ +a++ +++       +   +e+ ke +++ + + ++v + d+ e ++   +
  gi|330507505|ref|YP_004383933.1|  18 VLDLIEVNERAKIMDLGCSDGEFALRIAQKAKTL-------NIFGVEFLKEAAQRARSRgIRVCQADLNEILPlaAE 87 
                                       577788889999*****************99995.......556666777777777666678888887775544489 PP

                                       -EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHHHHS-- CS
                               MTS  97 kfdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLliVanrklgyeslleelfgnv 156
                                       +fd++  N  + + +      ++++i+e +++Lk+gG  +i + +  g +++l+ +fg+ 
  gi|330507505|ref|YP_004383933.1|  88 SFDVVHANQVLEHLS-----ETDRFIKEVHRILKPGGYAVISTPNLAGLHNILSLVFGKQ 142
                                       *****9996555544.....59******************9999999*******999975 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   7.5e-08   6.4e-05      94     187 ..      26     124 ..      17     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7.5e-08
                              DREV  94 edkklldlGaGdGeitkrvaptfee..vyatelsetmrdrlkkkkynvlsa..le.lqetdvkldlilclnlldrcf 165
                                       e  k++dlG  dGe + r+a+  +   ++  e  ++  +r + ++ +v  a  +e l  +   +d++ +  +l+   
  gi|330507505|ref|YP_004383933.1|  26 ERAKIMDLGCSDGEFALRIAQKAKTlnIFGVEFLKEAAQRARSRGIRVCQAdlNEiLPLAAESFDVVHANQVLEHLS 102
                                       6789***************99888666********************9865324555556889************** PP

                              DREV 166 dplklledirsalepngrviva 187
                                       ++ +++++++ +l+p g ++++
  gi|330507505|ref|YP_004383933.1| 103 ETDRFIKEVHRILKPGGYAVIS 124
                                       *****************99987 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.5e-07   0.00012      20     132 ..      16     123 ..       7     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.5e-07
                                       HHHHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG--..--S CS
                              TehB  20 sevveavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineak..lde 94 
                                         v++ +++ + +k++dlgc +g  +l ++ +     a   n   ++fl+e +++   ++i+    d+ne+     e
  gi|330507505|ref|YP_004383933.1|  16 KTVLDLIEVNERAKIMDLGCSDGEFALRIAQK-----AKTLNIFGVEFLKEAAQRARSRGIRVCQADLNEILplAAE 87 
                                       5689999*****************99998865.....66678889************************98432689 PP

                                       -EEEEEEESSGGGS-GGGHHHHHHHHHHTEEEEEEEEE CS
                              TehB  95 rydfilstvvlmfleaeripsiienmqectkvggynli 132
                                        +d + +  vl  l +    + i+++++  k+ggy +i
  gi|330507505|ref|YP_004383933.1|  88 SFDVVHANQVLEHLSE--TDRFIKEVHRILKPGGYAVI 123
                                       9**********99976..5799*************998 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     6e-06    0.0052       4      47 ..      29      72 ..      26     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6e-06
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHH CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiea 47
                                       ++++Gc  Gef +++A+k  + n++G+E  ++  +++ ++  +
  gi|330507505|ref|YP_004383933.1| 29 KIMDLGCSDGEFALRIAQKAKTLNIFGVEFLKEAAQRARSRGIR 72
                                      689**************************999988888776555 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.3e-07   0.00037      43     145 ..      26     124 ..       9     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.3e-07
                              NodS  43 siadalevGcaaGalterlapyckrltv..vdvveeaiararervkesshiswivsdvqqfs..tdekfdlivvaev 115
                                       + a+++++Gc+ G ++ r+a  +k l +  v+ ++ea +rar r      i   ++d++++   + e fd++   +v
  gi|330507505|ref|YP_004383933.1|  26 ERAKIMDLGCSDGEFALRIAQKAKTLNIfgVEFLKEAAQRARSRG-----IRVCQADLNEILplAAESFDVVHANQV 97 
                                       457899********************9855788999999999885.....556667777664225789********* PP

                              NodS 116 lyyiedvaelraavrnlvsllapdgqlvfG 145
                                       l ++++  ++   ++++ ++l+p+g+ v  
  gi|330507505|ref|YP_004383933.1|  98 LEHLSETDRF---IKEVHRILKPGGYAVIS 124
                                       *999999887...56666778888887765 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.1e-06    0.0035      27      84 ..      11      68 ..       5      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.1e-06
                                      -HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHH CS
                              DOT1 27 lpeflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaek 84
                                        e  ++vld +++++    +DLG   G+  l +a ++++ + +GvE  ++a++ a++
  gi|330507505|ref|YP_004383933.1| 11 DLENRKTVLDLIEVNERAKIMDLGCSDGEFALRIAQKAKTLNIFGVEFLKEAAQRARS 68
                                      55666899*********************************************98875 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     1e-05    0.0087     116     226 ..      27     132 ..      11     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                                       T-EEEEET-TTSHHHHHHHHCT-SE.EEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES CS
                    Methyltransf_9 116 grtildvGcgnGyhlwrmvgegakl.vvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsmG 190
                                         +i+d+Gc++G +  r++ +  +l ++G++  +      ea ++  +   r+ +  l  e lp   e+fd+v +  
  gi|330507505|ref|YP_004383933.1|  27 RAKIMDLGCSDGEFALRIAQKAKTLnIFGVEFLK------EAAQRARSRGIRVCQADLN-EILPLaAESFDVVHANQ 96 
                                       3479*************97765443266777433......6777777777777766654.667766789******** PP

                                       -GGG-S-HHHHHHHHHCTEEEEEEEEEEEE-BSS-T CS
                    Methyltransf_9 191 vlyhrrsPldhllqlkdqlvkgGelvletlvieGde 226
                                       vl h +     + +++  l+ gG  v+ t  + G +
  gi|330507505|ref|YP_004383933.1|  97 VLEHLSETDRFIKEVHRILKPGGYAVISTPNLAGLH 132
                                       ****9998888999************9998888755 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.7e-05     0.032     159     259 ..      24     124 ..      12     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.7e-05
                              PrmA 159 vkegeevlDvGtGSGiLaia.aakLgakkvvavDiDevAvkvake.NaelNkveaklevalseellkeekadvivaN 233
                                       v+e+++++D+G+  G  a+  a+k  + ++++v   + A + a++  +++ + + +   +l+  l + e++dv+ aN
  gi|330507505|ref|YP_004383933.1|  24 VNERAKIMDLGCSDGEFALRiAQKAKTLNIFGVEFLKEAAQRARSrGIRVCQADLNE--ILP--LAA-ESFDVVHAN 95 
                                       6777899*****9998888525677888999*9987777666654145554444433..233..333.78******* PP

                              PrmA 234 ILaevli...elaedikklvkeggllilS 259
                                        + e l    ++++++ +++k+gg++++S
  gi|330507505|ref|YP_004383933.1|  96 QVLEHLSetdRFIKEVHRILKPGGYAVIS 124
                                       999999633369**************998 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.047        40      27      51 ..      22      46 ..       8      69 .. 0.77
   2 ?    7.9   0.0    0.0023         2     126     173 ..      77     123 ..      60     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.047
                                      HHTSSSEEEEEES-TTTHHHHHHHH CS
                              CheR 27 aknekrvriwsagcssGeEpYslAm 51
                                      ++ ++r +i   gcs+Ge +  +A 
  gi|330507505|ref|YP_004383933.1| 22 IEVNERAKIMDLGCSDGEFALRIAQ 46
                                      4455899**********97777665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0023
                                       -TTT.-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
                              CheR 126 nlle.kksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLll 173
                                       +l+e    + +++Dv+ +  vl  ++e++  + ++++++ lkpgg+ ++
  gi|330507505|ref|YP_004383933.1|  77 DLNEiLPLAAESFDVVHANQVLEHLSETD--RFIKEVHRILKPGGYAVI 123
                                       555544567789*************9987..58************9877 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015      0.13      20      72 ..      25      80 ..       4     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                      -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.HHH...TTEEEECS-CCC CS
                              FtsJ 20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.apl...pgvttiqgditd 72
                                      ++  +++Dlg++ G ++  ++q+ + + ++++v   +  a++    g+++ q+d ++
  gi|330507505|ref|YP_004383933.1| 25 NERAKIMDLGCSDGEFALRIAQKAK-TLNIFGVEFLKEaAQRarsRGIRVCQADLNE 80
                                      3445699****************76.5*******95553444446788888999865 PP

>> NNMT_PNMT_TEMT  NNMT/PNMT/TEMT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018      0.15     123     217 ..      58     148 ..      42     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                       -HHHHHHHHHHHEEEEEE--TTSSSTTTTSS-SS..EEEEEEESSHHHH-SSHHHHHHHHHHHHTTEEEEEEEEEE. CS
                    NNMT_PNMT_TEMT 123 klqekeeklRklvkrvlkvdvhqspvvlagvqlpkkadvvvtifcleaacedleeylralrnlasllkpGGhlvlg. 198
                                        l+e ++++R++  rv ++d ++  ++ a     + +dvv +   le  +    e  r ++++ + lkpGG+ v+  
  gi|330507505|ref|YP_004383933.1|  58 FLKEAAQRARSRGIRVCQADLNEILPLAA-----ESFDVVHANQVLEHLS----ETDRFIKEVHRILKPGGYAVISt 125
                                       567888999999999***********999.....47****9998888655....557888999999******98741 PP

                                       ....EECS-SEEEETTEEEE--- CS
                    NNMT_PNMT_TEMT 199 ....gvleeseynvGekkfslla 217
                                           g  +  +  +G++ f+ + 
  gi|330507505|ref|YP_004383933.1| 126 pnlaGLHNILSLVFGKQPFTAHV 148
                                       11112333445566666676654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1590.22
//
Query:       gi|330507506|ref|YP_004383934.1|  [L=366]
Description: glycosyl transferase, group 1 family protein [Methanosaeta concilii GP6]
Scores for complete 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-36  123.1   0.0    1.3e-35  122.5   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    4.1e-26   92.0   0.0    1.3e-25   90.4   0.0    1.8  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.8e-20   73.7   0.0    2.7e-20   73.1   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    2.8e-11   44.1   0.0    5.8e-11   43.1   0.0    1.6  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    8.1e-10   38.9   0.0    1.8e-09   37.8   0.0    1.5  2  Glyco_trans_4_2  Glycosyl transferase 4-like
    1.5e-07   31.7   0.0    2.5e-07   31.0   0.0    1.3  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.18   11.9   0.0       0.95    9.6   0.0    2.1  2  DUF3880          DUF based on E. rectale Gene description (DU


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 !  122.5   0.0     5e-39   1.3e-35       3     171 ..     172     343 ..     170     344 .. 0.94

  Alignments for each domain:
  == domain 1  score: 122.5 bits;  conditional E-value: 5e-39
                                       HHHHHHTTTTTT-EEEEEE.SS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEE CS
                   Glycos_transf_1   3 ekkrkklgknekkkiilsv.grlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnvifl 78 
                                       +  r k++ ++++ ++lsv   + ++Kg+++l  a++  k+ + p+v+lv+ G g +++ ++++a++l+++dnv f 
  gi|330507506|ref|YP_004383934.1| 172 DAFRPKEAPPKGDIFFLSVlDEFHRYKGLEVLFAALKIMKQ-ELPDVRLVVGGRGCMFDHYRRMADSLGIGDNVSFA 247
                                       678999999********984689999***********9865.6********************************** PP

                                       ECCHSSSHHHHHHCESEEEEEESS...BSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-HHHHHHH CS
                   Glycos_transf_1  79 gevsredleellknadifvlpsis...EgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnnaealaea 151
                                       g+++ e+l+e+++ +++f+lps+    EgfGiv+lEAma+  pv+++  +g+++++ + g  G +v  n+ eala  
  gi|330507506|ref|YP_004383934.1| 248 GFIPSEKLIEYYNGCKLFALPSTDpsrEGFGIVPLEAMACERPVVVTEiMGMARDINECGA-GMVVRCNDKEALASS 323
                                       ************************************************8888888887777.*************** PP

                                       HHHHHHSHHHHHHHHHHHHH CS
                   Glycos_transf_1 152 irklledeelrerlgenark 171
                                       +  +l+d++l+ r+g ++rk
  gi|330507506|ref|YP_004383934.1| 324 MLAILKDDDLAGRMGAEGRK 343
                                       ****************9997 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.3   3.3e+03      32      72 ..     111     157 ..      98     174 .. 0.51
   2 !   90.4   0.0   5.2e-29   1.3e-25       4     134 .]     185     330 ..     182     330 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                                       EEEEEES---...........HHHHHHHTT-T.TEEEE---THHHHHHHH CS
                   Glyco_trans_1_4  32 vrlvivGdgprp.........eeleelaagleerveftGfvedlaellaa 72 
                                       ++  ivG+g ++          +l+ l+ + + ++++t  +  ++++l++
  gi|330507506|ref|YP_004383934.1| 111 YHNDIVGEG-WAgqiawiynkTALK-LLLKSAGGIIVTRNR-YVSPYLKD 157
                                       566677766.332232333223333.222334567777766.66666664 PP

  == domain 2  score: 90.4 bits;  conditional E-value: 5.2e-29
                                       EEEES---G..G.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHH CS
                   Glyco_trans_1_4   4 ilfvGrlee..nvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaella 71 
                                       i f++ l+e  ++kg+++l  a++ ++++  dvrlv+ G+g+   ++++++a+  g+ ++v+f+Gf+  e+l e+++
  gi|330507506|ref|YP_004383934.1| 185 IFFLSVLDEfhRYKGLEVLFAALKIMKQElpDVRLVVGGRGCmF-DHYRRMADslGIGDNVSFAGFIpsEKLIEYYN 260
                                       7778877445699**************99855********9964.5788777668999*********9777****** PP

                                       H-SEEEE--.....---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  72 aadvfvaPs.....egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                        +++f +Ps     egfg++ lEama+++pvV+t++ g+a+ +    +g++v  +d eala  +l++l+d
  gi|330507506|ref|YP_004383934.1| 261 GCKLFALPStdpsrEGFGIVPLEAMACERPVVVTEIMGMARDIneCGAGMVVRCNDKEALASSMLAILKD 330
                                       **********99988*********************99876564424679****************9987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.0     1e-23   2.7e-20       2     169 ..      14     172 ..      13     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 1e-23
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHa 78 
                                       GGve +v++L+r+L  +Gh+V v++ +++g+ +    +++  + +     ++   + +  ++l  +l re++D++H+
  gi|330507506|ref|YP_004383934.1|  14 GGVESYVRNLSRELIGMGHDVGVICADGPGENDID-QRIHTKTLKS----RGKIANTSINPYLPLALYREDFDILHT 85 
                                       9************************9999999999.4444444444....44444444455677777789******* PP

                    Glyco_transf_4  79 hspaalg..aallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviav.Seatadelrery 152
                                       h p ++   +++l +r+ ++ plVlt+H+       ++  + ++++++  ++ ll++a  +i++  +++  +l++ y
  gi|330507506|ref|YP_004383934.1|  86 HLPTPWSadWSGLISRL-KKRPLVLTYHNDI--VGEGWAGQIAWIYNKTALKLLLKSAGGIIVTrNRYVSPYLKD-Y 158
                                       *8877752255666665.9************..677888899999999999999*********845566666666.7 PP

                    Glyco_transf_4 153 gvppekitVipnGvDle 169
                                           +k+  +p G+D++
  gi|330507506|ref|YP_004383934.1| 159 A---SKVFFVPLGIDVD 172
                                       7...8899999999987 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 !   43.1   0.0   2.3e-14   5.8e-11       1     136 [.      14     146 ..      14     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 2.3e-14
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvv 77 
                                       gG++ yv++l+r+L   Gh+V v++++++++ +       r+h   +  r+   a+ +  + l  +l   re +d++
  gi|330507506|ref|YP_004383934.1|  14 GGVESYVRNLSRELIGMGHDVGVICADGPGEND----IDQRIHTKTLKSRG-KIANTSINPYLPLAL--YREDFDIL 83 
                                       8************************98888888....45578876666555.577778778888888..8******* PP

                   Glyco_trans_4_4  78 hahspt...aglaarlarrrrgiplvvtlhglllrrg.sgavrrly.ralerrllrradavlvv 136
                                       h+h pt   a + +++ r  ++ plv+t+h++ + +g +g  +++y +++ ++ll++a +++v+
  gi|330507506|ref|YP_004383934.1|  84 HTHLPTpwsADWSGLISR-LKKRPLVLTYHNDIVGEGwAGQIAWIYnKTALKLLLKSAGGIIVT 146
                                       ***998444445555556.99**********999877666666666888899999999999986 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   6.9e-13   1.8e-09      11     138 ..      18     146 ..      10     147 .. 0.84
   2 ?   -3.5   0.0       3.9     1e+04      63      77 ..     203     217 ..     193     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 6.9e-13
                   Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkgpleylkaf.klkklikkikPDvvhahyakpy 86 
                                        ++++l +eL   g++V vi+ +++  +++++++ih + lk  ++g++ + +++  l   + ++ +D++h+h ++p 
  gi|330507506|ref|YP_004383934.1|  18 SYVRNLSRELIGMGHDVGVICADGP-GENDIDQRIHTKTLK--SRGKIANTSINpYLPLALYREDFDILHTHLPTPW 91 
                                       578999****************999.788899*********..9999999999866655567889*******99888 PP

                   Glyco_trans_4_2  87 .gllgslaarlsgvipvvlsvwGldvlkfpkksk....lkklllklalkkatkvist 138
                                        + + +l++rl++  p+vl+ +  d+  ++ +++      k +lkl+lk+a  +i+t
  gi|330507506|ref|YP_004383934.1|  92 sADWSGLISRLKK-RPLVLTYH-NDIVGEGWAGQiawiYNKTALKLLLKSAGGIIVT 146
                                       5555668888888.********.8999998888877755556999999999999886 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.9
                   Glyco_trans_4_2  63 afklkklikkikPDv 77 
                                       +f+  k++k++ PDv
  gi|330507506|ref|YP_004383934.1| 203 LFAALKIMKQELPDV 217
                                       567789999999997 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 !   31.0   0.0   9.9e-11   2.5e-07       8      91 ..     274     359 ..     251     360 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 9.9e-11
                   Glyco_trans_1_2   8 sespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaeht 82 
                                       +e++  + +Ea+ac ++++++++ g+++ +++   +++++  d e la  + + l++++++ ++++++r+ +  +++
  gi|330507506|ref|YP_004383934.1| 274 REGFGIVPLEAMACERPVVVTEIMGMARDINECGAGMVVRcnDKEALASSMLAILKDDDLAGRMGAEGRKLAIGKYS 350
                                       3889999****************8888766666699999999*********************************** PP

                   Glyco_trans_1_2  83 ydhraeqll 91 
                                       ++++aeq+ 
  gi|330507506|ref|YP_004383934.1| 351 WRRAAEQIE 359
                                       *******95 PP

>> DUF3880  DUF based on E. rectale Gene description (DUF3880)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.83   2.1e+03      43      54 ..      70      81 ..      57     100 .. 0.82
   2 ?    9.6   0.0   0.00037      0.95      30      61 ..     151     182 ..     132     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.83
                           DUF3880 43 ylPLAanverld 54
                                      ylPLA   e +d
  gi|330507506|ref|YP_004383934.1| 70 YLPLALYREDFD 81
                                      9***98877665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00037
                           DUF3880  30 yeelkelGvknvyylPLAanverldpleaeae 61 
                                       ++ + +  +++v+++PL+ +v+ ++p ea ++
  gi|330507506|ref|YP_004383934.1| 151 VSPYLKDYASKVFFVPLGIDVDAFRPKEAPPK 182
                                       4666677789****************998873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2771.40
//
Query:       gi|330507507|ref|YP_004383935.1|  [L=314]
Description: family 2 glycosyl transferase [Methanosaeta concilii GP6]
Scores for complete sequence (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  106.7   0.0    6.8e-30  104.1   0.0    2.0  2  Glycos_transf_2  Glycosyl transferase family 2
    1.3e-20   74.3   0.0    1.8e-20   73.8   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.2e-07   31.0   0.0    3.8e-07   30.2   0.0    1.5  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    0.00015   21.3   0.0    0.00046   19.7   0.0    1.7  1  Glyco_transf_21  Glycosyl transferase family 21
      0.002   17.6   0.1       0.02   14.4   0.1    2.0  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   0.0   1.9e-33   6.8e-30       1     170 []       5     174 ..       5     174 .. 0.92
   2 ?    0.1   0.0      0.17   6.2e+02      95     114 ..     277     295 ..     275     311 .. 0.79

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 1.9e-33
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       sv++  yN +  l  +l sl++q +y+dfe+ivvD+gS+D+++e ++e    +p vr+ +++en G+ag+ n g+ra
  gi|330507507|ref|YP_004383935.1|   5 SVIVLNYNGKGFLDGCLSSLASQ-TYSDFEVIVVDNGSRDGSPEYVKEN---YPWVRLAKNDENLGFAGGTNVGIRA 77 
                                       8**********************.*************************...89*********************** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS....EEEECCHCCCCHCCCCCC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv....generlyfkerkrslkgn 150
                                       a+g+++++l+ D+  d  ++e+l++++ +++++v +++  + +g  +            + + ++   +++ +   +
  gi|330507507|ref|YP_004383935.1|  78 AKGEFVITLNNDSRADSRFIEELIKPMADPEVGVCAAKMLFPDGRINSAGICISRsgaaWDRGMFEPDRGQYEFVEE 154
                                       *****************************77766666666666666666665555999999999999999999999* PP

                                       STTCSTCCCEEEEHHHHHCH CS
                   Glycos_transf_2 151 lsfeigsaallrrealeell 170
                                       +++ + +aal+rre+l+e++
  gi|330507507|ref|YP_004383935.1| 155 VFGACAGAALYRREMLDEIG 174
                                       ****************9975 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.17
                                       THHHHHHHHHHH.TTCEEEE CS
                   Glycos_transf_2  95 dwleklvealekdgadvvlg 114
                                       d l+ +v+ +ek ++dvv+ 
  gi|330507507|ref|YP_004383935.1| 277 DALKGVVKMMEK-RKDVVCR 295
                                       78999*******.9999985 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 !   73.8   0.0     5e-24   1.8e-20       4     214 ..       4     213 ..       3     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 5e-24
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       ++v+V ++n    l  +l sl++q+y+++ev+vv+++s+++  e ++e   ++p v  r++ n++nlg+   + ++n
  gi|330507507|ref|YP_004383935.1|   4 ISVIVLNYNGKGFLDGCLSSLASQTYSDFEVIVVDNGSRDGSPEYVKE---NYPWV--RLAKNDENLGF---AGGTN 72 
                                       699*****************************************9998...9**97..66689999885...78899 PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrs..tl.......vsalgalefaerhlrf 148
                                        ++ra+k+++v+ ++ D++ + ++++ l   +++p+vg+  +++++  ++  ++        +a+++  f+ +  + 
  gi|330507507|ref|YP_004383935.1|  73 VGIRAAKGEFVITLNNDSRADSRFIEELIKPMADPEVGVCAAKMLFPDGRinSAgicisrsGAAWDRGMFEPDRGQY 149
                                       ********************************************9976664333667777799999999******** PP

                   Glyco_tranf_2_3 149 laarralgvltlnGsgslirrevlkelegldp.lflltdDyelglrlrragfrtayvpgaavrevfp 214
                                        ++ + +g+ +      l+rre+l+e++++d+  fl  +D++l++r+r ag++  yvpga v + ++
  gi|330507507|ref|YP_004383935.1| 150 EFVEEVFGACA---GAALYRREMLDEIGLFDEdFFLYLEDVDLAFRARLAGWKCLYVPGARVIHHHG 213
                                       ********976...4689**********9999778888***********************998765 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 !   30.2   0.0   1.1e-10   3.8e-07       2     126 ..      83     212 ..      82     264 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.1e-10
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgpvlvm.nvanwleelaalf...faedhgkdilvrealgrvvpsvG 74 
                                       ++ l  D++ +  +++e++  +a+pev+++  ++l+  ++  + +  +++     a+d g + + r ++  v  ++G
  gi|330507507|ref|YP_004383935.1|  83 VITLNNDSRADSRFIEELIKPMADPEVGVCAAKMLFPdGR--INSAGICISrsgAAWDRGMFEPDRGQYEFVEEVFG 157
                                       7788999999999********************9997333..44444444422447777777777776655555555 PP

                   Glyco_trans_2_3  75 sg...aflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkeks 126
                                       ++   a+ rr++l+e+g +d d++   ED d+++r++ +G+++ +vp++ v  ++
  gi|330507507|ref|YP_004383935.1| 158 ACagaALYRREMLDEIGLFDEDFFLYLEDVDLAFRARLAGWKCLYVPGARVIHHH 212
                                       54111578****************************************9554443 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.3e-07   0.00046      24     149 ..      73     206 ..      70     220 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-07
                   Glyco_transf_21  24 qaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaafl.......ntl.agvlq 92 
                                        +++aak ++++++  d r+++ ++eel ++++dp+vg V+++ +  +   + +a  +          +++ + + q
  gi|330507507|ref|YP_004383935.1|  73 VGIRAAKGEFVITLNNDSRADSRFIEELIKPMADPEVG-VCAAKMLFPDGRINSAGICISRsgaawdrGMFePDRGQ 148
                                       57899********************************9.56666666666655555555543222333333455555 PP

                   Glyco_transf_21  93 a.kl.sglgfavGksmalrreaLeaiGGfea.ladeLAeDyalgkllraaGlkvvlspap 149
                                       + ++ + +g + G+  ++rre L++iG f + +  +L eD  l+ + r aG+k   +p +
  gi|330507507|ref|YP_004383935.1| 149 YeFVeEVFGACAGA-ALYRREMLDEIGLFDEdFFLYL-EDVDLAFRARLAGWKCLYVPGA 206
                                       54452345666665.589***********76255555.9999999999999998777654 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   5.7e-06      0.02      14     198 ..      16     192 ..       5     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.7e-06
                   Glyco_tranf_2_2  14 yieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDa 90 
                                       ++   +   a++   ++e+ivvd+gS +   e v+        v l ++ d+  + a   N G+  a++++v+ l+ 
  gi|330507507|ref|YP_004383935.1|  16 FLDGCLSSLASQTYSDFEVIVVDNGSRDGSPEYVKENYPW---VRLAKN-DENLGFAGGTNVGIRAAKGEFVITLNN 88 
                                       4666665666666689*************87777754444...443333.567899999****************** PP

                   Glyco_tranf_2_2  91 DcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledllaakstlvkffapssss 167
                                       D    s  +e ++k +   ++  +  a + +p   +n +    + + +    ++ +  d    ++ + + f   +  
  gi|330507507|ref|YP_004383935.1|  89 DSRADSRFIEELIKPMADPEV-GVCAAKMLFPDGRINSAG-ICISRSGAAWDRGMFEPDRGQ-YEFVEEVFGACAGA 162
                                       ***999999999995544444.466788888888777654.566677766666777666554.77777788888899 PP

                   Glyco_tranf_2_2 168 ilinrraflevGGyDErfrGhgaEDfdlllR 198
                                       +l +r+++ e+G +DE f     ED dl  R
  gi|330507507|ref|YP_004383935.1| 163 ALYRREMLDEIGLFDEDF-FLYLEDVDLAFR 192
                                       999999999999999999.566788887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2143.31
//
Query:       gi|330507508|ref|YP_004383936.1|  [L=253]
Description: ABC transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-25   87.7  25.3    7.1e-25   87.7  25.3    1.4  2  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
       0.49   10.4   0.1       0.49   10.4   0.1    3.2  5  Gram_pos_anchor  LPXTG cell wall anchor motif


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 !   87.7  25.3   7.9e-29   7.1e-25       2     209 ..       9     213 ..       8     214 .. 0.86
   2 ?   -2.9   0.1      0.42   3.7e+03      29      35 ..     231     237 ..     222     246 .. 0.40

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 7.9e-29
                     ABC2_membrane   2 qikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnrpgllffsvlflafsaltsvapvfere 78 
                                       +ik+l+  +++  +++++lg++w+l++pll++lv+ +vf+n+ n ++    ++ll+++v + ++++ +s+a+  +++
  gi|330507508|ref|YP_004383936.1|   9 LIKILTISDLKVKYQSSVLGFAWSLLNPLLMMLVLYLVFSNVFNANQDNFALYLLIGIVSWRFMAIGSSAAMGAIVG 85 
                                       6899************************************98854444446************99999999999999 PP

                     ABC2_membrane  79 rgvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllisala 155
                                       +++l+ + + p   l + v+ + l++ ++ +l+ + +l+i     g+ +  ++lf+++ ++++l++ +++l+++al 
  gi|330507508|ref|YP_004383936.1|  86 KPSLVNKIYIPRQVLVTSVVLSNLISSILEFLVLVPLLIILGA--GISP-YILLFPFIHMIYFLIVYGISLILAALY 159
                                       9999988888886666666666666666666666666665555..4444.45************************* PP

                     ABC2_membrane 156 psfedasqlaslvllpllllsGffipidsm.pkwlqwiaylnPltyavealrsnl 209
                                       ++++d +q++ +++++ ++ls++++p++++ pk+l  ++ lnP+t +++++r +l
  gi|330507508|ref|YP_004383936.1| 160 VYYRDLNQIWDVLIQIGFFLSPIVYPLSTVpPKYLD-YYMLNPMTALIQMYRDVL 213
                                       ******************************668888.77*************987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.42
                     ABC2_membrane  29 plllalv 35 
                                        l++++v
  gi|330507508|ref|YP_004383936.1| 231 GLFIMVV 237
                                       1122222 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 ?   -4.3   0.8         2   1.8e+04      25      31 ..      37      43 ..      37      47 .. 0.48
   2 ?   -2.3   0.8      0.52   4.7e+03      20      32 ..      71      83 ..      71      86 .. 0.59
   3 ?   -3.4   0.8       1.1     1e+04      25      32 ..     122     129 ..     116     130 .. 0.68
   4 ?   -0.5   0.3      0.14   1.2e+03      18      37 ..     144     163 ..     142     163 .. 0.80
   5 ?   10.4   0.1   5.5e-05      0.49      19      37 ..     226     244 ..     222     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 2
                                      XXXXXXX CS
                   Gram_pos_anchor 25 llallgg 31
                                      ll++l+ 
  gi|330507508|ref|YP_004383936.1| 37 LLMMLVL 43
                                      4555554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.52
                                      XXXXXXXXXXXXX CS
                   Gram_pos_anchor 20 ltaaGllallggl 32
                                      ++a G+ a+ g++
  gi|330507508|ref|YP_004383936.1| 71 FMAIGSSAAMGAI 83
                                      5666766666655 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.1
                                       XXXXXXXX CS
                   Gram_pos_anchor  25 llallggl 32 
                                       ll++lg++
  gi|330507508|ref|YP_004383936.1| 122 LLIILGAG 129
                                       77888876 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.14
                                       XXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor  18 ifltaaGllallggllLlvk 37 
                                       +fl + G+ ++l++l ++++
  gi|330507508|ref|YP_004383936.1| 144 YFLIVYGISLILAALYVYYR 163
                                       57777798999999999886 PP

  == domain 5  score: 10.4 bits;  conditional E-value: 5.5e-05
                                       XXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor  19 fltaaGllallggllLlvk 37 
                                       ++ aaGl+++++g+l+++k
  gi|330507508|ref|YP_004383936.1| 226 VTIAAGLFIMVVGTLVFKK 244
                                       6889************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1700.34
//
Query:       gi|330507509|ref|YP_004383937.1|  [L=274]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-23   81.4   0.0    5.5e-22   78.8   0.0    2.0  1  ABC_tran      ABC transporter
    1.7e-06   28.1   0.2    6.6e-05   22.9   0.1    2.3  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.2e-05   25.9   0.0      2e-05   25.2   0.0    1.4  1  AAA_23        AAA domain
    2.5e-05   23.9   0.0    5.4e-05   22.9   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
    0.00067   20.1   0.2     0.0098   16.3   0.2    2.2  1  AAA           ATPase family associated with various cellular 
     0.0018   18.2   0.1      0.013   15.4   0.0    2.1  2  Rad17         Rad17 P-loop domain
     0.0026   17.7   0.3        1.3    8.9   0.0    2.2  2  NTPase_1      NTPase
     0.0029   17.1   0.2      0.055   12.9   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.012   15.7   0.2       0.22   11.6   0.2    2.5  1  AAA_14        AAA domain
      0.015   15.0   0.0      0.017   14.9   0.0    1.3  1  AAA_15        AAA ATPase domain
       0.02   14.8   0.0      0.038   13.9   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.041   14.3   0.0      0.059   13.8   0.0    1.4  1  AAA_16        AAA ATPase domain
      0.065   13.2   0.1       0.76    9.8   0.0    2.5  2  AAA_5         AAA domain (dynein-related subfamily)
        0.1   12.5   0.1       0.64    9.9   0.0    1.9  2  ATPase_2      ATPase domain predominantly from Archaea
       0.11   13.0   0.0       0.58   10.6   0.0    2.1  2  RNA_helicase  RNA helicase
       0.12   12.9   0.3       0.76   10.3   0.2    2.3  2  AAA_18        AAA domain
       0.17   11.6   0.1       0.58    9.8   0.1    1.9  1  AAA_30        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   5.2e-25   5.5e-22       1     135 [.      71     202 ..      71     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 5.2e-25
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltv 76 
                                       l++vs+ +k+ge+ +++G+nG+GKStLlk+lag l p++G+++++g             +i+ + +    ++pel++
  gi|330507509|ref|YP_004383937.1|  71 LQDVSFAVKHGETFGVIGPNGCGKSTLLKVLAGVLYPDSGRVEING-------------KIAPFLELgVGFQPELSA 134
                                       789***************************************5553.............333333322566667777 PP

                                       HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       r+n             e d++ +++++  +l+ +++ ++    +++S G+ +r+a a a+ ++p+++l+DE 
  gi|330507509|ref|YP_004383937.1| 135 RDNvylygaimglthkEVDQRYDEIMEFSELQRFENMKL----RNFSSGMYVRLAFATAIQTNPDVMLVDEV 202
                                       777777788999999999999******************....****************************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 !   22.9   0.1   6.3e-08   6.6e-05       3      55 ..      85     131 ..      84     143 .. 0.70
   2 ?    3.0   0.0     0.068        72     230     266 ..     169     202 ..     130     204 .. 0.80
   3 ?   -3.6   0.0       7.1   7.5e+03     288     299 ..     224     235 ..     212     238 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.3e-08
                            AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpe 55 
                                       ++iGpNg+GKS+LL+ l ++      + ++      +g+i+    l  + +pe
  gi|330507509|ref|YP_004383937.1|  85 GVIGPNGCGKSTLLKVLAGV------LYPDSGRVEINGKIAPFLELGVGFQPE 131
                                       69***************666......456666666666666666655555555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.068
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEp 266
                                        +  +r++S+G+   la++ta+   +   ++ l+DE+
  gi|330507509|ref|YP_004383937.1| 169 ENMKLRNFSSGMYVRLAFATAIQTNP---DVMLVDEV 202
                                       45567889****9888*******999...9******7 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 7.1
                            AAA_21 288 ngaQviltTHSp 299
                                        g  ++l++HS 
  gi|330507509|ref|YP_004383937.1| 224 AGKTILLVSHSL 235
                                       456778888886 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.9e-08     2e-05       7      55 ..      68     117 ..      64     229 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.9e-08
                            AAA_23   7 frsfrdqeidFsk.gltlItGpNGaGKTTildAiklaLygetprlsrksg 55 
                                       f+ ++d+++  ++   + ++GpNG+GK+T+l  +  +Ly +++r + + +
  gi|330507509|ref|YP_004383937.1|  68 FMALQDVSFAVKHgETFGVIGPNGCGKSTLLKVLAGVLYPDSGRVEINGK 117
                                       677777777776626899*********************99887765543 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 !   22.9   0.0   5.1e-08   5.4e-05      16      55 ..      75     115 ..      65     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.1e-08
                            AAA_29  16 tieidlkg.atlltGpsGsGKSTllDAiqalLvpak.kvrfN 55 
                                       ++ ++  g ++ ++Gp+G GKSTll  ++ +L+p++ +v+ N
  gi|330507509|ref|YP_004383937.1|  75 SFAVKH-GeTFGVIGPNGCGKSTLLKVLAGVLYPDSgRVEIN 115
                                       444443.35888**********************99888777 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 !   16.3   0.2   9.3e-06    0.0098       3      74 ..      86     209 ..      84     235 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.3e-06
                                       EESSTTSSHHHHHHHHHHHHTHE...................................................... CS
                               AAA   3 lyGppGtGKTllakavakelgve...................................................... 25 
                                       ++Gp G+GK++l k +a  l  +                                                      
  gi|330507509|ref|YP_004383937.1|  86 VIGPNGCGKSTLLKVLAGVLYPDsgrveingkiapflelgvgfqpelsardnvylygaimglthkevdqrydeimef 162
                                       68*****************8422222334455556666666666777777777777777777777777777775553 PP

                                       .....EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                               AAA  26 .....fleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                            f ++++          s + +r  f++a + + p ++++DE+ +++ ++
  gi|330507509|ref|YP_004383937.1| 163 selqrFENMKL------RNFSSGMYVRLAFATAIQTN-PDVMLVDEVLSVGDES 209
                                       33222222222......34457788888888888777.9999999998887766 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   1.2e-05     0.013      50      70 ..      86     106 ..      67     118 .. 0.83
   2 ?    0.2   0.0      0.56   5.9e+02     103     144 ..     162     205 ..     144     238 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                             Rad17  50 isGPsGCgkstvvkvLskelg 70 
                                       + GP GCgkst +kvL+  l 
  gi|330507509|ref|YP_004383937.1|  86 VIGPNGCGKSTLLKVLAGVLY 106
                                       78**************98775 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.56
                             Rad17 103 lsqiesfkeleLkd...akylklqklGddlrtdkklilvedlPnk 144
                                        s ++ f++++L++     y +l      ++t+  ++lv+++ ++
  gi|330507509|ref|YP_004383937.1| 162 FSELQRFENMKLRNfssGMYVRLA-FATAIQTNPDVMLVDEVLSV 205
                                       456666777777652113455555.66778888888888887644 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0045       4.8       3      25 ..      85     107 ..      83     125 .. 0.74
   2 !    8.9   0.0    0.0013       1.3      92     136 ..     189     236 ..     147     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0045
                                       EEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellks 25 
                                        + Gp G GK+Tl+k ++ +l  
  gi|330507509|ref|YP_004383937.1|  85 GVIGPNGCGKSTLLKVLAGVLYP 107
                                       577************99998853 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0013
                                       HH.HHH-EEEE---STT..GGG-HHHHHHHHHHHTTTSEEEEE--SS- CS
                          NTPase_1  92 al.seadviviDEiGkm..ElkskkfkeaveevLksekpvlavihrrk 136
                                       a+ +++dv+++DE+ +   E + kk +++++e+ k +k +l v h   
  gi|330507509|ref|YP_004383937.1| 189 AIqTNPDVMLVDEVLSVgdESFQKKCSDKIDEIRKAGKTILLVSHSLA 236
                                       334799*******87666699********************9999764 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 !   12.9   0.0   5.2e-05     0.055      26      45 ..      83     102 ..      64     112 .. 0.71
   2 ?    2.2   0.1     0.099     1e+02     147     201 ..     182     237 ..     144     252 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                                       EEEEEESTTSSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAil 45 
                                          ++GpNG+GKs ll  + 
  gi|330507509|ref|YP_004383937.1|  83 TFGVIGPNGCGKSTLLKVLA 102
                                       33599*********998765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.099
                                       HHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                             SMC_N 147 laLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreem 201
                                       + L fA+       ++l+De+ +  De+  kk ++ ++e +k    ++ +s++  +
  gi|330507509|ref|YP_004383937.1| 182 VRLAFATAIQTNPDVMLVDEVLSVGDESFQKKCSDKIDEIRKAgKTILLVSHSLAT 237
                                       456666655555567899*******************9999884455567776555 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   0.00021      0.22       5      41 ..      84     119 ..      80     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldde 41 
                                         + G+  +GK+tllk l+  l+ +++  ++in +  
  gi|330507509|ref|YP_004383937.1|  84 FGVIGPNGCGKSTLLKVLAGVLY-PDSGRVEINGKIA 119
                                       5799************9998888.6666666665555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.6e-05     0.017      27      44 ..      85     102 ..      68     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                            AAA_15  27 vliGkNnsGKSsileald 44 
                                        +iG+N++GKS++l++l 
  gi|330507509|ref|YP_004383937.1|  85 GVIGPNGCGKSTLLKVLA 102
                                       58*************995 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.6e-05     0.038      88     121 ..      69     103 ..      45     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                        +l++++ ++k+ +t  ++G+ G GKStL+++l++
  gi|330507509|ref|YP_004383937.1|  69 MALQDVSFAVKHgETFGVIGPNGCGKSTLLKVLAG 103
                                       66788888888879999***************987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.5e-05     0.059      22      63 ..      81     121 ..      66     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-05
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63 
                                       g  e   ++G+ G+GKs+l++ l+  l  d g + ++gk   +
  gi|330507509|ref|YP_004383937.1|  81 G--ETFGVIGPNGCGKSTLLKVLAGVLYPDSGRVeINGKIAPF 121
                                       4..556799***********99997777775666666665555 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 ?    9.8   0.0   0.00072      0.76       4      24 ..      86     107 ..      84     117 .. 0.82
   2 ?    0.3   0.0       0.6   6.3e+02      70      83 ..     217     230 ..     168     256 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00072
                                       EE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5   4 LvGppGtgKselaerlaaal.n 24 
                                       ++Gp G+gKs+l + la +l  
  gi|330507509|ref|YP_004383937.1|  86 VIGPNGCGKSTLLKVLAGVLyP 107
                                       59**************998862 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.6
                                       EEESGGG--HHHHH CS
                             AAA_5  70 vlDEveraesevln 83 
                                        +DE+ +a + +l 
  gi|330507509|ref|YP_004383937.1| 217 KIDEIRKAGKTILL 230
                                       35666666665555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00061      0.64      25      41 ..      86     102 ..      71     113 .. 0.86
   2 ?    0.2   0.0      0.57     6e+02      57     123 ..     165     231 ..     144     247 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00061
                          ATPase_2  25 iYGpegsGKtaLlkeii 41 
                                       + Gp g+GK++Llk ++
  gi|330507509|ref|YP_004383937.1|  86 VIGPNGCGKSTLLKVLA 102
                                       67***********9876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.57
                          ATPase_2  57 lreesiskldefieeeeekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiii 123
                                       l++ ++ kl++f    +++  ++ a++++     ++e+l+   +  +k+ ++ +++i+k gk i ++
  gi|330507509|ref|YP_004383937.1| 165 LQRFENMKLRNFSSGMYVRLAFATAIQTNPDVMLVDEVLSVGDESFQKKCSDKIDEIRKAGKTILLV 231
                                       4444444444554445555555555566666666777777777777788888888888888877776 PP

>> RNA_helicase  RNA helicase
   #    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      20 ..      86     103 ..      85     120 .. 0.85
   2 ?   -0.8   0.0       1.9     2e+03      49      68 ..     193     213 ..     165     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00055
                      RNA_helicase   3 lyGpsgeGKStlakeLak 20 
                                       + Gp+g+GKStl k La 
  gi|330507509|ref|YP_004383937.1|  86 VIGPNGCGKSTLLKVLAG 103
                                       67************9875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.9
                      RNA_helicase  49 gqevvvidDfgqvkdee.nps 68 
                                       +++v+++d++ +v de+ +++
  gi|330507509|ref|YP_004383937.1| 193 NPDVMLVDEVLSVGDESfQKK 213
                                       788999999988888864444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.3   1.4e+03      69      93 ..      17      47 ..       5      52 .. 0.70
   2 ?   10.3   0.2   0.00072      0.76       3      20 ..      86     103 ..      85     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                            AAA_18 69 s......aleegknlvidghlaeleseaakd 93
                                             + ++g+ +v++g+  +++ ++ k+
  gi|330507509|ref|YP_004383937.1| 17 LvkggigRGTNGNAIVVEGISKNFRIPKEKK 47
                                      244444467889999*****99999887776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00072
                            AAA_18   3 ltGtpGvGKttlakeLsk 20 
                                       + G+ G+GK+tl k L+ 
  gi|330507509|ref|YP_004383937.1|  86 VIGPNGCGKSTLLKVLAG 103
                                       89*************954 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   0.00055      0.58      20      49 ..      83     112 ..      73     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00055
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrv 49 
                                       +  + Gp G GK+t+lk+l+ ++  + grv
  gi|330507509|ref|YP_004383937.1|  83 TFGVIGPNGCGKSTLLKVLAGVLYPDSGRV 112
                                       66789**************98876665455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1844.99
//
Query:       gi|330507510|ref|YP_004383938.1|  [L=53]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); 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: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 398.84
//
Query:       gi|330507511|ref|YP_004383939.1|  [L=144]
Description: hypothetical protein MCON_1464 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-23   82.0   1.5    4.8e-23   81.7   1.5    1.1  1  LTD       Lamin Tail Domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   1.5   2.6e-27   4.8e-23      19     108 ..      47     139 ..      28     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 2.6e-27
                               LTD  19 gnnan....efvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsgttsasngskasssavwnn 90 
                                       + +++    e+ve++N++s++v+++gw+l+da+++ ytfp+    laag++vvv++g+g ++++n  +++s+ +wnn
  gi|330507511|ref|YP_004383939.1|  47 SPEKEnlddEWVEITNKGSSDVNMAGWTLADAQNHtYTFPDFA--LAAGAKVVVHTGEGDDDTENLFWDRSTSIWNN 121
                                       333334578*********************************6..******************************** PP

                               LTD  91 ggdavaLydasgevvdsv 108
                                       +gd ++L+d++g+ v+++
  gi|330507511|ref|YP_004383939.1| 122 SGDLAVLLDPEGNMVSQY 139
                                       **************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 965.10
//
Query:       gi|330507512|ref|YP_004383940.1|  [L=439]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-25   87.4   0.0    1.3e-24   86.3   0.0    1.6  1  Transposase_20  Transposase IS116/IS110/IS902 family
    9.3e-23   80.8   0.2    3.7e-22   78.9   0.0    2.0  2  DEDD_Tnp_IS110  Transposase
     0.0059   16.4   0.1      0.015   15.1   0.1    1.7  1  YfkB            YfkB-like domain
  ------ inclusion threshold ------
       0.12   11.3   0.1       0.79    8.6   0.0    2.1  2  UPF0261         Uncharacterised protein family (UPF0261)


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0     3e-28   1.3e-24       2      86 ..     249     334 ..     248     335 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 3e-28
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaai.r 77 
                                       ++++sipGi ++  +++l+eig+ r f++++qla+++Gl+p en+S++kkr+ +i+krG++++R +L+eaA++++  
  gi|330507512|ref|YP_004383940.1| 249 AIVMSIPGIAFISGSVILSEIGNYRDFQTPEQLAKWCGLNPGENESAGKKRKCGITKRGSKYIRVVLVEAAQTIAnM 325
                                       589********************************************************************999955 PP

                    Transposase_20  78 anpelrayy 86 
                                       +n  l ++y
  gi|330507512|ref|YP_004383940.1| 326 KNTGLSRFY 334
                                       569999888 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   8.3e-26   3.7e-22       1     151 [.       9     150 ..       9     152 .. 0.93
   2 ?   -1.5   0.0      0.46     2e+03      28      70 ..     323     366 ..     312     370 .. 0.63

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 8.3e-26
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G Dv+kd ++a+++  ++   ++e++ +++++l+++ ++ +a+ ++ +v++eatg y+ +++ + l++ i+++v n
  gi|330507512|ref|YP_004383940.1|   9 CGADVHKDLIVATITG-DEVPSIRENFGTTKSELDRFRNW-LADNKCEQVAFEATGVYWIPIYDV-LSRTIDTIVAN 82 
                                       799******9999984.66666778999999999999999.88999*************999998.6789******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLd 151
                                       pl++k +      ++K+D+kD+k IA l +  ++++ +++ +++ +eLr+ltr+r+ +vk+rt++knr+++ L 
  gi|330507512|ref|YP_004383940.1|  83 PLQIKSIP-----NDKSDSKDSKRIATLCL-NNQIKRSRVFSDEDRELRNLTRARSGYVKTRTQFKNRIHKYLS 150
                                       ******95.....8****************.****************************************996 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.46
                    DEDD_Tnp_IS110  28 pn.deeglealleklaakagevlvvveatghygallvaflleag 70 
                                       +n +  gl+++ ++l++k+++   +v    +   l++++l +++
  gi|330507512|ref|YP_004383940.1| 323 ANmKNTGLSRFYKRLSKKKEHNVAIVAVARKLICLIYHLLINQE 366
                                       44144678888888666666666666666666666666766665 PP

>> YfkB  YfkB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.4e-06     0.015      91     150 ..     317     377 ..     306     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-06
                              YfkB  91 gdeealgnikeekledvfekwke.sklakslnchcpavkclGpnvlvknayykevdfkkrk 150
                                         +++++n+k++ l+  +++ ++ ++ +  +     ++ cl   +l+++ +y+evd +krk
  gi|330507512|ref|YP_004383940.1| 317 EAAQTIANMKNTGLSRFYKRLSKkKEHNVAIVAVARKLICLIYHLLINQEFYQEVDCRKRK 377
                                       56789***************9873567788999999**********************998 PP

>> UPF0261  Uncharacterised protein family (UPF0261)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00018      0.79     195     224 ..      34      63 ..      30      64 .. 0.96
   2 ?   -0.4   0.1     0.096   4.3e+02     156     192 ..     311     347 ..     307     356 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00018
                           UPF0261 195 fGvttpavdairelLeeegyevlvFhAtGt 224
                                       fG+t+   d+ r+ L+++++e ++F AtG+
  gi|330507512|ref|YP_004383940.1|  34 FGTTKSELDRFRNWLADNKCEQVAFEATGV 63 
                                       9****************************6 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.096
                           UPF0261 156 lrkvLsnAaaaiaGmakaeekskeekeeeeekplvai 192
                                       +r vL +Aa+ ia m ++  ++  ++ ++++ + vai
  gi|330507512|ref|YP_004383940.1| 311 IRVVLVEAAQTIANMKNTGLSRFYKRLSKKKEHNVAI 347
                                       6889*************99999988877777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3277.17
//
Query:       gi|330507513|ref|YP_004383941.1|  [L=210]
Description: hypothetical protein MCON_1466 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   11.6   3.3        1.9    8.9   0.1    2.4  2  DUF1056   Protein of unknown function (DUF1056)


Domain annotation for each model (and alignments):
>> DUF1056  Protein of unknown function (DUF1056)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0001       1.9      12      39 ..      99     125 ..      92     127 .. 0.83
   2 ?    2.7   0.5    0.0088   1.6e+02       2      23 ..     185     203 ..     184     209 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0001
                           DUF1056  12 klfDVLlFiaamivltytaFlfnataGv 39 
                                       k f  LlF + +ivl+y+ F + + +G+
  gi|330507513|ref|YP_004383941.1|  99 KPFNALLF-SIAIVLVYALFWWRQGLGG 125
                                       55778888.7899**********99996 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0088
                           DUF1056   2 iFkrlfaliWklfDVLlFiaam 23 
                                       iF rl++    lf +LlFia  
  gi|330507513|ref|YP_004383941.1| 185 IFERLLGA---LFSILLFIAIC 203
                                       77777775...68899**9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1527.73
//
Query:       gi|330507514|ref|YP_004383942.1|  [L=178]
Description: pyruvate/ketoisovalerate oxidoreductase subunit gamma [Methanosaeta concilii GP6]
Scores for complete 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  136.8   0.2      9e-40  136.6   0.2    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 !  136.6   0.2     5e-44     9e-40       1     177 []      10     175 ..      10     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 136.6 bits;  conditional E-value: 5e-44
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGG CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldg 75 
                                       GGqG+vta++i+a aa++     qa++ +g e+rG+++++  ri+d+pi+ + +++e+d++++ d ++l+  ++++g
  gi|330507514|ref|YP_004383942.1|  10 GGQGSVTAAEIIAVAAFEDKRFSQAFPAFGVERRGAPVMAFARIADKPIRVRSQIYEPDYVIVQDVTLLDvvDVASG 86 
                                       9*************************************************99999**************99****** PP

                                       EEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHH CS
                               POR  76 lkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lpleale 151
                                       lkp+g ii+n+++  ++ + + k           ++v+++datkia e +g ++++Nt mlGa+++++g ++le+l 
  gi|330507514|ref|YP_004383942.1|  87 LKPDGKIIINTDRSGEQLKLDTK-----------AEVITIDATKIAMEVLG-RPIVNTTMLGAFCGASGeVGLESLN 151
                                       ***********664444444433...........369**************.************************* PP

                                       HHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 152 eaikkrfpkkkeviekNlkafragye 177
                                       +ai++rf++  e+ +kNl a++ +ye
  gi|330507514|ref|YP_004383942.1| 152 KAISERFRG--ELGKKNLLAIKTAYE 175
                                       ********9..8*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1300.11
//
Query:       gi|330507515|ref|YP_004383943.1|  [L=85]
Description: pyruvate oxidoreductase subunit delta [Methanosaeta concilii GP6]
Scores for complete 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-11   41.1  17.3    1.3e-05   24.8   2.5    2.2  2  Fer4      4Fe-4S binding domain
    2.6e-07   30.7  15.4    4.2e-07   30.0  15.1    1.5  1  Fer4_21   4Fe-4S dicluster domain
    2.3e-06   27.7  10.5     0.0061   16.7   3.3    2.1  2  Fer4_9    4Fe-4S dicluster domain
    1.4e-05   24.9  19.7     0.0025   17.8   7.7    2.3  2  Fer4_6    4Fe-4S binding domain
    2.9e-05   24.9  13.2      0.013   16.5   1.9    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    6.3e-05   23.5  15.3    0.00023   21.7  15.3    1.8  1  Fer4_7    4Fe-4S dicluster domain
    0.00019   21.3  13.1      0.062   13.4   2.8    2.5  2  Fer4_2    4Fe-4S binding domain
    0.00079   19.5  16.0      0.016   15.3  16.5    2.1  2  Fer4_10   4Fe-4S dicluster domain
     0.0015   19.1  13.2       0.16   12.5   2.3    2.2  2  Fer4_17   4Fe-4S dicluster domain
     0.0022   18.7  11.7       0.19   12.5   0.9    2.6  2  Fer4_15   4Fe-4S single cluster domain
     0.0076   16.7  14.3        0.2   12.3   1.9    2.5  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.031   14.8  13.8       0.38   11.3   4.0    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.09   13.2  16.6       0.41   11.1   3.8    2.2  3  Fer4_8    4Fe-4S dicluster domain
        4.1    8.6  19.6        3.8    8.7   6.2    2.5  2  Fer4_3    4Fe-4S binding domain
        7.5    7.5  14.7          9    7.2   2.2    2.2  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   7.1   7.1e-08   8.5e-05       1      23 [.      27      49 ..      27      50 .. 0.95
   2 !   24.8   2.5   1.1e-08   1.3e-05       2      24 .]      57      79 ..      56      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7.1e-08
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      +v+d   Ci+C +C+  CP g+I
  gi|330507515|ref|YP_004383943.1| 27 PVVDHKACIKCSLCAIYCPEGCI 49
                                      689*******************9 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.1e-08
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v d + C gC  C++ CP  AIt
  gi|330507515|ref|YP_004383943.1| 57 VPDLDYCKGCSVCANECPRMAIT 79
                                      5699*****************97 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0  15.1   3.5e-10   4.2e-07       2      59 .]      28      80 ..      27      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.5e-10
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                      ++d++ Ci+C +C+i C++    +i+  + +      d C GC +C++ CP   +i+m
  gi|330507515|ref|YP_004383943.1| 28 VVDHKACIKCSLCAIYCPE---GCIHQVDGQF-VPDLDYCKGCSVCANECP-RMAITM 80
                                      689***************8...6776555555.44679*************.699998 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   3.3   5.1e-06    0.0061      21      51 .]      12      49 ..       4      49 .. 0.69
   2 !   15.8   0.7   9.6e-06     0.011      35      51 .]      62      78 ..      50      82 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.1e-06
                            Fer4_9 21 aaerkarlraase.......eaCigCgaCveaCpkgai 51
                                      +++r+ +  a++        +aCi+C  C+  Cp+g+i
  gi|330507515|ref|YP_004383943.1| 12 CSTRITKTGAWRTfvpvvdhKACIKCSLCAIYCPEGCI 49
                                      4444444444444666666678*************987 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.6e-06
                            Fer4_9 35 aCigCgaCveaCpkgai 51
                                       C gC  C++ Cp+ ai
  gi|330507515|ref|YP_004383943.1| 62 YCKGCSVCANECPRMAI 78
                                      47777777777777655 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   7.7   2.1e-06    0.0025       1      24 []      26      49 ..      26      49 .. 0.95
   2 !   12.8   4.1   8.1e-05     0.096       5      24 .]      59      78 ..      59      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.1e-06
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      v+++d  +Ci C  C++ CPeg i
  gi|330507515|ref|YP_004383943.1| 26 VPVVDHKACIKCSLCAIYCPEGCI 49
                                      79*******************976 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.1e-05
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      d d C gC  C++ CP  ai
  gi|330507515|ref|YP_004383943.1| 59 DLDYCKGCSVCANECPRMAI 78
                                      5689************9887 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 !   14.0   3.9     6e-05     0.071       2      20 ..      34      52 ..      33      59 .. 0.88
   2 !   16.5   1.9     1e-05     0.013       2      20 ..      63      81 ..      62      85 .] 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++C  Ca  CP+++i++ 
  gi|330507515|ref|YP_004383943.1| 34 CIKCSLCAIYCPEGCIHQV 52
                                      ****************976 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++C  Ca+ CP  ai++ 
  gi|330507515|ref|YP_004383943.1| 63 CKGCSVCANECPRMAITMV 81
                                      ****************975 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7  15.3   1.9e-07   0.00023       1      50 [.      33      75 ..      33      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.9e-07
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50
                                      +Ci+C  C+ +Cp ++i   +        + + d ++C gC +C+++CP 
  gi|330507515|ref|YP_004383943.1| 33 ACIKCSLCAIYCPEGCIHQVDG-------QFVPDLDYCKGCSVCANECPR 75
                                      5****************99774.......588899**************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 !   13.4   2.8   5.2e-05     0.062       3      22 .]      27      46 ..      25      46 .. 0.91
   2 !   13.2   2.8   6.3e-05     0.075       6      21 ..      59      74 ..      55      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-05
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      +vvd  +Ci C+ C   CP+
  gi|330507515|ref|YP_004383943.1| 27 PVVDHKACIKCSLCAIYCPE 46
                                      899999*************5 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.3e-05
                            Fer4_2  6 dtdrCigCgaCvsaCP 21
                                      d d C gC+ C + CP
  gi|330507515|ref|YP_004383943.1| 59 DLDYCKGCSVCANECP 74
                                      6788************ PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3  16.5   1.4e-05     0.016       3      56 .]      28      74 ..      26      74 .. 0.89
   2 !   12.6   3.3   9.1e-05      0.11       5      21 ..      59      75 ..      55      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      v+d + Ci+C  C   CP          +   +++   +++ C gc  C+ +CP
  gi|330507515|ref|YP_004383943.1| 28 VVDHKACIKCSLCAIYCPE-------GCIHQVDGQFVPDLDYCKGCSVCANECP 74
                                      7899***************.......6677777777779**************9 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.1e-05
                           Fer4_10  5 dddtCirCgkCvkaCPa 21
                                      d d C +C  C + CP 
  gi|330507515|ref|YP_004383943.1| 59 DLDYCKGCSVCANECPR 75
                                      7899***********97 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   3.4   0.00016      0.19      44      59 ..      32      47 ..      11      49 .. 0.89
   2 !   12.5   2.3   0.00013      0.16       2      17 ..      63      78 ..      62      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      + Ci+C +C+ +CP+g
  gi|330507515|ref|YP_004383943.1| 32 KACIKCSLCAIYCPEG 47
                                      68************87 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00013
                           Fer4_17  2 CiqCgyClpeCpsyea 17
                                      C +C+ C++eCp++++
  gi|330507515|ref|YP_004383943.1| 63 CKGCSVCANECPRMAI 78
                                      9***********9876 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   3.9   0.00066      0.79       2      20 ..      28      46 ..      28      55 .. 0.87
   2 !   12.5   0.9   0.00016      0.19       4      20 ..      59      75 ..      56      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00066
                           Fer4_15  2 vvDrdaCigcglCvaeape 20
                                      vvD++aCi c lC+  +pe
  gi|330507515|ref|YP_004383943.1| 28 VVDHKACIKCSLCAIYCPE 46
                                      69***************98 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00016
                           Fer4_15  4 DrdaCigcglCvaeape 20
                                      D d C gc +C+ e+p+
  gi|330507515|ref|YP_004383943.1| 59 DLDYCKGCSVCANECPR 75
                                      8899***********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 !    9.5   4.9    0.0013       1.5       2      16 ..      32      46 ..      31      53 .. 0.91
   2 !   12.3   1.9   0.00016       0.2       2      15 ..      61      74 ..      60      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      + Ci C  C ++CP 
  gi|330507515|ref|YP_004383943.1| 32 KACIKCSLCAIYCPE 46
                                      57************6 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00016
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      + C gC +C + CP
  gi|330507515|ref|YP_004383943.1| 61 DYCKGCSVCANECP 74
                                      89***********9 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.0   0.00032      0.38       1      18 [.      29      46 ..      29      51 .. 0.96
   2 ?    8.9   2.3    0.0018       2.1       2      18 ..      59      75 ..      57      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      VD + Ci c +C+  +P+
  gi|330507515|ref|YP_004383943.1| 29 VDHKACIKCSLCAIYCPE 46
                                      899**************8 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0018
                           Fer4_13  2 DrdtCiacgaCvelaPd 18
                                      D d C +c +C++ +P 
  gi|330507515|ref|YP_004383943.1| 59 DLDYCKGCSVCANECPR 75
                                      6789************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 ?    8.9   4.2    0.0017         2       3      16 ..      32      45 ..      30      61 .. 0.73
   2 ?   10.8   3.7   0.00042       0.5       2      16 ..      60      74 ..      50      78 .. 0.71
   3 ?   11.1   3.8   0.00034      0.41       2      17 ..      60      75 ..      59      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0017
                            Fer4_8  3 ekCieCgaCqsaCp 16
                                      ++Ci+C++C   Cp
  gi|330507515|ref|YP_004383943.1| 32 KACIKCSLCAIYCP 45
                                      57788888877777 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00042
                            Fer4_8  2 lekCieCgaCqsaCp 16
                                      l++C +C+ C ++Cp
  gi|330507515|ref|YP_004383943.1| 60 LDYCKGCSVCANECP 74
                                      456666666666666 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00034
                            Fer4_8  2 lekCieCgaCqsaCpv 17
                                      l++C +C+ C ++Cp 
  gi|330507515|ref|YP_004383943.1| 60 LDYCKGCSVCANECPR 75
                                      6778888888888884 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.2    0.0032       3.8       1      14 [.      34      47 ..      34      50 .. 0.95
   2 ?    5.5   5.5     0.033        39       1      13 [.      63      75 ..      63      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0032
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+ C++C   CP+g
  gi|330507515|ref|YP_004383943.1| 34 CIKCSLCAIYCPEG 47
                                      ************98 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.033
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C gC+ C + CP 
  gi|330507515|ref|YP_004383943.1| 63 CKGCSVCANECPR 75
                                      9***********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 ?    6.5   4.4     0.012        15       2      17 ..      34      49 ..      33      57 .. 0.78
   2 ?    7.2   2.2    0.0075         9      78      94 ..      59      75 ..      49      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.012
                           Fer4_22  2 ClsCgaCtlvCptCsC 17
                                      C++C+ C++ Cp    
  gi|330507515|ref|YP_004383943.1| 34 CIKCSLCAIYCPEGCI 49
                                      ************7543 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0075
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                      +   C GC  C + cp 
  gi|330507515|ref|YP_004383943.1| 59 DLDYCKGCSVCANECPR 75
                                      5678***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 595.64
//
Query:       gi|330507516|ref|YP_004383944.1|  [L=405]
Description: pyruvate oxidoreductase subunit alpha [Methanosaeta concilii GP6]
Scores for complete 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-66  223.4   0.0    4.2e-66  223.0   0.0    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    5.5e-30  103.7   0.1    1.1e-29  102.8   0.1    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    1.9e-07   31.0   0.1    4.1e-07   29.9   0.1    1.5  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.0   0.0     7e-70   4.2e-66       2     229 ..      28     250 ..      27     252 .. 0.97

  Alignments for each domain:
  == domain 1  score: 223.0 bits;  conditional E-value: 7e-70
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       a++ +++dvi+aYPITP++ i+e+l++l+a+ge+ d  ++++ sE++a s  +G++a G r+   T +qGl+Lm+e 
  gi|330507516|ref|YP_004383944.1|  28 AVMCCRPDVISAYPITPQTHIVENLSQLVADGEL-DSAFLTVDSEFSALSLLVGSTACGGRGYSSTTSQGLALMYEV 103
                                       6788999**************************9.8***************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlf 153
                                       l+ ++g++lP+v++v++Ra+ ++ l+i++dq+D + ard+g++++++envqea d +l+A+++Ae+  +r+P++v++
  gi|330507516|ref|YP_004383944.1| 104 LYNVSGMRLPIVMTVANRAIGAP-LNIWNDQQDSIGARDVGWLQIYVENVQEAVDATLQAYKIAEDpeIRTPIMVCM 179
                                       ***********************.******************************************99********* PP

                                       EHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHH CS
                             POR_N 154 Dgfllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvveev 229
                                       Dgf+l+h +e+vel+d+e     ++e+l++ ++++  ldp++p+++g+ a p t+ e+r++++ea+++a + +e+v
  gi|330507516|ref|YP_004383944.1| 180 DGFILTHVYEPVELLDKE----KAREFLPDFKPAN-ILDPNNPLTFGAFADPSTYTEFRYQQFEAHQKALEKIEQV 250
                                       ******************....9999999999988.*******************************998888887 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 !  102.8   0.1   1.8e-33   1.1e-29       1     102 []     274     377 ..     274     377 .. 0.99

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 1.8e-33
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       Aevv+v++Gsv+gt+k+a+delR+eg+kvGl+++r +rPFP ++l+++l+++k ++vl++++++gse  l+++ kaa
  gi|330507516|ref|YP_004383944.1| 274 AEVVLVTLGSVIGTVKDAIDELRAEGLKVGLIKIRCYRPFPVAALRKALSGAKVIAVLEKDVAIGSEAGLLTDLKAA 350
                                       9**************************************************************************** PP

                                       TGGG..TSEEEEEE--GGG----HHHH CS
                           PFOR_II  78 lkks..kvkvvnfvaglgGrditvedi 102
                                        ++   + +++ f aglgGrdit++di
  gi|330507516|ref|YP_004383944.1| 351 FYNTqiRTPIIGFAAGLGGRDITLKDI 377
                                       ***99999****************997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   6.9e-11   4.1e-07       9      85 ..     273     348 ..     269     365 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 6.9e-11
                                       TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHH CS
                   Transketolase_C   9 gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaala 85 
                                         +v+lv+ Gs   ++ +A++eL++eg+++ ++ +r+ +p+  + +++++   + + v+e +v +g  ++ +++ l 
  gi|330507516|ref|YP_004383944.1| 273 DAEVVLVTLGSVIGTVKDAIDELRAEGLKVGLIKIRCYRPFPVAALRKALSGAKVIAVLEKDVAIG-SEAGLLTDLK 348
                                       579********************************************8888888888888777755.4455554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2816.13
//
Query:       gi|330507517|ref|YP_004383945.1|  [L=291]
Description: pyruvate oxidoreductase subunit beta [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-27   94.2   0.0    9.3e-27   93.7   0.0    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.0   5.2e-31   9.3e-27       2     153 .]      39     200 ..      38     200 .. 0.92

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 5.2e-31
                                       SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHH....HSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT- CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakl....akpdrevvaivGDGgflmi.lqelatavrrnl 73 
                                       +Gcl++++  +    + + +  + +++ + +  ++A+G+++      +d +vv+i GDG++++i +   + + +r++
  gi|330507517|ref|YP_004383945.1|  39 TGCLEVVTTPF----PESAWCVPWIHSLFENPAAVASGVEVmlkrRGQDTNVVVIGGDGSTFDIgMGSNSGMFERGH 111
                                       68999866655....566688899****************9864213489*************************** PP

                                       SEEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB......BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHH CS
                      TPP_enzyme_C  74 pitvvvlnNegygmtggq...qepfggkrksgpagk.....dlkpvdfaklaealGak.garvekadveeleealke 141
                                       ++++v+++Ne+y++tg q   ++pf   ++++p+g+       +++d+ ++a a+G++ +a+ ++a++ +l++++ke
  gi|330507517|ref|YP_004383945.1| 112 KVLYVCYDNEAYMNTGVQrsgSTPFCVHTTTTPSGSesmgnPRPKKDMPAIALAHGVPyVATASVAYPVDLRRKVKE 188
                                       ***********************************9***977999*************99999************** PP

                                       HHCSSSEEEEEE CS
                      TPP_enzyme_C 142 alekkgpaliev 153
                                       al+ +gp++i+v
  gi|330507517|ref|YP_004383945.1| 189 ALKANGPSYIQV 200
                                       **********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2128.37
//
Query:       gi|330507518|ref|YP_004383946.1|  [L=203]
Description: IMP cyclohydrolase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.8e-62  208.1   0.0      1e-61  207.9   0.0    1.0  1  IMP_cyclohyd  IMP cyclohydrolase-like protein


Domain annotation for each model (and alignments):
>> IMP_cyclohyd  IMP cyclohydrolase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.9   0.0   5.7e-66     1e-61       1     186 [.       2     185 ..       2     190 .. 0.98

  Alignments for each domain:
  == domain 1  score: 207.9 bits;  conditional E-value: 5.7e-66
                                       ---SEEEEEEETTEE.EEEEEEE-SS---EEEEEETTEEEEEE-TGGGGGT-TTSSEEEEEEETTEEEEESSTHHHH CS
                      IMP_cyclohyd   1 YvGRfivvgksedgkavaaYrvssRSfpnrnrvfredkirveptdeeklednpyiiYncvrvlddkavvtNGsqtdt 77 
                                       YvGR++v g+  +g+ ++aYrvssRSfpnr++ + +++i+v+p d+++l+ npyi+Ync+rv+dd+avvtNG++td+
  gi|330507518|ref|YP_004383946.1|   2 YVGRIVVAGRA-QGRSFVAYRVSSRSFPNRRAEVHDKSITVMPLDPADLARNPYISYNCIRVADDVAVVTNGTHTDM 77 
                                       9*********9.8888************************************************************* PP

                                       HHHHHHTSB-HHHHHHHHHHHH-S--STT---EEEEEE-SS.EEEEEEETTEEEEEE--..TTS-EEEESSS--S-E CS
                      IMP_cyclohyd  78 iaeklekgltardalalsLlaldyEkDdynTPRiagvvkeeeaalgivksdallvekvelkagegtliatYekgepk 154
                                       i+e++e g++  d++alsLla  +E+D+ +TPRiag v+ ++a+lgi ++d+l+v++ +l + ++ ++atYek++++
  gi|330507518|ref|YP_004383946.1|  78 ITERIEDGQSPGDSMALSLLAYGHERDELDTPRIAGAVRGNRAWLGIARKDELRVQQFRLDEDQALMVATYEKTNFE 154
                                       ***************************************************************************** PP

                                       E-----SSHHHHHHHHHHGGGSS-EEEEEEEE CS
                      IMP_cyclohyd 155 eveleaedaeeaaeelweslefenkVslavav 186
                                        v+++a d++ +a+++++ l+fe++V++a+a+
  gi|330507518|ref|YP_004383946.1| 155 DVSMSAWDVAGIARKAYD-LSFERPVCAAAAL 185
                                       ******************.*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1465.91
//
Query:       gi|330507519|ref|YP_004383947.1|  [L=296]
Description: formylmethanofuran--tetrahydromethanopterin formyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-64  215.4   1.1    3.4e-64  215.4   1.1    1.4  2  FTR_C     FTR, proximal lobe
    5.8e-60  201.3   0.1    1.6e-59  199.9   0.0    1.7  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   9.2e+03      20      37 ..      23      40 ..       9      42 .. 0.73
   2 !  215.4   1.1   3.8e-68   3.4e-64       1     148 [.     147     293 ..     147     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1
                                      EEEEESSHHHHHHHHHHH CS
                             FTR_C 20 llilaedqeaaleaaeaa 37
                                      + i+a +++ aleaa++a
  gi|330507519|ref|YP_004383947.1| 23 VQITAVTERWALEAAREA 40
                                      556777777888888776 PP

  == domain 2  score: 215.4 bits;  conditional E-value: 3.8e-68
                                       EEEEEES-EEEEEEEEEEEEEEEESSHHHHHHHHHHHHHHHHTSTTEE--SGGGEESS-EEES-S-TT-SEEE-GGG CS
                             FTR_C   1 geflieeklgvvkgvaGgnllilaedqeaaleaaeaaveaikkvegvitpFpGgivrsgSKvgskykflkastNeaf 77 
                                       g+f+ie+++g+v+g+aGgn+lil+++q++ l+aaeaa+++i+kv+g+itpFpGg+v+sgSKvgskykflkastN+af
  gi|330507519|ref|YP_004383947.1| 147 GDFIIENSFGAVEGIAGGNFLILGQNQMSGLMAAEAAIDSIRKVKGAITPFPGGVVSSGSKVGSKYKFLKASTNSAF 223
                                       8**************************************************************************** PP

                                       -TTSTT....----TT--EEEEEEEEESSHHHHHHHHHHHHHHHTTSTTEEEEE---STTSS-SEEEEGGG CS
                             FTR_C  78 cptlkekveeselpedveavlEiVidgldeeavaeamkagieaavkvegvlkisAgNygGkLGkykfkLke 148
                                       c++l+e+   + l edv++v+EiVi+g+d+ea+++am+agi+aa++v+g+lki+A+Ny+GkLG ++f L++
  gi|330507519|ref|YP_004383947.1| 224 CTSLREDG-VCVLAEDVSCVFEIVINGVDREAIENAMRAGIHAACQVPGILKITAANYEGKLGIHHFPLHS 293
                                       ******99.9***********************************************************97 PP

>> FTR  Formylmethanofuran-tetrahydromethanopterin formyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.9   0.0   1.8e-63   1.6e-59       1     140 [.       1     142 [.       1     144 [. 0.98
   2 ?   -1.8   0.0      0.29   2.6e+03      93     111 ..     231     251 ..     207     262 .. 0.72

  Alignments for each domain:
  == domain 1  score: 199.9 bits;  conditional E-value: 1.8e-63
                                       -EETTEEE-S-EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHSS-S-TTTSS-EEEESEEB-GGGSTTSS-EEEEEEE CS
                               FTR   1 leingveiedtfaEaFeikvtrviiTaatkkwakeaateatgfatsvigceaEagiervlspeetpDgRpGvailif 77 
                                       +eingv+i+dtfaEaF+ik++rv iTa t++wa eaa+eatgf+tsvigc+aEagie+ ++ +et DgRpGv+il++
  gi|330507519|ref|YP_004383947.1|   1 MEINGVQIDDTFAEAFPIKMARVQITAVTERWALEAAREATGFGTSVIGCPAEAGIECLVDGRETVDGRPGVNILLC 77 
                                       89*************************************************************************** PP

                                       ESSHHHHHHHHHHHHHHHTTTSTT-EEEE--..GG-SEEHHHHHHGGGTT--EEEEETTEEEEEE CS
                               FTR  78 aaskkklekqlleRigqcvLtapttavfngl..aeekiklgkklrffgDgyeiekelggrkvwri 140
                                       ++  k+le++ll R+gqcvLtapt+a+f+g+  ae+++++gkkl+ffgDgy++++e+ gr++w+i
  gi|330507519|ref|YP_004383947.1|  78 NMGFKNLENSLLMRLGQCVLTAPTAAAFSGMhdAEKQFDTGKKLSFFGDGYQKTEEMFGRNIWKI 142
                                       *******************************5555****************************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.29
                                       HHHTTTSTT-EEEE--GG..- CS
                               FTR  93 gqcvLtapttavfnglae..e 111
                                       g cvL    + vf+ + +  +
  gi|330507519|ref|YP_004383947.1| 231 GVCVLAEDVSCVFEIVINgvD 251
                                       668888888888888744443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2133.52
//
Query:       gi|330507520|ref|YP_004383948.1|  [L=122]
Description: hypothetical protein MCON_1474, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-28   99.8   0.1    1.1e-28   99.6   0.1    1.0  1  DUF2299   Uncharacterized conserved protein (DUF2299)


Domain annotation for each model (and alignments):
>> DUF2299  Uncharacterized conserved protein (DUF2299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   0.1   6.4e-33   1.1e-28      37     138 .]       1     101 [.       1     101 [. 0.99

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 6.4e-33
                                       EEEEEETT-SSEEEEEEEEE--HHHHHHHHHS-HHHHHHHHHHHHHHHTTTT-EEEEE-TTS--.-EEEEEEEEEGG CS
                           DUF2299  37 vdvikpkgksdvvvvgmgvkvseehkkalsslkeeerkeflselkrdLlrlcvdfqlipqdeelpqsiqvskeiykd 113
                                       +++i+p+g +d+vv+ + + +++ h+ka++ l +++++++++++++dLl+ + +f+++p +e++ +si +++eiy d
  gi|330507520|ref|YP_004383948.1|   1 MSIIQPQGHEDMVVIFSRIMLADVHQKAIMHLLPQQKERLMWQIRYDLLFRQSSFEIEPAGEDM-RSIRFTREIYYD 76 
                                       79*************************************************************9.************ PP

                                       G--HHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2299 114 gltknelldavkrvrnakllviwll 138
                                       gltk++l++a+++ +++ l+v+w++
  gi|330507520|ref|YP_004383948.1|  77 GLTKDRLMEAIRENFKCELYVVWKF 101
                                       ***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 948.27
//
Query:       gi|330507521|ref|YP_004383949.1|  [L=233]
Description: hypothetical protein MCON_1475 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-45  154.4   6.3    5.9e-45  154.2   6.3    1.0  1  SIMPL     Protein of unknown function (DUF541)


Domain annotation for each model (and alignments):
>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.2   6.3   3.3e-49   5.9e-45       2     200 .]      33     230 ..      32     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 154.2 bits;  conditional E-value: 3.3e-49
                             SIMPL   2 tVtGsaevevapDqatltlsvesegkdaaeakaevaekmnavlealkklgikekdiqtsslslkpeysy.....eng 73 
                                       +V G+++v++apD+at+ l+ve+++ +aaea++e+a  mn+ ++al  +gi e+++qts++sl +  ++      + 
  gi|330507521|ref|YP_004383949.1|  33 RVDGEGKVKAAPDMATIVLGVETRSTSAAEAAEENAILMNQTINALLDAGINESQMQTSRFSL-TTMPQdeprgADA 108
                                       79*********************************************88***********999.4444467788677 PP

                             SIMPL  74 knkitgyeasqsltvkfrdldklgevldaavka.aneingvsfslsdedelrdeareeAvkdArakAealAkalgvk 149
                                       +++++++ a++++tv+++++ ++g+vldaav+a  n+i+ v f+l+d+ ++ dea++ A+kdA++kA+++A+a+g++
  gi|330507521|ref|YP_004383949.1| 109 TQEPPTFLATNQVTVRLENTADVGRVLDAAVSAgSNSIQEVKFDLKDPTPQNDEAMTIAIKDAQRKAQVAASAAGLE 185
                                       77777799*************************999************999************************** PP

                             SIMPL 150 lgkvvsisesgsnpyappapamaaaaaaaasaatpfepgeievtasVtvvf 200
                                       lgk+++i++  + +y + a+++++     a++atp++pge+evtasV+ v+
  gi|330507521|ref|YP_004383949.1| 186 LGKILEITV--GYGYVMEASRSYSY----AMDATPIQPGEMEVTASVNLVY 230
                                       *******99..33455555555555....56*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1805.88
//
Query:       gi|330507522|ref|YP_004383950.1|  [L=232]
Description: hypothetical protein MCON_1476 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-26   94.5   3.9    1.3e-26   94.3   3.9    1.0  1  SIMPL          Protein of unknown function (DUF541)
  ------ inclusion threshold ------
      0.017   13.6   0.5       0.02   13.3   0.5    1.1  1  SP2            Structural protein 2
      0.065   13.2   0.1        2.3    8.3   0.0    2.4  2  DUF3783        Domain of unknown function (DUF3783)


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 !   94.3   3.9   2.2e-30   1.3e-26       1     158 [.      27     198 ..      27     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 2.2e-30
                             SIMPL   1 ItVtGsaevevapDqatltlsvesegkdaaeakaevaekmnavlealkklgikekdi...qtsslslkpeysy.... 70 
                                       +tV G ++v+v++D++t+++sves++++ ++a+ ev e mn+v++alkk+g+k+++i   q s++s  +  s+    
  gi|330507522|ref|YP_004383950.1|  27 LTVEGVGTVTVPADIVTISVSVESSNENITQAQYEVGEEMNRVISALKKAGVKDEEIlpgQGSGISSFQSSSKvckt 103
                                       59**********************************************99****99877666667775555556545 PP

                             SIMPL  71 .......engknkitg.....yeasqsltvkfrdldk..lgevldaavka.an.eingvsfslsdedelrdeareeA 131
                                              e              ++++s  ++++  d   +++vldaa +a an  + g    l+d++++r+ear++A
  gi|330507522|ref|YP_004383950.1| 104 vnnttvcE-------NvtesaSTLQRSTVIRLQAKDEsgIDKVLDAARSAgANaYVAGYY--LKDSSDARAEARKKA 171
                                       33222221.......221222358888888888677678***********9995466655..5566799******** PP

                             SIMPL 132 vkdArakAealAkalgvklgkvvsise 158
                                       ++dAr+ A a+A+ +g +lgk ++i  
  gi|330507522|ref|YP_004383950.1| 172 LADARKNAAAIAADAGGSLGKAMDIFA 198
                                       ********************9988865 PP

>> SP2  Structural protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   3.4e-06      0.02     470     559 ..      49     143 ..       8     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-06
                               SP2 470 klsfteltqtkiaasstydttdsdleraasqrvev....dtylsslipstplcnmvnntfscgns..daqavsisav 540
                                         s  ++tq++     +++   s l++a  +  e+     + +ss+  s+ +c+ vnnt  c n    a +  +s+v
  gi|330507522|ref|YP_004383950.1|  49 ESSNENITQAQYEVGEEMNRVISALKKAGVKDEEIlpgqGSGISSFQSSSKVCKTVNNTTVCENVteSASTLQRSTV 125
                                       44666788888888899999999999888888887433223467777889*************96224556789*** PP

                               SP2 541 avlaPncdksaldlnlrvt 559
                                         l  + d+s++d  l+ +
  gi|330507522|ref|YP_004383950.1| 126 IRLQAK-DESGIDKVLDAA 143
                                       ****99.****99877655 PP

>> DUF3783  Domain of unknown function (DUF3783)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00038       2.3      10      27 ..      63      81 ..      62      84 .. 0.86
   2 ?    2.3   0.0     0.028   1.7e+02      11      25 ..     134     148 ..     128     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00038
                           DUF3783 10 seeldklldalkkaglp.i 27
                                      +ee++++++alkkag++ +
  gi|330507522|ref|YP_004383950.1| 63 GEEMNRVISALKKAGVKdE 81
                                      69*************9853 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.028
                           DUF3783  11 eeldklldalkkagl 25 
                                         +dk+lda ++ag 
  gi|330507522|ref|YP_004383950.1| 134 SGIDKVLDAARSAGA 148
                                       559**********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1579.26
//
Query:       gi|330507523|ref|YP_004383951.1|  [L=265]
Description: fructose-bisphosphate aldolase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-59  200.2   0.0    4.2e-59  200.0   0.0    1.0  1  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.0   0.0   2.3e-63   4.2e-59       2     234 ..      22     236 ..      21     237 .. 0.99

  Alignments for each domain:
  == domain 1  score: 200.0 bits;  conditional E-value: 2.3e-63
                                       EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTE CS
                              DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqr 78 
                                       +i+++D++++ +++++       +d+ a+v++++++ga+avl + g+ ++++++y++d++l+++l+++  l +++++
  gi|330507523|ref|YP_004383951.1|  22 IIIPMDHGISVGPIAGL------IDMPATVDKVAEGGANAVLGHMGLPLHGHRGYGRDVGLIIHLSASSSLGPDPNH 92 
                                       79***************......9***************************************************** PP

                                       EEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHH CS
                              DeoC  79 dvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvae 155
                                       +v+ v++ve a++ GAdav+++v++   g+++e+++l +++rv+  c+++g+pli+++y+r++++k e+ + + v+ 
  gi|330507523|ref|YP_004383951.1|  93 KVL-VTDVEDAIRVGADAVSIHVNV---GADDEAEMLHDLGRVARSCDQWGIPLIAMMYPRGPKVKSEH-NVEHVKL 164
                                       ***.*********************...*****************************************.9999*** PP

                                       HHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEES CS
                              DeoC 156 AarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvlsG 229
                                       Aar+++elGaDi+K++++        ++ ++f++v++++ vp vv++GG+   +e+d+l++v  Av + g++Gv+ G
  gi|330507523|ref|YP_004383951.1| 165 AARIGSELGADIVKTNYT--------GSPDTFQEVVRGCSVP-VVIAGGPkmdTERDLLQMVYYAV-QVGGAGVAFG 231
                                       ******************........****************.***********************.********** PP

                                       HHHHT CS
                              DeoC 230 Raifq 234
                                       R++fq
  gi|330507523|ref|YP_004383951.1| 232 RNVFQ 236
                                       ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1874.05
//
Query:       gi|330507524|ref|YP_004383952.1|  [L=259]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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  137.7  13.2    9.4e-11   41.1   0.0    6.7  6  TPR_1         Tetratricopeptide repeat
    1.6e-33  112.0  14.1    1.8e-08   33.9   0.0    6.3  6  TPR_2         Tetratricopeptide repeat
    8.7e-32  108.5  17.0    7.3e-06   25.6   0.8    5.9  6  TPR_11        TPR repeat
    1.4e-30  102.9   8.5    2.6e-07   30.3   0.3    5.5  5  TPR_8         Tetratricopeptide repeat
    4.6e-20   71.7   9.5    3.9e-07   30.3   0.0    4.6  4  TPR_12        Tetratricopeptide repeat
    1.9e-19   68.6  12.0    6.6e-05   23.0   0.0    6.3  6  TPR_17        Tetratricopeptide repeat
    2.2e-19   69.8  17.5    8.3e-07   29.5   0.0    4.4  5  TPR_16        Tetratricopeptide repeat
    2.4e-17   62.1  13.7    5.2e-05   23.7   0.0    5.3  5  TPR_14        Tetratricopeptide repeat
    9.1e-17   61.0   7.9    2.6e-06   27.5   0.1    3.5  4  TPR_9         Tetratricopeptide repeat
    5.8e-13   49.1  14.5    0.00024   21.6   0.1    3.3  3  TPR_19        Tetratricopeptide repeat
    6.9e-08   32.6   2.6       0.49   11.1   0.1    5.1  5  TPR_6         Tetratricopeptide repeat
    5.3e-07   29.8   3.9      0.047   13.9   0.0    3.2  4  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    1.6e-06   27.7   9.2       0.14   12.2   0.0    4.7  5  TPR_7         Tetratricopeptide repeat
    3.3e-06   26.8  12.6       0.98    9.4   0.1    5.3  5  TPR_10        Tetratricopeptide repeat
    2.9e-05   24.0   1.0       0.03   14.4   0.7    3.1  2  SRP_TPR_like  Putative TPR-like repeat
    0.00042   19.4   6.6       0.15   11.0   0.1    2.9  3  NARP1         NMDA receptor-regulated protein 1
    0.00064   20.2   4.5        1.5    9.2   0.0    2.9  4  BTAD          Bacterial transcriptional activator domain
     0.0011   19.0   2.6        1.5    8.9   0.1    3.8  3  MIT           MIT (microtubule interacting and transport) dom
     0.0019   18.2   1.7        4.3    7.4   0.4    4.0  2  DUF3856       Domain of Unknown Function (DUF3856)
     0.0065   16.2   0.2       0.12   12.1   0.0    2.8  3  TOM20_plant   Plant specific mitochondrial import receptor su
     0.0099   16.2   8.5        1.5    9.2   0.2    3.2  3  TPR_20        Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.017   14.7   1.0         27    4.5   0.1    4.7  5  HTH_Bact      Helix-turn-helix bacterial domain
      0.099   12.7   0.1       0.45   10.6   0.0    2.1  1  TraI_2B       DNA relaxase TraI 2B/2B-like domain
       0.13   12.6   0.0        1.3    9.4   0.0    2.3  3  FRD2          Bacteriophage FRD2 protein
       0.62   10.2  10.1        7.5    6.7   0.1    4.9  6  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 ?    4.9   0.2     0.034        24      13      34 .]      36      57 ..      35      57 .. 0.89
   2 !   28.8   0.0   9.5e-10   6.8e-07       2      34 .]      59      91 ..      58      91 .. 0.95
   3 ?    5.1   1.1      0.03        22      14      31 ..     106     123 ..      92     124 .. 0.81
   4 !   37.2   0.4   2.1e-12   1.5e-09       1      32 [.     127     158 ..     127     160 .. 0.95
   5 !   23.2   0.0   5.7e-08   4.1e-05       2      34 .]     162     194 ..     161     194 .. 0.97
   6 !   41.1   0.0   1.3e-13   9.4e-11       1      34 []     195     228 ..     195     228 .. 0.98

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.034
                                      HTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1 13 klgkydeAleyyekALelnPnn 34
                                      ++g y  Al++ ++ L++n ++
  gi|330507524|ref|YP_004383952.1| 36 YNGSYPLALDDIDQYLKINQSD 57
                                      6899***************875 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 9.5e-10
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                       a+  ++n+++k+++y+eAle +++ ++l+ +n
  gi|330507524|ref|YP_004383952.1| 59 WAWSFRANLLLKMERYEEALESFDRIISLDQSN 91
                                      59****************************987 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.03
                                       TT-HHHHHHHHHHHHHHS CS
                             TPR_1  14 lgkydeAleyyekALeln 31 
                                       l++ +eAl+  e AL+++
  gi|330507524|ref|YP_004383952.1| 106 LNQDEEALASLEAALQID 123
                                       78889***********98 PP

  == domain 4  score: 37.2 bits;  conditional E-value: 2.1e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+a+yn+G+++ k+++y+e le+y+kA+ l+ 
  gi|330507524|ref|YP_004383952.1| 127 ANAWYNKGMVLEKMERYNESLEAYRKAIDLDG 158
                                       79****************************95 PP

  == domain 5  score: 23.2 bits;  conditional E-value: 5.7e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +a+y+ G++++  +++de l+  +kA+e nP+n
  gi|330507524|ref|YP_004383952.1| 162 RAWYRQGHVLLIVQRFDESLASLDKAVEFNPEN 194
                                       69*****************************97 PP

  == domain 6  score: 41.1 bits;  conditional E-value: 1.3e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a++ +G++++kl++ +eAl+++++A++l+P+n
  gi|330507524|ref|YP_004383952.1| 195 AEAWNDKGVVLRKLERNEEALDCFQRAIQLDPSN 228
                                       89******************************98 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.26   1.9e+02      12      32 ..      35      55 ..      32      57 .. 0.89
   2 !   23.1   0.0   7.1e-08   5.1e-05       3      33 ..      60      90 ..      59      91 .. 0.94
   3 !    7.1   0.8    0.0093       6.6      14      31 ..     106     123 ..      92     126 .. 0.81
   4 !   29.8   0.3   5.2e-10   3.7e-07       1      32 [.     127     158 ..     127     160 .. 0.94
   5 !   20.5   0.0   4.7e-07   0.00034       2      34 .]     162     194 ..     161     194 .. 0.97
   6 !   33.9   0.0   2.5e-11   1.8e-08       1      34 []     195     228 ..     195     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.26
                             TPR_2 12 yklgdyeeAleafekAleldP 32
                                      y++g y  Al++ ++ l+++ 
  gi|330507524|ref|YP_004383952.1| 35 YYNGSYPLALDDIDQYLKINQ 55
                                      899***************996 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 7.1e-08
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPn 33
                                      a+  ++++++k+ +yeeAle f++ ++ld  
  gi|330507524|ref|YP_004383952.1| 60 AWSFRANLLLKMERYEEALESFDRIISLDQS 90
                                      899*************************976 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0093
                             TPR_2  14 lgdyeeAleafekAleld 31 
                                       l++ eeAl+ +e+Al++d
  gi|330507524|ref|YP_004383952.1| 106 LNQDEEALASLEAALQID 123
                                       5677************98 PP

  == domain 4  score: 29.8 bits;  conditional E-value: 5.2e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       a a+yn G++++k+ +y+e lea++kA+ ld 
  gi|330507524|ref|YP_004383952.1| 127 ANAWYNKGMVLEKMERYNESLEAYRKAIDLDG 158
                                       689***************************96 PP

  == domain 5  score: 20.5 bits;  conditional E-value: 4.7e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +a+y++G +++  ++++e l+ ++kA+e +P+n
  gi|330507524|ref|YP_004383952.1| 162 RAWYRQGHVLLIVQRFDESLASLDKAVEFNPEN 194
                                       69*****************************97 PP

  == domain 6  score: 33.9 bits;  conditional E-value: 2.5e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       aea++  G +++kl + eeAl++f++A++ldP n
  gi|330507524|ref|YP_004383952.1| 195 AEAWNDKGVVLRKLERNEEALDCFQRAIQLDPSN 228
                                       89******************************87 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.18   1.3e+02       5      41 ..      35      71 ..      32      71 .. 0.86
   2 !   22.8   0.1   7.6e-08   5.4e-05       2      38 ..      66     102 ..      65     104 .. 0.93
   3 !   25.6   0.8     1e-08   7.3e-06       8      41 ..     107     140 ..     106     141 .. 0.94
   4 !   22.5   0.1   9.2e-08   6.6e-05       8      38 ..     141     171 ..     139     174 .. 0.92
   5 !   24.3   0.0   2.6e-08   1.8e-05       2      38 ..     169     205 ..     168     208 .. 0.87
   6 !   24.6   0.0     2e-08   1.5e-05       3      34 ..     204     235 ..     202     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.18
                            TPR_11  5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41
                                      y  G y+ A+ +  + lk+++++ +a++ ++++++k+
  gi|330507524|ref|YP_004383952.1| 35 YYNGSYPLALDDIDQYLKINQSDTWAWSFRANLLLKM 71
                                      78899999999999999*********99999988875 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 7.6e-08
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       +++ +  +yeeA+e++ + + ld++na ay+ ++l++
  gi|330507524|ref|YP_004383952.1|  66 NLLLKMERYEEALESFDRIISLDQSNAKAYNDRALVL 102
                                       7888999**************************9986 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 1e-08
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       ++ eeA++++++Al++d  na+a+yn G ++ k+
  gi|330507524|ref|YP_004383952.1| 107 NQDEEALASLEAALQIDALNANAWYNKGMVLEKM 140
                                       899*************************999886 PP

  == domain 4  score: 22.5 bits;  conditional E-value: 9.2e-08
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                        +y+e++eaY+kA++ld d  +a+y  G+++
  gi|330507524|ref|YP_004383952.1| 141 ERYNESLEAYRKAIDLDGDLDRAWYRQGHVL 171
                                       58***********************999886 PP

  == domain 5  score: 24.3 bits;  conditional E-value: 2.6e-08
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       +++   ++++e+++++ kA++++P+naea++  G+++
  gi|330507524|ref|YP_004383952.1| 169 HVLLIVQRFDESLASLDKAVEFNPENAEAWNDKGVVL 205
                                       56666689**************************997 PP

  == domain 6  score: 24.6 bits;  conditional E-value: 2e-08
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynL 34 
                                       +++++ ++eeA+ ++++A++ldP+n     nL
  gi|330507524|ref|YP_004383952.1| 204 VLRKLERNEEALDCFQRAIQLDPSNELYRENL 235
                                       78999********************9877776 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.4e-06    0.0031       3      33 ..      60      90 ..      60      91 .. 0.92
   2 !   11.8   0.3    0.0003      0.22       1      31 [.      92     123 ..      92     124 .. 0.94
   3 !   30.3   0.3   3.7e-10   2.6e-07       1      32 [.     127     158 ..     127     160 .. 0.94
   4 !   18.0   0.0   3.3e-06    0.0024       2      34 .]     162     194 ..     161     194 .. 0.97
   5 !   26.1   0.0     8e-09   5.7e-06       1      34 []     195     228 ..     195     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.4e-06
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      a+   ++++lk+++yeeA e++ + ++ld++
  gi|330507524|ref|YP_004383952.1| 60 AWSFRANLLLKMERYEEALESFDRIISLDQS 90
                                      577899**********************987 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0003
                                       CCHHHHHHHHH.HHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiy.lklgdyeeAkeyyekaleld 31 
                                       a+ay+  ++++   l++ eeA +++e al++d
  gi|330507524|ref|YP_004383952.1|  92 AKAYNDRALVLsGGLNQDEEALASLEAALQID 123
                                       789*****9998******************98 PP

  == domain 3  score: 30.3 bits;  conditional E-value: 3.7e-10
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a a+yn+g++++k+++y+e+ e+y+ka++ld 
  gi|330507524|ref|YP_004383952.1| 127 ANAWYNKGMVLEKMERYNESLEAYRKAIDLDG 158
                                       689***************************96 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 3.3e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +a+y+ g+++l  ++++e+ +++ ka+e +p+n
  gi|330507524|ref|YP_004383952.1| 162 RAWYRQGHVLLIVQRFDESLASLDKAVEFNPEN 194
                                       89*****************************86 PP

  == domain 5  score: 26.1 bits;  conditional E-value: 8e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       aea++ +g +++kl++ eeA  ++++a++ldp+n
  gi|330507524|ref|YP_004383952.1| 195 AEAWNDKGVVLRKLERNEEALDCFQRAIQLDPSN 228
                                       79******************************86 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   2.6   1.8e-07   0.00013       5      74 ..      60     122 ..      57     124 .. 0.90
   2 !   18.6   0.1   2.3e-06    0.0017       3      32 ..     127     156 ..     125     159 .. 0.90
   3 !   30.3   0.0   5.4e-10   3.9e-07       3      76 ..     161     226 ..     159     227 .. 0.91
   4 !   21.6   0.0   2.8e-07    0.0002       3      52 ..     195     239 ..     193     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.8e-07
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyr.algryeeAlelleealai 74 
                                       a++ +a++l++++ry+eAle +++ + + +      +   a ++++ + +++  l++ eeAl+ le al+i
  gi|330507524|ref|YP_004383952.1|  60 AWSFRANLLLKMERYEEALESFDRIISLDQ------S--NAKAYNDRALVLSgGLNQDEEALASLEAALQI 122
                                       67779********************77774......3..5899********7799**************98 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.3e-06
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                       a+a++n ++vl +++ry e+le ++ka+++
  gi|330507524|ref|YP_004383952.1| 127 ANAWYNKGMVLEKMERYNESLEAYRKAIDL 156
                                       7899999*****************999986 PP

  == domain 3  score: 30.3 bits;  conditional E-value: 5.4e-10
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        +a+++ ++vl+  +r+de+l+ l+ka+e       p++   a++ ++ g ++r+l+r eeAl+ +++a+++++
  gi|330507524|ref|YP_004383952.1| 161 DRAWYRQGHVLLIVQRFDESLASLDKAVEFN-----PEN---AEAWNDKGVVLRKLERNEEALDCFQRAIQLDP 226
                                       57899**********************6666.....765...9***************************9875 PP

  == domain 4  score: 21.6 bits;  conditional E-value: 2.8e-07
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLg 52 
                                       a a+n  ++vlr+l+r +eAl+++++a+++      p ++l+ + l++Lg
  gi|330507524|ref|YP_004383952.1| 195 AEAWNDKGVVLRKLERNEEALDCFQRAIQLD-----PSNELYRENLNDLG 239
                                       789988*********************9998.....77888888888887 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0082       5.9       4      34 .]      49      79 ..      47      79 .. 0.91
   2 !   12.7   0.0   0.00018      0.13       2      33 ..      81     113 ..      80     114 .. 0.86
   3 !   16.2   0.3   1.4e-05    0.0097       3      32 ..     117     146 ..     116     148 .. 0.89
   4 ?    6.9   0.0     0.013       9.1       1      31 [.     149     179 ..     149     182 .. 0.88
   5 !   23.0   0.0   9.2e-08   6.6e-05       3      33 ..     185     215 ..     184     216 .. 0.94
   6 ?    5.4   0.1     0.039        28       1      12 [.     217     228 ..     217     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0082
                            TPR_17  4 kaleldPnnadaynnLAelllknGdlmtArq 34
                                      + l+++ ++ +a+  +A+lllk  ++++A++
  gi|330507524|ref|YP_004383952.1| 49 QYLKINQSDTWAWSFRANLLLKMERYEEALE 79
                                      56899************************85 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00018
                            TPR_17   2 ylkaleldPnnadaynnLAelll.knGdlmtAr 33 
                                       + + + ld +na+ayn +A +l+  +++ ++A+
  gi|330507524|ref|YP_004383952.1|  81 FDRIISLDQSNAKAYNDRALVLSgGLNQDEEAL 113
                                       67899*****************88777777775 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.4e-05
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtA 32 
                                       + al++d  na+a++n++ +l+k  ++ + 
  gi|330507524|ref|YP_004383952.1| 117 EAALQIDALNANAWYNKGMVLEKMERYNES 146
                                       789*******************99998765 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.013
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                       +y+ka++ld +   a++  + +ll   ++++
  gi|330507524|ref|YP_004383952.1| 149 AYRKAIDLDGDLDRAWYRQGHVLLIVQRFDE 179
                                       59*******************9998777665 PP

  == domain 5  score: 23.0 bits;  conditional E-value: 9.2e-08
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtAr 33 
                                        ka+e +P na+a+n ++++l+k+ + ++A+
  gi|330507524|ref|YP_004383952.1| 185 DKAVEFNPENAEAWNDKGVVLRKLERNEEAL 215
                                       69************************99996 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.039
                            TPR_17   1 lylkaleldPnn 12 
                                       ++++a++ldP+n
  gi|330507524|ref|YP_004383952.1| 217 CFQRAIQLDPSN 228
                                       89********99 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.5   3.6e+02       8      27 ..      35      54 ..      31      65 .. 0.78
   2 !   22.5   3.6   1.8e-07   0.00013       4      64 ..      65     123 ..      64     129 .. 0.91
   3 !   18.7   1.1   2.9e-06    0.0021      14      64 ..     110     157 ..     105     159 .. 0.95
   4 !   27.1   0.1   6.5e-09   4.7e-06       1      65 [.     131     192 ..     131     193 .. 0.95
   5 !   29.5   0.0   1.2e-09   8.3e-07       1      67 [.     165     228 ..     165     229 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.5
                            TPR_16  8 lragdyddAaaaleaalkrd 27
                                      +++g y+ A+   +++lk +
  gi|330507524|ref|YP_004383952.1| 35 YYNGSYPLALDDIDQYLKIN 54
                                      78999************988 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.8e-07
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaal.rqgrlaeAaalyraalraa 64 
                                       a+++l+  +y++A++ +++ + +d     +a A++ +++++   ++  +eA+a ++aal+ +
  gi|330507524|ref|YP_004383952.1|  65 ANLLLKMERYEEALESFDRIISLD---QSNAKAYNDRALVLSgGLNQDEEALASLEAALQID 123
                                       99**********************...***************7779999999*****99766 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 2.9e-06
                            TPR_16  14 ddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                       ++A+a leaal  d    ++a A++++g ++ +  r+ e +++yr+a++ +
  gi|330507524|ref|YP_004383952.1| 110 EEALASLEAALQID---ALNANAWYNKGMVLEKMERYNESLEAYRKAIDLD 157
                                       69************...******************************9876 PP

  == domain 4  score: 27.1 bits;  conditional E-value: 6.5e-09
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +++++ + +  +y + ++a++ a+++d    d  +A++  g ++l  +r++e +a +++a++  p
  gi|330507524|ref|YP_004383952.1| 131 YNKGMVLEKMERYNESLEAYRKAIDLD---GDLDRAWYRQGHVLLIVQRFDESLASLDKAVEFNP 192
                                       789999*********************...99999***********************9998766 PP

  == domain 5  score: 29.5 bits;  conditional E-value: 1.2e-09
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       + +++ +l  +++d+ +a l+ a++ +   P++aeA++ +g+++ ++ r +eA++ +++a++ +p++
  gi|330507524|ref|YP_004383952.1| 165 YRQGHVLLIVQRFDESLASLDKAVEFN---PENAEAWNDKGVVLRKLERNEEALDCFQRAIQLDPSN 228
                                       6899999999*****************...**********************************987 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   6.2e-05     0.044       2      38 ..      59      95 ..      58     101 .. 0.91
   2 !    9.5   1.3    0.0027       1.9       3      40 ..      94     132 ..      92     136 .. 0.81
   3 !   14.2   0.3   8.5e-05     0.061       2      40 ..     128     166 ..     127     168 .. 0.94
   4 !   23.7   0.0   7.2e-08   5.2e-05       2      38 ..     162     198 ..     161     204 .. 0.94
   5 !   19.1   0.1   2.2e-06    0.0016       2      41 ..     196     235 ..     196     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.2e-05
                            TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeaw 38
                                      +a+  +a +ll  ++++eA++ ++r+++l+ ++a a+
  gi|330507524|ref|YP_004383952.1| 59 WAWSFRANLLLKMERYEEALESFDRIISLDQSNAKAY 95
                                      79999*************************9999887 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0027
                            TPR_14   3 allalaealla.lGdpdeAiallrralalaPddaeawll 40 
                                       a+ ++a +l   l + +eA+a l++al+ +  +a aw+ 
  gi|330507524|ref|YP_004383952.1|  94 AYNDRALVLSGgLNQDEEALASLEAALQIDALNANAWYN 132
                                       5666677776437899******************99986 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 8.5e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       +a++  + +l+  +++ e+++++r+a++l+ d ++aw++
  gi|330507524|ref|YP_004383952.1| 128 NAWYNKGMVLEKMERYNESLEAYRKAIDLDGDLDRAWYR 166
                                       799999*******************************87 PP

  == domain 4  score: 23.7 bits;  conditional E-value: 7.2e-08
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       +a+++ +++ll  +++de++a l++a++ +P++aeaw
  gi|330507524|ref|YP_004383952.1| 162 RAWYRQGHVLLIVQRFDESLASLDKAVEFNPENAEAW 198
                                       79*********************************** PP

  == domain 5  score: 19.1 bits;  conditional E-value: 2.2e-06
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       ea+ + + +l+ l++ +eA+++++ra++l+P+++ ++  l
  gi|330507524|ref|YP_004383952.1| 196 EAWNDKGVVLRKLERNEEALDCFQRAIQLDPSNELYRENL 235
                                       68999999*************************9998766 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   7.9e-06    0.0057      11      66 ..      40      95 ..      36     102 .. 0.85
   2 !   19.4   1.2   1.2e-06   0.00085       4      58 ..      67     122 ..      64     123 .. 0.92
   3 !   19.4   0.7   1.2e-06   0.00085      10      61 ..     108     159 ..     105     164 .. 0.93
   4 !   27.5   0.1   3.6e-09   2.6e-06       8      63 ..     174     229 ..     167     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.9e-06
                             TPR_9 11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66
                                      ++ al  ++  l ++  d   +  R+ ll +++++++Al+ +++ ++l+ +++ a+
  gi|330507524|ref|YP_004383952.1| 40 YPLALDDIDQYLKINQSDTWAWSFRANLLLKMERYEEALESFDRIISLDQSNAKAY 95
                                      67899999999999999999999999999999999999999999999888777665 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.2e-06
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGllla.qlGclsaAladLeaylal 58 
                                       +++  e++e+al+  +r++ l+   +  + dR+l+l   l++ ++Ala Lea+l++
  gi|330507524|ref|YP_004383952.1|  67 LLLKMERYEEALESFDRIISLDQSNAKAYNDRALVLSgGLNQDEEALASLEAALQI 122
                                       677889****************************99846**************986 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 1.2e-06
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       + e+ala +e  l+++   +  ++  G++l++++++++ l++   +++l++d
  gi|330507524|ref|YP_004383952.1| 108 QDEEALASLEAALQIDALNANAWYNKGMVLEKMERYNESLEAYRKAIDLDGD 159
                                       6689********************************************9986 PP

  == domain 4  score: 27.5 bits;  conditional E-value: 3.6e-09
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                        +++++ la ++  + ++P+ +e + d G++l +l++ ++Al++++++++l+p+++
  gi|330507524|ref|YP_004383952.1| 174 VQRFDESLASLDKAVEFNPENAEAWNDKGVVLRKLERNEEALDCFQRAIQLDPSNE 229
                                       5899999**********************************************875 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.4   4.8e-07   0.00034       3      59 ..      36      92 ..      34      99 .. 0.91
   2 !   13.1   3.6   0.00015      0.11       8      58 ..     110     160 ..     108     167 .. 0.91
   3 !   21.6   0.1   3.3e-07   0.00024       4      62 ..     174     232 ..     171     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.8e-07
                            TPR_19  3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59
                                      ++g y  Al+   q l+ +  + +a+   A++ll++ +++eA +  d++   d+ +a
  gi|330507524|ref|YP_004383952.1| 36 YNGSYPLALDDIDQYLKINQSDTWAWSFRANLLLKMERYEEALESFDRIISLDQSNA 92
                                      689999999999****************************************99963 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00015
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       +eAla le+alq d+ na+a+++   +l ++ +++e  ++  ++ + d d 
  gi|330507524|ref|YP_004383952.1| 110 EEALASLEAALQIDALNANAWYNKGMVLEKMERYNESLEAYRKAIDLDGDL 160
                                       58***************************************9999999993 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 3.3e-07
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                        ++++e la l +a + +p+naea+ +   +l +l + +eA ++ +++ + dp ++ y+
  gi|330507524|ref|YP_004383952.1| 174 VQRFDESLASLDKAVEFNPENAEAWNDKGVVLRKLERNEEALDCFQRAIQLDPSNELYR 232
                                       5799999**********************************************988886 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.017        12       7      28 ..      65      86 ..      60      88 .. 0.84
   2 ?    0.4   0.1       1.8   1.3e+03      13      28 ..     106     121 ..      92     123 .. 0.76
   3 !   11.1   0.1   0.00068      0.49       2      28 ..     129     155 ..     128     159 .. 0.93
   4 ?    1.1   0.0       1.1   7.8e+02       2      31 ..     163     192 ..     162     194 .. 0.77
   5 !    8.2   0.0     0.006       4.3       7      32 ..     202     227 ..     201     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.017
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  7 alsyrklgdtdkAlealerlik 28
                                      a +++k+ ++++Ale ++r+i+
  gi|330507524|ref|YP_004383952.1| 65 ANLLLKMERYEEALESFDRIIS 86
                                      56677778***********996 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHH CS
                             TPR_6  13 lgdtdkAlealerlik 28 
                                       l++ ++Al+ le  ++
  gi|330507524|ref|YP_004383952.1| 106 LNQDEEALASLEAALQ 121
                                       47999****9998875 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00068
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                       A y+ ++ ++k+ ++ ++lea+++ i+
  gi|330507524|ref|YP_004383952.1| 129 AWYNKGMVLEKMERYNESLEAYRKAID 155
                                       89*********88***********997 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 1.1
                                       HHHHHH.HHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   2 Alykla.lsyrklgdtdkAlealerlikeYP 31 
                                       A y+++  +++ + + d++l+ l++ ++  P
  gi|330507524|ref|YP_004383952.1| 163 AWYRQGhVLLIVQ-RFDESLASLDKAVEFNP 192
                                       7788885555678.99999999999988666 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       +  +rkl + ++Al+ ++r i+  P 
  gi|330507524|ref|YP_004383952.1| 202 GVVLRKLERNEEALDCFQRAIQLDPS 227
                                       5667887799************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 !   13.9   0.0   6.6e-05     0.047      19      81 ..      20      83 ..       5      84 .. 0.83
   2 !   12.1   0.6   0.00023      0.17       4      81 ..     108     186 ..     105     187 .. 0.84
   3 ?    5.0   0.0     0.041        29      37      81 ..     175     220 ..     159     221 .. 0.78
   4 ?    4.9   0.0     0.044        32      13      81 ..     185     220 ..     175     233 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.6e-05
                                      HH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3 19 etespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                      + +++e+  ++ ++ y ng y  A++ ++++ k+n ++  ++   A  llk+++yeeA+  +++
  gi|330507524|ref|YP_004383952.1| 20 MGQDAEHWIAKTKSDYYNGSYPLALDDIDQYlKINQSDTWAWSFRANLLLKMERYEEALESFDR 83
                                      55555555556677799******************************************98875 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00023
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       + ++A+  +e +l+ ++ ++++ y ++ +l ++++y++ +e +rka +l++   +++y  +++ll  ++++e +a L
  gi|330507524|ref|YP_004383952.1| 108 QDEEALASLEAALQIDALNANAWYNKGMVLEKMERYNESLEAYRKAiDLDGDLDRAWYRQGHVLLIVQRFDESLASL 184
                                       55677777888887888888888888999999999999999999999999999999999999999999999999999 PP

                                       -S CS
                            ANAPC3  80 ek 81 
                                       +k
  gi|330507524|ref|YP_004383952.1| 185 DK 186
                                       87 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.041
                                       T-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  37 gqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +++++ +  l+ka + n+++ +++  ++ +l kL++ eeA++++++
  gi|330507524|ref|YP_004383952.1| 175 QRFDESLASLDKAvEFNPENAEAWNDKGVVLRKLERNEEALDCFQR 220
                                       55666677778888888899999999999999*********99986 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.044
                                       HHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  13 erllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +++++                                  n+++ +++  ++ +l kL++ eeA++++++
  gi|330507524|ref|YP_004383952.1| 185 DKAVEF---------------------------------NPENAEAWNDKGVVLRKLERNEEALDCFQR 220
                                       444444.................................444444444445555555555555555543 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1    0.0022       1.6       2      30 ..      61      89 ..      60     103 .. 0.81
   2 ?    1.8   0.3      0.43   3.1e+02      12      28 ..     106     122 ..      94     127 .. 0.82
   3 !    7.5   0.1    0.0063       4.5       1      31 [.     129     157 ..     129     169 .. 0.84
   4 ?   -2.0   0.0       6.9   4.9e+03      14      20 ..     176     182 ..     158     195 .. 0.57
   5 !   12.2   0.0    0.0002      0.14       2      34 ..     198     228 ..     197     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0022
                             TPR_7  2 LlnLarlysrlGdyeeAielyeqsLaltk 30
                                      ++  a+l  ++ +yeeA+e + + + l+ 
  gi|330507524|ref|YP_004383952.1| 61 WSFRANLLLKMERYEEALESFDRIISLDQ 89
                                      667799****************9444443 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.43
                             TPR_7  12 lGdyeeAielyeqsLal 28 
                                       l++ eeA+  +e++L++
  gi|330507524|ref|YP_004383952.1| 106 LNQDEEALASLEAALQI 122
                                       7899*********8876 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0063
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       a++n + + +++ +y e +e y++  a++ d
  gi|330507524|ref|YP_004383952.1| 129 AWYNKGMVLEKMERYNESLEAYRK--AIDLD 157
                                       68899999****************..55543 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 6.9
                             TPR_7  14 dyeeAie 20 
                                       +++e + 
  gi|330507524|ref|YP_004383952.1| 176 RFDESLA 182
                                       3444333 PP

  == domain 5  score: 12.2 bits;  conditional E-value: 0.0002
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       ++  +++ ++l + eeA++++++  a+  dp++
  gi|330507524|ref|YP_004383952.1| 198 WNDKGVVLRKLERNEEALDCFQR--AIQLDPSN 228
                                       6667999****************..77666665 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.036        26       9      30 ..      65      86 ..      64      89 .. 0.87
   2 ?    6.3   1.1     0.013       9.4       2      31 ..      92     122 ..      92     124 .. 0.92
   3 !    8.3   0.2    0.0031       2.2       7      30 ..     132     155 ..     127     156 .. 0.91
   4 ?    1.9   0.0      0.31   2.2e+02       9      30 ..     168     189 ..     168     191 .. 0.86
   5 !    9.4   0.1    0.0014      0.98       6      30 ..     199     223 ..     195     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.036
                            TPR_10  9 analrqrgrydeAealleeala 30
                                      an+l ++ ry+eA++ +++ ++
  gi|330507524|ref|YP_004383952.1| 65 ANLLLKMERYEEALESFDRIIS 86
                                      89999*********98888776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                            TPR_10   2 AsslnNLanal.rqrgrydeAealleealai 31 
                                       A ++n+ a +l   +++ +eA+a le al+i
  gi|330507524|ref|YP_004383952.1|  92 AKAYNDRALVLsGGLNQDEEALASLEAALQI 122
                                       66899999999999***************97 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0031
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N +++l ++ ry+e+++ +++a++
  gi|330507524|ref|YP_004383952.1| 132 NKGMVLEKMERYNESLEAYRKAID 155
                                       6799******************96 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.31
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       +++l  ++r+de++a l++a++
  gi|330507524|ref|YP_004383952.1| 168 GHVLLIVQRFDESLASLDKAVE 189
                                       56777789************97 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.0014
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       n+ +++lr++ r +eA++ +++a++
  gi|330507524|ref|YP_004383952.1| 199 NDKGVVLRKLERNEEALDCFQRAIQ 223
                                       66699******************98 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.7   4.1e-05      0.03      17      70 ..      61     152 ..      40     163 .. 0.80
   2 ?    4.2   0.0      0.06        43      24      75 ..     171     225 ..     158     235 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.1e-05
                      SRP_TPR_like  17 kkfkvvaliklekyeeaLkllkkgs......................................alsedvrfEkaYvl 55 
                                         f++  l+k+e+yeeaL+  +                                         al+ +  + k  vl
  gi|330507524|ref|YP_004383952.1|  61 WSFRANLLLKMERYEEALESFDRIIsldqsnakayndralvlsgglnqdeealasleaalqidALNANAWYNKGMVL 137
                                       35799999**********99888766778888888899999999999999999988888899899999999999999 PP

                      SRP_TPR_like  56 Yklkkykkalkilkk 70 
                                        k+++y+++l+  +k
  gi|330507524|ref|YP_004383952.1| 138 EKMERYNESLEAYRK 152
                                       999999999887666 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.06
                      SRP_TPR_like  24 liklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkveaee 75 
                                       l+ +++++e+L  l+k+      + +   +k  vl kl++ ++al  ++++ + +
  gi|330507524|ref|YP_004383952.1| 171 LLIVQRFDESLASLDKAVefnPENAEAWNDKGVVLRKLERNEEALDCFQRAIQLD 225
                                       5667889999988888873333445667788889999999999998888776555 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.9     0.001      0.72      21      83 ..      41     103 ..      29     126 .. 0.71
   2 ?    2.7   1.6     0.065        46      18      67 ..     107     156 ..      87     167 .. 0.64
   3 !   11.0   0.1    0.0002      0.15      18      79 ..     175     236 ..     167     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHGG.G---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT. CS
                             NARP1  21 eeAlehLeekek.qivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakk 83 
                                         Al+ ++++ k +  D+ a+  ++a+lllk++r+eeA + + ++++  + n k y++   +++
  gi|330507524|ref|YP_004383952.1|  41 PLALDDIDQYLKiNQSDTWAW-SFRANLLLKMERYEEALESFDRIISLDQSNAKAYNDRALVLS 103
                                       567777777655134555555.69***********************99999988887666663 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.065
                                       THHHHHHHHHHHHGG.G---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             NARP1  18 gkleeAlehLeekek.qivDklavketkaelllkLgrkeeAeatyeaLler 67 
                                       ++ eeAl+ Le++ + + ++  a+  +k+ +l k++r++e+ ++y++ ++ 
  gi|330507524|ref|YP_004383952.1| 107 NQDEEALASLEAALQiDALNANAW-YNKGMVLEKMERYNESLEAYRKAIDL 156
                                       355777777777543033333333.46888888888888888888887764 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0002
                                       THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHH CS
                             NARP1  18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyegle 79 
                                       ++ +e+l+ L+++ +   ++ +  + k+ +l kL+r+eeA   +++ ++  p n+ Y e+l+
  gi|330507524|ref|YP_004383952.1| 175 QRFDESLASLDKAVEFNPENAEAWNDKGVVLRKLERNEEALDCFQRAIQLDPSNELYRENLN 236
                                       56789999999999999999999999*****************************9999987 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.57   4.1e+02      81     122 ..      43      84 ..      28      89 .. 0.65
   2 ?    1.1   0.0      0.67   4.8e+02      66      93 ..      62      89 ..      48     103 .. 0.69
   3 !    8.9   1.2    0.0027       1.9      74     124 ..     105     155 ..      86     163 .. 0.84
   4 !    9.2   0.0    0.0021       1.5      75     124 ..     174     223 ..     162     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  81 alaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       al++ ++ ++ +  + +++      l +++r +eALe ++r+
  gi|330507524|ref|YP_004383952.1|  43 ALDDIDQYLKINQSDTWAWSFRANLLLKMERYEEALESFDRI 84 
                                       555566666666666666666666677777888888877775 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.67
                                      HHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                              BTAD 66 ealaeaelrlGraeealaelealvaehP 93
                                        +a+++l+++r+eeal+  +++++++ 
  gi|330507524|ref|YP_004383952.1| 62 SFRANLLLKMERYEEALESFDRIISLDQ 89
                                      5566677777777777777777766665 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0027
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                        l++ eeala lea+++ + l+ +++      l +++r +e Le+Y+++ +
  gi|330507524|ref|YP_004383952.1| 105 GLNQDEEALASLEAALQIDALNANAWYNKGMVLEKMERYNESLEAYRKAID 155
                                       467899*****************************************9854 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0021
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       + r +e la l+++v+ +P + +++      l++++r++eAL  ++r+ +
  gi|330507524|ref|YP_004383952.1| 174 VQRFDESLASLDKAVEFNPENAEAWNDKGVVLRKLERNEEALDCFQRAIQ 223
                                       56888999**************************************9865 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.11        79      25      43 ..      72      92 ..      71     102 .. 0.75
   2 !    8.9   0.1    0.0021       1.5       8      33 ..     131     156 ..     125     156 .. 0.87
   3 ?    4.2   0.0     0.065        47      29      40 ..     213     225 ..     207     237 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.11
                               MIT 25 elYkealelLlqalk.e.kne 43
                                      e Y+eale +  +++   +n+
  gi|330507524|ref|YP_004383952.1| 72 ERYEEALESFDRIISlDqSNA 92
                                      789******999999544444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0021
                               MIT   8 vkkAveeDnagnyeeAlelYkealel 33 
                                        +k + +++ + y e le+Y++a++l
  gi|330507524|ref|YP_004383952.1| 131 YNKGMVLEKMERYNESLEAYRKAIDL 156
                                       57889999****************96 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.065
                               MIT  29 ealelLlqalk.e 40 
                                       eal+ ++ a++  
  gi|330507524|ref|YP_004383952.1| 213 EALDCFQRAIQlD 225
                                       4555555555532 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.4     0.006       4.3      58     128 ..      61     155 ..      51     161 .. 0.55
   2 ?    4.8   0.0     0.038        28      69     126 ..     175     221 ..     167     229 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHTT-HHHHHHHHHH........HHHHHHHH.....--TTSTHHHH.......HH.....HHHHHHHHH CS
                           DUF3856  58 haglsealaklgrydealesadk........alryfnrr.....GeleqdeGkl.......Wi.....aavfsrava 109
                                       ++  ++ l+k+ ry+eales d+        a  y + r     G l+qde  l        i     +a +++++ 
  gi|330507524|ref|YP_004383952.1|  61 WSFRANLLLKMERYEEALESFDRiisldqsnAKAYND-RalvlsGGLNQDEEALasleaalQIdalnaNAWYNKGMV 136
                                       5555666777777777777766422111111223333.324444667776643211111113311111345788888 PP

                                       HHHTT-HHHHHHHHHHHHH CS
                           DUF3856 110 leelGrkdealkafrmage 128
                                       le++ r++e+l+a+r+a +
  gi|330507524|ref|YP_004383952.1| 137 LEKMERYNESLEAYRKAID 155
                                       9999999999999988865 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.038
                                       T-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  69 grydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       +r+de+l s dka+++     e        W     +++v l +l r++eal+ f+ a
  gi|330507524|ref|YP_004383952.1| 175 QRFDESLASLDKAVEFNPENAE-------AW----NDKGVVLRKLERNEEALDCFQRA 221
                                       6777777777777654333333.......33....34666666666777777766665 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 ?   -1.1   0.1       1.9   1.4e+03      52      72 ..     110     130 ..      89     148 .. 0.82
   2 ?   -1.0   0.0       1.8   1.3e+03     114     134 ..     141     161 ..     137     189 .. 0.73
   3 !   12.1   0.0   0.00017      0.12      97     121 ..     212     236 ..     205     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHH-TT-HHHH CS
                       TOM20_plant  52 qdaiskleeallidPkkhdal 72 
                                       ++a++ le al id    +a 
  gi|330507524|ref|YP_004383952.1| 110 EEALASLEAALQIDALNANAW 130
                                       578888888888887776664 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHTHHHHHHHHH CS
                       TOM20_plant 114 dlyrkslelaakaPelhteih 134
                                       + y+ sle   ka +l  ++ 
  gi|330507524|ref|YP_004383952.1| 141 ERYNESLEAYRKAIDLDGDLD 161
                                       678889999999888766554 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHH-TT-HHHHHHHH CS
                       TOM20_plant  97 ekatqffqqavdedPdndlyrksle 121
                                       e a ++fq+a++ dP+n+lyr  l+
  gi|330507524|ref|YP_004383952.1| 212 EEALDCFQRAIQLDPSNELYRENLN 236
                                       7899*****************9986 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0067       4.8       8      54 ..      44      90 ..      40     101 .. 0.85
   2 ?    3.4   0.5      0.14     1e+02       3      44 ..     108     149 ..     106     168 .. 0.84
   3 !    9.2   0.2    0.0021       1.5       6      52 ..     179     225 ..     175     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0067
                            TPR_20  8 laeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54
                                      l+++++ l+ n +d  a    A++ll+ +ryeeAle + +i++ d++
  gi|330507524|ref|YP_004383952.1| 44 LDDIDQYLKINQSDTWAWSFRANLLLKMERYEEALESFDRIISLDQS 90
                                      567888888899999999999***************99999987765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.14
                            TPR_20   3 adapelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                       +d++ la+leaal+ +  + +a ++   +l + +ry e+le+
  gi|330507524|ref|YP_004383952.1| 108 QDEEALASLEAALQIDALNANAWYNKGMVLEKMERYNESLEA 149
                                       67788999***********99999999999999999999987 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0021
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrd 52 
                                       ++la+l++a++ np++ +a  d   +l + +r+eeAl+ + + ++ d
  gi|330507524|ref|YP_004383952.1| 179 ESLASLDKAVEFNPENAEAWNDKGVVLRKLERNEEALDCFQRAIQLD 225
                                       67999********************************9988887755 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      0.48   3.4e+02       1      13 [.      73      85 ..      73      91 .. 0.83
   2 ?    3.9   0.1     0.054        39      29      47 ..     130     148 ..     127     150 .. 0.85
   3 ?    4.5   0.1     0.037        27       1      14 [.     142     155 ..     142     157 .. 0.92
   4 ?    1.2   0.0      0.37   2.7e+02       1      15 [.     176     190 ..     176     195 .. 0.88
   5 ?   -0.8   0.0       1.7   1.2e+03       3      13 ..     212     222 ..     200     224 .. 0.56

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.48
                                      -HHHHHHHHHHHH CS
                          HTH_Bact  1 rYeeaLeqvnkAi 13
                                      rYeeaLe  ++ i
  gi|330507524|ref|YP_004383952.1| 73 RYEEALESFDRII 85
                                      7******999876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.054
                                       HHHHHHHHHHTT--HHHHH CS
                          HTH_Bact  29 yYqkgecleklgfseeeIk 47 
                                       +Y kg  lek++  +e+ +
  gi|330507524|ref|YP_004383952.1| 130 WYNKGMVLEKMERYNESLE 148
                                       6**********99888765 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.037
                                       -HHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAie 14 
                                       rY+e+Le  +kAi 
  gi|330507524|ref|YP_004383952.1| 142 RYNESLEAYRKAID 155
                                       7***********97 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.37
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       r++e+L   +kA+e 
  gi|330507524|ref|YP_004383952.1| 176 RFDESLASLDKAVEF 190
                                       689**********96 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHH CS
                          HTH_Bact   3 eeaLeqvnkAi 13 
                                       eeaL   ++Ai
  gi|330507524|ref|YP_004383952.1| 212 EEALDCFQRAI 222
                                       45555555555 PP

>> TraI_2B  DNA relaxase TraI 2B/2B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00063      0.45      12      35 ..     127     150 ..     121     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00063
                           TraI_2B  12 lrdtYreGmVlEdrsekketrery 35 
                                       +++ Y +GmVlE+ +  +e+ e y
  gi|330507524|ref|YP_004383952.1| 127 ANAWYNKGMVLEKMERYNESLEAY 150
                                       5678***********999998887 PP

>> FRD2  Bacteriophage FRD2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.4   9.9e+02      20      43 ..      77     100 ..      72     117 .. 0.86
   2 ?   -2.3   0.0       7.8   5.6e+03      29      59 ..     121     151 ..      99     158 .. 0.71
   3 ?    9.4   0.0    0.0018       1.3      20      62 ..     180     222 ..     168     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.4
                              FRD2  20 sldgfdyvteiicangeiynddgm 43 
                                       +l+ fd +  +  +n++ ynd ++
  gi|330507524|ref|YP_004383952.1|  77 ALESFDRIISLDQSNAKAYNDRAL 100
                                       6899999999999*******9765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.8
                              FRD2  29 eiicangeiynddgmgddyfelseeefycfr 59 
                                       +i + n++ + + gm  + +e  +e + ++r
  gi|330507524|ref|YP_004383952.1| 121 QIDALNANAWYNKGMVLEKMERYNESLEAYR 151
                                       5556667777777887777777777766666 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0018
                              FRD2  20 sldgfdyvteiicangeiynddgmgddyfelseeefycfreyk 62 
                                       sl  +d   e    n+e +nd g+    +e +ee + cf+   
  gi|330507524|ref|YP_004383952.1| 180 SLASLDKAVEFNPENAEAWNDKGVVLRKLERNEEALDCFQRAI 222
                                       788899999******************************8654 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 ?   -2.7   0.0       9.3   6.7e+03      15      30 ..      38      53 ..      35      56 .. 0.81
   2 ?    6.7   0.1      0.01       7.5      12      37 ..      69      94 ..      68     101 .. 0.90
   3 ?    1.5   0.3      0.43   3.1e+02      18      48 ..     110     140 ..     106     147 .. 0.77
   4 ?   -0.7   0.1       2.2   1.6e+03      13      25 ..     139     151 ..     137     158 .. 0.79
   5 ?    1.5   0.1      0.46   3.3e+02      15      37 ..     175     197 ..     174     211 .. 0.83
   6 ?    3.0   0.0      0.15     1e+02      13      35 ..     207     229 ..     202     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9.3
                                      T-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C 15 geYseArryvdalLei 30
                                      g Y  A+  +d+ L+i
  gi|330507524|ref|YP_004383952.1| 38 GSYPLALDDIDQYLKI 53
                                      7899999999999987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.01
                                      HHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C 12 yklgeYseArryvdalLeiEPenrQa 37
                                      +k+ +Y+eA++  d++++++ +n  a
  gi|330507524|ref|YP_004383952.1| 69 LKMERYEEALESFDRIISLDQSNAKA 94
                                      69****************99998765 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.43
                                       HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C  18 seArryvdalLeiEPenrQaqsLkeliedki 48 
                                       +eA+  ++a L+i+  n +a   k ++ +k+
  gi|330507524|ref|YP_004383952.1| 110 EEALASLEAALQIDALNANAWYNKGMVLEKM 140
                                       68999999*****999998865555555555 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.2
                                       HHT-HHHHHHHHH CS
                        Fis1_TPR_C  13 klgeYseArryvd 25 
                                       k+ +Y+e+++  +
  gi|330507524|ref|YP_004383952.1| 139 KMERYNESLEAYR 151
                                       8999999998765 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.46
                                       T-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenrQa 37 
                                       ++++e++  +d   e  Pen  a
  gi|330507524|ref|YP_004383952.1| 175 QRFDESLASLDKAVEFNPENAEA 197
                                       579999**************988 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.15
                                       HHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPenr 35 
                                       kl + +eA+ + ++ ++++P+n+
  gi|330507524|ref|YP_004383952.1| 207 KLERNEEALDCFQRAIQLDPSNE 229
                                       677779***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1626.16
//
Query:       gi|330507525|ref|YP_004383953.1|  [L=160]
Description: RDD domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-23   81.6   3.7    7.3e-23   81.3   3.7    1.1  1  RDD            RDD family
     0.0018   18.5   0.3        1.2    9.4   0.0    2.2  2  Glycophorin_A  Glycophorin A


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   3.7   8.1e-27   7.3e-23       2     140 ..      30     152 ..      29     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 8.1e-27
                               RDD   2 aslgrRllAfliDlvllliislllallivallnakasaneavagslllllllvlllvllvyqllllskkgqTlGkll 78 
                                        ++g Rl++++iD +++ +i + l  +++a        +  +  +  ++++++++++ ++y++ll+ +kgqT+Gk++
  gi|330507525|ref|YP_004383953.1|  30 QGIGIRLVSLVIDSIIFGLIFGALGNILGA--------GGMQGDMFPWYWGVLYFAIYIAYFTLLEGSKGQTVGKMI 98 
                                       68999*************************........7888999999999************************** PP

                               RDD  79 lglkvvdedgrklglaqaliRalllllllvlglslvlllllligflfvlf.srkrqalhDkla 140
                                       +++kvv+edg+++++ qa+ R++         l ++ +l+ +++ +++++ s+k+q+l D +a
  gi|330507525|ref|YP_004383953.1|  99 TKIKVVREDGSPIDMSQAFTRNI---------LRIIDGLFAYLIGAILIWrSDKQQRLGDSVA 152
                                       ***********************.........556655555555555555388889****988 PP

>> Glycophorin_A  Glycophorin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1   0.00064       5.8      28      76 ..       9      57 ..       3      59 .. 0.84
   2 !    9.4   0.0   0.00013       1.2      35      77 ..      98     138 ..      88     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00064
                                      XXXXXXXXXXXXXXXXX.XXXXSSSSSSS-TTHHHHHHHHHHHHHHHHH CS
                     Glycophorin_A 28 evseltirtevaaeqeetgereqlvhdFselvitliifgvmAgvigtil 76
                                      +v  ++++ e++++  e+ e + +      lvi  iifg + g +g il
  gi|330507525|ref|YP_004383953.1|  9 KVNIMAGQVELEVNGPEQMEYQGIGIRLVSLVIDSIIFGLIFGALGNIL 57
                                      566777888888888888888888889999****************998 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00013
                                       XXXXXXXXXX.XXXXSSSSSSS-TTHHHHHHHHHHHHHHHHHH CS
                     Glycophorin_A  35 rtevaaeqeetgereqlvhdFselvitliifgvmAgvigtill 77 
                                        t+++++ e+ g + ++ + F+   i  ii g  A +ig il+
  gi|330507525|ref|YP_004383953.1|  98 ITKIKVVRED-GSPIDMSQAFTR-NILRIIDGLFAYLIGAILI 138
                                       5778888888.**********87.6889*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1079.39
//
Query:       gi|330507526|ref|YP_004383954.1|  [L=387]
Description: glycosyl transferase, group 1 family protein [Methanosaeta concilii GP6]
Scores for complete 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-30  103.9   0.0    1.2e-29  103.1   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
    8.2e-28   97.5   0.4    1.8e-27   96.4   0.4    1.6  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.8e-23   83.4   0.0    3.6e-23   82.5   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
      1e-21   78.1   0.0    1.7e-21   77.4   0.0    1.4  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      5e-17   62.4   1.0    6.6e-08   32.5   0.0    2.2  2  Glyco_transf_5   Starch synthase catalytic domain
    7.3e-08   32.5   0.0    1.2e-07   31.9   0.0    1.4  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    3.5e-07   30.5   0.0    7.9e-07   29.4   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.024   14.1   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family


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 !  103.1   0.0   5.3e-33   1.2e-29       5     169 ..     199     358 ..     195     361 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 5.3e-33
                                       HHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECC CS
                   Glycos_transf_1   5 krkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgev 81 
                                       +++k+g+    +++l+ gr++ +Kg+dll++a++++ ++ +p+v +v++G+g ++ e +++a  l++ d ++flg+ 
  gi|330507526|ref|YP_004383954.1| 199 IKEKYGIHPLAPVVLFCGRMSVQKGPDLLVEAIPQVLRN-RPDVCFVFIGEGGMRSECEQKARYLGIADSCRFLGYT 274
                                       677888888899**************************9.************************************* PP

                                       HSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHS CS
                   Glycos_transf_1  82 sredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklled 158
                                       s  ++  l++++d++++ps++E+fG+v+lEA  a +pv+a++a     ++++ ++Gll     +e++a  i++++++
  gi|330507526|ref|YP_004383954.1| 275 SSAEKQMLINACDMMCVPSRNEPFGVVVLEAWDACKPVVATDA---VSIINNFQDGLLAYIQ-PESIAWCINRIISN 347
                                       ******************************************5...5799999999998887.************** PP

                                       HHHHHHHHHHH CS
                   Glycos_transf_1 159 eelrerlgena 169
                                       +++ ++l +++
  gi|330507526|ref|YP_004383954.1| 348 PKEMKHLARAG 358
                                       ***99999886 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.4   8.2e-31   1.8e-27       1     166 [.      16     185 ..      16     189 .. 0.72

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 8.2e-31
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev.......elvvrvprvplpllkrllrslaflrrlrrllkr 70 
                                       vGGv+ hv eL++aLarrGheV+++t+++d +++++         +v +++      ++ ++   a + r+ ++ + 
  gi|330507526|ref|YP_004383954.1|  16 VGGVAPHVSELSEALARRGHEVHIFTRRGDFESYDKIngvhyqrADVDDHGD---IVDQMNRMCDALYHRFGAVQQL 89 
                                       7***********************************6554433222222222...2222333333333333333333 PP

                    Glyco_transf_4  71 e.kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlk.plsrllralerrllrradrviavSeata 145
                                       + ++DvvH h+++++ +al +++  +++p+ lt+H+++  ++ ++  +   s  +   e++ +  a +vi++++ ++
  gi|330507526|ref|YP_004383954.1|  90 FgNFDVVHGHDWHPV-LALTRIKSDYHLPFLLTMHSTEW-GRNGNTFGyGISEEISHREWQGCYEAAKVIVTTRRMQ 164
                                       37************8.566777778*************4.3333222212233333346666*************** PP

                    Glyco_transf_4 146 delrerygvppekitVipnGv 166
                                       del++ y +p++ki +ipnG+
  gi|330507526|ref|YP_004383954.1| 165 DELMQIYSLPKDKIPIIPNGI 185
                                       ********************9 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 !   82.5   0.0   1.6e-26   3.6e-23       2     134 .]     210     347 ..     209     347 .. 0.86

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 1.6e-26
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaella 71 
                                       pv+lf+Gr+   +kg dll+ea+p+++++ + v +v++G+g  r +e+e++a+  g++++++f+G+   ++++ l++
  gi|330507526|ref|YP_004383954.1| 210 PVVLFCGRM-SVQKGPDLLVEAIPQVLRNrPdVCFVFIGEGGmR-SECEQKARylGIADSCRFLGYTssAEKQMLIN 284
                                       89*******.566**********888855336*******99966.59*9999889************8778****** PP

                                       H-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.T.TSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvggiaevv.g.engllvppgdpealaeailrLled 134
                                       a+d++++Ps  e fg+++lEa  a +pvVatd+     ++ + ++gll+   +pe++a  i r++++
  gi|330507526|ref|YP_004383954.1| 285 ACDMMCVPSrnEPFGVVVLEAWDACKPVVATDAVS---IInNfQDGLLAY-IQPESIAWCINRIISN 347
                                       *********999*******************9944...444348999986.4699999999998875 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 !   77.4   0.0   7.4e-25   1.7e-21       1     160 []      17     184 ..      17     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 7.4e-25
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaal.....ralrrllrqrre 72 
                                       gG++ +v el++aLa+rGheV+++t++++ +++    +gv++ r +v  +++ +  + ++     +++ ++ +q   
  gi|330507526|ref|YP_004383954.1|  17 GGVAPHVSELSEALARRGHEVHIFTRRGDFESY-DKINGVHYQRADVDDHGDIVDQMNRMcdalyHRFGAV-QQLFG 91 
                                       8************************98877777.6899**********99975554433322223444444.4667* PP

                   Glyco_trans_4_4  73 rpdvvhahsptaglaarlarrrrgiplvvtlhg.lllrrgsgavrrlyral...errllrradavlvvseaeaeelr 145
                                       ++dvvh h+++  la  +++   ++p+++t+h+  ++r g+++ + +  ++   e   +  a+ v+v+++ + +el 
  gi|330507526|ref|YP_004383954.1|  92 NFDVVHGHDWHPVLALTRIKSDYHLPFLLTMHStEWGRNGNTFGYGISEEIshrEWQGCYEAAKVIVTTRRMQDELM 168
                                       **********9999999999789*********73557778999999998885446678888**************** PP

                   Glyco_trans_4_4 146 a.lgvpadrvvvvpng 160
                                       + + +p d++ ++png
  gi|330507526|ref|YP_004383954.1| 169 QiYSLPKDKIPIIPNG 184
                                       *999***********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 !   32.5   0.0     3e-11   6.6e-08       1      45 [.       2      46 ..       2      60 .. 0.87
   2 !   28.7   0.4   4.3e-10   9.6e-07      98     180 ..      53     133 ..      45     171 .. 0.68

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3e-11
                    Glyco_transf_5  1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPryga 45
                                      +i ++++E    +k+GG+a +v++L++aLa++gh+v++++ r ++
  gi|330507526|ref|YP_004383954.1|  2 RIGMLSWESLYSIKVGGVAPHVSELSEALARRGHEVHIFTRRGDF 46
                                      688************************************987644 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 4.3e-10
                    Glyco_transf_5  98 eg.lYgdk.gedyednaerfalfsraalellekl..gwk.pdvihahDWhtalvpallkelykerglfkkiktvfti 169
                                       +g  Y+ +   d+ d  +++  ++ a  +    +   ++ +dv+h hDWh +l+   +k+ y       + ++++t 
  gi|330507526|ref|YP_004383954.1|  53 NGvHYQRAdVDDHGDIVDQMNRMCDALYHRFGAVqqLFGnFDVVHGHDWHPVLALTRIKSDY-------HLPFLLTM 122
                                       5556666555666666677777777766655554333325**************99999998.......49****** PP

                    Glyco_transf_5 170 HNlayqgrfpk 180
                                       H++++ ++ + 
  gi|330507526|ref|YP_004383954.1| 123 HSTEWGRNGNT 133
                                       *****998872 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   5.3e-11   1.2e-07      11     110 ..      21     126 ..      11     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 5.3e-11
                   Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkg.pleylk.a.......f.klkklikkikPDv 77 
                                       +h+++l ++La rg+eVh++t++++ + +++ +g+h +r +vd +g  +  ++ +       f ++ +l+   ++Dv
  gi|330507526|ref|YP_004383954.1|  21 PHVSELSEALARRGHEVHIFTRRGDFESYDKINGVHYQRADVDDHGdIVDQMNrMcdalyhrFgAVQQLFG--NFDV 95 
                                       79********************9999*****************6664333333343333333335555554..69** PP

                   Glyco_trans_4_2  78 vhahyakpygllgslaarlsgvipvvlsvwGld 110
                                       vh h   p+  l ++        p++l+++ + 
  gi|330507526|ref|YP_004383954.1|  96 VHGHDWHPVLALTRIK--SDYHLPFLLTMHSTE 126
                                       *****99987777773..333479999999775 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   3.5e-10   7.9e-07       4      89 ..     291     374 ..     282     377 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.5e-10
                   Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlae 80 
                                        psr+e + ++++Ea  +  +++++da ++ + f++g  ++ +  +e++a  i++ ++np+e + +a+a+  r+++e
  gi|330507526|ref|YP_004383954.1| 291 VPSRNEPFGVVVLEAWDACKPVVATDAVSIINNFQDG--LLAYIQPESIAWCINRIISNPKEMKHLARAGWTRIESE 365
                                       49999***********999999999998888888888..77777********************************* PP

                   Glyco_trans_1_2  81 htydhraeq 89 
                                       +++dh ae 
  gi|330507526|ref|YP_004383954.1| 366 FSWDHIAES 374
                                       ******985 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.1e-05     0.024      12      74 ..      24      86 ..      23      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE-.-S- CS
                         Epimerase 12 salvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihl.Aav 74
                                      s l +al+++g+ev+ ++r+ + +   +++ ++  ++d+ d+ ++ + +++ ++da +h  +av
  gi|330507526|ref|YP_004383954.1| 24 SELSEALARRGHEVHIFTRRGDFESYDKINGVHYQRADVDDHGDIVDQMNR-MCDALYHRfGAV 86
                                      67899***************999999999999***************9997.9******74544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2809.63
//
Query:       gi|330507527|ref|YP_004383955.1|  [L=327]
Description: galactose-1-phosphate uridylyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-14   53.6   0.0    1.1e-13   50.8   0.0    2.2  2  DUF4921          Domain of unknown function (DUF4921)
    2.8e-10   40.9   0.0    3.7e-09   37.3   0.0    2.2  1  GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-
      6e-08   32.6   0.0    9.9e-08   31.9   0.0    1.4  1  GalP_UDP_tr_C    Galactose-1-phosphate uridyl transferase, C-
      1e-07   31.5   1.1    7.3e-07   28.7   0.1    2.4  3  DUF4931          Domain of unknown function (DUF4931)
    2.2e-06   28.1   0.1    0.00026   21.4   0.0    2.7  2  DcpS_C           Scavenger mRNA decapping enzyme C-term bindi
    0.00076   20.2   0.0      0.046   14.5   0.0    2.2  2  HIT              HIT domain


Domain annotation for each model (and alignments):
>> DUF4921  Domain of unknown function (DUF4921)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.19   5.6e+02      44      62 ..      37      55 ..      18      67 .. 0.80
   2 !   50.8   0.0   3.7e-17   1.1e-13     204     387 ..     126     312 ..     118     321 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.19
                           DUF4921 44 eeacafcedrkletpPeka 62
                                      e+ c fc  +  +tpP  a
  gi|330507527|ref|YP_004383955.1| 37 EKDCPFCPGHEDRTPPTIA 55
                                      678*************765 PP

  == domain 2  score: 50.8 bits;  conditional E-value: 3.7e-17
                           DUF4921 204 iaftvdalkdl...ykrnryvrYvavfqnWLkpaGasfdhlhkqlvaiDergvqaeaeiarlrenPnl.ynelavdy 276
                                       +++ v+a +d    y++ + v+Y+++f+nW k +Gas+ h h ql+++     q++ e + +++     y ++ vd 
  gi|330507527|ref|YP_004383955.1| 126 LEMLVSAYTDRyrrYSTHEDVKYITIFKNWGKESGASLSHSHSQLITLPFLPPQMKREEEAISRSSFCpYCNI-VDR 201
                                       44555555555011667899*******************************9999998888866655416665.788 PP

                           DUF4921 277 aakhnlviaendhavafagfGhrypt.levysksatkePweqseeevravsdlvhalha...aagadvpcneeWhhr 349
                                        ++   ++aen+h + fa f    p    +  k +  +  +  +ee ++++ ++  +     ++ +d p n      
  gi|330507527|ref|YP_004383955.1| 202 ESASCRLVAENNHWILFAPFYSLMPYeTWILPKRHLGNLADLRDEEQKSLASMLAEILRilySTLDDPPYNLMI--- 275
                                       88888889************988774145778888888999999999999998865543011344444444433... PP

                           DUF4921 350 pidvdvpmpwrilikwrvstlaGfeggtkiylntisPa 387
                                         ++     + i i+  vs +aGfe +  iy+n + P+
  gi|330507527|ref|YP_004383955.1| 276 -FQLPKEYHFNIRIQPIVSRIAGFERSSGIYVNPVPPE 312
                                       .3444445677888889******************997 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   1.3e-12   3.7e-09      19     184 .]       9     177 ..       1     177 [. 0.70

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.3e-12
                   GalP_UDP_transf  19 ltgewvlvsphrtkrpwqgqqekiskdtlpekDklkcyLcPgnsrangefnpky..k.............stfvftn 80 
                                       +++e+ +++++r+krp         ++++p  D+  c++cPg +  +  + + y  +             +  vf n
  gi|330507527|ref|YP_004383955.1|   9 FLEEYCIIAAERNKRPSDFLV----AKAVPG-DEKDCPFCPGHEDRTPPTIAAYtdDgillqdetgsdlwQIRVFLN 80 
                                       566666677777777662222....222333.335688888877665555555532200000000000004455555 PP

                   GalP_UDP_transf  81 dFpalsedsnyikteaiaknilfkaepayGrceviifsskheltladlspkdikavvaaWqektaelkakeypkcvl 157
                                        +p + ++ + ++        ++ + p +G  evi+ s +h++   d  +k+++  v+a+++++   + +e +k++ 
  gi|330507527|ref|YP_004383955.1|  81 AYPTMIPRPEPPA-------AEWISLPGQGYHEVIVDSRDHRKNPRDFGKKHLEMLVSAYTDRYRRYSTHEDVKYIT 150
                                       5555555544444.......48******************************************************* PP

                   GalP_UDP_transf 158 ifENkGaamgvsnphPHgqiwaeehlp 184
                                       if N G + g+s+ h H+q+ + ++lp
  gi|330507527|ref|YP_004383955.1| 151 IFKNWGKESGASLSHSHSQLITLPFLP 177
                                       ********************9999987 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 !   31.9   0.0   3.3e-11   9.9e-08       5      84 ..     152     260 ..     135     316 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3.3e-11
                                       HHHHHHHH.SS-HHHHHHH...............................HHHHH-TTEEEE-SSEEEE--TT--ST CS
                     GalP_UDP_tr_C   5 fekYfagsngsillhdyvq...............................melaekervvelkdsflavvpylakWP 50 
                                       f+++ ++s g+ l+h + q                               +e a   r+v ++++++  +p++   P
  gi|330507527|ref|YP_004383955.1| 152 FKNWGKES-GASLSHSHSQlitlpflppqmkreeeaisrssfcpycnivdRESA-SCRLVAENNHWILFAPFYSLMP 226
                                       55666666.888888888888888888888888888888888888777544444.458999999************* PP

                                       T-EEEEESS--SSGGG--HHHHHHHHHHHHHHHH CS
                     GalP_UDP_tr_C  51 fevlllrkaevkslaeladeekedlaailkklar 84 
                                       +e+ +l+k++  +la+l dee++ la++l +++r
  gi|330507527|ref|YP_004383955.1| 227 YETWILPKRHLGNLADLRDEEQKSLASMLAEILR 260
                                       ***************************9998876 PP

>> DUF4931  Domain of unknown function (DUF4931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.41   1.2e+03      15      24 ..      35      44 ..      30      66 .. 0.74
   2 !   28.7   0.1   2.5e-10   7.3e-07      53     122 ..     105     174 ..     101     187 .. 0.93
   3 ?    0.3   0.0      0.12   3.4e+02       8      40 ..     181     217 ..     175     228 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.41
                           DUF4931 15 nketacPfcd 24
                                        e+ cPfc 
  gi|330507527|ref|YP_004383955.1| 35 GDEKDCPFCP 44
                                      56889****5 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 2.5e-10
                           DUF4931  53 qtvlietdeceedistyseehlrellrfgvkhwlelekseeyksvllfknhGPlsGGsikhahmqivGlk 122
                                         v++++ + +++  ++ + hl+ l++   +++     +e+ k + +fkn+G  sG s+ h+h q++ l 
  gi|330507527|ref|YP_004383955.1| 105 HEVIVDSRDHRKNPRDFGKKHLEMLVSAYTDRYRRYSTHEDVKYITIFKNWGKESGASLSHSHSQLITLP 174
                                       5699**************************************************************9885 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.12
                           DUF4931   8 kkPesirnketacPfc...dreklt.dildeegslil 40 
                                       k+ e+ + +++ cP+c   dre+ +  +++e+++ il
  gi|330507527|ref|YP_004383955.1| 181 KREEEAISRSSFCPYCnivDRESAScRLVAENNHWIL 217
                                       556677889999****444466554245555555555 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 ?    3.7   0.1     0.028        83      35      65 ..     104     135 ..      97     183 .. 0.63
   2 !   21.4   0.0   8.8e-08   0.00026       2      99 ..     193     288 ..     192     301 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.028
                                       EEEEEEESS.---SGGG--TTTTTHHHHHHHH CS
                            DcpS_C  35 lhllvipkr.dikslrdLtkehlpllkemrek 65 
                                       +h +++  r + k+ rd+ k+hl++l + +++
  gi|330507527|ref|YP_004383955.1| 104 YHEVIVDSRdHRKNPRDFGKKHLEMLVSAYTD 135
                                       56666655679999999999999998766554 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 8.8e-08
                                       -HHHHHHTTSS.-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T- CS
                            DcpS_C   2 wvfnilakgke.pervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynev 77 
                                       + +++++++++ + r+v e+++++++   +   ++   ++pkr++ +l dL++e+ + l++m  ++  ++ +   ++
  gi|330507527|ref|YP_004383955.1| 193 CPYCNIVDRESaSCRLVAENNHWILFAPFYSLMPYETWILPKRHLGNLADLRDEEQKSLASMLAEILRILYS---TL 266
                                       7799999999988999**************************************************999955...44 PP

                                       EEEEE--SCCCT--S-S--EEE CS
                            DcpS_C  78 daeelrvgvhyqPsvyhlHlHv 99 
                                       d    ++ +   P+ yh+ + +
  gi|330507527|ref|YP_004383955.1| 267 DDPPYNLMIFQLPKEYHFNIRI 288
                                       6666666666777777777655 PP

>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.04   1.2e+02      45      93 ..     123     171 ..     102     175 .. 0.71
   2 !   14.5   0.0   1.5e-05     0.046       5      75 ..     205     275 ..     201     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSSS-EEEEE CS
                               HIT  45 eeelakllsavkkvakalqkkfknkglrvvinngahagqsvahlHiHvi 93 
                                       ++ l +l+sa +   +   ++   k +++++n g+++g s  h H  +i
  gi|330507527|ref|YP_004383955.1| 123 KKHLEMLVSAYTDRYRRYSTHEDVKYITIFKNWGKESGASLSHSHSQLI 171
                                       5555555555555555555556678899*****************7555 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.5e-05
                                       -CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEE CS
                               HIT   5 pstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvi 75 
                                        +++v e+++ ++f    + +p  + ++pk+hl +l dl++ee++ l s+  ++ + l  ++    ++++i
  gi|330507527|ref|YP_004383955.1| 205 SCRLVAENNHWILFAPFYSLMPYETWILPKRHLGNLADLRDEEQKSLASMLAEILRILYSTLDDPPYNLMI 275
                                       67889999999999999999**********************************99888877766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2180.12
//
Query:       gi|330507528|ref|YP_004383956.1|  [L=415]
Description: glycosyl transferase, group 1 family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-31  109.7   0.0      4e-31  107.9   0.0    1.8  2  Glycos_transf_1  Glycosyl transferases group 1
    2.9e-24   86.0   0.0    1.1e-23   84.1   0.0    2.0  2  Glyco_transf_4   Glycosyltransferase Family 4
    4.9e-22   79.1   0.0    8.7e-22   78.3   0.0    1.4  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    2.3e-21   76.6   0.1    3.8e-21   75.9   0.1    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.4e-11   44.6   0.0    9.2e-11   41.9   0.0    2.2  1  Glyco_transf_5   Starch synthase catalytic domain
    7.1e-07   29.5   0.0    1.4e-06   28.6   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00023   21.2   0.0    0.00038   20.5   0.0    1.4  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
       0.22   10.0   0.0       0.32    9.5   0.0    1.1  1  Glycogen_syn     Glycogen synthase


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.75   1.7e+03      13      39 ..      70      96 ..      66     105 .. 0.85
   2 !  107.9   0.0   1.8e-34     4e-31       6     172 .]     214     383 ..     212     383 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.75
                                      TT-EEEEEESS-TTTTTHHHHHHHHHC CS
                   Glycos_transf_1 13 ekkkiilsvgrlekeKgvdllikafal 39
                                      ++ +i+ls   l+  +g+d+l+ +f  
  gi|330507528|ref|YP_004383956.1| 70 DGMEIFLSPQTLRWGQGLDYLLNLFSY 96
                                      6678999***************99985 PP

  == domain 2  score: 107.9 bits;  conditional E-value: 1.8e-34
                                       HHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH CS
                   Glycos_transf_1   6 rkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevs 82 
                                       r+++g++e++ +il+vgrle++Kg+  l  a+++++ +  ++vkl++ G g+     k +ae  ++   + ++ +v+
  gi|330507528|ref|YP_004383956.1| 214 RERYGFDEDDIVILFVGRLEPVKGIRELFSALPSVQSE-YNRVKLLVLGVGSLDGWAKVEAERQGN--ITLVTDFVD 287
                                       78899****************************99876.**********77777777777666655..899****** PP

                                       SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET..TTTHCHHCHTTT....SEEEE-TT-HHHHHHHHH CS
                   Glycos_transf_1  83 redleellknadifvlpsisEgfGivllEAmaaglpviasn..aggpaevvkdge....tGllvkpnnaealaeair 153
                                        e++   +  ad+ v+ps +E+fGiv+lEA a g+++++ +  ++g+ae+vk+      tG++v + ++++la +i+
  gi|330507528|ref|YP_004383956.1| 288 AEEKRLHYALADLCVFPSLYEPFGIVALEAAAMGKAAVVGAagTSGLAEIVKNPAedepTGVHVNARDPADLAWGIN 364
                                       ************************************999987889********9999******************** PP

                                       HHHHSHHHHHHHHHHHHHH CS
                   Glycos_transf_1 154 klledeelrerlgenarkr 172
                                        +led+e+   +g+narkr
  gi|330507528|ref|YP_004383956.1| 365 LALEDKERLLSWGKNARKR 383
                                       *****************97 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.0   4.9e-27   1.1e-23       1     169 [.      18     198 ..      18     199 .. 0.82
   2 ?   -1.8   0.0       1.2   2.7e+03     148     161 ..     213     226 ..     210     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 4.9e-27
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev..................elvvrvprvplpllkrllrsla 59 
                                       +GG ++++ +++r L ++G +Vtv++ g+++ ++ e                   e + ++   ++    ++l++l 
  gi|330507528|ref|YP_004383956.1|  18 YGGLGVYADNISRSLVALGQKVTVFSWGSKESPRHEMlvgvdvfremplamrdgmEIFLSPQTLRWGQGLDYLLNLF 94 
                                       6************************8777777777778899999999999988875555555555555555555555 PP

                    Glyco_transf_4  60 flrrl.rrllkre.kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrra 134
                                       ++ +l   +lk+e ++D++ +h++ al  +  a+rr  g pl+++vHgl+      +r+++ ++ + ale + l  a
  gi|330507528|ref|YP_004383956.1|  95 SYNQLaLDHLKEEdRFDLLVSHDWLALPGG-MAARR-EGTPLIYHVHGLE-----TGRSSNPNPQIVALEHKGLEVA 164
                                       55554157888889**********998555.55555.8************.....57777777888889******** PP

                    Glyco_transf_4 135 drviavSeatadelrerygvppekitVipnGvDle 169
                                       d vi+vSea+++el+   g++++ki+V ++GvD e
  gi|330507528|ref|YP_004383956.1| 165 DLVITVSEAMKRELAG-QGISEDKIRVCYHGVDCE 198
                                       ****************.****************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                    Glyco_transf_4 148 lrerygvppekitV 161
                                       lreryg+++++i++
  gi|330507528|ref|YP_004383956.1| 213 LRERYGFDEDDIVI 226
                                       899*******9986 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 !   78.3   0.0   3.9e-25   8.7e-22       1     157 [.      19     191 ..      19     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 3.9e-25
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhr.lpvprrps.....pladlaalral........ 63 
                                       gG g+y+ +++r+L+a+G  Vtv+  +  +++++++  gv v r +p+  r +      + +l++ ++l        
  gi|330507528|ref|YP_004383956.1|  19 GGLGVYADNISRSLVALGQKVTVFSWGSKESPRHEMLVGVDVFReMPLAMRDGmeiflSPQTLRWGQGLdyllnlfs 95 
                                       8************************8877777766666666654245443332222222222222222222222233 PP

                   Glyco_trans_4_4  64 .rrll...rqrrerpdvvhahsptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvv 136
                                         +l      ++ r+d++++h+++a + +++ar r g+pl++++hgl++ r s + ++++ ale+  l  ad+v++v
  gi|330507528|ref|YP_004383956.1|  96 yNQLAldhLKEEDRFDLLVSHDWLALPGGMAAR-REGTPLIYHVHGLETGRSSNPNPQIV-ALEHKGLEVADLVITV 170
                                       34433465579**************999*****.99***********9998899998888.9*************** PP

                   Glyco_trans_4_4 137 seaeaeelralgvpadrvvvv 157
                                       sea+ +el+ +g+  d+++v 
  gi|330507528|ref|YP_004383956.1| 171 SEAMKRELAGQGISEDKIRVC 191
                                       *******************96 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.1   1.7e-24   3.8e-21       3     134 .]     225     369 ..     223     369 .. 0.84

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 1.7e-24
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---....HHHHHHHTT-T.TEEEE---..THHHHHHHH- CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rp.eeleelaagleerveftGfv..edlaellaaa 73 
                                       vilfvGrl e+vkg++ l  a+p ++++ + v+l++ G g+ +  +++e++ +g  +   +t fv  e+++ ++a a
  gi|330507528|ref|YP_004383956.1| 225 VILFVGRL-EPVKGIRELFSALPSVQSEyNrVKLLVLGVGSlDGwAKVEAERQG--NITLVTDFVdaEEKRLHYALA 298
                                       89******.889**************88757*******8875334567654443..4488999999888******** PP

                                       SEEEE--..---SHHHHHHHHTT-EEEE-TGG..GTTT--......TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  74 dvfvaPs..egfglkllEamaaglpvVatdvg..giaevv......gengllvppgdpealaeailrLled 134
                                       d++v+Ps  e fg+++lEa+a+g++ V+ ++g  g+ae+v      + +g+ v+++dp++la  i   led
  gi|330507528|ref|YP_004383956.1| 299 DLCVFPSlyEPFGIVALEAAAMGKAAVVGAAGtsGLAEIVknpaedEPTGVHVNARDPADLAWGINLALED 369
                                       ***************************998854589****9765433689************999877776 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 !   41.9   0.0   4.1e-14   9.2e-11       1     230 [.       5     179 ..       5     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 4.1e-14
                    Glyco_transf_5   1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleevaelskaaedevevevekvkva 77 
                                       +i ++++E++p    GGL+  ++ +++ L +lg++v+v++ + ++ ++++     ++                v+v+
  gi|330507528|ref|YP_004383956.1|   5 RIAYFSTEYPP-LVYGGLGVYADNISRSLVALGQKVTVFSWGSKESPRHE----MLVG---------------VDVF 61 
                                       799********.99**************************9994444432....1111...............1112 PP

                    Glyco_transf_5  78 klkk....dgvdvyfldnpeffdreglYgdkgedyednaerfalfsraalelleklgwkpdvihahDWhtalvpall 150
                                       +       dg+++++  +     r   +   g++ ++  + f+ +++ al+ l++ + ++d+++ hDW +   ++ +
  gi|330507528|ref|YP_004383956.1|  62 REMPlamrDGMEIFLSPQTL---R---W---GQGLDYLLNLFS-YNQLALDHLKE-EDRFDLLVSHDWLALPGGMAA 127
                                       21111222577766533322...2...3...345555566666.89999******.889***********9999999 PP

                    Glyco_transf_5 151 kelykerglfkkiktvftiHNlayqgrfpkdelaalglpaedfekldglefygkvnflk.agivyadavttVSptya 226
                                       +           +++++++H l++ ++ ++++                     ++  l+  g+  ad v+tVS+ ++
  gi|330507528|ref|YP_004383956.1| 128 RREG--------TPLIYHVHGLETGRSSNPNP---------------------QIVALEhKGLEVADLVITVSEAMK 175
                                       9977........9************9988543.....................55555559**************** PP

                    Glyco_transf_5 227 kEil 230
                                       +E++
  gi|330507528|ref|YP_004383956.1| 176 RELA 179
                                       **97 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   6.1e-10   1.4e-06       3      91 ..     302     398 ..     300     399 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 6.1e-10
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltdda..egleelftpgk....evilfe..dleelaekiryllanpeerraiae 71 
                                       ++ps +e +  + +Eaaa+G  a++ +a  +gl+e++++      +++ +   d+++la  i+ +l++ e+  + ++
  gi|330507528|ref|YP_004383956.1| 302 VFPSLYEPFGIVALEAAAMGKAAVVGAAgtSGLAEIVKNPAedepTGVHVNarDPADLAWGINLALEDKERLLSWGK 378
                                       678999999*****************88********99888787766666668************************ PP

                   Glyco_trans_1_2  72 aarervlaehtydhraeqll 91 
                                       +ar+r++++++++++ae  l
  gi|330507528|ref|YP_004383956.1| 379 NARKRAQTNFSWQKAAESTL 398
                                       ***************99765 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 !   20.5   0.0   1.7e-07   0.00038      58     138 ..      91     170 ..      27     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.7e-07
                   Glyco_trans_4_2  58 leylka..fklkklikkikPDvvhahyakpygllgslaarlsgvipvvlsvwGldvlkfpkksklkklllklalkka 132
                                       l+++++  ++l  l +++ +D++  h  + ++l g++aar+ g  p+++ v+Gl + ++ ++++   +l++  l+ a
  gi|330507528|ref|YP_004383956.1|  91 LNLFSYnqLALDHLKEEDRFDLLVSHD-W-LALPGGMAARREG-TPLIYHVHGLETGRSSNPNPQIVALEHKGLEVA 164
                                       55554322467889999******9999.4.5799*********.************777777777888999999999 PP

                   Glyco_trans_4_2 133 tkvist 138
                                       ++vi+ 
  gi|330507528|ref|YP_004383956.1| 165 DLVITV 170
                                       999975 PP

>> Glycogen_syn  Glycogen synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00014      0.32     470     508 ..     299     339 ..     293     356 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00014
                                       SEEE---SSBSS-HHHHHHHHTT--EEEET..TBHHHHHHH CS
                      Glycogen_syn 470 hlGvfpsyyepwGytpaectvmGipsvttn..lsGfGcfme 508
                                        l vfps yep+G    e + mG  +v      sG+   ++
  gi|330507528|ref|YP_004383956.1| 299 DLCVFPSLYEPFGIVALEAAAMGKAAVVGAagTSGLAEIVK 339
                                       689********************998864311455555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3004.20
//
Query:       gi|330507529|ref|YP_004383957.1|  [L=594]
Description: hypothetical protein MCON_1486 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-17   63.3   0.0    1.3e-07   30.6   0.0    2.9  2  Glycogen_syn     Glycogen synthase
    6.9e-07   29.4   0.0    1.3e-06   28.5   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    0.00062   19.4   0.0     0.0042   16.6   0.0    2.3  2  Glycos_transf_1  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.034   14.6   0.0        0.2   12.1   0.0    2.3  3  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 !   28.1   0.0   1.7e-10   7.5e-07       4     337 ..      14     401 ..      11     408 .. 0.71
   2 !   30.6   0.0   2.9e-11   1.3e-07     441     550 ..     451     561 ..     432     591 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.7e-10
                                       TTTTS-SSCHHHHHHHHHH.....HHHHHHGGGE..EEEEE--T......TGGGGTEEE----SHH.....HHHHHH CS
                      Glycogen_syn   4 wevankvGGiytvlkskak.....vtteelGdny..tllGplke......qkarteveeleaenea.....lkkalk 62 
                                         v+nk+GGi+ v+ + a+     v+  el  ++  +++Gp         ++ r +v ++ a n+      l  +l 
  gi|330507529|ref|YP_004383957.1|  14 GPVSNKMGGIWNVVDAEATtlarlVAKGELDSEFriLVVGPNYPtagsdwNTGRNRVTDISALNRLdmgeeLALTLA 90 
                                       568999999999999988722222344555555421567885321111112334455555544433455559999** PP

                                       HHGGGT--EEEEEESSTT--E.EEEE-GGGGSTTHHHHH...........HHHHHHH----.....-TT-HHHHHHH CS
                      Glycogen_syn  63 slrekGvkvlyGrwlieGapk.vilfdldsaavkldewk...........aelwekvkigi.....peedretndai 122
                                        l++ G++ ++G+ + e  p   +lf+++  +  l +wk           +e ++  ++ +      ++  e n+ +
  gi|330507529|ref|YP_004383957.1|  91 ELNSLGMESVTGQRVEESVPIgYVLFNTNYYQSRLVRWKdremtlnnaikTEAFDLLGLDSmrfekEHYGWEYNHYL 167
                                       **************999999647999999888888877632222111111455665555541111145556789999 PP

                                       HHHHHHHHHHHHHHCT--..................--EEEEEEETGGGHHHHHHHHHTT..-SEEEEEEESS-HHH CS
                      Glycogen_syn 123 ilGflvalflkefrelee..................kkavvahfhewlaGvgliltrkrk..ldvatvftthatllG 179
                                        l + v+++++ + ++ e                   ++v a +h    G+    +r  k  ++v t+ t hat+ G
  gi|330507529|ref|YP_004383957.1| 168 NLSYAVSELVRILAQSPEestkkyadkavvefarsvMPRVRASLHCHEFGIFYAAARLEKlgIPVRTLCTFHATVPG 244
                                       999999998887776655667889999999999988899999999999999999988887335789*********** PP

                                       HHHHHTT---TTSTTS--HHHHHHHTT-HHHHHHHHHHHHHSSEEEESSHHHHHHHHHHSS---SEE----B-GGGT CS
                      Glycogen_syn 180 rylcagavdfynnldkfdvdkeaGkrqiyhrycleraaahtadvfttvseitaleaehllkrkpdvvlpnGlnvkkf 256
                                       r   ag    y  l+k   ++   + +    +    a a+ ad  t v + t  ea  l+ r   vv+ nG++v+  
  gi|330507529|ref|YP_004383957.1| 245 RT--AG----YRSLEKIRKNDSKMEPGTPLGFAALEALARYADGVTFVGDSTMKEAM-LFYRMKGVVIRNGIDVRV- 313
                                       *5..33....555555554444444455556666679999************99996.5667778999*****974. PP

                                       --TTTHHHHHHHHHHHHHHHHHHHTTT---S...-GGGEEEEEEESSS-TTTTTHHHHHHHHHHHHHHHHC---... CS
                      Glycogen_syn 257 salhefqnlhalkkekindfvrGhfyGhldf...dldktlyffiaGryefsnkGadifieslarlnyllkveks... 327
                                       + +    n +   +++i+df+   +y   +    + ++ + +f   r e +nkG   ++++l   ++ll+++     
  gi|330507529|ref|YP_004383957.1| 314 DRID--WNKKERCRARIQDFIINNLYKNCEGscpERENIIPVFSISRIEIENKGYPQLLDALVLQDHLLRHRMMgqr 388
                                       4443..4888999*************988752337899************************999999987543334 PP

                                       ...T-EEEEEEE- CS
                      Glycogen_syn 328 ...kktvvaflil 337
                                          ++ vv+fli 
  gi|330507529|ref|YP_004383957.1| 389 hadQTRVVCFLIA 401
                                       4437779999996 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 2.9e-11
                                       SEEEEEE-S---TTSSSS---HHHHHHH-SEEE---SSBSS-HHHHHHHHTT--EEEETTBHHHHHHHHH-T.TGGG CS
                      Glycogen_syn 441 rvkvvfhpeflsstspllgldyeefvrGchlGvfpsyyepwGytpaectvmGipsvttnlsGfGcfmeelie.dakd 516
                                        v  v++p++l  ++  lg+  +e + Gc  G+fps yep+  t  e    G ps+ +  +Gf   +++  +  +  
  gi|330507529|ref|YP_004383957.1| 451 SVAAVLYPQWLGPNDGGLGMRTDEVMAGCVAGIFPSQYEPFLLTALEAGREGTPSIVSRSAGFSDALKKVEHrVPGL 527
                                       47889**********************************************************98887654424566 PP

                                       GTEEEE--SSS-HHHHHHHHHHHHHHHHT--HHH CS
                      Glycogen_syn 517 yGiyivdrrfkslddsveqlaqflyefvkksrrq 550
                                        G+ +vd     ++++v + a  l  f++     
  gi|330507529|ref|YP_004383957.1| 528 GGVVVVDNIELQPQETVMDYALALDYFSRTYLED 561
                                       7899999999999999999988888887765555 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   2.9e-10   1.3e-06      76     168 ..     211     311 ..     196     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.9e-10
                    Glyco_transf_4  76 vHahspaalgaallalrrrlgiplVltvHglye...........krllkarlkplsrllralerrllrradrviavS 141
                                       +H+h ++ ++aa++  ++   +++ +t+H + +            r   ++  p+++l +a ++ l+r ad v+ v 
  gi|330507529|ref|YP_004383957.1| 211 LHCHEFGIFYAAARLEKLGIPVRTLCTFHATVPgrtagyrslekIRKNDSKMEPGTPLGFAALEALARYADGVTFVG 287
                                       5999977765554444435556669*************999987667777778************************ PP

                    Glyco_transf_4 142 eatadelrerygvppekitVipnGvDl 168
                                       ++t +e +  y+++    +Vi nG+D+
  gi|330507529|ref|YP_004383957.1| 288 DSTMKEAMLFYRMKG---VVIRNGIDV 311
                                       *999999999**998...9*******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 ?   -1.5   0.0      0.35   1.6e+03      18      38 ..     353     374 ..     345     393 .. 0.81
   2 !   16.6   0.0   9.3e-07    0.0042      88     135 ..     474     521 ..     470     545 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.35
                                       EEEESS-TTT.TTHHHHHHHHH CS
                   Glycos_transf_1  18 ilsvgrleke.Kgvdllikafa 38 
                                       ++s++r+e e Kg+ +l++a+ 
  gi|330507529|ref|YP_004383957.1| 353 VFSISRIEIEnKGYPQLLDALV 374
                                       68999999888*******9986 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9.3e-07
                                       HHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT CS
                   Glycos_transf_1  88 ellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdge 135
                                       e++  + + ++ps++E+f +++lEA   g+p i+s + g+++ +k+ e
  gi|330507529|ref|YP_004383957.1| 474 EVMAGCVAGIFPSQYEPFLLTALEAGREGTPSIVSRSAGFSDALKKVE 521
                                       5666677779******************************99998766 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 ?   -3.2   0.0       2.3     1e+04      15      34 ..     194     213 ..     189     242 .. 0.71
   2 ?   -3.0   0.0         2   9.2e+03      45      63 ..     272     289 ..     263     300 .. 0.63
   3 ?   12.1   0.0   4.5e-05       0.2      67     110 ..     473     519 ..     460     544 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.3
                                       GTHHHHHHHH.HHHH.HHEEE CS
                   Glyco_trans_1_4  15 kgvdllleav.pllrkkdvrl 34 
                                       k+v  +++ v p++r++ +++
  gi|330507529|ref|YP_004383957.1| 194 KAVVEFARSVmPRVRAS-LHC 213
                                       77777888888888855.443 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2
                                       HHHHHHTT-T.TEEEE--- CS
                   Glyco_trans_1_4  45 eleelaagleerveftGfv 63 
                                       +le+la +++++v+f+G  
  gi|330507529|ref|YP_004383957.1| 272 ALEALA-RYADGVTFVGDS 289
                                       455444.345778888765 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 4.5e-05
                                       HHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.T CS
                   Glyco_trans_1_4  67 aellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv.g 110
                                       +e++a +   ++Ps  e f l++lEa   g+p ++++ +g+++++ +
  gi|330507529|ref|YP_004383957.1| 473 DEVMAGCVAGIFPSqyEPFLLTALEAGREGTPSIVSRSAGFSDALkK 519
                                       6889999999****999********************9999997753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4113.51
//
Query:       gi|330507530|ref|YP_004383958.1|  [L=232]
Description: KaiC protein [Methanosaeta concilii GP6]
Scores for complete 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-46  155.9   0.2    1.2e-45  155.7   0.2    1.0  1  ATPase           KaiC
    2.5e-06   26.4   0.0    3.5e-06   25.9   0.0    1.1  1  GvpD             GvpD gas vesicle protein
    9.9e-05   22.0   0.0    0.00024   20.8   0.0    1.5  1  AAA_25           AAA domain
    0.00077   18.9   0.0     0.0013   18.1   0.0    1.6  2  DnaB_C           DnaB-like helicase C terminal domain
     0.0013   18.6   0.0     0.0022   17.8   0.0    1.3  1  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 
  ------ inclusion threshold ------
      0.012   14.8   0.9      0.022   14.1   0.9    1.4  1  Rad51            Rad51
      0.028   14.1   0.3      0.063   13.0   0.3    1.6  1  AAA_24           AAA domain
       0.03   14.0   0.2      0.052   13.3   0.2    1.3  1  Sigma54_activat  Sigma-54 interaction domain
      0.064   13.5   0.1       0.75   10.1   0.1    2.0  2  AAA_22           AAA domain
      0.066   12.4   0.1        0.1   11.7   0.1    1.2  1  DAP3             Mitochondrial ribosomal death-associated pro
      0.089   13.1   0.0       0.12   12.7   0.0    1.3  1  AAA_19           AAA domain
      0.094   13.1   1.0       0.67   10.3   1.0    2.1  1  AAA_16           AAA ATPase domain
       0.11   11.7   0.0       0.14   11.3   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.11   11.9   0.5        1.1    8.7   0.1    2.1  2  PhoH             PhoH-like protein
       0.14   12.2   0.2       0.51   10.4   0.2    1.9  1  AAA_14           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 !  155.7   0.2   9.7e-49   1.2e-45       2     227 ..       2     226 ..       1     229 [. 0.90

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 9.7e-49
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenak.slGwdlekl 77 
                                       k+gI+g+De++ gG+ +g+v  itG++GtGKt+fa qF+ +g+ + ge+g+++t  e+ae +r+++  s+Gwd+ +l
  gi|330507530|ref|YP_004383958.1|   2 KSGIPGFDEMVGGGFHQGTVNTITGSSGTGKTVFASQFIHHGIGQ-GEKGMIITPSESAEYMRREMMsSFGWDFGAL 77 
                                       89*******************************************.****************9886549******** PP

                            ATPase  78 eeegklaiidasesaeesaeekdkedleelieelaeai....keikakrvviDsitgl.ayeekeavaReilrqlvr 149
                                       e+ gkl +id++    + ++ +   d+  ++ ++++ +    +e k kr+ iD +t++ +  e + ++R+  + l+ 
  gi|330507530|ref|YP_004383958.1|  78 ENDGKLSLIDVTDPVLRLQK-SIDVDPVDFLINFRKLVerklQEEKPKRLFIDDLTAFfMAVEAPFKIRSLTDDLFG 153
                                       **********9998766555.55555555666666655110055677***********9****************** PP

                            ATPase 150 vlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikv 226
                                       +++  gvT + +       +a+g+++  e+ +d +  L++++i ++l R++ ++kmRg+k+ + + +++I+++gi+v
  gi|330507530|ref|YP_004383958.1| 154 TIRSSGVTCLVTIG-----TAFGTNQFLEYGADSATMLNRERIGNTLIRSIYVMKMRGSKIANSIRVLDISDDGISV 225
                                       *************9.....89******************************************************99 PP

                            ATPase 227 l 227
                                        
  gi|330507530|ref|YP_004383958.1| 226 S 226
                                       6 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.9e-09   3.5e-06      10     204 ..      19     217 ..      14     228 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.9e-09
                              GvpD  10 GktllikGaPGtGktlftlrgldv.lrresdvlyv.strvddetvseay...fsgeaeld...ktalldllkdplel 78 
                                       G    i G  GtGkt+f+ +++   + + ++ + +  + + +    e+      + ++l+   k  l+d+    l l
  gi|330507530|ref|YP_004383958.1|  19 GTVNTITGSSGTGKTVFASQFIHHgIGQGEKGMIItPSESAEYMRREMMssfGWDFGALEndgKLSLIDVTDPVLRL 95 
                                       5556799**************97526555544444145666666778876643366777644566777888777888 PP

                              GvpD  79 dldvdvPiekldlesllefvdeiaa..iatkl.iialdswelvyeylaerydsPediktvkndlvvlaresgvrlvl 152
                                       +  +dv      ++ l++f + ++     +k+  + +d   l   +     + P +i+ +++dl    r sgv  ++
  gi|330507530|ref|YP_004383958.1|  96 QKSIDVDP----VDFLINFRKLVERklQEEKPkRLFIDD--LTAFF--MAVEAPFKIRSLTDDLFGTIRSSGVTCLV 164
                                       88888755....566666655332200233331344455..33333..34568999****************98555 PP

                              GvpD 153 vleta..ansrleyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPft 204
                                          ta  +n+ ley +d    ln +      l+r++ + k+rG +i n ++ + 
  gi|330507530|ref|YP_004383958.1| 165 TIGTAfgTNQFLEYGADSATMLNRERI-GNTLIRSIYVMKMRGSKIANSIRVLD 217
                                       44444348999*******999974433.4579***************9876655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     2e-07   0.00024      25     156 ..      11     136 ..       2     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2e-07
                            AAA_25  25 lvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravg....ea 96 
                                        v+g    g+++ ++G +gtGKt++a++  ++   +G+           k +++   +s++ +rr +   +     a
  gi|330507530|ref|YP_004383958.1|  11 MVGGGFHQGTVNTITGSSGTGKTVFASQFIHHGIgQGE-----------KGMIITPSESAEYMRREMMSSFgwdfGA 76 
                                       56666689**************************7777...........4445544444445555555544333356 PP

                            AAA_25  97 lrddarllvldlagveslpLfakdrggtl..ltadvdaleaaieevegvrlvviDplsralg 156
                                       l+ d++l ++d+ +   l+L ++++ +++  l  + + +e++++e e+++ + iD l++++ 
  gi|330507530|ref|YP_004383958.1|  77 LENDGKLSLIDVTD-PVLRLQKSIDVDPVdfLINFRKLVERKLQE-EKPKRLFIDDLTAFFM 136
                                       6999*******977.699999999999999888888889999999.99*********99875 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 !   18.1   0.0   1.1e-06    0.0013       3      66 ..       2      64 ..       1     145 [. 0.73
   2 ?   -3.3   0.0       3.9   4.6e+03     202     236 ..     177     206 ..     173     212 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                                      XSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHH CS
                                      xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  3 stgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqR 66
                                      ++g   +D++++ G+++g++  i + +++Gkt++a +++++   + ++++++   e sa + ++R
  gi|330507530|ref|YP_004383958.1|  2 KSGIPGFDEMVGgGFHQGTVNTITGSSGTGKTVFASQFIHHGIGQGEKGMIITPSE-SA-EYMRR 64
                                      67888899998537*************************99776666665555444.22.23333 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.9
                                       CCCXSEEEEEEECCHHHHHHCHHCEEEEEEEEETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 202 eqdADvvlflyrdeyykedseekgkaeiiiaKhRn 236
                                       e  AD  ++l r+++ ++      +  i+++K R 
  gi|330507530|ref|YP_004383958.1| 177 EYGADSATMLNRERIGNTL-----IRSIYVMKMRG 206
                                       5668888888887665532.....34566666665 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 !   17.8   0.0   1.8e-06    0.0022      17     100 ..      36     123 ..      33     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                              MEDS  17 lvpfikaglargekvlyvasastldel.realrkagldvdaalesgqleildaeety...lrgggfdpermlealrr 89 
                                       +++fi+ g+ +gek ++++++++ + + re++++ g d  a+++ g+l+++d ++      ++   dp  +l ++r+
  gi|330507530|ref|YP_004383958.1|  36 ASQFIHHGIGQGEKGMIITPSESAEYMrREMMSSFGWDFGALENDGKLSLIDVTDPVlrlQKSIDVDPVDFLINFRK 112
                                       679*****************555555516677889********************9977777888999********* PP

                              MEDS  90 alakaladgya 100
                                        +++ l+++ +
  gi|330507530|ref|YP_004383958.1| 113 LVERKLQEEKP 123
                                       ***99966443 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.9   1.8e-05     0.022      22      56 ..       4      38 ..       1      49 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                      S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHH CS
                             Rad51 22 GskklDelLgGGietgsiteifGefrsGktqlcht 56
                                      G   +De++gGG++ g++  i G +++Gkt ++ +
  gi|330507530|ref|YP_004383958.1|  4 GIPGFDEMVGGGFHQGTVNTITGSSGTGKTVFASQ 38
                                      66789*************************99877 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   5.3e-05     0.063       6      30 ..      23      76 ..      19     146 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-05
                            AAA_24  6 liyGpsgiGKTtlakel.......gpkplfi......................d 30
                                       i+G+sg+GKT +a+++       g+k  +i                       
  gi|330507530|ref|YP_004383958.1| 23 TITGSSGTGKTVFASQFihhgigqGEKGMIItpsesaeymrremmssfgwdfgA 76
                                      699**************7777666555555545555555544444444444443 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   4.3e-05     0.052      26      77 ..      23      76 ..      15      82 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-05
                                      EEECSTTSSHHHHHHH.HHHHSTTTTS-EE..EEETTTS.-TTCHHHHHHEBSSSS CS
                   Sigma54_activat 26 litGesGtGKellara.iheaskrkekpfv..avncaai.peelleseLFGhekGa 77
                                       itG sGtGK+++a++ ih+   + ek ++    + a++  +e+++s  FG   Ga
  gi|330507530|ref|YP_004383958.1| 23 TITGSSGTGKTVFASQfIHHGIGQGEKGMIitPSESAEYmRREMMSS--FGWDFGA 76
                                      59***********9752777555555444411345555524445544..6666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00063      0.75       7      27 ..      21      41 ..      17      73 .. 0.85
   2 ?    1.4   0.0      0.29   3.5e+02      79     129 ..     111     167 ..      95     188 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00063
                            AAA_22  7 ilvvtGesGtGKTtllrrlle 27
                                      + ++tG sGtGKT+ + ++ +
  gi|330507530|ref|YP_004383958.1| 21 VNTITGSSGTGKTVFASQFIH 41
                                      5689**********9998876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.29
                            AAA_22  79 lealeqalraravielliiDEaqhlr.seealeeLrsllnl......srkgvqliLvG 129
                                       ++++e+ l++ +  + l iD+   ++   ea  ++rsl ++      s+  + l+ +G
  gi|330507530|ref|YP_004383958.1| 111 RKLVERKLQEEKP-KRLFIDDLTAFFmAVEAPFKIRSLTDDlfgtirSSGVTCLVTIG 167
                                       4555566666666.66666666665444555555555555555555444444444444 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   8.6e-05       0.1      28      62 ..      24      60 ..      17      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.6e-05
                                      EE-SSSSSTTTTHHHHHHHGGGS..--EEEEES-GGG CS
                              DAP3 28 ltGekgsGKSvlLlqalayAlek..gwvvlhvpeaed 62
                                      +tG  g+GK+v  +q +++++ +  + ++++ +e  +
  gi|330507530|ref|YP_004383958.1| 24 ITGSSGTGKTVFASQFIHHGIGQgeKGMIITPSESAE 60
                                      8********************9877555655555544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.9e-05      0.12       9      62 ..      18      67 ..      11     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.9e-05
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerl 62
                                      + +v  +t+  GtGKT    + +++ + +g    e+ +++++ + A    re +
  gi|330507530|ref|YP_004383958.1| 18 QGTVNTITGSSGTGKTVFASQFIHHGIGQG----EKGMIITPSESAEYMRREMM 67
                                      667889*******************99999....77899999887755545554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.0   0.00056      0.67      29     145 ..      24     132 ..      13     164 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00056
                            AAA_16  29 lsGesGvGKsslvrellralekd...ggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrekl 101
                                       ++G sG+GK+  + ++ ++  ++   g+i +  +  ++     +     + + +   + +l+++ + ++  +  +  
  gi|330507530|ref|YP_004383958.1|  24 ITGSSGTGKTVFASQFIHHGIGQgekGMIITPSESAEY-----MRReMMSSFGW--DFGALENDGKLSL-IDVTDPV 92 
                                       89***********9999876666554455555555555.....12224555533..5555655533322.2222211 PP

                            AAA_16 102 eealaavpelagaeasrllellkrll.allsrderplvlvlDdlq 145
                                       ++     ++  + ++ ++l  +++l+ ++l++ e+p  l++Ddl 
  gi|330507530|ref|YP_004383958.1|  93 LR----LQKSIDVDPVDFLINFRKLVeRKLQE-EKPKRLFIDDLT 132
                                       11....22222233368999999999888888.888999999986 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   0.00012      0.14       3      25 ..      21      43 ..      19      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                           DUF2075  3 vvlVtGvaGtGKtvvllnllael 25
                                      v  +tG +GtGKtv ++++++  
  gi|330507530|ref|YP_004383958.1| 21 VNTITGSSGTGKTVFASQFIHHG 43
                                      6689*************998765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00088       1.1      20      40 ..      20      40 ..      12      79 .. 0.83
   2 ?    1.5   0.0      0.15   1.8e+02      99     126 ..     190     217 ..     143     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00088
                                      SEEEEE--TTSSTTHHHHHHH CS
                              PhoH 20 divfaiGpaGtGKtylavala 40
                                      ++ +++G++GtGKt +a +  
  gi|330507530|ref|YP_004383958.1| 20 TVNTITGSSGTGKTVFASQFI 40
                                      67899***********98765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
                                       HHHTTSEEEEEGGGGTT--B-SEEEEE- CS
                              PhoH  99 llekgkievaplaymRGrTlndafvilD 126
                                        + +  i+ + +  mRG  +++++ +lD
  gi|330507530|ref|YP_004383958.1| 190 RIGNTLIRSIYVMKMRGSKIANSIRVLD 217
                                       55667788889999*********99998 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00043      0.51       3      32 ..      20      50 ..      18     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00043
                            AAA_14  3 kilvitGaRrvGKTtllkqlikell.vkkes 32
                                       + +itG   +GKT+++ q+i++ +   ++ 
  gi|330507530|ref|YP_004383958.1| 20 TVNTITGSSGTGKTVFASQFIHHGIgQGEKG 50
                                      6789*****************9988533333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1666.25
//
Query:       gi|330507531|ref|YP_004383959.1|  [L=534]
Description: replication factor C large subunit [Methanosaeta concilii GP6]
Scores for complete 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-14   52.0   0.0    2.8e-13   50.4   0.0    1.8  2  AAA             ATPase family associated with various cellula
    1.1e-05   25.8   0.0      0.091   13.0   0.0    2.8  2  AAA_22          AAA domain
    8.8e-05   23.0   0.8     0.0078   16.6   0.0    3.4  4  AAA_16          AAA ATPase domain
    0.00051   20.0   0.0      0.001   19.0   0.0    1.4  1  Rad17           Rad17 P-loop domain
     0.0027   18.0   0.2      0.011   16.1   0.1    2.1  2  AAA_assoc_2     AAA C-terminal domain
     0.0028   17.4   0.2     0.0097   15.6   0.1    1.9  1  AAA_30          AAA domain
     0.0031   17.0   0.6       0.33   10.4   0.5    2.4  2  PhoH            PhoH-like protein
     0.0037   16.9   0.1      0.061   12.9   0.0    2.4  2  AAA_25          AAA domain
     0.0047   16.9   0.0      0.016   15.2   0.0    2.0  1  AAA_5           AAA domain (dynein-related subfamily)
     0.0058   16.4   0.0      0.016   15.0   0.0    1.7  2  RuvB_N          Holliday junction DNA helicase RuvB P-loop do
     0.0075   16.6   0.2        3.4    8.0   0.0    2.8  2  AAA_19          AAA domain
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.031   14.3   0.0    1.4  1  AAA_14          AAA domain
      0.018   14.8   0.0      0.051   13.3   0.0    1.7  1  IstB_IS21       IstB-like ATP binding protein
      0.047   12.7   0.0       0.12   11.3   0.0    1.5  2  AAA_6           Hydrolytic ATP binding site of dynein motor r
      0.064   13.0   0.0        5.8    6.7   0.0    2.5  2  DEAD            DEAD/DEAH box helicase
      0.072   12.8   0.0       0.15   11.8   0.0    1.5  1  Cytidylate_kin  Cytidylate kinase
      0.099   12.9   0.1        1.1    9.5   0.0    2.4  2  AAA_28          AAA domain
       0.12   11.6   0.0        0.2   10.8   0.0    1.2  1  TIP49           TIP49 P-loop domain
       0.21   11.1   0.0       0.39   10.2   0.0    1.3  1  AAA_7           P-loop containing dynein motor region


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 !   50.4   0.0     3e-16   2.8e-13       1     121 [.      46     152 ..      46     161 .. 0.90
   2 ?   -2.6   0.0       7.5   7.1e+03      42      57 ..     407     422 ..     384     452 .. 0.67

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 3e-16
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka....kpsilfiDEidalaks 73 
                                       v+lyGp GtGKT++a a+a++++ +++e+++s+ +      ++  i+++   a++++    kp  +++DE+d+l+++
  gi|330507531|ref|YP_004383959.1|  46 VILYGPAGTGKTSAALALAHDFDWDYIEMNASDAR------TAGMIEKIAVPASRSQtfsgKPRLVILDEADNLHGT 116
                                       79*********************************......9999999999998888899999************** PP

                                       HTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS CS
                               AAA  74 rsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr 121
                                               ++  ++++l+ + +  +      vi+++n++ ++d+ l+ 
  gi|330507531|ref|YP_004383959.1| 117 A-------DRGGAAAMLRLVRNTLQ-----PVILIANEYYEIDKSLRD 152
                                       *.......78889999999998888.....69999*********9993 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.5
                                       HHHHHHHHHHHHHHTS CS
                               AAA  42 sekkirelfkeakeka 57 
                                       + kk++++f+ea + +
  gi|330507531|ref|YP_004383959.1| 407 GTKKVQNIFEEAMRIQ 422
                                       4567777777765444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   9.6e-05     0.091       6      40 ..      44      79 ..      43      98 .. 0.70
   2 !   11.0   0.0   0.00042      0.39      74     124 ..      80     135 ..      72     148 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.6e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee..erp 40
                                      g ++++G++GtGKT  +  l++ +d + ++e+   ++
  gi|330507531|ref|YP_004383959.1| 44 GAVILYGPAGTGKTSAALALAHDFD-WDYIEMnaSDA 79
                                      6789*****************9995.55555556333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00042
                            AAA_22  74 sseellealeqalrarav....ielliiDEaqhlr.s......eealeeLrsllnlsrkgvq 124
                                       ++  ++e+++  +++ ++    ++l+i+DEa++l  +      +++l+ +r+      ++ +
  gi|330507531|ref|YP_004383959.1|  80 RTAGMIEKIAVPASRSQTfsgkPRLVILDEADNLHgTadrggaAAMLRLVRN------TLQP 135
                                       66777788888888888889999***********661455444555554443......3444 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   8.2e-06    0.0078       7      47 ..      24      66 ..      18      82 .. 0.79
   2 ?    0.8   0.0      0.62   5.8e+02     134     161 ..     100     131 ..      76     139 .. 0.68
   3 ?   -1.9   0.0       4.1   3.8e+03      46      87 ..     172     180 ..     145     250 .. 0.51
   4 ?    1.0   0.1      0.52   4.9e+02      34      84 ..     337     373 ..     336     469 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.2e-06
                            AAA_16  7 eeleqLlsalervrsgrp..elvllsGesGvGKsslvrellra 47
                                      + ++ L++   ++ +++p  ++v+l+G++G+GK+s + +l++ 
  gi|330507531|ref|YP_004383959.1| 24 KAIDDLREWALSWERSEPitGAVILYGPAGTGKTSAALALAHD 66
                                      56677766666688888899***************99888875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.62
                            AAA_16 134 erplvlvlDdlq....wadeaslqllaaLlrl 161
                                       ++p +++lD+++     ad + ++++  L+r+
  gi|330507531|ref|YP_004383959.1| 100 GKPRLVILDEADnlhgTADRGGAAAMLRLVRN 131
                                       4599*******977777777777776666655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.1
                            AAA_16  46 ralekdggiflrgkcdqlesaipysalaqalareellrqlld 87 
                                       ra++++                                 ++ 
  gi|330507531|ref|YP_004383959.1| 172 RAICQA---------------------------------EGI 180
                                       233332.................................222 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.52
                            AAA_16  34 GvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrq 84 
                                        +G ++ vr++++++ ++    +  +c+ +      +a+a+      l+  
  gi|330507531|ref|YP_004383959.1| 337 RMGQTRKVRSIRDSAARK----IGRHCHVS------LAFARSE----LMDF 373
                                       689999999999999999....88888888......3333333....3222 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.1e-06     0.001       8      76 ..       6      74 ..       4      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                             Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrew 76
                                      +W eky+P +++++    k i++++ew  +    +     +++ GP+G gk+ +   L+  +  +++e 
  gi|330507531|ref|YP_004383959.1|  6 KWTEKYRPATLKQVLGNGKAIDDLREWALSWERSEPITGAVILYGPAGTGKTSAALALAHDFDWDYIEM 74
                                      6**************************8776555555568999***********999999998888874 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 ?   -2.5   0.0       7.2   6.8e+03      16      38 ..      72      94 ..      62     114 .. 0.70
   2 !   16.1   0.1   1.2e-05     0.011       4      52 ..     179     228 ..     176     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.2
                                      XXXXXXXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2 16 aeladGDaRkaLnlLElaaeaae 38
                                      +e+   DaR+a  +  +a+ a++
  gi|330507531|ref|YP_004383959.1| 72 IEMNASDARTAGMIEKIAVPASR 94
                                      56777899988555446665555 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.2e-05
                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXX CS
                       AAA_assoc_2   4 klkleddalealaeladGDaRkaLnlLElaaeaaeak.egkieitledle 52 
                                        +++++d l ++ae a+GD+R+ +n L++aae +e+  e++    + d++
  gi|330507531|ref|YP_004383959.1| 179 GIDCNPDLLVTIAERAGGDMRSGINDLQAAAEGQETLrEEDLATAQRDVK 228
                                       5788999************************9998653333333444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1     1e-05    0.0097      21     122 ..      46     139 ..      42     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEa 97 
                                       ++l GpAGtGKt a  al++ ++ +   + + A+ ++ A  ++ ++ ++as+ + +     g     + +l+i DEa
  gi|330507531|ref|YP_004383959.1|  46 VILYGPAGTGKTSAALALAHDFDWD--YIEMNASDARTAGMIE-KIAVPASRSQTFS----G-----KPRLVILDEA 110
                                       7999********9877776665544..5889999999987666.99********999....4.....459******9 PP

                            AAA_30  98 gmv....dtkqlaallkaaekagakvilv 122
                                         +    d   +aa+l+ ++++   vil+
  gi|330507531|ref|YP_004383959.1| 111 DNLhgtaDRGGAAAMLRLVRNTLQPVILI 139
                                       55443338888999999998877777776 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.5   0.00035      0.33      22      41 ..      46      65 ..      39      68 .. 0.88
   2 ?    4.2   0.0     0.026        25     100     132 ..      80     114 ..      68     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00035
                                      EEEE--TTSSTTHHHHHHHH CS
                              PhoH 22 vfaiGpaGtGKtylavalav 41
                                      v+  GpaGtGKt  a+ala 
  gi|330507531|ref|YP_004383959.1| 46 VILYGPAGTGKTSAALALAH 65
                                      7899************9985 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.026
                                       HHTTSEEEEEGGGGTT--B-SE..EEEE-SGGG-- CS
                              PhoH 100 lekgkievaplaymRGrTlnda..fvilDEAQntt 132
                                         +g+ie + +   R +T++ +  +vilDEA n++
  gi|330507531|ref|YP_004383959.1|  80 RTAGMIEKIAVPASRSQTFSGKprLVILDEADNLH 114
                                       4578889899999999999864349********86 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   6.4e-05     0.061      34      56 ..      44      66 ..      30      67 .. 0.90
   2 ?    1.1   0.0      0.27   2.6e+02     142     169 ..     101     129 ..      72     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.4e-05
                            AAA_25 34 elallaGapgtGKttlaldlala 56
                                      + ++l+G+ gtGKt +al la++
  gi|330507531|ref|YP_004383959.1| 44 GAVILYGPAGTGKTSAALALAHD 66
                                      679*****************975 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.27
                            AAA_25 142 gvrlvviDplsralgg.densnsdvgalv 169
                                       ++rlv++D  + ++g  d   ++++ +lv
  gi|330507531|ref|YP_004383959.1| 101 KPRLVILDEADNLHGTaDRGGAAAMLRLV 129
                                       49************997877777775555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.7e-05     0.016       2      38 ..      46      82 ..      45     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-05
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--H CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdtte 38
                                      v+L Gp GtgK++ a  la+ + + + +++ ++  t+
  gi|330507531|ref|YP_004383959.1| 46 VILYGPAGTGKTSAALALAHDFDWDYIEMNASDARTA 82
                                      8************************999988876555 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 !   15.0   0.0   1.7e-05     0.016       2      60 ..      12      70 ..      11      91 .. 0.84
   2 ?   -3.4   0.0       7.5   7.1e+03      55      74 ..     428     447 ..     427     454 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvk 60
                                      rP +l++ +g  k  ++l+    + ++ e     v+lyGp G Gkt+ a  +a++++ +
  gi|330507531|ref|YP_004383959.1| 12 RPATLKQVLGNGKAIDDLREWALSWERSEPITGAVILYGPAGTGKTSAALALAHDFDWD 70
                                      999**************99887766655666789*******************998754 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.5
                            RuvB_N  55 kelgvklkitsgPvlekagd 74 
                                       +e++   + +s P+l+k +d
  gi|330507531|ref|YP_004383959.1| 428 EEIELAWRKSSQPTLNKRSD 447
                                       578889999******99887 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.4     0.025        24      11      26 ..      44      59 ..      38     148 .. 0.91
   2 !    8.0   0.0    0.0036       3.4      24     116 ..     164     273 ..     163     293 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.025
                            AAA_19 11 kvllvtaGpGtGKTrv 26
                                      + +++ +++GtGKT  
  gi|330507531|ref|YP_004383959.1| 44 GAVILYGPAGTGKTSA 59
                                      56899*********75 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0036
                            AAA_19  24 TrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal.................ldfddl 83 
                                       ++++ ++++ + +++g++ ++ llv+ ++rA   +r  ++ l+a+a+    l +                 l++  +
  gi|330507531|ref|YP_004383959.1| 164 STTIAQALRAICQAEGIDCNPDLLVTIAERAGGDMRSGINDLQAAAEGQETLREedlataqrdvkssifrvLEVIYK 240
                                       689999999999*************************9999999965444443333344444444444444333333 PP

                            AAA_19  84 ltealelleeaeeekklqeee.llivDEfqdvde 116
                                        ++a e+le + + ++   e+ + +vDE   +  
  gi|330507531|ref|YP_004383959.1| 241 GNNAKEALEASYNLDES-PEDlINWVDENLPLAY 273
                                       33344444422222222.2232556777655555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.3e-05     0.031       4      78 ..      45     115 ..      43     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.3e-05
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpe 78 
                                       ++++ G+  +GKT  +  l+++      +++++n  d r++ + ++  ++    + +++ k ++++lDE+ ++ +
  gi|330507531|ref|YP_004383959.1|  45 AVILYGPAGTGKTSAALALAHDFD---WDYIEMNASDARTAGMIEKIAVPASRSQTFSG-KPRLVILDEADNLHG 115
                                       799****************98877...99********9998877554455444444777.99*******999865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.4e-05     0.051      49     134 ..      45     129 ..      24     145 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.4e-05
                         IstB_IS21  49 nivllGpsGvGKshlaialgveavra..glsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgll..p 121
                                       +++l Gp+G+GK+  a al+++   +  +++ +  r++ ++e++++      ++r ++   k++l+ilD+   l  +
  gi|330507531|ref|YP_004383959.1|  45 AVILYGPAGTGKTSAALALAHDFDWDyiEMNASDARTAGMIEKIAV-----PASRSQTFSGKPRLVILDEADNLhgT 116
                                       689****************997543311233334455555555544.....34555666677788888876544123 PP

                         IstB_IS21 122 ldqaeaellfevi 134
                                        d+  a+ +++++
  gi|330507531|ref|YP_004383959.1| 117 ADRGGAAAMLRLV 129
                                       4555556666665 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.12      37      77 ..      48      88 ..      40      96 .. 0.90
   2 ?   -2.8   0.0       2.5   2.3e+03     251     297 ..     138     184 ..     107     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                             AAA_6 37 paGpagtGKtEtvkdLakalakqvvvfncsdqldykslgki 77
                                      ++GpagtGKt +   La+ +    + +n sd+ ++ +++ki
  gi|330507531|ref|YP_004383959.1| 48 LYGPAGTGKTSAALALAHDFDWDYIEMNASDARTAGMIEKI 88
                                      68*****************************9999998887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.5
                             AAA_6 251 lvaeDvplfkglisdlFpgvelpesdyeeleeaieevlkekklqlee 297
                                       l+a+++   ++ ++d   g+++ +++++++ +a+++++++++++ ++
  gi|330507531|ref|YP_004383959.1| 138 LIANEYYEIDKSLRDATRGIQFRSVRSTTIAQALRAICQAEGIDCNP 184
                                       44555556666677777788888888888888888888888777665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.055        51      15      33 ..      44      62 ..      35      67 .. 0.85
   2 ?    6.7   0.0    0.0061       5.8     119     149 ..      99     129 ..      79     140 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.055
                                      CEEEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                              DEAD 15 gdvlvaaeTGsGKTlafli 33
                                      g v++ ++ G+GKT a+l 
  gi|330507531|ref|YP_004383959.1| 44 GAVILYGPAGTGKTSAALA 62
                                      579999*********9875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0061
                                       CTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 119 lsqvrflVlDEadrlldqgfsdfinrilnql 149
                                         + r+++lDEad+l     +    ++l+ +
  gi|330507531|ref|YP_004383959.1|  99 SGKPRLVILDEADNLHGTADRGGAAAMLRLV 129
                                       45679**********9987777777776666 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.15       3      29 ..      48      74 ..      46      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                      EE-STTSSHHHHHHHHHHHHT-EEEEH CS
                    Cytidylate_kin  3 iDGPagsGKssvaralaeklglkyldt 29
                                      + GPag+GK s a ala+ +++ y++ 
  gi|330507531|ref|YP_004383959.1| 48 LYGPAGTGKTSAALALAHDFDWDYIEM 74
                                      56**********************985 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0012       1.1       2      27 ..      46      72 ..      45      95 .. 0.84
   2 ?    0.3   0.1      0.76   7.2e+02      13      70 ..     165     223 ..     142     231 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvv 27
                                      +++ G+ +tGKT+ + aLa + ++ ++
  gi|330507531|ref|YP_004383959.1| 46 VILYGPAGTGKTSAALALAHDfDWDYI 72
                                      899****************87656555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.76
                            AAA_28  13 TtlleaLaar....gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaa 70 
                                       Tt+++aL a     g+ + p+   +i e  + + +  +   +dl a ae+++  + e++a a
  gi|330507531|ref|YP_004383959.1| 165 TTIAQALRAIcqaeGIDCNPDLLVTIAERAGGDMRSGI---NDLQAAAEGQETLREEDLATA 223
                                       77777777433334777777777777766654444433...455566666555555555554 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   0.00021       0.2      48      87 ..      42      78 ..      35      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 48 laGravLlaGpsgtGktalaiaiskelgedvpfvalsgse 87
                                      ++G av+l Gp+gtGkt+ a+a+++++     ++ +++s+
  gi|330507531|ref|YP_004383959.1| 42 ITG-AVILYGPAGTGKTSAALALAHDFD--WDYIEMNASD 78
                                      554.78899***************9986..5677777776 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 ?   10.2   0.0   0.00042      0.39      35      80 ..      45      87 ..      42      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                             AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqd 80
                                       v+l+Gp+GtGKt+ +  l + +d   + ++ +n s   +a ++ +
  gi|330507531|ref|YP_004383959.1| 45 AVILYGPAGTGKTSAALALAHDFD---WDYIEMNASDARTAGMIEK 87
                                      589***************999999...8888888888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3274.26
//
Query:       gi|330507532|ref|YP_004383960.1|  [L=155]
Description: pyridoxamine 5'-phosphate oxidase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-24   84.5   0.0    7.4e-24   84.3   0.0    1.0  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    1.7e-11   44.1   0.0    2.3e-11   43.7   0.0    1.1  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
    0.00059   19.4   0.0     0.0008   19.0   0.0    1.2  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like


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 !   84.3   0.0   1.2e-27   7.4e-24       2     140 ..      21     151 ..      20     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 1.2e-27
                                       HHHHHHHHHC-SEEEEEEEETTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGEE CS
                      Pyridox_ox_2   2 reeilalLdegevgrlafvddgepvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfnsl 77 
                                       ++e+ alL+++++grl+++++++p+++P+++v++++++y+h+   +r+++++ ++p +c+ v +++           
  gi|330507532|ref|YP_004383960.1|  21 DDECIALLSSARYGRLGLSREDQPYVVPMSFVYHEGKIYLHSRGMGRKVQYAAENPrICFQVDHLEK-----G---- 88 
                                       79***************************************************8888*******888.....4.... PP

                                       EEEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTTGGCSB---CCCCCT..EEEEEEEEEEEEEE CS
                      Pyridox_ox_2  78 nyrSVvvrGraeevtdeeekaealellvekivpgrwenlrpptrkelka..tsvlrlkieevsgr 140
                                       +++SV ++Grae+ +d e k++ ++ +++k + g+  ++   +r++l+    +++++ i+e++gr
  gi|330507532|ref|YP_004383960.1|  89 KWTSVNAFGRAELSDDIEAKQRMFDVFTRKGLGGHGGKSF--QRQDLERmdMTIWEIVIDELTGR 151
                                       5******************************999944444..344444444899**********9 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   3.8e-15   2.3e-11       2      86 ..      21     104 ..      20     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 3.8e-15
                                       HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT..GSEEEE CS
                    Putative_PNPOx   2 deelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde..lgrgvr 76 
                                       d+e+ ++l+++++++l+  +ed  P+v+p++++++ g+  i++++  + rk++  +enpr+++ ++  e  + ++v+
  gi|330507532|ref|YP_004383960.1|  21 DDECIALLSSARYGRLGLSREDQ-PYVVPMSFVYHEGK--IYLHSRGMGRKVQYAAENPRICFQVDHLEkgKWTSVN 94 
                                       789999************97777.**************..*****************************99999999 PP

                                       EEEEEEEESC CS
                    Putative_PNPOx  77 ieGtaelvsd 86 
                                         G+ael +d
  gi|330507532|ref|YP_004383960.1|  95 AFGRAELSDD 104
                                       9*****9876 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 !   19.0   0.0   1.3e-07    0.0008       9      97 ..      27     114 ..      20     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-07
                     Pyrid_ox_like   9 lvkdiktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsdeskkkyvsvs..Gtae 83 
                                       l+++++ + L++++ +++  + PM+     ++g+++  ++   +kv+  ++++++++ + + +k k+ sv+  G+ae
  gi|330507532|ref|YP_004383960.1|  27 LLSSARYGRLGLSR-EDQPYVVPMSFV--YHEGKIYLHSRGMGRKVQYAAENPRICFQVDHLEKGKWTSVNafGRAE 100
                                       67778888899986.6668889**985..678***********************************998555**** PP

                     Pyrid_ox_like  84 vvedrakieelWsp 97 
                                       +++d + ++ +++ 
  gi|330507532|ref|YP_004383960.1| 101 LSDDIEAKQRMFDV 114
                                       ****9999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1190.61
//
Query:       gi|330507533|ref|YP_004383961.1|  [L=496]
Description: acetyl-CoA carboxylase [Methanosaeta concilii GP6]
Scores for complete 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-75  252.1   0.0    5.1e-75  251.6   0.0    1.2  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    3.9e-46  156.1   0.2    1.1e-45  154.7   0.0    1.9  2  Biotin_carb_N    Biotin carboxylase, N-terminal domain
      2e-41  140.5   0.0    5.5e-41  139.0   0.0    1.8  2  Biotin_carb_C    Biotin carboxylase C-terminal domain
    5.7e-11   42.3   0.0    1.3e-10   41.2   0.0    1.6  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    6.8e-06   26.2   0.0    1.3e-05   25.3   0.0    1.5  1  ATP-grasp_3      ATP-grasp domain
    0.00041   20.0   0.0    0.00077   19.1   0.0    1.4  1  ATP-grasp        ATP-grasp domain
  ------ inclusion threshold ------
      0.032   14.0   0.0       0.07   12.9   0.0    1.5  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T


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 !  251.6   0.0     2e-78   5.1e-75       2     209 ..     118     323 ..     117     325 .. 0.99

  Alignments for each domain:
  == domain 1  score: 251.6 bits;  conditional E-value: 2e-78
                                       HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaaf 78 
                                       k +a++++k+++vp+vp+ +  +++ +ea+++a+ igyP+i+k+a+g+GG Gm+++ ++ee+  +++++++ a+ af
  gi|330507533|ref|YP_004383961.1| 118 KITARQTMKEAGVPIVPGIEEGINDPDEAMDLADGIGYPIILKPAAGGGGIGMKIVGSREEMLPALTSSQSVARNAF 194
                                       7899************************************************************************* PP

                                       STS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-E CS
                       CPSase_L_D2  79 gnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvv 155
                                       g++++++ek+l++p++iE+++l+D+ g +i+v +re+s+q+r+qk+ie+ Ps++++de r+++++ avk+++++g+ 
  gi|330507533|ref|YP_004383961.1| 195 GDDTIYIEKYLTEPRHIEFQILADEMGKTIYVSDRECSIQRRHQKLIEESPSPVMSDELRERMGSIAVKAAKAIGYA 271
                                       ***************************************************************************** PP

                                       EEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                       CPSase_L_D2 156 gagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                       +agtvef++++  +++y++E+NtRl+ve++++e++TG+dl+ke++ ia+g++L+
  gi|330507533|ref|YP_004383961.1| 272 SAGTVEFMYSR--GDFYFLEMNTRLQVEHPITEMVTGVDLAKEQILIAAGQPLN 323
                                       **********6..***************************************97 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 !  154.7   0.0   4.3e-49   1.1e-45       1     110 []       3     112 ..       3     112 .. 0.99
   2 ?   -3.5   0.0         6   1.5e+04      11      30 ..     258     277 ..     257     284 .. 0.74

  Alignments for each domain:
  == domain 1  score: 154.7 bits;  conditional E-value: 4.3e-49
                                       ---EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SE CS
                     Biotin_carb_N   1 kikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgada 77 
                                       +++k+lianrGeiA+r++ra+relgi +vavyse+d+n+l++++adeav +gp+++s+sYl+i++i+kaa e+ga+a
  gi|330507533|ref|YP_004383961.1|   3 MFNKILIANRGEIAIRVMRACRELGIPSVAVYSEADKNALFAKYADEAVFIGPSPSSQSYLKIDNIIKAALETGAEA 79 
                                       799************************************************************************** PP

                                       EE--SSTTTT-HHHHHHHHHTT-EESSS-HHHH CS
                     Biotin_carb_N  78 vhpGyGflsEnaefaeaveeagivfiGPsaeal 110
                                       +hpGyGflsEn+ fa++++e+givfiGP+++a+
  gi|330507533|ref|YP_004383961.1|  80 IHPGYGFLSENTVFASTCKENGIVFIGPPSTAI 112
                                       ****************************99876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6
                                       HHHHHHHHHHHHHTT-EEEE CS
                     Biotin_carb_N  11 GeiAvriiravrelgietva 30 
                                       G iAv+ ++a+   +  tv 
  gi|330507533|ref|YP_004383961.1| 258 GSIAVKAAKAIGYASAGTVE 277
                                       78999999998777777664 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 !  139.0   0.0   2.2e-44   5.5e-41       1     107 [.     337     443 ..     337     444 .. 0.99
   2 ?   -4.1   0.0       6.9   1.8e+04       3      12 ..     453     462 ..     453     466 .. 0.85

  Alignments for each domain:
  == domain 1  score: 139.0 bits;  conditional E-value: 2.2e-44
                                       EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EE CS
                     Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelri 77 
                                       e+RinaEdp ++f+p++G+++ ++ p+gpg+Rvdsgv++g+ ++pyyDsl++Kl++hg++r+ea+ar++raL e+ i
  gi|330507533|ref|YP_004383961.1| 337 ECRINAEDPLNDFSPAPGRIKGYRSPGGPGIRVDSGVYSGYLIPPYYDSLISKLVAHGKDRREAIARMERALYEYII 413
                                       8**************************************************************************** PP

                                       ESS-BSHHHHHHHHH-HHHHHT---TTTCC CS
                     Biotin_carb_C  78 eGvktnieflrailedeefakgeldtkfle 107
                                        Gvktn+ f++a+l++++f++g+++t+f++
  gi|330507533|ref|YP_004383961.1| 414 VGVKTNLIFHKAVLRNARFRSGDFNTGFIK 443
                                       ****************************98 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 6.9
                                       EEESEETTTT CS
                     Biotin_carb_C   3 RinaEdpekn 12 
                                       R+ aEd +kn
  gi|330507533|ref|YP_004383961.1| 453 RVAAEDHDKN 462
                                       999**99987 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 !   41.2   0.0     5e-14   1.3e-10      30     174 ..     148     292 ..     125     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 5e-14
                                       HHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT......-SCEEEEE--.ESEEEEEEEEETSSCEEE CS
                   Dala_Dala_lig_C  30 kveeelgypvfVKpareGSSvGvskveseeelkeaieeafky......dekvlvEeai.egreievavlgneklevs 99 
                                       ++ + +gyp++ Kpa  G  +G++ v s+ee+  a+ ++ +       d ++ +E+++ e r ie  +l +e  ++ 
  gi|330507533|ref|YP_004383961.1| 148 DLADGIGYPIILKPAAGGGGIGMKIVGSREEMLPALTSSQSVarnafgDDTIYIEKYLtEPRHIEFQILADEMGKTI 224
                                       567789*************************99888766543233344899*******9***********9888877 PP

                                       EEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C 100 evgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                        v ++    ++ + ++k ++++        +++e +e++  +a+ka ka++ +  + v f+++  g++++ E+Nt
  gi|330507533|ref|YP_004383961.1| 225 YVSDREC--SIQRRHQKLIEESP----SPVMSDELRERMGSIAVKAAKAIGYASAGTVEFMYS-RGDFYFLEMNT 292
                                       7776654..45567777764332....234688999*************************98.9*********9 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   4.9e-09   1.3e-05      19     159 ..     134     295 ..     115     297 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4.9e-09
                                       -............-EESS--SSSEEEEESS-------B--SS--TTE....................EEEE---SEE CS
                       ATP-grasp_3  19 P........tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve.............lvqefieGkp 74 
                                       P            ++ ++   +++++Kp+ G+gg ++ +v  +ee   a+ + +             + +   e ++
  gi|330507533|ref|YP_004383961.1| 134 PgieegindPDEAMDLADGIGYPIILKPAAGGGGIGMKIVGSREEMLPALTSSQsvarnafgddtiyIEKYLTEPRH 210
                                       454444331133344455569**********************99999999888899********988888889*** PP

                                       EEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H.HHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEE CS
                       ATP-grasp_3  75 lSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietel.keevvelaeevvekleglaGyvGvDlvlkdeepy 150
                                       +  ++l+d+    + +  r+   +++++     + +p+  ++ +e++ ++a ++ +++ g a+   v+++++ ++ y
  gi|330507533|ref|YP_004383961.1| 211 IEFQILADEMGKTIYVSDRECSIQRRHQKLIEESPSPVMSDElRERMGSIAVKAAKAI-GYASAGTVEFMYSRGDFY 286
                                       *******987777766666665555666666666666654444***************.****************** PP

                                       EEEEESS-- CS
                       ATP-grasp_3 151 viEvNPRlt 159
                                       ++E N Rl+
  gi|330507533|ref|YP_004383961.1| 287 FLEMNTRLQ 295
                                       *******97 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     3e-07   0.00077      14     159 ..     140     293 ..     125     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3e-07
                                       ECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEE CS
                         ATP-grasp  14 veskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlv 82 
                                       +++ +e+ ++a+ +g+p+++K +  g  G G ++v s+e++  al+          ++ ++++E++    + +   +
  gi|330507533|ref|YP_004383961.1| 140 INDPDEAMDLADGIGYPIILK-PAAGGGGIGMKIVGSREEMLPALTSSqsvarnafGDDTIYIEKYLTEPRHIEFQI 215
                                       778899999************.99999**********999988887777889999999******************* PP

                                       EEETTC-EEE--EEE.EEEE..TTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEE CS
                         ATP-grasp  83 vrsaeGetafypvve.tvqe..dgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnEl 156
                                         ++ G+t  +   e  +q+  ++ +++s  p  +s++  ++  +ia k+++++g++   +vE+ +   g+ ++ E+
  gi|330507533|ref|YP_004383961.1| 216 LADEMGKTIYVSDREcSIQRrhQKLIEESPSPV-MSDELRERMGSIAVKAAKAIGYASAGTVEFMYS-RGDFYFLEM 290
                                       ******976665433244441044556666665.78889999*********************8777.888888887 PP

                                       ESS CS
                         ATP-grasp 157 apR 159
                                         R
  gi|330507533|ref|YP_004383961.1| 291 NTR 293
                                       766 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.7e-05      0.07      46     112 ..     254     321 ..     225     337 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                      ATPgrasp_Ter  46 deelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgys.alaGvnlpylalklllgle 112
                                       +e++ ++a + a+++g +    v + + ++  + LE+N+R +    ++ +++Gv+l++  +  + g++
  gi|330507533|ref|YP_004383961.1| 254 RERMGSIAVKAAKAIGYASAGTVEFMYSRGDFYFLEMNTRLQVEHPITeMVTGVDLAKEQILIAAGQP 321
                                       567778999**********************************999883567******9999999942 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3620.87
//
Query:       gi|330507534|ref|YP_004383962.1|  [L=289]
Description: bifunctional protein birA [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-18   66.0   0.0      4e-18   65.6   0.0    1.2  1  BPL_LplA_LipB    Biotin/lipoate A/B protein ligase family
    5.2e-09   35.9   0.0      1e-08   34.9   0.0    1.5  1  BPL_LplA_LipB_2  Biotin/lipoate A/B protein ligase family
    3.8e-08   33.1   0.1    6.7e-08   32.3   0.1    1.4  1  BPL_C            Biotin protein ligase C terminal domain


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 !   65.6   0.0   6.7e-22     4e-18      19     131 .]      69     177 ..      53     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 6.7e-22
                                       GG--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-T CS
                     BPL_LplA_LipB  19 selesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegi 91 
                                       ++ esg++ +++ qt Gr    ++w+sp g++++sl+l+p+    + + +  +   + +av++a+       +  g 
  gi|330507534|ref|YP_004383962.1|  69 QKGESGTVILAEVQTRGRgrlsRHWESPSGGIWMSLILRPDI---PIALAYQINMAICVAVCRAI------SNLLGL 136
                                       34599**********************************887...42222222445556666666......5999** PP

                                       TEEEETTTEEEETTEEEEEEEEEEEE.TTS-EEEEEEEEEE CS
                     BPL_LplA_LipB  92 pvfikwpnDlyvngrKlaGiavtstr.gktlhhivigvgvn 131
                                       +  ikwpnDl+++ rK++Gi+ +++  g++l++ v+gvg+n
  gi|330507534|ref|YP_004383962.1| 137 NPGIKWPNDLLIGERKVGGILMEVQAeGERLEYAVVGVGIN 177
                                       **************************9************99 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 !   34.9   0.0   1.7e-12     1e-08      39     181 ..      97     232 ..      55     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.7e-12
                   BPL_LplA_LipB_2  39 adlleaAlvlaPevplakAaamlpvlmvalqdAlgalaPPevavhlewpgtilvngarvGgvrlaaseadeeevPdw 115
                                       +  + ++l+l P+ p+a A ++ +++ va++ A+  l    +   ++wp+++l+ + +vGg+ ++++ +   e  ++
  gi|330507534|ref|YP_004383962.1|  97 SGGIWMSLILRPDIPIALAYQINMAICVAVCRAISNLLG--LNPGIKWPNDLLIGERKVGGILMEVQAEG--ERLEY 169
                                       5567789***************************99876..444789****************9998755..55689 PP

                   BPL_LplA_LipB_2 116 lvvglelalekeseepGetpdetaLeeEGcaeveavalleslarhllawinrweedGfrpvhaewl 181
                                        vvg+ ++++ + +   ++  +t+L+ EG  ev+++al++   r ll+  + +e+ G  ++ +ew+
  gi|330507534|ref|YP_004383962.1| 170 AVVGVGINANIDPSAFPDDWMATSLSREGGSEVSRTALIQ---RTLLEIERAYENLGSMEIYDEWR 232
                                       9******999988866666788***************985...67777777899999999999997 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   1.1e-11   6.7e-08       1      47 [.     237     282 ..     237     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.1e-11
                                       STTSEEEEEETSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEEE CS
                             BPL_C   1 hsGqeVtlededgkveGiavGIdddGaLllktddglqpdinsGdisl 47 
                                       ++G+ V++  + g+++G ++++ +dGaLll+ dd+ ++ + +Gd+++
  gi|330507534|ref|YP_004383962.1| 237 TIGRMVRISANSGELVGEVEDLAEDGALLLRRDDE-LVRVLAGDCIH 282
                                       69*********************************.*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2103.10
//
Query:       gi|330507535|ref|YP_004383963.1|  [L=138]
Description: hypothetical protein MCON_1492 [Methanosaeta concilii GP6]
Scores for complete 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-09   35.8   0.0    7.6e-09   35.4   0.0    1.2  1  Prok-JAB  Prokaryotic homologs of the JAB domain
  ------ inclusion threshold ------
      0.038   13.9   0.0      0.049   13.6   0.0    1.4  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 !   35.4   0.0   8.5e-13   7.6e-09       8     117 ..      17     111 ..      10     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 8.5e-13
                          Prok-JAB   8 lvaharrahpeEtcGlllgkeseseevivvplvnewsnrfeipdpedslarlkfearerglevvgiwHSHpggsarP 84 
                                       ++++ r+++p E +Gll  + ++  ev + p             +  + a ++   +  +++v g +HSHp g+ rP
  gi|330507535|ref|YP_004383963.1|  17 ILEASRSTAPSEFAGLLQADGEIITEVLILPGT----------ESSRMSALVR-LYMLPNMQVAGSVHSHPSGALRP 82 
                                       778889999********9998444444444433..........4445555555.8999******************* PP

                          Prok-JAB  85 SetDrrdaaalarvkalliivgdkaeelrawrl 117
                                       Se D+  +++++   +++i+++    + ++w +
  gi|330507535|ref|YP_004383963.1|  83 SEPDLLFFSRTG--DYHIIVGPP--FDEQSWVC 111
                                       **********97..677777775..55569976 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.4e-06     0.049      69      90 ..      71      92 ..      24     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-06
                                      EEEE-TTS--S--HHHHHHHHH CS
                              RadC 69 laHnhPsgdlepSeeDieltkr 90
                                       +H hPsg l+pSe D+ +  r
  gi|330507535|ref|YP_004383963.1| 71 SVHSHPSGALRPSEPDLLFFSR 92
                                      59**************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       166  (0.00925874); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.58
# Mc/sec: 719.35
//
Query:       gi|330507536|ref|YP_004383964.1|  [L=143]
Description: cytidyltransferase-like domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-18   64.9   0.0    1.1e-17   64.6   0.0    1.1  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.14   12.0   0.1       0.63    9.9   0.1    2.3  2  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 !   64.6   0.0   1.2e-21   1.1e-17       1     141 [.       5     131 ..       5     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 1.2e-21
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       +a GtFD++H GH  +le+ k+l++e l+v+v+ d+++++k kp+ ++e+R +m+e +k vd++i  +  ++ r ++
  gi|330507536|ref|YP_004383964.1|   5 VATGTFDLLHPGHVLYLERSKALGDE-LVVIVARDVNVRHKAKPILPEEQRRRMIESLKPVDRAILGEVGDIFR-TI 79 
                                       589***********************.************999*******************************8.** PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHH CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkir 141
                                       ++l+pd  ++ +g d++ d      l+   + +++    r      v + ++++++ +Ss +i 
  gi|330507536|ref|YP_004383964.1|  80 EDLRPD--IITLGFDQHFDP-----LRLEHDLFRRGLHPRI-----VRIEEQEPCELCSSRRIV 131
                                       ******..*******99993.....4444444444444333.....558899999999988875 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1     7e-05      0.63       8      36 ..       3      31 ..       1     102 [. 0.85
   2 ?   -3.1   0.0       0.7   6.2e+03      48      66 ..     110     128 ..     108     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7e-05
                           FAD_syn  8 avvtlGnFDGvHlGHqallkkaveaakek 36
                                       vv+ G FD +H GH   l++ +++ +e 
  gi|330507536|ref|YP_004383964.1|  3 LVVATGTFDLLHPGHVLYLERSKALGDEL 31
                                      599************99999888877654 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.7
                           FAD_syn  48 hPrevlakekaparLttle 66 
                                       hPr v  +e++p++L + +
  gi|330507536|ref|YP_004383964.1| 110 HPRIVRIEEQEPCELCSSR 128
                                       8888888889999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1021.69
//
Query:       gi|330507537|ref|YP_004383965.1|  [L=154]
Description: Cytidylyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-14   54.6   0.0    1.5e-14   54.4   0.0    1.0  1  CTP_transf_like  Cytidylyltransferase-like
     0.0025   17.7   0.0      0.005   16.7   0.0    1.5  2  FAD_syn          FAD synthetase
  ------ inclusion threshold ------
       0.11   13.3   0.0       0.17   12.7   0.0    1.3  1  CAP              Cysteine-rich secretory protein family
       0.15   11.5   0.0        1.8    8.0   0.0    2.1  2  ATP-sulfurylase  ATP-sulfurylase


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 !   54.4   0.0   3.4e-18   1.5e-14       2     140 ..       6     140 ..       5     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 3.4e-18
                                       EEE--TT--HHHHHHHHHHHHHSSES.EEEEEESSTHCSST-.SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHH CS
                   CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleed.livgvpsdeppkkkk.kplasaeeRlemlelakevdevisvdpweltrev 76 
                                       +gGtFDpiH GHl+ll++a++l +   +++g++sde +++   +++ ++e R ++l++    ++ + +d+  +t+ +
  gi|330507537|ref|YP_004383965.1|   6 VGGTFDPIHDGHLALLRRAFELSGDGeVVIGLTSDEMARSSRtRSVRNYEVREKNLRAV--IKKCFGIDDVHITK-I 79 
                                       69*******************999879**************55****************..88899********7.9 PP

                                       HHHTTT......TEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHH CS
                   CTP_transf_like  77 lkklkp......dklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstki 140
                                       +++ +p      d  ++v++ ++l  +++ ++l+      +l + +++       +  +++   iSst++
  gi|330507537|ref|YP_004383965.1|  80 TDQCGPsiyecfD--FIVVSPETLPMAEKINRLRAKKNLPPLQISEIE-------YQMAQDKVRISSTRV 140
                                       9999997777777..999***9*9999777777777777777777777.......889999999****98 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-06     0.005      11      86 ..       6      80 ..       2      91 .. 0.76
   2 ?   -2.6   0.0         1   4.6e+03     146     157 ..     127     138 ..     105     139 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                           FAD_syn 11 tlGnFDGvHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklelleelgvdavlvvdFt 86
                                      + G FD +H GH all++a e++ + ++ +  +t ++  r+  +++  + ++ + + ++ + + +g+d v +++ t
  gi|330507537|ref|YP_004383965.1|  6 VGGTFDPIHDGHLALLRRAFELSGDGEVVIG-LTSDEMARSSRTRSVRNYEVREKNLRAVIKKCFGIDDVHITKIT 80
                                      4489******************987776655.66677777777767777778888888888788888877777655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1
                           FAD_syn 146 kveleeekisst 157
                                       ++ +++++isst
  gi|330507537|ref|YP_004383965.1| 127 QMAQDKVRISST 138
                                       346677888887 PP

>> CAP  Cysteine-rich secretory protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.8e-05      0.17       2      31 ..     105     134 ..     104     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHHHTT----EE-HHHHHHHHHHHH CS
                               CAP   2 eahNeyRaaaglppLkwdatLekaAqdhar 31 
                                       e +N +Ra+++lppL++++  +++Aqd++r
  gi|330507537|ref|YP_004383965.1| 105 EKINRLRAKKNLPPLQISEIEYQMAQDKVR 134
                                       579***********************9987 PP

>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0004       1.8      27      81 ..       9      69 ..       1      80 [. 0.62
   2 ?    3.4   0.0      0.01        46     100     167 ..      56     134 ..      37     150 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0004
                                      ESS---HHHHHHHHHHHHH.TSEE.....EEEEEB-SB-STTST.THHHHHHHHHHHHHHHS CS
                   ATP-sulfurylase 27 trnplHraHeellkralee.eadg.....lllhplvgptkpgdv.paevrvrayealieeyl 81
                                      t +p+H +H +ll+ra e  + dg     l    + + +++ +v ++evr +  +a+i++ +
  gi|330507537|ref|YP_004383965.1|  9 TFDPIHDGHLALLRRAFELsG-DGevvigLTSDEMARSSRTRSVrNYEVREKNLRAVIKKCF 69
                                      789**************9743.3332222333344444555554246677777777777655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHTT-SEEEE-TTTT-STC...........SS-TTHHHHHHHHCHHHCTSEEEE---EEEETTTTE CS
                   ATP-sulfurylase 100 prEallhaiirknyGcthfivGrdhagvgd...........fYgpydaqellakvagelgiepvkfeeavYckkege 165
                                        rE  l+a+i+k +G+  + + +    +g              ++  ++e +++++++ ++ p++++e+ Y +++++
  gi|330507537|ref|YP_004383965.1|  56 VREKNLRAVIKKCFGIDDVHITKITDQCGPsiyecfdfivvSPETLPMAEKINRLRAKKNLPPLQISEIEYQMAQDK 132
                                       57888888888888887766654444333332555555433223334455555666668888888888888888884 PP

                                       EE CS
                   ATP-sulfurylase 166 va 167
                                       v 
  gi|330507537|ref|YP_004383965.1| 133 VR 134
                                       43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1192.08
//
Query:       gi|330507538|ref|YP_004383966.1|  [L=354]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Methanosaeta concilii GP6]
Scores for complete 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-45  154.3   0.0      5e-45  154.0   0.0    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    3.1e-19   69.3   0.4    2.4e-14   53.6   0.1    2.4  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.3e-07   31.2   0.0    0.00056   19.3   0.0    2.3  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
    0.00035   21.1   0.0      0.052   14.0   0.0    2.3  2  XdhC_C         XdhC Rossmann domain
     0.0019   18.1   0.0        1.3    8.9   0.0    2.4  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
     0.0075   16.5   0.1       0.74   10.1   0.0    2.6  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.044   12.9   2.6       0.59    9.2   0.0    2.4  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
       0.14   11.2   2.0        7.9    5.4   0.0    2.5  2  GIDA           Glucose inhibited division protein A
       0.15   12.3   0.2        1.4    9.2   0.0    2.4  2  TrkA_N         TrkA-N 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 !  154.0   0.0   2.5e-48     5e-45       2     279 ..       2     268 ..       1     283 [. 0.81

  Alignments for each domain:
  == domain 1  score: 154.0 bits;  conditional E-value: 2.5e-48
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCCCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgielllg 72 
                                       +v+viGgG+AG ++ + +a   ++ tl+e  +     + l+++ l gva+ ++ a+      e   ++  g + + +
  gi|330507538|ref|YP_004383966.1|   2 KVAVIGGGIAGAELIRVAAPCPLEFTLIE-PKKQIEMQALYPEYLGGVARLQDLAAplkpfcE---RV--GAHHIQE 72 
                                       8***************************5.555556668888999999999998887753331...11..2222222 PP

                                       CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC..TTBEECCSECHHHHHHCCSS-TSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  73 eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv.aenvgklvrtldsaealklkllpkrivvv 148
                                        +++++ +g+ +v++      +  ++++d+ v+AtG+ ++ +gi Gv ++  +  +++ + a+++ +++ p+ri++ 
  gi|330507538|ref|YP_004383966.1|  73 -KALRL-EGS-TVVC------ERSQVEFDYAVIATGAAQNYFGIRGVeNTFSINTLEETKRARRFVEDNYPERIMIM 140
                                       .34444.333.6666......34579*********************444455555666666677777777****** PP

                                       S-SHHHHHHHHHHHHH.T-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSC CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 149 GgGyiGvElAaalakl.gkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledge 224
                                       G+G++GvE A+ la+   + ++++ear+r+l+++  + s+ +e+al k+Gv++ + t+v e++++        +d +
  gi|330507538|ref|YP_004383966.1| 141 GSGLTGVEAASILAESlDASIYVIEARERVLPQFSAQTSELVERALSKRGVNILTSTQVAEVKKDC----IMFTDDT 213
                                       ************75543889*******************************************887....5899999 PP

                                       EEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC....T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                       Pyr_redox_2 225 eidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva....g 279
                                        +d+d+ ++ +Gv+ps+ +  ++l l+  ++g+++vd++l+    +++aiGD+a    +
  gi|330507538|ref|YP_004383966.1| 214 CLDCDMAIWTAGVKPSQFI--QDLDLPK-KNGWLLVDPYLNL-KSNLFAIGDCAwveiD 268
                                       9***************977..8*****9.***********55.99*********76653 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0     4e-05      0.08       1      35 [.       2      36 ..       2      48 .. 0.88
   2 !   53.6   0.1   1.2e-17   2.4e-14       1      69 [.     136     205 ..     136     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      kv+v+GgG  g El  ++a    + t++e ++++ 
  gi|330507538|ref|YP_004383966.1|  2 KVAVIGGGIAGAELIRVAAPCPLEFTLIEPKKQIE 36
                                      79*****************************9997 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 1.2e-17
                                       EEEEECSSHHHHHHHHHHHH.TTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalae.lgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegs 69 
                                       +++++G+G++g+E+A++lae l ++++v+e+++++l+++ +++s+++++ l+k+g+++l++t+v+e++++
  gi|330507538|ref|YP_004383966.1| 136 RIMIMGSGLTGVEAASILAEsLDASIYVIEARERVLPQFSAQTSELVERALSKRGVNILTSTQVAEVKKD 205
                                       699***************998**********************************************976 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 !    9.7   0.0   0.00024      0.48      30      50 ..       2      22 ..       1      46 [. 0.82
   2 !   19.3   0.0   2.8e-07   0.00056      27      78 ..     133     200 ..     125     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00024
                                      EEEEESTSHHHHHHHHHHHHT CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakgl 50
                                      kv viGgG+aG + i++a+  
  gi|330507538|ref|YP_004383966.1|  2 KVAVIGGGIAGAELIRVAAPC 22
                                      89**************99865 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.8e-07
                                       ---EEEEESTSHHHHHHHHH.HHHTT-EEEEEESSHHHHHHHHHTTTCECEE...............H CS
                       AlaDh_PNT_C  27 epakvlviGgGvaGlqAiat.akglgakVtvlDvrparleqleslgakfvev...............l 78 
                                        p +++++G G  G++A+++ a +l+a+++v++ r+++l q+++  ++ ve                 
  gi|330507538|ref|YP_004383966.1| 133 YPERIMIMGSGLTGVEAASIlAESLDASIYVIEARERVLPQFSAQTSELVERalskrgvniltstqvA 200
                                       5789**************86599*******************99888877765555555555444441 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   2.6e-05     0.052       1      76 [.       3     109 ..       3     130 .. 0.77
   2 ?    4.9   0.0     0.018        36       2      45 ..     138     204 ..     137     230 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE................................. CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade................................. 44 
                                       ++++G+g  +++l+r+aa ++++ t+++p+++++ ++ +p   e                                 
  gi|330507538|ref|YP_004383966.1|   3 VAVIGGGIAGAELIRVAAPCPLEFTLIEPKKQIEMQALYP---Eylggvarlqdlaaplkpfcervgahhiqekalr 76 
                                       579****************************999666666...2233555566666677777777777777888888 PP

                                       ...-EEEE--S-HHHHHHHHHHHSSS--SEEEESS CS
                            XdhC_C  45 ...tavvvlthdhklDaealeaalrkkaayigllG 76 
                                          + vv+   + ++D++++++      +y+g+ G
  gi|330507538|ref|YP_004383966.1|  77 legSTVVCERSQVEFDYAVIATGA--AQNYFGIRG 109
                                       988777777778888888887777..455666655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.018
                                       EEE--STTHHHHHHH.HHHHTEEEEEEES-GGGG......-GGG-TT-SE........................- CS
                            XdhC_C   2 vifGaghvaqalarl.aaalgfrvtvvdpreefa......tkerfpeade........................t 45 
                                       +i+G g  + + a++ a++l+ +++v+++re++       t        +                        +
  gi|330507538|ref|YP_004383966.1| 138 MIMGSGLTGVEAASIlAESLDASIYVIEARERVLpqfsaqT--------SelveralskrgvniltstqvaevkK 204
                                       7999999998888862678************8553443331........12344444454444444444444433 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0029       5.9       1      34 [.       2      35 ..       2      44 .. 0.89
   2 !    8.9   0.0   0.00064       1.3       2      70 ..     137     209 ..     136     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0029
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      kvaviG G+ Ga++  v+a   le +l++ ++++
  gi|330507538|ref|YP_004383966.1|  2 KVAVIGGGIAGAELIRVAAPCPLEFTLIEPKKQI 35
                                      79*****************999999999988765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00064
                                       EEEE--SCCHHHHHHHHHHT.T-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-...HHHHCCCHHCEEEE CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasa.gleVvlvdiseealekalekieksleklvekgklk...eeeveaalarisft 70 
                                       + ++G+G+ G + a+++a++ + ++ +++ +e+ l +  ++ ++ +e++ +k+ ++     +v+++ +   + 
  gi|330507538|ref|YP_004383966.1| 137 IMIMGSGLTGVEAASILAESlDASIYVIEARERVLPQFSAQTSELVERALSKRGVNiltSTQVAEVKKDCIMF 209
                                       7799***************99***********************99999999888755555555554443333 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 ?    3.9   0.0     0.033        65       1      26 [.       5      30 ..       5      48 .. 0.77
   2 !   10.1   0.0   0.00037      0.74       1      31 [.     139     170 ..     139     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.033
                                      EE--SHHHHHHHHHHHCCTEEEEEE- CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvllle 26
                                      ++G+G++G+ + + +a   ++ +l+e
  gi|330507538|ref|YP_004383966.1|  5 VIGGGIAGAELIRVAAPCPLEFTLIE 30
                                      8*******866666665556666655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00037
                                       EE--SHHHHHHHHHHHCC.TEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLaka.gfdvlllekrdrl 31 
                                       I G+Gl+G  aA+ La+  ++++ ++e+r+r+
  gi|330507538|ref|YP_004383966.1| 139 IMGSGLTGVEAASILAESlDASIYVIEARERV 170
                                       77***************88**********985 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 ?    3.2   0.9      0.02        40     193     208 ..       2      17 ..       1      37 [. 0.89
   2 ?    9.2   0.0    0.0003      0.59     182     241 ..     125     186 ..      32     208 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.02
                       K_oxygenase 193 riaVvGsGqSaaeife 208
                                       ++aV+G+G  +ae+++
  gi|330507538|ref|YP_004383966.1|   2 KVAVIGGGIAGAELIR 17 
                                       79***********987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0003
                       K_oxygenase 182 lerkeellakkriaVvGsGqSaaeifedllrrqkk..velklvtrsealeplddspfvneif 241
                                       ++r  e++ ++ri+++GsG ++ e +  l+++ ++  + ++   r   ++ ++ s++v   +
  gi|330507538|ref|YP_004383966.1| 125 ARRFVEDNYPERIMIMGSGLTGVEAASILAESLDAsiYVIEARERVLPQFSAQTSELVERAL 186
                                       3333448999***************9999988663234444444444455555666665555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.004       7.9       1      19 [.       2      20 ..       2      52 .. 0.77
   2 ?    4.5   0.2    0.0079        16       2      20 ..     137     155 ..     136     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.004
                                      CEEEE-SSHHHHHHHHHHH CS
                              GIDA  1 dviViGgGhAGceAAlaaa 19
                                      +v ViGgG AG e    aa
  gi|330507538|ref|YP_004383966.1|  2 KVAVIGGGIAGAELIRVAA 20
                                      699********99655555 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0079
                                       EEEE-SSHHHHHHHHHHHH CS
                              GIDA   2 viViGgGhAGceAAlaaar 20 
                                       +++ G G+ G+eAA  +a+
  gi|330507538|ref|YP_004383966.1| 137 IMIMGSGLTGVEAASILAE 155
                                       789***********99886 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.47   9.4e+02       1      30 [.       3      32 ..       3      48 .. 0.75
   2 ?    9.2   0.0   0.00069       1.4       1      43 [.     137     180 ..     137     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.47
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESS CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkd 30
                                      +++iG G  G +l++       + +++i+ +
  gi|330507538|ref|YP_004383966.1|  3 VAVIGGGIAGAELIRVAAPcPLE-FTLIEPK 32
                                      689*********99977664444.7777765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00069
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSE CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreegle 43 
                                       i+i+G G +G + a  L e    +++vi+ +e+++ +++++  e
  gi|330507538|ref|YP_004383966.1| 137 IMIMGSGLTGVEAASILAEsLDASIYVIEARERVLPQFSAQTSE 180
                                       79*****************65567**********9999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2395.49
//
Query:       gi|330507539|ref|YP_004383967.1|  [L=147]
Description: hypothetical protein MCON_1496 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.039   14.0   0.0      0.071   13.2   0.0    1.4  1  HTH_7      Helix-turn-helix domain of resolvase
      0.051   13.6   0.0      0.079   12.9   0.0    1.3  1  HTH_Crp_2  Crp-like helix-turn-helix domain
       0.15   11.9   0.0       0.32   10.8   0.0    1.5  1  TetR_N     Bacterial regulatory proteins, tetR family
       0.17   11.8   0.0       0.28   11.1   0.0    1.4  1  MarR_2     MarR family


Domain annotation for each model (and alignments):
>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.6e-05     0.071      22      44 ..      31      53 ..      30      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                                      --STTTSSSS---SSSS--SS-- CS
                             HTH_7 22 isiskIAkevnisRsTvYRylad 44
                                      +s+++IA+  n+sR+T+ + +++
  gi|330507539|ref|YP_004383967.1| 31 YSKTDIAEGANLSRATLFKAWPK 53
                                      6899***************9987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.8e-05     0.079      20      54 ..      29      64 ..      17      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglis.rg 54
                                      ++ +++++A+  +l+r t+ ++  +L+   li+ ++
  gi|330507539|ref|YP_004383967.1| 29 FDYSKTDIAEGANLSRATLFKAWPKLEALDLITaTR 64
                                      789*****************************9655 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 ?   10.8   0.0   7.1e-05      0.32      21      42 ..      35      56 ..      30      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.1e-05
                                      HHHHHHTSSHHHHHHHTSSHHH CS
                            TetR_N 21 eIAkrAGvskgalYryFpsKee 42
                                      +IA+ A++s+++l++ +p  e+
  gi|330507539|ref|YP_004383967.1| 35 DIAEGANLSRATLFKAWPKLEA 56
                                      9**************9997555 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.3e-05      0.28       2      56 ..      11      65 ..      10      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.3e-05
                                      T--HHHHHHHHHHHCTTTSEE..EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdl..tvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      g++   + vL +L +++   +  + +++a+  +ls++++ ++  +L+a  L++ +++
  gi|330507539|ref|YP_004383967.1| 11 GIKSPVLKVLDFLMDNEC--FdySKTDIAEGANLSRATLFKAWPKLEALDLITATRS 65
                                      556666789999999996..355*****************************87765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1213.82
//
Query:       gi|330507540|ref|YP_004383968.1|  [L=83]
Description: hypothetical protein MCON_1497 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 697.43
//
Query:       gi|330507541|ref|YP_004383969.1|  [L=149]
Description: ribonuclease HI [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-14   52.8   0.0    3.6e-14   52.7   0.0    1.1  1  RVT_3     Reverse transcriptase-like
      9e-09   35.7   0.0    1.2e-08   35.2   0.0    1.2  1  RNase_H   RNase H


Domain annotation for each model (and alignments):
>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.0     4e-18   3.6e-14      11     122 ..      17     129 ..       5     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 4e-18
                             RVT_3  11 gaggagvvirdsnGevllagaek.lqgkasveeAElqALlrGLqlalklgirr.lvvegDsktvvqllngrekvkss 85 
                                       g ++ g++i+ ++  +  ++ +   ++++++ +AE+++Ll + +   + +i + +++ gDs+ v+++++g+ +v+s 
  gi|330507541|ref|YP_004383969.1|  17 GVAAYGYLICRDKEPIWKGFGAVgEGRGMTNNVAEYEGLLAAARWLNDEEIDEkIQIRGDSELVIKQMKGEYRVNSA 93 
                                       566778777777666666666666899****************99999999655*********************** PP

                             RVT_3  86 elanlldeirkllksfesvsvehipReqNrvAdalAk 122
                                         ++++ +i++ll    +vs++++pRe+N  Ad l++
  gi|330507541|ref|YP_004383969.1|  94 TSKRYVPQIKELLVGK-EVSFQWVPREKNEEADRLSR 129
                                       *************976.8***************9986 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   1.4e-12   1.2e-08       4     141 ..       2     131 ..       1     133 [. 0.68

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.4e-12
                                       EEEEEEEEEECTTTCE..EEEEEECTT.....EEEEEEEC.CCCHHHHHHHHHHHHHHH...TT.SCSEEEEEES-H CS
                           RNase_H   4 vvvYtDGsclgnpgeg..gagavlykeg...arnisaple.eaqtnnraELsAvieaLk...alksdekvniytDSk 71 
                                       ++vY DG c  ++  g   +g+++ +++   ++ + a  e    tnn aE + + +a +   + ++dek++i+ DS+
  gi|330507541|ref|YP_004383969.1|   2 ITVYFDGLCYPKNPGGvaAYGYLICRDKepiWKGFGAVGEgRGMTNNVAEYEGLLAAARwlnDEEIDEKIQIRGDSE 78 
                                       69*******98866662355666677765666666666667899******77777776521044677********** PP

                                       HHHHHHHCCCHHHHHTTSSSETTSSBHTTHHHHHHHHHCHCSSEEEEEE-SCCSSSTHHHHHHHHHHHHH CS
                           RNase_H  72 YvvkgitqwvhrwkknawkttseqkpvknkdlaellkelakkkkvqlkwvkgHaGvpkgNemaDrlAkea 141
                                        v+k ++    +  +   + +++      k +  ++kel   k+v+++wv+      ++Ne+aDrl + a
  gi|330507541|ref|YP_004383969.1|  79 LVIKQMK----GEYR--VNSATS------KRYVPQIKELLVGKEVSFQWVP----R-EKNEEADRLSRVA 131
                                       ****333....2222..212222......33444555556889*******9....4.68******98866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1049.05
//
Query:       gi|330507542|ref|YP_004383970.1|  [L=380]
Description: hypothetical protein MCON_1499 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.4e-51  172.8   0.0    8.2e-51  171.9   0.0    1.4  1  YhcG_C     YhcG PDDEXK nuclease domain
    1.8e-42  144.7   0.4    2.6e-42  144.2   0.4    1.2  1  DUF1016_N  DUF1016 N-terminal domain
  ------ inclusion threshold ------
      0.023   14.9   0.5        1.5    9.1   0.0    2.6  2  THDPS_N_2  Tetrahydrodipicolinate N-succinyltransferase N-ter


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 !  171.9   0.0   1.4e-54   8.2e-51       3     154 ..     200     350 ..     198     351 .. 0.94

  Alignments for each domain:
  == domain 1  score: 171.9 bits;  conditional E-value: 1.4e-54
                            YhcG_C   3 ilkdpyvldflelkeeykErelekalieklkkfllelGkgFafvgrqyrleveekefyidLlfYhlklkcyvvieLK 79 
                                       +++dpy+ldfl+l++ y+Er+le a++++l++fllelG++F+f++rq+r+++++++fy+dLlfYh++l+++v+ieLK
  gi|330507542|ref|YP_004383970.1| 200 VFRDPYLLDFLGLEDIYSERDLEAAILRELERFLLELGTDFSFIARQKRMTIGDRDFYLDLLFYHRSLHRLVAIELK 276
                                       68*************************************************************************** PP

                            YhcG_C  80 vgefkpedagklnlYlsaldeelkkeednptiGiilckekdktvveyalkeinkpigvseY..elpkelpeelkekl 154
                                        g+f+++++g+++lYl++ld+++++++++p+iG+ilc ek+++++e  l+  + +i v+eY  elp ++   l++kl
  gi|330507542|ref|YP_004383970.1| 277 LGSFDAAYKGQMELYLRWLDRYERRPGEEPPIGLILCGEKNREQIE-LLQLDRGEIRVAEYlvELPPRE--MLEAKL 350
                                       **********************************************.6788888*******77676666..666665 PP

>> DUF1016_N  DUF1016 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.2   0.4   4.4e-46   2.6e-42       2     137 .]      36     171 ..      35     171 .. 0.98

  Alignments for each domain:
  == domain 1  score: 144.2 bits;  conditional E-value: 4.4e-46
                         DUF1016_N   2 ikelieqarqkaakavnselvelyweiGkrive...kqeraeyGkkvikkLsedLkkefpevkGFsernlknmrqfy 75 
                                       i+ lieqa+ ++a++vnselv lyw+iGkri      ++raeyG+kv++ +se+L +e++  kGF ++n+ +m++f+
  gi|330507542|ref|YP_004383970.1|  36 IRPLIEQAKARVAQSVNSELVLLYWQIGKRIRYdlpAESRAEYGAKVVELVSERLAAEYG--KGFRRSNVFHMIHFA 110
                                       7889***************************999999***********************..*************** PP

                         DUF1016_N  76 eaykeeeilqqlvaqlsWshnllllekvkdeeerefYleeaieegWsrreLerqiksklyer 137
                                       e++++ +i+q+l+ qlsWsh+++++  +kd+ +r+fY+e+a  e+Ws+r+L+++i+ +lyer
  gi|330507542|ref|YP_004383970.1| 111 EVFDDAKIVQTLSGQLSWSHFIEII-YLKDPLQRQFYTEMARVERWSVRTLRKKIQGMLYER 171
                                       *************************.***********************************8 PP

>> THDPS_N_2  Tetrahydrodipicolinate N-succinyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.014        86       9      49 ..       4      53 ..       1      67 [. 0.62
   2 ?    9.1   0.0   0.00025       1.5      34      46 ..     324     342 ..     317     366 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.014
                                      HHHTGGG--S..SS--HHH.......HHHHHHHHHHHHTTSS-SEEEETT CS
                         THDPS_N_2  9 awerrdelep..etagaea.......raaveevleaLdaGelRvAekkdg 49
                                      a++ r+e +p  + a++e+       ++ v ++  ++++ ++RvA+  + 
  gi|330507542|ref|YP_004383970.1|  4 AFRMREEQDPagKIAESEEnevsvasEELVGSIRPLIEQAKARVAQSVNS 53
                                      55555555532222333334444444788999999**********97444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00025
                                       HHHHTTSS-SEE......E CS
                         THDPS_N_2  34 eaLdaGelRvAe......k 46 
                                        +Ld+Ge+RvAe      +
  gi|330507542|ref|YP_004383970.1| 324 LQLDRGEIRVAEylvelpP 342
                                       58**********6666551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2759.27
//
Query:       gi|330507543|ref|YP_004383971.1|  [L=107]
Description: hypothetical protein MCON_1500 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 772.29
//
Query:       gi|330507544|ref|YP_004383972.1|  [L=318]
Description: delta-aminolevulinic acid dehydratase [Methanosaeta concilii GP6]
Scores for complete 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-141  468.6   0.0     1e-140  468.5   0.0    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.5   0.0  5.6e-145    1e-140       2     316 ..       2     314 ..       1     315 [. 0.98

  Alignments for each domain:
  == domain 1  score: 468.5 bits;  conditional E-value: 5.6e-145
                                       --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE- CS
                              ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvp 78 
                                       +r+rrlr  + +re+v+et+l  ++l+ p+fv+e+ +e++ i+smpg+y+ s++++++e+  l +lg++avllFg+p
  gi|330507544|ref|YP_004383972.1|   2 RRMRRLRV-PGIREMVSETDLGIQNLVQPIFVDERITEPRMIESMPGQYHQSIESVAAEAGALEDLGVPAVLLFGLP 77 
                                       68899886.67****************************************************************** PP

                                       SS-BSS-GGGGSTTSHHHHHHHHHHHH-TTSEEEEEE-STTTBSS-SSSEEESS.EEHHHHHHHHHHHHHHHHHCT- CS
                              ALAD  79 eekdeegsealnedglvqrairaikeevpelvvitDvclceytshGhcgileekevdndetlellakvavsqaeaGa 155
                                       ++kde+gs+a+++dg++q+a+raike  ++l+vitD+clceytshGhcg+++ ++v+ndetl ll +vavsqa+aGa
  gi|330507544|ref|YP_004383972.1|  78 STKDEMGSAAADPDGVIQKAVRAIKEC-TSLLVITDLCLCEYTSHGHCGLVRGERVLNDETLPLLGEVAVSQAQAGA 153
                                       ************************976.99*********************************************** PP

                                       SEEEE-S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHHHHHHHHH CS
                              ALAD 156 divapSdmmDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansrealrevel 232
                                       divapS+mmD +v+air++Ld +gf +++ilsYsaKyaS+fYgPFr+aa+s  +fgdr+ Yqmdpan  eal ev+l
  gi|330507544|ref|YP_004383972.1| 154 DIVAPSGMMDHMVRAIRTSLDWEGFADTPILSYSAKYASTFYGPFREAAQSGFAFGDRRGYQMDPANFAEALWEVQL 230
                                       ***************************************************************************** PP

                                       HHHTT-SBEEEES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHTT-SEEEET CS
                              ALAD 233 dleeGADivmvKPalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEsllsikRAGadliltY 309
                                       d+eeGAD+vmvKPa++ylD++r+vke f +p+aayqvSGEY+mi+aaae+gwlde++++lEsl++ikRAGad+i+tY
  gi|330507544|ref|YP_004383972.1| 231 DIEEGADMVMVKPAMPYLDVLRAVKEMFGMPTAAYQVSGEYSMIQAAAERGWLDERAAFLESLMCIKRAGADMIITY 307
                                       ***************************************************************************** PP

                                       THHHHHH CS
                              ALAD 310 fakevak 316
                                       +ake+a+
  gi|330507544|ref|YP_004383972.1| 308 WAKEYAR 314
                                       ****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2405.10
//
Query:       gi|330507545|ref|YP_004383973.1|  [L=381]
Description: glutamyl-tRNA reductase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-39  134.1   0.1    3.3e-39  134.1   0.1    2.1  3  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
    2.7e-32  111.5   0.9    4.3e-32  110.9   0.1    1.8  2  GlutR_N        Glutamyl-tRNAGlu reductase, N-terminal domain
    4.9e-20   71.8   4.0    9.6e-20   70.8   4.0    1.5  1  GlutR_dimer    Glutamyl-tRNAGlu reductase, dimerisation domai
     0.0004   20.9   0.1     0.0021   18.6   0.0    2.3  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.014   14.9   0.1      0.034   13.6   0.1    1.7  1  Glu_dehyd_C    Glucose dehydrogenase C-terminus
      0.022   14.1   0.1       0.11   11.8   0.0    2.2  2  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
      0.057   12.8   0.0        0.1   11.9   0.0    1.5  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
       0.08   12.3   0.1       0.18   11.2   0.1    1.5  1  LVIVD          LVIVD repeat
        0.1   13.1   0.1       0.44   11.0   0.0    2.2  2  NAD_binding_7  Putative NAD(P)-binding
       0.14   11.5   0.2       0.27   10.5   0.2    1.4  1  ThiF           ThiF family
        0.2   11.2   3.1       0.42   10.2   3.1    1.5  1  HAUS6_N        HAUS augmin-like complex subunit 6 N-terminus


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 ?   -3.3   0.0       5.1   8.4e+03      40      56 ..      22      38 ..      13      57 .. 0.50
   2 !  134.1   0.1     2e-42   3.3e-39       1     138 []     128     262 ..     128     262 .. 0.99
   3 ?   -1.6   0.2       1.6   2.6e+03      54     101 ..     273     322 ..     266     329 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.1
                                      EEEESSHHHHHHHHHHH CS
                      Shikimate_DH 40 vvaNRtlerakelaeel 56
                                      vva R  +   +la++ 
  gi|330507545|ref|YP_004383973.1| 22 VVAPRGEKVLFDLAKKA 38
                                      34444444444444444 PP

  == domain 2  score: 134.1 bits;  conditional E-value: 2e-42
                                       HHHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-S CS
                      Shikimate_DH   1 elakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaead 77 
                                       +la+++l++lk+k vl+iGaGe++el+ ++Ll++++ +++v+NRtl+ a  lae+l+ge   a++++++ ++l+ ad
  gi|330507545|ref|YP_004383973.1| 128 DLAEEILGDLKGKSVLVIGAGETGELISRALLSREIGSLAVTNRTLSSAVCLAESLGGE---AVPFDDMPRRLHTAD 201
                                       59******************************************************999...*************** PP

                                       EEEE-SSSSS-SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHHH CS
                      Shikimate_DH  78 vvisataseepilekeeveealkkrkkplllvDiavPRdvepevaeledvrlytvDdLkev 138
                                       vvisat+++++il k+++e+a+++r+++ll++Dia+PRdv+++ ae+++v+l+++D Lk++
  gi|330507545|ref|YP_004383973.1| 202 VVISATSAPHYILLKSDIEMAMADRSNKLLIIDIANPRDVDQAAAEVSGVELHNIDSLKNI 262
                                       **********************************************************986 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.6
                                       HHHT.ET-EEEEGCGHHHHH..HT-SEEEE-SSSSS-SB-HHHHHCCHHH CS
                      Shikimate_DH  54 eelkgeeiealkleelkell..aeadvvisataseepilekeeveealkk 101
                                       e  + eei + +l+ l++    +ea+ +++   s+  +++ +ev++a++k
  gi|330507545|ref|YP_004383973.1| 273 EATRVEEIITEELQLLRAKYkrKEAEELLARLYSQAELIKDQEVRKAMNK 322
                                       44444445444444444333114555566666677777777777776655 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 !  110.9   0.1   2.6e-35   4.3e-32      33     146 .]       5     113 ..       1     113 [. 0.86
   2 ?   -2.2   0.1       1.9   3.2e+03      16      16 ..     308     308 ..     261     343 .. 0.61

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 2.6e-35
                           GlutR_N  33 kvkeaviLsTCNRtEiylsaeeeeeaseellellaevsleelkeklyvlegeeavrHlfrVasGLdSlvlGEdqIlg 109
                                       +v+e+++L+TCNR+E+y++a +    ++ l++l ++   +  ++ + +++++e++ Hl+r+asGL+S+++GEdqIlg
  gi|330507545|ref|YP_004383973.1|   5 RVEECAVLKTCNRVEVYVVAPRG---EKVLFDLAKK--ARVSSRIIDFHDHDESLLHLLRLASGLESMIIGEDQILG 76 
                                       678**************866554...4444444422..233447899****************************** PP

                           GlutR_N 110 QvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                                       Q+ke  + a +agt+g +Le+ f+kai+v+krvr+et
  gi|330507545|ref|YP_004383973.1|  77 QMKELTQIAMKAGTTGWMLETAFKKAIQVGKRVRKET 113
                                       ***********************************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                           GlutR_N  16 l 16 
                                       +
  gi|330507545|ref|YP_004383973.1| 308 A 308
                                       0 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   4.0   5.9e-23   9.6e-20       2      97 .]     277     377 ..     276     377 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 5.9e-23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S......--------TTHHHHHHHHHHHHHH CS
                       GlutR_dimer   2 AeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkkla....ldgedreelekltrslvnkllhept 74 
                                       +e+iI ee++ + a++k++e+++++++l+++ae i+++e+++a++kl+    l + ++++l +++rs+vnk+l ept
  gi|330507545|ref|YP_004383973.1| 277 VEEIITEELQLLRAKYKRKEAEELLARLYSQAELIKDQEVRKAMNKLSarhtLGEIEQQVLCDMSRSIVNKILSEPT 353
                                       8*************************************************9777777777***************** PP

                                       HHHHSS-TTTT.HHHHHHHHH... CS
                       GlutR_dimer  75 arLkeaedeee.ellealrrlFnl 97 
                                       ++Lk+a+++++ e+l+ l +lF l
  gi|330507545|ref|YP_004383973.1| 354 KSLKSAAERGDlEILKSLCELFRL 377
                                       ******777778**********86 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.8   7.8e+03      27      48 ..      19      40 ..      10      47 .. 0.71
   2 !   18.6   0.0   1.3e-06    0.0021       3      97 .]     143     238 ..     141     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.8
                                      CEEEEEESSCCCHHHHHHHHC- CS
                     F420_oxidored 27 eivvansrnpekaeelaeelgv 48
                                      e++v++ r ++ +  la+++ v
  gi|330507545|ref|YP_004383973.1| 19 EVYVVAPRGEKVLFDLAKKARV 40
                                      6777778888888888877665 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.3e-06
                                       EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHH.HHHHH-SEEEE-S-HHHHHHHH CS
                     F420_oxidored   3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdne.eaaeeadvvvlavkpedveevl 78 
                                        +iGaG+ ge + + ll++     ++  +++r+ ++a  lae+lg ++ + d     +  advv+ a    ++  + 
  gi|330507545|ref|YP_004383973.1| 143 LVIGAGETGELISRALLSRE--IGSLA-VTNRTLSSAVCLAESLGGEAVPFDDMpRRLHTADVVISATSAPHYILLK 216
                                       58*****************9..66666.56***************888886544156679*************9999 PP

                                       HHC...GHHHHTTSEEEEESSS CS
                     F420_oxidored  79 sel...akdalkgklvisvlag 97 
                                       s++   ++d +++ l+i+++++
  gi|330507545|ref|YP_004383973.1| 217 SDIemaMADRSNKLLIIDIANP 238
                                       999998999999999****997 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 ?   13.6   0.1   2.1e-05     0.034      11     114 ..     121     213 ..     113     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                       Glu_dehyd_C  11 siveKaielaeasrsafewepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsr 87 
                                       s+   a++lae++    + + +s+lv+GaG  G L   +l +  r++  + v++r  + + ++ l e+lG+  v   
  gi|330507545|ref|YP_004383973.1| 121 SVGSAAVDLAEEIL--GDLKGKSVLVIGAGETGELISRALLS--REIGSLAVTNR--TLSSAVCLAESLGGEAV--- 188
                                       66666666666554..467889***********888777764..78887878776..45678889*****9888... PP

                       Glu_dehyd_C  88 etpvdeipeaseemdlvvEaTGsakha 114
                                         p d++p   +  d+v+ aT +++ +
  gi|330507545|ref|YP_004383973.1| 189 --PFDDMPRRLHTADVVISATSAPHYI 213
                                       ..89*****************998766 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 ?   -2.3   0.0       1.5   2.4e+03      35      50 ..      62      77 ..      58      97 .. 0.78
   2 ?   11.8   0.0   6.9e-05      0.11      21      93 ..     124     213 ..     101     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                                      TT-EEEEE---TTTHH CS
                     THF_DHG_CYH_C 35 egkkvvvvGrsnivgk 50
                                      +g + +++G+ +i+g+
  gi|330507545|ref|YP_004383973.1| 62 SGLESMIIGEDQILGQ 77
                                      5788899999999997 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.9e-05
                                       HHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCT...........T-EEEEE-TTS......CCHHHHHCCS CS
                     THF_DHG_CYH_C  21 kgvvellketgielegkkvvvvGrsnivgkplallLlek...........natVtvchskt......kdlaeitrea 80 
                                        + v+l +e   +l+gk+v+v+G++++ +    +lL+++            + V +++s        +d+++ +++a
  gi|330507545|ref|YP_004383973.1| 124 SAAVDLAEEILGDLKGKSVLVIGAGETGELISRALLSREigslavtnrtlSSAVCLAESLGgeavpfDDMPRRLHTA 200
                                       678899999999************99876666777777577777776655555666666546667778999****** PP

                                       SEEEE-SS-TT-B CS
                     THF_DHG_CYH_C  81 divvvavGkpeli 93 
                                       d+v++a+  p+ i
  gi|330507545|ref|YP_004383973.1| 201 DVVISATSAPHYI 213
                                       ********99987 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.4e-05       0.1      29      98 ..     132     206 ..      98     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-05
                                       GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH..CHHHHTCEECSHHHH...HHH-SEEEE- CS
                      2-Hacid_dh_C  29 llgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee..eeeelgvelvsleel...laesDivslh 98 
                                           +l+gk v +iG+G+ G+ + + l + ++  +a+  +  +++   +e+lg e v ++++   l+++D+v+ +
  gi|330507545|ref|YP_004383973.1| 132 EILGDLKGKSVLVIGAGETGELISRALLSREIGSLAVTNRTLSSAvcLAESLGGEAVPFDDMprrLHTADVVISA 206
                                       44558***********************99995555554444444475666666666555542227777777654 PP

>> LVIVD  LVIVD repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00011      0.18      17      31 ..     224     238 ..     223     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                             LVIVD  17 AdqdngLvIvDISNp 31 
                                       Ad+ n L I+DI Np
  gi|330507545|ref|YP_004383973.1| 224 ADRSNKLLIIDIANP 238
                                       9*************9 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 ?   -2.9   0.0       5.8   9.5e+03      32      45 ..      19      29 ..      11      55 .. 0.60
   2 ?   11.0   0.0   0.00027      0.44       4      72 ..     136     210 ..     133     242 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.8
                     NAD_binding_7 32 kvtvvapevkeele 45
                                      +v vvap+     +
  gi|330507545|ref|YP_004383973.1| 19 EVYVVAPR---GEK 29
                                      56677776...223 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00027
                     NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklae.........eelekdlegadlviaatdd 71 
                                       dlkgk+vlv+G+Ge ++   r ll+ +     v+++    l++ v lae         +++++ l  ad+vi at+ 
  gi|330507545|ref|YP_004383973.1| 136 DLKGKSVLVIGAGETGELISRALLSREIGSLAVTNR---TLSSAVCLAEslggeavpfDDMPRRLHTADVVISATSA 209
                                       89**************99999998886544444444...33333333321111111114456668888888888876 PP

                     NAD_binding_7  72 r 72 
                                       +
  gi|330507545|ref|YP_004383973.1| 210 P 210
                                       5 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00017      0.27       8      48 ..     129     169 ..     116     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   8 lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlv 48 
                                       l+e+ +  L+ ++vl++GaG  G  + ++L    +g+l ++
  gi|330507545|ref|YP_004383973.1| 129 LAEEILGDLKGKSVLVIGAGETGELISRALLSREIGSLAVT 169
                                       6667777899**********************999999886 PP

>> HAUS6_N  HAUS augmin-like complex subunit 6 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.1   0.00026      0.42     143     202 ..     251     313 ..     226     341 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00026
                           HAUS6_N 143 qdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelkae.....k 202
                                        +l+++     +s++ +++++a+a+r+ + + e++qll+ k++  +ae+  l a+l  +      
  gi|330507545|ref|YP_004383973.1| 251 VELHNIDSLKNISRENMMQRMAEATRVEEIITEELQLLRAKYKRKEAEE--LLARLYSQaelikD 313
                                       578888888999*****************************99766554..45555433223232 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1112  (0.0620224); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2687.16
//
Query:       gi|330507546|ref|YP_004383974.1|  [L=233]
Description: siroheme synthase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   56.9   0.0    3.6e-15   56.3   0.0    1.3  1  NAD_binding_7  Putative NAD(P)-binding


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 !   56.3   0.0     2e-19   3.6e-15       1      94 [.      15     114 ..      15     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 2e-19
                     NAD_binding_7   1 lfldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele......elvkla....eeelekdlegadlvia 67 
                                       lfld++++ v+++GgG+vA+rk+  + ++   v+vv++ +   ++      ++ +l+    + ++++ l+ga+++i 
  gi|330507546|ref|YP_004383974.1|  15 LFLDMSQRLVVIFGGGKVAERKALLFSDY-GPVQVVSQSF---TPkllaskDRWELTecdlRVDFKRYLQGAFIAIP 87 
                                       79***************************.68*******5...4422233333334312235557888********* PP

                     NAD_binding_7  68 atddrelneriaeaakarrilvnvadk 94 
                                       at++ +ln+ i e+a + +ilvn++  
  gi|330507546|ref|YP_004383974.1|  88 ATSNSQLNRSIEEEAIRVGILVNRVEG 114
                                       ***************88******9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1601.26
//
Query:       gi|330507547|ref|YP_004383975.1|  [L=152]
Description: helix-turn-helix DNA binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-30  104.7   0.0    1.2e-29  102.3   0.0    1.9  2  AsnC_trans_reg2  AsnC-like ligand binding domain
     0.0027   17.5   1.3      0.005   16.7   0.2    2.0  2  HTH_AsnC-type    AsnC-type helix-turn-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 ?    0.1   0.0       0.1     9e+02      40      64 ..      21      45 ..      19      54 .. 0.85
   2 !  102.3   0.0   1.3e-33   1.2e-29       2      82 .]      62     146 ..      61     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.1
                   AsnC_trans_reg2 40 wpynlyfmvharseeeveevlaeia 64
                                       py ++  v +  e+e+ ++l+ ++
  gi|330507547|ref|YP_004383975.1| 21 RPYRVWGEVLGMGEDEIISRLRAME 45
                                      58999*9999999999999888876 PP

  == domain 2  score: 102.3 bits;  conditional E-value: 1.3e-33
                   AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeR....ewpynlyfmvharseeeveevlaeiaaatgledyev 74 
                                       lG+ anal+aw+vp e+v+e+++++a+ +evtHcYeR    +wpyn+y+mvh rs+ee+ +++++++++ g++dy v
  gi|330507547|ref|YP_004383975.1|  62 LGILANALIAWRVPPEKVDEAGAIFAAAEEVTHCYERataqDWPYNIYTMVHSRSREECLQIAERLSSRSGISDYIV 138
                                       8999*********************************99988*********************************** PP

                   AsnC_trans_reg2  75 LpstrefK 82 
                                       L+s++e+K
  gi|330507547|ref|YP_004383975.1| 139 LFSEKEYK 146
                                       *******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 !   16.7   0.2   5.5e-07     0.005       1      42 []       1      45 [.       1      45 [. 0.98
   2 ?   -1.4   0.1      0.23   2.1e+03      11      27 ..     120     127 ..     115     131 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.5e-07
                     HTH_AsnC-type  1 LDeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrLe 42
                                      +De+D+ +L+  q       ++y+  +e +G+ e++++ R+r++e
  gi|330507547|ref|YP_004383975.1|  1 MDELDLELLKVAQDGldlTERPYRVWGEVLGMGEDEIISRLRAME 45
                                      9************99****************************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.23
                     HTH_AsnC-type  11 aLqedaRisyaeLAerv 27 
                                       +Lq         +Aer+
  gi|330507547|ref|YP_004383975.1| 120 CLQ---------IAERL 127
                                       445.........45444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1178.98
//
Query:       gi|330507548|ref|YP_004383976.1|  [L=712]
Description: cell surface protein [Methanosaeta concilii GP6]
Scores for complete 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-61  205.8  48.3    1.3e-25   90.1  20.2    4.6  4  NosD        Periplasmic copper-binding protein (NosD)
    1.1e-57  194.4  90.6    2.8e-15   56.5   9.4    5.1  6  Beta_helix  Right handed beta helix region


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   2.7   1.7e-14   1.5e-10      23     155 ..      82     232 ..      59     235 .. 0.69
   2 !   59.3   7.1   3.7e-20   3.3e-16      40     157 ..     229     344 ..     225     352 .. 0.94
   3 !   41.7   0.2   8.9e-15     8e-11      26     154 ..     397     525 ..     365     527 .. 0.92
   4 !   90.1  20.2   1.4e-29   1.3e-25      15     212 ..     497     684 ..     491     709 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.7e-14
                              NosD  23 nsegseisnneisnsrdgi.lldnssnntitgntienlryGihlenses...................ntiedntls 79 
                                       n++g+ei + +i++sr+   l   s ++++ ++ti+ +++++  e+s++                   n++ ++ ++
  gi|330507548|ref|YP_004383976.1|  82 NAPGCEIYDLKINTSRSDAsLSLLSGDCQVIRCTISGEKAAVSSEGSNNtiancsisspagieifapdNRVLGCHIQ 158
                                       55556666666655555554445555556666666666666655555554444444444444444444899999999 PP

                              NosD  80 snesGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGill 155
                                       +++ G+ + ++s++ +e+ ti   +  G+l++ds+ n + nNti+ ++ G+ l++s++n+ +gN++++    Gi +
  gi|330507548|ref|YP_004383976.1| 159 GSGIGVRINQTSGCWVEDCTIAALQ--GVLIEDSDRNGVVNNTILTDGLGLVLTRSDGNVASGNNLSGAFVSGIDM 232
                                       9999999999998899999888873..6999999999999999999999999999999999999998888888765 PP

  == domain 2  score: 59.3 bits;  conditional E-value: 3.7e-20
                              NosD  40 gilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsssnntlenNtisnnenyGillsdssn 115
                                       gi + ns  n+i  n+ie ++ Gi l  +e++++++n++ +ne +Gi+  + s+ +l  N +++n n Gills+s++
  gi|330507548|ref|YP_004383976.1| 229 GIDMLNSRFNDIAANKIEGGKVGISLRVTEHCNVTSNWCLGNErAGIYGNEASGLMLAENDLIENGN-GILLSASAD 304
                                       778899*************************************9*********99**********99.********* PP

                              NosD 116 ntisnNtisnnnkGiflensssntitgNriesnqkiGillls 157
                                       n i+ N +s n +Gi+l++s +n +++N  e n  + +  ++
  gi|330507548|ref|YP_004383976.1| 305 NIIRSNLASHNVYGISLRGSAKNLLQDNLMELN-RYNLR-ID 344
                                       *********************************.88776.55 PP

  == domain 3  score: 41.7 bits;  conditional E-value: 8.9e-15
                              NosD  26 gseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisn 102
                                       + + +n +isns+ g+ll nss+++i+++ i  +++Gi l  s++++i+d+ +++++ G+   +s++  +    +++
  gi|330507548|ref|YP_004383976.1| 397 EISARNLTISNSSVGMLLVNSSGCRIQNSSIDLSEEGILLRASNDCIISDCRVRECNVGFDSRDSRGIQFVADHAQD 473
                                       4556899***********************************************************99777999999 PP

                              NosD 103 nenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGil 154
                                       +   G+ +++s n  + + + + +n+Gi+l +s   ++++++  +n k G+l
  gi|330507548|ref|YP_004383976.1| 474 CAAEGFRVDGSLNLLLLKCNSTASNSGISLHSSRLCRVQDCSAVRNAKEGLL 525
                                       9999******************************************999987 PP

  == domain 4  score: 90.1 bits;  conditional E-value: 1.4e-29
                              NosD  15 rgngiqlensegsei.snneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssne.sGialms 89 
                                       +++gi l +s+ +++  + +++n ++g+ll+ s+ +++ gn+  +++ Gi l++s+ + +e+n + sn+ +Gi++++
  gi|330507548|ref|YP_004383976.1| 497 SNSGISLHSSRLCRVqDCSAVRNAKEGLLLSLSHRCSLVGNQAASNDRGIALTGSNACALESNFAISNQkDGISIEQ 573
                                       579************6678899999999************************************999999******* PP

                              NosD  90 ssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiy 165
                                        s+  +++N+++nn + Gi+++ s+ ++is+N+   n+ +G++++ s+s  itgN+i snq  Gi  l ++++n +y
  gi|330507548|ref|YP_004383976.1| 574 LSDAEVKGNNATNNGQ-GIFVQSSKRSKISGNVLCnNSRYGLRMSTSTSCNITGNEICSNQIAGIN-LVDCTDNFLY 648
                                       **99**********99.*****************98999*********************999999.********** PP

                              NosD 166 nNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydg 212
                                        N+  +n ++ + d++ nn+W+               gGNyWsd + 
  gi|330507548|ref|YP_004383976.1| 649 HNIIRDNIIQNAADNG-NNHWDAGA----------EAGGNYWSDHEV 684
                                       ****999887777664.****7766..........789******875 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   6.0   7.8e-13     7e-09      32     158 .]      71     200 ..      35     200 .. 0.71
   2 !   56.5   9.4   3.1e-19   2.8e-15       2     157 ..     142     289 ..     141     290 .. 0.92
   3 !   46.3  11.5   4.5e-16     4e-12      26     156 ..     207     332 ..     206     352 .. 0.59
   4 !   23.6   2.3   4.2e-09   3.7e-05      36      91 ..     285     345 ..     278     387 .. 0.52
   5 !   53.9   0.7     2e-18   1.8e-14       8     157 ..     395     538 ..     391     539 .. 0.95
   6 !   49.6  22.4   4.2e-17   3.7e-13       6     147 ..     527     670 ..     523     679 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 7.8e-13
                                       S-.EEES........-EEES......-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-S CS
                        Beta_helix  32 snvvien........neian......nsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsG 94 
                                       ++v ie+        +ei++       s+  +++l s ++++ ++tis+ +  ++  +++snn+i n+ i+  +  G
  gi|330507548|ref|YP_004383976.1|  71 EGVSIEGplsinapgCEIYDlkintsRSDASLSLL-SGDCQVIRCTISGEK--AAVSSEGSNNTIANCSISSPA--G 142
                                       44444444444444466666555444444455555.388888888888888..666668888888888888884..7 PP

                                       EE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E. CS
                        Beta_helix  95 iylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNti 158
                                       i+++ +++n++ +++i + +  G+ i+++s ++ v+++ti      G+ + +s++ + v+nNti
  gi|330507548|ref|YP_004383976.1| 143 IEIF-APDNRVLGCHIQGSG-IGVRINQTS-GCWVEDCTIAAL--QGVLIEDSDR-NGVVNNTI 200
                                       8888.788899999886655.666666666.777788888855..5887777777.88888886 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 3.1e-19
                                       SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S CS
                        Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgas 78 
                                       gi+i   +n  + +++i++ +g G+ ++++s++ +e+++ia     G+ i+ s++n + nnti   +  g+ l+ ++
  gi|330507548|ref|YP_004383976.1| 142 GIEIFAPDN-RVLGCHIQG-SGIGVRINQTSGCWVEDCTIAA--LQGVLIEDSDRNGVVNNTILTDG-LGLVLTRSD 213
                                       676666666.79*******.7*********************..*******************9888.9******** PP

                                       --EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES CS
                        Beta_helix  79 nnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrn 155
                                       +n+ ++n+ +    sGi + +s  n+i  N i++ +  Gi+++ ++  ++vt N+  +n  aGi+ ++ s+ + +++
  gi|330507548|ref|YP_004383976.1| 214 GNVASGNNLSGAFVSGIDMLNSRFNDIAANKIEGGK-VGISLRVTE-HCNVTSNWCLGNERAGIYGNEASG-LMLAE 287
                                       ************************************.*********.9999*************6666666.88888 PP

                                       -E CS
                        Beta_helix 156 Nt 157
                                       N 
  gi|330507548|ref|YP_004383976.1| 288 ND 289
                                       85 PP

  == domain 3  score: 46.3 bits;  conditional E-value: 4.5e-16
                                       EEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S- CS
                        Beta_helix  26 iylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylnyssn 102
                                       + l  s+++v ++n++++   sGi++l+s  n i  n+i++++ +gi l+ + +  +  n +  n+++Giy n +s 
  gi|330507548|ref|YP_004383976.1| 207 LVLTRSDGNVASGNNLSGAFVSGIDMLNSRFNDIAANKIEGGK-VGISLRVTEHCNVTSNWCLGNERAGIYGNEASG 282
                                       4455555556666666666666666666666666666666666.666666666666666666666666666666666 PP

                                       -EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES- CS
                        Beta_helix 103 ntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnN 156
                                       + + +N + +n+ +Gi +++s+ ++ ++ N +++n+ +Gi + gs+  + +  N
  gi|330507548|ref|YP_004383976.1| 283 LMLAENDLIENG-NGILLSASA-DNIIRSNLASHNV-YGISLRGSAK-NLLQDN 332
                                       666666666666.666666666.5556666666666.6665555555.333333 PP

  == domain 4  score: 23.6 bits;  conditional E-value: 4.2e-09
                                       EES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-.......S CS
                        Beta_helix  36 ienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdn.......g 91 
                                       + +n++   +g+Gi ++ s++n+i+ n  s+n  +gi l+g+ +nl+++n ++ n       +
  gi|330507548|ref|YP_004383976.1| 285 LAENDLIE-NGNGILLSASADNIIRSNLASHNV-YGISLRGSAKNLLQDNLMELNrynlridD 345
                                       23344444.555555555555555555555555.55555555555555555555533333331 PP

  == domain 5  score: 53.9 bits;  conditional E-value: 2e-18
                                       S-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES CS
                        Beta_helix   8 ssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlien 84 
                                       + +++ +n tisn ++ G  l +ss+++i+n+ i   s++Gi ++ s++++is+++++++n +g+  +++ +  +  
  gi|330507548|ref|YP_004383976.1| 395 CREISARNLTISN-SSVGMLLVNSSGCRIQNSSIDL-SEEGILLRASNDCIISDCRVRECN-VGFDSRDSRGIQFVA 468
                                       5667899******.7***************999999.************************.*************** PP

                                       -EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E CS
                        Beta_helix  85 neitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNt 157
                                        +  d++  G+++++s n+ + +++ ++ + sGi++++s   ++v++++++ n+++G+ +  s + + +++N+
  gi|330507548|ref|YP_004383976.1| 469 DHAQDCAAEGFRVDGSLNLLLLKCNSTASN-SGISLHSSR-LCRVQDCSAVRNAKEGLLLSLSHR-CSLVGNQ 538
                                       ****************************99.*********.9999*************7777777.9999997 PP

  == domain 6  score: 49.6 bits;  conditional E-value: 4.2e-17
                                       -SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EE CS
                        Beta_helix   6 ngssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnli 82 
                                       + s+ +++ +n+  + ++ Gi l gs+ + +e+n   +n+ +Gi+i++ s++ +++n+ ++n+  gi ++ ++++ i
  gi|330507548|ref|YP_004383976.1| 527 SLSHRCSLVGNQAAS-NDRGIALTGSNACALESNFAISNQKDGISIEQLSDAEVKGNNATNNG-QGIFVQSSKRSKI 601
                                       556778999999999.6***************6666667***********************9.************* PP

                                       ES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT....---EEES-EEES-SSEEEE-TT- CS
                        Beta_helix  83 enneitdnggsGiylnyssnntienNiidnnagsGividdss....snvtvtnNtitnnkgaGiavvgs 147
                                       ++n   +n+++G+++++s+++ i++N i +n+ +Gi + d      + + +++N+i n++++G + ++ 
  gi|330507548|ref|YP_004383976.1| 602 SGNVLCNNSRYGLRMSTSTSCNITGNEICSNQIAGINLVDCTdnflYHNIIRDNIIQNAADNGNNHWDA 670
                                       ************************************999999899966669999999999888765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (712 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 5314.40
//
Query:       gi|330507549|ref|YP_004383977.1|  [L=417]
Description: response regulator domain with PAS sensor [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      9e-20   70.9   0.0      2e-19   69.8   0.0    1.6  1  Response_reg  Response regulator receiver domain
    1.9e-08   34.5   0.0    8.8e-08   32.3   0.0    2.2  3  PAS_9         PAS domain
    3.2e-08   33.8   0.0    8.8e-08   32.4   0.0    1.8  1  PAS_4         PAS fold
    3.6e-07   30.4   0.0    7.5e-07   29.4   0.0    1.5  1  PAS_3         PAS fold
    1.7e-05   24.8   0.0    4.5e-05   23.4   0.0    1.7  1  PAS           PAS fold
     0.0011   19.0   0.0     0.0055   16.7   0.0    2.2  2  PAS_8         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 !   69.8   0.0   6.8e-23     2e-19       1     103 [.       7     109 ..       7     114 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 6.8e-23
                                       EEEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlle.eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpvii 76 
                                       +li++Ddp  +el++  ++ ++++     a++g++ le++ ++++dli +D+ +pg+ Gl++l +ir+ dp++pv++
  gi|330507549|ref|YP_004383977.1|   7 ILIIEDDPEHAELIKMGFRrHDEF-FLNFAATGENGLEMISQDRYDLISVDLVLPGIGGLDVLVRIRRLDPDIPVVM 82 
                                       8******************76777.99************************************************** PP

                                       EESSTSHHHHHHHHHCTESEEEESSG- CS
                      Response_reg  77 ltahseeedavealkagaddflsKpfd 103
                                       +++h++ e+av a++  a ++++K ++
  gi|330507549|ref|YP_004383977.1|  83 VSGHGTTEMAVVAFENRATKYVVKSLE 109
                                       ************************875 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.7   1.4e+04      40      68 ..       9      36 ..       4      45 .. 0.63
   2 !   32.3   0.0   2.9e-11   8.8e-08       3     104 .]     155     251 ..     153     251 .. 0.90
   3 ?   -2.9   0.0       2.8   8.5e+03      88     102 ..     319     333 ..     314     335 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.7
                             PAS_9 40 f.vtdpeanerlraaleqgrkkerevevvl 68
                                      + ++dpe++e ++  +++++  e+  +   
  gi|330507549|ref|YP_004383977.1|  9 IiEDDPEHAELIKMGFRRHD--EFFLNFAA 36
                                      45677788887777777777..55555544 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 2.9e-11
                             PAS_9   3 gilidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       gi i   +g +   +N+ + +++G s++ +lg ++++l+ t+++ ++ +r   ++ +  +  +e    rk+g+  w+
  gi|330507549|ref|YP_004383977.1| 155 GIYIL-QEG-VFkLVNPRLGEIFGCSADSLLGMPFWQLI-TPDDIQCAIRLEKDRQS-GVPIYESRVLRKDGTCRWI 227
                                       56665.788.8889*************************.88888888888888888.9****************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                       +++  p+  ++++ v+  + l Dit+
  gi|330507549|ref|YP_004383977.1| 228 EFRTMPIEHEGQRAVL--GNLLDITD 251
                                       *******999888888..9*****96 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.8
                             PAS_9  88 ddgelvgiivilrDi 102
                                        +g +  +i +++Di
  gi|330507549|ref|YP_004383977.1| 319 LHGSVEVLIEFVNDI 333
                                       388999999999999 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   2.9e-11   8.8e-08      14     110 .]     161     254 ..     150     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2.9e-11
                             PAS_4  14 dgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlrd 90 
                                       +g++  +N++  e+fg+++++llG+++++l +++   + +  l++  +++ pi++  +l+ +g  r++e+r +P+ +
  gi|330507549|ref|YP_004383977.1| 161 EGVFKLVNPRLGEIFGCSADSLLGMPFWQLITPD-DIQCAIRLEKDRQSGVPIYESRVLRKDGTCRWIEFRTMPI-E 235
                                       79999************************99884.22333344555578889999998888**************.6 PP

                             PAS_4  91 esGevigvlvisrDiTerrr 110
                                       ++G+ ++vl+ + DiT+r++
  gi|330507549|ref|YP_004383977.1| 236 HEGQ-RAVLGNLLDITDRKE 254
                                       7999.9************85 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   2.5e-10   7.5e-07       4      81 ..     167     239 ..     164     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.5e-10
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdeng 80 
                                       v++r  ei+G s+++llg    + +l+ p+D++ + +  ++   +g p+  e R++rkdG+ rw+e r+ +i   +g
  gi|330507549|ref|YP_004383977.1| 167 VNPRLGEIFGCSADSLLGM--PFWQLITPDDIQCAIRLEKDRQ-SGVPI-YESRVLRKDGTCRWIEFRTMPI-EHEG 238
                                       89*****************..**********888888887765.55554.79********************.6666 PP

                             PAS_3  81 k 81 
                                       +
  gi|330507549|ref|YP_004383977.1| 239 Q 239
                                       6 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.5e-08   4.5e-05       4     113 .]     146     249 ..     145     249 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.5e-08
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       r+++e++ ++i ++   g++ +vN+   e++G s++ +lg ++  li ++    + ++  +l+++++++     s+ 
  gi|330507549|ref|YP_004383977.1| 146 RNVVENALAGIYIL-QEGVFKLVNPRLGEIFGCSADSLLGMPFWQLITPD----DIQCAIRLEKDRQSGVPIYESRV 217
                                       57899999999999.99******************************988....66777777777777777777777 PP

                                       C.TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 l.rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       l +dg+ +++e r+ p+ ++g++   +lg l di
  gi|330507549|ref|YP_004383977.1| 218 LrKDGTCRWIEFRTMPIEHEGQR--AVLGNLLDI 249
                                       789******************99..999999887 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.8e-06    0.0055       3      53 ..     145     195 ..     143     208 .. 0.86
   2 ?   -1.7   0.0       1.1   3.1e+03      28      37 ..     334     343 ..     306     362 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.8e-06
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlr 53 
                                       +r+++e++  gi ++ +g  +  vN++  e++G s + l+g++++ql++  +
  gi|330507549|ref|YP_004383977.1| 145 HRNVVENALAGIYILQEGV-FKLVNPRLGEIFGCSaDSLLGMPFWQLITPDD 195
                                       799**********998777.***************99999999998776655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                             PAS_8  28 qaalellGys 37 
                                       qa ++llG +
  gi|330507549|ref|YP_004383977.1| 334 QAGCDLLGKP 343
                                       5778888844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3017.01
//
Query:       gi|330507550|ref|YP_004383978.1|  [L=362]
Description: chorismate synthase [Methanosaeta concilii GP6]
Scores for 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-144  481.3   0.2   1.2e-144  481.1   0.2    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 !  481.1   0.2  6.4e-149  1.2e-144       1     327 []      10     355 ..      10     355 .. 0.97

  Alignments for each domain:
  == domain 1  score: 481.1 bits;  conditional E-value: 6.4e-149
                                       SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE CS
                   Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallie 77 
                                       +r+tt+GeShg+a+g+v+dg+pa+l+l+e diqkeLdrRrpgqs+++tqr+E+D+veilsG+fegkt+Gtpi++li+
  gi|330507550|ref|YP_004383978.1|  10 FRITTWGESHGRAVGVVLDGCPAELALTEYDIQKELDRRRPGQSRASTQRTEADRVEILSGIFEGKTTGTPISMLIW 86 
                                       89*************************************************************************** PP

                                       -TTS-..SSSSSTSBE-TTSTCHHHHHHC-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE. CS
                   Chorismate_synt  78 NkdqrskdyeeikevpRpgHADltyalkYgirdlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei. 153
                                       N+d++s +y+ ++++pRpgHAD++y++kYg rd+rgggrsSaReTa+rvaaGavakklL+++g+e++a+v+++g+i 
  gi|330507550|ref|YP_004383978.1|  87 NRDADSASYDLLRNRPRPGHADYAYQMKYGLRDHRGGGRSSARETAGRVAAGAVAKKLLQHFGVEVAAFVTELGGIk 163
                                       **************************************************************************888 PP

                                       ............CHHHHHTT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHH CS
                   Chorismate_synt 154 ............ekeaenpvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalm 218
                                                   ++ ++np+rcpd++aa +m+e+++ +++egdslGg+v+++++gvp+GlG+pvfdklda+Lakalm
  gi|330507550|ref|YP_004383978.1| 164 srtdsvdlaelrARVEANPIRCPDPNAAMRMMEQLDLVRQEGDSLGGMVTIIARGVPPGLGDPVFDKLDADLAKALM 240
                                       888888888775334788*********************************************************** PP

                                       TSTTEEEEEETTGGGGGGSBHHHHS--EEEE......SS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTT CS
                   Chorismate_synt 219 sipAvkgveiGsGfeaaelkGseanDeivlr......ktnnaGGieGGisnGepivvrvavKpipsiakeqktvdle 289
                                       s++Avk+veiG+G+ +a ++Gse+nD++ ++      + nnaGGi+GGis+G++iv+r+avKp+psiak+q+tvdl+
  gi|330507550|ref|YP_004383978.1| 241 SLGAVKAVEIGAGIGCAGMRGSEMNDPLRMEggkigfEGNNAGGILGGISTGMDIVCRIAVKPTPSIAKKQHTVDLA 317
                                       ****************************955667778**************************************** PP

                                       S-E-EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHHH CS
                   Chorismate_synt 290 tkeevelevkgrhDpcvvpravvvveamvalvladall 327
                                          ++e+e+kgrhDp + pr+v+v+eamva+vlad+ll
  gi|330507550|ref|YP_004383978.1| 318 AGMDAEIEIKGRHDPAIPPRMVPVAEAMVAIVLADHLL 355
                                       ************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2711.89
//
Query:       gi|330507551|ref|YP_004383979.1|  [L=589]
Description: molybdenum cofactor biosynthesis protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-38  129.9   0.5    1.1e-37  129.3   0.5    1.3  1  MoeA_N          MoeA N-terminal region (domain I and II)
    6.8e-26   90.7   0.0    1.4e-25   89.6   0.0    1.5  1  MoCF_biosynth   Probable molybdopterin binding domain
    1.3e-13   50.5   0.0    3.1e-12   46.0   0.0    2.3  1  PBP_like        PBP superfamily domain
    2.5e-10   40.4   0.0    8.5e-10   38.7   0.1    2.0  2  MoeA_C          MoeA C-terminal region (domain IV)
     0.0017   17.7   0.0       0.85    8.9   0.0    2.4  2  LysR_substrate  LysR substrate binding domain
  ------ inclusion threshold ------
      0.034   13.2   0.0      0.058   12.4   0.0    1.2  1  T2SSE           Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3   0.5   3.6e-41   1.1e-37       1     157 []       9     173 ..       9     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 3.6e-41
                                       B-HHHHHHHHHHH-HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--............. CS
                            MoeA_N   1 lsveealaiilaaleleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........ 68 
                                       +s++ea +ii+++l++ +e+ v+l  ++lg++lae+v++++dvP+f ++ mDGYAv ++++  a+e++p        
  gi|330507551|ref|YP_004383979.1|   9 ISLQEAKSIISDHLPPAREKaVAL-GSSLGCILAEKVISSQDVPGFGRASMDGYAVISQDTIVAREDRPvslrlags 84 
                                       689***********7767777***.8889************************************************ PP

                                       ......-S---TT-.EEEE-TTSB--TT--EEEEGGGE..E....EETTE...S--STTTTEE-TTSSB-TTSEEE- CS
                            MoeA_N  69 saageeperllpgg.avrimTGaplPegadaVvpvEdte.eeeaketvev...kavkpgenvrraGedikaGevllr 140
                                       +++g++pe ++++g a+++ TG+++P+gadaVv++E+   ++       v   +++ +genv+ aG+di+ Ge +l 
  gi|330507551|ref|YP_004383979.1|  85 VPMGRRPEIEISRGeAAEVSTGSMMPKGADAVVMIEYSLaQK-----GIVyirRPAFGGENVQAAGSDISFGEAVLF 156
                                       999999999999999**********************74221.....2224458999******************** PP

                                       TTBB--CCCHHHHHHCT CS
                            MoeA_N 141 agtrltpaeigllasvG 157
                                        gt + ++eig+la++G
  gi|330507551|ref|YP_004383979.1| 157 PGTPIAAREIGVLAALG 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 !   89.6   0.0   4.7e-29   1.4e-25       6     143 ..     197     321 ..     192     322 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 4.7e-29
                                       -HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHHHHHH CS
                     MoCF_biosynth   6 GdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpealaklf 82 
                                       G ell g+i+D n++++a+ +++ g++ + y+++pDd+e+++++ll+ +ee d+i+++G t++++ D+ ++++++++
  gi|330507551|ref|YP_004383979.1| 197 GRELLLGQIYDINSYTIAAGVEDCGARPRSYGILPDDKEQMARTLLRMAEECDMILVSGSTSAGAGDMIYQVIEEVG 273
                                       99*******************************************9999999************************* PP

                                       SEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  83 ekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                       e        +f++v+ kpgkp++++ +   +   gk+ igLPG+p ++ +++ e+  pa++
  gi|330507551|ref|YP_004383979.1| 274 E-------LIFHGVNFKPGKPTIFGII---R---GKPCIGLPGYPTSALTVFAELAAPAIR 321
                                       *.......8************999999...4...358******************999986 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0     1e-15   3.1e-12      12     192 ..     427     584 ..     417     585 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1e-15
                                       EEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BGGG CS
                          PBP_like  12 rvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkkitnwkd 88 
                                       r+   n+Gs+ G   l +g ad+a+++ + +e  + +            + +v   +re gl+++          + 
  gi|330507551|ref|YP_004383979.1| 427 RLMLLNTGSYRGRIYLEDGIADLAAVSSPLEEAPKGE------------AKVVWSGKRELGLIYRDP-------SAP 484
                                       6667788888888888888888888888887553333............445555578888888777.......345 PP

                                       C-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCCETTCCECCCGG-HCCCCCCECTT CS
                          PBP_like  89 ladaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVaagradvgvgieavaeelkgldfvp 165
                                       +  a  r+v+ +++S     f+++l++ gi+    + y + a++h a+aa+Va+grad g+g + +a ++ gl+f p
  gi|330507551|ref|YP_004383979.1| 485 VDPASQRIVGWPRDSAMKEAFEQALTEMGIGA---PVYVRLAKTHTAMAAIVASGRADLGFGEKEAASQA-GLGFKP 557
                                       6667789*********************9999...99******************************998.****** PP

                                       CE-EEEEEEEECTCCCSHHHHHHHHHH CS
                          PBP_like 166 laeerydlvvrkealddpevqaflefl 192
                                       + e ++ l+   + l  p++++++++l
  gi|330507551|ref|YP_004383979.1| 558 VVEDELYLLAGPKGLGNPRIKSLMSAL 584
                                       ***99999999999999*999999876 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 ?   -2.7   0.0       2.3   6.8e+03       4      23 ..      40      59 ..      39      69 .. 0.66
   2 !   38.7   0.1   2.9e-13   8.5e-10       4      72 .]     337     399 ..     334     399 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.3
                                      ESS-EE--SSS-EEEEEEEE CS
                            MoeA_C  4 laedlksdpgrreflRvilt 23
                                      lae++ s ++ + f R++++
  gi|330507551|ref|YP_004383979.1| 40 LAEKVISSQDVPGFGRASMD 59
                                      66777777777777777766 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 2.9e-13
                                       ESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                            MoeA_C   4 laedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                       la +l+ ++ r+++l v ++   g+  ++p+  +gSg +++la A+g i+ip+g+e+le G  V+v l+
  gi|330507551|ref|YP_004383979.1| 337 LAGPLRTEG-RQQMLAVGVS---GD-LVYPV-DKGSGSITTLALADGVIEIPAGVEFLEGGSPVQVRLF 399
                                       556666555.9999999999...88.9****.**********************************886 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00029      0.85      54     148 ..     445     534 ..     441     535 .. 0.77
   2 !    8.7   0.0   0.00034         1      49      87 ..     531     570 ..     528     579 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00029
                                       TSSSEEEEESSS.CCTTEEEEEEEEEEEEEEEETTSGGGGSSSECGGGGCTSEEEEESTTSTHHHHHHHHHHCTTEE CS
                    LysR_substrate  54 gelDlairagpp.edsglearpLaeeplvlvaspdhpLargepvsledLadeplilleegsglrdlledalreaglk 129
                                       g +Dla ++ p+ e       p +e ++v+   ++  L  ++p ++ d a ++ + ++++s++ +++e+al e g+ 
  gi|330507551|ref|YP_004383979.1| 445 GIADLAAVSSPLeE------APKGEAKVVWSGKRELGLIYRDPSAPVDPASQRIVGWPRDSAMKEAFEQALTEMGIG 515
                                       55555555555432......33455666666666655555788888899**************************** PP

                                       CEEEEEESSHHHHHHHHHT CS
                    LysR_substrate 130 prvalevnsleallalvaa 148
                                       + v +++  +++++a++ a
  gi|330507551|ref|YP_004383979.1| 516 APVYVRLAKTHTAMAAIVA 534
                                       **************99876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00034
                                       HHHHTTSSSEEEEESSS.CCTTEEEEEEEEEEEEEEEETT CS
                    LysR_substrate  49 dllaegelDlairagpp.edsglearpLaeeplvlvaspd 87 
                                       + +a+g++Dl++   +  +++gl + p+ e++l+l+a p 
  gi|330507551|ref|YP_004383979.1| 531 AIVASGRADLGFGEKEAaSQAGLGFKPVVEDELYLLAGPK 570
                                       5699********************************9986 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.9e-05     0.058     107     154 ..     226     273 ..     219     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                             T2SSE 107 dlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkein 154
                                        +g+ +++ke++a++l +  +e  +ilvsG T+ G   ++y +++e+ 
  gi|330507551|ref|YP_004383979.1| 226 SYGILPDDKEQMARTLLRMAEECDMILVSGSTSAGAGDMIYQVIEEVG 273
                                       678888999999999888879***************999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 3556.24
//
Query:       gi|330507552|ref|YP_004383980.1|  [L=341]
Description: DNA primase, large subunit [Methanosaeta concilii GP6]
Scores for complete 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  112.0   0.0    1.2e-31  110.1   0.0    1.7  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.0   6.7e-36   1.2e-31       2     260 ..     124     315 ..     123     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 6.7e-36
                                       EEEEEHHHHHHHTT-G........GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HH CS
                   DNA_primase_lrg   2 fykvpfedvldlvkrr........rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederek 70 
                                       ++k++f+++++ + r         ++ l +Gy+ +++ el +ll+e++r+++ k+l     +  ++     +  +e 
  gi|330507552|ref|YP_004383980.1| 124 PWKIHFSEYIRAAHRMhspkwkltNRDLSEGYLTVTDVELRRLLEEAIREKVLKGLPVSVDE--RI----CQGLEEY 194
                                       579*******99995568899***********************************993333..44....7777778 PP

                                       HHHHHCT--.............TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHH CS
                   DNA_primase_lrg  71 leellealsesyvaedvqeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldei 147
                                       l ++++ l+         ++ ++ki+   ++++++++fPpC++++l+++ k+ +l+h++r++l++Fl +i ++ de+
  gi|330507552|ref|YP_004383980.1| 195 LAPVKRDLE--------ALAAKQKID---LGEVKEGAFPPCIKKMLSEVSKGANLAHSARFALVSFLLQINMTPDEV 260
                                       999999999........444444443...47789999**************************************** PP

                                       HCCCHCHST..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S.-HHHH.HHHHHHHHHHTT CS
                   DNA_primase_lrg 148 lelwkeaftrteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahg.CpfrhdpdklktlLqeyg 222
                                       ++l+ ++     ++Fd+ ++ry+++h++G    +t+y+p+ C+++          ++g Cp    +d+l        
  gi|330507552|ref|YP_004383980.1| 261 IALFATS-----PDFDQdRTRYQVEHIAG--ATGTRYKPPACATM---------ATYGnCP---GEDDL-------- 310
                                       ******8.....*****************..88899*********.........9999999...56666........ PP

                                       ..HHHHHHHHHHHHTT.HHHHHHHHHHHHHS-TTT-SS CS
                   DNA_primase_lrg 223 lseediedilesvkegeyqvaCtkvFelthkcerdeik 260
                                                                      c+r  i+
  gi|330507552|ref|YP_004383980.1| 311 -------------------------------CRR--IR 315
                                       ...............................444..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 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:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2451.93
//
Query:       gi|330507553|ref|YP_004383981.1|  [L=244]
Description: DNA polymerase sliding clamp [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-16   60.2   0.0    1.6e-12   47.7   0.0    3.6  3  PCNA_C           Proliferating cell nuclear antigen, C-termin
    1.6e-15   57.0   0.5    3.5e-15   55.8   0.3    1.6  2  PCNA_N           Proliferating cell nuclear antigen, N-termin
    0.00016   21.3   0.0    0.00068   19.2   0.0    1.8  2  Rad9             Rad9
  ------ inclusion threshold ------
      0.068   13.3   0.1       0.36   10.9   0.2    2.2  2  DNA_pol3_beta    DNA polymerase III beta subunit, N-terminal 
       0.12   12.3   0.7       0.75    9.6   0.7    2.2  1  DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal 


Domain annotation for each model (and alignments):
>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.26   9.3e+02      25      45 ..      18      38 ..       6      57 .. 0.75
   2 !    6.2   0.0    0.0032        11      44      76 ..      60      93 ..      44     106 .. 0.87
   3 !   47.7   0.0   4.6e-16   1.6e-12       2     127 ..     122     239 ..     121     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.26
                                      HTTT-SEEEEEEETTEEEEEE CS
                            PCNA_C 25 lsqlsdsvvisvtkegvkfsa 45
                                      +s+l d+v  s++ +g+  +a
  gi|330507553|ref|YP_004383981.1| 18 VSSLVDEVKFSISENGLELKA 38
                                      677888888888888887776 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0032
                                      EE.EETTEEEEEEE--BEESSSGGGCBEEEESS- CS
                            PCNA_C 44 sa.sGdiGsasivlkqvkdvdkeeeavklelkep 76
                                      +a +G+iG   + l++v ++++  e v+lel+e 
  gi|330507553|ref|YP_004383981.1| 60 KAdQGEIGVDLVRLSDVLSMADRGENVQLELDEE 93
                                      5526***************************986 PP

  == domain 3  score: 47.7 bits;  conditional E-value: 4.6e-16
                                       ---SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EE CS
                            PCNA_C   2 ipdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvt 78 
                                       ipd++  a v+lp  e  r ++   ++sd v++ v+ eg    a+Gdi s ++++  ++ +        ++  e+  
  gi|330507553|ref|YP_004383981.1| 122 IPDLDLPAHVTLPGGELRRAVKAAEKVSDHVILGVSDEGFYMEAKGDIDSLKLKIPSTELL-------GMKPGEAR- 190
                                       9************************************************998777665544.......44444444. PP

                                       EEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                            PCNA_C  79 ltfalkYlaeftkatsLservtlslssevPlvveykikdvgllayllak 127
                                         f+l+Yl+++ k+ s + +vtl++  + Pl v +k+ +   ++ylla+
  gi|330507553|ref|YP_004383981.1| 191 SLFSLDYLQDMSKSISKAGEVTLEMGIDYPLRVTFKLGQSVDINYLLAP 239
                                       45*********************************************98 PP

>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.3   9.9e-19   3.5e-15       8     100 ..       7      98 ..       1     104 [. 0.91
   2 ?   -2.3   0.0      0.95   3.4e+03      15      39 ..     141     165 ..     136     178 .. 0.63

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 9.9e-19
                                       SHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTT CS
                            PCNA_N   8 qasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcann 84 
                                       +a  l+  ++++  lv+e+ f ++++G++l+a+D + va+vsl++ s++fe ++ D+   +gv+l  ls +l +a+ 
  gi|330507553|ref|YP_004383981.1|   7 NAETLRDAIDSVSSLVDEVKFSISENGLELKAVDPANVAMVSLKIGSDAFEYFKADQG-EIGVDLVRLSDVLSMADR 82 
                                       57779999************************************************86.79**************** PP

                                       TSEEEEEEETTSSEEE CS
                            PCNA_N  85 edsvtlkaedeadtla 100
                                        ++v l+ ++e+ +l+
  gi|330507553|ref|YP_004383981.1|  83 GENVQLELDEESHKLK 98 
                                       *******999988875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.95
                                       HHHHHTTTCSEEEEEEETTEEEEEE CS
                            PCNA_N  15 lleaikdlvneanfdcddsGislqa 39 
                                        + a   + +++ + ++d+G+ + a
  gi|330507553|ref|YP_004383981.1| 141 AVKAAEKVSDHVILGVSDEGFYMEA 165
                                       5555555566666666666666655 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.9e-07   0.00068       4      93 ..      14      96 ..      11     103 .. 0.75
   2 ?   -0.6   0.0      0.21   7.4e+02       1      28 [.     138     165 ..     138     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.9e-07
                              Rad9  4 alqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvKsvlsvfrslsakektvek 82
                                      a+ ++s + de+ + ise+glel++v+ ++ a +++++ ++ F+ ++    +q ++ + +  +  v+ s++      e+
  gi|330507553|ref|YP_004383981.1| 14 AIDSVSSLVDEVKFSISENGLELKAVDPANVAMVSLKIGSDAFEYFK---ADQGEIGVDLVRLSDVL-SMA---DRGEN 85
                                      78999***************************************993...33444444555555555.444...34455 PP

                              Rad9 83 vkisidekksr 93
                                      v++++de++ +
  gi|330507553|ref|YP_004383981.1| 86 VQLELDEESHK 96
                                      56666555555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.21
                              Rad9   1 laralqclsrigdelyleisedglelrt 28 
                                       l ra++++ +++d + l  s++g+ +++
  gi|330507553|ref|YP_004383981.1| 138 LRRAVKAAEKVSDHVILGVSDEGFYMEA 165
                                       5699*************99999998875 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 ?   10.9   0.2    0.0001      0.36      32     113 ..      24     112 ..       2     118 .. 0.81
   2 ?   -1.9   0.0      0.98   3.5e+03      74      92 ..     197     215 ..     187     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                                       EEEEEEETTEEEEEEE-SSEEEEEEEESEEE......EE-EEEEEEHHHHHHHHHHSSTTSEEEEEEET.TEEEEEE CS
                     DNA_pol3_beta  32 gvllevkdsqlsltgtDleisiestisaese......eeegkvlvparllldivkaLpndkkvkisvne.qklliik 101
                                        v+ ++++++l l++ D    + +++++ s+      + +g++ v    l+d+++  + +++v+++++e +++l i+
  gi|330507553|ref|YP_004383981.1|  24 EVKFSISENGLELKAVDPANVAMVSLKIGSDafeyfkADQGEIGVDLVRLSDVLSMADRGENVQLELDEeSHKLKIG 100
                                       5788899999999999987777777888877888888899****************************953333345 PP

                                       ETTEEEEEE-BE CS
                     DNA_pol3_beta 102 sgssrfslstls 113
                                       +gs  ++ls ++
  gi|330507553|ref|YP_004383981.1| 101 VGSLSYTLSLID 112
                                       888888887665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.98
                                       HHHHHHHHSSTTSEEEEEE CS
                     DNA_pol3_beta  74 llldivkaLpndkkvkisv 92 
                                       +l d+ k++++  +v++++
  gi|330507553|ref|YP_004383981.1| 197 YLQDMSKSISKAGEVTLEM 215
                                       6778888888877887776 PP

>> DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.7   0.00021      0.75      11      98 ..       3      92 ..       2     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00021
                                      EEEEEHHHHHHHHHHHHTTSSTSTGEEEEEEETTEEEEEEEETTSEEEEE..EEEEBEE...SS-EEEEEEHHHHHHHH CS
                   DNA_pol3_beta_3 11 kvtvdlkelkealkRvalladeknrkvrLsleegqlklsaensevgeaeE..evdvnye...GeeleiafNvsYlldal 84
                                      k++++ + l++a++ v+ l+d    +v+ s++e+ l+l+a ++    ++   + ++++e    ++ ei+     l d+l
  gi|330507553|ref|YP_004383981.1|  3 KAVINAETLRDAIDSVSSLVD----EVKFSISENGLELKAVDPANVAMVSlkIGSDAFEyfkADQGEIGVDLVRLSDVL 77
                                      578999**************8....9**************998766555543222222234566777777777777777 PP

                                      HHH-.SSEEEEEESS CS
                   DNA_pol3_beta_3 85 kale.teevelqltd 98
                                      +  + +e+v+l+l +
  gi|330507553|ref|YP_004383981.1| 78 SMADrGENVQLELDE 92
                                      766524667776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1782.84
//
Query:       gi|330507554|ref|YP_004383982.1|  [L=102]
Description: DNA-directed RNA polymerase subunit M [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-18   65.6  12.0    2.8e-17   62.3   3.3    3.1  3  TFIIS_C          Transcription factor S-II (TFIIS)
      4e-08   32.4  11.6      1e-06   27.9   0.7    2.8  3  zf-ribbon_3      zinc-ribbon domain
    1.3e-07   31.4  17.4    1.6e-07   31.1   4.2    3.1  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    0.00025   21.0  10.8      0.011   15.7  11.0    2.7  1  DZR              Double zinc ribbon
    0.00043   19.9  13.0        0.3   10.9   0.1    4.1  4  zinc_ribbon_2    zinc-ribbon domain
    0.00044   20.1   6.7       0.32   10.9   0.2    3.6  3  Nudix_N_2        Nudix N-terminal
    0.00079   19.3   8.6       0.14   12.1   1.4    2.3  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.001   19.0   1.0      0.001   19.0   1.0    3.1  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0016   18.6   9.1      0.052   13.8   2.2    2.7  2  IBR              IBR domain, a half RING-finger domain
     0.0022   17.5  12.7     0.0068   15.9   0.6    3.3  3  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0027   17.3   8.3        5.7    6.6   0.0    4.1  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
     0.0036   17.3  13.7        0.6   10.2   3.4    4.0  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain
     0.0041   17.0   7.6          3    7.9   0.1    3.5  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
     0.0053   16.4   7.5       0.65    9.7   1.0    3.3  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
     0.0057   16.5  17.0       0.39   10.7   0.7    4.1  3  zinc_ribbon_4    zinc-ribbon domain
     0.0069   16.3   9.3      0.071   13.1   1.3    2.8  2  zinc-ribbons_6   zinc-ribbons
  ------ inclusion threshold ------
       0.01   15.5   0.5       0.01   15.5   0.5    2.7  2  TackOD1          Thaumarchaeal output domain 1
      0.011   16.4   7.8      0.015   16.0   0.1    2.9  3  zinc_ribbon_15   zinc-ribbon family
      0.043   13.8   1.0      0.043   13.8   1.0    2.8  3  Prok-RING_1      Prokaryotic RING finger family 1
      0.046   13.4  15.0       0.26   11.0   2.4    4.0  3  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
      0.064   13.3  11.2       0.08   12.9   0.7    3.3  3  Ogr_Delta        Ogr/Delta-like zinc finger
      0.067   13.3  14.7       0.77    9.9   0.1    4.1  3  Zn-ribbon_8      Zinc ribbon domain
      0.075   13.1   2.5       0.88    9.6   0.2    2.9  3  zf-BED           BED zinc finger
      0.093   12.8   8.6       0.15   12.0   2.7    2.8  2  HypA             Hydrogenase/urease nickel incorporation, met
        0.1   12.5   0.4        0.1   12.5   0.4    2.3  3  DUF4428          Domain of unknown function (DUF4428)
       0.11   12.9   6.8        6.4    7.3   0.0    3.7  4  zf-IS66          zinc-finger binding domain of transposase IS
       0.13   12.1   6.0       0.35   10.8   0.0    3.3  4  DUF3797          Domain of unknown function (DUF3797)
       0.14   12.5   3.8       0.35   11.2   0.3    2.3  2  DUF3268          zinc-finger-containing domain
        0.2   11.8  12.2        1.4    9.0   0.1    3.6  3  UPF0547          Uncharacterised protein family UPF0547
       0.26   11.5   9.5        2.5    8.3   0.5    3.8  4  zf-RING_7        C4-type zinc ribbon domain
       0.33   10.9   7.6        1.1    9.2   1.1    3.0  3  PHD              PHD-finger
       0.38   10.5  15.7        8.7    6.2   0.1    4.2  4  Rubredoxin_2     Rubredoxin metal binding domain
        0.5   10.5   7.5        4.1    7.6   7.5    2.3  1  FYVE             FYVE zinc finger
       0.76    9.5  13.6       0.14   11.8   2.5    2.9  3  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.92   10.3  12.9         10    7.0   2.2    3.7  3  zf-3CxxC_2       Zinc-binding domain
        1.2    9.1   9.7         11    6.0   0.2    3.9  4  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
        1.2    9.3   9.8         30    4.8   0.0    3.6  3  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
        1.2    9.0  13.4        3.1    7.6   0.0    3.6  4  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
        1.4    9.6   8.9         20    5.9   8.9    2.5  1  RPA_interact_C   Replication protein A interacting C-terminal
        2.2    8.6   9.7        5.9    7.2   0.0    3.7  4  zf-LITAF-like    LITAF-like zinc ribbon domain
        4.4    8.0  16.6        6.8    7.5   1.7    3.9  4  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        4.6    7.6   9.5        3.3    8.0   2.1    2.8  2  Ribosomal_L32p   Ribosomal L32p protein family
        5.3    7.6  15.1        3.8    8.1   1.0    3.3  3  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
        6.7    6.5  10.7       0.83    9.4   1.0    2.5  3  Rep_fac-A_C      Replication factor-A C terminal domain
          8    6.6   7.8        1.3    9.1   1.3    2.5  2  DUF2318          Predicted membrane protein (DUF2318)


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1       0.3   1.2e+02       3       9 ..       4      10 ..       2      12 .. 0.81
   2 ?    5.8   0.1     0.031        12      29      37 ..      18      26 ..      13      27 .. 0.77
   3 !   62.3   3.3     7e-20   2.8e-17       2      39 .]      62      99 ..      61      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.3
                           TFIIS_C  3 CpkCgsr 9 
                                      Cp+C+s 
  gi|330507554|ref|YP_004383982.1|  4 CPQCKSM 10
                                      ****986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.031
                           TFIIS_C 29 ykCtkCghr 37
                                      ++C kCgh+
  gi|330507554|ref|YP_004383982.1| 18 MVCRKCGHK 26
                                      578888886 PP

  == domain 3  score: 62.3 bits;  conditional E-value: 7e-20
                           TFIIS_C  2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39
                                      +Cp+Cg++ ay++ +Q+RsaDE++++f++CtkC ++Wr
  gi|330507554|ref|YP_004383982.1| 62 RCPECGNNVAYWWLRQLRSADESEVRFFRCTKCSNTWR 99
                                      7************************************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 !   27.9   0.7   2.6e-09     1e-06       2      26 .]       1      27 [.       1      27 [. 0.95
   2 !   12.0   0.3   0.00026       0.1       2      12 ..      60      70 ..      59      71 .. 0.84
   3 ?   -1.7   0.4       5.2   2.1e+03      19      22 ..      91      94 ..      89      96 .. 0.60

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.6e-09
                       zf-ribbon_3  2 tvrCPnCGa.p.lssddnvCpyCGtkl 26
                                      + +CP+C++   ++++++vC +CG+kl
  gi|330507554|ref|YP_004383982.1|  1 MEFCPQCKSmMmPKDGMMVCRKCGHKL 27
                                      679******999*************97 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00026
                       zf-ribbon_3  2 tvrCPnCGapl 12
                                      t rCP+CG+++
  gi|330507554|ref|YP_004383982.1| 60 TARCPECGNNV 70
                                      689*****965 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5.2
                       zf-ribbon_3 19 CpyC 22
                                      C++C
  gi|330507554|ref|YP_004383982.1| 91 CTKC 94
                                      4444 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 !   31.1   4.2     4e-10   1.6e-07       1      33 [.       1      29 [.       1      32 [. 0.93
   2 ?    4.6   1.1     0.074        30       4       9 ..      63      68 ..      63      71 .. 0.96
   3 ?    4.0   0.2      0.12        46      16      28 ..      82      95 ..      78      97 .. 0.67

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4e-10
                                      EEBESTTTSBEEEEECSCCCEEEESSSS-EEES CS
                    RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepa 33
                                      ++FCp C++++ pk++  +    Cr+Cg + p+
  gi|330507554|ref|YP_004383982.1|  1 MEFCPQCKSMMMPKDGMMV----CRKCGHKLPK 29
                                      99*****************....****988775 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.074
                                      ESTTTS CS
                    RNA_POL_M_15KD  4 CpkCgN 9 
                                      Cp+CgN
  gi|330507554|ref|YP_004383982.1| 63 CPECGN 68
                                      *****9 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.12
                                      CSCCCE.EEESSSS CS
                    RNA_POL_M_15KD 16 dkegkn.feCrqCg 28
                                      d++ ++ f C +C+
  gi|330507554|ref|YP_004383982.1| 82 DESEVRfFRCTKCS 95
                                      34444469999996 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7  11.0   2.8e-05     0.011       1      38 [.       4      70 ..       4     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.8e-05
                               DZR  1 CpqCgeelppdar..fCseCgtklkavaa...........................edrCpsCgekv 38
                                      CpqC++ + p++   +C +Cg+kl+++++                             rCp+Cg  v
  gi|330507554|ref|YP_004383982.1|  4 CPQCKSMMMPKDGmmVCRKCGHKLPKANSeslvskteqlsrivpvleqesaglpttTARCPECGNNV 70
                                      ******9766554459********988779**********************************986 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   0.5     0.062        25      15      19 ..       3       7 ..       2      10 .. 0.78
   2 !   10.9   0.1   0.00076       0.3       2      10 ..      20      28 ..      14      32 .. 0.68
   3 !    8.6   0.1    0.0038       1.5       1       8 [.      62      69 ..      56      71 .. 0.77
   4 ?    2.7   0.2      0.29   1.1e+02       1       5 [.      90      94 ..      84      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.062
                     zinc_ribbon_2 15 FCpyC 19
                                      FCp+C
  gi|330507554|ref|YP_004383982.1|  3 FCPQC 7 
                                      78887 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00076
                     zinc_ribbon_2  2 CpnCGaelq 10
                                      C +CG++l+
  gi|330507554|ref|YP_004383982.1| 20 CRKCGHKLP 28
                                      677777766 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0038
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      +Cp+CG+ 
  gi|330507554|ref|YP_004383982.1| 62 RCPECGNN 69
                                      58888875 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.29
                     zinc_ribbon_2  1 fCpnC 5 
                                      +C++C
  gi|330507554|ref|YP_004383982.1| 90 RCTKC 94
                                      47777 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.046        18       2       8 ..       3       9 ..       2      14 .. 0.80
   2 ?    5.8   0.1     0.032        13       3      10 ..      20      27 ..      18      32 .. 0.78
   3 !   10.9   0.2   0.00081      0.32       3      29 ..      63      95 ..      63      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.046
                                     B-TTT-- CS
                         Nudix_N_2 2 FCsqCGt 8
                                     FC+qC +
  gi|330507554|ref|YP_004383982.1| 3 FCPQCKS 9
                                     9****76 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.032
                                      -TTT--B- CS
                         Nudix_N_2  3 CsqCGtpv 10
                                      C++CG+++
  gi|330507554|ref|YP_004383982.1| 20 CRKCGHKL 27
                                      78888776 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00081
                                      -TTT--B-E.....EE--TT-SS-EE.EETTTT CS
                         Nudix_N_2  3 CsqCGtpve.....lripdgDnreRl.vCpaCg 29
                                      C++CG+ v+     +   +++++ R+ +C++C+
  gi|330507554|ref|YP_004383982.1| 63 CPECGNNVAywwlrQLRSADESEVRFfRCTKCS 95
                                      ********9888744445888889963799997 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 !   11.4   0.9   0.00059      0.24      31      55 ..       4      26 ..       2      30 .. 0.94
   2 !   12.1   1.4   0.00036      0.14      27      56 ..      59      98 ..      46     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00059
                    OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfe 55
                                      C++C s + +  ++  ++C++Cg++
  gi|330507554|ref|YP_004383982.1|  4 CPQCKSMMMP--KDGMMVCRKCGHK 26
                                      **********..***********98 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00036
                    OrfB_Zn_ribbon 27 TSktCseCgsknke..........alsgrtfkCpnCgfea 56
                                      T  +C+eCg ++ +          + + r f+C++C  ++
  gi|330507554|ref|YP_004383982.1| 59 TTARCPECGNNVAYwwlrqlrsadESEVRFFRCTKCSNTW 98
                                      7789*****************9999999********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 ?    0.3   5.4       1.8   7.3e+02      21      45 ..       4      25 ..       2      26 .. 0.44
   2 ?    5.3   0.2     0.048        19      18      28 ..      16      29 ..       9      34 .. 0.75
   3 !   19.0   1.0   2.5e-06     0.001      19      45 ..      61      96 ..      52      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.8
                     Zn_Tnp_IS1595 21 CPhCgsrkayriktrglfqCkeCrk 45
                                      CP C+s      k+ g   C++C++
  gi|330507554|ref|YP_004383982.1|  4 CPQCKS--MMMPKD-GMMVCRKCGH 25
                                      666662..222222.4444444444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.048
                     Zn_Tnp_IS1595 18 g.fvCPhCgsr..k 28
                                      g  vC +Cg++  k
  gi|330507554|ref|YP_004383982.1| 16 GmMVCRKCGHKlpK 29
                                      4478*****87544 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 2.5e-06
                     Zn_Tnp_IS1595 19 fvCPhCgsr.kayrikt........rglfqCkeCrk 45
                                       +CP Cg+   ++ +++         + f+C +C+ 
  gi|330507554|ref|YP_004383982.1| 61 ARCPECGNNvAYWWLRQlrsadeseVRFFRCTKCSN 96
                                      78*******77777777999**************85 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   2.2   0.00013     0.052      20      47 ..       3      26 ..       1      27 [. 0.90
   2 !    8.3   0.7    0.0068       2.7      17      46 ..      59      96 ..      28     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00013
                               IBR 20 wCprpdCeaiieksegcksvtCskCgfe 47
                                       Cp  +C++++ +++g  ++ C+kCg++
  gi|330507554|ref|YP_004383982.1|  3 FCP--QCKSMMMPKDG--MMVCRKCGHK 26
                                      7*9..***********..889*****96 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0068
                               IBR 17 nlkwCprpdCeaii........eksegcks...vtCskCgf 46
                                      ++  Cp  +C++ +        ++ ++ ++    +C+kC+ 
  gi|330507554|ref|YP_004383982.1| 59 TTARCP--ECGNNVaywwlrqlRSADE-SEvrfFRCTKCSN 96
                                      367888..8888887888876522222.2234466888875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.6   1.7e-05    0.0068       3      30 ..       4      28 ..       2      40 .. 0.82
   2 ?    6.5   0.8     0.014       5.7       2       8 ..      62      68 ..      57      72 .. 0.61
   3 ?    3.6   5.6      0.12        46       2      25 ..      62      94 ..      61     102 .] 0.68

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-05
                                      ETTTTCEECHEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVle 30
                                      CP C+s ++   p+ g +vC +CG  l 
  gi|330507554|ref|YP_004383982.1|  4 CPQCKSMMM---PKDGMMVCRKCGHKLP 28
                                      ******665...888*********9986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                                      EETTTTC CS
                      TF_Zn_Ribbon  2 kCPnCgs 8 
                                      +CP+Cg+
  gi|330507554|ref|YP_004383982.1| 62 RCPECGN 68
                                      3555554 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.12
                                      EETTTTCEEC.........HEETSTTCE.EESSS CS
                      TF_Zn_Ribbon  2 kCPnCgstnl.........veDpergel.vCtdC 25
                                      +CP+Cg+  +           D+++  + +Ct+C
  gi|330507554|ref|YP_004383982.1| 62 RCPECGNN-VaywwlrqlrSADESEVRFfRCTKC 94
                                      6****985.3347778766555444444488888 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2     0.023       9.3       4      12 ..       3      11 ..       1      15 [. 0.83
   2 ?    6.6   0.1     0.015       5.8       3      15 ..      18      30 ..      16      34 .. 0.83
   3 ?    6.6   0.0     0.014       5.7       3      14 ..      61      72 ..      59      77 .. 0.78
   4 ?    1.1   0.2      0.78   3.1e+02       3       9 ..      89      95 ..      87     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.023
                            zf_UBZ  4 lCerCgkei 12
                                      +C++C++++
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSMM 11
                                      8*****987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                            zf_UBZ  3 ylCerCgkeipes 15
                                       +C +Cg+++p +
  gi|330507554|ref|YP_004383982.1| 18 MVCRKCGHKLPKA 30
                                      58*******9976 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.014
                            zf_UBZ  3 ylCerCgkeipe 14
                                        C++Cg ++  
  gi|330507554|ref|YP_004383982.1| 61 ARCPECGNNVAY 72
                                      57*****99875 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.78
                            zf_UBZ  3 ylCerCg 9 
                                      + C +C 
  gi|330507554|ref|YP_004383982.1| 89 FRCTKCS 95
                                      7899997 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 !   10.2   3.4    0.0015       0.6       4      26 .]       4      23 ..       4      23 .. 0.94
   2 ?    6.7   0.2     0.019       7.6       3      11 ..      62      70 ..      61      72 .. 0.84
   3 ?    4.2   0.3      0.12        47       1       9 [.      88      96 ..      88      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0015
                            zf-ACC  4 CpsCgemlykkeLernlyVCPkC 26
                                      Cp+C++m+  k+    ++VC+kC
  gi|330507554|ref|YP_004383982.1|  4 CPQCKSMMMPKDG---MMVCRKC 23
                                      **********985...******* PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.019
                            zf-ACC  3 KCpsCgeml 11
                                      +Cp+Cg+ +
  gi|330507554|ref|YP_004383982.1| 62 RCPECGNNV 70
                                      6*****976 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.12
                            zf-ACC  1 WtKCpsCge 9 
                                      +++C++C++
  gi|330507554|ref|YP_004383982.1| 88 FFRCTKCSN 96
                                      689****87 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   3.7    0.0077       3.1       5      27 ..       4      25 ..       3      27 .. 0.86
   2 !    7.9   0.1    0.0076         3       4      29 ..      62      98 ..      56      99 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0077
                    PhnA_Zn_Ribbon  5 CplCaSeytYedgallvCpeCah 27
                                      Cp+C+S      + ++vC +C+h
  gi|330507554|ref|YP_004383982.1|  4 CPQCKSMM-MPKDGMMVCRKCGH 25
                                      99999955.57888********9 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0076
                    PhnA_Zn_Ribbon  4 kCplCaSeytY...........edgallvCpeCahEw 29
                                       Cp+C+  ++Y            +   + C +C++ w
  gi|330507554|ref|YP_004383982.1| 62 RCPECGNNVAYwwlrqlrsadeSEVRFFRCTKCSNTW 98
                                      7999999999888888888766555667777777665 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 !    9.7   1.0    0.0016      0.65       3      26 ..       4      26 ..       3      27 .. 0.77
   2 !    7.3   0.0    0.0095       3.8      19      29 ..      62      72 ..      57      72 .. 0.80
   3 ?    1.7   0.2      0.54   2.2e+02      19      23 ..      90      94 ..      85      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0016
                                      -SSS--B----SSS----SSS--- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCGhR 26
                                      C +C++ +  k g    C++CGh+
  gi|330507554|ref|YP_004383982.1|  4 CPQCKSMMMPKDG-MMVCRKCGHK 26
                                      7788887777777.666******8 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0095
                                      --SSS-----B CS
                    DNA_RNApol_7kD 19 RCkeCGhRilY 29
                                      RC eCG  + Y
  gi|330507554|ref|YP_004383982.1| 62 RCPECGNNVAY 72
                                      9*****87755 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.54
                                      --SSS CS
                    DNA_RNApol_7kD 19 RCkeC 23
                                      RC++C
  gi|330507554|ref|YP_004383982.1| 90 RCTKC 94
                                      89999 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   5.6      0.16        62      19      34 ..      12      26 ..       3      28 .. 0.68
   2 ?    6.1   0.1     0.027        11      25      33 ..      60      68 ..      56      69 .. 0.79
   3 !   10.7   0.7   0.00098      0.39      26      36 .]      89      99 ..      83      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.16
                     zinc_ribbon_4 19 lpakgvkvrCskCghv 34
                                      +p++ +++ C kCgh+
  gi|330507554|ref|YP_004383982.1| 12 MPKD-GMMVCRKCGHK 26
                                      4455.5556*****97 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.027
                     zinc_ribbon_4 25 kvrCskCgh 33
                                       +rC+ Cg+
  gi|330507554|ref|YP_004383982.1| 60 TARCPECGN 68
                                      679999986 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00098
                     zinc_ribbon_4 26 vrCskCghvFr 36
                                       rC+kC++++r
  gi|330507554|ref|YP_004383982.1| 89 FRCTKCSNTWR 99
                                      69********7 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   1.3   0.00018     0.071       3      27 ..       4      28 ..       2      41 .. 0.88
   2 ?    6.3   1.4     0.023       9.3       2      24 ..      62      96 ..      61     101 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00018
                                      -SSS-S--EE-SSEEE-TTT--EEE CS
                    zinc-ribbons_6  3 CpeCqqelekrgeqyhCeaCqedlk 27
                                      Cp+C++ +  ++  + C++C ++l 
  gi|330507554|ref|YP_004383982.1|  4 CPQCKSMMMPKDGMMVCRKCGHKLP 28
                                      *********9999*******99765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.023
                                      --SSS-S--E.E-S...........SEEE-TTT-- CS
                    zinc-ribbons_6  2 kCpeCqqele.krg...........eqyhCeaCqe 24
                                       CpeC +++  +             + ++C +C++
  gi|330507554|ref|YP_004383982.1| 62 RCPECGNNVAyWWLrqlrsadesevRFFRCTKCSN 96
                                      69999999887544477888887777778888876 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.5   2.6e-05      0.01      88     116 ..       2      30 ..       1      43 [. 0.88
   2 ?    1.8   1.8      0.43   1.7e+02      98     152 ..      83      94 ..      55     102 .] 0.43

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-05
                           TackOD1  88 evCpkCkSidieeqelihhftCgnvgpee 116
                                       e Cp+CkS+ + ++ ++ + +Cg+  p+ 
  gi|330507554|ref|YP_004383982.1|   2 EFCPQCKSMMMPKDGMMVCRKCGHKLPKA 30 
                                       78*********************987764 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.43
                           TackOD1  98 ieeqelihhftCgnvgpeeeflkegkleCpkCktkLrhiGvDYdrplevykCnsC 152
                                        +e                                            ++++C +C
  gi|330507554|ref|YP_004383982.1|  83 ESEV-------------------------------------------RFFRCTKC 94 
                                       2222...........................................22222222 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.9       1.3   5.3e+02      80      85 ..       2       7 ..       1       8 [. 0.81
   2 ?   16.0   0.1   3.8e-05     0.015      35      75 ..      15      70 ..       8      74 .. 0.81
   3 ?    2.1   0.1      0.86   3.4e+02      65      74 ..      88      97 ..      75     101 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1.3
                    zinc_ribbon_15 80 kyCpkC 85
                                      ++Cp+C
  gi|330507554|ref|YP_004383982.1|  2 EFCPQC 7 
                                      799999 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.8e-05
                    zinc_ribbon_15 35 kpylacskCkslleaskelgkeiekkesse................kkeCknCgkev 75
                                      + +++c+kC+++l++ + +++ ++k+e+ +                + +C++Cg++v
  gi|330507554|ref|YP_004383982.1| 15 DGMMVCRKCGHKLPKAN-SESLVSKTEQLSrivpvleqesaglpttTARCPECGNNV 70
                                      7799**********998.444445555444699*********************998 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.86
                    zinc_ribbon_15 65 kkeCknCgke 74
                                        +C +C+++
  gi|330507554|ref|YP_004383982.1| 88 FFRCTKCSNT 97
                                      4566666654 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 ?   13.8   1.0   0.00011     0.043       6      27 ..       3      24 ..       1      29 [. 0.93
   2 ?    2.8   0.2      0.28   1.1e+02      23      27 ..      63      67 ..      58      71 .. 0.72
   3 ?   -0.6   0.1       3.4   1.3e+03       7      13 ..      91      97 ..      88     102 .] 0.66

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
                       Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCg 27
                                       Cp C+  + ++d + vC +Cg
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSMMMPKDGMMVCRKCG 24
                                      5********************9 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.28
                       Prok-RING_1 23 CpeCg 27
                                      CpeCg
  gi|330507554|ref|YP_004383982.1| 63 CPECG 67
                                      77777 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.4
                       Prok-RING_1  7 CpvCgke 13
                                      C+ C+++
  gi|330507554|ref|YP_004383982.1| 91 CTKCSNT 97
                                      7777665 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.4   0.00065      0.26       7      30 ..       4      26 ..       1      27 [. 0.73
   2 ?    4.9   0.6     0.054        21       6      13 ..      62      70 ..      62      73 .. 0.77
   3 ?    3.0   0.3      0.21        84       5      17 ..      89     100 ..      87     102 .] 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00065
                           zf-RRN7  7 CgvCgcrsftlddGfyyCrrChtq 30
                                      C++C +    + dG+++Cr C+++
  gi|330507554|ref|YP_004383982.1|  4 CPQCKS-MMMPKDGMMVCRKCGHK 26
                                      666666.33347**********96 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.054
                           zf-RRN7  6 pCgvCgc.r 13
                                      +C++Cg+ +
  gi|330507554|ref|YP_004383982.1| 62 RCPECGNnV 70
                                      7*****953 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.21
                           zf-RRN7   5 ppCgvCgcrsftl 17 
                                       ++C  C++ ++++
  gi|330507554|ref|YP_004383982.1|  89 FRCTKCSN-TWRE 100
                                       58*****9.5554 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 ?    3.6   1.0      0.17        67       2       9 ..       4      11 ..       3      13 .. 0.90
   2 ?    2.4   0.1       0.4   1.6e+02       2      18 ..      20      36 ..      19      45 .. 0.74
   3 ?   12.9   0.7    0.0002      0.08       1      35 [.      62      96 ..      62     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.17
                         Ogr_Delta  2 CPhCgapa 9 
                                      CP+C++ +
  gi|330507554|ref|YP_004383982.1|  4 CPQCKSMM 11
                                      *****987 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.4
                         Ogr_Delta  2 CPhCgapaaartsrnls 18
                                      C +Cg++    +s+ l 
  gi|330507554|ref|YP_004383982.1| 20 CRKCGHKLPKANSESLV 36
                                      77899988888877665 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.0002
                         Ogr_Delta  1 rCPhCgapaaartsrnl.skdvre.ryyqCsnfeCga 35
                                      rCP+Cg++ a +  r+l s+d  e r++ C+   C+ 
  gi|330507554|ref|YP_004383982.1| 62 RCPECGNNVAYWWLRQLrSADESEvRFFRCTK--CSN 96
                                      7******9999999887466666699999987..765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.4      0.13        54      29      34 ..       4       9 ..       1      16 [. 0.76
   2 ?    9.9   0.1    0.0019      0.77      24      36 ..      57      70 ..      48      71 .. 0.76
   3 ?    3.1   0.2      0.26     1e+02       6      13 ..      89      96 ..      88     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.13
                       Zn-ribbon_8 29 CPeCgs 34
                                      CP+C+s
  gi|330507554|ref|YP_004383982.1|  4 CPQCKS 9 
                                      ****98 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0019
                       Zn-ribbon_8 24 aplta.CPeCgsev 36
                                      +  ta CPeCg +v
  gi|330507554|ref|YP_004383982.1| 57 PTTTArCPECGNNV 70
                                      557888*****876 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.26
                       Zn-ribbon_8  6 YrCeeCgh 13
                                      +rC++C +
  gi|330507554|ref|YP_004383982.1| 89 FRCTKCSN 96
                                      89****86 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2    0.0022      0.88      13      29 ..      14      30 ..       6      44 .. 0.81
   2 ?    1.4   0.0      0.85   3.4e+02      15      27 ..      59      71 ..      54      73 .. 0.83
   3 ?    0.5   0.1       1.6   6.5e+02      16      25 ..      88      97 ..      81      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0022
                                      GSS--EETTTTEE---- CS
                            zf-BED 13 keqkavCryCgkilsrg 29
                                      k+++ vCr Cg +l   
  gi|330507554|ref|YP_004383982.1| 14 KDGMMVCRKCGHKLPKA 30
                                      789********998665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.85
                                      S--EETTTTEE-- CS
                            zf-BED 15 qkavCryCgkils 27
                                      + a+C  Cg++ +
  gi|330507554|ref|YP_004383982.1| 59 TTARCPECGNNVA 71
                                      6799*****9976 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.6
                                      --EETTTTEE CS
                            zf-BED 16 kavCryCgki 25
                                      + +C  C ++
  gi|330507554|ref|YP_004383982.1| 88 FFRCTKCSNT 97
                                      5689999875 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 ?    1.0   0.2       1.1   4.3e+02      89      96 ..       4      11 ..       1      17 [. 0.78
   2 ?   12.0   2.7   0.00039      0.15      69      95 ..      16      69 ..      10     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.1
                                      -TTTSSS- CS
                              HypA 89 CpkCgsad 96
                                      Cp+C+s  
  gi|330507554|ref|YP_004383982.1|  4 CPQCKSMM 11
                                      99999865 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00039
                                      -EEEETTTS-EEECHHH.HH..........................S-TTTSSS CS
                              HypA 69 vkvrCreCgkefeleek.al..........................rCpkCgsa 95
                                        + Cr+Cg++  ++++ +l                          rCp+Cg++
  gi|330507554|ref|YP_004383982.1| 16 GMMVCRKCGHKLPKANSeSLvskteqlsrivpvleqesaglptttaRCPECGNN 69
                                      6789********9886433378899**************************985 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   0.00026       0.1      11      43 ..      10      40 ..       3      46 .. 0.66
   2 ?   -0.8   0.0       3.7   1.5e+03       2       9 ..      63      70 ..      62      83 .. 0.70
   3 ?   -2.1   0.3       9.8   3.9e+03      23      28 ..      91      96 ..      89      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00026
                           DUF4428 11 llkrlkleDg.yvCkdClkKlseflsdvkikkil 43
                                      ++     +Dg  vC +C  Kl   +s+  ++k+ 
  gi|330507554|ref|YP_004383982.1| 10 MMM---PKDGmMVCRKCGHKLPKANSESLVSKTE 40
                                      555...68**78*********4444444444444 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.7
                           DUF4428  2 CaiCgkKi 9 
                                      C+ Cg+++
  gi|330507554|ref|YP_004383982.1| 63 CPECGNNV 70
                                      55566554 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 9.8
                           DUF4428 23 CkdClk 28
                                      C++C +
  gi|330507554|ref|YP_004383982.1| 91 CTKCSN 96
                                      999986 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 ?    2.6   0.1      0.46   1.8e+02       3      11 ..       3      11 ..       2      15 .. 0.72
   2 ?    7.3   0.0     0.016       6.4       3      26 ..      19      45 ..      18      50 .. 0.75
   3 ?    5.1   0.0     0.078        31       3       9 ..      62      68 ..      60      87 .. 0.78
   4 ?   -1.4   0.2       8.4   3.3e+03      41      45 ..      90      94 ..      89      97 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.46
                           zf-IS66  3 tCpcCGgll 11
                                       Cp+C + +
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSMM 11
                                      599998844 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.016
                           zf-IS66  3 tCpcCGg.llkpigedrvr..eeldip 26
                                      +C +CG+ l k   e  v+  e+l  +
  gi|330507554|ref|YP_004383982.1| 19 VCRKCGHkLPKANSESLVSktEQLSRI 45
                                      6******77888888878777777665 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.078
                           zf-IS66  3 tCpcCGg 9 
                                       Cp+CG 
  gi|330507554|ref|YP_004383982.1| 62 RCPECGN 68
                                      5999997 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 8.4
                           zf-IS66 41 aCpcC 45
                                      +C +C
  gi|330507554|ref|YP_004383982.1| 90 RCTKC 94
                                      56666 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.9      0.63   2.5e+02      16      21 ..       4       9 ..       2      20 .. 0.84
   2 ?   -1.7   0.0       7.1   2.8e+03      16      21 ..      20      25 ..      10      36 .. 0.74
   3 ?   10.8   0.0   0.00088      0.35      14      22 ..      61      69 ..      41      72 .. 0.80
   4 ?    0.4   0.0       1.5     6e+02      13      21 ..      88      96 ..      78      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.63
                           DUF3797 16 CPeCgN 21
                                      CP+C+ 
  gi|330507554|ref|YP_004383982.1|  4 CPQCKS 9 
                                      ****96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7.1
                           DUF3797 16 CPeCgN 21
                                      C +Cg 
  gi|330507554|ref|YP_004383982.1| 20 CRKCGH 25
                                      667764 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00088
                           DUF3797 14 vqCPeCgNn 22
                                      + CPeCgNn
  gi|330507554|ref|YP_004383982.1| 61 ARCPECGNN 69
                                      79******8 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.5
                           DUF3797 13 YvqCPeCgN 21
                                      +  C +C N
  gi|330507554|ref|YP_004383982.1| 88 FFRCTKCSN 96
                                      667888888 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.56   2.2e+02       3      21 ..      18      36 ..      16      47 .. 0.74
   2 ?   11.2   0.3   0.00087      0.35       2      37 ..      60      95 ..      59     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.56
                           DUF3268  3 trCpyCGekvilvsaseiY 21
                                      ++C+ CG+k   ++++++ 
  gi|330507554|ref|YP_004383982.1| 18 MVCRKCGHKLPKANSESLV 36
                                      6899999998888777766 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00087
                           DUF3268  2 ttrCpyCGekvilvsaseiYkerskgkllylCpkCd 37
                                      t rCp CG++v++   +++ ++ + +  ++ C+kC 
  gi|330507554|ref|YP_004383982.1| 60 TARCPECGNNVAYWWLRQLRSADESEVRFFRCTKCS 95
                                      689*****************9999999********7 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.4       0.1        40       3       6 ..       4       7 ..       1      10 [. 0.70
   2 ?    5.7   0.1     0.039        16      16      22 ..      19      25 ..      17      30 .. 0.76
   3 ?    9.0   0.1    0.0036       1.4      11      21 ..      57      67 ..      53      71 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.1
                           UPF0547 3 CPeC 6
                                     CP+C
  gi|330507554|ref|YP_004383982.1| 4 CPQC 7
                                     7777 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.039
                           UPF0547 16 fCphCGy 22
                                      +C+ CG+
  gi|330507554|ref|YP_004383982.1| 19 VCRKCGH 25
                                      6888888 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0036
                           UPF0547 11 PvaaqfCphCG 21
                                      P+ + +Cp+CG
  gi|330507554|ref|YP_004383982.1| 57 PTTTARCPECG 67
                                      66666677776 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.044        18      25      32 ..       3      10 ..       1      11 [. 0.80
   2 ?   -1.2   0.1       6.1   2.4e+03       2      10 ..      20      28 ..      19      30 .. 0.74
   3 ?    8.3   0.5    0.0064       2.5      16      30 ..      52      67 ..      43      67 .. 0.73
   4 ?    1.5   0.0       0.9   3.6e+02      16      29 ..      77      94 ..      74      95 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.044
                                      E-TTT--E CS
                         zf-RING_7 25 tCpeCGRI 32
                                      +Cp+C  +
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSM 10
                                      9****876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 6.1
                                      ETTT--B-- CS
                         zf-RING_7  2 CgGChmelp 10
                                      C  C+ +lp
  gi|330507554|ref|YP_004383982.1| 20 CRKCGHKLP 28
                                      777888887 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0064
                                      HHCCS.TB-EE-TTT- CS
                         zf-RING_7 16 elrag.devvtCpeCG 30
                                      e+++     ++CpeCG
  gi|330507554|ref|YP_004383982.1| 52 ESAGLpTTTARCPECG 67
                                      5555555569*****9 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.9
                                      HHCCSTB....-EE-TTT CS
                         zf-RING_7 16 elragde....vvtCpeC 29
                                      +lr +de     ++C  C
  gi|330507554|ref|YP_004383982.1| 77 QLRSADEsevrFFRCTKC 94
                                      455554444335777777 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.1    0.0027       1.1       1      23 [.       3      25 ..       3      28 .. 0.89
   2 ?    0.5   0.0       1.4   5.7e+02      45      50 ..      62      67 ..      49      70 .. 0.64
   3 ?    3.5   0.1      0.17        68      14      51 ..      87      96 ..      76      98 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0027
                                      SBTTTTSTTSTTSCEEEETTTSC CS
                               PHD  1 rCavCkkksdeeeelvqCdgCkr 23
                                      +C  Ck+    ++ +++C +C++
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSMMMPKDGMMVCRKCGH 25
                                      6999***8888999*******97 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.4
                                      SSTTTH CS
                               PHD 45 lCekCk 50
                                       C++C 
  gi|330507554|ref|YP_004383982.1| 62 RCPECG 67
                                      677775 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.17
                                      CEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTHT CS
                               PHD 14 elvqCdgCkrwfHqkClkppleseekpegewlCekCke 51
                                      +                             + C+kC++
  gi|330507554|ref|YP_004383982.1| 87 R----------------------------FFRCTKCSN 96
                                      3............................466777754 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3     0.085        34      17      22 ..       4       9 ..       3      10 .. 0.89
   2 ?    6.2   0.1     0.022       8.7       2      10 ..      19      27 ..      19      30 .. 0.82
   3 ?    5.9   0.6     0.027        11       2       8 ..      62      68 ..      62      74 .. 0.52
   4 ?    3.5   0.6      0.15        59       1       9 [.      89      97 ..      89     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.085
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp+C+s
  gi|330507554|ref|YP_004383982.1|  4 CPQCKS 9 
                                      ****98 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.022
                      Rubredoxin_2  2 vCsqCGfes 10
                                      vC++CG++ 
  gi|330507554|ref|YP_004383982.1| 19 VCRKCGHKL 27
                                      7*****975 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.027
                      Rubredoxin_2  2 vCsqCGf 8 
                                      +C +CG+
  gi|330507554|ref|YP_004383982.1| 62 RCPECGN 68
                                      4555555 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.15
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      ++C +C+++
  gi|330507554|ref|YP_004383982.1| 89 FRCTKCSNT 97
                                      89****986 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   7.5      0.01       4.1      11      48 ..       3      78 ..       1     100 [. 0.67

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.01
                                      B-TTT--B--SSS--EE-TTT--EE-STTS-EEE.EE......................................G CS
                              FYVE 11 kCeiCakkFsllrrrhhCrlCGkvvCekCssklvall......................................e 48
                                       C++C++          Cr CG+ + ++ s++lv+++                                       
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSMMMPKDGMMVCRKCGHKLPKANSESLVSKTeqlsrivpvleqesaglptttarcpecgnnvaywwlrqL 78
                                      69999999988899999*********99999999888777777777777555555555555555555555555542 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.5   0.00036      0.14       5      29 ..       3      25 ..       1      27 [. 0.96
   2 ?    5.3   0.2     0.038        15      22      29 ..      61      68 ..      58      70 .. 0.81
   3 ?   -1.6   0.3       5.4   2.2e+03      23      29 ..      90      96 ..      90      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00036
                     zf-NADH-PPase  5 FCgrCGaptepaeggwarvCpaCgl 29
                                      FC++C + ++p++g  ++vC  Cg+
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSMMMPKDG--MMVCRKCGH 25
                                      **************..********9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.038
                     zf-NADH-PPase 22 rvCpaCgl 29
                                       +Cp Cg+
  gi|330507554|ref|YP_004383982.1| 61 ARCPECGN 68
                                      58999997 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5.4
                     zf-NADH-PPase 23 vCpaCgl 29
                                      +C  C +
  gi|330507554|ref|YP_004383982.1| 90 RCTKCSN 96
                                      7999975 PP

>> zf-3CxxC_2  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.7       1.5   6.1e+02       8      16 ..      18      26 ..       1      38 [. 0.61
   2 ?    6.4   0.0     0.037        15      28      50 ..      61      83 ..      56      88 .. 0.81
   3 ?    7.0   2.2     0.025        10       8      17 ..      89      98 ..      86     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.5
                        zf-3CxxC_2  8 fkCekCgke 16
                                        C+kCg++
  gi|330507554|ref|YP_004383982.1| 18 MVCRKCGHK 26
                                      335555554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.037
                        zf-3CxxC_2 28 QeCkkCkekvepyklrekdkkkg 50
                                       +C +C+++v  + lr+++  ++
  gi|330507554|ref|YP_004383982.1| 61 ARCPECGNNVAYWWLRQLRSADE 83
                                      58************999776655 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.025
                        zf-3CxxC_2  8 fkCekCgkeW 17
                                      f+C+kC ++W
  gi|330507554|ref|YP_004383982.1| 89 FRCTKCSNTW 98
                                      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 ?    1.5   0.1      0.73   2.9e+02      27      33 ..       3       9 ..       1       9 [. 0.79
   2 ?    3.6   0.2      0.15        62      13      19 ..      19      25 ..      17      25 .. 0.80
   3 ?    6.0   0.2     0.027        11      25      32 ..      59      67 ..      56      70 .. 0.67
   4 ?    1.9   0.0      0.54   2.2e+02       8      17 ..      85      94 ..      80      97 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.73
                           DUF35_N 27 vCphCgs 33
                                      +Cp C s
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKS 9 
                                      8***965 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.15
                           DUF35_N 13 rCpdCGt 19
                                       C++CG+
  gi|330507554|ref|YP_004383982.1| 19 VCRKCGH 25
                                      7999997 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.027
                           DUF35_N 25 r.avCphCg 32
                                      + a Cp Cg
  gi|330507554|ref|YP_004383982.1| 59 TtARCPECG 67
                                      447777776 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.54
                           DUF35_N  8 rLvgqrCpdC 17
                                      ++++ rC++C
  gi|330507554|ref|YP_004383982.1| 85 EVRFFRCTKC 94
                                      5556699999 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   3.9     0.086        34      10      32 ..       3      26 ..       1      46 [. 0.61
   2 ?    4.8   0.0     0.076        30      25      32 ..      62      69 ..      54      77 .. 0.85
   3 ?    1.2   0.1       1.1   4.2e+02       9      18 ..      89      98 ..      81     102 .] 0.76

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.086
                      NOB1_Zn_bind 10 rChaCfkvt.kdmtkkFCpkCGnk 32
                                       C  C +++ ++   + C kCG+k
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSMMmPKDGMMVCRKCGHK 26
                                      355555544344555555666554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.076
                      NOB1_Zn_bind 25 FCpkCGnk 32
                                       Cp+CGn+
  gi|330507554|ref|YP_004383982.1| 62 RCPECGNN 69
                                      5*****97 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.1
                      NOB1_Zn_bind  9 lrChaCfkvt 18
                                       rC+ C ++ 
  gi|330507554|ref|YP_004383982.1| 89 FRCTKCSNTW 98
                                      5888887776 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   0.6     0.008       3.2       3      16 ..       3      16 ..       1      18 [. 0.84
   2 ?    1.8   0.4      0.54   2.1e+02       4      12 ..      20      28 ..      17      34 .. 0.81
   3 ?    7.6   0.0    0.0079       3.1       3      11 ..      62      70 ..      60      73 .. 0.83
   4 ?   -2.1   0.1       8.8   3.5e+03       4       8 ..      91      95 ..      88      97 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.008
                                      E-SSS--EEEEEE- CS
                    zf-C4_Topoisom  3 kCPkCggdLvlkrg 16
                                       CP+C++ ++ k g
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSMMMPKDG 16
                                      5******9998865 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.54
                                      -SSS--EEE CS
                    zf-C4_Topoisom  4 CPkCggdLv 12
                                      C kCg +L 
  gi|330507554|ref|YP_004383982.1| 20 CRKCGHKLP 28
                                      99***9985 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0079
                                      E-SSS--EE CS
                    zf-C4_Topoisom  3 kCPkCggdL 11
                                       CP+Cg+++
  gi|330507554|ref|YP_004383982.1| 62 RCPECGNNV 70
                                      6*****986 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 8.8
                                      -SSS- CS
                    zf-C4_Topoisom  4 CPkCg 8 
                                      C kC 
  gi|330507554|ref|YP_004383982.1| 91 CTKCS 95
                                      66775 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 ?    5.9   8.9     0.049        20       1      32 [.       3      34 ..       3      98 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.049
                    RPA_interact_C  1 lCPvCkkrklketsevifCe.Cglrletseesl 32
                                      +CP Ck+  +  ++ +++C+ Cg +l +++++ 
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSMMMP-KDGMMVCRkCGHKLPKANSES 34
                                      6****986554.567889988*****9953322 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 ?    2.9   0.4      0.34   1.4e+02      58      65 ..       3      10 ..       1      15 [. 0.68
   2 ?    2.7   0.1      0.39   1.5e+02      53      66 ..      14      27 ..       9      31 .. 0.75
   3 ?    7.2   0.0     0.015       5.9      55      69 ..      59      73 ..      53      74 .. 0.78
   4 ?   -0.1   0.1       2.8   1.1e+03       7      13 ..      90      96 ..      85     101 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.34
                     zf-LITAF-like 58 yCpnCgal 65
                                      +Cp+C+++
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSM 10
                                      57777765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.39
                     zf-LITAF-like 53 kdvehyCpnCgall 66
                                      kd    C +Cg++l
  gi|330507554|ref|YP_004383982.1| 14 KDGMMVCRKCGHKL 27
                                      66667899999887 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.015
                     zf-LITAF-like 55 vehyCpnCgallgty 69
                                      ++ +Cp+Cg+ ++++
  gi|330507554|ref|YP_004383982.1| 59 TTARCPECGNNVAYW 73
                                      556899999998887 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 2.8
                     zf-LITAF-like  7 dCpaCqq 13
                                       C +C++
  gi|330507554|ref|YP_004383982.1| 90 RCTKCSN 96
                                      3555544 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.093        37       4      13 ..       3      12 ..       2      17 .. 0.79
   2 ?    4.7   0.5      0.12        50       3      13 ..      18      29 ..      16      52 .. 0.68
   3 ?    7.5   1.7     0.017       6.8       3      13 ..      61      71 ..      59      91 .. 0.68
   4 ?    0.0   0.4       3.5   1.4e+03       4      11 ..      90      97 ..      87     102 .] 0.70

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.093
                           zf-ISL3  4 rCPnCgsktv 13
                                       CP+C+s ++
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSMMM 12
                                      6*****9876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.12
                           zf-ISL3  3 hrCPnCgsk.tv 13
                                      ++C++Cg k ++
  gi|330507554|ref|YP_004383982.1| 18 MVCRKCGHKlPK 29
                                      58*****99754 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.017
                           zf-ISL3  3 hrCPnCgsktv 13
                                       rCP+Cg+ ++
  gi|330507554|ref|YP_004383982.1| 61 ARCPECGNNVA 71
                                      79*****9877 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 3.5
                           zf-ISL3  4 rCPnCgsk 11
                                      rC +C ++
  gi|330507554|ref|YP_004383982.1| 90 RCTKCSNT 97
                                      78888776 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.1    0.0083       3.3      28      47 ..       3      25 ..       1      30 [. 0.86
   2 ?    3.7   0.1      0.19        75      24      34 ..      57      68 ..      50      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0083
                                      EETTTCCEECTT...C-BTTTTB CS
                    Ribosomal_L32p 28 ecpncgelklpH...rvcpscGy 47
                                       cp+c+++ +p+    vc +cG+
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSMMMPKdgmMVCRKCGH 25
                                      5**********977779999998 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.19
                                      -.-EEEETTTCC CS
                    Ribosomal_L32p 24 p.nlvecpncge 34
                                      p + ++cp+cg+
  gi|330507554|ref|YP_004383982.1| 57 PtTTARCPECGN 68
                                      547789****96 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 ?    1.0   0.4       1.6   6.4e+02       7      17 ..       3      13 ..       2      15 .. 0.86
   2 ?    8.1   1.0    0.0096       3.8       4      15 ..      16      27 ..      13      41 .. 0.89
   3 ?    7.4   1.1     0.016       6.4       6      31 ..      61      96 ..      58     101 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.6
                   Zn_ribbon_recom  7 rCgeCGspmtr 17
                                      +C +C s m  
  gi|330507554|ref|YP_004383982.1|  3 FCPQCKSMMMP 13
                                      7******9975 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0096
                   Zn_ribbon_recom  4 GllrCgeCGspm 15
                                      G+++C +CG+++
  gi|330507554|ref|YP_004383982.1| 16 GMMVCRKCGHKL 27
                                      99********97 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.016
                   Zn_ribbon_recom  6 lrCgeCGspmtr......rkrk.gkr...hyYrCst 31
                                       rC eCG++  +      r++  ++    ++ +Cs+
  gi|330507554|ref|YP_004383982.1| 61 ARCPECGNNVAYwwlrqlRSADeSEVrffRCTKCSN 96
                                      69*******766556333333333333444444444 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 ?    9.4   1.0    0.0021      0.83      21      53 ..       4      33 ..       2      40 .. 0.79
   2 ?   -0.9   0.1       3.2   1.3e+03      38      49 ..      61      72 ..      48      85 .. 0.69
   3 ?    1.1   3.1      0.74   2.9e+02      37      49 ..      88     100 ..      63     102 .] 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0021
                                      --STT---B-EEETTTEEEETTTTEEESS--EE CS
                       Rep_fac-A_C 21 CpsedCnkKvveeedgewrCekCdkeveepkyr 53
                                      Cp  +C k +++ +dg++ C kC +++++ +  
  gi|330507554|ref|YP_004383982.1|  4 CP--QC-KSMMMPKDGMMVCRKCGHKLPKANSE 33
                                      88..88.56777789*********999887655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.2
                                      EEETTTTEEESS CS
                       Rep_fac-A_C 38 wrCekCdkevee 49
                                       rC +C ++v+ 
  gi|330507554|ref|YP_004383982.1| 61 ARCPECGNNVAY 72
                                      689999888644 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.74
                                       EEEETTTTEEESS CS
                       Rep_fac-A_C  37 ewrCekCdkevee 49 
                                        +rC kC +++ e
  gi|330507554|ref|YP_004383982.1|  88 FFRCTKCSNTWRE 100
                                       39*****999866 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.3    0.0033       1.3      35      65 ..       2      31 ..       1      38 [. 0.78
   2 ?    1.3   0.7      0.94   3.8e+02      52      60 ..      89      97 ..      29     101 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0033
                           DUF2318 35 daCevCekkgYvqegeelvCknCgvrfalds 65
                                      + C  C+++  + ++  +vC++Cg ++ +++
  gi|330507554|ref|YP_004383982.1|  2 EFCPQCKSMM-MPKDGMMVCRKCGHKLPKAN 31
                                      5688887654.567889********998765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.94
                           DUF2318 52 lvCknCgvr 60
                                        C++C+++
  gi|330507554|ref|YP_004383982.1| 89 FRCTKCSNT 97
                                      345555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        62  (0.00345808); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 706.69
//
Query:       gi|330507555|ref|YP_004383983.1|  [L=221]
Description: amino acid-binding ACT domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-70  233.1   5.7    8.7e-70  233.1   5.7    2.0  3  DUF5612       Domain of unknown function (DUF5612)
    6.7e-09   35.4   0.4    2.2e-08   33.7   0.1    2.1  2  ACT           ACT domain
    0.00014   22.3   0.0    0.00049   20.6   0.0    2.0  1  ACT_4         ACT domain
     0.0023   17.9   0.0     0.0047   16.9   0.0    1.6  1  ACT_6         ACT domain
  ------ inclusion threshold ------
      0.058   12.8   0.2       0.78    9.1   0.0    2.2  2  Peripla_BP_1  Periplasmic binding proteins and sugar binding 


Domain annotation for each model (and alignments):
>> DUF5612  Domain of unknown function (DUF5612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.24   8.7e+02      95     113 ..       5      23 ..       2      42 .. 0.75
   2 ?   -0.4   0.1      0.26   9.2e+02      95     139 ..      19      63 ..      15      66 .. 0.72
   3 !  233.1   5.7   2.4e-73   8.7e-70       1     142 [.      79     219 ..      79     220 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.24
                                       -EEEEES-BSSHHHHSSEE CS
                           DUF5612  95 iivislnmaGsvtevadlv 113
                                       i vi+l+ +G + + a +v
  gi|330507555|ref|YP_004383983.1|   5 INVICLDRPGMLRDIAGVV 23 
                                       6788888888887777666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.26
                                       -EEEEES-BSSHHHHSSEEESSHHHHHHHHHHHH-TTS---GGGC CS
                           DUF5612  95 iivislnmaGsvtevadlvvtdpvqaGvlavmavadtavfdierv 139
                                       i  +  +m G++  + ++vv   +++   +v    d ++ d++r+
  gi|330507555|ref|YP_004383983.1|  19 IAGVVAKMGGNIVYTQQFVVERGINSDKASVYMEIDCSTQDVNRM 63 
                                       555667888888888888888888888777766666777777665 PP

  == domain 3  score: 233.1 bits;  conditional E-value: 2.4e-73
                                       E--HHHHT-EEEEEEE-HHHHHHHHHHHHHHHHHHHCTSS-EEEEEEE--SHHHHHHHHHHGGGSTTEEEEEEESSB CS
                           DUF5612   1 hkslkeifGkrviilGGGaqvaqvalGaiseadrhnirGerisvdtiplvGeeelaeaveavsrlprvkvlvlaGsl 77 
                                       h+++++i+G+rvii+GGGaqvaqva+Ga++eadrhn+rGerisvdtiplvGe ++a+av+avsrlpr+++lvlaG+l
  gi|330507555|ref|YP_004383983.1|  79 HDPFEKIYGSRVIIIGGGAQVAQVAVGAVNEADRHNLRGERISVDTIPLVGEVAIADAVSAVSRLPRASILVLAGAL 155
                                       6789************************************************************************* PP

                                       --THHHHHHHHHHHT.T-EEEEES-BSSHHHHSSEEESSHHHHHHHHHHHH-TTS---GGGCSS- CS
                           DUF5612  78 mGGkiteavkklkeekdiivislnmaGsvtevadlvvtdpvqaGvlavmavadtavfdiervkgk 142
                                       mGG+it++v++l+ee +i+vi+l+maGsv+ +ad+vvtdp+qaG++avm+va+tavfdi rv+g+
  gi|330507555|ref|YP_004383983.1| 156 MGGRITQEVARLQEE-GIPVIALKMAGSVPGQADMVVTDPIQAGTFAVMHVASTAVFDIARVRGR 219
                                       **************9.***********************************************97 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.1     6e-12   2.2e-08       3      49 ..       5      54 ..       3      69 .. 0.78
   2 ?   -2.1   0.0      0.94   3.4e+03      27      48 ..      72      93 ..      72     110 .. 0.59

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 6e-12
                                      EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT...ECEEEEEEEE CS
                               ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedk...vagivfvviv 49
                                      ++v + DrPG+L +++g++a++g Ni+  +q+ +e++       v + i 
  gi|330507555|ref|YP_004383983.1|  5 INVICLDRPGMLRDIAGVVAKMGGNIVYTQQFVVERGinsDKASVYMEID 54
                                      99*********************************997754444444444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.94
                                      EEEEEEEEEESTTECEEEEEEE CS
                               ACT 27 Nidsieqrssedkvagivfvvi 48
                                      +i+ ++++   +k+ g  +++i
  gi|330507555|ref|YP_004383983.1| 72 SITEVSVHDPFEKIYGSRVIII 93
                                      5777777777777444444444 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.4e-07   0.00049       8      78 ..       4      76 ..       1      77 [. 0.72

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.4e-07
                             ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkdvehLsrviakLraipgVisV 78
                                       ++v++ dr+g+L+di+ v++++++niv  +    ++   +  a++ +++   ++++++r+i+ L   +++++V
  gi|330507555|ref|YP_004383983.1|  4 AINVICLDRPGMLRDIAGVVAKMGGNIVYTQQFVVERginSDKASVYMEIDC-STQDVNRMIEELDGFDSITEV 76
                                      799************************9776655443333334444444443.567778888888888888777 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.3e-06    0.0047       5      40 ..       5      40 ..       2      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.3e-06
                             ACT_6  5 itvtGpdrpGltasLtsvlaefgvnilDieqavihg 40
                                      i+v+  drpG++ ++++v+a+ g ni+  +q v+++
  gi|330507555|ref|YP_004383983.1|  5 INVICLDRPGMLRDIAGVVAKMGGNIVYTQQFVVER 40
                                      999****************************99875 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 ?    0.8   0.0     0.072   2.6e+02     209     229 ..      58      78 ..      55     102 .. 0.88
   2 ?    9.1   0.0   0.00022      0.78      70     109 ..     162     201 ..     145     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.072
                                       GEEEEEESSGGGHHHHTSSS- CS
                      Peripla_BP_1 209 eevdsfiesvvvydgLkkaqd 229
                                       ++v+++ie+++++d+++++++
  gi|330507555|ref|YP_004383983.1|  58 QDVNRMIEELDGFDSITEVSV 78 
                                       89**************88765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00022
                                       HHHHHHHHHT-EEEEESS--B-TTTS-EEEE-HHHHHHHH CS
                      Peripla_BP_1  70 dditakaesgipvialedaidapdgvPcvipddtqagees 109
                                        ++ + +e+gipvial+ a+  p + ++v+ d  qag+ +
  gi|330507555|ref|YP_004383983.1| 162 QEVARLQEEGIPVIALKMAGSVPGQADMVVTDPIQAGTFA 201
                                       478889999**************999*********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1631.00
//
Query:       gi|330507556|ref|YP_004383984.1|  [L=82]
Description: glutaredoxin-like protein [Methanosaeta concilii GP6]
Scores for complete 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-05   23.0   0.0     0.0001   22.5   0.0    1.2  1  Glutaredoxin  Glutaredoxin
     0.0032   17.8   0.0     0.0037   17.6   0.0    1.2  1  DUF836        Glutaredoxin-like domain (DUF836)


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.1e-08    0.0001       3      40 ..       5      41 ..       4      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-08
                                      EEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHH CS
                      Glutaredoxin  3 lftkptCpyCkkakrlLkelgvkfeeidvdkdeeiree 40
                                      +++++ Cp C + k++L + g++fe id    +e+  e
  gi|330507556|ref|YP_004383984.1|  5 VYSTKSCPKCEQLKAALVKAGIAFENIDMGT-PEALTE 41
                                      8************************999766.455555 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   0.0   4.1e-07    0.0037       5      57 ..       6      59 ..       4      76 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.1e-07
                                      EE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CCCHC.....CCCTTTTEEEECT CS
                            DUF836  5 yskpgChlCeqakekLkelkleegleleviDIakdeelea.....kYgleipvlaleg 57
                                      ys++ C+ Ceq+k++L++++    +  e iD  + e l +      + l  pvl  e+
  gi|330507556|ref|YP_004383984.1|  6 YSTKSCPKCEQLKAALVKAG----IAFENIDMGTPEALTElringVFTLSAPVLQEED 59
                                      9****************765....6666888777777666555666777777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 623.73
//
Query:       gi|330507557|ref|YP_004383985.1|  [L=111]
Description: hypothetical protein MCON_1514 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 866.90
//
Query:       gi|330507558|ref|YP_004383986.1|  [L=76]
Description: archaeal histone [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-16   59.9   0.0    2.5e-16   59.7   0.0    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    1.2e-10   41.9   0.0    1.3e-10   41.7   0.0    1.0  1  Histone        Core histone H2A/H2B/H3/H4
    4.2e-09   36.3   0.0      5e-09   36.0   0.0    1.0  1  Bromo_TP       Bromodomain associated
      3e-07   30.5   0.0    3.5e-07   30.3   0.0    1.1  1  CENP-T_C       Centromere kinetochore component CENP-T histon
    2.3e-05   24.5   0.1    2.5e-05   24.4   0.1    1.1  1  TAF            TATA box binding protein associated factor (TA
    5.4e-05   23.2   0.0    6.6e-05   23.0   0.0    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
    0.00051   20.4   0.0    0.00056   20.2   0.0    1.1  1  CENP-S         CENP-S protein
  ------ inclusion threshold ------
      0.024   13.5   0.3      0.025   13.4   0.3    1.2  1  AAA_32         AAA domain


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   1.1e-19   2.5e-16       3      65 .]       4      65 ..       2      65 .. 0.98

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.1e-19
                                      XXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                     CBFD_NFYB_HMF  3 LPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                      LP+a+v ++++++ +a+++++ A++ +ae++e +  e+a+eAa  ++++krKt+kae+i+ Av
  gi|330507558|ref|YP_004383986.1|  4 LPVAPVSRLIREA-GAKRVSEGARDALAEVLESYGLEVAREAAGWANHAKRKTVKAEDIREAV 65
                                      9************.**********************************************998 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   5.8e-14   1.3e-10      65     129 ..       7      66 ..       1      68 [. 0.86

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 5.8e-14
                                       HHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                           Histone  65 lpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                       +p++R++re        +r+s  a +al+e+lE +  e++ eA+  a+haKR+T+ ++Di+ A++
  gi|330507558|ref|YP_004383986.1|   7 APVSRLIRE-----AGAKRVSEGARDALAEVLESYGLEVAREAAGWANHAKRKTVKAEDIREAVK 66 
                                       455555555.....556**********************************************98 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   2.2e-12     5e-09      12      71 ..       9      68 ..       5      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.2e-12
                                      HHHHHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHHHT CS
                          Bromo_TP 12 vsqileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvltLqel 71
                                      vs + +eaG +++ e+a ++L e++++Y +e++++a  +a+ha R +++ +D++ + +++
  gi|330507558|ref|YP_004383986.1|  9 VSRLIREAGAKRVSEGARDALAEVLESYGLEVAREAAGWANHAKRKTVKAEDIREAVKRV 68
                                      8999**************************************************998875 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.6e-10   3.5e-07       6      76 ..       2      67 ..       1      72 [. 0.92

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.6e-10
                          CENP-T_C  6 pslPaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmkr 76
                                      p lP+a v++l +++       +++++ a +al ++++ +   v+++ + +a+Ha+RKt++++D+   +kr
  gi|330507558|ref|YP_004383986.1|  2 PILPVAPVSRLIREA-----GAKRVSEGARDALAEVLESYGLEVAREAAGWANHAKRKTVKAEDIREAVKR 67
                                      89999***9999887.....4569*****************************************988887 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   1.1e-08   2.5e-05      17      66 .]      17      66 ..       1      66 [. 0.88

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.1e-08
                                      T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH- CS
                               TAF 17 GitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsALr 66
                                      G + +s+ a  +Lae +e    e+++eaa + +h+kR++  ++D+ +A++
  gi|330507558|ref|YP_004383986.1| 17 GAKRVSEGARDALAEVLESYGLEVAREAAGWANHAKRKTVKAEDIREAVK 66
                                      777888999999**99999999************************9986 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 !   23.0   0.0     3e-08   6.6e-05      11      68 ..       9      66 ..       5      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3e-08
                       TFIID-31kDa 11 ihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiq 68
                                      ++ ++++ g + ++e   + L ++   y  +v ++A   a+hak+k+v+++d+r A++
  gi|330507558|ref|YP_004383986.1|  9 VSRLIREAGAKRVSEGARDALAEVLESYGLEVAREAAGWANHAKRKTVKAEDIREAVK 66
                                      6789999*************************************************97 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.5e-07   0.00056      26      72 ..      21      67 ..       6      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.5e-07
                            CENP-S 26 atkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLlaRr 72
                                      +++ +  al+e+      ++a+    +a+HAkR+t++++D+   ++r
  gi|330507558|ref|YP_004383986.1| 21 VSEGARDALAEVLESYGLEVAREAAGWANHAKRKTVKAEDIREAVKR 67
                                      66666678888887778899999999**************9766665 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   1.1e-05     0.025     481     510 ..      38      67 ..       8      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                            AAA_32 481 adllrEAdywakkegaevveaehVekAlee 510
                                        ++ rEA+ wa+++++++v+ae++++A+++
  gi|330507558|ref|YP_004383986.1|  38 LEVAREAAGWANHAKRKTVKAEDIREAVKR 67 
                                       5899***********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 563.21
//
Query:       gi|330507559|ref|YP_004383987.1|  [L=634]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Methanosaeta concilii GP6]
Scores for complete 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-65  218.8   0.0    1.4e-64  218.2   0.0    1.3  1  GatB_N     GatB/GatE catalytic domain
    4.6e-21   75.3   0.2    9.1e-21   74.3   0.2    1.5  1  GatB_Yqey  GatB domain
    7.2e-11   42.2   0.2    2.8e-10   40.3   0.0    2.1  2  GAD        GAD domain
     0.0035   17.4   1.2     0.0071   16.4   1.2    1.4  1  YqeY       Yqey-like protein


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.2   0.0   3.1e-68   1.4e-64       2     272 ..      17     449 ..      16     450 .. 0.96

  Alignments for each domain:
  == domain 1  score: 218.2 bits;  conditional E-value: 3.1e-68
                                       EEEEEEEEEB--SB-SSSSSBSSSSCE.............STTSS--TTTTTS........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxx........................ RF
                            GatB_N   2 viGlEiHaqlktksKlFssasteeege.............epnsevsevdlal........................ 41 
                                       ++G+EiH+ql+t+ KlF++++t++ +e              ++se++e+d a+                        
  gi|330507559|ref|YP_004383987.1|  17 ICGIEIHQQLDTACKLFCGCPTAH-REvedsnfeffrylrPSRSELGEIDRAAleevlvsrkfhykcydttclvead 92 
                                       79*******************873.3234567888989844899999999999***********************9 PP

                                       ..TT..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEEE CS
                                       ..xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                            GatB_N  42 ..PGtlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrierih 114
                                         P   P  +n ea+e+++ +a  l ++i +e+ ++RK+++++++++g+Q+t+    + ++Gs+++ +  v+i+ ++
  gi|330507559|ref|YP_004383987.1|  93 eeP---PSqINPEALEISLVIARLLSMQIVDEVCTMRKMVIDGSNTSGFQRTA---YIGSKGSIQTnQGPVGIDILC 163
                                       998...888********************************************...688******97788******* PP

                                       EEE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 115 lEeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvr 191
                                       lEe+aa+ ++++ ++ +++l+R+G+pL+Ei t+pd+ sp++ar+v++ l+++lr++g +++++  G++R+DvNvS++
  gi|330507559|ref|YP_004383987.1| 164 LEEEAARIIEDRGDSLVYSLDRLGIPLVEIGTAPDIISPAHAREVASYLGMILRSTGRVKRGL--GTIRQDVNVSIK 238
                                       *************9*************************************************..************ PP

                                       TSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH....................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................... RF
                            GatB_N 192 eeekgeeegtrvEiKnlnslksiekaieyeierqiell....................................... 229
                                               g+rvEiK+++ l+ ++k++e e+ rq  ll                                       
  gi|330507559|ref|YP_004383987.1| 239 G-------GARVEIKGVQALNLVDKIVELEALRQHGLLqikeelirrgaavddtvfdvtslfsqtdskvlarsikkg 308
                                       4.......59******************************************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                            GatB_N 230 ............................................................................. 229
                                                                                                                    
  gi|330507559|ref|YP_004383987.1| 309 gvvlacrlagfaglvgrevqpgrrlgsemsdrakragvggifhsdelpaygvtaaevesvrvqlqagkeyavimvtg 385
                                       ***************************************************************************** PP

                                       ........................-EEEEEETTTTEEEEECC--.--...-EEE-TTS--EE--HHHH CS
                                       ........................xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 230 ........................qeTrkfdedkgetvslRske.eaedYryfpepdlppleiseeli 272
                                                               +eTr++ +d g ++++R+ + +a   r++pe+d+p ++i+e+++
  gi|330507559|ref|YP_004383987.1| 386 pedrarkamdavlvrareamelvpEETRRALPD-GCSEYMRPLPgSA---RMYPETDVPSVAINEQTL 449
                                       *********************************.**********555...**************9987 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.2     2e-24   9.1e-21       1     148 []     486     628 ..     486     628 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 2e-24
                                       HHHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXH CS
                         GatB_Yqey   1 dffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gksp 76 
                                       ++fee+v++++ ++++a   l+ +  el + g++i++  l+++++++ l l+aeg+I+k+   e++++l+e  ++s+
  gi|330507559|ref|YP_004383987.1| 486 QLFEEIVSHIQLSPSIAVRALETIPIELARDGVDISA--LSDNHFKDALGLVAEGRIAKEGLAELFRALAERpDRSA 560
                                       68********99*************************..9************************************* PP

                                       HHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  77 eeiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       +++    gL  +  e e+ k+v+ ++a +   ++ ++s+ e+a   l+G vMk+++Gkad++lv+ +lk+++
  gi|330507559|ref|YP_004383987.1| 561 ADAAAASGLAGVD-EVEVAKIVQAIVADK---MDLVRSKGERAAAPLMGLVMKELRGKADGALVSAILKKEI 628
                                       ***********95.6**************...999**********************************986 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   6.3e-14   2.8e-10       4      95 .]     304     394 ..     301     394 .. 0.96
   2 ?   -1.7   0.1      0.78   3.5e+03      54      81 ..     566     592 ..     560     593 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 6.3e-14
                                       HHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TTE CS
                               GAD   4 alksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeegD 79 
                                        +k+gg+v a r+ g +a+l+++e++++++++ e++++++   +v+g +++++++++ +t++ev+ ++ +++a ++ 
  gi|330507559|ref|YP_004383987.1| 304 SIKKGGVVLACRLAG-FAGLVGREVQPGRRLGSEMSDRAKRA-GVGGIFHSDELPAYgVTAAEVESVRVQLQAGKEY 378
                                       6899***********.8**********************976.********************************** PP

                                       EEEEEEEEHHHHHHHH CS
                               GAD  80 illfvAdkkktvnkal 95 
                                       ++++v ++++ + ka+
  gi|330507559|ref|YP_004383987.1| 379 AVIMVTGPEDRARKAM 394
                                       ************9998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.78
                                       ETTTCCCS-HHHHHHHHHHCT--TTEEE CS
                               GAD  54 tgpiakflteeevkklleavgaeegDil 81 
                                        +++a   +e ev k+++a+ a++ D++
  gi|330507559|ref|YP_004383987.1| 566 ASGLAGV-DEVEVAKIVQAIVADKMDLV 592
                                       5677777.99999999999999998886 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.2   1.6e-06    0.0071      95     142 ..     576     627 ..     571     628 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHH....TT--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH CS
                              YqeY  95 eiealvkeaiae....vgaesmkdmGkvmkalkpkvkGkaDgkkvsalvkek 142
                                       e++++v++++a+    v  ++ ++   +m++++++++GkaDg+ vsa++k++
  gi|330507559|ref|YP_004383987.1| 576 EVAKIVQAIVADkmdlVRSKGERAAAPLMGLVMKELRGKADGALVSAILKKE 627
                                       5556666555551111688999***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4373.51
//
Query:       gi|330507560|ref|YP_004383988.1|  [L=367]
Description: cell division control protein 6 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-11   44.2   0.1    1.6e-09   38.4   0.0    2.6  2  AAA_16         AAA ATPase domain
    8.3e-08   32.6   0.0      2e-07   31.4   0.0    1.5  1  AAA_22         AAA domain
    8.4e-05   23.0   0.0    0.00019   21.9   0.0    1.6  1  AAA            ATPase family associated with various cellular
    0.00024   20.6   0.0     0.0063   16.0   0.0    2.2  2  AAA_7          P-loop containing dynein motor region
    0.00042   20.2   0.1     0.0013   18.7   0.1    1.9  1  Cdc6_C         CDC6, C terminal winged helix domain
     0.0017   18.2   0.0     0.0034   17.2   0.0    1.6  2  AAA_11         AAA domain
     0.0059   16.5   0.0      0.012   15.5   0.0    1.4  1  NACHT          NACHT domain
  ------ inclusion threshold ------
      0.025   14.3   0.0      0.053   13.2   0.0    1.4  1  AAA_30         AAA domain
      0.041   12.9   0.0      0.069   12.2   0.0    1.3  1  T2SSE          Type II/IV secretion system protein
      0.053   12.7   0.0       0.12   11.5   0.0    1.5  2  DUF815         Protein of unknown function (DUF815)
      0.057   12.3   0.0       0.11   11.4   0.0    1.4  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.066   12.8   0.0       0.12   12.0   0.0    1.4  1  SRP54          SRP54-type protein, GTPase domain
      0.068   12.9   0.0       0.11   12.2   0.0    1.3  1  AAA_24         AAA domain
        0.1   11.9   0.0       0.15   11.3   0.0    1.2  1  DUF2075        Uncharacterized conserved protein (DUF2075)
       0.12   12.2   0.0       0.28   10.9   0.0    1.6  1  RuvB_N         Holliday junction DNA helicase RuvB P-loop dom
       0.12   12.7   0.0       0.28   11.6   0.0    1.6  1  RNA_helicase   RNA helicase
       0.14   11.0   0.0       0.35    9.6   0.0    1.6  2  AAA_35         AAA-like domain
       0.14   12.0   0.0       0.36   10.7   0.0    1.6  1  NTPase_1       NTPase


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 !   38.4   0.0   1.6e-12   1.6e-09       1     163 [.      23     160 ..      23     170 .. 0.65
   2 ?   -2.3   0.0       5.1   5.1e+03     124     124 ..     280     280 ..     220     336 .. 0.60

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.6e-12
                            AAA_16   1 rlvGReeeleqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekdg.gif.lrgkcdqlesaipysalaq 74 
                                       ++  Re++l+ L+ +++ ++  grp + l+ G++G+GK++ + +l++++e++   i+ +  +c+           ++
  gi|330507560|ref|YP_004383988.1|  23 QFLHRERQLDSLKFCIRpALQGGRPVNALCLGPPGTGKTTAIFKLFEEIEAHStRIVpVHVNCQMD--------STR 91 
                                       6889*************55555556*************************9953455566666666........444 PP

                            AAA_16  75 alareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwade.a 150
                                       ++ + +l++++ ++a                        ++  ++ +++ + ++ ++ +++ l++ lDd+  + +  
  gi|330507560|ref|YP_004383988.1|  92 YAVFYQLYKKIFEHAPP----------------------SSGISFKRVFEKVAQHSADEDKVLIVALDDINYLFPeK 146
                                       44445666666655111......................11145666666666555554555777777777444333 PP

                            AAA_16 151 slql.laaLlrlle 163
                                         +  l++Llr+ e
  gi|330507560|ref|YP_004383988.1| 147 EVDHvLYSLLRAHE 160
                                       33333666666655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.1
                            AAA_16 124 k 124
                                       +
  gi|330507560|ref|YP_004383988.1| 280 T 280
                                       2 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0     2e-10     2e-07       9     117 ..      51     157 ..      47     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2e-10
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdl.lrellralglelkaerlsseelleal 82 
                                       ++ G++GtGKTt + +l+e+ +++      + ++v  +v+++ ++++  + ++   +++++   +++ s ++++e++
  gi|330507560|ref|YP_004383988.1|  51 LCLGPPGTGKTTAIFKLFEEIEAH------STRIVpvHVNCQMDSTRYAVfYQLYKKIFEHAPPSSGISFKRVFEKV 121
                                       899*****************9775......7777788********88887366666666666666999********* PP

                            AAA_22  83 eqalraravielliiDEaqhlr.seealeeLrslln 117
                                       +q++ + +++ ++ +D++ +l+ ++e+   L sll 
  gi|330507560|ref|YP_004383988.1| 122 AQHSADEDKVLIVALDDINYLFpEKEVDHVLYSLLR 157
                                       *******99888999*****9864554444455444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.9e-07   0.00019       2      90 ..      51     156 ..      50     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.9e-07
                                       EEESSTTSSHHHHHHHHHHHHTHE...................EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.. CS
                               AAA   2 llyGppGtGKTllakavakelgve...................fleisgsellskyvgesekkirelfkeakeka.. 57 
                                       l  GppGtGKT+++  + +e++++                   ++    ++++++    s  +++ +f+++ +++  
  gi|330507560|ref|YP_004383988.1|  51 LCLGPPGTGKTTAIFKLFEEIEAHstrivpvhvncqmdstryaVFYQLYKKIFEHAPPSSGISFKRVFEKVAQHSad 127
                                       678*****************865544444444444444444443333344444557777777778888885555568 PP

                                       ..TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHH CS
                               AAA  58 ..kpsilfiDEidalaksrsgseseeeervvnqLl 90 
                                         k  i+ +D+i  l++++      e + v+  Ll
  gi|330507560|ref|YP_004383988.1| 128 edKVLIVALDDINYLFPEK------EVDHVLYSLL 156
                                       8666999*********999......4444444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.3e-06    0.0063      35      77 ..      49      91 ..      32     102 .. 0.82
   2 ?    2.0   0.0      0.13   1.3e+02      97     129 ..     127     159 ..     118     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.3e-06
                             AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanq 77
                                      + l+ Gp GtGKt+ i +l+++++  ++ ++ + ++ q+++++
  gi|330507560|ref|YP_004383988.1| 49 NALCLGPPGTGKTTAIFKLFEEIEAHSTRIVPVHVNCQMDSTR 91
                                      469*********************9999988888888888765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.13
                             AAA_7  97 pggkklvvFvDDlnmpakekygaqppiellRql 129
                                          k l+v +DD+n   +ek  +     llR +
  gi|330507560|ref|YP_004383988.1| 127 DEDKVLIVALDDINYLFPEKEVDHVLYSLLRAH 159
                                       567899*********999999999999999865 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 !   18.7   0.1   1.3e-06    0.0013      39      82 ..     320     362 ..     314     364 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHH CS
                            Cdc6_C  39 qrevsdllseLemlgileleksskGrregrtrkisLnvdpddvl 82 
                                        ++++++l++L++ +++++   ++G+r gr+r i+++++ +++l
  gi|330507560|ref|YP_004383988.1| 320 YTRFHEILNKLDAIRLINADFTGQGER-GRSRIIRVRYEAEEIL 362
                                       69***********************97.************9997 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.4e-06    0.0034      19      43 ..      49      86 ..      28     208 .. 0.71
   2 ?   -3.8   0.0       8.5   8.5e+03      73      98 ..     334     359 ..     332     365 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.4e-06
                            AAA_11 19 itliqGPPGtgKTktivellsqll.............s 43
                                       +l  GPPGtgKT++i +l++++              +
  gi|330507560|ref|YP_004383988.1| 49 NALCLGPPGTGKTTAIFKLFEEIEahstrivpvhvncQ 86
                                      56778*****************9744444444444440 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.5
                            AAA_11  73 rllrglldsegekykpkivRvgneee 98 
                                       rl++  ++++ge+ + +i+Rv  e+e
  gi|330507560|ref|YP_004383988.1| 334 RLINADFTGQGERGRSRIIRVRYEAE 359
                                       56665677889999999999988774 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   1.2e-05     0.012       6     115 ..      53     158 ..      50     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                                       EC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-C.....CHHHH CS
                             NACHT   6 qGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvse.....vwavl 76 
                                        G++G GKTt + kl +++ +         ++ +++++++s++ ++ + l + +f++ p++++ + +     v ++ 
  gi|330507560|ref|YP_004383988.1|  53 LGPPGTGKTTAIFKLFEEIEAHSTR----IVPVHVNCQMDSTRYAVfYQLYKKIFEHAPPSSGISFKrvfekVAQHS 125
                                       69*****************998844....58999*****99998777888888888888887776667666555555 PP

                                       CCSCCCEEEEEE-STT-SS-TCH.........HHHHHCT CS
                             NACHT  77 lelperlLlilDglDelvtdlgqkekqpvrtlLselirk 115
                                       +   + l   lD++++l  +      ++v+++L +l+r+
  gi|330507560|ref|YP_004383988.1| 126 ADEDKVLIVALDDINYLFPE------KEVDHVLYSLLRA 158
                                       55555555669999999973......457999*999997 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   5.3e-05     0.053      21      50 ..      50      79 ..      36      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                            AAA_30 21 avltGpAGtGKttalkalreaweaaggrvi 50
                                      a+  Gp+GtGKtta+ +l e +ea+  r++
  gi|330507560|ref|YP_004383988.1| 50 ALCLGPPGTGKTTAIFKLFEEIEAHSTRIV 79
                                      4568************99999998877766 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.9e-05     0.069     129     163 ..      47      81 ..      16      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.9e-05
                             T2SSE 129 rglilvsGgTgsGKttllyallkeinksderivtv 163
                                         + l  G+ g+GKtt +  l +ei++++ riv v
  gi|330507560|ref|YP_004383988.1|  47 PVNALCLGPPGTGKTTAIFKLFEEIEAHSTRIVPV 81 
                                       5678899*************************965 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.12      30      88 ..      24      82 ..      10      92 .. 0.89
   2 ?   -3.1   0.1       3.4   3.4e+03      96     119 ..     119     142 ..     116     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                            DUF815 30 LvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeegLrlieve 88
                                      +   ++q ++l+  ++  l+g +  n+L  G  GtGK + +  l++e+++++ r++ v+
  gi|330507560|ref|YP_004383988.1| 24 FLHRERQLDSLKFCIRPALQGGRPVNALCLGPPGTGKTTAIFKLFEEIEAHSTRIVPVH 82
                                      5566888889999999999************************************9987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.4
                            DUF815  96 pklvellrerperfilfvDDLsFe 119
                                       +k+ ++ +++++ +i+ +DD+ + 
  gi|330507560|ref|YP_004383988.1| 119 EKVAQHSADEDKVLIVALDDINYL 142
                                       567777778888899999998764 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   0.00011      0.11      19      55 ..      51      87 ..      46      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                     TrwB_AAD_bind 19 livGttGsGKtqalekllrairargdraivlDltGaf 55
                                      l +G  G+GKt+a+ kl ++i+a   r++ +  ++++
  gi|330507560|ref|YP_004383988.1| 51 LCLGPPGTGKTTAIFKLFEEIEAHSTRIVPVHVNCQM 87
                                      77899**********************9977666665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.12       4      49 ..      50      99 ..      47     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE....EESTSSTTHHHHHH CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllv....aaDtfRaaAveQLk 49
                                       l +G+ G+GKTt++ KL + ++++ ++++ v     +D  R a + QL 
  gi|330507560|ref|YP_004383988.1| 50 ALCLGPPGTGKTTAIFKLFEEIEAHSTRIVPVhvncQMDSTRYAVFYQLY 99
                                      5789****************999997665533111147999999999985 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   0.00011      0.11       3      75 ..      48     140 ..      46     148 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                            AAA_24   3 lkiliyGpsgiGKTtlakel.....gpkplfidtekGlksldadkfpdie..........................s 48 
                                       ++ l+ Gp+g+GKTt + +l                 + ++ + +++ ++                          s
  gi|330507560|ref|YP_004383988.1|  48 VNALCLGPPGTGKTTAIFKLfeeieA----------HSTRIVPVHVN-CQmdstryavfyqlykkifehappssgiS 113
                                       678999***********999544441..........33333333322.22333322222233344445555666666 PP

                            AAA_24  49 wedfldevvelaaeladyktlviDtid 75 
                                       ++ + ++v++ +a++++  ++ +D i+
  gi|330507560|ref|YP_004383988.1| 114 FKRVFEKVAQHSADEDKVLIVALDDIN 140
                                       666666666667777666666666665 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   0.00015      0.15       7      55 ..      53      98 ..      48     139 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                           DUF2075  7 tGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke 55
                                       G +GtGKt   ++l+ e+  +++  + v + vN  +++  r a+ ++ 
  gi|330507560|ref|YP_004383988.1| 53 LGPPGTGKTTAIFKLFEEI--EAHSTRIVPVHVN-CQMDSTRYAVFYQL 98
                                      599****************..4444444444444.44444444444444 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 ?   10.9   0.0   0.00028      0.28       7      60 ..      22      74 ..      18      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                            RuvB_N  7 eeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvk 60
                                      ++++ +e+  ++lk +i+ a + +++++  l  GpPG Gktt    + +e++++
  gi|330507560|ref|YP_004383988.1| 22 DQFLHRERQLDSLKFCIRPALQGGRPVNA-LCLGPPGTGKTTAIFKLFEEIEAH 74
                                      578888899999*********99999975.678*********887777777765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00029      0.28       4      29 ..      53      78 ..      50     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                      RNA_helicase  4 yGpsgeGKStlakeLakallkklklk 29
                                       Gp+g+GK+t++ +L ++++ ++  +
  gi|330507560|ref|YP_004383988.1| 53 LGPPGTGKTTAIFKLFEEIEAHSTRI 78
                                      7******************9988544 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.6   1.6e+03      39      68 ..      55      84 ..      52     105 .. 0.67
   2 ?    9.6   0.0   0.00036      0.35     126     155 ..     129     158 ..     106     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.6
                            AAA_35 39 pkkmGKtSLlarilakakqqgyktvsldlq 68
                                      p  +GKt  + ++ ++ ++++++ v + ++
  gi|330507560|ref|YP_004383988.1| 55 PPGTGKTTAIFKLFEEIEAHSTRIVPVHVN 84
                                      667788888888888888887777665544 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00036
                            AAA_35 126 dkplvLaldevdrlfeypeiakdflslLRs 155
                                       dk l++ald+++ lf ++e+ + + slLR+
  gi|330507560|ref|YP_004383988.1| 129 DKVLIVALDDINYLFPEKEVDHVLYSLLRA 158
                                       689**************************8 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00036      0.36       6      28 ..      54      76 ..      50      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                                      --TTSSHHHHHHHHHHHH...GG CS
                          NTPase_1  6 GppGvGKtTlvkkvlellkssgv 28
                                      GppG+GKtT + k+ e+++ +  
  gi|330507560|ref|YP_004383988.1| 54 GPPGTGKTTAIFKLFEEIEAHST 76
                                      9***************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); 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 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2479.95
//
Query:       gi|330507561|ref|YP_004383989.1|  [L=297]
Description: phosphate ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete sequence (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  10.2    1.1e-26   93.7  10.2    2.4  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   9.5      0.25   4.5e+03      23      61 ..      14      73 ..       1      86 [. 0.49
   2 !   93.7  10.2   6.4e-31   1.1e-26       1     182 [.      87     293 ..      87     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.25
                      BPD_transp_1 23 liivllslPsfvlaillvlvf.....................vilsilghlilpviilll 61
                                         +++++ s+++++l+++++                      + s+  +++lp+i+++l
  gi|330507561|ref|YP_004383989.1| 14 TLLFVSAITSILVMLLIFYFLihesipafselgiisllagmkWHPSGDIYGFLPLITASL 73
                                      334444555555555555555466666666666666665555444444444444444433 PP

  == domain 2  score: 93.7 bits;  conditional E-value: 6.4e-31
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf......vilsilghlilpviillllsaapyvrli 71 
                                       g++l+i++a   + + + +l p i++l ++Ps+v ++l v ++      +++   g +il++ ill ++++py + i
  gi|330507561|ref|YP_004383989.1|  87 GFPLAIYLAELAGPRSKAILKPAIELLAGVPSIVYGFLGVIILvsylqdSFDMLTGRSILAGSILLGVMFIPYLTTI 163
                                       789*******************************8888887778889999999************************ PP

                      BPD_transp_1  72 rraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgy 148
                                       +++alr++p +++e ++alGa+rwq++r+v++P+a + i + ++l++g+++g++++++++      g++   a+ +y
  gi|330507561|ref|YP_004383989.1| 164 CEDALRAVPGEFKEGSLALGANRWQTIRNVTIPAASSGITAAVLLNIGSIIGETMAVLLVV-----GNVARIASPYY 235
                                       *************************************************************.....66666666666 PP

                      BPD_transp_1 149 dyseis........................nggvlalviavlllnlvadilqrlldpr 182
                                       d+                            +++ l+l+++v +l+l+ad+  + + ++
  gi|330507561|ref|YP_004383989.1| 236 DIFDQGatftsviagemgevargsthyhalFAVGLILLLVVSILSLIADFARARIRKK 293
                                       6654445667778888888899****87777777777777777778877777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.22s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2097.03
//
Query:       gi|330507562|ref|YP_004383990.1|  [L=415]
Description: phosphate ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-22   78.7  12.7    4.4e-22   78.7  12.7    3.0  3  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2      0.21   3.8e+03     160     180 ..       8      28 ..       5      33 .. 0.47
   2 ?   -6.0   9.9         1   1.8e+04       4      80 ..      50     170 ..      47     204 .. 0.68
   3 !   78.7  12.7   2.5e-26   4.4e-22       3     183 ..     207     413 ..     205     415 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.21
                      BPD_transp_1 160 alviavlllnlvadilqrlld 180
                                       a+ +++ ++++v+ ++  +l+
  gi|330507562|ref|YP_004383990.1|   8 AASVVISAFLFVSSLICLILQ 28 
                                       444444444444444444444 PP

  == domain 2  score: -6.0 bits;  conditional E-value: 1
                      BPD_transp_1   4 lGilaalnrnkkldkllrpliivllslPsfv...........................laillvlvf.......... 43 
                                       lG+++  +++  ++ +l+++ ++l++  +f                            l++llvlv+          
  gi|330507562|ref|YP_004383990.1|  50 LGSYLT-MKGASVRTALLFILDILFCGSVFYlsysgalnpdfiikrplgvgasfeysfLLPLLVLVAsllcikdaln 125
                                       555565.6666677777777777765555554566666666666666666666666666666666667777778888 PP

                      BPD_transp_1  44 .............vilsilghlilpviillllsaapyvrlirraalrslp 80 
                                                    v       +i + ++l+++ ++++ ++i+++++ +++
  gi|330507562|ref|YP_004383990.1| 126 ivygytargrealV-----FLGIRMSAMLSIILLGGILFIIIYKGIWVIN 170
                                       88888887444332.....4456666666666666666666666665555 PP

  == domain 3  score: 78.7 bits;  conditional E-value: 2.5e-26
                      BPD_transp_1   3 llGilaa.....lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirra 74 
                                       +lGi aa     ++++ +l++l+++ + +l ++Ps+v +++ ++  ++ s +g + +++ i+l l ++p+++l+ ++
  gi|330507562|ref|YP_004383990.1| 207 PLGIGAAiylheYSKSERLNRLITIAVSCLNGVPSVVYGLFGLA--FLVSLFGVSLISGSIILGLINIPTIILTSQE 281
                                       67777777777**************************8888775..46799************************** PP

                      BPD_transp_1  75 alrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydys 151
                                       al+s+p +l+e + alGa++wq++rkvvlP+a+p i+tg+i+ ++ + g+++ + +++    ++ +   ++++y + 
  gi|330507562|ref|YP_004383990.1| 282 ALKSVPNSLREGSMALGATKWQTIRKVVLPSAMPGILTGVIMGVAKASGETAPIMWTA----VTFTASPVQMIYGVI 354
                                       ***************************************************9999988....555555555555443 PP

                      BPD_transp_1 152 eis...........................nggvlalviavlllnlvadilqrlldprv 183
                                         +                           +g++l+l+ +vl  nl+a ++  +  +++
  gi|330507562|ref|YP_004383990.1| 355 PDLfqpvnnlnyhllnliyflgawdvearaWGTALVLISLVLSTNLLAIVVRNYYRKKI 413
                                       3334677778899999********************************99999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2806.50
//
Query:       gi|330507563|ref|YP_004383991.1|  [L=157]
Description: hypothetical protein MCON_1521 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1209.42
//
Query:       gi|330507564|ref|YP_004383992.1|  [L=102]
Description: hypothetical protein MCON_1524 [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.1    1.7e-09   37.5   0.1    1.3  1  HTH_45        Winged helix-turn-helix
     0.0022   18.1   0.1     0.0026   17.9   0.1    1.2  1  HTH_34        Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.022   14.1   0.0    1.4  1  P53_tetramer  P53 tetramerisation motif
      0.057   13.8   0.0      0.074   13.4   0.0    1.1  1  Rrf2          Transcriptional regulator
       0.18   12.3   0.0       0.23   12.0   0.0    1.2  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 !   37.5   0.1   4.8e-13   1.7e-09       2      73 ..       7      90 ..       6      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 4.8e-13
                            HTH_45  2 RskleIiadILeaisegeak....kTkimykanLsykllnkYLdmLvekgli........kkskekYvlTekGlellek 68
                                      R  ++I++ +Le is+g++k    kT+i+  anL+   ++kY++mL + g+i          +   ++lT  G+  +e 
  gi|330507564|ref|YP_004383992.1|  7 RPAIKIVLKLLECISKGQSKgralKTHIIQCANLKTTSAEKYINMLKDAGYIeekrlawgAREVIVFELTPLGKSRYEW 85
                                      7889**********8655443344****************************777777665666778888888877777 PP

                            HTH_45 69 lkele 73
                                      +k+++
  gi|330507564|ref|YP_004383992.1| 86 FKTIN 90
                                      77766 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   7.3e-07    0.0026      19      70 ..      33      84 ..      14      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7.3e-07
                            HTH_34 19 elkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafk 70
                                       + ++ ++ +    + +++L++agYie +    g ++ +++++Tp G+++++
  gi|330507564|ref|YP_004383992.1| 33 HIIQCANLKTTSAEKYINMLKDAGYIEEKRLAWGAREVIVFELTPLGKSRYE 84
                                      555566666666678899******************************9987 PP

>> P53_tetramer  P53 tetramerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     6e-06     0.022      10      32 ..      69      93 ..      61      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6e-06
                      P53_tetramer 10 Ev..FtLqvRGRerYEmLkKineaL 32
                                      Ev  F L+  G++rYE++k in+ L
  gi|330507564|ref|YP_004383992.1| 69 EVivFELTPLGKSRYEWFKTINDEL 93
                                      5555778888************965 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.1e-05     0.074       7      59 ..      10      62 ..       4      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                                      HHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2  7 teyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      ++++l++l  ++k ++++ +  ++i ++ n++ + +ek +++L+ ag+++ +r
  gi|330507564|ref|YP_004383992.1| 10 IKIVLKLLECISKGQSKGRALKTHIIQCANLKTTSAEKYINMLKDAGYIEEKR 62
                                      566777888888888888788999*************************9876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.4e-05      0.23       9      67 ..      17      78 ..      12      79 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.4e-05
                            HTH_27  9 Lhlir..hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekr.vrlTdk 67
                                      L++i      +r+ ++ +++  n+  +++ + ++ L  +G++e+++ +   re+  ++lT+ 
  gi|330507564|ref|YP_004383992.1| 17 LECISkgQSKGRALKTHIIQCANLKTTSAEKYINMLKDAGYIEEKRLAWGAREVIvFELTPL 78
                                      5556563444555559**************************99998888888541567765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 827.07
//
Query:       gi|330507565|ref|YP_004383993.1|  [L=345]
Description: glycosyl transferase, group 2 family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-21   77.8   0.0    1.5e-21   77.4   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    3.2e-19   69.4   0.1    4.6e-19   68.9   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    3.7e-16   59.6   2.8    7.4e-16   58.6   2.8    1.5  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    5.4e-14   52.0   0.5    1.2e-13   50.9   0.3    1.6  2  Glyco_transf_21  Glycosyl transferase family 21
    5.1e-06   25.4  10.7    9.6e-06   24.5   0.0    2.1  2  Chitin_synth_2   Chitin synthase
    0.00048   20.6   0.5     0.0012   19.4   0.5    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.066   12.7   0.1       0.13   11.7   0.1    1.6  1  CodY             CodY GAF-like domain


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0   5.8e-25   1.5e-21       5     230 .]       4     230 ..       2     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 5.8e-25
                   Glyco_tranf_2_3   5 avlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                       + +Vp+ nee++l ++++ + +q  +++++ vv+d+++++t + a+     l+ + ++++ n +      ks aln+
  gi|330507565|ref|YP_004383993.1|   4 LTIVPAHNEEPTLDSCINGIRNQ-TIETDILVVCDNCTDKTEQLAQ----SLEVNTLKTINNVH-----KKSGALNQ 70 
                                       569*****************997.8999999999**9999877665....57766788886655.....59999*** PP

                   Glyco_tranf_2_3  82 alravk..sdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvflln..rstl....vsalgalefaerhlrfl 149
                                       al+ +   +dl+l+ D+Dt+++ ++l+ ++  + +++k gav  +   +    s++    +  l+++e+a   ++ +
  gi|330507565|ref|YP_004383993.1|  71 ALDKYLldYDLILVQDADTIIDHRLLENAVKEInKDKKLGAVCSKAGIKDimSSKWsellWWHLQRIEYA--TFDSS 145
                                       ***86666*************************9999999999888776442334444345555777765..55566 PP

                   Glyco_tranf_2_3 150 aarralgvltlnGsgslirrevlkele.gldp...lflltdDyelglrlrragfrtayvpgaavrevfpsslkayik 222
                                       +  +a+++  ++G   ++r++ l++ + ++++    +++t+Dyel+  l++ g++t  + +   +++ p +lk+++k
  gi|330507565|ref|YP_004383993.1| 146 RIETAGSIKVVHGMAAVYRTAALQQVKnKWGRiydENNITEDYELTICLKELGWKTTACMDMRAWTEVPVTLKELWK 222
                                       667777776679***************768888889***************************************** PP

                   Glyco_tranf_2_3 223 qrnRwvyg 230
                                       qr Rw +g
  gi|330507565|ref|YP_004383993.1| 223 QRVRWFRG 230
                                       *****875 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 !   68.9   0.1   1.8e-22   4.6e-19       3     169 ..       6     171 ..       5     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 1.8e-22
                                       EEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-.HHHHHHHHHHHH- CS
                   Glycos_transf_2   3 viptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenv.Gkagalnaglraa 78 
                                       ++p++Nee+tl  +++ +++q    + +i+vv D+ tD+t++++++l      v  ++  +nv  k+galn++l++ 
  gi|330507565|ref|YP_004383993.1|   6 IVPAHNEEPTLDSCINGIRNQ--TIETDILVVCDNCTDKTEQLAQSL-----EVNTLKTINNVhKKSGALNQALDKY 75 
                                       8********************..88888888888888**********.....799999999*99************6 PP

                                       -SS..EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS...EEEECCHCCCCHCCCCCC CS
                   Glycos_transf_2  79 tgd..yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv...generlyfkerkrslkgn 150
                                         d  +il+ DaD+++d   le  v++++kd + +++++   i++    ++  + +   ++ e   f   + ++ g+
  gi|330507565|ref|YP_004383993.1|  76 LLDydLILVQDADTIIDHRLLENAVKEINKDKKLGAVCSKAGIKDIMSSKWSELLWwhlQRIEYATFDSSRIETAGS 152
                                       66666**************************999999998888888888887777778989999999999******* PP

                                       STTCSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 151 lsfeigsaallrrealeel 169
                                       + +++g aa++r  al+++
  gi|330507565|ref|YP_004383993.1| 153 IKVVHGMAAVYRTAALQQV 171
                                       *************999875 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 !   58.6   2.8   2.9e-19   7.4e-16       2     182 ..      82     284 ..      81     339 .. 0.71

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2.9e-19
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaela.spevaivqgpvlvm.....nvanwleelaalffaedhgkdilvre.algrvvp 71 
                                       il+ DaDt ++   l+ ++ e+  + + ++v+ + ++        ++ l +++     + ++ + ++r  + g+   
  gi|330507565|ref|YP_004383993.1|  82 ILVQDADTIIDHRLLENAVKEINkDKKLGAVCSKAGIKdimssK-WSELLWWHLQ--RIEYATFDSSRIeTAGSIKV 155
                                       99*********************779999999887764332422.2233344443..33444455555526666777 PP

                   Glyco_trans_2_3  72 svGsgaflrrsalqevg.....gwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayG 143
                                       ++G  a+ r +alq+v       +d  e +++ED+++ + l ++G+++  + +   ++++p tl+  ++Qr Rw++G
  gi|330507565|ref|YP_004383993.1| 156 VHGMAAVYRTAALQQVKnkwgrIYD--ENNITEDYELTICLKELGWKTTACMDMRAWTEVPVTLKELWKQRVRWFRG 230
                                       88************99999965555..************************9999********************** PP

                   Glyco_trans_2_3 144 cel...eklillvrllgylgsllwsalp..lhlallllfslla..........l 182
                                         +    + i ++    yl ++l+  l     l++++l+ +l+          +
  gi|330507565|ref|YP_004383993.1| 231 GIDvlrTHGINKITITEYLQHILFIILTvlNVLIIYYLSVVLIsggqlgihplF 284
                                       722334333444444444444443332211122222222222233433443322 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.97   2.5e+03      16      38 ..      13      37 ..       3      40 .. 0.78
   2 !   50.9   0.3   4.8e-17   1.2e-13      15     172 ..      61     228 ..      49     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.97
                   Glyco_transf_21 16 npKvnnllqalea..akydllvisD 38
                                       p +  ++++++   +++d+lv++D
  gi|330507565|ref|YP_004383993.1| 13 EPTLDSCINGIRNqtIETDILVVCD 37
                                      556667888888888999******9 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 4.8e-17
                   Glyco_transf_21  15 vnpKvnnllqalea..akydllvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdakg......laaaleaa 82 
                                       v  K  +l+qal++    ydl+++ D+d++++   Le+ ++++ + +k g V+s     d  +      l+ +l++ 
  gi|330507565|ref|YP_004383993.1|  61 VHKKSGALNQALDKylLDYDLILVQDADTIIDHRLLENAVKEINKdKKLGAVCSKAGIKDIMSskwselLWWHLQRI 137
                                       567999***********************************9976599******98888877544444444444444 PP

                   Glyco_transf_21  83 flntl.agvlqaklsglgfavGksmalrreaLeai....GGfealadeLAeDyalgkllraaGlkvvlspapiaqts 154
                                         +t+ + ++   ++ ++ + G++ ++r++aL+++    G +     ++ eDy+l+ +l++ G+k+  + ++ a+t+
  gi|330507565|ref|YP_004383993.1| 138 EYATFdSSRIET-AGSIKVVHGMAAVYRTAALQQVknkwGRIYD-ENNITEDYELTICLKELGWKTTACMDMRAWTE 212
                                       443333555555.89*****************987222255555.789***************************** PP

                   Glyco_transf_21 155 vprrsslrallaRqlrWa 172
                                       vp   +l++l+++ +rW 
  gi|330507565|ref|YP_004383993.1| 213 VPV--TLKELWKQRVRWF 228
                                       *96..9***********6 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   3.8e-09   9.6e-06     201     310 ..      78     189 ..      48     197 .. 0.83
   2 ?    1.2   8.6     0.042   1.1e+02     343     476 ..     200     326 ..     190     338 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.8e-09
                    Chitin_synth_2 201 fyeivlmvdadtkvapdsltrlvaalvkdpeilglcGetkiankkeswvtai.....qvfeyyishhlskafesvfG 272
                                        y+ +l+ dadt +    l++ v ++ kd+++ ++c ++ i +  +s ++ +     q  ey  +   s   e   G
  gi|330507565|ref|YP_004383993.1|  78 DYDLILVQDADTIIDHRLLENAVKEINKDKKLGAVCSKAGIKDIMSSKWSELlwwhlQRIEYA-TF-DSSRIE-TAG 151
                                       5999*************************************9998886665411111444442.22.233344.57* PP

                    Chitin_synth_2 273 svtclPGcfslyrikaakgadgkwvPilvspeiveeys 310
                                       s+  + G  ++yr  a ++ ++kw  i+ +++i e+y 
  gi|330507565|ref|YP_004383993.1| 152 SIKVVHGMAAVYRTAALQQVKNKWGRIYDENNITEDYE 189
                                       ************************************95 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.042
                    Chitin_synth_2 343 ktvfvpqakcktvaPdtfkvllsqrrrwinstvhnllelvlvrdlcGtfcfsmrfvvfieligtvvlPvaiaftlyl 419
                                       kt+   + +++t +P t k l  qr rw    +  l     ++++  t+   ++ ++fi l+   vl v i++ l +
  gi|330507565|ref|YP_004383993.1| 200 KTTACMDMRAWTEVPVTLKELWKQRVRWFRGGIDVL-RTHGINKI--TITEYLQHILFIILT---VLNVLIIYYLSV 270
                                       566677889*********************999765.44566666..445568999998764...777888888888 PP

                    Chitin_synth_2 420 ivasilksklvpviplvllaivlGlpailivltarkleyvawll.vyllalPifnfvl 476
                                       +++s  +  + p+  l  + +++ l+++  +  a++++ +  ++ + +l + i+ ++ 
  gi|330507565|ref|YP_004383993.1| 271 VLISGGQLGIHPLFYL--VVAIVTLDGLYRLRYAENVKTIEIVIrLAILPFSIYMMLY 326
                                       8877766555555443..4456667776666666666666543323344444444443 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.5   4.5e-07    0.0012       1      84 [.      10      91 ..      10      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.5e-07
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgf.drilvydndstDgtrailkelpevkllhvdksyederrqvellkallarya.eadwvlv 77
                                      +ne+++L +++  +++  + ++ilv+++++tD+t ++ ++l+  + l++ ++++    +  +l+++l++y  + d +lv
  gi|330507565|ref|YP_004383993.1| 10 HNEEPTLDSCINGIRNQTIeTDILVVCDNCTDKTEQLAQSLEV-NTLKTINNVH---KKSGALNQALDKYLlDYDLILV 84
                                      59**************998457***************999743.3333333332...3455777777777425699*** PP

                   Glyco_tranf_2_4 78 vDaDEfl 84
                                       DaD ++
  gi|330507565|ref|YP_004383993.1| 85 QDADTII 91
                                      ***9765 PP

>> CodY  CodY GAF-like 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      0.13     108     170 ..      51     112 ..       3     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.2e-05
                                       SEEEEEEEEETTEEEEEEEEEESSS--THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              CodY 108 glttivPiegggeRLGtlilarvdkefedddliLaeyaaTvvGleilrekaeeiEeeaRkkav 170
                                       ++ t+  i+  +++ G+l  a  dk + d dliL++ a T++   +l+   +ei ++ +  av
  gi|330507565|ref|YP_004383993.1|  51 EVNTLKTINNVHKKSGALNQAL-DKYLLDYDLILVQDADTIIDHRLLENAVKEINKDKKLGAV 112
                                       4678999999999999998776.9******************************999876666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2524.36
//
Query:       gi|330507566|ref|YP_004383994.1|  [L=84]
Description: hypothetical protein MCON_1527 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.4   0.0      0.077   13.1   0.0    1.2  1  DUF150_C  RimP C-terminal SH3 domain


Domain annotation for each model (and alignments):
>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.3e-06     0.077       4      43 ..      21      56 ..      19      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-06
                          DUF150_C  4 aedFarflGelVkvklklpvegrkkftGkivevdeetitl 43
                                      + +F+++lG++V+v+ +    +   ++G   e  +++i++
  gi|330507566|ref|YP_004383994.1| 21 EDEFTQHLGKNVTVNVC----NMTVYQGNMTEWWNDSIVI 56
                                      678************99....9999999999999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 548.44
//
Query:       gi|330507567|ref|YP_004383995.1|  [L=337]
Description: rhodanese domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-23   81.2   0.0    3.8e-10   40.3   0.0    2.3  2  Rhodanese    Rhodanese-like domain
     0.0089   16.3   0.7      0.017   15.4   0.7    1.4  1  Uteroglobin  Uteroglobin family
  ------ inclusion threshold ------
       0.11   12.9   0.6       0.29   11.5   0.6    1.7  1  EAV_GP5      Envelope glycoprotein GP 5 of equine arteritis v
       0.17   11.9   0.0       0.49   10.4   0.0    1.7  1  DUF3895      Protein of unknown function (DUF3895)


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   8.4e-14   3.8e-10      20     106 ..     107     198 ..      90     199 .. 0.80
   2 !   38.6   0.0   2.8e-13   1.3e-09      10      95 ..     231     314 ..     222     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 8.4e-14
                         Rhodanese  20 RppeeYekghIpgAvnvskdtlsrakkseapllelpeellel.......gidnkktvvvy.....cdgggraaaa.. 82 
                                       ++   Y  + IpgAv++     s+ ++++ +  ++++ +++        gi++ +++vvy     c gg + +a+  
  gi|330507567|ref|YP_004383995.1| 107 SD---YPGSFIPGAVHI-----SYREFVDINNTACLKNISDIarilgdaGISRTDPLVVYgecqpCGGGPS-TATyv 174
                                       44...77899*******.....99999999999999999999999999************44333334444.33345 PP

                         Rhodanese  83 aallkklGyknvsvldGGfkawke 106
                                       ++ll+++G+++++vl+GG++aw e
  gi|330507567|ref|YP_004383995.1| 175 YWLLRYMGHEDIRVLNGGIDAWME 198
                                       88999***666***********87 PP

  == domain 2  score: 38.6 bits;  conditional E-value: 2.8e-13
                         Rhodanese  10 ekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel..gidnkktvvvycdgggraaaaaa 84 
                                       ++gk++++D+R+ ee+e+g Ipg++n+     ++ +  +++      el+    +++++k+vvv+  +g +a+  + 
  gi|330507567|ref|YP_004383995.1| 231 KSGKAQIVDARSVEEFERGTIPGSINI-----PYDEALDGKIIRAESELEGIfsNLTKNKPVVVFTTTGTKASVIWF 302
                                       456777*********************.....444444445555555555559999*************99555588 PP

                         Rhodanese  85 llkklGykn.vs 95 
                                        l  lGy   ++
  gi|330507567|ref|YP_004383995.1| 303 SLDMLGYDAkMY 314
                                       888888744355 PP

>> Uteroglobin  Uteroglobin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.7   3.8e-06     0.017       5      37 ..      15      49 ..      12      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-06
                                      XXXXXXXXXXXXXXXX..X---HHHHHHHHHHHHS CS
                       Uteroglobin  5 vvllLvalaLccyags..aegCpaleevvekfleg 37
                                       +++L+++aL+c+++s  + +C +l++  ++++++
  gi|330507567|ref|YP_004383995.1| 15 PAIMLLTVALFCSSASaeCYVCTFLDSLAKETITS 49
                                      4679********99664479**********99954 PP

>> EAV_GP5  Envelope glycoprotein GP 5 of equine arteritis virus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6   6.5e-05      0.29      52      71 ..      22      41 ..      19      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.5e-05
                           EAV_GP5 52 talyncsasktcwyctflde 71
                                       al+  sas  c+ ctfld 
  gi|330507567|ref|YP_004383995.1| 22 VALFCSSASAECYVCTFLDS 41
                                      589999************96 PP

>> DUF3895  Protein of unknown function (DUF3895)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00011      0.49      49      69 ..      35      55 ..      30      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                           DUF3895 49 vCvvLdqlakegvielvkkdg 69
                                      vC +Ld lake +  ++++d 
  gi|330507567|ref|YP_004383995.1| 35 VCTFLDSLAKETITSILSSDS 55
                                      9**************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2659.76
//
Query:       gi|330507568|ref|YP_004383996.1|  [L=465]
Description: carbohydrate kinase, YjeF-like protein [Methanosaeta concilii GP6]
Scores for complete 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-47  161.1   0.8    1.5e-46  158.9   0.8    2.2  3  Carb_kinase  Carbohydrate kinase
    5.7e-42  143.5   0.2    1.2e-40  139.2   0.0    2.2  2  YjeF_N       YjeF-related protein N-terminus
    0.00012   21.5   0.0    0.00019   20.9   0.0    1.2  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 ?   -2.8   0.0      0.59   3.5e+03     147     168 ..      63      84 ..      47      89 .. 0.71
   2 ?   -2.7   0.0      0.56   3.4e+03      57      85 ..     138     167 ..     130     180 .. 0.72
   3 !  158.9   0.8   2.5e-50   1.5e-46       2     243 ..     223     460 ..     222     461 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.59
                                       HHHHHHHHTTEEEEESTTSEEE CS
                       Carb_kinase 147 arelaqklnavvllkgekdviv 168
                                       a++    +na+v+l g +  i 
  gi|330507568|ref|YP_004383996.1|  63 AARHLSGYNATVYLLGRSRDIS 84 
                                       4445567999999999887665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.56
                                       TTS....--SSS-SEEEE-TT-SSSHCHHH CS
                       Carb_kinase  57 eqa.kileklerldavviGpGLgrdekikk 85 
                                       e    i+ + +++  v i +GLg+++++ +
  gi|330507568|ref|YP_004383996.1| 138 EAIdAINRSGKKVLSVDIPSGLGTNKAVRA 167
                                       444468888888888999999999998654 PP

  == domain 3  score: 158.9 bits;  conditional E-value: 2.5e-50
                                       EEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT....HTTTS....--SSS-SEEEE CS
                       Carb_kinase   2 lvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll....edeqa.kileklerldavvi 73 
                                       lvigG   ytGA+ l+alaalr+ga++v+va+   a++ +   +p++iv +l+    ++++     ++  + d+vv+
  gi|330507568|ref|YP_004383996.1| 223 LVIGG-GPYTGAPALTALAALRAGADIVTVAAPARAAKTISCFSPNLIVRELSedhlSANDLqPLQDLIAAHDVVVM 298
                                       78999.9**********************************************77764444433455567789**** PP

                                       -TT-SSSHCHHHHCHHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCH..HCCSHHHHHH CS
                       Carb_kinase  74 GpGLgrdekikklleevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivk..keddrlelar 148
                                       G+GLgr++ +  ++  +    e +viDAd+L         +    +   TPh++Ef+r+++ +++    ++r el+r
  gi|330507568|ref|YP_004383996.1| 299 GMGLGRHPDTRDAIASIIPLAEKVVIDADALL--------PGLPLKGLVTPHAGEFQRISGISLIdlDYKERTELVR 367
                                       ******************************97........445557889************9998778999****** PP

                                       HHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHH CS
                       Carb_kinase 149 elaqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdea 225
                                         a + ++++llkg++d+i + ++ v +n tg++++++GG+GDvLaG+ +a+ a +  ++ aa aaa+++g+a+d++
  gi|330507568|ref|YP_004383996.1| 368 GYAWERGVTILLKGKVDLITD-GEIVRANTTGNPGMTVGGTGDVLAGIAAAFYARAS-ALRAASAAAFVNGRAGDLV 442
                                       *******************99.9999*********************9999988877.9999*************** PP

                                       CCCT-TS-HCHHHHHHHC CS
                       Carb_kinase 226 aekkgvgmlatelskiip 243
                                         +kg gmlat++ + ip
  gi|330507568|ref|YP_004383996.1| 443 YLEKGFGMLATDVVEMIP 460
                                       **************9998 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.0     2e-44   1.2e-40       3     170 ..      25     178 ..      23     179 .. 0.91
   2 ?    2.3   0.0     0.023   1.4e+02      27      88 ..     220     280 ..     205     325 .. 0.60

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 2e-44
                            YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtv.llleeeekldedaeralell 78 
                                       +Lmenag+a+a+ + a +    ++k+v +++G+gnnGgd+++aArhL   g+++tv ll ++++  +e+a+r++e+l
  gi|330507568|ref|YP_004383996.1|  25 QLMENAGAAIAREVVASS----PGKRVAIVAGRGNNGGDAFVAARHL--SGYNATVyLLGRSRDISTEEARRNWEIL 95 
                                       8***********999998....9************************..5666666446778889************ PP

                            YjeF_N  79 kkaggkvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgt 155
                                       ++++ ++ e k++edl   +  ++dl++DA++G+g+rg +++  ae+i+ +n+s+++vl+vDiPSGl    G  +  
  gi|330507568|ref|YP_004383996.1|  96 ERLHLDLREIKDAEDL---MLDECDLIVDAIFGTGVRGRVSGLEAEAIDAINRSGKKVLSVDIPSGL----GTNK-- 163
                                       ********99999887...5578********************************************....5556.. PP

                            YjeF_N 156 avkadvtvtfgapkr 170
                                       av+ad++vtf+ pk+
  gi|330507568|ref|YP_004383996.1| 164 AVRADYVVTFHRPKP 178
                                       99***********97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.023
                            YjeF_N  27 kkvlvlvGsgnnGgdglaaArhLaqegak.Vtvllleeeekldedaeralellkkaggkvvee 88 
                                        ++lv+ G+  +G+ +l a + L ++ga+ Vtv     ++  +  +     +++++ ++ ++ 
  gi|330507568|ref|YP_004383996.1| 220 GRILVIGGGPYTGAPALTALAAL-RAGADiVTV-AAPARAAKTISCFSPNLIVRELSEDHLSA 280
                                       46777777779************.777774666.44344444444444444444454444444 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   3.2e-08   0.00019     141     219 ..     363     439 ..     341     461 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.2e-08
                                       HHHHHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHH CS
                                HK 141 vaavqkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykv 217
                                        + v+  A +++v++++ G+vD+++dg+ v   + G++ ++ + ++G +l+ + aaf a  ++ l aa +a  +   
  gi|330507568|ref|YP_004383996.1| 363 TELVRGYAWERGVTILLKGKVDLITDGEIVRANTTGNPGMT-VGGTGDVLAGIAAAFYARASA-LRAASAAAFVNGR 437
                                       67888999********************************7.9**************997654.4444444444445 PP

                                       HH CS
                                HK 218 Ag 219
                                       Ag
  gi|330507568|ref|YP_004383996.1| 438 AG 439
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3155.35
//
Query:       gi|330507569|ref|YP_004383997.1|  [L=142]
Description: molybdenum cofactor biosynthesis protein C [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-47  161.4   0.3    1.4e-47  161.2   0.3    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 !  161.2   0.3   7.6e-52   1.4e-47       1     136 []       1     141 [.       1     141 [. 0.98

  Alignments for each domain:
  == domain 1  score: 161.2 bits;  conditional E-value: 7.6e-52
                                       E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEE CS
                              MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkvevelele 77 
                                       mvd+++k+ + r+A+A+g+++l+e+tl++i+ +++kkGd la+ar+a+i+a+K+t++liplcHp+p+t   v lele
  gi|330507569|ref|YP_004383997.1|   1 MVDITSKSLVYRKATATGSIRLKESTLQAIRCGEIKKGDPLATARLAAILAVKETPRLIPLCHPIPITGLVVGLELE 77 
                                       9***********************************************************************99887 PP

                                       TTTTEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEESS CS
                              MoaC  78 eeeesveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKsgG 136
                                           +++ ++tv+  g+tGvemEALt+vsva+l+++DmvK ++k+       ++iee+r++eK +G
  gi|330507569|ref|YP_004383997.1|  78 --VMRIRATVTVTSVGRTGVEMEALTGVSVALLNIWDMVKYLEKDetgnypeTEIEEIRVLEKVKG 141
                                       ..799***************************************99*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1038.09
//
Query:       gi|330507570|ref|YP_004383998.1|  [L=114]
Description: hypothetical protein MCON_1532, partial [Methanosaeta concilii GP6]
Scores for complete 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   91.5   0.1    7.1e-26   91.4   0.1    1.0  1  SOUL       SOUL heme-binding protein
  ------ inclusion threshold ------
       0.01   16.1   0.0      0.014   15.7   0.0    1.2  1  GyrI-like  GyrI-like small molecule binding domain


Domain annotation for each model (and alignments):
>> SOUL  SOUL heme-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.1   7.9e-30   7.1e-26      62     167 ..       1     104 [.       1     105 [. 0.92

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 7.9e-30
                              SOUL  62 mtaPvvtkvkekevtmsfvlpskyqaeepPkPtddsrVkleevpertvavrrFsGfateeevkeeaeeLreaLekdg 138
                                       mtaPvvt+ +ek  +m+f++p++++ +++P+P ++s+V+++ v++rt+a++rFsG+++e +++++ e+L ++L+++g
  gi|330507570|ref|YP_004383998.1|   1 MTAPVVTTSTEKGLSMAFIMPERFDIQTIPRP-TSSNVEIRVVEPRTLATIRFSGYMNEGSYRDNLERLNKTLKERG 76 
                                       9*****98999**************99*****.666*******************99****************8788 PP

                              SOUL 139 ..geekkdsyvlaqYnppftppflrrNEvwi 167
                                          + ++    l+qYn+p tppf rrNE+++
  gi|330507570|ref|YP_004383998.1|  77 ilTKGEP---LLMQYNEPRTPPFYRRNEIAL 104
                                       7634346...*******************85 PP

>> GyrI-like  GyrI-like small molecule binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.0   1.6e-06     0.014       2      67 ..      36      98 ..      35     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-06
                                      CEEEEEE--EEEEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHCTT--SSEEEEEEEEE-STTCCCE CS
                         GyrI-like  2 eveivelpafrvvgirhrgdyneeggipklweelyawaseiklsnavspligvssdepeetedeel 67
                                      +vei+ +++++++ ir  g +ne+  + +  e+l++ ++e+++  +++pl+  + +ep  t++ + 
  gi|330507570|ref|YP_004383998.1| 36 NVEIRVVEPRTLATIRFSGYMNEGS-YRDNLERLNKTLKERGILTKGEPLLMQY-NEP-RTPPFYR 98
                                      699********************66.*****************96666655433.334.4555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.58
# Mc/sec: 596.27
//
Query:       gi|330507571|ref|YP_004383999.1|  [L=77]
Description: hypothetical protein MCON_1533 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 601.47
//
Query:       gi|330507572|ref|YP_004384000.1|  [L=119]
Description: death-on-curing family protein [Methanosaeta concilii GP6]
Scores for complete 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   30.4   0.2    0.00012   22.9   0.3    2.4  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 !   22.9   0.3   6.8e-09   0.00012      50      97 .]      33      77 ..       3      77 .. 0.72
   2 ?   -3.2   0.0      0.94   1.7e+04      37      54 ..      93     110 ..      83     116 .. 0.55

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.8e-09
                                      HHHHHHHCHHT-S-HHHHHHHHHHHHHHH--SSS-HHHHHHHHHHHHH CS
                               Fic 50 eelleylnelekeeplekaaalhyefekiHPFaDGNgRtarlllnllL 97
                                      + l++ +n  ++ + ++kaa +  +++++HPF+DG + t++ l++ +L
  gi|330507572|ref|YP_004384000.1| 33 DYLVSMIN--DEPDHFKKAALA-LHLIALHPFNDGQKKTGFQLADNIL 77
                                      44455666..555577777765.55889*************9999876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.94
                                       E---SCCCHHHHHHHHHH CS
                               Fic  37 salappeevpaeleelle 54 
                                        +l++ +e +  l+e+++
  gi|330507572|ref|YP_004384000.1|  93 GVLCKIAEYNCMLDEIER 110
                                       445555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 961.71
//
Query:       gi|330507573|ref|YP_004384001.1|  [L=111]
Description: hypothetical protein MCON_1536 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 819.01
//
Query:       gi|330507574|ref|YP_004384002.1|  [L=70]
Description: hypothetical protein MCON_1538 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.034   14.6   1.1      0.053   14.0   1.1    1.3  1  DUF104          Protein of unknown function DUF104
      0.043   13.8   0.0       0.09   12.7   0.0    1.6  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.1     6e-06     0.053      17      59 .]      18      67 ..      17      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6e-06
                            DUF104 17 LekvdLkEGeevkikIee.......akeilkklkgilkeadeeeleelle 59
                                      L +++L EG++v ++++        +k+++++l g +k  d++ +ee++e
  gi|330507574|ref|YP_004384002.1| 18 LSEINLCEGKRVALSVKGgellikpIKSLTDQLIGSIKLDDQKLIEEIIE 67
                                      6799*************999*99999999999999999889999999986 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     1e-05      0.09      11      44 ..      13      46 ..       9      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
                                      E-CCCHHHCCEECTCEEEEEECTTCCCCCCCHHS CS
                    MazE_antitoxin 11 iPkevrfelgireGdevelevdgdkiilrplksl 44
                                      +P  +  e ++ eG +v l+v+g+ ++++p+ksl
  gi|330507574|ref|YP_004384002.1| 13 LPSSILSEINLCEGKRVALSVKGGELLIKPIKSL 46
                                      899999999**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 539.46
//
Query:       gi|330507575|ref|YP_004384003.1|  [L=168]
Description: PIN domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-15   55.9   2.0    2.4e-14   53.9   2.0    1.8  1  PIN       PIN domain
    3.5e-05   24.4   0.2    7.3e-05   23.3   0.2    1.6  1  PIN_12    PIN domain
  ------ inclusion threshold ------
       0.15   12.9   0.0       0.16   12.8   0.0    1.2  1  PIN_3     PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   2.0     4e-18   2.4e-14       1     117 [.      14     158 ..      14     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 4e-18
                                       EEE-HHHHHHHH.TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS.....................SCHC CS
                               PIN   1 ivlDTsvliall.rgeekaeaarklleel....eelvtsalvlaEllyvlar.....................rksk 51 
                                       i++DT+++++   +  + ++++r+ l+++    +  +tsalvl E++++l                       ++++
  gi|330507575|ref|YP_004384003.1|  14 IFIDTNIFLYGAlDYTKYRATCRAFLQNIesgtYFAATSALVLNEIIHKLILaettktyhlrsesearkliedKSET 90 
                                       79********9998888888888888888888***********************************9996664444 PP

                                       HHHHHHHHHHHHH..HHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHH CS
                               PIN  52 rekaaelvellll..lsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfr 117
                                       +  +a++ +++    +  l i +id++  ++a +++++ygl + Da ++A++k +gi+ iat+D+df 
  gi|330507575|ref|YP_004384003.1|  91 ISSLARVWKTYAVirAYPLVIHSIDKATMDMATDLSSRYGLFISDASHLAVMKMNGISNIATNDNDFQ 158
                                       44444443333331144455555*******************************************97 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.2   1.2e-08   7.3e-05       1      57 [.      14      76 ..      14     126 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.2e-08
                            PIN_12  1 ifiDTnifld..effrlseeealkklleliesgkiklivpdivldEflknr.ekkiees....k 57
                                      ifiDTnifl     + +   + ++++l++iesg+   +++++vl+E+++++   +  ++    +
  gi|330507575|ref|YP_004384003.1| 14 IFIDTNIFLYgaLDYTKYR-ATCRAFLQNIESGTYFAATSALVLNEIIHKLiLAETTKTyhlrS 76
                                      9********6334455444.59**************************9996666665533220 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.6e-05      0.16       2      74 ..      14      89 ..      13     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                             PIN_3  2 vvlDtnvlldallfdsp...aarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakvale 74
                                      +++Dtn++l + l   +     r+ l+ +e+g++ + +s+ +l+E+   l   ++ +   lr++  a +l+++ +e
  gi|330507575|ref|YP_004384003.1| 14 IFIDTNIFLYGALDYTKyraTCRAFLQNIESGTYFAATSALVLNEIIHKLILAETTKTYHLRSESEARKLIEDKSE 89
                                      79*******99994444444555555555******************98844444444444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1324.94
//
Query:       gi|330507576|ref|YP_004384004.1|  [L=86]
Description: hypothetical protein MCON_1540 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.21s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 726.81
//
Query:       gi|330507577|ref|YP_004384005.1|  [L=534]
Description: CTP synthase [Methanosaeta concilii GP6]
Scores for complete 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-123  410.5   0.7   3.7e-123  410.0   0.7    1.2  1  CTP_synth_N    CTP synthase N-terminus
    1.3e-56  191.4   0.0    2.7e-56  190.4   0.0    1.5  1  GATase         Glutamine amidotransferase class-I
    3.7e-07   30.1   0.0    3.3e-05   23.7   0.0    2.8  2  Peptidase_C26  Peptidase C26
    0.00023   21.2   0.0     0.0006   19.9   0.0    1.5  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
       0.05   12.8   0.0       0.58    9.3   0.0    2.4  2  ArsA_ATPase    Anion-transporting ATPase
       0.11   12.4   0.0        0.2   11.6   0.0    1.5  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 !  410.0   0.7  1.2e-126  3.7e-123       1     265 []       2     264 ..       2     264 .. 0.99

  Alignments for each domain:
  == domain 1  score: 410.0 bits;  conditional E-value: 1.2e-126
                                       EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHH CS
                       CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfl 77 
                                       +yi+vtGGv+SglGkGi+aas+g+ll +rg+kvt+ikiDPY+n+dag +sp++hGEv+vl+dG+e+DlDlGnYeRfl
  gi|330507577|ref|YP_004384005.1|   2 RYIVVTGGVMSGLGKGITAASIGRLLMNRGYKVTAIKIDPYINIDAGLMSPFQHGEVYVLKDGGEVDLDLGNYERFL 78 
                                       7**************************************************************************** PP

                                       T----GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHH CS
                       CTP_synth_N  78 dikltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfle 154
                                       d++lt+++nittGk+y++viekerrG+ylGktvq+iph+t+eik+ri++v++    ++++ve+gGtvgdies+pfle
  gi|330507577|ref|YP_004384005.1|  79 DVELTRDHNITTGKVYSTVIEKERRGEYLGKTVQIIPHITEEIKKRIRQVSRDGGCEICLVEVGGTVGDIESMPFLE 155
                                       ***************************************************9989********************** PP

                                       HHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--G CS
                       CTP_synth_N 155 airqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvek 231
                                       a+rqlk+e  + n++++hvtl p   + ge+ktkptqhsvk +r+lG+qpd+iv+r+e++l  e+k+kia+fc+v+ 
  gi|330507577|ref|YP_004384005.1| 156 AMRQLKYEE-SGNIFFVHVTLAPST-TDGEQKTKPTQHSVKVMRELGLQPDMIVVRCENPLLPETKHKIAQFCDVPA 230
                                       ******996.89***********99.69************************************************* PP

                                       GGEEEEE--S-GGGHHHHHHHCTHHHHHHHHTT- CS
                       CTP_synth_N 232 eavisvkdvesiyevpllleeqglaelileklkl 265
                                       eavis+++ ++iy+vpl +e +g+a++i+++++l
  gi|330507577|ref|YP_004384005.1| 231 EAVISAHNSDDIYKVPLQMEAEGIAKYIMKEMRL 264
                                       ******************************9976 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.4   0.0     9e-60   2.7e-56       3     189 ..     306     526 ..     305     527 .. 0.94

  Alignments for each domain:
  == domain 1  score: 190.4 bits;  conditional E-value: 9e-60
                                       EESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH...THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEE CS
                            GATase   3 iDnydsvtenlvhalvelgvkvevvpidasaeeile...llknpdgilvsgGpgspgvegkieaikearenkiPiLG 76 
                                        D+y s+ e+l+ha++e+gv+ e+v+ida+++e  +   +l ++dgilv+gG+gs+g+egki+a+++are k+P+LG
  gi|330507577|ref|YP_004384005.1| 306 EDAYLSIRESLKHAGIEAGVRPEIVWIDAEDLEHGSsdlILREADGILVPGGFGSRGTEGKIKAVQYAREMKVPYLG 382
                                       69*******************************96676569************************************ PP

                                       ETHHHHHHHHHTTTEEE......................EEECEEEEEEEEEEEETTT........CGGTTTTSEEE CS
                            GATase  77 ICLGmQllaiefgrkvv......................kekekehhggtmrlgddet........allyglknevi 123
                                       IC+GmQl++ie++r+v                       ++++  ++g+tmrlg++++        +++yg+   + 
  gi|330507577|ref|YP_004384005.1| 383 ICFGMQLAVIEYARNVCgleeagstefgetphpviailpEQEKIRQMGATMRLGNYPAhllegslaHQIYGK-TNIV 458
                                       **************999999999999999999999****77779***************************9.99** PP

                                       EEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHH CS
                            GATase 124 erhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflik 189
                                       erhrHryevnp+    +e++g+++++++     lmei e ++ p f+g QFHPE++s+p++p+++f  +++
  gi|330507577|ref|YP_004384005.1| 459 ERHRHRYEVNPAyikPIEEKGMIFSGRNG---DLMEICEIPEhPfFFGSQFHPEMKSRPGKPSPPFLAFVE 526
                                       ***********999999*********993...4888888888888**********************9997 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.022        65      20      67 ..     307     357 ..     289     364 .. 0.72
   2 !   23.7   0.0   1.1e-08   3.3e-05      96     216 .]     368     509 ..     360     509 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.022
                     Peptidase_C26  20 aeesylaasyveavekagglpvllpiee...deedvkaildkldgllltGg 67 
                                        ++  +++s  +a  +ag++p +++i++   ++ + + il + dg+l++Gg
  gi|330507577|ref|YP_004384005.1| 307 DAYLSIRESLKHAGIEAGVRPEIVWIDAedlEHGSSDLILREADGILVPGG 357
                                       44455667777778899********99732234456789***********9 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 1.1e-08
                     Peptidase_C26  96 aLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe..............q.....saashavkv 153
                                       + ++ a e +vP lgiC G+ql  + +  ++   +ee  g t++ e+               q        +   ++
  gi|330507577|ref|YP_004384005.1| 368 KAVQYAREMKVPYLGICFGMQLAVIEYARNVCG-LEE-AGSTEFGETPhpviailpeqekirQmgatmRLGNYPAHL 442
                                       557788999*************98877766554.443.455556555555677777655444133334444555666 PP

                     Peptidase_C26 154 ekgsllaellgseeievnslHhqaike.....laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                        +gsl ++++g+++i     H+  ++      ++e+  + +  + +++E  e++e++ f++g Q+HPE
  gi|330507577|ref|YP_004384005.1| 443 LEGSLAHQIYGKTNIVERHRHRYEVNPayikpIEEKGMIFSGRNGDLMEICEIPEHP-FFFGSQFHPE 509
                                       6**********99999999999998877777799999999999999*********88.*********9 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     2e-07    0.0006       6      43 ..      10      47 ..       4     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2e-07
                                      SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannla 43
                                        +G GK  +aa+++r+l +rg++V +++ Dp  n +a
  gi|330507577|ref|YP_004384005.1| 10 VMSGLGKGITAASIGRLLMNRGYKVTAIKIDPYINIDA 47
                                      479*****************************988776 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00019      0.58       1     108 [.       1     118 [.       1     129 [. 0.71
   2 ?    0.8   0.0     0.074   2.2e+02     222     258 ..     188     227 ..     147     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00019
                                       -EEEEEEE..STTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HH..... CS
                       ArsA_ATPase   1 lkvilvgG..KGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpe..... 70 
                                       +++i+v+G    G GK   +a+++  l + g+kv  i  DP  ++   +   +++ +  v +    v++d       
  gi|330507577|ref|YP_004384005.1|   1 MRYIVVTGgvMSGLGKGITAASIGRLLMNRGYKVTAIKIDPYINIDAGLMSPFQHGEVYVLKDGGEVDLDLGnyerf 77 
                                       789999883447********************************999888888888888876544444444356666 PP

                                       ..HHHHHHHC.CHHGGGSCCHHHHHHHHHHHHHHTSSTTHH CS
                       ArsA_ATPase  71 ..veleeakq.evqkeeeallgleeledvlaeelaslPGid 108
                                         vel + ++  + k + ++++ e   + l ++++++P i 
  gi|330507577|ref|YP_004384005.1|  78 ldVELTRDHNiTTGKVYSTVIEKERRGEYLGKTVQIIPHIT 118
                                       55444444331333444555565666666666666666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.074
                                       HHHHHHHHHHHTT-EEEEEEE...EEE-TTCSSSTSHHHH CS
                       ArsA_ATPase 222 EteRaikeLkkygikvdaviv...NkllpeeeqenCefle 258
                                        t+ ++k + ++g++ d+++v   N llpe++++  +f++
  gi|330507577|ref|YP_004384005.1| 188 PTQHSVKVMRELGLQPDMIVVrceNPLLPETKHKIAQFCD 227
                                       5788899999999******99777779***9998777775 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.6e-05       0.2      12      47 ..      13      48 ..       2     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.6e-05
                            AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanattg 47
                                      G GK  t+  ++  l+++g+kv  + +Dp  n   g
  gi|330507577|ref|YP_004384005.1| 13 GLGKGITAASIGRLLMNRGYKVTAIKIDPYINIDAG 48
                                      88***************************9998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); 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:                         6  (0.000334653); expected 0.2 (1e-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 0.28s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 3837.60
//
Query:       gi|330507578|ref|YP_004384006.1|  [L=425]
Description: hypothetical protein MCON_1544 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3139.53
//
Query:       gi|330507579|ref|YP_004384007.1|  [L=60]
Description: hypothetical protein MCON_1545 [Methanosaeta concilii GP6]
Scores for complete 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-12   45.9   2.2    1.1e-11   45.1   2.2    1.4  1  Trm112p         Trm112p-like protein
  ------ inclusion threshold ------
      0.064   13.3   0.1      0.066   13.3   0.1    1.1  1  Elf1            Transcription elongation factor Elf1 like
       0.07   13.4   0.7       0.13   12.5   0.7    1.5  1  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase


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 !   45.1   2.2   1.8e-15   1.1e-11       1      68 []       2      49 ..       2      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.8e-15
                                      BTGGCCC-B-TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEEEEEETT CS
                           Trm112p  1 kllllniLaCpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgraYpIkdG 68
                                      k++ll+iLaCp+ckg L +e++ e++                     +i+ g+L C++c+ +YpI+dG
  gi|330507579|ref|YP_004384007.1|  2 KRDLLDILACPMCKGDLILEVFEENES--------------------EILAGKLCCRACNEIYPIEDG 49
                                      789**************6666666664....................9*******************9 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.1e-05     0.066      18      56 ..       5      45 ..       1      54 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                              Elf1 18 lptkFdCpfCnheksvevkldkkek..iaevsCkvCgesfe 56
                                      l     Cp+C+ +  +ev  +++++   +++ C+ C+e + 
  gi|330507579|ref|YP_004384007.1|  5 LLDILACPMCKGDLILEVFEENESEilAGKLCCRACNEIYP 45
                                      667789*******777776666666889********99775 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 ?   12.5   0.7   2.3e-05      0.13       5      32 ..      10      41 ..       9      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                                      --TTTT-TTTEE.ETT.......S-EEETTTT CS
                    Prim_Zn_Ribbon  5 pCPvCGGrDrFr.fddkdgr...GtwfCrqCg 32
                                      +CP+C+G      f++++     G   Cr C+
  gi|330507579|ref|YP_004384007.1| 10 ACPMCKGDLILEvFEENESEilaGKLCCRACN 41
                                      7***************99999*9********4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.28s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 445.95
//
Query:       gi|330507580|ref|YP_004384008.1|  [L=263]
Description: amidohydrolase 2 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-26   93.6   0.1    3.1e-26   92.8   0.1    1.3  1  Amidohydro_2  Amidohydrolase
  ------ inclusion threshold ------
       0.17   11.2   0.0        3.4    7.0   0.0    2.1  2  TatD_DNase    TatD related DNase


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.1   3.5e-30   3.1e-26       1     285 [.       3     258 ..       3     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 3.5e-30
                                       EEEEEEE..SHHHCCCCCCGGCTSCCCHHHHHCHHTSSECCC.EHCHHHHHHHHTSHHCHHHHHHHHHHHHHHHHHH CS
                      Amidohydro_2   1 iDvHaHllppeaairddgepngfdpeerlafmkragvdpqla.speallvlnaaagiaravivaalcrgannrvlae 76 
                                       iD HaH++pp              +    a+ ++  v ++    p++ll  ++ +giar v +     +++ + l +
  gi|330507580|ref|YP_004384008.1|   3 IDFHAHIYPPP-----------VAAKILPAARRKLKVEVPGSgAPQDLLGHMSRSGIARSVLLPLAKGREDVSSLND 68 
                                       89****98755...........3344444444444444333314667777788888888877777776666666666 PP

                                       HHH..HCTTCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGHHHHHHHHHHHT-EEEEE... CS
                      Amidohydro_2  77 aak..rpdrfvggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrldrpifealeelglpvdihtGp 151
                                       ++    + ++++++a+ p + e+  ael r +   g++Gv++ p  ++ +++++  + +++eal ++   +  htG 
  gi|330507580|ref|YP_004384008.1|  69 WILsvSDEGLIPFGAIHP-FMENLEAELDRLA-GCGVRGVKIMPLLQEFYPDDQCCE-RLYEALIKREMMLVTHTG- 141
                                       664223567777776666.*************.************************.****************99. PP

                                       .CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHH CS
                      Amidohydro_2 152 spewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrpnvyvklsglytellyfdspla 228
                                            +  ++e +    p+ +++v++ +P+lk+ laH+Gg+  + +  ++ll  + n y+++           s + 
  gi|330507580|ref|YP_004384008.1| 142 ---RDPLEREEVF--GTPERFARVVQCYPELKLLLAHLGGMRMWDESRRHLLPAGGNAYFDTAY--------VSFYL 205
                                       ...5555555555..78899999******************66666777788999999999966........7999* PP

                                       CHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHH CS
                      Amidohydro_2 229 dppalarlieavgpdrilfGsDyPhptleaepealalldlvallsdeerekilggNA 285
                                       d + +a li+ +g+dr++fGsDyP+  +++ +e ++ ldl    s+ e+e+il++NA
  gi|330507580|ref|YP_004384008.1| 206 DEKNMADLIQDIGADRVIFGSDYPWEIPGRAVEIIQRLDL----SEGEKEAILWKNA 258
                                       ***************************************9....************9 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.01        91       1     101 [.       3     147 ..       3     168 .. 0.56
   2 ?    7.0   0.0   0.00038       3.4     171     211 ..     193     233 ..     180     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.01
                                       EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEE..........EE-SSG.................GGHH.HHHHHHT CS
                        TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavv..........vvgtss.................kdsk.avlelak 49 
                                       iD H+H+  + +   +++il +a+++    v                +                 +d +    ++ +
  gi|330507580|ref|YP_004384008.1|   3 IDFHAHIYPPPV---AAKILPAARRKLKVEVPgsgapqdllgH----MsrsgiarsvllplakgrEDVSsLNDWILS 72 
                                       677777777554...4444433332222222222222222220....022223333333333344222213333444 PP

                                       T.TTTEEEEE---G...GGGGC.........................C.CCHHHHHHHHHHCCCTSEEEEEEEEEET CS
                        TatD_DNase  50 kypnkvyavlGiHP...nevde.........................asedlleelkelanvkhskvvaiGeiGLDy 98 
                                        +++ +++   iHP   n                             ++++ +e l e+  + + +++++  +G+D 
  gi|330507580|ref|YP_004384008.1|  73 VSDEGLIPFGAIHPfmeN---LeaeldrlagcgvrgvkimpllqefyPDDQCCERLYEA--LIKREMMLVTHTGRDP 144
                                       456668899999995530...23455669999999999998888887777888888888..8888888999999997 PP

                                       -CC CS
                        TatD_DNase  99 ysr 101
                                         r
  gi|330507580|ref|YP_004384008.1| 145 LER 147
                                       433 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00038
                                       TEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEE CS
                        TatD_DNase 171 gyyislsglltfknakelrelvkavpldrlLiETDaPyltp 211
                                       ++y+  + ++++ ++k++ +l++ +  dr++ ++D+P+  p
  gi|330507580|ref|YP_004384008.1| 193 NAYFDTAYVSFYLDEKNMADLIQDIGADRVIFGSDYPWEIP 233
                                       566777778889999***********************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1998.62
//
Query:       gi|330507581|ref|YP_004384009.1|  [L=375]
Description: DNA topoisomerase VI subunit A [Methanosaeta concilii GP6]
Scores for 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   57.8   0.1    1.6e-15   56.8   0.1    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 !   56.8   0.1   8.8e-20   1.6e-15       3      62 .]      84     148 ..      82     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 8.8e-20
                                       HHHHHHHHHHH.HHHHHTT--EEHHHHHHH....GGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
                            TP6A_N   3 faqllkvleli.helleegkvvTkRdiYYr....dvelFksQaesdrliddievllgvsReeLnv 62 
                                       + +++++ el+  e+l++++ +T+R+iYY     d ++F++Qaesdrli+d+e ++++ Re+++v
  gi|330507581|ref|YP_004384009.1|  84 ILKTVHLTELLiDEHLKNNRGSTLREIYYIsenwDIAKFHEQAESDRLIEDLEIVTDLHREDFHV 148
                                       56777777765499****************99999*****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2812.30
//
Query:       gi|330507582|ref|YP_004384010.1|  [L=611]
Description: DNA topoisomerase VI subunit B [Methanosaeta concilii GP6]
Scores for complete 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-63  212.1   0.0    5.9e-63  211.4   0.0    1.3  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    5.2e-37  126.5   0.0    1.3e-36  125.2   0.0    1.7  2  Top6b_C         Type 2 DNA topoisomerase 6 subunit B C-termin
    2.4e-11   44.1   0.0    7.8e-11   42.5   0.0    1.9  2  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    7.2e-07   29.1   0.0    1.5e-06   28.1   0.0    1.5  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
     0.0019   17.0   0.5     0.0035   16.2   0.0    1.6  2  FbpA            Fibronectin-binding protein A N-terminus (Fbp
  ------ inclusion threshold ------
       0.03   14.3   0.0      0.093   12.7   0.0    1.8  2  HATPase_c_2     Histidine kinase-like ATPase domain
       0.17   11.6   0.0       0.31   10.7   0.0    1.4  1  MAF_flag10      Protein of unknown function DUF115


Domain annotation for each model (and alignments):
>> Topo-VIb_trans  Topoisomerase VI B subunit, transducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.4   0.0   2.3e-66   5.9e-63       1     159 []     309     473 ..     309     473 .. 0.98

  Alignments for each domain:
  == domain 1  score: 211.4 bits;  conditional E-value: 2.3e-66
                    Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydega 77 
                                       P+ dclspigeeli++gl+ke++ +f+a++tr+++vy+g+pf+vEvg++yGGel +e ++eilRfaNrvPL+y++ga
  gi|330507582|ref|YP_004384010.1| 309 PPVDCLSPIGEELIRAGLEKEFRLDFIATTTRPVSVYSGNPFLVEVGLGYGGELAREGRIEILRFANRVPLVYQQGA 385
                                       899************************************************************************** PP

                    Topo-VIb_trans  78 dvitkavksinwkrYkleq......pedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkyls 148
                                       ++it+av+s++wk+Y+l+q      p +p+v+lvh+ast++Pf+se+K+a+ad++ei  ei+l l+evarkL++yls
  gi|330507582|ref|YP_004384010.1| 386 CAITHAVESVSWKNYSLSQsagsgiPVGPAVLLVHIASTNIPFTSESKDAVADMPEILVEIDLGLKEVARKLRRYLS 462
                                       ***************************************************************************** PP

                    Topo-VIb_trans 149 kkekekeekek 159
                                       +++  +e++ek
  gi|330507582|ref|YP_004384010.1| 463 RQSLLSERREK 473
                                       **988888765 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 ?   -4.2   0.0         7   1.8e+04      50      70 ..     221     241 ..     217     242 .. 0.85
   2 !  125.2   0.0     5e-40   1.3e-36       1     114 []     493     606 ..     493     606 .. 0.99

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 7
                                       --EES-----------EEE-S CS
                           Top6b_C  50 heilpaeieeaspeakvvemd 70 
                                       +e lp ++ +++p+++ +e++
  gi|330507582|ref|YP_004384010.1| 221 TESLPKKAYAIQPHPEGIELG 241
                                       788999999999999999998 PP

  == domain 2  score: 125.2 bits;  conditional E-value: 5e-40
                                       SSS---SHHHHHHHTT-EEEEEEE--SSS-.EEEEEEE---------EEE--EES-----------EEE-SSSEEE- CS
                           Top6b_C   1 dreepdidpvvArimgnvlvereveengdg.vevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlk 76 
                                       dr+epdi pvvA+imgn+lv re e++ dg ++v+l v+N+sd  ++f+lhe+l  ++e++sp akv+++++ yd++
  gi|330507582|ref|YP_004384010.1| 493 DRPEPDIGPVVAKIMGNLLVYRESEQQ-DGrISVRLVVENHSDLVRSFKLHELLGEKAEAISPPAKVISLGDGYDHH 568
                                       89***********************99.777********************************************** PP

                                       EEE---TT-EEEE----SS-GGGS--B----------- CS
                           Top6b_C  77 WelsvsageskvleYsvdseaeeelsliveGveeekvT 114
                                       W+lsv++g++++++Y++ ++++  ++ +veG++ e+vT
  gi|330507582|ref|YP_004384010.1| 569 WKLSVGPGQKAIISYQIGANSSGPAKPVVEGLDPEIVT 606
                                       ************************************99 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0     3e-14   7.8e-11       4      83 ..      34     121 ..      31     178 .. 0.76
   2 ?   -2.3   0.0       2.4   6.2e+03       9      33 ..     502     529 ..     497     540 .. 0.70

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 3e-14
                                       HHHHHHHHHHHHHHHHH...HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCH.....HCSTCHTS CS
                         HATPase_c   4 krLrqiisnlvdNavkf...atkageieveikaseddlvisveDnGiGipkedlkklfe.kfsq.....ddstkrgg 71 
                                       + L  +++++vdN++++   a+  ++i+v+ik+s +++++ veDnG+Gi +e+++++f+             ++rg+
  gi|330507582|ref|YP_004384010.1|  34 RALITCVKEAVDNSLDAcedAGILPDIFVQIKKSGEYFQVIVEDNGPGIVPEEIPRVFAkL-LYgsrfhTLRQSRGQ 109
                                       67899***********95444455599*****7669*******************777742.222455447778888 PP

                                       TSSSHHHHHHHH CS
                         HATPase_c  72 ggtGlGlsivkk 83 
                                       +g G+++ +  +
  gi|330507582|ref|YP_004384010.1| 110 QGIGISAGVLYS 121
                                       888887766654 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHH...HSTTTEEEEEEEE CS
                         HATPase_c   9 iisnlvdNavkf...atkageieveika 33 
                                       ++  +++N++ +   ++++g+i+v++ +
  gi|330507582|ref|YP_004384010.1| 502 VVAKIMGNLLVYresEQQDGRISVRLVV 529
                                       6777888888886554577777777664 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 !   28.1   0.0     6e-10   1.5e-06       6      83 ..      39     119 ..      35     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 6e-10
                       HATPase_c_3   6 AlaelvdNsldAdaen.....vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiG 76 
                                        + e vdNsldA         + ++++k  g+  ++ +eD+G G+ +ee+ +++ +l   s+  ++ ++s+G+ GiG
  gi|330507582|ref|YP_004384010.1|  39 CVKEAVDNSLDACEDAgilpdIFVQIKKS-GEYFQVIVEDNGPGIVPEEIPRVFaKLLYGSRF-HTLRQSRGQQGIG 113
                                       589********988888898877777775.689*******************77589999998.578********** PP

                       HATPase_c_3  77 lklAsls 83 
                                         +A++ 
  gi|330507582|ref|YP_004384010.1| 114 -ISAGVL 119
                                       .455433 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.4e-06    0.0035     153     238 ..     224     304 ..     214     332 .. 0.82
   2 ?   -4.0   0.2       1.8   4.5e+03     293     320 ..     462     489 ..     454     493 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-06
                                       STTXBXXXSXXXSXBXTTSXXH.HHHHHHHHH.S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH............ CS
                              FbpA 153 lpgekYelPpsqdklnPleaeeleefkellsk.kekdlvkaLvkafqGlspllaeelleragldketsakelseedl 228
                                       lp++ Y + p  ++++        e+ +ll+   +k+l+ +L ++f+ ++   a+el+++a ld+e + ++l+ +++
  gi|330507582|ref|YP_004384010.1| 224 LPKKAYAIQPHPEGIELG------ELIKLLRYtDKKKLRVFLKETFSSIGTISAQELCKKADLDPEAPPASLDHDEA 294
                                       455556555554444333......333444444669***************************************** PP

                                       ...HHHHHHH CS
                              FbpA 229 erlyealqel 238
                                        rl  a++++
  gi|330507582|ref|YP_004384010.1| 295 VRLLLAFKQI 304
                                       ***9999986 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.8
                                       X--SHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FbpA 293 erdrveqkrsdlekrveneleklekklk 320
                                        r+ + ++r + e++++++l +  kkl+
  gi|330507582|ref|YP_004384010.1| 462 SRQSLLSERREKEEIIRKILPRIAKKLS 489
                                       3444445555555555555555555554 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   3.6e-05     0.093      13     101 ..      18     113 ..       3     116 .. 0.76
   2 ?   -3.1   0.0       2.7     7e+03      37      62 ..     504     529 ..     471     535 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.6e-05
                       HATPase_c_2  13 evaeavlrraglseelldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdptee 89 
                                       e++e   r+    +++   +  +v+Ea+ N   +  + +   ++ v+++ ++e ++v v+D+Gpg  pe++p+  ++
  gi|330507582|ref|YP_004384010.1|  18 EFFEKN-RQILGFDSAPRALITCVKEAVDNSLDACEDAGILPDIFVQIKKSGEYFQVIVEDNGPGIVPEEIPRVFAK 93 
                                       333333.556666666778888***************99999999********************999988876665 PP

                       HATPase_c_2  90 ep........keslkegGrG 101
                                        +         +s+  +G+G
  gi|330507582|ref|YP_004384010.1|  94 LLygsrfhtlRQSRGQQGIG 113
                                       55666666666666666666 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.7
                       HATPase_c_2  37 eEactNavehayleapegpvevrles 62 
                                       + ++ N   +   e+++g+++vrl +
  gi|330507582|ref|YP_004384010.1| 504 AKIMGNLLVYRESEQQDGRISVRLVV 529
                                       55667777888888888888888655 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 ?   10.7   0.0   0.00012      0.31      55      88 ..      43      76 ..      31     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                        MAF_flag10 55 aadtalkaLlkegIkPDivvslDpqeasyevfke 88
                                      a+d +l a++++gI PDi+v + ++   ++v+ e
  gi|330507582|ref|YP_004384010.1| 43 AVDNSLDACEDAGILPDIFVQIKKSGEYFQVIVE 76
                                      899*****************99885555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.38
# Mc/sec: 4869.97
//
Query:       gi|330507583|ref|YP_004384011.1|  [L=76]
Description: AsnC family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-11   42.9   0.3      4e-11   42.7   0.3    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0003   20.8   1.2    0.00035   20.6   1.2    1.1  1  NapD            NapD protein
    0.00098   19.0   0.1     0.0011   18.9   0.1    1.2  1  GYD             GYD domain
  ------ inclusion threshold ------
      0.013   16.1   0.8        0.5   11.0   0.4    2.1  2  ACT_4           ACT domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.3     9e-15     4e-11       2      71 ..       7      72 ..       6      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 9e-15
                                      EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
                    AsnC_trans_reg  2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71
                                      +v++ pg+    +++  al+e++ ++ +y+v G++d+++++ v+ l  l+++++  ++++++v  t+t +
  gi|330507583|ref|YP_004384011.1|  7 MVKVVPGQ---EKTVYNALQEIDGIKDVYHVFGEFDFVVIIEVEGLSMLNKLVDV-IREIDNVNATQTVV 72
                                      69999999...*****************************************766.***********976 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.2   7.8e-08   0.00035       7      70 ..       7      71 ..       1      74 [. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.8e-08
                              NapD  7 vVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtieaiealpgVlsaslv 70
                                       V++ p++ + v +al++++g+ +v+++ +e   Vv+iE e    l + ++ i+++++V +++ v
  gi|330507583|ref|YP_004384011.1|  7 MVKVVPGQEKTVYNALQEIDGIkDVYHVFGEFDFVVIIEVEGLSMLNKLVDVIREIDNVNATQTV 71
                                      799******************879***********************************999876 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   2.4e-07    0.0011      16      64 ..       9      55 ..       3      74 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.4e-07
                               GYD 16 kdsperreeakealveslGgkleslyatlGeyDvvvivEapDdetaaal 64
                                      k  p +++++  al ++++g ++++y ++Ge+D+vvi+E++  +   +l
  gi|330507583|ref|YP_004384011.1|  9 KVVPGQEKTVYNAL-QEIDG-IKDVYHVFGEFDFVVIIEVEGLSMLNKL 55
                                      66677777788888.77766.78****************9876666655 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.018        81      64      79 ..      17      32 ..      13      35 .. 0.81
   2 ?   11.0   0.4   0.00011       0.5      48      76 ..      38      66 ..      33      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.018
                             ACT_4 64 rviakLraipgVisVe 79
                                      +v ++L++i+g+++V+
  gi|330507583|ref|YP_004384011.1| 17 TVYNALQEIDGIKDVY 32
                                      6778899999998885 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                             ACT_4 48 aeikitveVkdvehLsrviakLraipgVi 76
                                      +++ + +eV+ ++ L+++++ +r+i++V+
  gi|330507583|ref|YP_004384011.1| 38 FDFVVIIEVEGLSMLNKLVDVIREIDNVN 66
                                      777889*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 651.92
//
Query:       gi|330507584|ref|YP_004384012.1|  [L=296]
Description: hypothetical protein MCON_1550 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.5   1.8      0.017   13.2   1.8    1.1  1  DNA_pol_phi  DNA polymerase phi


Domain annotation for each model (and alignments):
>> DNA_pol_phi  DNA polymerase phi
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.8   9.7e-07     0.017     688     749 ..     194     261 ..     155     270 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.7e-07
                       DNA_pol_phi 688 elreklaealgesg........ededdddsdsDed.mdDeqMmaLDeqLaeiFkerkkaknkkkkekkeak 749
                                       + r+ +a al + +        +d+ + +s+ +++ m++e + +L e ++e F ++++a   k+ke  e+k
  gi|330507584|ref|YP_004384012.1| 194 RYRKMVARALASLKadlgktvgDDSGSLASSAESErMGEENGDELHEPIEEGFEAKPEA---KQKEMPEEK 261
                                       455666666666555555555677777778888888***********************...333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.34
# Mc/sec: 2577.45
//
Query:       gi|330507585|ref|YP_004384013.1|  [L=409]
Description: single-stranded DNA-binding replication protein A [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.019   15.0   0.0        1.4    8.9   0.0    2.6  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.064   13.1   0.1       0.19   11.6   0.0    1.8  2  RMI1_C           Recq-mediated genome instability protein 1, 


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 ?    3.1   0.0      0.01        92      23      72 ..     102     148 ..      96     155 .. 0.87
   2 ?    8.9   0.0   0.00016       1.4      23      72 ..     206     252 ..     199     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.01
                                       EEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEEEE CS
                   tRNA_anti-codon  23 lrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkvee 72 
                                       + Dg+g ++ v ++   ++ + +l  G+ +  +     +++g+ +++k ++
  gi|330507585|ref|YP_004384013.1| 102 VGDGSGAMKFVKWK---KSDLPDLVLGQSYSLKkVITDEFQGR-FSIKLNR 148
                                       579***********...99999999999999998888888998.9998876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00016
                                       EEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEEC.TTSSEEEEEEE CS
                   tRNA_anti-codon  23 lrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrr.pggelelkvee 72 
                                       + D+tg+i+ v +    ++ + nl+eG+ +  +  v+   +g+ +++k ++
  gi|330507585|ref|YP_004384013.1| 206 IGDETGSIKFVKWT---KADLANLEEGKSYLLRNLVTDEfQGR-FSVKLNR 252
                                       78************...****************8888773555.9999876 PP

>> RMI1_C  Recq-mediated genome instability protein 1, C-terminal OB-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.1e-05      0.19      45      85 ..     313     352 ..     287     367 .. 0.78
   2 ?   -3.4   0.0      0.86   7.7e+03     125     143 .]     388     406 ..     386     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.1e-05
                            RMI1_C  45 wqlkakisDGsaildvdlssevlteligfspaelkeslalk 85 
                                        ++ka+++DG  + dv +++e  ++l+g++  e  +++a++
  gi|330507585|ref|YP_004384013.1| 313 LRIKAVLDDGRRVQDVLINRETTERLVGLTLDE-ARMMAME 352
                                       356899**************************9.5677665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.86
                            RMI1_C 125 vleledvsesdleeLqkRl 143
                                       + el +v+es + eL++R+
  gi|330507585|ref|YP_004384013.1| 388 INELMPVTESSVDELMSRV 406
                                       5678899999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3155.96
//
Query:       gi|330507586|ref|YP_004384014.1|  [L=297]
Description: putative snoRNA binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-41  140.9   0.0    8.5e-41  139.9   0.0    1.4  1  Nop       snoRNA binding domain, fibrillarin


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   0.0   4.8e-45   8.5e-41      34     218 ..      84     266 ..      75     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 4.8e-45
                                       HHHHHHHHHHCCCCHCCT.HHTT.HHHHHHHHHHHHCHHHH.-SSS-S-HHHHH..HHHHHHHHHHHHHHHHHHHHH CS
                               Nop  34 nleYakvvkligneredlekkeedeelakevimaakvtast.smgaelseedlk..nikelcdrvleleelrkelle 107
                                       + + +++v++i   +e +     ++ l+++ +++ +   +   +g++l e  ++   +  +++++l+l e+rk+++e
  gi|330507586|ref|YP_004384014.1|  84 EQDLLQAVEAIDDMTEAI-----NL-LDERLYEWHRLHHQRiVHGKDLAELLCEdrIMGPFARSILRLMESRKSMEE 154
                                       555555555555333333.....12.555555555554444456666666554411356799*************** PP

                                       HHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HHHHCCCHHT-.--SSSCHHHCSHHHHHT CS
                               Nop 108 YlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaekalfralkkk.ntpkyGliyhselvqka 183
                                        ++ r +++APNlsaL G+ +aarLis aGgL++LakmP+s +q++Gaek+lf++l ++  +pk+G+i+ ++ v+ a
  gi|330507586|ref|YP_004384014.1| 155 EVSFRAEELAPNLSALAGPILAARLISRAGGLSRLAKMPSSRVQVMGAEKSLFKHLDGHaPSPKHGIIFRHPAVMGA 231
                                       *********************************************************7768**************77 PP

                                       S-CCCHHHHHHHHHHHHHHHHHHHHTT---.-SHHH CS
                               Nop 184 tppklkkkiaRllaaKvalaaRiDafsekd.gslGk 218
                                        p++l++k+aR+la K+alaaR+D +++++  +l  
  gi|330507586|ref|YP_004384014.1| 232 -PRRLRGKVARALAGKLALAARLDYYGASPsPDLAA 266
                                       .***********************765444344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 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:                        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 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2112.74
//
Query:       gi|330507587|ref|YP_004384015.1|  [L=211]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1629.53
//
Query:       gi|330507588|ref|YP_004384016.1|  [L=281]
Description: putative methanogenesis marker protein 8 [Methanosaeta concilii GP6]
Scores for complete 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-105  352.0   0.4   1.8e-105  351.8   0.4    1.0  1  DUF2099   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2099  Uncharacterized protein conserved in archaea (DUF2099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.8   0.4  9.8e-110  1.8e-105       1     257 []       2     255 ..       2     255 .. 0.99

  Alignments for each domain:
  == domain 1  score: 351.8 bits;  conditional E-value: 9.8e-110
                           DUF2099   1 HiiealgkarvvvkdgkvvevgepkikyCPlfkklrgikeitkeaikkniefrikefGlftkkRkleskedfvsfGa 77 
                                       H +e+lg++ ++v++ +v+e +ep i++CPlf+k+rgik++tke+  +n+efrike+G+f+++Rkle++ +fv+fGa
  gi|330507588|ref|YP_004384016.1|   2 HKMELLGRSAIKVSEEEVTEATEPVIEWCPLFDKVRGIKKVTKESAAANMEFRIKEHGMFSARRKLEMD-TFVGFGA 77 
                                       99*******************************************************************.******* PP

                           DUF2099  78 sEilstalkeglidaavivcdgaGtvivtnpelvqglggrisGlveTePieevierieeeggivldketaeidqveG 154
                                       sE ++t+l +g+idaav+vcdgaGtvi++n +lvqg+gg isGlveT+Pi+evi+ i++++g vl++e+++idq+eG
  gi|330507588|ref|YP_004384016.1|  78 SESMMTGLMRGIIDAAVTVCDGAGTVITSNGSLVQGMGGYISGLVETDPIPEVIKGIKSRDGHVLSPESGRIDQLEG 154
                                       ***************************************************************************** PP

                           DUF2099 155 vkkAiekgykkiavtvaeaedakklrelekeegvkilifavhttgiskeeaeelveaaDlvtacAskeireivkkka 231
                                       ++ Ai++gy ++avtva+a++a++lrele+++gv+i+i++vh+tgisk++a++l++aaD+vt+cAs++ire +   +
  gi|330507588|ref|YP_004384016.1| 155 AAYAISAGYCRFAVTVADAQTAERLRELERSTGVRIMIIGVHLTGISKDDARRLLKAADIVTSCASRHIREEAV--P 229
                                       ***********************************************************************999..9 PP

                           DUF2099 232 llqvgksvpvfaltekGkelilerlk 257
                                       l+qvg++vp+f+lt +Gkel++er+k
  gi|330507588|ref|YP_004384016.1| 230 LVQVGTAVPLFSLTPWGKELLVERAK 255
                                       ***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2214.69
//
Query:       gi|330507589|ref|YP_004384017.1|  [L=136]
Description: transcriptional regulator TrmB [Methanosaeta concilii GP6]
Scores for complete 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   19.8   0.0      0.001   18.9   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.078   12.9   0.1       0.18   11.7   0.1    1.6  1  MarR_2    MarR family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.1e-07     0.001       1      63 [.      31     100 ..      31     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-07
                                       HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEE CS
                              TrmB   1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYr 63 
                                       L k+GL+ + akv ++L    +at +ei   +++ ++ v  ++r+  +  +V+ +++r       +++Y+
  gi|330507589|ref|YP_004384017.1|  31 LMKIGLKRNVAKVLTYLAGVPEATSREIEIGSDLRQPEVSIAMREIRRLEWVRERDERnpgkgrpYRIYK 100
                                       6799*************************************************99999888888555776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     2e-05      0.18       2      60 ..      35      93 ..      34      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE..ESSSSS CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr..pgpeDk 60
                                      gl++  a vL +L+  p+   t +e++   +l ++ vs + ++  +  +v++r  ++p+ +
  gi|330507589|ref|YP_004384017.1| 35 GLKRNVAKVLTYLAGVPE--ATSREIEIGSDLRQPEVSIAMREIRRLEWVRERdeRNPGKG 93
                                      8899999**********9..9******************************9955555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1101.39
//
Query:       gi|330507590|ref|YP_004384018.1|  [L=370]
Description: cell division protein FtsZ [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-42  144.5   0.1    7.3e-42  143.8   0.1    1.3  1  Tubulin         Tubulin/FtsZ family, GTPase domain
    2.5e-33  114.2   1.1    7.8e-33  112.7   1.1    1.9  1  FtsZ_C          FtsZ family, C-terminal domain
     0.0044   16.9   0.3      0.011   15.7   0.3    1.8  1  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
        6.7    5.8   9.3        2.2    7.4   3.0    2.4  2  Tubulin_2       Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.8   0.1   1.6e-45   7.3e-42       2     196 ..      41     200 ..      40     201 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.8 bits;  conditional E-value: 1.6e-45
                                       EEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE- CS
                           Tubulin   2 iivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklll 78 
                                       i vig+G++G++++++l e      gi             +g +e++    a++td+q+l +i+a+      +++l+
  gi|330507590|ref|YP_004384018.1|  41 IRVIGCGGGGSNTIDRLAE-----CGI-------------QG-AELF----AVNTDAQHLLHINAD------RRFLI 88 
                                       789****************.....599.............77.8888....***************......***** PP

                                       -CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEE CS
                           Tubulin  79 gkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvv 155
                                       g   ++++gag+ p +g+eaa+e  +eir +v+++d+   +f+t +lgGGTG+G++pv++e+++e   +al++++v+
  gi|330507590|ref|YP_004384018.1|  89 GRRTTRGLGAGSLPAIGEEAAQEDIDEIRAAVDGADM---VFVTCGLGGGTGTGASPVVAEAAREA--GALTISIVT 160
                                       *************************************...**************************..********* PP

                                       E--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                           Tubulin 156 lPsefsevvvepynailalkelieesdavividNdaLlkil 196
                                       +P++  e++++++na+ +l++l+e sd+viv++Nd+Ll+++
  gi|330507590|ref|YP_004384018.1| 161 IPFSA-EGTIRMQNAEAGLNRLREVSDTVIVVPNDRLLDVV 200
                                       ***99.********************************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 !  112.7   1.1   1.7e-36   7.8e-33       1      94 [.     248     341 ..     248     342 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 1.7e-36
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       GvAm+g+Gea+ge++a++++ +a++spLLdvd+s A+++lvn+ ggsd+t++++e+v++++++++++ea++i+Ga+i
  gi|330507590|ref|YP_004384018.1| 248 GVAMIGMGEAQGEEKARDSVSKALRSPLLDVDVSCATSALVNVVGGSDMTITDAETVVDEVYQKINPEARIIWGAQI 324
                                       99*************************************************************************** PP

                                       -TT--SEEEEEEEEES- CS
                            FtsZ_C  78 deeledeirvtvvatgl 94 
                                       d++l+ ++r++ v+tg+
  gi|330507590|ref|YP_004384018.1| 325 DQNLDHTLRTMLVVTGV 341
                                       ****************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 !   15.7   0.3   2.4e-06     0.011      48      97 ..     110     160 ..     106     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-06
                                       TT-CCHHHHHHTT-SEEEES---TCCHHHH.HHHHHHHHHHCT--EEEEEE CS
                    NAD_binding_10  48 vtdvedlaealkgadaVvsalggggkdeeg.aknivdaakeagvkRfvlvs 97 
                                        +d +++++a++gad V+++ g gg++ +g    +++aa+eag   + +v+
  gi|330507590|ref|YP_004384018.1| 110 QEDIDEIRAAVDGADMVFVTCGLGGGTGTGaSPVVAEAAREAGALTISIVT 160
                                       5799*************9999888876677244556899999987776666 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4     0.029   1.3e+02       2      18 ..      43      59 ..      43      86 .. 0.86
   2 ?    7.4   3.0    0.0005       2.2     156     177 ..     124     145 ..      87     162 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.029
                         Tubulin_2  2 viGLGGtGgkvlaelrr 18
                                      viG+GG G++++++l++
  gi|330507590|ref|YP_004384018.1| 43 VIGCGGGGSNTIDRLAE 59
                                      7************9986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0005
                         Tubulin_2 156 lnvfVvgSLaGGTGSGiflDva 177
                                         vfV ++L GGTG G    va
  gi|330507590|ref|YP_004384018.1| 124 DMVFVTCGLGGGTGTGASPVVA 145
                                       47*************9876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 2990.52
//
Query:       gi|330507591|ref|YP_004384019.1|  [L=102]
Description: hypothetical protein MCON_1558 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-05   23.5   0.3    4.8e-05   22.8   0.3    1.4  1  HTH_24    Winged helix-turn-helix DNA-binding
     0.0012   19.2   0.1     0.0019   18.5   0.1    1.3  1  Rrf2      Transcriptional regulator
     0.0016   18.5   0.3     0.0033   17.5   0.1    1.5  2  DUF2250   Uncharacterized protein conserved in archaea (DUF22
     0.0021   18.0   0.2     0.0063   16.4   0.1    2.0  1  HTH_12    Ribonuclease R winged-helix domain
     0.0038   17.1   0.4     0.0068   16.2   0.4    1.5  1  HTH_5     Bacterial regulatory protein, arsR family
     0.0044   16.9   0.0     0.0072   16.2   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0047   17.3   0.0     0.0074   16.6   0.0    1.3  1  FaeA      FaeA-like protein
     0.0052   16.8   0.1     0.0096   16.0   0.1    1.5  1  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.023   14.3   0.1      0.033   13.9   0.1    1.3  1  GntR      Bacterial regulatory proteins, gntR family
      0.045   13.2   0.0      0.064   12.7   0.0    1.4  1  RepL      Firmicute plasmid replication protein (RepL)
       0.06   13.2   0.1      0.089   12.7   0.1    1.3  1  RuvB_C    RuvB C-terminal winged helix domain
      0.074   12.8   0.1         16    5.4   0.0    2.4  3  MerR      MerR 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 !   22.8   0.3   3.2e-08   4.8e-05       3      48 .]      17      62 ..      15      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.2e-08
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + ++ IL+ + +n  i +  LAe++ +++  v++ l+ Le+eGlIk
  gi|330507591|ref|YP_004384019.1| 17 QRHLLILKHVVENEPIGILKLAEETSIPSHKVRYSLRILEQEGLIK 62
                                      56789****************************************8 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   1.2e-06    0.0019       4      58 ..      10      64 ..       8      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                                      -HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2  4 sskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      s ++e+  + ll+L++  e+ep+ + ++ae+++i+ + ++  l+ L+++gl+k++
  gi|330507591|ref|YP_004384019.1| 10 SGELEMLQRHLLILKHVVENEPIGILKLAEETSIPSHKVRYSLRILEQEGLIKAT 64
                                      556677778999****************************************975 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.2e-06    0.0033       3      55 ..      12      64 ..      10      74 .. 0.91
   2 ?   -1.4   0.0       1.7   2.6e+03      32      42 ..      81      91 ..      63      98 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.2e-06
                           DUF2250  3 eleedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerv 55
                                      ele  +++l +lkh+ + ++   + +a+e+ ip ++vr  l+ Le+ GL++  
  gi|330507591|ref|YP_004384019.1| 12 ELEMLQRHLLILKHVVENEPIGILKLAEETSIPSHKVRYSLRILEQEGLIKAT 64
                                      5778899*******************************************875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
                           DUF2250 32 leipleevrel 42
                                      l+  +ee ++ 
  gi|330507591|ref|YP_004384019.1| 81 LDSMIEELSKR 91
                                      33333444444 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 !   16.4   0.1   4.2e-06    0.0063       4      54 ..      23      67 ..      20      81 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.2e-06
                            HTH_12  4 LkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgya 54
                                      Lk++ e+ +pig  ++aee       i    vRy Lr+le++gl++    +
  gi|330507591|ref|YP_004384019.1| 23 LKHVVEN-EPIGILKLAEE-----TSIPSHKVRYSLRILEQEGLIKATAPG 67
                                      5555553.45666666665.....56777888*************976655 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   4.6e-06    0.0068       5      46 ..      20      62 ..      17      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.6e-06
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      l ILk + e ++  +  laee+ ++  +v++ L++L+++GL++
  gi|330507591|ref|YP_004384019.1| 20 LLILKHVVEnEPIGILKLAEETSIPSHKVRYSLRILEQEGLIK 62
                                      56777777755577888************************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 !   16.2   0.0   4.8e-06    0.0072      15      54 ..      24      63 ..      13      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.8e-06
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      + +++++p  + ++aee+ +p  kv  +Lr Le+ Gl++ 
  gi|330507591|ref|YP_004384019.1| 24 KHVVENEPIGILKLAEETSIPSHKVRYSLRILEQEGLIKA 63
                                      66899********************************987 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     5e-06    0.0074       5      48 ..      22      64 ..      18      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5e-06
                                      HHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE CS
                              FaeA  5 IleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrs 48
                                      Il+++ + + p     +A+ +++    +Ry L  Le+eg ik +
  gi|330507591|ref|YP_004384019.1| 22 ILKHVVE-NEPIGILKLAEETSIPSHKVRYSLRILEQEGLIKAT 64
                                      999****.*********************************976 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   6.4e-06    0.0096      15      59 ..      22      66 ..      15      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.4e-06
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      il++  ++e+     lae+ +++   ++y Lr+Le+ gL++ + +
  gi|330507591|ref|YP_004384019.1| 22 ILKHVVENEPIGILKLAEETSIPSHKVRYSLRILEQEGLIKATAP 66
                                      677778888888889*************************98766 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.2e-05     0.033      10      56 ..      18      63 ..       6      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                                      HHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR 10 redIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglver 56
                                      r++++ +++  ++++    +La+e  +  + vR +Lr Le+egl+ +
  gi|330507591|ref|YP_004384019.1| 18 RHLLILKHVVENEPI-GILKLAEETSIPSHKVRYSLRILEQEGLIKA 63
                                      566777888889999.999*************************986 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.3e-05     0.064      80     112 ..      36      68 ..       7      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-05
                              RepL  80 elaeetgislktvsetlkileeanilkkkanGv 112
                                       +laeet i  + v+  l+ile+ +++k  a G+
  gi|330507591|ref|YP_004384019.1|  36 KLAEETSIPSHKVRYSLRILEQEGLIKATAPGA 68 
                                       79*************************999887 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     6e-05     0.089       9      67 ..      17      74 ..      11      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6e-05
                                      HHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEEEE-HHH CS
                            RuvB_C  9 ikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrGRilTkkg 67
                                      ++ L +lk+  +++p+g+  la+ ++++++++      +L +eglI+ t  G + T+++
  gi|330507591|ref|YP_004384019.1| 17 QRHLLILKHVVENEPIGILKLAEETSIPSHKVRYSL-RILEQEGLIKATAPGATTTHET 74
                                      57799999999*********************9655.8999********9999888876 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.015        23       4      18 ..      36      50 ..      32      50 .. 0.89
   2 ?    5.4   0.0     0.011        16      16      26 ..      52      62 ..      51      68 .. 0.85
   3 ?   -2.8   0.0       3.7   5.6e+03       2       9 ..      85      92 ..      85      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.015
                                      HHHHHHTTTHHHHHH CS
                              MerR  4 evAeltGvsprtLRy 18
                                       +Ae t ++++++Ry
  gi|330507591|ref|YP_004384019.1| 36 KLAEETSIPSHKVRY 50
                                      58************9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
                                      HHHHHHTTSST CS
                              MerR 16 LRyYEreGLip 26
                                      LR +E+eGLi+
  gi|330507591|ref|YP_004384019.1| 52 LRILEQEGLIK 62
                                      899*******5 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.7
                                      HHHHHHHH CS
                              MerR  2 IgevAelt 9 
                                      I e+++++
  gi|330507591|ref|YP_004384019.1| 85 IEELSKRA 92
                                      78999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 758.95
//
Query:       gi|330507592|ref|YP_004384020.1|  [L=546]
Description: DNA ligase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-26   91.3   0.0    1.8e-25   90.3   0.0    1.6  1  DNA_ligase_A_N   DNA ligase N terminus
    2.3e-14   53.5   0.0    3.7e-14   52.9   0.0    1.2  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
  ------ inclusion threshold ------
      0.067   13.5   0.0       0.14   12.5   0.0    1.5  1  UPF0016          Uncharacterized protein family UPF0016
       0.14   11.9   0.0       0.25   11.1   0.0    1.3  1  mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
        0.2   11.3   0.0       0.32   10.6   0.0    1.2  1  Peptidase_S51    Peptidase family S51


Domain annotation for each model (and alignments):
>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.0     5e-29   1.8e-25       7     173 .]       5     172 ..       2     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 5e-29
                                       HHHHHHCC..---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT--HHH CS
                    DNA_ligase_A_N   7 elfekiee.stkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealglskkk 78 
                                       ++ ++iee s+  r  k +++++++ ++   +pe l p++rL    l+P ++gre+g+g+  +a al e++  +   
  gi|330507592|ref|YP_004384020.1|   5 QIAQSIEElSSAPRSCKAELCSRLIVEM---KPELLCPTIRLllgqLWPPWEGREMGVGPEGVAAALEEISEEN--- 75 
                                       45555666555556689********443...699***********************************99866... PP

                                       HHHHHHHHS-HHHHHHHHHCCHHHH.------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHHHHHH CS
                    DNA_ligase_A_N  79 ikdalakvgDlgevaeevlskrstl.akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEakylir 153
                                       i    +++g++g vae++l+++ +   +++pl    v+e+L++++   gk+se++k ++l++l++ asp+E ky++r
  gi|330507592|ref|YP_004384020.1|  76 ISLLRDRMGEMGLVAEAALAEKGQHsLSSEPLQSMSVYEQLRRISLIrGKDSEQRKNALLRGLFQDASPLEGKYIAR 152
                                       55555568***********888777799****************9889***************************** PP

                                       HHCT---SS--HHHHHHHHH CS
                    DNA_ligase_A_N 154 iilkdlriglsektvldala 173
                                       ++l+++  g+++kt+l a+a
  gi|330507592|ref|YP_004384020.1| 153 TVLGNMLAGIGDKTMLAAFA 172
                                       *****************997 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 !   52.9   0.0     1e-17   3.7e-14      31     195 ..     250     414 ..     224     418 .. 0.82

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1e-17
                                       EEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEEEETTTTCBEHHHHHCHHH.HCHCCT CS
                    DNA_ligase_A_M  31 eRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElvavdketgeilpfqklasrk.kkkkkv 106
                                        R+qvh+ gd  ++fS r+k+it ++  l ++l+ + +    ++i+D+ l+ +  ++g++    ++ + + +++   
  gi|330507592|ref|YP_004384020.1| 250 LRVQVHNTGDGAYIFSSRQKNITTSLNGLAQRLSGMDD----EFIIDADLIGF--HEGKMCSQSEMLRYInRRRL-S 319
                                       69**********************99999888866554....6*********5..77788777777777634444.2 PP

                                       HHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB........--BTTTEEE--EEEESSHHHHHHHHHHHH CS
                    DNA_ligase_A_M 107 eeklkeaelclfvFDiLyldgesltdeplkeRrklLeeil........kesedrvelaeslevkdveeleelleeai 175
                                       ++  +++++ l+++D++y+ ge+ + +p++eRrk + ++l        + ++ + e +   +  + ++++  l++++
  gi|330507592|ref|YP_004384020.1| 320 RR--SSISPALLAYDLIYISGENTISLPFQERRKRMLKALgeprsmpfQGISATRECIVLEKELKKDSIQSHLDQMV 394
                                       33..589***************************9999999999888855554444444444556689********* PP

                                       HTTECEEEEEETT-CC-TTC CS
                    DNA_ligase_A_M 176 seglEGlvvKnpdskYepgk 195
                                       +eg  Gl+v++  + Y+pg+
  gi|330507592|ref|YP_004384020.1| 395 EEGGVGLMVRSLLGLYRPGE 414
                                       ******************96 PP

>> UPF0016  Uncharacterized protein family UPF0016
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     4e-05      0.14       8      27 ..     158     177 ..     152     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                           UPF0016   8 flaElGDkTqlaaalLaary 27 
                                       +la +GDkT+laa++La  +
  gi|330507592|ref|YP_004384020.1| 158 MLAGIGDKTMLAAFALAFCC 177
                                       7999*************866 PP

>> mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     7e-05      0.25      90     137 ..     325     371 ..     316     402 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7e-05
                                       EEEEEEEEEEEETTEEGTTSBHHHHHHHHHHHTHHHHHHHHHTTCCCC CS
                   mRNA_cap_enzyme  90 elryliyDivaingvtvaeeplskRleilkkelikprneekktgllet 137
                                       +++ l yD++ i+g +  + p+++R + + k l +pr     +g+  t
  gi|330507592|ref|YP_004384020.1| 325 SPALLAYDLIYISGENTISLPFQERRKRMLKALGEPRSMPF-QGISAT 371
                                       57899********************************9988.444444 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   8.9e-05      0.32      72     132 ..     320     378 ..     303     408 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.9e-05
                                       -HHHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB CS
                     Peptidase_S51  72 peeeieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivages 132
                                       +++ i   ll+ d+iy++G nt++L  + +++++ k+l e    +++  G+SA   ++  +
  gi|330507592|ref|YP_004384020.1| 320 RRSSISPALLAYDLIYISGENTISLPFQERRKRMLKALGEPR--SMPFQGISATRECIVLE 378
                                       456688899*****************************9976..99******976555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3903.71
//
Query:       gi|330507593|ref|YP_004384021.1|  [L=284]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.4e-10   39.7   0.0      1e-09   39.0   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
      3e-08   33.7   0.0     0.0014   18.4   1.9    2.2  2  DUF1848      Domain of unknown function (DUF1848)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   1.1e-13     1e-09       2     163 ..      23     184 ..      22     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.1e-13
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.... 74 
                                       +++ gC+++C +C+ ++     + +  +++ ++l+ +++ +a+   + +i  +   + yp+++++l   + +     
  gi|330507593|ref|YP_004384021.1|  23 NPYTGCPHGCLYCYASSY--IPRFHSCRPKVDLLRRLDREAAKVVPGLFIAISNSSDPYPPIEKELGLTRGCLrilk 97 
                                       6789************96..777777777777777777774444377888889999999999999988888888999 PP

                                       CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdriv 150
                                       ++++r+ ++t   l+  + +++l+ +    v++++ ++dd     +++ + ++++++l al  l +agi+ +  + +
  gi|330507593|ref|YP_004384021.1|  98 ERNFRVQIVTKSDLV-TRDIDLLAAMK-AAVAVTVTTLDDS-LSLRLEpGAPSPKRRLFALNELSRAGIPLSARIDP 171
                                       9**************.***********.*************.888888899*******************5555559 PP

                                       EBTTTSHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeeleel 163
                                       ++pG nd  +e+l
  gi|330507593|ref|YP_004384021.1| 172 IIPGINDCGIEDL 184
                                       *******988887 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.9   1.6e-07    0.0014     239     265 .]      11      37 ..       4      37 .. 0.91
   2 !   11.3   0.0   2.2e-05       0.2      65     208 ..     116     272 ..     101     278 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-07
                           DUF1848 239 rkeCgCveskDiGayntClhgCvYCYA 265
                                        + C+C +   +  y  C+hgC+YCYA
  gi|330507593|ref|YP_004384021.1|  11 SELCTCPAKLSLNPYTGCPHGCLYCYA 37 
                                       567***********************9 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.2e-05
                           DUF1848  65 leelkergiklyfqf.Tltdyeke.lepnvpsleerietfkelseklgkerviwRyDPilltek......ltvelhl 133
                                       ++ l +++  + + + Tl d  +  lep+ ps ++r+ +++els+      +  R DPi+   +      l  +lh 
  gi|330507593|ref|YP_004384021.1| 116 IDLLAAMKAAVAVTVtTLDDSLSLrLEPGAPSPKRRLFALNELSRAGI--PLSARIDPIIPGINdcgiedLVYSLHS 190
                                       55555544444444413444333369******************9754..4789*****965544566667777788 PP

                           DUF1848 134 ekfeklaeelk....gytekvviSfvdlykkvkrnlkk..k.lelrelseeekeelaeelaeiakklglelatCaek 203
                                         +++++++      + ++k++ +f +  + +k+ +++  +    + l ++ +++++e++a+ a+++g++ +tC e 
  gi|330507593|ref|YP_004384021.1| 191 AGVRHITSSTYkarpDSIKKITAAFPEEGAALKALFSRggRySGSSYLPADLRRSILEDVASHAHQTGITFSTCREG 267
                                       888888776654557899999999999999999999765534566677778889*********************99 PP

                           DUF1848 204 edlse 208
                                         ++e
  gi|330507593|ref|YP_004384021.1| 268 FAFEE 272
                                       87765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2079.13
//
Query:       gi|330507594|ref|YP_004384022.1|  [L=439]
Description: Cna protein B-type domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   2.6    5.5e-10   39.5   0.2    2.3  2  SdrD_B           SdrD B-like domain
     0.0053   17.0   2.6      0.015   15.5   0.1    2.9  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.013   15.8   0.0      0.013   15.8   0.0    2.9  2  SpaA             Prealbumin-like fold domain


Domain annotation for each model (and alignments):
>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2      0.82   4.9e+03      59      83 ..      43      67 ..      27      95 .. 0.53
   2 !   39.5   0.2   9.2e-14   5.5e-10       2      75 ..     342     415 ..     341     428 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.82
                            SdrD_B 59 eYkVeftapagytvtakkaGsddal 83
                                      +Y+   + ++ yt+t++   s++a 
  gi|330507594|ref|YP_004384022.1| 43 SYSAGSAGSQSYTATSAGVLSNTAA 67
                                      3444444444444444444333333 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 9.2e-14
                            SdrD_B   2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtak 75 
                                       +i  +V+eD ++nG+ + +e+g ++ tV+L + +g +++++ T+a+Gk+ F n  pG Y+++ +  ag+t+ + 
  gi|330507594|ref|YP_004384022.1| 342 TIEGVVFEDLDGNGVMNVNESGLANWTVNLEQPEGVIITSVNTSADGKFIFLNQLPGVYTIKEVLQAGWTLISP 415
                                       68899*********************************************************999999866544 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.4      0.31   1.9e+03      31      60 ..      35      62 ..      26      83 .. 0.60
   2 !   15.5   0.1   2.6e-06     0.015       1      52 [.     342     402 ..     342     405 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.31
                   CarboxypepD_reg 31 stttdadGafrlrglppgtysvtvsapGya 60
                                      ++ ++ + +++     +g+ s t++++G  
  gi|330507594|ref|YP_004384022.1| 35 TVASAGNQSYSAG--SAGSQSYTATSAGVL 62
                                      4444444444443..445555555555544 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.6e-06
                   CarboxypepD_reg   1 tisGrVtda.sgapi........agatVtvtnadtgtvastttdadGafrlrglppgtysv 52 
                                       ti+G V    +g+++        a+ tV +++ ++   +s+ t adG+f + +  pg y++
  gi|330507594|ref|YP_004384022.1| 342 TIEGVVFEDlDGNGVmnvnesglANWTVNLEQPEGVIITSVNTSADGKFIFLNQLPGVYTI 402
                                       57777765447777767777777********7777779*********************98 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   4.4         3   1.8e+04      69      69 ..     270     270 ..     180     334 .. 0.64
   2 ?   15.8   0.0   2.3e-06     0.013       3      61 ..     340     405 ..     338     424 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 3
                                       E CS
                              SpaA  69 l 69 
                                        
  gi|330507594|ref|YP_004384022.1| 270 A 270
                                       0 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.3e-06
                                       CCB-TS-EEEEEETT....TSCCCHCHHTT.......TTCCEESEEE-BTTSEEEEEEEESEEEEEEEE CS
                              SpaA   3 gkpLaGaeFtlykvd....tttdgkdalea......kktgtevttlttdenGkatfegLplGtYllvEt 61 
                                       g++++G++F+ ++ +    +++ g +   +      + +g  +t++ t ++Gk+ f +  +G Y+++E+
  gi|330507594|ref|YP_004384022.1| 340 GYTIEGVVFEDLDGNgvmnVNESGLA---NwtvnleQPEGVIITSVNTSADGKFIFLNQLPGVYTIKEV 405
                                       67899999999999975543333333...244588777888889999*********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.19s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 3733.63
//
Query:       gi|330507595|ref|YP_004384023.1|  [L=167]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.072   13.3   3.9        2.3    8.5   3.9    2.3  1  DUF333    Domain of unknown function (DUF333)


Domain annotation for each model (and alignments):
>> DUF333  Domain of unknown function (DUF333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.9   0.00013       2.3      28      47 ..      50      69 ..      34      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00013
                            DUF333 28 vgyCqlpdGkrceEwaLyrg 47
                                       g C +pdG  c+  ++yrg
  gi|330507595|ref|YP_004384023.1| 50 DGNCYFPDGGYCDLESFYRG 69
                                      377****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1218.95
//
Query:       gi|330507596|ref|YP_004384024.1|  [L=374]
Description: geranylgeranyl reductase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-09   36.8   0.0    8.7e-07   28.5   0.0    2.2  2  FAD_binding_3   FAD binding domain
    1.4e-08   34.5   0.0      2e-08   34.0   0.0    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
    2.6e-07   30.1   0.0    6.6e-07   28.7   0.0    1.6  2  Lycopene_cycl   Lycopene cyclase protein
    4.3e-07   29.5   0.2     0.0044   16.3   0.3    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    6.6e-07   28.5   0.7      0.003   16.5   0.1    2.8  2  Trp_halogenase  Tryptophan halogenase
    2.6e-06   26.9   0.0    4.1e-06   26.3   0.0    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.2e-06   25.8   0.0    6.9e-06   25.4   0.0    1.2  1  GIDA            Glucose inhibited division protein A
    7.5e-06   25.8   0.1     0.0038   16.9   0.2    2.4  2  DAO             FAD dependent oxidoreductase
    1.4e-05   24.0   0.1    0.00029   19.7   0.1    2.2  2  HI0933_like     HI0933-like protein
    3.6e-05   23.0   0.1    8.7e-05   21.8   0.1    1.6  2  FAD_binding_2   FAD binding domain
    4.5e-05   22.8   0.0    7.7e-05   22.0   0.0    1.3  1  Thi4            Thi4 family
    0.00019   21.6   0.0    0.00074   19.7   0.0    2.1  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0011   18.4   0.0     0.0017   17.7   0.0    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.068   13.7   0.0       0.22   12.1   0.0    1.9  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.076   13.5   0.0       0.32   11.5   0.0    2.0  2  XdhC_C          XdhC Rossmann domain
        0.1   11.9   0.0       0.21   11.0   0.0    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase


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 !   28.5   0.0   7.8e-10   8.7e-07       3     172 ..       3     153 ..       1     183 [. 0.81
   2 !    6.2   0.0    0.0048       5.4     280     307 ..     252     279 ..     247     299 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 7.8e-10
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealyne 79 
                                       d ++VGaGpaG ++a++ +  G +v+++ek +   ++p ++ l++r    l+ l l + + +++ + + ++ + + +
  gi|330507596|ref|YP_004384024.1|   3 DLVVVGAGPAGSTAARIAAGMGLKVLILEKEKFPRYKPCGGALSERATSWLD-LRLPEAVCEKAITGARIHYHEWVQ 78 
                                       568********************************************99995.899999999995555554444444 PP

                                       CCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEE CS
                     FAD_binding_3  80 lsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrak 156
                                                +++    ++  t+++ + +++ L+++a e+g++v f++ ++     e++v+ +  d+    +   r++
  gi|330507596|ref|YP_004384024.1|  79 --------DKVK---AYRLSTLINRSAFDQFLLQKAIETGASVSFSRVLN-YSSKEDHVSVQTDDQ----I--YRSR 137
                                       ........4555...88899*************************97554.778888876655444....4..5677 PP

                                       EEEE--GTT-HHHHHH CS
                     FAD_binding_3 157 YlvGaDGgrStvrktl 172
                                       +l+ a G +   r+++
  gi|330507596|ref|YP_004384024.1| 138 FLIVASGCQDSLRSRI 153
                                       8887777776666665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0048
                                       SSEETTEEE-GGGTEEE-STTSHHHHHH CS
                     FAD_binding_3 280 kyrkgrvflaGDAaHihpPtgGqGlNta 307
                                       + + grv+l GDAa  +    G G+  a
  gi|330507596|ref|YP_004384024.1| 252 RISLGRVLLTGDAASLVDSFSGEGIYYA 279
                                       6778***********9999999997655 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   1.8e-11     2e-08       1     140 [.       3     140 ..       3     148 .. 0.64

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.8e-11
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLve.....ergvlGGlltsglvatdignkaee...qvvtgiareflerlrq 69 
                                       D+vVvG+gpaG +AA  Aa +G kvl++e     +++ +GG l+  + ++++    e+   +++tg   +++e +++
  gi|330507596|ref|YP_004384024.1|   3 DLVVVGAGPAGSTAARIAAGMGLKVLILEkekfpRYKPCGGALSERATSWLDLRLPEAvceKAITGARIHYHEWVQD 79 
                                       99***************************4444445559********999999664446778899988888888866 PP

                      FAD_oxidored  70 rggarlkkrskwntfepevakavleeml....aeagvtvllntrlvevekegkriesvtveskegrktirAkvfi 140
                                       + +a   +r         +++++++++l     e g  v + ++l    ke  +  sv++     ++ +r+++ i
  gi|330507596|ref|YP_004384024.1|  80 KVKA---YR-----LSTLINRSAFDQFLlqkaIETGASVSFSRVLNYSSKE--DHVSVQTD----DQIYRSRFLI 140
                                       3333...22.....3344555555555511113344444444444444444..24455553....4555555555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   5.9e-10   6.6e-07       1     143 [.       3     147 ..       3     164 .. 0.76
   2 ?   -2.2   0.0       1.4   1.6e+03     243     296 ..     244     296 ..     222     338 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 5.9e-10
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga.....leecvehsWsgtivylddg 72 
                                       D+vv+GaGpAg   Aar+ +a +glkv+++e  + + + +       +++ +       e++ e+   g++++  + 
  gi|330507596|ref|YP_004384024.1|   3 DLVVVGAGPAGST-AARI-AAGMGLKVLILEKEKFPRYKP-CGGALSERATSWldlrlPEAVCEKAITGARIHYHEW 76 
                                       9**********65.7777.7**********7655443322.222222222222344424677799999********9 PP

                     Lycopene_cycl  73 kkillgraYg...rvsskrlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglas 143
                                        + ++  aY+    ++++ + + ll++ +e g++   ++v +   +e+ +++v   +++  r+r+ ++a+g   
  gi|330507596|ref|YP_004384024.1|  77 VQDKVK-AYRlstLINRSAFDQFLLQKAIETGASVSFSRVLNYSSKED-HVSVQ-TDDQIYRSRFLIVASGCQD 147
                                       999998.7753327******************************9999.55554.4567789*********554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                     Lycopene_cycl 243 iPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalre 296
                                       iP   gg+ +r+    vl  G aa+lv    G  +  +l+  ++ a ai +  ++
  gi|330507596|ref|YP_004384024.1| 244 IPQ--GGKKKRISLGrVLLTGDAASLVDSFSGEGIYYALRSGEMAARAIGEEKER 296
                                       555..55555554333777888888888888877777777777777777665554 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 !   16.3   0.3   3.9e-06    0.0044       1      31 [.       5      34 ..       5      37 .. 0.94
   2 !   11.0   0.0   0.00017      0.19     101     144 ..     112     154 ..     104     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.9e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      +++GaGPaG +aa  +  +gl ++lilEk++
  gi|330507596|ref|YP_004384024.1|  5 VVVGAGPAGSTAARIAAGMGL-KVLILEKEK 34
                                      79*******************.7******86 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00017
                       Pyr_redox_3 101 feeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnip 144
                                       f++V + ++++++ +v+t+ + y+++++i+A G  +   + +i+
  gi|330507596|ref|YP_004384024.1| 112 FSRVLNYSSKEDHVSVQTDDQIYRSRFLIVASGC-QDSLRSRIS 154
                                       6788899999***********************8.444445555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   2.7e-06     0.003       2      61 ..       4      60 ..       3      86 .. 0.75
   2 !    9.6   0.1   0.00032      0.36     141     371 ..      80     310 ..      58     360 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-06
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE--THHHHTHHHHT--HH CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeatipsirkllrlLgidee 61
                                      +v+vG+G+aG++aA + a ++   l+v+++e+e++++++   +++ +  +    L ++e+
  gi|330507596|ref|YP_004384024.1|  4 LVVVGAGPAGSTAARIAAGMG---LKVLILEKEKFPRYKPCGGALSERATSWLDLRLPEA 60
                                      79************9998888...9*************9888777777776666666666 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00032
                                       S-B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIII CS
                    Trp_halogenase 141 glsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqa 217
                                        ++a   +  ++++ +++fL + a + G  +   +v +   +e ++v s+++ d++ +  ++ i +sG +  l ++ 
  gi|330507596|ref|YP_004384024.1|  80 KVKAYRLSTLINRSAFDQFLLQKAIETGASVSFSRVLNYSSKE-DHV-SVQT-DDQIYRSRFLIVASGCQDSLRSRI 153
                                       5566666667899**********************97666554.455.5666.7888***********999988876 PP

                                       T---EEE-TTT----EEEEEEEE--H.---SSEE.......EEE-SSEEEEEEEETTEEEEEEE.E-TTTS-HHHHH CS
                    Trp_halogenase 218 LktgfedwsdvLltdrAlavqvesee.lvepytr.......ataekaGWtWkiPLqhrlgnGyv.yssahadddeAl 285
                                         +g  +  d+      l++++e ++  +e++ +             G  W  P ++ ++ G+   +s+     + +
  gi|330507596|ref|YP_004384024.1| 154 --SGKASRDDI---GVCLVTEIEADDrDIEARLGsfldihfG-IAGGGYGWIFPHRGYYSVGIGgLASQLRHPRMIM 224
                                       ..444444443...3456666666665444444422223211.2234566666666666655532455555566666 PP

                                       HHHHHHCT--TTTS-EEEE---.EEES-SEETTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BTT--HHHHH CS
                    Trp_halogenase 286 aellaeldgkleaeprkirftt.GrrkqawvknvvalGlasgfvePlestsihliqaalrrLlallpdksdepaaia 361
                                       + +l++ +++ ++  +   + + G++k++    v++ G+a++ v+   + +i+ + ++ +  ++ + +++ +++ + 
  gi|330507596|ref|YP_004384024.1| 225 KGFLENNGFDRDQIIHGHTIPQgGKKKRISLGRVLLTGDAASLVDSFSGEGIYYALRSGEMAARAIGEEKERDV-AR 300
                                       66666666666666655444441444555555555666666666666666666666666655555555543333.34 PP

                                       HHHHHHHHHH CS
                    Trp_halogenase 362 efnrevarel 371
                                        ++++ ++el
  gi|330507596|ref|YP_004384024.1| 301 LYEKRCNKEL 310
                                       5666555555 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 !   26.3   0.0   3.6e-09   4.1e-06       1     152 [.       2     196 ..       2     197 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.6e-09
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE..............TTHCHHHCSHHHHCHHHHHHHHHHHHH...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve..............legtclnggcllskallgvaedaeias...... 57 
                                       +d+vv+G+GpAG +aa+ +a  g+kv+++e              +e+++ + +  l++a+++ a  +  ++      
  gi|330507596|ref|YP_004384024.1|   2 FDLVVVGAGPAGSTAARIAAGMGLKVLILEkekfprykpcggalSERATSWLDLRLPEAVCEKAITGARIHyhewvq 78 
                                       589**************************755655555555666555555555555444444444444444788889 PP

                                       ....................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC CS
                                       ....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ....................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl 114
                                                              k +++g  +     v+++  ++ +v ++     d + +    l++A+G++  + 
  gi|330507596|ref|YP_004384024.1|  79 dkvkayrlstlinrsafdqfLLQKAIETGASVSFS-RVLNYSSKEDHVSVQ----TDDQIYRSRFLIVASGCQDSLR 150
                                       88888888777777666665222345555555555.666666666666663....4557999999******866655 PP

                                       .TCTTC....TTBEECCSECHHHHHHCCSS-T....SEEEEES-SH CS
                                       .xxxxx...xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                       Pyr_redox_2 115 .gipGv...aenvgklvrtldsaealklkllp....krivvvGgGy 152
                                         i G     + ++ lv +++ +++  ++ l      ++ + GgGy
  gi|330507596|ref|YP_004384024.1| 151 sRISGKasrDDIGVCLVTEIEADDRDIEARLGsfldIHFGIAGGGY 196
                                       5999887776777777777777777666666667667777777776 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   0.0   6.1e-09   6.9e-06       1     150 [.       3     145 ..       3     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 6.1e-09
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEEEEEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvrEidalggliikaadkagiqfril 77 
                                       d++V+G+G AG+ AA  aa +G+kvl++ +k +     +C  ++   a + l  +++  + ++ ka+  a+i+++  
  gi|330507596|ref|YP_004384024.1|   3 DLVVVGAGPAGSTAARIAAGMGLKVLIL-EKEKFPRYKPCGGALSERATSWL--DLRLPEAVCEKAITGARIHYHEW 76 
                                       689**********************999.44444455689999998898888..68888899999999999999999 PP

                                       STTS-CCC-EEEEEE-HHHHHHHH.HHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA  78 NrskGpavralraqvdrelyskev.teklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                        + k +a r   + ++r+++ + + ++++e+    ++   +v + + +e+  ++ v++d+++++++  ++a+G 
  gi|330507596|ref|YP_004384024.1|  77 VQDKVKAYRLS-TLINRSAFDQFLlQKAIETGA--SVSFSRVLNYSSKED--HVSVQTDDQIYRSRFLIVASGC 145
                                       99999999877.899999999975267777744..455556666655333..3345677888888899999997 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   3.4e-06    0.0038       1      32 [.       3      36 ..       3      60 .. 0.85
   2 !    6.1   0.0    0.0061       6.9     142     203 ..      89     146 ..      45     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.4e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSST CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdia 32
                                      d+v++G+G +G+++A+ +a  g  V++lek++++
  gi|330507596|ref|YP_004384024.1|  3 DLVVVGAGPAGSTAARIAAGMGlkVLILEKEKFP 36
                                      89****************9889********9764 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0061
                                       EEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGG CS
                               DAO 142 qvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaw 203
                                        ++  ++ ++l+++a + G+ + +  +v + + ++ + + v  +t+  + ++ + +++a G++
  gi|330507596|ref|YP_004384024.1|  89 LINRSAFDQFLLQKAIETGASVSFS-RVLNYSSKE-DHVSV--QTDdQIYRS-RFLIVASGCQ 146
                                       56889999****************9.999985542.23555..555355455.77******87 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   2.6e-07   0.00029       2      33 ..       3      34 ..       2      39 .. 0.92
   2 ?    2.0   0.0     0.061        68     114     164 ..      98     145 ..      92     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.6e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      d++v+G+G+AG  aA  aa  g +Vl+lek+k
  gi|330507596|ref|YP_004384024.1|  3 DLVVVGAGPAGSTAARIAAGMGLKVLILEKEK 34
                                      89****************************87 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.061
                                       HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       +ll+++ e+g ++  + +v + +++ed+ ++v+t +++ ++++ l++A+G 
  gi|330507596|ref|YP_004384024.1|  98 FLLQKAIETGASVSFS-RVLNYSSKEDH-VSVQT-DDQIYRSRFLIVASGC 145
                                       5677777777777765.56666676777.99**9.9*************96 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   7.8e-08   8.7e-05       1      32 [.       3      34 ..       3      56 .. 0.95
   2 ?   -2.2   0.0       1.5   1.7e+03      86     131 ..     260     303 ..     244     350 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.8e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                      D++V+G+G AG +AA  aa  Glkv+++eke+
  gi|330507596|ref|YP_004384024.1|  3 DLVVVGAGPAGSTAARIAAGMGLKVLILEKEK 34
                                      89****************************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                                       HH.THHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT CS
                     FAD_binding_2  86 ve.aapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaad 131
                                       ++  a+  vd +   g+ +   + g++++r  G+ +++  +++  + 
  gi|330507596|ref|YP_004384024.1| 260 LTgDAASLVDSFSGEGIYYAL-RSGEMAARAIGEEKER-DVAR-LYE 303
                                       444677777777777777777.6777777777777777.3333.333 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   6.9e-08   7.7e-05      19      50 ..       3      33 ..       1      45 [. 0.89

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.9e-08
                                      EEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4 19 DvvivGaGssGLtaayylakkpdlkvailers 50
                                      D+v+vGaG++G taa++ a   +lkv+ile++
  gi|330507596|ref|YP_004384024.1|  3 DLVVVGAGPAGSTAARIAAGM-GLKVLILEKE 33
                                      99**************99999.********85 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 !   19.7   0.0   6.6e-07   0.00074       1      28 [.       6      33 ..       6      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.6e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      +vGaG +G++aA+ +a  g++vl+lek 
  gi|330507596|ref|YP_004384024.1|  6 VVGAGPAGSTAARIAAGMGLKVLILEKE 33
                                      8*************************96 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.6e-06    0.0017      31      60 ..       4      33 ..       2      39 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.6e-06
                                      EEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvr 60
                                       +v+G+G aG  A+++a+g+g kV +l+++
  gi|330507596|ref|YP_004384024.1|  4 LVVVGAGPAGSTAARIAAGMGLKVLILEKE 33
                                      59************************9986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.22       2      36 ..       4      39 ..       3      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.T CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.r 36
                                      +vvvG+G  g  +A ++a +g kV ++e ++ ++ +
  gi|330507596|ref|YP_004384024.1|  4 LVVVGAGPAGSTAARIAAGMGLKVLILEKEKFPRyK 39
                                      79*************************999877755 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.32       1      31 [.       4      34 ..       4     128 .. 0.71
   2 ?   -1.1   0.0       2.3   2.6e+03      44      88 ..     305     362 ..     278     365 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-G CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpre 31
                                      lv++Gag+ +   ar+aa +g++v ++++++
  gi|330507596|ref|YP_004384024.1|  4 LVVVGAGPAGSTAARIAAGMGLKVLILEKEK 34
                                      79************************99877 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                                       E.........-EEEE--S-HHHHHHHHHHHSSS-....-SEEEESS-HHHHHHHCTTS CS
                            XdhC_C  44 e.........tavvvlthdhklDaealeaalrkk....aayigllGSrkkaarrlerl 88 
                                       +          ++++l++  +   +a +++l+++     +yi + ++++  + +++ l
  gi|330507596|ref|YP_004384024.1| 305 RcnkelgeelRYALILSQAMHRHPKAFSWMLERHnevlDRYIEIAAAKRSYKDFVRWL 362
                                       1445566667788888888888888888888643344334888888888777777665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.21      39      68 ..       4      33 ..       3      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                      EEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                      2-Hacid_dh_C 39 vGiiGlGrIGqavakrlkafgmkviaydrs 68
                                      + ++G+G  G+++a++++++g+kv++ ++ 
  gi|330507596|ref|YP_004384024.1|  4 LVVVGAGPAGSTAARIAAGMGLKVLILEKE 33
                                      679*********************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); 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:                        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 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2694.39
//
Query:       gi|330507597|ref|YP_004384025.1|  [L=111]
Description: nitrogen regulatory protein P-II [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-35  122.4   0.3    1.2e-35  122.2   0.3    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 !  122.2   0.3   6.5e-40   1.2e-35       1     102 []       6     107 ..       6     107 .. 0.99

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 6.5e-40
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       ieai+rpe+le+vkeaLe++gv +lt+te++GrG+qkg +  yrg ++ v+ll k+kle+ v de+v+ v++ai++a
  gi|330507597|ref|YP_004384025.1|   6 IEAIVRPERLERVKEALEEIGVVALTTTEIQGRGEQKGIKLQYRGGTMDVDLLTKLKLELYVADESVDPVLKAICDA 82 
                                       89*************************************************************************** PP

                                       H-SSSTTSEEEEEEEESEEEETTTT CS
                              P-II  78 aktgeiGDGkiFvlpveevirirtg 102
                                       a+tg++GDG+iFv+pve+ +++rtg
  gi|330507597|ref|YP_004384025.1|  83 ARTGKFGDGRIFVSPVERSVKVRTG 107
                                       ************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 853.41
//
Query:       gi|330507598|ref|YP_004384026.1|  [L=402]
Description: ammonium transporter [Methanosaeta concilii GP6]
Scores for complete 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-127  425.5  43.4   1.8e-127  425.4  43.4    1.0  1  Ammonium_transp  Ammonium Transporter Family
  ------ inclusion threshold ------
       0.15   10.4   1.0       0.24    9.7   1.0    1.3  1  CBP_BcsG         Cellulose biosynthesis protein BcsG


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 !  425.4  43.4    2e-131  1.8e-127       1     399 []       9     401 ..       9     401 .. 0.96

  Alignments for each domain:
  == domain 1  score: 425.4 bits;  conditional E-value: 2e-131
                                       HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-........ CS
                   Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfign........ 69 
                                       a++l+s+a+v++m++g++l+++glvr+k+v++++  ++l++a+ +l++v++Gysl+fg++  ++g ig         
  gi|330507598|ref|YP_004384026.1|   9 AWVLVSTAMVMLMTPGVGLFYGGLVRKKTVVSMIGLSFLAFALASLQWVFLGYSLSFGQD--IGGAIGAldylalng 83 
                                       7**********************************************************9..999999988866655 PP

                                       TTTTSCCGCCTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT- CS
                   Ammonium_transp  70 lglsaagvqdetlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgv 146
                                       +gl+ a +  ++l+++l+++fq++faa++++i ++avaer+++ +++++++l++tlvy p+ahwvw+ ggwla++g+
  gi|330507598|ref|YP_004384026.1|  84 IGLGEAPLA-GNLPHLLYVAFQMVFAAVTLAILTSAVAERVRLGSFIVLALLWTTLVYDPLAHWVWA-GGWLAQMGA 158
                                       555444443.4778888**************************************************.********* PP

                                       -.-SSSTTTTHHHHHHHHHHHHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.H CS
                   Ammonium_transp 147 liDfAgstvVHlvggvagLaaalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrarara 223
                                       l DfAg+tvVH+ +g+++La+a+v+gkr g +   ++ +++hn+p+a+lG+ lLwfgWfgFNaGsal+an+ a++ a
  gi|330507598|ref|YP_004384026.1| 159 L-DFAGGTVVHISSGFSALAIAMVIGKRVGFG---SYVMEPHNIPMAMLGAGLLWFGWFGFNAGSALGANGLAAS-A 230
                                       *.****************************99...9***************************************.* PP

                                       HHHHHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                   Ammonium_transp 224 avtTllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklk 300
                                        v+T+++aaagalt+ll s+lk gk++ lg+++G +AGlVAiT+a+++v+++gAl+iG+vAgvl+++++ +++   +
  gi|330507598|ref|YP_004384026.1| 231 LVVTNTSAAAGALTWLLSSWLK-GKPSALGMVSGGIAGLVAITPAAGFVDVLGALVIGAVAGVLCYMSL-LFRVSRG 305
                                       **********************.**********************************************.6****** PP

                                       C-CTTHHHHHHHHHHHHHHHHHHHHTSHHHCSSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                   Ammonium_transp 301 idDsldvvavHgvgGiwGllavgifaaekvvaskisggllsgegkqlvvqligilvilayafvvtlilllllklllg 377
                                       +d+s+d++avHg+gG+wG++a+gifa++ v+    ++gll+g+ +q+ vq++++ + ++yafvvt+ l++l++ ++g
  gi|330507598|ref|YP_004384026.1| 306 LDESCDAWAVHGMGGLWGAVATGIFATSAVN---SYTGLLQGNFNQFAVQIMAAGISVVYAFVVTYALAKLVDSFMG 379
                                       ****************************865...9****************************************** PP

                                       SB--HHHHHHSHHHHHHSSSSB CS
                   Ammonium_transp 378 LrvseeeeevglDvaehgetay 399
                                       Lrv+e+ee+vglD+++hge+ay
  gi|330507598|ref|YP_004384026.1| 380 LRVTEDEEYVGLDISQHGEKAY 401
                                       ********************99 PP

>> CBP_BcsG  Cellulose biosynthesis protein BcsG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.0   2.7e-05      0.24      91     130 ..     101     140 ..      97     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 2.7e-05
                          CBP_BcsG  91 inlkmllalivllivylllsqwirvttlvllalialsvle 130
                                       + ++m++a+++l+i+  ++++ +r+ ++++lal++++++ 
  gi|330507598|ref|YP_004384026.1| 101 VAFQMVFAAVTLAILTSAVAERVRLGSFIVLALLWTTLVY 140
                                       789********************************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2733.74
//
Query:       gi|330507599|ref|YP_004384027.1|  [L=227]
Description: hypothetical protein MCON_1568 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   12.5   0.1        2.2    8.7   0.0    2.1  2  Terminase_2  Terminase small subunit


Domain annotation for each model (and alignments):
>> Terminase_2  Terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00012       2.2      42      92 ..       4      54 ..       3     114 .. 0.77
   2 ?    1.7   0.1     0.018   3.3e+02      52      79 ..     197     224 ..     182     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00012
                       Terminase_2 42 kpkIkkaIreakaereertiieadeVlqellkiaraeitdevervklkdse 92
                                      k +I +aIreak+ + e  + +  +V++ +  ia +  ++++   k k+++
  gi|330507599|ref|YP_004384027.1|  4 KYEILQAIREAKKHLGEGSDFRIADVMETMEGIAPFLDKEVIIGLKCKNCD 54
                                      77999*************************999999888888844444443 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.018
                       Terminase_2  52 akaereertiieadeVlqellkiaraei 79 
                                       + a+++ r++++ d Vl+ ++k+ +++i
  gi|330507599|ref|YP_004384027.1| 197 LEANLQIRRQLDIDYVLEWIAKKRKMDI 224
                                       56778889************99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1734.49
//
Query:       gi|330507600|ref|YP_004384028.1|  [L=605]
Description: PIN domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   40.5   0.0      3e-10   39.6   0.0    1.3  1  T2SSE         Type II/IV secretion system protein
    7.7e-08   32.0   0.0    2.3e-07   30.5   0.0    1.8  1  KH_1          KH domain
    9.3e-08   32.6   0.0    2.1e-07   31.5   0.0    1.6  1  PIN           PIN domain
     0.0016   19.0   0.0     0.0036   17.8   0.0    1.6  1  AAA_18        AAA domain
     0.0021   18.3   0.0     0.0077   16.5   0.0    2.0  2  PIN_4         PIN domain
     0.0028   18.1   0.0      0.007   16.8   0.0    1.7  1  AAA_16        AAA ATPase domain
     0.0036   17.5   0.0      0.014   15.5   0.0    2.0  2  AAA_33        AAA domain
     0.0077   16.2   0.0      0.023   14.7   0.0    1.9  1  AAA_5         AAA domain (dynein-related subfamily)
     0.0085   15.9   0.4      0.037   13.9   0.1    2.3  1  KH_2          KH domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.052   13.4   0.0    2.0  1  KH_4          KH domain
      0.016   14.9   0.0      0.034   13.9   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.025   14.4   0.0      0.042   13.6   0.0    1.3  1  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.038   13.4   0.0      0.063   12.7   0.0    1.3  1  KTI12         Chromatin associated protein KTI12
      0.041   14.3   0.0       0.15   12.5   0.0    1.9  1  RNA_helicase  RNA helicase
      0.044   13.0   0.7      0.089   12.0   0.0    1.7  2  TIP49         TIP49 P-loop domain
      0.046   13.3   0.0       0.14   11.8   0.0    1.7  1  AAA_25        AAA domain
      0.047   13.4   0.0        0.1   12.3   0.0    1.5  1  AAA_24        AAA domain
      0.053   12.9   0.0        0.1   11.9   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.055   13.4   0.0       0.19   11.7   0.0    1.9  1  NTPase_1      NTPase
      0.067   13.6   0.0       0.16   12.4   0.0    1.6  1  AAA           ATPase family associated with various cellular 
      0.068   12.9   0.0       0.13   12.0   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein
       0.07   13.1   0.0       0.33   11.0   0.0    2.2  1  FliMN_C       Type III flagellar switch regulator (C-ring) Fl
       0.07   12.9   0.0       0.15   11.8   0.0    1.5  1  AAA_11        AAA domain
      0.078   13.0   0.0       0.17   11.9   0.0    1.5  1  AAA_14        AAA domain
      0.088   12.3   0.0       0.16   11.5   0.0    1.3  1  AAA_7         P-loop containing dynein motor region
      0.091   12.7   0.0       0.17   11.8   0.0    1.4  1  NACHT         NACHT domain
        0.1   12.9   0.0        0.3   11.4   0.0    1.7  1  AAA_22        AAA domain
       0.13   12.0   0.0       0.29   10.8   0.0    1.6  1  AAA_30        AAA domain
       0.23   12.2   0.4       0.57   10.9   0.4    1.6  1  NUP50         NUP50 (Nucleoporin 50 kDa)


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 !   39.6   0.0   4.8e-13     3e-10      68     247 ..     209     377 ..     163     398 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 4.8e-13
                             T2SSE  68 lqdarlpekgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKt 143
                                       +  a ++ + +r+ ++ +P + g e  ++R   ++++++d ++ + +lk +    l++    +  il++G+ gsGK+
  gi|330507600|ref|YP_004384028.1| 209 MGAAIIQIGPMRIAIAKPPFSDGlEITAVRP--VAKVSFDSYRHSSMLKTR----LKEG---QRGILIAGPPGSGKS 276
                                       445666688999***********99999994..556678999888776655....5666...7889*********** PP

                             T2SSE 144 tllyallkeinksderivtvEDpvEiqleganqvqlnakkakvtfadllraaLRlrPDrimvGEiRdketleilkAv 220
                                       t++  l +++ +++  + t+E p+ +q+  ++ +q  + ++++++++    +L  rPD  +  E+R +  +++   +
  gi|330507600|ref|YP_004384028.1| 277 TFAAGLAEYLLDCNYVVKTLESPRDLQVP-PEITQYGPLEGSMEASAD--ILLLVRPDYTIYDEVRKTRDFQVFADM 350
                                       *************999***********95.334444444444555544..467889*****************7666 PP

                             T2SSE 221 nTGHlgslsTlHansaagalerLeqlg 247
                                            g ++ +Han+++++l+rL   +
  gi|330507600|ref|YP_004384028.1| 351 RLAGVGMIGVVHANKPIDSLQRLLGRV 377
                                       6655666***************97544 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   3.7e-10   2.3e-07       3      42 ..     488     526 ..     486     539 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.7e-10
                                       EEEEGGGHHHHHHTGGGHHHHHHHHHH.T-EEEEESSTT.. CS
                              KH_1   3 rilvPsslvgriIGkgGsnIkeIreet.gakIkvpksedeg 42 
                                       +i+vP++ + r+IGk G+nI +I++ + g +I+v   +de+
  gi|330507600|ref|YP_004384028.1| 488 VIHVPQEDAARVIGKAGKNIDQIER-SlGMHIDVRA-RDEP 526
                                       799**********************.77*****984.3322 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   3.4e-10   2.1e-07       2     121 ..       6     120 ..       5     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3.4e-10
                                       EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.SCHCHHHHHHHHHHHHHHHTSEEEEBCHHH CS
                               PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar.rkskrekaaelvelllllsalkilpidaei 77 
                                       v DTsv+i   +g++ a+     l++  ++v++++v+aEl + ++  r+ + + ++el++l +l++a ki     +i
  gi|330507600|ref|YP_004384028.1|   6 VPDTSVVI---DGRVSARIKSGELQG-RRIVVPEAVVAELEAQANHgREIGLKGLEELRKLSELAKAGKIELEYVGI 78 
                                       67******...999999888888887.*******************9999999************************ PP

                                       HHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  78 aeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                       +    +i+l    + +Da+i  +A+e g++ + t D   +rva+
  gi|330507600|ref|YP_004384028.1|  79 RPNLDQIKLAG-GGEIDAMIRDVALELGASFL-TSDQVQSRVAE 120
                                       *********86.*****************999.****9999985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.8e-06    0.0036       1      24 [.     265     289 ..     265     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.8e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf 24 
                                       Il++G+pG+GK+t+a  L++ l  +
  gi|330507600|ref|YP_004384028.1| 265 ILIAGPPGSGKSTFAAGLAEYLlDC 289
                                       99****************9987555 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.2e-05    0.0077       2     127 ..       6     126 ..       5     130 .. 0.77
   2 ?   -2.0   0.0       6.5     4e+03       2      28 ..     385     411 ..     384     455 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-05
                             PIN_4   2 VlDTnvlLhdpealksf....keehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqtsa 74 
                                       V DT+v+++   +  ++     +  ++v+P  V+ EL+++ ++ +  e++ +  + +r l el +  + +l     +
  gi|330507600|ref|YP_004384028.1|   6 VPDTSVVIDGRVSA-RIksgeLQGRRIVVPEAVVAELEAQANHGR--EIGLKGLEELRKLSELAKAGKIELEYVGIR 79 
                                       89999999876443.33456779999**************99998..999999999999999998888888777777 PP

                             PIN_4  75 eelpee.eseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgiea 127
                                        +l++   + + + D +I +valel           ++ D+     A+a g+++
  gi|330507600|ref|YP_004384028.1|  80 PNLDQIkLAGGGEIDAMIRDVALELGASF-------LTSDQVQSRVAEAMGLDV 126
                                       7777764444789**********998764.......555655555666666665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.5
                             PIN_4   2 VlDTnvlLhdpealksfkeehdvviPi 28 
                                       V+DT v+++  e+ k ++ e  v +P 
  gi|330507600|ref|YP_004384028.1| 385 VVDTVVFIERGEVTKVLDVEFVVKVPS 411
                                       899999999988888775566565554 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     0.007      15      51 ..     253     289 ..     249     377 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                            AAA_16  15 ale.rvrsgrpelvllsGesGvGKsslvrellralekd 51 
                                       +l+ r+++g+ + +l+ G++G+GKs+ +  l+++l + 
  gi|330507600|ref|YP_004384028.1| 253 MLKtRLKEGQ-RGILIAGPPGSGKSTFAAGLAEYLLDC 289
                                       6773455555.9****************9999887765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         7   4.3e+03      18      39 ..      99     120 ..      96     153 .. 0.77
   2 !   15.5   0.0   2.3e-05     0.014       2      23 ..     265     286 ..     265     319 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7
                            AAA_33  18 rllkklgavllssdtlrrrlfg 39 
                                        ++ +lga +l+sd++ +r+++
  gi|330507600|ref|YP_004384028.1|  99 DVALELGASFLTSDQVQSRVAE 120
                                       5667899999999999998876 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.3e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkkl 23 
                                       +l+ G+pGsGKst+a +l++ l
  gi|330507600|ref|YP_004384028.1| 265 ILIAGPPGSGKSTFAAGLAEYL 286
                                       5789*************99654 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.8e-05     0.023       2      33 ..     265     297 ..     264     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-05
                                       EEEE--SSSSHHHHHHHGGGGB.S--EEEEE-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqlt 33 
                                       +l+ GppG+gKs++a  la+ l  ++++++ l 
  gi|330507600|ref|YP_004384028.1| 265 ILIAGPPGSGKSTFAAGLAEYLlDCNYVVKTLE 297
                                       7999****************9998888887765 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   5.9e-05     0.037      26      59 ..     486     519 ..     463     525 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-05
                                       EEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                              KH_2  26 rviiviresqpgivIGkgGsnikkigkelrkdie 59 
                                        ++i +  +  ++vIGk G+ni++i+  l+  i+
  gi|330507600|ref|YP_004384028.1| 486 SAVIHVPQEDAARVIGKAGKNIDQIERSLGMHID 519
                                       556666677889****************998885 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.5e-05     0.052      29      52 ..     485     508 ..     476     511 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.5e-05
                              KH_4  29 veielnvegedlGrvIGkrGrtld 52 
                                        +  ++v +ed +rvIGk G+++d
  gi|330507600|ref|YP_004384028.1| 485 SSAVIHVPQEDAARVIGKAGKNID 508
                                       566899****************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 ?   13.9   0.0   5.5e-05     0.034      21      38 ..     262     278 ..     248     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-05
                            AAA_29  21 lkgatlltGpsGsGKSTl 38 
                                       ++  +l++Gp GsGKST+
  gi|330507600|ref|YP_004384028.1| 262 QR-GILIAGPPGSGKSTF 278
                                       34.59************7 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 ?   13.6   0.0   6.8e-05     0.042       1      28 [.     267     294 ..     267     297 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.8e-05
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsva 28 
                                       ++Gp+GsGK+tf   l+e+l ++++ v+
  gi|330507600|ref|YP_004384028.1| 267 IAGPPGSGKSTFAAGLAEYLLDCNYVVK 294
                                       79*****************999977665 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001     0.063       4      33 ..     265     294 ..     264     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EE CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvv 33 
                                       +++ G P sGKst+a+ La++l + ++ v 
  gi|330507600|ref|YP_004384028.1| 265 ILIAGPPGSGKSTFAAGLAEYLLDCNYVVK 294
                                       799*******************98877765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00024      0.15       1      24 [.     265     288 ..     265     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallk 24 
                                       i++ Gp+g GKSt+a  La+ ll+
  gi|330507600|ref|YP_004384028.1| 265 ILIAGPPGSGKSTFAAGLAEYLLD 288
                                       6899***************99984 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014     0.089      49      74 ..     261     286 ..     250     294 .. 0.82
   2 ?   -2.6   0.2       3.8   2.4e+03     276     311 ..     384     424 ..     378     427 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  49 aGravLlaGpsgtGktalaiaiskel 74 
                                       + r++L+aGp+g+Gk+  a ++++ l
  gi|330507600|ref|YP_004384028.1| 261 GQRGILIAGPPGSGKSTFAAGLAEYL 286
                                       569******************99866 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.8
                                       XXXXXXXXXX..X.XXXXXXXXXXXX.XXXXXXXXX.XXXX CS
                             TIP49 276 eivpGvlfiD..e.vhmlDiecfsyl.nralesela.Pivi 311
                                       ++v  v+fi+  e +++lD+e    + +  +e +la P+++
  gi|330507600|ref|YP_004384028.1| 384 QVVDTVVFIErgEvTKVLDVEFVVKVpSGMVEADLArPVIV 424
                                       78888999973332468899876655134567777756665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00022      0.14      36      54 ..     265     283 ..     239     294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +l+aG+pg+GK+t+a  la
  gi|330507600|ref|YP_004384028.1| 265 ILIAGPPGSGKSTFAAGLA 283
                                       4679***********9997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017       0.1       5      22 ..     265     282 ..     262     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       ili Gp+g+GK+t+a+ l
  gi|330507600|ref|YP_004384028.1| 265 ILIAGPPGSGKSTFAAGL 282
                                       89*************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 ?   11.9   0.0   0.00017       0.1      21      47 ..     261     287 ..     255     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                      Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsllp 47 
                                       G+  +l++GppGsGK+  a+ l++ l 
  gi|330507600|ref|YP_004384028.1| 261 GQRGILIAGPPGSGKSTFAAGLAEYLL 287
                                       78899**************99987765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0003      0.19       2      31 ..     265     294 ..     264     300 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                       ++i GppG+GK+T+   ++e l + ++ v+
  gi|330507600|ref|YP_004384028.1| 265 ILIAGPPGSGKSTFAAGLAEYLLDCNYVVK 294
                                       789*****************9988888775 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00026      0.16       1      22 [.     265     286 ..     265     304 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00026
                                       EEEESSTTSSHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel 22 
                                       +l+ GppG GK+++a  +a+ l
  gi|330507600|ref|YP_004384028.1| 265 ILIAGPPGSGKSTFAAGLAEYL 286
                                       699***************9986 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 ?   12.0   0.0    0.0002      0.13      40      77 ..     255     292 ..     223     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                         IstB_IS21  40 tlsfiekkenivllGpsGvGKshlaialgveavragls 77 
                                       ++   e + +i++ Gp+G GKs +a+ l+      ++ 
  gi|330507600|ref|YP_004384028.1| 255 KTRLKEGQRGILIAGPPGSGKSTFAAGLAEYLLDCNYV 292
                                       5555566789******************9877766665 PP

>> FliMN_C  Type III flagellar switch regulator (C-ring) FliN C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00053      0.33      33      62 ..     542     571 ..     540     589 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00053
                                       EE--TTGGGCEEEEETTEEEEEEEEEEETT CS
                           FliMN_C  33 ipLdkpadepvevyvngkpiarGelgvvgg 62 
                                       + Ld  a+e v+v v++ p +++ +g+ g+
  gi|330507600|ref|YP_004384028.1| 542 LWLDGMAGESVDVSVGDEPAFTATVGRRGD 571
                                       5689999********************987 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   0.00024      0.15      19      43 ..     264     294 ..     246     333 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                            AAA_11  19 itliqGPPGtgKTktivellsqll......s 43 
                                         li GPPG+gK+++ ++l ++ll      +
  gi|330507600|ref|YP_004384028.1| 264 GILIAGPPGSGKSTFAAGLAEYLLdcnyvvK 294
                                       469*****************99975544431 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00027      0.17       5      80 ..     265     345 ..     262     352 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe....kllelileklke.......ekktylfl 70 
                                       ++i G+  +GK+t++  l++ ll  + +++  +l+++rd +   pe      le  +e   +        +  y + 
  gi|330507600|ref|YP_004384028.1| 265 ILIAGPPGSGKSTFAAGLAEYLL--DCNYVVKTLESPRDLQVP-PEitqyGPLEGSME---AsadilllVRPDYTIY 335
                                       789****************9999..889999999999996644.22122211223333...1223455557899999 PP

                            AAA_14  71 DEiqevpewe 80 
                                       DE+ + ++++
  gi|330507600|ref|YP_004384028.1| 336 DEVRKTRDFQ 345
                                       9999999887 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00025      0.16      18      66 ..     246     295 ..     241     300 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                             AAA_7  18 dtvrysyllelllkn.kkpvllvGptGtGKtviikdllkkldkekylslt 66 
                                       d+ r s +l++ lk+ ++ +l+ Gp G+GK++ +  l + l + +y+++t
  gi|330507600|ref|YP_004384028.1| 246 DSYRHSSMLKTRLKEgQRGILIAGPPGSGKSTFAAGLAEYLLDCNYVVKT 295
                                       78888888888666516789*************99988888777777665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00027      0.17       3      22 ..     265     284 ..     263     291 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       +++ G++GsGK+t++++la+
  gi|330507600|ref|YP_004384028.1| 265 ILIAGPPGSGKSTFAAGLAE 284
                                       899**************997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00049       0.3       4      27 ..     261     284 ..     257     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00049
                            AAA_22   4 tagilvvtGesGtGKTtllrrlle 27 
                                       +++ +++ G++G+GK+t ++ l+e
  gi|330507600|ref|YP_004384028.1| 261 GQRGILIAGPPGSGKSTFAAGLAE 284
                                       78889************9988776 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   0.00047      0.29      10      42 ..     254     286 ..     250     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00047
                            AAA_30  10 vealltsgdrvavltGpAGtGKttalkalreaw 42 
                                       +++ l++g+r  ++ Gp+G+GK+t  ++l+e +
  gi|330507600|ref|YP_004384028.1| 254 LKTRLKEGQRGILIAGPPGSGKSTFAAGLAEYL 286
                                       666778899999**************9999876 PP

>> NUP50  NUP50 (Nucleoporin 50 kDa)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   0.00092      0.57      25      48 ..     569     592 ..     563     602 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00092
                                       XXXXXXXXSHHHHCS-S-S---TT CS
                             NUP50  25 agtfkkAseevLakRkIkkakrrv 48 
                                       +g+ + A ++++akR Ikk+k+  
  gi|330507600|ref|YP_004384028.1| 569 RGDIRIAKSSEMAKRIIKKMKKGE 592
                                       688899***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 3860.18
//
Query:       gi|330507601|ref|YP_004384029.1|  [L=163]
Description: hypothetical protein MCON_1570 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1162.21
//
Query:       gi|330507602|ref|YP_004384030.1|  [L=227]
Description: hypothetical protein MCON_1571 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        7.9    7.1   8.9        5.5    7.6   7.2    1.7  2  Alpha_GJ  Alphavirus glycoprotein J


Domain annotation for each model (and alignments):
>> Alpha_GJ  Alphavirus glycoprotein J
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.27   4.9e+03      72      72 ..      43      43 ..      11      83 .. 0.55
   2 ?    7.6   7.2    0.0003       5.5      20      70 ..      74     121 ..      61     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.27
                          Alpha_GJ 72 a 72
                                      a
  gi|330507602|ref|YP_004384030.1| 43 A 43
                                      1 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0003
                          Alpha_GJ  20 tpkaalatgttatvgaanaaavanatganatsaaaastiaatvgapptdst 70 
                                        pka+ a   +a++ga n    + +t +nats + a+++a t++ pp++ +
  gi|330507602|ref|YP_004384030.1|  74 DPKASRAEAEAASIGAENE---SASTVDNATSEENATAMAETTELPPAEVA 121
                                       4667777766666666666...66888999999999999999998887753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1645.30
//
Query:       gi|330507603|ref|YP_004384031.1|  [L=877]
Description: DNA mismatch repair protein MutS [Methanosaeta concilii GP6]
Scores for 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-83  278.1   0.5    7.2e-83  277.3   0.5    1.4  1  MutS_V     MutS domain V
    5.3e-41  140.9   5.3    8.3e-41  140.3   4.2    1.8  2  MutS_III   MutS domain III
    3.3e-40  136.9   0.0    6.9e-40  135.8   0.0    1.6  1  MutS_I     MutS domain I
    4.9e-29  100.5   0.0    1.1e-28   99.4   0.0    1.6  1  MutS_IV    MutS family domain IV
    1.1e-13   51.7   0.2    6.6e-13   49.1   0.0    2.4  2  MutS_II    MutS domain II
     0.0014   18.6   0.0     0.0089   16.1   0.0    2.3  2  AAA_14     AAA domain
     0.0092   15.6   0.0      0.024   14.2   0.0    1.6  1  AAA_27     AAA domain
  ------ inclusion threshold ------
       0.06   13.8   0.5       0.37   11.3   0.0    2.4  3  AAA_23     AAA domain
      0.077   13.5   0.1       0.97   10.0   0.0    2.8  3  ABC_tran   ABC transporter
      0.092   12.5   0.0        0.2   11.4   0.0    1.5  1  AAA_29     P-loop containing region of AAA domain
       0.12   12.1   0.1       0.35   10.6   0.1    1.8  1  AAA_30     AAA domain
       0.14   12.1   3.0       0.18   11.8   0.6    2.4  2  T3SS_ExsE  Type III secretion system ExsE


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 !  277.3   0.5   4.8e-86   7.2e-83       1     188 []     610     797 ..     610     797 .. 0.99

  Alignments for each domain:
  == domain 1  score: 277.3 bits;  conditional E-value: 4.8e-86
                                       EEEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--T CS
                            MutS_V   1 llitGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknate 77 
                                       +++tGpnmaGkst++rq+al +++aq+Gsfvpa++a++s+vd++ftRvga Ddl+ g+stFmvEm+E+a+il++at+
  gi|330507603|ref|YP_004384031.1| 610 IILTGPNMAGKSTFMRQIALTAIMAQTGSFVPAAYASLSLVDQVFTRVGAYDDLSAGQSTFMVEMTEIAHILTSATR 686
                                       599************************************************************************** PP

                                       TSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEEEEEEE CS
                            MutS_V  78 kslvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavkeeeedivflykvk 154
                                       kslv+lDE+GRGtst+dGl++a+a+ eyl+e+ik+k++fatHyh+lt+l++ l+ v+n+++avke++ +i+fl++v 
  gi|330507603|ref|YP_004384031.1| 687 KSLVLLDEVGRGTSTFDGLSLAWAISEYLHESIKCKSVFATHYHQLTDLESILSGVRNYSIAVKEDKGTITFLRTVV 763
                                       ***************************************************************************** PP

                                       ES--SS--HHHHHHHTT--HHHHHHHHHHHHHTT CS
                            MutS_V 155 egaaeksyGikvaklaglPesvverArevlkele 188
                                       +ga++ksyG++va+lag+P++v +rA+++l+e+e
  gi|330507603|ref|YP_004384031.1| 764 PGATDKSYGVHVARLAGVPRTVTKRADQILREIE 797
                                       *****************************99986 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.3   4.2   5.6e-44   8.3e-41       2     191 .]     264     558 ..     263     558 .. 0.95
   2 ?   -1.5   0.0       1.7   2.6e+03      68      95 ..     722     750 ..     709     856 .. 0.62

  Alignments for each domain:
  == domain 1  score: 140.3 bits;  conditional E-value: 5.6e-44
                                       HHHHTTSSS-TTS.SSSS-HHHHH---SSHHHHHHHHHHHH--BS-HHHHHHHHHHHHH.T..TT.HHHHHHHHTT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                          MutS_III   2 TlrnLeilenlrggskegsLlgvldrTvTamGaRlLrewllqPltdleeInaRldaVee.leneelreelrellrrl 77 
                                       T+rnLei++n+r+ s++g+Ll++ld+T+TamGaR L +wl  Pl++ + I +Rld Vee  +++ l  +l e+l+  
  gi|330507603|ref|YP_004384031.1| 264 TVRNLEITRNIRDRSRRGTLLEFLDQTRTAMGARTLARWLQMPLQSEQAIARRLDGVEElASKSLLHRSLAEELKGT 340
                                       99********99999********************************************77788888899999**** PP

                                       --HHHHHHHHHTT---HHHHHHHHHHHHHHHTTTTT---SSTHHHHH............HHHHHHHHHHB-SS--SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxx RF
                          MutS_III  78 pDleRllsrislgkakardlkallealkaleelvallekeklaesee............eslaelleeaideeplal 142
                                       +DleRllsris ++a++++l+ l ++l+ l+ l+++l +++++ +++            +++ +l+e++i+e+p+ +
  gi|330507603|ref|YP_004384031.1| 341 SDLERLLSRISCKSASPKELSVLKSTLEMLPRLQEILMDDQSSAQSSylqdlssrlsplDDIVSLIERSIMEDPPVH 417
                                       ************99***********************999887776699888766655444449************* PP

                                       GGGS--B-T.................................................................... CS
                                       xxxxxxxxx.................................................................... RF
                          MutS_III 143 ekegedlra.................................................................... 151
                                        ++g+++r+                                                                    
  gi|330507603|ref|YP_004384031.1| 418 VRDGGVIREgydpeidqlrellrdgrgwisrlegsekertgikslkiafnnvfgyyievsranlhlvpqnyirkqtl 494
                                       ***************************************************************************** PP

                                       ........................HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH CS
                                       ........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III 152 ........................iealeqelfqelleeveealerlrrlaealaeLDvllSlA 191
                                                                 +leqelf ++++ v++++ ++++ a+alaeLDvl+SlA
  gi|330507603|ref|YP_004384031.1| 495 angerfvtpelkdmesrvlsaqerSVSLEQELFYKVRDLVASKAGVIQERATALAELDVLISLA 558
                                       *********************99999999***********9999*******************9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.7
                                       HHHHHH.HTT---HHHHHHHHHTT---HH CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III  68 eelrel.lrrlpDleRllsrislgkakar 95 
                                       ++++++  ++l Dle +ls + + +  ++
  gi|330507603|ref|YP_004384031.1| 722 KSVFAThYHQLTDLESILSGVRNYSIAVK 750
                                       44444435567788888887776544333 PP

>> MutS_I  MutS domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8   0.0   4.6e-43   6.9e-40       2     111 ..       8     118 ..       7     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 4.6e-43
                                       HHHHHHHCCCHH-TTCEEEEEETTEEEEECHHHHHHHHHCSSSSTT.ESSSSC..EEEEEEEHHHHHHHHHHHHHTT CS
                            MutS_I   2 plmkqylelkkkykdavlffrvGdfYelfgeDAviaareleitltkrkksseke.ipmagvPehalekylrkLvekg 77 
                                       plm+qy + kk y+da+l+frvGdfYe+f++DAvi+ar l+itlt+r+k+ + e ip agvP+h+l+ yl++L+++g
  gi|330507603|ref|YP_004384031.1|   8 PLMEQYYQNKKLYPDALLLFRVGDFYETFADDAVIVARDLNITLTSRQKDDQGEkIPLAGVPYHSLDAYLARLIRAG 84 
                                       9**********************************************96666666********************** PP

                                       -EEEEEEE-S-HHHHS.S--EEEEEEEBTTC-TT CS
                            MutS_I  78 ykVavveqtetpaekkgvvkrevvrviTpGtltd 111
                                       +kVa+++q+e+p+ ++g+vkr ++rv+TpGt+++
  gi|330507603|ref|YP_004384031.1|  85 HKVAICDQVEDPKLARGLVKRAITRVVTPGTIIE 118
                                       *******************************986 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4   0.0   7.2e-32   1.1e-28       1      92 []     427     518 ..     427     518 .. 0.99

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 7.2e-32
                                       TTSHHHHHHHHHHHHHHHHHHHHHCCCCCCCT-TTBEECCCSSSEEEEEE-TCCCTTT--SEEEEEECTCEEEEECC CS
                           MutS_IV   1 gfdeeLdelrdrleelekeleeleekereklgikslkveynkvlGyylevtrseakkvpkefirlqtlknserytta 77 
                                       g+d+e+d+lr++l++ + ++ +le +e+e++gikslk+ +n+v+Gyy+ev+r + + vp+++ir+qtl n+er++t+
  gi|330507603|ref|YP_004384031.1| 427 GYDPEIDQLRELLRDGRGWISRLEGSEKERTGIKSLKIAFNNVFGYYIEVSRANLHLVPQNYIRKQTLANGERFVTP 503
                                       8**************************************************************************** PP

                                       CHHHHHHHHHHHHHH CS
                           MutS_IV  78 elkkleaelleaeee 92 
                                       elk++e ++l+a+e+
  gi|330507603|ref|YP_004384031.1| 504 ELKDMESRVLSAQER 518
                                       ************986 PP

>> MutS_II  MutS domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   4.4e-16   6.6e-13       1     128 [.     128     239 ..     128     247 .. 0.82
   2 ?   -1.4   0.1       1.8   2.6e+03      34      60 ..     342     370 ..     332     407 .. 0.51

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 4.4e-16
                                       -EEEEEEEETTTSEEEEEEEETTTTEEEEEEEEE-HHHHHHHHHH-ESEEEEESS-SCCCHHHHHHCHCTTT-EEEE CS
                           MutS_II   1 nylaAisekregrrvGlafiDlstgefvvsefedfeeleaeLsrlsPkElllpedlsestaeeessklrelrsrvgv 77 
                                       n+laAi++   +  vGlaf+D+stgef ++e++   +l +eL+r+ P+E+l   +l+ + +             ++ 
  gi|330507603|ref|YP_004384031.1| 128 NFLAAIVK--GDENVGLAFVDVSTGEFLTTEVP-HNRLYSELARFRPAECLSAFSLHWEGT------------SLQI 189
                                       89*****9..66669******************.6*********************88854............6666 PP

                                       ESCCCCSHCCHHHHCHHHB--STTTTTTTGGG-HHHHHHHHHHHHHCCCCC CS
                           MutS_II  78 retvefesekaserleedfsvedldgfglekekklalaAlgalisYleetq 128
                                        e+  f+ e a+  l++ ++    + + l ++  l+ +A+ga++sYl    
  gi|330507603|ref|YP_004384031.1| 190 LEEPCFSAERAEAALADRYGPDWKERLRL-EGRGLSQRACGAVLSYLNASR 239
                                       66667888888888888887777677666.77788999********97655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                                       E-HHHHHHHHH..H-ESEEEEESS-SCCC CS
                           MutS_II  34 dfeeleaeLsr..lsPkElllpedlsest 60 
                                       d e+l++++s    sPkEl + ++ +e+ 
  gi|330507603|ref|YP_004384031.1| 342 DLERLLSRISCksASPKELSVLKSTLEML 370
                                       44444444432345566654444444443 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.4     2e+03      60      74 ..     251     264 ..     233     281 .. 0.75
   2 !   16.1   0.0     6e-06    0.0089       2      75 ..     607     697 ..     606     715 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.4
                            AAA_14  60 lkeekktylflDEiq 74 
                                       +++ +  y++lDE+ 
  gi|330507603|ref|YP_004384031.1| 251 IYS-GSDYMVLDEVT 264
                                       444.899******96 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 6e-06
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell......vkkesilyinldderd........kkladpe....kllelilekl 60 
                                       ++++++tG+  +GK+t+++q++ + +        +  +  ++l d+ +              +    +++ ++ e  
  gi|330507603|ref|YP_004384031.1| 607 NRLIILTGPNMAGKSTFMRQIALTAImaqtgsFVPAAYASLSLVDQVFtrvgayddL-----SagqsTFMVEMTEI- 677
                                       6899*****************999989777665556666666666666554443221.....13333333333332. PP

                            AAA_14  61 ke......ekktylflDEiqe 75 
                                        +       +k++++lDE+ +
  gi|330507603|ref|YP_004384031.1| 678 -AhiltsaTRKSLVLLDEVGR 697
                                       .0234456899*******976 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      12      46 ..     593     627 ..     587     633 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                            AAA_27  12 GkftdrsldfsaeeadlhliyGpNEAGKstalrAi 46 
                                       G f  + + +++++++l ++ GpN AGKst +r i
  gi|330507603|ref|YP_004384031.1| 593 GAFVPNDVLLDTDRNRLIILTGPNMAGKSTFMRQI 627
                                       7788888899999******************9965 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.1   1.7e+03     111     192 ..     337     367 ..     261     443 .. 0.52
   2 ?   11.3   0.0   0.00025      0.37      19      41 ..     607     629 ..     595     673 .. 0.89
   3 ?   -3.2   0.1       6.5   9.7e+03     133     143 ..     819     844 ..     783     875 .. 0.48

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                            AAA_23 111 lleideleqfisellgskkiilnlilflgqerfeefelkdkkerleelekeleeledekkllekleqekekekelee 187
                                       l ++++le+++s++ +++ +                                                    kel+ 
  gi|330507603|ref|YP_004384031.1| 337 LKGTSDLERLLSRISCKSAS---------------------------------------------------PKELSV 362
                                       22223333333332222222...................................................222222 PP

                            AAA_23 188 leeel 192
                                       l+++l
  gi|330507603|ref|YP_004384031.1| 363 LKSTL 367
                                       22222 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00025
                            AAA_23  19 kgltlItGpNGaGKTTildAikl 41 
                                       + l ++tGpN aGK+T+++ i l
  gi|330507603|ref|YP_004384031.1| 607 NRLIILTGPNMAGKSTFMRQIAL 629
                                       5799**************98876 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6.5
                            AAA_23 133 nlilflgqer...............f 143
                                       +li+f g e+                
  gi|330507603|ref|YP_004384031.1| 819 QLIFFDGNEDgntageverdkkdpiL 844
                                       45555555556554433332222220 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.5   9.7e+03      54      80 ..     474     512 ..     459     546 .. 0.66
   2 ?   10.0   0.0   0.00065      0.97       3      32 ..     599     628 ..     597     639 .. 0.84
   3 ?   -1.4   0.0         2     3e+03     107     134 ..     661     694 ..     642     696 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.5
                                       HHHCCHCEEEE-SS--S-TTSBHHHH............H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx............x RF
                          ABC_tran  54 leslrkeigvlpqepqlfpeltvren............e 80 
                                       +e++r+++  +pq+   +++l ++e+             
  gi|330507603|ref|YP_004384031.1| 474 IEVSRANLHLVPQNYIRKQTLANGERfvtpelkdmesrV 512
                                       567778888888886666666666666666555433330 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00065
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlklla 32 
                                       +v l+  +++++ ++G+n aGKSt+++ +a
  gi|330507603|ref|YP_004384031.1| 599 DVLLDTDRNRLIILTGPNMAGKSTFMRQIA 628
                                       66778889999***************9987 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2
                                       GGS-HHHHH....HHHHHHHH..HHTSSEEEEES CS
                                       xxxxxxxxx....xxxxxxxx..xxxxxxxxxxx RF
                          ABC_tran 107 ssLSgGqkq....rvalaral..lkkpkllllDE 134
                                         LS Gq      + ++a +l  +++++l+llDE
  gi|330507603|ref|YP_004384031.1| 661 DDLSAGQSTfmveMTEIAHILtsATRKSLVLLDE 694
                                       7788888764444567887762256788999998 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013       0.2      17      40 ..     602     625 ..     594     645 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                            AAA_29  17 ieidlkgatlltGpsGsGKSTllD 40 
                                       ++ d++  ++ltGp+ +GKST++ 
  gi|330507603|ref|YP_004384031.1| 602 LDTDRNRLIILTGPNMAGKSTFMR 625
                                       5666666899***********984 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   0.00023      0.35      15      98 ..     604     696 ..     600     733 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                            AAA_30  15 tsgdrvavltGpAGtGKttalkal.reaweaaggrviglAp.tgkaAkvLaeelgi......eastiakllkrlk.. 81 
                                       t+++r+ +ltGp  +GK+t ++++   a+ a+ g+ + +A  +    +++ + +g+        st    ++  +  
  gi|330507603|ref|YP_004384031.1| 604 TDRNRLIILTGPNMAGKSTFMRQIaLTAIMAQTGSFVPAAYaSLSLVDQVFTRVGAyddlsaGQSTFMVEMT--Eia 678
                                       67889*****************99634444444455544430334444444444422222112222222222..133 PP

                            AAA_30  82 ..grarlepgtllivDEag 98 
                                           ++ ++++l++ DE+g
  gi|330507603|ref|YP_004384031.1| 679 hiL-TSATRKSLVLLDEVG 696
                                       321.234556888888887 PP

>> T3SS_ExsE  Type III secretion system ExsE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6   0.00012      0.18      13      36 ..     296     319 ..     288     322 .. 0.92
   2 ?   -0.8   0.1         1   1.5e+03      15      34 ..     328     347 ..     320     348 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                       HHHHHHHCTT-TTHHHHHHHHHHT CS
                         T3SS_ExsE  13 armLaRnvAgdlrsEqaLQRLlDG 36 
                                       ar LaR + + l+sEqa+ R lDG
  gi|330507603|ref|YP_004384031.1| 296 ARTLARWLQMPLQSEQAIARRLDG 319
                                       899********************9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1
                                       HHHHHCTT-TTHHHHHHHHH CS
                         T3SS_ExsE  15 mLaRnvAgdlrsEqaLQRLl 34 
                                       +L R +A +l+    L RLl
  gi|330507603|ref|YP_004384031.1| 328 LLHRSLAEELKGTSDLERLL 347
                                       799********999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (877 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 5643.85
//
Query:       gi|330507604|ref|YP_004384032.1|  [L=571]
Description: DNA mismatch repair protein MutL [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-35  121.8   0.0    3.4e-35  121.0   0.0    1.5  1  MutL_C          MutL C terminal dimerisation domain
    2.4e-31  107.9   0.0    4.3e-31  107.1   0.0    1.4  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai
    2.5e-13   50.0   0.1    4.5e-13   49.2   0.1    1.4  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    2.1e-08   34.7   0.1    3.7e-08   33.8   0.1    1.5  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l


Domain annotation for each model (and alignments):
>> MutL_C  MutL C terminal dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.0   0.0   7.5e-39   3.4e-35       3     147 .]     384     528 ..     382     528 .. 0.96

  Alignments for each domain:
  == domain 1  score: 121.0 bits;  conditional E-value: 7.5e-39
                                       -EEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHCCHSSB-EEEEEEEEEEE--HHHHHHHHHCHHHHHHC CS
                            MutL_C   3 GkalgqvhgtyilaenedglvlvDqhaAherilyeklkeqlkeeelksQpLliPlvlelspeeaalleehkeeLakl 79 
                                       +k+lgq++  yi+ae+++glvl+DqhaA eri +e l e + e+ l +Q+L  P+++el ++e+ +l++ ke L  +
  gi|330507604|ref|YP_004384032.1| 384 LKILGQIKRLYIVAESDQGLVLIDQHAAAERIRFEGLEERYREG-LIRQELACPVTIELMASEEIMLSSWKEVLDDI 459
                                       689***************************************95.7******************************* PP

                                       T-EEEE-STTEEEEEEEECCCTTTSHHHHHHHHHHHHCCCSS.-H-HCCHHHHHHHHCTTSSSSSS--- CS
                            MutL_C  80 GfeleefgpnslivravPallrqqnleelirelleelaekgk.esleekleellatmachssvkagrrl 147
                                       Gfe+++fg++s+ vr+vPal + ++  e ++++l+el   gk     ++++e+l+ +ac++s+k g+ l
  gi|330507604|ref|YP_004384032.1| 460 GFEISSFGGRSYSVRSVPALGQRTESAESVHDVLKELFLRGKpGPDSSRRDEVLKLLACRGSIKSGKEL 528
                                       *************************************99999844569****************99876 PP

>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   0.0   9.6e-35   4.3e-31       2     114 ..     211     323 ..     210     328 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 9.6e-35
                                       HHHHHHHHHCCEEEEEEEETTEEEEEEEE-CCG-BTTGGEEEEEETTEEE--HHHHHHHHHHHHCCSSSSSB-EEEE CS
                    DNA_mis_repair   2 aavlgkevaenlleiekeeeqlkieGfiskpelsrskrdkqflfvNgRlvkskelkkaireaYkellpkgrypvvvL 78 
                                        +++g + ++ + +++++  +++ieG+i+++   r+++d++f+fvNgR+v+s+ ++ a+reaY++ +p g+ p++vL
  gi|330507604|ref|YP_004384032.1| 211 SRIFGLKAVAGMAPLQASGRGWRIEGMIGDAFNLRASPDRIFIFVNGRAVSSRPMAGALREAYRNIIPPGKSPIAVL 287
                                       5799************************************************************************* PP

                                       EEEESSGGEE-TSSTT----EETTHHCHHHHHHHHH CS
                    DNA_mis_repair  79 nleidpeevDvNvhPtKreVrfqdeeevieaieeal 114
                                       +lei+p+ vDvNvhP+Kre+r+ +e+e+++a++++ 
  gi|330507604|ref|YP_004384032.1| 288 SLEISPDLVDVNVHPAKREIRLLHENEICSAVTQEA 323
                                       ********************************9875 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 !   49.2   0.1     1e-16   4.5e-13       4     106 ..      25     128 ..      21     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1e-16
                       HATPase_c_3   4 ekAlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeak.rkstslGkkGi.Glk 78 
                                        +++ elv+Ns+dA a++v iev +    ++ i+++DdG+G+++++l  a++ +t+sk +  ++ +++G  G+ G  
  gi|330507604|ref|YP_004384032.1|  25 ASVVKELVENSIDAGAHKVLIEVRDG--GKSFIKVTDDGSGIDPDDLPLAFQKHTTSKISGaQDLETIGTLGFrGEA 99 
                                       689*********************95..689********************99999998652355567777766766 PP

                       HATPase_c_3  79 lAs.lslgkkltvitkkegesstltldvd 106
                                       lAs  s+++ ++v tk+++  s   l+++
  gi|330507604|ref|YP_004384032.1| 100 LASiASVSEAVEVRTKTRDALSGSYLRIE 128
                                       7761588999********99995544444 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 !   33.8   0.1   8.4e-12   3.7e-08       5      66 ..      23      87 ..      19     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 8.4e-12
                                      HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH......HCS CS
                         HATPase_c  5 rLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq......dds 66
                                      r   ++++lv+N++++   a+++ +e++ + ++  i+v+D+G Gi+++dl++ f+k+++      +d 
  gi|330507604|ref|YP_004384032.1| 23 RPASVVKELVENSIDA--GAHKVLIEVR-DGGKSFIKVTDDGSGIDPDDLPLAFQKHTTskisgaQDL 87
                                      56689**********6..7899999999.4478999*******************9999666533222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3693.65
//
Query:       gi|330507605|ref|YP_004384033.1|  [L=440]
Description: hypothetical protein MCON_1574 [Methanosaeta concilii GP6]
Scores for complete sequence (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   64.2   1.0    2.6e-17   63.4   1.0    1.5  1  AIRS_C    AIR synthase related protein, C-terminal domain
      3e-09   37.4   0.9    1.1e-08   35.6   0.9    2.0  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 !   63.4   1.0   2.9e-21   2.6e-17       1     153 [.     227     375 ..     227     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 2.9e-21
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgala 77 
                                       +pGdv+++t++ G g +  s++   +++e        ++d+ l  + +++ +al   + +++a++DvT+GG+ g+++
  gi|330507605|ref|YP_004384033.1| 227 RPGDVIMMTEGAGGGTIC-SAALYYNRHE--------VVDETLNIKFLEASEALLKVNARIHAMTDVTNGGIRGDAK 294
                                       79*********8877777.6666555554........778888889999999999999******************* PP

                                       HHHHTTTEEEEEECG......THHHHHHHH.HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEE CS
                            AIRS_C  78 emapasgvgaeidld......kvpifdele.splemllsensGrllvavppeeadavlaileeeglpeaavIGevta 147
                                       e+   +gv ++++++      ++++++ l+ +++++l +     ll+++ppeea+a+ a++++ g+ ++ +IG+v++
  gi|330507605|ref|YP_004384033.1| 295 EISYTAGVRLVFEEErmrklvNPRVLEMLNeLKIDYLGVSIDA-LLIIAPPEEAEAIAAAIRDVGV-KVDEIGRVEE 369
                                       ****************999999999999986666666666665.99********************.7********* PP

                                       SSSEEE CS
                            AIRS_C 148 keelsv 153
                                       +e+ ++
  gi|330507605|ref|YP_004384033.1| 370 GEGAYL 375
                                       998765 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 !   35.6   0.9   1.2e-12   1.1e-08       5      92 ..     116     215 ..     104     217 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.2e-12
                                       EEEEEEEEE.EECCTCCCC.HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EEE CS
                              AIRS   5 vvvttdshnrpvlvepvhf.iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvplv 74 
                                       ++vt+d  + ++ ++++ f +G  +  ++l+D+++mGA+P+all  + l       +l + ++g+a   e +gvpl+
  gi|330507605|ref|YP_004384033.1| 116 ITVTVD--GMHSRLSDYPFlAGFHVTRAALRDVYVMGAKPVALLSDVHLAddgdvsKLFDHIAGIATVSELIGVPLI 190
                                       367788..4444444455566********************9999999999*****99999**************** PP

                                       EEEEEEESS.......EEEEEEEEE CS
                              AIRS  75 gGdtsfsne.......ptisvtavG 92 
                                       +G t +  +       +t +v+avG
  gi|330507605|ref|YP_004384033.1| 191 TGSTLRIGGdmvigdrLTGCVGAVG 215
                                       **99876444555555666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 2402.41
//
Query:       gi|330507606|ref|YP_004384034.1|  [L=129]
Description: hypothetical protein MCON_1575 [Methanosaeta concilii GP6]
Scores for complete 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   16.9   0.0     0.0063   16.4   0.0    1.3  1  MarR_2         MarR family
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.028   14.3   0.0    1.8  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.015   15.0   0.2          2    8.1   0.0    2.0  2  Terpene_synth  Terpene synthase, N-terminal domain
      0.026   14.5   0.0      0.055   13.4   0.0    1.5  1  PadR           Transcriptional regulator PadR-like family
      0.042   13.5   0.1       0.11   12.1   0.0    1.6  1  SMC_ScpB       Segregation and condensation complex subunit S
       0.15   12.5   0.1          5    7.7   0.0    2.5  2  RuvA_C         RuvA, C-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 !   16.4   0.0   2.1e-06    0.0063       2      59 ..      24      79 ..      23      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.1e-06
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSS CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeD 59
                                      g+++     +a+L+ + +   t +e++r  +l ++ vs +l+ L +  ++e++ +  D
  gi|330507606|ref|YP_004384034.1| 24 GVPRKVSNMIAFLASGTE--ATSREIERGSDLRQPEVSIALRTLRKNNWIEEKMCRSD 79
                                      566666677889999998..9*******************************976666 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   9.4e-06     0.028      19      64 ..      38      90 ..      29      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.4e-06
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYra 64
                                      +  +at +ei + +++ ++ v  +Lr L +  ++e +  r        k+Yr 
  gi|330507606|ref|YP_004384034.1| 38 SGTEATSREIERGSDLRQPEVSIALRTLRKNNWIEEKMCRsdgtgrpMKVYRL 90
                                      56789******************************987555677774446765 PP

>> Terpene_synth  Terpene synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00066         2      54     111 ..      12      68 ..       2      76 .. 0.75
   2 ?    5.2   0.3    0.0049        15      29      65 ..      86     122 ..      70     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00066
                                       HHHHHHHHHHHTT-GGGGHHHHHHHHHHHHHT--T.T---SSSBHH..HHHHHHHHHHHT CS
                     Terpene_synth  54 ekLelidtLqrLGisyhFekEIkeiLdeiyrsweekkseeeeedle..tvAlaFrLLRqh 111
                                       + +e+++tL++LG+ ++ ++ I  +L +  ++ +++   e  +dl   +v++a r LR++
  gi|330507606|ref|YP_004384034.1|  12 RDIEVVETLKSLGVPRKVSNMIA-FLASGTEATSREI--ERGSDLRqpEVSIALRTLRKN 68 
                                       679**************999996.6777776655533..444455422799999999998 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0049
                                       HH--H....HHHHH---SSS--HHHHHHHHHHHHHHT CS
                     Terpene_synth  29 eaeklkeevrkllkavptvypkdeeekLelidtLqrL 65 
                                       ++ +lk  ++++l++ ++++ ++  + L+ i++L++L
  gi|330507606|ref|YP_004384034.1|  86 KVYRLKTPIEEILQHYEQQKMNEANQALQSIQRLKSL 122
                                       56779999*****98888666666699****999987 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.8e-05     0.055      37      65 ..      61      90 ..      44      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHTTSEEEEEE-S.TSSS-EEEEEE CS
                              PadR 37 aLkrLekeglvesewees.gegpprkyYrl 65
                                      aL++L+k++++e+++ +s g+g+p k+Yrl
  gi|330507606|ref|YP_004384034.1| 61 ALRTLRKNNWIEEKMCRSdGTGRPMKVYRL 90
                                      79***************99**********8 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.7e-05      0.11      87     138 ..      31      86 ..      14      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                          SMC_ScpB  87 etLaiIaykqpvtraeie...eiRGvnsdsvvrtLlerglieekg.rkeepgrpil 138
                                        ++a  a     t+ eie   ++R  +++ ++rtL + ++ieek  r++ +grp+ 
  gi|330507606|ref|YP_004384034.1|  31 NMIAFLASGTEATSREIErgsDLRQPEVSIALRTLRKNNWIEEKMcRSDGTGRPMK 86 
                                       5678888888888889973336999*****************98736677999975 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0017         5       5      18 ..      15      28 ..      15      47 .. 0.84
   2 ?    2.2   0.0     0.083   2.5e+02      18      29 ..     107     118 ..     105     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0017
                                      HHHHHHHHCTS-HH CS
                            RuvA_C  5 daveALlaLGYkek 18
                                      ++ve+L++LG ++k
  gi|330507606|ref|YP_004384034.1| 15 EVVETLKSLGVPRK 28
                                      89********9887 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.083
                                       HHHHHHHHHHHC CS
                            RuvA_C  18 keaekAvakvla 29 
                                       +ea++A++++ +
  gi|330507606|ref|YP_004384034.1| 107 NEANQALQSIQR 118
                                       79*****99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1315  (0.0733449); expected 358.6 (0.02)
Passed bias filter:                      748  (0.0417201); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 892.21
//
Query:       gi|330507607|ref|YP_004384035.1|  [L=165]
Description: TFIIE subunit alpha [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-19   68.9   0.6    4.2e-19   68.3   0.6    1.3  1  TFIIE_alpha   TFIIE alpha subunit
     0.0067   16.5   0.0      0.011   15.8   0.0    1.4  1  HTH_9         RNA polymerase III subunit RPC82 helix-turn-hel
     0.0098   15.3   0.0      0.016   14.6   0.0    1.4  1  RepL          Firmicute plasmid replication protein (RepL)
  ------ inclusion threshold ------
      0.011   15.5   0.2       0.14   12.0   0.0    2.2  2  HTH_IclR      IclR helix-turn-helix domain
      0.016   14.7   0.5      0.036   13.6   0.5    1.6  1  TF_Zn_Ribbon  TFIIB zinc-binding
      0.041   13.8   0.2       0.11   12.4   0.0    1.8  2  HTH_11        HTH domain
      0.048   13.6   0.7       0.16   12.0   0.0    2.1  3  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.056   13.2   0.1       0.12   12.1   0.1    1.6  1  HTH_DeoR      DeoR-like helix-turn-helix domain
      0.082   12.6   0.5       0.17   11.5   0.1    1.8  2  GntR          Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.6   2.1e-22   4.2e-19       8     105 .]      14     110 ..       2     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 2.1e-22
                                       HHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCC CS
                       TFIIE_alpha   8 rkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdv 84 
                                        k  gee   +++++  + e+t+e la++++i ln +r+ L+ Lye rl+ y+r+rd++ +w +y w++ +e+  ++
  gi|330507607|ref|YP_004384035.1|  14 NKLVGEEGLRIVECIP-EEEITDERLAELTGISLNTVRRTLYLLYEHRLAIYRRKRDPDSGWLTYLWQLCPENFDKA 89 
                                       45679**********9.89********************************************************** PP

                                       HHHHHHHHHHHHHHHHCCCTS CS
                       TFIIE_alpha  85 vkrkleevvkkLeeklekeen 105
                                       ++ + +++++kLee l  e++
  gi|330507607|ref|YP_004384035.1|  90 LQSEAKRLLRKLEERLAYEKE 110
                                       ****************99875 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 !   15.8   0.0   5.7e-06     0.011      32      59 ..      37      64 ..      24      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.7e-06
                                      HHHHHHSSTHHHHHHHHHHHHHTTSEEE CS
                             HTH_9 32 elvkktkLsldqVkksLvvLiqhrlVqy 59
                                       l+++t++sl+ V+++L++L  hrl+ y
  gi|330507607|ref|YP_004384035.1| 37 RLAELTGISLNTVRRTLYLLYEHRLAIY 64
                                      6899*********************998 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.2e-06     0.016      77     103 ..      34      60 ..      12      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.2e-06
                              RepL  77 tnRelaeetgislktvsetlkileean 103
                                       t  +lae tgisl+tv++tl  l e  
  gi|330507607|ref|YP_004384035.1|  34 TDERLAELTGISLNTVRRTLYLLYEHR 60 
                                       7789****************9998865 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     7e-05      0.14      23      47 ..      37      61 ..      21      64 .. 0.87
   2 ?    1.0   0.0      0.19   3.8e+02      33      45 ..      92     104 ..      91     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7e-05
                                      HHHHHHTS-HHHHHHHHHHHHHTTS CS
                          HTH_IclR 23 elArrtglpkStvhRlLqtLvelGy 47
                                       lA+ tg++  tv+R L  L e+++
  gi|330507607|ref|YP_004384035.1| 37 RLAELTGISLNTVRRTLYLLYEHRL 61
                                      79******************99987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHT CS
                          HTH_IclR  33 StvhRlLqtLvel 45 
                                       S + RlL+ L+e+
  gi|330507607|ref|YP_004384035.1|  92 SEAKRLLRKLEER 104
                                       8899******985 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   1.8e-05     0.036       2      29 ..     115     143 ..     114     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                       EETTTTCEECHEETSTTCEEESSS.SBEE CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdC.GlVl 29 
                                        C + + +++  +++ +++vC++C G++ 
  gi|330507607|ref|YP_004384035.1| 115 ACTEGCARFIFDEASDANFVCPFCqGSLE 143
                                       5777566665555999********99875 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.6e-05      0.11      14      42 ..      31      59 ..      22      73 .. 0.78
   2 ?   -2.3   0.0       2.2   4.5e+03      31      41 ..     153     163 ..     152     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.6e-05
                            HTH_11 14 gpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      + i+ e+LAe +++S  tvrr +  L e 
  gi|330507607|ref|YP_004384035.1| 31 EEITDERLAELTGISLNTVRRTLYLLYEH 59
                                      34999****************99887655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                            HTH_11  31 tvrrdIkaLee 41 
                                       ++ r I +L++
  gi|330507607|ref|YP_004384035.1| 153 AIERQITDLKA 163
                                       78999999997 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.9e-05      0.16      21      52 ..      32      63 ..      11      70 .. 0.81
   2 ?   -1.8   0.1       1.6   3.2e+03      40      48 ..      96     104 ..      92     112 .. 0.72
   3 ?   -2.5   0.0       2.7   5.3e+03      46      61 ..     146     160 ..     142     163 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.9e-05
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis 52
                                       +t e lA++ G++  tv r+l  L ++ l  
  gi|330507607|ref|YP_004384035.1| 32 EITDERLAELTGISLNTVRRTLYLLYEHRLAI 63
                                      6899******************9998888754 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                                       HHHHHHHHT CS
                         HTH_Crp_2  40 rilseLkre 48 
                                       r+l++L+++
  gi|330507607|ref|YP_004384035.1|  96 RLLRKLEER 104
                                       888888876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.7
                                       HHTTSEE.ETEEEEES- CS
                         HTH_Crp_2  46 kreglis.rgrririld 61 
                                       +++++++  +r  +i+d
  gi|330507607|ref|YP_004384035.1| 146 ENAKVVEaIER--QITD 160
                                       55556654343..3333 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 ?   12.1   0.1   6.1e-05      0.12      16      43 ..      34      61 ..      24      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.1e-05
                          HTH_DeoR 16 sveelvellgvSeaTiRRDLneLeeqgl 43
                                      + e+l+el g+S +T+RR L  L e  l
  gi|330507607|ref|YP_004384035.1| 34 TDERLAELTGISLNTVRRTLYLLYEHRL 61
                                      5589**************9988777655 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   8.7e-05      0.17      20      59 ..      29      67 ..      20      69 .. 0.87
   2 ?   -3.1   0.0       3.3   6.6e+03       4      13 ..     149     158 ..     147     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.7e-05
                                      TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR 20 pGdkLPsereLaaefgVsrttvReALrrLeaeglverrqg 59
                                      p++ + + + La+  g+s +tvR+ L  L +  l++ r++
  gi|330507607|ref|YP_004384035.1| 29 PEEEI-TDERLAELTGISLNTVRRTLYLLYEHRLAIYRRK 67
                                      77888.8899*****************9999999887765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.3
                                       HHHHHHHHHH CS
                              GntR   4 qvyerLredI 13 
                                       +v+e+++++I
  gi|330507607|ref|YP_004384035.1| 149 KVVEAIERQI 158
                                       5777887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      833  (0.046461); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1087.93
//
Query:       gi|330507608|ref|YP_004384036.1|  [L=133]
Description: hypothetical protein MCON_1579 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.7   0.0       0.09   12.7   0.0    1.5  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 ?   12.7   0.0     5e-06      0.09      23      60 ..      68     105 ..      64     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-06
                                       CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB  23 atadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60 
                                       ++ +e+  el+v+rs  Y + ++L+ +G+++ + g+++
  gi|330507608|ref|YP_004384036.1|  68 SEWRELLVELKVSRSAFYAMRNKLLGAGMITNKGGEYR 105
                                       66789999**********************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1051.52
//
Query:       gi|330507609|ref|YP_004384037.1|  [L=101]
Description: hypothetical protein MCON_1580 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-29  102.2   0.3    1.6e-29  102.0   0.3    1.1  1  DUF2551   Protein of unknown function (DUF2551)


Domain annotation for each model (and alignments):
>> DUF2551  Protein of unknown function (DUF2551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.3   8.9e-34   1.6e-29       2      82 ..      13      93 ..      12      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 8.9e-34
                           DUF2551  2 kkylerDksGiRrevLklfleakkltveeiyeklkekfdvsykgvasmvGliasrlGIlkvkkeskgeknvYsLkeeya 80
                                       ++l+ D++G+Rr vL+ +++++++tv +++e+++++++vs+k+vasm G+i srlGIl+++k+s++++++Y Lk+eya
  gi|330507609|ref|YP_004384037.1| 13 MNFLDLDSDGLRRVVLESMVQSQEFTVLSLHEEVSKEVNVSRKVVASMTGYIGSRLGILHMNKKSYRTPRTYALKDEYA 91
                                      69***************************************************************************** PP

                           DUF2551 81 dl 82
                                      d+
  gi|330507609|ref|YP_004384037.1| 92 DI 93
                                      97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 806.67
//
Query:       gi|330507610|ref|YP_004384038.1|  [L=125]
Description: hypothetical protein MCON_1581 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-05   25.2   3.1    2.6e-05   24.4   3.1    1.4  1  LIM            LIM domain
    0.00028   20.4   0.0    0.00047   19.7   0.0    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
     0.0066   16.2   0.0      0.011   15.5   0.0    1.3  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.019   14.9   4.6      0.041   13.8   4.6    1.5  1  zf-dskA_traR   Prokaryotic dksA/traR C4-type zinc finger
      0.025   14.6   3.1      0.052   13.6   3.1    1.5  1  DZR            Double zinc ribbon
      0.026   14.4   0.0      0.036   13.9   0.0    1.3  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.029   14.1   4.6      0.052   13.3   0.4    2.3  2  zinc_ribbon_2  zinc-ribbon domain
      0.063   12.8   0.0       0.11   12.1   0.0    1.3  1  Sigma70_r4     Sigma-70, region 4
      0.088   12.5   0.0       0.12   12.1   0.0    1.2  1  DUF4423        Domain of unknown function (DUF4423)
       0.12   12.1   0.0       0.21   11.3   0.0    1.4  1  HTH_DeoR       DeoR-like helix-turn-helix domain
       0.25   11.4   0.0       0.25   11.4   0.0    2.5  3  FeoC           FeoC like transcriptional regulator
       0.36   11.0   4.5       0.68   10.1   4.5    1.4  1  DUF1272        Protein of unknown function (DUF1272)
       0.78    9.4   5.9       0.31   10.7   1.4    2.2  2  zf_UBZ         Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   3.1   1.9e-08   2.6e-05      25      56 ..       3      34 ..       2      36 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.9e-08
                                      TTSB-TTT-SB-CTT.CEEETTEEEEHHHHHH CS
                               LIM 25 eCFtCsdCqkeLkegsfyekdgklyCkkdylk 56
                                      +C +C++C+k   e++++ ++gk +C+++y++
  gi|330507610|ref|YP_004384038.1|  3 DCIRCQKCGKDVPEDEVFATEGKTFCEDCYID 34
                                      7*****************************87 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.4e-07   0.00047       2      34 ..      66      98 ..      65     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.4e-07
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstv 34
                                       + +++I+e++q +++ +++++ +r +lS + +
  gi|330507610|ref|YP_004384038.1| 66 TDQQKEIYEYIQSQGKATMADIGKRFNLSEAEL 98
                                      6889*************************8755 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 !   15.5   0.0   8.1e-06     0.011       8      33 ..      72      97 ..      66     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.1e-06
                     HTH_AsnC-type  8 ILeaLqedaRisyaeLAervGlSest 33
                                      I e +q ++++++a++++r +lSe++
  gi|330507610|ref|YP_004384038.1| 72 IYEYIQSQGKATMADIGKRFNLSEAE 97
                                      77889*******************97 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 ?   13.8   4.6   2.9e-05     0.041       6      31 ..       7      32 ..       4      35 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                      zf-dskA_traR  6 CeeCGEpIpeaRlralPgarlCveCq 31
                                      C +CG+++pe  + a +g+++C +C 
  gi|330507610|ref|YP_004384038.1|  7 CQKCGKDVPEDEVFATEGKTFCEDCY 32
                                      *************************6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.1   3.8e-05     0.052      14      46 ..       6      43 ..       2      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                               DZR 14 fCseCgtklkavaa......edrCpsCgekvdpearfCp 46
                                       C++Cg+++++  +      +++C  C  +v+++ r+C+
  gi|330507610|ref|YP_004384038.1|  6 RCQKCGKDVPED-EvfategKTFCEDCYIDVNNRIRVCD 43
                                      6*******9854.3599999**************99997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.6e-05     0.036       5      57 ..      64     116 ..      59     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                                       HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB   5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57 
                                       GL++   ++Y ++ ++g+at+ +i ++ +++++  ++    L  + l + +k+
  gi|330507610|ref|YP_004384038.1|  64 GLTDQQKEIYEYIQSQGKATMADIGKRFNLSEAELNNQFAILRHCQLLKGKKE 116
                                       9*******************************999988887777777666665 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   3.8e-05     0.052       1      15 [.       6      20 ..       6      20 .. 0.95
   2 ?    2.2   0.4      0.12   1.6e+02      12      19 ..      24      31 ..      22      31 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                     zinc_ribbon_2  1 fCpnCGaelqdnakF 15
                                      +C +CG+ ++++++F
  gi|330507610|ref|YP_004384038.1|  6 RCQKCGKDVPEDEVF 20
                                      6***********998 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                     zinc_ribbon_2 12 nakFCpyC 19
                                      + +FC+ C
  gi|330507610|ref|YP_004384038.1| 24 GKTFCEDC 31
                                      66899998 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.8e-05      0.11       3      34 ..      63      95 ..      63      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.8e-05
                                      HHS-HHHHHHHHHHH.TTT--HHHHHHHHTS-H CS
                        Sigma70_r4  3 asLpererevlelrf.geglTleEIgerlgiSr 34
                                      + L+++++e+ e+     + T+++Ig+r+++S+
  gi|330507610|ref|YP_004384038.1| 63 DGLTDQQKEIYEYIQsQGKATMADIGKRFNLSE 95
                                      579************98888************7 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   8.6e-05      0.12      30      74 ..      76     117 ..      71     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.6e-05
                           DUF4423  30 lplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedg 74 
                                       ++ + + a+++ + kr++  +s++e ++   +L  ++llk +++g
  gi|330507610|ref|YP_004384038.1|  76 IQSQGK-ATMADIGKRFN--LSEAELNNQFAILRHCQLLKGKKEG 117
                                       555555.***********..********************99886 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.21       2      29 ..      69      96 ..      68     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                          HTH_DeoR  2 ieqilellkqqgklsveelvellgvSea 29
                                      +++i e++++qgk +  ++  +++ Sea
  gi|330507610|ref|YP_004384038.1| 69 QKEIYEYIQSQGKATMADIGKRFNLSEA 96
                                      789***********************96 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   1.2      0.75     1e+03      56      63 ..       6      13 ..       2      21 .. 0.74
   2 ?   -1.4   0.1       1.8   2.5e+03      57      61 ..      28      32 ..      14      54 .. 0.52
   3 ?   11.4   0.0   0.00018      0.25       3      33 ..      70     100 ..      69     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.75
                              FeoC 56 sCkkCggk 63
                                       C+kCg++
  gi|330507610|ref|YP_004384038.1|  6 RCQKCGKD 13
                                      59999964 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                              FeoC 57 CkkCg 61
                                      C+ C 
  gi|330507610|ref|YP_004384038.1| 28 CEDCY 32
                                      55543 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00018
                              FeoC   3 telkeyleergrvslkeLsrhfkaspealea 33 
                                       +e+ ey++ +g++ + ++ ++f+ s++ l+ 
  gi|330507610|ref|YP_004384038.1|  70 KEIYEYIQSQGKATMADIGKRFNLSEAELNN 100
                                       5889*********************998875 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.5   0.00049      0.68       7      39 ..       6      35 ..       3      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00049
                           DUF1272  7 nCecCdkdlppdseearicsyEctFCaeCaeev 39
                                      +C++C kd+p+d+   +  +   tFC++C   v
  gi|330507610|ref|YP_004384038.1|  6 RCQKCGKDVPEDE---VFATEGKTFCEDCYIDV 35
                                      7***********9...5556668******7655 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.4   0.00022      0.31       1      16 [.       3      18 ..       3      19 .. 0.88
   2 ?    0.4   0.2      0.36   4.9e+02       4       8 ..      27      31 ..      24      35 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                            zf_UBZ  1 dtylCerCgkeipese 16
                                      d++ C++Cgk +pe+e
  gi|330507610|ref|YP_004384038.1|  3 DCIRCQKCGKDVPEDE 18
                                      5789**********98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.36
                            zf_UBZ  4 lCerC 8 
                                      +Ce+C
  gi|330507610|ref|YP_004384038.1| 27 FCEDC 31
                                      8**** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      733  (0.0408835); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 884.90
//
Query:       gi|330507611|ref|YP_004384039.1|  [L=386]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-23   81.5   0.0    1.1e-22   79.7   0.0    2.0  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.4e-07   30.1   0.5    4.4e-07   30.1   0.5    1.7  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.035   14.1   0.1      0.089   12.8   0.1    1.6  1  DZR             Double zinc ribbon
      0.078   13.0   0.0       0.21   11.6   0.0    1.8  1  HypA            Hydrogenase/urease nickel incorporation, meta


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 !   79.7   0.0   2.6e-26   1.1e-22       1      67 [.     288     352 ..     288     353 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 2.6e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       f++lke+l+yka  +G+++++v+payTS+tC++Cg+ + +  +g+ fkCp Cg + d+D+n+a Ni+
  gi|330507611|ref|YP_004384039.1| 288 FYQLKEFLSYKALAAGVPLVLVDPAYTSQTCHQCGEHGIR--NGKSFKCPVCGWSGDADFNGAKNIA 352
                                       899*************************************..************************7 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1         1   4.5e+03      43      70 ..      93     128 ..      79     137 .. 0.67
   2 !   30.1   0.5   9.8e-11   4.4e-07      10     106 ..     161     255 ..     151     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1
                        OrfB_IS605  43 grrlksdykylakeiaelqsklkkskn........y 70 
                                       +  ++++ ++++++  e++ +l +s++        y
  gi|330507611|ref|YP_004384039.1|  93 SIDYDTRIFAFREKDEEISVTLLRSRQriklvlgdY 128
                                       556677778888888888888888875444444444 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 9.8e-11
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn..ykkasrklarlhrkr 84 
                                       +++    +++g+DlGi ++a++++++     + g+ +k  +  +a  +a lq+k+ k ++  ++++++ ++rl+ k 
  gi|330507611|ref|YP_004384039.1| 161 PEQIHVDTVLGVDLGITDIAVTSEGQ----KFGGKTIKLIKNHYASMRAVLQQKAVKGTRssRRRCRELQQRLSGKE 233
                                       667777899****************9....78999999999***********9998888889*************** PP

                        OrfB_IS605  85 srrrkhllhklathliktlkev 106
                                       +r  +   h+++++++ + +e+
  gi|330507611|ref|YP_004384039.1| 234 ARYQRQINHEISKAIVTRAQEI 255
                                       ****************999987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     2e-05     0.089      28      49 .]     315     338 ..     295     349 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                               DZR  28 edrCpsCgek.vdpearf.CpeCG 49 
                                       +++C +Cge  + ++++f Cp CG
  gi|330507611|ref|YP_004384039.1| 315 SQTCHQCGEHgIRNGKSFkCPVCG 338
                                       566666666666666666666666 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 ?   11.6   0.0   4.8e-05      0.21      57      95 ..     301     340 ..     242     351 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.8e-05
                                       TTT-EEE.EEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  57 legaeLe.ieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       ++g  L  ++    + +C++Cg+++  + k+++Cp Cg +
  gi|330507611|ref|YP_004384039.1| 301 AAGVPLVlVDPAYTSQTCHQCGEHGIRNGKSFKCPVCGWS 340
                                       45555553444556789*****9998777789*****965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2727.50
//
Query:       gi|330507612|ref|YP_004384040.1|  [L=105]
Description: hypothetical protein MCON_1584 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-10   40.5   3.1    2.5e-10   40.3   3.1    1.0  1  DUF1646   Protein of unknown function (DUF1646)


Domain annotation for each model (and alignments):
>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   3.1   1.4e-14   2.5e-10      95     173 ..      15      93 ..       3      97 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.4e-14
                           DUF1646  95 dklalkvfvfllivilGlassvisaivaavilaeivallplerkekvklvviasfaiGlGaaltPvGePlstiavsk 171
                                       +  +lk+++  ++ +lGl +  is ++a + l   v llp+er+ + +l++i++++i +Gaal  +  Pls ia  k
  gi|330507612|ref|YP_004384040.1|  15 KGTSLKALLTAIVAVLGLFAWTISPVLAFLALFGAVGLLPIERRVRTSLAIIGCISIVIGAALATMDFPLSQIAALK 91 
                                       5678999*******************************************************************999 PP

                           DUF1646 172 ln 173
                                       l 
  gi|330507612|ref|YP_004384040.1|  92 LM 93 
                                       85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 720.07
//
Query:       gi|330507613|ref|YP_004384041.1|  [L=576]
Description: membrane bound hydrogenase subunit [Methanosaeta concilii GP6]
Scores for 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  151.0  28.4    1.1e-43  149.5  28.4    1.8  1  Proton_antipo_M  Proton-conducting membrane transporter
     0.0006   19.2   6.6     0.0006   19.2   6.6    2.6  2  NADHdeh_related  NADH dehydrogenase I, subunit N related prot


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.5  28.4   1.3e-47   1.1e-43       1     283 [.     121     387 ..     121     398 .. 0.93

  Alignments for each domain:
  == domain 1  score: 149.5 bits;  conditional E-value: 1.3e-47
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       a+dL++ly+++E+++++++l+i    + +++ +A++ +++   +g +iLL gi++  + tg++ f+++  +      
  gi|330507613|ref|YP_004384041.1| 121 AGDLITLYFFWEIMSVASMLVIWHG-ATENAHSAGFRYIMWHIAGGIILLAGIVIYIASTGSITFDAIGWN------ 190
                                       78****************9998776.556**************************************9887...... PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqlllila 154
                                       s  + l+++l+++g+++ +++ plh Wlpday e+ + +s+ l+  + k +v++l+r +  +          l++l+
  gi|330507613|ref|YP_004384041.1| 191 SGSTYLAAMLIFLGFIINAGVPPLHAWLPDAYPESTVTGSVYLSIFTTKSAVYVLARGFTGFG--------PLMWLG 259
                                       99999**************************************889999*******9888888........9***** PP

                   Proton_antipo_M 155 iismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrd 231
                                       +i +++  + a+ +++++r+l yS i+++G+ml +++++t+ ++++a  h ++h++ k+llF+ +gsv  ++  t +
  gi|330507613|ref|YP_004384041.1| 260 AIMVIYPIFYAVLENNLRRVLSYSLINQVGFMLCGIGMGTALSLNGATSHAFAHIIYKSLLFMSVGSVLFRT-GTAK 335
                                       ********************************************************************6655.9*** PP

                   Proton_antipo_M 232 irayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslill 283
                                       i+++ggL+k+mP++ +  lv++ s+++ P+++gF+ k+++ +a+   +l ++
  gi|330507613|ref|YP_004384041.1| 336 ITDLGGLYKTMPLTTIFCLVGAASISAFPLFSGFVTKAMVVQASAFGGLAIV 387
                                       ****************************************998765554444 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 !   19.2   6.6   6.7e-08    0.0006      76     184 ..     109     216 ..      92     245 .. 0.87
   2 ?    0.3   4.8     0.043   3.9e+02     115     175 ..     300     359 ..     276     399 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.7e-08
                   NADHdeh_related  76 ivcglatlgavvtgdvfnftlflaliGianiGivaavkkefvleaafnyGlvaliatlplfggaalilastGtlsif 152
                                       +v + ++lg+v +gd+    +f  ++ +a + ++     e + +a f+y +  + + + l++g  + +astG ++  
  gi|330507613|ref|YP_004384041.1| 109 LVYAGSALGVVFAGDLITLYFFWEIMSVASMLVIWHGATENAHSAGFRYIMWHIAGGIILLAGIVIYIASTGSITF- 184
                                       56666899**************************999999999********9*********************985. PP

                   NADHdeh_related 153 elaklagdvlliaklllvlGvvGetGvaPfya 184
                                       +  + + +   +a++l+ lG + ++Gv P++a
  gi|330507613|ref|YP_004384041.1| 185 DAIGWNSGSTYLAAMLIFLGFIINAGVPPLHA 216
                                       555555556888999999***********987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.043
                   NADHdeh_related 115 efvleaafnyGlvaliatlplfggaalilastGtlsifelaklagdvlliaklllvlGvvG 175
                                          l+ a ++ +  +i    lf + + +l  tGt  i +l +l ++++l + ++ ++G + 
  gi|330507613|ref|YP_004384041.1| 300 ALSLNGATSHAFAHIIYKSLLFMSVGSVLFRTGTAKITDLGGLYKTMPL-TTIFCLVGAAS 359
                                       55688888888888999999********************999886554.56676666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3870.95
//
Query:       gi|330507614|ref|YP_004384042.1|  [L=57]
Description: hypothetical protein MCON_1587 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   14.1   0.0      0.045   13.8   0.0    1.1  1  UPF0697   Uncharacterised protein family UPF0697


Domain annotation for each model (and alignments):
>> UPF0697  Uncharacterised protein family UPF0697
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.5e-06     0.045       6      39 ..       9      42 ..       6      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-06
                           UPF0697  6 dysvheawneatnvyllvilvslglllyarknkr 39
                                      ++ v  aw+e t  y +  + ++++l+ya k  r
  gi|330507614|ref|YP_004384042.1|  9 QWPVEFAWQEVTAFYAIFGFSAFTFLIYAAKGLR 42
                                      567899***********************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 414.84
//
Query:       gi|330507615|ref|YP_004384043.1|  [L=397]
Description: hypothetical protein MCON_1589 [Methanosaeta concilii GP6]
Scores for 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-08   33.1   1.3       0.32   11.3   0.2    6.1  7  Colicin_E5  Colicin E5 ribonuclease domain
    8.2e-05   22.4  11.4       0.24   11.2   0.0    5.7  6  DUF2064     Uncharacterized protein conserved in bacteria (DU
     0.0081   16.6   0.7       0.15   12.5   0.1    3.0  3  DERM        Dermatopontin


Domain annotation for each model (and alignments):
>> Colicin_E5  Colicin E5 ribonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.91   5.4e+03      52      66 ..      28      44 ..      15      47 .. 0.55
   2 !    6.5   0.0    0.0017        10      32      68 ..      73     109 ..      71     114 .. 0.92
   3 ?    0.2   0.0      0.15   9.2e+02      32      67 ..     126     161 ..     125     168 .. 0.86
   4 ?    1.9   0.0     0.046   2.8e+02      42      67 ..     182     210 ..     165     214 .. 0.69
   5 ?    0.6   0.0      0.12     7e+02      32      67 ..     227     262 ..     225     265 .. 0.85
   6 !   11.3   0.2   5.3e-05      0.32      32      75 ..     279     322 ..     277     329 .. 0.91
   7 ?    3.1   0.0      0.02   1.2e+02      33      67 ..     344     378 ..     341     383 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.91
                        Colicin_E5 52 dsAtvYge..kdgkYvv 66
                                      d    Yg+  kdg+Y++
  gi|330507615|ref|YP_004384043.1| 28 DDVGTYGQqtKDGGYII 44
                                      33344554126899998 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0017
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvn 68 
                                       kt ++ +k +++t  gl+++    v   kd++Y++v 
  gi|330507615|ref|YP_004384043.1|  73 KTDAEGQKEWDRTYGGLGKDLGFFVQQTKDEGYIIVG 109
                                       7889999****************************96 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.15
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt ++ +  +++t  g + +   +v   +d++Y++ 
  gi|330507615|ref|YP_004384043.1| 126 KTDAKGNVLWDRTFGGSGEDLGFSVQQTNDDGYIIA 161
                                       56777788889999999999999***********96 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.046
                        Colicin_E5  42 nktsD.glrrnds..AtvYgekdgkYvvv 67 
                                       nk  D  ++r ds  A++   kdg+Y++ 
  gi|330507615|ref|YP_004384043.1| 182 NKQLDmATGRADSeaASIGLTKDGGYIIT 210
                                       33333146666643389999*******96 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.12
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt+s+ +  + kt  g +r+   +v   +dg+Y++ 
  gi|330507615|ref|YP_004384043.1| 227 KTNSKLHWDWLKTFGGPNRDLGLSVQETEDGGYIIA 262
                                       566666777889999999999*************95 PP

  == domain 6  score: 11.3 bits;  conditional E-value: 5.3e-05
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvndrtgevv 75 
                                       kt s+ d+ +++t  g + +  A+v   +dg+Y+v   +t ++ 
  gi|330507615|ref|YP_004384043.1| 279 KTDSKGDREWDRTFGGSNFDSGASVQQTRDGGYIVTGYNTTTID 322
                                       789999*****************************999998875 PP

  == domain 7  score: 3.1 bits;  conditional E-value: 0.02
                        Colicin_E5  33 tkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       t s+  + +n+t  g+r +   +v   +dg+Y++ 
  gi|330507615|ref|YP_004384043.1| 344 TDSEGIELWNETFGGTRNDWGNSVQETRDGGYIIT 378
                                       55666677999999**9999*************96 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 ?    3.5   0.2      0.01        61      96     112 ..      37      53 ..      33      60 .. 0.76
   2 ?   -2.9   0.0      0.96   5.7e+03      96     108 ..     100     112 ..      91     116 .. 0.80
   3 !   11.2   0.0     4e-05      0.24      63     107 ..     171     213 ..     137     222 .. 0.75
   4 !    4.5   0.2    0.0049        29      96     108 ..     254     266 ..     246     277 .. 0.85
   5 !    3.5   0.0    0.0097        58      95     108 ..     305     318 ..     298     338 .. 0.77
   6 ?    2.4   0.0     0.021   1.3e+02      96     108 ..     370     382 ..     367     391 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.01
                                       BTTSSEEEEEEEG-G.. CS
                           DUF2064  96 aeDGGYyllGlkkrlap 112
                                       ++DGGY++ G++++  +
  gi|330507615|ref|YP_004384043.1|  37 TKDGGYIITGYTSSYGA 53 
                                       68*********974444 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.96
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       ++D GY+++G kk
  gi|330507615|ref|YP_004384043.1| 100 TKDEGYIIVGGKK 112
                                       67889**999885 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 4e-05
                                       EEEEE-SS-TT--HHHHHHHHHHTTT-SEEEEEBTTSSEEEEEEE CS
                           DUF2064  63 pvlliGsDcpqltaalleqAfeaLeeadaVlgpaeDGGYyllGlk 107
                                       ++ +i  D+    ++ l+ A  + ++++a +g ++DGGY++ G++
  gi|330507615|ref|YP_004384043.1| 171 KAWIIKIDSQ--GNKQLDMATGRADSEAASIGLTKDGGYIITGYT 213
                                       5555555554..367899999999*******************98 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.0049
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       +eDGGY++ Gl++
  gi|330507615|ref|YP_004384043.1| 254 TEDGGYIIAGLTE 266
                                       79*********96 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.0097
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        + DGGY++ G+++
  gi|330507615|ref|YP_004384043.1| 305 QTRDGGYIVTGYNT 318
                                       578*********97 PP

  == domain 6  score: 2.4 bits;  conditional E-value: 0.021
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       + DGGY++ G+++
  gi|330507615|ref|YP_004384043.1| 370 TRDGGYIITGVTE 382
                                       57*********95 PP

>> DERM  Dermatopontin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.33     2e+03     117     135 ..      35      53 ..      16      68 .. 0.76
   2 ?   -0.4   0.0      0.24   1.4e+03      65      94 ..     153     179 ..     128     228 .. 0.51
   3 !   12.5   0.1   2.5e-05      0.15      55     139 ..     304     390 ..     278     395 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.33
                              DERM 117 sftapskrvitGvqsdfsn 135
                                       + t + +++itG +s++ +
  gi|330507615|ref|YP_004384043.1|  35 QQTKDGGYIITGYTSSYGA 53 
                                       4456678899999888865 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.24
                              DERM  65 tcpnnqyltgvesehsnskeDRrwkfqCar 94 
                                       t +++++++g +s  + +     w ++  +
  gi|330507615|ref|YP_004384043.1| 153 TNDDGYIIAGYTSFTNGK---KAWIIKIDS 179
                                       444444444444433333...234443333 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 2.5e-05
                              DERM  55 vnsydqeftftcpnnqyltgveseh...snskeDRrwkfqCartngatlsnCsttgylnsfdetlsftapskrvitG 128
                                        +  d++  +t  n + +  v s+    ++++  R+w +++ +  g +l n ++ g+ n++ ++++ t + +++itG
  gi|330507615|ref|YP_004384043.1| 304 QQTRDGGYIVTGYNTTTIDNVGSYSrlfNSDNIGRVWLIKTDSE-GIELWNETFGGTRNDWGNSVQETRDGGYIITG 379
                                       33334444445555556666655553334445579****98765.599***************************** PP

                              DERM 129 vqsdfsnskeD 139
                                       v+ ++ + keD
  gi|330507615|ref|YP_004384043.1| 380 VTESYGAGKED 390
                                       ***99999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2828.58
//
Query:       gi|330507616|ref|YP_004384044.1|  [L=500]
Description: membrane bound hydrogenase subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-58  198.3  26.6    1.6e-58  198.3  26.6    1.8  2  Proton_antipo_M  Proton-conducting membrane transporter
    4.4e-05   23.5   2.1    4.4e-05   23.5   2.1    2.8  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
       0.51   10.3   2.3        5.4    7.0   0.2    3.3  3  TRIQK            Triple QxxK/R motif-containing protein famil


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 ?   -3.4   0.1      0.73   4.4e+03     156     253 ..      39      45 ..      18      68 .. 0.57
   2 !  198.3  26.6   2.6e-62   1.6e-58       1     290 [.     130     420 ..     130     427 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.73
                   Proton_antipo_M 156 ismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrdi 232
                                       ++m                                                                          
  gi|330507616|ref|YP_004384044.1|  39 LAM-------------------------------------------------------------------------- 41 
                                       222.......................................................................... PP

                   Proton_antipo_M 233 rayggLakkmPilalvllvll 253
                                                        ++l+
  gi|330507616|ref|YP_004384044.1|  42 -----------------FLLV 45 
                                       .................2222 PP

  == domain 2  score: 198.3 bits;  conditional E-value: 2.6e-62
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       + +L++l++++E++ +++y L+    + p++l+A+ k++ + + +  +LL+gi++ y l+gt +f+       + ++
  gi|330507616|ref|YP_004384044.1| 130 SANLVTLFIFFEIITVSTYPLVIHE-QTPEALRAGHKYLAYLMPAGAFLLFGIMITYYLAGTKDFTPSGIRQLADAS 205
                                       679*******************988.778************************************987666456667 PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirllllla....vssneisql 149
                                        l +++l++++l+g++ K+a +p+h Wlp a + aP pvsall A  +vkagv++++r++  ++    + +  +  +
  gi|330507616|ref|YP_004384044.1| 206 PLVVTVLFFAFLLGFM-KAAWMPFHSWLPSA-MIAPSPVSALLhAVAVVKAGVFGIVRIVGYVIgmdlMQELGLWLI 280
                                       7778889999999997.**************.***********9999************999886422222233344 PP

                   Proton_antipo_M 150 llilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyer 226
                                       l+ +a  +m+++s+ a++q ++Kr lAyS+is+l y+++++a+ t +++++a++h+ +h+++k++lFl+ag++  ++
  gi|330507616|ref|YP_004384044.1| 281 LAGIAGFTMIVASFFAITQDNLKRRLAYSTISQLSYIILGAALLTRDSMQGAMLHIPFHGYMKITLFLCAGAILVAT 357
                                       55577789**************************************************************9997777 PP

                   Proton_antipo_M 227 ektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvas 290
                                          + i +++g+ k+mP++ l++ ++++++aG+Pp+ gF+sk+++  +a+av++   ++++  +
  gi|330507616|ref|YP_004384044.1| 358 -GKTRISEMAGIGKRMPLTMLAFSIAAIGMAGIPPVCGFISKLYLCLGAWAVGSPYGMIFLAVI 420
                                       .667799********************************************9887777764433 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 !   23.5   2.1   7.4e-09   4.4e-05      11      55 ..      69     115 ..      62     118 .. 0.86
   2 ?   -1.8   0.4      0.58   3.5e+03      21      39 ..     412     430 ..     409     431 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 7.4e-09
                   Proton_antipo_N  11 sieigfllDklsalmllvvtfvsllvhlYSigYMa..ddegyqRFfa 55 
                                       +i igf +D +  +++++ + + +lv +YSigYM+  ++  ++R+++
  gi|330507616|ref|YP_004384044.1|  69 DIYIGFKVDAFGEIFAITASSLWVLVSIYSIGYMRtlKEHAQTRYYF 115
                                       5789******************************8444777888875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.58
                   Proton_antipo_N  21 lsalmllvvtfvsllvhlY 39 
                                       + +++l+v+ + sll ++Y
  gi|330507616|ref|YP_004384044.1| 412 YGMIFLAVILISSLLDIVY 430
                                       6789999999999987777 PP

>> TRIQK  Triple QxxK/R motif-containing protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.2     7e+03      46      64 ..      27      45 ..      24      49 .. 0.55
   2 ?    0.7   0.0     0.082   4.9e+02      49      76 ..      80     107 ..      75     109 .. 0.83
   3 ?    7.0   0.2    0.0009       5.4      50      73 ..     463     486 ..     452     491 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                             TRIQK 46 sgikevllvlvailvllla 64
                                      + i+e+  + +++ ++ll+
  gi|330507616|ref|YP_004384044.1| 27 PNIREAWTIAASLAMFLLV 45
                                      5677766664444444443 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.082
                             TRIQK  49 kevllvlvailvlllalYalfflnlske 76 
                                        e++ ++++ l +l+++Y++ +++  ke
  gi|330507616|ref|YP_004384044.1|  80 GEIFAITASSLWVLVSIYSIGYMRTLKE 107
                                       6888899999*********999887665 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0009
                             TRIQK  50 evllvlvailvlllalYalfflnl 73 
                                        v l + ai+ l++ +Y  +f+++
  gi|330507616|ref|YP_004384044.1| 463 VVPLTITAIFSLIFFIYPNMFYIY 486
                                       566889************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3332.37
//
Query:       gi|330507617|ref|YP_004384045.1|  [L=141]
Description: membrane bound hydrogenase subunit [Methanosaeta concilii GP6]
Scores for complete 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-23   79.8   0.9    1.7e-22   79.1   0.9    1.3  1  Oxidored_q2    NADH-ubiquinone/plastoquinone oxidoreductase c
     0.0061   16.5   2.0     0.0061   16.5   2.0    1.9  2  DUF2108        Predicted membrane protein (DUF2108)
  ------ inclusion threshold ------
      0.077   12.9   1.9        5.8    6.9   0.1    2.4  2  Deltameth_res  Deltamethrin resistance


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 !   79.1   0.9   2.8e-26   1.7e-22       5     103 ..      16     129 ..      13     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 2.8e-26
                                       HHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC............................TTSCG CS
                       Oxidored_q2   5 liallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvi...............tnpatefadplp 66 
                                       +++l+++iGl   ++++nllk+ligl++ ++a++l +v +g   +++l                  ++   +++plp
  gi|330507617|ref|YP_004384045.1|  16 IAMLIIIIGLTATIVKENLLKKLIGLSIFQTAMFLWFVSLGDVGRNILTTwglktgtppilweqaAEKGYIYVNPLP 92 
                                       7899***************************************9999998************9887777789***** PP

                                       GHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-BCCG- CS
                       Oxidored_q2  67 qalvLtaivigaaetavgLallvrlyreygtddvqel 103
                                        +l+Lt iv++aa+tav+La+++r+y++ygt++ +e+
  gi|330507617|ref|YP_004384045.1|  93 NVLMLTGIVVSAATTAVALAIVIRIYQKYGTIEEDEI 129
                                       *********************************9998 PP

>> DUF2108  Predicted membrane protein (DUF2108)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.0     1e-06    0.0061       5      43 ..      16      54 ..      13      58 .. 0.92
   2 ?   -1.2   0.3      0.34     2e+03      54      63 ..     104     113 ..      93     120 .. 0.47

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-06
                           DUF2108  5 valalaliGaigvillkkpldKlimlalleaGlilliva 43
                                      +a+++++iG +++i+ ++ l+Kli l++ ++ ++l  v+
  gi|330507617|ref|YP_004384045.1| 16 IAMLIIIIGLTATIVKENLLKKLIGLSIFQTAMFLWFVS 54
                                      8999***************************99988776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.34
                           DUF2108  54 allePvstii 63 
                                       a   +v+  i
  gi|330507617|ref|YP_004384045.1| 104 AATTAVALAI 113
                                       2222333222 PP

>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1   0.00098       5.8      19      43 ..      10      34 ..       6      41 .. 0.89
   2 ?    5.4   0.2    0.0027        16      22      41 ..      93     112 ..      82     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00098
                     Deltameth_res 19 rkYNavLaaGiviligTialakesg 43
                                       kYN   a+ i+i + T++++ke+ 
  gi|330507617|ref|YP_004384045.1| 10 EKYNFWIAMLIIIIGLTATIVKENL 34
                                      59********************985 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0027
                     Deltameth_res  22 NavLaaGiviligTialake 41 
                                       N  +++Giv+ ++T a+a +
  gi|330507617|ref|YP_004384045.1|  93 NVLMLTGIVVSAATTAVALA 112
                                       8899***********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1058.19
//
Query:       gi|330507618|ref|YP_004384046.1|  [L=174]
Description: membrane bound hydrogenase subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-34  116.8   1.5    7.4e-34  116.6   1.5    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 !  116.6   1.5   4.2e-38   7.4e-34       1     143 [.      14     167 ..      14     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 4.2e-38
                              MNHE   1 llllflvWllltgs..........lgelllGlllallvalllrrll.....lplrrv...llrllayllvflweivk 59 
                                       ++++f++W+ll+++          l+    G+l al+v++l+++++      +   v   ++rl+ y+++ lw+i+ 
  gi|330507618|ref|YP_004384046.1|  14 FCVMFAFWMLLSAWtvyllepydlLKVSSRGILAALIVSFLTYEIFvpsrgEN---VllkIRRLIPYIGWELWQIYL 87 
                                       689*****************8885555589************99997755433...2556999************** PP

                              MNHE  60 anldVakrvlrpklpirpgivkvplrlksdlaltllansitltPGTltvdvdedrrvlyvHvldvedeeeeareeik 136
                                       a++dV+krvl+  lp++p+i++++++l+sd+al+++ansitltPGT+t+d++ ++++++vH++  e    + + +++
  gi|330507618|ref|YP_004384046.1|  88 ATIDVTKRVLG-ILPVDPRIIEFDTTLRSDFALVTFANSITLTPGTITIDIEPEKGRYIVHAIAKEP---AESLTVD 160
                                       **********8.56*************************************************6544...4445666 PP

                              MNHE 137 grlErrl 143
                                       +++++++
  gi|330507618|ref|YP_004384046.1| 161 QTMQKKV 167
                                       7777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1313.41
//
Query:       gi|330507619|ref|YP_004384047.1|  [L=89]
Description: membrane bound hydrogenase subunit [Methanosaeta concilii GP6]
Scores for complete sequence (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   64.1   3.3    1.1e-17   64.1   3.3    1.7  2  MrpF_PhaF      Multiple resistance and pH regulation protein 
  ------ inclusion threshold ------
       0.25   11.2   0.1       0.25   11.2   0.1    2.6  3  Deltameth_res  Deltamethrin resistance


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 ?   -0.8   0.2      0.23   2.1e+03      11      15 ..       9      13 ..       2      22 .. 0.48
   2 !   64.1   3.3   1.2e-21   1.1e-17       3      52 ..      32      81 ..      31      82 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.23
                         MrpF_PhaF 11 gtllv 15
                                      g++++
  gi|330507619|ref|YP_004384047.1|  9 GIIIA 13
                                      22222 PP

  == domain 2  score: 64.1 bits;  conditional E-value: 1.2e-21
                         MrpF_PhaF  3 RvvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarfl 52
                                      R+vA++++gt++++ll++++ + +rp ++d+al++A+++F+gt+++a++ 
  gi|330507619|ref|YP_004384047.1| 32 RIVAANVIGTKAIVLLIVVGYIIERPEFIDIALMYAVIAFIGTIIIAKYA 81
                                      9************************************************6 PP

>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.3     0.032   2.9e+02      25      40 ..       6      20 ..       4      26 .. 0.67
   2 ?   -1.0   0.2      0.19   1.7e+03      20      30 ..      29      39 ..      28      55 .. 0.63
   3 ?   11.2   0.1   2.8e-05      0.25      24      42 ..      63      81 ..      61      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.032
                     Deltameth_res 25 LaaGiviligTialak 40
                                      L++Gi+i ++Ti ++ 
  gi|330507619|ref|YP_004384047.1|  6 LVVGIII-ASTILVCS 20
                                      8888877.45666554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.19
                     Deltameth_res 20 kYNavLaaGiv 30
                                      ++N++ aa ++
  gi|330507619|ref|YP_004384047.1| 29 TFNRIVAANVI 39
                                      57777666555 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 2.8e-05
                     Deltameth_res 24 vLaaGiviligTialakes 42
                                       L+ +++++igTi++ak+ 
  gi|330507619|ref|YP_004384047.1| 63 ALMYAVIAFIGTIIIAKYA 81
                                      5999************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.18s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 773.38
//
Query:       gi|330507620|ref|YP_004384048.1|  [L=50]
Description: hypothetical protein MCON_1600 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 390.13
//
Query:       gi|330507621|ref|YP_004384049.1|  [L=83]
Description: hypothetical protein MCON_1601 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.071   13.0   0.0      0.094   12.6   0.0    1.3  1  PASTA     PASTA domain


Domain annotation for each model (and alignments):
>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.2e-06     0.094       2      32 ..      31      61 ..      30      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-06
                                      E--TTTTSBHHHHHHHHHHTT--CCCEEEEC CS
                             PASTA  2 tvPdvtGmsvdeAkatLkalGlkiktveets 32
                                      +v+ ++G + +eA+++L al l+i +++++s
  gi|330507621|ref|YP_004384049.1| 31 EVCRIRGIDESEAIEALDALALSIDEETYPS 61
                                      7999******************999999755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 647.85
//
Query:       gi|330507622|ref|YP_004384050.1|  [L=82]
Description: hypothetical protein MCON_1602 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.11   12.3   0.1       0.13   12.0   0.1    1.1  1  Endonuc-BglII  Restriction endonuclease BglII


Domain annotation for each model (and alignments):
>> Endonuc-BglII  Restriction endonuclease BglII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.5e-06      0.13      36      69 ..      14      50 ..       8      67 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.5e-06
                     Endonuc-BglII 36 enksdvkkrikellaakgWeeekrika...eseeene 69
                                      ++ks++++++++ll++kg+ +e+ri +   +s e + 
  gi|330507622|ref|YP_004384050.1| 14 KKKSKLRQEVEDLLEQKGFVMERRISVinlDSGEAHY 50
                                      589999*******************885543333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 627.35
//
Query:       gi|330507623|ref|YP_004384051.1|  [L=186]
Description: hypothetical protein MCON_1603 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   11.1   0.0         14    4.7   0.0    2.0  2  BPL_N     Biotin-protein ligase, N terminal


Domain annotation for each model (and alignments):
>> BPL_N  Biotin-protein ligase, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0009        16      43      84 ..      34      78 ..      25      83 .. 0.78
   2 ?    4.7   0.0   0.00077        14     194     223 ..     142     170 ..     136     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0009
                             BPL_N 43 kePWastcallVlPgG.aDlpYvreln..gegnrkikeyVekGGk 84
                                        P   +  ++ +P G a+  Y + l   +++ ++i+++V +GG 
  gi|330507623|ref|YP_004384051.1| 34 GSPFLPQYKMVMIPSGfANPDYSQILPglERMKSNIERFVMNGGV 78
                                      567778889999**993455588888855588999*********7 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.00077
                             BPL_N 194 sgeakkaAvvlckvgeGkalLtgvhpEfal 223
                                       ++++++a  v+ ++geG +++t+vh Ef++
  gi|330507623|ref|YP_004384051.1| 142 KDDKGRAILVMARHGEGLIVVTTVH-EFPA 170
                                       556677999***************9.6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1367.23
//
Query:       gi|330507624|ref|YP_004384052.1|  [L=135]
Description: CopG family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-34  116.5   4.6    6.4e-34  116.0   4.6    1.2  1  NikR_C           NikR C terminal nickel binding domain
    2.2e-10   40.1   0.1      4e-10   39.3   0.1    1.4  1  RHH_1            Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.052   13.7   0.0      0.093   12.8   0.0    1.5  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   4.6   1.1e-37   6.4e-34       1      77 []      53     129 ..      53     129 .. 0.99

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 1.1e-37
                                       EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEEE CS
                            NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltli 77 
                                       vGvit+vy h+qr+l e+lt+iqh++ d+i+sslhvhldhdncLevivl+Ge+++++  aek+++lkgVkhvklt++
  gi|330507624|ref|YP_004384052.1|  53 VGVITLVYSHSQRGLVENLTEIQHDSGDIIQSSLHVHLDHDNCLEVIVLRGEGKDVRVAAEKMMSLKGVKHVKLTTT 129
                                       7**************************************************************************86 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.1   6.7e-14     4e-10       1      37 [.       2      39 ..       2      40 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 6.7e-14
                                      EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                      r+ ++l+e+ll r+de++ +rg +SrSe IR+A+r+y+
  gi|330507624|ref|YP_004384052.1|  2 RIGVSLPEKLLSRFDEIILKRGySSRSEGIRDAIRNYI 39
                                      899*********************************97 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.6e-05     0.093      91     118 ..       2      30 ..       1      35 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                   HicB_lk_antitox  91 riNitlpervlkriDaavkaag.esRSgf 118
                                       ri ++lpe++l+r D+++ ++g +sRS  
  gi|330507624|ref|YP_004384052.1|   2 RIGVSLPEKLLSRFDEIILKRGySSRSEG 30 
                                       899***************99996799975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1028.03
//
Query:       gi|330507625|ref|YP_004384053.1|  [L=226]
Description: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-73  244.9   0.0    5.7e-73  244.8   0.0    1.0  1  Fibrillarin      Fibrillarin
     0.0069   15.5   0.0     0.0095   15.1   0.0    1.1  1  DREV             DREV methyltransferase
  ------ inclusion threshold ------
      0.024   15.4   0.0      0.035   14.8   0.0    1.3  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.8   0.0   9.5e-77   5.7e-73       4     225 ..       4     218 ..       1     219 [. 0.95

  Alignments for each domain:
  == domain 1  score: 244.8 bits;  conditional E-value: 9.5e-77
                                       ECSSTTEEEEETTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT.-S--S--TTSEEEEEST CS
                       Fibrillarin   4 heklegvyivkekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkg.lkelpikkgskvLYlGa 79 
                                       +e   g+yi++e++ arlat++  p   vYgE++     + yR W+p+rsKlaa ilkg  ++lp+k++s+vLYlGa
  gi|330507625|ref|YP_004384053.1|   4 EEIAPGIYILHERDGARLATRSSDP-VPVYGERIH----NGYRLWDPYRSKLAALILKGkWQTLPLKSNSRVLYLGA 75 
                                       67789******999999****9877.68****985....57****************9846899************* PP

                                       TTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHH CS
                       Fibrillarin  80 asGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqari 156
                                       ++GttvsHv+Div  eg+vyavefs r++r+l++++++Rkni+Pil+DA kPe+Y+ l+e vD++++Dvaq +qa+i
  gi|330507625|ref|YP_004384053.1|  76 STGTTVSHVADIVS-EGLVYAVEFSARSMRDLVRLCERRKNIIPILADAAKPEEYAPLLEPVDLVYQDVAQKNQAQI 151
                                       *************9.************************************************************** PP

                                       HHHHHHHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEEEE CS
                       Fibrillarin 157 laknaklflkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgkyk 225
                                       + +n+  +l +gg+l +++k+rs+d+t+ p++v ++e +kl+  gl+ ++ ++lep++ dh +v ++++
  gi|330507625|ref|YP_004384053.1| 152 ASLNCARYLGQGGELCLMLKSRSVDTTAPPQAVLQSELKKLE--GLELIKIMNLEPFHLDHWAVRARWN 218
                                       ****************************************96..899****************999875 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-06    0.0095      81     134 ..      53     111 ..      47     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-06
                              DREV  81 llaiekespasdqedkklldlGaGdGeitkrvaptfee..vyatelset.mrd..rlkk 134
                                       l+  +k +  + + + ++l lGa  G    +va+ ++e  vya e s + mrd  rl  
  gi|330507625|ref|YP_004384053.1|  53 LILKGKWQTLPLKSNSRVLYLGASTGTTVSHVADIVSEglVYAVEFSARsMRDlvRLCE 111
                                       5556677788888999******************************9752765334444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.8e-06     0.035       1      97 []      70     164 ..      70     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.8e-06
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC...CGBSSSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgda...edlpfedgsfDlvvssgal 74 
                                       vL lG+ tG+++ ++a+ ++++ v++v++s++ ++   + +e+++ n+  + +da   e++    + +Dlv+   + 
  gi|330507625|ref|YP_004384053.1|  70 VLYLGASTGTTVSHVADIVSEGLVYAVEFSARSMRDLVRLCERRK-NIIPILADAakpEEYAPLLEPVDLVYQD-V- 143
                                       899***************989********************7664.8988888885555566778899999983.3. PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                          ++++++ a  ++ar L +gG
  gi|330507625|ref|YP_004384053.1| 144 --AQKNQAQIASLNCARYLGQGG 164
                                       ..334455566677888877777 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:                      298  (0.0166211); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1669.69
//
Query:       gi|330507626|ref|YP_004384054.1|  [L=257]
Description: signal sequence peptidase I [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0001   22.2   0.0    0.00026   20.9   0.0    1.7  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 !   20.9   0.0   1.4e-08   0.00026       2      50 ..      49     118 ..      48     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-08
                                       XXSSTTCCTXXTTXEEEEECTS.................---TTSEEEEEETTCE....-EEEEEEEEET CS
                     Peptidase_S24   2 vpGdSMeptlldGdlilVdkfs.................epkrGdivvfrlpgee....eayiKrviglp 50 
                                       v+++SM p l+ Gd+ilV   s                   ++Gd++  r  g+e     +  K v g+p
  gi|330507626|ref|YP_004384054.1|  49 VESGSMVPNLNVGDIILVQGASrtevipwdegekmnytaFNNPGDVILYRPYGKEslnlFDQLKMVLGMP 118
                                       89*****************777888999999999999999999999999988888665555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1963.59
//
Query:       gi|330507627|ref|YP_004384055.1|  [L=540]
Description: DNA polymerase D, small subunit DP1 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-11   41.9   0.0    1.2e-10   41.1   0.0    1.3  1  DNA_pol_E_B      DNA polymerase alpha/epsilon subunit B
    3.8e-10   40.6   0.1    6.6e-10   39.8   0.1    1.4  1  Metallophos      Calcineurin-like phosphoesterase
    1.3e-08   35.2   0.0    2.7e-08   34.2   0.0    1.5  1  Metallophos_2    Calcineurin-like phosphoesterase superfamily
    0.00016   21.6   0.2    0.00033   20.6   0.2    1.6  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.077   13.0   0.1       0.18   11.9   0.1    1.5  1  DUF4539          Domain of unknown function (DUF4539)


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   3.3e-14   1.2e-10       2     204 ..     285     485 ..     284     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 3.3e-14
                                       EEEES--S-TT---...-HHHHHHHHHHH.....HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTH CS
                       DNA_pol_E_B   2 vivsglnldndnrs...leaLrkiLqgya....peesppdvlilaGnfvdaahkaiasskvstdekkenfdalalll 71 
                                       +++s+l++ ++ +     + ++++L+g a      +s+++ l++aG +vd      ++++  + +  +     ++  
  gi|330507627|ref|YP_004384055.1| 285 ILISDLHVGSKYFMdeaWQRFSDWLNGEAddpsGLASQVEYLVIAGDLVDGIGIYPGQQN--DLAIMDIYSQYEAAA 359
                                       578888888555547778999********99887899*************6555555554..345555566666667 PP

                                       HHHTTS-TTSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---E CS
                       DNA_pol_E_B  72 silesllekttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkre 148
                                         l+ + + +++++ Pg  D + + + Pq++lp+ + +  ++    + +v NP +++l ++ v+++ +  ++dl   
  gi|330507627|ref|YP_004384055.1| 360 GLLNAIRSDIKIIISPGNHDIVRQ-AEPQPALPPEVQKYFRPD---MLFVGNPAWVTLSGISVLIYHGRSIDDLVLR 432
                                       778888899***************.**********88888886...89************************99766 PP

                                       EESHHHHHS-HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEEE--- CS
                       DNA_pol_E_B 149 slkesntdverlrklvktildqrhlaPlaptlrpvswdkddalvleplPdvlvlpd 204
                                                 + +k++  +l+ rhl+P++ + +++  ++ d +v++  P +l ++ 
  gi|330507627|ref|YP_004384055.1| 433 LPGIAY---ANPEKAMIEMLRRRHLSPIYGSRVSIAPENEDHYVISHPPAILHCGH 485
                                       555444...7899********************************999*9998875 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.1   1.8e-13   6.6e-10       4     202 ..     285     487 ..     282     500 .. 0.63

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1.8e-13
                                       EEEESBTB...TTCCTHHHHHHHHHHHHHHH.....TTESEEEEESTSSSSS..............HHHHHHHHHHH CS
                       Metallophos   4 lvigDlHl...algggqlddllkllddllre.....ekpdlvllaGDlvdrg..............dlekellella 58 
                                       ++i+DlH+      ++ ++++ ++l+  +++     +++ ++++aGDlvd+                          
  gi|330507627|ref|YP_004384055.1| 285 ILISDLHVgskYFMDEAWQRFSDWLNGEADDpsglaSQVEYLVIAGDLVDGIgiypgqqndlaimdI---------- 351
                                       689****9999888899999999997774445555668899999*******9666666555555541.......... PP

                                       HHHHH...............TSEEEEEC-TTS..CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEE CS
                       Metallophos  59 alvky...............pipvylllGNHe..gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvl 118
                                           y               +i++++ +GNH+        +++ +   + ++ +r d  +++n+  + l +    vl
  gi|330507627|ref|YP_004384055.1| 352 ----YsqyeaaagllnairsDIKIIISPGNHDivR---QAEPQPALPPEVQKYFRPDMLFVGNPAWVTLSGI--SVL 419
                                       ....23334444555555669***********320...3333333333335566666666666666666666..99* PP

                                       EEESECEEETHHHHHHHHHHHSCHHHHCC......HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHH CS
                       Metallophos 119 llhGgspellvsldklgslnleleapepg......dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllk 189
                                       ++hG s+++         l+l+l+ +          e+l++             + sp+y gs  + ++e  + +  
  gi|330507627|ref|YP_004384055.1| 420 IYHGRSIDD---------LVLRLPGIAYAnpekamIEMLRR------------RHLSPIY-GSRVSIAPENEDHYVI 474
                                       ****95544.........44443333322332344444544............3445555.6666666666665555 PP

                                       HTTESEEEEESSS CS
                       Metallophos 190 kygvdlvisGHtH 202
                                        + + +  +GH+H
  gi|330507627|ref|YP_004384055.1| 475 SHPPAILHCGHVH 487
                                       5555555557777 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 !   34.2   0.0   7.4e-12   2.7e-08       4     150 ..     285     509 ..     283     524 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 7.4e-12
                     Metallophos_2   4 aiiSDlH..snldaleav.............lealkevgvdaiihaGD....................l..eeeepe 43 
                                       ++iSDlH  s+++  ea+             ++ l+++ v++++ aGD                    +  +e++  
  gi|330507627|ref|YP_004384055.1| 285 ILISDLHvgSKYFMDEAWqrfsdwlngeaddPSGLASQ-VEYLVIAGDlvdgigiypgqqndlaimdiYsqYEAAAG 360
                                       78*******78888888888888888888888888887.9********88888877777777776664244444445 PP

                     Metallophos_2  44 vleellelapvlaVrGNnD.......eev.veedvlreaaelgtdlpeeaelelagekvlliHgdpl.......... 102
                                        l+++++  ++++ +GN+D       +   +  +v++ + + +  + + a+++l g +vl++Hg             
  gi|330507627|ref|YP_004384055.1| 361 LLNAIRSDIKIIISPGNHDivrqaepQ-PaLPPEVQKYFRPDMLFVGNPAWVTLSGISVLIYHGRSIddlvlrlpgi 436
                                       77777776699999*****99877532.358888889999999999******************977********** PP

                     Metallophos_2 103 ............................gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgepr 150
                                                                   + +++ ++ +   + + +++ cGH H+ ++ + +gv  +n G  + + 
  gi|330507627|ref|YP_004384055.1| 437 ayanpekamiemlrrrhlspiygsrvsiA-PENEDHYV--ISHPPAILHCGHVHTVGIARYKGVAAINSGTWQSQT 509
                                       ***99999999999999999997766422.22222222..246888************************987764 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 !   20.6   0.2   9.2e-08   0.00033       1      56 [.     197     252 ..     197     260 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.2e-08
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.HHHHHHHTTS-TTSEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr.eeatklaenlkeGdvvrvtG 56 
                                       V++ G+v +i+   +++   i+l+D tg+i +v+ + +ea++   ++ ++ v++vtG
  gi|330507627|ref|YP_004384055.1| 197 VSLIGMVLDIR-NTSKGNRVIELEDPTGMIVAVIQKdGEAYEESGQIIPDEVIGVTG 252
                                       899*******8.88899*******************9999999999**********9 PP

>> DUF4539  Domain of unknown function (DUF4539)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   4.9e-05      0.18       6      41 ..     199     233 ..     197     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.9e-05
                           DUF4539   6 lvviiksintlnslgdalvtlkDptGeidgtihrkv 41 
                                       l++++  i   +s+g+  + l+DptG i ++i+++ 
  gi|330507627|ref|YP_004384055.1| 199 LIGMVLDI-RNTSKGNRVIELEDPTGMIVAVIQKDG 233
                                       67888888.66777789****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 3821.13
//
Query:       gi|330507628|ref|YP_004384056.1|  [L=134]
Description: hypothetical protein MCON_1609 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 954.36
//
Query:       gi|330507629|ref|YP_004384057.1|  [L=171]
Description: hypothetical protein MCON_1610 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1269.60
//
Query:       gi|330507630|ref|YP_004384058.1|  [L=429]
Description: thiamine biosynthesis protein ThiC [Methanosaeta concilii GP6]
Scores for complete 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  563.4   0.0   3.1e-169  563.2   0.0    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  563.2   0.0  1.7e-173  3.1e-169       1     417 [.       2     415 ..       2     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 563.2 bits;  conditional E-value: 1.7e-173
                      ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkek.pvaiGkglrtkvnaniGtsadasdiee 76 
                                       t +e+a +g++ +++e+va+ke+++p ++++ va+Gr+vip n++++   p++iG+ l +kvn+n+Gts++  + e 
  gi|330507630|ref|YP_004384058.1|   2 TLMEEASSGRVPQSIERVARKEGIDPAKLARLVAAGRVVIPGNVRREGLdPAGIGEMLAVKVNVNLGTSQNLDSAEV 78 
                                       789*******************************************6666*************************** PP

                      ThiC_Rad_SAM  77 EveKlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqaleekekkveelteeellevieeqaedGvd 153
                                       EveK+ +a +agad+vmdLstggd+d +r+kil++++vp+gtvpiYqa+++     +elt++ +++++e++a+dGvd
  gi|330507630|ref|YP_004384058.1|  79 EVEKALAASEAGADAVMDLSTGGDLDLVRKKILAAVKVPLGTVPIYQAAVK-----QELTSQGMFDALERHARDGVD 150
                                       *************************************************85.....589****************** PP

                      ThiC_Rad_SAM 154 fltiHagvtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaD 230
                                       f+t+Hagv++ +le+l+++ Rl+g+vSrgGsl+++++  +++enp+y+efd+llei++ey++tlSlgdglRpG+i+D
  gi|330507630|ref|YP_004384058.1| 151 FVTVHAGVNKISLERLRQDPRLMGLVSRGGSLTMKYIADTGEENPYYQEFDYLLEIAREYELTLSLGDGLRPGCIED 227
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 231 atdeaqlaelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsai 307
                                       a+d+a+++e+i+lgelvkrar+agvq+mveGPGHvp deie++v+++k+l+ +aP+y+lGplvtD+apgYDhit+a+
  gi|330507630|ref|YP_004384058.1| 228 ASDRAKYMEFIMLGELVKRARAAGVQAMVEGPGHVPADEIETSVRAMKHLTGGAPLYLLGPLVTDVAPGYDHITAAM 304
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 308 GaalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakg..lkkarerdkalskaRkeldwekqfel 382
                                       G+ +a++aGad+lC  tp+EHl lP++edv eG  +++iaahaadl++   +++ar++d ++s+aR++ldw+ qf++
  gi|330507630|ref|YP_004384058.1| 305 GGVIAGMAGADFLCATTPSEHLDLPNREDVIEGTYVTRIAAHAADLTRPgvRERARSWDLQMSRARAALDWDGQFQA 381
                                       ***********************************************9766899*********************** PP

                      ThiC_Rad_SAM 383 aldpekareireeklpeeeeaCsmCgekCavkive 417
                                       a++p++a++ir+++   e+++C+mC+e Ca+++++
  gi|330507630|ref|YP_004384058.1| 382 AINPARAKQIRHRRGL-ETDTCTMCSELCAIRLAK 415
                                       ************9986.99************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 3130.53
//
Query:       gi|330507631|ref|YP_004384059.1|  [L=212]
Description: metallo-beta-lactamase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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  102.6   0.0    3.5e-29  102.2   0.0    1.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.4e-07   31.2   0.0    2.4e-07   30.5   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0035   16.8   0.0     0.0052   16.3   0.0    1.2  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.038   13.9   0.0       0.15   12.0   0.0    1.8  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 !  102.2   0.0   7.7e-33   3.5e-29       5     197 .]      13     190 ..      10     190 .. 0.95

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 7.7e-33
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                        +n+yl+  d++ iL+D+G+ +  +++     ++ ++p +++ ++lTH H+DH G+++ l+eat++     ++e   
  gi|330507631|ref|YP_004384059.1|  13 DGNVYLV-LDEKPILVDAGMMAGPTLKNI---KKFIDPAKIELIVLTHCHHDHSGAAPALKEATGARLMLSEKEVGC 85 
                                       589****.9******************96...********************************************* PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCC CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetg 158
                                         +e a  a+ +++    ++++ k+d+++ e+ + + g + l+v+ +pgh+ g+++++ + +kvlf+GD+++  + g
  gi|330507631|ref|YP_004384059.1|  86 IGDELASVAYLFGQ----QAPEYKVDETLKEGMVLDIGEWKLEVMETPGHSTGSLCLYERTEKVLFSGDTVF--PDG 156
                                       ******99999998....6*****************************************************..555 PP

                                       CCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 159 ridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                        i++     +++++++ +++ +s+ +l +l+++v++pgH
  gi|330507631|ref|YP_004384059.1| 157 NIGR-----TDMFGGSTDELVRSIQRLTELDVKVMYPGH 190
                                       5555.....668*************************** PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   5.4e-11   2.4e-07       3     181 ..      25     193 ..      23     204 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 5.4e-11
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEE.EEHHHHH...HCCTTCG CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklply.apkgvla...vleanfv 75 
                                       iL+Dag   +++   +l++ ++  ++++i++++lth+H DH   ++ l+e ++  ++l+   k+v+    +l++   
  gi|330507631|ref|YP_004384059.1|  25 ILVDAGMM-AGP---TLKNIKKFIDPAKIELIVLTHCHHDHSGAAPALKEATG--ARLMlSEKEVGCigdELASV-A 94 
                                       89999998.344...45455678899************************666..45553445554411145544.4 PP

                                       HHHCHTTTTEEE.EEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHH CS
                     Lactamase_B_2  76 ylaleeepavnv.heldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeig 151
                                       yl+ +++p+ +v ++l+ g+ +++g+   ++++++ ++ s            +l++ + +++v+++gDt + ++ ig
  gi|330507631|ref|YP_004384059.1|  95 YLFGQQAPEYKVdETLKEGMVLDIGE--WKLEVMETPGHSTG----------SLCLYERTEKVLFSGDTVFPDGNIG 159
                                       55555556777724567888888885..45666666666655..........889999999*********9998888 PP

                                       ..HHHCT.-SEEEEE-S-SSTTHHHH.HHT---S CS
                     Lactamase_B_2 152 ..erlgg.adllllditayeddemir.hmgHltp 181
                                         +++gg  d l+  i ++++   +   +gH+++
  gi|330507631|ref|YP_004384059.1| 160 rtDMFGGsTDELVRSIQRLTELDVKVmYPGHMDI 193
                                       6556666688888888888887755577788876 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-06    0.0052       2      64 ..      18      77 ..      17      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-06
                     Lactamase_B_6  2 LeldnvkiLlDvGwdeskvslesalkelekvi..ptvdliLLshatlehlGayallyakfkskll 64
                                      L ld+  iL+D G+         +lk+++k i   +++li+L+h   +h Ga + l  + +++l+
  gi|330507631|ref|YP_004384059.1| 18 LVLDEKPILVDAGMMAG-----PTLKNIKKFIdpAKIELIVLTHCHHDHSGAAPALKEATGARLM 77
                                      6689999*******986.....369999**996669****************9988777666655 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.3e-05      0.15      17      74 ..      23     119 ..      15     204 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.3e-05
                     Lactamase_B_3  17 arilvDPf......kanlgyeppaeeaDlvlisqaledHa.hletlkql............................ 58 
                                       + ilvD +       +n++  +++ +++l+++++ + dH  ++++lk++                            
  gi|330507631|ref|YP_004384059.1|  23 KPILVDAGmmagptLKNIKKFIDPAKIELIVLTHCHHDHSgAAPALKEAtgarlmlsekevgcigdelasvaylfgq 99 
                                       556666555554445577788888************99972445566657777777766666666665555555555 PP

                     Lactamase_B_3  59 ....aenvkvleegeslevg 74 
                                           ++  ++l+eg  l++g
  gi|330507631|ref|YP_004384059.1| 100 qapeYKVDETLKEGMVLDIG 119
                                       54442222233333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1473.34
//
Query:       gi|330507632|ref|YP_004384060.1|  [L=382]
Description: acetylornithine aminotransferase [Methanosaeta concilii GP6]
Scores for complete 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-112  373.8   0.0   1.1e-111  373.4   0.0    1.1  1  Aminotran_3      Aminotransferase class-III
  ------ inclusion threshold ------
       0.09   11.3   0.0       0.13   10.7   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
       0.14   11.8   0.0       0.27   10.9   0.0    1.4  1  SERTA            SERTA motif


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 !  373.4   0.0  1.8e-115  1.1e-111      11     404 ..      24     380 ..      16     382 .] 0.97

  Alignments for each domain:
  == domain 1  score: 373.4 bits;  conditional E-value: 1.8e-115
                                       EEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-.. CS
                       Aminotran_3  11 lvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgl 87 
                                       +++ k+ G+ ++d +g++ylD+v++iav+ +Gh+hPk+v+ v+ qaa+l h+s +++ +e+++ lae+l  l++   
  gi|330507632|ref|YP_004384060.1|  24 VLLVKGSGAHVWDCEGREYLDFVAGIAVNSIGHCHPKLVETVSRQAAALIHTS-NLYYTENQVLLAEELKGLTGM-- 97 
                                       6789*************************************************.*******************99.. PP

                                       SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTB CS
                       Aminotran_3  88 dkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypd 164
                                       d+  ++nsG+e++e+AlKl r+      at ++ki+a + afHGrtlg+l++t++ + y++ f p+  e  +++y+d
  gi|330507632|ref|YP_004384060.1|  98 DRAYFCNSGAESIEAALKLVRR------ATGRAKIVAAERAFHGRTLGSLGLTHK-AAYREPFRPL-REAEFVPYND 166
                                       **********************......***************************.********96.578899***9 PP

                                       GGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTT CS
                       Aminotran_3 165 eevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrT 241
                                                         ea++++ + e+ Av +Ep+qge+Gv+v++ ++l+++r++c+++++lli DEvqtGfGrT
  gi|330507632|ref|YP_004384060.1| 167 -----------------SEAMKAAVTSETGAVFLEPVQGEAGVYVPDGDYLRTARDICDDQGALLILDEVQTGFGRT 226
                                       .................678888999*************************************************** PP

                                       SSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHH CS
                       Aminotran_3 242 GklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllenaq 318
                                       G +fA eh gv pD+++laKa++gGlp+ a+la+    + +++g+hgsTf+G pl ca+ala++++i eekl+e+ +
  gi|330507632|ref|YP_004384060.1| 227 GRWFAKEHSGVVPDIICLAKAIAGGLPMGAMLARGSSSESFQKGDHGSTFAGGPLICAAALATIDVIREEKLVERSE 303
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--HHHH CS
                       Aminotran_3 319 elgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitdeei 395
                                       elg++lk++ e+l+      +evRg+Glm++++l  + +    ++++ka++kGvli ++G++++rl+ppl++t+eei
  gi|330507632|ref|YP_004384060.1| 304 ELGRYLKSEIEKLN-----PREVRGLGLMVGLDLNCDCK----SLVEKALQKGVLINNTGEHTLRLIPPLVVTKEEI 371
                                       *************9.....578*************9999....8********************************* PP

                                       HHHHHHHHH CS
                       Aminotran_3 396 delleilkk 404
                                       d ++e + +
  gi|330507632|ref|YP_004384060.1| 372 DRVVEVIGE 380
                                       ***998865 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   2.2e-05      0.13      55     173 ..      85     217 ..      67     222 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-T..TEE.EEEESTSSHH....HHHHHHHTHHH....TTCEEE CS
                   Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailallka..Gde.ivvsddlYgg....tqrllkkvlkk....lgievk 120
                                         l e++  L g ++a+ ++sG  +i  a l+l++   G   iv+ + ++ g    +  l +k + +       e++
  gi|330507632|ref|YP_004384060.1|  85 VLLAEELKGLTGMDRAYFCNSGAESI-EAALKLVRRatGRAkIVAAERAFHGrtlgSLGLTHKAAYRepfrPLREAE 160
                                       5688999999**************99.55566665524432499988888653222334555555442211346899 PP

                                       EESTTSHHHHHHHCCTTEEEEEEESS.-TTTT----...HHHHHHHHHHTT-EEEEE CS
                   Cys_Met_Meta_PP 121 fvdtsdleelekaikentklvylEtp.tnpllkvvD...iekiaklakkagvlvvvD 173
                                       fv  +d e++++a++++t +v+lE + +   + v+D   +++  +++ ++g+l+++D
  gi|330507632|ref|YP_004384060.1| 161 FVPYNDSEAMKAAVTSETGAVFLEPVqGEAGVYVPDgdyLRTARDICDDQGALLILD 217
                                       ************************762445555655333444445555555555555 PP

>> SERTA  SERTA motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.5e-05      0.27      13      29 ..     337     353 ..     335     361 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.5e-05
                             SERTA  13 rdlvEpsLrRsVLInNt 29 
                                       + lvE  L++ VLInNt
  gi|330507632|ref|YP_004384060.1| 337 KSLVEKALQKGVLINNT 353
                                       6689************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2949.99
//
Query:       gi|330507633|ref|YP_004384061.1|  [L=351]
Description: histidinol-phosphate aminotransferase [Methanosaeta concilii GP6]
Scores for complete 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  159.1   0.0      2e-46  158.9   0.0    1.1  1  Aminotran_1_2  Aminotransferase class I and II
    2.3e-06   26.8   0.0    0.00044   19.2   0.0    2.1  2  Alliinase_C    Allinase
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.044   13.6   0.0    1.4  1  DUF3670        SNF2 Helicase protein


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.9   0.0   3.3e-50     2e-46       2     362 ..      37     345 ..      36     346 .. 0.93

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 3.3e-50
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       d+++Lgsne++++    ++p+v +a +       +  +y+ ++   el e la++ g        +e  +v g G +
  gi|330507633|ref|YP_004384061.1|  37 DIVKLGSNENPYG----PSPKVFEALQN-----VSPERYPEPE---ELMEGLARYTG-------SPEEMLVIGAGMD 94 
                                       789**********....*******9987.....88899*****...***********.......8999********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                        + ++l++l+ l++gd+ ++p+pt++ y+    l+g+e v  p       + d+   e+  k       + k+ +++
  gi|330507633|ref|YP_004384061.1|  95 GVMDTLTRLF-LEKGDRTFIPTPTFSYYEILTVLAGAEPVFSP------LGPDFRIQETVPK-------EAKMAFIC 157
                                       **********.********************************......5688876666444.......458***** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGy 232
                                       sp+NPtG ++++eel+ ll++++   +++f+DeaY +f+  sl       +v+++ nl++ ++lsKafGlaG R+Gy
  gi|330507633|ref|YP_004384061.1| 158 SPNNPTGNALKEEELCRLLETTE---AIVFLDEAYVEFAERSL-----AELVSRYENLVVGRTLSKAFGLAGMRLGY 226
                                       ******************55555...8**************54.....99*************************** PP

                                       EEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEE CS
                     Aminotran_1_2 233 ilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmfl 308
                                       +l  +++++   +++ pf   ss+  aa aaal d +    +++e+++++  +r +l +e+       ++sq+++++
  gi|330507633|ref|YP_004384061.1| 227 ALMPEWIAQEFCRAAPPFFGiSSASVAAGAAALADLD----FMNESVRKIRMERSRLQKEI-----RSYPSQANFLY 294
                                       ********************99999999999999977....8*****************98.....67********* PP

                                       EEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 309 ltdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                       l   +a+  +++++k l++ g++++ ++sf+   ++++R+tv  +t+ee+++++ a
  gi|330507633|ref|YP_004384061.1| 295 LKTEEAS--DSFAEKFLQK-GIIIRDCRSFRGagENHVRVTV--GTAEENDRFLAA 345
                                       9777766..**********.**********999*********..*******99977 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.4e-08   0.00044     136     209 ..     149     230 ..      89     241 .. 0.81
   2 !    5.7   0.0   0.00099       5.9     298     353 ..     286     340 ..     262     350 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.4e-08
                                       .S-EEEEEESS-TTT--.------....-TT-EEEEEE-TT-S...TTTS---S-B--SEEEEEHHHHHS-GGG-EE CS
                       Alliinase_C 136 peefielvtsPnnPdgl.lreavv....kgseakviyDlayYW...PhytpitskadedimLftlskltGhaGsrlG 204
                                       +e  + ++ sPnnP g+ l+e+ +    +++ea+v  D ay       ++++ s+ ++ ++  tlsk  G aG rlG
  gi|330507633|ref|YP_004384061.1| 149 KEAKMAFICSPNNPTGNaLKEEELcrllETTEAIVFLDEAYVEfaeRSLAELVSRYENLVVGRTLSKAFGLAGMRLG 225
                                       45678899******9964887644444599**********96412245788899999999999************** PP

                                       EEEES CS
                       Alliinase_C 205 Walvk 209
                                       +al+ 
  gi|330507633|ref|YP_004384061.1| 226 YALMP 230
                                       **975 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.00099
                                       EE---SEEEEEESSSS..-HHHHHHTTTEEEEEGGGG.TS-TTEEEEESSS-HHHHH CS
                       Alliinase_C 298 repsPayaWlkcekeededcaevlrekkiltrsGevf.eaesryvrlsllkrdddfd 353
                                        +++  + +lk+e+ +d+  ++ + +k+i+ r+ + f +a++++vr+++    ++ d
  gi|330507633|ref|YP_004384061.1| 286 YPSQANFLYLKTEEASDSFAEK-FLQKGIIIRDCRSFrGAGENHVRVTVGTA-EEND 340
                                       2344557789999777555555.555666666666553899*****986433.3334 PP

>> DUF3670  SNF2 Helicase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.4e-06     0.044      79     121 ..     164     206 ..     163     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.4e-06
                           DUF3670  79 deeLseeEldrLaeakrpLvrlrgqWvevdpeelrraleflkr 121
                                       ++ L+eeEl rL+e+++ +v l   +ve  ++ l+++ ++ ++
  gi|330507633|ref|YP_004384061.1| 164 GNALKEEELCRLLETTEAIVFLDEAYVEFAERSLAELVSRYEN 206
                                       5789******************************999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 2421.58
//
Query:       gi|330507634|ref|YP_004384062.1|  [L=167]
Description: hypothetical protein MCON_1615 [Methanosaeta concilii GP6]
Scores for complete 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   69.9   0.0    3.8e-19   69.5   0.0    1.2  1  AAA_18    AAA domain
     0.0012   19.1   0.1      0.003   17.8   0.0    1.8  2  AAA_28    AAA domain
     0.0045   17.1   0.0       0.13   12.4   0.0    2.3  1  UPF0180   Uncharacterised protein family (UPF0180)
     0.0072   16.0   0.1        0.3   10.7   0.0    2.2  2  CoaE      Dephospho-CoA kinase
     0.0086   16.5   1.5      0.029   14.8   1.5    2.1  1  AAA       ATPase family associated with various cellular acti
  ------ inclusion threshold ------
      0.017   15.4   0.4      0.043   14.1   0.4    1.8  1  AAA_22    AAA domain
      0.018   14.8   0.0      0.023   14.4   0.0    1.3  1  AAA_24    AAA domain
       0.02   15.3   0.4      0.067   13.6   0.4    1.8  1  AAA_16    AAA ATPase domain
      0.024   14.5   0.1      0.052   13.4   0.1    1.5  1  NTPase_1  NTPase
       0.07   13.3   0.5       0.42   10.8   0.1    2.1  2  AAA_33    AAA domain
      0.084   11.8   0.1        1.1    8.2   0.0    2.0  2  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.098   12.6   0.0       0.44   10.6   0.0    1.9  2  AAA_5     AAA domain (dynein-related subfamily)
       0.16   12.3   0.1       0.29   11.5   0.1    1.4  1  AAA_19    AAA domain
       0.16   11.6   0.0        2.6    7.7   0.0    2.1  2  PRK       Phosphoribulokinase / Uridine kinase family
       0.21   11.1   0.6       0.32   10.5   0.6    1.7  1  AAA_25    AAA domain


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.0   3.1e-22   3.8e-19       1     130 []       3     114 ..       3     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 3.1e-22
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknl 77 
                                       I+ltGtpG+GKtt+a+ L  r   ++ ++ +++e gl ++ dp+  + ++++d+d l++ l +++         +  
  gi|330507634|ref|YP_004384062.1|   3 IALTGTPGTGKTTVAHLLPYR---VIDINALVRE-GLNFGTDPK--RGCLEADMDGLAERLVEMDSD-------QIS 66 
                                       89****************999...8999999998.*********..**********66665555553.......667 PP

                            AAA_18  78 vidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeild 130
                                       +++gh ++++         +vL++ p +l  Rle+Rgy++ ki+en eae+ld
  gi|330507634|ref|YP_004384062.1|  67 ILEGHFSHHFAQWS-----IVLRLAPRKLESRLEERGYSPEKIRENLEAEALD 114
                                       *********99844.....9******************************985 PP

>> AAA_28  AAA 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     0.003       2      20 ..       3      21 ..       2      70 .. 0.77
   2 ?   -1.2   0.0       1.8   2.1e+03     133     154 ..      96     117 ..      75     143 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      i++tG+++tGKTt++  L 
  gi|330507634|ref|YP_004384062.1|  3 IALTGTPGTGKTTVAHLLP 21
                                      99************99886 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                            AAA_28 133 ereaiderlrealrelgipvii 154
                                       er  + e++re l++   +vi 
  gi|330507634|ref|YP_004384062.1|  96 ERGYSPEKIRENLEAEALDVIL 117
                                       3333344444444433333333 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00011      0.13      12      74 ..      90     144 ..      88     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                           UPF0180  12 vkeaLrekGYeVvdleteedaqsvdaiVvtGqdtnvmgiedtetkapvInAsgktaeeIlqev 74 
                                       +++ L+e+GY+ ++++++ +a+  d+i v+  +           ++  I+A+g+t++e+ + v
  gi|330507634|ref|YP_004384062.1|  90 LESRLEERGYSPEKIRENLEAEALDVILVEAVEYCQ--------RVDEIDATGRTPQEVADLV 144
                                       67899***********98889999999987654332........3334999999999999887 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00025       0.3       2      34 ..       2      31 ..       1      40 [. 0.78
   2 ?    3.6   0.0      0.04        47      27      56 ..      47      76 ..      40     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                                      EEEEEESTTSSHHHHHHHHHHTT-EEEEHHHHH CS
                              CoaE  2 ivgltGgiasGKstvanlfadlgvpivDaDlvA 34
                                       ++ltG  ++GK+tva+l+    + ++D  ++ 
  gi|330507634|ref|YP_004384062.1|  2 QIALTGTPGTGKTTVAHLLP---YRVIDINALV 31
                                      599*************9974...5566666555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.04
                                      EEEHHHHHHHTTCCTHHHHHHHHHHHGGGC CS
                              CoaE 27 ivDaDlvArqvvepgsealkkiveeFgeei 56
                                        D D +A ++ve +s + + +  +F ++ 
  gi|330507634|ref|YP_004384062.1| 47 EADMDGLAERLVEMDSDQISILEGHFSHHF 76
                                      56999***************9999998765 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   1.5   2.4e-05     0.029       2      18 ..       4      20 ..       3     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                                      EEESSTTSSHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakav 18
                                       l+G+pGtGKT++a+ +
  gi|330507634|ref|YP_004384062.1|  4 ALTGTPGTGKTTVAHLL 20
                                      699***********987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   3.6e-05     0.043       8      28 ..       3      23 ..       2     144 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleq 28
                                      +++tG +GtGKTt++  l ++
  gi|330507634|ref|YP_004384062.1|  3 IALTGTPGTGKTTVAHLLPYR 23
                                      689************998776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.9e-05     0.023       4      27 ..       2      25 ..       1      76 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                            AAA_24  4 kiliyGpsgiGKTtlakelgpkpl 27
                                      +i+++G +g+GKTt+a  l+++++
  gi|330507634|ref|YP_004384062.1|  2 QIALTGTPGTGKTTVAHLLPYRVI 25
                                      699*************99977765 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   0.4   5.6e-05     0.067      27      52 ..       3      52 ..       2     164 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.6e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekd........................g 52
                                      + l+G +G+GK++++  l+ ++ +                         g
  gi|330507634|ref|YP_004384062.1|  3 IALTGTPGTGKTTVAHLLPYRVIDInalvreglnfgtdpkrgcleadmdG 52
                                      579************99996444333444445555555544444444440 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.4e-05     0.052       2      18 ..       3      19 ..       2      34 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-05
                                      EEEE--TTSSHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkk 18
                                      +++TG pG+GKtT+ + 
  gi|330507634|ref|YP_004384062.1|  3 IALTGTPGTGKTTVAHL 19
                                      89************986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00035      0.42       4      19 ..       5      20 ..       3      68 .. 0.79
   2 ?    0.7   0.0      0.45   5.4e+02     102     134 ..      81     114 ..      61     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                            AAA_33  4 lvGlpGsGKstlaerl 19
                                      l G pG+GK+t+a+ l
  gi|330507634|ref|YP_004384062.1|  5 LTGTPGTGKTTVAHLL 20
                                      78**********9864 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.45
                            AAA_33 102 vvvetdeetlkeRlakRaang.ddrsevpeeald 134
                                       +v++  +++l++Rl++R  +  + r +++ eald
  gi|330507634|ref|YP_004384062.1|  81 IVLRLAPRKLESRLEERGYSPeKIRENLEAEALD 114
                                       6677788899999999988752455566666655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00092       1.1      31      50 ..       2      21 ..       1      35 [. 0.82
   2 ?    1.8   0.0     0.083     1e+02     116     135 ..     107     126 ..      89     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00092
                                      EEEEEE-TTSSHHHHHHHHH CS
                              MeaB 31 vvGltGvPGaGkstlvealg 50
                                      ++ ltG+PG+Gk t+ + l 
  gi|330507634|ref|YP_004384062.1|  2 QIALTGTPGTGKTTVAHLLP 21
                                      588***********987665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.083
                                       HHHHTT-SEEEEEEESSTTH CS
                              MeaB 116 lleaaGfDvvlietvGvGqs 135
                                        lea   Dv+l+e v   q 
  gi|330507634|ref|YP_004384062.1| 107 NLEAEALDVILVEAVEYCQR 126
                                       57899999999999987774 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   0.00036      0.44       3      20 ..       4      21 ..       2      33 .. 0.84
   2 ?   -0.2   0.0      0.79   9.4e+02      89     107 ..      94     112 ..      68     158 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00036
                                      EEE--SSSSHHHHHHHGG CS
                             AAA_5  3 lLvGppGtgKselaerla 20
                                       L G pGtgK+++a  l 
  gi|330507634|ref|YP_004384062.1|  4 ALTGTPGTGKTTVAHLLP 21
                                      699***********9885 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.79
                                       HHSSEEE..-SSSEEE--- CS
                             AAA_5  89 leerrllleeggelvkakn 107
                                       leer +++e+ +e   a++
  gi|330507634|ref|YP_004384062.1|  94 LEERGYSPEKIRENLEAEA 112
                                       3333333333333333333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00024      0.29      13      28 ..       3      18 ..       1      34 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                            AAA_19 13 llvtaGpGtGKTrvlk 28
                                      +++t+ pGtGKT+v +
  gi|330507634|ref|YP_004384062.1|  3 IALTGTPGTGKTTVAH 18
                                      689*********9865 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0022       2.6       2      19 ..       3      20 ..       2      37 .. 0.87
   2 ?    1.8   0.0      0.15   1.8e+02     146     168 ..      88     110 ..      79     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0022
                               PRK  2 IgvagsSGaGkttvarkl 19
                                      I+++g  G Gkttva+ l
  gi|330507634|ref|YP_004384062.1|  3 IALTGTPGTGKTTVAHLL 20
                                      99*************987 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.15
                               PRK 146 rklqRDiaeRGrsleavldsilr 168
                                       rkl+   +eRG+s e + +++++
  gi|330507634|ref|YP_004384062.1|  88 RKLESRLEERGYSPEKIRENLEA 110
                                       78888899*********998876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.6   0.00027      0.32      36      57 ..       3      24 ..       2     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00027
                            AAA_25 36 allaGapgtGKttlaldlalav 57
                                      ++l+G pgtGKtt+a  l + v
  gi|330507634|ref|YP_004384062.1|  3 IALTGTPGTGKTTVAHLLPYRV 24
                                      589***********97776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1125.84
//
Query:       gi|330507635|ref|YP_004384063.1|  [L=283]
Description: ribose-phosphate pyrophosphokinase [Methanosaeta concilii GP6]
Scores for 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   65.1   0.0    3.8e-15   55.8   0.0    2.2  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    1.2e-17   63.9   0.8    2.1e-17   63.1   0.8    1.3  1  Pribosyltran    Phosphoribosyl transferase domain
      1e-08   35.4   0.4    1.7e-08   34.7   0.4    1.3  1  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    6.2e-06   25.8   0.1      1e-05   25.1   0.1    1.3  1  UPRTase         Uracil phosphoribosyltransferase
    0.00087   18.8   0.2       0.13   11.8   0.1    2.3  2  PRTase_2        Phosphoribosyl transferase
  ------ inclusion threshold ------
        0.2   11.5   0.0       0.28   11.1   0.0    1.1  1  RCS1            Regulator of chromosome segregation 1


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 !   55.8   0.0   1.3e-18   3.8e-15       3     113 ..       2     107 ..       1     109 [. 0.92
   2 !    7.3   0.0    0.0014       4.2      10      75 ..     164     232 ..     155     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 1.3e-18
                    Pribosyltran_N   3 ifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasa 79 
                                       i+ g +s+ La ++a+ lg  l+ ++ ++f+dgE + ++   +  ++v iiqs+ ++   +l+ ll ++d ++    
  gi|330507635|ref|YP_004384063.1|   2 IIGGPASQLLAGRVAAILGEVLALCDYKTFPDGESYTQVTAPLD-DKVAIIQSTPTD--RDLVYLLQLLDICQ---E 72 
                                       889999*********************************98875.6799****9766..99***********8...5 PP

                    Pribosyltran_N  80 kritaViPylgysrqdrk.ksrepisaklvaklLe 113
                                       ++i +ViPy+gy+rqd+  k+ ep++a+ va+ L+
  gi|330507635|ref|YP_004384063.1|  73 SSIDLVIPYFGYARQDKIfKPGEPMTARAVARALN 107
                                       679****************************9885 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0014
                    Pribosyltran_N  10 keLaekiakrlgvelgkakvsrfadgEikveiee.svrgkdvfiiqsls..kpvndnlmelllmidalr 75 
                                        ++a+  a+ lg      + +r +  E+++  +e +vr++dv+i  ++     +  + +e+l+   a+r
  gi|330507635|ref|YP_004384063.1| 164 VAMARTAAAALGADSDYLQKTRLSGTEVRMAPKEiDVRDRDVVIFDDMIatGGTMATAIEMLRAQGAAR 232
                                       567888889999999999999************99**********999844334556667776666666 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.8   7.1e-21   2.1e-17      18     124 ..     141     239 ..     133     261 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 7.1e-21
                                       TTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE- CS
                      Pribosyltran  18 laaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVD 94 
                                       l+ae + + + k +vv+ +++g+v +a   a +L++  +y++k++ ++     a+        +++d++++ V+i D
  gi|330507635|ref|YP_004384063.1| 141 LLAENVASLGLKDPVVISPDKGAVAMARTAAAALGADSDYLQKTRLSGTEVRMAP--------KEIDVRDRDVVIFD 209
                                       7888889999***********************************9999999998........9************* PP

                                       SEESSSHHHHHHHHHHHCC-BSEEEEEEEE CS
                      Pribosyltran  95 DildtGgTllaalelLkekgpeevriavlv 124
                                       D+++tGgT+  a+e L+++g+++v +a+++
  gi|330507635|ref|YP_004384063.1| 210 DMIATGGTMATAIEMLRAQGAARVYLAAVH 239
                                       ************************999987 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.4   5.6e-12   1.7e-08      80     152 ..     199     271 ..     191     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 5.6e-12
                                       --TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHHH CS
                    Pribosyl_synth  80 dvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqkl 152
                                       dv  r  +i dd+i    ++  a e+l+++Ga ++y  a h +l+ +a  +l  s ++ v+ t+t+ + +  +
  gi|330507635|ref|YP_004384063.1| 199 DVRDRDVVIFDDMIATGGTMATAIEMLRAQGAARVYLAAVHPVLTGSAVLKLYRSGVEGVLATDTLDKGVSTV 271
                                       8999999**********************************************************98877654 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   3.4e-09     1e-05     116     158 ..     195     237 ..     181     272 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.4e-09
                           UPRTase 116 Pkki..aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvls 158
                                       Pk+i  ++r v++ D +iaTGg++a+ai++L+ +g+   ++ +++
  gi|330507635|ref|YP_004384063.1| 195 PKEIdvRDRDVVIFDDMIATGGTMATAIEMLRAQGAA--RVYLAA 237
                                       6666668999***********************8875..444444 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0048        14      29      91 ..     132     190 ..     114     196 .. 0.83
   2 !   11.8   0.1   4.3e-05      0.13     120     154 ..     201     235 ..     189     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0048
                          PRTase_2  29 pstvreagaaLaellaeakkeelpepvlvigfAEtAtaLghgvadaleeealylhtTRekvag 91 
                                       p+  ++a+  Lae++a    +   ++ +vi+    A+a++++ a+al ++  yl+ TR + ++
  gi|330507635|ref|YP_004384063.1| 132 PADNLDATPLLAENVA----SLGLKDPVVISPDKGAVAMARTAAAALGADSDYLQKTRLSGTE 190
                                       6777788888999998....34456668899999*************99*********87655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4.3e-05
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklprkryv 154
                                       +++ +v+ DD i+tG t++  i+ l+++  ++ y 
  gi|330507635|ref|YP_004384063.1| 201 RDRDVVIFDDMIATGGTMATAIEMLRAQGAARVYL 235
                                       6799*********************9997766554 PP

>> RCS1  Regulator of chromosome segregation 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.3e-05      0.28      81     115 ..     162     196 ..     155     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.3e-05
                              RCS1  81 glqaaarsAknalGavSQkiQescqsgtkslvetq 115
                                       g  a+ar+A  alGa S  +Q++  sgt++ +  +
  gi|330507635|ref|YP_004384063.1| 162 GAVAMARTAAAALGADSDYLQKTRLSGTEVRMAPK 196
                                       45699***********************9766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2014.38
//
Query:       gi|330507636|ref|YP_004384064.1|  [L=444]
Description: PmbA/TldD family protein [Methanosaeta concilii GP6]
Scores for complete 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-52  176.9   0.1    9.2e-52  176.6   0.1    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 !  176.6   0.1   5.1e-56   9.2e-52       1     279 []      28     314 ..      28     314 .. 0.91

  Alignments for each domain:
  == domain 1  score: 176.6 bits;  conditional E-value: 5.1e-56
                                       EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-.. CS
                         PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea.. 75 
                                       eaev+   ++s  v +++  ve +s+s   glg+r++++g++gf+s++d +   l+ ++  av++a+  + d+ +  
  gi|330507636|ref|YP_004384064.1|  28 EAEVYGMVGRSVDVDLRREYVEMASESYHCGLGLRAVVDGAVGFSSSSDMA--QLKFVAMSAVRSARARGRDDTWia 102
                                       69*********************************999******9977777..9**********************9 PP

                                       ..................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEE CS
                         PmbA_TldD  76 ..................eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldve 134
                                                         +++s+ee i+++++l +   ++d         ++  vs+ +  + ++ +++nS G+++ 
  gi|330507636|ref|YP_004384064.1| 103 lpqpervtepegiydrrlDKISPEECIDIAHSLLAGCNEVD---------GAEPVSGGVACVSGTGFVLNSQGIELV 170
                                       99999999999999999999999999998888876655555.........577788889999999************ PP

                                       EEEEEEEEEEEEEE...STCSETEEEEEEEE..SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHH CS
                         PmbA_TldD 135 qtrtrvslslsvia.d.dggsgdgmgggsgy..edleeedleeiaeeaaekalasleakplppgkypVvlspeavgs 207
                                       +t+t +++s+++ia + d        +gs++   +  e +++++++ a e+a+asl+    + g+++V+l p av++
  gi|330507636|ref|YP_004384064.1| 171 ETSTLMQASMEAIArReD------VATGSEFfnSRHLELSMKSVGRLAGEMARASLGGATGEGGRFDVLLRPLAVAE 241
                                       **************4433......4456666553333478888**************8888**************** PP

                                       HHHGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 208 llheavghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                       ll+ a+  +lead++++grS l+++lGe +ase l ivdd++  gg+ s++fD+EGvp+qrtvl+e+G+Lk++
  gi|330507636|ref|YP_004384064.1| 242 LLEGAFLTSLEADSIQKGRSSLRGRLGEMIASEDLMIVDDGLLpGGIDSSAFDGEGVPSQRTVLVERGILKGF 314
                                       **********************889*****************99***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       187  (0.01043); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3429.67
//
Query:       gi|330507637|ref|YP_004384065.1|  [L=256]
Description: hypothetical protein MCON_1618 [Methanosaeta concilii GP6]
Scores for 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-52  177.7   0.1    3.5e-52  177.5   0.1    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.5   0.1   1.9e-56   3.5e-52       2     212 ..      20     234 ..      19     235 .. 0.92

  Alignments for each domain:
  == domain 1  score: 177.5 bits;  conditional E-value: 1.9e-56
                                       EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEEEEE..TTT.SEEEEEEE CS
                              PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprlyak..dsgsrdllvlqg 74 
                                       i+G+pg+G+Vg+l++d+++e+l aek+ ei+s++ +p     p+v+v+e+   +  ++++ya+  ++g+ dll++ g
  gi|330507637|ref|YP_004384065.1|  20 IEGLPGVGHVGKLVADHMVEELHAEKIIEIYSPH-FP-----PQVMVKEDgtIKQVKNEIYARrgQNGEPDLLIIIG 90 
                                       9*********************************.**.....********7777778888***96666********* PP

                                       ....E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT........- CS
                              PAC2  75 ....repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees........e 139
                                            + +++ye +++  ld+ae+++v++++ Lgg+++g+       ++++v+gaat+ el+ee++++        +
  gi|330507637|ref|YP_004384065.1|  91 dyqsATNEGHYE-LTSIFLDIAESYKVRRIYALGGYGTGQFV-----DKSSVMGAATSIELVEEMKTQgvlfqeneP 161
                                       777777777777.************************99886.....5669**************73334555668* PP

                                       CEEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                              PAC2 140 yggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                       +ggi+g++glLl++++ rg+++++l++ +++yl+dPkaa+++l++ls +lg+ev +  Lee+a+e+e+ + +l
  gi|330507637|ref|YP_004384065.1| 162 GGGIIGVSGLLLGLGALRGLDVICLMGVTSGYLVDPKAASEVLRVLSGILGIEVGMHALEERAKEMEKIIGKL 234
                                       ********************************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1890.20
//
Query:       gi|330507638|ref|YP_004384066.1|  [L=257]
Description: translation initiation factor 2 subunit alpha [Methanosaeta concilii GP6]
Scores for complete 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-23   81.0   0.0    1.3e-22   80.1   0.0    1.4  1  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    3.6e-12   46.4   0.1    7.3e-12   45.5   0.1    1.5  1  S1           S1 RNA binding domain
     0.0036   17.4   1.9      0.006   16.7   1.9    1.3  1  LPD39        Large polyvalent protein associated domain 39
  ------ inclusion threshold ------
      0.033   14.6   0.0      0.098   13.0   0.0    1.7  1  DUF3662      Protein of unknown function (DUF2662)


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 !   80.1   0.0   2.8e-26   1.3e-22       3     116 .]     117     226 ..     116     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 2.8e-26
                                       HCTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHH CS
                       EIF_2_alpha   3 eevgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkea 78 
                                       ++v+  l++ y+++y a+ ++ai++ e+l++++++ee  + L +  + ++k++ v i++++++t+ ++dGve I++a
  gi|330507638|ref|YP_004384066.1| 117 KRVADSLMAAYDSLYLAMeEAAISGAEALNEADLTEEDVKILESLSRDNVKIPSVDISGYVDITSPAPDGVEVIRKA 193
                                       578999*********************************************************************** PP

                                       HHHHST.S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                       EIF_2_alpha  79 LkageeasneeeveeeeevkikliapPeYvltvetldk 116
                                       Lk++++ ++     ++ ++++++i++P+Y+++v+++d+
  gi|330507638|ref|YP_004384066.1| 194 LKQARRTKD-----KDATLSVSYIGAPRYRIHVTAPDY 226
                                       **8777444.....569******************997 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.1   1.6e-15   7.3e-12       3      75 .]       8      81 ..       7      81 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1.6e-15
                                      TTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1  3 ekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                      e g  v  +Vt+v+++GafV ++  +g +g++++se+++   ++ + +++++G+++  kvl+vd  r  i+ls+k
  gi|330507638|ref|YP_004384066.1|  8 EPGSLVVCTVTQVVDFGAFVSIDeyAGKQGLIHISEVASG-WIKYIRDHVREGQKIVCKVLNVDTSRHHIDLSLK 81
                                      677788889******************************9.9999****************************86 PP

>> LPD39  Large polyvalent protein associated domain 39
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.9   1.3e-06     0.006      88     166 ..      70     145 ..      39     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-06
                             LPD39  88 dATlagvDPsktfkaeaelkeeretlkeeperkaeyaeLrkrfeaLpeeakalYkkvRdaYkkqaeelrealeenie 164
                                       d +   +D s ++    ++++ re+++e ++++++++ L  +++  pe+ak +      aY+ ++ +++ea +   e
  gi|330507638|ref|YP_004384066.1|  70 DTSRHHIDLSLKD---VNEHQRREKIQEWKADQKAWKWLEMAYKDRPEDAKRVADSLMAAYDSLYLAMEEAAISGAE 143
                                       4556789999999...8999999999999****************************************99766555 PP

                             LPD39 165 ra 166
                                         
  gi|330507638|ref|YP_004384066.1| 144 AL 145
                                       54 PP

>> DUF3662  Protein of unknown function (DUF2662)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.2e-05     0.098      34      89 ..     197     251 ..     186     255 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                           DUF3662  34 rremddnarvvsrgrvlaPneYtveLspeDyerlasleeelaeeladllaehareq 89 
                                       +r  +d+ +++s + + aP +Y++++   Dy++ +s  ++ a+ +  ++++h  e 
  gi|330507638|ref|YP_004384066.1| 197 ARRTKDKDATLSVSYIGAP-RYRIHVTAPDYKHAESVLKKAAQAIVSYIEQHGGEG 251
                                       2455667789999999888.8******************************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1062  (0.0592336); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 1969.88
//
Query:       gi|330507639|ref|YP_004384067.1|  [L=55]
Description: 30S ribosomal protein S27 [Methanosaeta concilii GP6]
Scores for complete 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   87.9   1.9    2.7e-25   87.8   1.9    1.0  1  Ribosomal_S27e  Ribosomal protein S27
    0.00039   20.4   1.6    0.00049   20.1   1.6    1.2  1  zinc_ribbon_6   Zinc-ribbon
     0.0071   16.4   0.5     0.0075   16.3   0.5    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.028   14.3   0.9      0.038   13.9   0.9    1.2  1  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.056   13.0   2.3       0.18   11.4   0.1    2.1  2  Sgf11           Sgf11 (transcriptional regulation protein)
       0.11   12.5   2.1       0.94    9.6   0.1    2.1  2  zf-BED          BED zinc finger
       0.12   12.5   0.8       0.14   12.2   0.8    1.1  1  DUF1451         Zinc-ribbon containing domain
        0.3   10.9   4.0       0.71    9.7   4.0    1.6  1  ZZ              Zinc finger, ZZ type
       0.68    9.8   3.9         17    5.4   0.4    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   1.9   1.4e-28   2.7e-25       2      54 ..       2      54 ..       1      55 [] 0.96

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 1.4e-28
                                      S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEEE CS
                    Ribosomal_S27e  2 rskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqilerl 54
                                       skF++vkC dCene+v+F ha+tvvkC+ Cg++L+ePtGGka +k  ++e+l
  gi|330507639|ref|YP_004384067.1|  2 PSKFVKVKCNDCENEQVIFAHASTVVKCLVCGRTLAEPTGGKALIKTTVVEVL 54
                                      59**********************************************99987 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.6   2.4e-07   0.00049      26      54 ..       4      33 ..       1      34 [. 0.83

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.4e-07
                     zinc_ribbon_6 26 kkvkilCnDCekksevkfhv.lglkCkeCg 54
                                      k vk+ CnDCe+++ +  h    +kC  Cg
  gi|330507639|ref|YP_004384067.1|  4 KFVKVKCNDCENEQVIFAHAsTVVKCLVCG 33
                                      679************999972568***996 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.5   3.8e-06    0.0075      69     105 ..       6      45 ..       1      52 [. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.8e-06
                                       -EEEETTTS-EEE.CHH.H.HHS-TTTSSS-EEEEESSSE CS
                              HypA  69 vkvrCreCgkefe.lee.k.alrCpkCgsadveivsGeel 105
                                       vkv+C++C++e    ++ +  ++C  Cg++  e ++G+ l
  gi|330507639|ref|YP_004384067.1|   6 VKVKCNDCENEQViFAHaStVVKCLVCGRTLAEPTGGKAL 45 
                                       799******9988433333567********9999999876 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.9   1.9e-05     0.038      11      37 ..       7      35 ..       3      37 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                                      --B-TTT-SB-.-S.SSS-EEEETTT--E CS
                              C1_1 11 ptfCkhCgefl.wg.kekqglkCswCkll 37
                                      + +C+ C++    + ++++ +kC +C+++
  gi|330507639|ref|YP_004384067.1|  7 KVKCNDCENEQvIFaHASTVVKCLVCGRT 35
                                      579****86544556***********986 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.5      0.11   2.1e+02       4      11 ..       7      14 ..       4      16 .. 0.81
   2 ?   11.4   0.1   9.1e-05      0.18       2      15 ..      24      37 ..      23      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.11
                                      EEE-TTTS CS
                             Sgf11  4 yvtCpnCg 11
                                       v+C+ C+
  gi|330507639|ref|YP_004384067.1|  7 KVKCNDCE 14
                                      689*9996 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 9.1e-05
                                      C-EEE-TTTSSEEE CS
                             Sgf11  2 seyvtCpnCgRqia 15
                                      s+ v+C+ CgR+ a
  gi|330507639|ref|YP_004384067.1| 24 STVVKCLVCGRTLA 37
                                      789********987 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.4     0.045        90      16      25 ..       7      16 ..       1      19 [. 0.84
   2 ?    9.6   0.1   0.00047      0.94      14      28 ..      24      38 ..      18      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.045
                                      --EETTTTEE CS
                            zf-BED 16 kavCryCgki 25
                                      k++C+ C+++
  gi|330507639|ref|YP_004384067.1|  7 KVKCNDCENE 16
                                      89*****985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00047
                                      SS--EETTTTEE--- CS
                            zf-BED 14 eqkavCryCgkilsr 28
                                      +++++C  Cg++l+ 
  gi|330507639|ref|YP_004384067.1| 24 STVVKCLVCGRTLAE 38
                                      689********9986 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.8     7e-05      0.14     114     141 ..       7      35 ..       3      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7e-05
                           DUF1451 114 tlvCekCg.kelalkkteeippCpkCgat 141
                                       ++ C+ C+ +++ + +++++ +C  Cg t
  gi|330507639|ref|YP_004384067.1|   7 KVKCNDCEnEQVIFAHASTVVKCLVCGRT 35 
                                       679****825689*************987 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.0   0.00036      0.71       4      25 ..       7      32 ..       4      35 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00036
                                      -EE-TTT-S......EESSEEEESSS CS
                                ZZ  4 kytCdgCsea....pligvRyhclrc 25
                                      k++C+ C +     +++ ++++cl+c
  gi|330507639|ref|YP_004384067.1|  7 KVKCNDCENEqvifAHASTVVKCLVC 32
                                      79******97333356799******9 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.4    0.0084        17      28      37 ..       7      16 ..       4      18 .. 0.71
   2 ?    4.3   3.8     0.019        37       2      14 ..       9      21 ..       8      36 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0084
                           TFIIS_C 28 fykCtkCghr 37
                                       +kC++C+++
  gi|330507639|ref|YP_004384067.1|  7 KVKCNDCENE 16
                                      5788888764 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.019
                           TFIIS_C  2 kCpkCgsreayff 14
                                      kC+ C +++++f 
  gi|330507639|ref|YP_004384067.1|  9 KCNDCENEQVIFA 21
                                      7888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 416.69
//
Query:       gi|330507640|ref|YP_004384068.1|  [L=93]
Description: 50S ribosomal protein L44e [Methanosaeta concilii GP6]
Scores for complete 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   82.8   3.3    2.3e-23   82.4   3.3    1.1  1  Ribosomal_L44  Ribosomal protein L44
  ------ inclusion threshold ------
      0.029   14.6   0.1       0.27   11.5   0.0    2.1  2  C1_4           TFIIH C1-like domain
       0.11   13.0   1.2       0.11   13.0   1.2    2.4  2  Ribosomal_L33  Ribosomal protein L33
       0.23   11.4   3.6        8.6    6.4   1.0    2.3  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
        0.3   11.6   4.2        6.4    7.4   1.1    2.3  2  zf-H2C2_2      Zinc-finger double domain
       0.37   11.1   2.8       0.79   10.0   0.2    2.1  2  zf-LITAF-like  LITAF-like 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 !   82.4   3.3   7.8e-27   2.3e-23       1      76 []      16      91 ..      16      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 7.8e-27
                                      EEEEEEEEE-------SSSHHHHHHHH.H-SSS..GGGGS----.--SSBB--EEEEETTT--EEE----BBS--EEE CS
                     Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgyg..GqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfelv 76
                                      kHt ++ve+++kg++s+l++++R++ r  +g+g  G++++v+++ +K+tK+++lr++C eCkk++ +++++a+kf+lv
  gi|330507640|ref|YP_004384068.1| 16 KHTAQTVERVRKGRASTLTRITRQKLR-ANGIGnqGKFSKVPGG-DKPTKRLNLRYRCGECKKAHNRPGFKAGKFDLV 91
                                      8**************************.99**************.******************************996 PP

>> C1_4  TFIIH C1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.14   4.2e+02      27      34 ..      10      17 ..       3      35 .. 0.77
   2 ?   11.5   0.0   9.1e-05      0.27       4      34 ..      47      77 ..      44      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.14
                              C1_4 27 rCekCknd 34
                                       C+ Ck++
  gi|330507640|ref|YP_004384068.1| 10 YCPFCKKH 17
                                      47777765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.1e-05
                              C1_4  4 gCqkkfpklakkkkdeeltssryrCekCknd 34
                                      g q kf k+    k ++  ++ryrC++Ck+ 
  gi|330507640|ref|YP_004384068.1| 47 GNQGKFSKVPGGDKPTKRLNLRYRCGECKKA 77
                                      56677777777777778899********985 PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.2   3.5e-05      0.11      30      42 ..       7      19 ..       2      21 .. 0.84
   2 ?    0.6   0.7      0.26   7.7e+02      25      39 ..      62      76 ..      59      80 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.5e-05
                                      EEEEETTTTEEEE CS
                     Ribosomal_L33 30 lkKYcprcrkhtl 42
                                      l+ Ycp+c+kht 
  gi|330507640|ref|YP_004384068.1|  7 LNAYCPFCKKHTA 19
                                      677********95 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.26
                                      -S--EEEEEETTTTE CS
                     Ribosomal_L33 25 perLelkKYcprcrk 39
                                      ++rL+l+  c  c+k
  gi|330507640|ref|YP_004384068.1| 62 TKRLNLRYRCGECKK 76
                                      567777666666665 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   1.0    0.0029       8.6      20      34 ..      10      24 ..       4      43 .. 0.81
   2 ?    5.8   0.1    0.0044        13      37      45 ..      68      76 ..      47      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0029
                     Zn_Tnp_IS1595 20 vCPhCgsrkayrikt 34
                                       CP+C++ +a ++++
  gi|330507640|ref|YP_004384068.1| 10 YCPFCKKHTAQTVER 24
                                      5*****998888887 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0044
                     Zn_Tnp_IS1595 37 lfqCkeCrk 45
                                      +++C eC+k
  gi|330507640|ref|YP_004384068.1| 68 RYRCGECKK 76
                                      8******97 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.1    0.0021       6.4      16      25 ..      10      19 ..       2      20 .. 0.74
   2 ?    5.2   0.1     0.011        32      14      23 ..      68      77 ..      57      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0021
                         zf-H2C2_2 16 eCplCdkaFk 25
                                       Cp+C+k ++
  gi|330507640|ref|YP_004384068.1| 10 YCPFCKKHTA 19
                                      8******876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                         zf-H2C2_2 14 pyeCplCdka 23
                                      +y C +C+ka
  gi|330507640|ref|YP_004384068.1| 68 RYRCGECKKA 77
                                      49******98 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00026      0.79       5      26 ..       8      29 ..       4      39 .. 0.77
   2 ?    1.4   0.2      0.13     4e+02      56      64 ..      68      76 ..      63      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00026
                     zf-LITAF-like  5 qvdCpaCqqrvvTsveyksgkl 26
                                      + +Cp+C++++  +ve+  +  
  gi|330507640|ref|YP_004384068.1|  8 NAYCPFCKKHTAQTVERVRKGR 29
                                      579****999988888876655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.13
                     zf-LITAF-like 56 ehyCpnCga 64
                                      +++C++C++
  gi|330507640|ref|YP_004384068.1| 68 RYRCGECKK 76
                                      678999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 708.53
//
Query:       gi|330507641|ref|YP_004384069.1|  [L=188]
Description: hypothetical protein MCON_1622 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.6   0.1      0.059   13.1   0.1    1.1  1  VirE      Virulence-associated protein E
      0.058   13.9   1.1       0.11   12.9   0.3    1.9  2  Sld5      GINS complex protein


Domain annotation for each model (and alignments):
>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.6e-06     0.059      63     150 ..      10      98 ..       5     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-06
                              VirE  63 sgKstfleklgeewftdslksvedk.davekiqgvliveiaEleasnkaeveaiKafitrkkdkfrapygrkvedfp 138
                                         Ks+ l+ l e+++ +  +  ++  +++ +i   + ve + l+ + k e +++ + i ++ +k+ +   r++ +  
  gi|330507641|ref|YP_004384069.1|  10 ERKSAELQPLDEDFYQQVGTYLTGMgQELSQIIDPFSVEAQILQDTLKSERSSLNKLIDQRIKKIVRRALRNARSAS 86 
                                       67**************9998888752568899999******************************99999******* PP

                              VirE 139 resvlvgttNed 150
                                       re v+ g t e+
  gi|330507641|ref|YP_004384069.1|  87 REEVFSGMTAEE 98 
                                       *******99765 PP

>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   1.3e-05      0.11      31     109 .]       4      99 ..       1      99 [. 0.75
   2 ?   -1.8   0.0      0.47   4.2e+03      68      79 ..     131     142 ..     104     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                                       HHCCCHHTTSSSSTTTTTTHHH.HHHHHHHHHT...................HCHHHHHHHHHHHHHHHHHHHTHCH CS
                              Sld5  31 eailedetkssdlpslpphfle.lavkllelard..................ldelkrllrdllevRlakirkfaen 88 
                                       ++ l +e+ks++l+ l ++f++ ++++l+ + ++                  l+  ++ l++l+++R++ki   a  
  gi|330507641|ref|YP_004384069.1|   4 ANALREERKSAELQPLDEDFYQqVGTYLTGMGQElsqiidpfsveaqilqdtLKSERSSLNKLIDQRIKKIVRRALR 80 
                                       55566677776777777776652678899999876666667766666665565566799*************99999 PP

                                       HHHHHHTS-TCCHCCS-HHHH CS
                              Sld5  89 ledaagggggellsglseeEk 109
                                       ++ +a  + +e  sg+++eE+
  gi|330507641|ref|YP_004384069.1|  81 NARSA--SREEVFSGMTAEET 99 
                                       99999..78888889999995 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.47
                                       HHHHHHHHHHHH CS
                              Sld5  68 krllrdllevRl 79 
                                       k +lr++  vRl
  gi|330507641|ref|YP_004384069.1| 131 KDILREYEVVRL 142
                                       678888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1289.05
//
Query:       gi|330507642|ref|YP_004384070.1|  [L=395]
Description: DNA primase small subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-17   64.5   0.0    2.8e-16   60.1   0.0    2.1  1  DNA_primase_S    DNA primase small subunit
  ------ inclusion threshold ------
      0.091   12.6   0.0       0.27   11.1   0.0    1.8  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda


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 !   60.1   0.0   3.1e-20   2.8e-16       1     176 [.      89     328 ..      89     329 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 3.1e-20
                                       EEEEEETTT-.TT--HHHHHHHHHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE--TTEEES-HHHHHHHH CS
                     DNA_primase_S   1 FDiDmddyddcseatvcekcwkfvsvavkvldellredfgfk..dilwvfsgrrGfHcwvsdkdarpltdeeraaiv 75 
                                       FD+D+d++ +    ++  ++ ++ +++ k+l  ll  dfgf   +i +vfsg+rG+H++v+d ++ +++  er+++v
  gi|330507642|ref|YP_004384070.1|  89 FDLDADHLRG-AASSYAGMLEQVKRETLKLLSFLL-SDFGFAesKISVVFSGGRGYHIHVRDPRIYSFGGDERREVV 163
                                       9********9.777888888999999999998877.******999******************************** PP

                                       HH........................................................................... CS
                     DNA_primase_S  76 nylnly....................................................................rp. 83 
                                       +yl+                                                                       + 
  gi|330507642|ref|YP_004384070.1| 164 DYLSGRglvldrfiheapvegwgreggrrliapardspgwggrinrsiisfveglrtldepgavavltrvrgigPKk 240
                                       *7665578999999999999999999999999999999999999988888888887777777777776666664222 PP

                                       ....................................HCHHHHCT--------..................------- CS
                     DNA_primase_S  84 ...lhpflsrsmlkivkpvveeiileeqdpf.....eikkllrllpdkslrekkkweakedivlvllyprldeqvtk 152
                                          ++++l++        v eei   + d f      +k ll+ + d++              l   + ++de+vt+
  gi|330507642|ref|YP_004384070.1| 241 assFYRSLEGE------GVIEEIRRGNLDLFrgsagIWKLLLKECLDSEGVV-------VGLNLNQERGETDEPVTA 304
                                       33355555554......44555656666677888888888888888888776.......344477889********* PP

                                       ----------....---------. CS
                     DNA_primase_S 153 gikhllkapfcihgktgnvcvpld 176
                                       ++++l++ p+++hg++g +++pl+
  gi|330507642|ref|YP_004384070.1| 305 DVRRLIRCPGSLHGGSGLRVTPLS 328
                                       *********************996 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 ?   -3.1   0.0      0.82   7.3e+03      20      27 ..     216     223 ..     215     223 .. 0.85
   2 ?   11.1   0.0     3e-05      0.27       3      30 ..     230     259 ..     228     266 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.82
                   DNA_pol_lambd_f  20 kGirtled 27 
                                       +G+rtl++
  gi|330507642|ref|YP_004384070.1| 216 EGLRTLDE 223
                                       59****95 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3e-05
                   DNA_pol_lambd_f   3 FtkvyGVGpktAkkwyak..Girtledlra 30 
                                       +t+v G+Gpk+A+ +y+   G   +e++r+
  gi|330507642|ref|YP_004384070.1| 230 LTRVRGIGPKKASSFYRSleGEGVIEEIRR 259
                                       89**************86456666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2908.37
//
Query:       gi|330507643|ref|YP_004384071.1|  [L=244]
Description: nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-34  118.3   0.0    4.1e-34  118.1   0.0    1.1  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   0.0   2.3e-38   4.1e-34       1     260 [.       2     230 ..       2     231 .. 0.90

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 2.3e-38
                                       EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBS..SSHHHHHHHHBHSSSHHHHHHHHHHHHHT CS
                      CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgy..keeahfleaAeaglgetlallaalarkng 75 
                                       r+A+ Q +   ++  +nl+++l l+++A + ga+++v PElf+ g+  +  ++f e   +   e+l+ ++ala++ +
  gi|330507643|ref|YP_004384071.1|   2 RAALLQQTVLPCQDLKNLSQALYLASSALEMGAEILVYPELFLSGFcyEPIDRFWERG-TRAFEELDPFRALAKDSD 77 
                                       799999999999**********************************874444444433.46789************* PP

                                       EEEEEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEE CS
                      CN_hydrolase  76 iavvigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaai 152
                                       +++++ + + +         n +++ld++g   + + K+h f          e++ f  gd+i +++t+ g++G++i
  gi|330507643|ref|YP_004384071.1|  78 CLIIGSVRGGR--------SNLGFCLDRTGL--KLRPKIHPF--------GEEKKHFDGGDSISPIATRWGRVGLEI 136
                                       ******99974........677********9..8******66........679999999**9*************** PP

                                       GGGGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE CS
                      CN_hydrolase 153 CyeigfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaii 229
                                       Cy+ +fpe++r lal++a++lv+++    +  +  ++qw +l+ ara+en+++ +a+n + g         g+S+ii
  gi|330507643|ref|YP_004384071.1| 137 CYDLRFPEVARSLALQDADFLVTVA----QFPAQREEQWRALSLARAIENQIPHLACNWAEG---------GGSMII 200
                                       ***********************55....5667889999**************888888888.........****** PP

                                       -TTS-EEEECCSSSTEEEEEEEEHHHHHHHH CS
                      CN_hydrolase 230 dpdGrilaglgeeeegvliaeidladvratr 260
                                       + +G++la++   ee ++  e+dl++  ++r
  gi|330507643|ref|YP_004384071.1| 201 SARGTVLAEAESGEE-IIFGEVDLSERDQVR 230
                                       **********99997.********9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1876.57
//
Query:       gi|330507644|ref|YP_004384072.1|  [L=287]
Description: Ion transport protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-29  103.3   8.1    1.4e-29  103.0   8.1    1.0  1  Ion_trans    Ion transport protein
    8.3e-15   54.5   3.0    8.3e-15   54.5   3.0    2.1  2  Ion_trans_2  Ion channel
  ------ inclusion threshold ------
       0.13   11.8   0.1       0.23   11.1   0.1    1.4  1  Sgf11        Sgf11 (transcriptional regulation protein)


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 !  103.0   8.1   2.4e-33   1.4e-29       5     244 ..      27     250 ..      24     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 2.4e-33
                                       HHHHHHHHHHHHHHHHCCCSSSSHHHHC..HHHHHHHHHHHHHHHHHHHHHHHHHTH........HHHHHHCHSHHH CS
                         Ion_trans   5 elfilllillncvflaletyfpedelek..tileilelvftaiftlemllkilalgl........likkrYlrdpwn 71 
                                       +l  +ll++ln+v++ +et +   +     +i+e+++++ ++ift+e +l+i+++           +++r+  +p  
  gi|330507644|ref|YP_004384072.1|  27 NLALMLLVVLNVVAVIMETVQWLYS--AygPIFEAFNVFSIGIFTIEYILRIWSCIEdpiyrapqGNRLRFAITPLA 101
                                       7889*************99987733..236************************55566788888889********* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGGGHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Ion_trans  72 ilDflvvlpsllslvlseesllllsvlrlfrvlrllklisrleglrtlvtalirsvkdllnvlllllvvlfifalig 148
                                       ++D+++vlp++l +v     l  ++++rlfr++r+lkl  +++ l+t+   ++r  k+ l ++l++++vl+i +   
  gi|330507644|ref|YP_004384072.1| 102 MVDLIAVLPFYLPFVIA--DLRFVRAMRLFRLFRILKLAHYSRALQTFDD-VLRLKKEELGLMLFTIIVLLITSAGL 175
                                       ************99764..49**************************777.88888888889999999999888777 PP

                                       HHHHTTSCCCCCCSCCSTSSSTTTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHH CS
                         Ion_trans 149 vqlfkgklreknecaktwenpnngntnFdnfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsfll 225
                                       +                  +++ +   F ++++a++w ++++ t+g+gdi++ t  ++      + ++++++ ++ l
  gi|330507644|ref|YP_004384072.1| 176 MYEA---------------EHDAQPEAFASIPDAMWWGIVTLATVGYGDIYPITPWGR------LIGSVVVILGIGL 231
                                       4333...............45555677*******************************......************* PP

                                       HHHHHHHHHHHHHHHHHHH CS
                         Ion_trans 226 lNlliaviadnfqeltere 244
                                       ++l+ ++ a+ f +++ ++
  gi|330507644|ref|YP_004384072.1| 232 FALPAGLLAMGFVQVQAQR 250
                                       *************999876 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2      0.52   3.1e+03      63      78 ..      28      43 ..      26      48 .. 0.67
   2 !   54.5   3.0   1.4e-18   8.3e-15       2      74 ..     165     240 ..     162     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.52
                                      HHHHHHHHHHHHHHHH CS
                       Ion_trans_2 63 lalfalflavlgkvlt 78
                                      lal++l++ +++ v++
  gi|330507644|ref|YP_004384072.1| 28 LALMLLVVLNVVAVIM 43
                                      6677777777666665 PP

  == domain 2  score: 54.5 bits;  conditional E-value: 1.4e-18
                                       HHHHTCHHHHHHHHT..........T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2   2 vlllvlifgaviysl......eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflav 72 
                                       +++l+++++ ++y        e++    s+ da+++ +vtl T+GYGdi+p+t++grl+  v+++lG++lfal   +
  gi|330507644|ref|YP_004384072.1| 165 IIVLLITSAGLMYEAehdaqpEAFA---SIPDAMWWGIVTLATVGYGDIYPITPWGRLIGSVVVILGIGLFALPAGL 238
                                       5677777777777779976655555...********************************************98777 PP

                                       HH CS
                       Ion_trans_2  73 lg 74 
                                       l+
  gi|330507644|ref|YP_004384072.1| 239 LA 240
                                       66 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   3.8e-05      0.23       5      16 ..     259     270 ..     255     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.8e-05
                                       EE-TTTSSEEEG CS
                             Sgf11   5 vtCpnCgRqiaa 16 
                                        +Cp+CgRqi +
  gi|330507644|ref|YP_004384072.1| 259 LVCPYCGRQIEG 270
                                       69********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2122.83
//
Query:       gi|330507645|ref|YP_004384073.1|  [L=254]
Description: hypothetical protein MCON_1627 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   12.9   0.1        1.8    8.8   0.0    2.3  2  DUF3420   Domain of unknown function (DUF3420)


Domain annotation for each model (and alignments):
>> DUF3420  Domain of unknown function (DUF3420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.019   3.3e+02       7      16 ..     163     172 ..     160     174 .. 0.88
   2 ?    8.8   0.0    0.0001       1.8      11      28 ..     191     208 ..     190     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.019
                           DUF3420   7 LEKeLPievl 16 
                                       LEK+ P +++
  gi|330507645|ref|YP_004384073.1| 163 LEKRIPGDLI 172
                                       9*****9997 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0001
                           DUF3420  11 LPievlakIkelRlkssl 28 
                                       LP ev++ I+ +Rl s+ 
  gi|330507645|ref|YP_004384073.1| 191 LPGEVFTEIEAIRLLSGA 208
                                       9*************8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1927.47
//
Query:       gi|330507646|ref|YP_004384074.1|  [L=414]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   97.1   0.0    1.7e-27   96.5   0.0    1.3  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.044   13.9   0.1      0.078   13.1   0.1    1.3  1  Chorein_N     N-terminal region of Chorein or VPS13
      0.065   13.4   4.2       0.16   12.2   4.2    1.7  1  Dockerin_1    Dockerin type I 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 !   96.5   0.0   2.9e-31   1.7e-27      12     232 ..     121     353 ..     110     358 .. 0.91

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 2.9e-31
                                       HHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHHHS-EEE- CS
                      Peripla_BP_2  12 llalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedeellksgiptviv 88 
                                       l+ lG ++k vgvd+t+    +    +++ + vg+ +e+d+E+++ l+PDlv+  ++   td+ e++l +g  ++ +
  gi|330507646|ref|YP_004384074.1| 121 LAVLGGEEKAVGVDNTVGERVELFPRLSQLPAVGTTSEPDIESIISLQPDLVVTFTNAPSTDALEDKLPEGMAVLRF 197
                                       6778************988877754444************************************************* PP

                                       ---TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE........EEEE-TTS CS
                      Peripla_BP_2  89 essntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse.kpkpvlvfggade......ggyvvagsns 158
                                       + s   +sl e++ +lg ll+ +d  + +  ++d+ + +++++++ + +++ + v+++ ++       +    +s++
  gi|330507646|ref|YP_004384074.1| 198 DLSRS-SSLREEMAVLGFLLDDPDSTQRYLDWYDRYIGEIQDKAARIeDEDRARVLMERERsadtgpTARWAYASGT 273
                                       ***97.*****************************************97777777777777677766455566799* PP

                                       TTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH.......HHHT-S--HHHHT-SHHHHTSHHHHT CS
                      Peripla_BP_2 159 yigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr.......aeadnktgleflkenpllaelpAvkn 228
                                       +++dl+d +g+ nia+ +  ++++++  E +   dp+vi+  +        + ++ k+ ++++++++++ ++ Av+ 
  gi|330507646|ref|YP_004384074.1| 274 GFTDLVDLAGGINIASGY-MEGNKDLETEFVIDKDPQVIIGLSYkggykssDPESMKAYYDEIMKTEGFGNISAVRD 349
                                       ******************.*******************************99999********************** PP

                                       T-EE CS
                      Peripla_BP_2 229 grVy 232
                                       grV 
  gi|330507646|ref|YP_004384074.1| 350 GRVH 353
                                       **95 PP

>> Chorein_N  N-terminal region of Chorein or VPS13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.3e-05     0.078      15      75 ..      52     113 ..      47     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                         Chorein_N  15 eyvenldrdqlkvsl.wsGeveLenlkLkkealdklelPfevkegvigklrlkipwsnlksk 75 
                                       e +++ ++  +  ++ + G v L +l+L +e++++    +++++g+ ++l+l++p++++++ 
  gi|330507646|ref|YP_004384074.1|  52 EIINGSKEATMLSDVnLDGTVDLSDLQLAEELIEDRAERISLIDGNKQNLTLELPLERILTL 113
                                       555444555554445589*****************8889*****************999875 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   4.2   2.6e-05      0.16       5      52 ..      37      79 ..      34      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.6e-05
                                      TSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHH CS
                        Dockerin_1  5 NgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDall 52
                                      N D +++ +D+  i+  +n     +s++ +   DvN DG+v+  D++l
  gi|330507646|ref|YP_004384074.1| 37 NMDDRIDQTDIDYIQEIIN-----GSKEATMLSDVNLDGTVDLSDLQL 79
                                      89*****************.....9999999***********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 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:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2941.79
//
Query:       gi|330507647|ref|YP_004384075.1|  [L=86]
Description: hypothetical protein MCON_1629 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       173  (0.00964917); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 612.25
//
Query:       gi|330507648|ref|YP_004384076.1|  [L=162]
Description: riboflavin synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.7e-16   57.9   0.2    1.1e-15   57.7   0.2    1.1  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
      0.042   13.6   0.2       0.63    9.8   0.0    2.0  2  DUF2859        Protein of unknown function (DUF2859)


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 !   57.7   0.2   1.2e-19   1.1e-15       3     137 ..       3     128 ..       1     132 [. 0.82

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.2e-19
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHH CS
                     DMRL_synthase   3 riaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphf 79 
                                       ri+i  ++f      ++ ++a++++k+      +i+++tVPG  +lp+aak+l+e++++ d vialG  + G  +++
  gi|330507648|ref|YP_004384076.1|   3 RIGIADTTF---ARVDMARAAVSTIKKEAS--VQIVRYTVPGIKDLPVAAKRLLEEDDC-DIVIALG--MPGPADKD 71 
                                       777777777...666888999999998774..59*********************6445.*******..9******* PP

                                       HHHHHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTC...CCHHHHHHHHHHHHH CS
                     DMRL_synthase  80 eyvaeavskglmrvsldtgvPvifgvltvd.teeqaleraggka...gnkGeeaaeaalema 137
                                       +++a+++s+gl+ ++l t+     ++l v  +e++a++     a   +++ +e+a +al+++
  gi|330507648|ref|YP_004384076.1|  72 KMCAHEASSGLIMAQLMTN----KHILEVFvHEDEAKDEKTL-AwlaEKRTAEHALNALSLV 128
                                       ******************9....5666666666666666632.2456999999999999886 PP

>> DUF2859  Protein of unknown function (DUF2859)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.018   1.6e+02      99     133 ..      18      52 ..      12      55 .. 0.86
   2 ?    9.8   0.0     7e-05      0.63      77     111 ..     103     137 ..      74     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.018
                           DUF2859  99 vGlvvnvesaaalqelrelaeglelapasgddlae 133
                                          v +++++a++q +r  ++g++  p+++++l e
  gi|330507648|ref|YP_004384076.1|  18 RAAVSTIKKEASVQIVRYTVPGIKDLPVAAKRLLE 52 
                                       5567789999******************9999875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 7e-05
                           DUF2859  77 GdDalSraWLkqrraaLrelqAvGlvvnvesaaal 111
                                       ++D+   aWL+++r a ++l+A  lv + ++ ++l
  gi|330507648|ref|YP_004384076.1| 103 AKDEKTLAWLAEKRTAEHALNALSLVFHPQTLTRL 137
                                       57999*********************998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1140.33
//
Query:       gi|330507649|ref|YP_004384077.1|  [L=656]
Description: signal transduction histidine-protein kinase [Methanosaeta concilii GP6]
Scores for 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  111.0   0.0    7.9e-32  110.1   0.0    1.5  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    1.5e-27   96.0   0.1    3.9e-27   94.7   0.1    1.7  1  Response_reg  Response regulator receiver domain
    1.2e-21   77.1   0.0    4.1e-10   39.9   0.0    2.4  2  PAS_4         PAS fold
    3.2e-21   75.1   0.3    1.1e-20   73.5   0.1    2.1  2  HisKA         His Kinase A (phospho-acceptor) domain
    1.6e-15   57.2   0.0    4.8e-13   49.3   0.0    2.5  2  PAS_9         PAS domain
    7.1e-13   48.5   0.0    3.4e-08   33.5   0.0    2.4  2  PAS           PAS fold
    6.2e-12   45.6   0.0    5.1e-09   36.3   0.0    2.5  2  PAS_3         PAS fold
    5.8e-08   32.6   0.0    0.00015   21.7   0.0    2.8  2  PAS_8         PAS domain
     0.0011   18.8   0.0     0.0026   17.6   0.0    1.6  2  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
     0.0082   16.7   0.0        1.3    9.6   0.0    2.4  2  PAS_10        PAS domain
  ------ inclusion threshold ------
      0.094   12.8   0.0       0.21   11.7   0.0    1.5  1  PAS_11        PAS 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 !  110.1   0.0   4.8e-35   7.9e-32       1     110 [.     391     504 ..     391     506 .. 0.92

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 4.8e-35
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE....TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTST CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikase....ddlvisveDnGiGipkedlkklfekfsq.ddstkrggg 72 
                                       gd +rLrq++ nl++Navkf t++g +ev+++ +      +l++ v D+GiG+p+++l++lf++fsq d+s +r++g
  gi|330507649|ref|YP_004384077.1| 391 GDASRLRQVLANLLSNAVKF-TDKGFVEVSVRGNAipegFELRFDVLDTGIGMPQDKLDRLFMPFSQiDSSITRRYG 466
                                       7999****************.8788777777752255689************************************* PP

                                       SSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  73 gtGlGlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       gtGlGl+i+k+lv +mgG+iw +s+pg G+tftft++ 
  gi|330507649|ref|YP_004384077.1| 467 GTGLGLAISKRLVGMMGGRIWAKSNPGVGSTFTFTIKV 504
                                       **********************************9986 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   0.1   2.4e-30   3.9e-27       1     111 [.     539     651 ..     539     652 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 2.4e-30
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT...TTSEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed...pelpv 74 
                                       +l+++D+ +++++l q+l++ gy + + a++g ++l+ l+++++d++l+Di+mp+mdG+e++++i ++    + +++
  gi|330507649|ref|YP_004384077.1| 539 ILLAEDNAVNQMVLLQMLRKIGY-QADLASNGFDVLAALDRQAYDVVLMDIQMPDMDGFEATRRILARFpkmKRPRI 614
                                       89*********************.*****************************************77663666799* PP

                                       EEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  75 iiltahseeedavealkagaddflsKpfdpeeLlkal 111
                                       i+ltah+ + d++++l+ag+d++lsKp+++e+L +al
  gi|330507649|ref|YP_004384077.1| 615 IALTAHALNGDRERCLEAGMDGYLSKPVKIEDLQSAL 651
                                       *********************************9987 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   2.5e-13   4.1e-10       6     110 .]      38     141 ..      34     141 .. 0.94
   2 !   34.8   0.0   9.5e-12   1.5e-08       1     110 []     157     261 ..     157     261 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.5e-13
                             PAS_4   6 dalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhye 82 
                                       ++++v ++  r++y+N+a+a+++g+ p+el+G+++ el  ++d++ l +a  r  +ge++ +++   + +g   +++
  gi|330507649|ref|YP_004384077.1|  38 QGIVVSSEGWRFEYVNPAFARMVGRMPKELIGRSMDELIHPHDRPILIQARSRRQAGETSSYEARLIRSDGCVFPVQ 114
                                       6788888899***************************99999***********************9999******** PP

                             PAS_4  83 lrllPlrdesGevigvlvisrDiTerrr 110
                                       ++ +P    +G+  g +v ++D+Ter+r
  gi|330507649|ref|YP_004384077.1| 115 VTGTPR-WQDGKFFGSIVAVTDLTERKR 141
                                       *****6.78*****************97 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 9.5e-12
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       lds+pd ++ ld++g++l++ +   +++ ap+e ++Gk  ++++p+++ +  +++++ + ++++ + f+  l  +ge
  gi|330507649|ref|YP_004384077.1| 157 LDSIPDSIFLLDKEGNFLDYRTPNSSILYAPAELFMGKNIHSIMPQDLVELTMNNIEMARQSGKMQVFEYQLPANGE 233
                                       79******************999999*************************************************** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        +h+e r++     +G+  ++l+++rD+Ter+r
  gi|330507649|ref|YP_004384077.1| 234 IKHFEARINLC---EGG--DFLALVRDVTERKR 261
                                       ********996...345..6***********97 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 !   73.5   0.1   6.5e-24   1.1e-20       1      67 []     279     344 ..     279     344 .. 0.97
   2 ?   -2.9   0.0       4.6   7.5e+03      47      59 ..     392     404 ..     387     407 .. 0.65

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 6.5e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       ++++fla+++HE+rtPL+a++g + +L ++ +lt+e++ yle+++++++ l+++++d+Ld+s+i++g
  gi|330507649|ref|YP_004384077.1| 279 AKSEFLANMSHEIRTPLNAVIGLTGLLLDT-DLTPEQRNYLEIVRNSSDSLLSVINDILDFSKIDGG 344
                                       589************************996.9*********************************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.6
                                       HHHHHHHHHHHHH CS
                             HisKA  47 earrldhlvedlL 59 
                                        a rl++++ +lL
  gi|330507649|ref|YP_004384077.1| 392 DASRLRQVLANLL 404
                                       5667777777765 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   2.9e-16   4.8e-13       3     104 .]      39     138 ..      37     138 .. 0.88
   2 ?    5.5   0.0     0.012        20       1     104 []     161     258 ..     161     258 .. 0.64

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2.9e-16
                             PAS_9   3 gilidnpdg.rilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       gi++  ++g r +y+N+a++r+ G  p+e++g+s+++l+ ++ ++   ++a  ++   +  ++e  lir++g  f+v
  gi|330507649|ref|YP_004384077.1|  39 GIVVS-SEGwRFEYVNPAFARMVGRMPKELIGRSMDELI-HPHDRPILIQARSRRQAGETSSYEARLIRSDGCVFPV 113
                                       67765.8885777**************************.7777777777777777779****************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                       ++t +p + +dg+++g iv ++D+te
  gi|330507649|ref|YP_004384077.1| 114 QVTGTPRW-QDGKFFGSIVAVTDLTE 138
                                       *******6.67899999********8 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.012
                             PAS_9   1 pdgilidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirknge 74 
                                       pd+i++ +++g+ l y  +    l+   +e ++gk+i+ ++  +++  e   + +e+ r+  k + +e++l  + ge
  gi|330507649|ref|YP_004384077.1| 161 PDSIFLLDKEGNFLdYRTPNSSILY-APAELFMGKNIHSIM--PQDLVELTMNNIEMARQsgKMQVFEYQLPAN-GE 233
                                       78999999******77777777663.45666**********..4444444444444444445566777777765.66 PP

                             PAS_9  75 tfwvlltaspvkdddgelvgiivilrDite 104
                                         ++++++      +g+ ++  +++rD+te
  gi|330507649|ref|YP_004384077.1| 234 IKHFEARINLC---EGGDFL--ALVRDVTE 258
                                       66666666666...333344..78888876 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   2.1e-11   3.4e-08       6     101 ..      32     124 ..      27     136 .. 0.73
   2 !   12.8   0.0   5.6e-05     0.091       3      94 ..     153     242 ..     151     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.1e-11
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHH..HHTT-ECCCCEEEE CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqll..eqgeesrageisfk 80 
                                       ++ +   +i+v  e  r+ yvN+a++++ G  ++e++g+s+ +lih+ d    + +l q++  +q+ e +++e ++ 
  gi|330507649|ref|YP_004384077.1|  32 VMATVGQGIVVSSEGWRFEYVNPAFARMVGRMPKELIGRSMDELIHPHD----RPILIQARsrRQAGETSSYEARLI 104
                                       5667788999999999999**************************9985....344444430133444444455555 PP

                                       CTTSSEEEEEEEEEEEEETTE CS
                               PAS  81 lrdgrpihlevraspvrdagg 101
                                       + dg++++++v+ +p+    g
  gi|330507649|ref|YP_004384077.1| 105 RSDGCVFPVQVTGTPRWQD-G 124
                                       57************97544.4 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.6e-05
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                        r +l+s+pd if++D+ g++l   +   ++l  ++e  +gk++   ++ +    l+el  +++e +++s  +++ f
  gi|330507649|ref|YP_004384077.1| 153 NRLLLDSIPDSIFLLDKEGNFLDYRTPNSSILYAPAELFMGKNIHSIMPQD----LVELTMNNIEMARQSGKMQV-F 224
                                       6889*****************************************777766....99999999999999988888.8 PP

                                       EC...TTSSEEEEEEEEE CS
                               PAS  80 kl...rdgrpihlevras 94 
                                       ++    +g+++h+e r +
  gi|330507649|ref|YP_004384077.1| 225 EYqlpANGEIKHFEARIN 242
                                       888899999999998876 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   3.1e-12   5.1e-09       3      80 ..      51     124 ..      49     133 .. 0.89
   2 !    6.7   0.0    0.0053       8.6      14      73 ..     185     242 ..     183     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 3.1e-12
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirden 79 
                                       yv++++ +++G  p el+g+  s+ +l+hp Dr+ + +a  +  ++ +  + e R++r dG ++ v+ ++++   ++
  gi|330507649|ref|YP_004384077.1|  51 YVNPAFARMVGRMPKELIGR--SMDELIHPHDRPILIQARSRRQAGET-SSYEARLIRSDGCVFPVQVTGTPR-WQD 123
                                       9*******************..*******************9985555.689********************9.444 PP

                             PAS_3  80 g 80 
                                       g
  gi|330507649|ref|YP_004384077.1| 124 G 124
                                       4 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0053
                             PAS_3  14 yspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwvearar 73 
                                       y p+el     + +  + p+D  e ++++++ a ++g+   +ey  + ++Ge+ ++ear++
  gi|330507649|ref|YP_004384077.1| 185 YAPAELFMG--KNIHSIMPQDlVELTMNNIEMARQSGKMQVFEY-QLPANGEIKHFEARIN 242
                                       677777777..445555555559********9999999445677.5677********9986 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0     9e-08   0.00015       3      54 ..      29      81 ..      27      94 .. 0.75
   2 !    7.8   0.0     0.002       3.3       4      24 ..     154     174 ..     153     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 9e-08
                             PAS_8  3 lralfesspdgiavvdlgdrivdvNqaalellGys..adlkgellgqllpvlrp 54
                                        +++ ++ +gi+v  +g+r+ +vN+a++++ G +  ++l+g  +++l++ ++ 
  gi|330507649|ref|YP_004384077.1| 29 AHQVMATVGQGIVVSSEGWRFEYVNPAFARMVG-RmpKELIGRSMDELIHPHDR 81
                                      578999999****766888**************.85566666666555555444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.002
                             PAS_8   4 ralfesspdgiavvd.lgdriv 24 
                                       r l++s+pd+i+++d +g+ ++
  gi|330507649|ref|YP_004384077.1| 154 RLLLDSIPDSIFLLDkEGN-FL 174
                                       779***********96666.55 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 ?   -4.0   0.0       7.4   1.2e+04       8      17 ..     318     327 ..     317     332 .. 0.85
   2 !   17.6   0.0   1.6e-06    0.0026       4      79 ..     397     474 ..     394     485 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 7.4
                       HATPase_c_3   8 aelvdNsldA 17 
                                       +e+v+Ns d+
  gi|330507649|ref|YP_004384077.1| 318 LEIVRNSSDS 327
                                       69*****986 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.6e-06
                       HATPase_c_3   4 ekAlaelvdNsld.Adaenvkievnknr...gktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiG 76 
                                       +++la l+ N++   d   v+++v  n    g + ++ + D G Gm++++l++ + + ++  +  +  + +G  G+G
  gi|330507649|ref|YP_004384077.1| 397 RQVLANLLSNAVKfTDKGFVEVSVRGNAipeGFELRFDVLDTGIGMPQDKLDRLFMPFSQIDS--SITRRYGGTGLG 471
                                       689*********98999999999998764335559******************6665555444..257888999999 PP

                       HATPase_c_3  77 lkl 79 
                                       l  
  gi|330507649|ref|YP_004384077.1| 472 LAI 474
                                       544 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.027        45      20     105 ..      48     136 ..      33     137 .. 0.74
   2 !    9.6   0.0   0.00083       1.3       3      80 ..     155     234 ..     154     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.027
                            PAS_10  20 qirrFtpa.akklfklipadvGrpladihpkkavknveeviealrtgekdevevvv.pkngkwvlvrylpy.rdedg 93 
                                       ++ + +pa a+++ ++ ++ +Gr+++++ +++  + + +   + + ge+   e     ++g ++ v++    r +dg
  gi|330507649|ref|YP_004384077.1|  48 RFEYVNPAfARMVGRMPKELIGRSMDELIHPHDRPILIQARSRRQAGETSSYEARLiRSDGCVFPVQVTGTpRWQDG 124
                                       667778864678888888889******99988888888888888888886555544257777777776643277888 PP

                            PAS_10  94 eiaGvvetfvDi 105
                                       ++ G ++ ++D+
  gi|330507649|ref|YP_004384077.1| 125 KFFGSIVAVTDL 136
                                       888888888887 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00083
                            PAS_10   3 nlLnstpieltflDdnlqirrFtp.aakklfklipadvGrpladihpkkavknveeviealrtgek.devevvvpkn 77 
                                        lL+s+p ++  lD++ +++ + + +++ l+   +  +G ++ +i p++ v+ + + ie  r++ k ++ e++ p n
  gi|330507649|ref|YP_004384077.1| 155 LLLDSIPDSIFLLDKEGNFLDYRTpNSSILYAPAELFMGKNIHSIMPQDLVELTMNNIEMARQSGKmQVFEYQLPAN 231
                                       5899******************7725556666667789**********99998888777777665538888888877 PP

                            PAS_10  78 gkw 80 
                                       g++
  gi|330507649|ref|YP_004384077.1| 232 GEI 234
                                       754 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.21      30      89 ..      63     119 ..      56     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                            PAS_11  30 lekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktkskl 89 
                                        +k el+grs+ +L+hp+d+  l ++ +  +   ge++s   RL+ s++ +  v+ ++  
  gi|330507649|ref|YP_004384077.1|  63 MPK-ELIGRSMDELIHPHDRPILIQARSRRQ--AGETSSYEARLIRSDGCVFPVQVTGTP 119
                                       455.9****************9999877666..777777779999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 4922.85
//
Query:       gi|330507650|ref|YP_004384078.1|  [L=335]
Description: hypothetical protein MCON_1633 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2589.54
//
Query:       gi|330507651|ref|YP_004384079.1|  [L=165]
Description: rubrerythrin [Methanosaeta concilii GP6]
Scores for 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   75.3  14.5    8.9e-20   71.5  14.5    2.0  1  Rubrerythrin     Rubrerythrin
  ------ inclusion threshold ------
      0.017   15.0   0.5       0.61   10.0   0.0    2.5  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
      0.026   14.6   0.8      0.043   13.9   0.8    1.3  1  DZR              Double zinc ribbon
      0.072   13.0   5.1        2.5    8.0   5.1    2.1  1  Ferritin         Ferritin-like domain
       0.08   12.7   5.0        1.3    8.7   0.2    2.1  2  Haem_oxygenas_2  Iron-containing redox enzyme
       0.12   12.3   1.7        8.7    6.3   0.2    2.5  2  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
       0.47   10.5   6.7        6.1    7.0   0.4    2.6  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
        1.1    9.1   2.8         31    4.5   0.3    2.6  2  zf-C2H2_9        C2H2 type zinc-finger (1 copy)
        1.4    8.5   5.2          6    6.5   0.2    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
        1.6    8.6   4.3        1.8    8.5   1.4    2.4  2  Cys_rich_CPCC    Cysteine-rich CPCC
        2.6    8.6   6.1         19    5.9   0.3    2.8  2  Zn-C2H2_12       Autophagy receptor zinc finger-C2H2 domain
        3.6    8.2   5.5        7.6    7.2   0.1    3.1  3  zf-C2H2          Zinc finger, C2H2 type
        6.4    7.4   6.5        7.9    7.1   1.1    2.4  2  zf-H2C2_2        Zinc-finger double 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 !   71.5  14.5   6.5e-23   8.9e-20       1     135 [.       6     119 ..       6     121 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 6.5e-23
                                       HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS------- CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakp 76 
                                       ++L +A+agEs a r Y ++a +a+ egy q a+lF++ Ae+E+ Ha+++ ++l++++ ++e               
  gi|330507651|ref|YP_004384079.1|   6 DFLREAFAGESGANRKYSIFAAQADkEGYAQAARLFRAAAEAEAVHAANHLRALKAIKTTKE--------------- 67 
                                       79******************************************************988888............... PP

                                       TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  77 kflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrk 135
                                              nL+eai+g+++e ++my+++  +a++eg  +a+++f ++   E++H+ ++  
  gi|330507651|ref|YP_004384079.1|  68 -------NLREAIAGETHEFKDMYPEMIAIAKEEGARDAERSFNYANAVEEHHAWLYHD 119
                                       .......**********************************************988876 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00044      0.61       4      22 ..     124     142 ..     123     149 .. 0.85
   2 ?    2.9   0.2     0.069        94      14      21 ..     149     156 ..     143     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00044
                         zf-C2H2_3   4 LdlgqksfgasqCkeCgMv 22 
                                       Ld+ +  f    C++CgM+
  gi|330507651|ref|YP_004384079.1| 124 LDIQKEPFPYYVCPVCGMT 142
                                       788777888888******7 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.069
                         zf-C2H2_3  14 sqCkeCgM 21 
                                        +C++Cg 
  gi|330507651|ref|YP_004384079.1| 149 DKCPVCGV 156
                                       56****96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.8   3.1e-05     0.043      13      37 ..     134     157 ..     127     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.1e-05
                               DZR  13 rfCseCgtklkavaaedrCpsCgek 37 
                                        +C+ Cg +++  +a+d+Cp Cg k
  gi|330507651|ref|YP_004384079.1| 134 YVCPVCGMTVD-HKAPDKCPVCGVK 157
                                       579******97.7889******965 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.1    0.0018       2.5       4     111 ..       8      96 ..       5     126 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCSS CS
                          Ferritin   4 LneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkefgs 80 
                                       L+e++a e  a  +y  +a+ ++ +g+ + a +f+  ae e  ha   +  ++a+                      
  gi|330507651|ref|YP_004384079.1|   8 LREAFAGESGANRKYSIFAAQADKEGYAQAARLFRAAAEAEAVHAANHLRALKAIKT-------------------- 64 
                                       888889999999999999999999999999999999999999999655555555444.................... PP

                                       HHHHHHHHHHHHH.HHHHHHHHHHHHHHHTT- CS
                          Ferritin  81 veevleaalehek.kvteslrelielaeeegD 111
                                       ++e l++a++ e+ +  +++ e+i++a+eeg 
  gi|330507651|ref|YP_004384079.1|  65 TKENLREAIAGEThEFKDMYPEMIAIAKEEGA 96 
                                       33333333333321233344444444444444 PP

>> Haem_oxygenas_2  Iron-containing redox enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.9    0.0064       8.8     114     168 ..      23      75 ..      10      85 .. 0.77
   2 ?    8.7   0.2   0.00096       1.3      48      69 ..     110     131 ..      86     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0064
                   Haem_oxygenas_2 114 lklaeelrelgldeeapeyfdlHvtiDnaHaamaleaviellateepeeqedvle 168
                                        ++a+   + g   +a + f++ ++++++Haa  l +++++++t++++++e+++ 
  gi|330507651|ref|YP_004384079.1|  23 SIFAAQADKEGYA-QAARLFRAAAEAEAVHAANHL-RALKAIKTTKENLREAIAG 75 
                                       5555555555555.67899****************.9999***999777777764 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00096
                   Haem_oxygenas_2  48 ernHvelyrrllkalGldeepl 69 
                                       e++H+ ly+++l++l++++ep 
  gi|330507651|ref|YP_004384079.1| 110 EEHHAWLYHDMLEGLDIQKEPF 131
                                       445**************99986 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2    0.0063       8.7       3      11 ..     135     143 ..     135     146 .. 0.84
   2 ?    4.8   0.1     0.019        26       3       8 ..     150     155 ..     149     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0063
                                       B-TTT--BB CS
                      zf-FPG_IleRS   3 pCpRCwryi 11 
                                       +Cp+C++++
  gi|330507651|ref|YP_004384079.1| 135 VCPVCGMTV 143
                                       6*****996 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.019
                                       B-TTT- CS
                      zf-FPG_IleRS   3 pCpRCw 8  
                                       +Cp+C+
  gi|330507651|ref|YP_004384079.1| 150 KCPVCG 155
                                       9****9 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.4    0.0044       6.1       2       9 ..     136     143 ..     135     147 .. 0.83
   2 ?    6.0   1.3    0.0088        12       1       6 [.     150     155 ..     150     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0044
                    DNA_ligase_ZBD   2 CPvCGsav 9  
                                       CPvCG  v
  gi|330507651|ref|YP_004384079.1| 136 CPVCGMTV 143
                                       *****765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0088
                    DNA_ligase_ZBD   1 hCPvCG 6  
                                       +CPvCG
  gi|330507651|ref|YP_004384079.1| 150 KCPVCG 155
                                       6****9 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 ?    4.5   0.3     0.022        31       3      12 ..     135     144 ..     133     150 .. 0.84
   2 ?    4.4   0.1     0.024        33       3      15 ..     150     162 ..     148     165 .] 0.77

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.022
                                       B-TTT--B-S CS
                         zf-C2H2_9   3 lCPvCevkfn 12 
                                       +CPvC + ++
  gi|330507651|ref|YP_004384079.1| 135 VCPVCGMTVD 144
                                       7*****9987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.024
                                       B-TTT--B-SSHH CS
                         zf-C2H2_9   3 lCPvCevkfnswk 15 
                                        CPvC vk   +k
  gi|330507651|ref|YP_004384079.1| 150 KCPVCGVKGSMFK 162
                                       5******976555 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2    0.0044         6       1       8 [.     134     141 ..     133     147 .. 0.67
   2 ?    3.7   1.0     0.033        45       2       8 ..     150     156 ..     150     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0044
                                       EEETTTTC CS
                      TF_Zn_Ribbon   1 ykCPnCgs 8  
                                       y+CP+Cg 
  gi|330507651|ref|YP_004384079.1| 134 YVCPVCGM 141
                                       67777774 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.033
                                       EETTTTC CS
                      TF_Zn_Ribbon   2 kCPnCgs 8  
                                       kCP+Cg 
  gi|330507651|ref|YP_004384079.1| 150 KCPVCGV 156
                                       7****96 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.67   9.3e+02      39      54 ..      15      31 ..       5      50 .. 0.76
   2 ?    8.5   1.4    0.0013       1.8       1      25 [.     134     155 ..     134     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.67
                     Cys_rich_CPCC 39 eggaNk.vsLreArknf 54
                                      e+gaN+  s+  A++  
  gi|330507651|ref|YP_004384079.1| 15 ESGANRkYSIFAAQADK 31
                                      68899889999998765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0013
                     Cys_rich_CPCC   1 yqCpcCgyltleeeegsydiCpvCf 25 
                                       y Cp+Cg ++ +++  + d CpvC 
  gi|330507651|ref|YP_004384079.1| 134 YVCPVCGMTV-DHK--APDKCPVCG 155
                                       57*****755.555..578999995 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.1      0.04        55       2       7 ..     135     140 ..     135     142 .. 0.85
   2 ?    5.9   0.3     0.013        19       2       8 ..     150     156 ..     150     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.04
                        Zn-C2H2_12   2 eCPlCs 7  
                                       +CP+C+
  gi|330507651|ref|YP_004384079.1| 135 VCPVCG 140
                                       7****8 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
                        Zn-C2H2_12   2 eCPlCse 8  
                                       +CP+C++
  gi|330507651|ref|YP_004384079.1| 150 KCPVCGV 156
                                       7****85 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       2.9     4e+03       8      20 ..     101     113 ..     100     118 .. 0.78
   2 ?    7.2   0.1    0.0055       7.6       1      11 [.     134     144 ..     134     147 .. 0.83
   3 ?    2.5   0.3      0.17   2.4e+02       2       7 ..     150     155 ..     149     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.9
                                       EEESSHHHHHHHH CS
                           zf-C2H2   8 ksFkrksnLkrHi 20 
                                       +sF+     + H 
  gi|330507651|ref|YP_004384079.1| 101 RSFNYANAVEEHH 113
                                       7999999888886 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0055
                                       EEETTTTEEES CS
                           zf-C2H2   1 ykCpdCgksFk 11 
                                       y+Cp+Cg++  
  gi|330507651|ref|YP_004384079.1| 134 YVCPVCGMTVD 144
                                       9******9865 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.17
                                       EETTTT CS
                           zf-C2H2   2 kCpdCg 7  
                                       kCp+Cg
  gi|330507651|ref|YP_004384079.1| 150 KCPVCG 155
                                       8****9 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.1    0.0057       7.9      11      23 ..     129     142 ..     118     145 .. 0.84
   2 ?    2.6   0.5      0.15   2.1e+02      16      22 ..     150     156 ..     144     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0057
                         zf-H2C2_2  11 gekp.yeCplCdka 23 
                                        ++p y Cp+C+ +
  gi|330507651|ref|YP_004384079.1| 129 EPFPyYVCPVCGMT 142
                                       578989*****965 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.15
                         zf-H2C2_2  16 eCplCdk 22 
                                       +Cp+C+ 
  gi|330507651|ref|YP_004384079.1| 150 KCPVCGV 156
                                       8****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      787  (0.0438954); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); 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: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1310.52
//
Query:       gi|330507652|ref|YP_004384080.1|  [L=177]
Description: hypothetical protein MCON_1635 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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      0.083   12.9   0.0    2.0  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 ?   12.9   0.0   4.6e-06     0.083      19      82 ..      20      95 ..       3     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.6e-06
                                      EBSCSSSSSSSS-SEEEEET..TEEEEEEEEE...ESSSEEEE........EHHHHHHHHHHHHHHTCEEEEEEEET CS
                               Hjc 19 RsagSggatkplpDviAirg..dvvlviEvKs...skkeriyl........kkeqvekllefarkaggelllavklq 82
                                      R   S  a  +l D++   +  + +l+iE+Ks   +k + +y           +q+e+ ++f +++g + +lav l+
  gi|330507652|ref|YP_004384080.1| 20 RLRQSRFA-TQLADILVDSKiaEYYLAIECKSldaRKTRSLYFkqhfseasGGHQIERETDFITRSGRQGILAVELR 95
                                      66666666.5778887554422669******94323344778899999998899************99999998774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.34u 0.20s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 1514.13
//
Query:       gi|330507653|ref|YP_004384081.1|  [L=245]
Description: thymidylate synthase, methanogen type [Methanosaeta concilii GP6]
Scores for 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-18   64.5   0.0    1.3e-17   63.9   0.0    1.3  1  Thymidylat_synt  Thymidylate synthase


Domain annotation for each model (and alignments):
>> Thymidylat_synt  Thymidylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0     7e-22   1.3e-17      88     223 ..     107     239 ..      50     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 7e-22
                                       TB-SSSHHHHHHHBTSTTTSSB-HHHHHHHHHHHSTT-ST-EEE---GGGGGGSSS--SEEEEEEEE..SEETEEEE CS
                   Thymidylat_synt  88 gdlgpvYGkqwrkfkaeegkkidqlakvidqlkenpdsRriivsawnpaeldkmaLppChvlfqfyvkdkkegkLsl 164
                                          +  YG  +r ++ + +  +dq++  i++lke+p  Rr     w p    + +  pC+++  f+ +    g+L+l
  gi|330507653|ref|YP_004384081.1| 107 PGFEYTYGERLRAWRLPGTPPLDQIDMAIQRLKESPATRRATSVTWIPPVDGERNEVPCMIVDDFKLRG---GRLHL 180
                                       347899*****************************************8775568999**********54...57*** PP

                                       EEEEEEEETTTHHHHHHHHHHHHHHHHHHHHT-EEEEEEEEEEEEEEEGGGHHHHHHHH CS
                   Thymidylat_synt 165 qlyqRSaDvflGvpFNiasyalLthmlaqvtglkpgelihtigdaHiYsnhveqvkeql 223
                                        +  RS D++ + p N+   a L++  a+++g +pg++  t + aHiY+   + ++e+l
  gi|330507653|ref|YP_004384081.1| 181 AIFFRSHDFAGAYPANLYGLARLLEYAAREVGAQPGSISTTSSSAHIYEHDWDWIEEML 239
                                       ***************************************************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 2129.60
//
Query:       gi|330507654|ref|YP_004384082.1|  [L=337]
Description: hypothetical protein MCON_1638 [Methanosaeta concilii GP6]
Scores for complete 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-15   54.9  23.5    5.4e-07   29.7  11.5    3.8  4  Pentapeptide_3  Pentapeptide repeats (9 copies)
     0.0044   16.6   8.7      0.038   13.7   0.5    3.9  4  Pentapeptide    Pentapeptide repeats (8 copies)
  ------ inclusion threshold ------
      0.011   15.9   7.2      0.053   13.7   7.2    2.1  1  Pentapeptide_4  Pentapeptide repeats (9 copies)
        6.7    6.7   7.2         41    4.2   7.1    2.3  1  Ion_trans_2     Ion channel


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.79   3.5e+03      34      46 ..      26      38 ..      23      38 .. 0.84
   2 !   23.2   8.5   1.3e-08   5.6e-05       4      45 ..      60     102 ..      57     103 .. 0.91
   3 !   29.7  11.5   1.2e-10   5.4e-07       1      46 [.     101     146 ..     101     148 .. 0.89
   4 !   18.0   2.5   5.5e-07    0.0024       1      43 [.     123     164 ..     123     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.79
                    Pentapeptide_3 34 sgarFtgdvdFsg 46
                                      ++++++gd+d+++
  gi|330507654|ref|YP_004384082.1| 26 ENVIIYGDLDLHN 38
                                      6899999999975 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 1.3e-08
                    Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFs 45 
                                       ++ +g+++F+++ F+g ++F++++F + a+Fs++ F  d+ Fs
  gi|330507654|ref|YP_004384082.1|  60 SVIKGNVFFDHSAFQGLVDFDGTVFsQAANFSDSFFQEDAGFS 102
                                       677999*******************77**********999997 PP

  == domain 3  score: 29.7 bits;  conditional E-value: 1.2e-10
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsg 46 
                                       Fs+a+F+g a+F++a+F+  a+Fs+a+F++ dF +a F++   +s+
  gi|330507654|ref|YP_004384082.1| 101 FSQAQFHGEANFSRAHFTTEANFSRARFNDGDFGRAKFHRSFHLSN 146
                                       999**********************************997666666 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 5.5e-07
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvd 43 
                                       Fs+a+F +  dF +a F+++   sna+  + ++s+a+F+ d++
  gi|330507654|ref|YP_004384082.1| 123 FSRARFNDG-DFGRAKFHRSFHLSNARVYTLRLSDAIFEEDAS 164
                                       888999999.999999999955999999999999999988875 PP

>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.018        81      17      33 ..      78      95 ..      76      97 .. 0.76
   2 ?    2.8   0.1      0.02        92      16      23 ..     110     117 ..     103     118 .. 0.60
   3 !   13.7   0.5   8.4e-06     0.038       4      32 ..     119     148 ..     119     151 .. 0.87
   4 ?   -3.8   0.0       2.5   1.1e+04      33      38 ..     154     159 ..     152     160 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.018
                                      CCESEEECT-.B-TT-EE CS
                      Pentapeptide 17 nlsgAnLtgA.nlsgAdL 33
                                      ++ g++++ A n+s++ +
  gi|330507654|ref|YP_004384082.1| 78 DFDGTVFSQAaNFSDSFF 95
                                      788888888888888766 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.02
                                       CCCESEEE CS
                      Pentapeptide  16 anlsgAnL 23 
                                       an+s+A +
  gi|330507654|ref|YP_004384082.1| 110 ANFSRAHF 117
                                       44444444 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 8.4e-06
                                       TT-B-CCSCCEECCCESEEECT-.B-TT-E CS
                      Pentapeptide   4 sgAnLsganLsganlsgAnLtgA.nlsgAd 32 
                                       ++An+s a +++ ++ +A+++++  ls+A+
  gi|330507654|ref|YP_004384082.1| 119 TEANFSRARFNDGDFGRAKFHRSfHLSNAR 148
                                       589999999999999999999998888886 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 2.5
                                       ECCEEE CS
                      Pentapeptide  33 LsganL 38 
                                       Ls+a++
  gi|330507654|ref|YP_004384082.1| 154 LSDAIF 159
                                       455554 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   7.2   1.2e-05     0.053       8      69 ..      90     155 ..      64     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                    Pentapeptide_4   8 fnncklsn.vnFsearlrd.cnFtecrl.snvnFdecnlsdvdfaevdlkra.sFsgcnlknvnfs 69 
                                       f ++ + + + Fs+a++++ +nF+ +++ +++nF+++ ++d df  +++ r+  +s+ +  + ++s
  gi|330507654|ref|YP_004384082.1|  90 FSDSFFQEdAGFSQAQFHGeANFSRAHFtTEANFSRARFNDGDFGRAKFHRSfHLSNARVYTLRLS 155
                                       555666655788999999889999999999999999999999999999988755555555555554 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   7.1    0.0091        41      22      77 ..     281     335 ..     249     337 .] 0.72

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0091
                                       ---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2  22 kwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkvl 77 
                                       + s+ da+Yfs + ++     +i+ ++ +  ++t++++l G +l+alfl +++kv+
  gi|330507654|ref|YP_004384082.1| 281 SISINDAFYFSSMWFLGRAPQNISIIEGF-EFLTVFETLAGWLLMALFLVTMSKVM 335
                                       45777888888888877777777778777.9********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 2635.20
//
Query:       gi|330507655|ref|YP_004384083.1|  [L=1202]
Description: multi-sensor hybrid histidine kinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-32  112.1   0.5      4e-32  111.1   0.5    1.6  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    9.7e-28   96.6   1.2    3.9e-27   94.6   0.7    2.2  2  Response_reg  Response regulator receiver domain
    2.3e-21   76.5   0.0    3.6e-16   59.7   0.0    3.1  3  GAF_2         GAF domain
      3e-21   75.2   0.8    9.5e-21   73.6   0.0    2.4  2  HisKA         His Kinase A (phospho-acceptor) domain
    1.2e-20   73.8   0.0    1.5e-11   44.6   0.0    3.7  3  PAS_4         PAS fold
    2.7e-17   62.8   0.0    3.7e-13   49.6   0.0    3.6  3  PAS_3         PAS fold
    4.4e-14   52.6   0.0    0.00018   21.7   0.0    3.6  3  PAS_9         PAS domain
    8.6e-10   38.6   0.0    0.00031   20.7   0.0    3.8  3  PAS           PAS fold
      2e-09   38.2   0.0    1.7e-05   25.4   0.0    2.6  2  GAF           GAF domain
    0.00013   22.3   0.0       0.12   12.7   0.0    3.4  3  GAF_3         GAF domain
    0.00024   20.9   0.1    0.00049   19.9   0.1    1.5  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
     0.0017   18.3   0.0     0.0093   16.0   0.0    2.3  2  PAS_8         PAS domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.041   13.8   0.0    1.7  1  HATPase_c_5   GHKL 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 !  111.1   0.5   2.9e-35     4e-32       1     111 [.     934    1046 ..     934    1047 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 2.9e-35
                                        EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE.EE.TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTST CS
                         HATPase_c    1 gdekrLrqiisnlvdNavkfatkageieveika.se.ddlvisveDnGiGipkedlkklfekfsq.ddstkrggg 72  
                                        gd+ rL+qi+ nl++Navkf t+ g +++e+k  +e + l++sv+D+GiGi+k+d+kklf +fsq d+st+r++g
  gi|330507655|ref|YP_004384083.1|  934 GDSVRLQQILVNLLGNAVKF-TERGMVSLEVKMgDEpGMLHFSVTDTGIGISKSDMKKLFHSFSQvDASTSRKYG 1007
                                        799*****************.98888877777643379************************************* PP

                                        SSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                         HATPase_c   73 gtGlGlsivkklvelmgGeiwvesepgrGttftftlple 111 
                                        gtGlGl+i++ lve+mgG+iwvese g G+tf+f+++ e
  gi|330507655|ref|YP_004384083.1| 1008 GTGLGLAISRMLVEQMGGRIWVESEMGSGSTFHFQIKVE 1046
                                        **********************************99876 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.4   1.9e+03      88     109 ..     451     472 ..     441     473 .. 0.81
   2 !   94.6   0.7   2.8e-30   3.9e-27       1     111 [.    1080    1191 ..    1080    1192 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
                                       HHHHCTESEEEESSG-HHHHHH CS
                      Response_reg  88 ealkagaddflsKpfdpeeLlk 109
                                         l  g+++ ++K  ++eeL++
  gi|330507655|ref|YP_004384083.1| 451 TLLMSGMHKLIQKRRTEEELRQ 472
                                       56799**************998 PP

  == domain 2  score: 94.6 bits;  conditional E-value: 2.8e-30
                                        EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSE CS
                      Response_reg    1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelp 73  
                                        +l+++D+p+++++   +l++ gy + +++++g+ea++ l ++++d++l+D++mp+mdGle+++ i + d  + ++
  gi|330507655|ref|YP_004384083.1| 1080 ILLAEDNPVNMKVALLMLNKLGY-KADVVSNGEEAVQALSHKHYDVVLMDVQMPKMDGLEATRAILDMDlvDRPR 1153
                                        89*********************.*****************************************99998899** PP

                                        EEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg   74 viiltahseeedavealkagaddflsKpfdpeeLlkal 111 
                                        ++++ta++ e d++++l+ag+d+++sKp++++eL++al
  gi|330507655|ref|YP_004384083.1| 1154 ILAMTAYALEGDRKRCLDAGMDGYISKPVQIDELRAAL 1191
                                        ***********************************998 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   2.6e-19   3.6e-16       3     133 ..     321     457 ..     319     462 .. 0.81
   2 !   13.3   0.0   5.7e-05     0.079      55     137 ..     548     631 ..     479     632 .. 0.75
   3 ?   -2.3   0.0       3.7     5e+03      19      70 ..     690     744 ..     686     748 .. 0.71

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.6e-19
                                       HHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B--....-TT.HHHHHHHHTS-EEES CS
                             GAF_2   3 dleelldlvldelvel.gaalgyillvdddgg.lrlaawgeaeeefgaaldrpl....geg.lvgealrtgrpviln 72 
                                        l+el+d ++++ ++l g+++gy+ + d+ +g + +++w+ ++   ++a ++++    ge  l+ge+l+ +r+vi+n
  gi|330507655|ref|YP_004384083.1| 321 FLKELADYAIQAGAKLtGSRFGYLTFMDESEGiIFMSHWSKDPLPEDGADRSKMayhlGEPcLWGESLKRRRAVIVN 397
                                       589************978********999888555669996555555555443336778888*************** PP

                                       -GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHH CS
                             GAF_2  73 dleedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqi 133
                                       d      k++l  ++a + + ++vP++++g  +++++ ++nk+++++++d+++L++l++ +
  gi|330507655|ref|YP_004384083.1| 398 DNSIYCGKSHLSPDEAWVLRYISVPIMDKG-KIAIVAAVGNKEEEYNDADVRQLTLLMSGM 457
                                       *66667777777788888889*******99.666666669*****************9876 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.7e-05
                                       -TTH.HHHHHHHTS-EE.ES-.GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEE..S......--HHHHHHH CS
                             GAF_2  55 gegl.vgealrtgrpvi.lnd.leedpdkkglpaghaglrsflavPlisegrvvGvlnl..yankppafdeedlelL 126
                                       ++ + +++al  g p++ +++ +  dp +k   +++ g+ sfl +P++ e r  +v+++  +++++ +++e ++++L
  gi|330507655|ref|YP_004384083.1| 548 DQFIgWQDALSRGNPIQgITSkV-IDPGRKL--LEDNGIISFLLLPVFIERRFCAVISIddCHFER-RWTENEVAIL 620
                                       55544888888888888776622.2344433..68**************999*******7655555.4********* PP

                                       HHHHHHHHHHH CS
                             GAF_2 127 eelaeqiaiai 137
                                       ++ ae i+ a+
  gi|330507655|ref|YP_004384083.1| 621 QAAAESIGNAL 631
                                       ********997 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.7
                                       S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B--....-TTH.HHHHHHHTS-EE CS
                             GAF_2  19 gaalgyillvdddgglrlaawgeaeeefgaaldrpl....gegl.vgealrtgrpvi 70 
                                       ++a++y  l+ +d++   ++w+e + e    ++ +l    ++g  + +++++g+ ++
  gi|330507655|ref|YP_004384083.1| 690 NSAISYADLIHPDDR--DRVWSEIQQETEKGTPFRLtyriNAGSeTKWVWEHGQGIF 744
                                       466677667665555..5699999999988887755556688855999999998777 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 ?   -2.5   0.2         4   5.4e+03      21      52 ..     621     647 ..     617     651 .. 0.73
   2 !   73.6   0.0   6.9e-24   9.5e-21       1      67 []     822     887 ..     822     887 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4
                                       HHHHHHHHC..T-HSSCHHHHHHHHHHHHHHH CS
                             HisKA  21 lgnaeaLkregklteelkeyletiesearrld 52 
                                       +++ae + +       l++  e++ +e++r++
  gi|330507655|ref|YP_004384083.1| 621 QAAAESIGN-----ALLRRRTEVALRESKRML 647
                                       555555555.....678889999999999997 PP

  == domain 2  score: 73.6 bits;  conditional E-value: 6.9e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       s+g+fla+++HE+rtP+++++g a +L ++ +l++e+++y++ti+s+++ l+++++d+Ld+s+i +g
  gi|330507655|ref|YP_004384083.1| 822 SMGEFLAYMSHEIRTPMNSVIGLAGLLLET-NLSPEQRDYVQTIHSSGDALLSIINDILDFSKINEG 887
                                       689***********************9885.9********************************876 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   1.1e-14   1.5e-11       5     109 ..      70     172 ..      66     173 .. 0.94
   2 !    9.7   0.0    0.0007      0.97       1      48 [.     185     233 ..     185     254 .. 0.84
   3 !   15.2   0.0   1.4e-05      0.02       3     109 ..     653     764 ..     651     765 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.1e-14
                             PAS_4   5 pdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhy 81 
                                       p++l+  d+ +r+++++ +     g+++  +lGkt+++++++  a+r +r+ +rv+e++ p++ + +   +g e+++
  gi|330507655|ref|YP_004384083.1|  70 PCCLFLQDRGLRYTWLSFERPP--GMDGLLALGKTDEDIFSPAEADRQRRIKERVIETGNPARGEVHISKDGMEQYL 144
                                       5666666**********99666..9**************************************************** PP

                             PAS_4  82 elrllPlrdesGevigvlvisrDiTerr 109
                                       +  ++P+ de+G+++gv + + D+Terr
  gi|330507655|ref|YP_004384083.1| 145 DYVYYPWQDEDGRTLGVAGCIKDVTERR 172
                                       ***************************8 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0007
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaae.lfgappeellGktlaellpeed 48 
                                       ++s+p a++ +d +gr++y+N+   + ++  ++  ++G + +++ +e+ 
  gi|330507655|ref|YP_004384083.1| 185 VESSPTAIVLFDFEGRIEYVNPLLLQsCGYDDASPVMGWSIFDFTNEDG 233
                                       699*******************977768888888889988888877764 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 1.4e-05
                             PAS_4   3 slpdalavl..dpdgrvlyaNaaaaelfgappeellGktla...ellpeedaarleralrrvlegeepiefleelll 74 
                                       +lp + + +  d++ ++++++    el g+p  ell  +     +l  ++d++r+ + +++  e ++p + +   + 
  gi|330507655|ref|YP_004384083.1| 653 NLPGMAYRCrnDRQRTMEFVSDGCLELTGRPSPELLHNSAIsyaDLIHPDDRDRVWSEIQQETEKGTPFRLTYRINA 729
                                       67778888888999999999999999888887777766655466888888*************************** PP

                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       + e++++  +   ++d+sG+ +++ ++++DiTer+
  gi|330507655|ref|YP_004384083.1| 730 GSETKWVWEHGQGIFDASGKLLALEGFIHDITERK 764
                                       99999999999**********************97 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.021        29      28      87 ..     105     163 ..      97     165 .. 0.91
   2 ?    4.0   0.0     0.043        59       3      85 ..     203     284 ..     201     288 .. 0.84
   3 !   49.6   0.0   2.7e-16   3.7e-13       3      88 ..     671     756 ..     669     757 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.021
                             PAS_3  28 dlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengkpvrvig 87 
                                       d+  p + +r r+  ++++++g p  ge+  + kdG   +++  +++ +de+g+ + v g
  gi|330507655|ref|YP_004384083.1| 105 DIFSPAEADRQRRIKERVIETGNPARGEV-HISKDGMEQYLDYVYYPWQDEDGRTLGVAG 163
                                       67789999999*****************9.679*********************999988 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.043
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirden 79 
                                       yv++   +  Gy++++      s+ d+   +  +++re +  +l +++ ++ge  i+  dG+y+  e  ++ i   +
  gi|330507655|ref|YP_004384083.1| 203 YVNPLLLQSCGYDDASPVMG-WSIFDFTNEDGKSKLREVIIPVLLSQGNWQGELPIQGTDGQYYTAEMICTRIAAYS 278
                                       77888888889999988877.67999999999*********99999999****************999999996666 PP

                             PAS_3  80 gkpvrv 85 
                                       g  v++
  gi|330507655|ref|YP_004384083.1| 279 GGSVYF 284
                                       655554 PP

  == domain 3  score: 49.6 bits;  conditional E-value: 2.7e-16
                             PAS_3   3 yvserveeilGyspeellgk.veswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +vs+ + e++G  + ell++   s++dl+hp+Dr+rv++++q+  +kg+p+   yRi ++  e+ wv+++++ i+d 
  gi|330507655|ref|YP_004384083.1| 671 FVSDGCLELTGRPSPELLHNsAISYADLIHPDDRDRVWSEIQQETEKGTPFRLTYRI-NAGSETKWVWEHGQGIFDA 746
                                       89******************9**********************************86.8999*************** PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +gk + + g+
  gi|330507655|ref|YP_004384083.1| 747 SGKLLALEGF 756
                                       ***9999887 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00085       1.2      32     104 .]      99     170 ..      92     170 .. 0.81
   2 !   21.7   0.0   1.3e-07   0.00018       2      95 ..     190     284 ..     189     290 .. 0.78
   3 !   17.2   0.0   3.3e-06    0.0046      10     104 .]     666     762 ..     656     762 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00085
                             PAS_9  32 lgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                       lgk  +d+f  +++++ ++ +++++e+g   + ++ev++ ++  e+++ +   +p +d+dg+  g++++++D+te
  gi|330507655|ref|YP_004384083.1|  99 LGKTDEDIFspAEADRQRRIKERVIETGN--PARGEVHISKDGMEQYL-DYVYYPWQDEDGRTLGVAGCIKDVTE 170
                                       67777888876666677777777788887..88888888777666666.9999*********************8 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.3e-07
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGys.peevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirknget 75 
                                       ++i++ + +gri+y+N+ +l+  Gy+ +  v+g si+d+   +++++++lr+++         +++e+ ++  +g++
  gi|330507655|ref|YP_004384083.1| 190 TAIVLFDFEGRIEYVNPLLLQSCGYDdASPVMGWSIFDFT--NEDGKSKLREVIIPVLLsqGNWQGELPIQGTDGQY 264
                                       678886699***************997888**********..555555555554333333568************** PP

                             PAS_9  76 fwvlltaspvkdddgelvgi 95 
                                       + +++ ++++   +g+ v +
  gi|330507655|ref|YP_004384083.1| 265 YTAEMICTRIAAYSGGSVYF 284
                                       *********96666666654 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 3.3e-06
                             PAS_9  10 dgrilyaNeaalrllGyspeevlgks...itdlfvtdpeanerlraaleqgrkkerevevvlirkng.etfwvllta 82 
                                       + ++++++++ l+l+G  + e+l+ s   + dl+  +p++++r++  ++q ++k   + ++++ + g et wv  + 
  gi|330507655|ref|YP_004384083.1| 666 QRTMEFVSDGCLELTGRPSPELLHNSaisYADLI--HPDDRDRVWSEIQQETEKGTPFRLTYRINAGsETKWVWEHG 740
                                       44677*************99999999999*****..99999999999999998888899998888889999999*** PP

                             PAS_9  83 spvkdddgelvgiivilrDite 104
                                         ++d++g+l ++ ++++Dite
  gi|330507655|ref|YP_004384083.1| 741 QGIFDASGKLLALEGFIHDITE 762
                                       ************99*******8 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.027        37      49     113 .]     105     168 ..     101     168 .. 0.88
   2 !   20.7   0.0   2.3e-07   0.00031       2     101 ..     180     279 ..     177     288 .. 0.87
   3 !    8.9   0.0    0.0011       1.5      26     113 .]     672     760 ..     662     760 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.027
                                       GBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  49 liheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +i+ + +a+++++++++  ++ ++  ge+ + + dg + +l+    p  d++g+ lg+ g ++d+
  gi|330507655|ref|YP_004384083.1| 105 DIFSPAEADRQRRIKERVIETGNPARGEVHISK-DGMEQYLDYVYYPWQDEDGRTLGVAGCIKDV 168
                                       566666677889999999888888899**9***.**************************99997 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsr.eevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       ++++ +es+p++i++ D  gri yvN+   + +G++  + v+g s++d+ +e+  ++l+e +  +l+++ +++++  
  gi|330507655|ref|YP_004384083.1| 180 RMVQSVESSPTAIVLFDFEGRIEYVNPLLLQSCGYDDaSPVMGWSIFDFTNEDGKSKLREVIIPVLLSQGNWQGELP 256
                                       56666778*****************************9***************999999999999999999999777 PP

                                       EEECTTSSEEEEEEEEEEEEETTE CS
                               PAS  78 sfklrdgrpihlevraspvrdagg 101
                                          + dg ++ +e+ ++ +   +g
  gi|330507655|ref|YP_004384083.1| 257 IQGT-DGQYYTAEMICTRIAAYSG 279
                                       6666.9999999998887776666 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0011
                                       ECHHHHHHHSSTHHHCTTS...BGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC.TTSSEEEEEEEEEEEEE CS
                               PAS  26 vNaaaeellGlsreevlgk...slldliheeddaelaelleqlleqgeesrageisfkl.rdgrpihlevraspvrd 98 
                                       v++   el+G +  e+l+    s+ dlih++d   + +  ++  +++e+++ ++ + +     +++++  +   ++d
  gi|330507655|ref|YP_004384083.1| 672 VSDGCLELTGRPSPELLHNsaiSYADLIHPDD---RDRVWSEIQQETEKGTPFRLTYRInAGSETKWVWEHGQGIFD 745
                                       55556688999998888872225789999986...5666666666777777788888888899999*********** PP

                                       TTEEEEEEEEEEEES CS
                               PAS  99 aggeilgflgvlrdi 113
                                       a+g++l + g+++di
  gi|330507655|ref|YP_004384083.1| 746 ASGKLLALEGFIHDI 760
                                       *************98 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00078       1.1       5     122 ..     325     450 ..     322     455 .. 0.60
   2 !   25.4   0.0   1.3e-08   1.7e-05      16     133 .]     506     631 ..     494     631 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00078
                                       HHHHHHHHHHHHHTESEEEE.EEEEETTEEECEEEEECCEEEETTSHHHH...............HHHHHSSSEEES CS
                               GAF   5 lldtvveelrellgadrval.ylpdydGlhydipqasrwlfmkngrgicg...............qvlatgqplvip 65 
                                       l+d +++  ++l+g + + l ++++++G    i   s+w+ ++ ++  ++               + l+ +++++++
  gi|330507655|ref|YP_004384083.1| 325 LADYAIQAGAKLTGSRFGYLtFMDESEG----IIFMSHWSKDPLPEDGADrskmayhlgepclwgESLKRRRAVIVN 397
                                       5555666667778877777766777777....444444522222222122222223333344466************ PP

                                       TGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE.SSSCSHHHHHHHH CS
                               GAF  66 dstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhn.psppftreelell 122
                                          + + ++   +++  e++  r +++vP++++g+ +++++++  + +++++++++ l
  gi|330507655|ref|YP_004384083.1| 398 ---DNSIYCGKSHLSPDEAWVLR-YISVPIMDKGK-IAIVAAVGnKEEEYNDADVRQL 450
                                       ...56666665555556666665.***********.6666655524447888887766 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.3e-08
                                       HHTESEEEEEE.EEETTEEECEEEEECCEEEET..TSHHHH........HHHHHSSSEEESTGGTSTTHHTTHHHHH CS
                               GAF  16 llgadrvalyl.pdydGlhydipqasrwlfmkn..grgicg........qvlatgqplvipdstpdprfaqynrrdl 81 
                                         g dr +++  +++ G +   +++ +wl+ +    rg++          +l+ g p++     ++    +   r+l
  gi|330507655|ref|YP_004384083.1| 506 SIGSDRITILEsAEWTGTESVFEESIQWLREPAepFRGRISwdqfigwqDALSRGNPIQGI---TSKVIDP--GRKL 577
                                       5678888886665677763348888888555555545533344444488888888888877...4444444..5679 PP

                                       HHHTTESEEEEEEEEETTEEEEEEEEEE...SSSCSHHHHHHHHHHHHHHHHHHH CS
                               GAF  82 lenmgirsslvvPlvndgelwGllvlhn...psppftreelellqvladqvaval 133
                                       le  gi+s+l +P++ +++  +++++++   +++ +t++e+++lq+ a+ +++al
  gi|330507655|ref|YP_004384083.1| 578 LEDNGIISFLLLPVFIERRFCAVISIDDchfERR-WTENEVAILQAAAESIGNAL 631
                                       999*************************665555.*****************997 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.3   1.8e+03      51      99 ..     113     163 ..      94     182 .. 0.75
   2 !   12.7   0.0   8.6e-05      0.12       3     121 ..     323     455 ..     322     458 .. 0.76
   3 ?    5.0   0.0     0.022        30      81     129 .]     584     633 ..     533     633 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.3
                             GAF_3  51 dedsalarralssgevvsepsfaeedglpd.raalavPLvagr.qviGvla 99 
                                       d++   + r++++g+++ +     +dg+++   +++ P ++++ +++Gv +
  gi|330507655|ref|YP_004384083.1| 113 DRQRRIKERVIETGNPARGEVHISKDGMEQyLDYVYYPWQDEDgRTLGVAG 163
                                       566667789999999998888777788765267899999999999999976 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.6e-05
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse.......sld.edsalarralssgevvseps 71 
                                       +el++ ++++++kl+g+ +g l   d + + +  +++w   p ++        +    + +l+ + l+++ +v++++
  gi|330507655|ref|YP_004384083.1| 323 KELADYAIQAGAKLTGSRFGYLTFMD-ESEGIIFMSHWSKDPLPEDgadrskmAYHlGEPCLWGESLKRRRAVIVND 398
                                       789999999*************9999.66999999999555555558777755555566777779999999999966 PP

                             GAF_3  72 f......aeedglpdraa....lavPLvagrqviGvlalastkprafdaedlelleslAr 121
                                                   +pd+a     + vP+++  + i ++a+  +k+++++++d++ l  l++
  gi|330507655|ref|YP_004384083.1| 399 NsiycgkS--HLSPDEAWvlryISVPIMD-KGKIAIVAAVGNKEEEYNDADVRQLTLLMS 455
                                       53443221..233443323333778****.*************************99986 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.022
                             GAF_3  81 raalavPLvagrqviGvlalast.kprafdaedlelleslArqiataier 129
                                        + l++P+ ++r+   v+ +     +r +++ +++ l++ A  i++a+ r
  gi|330507655|ref|YP_004384083.1| 584 ISFLLLPVFIERRFCAVISIDDChFERRWTENEVAILQAAAESIGNALLR 633
                                       456999****99********76515777*******************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 !   19.9   0.1   3.5e-07   0.00049       6     110 ..     942    1050 ..     937    1069 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.5e-07
                       HATPase_c_3    6 AlaelvdNsld.Adaenvkievnknr.gktgeivieDdGkGmseeelknalr.latsskeakrkstslGkkGiGl 77  
                                         l+ l+ N++   +   v++ev+  +      ++++D G G+s++++k+ +  + + + +   +s+++G  G+Gl
  gi|330507655|ref|YP_004384083.1|  942 ILVNLLGNAVKfTERGMVSLEVKMGDePGMLHFSVTDTGIGISKSDMKKLFHsFSQVDAS---TSRKYGGTGLGL 1013
                                        57788888888666666777777554123589*****************88626666666...89*********7 PP

                       HATPase_c_3   78 klAsl...slgkkltvitk.kegesstltldvdkidk 110 
                                          + +   ++g ++ v++   +g++ +++++v+ ++ 
  gi|330507655|ref|YP_004384083.1| 1014 AISRMlveQMGGRIWVESEmGSGSTFHFQIKVEESSG 1050
                                        6554422245666777774133444455555555444 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.7e-06    0.0093       7      41 ..     185     217 ..     177     240 .. 0.80
   2 ?   -2.4   0.0         4   5.5e+03      25      56 ..     671     703 ..     657     713 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.7e-06
                             PAS_8   7 fesspdgiavvd.lgdrivdvNqaalellGysadlk 41 
                                       +essp +i+++d +g+ i +vN+  l+ +Gy+  + 
  gi|330507655|ref|YP_004384083.1| 185 VESSPTAIVLFDfEGR-IEYVNPLLLQSCGYD--DA 217
                                       89**********9999.*************98..33 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4
                             PAS_8  25 dvNqaalellGys.adlkgellgqllpvlrpll 56 
                                       +v +  lel+G + ++l+      + + ++p  
  gi|330507655|ref|YP_004384083.1| 671 FVSDGCLELTGRPsPELLHNSAISYADLIHPDD 703
                                       588888999998866655555555555555555 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     3e-05     0.041       5      98 ..     938    1043 ..     935    1046 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-05
                       HATPase_c_5    5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg......ek......kklesskskkeeh 67  
                                         l  il nlL NA+   ++      ++++++  + ++l +s++ +  g      +k      +   s+++k +  
  gi|330507655|ref|YP_004384083.1|  938 RLQQILVNLLGNAVKFTERGM---VSLEVKMGDEPGMLHFSVTDTGIGisksdmKKlfhsfsQVDASTSRKYGGT 1009
                                        57889*********9988855...6899999999999999999995555555551134334344458899999** PP

                       HATPase_c_5   68 GiGlksireivkkykgnlsieaedg...lFtlsv 98  
                                        G+Gl   r +v++ +g +++e e g   +F+ ++
  gi|330507655|ref|YP_004384083.1| 1010 GLGLAISRMLVEQMGGRIWVESEMGsgsTFHFQI 1043
                                        *******************999876444566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1202 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:                        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: 0.81u 0.23s 00:00:01.04 Elapsed: 00:00:00.98
# Mc/sec: 3705.71
//
Query:       gi|330507656|ref|YP_004384084.1|  [L=174]
Description: hypothetical protein MCON_1640 [Methanosaeta concilii GP6]
Scores for complete 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   21.6   0.0    0.00035   20.4   0.0    1.6  1  MarR_2           MarR family
    0.00083   19.2   0.0     0.0028   17.5   0.0    1.9  2  HTH_5            Bacterial regulatory protein, arsR family
    0.00098   18.6   0.0     0.0022   17.5   0.0    1.6  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0016   18.3   0.0     0.0034   17.3   0.0    1.5  1  MarR             MarR family
     0.0027   17.7   0.0     0.0059   16.6   0.0    1.5  1  HTH_20           Helix-turn-helix domain
     0.0056   17.0   0.0      0.012   16.0   0.0    1.5  1  Penicillinase_R  Penicillinase repressor
     0.0066   16.3   0.0      0.012   15.4   0.0    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0079   16.0   1.6      0.022   14.6   0.0    2.3  3  HTH_IclR         IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.022   14.8   0.0      0.059   13.5   0.0    1.7  1  DprA_WH          DprA winged helix domain
      0.045   14.2   0.1       0.22   12.1   0.0    2.1  2  HTH_27           Winged helix DNA-binding domain
      0.051   13.5   0.0        0.1   12.6   0.0    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
        0.1   12.3   0.0        0.2   11.3   0.0    1.5  1  GntR             Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.3e-07   0.00035      18      61 ..      49      89 ..      35      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-07
                                      TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      p   l++ +l++++g+sks+vs     L++ GLv r+  p+DkR
  gi|330507656|ref|YP_004384084.1| 49 P---LSMDQLVEETGYSKSTVSTNMGILERIGLVKRVVIPGDKR 89
                                      3...99*******************************5555999 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.2   3.3e+03      20      32 ..      31      43 ..      29      44 .. 0.86
   2 !   17.5   0.0   1.9e-06    0.0028      15      46 ..      49      80 ..      42      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.2
                                      HHHHHHTS-HHHH CS
                             HTH_5 20 elaeelglsqstv 32
                                       +++++g+ q+t+
  gi|330507656|ref|YP_004384084.1| 31 GCCDAVGVLQGTL 43
                                      5899****99996 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.9e-06
                                      SEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 15 elcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +l+  +l+ee+g s+stvS    +L+  GLV+
  gi|330507656|ref|YP_004384084.1| 49 PLSMDQLVEETGYSKSTVSTNMGILERIGLVK 80
                                      78889*************************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 !   17.5   0.0   1.5e-06    0.0022      18      48 .]      50      80 ..      49      80 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                            HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +s+ +L e++g S+stv++ +  Le+ Gl+k
  gi|330507656|ref|YP_004384084.1| 50 LSMDQLVEETGYSKSTVSTNMGILERIGLVK 80
                                      7999*************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.3e-06    0.0034      17      57 ..      49      89 ..      48      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-06
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTT CS
                              MarR 17 plsvseLakklgvskstvtrvldrLekkGlieRskspeDrR 57
                                      pls+ +L +  g skstv++    Le+ Gl++R   p+D+R
  gi|330507656|ref|YP_004384084.1| 49 PLSMDQLVEETGYSKSTVSTNMGILERIGLVKRVVIPGDKR 89
                                      678899**********************************9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.9e-06    0.0059      21      57 ..      46      82 ..      34      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.9e-06
                                      TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 21 raegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      ++ +l+  +l e+ + sk+t+s ++ +Le+ gLv++v
  gi|330507656|ref|YP_004384084.1| 46 TGVPLSMDQLVEETGYSKSTVSTNMGILERIGLVKRV 82
                                      67899999**************************987 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.8e-06     0.012      25      81 ..      53     111 ..      51     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.8e-06
                                       HT--GGG---HHHHHHHHHHHHHTTS-EEEEE..TTEEEEE----XXXXXXXXXXXXXX CS
                   Penicillinase_R  25 eeleeekelaysTVktllrrLvkKgllsreke..grafiYsplvseeeavasavkqlld 81 
                                       ++l ee+  ++sTV t ++ L++ gl++r      +++ Y p+++ + ++  +  ++ +
  gi|330507656|ref|YP_004384084.1|  53 DQLVEETGYSKSTVSTNMGILERIGLVKRVVIpgDKRYHYIPVTDADSLRGDMIANIRQ 111
                                       678899999********************9877689*********99998887776655 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   8.3e-06     0.012      21      67 ..      48      95 ..      42      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.3e-06
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE--H CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYravdp 67
                                       p+++d++ ee+g ++s+v   +  Le+ GlV+r+     k+Y+++++
  gi|330507656|ref|YP_004384084.1| 48 VPLSMDQLVEETGYSKSTVSTNMGILERIGLVKRVVIPgDKRYHYIPV 95
                                      58899******************************9887889998885 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.4e-05     0.022      18      50 ..      49      81 ..      42      82 .. 0.92
   2 ?   -2.3   0.1       2.6   3.9e+03       8      19 ..     116     127 ..     116     129 .. 0.80
   3 ?   -1.0   0.1         1   1.6e+03       8      18 ..     154     164 ..     153     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                                      S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +l+  +l ++tg +kStv+  +  L++ G+v++
  gi|330507656|ref|YP_004384084.1| 49 PLSMDQLVEETGYSKSTVSTNMGILERIGLVKR 81
                                      578899*************************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.6
                                       HHCT-CTTBSS- CS
                          HTH_IclR   8 iLdalaeapqel 19 
                                       iL+al ++  +l
  gi|330507656|ref|YP_004384084.1| 116 ILNALDRTEADL 127
                                       899999998876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1
                                       HHCT-CTTBSS CS
                          HTH_IclR   8 iLdalaeapqe 18 
                                       +Ld++++++ e
  gi|330507656|ref|YP_004384084.1| 154 LLDLISRHNTE 164
                                       89***999876 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.9e-05     0.059      24      57 ..      48      81 ..      44      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-05
                           DprA_WH 24 ePvhvDqLvrrtglpaaevsaaLleLELaGlver 57
                                       P+++DqLv++tg + ++vs+    LE  Glv+r
  gi|330507656|ref|YP_004384084.1| 48 VPLSMDQLVEETGYSKSTVSTNMGILERIGLVKR 81
                                      599*******************999998888877 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.22      23      67 ..      54      98 ..      45      98 .. 0.92
   2 ?   -1.3   0.0       2.2   3.2e+03      17      32 ..     150     165 ..     140     167 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                            HTH_27 23 dlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdk 67
                                      +l++ + +++s++s ++  L++ GLv+r   + d+r+  + +Td+
  gi|330507656|ref|YP_004384084.1| 54 QLVEETGYSKSTVSTNMGILERIGLVKRVVIPGDKRYHYIPVTDA 98
                                      79999********************************99999985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                            HTH_27  17 rrkkladlcgrlnved 32 
                                         +kl dl+ r+n+ed
  gi|330507656|ref|YP_004384084.1| 150 QNDKLLDLISRHNTED 165
                                       4456689999999887 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 ?   12.6   0.0   6.7e-05       0.1      19      66 ..      47     102 ..      27     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.7e-05
                                       EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E..T.EE...EEES-HHHHH CS
                         HTH_Crp_2  19 elpltqeelAsmlGltretvsrilseLkreglis..r..g.rr...irildleaLr 66 
                                        +pl++++l +  G + +tvs  ++ L+r gl++     g +r   i ++d + Lr
  gi|330507656|ref|YP_004384084.1|  47 GVPLSMDQLVEETGYSKSTVSTNMGILERIGLVKrvVipGdKRyhyIPVTDADSLR 102
                                       479*******************************6415533323477788888776 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014       0.2      18      57 ..      44      82 ..      38      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                      S-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 18 lrpGdkLPsereLaaefgVsrttvReALrrLeaeglverr 57
                                      +  G +L s  +L++e g s++tv   +  Le+ glv r 
  gi|330507656|ref|YP_004384084.1| 44 FLTGVPL-SMDQLVEETGYSKSTVSTNMGILERIGLVKRV 82
                                      6678899.9****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1221.05
//
Query:       gi|330507657|ref|YP_004384085.1|  [L=792]
Description: hydrophobe/amphiphile efflux-3 (HAE3) family transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-48  162.9  18.4    6.7e-24   84.4  11.2    2.4  2  MMPL            MMPL family
    1.2e-11   43.1  20.3    5.7e-07   27.6   2.4    3.0  3  ACR_tran        AcrB/AcrD/AcrF family
    1.5e-09   37.9  12.2    4.7e-06   26.5   1.7    2.6  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
      3e-08   33.3   8.5      3e-08   33.3   8.5    2.7  2  SecD_SecF       Protein export membrane protein
  ------ inclusion threshold ------
       0.77    9.3   6.1        6.8    6.2   0.3    2.9  3  CD34_antigen    CD34/Podocalyxin family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   0.7   7.7e-27   2.8e-23      49     305 ..     117     375 ..      83     416 .. 0.89
   2 !   84.4  11.2   1.9e-27   6.7e-24      97     295 ..     566     759 ..     549     774 .. 0.86

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 7.7e-27
                              MMPL  49 avdelvdelkkdtkhvgevsdf......lsdpdvaaafvSkDgkaaralvtlegdpgsteadesvaairaaveearp 119
                                        + ++v++ +k++++++++ d       ls +d+  a++ +D + + + ++l  +  ++e+ e +++ +  +  a+ 
  gi|330507657|ref|YP_004384085.1| 117 SIADIVADTEKESSGIRAIPDQerideiLSADDLILAAILPDRSHTMLSIELPVSLTESEQGELYQETKGQLLLASF 193
                                       5677888889999999999999888888888888888999********************************99999 PP

                              MMPL 120 leglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllg 196
                                       +++++  vtG +a+++ ++   +++ + i ++++ + +v Lli++  +   llp+  v ++++ ++g  + l ++ +
  gi|330507657|ref|YP_004384085.1| 194 PADTRLTVTGDPALMNSITAEMAESNGPILLLAAFLMIVALLITFNQVKWSLLPIPIVFLGVGWTFGA-MGLLHIPF 269
                                       ********************************************************************.55555544 PP

                              MMPL 197 lelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvl 273
                                         +s++    ++ +li++G+DYa+ +  R+ ee  +  + ++av ++v+ + k v++a ++  i +++L+++++p++
  gi|330507657|ref|YP_004384085.1| 270 TMVSMS----AFPVLIGIGIDYAIQFQNRINEEFTRTGQPQKAVVETVKHVTKPVIIALIITSIGFISLLTSSIPMI 342
                                       444444....67799************************************************************** PP

                              MMPL 274 aqvGvaialGvlvdvlivlTll.PAllvllGra 305
                                       + +G+ + +G+++ +l +l +    l   +G++
  gi|330507657|ref|YP_004384085.1| 343 RDFGLLCLIGLILCFLSALFVGvTILYIAVGKR 375
                                       ******************999977777777877 PP

  == domain 2  score: 84.4 bits;  conditional E-value: 1.9e-27
                              MMPL  97 dpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallp 173
                                       + g++ +d+ +++i + ++  +p++g+ v+ tG a++++ +  a ++ ++ +++ +l++i+++Ll +yr l+ allp
  gi|330507657|ref|YP_004384085.1| 566 NLGTEGSDRLMKEIDKDIAWNPPPAGVSVRMTGDAVVMTTVITALTKGRTEMTLFGLLLIFIVLLAIYRDLIKALLP 642
                                       3344444444555555555555******************************************************* PP

                              MMPL 174 lltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkv 250
                                       +l  +v ++   g+     +++g++ +  ++  l +l+++vG+ Ya+l++ R+ eel++  + ++a+ +a + +g++
  gi|330507657|ref|YP_004384085.1| 643 VLPMLVVIGWMGGV----MYISGMKYTPLTAC-LGALILGVGSEYAILMMERFYEELEKIGEPRKALSTATRAIGSA 714
                                       99877766666555....78999998777665.568899********************99999************* PP

                              MMPL 251 vtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll 295
                                        +a+Glt ++ +++L  + + + +++G++  l+++++++ ++T+ 
  gi|330507657|ref|YP_004384085.1| 715 LIASGLTTIFGFAALISSPFLITNNFGMVTVLAIVFALATTFTVF 759
                                       **************************************9999985 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   2.4   1.6e-10   5.7e-07     308     497 ..     191     383 ..     175     406 .. 0.82
   2 !    2.9   0.0    0.0046        16       1      33 [.     413     445 ..     413     454 .. 0.93
   3 !   17.2   9.4   2.2e-07   0.00078     311     479 ..     589     762 ..     566     777 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.6e-10
                                       GGSSTTEEEEEEEESHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                          ACR_tran 308 eslPegveivvvydrtefvrasieeVvkt...LleaivLvvlvvflFLqnlratlipaiavPlsllgtfavlkalgf 381
                                       +s+P++  ++v+ d + + + + e  + +   Ll+a+ L ++ +++  ++++ +l p  +v l +  tf ++ +l +
  gi|330507657|ref|YP_004384085.1| 191 ASFPADTRLTVTGDPALMNSITAEMAESNgpiLLLAAFLMIVALLITFNQVKWSLLPIPIVFLGVGWTFGAMGLLHI 267
                                       67888888888888876654444444444334899**********************9999999999********** PP

                                       -BCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHH CS
                          ACR_tran 382 slNlltLfgLvlAiGlvvDdAiVvvEnierkleeegekpleaalksmkeiqgalvaialvllavflPilflgGveGk 458
                                          + ++ +  + iG+ +D Ai     i ++      +p++a+ +++k ++ +++   ++ ++ f+ +l+ +     
  gi|330507657|ref|YP_004384085.1| 268 PFTMVSMSAFPVLIGIGIDYAIQFQNRINEEFTR-TGQPQKAVVETVKHVTKPVIIALIITSIGFISLLTSSI---P 340
                                       ********************************99.77899***************999999999987776443...4 PP

                                       HHHHHH....HHHHHHHHHHHHHHHCCHHHHHHHHS---STT- CS
                          ACR_tran 459 lfrqfa....ltivlaillsvlvaltltPalcallLkerkeek 497
                                       + r+f+    + ++l+ l +++v +t+   +++  L+++   k
  gi|330507657|ref|YP_004384085.1| 341 MIRDFGllclIGLILCFLSALFVGVTILYIAVGKRLNHQPIDK 383
                                       4555552112467777788888888887777777776666555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0046
                                       -HHHHHTSHHHHHHHHHHHHHHHHHHHCTSSBE CS
                          ACR_tran   1 iikffikrpifalvlaliilllGilsilslPvd 33 
                                       i+ f i+r  ++l lal++ l+Gi+s  ++Pvd
  gi|330507657|ref|YP_004384085.1| 413 ISGFCIERWQLVLALALLLSLAGIYSDTQVPVD 445
                                       57899***************************9 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 2.2e-07
                                       STTEEEEEEEES...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHH..HHHHHHHHHTT-- CS
                          ACR_tran 311 Pegveivvvydr...tefvrasieeVvktLleaivLvvlvvflFLqnlratlipaiavPlsl..lgtfavlkalgfs 382
                                       P+gv+++++ d    t+++ a  +   +  l +++L+++v++   ++l  +l p++ + +++  +g+++ ++ ++++
  gi|330507657|ref|YP_004384085.1| 589 PAGVSVRMTGDAvvmTTVITALTKGRTEMTLFGLLLIFIVLLAIYRDLIKALLPVLPMLVVIgwMGGVMYISGMKYT 665
                                       56666666655422134444444444455678*********************997554444339999999999999 PP

                                       BCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHH CS
                          ACR_tran 383 lNlltLfgLvlAiGlvvDdAiVvvEnierkleeegekpleaalksmkeiqgalvaialvllavflPilflgGveGkl 459
                                         +  L++L l++G     Ai ++E  +++le+   +p++a   +++ i++al+a+ l+ +  f  +++   ++ + 
  gi|330507657|ref|YP_004384085.1| 666 PLTACLGALILGVGS--EYAILMMERFYEELEK-IGEPRKALSTATRAIGSALIASGLTTIFGFAALISSPFLITNN 739
                                       99999******9998..89**************.7889******************999988777665544444433 PP

                                       H...HHHHHHHHHHHHHHHHHHH CS
                          ACR_tran 460 f...rqfaltivlaillsvlval 479
                                       f     +a+  +la+  +v+v+l
  gi|330507657|ref|YP_004384085.1| 740 FgmvTVLAIVFALATTFTVFVVL 762
                                       30004444444444444444444 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 !   26.5   1.7   1.3e-09   4.7e-06      13     140 ..     248     375 ..     239     386 .. 0.86
   2 !   15.8   3.3   2.7e-06    0.0096      23     140 ..     653     771 ..     638     782 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.3e-09
                                       HHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCH.HHHHHHHHHHHCCCCHHC CS
                    Sterol-sensing  13 viivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrslde.seriaealgevgpsillt 88 
                                       + iv l v  ++g + +l +++t++++  +P  ++ +g+d    + + +++   ++ + ++ + e++++v   +++ 
  gi|330507657|ref|YP_004384085.1| 248 IPIVFLGVGWTFGAMGLLHIPFTMVSMSAFPV-LIGIGIDYAIQFQNRINEEFTRTGQpQKAVVETVKHVTKPVIIA 323
                                       6689999************************5.57********9999998776666554999*********999999 PP

                                       CCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHH CS
                    Sterol-sensing  89 sltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldirre 140
                                       ++  ++ ++  + +++p ++ F l + +++++ Fl  +++ v++L + + ++
  gi|330507657|ref|YP_004384085.1| 324 LIITSIGFISLLTSSIPMIRDFGLLCLIGLILCFLSALFVGVTILYIAVGKR 375
                                       999999988666899*****************************99887655 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.7e-06
                                       HCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCH.HHHHHHHHHHHCCCCHHCCCHHHHHHHH CS
                    Sterol-sensing  23 slgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrslde.seriaealgevgpsilltsltellalll 98 
                                         g++++ g+++t++++  l  l+l vg +   ++++ + +  ++  e  + +  a + +g +++++ lt ++ ++ 
  gi|330507657|ref|YP_004384085.1| 653 MGGVMYISGMKYTPLTA-CLGALILGVGSEYAILMMERFYEELEKIGEpRKALSTATRAIGSALIASGLTTIFGFAA 728
                                       56899999*******99.999*********98888888777777776658899999999999999999*99999986 PP

                                       HHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHH.HHHHHHH CS
                    Sterol-sensing  99 galtdvpavqeFclfaavavlvdFllqitfFvavL.sldirre 140
                                        +++ +   ++F + +++a+++  +   t+Fv ++  +++rre
  gi|330507657|ref|YP_004384085.1| 729 LISSPFLITNNFGMVTVLAIVFALATTFTVFVVLIyRMELRRE 771
                                       667888899**********************987625677776 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   8.5   8.3e-12     3e-08      28     184 ..     214     369 ..     197     374 .. 0.86
   2 ?   -5.5  11.4         5   1.8e+04      20     174 ..     601     754 ..     590     769 .. 0.68

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 8.3e-12
                                       HHHHH.HHHHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSSHHHH CS
                         SecD_SecF  28 elaek.avlallialvliliyvalrF.ewrvalaaiialvhDviitvgvlsllgievdlatvaalLtiiGYSvndtv 102
                                       e+ae+ + + ll+a+++i + + + F + ++ l  i  ++  v  t g++ ll+i++++ +++a  ++iG  ++  +
  gi|330507657|ref|YP_004384085.1| 214 EMAESnGPILLLAAFLMI-VALLITFnQVKWSLLPIPIVFLGVGWTFGAMGLLHIPFTMVSMSAFPVLIGIGIDYAI 289
                                       555540445555555555.55555552679*********************************************** PP

                                       HHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTTTHHHHH CS
                         SecD_SecF 103 vvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgtyssifia 179
                                          +r+ e++++  + + ++++ + +++  +  i++ ++t +  ++ll     +++df l  l+Gli+  +s++f+ 
  gi|330507657|ref|YP_004384085.1| 290 QFQNRINEEFTR--TGQPQKAVVETVKHVTKPVIIALIITSIGFISLLTSSIPMIRDFGLLCLIGLILCFLSALFVG 364
                                       *********998..6777888888999999999*******************************************9 PP

                                       HHHHH CS
                         SecD_SecF 180 splll 184
                                        ++l+
  gi|330507657|ref|YP_004384085.1| 365 VTILY 369
                                       99986 PP

  == domain 2  score: -5.5 bits;  conditional E-value: 5
                                       EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHH.HHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTT CS
                         SecD_SecF  20 tvgpsvskelaekavlallialvliliyvalrFewrv.alaaiialvhDviitvgvlsllgievdlatvaalLtiiG 95 
                                       +v  +v   l++      l+ l+li+i++  ++++ + al  ++ ++  +  + gv+ + g++ ++ t      i+G
  gi|330507657|ref|YP_004384085.1| 601 VVMTTVITALTKGRTEMTLFGLLLIFIVLLAIYRDLIkALLPVLPMLVVIGWMGGVMYISGMKYTPLTACLGALILG 677
                                       56666667777777777788888899988888887763777888899999999999999999998765433334788 PP

                                       SSSHHHHHHHHHHHHHHHH--S.S-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTT CS
                         SecD_SecF  96 YSvndtvvvfdrvrenlrkkkr.atlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivg 171
                                          +  +++++r  e+l+k  + +++   + +++ + L    +  ltt++  +al+  +  + ++f ++ ++++++ 
  gi|330507657|ref|YP_004384085.1| 678 VGSEYAILMMERFYEELEKIGEpRKALSTATRAIGSALI---ASGLTTIFGFAALISSPFLITNNFGMVTVLAIVFA 751
                                       888999999999999999853314445555666666665...55555555666665555566666666666666554 PP

                                       TTT CS
                         SecD_SecF 172 tys 174
                                         +
  gi|330507657|ref|YP_004384085.1| 752 LAT 754
                                       443 PP

>> CD34_antigen  CD34/Podocalyxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3    0.0019       6.8      85     125 ..     298     338 ..     290     343 .. 0.85
   2 ?    5.6   0.1    0.0028        10     102     147 ..     344     389 ..     337     399 .. 0.87
   3 ?   -3.9   0.2       2.4   8.7e+03     101     127 ..     738     764 ..     730     771 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0019
                      CD34_antigen  85 nltsvkeaqeedirseqdyskkllialvtsglllaiLlvag 125
                                       ++t + + q+  +++ ++ +k+++ial+++++  + Ll+  
  gi|330507657|ref|YP_004384085.1| 298 EFTRTGQPQKAVVETVKHVTKPVIIALIITSIGFISLLTSS 338
                                       56777778888889999***************999998865 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0028
                      CD34_antigen 102 dyskkllialvtsglllaiLlvagyYgclhrRlskskagerLgEel 147
                                       d++ + li l++  l + +++v+ +Y+ + +Rl  ++  ++ + + 
  gi|330507657|ref|YP_004384085.1| 344 DFGLLCLIGLILCFLSALFVGVTILYIAVGKRLNHQPIDKHSTQDT 389
                                       789999******9999999****************99999966665 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 2.4
                      CD34_antigen 101 qdyskkllialvtsglllaiLlvagyY 127
                                       +++++ ++ a+v      + + v ++Y
  gi|330507657|ref|YP_004384085.1| 738 NNFGMVTVLAIVFALATTFTVFVVLIY 764
                                       567888888888844444556667777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (792 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.80u 0.27s 00:00:01.07 Elapsed: 00:00:00.44
# Mc/sec: 5400.83
//
Query:       gi|330507658|ref|YP_004384086.1|  [L=184]
Description: hypothetical protein MCON_1642 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.9   0.0      0.032   14.0   0.0    1.4  1  HTH_IclR   IclR helix-turn-helix domain
      0.042   13.4   0.0       0.07   12.7   0.0    1.4  1  HTH_24     Winged helix-turn-helix DNA-binding
       0.11   12.5   0.0       0.26   11.3   0.0    1.7  1  DASH_Dad4  DASH complex subunit Dad4
        0.4   11.1   5.0       0.74   10.3   0.3    2.6  2  LPP        Lipoprotein leucine-zipper


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.2e-06     0.032       7      35 ..      98     126 ..      95     131 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.2e-06
                                       HHHCT-CTTBSS-BHHHHHHHHTS-HHHH CS
                          HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStv 35 
                                       +++d+ ae p++ t sel + +gl+k+tv
  gi|330507658|ref|YP_004384086.1|  98 SLIDIMAEKPGRYTTSELVDMLGLNKTTV 126
                                       5899************************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 ?   12.7   0.0   1.6e-05      0.07       2      42 ..      93     134 ..      92     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                            HTH_24   2 detdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLe 42 
                                       d   r ++ ++ ++p+  + +eL ++lgl ++tv   +kr  
  gi|330507658|ref|YP_004384086.1|  93 DNHARSLIDIMAEKPGrYTTSELVDMLGLNKTTVISVMKRAL 134
                                       66678888999999999*******************999965 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.9e-05      0.26       9      36 ..      46      73 ..      40      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.9e-05
                         DASH_Dad4  9 qsalLsRIiknvekLnesvvelnkelee 36
                                         lL R+i  v++L++ v +l++++++
  gi|330507658|ref|YP_004384086.1| 46 DVELLGRLIDQVDRLSKEVSDLKSQFRT 73
                                      5689******************999876 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.4     0.043   1.9e+02      12      31 ..      29      48 ..      24      52 .. 0.81
   2 ?   10.3   0.3   0.00016      0.74       8      27 ..      56      75 ..      50      98 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.043
                               LPP 12 Lkskvdqlssdvnsakaaaq 31
                                      L s +d++s+d++s k++++
  gi|330507658|ref|YP_004384086.1| 29 LVSAIDKMSQDMDSKKSDVE 48
                                      56778899999988888875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00016
                               LPP  8 qVsqLkskvdqlssdvnsak 27
                                      qV +L+++v+ l+s+    +
  gi|330507658|ref|YP_004384086.1| 56 QVDRLSKEVSDLKSQFRTRQ 75
                                      55555555555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1122  (0.0625802); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1422.05
//
Query:       gi|330507659|ref|YP_004384087.1|  [L=287]
Description: haloacid dehalogenase domain-containing protein hydrolase [Methanosaeta concilii GP6]
Scores for 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-17   63.6   0.0    1.6e-16   61.3   0.0    1.9  1  Hydrolase       haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.018   14.1   0.0      0.028   13.5   0.0    1.3  1  Asparaginase_2  Asparaginase
      0.024   14.4   0.0      0.077   12.7   0.0    1.8  2  Hydrolase_3     haloacid dehalogenase-like hydrolase
       0.23   11.5   0.0        1.7    8.7   0.0    2.1  1  HAD_2           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 !   61.3   0.0   3.5e-20   1.6e-16       4     210 .]       7     227 ..       5     227 .. 0.62

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 3.5e-20
                                       EEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH............................HHCHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................xxxxxxxxxxxxxxx RF
                         Hydrolase   4 vvfDkdGTLttgepsvedvivsaalalaaaletg............................sehpigkalvaaaka 52 
                                       vv+D+ GT+ +  ++ +d+   +      +le +                             +hpi   +    + 
  gi|330507659|ref|YP_004384087.1|   7 VVMDVAGTIMRMYRVAKDIPGDI------ILEKVvtwelimeksgralvvpqidpdmiiscnPDHPIRVLVLGREDC 77 
                                       66666666666665555533333......111111111222222333333344444555454555555555444444 PP

                                       HHHHHHHHHHETTTE.HHHHTHHHHHHHH.HCHHHHHHH.HHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHH CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  53 rsgaltgfatfigrg.ayaigkpewltal.dippdlgaa.igsaqsqgrtvallqaralavftiadplkvkpeaaea 126
                                       +++++++ + ++++  ++++ +p  +++l +    ++a+  g + ++g +v  +  +    ++i+    ++p+++ +
  gi|330507659|ref|YP_004384087.1|  78 IKISCSSSQISPDEVlRILKSSPVKMRELqEACAIVKAKcPGNYRTAGFIVDHD--HGEIAYAISTGGIPFPGLERV 152
                                       455555555544554566666666666664333333333133344444444444..6666677778888******** PP

                                       HHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES...STTTSHHHHHHHHHHHTSTGGGEEEEESSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 127 vasLkaagievvlltgdnpetaeraanqlGddyfdaviasdiet...vakpspegkvaaireLqgkpeevamVGDgv 200
                                       +  Lka+g +v+l++gd+++  ++ ++ lG           i+       ++p+ k++++ eL+++  +v+mVGDg+
  gi|330507659|ref|YP_004384087.1| 153 LLDLKAMGADVYLASGDSRRSLNS-LDDLG-----------IDPsrmNPVANPWRKKEIVAELKERYGHVVMVGDGL 217
                                       ***********************5.55579...........666657666699************************ PP

                                       HHHHHHHHTT CS
                                       xxxxxxxxxx RF
                         Hydrolase 201 nDaaalaaAg 210
                                       nD+ al+aA+
  gi|330507659|ref|YP_004384087.1| 218 NDIYALKAAD 227
                                       *********8 PP

>> Asparaginase_2  Asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.2e-06     0.028     169     203 ..     112     152 ..      79     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.2e-06
                                       T......TT---EEEEEE-TTS-EEEEEEE--STTB-TTEE CS
                    Asparaginase_2 169 k......aklgTvGaValDsegnlAaaTSTgGltnklvGRv 203
                                               +++T G ++ + +g++A a STgG+ +    Rv
  gi|330507659|ref|YP_004384087.1| 112 IvkakcpGNYRTAGFIVDHDHGEIAYAISTGGIPFPGLERV 152
                                       02344458899*********************988777776 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.51   2.3e+03      22      46 ..     151     175 ..     147     187 .. 0.76
   2 ?   12.7   0.0   1.7e-05     0.077     195     227 ..     199     231 ..     195     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.51
                                       HHHHHHHHTTSEEEEE-SS-HHHHH CS
                       Hydrolase_3  22 eaikklkekgikvviATGRslravl 46 
                                       +++  lk+ g  v +A+G s r++ 
  gi|330507659|ref|YP_004384087.1| 151 RVLLDLKAMGADVYLASGDSRRSLN 175
                                       56778899999*******8877654 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.7e-05
                                       HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEE CS
                       Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvA 227
                                       ++ el+    +v+ +GDg NDi  L+aa+lgv 
  gi|330507659|ref|YP_004384087.1| 199 IVAELKERYGHVVMVGDGLNDIYALKAADLGVL 231
                                       556666777799*******************95 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00037       1.7     142     176 ..     197     231 ..     140     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00037
                             HAD_2 142 ekaleklklkkeeviyvGDsptDieaakkagikvi 176
                                       ++++ +lk    +v++vGD  +Di a k+a + v+
  gi|330507659|ref|YP_004384087.1| 197 KEIVAELKERYGHVVMVGDGLNDIYALKAADLGVL 231
                                       4677788888899*************999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1915.31
//
Query:       gi|330507660|ref|YP_004384088.1|  [L=233]
Description: hypothetical protein MCON_1644 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1705.35
//
Query:       gi|330507661|ref|YP_004384089.1|  [L=69]
Description: AbrB family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.22s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 592.06
//
Query:       gi|330507662|ref|YP_004384090.1|  [L=102]
Description: 30S ribosomal protein S10 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-25   88.9   0.0    2.2e-25   88.7   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 !   88.7   0.0   1.2e-29   2.2e-25       1      97 [.       5      98 ..       5      99 .. 0.99

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 1.2e-29
                                      EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHH CS
                     Ribosomal_S10  1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketi 78
                                      rirl+++++  L++++++++ +a+++g+ + gp+plPtkr  v+ +ksp ++ + +++++e+r+hkRlid+ da+++ +
  gi|330507662|ref|YP_004384090.1|  5 RIRLSGTNPLMLDDICNQVKGIAQRTGVHMAGPIPLPTKRMVVPCRKSPDGEgTATWDHWEMRVHKRLIDL-DADERAL 82
                                      8**********************************************************************.8****** PP

                                      HHHS-...S---SS-EEEE CS
                     Ribosomal_S10 79 dtllkllqlnlpegVsvev 97
                                      ++l++   +++p+ V++e+
  gi|330507662|ref|YP_004384090.1| 83 RQLMR---IQVPKNVNIEI 98
                                      *****...*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 790.85
//
Query:       gi|330507663|ref|YP_004384091.1|  [L=424]
Description: translation elongation factor EF-1 subunit alpha [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-53  181.7   0.0    1.6e-53  181.2   0.0    1.1  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    6.2e-38  129.6   0.4    2.4e-37  127.7   0.0    2.1  3  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    3.9e-16   59.2   1.8      2e-15   57.0   0.3    2.8  4  GTP_EFTU_D2  Elongation factor Tu domain 2
    1.4e-05   25.2   0.0     0.0003   20.8   0.0    2.4  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0037   17.1   0.4     0.0099   15.8   0.4    1.7  1  GTP_EFTU_D4  Elongation factor Tu domain 4
  ------ inclusion threshold ------
      0.042   13.2   0.0       0.13   11.6   0.0    1.7  1  Gtr1_RagA    Gtr1/RagA G protein conserved region


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 !  181.2   0.0   5.3e-57   1.6e-53       1     188 [.       5     213 ..       5     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 181.2 bits;  conditional E-value: 5.3e-57
                                       TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH.HHHST............HCHSHHHHHHTSCSSCEEEEEE CS
                          GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka.eeerv............lDtlkeErergiTiksaaisle 64 
                                       k+++n+++ighvDhGK+T+++rL+++tga++ +  ++ ++e++            +D+lkeErerg+Ti++a+  ++
  gi|330507663|ref|YP_004384091.1|   5 KPHLNLAFIGHVDHGKSTTVGRLMFETGAVDPHVIDEyKKEAAskgkatfefawvMDSLKEERERGVTIDIAHHRFD 81 
                                       579****************************9888875223336789999*************************** PP

                                       TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST..... CS
                          GTP_EFTU  65 ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl..... 135
                                         t+ky ++++D+PGH+dF+k++i+g++++D avl+v++ +Gv++qt+e++ l +++gv+ ++v++NK+D +     
  gi|330507663|ref|YP_004384091.1|  82 --TAKYYFTVVDCPGHRDFVKNMITGASQADAAVLIVAVPDGVMAQTKEHVFLSRTLGVNqLVVAMNKIDATtppyd 156
                                       ..**********************************************************************9***9 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............HHHHHH CS
                          GTP_EFTU 136 kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............tlleal 188
                                       +++++e++eev  kl      l+ +g+k + ++p+++ S+l g+++             tlleal
  gi|330507663|ref|YP_004384091.1| 157 EKRYNEVKEEVG-KL------LKMVGYKVD-DIPFIPLSGLMGDNLAkastntpwykgpTLLEAL 213
                                       999999999999.55......578888885.9************988777777777777777776 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       1.8   5.3e+03       9      56 ..     110     155 ..     103     167 .. 0.62
   2 ?   -2.0   0.0       1.5   4.5e+03      60      79 ..     256     275 ..     245     293 .. 0.58
   3 !  127.7   0.0     8e-41   2.4e-37       3     111 ..     315     421 ..     313     422 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.8
                                       EEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB- CS
                       GTP_EFTU_D3   9 eAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekv 56 
                                       +A v+i+     + + +  + v+  rt  v+  vv++ +k+d  t   
  gi|330507663|ref|YP_004384091.1| 110 DAAVLIVAV-PDGVMAQTKEHVFLSRTLGVNQLVVAM-NKIDATTPPY 155
                                       566666666.444555555678888888888877777.7777666555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                                       -SSCCSTT-CEEEEEEECCE CS
                       GTP_EFTU_D3  60 kpefvkpGdnvivevelikp 79 
                                       + ++v +  nv+ ev+ i++
  gi|330507663|ref|YP_004384091.1| 256 NDKIVFQPANVTGEVKSIEM 275
                                       55555555555555544443 PP

  == domain 3  score: 127.7 bits;  conditional E-value: 8e-41
                                       EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCE CS
                       GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikp 79 
                                       + +++f+Aq+++l++  +++i agY+pv++++ta+++++ +++l+kld++++ v+e++p f+k Gd++i+ v+++kp
  gi|330507663|ref|YP_004384091.1| 315 TVAKEFKAQIVVLQH--PSAISAGYTPVFHCHTAQIACTLTAILAKLDPRSGAVKEENPAFIKAGDAAIIMVTPSKP 389
                                       6789***********..************************************************************ PP

                                       EEE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  80 ialekgseypqlGrFaiReggrTvaaGvvtei 111
                                       +++e ++e+pqlGrFaiR++g+TvaaG+ +++
  gi|330507663|ref|YP_004384091.1| 390 MVIEPVKEIPQLGRFAIRDMGTTVAAGMCMSV 421
                                       ***************************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 ?   -0.7   0.0      0.64   1.9e+03      22      46 ..      13      35 ..       9      45 .. 0.79
   2 ?   -2.4   0.0       2.2   6.7e+03      44      63 ..     157     176 ..     140     179 .. 0.62
   3 !   57.0   0.3   6.5e-19     2e-15       1      73 [.     241     307 ..     241     308 .. 0.96
   4 ?   -3.6   0.0       5.2   1.6e+04      13      30 ..     374     389 ..     374     398 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.64
                                      EC.TCTTSEEEEEEEEEEEEETEEES CS
                       GTP_EFTU_D2 22 lg.ndtskkeivtrissletfheded 46
                                      +g +d +k+   t++++l  + + +d
  gi|330507663|ref|YP_004384091.1| 13 IGhVDHGKS---TTVGRLMFETGAVD 35
                                      465788899...******99888776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.2
                                       EESEEETTSEEEEEEEESSC CS
                       GTP_EFTU_D2  44 dedeavaganaGvivaikgl 63 
                                       +++  ++ + +G +++++g+
  gi|330507663|ref|YP_004384091.1| 157 EKRYNEVKEEVGKLLKMVGY 176
                                       34444666666666666665 PP

  == domain 3  score: 57.0 bits;  conditional E-value: 6.5e-19
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       Gtv  grv++G+++k+d++++ + n t      ++++s+e++he++ ea +g+n+G +v+++  +d i++Gd+ 
  gi|330507663|ref|YP_004384091.1| 241 GTVPVGRVETGVMRKNDKIVFQPaNVT------GEVKSIEMHHEEVPEAFPGDNIGWNVRGVSKKD-IRRGDVC 307
                                       99*******************887777......99*******************************.*****95 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 5.2
                                       EETTEEEEEECTCTTSEE CS
                       GTP_EFTU_D2  13 lkkGdevrilgndtskke 30 
                                       +k Gd   i  + t+ k+
  gi|330507663|ref|YP_004384091.1| 374 IKAGDAAII--MVTPSKP 389
                                       688999999..8887775 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     1e-07    0.0003       2      90 ..      10     122 ..       9     182 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1e-07
                                       EEEEESTTSSHHHHHHHHH....................T...........STEEESSSTTSSSSEEEEEEEETTEE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinalt....................g...........ekaivsdkpgtTrdinegrvklkgke 47 
                                        a++G+   GKSt + +l+                    +           +  + +++ g+T+di ++r+++ +  
  gi|330507663|ref|YP_004384091.1|  10 LAFIGHVDHGKSTTVGRLMfetgavdphvideykkeaasKgkatfefawvmDSLKEERERGVTIDIAHHRFDTAKYY 86 
                                       588999999999999999866666666666665555544055555555443577899999************99999 PP

                                       EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCS CS
                          MMR_HSR1  48 ielvDtpGliegaseekglgkaflaleeadlillvvdaseekl 90 
                                       +++vD+pG    +     +++ +    +ad+++l+v +  +++
  gi|330507663|ref|YP_004384091.1|  87 FTVVDCPGH-R-D----FVKNMITGASQADAAVLIVAVP-DGV 122
                                       ********2.2.1....2233333333344444444322.212 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 !   15.8   0.4   3.3e-06    0.0099      21      84 ..     245     306 ..     231     307 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.3e-06
                                       EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-E CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdi 84 
                                       vG +v +Gv++ + k++ +  +  Ge+++i+ +++++ ea  G++++  ++g    ++i  gd+
  gi|330507663|ref|YP_004384091.1| 245 VG-RVETGVMRKNDKIVFQPANVTGEVKSIEMHHEEVPEAFPGDNIGWNVRGVS-KKDIRRGDV 306
                                       88.9********************************************999965.777888875 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 ?   11.6   0.0   4.3e-05      0.13      29      68 ..      67     105 ..      60     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.3e-05
                         Gtr1_RagA  29 lrlgatidveksevrflgnltlnlwDcgGqeafveeylss 68 
                                       ++ g+tid+ ++++  +++ ++ ++Dc+G ++fv+++++ 
  gi|330507663|ref|YP_004384091.1|  67 RERGVTIDIAHHRFD-TAKYYFTVVDCPGHRDFVKNMITG 105
                                       56689******9995.7889****************7653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); 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:                         6  (0.000334653); expected 0.2 (1e-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 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3050.37
//
Query:       gi|330507664|ref|YP_004384092.1|  [L=731]
Description: translation elongation factor aEF-2 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.4e-62  208.2   0.2    1.4e-61  207.5   0.2    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    3.8e-27   94.5   0.0    3.4e-26   91.4   0.0    2.6  2  EFG_IV       Elongation factor G, domain IV
    3.4e-25   87.9   1.6      5e-25   87.4   0.5    2.0  2  EFG_II       Elongation Factor G, domain II
    6.4e-25   87.0   0.1    3.1e-24   84.8   0.0    2.2  2  EFG_C        Elongation factor G C-terminus
    5.3e-15   55.6   1.7    1.6e-14   54.0   1.7    1.9  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00035   20.6   0.0    0.00084   19.4   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0032   17.3   0.1      0.016   15.0   0.1    2.2  3  RF3_C        Class II release factor RF3, C-terminal domain
  ------ inclusion threshold ------
      0.057   13.0   0.0       0.12   11.9   0.0    1.5  1  Ras          Ras 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 !  207.5   0.2   6.2e-65   1.4e-61       3     193 ..      21     257 ..      19     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 207.5 bits;  conditional E-value: 6.2e-65
                                       EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEET..TCSSEEEEEEEE CS
                          GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaislek..etkkylinliDt 77 
                                       irnigi++h+DhGKtTL+d+Ll  +g+is+    a+++ ++D+ + E++rgiTi++a++s+ +  ++k+ylin+iDt
  gi|330507664|ref|YP_004384092.1|  21 IRNIGIVAHIDHGKTTLSDNLLGGAGMISM--DLAGKQLFMDFDPLEQARGITIDAANVSMVHevDGKEYLINMIDT 95 
                                       8*****************************..777889************************5479*********** PP

                                       SSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH. CS
                          GTP_EFTU  78 PGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk. 153
                                       PGHvdF  +v+r++r++Dgav+vvdaveG +pqte+vlr+alkegv++++f+NK+Dr+++elk  ++++  +l ++ 
  gi|330507664|ref|YP_004384092.1|  96 PGHVDFGGDVTRAMRAVDGAVVVVDAVEGAMPQTETVLRQALKEGVRPVLFVNKVDRMINELKVEKKDMAARLGKVi 172
                                       *************************************************************************9995 PP

                                       ...........HHHHHHHHHTTT..........TTEEEEEEBTTTTBTHH........................... CS
                          GTP_EFTU 154 ...........eeklekygekge..........kevpvvfgSalkgegvk........................... 182
                                                  e          e           + +++fgSal +++++                           
  gi|330507664|ref|YP_004384092.1| 173 dnvnklilgmdE----------EkykagwkldaAKGNIAFGSALYNWAISvpqmkktgigfdqvvdychegkmkela 239
                                       555555555542..........145555555568999**********887777777777777777777777777777 PP

                                       .......HHHHHHHHHSH CS
                          GTP_EFTU 183 .......tllealvellp 193
                                              ++ +++v++lp
  gi|330507664|ref|YP_004384092.1| 240 ekvplyiAVNDMVVKFLP 257
                                       777666666666666666 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 !   91.4   0.0   1.5e-29   3.4e-26       4     120 ..     509     617 ..     506     618 .. 0.91
   2 ?   -1.4   0.0      0.85   1.9e+03      20      60 ..     679     716 ..     673     722 .. 0.73

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 1.5e-29
                                       ESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS CS
                            EFG_IV   4 ayrEtirkpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplag 80 
                                       +++    +++ er++ l++  g+d+++a+ i   +      +n++ ++tkg+q+++e++e++ +Gf+ealk+Gp+++
  gi|330507664|ref|YP_004384092.1| 509 SMK----MEEIERRKLLIE-NGMDKDEARNISGYYG-----TNILLNMTKGIQYLRETMELILEGFEEALKNGPICR 575
                                       555....555545666666.8*************99.....8*********************************** PP

                                       --EESEEEEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC CS
                            EFG_IV  81 epvtdvkvtLldgslhe..vdsseaafkpaarralkeallkA 120
                                       epv+++k++++d++lhe  v++++a+++pa+r+a+++++l+A
  gi|330507664|ref|YP_004384092.1| 576 EPVQGIKAKIMDVKLHEdaVHRGPAQVIPAVRQAVQAGILMA 617
                                       **************************************9988 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.85
                                       CCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCC CS
                            EFG_IV  20 lkkqsggdgqyakvileiePleegsgnefvdetkggqvpke 60 
                                       +   ++g+  +++    +ePl+    n + +++k+++  k 
  gi|330507664|ref|YP_004384092.1| 679 IRSATEGRALWSTEFAGFEPLP---ANLLLETVKQIRTRKG 716
                                       55667889999999999****9...7777777776666555 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 !   87.4   0.5   2.2e-28     5e-25       1      74 [.     387     460 ..     387     461 .. 0.97
   2 ?   -3.4   0.0       4.9   1.1e+04      41      51 ..     554     564 ..     550     566 .. 0.82

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 2.2e-28
                            EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                       ++ePv+++a+e+k+ +d  k+ ++L+++++EDptl+v+ +eeT+e +++GmGelHl+++v+rl+r+ +ve++++
  gi|330507664|ref|YP_004384092.1| 387 VSEPVMTVAVEAKNTRDLPKVVEVLRQIAKEDPTLQVTINEETGEHLMAGMGELHLDVTVTRLQRDRGVELKTS 460
                                       689*******************************************************************9986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.9
                            EFG_II  41 eeTketilsGm 51 
                                       +eT e+il+G 
  gi|330507664|ref|YP_004384092.1| 554 RETMELILEGF 564
                                       79******996 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 ?   -1.5   0.0       1.2   2.6e+03       3      15 ..     388     400 ..     386     413 .. 0.81
   2 !   84.8   0.0   1.4e-27   3.1e-24       1      85 [.     620     703 ..     620     707 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                       EEEEEEEEEEEEC CS
                             EFG_C   3 lEPivkveievpe 15 
                                        EP+++v +e+ +
  gi|330507664|ref|YP_004384092.1| 388 SEPVMTVAVEAKN 400
                                       6*******99875 PP

  == domain 2  score: 84.8 bits;  conditional E-value: 1.4e-27
                                       EEEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEE CS
                             EFG_C   1 vllEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsg 77 
                                       vllEP+++v i+vp++ +g ++s+++ rrG i++m+++ +++vi++ ++P+a+++gf+ ++rs+T+G++ +s+ef+g
  gi|330507664|ref|YP_004384092.1| 620 VLLEPFQNVYIQVPQDQMGGAMSEIQGRRGVILNMDSQ-GDMVILKSKMPVAQMFGFSGAIRSATEGRALWSTEFAG 695
                                       59************************************.************************************** PP

                                       EEE--HHH CS
                             EFG_C  78 Yeevpgdk 85 
                                       +e++p ++
  gi|330507664|ref|YP_004384092.1| 696 FEPLPANL 703
                                       ****9876 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 !   54.0   1.7   7.2e-18   1.6e-14       1      73 [.     306     372 ..     306     373 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 7.2e-18
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       G+va+gr++sGtl++G+e+++ g  +t       ri+++ + ++ e+ +v++ +aG+i+a+ gl da ivG+t+
  gi|330507664|ref|YP_004384092.1| 306 GEVATGRLFSGTLRRGMELYVSGfGGT------NRIQQTGVVMGAERVEVEEIPAGNIAAVTGLRDA-IVGSTI 372
                                       89*******************886665......9********************************8.*****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 !   19.4   0.0   3.7e-07   0.00084       2     113 ..      24     148 ..      23     149 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.7e-07
                                       EEEEESTTSSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEEETTEE.........EEEEEC CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg................ekaivsdkpgtTrdinegrvklkgke.........ielvDt 53 
                                       ++iv +   GK+tL   l+g                +    ++  g T+d     +               i+++Dt
  gi|330507664|ref|YP_004384092.1|  24 IGIVAHIDHGKTTLSDNLLGgagmismdlagkqlfmDFDPLEQARGITIDAANVSM-----VhevdgkeylINMIDT 95 
                                       788888899*********98555554444443333223344555566666533333.....03333334559***** PP

                                       GGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                          MMR_HSR1  54 pGliegaseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvln 113
                                       pG ++    + ++++a++    +d +++vvda e+   p+ e++ +   +++ + +l +n
  gi|330507664|ref|YP_004384092.1|  96 PGHVD---FGGDVTRAMR---AVDGAVVVVDAVEG-AMPQTETVLRQALKEGVRPVLFVN 148
                                       **665...2223444444...58********9955.555555555444444444455555 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   7.3e-06     0.016      13      80 ..     394     461 ..     381     478 .. 0.82
   2 ?   -1.9   0.0       1.2   2.8e+03      35      46 ..     496     507 ..     476     515 .. 0.80
   3 ?   -3.4   0.0       3.6     8e+03      96     122 ..     639     665 ..     626     670 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.3e-06
                                       EEEEESSGGGHHHHHHHHHHHHHCT.SSEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEEE CS
                             RF3_C  13 arvrlkdplkrkqlrkgleqLaeEG.avqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrles 80 
                                         v++k++    +  + l+q+a+E  + qv  +e ++ e +++ +G+L ++V  +Rl++  gve+++++
  gi|330507664|ref|YP_004384092.1| 394 VAVEAKNTRDLPKVVEVLRQIAKEDpTLQVTINE-ETGEHLMAGMGELHLDVTVTRLQRDRGVELKTSP 461
                                       56888888888899999*****998356777666.678899999****************999998765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                       HCTSSEEEEET. CS
                             RF3_C  35 eEGavqvfkeee 46 
                                       eEG++q +ke +
  gi|330507664|ref|YP_004384092.1| 496 EEGVIQSLKEGK 507
                                       799999888754 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.6
                                       HHHHHHHHHCGGGEEEETTS-EEEEES CS
                             RF3_C  96 kkleelkkkseselvkdkkgrpvlLfe 122
                                        +++e++ ++++ l  d++g++v+L +
  gi|330507664|ref|YP_004384092.1| 639 GAMSEIQGRRGVILNMDSQGDMVILKS 665
                                       457888888889999999999999865 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.5e-05      0.12      28     117 ..      68     153 ..      58     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.5e-05
                                       CTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTT CS
                               Ras  28 yesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeikrvaeen 104
                                          Ti +++ +   evdgke+ +++ DT G  +f    +  +r ++g+++v d  + +   + ++    +++  +e 
  gi|330507664|ref|YP_004384092.1|  68 RGITIDAANVSMVHEVDGKEYLINMIDTPGHVDFGGDVTRAMRAVDGAVVVVDAVEGA-MPQTETV---LRQALKEG 140
                                       557999999999***************************************9976654.3333333...33344456 PP

                                       SEEEEEEETTTGG CS
                               Ras 105 vpivLvGnKvDle 117
                                       v  vL  nKvD  
  gi|330507664|ref|YP_004384092.1| 141 VRPVLFVNKVDRM 153
                                       6778888888844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (731 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 4793.11
//
Query:       gi|330507665|ref|YP_004384093.1|  [L=459]
Description: aspartate kinase, monofunctional class [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-44  150.5   1.2    7.3e-44  150.2   0.0    1.8  2  AA_kinase       Amino acid kinase family
    3.1e-21   74.8   1.1    6.3e-10   38.7   0.2    2.9  2  ACT             ACT domain
    4.3e-21   74.5   1.7    2.8e-09   36.6   0.1    3.1  3  ACT_7           ACT domain
    3.9e-05   24.6   0.6       0.16   12.9   0.1    2.9  3  LytR_C          LytR cell envelope-related transcriptional at
  ------ inclusion threshold ------
       0.09   13.1   2.0        4.1    7.8   0.2    2.9  3  Nitro_FeMo-Co   Dinitrogenase iron-molybdenum cofactor
        0.1   12.8   4.6        4.3    7.6   0.2    2.8  2  Asparaginase_C  Glutaminase/Asparaginase 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 !  150.2   0.0   2.4e-47   7.3e-44       5     240 ..       1     281 [.       1     282 [. 0.90
   2 ?   -1.8   0.2      0.64   1.9e+03      45      45 ..     352     352 ..     302     451 .. 0.60

  Alignments for each domain:
  == domain 1  score: 150.2 bits;  conditional E-value: 2.4e-47
                                       EEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHHTCCCCCHHHC.........E..HHHHH CS
                         AA_kinase   5 vKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllalksglssgelaa.....glrstleeage 75 
                                       +K+GG s++d+++  lr++ + +a +  ++n++v+V+++  ++td+lla ++   s+++ +     ++r t+     
  gi|330507665|ref|YP_004384093.1|   1 MKFGGVSVADGNR--LRHVGDLVAHF-HRDNEIVLVTSAlQGVTDELLACARRAASEGNVSdvmdfMERITDRHNQA 74 
                                       6************..***********.999*******************9333333333324666644444444333 PP

                                       HHHH.......................................HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECC CS
                         AA_kinase  76 vatr.......................................dalaslgerlvaallaaglpavglsaaaldatea 113
                                       +a                                         d++   ge+l a +l+  l+++g+ ++ ++ +ea
  gi|330507665|ref|YP_004384093.1|  75 IADAiqnpaiakevqgiiseklsllekayigicylgeltrrslDYISGYGEQLAAPILSGVLRDMGIESQHYTGREA 151
                                       3333666899999**************************************************************** PP

                                       CE......HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESSS CS
                         AA_kinase 114 gr....degsdgnvesvdaeaieelleagvvpvltgfigldeege...lgrgssDtiaallAealgAdkliiltdVd 183
                                       g+    ++g ++++e+      ++ll  + vpv+tgfi+ de+g    lgrg+sD +a+l+++a++Ad+++++++++
  gi|330507665|ref|YP_004384093.1| 152 GIitdsNYGDARPLEKTYGLIPQKLLPLKGVPVVTGFIAQDEKGTnttLGRGGSDLSASLIGAAINADEIWFWKETS 228
                                       *****9999999999988888888886666*********************************************** PP

                                       SCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEE CS
                         AA_kinase 184 GVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvIt 240
                                       G+++ dpk+vp a+ +p+is++ea+e    l+++G+kv+hp+a+++a ++gipv+++
  gi|330507665|ref|YP_004384093.1| 229 GIMTTDPKIVPEAKTIPTISYREAME----LSYFGAKVLHPRAIEPAIKKGIPVRVK 281
                                       **************************....*************************96 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.64
                                       H CS
                         AA_kinase  45 s 45 
                                       s
  gi|330507665|ref|YP_004384093.1| 352 S 352
                                       1 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.2   2.1e-13   6.3e-10      11      60 ..     327     373 ..     321     376 .. 0.88
   2 !   33.8   0.0   6.9e-12   2.1e-08       6      64 ..     399     451 ..     397     454 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.1e-13
                                       TTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHH CS
                               ACT  11 PGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevle 60 
                                        G++ar f+ala++giNi++i+q+sse    +i++v++++ +++++e+l+
  gi|330507665|ref|YP_004384093.1| 327 LGVAARAFTALAEAGINIVMISQGSSEA---NISMVIEEGQADRADEALR 373
                                       59************************97...8888888888888888875 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 6.9e-12
                                       EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT   6 gvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64 
                                       g+++ PG++arvf a++++ iN+++i+q+s        +++ +vv  +d e ++++l++
  gi|330507665|ref|YP_004384093.1| 399 GMAGTPGVAARVFKAMGQAKINVVMISQASG------QHNISFVVASADGERAVRELHR 451
                                       58899**************************......7888888888888888888876 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.88   2.6e+03      20      40 ..      88     108 ..      79     111 .. 0.83
   2 !   36.6   0.1   9.5e-13   2.8e-09       9      64 ..     316     373 ..     311     374 .. 0.96
   3 !   35.7   0.0   1.8e-12   5.4e-09       3      65 .]     387     451 ..     385     451 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.88
                                       S--HHHHHHHHHHTTT---EE CS
                             ACT_7  20 vtGivaklaspLaeagIsifq 40 
                                       v Gi+++  s L +a I i +
  gi|330507665|ref|YP_004384093.1|  88 VQGIISEKLSLLEKAYIGICY 108
                                       669999999999999999987 PP

  == domain 2  score: 36.6 bits;  conditional E-value: 9.5e-13
                                       EEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHH CS
                             ACT_7   9 lsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLh 64 
                                       l+++g+g+ + + G++a+ +++LaeagI+i +iS   ++  ++ +++e ++++A eaL+
  gi|330507665|ref|YP_004384093.1| 316 LNISGAGMIG-TLGVAARAFTALAEAGINIVMISqgsSEANISMVIEEGQADRADEALR 373
                                       89******88.********************************************9998 PP

  == domain 3  score: 35.7 bits;  conditional E-value: 1.8e-12
                                       EEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHHH CS
                             ACT_7   3 edgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLhe 65 
                                       ++++ ++ v gsg+++ ++G++a+++++  +a+I++ +iS    ++ ++++V ++d e+Av+ Lh+
  gi|330507665|ref|YP_004384093.1| 387 DHDVCTVAVTGSGMAG-TPGVAARVFKAMGQAKINVVMISqasGQHNISFVVASADGERAVRELHR 451
                                       678889********99.************************98999****************9995 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         6   1.8e+04      54      67 ..      71      84 ..      54      89 .. 0.70
   2 !   12.9   0.1   5.5e-05      0.16       3      69 ..     312     383 ..     311     399 .. 0.67
   3 !    9.1   0.0   0.00087       2.6      10      65 ..     401     456 ..     393     459 .] 0.80

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6
                            LytR_C 54 aakalaaalglgel 67
                                       ++a+a+a++ +++
  gi|330507665|ref|YP_004384093.1| 71 HNQAIADAIQNPAI 84
                                      45688888877764 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.5e-05
                            LytR_C   3 kVeVlNgtg.....vsGlAarvadaLeerGftvgevgn.agnadee.ttivyreaaaaaakalaaalglgelqe 69 
                                       kVe lN +g     + G+Aar+ +aL+e+G +++ +++ +++a  + + ++ + +a++a +al+++++   ++e
  gi|330507665|ref|YP_004384093.1| 312 KVELLNISGagmigTLGVAARAFTALAEAGINIVMISQgSSEA--NiSMVIEEGQADRADEALRSEFPRDVVKE 383
                                       5777777777777799*******************88525555..23666633333357779999996555333 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00087
                            LytR_C  10 tgvsGlAarvadaLeerGftvgevgnagnadeettivyreaaaaaakalaaalglg 65 
                                       +g++G+Aarv +a+ ++  +v+ +++a+ + + + +v+++++++a ++l +++glg
  gi|330507665|ref|YP_004384093.1| 401 AGTPGVAARVFKAMGQAKINVVMISQASGQHNISFVVASADGERAVRELHREFGLG 456
                                       589********************997666633377776454556999999999955 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 ?    7.8   0.2    0.0014       4.1      49      93 ..     315     359 ..     305     361 .. 0.86
   2 ?   -2.1   0.0       1.7     5e+03      48      65 ..     383     400 ..     375     423 .. 0.66
   3 ?    3.6   0.0     0.029        86      49      73 ..     427     451 ..     412     453 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0014
                                       HHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES-SSBHHHHHHHH CS
                     Nitro_FeMo-Co  49 llaeegvdvvivgkiGpralakleaagievykgaggtveealkev 93 
                                       ll  +g+ ++ + ++  ra+++l++agi +++ + g+ e+ +  v
  gi|330507665|ref|YP_004384093.1| 315 LLNISGAGMIGTLGVAARAFTALAEAGINIVMISQGSSEANISMV 359
                                       555589999999999*****************9999999888766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.7
                                       HHHHHTT-SEEEESSSCH CS
                     Nitro_FeMo-Co  48 qllaeegvdvvivgkiGp 65 
                                       ++ ++++v +v v + G 
  gi|330507665|ref|YP_004384093.1| 383 EISHDHDVCTVAVTGSGM 400
                                       445558887777777664 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.029
                                       HHHHTT-SEEEESSSCHHHHHHHCT CS
                     Nitro_FeMo-Co  49 llaeegvdvvivgkiGpralaklea 73 
                                          +++++ v++++ G+ra+++l +
  gi|330507665|ref|YP_004384093.1| 427 ASGQHNISFVVASADGERAVRELHR 451
                                       45569****************9976 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 ?    7.6   0.2    0.0014       4.3      28      76 ..     315     365 ..     299     377 .. 0.78
   2 ?    6.2   0.5    0.0038        11      13      62 ..     378     428 ..     371     446 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                                       EEEEBTTTB--H..HHHHHHHHHHTTT-EEEEEESSSBS-----H.....H CS
                    Asparaginase_C  28 vlegtGvGnlps..allealkeakargivvvatsqcpsgsvsnseyeagke 76 
                                       +l + G+G + +  +  +a+  + ++gi +v++sq +s+     + e+g++
  gi|330507665|ref|YP_004384093.1| 315 LLNISGAGMIGTlgVAARAFTALAEAGINIVMISQGSSEANISMVIEEGQA 365
                                       78999******9999999999999***********9988655555555554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0038
                                       HHHHHHHHHT.T--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSS CS
                    Asparaginase_C  13 tkvlkallkk.gakGvvlegtGvGnlpsallealkeakargivvvatsqcp 62 
                                        +v+k++ +   +  v + g G+ + p +  +++k + +++i vv++sq +
  gi|330507665|ref|YP_004384093.1| 378 RDVVKEISHDhDVCTVAVTGSGMAGTPGVAARVFKAMGQAKINVVMISQAS 428
                                       55666553222333344555555556669999999999***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3171.54
//
Query:       gi|330507666|ref|YP_004384094.1|  [L=331]
Description: phosphoribosylformylglycinamidine cyclo-ligase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-23   81.5   0.0    1.3e-22   80.6   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain
    1.8e-16   60.5   1.1    3.3e-16   59.7   1.1    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 !   80.6   0.0   1.4e-26   1.3e-22       1     149 [.     169     323 ..     169     328 .. 0.90

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.4e-26
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT......TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds......avqlgdvlleptliyvkralaalkglvkaahDvTgGG 71 
                                       k Gdvl++++s+Gl+++g+ l+r i++++g  ++      ++ +g++ll+pt+iy+   +   + +v++++++Tg G
  gi|330507666|ref|YP_004384094.1| 169 KKGDVLVGVPSSGLHSNGYTLARAIVAQSGYTYFdrlpggEKSIGEELLVPTRIYHEVVELVGRCDVHGLAHITGSG 245
                                       68****************************9999*****5555************987777768************9 PP

                                       HHHHHHHHHHTTTEEEEEECG..THHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEE CS
                            AIRS_C  72 Llgalaemapasgvgaeidld..kvpifdele.....splemllsensGrllvavppeea.davlaileeeglpeaa 140
                                       Ll  l ++   s++g+ei+ +    pif+ l+     ++lem+ ++n+G ++++v +ee+ +++++i++       +
  gi|330507666|ref|YP_004384094.1| 246 LLK-LRRI---SNLGFEITDPlePQPIFHFLQeqgrvEDLEMYQTFNMGMGFLVVLAEEEaQEACRIMGP----GSR 314
                                       995.6777...67888888888899******9*******************9999999999********4....479 PP

                                       EEEEEEESS CS
                            AIRS_C 141 vIGevtake 149
                                       vIG v++++
  gi|330507666|ref|YP_004384094.1| 315 VIGSVVGEG 323
                                       *****9874 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 !   59.7   1.1   3.7e-20   3.3e-16       4      94 .]      54     157 ..      39     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 3.7e-20
                                       EEEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT- CS
                              AIRS   4 avvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgv 71 
                                       a+++ttd+++++vl+++       +G  ++a+n++Dl+a GA+P+a++++la++      +e+++ gla++ae  ++
  gi|330507666|ref|YP_004384094.1|  54 ALAMTTDGVGSKVLIANAISkwdtVGIDCIAMNVNDLYAIGAEPIAFVDYLAVEkvdpeRAEQIAIGLARGAELSNM 130
                                       479************775555677***************************************************** PP

                                       EEEEEEEEEESS....EEEEEEEEEEE CS
                              AIRS  72 plvgGdtsfsne....ptisvtavGlv 94 
                                        +vgG+t++ +e    + ++ ta+G+v
  gi|330507666|ref|YP_004384094.1| 131 TIVGGETASLPEiirgFDLAGTAIGVV 157
                                       **********99999999*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2537.77
//
Query:       gi|330507667|ref|YP_004384095.1|  [L=258]
Description: carbon monoxide dehydrogenase accessory protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-19   69.4   0.0    4.3e-19   68.8   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    2.2e-12   47.3   0.0    4.1e-11   43.1   0.0    2.1  1  AAA_31       AAA domain
      6e-11   42.3   0.6    2.3e-07   30.5   1.1    3.0  2  ParA         NUBPL iron-transfer P-loop NTPase
    2.6e-09   36.7   0.2    6.7e-08   32.1   0.0    2.3  2  ArsA_ATPase  Anion-transporting ATPase
    7.3e-08   32.2   0.0    0.00017   21.1   0.1    2.1  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    1.9e-05   24.3   0.2     0.0001   21.9   0.2    2.1  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    2.7e-05   24.0   0.0    0.00012   21.9   0.0    1.9  2  AAA_24       AAA domain
     0.0019   17.9   0.2     0.0071   16.0   0.1    1.9  2  SRP54        SRP54-type protein, GTPase domain
     0.0043   16.1   0.3     0.0093   15.0   0.1    1.7  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0044   16.8   0.0      0.017   14.9   0.0    1.9  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
     0.0059   17.2   0.0     0.0096   16.5   0.0    1.4  1  AAA_18       AAA domain
     0.0072   16.3   0.2       0.03   14.2   0.0    2.0  2  NTPase_1     NTPase
     0.0073   16.7   0.0      0.015   15.7   0.0    1.5  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.017   15.0   0.1      0.029   14.3   0.1    1.3  1  NACHT        NACHT domain
      0.018   15.2   0.6       0.09   12.9   0.1    2.2  3  DUF87        Helicase HerA, central domain
      0.019   14.8   0.1       0.21   11.4   0.0    2.1  2  AAA_26       AAA domain
       0.03   14.0   0.3      0.055   13.2   0.3    1.7  1  AAA_30       AAA domain
      0.047   13.3   0.2      0.074   12.7   0.2    1.3  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
       0.05   13.4   0.1       0.09   12.5   0.1    1.4  1  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.061   12.5   0.3       0.12   11.6   0.3    1.5  1  NB-ARC       NB-ARC domain
      0.062   13.0   0.2       0.14   11.9   0.0    1.6  2  IstB_IS21    IstB-like ATP binding protein
      0.065   13.1   0.0       0.12   12.3   0.0    1.4  1  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.069   13.4   0.0       0.11   12.7   0.0    1.4  1  AAA_28       AAA domain
       0.14   12.7   0.0       0.23   12.0   0.0    1.4  1  ABC_tran     ABC transporter
       0.14   11.7   0.2        1.9    8.0   0.1    2.1  2  AAA_25       AAA domain
       0.17   11.4   0.1        8.8    5.8   0.0    2.3  2  GTP_EFTU     Elongation factor Tu GTP binding domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.0   6.2e-22   4.3e-19       2     126 ..       3     225 ..       2     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 6.2e-22
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       +++s+kGGvGKTtla +Lar++ar+g++Vl++DaDp +n+ + + g     +p                        
  gi|330507667|ref|YP_004384095.1|   3 IAISGKGGVGKTTLAGTLARLFARDGYNVLAIDADPSMNLGS-ALGIPDLPKPvtehkdlveeragmpmgmfkmnpk 78 
                                       578*************************************99.4554444444777888999999************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|330507667|ref|YP_004384095.1|  79 vddvvgmcgctgpdnvklvvmgtidsggsgcmcpanafvkallrhvitrekdlvildmeagiehlgratargvdami 155
                                       ***************************************************************************** PP

                                       ...........CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCC CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...........dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavae 120
                                                  +++r+ +l +++g      +   + v+n+ d +       + l       g+pvlg ip+d  ++e
  gi|330507667|ref|YP_004384095.1| 156 avvepgmrsieTVERIMQLGKEIG------ISRYFAVINKADDP--GPV-ADKLSAM----GIPVLGTIPFDRCLVE 219
                                       ****94444444444444444444......779*********99..553.3444333....**************** PP

                                       CCHHTS CS
                                       xxxxxx RF
                              CbiA 121 aparge 126
                                       a+  g 
  gi|330507667|ref|YP_004384095.1| 220 ADLAGT 225
                                       *99887 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   5.9e-14   4.1e-11       8     163 ..       6     174 ..       2     183 .. 0.66

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 5.9e-14
                            AAA_31   8 nqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgi.ekneiektlyevlieeknikeaiiktkvenldl 83 
                                         KGGvGKTT +  la  +a+ g+ vL +D+Dp  n+ ++lgi +  +  ++  +++ e++ +   + k + +  d+
  gi|330507667|ref|YP_004384095.1|   6 SGKGGVGKTTLAGTLARLFARDGYNVLAIDADPSMNLGSALGIpDLPKPVTEHKDLVEERAGMPMGMFKMNPKVDDV 82 
                                       57****************************************94333322222223224444444444333222232 PP

                            AAA_31  84 i..pssidLaeaeielvelekk.........eeilkellekv.kdeYDyiiiDcpPsLglltenaLvasdsviipvq 148
                                       +   + +   +++  ++++ ++         +  +k ll++v   e D++i+D+   ++ l +      d +i +v+
  gi|330507667|ref|YP_004384095.1|  83 VgmCGCTGPDNVKLVVMGTIDSggsgcmcpaNAFVKALLRHViTREKDLVILDMEAGIEHLGRATARGVDAMIAVVE 159
                                       21122222333333333333335555555534445777766515678999999999999999999999999999999 PP

                            AAA_31 149 aeayaleGleqllkt 163
                                       +  +++e++e++++ 
  gi|330507667|ref|YP_004384095.1| 160 PGMRSIETVERIMQL 174
                                       999999999988875 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   1.1   3.3e-10   2.3e-07       9     165 ..       5     180 ..       1     191 [. 0.66
   2 ?    4.7   0.0     0.025        17     198     244 ..     200     244 ..     192     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.3e-10
                              ParA   9 lSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee........................ekpeqs 61 
                                       +SgKGGVGK+t+a +lA  +a+ g++v  +DaD    ++ + lg+ +                         +p+++
  gi|330507667|ref|YP_004384095.1|   5 ISGKGGVGKTTLAGTLARLFARDGYNVLAIDADPS-MNLGSALGIPDlpkpvtehkdlveeragmpmgmfkMNPKVD 80 
                                       7********************************53.44445555555544444444555554444444443222222 PP

                              ParA  62 .ekkliPvea.kgikvmSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklpl 136
                                          ++  ++  +++k++ +g++ +   +  +     +++++k ll++v   e D++i+D+  G   e+l  a    +
  gi|330507667|ref|YP_004384095.1|  81 dVVGMCGCTGpDNVKLVVMGTIDS-GGSGCM---CPANAFVKALLRHVITREKDLVILDMEAG--IEHLGRATARGV 151
                                       112233333345555555555444.333222...12577889999999999999999999655..478888888888 PP

                              ParA 137 agaviVttpqevaladvkkaiemfkkvkv 165
                                       ++++ V  p   +++ v++ +++ k++ +
  gi|330507667|ref|YP_004384095.1| 152 DAMIAVVEPGMRSIETVERIMQLGKEIGI 180
                                       99999999999999999999988888776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.025
                              ParA 198 aeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiaek 244
                                        +++g+p+lg+ip+d  ++ea  +g+p + ++   +  +++++i ek
  gi|330507667|ref|YP_004384095.1| 200 LSAMGIPVLGTIPFDRCLVEADLAGTPPIDAD--CPSVQSIKRIKEK 244
                                       56799****************99999988664..6666666666655 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   9.8e-11   6.7e-08       4      48 ..       3      47 ..       1      66 [. 0.90
   2 ?    2.3   0.0      0.11        76     208     244 ..     153     189 ..     114     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 9.8e-11
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHT CS
                       ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfd 48
                                      i ++GKGGVGKtt++ ++a   ++ g++vl i  DP  +l  ++ 
  gi|330507667|ref|YP_004384095.1|  3 IAISGKGGVGKTTLAGTLARLFARDGYNVLAIDADPSMNLGSALG 47
                                      789************************************987765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.11
                                       EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                       ArsA_ATPase 208 sfrlVvipEklslkEteRaikeLkkygikvdavivNk 244
                                       ++++Vv p   s++  eR ++  k++gi+    ++Nk
  gi|330507667|ref|YP_004384095.1| 153 AMIAVVEPGMRSIETVERIMQLGKEIGISRYFAVINK 189
                                       57899999999*********99999999999999997 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   2.5e-07   0.00017       4      44 ..       3      42 ..       1      50 [. 0.87
   2 !    9.3   0.0    0.0011      0.73     104     154 ..     116     167 ..      91     242 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.5e-07
                          CBP_BcsQ  4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlL 44
                                      +a++G +GGvG+t+l+++La+ + + g++vl+iD+ p+  L
  gi|330507667|ref|YP_004384095.1|  3 IAISG-KGGVGKTTLAGTLARLFARDGYNVLAIDADPSMNL 42
                                      56666.8****************************998665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
                          CBP_BcsQ 104 allaalke.lkeqyrwillDlpagasaltrellaladlvllvvepdanchvr 154
                                        ++a l++ ++++ ++++lD+ ag ++l r++ +  d +++vvep + +   
  gi|330507667|ref|YP_004384095.1| 116 FVKALLRHvITREKDLVILDMEAGIEHLGRATARGVDAMIAVVEPGMRSIET 167
                                       44444544145899*******************************9877544 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.2   1.5e-07    0.0001       1      41 [.       1      41 [.       1     251 [. 0.79

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.5e-07
                         Fer4_NifH  1 rkiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaD 41
                                      +kiai GkGG+Gk+t +  l+  +a++g  vl +  DP  +
  gi|330507667|ref|YP_004384095.1|  1 MKIAISGKGGVGKTTLAGTLARLFARDGYNVLAIDADPSMN 41
                                      69************************************876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.7e-07   0.00012       4      75 ..       2     103 ..       1     111 [. 0.79
   2 ?   -0.4   0.0       1.1   7.8e+02      23      44 ..     128     149 ..     116     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-07
                            AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.swedfldevvel............. 59 
                                       ki+i G+ g+GKTtla +l       g+++l id + +++   a  +pd++  +++ +d v+e              
  gi|330507667|ref|YP_004384095.1|   2 KIAISGKGGVGKTTLAGTLarlfardGYNVLAIDADPSMNLGSALGIPDLPkPVTEHKDLVEERagmpmgmfkmnpk 78 
                                       99*************************************99999999998887888888887776666666666666 PP

                            AAA_24  60 .........aaeladyktlviDtid 75 
                                                 + +++ k +v  tid
  gi|330507667|ref|YP_004384095.1|  79 vddvvgmcgCTGPDNVKLVVMGTID 103
                                       6666666666666666666666666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                            AAA_24  23 gpkplfidtekGlksldadkfp 44 
                                       +++ +++d+e+G  +l  +   
  gi|330507667|ref|YP_004384095.1| 128 EKDLVILDMEAGIEHLGRATAR 149
                                       4788999*****9998877655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1     1e-05    0.0071       4      38 ..       3      37 ..       1      39 [. 0.92
   2 ?   -0.9   0.0       1.5     1e+03      71     112 ..     116     158 ..     107     181 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      i++ G  G+GKTt ++ La+l+ ++g++vl + aD
  gi|330507667|ref|YP_004384095.1|  3 IAISGKGGVGKTTLAGTLARLFARDGYNVLAIDAD 37
                                      778999***********************988777 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHTTSSEEEEEE.--SSTTHHHHHHHHHHHHHHH CS
                             SRP54  71 vakeavekakeekidvvlvDT.aGrlqndkelmeelkkikkvv 112
                                       ++k+ +++   ++ d+v++D  aG  +  ++  + ++++  vv
  gi|330507667|ref|YP_004384095.1| 116 FVKALLRHVITREKDLVILDMeAGIEHLGRATARGVDAMIAVV 158
                                       5666677788888899999954777776666666666666655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.3e-05    0.0093      31      77 ..       2      46 ..       1      62 [. 0.85
   2 ?   -3.7   0.0       6.5   4.5e+03     172     180 ..     185     193 ..     183     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------ CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsil 77
                                      ++ + G  G+Gk tl   l+  ++r G+ v  +  DPs   + Gs l
  gi|330507667|ref|YP_004384095.1|  2 KIAISGKGGVGKTTLAGTLARLFARDGYNVLAIDADPSM--NLGSAL 46
                                      58899***********************98777777764..445555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.5
                                       EEEE---HH CS
                              MeaB 172 ivvnkaDkk 180
                                        v+nkaD +
  gi|330507667|ref|YP_004384095.1| 185 AVINKADDP 193
                                       699***955 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.5e-05     0.017       1      34 [.       7      40 ..       7      49 .. 0.91
   2 ?   -1.2   0.0       2.2   1.5e+03      10      37 ..     116     143 ..     114     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGq 34
                                      G+  +GK+Tla +L+   +r g++++ +D+D+  
  gi|330507667|ref|YP_004384095.1|  7 GKGGVGKTTLAGTLARLFARDGYNVLAIDADPSM 40
                                      66789**************************976 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.2
                            CLP1_P  10 larlLlNyalrkgrkpvyvDlDvGqsei 37 
                                       +++ Ll  ++ +++  v++D+  G  ++
  gi|330507667|ref|YP_004384095.1| 116 FVKALLRHVITREKDLVILDMEAGIEHL 143
                                       7888899999999999999988886665 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   1.4e-05    0.0096       1      29 [.       3      32 ..       3      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.gvnlr 29
                                      I+++G+ GvGKttla  L+++ +  g+n+ 
  gi|330507667|ref|YP_004384095.1|  3 IAISGKGGVGKTTLAGTLARLFARdGYNVL 32
                                      89****************999544755554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.4e-05      0.03       1      30 [.       2      31 ..       2      44 .. 0.93
   2 ?   -0.8   0.1       1.8   1.3e+03      90     114 ..     122     147 ..     113     187 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-05
                                      EEEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkv 30
                                      k++i+G+ GvGKtTl   +++l +++g++v
  gi|330507667|ref|YP_004384095.1|  2 KIAISGKGGVGKTTLAGTLARLFARDGYNV 31
                                      689**********************99998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                                       HHHH.HHH-EEEE-.--STTGGG-HHH CS
                          NTPase_1  90 rkal.seadviviD.EiGkmElkskkf 114
                                       r+ + +e+d++++D E G +E   +  
  gi|330507667|ref|YP_004384095.1| 122 RHVItREKDLVILDmEAG-IEHLGRAT 147
                                       333357888888883333.34333333 PP

>> AAA_16  AAA ATPase 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     0.015      28      63 ..       4      39 ..       2      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-05
                            AAA_16 28 llsGesGvGKsslvrellralekdggiflrgkcdql 63
                                       +sG  GvGK++l+ +l+r + +dg  +l+ ++d +
  gi|330507667|ref|YP_004384095.1|  4 AISGKGGVGKTTLAGTLARLFARDGYNVLAIDADPS 39
                                      69****************999999766676666665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   4.2e-05     0.029       3      30 ..       3      30 ..       2      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-05
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklp 30
                                      +++ G+ G+GKTtL+  la++ a++ ++
  gi|330507667|ref|YP_004384095.1|  3 IAISGKGGVGKTTLAGTLARLFARDGYN 30
                                      689******************9998765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00013      0.09      25      60 ..       2      36 ..       1      38 [. 0.92
   2 ?   -0.6   0.0       1.7   1.2e+03      39      61 ..     116     137 ..     115     155 .. 0.79
   3 ?   -2.4   0.0       5.8     4e+03     161     179 ..     234     252 ..     217     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                             DUF87 25 HlAilgsTGsGKSntvavLleellekkgatililDp 60
                                       +Ai g+ G+GK+++++ L +  + ++g+++l +D+
  gi|330507667|ref|YP_004384095.1|  2 KIAISGKGGVGKTTLAGTLARLFA-RDGYNVLAIDA 36
                                      58*****************99999.99*****9997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                             DUF87  39 tvavLleellekkgatililDpH 61 
                                       +v+ Ll+ ++ ++   ++ilD+ 
  gi|330507667|ref|YP_004384095.1| 116 FVKALLRHVI-TREKDLVILDME 137
                                       5777777777.777777888774 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.8
                             DUF87 161 knqaiarlldkledllrkg 179
                                       + q+i+r+++kle+++ ++
  gi|330507667|ref|YP_004384095.1| 234 SVQSIKRIKEKLEEMFGEN 252
                                       5678888888888887655 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.38   2.6e+02      11      32 ..      10      31 ..       3      32 .. 0.86
   2 ?   11.4   0.0   0.00031      0.21     132     195 ..     155     218 ..     148     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.38
                            AAA_26 11 gvGKTvvslgLvralkrkgvkv 32
                                      gvGKT+++  L+r + r g++v
  gi|330507667|ref|YP_004384095.1| 10 GVGKTTLAGTLARLFARDGYNV 31
                                      8*************99888876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00031
                            AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNkvrnpenvetlekksgipvlGvvPylpdle 195
                                       i V+ +g ++i+ +   +++ ++ ++     ++Nk  +p +v+   ++ gipvlG++P ++ l 
  gi|330507667|ref|YP_004384095.1| 155 IAVVEPGMRSIETVERIMQLGKEIGISRYFAVINKADDPGPVADKLSAMGIPVLGTIPFDRCLV 218
                                       55666666666666666666666677777789****9**9999999999*********998775 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3     8e-05     0.055      22      68 ..       4      48 ..       2     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8e-05
                            AAA_30 22 vltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgi 68
                                      ++ G  G GKtt+ ++l+++++++g++v  lA  +  + +L+ +lgi
  gi|330507667|ref|YP_004384095.1|  4 AISGKGGVGKTTLAGTLARLFARDGYNV--LAIDADPSMNLGSALGI 48
                                      5899*********************987..56677777777777776 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   0.2   0.00011     0.074      16      84 ..       2     195 ..       1     207 [. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                       EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE............................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................ RF
                       ATP-synt_ab  16 rtlipgafgvGktvisqslskqsnsddaiiyvg............................................ 48 
                                       +++i g+ gvGkt+++ +l++    d + +++                                             
  gi|330507667|ref|YP_004384095.1|   2 KIAISGKGGVGKTTLAGTLARLFARDGYNVLAIdadpsmnlgsalgipdlpkpvtehkdlveeragmpmgmfkmnpk 78 
                                       689*******************9888899999999****************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                       ATP-synt_ab  49 ............................................................................. 48 
                                                                                                                    
  gi|330507667|ref|YP_004384095.1|  79 vddvvgmcgctgpdnvklvvmgtidsggsgcmcpanafvkallrhvitrekdlvildmeagiehlgratargvdami 155
                                       ***************************************************************************** PP

                                       ....ESEEHHHHHHHHHHCHHSSGGGGEEEEEEETTS-HH CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  49 ....iGergnevaevleefpegtimkrtvlvantsnepva 84 
                                            G r+ e  e ++++ ++  ++r   v+n++++p  
  gi|330507667|ref|YP_004384095.1| 156 avvePGMRSIETVERIMQLGKEIGISRYFAVINKADDPGP 195
                                       *999999***********99999************99854 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00013      0.09       1      36 [.       5      40 ..       5      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAa 36
                                      + G  G+GKtt+ g+l+ ++   g++v  +  DP  
  gi|330507667|ref|YP_004384095.1|  5 ISGKGGVGKTTLAGTLARLFARDGYNVLAIDADPSM 40
                                      57999****************************975 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00017      0.12      23      39 ..       3      19 ..       1      27 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                      EEEEESTTSSHHHHHHH CS
                            NB-ARC 23 valvGmgGvGKttlakq 39
                                      +a++G+gGvGKttla  
  gi|330507667|ref|YP_004384095.1|  3 IAISGKGGVGKTTLAGT 19
                                      79************965 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.14      50      79 ..       3      32 ..       1      42 [. 0.91
   2 ?   -2.6   0.0       5.8     4e+03     109     127 ..     129     148 ..     118     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                         IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvl 79
                                      i++ G  GvGK+ la +l++  +r+g++vl
  gi|330507667|ref|YP_004384095.1|  3 IAISGKGGVGKTTLAGTLARLFARDGYNVL 32
                                      7999***********************998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.8
                         IstB_IS21 109 vdllilD.dlgllpldqaea 127
                                        dl+ilD + g+++l +a a
  gi|330507667|ref|YP_004384095.1| 129 KDLVILDmEAGIEHLGRATA 148
                                       48888887777777776665 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   0.00018      0.12       2      33 ..       3      34 ..       2      39 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgti 33
                                      ++i gk g GKTtL   l + +++ g++v +i
  gi|330507667|ref|YP_004384095.1|  3 IAISGKGGVGKTTLAGTLARLFARDGYNVLAI 34
                                      6899************************9877 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017      0.11       1      27 [.       2      32 ..       2      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                            AAA_28  1 kivitGgestGKTtlleaLa...ar.gypvv 27
                                      ki+i+G  + GKTtl+  La   ar gy+v+
  gi|330507667|ref|YP_004384095.1|  2 KIAISGKGGVGKTTLAGTLArlfARdGYNVL 32
                                      79**************999955544698876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00033      0.23      13      37 ..       2      26 ..       1      67 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00033
                                      EEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkp 37
                                      k+ai G+ G GK+tL+ +la+l   
  gi|330507667|ref|YP_004384095.1|  2 KIAISGKGGVGKTTLAGTLARLFAR 26
                                      689****************998765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0028       1.9      37      58 ..       4      25 ..       2      37 .. 0.84
   2 ?    1.5   0.0      0.28     2e+02     127     165 ..     114     151 ..      89     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0028
                            AAA_25 37 llaGapgtGKttlaldlalava 58
                                      ++ G +g+GKttla  la   a
  gi|330507667|ref|YP_004384095.1|  4 AISGKGGVGKTTLAGTLARLFA 25
                                      789***********99987665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.28
                            AAA_25 127 tadvdaleaaieevegvrlvviDplsralggdensnsdv 165
                                       +a+v+al +++    + +lv++D+ + + + +   ++ v
  gi|330507667|ref|YP_004384095.1| 114 NAFVKALLRHVIT-REKDLVILDMEAGIEHLGRATARGV 151
                                       6788999999999.569******8666555555555555 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 ?    3.1   0.1     0.088        61       5      24 ..       2      21 ..       1      32 [. 0.85
   2 ?    5.8   0.0     0.013       8.8      90     137 ..     147     195 ..     141     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.088
                                      EEEEEESTTSSHHHHHHHHH CS
                          GTP_EFTU  5 nigiighvDhGKtTLtdrLl 24
                                      +i+i g    GKtTL ++L 
  gi|330507667|ref|YP_004384095.1|  2 KIAISGKGGVGKTTLAGTLA 21
                                      5789999999******9996 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                                       HHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGSTHH CS
                          GTP_EFTU  90 glrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrlka 137
                                       ++r +D ++ vv+      +  e++++l ++ g+   + +iNK+D ++ 
  gi|330507667|ref|YP_004384095.1| 147 TARGVDAMIAVVEPGMRSIETVERIMQLGKEIGISrYFAVINKADDPGP 195
                                       57889999999999999999999999999*****9999*******9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); 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 0.25s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 1972.69
//
Query:       gi|330507668|ref|YP_004384096.1|  [L=676]
Description: ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     1e-153  512.6   0.0   1.5e-151  505.5   0.0    2.3  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    1.2e-23   82.9   0.0    3.6e-23   81.4   0.0    1.9  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
    1.4e-20   73.6   1.9    3.7e-20   72.3   1.9    1.7  1  ATP-cone         ATP cone domain


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  505.5   0.0  2.5e-155  1.5e-151       1     524 []     190     652 ..     190     652 .. 0.97

  Alignments for each domain:
  == domain 1  score: 505.5 bits;  conditional E-value: 2.5e-155
                                       EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRr 77 
                                       s+Cfvl v+dsl +I++++k++al++++ggG+G+++s+lR+k+++v+ t+g asGpvsfm+++d+ +dv+kqgG+Rr
  gi|330507668|ref|YP_004384096.1| 190 SACFVLPVTDSLPGIFDALKNMALIHQSGGGTGFSFSRLRPKDDVVRATGGVASGPVSFMRIFDTATDVIKQGGRRR 266
                                       79*************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC  78 GAamvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygeefeee 154
                                       GA+m++l+v+HpDi++fi+aKe+        l+n+n+sv  +d+Fme+ + ++++ L++Prt               
  gi|330507668|ref|YP_004384096.1| 267 GANMGILRVDHPDIMEFIEAKER-----PGFLENFNLSVAATDEFMEKSRGEGEIDLINPRT--------------- 323
                                       *********************66.....77*******************************3............... PP

                                       .............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 155 yeeleekakikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyesvavCn 231
                                                ++  + ka eL+  ia+saw+ g+Pg++f+D+iN++++l     g+I+atN+CgE+pll+yes   Cn
  gi|330507668|ref|YP_004384096.1| 324 --------GLAGGRLKAAELLGLIATSAWRGGDPGIIFIDRINAAHPL----PGEIEATNPCGEQPLLPYES---CN 385
                                       ........233359**********************************....489*****************...** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 232 LasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladalaklgip 308
                                       L+sinL+++v      k e dwd+l++ + l+vr+Ld+vid+n++plp+ie++t ++R+iGlGvmg+ad+l++++i 
  gi|330507668|ref|YP_004384096.1| 386 LGSINLSRLV-----RKGELDWDRLAELVSLAVRFLDDVIDMNRFPLPQIEEATLSRRKIGLGVMGFADMLIQMNIS 457
                                       **********.....579*********************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 309 ydseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdefeekekedweeLreeikkyGlrnam 385
                                       y s++a+++a+k++ +++ +a  +S++l +erg+fplf++s+ + g              w+          +rna+
  gi|330507668|ref|YP_004384096.1| 458 YASPQAVALAEKLMGFISEHARAQSARLGEERGSFPLFDSSRLR-G--------------WS---------AMRNAT 510
                                       ****************************************9985.4..............43.........49**** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                   Ribonuc_red_lgC 386 vtalaPTgsiSliagtssgiePifalvykksvtvge.flevnpvfeeeLkklglwseellkki..lesvqgleeipe 459
                                       vt++aPTg+iS+iagtssgieP+fal+++++v +g  +lev p fe+   ++g+++ +l+ ++   +svq++  +p+
  gi|330507668|ref|YP_004384096.1| 511 VTTIAPTGTISIIAGTSSGIEPLFALAFVRRVLEGArLLEVSPLFEKMAMERGIYTPDLKVELawRGSVQEIAGLPQ 587
                                       **********************************654*************************988899********* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 460 eikrvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                       ++k++f+taldi++++h+++qaa qk+ d+++Skt+nlp eatv+dv ++y lA++lG+Kgvt++
  gi|330507668|ref|YP_004384096.1| 588 DLKELFRTALDISAQQHVRIQAAFQKYTDNAVSKTVNLPAEATVSDVLQVYRLAYDLGCKGVTVF 652
                                       ***************************************************************96 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.0     6e-27   3.6e-23       2      83 .]     108     187 ..     107     187 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 6e-27
                   Ribonuc_red_lgN   2 kltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealydkleedkdlaeefydlmssqkflpasPtlmna 78 
                                       kl++na++vl++rYll+de+g++vE+p +mf RvA ++  ae +y  + +++++   f ++m +++flp+sPtlmn+
  gi|330507668|ref|YP_004384096.1| 108 KLSVNAAEVLKKRYLLRDERGDVVETPGEMFGRVADHISKAESKY--GGDVESYRSLFLQMMRNLEFLPNSPTLMNS 182
                                       789****************************************98..899999999********************* PP

                   Ribonuc_red_lgN  79 Gtelg 83 
                                       + elg
  gi|330507668|ref|YP_004384096.1| 183 RLELG 187
                                       99876 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   1.9   6.2e-24   3.7e-20       2      86 .]       4      93 ..       3      93 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 6.2e-24
                                      EEE-TTS-EEE--HHHHHHHHHHHHHH....-HHHHHHHHHHHHHHHHHHHIIT.-BHHHHHHHHHHHHHHSS-HHHHH CS
                          ATP-cone  2 kViKRdGtvepfdvekIkraiekAceg....seeeideiaeeveaevrkrlrdg.isteeIqdlvektliehpdyavaa 75
                                      +++KR G+v++f  ekI+ ai+kA+++    +e+   ++ae+v++e+++r+ ++ + +eeIqdlve++li +++ +va+
  gi|330507668|ref|YP_004384096.1|  4 RIRKREGRVVEFQTEKIALAISKAFRAvgreEEDAPFRLAERVAKEAEERFSRTiPGVEEIQDLVERALISAGYADVAK 82
                                      69**************************9877777999************9999899********************** PP

                                      HHHHHHHHHHH CS
                          ATP-cone 76 ayilyrnlrke 86
                                      ayilyr++r+e
  gi|330507668|ref|YP_004384096.1| 83 AYILYRQKRTE 93
                                      ********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (676 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 4643.98
//
Query:       gi|330507669|ref|YP_004384097.1|  [L=236]
Description: hypothetical protein MCON_1655 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-58  195.8   0.1    8.3e-58  195.6   0.1    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 !  195.6   0.1   4.6e-62   8.3e-58       1     213 []       9     225 ..       9     225 .. 0.98

  Alignments for each domain:
  == domain 1  score: 195.6 bits;  conditional E-value: 4.6e-62
                    DNA_alkylation   1 ikaeLealadpekaeemqryfkegdeflGvkvpelrklakeffkelkle..eelqelaeeLwksperEerllAldll 75 
                                       +++eL +  d++++   +r+fke+ +f+Gvk+  +rk+a ++f+e+k +   ++++l+eeL+ s++ Ee ++A++++
  gi|330507669|ref|YP_004384097.1|   9 LRQELIEGIDEKTRDGASRFFKEEVRFYGVKSSLVRKIATKYFREIKGRdkGKIFTLCEELLCSDYGEEAFIAFEWA 85 
                                       589********************************************99999999********************** PP

                    DNA_alkylation  76 tqakkklaeadlelyeklve.tinnWdlvDslaskivgalladkperrdllkeWaksenlWerRaAivatlklikk. 150
                                       +  + +++++d+  +e ++e ++nnW+ +D+l+++++g++++ +p+  ++l  Wa+s+n+W+rRa++v+++  +++ 
  gi|330507669|ref|YP_004384097.1|  86 YSLRSQYEPSDFFIFEGWLErYVNNWAKCDTLCNHTLGSFIELYPQYMEKLFGWARSDNRWVRRASAVTLILPARRg 162
                                       ****************************************************************************7 PP

                    DNA_alkylation 151 tdlellleiaeelladkedfiqkAiGwaLrelsktdpdlveeFlekhakrmprlslreAiekl 213
                                       + l + + ia+ ll dk+d++qk++Gw+L+e+s+ ++++v+++++k+++ mpr+slr+Aiek+
  gi|330507669|ref|YP_004384097.1| 163 DFLPEAFMIADILLLDKDDMVQKGYGWLLKEASRAHQAEVFDYVMKNKAVMPRTSLRYAIEKM 225
                                       7789*********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1857.64
//
Query:       gi|330507670|ref|YP_004384098.1|  [L=76]
Description: hypothetical protein MCON_1656 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.6   0.2      0.054   13.3   0.2    1.3  1  Synaptonemal_3  Synaptonemal complex central element protein 


Domain annotation for each model (and alignments):
>> Synaptonemal_3  Synaptonemal complex central element protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2     3e-06     0.054      10      45 ..       6      41 ..       1      72 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-06
                    Synaptonemal_3 10 qyedfskeslqlnkdleklteqmedvsvkltwmayd 45
                                        +++s  ++ +n  le + e++e++s+   +m + 
  gi|330507670|ref|YP_004384098.1|  6 VLQEISDTLISINDCLEGIGEELEEISMASKMMIFF 41
                                      5678999999******************99988763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 578.81
//
Query:       gi|330507671|ref|YP_004384099.1|  [L=450]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-25   89.8   0.0    3.3e-25   89.0   0.0    1.4  1  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
      0.014   14.7   0.3      0.021   14.1   0.3    1.3  1  DDE_Tnp_2    Archaeal putative transposase ISC1217
      0.019   13.3   0.0       0.03   12.6   0.0    1.2  1  DDE_Tnp_1_4  Transposase DDE domain group 1
      0.075   13.0   1.0        1.4    8.9   0.1    2.8  3  Tudor_FRX1   Fragile X mental retardation Tudor 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 !   89.0   0.0   7.3e-29   3.3e-25       2     212 ..     133     371 ..     132     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 7.3e-29
                         DDE_Tnp_1   2 skrevlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkq..lldelrprk 76 
                                       s+r+v i D+t +r +++ +d+++     k  +g+k+  ++++    + s+ i p n++d+k+lk   ++      k
  gi|330507671|ref|YP_004384099.1| 133 SFRDVMIQDSTIIRLHKSLADKWPATRSRKVAAGVKVAFLTSAIANSPKSISILPENTNDVKTLKIgpWV------K 203
                                       6899***************9999988899999********************************995555......7 PP

                         DDE_Tnp_1  77 gklvlaDaGYasaelldtleekgvdyiirlkkntklyrk.............gaeskrrgrlrkhdrnkiltksqkr 140
                                       + ++l D G+ +++l+ ++ e+g+++++rlk+n++ ++              + +++++ +l+k d    ++ + ++
  gi|330507671|ref|YP_004384099.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVgtnqvrntrgvdlNGKHLKDIKLEKSDDIFDVNVEVSF 280
                                       789************************************99777666666663444444444444444444444444 PP

                         DDE_Tnp_1 141 rnk...................skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrgl 198
                                       +++                    +++++++ y+tn++s+ l a+eva+ y+ Rw++E +Fk+lk+++ ld   ++++
  gi|330507671|ref|YP_004384099.1| 281 DRRsyrgeskkdnkifrlvaiyNTEAEEHHFYLTNISSDILNASEVAAVYSGRWEVELIFKELKSRYALDQITTKSP 357
                                       4447777777777799999999999**************************************************** PP

                         DDE_Tnp_1 199 nrveaqllllllal 212
                                        ++ea ++  +l+l
  gi|330507671|ref|YP_004384099.1| 358 YAIEALIWVSILTL 371
                                       *******9998876 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   4.6e-06     0.021     219     288 ..     274     346 ..     202     384 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                         DDE_Tnp_2 219 rhvpvaelPeGeylveyl.dtvikllvlddykkdgrrylfstdln...dtdediittWenrWdievlirelkal 288
                                        +v+v+ + + +y  e   d+ i  lv +   + +  +++ t++    + + ++ + +  rW++e +++elk+ 
  gi|330507671|ref|YP_004384099.1| 274 VNVEVS-FDRRSYRGESKkDNKIFRLVAIYNTEAEEHHFYLTNISsdiLNASEVAAVYSGRWEVELIFKELKSR 346
                                       445543.7777888887767777767777777888999**999973335799********************73 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.6e-06      0.03     217     368 ..     204     372 ..     197     399 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.6e-06
                       DDE_Tnp_1_4 217 kilvRgDSafarpellkwceergvdYviglaknsrlealiaelvekakteaaekkek................erey 277
                                       +i++  D +f + +l++ + e+g ++v +l++n++     ++ v +++  + + k+                 e+++
  gi|330507671|ref|YP_004384099.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVGTNQVRNTRGVDLNGKHLkdikleksddifdvnvEVSF 280
                                       578889999**********************999877766666666666666654436799999999**99999999 PP

                       DDE_Tnp_1_4 278 refayqaesWskerrVvakaerpaeglnlrfvvTsla..klspeelyeqlYcaRGemEnrIKeakldlaadrtsshs 352
                                        +  y+ es + ++   + a +++e  +++f +T+++   l+++e+   +Y  R e+E  +Ke k+  a+d++ ++s
  gi|330507671|ref|YP_004384099.1| 281 DRRSYRGESKKDNKIFRLVAIYNTEAEEHHFYLTNISsdILNASEVA-AVYSGRWEVELIFKELKSRYALDQITTKS 356
                                       99999999855444333334455556667999****99888999999.9*************************999 PP

                       DDE_Tnp_1_4 353 faaNqlrlllsalAyn 368
                                         a ++ +++s l   
  gi|330507671|ref|YP_004384099.1| 357 PYAIEALIWVSILTLL 372
                                       9999988888887654 PP

>> Tudor_FRX1  Fragile X mental retardation Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00031       1.4      17      36 ..      22      41 ..      18      44 .. 0.88
   2 ?    1.1   0.0     0.085   3.8e+02      18      31 ..     269     282 ..     257     291 .. 0.89
   3 ?   -2.6   0.0       1.2   5.4e+03      13      36 ..     313     337 ..     311     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00031
                        Tudor_FRX1 17 vkdvhedsltvaFennWqpe 36
                                       kd+ e++lt +Fe +W  +
  gi|330507671|ref|YP_004384099.1| 22 EKDIVEQELTRMFESKWIRD 41
                                      59***************765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.085
                        Tudor_FRX1  18 kdvhedsltvaFen 31 
                                        d+++ ++ v+F+ 
  gi|330507671|ref|YP_004384099.1| 269 DDIFDVNVEVSFDR 282
                                       59**********96 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.2
                        Tudor_FRX1  13 ykafvkdvhed.sltvaFennWqpe 36 
                                       +  +  d+++  ++ +++   W  e
  gi|330507671|ref|YP_004384099.1| 313 LTNISSDILNAsEVAAVYSGRWEVE 337
                                       5566778888526888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3208.81
//
Query:       gi|330507672|ref|YP_004384100.1|  [L=222]
Description: peptidase M50 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-09   37.5   7.4    0.00012   21.4   0.6    2.8  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 !   18.3   1.3   6.1e-08    0.0011      10     108 ..      48     154 ..      38     158 .. 0.73
   2 !   21.4   0.6   6.8e-09   0.00012     187     219 ..     164     196 ..     154     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.1e-08
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                     Peptidase_M50  10 vvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeaka........ 78 
                                        ++HEl+H ++A+ +g+  e  + ++G  l+          +++ p G+ V ++  +p  ++  +++          
  gi|330507672|ref|YP_004384100.1|  48 FLLHELAHKFTAQHFGYLAEYRANLLGLGLAVAS--AFAGLLIAAP-GA-VMISRSRPPVQTYIQDSIYgstvpdpf 120
                                       689*************998876655555553333..2333477888.77.55555554444333333336999***9 PP

                                       ....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  79 ....flkkspwqrllivlAGplanfilailvfvv 108
                                           ++++   + lli lAGp++n++la ++f++
  gi|330507672|ref|YP_004384100.1| 121 hqeeLASQLKREMLLISLAGPMTNIVLAAFFFIL 154
                                       9999999999999******************986 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 6.8e-09
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 187 glssflqllalisvnLgilNLlPipvLDGghll 219
                                        + + + ++ +i+++L+ +N+lP+ +LDG +++
  gi|330507672|ref|YP_004384100.1| 164 VWAQAITFALFINLILAAFNMLPFGPLDGKKIF 196
                                       5668899***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1535.31
//
Query:       gi|330507673|ref|YP_004384101.1|  [L=84]
Description: hypothetical protein MCON_1659 [Methanosaeta concilii GP6]
Scores for complete 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   0.3     0.0033   17.3   0.3    1.4  1  VbhA      Antitoxin VbhA


Domain annotation for each model (and alignments):
>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.3   1.8e-07    0.0033      25      40 ..      24      39 ..      22      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-07
                              VbhA 25 adleayvrGeIdadEl 40
                                      a l++y+rGeId+dE+
  gi|330507673|ref|YP_004384101.1| 24 AILNRYARGEIDLDEA 39
                                      789************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 671.39
//
Query:       gi|330507674|ref|YP_004384102.1|  [L=364]
Description: hypothetical protein MCON_1660 [Methanosaeta concilii GP6]
Scores for complete 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-11   41.8   0.0    0.00036   19.9   0.0    2.2  2  Glyco_trans_1_3  Glycosyl transferase family 1
    0.00011   22.3   0.0    0.00016   21.7   0.0    1.2  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
    0.00015   21.8   0.0    0.00033   20.7   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
      0.043   14.3   0.0      0.073   13.5   0.0    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
       0.12   12.5   0.0        4.9    7.2   0.0    2.2  2  MTS_N            Methyltransferase small domain N-terminal
       0.12   12.0   0.1         23    4.6   0.1    2.7  3  NAT              NAT, N-acetyltransferase, of N-acetylglutama
       0.13   13.1   0.0        2.3    9.1   0.0    2.3  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


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 !   19.9   0.0   1.4e-07   0.00036      11      48 ..      12      51 ..       9     117 .. 0.74
   2 !   19.8   0.0   1.5e-07   0.00039     215     300 ..     229     318 ..     212     336 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.4e-07
                   Glyco_trans_1_3 11 GaGhasRsrvvlehLar.ghevkvvvsgraldvLekef.d 48
                                      G Gh++R   ++e L+r ghev + +sg al+ L++ef +
  gi|330507674|ref|YP_004384102.1| 12 GLGHSTRDIPIIEELIRrGHEVTIGTSGNALTLLKREFpE 51
                                      89*************777*****************99943 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.5e-07
                   Glyco_trans_1_3 215 klg.vefvvYglrrd..teeekegnltykafseegFleDLataraviagagftLmtealyLkk.PlLavPvarqFeq 287
                                       kl+ +++v+ g +++  +e+  e   ++   s e  +e + +ar +i+ +g+t m e + L k   L +P  +q eq
  gi|330507674|ref|YP_004384102.1| 229 KLPgEKVVLLGSPQKerHEKLDEHTTVHSYLSTEDKVEMMNRARFLITRSGYTTMMEMVELDKkHGLFIPTPGQTEQ 305
                                       4443677778877664455666777889999******************************76167*********** PP

                   Glyco_trans_1_3 288 vlnalyLerlgyG 300
                                           +y  r+g+ 
  gi|330507674|ref|YP_004384102.1| 306 EYLSRYYARQGWF 318
                                       *999999998865 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 !   21.7   0.0   6.2e-08   0.00016      43     159 ..     242     350 ..     208     358 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 6.2e-08
                                       C---STT-TTTTCEEEEEESSSSHHHHHHHH-EEEECS-CHHHHHHHHTT--E.EEE--TT....S-HHHHHHHHHH CS
                   Glyco_tran_28_C  43 leevkikveeltlkvevfefidkmaeaikaadLvIsRAGagtiaEllalgkpl.IlvplpeaaenhqdnNakeleka 118
                                       ++e + k+ e t +v+ +  +++ +e + +a   I+R+G +t +E++ l k++ +++p p ++  +q++  ++ +++
  gi|330507674|ref|YP_004384102.1| 242 QKERHEKLDEHT-TVHSYLSTEDKVEMMNRARFLITRSGYTTMMEMVELDKKHgLFIPTPGQT--EQEYLSRYYARQ 315
                                       344444455553.555555566799************************986449******88..999999999999 PP

                                       HHHHSSEEEE-STTCHHHHHHHHCCS---S---SSCH..CH CS
                   Glyco_tran_28_C 119 gaalvleqkeltpekLeeallelaaeklrlaekskasaask 159
                                       g      q++l   +L + ++e ++ +  ++++++a     
  gi|330507674|ref|YP_004384102.1| 316 GWFFSRSQYKL---RLPQDVQEAMNYQGFPEMTKTAE---N 350
                                       99888888888...89999999888888777777774...3 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.3e-07   0.00033      12     140 ..      23     158 ..      21     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.3e-07
                    Glyco_transf_4  12 araLarrGheVtvvtpgddgpleeev.........elvvrvprvplpllk.rllrslaflrrlrrllkre....... 71 
                                       +++L rrGheVt+ t+g    l +++         +++ ++ +  +++l+  +  ++  lr+l+r  k+        
  gi|330507674|ref|YP_004384102.1|  23 IEELIRRGHEVTIGTSGNALTLLKREfpecdfitfKDYPAPYSSTRFFLPkFAASIPILLRALARERKKLdeilsvn 99 
                                       689****************99999999**888777333333333333333033333344444433333334457777 PP

                    Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviav 140
                                       k+D++ + + + + ++       ++ip  +  H l     l+++l p++ l   +  +++ + d vi++
  gi|330507674|ref|YP_004384102.1| 100 KFDLIISDNRMGV-YS-------HDIPSYFISHQLR--FSLPQYLYPFEMLTIPVNSFVHVKFDGVIVP 158
                                       *****88887665.33.......6999999999998..5778888888888888888888888888886 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 ?   13.5   0.0   2.8e-05     0.073      10      71 ..      22      89 ..      14     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-05
                   Glyco_trans_4_4 10 laraLaarGheVtvltpapapgapeleedgvrvhrl...pvprrps...pladlaalralrrllrqrr 71
                                      ++++L +rGheVt+ t++ a     +e + +  + +   p+p+++    +++ +a+++ l r+l+++r
  gi|330507674|ref|YP_004384102.1| 22 IIEELIRRGHEVTIGTSGNALTLLKREFPECDFITFkdyPAPYSSTrffLPKFAASIPILLRALARER 89
                                      689****************9998888888888886633378888864444455667788888883333 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 ?    3.0   0.0     0.038        98      59     114 ..      52     114 ..      16     118 .. 0.69
   2 ?    7.2   0.0    0.0019       4.9       2      40 ..     221     258 ..     220     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.038
                                       EEE-SS--HHTT-SEEEEE--SSHHHHHHHHHHHHTTS-TT-EE.......EEEEEGGGTGGG CS
                             MTS_N  59 vefgleleaeskfdlvilylpKaKeeakylLalllsklkkgtei.......lvVGenksGvks 114
                                       ++f +  +  + + +  ++lpK  + + +lL++l+ + kk  ei       l++ +n+ Gv s
  gi|330507674|ref|YP_004384102.1|  52 CDFITFKDYPAPYSSTRFFLPKFAASIPILLRALARERKKLDEIlsvnkfdLIISDNRMGVYS 114
                                       5554444444677888899**************999988888883333333477888888876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0019
                                       HHHHTTHHHHTT-EEEEEE---SSHHHHS--SEEEEEE. CS
                             MTS_N   2 qvllRnlelfenksvllageieddlpkelkkasksvtvl 40 
                                       ++++++ +++ +++v+l+g+++ +  ++l+++++ v+ +
  gi|330507674|ref|YP_004384102.1| 221 EIIMKQVQKLPGEKVVLLGSPQKERHEKLDEHTT-VHSY 258
                                       799***********************99998776.4432 PP

>> NAT  NAT, N-acetyltransferase, of N-acetylglutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.2   8.2e+03      15      31 ..      26      42 ..      25      63 .. 0.70
   2 ?    4.5   0.0    0.0097        25      34      86 ..     166     216 ..     142     286 .. 0.83
   3 ?    4.6   0.1    0.0088        23     132     167 ..     316     354 ..     311     357 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.2
                                      EEE---XEEEESSCCCS CS
                               NAT 15 lirrGlkvitvkslkel 31
                                      lirrG +v+  +s + l
  gi|330507674|ref|YP_004384102.1| 26 LIRRGHEVTIGTSGNAL 42
                                      67777777776666555 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0097
                                       CCHHHHHHTTSTTTSSXHHHHHHHHHTSXEEEEEETTXSEEEEE.....EXSS CS
                               NAT  34 lekLksliedsfkrkldvkdYldrlkgkiakiyiaedyeglAivtwedpkeek 86 
                                        ++L+  +++s+ + ++++ Y+  + ++  k+ ++ed++ l iv    p++++
  gi|330507674|ref|YP_004384102.1| 166 QPNLSGKLSRSRLDATNKRAYFAGIFTSTRKMNLDEDLDYLIIVSG--PEPQR 216
                                       567888899999999*****************************54..44433 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0088
                                       HHHHHCXSEEEE...ETTEEEEEESXXXHHHHHHHHHHH CS
                               NAT 132 kWyfersdGslk...ksqwvlfWyGlkdlkeveelvesf 167
                                        W+f+rs+  l+   + q+ + ++G+ +++++ e v+++
  gi|330507674|ref|YP_004384102.1| 316 GWFFSRSQYKLRlpqDVQEAMNYQGFPEMTKTAENVKRL 354
                                       6*********999988899******99999999888765 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.11   2.7e+02      49      78 ..     188     218 ..     172     231 .. 0.68
   2 ?    9.1   0.0   0.00089       2.3      21      54 ..     228     280 ..     219     315 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.11
                                       E.EESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA  49 e.aysdleelladpeidavivatpngtheel 78 
                                       +  +++ +++  d++ d++i+++ ++ ++  
  gi|330507674|ref|YP_004384102.1| 188 AgIFTSTRKMNLDEDLDYLIIVSGPEPQRTK 218
                                       3478899999999**********99543332 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00089
                                       HTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS...................H CS
                      GFO_IDH_MocA  21 esqrleevvalldpdaeraeavaesfgveaysd...................l 54 
                                       ++ ++e+vv l +p++er+e++ e++ v++y +                   +
  gi|330507674|ref|YP_004384102.1| 228 QKLPGEKVVLLGSPQKERHEKLDEHTTVHSYLStedkvemmnrarflitrsgY 280
                                       445889***********************888844444444444444444441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2553.01
//
Query:       gi|330507675|ref|YP_004384103.1|  [L=182]
Description: hypothetical protein MCON_1661 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.2   0.4       0.42   10.6   0.2    2.1  2  RHH_3     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0     0.054   9.7e+02      10      23 ..      10      23 ..       6      25 .. 0.85
   2 ?   10.6   0.2   2.3e-05      0.42      22      42 ..     141     161 ..     138     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.054
                             RHH_3 10 dpelaekLkaLSek 23
                                      + el + L+ LS++
  gi|330507675|ref|YP_004384103.1| 10 CQELIYWLELLSRR 23
                                      6899999*****98 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 2.3e-05
                             RHH_3  22 ekTrIprSklldeAiellLek 42 
                                       e+++ +++++l+++i+ll+++
  gi|330507675|ref|YP_004384103.1| 141 ERLMERKARYLEQMIDLLPKE 161
                                       5666689***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1355.49
//
Query:       gi|330507676|ref|YP_004384104.1|  [L=454]
Description: histone deacetylase family protein [Methanosaeta concilii GP6]
Scores for complete 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-64  217.6   0.0    3.9e-64  217.0   0.0    1.3  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.0   0.0   2.2e-68   3.9e-64      76     295 ..      70     282 ..      26     294 .. 0.89

  Alignments for each domain:
  == domain 1  score: 217.0 bits;  conditional E-value: 2.2e-68
                                       SSSSSTHCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-B..TTBSS-HHHHHHHHHHHCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  76 lldddtpvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseas..GFClvNnvaiaikylqakhe 150
                                       +++d   v++++ +a l+a+g++l+++da+ +g+++++f+lvrPpgHH+++   +  GFC +Nn+ai ++yl+ k++
  gi|330507676|ref|YP_004384104.1|  70 CVPD---VESQVTEAHLIAAGSTLTLADALEKGEIRNGFALVRPPGHHSMRVVHGnrGFCNINNMAILVEYLRTKYG 143
                                       3444...7889999***********************************87776668******************** PP

                                       SS-EEEEE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 151 lkrvailDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfe 227
                                       +kr a++D DvHhG+Gt+e+f++dp+vl++S+H+ ++++yPg+g ++++g  ++   +lnvpl++gt+de +++v++
  gi|330507676|ref|YP_004384104.1| 144 HKRLAVIDTDVHHGDGTQEIFWHDPEVLCISFHQDGHTLYPGSGFVNEIGGPQALARTLNVPLPPGTTDEGIHYVLD 220
                                       **************************************************999999********************* PP

                                       HCHHHHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S---H.HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                     Hist_deacetyl 228 eilrpvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkvkkvvllleGGYnl.ea 295
                                       +++ p+leefkPdl+l saG D + +dpl++++ s++gy++l +kla         +++leGGY   +a
  gi|330507676|ref|YP_004384104.1| 221 NLILPILEEFKPDLVLNSAGQDNHYTDPLANMRFSANGYARLNEKLAP-------DICVLEGGYAVeTA 282
                                       *******************************************99953.......38*******99444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3314.04
//
Query:       gi|330507677|ref|YP_004384105.1|  [L=558]
Description: hydantoinase/oxoprolinase [Methanosaeta concilii GP6]
Scores for complete 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-44  149.8  10.0    6.5e-41  140.5   3.9    2.8  3  Hydantoinase_A  Hydantoinase/oxoprolinase
      2e-29  102.6   7.2    1.6e-26   93.1   3.4    3.4  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    3.1e-05   22.8   5.4      0.013   14.1   0.1    3.1  3  MutL            MutL protein
      0.002   18.5   5.8       0.67   10.4   0.2    3.4  2  FtsA            Cell division protein FtsA
     0.0069   15.9   1.3       0.12   11.8   0.0    2.7  3  Ppx-GppA        Ppx/GppA phosphatase family
  ------ inclusion threshold ------
      0.067   12.2   0.2      0.067   12.2   0.2    2.8  3  DDR             Diol dehydratase reactivase ATPase-like domai
      0.076   12.5  12.6         20    4.6  12.6    3.3  1  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
       0.11   11.7   1.7        1.8    7.7   0.1    2.6  2  StbA            StbA protein
        1.9    7.2   7.9       0.19   10.5   0.3    2.6  3  MreB_Mbl        MreB/Mbl protein


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   4.4e-05     0.087      80     102 ..       3      25 ..       1      60 [. 0.84
   2 !  140.5   3.9   3.3e-44   6.5e-41       2     288 ..     182     461 ..     181     463 .. 0.92
   3 ?   -2.5   0.0       1.2   2.3e+03     171     219 ..     482     522 ..     475     535 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                    Hydantoinase_A  80 kvItfDmGGTstDvslikdgeve 102
                                        +I++D+GGT+tD+ l++  +ve
  gi|330507677|ref|YP_004384105.1|   3 MLIGIDVGGTTTDAVLVDGSRVE 25 
                                       68**************9955554 PP

  == domain 2  score: 140.5 bits;  conditional E-value: 3.3e-44
                    Hydantoinase_A   2 tetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklage 78 
                                       + t+ ++ + ++ + +++  ++ +le+r ++a+++++++dGg+++++   + pveti SGPaa+++g+ a   ++  
  gi|330507677|ref|YP_004384105.1| 182 AATTKLTLATKESYARFALAISRALEERRITAPVYILKADGGTLPLEGSLQMPVETIFSGPAASIMGVMA--LTPPG 256
                                       66777777778888999999**************************************************..77777 PP

                    Hydantoinase_A  79 kkvItfDmGGTstDvslikdgevevsletei.agvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpa 154
                                       +  +++D+GGT+tD++li +g++  s++      + ++++a ++r+v++gG+s +    ++ l vgp+  g+     
  gi|330507677|ref|YP_004384105.1| 257 QTSVVVDIGGTTTDLALILSGSPLLSSKGARvDSMLTHVRAFAVRSVAIGGDSAV-DVAEDGLTVGPQRNGSPFCL- 331
                                       7899*******************99988654499*********************.777899*****987764444. PP

                    Hydantoinase_A 155 cyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegilsvavenmanavrk 231
                                           Ggt +t TDa  vLGr                d e a++a++ +a ++n ++e++Ae +l+ +ve++a++v++
  gi|330507677|ref|YP_004384105.1| 332 ----GGTGPTPTDALRVLGRSSVG------------DLERAKEAMAGVASRMNCTAEKAAEMVLDSVVEKIASQVNE 392
                                       ....6667***********97766............567************************************** PP

                    Hydantoinase_A 232 l.............svergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvr 288
                                       +             +  ++ + +  ++v++GGa++ +++ +a +l v +++ +++  v++a+G+a+A+ +
  gi|330507677|ref|YP_004384105.1| 393 MfreweqepayriwEIMKKEKLEAQNVVGVGGAAPALVPLIASRLKVASIVPEHA-AVANAIGAAVARPT 461
                                       **************999********************************988887.***********976 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.2
                    Hydantoinase_A 171 vLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegils 219
                                       ++G++++++++          ++larr + e a +l  ++ee A+++l 
  gi|330507677|ref|YP_004384105.1| 482 IMGKVNEKQMS------LAQAEQLARRLLVERAGRL--GIEEYAAEALV 522
                                       67888888777......5567778888887777777..57777777664 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 !   93.1   3.4   7.8e-30   1.6e-26       2     177 ..       5     160 ..       4     161 .. 0.92
   2 !    7.4   0.1    0.0016       3.2       2      18 ..     260     276 ..     259     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 7.8e-30
                        Hydant_A_N   2 igIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkger 78 
                                       igIDvGGT TDav++d+  ++ +++ +++  ++    ++ al+e+ +  + + ski+ v+++TT+ tN++ e+k ++
  gi|330507677|ref|YP_004384105.1|   5 IGIDVGGTTTDAVLVDGS-RVEKTAYVPTDHNDLLGCLLGALDELVR--GVDVSKIERVVLSTTLITNMIAEKKTDP 78 
                                       8***************88.*************************965..5778************************ PP

                        Hydant_A_N  79 vaLittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiav 155
                                       vaL+ + g     +  +                   + + +d+ ++++g+++++l+e++++ a++++k++gv+ +av
  gi|330507677|ref|YP_004384105.1|  79 VALVLIPGPGTNPQDYNL-----------------GQSIILDGAIDFRGKEIDRLNESQIKDAAARIKESGVSRVAV 138
                                       ******998766544433.................566779************************************ PP

                        Hydant_A_N 156 vllhSylnpehElrvaeiarei 177
                                       v  +S +np+hE++v +i+++i
  gi|330507677|ref|YP_004384105.1| 139 VGKFSQRNPAHEEKVSQIMSQI 160
                                       ******************9876 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0016
                        Hydant_A_N   2 igIDvGGTfTDavalde 18 
                                       + +D+GGT TD+ ++  
  gi|330507677|ref|YP_004384105.1| 260 VVVDIGGTTTDLALILS 276
                                       78*********988765 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.2    0.0002       0.4     249     275 ..       4      29 ..       1      81 [. 0.54
   2 !   14.1   0.1   6.4e-06     0.013     222     272 ..     236     282 ..     226     294 .. 0.81
   3 ?   -0.3   0.1      0.15   3.1e+02     317     392 ..     354     425 ..     342     435 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0002
                              MutL 249 llvvDvGGaTTdvhsvaegspekekvl 275
                                       l+++DvGG+TTd   v +gs  +++  
  gi|330507677|ref|YP_004384105.1|   4 LIGIDVGGTTTDAVLV-DGSRVEKTAY 29 
                                       5677777777777777.4433333222 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.4e-06
                              MutL 222 aeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspeke 272
                                       ++i   PaA + +v +l     +     +vvD+GG+TTd+  +++gsp  +
  gi|330507677|ref|YP_004384105.1| 236 ETIFSGPAASIMGVMALTPP-GQ---TSVVVDIGGTTTDLALILSGSPLLS 282
                                       67788899999999999993.33...58**************999988655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.15
                              MutL 317 eelrerlenlmerpktiPkteeelaldealareavelaverHagtleelytplgrvvvqegkdltavkliigtGGv 392
                                       e+ +e+++ +++r++  +++++e+ ld+ + ++a ++       + e    p  r++    k+  + + ++g GG+
  gi|330507677|ref|YP_004384105.1| 354 ERAKEAMAGVASRMNCTAEKAAEMVLDSVVEKIASQVN----EMFREWEQEPAYRIWEIMKKEKLEAQNVVGVGGA 425
                                       66778888888999999999999999999999999888....5555566678889999999999999999999996 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.2   0.00034      0.67       1      30 [.       5      34 ..       5      64 .. 0.90
   2 !    8.5   1.4    0.0013       2.6       1      22 [.     260     281 ..     260     529 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00034
                                      EEEEE-SSSEEEEEEETTEEEEEEEES--H CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              FtsA  1 alvDiGagktdvavaedgalvhlrvigvgg 30
                                      +++D+G+++td+++++++++ +++++++  
  gi|330507677|ref|YP_004384105.1|  5 IGIDVGGTTTDAVLVDGSRVEKTAYVPTDH 34
                                      58***********************99854 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0013
                                       EEEEE-SSSEEEEEEETTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                              FtsA   1 alvDiGagktdvavaedgalvh 22 
                                       ++vDiG+++td+a++  g++  
  gi|330507677|ref|YP_004384105.1| 260 VVVDIGGTTTDLALILSGSPLL 281
                                       79***********998887543 PP

>> Ppx-GppA  Ppx/GppA phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.063   1.2e+02     115     136 ..       5      26 ..       2      31 .. 0.88
   2 ?   -3.3   0.0       2.4   4.8e+03      44      63 ..     121     140 ..     112     160 .. 0.81
   3 !   11.8   0.0   6.1e-05      0.12     100     132 ..     245     277 ..     231     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.063
                                       EEEEEETTEEEEEEEETTEEEE CS
                          Ppx-GppA 115 lviDiGGGStElvlgeekevsk 136
                                       + iD+GG  t+ vl+++  v+k
  gi|330507677|ref|YP_004384105.1|   5 IGIDVGGTTTDAVLVDGSRVEK 26 
                                       679*************999887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.4
                                       HHHHHHHCCCTTGCCEEEEE CS
                          Ppx-GppA  44 LkefaellqkfkvenvrvVA 63 
                                       +k+ a ++++++v++v vV+
  gi|330507677|ref|YP_004384105.1| 121 IKDAAARIKESGVSRVAVVG 140
                                       77888899999999999987 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 6.1e-05
                                       HHHHHHHHT---SSEEEEEEETTEEEEEEEETT CS
                          Ppx-GppA 100 iylgvvssllekgrglviDiGGGStElvlgeek 132
                                       +++gv++ ++  +  +v+DiGG  t+l+l+ + 
  gi|330507677|ref|YP_004384105.1| 245 SIMGVMALTPPGQTSVVVDIGGTTTDLALILSG 277
                                       689*************************99665 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 ?   -0.3   0.1      0.21   4.1e+02     138     153 ..       7      22 ..       2      30 .. 0.79
   2 ?   12.2   0.2   3.4e-05     0.067     103     151 ..     227     275 ..     224     296 .. 0.85
   3 ?   -1.3   0.1      0.41   8.2e+02     274     315 ..     415     454 ..     353     464 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.21
                               DDR 138 lDlGaGstDaalieee 153
                                       +D+G+ +tDa l++ +
  gi|330507677|ref|YP_004384105.1|   7 IDVGGTTTDAVLVDGS 22 
                                       8********9999865 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.4e-05
                               DDR 103 leeelgvkvevggvEaemAilG..alttPGtekplailDlGaGstDaalie 151
                                       le +l+++ve+  + + + i+G  alt PG +  ++++D+G+ +tD ali 
  gi|330507677|ref|YP_004384105.1| 227 LEGSLQMPVETIFSGPAASIMGvmALTPPGQT--SVVVDIGGTTTDLALIL 275
                                       56789999999999999999997789999965..799*********99985 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.41
                               DDR 274 didfvvlvGgsalDfEipelvtdalaeygivaGrgnirgveG 315
                                       + ++vv vGg+a    +  l++++l+ ++iv  ++ + +  G
  gi|330507677|ref|YP_004384105.1| 415 EAQNVVGVGGAAP--ALVPLIASRLKVASIVPEHAAVANAIG 454
                                       4566777777775..466677777777777777776666666 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 ?    4.6  12.6    0.0099        20       1     264 [.       5     456 ..       5     458 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0099
                                       EEEEE-SSEEEEEEEETTTEEEEEEEE--................................................ CS
                       BcrAD_BadFG   1 vGiDgGsTttkavlmdekgevlgrgitns................................................ 29 
                                       +GiD+G+Ttt avl+d +     ++  ++                                                
  gi|330507677|ref|YP_004384105.1|   5 IGIDVGGTTTDAVLVDGSRV--EKTAYVPtdhndllgcllgaldelvrgvdvskiervvlsttlitnmiaekktdpv 79 
                                       7**************96633..3333333345666666666666555555555555555555555555555555555 PP

                                       ..................................TTS-HHH.........HHHHHHHHHHT--GGG........... CS
                       BcrAD_BadFG  30 ..................................anlesvrfeaaekvleealtealerageeead........... 61 
                                                                         +                                          
  gi|330507677|ref|YP_004384105.1|  80 alvlipgpgtnpqdynlgqsiildgaidfrgkeiD------------------------------Rlnesqikdaaa 126
                                       55555555555555555555555554444444441..............................044444444444 PP

                                       ............................................................................. CS
                       BcrAD_BadFG  62 ............................................................................. 61 
                                                                                                                    
  gi|330507677|ref|YP_004384105.1| 127 rikesgvsrvavvgkfsqrnpaheekvsqimsqilpgskielghrvsghlnfprraattkltlatkesyarfalais 203
                                       44444444444444444444555555555555555555555556777777777777777777777777777888888 PP

                                       ...........................................ECEE..EEESTTCCCTCTTBSEEE-........H CS
                       BcrAD_BadFG  62 ...........................................ieetylvgtgyGratlpekfekeiirs......e 89 
                                                                                  +  ++l+  g   + ++  ++  + +       +
  gi|330507677|ref|YP_004384105.1| 204 raleerritapvyilkadggtlplegslqmpvetifsgpaasiMGVMALTPPGQTSVVVD--IGGTTTDLalilsgS 278
                                       887777777777777777777777777777777777777777766666666666666665..333333333455565 PP

                                       HHHHHHHHHH..H-TT--..EE..EEEETTEEEEEEEE.TTEEEEEEEESS--TTSHHHHHHHHHHHT--TTTHHHH CS
                       BcrAD_BadFG  90 ilvhgdGava..lypgtr..tv..ldigGqdskgiqid.kgkvenfqmndrcaageGrylgiiadelnmglreldgl 159
                                        l+ ++Ga +  +  ++r  +v  + igG   + ++ d      +  +  +c++g+G     + ++l+ +     ++
  gi|330507677|ref|YP_004384105.1| 279 PLLSSKGARVdsMLTHVRafAVrsVAIGGDSAVDVAEDgLTVGPQRNGSPFCLGGTGPTPTDALRVLGRSSVGDLER 355
                                       55555555432244444455332245666555555555333333445555777777777777777777776666667 PP

                                       HTT--S-------SHH..HHHHHHHHH.HHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG-HHHH CS
                       BcrAD_BadFG 160 aekatkkarinstcav..faeaelrda.lsggekaedIlaglhraialrvialisrsggvtdevtltGGvakneaav 233
                                       a++a++  +++  c++   ae++l +  ++     ++ +++  ++ a r+++++++++ + ++v+ +GG a +    
  gi|330507677|ref|YP_004384105.1| 356 AKEAMAGVASRMNCTAekAAEMVLDSVvEKIASQVNEMFREWEQEPAYRIWEIMKKEKLEAQNVVGVGGAAPA---- 428
                                       7777755444444444114444444431333444566777777777777777777777777778888888777.... PP

                                       HHH.....HHHH-S-EE--GGGGGHHHHHHH CS
                       BcrAD_BadFG 234 kelrklvkenygevkininpdsiytgalGAa 264
                                         l +l+ ++       ++ ++ ++ a+GAa
  gi|330507677|ref|YP_004384105.1| 429 --LVPLIASRLKV-ASIVPEHAAVANAIGAA 456
                                       ..66667666554.34567777777777776 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.036        71     166     187 ..       5      27 ..       1      81 [. 0.69
   2 ?    7.7   0.1    0.0009       1.8     163     182 ..     257     276 ..     242     284 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.036
                              StbA 166 LiiDlGGttLDvakvrg.klegi 187
                                       + iD+GGtt D   v g ++e+ 
  gi|330507677|ref|YP_004384105.1|   5 IGIDVGGTTTDAVLVDGsRVEKT 27 
                                       449********999987234544 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0009
                              StbA 163 eslLiiDlGGttLDvakvrg 182
                                       + ++++D+GGtt D+a + +
  gi|330507677|ref|YP_004384105.1| 257 QTSVVVDIGGTTTDLALILS 276
                                       5789************9976 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2      0.91   1.8e+03     150     163 ..       7      19 ..       3      29 .. 0.68
   2 ?   10.5   0.3   9.3e-05      0.19     145     166 ..     257     278 ..     235     305 .. 0.75
   3 ?    0.6   0.1     0.096   1.9e+02     225     317 ..     357     457 ..     354     465 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.91
                                       EEE-SS-EEEEEEE CS
                          MreB_Mbl 150 vdiGggttevavis 163
                                       +d+Gg tt+  v+ 
  gi|330507677|ref|YP_004384105.1|   7 IDVGGTTTDA-VLV 19 
                                       7899988884.444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.3e-05
                                       S-EEEEEE-SS-EEEEEEETTE CS
                          MreB_Mbl 145 sgnmvvdiGggttevavislgg 166
                                       + ++vvdiGg tt++a+i  g+
  gi|330507677|ref|YP_004384105.1| 257 QTSVVVDIGGTTTDLALILSGS 278
                                       6799************886665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.096
                                       EETTTTCEEEEEEEHHHHHH.HHHHHHHHHHHHHHHHHHTS-HH...HHHHHHHH....-EEEESGGGGSBTHHHHH CS
                          MreB_Mbl 225 rdlvtglpkevevsseevre.alkepvsaiveavkevLektppe...Laadivdr....givltGGgallkgldkll 293
                                       ++ + g++ +++ ++e+ +e +l ++v++i ++v+e+ ++   e    + +i+++    +  ++G g+    l  l+
  gi|330507677|ref|YP_004384105.1| 357 KEAMAGVASRMNCTAEKAAEmVLDSVVEKIASQVNEMFREWEQEpayRIWEIMKKekleAQNVVGVGGAAPALVPLI 433
                                       56778888888888877766256677889999999887655544000445666552222234556666667788888 PP

                                       HHHHSS-EEE-SSTTTHHHHHHHH CS
                          MreB_Mbl 294 seetglpvkvaedpltcvakGtgk 317
                                        +++++  +v e++  + a G++ 
  gi|330507677|ref|YP_004384105.1| 434 ASRLKVASIVPEHAAVANAIGAAV 457
                                       888888888888887777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 3692.07
//
Query:       gi|330507678|ref|YP_004384106.1|  [L=256]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete 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   61.5  20.6    7.8e-17   61.2  20.6    1.1  1  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.039   12.3   3.0      0.052   11.9   3.0    1.2  1  MFS_3     Transmembrane secretion effector
      0.065   12.9   0.7      0.094   12.4   0.7    1.1  1  RTX       N-terminal domain in RTX protein
       0.23   11.8   5.2        1.3    9.4   2.3    2.6  2  DUF2484   Protein of unknown function (DUF2484)


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 !   61.2  20.6   1.7e-20   7.8e-17       5     182 ..      13     190 ..       9     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1.7e-20
                             MFS_1   5 aflsalarsilgpalplalaed..lgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg.ll 77 
                                        +++ ++++++ p++ ++++     g s  ++gl+ +l+ ++ ++ +lp+G+ +dr + +  +l++g +l+a   l+
  gi|330507678|ref|YP_004384106.1|  13 DIFVLTGFGLIQPIIAIYINGGgvAGGSMLSAGLASALFLFTKSLVQLPFGHYVDRQSDKTkWLFVGTILMAGVpLI 89 
                                       5677888888899998877443225577788*************************888888999999999999444 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       + + ass++ ++++ v+ Glg+g+++p+ + l ++   k + ++  +++s++++lG++ + +lg+++as +g++a+f
  gi|330507678|ref|YP_004384106.1|  90 YVS-ASSIYHIYIAEVIYGLGSGLAYPTWLGLWSANLDKGQESFQWSVYSTATGLGTAATGALGAAVASFVGFSATF 165
                                       444.48888******************************************************************** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrk 182
                                       +++++++ll+++   +l++ ++++ +r 
  gi|330507678|ref|YP_004384106.1| 166 ILAGVLCLLGCI---ALFYLDYKNGWRR 190
                                       **********99...7777777777765 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.0   1.2e-05     0.052      63     184 ..      60     178 ..      29     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                             MFS_3  63 ilaGalaD.nfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvp 138
                                       ++ G   D + d+ k l+++ +l+a v ++      +   s + + +  ++ g+G+ l  P+W    +  +++ + +
  gi|330507678|ref|YP_004384106.1|  60 LPFGHYVDrQSDKTKWLFVGTILMAGVPLIY-----VSASSIYHIYIAEVIYGLGSGLAYPTWLGLWSANLDKGQES 131
                                       5556656623578899999998888776543.....444567788899999********************999988 PP

                             MFS_3 139 aAvaLnsvginiaRsvGPAlgGvlvaavGaalafavn.alsylaliv 184
                                           + s    +  ++  Alg  + ++vG  ++f ++ +l+ l  i+
  gi|330507678|ref|YP_004384106.1| 132 FQWSVYSTATGLGTAATGALGAAVASFVGFSATFILAgVLCLLGCIA 178
                                       888889999999999999****************9872556665554 PP

>> RTX  N-terminal domain in RTX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.7   2.1e-05     0.094      64     117 ..     123     176 ..     120     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.1e-05
                               RTX  64 aelyrekktieaaltaistvldvvsavvsaaaaasgVGaPvallvalitglisg 117
                                       a+l ++++  + +++++ t l++ ++++ +aa+as VG   + ++a++  l+  
  gi|330507678|ref|YP_004384106.1| 123 ANLDKGQESFQWSVYSTATGLGTAATGALGAAVASFVGFSATFILAGVLCLLGC 176
                                       6788999999****************************9999999999887765 PP

>> DUF2484  Protein of unknown function (DUF2484)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.043   1.9e+02      25      42 ..      73      90 ..      68     105 .. 0.86
   2 ?    9.4   2.3    0.0003       1.3       6      58 ..     144     196 ..     139     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.043
                           DUF2484 25 whwsaaivLialgipllg 42
                                       +w ++ +++++g+pl++
  gi|330507678|ref|YP_004384106.1| 73 TKWLFVGTILMAGVPLIY 90
                                      578889999******985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0003
                           DUF2484   6 llavlWvlvAavvallplRwhwsaaivLialgipllgyvtyehGPwwgllvll 58 
                                        +a++ +l Aav+ ++     +  a vL +lg   l y+ y++G+   +++l+
  gi|330507678|ref|YP_004384106.1| 144 GTAATGALGAAVASFVGFSATFILAGVLCLLGCIALFYLDYKNGWRRIMAMLV 196
                                       56777778888888888888888999*******************99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1889.13
//
Query:       gi|330507679|ref|YP_004384107.1|  [L=470]
Description: Na+/solute symporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-46  158.4  32.7    3.4e-46  157.9  32.7    1.2  1  SSF          Sodium:solute symporter family
  ------ inclusion threshold ------
      0.067   12.0   0.5       0.11   11.3   0.5    1.2  1  Calici_PP_N  Viral polyprotein N-terminal


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 !  157.9  32.7   3.8e-50   3.4e-46       1     404 [.      29     422 ..      29     424 .. 0.90

  Alignments for each domain:
  == domain 1  score: 157.9 bits;  conditional E-value: 3.8e-50
                               SSF   1 yflagrslt.gfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr....nagalTlp 72 
                                       + l++r+++ + v+g++ +a + saasf+G+ G + a G+ +v++   + +++  + +++a+r      ++ a T+p
  gi|330507679|ref|YP_004384107.1|  29 FVLSNRNIAyPAVIGIAYTAAYFSAASFLGGGGYGLAAGMPWVIFCSLFHVGFACIAWIMAGRIWtmakQYDAKTVP 105
                                       56788888735899*********************************************999988889999****** PP

                               SSF  73 dylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdti 149
                                       ++l+ R+++    v+l+++ +l++ t++l   + g a l++ ++G++y  ++l+ +a++a+Y +iGGl A++++  i
  gi|330507679|ref|YP_004384107.1| 106 QLLERRYNSPLGKVILAII-MLILYTVYLVPIFKGCATLFQGMIGVSYLEGLLITVAIVAIYYAIGGLPAIIWVGFI 181
                                       ********99866666655.5566688999999******************************************** PP

                               SSF 150 qavlmlvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvRfl 226
                                       q+vlml+ga++l ++ +++ Ggl+          p   d+l  ++l++  + ++++ +   + lG+  lp  l+ ++
  gi|330507679|ref|YP_004384107.1| 182 QGVLMLIGAVFLYGGLISAGGGLDIWE-----RIP--LDVLSMNGLNIPWQQTFGQAF--SISLGLLALPDLLIMIF 249
                                       **************9999988987543.....345..466666676677777788887..7899************* PP

                               SSF 227 aakdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlA 303
                                       +a d++ ++ + +++ i +++  + ++s+++ a     a  + + + +++++  +p  +  +lp+++ G++l ++++
  gi|330507679|ref|YP_004384107.1| 250 SARDKRVVRFAGIYGPISIAIYSVCIFSLGILAYGALSA--EQIAPFLKNPDGLVPFVATLILPKGFDGIILLAAIS 324
                                       *******************99999999999999887777..99********************************** PP

                               SSF 304 aimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasa 380
                                       a mst+++++l++++++t D+   + +     +++++ + r+i + +  +a + a++ +q+ ++ lv++ ++++a +
  gi|330507679|ref|YP_004384107.1| 325 AAMSTMSAIVLVTATSLTSDILRYLNPGI--ADRKVLLLTRMIGVAILIIAAVSAINVPQQ-IVPLVAVSMGIIACC 398
                                       *********************99999988..66777777888888888899999*******.*************** PP

                               SSF 381 vlavillalfwkrvneqGAlagli 404
                                       vl  + l++fw+r ne G +a+l+
  gi|330507679|ref|YP_004384107.1| 399 VLVPLFLGIFWQRGNETGFIASLL 422
                                       ******************988876 PP

>> Calici_PP_N  Viral polyprotein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   1.2e-05      0.11     177     213 ..     389     425 ..     370     430 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.2e-05
                       Calici_PP_N 177 wtfmgvvemvvlllelfgifwnppdvsnfiasllpdf 213
                                          mg++   vl+  ++gifw+  + + fiasll  f
  gi|330507679|ref|YP_004384107.1| 389 AVSMGIIACCVLVPLFLGIFWQRGNETGFIASLLASF 425
                                       5679********99999*****************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 3284.66
//
Query:       gi|330507680|ref|YP_004384108.1|  [L=88]
Description: hypothetical protein MCON_1667 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-38  129.4   0.4    5.7e-38  129.1   0.4    1.1  1  MC1       Non-histone chromosomal protein MC1


Domain annotation for each model (and alignments):
>> MC1  Non-histone chromosomal protein MC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.1   0.4   3.2e-42   5.7e-38       1      96 []       3      88 .]       3      88 .] 0.98

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 3.2e-42
                               MC1  1 dkrnfalrdedGeeisvfsGkqPrqaaLkaarrletadseeeakeeeirLrekGtkkvhiyegkaeeeeaPddkpdWle 79
                                      ++rnfalrd++G+ei+vf+Gk+PrqaaLkaa+r+ t+          i+Lre+Gtkkvhi++g++ ++++P+ +p+W++
  gi|330507680|ref|YP_004384108.1|  3 EMRNFALRDAQGNEIGVFTGKSPRQAALKAANRGYTE----------IKLRERGTKKVHIFSGERVQVDKPAGAPAWMP 71
                                      68*********************************99..........******************************** PP

                               MC1 80 dkitkanvskqgiekle 96
                                      dki+k++v+k+giekl+
  gi|330507680|ref|YP_004384108.1| 72 DKIWKPKVKKEGIEKLD 88
                                      ***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 610.38
//
Query:       gi|330507681|ref|YP_004384109.1|  [L=434]
Description: aspartyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete 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-87  292.8   0.0    3.2e-87  292.6   0.0    1.0  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    5.4e-12   45.5   0.0      1e-11   44.7   0.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    0.00065   19.2   0.1       0.12   11.8   0.1    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 !  292.6   0.0   5.3e-91   3.2e-87       3     313 ..     119     428 ..     117     429 .. 0.95

  Alignments for each domain:
  == domain 1  score: 292.6 bits;  conditional E-value: 5.3e-91
                                       CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqsp 79 
                                       ++rl+ r++d+r++ v + +++ s v+ ++r+y++++g +e+ tP ++ ++te+g  lF +   e  ke f L+qsp
  gi|330507681|ref|YP_004384109.1| 119 DTRLDSRFMDIRRPCVLAAFEIESAVLCSLRDYFHKKGIVEVFTPKIVAAATEGGTDLFPISYFE--KEAF-LNQSP 192
                                       799**********************************************************4333..4666.***** PP

                                       HHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  80 qlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefv 156
                                       qly+++l+ ag+drv++i++ FRaE+++t+rhl+E ++i++e+sf++++d+m++lee +    + v +++++++e  
  gi|330507681|ref|YP_004384109.1| 193 QLYKQMLMGAGMDRVYEIGPIFRAEEHDTRRHLNEAISIDLEVSFADDKDVMEILEEAVAGAYSYVADNCRRQLEVL 269
                                       ******************************************************************99997777666 PP

                                       TTTTSEE-SSS-EEEEHHHHHHHHHTS.......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 157 irrnskdlkkpfkrltykeaieklnei.......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddkk 226
                                       + +  + ++ pfkr+ty+ a+e ++e+       g+dld++ er+l + ++ e +f++d+P+++kp+y+   ed+++
  gi|330507681|ref|YP_004384109.1| 270 NME-LEVPRLPFKRITYTRALELAEEKagarmqwGDDLDTETERFLGE-SIGEHYFLIDWPSSIKPYYTLPYEDKPE 344
                                       655.4566777************9998*********************.999************************* PP

                                       BBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 227 ltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgses 303
                                       + +++Dl+ + +El++G++R++d+ +l e++k+kgld   ++ f++yl+a++yG+pph+G+glGl+Rlvm++l++e+
  gi|330507681|ref|YP_004384109.1| 345 ICRGFDLMHPRMELASGAQRVHDYSLLVERIKEKGLD---PDGFEFYLRAFRYGMPPHAGWGLGLSRLVMTMLNLEN 418
                                       *************************************...************************************* PP

                                       GGGCSSS-XX CS
                                       xxxxxxxxxx RF
                       tRNA-synt_2 304 IrdviaFPkl 313
                                       Ird+++FP+ 
  gi|330507681|ref|YP_004384109.1| 419 IRDAVIFPRD 428
                                       ********96 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   1.7e-15     1e-11       2      76 .]      21      99 ..      20      99 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.7e-15
                                      EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEEE CS
                   tRNA_anti-codon  2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrr...pggelelkveei 73
                                       +aG  + i  r+ g+++f++lrD++g+ q++l +    ++++k+a ++ +++vv v+G vk+    p+g +e+  +ei
  gi|330507681|ref|YP_004384109.1| 21 MLAGFAHEI--RDLGGIAFLVLRDREGMAQITLVKkllgKDVFKMARSISRESVVMVRGNVKAEakaPRG-YEILPTEI 96
                                      57899999*..*******************************************************9*9*.******** PP

                                      EEE CS
                   tRNA_anti-codon 74 ell 76
                                      ++l
  gi|330507681|ref|YP_004384109.1| 97 QVL 99
                                      986 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0029        17     103     155 ..     206     254 ..     188     260 .. 0.80
   2 !   11.8   0.1     2e-05      0.12     212     234 ..     400     422 ..     393     430 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0029
                                       EEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTS CS
                      tRNA-synt_2d 103 kiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfga 155
                                       ++  ig +fR ++ D ++    h  e + +d +vs+ad k v+e l +++ ga
  gi|330507681|ref|YP_004384109.1| 206 RVYEIGPIFRAEEHDTRR----HLNEAISIDLEVSFADDKDVMEILEEAVAGA 254
                                       7778999******66554....5679***************999988877765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2e-05
                                       EEEEEEHHHHHHHHHT-SSGHHH CS
                      tRNA-synt_2d 212 fafGlGveRlamlkygieDiRel 234
                                       +++GlG+ Rl m ++++e+iR+ 
  gi|330507681|ref|YP_004384109.1| 400 AGWGLGLSRLVMTMLNLENIRDA 422
                                       68*******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3256.39
//
Query:       gi|330507682|ref|YP_004384110.1|  [L=68]
Description: hypothetical protein MCON_1669 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   12.6   1.7       0.15   12.5   1.7    1.1  1  DUF805    Protein of unknown function (DUF805)


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 ?   12.5   1.7   8.4e-06      0.15       4      60 ..       4      62 ..       1      68 [] 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-06
                            DUF805  4 fkGRasRsefw..wfvlfllllvivlallaavlaaaavasalsvvlallllvpslavtv 60
                                      +++ +s+++fw  +f+l  +ll+  +  la ++    + ++l ++ a++++++ l+ ++
  gi|330507682|ref|YP_004384110.1|  4 LHDLLSQKDFWilLFFLGWVLLNWPMLSLADAIILLGMPAILVYISAVWMILILLMYLF 62
                                      55667899***998999999999998888887766666777777777777776666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 485.75
//
Query:       gi|330507683|ref|YP_004384111.1|  [L=1061]
Description: Na+/solute symporter [Methanosaeta concilii GP6]
Scores for complete 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  180.9   0.2    2.1e-37  127.9   0.0    2.7  3  DUF835    Protein of unknown function (DUF835)


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0      0.46   8.2e+03      53      70 ..     582     599 ..     576     602 .. 0.77
   2 !   50.1   0.1   1.2e-17   2.2e-13       8      95 ..     648     736 ..     645     749 .. 0.94
   3 !  127.9   0.0   1.2e-41   2.1e-37       3     136 .]     921    1056 ..     919    1056 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.46
                            DUF835  53 entvsPtnlekltetivk 70 
                                        +tvsP++l++l ++ +k
  gi|330507683|ref|YP_004384111.1| 582 RETVSPRQLQELWNQFEK 599
                                       57999*999999777666 PP

  == domain 2  score: 50.1 bits;  conditional E-value: 1.2e-17
                            DUF835   8 akeilsdlvkegvkvlaitRenpkkirekvkienvkviwltkvee.entvsPtnlekltetivkflkeaekgvvliD 83 
                                       a+e+++d++++gv++l+it ++p+++r + + +++++i l+++++  + +sP+nl+ l  ti++f+++  +++vliD
  gi|330507683|ref|YP_004384111.1| 648 AYEVFTDQITHGVEGLCITHSSPEEVRLRWGFKETPIIKLSDEKRsDRYISPRNLPLLFITIKSFVDSSRNSIVLID 724
                                       6799****************************************64889**************************** PP

                            DUF835  84 gleyLvlengFe 95 
                                       ++e Lv en F+
  gi|330507683|ref|YP_004384111.1| 725 SIEKLVNENMFK 736
                                       *********997 PP

  == domain 3  score: 127.9 bits;  conditional E-value: 1.2e-41
                            DUF835    3 kkkekakeilsdlvkegvkvlaitRenpkkirekvkienvkviwltkvee..entvsPtnlekltetivkflkea 75  
                                        +k +k+ e++s+lv +g+++l+++R+np++++e+++i+  +viwlt+++e  ++tv+Ptn+++l ++i++fl++a
  gi|330507683|ref|YP_004384111.1|  921 EKPKKSLEVFSELVAHGMEGLCLSRHNPETLQERFSIPPETVIWLTQKSEpgYRTVDPTNFPRLSGMISEFLDQA 995 
                                        6788999*****************************************985688********************* PP

                            DUF835   76 ekgvvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalLkref 136 
                                        +  ++l++g+ yL++++++e+vl+f++  +D +++kn++++++id+  l++kel+ L +e+
  gi|330507683|ref|YP_004384111.1|  996 NYPIILLEGMGYLITQSNYETVLRFVQFQRDEIAMKNAIMLIHIDPLSLDTKELHRLASEM 1056
                                        **********************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1061 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); 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):               1  [number of targets reported over threshold]
# CPU time: 0.77u 0.27s 00:00:01.04 Elapsed: 00:00:00.43
# Mc/sec: 7329.98
//
Query:       gi|330507684|ref|YP_004384112.1|  [L=80]
Description: hypothetical protein MCON_1671 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-09   35.9  20.3    7.5e-09   35.7  20.3    1.1  1  BofA      SigmaK-factor processing regulatory protein BofA
  ------ inclusion threshold ------
        1.6    7.7   7.3        1.7    7.6   7.3    1.1  1  DuoxA     Dual oxidase maturation factor


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 !   35.7  20.3   8.3e-13   7.5e-09       3      74 ..       7      75 ..       4      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 8.3e-13
                              BofA  3 illlllvikllkkplkillkllinavlGlvlLflvNllgavfglhipiNlitaliagflGipGvilLillkl 74
                                      +ll++++i   +  l+ l +++ina+ Gl +Lfl+N   +++   i+++++ +li+g++G  G+ilL+ l++
  gi|330507684|ref|YP_004384112.1|  7 VLLAVVLIFGAFLLLRSLKNFVINAIAGLFILFLAN---QFISADIGYSWLVILICGIGGAVGAILLLALHF 75
                                      44555555555688899*******************...*******************************97 PP

>> DuoxA  Dual oxidase maturation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   7.3   0.00019       1.7     201     265 ..      11      76 ..       1      78 [. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00019
                             DuoxA 201 mllltgallllalliyslvlpkcelvipl.eaavletefgwsfwlvlatGllclllgliilvldlv 265
                                       ++l+ ga+lll  l  +++     l i +  ++ +++++g s+ ++l++G+   + ++++l+l+++
  gi|330507684|ref|YP_004384112.1|  11 VVLIFGAFLLLRSLKNFVINAIAGLFILFlANQFISADIGYSWLVILICGIGGAVGAILLLALHFI 76 
                                       3455666666655554455555555555536667*********************99999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 601.54
//
Query:       gi|330507685|ref|YP_004384113.1|  [L=409]
Description: orc1/cdc6 family replication initiation protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-21   73.9   0.4    2.5e-20   72.2   0.4    1.9  1  Cdc6_C           CDC6, C terminal winged helix domain
    2.1e-13   51.0   0.7    1.9e-11   44.6   0.0    3.0  2  AAA_16           AAA ATPase domain
      4e-13   49.8   0.0    9.3e-13   48.6   0.0    1.5  1  AAA_22           AAA domain
    3.4e-10   40.4   0.0    1.1e-09   38.8   0.0    1.8  1  AAA              ATPase family associated with various cellul
    1.7e-06   27.6   0.1      4e-06   26.4   0.0    1.6  2  TniB             Bacterial TniB protein
    5.4e-06   26.5   2.2    3.6e-05   23.8   1.0    2.4  2  ATPase_2         ATPase domain predominantly from Archaea
    9.2e-06   25.7   0.0      2e-05   24.5   0.0    1.6  1  NACHT            NACHT domain
    4.8e-05   23.2   0.2      0.021   14.6   0.0    2.8  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00016   21.0   0.5      0.013   14.8   0.0    2.2  2  KAP_NTPase       KAP family P-loop domain
    0.00034   20.4   0.1    0.00089   19.0   0.0    1.7  2  Sigma54_activat  Sigma-54 interaction domain
    0.00069   18.9   0.0     0.0013   18.0   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
     0.0019   17.5   0.0     0.0031   16.7   0.0    1.4  1  NB-ARC           NB-ARC domain
     0.0036   17.8   0.0       0.01   16.3   0.0    1.9  1  AAA_18           AAA domain
     0.0036   16.8   0.0     0.0065   16.0   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
     0.0044   16.3   0.0     0.0062   15.8   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0069   16.2   0.7      0.027   14.2   0.1    2.2  2  DEAD             DEAD/DEAH box helicase
     0.0072   15.6   0.0      0.036   13.4   0.0    2.0  2  Zeta_toxin       Zeta toxin
  ------ inclusion threshold ------
       0.01   15.1   0.0      0.019   14.2   0.0    1.4  1  TIP49            TIP49 P-loop domain
      0.017   15.5   0.0      0.052   13.9   0.0    1.8  1  RNA_helicase     RNA helicase
      0.019   15.1   1.0       0.11   12.6   0.2    2.5  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.023   14.7   0.0      0.048   13.7   0.0    1.6  1  ResIII           Type III restriction enzyme, res subunit
      0.028   14.2   0.4      0.028   14.2   0.4    1.9  2  AAA_24           AAA domain
      0.034   14.0   0.0       0.11   12.4   0.0    1.8  1  DUF2498          Protein of unknown function (DUF2498)
      0.039   14.0   0.0      0.086   12.8   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.048   13.7   0.2       0.49   10.5   0.2    2.4  2  Trans_reg_C      Transcriptional regulatory protein, C termin
      0.054   13.5   0.2       0.38   10.8   0.2    2.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.057   13.8   0.1       0.18   12.1   0.1    1.9  1  AAA_assoc_2      AAA C-terminal domain
      0.078   12.8   0.0       0.46   10.3   0.0    2.0  2  Bac_DnaA         Bacterial dnaA  protein
       0.19   11.8   2.5        3.8    7.6   0.3    2.9  3  DUF87            Helicase HerA, central 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 !   72.2   0.4     4e-23   2.5e-20       1      76 [.     305     378 ..     305     385 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 4e-23
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnv 76 
                                       L++++ll++ +g++ +tt+ vy++Yk+lC   + d lt+r++ dl++eL+mlgil + + skGr +grt++i+L+v
  gi|330507685|ref|YP_004384113.1| 305 LYSIILLEE-QGTRNITTSAVYNMYKQLCPLVETDFLTHRRITDLIAELDMLGILHTIVISKGR-YGRTKEITLSV 378
                                       89*******.*****************************************************9.*********98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   3.1e-14   1.9e-11       1     164 [.      33     171 ..      33     180 .. 0.76
   2 ?    0.3   0.1       1.3   8.3e+02      44     116 ..     215     286 ..     195     307 .. 0.49

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 3.1e-14
                            AAA_16   1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd.....ggiflrgkcdqlesaipysa 71 
                                       +l+ Ree+++ L+s+l ++ +g++ ++vl++G  G+GK+++++ + ++le++     ++++++ +c+    ++ y  
  gi|330507685|ref|YP_004384113.1|  33 KLPHREEQINNLASILVPALRGETpSNVLIYGKTGTGKTAVAKYVGKELEEAsfedmKCVVIYINCEVV--DTQY-- 105
                                       5899*******************99*************************99999988999*******9..5445.. PP

                            AAA_16  72 laqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwad 148
                                         ++l + +l r  +++        w++                  +++++++++l+  +  +  +v+ lD+++++ 
  gi|330507685|ref|YP_004384113.1| 106 --RIL-A-HLARHFDRD---IPMTGWPT-----------------DQVYAEFRNALDEEK--QV-VVIMLDEVDKLV 155
                                       ..444.3.555555555...33445666.................566777777772222..23.888888888888 PP

                            AAA_16 149 easlqllaaLlrlles 164
                                           ++l++L r  ++
  gi|330507685|ref|YP_004384113.1| 156 RKGDDVLYNLSRVNSD 171
                                       8888888888776554 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.3
                            AAA_16  44 llralekd.ggiflrgkcdqlesaipysa.laqalareellrqlldeaesaele.awrekleealaavpelagaea 116
                                       +++ le++ ++ f +g  +++   ip+ a +a +    +  r+l+    s el+ ++r +  +++  v++++++++
  gi|330507685|ref|YP_004384113.1| 215 IREILEQRaNVAFCSGSLQES--VIPLCAaFAAQEHG-DARRALDLLRISGELAeRARSTVVTEV-HVRQARDKIE 286
                                       444444442255555555555..66663325544434.333333333233222202222222222.3444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   1.5e-15   9.3e-13       4     117 ..      56     169 ..      53     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.5e-15
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelle 80 
                                       t + ++++G +GtGKT +++ + ++l+ ea+ e+++  v+++++ +  ++  +l +l+r ++++    +  ++++++
  gi|330507685|ref|YP_004384113.1|  56 TPSNVLIYGKTGTGKTAVAKYVGKELE-EASFEDMKCVVIYINCEVVDTQYRILAHLARHFDRDIPMTGWPTDQVYA 131
                                       567789*******************95.56677789999**************************99889999999* PP

                            AAA_22  81 aleqalraravielliiDEaqhlr..seealeeLrslln 117
                                        +++al++ + ++++++DE+++l    +++l +L s++n
  gi|330507685|ref|YP_004384113.1| 132 EFRNALDEEKQVVVIMLDEVDKLVrkGDDVLYNL-SRVN 169
                                       **********99**********876559999999.4444 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 !   38.8   0.0   1.7e-12   1.1e-09       1     112 [.      60     186 ..      60     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.7e-12
                                       EEEESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCS.SS......................STTHHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelg.vefleisgsell.sk......................yvgesekkirelfkea 53 
                                       vl+yG  GtGKT++ak v kel+ ++f  +++  +  +                       + g   +++ + f++a
  gi|330507685|ref|YP_004384113.1|  60 VLIYGKTGTGKTAVAKYVGKELEeASFEDMKCVVIYiNCevvdtqyrilahlarhfdrdipMTGWPTDQVYAEFRNA 136
                                       79*******************85444444444444422244444699**************7787888888777777 PP

                                       HHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSG CS
                               AAA  54 keka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrp 112
                                         ++ + +++++DE+d+l+++         ++v+  L ++ +++ +  s+v +ig++n+ 
  gi|330507685|ref|YP_004384113.1| 137 LDEEkQVVVIMLDEVDKLVRKG--------DDVLYNLSRVNSDLLR--SRVSIIGISNDL 186
                                       4333246************999........7788888888888877..589999999984 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   6.5e-09     4e-06      18     132 ..      39     155 ..      32     184 .. 0.82
   2 ?   -2.9   0.0       6.1   3.8e+03     132     151 ..     280     299 ..     268     332 .. 0.54

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 6.5e-09
                              TniB  18 eilerLeeLle.ypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLea 93 
                                       e +++L+++l  + + + ++n+l++G++ +GKt+++ k+  ++ +e + ++ k+ v+++++    ++ r+ a++ ++
  gi|330507685|ref|YP_004384113.1|  39 EQINNLASILVpALRGETPSNVLIYGKTGTGKTAVA-KYVGKELEEASFEDMKCVVIYINCEVVDTQYRILAHLARH 114
                                       455566555440455666799************876.67888888888899999*********************** PP

                              TniB  94 lgaplkar.arvskleqqvlrllr.elkvrvLiiDEihnll 132
                                       +  ++  + + +++ +++  + l+ e +v v+++DE+++l+
  gi|330507685|ref|YP_004384113.1| 115 FDRDIPMTgWPTDQVYAEFRNALDeEKQVVVIMLDEVDKLV 155
                                       **99987735888999999999962578999*******987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.1
                              TniB 132 lagsarkqreflnalksLgn 151
                                        a    +q ++ +++k+L  
  gi|330507685|ref|YP_004384113.1| 280 QARDKIEQDRVEEVIKTLPT 299
                                       33334444444444444433 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   1.0   5.8e-08   3.6e-05       4     152 ..      37     172 ..      35     190 .. 0.80
   2 ?   -2.9   0.0       8.5   5.3e+03      83      99 ..     282     301 ..     243     317 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.8e-08
                          ATPase_2   4 Rekelkeleeil....erepneiyfiYGpegsGKtaLlkeiienledkdk....yviyyialreesiskldefieee 72 
                                       Re+ +++l +il    + e+ + ++iYG  g GKta+ k + ++le+ ++     v+ yi+ + +++++        
  gi|330507685|ref|YP_004384113.1|  37 REEQINNLASILvpalRGETPSNVLIYGKTGTGKTAVAKYVGKELEEASFedmkCVVIYINCEVVDTQYRILA---- 109
                                       9999999998853333899999***********************9988866766778888888877776665.... PP

                          ATPase_2  73 eekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnli 149
                                            l++++  ++p +             ++  +++ +++ ++++ ++i++De+ kl+    ++  +++++L ++ 
  gi|330507685|ref|YP_004384113.1| 110 ----HLARHFDRDIPMTGW---------PTDQVYAEFRNALDEEKQVVVIMLDEVDKLV----RKGDDVLYNLSRVN 169
                                       ....577777777777666.........55788899999999998889**********9....67778888887776 PP

                          ATPase_2 150 esl 152
                                        +l
  gi|330507685|ref|YP_004384113.1| 170 SDL 172
                                       655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.5
                          ATPase_2  83 giavpkaeleeilk...eks 99 
                                        ++++++++ee++k   ++s
  gi|330507685|ref|YP_004384113.1| 282 RDKIEQDRVEEVIKtlpTQS 301
                                       34444444444444333333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   3.3e-08     2e-05       3      99 ..      60     160 ..      58     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.3e-08
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-C....CHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvse....vwa 74 
                                       v++ G+ G GKT+ ++ +  ++ e   +    ++v+++++  + ++ ++  +la++  ++ p  + p ++    +++
  gi|330507685|ref|YP_004384113.1|  60 VLIYGKTGTGKTAVAKYVGKELEEASFEDM-KCVVIYINCEVVDTQYRIlAHLARHFDRDIPMTGWPTDQvyaeFRN 135
                                       89***********************97776.5**************9999899999999999988888888887888 PP

                                       HHCCSCCCEEEEEE-STT-SS-TCH CS
                             NACHT  75 vllelperlLlilDglDelvtdlgq 99 
                                        l e ++ +++ lD +D+lv++ + 
  gi|330507685|ref|YP_004384113.1| 136 ALDEEKQVVVIMLDEVDKLVRKGDD 160
                                       8899999999**********97665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.4e-05     0.021      23      59 ..      49      83 ..      25     107 .. 0.81
   2 ?    5.7   0.0     0.018        11      53     106 ..     111     164 ..     103     172 .. 0.87
   3 ?   -2.9   0.0       7.9   4.9e+03     114     132 ..     360     378 ..     346     380 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.4e-05
                            RuvB_N 23 ieaakkreealdhvllyGpPGlGkttlakiiakelgv 59
                                      +     r+e+   vl+yG  G Gkt++ak + kel+ 
  gi|330507685|ref|YP_004384113.1| 49 VP--ALRGETPSNVLIYGKTGTGKTAVAKYVGKELEE 83
                                      33..46999*************************975 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.018
                            RuvB_N  53 iakelgvklkitsgPvlekagdlaalltnleekdvlfideihrlsraveevlys 106
                                       +a+ ++ ++ +t  P+ +  +++   l + ++  v+++de+ +l r+ ++vly+
  gi|330507685|ref|YP_004384113.1| 111 LARHFDRDIPMTGWPTDQVYAEFRNALDEEKQVVVIMLDEVDKLVRKGDDVLYN 164
                                       5777888888888888888899999999999999*******************6 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 7.9
                            RuvB_N 114 divigkGpsarsikldlpk 132
                                        ivi kG+  r+ +++l+ 
  gi|330507685|ref|YP_004384113.1| 360 TIVISKGRYGRTKEITLSV 378
                                       5899999999999998875 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 !   14.8   0.0   2.1e-05     0.013       2      48 ..      38      85 ..      37     114 .. 0.82
   2 ?    4.4   0.3     0.031        19     159     185 ..     128     154 ..     115     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                        KAP_NTPase  2 dlyasaladilseptl..atpivvgLygkWGsGKssllnkledelkefa 48
                                      +  +++la il+ p+l  +tp+ v +ygk G+GK+++ + + +el+e +
  gi|330507685|ref|YP_004384113.1| 38 EEQINNLASILV-PALrgETPSNVLIYGKTGTGKTAVAKYVGKELEEAS 85
                                      6789********.889999*************************99985 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.031
                        KAP_NTPase 159 elladmektLdalqkrlVvviDdLDrc 185
                                       +++a++ ++Ld++++ +V+ +D+ D +
  gi|330507685|ref|YP_004384113.1| 128 QVYAEFRNALDEEKQVVVIMLDEVDKL 154
                                       578999*******************87 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.4e-06   0.00089      20      59 ..      55      99 ..      36     111 .. 0.69
   2 ?   -3.1   0.0       8.7   5.4e+03      96     110 ..     145     159 ..     139     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-06
                                      TSSS-EEEECSTTSSHHHHHHHHHH.....HSTTTTS-EEEEETT CS
                   Sigma54_activat 20 ktdlsvlitGesGtGKellaraihe.....askrkekpfvavnca 59
                                      +t+++vli G++GtGK+ +a+ + +     + +  +  ++ +nc 
  gi|330507685|ref|YP_004384113.1| 55 ETPSNVLIYGKTGTGKTAVAKYVGKeleeaSFEDMKCVVIYINCE 99
                                      5679*****************997733321112223345556665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.7
                                       EEEEETGGGS-HHHH CS
                   Sigma54_activat  96 tlfLDeigelplelQ 110
                                       +++LDe+ +l  ++ 
  gi|330507685|ref|YP_004384113.1| 145 VIMLDEVDKLVRKGD 159
                                       6899**999977665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     2e-06    0.0013      29     102 ..      33     111 ..      25     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                            DUF815  29 dLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg.....Lrlievekedlkelpklve 100
                                       +L   ++q ++l +     l+g++ +nvL++G+ GtGK ++ k + +e++e++       +i ++ e +++  ++++
  gi|330507685|ref|YP_004384113.1|  33 KLPHREEQINNLASILVPALRGETPSNVLIYGKTGTGKTAVAKYVGKELEEASfedmkCVVIYINCEVVDTQYRILA 109
                                       56667888888888888999*************************99999887666444455566666655555555 PP

                            DUF815 101 ll 102
                                       +l
  gi|330507685|ref|YP_004384113.1| 110 HL 111
                                       55 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     5e-06    0.0031      22     112 ..      59     151 ..      37     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5e-06
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS...HHHH CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddleekeeves...lkrk 95 
                                        v ++G+ G GKt +ak + ++    e  F+ +  vv+  + +  + + +il++L ++  d+++  ++ +      +
  gi|330507685|ref|YP_004384113.1|  59 NVLIYGKTGTGKTAVAKYVGKE--LEEASFEDMKCVVIYINCEVVDTQYRILAHLARH-FDRDIPMTGWPtdqVYAE 132
                                       688****************999..44559*9999999999999999999999999777.666666666555668999 PP

                                       HHHHCCCT..TEEEEEEEE CS
                            NB-ARC  96 lvrlLltk..rfllvlDDV 112
                                        +++L +    ++++lD V
  gi|330507685|ref|YP_004384113.1| 133 FRNALDEEkqVVVIMLDEV 151
                                       9****88732344566766 PP

>> AAA_18  AAA 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      0.01       1      68 [.      60     137 ..      60     179 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.gvnlrdvakenglllevdpe........aldeskrldedkldklldaleen 67 
                                       +l+ G+ G+GKt +ak++ k+l +   +  ++v+   +++  ++++         +d+   +  + +d++  +++++
  gi|330507685|ref|YP_004384113.1|  60 VLIYGKTGTGKTAVAKYVGKELeEAsFEDMKCVVIYINCEVVDTQYrilahlarHFDRDIPMTGWPTDQVYAEFRNA 136
                                       79****************99985557444444444444444444444443344445555555555555555555554 PP

                            AAA_18  68 s 68 
                                        
  gi|330507685|ref|YP_004384113.1| 137 L 137
                                       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 !   16.0   0.0   1.1e-05    0.0065      34      65 ..      58      89 ..      47     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsl 65
                                       +vl++G+tGtGKt+++k + k+l++ ++  +
  gi|330507685|ref|YP_004384113.1| 58 SNVLIYGKTGTGKTAVAKYVGKELEEASFEDM 89
                                      68******************999998776544 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     1e-05    0.0062       3     105 ..      59     159 ..      57     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                           DUF2075   3 vvlVtGvaGtGKtvvllnllael.eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefk 78 
                                        vl+ G++GtGKt v+  +  el e + e+ + v+++ N + v++ ++ la  +  +++++++        ++   +
  gi|330507685|ref|YP_004384113.1|  59 NVLIYGKTGTGKTAVAKYVGKELeEASFEDMKCVVIYINCEVVDTQYRILAHLA--RHFDRDIPMTGWPTDQVY-AE 132
                                       689********************666669999999************9998888..666666665554444444.22 PP

                           DUF2075  79 kaeekkeepkedvvivDEAhrlltksd 105
                                        +++ +ee+++ v+  DE  +l  k+d
  gi|330507685|ref|YP_004384113.1| 133 FRNALDEEKQVVVIMLDEVDKLVRKGD 159
                                       234556778888889999999988776 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   4.4e-05     0.027      15     121 ..      58     167 ..      40     173 .. 0.77
   2 ?   -1.9   0.0       3.8   2.4e+03     141     151 ..     289     299 ..     252     377 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-05
                                       CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST..SEEEEEETTSSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid..lrvlliiggvaard 89 
                                        +vl+ ++TG+GKT+++   v +++ e+ + +  k++++    e +  +++ l  +  + d  + +  + +++ + +
  gi|330507685|ref|YP_004384113.1|  58 SNVLIYGKTGTGKTAVAKY-VGKEL-EEASFEDMKCVVIYINCEVVDTQYRILAHLARHFDrdIPMTGWPTDQVYAE 132
                                       69************99654.45566.44899999***********************99774466666667777888 PP

                                       HHHHHHTTCSEEEEEHHHHHHHHHCTS...SHCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                              DEAD  90 qlskldngvdivvgtpgrlddllstgk...lnlsq 121
                                        +++ld++ ++vv   + +d+l+++g     nls+
  gi|330507685|ref|YP_004384113.1| 133 FRNALDEEKQVVVIMLDEVDKLVRKGDdvlYNLSR 167
                                       8889999999***9999999999555422255555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.8
                                       HHHHHHHHSHH CS
                                       xxxxxxxxxxx RF
                              DEAD 141 finrilnqlpq 151
                                        +++++++lp+
  gi|330507685|ref|YP_004384113.1| 289 RVEEVIKTLPT 299
                                       33333333322 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   5.8e-05     0.036      12      42 ..      53      87 ..      42      97 .. 0.81
   2 ?   -0.7   0.0       1.1     7e+02      34      75 ..     131     172 ..     128     181 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.8e-05
                        Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdele....r 42
                                      ++e+P  +l+ G +G GK+++a+++ +ele    +
  gi|330507685|ref|YP_004384113.1| 53 RGETPSNVLIYGKTGTGKTAVAKYVGKELEeasfE 87
                                      6799***********************99855444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                        Zeta_toxin  34 ellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkasel 75 
                                       ++++++l+++++vv++  D++ +l ++ +++l + ++ +s+l
  gi|330507685|ref|YP_004384113.1| 131 AEFRNALDEEKQVVVIMLDEVDKLVRKGDDVLYNLSRVNSDL 172
                                       667888999999999999998888777666666555555555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.1e-05     0.019      52      94 ..      59     101 ..      40     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevy.slevk 94 
                                        vL+ G++gtGkta+a  + kel  +  f  ++   +y  +ev 
  gi|330507685|ref|YP_004384113.1|  59 NVLIYGKTGTGKTAVAKYVGKELE-EASFEDMKCVVIYiNCEVV 101
                                       69*********************8.6789999998888335655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   8.5e-05     0.052       1      31 [.      60      90 ..      60     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.5e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkk 31
                                      +++yG++g+GK+ +ak++ k+l++++ ++ k
  gi|330507685|ref|YP_004384113.1| 60 VLIYGKTGTGKTAVAKYVGKELEEASFEDMK 90
                                      689*******************987744444 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00018      0.11       4      89 ..      58     160 ..      55     174 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                       --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---......----THHHHHHHHHTTT-HHHHTTS.... CS
                             AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselle......eeevehlvsrligappgyvgaeegG.... 70 
                                       +++l+ g+tg+Gkt +ak + + l+     +    d++ +         +   +++++l  a+ ++      G    
  gi|330507685|ref|YP_004384113.1|  58 SNVLIYGKTGTGKTAVAKYVGKELE-----EASFEDMKCVVIyincevVDTQYRILAHL--ARHFDRDIPMTGwptd 127
                                       6899999*******98887777777.....45555555555522211111112222222..2233333333337777 PP

                                       .................EEEEETGGG----.------ CS
                             AAA_2  71 .................ivllDEidKihpk.essgad 89 
                                                        +++lDE+dK  +k +    d
  gi|330507685|ref|YP_004384113.1| 128 qvyaefrnaldeekqvvVIMLDEVDKLVRKgD----D 160
                                       78888888999999999**********99533....3 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.8e-05     0.048       5      68 ..      37     102 ..      33     175 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-05
                                       -HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S......-EEEEESSHHHHH CS
                            ResIII   5 reyQeeaienll.eklkskrdkrglikmaTGtGKTlvaaklierllkkgkee.kflflvprkslle 68 
                                       re Q++ + ++l  +l  +   ++li   TGtGKT va  + ++l ++  e+ k++++  + ++++
  gi|330507685|ref|YP_004384113.1|  37 REEQINNLASILvPALRGETPSNVLIYGKTGTGKTAVAKYVGKELEEASFEDmKCVVIYINCEVVD 102
                                       5555555555555455558999****************9999999888776676666655555544 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   4.5e-05     0.028       3      79 ..      58     156 ..      56     171 .. 0.59
   2 ?   -2.4   0.1       5.2   3.2e+03     143     181 ..     280     318 ..     265     328 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.5e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.........................swedfld 54 
                                        ++liyG+ g+GKT +ak  g++     +e+   +  +  + ++e                           ++++ 
  gi|330507685|ref|YP_004384113.1|  58 SNVLIYGKTGTGKTAVAKYVGKELEEASFEDM--KCVV-IYINCEvvdtqyrilahlarhfdrdipmtgwPTDQVYA 131
                                       579****************9555555555551..1122.22223333344444444444444455555443344444 PP

                            AAA_24  55 evvelaaeladyktlviDtidelee 79 
                                       e+    +e+++  ++ +D +d+l++
  gi|330507685|ref|YP_004384113.1| 132 EFRNALDEEKQVVVIMLDEVDKLVR 156
                                       4444477777777888888888876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.2
                            AAA_24 143 akytrlepklgkktanelkeevDlvlranlkredkvger 181
                                       ++ +++e++  + + + l++++ lvl+  +  e+++++ 
  gi|330507685|ref|YP_004384113.1| 280 QARDKIEQDRVEEVIKTLPTQSKLVLYSIILLEEQGTRN 318
                                       566677777777777778888888888776655555543 PP

>> DUF2498  Protein of unknown function (DUF2498)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00017      0.11      41      70 ..     304     333 ..     279     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                           DUF2498  41 vFkGeyfldeqglPtekttavFnmfkyLah 70 
                                       v      l+eqg     t av+nm+k+L  
  gi|330507685|ref|YP_004384113.1| 304 VLYSIILLEEQGTRNITTSAVYNMYKQLCP 333
                                       55556689*******************975 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014     0.086       3      44 ..      37      82 ..      35      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                                      SHHHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  3 seeetealgkklakal....gdvilLeGdLGaGKTtlvrglakalg 44
                                      +ee++++l++ l  al     + +l++G+ G+GKT+ ++ + k+l+
  gi|330507685|ref|YP_004384113.1| 37 REEQINNLASILVPALrgetPSNVLIYGKTGTGKTAVAKYVGKELE 82
                                      68899999999999888544345*****************999885 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.7     1e+03       9      22 ..     103     116 ..      98     120 .. 0.85
   2 ?   10.5   0.2   0.00079      0.49      42      71 ..     270     298 ..     255     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHTTT CS
                       Trans_reg_C   9 kefklLelLlenpg 22 
                                       +++++L+ L+++ +
  gi|330507685|ref|YP_004384113.1| 103 TQYRILAHLARHFD 116
                                       79*********965 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00079
                                       HTHHHHHHHHHHHHHHHTTTTSSSSEEEET CS
                       Trans_reg_C  42 ddrtvdvhisrLRkkLeddekkprlIetvr 71 
                                       ++ + +vh+++ R+k+e+d   +++I+t++
  gi|330507685|ref|YP_004384113.1| 270 STVVTEVHVRQARDKIEQDR-VEEVIKTLP 298
                                       445558************65.6679*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 ?   10.8   0.2   0.00061      0.38       1      24 [.      59      90 ..      59     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00061
                                      EEEEE--SSSSHHHHHHHGGGGB........S CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal........n 24
                                      +vl+ G++GtgK+ +a+++ + l        +
  gi|330507685|ref|YP_004384113.1| 59 NVLIYGKTGTGKTAVAKYVGKELeeasfedmK 90
                                      69***************998888643333333 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 ?   12.1   0.1    0.0003      0.18      16      55 ..     244     294 ..     232     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0003
                                       XXXXXXXXXXXXXXXXXXXXXXXX............XXXXXXXXXXXXXXX CS
                       AAA_assoc_2  16 aeladGDaRkaLnlLElaaeaaeak...........egkieitledleeal 55 
                                       a+  +GDaR+aL lL +  e ae++           + + +i+++ +ee++
  gi|330507685|ref|YP_004384113.1| 244 AAQEHGDARRALDLLRISGELAERArstvvtevhvrQARDKIEQDRVEEVI 294
                                       55668***********99998887555566666666666666666666665 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00074      0.46      35      73 ..      58      99 ..      38     119 .. 0.78
   2 ?   -0.0   0.0       1.1   6.7e+02      96     122 ..     141     168 ..     124     259 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00074
                                      --EEEE-SSSSSHHHHHHHHHHHHHH.HSSSS-..EEEEEHH CS
                          Bac_DnaA 35 nPlfiygevGlGktHLlkaignevle.napelr..vvYltae 73
                                        ++iyg++G Gkt + k +g+e++e ++++++  v+Y++ e
  gi|330507685|ref|YP_004384113.1| 58 SNVLIYGKTGTGKTAVAKYVGKELEEaSFEDMKcvVIYINCE 99
                                      5699******************99872456666446677766 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                                       TT-SEEEEE-GGGGTT-H.HHHHHHHHH CS
                          Bac_DnaA  96 rkvDvLliDDiqflagke.ktqeelfht 122
                                       ++v v+++D++  l +k  ++  +l  +
  gi|330507685|ref|YP_004384113.1| 141 KQVVVIMLDEVDKLVRKGdDVLYNLSRV 168
                                       2444455555555555431233334444 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3    0.0061       3.8      26      50 ..      60      86 ..      58     104 .. 0.80
   2 ?    2.3   0.0      0.25   1.6e+02     163     215 ..     102     155 ..      76     168 .. 0.74
   3 ?    0.6   0.0      0.83   5.1e+02     101     195 ..     256     353 ..     251     380 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0061
                             DUF87 26 lAilgsTGsGKSntvavLleelle..k 50
                                      ++i g+TG+GK+  +++  +el e  +
  gi|330507685|ref|YP_004384113.1| 60 VLIYGKTGTGKTAVAKYVGKELEEasF 86
                                      689************998888765553 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.25
                             DUF87 163 qaiarlldkledllrkggsf.snsstdliallleklekegkitiidlsgvdela 215
                                       +++ r+l++l + +++ +   +  +++++a+  + l++e+++++i l +vd+l+
  gi|330507685|ref|YP_004384113.1| 102 DTQYRILAHLARHFDRDIPMtGWPTDQVYAEFRNALDEEKQVVVIMLDEVDKLV 155
                                       556666666655554444444566778899999999*************99886 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.83
                             DUF87 101 elldlleeddkpaaavqrsvleealdqakakeekeklssdepveklleelk........kekeelrklknqaiarll 169
                                       +ll++++e   +++a+++ v e  ++qa+   ++e+  ++e +++l  + k         e+++ r++ ++a  ++ 
  gi|330507685|ref|YP_004384113.1| 256 DLLRISGE--LAERARSTVVTEVHVRQAR--DKIEQDRVEEVIKTLPTQSKlvlysiilLEEQGTRNITTSAVYNMY 328
                                       66666666..6666666667777777777..7778888888888887777788888888888899999999999999 PP

                             DUF87 170 dkledllrkggsfsnsstdliallle 195
                                       ++l  l ++  + +   tdlia+l +
  gi|330507685|ref|YP_004384113.1| 329 KQLCPLVETDFLTHRRITDLIAEL-D 353
                                       999988888888888888888877.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 2607.36
//
Query:       gi|330507686|ref|YP_004384114.1|  [L=69]
Description: hypothetical protein MCON_1675 [Methanosaeta concilii GP6]
Scores for complete 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-30  102.5   2.6      1e-29  102.4   2.6    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)


Domain annotation for each model (and alignments):
>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4   2.6   5.7e-34     1e-29      16      81 .]       1      66 [.       1      66 [. 0.98

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 5.7e-34
                                      HT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
                           UPF0147 16 iedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEti 81
                                      ++d++vPrniRr+a+ +k+ L+de+ + a++aa+aisiLdeisnDpn+Plh+Rtliw+v s+LEti
  gi|330507686|ref|YP_004384114.1|  1 MSDDAVPRNIRRSAESVKTILMDESVNEAIKAASAISILDEISNDPNIPLHTRTLIWNVASQLETI 66
                                      689*************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 540.35
//
Query:       gi|330507687|ref|YP_004384115.1|  [L=156]
Description: hypothetical protein MCON_1676 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-10   40.7   1.9    4.2e-10   39.6   1.9    1.6  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (


Domain annotation for each model (and alignments):
>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   1.9   2.3e-14   4.2e-10       2      39 ..       9      43 ..       8      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 2.3e-14
                     Auto_anti-p27  2 kmgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaC 39
                                      k+ +lL +G tMLa+++ +Cg+PL+r   +g+++C++C
  gi|330507687|ref|YP_004384115.1|  9 KITRLLERGCTMLATHH-DCGAPLFR--CQGEIVCPVC 43
                                      899************99.5*******..789******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1146.18
//
Query:       gi|330507688|ref|YP_004384116.1|  [L=404]
Description: hypothetical protein MCON_1677 [Methanosaeta concilii GP6]
Scores for 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-09   35.2   0.0    1.6e-08   34.4   0.0    1.4  1  Ada_Zn_binding  Metal binding domain of Ada


Domain annotation for each model (and alignments):
>> Ada_Zn_binding  Metal binding domain of Ada
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0     9e-13   1.6e-08      18      64 ..     357     404 .]     344     404 .] 0.87

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 9e-13
                                       EEEETTTTEEE-TT-SSS.-S-SCCEEEESSHHHHHHTT-EEETTTTT CS
                    Ada_Zn_binding  18 vyavkttgiyCrpsCpar.lPkrenveFfdtaaeAeaagfrpCkrcrP 64 
                                       +++  t + y  p+C+   + k+en ++f++a+eA+++g+ pCk c+P
  gi|330507688|ref|YP_004384116.1| 357 FVGSSTSKKYHLPDCRYAlKIKQENKVYFQSAEEAKSQGYLPCKSCHP 404
                                       68999**********9661567*************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 2802.26
//
Query:       gi|330507689|ref|YP_004384117.1|  [L=190]
Description: precorrin-6y C5,15-methyltransferase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-20   73.2   0.5    8.8e-19   68.3   0.5    2.5  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.5   4.9e-23   8.8e-19       4     209 ..       3     173 ..       1     177 [. 0.79

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 4.9e-23
                      TP_methylase   4 lVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragk 80 
                                       +VGvG+ +p  +T++A +a+ +a +++g++ r  +++++++++       +           +ei e ++++    +
  gi|330507689|ref|YP_004384117.1|   3 IVGVGI-GPGMMTQEAEEAIGRARLIYGSK-RSIDLAREYIDP-------D--------CIVREI-EDYKRLSSLPE 61 
                                       555555.3466*******************.999999888743.......1........223333.33455555556 PP

                      TP_methylase  81 dVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeereleal 157
                                       ++v+l++GDP+++g g                +viPG+sslq a+arl+i+  +   ++ +  ++++   ++ ++  
  gi|330507689|ref|YP_004384117.1|  62 EAVVLSTGDPMLSGLGYL-----P-------GRVIPGISSLQVACARLKISELDVVPITVHG-RRMD---PEAIASE 122
                                       69************9544.....2.......38******************99888888888.5544...5556666 PP

                      TP_methylase 158 langdtlvllkapr.klaelaelLkealyddttpvavveragtedervvrgtl 209
                                       l+++ +++ll++ + +l+ +++lL e+  +  + v +  ++g+++er+ rg+ 
  gi|330507689|ref|YP_004384117.1| 123 LSRNKSVFLLTDDStDLEGVCRLLEER--GLARSVLALTDLGYPQERIERGST 173
                                       6778888888888868***********..8899****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1388.90
//
Query:       gi|330507690|ref|YP_004384118.1|  [L=341]
Description: putative cobalt-precorrin-6A synthase (deacetylating) [Methanosaeta concilii GP6]
Scores for complete 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  158.6   1.4    2.2e-46  158.2   1.4    1.1  1  CbiD      CbiD
  ------ inclusion threshold ------
      0.037   13.8   0.1      0.096   12.5   0.1    1.7  1  TruB_C    tRNA Pseudouridine synthase II, C terminal


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 !  158.2   1.4   2.4e-50   2.2e-46       1     224 [.      49     263 ..      49     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 158.2 bits;  conditional E-value: 2.4e-50
                              CbiD   1 lrsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleeeaavikdaGddp.DvTngaeivae 76 
                                       l++G+TtG++AaAAak+A++ l+  +++e++e+++p+g+ ++++   v++++  +  +kd+Gd+  DvT g+ i a+
  gi|330507690|ref|YP_004384118.1|  49 LKRGLTTGTTAAAAAKGAVVSLV--RATESLEVMTPAGIPVSVS---VKAENGYCNARKDGGDHQsDVTAGLGISAR 120
                                       589*******************6..5679*********999999...5554445*********866*********** PP

                              CbiD  77 ve..eeieiegGeGvGrvtkpgLevevgeaAInpvprkmieenveevleea.kegvevtisvpeGeelAkkTlNprl 150
                                        e  +e ++ +G G+Gr+   gL  ++g++AI+p ++ +i  +++e l+ +  e+v+v+i vp+Ge+++++TlNp+l
  gi|330507690|ref|YP_004384118.1| 121 AEpsGETVLLAGAGIGRIGAGGLCDQIGRPAISPSAKGQIMMAISEGLKVTgLEHVRVEIWVPQGERISRQTLNPKL 197
                                       ****7799****************************************9888679********************** PP

                              CbiD 151 GivgGiSiLGTtGivepmSeeallesireelkvaaaeglkelvlvtGnkgeklakkklglpeealvkvsnfvge 224
                                       Gi+gGiSiLG tG vep+ e+ l+++ +eelk       k++v++tG++g kl +    +p+++ v ++n +g 
  gi|330507690|ref|YP_004384118.1| 198 GIMGGISILGSTGFVEPWNEH-LINERAEELKG-----AKKVVVSTGRTGLKLSRI--LFPDHEAVLMGNQLGR 263
                                       *****************9776.55555667765.....5789**********9998..69**********9986 PP

>> TruB_C  tRNA Pseudouridine synthase II, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.1e-05     0.096      14      45 ..      43      74 ..      41      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.1e-05
                                      HHTT---B-----S-EEEE-TTS-EEEEEEEE CS
                            TruB_C 14 lrhGrrLeaagikgvvAaiaPdGrliALleer 45
                                      l+ G+ L++  + g++Aa a+ G ++ L+++ 
  gi|330507690|ref|YP_004384118.1| 43 LSSGQLLKRGLTTGTTAAAAAKGAVVSLVRAT 74
                                      788999***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2312.31
//
Query:       gi|330507691|ref|YP_004384119.1|  [L=210]
Description: precorrin-8X methylmutase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-60  203.2   0.1    3.6e-60  203.0   0.1    1.0  1  CbiC      Precorrin-8X methylmutase


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.0   0.1     2e-64   3.6e-60       2     195 ..      18     203 ..      17     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 203.0 bits;  conditional E-value: 2e-64
                                       HHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HHH CS
                              CbiC   2 IeaeSfaiideelgeeelseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitkkr 78 
                                       I ++S ++i + +g++   + e+++++R++ at+d++ a+++rf++d  +agl+al++gapi++D++mv+aG+ kk 
  gi|330507691|ref|YP_004384119.1|  18 ISRKSRELISSMIGDR---SLEDRITQRCVIATGDPSTADIMRFQNDPFQAGLKALERGAPIYVDIKMVQAGVLKKG 91 
                                       99************88...99****************************************************9999 PP

                                       HHTTC-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE---- CS
                              CbiC  79 leklgnevlclladpevaelakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPvG 155
                                       +++   ++  ++++    ela+++gitr++a++ ++ e+l+g+i viGnAP+ALl+l+el+e+g+v+p lvigvPvG
  gi|330507691|ref|YP_004384119.1|  92 HTS---PIEAFIDKG--DELAASRGITRTSAGVFALNEKLSGSIAVIGNAPSALLTLCELMESGRVQPDLVIGVPVG 163
                                       877...899999998..789********************************************************* PP

                                       SCCHHHHHHHHHCSSS-EEEESSS---HHHHHHHHHHHHH CS
                              CbiC 156 FvgaaesKealaesevpyitveGrkGGsavAaaivnaLle 195
                                       Fv+a esKe+l+e  vp+i + G++GG+++A+a++n++++
  gi|330507691|ref|YP_004384119.1| 164 FVNALESKERLREIPVPSISTAGTRGGTPIAVAAINEIIN 203
                                       *************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1651.73
//
Query:       gi|330507692|ref|YP_004384120.1|  [L=476]
Description: cobalt-precorrin-3B C(17)-methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-63  213.8   1.6    8.9e-34  117.3   0.2    2.1  2  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.022   14.2   0.0      0.055   12.9   0.0    1.7  1  DUF4244       Protein of unknown function (DUF4244)


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.3   0.2   9.9e-38   8.9e-34       1     211 [.      17     214 ..      17     216 .. 0.87
   2 !   96.2   0.1   2.8e-31   2.5e-27       3     212 ..     250     438 ..     248     439 .. 0.82

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 9.9e-38
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       +l +VG+GpGd+ l T++A++a+k ad v+g++  +l++++dll+ +        +  ++  ++  + ++a  ++l 
  gi|330507692|ref|YP_004384120.1|  17 RLSIVGIGPGDASLRTLAAVDAIKGADYVVGYR-PYLKLIEDLLPGK--------EVYSSGMGKETDRVRAALDLLS 84 
                                       588******************************.**********763........3333333445556677788888 PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeer 152
                                       +g  V+l++sGD +vyg+++  + + ++  +  eveviPGv+s++aaa+r+g+   e   v s++  l++++++e r
  gi|330507692|ref|YP_004384120.1|  85 RGP-VALVSSGDANVYGMAGLGL-EMAE--HPAEVEVIPGVTSFTAAACRAGLLFRECVAVISLSdlLTPWQDIEGR 157
                                       886.******************9.5566..6789*********************************9****88877 PP

                      TP_methylase 153 eleallangdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtlee 211
                                       ++ a  a+++  v+l++pr  ++  +lL++  +y++  +v v++++g+e+er++ +t ++
  gi|330507692|ref|YP_004384120.1| 158 LRQA--ADFGMPVALYNPRSRKRDWQLLRALnIYEKR-DVLVAKEVGREGERLFWTTAAA 214
                                       7755..4589999999***************988855.***************9888765 PP

  == domain 2  score: 96.2 bits;  conditional E-value: 2.8e-31
                      TP_methylase   3 ylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal..aealr 77 
                                        lVG+GpG+ + lT +A+ +l +++ +lg++ r+l ++ d++ e+       ++         +  a+     +++r
  gi|330507692|ref|YP_004384120.1| 250 NLVGTGPGGQANLTAEARTILSSSEKILGAE-RYLNLIGDYPGEK------VAHAGPCP---ERSYARFQeaEQLAR 316
                                       69*****************************.*******998762......22222222...333333334488999 PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerel 154
                                       +gk++ +l++GDP+++++g +++  l++  + ++v++ PGvs+++++aar+g+pl+ ++  ls l    +++e+  l
  gi|330507692|ref|YP_004384120.1| 317 SGKKASILTGGDPSIFSAGWRIM-DLAR--NRLPVHISPGVSAFSSVAARAGAPLSGDFALLSQL----DNPEAPSL 386
                                       999********************.6776..5689**********************999999999....33344444 PP

                      TP_methylase 155 eallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                        a   ++++ v++++++   e+ ++L+e   ++++ va+++++ +++e+++  + eel
  gi|330507692|ref|YP_004384120.1| 387 LA---AAGFGVVIYNVK-GHEVQAFLQEL--EPERAVALARDVARKGEEMIIMKAEEL 438
                                       33...346777777887.899*****999..7788****************9999987 PP

>> DUF4244  Protein of unknown function (DUF4244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.2e-06     0.055      22      48 ..     386     411 ..     383     412 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.2e-06
                           DUF4244  22 tlAAvafAavLykvvtsdsVrsaLtgi 48 
                                       +lAA++f++v y v ++ +V++ L+++
  gi|330507692|ref|YP_004384120.1| 386 LLAAAGFGVVIYNV-KGHEVQAFLQEL 411
                                       69**********96.9*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3338.31
//
Query:       gi|330507693|ref|YP_004384121.1|  [L=255]
Description: cobalamin (vitamin B12) biosynthesis CbiG protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.2    1.7e-27   96.3   0.2    1.3  1  CbiG_C    Cobalamin synthesis G C-terminus
    8.7e-27   92.9   0.1    2.3e-26   91.6   0.1    1.8  1  CbiG_N    Cobalamin synthesis G N-terminal


Domain annotation for each model (and alignments):
>> CbiG_C  Cobalamin synthesis G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.2   1.9e-31   1.7e-27       1     115 [.     140     252 ..     140     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 1.9e-31
                                       EEEEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHHCSCT- CS
                            CbiG_C   1 lvvGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaavevpnps 77 
                                       lv+G+G+r+g+s ee+ +ai++al+e g ++e++a lat  lK++e+glle+a++l+ +++++s+eeL++ +  +ps
  gi|330507693|ref|YP_004384121.1| 140 LVLGVGARKGVSSEEVLQAIDQALAESGRKREDIAFLATAWLKKEEEGLLEAAKSLDREIVFLSREELNSQKPSTPS 216
                                       79*********************************************************************987787 PP

                                       CHHHCCCSSS-HHHHHHHHHC.EECSCEEEETTEEEEE CS
                            CbiG_C  78 efvkkevGvpsVaEaaAllaaarllvpKqakggvTvAi 115
                                        +  + +G+ +VaE+a l+ a+rl++pK+a+g+vTvAi
  gi|330507693|ref|YP_004384121.1| 217 RA--EDLGLAGVAEPAVLALAKRLILPKKAYGRVTVAI 252
                                       75..68*******************************9 PP

>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.1   2.6e-30   2.3e-26       4      82 .]       2      79 ..       1      79 [. 0.98

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 2.6e-30
                                      HHHCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XXXXX. CS
                            CbiG_N  4 relfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviTtatd 82
                                      ++l+++yd lv+i+a+Giv R+++ +l+dK++D +Vv+vd+a + ++++++Gh +gAn+lA  +a+ +g  p+iTtatd
  gi|330507693|ref|YP_004384121.1|  2 KRLLEKYDLLVAIMAVGIVTRSLCRHLQDKWRDRPVVAVDSALSCAVPVVGGH-HGANDLALLLAERMGLYPAITTATD 79
                                      67899************************************************.************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2014.07
//
Query:       gi|330507694|ref|YP_004384122.1|  [L=236]
Description: precorrin-4 C11-methyltransferase [Methanosaeta concilii GP6]
Scores for complete 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  160.3   0.2    7.1e-47  160.1   0.2    1.0  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 !  160.1   0.2   3.9e-51   7.1e-47       1     212 [.       2     201 ..       2     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: 160.1 bits;  conditional E-value: 3.9e-51
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       k+y+VG+GpGdpel+Tv++ r+l++ad+v++++s++   ll+ l+           ++++++   ee +++++e lr
  gi|330507694|ref|YP_004384122.1|   2 KVYFVGAGPGDPELITVKGKRLLEEADLVVYAGSLVNPQLLEGLRA---------IKVDSNGLSIEETQAKMVEFLR 69 
                                       79*******************************9977777666654.........678899999************* PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeer 152
                                       agk+Vv+l+sGDP++yg+  e ++ l++   gievev+PGvssl aa a+l++ lt +g + s++  +p+  + +++
  gi|330507694|ref|YP_004384122.1|  70 AGKKVVRLHSGDPSIYGAILEQMKPLEE--MGIEVEVVPGVSSLFAASAALKTQLTLKGISESLIvtRPKGTTLAKD 144
                                       ****************************..************************************98888999999 PP

                      TP_methylase 153 eleallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                       +l  l+  g+t++++ + +k+ ++++ L +   + ttpvavv +a+++d++v  gt+ ++
  gi|330507694|ref|YP_004384122.1| 145 DLPTLSRLGTTMAIFLGIDKIRDIVQSL-DL--PGTTPVAVVYHASWPDQQVLCGTIDDI 201
                                       99999999********************.66..5578*******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1690.12
//
Query:       gi|330507695|ref|YP_004384123.1|  [L=202]
Description: uroporphyrin-III C/tetrapyrrole methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-29  102.0   0.0    1.5e-28  100.2   0.0    1.7  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 !  100.2   0.0   8.4e-33   1.5e-28       1     208 [.       1     185 [.       1     188 [. 0.90

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 8.4e-33
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       +l+++ +GpGdp llT +A++alk+++ v+ +++ a e+++++  ++  l +pm +++ +l + ++++a+++a+++ 
  gi|330507695|ref|YP_004384123.1|   1 MLIGISLGPGDPQLLTFKAAAALKSCKRVYVPGEMAAELARPYSSPQ-ILDFPMIQDELELKRIWQKNADIIAQDAG 76 
                                       79*******************************77******998775.999******9999999************* PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerel 154
                                       + + V ++++GD + ++t+s+l + +++r++gie+++iPGv  + a+a+r+++pl+ ++ v++ +          ++
  gi|330507695|ref|YP_004384123.1|  77 TSQ-VGFACIGDINTFSTFSHLKRVIEERHPGIEIQTIPGVGVVPALASRFDVPLERSFLVSDGS----------QV 142
                                       *96.****************************************************666666555..........22 PP

                      TP_methylase 155 eallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgt 208
                                              ++++ +ka+r + +lae+L+e+  + + + +++ r+ t++er+vrg 
  gi|330507695|ref|YP_004384123.1| 143 -------QSVIRIKATR-PRKLAEELREE--GYE-DFTLGMRLFTPEERIVRGE 185
                                       .......7788888888.99999999999..434.7999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1503.17
//
Query:       gi|330507696|ref|YP_004384124.1|  [L=170]
Description: hypothetical protein MCON_1685 [Methanosaeta concilii GP6]
Scores for complete 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   27.2   0.0    3.7e-06   26.8   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    6.8e-05   23.5   0.0    0.00012   22.7   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    8.9e-05   23.1   0.0    0.00018   22.1   0.0    1.5  2  Methyltransf_11  Methyltransferase domain
      9e-05   22.0   0.0    0.00013   21.5   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00011   21.7   0.0    0.00015   21.2   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0033   17.3   0.0     0.0047   16.8   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.018   14.6   0.0      0.029   13.9   0.0    1.3  1  MTS              Methyltransferase small domain
      0.035   13.7   0.0      0.058   13.0   0.0    1.3  1  NodS             Nodulation protein S (NodS)
      0.069   13.9   0.0       0.13   13.0   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
      0.085   12.5   0.0       0.13   11.9   0.0    1.2  1  N6_N4_Mtase      DNA methylase
      0.096   12.2   0.0       0.15   11.6   0.0    1.3  1  DOT1             Histone methylation protein DOT1
       0.14   13.2   0.0       0.22   12.6   0.0    1.3  1  Methyltransf_24  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 !   26.8   0.0   2.5e-09   3.7e-06       7      68 ..      28      82 ..      22     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.5e-09
                   Methyltransf_31  7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.lek 68
                                      +lD+GCG+G+ ++++    +   +++G+D+ +eai+l+re  ++ +     F  g++ee ++ 
  gi|330507696|ref|YP_004384124.1| 28 FLDIGCGSGAVSLAAS---CYTDRIYGLDRRPEAINLSRELVECGK-----FLLGEAEEiIPR 82
                                      79**********9999...56678****************977655.....456666666665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   7.9e-08   0.00012       2      58 ..      29      79 ..      28      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.9e-08
                                      EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGB CS
                   Methyltransf_25  2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedl 58
                                      Ld+GcG+G ++la++      +++g+D  +e+++  re +e      +f+ g+ae++
  gi|330507696|ref|YP_004384124.1| 29 LDIGCGSGAVSLAASCYT--DRIYGLDRRPEAINLSRELVE----CGKFLLGEAEEI 79
                                      9*******9999998664..*****************9994....457777777765 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.2e-07   0.00018       1      54 [.      29      78 ..      29      91 .. 0.84
   2 ?   -3.0   0.0       8.3   1.2e+04      76      86 ..     132     142 ..     122     149 .. 0.52

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.2e-07
                                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaek 54
                                      Ld+GcG+G+++ a   +  r++g+D  +e+++l++e ++  +    f+ ++ae+
  gi|330507696|ref|YP_004384124.1| 29 LDIGCGSGAVSLAASCYTDRIYGLDRRPEAINLSRELVECGK----FLLGEAEE 78
                                      8**************888*************99999888766....57777766 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.3
                                       CHHHHHHHHHH CS
                   Methyltransf_11  76 dpekalkeiaR 86 
                                       + e +++ei +
  gi|330507696|ref|YP_004384124.1| 132 KKEGIFREILQ 142
                                       34445555554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   8.8e-08   0.00013     159     203 ..      22      65 ..      11      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.8e-08
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeN 203
                                       +++g+ +lD+G+GSG  ++aa+   +++++++D  + A++ ++e 
  gi|330507696|ref|YP_004384124.1|  22 IRPGDLFLDIGCGSGAVSLAASCY-TDRIYGLDRRPEAINLSREL 65 
                                       6889999*************9976.789************99985 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   9.7e-08   0.00015      49      92 ..      11      53 ..       6      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 9.7e-08
                                      HHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEE CS
                              CMAS 49 aKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglT 92
                                      + ++++++kl ++pG+  LdiGcG G++   a++ y  ++ gl 
  gi|330507696|ref|YP_004384124.1| 11 ENIHIAMGKLAIRPGDLFLDIGCGSGAVSL-AASCYTDRIYGLD 53
                                      568899********************9865.6677787887775 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.1e-06    0.0047      21      61 ..      23      63 ..       7     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.1e-06
                   Methyltransf_23 21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae 61
                                      r+g   LdiGcG+G ++  ++ +   ++g D +pea+++ +
  gi|330507696|ref|YP_004384124.1| 23 RPGDLFLDIGCGSGAVSLAASCYTDRIYGLDRRPEAINLSR 63
                                      555667********999977777669***********9876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     2e-05     0.029      35      75 ..      28      66 ..      15      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                                      EEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHH CS
                               MTS 35 vlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenl 75
                                       lD+GcG G++++a+   +++  +  +d   +A+++++e +
  gi|330507696|ref|YP_004384124.1| 28 FLDIGCGSGAVSLAASCYTDR--IYGLDRRPEAINLSRELV 66
                                      79********99988776666..9***********999865 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.9e-05     0.058      27      85 ..      10      66 ..       4      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.9e-05
                              NodS 27 eqerlaqilrlslaqgsiadalevGcaaGalterlapyckrltvvdvveeaiararerv 85
                                      e++ + ++ +l+++ g++   l++Gc +Ga++   + y++r+  +d  +eai+ +re v
  gi|330507696|ref|YP_004384124.1| 10 EENIHIAMGKLAIRPGDL--FLDIGCGSGAVSLAASCYTDRIYGLDRRPEAINLSRELV 66
                                      667788888888888887..69*******************************999866 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.9e-05      0.13       1      36 [.      29      62 ..      29      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.9e-05
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaieda 36
                                      L+iGcG+G+++ a   +  + +++g+D  p+ai+  
  gi|330507696|ref|YP_004384124.1| 29 LDIGCGSGAVSLAASCY--TDRIYGLDRRPEAINLS 62
                                      8*******999888888..*************9443 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.7e-05      0.13     186     230 ..      19      63 ..      12      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.7e-05
                                       HHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                       N6_N4_Mtase 186 klstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelae 230
                                       kl  ++gd+ lD  +GSG    aa     + +G +  +e+++l+ 
  gi|330507696|ref|YP_004384124.1|  19 KLAIRPGDLFLDIGCGSGAVSLAASCYTDRIYGLDRRPEAINLSR 63 
                                       57789***********************************99875 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.15      32      65 ..      14      47 ..       7      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                      HHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH- CS
                              DOT1 32 sevldkvnlkkedvFvDLGSGvGnvvlqaalevg 65
                                         + k+ +++ d+F+D+G G G v l a+ ++ 
  gi|330507696|ref|YP_004384124.1| 14 HIAMGKLAIRPGDLFLDIGCGSGAVSLAASCYTD 47
                                      55678999***************99988777654 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00015      0.22       2     104 ..      30     117 ..      29     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                   Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalareaglddrvrlikadseealaslaagsiDllfiDgg 78 
                                        iG  +G  ++ l+ a + ++  r++ +d  p   ea +l re  l +  +++ +++ee +++l    +D  fi g 
  gi|330507696|ref|YP_004384124.1|  30 DIG--CGSGAVSLA-ASCYTD--RIYGLDRRP---EAINLSRE--LVECGKFLLGEAEEIIPRLP--AVDRCFIGGT 94 
                                       699..777677776.555555..69*******...86666665..********************..8******998 PP

                   Methyltransf_24  79 haaeavledleallprlapggvvlfd 104
                                          +   ++l++ll++ +pg+++++d
  gi|330507696|ref|YP_004384124.1|  95 ---RGIDRFLPLLLEKASPGCMIVVD 117
                                       ...99999****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1245.56
//
Query:       gi|330507697|ref|YP_004384125.1|  [L=304]
Description: hypothetical protein MCON_1686 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-30  106.9   0.0    1.3e-30  106.5   0.0    1.1  1  ATP-grasp_3  ATP-grasp domain
    0.00068   19.0   0.0       0.41    9.8   0.0    2.1  2  ATPgrasp_ST  Sugar-transfer associated ATP-grasp


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 !  106.5   0.0   1.5e-34   1.3e-30       1     161 []     108     262 ..     108     262 .. 0.92

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 1.5e-34
                                       HTSHHHHHHHHTTT.S---....-.EESS--SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEE CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvPtklea.eeleeeekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplS 76 
                                       a+dKl ++++L ++gv+v + +   + +++   ++vvKpr+G+g+e+vr+    ++        e+v ++ eG +lS
  gi|330507697|ref|YP_004384125.1| 108 AADKLLSTQALARSGVPVAEIVDRpDPVDKGCLQYVVKPRTGSGSEGVRISSFVRAGP-----EEIVTRYHEGLHLS 179
                                       79************99999555541444555779********************7777.....459*********** PP

                                       EEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEE CS
                       ATP-grasp_3  77 vsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkdeepyviE 153
                                       +s+++ +e +l+l++nrqli++a  +++y+G+ +p++t ++ e+ e+ae++   l  l+Gy+G+D vl +  p  ++
  gi|330507697|ref|YP_004384125.1| 180 ASFIVGKEGFLPLTLNRQLIDFADGKMRYQGSQVPYRTPRAAEIWEAAEKAADVL-ALRGYAGIDYVLGE-RPWAVD 254
                                       *******************************************************.**************.****** PP

                                       EESS--GG CS
                       ATP-grasp_3 154 vNPRltts 161
                                       vN+R+tts
  gi|330507697|ref|YP_004384125.1| 255 VNARPTTS 262
                                       ******97 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 !    7.0   0.0   0.00034         3      15      81 ..     104     160 ..      97     172 .. 0.85
   2 !    9.8   0.0   4.6e-05      0.41     207     274 ..     198     267 ..     184     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00034
                       ATPgrasp_ST  15 efplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvite 81 
                                       ++ l +dKl+ ++ + r g++v +          +++ + + k++  ++v+Kp  gsg +G+++ ++
  gi|330507697|ref|YP_004384125.1| 104 AASLAADKLLSTQALARSGVPVAE---------IVDRPDPVDKGC-LQYVVKPRTGSGSEGVRISSF 160
                                       567778999999999999999999.........888999999999.559*************99876 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 4.6e-05
                       ATPgrasp_ST 207 ieeHPdTgvklsglqi....PnweevlelaakaaeklpglgylGwDivldeekgplllElNarpglaivqia 274
                                           +d +++ +g q+    P  +e+ e a kaa+ l   gy G+D vl e + p  + +Narp  +i+ ia
  gi|330507697|ref|YP_004384125.1| 198 LIDFADGKMRYQGSQVpyrtPRAAEIWEAAEKAADVLALRGYAGIDYVLGE-R-PWAVDVNARPTTSIIGIA 267
                                       5556778888888888444456789**********999999********76.5.8*********99997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2151.39
//
Query:       gi|330507698|ref|YP_004384126.1|  [L=66]
Description: hypothetical protein MCON_1687 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 515.77
//
Query:       gi|330507699|ref|YP_004384127.1|  [L=53]
Description: hypothetical protein MCON_1688, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       129  (0.00719505); expected 358.6 (0.02)
Passed bias filter:                      120  (0.00669307); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 384.59
//
Query:       gi|330507700|ref|YP_004384128.1|  [L=337]
Description: PfkB domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-55  188.2   0.3    2.4e-55  188.0   0.3    1.0  1  PfkB          pfkB family carbohydrate kinase
    0.00013   21.4   0.1    0.00025   20.5   0.1    1.4  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
      0.029   14.1   1.2       0.29   10.9   0.0    3.0  4  Robl_LC7      Roadblock/LC7 domain


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 !  188.0   0.3   4.1e-59   2.4e-55       4     301 ..      24     321 ..      21     322 .. 0.93

  Alignments for each domain:
  == domain 1  score: 188.0 bits;  conditional E-value: 4.1e-59
                                       EEEEEEEEEEEEEECSSH..........TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHH CS
                              PfkB   4 vvviGealidliavsekl..........egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflle 70 
                                       v+v+G +++dlia sek+          +++ ++  ++++  GG++ N A++la lg  ++ +g vG+ ++Ge++l+
  gi|330507700|ref|YP_004384128.1|  24 VLVVGGIIVDLIARSEKFkvvndnlcfpFDSKITLDQLSQDTGGSAHNLATNLAELGTTTYILGSVGKEDHGEEYLR 100
                                       899************************888888******************************************** PP

                                       HHHHTTEEETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHH CS
                              PfkB  71 elkkegvdtdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeav 147
                                       +l+ +g  t+yv  +e+  tg+ l+++ + ge t+++ rga+a l +e+l  + + + + d  ++ +l+s+  + a+
  gi|330507700|ref|YP_004384128.1| 101 NLRIHGAITKYVTLKEG-LTGMSLVFLYN-GEKTVLTSRGANALLGEEDL--NPEVFDKIDTMVLTSLISQ-ENMAL 172
                                       *********99996666.**********7.7****************987..9999999*******95444.56677 PP

                                       HHHHHHHHHHTTEEEEEECESSSHH...HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSS CS
                              PfkB 148 leelaeaaknggtfdpnlldplgaq...fkeallellaladllkpneeElealtgekledieealaalhklkakgak 221
                                       +++++e ak+ g  ++++ +p+ +      e+l++++  ++++++n +E   +tgek  d+++a+++l+     ga+
  gi|330507700|ref|YP_004384128.1| 173 MKKAIEEAKKRG--IYIITNPSMSMvnhRPEELKHAMHNSQVIIMNGKESMLITGEK--DVDSAIKKLKD---YGAE 242
                                       777777777777..899999999878888899*************************..99999999988...999* PP

                                       EEEEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTC CS
                              PfkB 222 tvvvtlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaias 298
                                       tv+vtl ++Galv +++ +++vp+ +kvkvvDttG GDsf++gf+ a  +g s eea++fa+avAal++ ++ga+++
  gi|330507700|ref|YP_004384128.1| 243 TVIVTLDVRGALVLDNERTFRVPS-YKVKVVDTTGGGDSFTAGFIHAKYHGYSNEEAVKFASAVAALNIVTPGASTD 318
                                       ************************.9*************************************************99 PP

                                       SCC CS
                              PfkB 299 lpt 301
                                       lp+
  gi|330507700|ref|YP_004384128.1| 319 LPS 321
                                       985 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   4.2e-08   0.00025     111     226 ..     202     304 ..     158     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.2e-08
                                       HHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEE CS
                      Phos_pyr_kin 111 alkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveele 187
                                        lk+  ++ ++vi+ N +E   ++g     e+d+++a kkl ++ga++V+++             +++d+e++++++
  gi|330507700|ref|YP_004384128.1| 202 ELKH-AMHNSQVIIMNGKESMLITG-----EKDVDSAIKKLKDYGAETVIVTLDVR----G---ALVLDNERTFRVP 265
                                       4444.778899*********99999.....99******************987752....2...3567********* PP

                                       EE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHH CS
                      Phos_pyr_kin 188 aerietknthGtGCtlssaiaaelakgesleeAvkkAke 226
                                       + +++  +t G G+++ +       +g+s eeAvk A +
  gi|330507700|ref|YP_004384128.1| 266 SYKVKVVDTTGGGDSFTAGFIHAKYHGYSNEEAVKFASA 304
                                       ******************9999999**********9975 PP

>> Robl_LC7  Roadblock/LC7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.86   5.2e+03      39      60 ..     159     181 ..     153     184 .. 0.64
   2 ?   -1.7   0.0      0.43   2.6e+03      65      87 ..     201     223 ..     195     224 .. 0.81
   3 ?   -0.6   0.0      0.19   1.2e+03      14      24 ..     249     259 ..     246     259 .. 0.89
   4 ?   10.9   0.0   4.9e-05      0.29      25      66 ..     284     327 ..     282     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.86
                                       HHHHHHHH.HHHHHHHHHHHHCT CS
                          Robl_LC7  39 dqlAalas.gllsaakaaarelg 60 
                                        +l +l+s  +++++k+a++e +
  gi|330507700|ref|YP_004384128.1| 159 MVLTSLISqENMALMKKAIEEAK 181
                                       55555554158999999988765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.43
                                       CEEEEEETTEEEEEEECTTTEEE CS
                          Robl_LC7  65 kelliegkkgelyltpagegalL 87 
                                       +el + +++ ++++++ +e +l+
  gi|330507700|ref|YP_004384128.1| 201 EELKHAMHNSQVIIMNGKESMLI 223
                                       67788999999***999996665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.19
                                       TECEEEEEETT CS
                          Robl_LC7  14 gvrgalvvskd 24 
                                       +vrgalv++++
  gi|330507700|ref|YP_004384128.1| 249 DVRGALVLDNE 259
                                       69*******96 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 4.9e-05
                                       S-EEEE.CCSSSS-HHHHHHHHHHHHHHHHHHHHHCT.SSSECE CS
                          Robl_LC7  25 Glviat.stldnddadqlAalasgllsaakaaarelg.egelke 66 
                                       G++ a  ++++n++a+++A+++++l + + +a+++l+ e+++ e
  gi|330507700|ref|YP_004384128.1| 284 GFIHAKyHGYSNEEAVKFASAVAALNIVTPGASTDLPsENDVVE 327
                                       66666679*****************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2388.34
//
Query:       gi|330507701|ref|YP_004384129.1|  [L=255]
Description: hypothetical protein MCON_1690 [Methanosaeta concilii GP6]
Scores for complete 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-68  229.3  16.9    5.2e-68  228.9  16.9    1.0  1  DUF1624        Protein of unknown function (DUF1624)
    3.7e-07   29.4  12.3    8.7e-05   21.6  10.4    2.5  2  OpgC_C         OpgC protein
    6.4e-07   28.7  30.9    0.00024   20.3  13.2    2.7  2  Acyl_transf_3  Acyltransferase family


Domain annotation for each model (and alignments):
>> DUF1624  Protein of unknown function (DUF1624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.9  16.9   8.8e-72   5.2e-68       2     223 .]       9     235 ..       9     235 .. 0.97

  Alignments for each domain:
  == domain 1  score: 228.9 bits;  conditional E-value: 8.8e-72
                           DUF1624   2 ieeiDalRGiAlilMiifHflfdLeffgylavslatsglwvvfarliaslFlfiaGvslvlahskslrw.......r 71 
                                       ++e+D+lRG+A+++M+ifH+ +dL+ff++ +++l+  g+w+++ar++aslFl+++G+sl+l++s+++          
  gi|330507701|ref|YP_004384129.1|   9 LWEVDFLRGLAIVMMVIFHLAYDLDFFRIHEIDLS-GGFWFYLARFTASLFLLLVGISLTLSYSRAKLAgqrnqypF 84 
                                       59*********************************.***************************99887788999999 PP

                           DUF1624  72 kflkRglkilaaallitaatylllpdsfivFGiLhlialalllallflrlpkalllllallilalglllreaifdlp 148
                                       + lkR l i+ +al it++ty+++ ++fivFGiLhli +++lla+++lrl++ +lll++++il lgl+++e  +d+ 
  gi|330507701|ref|YP_004384129.1|  85 RLLKRSLWIMSLALGITLVTYIVIGRGFIVFGILHLISISILLAYPLLRLGRMNLLLGLAAIL-LGLYIQELEVDFF 160
                                       9********************************************************666666.59*********** PP

                           DUF1624 149 lllwlglssekfetndYvplfPWfgvvllGialgkllyekgkrrlklpslpkaklvrplallGrhsLliYlihqp 223
                                       +l+wlgl++++f+++dYvpl+PWfgvvl+G+a g+lly+++ rr+ lp++++ + vr l++lGr+sL+iY++hqp
  gi|330507701|ref|YP_004384129.1| 161 WLIWLGLAPRSFTSLDYVPLLPWFGVVLMGMAGGALLYKDLGRRFPLPDISAWPPVRGLIFLGRNSLAIYILHQP 235
                                       **************************************************************************9 PP

>> OpgC_C  OpgC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6  10.4   1.5e-08   8.7e-05       3     129 ..      10     141 ..       9     167 .. 0.82
   2 !    7.0   0.0    0.0004       2.4     294     317 ..     213     236 ..     180     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.5e-08
                            OpgC_C   3 lrlDlfRGlalvlivvdHipgsvlskltlrnfGfsda.........AevFVflSGlavglvYgraaeregalaaaar 70 
                                       +++D++RGla+v++v+ H+  ++   + ++++ +s +         A +F +l G+++ l Y+ra  + ++++   r
  gi|330507701|ref|YP_004384129.1|  10 WEVDFLRGLAIVMMVIFHLAYDLD-FFRIHEIDLSGGfwfylarftASLFLLLVGISLTLSYSRAKLAGQRNQYPFR 85 
                                       79*****************55532.2444444443322222224449****************************** PP

                            OpgC_C  71 ilrRawelYvahiallvlvlaliallallfeesdlieelnlepllekplealvalllLk 129
                                       +l+R + +   +++++++++++i   +++f    +++ ++++ ll+ pl  l ++ lL+
  gi|330507701|ref|YP_004384129.1|  86 LLKRSLWIMSLALGITLVTYIVIGRGFIVF---GILHLISISILLAYPLLRLGRMNLLL 141
                                       ***********************9999977...89999999999999998887776664 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0004
                            OpgC_C 294 aavlrplillGrhsLavFvvgvvl 317
                                       ++++r li lGr+sLa+++++  l
  gi|330507701|ref|YP_004384129.1| 213 WPPVRGLIFLGRNSLAIYILHQPL 236
                                       678899**************9755 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3  13.2     4e-08   0.00024       3     100 ..      11     112 ..       9     127 .. 0.79
   2 !   10.1  13.0   5.1e-05       0.3     246     312 ..     159     245 ..     112     254 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4e-08
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxx RF
                     Acyl_transf_3   3 ylDllRgiAillVvflHaliayspdagrgspiqasqssqiaflggfgvplFFllSGffla......amlyrrrglsk 73 
                                       ++D lRg+Ai+++v++H ++ ++ +  +  +    ++   ++l +f  +lF+ll G  l+      +    r  ++ 
  gi|330507701|ref|YP_004384129.1|  11 EVDFLRGLAIVMMVIFHLAYDLDFFRIHEIDLSGGFW---FYLARFTASLFLLLVGISLTlsysraKLAGQRNQYPF 84 
                                       68******************77665555554444433...49******************99999877777777777 PP

                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3  74 likrRilrll.iplliwllliillialv 100
                                        + +R l ++ ++l i+l+++i++   +
  gi|330507701|ref|YP_004384129.1|  85 RLLKRSLWIMsLALGITLVTYIVIGRGF 112
                                       7788888888899999999998887655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 5.1e-05
                                       x............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxx RF
                     Acyl_transf_3 246 g............gglvasvliqsaslllvslgimllllllfalpsrsafk............llrylgkiSygiYl 298
                                                     +    +l + + l+++ + +m+    +++++++ +++             l++lg++S++iY+
  gi|330507701|ref|YP_004384129.1| 159 FfwliwlglaprsFT----SLDYVPLLPWFGVVLMGMAGGALLYKDLGRRFplpdisawppvrGLIFLGRNSLAIYI 231
                                       044444433222222....455555555555555555555555555555555667778799999************* PP

                                       xxxxxxxxxxxxxx RF
                     Acyl_transf_3 299 iHlpllmllqkllr 312
                                       +H+pll  l +l  
  gi|330507701|ref|YP_004384129.1| 232 LHQPLLLGLIYLAE 245
                                       *******9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); 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:                         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 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1882.98
//
Query:       gi|330507702|ref|YP_004384130.1|  [L=239]
Description: acylphosphatase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-18   67.0   1.9      3e-18   66.0   0.1    2.3  3  Acylphosphatase  Acylphosphatase
    3.3e-05   24.0   5.2       0.14   12.2   0.3    2.9  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    8.8e-05   22.6  10.3    0.00016   21.8   8.4    2.1  1  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
    0.00018   21.5  15.7     0.0003   20.7  15.5    1.5  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
     0.0009   19.4   6.7     0.0044   17.2   1.1    4.1  2  Halo_GVPC        Halobacterial gas vesicle protein C (GVPC) r
     0.0023   17.2  11.1     0.0054   16.0  11.1    1.6  1  DLP_helical      Dynamin-like helical domain
  ------ inclusion threshold ------
      0.013   15.0   6.7      0.054   13.0   2.2    2.7  2  Fzo_mitofusin    fzo-like conserved region
      0.021   14.7   5.9      0.032   14.1   5.9    1.4  1  PIN_8            PIN like domain
      0.031   13.8  10.9      0.041   13.3  10.9    1.3  1  Golgin_A5        Golgin subfamily A member 5
      0.037   13.4  12.1      0.025   13.9  10.1    1.7  2  DUF4407          Domain of unknown function (DUF4407)
      0.038   12.0   6.0      0.051   11.5   6.0    1.1  1  Prominin         Prominin
      0.043   14.4  11.6       0.14   12.8   8.0    2.5  2  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
      0.045   13.6   0.1        4.7    7.1   0.1    2.3  2  DUF720           Protein of unknown function (DUF720)
      0.054   13.5   0.7        1.1    9.2   0.5    2.3  2  ApoO             Apolipoprotein O
      0.063   12.8   0.7       0.24   10.9   0.7    1.8  1  Lant_dehydr_C    Lantibiotic biosynthesis dehydratase C-term
      0.081   11.2   1.3       0.18   10.0   0.1    1.9  2  Fusion_gly       Fusion glycoprotein F0
      0.083   13.0   4.5        0.1   12.7   2.4    2.1  2  DUF148           Domain of unknown function DUF148
      0.087   12.9  13.9       0.66   10.0   2.6    3.0  3  DUF1664          Protein of unknown function (DUF1664)
        0.1   11.5  16.3       0.57    9.0   8.4    2.0  2  Spc7             Spc7 kinetochore protein
       0.11   13.0  12.3        3.9    8.1   0.6    3.0  2  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.12   12.4  15.6        2.9    7.9   8.6    2.4  2  DUF1640          Protein of unknown function (DUF1640)
       0.15   11.3   0.7        0.3   10.4   0.6    1.5  1  GCS2             Glutamate-cysteine ligase family 2(GCS2)
       0.24   11.3   3.0        9.8    6.1   0.6    2.5  2  DUF1706          Protein of unknown function (DUF1706)
       0.27    8.7  13.6        0.6    7.5  13.5    1.6  1  DUF3584          Protein of unknown function (DUF3584)
       0.27   10.3  13.7          2    7.4  13.7    2.0  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.32   11.1   9.0        1.9    8.6   2.1    3.6  3  Vps51            Vps51/Vps67
       0.34   11.1   5.4       0.42   10.8   0.7    2.5  2  DUF3958          Protein of unknown function (DUF3958)
       0.38   11.5  11.0        1.3    9.8   5.6    2.9  3  DUF2203          Uncharacterized conserved protein (DUF2203)
       0.39   10.8  12.3       0.39   10.8   6.4    2.7  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.63   10.6  19.8        3.2    8.3   5.7    3.8  2  YtxH             YtxH-like protein
       0.83    9.6  18.2        1.9    8.4   1.0    2.7  2  RRF              Ribosome recycling factor
       0.96   10.3  17.5        1.9    9.4   4.8    3.2  3  FliT             Flagellar protein FliT
          1    9.9   8.1        6.7    7.2   2.4    3.0  3  Arm-DNA-bind_5   Arm DNA-binding domain
        1.1    9.9  13.4         25    5.5   1.0    2.8  2  DUF883           Bacterial protein of unknown function (DUF88
        2.5    8.3  10.7         10    6.4   1.1    3.3  3  Cnn_1N           Centrosomin N-terminal motif 1
        2.7    8.3   7.1        7.6    6.9   4.9    2.3  2  DUF2390          Protein of unknown function (DUF2390)
        2.8    7.8  20.8        1.6    8.6   1.8    3.5  3  CdvA             CdvA-like coiled-coil domain
        4.4    7.6  18.9        6.5    7.1   0.1    4.5  3  DUF3618          Protein of unknown function (DUF3618)
        4.7    7.4  11.1        7.8    6.7   2.8    3.2  3  Med9             RNA polymerase II transcription mediator com
        4.7    7.4   5.9          4    7.6   3.2    2.2  2  IFP_35_N         Interferon-induced 35 kDa protein (IFP 35) N
          5    6.8   9.7        4.2    7.0   8.1    1.7  1  Med4             Vitamin-D-receptor interacting Mediator subu
        5.2    6.2   5.4          4    6.6   3.4    1.7  3  TMPIT            TMPIT-like protein
        5.2    7.6  11.0        3.3    8.2   1.8    3.2  3  NPV_P10          Nucleopolyhedrovirus P10 protein
        6.7    7.0   9.7         12    6.1   1.7    3.2  3  DUF3216          Protein of unknown function (DUF3216)
        7.5    6.7  10.0         42    4.3   3.0    2.4  2  Fib_alpha        Fibrinogen alpha/beta chain family
        8.1    6.8  14.6         23    5.4   2.7    2.3  2  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
        9.7    6.6  10.9        0.4   11.0   2.8    2.7  2  RICH             RICH domain


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.1   7.8e-21     3e-18       2      83 ..       5      86 ..       4      88 .. 0.97
   2 ?   -0.7   0.1         5   1.9e+03      51      59 ..     137     145 ..      98     179 .. 0.63
   3 ?   -1.2   0.1       7.5   2.9e+03      50      61 ..     190     201 ..     150     221 .. 0.54

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 7.8e-21
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      +++++G+VQ+ g+R+ v ++A+++gl+Gyv+Nl+dg+V++vaeg++ ++ ++l+++  +++ ++v +++ e +++++ef
  gi|330507702|ref|YP_004384130.1|  5 TAYISGKVQKTGYRARVVSIARDFGLTGYVQNLDDGRVKVVAEGQDYDLGSLLAAIDIKNTLIQVADIQKEYSAAANEF 83
                                      679**************************************************************************** PP

                   Acylphosphatase 81 kdF 83
                                      ++F
  gi|330507702|ref|YP_004384130.1| 84 QGF 86
                                      999 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 5
                   Acylphosphatase  51 ekfleelks 59 
                                       e+++ee+++
  gi|330507702|ref|YP_004384130.1| 137 EELKEEIRA 145
                                       344444444 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 7.5
                   Acylphosphatase  50 vekfleelksgp 61 
                                        + + e++ s +
  gi|330507702|ref|YP_004384130.1| 190 ADLLAEKIDSAK 201
                                       222333333333 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.3    0.0004      0.15      12      92 ..      47     126 ..      34     130 .. 0.79
   2 !    7.8   0.1    0.0085       3.3      20      85 ..     116     177 ..     111     183 .. 0.72
   3 !   12.2   0.3   0.00036      0.14      24      99 ..     156     235 ..     149     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0004
                      Baculo_PEP_C  12 gnqfldLtnvLnairlqnvqi.laqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneL 87 
                                        +q  dL  +L+ai  +n+ i +a++++   a +++++ + + ++  + e d+r+d++++ L+  l ++++++ +e+
  gi|330507702|ref|YP_004384130.1|  47 EGQDYDLGSLLAAIDIKNTLIqVADIQKEYSAAANEFQGFFKVVSG-SGETDQRIDQAAELLK-ELISVNKDVLKEI 121
                                       57899*******9988777552299999999999999999886666.9999****99877665.5667898888888 PP

                      Baculo_PEP_C  88 tnlns 92 
                                       +++  
  gi|330507702|ref|YP_004384130.1| 122 KATRV 126
                                       87765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0085
                      Baculo_PEP_C  20 nvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrn 85 
                                       +vL+ i++  v++  ++ ++ +++++++ a  +++k+   e+    +++  +L+d +    d+l+ 
  gi|330507702|ref|YP_004384130.1| 116 DVLKEIKATRVELKDEIRATREELKEEIRATRDEVKATRDEV----KATRVELKDEIRVTRDDLKA 177
                                       589999999999999999999999999999999999955554....45555555555544455544 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00036
                      Baculo_PEP_C  24 airlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq....dtlrneLtnlnsiltn 96 
                                        +++  v++  ++  + d+++ ++  + +++ks+   l++++d++ +++  ++  +     d+l+++L  ++ ++++
  gi|330507702|ref|YP_004384130.1| 156 EVKATRVELKDEIRVTRDDLKAEIVGVRDQVKSSADLLAEKIDSAKEEIAVSIDDIRsdyrDDLTERLAKIEEDISQ 232
                                       56777888888999999999999999999999999999999999999999999999999999999999999999988 PP

                      Baculo_PEP_C  97 Lls 99 
                                       + +
  gi|330507702|ref|YP_004384130.1| 233 IKA 235
                                       765 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 !   21.8   8.4   4.2e-07   0.00016      19     129 ..     102     212 ..      79     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.2e-07
                         ApoLp-III  19 sqeevvetiKensenlvdqlkqvikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQsg 95 
                                       ++ e ++++    + +++++k++  +l++e+  + +el+e ++ ++++++ t+d++++ + e+k ++  ++  + + 
  gi|330507702|ref|YP_004384130.1| 102 QAAELLKELISVNKDVLKEIKATRVELKDEIRATREELKEEIRATRDEVKATRDEVKATRVELKDEIRVTRDDLKAE 178
                                       45566666666778899999999999999999999999999999999999999999999999999999999999998 PP

                         ApoLp-III  96 vqslvkesqklaeslkensqeakeklakaikqay 129
                                       +  +  +++  a  l e++  ake++a  i  + 
  gi|330507702|ref|YP_004384130.1| 179 IVGVRDQVKSSADLLAEKIDSAKEEIAVSIDDIR 212
                                       8777777777777777777777777766655443 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7  15.5   7.9e-07    0.0003      11     141 ..     101     230 ..      93     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 7.9e-07
                                       HHHCCHHHCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHH CS
                    Apolipoprotein  11 ayaeeleeqlaplaqelrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerla 87 
                                        +a+el + l ++++++ + + +   el++++ra  ee+++ + + rdev+++  +++++ r +l+  ++  r+ l+
  gi|330507702|ref|YP_004384130.1| 101 DQAAELLKELISVNKDVLKEIKATRVELKDEIRATREELKEEIRATRDEVKAT-RDEVKATRVELKDEIRVTRDDLK 176
                                       57889999999999999999******************************876.789999***************** PP

                                       HCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-- CS
                    Apolipoprotein  88 adaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkesl 141
                                       a++  +++q+++ a+ l e+++++ e++   ++ ++ + r++l erl  ++e +
  gi|330507702|ref|YP_004384130.1| 177 AEIVGVRDQVKSSADLLAEKIDSAKEEIAVSIDDIRSDYRDDLTERLAKIEEDI 230
                                       *******************************************99999888765 PP

>> Halo_GVPC  Halobacterial gas vesicle protein C (GVPC) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       4.8   1.8e+03       3       9 ..      55      61 ..      54      61 .. 0.86
   2 !   17.2   1.1   1.1e-05    0.0044       9      30 ..     137     158 ..     128     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 4.8
                         Halo_GVPC  3 aLlaaIa 9 
                                      +LlaaI+
  gi|330507702|ref|YP_004384130.1| 55 SLLAAID 61
                                      8*****7 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.1e-05
                         Halo_GVPC   9 aafreefdatqdaFeaYadeFa 30 
                                       ++++ee++at+d+  a++de+ 
  gi|330507702|ref|YP_004384130.1| 137 EELKEEIRATRDEVKATRDEVK 158
                                       68899**************975 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  11.1   1.4e-05    0.0054      63     177 ..     109     232 ..      94     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                       DLP_helical  63 tkksvirdvlerqlpeaeerleelekevekleesakriekelaelkkeieearielreelkayfsdLilqvkgl..s 137
                                         +sv +dvl++  ++  e  +e+ + +e+l+e+ + +++e++ ++ e++ +r el++e++  ++dL  ++ g+  +
  gi|330507702|ref|YP_004384130.1| 109 ELISVNKDVLKEIKATRVELKDEIRATREELKEEIRATRDEVKATRDEVKATRVELKDEIRVTRDDLKAEIVGVrdQ 185
                                       45899******99999999999*************************************************998334 PP

                       DLP_helical 138 letieeFlereiGdegivvgtkl.......eneferqlekiseeisk 177
                                       +++ +++l ++i +  +++   +       + +++++l ki e+is+
  gi|330507702|ref|YP_004384130.1| 186 VKSSADLLAEKIDSAKEEIAVSIddirsdyRDDLTERLAKIEEDISQ 232
                                       67888888888876666555544111000033344444444444444 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.2   0.00014     0.054      91     144 ..     113     167 ..      97     177 .. 0.79
   2 ?    4.4   0.9     0.063        24      98     130 ..     156     188 ..     151     238 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                     Fzo_mitofusin  91 cshqvqqelsstfarlcqqvdetekeleeeikelekeiekl.eevqkkakllrnk 144
                                       +++ v +e++ t  +l+ +++ t++el+eei++ + e+++  +ev+ +   l+++
  gi|330507702|ref|YP_004384130.1| 113 VNKDVLKEIKATRVELKDEIRATREELKEEIRATRDEVKATrDEVKATRVELKDE 167
                                       67899********************************997624555555556665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.063
                     Fzo_mitofusin  98 elsstfarlcqqvdetekeleeeikelekeiek 130
                                       e++ t  +l+ +++ t+++l++ei  ++ ++++
  gi|330507702|ref|YP_004384130.1| 156 EVKATRVELKDEIRVTRDDLKAEIVGVRDQVKS 188
                                       556666666666666666666666666666554 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   5.9   8.3e-05     0.032      18     136 ..      95     210 ..      64     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.3e-05
                             PIN_8  18 etrkdllkvlekladrlwvPhqvalEfqrnresviskekkayedlekeleklkkaaekkleealkkwakkkald... 91 
                                       et +++ ++ e l++ + v   v++E    r ++ ++ +++ e+l++e+++ ++++++     ++++ k ++++   
  gi|330507702|ref|YP_004384130.1|  95 ETDQRIDQAAELLKELISVNKDVLKEIKATRVELKDEIRATREELKEEIRATRDEVKA-----TRDEVKATRVElkd 166
                                       6677777788888888888888888888888888888888888888888888888883.....33333333333335 PP

                             PIN_8  92 .teelrkelkkqleelkeelkaeleelkksskadkeedpilkklee 136
                                         + +r++lk+++  +++++k +++ l +++++ k  ++i   +++
  gi|330507702|ref|YP_004384130.1| 167 eIRVTRDDLKAEIVGVRDQVKSSADLLAEKIDSAK--EEIAVSIDD 210
                                       56777777888888888877555555555555554..333333333 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 ?   13.3  10.9   0.00011     0.041      17     158 ..      98     236 ..      63     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                         Golgin_A5  17 arILQsKekliasLkegsgeeglesstalsael.delkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslr 92 
                                       +rI Q+ e l+++L + + ++ l+  +a+ +el de+++ r+ l+ee+ +++ +++  r e++ +  + + e++ +r
  gi|330507702|ref|YP_004384130.1|  98 QRIDQAAE-LLKELISVN-KDVLKEIKATRVELkDEIRATREELKEEIRATRDEVKATRDEVKATRVELKDEIRVTR 172
                                       56666666.555555433.4445555556666647889999999999999999999999999999999999999999 PP

                         Golgin_A5  93 eqlqeleeqleeerkakee.veaelerlkeelryleeelvrskatlqsrikdrekeieklrnqlttk 158
                                       + l+     ++ + k++ + + +++ + kee+ +  ++ +   ++++  +++r ++ie+  +q++ k
  gi|330507702|ref|YP_004384130.1| 173 DDLKAEIVGVRDQVKSSADlLAEKIDSAKEEIAVSIDDIR---SDYRDDLTERLAKIEEDISQIKAK 236
                                       8888777777766666655145678999999999888876...445555555555555555555544 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1         1   3.8e+02     153     197 ..      73     116 ..      59     130 .. 0.39
   2 ?   13.9  10.1   6.6e-05     0.025     115     225 ..     116     236 ..     103     239 .] 0.69

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1
                           DUF4407 153 earldalraeaqkeldgtk....gtgttgvaGkgpaakekkaqldaaqa 197
                                       +++++a+ +e+q    g +    g+g+t +++  +aa+  k+ +   + 
  gi|330507702|ref|YP_004384130.1|  73 QKEYSAAANEFQ----GFFkvvsGSGET-DQRIDQAAELLKELISVNKD 116
                                       333333333333....222222244433.23333333333333333333 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.6e-05
                           DUF4407 115 eqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaq 191
                                          +e+k+ + +l+++ +a+ +el+++i+a + e++a +++++a+r e+++e+  t+ +    +a    + ++ k+ 
  gi|330507702|ref|YP_004384130.1| 116 DVLKEIKATRVELKDEIRATREELKEEIRATRDEVKATRDEVKATRVELKDEIRVTRDDL---KAEIVGVRDQVKSS 189
                                       445677777778888899************************************877444...44444445555555 PP

                           DUF4407 192 ldaaqaelaelkakld.............atarlaalraelaeleae 225
                                       +d + ++++++k+++               t+rla+ ++ +++++a+
  gi|330507702|ref|YP_004384130.1| 190 ADLLAEKIDSAKEEIAvsiddirsdyrddLTERLAKIEEDISQIKAK 236
                                       55555555555555444444443555566666666666666666655 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   6.0   0.00013     0.051     244     373 ..     100     235 ..      95     238 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                          Prominin 244 llenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcl...... 314
                                       + ++ +  ke+++  ++++ke++ +  +L+d +r+ +++l++ +    ++ e + +++++++++++++ ++      
  gi|330507702|ref|YP_004384130.1| 100 IDQAAELLKELISVNKDVLKEIKATRVELKDEIRATREELKEEIRA--TRDEVKATRDEVKATRVELKDEIrvtrdd 174
                                       44555555555555567899*********************99999..44688888888888888888888644433 PP

                          Prominin 315 ..dqlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgre 373
                                          ++  v +++++  ++l+++++s+ +e   ++++i++  +++++e ++++ ++++++++
  gi|330507702|ref|YP_004384130.1| 175 lkAEIVGVRDQVKSSADLLAEKIDSAKEEIAVSIDDIRSDYRDDLTERLAKIEEDISQIKA 235
                                       4445556666666666666666666666666666666666666666666666666666654 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 ?   12.8   8.0   0.00036      0.14       3      70 ..     109     177 ..     103     195 .. 0.80
   2 ?    3.1   0.1      0.38   1.4e+02      19      55 ..     191     227 ..     177     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00036
                    HIP1_clath_bdg   3 dLLrKnAevtkqlsvarqa.qeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelar 70 
                                       +L+  n +v k + ++r + ++e+ ++++el+ee+++ ++e +   +e k +  +Lk e+  +r++l+ 
  gi|330507702|ref|YP_004384130.1| 109 ELISVNKDVLKEIKATRVElKDEIRATREELKEEIRATRDEVKATRDEVKATRVELKDEIRVTRDDLKA 177
                                       455669999999999998647899999999999999999999999999999999999999999988876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.38
                    HIP1_clath_bdg  19 rqaqeeverekkeleeelerlkeeaerkleeqkeele 55 
                                           e ++ +k+e++ ++++++++ +  l e+  ++e
  gi|330507702|ref|YP_004384130.1| 191 DLLAEKIDSAKEEIAVSIDDIRSDYRDDLTERLAKIE 227
                                       4455678888888888888888888888888877776 PP

>> DUF720  Protein of unknown function (DUF720)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1     0.012       4.7      73     118 ..      69     113 ..      35     119 .. 0.81
   2 ?    4.8   0.0     0.062        24      66     102 ..     129     165 ..     110     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.012
                            DUF720  73 Reaiqdqlsaarqraqvisssvntnsniiqqilqavsaliktlsdv 118
                                          iq++ saa ++ q   + v+      q+i qa   l+k l++v
  gi|330507702|ref|YP_004384130.1|  69 VADIQKEYSAAANEFQGFFKVVSGSGETDQRIDQAA-ELLKELISV 113
                                       467*******************99988888888875.588999988 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.062
                            DUF720  66 NqavsAsReaiqdqlsaarqraqvisssvntnsniiq 102
                                         ++ A Re +++++ a r++ ++   +v ++  +++
  gi|330507702|ref|YP_004384130.1| 129 KDEIRATREELKEEIRATRDEVKATRDEVKATRVELK 165
                                       45799***********************999987766 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.5    0.0028       1.1      12      57 ..     124     169 ..     109     177 .. 0.86
   2 ?    3.3   0.0       0.2        76      13      50 ..     172     209 ..     163     226 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0028
                              ApoO  12 ptdrLeegvrslRkslepytsavqdelnkvkskvetaeqsvtdtia 57 
                                        + +L+  +r +R++l++++ a+ de++ +++ v+ +   ++d+i 
  gi|330507702|ref|YP_004384130.1| 124 TRVELKDEIRATREELKEEIRATRDEVKATRDEVKATRVELKDEIR 169
                                       45679999**************************999999999886 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.2
                              ApoO  13 tdrLeegvrslRkslepytsavqdelnkvkskvetaeq 50 
                                       +d L++ +  +R ++++ ++ + ++++++k+ +  +  
  gi|330507702|ref|YP_004384130.1| 172 RDDLKAEIVGVRDQVKSSADLLAEKIDSAKEEIAVSID 209
                                       34555556666666666666666666666665554444 PP

>> Lant_dehydr_C  Lantibiotic biosynthesis dehydratase C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7   0.00063      0.24     192     262 ..     113     178 ..      80     238 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00063
                                       HHHTSTTHHH.HHHHHHHHHHHTHHHHHHHHHHHHHHHH-SSS-SS.....HHHHHHHHHHHHHHHHHHHH CS
                     Lant_dehydr_C 192 flaefsdtkkalrealdrkyraqrealearlravlaaaaepesegesadlppflaewaerlrelrrrleal 262
                                         + + ++ ka+r +l++++ra+re+l++ +ra++++++++++e +     +   e+  + r +r++l+a 
  gi|330507702|ref|YP_004384130.1| 113 VNKDVLKEIKATRVELKDEIRATREELKEEIRATRDEVKATRDEVK-----ATRVELKDEIRVTRDDLKAE 178
                                       4455556667799999999999999999999999999997655555.....45557777777777777664 PP

>> Fusion_gly  Fusion glycoprotein F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.74   2.8e+02      45      76 ..      97     127 ..      67     148 .. 0.76
   2 ?   10.0   0.1   0.00047      0.18     411     454 ..     152     195 ..     142     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.74
                                       CCHHHHHHHHHHHHHHHHHHHHHHHHCCEEEG CS
                        Fusion_gly  45 kkeleeykkaltelltpiadalnkieaeitvk 76 
                                        + +++  ++l+el+++ +d l++i+a  +v+
  gi|330507702|ref|YP_004384130.1|  97 DQRIDQAAELLKELISVNKDVLKEIKAT-RVE 127
                                       5678888888888888888888888866.322 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00047
                                       SS-TTTTCCGS----B---SHHHHHHHHHHHHHHHHHHHHHHHH CS
                        Fusion_gly 411 lanveaknlsiklgppisveevdisaelskvnesleqskdllee 454
                                       ++  e+k  +++l+ +i v ++d++ae+  v +++++s dll+e
  gi|330507702|ref|YP_004384130.1| 152 ATRDEVKATRVELKDEIRVTRDDLKAEIVGVRDQVKSSADLLAE 195
                                       56789999********************************9976 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.4   0.00027       0.1       4     101 ..      84     179 ..      81     187 .. 0.84
   2 ?   -0.4   0.0       3.2   1.2e+03      29      53 ..     213     228 ..     183     237 .. 0.45

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00027
                            DUF148   4 keffaIlknenltiaeieeqleawaekygv.tdeykefeakvkaqkeevkknvtavisnLssvqekleaIldnkslT 79 
                                       + ff++++ +  t++ i+++ e + e  +v +d +ke +a++ + k+e+++  ++  +++ +  ++++a  d+ + T
  gi|330507702|ref|YP_004384130.1|  84 QGFFKVVSGSGETDQRIDQAAELLKELISVnKDVLKEIKATRVELKDEIRATREELKEEIRATRDEVKATRDEVKAT 160
                                       6789999888888888887777777766661567899**************************************** PP

                            DUF148  80 rkeqkeaieelkkqypkevstl 101
                                       r e k++i+ +++ +++e   +
  gi|330507702|ref|YP_004384130.1| 161 RVELKDEIRVTRDDLKAE---I 179
                                       ***********9999999...4 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.2
                            DUF148  29 ekygvtdeykefeakvkaqkeevkk 53 
                                       +         +++ +++++ +++++
  gi|330507702|ref|YP_004384130.1| 213 S---------DYRDDLTERLAKIEE 228
                                       2.........222222222222222 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       3.4   1.3e+03      83     115 ..      63      95 ..      57     103 .. 0.77
   2 ?    6.7   5.4     0.019       7.2      53     104 ..     117     165 ..      95     179 .. 0.53
   3 ?   10.0   2.6    0.0017      0.66      54     122 ..     165     235 ..     162     238 .. 0.50

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.4
                           DUF1664  83 keikeevtevredlseigedvesvkeavegles 115
                                       k++  +v++++++ s+  ++++   ++v+g ++
  gi|330507702|ref|YP_004384130.1|  63 KNTLIQVADIQKEYSAAANEFQGFFKVVSGSGE 95 
                                       566678999999999999999999999987655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.019
                           DUF1664  53 vseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedve 104
                                       v ++++at+ +L+++i       +e ke ++++++ev++ r+++++++ +++
  gi|330507702|ref|YP_004384130.1| 117 VLKEIKATRVELKDEIRATR---EELKEEIRATRDEVKATRDEVKATRVELK 165
                                       34445555555554444333...33333344445555555555544444433 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0017
                           DUF1664  54 seslaatkrhLssridrvdkkldeqkei.skeikeevtevredlseigedve.svkeavegleskleriee 122
                                       +++++ t+++L+++i  v +++++++++ +++i++  +e+   +++i++d +  + e   ++e+ +++i++
  gi|330507702|ref|YP_004384130.1| 165 KDEIRVTRDDLKAEIVGVRDQVKSSADLlAEKIDSAKEEIAVSIDDIRSDYRdDLTERLAKIEEDISQIKA 235
                                       45555555555555555555555555431344555555555555555555431455555555555555544 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   8.4    0.0015      0.57     178     250 ..      95     168 ..      68     173 .. 0.63
   2 ?    8.5   2.7    0.0021      0.81     167     242 ..     163     236 ..     158     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                              Spc7 178 eleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkela.elqeqleeleekieelkeqkseleeei 250
                                       e  +++++  e  +el s++k+ L+e++ + +elk ei++ ++el+ e ++ ++e++++ +e+k+ + el++ei
  gi|330507702|ref|YP_004384130.1|  95 ETDQRIDQAAELLKELISVNKDVLKEIKATRVELKDEIRATREELKeEIRATRDEVKATRDEVKATRVELKDEI 168
                                       34444444444555566777777777777777777777766666541355666666666666666666666666 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0021
                              Spc7 167 ellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeq 242
                                       el++e++  +++l++e+   ++++++ +++  e++ +++ee+a    +i+  ++  ++l+e+l+++ee+i+++k++
  gi|330507702|ref|YP_004384130.1| 163 ELKDEIRVTRDDLKAEIVGVRDQVKSSADLLAEKIDSAKEEIAVSIDDIR--SDYRDDLTERLAKIEEDISQIKAK 236
                                       67889999999***************999********************9..88889**************99986 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 ?    8.1   5.2     0.011         4      35      96 ..     103     165 ..      66     179 .. 0.56
   2 ?    8.1   0.6      0.01       3.9       6      61 ..     182     234 ..     179     239 .] 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.011
                      Syntaxin-6_N  35 tseeldetrteLrkalrsiewdledLeetvriveknpsk.fkidekelsrrrafveevreevk 96 
                                         e l+e+ +  +  l++i+ +  +L++ +r+ +++ ++  + + +e++  r+ v+++r e+k
  gi|330507702|ref|YP_004384130.1| 103 AAELLKELISVNKDVLKEIKATRVELKDEIRATREELKEeIRATRDEVKATRDEVKATRVELK 165
                                       333333333334556666666666666666666555444466666666666666666666655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.01
                      Syntaxin-6_N   6 vkeeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLe 61 
                                       v+++V++s++ +++ +++ ++   +   s  +  ++ r++L + l +ie+d+++++
  gi|330507702|ref|YP_004384130.1| 182 VRDQVKSSADLLAEKIDSAKEEIAV---SIDDIRSDYRDDLTERLAKIEEDISQIK 234
                                       7899999999999999999763333...568889999***************9886 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   8.6    0.0077       2.9      60     146 ..     104     186 ..      95     189 .. 0.76
   2 ?    7.4  12.2     0.011       4.2      58     144 ..     124     213 ..     121     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0077
                           DUF1640  60 selrkevqisersefaalrseteklqreleklkqkLreeidklkadirldlnleKgrireelakleakiqelnnkid 136
                                       +el ke+ + ++   +++++ + +l+ e+ + +++L+eei  ++++++      + ++++   +l+++i+ +   ++
  gi|330507702|ref|YP_004384130.1| 104 AELLKELISVNKDVLKEIKATRVELKDEIRATREELKEEIRATRDEVK----ATRDEVKATRVELKDEIRVTRDDLK 176
                                       677788888888888888888888999999999999999888888854....5677777777777777777777777 PP

                           DUF1640 137 revsalrtei 146
                                        e+  +r ++
  gi|330507702|ref|YP_004384130.1| 177 AEIVGVRDQV 186
                                       7777777665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                           DUF1640  58 alselrkevqise...rsefaalrseteklqreleklkqkLreeidklkadirldlnleKgrireelakleakiqel 131
                                          el++e++  +   ++e+ a r e ++ + e+++ + +L++ei  +++d + ++   + +++     l +ki+  
  gi|330507702|ref|YP_004384130.1| 124 TRVELKDEIRATReelKEEIRATRDEVKATRDEVKATRVELKDEIRVTRDDLKAEIVGVRDQVKSSADLLAEKIDSA 200
                                       55678888887776667899999999999999999999999999999999999999999999999999999999888 PP

                           DUF1640 132 nnkidrevsalrt 144
                                       ++ i  ++ ++r+
  gi|330507702|ref|YP_004384130.1| 201 KEEIAVSIDDIRS 213
                                       8888888877775 PP

>> GCS2  Glutamate-cysteine ligase family 2(GCS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00079       0.3      33      77 ..     112     156 ..      89     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00079
                                       S.SSEEEE-SSTTEEEEE--SBSSHHHHHHHHHHHHHHHHHHHHH CS
                              GCS2  33 seggsvvkelpegqvElstapleslaeaaeeisadleelrsvade 77 
                                       s ++ v ke++   vEl+  + ++ +e+ eei+a+++e+++  de
  gi|330507702|ref|YP_004384130.1| 112 SVNKDVLKEIKATRVELKDEIRATREELKEEIRATRDEVKATRDE 156
                                       345799*********************************987665 PP

>> DUF1706  Protein of unknown function (DUF1706)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.6     0.026       9.8       4      37 ..     122     155 ..     119     161 .. 0.82
   2 ?    5.7   0.1     0.033        13       4      38 ..     158     199 ..     156     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.026
                                       SSSHHHHHHHHHHHHHHHHHTTTTS-GGGT...T CS
                           DUF1706   4 pqsKeeLleaieknfekLiklidsipeeekkape 37 
                                       ++++ eL+++i+ ++e+L ++i++  +e k +++
  gi|330507702|ref|YP_004384130.1| 122 KATRVELKDEIRATREELKEEIRATRDEVKATRD 155
                                       57999*****************999999886654 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.033
                                       SSSHHHHHHHHHHHHHHHHHTTTTS-GGGT..........T- CS
                           DUF1706   4 pqsKeeLleaieknfekLiklidsipeeekkap.......ee 38 
                                       ++++ eL+++i+ ++++L ++i  + ++ k+++       + 
  gi|330507702|ref|YP_004384130.1| 158 KATRVELKDEIRVTRDDLKAEIVGVRDQVKSSAdllaekiDS 199
                                       67999*****************99999999877555443333 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  13.5    0.0016       0.6     619     765 ..     115     222 ..      67     238 .. 0.42

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0016
                           DUF3584 619 eakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklekaiaerkqqaeeqlqkldaqlkq 695
                                       ++  k++ +                                        +++l+  i + +++ +e+++    + k+
  gi|330507702|ref|YP_004384130.1| 115 KDVLKEIKA---------------------------------------TRVELKDEIRATREELKEEIRATRDEVKA 152
                                       333333333.......................................33333333333333333333333333333 PP

                           DUF3584 696 leeqqkaaleelkedlseerlekkakwqevvgeldeqlaelkkaieaartqakarlkeleeaykreLksk 765
                                          + ka   elk++++  r + ka++  v  + + + + l ++i++a+++ +  ++ +  +y+++L ++
  gi|330507702|ref|YP_004384130.1| 153 TRDEVKATRVELKDEIRVTRDDLKAEIVGVRDQVKSSADLLAEKIDSAKEEIAVSIDDIRSDYRDDLTER 222
                                       3333333333333333333333333333333333333333333333333333333333333333333332 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  13.7    0.0053         2      43     126 ..      98     198 ..      60     238 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0053
                             Atg14  43 kkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk....... 112
                                       ++i++a       e l++ i  +k+ l+e+k+++ +l   + e+++++++lk+ei++++ ++++ +d++k       
  gi|330507702|ref|YP_004384130.1|  98 QRIDQAA------ELLKELISVNKDVLKEIKATRVEL---KDEIRATREELKEEIRATRDEVKATRDEVKatrvelk 165
                                       2222222......333355555566666666665555...4567778888888888888888888888885555444 PP

                             Atg14 113 ...................kRrsdleslqnele 126
                                                          + +s++++l +++ 
  gi|330507702|ref|YP_004384130.1| 166 deirvtrddlkaeivgvrdQVKSSADLLAEKID 198
                                       444444443333333333333333333333333 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.1    0.0049       1.9      10      44 ..     105     141 ..      96     153 .. 0.77
   2 ?    4.3   0.3      0.11        43      19      46 ..     152     179 ..     144     195 .. 0.88
   3 ?   -0.1   0.0       2.6     1e+03      57      71 ..     220     234 ..     188     238 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0049
                             Vps51  10 ayvrellakst..lkellkveasllseiraldselka 44 
                                       ++++el++ ++  lke+++++ +l+ eira+ +elk+
  gi|330507702|ref|YP_004384130.1| 105 ELLKELISVNKdvLKEIKATRVELKDEIRATREELKE 141
                                       5555565555444899999999999999999999997 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.11
                             Vps51  19 stlkellkveasllseiraldselkalV 46 
                                       +t +e+++++ +l+ eir +  +lka +
  gi|330507702|ref|YP_004384130.1| 152 ATRDEVKATRVELKDEIRVTRDDLKAEI 179
                                       667899*******************866 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.6
                             Vps51  57 sdtIrkmksemdkld 71 
                                       ++ ++k+++++++++
  gi|330507702|ref|YP_004384130.1| 220 TERLAKIEEDISQIK 234
                                       233333333333333 PP

>> DUF3958  Protein of unknown function (DUF3958)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7    0.0011      0.42      22      99 ..      64     141 ..      52     150 .. 0.90
   2 ?    2.2   0.1      0.54   2.1e+02      63      98 ..     152     187 ..     147     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0011
                           DUF3958  22 kelkkqeqlkeeyeehfnqskrlfdelletfrkdeeshlfeklrdevqrlsrklredLEeeeeeLkrekrqLedqee 98 
                                         l ++  +++ey    n+ + +f+ ++   ++d++     +l +e+++ ++++ +++  ++ eLk e r+ ++++ 
  gi|330507702|ref|YP_004384130.1|  64 NTLIQVADIQKEYSAAANEFQGFFKVVSGSGETDQRIDQAAELLKELISVNKDVLKEIKATRVELKDEIRATREELK 140
                                       566678899*************************************************************9999987 PP

                           DUF3958  99 e 99 
                                       e
  gi|330507702|ref|YP_004384130.1| 141 E 141
                                       7 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.54
                           DUF3958  63 klrdevqrlsrklredLEeeeeeLkrekrqLedqee 98 
                                       + rdev  +  +l++++  +++ Lk e + ++dq+ 
  gi|330507702|ref|YP_004384130.1| 152 ATRDEVKATRVELKDEIRVTRDDLKAEIVGVRDQVK 187
                                       5799999999*****************999999985 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.4    0.0065       2.5      10      78 ..      64     130 ..      60     134 .. 0.84
   2 ?    9.8   5.6    0.0033       1.3       7      78 ..     102     166 ..      95     179 .. 0.71
   3 ?    2.2   0.4      0.76   2.9e+02      24      69 ..     181     233 ..     167     238 .. 0.43

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0065
                           DUF2203  10 alLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkd 78 
                                       ++L ++ ++ +e+ a+++e++   + ++ + ++ ++    ++++ l+el +  +++++ei+++ ve+kd
  gi|330507702|ref|YP_004384130.1|  64 NTLIQVADIQKEYSAAANEFQGFFKVVSGSGETDQR--IDQAAELLKELISVNKDVLKEIKATRVELKD 130
                                       678889999999999999999988877777766543..78899999**********************9 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0033
                           DUF2203   7 eAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkd 78 
                                       +A +lL +l ++ +++    ke++ ++ el+++ ++    +++el++e+++ ++e++++ +e++++ ve+kd
  gi|330507702|ref|YP_004384130.1| 102 QAAELLKELISVNKDVL---KEIKATRVELKDEIRA----TREELKEEIRATRDEVKATRDEVKATRVELKD 166
                                       44444444444444443...4444444455554444....3889***************************9 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.76
                           DUF2203  24 alrkeleeleeeleeakaeaekse.......aaeleaeleeleaeieelveei 69 
                                        +r+++++ ++ l+e+ ++a+++        ++  + +l+e  a+iee +++i
  gi|330507702|ref|YP_004384130.1| 181 GVRDQVKSSADLLAEKIDSAKEEIavsiddiRSDYRDDLTERLAKIEEDISQI 233
                                       44444444444444444433322222233333333333333333333333333 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 ?   10.8   6.4     0.001      0.39      52     109 ..     114     172 ..      95     177 .. 0.85
   2 ?    2.9   0.4      0.29   1.1e+02      67      94 ..     184     211 ..     170     237 .. 0.43

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.001
                        TPR_MLP1_2  52 haedvkelqalreel.nelkaeiaelkaeaesakaeleeseesweeqkeelekelsele 109
                                       +++ +ke++a+r el +e++a+++elk+e  +++ e+++ + + + ++ el++e++ ++
  gi|330507702|ref|YP_004384130.1| 114 NKDVLKEIKATRVELkDEIRATREELKEEIRATRDEVKATRDEVKATRVELKDEIRVTR 172
                                       45668999999999978999**********************************98765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.29
                        TPR_MLP1_2  67 nelkaeiaelkaeaesakaeleeseesw 94 
                                       +++k+ +  l ++ +sak+e++ s   +
  gi|330507702|ref|YP_004384130.1| 184 DQVKSSADLLAEKIDSAKEEIAVSIDDI 211
                                       3444444444444444444444443333 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0  10.8      0.81   3.1e+02      25      66 ..     134     171 ..      61     179 .. 0.72
   2 ?    8.3   5.7    0.0085       3.2      25      72 ..     170     206 ..     158     237 .. 0.55

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.81
                              YtxH  25 etRkdlkekaddlkekakelleeakekakekaedlkekvkek 66 
                                        tR++lke+  ++++ +k + +e+    k +  +lk++++ +
  gi|330507702|ref|YP_004384130.1| 134 ATREELKEEIRATRDEVKATRDEV----KATRVELKDEIRVT 171
                                       344444444444444444443333....55555555555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0085
                              YtxH  25 etRkdlkekaddlkekakelleeakekakekaedlkekvkekadelke 72 
                                        tR+dlk +   +++++           k++a+ l+ek+++  +e++ 
  gi|330507702|ref|YP_004384130.1| 170 VTRDDLKAEIVGVRDQV-----------KSSADLLAEKIDSAKEEIAV 206
                                       35555555555555555...........55555555555444444432 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   8.6     0.015       5.6      92     142 ..     115     167 ..     112     185 .. 0.79
   2 ?    8.4   1.0     0.005       1.9      92     132 ..     191     231 ..     179     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..S-HHHHHHHHHHHHHH CS
                               RRF  92 kelvkeakkaaekakvairniRrdankklkklekk..iseDdvkkaekeiqkl 142
                                       k++ ke+k+   + k++ir  R++ ++++++ + +   ++D+vk    e+++ 
  gi|330507702|ref|YP_004384130.1| 115 KDVLKEIKATRVELKDEIRATREELKEEIRATRDEvkATRDEVKATRVELKDE 167
                                       7899*************************876665556777777776666554 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.005
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS-HHHH CS
                               RRF  92 kelvkeakkaaekakvairniRrdankklkklekkiseDdv 132
                                       + l++++ +a e++ v+i +iR+d++++l +   ki eD  
  gi|330507702|ref|YP_004384130.1| 191 DLLAEKIDSAKEEIAVSIDDIRSDYRDDLTERLAKIEEDIS 231
                                       5688999999*******************877667877764 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.8     0.005       1.9      33      77 ..     104     148 ..      67     154 .. 0.55
   2 ?    6.8   2.4     0.031        12      38      81 ..     134     177 ..     133     179 .. 0.89
   3 ?    3.9   1.8      0.26        98      31      77 ..     190     235 ..     174     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.005
                                       ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTHH CS
                              FliT  33 aplspaereekrellrrilandaeirallqprldelqkllgalrr 77 
                                       a+l  ++     ++l++i a   e+++ +++ ++el+++++a+r 
  gi|330507702|ref|YP_004384130.1| 104 AELLKELISVNKDVLKEIKATRVELKDEIRATREELKEEIRATRD 148
                                       133333334444444455555555555555555555555555555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.031
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTHHHHHH CS
                              FliT  38 aereekrellrrilandaeirallqprldelqkllgalrrqrka 81 
                                       a ree+ e +r  +++ +++r+ +++ + el+++++ +r   ka
  gi|330507702|ref|YP_004384130.1| 134 ATREELKEEIRATRDEVKATRDEVKATRVELKDEIRVTRDDLKA 177
                                       56899999999************************999887665 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.26
                                       --ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTHH CS
                              FliT  31 daaplspaereekrellrrilandaeirallqprldelqkllgalrr 77 
                                       + + l++    +k+e+   i ++    r+ l +rl+++++++++++ 
  gi|330507702|ref|YP_004384130.1| 190 A-DLLAEKIDSAKEEIAVSIDDIRSDYRDDLTERLAKIEEDISQIKA 235
                                       4.6677777888899999999999999**************999875 PP

>> Arm-DNA-bind_5  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   2.4     0.018       6.7      45      80 ..     116     151 ..     104     159 .. 0.78
   2 ?    1.3   0.0       1.3   4.8e+02      53      84 ..     158     192 ..     147     194 .. 0.70
   3 ?    4.6   0.4      0.12        44      49      78 ..     184     214 ..     158     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.018
                    Arm-DNA-bind_5  45 gkvkerepntlelnskirqerekledivrklrqkek 80 
                                         +ke +  + el+ +ir+ re+l++++r+ r++ k
  gi|330507702|ref|YP_004384130.1| 116 DVLKEIKATRVELKDEIRATREELKEEIRATRDEVK 151
                                       344677777999*****************9998866 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.3
                    Arm-DNA-bind_5  53 n..tlelnskirqerekledivrklrqkek.tael 84 
                                       +  + el+ +ir  r+ l+ ++   r++ k +a+l
  gi|330507702|ref|YP_004384130.1| 158 KatRVELKDEIRVTRDDLKAEIVGVRDQVKsSADL 192
                                       23478899999999999888888888888766665 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.12
                    Arm-DNA-bind_5  49 erepn.tlelnskirqerekledivrklrqk 78 
                                       ++ +  +  l++ki++ +e+++  ++++r++
  gi|330507702|ref|YP_004384130.1| 184 DQVKSsADLLAEKIDSAKEEIAVSIDDIRSD 214
                                       4444467789999999999999999998876 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   9.8     0.099        38      15      56 ..     118     159 ..      94     199 .. 0.59
   2 ?    5.5   1.0     0.067        25      11      49 ..     179     217 ..     162     237 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.099
                            DUF883  15 eellkeaadeageeaeelRerleerlerarerlrdaeeavae 56 
                                        + +k++  e ++e+++ Re+l+e+++++r+++++++++v++
  gi|330507702|ref|YP_004384130.1| 118 LKEIKATRVELKDEIRATREELKEEIRATRDEVKATRDEVKA 159
                                       333333444445555555566666666666666655555544 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.067
                            DUF883  11 ladleellkeaadeageeaeelRerleerlerarerlrd 49 
                                       +  +++ +k++ad  +e++++++e++  ++++ r+  rd
  gi|330507702|ref|YP_004384130.1| 179 IVGVRDQVKSSADLLAEKIDSAKEEIAVSIDDIRSDYRD 217
                                       333344455666666666666666666666666665554 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   3.5     0.055        21      36      69 ..     116     149 ..      91     153 .. 0.71
   2 ?    6.4   1.1     0.027        10      35      62 ..     148     178 ..     139     190 .. 0.76
   3 ?    1.0   0.1       1.3   4.8e+02      18      44 ..     174     203 ..     174     235 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.055
                            Cnn_1N  36 eqkeellkenielkveveslqkelkekkkllrea 69 
                                       +  +e+ ++++elk+e+   + elke  +  r+ 
  gi|330507702|ref|YP_004384130.1| 116 DVLKEIKATRVELKDEIRATREELKEEIRATRDE 149
                                       5567888889999999999999999877666665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.027
                            Cnn_1N  35 e...eqkeellkenielkveveslqkelkek 62 
                                       +    +++e+ ++++elk+e+   +++lk+ 
  gi|330507702|ref|YP_004384130.1| 148 DevkATRDEVKATRVELKDEIRVTRDDLKAE 178
                                       3455789999***********9999999875 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.3
                            Cnn_1N  18 dLKLriyfLeerleklse...eqkeellke 44 
                                       dLK +i   +++++ +++   e+++++ +e
  gi|330507702|ref|YP_004384130.1| 174 DLKAEIVGVRDQVKSSADllaEKIDSAKEE 203
                                       677777777777777777665444444443 PP

>> DUF2390  Protein of unknown function (DUF2390)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.9      0.02       7.6      53      97 ..     116     164 ..      93     170 .. 0.62
   2 ?    4.9   1.3     0.086        33      43     102 ..     142     197 ..     139     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.02
                           DUF2390  53 aleaavaewreevvkplRalRralkaaase.dea.ealreqlka..vEL 97 
                                       ++ +++++ r e+  ++Ra R++lk++ ++ +++ +a r+++ka  vEL
  gi|330507702|ref|YP_004384130.1| 116 DVLKEIKATRVELKDEIRATREELKEEIRAtRDEvKATRDEVKAtrVEL 164
                                       4455566666666666677777777666665334566666666422455 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.086
                           DUF2390  43 graldaeelaaleaavaewreevvkplRalRralkaaasedeaealreqlka.vELeaErv 102
                                       +++++++e++a +++v++ r e+  ++R  R  lka+        +r+q+k+ + L aE++
  gi|330507702|ref|YP_004384130.1| 142 EIRATRDEVKATRDEVKATRVELKDEIRVTRDDLKAEIV-----GVRDQVKSsADLLAEKI 197
                                       567788899999999999999999999999999999987.....57777764256777765 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.6     0.031        12      23      59 ..     110     146 ..      97     151 .. 0.77
   2 ?    5.7   7.5     0.032        12       5      58 ..     117     170 ..     114     193 .. 0.80
   3 ?    8.6   1.8    0.0041       1.6       8      61 ..     178     235 ..     177     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.031
                              CdvA  23 ikekleealkklkekakelkeklkkrlkeledqiksl 59 
                                       +    ++ lk++k+++ elk+++++  +el+++i+++
  gi|330507702|ref|YP_004384130.1| 110 LISVNKDVLKEIKATRVELKDEIRATREELKEEIRAT 146
                                       4444578899999999999999999999999999876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.032
                              CdvA   5 ALeeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqiks 58 
                                       +L+e+ ++    k++ +  +e+l+e++++ +++ k+ ++++k+   el+d+i+ 
  gi|330507702|ref|YP_004384130.1| 117 VLKEIKATRVELKDEIRATREELKEEIRATRDEVKATRDEVKATRVELKDEIRV 170
                                       567777777777888888888888888888888888888888888888888875 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0041
                              CdvA   8 eLvsegdipkstyeeikekleealkklkekakel....keklkkrlkeledqikslek 61 
                                       e+v   d  ks ++ + ek+++a +++    +++    ++ l++rl+++e+ i++++ 
  gi|330507702|ref|YP_004384130.1| 178 EIVGVRDQVKSSADLLAEKIDSAKEEIAVSIDDIrsdyRDDLTERLAKIEEDISQIKA 235
                                       67888889999999999999999999887777772222579*************9985 PP

>> DUF3618  Protein of unknown function (DUF3618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       1.6     6e+02      10      21 ..     120     131 ..     119     134 .. 0.80
   2 ?    6.3   5.5      0.03        12       3      25 ..     135     157 ..     133     161 .. 0.89
   3 ?    7.1   0.1     0.017       6.5       3      30 ..     171     198 ..     170     202 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.6
                           DUF3618  10 dIertRaeLaeT 21 
                                       +I +tR eL   
  gi|330507702|ref|YP_004384130.1| 120 EIKATRVELKDE 131
                                       9******99765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.03
                           DUF3618   3 dpeeIerdIertRaeLaeTvdeL 25 
                                       ++ee++++I +tR+e  +T de 
  gi|330507702|ref|YP_004384130.1| 135 TREELKEEIRATRDEVKATRDEV 157
                                       79*************99998875 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.017
                           DUF3618   3 dpeeIerdIertRaeLaeTvdeLaarad 30 
                                       ++++++++I   R++  +  d La++ d
  gi|330507702|ref|YP_004384130.1| 171 TRDDLKAEIVGVRDQVKSSADLLAEKID 198
                                       689**********************965 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 ?    6.7   2.8     0.021       7.8      23      71 ..      99     155 ..      91     162 .. 0.75
   2 ?    3.6   0.1      0.19        71      44      74 ..     163     194 ..     155     196 .. 0.83
   3 ?    3.0   0.7      0.29   1.1e+02      23      69 ..     185     236 ..     183     238 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.021
                              Med9  23 dletktgelrhkLkkarelirelpg........idrsveeqeaeieeleeqlakKre 71 
                                        +++++  l+  ++  + +++e++         i  + ee ++ei++ ++++++ r+
  gi|330507702|ref|YP_004384130.1|  99 RIDQAAELLKELISVNKDVLKEIKAtrvelkdeIRATREELKEEIRATRDEVKATRD 155
                                       566666666666666666666666666666669999999999999999999998876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.19
                              Med9  44 elpg.idrsveeqeaeieeleeqlakKrelLk 74 
                                       el++ i  + ++ +aei   ++q++   +lL+
  gi|330507702|ref|YP_004384130.1| 163 ELKDeIRVTRDDLKAEIVGVRDQVKSSADLLA 194
                                       455559999****************9999997 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.29
                              Med9  23 dletktgelrhkLkkarelir.elpg....idrsveeqeaeieeleeqlakK 69 
                                       +++++++ l  k+++a+e i+ ++++          e++a+iee   q+++K
  gi|330507702|ref|YP_004384130.1| 185 QVKSSADLLAEKIDSAKEEIAvSIDDirsdYRDDLTERLAKIEEDISQIKAK 236
                                       5677888899999999999983455554444555666777777666666665 PP

>> IFP_35_N  Interferon-induced 35 kDa protein (IFP 35) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   3.2      0.01         4       1      48 [.     117     164 ..     117     179 .. 0.91
   2 ?   -1.1   0.0       5.3     2e+03      12      25 ..     219     232 ..     208     238 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.01
                          IFP_35_N   1 liaeitkeniqLkeeiqkLeaELQettrefqikediPetKikftsvEt 48 
                                       +++ei+    +Lk+ei+    EL e+ r  +    + ++ +k t vE 
  gi|330507702|ref|YP_004384130.1| 117 VLKEIKATRVELKDEIRATREELKEEIRATRDEVKATRDEVKATRVEL 164
                                       689*************************99989999999999999985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5.3
                          IFP_35_N  12 LkeeiqkLeaELQe 25 
                                       L e++ k+e ++ +
  gi|330507702|ref|YP_004384130.1| 219 LTERLAKIEEDISQ 232
                                       66666666665544 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 ?    7.0   8.1     0.011       4.2       2      86 ..     105     189 ..     104     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                              Med4   2 klaekLlaaddelskslk..eleehqknearilqLraeveslDekikeivksLkeyekeLkavpdqenskldtasik 76 
                                       +l+++L+++++   k +k  ++e  ++++a  ++L++e+ +  +++k +  ++k  + eLk ++ + + +l  +   
  gi|330507702|ref|YP_004384130.1| 105 ELLKELISVNKDVLKEIKatRVELKDEIRATREELKEEIRATRDEVKATRDEVKATRVELKDEIRVTRDDL--KAEI 179
                                       6899*************95568999***************************************9999998..7777 PP

                              Med4  77 laekrevdse 86 
                                        + + +v+s+
  gi|330507702|ref|YP_004384130.1| 180 VGVRDQVKSS 189
                                       7777777654 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   2.4     0.092        35      30      80 ..      95     148 ..      61     165 .. 0.38
   2 ?    6.6   3.4     0.011         4      14      92 ..     118     196 ..     102     213 .. 0.81
   3 ?    1.0   0.2      0.52     2e+02      29      85 ..     187     233 ..     155     237 .. 0.39

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.092
                             TMPIT  30 klqskcskeikkqkkrlkelksslkklkks...vkeeeeeeveelkeelkerkk 80 
                                       +  +++ ++++  k+ ++  k+ lk++k++   +k+e + + eelkee++ ++ 
  gi|330507702|ref|YP_004384130.1|  95 ETDQRIDQAAELLKELISVNKDVLKEIKATrveLKDEIRATREELKEEIRATRD 148
                                       222222222222222222222222222222111223333333334443333333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                             TMPIT  14 leetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesllp 90 
                                       l+e + +  +  +e+ +  +++++ei+  + ++k+ ++++k ++ ++k+e + + ++lk+e+   + ++k+ ++ll 
  gi|330507702|ref|YP_004384130.1| 118 LKEIKATRVELKDEIRATREELKEEIRATRDEVKATRDEVKATRVELKDEIRVTRDDLKAEIVGVRDQVKSSADLLA 194
                                       45555555777788899999999999999999999999999999999999999999999999999999999998888 PP

                             TMPIT  91 kk 92 
                                       +k
  gi|330507702|ref|YP_004384130.1| 195 EK 196
                                       77 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.52
                             TMPIT  29 sklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkev 85 
                                       +++ + ++++i++ k+          ++  s+++ +++  ++l+e+l+++++ ++++
  gi|330507702|ref|YP_004384130.1| 187 KSSADLLAEKIDSAKE----------EIAVSIDDIRSDYRDDLTERLAKIEEDISQI 233
                                       2222222222222222..........2222222333334444444444444433333 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   0.3       3.4   1.3e+03      42      42 ..      98      98 ..      55     141 .. 0.57
   2 ?    8.2   1.8    0.0087       3.3      10      66 ..     140     194 ..     137     202 .. 0.92
   3 ?    4.5   0.2      0.12        47      25      62 ..     206     234 ..     193     237 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 3.4
                           NPV_P10 42 e 42
                                      +
  gi|330507702|ref|YP_004384130.1| 98 Q 98
                                      2 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0087
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                       +++i+a+ d V+a  ++v+  + +l+d  e+    d++ a++  + ++v++  d+L 
  gi|330507702|ref|YP_004384130.1| 140 KEEIRATRDEVKATRDEVKATRVELKD--EIRVTRDDLKAEIVGVRDQVKSSADLLA 194
                                       689************************..9********************9999998 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.12
                           NPV_P10  25 qqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                        ++dd++++ +d  +l+e+L +       +e+ +++I+
  gi|330507702|ref|YP_004384130.1| 206 VSIDDIRSDYRD--DLTERLAK-------IEEDISQIK 234
                                       345666666666..45555555.......555555553 PP

>> DUF3216  Protein of unknown function (DUF3216)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.7     0.033        12      62      82 ..     125     144 ..     105     149 .. 0.58
   2 ?    4.7   1.2     0.093        36      60      86 ..     147     173 ..     139     178 .. 0.80
   3 ?   -1.4   0.0       7.3   2.8e+03      66      81 ..     193     208 ..     184     236 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHHHHHHH---- CS
                           DUF3216  62 kvkellekvkakreeleellr 82 
                                       +v el ++++a reel+e +r
  gi|330507702|ref|YP_004384130.1| 125 RV-ELKDEIRATREELKEEIR 144
                                       22.456666666666666666 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.093
                                       -HHHHHHHHHHHHHHHHHH----XXXX CS
                           DUF3216  60 eekvkellekvkakreeleellrkpri 86 
                                        + vk   ++vka r el++ +r  r 
  gi|330507702|ref|YP_004384130.1| 147 RDEVKATRDEVKATRVELKDEIRVTRD 173
                                       567889999999999999999998775 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 7.3
                                       HHHHHHHHHHHHH--- CS
                           DUF3216  66 llekvkakreeleell 81 
                                       l ek+ +++ee+   +
  gi|330507702|ref|YP_004384130.1| 193 LAEKIDSAKEEIAVSI 208
                                       4556666666654444 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 ?    4.3   3.0      0.11        42      51     116 ..      97     162 ..      60     166 .. 0.56
   2 ?    2.1   9.9      0.55   2.1e+02      22     128 ..     128     233 ..      95     237 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHH CS
                         Fib_alpha  51 tkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneq 116
                                        + +++  + +k+ +  ++   k+ + +  ++++e++   ++lke+i a+  ++++ ++ +++ ++
  gi|330507702|ref|YP_004384130.1|  97 DQRIDQAAELLKELISVNKDVLKEIKATRVELKDEIRATREELKEEIRATRDEVKATRDEVKATRV 162
                                       333444444444444444444444455555566666666666666666666666666665555555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.55
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH........HHHHHHHHHHHHHCC CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn........dnvikksskeleeei 90 
                                       l+d +  +++++k++++  ++e++        +++ vk+++  l+++ + ++d            +k+s++ l e+i
  gi|330507702|ref|YP_004384130.1| 128 LKDEIRATREELKEEIRATRDEVK-------ATRDEVKATRVELKDEIRVTRDDlkaeivgvRDQVKSSADLLAEKI 197
                                       444444444444444444444444.......4444444444444433333333220001123555555666666666 PP

                                       CHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  91 lrlketidaqesnirvLqnvlesneqkiqkLeqdidqk 128
                                          ke+i   +  ir   +  +++ ++++k+e+di+q 
  gi|330507702|ref|YP_004384130.1| 198 DSAKEEIAVSIDDIRS--DYRDDLTERLAKIEEDISQI 233
                                       6666666555555553..44455666777777777664 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 ?    5.4   2.7      0.06        23      32      71 ..     101     142 ..      61     145 .. 0.65
   2 ?    3.9  13.5      0.18        67      38      76 ..     127     165 ..      94     237 .. 0.48

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.06
                       Uso1_p115_C  32 esleqk..eakkaaesqakeleaenkklekeleklraelkee 71 
                                        ++++   e    ++ + ke++a++ +l++e+ ++r+elkee
  gi|330507702|ref|YP_004384130.1| 101 DQAAELlkELISVNKDVLKEIKATRVELKDEIRATREELKEE 142
                                       222222322344466666777777777777777777777766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.18
                       Uso1_p115_C  38 eakkaaesqakeleaenkklekeleklraelkeekekek 76 
                                       e k ++++  +el++e+ ++++e++++r e+k+ + + k
  gi|330507702|ref|YP_004384130.1| 127 ELKDEIRATREELKEEIRATRDEVKATRDEVKATRVELK 165
                                       333334444444444444444444444444443332222 PP

>> RICH  RICH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.8    0.0011       0.4      30      82 ..      99     151 ..      95     159 .. 0.83
   2 ?   -0.2   0.2       3.5   1.3e+03       3      22 ..     211     230 ..     182     237 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0011
                              RICH  30 khtqnvaLikkLseIkteyLyelkvlkekskaeleelvsktkaeldaafekfk 82 
                                       +  q  +L+k+L  +++  L+e+k    + k e+  + ++ k+e+ a+ +++k
  gi|330507702|ref|YP_004384130.1|  99 RIDQAAELLKELISVNKDVLKEIKATRVELKDEIRATREELKEEIRATRDEVK 151
                                       667999*******************9999998888877888887777665555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 3.5
                              RICH   3 eskkakdeVkeylekiLsei 22 
                                       +++ ++d+ +e l ki ++i
  gi|330507702|ref|YP_004384130.1| 211 IRSDYRDDLTERLAKIEEDI 230
                                       33333444444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1854  (0.103408); expected 358.6 (0.02)
Passed bias filter:                      777  (0.0433376); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                        57  (0.00317921); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 0.88u 0.30s 00:00:01.18 Elapsed: 00:00:00.45
# Mc/sec: 1585.85
//
Query:       gi|330507703|ref|YP_004384131.1|  [L=337]
Description: transcription initiation factor IIB [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-44  147.7   3.2    1.4e-21   76.3   1.0    2.3  2  TFIIB           Transcription factor TFIIB repeat
    7.4e-19   67.0   1.3    7.4e-19   67.0   1.3    1.8  2  TF_Zn_Ribbon    TFIIB zinc-binding
    8.3e-05   22.0   0.1      0.048   13.2   0.1    3.1  2  Sigma70_r4      Sigma-70, region 4
     0.0089   15.8   2.3      0.063   13.1   0.1    3.1  3  HTH_AsnC-type   AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   16.3   0.0       0.65   10.6   0.0    2.4  2  RPA_interact_C  Replication protein A interacting C-terminal
      0.012   15.3   0.4      0.033   13.9   0.4    1.6  1  Ribosomal_S27e  Ribosomal protein S27
      0.018   15.1   0.0        9.1    6.4   0.0    2.4  2  Cyclin_C        Cyclin, C-terminal domain
      0.022   14.5   0.0        1.8    8.3   0.0    2.3  2  Cyclin_N        Cyclin, N-terminal domain
      0.043   12.4   0.2      0.064   11.8   0.2    1.2  1  Terminase_GpA   Phage terminase large subunit (GpA)
      0.044   13.8   2.2         12    6.0   0.0    3.6  3  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.055   13.3   0.4       0.78    9.6   0.4    2.4  2  eIF-5_eIF-2B    Domain found in IF2B/IF5
      0.057   13.5   0.0       0.11   12.5   0.0    1.5  1  RB_B            Retinoblastoma-associated protein B domain
      0.061   13.4   0.1        3.8    7.7   0.0    3.6  4  HTH_3           Helix-turn-helix
      0.086   13.4   0.4        1.7    9.2   0.3    2.5  2  Stc1            Stc1 domain
       0.11   12.4   0.4       0.28   11.1   0.4    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.15   12.2   0.0         11    6.3   0.0    2.7  2  DUF5419         Family of unknown function (DUF5419)
       0.22   11.6   5.1        5.9    7.1   3.4    2.8  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
       0.51    9.8   3.5        8.6    5.9   3.5    2.4  1  zf-ribbon_3     zinc-ribbon domain
       0.56   10.4   4.7        1.8    8.7   0.3    3.1  3  Zn-ribbon_8     Zinc ribbon domain
          1    9.6   3.3        5.8    7.2   1.5    2.3  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
        1.2    9.3   4.1         26    5.0   0.1    2.9  3  SR1P            SR1 protein
        1.5    8.8   3.9        5.6    6.9   0.5    2.5  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
        2.6    8.5  11.1        5.6    7.4   0.1    4.2  4  HTH_31          Helix-turn-helix domain
        5.6    6.9   7.0        1.9    8.4   0.1    3.5  3  HTH_23          Homeodomain-like domain
        9.4    6.3   6.3        2.2    8.3   2.5    1.9  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon


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 !   76.3   1.0     2e-24   1.4e-21       2      71 .]     157     226 ..     156     226 .. 0.98
   2 !   71.6   0.0   5.8e-23   4.1e-20       1      71 []     250     320 ..     250     320 .. 0.99

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 2e-24
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                        r+a+al+L+  V++ A  ++++a++++++ Grs +g+aAA+ly Acr+++v rt+ ei++v++Vs k+i
  gi|330507703|ref|YP_004384131.1| 157 DRMASALGLSRNVRETAAVVYRKAVDKNLIRGRSIEGVAAAALYAACRQCNVPRTLDEIAEVSRVSRKEI 226
                                       69*****************************************************************997 PP

  == domain 2  score: 71.6 bits;  conditional E-value: 5.8e-23
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i+rf++ l+L+ +V+ +  e++++a+e+++++Gr p+g+aAA++yiA+ +++ +rtq+e+++v+ V+e+ti
  gi|330507703|ref|YP_004384131.1| 250 IPRFCSGLNLKGEVQAKGIEILRQAAEKELTSGRGPTGVAAAAIYIASILCGDRRTQREVADVAGVTEVTI 320
                                       89*******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   1.3     1e-21   7.4e-19       3      43 .]      41      81 ..      39      81 .. 0.98
   2 ?   -3.2   0.1       8.6   6.2e+03       3      10 ..     203     210 ..     202     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 1e-21
                                      ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      CP+C+s +lv+D+er+elvC+dCGlV+++n id gpewr+f
  gi|330507703|ref|YP_004384131.1| 41 CPECKSHTLVRDYERAELVCSDCGLVIDENFIDQGPEWRAF 81
                                      ***************************************98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.6
                                       ETTTTCEE CS
                      TF_Zn_Ribbon   3 CPnCgstn 10 
                                       C  C+ ++
  gi|330507703|ref|YP_004384131.1| 203 CRQCNVPR 210
                                       99999876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.02        14      20      35 ..     209     224 ..     202     231 .. 0.86
   2 !   13.2   0.1   6.7e-05     0.048      18      43 ..     301     326 ..     293     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.02
                                       T--HHHHHHHHTS-HH CS
                        Sigma70_r4  20 glTleEIgerlgiSre 35 
                                       ++Tl EI+e+  +Sr 
  gi|330507703|ref|YP_004384131.1| 209 PRTLDEIAEVSRVSRK 224
                                       79*********99996 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.7e-05
                                       TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekr 43 
                                       g+ +T+ E++++ g+++ ++r + k+
  gi|330507703|ref|YP_004384131.1| 301 GDRRTQREVADVAGVTEVTIRNRYKE 326
                                       5679*******************987 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.8   1.3e+03      23      31 ..     159     167 ..     156     168 .. 0.84
   2 ?   -0.0   0.0       1.1     8e+02      15      36 ..     207     228 ..     205     231 .. 0.73
   3 !   13.1   0.1   8.8e-05     0.063      17      41 ..     303     327 ..     301     328 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.8
                     HTH_AsnC-type  23 LAervGlSe 31 
                                       +A ++GlS+
  gi|330507703|ref|YP_004384131.1| 159 MASALGLSR 167
                                       799*****8 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                     HTH_AsnC-type  15 daRisyaeLAervGlSestvlr 36 
                                       +  ++  e+Ae   +S+ ++ r
  gi|330507703|ref|YP_004384131.1| 207 NVPRTLDEIAEVSRVSRKEIGR 228
                                       5667888999988888887766 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 8.8e-05
                     HTH_AsnC-type  17 RisyaeLAervGlSestvlrRvrrL 41 
                                       R++ +e+A+  G++e t+++R++ L
  gi|330507703|ref|YP_004384131.1| 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 ?   10.6   0.0   0.00091      0.65       2      27 ..      41      69 ..      40     129 .. 0.83
   2 ?    3.5   0.0      0.15   1.1e+02      64      78 ..     194     208 ..     154     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00091
                    RPA_interact_C  2 CPvCkkrklkets..evifCe.Cglrlet 27
                                      CP Ck++ l ++     ++C+ Cgl ++ 
  gi|330507703|ref|YP_004384131.1| 41 CPECKSHTLVRDYerAELVCSdCGLVIDE 69
                                      *********98553477***99***9987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.15
                    RPA_interact_C  64 egveaLlaeCeeCdf 78 
                                          +aL+a C++C++
  gi|330507703|ref|YP_004384131.1| 194 VAAAALYAACRQCNV 208
                                       56789********86 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   4.6e-05     0.033       7      36 ..      38      67 ..      35      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                                      EEE-TTTS-EEEEESS-SS-EEESSSTCEE CS
                    Ribosomal_S27e  7 dvkCpdCenetvvFshaatvvkCisCgkvL 36
                                       v Cp+C+  t v +       C  Cg v+
  gi|330507703|ref|YP_004384131.1| 38 TVECPECKSHTLVRDYERAELVCSDCGLVI 67
                                      699************************876 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.016        12      47      83 ..     194     230 ..     190     238 .. 0.88
   2 ?    6.4   0.0     0.013       9.1      47      88 ..     288     329 ..     283     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.016
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcv 83 
                                       +Aaaal++a+++ n p   +++ +++++s +++   +
  gi|330507703|ref|YP_004384131.1| 194 VAAAALYAACRQCNVPRTLDEIAEVSRVSRKEIGRTY 230
                                       7***************999999999999988886655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcvelile 88 
                                       +Aaaa+++a+   ++   ++++  + g+++  +++ ++ ++e
  gi|330507703|ref|YP_004384131.1| 288 VAAAAIYIASILCGDRRTQREVADVAGVTEVTIRNRYKELAE 329
                                       8***********9**********************9999987 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0025       1.8      40     111 ..     158     226 ..     137     241 .. 0.81
   2 ?    3.6   0.0     0.072        52      34      86 ..     246     298 ..     233     331 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0025
                                       HHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHH CS
                          Cyclin_N  40 evaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeei 111
                                       ++a+ + l++++  +a++++ + + k+ ++ + ++ v+a++L+ A++  ++ p +l++++ ++   ++++ei
  gi|330507703|ref|YP_004384131.1| 158 RMASALGLSRNVRETAAVVYRKAVDKNLIRGRSIEGVAAAALYAACRQCNV-PRTLDEIAEVS--RVSRKEI 226
                                       677788899999999********************************9888.88888888774..3555555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.072
                                       HHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHH CS
                          Cyclin_N  34 lidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaK 86 
                                        id++ + ++ ++l+ e+ +  +++l +  +k+ ++ +    v+a+++++A+ 
  gi|330507703|ref|YP_004384131.1| 246 PIDYIPRFCSGLNLKGEVQAKGIEILRQAAEKELTSGRGPTGVAAAAIYIASI 298
                                       589999*************************9999999*************95 PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2     9e-05     0.064     182     240 ..      21      70 ..      14     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9e-05
                     Terminase_GpA 182 tsriealyeesdqr.ryyvpCphCgelqelsferlkwpegeaeekaryvCphcgslieeh 240
                                        +r+ ++ e+ d+  ++ v+Cp+C+++  ++          + e a++vC++cg +i+e+
  gi|330507703|ref|YP_004384131.1|  21 RTRLRREKEKVDEFeKFTVECPECKSHTLVR----------DYERAELVCSDCGLVIDEN 70 
                                       5677778888888669**********99998..........4678************997 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.3      0.26   1.8e+02      26      58 ..     158     192 ..     127     202 .. 0.68
   2 ?    3.3   0.0      0.12        84      12      42 ..     203     230 ..     194     240 .. 0.78
   3 ?    6.0   0.0     0.016        12      23      48 ..     305     330 ..     295     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.26
                                       HHHHHTTSSH...HHHHHHHHHHHHTTSEEETEEEE CS
                         HTH_Crp_2  26 elAsmlGltr...etvsrilseLkreglisrgrrir 58 
                                        +As lGl+r   et   + ++  +++li+ +  i+
  gi|330507703|ref|YP_004384131.1| 158 RMASALGLSRnvrETAAVVYRKAVDKNLIRGRS-IE 192
                                       589999998533378888888888888887554.55 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.12
                                       CTTTCEEEEEHHHHHHHHHTTSSHHHHHHHH CS
                         HTH_Crp_2  12 eraggeielpltqeelAsmlGltretvsril 42 
                                       +r   ++++p t +e+A+   ++r  + r+ 
  gi|330507703|ref|YP_004384131.1| 203 CR---QCNVPRTLDEIAEVSRVSRKEIGRTY 230
                                       33...478999*************9998876 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.016
                                       HHHHHHHHTTSSHHHHHHHHHHHHHT CS
                         HTH_Crp_2  23 tqeelAsmlGltretvsrilseLkre 48 
                                       tq+e A+  G+t +t+    +eL +e
  gi|330507703|ref|YP_004384131.1| 305 TQREVADVAGVTEVTIRNRYKELAEE 330
                                       9***************9999999875 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4    0.0011      0.78      77     115 ..      28      64 ..       3      66 .. 0.76
   2 ?    0.9   0.0      0.56     4e+02      85      98 ..     198     211 ..     154     224 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHTSTSSSTSTCEEECCS.SSCEEEEESSST CS
                      eIF-5_eIF-2B  77 eklldkyieeyVlCkeCkspeteleke.erllvlkCkaCg 115
                                       ++++d++ +  V C+eCks+  +l+++ er   l C+ Cg
  gi|330507703|ref|YP_004384131.1|  28 KEKVDEFEKFTVECPECKSH--TLVRDyERAE-LVCSDCG 64 
                                       67788898888*******96..3566515665.99****9 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.56
                                       HHHTSTSSSTSTCE CS
                      eIF-5_eIF-2B  85 eeyVlCkeCkspet 98 
                                         y  C++C+ p t
  gi|330507703|ref|YP_004384131.1| 198 ALYAACRQCNVPRT 211
                                       35889999999887 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00016      0.11      10      96 ..     149     233 ..     141     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                              RB_B  10 yklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqp 86 
                                       +  a + l ++ + L ls+++re +  + ++++  +++l++ R ++ +  +a+Y+ ++ ++  +++ ei +  r + 
  gi|330507703|ref|YP_004384131.1| 149 LAFALSELDRMASALGLSRNVRETAAVVYRKAV--DKNLIRGRSIEGVAAAALYAACRQCNVPRTLDEIAEVSRVSR 223
                                       66788899999999*****99999988877776..568*********************************999999 PP

                              RB_B  87 qasskvyrsv 96 
                                       ++  ++yr v
  gi|330507703|ref|YP_004384131.1| 224 KEIGRTYRFV 233
                                       9999988877 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         3   2.1e+03      39      51 ..     154     166 ..     150     168 .. 0.76
   2 ?    0.4   0.0         1   7.2e+02      11      27 ..     211     227 ..     202     228 .. 0.85
   3 ?    7.7   0.0    0.0053       3.8      11      27 ..     305     321 ..     303     325 .. 0.92
   4 ?   -2.4   0.0       7.1   5.1e+03      13      21 ..     325     333 ..     322     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3
                                       HHHHHHHHHHTSE CS
                             HTH_3  39 etlkklakaLgvs 51 
                                       + l ++a aLg+s
  gi|330507703|ref|YP_004384131.1| 154 SELDRMASALGLS 166
                                       5678888888876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1
                                       HHHHHHHHHTSSHHHHH CS
                             HTH_3  11 sqeeLAeklGvsrstis 27 
                                       ++ e+Ae++ vsr  i 
  gi|330507703|ref|YP_004384131.1| 211 TLDEIAEVSRVSRKEIG 227
                                       67899999999998876 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0053
                                       HHHHHHHHHTSSHHHHH CS
                             HTH_3  11 sqeeLAeklGvsrstis 27 
                                       +q+e+A+++Gv+  ti+
  gi|330507703|ref|YP_004384131.1| 305 TQREVADVAGVTEVTIR 321
                                       9*************997 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 7.1
                                       HHHHHHHTS CS
                             HTH_3  13 eeLAeklGv 21 
                                       +eLAe+l++
  gi|330507703|ref|YP_004384131.1| 325 KELAEELDI 333
                                       899999976 PP

>> Stc1  Stc1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3    0.0024       1.7      23      61 ..      21      66 ..       6      72 .. 0.78
   2 ?    1.1   0.0      0.82   5.9e+02      47      74 ..     195     222 ..     164     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0024
                                      TTEEEE-S-........----TTTS-----E......EE-SSS--E CS
                              Stc1 23 ekklaeekakvkkaks.kikCkectakqate......leCsaCqkt 61
                                      +++l++ek+kv+++++ +++C ec+++  +       l Cs C+ +
  gi|330507703|ref|YP_004384131.1| 21 RTRLRREKEKVDEFEKfTVECPECKSHTLVRdyeraeLVCSDCGLV 66
                                      555666688899998889*******998776777777******865 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.82
                                       -----EEE-SSS--EEESTTS-HHHHHS CS
                              Stc1  47 akqateleCsaCqktkpldeFsksqrrk 74 
                                       a +a    C  C+  ++lde ++ +r +
  gi|330507703|ref|YP_004384131.1| 195 AAAALYAACRQCNVPRTLDEIAEVSRVS 222
                                       4455557788888888888777766655 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   0.4   0.00039      0.28      21      57 ..      30      68 ..      18      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                    OrfB_Zn_ribbon 21 evnpay.TSktCseCgsk.nkealsgrtfkCpnCgfead 57
                                      +v+++     +C+eC s  + ++ ++ +++C++Cg+++d
  gi|330507703|ref|YP_004384131.1| 30 KVDEFEkFTVECPECKSHtLVRDYERAELVCSDCGLVID 68
                                      55665555689****865155599***********9987 PP

>> DUF5419  Family of unknown function (DUF5419)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.18   1.3e+02      27      44 ..     108     125 ..      96     129 .. 0.81
   2 ?    6.3   0.0     0.015        11       9      37 ..     153     182 ..     146     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.18
                           DUF5419  27 fADWrYavAftnGiapRq 44 
                                       + DWr ++ +   i+ ++
  gi|330507703|ref|YP_004384131.1| 108 MIDWRNRDSYGKTISSKN 125
                                       67********99888765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.015
                           DUF5419   9 LDieldkitggiGLtrn..DfADWrYavAft 37 
                                       L  eld++  ++GL+rn  + A   Y+ A +
  gi|330507703|ref|YP_004384131.1| 153 LS-ELDRMASALGLSRNvrETAAVVYRKAVD 182
                                       55.9************855677777777766 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.4    0.0082       5.9       3      26 .]      40      63 ..      39      63 .. 0.93
   2 ?    3.2   0.0      0.13        92       9      20 ..     174     185 ..     173     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0082
                            zf-ACC  3 KCpsCgemlykkeLernlyVCPkC 26
                                       Cp+C++ ++ ++ er   VC  C
  gi|330507703|ref|YP_004384131.1| 40 ECPECKSHTLVRDYERAELVCSDC 63
                                      6***************99999988 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                            zf-ACC   9 emlykkeLernl 20 
                                       +++y+k +++nl
  gi|330507703|ref|YP_004384131.1| 174 AVVYRKAVDKNL 185
                                       79*********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 ?    5.9   3.5     0.012       8.6       2      25 ..      38      66 ..      37      67 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                       zf-ribbon_3  2 tvrCPnCGap..l...ssddnvCpyCGtk 25
                                      tv+CP+C+++  +   +    vC  CG +
  gi|330507703|ref|YP_004384131.1| 38 TVECPECKSHtlVrdyERAELVCSDCGLV 66
                                      89******952232222234577777766 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3    0.0025       1.8      25      38 ..      36      51 ..      25      53 .. 0.73
   2 ?    1.8   0.1      0.38   2.7e+02       5      14 ..      57      66 ..      52      77 .. 0.70
   3 ?   -0.9   0.0       2.7   1.9e+03      28      33 ..     201     207 ..     191     212 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0025
                       Zn-ribbon_8 25 plta.CPeCgs.evrr 38
                                      + t+ CPeC+s ++ r
  gi|330507703|ref|YP_004384131.1| 36 KFTVeCPECKShTLVR 51
                                      45677******99888 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.38
                       Zn-ribbon_8  5 eYrCeeCghe 14
                                      e  C +Cg +
  gi|330507703|ref|YP_004384131.1| 57 ELVCSDCGLV 66
                                      3458888755 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.7
                       Zn-ribbon_8  28 a.CPeCg 33 
                                       a C +C+
  gi|330507703|ref|YP_004384131.1| 201 AaCRQCN 207
                                       4477774 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.5    0.0081       5.8      17      40 .]      40      64 ..      38      64 .. 0.92
   2 ?    1.5   0.0      0.46   3.3e+02      16      25 ..     201     210 ..     197     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0081
                     Auto_anti-p27 17 tCpvC.gvPLmrdrkggkvyCvaCd 40
                                       Cp+C +  L+rd ++ +++C  C+
  gi|330507703|ref|YP_004384131.1| 40 ECPECkSHTLVRDYERAELVCSDCG 64
                                      6*****9******9899*****996 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.46
                     Auto_anti-p27  16 etCpvCgvPL 25 
                                       + C +C+vP 
  gi|330507703|ref|YP_004384131.1| 201 AACRQCNVPR 210
                                       46******96 PP

>> SR1P  SR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       4.9   3.5e+03      30      35 ..      41      46 ..      27      47 .. 0.59
   2 ?    5.0   0.1     0.037        26       5      14 ..      59      68 ..      58      71 .. 0.92
   3 ?    4.5   0.0     0.052        37      22      32 ..     197     207 ..     190     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.9
                              SR1P 30 qceCkk 35
                                      ++eCk+
  gi|330507703|ref|YP_004384131.1| 41 CPECKS 46
                                      578875 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.037
                              SR1P  5 vCqtCnatId 14
                                      vC++C+ +Id
  gi|330507703|ref|YP_004384131.1| 59 VCSDCGLVID 68
                                      9********9 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.052
                              SR1P  22 ttLYgtCnqce 32 
                                       + LY+ C qc+
  gi|330507703|ref|YP_004384131.1| 197 AALYAACRQCN 207
                                       579****9775 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5    0.0078       5.6       4      28 ..      41      64 ..      36      66 .. 0.80
   2 ?    2.1   0.2      0.25   1.8e+02      23      28 ..     202     207 ..     195     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0078
                                      ESTTTSBEEEEECSCCCEEEESSSS CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCg 28
                                      Cp+C+++ l+++ +    + C+ Cg
  gi|330507703|ref|YP_004384131.1| 41 CPECKSHTLVRDYERAE-LVCSDCG 64
                                      *******9988655543.4599997 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.25
                                       EESSSS CS
                    RNA_POL_M_15KD  23 eCrqCg 28 
                                       +CrqC 
  gi|330507703|ref|YP_004384131.1| 202 ACRQCN 207
                                       8***95 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4       6.2   4.5e+03      10      18 ..      19      27 ..      12      61 .. 0.62
   2 ?    4.5   0.1     0.061        44      44      62 ..     153     171 ..     131     173 .. 0.83
   3 ?    1.6   0.1       0.5   3.6e+02      16      33 ..     211     228 ..     187     235 .. 0.82
   4 ?    7.4   0.1    0.0079       5.6      10      32 ..     272     321 ..     269     322 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.2
                            HTH_31 10 ReraGLsqe 18
                                       er +L++e
  gi|330507703|ref|YP_004384131.1| 19 KERTRLRRE 27
                                      556666655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.061
                            HTH_31  44 pavlealaralgldpaera 62 
                                       ++ l+++a algl+++ r+
  gi|330507703|ref|YP_004384131.1| 153 LSELDRMASALGLSRNVRE 171
                                       5799**********99887 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.5
                            HTH_31  16 sqeevAerlgvsestlsr 33 
                                       +++e Ae ++vs+  ++r
  gi|330507703|ref|YP_004384131.1| 211 TLDEIAEVSRVSRKEIGR 228
                                       778889999999888877 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0079
                            HTH_31  10 Rera...........................GLsqeevAerlgvsestls 32 
                                       R++a                           + +q+evA+ +gv+e t++
  gi|330507703|ref|YP_004384131.1| 272 RQAAekeltsgrgptgvaaaaiyiasilcgdRRTQREVADVAGVTEVTIR 321
                                       555555566666666666666777777777788************99986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.9       6.2   4.4e+03      30      40 ..     125     135 ..     124     142 .. 0.74
   2 ?   -0.0   0.1       1.2   8.3e+02      17      27 ..     220     230 ..     210     238 .. 0.53
   3 ?    8.4   0.1    0.0026       1.9      17      40 ..     303     326 ..     293     332 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.2
                            HTH_23  30 srrTvyrwlkr 40 
                                       +r ++yr +k+
  gi|330507703|ref|YP_004384131.1| 125 NRAQLYRLRKW 135
                                       57788888887 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.2
                            HTH_23  17 GlsvreIAreL 27 
                                       + s++eI r +
  gi|330507703|ref|YP_004384131.1| 220 RVSRKEIGRTY 230
                                       55555555555 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0026
                            HTH_23  17 GlsvreIAreLgvsrrTvyrwlkr 40 
                                       + ++re+A+  gv++ T+++  k 
  gi|330507703|ref|YP_004384131.1| 303 RRTQREVADVAGVTEVTIRNRYKE 326
                                       679****************65554 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.5    0.0031       2.2       5      26 ..      41      64 ..      40      65 .. 0.91
   2 ?   -2.7   0.1       8.6   6.2e+03       4       9 ..     202     207 ..     200     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0031
                    PhnA_Zn_Ribbon  5 CplCaSeytY...edgallvCpeCa 26
                                      Cp+C+S +t+    ++a lvC++C+
  gi|330507703|ref|YP_004384131.1| 41 CPECKS-HTLvrdYERAELVCSDCG 64
                                      *****9.78889999*********7 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.6
                    PhnA_Zn_Ribbon   4 kCplCa 9  
                                       +C +C+
  gi|330507703|ref|YP_004384131.1| 202 ACRQCN 207
                                       699997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      767  (0.0427799); 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):              25  [number of targets reported over threshold]
# CPU time: 0.74u 0.36s 00:00:01.10 Elapsed: 00:00:00.58
# Mc/sec: 1736.39
//
Query:       gi|330507704|ref|YP_004384132.1|  [L=94]
Description: hypothetical protein MCON_1694 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-17   61.8   0.0    6.5e-17   61.7   0.0    1.0  1  Gar1      Gar1/Naf1 RNA binding region


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   3.6e-21   6.5e-17      21     107 ..       2      88 ..       1      94 [] 0.85

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 3.6e-21
                                       EEEEEEEEEETTEEEEEE--..-S--B--BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHHHHHTTTTS CS
                              Gar1  21 leiGtvssivenevvikstt..sgekkvldfnsilflenktqiGkVdEifGpvnepyysVklnsseeikaksfkvgd 95 
                                       + +Gt  ++v+n+++++s +   +e+ ++  ns + ++++t +GkV++ifGp+  py  V++n   +  a   ++g+
  gi|330507704|ref|YP_004384132.1|   2 KRLGTALHVVQNKLIVQSEEivGSETAIPRGNSWVVDQKRTRVGKVFDIFGPIDRPYIIVRPN--RGTDA-AAHIGK 75 
                                       579**************98633457799***********************************..55555.569*** PP

                                       EEEEE-X...XXX CS
                              Gar1  96 kvyiapd.lpler 107
                                       k+yi+ +   +++
  gi|330507704|ref|YP_004384132.1|  76 KLYIDEApGRDSK 88 
                                       *****98555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 523.38
//
Query:       gi|330507705|ref|YP_004384133.1|  [L=320]
Description: GTP-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-43  147.3   0.1    4.2e-42  143.8   0.1    2.1  1  NOG1_N     NOG1 N-terminal helical domain
    1.2e-21   76.2   0.0    2.2e-21   75.4   0.0    1.5  1  NOG1       Nucleolar GTP-binding protein 1 (NOG1)
    6.9e-21   74.5   0.0    1.2e-20   73.7   0.0    1.4  1  MMR_HSR1   50S ribosome-binding GTPase
    4.1e-12   45.9   0.0      6e-12   45.4   0.0    1.2  1  FeoB_N     Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.061   12.6   0.0      0.089   12.1   0.0    1.2  1  AIG1       AIG1 family
      0.071   13.2   0.1         12    5.9   0.0    2.3  2  Dynamin_N  Dynamin family
       0.12   12.0   0.0         28    4.3   0.0    2.8  3  Ras        Ras 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 !  143.8   0.1   1.7e-45   4.2e-42       1     160 []       2     145 ..       2     145 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.8 bits;  conditional E-value: 1.7e-45
                            NOG1_N   1 FekiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrel 77 
                                       Fe++pt+pts+el+dk++rra+raa +                ++v +a n+lsd+L+++++kfP++++l+pFyre+
  gi|330507705|ref|YP_004384133.1|   2 FERLPTIPTSQELLDKSFRRATRAADNE---------------SMVLNAGNILSDNLANLIRKFPSFENLPPFYREM 63 
                                       9**********************98766...............367899**************************** PP

                            NOG1_N  78 ldvlvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLr 154
                                       ++++v++d++++sL+++ wa++ +r i++eyv+k+++a+  + +  lr++afgr +sv+++++k++ fL+ +r+ Lr
  gi|330507705|ref|YP_004384133.1|  64 VEITVGVDKIRISLSRLRWASRQTRLITREYVGKIRRARGTD-STPLRKSAFGRFSSVMRSIEKDMLFLNSARNLLR 139
                                       ****************************************66.9********************************* PP

                            NOG1_N 155 kLpaiD 160
                                       k+p+iD
  gi|330507705|ref|YP_004384133.1| 140 KMPTID 145
                                       *****9 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   8.8e-25   2.2e-21       1      58 []     215     271 ..     215     271 .. 0.99

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 8.8e-25
                              NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                       eIE+q++aAL hl+++vl++lDpse+cgy+l++Ql+L e++ + ++  p+++v+nK+D
  gi|330507705|ref|YP_004384133.1| 215 EIERQTVAALSHLQGVVLYILDPSEHCGYPLDSQLRLAEDLSNWIR-LPMLIVANKVD 271
                                       6*********************************************.9*********9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.0   4.6e-24   1.2e-20       2     114 .]     151     269 ..     150     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 4.6e-24
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHC. CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflalee. 75 
                                       ++i+G+pNvGKS++i ++tg+k +v+++p+tTr i+ g++  ++k++++vDtpGl++  ++++++ ++++++al   
  gi|330507705|ref|YP_004384133.1| 151 ILIAGYPNVGKSSFIIRITGAKPEVASYPFTTRGIIVGHFVRDDKRYQVVDTPGLLDrpMSERNEIERQTVAALSHl 227
                                       89**************************************9999**********99653333333444444444444 PP

                                       TSEEEEEEETT.......TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  76 adlillvvdas.......eeklkpldeeleelleeakkplilvlnk 114
                                         ++l+++d s       +++  +l e+l ++++    p+++v+nk
  gi|330507705|ref|YP_004384133.1| 228 QGVVLYILDPSehcgyplDSQ-LRLAEDLSNWIR---LPMLIVANK 269
                                       499999999776555543222.345588888875...899999998 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 !   45.4   0.0   2.3e-15     6e-12       2     119 ..     150     274 ..     149     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2.3e-15
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH..C CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll..e 76 
                                       t+ ++G pnvGk++++ ++tgak +v+ +p +t     g++  ++k++++vD PG  +  ++se +++ r++++  +
  gi|330507705|ref|YP_004384133.1| 150 TILIAGYPNVGKSSFIIRITGAKPEVASYPFTTRGIIVGHFVRDDKRYQVVDTPGLLD-RPMSERNEIERQTVAalS 225
                                       6899***************************************************987.789999999999887446 PP

                                       TSSSEEEEEEEGGG.....HHHHHHHHHHHHH.TTSSEEEEEETHHHHH CS
                            FeoB_N  77 eepdvvvnvvdatn.....lernLyLtlqlle.lgvpvvlalnmideae 119
                                       + + vv+ ++d ++     l+ +L L  +l + +++p++++ n++d  +
  gi|330507705|ref|YP_004384133.1| 226 HLQGVVLYILDPSEhcgypLDSQLRLAEDLSNwIRLPMLIVANKVDIKR 274
                                       6688999****76544455899999999998846799999999999765 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.5e-05     0.089       2      76 ..     150     223 ..     149     239 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEE.EETTEEEEEEE--SCCCTTCC.HHCHHHHHHHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksr.twdgkkinViDTPglfdlsvs.adkiskeivrc 76 
                                       ti++ G   +GkS+ +  i g k    ++++ + t++   +   ++d+k+ +V+DTPgl+d   s  ++i+++ v  
  gi|330507705|ref|YP_004384133.1| 150 TILIAGYPNVGKSSFIIRITGAKP---EVASYPFTTRGIIVGHfVRDDKRYQVVDTPGLLDRPMSeRNEIERQTVAA 223
                                       678888888888888777777765...33334555555444444999**************8875245555555543 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0046        12       1      37 [.     151     187 ..     151     198 .. 0.74
   2 ?    5.6   0.0    0.0057        15     100     124 ..     194     218 ..     184     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0046
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EE CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrple 37 
                                       i++ G  + GKSS++  ++g++  + +   tTr +++
  gi|330507705|ref|YP_004384133.1| 151 ILIAGYPNVGKSSFIIRITGAKPEVASYPFTTRGIIV 187
                                       567788899************9555555566665554 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0057
                                       S-SEEEEE---B-SSSGTTSHHHHH CS
                         Dynamin_N 100 vkgltlvDlPGldsvnkrdqelvke 124
                                       +k++ +vD+PGl +++  + + +++
  gi|330507705|ref|YP_004384133.1| 194 DKRYQVVDTPGLLDRPMSERNEIER 218
                                       678899******9999888865554 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.39     1e+03      83     126 ..      49      94 ..      45     105 .. 0.71
   2 ?    4.0   0.0     0.013        34       2      22 ..     151     171 ..     150     207 .. 0.79
   3 ?    4.3   0.0     0.011        28     102     127 ..     260     286 ..     244     297 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.39
                                       BHHHHHTHHHHHHHHHHHST..TTSEEEEEEETTTGGGG-SS-HHH CS
                               Ras  83 sresfenvkkwveeikrvae..envpivLvGnKvDleekravstee 126
                                       +  sfen+  +++e+ +++   +++ i L   +   +++r +++e 
  gi|330507705|ref|YP_004384133.1|  49 KFPSFENLPPFYREMVEITVgvDKIRISLSRLRWASRQTRLITREY 94 
                                       5668999999988888877667677777777777777777776665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.013
                                       EEEEESTTSSHHHHHHHHHHS CS
                               Ras   2 lvlvGdsavGKtslllrfvkd 22 
                                       +++ G  +vGK+s+++r +  
  gi|330507705|ref|YP_004384133.1| 151 ILIAGYPNVGKSSFIIRITGA 171
                                       67889***********98755 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.011
                                       TTTSEEEEEEETTTGGG...G-SS-HHHH CS
                               Ras 102 eenvpivLvGnKvDlee...kravsteeg 127
                                       +  +p+++v+nKvD+++     ++ste+g
  gi|330507705|ref|YP_004384133.1| 260 R--LPMLIVANKVDIKRysdLAEMSTETG 286
                                       3..89**********98544445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2336.46
//
Query:       gi|330507706|ref|YP_004384134.1|  [L=167]
Description: methylase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-12   46.0   0.0    4.4e-11   42.6   0.0    2.1  1  MTS              Methyltransferase small domain
    1.7e-09   38.3   0.0    1.1e-08   35.7   0.0    2.0  2  Methyltransf_25  Methyltransferase domain
      3e-08   33.7   0.0    3.1e-07   30.4   0.0    2.0  1  Methyltransf_23  Methyltransferase domain
    1.5e-07   31.4   0.0    1.9e-07   31.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.7e-06   28.6   0.0    1.1e-05   25.9   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
    3.2e-05   23.5   0.0    3.9e-05   23.2   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    4.1e-05   24.3   0.0      0.001   19.8   0.0    2.4  2  Methyltransf_12  Methyltransferase domain
    0.00019   21.1   0.0    0.00031   20.4   0.0    1.4  1  NodS             Nodulation protein S (NodS)
    0.00024   20.8   0.5     0.0026   17.4   0.5    2.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00036   20.2   0.0    0.00049   19.8   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
     0.0016   17.6   0.0      0.002   17.3   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0022   17.9   0.0     0.0043   16.9   0.0    1.5  1  UPF0146          Uncharacterised protein family (UPF0146)
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.027   14.1   0.0    1.4  1  TPMT             Thiopurine S-methyltransferase (TPMT)
      0.037   14.0   0.0      0.049   13.6   0.0    1.1  1  Methyltransf_32  Methyltransferase domain
      0.057   12.4   0.0      0.073   12.1   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.068   12.4   0.0       0.15   11.3   0.0    1.4  2  N6_Mtase         N-6 DNA Methylase
      0.077   12.7   0.0       0.25   11.0   0.0    1.7  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
      0.078   12.9   0.0       0.11   12.5   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
      0.097   12.5   0.0        0.1   12.4   0.0    1.2  1  N6-adenineMlase  Probable N6-adenine methyltransferase
       0.12   12.0   0.0        2.2    7.9   0.0    2.7  1  UPF0020          Putative RNA methylase family UPF0020
       0.12   12.9   0.0       0.17   12.4   0.0    1.3  1  Eco57I           Eco57I restriction-modification methylase
       0.13   12.0   0.0       0.27   10.9   0.0    1.5  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.13   12.0   0.0       0.32   10.7   0.0    1.6  2  Met_10           Met-10+ like-protein
       0.15   11.8   0.0       0.21   11.3   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
       0.18   10.9   0.0        0.4    9.7   0.0    1.5  2  Pox_MCEL         mRNA capping enzyme
       0.19   11.0   0.0       0.28   10.5   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family


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 !   42.6   0.0   6.4e-14   4.4e-11      31     113 ..      10      83 ..       2     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 6.4e-14
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPf 107
                                        +++vl +GcG G+++++la++ ++  ++++d++ +A+++++e        vev+ sd++e +  +kfdli+ NPP+
  gi|330507706|ref|YP_004384134.1|  10 PEDHVLEVGCGSGLVSLELARQVES--LVALDINPHAVRATRER------GVEVIRSDLFEGIR-GKFDLIIFNPPY 77 
                                       6789*****************8888..9**********998763......379***********.***********9 PP

                                       TTTCHC CS
                               MTS 108 hagkat 113
                                          k++
  gi|330507706|ref|YP_004384134.1|  78 LPTKQA 83 
                                       776664 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   1.6e-11   1.1e-08       1      78 [.      14      79 ..      14      97 .. 0.83
   2 ?    0.2   0.0       1.8   1.2e+03      81      97 .]     103     119 ..      98     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.6e-11
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhls 78
                                      vL++GcG+G ++l+la+++  ++++++Di++ +++a+rer       ve+++ d+ +     g+fDl++ +    +l+
  gi|330507706|ref|YP_004384134.1| 14 VLEVGCGSGLVSLELARQV--ESLVALDINPHAVRATRERG------VEVIRSDLFEG--IRGKFDLIIFN--PPYLP 79
                                      9*****************9..9******************9......99999998443..35789999884..24444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                        + ++l  +a++L+pgG
  gi|330507706|ref|YP_004384134.1| 103 TIGRFLLDLAEHLRPGG 119
                                       566788899999***99 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   4.5e-10   3.1e-07      19     124 ..       7     130 ..       1     159 [. 0.72

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 4.5e-10
                   Methyltransf_23  19 klraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaepqgkfdlIvlrevle 93 
                                       + r+   vL++GcG+G ++ +l++++ s+++ D++p+av   +  +    ++d f     +   gkfdlI+ +    
  gi|330507706|ref|YP_004384134.1|   7 EARPEDHVLEVGCGSGLVSLELARQVESLVALDINPHAVRATRerGVEVIRSDLF-----EGIRGKFDLIIFNPPYL 78 
                                       4678889********************************9887775555555555.....33467999998875443 PP

                   Methyltransf_23  94 hvpdpp.....................ellrqiatllkpgGylllseplasl 124
                                         +  +                     + l  +a++l+pgG++ll+ +  s 
  gi|330507706|ref|YP_004384134.1|  79 PTKQAErsdqwinyaldggesgretigRFLLDLAEHLRPGGRALLLISSLSG 130
                                       3333334566667777777777777778888888888888888887765554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   2.8e-10   1.9e-07       4      82 ..      11      75 ..       8     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.8e-10
                   Methyltransf_31  4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsn 81
                                      + +vl++GCG+G  ++ela+++ +   +v +Di+++a++  re+        ve+ ++d +e +       kfDli+ n
  gi|330507706|ref|YP_004384134.1| 11 EDHVLEVGCGSGLVSLELARQVES---LVALDINPHAVRATRER-------GVEVIRSDLFEgIR-----GKFDLIIFN 74
                                      568****************77655...****************8.......99*********999.....99*****99 PP

                   Methyltransf_31 82 e 82
                                       
  gi|330507706|ref|YP_004384134.1| 75 P 75
                                      3 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.7e-08   1.1e-05       1      49 [.      15      57 ..      15      75 .. 0.82
   2 ?    0.3   0.0       1.7   1.2e+03      79      95 ..     106     122 ..      91     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.7e-08
                                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETT CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvv 49
                                      L+vGcG+G+++ +la++++++v++D+++ ++++ +e+++e       ++
  gi|330507706|ref|YP_004384134.1| 15 LEVGCGSGLVSLELARQVESLVALDINPHAVRATRERGVEV------IR 57
                                      89*****************************9998888665......44 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.7
                                       HHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  79 kalkeiaRvLkpgGllv 95 
                                       ++l  +a  L+pgG+ +
  gi|330507706|ref|YP_004384134.1| 106 RFLLDLAEHLRPGGRAL 122
                                       678888999*****875 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   5.7e-08   3.9e-05     159     202 ..       8      50 ..       1      74 [. 0.85

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.7e-08
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvake 202
                                        +++++vl vG+GSG+ ++  a+   ++ va+Di++ Av++++e
  gi|330507706|ref|YP_004384134.1|   8 ARPEDHVLEVGCGSGLVSLELAR-QVESLVALDINPHAVRATRE 50 
                                       57889*************98877.6899*************997 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.5e-06     0.001       1      43 [.      15      55 ..      15      75 .. 0.78
   2 ?    1.9   0.0      0.54   3.7e+02      81      98 ..     103     120 ..      88     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.5e-06
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakr 43
                                      Le+GcG+G ++ +l+++    +++++Di+p+a+ +++e+  + 
  gi|330507706|ref|YP_004384134.1| 15 LEVGCGSGLVSLELARQ--VESLVALDINPHAVRATRERGVEV 55
                                      8****************..88888*********7777665444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.54
                   Methyltransf_12  81 direvldnirklLkpgGr 98 
                                       +i ++l  ++++L+pgGr
  gi|330507706|ref|YP_004384134.1| 103 TIGRFLLDLAEHLRPGGR 120
                                       566788999********7 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.5e-07   0.00031      45      87 ..      12      54 ..       1      74 [. 0.83

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.5e-07
                              NodS 45 adalevGcaaGalterlapyckrltvvdvveeaiararervke 87
                                       ++levGc +G ++ +la   ++l  +d+ ++a+  +rer  e
  gi|330507706|ref|YP_004384134.1| 12 DHVLEVGCGSGLVSLELARQVESLVALDINPHAVRATRERGVE 54
                                      679************************************9655 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.5   3.8e-06    0.0026      40     124 ..       9      78 ..       2      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.8e-06
                                       HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEE CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdi 116
                                         + +vL++ +GsG ++lE l R++++ v+++ +++av++ +e        + +++++ d +e ++ +      fd+
  gi|330507706|ref|YP_004384134.1|   9 RPEDHVLEVGCGSGLVSLE-LARQVESLVALDINPHAVRATRER-------G-VEVIRSDLFEGIRGK------FDL 70 
                                       56789**************.89***************9987764.......2.456666666666444......888 PP

                                       EEE--SSS CS
                     Cons_hypoth95 117 vflDPPya 124
                                       + ++PPy 
  gi|330507706|ref|YP_004384134.1|  71 IIFNPPYL 78 
                                       88888885 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   7.1e-07   0.00049      12      81 ..       9      73 ..       2      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.1e-07
                              MetW 12 kpgsrvldlGcGdGellellkeekqvdg.rGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvl 81
                                      +p+ +vl++GcG G +   l+  +qv++   l+++ ++v ++ ++G++vi+ dl +++      +fd++++
  gi|330507706|ref|YP_004384134.1|  9 RPEDHVLEVGCGSGLV--SLELARQVESlVALDINPHAVRATRERGVEVIRSDLFEGIR----GKFDLIIF 73
                                      78899*********65..3444678876357999*******************998875....35666655 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.9e-06     0.002      29      70 ..       9      50 ..       1      63 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.9e-06
                                      GTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHC CS
                            RrnaAD 29 eekltvleigpGkGilTeeLakrakqvvvlElderLakllqk 70
                                      ++++ vle+g G G+ + eLa +++++v+l + ++ +  +++
  gi|330507706|ref|YP_004384134.1|  9 RPEDHVLEVGCGSGLVSLELARQVESLVALDINPHAVRATRE 50
                                      599*****************************9998888887 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.3e-06    0.0043       8      62 ..       4      62 ..       1      68 [. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.3e-06
                                      HHHHS-SS.EEEEET-TT--HHHHHHHHHS-EEEEE-SS-S........STTEE---SSS CS
                           UPF0146  8 iaeenarg.kvvEvGiGrkldvaealakrgvdlvatDikek..kak..egvrivrDDvtd 62
                                      +++e+ ++ +v EvG G  l v+ +la++   lva Di+++  +a    gv+++r D+++
  gi|330507706|ref|YP_004384134.1|  4 AIKEARPEdHVLEVGCGSGL-VSLELARQVESLVALDINPHavRATreRGVEVIRSDLFE 62
                                      5666766669*******976.9*******999********96633334789999999986 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     4e-05     0.027      35      80 ..       8      52 ..       2      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-05
                                      -S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHT CS
                              TPMT 35 akaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeean 80
                                      a ++ +vl  +CG++l    lA q +++v++++ + Av++  +e++
  gi|330507706|ref|YP_004384134.1|  8 ARPEDHVLEVGCGSGLVSLELARQVESLVALDINPHAVRAT-RERG 52
                                      5677789999****************************994.5554 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     7e-05     0.049      21      75 ..       6      56 ..       1      67 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-05
                   Methyltransf_32 21 akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75
                                      ++++++ +v++vG+G g  s  la    +   ++v++d++ + v+++++r  ++ 
  gi|330507706|ref|YP_004384134.1|  6 KEARPEDHVLEVGCGSGLVSLELAR---Q-VESLVALDINPHAVRATRERGVEVI 56
                                      45788999*****************...4.4589**************9987765 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 ?   12.1   0.0   0.00011     0.073     202     239 ..      11      48 ..       2      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                   tRNA_U5-meth_tr 202 kgdllelycGnGnfslalarnfekvlateiakssveaa 239
                                       ++ +le+ cG G  sl lar++e ++a +i   +v a+
  gi|330507706|ref|YP_004384134.1|  11 EDHVLEVGCGSGLVSLELARQVESLVALDINPHAVRAT 48 
                                       5679**************************99988876 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.7   2.6e+03      43      69 ..       7      33 ..       3      46 .. 0.75
   2 ?   11.3   0.0   0.00021      0.15     116     183 ..      57     125 ..      38     129 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.7
                          N6_Mtase 43 epksgesvyDpacGsggllvqaekvlk 69
                                      e +++  v+   cGsg + ++ +++++
  gi|330507706|ref|YP_004384134.1|  7 EARPEDHVLEVGCGSGLVSLELARQVE 33
                                      556666799999999987777777765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00021
                          N6_Mtase 116 ekpkfe.kdkkfdvvvaNppfnqkewkektlekderfrea..vapksnadla..fllhiieslkpkGraavvl 183
                                        ++ fe    kfd ++ Npp+  +    k+ e+ +++ ++     +s +++   fll + e+l+p+Gra +++
  gi|330507706|ref|YP_004384134.1|  57 RSDLFEgIRGKFDLIIFNPPYLPT----KQAERSDQWINYalDGGESGRETIgrFLLDLAEHLRPGGRALLLI 125
                                       56666656789**********999....55555556766644333455555568**************97765 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00036      0.25      14      56 ..       7      46 ..       2      63 .. 0.83
   2 ?   -1.0   0.0       1.6   1.1e+03     178     193 ..      68      83 ..      52      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00036
                                      CCS-..--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHH CS
                   MethyltransfD12 14 elipkdkgktfvepFaGggaVffeakkqgkkvlinDinedlin 56
                                      e  p   ++++ e+ +G+g V++e+ +q++  ++ Din++ + 
  gi|330507706|ref|YP_004384134.1|  7 EARP---EDHVLEVGCGSGLVSLELARQVESLVALDINPHAVR 46
                                      4444...46899999***********************99765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                                       E.EEEE--S-T.S... CS
                   MethyltransfD12 178 ddivYlDPPYnprqyt 193
                                        d++ + PPY p+++ 
  gi|330507706|ref|YP_004384134.1|  68 FDLIIFNPPYLPTKQA 83 
                                       4577788****97765 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015      0.11       6      56 ..       2      50 ..       1      65 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                   Methyltransf_18  6 kaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekake 56
                                      +a ++  +++++v+ +G+  g+++++l+  +++++ +a Din++++++ +e
  gi|330507706|ref|YP_004384134.1|  2 QAAIKEARPEDHVLEVGCGSGLVSLELA--RQVESLVALDINPHAVRATRE 50
                                      55666677899****************9..57899********99988776 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015       0.1      83     116 ..      62      95 ..      27     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                   N6-adenineMlase  83 eelkgkfdviviDPPFlseeclkklaktaklllk 116
                                       e ++gkfd+i++ PP+l  + +++  + +++ l 
  gi|330507706|ref|YP_004384134.1|  62 EGIRGKFDLIIFNPPYLPTKQAERSDQWINYALD 95 
                                       55699************99999998888777655 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0032       2.2     113     137 ..      62      83 ..       4     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0032
                                       GG--STTS---EEEE---------- CS
                           UPF0020 113 akLrlkegevdvivtnpPYGerlgs 137
                                         +r   g++d+i+ npPY    ++
  gi|330507706|ref|YP_004384134.1|  62 EGIR---GKFDLIIFNPPYLPTKQA 83 
                                       3444...789999999999765554 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00025      0.17       2      20 ..      67      85 ..      66     127 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00025
                            Eco57I  2 kfdviiGNPPYqeseakke 20
                                      kfd ii NPPY  +++ ++
  gi|330507706|ref|YP_004384134.1| 67 KFDLIIFNPPYLPTKQAER 85
                                      8**********98874433 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00039      0.27      72      97 ..       9      34 ..       2      58 .. 0.82
   2 ?   -2.7   0.0         6   4.1e+03     159     174 ..     111     126 ..     110     147 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00039
                                      -TT-EEEEES-TTSHHHHHHHHHHCT CS
                              PCMT 72 kkgarvLevGsGsGyltavlarlvge 97
                                      ++ ++vLevG+GsG  +  lar v++
  gi|330507706|ref|YP_004384134.1|  9 RPEDHVLEVGCGSGLVSLELARQVES 34
                                      5789**********999888888765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6
                                       HHHTEEEEEEEEEEES CS
                              PCMT 159 lidQLkeGGrlvvPvg 174
                                       l + L +GGr ++ + 
  gi|330507706|ref|YP_004384134.1| 111 LAEHLRPGGRALLLIS 126
                                       5678899999877665 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00046      0.32      95     139 ..       5      47 ..       2      56 .. 0.89
   2 ?   -2.2   0.0       4.1   2.8e+03      52      67 ..     132     147 ..     101     156 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00046
                                       HTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHH CS
                            Met_10  95 aklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvky 139
                                       +k +++ + V++v  G G  ++ +a+  + + ++a d+nP++v+ 
  gi|330507706|ref|YP_004384134.1|   5 IKEARPEDHVLEVGCGSGLVSLELAR--QVESLVALDINPHAVRA 47 
                                       5678899******************9..88899*********985 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.1
                                       --EEEEEES-.SEEEE CS
                            Met_10  52 felevlaGsdstetih 67 
                                        e+e++aG++ ++t++
  gi|330507706|ref|YP_004384134.1| 132 EEVEMMAGDAGLITER 147
                                       5677777766666654 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0003      0.21      45      68 ..       9      32 ..       2      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                   Methyltransf_16 45 lsklsvlELGsGtGlvGlavaell 68
                                      + + +vlE+G G+Glv l +a+++
  gi|330507706|ref|YP_004384134.1|  9 RPEDHVLEVGCGSGLVSLELARQV 32
                                      56789**************99984 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00059       0.4      66     108 ..      12      54 ..       2      74 .. 0.76
   2 ?   -2.3   0.0       2.7   1.8e+03     167     183 ..     106     122 ..     100     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00059
                          Pox_MCEL  66 lkvLdldcgkGgDLeKyekg.eIsklvatDiaeesieeckeRY.n 108
                                        +vL+++cg G  L   e + ++++lva Di+ ++++ ++eR  +
  gi|330507706|ref|YP_004384134.1|  12 DHVLEVGCGSG--LVSLELArQVESLVALDINPHAVRATRERGvE 54 
                                       579*****999..56665542699*****************9743 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.7
                          Pox_MCEL 167 tvlrNvaellasGGkvl 183
                                       + l  +ae l++GG+ l
  gi|330507706|ref|YP_004384134.1| 106 RFLLDLAEHLRPGGRAL 122
                                       678899********977 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0004      0.28      44      92 ..       7      52 ..       2      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0004
                                      -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHH CS
                   Ubie_methyltran 44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekkl 92
                                        ++  +vl+v +G+g ++++l+++v++   +v lDin++ ++ ++++ 
  gi|330507706|ref|YP_004384134.1|  7 EARPEDHVLEVGCGSGLVSLELARQVES---LVALDINPHAVRATRERG 52
                                      4566779*****************9996...789999999999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1224.74
//
Query:       gi|330507707|ref|YP_004384135.1|  [L=261]
Description: hypothetical protein MCON_1697 [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.0    1.9e-11   44.0   0.0    1.4  1  PLDc_2        PLD-like domain
     0.0027   17.1   0.0     0.0051   16.2   0.0    1.4  1  RE_NgoFVII    NgoFVII restriction endonuclease
  ------ inclusion threshold ------
      0.017   15.3   0.0      0.035   14.3   0.0    1.5  1  PLDc          Phospholipase D Active site motif
       0.13   11.9  11.2        0.2   11.3  11.2    1.2  1  Lebercilin    Ciliary protein causing Leber congenital amauro
       0.45   11.3   6.5       0.83   10.4   6.5    1.3  1  Occludin_ELL  Occludin homology domain


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   5.3e-15   1.9e-11       1     130 [.     129     253 ..     129     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 5.3e-15
                            PLDc_2   1 liqliksAkksidiatyyf..vsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvf 75 
                                       l+++++ A+ ++ ++++ +  ++   i++ l k  +rg ++ + ++ +++   +    +   ++  +++ g e+ + 
  gi|330507707|ref|YP_004384135.1| 129 LCRMLEAARFEVVVVSPWIkrQTWNRIAAPLQKFFRRGGRLVVFMRGRES---DYSSGMSDDIQDEVRRLGGELLF- 201
                                       56778888888888888884444444677788899999999999998443...33334555555555666888444. PP

                            PLDc_2  76 etllgslHaKlylidgktvivGSsNltkrgldlnlElnvviedkelakeleeeFe 130
                                           + lHaK+y+id+k +iv+S+Nl++ g d n+E++v++ d+++++ + ++ +
  gi|330507707|ref|YP_004384135.1| 202 -V--RPLHAKIYMIDRKEAIVTSANLSQGGIDDNYEAGVWLNDPQVIHDICSYVD 253
                                       .2..568*************************************99998877766 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.4e-06    0.0051      76     135 ..     201     255 ..     185     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-06
                                       SSSXBXXXEEEEEET.TEEEEEEESXXSXXTTSXXXSBXEEEEEE.HHHHHHHHHHHHHH CS
                        RE_NgoFVII  76 ysvkvHsKlYiwkkdgkplsAliGSANlssnglrtrqrEtlvdldtedafkeldeyiqsl 135
                                        + + H+K+Y+  ++    +A++ SANls+ g   + +E+ v l++ + ++ + +y+++l
  gi|330507707|ref|YP_004384135.1| 201 FVRPLHAKIYMIDRK----EAIVTSANLSQGGI-DDNYEAGVWLNDPQVIHDICSYVDDL 255
                                       34499*******999....9*********9886.67889999999988888888888766 PP

>> PLDc  Phospholipase D Active site motif
   #    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       5      25 ..     205     225 ..     204     227 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.8e-06
                                       E---EEEETTTEEEEE---SS CS
                              PLDc   5 hHqKivivDdrvafvGgaNLc 25 
                                       +H+Ki+++D + a+v++aNL 
  gi|330507707|ref|YP_004384135.1| 205 LHAKIYMIDRKEAIVTSANLS 225
                                       7******************96 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3  11.2   5.5e-05       0.2      75     153 ..      34     108 ..      23     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.5e-05
                        Lebercilin  75 rlRksqekerelekklkekeaellrlkdklkklkkLsedknLaereeLqkkLeeleakle.ekeekikeLerklele 150
                                        +R++q  +++l  +l+eke++l +l++++ +l kL   +nL+  eeL+k     +  +e +++e+++ Le +l  +
  gi|330507707|ref|YP_004384135.1|  34 GYRQMQMDVEQLRGRLREKEMKLDQLQRECAHLLKLK-SRNLDLEEELKKT----KRSAEyNSSERLQYLESYLARQ 105
                                       579********************************98.8999656665554....4444424567788888777776 PP

                        Lebercilin 151 eks 153
                                       e++
  gi|330507707|ref|YP_004384135.1| 106 EQN 108
                                       665 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   6.5   0.00023      0.83      22      89 ..      33     102 ..      29     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                      Occludin_ELL  22 keYkelhaeleevskkfseLerelkelkegsk...eykkieeeilqeykklkkdpeyqekkkrceyLkekL 89 
                                       + Y++++ ++e+++ +++e e +l++l+++     + k+++ ++ +e+kk k+++ey +  +r++yL++ L
  gi|330507707|ref|YP_004384135.1|  33 AGYRQMQMDVEQLRGRLREKEMKLDQLQRECAhllKLKSRNLDLEEELKKTKRSAEYNS-SERLQYLESYL 102
                                       56**************************99998888888999999************86.57999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1296  (0.0722851); expected 358.6 (0.02)
Passed bias filter:                      840  (0.0468515); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1893.61
//
Query:       gi|330507708|ref|YP_004384136.1|  [L=559]
Description: thermosome subunit gamma [Methanosaeta concilii GP6]
Scores for complete 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-169  564.1  19.9   2.8e-169  563.9  19.9    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.096   12.7   0.2        3.7    7.6   0.0    2.4  2  AAA_5       AAA domain (dynein-related subfamily)


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 !  563.9  19.9  3.1e-173  2.8e-169       1     489 [.      34     521 ..      34     523 .. 0.98

  Alignments for each domain:
  == domain 1  score: 563.9 bits;  conditional E-value: 3.1e-173
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++v++++GPkGmdK+lv+++g+v++TnDG+tilke++++hPaak+l+eaa++qd+evGDGTttv++LageLl++a
  gi|330507708|ref|YP_004384136.1|  34 VANAVRSSMGPKGMDKLLVDSIGDVTITNDGVTILKEMDVQHPAAKMLIEAAKTQDKEVGDGTTTVAVLAGELLRKA 110
                                       689************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCH CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.kli 153
                                       e l++++vhpt i++gy++a+++a+++ k+i  +++ +e dr  L ++art++++kl ++   +++  +vd v +++
  gi|330507708|ref|YP_004384136.1| 111 EVLLDQKVHPTMIVQGYRMAADEAVKIAKSI--AFEAQESDRVLLERIARTAMTGKLADSPDSKMAGYAVDLVlNAT 185
                                       *******************************..9999999********************999***99999995555 PP

                                       CCCS..EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCC CS
                        Cpn60_TCP1 154 eene..keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdae 228
                                       e+    + +d++r++v+k+ g+s  dse++eG+v+dk++++++mp+k+++akv+ll++++e + tetkt+v++++ +
  gi|330507708|ref|YP_004384136.1| 186 EDYGdkRVFDMDRVNVEKKVGESTADSEIIEGVVIDKEIVHQNMPRKVTDAKVALLSCPIESKDTETKTEVQITSSD 262
                                       54449999********************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGG CS
                        Cpn60_TCP1 229 eleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledlt 305
                                       +++ ++++e+k ++e  +k+i+sg+nvv+cqkgiddla+h+la++g+lalrrv kkdl++lakatGa++v+sl++l+
  gi|330507708|ref|YP_004384136.1| 263 QFQMFMEHEKKRVKEAADKVIASGANVVFCQKGIDDLAQHYLAQAGVLALRRVIKKDLDKLAKATGANIVTSLDELK 339
                                       ***************************************************************************** PP

                                       CGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHH CS
                        Cpn60_TCP1 306 peelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatele 382
                                       p++lG+a  vee+++gs  +t+i++ +++++at+llrg t++vld +era++dAl++v+ ++ed+k+v+GG+a e+e
  gi|330507708|ref|YP_004384136.1| 340 PSDLGSAALVEERRVGSGIMTFITG-TKKSAATLLLRGGTQQVLDGLERALDDALHAVADVVEDKKLVVGGAAPEIE 415
                                       ************************9.7888*********************************************** PP

                                       HHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTX CS
                        Cpn60_TCP1 383 lakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagv 459
                                       +a +l+eya +++g+eqla+ +fa+A+e++pktLaeNaG+d+i+ + +l+++h++++ + g+++ +ge++d+ e gv
  gi|330507708|ref|YP_004384136.1| 416 IALRLREYAATLKGREQLAVAKFAEAMEIVPKTLAENAGFDAIDKVVELKSRHSSNK-NIGLNAYTGETVDMYELGV 491
                                       *********************************************************.******************* PP

                                       EEEHHHHHHHHHHHHHHHHHHHCEEEEEXX CS
                        Cpn60_TCP1 460 vDplkvkrqalksAteaastiLrideiika 489
                                       v+pl+vk qa+ sAt+aa++iLrid+++  
  gi|330507708|ref|YP_004384136.1| 492 VEPLRVKIQAILSATDAACLILRIDDVLAS 521
                                       ***************************875 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 ?    2.6   0.1     0.013   1.2e+02      28      76 ..     110     158 ..      91     164 .. 0.79
   2 ?    7.6   0.0   0.00041       3.7      34      97 ..     341     408 ..     320     436 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.013
                                       EEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG CS
                             AAA_5  28 eyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEver 76 
                                        +v+l ++  ++ ++++++++ ++++   +++  +a+e++ ++l+ + r
  gi|330507708|ref|YP_004384136.1| 110 AEVLLDQKVHPTMIVQGYRMAADEAVKIAKSIAFEAQESDRVLLERIAR 158
                                       57999****************7777777666666999999999987766 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00041
                                       TT--HHHHH--B--.........--------....G-SEEEEESGGG--HHHHHHHHHHHHSSEEE.. CS
                             AAA_5  34 rdtteedlkgrreikngttslvdsplvraar....egeilvlDEveraesevlnsLlslleerrllle 97 
                                       +d+ ++ l+ +r++ +g   +  +  + aa+     g   vlD++era +++l ++  + e+++l + 
  gi|330507708|ref|YP_004384136.1| 341 SDLGSAALVEERRVGSGIMTFITGTKKSAATlllrGGTQQVLDGLERALDDALHAVADVVEDKKLVVG 408
                                       6777888888899988888888888888888888899999***********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 4130.53
//
Query:       gi|330507709|ref|YP_004384137.1|  [L=64]
Description: cold shock DNA binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-18   64.6   2.2    5.7e-18   64.5   2.2    1.0  1  CSD       'Cold-shock' DNA-binding domain


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   2.2   3.2e-22   5.7e-18       2      65 ..       3      63 ..       2      64 .] 0.97

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 3.2e-22
                                      EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                               CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                       GtVk fn+ k+fGFI+ +dg+ d FvHv+ ++      ++eg++V+F+v+eg+kgp+A +V k
  gi|330507709|ref|YP_004384137.1|  3 DGTVKFFNRVKNFGFIAGDDGK-DYFVHVTGLKPGV--AIDEGDKVSFDVIEGEKGPKADKVEK 63
                                      6********************9.*************..************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 527.69
//
Query:       gi|330507710|ref|YP_004384138.1|  [L=199]
Description: transmembrane protein [Methanosaeta concilii GP6]
Scores for complete 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-42  141.6  13.6    3.1e-23   81.9   3.1    2.1  2  UPF0016      Uncharacterized protein family UPF0016
    0.00076   19.2  12.8       0.18   11.4   3.6    2.2  2  TauE         Sulfite exporter TauE/SafE
      0.009   16.2   0.8      0.009   16.2   0.8    2.4  2  DUF2304      Uncharacterized conserved protein (DUF2304)
  ------ inclusion threshold ------
      0.057   13.6   0.3      0.057   13.6   0.3    4.0  4  DUF3784      Domain of unknown function (DUF3784)
      0.064   13.4   1.9       0.12   12.6   1.9    1.4  1  L_HMGIC_fpl  Lipoma HMGIC fusion partner-like protein
       0.39   10.7  15.6       0.31   11.0   6.5    2.2  2  Colicin_V    Colicin V production protein
       0.64    9.6   4.8       0.48   10.0   2.9    1.7  1  PIRT         Phosphoinositide-interacting protein family
        5.4    7.1  11.0        1.4    9.0   3.7    2.6  3  SirB         Invasion gene expression up-regulator, SirB
          6    6.8   7.5         23    4.9   0.3    2.5  2  RseC_MucC    Positive regulator of sigma(E), RseC/MucC
        8.6    6.1  11.7       0.12   12.1   3.4    1.9  2  Claudin_2    PMP-22/EMP/MP20/Claudin tight junction


Domain annotation for each model (and alignments):
>> UPF0016  Uncharacterized protein family UPF0016
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   2.9   2.2e-21   3.9e-18       4      75 .]      12      84 ..       9      84 .. 0.97
   2 !   81.9   3.1   1.7e-26   3.1e-23       2      75 .]     109     182 ..     108     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 2.2e-21
                           UPF0016  4 flliflaElGDkTqlaaalLaary.kplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75
                                      +++i laE+GDkTql ++lL++r+ +++p ++G++lA+++ +++++l+Gs++++ +p +l++l+++ +F+lfG
  gi|330507710|ref|YP_004384138.1| 12 LIAIGLAEMGDKTQLSVILLSSRTrEYIPLLAGVMLAFLITDGFAILIGSWMTGIIPLDLLKLISGGVFILFG 84
                                      67899*******************99**********************************************9 PP

  == domain 2  score: 81.9 bits;  conditional E-value: 1.7e-26
                           UPF0016   2 aaflliflaElGDkTqlaaalLaarykplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75 
                                       + f+lifl+E+GDkTq+a al+a++y+p+ Vf+G+++Al++ +v++++lG+ ++++++++l+ ++a+ lFl++G
  gi|330507710|ref|YP_004384138.1| 109 SGFSLIFLSEWGDKTQIASALFATEYNPIMVFIGVMAALFILSVMAIYLGQIISQKVDRKLVSRIAGTLFLIIG 182
                                       679*********************************************************************98 PP

>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   5.1   0.00014      0.25      65     114 ..      45     117 ..      23     148 .. 0.63
   2 !   11.4   3.6   9.8e-05      0.18     191     235 ..     140     184 ..     122     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                              TauE  65 lllllllgsliGallGallllllpsellkllfgvlllllallmllrkkr.......................s 114
                                       ++l +l+    ++l+G+++   +p +llkl+ g + +l+++l+l+  ++                       s
  gi|330507710|ref|YP_004384138.1|  45 VMLAFLITDGFAILIGSWMTGIIPLDLLKLISGGVFILFGALILRGDQKeaeeerglssgnallsgfsliflS 117
                                       456666666778999*****************************96665445554444444444444433330 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 9.8e-05
                              TauE 191 dwpllllllpgallGallGarlarrlsertlrrlfallllvlgvk 235
                                        + ++++l + ++  ++lG+ ++++++++ + r+ ++l l++g+ 
  gi|330507710|ref|YP_004384138.1| 140 FIGVMAALFILSVMAIYLGQIISQKVDRKLVSRIAGTLFLIIGIA 184
                                       3333444999999***************************99985 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.8     5e-06     0.009       4      84 ..      74     156 ..      71     176 .. 0.72
   2 ?    1.3   3.6      0.22     4e+02       4      49 ..     148     193 ..     147     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5e-06
                           DUF2304   4 iiliivsvllllliirlvrkkklkleysll...wlllalilivlslfpqiltvlanllGvgrgtnllfllgivfllv 77 
                                       +i+  v +l+ +li+r   +k+ ++e+ l     ll ++ li+ls + + +++ + l+ +++++ ++f+ ++++l++
  gi|330507710|ref|YP_004384138.1|  74 LISGGVFILFGALILRG-DQKEAEEERGLSsgnALLSGFSLIFLSEWGDKTQIASALFATEYNPIMVFIGVMAALFI 149
                                       55666666666666665.6777777777763336999********************************99999999 PP

                           DUF2304  78 ilfslsl 84 
                                       +++    
  gi|330507710|ref|YP_004384138.1| 150 LSVMAIY 156
                                       8775443 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.22
                           DUF2304   4 iiliivsvllllliirlvrkkklkleysllwlllalilivlslfpq 49 
                                       +il +++++l  +i ++v +k ++     l+l++++++i+  l p 
  gi|330507710|ref|YP_004384138.1| 148 FILSVMAIYLGQIISQKVDRKLVSRIAGTLFLIIGIAIILSLLAPY 193
                                       5788888888888999999998888888888888888888888775 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.4      0.63   1.1e+03      52      73 ..      41      56 ..      21      73 .. 0.51
   2 ?    1.3   0.5      0.23   4.1e+02       1      17 [.      74      90 ..      74      95 .. 0.81
   3 ?   -0.4   3.9      0.74   1.3e+03      64      89 ..     132     157 ..     107     162 .. 0.63
   4 ?   13.6   0.3   3.2e-05     0.057      35      63 ..     163     191 ..     159     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.63
                           DUF3784 52 ligilflllgllsaiesealli 73
                                      l++ ++l++ +         ++
  gi|330507710|ref|YP_004384138.1| 41 LLAGVMLAFLIT------DGFA 56
                                      333333333333......1111 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.23
                           DUF3784  1 lilallflilGilflkg 17
                                      li++++f+++G l+l g
  gi|330507710|ref|YP_004384138.1| 74 LISGGVFILFGALILRG 90
                                      57899999999999866 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.74
                           DUF3784  64 saiesealliialiviiiiviylivy 89 
                                         ++  +++i+++++++i+++++i++
  gi|330507710|ref|YP_004384138.1| 132 TEYNPIMVFIGVMAALFILSVMAIYL 157
                                       44556666677777777777776654 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 3.2e-05
                           DUF3784  35 ekydekklsrfmgivllligilflllgll 63 
                                       +k+d k +sr +g ++l+igi+++l+ l 
  gi|330507710|ref|YP_004384138.1| 163 QKVDRKLVSRIAGTLFLIIGIAIILSLLA 191
                                       699*****************666666554 PP

>> L_HMGIC_fpl  Lipoma HMGIC fusion partner-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.9   6.7e-05      0.12      65     125 ..     125     190 ..     115     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.7e-05
                       L_HMGIC_fpl  65 ipssa....wkaaavlvalgill.lllvlllslltlcrqsilkksvfkicallqlvaglllllgll 125
                                       i+s      ++  +v++++  +l +l+v+ + l  +++q++  k v +i+++l l+ g+ ++l+ll
  gi|330507710|ref|YP_004384138.1| 125 IASALfateYNPIMVFIGVMAALfILSVMAIYLGQIISQKVDRKLVSRIAGTLFLIIGIAIILSLL 190
                                       4444423337788999999999989999*********************************99876 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.6      0.01        18      28      73 ..      42      87 ..       9      90 .. 0.64
   2 ?   11.0   6.5   0.00017      0.31      59     115 ..     134     191 ..     106     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.01
                         Colicin_V 28 llgwvvafvvasllypslaellaelilspalaaiiaflllfllvll 73
                                      l+g+++af+++  ++  ++ +++ +i+   l  i + + +++++l+
  gi|330507710|ref|YP_004384138.1| 42 LAGVMLAFLITDGFAILIGSWMTGIIPLDLLKLISGGVFILFGALI 87
                                      4566666666666666666666664333333333333666666555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00017
                         Colicin_V  59 aaiiaflllfllvllivsllgallsklvsktglgl.ldrllGaifGllkglllvvlll 115
                                       ++ i  ++ ++++l+i+s+++ +l++++s+++ +  + r++G +f ++ ++++++ll 
  gi|330507710|ref|YP_004384138.1| 134 YNPIMVFIGVMAALFILSVMAIYLGQIISQKVDRKlVSRIAGTLFLIIGIAIILSLLA 191
                                       6677788888899999999999999999777777669999999999999999999543 PP

>> PIRT  Phosphoinositide-interacting protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.9   0.00027      0.48      48      99 ..     135     187 ..     112     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
                              PIRT  48 kpiiv.lsvGgavfllGvvittlsrnstlknkdkevfklsGpaflslGlmllv 99 
                                        pi+v + v +a+f+l v+   l +    k + k v++++G  fl +G+ +++
  gi|330507710|ref|YP_004384138.1| 135 NPIMVfIGVMAALFILSVMAIYLGQIISQKVDRKLVSRIAGTLFLIIGIAIIL 187
                                       4665527899*************9999999999999************98765 PP

>> SirB  Invasion gene expression up-regulator, SirB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.4      0.14   2.5e+02      50      73 ..      41      66 ..      16      99 .. 0.56
   2 ?    0.1   0.0      0.47   8.4e+02      13      33 ..      74      94 ..      69     124 .. 0.68
   3 ?    9.0   3.7   0.00079       1.4       9      60 ..     138     189 ..     137     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.14
                              SirB 50 llsgiaLlvllglspf..tkaWltaK 73
                                      ll+g++L++l+         +W+t  
  gi|330507710|ref|YP_004384138.1| 41 LLAGVMLAFLITDGFAilIGSWMTGI 66
                                      56666666665322112234455532 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.47
                              SirB 13 llslllFilrgllllkgsall 33
                                      l+s  +Fil g+l l+g ++ 
  gi|330507710|ref|YP_004384138.1| 74 LISGGVFILFGALILRGDQKE 94
                                      467777777777777655543 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00079
                              SirB   9 lllvllslllFilrgllllkgsallqkkllkilphivdtlLllsgiaLlvll 60 
                                       ++++ +  +lFil +++ + g+   qk   k+++ i  tl+l+ gia+++ l
  gi|330507710|ref|YP_004384138.1| 138 MVFIGVMAALFILSVMAIYLGQIISQKVDRKLVSRIAGTLFLIIGIAIILSL 189
                                       67889999**************************************988764 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3     0.013        23      80     122 ..      55      99 ..      37     103 .. 0.71
   2 ?    4.8   1.8     0.014        25      68     111 ..     145     186 ..     118     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.013
                         RseC_MucC  80 lgallgsall..gssellaalgallglvlgflivrllskrlkkks 122
                                       +++l+gs+++  +  +ll ++ + +++++g li+r  +k++++++
  gi|330507710|ref|YP_004384138.1|  55 FAILIGSWMTgiIPLDLLKLISGGVFILFGALILRGDQKEAEEER 99 
                                       344455555566799*******************99998877665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.014
                         RseC_MucC  68 llvYllPllllilgallgsallgssellaalgallglvlgfliv 111
                                       + +++l ++++ lg ++ + +  + +l++ +++ l+l++g+ i+
  gi|330507710|ref|YP_004384138.1| 145 AALFILSVMAIYLGQIISQKV--DRKLVSRIAGTLFLIIGIAII 186
                                       445555555555555555555..899999999999999999887 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 ?   -1.5   1.3      0.96   1.7e+03     101     136 ..      48      87 ..      25      90 .. 0.64
   2 ?   12.1   3.4   6.6e-05      0.12      75     141 ..     127     190 ..     109     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.96
                         Claudin_2 101 vlivlavvlgllallkqsv....lllkaagilfllagvlg 136
                                        ++++  +++l++++ +      ll +  g++f+l g+l+
  gi|330507710|ref|YP_004384138.1|  48 AFLITDGFAILIGSWMTGIipldLLKLISGGVFILFGALI 87 
                                       3345555666666666665555566666677777766666 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6.6e-05
                         Claudin_2  75 eeivsisatsllalarfvqvlliLslvlivlavvlgllallkqsvlllkaagilfllagvlgllavv 141
                                       +  + +++ + + +++++++l+iLs+++i l+ +   ++    ++l+ + ag+lfl+ g+ + l+++
  gi|330507710|ref|YP_004384138.1| 127 SALFATEYNPIMVFIGVMAALFILSVMAIYLGQI---ISQKVDRKLVSRIAGTLFLIIGIAIILSLL 190
                                       55677899999**************999999864...344444558999999****99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 1539.78
//
Query:       gi|330507711|ref|YP_004384139.1|  [L=602]
Description: translation initiation factor aIF-2 [Methanosaeta concilii GP6]
Scores for complete 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  114.6   0.0    3.6e-32  111.5   0.0    2.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    5.2e-31  106.4   6.2    5.4e-31  106.3   3.5    2.3  2  GTP_EFTU_D4  Elongation factor Tu domain 4
    2.3e-20   72.7   1.0    1.2e-19   70.3   0.2    2.3  2  IF-2         Translation-initiation factor 2
    5.8e-10   39.4   4.4    3.5e-07   30.5   0.0    3.2  3  GTP_EFTU_D2  Elongation factor Tu domain 2
    6.4e-07   29.4   0.0    1.8e-06   28.0   0.0    1.9  1  MMR_HSR1     50S ribosome-binding GTPase
      0.007   16.2   0.0      0.027   14.2   0.0    1.8  2  ATP_bind_1   Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.058   13.4   0.1        0.5   10.4   0.0    2.3  2  Dynamin_N    Dynamin family
       0.14   12.0   1.2        1.1    9.2   0.2    2.7  2  RsgA_GTPase  RsgA GTPase
       0.16   11.7   0.0       0.78    9.5   0.0    2.1  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati


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 !  111.5   0.0   1.8e-35   3.6e-32       4     191 ..      21     227 ..      18     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 1.8e-35
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSS CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGH 80 
                                         ++++ghvDhGKtTL+d++  ++ a  ++g  ++        ++E    +  + +  ++ ke +   + +iDtPGH
  gi|330507711|ref|YP_004384139.1|  21 PIVVVMGHVDHGKTTLLDKIRGTAVAKGEAGLITQ-----HIGATEVPLDVVQDFCGSHFGKEIEIPGLLFIDTPGH 92 
                                       5799*****************88888777665554.....556677777777888888888889999********** PP

                                       GGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHH CS
                          GTP_EFTU  81 vdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeiveev 146
                                         F++  +rg + +D+avl+vd++eG +pqt e l ++++ ++p++v+ NKmDr+            ++lk + e v
  gi|330507711|ref|YP_004384139.1|  93 HAFTSMRSRGGSLADLAVLIVDVNEGFQPQTIESLSILKRFKTPFVVAANKMDRIggwhtttnapfAKSLKVQSERV 169
                                       ***********************************************************999988877777777777 PP

                                       HHHHHHH....HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 147 kqklsrk....eeklekygekge.........kevpvvfgSalkgegvktllealvel 191
                                       ++ l+++     ++l kyg++++         ++v +v++Sa++gegv +ll  lv l
  gi|330507711|ref|YP_004384139.1| 170 SEILDTRlyelVGELYKYGFDADrydritdftRTVGIVPISAITGEGVPDLLMILVGL 227
                                       777765577777778888888779999999999******************9988865 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.69   1.4e+03      30      54 ..     232     255 ..     222     258 .. 0.77
   2 !  106.3   3.5   2.7e-34   5.4e-31       1      86 []     474     559 ..     474     559 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.69
                                       EETT-EEEETTE.EEEEEEEEEETT CS
                       GTP_EFTU_D4  30 ikpgvklikedGrevGeilqiqdkg 54 
                                       +k +++l +++G  vG+il++++++
  gi|330507711|ref|YP_004384139.1| 232 LKDNLQL-TATGPGVGTILEVKEEK 255
                                       6666777.679999******99875 PP

  == domain 2  score: 106.3 bits;  conditional E-value: 2.7e-34
                                       S-CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTT CS
                       GTP_EFTU_D4   1 rPgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGr 77 
                                       rPg ++ilp++vfr+s+pa+vGv+v+gG+++++v+l++edG +vG+i+ iq ++++   a+ Gqevaisi+g++vGr
  gi|330507711|ref|YP_004384139.1| 474 RPGAVRILPDCVFRQSKPAVVGVQVIGGIVRTQVNLMREDGANVGVIKGIQAHNENQGSATVGQEVAISIDGPTVGR 550
                                       7**************************************************************************** PP

                                       S--TT-EEE CS
                       GTP_EFTU_D4  78 qikegdily 86 
                                       qi+egdily
  gi|330507711|ref|YP_004384139.1| 551 QIHEGDILY 559
                                       ********9 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.2   6.1e-23   1.2e-19       5     104 ..     355     453 ..     351     454 .. 0.92
   2 ?    0.1   0.0      0.42   8.4e+02      40      76 ..     537     576 ..     518     587 .. 0.81

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 6.1e-23
                                       HHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHHST....EEEEEESSSCT CS
                              IF-2   5 feeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasasn....aiiigFnvkvs 77 
                                       ++++  ++++ ++iik+D+ GsleAl   L+        +++ +++vG+i+++Dv  a+a n    + i+gFnv++ 
  gi|330507711|ref|YP_004384139.1| 355 LDAVRIDTENEGLIIKSDTIGSLEALVGELKAR-----DIHIHYADVGPISRRDVIRAAAINdpllSAILGFNVDIL 426
                                       566666778899*******************98.....5*********************777999*********** PP

                                       HHHHHCCCCCTSEEEEESSHHHHHHHH CS
                              IF-2  78 kkakklaekegvkirlynvIYkliddv 104
                                       ++a ++++k +v ++++++IY +i+ +
  gi|330507711|ref|YP_004384139.1| 427 PDALNEIQKTNVPVFSSDIIYTIIESY 453
                                       ************************987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.42
                                       SSTEEEECEEEESS.B-HHHHHHHHH..STEEEEEESSSC CS
                              IF-2  40 eevkvkvihsgvGa.itesDvelasa..snaiiigFnvkv 76 
                                       +ev +++    vG  i+e D+ +++   ++a i+  ++k+
  gi|330507711|ref|YP_004384139.1| 537 QEVAISIDGPTVGRqIHEGDILYVNIpeKHARIVELELKP 576
                                       789999999999955*******999855558888776665 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 ?   -2.3   0.0       3.1   6.2e+03      48      59 ..      44      55 ..      23      83 .. 0.65
   2 !   30.5   0.0   1.7e-10   3.5e-07       1      73 [.     258     335 ..     258     336 .. 0.93
   3 !    7.9   1.8     0.002       3.9      18      74 .]     506     559 ..     492     559 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.1
                                      EETTSEEEEEEE CS
                       GTP_EFTU_D2 48 avaganaGviva 59
                                      ava + aG+i+ 
  gi|330507711|ref|YP_004384139.1| 44 AVAKGEAGLITQ 55
                                      455555555554 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 1.7e-10
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE..........ETTSEEEEEEEESSCCSGS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededea..........vaganaGvivaikgledai 67 
                                       Gt+ ++++y+G++  Gd+v +   +ts+++ vt+i++l+++++ + e            + a+ Gv+v +++l++a 
  gi|330507711|ref|YP_004384139.1| 258 GTTLDVILYNGEFFAGDTVIV---GTSREPLVTKIRALLKPKP-LAEIrseerflpvkHVSAASGVKVSAPKLDNA- 329
                                       89******************9...57799************55.6666699************************8. PP

                                       STTCEE CS
                       GTP_EFTU_D2  68 ivGdtl 73 
                                       ++G+t+
  gi|330507711|ref|YP_004384139.1| 330 LAGSTI 335
                                       *****8 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.002
                                       EEEEEC.TCTTSEE.EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                       GTP_EFTU_D2  18 evrilg.ndtskke.ivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                       +v +++ +     +  v+ i+++++++e++  a +g+ + + + ++ +   i  Gd+l+
  gi|330507711|ref|YP_004384139.1| 506 QVNLMReD-----GaNVGVIKGIQAHNENQGSATVGQEVAISIDGPTVGRQIHEGDILY 559
                                       45553322.....13799**************************************997 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   9.3e-10   1.8e-06       2     114 .]      23     143 ..      22     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 9.3e-10
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE...............EEEEECGGCSSHHHHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke...............ielvDtpGliegasee 63 
                                       v+++G+   GK+tL+ ++ g+++  ++    T++i   +v l+  +               + ++DtpG  +     
  gi|330507711|ref|YP_004384139.1|  23 VVVMGHVDHGKTTLLDKIRGTAVAKGEAGLITQHIGATEVPLDVVQdfcgshfgkeieipgLLFIDTPG-HH----- 93 
                                       899****************9888888888888888888777553223555556666666669*******.44..... PP

                                       HHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  64 kglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                         ++    +  + adl++l+vd++ e+++p+  e  ++l++ k p+++++nk
  gi|330507711|ref|YP_004384139.1|  94 -AFTSMRSRGGSlADLAVLIVDVN-EGFQPQTIESLSILKRFKTPFVVAANK 143
                                       .2333333333348********87.88************99*******9998 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         1     2e+03       1      18 [.      25      42 ..      25      50 .. 0.80
   2 !   14.2   0.0   1.4e-05     0.027      66     231 ..      58     220 ..      44     224 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1
                        ATP_bind_1  1 vvGpaGsGKttfvgalse 18
                                      v+G++  GKtt+  ++  
  gi|330507711|ref|YP_004384139.1| 25 VMGHVDHGKTTLLDKIRG 42
                                      899999******988765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.4e-05
                        ATP_bind_1  66 galvvaleflresl.dwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkf 141
                                       ga+ v l+++++ +  ++ +e+  e   +l +DtPG   +  +++ +         + a  +v +vD++   +p   
  gi|330507711|ref|YP_004384139.1|  58 GATEVPLDVVQDFCgSHFGKEI--EIPGLLFIDTPGHHAFTSMRSRGG--------SLADLAVLIVDVNEGFQPQ-- 122
                                       5666666666666655556666..33379999*************999........77789999**998766654.. PP

                        ATP_bind_1 142 isgllsalsamlrlelPhvvvlnkfDllkek.lekeleffedvealslllekee.........ekykklae.aiael 207
                                          ++ +ls++ r ++P+vv+ nk+D +    ++ +  f + ++  s+   +           e yk+ +  +  + 
  gi|330507711|ref|YP_004384139.1| 123 ---TIESLSILKRFKTPFVVAANKMDRIGGWhTTTNAPFAKSLKVQSERVSEILdtrlyelvgELYKYGFDaDRYDR 196
                                       ...44558******************876444333333333222222222111123445555533443332023345 PP

                        ATP_bind_1 208 leefalvlrflplssekeesiedl 231
                                       +++f+++  ++p+s+ ++e++ dl
  gi|330507711|ref|YP_004384139.1| 197 ITDFTRTVGIVPISAITGEGVPDL 220
                                       555555556666666666666555 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00025       0.5       1      34 [.      23      56 ..      23      64 .. 0.91
   2 ?   -0.2   0.0      0.46   9.2e+02     100     113 ..      81      94 ..      76     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00025
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                                      ++v+G++ +GK+++l+++ g ++   +++++T+ 
  gi|330507711|ref|YP_004384139.1| 23 VVVMGHVDHGKTTLLDKIRGTAVAKGEAGLITQH 56
                                      79********************999999988875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.46
                                       S-SEEEEE---B-S CS
                         Dynamin_N 100 vkgltlvDlPGlds 113
                                        +gl ++D+PG + 
  gi|330507711|ref|YP_004384139.1|  81 IPGLLFIDTPGHHA 94 
                                       57899******875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2   0.00053       1.1      94     125 ..      15      46 ..       2      98 .. 0.71
   2 ?   -0.1   0.0      0.37   7.4e+02      17      59 ..     107     147 ..      95     168 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00053
                                       HHHCTTSEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  94 kellkdktsvlvGqSGvGKStLinallpelel 125
                                       +++l+  ++v++G+   GK+tL++++++++ +
  gi|330507711|ref|YP_004384139.1|  15 QSNLRTPIVVVMGHVDHGKTTLLDKIRGTAVA 46 
                                       6889999********************98432 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.37
                                       -EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG- CS
                       RsgA_GTPase  17 dqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDll 59 
                                       d ++++v ++ + +++++++  L ++++ + + v++ nK+D +
  gi|330507711|ref|YP_004384139.1| 107 DLAVLIVDVN-EGFQPQTIE-SLSILKRFKTPFVVAANKMDRI 147
                                       6777888887.788888887.5778888888888888888865 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00039      0.78       4      26 ..      23      45 ..      20      71 .. 0.84
   2 ?   -1.7   0.0       1.1   2.1e+03      40      48 ..      86      94 ..      79     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00039
                         PduV-EutP  4 illiGkvgsGKttLtqalkgeel 26
                                      ++++G+v+ GKttL  +++g ++
  gi|330507711|ref|YP_004384139.1| 23 VVVMGHVDHGKTTLLDKIRGTAV 45
                                      899***************99876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                         PduV-EutP 40 viDtPGeyl 48
                                      +iDtPG ++
  gi|330507711|ref|YP_004384139.1| 86 FIDTPGHHA 94
                                      69***9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 3274.91
//
Query:       gi|330507712|ref|YP_004384140.1|  [L=143]
Description: nucleoside diphosphate kinase [Methanosaeta concilii GP6]
Scores for complete 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-52  174.5   0.0    1.1e-51  174.4   0.0    1.0  1  NDK       Nucleoside diphosphate kinase


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.4   0.0   6.2e-56   1.1e-51       6     134 ..       1     129 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 174.4 bits;  conditional E-value: 6.2e-56
                                       EE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHHHH CS
                               NDK   6 liKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedaiek 82 
                                       ++KPd+v+rgl+g+i++r+eekg+kiva+k+  + e++a+ehYaeh gk+f+++lv+f+tsgp v lv+eg+ ai++
  gi|330507712|ref|YP_004384140.1|   1 MVKPDGVQRGLVGKILQRIEEKGFKIVAMKLAAMPEAKAKEHYAEHVGKKFYQDLVDFITSGPSVSLVVEGRGAIAA 77 
                                       89*************************************************************************** PP

                                       HHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTGGG CS
                               NDK  83 vreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFkeee 134
                                       +r++ Gatnp ea pgtiR+d+g+++g+N+vHgSds++sa rei+l F+++e
  gi|330507712|ref|YP_004384140.1|  78 MRKMNGATNPVEAVPGTIRGDWGIETGRNVVHGSDSPASASREIALHFDPSE 129
                                       ************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1130.95
//
Query:       gi|330507713|ref|YP_004384141.1|  [L=56]
Description: 50S ribosomal protein L24e [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-19   68.1   1.8    6.4e-19   67.9   1.8    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
    0.00011   22.2   0.5    0.00015   21.8   0.5    1.1  1  YHS             YHS domain
    0.00096   19.0   2.7     0.0013   18.6   2.7    1.2  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
     0.0015   17.5   0.1     0.0015   17.5   0.1    1.0  1  SerH            Cell surface immobilisation antigen SerH
  ------ inclusion threshold ------
      0.034   14.5   0.2      0.037   14.3   0.2    1.1  1  DUF3268         zinc-finger-containing domain
      0.043   14.1   0.5      0.047   14.0   0.5    1.1  1  Ta0938          Ta0938
      0.048   13.3   0.0      0.049   13.2   0.0    1.0  1  Ras             Ras family
      0.087   12.3   3.7       0.21   11.1   3.7    1.6  1  zf-FLZ          zinc-finger of the FCS-type, C2-C2
       0.11   12.4   4.5       0.25   11.2   4.5    1.6  1  VATC            Vms1-associating treble clef domain
       0.19   11.5   1.0       0.19   11.5   1.0    2.2  3  zf-C2H2_10      C2H2 zinc-finger


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 !   67.9   1.8   3.6e-22   6.4e-19       1      53 [.       1      53 [.       1      55 [. 0.96

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 3.6e-22
                                      XXX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTST CS
                    Ribosomal_L24e  1 mktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrnPrklkWTk 53
                                      m+ +kCsF+ + i+PG+Gk++ ++Dg+vf+F+s+Kce+++   r  r++kW +
  gi|330507713|ref|YP_004384141.1|  1 MEERKCSFCNKTIEPGTGKLYAKKDGTVFFFCSAKCENNVALGRVTRRIKWAR 53
                                      7889***********************************************86 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.5   8.5e-08   0.00015       6      35 ..       9      38 ..       8      39 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.5e-08
                               YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCkd 35
                                      c +++++++ + + + +G+ ++FcS++C++
  gi|330507713|ref|YP_004384141.1|  9 CNKTIEPGTGKLYAKKDGTVFFFCSAKCEN 38
                                      999*************************86 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.7   7.1e-07    0.0013       4      37 ..       4      36 ..       2      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.1e-07
                            zf-FCS  4 krCwfCkkyikgkpeftyvlendgvvgqFCStsC 37
                                      ++C+fC+k i+ ++    +  +dg v  FCS  C
  gi|330507713|ref|YP_004384141.1|  4 RKCSFCNKTIEPGT-GKLYAKKDGTVFFFCSAKC 36
                                      69********9999.689999**********999 PP

>> SerH  Cell surface immobilisation antigen SerH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   8.2e-07    0.0015     158     193 ..       4      39 ..       1      52 [. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.2e-07
                              SerH 158 anCaaCattaspkgknvfAnsaGsaCvassasCgss 193
                                        +C+ C++t +p + +++A ++G+     sa C++ 
  gi|330507713|ref|YP_004384141.1|   4 RKCSFCNKTIEPGTGKLYAKKDGTVFFFCSAKCENN 39 
                                       568888888888888888888888888888888765 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   2.1e-05     0.037       3      46 ..       4      46 ..       2      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                           DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylC.pkCdayvgvhkgt 46
                                       +C++C +++      ++Y +++ g++++ C  kC+  v + + t
  gi|330507713|ref|YP_004384141.1|  4 RKCSFCNKTIE-PGTGKLY-AKKDGTVFFFCsAKCENNVALGRVT 46
                                      68****87665.56678**.999999*****99***999876655 PP

>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   2.6e-05     0.047      14      61 ..       3      52 ..       1      55 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                                      GGS-SS---S-....--SS-B-TT--BSSS--SSSS-TTS-THHHHHHHHHH CS
                            Ta0938 14 ekgcalcgatw....gdyyeevdgeklffccdicakefvnllnevkkrtgls 61
                                      e+ c++c  t     g+ y++ dg  +ffc   c ++    l +v +r+++ 
  gi|330507713|ref|YP_004384141.1|  3 ERKCSFCNKTIepgtGKLYAKKDGTVFFFCSAKCENNV--ALGRVTRRIKWA 52
                                      77899999885444499**************9998765..467777777776 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.7e-05     0.049     114     150 ..       6      41 ..       2      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.7e-05
                                       TTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHH CS
                               Ras 114 vDleekravsteegeelakelglkfletSAktnenve 150
                                       +    +++++  +g+ +ak+ g+ f+ +SAk ++nv 
  gi|330507713|ref|YP_004384141.1|   6 CSFC-NKTIEPGTGKLYAKKDGTVFFFCSAKCENNVA 41 
                                       5555.489999************************95 PP

>> zf-FLZ  zinc-finger of the FCS-type, C2-C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.7   0.00012      0.21      14      45 ..       4      38 ..       4      42 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                            zf-FLZ 14 saCflCkkkLgegk.DiymYrGdka..FCSeeCRq 45
                                      ++C++C+k +++g    y  +  +   FCS+ C +
  gi|330507713|ref|YP_004384141.1|  4 RKCSFCNKTIEPGTgKLYAKKDGTVffFCSAKCEN 38
                                      58***********967777775554447****965 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.5   0.00014      0.25       4      31 ..       4      36 ..       2      39 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                              VATC  4 lrCsiCgeslegkv..yFekfd...frYCstkC 31
                                      ++Cs+C++ +e+ +   + k d   f +Cs kC
  gi|330507713|ref|YP_004384141.1|  4 RKCSFCNKTIEPGTgkLYAKKDgtvFFFCSAKC 36
                                      79*********8555566666655589****** PP

>> zf-C2H2_10  C2H2 zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.0   0.00011      0.19       5      12 ..       5      12 ..       4      12 .. 0.92
   2 ?   -3.7   0.4       5.8     1e+04       8       9 ..      31      32 ..      31      33 .. 0.43
   3 ?   -0.8   0.2      0.73   1.3e+03      17      20 ..      34      37 ..      34      38 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                        zf-C2H2_10  5 tCSYChet 12
                                      +CS+C++t
  gi|330507713|ref|YP_004384141.1|  5 KCSFCNKT 12
                                      7*****97 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.8
                        zf-C2H2_10  8 YC 9 
                                      +C
  gi|330507713|ref|YP_004384141.1| 31 FC 32
                                      55 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.73
                        zf-C2H2_10 17 AkCe 20
                                      AkCe
  gi|330507713|ref|YP_004384141.1| 34 AKCE 37
                                      89*8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 451.69
//
Query:       gi|330507714|ref|YP_004384142.1|  [L=70]
Description: 30S ribosomal protein S28e [Methanosaeta concilii GP6]
Scores for complete 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-29  100.7   0.6    3.5e-29  100.6   0.6    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 !  100.6   0.6     2e-33   3.5e-29       3      64 .]       6      67 ..       4      67 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 2e-33
                                      -EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                    Ribosomal_S28e  3 aklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                        +AeVi+v+g tG++Ge++q+++++leg++kgrii+Rn +GP+r GD+L+LlEt+rEA++L
  gi|330507714|ref|YP_004384142.1|  6 GIPAEVIEVIGVTGMHGEAMQIKCRILEGNNKGRIITRNSMGPIRIGDVLMLLETAREAKKL 67
                                      679*********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 525.50
//
Query:       gi|330507715|ref|YP_004384143.1|  [L=122]
Description: 50S ribosomal protein L7Ae [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-25   88.1   0.4    2.8e-25   87.9   0.4    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
    1.8e-05   24.5   0.1    2.4e-05   24.1   0.1    1.2  1  PELOTA_1        PELOTA RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.4   3.1e-29   2.8e-25       3      93 ..      19     109 ..      17     111 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 3.1e-29
                                       HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSE CS
                    Ribosomal_L7Ae   3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrp 79 
                                         e+l++a+++g++++G++e+tka+erg a lvi+ edv+p+e++++++alc+ek+ py++vk + eLG+++g+ + 
  gi|330507715|ref|YP_004384143.1|  19 SLEALELARDTGRIKKGTNEATKAIERGVARLVIVGEDVQPPEIVAHIPALCEEKKTPYIYVKKQSELGAAAGLGVK 95 
                                       56899************************************************************************ PP

                                       CSEEEEEESTTTHH CS
                    Ribosomal_L7Ae  80 vsalaikdegdskd 93 
                                       ++a+ai+++g+ k+
  gi|330507715|ref|YP_004384143.1|  96 SAAAAIVEPGKGKE 109
                                       ********998665 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   2.7e-09   2.4e-05      17      71 ..      27      83 ..      15      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.7e-09
                          PELOTA_1 17 edinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpdl 71
                                      +d+ +iK g  EaT+++ R v + v+v ++ +  + +ah+ +L++ek++p+  v+++
  gi|330507715|ref|YP_004384143.1| 27 RDTGRIKKGTNEATKAIERGVARLVIVGEDVQppEIVAHIPALCEEKKTPYIYVKKQ 83
                                      6899************************988865679************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 868.09
//
Query:       gi|330507716|ref|YP_004384144.1|  [L=285]
Description: hypothetical protein MCON_1708 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1946.43
//
Query:       gi|330507717|ref|YP_004384145.1|  [L=483]
Description: dihydropteroate synthase-like protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.6e-09   35.8   0.1    1.4e-08   34.7   0.1    1.6  1  Pterin_bind  Pterin binding enzyme
    7.2e-09   35.7   0.0    1.5e-08   34.7   0.0    1.6  1  DUF4346      Domain of unknown function (DUF4346)
     0.0065   16.0   0.5       0.17   11.3   0.0    2.6  3  PEP_mutase   Phosphoenolpyruvate phosphomutase
  ------ inclusion threshold ------
      0.069   12.3   0.0       0.13   11.4   0.0    1.4  1  DUF561       Protein of unknown function (DUF561)


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 !   34.7   0.1   3.1e-12   1.4e-08      20     131 ..     154     254 ..     145     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.1e-12
                                       HHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHTTSEE CS
                       Pterin_bind  20 ldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDttkaevaeaAlkagadi 96 
                                        ++ ++++r   e+GAd++D+g+      a+  +++++l++  +v +       +pisiD +++e + a+++agad+
  gi|330507717|ref|YP_004384145.1| 154 DEDLVERIRYFEEQGADLIDLGASLD---ATSASVKRALKKAREVTA-------LPISIDAVRPELICAGIEAGADM 220
                                       5778999999************9776...678888888888888877.......8********************** PP

                                       EEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTT CS
                       Pterin_bind  97 vNdvsgeerdpkmlelvaeagaavvvmhmrgtpkt 131
                                       + + +ge+  p + + vaeag + vv    g    
  gi|330507717|ref|YP_004384145.1| 221 ILSLNGEN-LPLVGSRVAEAGIPAVVIPGPGSVTL 254
                                       ********.****************9876655444 PP

>> DUF4346  Domain of unknown function (DUF4346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   3.3e-12   1.5e-08      73     118 .]     432     474 ..     397     474 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.3e-12
                           DUF4346  73 akelcvkileeeeelpvtkldhaaYlGRelqraeaaLlsgkeYiqD 118
                                       a+++   ++++     + +ldha YlGRel rae+aL  g++YiqD
  gi|330507717|ref|YP_004384145.1| 432 ARKVLNTLIDR---GLIGRLDHAGYLGRELERAEIALRLGRSYIQD 474
                                       55555555544...5699***************************9 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.03   1.3e+02     155     175 ..     154     174 ..     137     208 .. 0.68
   2 !   11.3   0.0   3.9e-05      0.17     166     208 ..     214     256 ..     211     268 .. 0.92
   3 ?   -2.9   0.0      0.81   3.6e+03     166     195 ..     327     358 ..     324     369 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.03
                        PEP_mutase 155 leeaieRaraYaeAGAdgvfv 175
                                        e+ +eR r + e GAd +  
  gi|330507717|ref|YP_004384145.1| 154 DEDLVERIRYFEEQGADLIDL 174
                                       578899999999999998854 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.9e-05
                        PEP_mutase 166 aeAGAdgvfvpglqkdaeiaelvaavdvplnvvplkgtlsvae 208
                                        eAGAd+++   +++ + +++ va+ ++p +v+p++g+++++e
  gi|330507717|ref|YP_004384145.1| 214 IEAGADMILSLNGENLPLVGSRVAEAGIPAVVIPGPGSVTLEE 256
                                       59********************************988888776 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.81
                        PEP_mutase 166 aeAGAdgvfvpglqkdae..iaelvaavdvpl 195
                                       +e GA+ +f p  + +a+  i+el+ a ++++
  gi|330507717|ref|YP_004384145.1| 327 MEVGASLLFTPEYSAKAKgsIHELAVASRMMV 358
                                       78899999999886665545888887765544 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.9e-05      0.13      51      85 ..     187     221 ..     161     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                            DUF561  51 klvkkvksvsniPiCvsaveakllleavkaGadlv 85 
                                       + +kk ++v+ +Pi + av ++l+   + aGad++
  gi|330507717|ref|YP_004384145.1| 187 RALKKAREVTALPISIDAVRPELICAGIEAGADMI 221
                                       5578999**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 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:                        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 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3268.83
//
Query:       gi|330507718|ref|YP_004384146.1|  [L=117]
Description: hypothetical protein MCON_1710 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-31  107.0   0.0    5.4e-31  106.9   0.0    1.0  1  DUF473    Protein of unknown function (DUF473)


Domain annotation for each model (and alignments):
>> DUF473  Protein of unknown function (DUF473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   0.0     3e-35   5.4e-31      13     115 ..       1     103 [.       1     106 [. 0.96

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 3e-35
                            DUF473  13 vieeLkknklrtielrsahNvitllklevgdlvFlTsvsleDltkGteGiiaevlsveistkrvvessesfieErEt 89 
                                       +i+e++  ++rt+e+rs++N++++ ++++g+ +F+T+ s+ D+++Gt+G+i++++ ++++t+r+++s e+++eE+E+
  gi|330507718|ref|YP_004384146.1|   1 MIKEILAARVRTVEIRSPNNFFAIYNCQPGERIFITDSSALDVVPGTTGLITTIKALQVITHRTIQSGENYYEESES 77 
                                       599************************************************************************** PP

                            DUF473  90 tvarvqlkllglgrvrevkeeellkp 115
                                       ++ar+ql+l+g+grvr++ + e ++p
  gi|330507718|ref|YP_004384146.1|  78 QAARLQLQLVGVGRVRRIASIEPATP 103
                                       ******************99877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 877.69
//
Query:       gi|330507719|ref|YP_004384147.1|  [L=247]
Description: hypothetical protein MCON_1711 [Methanosaeta concilii GP6]
Scores for complete 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  165.0   0.1    2.6e-48  164.8   0.1    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.8   0.1   1.5e-52   2.6e-48       1     212 [.      21     223 ..      21     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 1.5e-52
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEE... CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqg... 74 
                                       Li+GfpgiG+Vg +a +++++ l+++++g+ +s+y +p     p +++ +g+  +p+r+y +   s+ ++vl+    
  gi|330507719|ref|YP_004384147.1|  21 LIEGFPGIGLVGNIASQYIVNDLKMTYIGAMNSKY-FP-----PLAVLLGGVVNMPVRIYEDA--SKGVVVLTAdip 89 
                                       8**********************************.**.....*****************664..69*******997 PP

                                       E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH.CT...-CEEEEHHH CS
                              PAC2  75 repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele.es...eyggivgit 147
                                       ++p + ye + ++++ wae+++v+e ++L+g+  ++       ++ +v+ga++++ell+++  ++   e g+i+git
  gi|330507719|ref|YP_004384147.1|  90 IHPLASYE-VGREIVAWAESIDVQELICLAGITVMD-------DQNRVFGAVSRQELLDKIRgKAeifEIGTITGIT 158
                                       77777777.************************664.......4559**************5333689********* PP

                                       HHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                              PAC2 148 glLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                       g+++++++ r++pav+ll+e+    pdP++a+a++e ++k++gl v+t +L e+aee+e q+++l
  gi|330507719|ref|YP_004384147.1| 159 GSIMNECRIRNLPAVCLLGETASAEPDPRSAIAAIETINKIYGLGVNTAKLAEQAEEIEVQMAQL 223
                                       **************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      789  (0.0440069); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 1969.54
//
Query:       gi|330507720|ref|YP_004384148.1|  [L=693]
Description: CoA-binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-74  249.1   0.1    6.8e-74  248.1   0.0    1.5  2  ATP-grasp_5    ATP-grasp domain
    2.4e-44  150.5   0.2    1.3e-43  148.1   0.3    2.2  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    2.2e-21   76.5   0.1    8.2e-21   74.7   0.0    2.1  2  CoA_binding_2  CoA binding domain
    3.4e-14   53.3   0.1    1.3e-13   51.4   0.0    2.1  2  CoA_binding    CoA binding domain
    5.4e-06   26.1   0.0      1e-05   25.2   0.0    1.5  1  ATP-grasp_2    ATP-grasp domain
  ------ inclusion threshold ------
      0.012   16.4   0.1      0.091   13.6   0.0    2.4  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo


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 !  248.1   0.0   2.3e-77   6.8e-74       1     222 []      13     228 ..      13     228 .. 0.98
   2 ?   -3.4   0.0       1.8   5.5e+03      61      91 ..     659     688 ..     656     692 .. 0.77

  Alignments for each domain:
  == domain 1  score: 248.1 bits;  conditional E-value: 2.3e-77
                       ATP-grasp_5   1 kalaegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeev 77 
                                       +a++++rt+L e+e+k++le +gi+++ + +a+++eeave+++++  pv+lK+ spd++hK+d+gGv+l l+++++v
  gi|330507720|ref|YP_004384148.1|  13 QAKSADRTYLMEHESKAILEELGISTTGSVVARTEEEAVEIFKSLASPVALKVLSPDVVHKSDAGGVKLHLNEENDV 89 
                                       588999*********************************************************************** PP

                       ATP-grasp_5  78 raaaeeilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstla 154
                                       r+a+++i++++    +++ +eg++Vq+ma+  g+E ivgv++Dp+FGpv++fGlGG+ vevlkdv+++  p+++++a
  gi|330507720|ref|YP_004384148.1|  90 RRAYRDIVSSF----QGKPVEGISVQKMAP-TGIEAIVGVANDPTFGPVLMFGLGGVFVEVLKDVSFRSIPITRSDA 161
                                       **********9....5589***********.********************************************** PP

                       ATP-grasp_5 155 reliertkaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDarirl 222
                                       +e+ie+++ + llkg rg+  ad++al++ll+r+s+ v   p+I e+d+nP++ +++g++++Dari l
  gi|330507720|ref|YP_004384148.1| 162 QEMIEEIRGYSLLKGSRGH-SADIEALKDLLMRISDFVNLEPRIWEMDLNPVFLYPHGCTVVDARIIL 228
                                       *******************.*********************************************976 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.8
                       ATP-grasp_5  61 KtdvgGvrlnlkdaeevraaaeeilervkek 91 
                                       K +  G+ + ++++e+v++a+  + +++k+ 
  gi|330507720|ref|YP_004384148.1| 659 KMEKAGIPV-FSTPEQVADALGIMYRHYKRV 688
                                       556667777.899999999999998888764 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 !  148.1   0.3   4.3e-47   1.3e-43       1     137 [.     394     529 ..     394     530 .. 0.95
   2 ?   -2.0   0.0      0.94   2.8e+03      72      91 ..     630     650 ..     627     655 .. 0.82

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 4.3e-47
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarr 77 
                                       +G+i+l+sq G  a a + w  ++ ++f  ++++Gn++d++++d++e++++d++++vi++ylEs++ gr+f++ ar+
  gi|330507720|ref|YP_004384148.1| 394 QGNIGLVSQAGVCA-AGMLWGLRHIMDFGIIATIGNKLDINETDIMEAVSKDENINVICMYLESVKGGRRFIDQARQ 469
                                       59*******99655.5566888888**************************************************** PP

                      Succ_CoA_lig  78 aarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaael 137
                                       ++ kkp+vvlksGr+eag++a+asht++lag+d++++a+frq+G++r+++ e +f++ ++
  gi|330507720|ref|YP_004384148.1| 470 ITMKKPIVVLKSGRTEAGKKAVASHTASLAGNDQIYSAVFRQSGIIRARDYEHMFNLSRA 529
                                       *******************************************************99775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.94
                      Succ_CoA_lig  72 lsaarraark.kpvvvlksGr 91 
                                       +++++++  k kp++++ +G+
  gi|330507720|ref|YP_004384148.1| 630 VDTLKSIDYKgKPIIACVAGK 650
                                       56778888899******9997 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.0   2.8e-24   8.2e-21       2     115 ..     252     377 ..     251     378 .. 0.96
   2 ?   -3.5   0.0       4.9   1.5e+04      57      79 ..     615     637 ..     599     653 .. 0.68

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 2.8e-24
                                       -EEEET--S-TTSHHHHHHHHHHH...HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHH CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle...hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkea 75 
                                       +iaV+Gas +pgk g  v+ +l++   +g   +p+np++eei+g k+y+++++ pe vd++ +++ +  t+++v+e+
  gi|330507720|ref|YP_004384148.1| 252 SIAVIGASGTPGKLGWNVFTNLVShkfKG-MLYPINPRAEEIHGIKAYPRISAVPERVDVAIILVSAGMTADVVEEC 327
                                       8***********************66666.79********************758********************** PP

                                       HHH--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHHH CS
                     CoA_binding_2  76 lalgakavwlqpg..........sedeeaaelaeeagirvvgdrCilveg 115
                                       +++g++ +++ ++            + ++ e+a+++g+r++g++C ++++
  gi|330507720|ref|YP_004384148.1| 328 CQCGVRYIVVESAgfaelgpegkKIELQMKEIADRYGVRLLGPNCSGIIN 377
                                       ************9*********************************9975 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.9
                                       -EEEE-S-HHHHGGGHHHHHHH- CS
                     CoA_binding_2  57 dlvdvftppeatpeivkealalg 79 
                                        +  v++++e++ ++v+ +++++
  gi|330507720|ref|YP_004384148.1| 615 GSFIVILQAEILDSYVDTLKSID 637
                                       35667777777777777777765 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   4.4e-17   1.3e-13       3      94 ..     250     339 ..     248     341 .. 0.96
   2 ?   -3.3   0.0       5.3   1.6e+04      40      56 ..     657     673 ..     655     679 .. 0.67

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 4.4e-17
                                       TEEEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHH CS
                       CoA_binding   3 dtkviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqe 77 
                                       + +++viGa+g+ ++++  +f +  + ++k +++++npr  ++e++g+++y+ ++ ++e+  vdva+i+v+a   ++
  gi|330507720|ref|YP_004384148.1| 250 PQSIAVIGASGTPGKLGwNVFTNLVSHKFKgMLYPINPR--AEEIHGIKAYPRISAVPER--VDVAIILVSAGMTAD 322
                                       679************************************..*******************..*************** PP

                                       HHHHHHHTT-SEEEEES CS
                       CoA_binding  78 avdelveagikgiviit 94 
                                       +v+e+ + g++ iv+ +
  gi|330507720|ref|YP_004384148.1| 323 VVEECCQCGVRYIVVES 339
                                       *************9865 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.3
                                       TTTCEETTEEEESCHHH CS
                       CoA_binding  40 kvgtevlglpvyksvde 56 
                                        +  e  g+pv+ + ++
  gi|330507720|ref|YP_004384148.1| 657 VIKMEKAGIPVFSTPEQ 673
                                       56678889999965554 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.3e-09     1e-05       2     136 ..      22     147 ..      21     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.3e-09
                                       E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE.--SSSTCCCTTCEEEESS.HHHHHHHHHCCT CS
                       ATP-grasp_2   2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKa.QvlaGGRGKagGvklvks.keeakeaakell 76 
                                       l E+++k il++ g++++ + va+++eea e++k+l + + ++K     +  +  agGvkl  + ++++++a ++++
  gi|330507720|ref|YP_004384148.1|  22 LMEHESKAILEELGISTTGSVVARTEEEAVEIFKSLASPV-ALKVlSPDVVHKSDAGGVKLHLNeENDVRRAYRDIV 97 
                                       79***********************************998.66651345667899*****97550556666666655 PP

                                       TSEEE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHH CS
                       ATP-grasp_2  77 gkelvtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEeva 136
                                       + +        +Gk+ve + v+++ ++  E+ +++  D +  ++v+++   GGv +E + 
  gi|330507720|ref|YP_004384148.1|  98 S-SF-------QGKPVEGISVQKMAPTGIEAIVGVANDPT-FGPVLMFG-LGGVFVEVLK 147
                                       4.34.......49999999999999999999999887754.45666654.5777666655 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     3e-05     0.091       3      92 ..     253     338 ..     251     339 .. 0.87
   2 ?   -0.6   0.0      0.76   2.3e+03      44      74 ..     428     458 ..     422     492 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-05
                                       EEEETTSHH.HHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA   3 vaiiGaGki.gskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheel 78 
                                       +a+iGa    g+  ++ + +    ++  + l p ++rae++    g++ay  ++++++  ++d++i+ + +g  +++
  gi|330507720|ref|YP_004384148.1| 253 IAVIGASGTpGKLGWNVFTNL-VSHKFKGMLYPINPRAEEI---HGIKAYPRISAVPE--RVDVAIILVSAGMTADV 323
                                       899**9555488888666666.788**************99...9*************..***************** PP

                                       HHHHHHTT-.EEEEE CS
                      GFO_IDH_MocA  79 akaaleagk.hvllE 92 
                                       ++++ + g+  +++E
  gi|330507720|ref|YP_004384148.1| 324 VEECCQCGVrYIVVE 338
                                       ******999666665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.76
                                       HHTTHEEESSHHHHHTCTTESEEEE-S-GGG CS
                      GFO_IDH_MocA  44 esfgveaysdleelladpeidavivatpngt 74 
                                       ++++++  + +e++++d++i++++    + +
  gi|330507720|ref|YP_004384148.1| 428 NKLDINETDIMEAVSKDENINVICMYLESVK 458
                                       566677777799999*******998887743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (693 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4997.01
//
Query:       gi|330507721|ref|YP_004384149.1|  [L=197]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.6   0.1      0.082   13.1   0.1    1.4  1  TrbH      Conjugal transfer protein TrbH


Domain annotation for each model (and alignments):
>> TrbH  Conjugal transfer protein TrbH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.6e-06     0.082      46     106 ..     115     172 ..      66     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-06
                              TrbH  46 kGyavlefaperakaaaeataaeatglpLryvldeakssnlyrltllvGsqsisrayleqn 106
                                       +Gy++l  + ++a+ +   +a++  g  +   ++ ++s++lyrl+l++   s+  +++ + 
  gi|330507721|ref|YP_004384149.1| 115 SGYGILMQNGNAAQVT---AAGTILGDRVALFVSPVQSQGLYRLSLTITPGSMNGSFVYTA 172
                                       6899887777776666...6777778889999*****************999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1492.84
//
Query:       gi|330507722|ref|YP_004384150.1|  [L=107]
Description: hypothetical protein MCON_1715 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 893.12
//
Query:       gi|330507723|ref|YP_004384151.1|  [L=445]
Description: signal sequence recognition 54 kDa protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-68  230.3   4.3    1.5e-68  230.3   4.3    1.6  2  SRP54            SRP54-type protein, GTPase domain
    3.8e-27   94.8   1.9    3.8e-27   94.8   1.9    2.5  2  SRP_SPB          Signal peptide binding domain
      3e-21   75.4   0.5    1.1e-20   73.6   0.3    2.2  2  SRP54_N          SRP54-type protein, helical bundle domain
    8.7e-08   32.3   0.0    4.4e-07   30.0   0.0    2.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      2e-05   24.3   2.4    0.00023   20.8   2.4    2.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00076   19.5   0.9     0.0095   16.0   0.9    2.5  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0011   18.0   0.2      0.003   16.6   0.2    1.8  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0013   18.6   0.1     0.0033   17.4   0.1    1.7  1  APS_kinase       Adenylylsulphate kinase
      0.002   18.5   0.4     0.0061   17.0   0.2    2.0  1  AAA_16           AAA ATPase domain
      0.003   17.7   0.0     0.0067   16.6   0.0    1.8  1  AAA_33           AAA domain
     0.0031   18.0   0.0       0.01   16.4   0.0    1.9  1  AAA_18           AAA domain
     0.0038   17.0   1.2      0.012   15.4   0.9    2.0  1  AAA_30           AAA domain
     0.0041   17.4   0.0      0.014   15.7   0.0    2.0  1  AAA_22           AAA domain
     0.0045   16.9   0.0      0.011   15.6   0.0    1.6  1  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0046   16.3   0.0      0.011   15.0   0.0    1.6  1  Zeta_toxin       Zeta toxin
     0.0056   16.0   0.2      0.047   13.0   0.0    2.2  2  AAA_8            P-loop containing dynein motor region D4
     0.0058   16.0   0.0      0.012   14.9   0.0    1.5  1  6PF2K            6-phosphofructo-2-kinase
     0.0083   15.9   0.1      0.022   14.5   0.0    1.9  2  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.014   15.3   0.2       0.06   13.3   0.2    2.1  1  AAA_31           AAA domain
      0.015   14.9   0.1       0.22   11.2   0.1    2.6  2  Thymidylate_kin  Thymidylate kinase
       0.02   14.3   0.2          1    8.8   0.1    2.5  2  SRPRB            Signal recognition particle receptor beta su
      0.024   13.6   0.1      0.054   12.4   0.1    1.5  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.027   14.2   0.0      0.042   13.5   0.0    1.4  1  AAA_15           AAA ATPase domain
      0.029   13.8   0.0      0.076   12.4   0.0    1.6  1  KTI12            Chromatin associated protein KTI12
      0.039   14.2   0.6       0.22   11.7   0.0    2.3  2  AAA_28           AAA domain
      0.045   13.7   0.0       0.13   12.3   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
       0.07   12.3   0.1       0.15   11.1   0.1    1.8  1  G-alpha          G-protein alpha subunit
      0.072   13.1   0.0       0.15   12.0   0.0    1.7  1  ResIII           Type III restriction enzyme, res subunit
      0.074   13.4   0.6       0.26   11.6   0.1    2.1  2  AAA_19           AAA domain
      0.095   12.6   0.2       0.42   10.5   0.0    2.2  2  NTPase_1         NTPase
       0.11   12.9   1.4          1    9.8   0.7    3.0  2  AAA              ATPase family associated with various cellul
       0.13   12.0   1.0        2.3    8.0   0.1    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
          3    8.3   5.6        2.2    8.7   0.8    3.2  3  AAA_17           AAA domain


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       9.8   5.3e+03      79      97 ..      18      36 ..      11      55 .. 0.64
   2 !  230.3   4.3   2.7e-71   1.5e-68       2     196 .]      98     290 ..      97     290 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.8
                                      HHHTTSSEEEEEE--SSTT CS
                             SRP54 79 akeekidvvlvDTaGrlqn 97
                                      a ++kid  lvD a r  +
  gi|330507723|ref|YP_004384151.1| 18 ASANKIDKALVDEAVREIQ 36
                                      4556677777777766544 PP

  == domain 2  score: 230.3 bits;  conditional E-value: 2.7e-71
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                       + i+lvGlqG+GKTtt+aKLa  ++++g ++++++aDtfRa+A++QLk+l ek g+ ++++k ++d+ ava++++e+
  gi|330507723|ref|YP_004384151.1|  98 QNIMLVGLQGSGKTTTAAKLATFFQRKGLRTAVICADTFRAGAYDQLKALCEKQGIFFYGEKGNTDAPAVARNGLEA 174
                                       579*************************************************************************9 PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                        k+  +d+ +vDTaGr++ + +l++e+k+i+ vv++d++llv+da++gq+a +qakaF+eav+itgvi+tklDg+ak
  gi|330507723|ref|YP_004384151.1| 175 TKK--YDIRIVDTAGRHALEGDLIQEMKDIHAVVNADQKLLVMDAALGQQASEQAKAFNEAVNITGVIITKLDGTAK 249
                                       998..************************************************************************ PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       gG+als++ae+k+ ++figvGe+  dle+f+++r++sr+lg
  gi|330507723|ref|YP_004384151.1| 250 GGGALSAVAETKTSVAFIGVGETPADLERFEADRFISRMLG 290
                                       **************************************985 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       8.7   4.7e+03      11      26 ..     285     300 ..     280     314 .. 0.74
   2 !   94.8   1.9     7e-30   3.8e-27       1      98 [.     319     419 ..     319     420 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 8.7
                                       HHHHHCCCCCCHHHHC CS
                           SRP_SPB  11 lqqikkmGplskllsm 26 
                                       ++++  mG+++ l++ 
  gi|330507723|ref|YP_004384151.1| 285 ISRMLGMGDIKTLIER 300
                                       5678889999998875 PP

  == domain 2  score: 94.8 bits;  conditional E-value: 7e-30
                                       SSCTHHHHHHHHHHHCCCCCCHHHHCCC..........H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHH CS
                           SRP_SPB   1 eftlrdlleqlqqikkmGplskllsmiPgmsae.....akaeeeaekklkrieaiidSMTkeErdspekllkesRkr 72 
                                       +ftl+d+++q++ ++k+Gpl+++++m+P m+        k+ ++++++l+++ +++dSMT++E+d+p+ ++++sR++
  gi|330507723|ref|YP_004384151.1| 319 KFTLKDMYQQMEAMNKLGPLKQIMQMLP-MGGLgfelsDKEYQMTKDRLDKYRVVMDSMTAAELDDPK-IITASRIK 393
                                       6***************************.34445777544448899**********************.8889**** PP

                                       HHHHHTTS-HHHHHHHHHHHHHHHHH CS
                           SRP_SPB  73 RiArGsGtsvqevnellkqfeqmkkm 98 
                                       Ri++GsG s + v+ellk+++ m+k 
  gi|330507723|ref|YP_004384151.1| 394 RISQGSGASPDLVRELLKSHQAMQKA 419
                                       ***********************996 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.3   2.1e-23   1.1e-20       1      75 []       6      83 ..       6      83 .. 0.97
   2 ?   -1.8   0.0       7.1   3.8e+03      57      72 ..     407     421 ..     390     422 .. 0.72

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 2.1e-23
                                      HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                           SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                                      Lg++l++alkk+ ++ kid+++++ea++e+++aLl+aDV+vk+v++l + +k +a+ ek    ++p+++v++iv++eL
  gi|330507723|ref|YP_004384151.1|  6 LGGSLRNALKKIASANKIDKALVDEAVREIQRALLQADVNVKLVMQLSNTIKSRALDEKPapgMNPREHVINIVYQEL 83
                                      799**************************************************9999555*****************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.1
                                       CTTSS-HHHHHHHHHH CS
                           SRP54_N  57 gekklkpkqqvkkivk 72 
                                       + + lk++q+++k++k
  gi|330507723|ref|YP_004384151.1| 407 R-ELLKSHQAMQKALK 421
                                       3.44788888888886 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   8.1e-10   4.4e-07       9     108 ..     107     266 ..     104     335 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 8.1e-10
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       G+GKTt+aa+La+ ++r+glr++++ aD+ +  +   ++l     +                               
  gi|330507723|ref|YP_004384151.1| 107 GSGKTTTAAKLATFFQRKGLRTAVICADTFRAGAY--DQL-----Kalcekqgiffygekgntdapavarngleatk 176
                                       99**************************9955543..222.....12334467788888888888************ PP

                                       .......................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TT CS
                                       .......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 .......................................dlkrllellealgkkkalllkiagvvlnrvdgeneetl 92 
                                                                              d+   ++ +++  k ++ +++i gv++++ dg +    
  gi|330507723|ref|YP_004384151.1| 177 kydirivdtagrhalegdliqemkdihavvnadqkllvmDAAL-GQQASEQAKAFNEAVNITGVIITKLDGTAKGGG 252
                                       ******************************7777777665544.33333333345555*************988877 PP

                                       CHHHHHHHHHHCTS-E CS
                                       xxxxxxxxxxxxxxxx RF
                              CbiA  93 lkealeelkqrygvpv 108
                                         +a++e+k    v +
  gi|330507723|ref|YP_004384151.1| 253 ALSAVAETKT--SVAF 266
                                       7777777664..5555 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 !   20.8   2.4   4.3e-07   0.00023       3     157 ..     100     252 ..      98     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.3e-07
                                       EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkeleale 77 
                                       ++l+G  GsGKTt   +l    +r+gl++avi  +    +   +l + ++++   +  G    t   d+ +++++ +
  gi|330507723|ref|YP_004384151.1| 100 IMLVGLQGSGKTTTAAKLAtfFQRKGLRTAVICADTFRAGAYDQLKALCEKQ-GIFFYGEKGNT---DAPAVARNGL 172
                                       6899*************9989899***********99887777666666444.22334444445...7888887777 PP

                                       HHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHH CS
                              cobW  78 ereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDll 153
                                       e  +++d+ ++ t G  a    ++ + +++++ +++d ++ v+Da +l ++ +++++ +++ ++ + + +++K D  
  gi|330507723|ref|YP_004384151.1| 173 EATKKYDIRIVDTAGrHALEGDLIQEMKDIHAVVNADQKLLVMDA-ALGQQASEQAKAFNEAVNITGV-IITKLDGT 247
                                       77779**********98888888788*******************.6668888888888888888775.67899987 PP

                                       CHC.. CS
                              cobW 154 dee.a 157
                                        +   
  gi|330507723|ref|YP_004384151.1| 248 AKGgG 252
                                       76654 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.9   1.8e-05    0.0095       2     100 ..     100     230 ..      99     243 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-05
                                       EEEEESTTSSHHHHHHHHH....................T..........STE.EESSSTTSSSSEEEEEEE...ET CS
                          MMR_HSR1   2 vaivGrpNvGKStLinalt....................g..........eka.ivsdkpgtTrdinegrvk...lk 44 
                                       +++vG   +GK+t   +l                     g          ++      ++g T  +  +r     +k
  gi|330507723|ref|YP_004384151.1| 100 IMLVGLQGSGKTTTAAKLAtffqrkglrtavicadtfraGaydqlkalceKQGiFFYGEKGNTDAPAVARNGleaTK 176
                                       77888888888888888873333333322222222222202222222221221022333444444444432222333 PP

                                       TEEEEEEECGGCSSHHHHHH..HHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHH CS
                          MMR_HSR1  45 gkeielvDtpGliegaseek..glgkaflaleeadlillvvdaseeklkpldeeleel 100
                                       + +i++vDt+G  + a e+   ++ k+++a+ +ad  llv+da+ +  ++  e+ +++
  gi|330507723|ref|YP_004384151.1| 177 KYDIRIVDTAG-RH-ALEGDliQEMKDIHAVVNADQKLLVMDAALG--QQASEQAKAF 230
                                       467********.54.222333688899999999*********8833..3333333333 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   5.5e-06     0.003      30      67 ..      98     135 ..      81     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.5e-06
                                       EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                              MeaB  30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavDP 67 
                                       q + l G+ G+Gk t+  +l++ ++r+G r av+  D 
  gi|330507723|ref|YP_004384151.1|  98 QNIMLVGLQGSGKTTTAAKLATFFQRKGLRTAVICADT 135
                                       678899****************************9883 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     6e-06    0.0033       4      49 ..      99     144 ..      96     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6e-06
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                        APS_kinase   4 vvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49 
                                        ++l Gl gsGK+t a +l++  ++kg ++ ++  d+ R g + +L
  gi|330507723|ref|YP_004384151.1|  99 NIMLVGLQGSGKTTTAAKLATFFQRKGLRTAVICADTFRAGAYDQL 144
                                       5899***********************************9987776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   1.1e-05    0.0061      25      82 ..      98     153 ..      72     236 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareell 82 
                                       ++++l+G +G+GK++ + +l++ ++++g  ++   +d + +a +y++l  ++++ + +
  gi|330507723|ref|YP_004384151.1|  98 QNIMLVGLQGSGKTTTAAKLATFFQRKGLRTAVICADTF-RAGAYDQLKALCEK-QGI 153
                                       7899******************99999766666666666.33345554444433.222 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.2e-05    0.0067       2      37 ..     100     140 ..     100     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
                            AAA_33   2 vllvGlpGsGKstlaerl...lkklg..avllssdtlrrrl 37 
                                       ++lvGl+GsGK+t a +l    ++ g  + ++  dt+r   
  gi|330507723|ref|YP_004384151.1| 100 IMLVGLQGSGKTTTAAKLatfFQRKGlrTAVICADTFRAGA 140
                                       79***************955545555777777777766544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.9e-05      0.01       1      92 [.     100     228 ..     100     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-05
                            AAA_18   1 IlltGtpGvGKttlakeL....skrlgf..............gvnlrdvakenglllevdpe......aldeskrld 53 
                                       I+l G +G+GKtt a  L    +++ g+               ++l+ ++ + g+ ++ ++         ++ +++ 
  gi|330507723|ref|YP_004384151.1| 100 IMLVGLQGSGKTTTAAKLatffQRK-GLrtavicadtfragaYDQLKALCEKQGIFFYGEKGntdapaVARNGLEAT 175
                                       89****************6666444.236688899988888888888888888888888877788887777777777 PP

                            AAA_18  54 edkldklldaleenss..............aleegknlvidghlaeleseaak 92 
                                       ++++ +++d+  +++                ++++k lv+d  l++  se+ak
  gi|330507723|ref|YP_004384151.1| 176 KKYDIRIVDTAGRHALegdliqemkdihavVNADQKLLVMDAALGQQASEQAK 228
                                       77777777777777777777777778888877778888888888777777665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.9   2.1e-05     0.012      21      99 ..     100     188 ..      95     245 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-05
                            AAA_30  21 avltGpAGtGKttalkalreaweaag.grviglAptgkaAkv..La...eelgi.....eastiakllkrlk.grar 85 
                                        +l+G  G+GKtt+ ++l+  ++++g ++ +++A t +a +   L+   e+ gi     +++t a  + r++ +   
  gi|330507723|ref|YP_004384151.1| 100 IMLVGLQGSGKTTTAAKLATFFQRKGlRTAVICADTFRAGAYdqLKalcEKQGIffygeKGNTDAPAVARNGlE--- 173
                                       5799*********************8677789999988754222664444555555666888888888776642... PP

                            AAA_30  86 lepg.tllivDEagm 99 
                                        +++ ++ ivD ag 
  gi|330507723|ref|YP_004384151.1| 174 ATKKyDIRIVDTAGR 188
                                       233337777776665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.6e-05     0.014       5      33 ..      97     125 ..      95     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeea 33 
                                       ++ ++++G  G+GKTt++++l+  +++  
  gi|330507723|ref|YP_004384151.1|  97 KQNIMLVGLQGSGKTTTAAKLATFFQRKG 125
                                       6789*******************997543 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     2e-05     0.011       2      33 ..     100     131 ..      99     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-05
                              MobB   2 lgivgksgsGKTtLleklipelkarglrvgti 33 
                                       + +vg +gsGKTt   kl + ++++glr ++i
  gi|330507723|ref|YP_004384151.1| 100 IMLVGLQGSGKTTTAAKLATFFQRKGLRTAVI 131
                                       679***************************98 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.1e-05     0.011      16      56 ..      97     138 ..      91     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe 56 
                                       +  i+l+G +G+GK+++a++l++ ++ ++ +  ++ +D++R+
  gi|330507723|ref|YP_004384151.1|  97 KQNIMLVGLQGSGKTTTAAKLATFFQrKGLRTAVICADTFRA 138
                                       56799********************9788899********96 PP

>> AAA_8  P-loop containing dynein motor region D4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   8.7e-05     0.047      23      78 ..      96     152 ..      84     156 .. 0.77
   2 ?    0.2   0.0      0.71   3.9e+02     101     163 ..     284     346 ..     277     353 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.7e-05
                             AAA_8  23 prghaLlvGvgGsGrqs.ltkLAafiaelelfqievtkkykekefredlkkllkkag 78 
                                       ++ +++lvG++GsG+ +  +kLA+f ++  l++  +  +  ++   ++lk l++k g
  gi|330507723|ref|YP_004384151.1|  96 KKQNIMLVGLQGSGKTTtAAKLATFFQRKGLRTAVICADTFRAGAYDQLKALCEKQG 152
                                       6789***********862689*****9998887776655555555566776666655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.71
                             AAA_8 101 dinnlLntGevpnLfskeekeeiieelrkeakkqgvedskesllnffikrvrenLhivlcmsp 163
                                        i+ +L  G++ +L ++ ++ +  +e+  e  ++g+ + k+   ++ + +    L+ ++ m p
  gi|330507723|ref|YP_004384151.1| 284 FISRMLGMGDIKTLIERAQEVQTEQEVDVESLMRGKFTLKDMYQQMEAMNKLGPLKQIMQMLP 346
                                       6899***********999988888888876666555555555555555555555555555555 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.2e-05     0.012      13      58 ..      97     142 ..      91     178 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHS CS
                             6PF2K  13 klvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreask 58 
                                       k  i+lvGL   gKt+++ kl  + +  g+rt v  +  +r  a  
  gi|330507723|ref|YP_004384151.1|  97 KQNIMLVGLQGSGKTTTAAKLATFFQRKGLRTAVICADTFRAGAYD 142
                                       56799********************999888877544444443333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.1e-05     0.022       1      74 [.      96     186 ..      96     239 .. 0.70
   2 ?   -3.0   0.0       9.3     5e+03      60      77 ..     363     379 ..     304     401 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-05
                            AAA_24   1 kklkiliyGpsgiGKTtlakelgpkplfidtek.Glksldadkfpdieswedfldevvel................. 59 
                                       kk++i+++G +g+GKTt+a++l   + f++  +  ++ + ad f  + ++++++  +++                  
  gi|330507723|ref|YP_004384151.1|  96 KKQNIMLVGLQGSGKTTTAAKL---ATFFQRKGlRTAVICADTFR-AGAYDQLKALCEKQgiffygekgntdapava 168
                                       5899******************...44444443244444444443.2255555555555566666666666666666 PP

                            AAA_24  60 ...aaeladyktlviDti 74 
                                           ++ ++y++ ++Dt+
  gi|330507723|ref|YP_004384151.1| 169 rngLEATKKYDIRIVDTA 186
                                       666555555666666665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.3
                            AAA_24  60 aaeladyktlviDtidel 77 
                                       ++ l++y+ +v D+ + +
  gi|330507723|ref|YP_004384151.1| 363 KDRLDKYR-VVMDSMTAA 379
                                       44444443.456666666 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   0.00011      0.06      12      47 ..     107     169 ..     102     236 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt...........................g 47 
                                       G GKTTt+ +la ++ ++g ++ ++ +D+  + +                            +
  gi|330507723|ref|YP_004384151.1| 107 GSGKTTTAAKLATFFQRKGLRTAVICADTFRAGAYdqlkalcekqgiffygekgntdapavaR 169
                                       99***********************99986665555555555555555555555444444443 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1    0.0004      0.22       3      27 ..     104     129 ..     102     133 .. 0.89
   2 ?    0.2   0.0      0.98   5.3e+02      15      86 ..     143     216 ..     140     223 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                                       ESTTSSHHHHHHHHHHHHHHTTE..E CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik.v 27 
                                       Gl G+GKtt a++l+  ++++g++ +
  gi|330507723|ref|YP_004384151.1| 104 GLQGSGKTTTAAKLATFFQRKGLRtA 129
                                       99*******************98743 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.98
                                       HHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHH....HHHHHHHHHHHTTHHHHHHHHHTT-EEEEE CS
                   Thymidylate_kin  15 llkerlkeegikvvltrepggteiGekirelllkeeeleeqt....eallfaadriehleekikpalkqgktvivd 86 
                                        lk+ ++++gi  ++  e+g+t+   ++r+ l+ +++++           +  d i+++ + +   ++++k++++d
  gi|330507723|ref|YP_004384151.1| 143 QLKALCEKQGI--FFYGEKGNTDAPAVARNGLEATKKYDIRIvdtaGRHALEGDLIQEMKDIHAVVNADQKLLVMD 216
                                       57788888885..899999999999999999985544443332322223334455666666666666666666666 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 ?    8.8   0.1    0.0018         1       3      26 ..      97     120 ..      95     145 .. 0.84
   2 ?    2.9   0.0      0.12        64      44      89 ..     173     221 ..     158     241 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                                       --EEEEE-STTSSHHHHHHHHHHS CS
                             SRPRB   3 kpavllvGlsdsGKTslftrLttd 26 
                                       k++++lvGl+ sGKT+   +L t 
  gi|330507723|ref|YP_004384151.1|  97 KQNIMLVGLQGSGKTTTAAKLATF 120
                                       7899************99999875 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.12
                                       ...GGTT-SEEEETT-GCCSHHHHHHHHHHGG...EEEEEEEEETTS-H CS
                             SRPRB  44 ksekgskltliDfPGheklrqklleklkakss...lkglvfvvDStidp 89 
                                       +++k+  ++++D  G + l  +l++++k+ +    + + + v+D++  +
  gi|330507723|ref|YP_004384151.1| 173 EATKKYDIRIVDTAGRHALEGDLIQEMKDIHAvvnADQKLLVMDAALGQ 221
                                       67899999*****************998876531234456677766655 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1    0.0001     0.054      14      48 ..      96     130 ..      91     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                     TrwB_AAD_bind  14 etqhilivGttGsGKtqalekllrairargdraiv 48 
                                        +q i++vG +GsGKt+++ kl +  +++g r  v
  gi|330507723|ref|YP_004384151.1|  96 KKQNIMLVGLQGSGKTTTAAKLATFFQRKGLRTAV 130
                                       4789********************99999966433 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.8e-05     0.042      17      50 ..      91     124 ..      89     234 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.8e-05
                            AAA_15  17 veidlseeltvliGkNnsGKSsilealdlFlnnk 50 
                                       ++i+l+++   l+G ++sGK++ +  l  F+++k
  gi|330507723|ref|YP_004384151.1|  91 ADIPLKKQNIMLVGLQGSGKTTTAAKLATFFQRK 124
                                       5799***999**********************88 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014     0.076       4      41 ..     100     137 ..      99     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                                       ++l Gl  sGK+t a++La+ ++ ++ +  vi  ++++
  gi|330507723|ref|YP_004384151.1| 100 IMLVGLQGSGKTTTAAKLATFFQRKGLRTAVICADTFR 137
                                       7899*************************999988877 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00041      0.22       1      32 [.      99     137 ..      99     151 .. 0.72
   2 ?   -0.6   0.1       2.5   1.4e+03      20      70 ..     173     229 ..     167     238 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00041
                            AAA_28   1 kivitGgestGKTtlleaLa...ar...gypvv.pEaar 32 
                                       +i+++G +++GKTt++++La   +r    + v+ ++++r
  gi|330507723|ref|YP_004384151.1|  99 NIMLVGLQGSGKTTTAAKLAtffQRkglRTAVIcADTFR 137
                                       5899****************7664453333344555555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.5
                            AAA_28  20 aar...gypvvpEaareileeklakgedalpwv...edllafaervleeqleeeaaa 70 
                                       +a+   ++++v  a+r  le  l ++ +++++v   +++l + ++ l +q++e+a+a
  gi|330507723|ref|YP_004384151.1| 173 EATkkyDIRIVDTAGRHALEGDLIQEMKDIHAVvnaDQKLLVMDAALGQQASEQAKA 229
                                       444444778888899999998887766666655444577888888888888777776 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00024      0.13       1      26 [.      99     124 ..      99     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00024
                                       EEEEE--SSSSHHHHHHHGGGGBS-- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnre 26 
                                       +++LvG +G+gK++ a +la +++r+
  gi|330507723|ref|YP_004384151.1|  99 NIMLVGLQGSGKTTTAAKLATFFQRK 124
                                       689******************99654 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00028      0.15      23      54 ..      97     129 ..      89     378 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                                       EEEEEEEESTTSSHHHHHHHHHHHCS--.--HH CS
                           G-alpha  23 evkllllGqseSGKsTilkqlkllykkg.fsee 54 
                                       + +++l+G ++SGK+T+  +l ++++ +  ++ 
  gi|330507723|ref|YP_004384151.1|  97 KQNIMLVGLQGSGKTTTAAKLATFFQRKgLRTA 129
                                       359**************9999987755424444 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 ?   12.0   0.0   0.00028      0.15      21      53 ..      85     126 ..      20     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00028
                                       ...........TTSEEEEEESTTSTHHHHHHHHHHHH-S... CS
                            ResIII  21 s.........krdkrglikmaTGtGKTlvaaklierllkkgk 53 
                                       +          ++++++++   G+GKT +aakl+  +++kg 
  gi|330507723|ref|YP_004384151.1|  85 NlvgrgadipLKKQNIMLVGLQGSGKTTTAAKLATFFQRKGL 126
                                       24445555555678999****************998888765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00048      0.26       8      62 ..      95     148 ..      89     241 .. 0.63
   2 ?   -1.5   0.0       5.4   2.9e+03      20      63 ..     290     333 ..     285     389 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00048
                            AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerl 62 
                                       lk++++++++  G+GKT++  +  + +++ g +  + i + +f   A ++l+  +
  gi|330507723|ref|YP_004384151.1|  95 LKKQNIMLVGLQGSGKTTTAAKLATFFQRKG-LRTAVICADTFRAGAYDQLKALC 148
                                       688999***********99877766666666.64455555555555666666544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.4
                            AAA_19  20 GtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerla 63 
                                       G+G  ++l ++ ++++ +++v++e+++   ft + + +  e+++
  gi|330507723|ref|YP_004384151.1| 290 GMGDIKTLIERAQEVQTEQEVDVESLMRGKFTLKDMYQQMEAMN 333
                                       66666777777777777777777777777777666555555553 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00077      0.42       1      39 [.      99     137 ..      99     142 .. 0.85
   2 ?   -2.1   0.0       5.7   3.1e+03      92     127 ..     174     211 ..     163     237 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00077
                                       EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39 
                                       ++++ G +G+GKtT   k++   +++g++ + + +   r
  gi|330507723|ref|YP_004384151.1|  99 NIMLVGLQGSGKTTTAAKLATFFQRKGLRTAVICADTFR 137
                                       58999**********************998766666555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.7
                                       HHHHH-EEEE---STTGGG-HHHH..HHHHHHHTTTSE CS
                          NTPase_1  92 alseadviviDEiGkmElkskkfk..eaveevLksekp 127
                                       a ++ d+ ++D  G+  l+   ++  + ++ v++ ++ 
  gi|330507723|ref|YP_004384151.1| 174 ATKKYDIRIVDTAGRHALEGDLIQemKDIHAVVNADQK 211
                                       56788888888888754444444311456666664444 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   0.7    0.0019         1       1      25 [.     100     124 ..     100     290 .. 0.82
   2 ?   -1.5   0.0       5.7   3.1e+03      25      55 ..     385     415 ..     365     420 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0019
                                       EEEESSTTSSHHHHHHHHHHHHTHE CS
                               AAA   1 vllyGppGtGKTllakavakelgve 25 
                                       ++l+G  G GKT++a  +a+ ++++
  gi|330507723|ref|YP_004384151.1| 100 IMLVGLQGSGKTTTAAKLATFFQRK 124
                                       689***************9876544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.7
                                       EEEEEETTTCSSSSTTHHHHHHHHHHHHHHH CS
                               AAA  25 efleisgsellskyvgesekkirelfkeake 55 
                                       ++++ s  + +s+  g+s++ +rel+k+ ++
  gi|330507723|ref|YP_004384151.1| 385 KIITASRIKRISQGSGASPDLVRELLKSHQA 415
                                       4556666666677888888889988887655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0042       2.3       2      21 ..      98     117 ..      97     123 .. 0.88
   2 ?    1.9   0.1      0.31   1.7e+02      39     102 ..     181     247 ..     173     268 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0042
                         PduV-EutP   2 kkilliGkvgsGKttLtqal 21 
                                       ++i+l+G  gsGKtt + +l
  gi|330507723|ref|YP_004384151.1|  98 QNIMLVGLQGSGKTTTAAKL 117
                                       68*************98877 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.31
                         PduV-EutP  39 eviDtPGeylenrklysalivt..saeadvialvqdateeesvfppgfasvfnkeviG.iitkidla 102
                                       +++Dt G ++ +  l + ++ +   ++ad   lv+da   ++   ++ a   + ++ G iitk+d +
  gi|330507723|ref|YP_004384151.1| 181 RIVDTAGRHALEGDLIQEMKDIhaVVNADQKLLVMDAALGQQASEQAKAFNEAVNITGvIITKLDGT 247
                                       6799999999999998888654116789998999988766655444444444445677357999965 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.4   1.3e+03      59      84 ..      11      36 ..       7      59 .. 0.65
   2 ?    8.7   0.8     0.004       2.2       1      17 [.     103     119 ..     103     234 .. 0.86
   3 ?   -1.7   0.0       6.4   3.5e+03     111     128 ..     383     402 ..     353     434 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.4
                                      HHHHHHHHHHHHSSEEEEEE-SEEEE CS
                            AAA_17 59 keaaekiaeeakkkgvlvdghprike 84
                                      ++a +kia ++k +++lvd   r  +
  gi|330507723|ref|YP_004384151.1| 11 RNALKKIASANKIDKALVDEAVREIQ 36
                                      56777777777777777777666433 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.004
                                       EE-TTSSHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklve 17 
                                       +G+ GsGK+t ++kl+ 
  gi|330507723|ref|YP_004384151.1| 103 VGLQGSGKTTTAAKLAT 119
                                       79*************85 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 6.4
                                       -HHHHHHHHHHH..TTST-T CS
                            AAA_17 111 dpeeilerrlkd..rtrgrd 128
                                       dp+ i++ r+k+  +++g +
  gi|330507723|ref|YP_004384151.1| 383 DPKIITASRIKRisQGSGAS 402
                                       34444444555433334433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); 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: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 2956.15
//
Query:       gi|330507724|ref|YP_004384152.1|  [L=190]
Description: hypothetical protein MCON_1717 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1314.76
//
Query:       gi|330507725|ref|YP_004384153.1|  [L=352]
Description: Papain family cysteine protease [Methanosaeta concilii GP6]
Scores for complete 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  125.7   0.0    3.6e-36  125.3   0.0    1.1  1  Peptidase_C1  Papain family cysteine protease


Domain annotation for each model (and alignments):
>> Peptidase_C1  Papain family cysteine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.3   0.0     2e-40   3.6e-36       2     212 ..      41     240 ..      40     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 2e-40
                                       TSCEETTT.TTTG.SG---B-TSSBTHHHHHHHHHHHHHHHHHHS..SS---B-HHHHHHHSTTTSTGGGBB-HHHH CS
                      Peptidase_C1   2 pesvDwre.kgga.vtpvkdqgsCGsCWafsavgaledrlaiktk..kklvslSeqelvdCskeenegCnGGlmena 74 
                                       p+s+Dwr+ +g    tp++dqg+C s+ af++++ +e++++i+++  k + +lSe  l    +     C+ G +   
  gi|330507725|ref|YP_004384153.1|  41 PSSFDWRSiEGEDfTTPIRDQGKCSSSVAFATIALMESMIKIANQdpKLQPDLSEAYLFPRGG---GKCESGAQFGR 114
                                       99******7555579*****************************9988899*******98755...78999999999 PP

                                       HHHHHHTEBEBTTTS--SSSCSSS-CGCGGGSEEBEESEEEEEESSBHHHHHHHHHHHSSEEEEEECCSHHHHTEES CS
                      Peptidase_C1  75 feyikkggivtekdypYkakeggkCkkkkkkekvakikgygkvkenseealkkalakngPvsvaidaseedfqlYks 151
                                       +  + ++g+++e + pY +   + C   k++   + i+  +++ +   e+ k+++a++gP+   + +++ df  + +
  gi|330507725|ref|YP_004384153.1| 115 MLTAAESGVCDELCCPYAGDW-KPCPDFKSRL--TAITFSETIFS--PEQAKAHIASTGPLMSGMAVYA-DFFEHDG 185
                                       99999**************99.68*9998763..46666666555..47899*****************.6****** PP

                                       SEESSTSCETSS-EEEEEEEEEEEETTEEEEEEE-SBTTTSTBTTEEEEESSSSTGGGTTS CS
                      Peptidase_C1 152 GvyketecsktelnhavlivGygvengkkyWivkNsWgtdwgekGYiriargknnecgies 212
                                       G+y++ +  +   nha+livGy++  g+++Wi kNsWg +wge G++ri++g   ecgi s
  gi|330507725|ref|YP_004384153.1| 186 GIYSQ-DYGNFVGNHAILIVGYDE--GEDCWIGKNSWGLTWGEGGWFRIKQG---ECGIGS 240
                                       ****9.6666778*********86..69**********************88...899976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2577.97
//
Query:       gi|330507726|ref|YP_004384154.1|  [L=149]
Description: hypothetical protein MCON_1720 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1023.99
//
Query:       gi|330507727|ref|YP_004384155.1|  [L=120]
Description: hypothetical protein MCON_1721 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   15.9   0.0      0.012   15.9   0.0    1.1  1  Mre11_DNA_bind  Mre11 DNA-binding presumed domain


Domain annotation for each model (and alignments):
>> Mre11_DNA_bind  Mre11 DNA-binding presumed domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0   6.9e-07     0.012      52      97 ..      53      98 ..      12     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.9e-07
                                      HHHHHSSSTTS------EEEEEEE-TTT-----HHHHHHC.CCTTBS CS
                    Mre11_DNA_bind 52 aeeeweeeaeeeepplPLiRLrVdysggfevenpqrfgqr.FvgkVA 97
                                        +   +e+e+++++l LiR+ Vd +      + qrf qr +v +V 
  gi|330507727|ref|YP_004384155.1| 53 ICSLCIKEDEQRDMRLSLIRVQVDAE-LKMNQDIQRFQQRrYVAQVI 98
                                      333447899*****************.55567899999864777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 893.46
//
Query:       gi|330507728|ref|YP_004384156.1|  [L=195]
Description: hypothetical protein MCON_1722 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-17   62.4   0.0    7.3e-17   62.2   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    1.8e-06   28.0   0.0    1.2e-05   25.3   0.0    1.9  1  CTP_transf_3     Cytidylyltransferase
    0.00063   19.4   0.0    0.00093   18.8   0.0    1.4  1  NTP_transferase  Nucleotidyl transferase
      0.006   15.8   0.2      0.013   14.7   0.0    1.5  2  CofC             Guanylyl transferase CofC like


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0   1.6e-20   7.3e-17       4     119 ..       1     117 [.       1     141 [. 0.91

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.6e-20
                                       EEESS-TTTTT.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHHH CS
                      NTP_transf_3   4 LAGGrSsRmgg.dKallplggkpllervldalraagvdevvvvggd..eevlaalarlgvrvvededpgkgplasla 77 
                                       +AGGr+sR+++ +K+++ + g++l+e+v+ al++++v++++v++ +  +  +a +++  ++vv  +  g g +  + 
  gi|330507728|ref|YP_004384156.1|   1 MAGGRGSRLNRgEKPMVTIFGRRLIEYVALALEDSSVEKIYVATTEnvPLTRAWARDWSLSVVDTP--GMGFVPDMI 75 
                                       59********77*******************************97756778888888888888886..9******** PP

                                       HHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEE CS
                      NTP_transf_3  78 aalraaadadavlvlacDmPlltpelverllaaaaasgadvv 119
                                       +a+++a  +d+++v+++D+Pl+t+el++++++ ++++++ ++
  gi|330507728|ref|YP_004384156.1|  76 SAVNEAMVTDPIMVIMADLPLITSELIDTIIEVYEERPEPAL 117
                                       *****99**************************998887664 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   2.8e-09   1.2e-05      15     125 ..      13     119 ..       7     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.8e-09
                                       TGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTT..SEEEE--TTCSSHHHHHHHHHHHHTTT.T CS
                      CTP_transf_3  15 gKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefg..asvlvtrsslesdterflevvkaflmsen 89 
                                       +K++  ++g++li+yv  a+ +s + ek++vaT+++     a ++    sv+ t++     +  + ++++a+     
  gi|330507728|ref|YP_004384156.1|  13 EKPMVTIFGRRLIEYVALALEDSSV-EKIYVATTENVPLTRAWARDwsLSVVDTPG-----MGFVPDMISAVNEAMV 83 
                                       6*********************888.********9865555555541166665554.....4444444444444444 PP

                                       TSEEEEE-TT-TT--HHHHHHHHHHHHHSTTSSEEE CS
                      CTP_transf_3  90 eeiivnlqGdnPllqeevikkaietlkenqedylst 125
                                        + i+ + +d Pl+ +e+i+ +ie ++e++e+ lst
  gi|330507728|ref|YP_004384156.1|  84 TDPIMVIMADLPLITSELIDTIIEVYEERPEPALST 119
                                       458899999********************9987766 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.1e-07   0.00093       5      62 ..       1      52 [.       1     119 [. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.1e-07
                                      E--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHH CS
                   NTP_transferase  5 LaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflve 62
                                      +aGG+G+RL    ++  k++v++ g  rli++++ +l +s++e+ i+v t e+ +l +
  gi|330507728|ref|YP_004384156.1|  1 MAGGRGSRL----NRGEKPMVTIFGR-RLIEYVALALEDSSVEK-IYVATTENVPLTR 52
                                      8********....69***********.*****************.6666666655444 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.8e-06     0.013      75     112 ..      74     108 ..      58     113 .. 0.85
   2 ?   -2.4   0.0      0.49   2.2e+03     166     180 ..     170     184 ..     157     193 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.8e-06
                              CofC  75 lntavekafeeieekeviiipsdiPlikkedvkdllel 112
                                       + +av++a+     +++++i++d+Pli+ e ++ ++e 
  gi|330507728|ref|YP_004384156.1|  74 MISAVNEAM---VTDPIMVIMADLPLITSELIDTIIEV 108
                                       556777774...489******************99986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.49
                              CofC 166 sfylsvdinteedlg 180
                                          l+v++n +edl 
  gi|330507728|ref|YP_004384156.1| 170 RIELAVNVNVAEDLR 184
                                       555778888888863 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1426.82
//
Query:       gi|330507729|ref|YP_004384157.1|  [L=254]
Description: cobalamin 5'-phosphate synthase [Methanosaeta concilii GP6]
Scores for complete 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-40  137.1  20.2      1e-39  136.9  20.2    1.0  1  CobS             Cobalamin-5-phosphate synthase
  ------ inclusion threshold ------
      0.013   15.4   4.3      0.013   15.4   4.3    2.9  3  RseC_MucC        Positive regulator of sigma(E), RseC/MucC
      0.081   13.2   0.2      0.081   13.2   0.2    2.9  3  DUF3267          Putative zincin peptidase
        9.9    6.4   9.1         23    5.2   1.8    2.5  2  TMEM191C         TMEM191C family


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 !  136.9  20.2   2.3e-43     1e-39       2     203 ..      12     239 ..      11     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 2.3e-43
                              CobS   2 lsflTrlPvp.......elaralaffPlvGlllGlll.llallllllll.llaallavaalvlltgglHlDGlaDta 69 
                                       +++l+ +Pv        +l + +++fPlvGl+lG++l  + +++l++++ +l a+++++a+++l g++H+DGlaD+a
  gi|330507729|ref|YP_004384157.1|  12 FGWLSAIPVGismegveALMNHVYVFPLVGLVLGAILgTVSYIALQAFPaSLVAVVVIVAIYWLCGINHIDGLADFA 88 
                                       789******876655444467999*************99999999888886677777778899************** PP

                              CobS  70 DglgsgrdrerrleImkDsrvGafGvlalvlvlllkvaalaala.......lllapvlsRlaallaiallpyaeegl 139
                                       Dg++++++re+++++mkD  +G++G l +v+++l+ +a+l++l+       ll+a+v ++ a++ ++a++ + ++g+
  gi|330507729|ref|YP_004384157.1|  89 DGVIAHGTREKKIAAMKDVYMGTGGGLYIVVLILAAFAVLSSLPerllplaLLTAEVSAKEAMISFAAFSSSLQKGF 165
                                       ***9999********************************9777777788888899****************8899** PP

                              CobS 140 galfaeaqkk......lv..llal....avlllllalllaallvalllrrlarrklggvtGDvlGavieltellvl 203
                                       g++++++++k      lv  +  +    a+ +l la+l+aa l+al+l ++++r++gg tGD +Ga++e++++++l
  gi|330507729|ref|YP_004384157.1| 166 GQIMIQRTDKgqfllgLVisA--VicslALGALGLAILAAAQLAALYLVWVSKRNFGGATGDGIGATNEIARVTAL 239
                                       *****9666667655422221..133322222222455666668889999**********************9987 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 ?   15.4   4.3   2.9e-06     0.013      56     110 ..      20      75 ..      16      82 .. 0.77
   2 ?   -2.1   0.5      0.75   3.4e+03      72      72 ..     135     135 ..     107     170 .. 0.59
   3 ?    3.0   4.0     0.021        92      75     113 ..     179     216 ..     178     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-06
                         RseC_MucC  56 vgieeksllkaallvYllPllllilgallgsall.gssellaalgallglvlgfli 110
                                       vgi+ + +   +  vY++Pl++l+lga+lg++   + + + a l+a++++v+ +++
  gi|330507729|ref|YP_004384157.1|  20 VGISMEGVEALMNHVYVFPLVGLVLGAILGTVSYiALQAFPASLVAVVVIVAIYWL 75 
                                       66666666677778****************99887677777777777777776665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.75
                         RseC_MucC  72 l 72 
                                       l
  gi|330507729|ref|YP_004384157.1| 135 L 135
                                       2 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.021
                         RseC_MucC  75 llllilgallgsallgssellaalgallglvlgflivrl 113
                                       ll+l+++a+++s++ ++  +la+l+a  +++l++++v +
  gi|330507729|ref|YP_004384157.1| 179 LLGLVISAVICSLA-LGALGLAILAAAQLAALYLVWVSK 216
                                       799***********.699999999999999999999875 PP

>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   2.2      0.29   1.3e+03      60      85 ..      47      72 ..      29      87 .. 0.62
   2 ?   -0.4   0.2      0.32   1.4e+03      81      90 ..     121     130 ..     103     163 .. 0.54
   3 ?   13.2   0.2   1.8e-05     0.081      47     103 ..     175     236 ..     164     240 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.29
                           DUF3267 60 llgilllllalllpsstlllllllal 85
                                      +lg++ ++++ ++p s  ++++++a+
  gi|330507729|ref|YP_004384157.1| 47 ILGTVSYIALQAFPASLVAVVVIVAI 72
                                      55666666666666554433333333 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.32
                           DUF3267  81 lllalnaags 90 
                                       +l+a+ +++s
  gi|330507729|ref|YP_004384157.1| 121 ILAAFAVLSS 130
                                       2222222222 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 1.8e-05
                           DUF3267  47 kkqfiiillaPfvl....lgilllllalllpsstlllllllalnaagsagD.lliallllka 103
                                       k qf++ l+  +v+    lg+l+l+++++++ ++l+l++++  n++g++gD + +++ + ++
  gi|330507729|ref|YP_004384157.1| 175 KGQFLLGLVISAVIcslaLGALGLAILAAAQLAALYLVWVSKRNFGGATGDgIGATNEIARV 236
                                       66666666666666111145566666666666666****************99888887776 PP

>> TMEM191C  TMEM191C family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.8    0.0057        26      44      87 ..     108     151 ..      92     162 .. 0.82
   2 ?    5.2   1.8    0.0051        23      35      80 ..     170     215 ..     159     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0057
                          TMEM191C  44 lfGgagaaalrlwalgalqtllllPlgflalpllylvlvksdav 87 
                                        +G+ g+  + + +l+a+ +l  lP  +l l+ll   +  ++a+
  gi|330507729|ref|YP_004384157.1| 108 YMGTGGGLYIVVLILAAFAVLSSLPERLLPLALLTAEVSAKEAM 151
                                       4677778889999*********************9887777765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0051
                          TMEM191C  35 varadcekrlfGgagaaalrlwalgalqtllllPlgflalpllylv 80 
                                       + r+d  + l+G   +a++   algal + +l    + al l+++ 
  gi|330507729|ref|YP_004384157.1| 170 IQRTDKGQFLLGLVISAVICSLALGALGLAILAAAQLAALYLVWVS 215
                                       679999*********************9999998888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 1828.47
//
Query:       gi|330507730|ref|YP_004384158.1|  [L=151]
Description: alpha-ribazole phosphatase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-06   28.2   0.0    1.8e-06   28.0   0.0    1.1  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 !   28.0   0.0     1e-10   1.8e-06      42     141 ..      43     139 ..       4     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1e-10
                                       H...HHHHHHHHHHHHHHHHHHT.-S-.......HHT-TT--HHHHTTHHHHH........TTHHHHHHHHHHHHS- CS
                              PgpA  42 l...llilllflvGiwackktek.elg.......ekDpgeiviDEvvgqwiallllpatllalllafilFrlfDivK 107
                                       +   ++++ll+++++ ++ + e+ +l        e+D + ++ DEv+g++ia       +++   +++ +  +D++K
  gi|330507730|ref|YP_004384158.1|  43 AlsdPNLALLIYAALLLEVEGERrNLPnlkpsdyENDLTCLIADEVIGLSIAK------YVGGYKGLFDYVRYDKAK 113
                                       2345566666666666666666655556779999*******************......4566999*********** PP

                                       -THHHHTSSS.-S---TTHHHHHHHHHHHHHHHH CS
                              PgpA 108 pgpigwldrklkgglgvmlDDllAgiaaalvlal 141
                                       pg++++l          +lDD+lAg+++++   +
  gi|330507730|ref|YP_004384158.1| 114 PGILSRLGP--------FLDDALAGLIGGVSANM 139
                                       ******977........9*********9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1242.94
//
Query:       gi|330507731|ref|YP_004384159.1|  [L=116]
Description: hypothetical protein MCON_1725 [Methanosaeta concilii GP6]
Scores for complete 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  156.0   0.1      3e-46  155.9   0.1    1.0  1  Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen r
  ------ inclusion threshold ------
      0.069   13.3   0.0         15    5.8   0.0    2.1  2  HisG_C         HisG, C-terminal domain
       0.13   12.3   0.2       0.55   10.3   0.2    1.8  1  Bcr-Abl_Oligo  Bcr-Abl oncoprotein oligomerisation domain


Domain annotation for each model (and alignments):
>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.9   0.1     5e-50     3e-46       1     106 [.       1     106 [.       1     107 [. 0.99

  Alignments for each domain:
  == domain 1  score: 155.9 bits;  conditional E-value: 5e-50
                     Nit_Regul_Hom   1 mkvllklfvesenlgkvinalseagitGfylieYkGlsPqewkgflleedpesaikiikdlseeavlintvvdeekv 77 
                                       mk+++k+fv++e+l++vin+l+e gitGfylieY+G++P++wk+f+l+edp++a+k+i+d+se++v++ntvv  +k+
  gi|330507731|ref|YP_004384159.1|   1 MKTMVKIFVDHEHLVRVINSLTELGITGFYLIEYQGMAPTNWKSFQLSEDPDMALKAIRDHSEPGVMVNTVVGPDKC 77 
                                       8**************************************************************************** PP

                     Nit_Regul_Hom  78 ekikeeleeklkderytiieipvekikvn 106
                                       +++ +elee+lk+ r+tii ++v++ikv+
  gi|330507731|ref|YP_004384159.1|  78 QRLIKELEEALKGIRFTIIGHQVNSIKVK 106
                                       ***************************97 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0032        19      41      64 ..       4      27 ..       2      33 .. 0.89
   2 ?    5.8   0.0    0.0025        15      36      61 ..      62      87 ..      53      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0032
                                      EEEEEEECCCHHHHHHHHHCTT-E CS
                            HisG_C 41 aVsavveekevaevideLkaaGAs 64
                                       V++ v+ + + +vi+ L+++G +
  gi|330507731|ref|YP_004384159.1|  4 MVKIFVDHEHLVRVINSLTELGIT 27
                                      699******************965 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0025
                                      SS-EEEEEEEEECCCHHHHHHHHHCT CS
                            HisG_C 36 degwvaVsavveekevaevideLkaa 61
                                      +e  v V++vv  ++++++i+eL++a
  gi|330507731|ref|YP_004384159.1| 62 SEPGVMVNTVVGPDKCQRLIKELEEA 87
                                      566799*****************986 PP

>> Bcr-Abl_Oligo  Bcr-Abl oncoprotein oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   9.3e-05      0.55      13      59 ..      45     100 ..      38     110 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.3e-05
                     Bcr-Abl_Oligo  13 fPeeevPkmeLdsvedieqe..L.......erCkaslrrLekelneekfkviyLqt 59 
                                       f  +e P m L++++d  +   +       ++C+  +++Le+ l+  +f +i  q 
  gi|330507731|ref|YP_004384159.1|  45 FQLSEDPDMALKAIRDHSEPgvMvntvvgpDKCQRLIKELEEALKGIRFTIIGHQV 100
                                       6667778888888887544211022223449********************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 860.98
//
Query:       gi|330507732|ref|YP_004384160.1|  [L=75]
Description: NifU-like domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-23   81.7   0.6    3.6e-23   81.5   0.6    1.0  1  NifU            NifU-like domain
     0.0068   16.5   0.1       0.03   14.5   0.1    2.0  1  FeS_assembly_P  Iron-sulfur cluster assembly protein


Domain annotation for each model (and alignments):
>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.6     4e-27   3.6e-23       1      67 []       8      73 ..       8      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 4e-27
                                      HHHHHHH.HGGG--GG--EEEEEEEETTEEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EEE CS
                              NifU  1 ieevleeeirPaLasdGGdielvdvdegvVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeVe 67
                                      +e++l + ir  L+ dGGd+elvd+ +g+V+vrlqG C+gCp s++tlk+ iek L + v  +k V+
  gi|330507732|ref|YP_004384160.1|  8 VEAALGK-IREGLRVDGGDVELVDISDGIVTVRLQGHCAGCPFSQMTLKNFIEKELVKSVAGIKGVV 73
                                      789999*.*******************************************************9985 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.4e-06      0.03      21      68 ..      21      70 ..       5      75 .] 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-06
                                      CCCT---EEEE-T-EEEEEE--SSTT-T.THHHHHHHHHHHHC..STT-- CS
                    FeS_assembly_P 21 vslglvreidieggkVsvditltypacs.laeairadaeaalr.alpgve 68
                                      v+ g v+ +di++g V+v ++   ++c+ +   +++ +e+ l  +++g++
  gi|330507732|ref|YP_004384160.1| 21 VDGGDVELVDISDGIVTVRLQGHCAGCPfSQMTLKNFIEKELVkSVAGIK 70
                                      56777888********************7666666667776666777733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 549.31
//
Query:       gi|330507733|ref|YP_004384161.1|  [L=56]
Description: LSM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-14   53.0   0.1    2.2e-14   52.9   0.1    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 !   52.9   0.1   1.3e-18   2.2e-14      20      67 .]       8      54 ..       3      54 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.3e-18
                                      EEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                               LSM 20 elrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                      +l+G+L ++D+++Nl+L +++e + ++ ++r+lg v++RGnni+lis+
  gi|330507733|ref|YP_004384161.1|  8 VLEGVLNSVDEYLNLHLLETVELIGGE-KTRSLGSVILRGNNIILISP 54
                                      689*********************999.******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       163  (0.00909142); expected 358.6 (0.02)
Passed bias filter:                      152  (0.00847788); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 446.38
//
Query:       gi|330507734|ref|YP_004384162.1|  [L=133]
Description: hypothetical protein MCON_1728 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00056   20.0   0.0    0.00081   19.5   0.0    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
    0.00094   19.0   0.0     0.0017   18.2   0.0    1.3  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.097   12.6   0.0       0.14   12.1   0.0    1.3  1  MarR            MarR family


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 !   19.5   0.0   1.3e-07   0.00081      14      51 ..      12      49 ..       6      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-07
                    B-block_TFIIIC 14 sRysGitqsdLakeskqdprslfyrlksLekkgLIvkq 51
                                      s  +G +qsdL+k++k+d+r+   ++ +L k   I++ 
  gi|330507734|ref|YP_004384162.1| 12 SHPEGALQSDLWKALKIDSRKCSRIVAKLLKDRHITRE 49
                                      5568***************************9999986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.8e-07    0.0017      10      57 ..       6      52 ..       5      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.8e-07
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgp 57
                                      +L ++  +p++   +++l ++l+++    sri+++L +  +++r+  +
  gi|330507734|ref|YP_004384162.1|  6 ALDYIKSHPEG-ALQSDLWKALKIDSRKCSRIVAKLLKDRHITREVES 52
                                      6899999*998.7******************************99655 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.3e-05      0.14      12      50 ..      10      49 ..       5      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                                      HHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 12 lyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      ++++++ + +s+L+k+l++++   +r++ +L k+  i+R+
  gi|330507734|ref|YP_004384162.1| 10 IKSHPEgALQSDLWKALKIDSRKCSRIVAKLLKDRHITRE 49
                                      66666657788**********************9888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1042.01
//
Query:       gi|330507735|ref|YP_004384163.1|  [L=102]
Description: protein translation initiation factor SUI1-like protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-22   80.0   2.5    1.8e-22   79.7   2.5    1.1  1  SUI1      Translation initiation factor SUI1
     0.0027   18.0   0.6     0.0043   17.3   0.6    1.5  1  Img2      Mitochondrial large subunit ribosomal protein (Img2
  ------ inclusion threshold ------
      0.021   14.5   1.3      0.023   14.4   1.3    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 !   79.7   2.5   2.9e-26   1.8e-22       2      76 ..      25      95 ..      24      96 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 2.9e-26
                              SUI1  2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygv 76
                                      +++i +++++r+ +K vT+++g+++ +idl++l+ +lk+k+ac+g+v kd+   i++QG+++++++++L++k g+
  gi|330507735|ref|YP_004384163.1| 25 QQRIVVKVQKRRYGKEVTVIQGIDPHEIDLQELCTHLKSKLACGGTV-KDS--LIELQGNHIQRIKDILVKK-GF 95
                                      899*******************************************9.888..8*****************9.86 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.6   7.1e-07    0.0043      19      80 .]      33      95 ..      13      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.1e-07
                              Img2 19 vkrggtkkltvirkieG...DiaalredLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                       kr+  k++tvi+ i+    D+++l ++L++ l+  +  + + + ie++G++ +++k++L +kgF
  gi|330507735|ref|YP_004384163.1| 33 QKRRYGKEVTVIQGIDPheiDLQELCTHLKSKLA--CGGTVKDSLIELQGNHIQRIKDILVKKGF 95
                                      4666778899999996544499999999999999..88888999********************9 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.3   3.8e-06     0.023       2      29 ..       4      30 ..       3      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-06
                               DTW  2 elCerCllpaevclcsslppleklpikv 29
                                      ++C+ C lp+e+c+c+++ + e+++i v
  gi|330507735|ref|YP_004384163.1|  4 QMCAVCGLPQELCICEEVAK-EQQRIVV 30
                                      68*****************9.6664443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 884.47
//
Query:       gi|330507736|ref|YP_004384164.1|  [L=786]
Description: hypothetical protein MCON_1730 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-11   43.7   0.0    6.1e-06   26.6   0.0    2.4  2  VWA           von Willebrand factor type A domain
    9.1e-11   42.4   0.0    2.5e-10   40.9   0.0    1.8  1  VWA_2         von Willebrand factor type A domain
    2.5e-10   40.2   0.0    0.00038   20.0   0.0    2.4  2  GATase1_like  Putative glutamine amidotransferase
     0.0029   17.8   0.1      0.031   14.5   0.0    2.8  3  Big_3_5       Bacterial Ig-like domain (group 3)
  ------ inclusion threshold ------
       0.12   12.9   0.0       0.29   11.7   0.0    1.6  1  Usp           Universal stress protein family


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 !   14.5   0.0   8.7e-06     0.031     106     143 ..     121     159 ..     114     181 .. 0.86
   2 !   26.6   0.0   1.7e-09   6.1e-06       2     162 ..     355     518 ..     355     529 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.7e-06
                                       EEEEEESS--CSS.HTHHHHHHHHGCTEEEEEEEESSSH CS
                               VWA 106 viilltdGksndg.dpkeaaneakeqgikvfavGvgnad 143
                                        i+l+tdG+sn+g ++++a++ a++++ +vfa+ ++ + 
  gi|330507736|ref|YP_004384164.1| 121 TILLVTDGYSNSGrSLEDALALARSSNSTVFALDIDPVK 159
                                       589*********88******************9986554 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 1.7e-09
                                       EEEEEE-STTS.......CHHHHHHHHHHHHHHHHHHTB..TTTTEEEEEEEESSSEEEEEETTSHC.HHHHHHHHH CS
                               VWA   2 ivfvlDgSgsm.......geenfekvkefikklveklev..gpegtrvglvqfssevktefslndys.skeellsal 68 
                                       ++fvlD S s        g     + +++ k l+ +l    + ++ +vglv f++ ++ +++    s s++ l++ +
  gi|330507736|ref|YP_004384164.1| 355 LIFVLDISFSLlstltkdGT----TLLDYEKALAVELLHspQFQDYNVGLVVFGTRAYNVIDPVPLSrSQNVLADRI 427
                                       68999999999555433222....44444444444444223477889*********99998888855599******* PP

                                       HTGSGGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS.SHTHHHHHHHHGC.TEEEEEEEE..SS CS
                               VWA  69 nnlkysgggttntgkalkyaleklfkssagaRenakkviilltdGksnd.gdpkeaaneakeq.gikvfavGv..gn 141
                                        +l   g+++++++++l+ a++ ++++s g     +  +i+l+dG+ +  gd+   ++e+ ++ +i++  + v    
  gi|330507736|ref|YP_004384164.1| 428 ATLAPTGTENSYLDSGLELARD-MIQASGG-----EGEMIVLSDGNLQNyGDVVVRSKELIREmNITTRLIQVqaIP 498
                                       ******************9998.7777777.....789*********776888888888777779999999996544 PP

                                       SHHHHHHHHHSSSSCHHCEEE CS
                               VWA 142 adekelLnkiasepgeghvft 162
                                         + +   +ias++g++++++
  gi|330507736|ref|YP_004384164.1| 499 GATGS-FPDIASSTGSEFTYF 518
                                       55555.888888888555543 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 !   40.9   0.0   7.1e-14   2.5e-10       1     107 []     355     467 ..     355     467 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 7.1e-14
                             VWA_2   1 lvfvlDtSgSmrng..dygptrleaakdaveallk..slpgdrvglvtfsdgpevlipl...tkdkakilnalrnle 70 
                                       l+fvlD S S  ++  + g+t l++ k+++ +ll+  ++++ +vglv+f+++++ +i++   +++++ + +++  l 
  gi|330507736|ref|YP_004384164.1| 355 LIFVLDISFSLLSTltKDGTTLLDYEKALAVELLHspQFQDYNVGLVVFGTRAYNVIDPvplSRSQNVLADRIATLA 431
                                       69*********88743448****************5555566*********999998764447************** PP

                             VWA_2  71 ak.gggtnlaaaLqlarkalkkrrkgekrvivlitDge 107
                                       ++ + +++l+++L+lar+++++   g + ++++++Dg+
  gi|330507736|ref|YP_004384164.1| 432 PTgTENSYLDSGLELARDMIQAS--GGEGEMIVLSDGN 467
                                       **9999***************77..79*********95 PP

>> GATase1_like  Putative glutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.1e-07    0.0018      96     184 ..     303     384 ..     287     404 .. 0.85
   2 !   20.0   0.0     1e-07   0.00038     157     226 ..     548     615 ..     531     633 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.1e-07
                      GATase1_like  96 rlkllkdyvaeGggllmvGGylsfqGidgkarykktpvedvlPvtcldvddrvevPeGlaaevvasehpvlkglsse 172
                                        l  l+dyv eGggl++vGG  s+       +y+++++e  lPv+ ++   r e  + l+  v++ + ++l++l+++
  gi|330507736|ref|YP_004384164.1| 303 SLDRLEDYVREGGGLVVVGGKNSYD----LGEYRNSTLERFLPVQSFPS--RFEGGKTLI-FVLDISFSLLSTLTKD 372
                                       678899*****************97....468*************9995..888776655.4678899999999999 PP

                      GATase1_like 173 wPkllGynevea 184
                                         +ll y++  a
  gi|330507736|ref|YP_004384164.1| 373 GTTLLDYEKALA 384
                                       999999988765 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1e-07
                      GATase1_like 157 evvasehpvlkglssewPkllGyneveakdnaevlatvsedshPllvvGeygkGrtaaftsdisphwlsp 226
                                        vv+++h +++ l     ++ G+n+v++k+++  l  +++ ++P+l v +yg Gr+aa t+d +  w   
  gi|330507736|ref|YP_004384164.1| 548 AVVNQNHYITTDLEL-NATITGFNDVTPKPGSLRLVALTD-GKPVLTVWRYGLGRVAALTTDNGISWAGL 615
                                       578899999999995.57899**********999988875.59************************865 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 !   14.5   0.0   8.5e-06     0.031       1      74 [.     169     241 ..     169     256 .. 0.84
   2 ?   -2.6   0.1       1.8   6.5e+03       7      29 ..     557     580 ..     553     608 .. 0.64
   3 ?   -1.6   0.0      0.91   3.3e+03      58      71 ..     674     687 ..     649     693 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.5e-06
                                       -S-EETTSEEEEEEE--CCCCTTS--EEEEEETTEE-SS-EE--TTSEEEEEE..E-SS-EEEEEEEEEE-TTS-- CS
                           Big_3_5   1 ptsvtagqtvtltatVtaasggtptGtVtftdggttlgtavllsanGtAtltv..salaaGthsitAtYsGdanya 74 
                                       p++++ g ++ + ++V ++   + +G  +++ +++++ + +  + nG+A++++  s+l++G+h + A+ ++d + a
  gi|330507736|ref|YP_004384164.1| 169 PNTAVLGGDYPFRVMVRSS--LDYSGPLSVYADEKKIYSDQIQA-NGSASIKIshSFLETGNHILRAVIAPDMQPA 241
                                       789999***********99..89****************99877.9***99874477**********977776555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
                                       TSEEEEEEE--CCCCTTS-.-EEE CS
                           Big_3_5   7 gqtvtltatVtaasggtpt.GtVt 29 
                                        ++ +l+at+t+ +  tp  G+  
  gi|330507736|ref|YP_004384164.1| 557 TTDLELNATITGFNDVTPKpGSLR 580
                                       567888999998776554435444 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.91
                                       -EEEEEEEEEE-TT CS
                           Big_3_5  58 aGthsitAtYsGda 71 
                                        G + +tAt+++++
  gi|330507736|ref|YP_004384164.1| 674 IGDNRYTATFTPNS 687
                                       57777777777654 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     8e-05      0.29       4      43 ..     121     160 ..     120     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8e-05
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSH CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidpra 43 
                                       +Il+++Dg ++s + le Al+la+++++++++l + + + 
  gi|330507736|ref|YP_004384164.1| 121 TILLVTDGYSNSGRSLEDALALARSSNSTVFALDIDPVKG 160
                                       79******************************98877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (786 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 5195.23
//
Query:       gi|330507737|ref|YP_004384165.1|  [L=580]
Description: hypothetical protein MCON_1731 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-18   65.1   6.8      7e-18   64.8   1.6    2.3  2  BatA      Aerotolerance regulator N-terminal
    0.00095   19.8   0.0      0.002   18.8   0.0    1.5  1  VWA_2     von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.032   13.1   0.1      0.052   12.5   0.1    1.2  1  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   1.6   1.2e-21     7e-18       1      77 []       1      76 [.       1      76 [. 0.98
   2 ?    2.9   0.3     0.023   1.4e+02       6      27 ..     556     578 ..     552     580 .] 0.50

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.2e-21
                              BatA  1 MlpFlnPllLlallllplpiillyllkrrpqevvfsslrlleevekdeea.lqrlkknllllLrllalallvlalArP 77
                                      M pF nP++Ll+ll +++ ++++yl++++p+e++fss+++l+e e +++a l+rl  + l++++lla++ l la A+P
  gi|330507737|ref|YP_004384165.1|  1 M-PFSNPIALLGLLGIIP-LVIIYLIRPQPKEIRFSSIQFLREGEAKRTAvLSRLISDPLFWVQLLAICSLSLAAAGP 76
                                      9.9***********9999.9*************************999999**************************9 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.023
                              BatA   6 nPllLlall.llplpiillyllk 27 
                                       +P++ ++++ +++l ++++++++
  gi|330507737|ref|YP_004384165.1| 556 SPWVIALAAlAIILELAIMRWRR 578
                                       78866444413333344444443 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 !   18.8   0.0   3.3e-07     0.002       1     105 [.      88     179 ..      88     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.3e-07
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtn 77 
                                       lv+vlD+S+Sm+++      ++ a+++++++l++    r++++  ++ p+++++  + +a+ ++ l + ++ +   +
  gi|330507737|ref|YP_004384165.1|  88 LVVVLDGSASMQSS------FSPAQNIIRSYLDR--YERISIILAKNVPQTVLTEGS-PAEARDQLPQFKPAAVSAD 155
                                       79***********9......*************9..569****99999999987555.99***************** PP

                             VWA_2  78 laaaLqlarkalkkrrkgekrvivlitD 105
                                       l +aL +a+ +l ++       i+l++D
  gi|330507737|ref|YP_004384165.1| 156 LSSALTQASILLGST----GGDILLVSD 179
                                       *********999966....588888888 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   8.6e-06     0.052     158     225 ..       8      75 ..       6     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.6e-06
                             MFS_1 158 aivsllafv.lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg 225
                                       a+++ll+++ l++++l +++p++ r+s+++ + + g+a+ + +++ l +dp +w+ l+a+++ +++ +g
  gi|330507737|ref|YP_004384165.1|   8 ALLGLLGIIpLVIIYLIRPQPKEIRFSSIQFL-REGEAKRTAVLSRLISDPLFWVQLLAICSLSLAAAG 75 
                                       7889999889999******************5.33333333357*******999444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 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:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 4080.04
//
Query:       gi|330507738|ref|YP_004384166.1|  [L=153]
Description: tungsten formylmethanofuran dehydrogenase subunit G [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-13   49.3   3.1    2.8e-13   49.3   3.1    2.5  2  FeS           Putative Fe-S cluster
    8.2e-09   34.9  20.2    1.7e-07   30.7   4.6    3.3  3  Fer4          4Fe-4S binding domain
    1.1e-08   35.5  13.8    2.1e-05   25.0   5.8    2.7  2  Fer4_7        4Fe-4S dicluster domain
    4.2e-08   33.2   8.7    4.2e-08   33.2   8.7    2.8  2  Fer4_10       4Fe-4S dicluster domain
    1.3e-06   28.4  12.1    0.00039   20.5   4.7    2.9  2  Fer4_9        4Fe-4S dicluster domain
    1.8e-05   24.6  20.3    0.00011   22.1   3.2    3.2  3  Fer4_6        4Fe-4S binding domain
    2.5e-05   24.4  20.2    9.3e-05   22.6   2.5    3.7  3  Fer4_4        4Fe-4S binding domain
    3.4e-05   24.2  19.6    0.00067   20.1   6.8    2.4  2  Fer4_8        4Fe-4S dicluster domain
    8.5e-05   22.4  16.8    0.00039   20.3   2.3    3.3  3  Fer4_2        4Fe-4S binding domain
    0.00023   21.2  13.3    0.00037   20.5   1.0    3.0  3  Fer4_21       4Fe-4S dicluster domain
    0.00059   20.3  10.9     0.0047   17.4   3.9    2.6  2  Fer4_17       4Fe-4S dicluster domain
     0.0013   19.6  17.7        0.1   13.6   0.6    2.9  2  Fer4_16       4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
       0.02   15.8  22.8        0.2   12.7   6.1    3.4  3  Fer4_3        4Fe-4S binding domain
      0.064   13.3   0.7       0.13   12.4   0.0    1.8  2  Exonuc_VII_S  Exonuclease VII small subunit
      0.089   12.5   0.1       0.13   11.9   0.1    1.3  1  LID           LIM interaction domain (LID)
       0.18   12.0   3.9       0.99    9.6   0.3    2.4  2  Fer4_18       4Fe-4S dicluster domain
          4    8.0  12.7       0.76   10.4   1.7    2.9  3  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   3.1   2.6e-16   2.8e-13       1      33 []      11      43 ..      11      43 .. 0.99
   2 ?   -3.1   1.1       6.1   6.4e+03       6      14 ..     138     145 ..     138     150 .. 0.61

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2.6e-16
                               FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                      LP+tNC++CG p+CmafA  l+  e++le+C+p
  gi|330507738|ref|YP_004384166.1| 11 LPKTNCKKCGLPTCMAFAVGLLGREKKLEECTP 43
                                      9******************************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.1
                               FeS   6 CgaCGypgC 14 
                                       C aC   +C
  gi|330507738|ref|YP_004384166.1| 138 CNACTA-TC 145
                                       666643.55 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.5      0.43   4.6e+02       7      12 ..      15      20 ..      13      21 .. 0.74
   2 !   30.7   4.6   1.7e-10   1.7e-07       2      22 ..      73      93 ..      72      94 .. 0.94
   3 !   13.0   1.4   6.7e-05     0.071       9      24 .]     136     151 ..     136     151 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.43
                                      TSSS-T CS
                              Fer4  7 kCigCG 12
                                       C +CG
  gi|330507738|ref|YP_004384166.1| 15 NCKKCG 20
                                      688998 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 1.7e-10
                                      EEETTTSSS-THHHHHSTTTE CS
                              Fer4  2 videekCigCGaCvevCPvgA 22
                                      vi++ekC gCG+Cv +CPv++
  gi|330507738|ref|YP_004384166.1| 73 VIHPEKCFGCGNCVIACPVNV 93
                                      89*****************96 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 6.7e-05
                                       SS-THHHHHSTTTEEE CS
                              Fer4   9 igCGaCvevCPvgAIt 24 
                                       i C+aC   CP  AI+
  gi|330507738|ref|YP_004384166.1| 136 ILCNACTATCPSKAIE 151
                                       78************96 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   5.8     2e-08   2.1e-05       4      52 .]      15      93 ..      14      93 .. 0.58
   2 !   14.5   1.0   3.8e-05      0.04       3      19 ..     136     152 ..     136     153 .] 0.90

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2e-08
                            Fer4_7  4 gCgaCv.aaCpvkaieldeeenek..........gtekv......................eidpekClgCgaCvavCP 49
                                      +C++C  ++C++ a+ l  +e++           +   +                      +i+pekC gCg+Cv +CP
  gi|330507738|ref|YP_004384166.1| 15 NCKKCGlPTCMAFAVGLLGREKKLeectplfeekK---YeaklaklkeivaplesasetglVIHPEKCFGCGNCVIACP 90
                                      68888558887666665543222222333332220...122233334445555555556669***************** PP

                            Fer4_7 50 tga 52
                                      +++
  gi|330507738|ref|YP_004384166.1| 91 VNV 93
                                      986 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.8e-05
                            Fer4_7   3 igCgaCvaaCpvkaiel 19 
                                       i C+aC+a+Cp+kaie+
  gi|330507738|ref|YP_004384166.1| 136 ILCNACTATCPSKAIEF 152
                                       56************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 ?    1.3   2.2      0.36   3.8e+02       6      17 ..      13      26 ..       8      45 .. 0.77
   2 !   33.2   8.7     4e-11   4.2e-08       3      56 .]      73     146 ..      71     146 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.36
                           Fer4_10  6 ddtCirCg..kCvk 17
                                      +  C +Cg  +C++
  gi|330507738|ref|YP_004384166.1| 13 KTNCKKCGlpTCMA 26
                                      56677777666665 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 4e-11
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.............tsvgakgeaseeeavrkkvekCtg.......cgaCveaCP 56 
                                       vi +++C +Cg+Cv aCP+++             ++++++   +++ +v  ++++C +       c aC++ CP
  gi|330507738|ref|YP_004384166.1|  73 VIHPEKCFGCGNCVIACPVNVaaeptrvgaglgpEGDRVILRVEDGVVVANNLQECKRfgpnkilCNACTATCP 146
                                       899****************99*************99999999999999999*******99999999*******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 !   20.5   4.7   3.7e-07   0.00039       3      49 ..      14      92 ..      14      94 .. 0.67
   2 !   10.9   0.8   0.00037      0.39      37      51 .]     136     150 ..     116     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.7e-07
                            Fer4_9  3 tgCgaC.veaCpagvvvedaaerkarlraase................................eaCigCgaCveaCpk 48
                                      t+C++C  + C a +v     e+k +  ++                                  e+C+gCg Cv aCp 
  gi|330507738|ref|YP_004384166.1| 14 TNCKKCgLPTCMAFAVGLLGREKKLEE-CTPLfeekkyeaklaklkeivaplesasetglvihpEKCFGCGNCVIACPV 91
                                      578888778885555544444333332.2222345556666666666777888888899*******************8 PP

                            Fer4_9 49 g 49
                                      +
  gi|330507738|ref|YP_004384166.1| 92 N 92
                                      7 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00037
                            Fer4_9  37 igCgaCveaCpkgai 51 
                                       i C+aC++ Cp++ai
  gi|330507738|ref|YP_004384166.1| 136 ILCNACTATCPSKAI 150
                                       569999999999887 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.2      0.47   4.9e+02       8      16 ..      15      25 ..      13      26 .. 0.75
   2 !   22.1   3.2   1.1e-07   0.00011       3      23 ..      73      93 ..      72      95 .. 0.91
   3 !   12.1   1.5   0.00015      0.15      10      24 .]     136     150 ..     126     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.47
                            Fer4_6  8 kCigCgd..Cv 16
                                      +C  Cg   C+
  gi|330507738|ref|YP_004384166.1| 15 NCKKCGLptCM 25
                                      79999977776 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.1e-07
                            Fer4_6  3 eidpdkCigCgdCvrvCPega 23
                                      +i p+kC gCg+Cv++CP ++
  gi|330507738|ref|YP_004384166.1| 73 VIHPEKCFGCGNCVIACPVNV 93
                                      789***************875 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00015
                            Fer4_6  10 igCgdCvrvCPegai 24 
                                       i C++C++ CP +ai
  gi|330507738|ref|YP_004384166.1| 136 ILCNACTATCPSKAI 150
                                       58**********998 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   0.7      0.25   2.6e+02       3      12 ..      15      26 ..      13      27 .. 0.58
   2 !   22.6   2.5   8.8e-08   9.3e-05       1      17 []      76      92 ..      76      96 .. 0.93
   3 !    9.1   2.8    0.0019         2       5      16 ..     136     147 ..     125     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.25
                            Fer4_4  3 rCigCg..sCva 12
                                      +C  Cg   C+a
  gi|330507738|ref|YP_004384166.1| 15 NCKKCGlpTCMA 26
                                      577777444766 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 8.8e-08
                            Fer4_4  1 qerCigCgsCvaaCPqg 17
                                      +e+C+gCg Cv+aCP++
  gi|330507738|ref|YP_004384166.1| 76 PEKCFGCGNCVIACPVN 92
                                      69*************75 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0019
                            Fer4_4   5 igCgsCvaaCPq 16 
                                       i C +C+a+CP+
  gi|330507738|ref|YP_004384166.1| 136 ILCNACTATCPS 147
                                       67*********7 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   4.9   8.1e-06    0.0086       4      65 .]      15      93 ..      13      93 .. 0.75
   2 !   20.1   6.8   6.3e-07   0.00067       3      64 ..      77     148 ..      75     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.1e-06
                            Fer4_8  4 kCieCg..aCq.............saC.pvlrrtkkhlldargeaae.....dvqeeqvlee..eealwsCttcgaCte 59
                                      +C +Cg   C+             ++C p+++++k + + a+ + +            +  +      ++C +cg+C+ 
  gi|330507738|ref|YP_004384166.1| 15 NCKKCGlpTCMafavgllgrekklEECtPLFEEKKYEAKLAKLKEIVaplesA----SE--TglVIHPEKCFGCGNCVI 87
                                      79999977799999999999999988988888888777777777665433321....22..2346789*********** PP

                            Fer4_8 60 vCpvgi 65
                                      +Cpv++
  gi|330507738|ref|YP_004384166.1| 88 ACPVNV 93
                                      ***986 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.3e-07
                            Fer4_8   3 ekCieCgaCqsaCp...vlrrtk.khlldargeaaedvqeeqvleeeealwsC.......ttcgaCtevCpvg 64 
                                       ekC +Cg C  aCp   +++ t+    l ++g++    + e+++  +++l++C         c+aCt  Cp +
  gi|330507738|ref|YP_004384166.1|  77 EKCFGCGNCVIACPvnvAAEPTRvGAGLGPEGDRVI-LRVEDGVVVANNLQECkrfgpnkILCNACTATCPSK 148
                                       69************4444444555555566666666.666666666*******999999999*********86 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.15   1.6e+02       9      16 ..      15      24 ..       8      27 .. 0.68
   2 !   20.3   2.3   3.7e-07   0.00039       4      21 ..      73      90 ..      71      91 .. 0.90
   3 !    7.9   1.9    0.0033       3.5      12      21 ..     137     146 ..     120     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.15
                            Fer4_2  9 rCigCg..aC 16
                                      +C  Cg  +C
  gi|330507738|ref|YP_004384166.1| 15 NCKKCGlpTC 24
                                      5777776666 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 3.7e-07
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      v+ +++C gCg Cv aCP
  gi|330507738|ref|YP_004384166.1| 73 VIHPEKCFGCGNCVIACP 90
                                      6789************** PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0033
                            Fer4_2  12 gCgaCvsaCP 21 
                                        C+aC+  CP
  gi|330507738|ref|YP_004384166.1| 137 LCNACTATCP 146
                                       3****999** 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   0.3         1   1.1e+03      10      15 ..      15      20 ..      10      43 .. 0.70
   2 !   20.5   1.0   3.6e-07   0.00037      35      53 ..      73      91 ..      59      96 .. 0.64
   3 !    8.1   0.8    0.0027       2.9      10      57 ..     137     150 ..     122     153 .] 0.67

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1
                           Fer4_21 10 gCgkCl 15
                                      +C+kC 
  gi|330507738|ref|YP_004384166.1| 15 NCKKCG 20
                                      455553 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.6e-07
                           Fer4_21 35 kvvedeCvGCnlCssvCPv 53
                                       +  ++C GC  C++ CPv
  gi|330507738|ref|YP_004384166.1| 73 VIHPEKCFGCGNCVIACPV 91
                                      4445666666666666665 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0027
                           Fer4_21  10 gCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                        C+ C+ +C+                                   ++i
  gi|330507738|ref|YP_004384166.1| 137 LCNACTATCPS----------------------------------KAI 150
                                       45555555554..................................444 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   3.9   4.4e-06    0.0047       1      60 [.      15      93 ..      15      94 .. 0.71
   2 ?    6.6   0.6     0.011        12      48      58 ..     137     147 ..     134     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.4e-06
                           Fer4_17  1 rCiqCgy..Clp.............eCpsyeaydnepkkllraakl.glleeaeke...ekaslCieCgeCerkCPqgl 60
                                      +C +Cg   C++             eC  + + +++++kl++  ++ + le a++       ++C +Cg+C+ +CP ++
  gi|330507738|ref|YP_004384166.1| 15 NCKKCGLptCMAfavgllgrekkleECTPLFEEKKYEAKLAKLKEIvAPLESASETglvIHPEKCFGCGNCVIACPVNV 93
                                      69999976799988888888888888887777677777666665555333443332344577**************886 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                           Fer4_17  48 eCgeCerkCPq 58 
                                        C+ C++ CP+
  gi|330507738|ref|YP_004384166.1| 137 LCNACTATCPS 147
                                       58888888886 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3  10.6    0.0021       2.2      51      67 .]      70      92 ..      14      92 .. 0.48
   2 !   13.6   0.6   9.7e-05       0.1       5      18 ..     138     151 ..     115     153 .] 0.92

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0021
                           Fer4_16 51 q......eaitgCdiCqdvCPan 67
                                             e+++gC++C+ +CP+n
  gi|330507738|ref|YP_004384166.1| 70 TglvihpEKCFGCGNCVIACPVN 92
                                      2345556899***********98 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.7e-05
                           Fer4_16   5 CgkCaevCPtnaik 18 
                                       C++C+ +CP++ai+
  gi|330507738|ref|YP_004384166.1| 138 CNACTATCPSKAIE 151
                                       99*********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 ?    1.3   1.0      0.84   8.9e+02       1       8 [.      16      25 ..      16      27 .. 0.79
   2 ?   12.7   6.1   0.00019       0.2       1      14 [.      79      92 ..      79      93 .. 0.95
   3 ?   12.1   1.3   0.00028       0.3       3      15 .]     137     149 ..     136     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.84
                            Fer4_3  1 CtgCg..aCv 8 
                                      C  Cg  +C+
  gi|330507738|ref|YP_004384166.1| 16 CKKCGlpTCM 25
                                      999*966698 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00019
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C gCg Cv +CPv+
  gi|330507738|ref|YP_004384166.1| 79 CFGCGNCVIACPVN 92
                                      99**********98 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00028
                            Fer4_3   3 gCgaCvevCPvgA 15 
                                        C+aC   CP++A
  gi|330507738|ref|YP_004384166.1| 137 LCNACTATCPSKA 149
                                       7**********98 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 ?   -1.9   0.1       3.5   3.6e+03      21      31 ..      37      47 ..      35      47 .. 0.69
   2 ?   12.4   0.0   0.00012      0.13       1      17 [.      50      66 ..      50      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.5
                      Exonuc_VII_S 21 sLeeslklyee 31
                                       Lee   l+ee
  gi|330507738|ref|YP_004384166.1| 37 KLEECTPLFEE 47
                                      47777777776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00012
                      Exonuc_VII_S  1 FEealaeLeeIvekLEs 17
                                      +E++la+L+eIv+ LEs
  gi|330507738|ref|YP_004384166.1| 50 YEAKLAKLKEIVAPLES 66
                                      9***************7 PP

>> LID  LIM interaction domain (LID)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00013      0.13       2      27 ..      91     116 ..      90     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                               LID   2 VMVVsEPSmMGgdFGeeDERvIsRlE 27 
                                       V V  EP   G + G e  RvI R+E
  gi|330507738|ref|YP_004384166.1|  91 VNVAAEPTRVGAGLGPEGDRVILRVE 116
                                       56889********************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 ?    9.6   0.3   0.00094      0.99      59      75 ..      77      93 ..      40     101 .. 0.82
   2 ?    3.5   0.3     0.075        80      60      73 ..     134     147 ..     108     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00094
                           Fer4_18 59 gdcidcescvkvcPtgi 75
                                       +c  c+ cv  cP+++
  gi|330507738|ref|YP_004384166.1| 77 EKCFGCGNCVIACPVNV 93
                                      57999999999999987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.075
                           Fer4_18  60 dcidcescvkvcPt 73 
                                       + i c++c + cP 
  gi|330507738|ref|YP_004384166.1| 134 NKILCNACTATCPS 147
                                       5689********97 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       4.1   4.3e+03       8      13 ..      15      20 ..      13      37 .. 0.63
   2 ?   10.4   1.7   0.00072      0.76       4      17 ..      77      90 ..      74      99 .. 0.89
   3 ?    4.6   0.7     0.047        50       8      18 ..     137     147 ..     124     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.1
                           Fer4_13  8 acgaCv 13
                                      +c++C+
  gi|330507738|ref|YP_004384166.1| 15 NCKKCG 20
                                      445554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00072
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      ++C +cg+Cv ++P
  gi|330507738|ref|YP_004384166.1| 77 EKCFGCGNCVIACP 90
                                      89************ PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.047
                           Fer4_13   8 acgaCvelaPd 18 
                                        c+aC +++P 
  gi|330507738|ref|YP_004384166.1| 137 LCNACTATCPS 147
                                       58888888884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 801.76
//
Query:       gi|330507739|ref|YP_004384167.1|  [L=412]
Description: tungsten formylmethanofuran dehydrogenase subunit B [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0052   16.5   0.0        4.6    7.0   0.0    2.5  2  TPP_enzyme_M   Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.071   12.1   0.0        1.5    7.7   0.0    2.3  2  Molybdopterin  Molybdopterin oxidoreductase
       0.16   11.8   0.0       0.35   10.8   0.0    1.5  1  TRSP           TRSP domain C terminus to PRTase_2


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 !    6.9   0.0    0.0008       4.8       1      40 [.      66     104 ..      66     110 .. 0.82
   2 !    7.0   0.0   0.00077       4.6      68     113 ..     312     356 ..     302     370 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0008
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT- CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgi 40 
                                       ie+aae+l++a+ pvi+  + +   +a+e   +la k+g+
  gi|330507739|ref|YP_004384167.1|  66 IERAAEILRNASAPVIYGWSNCT-LEAQEVGLALAAKIGA 104
                                       79**************9877776.6777777777777776 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00077
                                       CHHHHHHHHH-SEEEEES-S.SSTCCCTTTTTTTTTT-EEEEEESSC CS
                      TPP_enzyme_M  68 skaanealeeaDlvlalGar.fddirttgsepefapeakiihididp 113
                                       +++  ea++ aD +l+lG++ + d    g  ++fa    i+ id+ +
  gi|330507739|ref|YP_004384167.1| 312 APSLVEAVKGADGILVLGSDpLLD-LPLGLARAFAAA-PIVAIDPRR 356
                                       678899************987667.677777777744.899998876 PP

>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.013        78      71     129 ..     100     155 ..      55     186 .. 0.78
   2 ?    7.7   0.0   0.00025       1.5     108     159 ..     318     362 ..     293     373 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.013
                                       -EEE-BEECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG.-SEEEEESS-HHHHSHHH CS
                     Molybdopterin  71 gknlsfydwyadlppasaqqtigsdsrsnyessnpledlen.sdliilwGsNvreerpil 129
                                        k+++f+d+   ++ ++  + i     s  + s++l d+ n +d  i wGs++  ++p  
  gi|330507739|ref|YP_004384167.1| 100 AKIGAFVDDPSSYCEGQLMERI----LSGKIPSCTLDDVRNfADTSIFWGSDPSSTQPRH 155
                                       3445578888888877765333....334578899999999899*********9999865 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00025
                                       GGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HCGGGCS CS
                     Molybdopterin 108 dlensdliilwGsNvreerpilnarirkaalkkkakvivigpryaellkfad 159
                                        +  +d i++ Gs++    p+     +++a+ + a +++i+pr +  l+ ++
  gi|330507739|ref|YP_004384167.1| 318 AVKGADGILVLGSDPLLDLPLG----LARAFAA-APIVAIDPRRS--LTADV 362
                                       5667999***************....8999995.*********99..67665 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 ?   10.8   0.0   5.8e-05      0.35      23      57 ..     312     346 ..     298     359 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.8e-05
                              TRSP  23 aaklraalekaervlvLGteElmylPlrlAaalae 57 
                                       a +l +a++ a+ +lvLG++ l+ lPl lA+a+a+
  gi|330507739|ref|YP_004384167.1| 312 APSLVEAVKGADGILVLGSDPLLDLPLGLARAFAA 346
                                       4556666678899******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2603.83
//
Query:       gi|330507740|ref|YP_004384168.1|  [L=128]
Description: tungsten formylmethanofuran dehydrogenase subunit D [Methanosaeta concilii GP6]
Scores for 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   30.5   0.0    3.2e-07   30.4   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 !   30.4   0.0   1.8e-11   3.2e-07       4      94 ..       8      90 ..       5     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.8e-11
                                      EEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEE.SSB-TTEEEEESSHC CS
                   Molydop_binding  4 itgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvt.ervrpGvvfmpfgww 81
                                      +t++   q+ ++ +  +++++ k +   + +   d+a lG+++G +V +e++  +++++a  + +  +pG +fm    w
  gi|330507740|ref|YP_004384168.1|  8 VTYQDIFQYGAGKMGLHSEEYLKLSA-SIILDKGDMASLGVAEGGKVLLENELNRIVLNATASvDKPHPGLAFMIKSPW 85
                                      7999999******************9.*******************************99555155************* PP

                                      C.....S-GHCTS CS
                   Molydop_binding 82 eagekggnaNalt 94
                                      +        N+l 
  gi|330507740|ref|YP_004384168.1| 86 S--------NQLE 90
                                      9........4433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 962.26
//
Query:       gi|330507741|ref|YP_004384169.1|  [L=304]
Description: ornithine carbamoyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-53  178.5   0.0    1.2e-52  178.1   0.0    1.1  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    1.4e-47  161.4   0.0      2e-47  160.9   0.0    1.3  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.1   0.0   1.4e-56   1.2e-52       1     156 [.     145     295 ..     145     296 .. 0.98

  Alignments for each domain:
  == domain 1  score: 178.1 bits;  conditional E-value: 1.4e-56
                                       CC.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE CS
                            OTCace   1 kglkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvyt 77 
                                       +gl+i ++Gd+ nnv+nsli + a+l m++++++P+g+ p+ e+leea++     ggs  + e++eea+ gaDv++t
  gi|330507741|ref|YP_004384169.1| 145 DGLQIGWIGDG-NNVCNSLILASAILRMEITVASPPGYGPKAEILEEARAL----GGSPRVVEEPEEAAGGADVLVT 216
                                       599********.*********************************999987....9********************* PP

                                       --SSETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHH CS
                            OTCace  78 dvwvsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAll 154
                                       d+wvsmg+e+e+ erl+ +  yq++++l++la + ai lHcLPa+rg+E+tdeV+d+prs vf++aeNr+ht kA++
  gi|330507741|ref|YP_004384169.1| 217 DTWVSMGDEAEEAERLRVFGRYQINSQLMDLAGDGAIALHCLPAHRGQEITDEVMDGPRSRVFDEAENRMHTSKAVM 293
                                       ***************************************************************************** PP

                                       HH CS
                            OTCace 155 vl 156
                                       ++
  gi|330507741|ref|YP_004384169.1| 294 AW 295
                                       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 !  160.9   0.0   2.3e-51     2e-47       2     147 ..       2     138 ..       1     139 [. 0.96

  Alignments for each domain:
  == domain 1  score: 160.9 bits;  conditional E-value: 2.3e-51
                                       -BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSC CS
                          OTCace_N   2 hllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediq 78 
                                       +l+s++dls e+i +l++ a+++++++   ++ + l+gk+la++Fe+pStRTrvS evAa +lGg++l+ls a+++q
  gi|330507741|ref|YP_004384169.1|   2 NLISIADLSGEDILRLIQSAEAFRARR--GRHGQPLEGKSLAMIFEKPSTRTRVSLEVAAWELGGHPLYLS-ANELQ 75 
                                       69**********************886..589999************************************.889** PP

                                       TTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                          OTCace_N  79 lssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                       l+     r+E+++Dtarvlsryv++i +R++++ ++ +la++asvpviNa+ +d eHP+Q+LaDl+t+ 
  gi|330507741|ref|YP_004384169.1|  76 LG-----RGETIADTARVLSRYVHGITARVHSHGTVLQLAEHASVPVINAL-SDWEHPLQILADLQTMS 138
                                       *9.....78**********************9999****************.***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2260.76
//
Query:       gi|330507742|ref|YP_004384170.1|  [L=146]
Description: nucleotidyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-11   43.7   0.0      3e-11   43.2   0.0    1.1  1  Polbeta       Polymerase beta, Nucleotidyltransferase
      2e-10   40.8   0.0    2.8e-10   40.3   0.0    1.2  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   3.4e-15     3e-11      11      90 ..      24     100 ..      15     101 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 3.4e-15
                                       HHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS-EEE CS
                           Polbeta  11 keielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeilkegkll 87 
                                       k +  ++l+GS+a+g+a ++SDiDl+++  e    e+++ l+ e+ +   ++k Dl +++  p++++  +++eg +l
  gi|330507742|ref|YP_004384170.1|  24 KRVLGVLLYGSWARGDAGPDSDIDLCLVAPEA---EDRAGLWREFVSHLRSEKYDLRIFEILPLYIKMAVIEEGSVL 97 
                                       57899*************************99...999*******999899************************** PP

                                       ES- CS
                           Polbeta  88 ysk 90 
                                        s+
  gi|330507742|ref|YP_004384170.1|  98 WSR 100
                                       986 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   3.2e-14   2.8e-10      13      92 ..      23      94 ..       8      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 3.2e-14
                                      T..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCTEEEEEE CS
                      NTP_transf_2 13 p..vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpllvksil 89
                                         v  v l+GS arG+a+++SDiDl++v pe           ++   +++f++ l+  ++dl+++e+l+ +++++ + 
  gi|330507742|ref|YP_004384170.1| 23 EkrVLGVLLYGSWARGDAGPDSDIDLCLVAPEAE---------DRAGLWREFVSHLRSEKYDLRIFEILP-LYIKMAVI 91
                                      145899***************************3.........689999********************9.99999988 PP

                                      CEE CS
                      NTP_transf_2 90 eer 92
                                      ee+
  gi|330507742|ref|YP_004384170.1| 92 EEG 94
                                      886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1057.20
//
Query:       gi|330507743|ref|YP_004384171.1|  [L=194]
Description: hypothetical protein MCON_1737 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   0.3          4    7.5   0.0    2.2  2  Thg1      tRNAHis guanylyltransferase


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 ?    5.3   0.1    0.0011        19      38      80 ..      73     121 ..      66     134 .. 0.68
   2 ?    7.5   0.0   0.00022         4      61      92 ..     154     185 ..     145     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0011
                              Thg1  38 ekPnDeral..klmneaakelvkef....edivlaYgqSDEislvlske 80 
                                       ++P D ++   + mn+ a +l+ +f    e+i l Y++ +E+   +++ 
  gi|330507743|ref|YP_004384171.1|  73 KQPEDLNISneDFMNANAMNLLMKFysgfENINLTYTNAEEFLNNFQSL 121
                                       6676666652258999999888776432247**********96555554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00022
                              Thg1  61 edivlaYgqSDEislvlsketklynrraqklv 92 
                                       + i++  ++SDE+  ++ +e k+y+r+++k +
  gi|330507743|ref|YP_004384171.1| 154 NYIIICSTESDEMMALIMRELKVYAREESKAA 185
                                       4578899*********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1303.22
//
Query:       gi|330507744|ref|YP_004384172.1|  [L=344]
Description: TPR repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-20   71.9   0.5     0.0014   18.6   0.1    5.8  5  TPR_2            Tetratricopeptide repeat
    2.5e-20   71.9   6.5    1.4e-07   31.1   0.0    5.0  5  TPR_11           TPR repeat
      3e-20   71.1   0.2    1.7e-06   28.0   0.0    4.8  4  TPR_17           Tetratricopeptide repeat
    8.6e-20   69.7   4.2     0.0039   17.0   0.0    5.5  5  TPR_1            Tetratricopeptide repeat
      7e-18   63.3   3.6     0.0024   17.9   0.0    5.2  5  TPR_8            Tetratricopeptide repeat
    7.4e-12   45.0   0.0    0.00029   21.4   0.0    4.5  4  TPR_14           Tetratricopeptide repeat
    1.7e-11   44.1   0.0      8e-05   22.7   0.0    2.9  3  TPR_9            Tetratricopeptide repeat
    2.4e-10   40.7   0.0    2.8e-05   24.5   0.0    3.4  3  TPR_19           Tetratricopeptide repeat
    3.1e-10   40.5   0.0     0.0026   18.4   0.0    3.3  3  TPR_16           Tetratricopeptide repeat
      2e-09   36.9   0.3    7.7e-05   21.8   0.0    3.0  3  NARP1            NMDA receptor-regulated protein 1
    8.3e-07   29.1   0.0    8.2e-06   26.0   0.0    2.2  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    0.00019   21.5   0.0      0.024   14.7   0.0    3.6  4  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
     0.0002   21.6   0.0         11    6.4   0.0    3.6  3  TPR_12           Tetratricopeptide repeat
     0.0013   18.6   0.0        2.3    8.5   0.0    3.9  4  TPR_7            Tetratricopeptide repeat
      0.005   17.3   0.1        1.2    9.6   0.0    2.4  2  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0063   16.5   0.2      0.013   15.5   0.2    1.5  1  SRP_TPR_like     Putative TPR-like repeat
  ------ inclusion threshold ------
      0.015   15.0   9.2       0.22   11.3   0.0    3.8  3  PPTA             Protein prenyltransferase alpha subunit repe
      0.031   13.3   0.1       0.22   10.5   0.0    2.0  2  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
      0.053   13.2   0.0       0.23   11.1   0.0    1.9  1  HrpB1_HrpK       Bacterial type III secretion protein (HrpB1_


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 !   13.1   0.0   8.6e-05     0.081      18      34 .]      32      48 ..      16      48 .. 0.87
   2 !   14.7   0.0   2.7e-05     0.025       1      34 []      49      82 ..      49      82 .. 0.96
   3 ?    1.8   0.0      0.34   3.2e+02      16      32 ..     228     244 ..     227     245 .. 0.87
   4 !   16.2   0.0   8.3e-06    0.0079       7      34 .]     253     280 ..     249     280 .. 0.92
   5 !   18.6   0.1   1.5e-06    0.0014       2      32 ..     282     312 ..     281     313 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.6e-05
                             TPR_2 18 eeAleafekAleldPnn 34
                                      e A+++++k++eldP+n
  gi|330507744|ref|YP_004384172.1| 32 EAAIRCYDKVIELDPKN 48
                                      89*************97 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.7e-05
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      a a+yn G ++  + + +e l+af+ A+ l P++
  gi|330507744|ref|YP_004384172.1| 49 ATAWYNKGVILSSQFKQNESLAAFNIAINLSPED 82
                                      679*****************************86 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.34
                             TPR_2  16 dyeeAleafekAleldP 32 
                                       ++   lea +kAle dP
  gi|330507744|ref|YP_004384172.1| 228 RFSSSLEAVDKALEFDP 244
                                       6777899*******999 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 8.3e-06
                             TPR_2   7 lGlayyklgdyeeAleafekAleldPnn 34 
                                        +++++  g++eeA++  + Al++dP n
  gi|330507744|ref|YP_004384172.1| 253 KARVLIDCGEFEEAIKIIDNALKIDPSN 280
                                       68999*********************87 PP

  == domain 5  score: 18.6 bits;  conditional E-value: 1.5e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       ea+   G++++k+ +y eA++ ++ A eld 
  gi|330507744|ref|YP_004384172.1| 282 EAWQTKGYILMKQENYTEAIKNLNIANELDN 312
                                       89********************999988886 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   1.5e-10   1.4e-07      11      38 ..      32      59 ..      24      62 .. 0.91
   2 !    9.6   0.2   0.00073      0.69       9      36 ..      64      91 ..      64      94 .. 0.91
   3 ?   -1.5   0.0       2.2   2.1e+03      18      25 ..     237     244 ..     227     246 .. 0.79
   4 !   16.8   0.0   4.3e-06    0.0041       2      31 ..     255     284 ..     254     285 .. 0.93
   5 !   13.1   0.6   5.9e-05     0.056       1      26 [.     288     313 ..     288     316 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.5e-10
                            TPR_11 11 eeAieaYkkAlkldPdnaeayynLGlay 38
                                      e+Ai +Y k ++ldP+na+a+yn G+++
  gi|330507744|ref|YP_004384172.1| 32 EAAIRCYDKVIELDPKNATAWYNKGVIL 59
                                      89***********************987 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00073
                            TPR_11  9 kyeeAieaYkkAlkldPdnaeayynLGl 36
                                      k +e+++a++ A++l+P++ +a+++ Gl
  gi|330507744|ref|YP_004384172.1| 64 KQNESLAAFNIAINLSPEDSNAWNAKGL 91
                                      5689********************9986 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.2
                            TPR_11  18 kkAlkldP 25 
                                        kAl++dP
  gi|330507744|ref|YP_004384172.1| 237 DKALEFDP 244
                                       69****99 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 4.3e-06
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeay 31 
                                       +++ + G++eeAi+   +Alk+dP+n ea+
  gi|330507744|ref|YP_004384172.1| 255 RVLIDCGEFEEAIKIIDNALKIDPSNHEAW 284
                                       67899*********************9986 PP

  == domain 5  score: 13.1 bits;  conditional E-value: 5.9e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPd 26 
                                       G+++++q +y+eAi++++ A +ld++
  gi|330507744|ref|YP_004384172.1| 288 GYILMKQENYTEAIKNLNIANELDNN 313
                                       89******************999987 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.8e-09   1.7e-06       1      25 [.      37      64 ..      37      72 .. 0.84
   2 ?    6.1   0.1     0.017        16       5      21 ..      75      91 ..      71     126 .. 0.83
   3 !   10.6   0.0   0.00064      0.61       4      34 .]     238     268 ..     236     268 .. 0.95
   4 !   20.6   0.0   4.1e-07   0.00039       3      34 .]     271     302 ..     269     302 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.8e-09
                            TPR_17  1 lylkaleldPnnadaynnLAelll...k 25
                                      +y k++eldP+na a++n++++l+   k
  gi|330507744|ref|YP_004384172.1| 37 CYDKVIELDPKNATAWYNKGVILSsqfK 64
                                      8**********************94443 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.017
                            TPR_17  5 aleldPnnadaynnLAe 21
                                      a+ l P +++a+n ++ 
  gi|330507744|ref|YP_004384172.1| 75 AINLSPEDSNAWNAKGL 91
                                      79999********9986 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00064
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtArq 34 
                                       kale dP + d++ ++A++l   G++++A++
  gi|330507744|ref|YP_004384172.1| 238 KALEFDPISLDPMILKARVLIDCGEFEEAIK 268
                                       9****************************85 PP

  == domain 4  score: 20.6 bits;  conditional E-value: 4.1e-07
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtArq 34 
                                        +al++dP+n +a++ ++++l k+ ++ +A++
  gi|330507744|ref|YP_004384172.1| 271 DNALKIDPSNHEAWQTKGYILMKQENYTEAIK 302
                                       689**************************985 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   7.1e-06    0.0067      18      34 .]      32      48 ..      31      48 .. 0.94
   2 !   17.0   0.0   4.1e-06    0.0039       1      34 []      49      82 ..      49      82 .. 0.95
   3 ?    2.1   0.0       0.2   1.9e+02      17      32 ..     229     244 ..     227     245 .. 0.83
   4 !   15.8   0.0   9.7e-06    0.0092       8      34 .]     254     280 ..     251     280 .. 0.89
   5 !   15.3   0.2   1.4e-05     0.013       2      25 ..     282     305 ..     281     312 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.1e-06
                                      HHHHHHHHHHHHHSTTH CS
                             TPR_1 18 deAleyyekALelnPnn 34
                                      + A+ +y+k++el+P+n
  gi|330507744|ref|YP_004384172.1| 32 EAAIRCYDKVIELDPKN 48
                                      78*************98 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 4.1e-06
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a a+yn+G+++ ++ k +e l++++ A+ l P++
  gi|330507744|ref|YP_004384172.1| 49 ATAWYNKGVILSSQFKQNESLAAFNIAINLSPED 82
                                      679***************************9986 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHST CS
                             TPR_1  17 ydeAleyyekALelnP 32 
                                       +   le+ +kALe +P
  gi|330507744|ref|YP_004384172.1| 229 FSSSLEAVDKALEFDP 244
                                       666789999*****99 PP

  == domain 4  score: 15.8 bits;  conditional E-value: 9.7e-06
                                       HHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   8 GnayfklgkydeAleyyekALelnPnn 34 
                                       + ++   g+++eA++  + AL+++P+n
  gi|330507744|ref|YP_004384172.1| 254 ARVLIDCGEFEEAIKIIDNALKIDPSN 280
                                       5677889******************98 PP

  == domain 5  score: 15.3 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHHTT-HHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyye 25 
                                       +a+  +G++++k+++y eA++  +
  gi|330507744|ref|YP_004384172.1| 282 EAWQTKGYILMKQENYTEAIKNLN 305
                                       799*****************9765 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00022      0.21      17      34 .]      31      48 ..      25      48 .. 0.92
   2 !   13.7   0.0     6e-05     0.057       1      34 []      49      82 ..      49      82 .. 0.95
   3 ?   -0.5   0.0       2.1     2e+03      18      32 ..     230     244 ..     227     245 .. 0.80
   4 !   17.9   0.0   2.6e-06    0.0024       6      34 .]     252     280 ..     248     280 .. 0.93
   5 !   16.1   0.2   9.8e-06    0.0092       2      32 ..     282     312 ..     281     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                                      HHHHHHHHHHHHHHHHH. CS
                             TPR_8 17 yeeAkeyyekaleldpdn 34
                                       e+A+ +y k++eldp+n
  gi|330507744|ref|YP_004384172.1| 31 SEAAIRCYDKVIELDPKN 48
                                      599*************97 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6e-05
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      a a+yn+g i++++ + +e+ ++++ a+ l+p++
  gi|330507744|ref|YP_004384172.1| 49 ATAWYNKGVILSSQFKQNESLAAFNIAINLSPED 82
                                      679****************************985 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHH CS
                             TPR_8  18 eeAkeyyekaleldp 32 
                                        ++ e+  kale dp
  gi|330507744|ref|YP_004384172.1| 230 SSSLEAVDKALEFDP 244
                                       56778999****998 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 2.6e-06
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++++++++ g++eeA++ +  al++dp+n
  gi|330507744|ref|YP_004384172.1| 252 LKARVLIDCGEFEEAIKIIDNALKIDPSN 280
                                       799************************86 PP

  == domain 5  score: 16.1 bits;  conditional E-value: 9.8e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ea++ +g+i++k+++y eA++ ++ a eld 
  gi|330507744|ref|YP_004384172.1| 282 EAWQTKGYILMKQENYTEAIKNLNIANELDN 312
                                       89*******************9998888876 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     3e-05     0.029      13      42 ..      27      56 ..      16      58 .. 0.83
   2 ?    0.9   0.0       1.2   1.1e+03      19      40 ..      67      88 ..      61      91 .. 0.86
   3 !   21.4   0.0     3e-07   0.00029       8      40 ..     254     286 ..     250     290 .. 0.91
   4 ?    5.8   0.0     0.031        30       2      27 ..     282     307 ..     281     313 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-05
                            TPR_14 13 alGdpdeAiallrralalaPddaeawllla 42
                                       ++  ++Ai++++++++l+P++a+aw+  +
  gi|330507744|ref|YP_004384172.1| 27 SSDFSEAAIRCYDKVIELDPKNATAWYNKG 56
                                      4556789*******************9776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.2
                            TPR_14 19 eAiallrralalaPddaeawll 40
                                      e++a+++ a+ l P+d  aw +
  gi|330507744|ref|YP_004384172.1| 67 ESLAAFNIAINLSPEDSNAWNA 88
                                      67899************99965 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 3e-07
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawll 40 
                                       a++l   G+++eAi++ + al+ +P++ eaw  
  gi|330507744|ref|YP_004384172.1| 254 ARVLIDCGEFEEAIKIIDNALKIDPSNHEAWQT 286
                                       89*****************************75 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.031
                            TPR_14   2 eallalaeallalGdpdeAiallrra 27 
                                       ea++  + +l+ ++++ eAi+ l+ a
  gi|330507744|ref|YP_004384172.1| 282 EAWQTKGYILMKQENYTEAIKNLNIA 307
                                       89******************988766 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.3e-06    0.0031       7      65 ..      27      85 ..      22      90 .. 0.91
   2 ?    5.0   0.0     0.028        26       8      49 ..     226     267 ..     224     268 .. 0.94
   3 !   22.7   0.0   8.5e-08     8e-05       6      55 ..     258     307 ..     252     320 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.3e-06
                             TPR_9  7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                                      +++ +e+a+++++ ++ l+P+ +  ++  G++l  +   ++ la+++ ++ l+p++  a
  gi|330507744|ref|YP_004384172.1| 27 SSDFSEAAIRCYDKVIELDPKNATAWYNKGVILSSQFKQNESLAAFNIAINLSPEDSNA 85
                                      566689***********************************************999876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.028
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAl 49 
                                       +e+++  l++v+  l ++P + +     +++l   G +++A+
  gi|330507744|ref|YP_004384172.1| 226 PERFSSSLEAVDKALEFDPISLDPMILKARVLIDCGEFEEAI 267
                                       6899999********************************997 PP

  == domain 3  score: 22.7 bits;  conditional E-value: 8.5e-08
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeay 55 
                                       i   ++e+a+++++  l ++P  +e +   G +l++++++ +A++ L+ +
  gi|330507744|ref|YP_004384172.1| 258 IDCGEFEEAIKIIDNALKIDPSNHEAWQTKGYILMKQENYTEAIKNLNIA 307
                                       777789***************************************99865 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0091       8.6       8      38 ..      32      62 ..      27      90 .. 0.74
   2 !   21.8   0.0   2.2e-07    0.0002      11      62 ..     233     285 ..     226     288 .. 0.89
   3 !   24.5   0.0     3e-08   2.8e-05       3      56 ..     259     312 ..     257     318 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0091
                            TPR_19  8 aeAlalleqalqedpknaearllLAeallal 38
                                      ++A++ + ++++ dpkna a+++   +l ++
  gi|330507744|ref|YP_004384172.1| 32 EAAIRCYDKVIELDPKNATAWYNKGVILSSQ 62
                                      578999****************987777666 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.2e-07
                            TPR_19  11 lalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.arya 62 
                                       l++  +al+ dp +++  +l A++l+  g+++eA++++d +++ dp + ++++
  gi|330507744|ref|YP_004384172.1| 233 LEAVDKALEFDPISLDPMILKARVLIDCGEFEEAIKIIDNALKIDPSNhEAWQ 285
                                       678899****************************************9746665 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 3e-08
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                       + g ++eA+++  +al+ dp n ea+     +l+++ +++eA++ L+ + e d 
  gi|330507744|ref|YP_004384172.1| 259 DCGEFEEAIKIIDNALKIDPSNHEAWQTKGYILMKQENYTEAIKNLNIANELDN 312
                                       5599****************************************9987766665 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.4e-06    0.0032       6      61 ..      24      76 ..      20      83 .. 0.81
   2 ?    1.0   0.0      0.76   7.1e+02      15      42 ..      67      91 ..      66      99 .. 0.83
   3 !   18.4   0.0   2.7e-06    0.0026       3      54 ..     253     301 ..     251     310 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.4e-06
                            TPR_16  6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61
                                      +++ +   ++A++ ++ ++++d   P +a A++++g+++  q    e +a+++ a+
  gi|330507744|ref|YP_004384172.1| 24 DYFSSDFSEAAIRCYDKVIELD---PKNATAWYNKGVILSSQFKQNESLAAFNIAI 76
                                      566677789*************...**************98866666666666665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.76
                            TPR_16 15 dAaaaleaalkrdpssPdaaeAllllgd 42
                                      + +aa+++a+ +    P++  A++++g+
  gi|330507744|ref|YP_004384172.1| 67 ESLAAFNIAINLS---PEDSNAWNAKGL 91
                                      5789999***9**...999999999886 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 2.7e-06
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                                       +ar +++ g++++A++  + alk d   P ++eA+  +g ++ +q +++eA+
  gi|330507744|ref|YP_004384172.1| 253 KARVLIDCGEFEEAIKIIDNALKID---PSNHEAWQTKGYILMKQENYTEAI 301
                                       79999999*****************...***********************9 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.098        92     208     239 ..      31      62 ..      15      83 .. 0.77
   2 !   21.8   0.0   8.1e-08   7.7e-05     191     256 ..     213     277 ..     203     277 .. 0.89
   3 !   20.8   0.2   1.6e-07   0.00015     206     264 ..     261     318 ..     259     337 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.098
                                       SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHT CS
                             NARP1 208 rekAleyidkaiehtptlvelyltKarilkha 239
                                        e A+++ dk ie +p+    +++K+ il  +
  gi|330507744|ref|YP_004384172.1|  31 SEAAIRCYDKVIELDPKNATAWYNKGVILSSQ 62 
                                       5699**********************998765 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 8.1e-08
                                       HHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 191 llwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                         +++ +++q y   ++ + +le +dka+e +p +++ ++ Kar+l   G++++A++++++a k+D
  gi|330507744|ref|YP_004384172.1| 213 TAFTVKLISQSYSP-ERFSSSLEAVDKALEFDPISLDPMILKARVLIDCGEFEEAIKIIDNALKID 277
                                       46888888998875.567799*****************************************9988 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 1.6e-07
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHHHH CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyiNs 264
                                       g+ e+A+++id+a++ +p+  e ++tK+ il ++ + ++A++ ++ a +lD++  yi s
  gi|330507744|ref|YP_004384172.1| 261 GEFEEAIKIIDNALKIDPSNHEAWQTKGYILMKQENYTEAIKNLNIANELDNNG-YIIS 318
                                       67799**********************************************864.5555 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.83   7.9e+02       8      66 ..      34      59 ..      12      85 .. 0.61
   2 !   26.0   0.0   8.7e-09   8.2e-06       9      79 ..     233     304 ..     227     306 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.83
                                      HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHH CS
                            ANAPC3  8 AiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcl 66
                                      Ai +++++ +                                 l++k+  ++y ++  l
  gi|330507744|ref|YP_004384172.1| 34 AIRCYDKVIE---------------------------------LDPKNATAWYNKGVIL 59
                                      4445555554.................................4444444444444333 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 8.7e-09
                                       HHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   9 iflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       +   +++l+ ++ s++   l+A +l   g++++A++++++a k+++++++++ +++  l k+++y eAi+ L
  gi|330507744|ref|YP_004384172.1| 233 LEAVDKALEFDPISLDPMILKARVLIDCGEFEEAIKIIDNAlKIDPSNHEAWQTKGYILMKQENYTEAIKNL 304
                                       5667888899999999999**************************************************998 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 ?    0.5   0.0      0.67   6.3e+02      19      35 ..      33      49 ..      23      51 .. 0.83
   2 ?   -0.3   0.0       1.2   1.1e+03      16      32 ..     228     244 ..     224     254 .. 0.89
   3 !   14.7   0.0   2.5e-05     0.024      15      39 ..     261     285 ..     259     295 .. 0.89
   4 ?   -1.0   0.0       2.1     2e+03      12      22 ..     292     302 ..     291     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.67
                                      HHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C 19 eArryvdalLeiEPenr 35
                                       A r+ d ++e++P+n 
  gi|330507744|ref|YP_004384172.1| 33 AAIRCYDKVIELDPKNA 49
                                      478999*********96 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                                       -HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEP 32 
                                       ++s +++ vd  Le +P
  gi|330507744|ref|YP_004384172.1| 228 RFSSSLEAVDKALEFDP 244
                                       68999*********999 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 2.5e-05
                                       T-HHHHHHHHHHHHHHTTS-HHHHH CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenrQaqs 39 
                                       ge++eA + +d  L+i+P+n+ a +
  gi|330507744|ref|YP_004384172.1| 261 GEFEEAIKIIDNALKIDPSNHEAWQ 285
                                       89*******************9965 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 2.1
                                       HHHT-HHHHHH CS
                        Fis1_TPR_C  12 yklgeYseArr 22 
                                       +k+ +Y+eA +
  gi|330507744|ref|YP_004384172.1| 292 MKQENYTEAIK 302
                                       5999****977 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.043        41      20      73 ..      32      77 ..      23      81 .. 0.75
   2 ?    6.4   0.0     0.012        11       9      32 ..     253     276 ..     247     284 .. 0.88
   3 ?    6.4   0.0     0.012        11       9      27 ..     287     305 ..     280     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.043
                            TPR_12 20 deAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73
                                      + A+++++k++e+      p+    at+ +n g +++ + ++ e l++++ a++
  gi|330507744|ref|YP_004384172.1| 32 EAAIRCYDKVIELD-----PK---NATAWYNKGVILSSQFKQNESLAAFNIAIN 77
                                      45666666665555.....54...59999*******999999999999986665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.012
                            TPR_12   9 laavlrrlgrydeAlellekalei 32 
                                        a vl   g+++eA+++ + al i
  gi|330507744|ref|YP_004384172.1| 253 KARVLIDCGEFEEAIKIIDNALKI 276
                                       799999****************98 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.012
                            TPR_12   9 laavlrrlgrydeAlelle 27 
                                        + +l+++++y+eA+++l+
  gi|330507744|ref|YP_004384172.1| 287 KGYILMKQENYTEAIKNLN 305
                                       7899************987 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.078        74      16      35 ..      32      49 ..      31      50 .. 0.82
   2 ?   -1.7   0.0       4.3     4e+03       1      20 [.      51      70 ..      51      83 .. 0.70
   3 !    8.5   0.0    0.0024       2.3       6      31 ..     254     279 ..     252     283 .. 0.79
   4 ?    0.7   0.0      0.74   6.9e+02       6      20 ..     288     302 ..     283     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.078
                             TPR_7 16 eeAielyeqsLaltkdpeda 35
                                      e Ai++y +  +++ dp +a
  gi|330507744|ref|YP_004384172.1| 32 EAAIRCYDK--VIELDPKNA 49
                                      68*******..888888765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.3
                             TPR_7  1 aLlnLarlysrlGdyeeAie 20
                                      a++n +++ s++ +  e + 
  gi|330507744|ref|YP_004384172.1| 51 AWYNKGVILSSQFKQNESLA 70
                                      68899999999877666555 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0024
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                       ar+  ++G++eeAi++   +L ++ +
  gi|330507744|ref|YP_004384172.1| 254 ARVLIDCGEFEEAIKIIDNALKIDPS 279
                                       788999***********995555544 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.74
                             TPR_7   6 arlysrlGdyeeAie 20 
                                       + +  ++ +y eAi+
  gi|330507744|ref|YP_004384172.1| 288 GYILMKQENYTEAIK 302
                                       678899*******96 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.026        24      79     128 ..      25      74 ..       8      81 .. 0.85
   2 !    9.6   0.0    0.0013       1.2      72     121 ..     250     299 ..     216     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.026
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHH CS
                   Alkyl_sulf_dimr  79 alkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRni 128
                                       +++++  ++a+   +++++ dp+na+a   k  +l +  +q+es ++ ni
  gi|330507744|ref|YP_004384172.1|  25 YFSSDFSEAAIRCYDKVIELDPKNATAWYNKGVILSSQFKQNESLAAFNI 74 
                                       4555667899999*****************************99999887 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
                   Alkyl_sulf_dimr  72 vlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                                       ++ ka+  +++g+++ a++++++++  dp+n+ea + k  +l +  + +e
  gi|330507744|ref|YP_004384172.1| 250 MILKARVLIDCGEFEEAIKIIDNALKIDPSNHEAWQTKGYILMKQENYTE 299
                                       567899999**************************999887766555544 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 !   15.5   0.2   1.4e-05     0.013      19      89 ..     250     325 ..     228     340 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                      SRP_TPR_like  19 f..kvvaliklekyeeaLkllkkgsal...sedvrfEkaYvlYklkkykkalkilkkveaeekvkvlksqvlYrlg 89 
                                          k+  li  + +eea+k+++++ ++   +++    k Y+l k ++y++a k l+ +++ ++   + s +     
  gi|330507744|ref|YP_004384172.1| 250 MilKARVLIDCGEFEEAIKIIDNALKIdpsNHEAWQTKGYILMKQENYTEAIKNLNIANELDNNGYIISSISKNSI 325
                                       35588899*************99875522145566789*****************999988877777777665443 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00023      0.22       7      20 ..      40      53 ..      39      60 .. 0.90
   2 ?   -1.9   0.2       3.4   3.2e+03       8      20 ..      75      87 ..      74      87 .. 0.87
   3 ?    8.0   0.1    0.0026       2.5       3      20 ..     268     285 ..     266     286 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                                      HHHHH-TT-CHHHH CS
                              PPTA  7 kliekdpkNYsaWn 20
                                      k+ie+dpkN +aW+
  gi|330507744|ref|YP_004384172.1| 40 KVIELDPKNATAWY 53
                                      79***********8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.4
                                      HHHH-TT-CHHHH CS
                              PPTA  8 liekdpkNYsaWn 20
                                      +i++ p +  aWn
  gi|330507744|ref|YP_004384172.1| 75 AINLSPEDSNAWN 87
                                      6888999999**8 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0026
                                       HHHHHHHHH-TT-CHHHH CS
                              PPTA   3 eltekliekdpkNYsaWn 20 
                                       + ++++++ dp+N  aW+
  gi|330507744|ref|YP_004384172.1| 268 KIIDNALKIDPSNHEAWQ 285
                                       6689*************6 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.26   2.5e+02     249     299 ..      64     119 ..      25     162 .. 0.66
   2 ?   10.5   0.0   0.00023      0.22     224     292 ..     237     305 ..     227     316 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.26
                                       --HHHHHHHHHHHHH-TT-HHHHHH.HHHHHH..HTT-HHHH.HHHHHT.----SS CS
                             ChAPs 249 keelAlevakravksaPsefktWal.LvkvYi..kledienA.LltLNs.cPmfty 299
                                       k++  l++ + a++++P +++ W       Y+  +l++i +  L+ LN+  P+ + 
  gi|330507744|ref|YP_004384172.1|  64 KQNESLAAFNIAINLSPEDSNAWNAkGLGLYVgaRLNQIVDDlLIDLNTeYPIINN 119
                                       44445555677899999999999641455666335677644404457753455554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00023
                                       HHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                             ChAPs 224 neeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienALltLN 292
                                        ++le ++ + + ++l+a  l++  + e A+++ ++a k+ Ps+ + W +   + +k+e++ +A+  LN
  gi|330507744|ref|YP_004384172.1| 237 DKALEFDPISLDPMILKARVLIDCGEFEEAIKIIDNALKIDPSNHEAWQTKGYILMKQENYTEAIKNLN 305
                                       566667777778889999********************************999999*********9999 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00024      0.23      23      71 ..     259     307 ..     238     320 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                        HrpB1_HrpK  23 asedtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLrev 71 
                                       + +++e+a +++d    + P++ e+    g +l+++++++eA++ L+  
  gi|330507744|ref|YP_004384172.1| 259 DCGEFEEAIKIIDNALKIDPSNHEAWQTKGYILMKQENYTEAIKNLNIA 307
                                       667899999999999999*************************999755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2321.64
//
Query:       gi|330507745|ref|YP_004384173.1|  [L=128]
Description: hypothetical protein MCON_1739 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00018   20.8   0.2    0.00021   20.6   0.2    1.1  1  RepC      Replication protein C (RepC)
     0.0033   17.3   0.4     0.0039   17.1   0.4    1.0  1  DUF445    Protein of unknown function (DUF445)


Domain annotation for each model (and alignments):
>> RepC  Replication protein C (RepC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   2.4e-08   0.00021      25     103 ..      38     116 ..      21     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.4e-08
                              RepC  25 rGerkrlkldvayeygegerlefkgkeplGvddlrilqGlvalaGpkGlvlkaetkseagkqlrlllepkfdavekd 101
                                         +  rl ld+a +     +le + ++pl  d   il+ l+   G+k l   a  k + +kql+ +l   +d +e++
  gi|330507745|ref|YP_004384173.1|  38 TADIERLALDIALDRQRLTKLEKVEPQPLQKDRGEILRALIVANGGKMLAKDARQKMHLSKQLFSMLINSMDDIETK 114
                                       57889*************************************************************99999999987 PP

                              RepC 102 al 103
                                        l
  gi|330507745|ref|YP_004384173.1| 115 PL 116
                                       65 PP

>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   4.4e-07    0.0039     191     289 ..      16     115 ..       6     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.4e-07
                            DUF445 191 ltsilekvksdpdh..llreeedkkvreliadllndpelaakveklkkkklsdlevqeyeealwealkdlllkdlne 265
                                        ++i+++v+s  d+   l+ ++++ +++l+ d++ d +  +k+ek+  + l++ + ++    +++++ ++l kd+++
  gi|330507745|ref|YP_004384173.1|  16 FKVIVQEVHSLRDQiaALEARQTADIERLALDIALDRQRLTKLEKVEPQPLQKDRGEILRALIVANGGKMLAKDARQ 92 
                                       5667777776655411678888999**************************************************** PP

                            DUF445 266 eesllrerisklleklgeklaedp 289
                                       +   l +++ ++l + ++ ++++p
  gi|330507745|ref|YP_004384173.1|  93 KM-HLSKQLFSMLINSMDDIETKP 115
                                       66.***********9999999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 872.50
//
Query:       gi|330507746|ref|YP_004384174.1|  [L=196]
Description: putative integrase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-09   36.5   0.0      7e-09   35.7   0.0    1.4  1  Phage_integrase  Phage integrase family
      8e-07   29.5   0.1    2.2e-06   28.0   0.1    1.7  1  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
     0.0026   18.0   0.5     0.0095   16.2   0.5    1.9  1  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 !   35.7   0.0   1.2e-12     7e-09       2      87 ..      98     178 ..      97     194 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.2e-12
                                       HHHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHH CS
                   Phage_integrase   2 vltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseeale 78 
                                       +++e++++++++a+ +   i+  ++l++ +   lR+sE+++L+ +d+dl n++i++  r gK+ k+ ++ l++    
  gi|330507746|ref|YP_004384174.1|  98 YFDENDIRAIFNAITN---IKYLCVLQIGFYASLRASEVANLDDSDIDLINKTIRI--RGGKNDKDAILYLNDICID 169
                                       57899***********...*************************************..******************* PP

                                       HHHHHHHHH CS
                   Phage_integrase  79 llkellska 87 
                                        l+++l+++
  gi|330507746|ref|YP_004384174.1| 170 TLRKYLKVR 178
                                       ****99998 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 !   28.0   0.1   3.8e-10   2.2e-06       3      69 ..       9      71 ..       8      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.8e-10
                   Phage_int_SAM_4  3 erfrealrlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqknaln 69
                                      +rf +++r+ g++++Ti+ Y++ ++r+l+f++  +p+    +d+e++  +L+ +r+ls s+++n+  
  gi|330507746|ref|YP_004384174.1|  9 NRFEHHIRSMGFRDSTINDYVNRLRRYLAFCDTISPDL---ADAERFRDSLI-DRRLSRSSINNYSF 71
                                      68999***************************667765...7999*******.***********954 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 !   16.2   0.5   1.6e-06    0.0095       3      78 ..      10      78 ..       8      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-06
                                      HHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHH CS
                   Phage_int_SAM_1  3 qfleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfq 78
                                      +f+++++   g+   T+++Y+++Lrr+l f ++       + + +d  +f + l +++ls++s++++   +++++q
  gi|330507746|ref|YP_004384174.1| 10 RFEHHIR-SMGFRDSTINDYVNRLRRYLAFCDT------ISPDLADAERFRDSLIDRRLSRSSINNYSFVMKNYHQ 78
                                      5666665.678899*******************......5556666677777888888899****99999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1368.70
//
Query:       gi|330507747|ref|YP_004384175.1|  [L=474]
Description: transposase, IS4 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-19   70.1   0.0    4.7e-19   68.9   0.0    1.6  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 !   68.9   0.0   2.6e-23   4.7e-19       7     213 ..     175     409 ..     170     410 .. 0.79

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 2.6e-23
                         DDE_Tnp_1   7 livDattvrvpgtkedarwgykggk.ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvla 82 
                                       l+ D +tv ++++  +a  gy++gk + + +++ + ++  +gl++ +++ pg+v d+k l   + e+r+ +g +v+ 
  gi|330507747|ref|YP_004384175.1| 175 LVYDLSTVLTRSSINFAEIGYNKGKvHVPQINIALFCSMTTGLPTMIRTLPGSVRDIKSLYNSILEARK-EGGTVVL 250
                                       6677788888888888888***9999************************************9999999.******* PP

                         DDE_Tnp_1  83 DaGYasaelldtleekgvdyiirlkkntklyrk..........................gaeskrrgrlrkhdrnki 133
                                       D+G++s++++++l ekg+++i++++ n++ly +                                            
  gi|330507747|ref|YP_004384175.1| 251 DRGFFSKGTIQFLLEKGMNFILPARRNSRLYNTgidlsghmfyqkrlikcgkrknenifL----------------- 310
                                       *******************************99777766555554444444433333330................. PP

                         DDE_Tnp_1 134 ltksqkrrnk...............................skkekgdvyyvtntnsellsaeevaelyrlRwqiEr 179
                                                +                               s++++g     + +++ +++++e+   y+ R +iE 
  gi|330507747|ref|YP_004384175.1| 311 ---------YlfedqqlkleenttlyrkldedkideidltnSQERAGKI---LIVSNLDSDPKEIFMQYKSRDRIEK 375
                                       .........0233344444455555555555555666655555555555...55555556***************** PP

                         DDE_Tnp_1 180 vFkwlkrkfgldrlryrglnrveaqllllllaln 213
                                        F + k++++ d l++ + + ++ ++++ +l+l 
  gi|330507747|ref|YP_004384175.1| 376 LFDTYKNSLHSDILYLQDNESIFGHIFISFLSLY 409
                                       *****************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3380.95
//
Query:       gi|330507748|ref|YP_004384176.1|  [L=404]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete 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-141  469.0   0.0   6.2e-141  468.8   0.0    1.0  1  DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
    1.3e-05   25.3   0.0    4.2e-05   23.7   0.0    1.8  1  HTH_Tnp_Tc3_2    Transposase
     0.0004   20.4   0.0    0.00094   19.3   0.0    1.6  1  HTH_21           HTH-like domain
     0.0011   19.5   0.0      0.003   18.2   0.0    1.8  1  HTH_32           Homeodomain-like domain
     0.0026   17.7   0.4      0.009   15.9   0.1    2.1  2  HTH_12           Ribonuclease R winged-helix domain
      0.009   16.1   0.0      0.014   15.5   0.0    1.3  1  GSH-S_N          Prokaryotic glutathione synthetase, N-termin
  ------ inclusion threshold ------
      0.014   14.0   0.0      0.023   13.3   0.0    1.3  1  UPF0236          Uncharacterised protein family (UPF0236)
      0.017   14.8   0.4      0.061   13.0   0.2    2.0  3  HTH_33           Winged helix-turn helix


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.8   0.0  2.8e-144  6.2e-141       1     308 []      91     398 ..      91     398 .. 1.00

  Alignments for each domain:
  == domain 1  score: 468.8 bits;  conditional E-value: 2.8e-144
                   DDE_Tnp_ISAZ013   1 dleelvepetrgdpesplrwttkslrklaeeLkeqghkvsaetvaelLkelgyslqsnrKtkegkkhpdrdaqFeki 77 
                                       dle+++e++t+gdp+s l+wt ks++++aeeL+++g+kvs++tv++lLke+gyslq+nrK+ egk+ p+rd+qF+++
  gi|330507748|ref|YP_004384176.1|  91 DLEKIMEESTAGDPMSLLKWTYKSTYAIAEELQSRGYKVSHDTVRRLLKESGYSLQANRKNLEGKSGPERDTQFRYV 167
                                       79*************************************************************************** PP

                   DDE_Tnp_ISAZ013  78 nekvkeaqeagqpvisvdtkkkeliGefkrsGkewrpkgepaevkdhdfvskeegkaipyGiydlaenegwvsvgtd 154
                                       +++++++ +ag+pvisvd+kkkel+G++k+sG++wr+kg+p+ v+++df+sk+ g+aipyG+yd+++neg+v++g++
  gi|330507748|ref|YP_004384176.1| 168 SSQAAKFIDAGDPVISVDAKKKELVGNYKNSGRTWRQKGQPELVNVYDFPSKAIGAAIPYGVYDPKRNEGVVNIGKS 244
                                       ***************************************************************************** PP

                   DDE_Tnp_ISAZ013 155 kdtaefavesirrwWqevgkarypkakrllitaDaggsnssrsrlwkkelqkladelgleiqvahfPpgtskwnkiE 231
                                       ++taefavesir+wW+ vgk+ry+ +k+lli+aD+ggsn+sr+r wk  lq+lade+g++i+v+hfPpgtskwnkiE
  gi|330507748|ref|YP_004384176.1| 245 HNTAEFAVESIRQWWNLVGKYRYAGCKNLLICADGGGSNGSRNRGWKFFLQQLADEIGITITVSHFPPGTSKWNKIE 321
                                       ***************************************************************************** PP

                   DDE_Tnp_ISAZ013 232 hRlfshitqnwrgrpltsvevvvnliaatttkkglkveaeldeksyetGikvskeemealeierdelhgewnytiap 308
                                       h++fs+i++nwrg+pl+s+e++++li++t+tkkgl++ea+ld+++yetGik+ +e+m++l+i+ +el++ wny+i+p
  gi|330507748|ref|YP_004384176.1| 322 HCMFSFISMNWRGKPLSSYETIIKLIGSTKTKKGLRIEARLDDRDYETGIKILDEDMARLKISVHELYPMWNYSIEP 398
                                       ***************************************************************************98 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.9e-08   4.2e-05      14      51 ..     113     150 ..      96     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.9e-08
                     HTH_Tnp_Tc3_2  14 itlreLanelkeeGksvsreTirrrLrkaglkkrkprk 51 
                                       ++  ++a+el+++G +vs+ T+rr L+++g++ +  rk
  gi|330507748|ref|YP_004384176.1| 113 KSTYAIAEELQSRGYKVSHDTVRRLLKESGYSLQANRK 150
                                       57779*****999******************9888777 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.2e-07   0.00094      26      59 ..     118     150 ..     116     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.2e-07
                            HTH_21  26 iwaeLrreggvrvnhkrVrRlMrelGLrgvqrrk 59 
                                       i+ eL+ +g+ +v+h +VrRl +e G+  + +rk
  gi|330507748|ref|YP_004384176.1| 118 IAEELQSRGY-KVSHDTVRRLLKESGYSLQANRK 150
                                       6789****77.6**************99888887 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.3e-06     0.003      20      73 .]      73     138 ..      51     138 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                            HTH_32  20 rprrgrpr..klsdevrariiallreep.........rWsprq...laarlaeregvkvShstvyriL 73 
                                       +p +gr+r     + +   + ++  ee+         +W+++    +a++l + +g+kvSh tv+r+L
  gi|330507748|ref|YP_004384176.1|  73 KPGGGRKRvaDREPNLLNDLEKIM-EEStagdpmsllKWTYKStyaIAEEL-QSRGYKVSHDTVRRLL 138
                                       344557764435555666666666.433467779999997777777*****.8889**********98 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     4e-06     0.009      17      40 ..     116     139 ..     107     149 .. 0.92
   2 ?   -2.9   0.0       3.1     7e+03      18      31 ..     357     370 ..     346     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4e-06
                            HTH_12  17 keiaeeLkkrgydigeravRyrLr 40 
                                        +iaeeL+ rgy+++  +vR+ L+
  gi|330507748|ref|YP_004384176.1| 116 YAIAEELQSRGYKVSHDTVRRLLK 139
                                       68*******************998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.1
                            HTH_12  18 eiaeeLkkrgydig 31 
                                       +i+  L +r+y+ g
  gi|330507748|ref|YP_004384176.1| 357 RIEARLDDRDYETG 370
                                       68888999998765 PP

>> GSH-S_N  Prokaryotic glutathione synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.4e-06     0.014       8      60 ..     103     156 ..      96     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.4e-06
                           GSH-S_N   8 dplesikikkDttfalmleaqarghevfvleaadLslreg.katararkvevke 60 
                                       dp++ +k +  +t+a+++e q+rg++v + ++++L  ++g +++a+ +++e k+
  gi|330507748|ref|YP_004384176.1| 103 DPMSLLKWTYKSTYAIAEELQSRGYKVSHDTVRRLLKESGySLQANRKNLEGKS 156
                                       9999***999*************************9987723455555555533 PP

>> UPF0236  Uncharacterised protein family (UPF0236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     1e-05     0.023     139     230 ..     119     216 ..     110     222 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                           UPF0236 139 aeklerivcqekvskeairqlvleigvalaaaekevkveikekrkvRvLyieaDg.lfvsrq......dgkkeeerl 208
                                       ae+l+++    kvs++++r+l  e g +l+a +k+ + + + +r+  + y+      f+         d kk+e   
  gi|330507748|ref|YP_004384176.1| 119 AEELQSR--GYKVSHDTVRRLLKESGYSLQANRKNLEGKSGPERDTQFRYVSSQAaKFIDAGdpvisvDAKKKELVG 193
                                       4555333..3589**********************************999976531344433233322334444444 PP

                           UPF0236 209 lviheGrk.ekgsrleLvnrrdy 230
                                        +   Gr+ ++ ++ eLvn+ d+
  gi|330507748|ref|YP_004384176.1| 194 NYKNSGRTwRQKGQPELVNVYDF 216
                                       45666755356677778887665 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.3   2.9e+03      23      40 ..      97     114 ..      94     122 .. 0.83
   2 ?   13.0   0.2   2.7e-05     0.061      10      39 ..     118     146 ..     111     159 .. 0.86
   3 ?   -3.7   0.0       4.3   9.5e+03      13      26 ..     296     309 ..     295     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.3
                            HTH_33  23 svsgvyrlLkrlGfsyqk 40 
                                       ++s+ ++ +  l+++y++
  gi|330507748|ref|YP_004384176.1|  97 EESTAGDPMSLLKWTYKS 114
                                       6788888999999**997 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.7e-05
                            HTH_33  10 laqlieerfgvsysvsgvyrlLkrlGfsyq 39 
                                       +a+ ++ r g ++s+ +v+rlLk+ G+s q
  gi|330507748|ref|YP_004384176.1| 118 IAEELQSR-GYKVSHDTVRRLLKESGYSLQ 146
                                       66666666.99*****************99 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.3
                            HTH_33  13 lieerfgvsysvsg 26 
                                        ++++ g++++vs+
  gi|330507748|ref|YP_004384176.1| 296 QLADEIGITITVSH 309
                                       5789999*999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2908.67
//
Query:       gi|330507749|ref|YP_004384177.1|  [L=207]
Description: hypothetical protein MCON_1744 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-07   31.5   0.2    9.4e-05   22.8   0.1    2.2  2  DDE_Tnp_IS1  IS1 transposase
    0.00085   19.1   0.2     0.0018   18.0   0.2    1.6  1  rve_3        Integrase core domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS1  IS1 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0   0.00083       7.4      31      77 ..       5      53 ..       1      66 [. 0.82
   2 !   22.8   0.1     1e-08   9.4e-05      82     125 ..     109     153 ..      79     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00083
                       DDE_Tnp_IS1 31 rktvlayvfgertdetlrellallsp..fdvviltsddwglyerelkkd 77
                                       + vl++v ger++++  +l+   +     + ++++d+   y + l+k+
  gi|330507749|ref|YP_004384177.1|  5 SRLVLSHVVGERSQKSSDQLIKNTAKklSSIPLFVTDGLKFYIKSLRKQ 53
                                      5679****************9765542258999*********9999886 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1e-08
                       DDE_Tnp_IS1  82 sk.iytqriernnltlrtrlkrlarkslsfsksvelhekvigtyl 125
                                       sk i t  ier nlt r+  +r++rk++ fsk  e  ++ +  y+
  gi|330507749|ref|YP_004384177.1| 109 SKmISTSYIERLNLTCRQDNNRISRKTIGFSKKAEELDHQMTLYF 153
                                       55245889************************9987777666665 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2     2e-07    0.0018      17      65 ..     115     168 ..     110     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-07
                             rve_3  17 glvEsfngtlrdellneel.....frslaearekleawredYNteRPHssLgyk 65 
                                        ++E++n t r+     +       ++ +e++++++ +++ YN+ R H+sL+yk
  gi|330507749|ref|YP_004384177.1| 115 SYIERLNLTCRQDNNRISRktigfSKKAEELDHQMTLYFACYNYCRKHRSLKYK 168
                                       589********998877778899878999***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1436.57
//
Query:       gi|330507750|ref|YP_004384178.1|  [L=257]
Description: hypothetical protein MCON_1745 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1933.04
//
Query:       gi|330507751|ref|YP_004384179.1|  [L=292]
Description: hypothetical protein MCON_1746 [Methanosaeta concilii GP6]
Scores for complete sequence (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    1.3e-06   28.0   0.0    2.0  1  CHAT           CHAT domain
  ------ inclusion threshold ------
      0.043   13.0   0.0      0.052   12.7   0.0    1.2  1  Peptidase_C25  Peptidase family C25
      0.096   12.9   0.0       0.23   11.7   0.0    1.6  1  PGM_PMM_IV     Phosphoglucomutase/phosphomannomutase, C-termi


Domain annotation for each model (and alignments):
>> CHAT  CHAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   2.2e-10   1.3e-06     108     267 ..     115     263 ..      89     274 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.2e-10
                                       xxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CHAT 108 aEaeaiakllaegel....kvllgeaatesalksals.rryrvvHfatHgvfnanpplqsglvlsaenseedglLta 179
                                       +E++ i   +++++     ++ +  a++++ +++al+  r+++vHf++Hg+++      + ++  +++  + ++++ 
  gi|330507751|ref|YP_004384179.1| 115 EEVREITSKIRASKFrdsiELVSEWAVRPDDILQALNeVRPEIVHFCGHGSSS------GEIIVVDSTG-SPKPISN 184
                                       45666666655554456645666666699*******99***************......7777776555.6667777 PP

                                       xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CHAT 180 eeilelnldg....aelVvLsACqtglgevidgegvlgLaralllaGarsviaslwpVddeatalLmkrfyqnllag 252
                                       e i++l +++    +++V ++AC +     +++e+++ +        + ++i++  ++ d a+++++++fy+++  g
  gi|330507751|ref|YP_004384179.1| 185 EAIRSL-FETmkdnIKIVLINACYSR----TQAESIVNV--------IDCAIGMNTSIGDLAAITFAAAFYRAIGFG 248
                                       777762.2223346************....456777766........79**************************** PP

                                       xxxxxxxxxxxxxxx RF
                              CHAT 253 lskaeALreaqlkll 267
                                       +s+ eA  + ++++l
  gi|330507751|ref|YP_004384179.1| 249 RSVQEAFYQGRTAML 263
                                       ******999998887 PP

>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.7e-06     0.052     225     316 ..     139     242 ..      88     271 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.7e-06
                                       .....TTTTHHHHH.--SEEEEES-EETTEE........TTTTEEHHHHHT-..--TT--EEEEEESSSTT-TTSSS CS
                     Peptidase_C25 225 l.lttqnllkalnq.GvlfvnytGHGsetaw........adeslstndisal..tntnklpiaitaaCltgafdeet 289
                                       + ++++++l+aln+  + +v++ GHGs+++         + + +s++ i +l  t +++  i++ +aC++    e+ 
  gi|330507751|ref|YP_004384179.1| 139 WaVRPDDILQALNEvRPEIVHFCGHGSSSGEiivvdstgSPKPISNEAIRSLfeTMKDNIKIVLINACYSRTQAESI 215
                                       4467889******8799************888888877555558*******94445569*********987665555 PP

                                       -.-HHHHHHHSTTSSEEEEEEESS--- CS
                     Peptidase_C25 290 krsfgeklvlnangGavayigatrlgy 316
                                        + +  ++ +n + G  a i+     y
  gi|330507751|ref|YP_004384179.1| 216 VNVIDCAIGMNTSIGDLAAITFAAAFY 242
                                       445555555555555555555555555 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 ?   11.7   0.0   3.9e-05      0.23      24      71 ..      40      89 ..      13      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.9e-05
                                      HCCCCCCCCGCCEEEE.EEEETTCCE..EEEEEEESSHHHHHHHHHHHHH CS
                        PGM_PMM_IV 24 sikeglkilledGrrlavRpSGTepl..lrvyvEaksdeelarlaeevae 71
                                      +i++++ +l + G + ++R+ GT p+  l v++E++ + + +++++++++
  gi|330507751|ref|YP_004384179.1| 40 EINDAINYLEGQGAIEVLRACGTAPYdfLSVRIETPGRILYHHIKDKIYK 89
                                      689*********************************99999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2033.63
//
Query:       gi|330507752|ref|YP_004384180.1|  [L=99]
Description: hypothetical protein MCON_1747 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   14.6   0.1      0.022   14.5   0.1    1.1  1  O-FucT    GDP-fucose protein O-fucosyltransferase


Domain annotation for each model (and alignments):
>> O-FucT  GDP-fucose protein O-fucosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.2e-06     0.022      49      96 ..      17      72 ..       6      97 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-06
                            O-FucT 49 qnrlpFsdfFdiesLkkdvrviemeeflk.............elppelwsaekrksvckea 96
                                      ++++pF+d+F++  + ++++ +++++ ++             ++p+e        ++ +e 
  gi|330507752|ref|YP_004384180.1| 17 THNVPFDDLFNVRFMTEYTEFVTIDDMFEsagfkvdneedfnNIPEEKL-----DKFIREH 72
                                      679*************************944444444444443332111.....2233333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 723.30
//
Query:       gi|330507753|ref|YP_004384181.1|  [L=84]
Description: hypothetical protein MCON_1748 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00024   21.2   0.0    0.00028   21.0   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.6e-08   0.00028       8      61 ..      18      71 ..      12      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.6e-08
                   HicB_lk_antitox  8 dedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipepssi 61
                                       ed +y  +v  l+G++ +gdt+ee  ++   aie ++   +  g+ ip    i
  gi|330507753|ref|YP_004384181.1| 18 LEDGTYMATVAGLQGVIAVGDTIEECRDDLIGAIEGWVALGLRLGHPIPPIDGI 71
                                      57889999*******************************999999999987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 636.08
//
Query:       gi|330507754|ref|YP_004384182.1|  [L=423]
Description: hypothetical protein MCON_1750 [Methanosaeta concilii GP6]
Scores for 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-23   82.7   0.5    7.5e-23   82.1   0.5    1.3  1  Trypsin_2      Trypsin-like peptidase domain
    3.6e-11   42.4  10.7    9.7e-07   28.4   0.1    3.5  3  TPR_1          Tetratricopeptide repeat
    9.5e-11   41.0   8.9    1.2e-07   31.3   0.1    2.9  3  TPR_2          Tetratricopeptide repeat
    9.7e-08   31.6   4.8    8.7e-05   22.4   0.1    2.7  2  TPR_8          Tetratricopeptide repeat
    2.9e-07   30.5   0.9    1.5e-06   28.2   0.9    1.9  1  Trypsin        Trypsin
    0.00013   22.1   1.1        0.1   13.0   0.1    2.9  2  TPR_17         Tetratricopeptide repeat
      0.001   19.3   2.3         45    4.4   0.3    2.2  1  TPR_12         Tetratricopeptide repeat
     0.0022   17.7   2.1     0.0038   16.9   0.2    2.3  2  TPR_11         TPR repeat
     0.0061   17.2   0.3       0.01   16.5   0.3    1.3  1  TPR_16         Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.063   13.4   0.0    2.0  1  TPR_9          Tetratricopeptide repeat
      0.016   13.8   1.0       0.28    9.8   0.3    2.1  2  Peptidase_S46  Peptidase S46
      0.017   14.9   0.3      0.039   13.8   0.3    1.6  1  Peptidase_S7   Peptidase S7, Flavivirus NS3 serine protease
       0.06   13.1   0.0       0.13   12.0   0.0    1.5  1  Peptidase_S29  Hepatitis C virus NS3 protease
        0.1   13.2   0.1        0.5   10.9   0.1    2.0  2  TPR_19         Tetratricopeptide repeat
       0.12   12.7   5.3      0.098   12.9   3.0    1.8  2  ANAPC3         Anaphase-promoting complex, cyclosome, subunit


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.5   6.3e-26   7.5e-23       1     150 []     109     236 ..     109     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 6.3e-26
                         Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpak.vvaadpel.DlAllkvssderaglpplpl 75 
                                       GsGf++++dg i+T++Hv+++ ++a v         +++d+++++++ v a +  + DlA + + s ++ ++  l +
  gi|330507754|ref|YP_004384182.1| 109 GSGFIISKDGGIVTCYHVMRGYSTAIV---------TTSDEKKFQVRnVTALNK-SdDLARISL-SVDNHSFSNLNV 174
                                       9********88****************.........666666666662666664.46*******.999999999999 PP

                         Trypsin_2  76 gpsealkggepvyvvGyplggeksgsvssGivsgvvesesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                        ++++ +g ++++++G plg  k  +vs+Givs++++          + +q +a++spGsSGGp+f+ +G+v+G+
  gi|330507754|ref|YP_004384182.1| 175 NTTTPEVG-QDIIAIGGPLGLAK--TVSEGIVSAIRN----------NTIQITAPISPGSSGGPVFNMRGEVIGI 236
                                       99775555.5*************..9***********..........***************************8 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3     0.011        13      13      34 .]     321     342 ..     318     342 .. 0.89
   2 !   28.4   0.1   8.1e-10   9.7e-07       3      33 ..     345     375 ..     343     376 .. 0.96
   3 !   12.5   2.1   8.2e-05     0.098       4      25 ..     380     401 ..     378     402 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                                       HTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  13 klgkydeAleyyekALelnPnn 34 
                                        ++ky+e +++++  L  +P++
  gi|330507754|ref|YP_004384182.1| 321 FKNKYKETIQCCDYILDEDPSF 342
                                       579**************99986 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 8.1e-10
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       a++ +G+a+++l +y+eAl ++++ +el+P+
  gi|330507754|ref|YP_004384182.1| 345 AWNMKGLALYYLTRYEEALSCFNESIELDPS 375
                                       9*****************************7 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 8.2e-05
                                       HHHHHHHHHHTT-HHHHHHHHH CS
                             TPR_1   4 lynlGnayfklgkydeAleyye 25 
                                       + n+G+a+ kl +y eA e++ 
  gi|330507754|ref|YP_004384182.1| 380 WQNKGAALKKLHRYAEAKEAFA 401
                                       99*****************995 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       9.4   1.1e+04      12      32 ..     320     340 ..     318     341 .. 0.69
   2 !   31.3   0.1   9.9e-11   1.2e-07       2      32 ..     344     374 ..     343     376 .. 0.95
   3 !   12.6   2.9   9.8e-05      0.12       3      26 ..     379     402 ..     377     402 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.4
                             TPR_2  12 yklgdyeeAleafekAleldP 32 
                                       y +++y+e +++++  l  dP
  gi|330507754|ref|YP_004384182.1| 320 YFKNKYKETIQCCDYILDEDP 340
                                       556778877777777777777 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 9.9e-11
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                        a+++ Gla+y+l +yeeAl +f++++eldP
  gi|330507754|ref|YP_004384182.1| 344 LAWNMKGLALYYLTRYEEALSCFNESIELDP 374
                                       59***************************** PP

  == domain 3  score: 12.6 bits;  conditional E-value: 9.8e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafek 26 
                                       ++ n G a+ kl +y+eA+eaf k
  gi|330507754|ref|YP_004384182.1| 379 YWQNKGAALKKLHRYAEAKEAFAK 402
                                       89*******************976 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   7.3e-08   8.7e-05       3      33 ..     345     375 ..     344     376 .. 0.97
   2 !    9.9   1.2   0.00074      0.89       3      26 ..     379     402 ..     377     402 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.3e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++++g+++  l +yeeA +++++ +eldp+
  gi|330507754|ref|YP_004384182.1| 345 AWNMKGLALYYLTRYEEALSCFNESIELDPS 375
                                       8****************************96 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00074
                                       HHHHHHHHHHHTT-HHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyek 26 
                                       +++n+g +++kl +y eAke++ k
  gi|330507754|ref|YP_004384182.1| 379 YWQNKGAALKKLHRYAEAKEAFAK 402
                                       79*******************976 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.9   1.3e-09   1.5e-06      28     213 ..     110     252 ..      95     259 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.3e-09
                                       EEEEEETT.EEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBSS CS
                           Trypsin  28 gGslisen.wvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgdt 103
                                       +G++is++  ++T  H++++ ++  +      ++ s++  +k++v++v+     n+s+   D+a + l+ +   +++
  gi|330507754|ref|YP_004384182.1| 110 SGFIISKDgGIVTCYHVMRG-YSTAI------VTTSDE--KKFQVRNVTA---LNKSD---DLARISLSVD---NHS 168
                                       69******9**********9.33333......333444..7999999766...88888...**********...999 PP

                                       BHCCBBCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBCTTTT CS
                           Trypsin 104 vrpiclpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsretcksaykgkvtenmlcagakeggkdacqGD 180
                                        + ++  ++ +  +vg+ ++++G +        +t+ e+ v++             +++n++++ a      + +G 
  gi|330507754|ref|YP_004384182.1| 169 FSNLNVNTTTP--EVGQDIIAIGGPLG--L--AKTVSEGIVSA-------------IRNNTIQITA-----PISPGS 221
                                       99999999555..99*99999999885..2..24566666655.............5567888888.....6999** PP

                                       TTSEEEETTTEEEEEEEEESSSSCTTSEEEEEE CS
                           Trypsin 181 SGGPlvcsdgelvGivswgkgcakgnrpgvytk 213
                                       SGGP++++ ge++Gi s   + +++   +++++
  gi|330507754|ref|YP_004384182.1| 222 SGGPVFNMRGEVIGIASSQMKNGQN--LNFAIP 252
                                       *****************98554444..455555 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0071       8.5       5      33 ..     335     363 ..     331     364 .. 0.88
   2 !   13.0   0.1   8.8e-05       0.1       1      34 []     365     398 ..     365     398 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0071
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmtAr 33 
                                        l+ dP+   a+n+++ +l+ + ++++A+
  gi|330507754|ref|YP_004384182.1| 335 ILDEDPSFHLAWNMKGLALYYLTRYEEAL 363
                                       5788****************999999996 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.8e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       ++ +++eldP+    ++n++ +l+k++++++A++
  gi|330507754|ref|YP_004384182.1| 365 CFNESIELDPSMGAYWQNKGAALKKLHRYAEAKE 398
                                       799*****************************86 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.037        45       8      27 ..     382     401 ..     375     403 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.037
                            TPR_12   8 nlaavlrrlgrydeAlelle 27 
                                       n +a+l +l ry+eA e + 
  gi|330507754|ref|YP_004384182.1| 382 NKGAALKKLHRYAEAKEAFA 401
                                       67888888888888887775 PP

>> TPR_11  TPR repeat
   #    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      28      41 ..     310     323 ..     308     329 .. 0.86
   2 !   16.9   0.2   3.1e-06    0.0038       1      40 [.     350     389 ..     350     390 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1
                            TPR_11  28 aeayynLGlayykq 41 
                                       a +yy++ ++y+k+
  gi|330507754|ref|YP_004384182.1| 310 AYIYYCMDQLYFKN 323
                                       78999999999987 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.1e-06
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       G a+y + +yeeA+ ++++ ++ldP+    + n G+a+ k
  gi|330507754|ref|YP_004384182.1| 350 GLALYYLTRYEEALSCFNESIELDPSMGAYWQNKGAALKK 389
                                       7899999******************998888888888877 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   8.4e-06      0.01       2      57 ..     348     400 ..     347     405 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.4e-06
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaaly 57 
                                       ++++a++++ +y++A+  +++ +++d   P   + + ++g a+ ++ r+aeA +++
  gi|330507754|ref|YP_004384182.1| 348 MKGLALYYLTRYEEALSCFNESIELD---PSMGAYWQNKGAALKKLHRYAEAKEAF 400
                                       7899**********************...***********************7544 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.3e-05     0.063       9      61 ..     323     375 ..     321     401 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.3e-05
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       +++ +++++++ +l  +P  +  +   Gl+l+ l ++++Al +++  ++l+p+
  gi|330507754|ref|YP_004384182.1| 323 NKYKETIQCCDYILDEDPSFHLAWNMKGLALYYLTRYEEALSCFNESIELDPS 375
                                       5678899***************************************9999995 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.039        46      46      70 ..     106     130 ..      98     165 .. 0.83
   2 ?    9.8   0.3   0.00023      0.28     630     651 ..     216     237 ..     210     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.039
                                       TTTEE-EE-STT-EEEE-HHHHHHH CS
                     Peptidase_S46  46 lggCtasfVSpeGLvlTNHHCayga 70 
                                       lg  ++ ++S++G ++T  H+++g 
  gi|330507754|ref|YP_004384182.1| 106 LGQGSGFIISKDGGIVTCYHVMRGY 130
                                       6889****************98764 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00023
                                       ---TT-TT-EEE-TTS-EEEEE CS
                     Peptidase_S46 630 DitGGNSGSPvlngkgelvGla 651
                                        i  G SG Pv+n +ge++G+a
  gi|330507754|ref|YP_004384182.1| 216 PISPGSSGGPVFNMRGEVIGIA 237
                                       5778****************97 PP

>> Peptidase_S7  Peptidase S7, Flavivirus NS3 serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   3.2e-05     0.039      93     116 ..     217     240 ..     124     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                                       XXTT-TTSEEE-TTSXEEEECEEE CS
                      Peptidase_S7  93 lssGsSGSlvlnqnkqivgiYfat 116
                                        s+GsSG +v+n +++++gi +  
  gi|330507754|ref|YP_004384182.1| 217 ISPGSSGGPVFNMRGEVIGIASSQ 240
                                       789*****************7765 PP

>> Peptidase_S29  Hepatitis C virus NS3 protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.13     102     133 ..     216     245 ..     198     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                     Peptidase_S29 102 elselkGssGsPilCdsGhvvGllvaavcsgg 133
                                       ++s   GssG+P++  +G v+G+  + +++g 
  gi|330507754|ref|YP_004384182.1| 216 PIS--PGSSGGPVFNMRGEVIGIASSQMKNGQ 245
                                       554..5*****************999887765 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.5     3e+03      38      57 ..     322     341 ..     312     352 .. 0.73
   2 ?   10.9   0.1   0.00042       0.5       6      50 ..     358     402 ..     353     406 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.5
                            TPR_19  38 lgqldeAealLdalpeedpd 57 
                                        + ++e ++++d +++edp 
  gi|330507754|ref|YP_004384182.1| 322 KNKYKETIQCCDYILDEDPS 341
                                       57777778888888888886 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00042
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLda 50 
                                       +y+eAl+ + + ++ dp +++ + +   al +l +++eA+++ ++
  gi|330507754|ref|YP_004384182.1| 358 RYEEALSCFNESIELDPSMGAYWQNKGAALKKLHRYAEAKEAFAK 402
                                       79***************************************9875 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.0   9.9e-05      0.12      28      80 ..     314     367 ..     299     369 .. 0.82
   2 ?   12.9   3.0   8.2e-05     0.098       2      79 ..     322     400 ..     321     402 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.9e-05
                                       HH.HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  28 ll.AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +   + +   ++yk+ ++ ++   +++++ + ++  ++ +l+ L +yeeA++++ 
  gi|330507754|ref|YP_004384182.1| 314 YCmDQLY-FKNKYKETIQCCDYIlDEDPSFHLAWNMKGLALYYLTRYEEALSCFN 367
                                       3334445.5568***********99999999********************9987 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.2e-05
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       +n+yk+ i +++ +l  ++  + +  +++l+ly + +y++A+  ++++ +l+++  +++  ++ +l kL++y eA  
  gi|330507754|ref|YP_004384182.1| 322 KNKYKETIQCCDYILDEDPSFHLAWNMKGLALYYLTRYEEALSCFNESiELDPSMGAYWQNKGAALKKLHRYAEAKE 398
                                       5889999999999998889999999999********************7777777788888888888*******987 PP

                                       HH CS
                            ANAPC3  78 aL 79 
                                       a+
  gi|330507754|ref|YP_004384182.1| 399 AF 400
                                       76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); 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 0.23s 00:00:00.78 Elapsed: 00:00:00.38
# Mc/sec: 3358.17
//
Query:       gi|330507755|ref|YP_004384183.1|  [L=70]
Description: hypothetical protein MCON_1753 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 528.27
//
Query:       gi|330507756|ref|YP_004384184.1|  [L=136]
Description: hypothetical protein MCON_1754 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-12   46.8   2.3    4.3e-12   46.6   2.3    1.0  1  PIN       PIN domain
  ------ inclusion threshold ------
       0.11   12.5   0.1        1.3    9.1   0.0    2.1  2  Mut7-C    Mut7-C RNAse domain
       0.13   13.0   1.1       0.24   12.2   1.1    1.6  1  PIN_3     PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   2.3   7.2e-16   4.3e-12       1     121 [.       5     128 ..       5     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 7.2e-16
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHH.HHTSEEE CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar.....rkskrekaaelvellll.lsalkil 71 
                                       +vlD+sv+ a++++e+ + +a ++ ++ ++l+t +l++aE+ +v+++     + +k + +a++++ +    +a++++
  gi|330507756|ref|YP_004384184.1|   5 VVLDSSVIAAMFFREDASTRAIQAAAK-SDLITLDLAIAEVGNVASKqvafcGGDKDLTLAAFKKCQSFiSEACELI 80 
                                       69**********999999666666665.************************999999999999999998******* PP

                                       EBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  72 pidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                          ++++ ea+ i+l+++   +D l +A A+e++ +l+ t D+++++ ak
  gi|330507756|ref|YP_004384184.1|  81 R-AEDLTMEAYIISLEAKTAFYDSLFLAAAEESQVPLL-TLDRKLYERAK 128
                                       *.************************************.*****999887 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.029   1.7e+02      30      70 ..      57      97 ..      14     104 .. 0.78
   2 ?    9.1   0.0   0.00021       1.3      31      62 ..     102     133 ..      93     136 .] 0.76

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.029
                            Mut7-C 30 edeellalaakekrillTrdreLlkraklkkgvlltsrdve 70
                                       d++l   a k+ + +++  +eL++ ++l+ ++++ s + +
  gi|330507756|ref|YP_004384184.1| 57 GDKDLTLAAFKKCQSFISEACELIRAEDLTMEAYIISLEAK 97
                                      57778888888888899999999999998888777666655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00021
                            Mut7-C  31 deellalaakekrillTrdreLlkraklkkgv 62 
                                       d+  la a++ +  llT dr+L++rakl+k+v
  gi|330507756|ref|YP_004384184.1| 102 DSLFLAAAEESQVPLLTLDRKLYERAKLTKNV 133
                                       44456666777777*************99875 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.1     4e-05      0.24       1     115 [.       4     121 ..       4     122 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4e-05
                             PIN_3   1 rvvlDtnvlldallfdspaarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakva...le 74 
                                       +vvlD++v+ +++ +++ + r+i +a+++  itl     ++ E+ +v+++++a+  +  + +  +a+  k++   +e
  gi|330507756|ref|YP_004384184.1|   4 KVVLDSSVIAAMFFREDASTRAIQAAAKSDLITL---DLAIAEVGNVASKQVAF--CGGDKDLTLAAFKKCQsfiSE 75 
                                       69******99999977766666666667777777...66777888777666444..555555555555566544433 PP

                             PIN_3  75 r......kavapdaelrpllkcrDpdDqkvlelAlaaradvlVTkdr 115
                                       +      ++ + +a   +l ++  + D  +l++A +  +  l+T dr
  gi|330507756|ref|YP_004384184.1|  76 AceliraEDLTMEAYIISLEAKTAFYDSLFLAAAEES-QVPLLTLDR 121
                                       3777744333333333334444477788888777776.666667776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1107.11
//
Query:       gi|330507757|ref|YP_004384185.1|  [L=59]
Description: hypothetical protein MCON_1755 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   1.4       0.21   11.7   0.1    2.0  2  Vault_4        Major Vault Protein repeat domain
      0.071   13.3   1.8      0.073   13.2   1.8    1.0  1  Kinesin_assoc  Kinesin-associated


Domain annotation for each model (and alignments):
>> Vault_4  Major Vault Protein repeat domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1    0.0078        70      36      53 ..       9      26 ..       1      29 [. 0.79
   2 ?   11.7   0.1   2.3e-05      0.21      29      54 ..      30      57 ..      27      59 .] 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0078
                           Vault_4 36 lWeKeLpedVeeLlaeak 53
                                       W+ e+ ++Ve++++e+k
  gi|330507757|ref|YP_004384185.1|  9 NWQVEIRQSVERIVREKK 26
                                      5*************9987 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.3e-05
                           Vault_4 29 mlteeEelWeKeLpedV..eeLlaeakd 54
                                      +l e  elWe ++p+++   e+++e +d
  gi|330507757|ref|YP_004384185.1| 30 LLAEAKELWEDQIPNKIgaAEMIREDRD 57
                                      7999***********9844689999888 PP

>> Kinesin_assoc  Kinesin-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.8   8.2e-06     0.073      95     133 ..      16      58 ..       2      59 .] 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.2e-06
                     Kinesin_assoc  95 aseeaierlketekiiaelnetWee....klrkteairlerea 133
                                        s e i r k+ +k++ae  e We+    k+  +e ir +r+a
  gi|330507757|ref|YP_004384185.1|  16 QSVERIVREKKKQKLLAEAKELWEDqipnKIGAAEMIREDRDA 58 
                                       445677889999************8333355667888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1180  (0.0658152); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 454.89
//
Query:       gi|330507758|ref|YP_004384186.1|  [L=208]
Description: isochorismatase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-27   95.1   0.1    6.6e-27   94.8   0.1    1.1  1  Isochorismatase  Isochorismatase family
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.21   11.6   0.0    1.5  1  Sigma70_r1_1     Sigma-70 factor, region 1.1


Domain annotation for each model (and alignments):
>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.1   7.4e-31   6.6e-27       2     174 ..      31     201 ..      30     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 7.4e-31
                   Isochorismatase   2 alvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgael 78 
                                       al+v+ +qndf+e+g+    ++s+++  ink + ++r     vi+++d h+      + +  k++ h++ gt gae+
  gi|330507758|ref|YP_004384186.1|  31 ALIVVEPQNDFTEGGALPAQNASEAITVINKIIPRFR----YVIASKDWHP----PDHCSFAKWPMHCIAGTIGAEF 99 
                                       9***********************************9....5*********....88889999************** PP

                   Isochorismatase  79 vpelaplegdvvvdKt......rfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAva 149
                                       + +l ++    +++K        +s f+++ l+++L++ +i++++++G+  dvCV  ta++a+ lG+++++v DA+ 
  gi|330507758|ref|YP_004384186.1| 100 HFSLDQRNIRTIIHKGverdddAYSVFENSHLEAMLRADNIRRVYITGFVLDVCVYETAVSAIALGFDTYIVLDATK 176
                                       *******999999998999999******************************************************* PP

                   Isochorismatase 150 alspelhdaalkrlkqafatvitte 174
                                           ++ +  ++++++a+ +vi ++
  gi|330507758|ref|YP_004384186.1| 177 PAYHDQLEETMAKIRDAGIKVIYSA 201
                                       ******9999********9999776 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.4e-05      0.21      36      58 ..     180     202 ..     172     208 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHHHCCT-EEE-SS- CS
                      Sigma70_r1_1  36 seqiediiemLedmgIdvveeae 58 
                                        +q+e++++++ d+gI+v+ +a+
  gi|330507758|ref|YP_004384186.1| 180 HDQLEETMAKIRDAGIKVIYSAD 202
                                       69****************98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1373.60
//
Query:       gi|330507759|ref|YP_004384187.1|  [L=213]
Description: putative peroxiredoxin [Methanosaeta concilii GP6]
Scores for complete 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  111.0   0.0    4.5e-32  110.6   0.0    1.2  1  AhpC-TSA    AhpC/TSA family
    4.5e-17   62.1   0.0    6.3e-17   61.7   0.0    1.1  1  Redoxin     Redoxin
    1.1e-06   28.3   1.1    2.8e-06   27.1   1.1    1.7  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.23   11.5   0.0    1.4  1  DUF2375     Protein of unknown function (DUF2375)
       0.18   11.9   0.0       0.22   11.6   0.0    1.3  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   0.0   1.3e-35   4.5e-32       2     123 ..       5     133 ..       4     134 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 1.3e-35
                                       TSB----EEESTTCEEEECHHH.TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHH CS
                          AhpC-TSA   2 gdkapdfelknadgetvslsdy.kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfi 77 
                                       gd++pd++++++  +t++l d  +gk+ +lf +p+d++pvCtte  a+ak++e+f+e++ e+ig+s+d++++h k++
  gi|330507759|ref|YP_004384187.1|   5 GDRFPDMTVQTTA-GTMELPDAyAGKWFILFSHPGDFTPVCTTEFVAFAKRHEQFRENNTELIGLSIDQVQAHMKWV 80 
                                       99********987.99***6655****************************************************** PP

                                       HH-H.......SSEEEE-TTSHHHHHTT-EETT.TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  78 ekes......lnfpllsDeegkvakaygvlkee.kglalratfvidkegkiry 123
                                       e ++      ++fp+++D +g vak++g+++++    ++ra+f+id+ g+ir 
  gi|330507759|ref|YP_004384187.1|  81 EWINdtlktnITFPIIADGTGRVAKQLGMIHPAkGSNTVRAVFIIDPSGTIRT 133
                                       ******************************99977899*************95 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   1.7e-20   6.3e-17       3     137 ..       5     141 ..       3     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.7e-20
                                       TSBB---ECCEETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHH CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvke 78 
                                       gd++Pd t   ++t   + +l + ++gk  ++++ pg f+P+C++e ++++k  e+++e++ + +++++d+ +  ++
  gi|330507759|ref|YP_004384187.1|   5 GDRFPDMT---VQTTAGTMELPDaYAGKWFILFSHPGDFTPVCTTEFVAFAKRHEQFRENNTELIGLSIDQVQAHMK 78 
                                       9*******...5688889999999**************************************************888 PP

                                       HHHH......TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCH CS
                           Redoxin  79 fwgk......eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepe 137
                                       +++       ++++fp+++Dg++ ++k+lG+   ++ s+    +++++id  g ++ + + p ++
  gi|330507759|ref|YP_004384187.1|  79 WVEWindtlkTNITFPIIADGTGRVAKQLGMIHPAKGSN--TVRAVFIIDPSGTIRTILYYPQEV 141
                                       7777777999999*****************776665555..8***********999887776664 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 !   27.1   1.1   7.8e-10   2.8e-06       1      30 [.     154     187 ..     154     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 7.8e-10
                                       HHHHHHHHT-BB-TTT.T.....BT-EEE---SSH CS
                        1-cysPrx_C   1 ALQladkhgvatPAnWkp.....GdkvivpPpate 30 
                                       ALQ+ad++ va PAnW p      d vi+pPp+ e
  gi|330507759|ref|YP_004384187.1| 154 ALQVADQNRVAMPANW-PnneliADGVIIPPPTNE 187
                                       9***************.988888899998886544 PP

>> DUF2375  Protein of unknown function (DUF2375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.5e-05      0.23       7      42 ..     132     169 ..     126     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.5e-05
                           DUF2375   7 VTvlYyeapallllhnav..lkslpvsesGrviiPqeF 42 
                                        T+lYy ++++  + + +  ++ l+v ++ rv +P+++
  gi|330507759|ref|YP_004384187.1| 132 RTILYYPQEVGRNMDEILrtVRALQVADQNRVAMPANW 169
                                       69*********999884322789************976 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.2e-05      0.22       4      55 ..      53     117 ..      50     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.2e-05
                        AhpC-TSA_2   4 rdkpeldaagvklvaigigdps.akkFvkl......tgfpfelyvDpsaklyqalglk......r 55 
                                       ++ +++++++++l++ +i++++   k+v+       t++ f++++D ++ + ++lg+       +
  gi|330507759|ref|YP_004384187.1|  53 KRHEQFRENNTELIGLSIDQVQaHMKWVEWindtlkTNITFPIIADGTGRVAKQLGMIhpakgsN 117
                                       6789*****************768888876777999********************975555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1575.83
//
Query:       gi|330507760|ref|YP_004384188.1|  [L=123]
Description: RelE/StbE family addiction module toxin [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-07   30.5   0.0    6.9e-07   29.8   0.0    1.3  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
    7.5e-07   29.0   0.3    2.8e-06   27.2   0.1    1.8  2  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
    0.00059   20.1   0.0      0.001   19.3   0.0    1.3  1  YafQ_toxin       Bacterial toxin of type II toxin-antitoxin s


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   1.1e-10   6.9e-07      10      90 .]      14      84 ..       7      84 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.1e-10
                                      HHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTCCTTEEEEEECTEEEEEEEETSTTEEEEEEEEEHHH CS
                        ParE_toxin 10 dlkkiadyiardgpaakrfldaleealellaenpalgrprrelglkglrririgdyriiYriddeelvvvilrvlhrse 88
                                      ++kk+ +         + + +++ ++++++ enp++g+p +  +lkglr  ++++++iiY +  ++ +v +++v h+++
  gi|330507760|ref|YP_004384188.1| 14 QFKKLTKK-------DAALEQRFGKKIKAICENPEIGEP-KSHNLKGLRGDHVDPFVIIYGVF-GDFIV-FVHVDHHDK 82
                                      44444443.......566777777778888888888888.444488***************96.66888.*******98 PP

                                      HC CS
                        ParE_toxin 89 dy 90
                                      +y
  gi|330507760|ref|YP_004384188.1| 83 AY 84
                                      86 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   4.7e-10   2.8e-06       5      48 ..       9      55 ..       6      59 .. 0.88
   2 ?   -0.5   0.0       0.2   1.2e+03      47      67 ..      73      93 ..      69     109 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.7e-10
                   ParE-like_toxin  5 rrfkkalkklkek...lkadldkavkeiiedPelGeeKkGDLsgvfv 48
                                      ++f+k+ kkl +k   l++++ k++k+i+e+Pe+Ge+K   L+g++ 
  gi|330507760|ref|YP_004384188.1|  9 SHFHKQFKKLTKKdaaLEQRFGKKIKAICENPEIGEPKSHNLKGLRG 55
                                      68999999998875567899***********************9985 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.2
                   ParE-like_toxin 47 fvykfklnkqltllaYeldek 67
                                        +++  +++ +  aYe+ + 
  gi|330507760|ref|YP_004384188.1| 73 VFVHVDHHDKAYAAAYEIAKA 93
                                      445567778888888888765 PP

>> YafQ_toxin  Bacterial toxin of type II toxin-antitoxin system, YafQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.7e-07     0.001       7      85 ..       9      82 ..       5      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-07
                                      HHHHHHHHHHHHTT--HH.HHHHHHHHHHTT-S--GGG--EE-SSS-TTEEEEEEETTEEEEEEE-SSEEEEEEEE-HH CS
                        YafQ_toxin  7 kqfkkdlkrlkkrkkdle.klkevlklLaegepLpekyrdHaLkgnwkgyrecHikpDllLiYrleddelvlvrlGsHs 84
                                      ++f+k++k+l k+   le ++ + +k++ e+ ++  + + H+Lkg     r  H+ p +++iY +  d +v+v ++ H+
  gi|330507760|ref|YP_004384188.1|  9 SHFHKQFKKLTKKDAALEqRFGKKIKAICENPEI-GEPKSHNLKG----LRGDHVDP-FVIIYGVFGDFIVFVHVDHHD 81
                                      68*********8888777699************9.56799**996....78889999.********************9 PP

                                      H CS
                        YafQ_toxin 85 e 85
                                      +
  gi|330507760|ref|YP_004384188.1| 82 K 82
                                      7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 890.56
//
Query:       gi|330507761|ref|YP_004384189.1|  [L=62]
Description: hypothetical protein MCON_1762 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       371  (0.0206927); 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:                         0  (0); expected 0.2 (1e-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: 478.54
//
Query:       gi|330507762|ref|YP_004384190.1|  [L=852]
Description: cation transporting P-type ATPase [Methanosaeta concilii GP6]
Scores for complete 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-44  150.0   0.3    4.9e-44  150.0   0.3    3.0  4  E1-E2_ATPase     E1-E2 ATPase
    2.6e-34  118.5   7.2    5.7e-34  117.4   7.2    1.6  1  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    1.9e-28  100.2   0.0      4e-28   99.1   0.0    1.6  1  Hydrolase        haloacid dehalogenase-like hydrolase
    2.4e-10   39.9   0.0    7.3e-10   38.4   0.0    1.9  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    4.9e-07   29.7   0.3     0.0001   22.1   0.3    2.4  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    1.6e-06   28.1   0.0    3.4e-06   27.0   0.0    1.6  1  Cation_ATPase    Cation transport ATPase (P-type)
    0.00025   21.5   0.0    0.00063   20.2   0.0    1.8  1  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.055   13.9   0.0      0.055   13.9   0.0    3.6  4  PhoR             Phosphate regulon sensor protein PhoR


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 !  150.0   0.3   2.2e-47   4.9e-44       2     180 ..     101     295 ..     100     296 .. 0.98
   2 ?   -0.9   0.0      0.45     1e+03      94     145 ..     626     677 ..     620     698 .. 0.81
   3 ?   -1.1   0.3      0.52   1.2e+03     120     148 ..     726     754 ..     715     770 .. 0.54
   4 ?   -2.4   0.6       1.3   2.9e+03     123     156 ..     791     824 ..     735     827 .. 0.61

  Alignments for each domain:
  == domain 1  score: 150.0 bits;  conditional E-value: 2.2e-47
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-............. CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek............. 64 
                                       +++p+a virdg e++i+ +++vpGD+++l +gdrvpaD+++++ ++ + des+LTGEs+ v+k             
  gi|330507762|ref|YP_004384190.1| 101 MSSPRALVIRDGVEKRIAGRDVVPGDLIVLAEGDRVPADAVLLSCTNlSADESLLTGESVSVRKvcsetdspvmarp 177
                                       68899******************************************9***************************99 PP

                                       ..G-TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-ST CS
                      E1-E2_ATPase  65 ..ekgdmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvfliall 139
                                         +    v+sG+ vv+g+ +av+ atg +te+gki r++e+ ksk+t lqk+ + l++ l++++l ++llv+++  +
  gi|330507762|ref|YP_004384190.1| 178 ggDDLPFVYSGSLVVQGQGVAVARATGINTEIGKIGRALEQVKSKETALQKETNLLVRNLALLGLGLCLLVVVAYGI 254
                                       9889999********************************************************************** PP

                                       TTSSTTHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 140 lgkslaeallralallvaaiPcaLplavplalalgarrlak 180
                                       +++++ + +l ++++++a++P+ +p+++++ lalga+r ++
  gi|330507762|ref|YP_004384190.1| 255 TRGNWLQGVLAGITTAMAVLPEEFPVVLTVFLALGAWRISQ 295
                                       *************************************9876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.45
                                       TTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT CS
                      E1-E2_ATPase  94 lgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla 145
                                       ++ i++++++ ++   +++k +  + ++ vp++ + ++ v+l ++l++ ++ 
  gi|330507762|ref|YP_004384190.1| 626 FSSIVKAIKSGRRIFDNIKKAMAYILAIHVPIAGISLIPVLLGWPLIFFPVH 677
                                       7889999999999999999999999999999999999999999988877665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.52
                                       HHHHHHHHHHHHHHHHS-STTTSSTT..HHH CS
                      E1-E2_ATPase 120 kvlvpvvlliallvflialllgksla..eal 148
                                       + l+++v+++a++   + l++g++ a  +al
  gi|330507762|ref|YP_004384190.1| 726 QGLSVLVIVMAVF--TVSLYRGQGEAeaRAL 754
                                       4455555555554..4444555444433333 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHH CS
                      E1-E2_ATPase 123 vpvvlliallvflialllgkslaeallralallv 156
                                       v+ + l++l+++++ ++l++   +a l+ +++++
  gi|330507762|ref|YP_004384190.1| 791 VVGGALVFLAMAIYVPFLREIFSFAYLHLIDIAI 824
                                       3333455555555555555555577777777776 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 !  117.4   7.2   2.5e-37   5.7e-34       1     182 []     670     842 ..     670     842 .. 0.95

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 2.5e-37
                   Cation_ATPase_C   1 plplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfg 77 
                                       pl++ ++++ +++L++D  +++a+  ep+e+d+m+rpPr++++pl+s++ l+ +l+qgl +++++++vf + l+  g
  gi|330507762|ref|YP_004384190.1| 670 PLIFFPVHVVFLELIIDPACSIAFEAEPEEADVMDRPPRDPNAPLFSSHALVLSLLQGLSVLVIVMAVFTVSLY-RG 745
                                       7899*****************************************************************99998.55 PP

                   Cation_ATPase_C  78 isekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgt 154
                                       + e e       a++++++tl++++++ +l+ rs ++++++ ++ + n+ l++++ ++l+++++ +yvp+l+++f++
  gi|330507762|ref|YP_004384190.1| 746 QGEAE-------ARALTYTTLIFANLALILANRSWTRTILETMS-TPNPALWWVVGGALVFLAMAIYVPFLREIFSF 814
                                       55545.......*****************************555.59****************************** PP

                   Cation_ATPase_C 155 aplsleewlialllalvvllvdelvKll 182
                                       a l l + +i+++ +++++l++e++K++
  gi|330507762|ref|YP_004384190.1| 815 AYLHLIDIAICFASGIASILWFEALKIF 842
                                       *************************987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1   0.0   1.8e-31     4e-28       3     210 .]     314     600 ..     312     600 .. 0.77

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 1.8e-31
                                       EEEEESBTTTBCHHHHHHHHHHHH.................................................CHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.................................................xxxx RF
                         Hydrolase   3 tvvfDkdGTLttgepsvedvivsa.................................................alal 30 
                                       +++ Dk+GTLt  ++ v+++++s                                                  +  +
  gi|330507762|ref|YP_004384190.1| 314 VLCTDKTGTLTLNRMKVKKIFASGqsvelddgrdnlpeaiheviefsilasqmdpfdpmekafkklgedylakTEHI 390
                                       7899********************99999999888866666655555555555555555555554433333333333 PP

                                       HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHH.....HCHHHHHHHHHHHHHHCHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  31 aaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewltal.....dippdlgaaigsaqsqgrtval 102
                                        +  e++ e p+ k+l a     + +  +  +      +a+g pe +++l     d +++l ++i++   +g  v  
  gi|330507762|ref|YP_004384190.1| 391 HRDWELVREYPLSKKLLAMSRVWRSSSGNEYV-----IAAKGAPEAIAELchidpDREKELSNNIQTMANEGMRVLG 462
                                       33333336666666665555555444444444.....89************77777778888888888888888888 PP

                                       H.................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT...... CS
                                       x.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                         Hydrolase 103 l.................qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG...... 156
                                       +                 + + l+++ ++dp  v+p++ ea+++  +agi+vv++tgd p ta+++a+q+G      
  gi|330507762|ref|YP_004384190.1| 463 VakasfqktdlpdgqhdfEFEFLGLIGMEDP--VRPGVPEAIKECYSAGIRVVMITGDYPGTAQAIARQIGlptdkv 537
                                       8*****99999999888877***********..**************************************999755 PP

                                       .....GGGESEEEEHHCES...........STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       .....xxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 157 .....ddyfdaviasdiet...........vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                                    a+  +            ++ + pe+k+++++ L++++e vam GDgvnDa+al+aA+
  gi|330507762|ref|YP_004384190.1| 538 itgpeL-------AILSDQelqekvrdiclFSRVVPEQKLRLVKALKANGEVVAMTGDGVNDAPALKAAD 600
                                       554332.......222222344456669999999***********************************8 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 !   38.4   0.0   3.2e-13   7.3e-10      13      68 ..       5      60 ..       1      61 [. 0.92

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 3.2e-13
                   Cation_ATPase_N 13 LetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalv 68
                                      ++     GLt+aeaa++lk+ G Nel+  k++s++++ ++ ++ p+ +lL++++lv
  gi|330507762|ref|YP_004384190.1|  5 FDIKTAGGLTEAEAAKLLKEVGYNELPSTKPRSAFAIAFEVVKEPMFLLLVAGGLV 60
                                      5555678*********************************************9997 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0083        19      20      55 ..     498     533 ..     487     540 .. 0.86
   2 !   22.1   0.3   4.6e-08    0.0001     194     255 .]     571     633 ..     569     633 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0083
                                       HHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                       Hydrolase_3  20 tkeaikklkekgikvviATGRslravlpvleelgld 55 
                                         eaik++ ++gi vv  TG  + +++ +++++gl 
  gi|330507762|ref|YP_004384190.1| 498 VPEAIKECYSAGIRVVMITGDYPGTAQAIARQIGLP 533
                                       569************************999999986 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 4.6e-08
                                       HHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEET.TS-HHHHHHSSEEE--GGGTHHHHHH CS
                       Hydrolase_3 194 klakelnisleeviafGDgeNDieMLeaaglgvAmg.naseevkkaAdyvtksnnedGVakal 255
                                       +l+k l+ + e v+  GDg ND + L+aa++g+Amg  +++ + + A+ v  + + ++++ka+
  gi|330507762|ref|YP_004384190.1| 571 RLVKALKANGEVVAMTGDGVNDAPALKAADIGIAMGgRGTDVARESASLVLLDDDFSSIVKAI 633
                                       58899******************************64899999*******9999999999987 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 !   27.0   0.0   1.5e-09   3.4e-06      22      88 ..     370     436 ..     369     438 .. 0.97

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.5e-09
                     Cation_ATPase  22 nktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilkrC 88 
                                       ++ E A  +l e+   +te + ++++ v+e+p +++   ms v + ++ +++++  KGApe i + C
  gi|330507762|ref|YP_004384190.1| 370 DPMEKAFKKLGEDYLAKTEHIHRDWELVREYPLSKKLLAMSRVWRSSSGNEYVIAAKGAPEAIAELC 436
                                       689**************************************************************99 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.8e-07   0.00063      87     188 .]     495     597 ..     382     597 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.8e-07
                               HAD  87 dpgalellaahraaGdrvvvvSgglrplvepllaelg..adevlat.elevdd......rltgelglegkpvrgegk 154
                                       +pg+ e+++++ +aG+rvv+++g +   +++++++ g   d v+   el+         ++     l+  +v  e+k
  gi|330507762|ref|YP_004384190.1| 495 RPGVPEAIKECYSAGIRVVMITGDYPGTAQAIARQIGlpTDKVITGpELAILSdqelqeKVRDI-CLFSRVV-PEQK 569
                                       477777777666*************************887777666555554444444433333.2333333.3577 PP

                               HAD 155 vaalrewlaaegegidleevvay.GDspsDlpllr 188
                                       ++ +++ l+a+g      evva  GD+++D p+l+
  gi|330507762|ref|YP_004384190.1| 570 LRLVKA-LKANG------EVVAMtGDGVNDAPALK 597
                                       777777.33333......277777*********96 PP

>> PhoR  Phosphate regulon sensor protein PhoR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.5e-05     0.055       9      63 ..      50     106 ..      46     117 .. 0.90
   2 ?   -3.8   4.6       7.8   1.8e+04       9      39 ..     242     272 ..     235     303 .. 0.68
   3 ?   -4.8   0.9         8   1.8e+04      13      20 ..     728     735 ..     718     743 .. 0.38
   4 ?   -1.5   0.9       1.6   3.5e+03      13      35 ..     784     804 ..     772     819 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                              PhoR   9 lallllaallvgllvgalaalll..lalllllawhlyqllrLsrWLrkpkklepPdg 63 
                                       ++lll+a  lv +l+g l+ +l+   ++l++++ ++yq ++ +r L++ ++++ P++
  gi|330507762|ref|YP_004384190.1|  50 MFLLLVAGGLVYFLLGDLQEALIlmGSVLVVMGITFYQERKTERALEALRDMSSPRA 106
                                       578888889************99777899999***************9999999986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.8
                              PhoR   9 lallllaallvgllvgalaallllallllla 39 
                                       l l+ll++++ g+  g++   +l+++  ++a
  gi|330507762|ref|YP_004384190.1| 242 LGLCLLVVVAYGITRGNWLQGVLAGITTAMA 272
                                       4455555557777777777777655554443 PP

  == domain 3  score: -4.8 bits;  conditional E-value: 8
                              PhoR  13 llaallvg 20 
                                       l ++++v+
  gi|330507762|ref|YP_004384190.1| 728 LSVLVIVM 735
                                       22222222 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.6
                              PhoR  13 llaallvgllvgalaallllall 35 
                                         +a  ++++vg    +l++a+ 
  gi|330507762|ref|YP_004384190.1| 784 PNPA--LWWVVGGALVFLAMAIY 804
                                       4455..67777766666654433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (852 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); 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: 0.76u 0.26s 00:00:01.02 Elapsed: 00:00:00.42
# Mc/sec: 6055.59
//
Query:       gi|330507763|ref|YP_004384191.1|  [L=140]
Description: hypothetical protein MCON_1765 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-35  121.9   0.0    1.5e-35  121.7   0.0    1.0  1  SnoaL     SnoaL-like polyketide cyclase
    6.2e-20   71.7   0.0    7.3e-20   71.5   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 !  121.7   0.0   1.7e-39   1.5e-35       2     126 .]       9     132 ..       8     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.7 bits;  conditional E-value: 1.7e-39
                                       HHHHHHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEE CS
                             SnoaL   2 lvlrfyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltft 78 
                                        vlrf+ee  ++gdl+a+del+a++++ h+p   +a G++g+ +++++ + af  l+v+ved+vae+dkvaar t++
  gi|330507763|ref|YP_004384191.1|   9 IVLRFFEEGPSKGDLRAADELLAPNFALHTPL-PSAPGIKGMNDVITACRSAFEHLNVTVEDMVAEEDKVAARFTAR 84 
                                       589**************************888.899***************************************** PP

                                       EEESSEBTTBE-TT-EEEEEEEEEEEEETTEEEEEEEEECHHHHHHHC CS
                             SnoaL  79 GthtgeflGipptGkkvkfeeitllrvedGkIveewdviDllgllrQl 126
                                       G h+g+f+++ ptGk++++++i+++r+e+GkI+e w+ ++llgl++Ql
  gi|330507763|ref|YP_004384191.1|  85 GIHKGAFMDLVPTGKSITMTGIEIFRIENGKIAELWGEANLLGLMQQL 132
                                       ***********************************************8 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   8.1e-24   7.3e-20       3     101 ..      12     118 ..      10     119 .. 0.94

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 8.1e-24
                                       HHHH.HHHTTCHHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEE.. CS
                           SnoaL_2   3 afla.alnagdldalaalfapdvvwedpggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgt.. 76 
                                       +f++   ++gdl a+++l+ap++ ++ p+++  G++++ + ++a + af++l+++++d+va++d+va+++t++g   
  gi|330507763|ref|YP_004384191.1|  12 RFFEeGPSKGDLRAADELLAPNFALHTPLPSAPGIKGMNDVITACRSAFEHLNVTVEDMVAEEDKVAARFTARGIhk 88 
                                       5665456799*******************9*******************************************99** PP

                                       .....EETTSSEEEEEEEEEEEEETTEEEE CS
                           SnoaL_2  77 .....ipatgrgvtvrgvdvfrvrdGkive 101
                                              +tg+ +t++g+++fr+++Gki+e
  gi|330507763|ref|YP_004384191.1|  89 gafmdLVPTGKSITMTGIEIFRIENGKIAE 118
                                       ****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1141.68
//
Query:       gi|330507764|ref|YP_004384192.1|  [L=318]
Description: TPR repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-38  127.9   0.2    2.4e-08   33.5   0.1    6.3  6  TPR_1      Tetratricopeptide repeat
    2.3e-36  120.9   0.3    2.1e-07   30.5   0.0    6.4  6  TPR_2      Tetratricopeptide repeat
    8.8e-30  100.4   4.3      1e-06   28.5   0.0    6.4  6  TPR_8      Tetratricopeptide repeat
    1.6e-28   98.1   5.0      1e-05   25.1   0.2    5.7  5  TPR_11     TPR repeat
      8e-27   91.7   0.2    0.00013   22.1   0.0    5.5  5  TPR_17     Tetratricopeptide repeat
    3.8e-22   78.6   0.0    1.1e-07   32.4   0.1    3.4  3  TPR_16     Tetratricopeptide repeat
    1.6e-18   66.8   2.7    2.8e-08   33.9   0.1    4.7  4  TPR_12     Tetratricopeptide repeat
    2.9e-18   66.1   0.0    2.2e-05   24.8   0.0    3.3  3  TPR_19     Tetratricopeptide repeat
      9e-15   54.1   0.7       0.11   13.4   0.0    6.0  6  TPR_14     Tetratricopeptide repeat
    1.6e-11   44.2   0.0     0.0082   16.3   0.0    3.7  4  TPR_9      Tetratricopeptide repeat
    2.1e-10   39.9   2.1     0.0029   17.5   0.0    5.3  5  TPR_7      Tetratricopeptide repeat
    6.2e-10   39.2   0.1     0.0054   16.9   0.0    3.3  3  ANAPC3     Anaphase-promoting complex, cyclosome, subunit 3
    1.2e-09   38.2   1.7       0.06   14.0   0.0    4.7  4  TPR_6      Tetratricopeptide repeat
    1.6e-09   37.3   3.9      0.042   13.7   0.1    4.9  5  TPR_10     Tetratricopeptide repeat
    5.9e-08   33.3   0.0     0.0089   16.5   0.0    3.0  3  BTAD       Bacterial transcriptional activator domain
    9.7e-08   32.2   0.3        1.6    8.8   0.0    4.8  4  DUF3856    Domain of Unknown Function (DUF3856)
    3.7e-05   24.0   0.5        5.3    8.0   0.0    3.9  3  TPR_4      Tetratricopeptide repeat
    0.00013   21.9   2.2          3    8.0   0.0    4.2  4  MIT        MIT (microtubule interacting and transport) domain
     0.0084   15.3   1.1        0.1   11.8   0.7    2.3  2  TPR_15     Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.017   15.1   0.5        2.6    8.2   0.0    4.0  4  TPR_3      Tetratricopeptide repeat
      0.049   13.9   0.0        3.5    7.9   0.0    2.9  3  NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
      0.071   12.0   0.2        9.4    5.0   0.0    2.4  2  NARP1      NMDA receptor-regulated protein 1
      0.099   12.9   0.3         45    4.6   0.1    4.2  4  PPR        PPR repeat
        0.3   10.6   2.4        8.3    6.0   0.0    3.6  5  SHNi-TPR   SHNi-TPR


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0062       4.6       2      34 .]      27      59 ..      26      59 .. 0.93
   2 !   26.5   0.0   4.9e-09   3.7e-06       1      34 []      60      93 ..      60      93 .. 0.93
   3 !   15.5   0.0   1.5e-05     0.011       1      34 []      94     127 ..      94     127 .. 0.97
   4 !   33.5   0.1   3.2e-11   2.4e-08       3      31 ..     130     158 ..     129     160 .. 0.94
   5 !   22.6   0.0   8.5e-08   6.3e-05       7      33 ..     168     194 ..     167     195 .. 0.95
   6 !   14.7   0.0   2.8e-05     0.021       2      24 ..     197     219 ..     196     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0062
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                      + +  +G+  + +g ++eA   ++ A +++P+n
  gi|330507764|ref|YP_004384192.1| 27 EYWLTKGAEEYVNGSLKEAFRSFDNATTVDPEN 59
                                      579999999**********************97 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 4.9e-09
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a +++ +G+a+  l++y+eA+  y+k ++++ +n
  gi|330507764|ref|YP_004384192.1| 60 ATVWFARGMALSGLKRYEEAISSYNKSIRIDDKN 93
                                      568***************************9776 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+++y ++    + g+ ++ l+ y++ L+++P+n
  gi|330507764|ref|YP_004384192.1|  94 ADVWYARATDESYIGRMNDSLASYDQSLQIDPEN 127
                                       799*****************************97 PP

  == domain 4  score: 33.5 bits;  conditional E-value: 3.2e-11
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                                       ++y +Gn +++lg+y+eA+ +y++A+ ++
  gi|330507764|ref|YP_004384192.1| 130 VWYDKGNSLQELGRYEEAITCYDQAILID 158
                                       7*************************998 PP

  == domain 5  score: 22.6 bits;  conditional E-value: 8.5e-08
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnPn 33 
                                       +G+a+ +lg+y+eAl+ +e+ + ++Pn
  gi|330507764|ref|YP_004384192.1| 168 KGYALGELGRYEEALQSFEESVDIYPN 194
                                       79************************9 PP

  == domain 6  score: 14.7 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHHHHTT-HHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyy 24 
                                       +++y++++a+++lg+ +eA+e+ 
  gi|330507764|ref|YP_004384192.1| 197 QSWYGKALALRSLGRTQEAEEAW 219
                                       68******************986 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0069       5.2       2      34 .]      27      59 ..      26      59 .. 0.95
   2 !   26.4   0.0     6e-09   4.5e-06       1      34 []      60      93 ..      60      93 .. 0.94
   3 !   13.6   0.0   7.5e-05     0.056       1      34 []      94     127 ..      94     127 .. 0.97
   4 !   30.5   0.0   2.8e-10   2.1e-07       3      33 ..     130     160 ..     129     161 .. 0.94
   5 !   23.3   0.0   5.7e-08   4.3e-05       4      33 ..     165     194 ..     162     195 .. 0.92
   6 !   11.8   0.1   0.00028      0.21       3      25 ..     198     220 ..     196     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0069
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPnn 34
                                      e++   G   y +g ++eA + f+ A   dP+n
  gi|330507764|ref|YP_004384192.1| 27 EYWLTKGAEEYVNGSLKEAFRSFDNATTVDPEN 59
                                      789999*************************97 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 6e-09
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      a +++++G+a+  l++yeeA+  ++k++++d +n
  gi|330507764|ref|YP_004384192.1| 60 ATVWFARGMALSGLKRYEEAISSYNKSIRIDDKN 93
                                      579***************************9876 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 7.5e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+++y+++    + g+ ++ l+ ++++l++dP+n
  gi|330507764|ref|YP_004384192.1|  94 ADVWYARATDESYIGRMNDSLASYDQSLQIDPEN 127
                                       789*****************************97 PP

  == domain 4  score: 30.5 bits;  conditional E-value: 2.8e-10
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       ++y  G+++ +lg+yeeA+ ++++A+ +d n
  gi|330507764|ref|YP_004384192.1| 130 VWYDKGNSLQELGRYEEAITCYDQAILIDGN 160
                                       7*************************99976 PP

  == domain 5  score: 23.3 bits;  conditional E-value: 5.7e-08
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                       +   G+a+ +lg+yeeAl+ fe+++ ++Pn
  gi|330507764|ref|YP_004384192.1| 165 WDSKGYALGELGRYEEALQSFEESVDIYPN 194
                                       6778*************************9 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 0.00028
                             TPR_2   3 alynlGlayyklgdyeeAleafe 25 
                                        +y  +la++ lg+ +eA+ea+ 
  gi|330507764|ref|YP_004384192.1| 198 SWYGKALALRSLGRTQEAEEAWS 220
                                       7*******************985 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.44   3.3e+02      15      34 .]      40      59 ..      26      59 .. 0.86
   2 !   28.5   0.0   1.4e-09     1e-06       1      34 []      60      93 ..      60      93 .. 0.94
   3 ?    6.2   0.0     0.019        14      12      34 .]     105     127 ..      94     127 .. 0.81
   4 !   26.6   0.1   5.6e-09   4.2e-06       3      32 ..     130     159 ..     130     160 .. 0.94
   5 !   22.0   0.0   1.6e-07   0.00012       4      33 ..     165     194 ..     162     195 .. 0.92
   6 !   11.1   0.1   0.00049      0.37       2      23 ..     197     218 ..     196     218 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.44
                                      T-HHHHHHHHHHHHHHHHH. CS
                             TPR_8 15 gdyeeAkeyyekaleldpdn 34
                                      g ++eA  ++  a++ dp+n
  gi|330507764|ref|YP_004384192.1| 40 GSLKEAFRSFDNATTVDPEN 59
                                      8899**************86 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 1.4e-09
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      a +++  g++++ l++yeeA+++y+k +++d +n
  gi|330507764|ref|YP_004384192.1| 60 ATVWFARGMALSGLKRYEEAISSYNKSIRIDDKN 93
                                      579***************************9875 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.019
                                       HHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  12 lklgdyeeAkeyyekaleldpdn 34 
                                       +  g+++ + ++y + l++dp+n
  gi|330507764|ref|YP_004384192.1| 105 SYIGRMNDSLASYDQSLQIDPEN 127
                                       56799****************86 PP

  == domain 4  score: 26.6 bits;  conditional E-value: 5.6e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ++y +g+ +++lg+yeeA+ +y +a+ +d 
  gi|330507764|ref|YP_004384192.1| 130 VWYDKGNSLQELGRYEEAITCYDQAILIDG 159
                                       6*************************9985 PP

  == domain 5  score: 22.0 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +  +g+++ +lg+yeeA +++e+ +++ p+
  gi|330507764|ref|YP_004384192.1| 165 WDSKGYALGELGRYEEALQSFEESVDIYPN 194
                                       7789************************98 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.00049
                                       CHHHHHHHHHHHTT-HHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkey 23 
                                       +++y +++++++lg+ +eA+e+
  gi|330507764|ref|YP_004384192.1| 197 QSWYGKALALRSLGRTQEAEEA 218
                                       79*****************985 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.9e-06    0.0029       4      38 ..      36      70 ..      33      73 .. 0.90
   2 !   25.1   0.2   1.4e-08     1e-05       9      35 ..      75     101 ..      73     102 .. 0.94
   3 !   17.0   0.0   4.6e-06    0.0035       8      42 .]     108     142 ..     106     142 .. 0.95
   4 !   22.9   0.2   6.9e-08   5.1e-05       1      24 [.     135     158 ..     135     160 .. 0.92
   5 !   18.5   0.1   1.6e-06    0.0012       1      40 [.     169     208 ..     169     210 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.9e-06
                            TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                                       y  G ++eA  ++ +A   dP+na++++++G a+
  gi|330507764|ref|YP_004384192.1| 36 EYVNGSLKEAFRSFDNATTVDPENATVWFARGMAL 70
                                      6778****************************775 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.4e-08
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLG 35 
                                       +yeeAi +Y+k +++d +na+++y+++
  gi|330507764|ref|YP_004384192.1|  75 RYEEAISSYNKSIRIDDKNADVWYARA 101
                                       8***********************986 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 4.6e-06
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+ ++++++Y + l++dP+n  ++y  G+ ++++G
  gi|330507764|ref|YP_004384192.1| 108 GRMNDSLASYDQSLQIDPENKFVWYDKGNSLQELG 142
                                       88999**************************9998 PP

  == domain 4  score: 22.9 bits;  conditional E-value: 6.9e-08
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkld 24 
                                       G+ + e+G+yeeAi++Y +A+ +d
  gi|330507764|ref|YP_004384192.1| 135 GNSLQELGRYEEAITCYDQAILID 158
                                       89999****************777 PP

  == domain 5  score: 18.5 bits;  conditional E-value: 1.6e-06
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       G+a+ e+G+yeeA++++++ +++ P++   +y+ +la+  
  gi|330507764|ref|YP_004384192.1| 169 GYALGELGRYEEALQSFEESVDIYPNSSQSWYGKALALRS 208
                                       788889***************************9999855 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.7e-05     0.012       2      33 ..      49      80 ..      48      81 .. 0.92
   2 !   12.9   0.0   0.00015      0.11       2      21 ..      83     102 ..      82     102 .. 0.95
   3 !   19.2   0.0   1.4e-06    0.0011       2      33 ..     117     148 ..     116     149 .. 0.97
   4 !   14.9   0.0   3.4e-05     0.026       1      34 []     150     183 ..     150     183 .. 0.98
   5 !   22.1   0.0   1.8e-07   0.00013       2      34 .]     185     217 ..     184     217 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-05
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      + +a   dP na +++ ++ +l+ ++++++A+
  gi|330507764|ref|YP_004384192.1| 49 FDNATTVDPENATVWFARGMALSGLKRYEEAI 80
                                      5678889***********************97 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00015
                            TPR_17   2 ylkaleldPnnadaynnLAe 21 
                                       y k++++d +nad+++ +A+
  gi|330507764|ref|YP_004384192.1|  83 YNKSIRIDDKNADVWYARAT 102
                                       99***************996 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 1.4e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y ++l++dP n  +++ +++ l ++G++++A+
  gi|330507764|ref|YP_004384192.1| 117 YDQSLQIDPENKFVWYDKGNSLQELGRYEEAI 148
                                       99****************************97 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 3.4e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a+ +d n + ++  ++++l ++G++++A+q
  gi|330507764|ref|YP_004384192.1| 150 CYDQAILIDGNWSRPWDSKGYALGELGRYEEALQ 183
                                       8*******************************97 PP

  == domain 5  score: 22.1 bits;  conditional E-value: 1.8e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       ++++++++Pn++ +++ +A +l+++G++++A++
  gi|330507764|ref|YP_004384192.1| 185 FEESVDIYPNSSQSWYGKALALRSLGRTQEAEE 217
                                       799****************************96 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   2.8e-08   2.1e-05       3      66 ..      32      92 ..      30      94 .. 0.89
   2 !   17.1   0.0   8.6e-06    0.0064       1      60 [.      98     154 ..      98     162 .. 0.85
   3 !   32.4   0.1   1.4e-10   1.1e-07       3      56 ..     168     219 ..     167     224 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.8e-08
                            TPR_16  3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66
                                      ++ + + +g   +A + ++ a+  d   P++a  ++++g a+  ++r++eA+  y++ +r + +
  gi|330507764|ref|YP_004384192.1| 32 KGAEEYVNGSLKEAFRSFDNATTVD---PENATVWFARGMALSGLKRYEEAISSYNKSIRIDDK 92
                                      567788999999999**********...************************999888877665 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 8.6e-06
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                       +a+a++  + g+  d +a +++ l  d   P++   ++ +g+++ ++gr++eA+  y+ a
  gi|330507764|ref|YP_004384192.1|  98 YARATDESYIGRMNDSLASYDQSLQID---PENKFVWYDKGNSLQELGRYEEAITCYDQA 154
                                       788899999999999999999999999...888889999999999999999999777665 PP

  == domain 3  score: 32.4 bits;  conditional E-value: 1.4e-10
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.al 56 
                                       +++a+ ++g+y++A+  +e+ ++ +   P   ++++++++a+  +gr +eA+ a+
  gi|330507764|ref|YP_004384192.1| 168 KGYALGELGRYEEALQSFEESVDIY---PNSSQSWYGKALALRSLGRTQEAEeAW 219
                                       68999********************...99999*******************666 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-05     0.009      42      76 ..      57      91 ..      34      92 .. 0.84
   2 ?    5.1   0.0     0.038        28       4      32 ..      95     123 ..      93     129 .. 0.81
   3 !   33.9   0.1   3.8e-11   2.8e-08       6      76 ..     131     193 ..     129     194 .. 0.94
   4 !   23.3   0.2   7.6e-08   5.7e-05      10      66 ..     169     217 ..     162     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                            TPR_12 42 pltattlrnLgrlyralgryeeAlelleealaiae 76
                                      p+ at+ ++ g++++ l+ryeeA++ ++++++i+ 
  gi|330507764|ref|YP_004384192.1| 57 PENATVWFARGMALSGLKRYEEAISSYNKSIRIDD 91
                                      566999999*********************99975 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.038
                            TPR_12   4 talnnlaavlrrlgrydeAlellekalei 32 
                                        +++ +a+ + + gr+ ++l+ ++++l+i
  gi|330507764|ref|YP_004384192.1|  95 DVWYARATDESYIGRMNDSLASYDQSLQI 123
                                       56778888888999999999999999998 PP

  == domain 3  score: 33.9 bits;  conditional E-value: 3.8e-11
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       ++  ++ l++lgry+eA++++++a+ i      +++   ++     g ++ +lgryeeAl+ +ee+++i++
  gi|330507764|ref|YP_004384192.1| 131 WYDKGNSLQELGRYEEAITCYDQAILID-----GNW---SRPWDSKGYALGELGRYEEALQSFEESVDIYP 193
                                       56789*******************9999.....888...8999**************************97 PP

  == domain 4  score: 23.3 bits;  conditional E-value: 7.6e-08
                            TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAle 66 
                                       + +l +lgry+eAl+ +e++++i+     p++   +++ ++ + ++r lgr++eA+e
  gi|330507764|ref|YP_004384192.1| 169 GYALGELGRYEEALQSFEESVDIY-----PNS---SQSWYGKALALRSLGRTQEAEE 217
                                       667889******************.....553...5566666666666666666655 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.8e-06    0.0036       4      66 ..      39     101 ..      37     102 .. 0.95
   2 !   19.6   0.0   1.3e-06   0.00099      11      60 ..     114     163 ..     108     169 .. 0.90
   3 !   24.8   0.0     3e-08   2.2e-05       5      50 ..     176     221 ..     174     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.8e-06
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66 
                                       +g + eA + + +a + dp+na ++ +   al  l++++eA+   ++  + d ++a+++ ++A
  gi|330507764|ref|YP_004384192.1|  39 NGSLKEAFRSFDNATTVDPENATVWFARGMALSGLKRYEEAISSYNKSIRIDDKNADVWYARA 101
                                       6999*************************************************9999998776 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.3e-06
                            TPR_19  11 lalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                       la + q lq dp+n  ++++  + l +lg+++eA+ + d++ + d +++r
  gi|330507764|ref|YP_004384192.1| 114 LASYDQSLQIDPENKFVWYDKGNSLQELGRYEEAITCYDQAILIDGNWSR 163
                                       77899***************************************999876 PP

  == domain 3  score: 24.8 bits;  conditional E-value: 3e-08
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLda 50 
                                       g+y+eAl+ +e+  + +p+++  +++ A al +lg+++eAe++ ++
  gi|330507764|ref|YP_004384192.1| 176 GRYEEALQSFEESVDIYPNSSQSWYGKALALRSLGRTQEAEEAWST 221
                                       9****************************************97555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0013      0.96       8      41 ..      33      66 ..      26      69 .. 0.83
   2 !   13.4   0.0   0.00015      0.11       4      42 ..      63     101 ..      62     103 .. 0.94
   3 ?    1.1   0.0       1.3   9.4e+02      19      39 ..     112     132 ..     107     135 .. 0.83
   4 !   11.2   0.0   0.00075      0.56       4      30 ..     131     157 ..     128     170 .. 0.88
   5 !   12.2   0.0   0.00035      0.26       8      40 ..     169     201 ..     162     204 .. 0.84
   6 ?    5.1   0.2     0.066        49       3      24 ..     198     219 ..     196     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                            TPR_14  8 aeallalGdpdeAiallrralalaPddaeawlll 41
                                      ++ ++ +G ++eA + ++ a   +P++a++w++ 
  gi|330507764|ref|YP_004384192.1| 33 GAEEYVNGSLKEAFRSFDNATTVDPENATVWFAR 66
                                      555566899**********************975 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00015
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       + a++ al  l +++eAi  +++ ++ + ++a++w++ a
  gi|330507764|ref|YP_004384192.1|  63 WFARGMALSGLKRYEEAISSYNKSIRIDDKNADVWYARA 101
                                       8999*******************************9877 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.3
                            TPR_14  19 eAiallrralalaPddaeawl 39 
                                       +++a +++ l+ +P++  +w+
  gi|330507764|ref|YP_004384192.1| 112 DSLASYDQSLQIDPENKFVWY 132
                                       67899**********988876 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00075
                            TPR_14   4 llalaeallalGdpdeAiallrralal 30 
                                       +++ +  l +lG+++eAi+++++a+  
  gi|330507764|ref|YP_004384192.1| 131 WYDKGNSLQELGRYEEAITCYDQAILI 157
                                       9999*******************9865 PP

  == domain 5  score: 12.2 bits;  conditional E-value: 0.00035
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawll 40 
                                       + al +lG+++eA++ +++ ++ +P++ + w+ 
  gi|330507764|ref|YP_004384192.1| 169 GYALGELGRYEEALQSFEESVDIYPNSSQSWYG 201
                                       677889********************9887765 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.066
                            TPR_14   3 allalaeallalGdpdeAiall 24 
                                        ++  a al+ lG+++eA+++ 
  gi|330507764|ref|YP_004384192.1| 198 SWYGKALALRSLGRTQEAEEAW 219
                                       5888999***********9985 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00019      0.14      13      65 ..      44      96 ..      38     102 .. 0.86
   2 !   16.3   0.0   1.1e-05    0.0082      14      59 ..     113     158 ..     108     167 .. 0.90
   3 !   12.9   0.0   0.00013     0.094      12      63 ..     145     196 ..     145     198 .. 0.93
   4 !   10.9   0.1   0.00052      0.39      10      56 ..     177     223 ..     174     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                             TPR_9 13 ralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                                      +a +  +    ++P+ +  ++ RG++l  l ++++A+   +  ++++++++d+
  gi|330507764|ref|YP_004384192.1| 44 EAFRSFDNATTVDPENATVWFARGMALSGLKRYEEAISSYNKSIRIDDKNADV 96
                                      67788889999***************************999988888877775 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.1e-05
                             TPR_9  14 alavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                        la ++  l+++P+    ++d G  l++lG++++A+ + ++++ ++
  gi|330507764|ref|YP_004384192.1| 113 SLASYDQSLQIDPENKFVWYDKGNSLQELGRYEEAITCYDQAILID 158
                                       68999**********************************9998765 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00013
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       e+a+ +++  +l++ +  + +   G +l +lG++++Al+ +e  +++ p+  
  gi|330507764|ref|YP_004384192.1| 145 EEAITCYDQAILIDGNWSRPWDSKGYALGELGRYEEALQSFEESVDIYPNSS 196
                                       5799***************************************999999765 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00052
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl 56 
                                       ++e+al+  e  + + P++ + ++  +l+l  lG++++A ++  +y 
  gi|330507764|ref|YP_004384192.1| 177 RYEEALQSFEESVDIYPNSSQSWYGKALALRSLGRTQEAEEAWSTYR 223
                                       7899***********************************99877775 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.016        12       5      30 ..      66      91 ..      62      96 .. 0.77
   2 ?   -0.7   0.0       2.6     2e+03      13      29 ..     108     124 ..     105     128 .. 0.81
   3 !   17.5   0.0   3.9e-06    0.0029       6      28 ..     135     155 ..     130     160 .. 0.84
   4 !    7.3   0.0    0.0071       5.3       8      25 ..     171     188 ..     165     195 .. 0.84
   5 ?    3.3   0.1      0.13        97       6      20 ..     203     217 ..     198     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.016
                             TPR_7  5 LarlysrlGdyeeAielyeqsLaltk 30
                                       + + s l +yeeAi+ y +s+++++
  gi|330507764|ref|YP_004384192.1| 66 RGMALSGLKRYEEAISSYNKSIRIDD 91
                                      5667777889*********9877765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.6
                             TPR_7  13 GdyeeAielyeqsLalt 29 
                                       G++ + +  y qsL+++
  gi|330507764|ref|YP_004384192.1| 108 GRMNDSLASYDQSLQID 124
                                       788899999***99887 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 3.9e-06
                             TPR_7   6 arlysrlGdyeeAielyeqsLal 28 
                                       ++  ++lG+yeeAi++y q  a+
  gi|330507764|ref|YP_004384192.1| 135 GNSLQELGRYEEAITCYDQ--AI 155
                                       78899**************..54 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0071
                             TPR_7   8 lysrlGdyeeAielyeqs 25 
                                       +  +lG+yeeA++ +e+s
  gi|330507764|ref|YP_004384192.1| 171 ALGELGRYEEALQSFEES 188
                                       66689***********95 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.13
                             TPR_7   6 arlysrlGdyeeAie 20 
                                       a + ++lG+++eA+e
  gi|330507764|ref|YP_004384192.1| 203 ALALRSLGRTQEAEE 217
                                       78999********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 !    7.7   0.0    0.0054       4.1      34      81 ..      37      85 ..      28      86 .. 0.89
   2 !   10.7   0.0   0.00063      0.47      49      80 ..     120     152 ..     108     154 .. 0.85
   3 !   16.9   0.0   7.2e-06    0.0054      30      78 ..     169     218 ..     167     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0054
                                      HHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3 34 ylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                      y ng  k+A++ +++a   ++++  +++  + +l  Lk+yeeAi+ + k
  gi|330507764|ref|YP_004384192.1| 37 YVNGSLKEAFRSFDNAtTVDPENATVWFARGMALSGLKRYEEAISSYNK 85
                                      6689999*********9999999999999999************98765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00063
                                       T.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  49 a.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       + +++++++ ++y ++ +l +L++yeeAi++++
  gi|330507764|ref|YP_004384192.1| 120 SlQIDPENKFVWYDKGNSLQELGRYEEAITCYD 152
                                       44678899999*******************987 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 7.2e-06
                                       HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       +++l ++g+y++A++ ++++ +++++s +++y +A +l  L++ +eA+ a
  gi|330507764|ref|YP_004384192.1| 169 GYALGELGRYEEALQSFEESvDIYPNSSQSWYGKALALRSLGRTQEAEEA 218
                                       6778889****************************************986 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.13     1e+02       4      25 ..      64      85 ..      61      90 .. 0.84
   2 !    9.6   0.0    0.0021       1.5       4      27 ..     132     155 ..     129     157 .. 0.88
   3 !   14.0   0.0     8e-05      0.06       7      33 .]     169     195 ..     168     195 .. 0.93
   4 ?    6.2   0.1     0.025        18       2      25 ..     198     221 ..     197     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.13
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  4 yklalsyrklgdtdkAlealer 25
                                      + +++++  l+++++A+  +++
  gi|330507764|ref|YP_004384192.1| 64 FARGMALSGLKRYEEAISSYNK 85
                                      67899999999*******9997 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   4 yklalsyrklgdtdkAlealerli 27 
                                       y  + s+++lg++++A++ +++ i
  gi|330507764|ref|YP_004384192.1| 132 YDKGNSLQELGRYEEAITCYDQAI 155
                                       667999***99*********9987 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 8e-05
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPdS 33 
                                       ++++ +lg++++Al+ +e+ ++ YP+S
  gi|330507764|ref|YP_004384192.1| 169 GYALGELGRYEEALQSFEESVDIYPNS 195
                                       67888999******************9 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealer 25 
                                       + y  al++r+lg+t++A ea+  
  gi|330507764|ref|YP_004384192.1| 198 SWYGKALALRSLGRTQEAEEAWST 221
                                       67999******99*****998765 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.051        38       9      30 ..      67      88 ..      66      89 .. 0.84
   2 ?   -2.9   0.0       9.4     7e+03      16      31 ..     108     123 ..     105     123 .. 0.79
   3 !   10.7   0.0   0.00049      0.37       9      29 ..     135     155 ..     133     157 .. 0.93
   4 !   13.7   0.1   5.7e-05     0.042       9      32 ..     169     192 ..     168     192 .. 0.94
   5 ?    5.6   0.1      0.02        15       9      23 ..     203     217 ..     202     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.051
                            TPR_10  9 analrqrgrydeAealleeala 30
                                      ++al+ ++ry+eA   + ++++
  gi|330507764|ref|YP_004384192.1| 67 GMALSGLKRYEEAISSYNKSIR 88
                                      89***********887777766 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.4
                            TPR_10  16 grydeAealleealai 31 
                                       gr ++++a ++++l+i
  gi|330507764|ref|YP_004384192.1| 108 GRMNDSLASYDQSLQI 123
                                       7778888889999886 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00049
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       +n l+++gry+eA   +++a+
  gi|330507764|ref|YP_004384192.1| 135 GNSLQELGRYEEAITCYDQAI 155
                                       899*****************8 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 5.7e-05
                            TPR_10   9 analrqrgrydeAealleealair 32 
                                       + al ++gry+eA++ +ee+++i+
  gi|330507764|ref|YP_004384192.1| 169 GYALGELGRYEEALQSFEESVDIY 192
                                       67999****************998 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.02
                            TPR_10   9 analrqrgrydeAea 23 
                                       a alr++gr +eAe+
  gi|330507764|ref|YP_004384192.1| 203 ALALRSLGRTQEAEE 217
                                       789**********97 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.071        53      73     122 ..      37      86 ..      29      96 .. 0.88
   2 !   10.4   0.0    0.0009      0.67      54     122 ..      86     154 ..      66     157 .. 0.81
   3 !   16.5   0.0   1.2e-05    0.0089      73     125 ..     173     225 ..     167     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.071
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                          G  +ea +  +++++ +P + + + +   Al  + r +eA+  Y++ 
  gi|330507764|ref|YP_004384192.1|  37 YVNGSLKEAFRSFDNATTVDPENATVWFARGMALSGLKRYEEAISSYNKS 86 
                                       55688899999************************************975 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0009
                                       HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  54 rerleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                         r++++  ++  a+a  e+++Gr ++ la +++ ++ +P +   +      l  +Gr +eA++ Y+++
  gi|330507764|ref|YP_004384192.1|  86 SIRIDDKNADVWYARATDESYIGRMNDSLASYDQSLQIDPENKFVWYDKGNSLQELGRYEEAITCYDQA 154
                                       4477788888889999999********************************************999875 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.2e-05
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                        +lGr+eeal+  e+ v+ +P   +++    +Al+ +Gr++eA e++ ++r+l
  gi|330507764|ref|YP_004384192.1| 173 GELGRYEEALQSFEESVDIYPNSSQSWYGKALALRSLGRTQEAEEAWSTYRDL 225
                                       589*********************************************99987 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0037       2.8      95     127 ..      59      87 ..      33     100 .. 0.71
   2 !    6.8   0.0    0.0089       6.7     104     126 ..     132     154 ..     105     159 .. 0.89
   3 !    8.8   0.0    0.0021       1.6     103     128 ..     165     190 ..     158     196 .. 0.80
   4 ?    2.4   0.0       0.2   1.5e+02     104     124 ..     200     220 ..     196     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0037
                                       HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  95 eGklWiaavfsravaleelGrkdealkafrmag 127
                                       +   W    f r++al++l r++ea+ +++++ 
  gi|330507764|ref|YP_004384192.1|  59 NATVW----FARGMALSGLKRYEEAISSYNKSI 87 
                                       54444....679999999999999999998865 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0089
                                       HHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrma 126
                                       ++++ +l+elGr++ea+  + +a
  gi|330507764|ref|YP_004384192.1| 132 YDKGNSLQELGRYEEAITCYDQA 154
                                       789999**********9999876 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 103 vfsravaleelGrkdealkafrmage 128
                                         s++ al elGr++eal++f+ +++
  gi|330507764|ref|YP_004384192.1| 165 WDSKGYALGELGRYEEALQSFEESVD 190
                                       56899999999999999999987665 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.2
                                       HHHHHHHHHTT-HHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafr 124
                                       + +a al +lGr++ea +a+ 
  gi|330507764|ref|YP_004384192.1| 200 YGKALALRSLGRTQEAEEAWS 220
                                       6799*********99987765 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.049        37       7      24 ..     134     151 ..     130     153 .. 0.78
   2 !    8.0   0.0     0.007       5.3       8      26 .]     169     187 ..     167     187 .. 0.86
   3 ?    6.2   0.1     0.027        20       5      24 ..     200     219 ..     196     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.049
                             TPR_4   7 LArallalGdldeArall 24 
                                        +  l++lG+++eA +  
  gi|330507764|ref|YP_004384192.1| 134 KGNSLQELGRYEEAITCY 151
                                       57889*********7665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.007
                             TPR_4   8 ArallalGdldeAraller 26 
                                       + al +lG+++eA++ +e+
  gi|330507764|ref|YP_004384192.1| 169 GYALGELGRYEEALQSFEE 187
                                       57999*********98775 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.027
                             TPR_4   5 laLArallalGdldeArall 24 
                                       ++ A al  lG+  eA++++
  gi|330507764|ref|YP_004384192.1| 200 YGKALALRSLGRTQEAEEAW 219
                                       67899************976 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 ?   -1.6   0.0       3.9   2.9e+03      12      30 ..      34      52 ..      30      54 .. 0.75
   2 ?    5.7   0.0      0.02        15      18      32 ..      74      88 ..      68      89 .. 0.90
   3 !    8.0   0.0     0.004         3      17      31 ..     141     155 ..     135     157 .. 0.89
   4 ?    4.5   0.1     0.049        37      17      32 ..     175     190 ..     168     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.9
                               MIT 12 veeDnagnyeeAlelYkea 30
                                      +ee  +g  +eA++ + +a
  gi|330507764|ref|YP_004384192.1| 34 AEEYVNGSLKEAFRSFDNA 52
                                      5566688899999998887 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                               MIT 18 gnyeeAlelYkeale 32
                                      + yeeA++ Y ++++
  gi|330507764|ref|YP_004384192.1| 74 KRYEEAISSYNKSIR 88
                                      78**********986 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.004
                               MIT  17 agnyeeAlelYkeal 31 
                                        g yeeA+ +Y +a+
  gi|330507764|ref|YP_004384192.1| 141 LGRYEEAITCYDQAI 155
                                       689***********8 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.049
                               MIT  17 agnyeeAlelYkeale 32 
                                        g yeeAl+ ++e+++
  gi|330507764|ref|YP_004384192.1| 175 LGRYEEALQSFEESVD 190
                                       689**********998 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.04        30     131     181 ..      40      95 ..      25      99 .. 0.54
   2 !   11.8   0.7   0.00014       0.1     144     268 ..      92     216 ..      70     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.04
                            TPR_15 131 ellksle....eeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsse 181
                                         lk++     +  ++  ++a++++ar+ + +   + ++A+  y + ++ ++++++
  gi|330507764|ref|YP_004384192.1|  40 GSLKEAFrsfdNATTVDpENATVWFARGMALSGLKRYEEAISSYNKSIRIDDKNAD 95 
                                       33444331110222233566667777777777777777777666666666666554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00014
                            TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLw 217
                                       ++a +++ara  ++  g+ +++l  y + l+ +p+++ +       l +lgr++e   ++  + ++     + ++ w
  gi|330507764|ref|YP_004384192.1|  92 KNADVWYARATDESYIGRMNDSLASYDQSLQIDPENKFVWYDKGNSLQELGRYEE---AITCYDQAIlidGNWSRPW 165
                                       7788999999999999999999999999999999988777777778999999996...9999998887766677778 PP

                            TPR_15 218 gplaaAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAw 268
                                          + Al  Lgr+++AL+ ++   +  +++       A al   gr++eA+
  gi|330507764|ref|YP_004384192.1| 166 DSKGYALGELGRYEEALQSFEESVDIYPNSSQSWYGKALALRSLGRTQEAE 216
                                       888999999999999999999998888888777777777777777776665 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.3   9.6e+02      15      26 ..      74      83 ..      73      93 .. 0.72
   2 ?    8.2   0.0    0.0034       2.6       9      29 ..     136     154 ..     131     159 .. 0.80
   3 ?    0.2   0.0       1.1   8.2e+02      14      23 ..     175     184 ..     169     186 .. 0.79
   4 ?   -0.1   0.0       1.3   9.9e+02       4      25 ..     199     220 ..     196     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.3
                                      T-HHHHHHH..H CS
                             TPR_3 15 kkyqeArelfsY 26
                                      k+y+eA+    Y
  gi|330507764|ref|YP_004384192.1| 74 KRYEEAISS--Y 83
                                      99****987..4 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0034
                                       HHHHHTT-HHHHHHH..HHHH CS
                             TPR_3   9 aefynkkkyqeArelfsYall 29 
                                        +++  ++y+eA+  ++  ++
  gi|330507764|ref|YP_004384192.1| 136 NSLQELGRYEEAITCYD--QA 154
                                       5799***********77..87 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.1
                                       TT-HHHHHHH CS
                             TPR_3  14 kkkyqeArel 23 
                                        ++y+eA++ 
  gi|330507764|ref|YP_004384192.1| 175 LGRYEEALQS 184
                                       69*****987 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHTT-HHHHHHH.. CS
                             TPR_3   4 lysyAaefynkkkyqeArelfs 25 
                                       +y+ A ++ + ++ qeA+e+ s
  gi|330507764|ref|YP_004384192.1| 199 WYGKALALRSLGRTQEAEEAWS 220
                                       77777777788999***99976 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.32   2.4e+02      22      34 ..      74      86 ..      65      92 .. 0.83
   2 ?    7.9   0.0    0.0046       3.5      16      34 ..     136     154 ..     132     163 .. 0.83
   3 ?   -1.3   0.0       3.6   2.7e+03      21      32 ..     175     186 ..     167     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.32
                         NRBF2_MIT 22 Gkyeeaischkka 34
                                       +yeeais ++k+
  gi|330507764|ref|YP_004384192.1| 74 KRYEEAISSYNKS 86
                                      58******99996 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0046
                         NRBF2_MIT  16 drllaaGkyeeaischkka 34 
                                       + l   G+yeeai+c+ +a
  gi|330507764|ref|YP_004384192.1| 136 NSLQELGRYEEAITCYDQA 154
                                       566778*********9987 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.6
                         NRBF2_MIT  21 aGkyeeaischk 32 
                                        G+yeea+   +
  gi|330507764|ref|YP_004384192.1| 175 LGRYEEALQSFE 186
                                       599***997665 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.015        11     182     262 ..      52     130 ..      29     150 .. 0.78
   2 ?    5.0   0.0     0.013       9.4      16     253 ..     174     223 ..     165     286 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                                       SS----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT CS
                             NARP1 182 dsekepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDla 258
                                        ++ +pe+a +w    +A     l+++e+A++  +k i+ +++  ++++++a+     G +++  +  +++ ++D +
  gi|330507764|ref|YP_004384192.1|  52 ATTVDPENATVWFARGMA--LSGLKRYEEAISSYNKSIRIDDKNADVWYARATDESYIGRMNDSLASYDQSLQIDPE 126
                                       335666777667666555..56799999************************9999999999999999999999999 PP

                                       -HHH CS
                             NARP1 259 DRyi 262
                                        +++
  gi|330507764|ref|YP_004384192.1| 127 NKFV 130
                                       8887 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.013
                                       HHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHH CS
                             NARP1  16 eagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeal 92 
                                       e                                                                            
  gi|330507764|ref|YP_004384192.1| 174 E---------------------------------------------------------------------------- 174
                                       3............................................................................ PP

                                       HHHHHHTTTS-TT-SHHHHTHHHH--HHHHHHHHHHHHHHHHHCT-TTHHHHHGGGGGGSCHHHHHHHHHHHHHTTT CS
                             NARP1  93 lalydelaekyprsdaprRlpLdfleGeeFkelvdkYlrkaLrkgvPslfanlksLYedkeKvkileelvegyvksl 169
                                                                                                                    
  gi|330507764|ref|YP_004384192.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       TTSSSSTTGG.GSS----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                             NARP1 170 ktsgklsesdnedsekepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAa 246
                                                                          lg++e+Al+  ++ ++  p++ + ++ Ka  l+  G  ++A 
  gi|330507764|ref|YP_004384192.1| 175 -----------------------------------LGRYEEALQSFEESVDIYPNSSQSWYGKALALRSLGRTQEAE 216
                                       ...................................444555555555555555555555555555555555555555 PP

                                       HHHHHHH CS
                             NARP1 247 evmeear 253
                                       e+  + r
  gi|330507764|ref|YP_004384192.1| 217 EAWSTYR 223
                                       5444444 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       4.8   3.5e+03      11      24 ..      71      84 ..      68      88 .. 0.71
   2 ?    1.7   0.0      0.49   3.7e+02      13      25 ..     141     153 ..     136     155 .. 0.85
   3 ?    4.6   0.1      0.06        45       9      25 ..     171     187 ..     170     190 .. 0.88
   4 ?   -0.2   0.0         2   1.5e+03       9      22 ..     208     221 ..     205     226 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.8
                               PPR 11 cknGkleeAlelfk 24
                                      +   ++eeA++ ++
  gi|330507764|ref|YP_004384192.1| 71 SGLKRYEEAISSYN 84
                                      55678999988665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.49
                               PPR  13 nGkleeAlelfke 25 
                                        G++eeA+ ++++
  gi|330507764|ref|YP_004384192.1| 141 LGRYEEAITCYDQ 153
                                       79******99985 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.06
                               PPR   9 gycknGkleeAlelfke 25 
                                       +++  G++eeAl+ f+e
  gi|330507764|ref|YP_004384192.1| 171 ALGELGRYEEALQSFEE 187
                                       68899*******99988 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2
                               PPR   9 gycknGkleeAlel 22 
                                       ++++  + eeA + 
  gi|330507764|ref|YP_004384192.1| 208 SLGRTQEAEEAWST 221
                                       45555555555555 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1        10   7.4e+03       3      11 ..      16      24 ..      16      24 .. 0.85
   2 ?    1.6   0.0      0.26   1.9e+02      16      30 ..      75      89 ..      74      93 .. 0.89
   3 ?   -0.6   0.0       1.3   9.5e+02      13      25 ..     140     152 ..     139     156 .. 0.73
   4 ?    6.0   0.0     0.011       8.3      15      31 ..     176     192 ..     172     195 .. 0.90
   5 ?   -2.7   0.0       5.7   4.3e+03      24      31 ..     200     207 ..     200     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 10
                          SHNi-TPR  3 vydlLGEis 11
                                      +++ LG+++
  gi|330507764|ref|YP_004384192.1| 16 CLTGLGDVG 24
                                      7889***96 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.26
                          SHNi-TPR 16 nFpqAveDlrkaLeL 30
                                      ++++A++ ++k++ +
  gi|330507764|ref|YP_004384192.1| 75 RYEEAISSYNKSIRI 89
                                      8**********9865 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.3
                          SHNi-TPR  13 EnenFpqAveDlr 25 
                                       E +++++A++ ++
  gi|330507764|ref|YP_004384192.1| 140 ELGRYEEAITCYD 152
                                       5579999998665 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.011
                          SHNi-TPR  15 enFpqAveDlrkaLeLr 31 
                                       +++++A++ ++++++++
  gi|330507764|ref|YP_004384192.1| 176 GRYEEALQSFEESVDIY 192
                                       79************997 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 5.7
                          SHNi-TPR  24 lrkaLeLr 31 
                                       + kaL+Lr
  gi|330507764|ref|YP_004384192.1| 200 YGKALALR 207
                                       789****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2230.06
//
Query:       gi|330507765|ref|YP_004384193.1|  [L=402]
Description: SufBD domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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  163.9   0.0    5.5e-48  163.5   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 !  163.5   0.0     3e-52   5.5e-48       2     218 .]     152     374 ..     151     374 .. 0.94

  Alignments for each domain:
  == domain 1  score: 163.5 bits;  conditional E-value: 3e-52
                           UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakl 66 
                                       q +++++++eeg+e+++i   +gc            gv+e ++++nAk+++++v++w++++ + +++ ++ ++  +l
  gi|330507765|ref|YP_004384193.1| 152 QRVHNIVIAEEGSELHVI---TGCttpahvqrglhiGVSEYYIQKNAKVSFTMVHSWGKEVEVRPRTGVTIAEGGSL 225
                                       789***************...999999999999999*********************************88887778 PP

                           UPF0051  67 elttvslggkltrk.epsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgki 142
                                         +++ l    t++  p+++l+g+ga a++n++++++ + ++d+++ v +n+p+ts++ +s+ v+  ++ ++ rg++
  gi|330507765|ref|YP_004384193.1| 226 YNNYIMLRPVKTLQtFPTANLAGRGAVASFNTVIYSTMG-NIDVGSDVFLNAPETSAESISRVVCM-GGDVIARGRM 300
                                       88888887776655389*******************997.6*************************.599******* PP

                           UPF0051 143 kvrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                         +    +++ah e+  Llls+++r+++iPel  +  d  +sH+A+vG+i+ee+l YLm+RGls e+A+++ivrgf
  gi|330507765|ref|YP_004384193.1| 301 --TGTVPGARAHLECVGLLLSNEGRIYSIPELDGHCRDLDMSHEAAVGRISEEELEYLMARGLSSEQATSVIVRGF 374
                                       ..8889*********************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3049.60
//
Query:       gi|330507766|ref|YP_004384194.1|  [L=247]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-24   86.6   0.0    3.4e-24   85.9   0.0    1.3  1  ABC_tran     ABC transporter
    4.4e-09   36.6   0.7     0.0018   18.2   0.2    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00076   20.0   1.1      0.003   18.1   0.6    2.0  2  AAA_23       AAA domain
    0.00096   18.6   1.3       0.87    9.0   0.1    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0014   18.6   0.0     0.0022   17.9   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
     0.0068   16.8   0.3      0.024   15.1   0.3    2.0  1  AAA          ATPase family associated with various cellular a
     0.0075   16.0   0.0      0.015   15.1   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.026   13.2   0.0      0.044   12.4   0.0    1.3  1  AAA_13       AAA domain
      0.039   13.5   0.0      0.069   12.7   0.0    1.4  1  AAA_25       AAA domain
      0.048   13.4   0.0      0.098   12.4   0.0    1.5  1  AAA_30       AAA domain
      0.054   13.9   0.0      0.077   13.4   0.0    1.5  1  AAA_16       AAA ATPase domain
      0.082   12.6   0.1       0.13   12.0   0.1    1.5  1  AAA_15       AAA ATPase domain
      0.093   13.0   0.3       0.46   10.8   0.3    2.1  1  AAA_22       AAA domain
        0.1   12.3   0.0       0.19   11.5   0.0    1.4  1  RuvB_N       Holliday junction DNA helicase RuvB P-loop domai
       0.13   12.8   0.0        5.4    7.6   0.0    2.2  2  AAA_18       AAA domain
       0.15   12.3   0.0       0.21   11.8   0.0    1.3  1  AAA_28       AAA domain
       0.15   12.0   0.1        1.1    9.1   0.0    2.0  2  NACHT        NACHT domain
        0.2   10.5   0.0       0.27   10.0   0.0    1.1  1  DLIC         Dynein light intermediate chain (DLIC)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.0   3.4e-27   3.4e-24       1     136 [.      22     161 ..      22     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 3.4e-27
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpel 74 
                                       lkn +l ++ ge++a++G+nG+GK+tLl+++ag  +   ++G+i +++kd+++    e++r  ig+ +q p   ++l
  gi|330507766|ref|YP_004384194.1|  22 LKNFNLRINSGETHALFGPNGTGKTTLLNVIAGIPRYtiDKGRIIFKEKDITHmSMDERARLGIGMAFQRPPAIRGL 98 
                                       79*******************************9777669*************889999****************** PP

                                       BHHHH....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++++     + +++ e +l+k++ + ++++ v    + +SgG+ +r +++++l+++p+l++lDEp 
  gi|330507766|ref|YP_004384194.1|  99 RLKDLitiiNPQADTESILKKMDFEAFAERDV---NRGFSGGEVKRSEMVQLLAQQPDLVMLDEPD 161
                                       99999***999********************9...799**************************95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   1.8e-06    0.0018       3      22 ..      36      55 ..      35      87 .. 0.78
   2 !   16.8   0.0   4.8e-06    0.0048     247     295 ..     144     197 ..      96     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                      +l GpNg+GK++LL  + ++
  gi|330507766|ref|YP_004384194.1| 36 ALFGPNGTGKTTLLNVIAGI 55
                                      799**************887 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.8e-06
                            AAA_21 247 lltallralkkgsllliDEpEngLHPkllrrllellkelsr........ngaQvilt 295
                                       ++ +l++++   +l+ +DEp++g + + ++ + + +++l++        +++ +i+t
  gi|330507766|ref|YP_004384194.1| 144 MVQLLAQQP---DLVMLDEPDSGVDLENIKLIGDAINQLTQkdqrpsyrTKSGIIIT 197
                                       555555555...9***********************999998887885444444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.6   3.1e-06     0.003      13      40 ..      25      53 ..      15      55 .. 0.74
   2 ?    0.0   0.0         1     1e+03     154     176 ..      99     130 ..      60     191 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.1e-06
                            AAA_23 13 qeidFsk.gltlItGpNGaGKTTildAik 40
                                      +++  ++    +++GpNG+GKTT+l+ i 
  gi|330507766|ref|YP_004384194.1| 25 FNLRINSgETHALFGPNGTGKTTLLNVIA 53
                                      4444444145599************9885 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1
                            AAA_23 154 rleelekeleeledekkllekl.........e 176
                                       rl++l++ ++ + d+++ l+k           
  gi|330507766|ref|YP_004384194.1|  99 RLKDLITIINPQADTESILKKMdfeafaerdV 130
                                       66667777777666666666654444443330 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1   0.00088      0.87      25      44 ..      33      52 ..       9      60 .. 0.80
   2 !    8.6   0.2    0.0012       1.1     138     191 ..     135     184 ..     108     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00088
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                      +  a+ GpNG GK+ ll+ i
  gi|330507766|ref|YP_004384194.1| 33 ETHALFGPNGTGKTTLLNVI 52
                                      46789*********999876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0012
                                       -HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 138 SgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQ 191
                                       SgGe + + +  l+A    ++  l++lDe d+  D +n+k + + +++ +++ Q
  gi|330507766|ref|YP_004384194.1| 135 SGGEVKRSEMVQLLA----QQPDLVMLDEPDSGVDLENIKLIGDAINQLTQKDQ 184
                                       555555555444444....334599***********************999877 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.2e-06    0.0022      74     121 ..       6      54 ..       1      75 [. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.2e-06
                                       HTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  74 algyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                        l++e l vs  +k+ l++ + ++++ +t +l G+ G GK+tL+n++++
  gi|330507766|ref|YP_004384194.1|   6 LLEIEDLSVSIGSKQVLKNFNLRINSgETHALFGPNGTGKTTLLNVIAG 54 
                                       566777888999999999999999988*******************987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   2.4e-05     0.024       3      21 ..      37      55 ..      35     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-05
                                      EESSTTSSHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavake 21
                                      l+Gp GtGKT+l + +a  
  gi|330507766|ref|YP_004384194.1| 37 LFGPNGTGKTTLLNVIAGI 55
                                      89**************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 !   15.1   0.0   1.5e-05     0.015      16      40 ..      26      50 ..      20      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllD 40
                                       ++i+  +++ l Gp+G+GK+Tll 
  gi|330507766|ref|YP_004384194.1| 26 NLRINSGETHALFGPNGTGKTTLLN 50
                                      5677755599*************95 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.4e-05     0.044      21      41 ..      37      57 ..      26      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.4e-05
                            AAA_13 21 iYGwNGaGKTtLSrllrslel 41
                                      ++G NG+GKTtL ++++ + +
  gi|330507766|ref|YP_004384194.1| 37 LFGPNGTGKTTLLNVIAGIPR 57
                                      79**************98743 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.9e-05     0.069      29      50 ..      28      49 ..       9      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-05
                            AAA_25 29 llpagelallaGapgtGKttla 50
                                       +  ge+++l+G+ gtGKttl+
  gi|330507766|ref|YP_004384194.1| 28 RINSGETHALFGPNGTGKTTLL 49
                                      57889***************98 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   9.9e-05     0.098      16      40 ..      31      54 ..      22      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.9e-05
                            AAA_30 16 sgdrvavltGpAGtGKttalkalre 40
                                      sg  +++l Gp GtGKtt+l++++ 
  gi|330507766|ref|YP_004384194.1| 31 SG-ETHALFGPNGTGKTTLLNVIAG 54
                                      44.488999************9976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.7e-05     0.077      15      46 ..      24      54 ..      18     186 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.7e-05
                            AAA_16 15 ale.rvrsgrpelvllsGesGvGKsslvrellr 46
                                       ++ r++sg  e   l G+ G+GK++l++ ++ 
  gi|330507766|ref|YP_004384194.1| 24 NFNlRINSG--ETHALFGPNGTGKTTLLNVIAG 54
                                      455456666..566789***********98874 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00013      0.13      14      46 ..      22      55 ..      20     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlF 46
                                      lk++ + +++  +  l G+N++GK+++l+++  +
  gi|330507766|ref|YP_004384194.1| 22 LKNFNLRINSGeTHALFGPNGTGKTTLLNVIAGI 55
                                      567777777765779**************99544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00046      0.46       9      24 ..      36      51 ..      29     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                            AAA_22  9 vvtGesGtGKTtllrr 24
                                      +++G+ GtGKTtll+ 
  gi|330507766|ref|YP_004384194.1| 36 ALFGPNGTGKTTLLNV 51
                                      69***********975 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019      0.19      34      75 ..      33      72 ..       9      82 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                            RuvB_N 34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdl 75
                                      +   l+Gp G Gkttl ++ia     +  i  g ++ k++d+
  gi|330507766|ref|YP_004384194.1| 33 ETHALFGPNGTGKTTLLNVIAGIPRYT--IDKGRIIFKEKDI 72
                                      344578**************9654433..3445555555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0054       5.4       3      18 ..      37      52 ..      36      83 .. 0.87
   2 ?    3.3   0.0      0.12   1.2e+02      25     115 ..     142     237 ..     116     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0054
                            AAA_18  3 ltGtpGvGKttlakeL 18
                                      l G+ G+GKttl + +
  gi|330507766|ref|YP_004384194.1| 37 LFGPNGTGKTTLLNVI 52
                                      88**********8766 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.12
                            AAA_18  25 gvnlrdvakenglllevdpealdeskrldedkldklldaleenss..aleegknlvidghlaeleseaakdikk... 96 
                                       ++ ++ +a++ +l+  ++p+  +  + ++++    ++++l + ++  +++  + ++i  +   l +++a +++    
  gi|330507766|ref|YP_004384194.1| 142 SEMVQLLAQQPDLVMLDEPD--SGVDLENIKLIGDAINQLTQKDQrpSYRTKSGIIITHFGHILDYMKADRAHVmlg 216
                                       55667788888999999999..8888888888888999999988899777777778877777777777766665777 PP

                            AAA_18  97 ..vvLtaspeelleRlekRgy 115
                                         +v   +p e le ++k gy
  gi|330507766|ref|YP_004384194.1| 217 gaIVCSGNPGEILEQIKKSGY 237
                                       777777777777777777776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00022      0.21       3      20 ..      36      53 ..      34     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                            AAA_28  3 vitGgestGKTtlleaLa 20
                                      +++G+ +tGKTtll+ +a
  gi|330507766|ref|YP_004384194.1| 36 ALFGPNGTGKTTLLNVIA 53
                                      799***********9888 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0011       1.1       3      21 ..      35      53 ..      33      57 .. 0.87
   2 ?    0.6   0.0      0.48   4.8e+02      70      99 ..     142     185 ..     127     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                       +l G++G GKTtLl  +a
  gi|330507766|ref|YP_004384194.1| 35 HALFGPNGTGKTTLLNVIA 53
                                      5788***********9886 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.48
                                       -CCHHHHCCSCCCEE..............EEEE-STT-SS-TCH CS
                             NACHT  70 sevwavllelperlL..............lilDglDelvtdlgq 99 
                                       se++++l+++p+ ++              li D++++l ++++ 
  gi|330507766|ref|YP_004384194.1| 142 SEMVQLLAQQPDLVMldepdsgvdlenikLIGDAINQLTQKDQR 185
                                       45566666666666678888888999999999999999997776 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00027      0.27      21      76 ..      28      84 ..       9      88 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
                              DLIC 21 klPsgksvlvlGedgsGkttliaklqGveeekkGrG.leylyldvkdedrddltrln 76
                                      ++ sg +  ++G +g+Gkttl+  + G+  +   +G + +   d+    +d+ +rl+
  gi|330507766|ref|YP_004384194.1| 28 RINSGETHALFGPNGTGKTTLLNVIAGIPRYTIDKGrIIFKEKDITHMSMDERARLG 84
                                      677899999*******************98865444234555566666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1818.27
//
Query:       gi|330507767|ref|YP_004384195.1|  [L=213]
Description: hypothetical protein MCON_1769 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1600.11
//
Query:       gi|330507768|ref|YP_004384196.1|  [L=427]
Description: diaminopimelate decarboxylase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-55  187.9   0.0    2.5e-55  187.5   0.0    1.1  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    3.5e-24   84.9   0.0      4e-24   84.7   0.0    1.3  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina
      4e-13   49.5   0.0    5.7e-13   49.0   0.0    1.2  1  Ala_racemase_N   Alanine racemase, N-terminal domain


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.5   0.0   4.3e-59   2.5e-55       3     247 .]      40     288 ..      38     288 .. 0.97

  Alignments for each domain:
  == domain 1  score: 187.5 bits;  conditional E-value: 4.3e-59
                                       HHHHHHHHHHHHCTCCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHHHH CS
                     Orn_Arg_deC_N   3 sierklkrwkkalprikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqreelrya 79 
                                       +++++++r+++a+p+++ ++avKan +la+l++ a++G+g d+ S +El lv  ag++ + i f ++ k++++  +a
  gi|330507768|ref|YP_004384196.1|  40 RLRENIRRYHRAFPDAEKYFAVKANGNLAILQVAAQEGMGADIFSAGELSLVRLAGIPRDMILFNGNSKSEKDHIAA 116
                                       68999************************************************************************ PP

                                       HHCTHTEEEESSHHHHHHHHHHHCC....EEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHHHTTE CS
                     Orn_Arg_deC_N  80 lekgvkvvtvdnveeleklaklape....akvllRiktdvsaatcelistggessKFGaaleeavealleaakeenl 152
                                       l+ gv+ + vd+ eele+la++a +    a++l R++++vs +t++ i+tg +ssKFG+ +e+ + ++++a++ e++
  gi|330507768|ref|YP_004384196.1| 117 LQAGVR-ISVDSNEELEHLARTARNldseAEILFRVNPNVSPKTHPKIATGLRSSKFGIPAEQVAGTYKRAMELEGI 192
                                       ******.99***************99999********************************9*************** PP

                                       EEEEEE---BSSC-SCHHHHHHHHHHHHHHHHHHHHT---SEEE--S-BS-HCSTTSSSSTHHHHHHHHHHHHHHHH CS
                     Orn_Arg_deC_N 153 qlvGvsfHvGSgvsdleafvkavekalklfdelaelGvklkiLdvGGGfgveyeeeeeplkleeiaekirealeeaf 229
                                       + vG+++H+GS++ d+++f++a+ +++ +   ++  G +++ +d+GGG+g++y+ ++ +   ++ a+++ + +++ +
  gi|330507768|ref|YP_004384196.1| 193 KPVGLHCHIGSQILDTAPFAEAAGRMMDITRAVVAEGGNVERIDLGGGLGIQYQPDSTAPLPSDLAKAVLPVIQDSC 269
                                       ******************************************************87766666*************** PP

                                       H.TSSS-EEEE--SHHHHG CS
                     Orn_Arg_deC_N 230 p.gdkevtiiaEpGRalva 247
                                       +  +  +++i+EpGR++va
  gi|330507768|ref|YP_004384196.1| 270 RdMGIFPQLILEPGRSIVA 288
                                       *877779**********98 PP

>> Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-terminal sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.0   6.7e-28     4e-24       5      98 .]     248     377 ..      27     377 .. 0.71

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 6.7e-28
                                       E........................................GGEEEEEEEEEEEEETCEEEEEES--TTTS-HHHHC CS
                                       x........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC   5 d........................................eagvLvtrViavkesekkkfvivdaGmndllrpaly 41 
                                       d                                        ++ +++t V+ vk+ +  +fv vdaG+n l+rp ly
  gi|330507768|ref|YP_004384196.1| 248 DstaplpsdlakavlpviqdscrdmgifpqlilepgrsivaDSTIMLTGVNVVKRAHV-NFVAVDAGFNVLARPMLY 323
                                       0555555555555555555555555555555555555555578999********9987.8***************** PP

                                       TT-S-E.ESBTT-SCEEC.EEEEEEEE-SSSSTT-EEEEEEEEEE--TT-EEEESS-S CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC  42 gsfhei.pvkeeeaekeeeeeeevdvvGptCesgDvlakdrelpelevGdllafedaG 98 
                                       +s+h++ +++    ++ee+ ee++++vGp+Ce+gDvla+dr+lp+l +Gd laf daG
  gi|330507768|ref|YP_004384196.1| 324 DSYHHVlAAN----RAEEQGEETYTIVGPICETGDVLARDRRLPRLVRGDTLAFLDAG 377
                                       ******4443....345566789*********************************99 PP

>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   9.5e-17   5.7e-13       3     180 ..      38     225 ..      36     247 .. 0.81

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 9.5e-17
                                       HHHHHHHHHHHHHHSCTTSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTSCSEEEEESC..S CS
                    Ala_racemase_N   3 ldalrhNlrrlralagpgaklmavvKanayghgavevaralaeggadgfgvatleEalelreagitapilvleg..f 77 
                                         +lr+N+rr  +++ p+a+ +  vKan+  + +++va  ++  gad f   +  E+  +r agi +++++++g   
  gi|330507768|ref|YP_004384196.1|  38 ERRLRENIRRYHRAF-PDAEKYFAVKANGN-LAILQVAA-QEGMGADIF---SAGELSLVRLAGIPRDMILFNGnsK 108
                                       579************.88999999***654.44445555.443457755...677888*******999999999754 PP

                                       TGGGHHHHHHTTEEEEESSHHHHHHHHHHHHH............TTS-EEEEEEBESSSS..SSSBSCHHHHHHHHH CS
                    Ala_racemase_N  78 speelaalaeydltvtvdsleqlealaaaare............agkplrvhlkidtgmg..RlGftpeeleellea 140
                                       s+++  a++++++ + vds e+le la+ ar+             +   + h ki tg+   + G+++e+++  +++
  gi|330507768|ref|YP_004384196.1| 109 SEKDHIAALQAGVRISVDSNEELEHLARTARNldseaeilfrvnPNVSPKTHPKIATGLRssKFGIPAEQVAGTYKR 185
                                       55555566678********************************99999**********999**************** PP

                                       HHHTTTEEEEEEE-S-SST..TSTSHHHHHHHHHHHHHHHHH CS
                    Ala_racemase_N 141 laalpglrleglmtHfasa..depdeeteaqlarfeealeel 180
                                       + +l+g++++gl  H +s   d+  +++++   r+ +++ ++
  gi|330507768|ref|YP_004384196.1| 186 AMELEGIKPVGLHCHIGSQilDT--APFAEAAGRMMDITRAV 225
                                       ***************99975444..34555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2791.11
//
Query:       gi|330507769|ref|YP_004384197.1|  [L=518]
Description: hypothetical protein MCON_1771 [Methanosaeta concilii GP6]
Scores for complete 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-49  165.0  55.1    2.5e-16   59.4   2.9    6.8  7  TM_helix     Conserved TM helix
  ------ inclusion threshold ------
      0.093   12.0   3.0       0.88    8.8   3.0    2.4  1  7tm_1        7 transmembrane receptor (rhodopsin family)
          9    6.3  61.8       0.47   10.4   0.7    7.1  6  Colicin_V    Colicin V production protein


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 !   35.8   0.7   9.5e-13   5.7e-09      16      49 ..      41      74 ..      35      75 .. 0.95
   2 !   44.0   2.6   2.6e-15   1.5e-11       1      49 [.     122     170 ..     122     170 .. 0.98
   3 !   50.2   2.7   3.1e-17   1.9e-13       1      49 [.     216     264 ..     216     265 .. 0.95
   4 ?   -5.9   2.9         3   1.8e+04      12      22 ..     282     292 ..     280     294 .. 0.59
   5 !   59.4   2.9   4.2e-20   2.5e-16       1      49 [.     311     359 ..     311     360 .. 0.98
   6 !   11.3   0.7   4.3e-05      0.26       5      38 ..     408     441 ..     406     455 .. 0.82
   7 ?   -1.1   0.3      0.33     2e+03      17      25 ..     486     494 ..     475     517 .. 0.68

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 9.5e-13
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                          TM_helix 16 nLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49
                                      n++ A++IL+vGwi+A +vs l++k l++t +d+
  gi|330507769|ref|YP_004384197.1| 41 NIFSALIILVVGWIVALIVSSLIGKALRRTAMDE 74
                                      9*****************************9997 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 2.6e-15
                                       XXXXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                          TM_helix   1 nplnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49 
                                       +pln++l+ +++++P+L++A+lI++v+ ++A +++r+v  +l++++id+
  gi|330507769|ref|YP_004384197.1| 122 QPLNEMLTVVFAYIPKLFAALLIAIVAIVLAMVLKRVVLTVLRSANIDE 170
                                       7**********************************************96 PP

  == domain 3  score: 50.2 bits;  conditional E-value: 3.1e-17
                                       XXXXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                          TM_helix   1 nplnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49 
                                       +pl+ +  + l+flPnL++A++ILlvGw++A++v +++t ll ++g ++
  gi|330507769|ref|YP_004384197.1| 216 EPLQVMMAKMLGFLPNLLAAAAILLVGWFLARIVQKILTGLLLAVGSER 264
                                       599*****************************************99876 PP

  == domain 4  score: -5.9 bits;  conditional E-value: 3
                                       TTHSHHHHHHH CS
                          TM_helix  12 sflPnLvgAil 22 
                                       + ++ +v A++
  gi|330507769|ref|YP_004384197.1| 282 GLIGLIVYALI 292
                                       55666777766 PP

  == domain 5  score: 59.4 bits;  conditional E-value: 4.2e-20
                                       XXXXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                          TM_helix   1 nplnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49 
                                       +pl+n+ln++l++lP  +gAilIL+++++++k+v+ lvt+lla++g+d 
  gi|330507769|ref|YP_004384197.1| 311 QPLSNMLNQILAALPSAFGAILILAIAYVLGKIVAELVTNLLAAAGFDS 359
                                       7**********************************************96 PP

  == domain 6  score: 11.3 bits;  conditional E-value: 4.3e-05
                                       SXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHH CS
                          TM_helix   5 nllnellsflPnLvgAilILlvGwiiAkfvsrlv 38 
                                       +l+ e++ f +++++ ++IL+ G ++A+++ + v
  gi|330507769|ref|YP_004384197.1| 408 DLIYEFIVFAGRVLVGLVILATGIYLANLAYDTV 441
                                       567799**********************998877 PP

  == domain 7  score: -1.1 bits;  conditional E-value: 0.33
                                       HHHHHHHHH CS
                          TM_helix  17 LvgAilILl 25 
                                       L+gAi++++
  gi|330507769|ref|YP_004384197.1| 486 LLGAIAVAV 494
                                       555555543 PP

>> 7tm_1  7 transmembrane receptor (rhodopsin family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.0   0.00015      0.88     145     217 ..      38     109 ..      27     392 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCHHHHSHCCHHHHHHCTTCHHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             7tm_1 145 svyiifsavlsfilPllvivilyarifrtvlktsrtktsksknggsstpplkavrekkaartlgivvavfivc 217
                                       ++ +ifsa++  ++  +v +i+   i +++++t+  ++  +   g+++ + + ++++ ++r++ +v++ f+++
  gi|330507769|ref|YP_004384197.1|  38 MSSNIFSALIILVVGWIVALIVSSLIGKALRRTAMDEKIARVAVGEERAR-SIDSNRWITRIIYYVLLFFVIV 109
                                       5779**********************************966555555554.4555566666666666666553 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7   7.8e-05      0.47      48      89 ..      34      70 ..      16      82 .. 0.67
   2 ?    8.4  11.0   0.00033         2      25     116 ..      47     153 ..      43     157 .. 0.76
   3 ?    4.8   1.3    0.0043        26      25      75 ..     139     206 ..     135     217 .. 0.79
   4 ?    9.7   7.8   0.00013       0.8      60     127 ..     231     310 ..     214     315 .. 0.84
   5 ?    6.8   2.2    0.0011       6.3      42      94 ..     310     360 ..     306     367 .. 0.80
   6 ?   -4.9  13.4         3   1.8e+04      25      77 ..     421     472 ..     384     516 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.8e-05
                         Colicin_V 48 llaelilspalaaiiaflllfllvllivsllgallsklvskt 89
                                      +++     p   +i++ l++++++++++ ++++l++k++++t
  gi|330507769|ref|YP_004384197.1| 34 IFG-----PMSSNIFSALIILVVGWIVALIVSSLIGKALRRT 70
                                      333.....4556777777777777777777777777776544 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00033
                         Colicin_V  25 vlsllgwvvafvvasllypslaellae...............lilspalaaiiaflllfllvllivsllgallsklv 86 
                                       ++ ++gw+va++v sl ++ l     +               + +++++ +ii ++llf+++++++  lg  l    
  gi|330507769|ref|YP_004384197.1|  47 IILVVGWIVALIVSSLIGKALRRTAMDekiarvavgeerarsIDSNRWITRIIYYVLLFFVIVAFFETLGLTLVAQP 123
                                       5667888888888888888888888889*************98899999*********************9999955 PP

                         Colicin_V  87 sktglglldrllGaifGllkglllvvllll 116
                                          +l  +   +  +f +l +++++++l +
  gi|330507769|ref|YP_004384197.1| 124 LNEMLTVVFAYIPKLFAALLIAIVAIVLAM 153
                                       555555555555555555555555554433 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0043
                         Colicin_V  25 vlsllgwvvafvvasllypslaellae.................lilspalaaiiaflllfllvlliv 75 
                                       +++ll  +va+v+a  l   +   l++                 + ls+++ +i+ +l+l+l+  +++
  gi|330507769|ref|YP_004384197.1| 139 FAALLIAIVAIVLAMVLKRVVLTVLRSanidedigskaglerkeMPLSQTISEIVFYLVLLLFLPMVL 206
                                       67899999******************99***********98888556788888888855555544443 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.00013
                         Colicin_V  60 aiiaflllfllvllivsllgallsk.........lvsktglgll..drllGaifGllkglllvv.llllllalvplp 124
                                       +++a ++++l+++++++++ ++l++         l +k+gl+++   r l +++Gl+  +l+++ +l+++l++ +l 
  gi|330507769|ref|YP_004384197.1| 231 NLLAAAAILLVGWFLARIVQKILTGlllavgserLSEKVGLSRVlgERGLAGLIGLIVYALILIpVLMAALQALDLV 307
                                       78999********************88777777666778888844478999******************99998887 PP

                         Colicin_V 125 kvq 127
                                       +v+
  gi|330507769|ref|YP_004384197.1| 308 SVT 310
                                       764 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.0011
                         Colicin_V  42 ypslaellaelilspalaaiiaflllfllvllivsllgallsklvsktglgll 94 
                                        ++l+++l+++   +al ++++ +l++ ++++++++++ l+++l+ + g   +
  gi|330507769|ref|YP_004384197.1| 310 TQPLSNMLNQI--LAALPSAFGAILILAIAYVLGKIVAELVTNLLAAAGFDSI 360
                                       68899999995..5788899999999999999999999999999887776655 PP

  == domain 6  score: -4.9 bits;  conditional E-value: 3
                         Colicin_V  25 vlsllgwvvafvvasllypslaellaelilspalaaiiaf.lllfllvllivsl 77 
                                       +++l+ ++ ++++a l y+++ +  ++  + + la+++ + +l+f +++++ ++
  gi|330507769|ref|YP_004384197.1| 421 LVGLVILATGIYLANLAYDTVMASNTS--QAKMLAQAARIsVLIFSGAMALRHM 472
                                       456777777777777777777777777..5666666666656666666666443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1357  (0.0756874); 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:                        19  (0.00105974); expected 0.2 (1e-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 0.31s 00:00:01.09 Elapsed: 00:00:00.45
# Mc/sec: 3436.38
//
Query:       gi|330507770|ref|YP_004384198.1|  [L=345]
Description: hypothetical protein MCON_1772 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2610.96
//
Query:       gi|330507771|ref|YP_004384199.1|  [L=134]
Description: hypothetical protein MCON_1773 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 00:00:00.40
# Mc/sec: 1010.28
//
Query:       gi|330507772|ref|YP_004384200.1|  [L=131]
Description: hypothetical protein MCON_1774 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1005.13
//
Query:       gi|330507773|ref|YP_004384201.1|  [L=201]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (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  109.2   0.0    1.9e-31  108.8   0.0    1.1  1  DDE_3     DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.063   13.5   0.0       0.12   12.5   0.0    1.5  1  rve_2     Integrase core domain
       0.11   12.3   0.3        2.3    8.1   0.0    2.5  3  rve_3     Integrase core domain


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8   0.0   3.2e-35   1.9e-31      15     145 ..      10     171 ..       2     172 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 3.2e-35
                             DDE_3  15 vrrrawakkGkrer.leeygrrgrvnligaldekgglaf.vtfeetlnaedfaeflerlletalqakkivlilDnas 89 
                                         +  ++ +Gk er ++ey+r+g++++i+++ +++g++  + + +t+n++df+ ++++++e+ l+  +++++ Dn++
  gi|330507773|ref|YP_004384201.1|  10 KHPGLPMAPGKVERrEFEYIRHGTQSFIVSFAVANGKVDtISCGDTRNEDDFVSHIKEVVERSLSTSRWHFVADNLN 86 
                                       5666799********************************99************************************ PP

                             DDE_3  90 iHkseslrelveee.............................adrlellylPpySPelNpiEivwsklkrellkrr 137
                                       iHksesl+++v++                              +++++++y+P ++++ N++Ei++s+l+r+ll+r+
  gi|330507773|ref|YP_004384201.1|  87 IHKSESLVRYVADVsdldidlgikgrdgilksietresfladpSHSIVFHYTPIHASWMNQVEIWFSILVRKLLRRA 163
                                       ***************************************************************************** PP

                             DDE_3 138 sfksldeL 145
                                       sf s+ +L
  gi|330507773|ref|YP_004384201.1| 164 SFASINDL 171
                                       ****9998 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     2e-05      0.12       3      36 ..     151     184 ..     149     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
                             rve_2   3 fFgsLKtElvygetfktleeleaaiedYIewYNn 36 
                                        F +L ++l++ + f++++ l+a++  ++e++N+
  gi|330507773|ref|YP_004384201.1| 151 WFSILVRKLLRRASFASINDLNAKVLAFVEYFNK 184
                                       699999***************************7 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.04   2.4e+02       5      21 ..       7      23 ..       4      29 .. 0.88
   2 ?   -3.4   0.0       1.5   8.9e+03      19      33 ..      69      83 ..      67      93 .. 0.65
   3 ?    8.1   0.0   0.00038       2.3      24      55 ..     153     184 ..     131     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.04
                             rve_3  5 lsyiapgkPqqNglvEs 21
                                      l++ +pg P+  g+vE+
  gi|330507773|ref|YP_004384201.1|  7 LERKHPGLPMAPGKVER 23
                                      56789***********9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                             rve_3 19 vEsfngtlrdellne 33
                                      vE++  t r +++  
  gi|330507773|ref|YP_004384201.1| 69 VERSLSTSRWHFVAD 83
                                      677777766666554 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00038
                             rve_3  24 gtlrdellneelfrslaearekleawredYNt 55 
                                         l ++ll + +f s++++++k+ a++e++N+
  gi|330507773|ref|YP_004384201.1| 153 SILVRKLLRRASFASINDLNAKVLAFVEYFNK 184
                                       556678899999*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1487.32
//
Query:       gi|330507774|ref|YP_004384202.1|  [L=432]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-138  443.4  49.3    8.5e-13   47.5   0.2   12.0 12  TPR_1            Tetratricopeptide repeat
   6.3e-110  350.7  42.3    1.9e-09   36.9   0.1   12.0 12  TPR_2            Tetratricopeptide repeat
   3.3e-102  333.9  72.4    6.5e-13   48.1   3.7   12.0 12  TPR_11           TPR repeat
    4.2e-98  313.5  42.6    1.2e-08   34.4   0.1   12.1 12  TPR_8            Tetratricopeptide repeat
      1e-79  257.3  34.3    8.4e-07   28.9   0.0   11.4 11  TPR_17           Tetratricopeptide repeat
    4.7e-72  232.5  24.7    2.6e-06   27.8   0.0   12.1 12  TPR_14           Tetratricopeptide repeat
    1.2e-69  230.6  25.1    2.5e-13   50.4   0.1    7.2  7  TPR_16           Tetratricopeptide repeat
    9.3e-58  192.7  32.7    4.7e-10   39.8   0.3    7.3  7  TPR_19           Tetratricopeptide repeat
      1e-54  182.7  25.6    1.3e-08   35.0   0.3    9.7  7  TPR_12           Tetratricopeptide repeat
    3.9e-43  142.3  14.9     0.0019   18.1   0.1   12.1 12  TPR_7            Tetratricopeptide repeat
      8e-41  138.2  19.1    1.4e-07   31.6   0.3    6.3  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    1.1e-40  137.6   5.1      2e-05   24.7   1.2    7.3  8  TPR_9            Tetratricopeptide repeat
    3.4e-38  128.5  27.2     0.0076   16.1   0.1   12.1 12  TPR_10           Tetratricopeptide repeat
    5.8e-36  120.8  23.3      0.027   15.1   0.3   12.1 12  TPR_6            Tetratricopeptide repeat
    1.4e-25   89.1  14.3      0.061   13.4   0.0   11.2 11  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
      4e-23   82.1  16.9      0.011   15.8   0.2   11.5  8  DUF3856          Domain of Unknown Function (DUF3856)
    4.5e-21   75.4  13.6     0.0012   17.9   0.1    5.8  6  NARP1            NMDA receptor-regulated protein 1
      2e-20   73.7   0.4      0.024   15.1   0.0    6.0  6  BTAD             Bacterial transcriptional activator domain
    8.7e-20   69.3   7.9       0.15   12.7   0.3   11.4 11  TPR_4            Tetratricopeptide repeat
    8.2e-18   64.0  32.8      0.014   15.4   0.1   12.4 12  TPR_3            Tetratricopeptide repeat
      2e-17   63.3   2.6      0.021   14.8   0.0    6.7  5  SRP_TPR_like     Putative TPR-like repeat
    8.3e-14   51.7  26.3      0.013   15.2   0.4    7.4  8  TPR_21           Tetratricopeptide repeat-like domain
    2.4e-13   50.0   3.8        3.7    7.7   0.0   10.5 11  ANAPC5           Anaphase-promoting complex subunit 5
    1.8e-11   44.0   0.0        2.3    8.2   0.0    5.5  5  DUF627           Protein of unknown function (DUF627)
    1.5e-10   40.5   2.2        1.1    9.0   0.0    8.8 11  Lambda_Kil       Bacteriophage lambda Kil protein
    9.6e-09   35.2  41.6          2    8.5   0.2   11.9 12  MIT              MIT (microtubule interacting and transport) 
    1.4e-08   34.8  19.8        2.1    8.6   0.1   10.6 11  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
      3e-08   33.4   1.7         46    4.6   0.0   10.4 11  PPR              PPR repeat
    2.7e-07   30.0  31.4         18    5.0   0.2   11.6 11  HTH_Bact         Helix-turn-helix bacterial domain
    5.2e-07   29.8   7.0         11    6.1   0.0    7.9  8  Mo-co_dimer      Mo-co oxidoreductase dimerisation domain
    2.4e-06   27.2   2.2       0.87    8.9   0.0    4.7  4  TPR_MalT         MalT-like TPR region
    2.8e-06   27.0   0.0          5    6.4   0.0    5.2  6  Coatomer_E       Coatomer epsilon subunit
    7.1e-06   26.0  11.0         17    5.5   0.0    7.3  7  DUF982           Protein of unknown function (DUF982)
    7.5e-06   25.8  17.7        2.7    7.8   0.0    8.8 10  DUF5113          Domain of unknown function (DUF5113)
    1.1e-05   25.5  24.2       0.77    9.6   0.2    8.5  8  Wzy_C_2          Virulence factor membrane-bound polymerase, 
    1.8e-05   24.1  14.5       0.13   11.5   0.2    4.6  5  TPR_15           Tetratricopeptide repeat
    3.2e-05   24.4   4.9         29    5.1   0.0    6.0  6  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    0.00025   21.7   0.0         11    6.8   0.0    5.2  6  TetR_C_15        Tetracyclin repressor-like, C-terminal domai
    0.00039   20.7   1.2         24    5.4   0.0    6.0  6  FERM_C           FERM C-terminal PH-like domain
     0.0005   19.4  18.2        2.4    7.3   0.1    6.7  8  FAT              FAT domain
    0.00087   19.6  12.3         10    6.5   1.3    5.7  6  TPR_20           Tetratricopeptide repeat
    0.00097   18.8   7.9         68    3.3   0.0    8.2 10  SPOB_a           Sensor_kinase_SpoOB-type, alpha-helical doma
      0.007   16.5  11.9         61    3.9   0.0    7.6  9  DUF1510          Domain of unknown function (DUF1510)
     0.0079   16.0   8.8         30    4.5   0.0    6.3  6  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
  ------ inclusion threshold ------
      0.012   15.4  16.9        8.1    6.1   0.1    7.7 10  RPN7             26S proteasome subunit RPN7
       0.07   13.1   0.0          7    6.6   0.0    3.6  3  Trm56            tRNA ribose 2'-O-methyltransferase, aTrm56
       0.22   11.3  11.1         77    3.1   0.1    6.3  5  Vta1_C           Vta1 C-terminal domain
       0.22   11.8   2.4         24    5.2   0.1    3.5  3  PHP              PHP domain
       0.44   10.8   1.7    2.2e+02    2.1   0.0    4.9  3  SpoVAC_SpoVAEB   SpoVAC/SpoVAEB sporulation membrane protein


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   3.2e-10   1.2e-07       1      34 []      29      62 ..      29      62 .. 0.94
   2 !   43.1   0.7   5.8e-14   2.1e-11       1      34 []      63      96 ..      63      96 .. 0.97
   3 !   40.9   0.4   2.9e-13     1e-10       1      34 []      97     130 ..      97     130 .. 0.97
   4 !   39.3   0.4   8.9e-13   3.3e-10       1      34 []     131     164 ..     131     164 .. 0.96
   5 !   42.2   0.1   1.2e-13   4.3e-11       1      34 []     165     198 ..     165     198 .. 0.98
   6 !   37.9   0.0   2.6e-12   9.6e-10       1      34 []     199     232 ..     199     232 .. 0.97
   7 !   44.2   0.1   2.6e-14   9.5e-12       1      33 [.     233     265 ..     233     266 .. 0.97
   8 !   38.5   0.1   1.6e-12   5.9e-10       1      33 [.     267     299 ..     267     300 .. 0.97
   9 !   47.4   0.2   2.6e-15   9.6e-13       1      34 []     301     334 ..     301     334 .. 0.97
  10 !   30.1   0.3   7.3e-10   2.7e-07       1      34 []     335     368 ..     335     368 .. 0.94
  11 !   47.5   0.2   2.3e-15   8.5e-13       1      34 []     369     402 ..     369     402 .. 0.97
  12 !   31.4   0.2     3e-10   1.1e-07       1      25 [.     403     427 ..     403     429 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 3.2e-10
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a  +  +Gna+  l +ydeA+++y++A++++P++
  gi|330507774|ref|YP_004384202.1| 29 AAEWLEKGNAFVMLSMYDEAIQAYDQAISIDPQD 62
                                      56799***************************86 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 5.8e-14
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a+a+ n+G a++ lg+ydeA+++y++A++++P++
  gi|330507774|ref|YP_004384202.1| 63 AYAWSNKGEALRALGRYDEAIQAYDQAISIDPQY 96
                                      79******************************86 PP

  == domain 3  score: 40.9 bits;  conditional E-value: 2.9e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a+ n+G a++ lgkydeA+ ++++A+++nP++
  gi|330507774|ref|YP_004384202.1|  97 AYAWSNKGEALRALGKYDEAINACDQAISINPQD 130
                                       79******************************86 PP

  == domain 4  score: 39.3 bits;  conditional E-value: 8.9e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a+  +Gna++ lgkydeA+ +y++A++++P++
  gi|330507774|ref|YP_004384202.1| 131 AFAWTIKGNALYDLGKYDEAINAYDQAISIDPQY 164
                                       679*****************************86 PP

  == domain 5  score: 42.2 bits;  conditional E-value: 1.2e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a+ n+G a+ +lgkydeA++++++A++++P+n
  gi|330507774|ref|YP_004384202.1| 165 AYAWSNKGTALGHLGKYDEAIKACDQAISIDPQN 198
                                       79******************************97 PP

  == domain 6  score: 37.9 bits;  conditional E-value: 2.6e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a+yn+G ++  lgkydeA++ +++A++++P++
  gi|330507774|ref|YP_004384202.1| 199 AYAWYNKGTVLGILGKYDEAIKPFDQAISIDPQF 232
                                       79******************************86 PP

  == domain 7  score: 44.2 bits;  conditional E-value: 2.6e-14
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+a+yn+G a+ +lgkydeA++++++A++++P+
  gi|330507774|ref|YP_004384202.1| 233 AEAWYNKGTALGRLGKYDEAIKACDQAISIDPQ 265
                                       89******************************7 PP

  == domain 8  score: 38.5 bits;  conditional E-value: 1.6e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+++  +G a++ lgkydeA+++y++A+++nP+
  gi|330507774|ref|YP_004384202.1| 267 AETWTIKGIALYDLGKYDEAIQAYDQAISINPQ 299
                                       799*****************************6 PP

  == domain 9  score: 47.4 bits;  conditional E-value: 2.6e-15
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a+yn+G+a+  lgkydeA++++++A+++nP++
  gi|330507774|ref|YP_004384202.1| 301 AEAWYNKGVALTALGKYDEAIKACDQAISINPQD 334
                                       89******************************86 PP

  == domain 10  score: 30.1 bits;  conditional E-value: 7.3e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a+  +G a++ lgkydeA+++y++A ++nP++
  gi|330507774|ref|YP_004384202.1| 335 AFAWTIKGIALYDLGKYDEAIQAYDQANRINPQF 368
                                       679************************9999986 PP

  == domain 11  score: 47.5 bits;  conditional E-value: 2.3e-15
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a+yn+G+a+  lgkydeA++++++A+++nP++
  gi|330507774|ref|YP_004384202.1| 369 AEAWYNKGVALTALGKYDEAIKACDQAISINPQF 402
                                       89******************************86 PP

  == domain 12  score: 31.4 bits;  conditional E-value: 3e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyye 25 
                                       a+a+yn+G+++  lgkydeA++++e
  gi|330507774|ref|YP_004384202.1| 403 AEAWYNKGVVLKALGKYDEAIKAFE 427
                                       89**********************8 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     2e-07   7.1e-05       1      34 []      29      62 ..      29      62 .. 0.94
   2 !   36.0   0.8     1e-11   3.7e-09       1      34 []      63      96 ..      63      96 .. 0.96
   3 !   33.4   0.2   7.1e-11   2.6e-08       1      34 []      97     130 ..      97     130 .. 0.97
   4 !   33.9   0.2   4.9e-11   1.8e-08       1      34 []     131     164 ..     131     164 .. 0.95
   5 !   31.2   0.0   3.4e-10   1.3e-07       1      34 []     165     198 ..     165     198 .. 0.97
   6 !   24.3   0.0   5.7e-08   2.1e-05       1      33 [.     199     231 ..     199     232 .. 0.96
   7 !   34.4   0.1   3.3e-11   1.2e-08       1      33 [.     233     265 ..     233     266 .. 0.97
   8 !   32.0   0.0   1.9e-10   7.1e-08       1      33 [.     267     299 ..     267     300 .. 0.95
   9 !   36.9   0.1   5.3e-12   1.9e-09       1      34 []     301     334 ..     301     334 .. 0.97
  10 !   28.3   0.2     3e-09   1.1e-06       1      33 [.     335     367 ..     335     368 .. 0.95
  11 !   36.1   0.1   9.1e-12   3.3e-09       1      33 [.     369     401 ..     369     402 .. 0.97
  12 !   25.6   0.5   2.2e-08   8.2e-06       1      25 [.     403     427 ..     403     432 .] 0.94

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2e-07
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      a  + + G+a   l  y+eA++a+++A+++dP++
  gi|330507774|ref|YP_004384202.1| 29 AAEWLEKGNAFVMLSMYDEAIQAYDQAISIDPQD 62
                                      567999**************************86 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 1e-11
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      a+a+ n G+a+++lg+y+eA++a+++A+++dP++
  gi|330507774|ref|YP_004384202.1| 63 AYAWSNKGEALRALGRYDEAIQAYDQAISIDPQY 96
                                      78******************************85 PP

  == domain 3  score: 33.4 bits;  conditional E-value: 7.1e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+a+ n G+a+++lg+y+eA++a+++A++++P++
  gi|330507774|ref|YP_004384202.1|  97 AYAWSNKGEALRALGKYDEAINACDQAISINPQD 130
                                       78******************************86 PP

  == domain 4  score: 33.9 bits;  conditional E-value: 4.9e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a a+   G+a+y lg+y+eA++a+++A+++dP++
  gi|330507774|ref|YP_004384202.1| 131 AFAWTIKGNALYDLGKYDEAINAYDQAISIDPQY 164
                                       679999**************************85 PP

  == domain 5  score: 31.2 bits;  conditional E-value: 3.4e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+a+ n G a+ +lg+y+eA++a+++A+++dP+n
  gi|330507774|ref|YP_004384202.1| 165 AYAWSNKGTALGHLGKYDEAIKACDQAISIDPQN 198
                                       78******************************97 PP

  == domain 6  score: 24.3 bits;  conditional E-value: 5.7e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+a+yn G ++  lg+y+eA++ f++A+++dP+
  gi|330507774|ref|YP_004384202.1| 199 AYAWYNKGTVLGILGKYDEAIKPFDQAISIDPQ 231
                                       78******************************7 PP

  == domain 7  score: 34.4 bits;  conditional E-value: 3.3e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       aea+yn G a+ +lg+y+eA++a+++A+++dP+
  gi|330507774|ref|YP_004384202.1| 233 AEAWYNKGTALGRLGKYDEAIKACDQAISIDPQ 265
                                       89******************************7 PP

  == domain 8  score: 32.0 bits;  conditional E-value: 1.9e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       ae +   G a+y lg+y+eA++a+++A++++P+
  gi|330507774|ref|YP_004384202.1| 267 AETWTIKGIALYDLGKYDEAIQAYDQAISINPQ 299
                                       6889999*************************7 PP

  == domain 9  score: 36.9 bits;  conditional E-value: 5.3e-12
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       aea+yn G a+ +lg+y+eA++a+++A++++P++
  gi|330507774|ref|YP_004384202.1| 301 AEAWYNKGVALTALGKYDEAIKACDQAISINPQD 334
                                       89******************************86 PP

  == domain 10  score: 28.3 bits;  conditional E-value: 3e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a+   G a+y lg+y+eA++a+++A +++P+
  gi|330507774|ref|YP_004384202.1| 335 AFAWTIKGIALYDLGKYDEAIQAYDQANRINPQ 367
                                       679999**************************7 PP

  == domain 11  score: 36.1 bits;  conditional E-value: 9.1e-12
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       aea+yn G a+ +lg+y+eA++a+++A++++P+
  gi|330507774|ref|YP_004384202.1| 369 AEAWYNKGVALTALGKYDEAIKACDQAISINPQ 401
                                       89******************************7 PP

  == domain 12  score: 25.6 bits;  conditional E-value: 2.2e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafe 25 
                                       aea+yn G ++ +lg+y+eA++afe
  gi|330507774|ref|YP_004384202.1| 403 AEAWYNKGVVLKALGKYDEAIKAFE 427
                                       89**********************8 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.2   1.9e-12   7.1e-10       1      42 []      36      77 ..      36      77 .. 0.94
   2 !   43.5   2.7   4.8e-14   1.8e-11       1      38 [.      70     107 ..      70     107 .. 0.97
   3 !   24.6   0.4   4.1e-08   1.5e-05       1      29 [.     104     132 ..     104     135 .. 0.93
   4 !   48.1   3.7   1.8e-15   6.5e-13       1      42 []     138     179 ..     138     179 .. 0.95
   5 !   31.7   0.6   2.5e-10   9.1e-08       7      37 ..     178     208 ..     175     210 .. 0.94
   6 !   37.2   0.1   4.7e-12   1.7e-09       7      42 .]     212     247 ..     211     247 .. 0.97
   7 !   20.8   0.3     6e-07   0.00022       7      39 ..     246     278 ..     245     278 .. 0.90
   8 !   45.6   2.1   1.1e-14     4e-12       3      42 .]     276     315 ..     274     315 .. 0.94
   9 !   22.2   0.5   2.2e-07   8.2e-05       3      39 ..     310     346 ..     309     346 .. 0.88
  10 !   41.9   2.8   1.5e-13   5.6e-11       3      38 ..     344     379 ..     342     381 .. 0.95
  11 !   39.5   0.1   8.6e-13   3.1e-10       3      42 .]     378     417 ..     376     417 .. 0.95
  12 !    7.4   0.1    0.0095       3.5       4      18 ..     413     427 ..     412     429 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.9e-12
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      G+a++ +  y+eAi+aY +A+ +dP++a a++n G+a+ ++G
  gi|330507774|ref|YP_004384202.1| 36 GNAFVMLSMYDEAIQAYDQAISIDPQDAYAWSNKGEALRALG 77
                                      899999999****************************97776 PP

  == domain 2  score: 43.5 bits;  conditional E-value: 4.8e-14
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       G a++++G+y+eAi+aY +A+ +dP++a a++n G+a+
  gi|330507774|ref|YP_004384202.1|  70 GEALRALGRYDEAIQAYDQAISIDPQYAYAWSNKGEAL 107
                                       899********************************985 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 4.1e-08
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnae 29 
                                       G a++++Gky+eAi+a  +A+ ++P++a 
  gi|330507774|ref|YP_004384202.1| 104 GEALRALGKYDEAINACDQAISINPQDAF 132
                                       899***********************995 PP

  == domain 4  score: 48.1 bits;  conditional E-value: 1.8e-15
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+a+y++Gky+eAi+aY +A+ +dP++a a++n G a+  +G
  gi|330507774|ref|YP_004384202.1| 138 GNALYDLGKYDEAINAYDQAISIDPQYAYAWSNKGTALGHLG 179
                                       9**********************************9987665 PP

  == domain 5  score: 31.7 bits;  conditional E-value: 2.5e-10
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       +Gky+eAi+a  +A+ +dP+na a+yn G +
  gi|330507774|ref|YP_004384202.1| 178 LGKYDEAIKACDQAISIDPQNAYAWYNKGTV 208
                                       6**************************9976 PP

  == domain 6  score: 37.2 bits;  conditional E-value: 4.7e-12
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +Gky+eAi+ + +A+ +dP++aea+yn G a+ ++G
  gi|330507774|ref|YP_004384202.1| 212 LGKYDEAIKPFDQAISIDPQFAEAWYNKGTALGRLG 247
                                       7*******************************9998 PP

  == domain 7  score: 20.8 bits;  conditional E-value: 6e-07
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       +Gky+eAi+a  +A+ +dP+ ae +   G a+y
  gi|330507774|ref|YP_004384202.1| 246 LGKYDEAIKACDQAISIDPQLAETWTIKGIALY 278
                                       7**********************9987777766 PP

  == domain 8  score: 45.6 bits;  conditional E-value: 1.1e-14
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       a+y++Gky+eAi+aY +A+ ++P+ aea+yn G+a+ ++G
  gi|330507774|ref|YP_004384202.1| 276 ALYDLGKYDEAIQAYDQAISINPQIAEAWYNKGVALTALG 315
                                       89*********************************98877 PP

  == domain 9  score: 22.2 bits;  conditional E-value: 2.2e-07
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       a++++Gky+eAi+a  +A+ ++P++a a+   G a+y
  gi|330507774|ref|YP_004384202.1| 310 ALTALGKYDEAIKACDQAISINPQDAFAWTIKGIALY 346
                                       6889**********************88877776665 PP

  == domain 10  score: 41.9 bits;  conditional E-value: 1.5e-13
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       a+y++Gky+eAi+aY +A +++P++aea+yn G+a+
  gi|330507774|ref|YP_004384202.1| 344 ALYDLGKYDEAIQAYDQANRINPQFAEAWYNKGVAL 379
                                       89*******************************996 PP

  == domain 11  score: 39.5 bits;  conditional E-value: 8.6e-13
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       a++++Gky+eAi+a  +A+ ++P++aea+yn G+++ ++G
  gi|330507774|ref|YP_004384202.1| 378 ALTALGKYDEAIKACDQAISINPQFAEAWYNKGVVLKALG 417
                                       899*********************************9998 PP

  == domain 12  score: 7.4 bits;  conditional E-value: 0.0095
                            TPR_11   4 yyeqGkyeeAieaYk 18 
                                       + ++Gky+eAi+a++
  gi|330507774|ref|YP_004384202.1| 413 LKALGKYDEAIKAFE 427
                                       5689*******9875 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.1e-05    0.0041       4      34 .]      32      62 ..      32      62 .. 0.86
   2 !   32.2   0.4   1.8e-10   6.7e-08       2      33 ..      64      95 ..      63      96 .. 0.95
   3 !   28.2   0.2   3.4e-09   1.2e-06       2      34 .]      98     130 ..      97     130 .. 0.95
   4 !   29.3   0.2   1.5e-09   5.6e-07       3      33 ..     133     163 ..     133     164 .. 0.96
   5 !   28.4   0.1   2.9e-09   1.1e-06       2      34 .]     166     198 ..     165     198 .. 0.95
   6 !   26.4   0.0   1.2e-08   4.5e-06       1      33 [.     199     231 ..     199     232 .. 0.95
   7 !   34.3   0.1   3.7e-11   1.4e-08       1      33 [.     233     265 ..     233     266 .. 0.97
   8 !   27.9   0.1   4.2e-09   1.5e-06       1      33 [.     267     299 ..     267     300 .. 0.96
   9 !   34.4   0.1   3.4e-11   1.2e-08       1      34 []     301     334 ..     301     334 .. 0.97
  10 !   21.7   0.1   4.1e-07   0.00015       3      33 ..     337     367 ..     337     368 .. 0.94
  11 !   33.8   0.1   5.3e-11   1.9e-08       1      33 [.     369     401 ..     369     402 .. 0.97
  12 !   23.9   0.3   7.9e-08   2.9e-05       1      25 [.     403     427 ..     403     430 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  4 yynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      ++ +g++   l  y+eA+++y +a+++dp++
  gi|330507774|ref|YP_004384202.1| 32 WLEKGNAFVMLSMYDEAIQAYDQAISIDPQD 62
                                      5667777777889****************86 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 1.8e-10
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                                       a+ n+g +++ lg+y+eA+++y +a+++dp+
  gi|330507774|ref|YP_004384202.1| 64 YAWSNKGEALRALGRYDEAIQAYDQAISIDPQ 95
                                      69*****************************8 PP

  == domain 3  score: 28.2 bits;  conditional E-value: 3.4e-09
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        a+ n+g +++ lg+y+eA+ ++ +a++++p++
  gi|330507774|ref|YP_004384202.1|  98 YAWSNKGEALRALGKYDEAINACDQAISINPQD 130
                                       69*****************************86 PP

  == domain 4  score: 29.3 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+  +g+++ +lg+y+eA+ +y +a+++dp+
  gi|330507774|ref|YP_004384202.1| 133 AWTIKGNALYDLGKYDEAINAYDQAISIDPQ 163
                                       7999**************************8 PP

  == domain 5  score: 28.4 bits;  conditional E-value: 2.9e-09
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        a+ n+g ++  lg+y+eA++++ +a+++dp+n
  gi|330507774|ref|YP_004384202.1| 166 YAWSNKGTALGHLGKYDEAIKACDQAISIDPQN 198
                                       69*****************************96 PP

  == domain 6  score: 26.4 bits;  conditional E-value: 1.2e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a a+yn+g ++  lg+y+eA++ + +a+++dp+
  gi|330507774|ref|YP_004384202.1| 199 AYAWYNKGTVLGILGKYDEAIKPFDQAISIDPQ 231
                                       569*****************************7 PP

  == domain 7  score: 34.3 bits;  conditional E-value: 3.7e-11
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       aea+yn+g ++  lg+y+eA++++ +a+++dp+
  gi|330507774|ref|YP_004384202.1| 233 AEAWYNKGTALGRLGKYDEAIKACDQAISIDPQ 265
                                       79******************************7 PP

  == domain 8  score: 27.9 bits;  conditional E-value: 4.2e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ae +  +g ++ +lg+y+eA+++y +a++++p+
  gi|330507774|ref|YP_004384202.1| 267 AETWTIKGIALYDLGKYDEAIQAYDQAISINPQ 299
                                       7899****************************7 PP

  == domain 9  score: 34.4 bits;  conditional E-value: 3.4e-11
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       aea+yn+g ++  lg+y+eA++++ +a++++p++
  gi|330507774|ref|YP_004384202.1| 301 AEAWYNKGVALTALGKYDEAIKACDQAISINPQD 334
                                       79******************************86 PP

  == domain 10  score: 21.7 bits;  conditional E-value: 4.1e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+  +g ++ +lg+y+eA+++y +a +++p+
  gi|330507774|ref|YP_004384202.1| 337 AWTIKGIALYDLGKYDEAIQAYDQANRINPQ 367
                                       6899999***********************7 PP

  == domain 11  score: 33.8 bits;  conditional E-value: 5.3e-11
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       aea+yn+g ++  lg+y+eA++++ +a++++p+
  gi|330507774|ref|YP_004384202.1| 369 AEAWYNKGVALTALGKYDEAIKACDQAISINPQ 401
                                       79******************************7 PP

  == domain 12  score: 23.9 bits;  conditional E-value: 7.9e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyye 25 
                                       aea+yn+g +++ lg+y+eA++++e
  gi|330507774|ref|YP_004384202.1| 403 AEAWYNKGVVLKALGKYDEAIKAFE 427
                                       79**********************8 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.1   2.4e-09   8.8e-07       1      34 []      51      84 ..      51      84 .. 0.97
   2 !   26.0   0.4   2.1e-08   7.6e-06       1      33 [.      85     117 ..      85     118 .. 0.96
   3 !   20.1   0.1   1.6e-06   0.00058       2      33 ..     120     151 ..     119     152 .. 0.95
   4 !   26.1   0.1   1.9e-08   7.1e-06       1      34 []     153     186 ..     153     186 .. 0.96
   5 !   28.9   0.0   2.3e-09   8.4e-07       2      34 .]     188     220 ..     187     220 .. 0.95
   6 !   27.1   0.0   9.2e-09   3.4e-06       2      34 .]     222     254 ..     222     254 .. 0.95
   7 !   18.4   0.0   5.5e-06     0.002       2      34 .]     256     288 ..     255     288 .. 0.96
   8 !   27.1   0.1   8.8e-09   3.2e-06       1      34 []     289     322 ..     289     322 .. 0.96
   9 !   20.2   0.0   1.4e-06   0.00051       2      34 .]     324     356 ..     323     356 .. 0.96
  10 !   23.8   0.3     1e-07   3.7e-05       2      34 .]     358     390 ..     357     390 .. 0.95
  11 !   28.4   0.0   3.6e-09   1.3e-06       2      34 .]     392     424 ..     391     424 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.4e-09
                            TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtArq 34
                                      +y +a+ +dP +a+a+ n++e+l+ +G++++A+q
  gi|330507774|ref|YP_004384202.1| 51 AYDQAISIDPQDAYAWSNKGEALRALGRYDEAIQ 84
                                      59******************************98 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 2.1e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y +a+ +dP +a+a+ n++e+l+ +G++++A+
  gi|330507774|ref|YP_004384202.1|  85 AYDQAISIDPQYAYAWSNKGEALRALGKYDEAI 117
                                       59*****************************97 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 1.6e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + +a+ ++P +a a++ ++++l+ +G++++A+
  gi|330507774|ref|YP_004384202.1| 120 CDQAISINPQDAFAWTIKGNALYDLGKYDEAI 151
                                       789***************************97 PP

  == domain 4  score: 26.1 bits;  conditional E-value: 1.9e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a+ +dP +a+a+ n++++l ++G++++A++
  gi|330507774|ref|YP_004384202.1| 153 AYDQAISIDPQYAYAWSNKGTALGHLGKYDEAIK 186
                                       59******************************85 PP

  == domain 5  score: 28.9 bits;  conditional E-value: 2.3e-09
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +a+ +dP na+a++n++++l  +G++++A++
  gi|330507774|ref|YP_004384202.1| 188 CDQAISIDPQNAYAWYNKGTVLGILGKYDEAIK 220
                                       789****************************85 PP

  == domain 6  score: 27.1 bits;  conditional E-value: 9.2e-09
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +a+ +dP  a+a++n++++l ++G++++A++
  gi|330507774|ref|YP_004384202.1| 222 FDQAISIDPQFAEAWYNKGTALGRLGKYDEAIK 254
                                       679****************************85 PP

  == domain 7  score: 18.4 bits;  conditional E-value: 5.5e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +a+ +dP  a+ ++ ++ +l+ +G++++A+q
  gi|330507774|ref|YP_004384202.1| 256 CDQAISIDPQLAETWTIKGIALYDLGKYDEAIQ 288
                                       789****************************98 PP

  == domain 8  score: 27.1 bits;  conditional E-value: 8.8e-09
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a+ ++P  a+a++n++++l  +G++++A++
  gi|330507774|ref|YP_004384202.1| 289 AYDQAISINPQIAEAWYNKGVALTALGKYDEAIK 322
                                       59******************************85 PP

  == domain 9  score: 20.2 bits;  conditional E-value: 1.4e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +a+ ++P +a a++ ++ +l+ +G++++A+q
  gi|330507774|ref|YP_004384202.1| 324 CDQAISINPQDAFAWTIKGIALYDLGKYDEAIQ 356
                                       789****************************98 PP

  == domain 10  score: 23.8 bits;  conditional E-value: 1e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y +a +++P  a+a++n++++l  +G++++A++
  gi|330507774|ref|YP_004384202.1| 358 YDQANRINPQFAEAWYNKGVALTALGKYDEAIK 390
                                       99999**************************85 PP

  == domain 11  score: 28.4 bits;  conditional E-value: 3.6e-09
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +a+ ++P  a+a++n++++l+ +G++++A++
  gi|330507774|ref|YP_004384202.1| 392 CDQAISINPQFAEAWYNKGVVLKALGKYDEAIK 424
                                       789****************************85 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.3e-06   0.00046       2      41 ..      30      69 ..      29      72 .. 0.90
   2 !   24.6   1.2   7.3e-08   2.7e-05       6      41 ..      68     103 ..      65     106 .. 0.88
   3 !   24.0   0.1   1.1e-07   4.2e-05       4      39 ..     100     135 ..      97     138 .. 0.90
   4 !   21.2   0.1   9.1e-07   0.00033       4      39 ..     134     169 ..     133     176 .. 0.88
   5 !   20.8   0.0   1.3e-06   0.00047       8      42 ..     172     206 ..     167     209 .. 0.87
   6 !   18.4   0.0   7.2e-06    0.0026      13      42 ..     211     240 ..     205     243 .. 0.89
   7 !   21.2   0.0   9.4e-07   0.00034       2      39 ..     234     271 ..     234     275 .. 0.94
   8 !   25.8   0.1     3e-08   1.1e-05       2      42 ..     268     308 ..     267     310 .. 0.90
   9 !   25.7   0.0   3.3e-08   1.2e-05       2      39 ..     302     339 ..     301     343 .. 0.94
  10 !   22.5   0.2   3.5e-07   0.00013       4      42 ..     338     376 ..     337     378 .. 0.89
  11 !   27.8   0.0   7.2e-09   2.6e-06       2      42 ..     370     410 ..     370     412 .. 0.94
  12 !   11.2   0.0    0.0015      0.53       2      27 ..     404     429 ..     404     432 .] 0.90

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.3e-06
                            TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeawlll 41
                                      + +l+ + a+  l  +deAi+++++a++ +P+da aw   
  gi|330507774|ref|YP_004384202.1| 30 AEWLEKGNAFVMLSMYDEAIQAYDQAISIDPQDAYAWSNK 69
                                      579999******************************9665 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 7.3e-08
                            TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawlll 41 
                                         +eal+alG++deAi+++++a++ +P+ a aw   
  gi|330507774|ref|YP_004384202.1|  68 NKGEALRALGRYDEAIQAYDQAISIDPQYAYAWSNK 103
                                       5689***************************99665 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 1.1e-07
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +   +eal+alG++deAi+++++a++ +P+da aw+
  gi|330507774|ref|YP_004384202.1| 100 WSNKGEALRALGKYDEAINACDQAISINPQDAFAWT 135
                                       556689**************************9996 PP

  == domain 4  score: 21.2 bits;  conditional E-value: 9.1e-07
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +   + al+ lG++deAi+++++a++ +P+ a aw 
  gi|330507774|ref|YP_004384202.1| 134 WTIKGNALYDLGKYDEAINAYDQAISIDPQYAYAWS 169
                                       5566899*************************9995 PP

  == domain 5  score: 20.8 bits;  conditional E-value: 1.3e-06
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                                       + al +lG++deAi+++++a++ +P++a aw+  +
  gi|330507774|ref|YP_004384202.1| 172 GTALGHLGKYDEAIKACDQAISIDPQNAYAWYNKG 206
                                       5677799************************8765 PP

  == domain 6  score: 18.4 bits;  conditional E-value: 7.2e-06
                            TPR_14  13 alGdpdeAiallrralalaPddaeawllla 42 
                                        lG++deAi+ +++a++ +P++aeaw+  +
  gi|330507774|ref|YP_004384202.1| 211 ILGKYDEAIKPFDQAISIDPQFAEAWYNKG 240
                                       589***********************9765 PP

  == domain 7  score: 21.2 bits;  conditional E-value: 9.4e-07
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       ea++  + al +lG++deAi+++++a++ +P+ ae+w+
  gi|330507774|ref|YP_004384202.1| 234 EAWYNKGTALGRLGKYDEAIKACDQAISIDPQLAETWT 271
                                       68999999***************************997 PP

  == domain 8  score: 25.8 bits;  conditional E-value: 3e-08
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       e +   + al+ lG++deAi+++++a++ +P+ aeaw+  +
  gi|330507774|ref|YP_004384202.1| 268 ETWTIKGIALYDLGKYDEAIQAYDQAISINPQIAEAWYNKG 308
                                       56777799*****************************9765 PP

  == domain 9  score: 25.7 bits;  conditional E-value: 3.3e-08
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       ea++  + al alG++deAi+++++a++ +P+da aw+
  gi|330507774|ref|YP_004384202.1| 302 EAWYNKGVALTALGKYDEAIKACDQAISINPQDAFAWT 339
                                       89********************************9996 PP

  == domain 10  score: 22.5 bits;  conditional E-value: 3.5e-07
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +   + al+ lG++deAi+++++a + +P++aeaw+  +
  gi|330507774|ref|YP_004384202.1| 338 WTIKGIALYDLGKYDEAIQAYDQANRINPQFAEAWYNKG 376
                                       5566899****************************9765 PP

  == domain 11  score: 27.8 bits;  conditional E-value: 7.2e-09
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       ea++  + al alG++deAi+++++a++ +P++aeaw+  +
  gi|330507774|ref|YP_004384202.1| 370 EAWYNKGVALTALGKYDEAIKACDQAISINPQFAEAWYNKG 410
                                       6999999******************************9765 PP

  == domain 12  score: 11.2 bits;  conditional E-value: 0.0015
                            TPR_14   2 eallalaeallalGdpdeAiallrra 27 
                                       ea++  + +l alG++deAi++++  
  gi|330507774|ref|YP_004384202.1| 404 EAWYNKGVVLKALGKYDEAIKAFESG 429
                                       69999999***************976 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   2.6   3.2e-12   1.2e-09       3      67 ..      35      96 ..      33      97 .. 0.91
   2 !   39.3   2.3     2e-12   7.5e-10       3      68 .]      69     131 ..      67     131 .. 0.96
   3 !   43.8   0.2   8.1e-14     3e-11       4      68 .]     138     199 ..     137     199 .. 0.97
   4 !   33.2   0.0   1.7e-10   6.3e-08      10      66 ..     212     265 ..     203     267 .. 0.91
   5 !   50.4   0.1   6.8e-16   2.5e-13       4      68 .]     274     335 ..     273     335 .. 0.96
   6 !   45.2   0.6     3e-14   1.1e-11       4      65 ..     342     400 ..     341     401 .. 0.95
   7 !   33.8   0.1   1.1e-10     4e-08      10      59 ..     382     428 ..     381     432 .] 0.93

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 3.2e-12
                            TPR_16  3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                                      +++a++ +  yd+A+ a+++a+  d   P++a A+ ++g+a+ ++gr++eA+++y+ a+  +p++
  gi|330507774|ref|YP_004384202.1| 35 KGNAFVMLSMYDEAIQAYDQAISID---PQDAYAWSNKGEALRALGRYDEAIQAYDQAISIDPQY 96
                                      5666666667***************...********************************99997 PP

  == domain 2  score: 39.3 bits;  conditional E-value: 2e-12
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       ++ a++++g+yd+A+ a+++a+  d   P+ a A+ ++g+a+ ++g ++eA+ +++ a+   p+++
  gi|330507774|ref|YP_004384202.1|  69 KGEALRALGRYDEAIQAYDQAISID---PQYAYAWSNKGEALRALGKYDEAINACDQAISINPQDA 131
                                       7899*********************...******************************99999985 PP

  == domain 3  score: 43.8 bits;  conditional E-value: 8.1e-14
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       ++a++++g+yd+A++a+++a+  d   P+ a A+ ++g a+ ++g ++eA+ +++ a+  +p+++
  gi|330507774|ref|YP_004384202.1| 138 GNALYDLGKYDEAINAYDQAISID---PQYAYAWSNKGTALGHLGKYDEAIKACDQAISIDPQNA 199
                                       89**********************...***********************************985 PP

  == domain 4  score: 33.2 bits;  conditional E-value: 1.7e-10
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       +g+yd+A++ +++a+  d   P+ aeA++++g a+ r+g ++eA+ +++ a+  +p+
  gi|330507774|ref|YP_004384202.1| 212 LGKYDEAIKPFDQAISID---PQFAEAWYNKGTALGRLGKYDEAIKACDQAISIDPQ 265
                                       79****************...*******************************99997 PP

  == domain 5  score: 50.4 bits;  conditional E-value: 6.8e-16
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       + a++++g+yd+A+ a+++a+  +   P+ aeA++++g+a+ ++g ++eA+ +++ a+   p+++
  gi|330507774|ref|YP_004384202.1| 274 GIALYDLGKYDEAIQAYDQAISIN---PQIAEAWYNKGVALTALGKYDEAIKACDQAISINPQDA 335
                                       789*********************...*******************************9999985 PP

  == domain 6  score: 45.2 bits;  conditional E-value: 3e-14
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       + a++++g+yd+A+ a+++a + +   P+ aeA++++g+a+ ++g ++eA+ +++ a+   p
  gi|330507774|ref|YP_004384202.1| 342 GIALYDLGKYDEAIQAYDQANRIN---PQFAEAWYNKGVALTALGKYDEAIKACDQAISINP 400
                                       789*********************...****************************9987776 PP

  == domain 7  score: 33.8 bits;  conditional E-value: 1.1e-10
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyra 59 
                                       +g+yd+A++a ++a+  +   P+ aeA++++g+++ ++g ++eA+ ++++
  gi|330507774|ref|YP_004384202.1| 382 LGKYDEAIKACDQAISIN---PQFAEAWYNKGVVLKALGKYDEAIKAFES 428
                                       79****************...************************88876 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   2.4   1.8e-09   6.6e-07       7      49 ..      45      87 ..      39      88 .. 0.95
   2 !   39.1   2.1   2.2e-12   8.1e-10       2      59 ..      74     131 ..      73     139 .. 0.92
   3 !   35.1   1.1   3.8e-11   1.4e-08       1      62 [.     141     202 ..     141     206 .. 0.95
   4 !   30.8   0.0   8.6e-10   3.2e-07       5      58 ..     213     266 ..     211     274 .. 0.93
   5 !   39.8   0.3   1.3e-12   4.7e-10       1      59 [.     277     335 ..     277     343 .. 0.93
   6 !   33.2   1.8   1.5e-10   5.7e-08       1      50 [.     345     394 ..     345     395 .. 0.95
   7 !   32.5   0.1   2.6e-10   9.4e-08       3      48 ..     381     426 ..     379     429 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.8e-09
                            TPR_19  7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLd 49
                                      y+eA++++ qa++ dp++a+a+ +  eal alg++deA+++ d
  gi|330507774|ref|YP_004384202.1| 45 YDEAIQAYDQAISIDPQDAYAWSNKGEALRALGRYDEAIQAYD 87
                                      9**************************************9876 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 2.2e-12
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                        a g+y+eA++++ qa++ dp++a+a+ +  eal alg +deA++++d++   +p+da
  gi|330507774|ref|YP_004384202.1|  74 RALGRYDEAIQAYDQAISIDPQYAYAWSNKGEALRALGKYDEAINACDQAISINPQDA 131
                                       678****************************************************986 PP

  == domain 3  score: 35.1 bits;  conditional E-value: 3.8e-11
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       l++ g+y+eA++++ qa++ dp++a+a+ +   al  lg +deA++++d++   dp++a+++
  gi|330507774|ref|YP_004384202.1| 141 LYDLGKYDEAINAYDQAISIDPQYAYAWSNKGTALGHLGKYDEAIKACDQAISIDPQNAYAW 202
                                       5788*****************************************************87765 PP

  == domain 4  score: 30.8 bits;  conditional E-value: 8.6e-10
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       g+y+eA++ + qa++ dp+ aea+++   al  lg +deA++++d++   dp+ 
  gi|330507774|ref|YP_004384202.1| 213 GKYDEAIKPFDQAISIDPQFAEAWYNKGTALGRLGKYDEAIKACDQAISIDPQL 266
                                       89*********************************************9999985 PP

  == domain 5  score: 39.8 bits;  conditional E-value: 1.3e-12
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                       l++ g+y+eA++++ qa++ +p+ aea+++   al alg +deA++++d++   +p+da
  gi|330507774|ref|YP_004384202.1| 277 LYDLGKYDEAIQAYDQAISINPQIAEAWYNKGVALTALGKYDEAIKACDQAISINPQDA 335
                                       5788***************************************************9986 PP

  == domain 6  score: 33.2 bits;  conditional E-value: 1.5e-10
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLda 50 
                                       l++ g+y+eA++++ qa   +p+ aea+++   al alg +deA++++d+
  gi|330507774|ref|YP_004384202.1| 345 LYDLGKYDEAIQAYDQANRINPQFAEAWYNKGVALTALGKYDEAIKACDQ 394
                                       5788******************************************9997 PP

  == domain 7  score: 32.5 bits;  conditional E-value: 2.6e-10
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealL 48 
                                       a g+y+eA+++  qa++ +p+ aea+++   +l alg +deA+++ 
  gi|330507774|ref|YP_004384202.1| 381 ALGKYDEAIKACDQAISINPQFAEAWYNKGVVLKALGKYDEAIKAF 426
                                       679***************************************9986 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.015       5.5      52      75 ..      36      59 ..      27      61 .. 0.77
   2 !   21.2   0.5   7.1e-07   0.00026       4      32 ..      64      92 ..      61      98 .. 0.83
   3 !   30.9   0.7   6.7e-10   2.5e-07       3      76 ..      97     162 ..      95     163 .. 0.92
   4 !   31.4   0.0   4.6e-10   1.7e-07       3      76 ..     165     230 ..     163     231 .. 0.93
   5 !   35.0   0.3   3.6e-11   1.3e-08       2      74 ..     232     296 ..     231     299 .. 0.92
   6 !   31.1   1.0   5.7e-10   2.1e-07       1      71 [.     299     361 ..     299     366 .. 0.90
   7 !   31.4   0.2   4.6e-10   1.7e-07       2      72 ..     368     430 ..     367     432 .] 0.92

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.015
                            TPR_12 52 grlyralgryeeAlelleealaia 75
                                      g ++ +l  y+eA++++ +a+ i+
  gi|330507774|ref|YP_004384202.1| 36 GNAFVMLSMYDEAIQAYDQAISID 59
                                      666777888888888888888776 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 7.1e-07
                            TPR_12  4 talnnlaavlrrlgrydeAlellekalei 32
                                       a++n +++lr+lgrydeA++ +++a+ i
  gi|330507774|ref|YP_004384202.1| 64 YAWSNKGEALRALGRYDEAIQAYDQAISI 92
                                      57889999999999999999999999877 PP

  == domain 3  score: 30.9 bits;  conditional E-value: 6.7e-10
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a a++n +++lr+lg+ydeA+  +++a+ i      p+    a +    g +++ lg+y+eA++++ +a+ i++
  gi|330507774|ref|YP_004384202.1|  97 AYAWSNKGEALRALGKYDEAINACDQAISIN-----PQ---DAFAWTIKGNALYDLGKYDEAINAYDQAISIDP 162
                                       67899**********************9999.....87...5999999*********************99876 PP

  == domain 4  score: 31.4 bits;  conditional E-value: 4.6e-10
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a a++n +++l +lg+ydeA++ +++a+ i      p++   a + +n g+++  lg+y+eA++ + +a+ i++
  gi|330507774|ref|YP_004384202.1| 165 AYAWSNKGTALGHLGKYDEAIKACDQAISID-----PQN---AYAWYNKGTVLGILGKYDEAIKPFDQAISIDP 230
                                       67899**********************9999.....987...889************************99976 PP

  == domain 5  score: 35.0 bits;  conditional E-value: 3.6e-11
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        a a++n +++l rlg+ydeA++ +++a+ i      p+   +a+t    g++++ lg+y+eA++++ +a+ i
  gi|330507774|ref|YP_004384202.1| 232 FAEAWYNKGTALGRLGKYDEAIKACDQAISID-----PQ---LAETWTIKGIALYDLGKYDEAIQAYDQAISI 296
                                       58999***********************9999.....75...999*************************987 PP

  == domain 6  score: 31.1 bits;  conditional E-value: 5.7e-10
                            TPR_12   1 dvatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                       ++a a++n +++l++lg+ydeA++ +++a+ i      p+    a +    g++++ lg+y+eA++++ +a
  gi|330507774|ref|YP_004384202.1| 299 QIAEAWYNKGVALTALGKYDEAIKACDQAISIN-----PQD---AFAWTIKGIALYDLGKYDEAIQAYDQA 361
                                       6899*************************9999.....875...8888888888889***********998 PP

  == domain 7  score: 31.4 bits;  conditional E-value: 4.6e-10
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                        a a++n +++l++lg+ydeA++ +++a+ i      p+    a++ +n g ++ alg+y+eA++++e  +
  gi|330507774|ref|YP_004384202.1| 368 FAEAWYNKGVALTALGKYDEAIKACDQAISIN-----PQ---FAEAWYNKGVVLKALGKYDEAIKAFESGY 430
                                       58999***********************9999.....75...6999*********************9866 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0062       2.3       6      35 ..      36      63 ..      31      64 .. 0.83
   2 !   18.1   0.1   5.1e-06    0.0019       1      31 [.      65      93 ..      65      95 .. 0.87
   3 !   14.8   0.0     6e-05     0.022       1      30 [.      99     126 ..      99     131 .. 0.85
   4 !   12.2   0.0   0.00039      0.14       6      31 ..     138     161 ..     133     163 .. 0.83
   5 !   11.4   0.0   0.00073      0.27       1      34 [.     167     198 ..     167     200 .. 0.87
   6 ?    3.3   0.0      0.28     1e+02      12      32 ..     212     230 ..     201     234 .. 0.78
   7 !   13.2   0.0   0.00019      0.07       1      32 [.     235     264 ..     235     268 .. 0.85
   8 !   11.0   0.0   0.00093      0.34       7      32 ..     275     298 ..     269     302 .. 0.79
   9 !   14.3   0.0   8.4e-05     0.031       1      30 [.     303     330 ..     303     335 .. 0.85
  10 !    8.9   0.0    0.0044       1.6       7      27 ..     343     361 ..     337     369 .. 0.84
  11 !   13.7   0.0   0.00013     0.049       1      28 [.     371     396 ..     371     403 .. 0.89
  12 !   10.4   0.0    0.0015      0.53       1      23 [.     405     427 ..     405     429 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0062
                             TPR_7  6 arlysrlGdyeeAielyeqsLaltkdpeda 35
                                      +++++ l  y+eAi+ y q  a+  dp+da
  gi|330507774|ref|YP_004384202.1| 36 GNAFVMLSMYDEAIQAYDQ--AISIDPQDA 63
                                      677777899**********..988888875 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 5.1e-06
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31
                                      a++n +++ ++lG+y+eAi+ y q  a+  d
  gi|330507774|ref|YP_004384202.1| 65 AWSNKGEALRALGRYDEAIQAYDQ--AISID 93
                                      7899********************..66544 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 6e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       a++n +++ ++lG+y+eAi  + q  a+  
  gi|330507774|ref|YP_004384202.1|  99 AWSNKGEALRALGKYDEAINACDQ--AISI 126
                                       7899********************..6654 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00039
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                       +++  +lG+y+eAi  y q  a+  d
  gi|330507774|ref|YP_004384202.1| 138 GNALYDLGKYDEAINAYDQ--AISID 161
                                       788999*************..66544 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 0.00073
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       a++n + +   lG+y+eAi+ + q  a+  dp++
  gi|330507774|ref|YP_004384202.1| 167 AWSNKGTALGHLGKYDEAIKACDQ--AISIDPQN 198
                                       67899999999*************..88877776 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.28
                             TPR_7  12 lGdyeeAielyeqsLaltkdp 32 
                                       lG+y+eAi+ + q  a+  dp
  gi|330507774|ref|YP_004384202.1| 212 LGKYDEAIKPFDQ--AISIDP 230
                                       8*******98888..665555 PP

  == domain 7  score: 13.2 bits;  conditional E-value: 0.00019
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       a++n + +  rlG+y+eAi+ + q  a+  dp
  gi|330507774|ref|YP_004384202.1| 235 AWYNKGTALGRLGKYDEAIKACDQ--AISIDP 264
                                       6899999*****************..666555 PP

  == domain 8  score: 11.0 bits;  conditional E-value: 0.00093
                             TPR_7   7 rlysrlGdyeeAielyeqsLaltkdp 32 
                                        +  +lG+y+eAi+ y q  a+   p
  gi|330507774|ref|YP_004384202.1| 275 IALYDLGKYDEAIQAYDQ--AISINP 298
                                       56678*************..776555 PP

  == domain 9  score: 14.3 bits;  conditional E-value: 8.4e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       a++n +++  +lG+y+eAi+ + q  a+  
  gi|330507774|ref|YP_004384202.1| 303 AWYNKGVALTALGKYDEAIKACDQ--AISI 330
                                       789*********************..6654 PP

  == domain 10  score: 8.9 bits;  conditional E-value: 0.0044
                             TPR_7   7 rlysrlGdyeeAielyeqsLa 27 
                                        +  +lG+y+eAi+ y q  a
  gi|330507774|ref|YP_004384202.1| 343 IALYDLGKYDEAIQAYDQ--A 361
                                       56678***********99..5 PP

  == domain 11  score: 13.7 bits;  conditional E-value: 0.00013
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       a++n +++  +lG+y+eAi+ + q  a+
  gi|330507774|ref|YP_004384202.1| 371 AWYNKGVALTALGKYDEAIKACDQ--AI 396
                                       789*******************99..54 PP

  == domain 12  score: 10.4 bits;  conditional E-value: 0.0015
                             TPR_7   1 aLlnLarlysrlGdyeeAielye 23 
                                       a++n +++  +lG+y+eAi+ +e
  gi|330507774|ref|YP_004384202.1| 405 AWYNKGVVLKALGKYDEAIKAFE 427
                                       78999***************998 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 !   13.2   0.1   0.00021     0.076      29      80 ..      35      87 ..      14      89 .. 0.84
   2 !   31.6   0.3   3.8e-10   1.4e-07      24      80 ..      95     155 ..      88     157 .. 0.88
   3 !   17.5   0.1   9.9e-06    0.0036      29      77 ..     171     220 ..     156     225 .. 0.85
   4 !   29.9   0.1   1.3e-09   4.7e-07      19      80 ..     229     291 ..     222     293 .. 0.92
   5 !   29.8   0.3   1.4e-09   5.1e-07      21      80 ..     299     359 ..     290     361 .. 0.90
   6 !   26.5   0.2   1.5e-08   5.5e-06      20      80 ..     366     427 ..     361     429 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00021
                                      HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3 29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80
                                      ++ ++  ++ y++A++ +++a  +++++  ++  ++++l +L++y+eAi+a++
  gi|330507774|ref|YP_004384202.1| 35 KGNAFVMLSMYDEAIQAYDQAiSIDPQDAYAWSNKGEALRALGRYDEAIQAYD 87
                                      37788888999**********999999999999999*************9987 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 3.8e-10
                                       HHHHH...HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  24 edayl...lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       + ay+   ++++l  +g+y++A++ +++a  +n+++  ++ +++ +l++L+ky+eAi+a++
  gi|330507774|ref|YP_004384202.1|  95 QYAYAwsnKGEALRALGKYDEAINACDQAiSINPQDAFAWTIKGNALYDLGKYDEAINAYD 155
                                       555553445999**********************************************987 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 9.9e-06
                                       HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3  29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       ++ +l ++g+y++A++ +++a  +++++  ++y ++ +l  L+ky+eAi+
  gi|330507774|ref|YP_004384202.1| 171 KGTALGHLGKYDEAIKACDQAiSIDPQNAYAWYNKGTVLGILGKYDEAIK 220
                                       4788999*****************************************97 PP

  == domain 4  score: 29.9 bits;  conditional E-value: 1.3e-09
                                       HH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  19 etespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +++ +e+ y ++ +l ++g+y++A++ +++a  ++++  + + +++ +l++L+ky+eAi+a++
  gi|330507774|ref|YP_004384202.1| 229 DPQFAEAWYNKGTALGRLGKYDEAIKACDQAiSIDPQLAETWTIKGIALYDLGKYDEAIQAYD 291
                                       67888999999*************************************************987 PP

  == domain 5  score: 29.8 bits;  conditional E-value: 1.4e-09
                                       --HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  21 espedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       + +e+ y ++ +l  +g+y++A++ +++a  +n+++  ++ +++ +l++L+ky+eAi+a++
  gi|330507774|ref|YP_004384202.1| 299 QIAEAWYNKGVALTALGKYDEAIKACDQAiSINPQDAFAWTIKGIALYDLGKYDEAIQAYD 359
                                       556777888999**********************************************987 PP

  == domain 6  score: 26.5 bits;  conditional E-value: 1.5e-08
                                       H--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  20 tespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       ++ +e+ y ++ +l  +g+y++A++ +++a  +n++  +++y ++ +l +L+ky+eAi+a+e
  gi|330507774|ref|YP_004384202.1| 366 PQFAEAWYNKGVALTALGKYDEAIKACDQAiSINPQFAEAWYNKGVVLKALGKYDEAIKAFE 427
                                       677788888999************************************************98 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   1.2   5.4e-08     2e-05      11      61 ..      45      95 ..      41     109 .. 0.94
   2 !   20.0   0.0   1.5e-06   0.00054       9      61 ..     111     163 ..     104     168 .. 0.93
   3 !   22.6   0.0   2.3e-07   8.6e-05      10      61 ..     180     231 ..     171     237 .. 0.94
   4 !   24.1   0.0   8.3e-08     3e-05       9      61 ..     247     299 ..     239     304 .. 0.92
   5 !   21.0   0.0   7.5e-07   0.00027      12      63 ..     284     335 ..     283     340 .. 0.95
   6 !   20.4   0.0   1.1e-06   0.00041       9      61 ..     315     367 ..     307     372 .. 0.91
   7 !   16.7   0.0   1.6e-05     0.006       9      61 ..     349     401 ..     340     401 .. 0.90
   8 !   19.5   0.0   2.2e-06   0.00079       9      53 ..     383     427 ..     375     431 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5.4e-08
                             TPR_9 11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61
                                      +++a+++++  + ++P+d++ +   G +l  lG++ +A+++ +++++++p+
  gi|330507774|ref|YP_004384202.1| 45 YDEAIQAYDQAISIDPQDAYAWSNKGEALRALGRYDEAIQAYDQAISIDPQ 95
                                      689**********************************************96 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.5e-06
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                        ++++a+ +++  + ++P+d+  +   G +l+ lG + +A+++ +++++++p+
  gi|330507774|ref|YP_004384202.1| 111 GKYDEAINACDQAISINPQDAFAWTIKGNALYDLGKYDEAINAYDQAISIDPQ 163
                                       5799***********************************************97 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 2.3e-07
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       ++++a+++++  + ++P+ ++ ++  G +l  lG + +A++ ++++++++p+
  gi|330507774|ref|YP_004384202.1| 180 KYDEAIKACDQAISIDPQNAYAWYNKGTVLGILGKYDEAIKPFDQAISIDPQ 231
                                       6899**********************************************97 PP

  == domain 4  score: 24.1 bits;  conditional E-value: 8.3e-08
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                        ++++a+++++  + ++P+ +e +   G++l+ lG + +A+++ +++++++p+
  gi|330507774|ref|YP_004384202.1| 247 GKYDEAIKACDQAISIDPQLAETWTIKGIALYDLGKYDEAIQAYDQAISINPQ 299
                                       6899*********************************************9997 PP

  == domain 5  score: 21.0 bits;  conditional E-value: 7.5e-07
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       ++a+++++  + ++P+ +e ++  G++l  lG + +A+++ +++++++p+++
  gi|330507774|ref|YP_004384202.1| 284 DEAIQAYDQAISINPQIAEAWYNKGVALTALGKYDEAIKACDQAISINPQDA 335
                                       789**********************************************987 PP

  == domain 6  score: 20.4 bits;  conditional E-value: 1.1e-06
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                        ++++a+++++  + ++P+d+  +   G++l+ lG + +A+++ +++ +++p+
  gi|330507774|ref|YP_004384202.1| 315 GKYDEAIKACDQAISINPQDAFAWTIKGIALYDLGKYDEAIQAYDQANRINPQ 367
                                       5799****************************************999888886 PP

  == domain 7  score: 16.7 bits;  conditional E-value: 1.6e-05
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                        ++++a+++++    ++P+ +e ++  G++l  lG + +A+++ +++++++p+
  gi|330507774|ref|YP_004384202.1| 349 GKYDEAIQAYDQANRINPQFAEAWYNKGVALTALGKYDEAIKACDQAISINPQ 401
                                       6899***************************************9999998885 PP

  == domain 8  score: 19.5 bits;  conditional E-value: 2.2e-06
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLe 53 
                                        ++++a+++++  + ++P+ +e ++  G++l  lG + +A++++e
  gi|330507774|ref|YP_004384202.1| 383 GKYDEAIKACDQAISINPQFAEAWYNKGVVLKALGKYDEAIKAFE 427
                                       5799**************************************998 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.91   3.3e+02      18      31 ..      45      58 ..      43      61 .. 0.85
   2 !   15.9   0.4   2.5e-05     0.009       6      31 ..      67      92 ..      63      92 .. 0.92
   3 !   14.1   0.2   8.9e-05     0.033       6      31 ..     101     126 ..      97     127 .. 0.92
   4 !   16.1   0.1   2.1e-05    0.0076       9      31 ..     138     160 ..     138     160 .. 0.96
   5 !   10.7   0.0    0.0011      0.39       6      31 ..     169     194 ..     165     194 .. 0.92
   6 !    9.4   0.0    0.0026      0.96       8      31 ..     205     228 ..     203     228 .. 0.90
   7 !   10.3   0.0    0.0014      0.51       7      31 ..     238     262 ..     235     262 .. 0.92
   8 !   15.4   0.1   3.4e-05     0.012       9      31 ..     274     296 ..     273     297 .. 0.95
   9 !   13.0   0.1   0.00019      0.07       7      31 ..     306     330 ..     301     331 .. 0.93
  10 !   10.5   0.2    0.0012      0.44       9      28 ..     342     361 ..     342     362 .. 0.95
  11 !   13.0   0.0    0.0002     0.073       7      31 ..     374     398 ..     370     399 .. 0.93
  12 ?    6.3   0.0     0.025       9.2       7      26 ..     408     427 ..     405     430 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.91
                            TPR_10 18 ydeAealleealai 31
                                      ydeA + +++a++i
  gi|330507774|ref|YP_004384202.1| 45 YDEAIQAYDQAISI 58
                                      78999999999876 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.5e-05
                            TPR_10  6 nNLanalrqrgrydeAealleealai 31
                                      +N + alr++grydeA + +++a++i
  gi|330507774|ref|YP_004384202.1| 67 SNKGEALRALGRYDEAIQAYDQAISI 92
                                      57899******************986 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 8.9e-05
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       +N + alr++g+ydeA + +++a++i
  gi|330507774|ref|YP_004384202.1| 101 SNKGEALRALGKYDEAINACDQAISI 126
                                       57899*******************97 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 2.1e-05
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       +nal+++g+ydeA + +++a++i
  gi|330507774|ref|YP_004384202.1| 138 GNALYDLGKYDEAINAYDQAISI 160
                                       89*******************86 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.0011
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       +N + al ++g+ydeA + +++a++i
  gi|330507774|ref|YP_004384202.1| 169 SNKGTALGHLGKYDEAIKACDQAISI 194
                                       57899******************986 PP

  == domain 6  score: 9.4 bits;  conditional E-value: 0.0026
                            TPR_10   8 LanalrqrgrydeAealleealai 31 
                                        + +l  +g+ydeA +++++a++i
  gi|330507774|ref|YP_004384202.1| 205 KGTVLGILGKYDEAIKPFDQAISI 228
                                       5889999**************986 PP

  == domain 7  score: 10.3 bits;  conditional E-value: 0.0014
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N + al ++g+ydeA + +++a++i
  gi|330507774|ref|YP_004384202.1| 238 NKGTALGRLGKYDEAIKACDQAISI 262
                                       56899*****************986 PP

  == domain 8  score: 15.4 bits;  conditional E-value: 3.4e-05
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       ++al+++g+ydeA + +++a++i
  gi|330507774|ref|YP_004384202.1| 274 GIALYDLGKYDEAIQAYDQAISI 296
                                       89*******************97 PP

  == domain 9  score: 13.0 bits;  conditional E-value: 0.00019
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N ++al+++g+ydeA + +++a++i
  gi|330507774|ref|YP_004384202.1| 306 NKGVALTALGKYDEAIKACDQAISI 330
                                       6699*******************97 PP

  == domain 10  score: 10.5 bits;  conditional E-value: 0.0012
                            TPR_10   9 analrqrgrydeAealleea 28 
                                       ++al+++g+ydeA + +++a
  gi|330507774|ref|YP_004384202.1| 342 GIALYDLGKYDEAIQAYDQA 361
                                       89**************9997 PP

  == domain 11  score: 13.0 bits;  conditional E-value: 0.0002
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N ++al+++g+ydeA + +++a++i
  gi|330507774|ref|YP_004384202.1| 374 NKGVALTALGKYDEAIKACDQAISI 398
                                       6699*******************97 PP

  == domain 12  score: 6.3 bits;  conditional E-value: 0.025
                            TPR_10   7 NLanalrqrgrydeAealle 26 
                                       N +++l ++g+ydeA + +e
  gi|330507774|ref|YP_004384202.1| 408 NKGVVLKALGKYDEAIKAFE 427
                                       6699***********99877 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.017       6.4       7      32 ..      36      61 ..      30      62 .. 0.83
   2 !   15.1   0.3   7.3e-05     0.027       5      32 ..      68      95 ..      64      96 .. 0.88
   3 !   10.0   0.0     0.003       1.1       5      32 ..     102     129 ..      98     130 .. 0.89
   4 !   11.0   0.1    0.0015      0.56       7      32 ..     138     163 ..     136     164 .. 0.90
   5 ?    7.2   0.0     0.023       8.6       7      32 ..     172     197 ..     163     198 .. 0.79
   6 ?    4.4   0.0      0.19        71       4      31 ..     203     230 ..     199     231 .. 0.70
   7 !   12.5   0.0   0.00051      0.18       1      31 [.     234     264 ..     234     265 .. 0.93
   8 !   12.6   0.1   0.00045      0.16       7      32 ..     274     299 ..     272     299 .. 0.90
   9 !   13.0   0.0   0.00034      0.12       1      32 [.     302     333 ..     302     334 .. 0.95
  10 !    8.8   0.1    0.0076       2.8       7      30 ..     342     365 ..     340     367 .. 0.83
  11 !   12.6   0.0   0.00048      0.17       1      32 [.     370     401 ..     370     401 .. 0.94
  12 !   11.7   0.0    0.0009      0.33       1      24 [.     404     427 ..     404     428 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.017
                                      HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  7 alsyrklgdtdkAlealerlikeYPd 32
                                      + ++ +l  +d+A++a+++ i+  P+
  gi|330507774|ref|YP_004384202.1| 36 GNAFVMLSMYDEAIQAYDQAISIDPQ 61
                                      566677779************99886 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7.3e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  5 klalsyrklgdtdkAlealerlikeYPd 32
                                      + ++++r+lg++d+A++a+++ i+  P+
  gi|330507774|ref|YP_004384202.1| 68 NKGEALRALGRYDEAIQAYDQAISIDPQ 95
                                      5699****99*************99886 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   5 klalsyrklgdtdkAlealerlikeYPd 32 
                                       + ++++r+lg++d+A+ a ++ i+  P+
  gi|330507774|ref|YP_004384202.1| 102 NKGEALRALGKYDEAINACDQAISINPQ 129
                                       5699****99*************99996 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + +++ lg++d+A+ a+++ i+  P+
  gi|330507774|ref|YP_004384202.1| 138 GNALYDLGKYDEAINAYDQAISIDPQ 163
                                       67899999*************99886 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + ++  lg++d+A++a ++ i+  P+
  gi|330507774|ref|YP_004384202.1| 172 GTALGHLGKYDEAIKACDQAISIDPQ 197
                                       55666679*************99997 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlikeYP 31 
                                       y+ +  +  lg++d+A++ +++ i+  P
  gi|330507774|ref|YP_004384202.1| 203 YNKGTVLGILGKYDEAIKPFDQAISIDP 230
                                       44444444348************99888 PP

  == domain 7  score: 12.5 bits;  conditional E-value: 0.00051
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                       +A y+ + ++ +lg++d+A++a ++ i+  P
  gi|330507774|ref|YP_004384202.1| 234 EAWYNKGTALGRLGKYDEAIKACDQAISIDP 264
                                       799*********9*************99888 PP

  == domain 8  score: 12.6 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + +++ lg++d+A++a+++ i+  P+
  gi|330507774|ref|YP_004384202.1| 274 GIALYDLGKYDEAIQAYDQAISINPQ 299
                                       67899999*************99885 PP

  == domain 9  score: 13.0 bits;  conditional E-value: 0.00034
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       +A y+ + ++ +lg++d+A++a ++ i+  P+
  gi|330507774|ref|YP_004384202.1| 302 EAWYNKGVALTALGKYDEAIKACDQAISINPQ 333
                                       799*********9**************99996 PP

  == domain 10  score: 8.8 bits;  conditional E-value: 0.0076
                                       HHHHHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeY 30 
                                       + +++ lg++d+A++a+++  +  
  gi|330507774|ref|YP_004384202.1| 342 GIALYDLGKYDEAIQAYDQANRIN 365
                                       67899999*********9976555 PP

  == domain 11  score: 12.6 bits;  conditional E-value: 0.00048
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       +A y+ + ++ +lg++d+A++a ++ i+  P+
  gi|330507774|ref|YP_004384202.1| 370 EAWYNKGVALTALGKYDEAIKACDQAISINPQ 401
                                       799*********9**************99885 PP

  == domain 12  score: 11.7 bits;  conditional E-value: 0.0009
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAleale 24 
                                       +A y+ +  +++lg++d+A++a+e
  gi|330507774|ref|YP_004384202.1| 404 EAWYNKGVVLKALGKYDEAIKAFE 427
                                       799*********9**********8 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.88   3.2e+02      16      34 ..      44      62 ..      40      65 .. 0.89
   2 ?    4.9   0.1     0.076        28      14      33 ..      76      95 ..      72      99 .. 0.92
   3 ?    6.2   0.0     0.029        11      14      34 ..     110     130 ..     106     133 .. 0.92
   4 ?    6.3   0.1     0.028        10      10      33 ..     140     163 ..     138     167 .. 0.91
   5 !   12.6   0.0   0.00029      0.11      14      35 ..     178     199 ..     173     201 .. 0.88
   6 ?    4.8   0.0     0.083        30      14      37 ..     212     235 ..     212     236 .. 0.93
   7 !   12.8   0.0   0.00026     0.094       5      33 ..     237     265 ..     233     269 .. 0.86
   8 !    7.8   0.0    0.0093       3.4       9      34 ..     275     300 ..     273     304 .. 0.90
   9 !   11.5   0.0   0.00067      0.24       3      34 ..     303     334 ..     301     337 .. 0.90
  10 ?    5.8   0.1     0.039        14       9      37 ..     343     371 ..     341     372 .. 0.90
  11 !   13.4   0.0   0.00017     0.061       3      37 ..     371     405 ..     369     406 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.88
                                      -HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C 16 eYseArryvdalLeiEPen 34
                                       Y+eA +  d+ ++i+P+ 
  gi|330507774|ref|YP_004384202.1| 44 MYDEAIQAYDQAISIDPQD 62
                                      6****************85 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.076
                                      HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPe 33
                                      lg+Y+eA +  d+ ++i+P+
  gi|330507774|ref|YP_004384202.1| 76 LGRYDEAIQAYDQAISIDPQ 95
                                      89*****************8 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.029
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                       lg+Y+eA + +d+ ++i P+ 
  gi|330507774|ref|YP_004384202.1| 110 LGKYDEAINACDQAISINPQD 130
                                       89****************985 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.028
                                       HHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPe 33 
                                       + y lg+Y+eA +  d+ ++i+P+
  gi|330507774|ref|YP_004384202.1| 140 ALYDLGKYDEAINAYDQAISIDPQ 163
                                       6788*******************8 PP

  == domain 5  score: 12.6 bits;  conditional E-value: 0.00029
                                       HT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenr 35 
                                       lg+Y+eA + +d+ ++i+P+n 
  gi|330507774|ref|YP_004384202.1| 178 LGKYDEAIKACDQAISIDPQNA 199
                                       89******************95 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.083
                                       HT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQa 37 
                                       lg+Y+eA +  d+ ++i+P++  a
  gi|330507774|ref|YP_004384202.1| 212 LGKYDEAIKPFDQAISIDPQFAEA 235
                                       799****************99766 PP

  == domain 7  score: 12.8 bits;  conditional E-value: 0.00026
                                       HHHHHHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C   5 YylAlGhyklgeYseArryvdalLeiEPe 33 
                                       Y    +  +lg+Y+eA + +d+ ++i+P+
  gi|330507774|ref|YP_004384202.1| 237 YNKGTALGRLGKYDEAIKACDQAISIDPQ 265
                                       66667788********************7 PP

  == domain 8  score: 7.8 bits;  conditional E-value: 0.0093
                                       HHHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPen 34 
                                       ++ y lg+Y+eA +  d+ ++i P+ 
  gi|330507774|ref|YP_004384202.1| 275 IALYDLGKYDEAIQAYDQAISINPQI 300
                                       899********************986 PP

  == domain 9  score: 11.5 bits;  conditional E-value: 0.00067
                                       HHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C   3 clYylAlGhyklgeYseArryvdalLeiEPen 34 
                                         Y   ++ + lg+Y+eA + +d+ ++i P+ 
  gi|330507774|ref|YP_004384202.1| 303 AWYNKGVALTALGKYDEAIKACDQAISINPQD 334
                                       568889999********************985 PP

  == domain 10  score: 5.8 bits;  conditional E-value: 0.039
                                       HHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPenrQa 37 
                                       ++ y lg+Y+eA +  d+  +i P++  a
  gi|330507774|ref|YP_004384202.1| 343 IALYDLGKYDEAIQAYDQANRINPQFAEA 371
                                       899****************9999998765 PP

  == domain 11  score: 13.4 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C   3 clYylAlGhyklgeYseArryvdalLeiEPenrQa 37 
                                         Y   ++ + lg+Y+eA + +d+ ++i P++  a
  gi|330507774|ref|YP_004384202.1| 371 AWYNKGVALTALGKYDEAIKACDQAISINPQFAEA 405
                                       568889999*********************99766 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1    0.0013      0.49      51      82 ..      59      90 ..      51      96 .. 0.76
   2 ?    6.5   0.0     0.023       8.3      56      82 ..      98     124 ..      92     127 .. 0.75
   3 !   12.6   0.2   0.00029      0.11      53     125 ..     129     190 ..     122     195 .. 0.77
   4 ?    7.3   0.0     0.013       4.7      57      83 ..     167     193 ..     161     229 .. 0.59
   5 !    8.2   0.1    0.0069       2.5      64     126 ..     242     293 ..     235     302 .. 0.65
   6 !    9.7   0.1    0.0022      0.82      64     126 ..     276     327 ..     267     331 .. 0.69
   7 !   15.8   0.2   3.1e-05     0.011      51     126 ..     331     395 ..     324     399 .. 0.83
   8 !    9.4   0.1    0.0029       1.1      64     124 ..     378     427 ..     378     431 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0013
                                      HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 51 eGfdalchaglsealaklgrydealesadkal 82
                                      +  da +++   eal  lgrydea+++ d+a+
  gi|330507774|ref|YP_004384202.1| 59 DPQDAYAWSNKGEALRALGRYDEAIQAYDQAI 90
                                      55688888888888888888888888888776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  56 lchaglsealaklgrydealesadkal 82 
                                        +++   eal  lg+ydea+++ d+a+
  gi|330507774|ref|YP_004384202.1|  98 YAWSNKGEALRALGKYDEAINACDQAI 124
                                       556666788888888888888888876 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00029
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                           DUF3856  53 fdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrm 125
                                        da++++   +al  lg+ydea+++ d+a+         +     ++  a  ++++al  lG++dea+ka  +
  gi|330507774|ref|YP_004384202.1| 129 QDAFAWTIKGNALYDLGKYDEAINAYDQAISI-------D----PQYAYAWSNKGTALGHLGKYDEAIKACDQ 190
                                       69*************************99863.......2....34555556778888888888888777655 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  57 chaglsealaklgrydealesadkalr 83 
                                       +++    al +lg+ydea+++ d+a+ 
  gi|330507774|ref|YP_004384202.1| 167 AWSNKGTALGHLGKYDEAIKACDQAIS 193
                                       455556677777777777777777764 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.0069
                                       HHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       al +lg+ydea+++ d+a+         + +  + W      ++ al +lG++dea++a+ +a
  gi|330507774|ref|YP_004384202.1| 242 ALGRLGKYDEAIKACDQAISI-------DPQLAETW----TIKGIALYDLGKYDEAIQAYDQA 293
                                       666777777777777777653.......22333344....34777777788888887777766 PP

  == domain 6  score: 9.7 bits;  conditional E-value: 0.0022
                                       HHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       al  lg+ydea+++ d+a+         + +       a ++++val  lG++dea+ka  +a
  gi|330507774|ref|YP_004384202.1| 276 ALYDLGKYDEAIQAYDQAISI-------NPQIA----EAWYNKGVALTALGKYDEAIKACDQA 327
                                       666777777777777777653.......22222....34589999999999999999987665 PP

  == domain 7  score: 15.8 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  51 eGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       +  da++++    al  lg+ydea+++ d+a r        +     ++  a ++++val  lG++dea+ka  +a
  gi|330507774|ref|YP_004384202.1| 331 NPQDAFAWTIKGIALYDLGKYDEAIQAYDQANRI-------N----PQFAEAWYNKGVALTALGKYDEAIKACDQA 395
                                       5679************************999542.......3....35666779****************998766 PP

  == domain 8  score: 9.4 bits;  conditional E-value: 0.0029
                                       HHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafr 124
                                       al+ lg+ydea+++ d+a+         +     ++  a ++++v l+ lG++dea+kaf+
  gi|330507774|ref|YP_004384202.1| 378 ALTALGKYDEAIKACDQAISI-------N----PQFAEAWYNKGVVLKALGKYDEAIKAFE 427
                                       566777788888777777753.......2....345567799****************997 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.3   0.00096      0.35     207     266 ..      44     103 ..      37     122 .. 0.74
   2 !   12.5   0.1   0.00013     0.049     205     261 ..      76     132 ..      68     140 .. 0.94
   3 !   17.4   0.1   4.5e-06    0.0016     204     261 ..     143     200 ..     125     205 .. 0.89
   4 !   16.3   0.0   9.7e-06    0.0035     205     257 ..     212     264 ..     200     266 .. 0.93
   5 !   16.1   0.2   1.1e-05     0.004     204     261 ..     279     336 ..     266     341 .. 0.92
   6 !   17.9   0.1   3.2e-06    0.0012     204     251 ..     381     428 ..     353     431 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00096
                                       -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHHHHHH CS
                             NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyiNskc 266
                                        +++A++  d+ai+ +p+    + +K++ l+  G  ++A+++ ++a ++D +  y  s+ 
  gi|330507774|ref|YP_004384202.1|  44 MYDEAIQAYDQAISIDPQDAYAWSNKGEALRALGRYDEAIQAYDQAISIDPQYAYAWSNK 103
                                       578899999999999999999999999999999999999999999999888777765554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00013
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRy 261
                                       lg++++A++  d+ai+ +p+    + +K++ l+  G  ++A+++ ++a ++  +D +
  gi|330507774|ref|YP_004384202.1|  76 LGRYDEAIQAYDQAISIDPQYAYAWSNKGEALRALGKYDEAINACDQAISINPQDAF 132
                                       7899*********************************************99999976 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 4.5e-06
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HH CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRy 261
                                        lg++++A++  d+ai+ +p+    + +K++ l h G  ++A+++ ++a ++D +  y
  gi|330507774|ref|YP_004384202.1| 143 DLGKYDEAINAYDQAISIDPQYAYAWSNKGTALGHLGKYDEAIKACDQAISIDPQNAY 200
                                       4799*************************************************98776 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 9.7e-06
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                       lg++++A++  d+ai+ +p++ e +++K++ l + G  ++A+++ ++a ++D 
  gi|330507774|ref|YP_004384202.1| 212 LGKYDEAIKPFDQAISIDPQFAEAWYNKGTALGRLGKYDEAIKACDQAISIDP 264
                                       6899********************************************99995 PP

  == domain 5  score: 16.1 bits;  conditional E-value: 1.1e-05
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HH CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRy 261
                                        lg++++A++  d+ai+ +p++ e +++K+  l   G  ++A+++ ++a ++  +D +
  gi|330507774|ref|YP_004384202.1| 279 DLGKYDEAIQAYDQAISINPQIAEAWYNKGVALTALGKYDEAIKACDQAISINPQDAF 336
                                       4799**********************************************99999976 PP

  == domain 6  score: 17.9 bits;  conditional E-value: 3.2e-06
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmee 251
                                        lg++++A++  d+ai+ +p++ e +++K+ +lk  G  ++A+++ e+
  gi|330507774|ref|YP_004384202.1| 381 ALGKYDEAIKACDQAISINPQFAEAWYNKGVVLKALGKYDEAIKAFES 428
                                       5899***************************************99886 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00038      0.14      74     122 ..      41      89 ..      26      93 .. 0.90
   2 !   14.0   0.0   0.00014     0.052      68     122 ..     103     157 ..      95     160 .. 0.93
   3 ?    2.2   0.0      0.61   2.2e+02      71     121 ..     174     224 ..     165     228 .. 0.80
   4 !   15.1   0.0   6.6e-05     0.024      62     122 ..     233     293 ..     224     296 .. 0.89
   5 !   15.0   0.0   6.8e-05     0.025      71     124 ..     310     363 ..     296     367 .. 0.92
   6 ?    7.9   0.0     0.011         4      56     122 ..     363     429 ..     360     432 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00038
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        l  ++ea++ ++++++ +P +  ++    +Al+++Gr  eA+++Y+++
  gi|330507774|ref|YP_004384202.1|  41 MLSMYDEAIQAYDQAISIDPQDAYAWSNKGEALRALGRYDEAIQAYDQA 89 
                                       566789****************************************987 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00014
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  68 laeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                         ea+ +lG+++ea+   +++++ +P +  ++     Al+ +G+  eA+++Y+++
  gi|330507774|ref|YP_004384202.1| 103 KGEALRALGKYDEAINACDQAISINPQDAFAWTIKGNALYDLGKYDEAINAYDQA 157
                                       568999**********************************************987 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.61
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                       a+ +lG+++ea++  +++++ +P +  ++    + l  +G+  eA++ +++
  gi|330507774|ref|YP_004384202.1| 174 ALGHLGKYDEAIKACDQAISIDPQNAYAWYNKGTVLGILGKYDEAIKPFDQ 224
                                       5668999999***99999999999998888877777777777777776665 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 6.6e-05
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  62 lealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        ea      a+ rlG+++ea++  +++++ +P   +++     Al+ +G+  eA+++Y+++
  gi|330507774|ref|YP_004384202.1| 233 AEAWYNKGTALGRLGKYDEAIKACDQAISIDPQLAETWTIKGIALYDLGKYDEAIQAYDQA 293
                                       5566666678889*********************************************987 PP

  == domain 5  score: 15.0 bits;  conditional E-value: 6.8e-05
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       a+++lG+++ea++  +++++ +P +  ++     Al+ +G+  eA+++Y+++ r
  gi|330507774|ref|YP_004384202.1| 310 ALTALGKYDEAIKACDQAISINPQDAFAWTIKGIALYDLGKYDEAIQAYDQANR 363
                                       7899**********************************************9876 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  56 rleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       r++ ++ ea      a+++lG+++ea++  +++++ +P   +++      l ++G+  eA++++e+ 
  gi|330507774|ref|YP_004384202.1| 363 RINPQFAEAWYNKGVALTALGKYDEAIKACDQAISINPQFAEAWYNKGVVLKALGKYDEAIKAFESG 429
                                       666677777777788999*********************99999999999***********999976 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.3   0.00042      0.15       2      25 ..      64      87 ..      63      88 .. 0.86
   2 ?    8.4   0.0     0.011       3.9       2      20 ..      98     116 ..      97     122 .. 0.89
   3 ?    3.3   0.0      0.48   1.8e+02       8      20 ..     138     150 ..     131     156 .. 0.83
   4 ?    4.7   0.0      0.16        59       2      20 ..     166     184 ..     165     185 .. 0.91
   5 ?    0.5   0.0       3.8   1.4e+03       2      20 ..     200     218 ..     199     218 .. 0.90
   6 ?    5.7   0.0     0.079        29       2      20 ..     234     252 ..     233     253 .. 0.92
   7 ?    4.6   0.0      0.18        65       8      25 ..     274     291 ..     267     292 .. 0.82
   8 ?    5.5   0.0     0.087        32       2      20 ..     302     320 ..     301     321 .. 0.92
   9 ?    4.8   0.0      0.15        56       7      25 ..     341     359 ..     335     360 .. 0.80
  10 ?    5.5   0.0     0.087        32       2      20 ..     370     388 ..     369     389 .. 0.92
  11 ?    4.1   0.0      0.25        93       2      20 ..     404     422 ..     403     424 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00042
                             TPR_4  2 rallaLArallalGdldeAralle 25
                                      +a ++ ++al alG++deA ++ +
  gi|330507774|ref|YP_004384202.1| 64 YAWSNKGEALRALGRYDEAIQAYD 87
                                      789999*************77665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.011
                             TPR_4   2 rallaLArallalGdldeA 20 
                                       +a ++ ++al alG +deA
  gi|330507774|ref|YP_004384202.1|  98 YAWSNKGEALRALGKYDEA 116
                                       789999************9 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.48
                             TPR_4   8 ArallalGdldeA 20 
                                       + al++lG +deA
  gi|330507774|ref|YP_004384202.1| 138 GNALYDLGKYDEA 150
                                       789*********9 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.16
                             TPR_4   2 rallaLArallalGdldeA 20 
                                       +a ++ + al +lG +deA
  gi|330507774|ref|YP_004384202.1| 166 YAWSNKGTALGHLGKYDEA 184
                                       688999************9 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 3.8
                             TPR_4   2 rallaLArallalGdldeA 20 
                                       +a ++ + +l  lG +deA
  gi|330507774|ref|YP_004384202.1| 200 YAWYNKGTVLGILGKYDEA 218
                                       78899999**********9 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.079
                             TPR_4   2 rallaLArallalGdldeA 20 
                                        a ++ + al +lG +deA
  gi|330507774|ref|YP_004384202.1| 234 EAWYNKGTALGRLGKYDEA 252
                                       68999*************9 PP

  == domain 7  score: 4.6 bits;  conditional E-value: 0.18
                             TPR_4   8 ArallalGdldeAralle 25 
                                       + al++lG +deA ++ +
  gi|330507774|ref|YP_004384202.1| 274 GIALYDLGKYDEAIQAYD 291
                                       78***********77665 PP

  == domain 8  score: 5.5 bits;  conditional E-value: 0.087
                             TPR_4   2 rallaLArallalGdldeA 20 
                                        a ++ + al alG +deA
  gi|330507774|ref|YP_004384202.1| 302 EAWYNKGVALTALGKYDEA 320
                                       68999*************9 PP

  == domain 9  score: 4.8 bits;  conditional E-value: 0.15
                             TPR_4   7 LArallalGdldeAralle 25 
                                        + al++lG +deA ++ +
  gi|330507774|ref|YP_004384202.1| 341 KGIALYDLGKYDEAIQAYD 359
                                       589***********77665 PP

  == domain 10  score: 5.5 bits;  conditional E-value: 0.087
                             TPR_4   2 rallaLArallalGdldeA 20 
                                        a ++ + al alG +deA
  gi|330507774|ref|YP_004384202.1| 370 EAWYNKGVALTALGKYDEA 388
                                       68999*************9 PP

  == domain 11  score: 4.1 bits;  conditional E-value: 0.25
                             TPR_4   2 rallaLArallalGdldeA 20 
                                        a ++ + +l alG +deA
  gi|330507774|ref|YP_004384202.1| 404 EAWYNKGVVLKALGKYDEA 422
                                       689999************9 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.042        15      17      36 .]      45      62 ..      44      62 .. 0.88
   2 !    8.5   0.1    0.0053       1.9      15      34 ..      77      94 ..      75      95 .. 0.82
   3 ?    3.5   0.0       0.2        74      15      23 ..     111     119 ..     109     130 .. 0.81
   4 !   15.1   0.1   4.7e-05     0.017      10      34 ..     140     162 ..     138     163 .. 0.85
   5 ?    2.9   0.0       0.3   1.1e+02      15      36 .]     179     198 ..     177     198 .. 0.80
   6 ?    3.5   0.0       0.2        74      15      33 ..     213     229 ..     211     231 .. 0.80
   7 ?    1.6   0.0      0.78   2.9e+02      15      23 ..     247     255 ..     245     265 .. 0.78
   8 !   13.8   0.1   0.00012     0.043      10      29 ..     276     293 ..     274     298 .. 0.86
   9 ?    1.7   0.0      0.73   2.7e+02      15      23 ..     315     323 ..     308     334 .. 0.83
  10 !   15.4   0.1   3.8e-05     0.014      10      32 ..     344     364 ..     342     367 .. 0.84
  11 ?    1.4   0.1      0.94   3.4e+02      15      23 ..     383     391 ..     373     396 .. 0.87
  12 ?    3.5   0.1       0.2        75      15      24 ..     417     426 ..     407     427 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.042
                                      HHHHHHH..HHHHHHH-TT- CS
                             TPR_3 17 yqeArelfsYallaildken 36
                                      y+eA+++++  ++  +d+++
  gi|330507774|ref|YP_004384202.1| 45 YDEAIQAYD--QAISIDPQD 62
                                      9******77..*99999876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0053
                                      T-HHHHHHH..HHHHHHH-T CS
                             TPR_3 15 kkyqeArelfsYallaildk 34
                                      ++y+eA+++++  ++  +d+
  gi|330507774|ref|YP_004384202.1| 77 GRYDEAIQAYD--QAISIDP 94
                                      9********77..9977765 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.2
                                       T-HHHHHHH CS
                             TPR_3  15 kkyqeArel 23 
                                       +ky+eA+++
  gi|330507774|ref|YP_004384202.1| 111 GKYDEAINA 119
                                       9******98 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 4.7e-05
                                       HHHHTT-HHHHHHH..HHHHHHH-T CS
                             TPR_3  10 efynkkkyqeArelfsYallaildk 34 
                                       ++y+ +ky+eA+++++  ++  +d+
  gi|330507774|ref|YP_004384202.1| 140 ALYDLGKYDEAINAYD--QAISIDP 162
                                       68************77..9977765 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.3
                                       T-HHHHHHH..HHHHHHH-TT- CS
                             TPR_3  15 kkyqeArelfsYallaildken 36 
                                       +ky+eA+ + +  ++  +d++n
  gi|330507774|ref|YP_004384202.1| 179 GKYDEAIKACD--QAISIDPQN 198
                                       9******9977..777777766 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.2
                                       T-HHHHHHH..HHHHHHH- CS
                             TPR_3  15 kkyqeArelfsYallaild 33 
                                       +ky+eA+  f+  ++  +d
  gi|330507774|ref|YP_004384202.1| 213 GKYDEAIKPFD--QAISID 229
                                       9******9988..887666 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.78
                                       T-HHHHHHH CS
                             TPR_3  15 kkyqeArel 23 
                                       +ky+eA+ +
  gi|330507774|ref|YP_004384202.1| 247 GKYDEAIKA 255
                                       9*****987 PP

  == domain 8  score: 13.8 bits;  conditional E-value: 0.00012
                                       HHHHTT-HHHHHHH..HHHH CS
                             TPR_3  10 efynkkkyqeArelfsYall 29 
                                       ++y+ +ky+eA+++++  ++
  gi|330507774|ref|YP_004384202.1| 276 ALYDLGKYDEAIQAYD--QA 293
                                       79************77..76 PP

  == domain 9  score: 1.7 bits;  conditional E-value: 0.73
                                       T-HHHHHHH CS
                             TPR_3  15 kkyqeArel 23 
                                       +ky+eA+ +
  gi|330507774|ref|YP_004384202.1| 315 GKYDEAIKA 323
                                       9*****976 PP

  == domain 10  score: 15.4 bits;  conditional E-value: 3.8e-05
                                       HHHHTT-HHHHHHH..HHHHHHH CS
                             TPR_3  10 efynkkkyqeArelfsYallail 32 
                                       ++y+ +ky+eA+++++  +++ +
  gi|330507774|ref|YP_004384202.1| 344 ALYDLGKYDEAIQAYD--QANRI 364
                                       79************77..99865 PP

  == domain 11  score: 1.4 bits;  conditional E-value: 0.94
                                       T-HHHHHHH CS
                             TPR_3  15 kkyqeArel 23 
                                       +ky+eA+ +
  gi|330507774|ref|YP_004384202.1| 383 GKYDEAIKA 391
                                       9*****975 PP

  == domain 12  score: 3.5 bits;  conditional E-value: 0.2
                                       T-HHHHHHH. CS
                             TPR_3  15 kkyqeArelf 24 
                                       +ky+eA+ +f
  gi|330507774|ref|YP_004384202.1| 417 GKYDEAIKAF 426
                                       9******995 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0056         2      19      66 ..     100     152 ..      48     165 .. 0.50
   2 !   11.0   0.0   0.00089      0.33       6      70 ..     155     224 ..     151     234 .. 0.66
   3 !   10.2   0.0    0.0015      0.56      20      67 ..     239     289 ..     219     296 .. 0.74
   4 !   14.8   0.0   5.8e-05     0.021       4      70 ..     289     360 ..     287     368 .. 0.81
   5 !   14.7   0.1   6.2e-05     0.023       5      69 ..     358     427 ..     355     431 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0056
                      SRP_TPR_like  19 f..kvvaliklekyeeaLkllkkgsalsedvrfE...kaYvlYklkkykkalk 66 
                                       +  k  al  l+ky+ea+++++++ +++ +  f    k  +lY l ky +a +
  gi|330507774|ref|YP_004384202.1| 100 WsnKGEALRALGKYDEAINACDQAISINPQDAFAwtiKGNALYDLGKYDEAIN 152
                                       12344445555555555555555554444444332224455555555555544 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00089
                      SRP_TPR_like   6 ekilrlegkelkkf..kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkk 70 
                                       ++ + ++ +    +  k +al +l+ky+ea+k+++++      +    + k  vl  l ky +a k +++
  gi|330507774|ref|YP_004384202.1| 155 DQAISIDPQYAYAWsnKGTALGHLGKYDEAIKACDQAIsidPQNAYAWYNKGTVLGILGKYDEAIKPFDQ 224
                                       5555554433222256999****************99822223344556666666667888888776655 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0015
                      SRP_TPR_like  20 kvvaliklekyeeaLkllkkgs....alsedvrfEkaYvlYklkkykkalki 67 
                                       k +al +l+ky+ea+k+++++     +l+e +   k  +lY l ky +a + 
  gi|330507774|ref|YP_004384202.1| 239 KGTALGRLGKYDEAIKACDQAIsidpQLAE-TWTIKGIALYDLGKYDEAIQA 289
                                       889999************998734433443.445689999*****9999875 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 5.8e-05
                      SRP_TPR_like   4 eyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsalsedvrfE...kaYvlYklkkykkalkilkk 70 
                                       +y++ + ++ ++ + +  k val  l+ky+ea+k+++++ +++ +  f    k  +lY l ky +a +  ++
  gi|330507774|ref|YP_004384202.1| 289 AYDQAISINPQIAEAWynKGVALTALGKYDEAIKACDQAISINPQDAFAwtiKGIALYDLGKYDEAIQAYDQ 360
                                       67777777777777667799******************99898877775334889**********9987665 PP

  == domain 5  score: 14.7 bits;  conditional E-value: 6.2e-05
                      SRP_TPR_like   5 yekilrlegkelkkf..kvvaliklekyeeaLkllkkgsals...edvrfEkaYvlYklkkykkalkilk 69 
                                       y++  r++ +  + +  k val  l+ky+ea+k+++++ +++    +  + k  vl  l ky +a k ++
  gi|330507774|ref|YP_004384202.1| 358 YDQANRINPQFAEAWynKGVALTALGKYDEAIKACDQAISINpqfAEAWYNKGVVLKALGKYDEAIKAFE 427
                                       6666666554444446799*****************998776222456799999************9887 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.085        31     152     177 ..      35      60 ..      15      66 .. 0.82
   2 !    7.8   3.4    0.0068       2.5     130     175 ..      46      92 ..      45     108 .. 0.76
   3 ?    3.4   0.0      0.15        54     151     175 ..     102     126 ..      93     132 .. 0.85
   4 !   15.2   0.4   3.5e-05     0.013     125     174 ..     109     159 ..     104     170 .. 0.85
   5 ?    3.9   0.0       0.1        38     126     174 ..     178     227 ..     172     244 .. 0.84
   6 !   12.4   0.1   0.00026     0.094     127     174 ..     247     295 ..     242     303 .. 0.87
   7 !   12.8   0.2   0.00019     0.069     124     173 ..     312     362 ..     308     372 .. 0.86
   8 !    8.5   0.2    0.0041       1.5     124     174 ..     380     431 ..     375     432 .] 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.085
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaale 177
                                       +G+++v     deA +aY++A++   
  gi|330507774|ref|YP_004384202.1|  35 KGNAFVMLSMYDEAIQAYDQAISIDP 60 
                                       9********************97655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0068
                            TPR_21 130 deAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       deA+++ +++ + +  +a +   +G++l a g+ deA +aY++A++ 
  gi|330507774|ref|YP_004384202.1|  46 DEAIQAYDQAiSIDPQDAYAWSNKGEALRALGRYDEAIQAYDQAISI 92 
                                       66666664431335566666778*********************975 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.15
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaa 175
                                        +G++l a gk deA +a ++A++ 
  gi|330507774|ref|YP_004384202.1| 102 NKGEALRALGKYDEAINACDQAISI 126
                                       59****************9999875 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 3.5e-05
                            TPR_21 125 aekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       a +kydeA+++ +++ + +  +a +  ++G++l+  gk deA +aY++A++
  gi|330507774|ref|YP_004384202.1| 109 ALGKYDEAINACDQAISiNPQDAFAWTIKGNALYDLGKYDEAINAYDQAIS 159
                                       6799*******9776542778888889**********************97 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.1
                            TPR_21 126 ekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                        +kydeA+k+ +++ + +  +a +   +G +l   gk deA + +++A++
  gi|330507774|ref|YP_004384202.1| 178 LGKYDEAIKACDQAISiDPQNAYAWYNKGTVLGILGKYDEAIKPFDQAIS 227
                                       5899*****997765526677777788*****************999986 PP

  == domain 6  score: 12.4 bits;  conditional E-value: 0.00026
                            TPR_21 127 kkydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       +kydeA+k+ +++ + +   a+   ++G +l+  gk deA +aY++A++
  gi|330507774|ref|YP_004384202.1| 247 GKYDEAIKACDQAiSIDPQLAETWTIKGIALYDLGKYDEAIQAYDQAIS 295
                                       89********7651568899999************************86 PP

  == domain 7  score: 12.8 bits;  conditional E-value: 0.00019
                            TPR_21 124 laekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAl 173
                                        a +kydeA+k+ +++ + +  +a +  ++G +l+  gk deA +aY++A 
  gi|330507774|ref|YP_004384202.1| 312 TALGKYDEAIKACDQAISiNPQDAFAWTIKGIALYDLGKYDEAIQAYDQAN 362
                                       6789*********776552778888889*********************96 PP

  == domain 8  score: 8.5 bits;  conditional E-value: 0.0041
                            TPR_21 124 laekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                        a +kydeA+k+ +++ + +   a++   +G +l a gk deA +a++ +++
  gi|330507774|ref|YP_004384202.1| 380 TALGKYDEAIKACDQAISiNPQFAEAWYNKGVVLKALGKYDEAIKAFESGYQ 431
                                       6789*********8765423344555567******************98875 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       3.2   1.2e+03      53      70 ..      41      58 ..      30      63 .. 0.83
   2 ?    6.4   0.0     0.026       9.5      37      70 ..      93     126 ..      63     131 .. 0.76
   3 ?    2.9   0.0      0.31   1.1e+02      52      70 ..     142     160 ..     133     164 .. 0.91
   4 ?    7.7   0.0      0.01       3.7      39      71 ..     163     195 ..     159     202 .. 0.89
   5 ?    1.9   0.0      0.64   2.3e+02      42      70 ..     200     228 ..     197     234 .. 0.84
   6 ?    3.4   0.0      0.21        78      52      70 ..     244     262 ..     229     276 .. 0.81
   7 ?    3.5   0.0      0.21        77      52      70 ..     278     296 ..     272     303 .. 0.89
   8 ?    4.0   0.0      0.14        52      51      71 ..     311     331 ..     297     350 .. 0.86
   9 ?   -0.1   0.0       2.6   9.6e+02      52      70 ..     346     364 ..     336     367 .. 0.84
  10 ?    5.4   0.1     0.053        19      37      70 ..     365     398 ..     350     405 .. 0.79
  11 ?    1.3   0.0         1   3.7e+02      43      65 ..     405     427 ..     399     429 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.2
                            ANAPC5 53 dfghneeAvkaleeairl 70
                                       ++ ++eA++a   ai++
  gi|330507774|ref|YP_004384202.1| 41 MLSMYDEAIQAYDQAISI 58
                                      567899*******99987 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.026
                            ANAPC5  37 kksyqyalLnlaslhadfghneeAvkaleeairl 70 
                                         +y ya  n      ++g+++eA++a   ai++
  gi|330507774|ref|YP_004384202.1|  93 DPQYAYAWSNKGEALRALGKYDEAINACDQAISI 126
                                       567999999999999999************9998 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.31
                            ANAPC5  52 adfghneeAvkaleeairl 70 
                                       +d+g+++eA++a   ai++
  gi|330507774|ref|YP_004384202.1| 142 YDLGKYDEAINAYDQAISI 160
                                       789**************97 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.01
                            ANAPC5  39 syqyalLnlaslhadfghneeAvkaleeairlA 71 
                                       +y ya  n  +   ++g+++eA+ka   ai++ 
  gi|330507774|ref|YP_004384202.1| 163 QYAYAWSNKGTALGHLGKYDEAIKACDQAISID 195
                                       69999999999999****************985 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.64
                            ANAPC5  42 yalLnlaslhadfghneeAvkaleeairl 70 
                                       ya  n  ++   +g+++eA+k +  ai++
  gi|330507774|ref|YP_004384202.1| 200 YAWYNKGTVLGILGKYDEAIKPFDQAISI 228
                                       6666777777789**************97 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.21
                            ANAPC5  52 adfghneeAvkaleeairl 70 
                                        ++g+++eA+ka   ai++
  gi|330507774|ref|YP_004384202.1| 244 GRLGKYDEAIKACDQAISI 262
                                       579**************98 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.21
                            ANAPC5  52 adfghneeAvkaleeairl 70 
                                       +d+g+++eA++a   ai++
  gi|330507774|ref|YP_004384202.1| 278 YDLGKYDEAIQAYDQAISI 296
                                       789**************98 PP

  == domain 8  score: 4.0 bits;  conditional E-value: 0.14
                            ANAPC5  51 hadfghneeAvkaleeairlA 71 
                                        +++g+++eA+ka   ai++ 
  gi|330507774|ref|YP_004384202.1| 311 LTALGKYDEAIKACDQAISIN 331
                                       5679**************985 PP

  == domain 9  score: -0.1 bits;  conditional E-value: 2.6
                            ANAPC5  52 adfghneeAvkaleeairl 70 
                                       +d+g+++eA++a   a r+
  gi|330507774|ref|YP_004384202.1| 346 YDLGKYDEAIQAYDQANRI 364
                                       789********99888665 PP

  == domain 10  score: 5.4 bits;  conditional E-value: 0.053
                            ANAPC5  37 kksyqyalLnlaslhadfghneeAvkaleeairl 70 
                                       + ++  a  n  +  +++g+++eA+ka   ai++
  gi|330507774|ref|YP_004384202.1| 365 NPQFAEAWYNKGVALTALGKYDEAIKACDQAISI 398
                                       45667778888888899***************98 PP

  == domain 11  score: 1.3 bits;  conditional E-value: 1
                            ANAPC5  43 alLnlaslhadfghneeAvkale 65 
                                       a  n  ++  ++g+++eA+ka+e
  gi|330507774|ref|YP_004384202.1| 405 AWYNKGVVLKALGKYDEAIKAFE 427
                                       666777788899*********97 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.012       4.6      62     106 ..      82     126 ..      78     128 .. 0.95
   2 ?    6.9   0.0     0.017       6.2      62     106 ..     150     194 ..     147     196 .. 0.95
   3 !    8.2   0.0    0.0064       2.3      62     106 ..     218     262 ..     215     264 .. 0.95
   4 ?    7.5   0.0     0.011       3.9      62     106 ..     286     330 ..     283     332 .. 0.95
   5 ?    6.9   0.0     0.017       6.2      62     106 ..     354     398 ..     351     400 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.012
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakraLsv 106
                                       +++++ +a ++   yA    + ++ l+   +Y +a++ + +a+s+
  gi|330507774|ref|YP_004384202.1|  82 AIQAYDQAISIDPQYAYAWSNKGEALRALGKYDEAINACDQAISI 126
                                       89****************************************998 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.017
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakraLsv 106
                                       +++++ +a ++   yA    + +  lg   +Y +a+k + +a+s+
  gi|330507774|ref|YP_004384202.1| 150 AINAYDQAISIDPQYAYAWSNKGTALGHLGKYDEAIKACDQAISI 194
                                       8999**************************************998 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0064
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakraLsv 106
                                       ++++f +a ++    A+  ++ +  lg   +Y +a+k + +a+s+
  gi|330507774|ref|YP_004384202.1| 218 AIKPFDQAISIDPQFAEAWYNKGTALGRLGKYDEAIKACDQAISI 262
                                       8999**************************************998 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.011
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakraLsv 106
                                       +++++ +a ++    A+  ++ +  l    +Y +a+k + +a+s+
  gi|330507774|ref|YP_004384202.1| 286 AIQAYDQAISINPQIAEAWYNKGVALTALGKYDEAIKACDQAISI 330
                                       89****************************************998 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.017
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakraLsv 106
                                       +++++ +a ++    A+  ++ +  l    +Y +a+k + +a+s+
  gi|330507774|ref|YP_004384202.1| 354 AIQAYDQANRINPQFAEAWYNKGVALTALGKYDEAIKACDQAISI 398
                                       89****************************************998 PP

>> Lambda_Kil  Bacteriophage lambda Kil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0029       1.1      23      37 ..      44      58 ..      42      60 .. 0.94
   2 ?    5.6   0.0     0.032        12      24      37 ..      79      92 ..      76      96 .. 0.88
   3 ?   -1.0   0.0       3.7   1.4e+03      24      37 ..     113     126 ..     111     127 .. 0.87
   4 ?    4.4   0.0     0.077        28      20      37 ..     143     160 ..     141     164 .. 0.86
   5 ?    0.4   0.0       1.4     5e+02      18      37 ..     175     194 ..     172     196 .. 0.86
   6 ?   -2.3   0.0       9.3   3.4e+03      22      37 ..     213     228 ..     207     229 .. 0.79
   7 ?   -0.3   0.0       2.3   8.4e+02      19      37 ..     244     262 ..     241     264 .. 0.82
   8 ?    6.7   0.0     0.014       5.2      20      37 ..     279     296 ..     275     298 .. 0.88
   9 ?   -1.5   0.0       5.3     2e+03      24      37 ..     317     330 ..     315     331 .. 0.85
  10 ?    0.0   0.0       1.8   6.5e+02      20      34 ..     347     361 ..     344     364 .. 0.83
  11 ?   -1.5   0.0       5.3     2e+03      24      37 ..     385     398 ..     383     399 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0029
                        Lambda_Kil 23 MfleAvdayKkavli 37
                                      M+ eA +ay +a++i
  gi|330507774|ref|YP_004384202.1| 44 MYDEAIQAYDQAISI 58
                                      9*************8 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.032
                        Lambda_Kil 24 fleAvdayKkavli 37
                                      + eA +ay +a++i
  gi|330507774|ref|YP_004384202.1| 79 YDEAIQAYDQAISI 92
                                      679**********9 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3.7
                        Lambda_Kil  24 fleAvdayKkavli 37 
                                       + eA +a  +a++i
  gi|330507774|ref|YP_004384202.1| 113 YDEAINACDQAISI 126
                                       66999*******98 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.077
                        Lambda_Kil  20 DekMfleAvdayKkavli 37 
                                       D + + eA +ay +a++i
  gi|330507774|ref|YP_004384202.1| 143 DLGKYDEAINAYDQAISI 160
                                       567789***********9 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 1.4
                        Lambda_Kil  18 lGDekMfleAvdayKkavli 37 
                                       lG  + + eA  a  +a++i
  gi|330507774|ref|YP_004384202.1| 175 LGHLGKYDEAIKACDQAISI 194
                                       67778899**********98 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 9.3
                        Lambda_Kil  22 kMfleAvdayKkavli 37 
                                       + + eA   + +a++i
  gi|330507774|ref|YP_004384202.1| 213 GKYDEAIKPFDQAISI 228
                                       5677999999999998 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 2.3
                        Lambda_Kil  19 GDekMfleAvdayKkavli 37 
                                       G  + + eA  a  +a++i
  gi|330507774|ref|YP_004384202.1| 244 GRLGKYDEAIKACDQAISI 262
                                       55567889*********98 PP

  == domain 8  score: 6.7 bits;  conditional E-value: 0.014
                        Lambda_Kil  20 DekMfleAvdayKkavli 37 
                                       D + + eA +ay +a++i
  gi|330507774|ref|YP_004384202.1| 279 DLGKYDEAIQAYDQAISI 296
                                       667789***********9 PP

  == domain 9  score: -1.5 bits;  conditional E-value: 5.3
                        Lambda_Kil  24 fleAvdayKkavli 37 
                                       + eA  a  +a++i
  gi|330507774|ref|YP_004384202.1| 317 YDEAIKACDQAISI 330
                                       569999999***98 PP

  == domain 10  score: 0.0 bits;  conditional E-value: 1.8
                        Lambda_Kil  20 DekMfleAvdayKka 34 
                                       D + + eA +ay +a
  gi|330507774|ref|YP_004384202.1| 347 DLGKYDEAIQAYDQA 361
                                       5677889*****997 PP

  == domain 11  score: -1.5 bits;  conditional E-value: 5.3
                        Lambda_Kil  24 fleAvdayKkavli 37 
                                       + eA  a  +a++i
  gi|330507774|ref|YP_004384202.1| 385 YDEAIKACDQAISI 398
                                       569999999***98 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 ?    4.6   0.1     0.093        34      20      31 ..      45      56 ..      42      58 .. 0.90
   2 ?    7.4   0.4     0.012       4.5      16      31 ..      75      90 ..      61      92 .. 0.78
   3 ?    5.6   0.0     0.045        17      16      40 ..     102     127 ..      97     139 .. 0.83
   4 ?    7.6   0.2     0.011         4      18      31 ..     145     158 ..     141     160 .. 0.90
   5 ?    1.4   0.1      0.93   3.4e+02      10      31 ..     171     192 ..     163     194 .. 0.69
   6 ?    1.8   0.0      0.68   2.5e+02      17      31 ..     212     226 ..     197     228 .. 0.76
   7 ?    1.3   0.0      0.99   3.6e+02      17      31 ..     246     260 ..     233     269 .. 0.73
   8 !    8.5   0.2    0.0055         2      18      31 ..     281     294 ..     273     296 .. 0.89
   9 ?    4.1   0.0      0.13        48      22      40 ..     312     331 ..     306     344 .. 0.77
  10 ?    6.2   0.6     0.029        11      17      30 ..     348     361 ..     333     364 .. 0.84
  11 ?    3.7   0.1      0.17        64      22      39 ..     380     397 ..     374     411 .. 0.74
  12 ?    4.2   0.1      0.13        47      10      31 ..     409     430 ..     401     432 .] 0.72

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.093
                               MIT 20 yeeAlelYkeal 31
                                      y+eA+++Y +a+
  gi|330507774|ref|YP_004384202.1| 45 YDEAIQAYDQAI 56
                                      9**********8 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.012
                               MIT 16 nagnyeeAlelYkeal 31
                                        g y+eA+++Y +a+
  gi|330507774|ref|YP_004384202.1| 75 ALGRYDEAIQAYDQAI 90
                                      5699***********8 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.045
                               MIT  16 nagnyeeAlelYkealelLlqalk.e 40 
                                       n+g+   Al +Y ea++ + qa++ +
  gi|330507774|ref|YP_004384202.1| 102 NKGEALRALGKYDEAINACDQAISiN 127
                                       67777889**************9844 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.011
                               MIT  18 gnyeeAlelYkeal 31 
                                       g+y+eA+++Y +a+
  gi|330507774|ref|YP_004384202.1| 145 GKYDEAINAYDQAI 158
                                       8************9 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.93
                               MIT  10 kAveeDnagnyeeAlelYkeal 31 
                                       k + +   g+y+eA+++  +a+
  gi|330507774|ref|YP_004384202.1| 171 KGTALGHLGKYDEAIKACDQAI 192
                                       5555566789999998766666 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.68
                               MIT  17 agnyeeAlelYkeal 31 
                                        g+y+eA++ + +a+
  gi|330507774|ref|YP_004384202.1| 212 LGKYDEAIKPFDQAI 226
                                       589999999888887 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.99
                               MIT  17 agnyeeAlelYkeal 31 
                                        g+y+eA+++  +a+
  gi|330507774|ref|YP_004384202.1| 246 LGKYDEAIKACDQAI 260
                                       577777777655555 PP

  == domain 8  score: 8.5 bits;  conditional E-value: 0.0055
                               MIT  18 gnyeeAlelYkeal 31 
                                       g+y+eA+++Y +a+
  gi|330507774|ref|YP_004384202.1| 281 GKYDEAIQAYDQAI 294
                                       9************9 PP

  == domain 9  score: 4.1 bits;  conditional E-value: 0.13
                               MIT  22 eAlelYkealelLlqalk.e 40 
                                       +Al +Y ea++ + qa++ +
  gi|330507774|ref|YP_004384202.1| 312 TALGKYDEAIKACDQAISiN 331
                                       68889999999999998743 PP

  == domain 10  score: 6.2 bits;  conditional E-value: 0.029
                               MIT  17 agnyeeAlelYkea 30 
                                        g+y+eA+++Y +a
  gi|330507774|ref|YP_004384202.1| 348 LGKYDEAIQAYDQA 361
                                       69**********98 PP

  == domain 11  score: 3.7 bits;  conditional E-value: 0.17
                               MIT  22 eAlelYkealelLlqalk 39 
                                       +Al +Y ea++ + qa++
  gi|330507774|ref|YP_004384202.1| 380 TALGKYDEAIKACDQAIS 397
                                       688888888888888887 PP

  == domain 12  score: 4.2 bits;  conditional E-value: 0.13
                               MIT  10 kAveeDnagnyeeAlelYkeal 31 
                                       k v +   g+y+eA+++++++ 
  gi|330507774|ref|YP_004384202.1| 409 KGVVLKALGKYDEAIKAFESGY 430
                                       5566666788888888887775 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.055        20      10      34 ..      65      89 ..      60      94 .. 0.85
   2 !    8.6   0.1    0.0057       2.1       8      34 ..      97     124 ..      91     140 .. 0.77
   3 ?    3.2   0.0      0.28     1e+02      14      34 ..     137     157 ..     131     163 .. 0.82
   4 ?    2.6   0.1      0.43   1.6e+02      11      33 ..     168     190 ..     161     201 .. 0.74
   5 ?    0.2   0.0       2.4     9e+02      20      33 ..     211     224 ..     196     228 .. 0.78
   6 ?    1.5   0.1      0.98   3.6e+02      20      33 ..     245     258 ..     231     269 .. 0.76
   7 ?    2.4   0.0      0.49   1.8e+02      18      35 ..     277     294 ..     264     303 .. 0.79
   8 ?    4.9   0.1     0.082        30      17      34 ..     310     328 ..     298     344 .. 0.74
   9 ?    2.3   0.0      0.56     2e+02      19      35 ..     346     362 ..     339     372 .. 0.83
  10 ?    4.1   0.1      0.15        53      17      33 ..     378     394 ..     367     401 .. 0.77
  11 ?    2.0   0.0       0.7   2.5e+02      18      30 ..     413     425 ..     401     429 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.055
                         NRBF2_MIT 10 qqsrkadrllaaGkyeeaischkka 34
                                        s k + l a G+y+eai  + +a
  gi|330507774|ref|YP_004384202.1| 65 AWSNKGEALRALGRYDEAIQAYDQA 89
                                      5688999************998877 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0057
                         NRBF2_MIT   8 ahqqsrkadrllaaGkyeeai.schkka 34 
                                       a+  s k + l a Gky+eai +c +  
  gi|330507774|ref|YP_004384202.1|  97 AYAWSNKGEALRALGKYDEAInACDQAI 124
                                       66678999*************4455544 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.28
                         NRBF2_MIT  14 kadrllaaGkyeeaischkka 34 
                                       k + l   Gky+eai  + +a
  gi|330507774|ref|YP_004384202.1| 137 KGNALYDLGKYDEAINAYDQA 157
                                       56678889*******998877 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.43
                         NRBF2_MIT  11 qsrkadrllaaGkyeeaischkk 33 
                                        s k   l   Gky+eai    +
  gi|330507774|ref|YP_004384202.1| 168 WSNKGTALGHLGKYDEAIKACDQ 190
                                       56677777788*******64443 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 2.4
                         NRBF2_MIT  20 aaGkyeeaischkk 33 
                                         Gky+eai    +
  gi|330507774|ref|YP_004384202.1| 211 ILGKYDEAIKPFDQ 224
                                       579******87665 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.98
                         NRBF2_MIT  20 aaGkyeeaischkk 33 
                                         Gky+eai    +
  gi|330507774|ref|YP_004384202.1| 245 RLGKYDEAIKACDQ 258
                                       569******64443 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.49
                         NRBF2_MIT  18 llaaGkyeeaischkkaa 35 
                                       l   Gky+eai  + +a 
  gi|330507774|ref|YP_004384202.1| 277 LYDLGKYDEAIQAYDQAI 294
                                       6678*******9988875 PP

  == domain 8  score: 4.9 bits;  conditional E-value: 0.082
                         NRBF2_MIT  17 rllaaGkyeeai.schkka 34 
                                        l a Gky+eai +c +  
  gi|330507774|ref|YP_004384202.1| 310 ALTALGKYDEAIkACDQAI 328
                                       68899*******4465544 PP

  == domain 9  score: 2.3 bits;  conditional E-value: 0.56
                         NRBF2_MIT  19 laaGkyeeaischkkaa 35 
                                          Gky+eai  + +a 
  gi|330507774|ref|YP_004384202.1| 346 YDLGKYDEAIQAYDQAN 362
                                       567*******9998886 PP

  == domain 10  score: 4.1 bits;  conditional E-value: 0.15
                         NRBF2_MIT  17 rllaaGkyeeaischkk 33 
                                        l a Gky+eai    +
  gi|330507774|ref|YP_004384202.1| 378 ALTALGKYDEAIKACDQ 394
                                       58899*******64443 PP

  == domain 11  score: 2.0 bits;  conditional E-value: 0.7
                         NRBF2_MIT  18 llaaGkyeeaisc 30 
                                       l a Gky+eai  
  gi|330507774|ref|YP_004384202.1| 413 LKALGKYDEAIKA 425
                                       7799******975 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       2.5   9.1e+02       8      25 ..      37      54 ..      37      58 .. 0.84
   2 ?    0.8   0.0         2   7.3e+02      13      25 ..      76      88 ..      71      92 .. 0.81
   3 ?    1.1   0.0       1.6   5.7e+02       9      25 ..     140     156 ..     139     160 .. 0.80
   4 ?    3.0   0.0       0.4   1.4e+02       9      22 ..     174     187 ..     173     193 .. 0.85
   5 ?   -0.4   0.0       4.7   1.7e+03      10      21 ..     209     220 ..     207     224 .. 0.83
   6 ?    4.6   0.0      0.13        46       9      22 ..     242     255 ..     241     261 .. 0.85
   7 ?    1.2   0.0       1.5   5.3e+02      12      25 ..     279     292 ..     275     297 .. 0.80
   8 ?    0.3   0.0       2.9   1.1e+03      11      22 ..     312     323 ..     310     329 .. 0.78
   9 ?    0.6   0.0       2.3   8.6e+02      13      24 ..     348     359 ..     344     363 .. 0.82
  10 ?    0.3   0.0       2.9   1.1e+03      11      22 ..     380     391 ..     378     397 .. 0.78
  11 ?    1.7   0.0         1   3.7e+02      13      24 ..     416     427 ..     412     428 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2.5
                               PPR  8 sgycknGkleeAlelfke 25
                                      ++++   +++eA++ +++
  gi|330507774|ref|YP_004384202.1| 37 NAFVMLSMYDEAIQAYDQ 54
                                      6889999*****998876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 2
                               PPR 13 nGkleeAlelfke 25
                                       G+++eA++ +++
  gi|330507774|ref|YP_004384202.1| 76 LGRYDEAIQAYDQ 88
                                      79*****998876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.6
                               PPR   9 gycknGkleeAlelfke 25 
                                       ++   Gk++eA+  +++
  gi|330507774|ref|YP_004384202.1| 140 ALYDLGKYDEAINAYDQ 156
                                       66778******988875 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.4
                               PPR   9 gycknGkleeAlel 22 
                                       ++++ Gk++eA++ 
  gi|330507774|ref|YP_004384202.1| 174 ALGHLGKYDEAIKA 187
                                       7999*******985 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 4.7
                               PPR  10 ycknGkleeAle 21 
                                       ++  Gk++eA++
  gi|330507774|ref|YP_004384202.1| 209 LGILGKYDEAIK 220
                                       5678******86 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.13
                               PPR   9 gycknGkleeAlel 22 
                                       ++++ Gk++eA++ 
  gi|330507774|ref|YP_004384202.1| 242 ALGRLGKYDEAIKA 255
                                       89*********985 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 1.5
                               PPR  12 knGkleeAlelfke 25 
                                         Gk++eA++ +++
  gi|330507774|ref|YP_004384202.1| 279 DLGKYDEAIQAYDQ 292
                                       57*******99886 PP

  == domain 8  score: 0.3 bits;  conditional E-value: 2.9
                               PPR  11 cknGkleeAlel 22 
                                          Gk++eA++ 
  gi|330507774|ref|YP_004384202.1| 312 TALGKYDEAIKA 323
                                       568******985 PP

  == domain 9  score: 0.6 bits;  conditional E-value: 2.3
                               PPR  13 nGkleeAlelfk 24 
                                        Gk++eA++ ++
  gi|330507774|ref|YP_004384202.1| 348 LGKYDEAIQAYD 359
                                       79*****99887 PP

  == domain 10  score: 0.3 bits;  conditional E-value: 2.9
                               PPR  11 cknGkleeAlel 22 
                                          Gk++eA++ 
  gi|330507774|ref|YP_004384202.1| 380 TALGKYDEAIKA 391
                                       568******985 PP

  == domain 11  score: 1.7 bits;  conditional E-value: 1
                               PPR  13 nGkleeAlelfk 24 
                                        Gk++eA++ f+
  gi|330507774|ref|YP_004384202.1| 416 LGKYDEAIKAFE 427
                                       69******9997 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 ?    3.5   0.1      0.15        54       2      15 ..      45      58 ..      44      62 .. 0.92
   2 ?    4.7   0.2      0.06        22       1      15 [.      78      92 ..      78      96 .. 0.92
   3 ?    4.0   0.0     0.099        36       1      15 [.     112     126 ..     112     131 .. 0.89
   4 ?    3.1   0.1      0.19        70       1      15 [.     146     160 ..     146     164 .. 0.91
   5 ?    4.7   0.0     0.061        22       1      15 [.     180     194 ..     180     199 .. 0.88
   6 ?    3.0   0.0       0.2        73       1      15 [.     214     228 ..     214     233 .. 0.91
   7 ?    4.5   0.0     0.069        25       1      15 [.     248     262 ..     248     267 .. 0.90
   8 ?    5.0   0.2     0.049        18       1      16 [.     282     297 ..     282     302 .. 0.86
   9 ?    4.8   0.0     0.059        22       1      15 [.     316     330 ..     316     335 .. 0.89
  10 ?   -0.5   0.1       2.6   9.6e+02       1      12 [.     350     361 ..     350     365 .. 0.87
  11 ?    5.0   0.1      0.05        18       1      16 [.     384     399 ..     384     426 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.15
                                      HHHHHHHHHHHHHH CS
                          HTH_Bact  2 YeeaLeqvnkAiei 15
                                      Y+ea++  ++Ai i
  gi|330507774|ref|YP_004384202.1| 45 YDEAIQAYDQAISI 58
                                      ************87 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.06
                                      -HHHHHHHHHHHHHH CS
                          HTH_Bact  1 rYeeaLeqvnkAiei 15
                                      rY+ea++  ++Ai i
  gi|330507774|ref|YP_004384202.1| 78 RYDEAIQAYDQAISI 92
                                      7************87 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.099
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y+ea++  ++Ai i
  gi|330507774|ref|YP_004384202.1| 112 KYDEAINACDQAISI 126
                                       6************87 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.19
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y+ea++  ++Ai i
  gi|330507774|ref|YP_004384202.1| 146 KYDEAINAYDQAISI 160
                                       6************87 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.061
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y+ea++  ++Ai i
  gi|330507774|ref|YP_004384202.1| 180 KYDEAIKACDQAISI 194
                                       6************87 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.2
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y+ea++  ++Ai i
  gi|330507774|ref|YP_004384202.1| 214 KYDEAIKPFDQAISI 228
                                       6************87 PP

  == domain 7  score: 4.5 bits;  conditional E-value: 0.069
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y+ea++  ++Ai i
  gi|330507774|ref|YP_004384202.1| 248 KYDEAIKACDQAISI 262
                                       6************87 PP

  == domain 8  score: 5.0 bits;  conditional E-value: 0.049
                                       -HHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiS 16 
                                       +Y+ea++  ++Ai i 
  gi|330507774|ref|YP_004384202.1| 282 KYDEAIQAYDQAISIN 297
                                       6************986 PP

  == domain 9  score: 4.8 bits;  conditional E-value: 0.059
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y+ea++  ++Ai i
  gi|330507774|ref|YP_004384202.1| 316 KYDEAIKACDQAISI 330
                                       6************87 PP

  == domain 10  score: -0.5 bits;  conditional E-value: 2.6
                                       -HHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkA 12 
                                       +Y+ea++  ++A
  gi|330507774|ref|YP_004384202.1| 350 KYDEAIQAYDQA 361
                                       6*******9999 PP

  == domain 11  score: 5.0 bits;  conditional E-value: 0.05
                                       -HHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiS 16 
                                       +Y+ea++  ++Ai i 
  gi|330507774|ref|YP_004384202.1| 384 KYDEAIKACDQAISIN 399
                                       6************875 PP

>> Mo-co_dimer  Mo-co oxidoreductase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.94   3.4e+02     103     123 ..      48      69 ..      38      75 .. 0.79
   2 ?    3.5   0.0      0.19        69      98     124 ..     111     138 ..      78     143 .. 0.70
   3 ?    0.0   0.0       2.1   7.7e+02     103     124 ..     150     172 ..     141     177 .. 0.81
   4 ?    1.7   0.0      0.65   2.4e+02     101     120 ..     182     202 ..     162     213 .. 0.76
   5 ?    5.4   0.0     0.046        17     102     125 ..     251     275 ..     235     279 .. 0.88
   6 ?    0.0   0.0       2.2   7.9e+02     103     124 ..     286     308 ..     275     313 .. 0.77
   7 ?    6.1   0.0     0.029        11      99     125 ..     316     343 ..     299     347 .. 0.77
   8 ?    4.4   0.0     0.097        36      78     125 ..     364     411 ..     346     416 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.94
                                       EEEEEETT--B--S.HHH--TT CS
                       Mo-co_dimer 103 lvravDealnvqPe.emiwnvl 123
                                       +++a D+a+++ P+ +  w+  
  gi|330507774|ref|YP_004384202.1|  48 AIQAYDQAISIDPQdAYAWSNK 69 
                                       6899**********44558755 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.19
                                       .E.EEEEEEEETT--B--S.HHH--TT- CS
                       Mo-co_dimer  98 kekeilvravDealnvqPe.emiwnvlg 124
                                        + + ++ a D+a+++ P+ +  w + g
  gi|330507774|ref|YP_004384202.1| 111 GKYDEAINACDQAISINPQdAFAWTIKG 138
                                       4455577899999999999667898887 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 2.1
                                       EEEEEETT--B--S.HHH--TT- CS
                       Mo-co_dimer 103 lvravDealnvqPe.emiwnvlg 124
                                       ++ a D+a+++ P+ +  w+  g
  gi|330507774|ref|YP_004384202.1| 150 AINAYDQAISIDPQyAYAWSNKG 172
                                       57899********9777898766 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.65
                                       EEEEEEEETT--B--S.HHH- CS
                       Mo-co_dimer 101 eilvravDealnvqPe.emiw 120
                                       + +++a D+a+++ P+ +  w
  gi|330507774|ref|YP_004384202.1| 182 DEAIKACDQAISIDPQnAYAW 202
                                       5579***********944456 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.046
                                       EEEEEEETT--B--S.HHH--TT-- CS
                       Mo-co_dimer 102 ilvravDealnvqPe.emiwnvlgm 125
                                        +++a D+a+++ P+ + +w + g+
  gi|330507774|ref|YP_004384202.1| 251 EAIKACDQAISIDPQlAETWTIKGI 275
                                       579************99*****997 PP

  == domain 6  score: 0.0 bits;  conditional E-value: 2.2
                                       EEEEEETT--B--S.HHH--TT- CS
                       Mo-co_dimer 103 lvravDealnvqPe.emiwnvlg 124
                                       +++a D+a+++ P+ +  w   g
  gi|330507774|ref|YP_004384202.1| 286 AIQAYDQAISINPQiAEAWYNKG 308
                                       6899*********9877776555 PP

  == domain 7  score: 6.1 bits;  conditional E-value: 0.029
                                       E.EEEEEEEETT--B--S.HHH--TT-- CS
                       Mo-co_dimer  99 ekeilvravDealnvqPe.emiwnvlgm 125
                                       + + +++a D+a+++ P+ +  w + g+
  gi|330507774|ref|YP_004384202.1| 316 KYDEAIKACDQAISINPQdAFAWTIKGI 343
                                       445579************7789***997 PP

  == domain 8  score: 4.4 bits;  conditional E-value: 0.097
                                       TS-TTS-EEEEEEEEESS...E.EEEEEEEETT--B--S.HHH--TT-- CS
                       Mo-co_dimer  78 retafcwvfweldvevselakekeilvravDealnvqPe.emiwnvlgm 125
                                        +  f+   ++  v ++ l  + + +++a D+a+++ P+ +  w   g+
  gi|330507774|ref|YP_004384202.1| 364 INPQFAEAWYNKGVALTALG-KYDEAIKACDQAISINPQfAEAWYNKGV 411
                                       45567777788888888874.456689***********98778866665 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2      0.03        11      60     108 ..      42      91 ..      22     100 .. 0.76
   2 ?    4.2   0.0     0.062        23      54     107 ..     104     158 ..      92     169 .. 0.52
   3 ?    3.8   0.0     0.083        30      15     155 ..     179     300 ..     171     314 .. 0.63
   4 !    8.9   0.0    0.0024      0.87      12     109 ..     312     398 ..     306     406 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.03
                          TPR_MalT  60 lqalqeaeklarqadsl.hvallallqqaeilvaqGrLheAletyeqalq 108
                                       l+++ ea+++ +qa s+ ++ ++a    +e l+a Gr +eA++ y qa+ 
  gi|330507774|ref|YP_004384202.1|  42 LSMYDEAIQAYDQAISIdPQDAYAWSNKGEALRALGRYDEAIQAYDQAIS 91 
                                       5666777777766666633357777888*******************997 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.062
                          TPR_MalT  54 GdleaAlqalqeaeklarqadsl.hvallallqqaeilvaqGrLheAletyeqal 107
                                       G+  +Al  + ea+ + +qa s+ ++ ++a +  ++ l   G+ +eA++ y qa+
  gi|330507774|ref|YP_004384202.1| 104 GEALRALGKYDEAINACDQAISInPQDAFAWTIKGNALYDLGKYDEAINAYDQAI 158
                                       4444444444444444433333312223444444666666666666666666665 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.083
                          TPR_MalT  15 gdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilv 91 
                                       g+ ++a++ + qA+++ p++++ +      vlG    + G+ ++A + + +a+++       ++ + a +  +  l 
  gi|330507774|ref|YP_004384202.1| 179 GKYDEAIKACDQAISIDPQNAYAWYNKG-TVLG----ILGKYDEAIKPFDQAISID------PQFAEAWYNKGTALG 244
                                       6667777888888887777776554333.2334....6667777777777777665......334455556666666 PP

                          TPR_MalT  92 aqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql 155
                                         G+ +eA++ + qa+  ++ q  + + + g++       ly+ ++ +eA q+ +++i +  q 
  gi|330507774|ref|YP_004384202.1| 245 RLGKYDEAIKACDQAIS-IDPQLAETWTIKGIA-------LYDLGKYDEAIQAYDQAISINPQI 300
                                       77788888888888887.555555555555555.......666667777777777777666655 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0024
                          TPR_MalT  12 iasgdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqae 88 
                                       +a g+ ++a++ + qA+++ p+d++ + i      G a    G+ ++A qa+ +a ++       ++ + a +  + 
  gi|330507774|ref|YP_004384202.1| 312 TALGKYDEAIKACDQAISINPQDAFAWTIK-----GIALYDLGKYDEAIQAYDQANRIN------PQFAEAWYNKGV 377
                                       56789999***************9887644.....455555778888999988888876......446778888899 PP

                          TPR_MalT  89 ilvaqGrLheAletyeqalql 109
                                        l+a G+ +eA++ + qa+  
  gi|330507774|ref|YP_004384202.1| 378 ALTALGKYDEAIKACDQAISI 398
                                       999999999999999999975 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.75   2.7e+02     203     256 ..      33      84 ..      25      95 .. 0.81
   2 ?    1.7   0.0      0.39   1.4e+02     213     256 ..      75     118 ..      68     137 .. 0.89
   3 ?    4.8   0.0     0.043        16     213     256 ..     143     186 ..     130     200 .. 0.88
   4 ?    1.5   0.0      0.44   1.6e+02     214     255 ..     212     253 ..     203     265 .. 0.90
   5 ?    4.0   0.0     0.076        28     212     256 ..     278     322 ..     267     336 .. 0.86
   6 ?    6.4   0.0     0.014         5     183     256 ..     351     424 ..     333     431 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.75
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 203 llngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                       l++g+A v l    y+eA +   +a+  d++d+ + +N   a   lg+ +e+++
  gi|330507774|ref|YP_004384202.1|  33 LEKGNAFVMLS--MYDEAIQAYDQAISIDPQDAYAWSNKGEALRALGRYDEAIQ 84 
                                       66777777665..599****************9999999888888888777765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.39
                                       HTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 213 llgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                       +lgry+eA +   +a+  d++++ + +N   a   lgk +e+++
  gi|330507774|ref|YP_004384202.1|  75 ALGRYDEAIQAYDQAISIDPQYAYAWSNKGEALRALGKYDEAIN 118
                                       5799************************9999999999998876 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.043
                                       HTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 213 llgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                        lg+y+eA +   +a+  d++++ + +N  +a  hlgk +e+++
  gi|330507774|ref|YP_004384202.1| 143 DLGKYDEAINAYDQAISIDPQYAYAWSNKGTALGHLGKYDEAIK 186
                                       4689**********************************988864 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.44
                                       TT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHH CS
                        Coatomer_E 214 lgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevs 255
                                       lg+y+eA +   +a+  d++ +e+  N  +a   lgk +e++
  gi|330507774|ref|YP_004384202.1| 212 LGKYDEAIKPFDQAISIDPQFAEAWYNKGTALGRLGKYDEAI 253
                                       789**********************************98876 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.076
                                       HHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 212 lllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                         lg+y+eA +   +a+  +++ +e+  N  va + lgk +e+++
  gi|330507774|ref|YP_004384202.1| 278 YDLGKYDEAIQAYDQAISINPQIAEAWYNKGVALTALGKYDEAIK 322
                                       56899**********************************988764 PP

  == domain 6  score: 6.4 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 183 iqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                       + +A   +++ +   ++       k v+  +lg+y+eA +   +a+  +++ +e+  N  v+ + lgk +e+++
  gi|330507774|ref|YP_004384202.1| 351 YDEAIQAYDQANRINPQFAEAWYNKGVALTALGKYDEAIKACDQAISINPQFAEAWYNKGVVLKALGKYDEAIK 424
                                       5555555555554444445555677888899999************************9999999999988875 PP

>> DUF982  Protein of unknown function (DUF982)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       9.9   3.6e+03      37      50 ..      44      57 ..      27      67 .. 0.70
   2 ?    4.3   0.0      0.11        40      37      50 ..     112     125 ..     105     135 .. 0.89
   3 ?    5.5   0.0     0.048        18      37      50 ..     180     193 ..     174     202 .. 0.83
   4 ?    5.4   0.1     0.052        19      37      51 ..     248     262 ..     242     272 .. 0.85
   5 ?   -1.0   0.0       5.3   1.9e+03      37      58 ..     282     303 ..     264     305 .. 0.72
   6 ?    4.7   0.0     0.084        31      37      50 ..     316     329 ..     314     338 .. 0.89
   7 ?    5.5   0.0     0.046        17      37      57 ..     384     404 ..     381     407 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 9.9
                                      HHHHHHHHHHHHHT CS
                            DUF982 37 ayeaAlkaCrdAld 50
                                       y++A++a ++A++
  gi|330507774|ref|YP_004384202.1| 44 MYDEAIQAYDQAIS 57
                                      57888888777775 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHT CS
                            DUF982  37 ayeaAlkaCrdAld 50 
                                       +y++A++aC++A++
  gi|330507774|ref|YP_004384202.1| 112 KYDEAINACDQAIS 125
                                       69**********96 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.048
                                       HHHHHHHHHHHHHT CS
                            DUF982  37 ayeaAlkaCrdAld 50 
                                       +y++A+kaC++A++
  gi|330507774|ref|YP_004384202.1| 180 KYDEAIKACDQAIS 193
                                       69**********97 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.052
                                       HHHHHHHHHHHHHTT CS
                            DUF982  37 ayeaAlkaCrdAldg 51 
                                       +y++A+kaC++A++ 
  gi|330507774|ref|YP_004384202.1| 248 KYDEAIKACDQAISI 262
                                       69**********975 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 5.3
                                       HHHHHHHHHHHHHTT-S-HHHH CS
                            DUF982  37 ayeaAlkaCrdAldgdvpveeA 58 
                                       +y++A++a ++A++   +++eA
  gi|330507774|ref|YP_004384202.1| 282 KYDEAIQAYDQAISINPQIAEA 303
                                       7999999999999866666666 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.084
                                       HHHHHHHHHHHHHT CS
                            DUF982  37 ayeaAlkaCrdAld 50 
                                       +y++A+kaC++A++
  gi|330507774|ref|YP_004384202.1| 316 KYDEAIKACDQAIS 329
                                       69**********96 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHHHTT-S-HHH CS
                            DUF982  37 ayeaAlkaCrdAldgdvpvee 57 
                                       +y++A+kaC++A++   + +e
  gi|330507774|ref|YP_004384202.1| 384 KYDEAIKACDQAISINPQFAE 404
                                       69**********986655555 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.3   8.2e+02       3      28 ..      31      56 ..      27      62 .. 0.56
   2 ?    4.7   0.5     0.067        24       8      53 ..      63     107 ..      52     116 .. 0.80
   3 ?    2.9   0.1      0.23        84       7      36 ..      96     125 ..      93     129 .. 0.88
   4 ?    0.7   0.1       1.1   4.2e+02      15      41 ..     138     164 ..     129     178 .. 0.75
   5 ?    2.0   0.0      0.43   1.6e+02       7      36 ..     164     193 ..     154     195 .. 0.85
   6 ?    5.2   0.0     0.046        17       8      56 ..     199     246 ..     196     256 .. 0.81
   7 ?    1.0   0.0      0.92   3.4e+02       7      36 ..     266     295 ..     264     299 .. 0.83
   8 ?    4.9   0.1     0.055        20       6      36 ..     299     329 ..     297     334 .. 0.93
   9 ?   -2.0   0.0       7.5   2.7e+03      18      35 ..     345     362 ..     333     374 .. 0.71
  10 !    7.8   0.0    0.0074       2.7       6      54 ..     367     414 ..     362     428 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.3
                           DUF5113  3 dllqiandYanlayylnvegeyeeAL 28
                                      ++l++ n+++ l +y  + + y++A+
  gi|330507774|ref|YP_004384202.1| 31 EWLEKGNAFVMLSMYDEAIQAYDQAI 56
                                      34555555555555555555555554 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.067
                           DUF5113   8 andYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtl 53 
                                       a ++ n + +l + g+y+eA++  d+a+++  ++   +++k  + l
  gi|330507774|ref|YP_004384202.1|  63 AYAWSNKGEALRALGRYDEAIQAYDQAISIDPQYAYAWSNKG-EAL 107
                                       566789999999****************98777777777665.455 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.23
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsale 36 
                                        a ++ n + +l + g+y+eA++  d+a++
  gi|330507774|ref|YP_004384202.1|  96 YAYAWSNKGEALRALGKYDEAINACDQAIS 125
                                       5677889999999***************97 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.1
                           DUF5113  15 ayylnvegeyeeALeyldsaleylNah 41 
                                       +++l+  g+y+eA++  d+a+++  ++
  gi|330507774|ref|YP_004384202.1| 138 GNALYDLGKYDEAINAYDQAISIDPQY 164
                                       566677799***********9875555 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.43
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsale 36 
                                        a ++ n +++l   g+y+eA++  d+a++
  gi|330507774|ref|YP_004384202.1| 164 YAYAWSNKGTALGHLGKYDEAIKACDQAIS 193
                                       466677899999999*************97 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.046
                           DUF5113   8 andYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtldkl 56 
                                       a ++ n ++ l + g+y+eA++ +d+a+++  ++ e +++k +  l +l
  gi|330507774|ref|YP_004384202.1| 199 AYAWYNKGTVLGILGKYDEAIKPFDQAISIDPQFAEAWYNKGT-ALGRL 246
                                       5567789999999****************99999999998873.56555 PP

  == domain 7  score: 1.0 bits;  conditional E-value: 0.92
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsale 36 
                                        a+++   + +l+  g+y+eA++  d+a++
  gi|330507774|ref|YP_004384202.1| 266 LAETWTIKGIALYDLGKYDEAIQAYDQAIS 295
                                       5677777788888899***********997 PP

  == domain 8  score: 4.9 bits;  conditional E-value: 0.055
                           DUF5113   6 qiandYanlayylnvegeyeeALeyldsale 36 
                                       qia+++ n + +l + g+y+eA++  d+a++
  gi|330507774|ref|YP_004384202.1| 299 QIAEAWYNKGVALTALGKYDEAIKACDQAIS 329
                                       7999*************************97 PP

  == domain 9  score: -2.0 bits;  conditional E-value: 7.5
                           DUF5113  18 lnvegeyeeALeyldsal 35 
                                       l+  g+y+eA++  d+a 
  gi|330507774|ref|YP_004384202.1| 345 LYDLGKYDEAIQAYDQAN 362
                                       555689999999999884 PP

  == domain 10  score: 7.8 bits;  conditional E-value: 0.0074
                           DUF5113   6 qiandYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtld 54 
                                       q a+++ n + +l + g+y+eA++  d+a+++  ++ e +++k    l+
  gi|330507774|ref|YP_004384202.1| 367 QFAEAWYNKGVALTALGKYDEAIKACDQAISINPQFAEAWYNKGV-VLK 414
                                       5789999999*********************99999999998874.554 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   1.8    0.0027      0.99     124     181 ..      43     101 ..      20     105 .. 0.86
   2 ?    5.5   0.0      0.04        15     151     180 ..     105     134 ..     101     140 .. 0.91
   3 ?    2.6   0.3      0.32   1.2e+02     150     180 ..     172     202 ..     146     207 .. 0.77
   4 ?   -0.7   0.0       3.1   1.1e+03     152     180 ..     242     270 ..     233     274 .. 0.86
   5 ?    3.9   0.1      0.12        44     152     180 ..     276     304 ..     249     309 .. 0.88
   6 !    9.6   0.2    0.0021      0.77     126     180 ..     283     338 ..     279     343 .. 0.86
   7 ?    2.6   0.2       0.3   1.1e+02     153     180 ..     345     372 ..     342     377 .. 0.87
   8 ?    3.2   0.7       0.2        75     148     180 ..     374     406 ..     352     411 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0027
                           Wzy_C_2 124 enlaaklalarklihlsPepav.ierlilslallGdedeAeqilararalfpeedakwv 181
                                       +++++ ++++ ++i   P+ a   ++  ++l +lG+ deA q +++a+ + p+++++w+
  gi|330507774|ref|YP_004384202.1|  43 SMYDEAIQAYDQAISIDPQDAYaWSNKGEALRALGRYDEAIQAYDQAISIDPQYAYAWS 101
                                       57788899999999999988752588999*****************************4 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.04
                           Wzy_C_2 151 lslallGdedeAeqilararalfpeedakw 180
                                       ++l +lG+ deA    ++a+ + p+++++w
  gi|330507774|ref|YP_004384202.1| 105 EALRALGKYDEAINACDQAISINPQDAFAW 134
                                       68999************************* PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.32
                           Wzy_C_2 150 ilslallGdedeAeqilararalfpeedakw 180
                                         +l  lG+ deA +  ++a+ + p+++++w
  gi|330507774|ref|YP_004384202.1| 172 GTALGHLGKYDEAIKACDQAISIDPQNAYAW 202
                                       5678889*********************999 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 3.1
                           Wzy_C_2 152 slallGdedeAeqilararalfpeedakw 180
                                       +l  lG+ deA +  ++a+ + p+ +++w
  gi|330507774|ref|YP_004384202.1| 242 ALGRLGKYDEAIKACDQAISIDPQLAETW 270
                                       67889*************99988888888 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.12
                           Wzy_C_2 152 slallGdedeAeqilararalfpeedakw 180
                                       +l  lG+ deA q +++a+ + p+ +++w
  gi|330507774|ref|YP_004384202.1| 276 ALYDLGKYDEAIQAYDQAISINPQIAEAW 304
                                       56679**********************99 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.0021
                           Wzy_C_2 126 laaklalarklihlsPepa.vierlilslallGdedeAeqilararalfpeedakw 180
                                       +++ ++++ ++i   P+ a   ++  ++l +lG+ deA +  ++a+ + p+++++w
  gi|330507774|ref|YP_004384202.1| 283 YDEAIQAYDQAISINPQIAeAWYNKGVALTALGKYDEAIKACDQAISINPQDAFAW 338
                                       678889999999999987624688899***************************** PP

  == domain 7  score: 2.6 bits;  conditional E-value: 0.3
                           Wzy_C_2 153 lallGdedeAeqilararalfpeedakw 180
                                       l  lG+ deA q +++a  + p+ +++w
  gi|330507774|ref|YP_004384202.1| 345 LYDLGKYDEAIQAYDQANRINPQFAEAW 372
                                       5568****************99999999 PP

  == domain 8  score: 3.2 bits;  conditional E-value: 0.2
                           Wzy_C_2 148 rlilslallGdedeAeqilararalfpeedakw 180
                                       +  ++l +lG+ deA +  ++a+ + p+ +++w
  gi|330507774|ref|YP_004384202.1| 374 NKGVALTALGKYDEAIKACDQAISINPQFAEAW 406
                                       45589999*****************99999999 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2     0.003       1.1     143     178 ..      59      95 ..      27      99 .. 0.83
   2 !   11.5   0.2   0.00035      0.13     146     239 ..      97     190 ..      94     220 .. 0.79
   3 ?    2.9   0.0      0.15        53     146     235 ..     199     288 ..     172     299 .. 0.43
   4 !    8.8   1.8    0.0023      0.85     148     249 ..     235     336 ..     223     361 .. 0.79
   5 !    6.8   2.3    0.0094       3.4     149     263 ..     304     411 ..     299     427 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.003
                            TPR_15 143 e.qsaafllaraelyrqegqtdaAlrdyreAlalapd 178
                                         q+a+ ++  +e+ r+ g+ d+A+++y +A++ +p+
  gi|330507774|ref|YP_004384202.1|  59 DpQDAYAWSNKGEALRALGRYDEAIQAYDQAISIDPQ 95 
                                       2699*****************************9997 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00035
                            TPR_15 146 aafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgp 219
                                       a+ ++  +e+ r+ g+ d+A+++  +A++ +p+++ +      +l Dlg+++e   ++ a+ ++     + a  w  
  gi|330507774|ref|YP_004384202.1|  97 AYAWSNKGEALRALGKYDEAINACDQAISINPQDAFAWTIKGNALYDLGKYDE---AINAYDQAIsidPQYAYAWSN 170
                                       78899999999999999999999999999999988777777778899999997...999999988444444555666 PP

                            TPR_15 220 laaAlllLgrpkkALeylrk 239
                                        ++Al  Lg++++A +   +
  gi|330507774|ref|YP_004384202.1| 171 KGTALGHLGKYDEAIKACDQ 190
                                       78899999999888776655 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.15
                            TPR_15 146 aafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasL...wgp 219
                                       a+ ++  + +    g+ d+A++ + +A++ +p+ +e+  +   +l  lg+++   e++ka  ++ + d++L   w  
  gi|330507774|ref|YP_004384202.1| 199 AYAWYNKGTVLGILGKYDEAIKPFDQAISIDPQFAEAWYNKGTALGRLGKYD---EAIKACDQAISIDPQLaetWTI 272
                                       4555555555555555555555555555555543222222222222222222...2444444433222222000222 PP

                            TPR_15 220 laaAlllLgrpkkALe 235
                                        + Al  Lg++++A +
  gi|330507774|ref|YP_004384202.1| 273 KGIALYDLGKYDEAIQ 288
                                       2334444444444444 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0023
                            TPR_15 148 fllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgpl...a 221
                                        ++  + +  + g+ d+A+++  +A++ +p+ +e       +l Dlg+++e   +++a+ ++ + ++++ ++    +
  gi|330507774|ref|YP_004384202.1| 235 AWYNKGTALGRLGKYDEAIKACDQAISIDPQLAETWTIKGIALYDLGKYDE---AIQAYDQAISINPQIAEAWynkG 308
                                       5777778888999*****************96655555556899******7...******99966666666543338 PP

                            TPR_15 222 aAlllLgrpkkALeylrkqakenrkdpl 249
                                        Al +Lg++++A +   +  + n++d+ 
  gi|330507774|ref|YP_004384202.1| 309 VALTALGKYDEAIKACDQAISINPQDAF 336
                                       9**********************99974 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.0094
                            TPR_15 149 llaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgplaaAll 225
                                       ++  + + ++ g+ d+A+++  +A++ +p+++ +      +l Dlg+++e   +++a+ ++    +++ + +a A+ 
  gi|330507774|ref|YP_004384202.1| 304 WYNKGVALTALGKYDEAIKACDQAISINPQDAFAWTIKGIALYDLGKYDE---AIQAYDQA----NRINPQFAEAWY 373
                                       6666677788999*****************9888777778999******7...99999877....778888888888 PP

                            TPR_15 226 lLgrpkkALeylrkqakenrkdplwllaYADaleqagr 263
                                         g    AL  +    k+  + +++  ++A+a + +g 
  gi|330507774|ref|YP_004384202.1| 374 NKGVALTALGKYDEAIKACDQAISINPQFAEAWYNKGV 411
                                       88888888888888888888888888888888887775 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1      0.11        39      73     123 ..      33      83 ..      17      88 .. 0.79
   2 ?    5.1   0.0     0.078        29      75     125 ..     103     153 ..      96     160 .. 0.89
   3 ?    3.4   0.0      0.27        99      82     121 ..     178     217 ..     165     221 .. 0.86
   4 ?    3.1   0.0      0.33   1.2e+02      78     117 ..     276     315 ..     233     323 .. 0.58
   5 ?    1.6   0.0      0.94   3.4e+02      78     123 ..     310     355 ..     300     364 .. 0.84
   6 ?    3.0   0.0      0.35   1.3e+02      77     123 ..     377     423 ..     355     428 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.11
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  73 lekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       lek ++ +    y  a++  ++++  dp++a a + k +al++lg+  e+ 
  gi|330507774|ref|YP_004384202.1|  33 LEKGNAFVMLSMYDEAIQAYDQAISIDPQDAYAWSNKGEALRALGRYDEAI 83 
                                       44444444555588888889999999*******************998876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.078
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHH CS
                   Alkyl_sulf_dimr  75 kakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatw 125
                                       k ++ ++ g+y  a++ +++++  +p++a a ++k +al  lg+  e+ ++
  gi|330507774|ref|YP_004384202.1| 103 KGEALRALGKYDEAINACDQAISINPQDAFAWTIKGNALYDLGKYDEAINA 153
                                       5566778899*********************************99988775 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.27
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
                   Alkyl_sulf_dimr  82 egdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                                        g+y  a++ +++++  dp+na a   k  +l  lg+  e
  gi|330507774|ref|YP_004384202.1| 178 LGKYDEAIKACDQAISIDPQNAYAWYNKGTVLGILGKYDE 217
                                       589999******************9999999998888766 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.33
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlg 117
                                       + ++ g+y  a++  ++++  +p+ aea   k  al++lg
  gi|330507774|ref|YP_004384202.1| 276 ALYDLGKYDEAIQAYDQAISINPQIAEAWYNKGVALTALG 315
                                       3445555555555555555555555555555555555555 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.94
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       +  + g+y  a++ +++++  +p++a a ++k  al  lg+  e+ 
  gi|330507774|ref|YP_004384202.1| 310 ALTALGKYDEAIKACDQAISINPQDAFAWTIKGIALYDLGKYDEAI 355
                                       5567799999****************99999999999999887765 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.35
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  77 kealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                        +  + g+y  a++ +++++  +p+ aea   k  +l++lg+  e+ 
  gi|330507774|ref|YP_004384202.1| 377 VALTALGKYDEAIKACDQAISINPQFAEAWYNKGVVLKALGKYDEAI 423
                                       5566779999******************************9988765 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       1.7   6.2e+02       7      41 ..      80     115 ..      43     125 .. 0.79
   2 ?   -0.3   0.0       4.8   1.8e+03       7      42 ..     148     184 ..     147     193 .. 0.81
   3 ?    3.1   0.0      0.43   1.6e+02       7      43 ..     216     253 ..     215     261 .. 0.83
   4 ?    2.5   0.0      0.67   2.5e+02       7      42 ..     284     320 ..     283     329 .. 0.82
   5 ?    6.8   0.0      0.03        11       7      42 ..     352     388 ..     351     397 .. 0.82
   6 ?   -0.6   0.0         6   2.2e+03       7      30 ..     386     409 ..     385     424 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.7
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgel.elve 41 
                                       d+ ++a+ +a + +p++  +++    +l++l + +e
  gi|330507774|ref|YP_004384202.1|  80 DEAIQAYDQAISIDPQYAYAWSNKGEALRALgKYDE 115
                                       678888889999999998888888877777744444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 4.8
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgel.elvea 42 
                                       d+ + a+ +a + +p++  +++   ++lg l + +ea
  gi|330507774|ref|YP_004384202.1| 148 DEAINAYDQAISIDPQYAYAWSNKGTALGHLgKYDEA 184
                                       678999****************999999998555555 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.43
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgel.elveal 43 
                                       d+ + ++ +a + +p++ ++++   ++lg+l + +ea 
  gi|330507774|ref|YP_004384202.1| 216 DEAIKPFDQAISIDPQFAEAWYNKGTALGRLgKYDEAI 253
                                       678999*********************99996665554 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.67
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgel.elvea 42 
                                       d+ ++a+ +a + np++ ++++    +l++l + +ea
  gi|330507774|ref|YP_004384202.1| 284 DEAIQAYDQAISINPQIAEAWYNKGVALTALgKYDEA 320
                                       7899******************999999888555554 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.03
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgel.elvea 42 
                                       d+ ++a+ +a+r np++ ++++    +l++l + +ea
  gi|330507774|ref|YP_004384202.1| 352 DEAIQAYDQANRINPQFAEAWYNKGVALTALgKYDEA 388
                                       789*******************999999888555554 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 6
                         TetR_C_15   7 dalvdallaahrenpalrrvllee 30 
                                       d+ + a  +a + np++ ++++  
  gi|330507774|ref|YP_004384202.1| 386 DEAIKACDQAISINPQFAEAWYNK 409
                                       678999999************975 PP

>> FERM_C  FERM C-terminal PH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.065        24       4      35 ..      37      68 ..      34      71 .. 0.89
   2 ?    2.2   0.0      0.66   2.4e+02       9      35 ..      76     102 ..      68     104 .. 0.84
   3 ?    1.0   0.0       1.5   5.6e+02       9      34 ..     110     135 ..     102     142 .. 0.84
   4 ?    2.4   0.0      0.55     2e+02       9      35 ..     144     170 ..     136     173 .. 0.85
   5 ?    0.2   0.0       2.8     1e+03       9      33 ..     178     202 ..     170     204 .. 0.81
   6 ?    0.5   0.0       2.2     8e+02      10      34 ..     315     339 ..     308     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.065
                                      --EEEEEE-SSEEEEEBTTBSSS-SEEEEGGG CS
                            FERM_C  4 gteliLgisakGilvyekqnkitpklafpWre 35
                                      +  ++L++  + i+ y++   i p+ a+ W++
  gi|330507774|ref|YP_004384202.1| 37 NAFVMLSMYDEAIQAYDQAISIDPQDAYAWSN 68
                                      566899************************85 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.66
                                       EEE-SSEEEEEBTTBSSS-SEEEEGGG CS
                            FERM_C   9 LgisakGilvyekqnkitpklafpWre 35 
                                       Lg   + i+ y++   i p+ a+ W++
  gi|330507774|ref|YP_004384202.1|  76 LGRYDEAIQAYDQAISIDPQYAYAWSN 102
                                       6666677999***************85 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.5
                                       EEE-SSEEEEEBTTBSSS-SEEEEGG CS
                            FERM_C   9 LgisakGilvyekqnkitpklafpWr 34 
                                       Lg   + i+ +++   i+p+ af W 
  gi|330507774|ref|YP_004384202.1| 110 LGKYDEAINACDQAISINPQDAFAWT 135
                                       66666779999999***********6 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.55
                                       EEE-SSEEEEEBTTBSSS-SEEEEGGG CS
                            FERM_C   9 LgisakGilvyekqnkitpklafpWre 35 
                                       Lg   + i+ y++   i p+ a+ W++
  gi|330507774|ref|YP_004384202.1| 144 LGKYDEAINAYDQAISIDPQYAYAWSN 170
                                       6666677999***************85 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 2.8
                                       EEE-SSEEEEEBTTBSSS-SEEEEG CS
                            FERM_C   9 LgisakGilvyekqnkitpklafpW 33 
                                       Lg   + i+ +++   i p++a+ W
  gi|330507774|ref|YP_004384202.1| 178 LGKYDEAIKACDQAISIDPQNAYAW 202
                                       555666688899999********** PP

  == domain 6  score: 0.5 bits;  conditional E-value: 2.2
                                       EE-SSEEEEEBTTBSSS-SEEEEGG CS
                            FERM_C  10 gisakGilvyekqnkitpklafpWr 34 
                                       g   + i+ +++   i+p+ af W 
  gi|330507774|ref|YP_004384202.1| 315 GKYDEAIKACDQAISINPQDAFAWT 339
                                       555566888999999*********5 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.41   1.5e+02     254     290 ..      32      67 ..      25      69 .. 0.76
   2 ?    6.6   0.2      0.01       3.7     250     291 ..      68     102 ..      59     117 .. 0.85
   3 ?    2.4   0.2       0.2        73     267     291 ..     146     170 ..     127     193 .. 0.81
   4 ?   -1.3   0.1       2.7     1e+03     251     291 ..     171     204 ..     162     209 .. 0.82
   5 ?    2.8   0.0      0.15        54     260     291 ..     214     238 ..     195     255 .. 0.83
   6 !    7.3   0.1    0.0064       2.4     245     291 ..     267     306 ..     261     323 .. 0.79
   7 ?    5.3   0.2     0.026       9.5     267     291 ..     350     374 ..     337     390 .. 0.84
   8 ?    3.9   0.4      0.07        25     239     291 ..     363     408 ..     353     428 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.41
                                       CCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTC CS
                               FAT 254 wqealqkldwseekieeilqsysaateidpswykawh 290
                                       w+e+ + +  +    +e+ q+y +a +idp+ + aw 
  gi|330507774|ref|YP_004384202.1|  32 WLEKGNAF-VMLSMYDEAIQAYDQAISIDPQDAYAWS 67 
                                       55555554.34445899*************9999997 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                                       TCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 250 kkGewqealqkldwseekieeilqsysaateidpswykawht 291
                                        kGe ++al++        +e+ q+y +a +idp+ + aw +
  gi|330507774|ref|YP_004384202.1|  68 NKGEALRALGR-------YDEAIQAYDQAISIDPQYAYAWSN 102
                                       68999999999.......99*****************9**87 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.2
                                       .-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 267 kieeilqsysaateidpswykawht 291
                                       k +e+ ++y +a +idp+ + aw +
  gi|330507774|ref|YP_004384202.1| 146 KYDEAINAYDQAISIDPQYAYAWSN 170
                                       4799***************99**87 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 2.7
                                       CCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 251 kGewqealqkldwseekieeilqsysaateidpswykawht 291
                                       kG  + +l+k        +e+ ++  +a +idp+ + aw++
  gi|330507774|ref|YP_004384202.1| 171 KGTALGHLGK-------YDEAIKACDQAISIDPQNAYAWYN 204
                                       5666666777.......899999999999999999999985 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.15
                                       CCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 260 kldwseekieeilqsysaateidpswykawht 291
                                       k        +e+ + + +a +idp+ ++aw++
  gi|330507774|ref|YP_004384202.1| 214 K-------YDEAIKPFDQAISIDPQFAEAWYN 238
                                       4.......789*******************97 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.0064
                                       HHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 245 arcylkkGewqealqkldwseekieeilqsysaateidpswykawht 291
                                       a++ + kG  +  l+k        +e+ q+y +a +i+p++++aw++
  gi|330507774|ref|YP_004384202.1| 267 AETWTIKGIALYDLGK-------YDEAIQAYDQAISINPQIAEAWYN 306
                                       6666666766666666.......89********************97 PP

  == domain 7  score: 5.3 bits;  conditional E-value: 0.026
                                       .-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 267 kieeilqsysaateidpswykawht 291
                                       k +e+ q+y +a++i+p+ ++aw++
  gi|330507774|ref|YP_004384202.1| 350 KYDEAIQAYDQANRINPQFAEAWYN 374
                                       4799*******************97 PP

  == domain 8  score: 3.9 bits;  conditional E-value: 0.07
                                       ....HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 239 eftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykawht 291
                                        ++ + a++   kG  ++al+k        +e+ ++  +a +i+p+ ++aw++
  gi|330507774|ref|YP_004384202.1| 363 RINPQFAEAWYNKGVALTALGK-------YDEAIKACDQAISINPQFAEAWYN 408
                                       3344446666666666666666.......667777777777777777777765 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.3     0.028        10       6      70 ..      47     116 ..      44     125 .. 0.81
   2 ?    3.4   0.1      0.27     1e+02       7      52 ..     116     161 ..     111     174 .. 0.84
   3 ?    4.8   0.0     0.098        36       6      56 ..     183     233 ..     179     263 .. 0.82
   4 ?    4.7   0.1      0.11        39       6      44 ..     285     323 ..     281     335 .. 0.89
   5 ?    1.0   0.3       1.5   5.6e+02       7      43 ..     320     356 ..     318     371 .. 0.88
   6 ?    4.1   0.2      0.17        60       8      57 ..     355     404 ..     347     427 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.028
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw.....eddaarkqllkifea 70 
                                       + +++ ++a+  +p+d  a  +  +al a gry+eA+++  + ++ d ++     ++++a ++l k+ ea
  gi|330507774|ref|YP_004384202.1|  47 EAIQAYDQAISIDPQDAYAWSNKGEALRALGRYDEAIQAYDQAISIDPQYayawsNKGEALRALGKYDEA 116
                                       5689999******************************999999888888866666666666666555555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.27
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrd 52 
                                        + + ++a+  np+d  a     +al+  g+y+eA+++  + ++ d
  gi|330507774|ref|YP_004384202.1| 116 AINACDQAISINPQDAFAWTIKGNALYDLGKYDEAINAYDQAISID 161
                                       6788999*********999999*************99866666655 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.098
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwe 56 
                                       + +++ ++a+  +p++  a ++  ++l   g+y+eA++ + + ++ d +++
  gi|330507774|ref|YP_004384202.1| 183 EAIKACDQAISIDPQNAYAWYNKGTVLGILGKYDEAIKPFDQAISIDPQFA 233
                                       56889999*****************************99988888888873 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.11
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                       + +++ ++a+  np+  +a ++   al a g+y+eA+++
  gi|330507774|ref|YP_004384202.1| 285 EAIQAYDQAISINPQIAEAWYNKGVALTALGKYDEAIKA 323
                                       5789999*****************************975 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 1.5
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAle 43 
                                        +++ ++a+  np+d  a      al+  g+y+eA++
  gi|330507774|ref|YP_004384202.1| 320 AIKACDQAISINPQDAFAWTIKGIALYDLGKYDEAIQ 356
                                       57889999*******9999999999999999999997 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.17
                            TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwed 57 
                                       +++ ++a   np+  +a ++   al a g+y+eA+++  + ++ + ++++
  gi|330507774|ref|YP_004384202.1| 355 IQAYDQANRINPQFAEAWYNKGVALTALGKYDEAIKACDQAISINPQFAE 404
                                       56666666667777777777777777777777777666555555555533 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 ?   -1.8   0.0       7.3   2.7e+03      35      45 ..      75      85 ..      72      91 .. 0.74
   2 ?    1.0   0.0      0.95   3.5e+02      35      50 ..     109     124 ..     105     126 .. 0.86
   3 ?   -0.2   0.0       2.3   8.4e+02      33      46 ..     141     154 ..     136     159 .. 0.76
   4 ?    2.4   0.0      0.34   1.3e+02      35      50 ..     177     192 ..     173     194 .. 0.87
   5 ?    1.5   0.0      0.67   2.5e+02      35      50 ..     245     260 ..     241     262 .. 0.86
   6 ?   -0.7   0.0       3.3   1.2e+03      33      45 ..     277     289 ..     275     295 .. 0.76
   7 ?    3.3   0.0      0.19        68      33      50 ..     311     328 ..     310     330 .. 0.89
   8 ?   -1.1   0.0       4.5   1.6e+03      33      44 ..     345     356 ..     344     363 .. 0.77
   9 ?    3.3   0.0      0.19        68      33      50 ..     379     396 ..     378     398 .. 0.89
  10 ?   -2.1   0.0       8.9   3.2e+03      35      44 ..     415     424 ..     413     430 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 7.3
                            SPOB_a 35 qLgkydkaeey 45
                                      +Lg+yd+a + 
  gi|330507774|ref|YP_004384202.1| 75 ALGRYDEAIQA 85
                                      799***99765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.95
                            SPOB_a  35 qLgkydkaeeyieevv 50 
                                       +Lgkyd+a + +++++
  gi|330507774|ref|YP_004384202.1| 109 ALGKYDEAINACDQAI 124
                                       79*******9999986 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.3
                            SPOB_a  33 ylqLgkydkaeeyi 46 
                                       + +Lgkyd+a +  
  gi|330507774|ref|YP_004384202.1| 141 LYDLGKYDEAINAY 154
                                       579******97755 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.34
                            SPOB_a  35 qLgkydkaeeyieevv 50 
                                       +Lgkyd+a + +++++
  gi|330507774|ref|YP_004384202.1| 177 HLGKYDEAIKACDQAI 192
                                       8**********99986 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.67
                            SPOB_a  35 qLgkydkaeeyieevv 50 
                                        Lgkyd+a + +++++
  gi|330507774|ref|YP_004384202.1| 245 RLGKYDEAIKACDQAI 260
                                       69********999986 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 3.3
                            SPOB_a  33 ylqLgkydkaeey 45 
                                       + +Lgkyd+a + 
  gi|330507774|ref|YP_004384202.1| 277 LYDLGKYDEAIQA 289
                                       5689****99765 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.19
                            SPOB_a  33 ylqLgkydkaeeyieevv 50 
                                       +++Lgkyd+a + +++++
  gi|330507774|ref|YP_004384202.1| 311 LTALGKYDEAIKACDQAI 328
                                       789**********99986 PP

  == domain 8  score: -1.1 bits;  conditional E-value: 4.5
                            SPOB_a  33 ylqLgkydkaee 44 
                                       + +Lgkyd+a +
  gi|330507774|ref|YP_004384202.1| 345 LYDLGKYDEAIQ 356
                                       5689****9976 PP

  == domain 9  score: 3.3 bits;  conditional E-value: 0.19
                            SPOB_a  33 ylqLgkydkaeeyieevv 50 
                                       +++Lgkyd+a + +++++
  gi|330507774|ref|YP_004384202.1| 379 LTALGKYDEAIKACDQAI 396
                                       789**********99986 PP

  == domain 10  score: -2.1 bits;  conditional E-value: 8.9
                            SPOB_a  35 qLgkydkaee 44 
                                       +Lgkyd+a +
  gi|330507774|ref|YP_004384202.1| 415 ALGKYDEAIK 424
                                       699***9976 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.22        81      28      57 ..      45      72 ..      34      92 .. 0.82
   2 ?    0.1   0.0       2.4   8.8e+02      28      52 ..      79     103 ..      76     113 .. 0.78
   3 ?    3.9   0.0      0.17        61      28      54 ..     113     139 ..     108     146 .. 0.91
   4 ?   -0.7   0.0       4.6   1.7e+03      28      51 ..     147     170 ..     142     180 .. 0.82
   5 ?    3.4   0.0      0.24        86      28      52 ..     181     205 ..     176     210 .. 0.90
   6 ?    0.5   0.0       1.9   6.9e+02      28      52 ..     249     273 ..     245     277 .. 0.91
   7 ?   -0.7   0.0       4.5   1.6e+03      28      51 ..     283     306 ..     278     316 .. 0.83
   8 ?    3.1   0.0      0.29   1.1e+02      28      52 ..     317     341 ..     312     346 .. 0.92
   9 ?   -1.1   0.0         6   2.2e+03      28      50 ..     385     407 ..     382     422 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.22
                           DUF1510 28 wnEmekavskatglsednmivwwlgnggsp 57
                                      ++E  +a  +a+ ++ ++ + w    +g++
  gi|330507774|ref|YP_004384202.1| 45 YDEAIQAYDQAISIDPQDAYAWSN--KGEA 72
                                      7899***************99964..4555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.4
                           DUF1510  28 wnEmekavskatglsednmivwwlg 52 
                                       ++E  +a  +a+ ++ +  + w  +
  gi|330507774|ref|YP_004384202.1|  79 YDEAIQAYDQAISIDPQYAYAWSNK 103
                                       78999*********98887777543 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.17
                           DUF1510  28 wnEmekavskatglsednmivwwlgng 54 
                                       ++E  +a  +a+ ++ ++   w ++ +
  gi|330507774|ref|YP_004384202.1| 113 YDEAINACDQAISINPQDAFAWTIKGN 139
                                       7899*******************9876 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 4.6
                           DUF1510  28 wnEmekavskatglsednmivwwl 51 
                                       ++E  +a  +a+ ++ +  + w  
  gi|330507774|ref|YP_004384202.1| 147 YDEAINAYDQAISIDPQYAYAWSN 170
                                       789999********9888777754 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.24
                           DUF1510  28 wnEmekavskatglsednmivwwlg 52 
                                       ++E  ka  +a+ ++ +n + w+ +
  gi|330507774|ref|YP_004384202.1| 181 YDEAIKACDQAISIDPQNAYAWYNK 205
                                       7899******************865 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 1.9
                           DUF1510  28 wnEmekavskatglsednmivwwlg 52 
                                       ++E  ka  +a+ ++ +   +w ++
  gi|330507774|ref|YP_004384202.1| 249 YDEAIKACDQAISIDPQLAETWTIK 273
                                       7899************999999986 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 4.5
                           DUF1510  28 wnEmekavskatglsednmivwwl 51 
                                       ++E  +a  +a+ ++ +    w+ 
  gi|330507774|ref|YP_004384202.1| 283 YDEAIQAYDQAISINPQIAEAWYN 306
                                       78999*********9988777764 PP

  == domain 8  score: 3.1 bits;  conditional E-value: 0.29
                           DUF1510  28 wnEmekavskatglsednmivwwlg 52 
                                       ++E  ka  +a+ ++ ++   w ++
  gi|330507774|ref|YP_004384202.1| 317 YDEAIKACDQAISINPQDAFAWTIK 341
                                       7899******************997 PP

  == domain 9  score: -1.1 bits;  conditional E-value: 6
                           DUF1510  28 wnEmekavskatglsednmivww 50 
                                       ++E  ka  +a+ ++ +    w+
  gi|330507774|ref|YP_004384202.1| 385 YDEAIKACDQAISINPQFAEAWY 407
                                       78999*********998877776 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.39   1.4e+02      10      21 ..      25      36 ..      24      38 .. 0.92
   2 ?    0.8   0.0       1.2   4.4e+02      11      21 ..     196     206 ..     194     208 .. 0.88
   3 ?    1.3   0.0      0.87   3.2e+02      11      21 ..     230     240 ..     228     242 .. 0.85
   4 ?    4.5   0.0     0.082        30      11      22 ..     298     309 ..     295     310 .. 0.88
   5 ?    2.5   0.0      0.35   1.3e+02      11      22 ..     366     377 ..     364     378 .. 0.85
   6 ?    2.6   0.0      0.34   1.2e+02      11      22 ..     400     411 ..     397     412 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.39
                   DNA_pol_lambd_f 10 GpktAkkwyakG 21
                                      G++tA +w +kG
  gi|330507774|ref|YP_004384202.1| 25 GQQTAAEWLEKG 36
                                      99*******998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.2
                   DNA_pol_lambd_f  11 pktAkkwyakG 21 
                                       p+ A  wy+kG
  gi|330507774|ref|YP_004384202.1| 196 PQNAYAWYNKG 206
                                       78899*****9 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.87
                   DNA_pol_lambd_f  11 pktAkkwyakG 21 
                                       p+ A+ wy+kG
  gi|330507774|ref|YP_004384202.1| 230 PQFAEAWYNKG 240
                                       5679******9 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.082
                   DNA_pol_lambd_f  11 pktAkkwyakGi 22 
                                       p++A+ wy+kG+
  gi|330507774|ref|YP_004384202.1| 298 PQIAEAWYNKGV 309
                                       899********7 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.35
                   DNA_pol_lambd_f  11 pktAkkwyakGi 22 
                                       p+ A+ wy+kG+
  gi|330507774|ref|YP_004384202.1| 366 PQFAEAWYNKGV 377
                                       678********7 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.34
                   DNA_pol_lambd_f  11 pktAkkwyakGi 22 
                                       p+ A+ wy+kG+
  gi|330507774|ref|YP_004384202.1| 400 PQFAEAWYNKGV 411
                                       778*******97 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.42   1.5e+02      35      63 ..      28      56 ..      24      61 .. 0.88
   2 ?   -0.0   0.1       1.7   6.2e+02      38      63 ..      65      90 ..      49      97 .. 0.83
   3 ?    2.1   0.2      0.37   1.3e+02      15      62 ..      75     123 ..      62     129 .. 0.72
   4 ?    1.5   0.0      0.59   2.2e+02      42      63 ..     137     158 ..     131     163 .. 0.83
   5 ?    0.5   0.1       1.2   4.2e+02      20      61 ..     148     190 ..     143     198 .. 0.58
   6 ?    2.1   0.0      0.39   1.4e+02      31      62 ..     228     259 ..     212     268 .. 0.85
   7 ?    1.5   0.1       0.6   2.2e+02      33      62 ..     264     293 ..     245     297 .. 0.71
   8 ?    4.6   0.2     0.067        24      19      62 ..     283     327 ..     278     331 .. 0.81
   9 ?    6.1   0.1     0.022       8.1      18      62 ..     350     395 ..     341     401 .. 0.90
  10 ?   -0.6   0.0       2.6   9.4e+02      36      60 ..     403     427 ..     397     431 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.42
                                      HHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7 35 irrakldlaehYlkigdleeAlkaysrir 63
                                      +++ +l++++ +++   ++eA++ay +++
  gi|330507774|ref|YP_004384202.1| 28 TAAEWLEKGNAFVMLSMYDEAIQAYDQAI 56
                                      677899*******************9964 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.7
                                      HHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7 38 akldlaehYlkigdleeAlkaysrir 63
                                      a+ +++e     g ++eA++ay +++
  gi|330507774|ref|YP_004384202.1| 65 AWSNKGEALRALGRYDEAIQAYDQAI 90
                                      667888888999**********9864 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHHHH.HTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7  15 eleeLdaelkdak.enlgkeeirrakldlaehYlkigdleeAlkaysri 62 
                                        l + d+ ++ +    +++ + + a+ +++e     g+++eA++a+ ++
  gi|330507774|ref|YP_004384202.1|  75 ALGRYDEAIQAYDqAISIDPQYAYAWSNKGEALRALGKYDEAINACDQA 123
                                       4555666666666566777777888888888888888888888888775 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.59
                                       HHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  42 laehYlkigdleeAlkaysrir 63 
                                       +++  ++ g+++eA++ay +++
  gi|330507774|ref|YP_004384202.1| 137 KGNALYDLGKYDEAINAYDQAI 158
                                       67778899**********9964 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 1.2
                                       HHHHHHHH.HTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHT CS
                              RPN7  20 daelkdak.enlgkeeirrakldlaehYlkigdleeAlkaysr 61 
                                       d+ ++ +    +++ + + a+ +++      g+++eA+ka+ +
  gi|330507774|ref|YP_004384202.1| 148 DEAINAYDqAISIDPQYAYAWSNKGTALGHLGKYDEAIKACDQ 190
                                       4444444434445555555666666666666777777777665 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.39
                                       -HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7  31 gkeeirrakldlaehYlkigdleeAlkaysri 62 
                                       ++ + ++a+++++    + g+++eA+ka+ ++
  gi|330507774|ref|YP_004384202.1| 228 IDPQFAEAWYNKGTALGRLGKYDEAIKACDQA 259
                                       6677889999999999************9886 PP

  == domain 7  score: 1.5 bits;  conditional E-value: 0.6
                                       HHHHHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7  33 eeirrakldlaehYlkigdleeAlkaysri 62 
                                        + ++++  ++   ++ g+++eA++ay ++
  gi|330507774|ref|YP_004384202.1| 264 PQLAETWTIKGIALYDLGKYDEAIQAYDQA 293
                                       555566666666678889999999999886 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.067
                                       HHHHHHHHH.HTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7  19 Ldaelkdak.enlgkeeirrakldlaehYlkigdleeAlkaysri 62 
                                        d+ ++ +    ++  +i++a+++++   +  g+++eA+ka+ ++
  gi|330507774|ref|YP_004384202.1| 283 YDEAIQAYDqAISINPQIAEAWYNKGVALTALGKYDEAIKACDQA 327
                                       5666666665667888999*********************99886 PP

  == domain 9  score: 6.1 bits;  conditional E-value: 0.022
                                       HHHHHHHHHH.HTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7  18 eLdaelkdak.enlgkeeirrakldlaehYlkigdleeAlkaysri 62 
                                       + d+ ++ +   n +  + ++a+++++   +  g+++eA+ka+ ++
  gi|330507774|ref|YP_004384202.1| 350 KYDEAIQAYDqANRINPQFAEAWYNKGVALTALGKYDEAIKACDQA 395
                                       678889999889******************************9886 PP

  == domain 10  score: -0.6 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHCT-HHHHHHHHH CS
                              RPN7  36 rrakldlaehYlkigdleeAlkays 60 
                                       ++a+++++      g+++eA+ka++
  gi|330507774|ref|YP_004384202.1| 403 AEAWYNKGVVLKALGKYDEAIKAFE 427
                                       6788888888889999999999987 PP

>> Trm56  tRNA ribose 2'-O-methyltransferase, aTrm56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.019         7      14      46 ..      26      58 ..      18      89 .. 0.88
   2 ?    1.4   0.0       0.8   2.9e+02      15      46 ..     163     194 ..     153     213 .. 0.86
   3 ?   -1.6   0.0       6.8   2.5e+03      15      45 ..     299     329 ..     264     337 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.019
                                      HHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC CS
                             Trm56 14 kklikefkkeggivvhltmyGenieevieeikk 46
                                      +++  e+ ++g   v l+my e i+   + i+ 
  gi|330507774|ref|YP_004384202.1| 26 QQTAAEWLEKGNAFVMLSMYDEAIQAYDQAISI 58
                                      567889*******************99888864 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.8
                                       HHHHC-S...SEEEEE-TTSEEHHHHHHHHHC CS
                             Trm56  15 klikefkkeggivvhltmyGenieevieeikk 46 
                                       ++   ++++g  + hl  y e i+ + + i+ 
  gi|330507774|ref|YP_004384202.1| 163 QYAYAWSNKGTALGHLGKYDEAIKACDQAISI 194
                                       567789*99***************99998865 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 6.8
                                       HHHHC-S...SEEEEE-TTSEEHHHHHHHHH CS
                             Trm56  15 klikefkkeggivvhltmyGenieevieeik 45 
                                       ++ + + ++g  +  l  y e i+ + + i+
  gi|330507774|ref|YP_004384202.1| 299 QIAEAWYNKGVALTALGKYDEAIKACDQAIS 329
                                       4456677777777777777777777766665 PP

>> Vta1_C  Vta1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       3.2   1.2e+03      24      35 ..     114     125 ..     113     126 .. 0.78
   2 ?    3.1   0.1      0.21        77       4      16 ..     181     193 ..     180     194 .. 0.63
   3 ?    3.1   0.1      0.21        77       4      16 ..     249     261 ..     248     262 .. 0.63
   4 ?    3.1   0.1      0.21        77       4      16 ..     317     329 ..     316     330 .. 0.63
   5 ?    3.1   0.1      0.21        77       4      16 ..     385     397 ..     384     398 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.2
                            Vta1_C  24 etAiknLqeALk 35 
                                       ++Ai  + +A++
  gi|330507774|ref|YP_004384202.1| 114 DEAINACDQAIS 125
                                       789999999987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.21
                            Vta1_C   4 iaeAqKhaKfAiS 16 
                                       ++eA K++ +AiS
  gi|330507774|ref|YP_004384202.1| 181 YDEAIKACDQAIS 193
                                       5666666666666 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.21
                            Vta1_C   4 iaeAqKhaKfAiS 16 
                                       ++eA K++ +AiS
  gi|330507774|ref|YP_004384202.1| 249 YDEAIKACDQAIS 261
                                       5666666666666 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.21
                            Vta1_C   4 iaeAqKhaKfAiS 16 
                                       ++eA K++ +AiS
  gi|330507774|ref|YP_004384202.1| 317 YDEAIKACDQAIS 329
                                       5666666666666 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.21
                            Vta1_C   4 iaeAqKhaKfAiS 16 
                                       ++eA K++ +AiS
  gi|330507774|ref|YP_004384202.1| 385 YDEAIKACDQAIS 397
                                       5666666666666 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       4.6   1.7e+03      22      50 ..     129     157 ..     116     169 .. 0.83
   2 ?    4.3   0.1      0.12        43      22      50 ..     265     293 ..     254     329 .. 0.90
   3 ?    5.2   0.1     0.066        24      22      51 ..     333     362 ..     322     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 4.6
                                       HHHHHCT-SEEEEEEEEBTTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  22 kkakelglkaiaiTDhgnlfgyvefykaa 50 
                                       + a ++ +k  a+ D g +++++++y +a
  gi|330507774|ref|YP_004384202.1| 129 QDAFAWTIKGNALYDLGKYDEAINAYDQA 157
                                       66888999999***********9999988 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.12
                                       HHHHHCT-SEEEEEEEEBTTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  22 kkakelglkaiaiTDhgnlfgyvefykaa 50 
                                       + a+ + +k ia+ D g +++++++y +a
  gi|330507774|ref|YP_004384202.1| 265 QLAETWTIKGIALYDLGKYDEAIQAYDQA 293
                                       56899*********************998 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.066
                                       HHHHHCT-SEEEEEEEEBTTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  22 kkakelglkaiaiTDhgnlfgyvefykaak 51 
                                       + a ++ +k ia+ D g +++++++y +a+
  gi|330507774|ref|YP_004384202.1| 333 QDAFAWTIKGIALYDLGKYDEAIQAYDQAN 362
                                       678899*********************993 PP

>> SpoVAC_SpoVAEB  SpoVAC/SpoVAEB sporulation membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.89   3.2e+02      42      64 ..     308     330 ..     299     347 .. 0.81
   2 ?    0.7   0.0       1.7   6.1e+02      42      60 ..     376     394 ..     372     403 .. 0.85
   3 ?    2.1   0.0       0.6   2.2e+02      42      61 ..     410     429 ..     406     431 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.89
                    SpoVAC_SpoVAEB  42 galltglgvYdklvkfagaGalv 64 
                                       g+ lt+lg Yd+ +k +    ++
  gi|330507774|ref|YP_004384202.1| 308 GVALTALGKYDEAIKACDQAISI 330
                                       899*********99988766554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.7
                    SpoVAC_SpoVAEB  42 galltglgvYdklvkfaga 60 
                                       g+ lt+lg Yd+ +k +  
  gi|330507774|ref|YP_004384202.1| 376 GVALTALGKYDEAIKACDQ 394
                                       899*********9998765 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.6
                    SpoVAC_SpoVAEB  42 galltglgvYdklvkfagaG 61 
                                       g++l++lg Yd+ +k ++ G
  gi|330507774|ref|YP_004384202.1| 410 GVVLKALGKYDEAIKAFESG 429
                                       89************999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        51  (0.00284455); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              49  [number of targets reported over threshold]
# CPU time: 1.10u 0.30s 00:00:01.40 Elapsed: 00:00:00.62
# Mc/sec: 2084.58
//
Query:       gi|330507775|ref|YP_004384203.1|  [L=104]
Description: hypothetical protein MCON_1781 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-07   29.0   0.2    9.8e-07   29.0   0.2    1.3  2  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0009   18.8   0.1     0.0011   18.6   0.1    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       0.9   8.1e+03     130     141 ..      18      29 ..       7      34 .. 0.53
   2 !   29.0   0.2   1.1e-10   9.8e-07      24      80 ..      43      94 ..      35     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.9
                                       STSCCEEEEEET CS
                       Lactamase_B 130 ghghghgvveyg 141
                                       g +++h+v++++
  gi|330507775|ref|YP_004384203.1|  18 GVTGSHMVLHAR 29 
                                       344444444444 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 1.1e-10
                                      SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B 24 tsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80
                                      ++t++++        g +p++++a ilTH+H+DH G  + ++++    ++++ ++++
  gi|330507775|ref|YP_004384203.1| 43 GDTDRNQDG-----FGHDPNRLKAMILTHAHVDHSGRIPLFINEGFKGSVCCTHATR 94
                                      444444444.....899***************************9999998887765 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 !   18.6   0.1   1.2e-07    0.0011       4      52 ..      34      80 ..      31      98 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-07
                                      EES--TTHHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCC CS
                     Lactamase_B_2  4 LiDagpdlrqqalralqPve.lrdelppidaVllthaHyDHlaglltlre 52
                                       iDag+   +  + +   +    +++++++a +lthaH+DH   ++ +  
  gi|330507775|ref|YP_004384203.1| 34 GIDAGLFQGGD-TDRN--QDgFGHDPNRLKAMILTHAHVDHSGRIPLFIN 80
                                      56666542222.3332..3336899****************976665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 764.75
//
Query:       gi|330507776|ref|YP_004384204.1|  [L=775]
Description: hydrophobe/amphiphile efflux-3 (HAE3) family efflux transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.9e-44  149.6  21.0    6.1e-24   84.6   9.0    2.5  2  MMPL       MMPL family
    3.1e-06   25.2  26.9    6.1e-06   24.2   5.0    2.4  2  ACR_tran   AcrB/AcrD/AcrF family
    1.2e-05   24.8   5.3    1.2e-05   24.8   5.3    2.6  2  SecD_SecF  Protein export membrane protein


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 !   72.4   2.0   5.2e-24   3.1e-20      63     292 ..     103     352 ..      63     398 .. 0.81
   2 !   84.6   9.0     1e-27   6.1e-24     103     322 ..     545     772 ..     526     774 .. 0.78

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 5.2e-24
                              MMPL  63 hvgevsdf.......................lsdpdvaaafvSkDgkaaralvtlegdpgsteadesvaai....ra 112
                                       +v++++d+                       l++  +  a + +D   +r+++ +     st+++e+ +++    ++
  gi|330507776|ref|YP_004384204.1| 103 GVQSAADWiadeeykrtgirqipsqerideiLANAGTSIAHLMPDRGHTRIIIGMPT--TSTLTEEQRNRLlletEN 177
                                       455666667777776666666666666666666777888888899999999999884..455555555544111166 PP

                              MMPL 113 aveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvl 189
                                       av+ a+ + g  v +tG +   a + ++ ++  + i ++  ++ +v Ll+ +r +   llpl +v+++++ +lg  +
  gi|330507776|ref|YP_004384204.1| 178 AVDYAEFPPGYGVTITGDPSFQAAIVQMMNSTNGQILALCGLLMIVALLLFFRHVRWSLLPLPVVLLGIVWTLGA-M 253
                                       7777779***************************9999999999999****************************.3 PP

                              MMPL 190 ilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLv 266
                                        l ++  ++++tf+   ++ ++i++G+DYa+ +  R+ eel +g++  +a  r+v+ ++  v+ a  +  + +++L+
  gi|330507776|ref|YP_004384204.1| 254 GLLHI-RMGMTTFA---AFPIMIGIGIDYAIQFHNRIDEELSKGKSVLQASTRTVKYVAIPVLVALTVTEAGFFSLL 326
                                       33333.56666666...799********************************************999999******* PP

                              MMPL 267 varlpvlaqvGvaialGvlvdvlivl 292
                                        +++p+ + +G ++ +G+++  l +l
  gi|330507776|ref|YP_004384204.1| 327 SSSVPSTQDFGKMCMIGLVMCYLSAL 352
                                       ********************999886 PP

  == domain 2  score: 84.6 bits;  conditional E-value: 1e-27
                              MMPL 103 adesvaairaaveear....pleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallpll 175
                                       + e ++++ +  e+      p+ g+ v++tG++++++ ++da ++ +  + +++l +i+v+Ll++yr l+ allp+l
  gi|330507776|ref|YP_004384204.1| 545 GTEGMERLVRSYEDDLawhtPPPGVSVRITGQPVLMTTVMDALTEGRVEMSLLGLFLIFVLLLLIYRDLIRALLPVL 621
                                       444444444444444455569******************************************************98 PP

                              MMPL 176 tvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvt 252
                                         +v     +g + ++ +  gl+ +  +++l  +l+++vG+ Ya+l++ R+ eel++  +  +a+  + +++g++ +
  gi|330507776|ref|YP_004384204.1| 622 PMLV----VIGWMGLVMYYGGLKYTPLTATL-GALVLGVGSEYAILMMERFYEELENVGNPIDALKITANRIGSALV 693
                                       7655....44554456777788877766665.6899***************************************** PP

                              MMPL 253 aaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll..PAllvllGraalakprrkrkk........rwW 319
                                       a+G+ v++ + +L ++ +++++++Gv+  ++v++++  ++T+    A+ + + r +l  + + + k         +W
  gi|330507776|ref|YP_004384204.1| 694 ASGMAVIFGFGALIASPFNIISNFGVVTVMSVVLALVTTFTVFvvLAIRMEVQREVLE-NAKLEMKraialinnQRW 769
                                       ***************************9999999999888876223333333333233.333333346666777777 PP

                              MMPL 320 rrl 322
                                       rr+
  gi|330507776|ref|YP_004384204.1| 770 RRI 772
                                       765 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   5.0     1e-09   6.1e-06     310     481 ..     184     358 ..     180     361 .. 0.80
   2 !    6.3  13.9   0.00027       1.6     334     486 ..     592     740 ..     563     765 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1e-09
                                       SSTTEEEEEEEESH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHTT--B CS
                          ACR_tran 310 lPegveivvvydrt...efvrasieeVvktLleaivLvvlvvflFLqnlratlipaiavPlsllgtfavlkalgfsl 383
                                       +P g+ ++++ d +    +v+   ++  + L +  +L ++ ++lF + +r +l p+ +v l ++ t+ ++ +l + +
  gi|330507776|ref|YP_004384204.1| 184 FPPGYGVTITGDPSfqaAIVQMMNSTNGQILALCGLLMIVALLLFFRHVRWSLLPLPVVLLGIVWTLGAMGLLHIRM 260
                                       6666666666664421133333333334456677789**************************************** PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHH CS
                          ACR_tran 384 NlltLfgLvlAiGlvvDdAiVvvEnierkleeegekpleaalksmkeiqgalvaialvllavflPilflgGveGklf 460
                                        + t  +  + iG+ +D Ai     i ++l++ g++ l+a+ +++k ++ +++    v  a f  +l+ +    + f
  gi|330507776|ref|YP_004384204.1| 261 GMTTFAAFPIMIGIGIDYAIQFHNRIDEELSK-GKSVLQASTRTVKYVAIPVLVALTVTEAGFFSLLSSSVPSTQDF 336
                                       ********************************.******************98888887777777777666666666 PP

                                       HHH.HHHHHHHHHHHHHHHHCC CS
                          ACR_tran 461 rqf.altivlaillsvlvaltl 481
                                        ++  + +v++ l +++v lt+
  gi|330507776|ref|YP_004384204.1| 337 GKMcMIGLVMCYLSALFVNLTI 358
                                       6652467777777777777776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00027
                                       HHHHHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHH..TT--BCHHHHHHHHHHHHHHHHHHHHHHHH CS
                          ACR_tran 334 vktLleaivLvvlvvflFLqnlratlipaiavPlsllgtfavlka..lgfslNlltLfgLvlAiGlvvDdAiVvvEn 408
                                       v+  l+++ L+++ ++l  ++l  +l p++ + +++     v++   l+++  + tL++Lvl++G     Ai ++E 
  gi|330507776|ref|YP_004384204.1| 592 VEMSLLGLFLIFVLLLLIYRDLIRALLPVLPMLVVIGWMGLVMYYggLKYTPLTATLGALVLGVGS--EYAILMMER 666
                                       4455789********************98755444433334444411455666779******9998..89******* PP

                                       HHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                          ACR_tran 409 ierkleeegekpleaalksmkeiqgalvaialvllavflPilflgGveGklfrqfaltivlaillsvlvaltltPal 485
                                        +++le+   +p  a + +++ i++alva+ +   av   + +l  +  ++  +f++  v++++l+++   t+  +l
  gi|330507776|ref|YP_004384204.1| 667 FYEELEN-VGNPIDALKITANRIGSALVASGM---AVIFGFGALIASPFNIISNFGVVTVMSVVLALVTTFTVFVVL 739
                                       *******.8899****************9986...555666788888889999999999999999999888876555 PP

                                       H CS
                          ACR_tran 486 c 486
                                       +
  gi|330507776|ref|YP_004384204.1| 740 A 740
                                       4 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   5.3     2e-09   1.2e-05      33     187 ..     212     363 ..     203     365 .. 0.83
   2 ?    0.2   1.4     0.068   4.1e+02      54      79 ..     715     740 ..     670     751 .. 0.50

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2e-09
                                       HHHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSSHHHHHHHHHHH CS
                         SecD_SecF  33 avlallialvliliyvalrFewrvalaaiialvhDviitvgvlsllgievdlatvaalLtiiGYSvndtvvvfdrvr 109
                                        +lal + l+++++ +++r   r+ l  +  ++  ++ t+g++ ll+i + ++t aa   +iG  ++  +   +r+ 
  gi|330507776|ref|YP_004384204.1| 212 QILALCGLLMIVALLLFFRH-VRWSLLPLPVVLLGIVWTLGAMGLLHIRMGMTTFAAFPIMIGIGIDYAIQFHNRID 287
                                       56677777776666666664.57888889999999****************************************** PP

                                       HHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTTTHHHHHHHHHHHH CS
                         SecD_SecF 110 enlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgtyssifiasplllll 186
                                       e+l k   +++ ++  + ++      +++  +t    ++ll     s +df  + ++Gl++  +s++f++ ++l++ 
  gi|330507776|ref|YP_004384204.1| 288 EELSK--GKSVLQASTRTVKYVAIPVLVALTVTEAGFFSLLSSSVPSTQDFGKMCMIGLVMCYLSALFVNLTILYQS 362
                                       **998..66677777777776666666666667777888888889****************************9876 PP

                                       H CS
                         SecD_SecF 187 k 187
                                       +
  gi|330507776|ref|YP_004384204.1| 363 E 363
                                       5 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.068
                                       HHHHHHHHHHHHHHHHHHHHHHHHTT CS
                         SecD_SecF  54 wrvalaaiialvhDviitvgvlsllg 79 
                                        ++++  ++++v  +++t +v+++l 
  gi|330507776|ref|YP_004384204.1| 715 SNFGVVTVMSVVLALVTTFTVFVVLA 740
                                       22333333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (775 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.48
# Mc/sec: 4904.60
//
Query:       gi|330507777|ref|YP_004384205.1|  [L=350]
Description: hypothetical protein MCON_1783 [Methanosaeta concilii GP6]
Scores for complete 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-07   30.3   0.0      0.044   14.0   0.0    3.6  4  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
  ------ inclusion threshold ------
       0.22   11.7   0.9       0.76    9.9   0.5    2.0  2  DUF2012      Protein of unknown function (DUF2012)


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 ?    0.2   0.0      0.11   9.4e+02       2      17 ..      55      70 ..      54      72 .. 0.90
   2 !   11.1   0.0   3.9e-05      0.35      44      78 ..     126     162 ..     117     163 .. 0.79
   3 ?   -2.6   0.0      0.77   6.9e+03      49      60 ..     196     207 ..     178     212 .. 0.58
   4 !   14.0   0.0     5e-06     0.044       4      79 .]     225     299 ..     222     299 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.11
                       NPCBM_assoc  2 epGetvtltltvtndg 17
                                      ++G+tvtl l +tn g
  gi|330507777|ref|YP_004384205.1| 55 KRGDTVTLYLDLTNYG 70
                                      79************98 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.9e-05
                       NPCBM_assoc  44 aaslapGetvea..tvkVtppagaaaGdyevtakarl 78 
                                       ++sl+ G+++++  ++++++++ a aG+y++ ++ ++
  gi|330507777|ref|YP_004384205.1| 126 VESLKSGDKTQSplKFTIKIGEHAPAGEYPLHLNMTY 162
                                       3488888887754499***************999876 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.77
                       NPCBM_assoc  49 pGetveatvkVt 60 
                                       +++tv +t++V+
  gi|330507777|ref|YP_004384205.1| 196 ANQTVPVTIRVK 207
                                       444444554443 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 5e-06
                       NPCBM_assoc   4 GetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakarlt 79 
                                       G+++++ +t +n g++++++   +ls  +  + ++ + a +  l+pG ++++ +++ + ++a a dy +  ++++t
  gi|330507777|ref|YP_004384205.1| 225 GKKQEIHATYKNIGEDPVRDAVARLSIFKPFS-STDDQAFIGNLDPGNETTVLFRMDVDSDATAKDYGISSEIKYT 299
                                       999*****************999999977777.668888888***************************9999986 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.19   1.7e+03      61      97 ..     107     143 ..      98     148 .. 0.81
   2 ?    9.9   0.5   8.5e-05      0.76      36     111 ..     148     220 ..     140     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.19
                           DUF2012  61 kdkgkakasklrivetaevnvvdesgneesyplkika 97 
                                       +    ++a+++++ +  +v+ + +sg ++++plk+++
  gi|330507777|ref|YP_004384205.1| 107 TATLISQAPQIEVKSGDQVVESLKSGDKTQSPLKFTI 143
                                       5556678899999999999999999999999999876 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 8.5e-05
                           DUF2012  36 dlpegsYlLevespeyvFepyrVdvkdkgkakasklrivetaevnvvdesgneesyplkikavarreyyeerekfs 111
                                       + p+g+Y L+++  +   +++rV  +  +++ +     +++++v  v ++  ++++p++i++++++++ ++ ++ +
  gi|330507777|ref|YP_004384205.1| 148 HAPAGEYPLHLNMTYDYQDNVRVYAS--KLVTEGGTSTFSNYRVSYVYQKA-NQTVPVTIRVKKQADFVIQNTTAE 220
                                       7899******9976555555776666..77777778889999997766655.5789************99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2554.29
//
Query:       gi|330507778|ref|YP_004384206.1|  [L=131]
Description: RDD domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   4.4    1.6e-14   54.3   4.4    1.1  1  RDD       RDD family


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   4.4   9.2e-19   1.6e-14       1     140 [.       6     122 ..       6     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 9.2e-19
                               RDD   1 laslgrRllAfliDlvllliislllallivallnakasaneavagslllllllvlllvllvyqllllskkgqTlGkl 77 
                                       las+++R++A+liD++l+ +i   ++l++++           ++++l ++l+l+ l+  +vy++ l+ ++gq+lGk+
  gi|330507778|ref|YP_004384206.1|   6 LASWSDRFWAWLIDVLLMGLIWHRVVLVLGI-----------DPMHLDAMLILSGLI--FVYWTALEGYRGQSLGKM 69 
                                       59*****************************...........899999998888875..8999************** PP

                               RDD  78 llglkvvdedgrklglaqaliRalllllllvlglslvlllllligflfvlf..srkrqalhDkla 140
                                       ll + vv   g+ +g+  + + ++              ++ll+++ l+ lf  ++krq+l  kl+
  gi|330507778|ref|YP_004384206.1|  70 LLNIVVVGPYGEAIGFRDSALQSF------------GKAFLLPVDCLIGLFafRGKRQRLFNKLS 122
                                       **********************98............4444455555544444499***9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 948.01
//
Query:       gi|330507779|ref|YP_004384207.1|  [L=246]
Description: 4Fe-4S ferredoxin, iron-sulfur binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-13   50.4  12.5    1.3e-11   44.3   2.2    3.4  4  Fer4_5    4Fe-4S binding domain
      3e-07   30.9  11.4    0.00016   22.2   0.6    2.4  2  Fer4_7    4Fe-4S dicluster domain
    1.7e-05   24.9  15.1    5.6e-05   23.2  14.3    2.1  2  Fer4_9    4Fe-4S dicluster domain
    0.00016   21.9   9.6    0.00016   21.9   9.6    2.2  2  Fer4_18   4Fe-4S dicluster domain
    0.00019   21.1  22.4     0.0012   18.6   6.1    3.6  4  Fer4      4Fe-4S binding domain
    0.00041   20.8  17.1     0.0061   17.1   4.6    2.6  2  Fer4_17   4Fe-4S dicluster domain
    0.00065   20.0  20.8       0.11   13.1   1.7    3.9  4  Fer4_4    4Fe-4S binding domain
    0.00097   19.2  17.3     0.0018   18.4  15.2    2.5  3  Fer4_10   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.022   15.7  14.9       0.59   11.1   4.0    3.0  3  Fer4_16   4Fe-4S double cluster binding domain
      0.039   14.0   2.3      0.039   14.0   2.3    2.8  2  Fer4_6    4Fe-4S binding domain
       0.15   12.5  20.0        0.3   11.6   3.5    2.6  3  Fer4_8    4Fe-4S dicluster domain
       0.21   11.7  19.8        1.8    8.7   4.5    3.1  3  Fer4_21   4Fe-4S dicluster domain
       0.25   11.5  23.4      0.099   12.8   3.6    3.0  3  Fer4_2    4Fe-4S binding 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 ?   -3.8   0.7       9.3   1.3e+04       6      13 ..      16      23 ..      13      28 .. 0.39
   2 !   44.3   2.2   9.1e-15   1.3e-11       3      38 ..      44      79 ..      42      87 .. 0.88
   3 ?   -1.4   0.4       1.7   2.3e+03       9      17 ..      99     107 ..      96     114 .. 0.51
   4 !   18.6   2.9   9.5e-07    0.0013       9      42 ..     145     178 ..     137     184 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 9.3
                            Fer4_5  6 lilflaiv 13
                                      ++ f+++ 
  gi|330507779|ref|YP_004384207.1| 16 ILSFVLLP 23
                                      23333333 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 9.1e-15
                            Fer4_5  3 llllilflaivlvtllfGRafCgWiCPfGalqella 38
                                        +li f+++++ +ll+GR++CgW+CP G lqe++ 
  gi|330507779|ref|YP_004384207.1| 44 TGGLIVFVLLFISSLLLGRLWCGWLCPGGGLQEIYI 79
                                      6799*****************************986 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.7
                            Fer4_5   9 flaivlvtl 17 
                                       fl+i++++l
  gi|330507779|ref|YP_004384207.1|  99 FLFILFIPL 107
                                       334444333 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 9.5e-07
                            Fer4_5   9 flaivlvtllfGR.afCgWiCPfGalqellakllr 42 
                                        +++ +++ll G+ afC ++CP+ ++  + +k +r
  gi|330507779|ref|YP_004384207.1| 145 IAFFTAFALLAGKrAFCHYFCPIAVILITGRK-IR 178
                                       33666667775555********9988766665.55 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.6   1.1e-07   0.00016       7      50 ..     160     207 ..     158     209 .. 0.76
   2 !   12.5   4.6   0.00012      0.17       2      19 ..     225     242 ..     224     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.1e-07
                            Fer4_7   7 aCvaaCpvkaieldeeenek....gtekveidpekClgCgaCvavCPt 50 
                                       +C   Cp  +i ++ ++  +    +  ++  d+ +C++C++C a+CP 
  gi|330507779|ref|YP_004384207.1| 160 FCHYFCPIAVILITGRKIRDlfrwPALQLSSDAGRCSNCRRCSATCPM 207
                                       7***********9998555544222234466788*************6 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00012
                            Fer4_7   2 CigCgaCvaaCpvkaiel 19 
                                       Ci Cg Cv++C+ +ai++
  gi|330507779|ref|YP_004384207.1| 225 CILCGCCVDVCSENAISY 242
                                       ***************986 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2   1.7e+03       8      17 ..     161     170 ..     158     183 .. 0.77
   2 !   23.2  14.3   4.1e-08   5.6e-05       1      51 []     194     240 ..     194     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                            Fer4_9   8 CveaCpagvv 17 
                                       C++ Cp  v+
  gi|330507779|ref|YP_004384207.1| 161 CHYFCPIAVI 170
                                       8889987766 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 4.1e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +C +C++C + Cp+ + v+  +++ +  +     +Ci Cg Cv++C ++ai
  gi|330507779|ref|YP_004384207.1| 194 RCSNCRRCSATCPMSLDVNLMVRQGIMENS----ECILCGCCVDVCSENAI 240
                                       5***************98777777766543....5************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 ?   -0.5   0.2         1   1.4e+03       4      13 ..     159     168 ..     157     173 .. 0.80
   2 !   21.9   9.6   1.1e-07   0.00016      52      97 ..     186     237 ..     171     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1
                           Fer4_18   4 dvcvyvcPya 13 
                                        +c y cP a
  gi|330507779|ref|YP_004384207.1| 159 AFCHYFCPIA 168
                                       69*****987 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.1e-07
                           Fer4_18  52 erkekgagdcidcescvkvcPtgidi....rkGl..qleciscllcidacdk 97 
                                       ++ +++ag c +c+ c + cP+ +d+    r+G+    eci c+ c+d c++
  gi|330507779|ref|YP_004384207.1| 186 LQLSSDAGRCSNCRRCSATCPMSLDVnlmvRQGImeNSECILCGCCVDVCSE 237
                                       56678899***************9954444999844579***********75 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.8   3.8e+03      14      21 ..      65      72 ..      64      74 .. 0.75
   2 ?   -0.3   0.2      0.81   1.1e+03      14      23 ..     161     170 ..     160     171 .. 0.83
   3 !   12.3   1.2   8.1e-05      0.11       4      19 ..     191     206 ..     189     208 .. 0.92
   4 !   18.6   6.1   8.7e-07    0.0012       6      24 .]     223     241 ..     220     241 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.8
                                      HHHHSTTT CS
                              Fer4 14 CvevCPvg 21
                                      C   CP g
  gi|330507779|ref|YP_004384207.1| 65 CGWLCPGG 72
                                      77789965 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.81
                                       HHHHSTTTEE CS
                              Fer4  14 CvevCPvgAI 23 
                                       C   CP  +I
  gi|330507779|ref|YP_004384207.1| 161 CHYFCPIAVI 170
                                       8999**8877 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 8.1e-05
                                       ETTTSSS-THHHHHST CS
                              Fer4   4 deekCigCGaCvevCP 19 
                                       d  +C +C +C   CP
  gi|330507779|ref|YP_004384207.1| 191 DAGRCSNCRRCSATCP 206
                                       789************* PP

  == domain 4  score: 18.6 bits;  conditional E-value: 8.7e-07
                                       TTSSS-THHHHHSTTTEEE CS
                              Fer4   6 ekCigCGaCvevCPvgAIt 24 
                                       + Ci CG Cv+vC  +AI+
  gi|330507779|ref|YP_004384207.1| 223 SECILCGCCVDVCSENAIS 241
                                       78***************95 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   4.6   4.4e-06    0.0061      39      61 .]     188     210 ..     159     210 .. 0.80
   2 !    9.0   4.6    0.0014         2       1      16 [.     224     239 ..     220     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.4e-06
                           Fer4_17  39 keekaslCieCgeCerkCPqgld 61 
                                        ++ a++C++C++C++ CP++ld
  gi|330507779|ref|YP_004384207.1| 188 LSSDAGRCSNCRRCSATCPMSLD 210
                                       457899***************97 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                           Fer4_17   1 rCiqCgyClpeCpsye 16 
                                       +Ci Cg+C+++C+ ++
  gi|330507779|ref|YP_004384207.1| 224 ECILCGCCVDVCSENA 239
                                       5999999999998765 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.8   5.2e+03      11      15 ..      28      32 ..      28      39 .. 0.82
   2 ?    4.2   0.0     0.053        73      10      15 ..     161     166 ..     156     179 .. 0.86
   3 !   13.1   1.7   7.9e-05      0.11       3      16 ..     194     207 ..     192     214 .. 0.92
   4 !    9.8   6.8   0.00089       1.2       3      15 ..     224     236 ..     221     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.8
                            Fer4_4 11 vaaCP 15
                                      +++CP
  gi|330507779|ref|YP_004384207.1| 28 YISCP 32
                                      57899 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.053
                            Fer4_4  10 CvaaCP 15 
                                       C+++CP
  gi|330507779|ref|YP_004384207.1| 161 CHYFCP 166
                                       *****9 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 7.9e-05
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       rC +C++C a+CP+
  gi|330507779|ref|YP_004384207.1| 194 RCSNCRRCSATCPM 207
                                       9************6 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00089
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                        Ci Cg+Cv++C+
  gi|330507779|ref|YP_004384207.1| 224 ECILCGCCVDVCS 236
                                       6***********7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.2   4.4e+03      18      23 ..      30      35 ..      28      47 .. 0.63
   2 ?   -2.1   0.0       3.1   4.3e+03      15      21 ..     161     167 ..     160     179 .. 0.72
   3 !   18.4  15.2   1.3e-06    0.0018       4      55 ..     190     235 ..     187     236 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.2
                           Fer4_10 18 aCPadl 23
                                      +CP+ +
  gi|330507779|ref|YP_004384207.1| 30 SCPVII 35
                                      799955 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                           Fer4_10  15 CvkaCPa 21 
                                       C  +CP 
  gi|330507779|ref|YP_004384207.1| 161 CHYFCPI 167
                                       7778987 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.3e-06
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                        d+ +C +C++C + CP+   s +++    ++ +     ++C+ cg Cv++C
  gi|330507779|ref|YP_004384207.1| 190 SDAGRCSNCRRCSATCPM---SLDVNLMVRQGIM---ENSECILCGCCVDVC 235
                                       68899*************...2222222222222...3457*********** PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.3   3.1e+03       8      17 ..     161     170 ..     157     179 .. 0.73
   2 ?   10.2   1.2   0.00081       1.1       1      14 [.     194     207 ..     185     209 .. 0.79
   3 ?   11.1   4.0   0.00043      0.59       2      18 ..     225     241 ..     224     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.3
                           Fer4_16   8 CaevCPtnai 17 
                                       C   CP ++i
  gi|330507779|ref|YP_004384207.1| 161 CHYFCPIAVI 170
                                       6667777666 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00081
                           Fer4_16   1 rCgtCgkCaevCPt 14 
                                       rC +C++C  +CP 
  gi|330507779|ref|YP_004384207.1| 194 RCSNCRRCSATCPM 207
                                       57778888888875 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00043
                           Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                       C+ Cg C++vC +nai+
  gi|330507779|ref|YP_004384207.1| 225 CILCGCCVDVCSENAIS 241
                                       ****************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 ?   14.0   2.3   2.9e-05     0.039       5      21 ..     191     207 ..     189     211 .. 0.90
   2 ?   10.2   7.4   0.00045      0.62       9      24 .]     225     240 ..     222     240 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-05
                            Fer4_6   5 dpdkCigCgdCvrvCPe 21 
                                       d+ +C  C++C + CP+
  gi|330507779|ref|YP_004384207.1| 191 DAGRCSNCRRCSATCPM 207
                                       7789************7 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00045
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       Ci Cg Cv+vC e+ai
  gi|330507779|ref|YP_004384207.1| 225 CILCGCCVDVCSENAI 240
                                       ***************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 ?   10.7   5.3   0.00041      0.56      45      64 ..     189     208 ..     159     209 .. 0.70
   2 ?   11.6   3.5   0.00022       0.3       3      19 ..     193     209 ..     191     222 .. 0.68
   3 ?    6.6   6.9    0.0078        11      49      63 ..     223     237 ..     211     240 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00041
                            Fer4_8  45 eealwsCttcgaCtevCpvg 64 
                                          +++C++c++C+  Cp++
  gi|330507779|ref|YP_004384207.1| 189 SSDAGRCSNCRRCSATCPMS 208
                                       45578999999999999986 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00022
                            Fer4_8   3 ekCieCgaCqsaCpvlr 19 
                                        +C +C +C ++Cp+  
  gi|330507779|ref|YP_004384207.1| 193 GRCSNCRRCSATCPMSL 209
                                       46777777777777655 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0078
                            Fer4_8  49 wsCttcgaCtevCpv 63 
                                        +C  cg+C++vC +
  gi|330507779|ref|YP_004384207.1| 223 SECILCGCCVDVCSE 237
                                       467777777777765 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.7   1.1e+04      14      26 ..      65      77 ..      64      85 .. 0.64
   2 ?    8.7   4.5    0.0013       1.8      14      53 ..     161     207 ..     158     213 .. 0.59
   3 ?    7.1   7.1    0.0043       5.9       4      23 ..     221     240 ..     218     243 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.7
                           Fer4_21 14 CliaCedtshqai 26
                                      C   C+ ++ q i
  gi|330507779|ref|YP_004384207.1| 65 CGWLCPGGGLQEI 77
                                      5556666666655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0013
                           Fer4_21  14 CliaCedtshqaieidaktvl........kvvedeCvGCnlCssvCPv 53 
                                       C+  C+  ++  i++ + + l           + +C  C  Cs+ CP+
  gi|330507779|ref|YP_004384207.1| 161 CHYFCP-IAVILITGRKIRDLfrwpalqlSSDAGRCSNCRRCSATCPM 207
                                       777777.3444443332221133333322445679************7 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0043
                           Fer4_21   4 dedkCigCgkCliaCedtsh 23 
                                       ++++Ci Cg C+ +C+++++
  gi|330507779|ref|YP_004384207.1| 221 ENSECILCGCCVDVCSENAI 240
                                       67889999999999998764 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.3       4.9   6.7e+03      16      21 ..     161     166 ..     160     166 .. 0.83
   2 ?   12.8   3.6   7.1e-05     0.099       6      21 ..     191     206 ..     187     207 .. 0.88
   3 ?    8.7   6.3    0.0014       1.9       7      20 ..     223     235 ..     219     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.9
                            Fer4_2  16 CvsaCP 21 
                                       C   CP
  gi|330507779|ref|YP_004384207.1| 161 CHYFCP 166
                                       888999 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.1e-05
                            Fer4_2   6 dtdrCigCgaCvsaCP 21 
                                       d+ rC +C+ C   CP
  gi|330507779|ref|YP_004384207.1| 191 DAGRCSNCRRCSATCP 206
                                       6679*******888** PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0014
                            Fer4_2   7 tdrCigCgaCvsaC 20 
                                       ++ Ci Cg Cv++C
  gi|330507779|ref|YP_004384207.1| 223 SE-CILCGCCVDVC 235
                                       55.*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1736.93
//
Query:       gi|330507780|ref|YP_004384208.1|  [L=112]
Description: cupin domain-containing protein [Methanosaeta concilii GP6]
Scores for 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    4.2e-13   48.8   0.1    1.2  1  Cupin_2          Cupin domain
     0.0095   15.8   0.0      0.011   15.6   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
  ------ inclusion threshold ------
      0.054   13.4   0.1      0.065   13.1   0.1    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
       0.12   12.2   0.0       0.15   11.9   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding


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 !   48.8   0.1   9.3e-17   4.2e-13       2      70 ..      33     100 ..      32     101 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 9.3e-17
                                       EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       +++l+pGes + h+ p    +fyVleG g++++++e+ + +a+ ++  pa+ pHr+ N+++   r+lvv
  gi|330507780|ref|YP_004384208.1|  33 HITLQPGESLKKHITPVD-VIFYVLEGVGVVEIGEEKAVAGADTLIESPAKIPHRWMNESNSVTRILVV 100
                                       679**************8.***********************************************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 !   15.6   0.0   2.5e-06     0.011      11      65 ..      37      91 ..      28     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-06
                                      STT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-T CS
                      AraC_binding 11 ypdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesds 65
                                       p++s ++h  +  vi yv+eG+g ++++++   +g+++l+  p   pH+   +s
  gi|330507780|ref|YP_004384208.1| 37 QPGESLKKHITPVDVIFYVLEGVGVVEIGEEKAVAGADTLIESPAKIPHRWMNES 91
                                      577788899999999**********************************976666 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.4e-05     0.065      54     136 ..      20     101 ..       4     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                   MannoseP_isomer  54 yevldegeryqvkritvkPgeklslqkhhhraeh.WvvvkGtakvtvddevlllkenestyiplgaihrlenpGkip 129
                                        ++++ +e+ qv +it++Pge  sl+kh    +  + v++G+  v++++e+++  ++  +  p+   hr  n  +  
  gi|330507780|ref|YP_004384208.1|  20 ARSISDTESAQVVHITLQPGE--SLKKHITPVDViFYVLEGVGVVEIGEEKAVAGADTLIESPAKIPHRWMNESNSV 94 
                                       4789999*************9..5688888776427799*************9999999999999999999998877 PP

                   MannoseP_isomer 130 lelievq 136
                                        +++ v+
  gi|330507780|ref|YP_004384208.1|  95 TRILVVK 101
                                       7776665 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 ?   11.9   0.0   3.4e-05      0.15      33      83 ..      21      78 ..      14     109 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                                      HHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC....HHHH...HHHHHH CS
                    NAD_binding_10 33 aeleaeeglevvegdvtdvedlaealkgadaVvsalggggk....deeg...aknivd 83
                                       +++++e ++vv++ ++  e+l+++++ +d+++  l g g     +e++   a+++++
  gi|330507780|ref|YP_004384208.1| 21 RSISDTESAQVVHITLQPGESLKKHITPVDVIFYVLEGVGVveigEEKAvagADTLIE 78
                                      45667899****************************6655533331111334444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 801.25
//
Query:       gi|330507781|ref|YP_004384209.1|  [L=664]
Description: sodium/hydrogen exchanger [Methanosaeta concilii GP6]
Scores for complete 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-60  202.7  52.3    9.6e-60  202.4  52.3    1.1  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
    5.6e-22   78.2   0.1    1.4e-21   76.9   0.1    1.7  2  TrkA_N          TrkA-N domain
    3.5e-14   52.4   0.0    3.2e-13   49.3   0.0    2.7  3  TrkA_C          TrkA-C domain
  ------ inclusion threshold ------
       0.03   14.5   0.0      0.056   13.6   0.0    1.4  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy


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 !  202.4  52.3   2.1e-63   9.6e-60       3     375 ..      11     373 ..       9     379 .. 0.94

  Alignments for each domain:
  == domain 1  score: 202.4 bits;  conditional E-value: 2.1e-63
                                       HHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHH CS
                    Na_H_Exchanger   3 llillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksi 79 
                                       ++++l++lv++++++++ p ivg+i++G l Gp glgli+   e+++vl+e+g+illlF +Gle++l++l++++k +
  gi|330507781|ref|YP_004384209.1|  11 VIFVLSVLVLFIFHKVRAPAIVGFIFTGALAGPQGLGLIQAI-EQVDVLAEIGVILLLFTIGLEISLKDLMQMKKYV 86 
                                       455556666668******************************.********************************** PP

                                       HHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCC CS
                    Na_H_Exchanger  80 lllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavav 156
                                       l++++l+v++++++  ++l +   +g p+  a+l+g+++s++++++vl+i +++ ++ +  g+++lg+++++D++ v
  gi|330507781|ref|YP_004384209.1|  87 LVGGTLQVALAILA-VYALLI--YFGQPVGTAILIGFLVSVSSTAIVLRIIQKKSEMYTPQGRTILGILIFQDIAIV 160
                                       ***********999.444443..3688************************************************** PP

                                       CCCHHHHHHTX.XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHT CS
                    Na_H_Exchanger 157 vllavllalak.eeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallael 232
                                       +l   ++ l +  +   e+ ll l++ +++va++++ +++++++ l  i r+  ddrel++l  +++++++a++++l
  gi|330507781|ref|YP_004384209.1| 161 PLMLAVPLLPGaVGEVPESPLLILAKGLALVALVIISAKWLVPLALYHIART--DDRELFLLSLVAICFAVAWATSL 235
                                       *****99998787888899999999******************999999999..*********************** PP

                                       SXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHH CS
                    Na_H_Exchanger 233 lgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgril 309
                                        g+s  lgaflaGl++se+ +s+++  ++ ++r ++f  +fFv+vG+ ld+++l   l ++++++l+   ++l + l
  gi|330507781|ref|YP_004384209.1| 236 AGLSLGLGAFLAGLTISESQYSHQAFGNVLPLR-DAFTSFFFVSVGMLLDVNFL---LANPLYIILLASGVMLLKSL 308
                                       *********************************.9*******************...9******************* PP

                                       HHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHH CS
                    Na_H_Exchanger 310 avflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlsl 375
                                        + + + ++gl+lr a+++g++++q+g+++++l  +g   gl+++ely +++ v+++t++ +++s+
  gi|330507781|ref|YP_004384209.1| 309 IAGATVAIMGLPLRIAVLVGLALSQIGEFSFVLSKVGLEYGLISQELYRIFLDVAVLTMV-ATSSI 373
                                       ***********************************************************9.44444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.1   3.2e-25   1.4e-21       2     114 ..     412     524 ..     411     526 .. 0.98
   2 ?   -3.7   0.0       3.1   1.4e+04      45      69 ..     590     614 ..     578     620 .. 0.66

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 3.2e-25
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanil 78 
                                       iiiG+G  Gr++a   +++ +++v++d d+e+v++  ++g ++ +gdat+e+vL + g+++a+++++a++d +++  
  gi|330507781|ref|YP_004384209.1| 412 IIIGYGVNGRNVALSAKSEAIPYVIVDIDPETVKSGLRNGEPIRYGDATQEHVLLSTGVKSARVIVIAISDRTETRR 488
                                       9*****************8888******************************************************* PP

                                       HHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEE CS
                            TrkA_N  79 avllakelnpkkkiiaraqdpehaellkklgadvvi 114
                                       +++la+ lnp+++ii r+++  +  +l++lga++vi
  gi|330507781|ref|YP_004384209.1| 489 MTELARRLNPDIYIIDRTRYINEMSALYNLGANEVI 524
                                       **********************************99 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.1
                                       EES-TTSHHHHHHTTGGGESEEEE- CS
                            TrkA_N  45 vvgdatdeevLeeagiekadaviaa 69 
                                         g+++    L+e+g+ ++ + + a
  gi|330507781|ref|YP_004384209.1| 590 PAGSPAAGRSLKEIGLREIGISLLA 614
                                       4566667777888888777665555 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.61   2.7e+03      27      47 ..     128     149 ..     123     149 .. 0.81
   2 ?   -4.1   0.0       3.3   1.5e+04      12      21 ..     246     255 ..     244     262 .. 0.83
   3 !   49.3   0.0   7.1e-17   3.2e-13       3      65 ..     586     649 ..     584     654 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.61
                                       -EEEEEE-T.-EEES--TT-B- CS
                            TrkA_C  27 vlvvairRg.geliipsgdtvL 47 
                                       ++v++i  +  e++ p g t+L
  gi|330507781|ref|YP_004384209.1| 128 AIVLRIIQKkSEMYTPQGRTIL 149
                                       789999544479******9997 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3.3
                                       GTTSBHHHHT CS
                            TrkA_C  12 lvGktlkeln 21 
                                       l+G t++e++
  gi|330507781|ref|YP_004384209.1| 246 LAGLTISESQ 255
                                       79999*9975 PP

  == domain 3  score: 49.3 bits;  conditional E-value: 7.1e-17
                                       EEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHH CS
                            TrkA_C   3 evtvpagsplvGktlkelnlrargvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlael 65 
                                        ++vpagsp +G++lke++lr+ g+ ++a+ R+ +++ +p++++vL+++D+ +++gs ++la +
  gi|330507781|ref|YP_004384209.1| 586 TIKVPAGSPAAGRSLKEIGLREIGISLLAVNREsQVINHPDESFVLQPDDLAIILGSEAQLASV 649
                                       689***************************9999**************************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 ?   13.6   0.0   1.2e-05     0.056       4      90 ..     413     506 ..     410     515 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                                       EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........EEE-SSHHHHHHHCSEEEE-SSSHHHHHHH CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........akaaesieelvasldvvitmvkagkavdev 72 
                                       +iG Gv G+n al  +++ +  ++++ ++e v++ + +g         + +  ++  v+s++v+++ +++ ++++ +
  gi|330507781|ref|YP_004384209.1| 413 IIGYGVNGRNVALSAKSEAIPYVIVDIDPETVKSGLRNGepirygdaTQEHVLLSTGVKSARVIVIAISDRTETRRM 489
                                       7*************************************99988777555555566778888************9987 PP

                                       HHSHCCC--TT-EEEE-S CS
                     NAD_binding_2  73 iegllealkkgdilidgs 90 
                                       + +l+++l+++ ++id +
  gi|330507781|ref|YP_004384209.1| 490 T-ELARRLNPDIYIIDRT 506
                                       5.689**********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (664 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 4261.87
//
Query:       gi|330507782|ref|YP_004384210.1|  [L=503]
Description: monovalent cation:proton antiporter-2 (CPA2) family transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-57  193.8  42.9    4.8e-57  193.5  42.9    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
    1.4e-10   40.9   0.1    2.5e-10   40.0   0.1    1.5  1  TrkA_C          TrkA-C domain
  ------ inclusion threshold ------
      0.029   14.4   1.8      0.029   14.4   1.8    4.4  5  DUF4229         Protein of unknown function (DUF4229)


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 !  193.5  42.9   8.1e-61   4.8e-57       3     379 ..      12     387 ..       8     389 .. 0.92

  Alignments for each domain:
  == domain 1  score: 193.5 bits;  conditional E-value: 8.1e-61
                                       HHHHHHHHHHHH.HHHTTSXHHHHHHHHHHHHTTTTTS.......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTH CS
                    Na_H_Exchanger   3 llillallvgll.arrlklpeivgliiaGlllGpsglg.l.iepseedlevlselglilllFlaGleldlrelrknl 76 
                                       +++ll+++v    ++ l++p +v+++++G+l G  g+g + ++++    ++l ++ li++lF  Gl ++++e++ +l
  gi|330507782|ref|YP_004384210.1|  12 AVMLLLSVVSSKaSTQLGVPTLVLFLLIGMLAGSDGPGgIeFNNP-WLAQYLGTVALIFILFSGGLDTKWKEIKPVL 87 
                                       4444455555544*************************7446666.899**************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC..CCCTSTCCCCCCHHHHHHHHH CS
                    Na_H_Exchanger  77 ksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailk.eegrvperlgtlllgesvlnD 152
                                       +  ++l+++gv +t++++G+++y+  +l+++llea+l++ai+s td+++v +il+ ++  ++ +l+ ll+ es+ nD
  gi|330507782|ref|YP_004384210.1|  88 WRGVILSTIGVMLTAIIVGYAAYY--VLDFSLLEAMLLAAIISSTDAAAVFSILRsKQISLKGDLRPLLELESGSND 162
                                       ***********************8..89**************************988999***************** PP

                                       HHCCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.CTHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 153 avavvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft.dddrelevllvlllallaal 228
                                        +a++l+++l+al+   +g+ +s  +l+  f+   ++g ++g  +g  +++i  ++  d r l++ll++ l+ll+++
  gi|330507782|ref|YP_004384210.1| 163 PMAIFLTTSLIALI---TGAIASPTTLISMFAQQMALGAVFGYMMGRGMAVIVNRIrLDYRGLYPLLTISLVLLTYA 236
                                       **************...999999999999999999999999999999999888888889****************** PP

                                       HHHTSXXXHHHHHHHHHHHHHHHHHHTT..HHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 229 laellgvsgilgaflaGlvlseyefsnk..lseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvai 303
                                       l+ +lg  g l++ +aGl l+ ++f +k  l  + +s++ +l+ +++F+ +Gl ++++ l   +   i +++ +v++
  gi|330507782|ref|YP_004384210.1| 237 LTAALGGNGFLAVYIAGLSLGSHSFIHKrsLIDDHDSMA-WLMQIVMFLTLGLLVFPSKLI--PVAGIGLFICFVLM 310
                                       *********************888877767888899999.********************4..66666677777888 PP

                                       HTHHHHHHHHHTTTX.SSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTT.SSTTTCSTSXHHHHHHHHHHHH CS
                    Na_H_Exchanger 304 llgrilavflllrll.glslrealiigfgglqrgavalalaalgpalgllarel.yallivvvlftvlvqGlslkpl 378
                                       +l+r++av+++l  + + +++e++++++ gl rg+v ++la +   +g+ ++++ ++++++vvl++vlvqG+s++++
  gi|330507782|ref|YP_004384210.1| 311 FLARPMAVLICLLPFrKMPIKERVMLSWVGL-RGSVPIILATFPLISGVQKADMiFNVVFFVVLTSVLVQGSSIPFF 386
                                       88********9999989**************.******************************************998 PP

                                       H CS
                    Na_H_Exchanger 379 l 379
                                        
  gi|330507782|ref|YP_004384210.1| 387 A 387
                                       6 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.1   4.1e-14   2.5e-10       2      68 ..     416     481 ..     415     483 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 4.1e-14
                                       EEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                       v ++v +gs  +Gk +++lnl++ +  ++ +rR+g++i p+g+tvL+ GD+l v +s  +l+ lr+l
  gi|330507782|ref|YP_004384210.1| 416 VKLKVLSGSSADGKQIADLNLPD-DTWIAVLRREGHPIRPGGSTVLKGGDRLSVQSSGPSLDLLRSL 481
                                       67899******************.**********************************999999987 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   3.2       1.1   6.9e+03      10      37 ..       9      38 ..       6      45 .. 0.50
   2 ?   14.4   1.8   4.9e-06     0.029      12      54 ..      98     140 ..      95     143 .. 0.91
   3 ?   -2.9   0.5       1.3   7.6e+03      36      46 ..     172     182 ..     165     200 .. 0.54
   4 ?   -3.7   3.8       2.3   1.4e+04      27      45 ..     291     309 ..     274     328 .. 0.54
   5 ?   -1.8   0.5      0.57   3.4e+03      31      41 ..     367     377 ..     347     390 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                           DUF4229 10 Lfvvltavillvarliglp..vpllvaall 37
                                      L v++++++ +v   + ++  vp lv++ll
  gi|330507782|ref|YP_004384210.1|  9 LGVAVMLLLSVVSSKASTQlgVPTLVLFLL 38
                                      444444444444444444455777766655 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.9e-06
                           DUF4229  12 vvltavillvarliglpvpllvaallAlvvalplSmvllkklR 54 
                                       v+lta+i++ a   +l++ ll a+llA++++      +++ lR
  gi|330507782|ref|YP_004384210.1|  98 VMLTAIIVGYAAYYVLDFSLLEAMLLAAIISSTDAAAVFSILR 140
                                       89*****************************998888888887 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.3
                           DUF4229  36 llAlvvalplS 46 
                                       l+Al+  ++ S
  gi|330507782|ref|YP_004384210.1| 172 LIALITGAIAS 182
                                       33333333333 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 2.3
                           DUF4229  27 lpvpllvaallAlvvalpl 45 
                                        p++l+ +a ++l + ++l
  gi|330507782|ref|YP_004384210.1| 291 FPSKLIPVAGIGLFICFVL 309
                                       4444444444444444444 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 0.57
                           DUF4229  31 llvaallAlvv 41 
                                       ++  ++l  v+
  gi|330507782|ref|YP_004384210.1| 367 VVFFVVLTSVL 377
                                       33333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 3030.91
//
Query:       gi|330507783|ref|YP_004384211.1|  [L=334]
Description: putative K+-dependent Na+/Ca++ exchanger-like protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-50  171.2  33.6    3.6e-28   98.4   9.7    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 !   79.0  15.9     2e-26   3.5e-22       3     148 ..       4     141 ..       3     144 .. 0.92
   2 !   98.4   9.7     2e-32   3.6e-28       2     150 ..     187     330 ..     186     331 .. 0.90

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 2e-26
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       +++f+++ll+++v+a+++v+ a+ +a  lgi++ ++Glt++++g+s+pEl++ i+a l+g++ la++n+ G n++n+
  gi|330507783|ref|YP_004384211.1|   4 VMIFFAGLLALIVGAELIVRGASRLAALLGINPLLIGLTIVSIGTSMPELAVGITAGLQGSGPLAVANIAGTNLVNI 80 
                                       579************************9************************************************* PP

                                       HTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvl 148
                                       l+++Gl+ali +l  + + l ldl++++++a++l  + l+        g+lt leg++++++ a+y++ 
  gi|330507783|ref|YP_004384211.1|  81 LFILGLSALIRPLALHLQVLSLDLPMMIVAAAAL--AGLASD------GVLTPLEGVLMVGASAIYTLA 141
                                       **********998888888999998877777777..446656......*************99999875 PP

  == domain 2  score: 98.4 bits;  conditional E-value: 2e-32
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   2 lfvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifn 78 
                                       +++++i+++++ +++ad+lv+ a+ +a+ ++i+++++Gl ++A+g+s+pEl+++i+a l++e d+aign+lGs i n
  gi|330507783|ref|YP_004384211.1| 187 YVAMLIAGMAITAIGADWLVDGATGLARMIDIPEAIIGLSIVAIGTSAPELFTTIVATLRDERDVAIGNLLGSSIYN 263
                                       7899************************************************************************* PP

                                       HHTHHHHHHHHHH..BTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  79 lllviGlialigs..lkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                       +llv+Gl+al ++  l v ++   +d++l+ lval+++ ++l+        +r+++leg + +++Y++yl+++l
  gi|330507783|ref|YP_004384211.1| 264 ILLVLGLAALAAPtgLAVTRQLQLFDIPLMTLVALACVPVFLT-G------RRISRLEGGLGVAAYLIYLIWLL 330
                                       ***********99885555555579998888877777443333.5......9******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); 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:                         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: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.59
# Mc/sec: 1708.75
//
Query:       gi|330507784|ref|YP_004384212.1|  [L=374]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-22   77.5   0.0    1.9e-21   76.5   0.0    1.5  1  OrfB_IS605      Probable transposase
    1.5e-21   76.1   0.0    3.7e-21   74.8   0.0    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.5e-19   68.5   2.3    5.3e-19   67.4   2.3    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0032   17.4   0.2     0.0057   16.7   0.2    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.064   12.7   0.6       0.83    9.1   0.1    2.3  2  zf-ribbon_3     zinc-ribbon domain
      0.082   12.7   0.1          2    8.2   0.0    2.3  2  zinc_ribbon_2   zinc-ribbon domain
        0.1   12.1   0.3        2.8    7.5   0.0    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.13   11.9   2.8         11    5.6   0.2    3.1  3  RecR            RecR protein
        0.2   11.3   0.7       0.42   10.3   0.7    1.5  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   9.3e-25   1.9e-21       3     117 ..     165     277 ..     163     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 9.3e-25
                        OrfB_IS605   3 pveveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        ve+e++ +p+ k ++ +g+D+G++ +at+++++   ++ ++r++++++ +la+ +++l++  k++  +kka r + 
  gi|330507784|ref|YP_004384212.1| 165 SVEIEDQlKPPWKDGSLVGVDVGLESFATLSNGE---TIANPRFFREEETELARVQRKLSKAPKGTPERKKALRMVE 238
                                       6899999666779999******************...**************************************** PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       r+h++++++r +++hk++++l+++   ++ e+L ++nm 
  gi|330507784|ref|YP_004384212.1| 239 RVHERIANKRYDFAHKVSRYLVNRFGLIAFEDLSIQNML 277
                                       *************************************97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0   1.9e-24   3.7e-21       1      68 [.     291     358 ..     291     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.9e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++ l +  +yka  +G  v++v+p++TSk Cs+Cg  ++++ls+r++ Cp+Cg+++drD+nAaiNil+
  gi|330507784|ref|YP_004384212.1| 291 WNMLVTLTSYKAVSAGSMVVLVDPRNTSKMCSRCGILVEKTLSDRVHSCPQCGLSLDRDWNAAINILR 358
                                       667777889*********************************************************97 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   2.3   2.7e-22   5.3e-19       1      47 []       1      46 [.       1      46 [. 0.99

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 2.7e-22
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkayk+r+yPT+ Q++k++rt++ +R+ YN+ La+rk+a+e+egk
  gi|330507784|ref|YP_004384212.1|  1 M-LKAYKFRIYPTKSQRTKMERTLDLCRWTYNQTLAYRKDAWEKEGK 46
                                      8.*******************************************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   2.9e-06    0.0057      10      44 ..     316     352 ..     312     355 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.9e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + +++Cs+Cg  ++++ +   + Cp+Cg ++d +++ 
  gi|330507784|ref|YP_004384212.1| 316 NTSKMCSRCGILVEKTLSdrVHSCPQCGLSLDRDWNA 352
                                       6789*********9877799************99986 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      0.13   2.5e+02       5       9 ..     321     325 ..     317     331 .. 0.70
   2 ?    9.1   0.1   0.00042      0.83       4      17 ..     338     351 ..     335     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.13
                       zf-ribbon_3   5 CPnCG 9  
                                       C++CG
  gi|330507784|ref|YP_004384212.1| 321 CSRCG 325
                                       77777 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00042
                       zf-ribbon_3   4 rCPnCGaplssddn 17 
                                       +CP+CG  l+ d+n
  gi|330507784|ref|YP_004384212.1| 338 SCPQCGLSLDRDWN 351
                                       7*****98899998 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.1     2e+02      15      20 ..     320     325 ..     315     328 .. 0.70
   2 ?    8.2   0.0     0.001         2       7      20 ..     330     343 ..     329     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.1
                     zinc_ribbon_2  15 FCpyCG 20 
                                        C++CG
  gi|330507784|ref|YP_004384212.1| 320 MCSRCG 325
                                       577776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.001
                     zinc_ribbon_2   7 aelqdnakFCpyCG 20 
                                       ++l+d++  Cp+CG
  gi|330507784|ref|YP_004384212.1| 330 KTLSDRVHSCPQCG 343
                                       6799*********9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0014       2.8      11      31 ..     310     330 ..     305     335 .. 0.84
   2 ?    2.2   0.0     0.064   1.3e+02      21      29 ..     338     346 ..     337     349 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0014
                                       CHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon  11 lveDpergelvCtdCGlVled 31 
                                       +++Dp ++   C++CG ++e 
  gi|330507784|ref|YP_004384212.1| 310 VLVDPRNTSKMCSRCGILVEK 330
                                       689***999*******99996 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.064
                                       EESSSSBEE CS
                      TF_Zn_Ribbon  21 vCtdCGlVl 29 
                                        C+ CGl l
  gi|330507784|ref|YP_004384212.1| 338 SCPQCGLSL 346
                                       588888765 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.44   8.8e+02       5      16 ..      71      82 ..      69      84 .. 0.89
   2 ?    5.1   0.1    0.0082        16      13      28 ..     315     330 ..     310     332 .. 0.76
   3 ?    5.6   0.2    0.0057        11      12      23 ..     332     343 ..     330     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.44
                                      HHHHHHHHHHH- CS
                              RecR  5 LaeaLqeakekv 16
                                      ++++Lq+a e+v
  gi|330507784|ref|YP_004384212.1| 71 FSQTLQNAQERV 82
                                      89*******998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0082
                                       HHH-EE-TTT--EESS CS
                              RecR  13 kekvrhCsrCgnltee 28 
                                       +++ + CsrCg l e+
  gi|330507784|ref|YP_004384212.1| 315 RNTSKMCSRCGILVEK 330
                                       667799*****99776 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0057
                                       HHHH-EE-TTT- CS
                              RecR  12 akekvrhCsrCg 23 
                                       + ++v+ C++Cg
  gi|330507784|ref|YP_004384212.1| 332 LSDRVHSCPQCG 343
                                       6799*******9 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 ?   10.3   0.7   0.00021      0.42       6      29 ..     321     344 ..     316     345 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                     zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCgl 29 
                                       C+rCG  +e+   ++   Cp+Cgl
  gi|330507784|ref|YP_004384212.1| 321 CSRCGILVEKTLSDRVHSCPQCGL 344
                                       **********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2187.10
//
Query:       gi|330507785|ref|YP_004384213.1|  [L=323]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-15   56.9   0.0    4.4e-15   56.4   0.0    1.2  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0   2.5e-19   4.4e-15       1     162 [.      93     247 ..      93     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2.5e-19
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC.C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla.v 75 
                                       +++++ C ++C+fCa+p     +  g+++s e+++e +ke+    g  + + l++g+     +++e +++l++    
  gi|330507785|ref|YP_004384213.1|  93 ITISERCIYDCKFCAVP-----RLMGKVKSHERVMEMAKEA-MATGrLESISLTSGTEVSPQHEAERVAALVRDLlP 163
                                       67899************.....6899999999999999999.78888*******99888888888888888888788 PP

                                       CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivg 151
                                        g+ i v++n++     + + ll++g d v  +le++d + + + + +g +++e+++ale + e+ +++ v++++++
  gi|330507785|ref|YP_004384213.1| 164 FGLPIGVSVNPFPG---VNRILLDAGADEVKYNLETVDRDIFAQVC-PGLSYQEIMDALEEAVELFGPNhVFSNVII 236
                                       88888888888886...88***************************.******************7777******** PP

                                       BTTTSHHHHHH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 152 lpGendeelee 162
                                       + Ge+d+ l++
  gi|330507785|ref|YP_004384213.1| 237 GLGESDQSLRQ 247
                                       ******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1866.84
//
Query:       gi|330507786|ref|YP_004384214.1|  [L=162]
Description: hypothetical protein MCON_1793 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.041   14.4   0.1      0.073   13.5   0.1    1.5  1  NERD      Nuclease-related domain


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 ?   13.5   0.1   4.1e-06     0.073       2      61 ..      16      73 ..      15     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-06
                              NERD  2 gaegEravakeLkelkedeylvlhdvrlrpgtgeiDhlvispkgifviEvKnwsGwifgd 61
                                      g+  E  + +++k+l+++  +++  v++r+++g  D+  +++++ ++ E+Kn++ +i++ 
  gi|330507786|ref|YP_004384214.1| 16 GKLSEFYAYRYIKHLEAE--HIIEEVEWRDTDGRPDFEFLYNGKKYLMECKNLRNKIYKR 73
                                      677788888999988555..899*****99988*********************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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: 00:00:00.43
# Mc/sec: 1131.35
//
Query:       gi|330507787|ref|YP_004384215.1|  [L=59]
Description: hypothetical protein MCON_1794 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.024   14.9   0.0      0.032   14.4   0.0    1.2  1  Catalase-rel  Catalase-related immune-responsive


Domain annotation for each model (and alignments):
>> Catalase-rel  Catalase-related immune-responsive
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.8e-06     0.032      21      50 ..      11      40 ..       3      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-06
                                      HHHHHHHHHHHHHHTTSS-HHHHHHHHHHH CS
                      Catalase-rel 21 eekerlvnniafelskvedeeiqerqlehf 50
                                       e+  l++n+++el++ + e +++ +l+ +
  gi|330507787|ref|YP_004384215.1| 11 PEQWALIENFRGELGNGDAEIVRNIVLAWL 40
                                      68999*************888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 463.18
//
Query:       gi|330507788|ref|YP_004384216.1|  [L=312]
Description: DNA methylase [Methanosaeta concilii GP6]
Scores for complete 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-38  131.5   0.1    4.5e-38  131.2   0.1    1.0  1  N6_N4_Mtase  DNA methylase
  ------ inclusion threshold ------
      0.041   13.6   0.1         13    5.4   0.0    2.6  3  UPF0020      Putative RNA methylase family UPF0020
      0.054   12.7   0.0        3.8    6.7   0.0    2.1  2  N6_Mtase     N-6 DNA Methylase


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2   0.1   7.6e-42   4.5e-38       1     229 [.      52     303 ..      52     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 7.6e-42
                                       EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT......HHHHHHHH CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk......elkalade 71 
                                       v+livt+pPY ++ +     ++ ++ + ++y++++  ++++  rvL +dgs++ini+ s            ++l+ e
  gi|330507788|ref|YP_004384216.1|  52 VNLIVTSPPYALVYK-----KEYGNVDANAYVKWFMDFADQFLRVLTEDGSLVINIGGSWNRGkptrstYQFELIIE 123
                                       89*************.....89999999*******************************988899***977777778 PP

                                       HTT-EEEEEEEEEEESSSTTTSTCC......S-B--EEEEEEEESSTT-..---GGGSSBSS-HHHHHHHHHH..CH CS
                       N6_N4_Mtase  72 ifggffllnvivwkkpnsmpesnkd......rltsthEyilvfsknkkyllkfnldaikvpyeekdklekrga..yt 140
                                        +++f l++   w +p ++p+++++      r++++ E++l++sk+     k +  +i +py++  ++  ++   ++
  gi|330507788|ref|YP_004384216.1| 124 LAKKFHLAQEFYWYNPAKLPAPAEWvtvrriRVKDSVELVLWLSKSPFP--KADNRKILQPYSKDMQRLIERGyvAK 198
                                       7778************999998888999999******************..77777777777766665555545999 PP

                                       HHCC-B--BSEE...................E-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS-TT-EEEET CS
                       N6_N4_Mtase 141 skkkgkkiediW...................dlseiqsnekkskgdtkkkHpaqkPvallerlIklstkkgdivlDp 198
                                       + + g++i+ ++                    +s + +++k+s+    k Hpa +P +l++  I+ +t++gd+v+Dp
  gi|330507788|ref|YP_004384216.1| 199 KRPSGHNITSKFqrdnkgaippnllqvgnndANSPYLQKCKESN---MKPHPARFPKELPQLFIDFLTDQGDVVMDP 272
                                       9******************9999999999886777777777766...479*************************** PP

                                       T-TTTHHHHHHHHTT-EEEEEESSHHHHHHH CS
                       N6_N4_Mtase 199 FaGSGtTavaakelgrkfiGieieeeyvela 229
                                       F+GS  T+++a+  +r++iGie  e y++++
  gi|330507788|ref|YP_004384216.1| 273 FCGSNMTGIVAETRKRRWIGIESIEDYLKAS 303
                                       ***************************9876 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0025        15     117     135 ..      47      65 ..      32     103 .. 0.71
   2 ?   -2.4   0.0      0.54   3.3e+03      43      94 ..     190     240 ..     189     244 .. 0.50
   3 ?    5.4   0.0    0.0021        13      27      39 ..     264     276 ..     262     288 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0025
                                       STTS---EEEE-------- CS
                           UPF0020 117 lkegevdvivtnpPYGerl 135
                                        +e++v++ivt pPY    
  gi|330507788|ref|YP_004384216.1|  47 MPESSVNLIVTSPPYALVY 65 
                                       45789**********7554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.54
                                       HHHHHHHHTT--TTTT----SSHHHHHHHHHH.....HH--EEEEES-HHHHHHHHH CS
                           UPF0020  43 lIEaallganiapgllrefvlelkaeaeeear.....aelklygsDldrrvvqgare 94 
                                       lIE++ ++++++ g +      + ++ +++++     + l++   D ++ ++q+++e
  gi|330507788|ref|YP_004384216.1| 190 LIERGYVAKKRPSGHN------ITSKFQRDNKgaippNLLQVGNNDANSPYLQKCKE 240
                                       5777777777775444......22222222222223455555556666666666664 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0021
                                       -TTS-EEETT-TT CS
                           UPF0020  27 kpgepllDPmCGs 39 
                                       ++g++ +DP+CGs
  gi|330507788|ref|YP_004384216.1| 264 DQGDVVMDPFCGS 276
                                       57999*******9 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0    0.0047        28     109     143 ..      35      68 ..      29      88 .. 0.76
   2 ?    6.7   0.0   0.00063       3.8      31      58 ..     251     277 ..     248     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0047
                          N6_Mtase 109 irlgdtlekpkfekdkkfdvvvaNppfnqkewkek 143
                                       + l+d+le  k + +++++ +v+ pp+    +k++
  gi|330507788|ref|YP_004384216.1|  35 AYLADSLEVMKNMPESSVNLIVTSPPYALV-YKKE 68 
                                       567899999999999************987.6443 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00063
                          N6_Mtase  31 PrevsklivellepksgesvyDpacGsg 58 
                                       P+e+ +l ++ l ++ + +v+Dp cGs+
  gi|330507788|ref|YP_004384216.1| 251 PKELPQLFIDFLTDQGD-VVMDPFCGSN 277
                                       9999********99988.7********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2442.08
//
Query:       gi|330507789|ref|YP_004384217.1|  [L=215]
Description: Isoprenylcysteine carboxyl methyltransferase (ICMT) family protein [Methanosaeta concilii GP6]
Scores for complete 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   47.5   0.7    1.9e-12   47.5   0.7    2.3  3  PEMT             Phospholipid methyltransferase
    1.7e-09   37.9   4.6    1.9e-09   37.8   0.8    2.4  2  ICMT             Isoprenylcysteine carboxyl methyltransferase
  ------ inclusion threshold ------
      0.016   14.9   1.6      0.016   14.9   1.6    1.5  2  DUF1345          Protein of unknown function (DUF1345)
      0.017   13.9   0.3      0.017   13.9   0.3    2.2  2  ERG4_ERG24       Ergosterol biosynthesis ERG4/ERG24 family
      0.098   12.6   0.2        0.3   11.1   0.2    1.8  1  Holin_BhlA       BhlA holin family
       0.15   12.7   0.1       0.15   12.7   0.1    1.7  2  WBP-1            WW domain-binding protein 1
       0.18   11.8   3.2       0.35   10.8   3.2    1.5  1  Abhydrolase_9_N  Alpha/beta-hydrolase family N-terminus
        2.2    8.1  17.2        1.4    8.7   5.6    2.1  2  FA_desaturase    Fatty acid desaturase


Domain annotation for each model (and alignments):
>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3      0.47   1.1e+03      75      98 ..      31      53 ..       8      58 .. 0.59
   2 ?   -3.3   0.1       5.5   1.2e+04       9      17 ..      75      83 ..      68      90 .. 0.47
   3 !   47.5   0.7   8.3e-16   1.9e-12       5      99 ..     103     193 ..     100     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.47
                              PEMT 75 glllallvllvylialkfvEephl 98
                                      + +l+l +l+++  +lk  E ++l
  gi|330507789|ref|YP_004384217.1| 31 WAVLVLPMLVAVCYFLK-HEPEML 53
                                      24444445555555555.565555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.5
                              PEMT  9 lialglllv 17
                                      li++  +++
  gi|330507789|ref|YP_004384217.1| 75 LIIIAGFVA 83
                                      333333332 PP

  == domain 3  score: 47.5 bits;  conditional E-value: 8.3e-16
                              PEMT   5 lGlllialglllvlssiealgefgtfygdfFlelmdklvtsGiYrylnnPeyvgstlgflGlaLitgsaaglllall 81 
                                       ++ + +++g++lvl+++++ +++   ++    ++ ++++++G+Y ++++P+y+g+++++l++ ++ gs+++l + +l
  gi|330507789|ref|YP_004384217.1| 103 FADAAVFFGYILVLWVFKENSYASRIIQI---SEGQRVISTGPYAIIRHPMYLGVLAMYLATPIALGSWWALPIFAL 176
                                       6778899*******************884...7899**********************************9999988 PP

                              PEMT  82 vllvylialkfvEephla 99 
                                       ++ ++ + ++  Ee+ l 
  gi|330507789|ref|YP_004384217.1| 177 SVPFICWRII-AEERLLL 193
                                       8888888888.7887765 PP

>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.21   4.7e+02      51      66 ..      27      42 ..      13      59 .. 0.86
   2 !   37.8   0.8   8.7e-13   1.9e-09       5      92 ..     108     192 ..     100     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.21
                              ICMT 51 lfvilelatllLlcna 66
                                      +++++++ +l++l+  
  gi|330507789|ref|YP_004384217.1| 27 GWLYWAVLVLPMLVAV 42
                                      8999999999999865 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 8.7e-13
                              ICMT   5 vllaqalrlvvmatlGeiwttrvailpdhklvksglykylrHPnYllfvilelatllLlcnakltalvllalvalll 81 
                                       v ++++l l+v ++  ++ + +++i+++++++ +g+y+++rHP Yl+ +++ lat + l +    al ++al + ++
  gi|330507789|ref|YP_004384217.1| 108 VFFGYILVLWVFKE-NSYASRIIQISEGQRVISTGPYAIIRHPMYLGVLAMYLATPIALGSW--WALPIFALSVPFI 181
                                       56777777777765.5677778888**********************888888887777777..6778888889999 PP

                              ICMT  82 fvRikeEekaL 92 
                                         Ri +Ee+ L
  gi|330507789|ref|YP_004384217.1| 182 CWRIIAEERLL 192
                                       9*******998 PP

>> DUF1345  Protein of unknown function (DUF1345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.6     7e-06     0.016       7      99 ..      29     120 ..      23     138 .. 0.66
   2 ?   -3.7   0.4       3.7   8.3e+03      78      95 ..     155     172 ..     149     176 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7e-06
                           DUF1345   7 igwdlaalvylvlvllvllradaeelrkraerede..srvlilllvllaalaslvaivlllasakaekpaekllhla 81 
                                       ++w +++l +lv+v++ l ++++e l++r + +++  ++++i+  + l ++a +vai++ l  ++  ++   +  ++
  gi|330507789|ref|YP_004384217.1|  29 LYWAVLVLPMLVAVCYFL-KHEPEMLERRMNLQERekEQIAIVNAISLIIIAGFVAIAIDLRLHGL-NAIP-VHLVL 102
                                       578888887777777766.56788887776655551155566666888888889999998855554.3333.46666 PP

                           DUF1345  82 lavatvvlsWllvhtvfa 99 
                                       +a a+v+ + +lv  vf 
  gi|330507789|ref|YP_004384217.1| 103 FADAAVFFGYILVLWVFK 120
                                       677777777777777775 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.7
                           DUF1345  78 lhlalavatvvlsWllvh 95 
                                       l++ la    + sW ++ 
  gi|330507789|ref|YP_004384217.1| 155 LAMYLATPIALGSWWALP 172
                                       566677777788887765 PP

>> ERG4_ERG24  Ergosterol biosynthesis ERG4/ERG24 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.8     0.018        40      66     158 ..      25     119 ..      12     127 .. 0.74
   2 ?   13.9   0.3   7.7e-06     0.017     340     431 ..     126     214 ..     119     215 .] 0.69

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.018
                        ERG4_ERG24  66 werklftvfllfyvlqavlylll..pGkvveGleLsngkkLkYkinalaslllvlaillvlqvtelfeltvlidnfv 140
                                       w+  l+   l+  +l av y l   p +  + ++L++ +k +  i    sl++++  ++++ + +l  l+ +  + v
  gi|330507789|ref|YP_004384217.1|  25 WQGWLYWAVLVLPMLVAVCYFLKhePEMLERRMNLQEREKEQIAIVNAISLIIIAGFVAIAIDLRLHGLNAIPVHLV 101
                                       444444444455566677776652245555667888888888777666689999999999999************** PP

                        ERG4_ERG24 141 qlisvailfafalaivlY 158
                                        ++ +a+ f+++l ++++
  gi|330507789|ref|YP_004384217.1| 102 LFADAAVFFGYILVLWVF 119
                                       ***********9998886 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.7e-06
                        ERG4_ERG24 340 lkyiqtktGskLlvsGWyglarkinYlgDwlqslswsLatgfqsvlpyf.yvlyFlvlLvhRelRDeekCkkkYGed 415
                                        ++iq ++G++++ +G y++ r++ Ylg + + l+  +a g    lp f  ++ F++  +  e R       +    
  gi|330507789|ref|YP_004384217.1| 126 SRIIQISEGQRVISTGPYAIIRHPMYLGVLAMYLATPIALGSWWALPIFaLSVPFICWRIIAEERL----LLRDLPG 198
                                       5789************************99988877666666666666634566766555444432....3333344 PP

                        ERG4_ERG24 416 weeYkkkvpykiipyv 431
                                       + eY+++ +y++ p+v
  gi|330507789|ref|YP_004384217.1| 199 YLEYCQERRYRLLPHV 214
                                       5566666666666666 PP

>> Holin_BhlA  BhlA holin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00013       0.3      15      52 ..      31      74 ..      24      75 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                        Holin_BhlA 15 wavLfv...vllvYilkkqe...kreekqeerekkyqeiikklt 52
                                      wavL     v++ Y+lk++    +r  +++erek++ +i++ ++
  gi|330507789|ref|YP_004384217.1| 31 WAVLVLpmlVAVCYFLKHEPemlERRMNLQEREKEQIAIVNAIS 74
                                      9999762115567****8752224666677*********99886 PP

>> WBP-1  WW domain-binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   6.6e-05      0.15      18      62 ..      24      70 ..      20      99 .. 0.64
   2 ?   -3.2   0.2         6   1.3e+04      22      41 ..     168     187 ..     167     205 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.6e-05
                             WBP-1 18 yyElwwfwlvwtllillsCicalakrrak...lrleqqerqreinlva 62
                                      y   w++w v++ l +l+ +c + k + +   +r++ qer++e++ + 
  gi|330507789|ref|YP_004384217.1| 24 YWQGWLYWAVLV-LPMLVAVCYFLKHEPEmleRRMNLQEREKEQIAIV 70
                                      444566666555.44588888888866665557777777777544433 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6
                             WBP-1  22 wwfwlvwtllillsCicala 41 
                                       ww + +++l + ++C  ++a
  gi|330507789|ref|YP_004384217.1| 168 WWALPIFALSVPFICWRIIA 187
                                       67666777666677754444 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 ?   10.8   3.2   0.00016      0.35      52     144 ..      27     118 ..       4     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                   Abhydrolase_9_N  52 lrlalavvalvvllvalvlaarwQrelralmgaeplgaaeyllvllvallvfalllllgrllralvrllarllgrvl 128
                                        +l +av++l +l+++ ++ ++  + l++ m++++++  + + v +++l+++a +++++  lr         ++ vl
  gi|330507789|ref|YP_004384217.1|  27 GWLYWAVLVLPMLVAVCYFLKHEPEMLERRMNLQEREKEQIAIVNAISLIIIAGFVAIAIDLRLHGLNA-IPVHLVL 102
                                       46666777778888888899999999******************************9987666443322.3566777 PP

                   Abhydrolase_9_N 129 prrvaavlgvlvvvvl 144
                                        + +a ++g ++v+++
  gi|330507789|ref|YP_004384217.1| 103 FADAAVFFGYILVLWV 118
                                       7777778887777776 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   5.6   0.00062       1.4      87     179 ..      23     117 ..       8     126 .. 0.61
   2 ?    3.7   5.2      0.02        46     140     184 ..     144     188 ..     117     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00062
                     FA_desaturase  87 srfeglfryllrlllgllvlgwllalvlglwlrrlarrrapsksrrrkwrllawlllllawlglwlalllllglall 163
                                       ++++g+ ++++  l +l+++ ++l++ + ++ rr+  +++ ++++   +++ a+ l+++  +g+++ ++ l  ++l+
  gi|330507789|ref|YP_004384217.1|  23 RYWQGWLYWAVLVLPMLVAVCYFLKHEPEMLERRMNLQEREKEQI---AIVNAISLIII--AGFVAIAIDLRLHGLN 94 
                                       789999999999999999999888887666666666666655554...33444444444..4555555444444444 PP

                     FA_desaturase 164 .......lwlvplllllfllalv 179
                                              l++ ++++++ +l+l+
  gi|330507789|ref|YP_004384217.1|  95 aipvhlvLFADAAVFFGYILVLW 117
                                       45777443333355555555544 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.02
                     FA_desaturase 140 wlllllawlglwlalllllglalllwlvplllllfllalvlnyve 184
                                       + +  + +lg+++++l+ +  ++++w++p+++l + + +++ ++e
  gi|330507789|ref|YP_004384217.1| 144 AIIRHPMYLGVLAMYLATPIALGSWWALPIFALSVPFICWRIIAE 188
                                       455566678888888887777777**********99999987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); 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:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1467.11
//
Query:       gi|330507790|ref|YP_004384218.1|  [L=212]
Description: hypothetical protein MCON_1798 [Methanosaeta concilii GP6]
Scores for complete 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-17   62.6   0.1    8.3e-16   58.3   0.2    2.0  2  LTD       Lamin Tail Domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.2   4.6e-20   8.3e-16       8     110 ..      39     135 ..      32     136 .. 0.91
   2 ?    1.9   0.0     0.016   2.8e+02      28      43 ..     181     196 ..     170     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 4.6e-20
                               LTD   8 vvIsevmedgagnnanefvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsgttsasngskas 83 
                                       v+I  v ++ a+    ++ve++N +s  ++L gw+l++  ++ y fp++  tl+ag+++ v+s++g++s+s+    +
  gi|330507790|ref|YP_004384218.1|  39 VKIISVSYQDAD----QWVEIANMGSGLMNLDGWSLKNRENQsYAFPANF-TLKAGSTARVHSKEGSNSSSDL--YN 108
                                       667777775533....9***********************99*******9.*************999988888..68 PP

                               LTD  84 ssavwnnggdavaLydasgevvdsvgy 110
                                       s++ w++ gd+++L d +g++++++ y
  gi|330507790|ref|YP_004384218.1| 109 SALFWSEMGDTATLEDIAGRIISQYRY 135
                                       99**********************988 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.016
                               LTD  28 lyNtsskavdLsgwkl 43 
                                       l  +ss++v+L+g+++
  gi|330507790|ref|YP_004384218.1| 181 LRSSSSTPVNLTGHTF 196
                                       5668999******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1627.22
//
Query:       gi|330507791|ref|YP_004384219.1|  [L=205]
Description: G-D-S-L family lipolytic protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-29  103.5   0.0    2.1e-29  103.2   0.0    1.1  1  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
    1.1e-18   68.0   0.0    1.3e-18   67.7   0.0    1.1  1  Lipase_GDSL    GDSL-like Lipase/Acylhydrolase
     0.0019   18.4   0.0     0.0032   17.6   0.0    1.4  1  Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family
  ------ inclusion threshold ------
      0.019   14.2   0.0      0.029   13.6   0.0    1.3  1  OSK            OSK domain


Domain annotation for each model (and alignments):
>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   4.6e-33   2.1e-29       1     179 []      26     196 ..      26     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 4.6e-33
                                       EEESHHHHTCTTBCCHCHHCCCCCCCHHHTT...-EEEEE.EEHCCH-H..HHHHHHHH.CTGGG-TSEEEEE--CC CS
                     Lipase_GDSL_2   1 alGDSiTaGygadgggrsypaylarllaarl...gldvvnnlgvsGattallrllerlr.dllrlkpdlvtiliGtN 73 
                                       ++GDSiTaGy   +  r++p++l + l++r+   + + +n  g+sG+t+  ++ l rl+ ++l ++pdlvti++G+N
  gi|330507791|ref|YP_004384219.1|  26 CFGDSITAGY---AVRRGFPSFLLESLRQRFpdsKIEMIN-SGISGDTS--QDGLSRLDwAVLSYEPDLVTINFGIN 96 
                                       9*********...889***************654444555.********..999999999***************** PP

                                       CCCTT--HHHHHHH..HHHHHHHHCCC...GEEECEEEEE-TTT-TTSTCCHHHHHHHHHHHHHHHHHHCT-EEE-H CS
                     Lipase_GDSL_2  74 DlgrgvpaaaaaandnleelidalraaapgarilvlgplpptpeaaadarelnaviaaynealrevaaeegvpfvDl 150
                                       D+  g + ++++ n  l  +++++ra  p+  il    l ++p ++++    ++++ +y +++++va+e +v fvD+
  gi|330507791|ref|YP_004384219.1|  97 DCVLGLSLEEFEMN--LVVMVRRIRAG-PDSEIL---LLSSQPLESPPY---DQRVLDYYQTVERVAKEMNVGFVDV 164
                                       **************..*********99.**9999...444444444443...45889******************** PP

                                       HHHH...HHCCCCCGGBBTTS.SSB-HHHHHH CS
                     Lipase_GDSL_2 151 hdal...adsgerladlladdglHPnaaGyrl 179
                                       ++a+    + g +l+ l  ++  HPn+aGyr+
  gi|330507791|ref|YP_004384219.1| 165 YGAWmkrVQAGMPLDSLILPGLDHPNEAGYRI 196
                                       66662225566777777777779*******96 PP

>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.0     3e-22   1.3e-18       1     200 []      24     201 ..      24     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 3e-22
                                       EEEEESHHHHTT......THHHHHHHCCCCEECCCTTC.GCEEEEEEECTTHHHHHHHCCHECTTTECHHHHHCTTS CS
                                       xxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Lipase_GDSL   1 ivafGDSltdGd......gaatlntiqlktpknlnefdlaldrianignkgasdnelqqllnkyplkseqlkalhpd 71 
                                       iv+fGDS+t+G+       +  l++ + ++p++          + n g+ g+ ++    +l       +   ++ pd
  gi|330507791|ref|YP_004384219.1|  24 IVCFGDSITAGYavrrgfPSFLLESLRQRFPDSKI-------EMINSGISGDTSQDGLSRL------DWAVLSYEPD 87 
                                       8*********9988885444455555566666555.......4588889888888888888......99******** PP

                                       EEEEE--CTCC-EECSSCTTTCEEHHHHHHHHHHHHHHHHHHHHTTEEEEEEE-SSTCHCTCCCCHCCHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Lipase_GDSL  72 lviislGtNDsnlgkkstdaakkeaeeyiknlreaikelkeegapkaivvlvsppglgpqeekdakklgekgnefvg 148
                                       lv+i++G ND+          +++ ee+  nl  ++++++ +g++  i +l+s+p  +p            + ++v 
  gi|330507791|ref|YP_004384219.1|  88 LVTINFGINDC--------VLGLSLEEFEMNLVVMVRRIR-AGPDSEILLLSSQPLESP-----------PYDQRVL 144
                                       ***********........*********************.887777777788888888...........9****** PP

                                       HHHHHHHHHHHHCTEEEECHHHHHHHTHCCGCHCHTSS......SB-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx RF
                       Lipase_GDSL 149 eynqrlndlaekdgfavvDlydelqglsgieqlkaDgl......Hpsekgyeklaell 200
                                        y q ++ +a+++++ +vD+y  + ++ +++ +  D l      Hp+e+gy+++ae+l
  gi|330507791|ref|YP_004384219.1| 145 DYYQTVERVAKEMNVGFVDVYGAWMKRVQAGMPL-DSLilpgldHPNEAGYRIIAEEL 201
                                       ***************************9999999.888888888***********975 PP

>> Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.2e-07    0.0032       3     172 ..      23     200 ..      21     204 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.2e-07
                     Lipase_GDSL_3   3 pivvYGsSitqGasasRpglayt.ailsrkl...grevvnLgfsGnalle..aeladvlaevdasvfvldllpN... 70 
                                        iv +G Sit G +  R   ++    l +++   + e++n g+sG +  +  + l  ++ + ++++  +++  N   
  gi|330507791|ref|YP_004384219.1|  23 TIVCFGDSITAGYAVRRGFPSFLlESLRQRFpdsKIEMINSGISGDTSQDglSRLDWAVLSYEPDLVTINFGINdcv 99 
                                       599*********98888766665144555554436799******997655333444455555556666655555555 PP

                     Lipase_GDSL_3  71 ..asaeeirerleyfvktlrkahPktpillvedlsttkglvdeklekeveaknkaleelvkklkkekekklylissk 145
                                          s ee++  l  +v+++r a P+  ill+ +   ++  +d+++ + +++ +++ +e+       ++ + ++   +
  gi|330507791|ref|YP_004384219.1| 100 lgLSLEEFEMNLVVMVRRIR-AGPDSEILLLSSQPLESPPYDQRVLDYYQTVERVAKEMNVGF--VDVYGAWMKRVQ 173
                                       55*****************9.579********9999999999976666666555555543332..233333344444 PP

                     Lipase_GDSL_3 146 ellgkdeeatvdgiHpsdlGllryada 172
                                       + +  d+       Hp++ G+  +a++
  gi|330507791|ref|YP_004384219.1| 174 AGMPLDSLILPGLDHPNEAGYRIIAEE 200
                                       445556666666677777777666665 PP

>> OSK  OSK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.5e-06     0.029      45     119 ..      58     135 ..      45     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-06
                                       S-EETEEETT--HHHHHHHHHT----T..-EEEEE--HHHHHTT--HHHHHHHHHHHHHHHHHT.T-EEEEE----- CS
                               OSK  45 vlqsGlciSGlTiseaakrlekielis..srvvvnlGsvDilngktlvelehDlteLlkelrer.nvaiilttlaPl 118
                                       + +    iSG T ++  +rl+ + l    + v +n G  D + g +l+e+e+ l  +++++r   +++i+l    Pl
  gi|330507791|ref|YP_004384219.1|  58 IEMINSGISGDTSQDGLSRLDWAVLSYepDLVTINFGINDCVLGLSLEEFEMNLVVMVRRIRAGpDSEILLLSSQPL 134
                                       44444559************976544337999*****************************9987888888888887 PP

                                       G CS
                               OSK 119 a 119
                                        
  gi|330507791|ref|YP_004384219.1| 135 E 135
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1433.89
//
Query:       gi|330507792|ref|YP_004384220.1|  [L=258]
Description: tryptophan synthase subunit alpha [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-78  263.1   0.0    2.1e-78  262.8   0.0    1.0  1  Trp_syntA     Tryptophan synthase alpha chain
    0.00064   19.3   0.2     0.0013   18.3   0.1    1.5  2  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.026   13.7   0.1      0.095   11.9   0.1    1.9  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
      0.048   13.1   0.0       0.15   11.5   0.0    1.7  2  PcrB          PcrB family
       0.15   12.4   0.0        5.4    7.4   0.0    2.3  2  Radical_SAM   Radical SAM superfamily


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 !  262.8   0.0   5.9e-82   2.1e-78       8     249 ..       9     247 ..       4     255 .. 0.93

  Alignments for each domain:
  == domain 1  score: 262.8 bits;  conditional E-value: 5.9e-82
                                       TB-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHH CS
                         Trp_syntA   8 nraafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkk 84 
                                       +   ++ y+  gdp+   + e+++ l +agad+iElGlp sdP+adGP+Iqaa++ra+a+g++++  +++ ee++  
  gi|330507792|ref|YP_004384220.1|   9 KGPLLIVYLCSGDPSPGATPELVRRLVRAGADIIELGLPHSDPIADGPTIQAAAQRAIAAGMNTDVYFQVAEEAD-- 83 
                                       66789********************************************************************99.. PP

                                       CSSS-EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHH CS
                         Trp_syntA  85 evevPivlltylnlvlsygeerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkevve 161
                                        v vP v+++y+n+v+++g erf ++++  g++g+ivpDlP+eea++l+ea+ k+g++l+ lvap+t+ +r++ ++e
  gi|330507792|ref|YP_004384220.1|  84 -VPVPKVFMGYYNMVYARGLERFARDCARCGITGMIVPDLPPEEAAPLKEACGKHGVDLIYLVAPNTPPARIDLIAE 159
                                       .**************************************************************************** PP

                                       H--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHC.T CS
                         Trp_syntA 162 qaegfvYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkkiee.e 236
                                       ++ gf Y+v+r+GvTga+++v +++ +l+ r+     +P+avGFGist++q+++v+ ++ad++ivGSa v+ i++ +
  gi|330507792|ref|YP_004384220.1| 160 ETGGFLYLVARTGVTGARSEVLQDTRDLILRVPGK--KPKAVGFGISTPDQAAEVIrAGADAAIVGSACVDLIARgR 234
                                       *****************************999876..5******************9****************9643 PP

                                       TTSHHHHHHHHHH CS
                         Trp_syntA 237 aeekeqaleklee 249
                                       ++e e+ + ++++
  gi|330507792|ref|YP_004384220.1| 235 IDELEALVGEMKK 247
                                       4444444433333 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.7   6.2e+03     176     194 ..      68      86 ..      66      86 .. 0.84
   2 !   18.3   0.1   3.6e-07    0.0013      62     107 ..     185     228 ..     167     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.7
                                       S---HHHHHHHHHHHSSEE CS
                      His_biosynth 176 sGpdleltkelaeavkipv 194
                                       +G++ +++ ++ae+ ++pv
  gi|330507792|ref|YP_004384220.1|  68 AGMNTDVYFQVAEEADVPV 86 
                                       6899999999999999987 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3.6e-07
                                       HHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
                      His_biosynth  62 ldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavk 107
                                        dl+ ++  +   p  vG GI++ ++++e+++agad  i+g+a v+
  gi|330507792|ref|YP_004384220.1| 185 RDLILRVPGK--KPKAVGFGISTPDQAAEVIRAGADAAIVGSACVD 228
                                       5677777777..8899***************************986 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      0.55     2e+03     155     172 ..      27      44 ..      25      48 .. 0.61
   2 ?   11.9   0.1   2.6e-05     0.095     153     177 ..     203     227 ..     190     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.55
                                       SHHHHHHHHTT--SEEEE CS
                              NanE 155 tPekakkaieiGvdavvv 172
                                       tPe+ ++ ++ G+d + +
  gi|330507792|ref|YP_004384220.1|  27 TPELVRRLVRAGADIIEL 44 
                                       566666666666665554 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.6e-05
                                       --SHHHHHHHHTT--SEEEE-HHHH CS
                              NanE 153 intPekakkaieiGvdavvvGsait 177
                                       i tP++a+++i+ G+da +vGsa  
  gi|330507792|ref|YP_004384220.1| 203 ISTPDQAAEVIRAGADAAIVGSACV 227
                                       78********************965 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.48   1.7e+03      10      36 ..      18      44 ..      13      48 .. 0.78
   2 ?   11.5   0.0   4.1e-05      0.15     182     211 ..     196     226 ..     164     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.48
                                      EEE-TTSS-CHHHHHHHHCTT-SEEEE CS
                              PcrB 10 tklDPeeenpdEiveiviesgtDavmi 36
                                         DP    + E v+ +++ g+D + +
  gi|330507792|ref|YP_004384220.1| 18 CSGDPSPGATPELVRRLVRAGADIIEL 44
                                      555888888899999999999998765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.1e-05
                                       EEEEESS--SHHHHHHHHCC.SSEEEE-CHH CS
                              PcrB 182 rlivGGGirsaEkAkevvea.ADvivvGnvv 211
                                          vG Gi  +++A+ev++a AD+ +vG + 
  gi|330507792|ref|YP_004384220.1| 196 PKAVGFGISTPDQAAEVIRAgADAAIVGSAC 226
                                       456999**********************875 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0015       5.4      86     115 ..      24      52 ..       8     101 .. 0.78
   2 ?    3.0   0.0     0.032   1.1e+02      41     102 ..     105     166 ..      96     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0015
                                       SSCHGHHHHHHHHHTT-SEEEEEEBSSSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  86 gtlpdeeklerllelgvdrvslgleaadde 115
                                       ++   +e ++rl+++g d ++lgl + d+ 
  gi|330507792|ref|YP_004384220.1|  24 PGAT-PELVRRLVRAGADIIELGLPHSDPI 52 
                                       3333.9*********************997 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.032
                                       HHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT....- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                       Radical_SAM  41 lkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelg....v 102
                                       + a++ ++  i g+  p+l p+++  l++++ +   g+ + + + + +p +  +++++e       
  gi|330507792|ref|YP_004384220.1| 105 F-ARDCARCGITGMIVPDLPPEEAAPLKEACGK--HGVDLIYLVAPNTP-PARIDLIAEETggflY 166
                                       4.344477778888899999999999*****99..69999888888888.9999999987733333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); 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:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1807.90
//
Query:       gi|330507793|ref|YP_004384221.1|  [L=393]
Description: tryptophan synthase subunit beta [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-38  132.6   0.2    2.5e-38  132.2   0.2    1.2  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 !  132.2   0.2   1.4e-42   2.5e-38       4     293 ..      53     377 ..      50     378 .. 0.83

  Alignments for each domain:
  == domain 1  score: 132.2 bits;  conditional E-value: 1.4e-42
                                       CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                              PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlk 80 
                                       + +pT l  +p+ls++lg++++lK+E+l ++g++K++      + +k+  +++ ++e+++G+hg+a+A+++a+lG++
  gi|330507793|ref|YP_004384221.1|  53 AGRPTSLYLAPNLSRKLGCRVYLKREDLMHGGAHKLNNTLGQALVAKNMGKTRLIAETGAGQHGVATAIVGAKLGFE 129
                                       679*************************************77777666669999999999***************** PP

                                       EEEEEETTS-...HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHH......STTCEE--TTT.......SHH... CS
                              PALP  81 vtivvpadas...pekvallrllGaevvevggdydeavaaaaelaae......gegaylvsqfd.......npt... 138
                                         +++ + +    + +v +++l+Gaev+ v ++  + ++a++e++++              ++        +p    
  gi|330507793|ref|YP_004384221.1| 130 TQVYMGEVDIerqKMNVYRMELMGAEVIPVRSGSRTLKDAINEALRDwassfeH------THYLlgtaagaHPFpsm 200
                                       ****99999955569***************999888888888888885555442......33333222456444554 PP

                                       HHHHHHTHHHHHH....HHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEEC.TTCGGTTCC.S..S.SS CS
                              PALP 139 viegygtiglEil....eqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepe.gsdalarsl.ragrrvt 209
                                       v + ++ ig+E      e  g+ pd +v++vGgG++++Gi +++ +   dvr+i+ve+  + + + + + ++g  + 
  gi|330507793|ref|YP_004384221.1| 201 VRDFQSVIGQEAReqilEAEGRLPDSIVACVGGGSNAMGIFTPFLK--DDVRLIAVEAGgRGPGMSDKMaDNGASLG 275
                                       6666********844446666************************8..68*********878888888855555555 PP

                                       ..B......................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-H CS
                              PALP 210 vpvs.....................dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvep 265
                                       + +                       + a gl+ + ++++   l+++        +d +ale+ r l r egi++  
  gi|330507793|ref|YP_004384221.1| 276 YGTDgilhgaltkilqdpygqilesYSVAAGLDYPGVGPELAFLAEKGRVLPRLADDRTALEGFRALSRLEGIIPAL 352
                                       55558999999999999**999999999*******6665555588787778999*********************** PP

                                       HHHHHHHHHHHHHHHCCTTCEEEEEEE- CS
                              PALP 266 ssaaalaalklreagelkegdrvvvilt 293
                                        sa+a+  + lre ++l++   v++ ++
  gi|330507793|ref|YP_004384221.1| 353 ESAHAIGYA-LREPESLGDL--VIINVS 377
                                       *******99.9999998877..665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2853.68
//
Query:       gi|330507794|ref|YP_004384222.1|  [L=69]
Description: exodeoxyribonuclease VII, small subunit [Methanosaeta concilii GP6]
Scores for complete 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-18   65.6   5.1    4.6e-18   65.0   5.1    1.1  1  Exonuc_VII_S  Exonuclease VII small subunit
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.14   12.4   0.0    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 !   65.0   5.1   5.1e-22   4.6e-18       2      51 ..       9      58 ..       9      58 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 5.1e-22
                      Exonuc_VII_S  2 EealaeLeeIvekLEsgelsLeeslklyeeGvkLlkeCekkLdeaeqkve 51
                                      E+al+eLe Iv++LE+g++sLe+sl+lye+G++L++ C+ +Ld a++++e
  gi|330507794|ref|YP_004384222.1|  9 EDALEELERIVSELEEGKMSLEKSLELYERGMRLVRVCNLRLDSAQRRIE 58
                                      89**********************************************97 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.6e-05      0.14      38      78 ..      24      64 ..       7      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                              KxDL 38 lsqerlaklrarfkqgtkllkevkkdLesifkkirslkakl 78
                                      + +  l+k  + +++g++l++  +  L+s +++i+ l+ +l
  gi|330507794|ref|YP_004384222.1| 24 EGKMSLEKSLELYERGMRLVRVCNLRLDSAQRRIECLTGEL 64
                                      3455899999*************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 488.28
//
Query:       gi|330507795|ref|YP_004384223.1|  [L=401]
Description: exodeoxyribonuclease VII, large subunit [Methanosaeta concilii GP6]
Scores for complete 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-79  265.8   0.0    2.9e-71  240.5   0.2    2.1  2  Exonuc_VII_L     Exonuclease VII, large subunit
      1e-26   92.9   0.0    1.8e-26   92.2   0.0    1.4  1  tRNA_anti_2      OB-fold nucleic acid binding domain
    3.6e-06   26.9   0.0      1e-05   25.4   0.0    1.8  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.004   17.2   0.0     0.0079   16.2   0.0    1.4  1  DUF4539          Domain of unknown function (DUF4539)


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 !  240.5   0.2   6.4e-75   2.9e-71       1     217 [.     124     338 ..     124     339 .. 0.95
   2 !   29.6   0.0   1.1e-10     5e-07     240     302 ..     326     387 ..     320     389 .. 0.90

  Alignments for each domain:
  == domain 1  score: 240.5 bits;  conditional E-value: 6.4e-75
                      Exonuc_VII_L   1 lfdeerkkplpklpkrigvvtsptgaairDilrtlkrrgplveillfpalvQGeeaaaeiikalekanalkeaDvli 77 
                                       lfd+e+k+plp +p+rig+vts +gaa+rD++rt+  +    +i++ pa+vQGe+a+++i++al +++   + D++i
  gi|330507795|ref|YP_004384223.1| 124 LFDQEQKRPLPLYPERIGIVTSLQGAALRDVVRTIGPYPA--RIIISPARVQGEKAEESIVSALLALQ--GRTDLII 196
                                       8***********************************9877..**********************6665..6679*** PP

                      Exonuc_VII_L  78 iaRGGGSleDLwaFndeelaraiaaskiPvisavGHEtDttiaDfvAdlrapTPtaaAelvvpdkaeleeqleeler 154
                                       ++RGGGS eDLw+Fn+e +ara++a+  PvisavGHEtD+ti+Df+Ad+ra+TPtaaA+++vpd a+l+ +le+ + 
  gi|330507795|ref|YP_004384223.1| 197 VCRGGGSAEDLWCFNSEVVARAVFACDSPVISAVGHETDVTITDFAADMRAATPTAAAKIAVPDVADLKIRLEQSQV 273
                                       ***************************************************************************** PP

                      Exonuc_VII_L 155 rlekaikrlleekkqrleklasrl..kspeellerkrqrldeleerleralkkqlkkkrerleel 217
                                       r+ +a+ + le+k++rle ++++l  ++  +++ + rqrld+l++ l+ a+++ lk++++rl+ +
  gi|330507795|ref|YP_004384223.1| 274 RIMRALWTSLERKEERLEYIQRSLspSRMYSITGDLRQRLDHLSDGLDLAQAEMLKARKTRLDAA 338
                                       ************************533666688888*************99999***99999876 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1.1e-10
                      Exonuc_VII_L 240 elleekkerleeleeklealsplkvLkrGyaivrkedgkvvtsakdlkkgdeleirladgevk 302
                                       e+l+++k+rl++++ kl+a++p+++L+rGya+vr+ ++ +v   +d+ +g+e+e+ l +g ++
  gi|330507795|ref|YP_004384223.1| 326 EMLKARKTRLDAAKGKLAAVGPRATLQRGYALVRS-KKGLVVAWDDVLPGEEVELILGRGALR 387
                                       47999*****************************8.5889999*************9999876 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.0     4e-30   1.8e-26       1      94 [.       5      99 ..       5     100 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 4e-30
                       tRNA_anti_2  1 lsVseltraikell..eaelkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgr 77
                                      ++V++l+++i+e+l  +++l++ +w +Ge+sn+ +++sgh+YftLkD +++is+v+f+++  +++++l++Gm+Vl+ g 
  gi|330507795|ref|YP_004384223.1|  5 FTVTNLNERIRERLenDPRLHD-LWAQGEVSNFVHHRSGHMYFTLKDRDSQISCVLFKGNIGQVETELRNGMNVLLFGD 82
                                      79************98899966.**********7677****************************************** PP

                       tRNA_anti_2 78 lsvYeprGsyqlivedi 94
                                      ++vY p+G++ql+++ i
  gi|330507795|ref|YP_004384223.1| 83 VAVYRPQGRVQLVARAI 99
                                      **************988 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   2.3e-09     1e-05       4      73 ..      30      99 ..      27     101 .. 0.90
   2 ?   -3.3   0.0       2.1   9.3e+03      37      60 ..     288     311 ..     265     317 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.3e-09
                                      EEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEEC..TTSSEEEEEEEE CS
                   tRNA_anti-codon  4 aGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrr..pggelelkveei 73
                                      +G+v++    + +++++++l+D+  +i +vlf+++  ++  +l++G+ v  +G v  +  +g+ ++l++  i
  gi|330507795|ref|YP_004384223.1| 30 QGEVSNFV-HHRSGHMYFTLKDRDSQISCVLFKGNIGQVETELRNGMNVLLFGDVAVYrpQGR-VQLVARAI 99
                                      68888885.77899********************************************96666.***99877 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                                       HHHHHHHTTS-TTSEEEEEEEEEE CS
                   tRNA_anti-codon  37 eeatklaenlkeGdvvrvtGrvkr 60 
                                       e  ++++ +l +   + +tG ++ 
  gi|330507795|ref|YP_004384223.1| 288 ERLEYIQRSLSPSRMYSITGDLRQ 311
                                       445566667777777778887765 PP

>> DUF4539  Domain of unknown function (DUF4539)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.8e-06    0.0079      16      68 ..      38      91 ..      31      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-06
                           DUF4539 16 lnslgdalvtlkDptGeidgtihrkvleeygkdlsvGa.vllLkqVsvfspsrr 68
                                      ++++g +  tlkD   +i +++ +  + + + +l+ G+ vll  +V+v++p+ r
  gi|330507795|ref|YP_004384223.1| 38 HHRSGHMYFTLKDRDSQISCVLFKGNIGQVETELRNGMnVLLFGDVAVYRPQGR 91
                                      5666789******************************8466667******9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2847.81
//
Query:       gi|330507796|ref|YP_004384224.1|  [L=228]
Description: cobalamin biosynthesis protein CbiM [Methanosaeta concilii GP6]
Scores for complete 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-54  184.4  21.5    2.6e-54  184.2  21.5    1.0  1  CbiM      Cobalt uptake substrate-specific transmembrane regi
  ------ inclusion threshold ------
       0.17   12.4   0.3       0.17   12.4   0.3    2.2  2  DUF4231   Protein of unknown function (DUF4231)


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 !  184.2  21.5   2.9e-58   2.6e-54       4     206 ..       2     207 ..       1     208 [. 0.96

  Alignments for each domain:
  == domain 1  score: 184.2 bits;  conditional E-value: 2.9e-58
                              CbiM   4 dgiLspavllaayavalallalalrrlrkeldear..vpllallaafifaaqminipipggtslHllgavlaaiLlG 78 
                                       +g+L+ +++ ++++++l+++a+++++++k ++e+r  +plla+ +af+f+++++++p  +g+++H++g+++ aiL+G
  gi|330507796|ref|YP_004384224.1|   2 EGFLPHPWWEIWLIISLPVVAWGVYKMNKMVKENReiLPLLAVSGAFVFVLSSLKMPSVTGSCSHPTGTGMGAILFG 78 
                                       8*******************************88889**************************************** PP

                              CbiM  79 pwaaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaall 155
                                       pw++++  a+vl+ qal++++GG+t+LGaNi++m+++g+l++ylv+  l ++  s  ++ l++flaa+l+ + ++++
  gi|330507796|ref|YP_004384224.1|  79 PWITAVLSAIVLIYQALFLAHGGLTTLGANIFSMGIAGPLIGYLVFV-LAKR--SGLNMYLSVFLAAMLADWTTYVV 152
                                       ***********************************************.6666..789******************** PP

                              CbiM 156 valelalsgleas....lsltaalaamllvhlpvgilEgviTaaivkalkkvrpe 206
                                       ++++lal+  +as    +s++a++a+++++++p++++Eg++Ta+++k+l ++r +
  gi|330507796|ref|YP_004384224.1| 153 TSMQLALAFPAASggvvASFQAFMAIFAITQVPLAVVEGAVTALMFKYLVRLRGD 207
                                       ********6666689999*********************************9976 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   1.9e-05      0.17       8      64 ..      26      96 ..      20      99 .. 0.85
   2 ?   -0.2   1.5      0.16   1.4e+03      19      61 ..     154     173 ..     129     200 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                           DUF4231  8 kkasrakrrfrllrlitivlgallpilvs..............sklgagvsvlkiltallsalvailaale 64
                                       k++++++  r +  +++v ga++ +l+s              ++ +    + +++ta+lsa+v i +al 
  gi|330507796|ref|YP_004384224.1| 26 YKMNKMVKENREILPLLAVSGAFVFVLSSlkmpsvtgscshptGTGMGAILFGPWITAVLSAIVLIYQALF 96
                                      577777777777777899999999999999**********9997778889999*************99985 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.16
                           DUF4231  19 llrlitivlgallpilvssklgagvsvlkiltallsalvaila 61 
                                       +++l++++ +a   +++s                        +
  gi|330507796|ref|YP_004384224.1| 154 SMQLALAFPAASGGVVAS-----------------------FQ 173
                                       222222222222222222.......................22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1619.70
//
Query:       gi|330507797|ref|YP_004384225.1|  [L=107]
Description: cobalt transport protein [Methanosaeta concilii GP6]
Scores for complete 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   91.8   0.5    2.5e-26   91.5   0.5    1.1  1  CbiN      Cobalt transport protein component CbiN
  ------ inclusion threshold ------
       0.12   12.3   0.2       0.13   12.2   0.2    1.2  1  PgpA      Phosphatidylglycerophosphatase A
       0.38   10.7   1.2       0.58   10.1   1.2    1.3  1  PsbI      Photosystem II reaction centre I protein (PSII 4.8 


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 !   91.5   0.5   4.1e-30   2.5e-26       3      67 .]       5      73 ..       3      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 4.1e-30
                              CbiN  3 lllllvvllavvplflv...kgaeFgGaDdqaeevIeei.apdyepwfeplweppsGEiESlLFalQAA 67
                                      +++l+vv+l+ + ++++    ++e++GaDdq e+vI e+ +  yepw +plweppsGEiESlLFalQAA
  gi|330507797|ref|YP_004384225.1|  5 IIVLVVVALFTAIFVYQstsGEHEWAGADDQSEKVIDELtGGTYEPWSSPLWEPPSGEIESLLFALQAA 73
                                      6899999********997655556***************999**************************8 PP

>> PgpA  Phosphatidylglycerophosphatase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   2.2e-05      0.13      41      79 ..       5      46 ..       1      85 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                                      HHHHHHHHHHHHHHHHHHHHT-S-...HHT-TT--HHHHTTH CS
                              PgpA 41 llllilllflvGiwackktekelg...ekDpgeiviDEvvgq 79
                                      +++l++++++++i++ ++t+ e +    +D++e viDE+ g 
  gi|330507797|ref|YP_004384225.1|  5 IIVLVVVALFTAIFVYQSTSGEHEwagADDQSEKVIDELTGG 46
                                      4568888999999999888876655669***********995 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 ?   10.1   1.2   9.7e-05      0.58       4      21 ..       3      20 ..       1      25 [. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.7e-05
                              PsbI  4 LKivVyivViffvslFvF 21
                                      L i+V +vV++f ++Fv+
  gi|330507797|ref|YP_004384225.1|  3 LEIIVLVVVALFTAIFVY 20
                                      779*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 776.31
//
Query:       gi|330507798|ref|YP_004384226.1|  [L=264]
Description: cobalt ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete 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  126.0  12.7    2.3e-36  125.5  12.7    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 !  125.5  12.7   1.3e-40   2.3e-36       6     211 ..      15     221 ..      10     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 125.5 bits;  conditional E-value: 1.3e-40
                                       CS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---..HHHHHHHCCCHCHHHHHHHHHHE....... CS
                              CbiQ   6 hrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp..rvlaqalilpllflllgllillfqlitteg 80 
                                       ++ ++ +kl+  +  +++ v + ++ ++++++a + l++l+ ++   r++++ l lpl f ll+  ++++  +  +g
  gi|330507798|ref|YP_004384226.1|  15 RETSAHLKLFLGLGAIIICVSSVTPPAPVFVAASMSLIILILAKIpiRIYSRLLLLPLSFALLSSTVVAL--MHGSG 89 
                                       55666667766666666666666666666666666555555554445***************99999999..89999 PP

                                       EECTTEEE......E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHH CS
                              CbiQ  81 efvfaggg...qisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLl 154
                                       e++++      +i+i  +G   +lll  R++  ++ l+++alTTp++e+++ l++l++P+ ++++ + +yR+if++l
  gi|330507798|ref|YP_004384226.1|  90 EMLYSMQLfglEIGIRVDGAALALLLIARTFGGMCSLFFIALTTPMIEIFAVLKSLRIPESVIELSMMIYRYIFVFL 166
                                       999987766799***************************************************************** PP

                                       HHHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                              CbiQ 155 eevqrikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                       + +  i+ Aq +Rlgd   g r+sl+s  +l+  lflr+++++er+  Am+aR+Y+g
  gi|330507798|ref|YP_004384226.1| 167 DQAAMIHSAQVMRLGDL--GTRSSLNSFSMLASVLFLRSWEQGERLIVAMDARCYDG 221
                                       *****************..*************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1687.33
//
Query:       gi|330507799|ref|YP_004384227.1|  [L=407]
Description: cobalt import ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-31  107.8   0.0    1.3e-30  106.7   0.0    1.6  2  ABC_tran     ABC transporter
    1.3e-16   61.3   0.1    2.7e-11   43.8   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.7e-07   30.9   0.0    0.00063   19.2   0.0    2.3  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0013   18.6   0.0     0.0023   17.8   0.0    1.3  1  MukB         MukB N-terminal
     0.0023   17.6   0.0     0.0054   16.4   0.0    1.6  1  AAA_29       P-loop containing region of AAA domain
     0.0031   17.3   0.0      0.038   13.7   0.0    2.0  2  AAA_15       AAA ATPase domain
  ------ inclusion threshold ------
      0.017   15.4   0.0      0.062   13.6   0.0    2.0  1  AAA_22       AAA domain
      0.017   15.3   0.1       0.24   11.7   0.1    2.4  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.028   14.9   0.0      0.048   14.2   0.0    1.4  1  AAA_23       AAA domain
      0.029   14.1   0.0      0.054   13.2   0.0    1.4  1  AAA_24       AAA domain
      0.049   14.0   0.0      0.091   13.1   0.0    1.6  1  AAA_16       AAA ATPase domain
       0.17   11.8   0.0       0.36   10.7   0.0    1.5  1  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7   0.0   8.9e-34   1.3e-30       1     137 []      21     169 ..      21     169 .. 0.94
   2 ?   -3.3   0.0       8.2   1.2e+04      22      42 ..     349     369 ..     349     384 .. 0.58

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 8.9e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe..pqlfpe 73 
                                       l+nvsl++ eg+k+a+vG+nGaGKStL+ ++ g l+p++Ge+l++++ l++  ++l+++r+++g+++q+  +qlf  
  gi|330507799|ref|YP_004384227.1|  21 LSNVSLTIGEGRKIALVGPNGAGKSTLMLMFNGILRPDAGEVLFRNERLDYdsRSLRKVRQRVGMVFQNsdDQLFAP 97 
                                       78************************************************998999*************99999999 PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       + v++              + ++ +  al+ +gl++ + ++     ++LSgG+k+r a+a +l+ +p++++lDEpt+
  gi|330507799|ref|YP_004384227.1|  98 T-VYQDvafgpvnlrfppeKVKRYVGYALQYVGLSGYERRPP----HHLSGGEKKRAAIAGILAMEPEVMILDEPTS 169
                                       9.66666**********9777777************999998....*****************************96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.2
                                       SSHHHHHHHHTTSS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  22 aGKStLlkllagllkpteGei 42 
                                       aGKS L+ +  g++ + + +i
  gi|330507799|ref|YP_004384227.1| 349 AGKSCLVLTSQGMMGQVQKRI 369
                                       677777766555554444444 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   7.7e-06     0.011       3      24 ..      35      56 ..      34      80 .. 0.75
   2 !   43.8   0.0   1.8e-14   2.7e-11     226     299 ..     130     200 ..      57     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.7e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                      +l+GpNg+GKS+L+  + ++ r
  gi|330507799|ref|YP_004384227.1| 35 ALVGPNGAGKSTLMLMFNGILR 56
                                      79***********999877765 PP

  == domain 2  score: 43.8 bits;  conditional E-value: 1.8e-14
                            AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                        +++  +p+++lS G k+ +a++ +l+  +    + ++DEp ++L+P+  ++++e+l+el+ +g  +i++TH+ 
  gi|330507799|ref|YP_004384227.1| 130 LSGYERRPPHHLSGGEKKRAAIAGILAMEP---EVMILDEPTSNLDPATSEEIMEMLDELNLGGKTLIISTHDV 200
                                       5677889************99999999988...9**************************************95 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00036      0.53      27      41 ..      34      48 ..      19     100 .. 0.80
   2 !   19.2   0.0   4.2e-07   0.00063     136     199 ..     140     199 ..      62     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00036
                                      EEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnll 41
                                       a+vGpNG+GKs l+
  gi|330507799|ref|YP_004384227.1| 34 IALVGPNGAGKSTLM 48
                                      689*********997 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 4.2e-07
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                        LSgGek+ +a+a ++A++   p+ +++lDe  ++LD +  +++ e+l+e +     ++is ++
  gi|330507799|ref|YP_004384227.1| 140 HLSGGEKKRAAIAGILAME---PE-VMILDEPTSNLDPATSEEIMEMLDELNLGGKTLIISTHD 199
                                       7************999975...54.679**********************99987777777654 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.5e-06    0.0023      30      62 ..      35      67 ..      31      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-06
                                      HHHS--SHHHHHHHHHHHHHHS--TTT------ CS
                              MukB 30 tlsGgnGaGksttmaafvtaliPdlsllhfrnt 62
                                      +l G nGaGkst m  f  +l Pd   + frn 
  gi|330507799|ref|YP_004384227.1| 35 ALVGPNGAGKSTLMLMFNGILRPDAGEVLFRNE 67
                                      799****************************95 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.6e-06    0.0054      17      39 ..      26      48 ..      19      64 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.6e-06
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTll 39
                                      ++i + g  + l+Gp+G+GKSTl+
  gi|330507799|ref|YP_004384227.1| 26 LTIGE-GrKIALVGPNGAGKSTLM 48
                                      55553.44899************8 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   2.6e-05     0.038      12      48 ..      19      56 ..      19      95 .. 0.83
   2 ?    1.3   0.0      0.15   2.2e+02     325     365 ..     160     199 ..     156     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                            AAA_15 12 Rslkdveidlsee.ltvliGkNnsGKSsilealdlFln 48
                                      R+l++v++ + e     l+G+N++GKS+++ +++ +l 
  gi|330507799|ref|YP_004384227.1| 19 RALSNVSLTIGEGrKIALVGPNGAGKSTLMLMFNGILR 56
                                      8899999999999999*************999876666 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                            AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                        + +++EP  +L p   +++++ l el   +k  +ii+TH 
  gi|330507799|ref|YP_004384227.1| 160 EVMILDEPTSNLDPATSEEIMEMLDELNLGGK-TLIISTHD 199
                                       56789**********************99999.9******6 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.2e-05     0.062       8     111 ..      34     185 ..      28     209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskdllrellralglelka............ 70 
                                       ++++G+ G+GK+tl+ ++   l  +++a e   r e + ++  s+ + ++   +++++ +++l a            
  gi|330507799|ref|YP_004384227.1|  34 IALVGPNGAGKSTLMLMFNGIL--RPDAGEvlFRNERLDYDSRSLRKVRQRVGMVFQNSDDQLFAptvyqdvafgpv 108
                                       899***************9999..55555577888888888888888888888888888888888888888888888 PP

                            AAA_22  71 .........................erlsseell.ealeqalrarav...ielliiDEaqh.lr...s...eealee 111
                                                                er   ++l      +a+ a      +e++i+DE    l+   s   +e+l e
  gi|330507799|ref|YP_004384227.1| 109 nlrfppekvkryvgyalqyvglsgyERRPPHHLSgGEKKRAAIAGILamePEVMILDEPTSnLDpatSeeiMEMLDE 185
                                       88887777777777777777766664444444444333333333333466777777777666766543334444444 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   0.00016      0.24      31      89 ..     139     184 ..     115     185 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                           SbcCD_C  31 gtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                         lSGGek         aa+a  +         +++++LDE  s+lD+ ++++++e+l+
  gi|330507799|ref|YP_004384227.1| 139 HHLSGGEK-------KRAAIAGILAM------EPEVMILDEPTSNLDPATSEEIMEMLD 184
                                       55666666.......22333333333......4789********************986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.2e-05     0.048      23      37 ..      35      49 ..      17     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-05
                            AAA_23 23 lItGpNGaGKTTild 37
                                      +++GpNGaGK+T++ 
  gi|330507799|ref|YP_004384227.1| 35 ALVGPNGAGKSTLML 49
                                      789**********85 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.6e-05     0.054       2      24 ..      31      52 ..      30      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                            AAA_24  2 klkiliyGpsgiGKTtlakelgp 24
                                      ++ki+++Gp+g+GK+tl++++ +
  gi|330507799|ref|YP_004384227.1| 31 GRKIALVGPNGAGKSTLMLMF-N 52
                                      689***************999.3 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   6.1e-05     0.091      20      63 ..      27      72 ..      18     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.1e-05
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekd..ggiflrgkcdql 63
                                        g+++ + l+G+ G GKs+l+ ++   l+ d  +++f +++ d  
  gi|330507799|ref|YP_004384227.1| 27 TIGEGRKIALVGPNGAGKSTLMLMFNGILRPDagEVLFRNERLDYD 72
                                      457778899*************999988887764366655555555 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   0.00024      0.36      99     121 ..      30      53 ..       4      71 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                                       T.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallp 121
                                       + + ++lvG+ G+GKStL+ ++++
  gi|330507799|ref|YP_004384227.1|  30 EgRKIALVGPNGAGKSTLMLMFNG 53 
                                       448899************976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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 0.31s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2731.12
//
Query:       gi|330507800|ref|YP_004384228.1|  [L=279]
Description: hypothetical protein MCON_1809 [Methanosaeta concilii GP6]
Scores for complete 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-17   61.2   1.8    1.2e-16   60.6   1.8    1.3  1  AIRC      AIR carboxylase
     0.0053   16.6   0.1      0.011   15.6   0.1    1.5  1  VbhA      Antitoxin VbhA
  ------ inclusion threshold ------
       0.12   12.4   0.0        0.2   11.7   0.0    1.3  1  DUF2089   Protein of unknown function (DUF2089)


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 !   60.6   1.8     2e-20   1.2e-16       1     133 [.     144     275 ..     144     279 .] 0.87

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 2e-20
                                       EEEEEESSGGGHHHHHHHHHHHHHTT-....EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHH CS
                              AIRC   1 kVgiimGSdsDlevmkkaaeilkelgv....eyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvva 73 
                                       +V+i+ + + D++v+++a  + +e+g     ey+v v+  hr    l+++a+       ++++++AG++  Lp vva
  gi|330507800|ref|YP_004384228.1| 144 RVAILAAGTADIPVAEEARVVAEEMGCqvlrEYDVGVAGIHRLFPCLERMAD------ADAFVVAAGREGTLPAVVA 214
                                       599*********************999788889********98777776665......578**************** PP

                                       HHSSS-EEEEEE--S...TTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT-HH CS
                              AIRC  74 slttlPVigvPvksk...alkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkdee 133
                                       +l++ PVig Pv++       g  +l+S++q +s ++v++v+   +  A+ +Aa+i   k ++
  gi|330507800|ref|YP_004384228.1| 215 GLVNAPVIGLPVSTGygiGGGGKAALYSMLQSCSVLTVVNVD--AGFVAGAYAAKIARQKAHK 275
                                       *************95222468899**************9999..8899999999998776654 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.8e-06     0.011      23      47 .]      25      49 ..      23      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-06
                              VbhA 23 tvadleayvrGeIdadElvrrvraR 47
                                       ++ le y rGeI+++E+++++r R
  gi|330507800|ref|YP_004384228.1| 25 NREILESYRRGEISLEEALKQIRVR 49
                                      5899*****************9987 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.4e-05       0.2      88     114 .]      21      47 ..       9      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                           DUF2089  88 eeeerkeileklekgeisveeAlerLk 114
                                       + e+++eile+ ++geis+eeAl++++
  gi|330507800|ref|YP_004384228.1|  21 KMESNREILESYRRGEISLEEALKQIR 47 
                                       346799******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2084.96
//
Query:       gi|330507801|ref|YP_004384229.1|  [L=405]
Description: hypothetical protein MCON_1810 [Methanosaeta concilii GP6]
Scores for complete 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-05   22.9   0.0        0.2   11.9   0.0    2.4  2  PHP        PHP domain
  ------ inclusion threshold ------
      0.035   13.8   0.0      0.085   12.6   0.0    1.6  1  PHP_C      PHP-associated
       0.23   10.5   0.3       0.35    9.9   0.3    1.2  1  Tmemb_55A  Transmembrane protein 55A


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 !   11.9   0.0   3.3e-05       0.2       1      34 [.       6      40 ..       6      91 .. 0.93
   2 !    9.1   0.0   0.00025       1.5      15      65 ..     120     171 ..     107     375 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.3e-05
                                      EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEE CS
                                      xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteys.lldgalsieelvkkakelglkaiai 34
                                      dlH+H+ ys +++g +++ +++k a+ +g k ++ 
  gi|330507801|ref|YP_004384229.1|  6 DLHIHSRYSmAVSGDMELGQIAKGAAHKGVKIVGT 40
                                      89********999****************998875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00025
                                       H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEE.EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                               PHP  15 lsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpi.iGle 65 
                                       ++i +lv +a+ l  +a a+T   ++++y +  +++ ++++++i+ i +Gl 
  gi|330507801|ref|YP_004384229.1| 120 AQIADLVFEAEGLIGPAHAFTPWTGMYAYHRSLSECYQEKADRIRFIeLGLS 171
                                       34799999****************************8888888887644555 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.4e-05     0.085       7      28 ..     177     198 ..     173     206 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                             PHP_C   7 ArrfAeklglpgtgGSDAHrle 28 
                                       A+r+Ae  ++ ++ +SDAH+++
  gi|330507801|ref|YP_004384229.1| 177 ADRIAELSDKTFLSNSDAHSPR 198
                                       99*****************997 PP

>> Tmemb_55A  Transmembrane protein 55A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.3   5.8e-05      0.35     146     178 ..     244     276 ..     217     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 5.8e-05
                         Tmemb_55A 146 gvrviCghCkntflftelsrtlarCPhCrkvss 178
                                         r  C+ C + f  +e++  + rC hC+ +  
  gi|330507801|ref|YP_004384229.1| 244 YNRTACTRCFHHFSAKEMNDLMGRCSHCQGLIK 276
                                       57999***********************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.21s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3124.13
//
Query:       gi|330507802|ref|YP_004384230.1|  [L=288]
Description: hypothetical protein MCON_1811 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2381.40
//
Query:       gi|330507803|ref|YP_004384231.1|  [L=618]
Description: glycosyl transferase, group 2 family protein [Methanosaeta concilii GP6]
Scores for complete 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-52  176.5   0.6    7.3e-28   97.5   0.1    2.4  2  Glycos_transf_2  Glycosyl transferase family 2
    2.4e-27   96.3   0.0    1.6e-13   51.1   0.0    2.7  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    8.2e-20   71.4   5.1    3.2e-09   36.6   0.3    3.8  3  Glyco_tranf_2_2  Glycosyltransferase like family 2
    3.1e-11   43.6   0.1    6.6e-05   22.9   0.0    2.6  2  Glyco_trans_2_3  Glycosyl transferase family group 2
    3.8e-07   30.0   0.2    2.7e-06   27.2   0.0    2.3  2  Glyco_tranf_2_5  Glycosyltransferase like family
      0.001   18.7   0.0     0.0068   16.0   0.0    2.2  2  Glyco_transf_7C  N-terminal domain of galactosyltransferase
     0.0015   18.0   0.0      0.043   13.3   0.0    2.5  2  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
       0.06   12.1   0.1        1.4    7.6   0.0    2.1  2  GNT-I            GNT-I family


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   0.1   3.2e-31   7.3e-28       1     169 [.      96     256 ..      96     257 .. 0.87
   2 !   77.2   0.1   5.5e-25   1.2e-21       1     169 [.     350     526 ..     350     527 .. 0.95

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 3.2e-31
                                       EEEEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-.SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNe.ektlletlesllaqdpypdfeiivvDDgS.tDetveileelakedprvrvirreenvGkagalnagl 75 
                                       s+++p+ N  e+ l+ ++es+l q  y+++e++++DDgS + + +e l  ++++d r++v  ++en+G +ga n++l
  gi|330507803|ref|YP_004384231.1|  96 SIIVPVLNTrEEWLRSSIESVLHQ-IYDNWELCIADDGSdQPHIKETLNCYQQKDARIKVKYLNENQGVSGASNEAL 171
                                       8***********************.**************************************************** PP

                                       HH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCST CS
                   Glycos_transf_2  76 raatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnls 152
                                       ++a+g++i flD Dd+  p+ l ++v  l++ +a   +  ++  +    ++ ++         yf+     ++  ++
  gi|330507803|ref|YP_004384231.1| 172 AMASGEFIGFLDHDDQLLPNALYEVVLMLNR-NA--SADFIYSDEILISKRGKP------VFAYFRPDFSLDYMLSH 239
                                       *******************************.77..444444444444444443......34566666666677888 PP

                                       TCSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 153 feigsaallrrealeel 169
                                       ++i ++ ++r ++l+++
  gi|330507803|ref|YP_004384231.1| 240 CYIVHFVVIRASILKKI 256
                                       88999999999988886 PP

  == domain 2  score: 77.2 bits;  conditional E-value: 5.5e-25
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-.SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgS.tDetveileelakedprvrvirreenvGkagalnaglr 76 
                                       s++ipt  + ++l++++es+ ++  y+++eii+vD+ S ++et++ l+ l   ++  r+i+ +e++ +++  n +++
  gi|330507803|ref|YP_004384231.1| 350 SIIIPTKDRIDLLKRCIESIQNRSSYDNYEIIIVDNMSqEEETAAYLDGL---GKSYRIIKFNEKFNYSKLNNYAAE 423
                                       8*************************************************...67********************** PP

                                       H--SSEEEEEESSEEE-TT.HHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.........EEEECCHCCCC CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpd.wleklvealekdgadvvlgqrprifgetdeiernkrv.........generlyfker 143
                                        a+g+ +lfl+ D e+    wle ++e  ++d+ ++v ++  + + +  +     ++         + +++  ++ +
  gi|330507803|ref|YP_004384231.1| 424 FARGEHLLFLNNDIEVLNSdWLEAMLEQSQRDEIGCVGAKLLYPDRKIQHVGVVVGWggraehiykWLHSNDIGYMG 500
                                       **************999888**********************99999999999988899999999888888889999 PP

                                       HCCCCCCSTTCSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 144 krslkgnlsfeigsaallrrealeel 169
                                       ++   +n s ++  +++lr+++++e+
  gi|330507803|ref|YP_004384231.1| 501 HFVSIRNYSAVTAACMMLRKSIFNEV 526
                                       99999999999999999999999887 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 !   41.9   0.0   4.7e-14   1.1e-10       1     209 [.      93     307 ..      92     322 .. 0.77
   2 !   51.1   0.0   7.2e-17   1.6e-13       1     216 [.     347     568 ..     346     594 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 4.7e-14
                   Glyco_tranf_2_3   1 prdlavlVptfneed.vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgks 76 
                                       p  ++++Vp++n  +  l++ +es+l q y++ e+++ +d+sd+  +++     ++  d+r++v    +n g+ g+s
  gi|330507803|ref|YP_004384231.1|  93 PK-ISIIVPVLNTREeWLRSSIESVLHQIYDNWELCIADDGSDQPHIKETLNCYQQK-DARIKVKYLNENQGVSGAS 167
                                       45.9********87758888***********************87765443433333.4455543334556766666 PP

                   Glyco_tranf_2_3  77 ralnealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaa 151
                                       +   eal +++++++ ++D D+ + P++l  ++  + + +++++++ ++ +   r + v a+ +  f  +++  l++
  gi|330507803|ref|YP_004384231.1| 168 N---EALAMASGEFIGFLDHDDQLLPNALYEVVLMLnRNASADFIYSDEiLISKRGKPVFAYFRPDFSLDYM--LSH 239
                                       6...*******************************99999******88857777888877676667777777..333 PP

                   Glyco_tranf_2_3 152 rralgvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaa.................v 209
                                        +          +++ir+++lk ++g+++ f +  Dy+l lr+ ++   +   p+ +                 v
  gi|330507803|ref|YP_004384231.1| 240 CYI-------VHFVVIRASILKKIGGFRAEFKVSQDYDLFLRVLSQTRNVLHIPKILyrwrqyesstghllkerV 307
                                       333.......34679******************************999999888887655555555444444444 PP

  == domain 2  score: 51.1 bits;  conditional E-value: 7.2e-17
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesll.aqeyprvevvvvvdesd.aetlevaeelaaalpdvrvrvvvnarnlgstgk 75 
                                       p  +++++pt ++ d l +++es+  +++y+++e+++v+++s+ +et++ +++l + +     r++   +    ++k
  gi|330507803|ref|YP_004384231.1| 347 PK-ISIIIPTKDRIDLLKRCIESIQnRSSYDNYEIIIVDNMSQeEETAAYLDGLGKSY-----RIIKFNE-KFNYSK 416
                                       45.9*********************5556**********9977377899999976666.....5555544.455899 PP

                   Glyco_tranf_2_3  76 sralnealravksdlvllvDdDtvv.ePdtlkrllqffltpkvgavgtpvfllnrs..tl...............vs 134
                                        +  n a + ++++++l+++ D  v   d l+++l + +++++g+vg++ +   r+  ++               + 
  gi|330507803|ref|YP_004384231.1| 417 LN--NYAAEFARGEHLLFLNNDIEVlNSDWLEAMLEQSQRDEIGCVGAKLLYPDRKiqHVgvvvgwggraehiykWL 491
                                       99..77888899***********999************99*******998775555543377677677666666666 PP

                   Glyco_tranf_2_3 135 algalefaerhlrflaarralgvltlnGsgslirrevlkelegldplfllt.dDyelglrlrragfrtayvpgaavr 210
                                        ++++ +  ++    + r++  v+    ++++ r +++ e +g+d++f ++  D++l+lr+r+ g+   + p+a+  
  gi|330507803|ref|YP_004384231.1| 492 HSNDIGYMGHFV---SIRNYSAVT---AACMMLRKSIFNEVGGFDERFEIGfGDVDLCLRVRELGYENLFTPYAELL 562
                                       666666665555...455555554...59**********************99*********************999 PP

                   Glyco_tranf_2_3 211 evfpss 216
                                       +++ ++
  gi|330507803|ref|YP_004384231.1| 563 HYESAT 568
                                       985433 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 !   36.6   0.3   1.4e-12   3.2e-09       1     219 [.      96     294 ..      96     327 .. 0.83
   2 !   16.9   0.1   1.5e-06    0.0035      16     107 ..     366     453 ..     350     474 .. 0.75
   3 !   16.5   0.0     2e-06    0.0044     165     218 ..     513     566 ..     488     580 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.4e-12
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssi...idlnllvylkdeddkayslaaarN 74 
                                       s+++p+ + +e+ +++  +    ++  ++ el + ddgS ++ ++e  +    +d++ +v + +e     + + a N
  gi|330507803|ref|YP_004384231.1|  96 SIIVPVLNTREE-WLRSSIESVLHQIYDNWELCIADDGSDQPHIKETLNCyqqKDARIKVKYLNE---NQGVSGASN 168
                                       799*****9999.******7777776689*************99887665122445666655566...45788889* PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledll 151
                                            a ++++ FlD D+   ++ +  ++       l++n  a  +++   l+ +  + ++ +     + ++  d +
  gi|330507803|ref|YP_004384231.1| 169 EALAMASGEFIGFLDHDDQLLPNALYEVVL-----MLNRNASADFIYSDEILISKRGKPVFAY----FRPDFSLDYM 236
                                       ******************999999877766.....799***************9999888875....6777777888 PP

                   Glyco_tranf_2_2 152 aakstlvkffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykara 219
                                         +  +v+f       ++i+   + ++GG+  +f  + + D+dl+lR++ + +++    +++ly+ r+
  gi|330507803|ref|YP_004384231.1| 237 LSHCYIVHF-------VVIRASILKKIGGFRAEF--KVSQDYDLFLRVLSQTRNV-LHIPKILYRWRQ 294
                                       855555555.......6899999***********..9******************.666688888775 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.5e-06
                   Glyco_tranf_2_2  16 eervlqkakyydeeielivvddgSsek.fleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaD 91 
                                        e + ++ +y  ++ e+i+vd+ S e+ ++  +  + +    + +++     +  ++  N  a+ a ++ +lFl+ D
  gi|330507803|ref|YP_004384231.1| 366 IESIQNRSSY--DNYEIIIVDNMSQEEeTAAYLDGLGKSYRIIKFNE----KFNYSKLNNYAAEFARGEHLLFLNND 436
                                       4677888888..79**********97615555555555555554444....5999999******************* PP

                   Glyco_tranf_2_2  92 .cfissDkfekilklit 107
                                            sD +e++l+  +
  gi|330507803|ref|YP_004384231.1| 437 iEVLNSDWLEAMLEQSQ 453
                                       44789*******99544 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 2e-06
                   Glyco_tranf_2_2 165 sssilinrraflevGGyDErfrGhgaEDfdlllRla.kaikslekmpvellykar 218
                                       +  +++++  f evGG+DErf   g  D dl lR+  + +++l  + +ell+ ++
  gi|330507803|ref|YP_004384231.1| 513 AACMMLRKSIFNEVGGFDERF-EIGFGDVDLCLRVReLGYENLFTPYAELLHYES 566
                                       567899***************.88999*****99962457787777777765544 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 !   17.7   0.1   1.1e-06    0.0026       2     121 ..     179     290 ..     178     318 .. 0.70
   2 !   22.9   0.0   2.9e-08   6.6e-05      31     143 ..     471     595 ..     462     614 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelas.pevaivqgp.vlvm.nvanwleelaalffaedhgkdilvrealgrvvpsvGs 75 
                                       i +lD D+ l p+ l+e++ +l +   ++++    +l+  ++++++       f++d+   +l+ +++        +
  gi|330507803|ref|YP_004384231.1| 179 IGFLDHDDQLLPNALYEVVLMLNRnASADFIYSDeILISkRGKPVF-AYFRPDFSLDY---MLSHCYI-------VH 244
                                       6678999999999999999999863466655544255652445555.33333343333...3344444.......48 PP

                   Glyco_trans_2_3  76 gaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpes.l 121
                                        +++r+s l+++gg++  e+ vs D+d+ lr +++  +v ++p    
  gi|330507803|ref|YP_004384231.1| 245 FVVIRASILKKIGGFR-AEFKVSQDYDLFLRVLSQTRNVLHIPKIlY 290
                                       9***************.99*****************99999987752 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 2.9e-08
                   Glyco_trans_2_3  31 vqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalqevggwdgdessvsEDfdmglrl 107
                                       +q+  +v++++   e++++   ++d+g ++++ +++ +   ++ ++++lr s ++evgg+d +++    D d++lr 
  gi|330507803|ref|YP_004384231.1| 471 IQHVGVVVGWGGRAEHIYKWLHSNDIGYMGHF-VSIRNYSAVTAACMMLRKSIFNEVGGFDERFEIGFGDVDLCLRV 546
                                       79999999999999999999999999999999.6999999999******************9988999********* PP

                   Glyco_trans_2_3 108 qrkGyrvrfvpes..lvkeksplt...........lraalrQrkRwayG 143
                                       +++Gy   f p++  l +e+  +             + ++ +++ ++ G
  gi|330507803|ref|YP_004384231.1| 547 RELGYENLFTPYAelLHYESATRGrsfsfdphpndTKRFIERWQEYIKG 595
                                       **********999865566655556788888888899999999999988 PP

>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.36   8.2e+02      28      76 ..     150     198 ..     139     205 .. 0.80
   2 !   27.2   0.0   1.2e-09   2.7e-06       3     179 ..     380     555 ..     360     586 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.36
                   Glyco_tranf_2_5  28 yeveiiairnaksiaeaynkalsasdakykvYlhqDvliinkdfikdll 76 
                                         + +  +++++ +  a n+al+ ++ ++  +l++D  ++ + + + +l
  gi|330507803|ref|YP_004384231.1| 150 ARIKVKYLNENQGVSGASNEALAMASGEFIGFLDHDDQLLPNALYEVVL 198
                                       56667778888999999****************9998887766666555 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 1.2e-09
                   Glyco_tranf_2_5   3 ivcvnneelyeeclsylenlevpegyeveiiairnaksiaeaynkalsasdakykvYlhqDvliinkdfikdlleiF 79 
                                       i+ v+n ++ ee  +yl+ l    g ++ ii+ +++ ++ +  n a++ ++ + +++l++D+ ++n+d+++ +le+ 
  gi|330507803|ref|YP_004384231.1| 380 IIIVDNMSQEEETAAYLDGL----GKSYRIIKFNEKFNYSKLNNYAAEFARGEHLLFLNNDIEVLNSDWLEAMLEQS 452
                                       56666666667767777766....678999**********************************************9 PP

                   Glyco_tranf_2_5  80 kkdkkiGmiG...vvGakslpesgvwweskkkvgkvietskeeakelraeeeeseyeeVeaidGllmatqydv.... 149
                                        + ++iG +G   +   +++++ gv++    +  ++++  +++   ++   +  ++++ +a+    m++++++    
  gi|330507803|ref|YP_004384231.1| 453 -QRDEIGCVGaklLYPDRKIQHVGVVVGWGGRAEHIYKWLHSNDIGYMG--HFVSIRNYSAVTAACMMLRKSIfnev 526
                                       .99******9666678999999996554444566666665555555553..33467778888889********9999 PP

                   Glyco_tranf_2_5 150 .pwredlftgfhfYdvsqslefekagykvvV 179
                                         ++e  f +  f dv+ +l++++ gy+++ 
  gi|330507803|ref|YP_004384231.1| 527 gGFDER-F-EIGFGDVDLCLRVRELGYENLF 555
                                       999999.5.57899*************9864 PP

>> Glyco_transf_7C  N-terminal domain of galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.85   1.9e+03      25      57 ..     247     277 ..     235     295 .. 0.74
   2 !   16.0   0.0     3e-06    0.0068      16      61 ..     508     552 ..     501     578 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.85
                   Glyco_transf_7C  25 alrkedfekiNGfsntfwgWGgEDdelyaRlak 57 
                                       ++r +  +ki+Gf  +f      D +l+ R+++
  gi|330507803|ref|YP_004384231.1| 247 VIRASILKKIGGFRAEFKV--SQDYDLFLRVLS 277
                                       6667778899999888865..556666666655 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3e-06
                   Glyco_transf_7C  16 yekyfgGvlalrkedfekiNGfsntfwgWGgEDdelyaRlakkgle 61 
                                       y+ +    ++lrk+ f +++Gf+++f   G  D +l+ R+++ g+e
  gi|330507803|ref|YP_004384231.1| 508 YSAVTAACMMLRKSIFNEVGGFDERFEI-GFGDVDLCLRVRELGYE 552
                                       677777889****************986.888*********99987 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 ?    1.9   0.0      0.06   1.3e+02     105     130 ..     245     269 ..     166     295 .. 0.82
   2 !   13.3   0.0   1.9e-05     0.043      15     121 ..     412     531 ..     402     553 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.06
                   Glyco_transf_21 105 smalrreaLeaiGGfealadeLAeDy 130
                                       ++++r ++L++iGGf+a   ++  Dy
  gi|330507803|ref|YP_004384231.1| 245 FVVIRASILKKIGGFRA-EFKVSQDY 269
                                       5678999********99.55566665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.9e-05
                   Glyco_transf_21  15 vnp.KvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdak........glaaaleaa 82 
                                        n+ K+nn +  +++ ++ l++ +D  v +++d Le +l++ +++++g+V +  ++ d+k        g++++ e  
  gi|330507803|ref|YP_004384231.1| 412 FNYsKLNNYAAEFARGEHLLFLNNDIEV-LNSDWLEAMLEQSQRDEIGCVGAKLLYPDRKiqhvgvvvGWGGRAEHI 487
                                       5544888888888888888888888876.599*******************98888887755554444488888777 PP

                   Glyco_transf_21  83 fl....ntlagvlqa..klsglgfavGksmalrreaLeaiGGfea 121
                                       +     n   g++    +    + ++ ++m+lr++++ ++GGf +
  gi|330507803|ref|YP_004384231.1| 488 YKwlhsN-DIGYMGHfvSIRNYSAVTAACMMLRKSIFNEVGGFDE 531
                                       7433332.234444423367999********************75 PP

>> GNT-I  GNT-I family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.025        57      90     148 ..      90     148 ..      30     162 .. 0.73
   2 ?    7.6   0.0   0.00061       1.4      91     139 ..     345     392 ..     302     415 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.025
                             GNT-I  90 qakdviavlv.lacsradavrrtvekllkyrpsaekfPlivsqdcsne.evkkevlsygdk 148
                                       + ++ i+++v +   r + +r ++e++l+     + + l ++ d+s++ ++k++   y +k
  gi|330507803|ref|YP_004384231.1|  90 EYRPKISIIVpVLNTREEWLRSSIESVLH--QIYDNWELCIADDGSDQpHIKETLNCYQQK 148
                                       345666666624567999**********8..57899********98863677777778655 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00061
                             GNT-I  91 akdviavlvlacsradavrrtvekllkyrpsaekfPlivsqdcsneevk 139
                                        ++ i++++ + +r d ++r++e++ + r+s + + +i+  + s+ee  
  gi|330507803|ref|YP_004384231.1| 345 DRPKISIIIPTKDRIDLLKRCIESI-QNRSSYDNYEIIIVDNMSQEEET 392
                                       4678999****************96.789********999988876543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.22s 00:00:00.83 Elapsed: 00:00:00.36
# Mc/sec: 5144.07
//
Query:       gi|330507804|ref|YP_004384232.1|  [L=1234]
Description: methyltransferase/glycosyl transferase fusion protein [Methanosaeta concilii GP6]
Scores for complete 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-45  155.1   1.5    2.2e-22   79.7   0.6    2.8  2  Glycos_transf_2  Glycosyl transferase family 2
    3.5e-22   79.4   0.0    4.8e-12   46.3   0.0    2.6  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
      5e-17   62.0   0.0    1.8e-16   60.1   0.0    2.0  1  Glycos_transf_1  Glycosyl transferases group 1
      5e-13   49.7   0.0    1.2e-12   48.4   0.0    1.6  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.3e-11   43.7  10.0    6.9e-07   29.0   0.1    3.9  3  Glyco_tranf_2_2  Glycosyltransferase like family 2
      5e-11   43.1   0.0    5.2e-09   36.6   0.0    3.2  2  Methyltransf_11  Methyltransferase domain
    4.8e-08   32.6   0.0      1e-07   31.5   0.0    1.5  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.2e-07   30.3   0.0    9.8e-07   28.7   0.0    1.8  1  Glyco_tranf_2_5  Glycosyltransferase like family
    2.8e-06   27.6   0.0    1.2e-05   25.6   0.0    2.1  1  Glyco_trans_1_2  Glycosyl transferases group 1
    3.6e-06   27.6   0.0    0.00017   22.2   0.0    2.9  2  Methyltransf_25  Methyltransferase domain
    9.6e-06   25.5   0.9    9.6e-05   22.2   0.0    2.7  3  Methyltransf_31  Methyltransferase domain
    9.9e-05   22.0   0.0     0.0004   20.0   0.0    2.0  2  Glyco_trans_4_5  Glycosyl-transferase family 4
     0.0075   17.0   0.0      0.049   14.4   0.0    2.5  2  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.027   14.3   0.0    1.6  1  Methyltransf_8   Hypothetical methyltransferase
      0.018   14.9   0.0       0.07   13.0   0.0    2.0  2  Glyco_trans_2_3  Glycosyl transferase family group 2
        0.1   12.2   0.0       0.26   10.8   0.0    1.7  1  MetW             Methionine biosynthesis protein MetW
       0.13   12.5   0.4       0.45   10.7   0.3    2.0  1  DUF1492          Protein of unknown function (DUF1492)
       0.15   12.3   3.3       0.28   11.5   0.1    3.2  2  DUF5461          Family of unknown function (DUF5461)
       0.17   12.0   0.1        7.8    6.6   0.0    2.8  3  DUF4951          Domian of unknown function (DUF4951)
       0.46   10.8   2.4        0.5   10.7   0.5    2.0  2  PVL_ORF50        PVL ORF-50-like family


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.6   2.4e-25   2.2e-22       1     155 [.     184     333 ..     184     345 .. 0.87
   2 !   73.5   0.0   1.9e-23   1.7e-20       1     115 [.     603     715 ..     603     782 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 2.4e-25
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       ++++pt+N    +++++es++ q +y+++ +ivv+Dg  ++ ++i++e++  d r+++i  +++ Gk+ +ln g+ +
  gi|330507804|ref|YP_004384232.1| 184 DIIMPTFNGRGSIRRAIESVIYQ-TYQNWNLIVVNDGG-EDIKDIIDEFS--DSRIKYICSDHK-GKSHSLNVGINR 255
                                       69*********************.*************9.899*******6..8*********88.************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                       ++gd+i +lD+Dd+  p +le l++a+ + g d ++  ++    +++ +e n+ +++++ +       + ++n+ ++
  gi|330507804|ref|YP_004384232.1| 256 SSGDFIGYLDDDDILYPMHLEVLINAAIDQGCDFIYNDWYEVCIDEFGREINRYFEFRNDVSPSMLILKNYINHKCI 332
                                       *********************************99999998888888888887766666666666666666665555 PP

                                       S CS
                   Glycos_transf_2 155 i 155
                                        
  gi|330507804|ref|YP_004384232.1| 333 L 333
                                       5 PP

  == domain 2  score: 73.5 bits;  conditional E-value: 1.9e-23
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       ++vi+++N  + ++ +l s+++   +  +++i+vDDgS + t+++l+++a   ++  ++r++  +G+  a n+glr+
  gi|330507804|ref|YP_004384232.1| 603 DIVICIHNALDDVKSCLMSVIKY-SPHIYTLILVDDGSDETTKSFLQDFA-LHHDAFLLRNDVARGYTFAANQGLRN 677
                                       69********************9.*************************7.7************************* PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEE CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgq 115
                                       +tg+y+++l++D++++ dwl +++e +e d++ +++g 
  gi|330507804|ref|YP_004384232.1| 678 STGKYVILLNSDTIVSADWLDRMLECAESDERIGIVGP 715
                                       *****************************888666664 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 !   30.1   0.0   4.8e-10   4.3e-07       6     121 ..     185     291 ..     181     295 .. 0.92
   2 !   46.3   0.0   5.4e-15   4.8e-12       6     217 ..     604     826 ..     600     834 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.8e-10
                   Glyco_tranf_2_3   6 vlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                       ++ ptfn    +++ +es++ q+y +  ++vv d++++   + ++e    ++d r++++  ++    +gks++ln +
  gi|330507804|ref|YP_004384232.1| 185 IIMPTFNGRGSIRRAIESVIYQTYQNWNLIVVNDGGEDI-KDIIDE----FSDSRIKYICSDH----KGKSHSLNVG 252
                                       789***************************998877655.788998....9********8888....79******** PP

                   Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrllqffltpkvgavg 121
                                       +++ ++d++  +DdD+++ P  l++l +++ ++++++++
  gi|330507804|ref|YP_004384232.1| 253 INRSSGDFIGYLDDDDILYPMHLEVLINAAIDQGCDFIY 291
                                       ******************************999999986 PP

  == domain 2  score: 46.3 bits;  conditional E-value: 5.4e-15
                   Glyco_tranf_2_3   6 vlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                       ++++  n+ d++ ++l+s+++++ + + +++v+d+sd+ t ++++ +a  +++    +++n+     +g+  a n++
  gi|330507804|ref|YP_004384232.1| 604 IVICIHNALDDVKSCLMSVIKYSPHIYTLILVDDGSDETTKSFLQDFALHHDAF---LLRNDVA---RGYTFAANQG 674
                                       889999999************76666********************99999886...5555443...45555669** PP

                   Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavg.tpvfllnrstl........vsalgalefaerhlrfl 149
                                       lr+ ++++v+l+++Dt+v+ d l+r+l  +  ++++g+vg  +  +   s +        ++ +++l  ++    ++
  gi|330507804|ref|YP_004384232.1| 675 LRNSTGKYVILLNSDTIVSADWLDRMLECAeSDERIGIVGpLSNTASWQS-VpkiescgdWA-SNDLPENI--SIHM 747
                                       ******************************88889****95444333344.33666765544.35543232..2223 PP

                   Glyco_tranf_2_3 150 aar........ralgvltlnGsgslirrevlkelegldp.lfllt..dDyelglrlrragfrtayvpgaavrevfps 215
                                        a+         + ++++lnG ++li re+  +++ +d+ +f  +  + ++++  +r++ ++ a++ ++ +++ + +
  gi|330507804|ref|YP_004384232.1| 748 MADligkyscrCYPKIPFLNGFCLLIKRELINQIGYFDEdSFGAGygEENDYCIQARKTQWHLAVADDVYIYHKQSR 824
                                       3332334333233479*******************999986666666**************************9665 PP

                   Glyco_tranf_2_3 216 sl 217
                                       s 
  gi|330507804|ref|YP_004384232.1| 825 SY 826
                                       54 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 !   60.1   0.0     2e-19   1.8e-16      81     165 ..    1124    1208 ..    1081    1213 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 2e-19
                                        CHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHH CS
                   Glycos_transf_1   81 vsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkl 155 
                                        ++re +++l++  difv  s++ ++G+++lEAma+g +vi+  +gg+ + vkdg +G+l+++++  +  +a++kl
  gi|330507804|ref|YP_004384232.1| 1124 LKREWMPHLFNEIDIFVDFSTYQAMGLTALEAMACGSAVIVPRNGGCQDFVKDGINGFLIDTTDRRSCTDALEKL 1198
                                        56667999******************************************************************* PP

                                        HHSHHHHHHH CS
                   Glycos_transf_1  156 ledeelrerl 165 
                                        ++de+lr+++
  gi|330507804|ref|YP_004384232.1| 1199 INDEKLRKKM 1208
                                        *******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 !   48.4   0.0   1.3e-15   1.2e-12       5     134 .]    1062    1201 ..    1059    1201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.3e-15
                                        EEES--.-G..G.GTHHHHHHHHHHHH.H..H.EEEEEES---..HHHHHHHTT-T.T.EEEE---.TH.HHHHH CS
                   Glyco_trans_1_4    5 lfvGrl.ee..nvkgvdllleavpllrkk..d.vrlvivGdgprpeeleelaagleer.veftGfv.ed.laell 70  
                                        +f+G++ ++  ++ + ++ le +++++k   d ++++  G + +++ l  l +  ++  +  +G +  + ++ l+
  gi|330507804|ref|YP_004384232.1| 1062 IFIGAMiRPstPRRNPRFTLEILEEIKKLygDkINIITFGCS-NDDFLS-L-NPCRDIpINHMGVLkREwMPHLF 1133
                                        69999977789999************9665436888888844.543443.3.323333499999886336***** PP

                                        HH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4   71 aaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134 
                                        ++ d+fv  s  + +gl++lEama+g +v++ + gg++++v  g ng+l++  d  + ++a+++L++d
  gi|330507804|ref|YP_004384232.1| 1134 NEIDIFVDFStyQAMGLTALEAMACGSAVIVPRNGGCQDFVkdGINGFLIDTTDRRSCTDALEKLIND 1201
                                        ********99888****************************************************997 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 !   17.8   1.1     2e-06    0.0018      18     202 ..     202     364 ..     184     384 .. 0.72
   2 ?   -2.4   0.2       2.9   2.6e+03     106     172 ..     445     513 ..     437     515 .. 0.69
   3 !   29.0   0.1   7.6e-10   6.9e-07       2     191 ..     604     795 ..     603     827 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2e-06
                   Glyco_tranf_2_2  18 rvlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaDcfi 94 
                                        v  ++    ++ +livv+dg  + + + +  + d + +   +d      +++ + N G++++ +d++ +lD D+  
  gi|330507804|ref|YP_004384232.1| 202 SVIYQTY---QNWNLIVVNDGGED-IKDIIDEFSDSRIKYICSDH----KGKSHSLNVGINRSSGDFIGYLDDDDIL 270
                                       3344444...599*******9865.5999*******999866766....3788889********************* PP

                   Glyco_tranf_2_2  95 ssDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledllaakstlvkffapssssilin 171
                                        + ++e +++ +  +    + +      + ++ +e +  +   +d+  s ++l++ +            +   il +
  gi|330507804|ref|YP_004384232.1| 271 YPMHLEVLINAAIDQGCDFIYNDWYEVCIDEFGREINRYFEFRNDVSPSMLILKNYI------------NHKCILHR 335
                                       ******999955445555555555555555555555555555555555555553322............35678888 PP

                   Glyco_tranf_2_2 172 rraflevGGyDErfrGhgaEDfdlllRlaka 202
                                       r  + +vG yDE +      D+d++ Rl+ a
  gi|330507804|ref|YP_004384232.1| 336 RCLLNKVGLYDEDL--DILIDWDMIRRLTFA 364
                                       999999********..9999******99865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.9
                   Glyco_tranf_2_2 106 itikklrenid.aavvlpvvdlnkedsevlkdvedltassrvledllaakstlvkffapss.ssilinr 172
                                       ++  ++++n + + ++  +  lnke+se + +      +++vl+  +a  +  +  ++ +  ++ +i+r
  gi|330507804|ref|YP_004384232.1| 445 LHEHEISQNKEkSELISQLQSLNKEKSELISQLHLARYRAHVLDIEIAEIKRSISWIITNRfNNSVIER 513
                                       4556777776525678888999******99999999999999954455444444455555557777776 PP

  == domain 3  score: 29.0 bits;  conditional E-value: 7.6e-10
                   Glyco_tranf_2_2   2 vviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGas 78 
                                       +vi++++  +   ++  ++   ky      li+vddgS e + + ++ +  ++    l++    a + + a N+G  
  gi|330507804|ref|YP_004384232.1| 604 IVICIHNALDD--VKSCLMSVIKYSPHIYTLILVDDGSDETTKSFLQDFALHHDAFLLRND--VARGYTFAANQGLR 676
                                       79999999999..999999999997777899*****************9887777776666..555666667***** PP

                   Glyco_tranf_2_2  79 kaesdlvlFlDaDcfissDkfekilklitikklrenidaa.vvlpvvdlnkedsevlkdvedl..tassrvledlla 152
                                       ++ + +v+ l++D  +s D ++++l+ +++ +   ++  +    ++    k +s      +dl   +s++++ dl+ 
  gi|330507804|ref|YP_004384232.1| 677 NSTGKYVILLNSDTIVSADWLDRMLECAESDERIGIVGPLsNTASWQSVPKIESCGDWASNDLpeNISIHMMADLIG 753
                                       **************************998876444443221234566555544443334444311577788899999 PP

                   Glyco_tranf_2_2 153 akstlvkffap..ssssilinrraflevGGyDErfrGhga.E 191
                                        +s      +p  ++  +li+r+ + ++G +DE   G g+ E
  gi|330507804|ref|YP_004384232.1| 754 KYSCRCYPKIPflNGFCLLIKRELINQIGYFDEDSFGAGYgE 795
                                       998876643331167788999999999999999888888742 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   5.9e-12   5.2e-09      44      96 .]      68     120 ..      30     120 .. 0.90
   2 ?    2.4   0.0      0.27   2.4e+02      17      68 ..     919     967 ..     907     979 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 5.9e-12
                                       EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  44 kvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGllvi 96 
                                       k++f+ a  ++l f+d+sfD  ++ e+lh+  d++k+l+e++Rv k+gG++++
  gi|330507804|ref|YP_004384232.1|  68 KIQFLIAGGTNLSFRDSSFDSAIIAEALHTAIDLKKILEEAVRVIKNGGRIIV 120
                                       6899**********************************************986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.27
                                       TTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEE CS
                   Methyltransf_11  17 rgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvss 68 
                                        g rv  ++l++  +k     +s ++l++ ++ +++ ++p+  + fD+v+++
  gi|330507804|ref|YP_004384232.1| 919 MGVRVSLFNLTEHGVKFQ---QSFPDLRIPVIYGSINEVPLIAADFDAVIAT 967
                                       555555566666666332...22233368899*****************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 !   31.5   0.0   1.2e-10     1e-07      98     153 ..      67     122 ..      59     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.2e-10
                                       STEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran  98 inieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                        +i+fl a + +L f d sfD+  ++  l    D +k L+ea rv+k GGr++vl 
  gi|330507804|ref|YP_004384232.1|  67 NKIQFLIAGGTNLSFRDSSFDSAIIAEALHTAIDLKKILEEAVRVIKNGGRIIVLA 122
                                       48***************************************************995 PP

>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.1e-09   9.8e-07      35     195 ..     659     826 ..     650     838 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.1e-09
                   Glyco_tranf_2_5  35 irna..ksiaeaynkalsasdakykvYlhqDvliinkdfikdlleiFkkdkkiGmiGvvGakslpesg.vww.eskk 107
                                       +rn     ++ a n++l++s  ky++ l+ D+ i++ d++ ++le  ++d++iG++G + +++  +s   +  ++++
  gi|330507804|ref|YP_004384232.1| 659 LRNDvaRGYTFAANQGLRNSTGKYVILLNSDT-IVSADWLDRMLECAESDERIGIVGPLSNTASWQSVpKIEsCGDW 734
                                       55544488999********************8.7899********************88877666655344446666 PP

                   Glyco_tranf_2_5 108 kvgkvietsk.eeakelraeeeeseyeeVeaidGllmatqydv.....pwredlftgfhfYdvsqslefekagykvv 178
                                           + e+ + + + +l+ +++ + y ++ +++G+ +++++++      ++ed f   +    + +++ +k + + +
  gi|330507804|ref|YP_004384232.1| 735 ASNDLPENISiHMMADLIGKYSCRCYPKIPFLNGFCLLIKRELinqigYFDEDSFGAGYGEENDYCIQARKTQWHLA 811
                                       666666554304455555599999******************9999999*******************999988777 PP

                   Glyco_tranf_2_5 179 VpnqekpWvihdsgfkk 195
                                       V   ++++++h++  + 
  gi|330507804|ref|YP_004384232.1| 812 V--ADDVYIYHKQSRSY 826
                                       7..46777777655433 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.3e-08   1.2e-05       7      77 ..    1144    1216 ..    1110    1219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.3e-08
                   Glyco_trans_1_2    7 rsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarerv 77  
                                         +  + l  +Ea+acG+ +++ +  g ++++++g  ++l++  d  ++ +++++l++++++r+++  + + +v
  gi|330507804|ref|YP_004384232.1| 1144 TYQAMGLTALEAMACGSAVIVPRNGGCQDFVKDGINGFLIDttDRRSCTDALEKLINDEKLRKKMCSQSIIDV 1216
                                        455667889*******************************************************998877765 PP

>> Methyltransf_25  Methyltransferase 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   0.00017      47      97 .]      68     116 ..      56     116 .. 0.89
   2 ?    1.8   0.0      0.46   4.1e+02      45      72 ..     941     968 ..     914     980 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.9e-07
                                       TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  47 nvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                       +++f+ +  ++l+f d+sfD  +++ alh     dl+k+l+e+ rv+k+gG
  gi|330507804|ref|YP_004384232.1|  68 KIQFLIAGGTNLSFRDSSFDSAIIAEALHT--AIDLKKILEEAVRVIKNGG 116
                                       89**********************988987..3589**************9 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.46
                                       TTTEEEEESBCCGBSSSTTTEEEEEEES CS
                   Methyltransf_25  45 glnvefvqgdaedlpfedgsfDlvvssg 72 
                                       +l++ ++ g+++++p+ ++ fD+v+++ 
  gi|330507804|ref|YP_004384232.1| 941 DLRIPVIYGSINEVPLIAADFDAVIATI 968
                                       45899999*****************964 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.1e-07   9.6e-05      56     117 ..      69     127 ..      63     183 .. 0.77
   2 ?   -2.7   0.0       4.9   4.4e+03      89     112 ..     455     478 ..     413     508 .. 0.62
   3 ?    0.1   0.0      0.68   6.1e+02      68     100 ..     596     625 ..     582     655 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.1e-07
                   Methyltransf_31  56 veFeqgdieeleklledekfDlilsnevlnaladpdkileeiervlkpggilliedprllae 117
                                       ++F ++  ++l+  + d++fD  +  e+l++  d++kilee+ rv+k+gg++++   + +++
  gi|330507804|ref|YP_004384232.1|  69 IQFLIAGGTNLS--FRDSSFDSAIIAEALHTAIDLKKILEEAVRVIKNGGRIIVLAEN-WDR 127
                                       566666667777..99*************************************88777.222 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.9
                   Methyltransf_31  89 dpdkileeiervlkpggilliedp 112
                                       ++ + + +++++ k++++l+++ +
  gi|330507804|ref|YP_004384232.1| 455 EKSELISQLQSLNKEKSELISQLH 478
                                       444455566666666666665444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.68
                   Methyltransf_31  68 klledekfDlilsnevlnaladpdkileeierv 100
                                        ++e +++D++++  + nal d +++l++++++
  gi|330507804|ref|YP_004384232.1| 596 RHYE-KNVDIVIC--IHNALDDVKSCLMSVIKY 625
                                       3356.899**999..579999999999999987 PP

>> Glyco_trans_4_5  Glycosyl-transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.1   2.8e+03      75      92 ..     684     703 ..     670     710 .. 0.73
   2 !   20.0   0.0   4.4e-07    0.0004       1      91 [.     889     980 ..     889    1021 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.1
                   Glyco_trans_4_5  75 vvln..tvvaakwidqllee 92 
                                       ++ln  t+v+a+w+d +le 
  gi|330507804|ref|YP_004384232.1| 684 ILLNsdTIVSADWLDRMLEC 703
                                       555533899999**999984 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 4.4e-07
                   Glyco_trans_4_5   1 kgkrvllishelsltGaPlvlmelatlLrsvgaevvvltlskkgg.llkeladrgikvleakaeelfklalkaDlvv 76 
                                       kgk++l+i    + tG+  v+++ a  L ++g  v++  l ++g    + + d +i+v+   ++e   +a+++D+v+
  gi|330507804|ref|YP_004384232.1| 889 KGKSLLIILPIMEPTGGAYVIIQEAYALIEMGVRVSLFNLTEHGVkFQQSFPDLRIPVIYGSINEVPLIAADFDAVI 965
                                       69**********************************9998776644899**************************** PP

                   Glyco_trans_4_5  77 lntvvaakwidqlle 91 
                                       +    ++ wi +l  
  gi|330507804|ref|YP_004384232.1| 966 ATINNSVYWIASLNS 980
                                       *99899999988765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.5e-05     0.049      54      99 .]      75     118 ..      59     118 .. 0.79
   2 ?   -2.3   0.0       8.5   7.6e+03      64      77 ..     595     613 ..     560     624 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.5e-05
                   Methyltransf_12  54 ealdlldldggssfDlvvasnvlhhlkdirevldnirklLkpgGrl 99 
                                         ++l+ +d  ssfD  +++++lh   d++++l+++ +++k+gGr+
  gi|330507804|ref|YP_004384232.1|  75 GGTNLSFRD--SSFDSAIIAEALHTAIDLKKILEEAVRVIKNGGRI 118
                                       444555554..5********************************86 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.5
                   Methyltransf_12  64 g....ssfDlvvas.nvlh 77 
                                       +    + +D+v+++ n+l 
  gi|330507804|ref|YP_004384232.1| 595 KrhyeKNVDIVICIhNALD 613
                                       0334479999999856655 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.1e-05     0.027     115     168 ..      78     133 ..      73     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                                       S-S--TT-EEEEEEES---.SS-HHHHHHHHHHHEEEEEEE.EEEEEGGG-S-HHH CS
                    Methyltransf_8 115 kvPledesvdvavfclslm.gtnladflkeanrvlkvGGll.kvaevksrfesvkl 168
                                       ++   d+s d a++  +l  + +l++ l+ea rv+k+GG +  +ae   r++s++ 
  gi|330507804|ref|YP_004384232.1|  78 NLSFRDSSFDSAIIAEALHtAIDLKKILEEAVRVIKNGGRIiVLAENWDRISSGEN 133
                                       567889********999972569****************761569******97764 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 ?   -2.0   0.1       3.1   2.8e+03       2      37 ..     261     290 ..     260     380 .. 0.62
   2 ?   13.0   0.0   7.8e-05      0.07       1     137 [.     682     833 ..     682     857 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.1
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgpvlv 37 
                                       i +lD+D+ l p  l+ +++   ++ +++      +
  gi|330507804|ref|YP_004384232.1| 261 IGYLDDDDILYPMHLEVLINAAIDQGCDF------I 290
                                       56788888888888887766443323333......3 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.8e-05
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelas.pevaivqgpvlvm..nvanwleelaalf............faedhgkdilv 62 
                                       +++ll +Dt +++d l + ++  +s  +++iv   +  +  ++ + +e + +              +a+ +gk  + 
  gi|330507804|ref|YP_004384232.1| 682 YVILLNSDTIVSADWLDRMLECAESdERIGIVGPLSNTAswQSVPKIESCGDWAsndlpenisihmMADLIGKY-SC 757
                                       7999***************9999962566666533222123444444444444444444443333277777764.77 PP

                   Glyco_trans_2_3  63 realgrvvpsvGsgaflrrsalqevggwdgdes..svsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQr 137
                                       r++++ + ++ G + ++ r++++++g++d d++    +E  d ++ +++  +++  ++++ ++ k ++++ + +r +
  gi|330507804|ref|YP_004384232.1| 758 RCYPKIP-FLNGFCLLIKRELINQIGYFDEDSFgaGYGEENDYCIQARKTQWHLAVADDVYIYHKQSRSYSDDRRKK 833
                                       7776444.577******************554455789*************************99999998887765 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00029      0.26      70     104 ..      80     114 ..       8     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                              MetW  70 nfedksfdyvvlsqtlqatrnpkevldellrigrr 104
                                        f+d+sfd ++++ +l +  + k++l+e +r+ ++
  gi|330507804|ref|YP_004384232.1|  80 SFRDSSFDSAIIAEALHTAIDLKKILEEAVRVIKN 114
                                       699****************************9553 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00051      0.45      38      85 ..     405     452 ..     393     467 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00051
                           DUF1492  38 taeaikkklelqrlidklensdsrsvLrmvyidkltvwqvidklnisr 85 
                                          +ikk  el+    +l++s s ++L+  y ++  ++q++++ +is+
  gi|330507804|ref|YP_004384232.1| 405 LEIIIKKTCELHADEMELNESISDAMLSFSYYHQFRIDQILHEHEISQ 452
                                       344689999*************************************97 PP

>> DUF5461  Family of unknown function (DUF5461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00031      0.28       4      73 ..     221     284 ..     218     295 .. 0.86
   2 ?   -2.1   0.1       5.6     5e+03      11      30 ..    1088    1106 ..    1083    1109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                           DUF5461   4 eaikkllqkyfkdkkiekilllpseedvkkdyiigrvgiirisktyiGivlvdGvkipfvaevhlnnkid 73 
                                       e ik ++   f+d++i+ i   +s+ + k + +   vgi+r s  +iG++  d +  p+  ev  n+ id
  gi|330507804|ref|YP_004384232.1| 221 EDIKDIID-EFSDSRIKYI---CSDHKGKSHSLN--VGINRSSGDFIGYLDDDDILYPMHLEVLINAAID 284
                                       66777765.6999998865...999999988887..******************************9987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.6
                           DUF5461   11 qkyfkdkkiekilllpseed 30  
                                        +k + d ki+ i + +s+ d
  gi|330507804|ref|YP_004384232.1| 1088 KKLYGD-KINIITFGCSNDD 1106
                                        556655.7*********987 PP

>> DUF4951  Domian of unknown function (DUF4951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.26   2.4e+02      27      63 ..     100     136 ..      79     150 .. 0.84
   2 ?   -3.0   0.0       8.6   7.7e+03      45      76 ..     456     487 ..     440     493 .. 0.67
   3 ?    6.6   0.0    0.0087       7.8       6      77 ..     502     575 ..     498     581 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.26
                           DUF4951  27 rleniqredveiikqkGvtlemikawqefyeqeaqrd 63 
                                        l++i +e v +ik+ G  + +++ w+     e  ++
  gi|330507804|ref|YP_004384232.1| 100 DLKKILEEAVRVIKNGGRIIVLAENWDRISSGENAKS 136
                                       588999********************98877666665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.6
                           DUF4951  45 tlemikawqefyeqeaqrdannPtaryrarlm 76 
                                         e+i   q+  ++++    +   aryra+++
  gi|330507804|ref|YP_004384232.1| 456 KSELISQLQSLNKEKSELISQLHLARYRAHVL 487
                                       45666666666666666666667899999876 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0087
                           DUF4951   6 slnafGkwiiGwGtGaegarqrleniqredveiikqkGvt..lemikawqefyeqeaqrdannPtaryrarlmk 77 
                                       + n f + +i      e  r+r  ++  + + i+ ++G +  l+  ++ + +y   a+++ +nP   +r  +m 
  gi|330507804|ref|YP_004384232.1| 502 ITNRFNNSVIERALPHESKRRRWYDLGLKAMRILANDGFStlLQEYRSRNAYYCSIAHKESENPENTFRETVMD 575
                                       66888999999999999999999999999999**99997633566789999******************99996 PP

>> PVL_ORF50  PVL ORF-50-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       8.7   7.8e+03      18      38 ..     136     156 ..     125     184 .. 0.68
   2 ?   10.7   0.5   0.00055       0.5       6      69 ..     410     472 ..     406     500 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.7
                         PVL_ORF50  18 liekygitpelvakrvkdkle 38 
                                        i k+ i +el+++  k  ++
  gi|330507804|ref|YP_004384232.1| 136 SISKEVINAELMQYTRKVTWH 156
                                       477777888888777776665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00055
                         PVL_ORF50   6 ikpkkltkreveliekygitpelvakrvkdkleldealdarkdsrlkeekekv.kskileeekke 69 
                                       +k+  l   e+el  ++ i+  +++  + ++++ d++l+ ++ s+ ke+ e + + + l++ek e
  gi|330507804|ref|YP_004384232.1| 410 KKTCELHADEMEL--NESISDAMLSFSYYHQFRIDQILHEHEISQNKEKSELIsQLQSLNKEKSE 472
                                       5666777888885..5679*****************************99975134555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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: 0.82u 0.26s 00:00:01.08 Elapsed: 00:00:00.44
# Mc/sec: 8438.59
//
Query:       gi|330507805|ref|YP_004384233.1|  [L=505]
Description: dolichyl-phosphate-mannose-protein mannosyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-19   69.3  19.6    4.1e-19   69.3  19.6    3.2  2  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
    3.6e-12   46.4  20.6    3.6e-12   46.4  20.6    2.5  2  PMT       Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3  19.6   4.6e-23   4.1e-19       4     159 .]      61     221 ..      57     222 .. 0.86
   2 ?   -4.4   7.7         2   1.8e+04      82     145 ..     345     367 ..     278     383 .. 0.53

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 4.6e-23
                             PMT_2   4 Pliawllalftklf...gf..selairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpd 75 
                                        ++ wl  ++ k+f   gf  +   +r +++ +++l+i+l++  +r lf++++all+a l+++ p+++a s+l+ +d
  gi|330507805|ref|YP_004384233.1|  61 VVTMWLSGISIKIFdgsGFpeKLSFARAPTVMVTSLSIILIFYFIRVLFNTKIALLSATLISLDPFLLAHSRLIHLD 137
                                       5789**********87766534556899************************************************* PP

                             PMT_2  76 aplvllwalalylllraleknklkywllagvlfGlgflsKytaallliaallyllis.arrilkekkpylalllall 151
                                       a+l+ +++l+l+ l+ +l+k++ + ++++g+++Gl++l+K+ a++ll   + ++++   + +++++  y++ +++l+
  gi|330507805|ref|YP_004384233.1| 138 AMLTTFMLLCLLSLMSFLKKPRKEFLIMTGIFLGLAILTKMPAIFLLAF-MPFVVFFlSNDTMAKSFNYVIFIIILA 213
                                       **********************888899******************994.334444434579999999997777777 PP

                             PMT_2 152 lfspvliw 159
                                       ++  +l w
  gi|330507805|ref|YP_004384233.1| 214 AMTFFLFW 221
                                       76555766 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 2
                             PMT_2  82 walalylllraleknklkywllagvlfGlgflsKytaallliaallyllisarrilkekkpyl.a 145
                                       +a+ +                                         y +++  +i k++++yl +
  gi|330507805|ref|YP_004384233.1| 345 VAIGM-----------------------------------------YCFFR-VHINKKSVFYLlM 367
                                       22223.........................................33333.3344444444433 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4  20.6     4e-16   3.6e-12      83     232 ..      84     225 ..      65     233 .. 0.87
   2 ?   -2.1   5.2      0.26   2.3e+03      87     173 ..     285     370 ..     279     378 .. 0.59

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 4e-16
                               PMT  83 vslRlfsallgslivplvyltllelgfskltallaallvllenslitlsryilldspLlfftllsmyclvkferkap 159
                                       +++R+ + +++sl+ +l +++ +   f+  +all+a+l  l++ l++ sr+i ld++L+ f+ll +++l+ f     
  gi|330507805|ref|YP_004384233.1|  84 SFARAPTVMVTSLSIILIFYFIRV-LFNTKIALLSATLISLDPFLLAHSRLIHLDAMLTTFMLLCLLSLMSF----- 154
                                       67899999**********999875.5889*******************************************..... PP

                               PMT 160 fsrswwlwllltgvalglavsvKwvglftvllvgllliwelwqllgdkslllksivkhllaralaliviPvtl 232
                                       + +     l++tg+ lgla+++K++++f++  ++  +++ l +  + ks+ ++ i++++la ++++++ P+++
  gi|330507805|ref|YP_004384233.1| 155 LKKPRKEFLIMTGIFLGLAILTKMPAIFLL-AFMPFVVFFLSNDTMAKSFNYV-IFIIILAAMTFFLFWPAMW 225
                                       577788889******************999.7777777778888889999999.7666666666666666665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.26
                               PMT  87 lfsallgslivplvyltllelgfskltallaallvllensli..tlsryilldspLl.fftllsmyclvkferkapf 160
                                       +++++l ++i  l  ++l   +++ ++  l  +l++ + +l   +  ryil   p + +  + +myc+ +++     
  gi|330507805|ref|YP_004384233.1| 285 FLPIFLVMFIKKLFKNGLDYVNKNLIVLCLYIILFAAQMILSlkAFPRYILPVFPVVdIIVAIGMYCFFRVH----I 357
                                       455555566666666666666665555555555555444333114457777777776234456899998888....5 PP

                               PMT 161 srswwlwllltgv 173
                                        ++  + ll+ g+
  gi|330507805|ref|YP_004384233.1| 358 NKKSVFYLLMSGI 370
                                       6666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1032  (0.0575604); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 3733.60
//
Query:       gi|330507806|ref|YP_004384234.1|  [L=310]
Description: glycosyl transferase, group 2 family protein [Methanosaeta concilii GP6]
Scores for complete 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-36  123.4   0.4    1.2e-35  122.8   0.4    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    1.4e-10   41.1   0.1    1.9e-10   40.7   0.1    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    3.1e-05   24.0   0.0    4.4e-05   23.5   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0025   17.3   0.0      0.013   15.0   0.0    1.9  2  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
      0.016   15.7   0.1      0.028   14.9   0.1    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.8   0.4   3.4e-39   1.2e-35       1     168 [.       3     165 ..       3     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 122.8 bits;  conditional E-value: 3.4e-39
                                       EEEEEESS-TTTHHHHHHHHHHH..GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq..dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnagl 75 
                                       s+vip yNee++++e++++l++     ++ +e++++DDgStD++ + l e+ k+++ +++++  +n+G+ +a+ ag+
  gi|330507806|ref|YP_004384234.1|   3 SIVIPLYNEEENIQELYRRLIDVldSMRESYEVLFIDDGSTDGSYARLLEIKKNNESIKIVKFRRNFGQTAAIHAGF 79 
                                       8***********************99*************************************************** PP

                                       HH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCST CS
                   Glycos_transf_2  76 raatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnls 152
                                       ++a+g++i++lDaD++ dp++++++v++l++ + dvv+g r+ ++++ +++         +r+ +  r++ ++ +++
  gi|330507806|ref|YP_004384234.1|  80 DYAQGEIIATLDADLQNDPQDIPDMVKKLNDLDLDVVCGWRYQRQDKFHKKIL-------SRFANGLRRNLTGESIH 149
                                       *********************************************99999997.......589************** PP

                                       TCSTCCCEEEEHHHHH CS
                   Glycos_transf_2 153 feigsaallrrealee 168
                                       +  ++ +++r+e++++
  gi|330507806|ref|YP_004384234.1| 150 DSGCTLRVYRKESVRD 165
                                       ************9976 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 !   40.7   0.1   5.4e-14   1.9e-10       1     104 [.       3     106 ..       3     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 5.4e-14
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyyd...eeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarN 74 
                                       s+vipl+++ee+  i+e  ++     d   e  e++++ddgS++     +  i++ n  + + +   + ++++aa  
  gi|330507806|ref|YP_004384234.1|   3 SIVIPLYNEEEN--IQELYRRLIDVLDsmrESYEVLFIDDGSTDGSYARLLEIKKNNESIKIVKF-RRNFGQTAAIH 76 
                                       79**********..**988666555552226789**************************87776.78********* PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfissDkfekilk 104
                                        G+++a+++++  lDaD    +  +  ++k
  gi|330507806|ref|YP_004384234.1|  77 AGFDYAQGEIIATLDADLQNDPQDIPDMVK 106
                                       *****************8877777766666 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   1.2e-08   4.4e-05       4     109 ..       2     105 ..       1     129 [. 0.81

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.2e-08
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesll...aqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77 
                                       +++++p +nee+ + e+ + l+    +++ ++ev +++d+s+++  +++ e+ ++ +   +++v   rn g t++++
  gi|330507806|ref|YP_004384234.1|   2 ISIVIPLYNEEENIQELYRRLIdvlDSMRESYEVLFIDDGSTDGSYARLLEIKKNNES--IKIVKFRRNFGQTAAIH 76 
                                       79**********6666655555300555678********************9777765..68999999989877777 PP

                   Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvvePdtlkrll 109
                                           +++ +++++++ +D+D   +P  ++ ++
  gi|330507806|ref|YP_004384234.1|  77 ---AGFDYAQGEIIATLDADLQNDPQDIPDMV 105
                                       ...*****************998887766555 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 !   15.0   0.0   3.6e-06     0.013      21      84 ..      74     136 ..      64     153 .. 0.82
   2 ?   -0.4   0.0       0.2     7e+02      58      95 ..     188     227 ..     182     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-06
                   Glyco_transf_21  21 nllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaafl 84 
                                       +++ ++++a+ +++ ++D+d   +p+ + +++++l d +  +V++  +  +++++++++ + f 
  gi|330507806|ref|YP_004384234.1|  74 AIHAGFDYAQGEIIATLDADLQNDPQDIPDMVKKLNDLDLDVVCGWRYQ-RQDKFHKKILSRFA 136
                                       5788999*************************************98765.45555555555554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.2
                   Glyco_transf_21  58 pkvglVtslpvgsdakglaaaleaafl.ntlagvlqa.kl 95 
                                       ++ ++V++  +  ++k  +++l + f+   + +++q+ ++
  gi|330507806|ref|YP_004384234.1| 188 DEHKVVHHERYRGQTKYNWRRLTRGFFdLVVVAFWQRySF 227
                                       4678899999999999999999999995577888888555 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 ?   14.9   0.1   7.8e-06     0.028      21      81 ..      34      93 ..       9     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.8e-06
                   Glyco_tranf_2_4 21 rilvydndstDgtrail....kelpevkllhvdksyederrqvellkallaryaeadwvlvvDaD 81
                                      ++l++d++stDg++a l    k+++ +k+++++ ++     q ++++a + +ya+++ ++++DaD
  gi|330507806|ref|YP_004384234.1| 34 EVLFIDDGSTDGSYARLleikKNNESIKIVKFRRNFG----QTAAIHAGF-DYAQGEIIATLDAD 93
                                      5999*************55433356699999999997....566666666.77889999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2150.79
//
Query:       gi|330507807|ref|YP_004384235.1|  [L=318]
Description: NAD-dependent nucleotide sugar epimerase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-63  214.3   0.0    9.4e-63  212.6   0.0    1.6  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    5.4e-62  209.4   0.0    6.5e-62  209.1   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.7e-32  112.6   0.0    2.2e-32  112.2   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    8.3e-20   71.1   0.0    5.7e-19   68.4   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    8.8e-15   54.5   0.0    1.3e-14   54.0   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    1.3e-11   44.7   0.0      3e-11   43.5   0.0    1.6  1  NAD_binding_10   NAD(P)H-binding
    1.1e-10   41.5   0.0    1.8e-10   40.8   0.0    1.4  1  NmrA             NmrA-like family
    2.6e-10   39.9   0.1      4e-09   36.0   0.1    2.5  1  NAD_binding_4    Male sterility protein
    6.1e-05   22.6   0.0    9.9e-05   21.9   0.0    1.3  1  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.079   12.9   0.0       0.17   11.8   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 !  212.6   0.0   5.2e-66   9.4e-63       2     331 ..       7     303 ..       6     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 212.6 bits;  conditional E-value: 5.2e-66
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTH.HHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntg.riehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       +TG+aGfiGsyl+e++++ g++v  +++ ++ ++ + + ++++   +++++en++l kgD+ D++ ++++l+ +  d
  gi|330507807|ref|YP_004384235.1|   7 VTGGAGFIGSYLVERFINDGHDVLCLDNFDNYYDPAiKRDNVT---RFKNKENFTLLKGDILDRDMVHKALNGA--D 78 
                                       9**************************9988776431344444...567789********************99..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        v++LAAq  V+ s+++P ++ e+n +Gtl++L+a+ ++g++   r++ aS+s +YGkv+  p++E++p  P sPY+
  gi|330507807|ref|YP_004384235.1|  79 CVFHLAAQAGVRASVKDPIKVHEINTMGTLNILQAALDCGVK---RLVYASSSSIYGKVKYLPFDESHPRVPVSPYG 152
                                       ****************************************96...9******************************* PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                        +Kl+a+  ++ + e ygl +v+ ++f  ++pr+ ++     i+ ++ r+++   +  ++G ++++Rd+++++D+v 
  gi|330507807|ref|YP_004384235.1| 153 LSKLMAEEYCRIFSEIYGLETVSLRYFTVYGPRMRPD---LAISIFANRALQ-DLPLEIFGPGEKTRDFTYIDDVVC 225
                                       *********************************8665...446555555555.5577779***************** PP

                                       HHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B CS
                     GDP_Man_Dehyd 232 amwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllg 308
                                       a  l+++ ++   ++i++g+  sv+e++el ++ +g                      + ++ ++ +  g+++ +++
  gi|330507807|ref|YP_004384235.1| 226 ANALAMKCNR-GVFNIGSGHRISVKELAELIIQLTGS---------------------RSKIVFREDARGDAQHTWA 280
                                       ******9987.79************999965555543.....................3456677888899****** PP

                                       -THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 309 daskakeeLgWkpkvsfeelvre 331
                                       ++++ak +LgW+ kv++ee++++
  gi|330507807|ref|YP_004384235.1| 281 NTDRAKVKLGWSSKVGIEEGLKR 303
                                       ********************986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.1   0.0   3.6e-65   6.5e-62       1     241 []       5     241 ..       5     241 .. 0.97

  Alignments for each domain:
  == domain 1  score: 209.1 bits;  conditional E-value: 3.6e-65
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..........EEEE--TT-HHHHHHHHHHHT-SE CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl..........elveldltdrsalerlfkeeqpda 67 
                                       i+VtG++GfiGs+lv+++ + g++v++ld+  +    a ++d           +l ++d++dr+ ++++++  ++d+
  gi|330507807|ref|YP_004384235.1|   5 IVVTGGAGFIGSYLVERFINDGHDVLCLDNFDNYYDPAIKRDNvtrfknkenfTLLKGDILDRDMVHKALN--GADC 79 
                                       89*****************************99998888888889**************************..9*** PP

                                       EEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHH CS
                         Epimerase  68 vihlAavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaa 144
                                       v+hlAa++gv+as++dp ++ e+n++gtln+l+aa ++gvkrl+++sSs++YGk++  p +e+    p  p spY++
  gi|330507807|ref|YP_004384235.1|  80 VFHLAAQAGVRASVKDPIKVHEINTMGTLNILQAALDCGVKRLVYASSSSIYGKVKYLPFDESH---PRVPVSPYGL 153
                                       ***********************************************************99999...99******** PP

                                       HHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHH CS
                         Epimerase 145 aKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaea 221
                                       +Kl++e++++ + + ygl++++lr+f++yGpr    +++  i+ +++++l+   ++ ++g g+  Rdf y++Dv+ a
  gi|330507807|ref|YP_004384235.1| 154 SKLMAEEYCRIFSEIYGLETVSLRYFTVYGPR---MRPDLAISIFANRALQDL-PLEIFGPGEKTRDFTYIDDVVCA 226
                                       ********************************...8899**************.*********************** PP

                                       HHHHHHHHTT-STTEEEEES CS
                         Epimerase 222 illvlehvdagdkgeiyniG 241
                                       + l+++      +++++niG
  gi|330507807|ref|YP_004384235.1| 227 NALAMKC-----NRGVFNIG 241
                                       *****98.....45699998 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 !  112.2   0.0   1.2e-35   2.2e-32       1     230 [.       6     232 ..       6     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 1.2e-35
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrlee.lkevrvlDlrespel.leelskvnvkk...viegDvtdkdkleealegvdvvih 72 
                                       vvtGgaGF+G++lv+++++ ++ +  +  +D   +p + +++++++++k+   +++gD++d d +++al+g+d+v+h
  gi|330507807|ref|YP_004384235.1|   6 VVTGGAGFIGSYLVERFINDGHdVLCLDNFDNYYDPAIkRDNVTRFKNKEnftLLKGDILDRDMVHKALNGADCVFH 82 
                                       8******************99745555566655555541566677777666779*********************** PP

                         3Beta_HSD  73 laslvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaype 148
                                       la+   v+  +    ++ ++n  GT n+l+a++++gv++lvY Ss ++ g+ ++  +    dE+  ++ +++++y  
  gi|330507807|ref|YP_004384235.1|  83 LAAQAGVRAsVKDPIKVHEINTMGTLNILQAALDCGVKRLVYASSSSIYGK-VKYLP---FDES--HPRVPVSPYGL 153
                                       ****99998456667899*****************************9999.33333...4565..677999***** PP

                         3Beta_HSD 149 sKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgNvaw 223
                                       sK +aE++        ++++  l T++LR  ++yG++ +  l    + + a + l l   g  e + d++Y + v+ 
  gi|330507807|ref|YP_004384235.1| 154 SKLMAEEYCR-----IFSEIYGLETVSLRYFTVYGPRMRpdLAISIFANRALQDLPLEIFGPGEKTRDFTYIDDVVC 225
                                       ********85.....5666888**************976223334444555556688899999999*********** PP

                         3Beta_HSD 224 ahilAar 230
                                       a  lA++
  gi|330507807|ref|YP_004384235.1| 226 ANALAMK 232
                                       ****987 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.0   3.2e-22   5.7e-19       1     252 [.       5     264 ..       5     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 3.2e-22
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       ++vtG++G iGs lv+++++     + l + d +   +i++++ +++k+k+    ++ + gd+ d++ ++kal+  +
  gi|330507807|ref|YP_004384235.1|   5 IVVTGGAGFIGSYLVERFINDGHDVLCLDNFDNYYDPAIKRDNVTRFKNKEN---FTLLKGDILDRDMVHKALN--G 76 
                                       79********************99999999999999******9888888543...45788**************..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEG....GGSS..........--SHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStD....KAvn..........PtnvmGa 140
                                        d+vfh AA   V +  + p+++ + N +gt n+++aa+++gvk++v+ S+     K  +          P++ +G+
  gi|330507807|ref|YP_004384235.1|  77 ADCVFHLAAQAGVRASVKDPIKVHEINTMGTLNILQAALDCGVKRLVYASSSsiygKVKYlpfdeshprvPVSPYGL 153
                                       *************************************************98522222221223333334499***** PP

                                       HHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGT...TSSHHHHHHHHHTTSSEEES-T.T-EEEEE-HHHHHHHH CS
                   Polysacc_synt_2 141 tKrlaekllqalakeseekktkfvvvRfGNVlgSr...GSviplFkkqikeggpvtvTdp.emtRyfmtieeavqLv 213
                                       +K++ae ++  +++       + v  R+  V g r      i +F ++  ++ p+ +  p e tR f  i++ v   
  gi|330507807|ref|YP_004384235.1| 154 SKLMAEEYCRIFSEIY---GLETVSLRYFTVYGPRmrpDLAISIFANRALQDLPLEIFGPgEKTRDFTYIDDVV--C 225
                                       *************999...67778888888888772223579***************987579********986..6 PP

                                       HHHHHH--SS-EEEE--.-EEEHHHHHHHH......... CS
                   Polysacc_synt_2 214 lqalalakggeifvldmGepvkivdlakalielsgleek 252
                                        +ala+  +  +f    G+ +++++la+ +i+l+g ++k
  gi|330507807|ref|YP_004384235.1| 226 ANALAMKCNRGVFNIGSGHRISVKELAELIIQLTGSRSK 264
                                       8999999999************************98665 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 !   54.0   0.0   7.2e-18   1.3e-14       3     235 ..       5     263 ..       3     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 7.2e-18
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.........................T--TTSHHHHHHHHHHH--SE CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre.........................eldltdaeavaellkeakpdv 54 
                                       i+vtG+ G +Gs L++++ ++g++vl l++                          + d+ d++ v+++l+    d+
  gi|330507807|ref|YP_004384235.1|   5 IVVTGGAGFIGSYLVERFINDGHDVLCLDNFdnyydpaikrdnvtrfknkenftllKGDILDRDMVHKALNG--ADC 79 
                                       89**************************77789*************************************99..677 PP

                                       EEE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHH CS
                     RmlD_sub_bind  55 vvnaAAytavDkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrpYeeddetsPlnvYGrtKl 130
                                       v ++AA   v +  +++ + +++n  ++ ++ +aa  +g++ L++ S+  ++   k  p+ e+++  P++ YG +Kl
  gi|330507807|ref|YP_004384235.1|  80 VFHLAAQAGVRASVKDPIKVHEINTMGTLNILQAALDCGVKrLVYASSSSIYGKVKYLPFDESHPRVPVSPYGLSKL 156
                                       ***************************************955**********999********************** PP

                                       HHHHHHHH....H-SSEEEEEE-SEESS.SSS-H.HHHHHHHHHH-SEEEEES..S-EE--EEHHHHHHHHHHHHHH CS
                     RmlD_sub_bind 131 aGEqavla....agkkalivRtswvyge.kgknf.vktmlrlakereelkvva..DqlgsPTsardlAevllqllek 199
                                         E+  +     +g +++ +R   vyg   + ++ ++ + ++a ++ +l+++    +++  T+ +d+  v++++l+ 
  gi|330507807|ref|YP_004384235.1| 157 MAEEYCRIfseiYGLETVSLRYFTVYGPrMRPDLaISIFANRALQDLPLEIFGpgEKTRDFTYIDDV--VCANALAM 231
                                       ****998766677889999*******98544455155667888999999998522566666777766..45555655 PP

                                       CHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTT CS
                     RmlD_sub_bind 200 aaeekelagvyHlanegetswlefArailkeagads 235
                                       +++     gv+ +++   +s  e+A+ i++ +g++s
  gi|330507807|ref|YP_004384235.1| 232 KCN----RGVFNIGSGHRISVKELAELIIQLTGSRS 263
                                       555....89999999999999999999999888766 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 !   43.5   0.0   1.7e-14     3e-11       1     130 [.       9     161 ..       9     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.7e-14
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT..........HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..........peklaeleaeeglevvegdvtdvedlaealkgadaVvsa 67 
                                       G+ G +G++lv++ +++g h+v  l  n           + +++++++e+ ++++gd++d + + +al+gad V+  
  gi|330507807|ref|YP_004384235.1|   9 GGAGFIGSYLVERFINDG-HDVLCL-DNfdnyydpaikRDNVTRFKNKENFTLLKGDILDRDMVHKALNGADCVFHL 83 
                                       999**************5.**9666.4434466655555777899999**************************999 PP

                                       ---TCCHHHH.............HHHHHHHHHHCT--EEEEEEETTTTSGCGC.HHHHHHHH.CCHHHHHHHHHHHH CS
                    NAD_binding_10  68 lggggkdeeg.............aknivdaakeagvkRfvlvsaigvgdevpg.efgewnke.llkaylaakraaee 129
                                       +++ g ++ +             + ni++aa   gvkR+v+ s+  ++ +v+  +f+e   +  +++y   k  aee
  gi|330507807|ref|YP_004384235.1|  84 AAQAGVRASVkdpikvheintmgTLNILQAALDCGVKRLVYASSSSIYGKVKYlPFDESHPRvPVSPYGLSKLMAEE 160
                                       96666633333445566667778************************987664145555444234566566666666 PP

                                       H CS
                    NAD_binding_10 130 l 130
                                       +
  gi|330507807|ref|YP_004384235.1| 161 Y 161
                                       6 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   9.8e-14   1.8e-10       1     103 [.       5     128 ..       5     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 9.8e-14
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S........-SHHHHHHHHSTTEEE.ES-TT-HHHHHHHHTT-SEE CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdt........kselakslkeaGvelv.kgdlddkeslvealkgvdvv 68 
                                       I+v+G++G +G+++v+ ++++gh+v  l            k+++++ +k++ + ++ kgd+ d++++++al+g+d v
  gi|330507807|ref|YP_004384235.1|   5 IVVTGGAGFIGSYLVERFINDGHDVLCLDN-FdnyydpaiKRDNVTRFKNKENFTLlKGDILDRDMVHKALNGADCV 80 
                                       89***********************98854.2478999************9998777******************** PP

                                       EE---GG.............S-HHHHHHHHHHHHHHHS-SEEEEEE-- CS
                              NmrA  69 fsvtgfy.............skeiedgkklvdAakeaGvkhfiySslg 103
                                       f   + +             + ++    ++ +Aa   Gvk+++y+s  
  gi|330507807|ref|YP_004384235.1|  81 FHLAAQAgvrasvkdpikvhEINTMGTLNILQAALDCGVKRLVYASSS 128
                                       **999889999999999864444555679***************9865 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.1   2.2e-12     4e-09       1     206 [.       7     181 ..       7     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.2e-12
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TG+ GF+G++L+e+ +++     + +l   ++  +++ +  +++++++         +e+ + ++GD+      L+
  gi|330507807|ref|YP_004384235.1|   7 VTGGAGFIGSYLVERFINDGH--DVLCLDNFDNYYDPAIKR-DNVTRFKN--------KENFTLLKGDI------LD 66 
                                       7******************99..799998777765555554.44444443........56778******......66 PP

                                       HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                        + +++  +  d+++h aA+  + +++k+   + ++N++Gt ++l+ a  +  +  l++ S++ ++g+ +       
  gi|330507807|ref|YP_004384235.1|  67 RDMVHKALNGADCVFHLAAQAGVRASVKDpikVHEINTMGTLNILQAALDCGVK-RLVYASSSSIYGKVKYL----- 137
                                       67899999***************9999985556789***************999.99999998777777732..... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EE CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsii 206
                                                    ++++ +     Y  sK +aE+ +r  ++  gl +v +R  ++
  gi|330507807|ref|YP_004384235.1| 138 -----------PFDESHPRVPVSPYGLSKLMAEEYCRIFSEIYGLETVSLRYFTV 181
                                       ...........33445556666799999999999998888777777777776555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   5.5e-08   9.9e-05       2     122 ..       4     117 ..       3     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.5e-08
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT....TSEEEEEE-TTTSHHHHHHHHHHHHHH CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee....gakalaiqvDvtdreevealvekavkk 74 
                                        ++vtG+++ IG  ++++++++G +v+++d+ ++    ++k  + +    +++++ +++D+ dr+ v ++++ a   
  gi|330507807|ref|YP_004384235.1|   4 SIVVTGGAGFIGSYLVERFINDGHDVLCLDNFDNYYDPAIKRDNVTrfknKENFTLLKGDILDRDMVHKALNGA--- 77 
                                       589*************************9999888877776544444555788****************99999... PP

                                       HSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHH CS
                         adh_short  75 lgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpa 122
                                        + +  L + AG+       + s ++  +v e+N +g++++ +a+l+ 
  gi|330507807|ref|YP_004384235.1|  78 -DCVFHLAAQAGV-------RASVKDPIKVHEINTMGTLNILQAALDC 117
                                       .788889999999.......78899999999*********99999976 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.6e-05      0.17       3      90 ..       5      85 ..       3     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.6e-05
                                      EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHH.HHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedsk.aliaelealgaevevvaaDvsdkdavealleeikaeep 80
                                       ++tGG+G +G  l++  +++g   l l   ++  d++ k ++++++++   + ++++ D+ d+d v+++l+ ++    
  gi|330507807|ref|YP_004384235.1|  5 IVVTGGAGFIGSYLVERFINDGHDVLCLDNFDNYYDPAIKrDNVTRFKN-KENFTLLKGDILDRDMVHKALNGAD---- 78
                                      68**************************998876555544156666665.568999***********99999886.... PP

                                      ---EEEE--- CS
                                KR 81 pikGvihaAg 90
                                          v+h A 
  gi|330507807|ref|YP_004384235.1| 79 ---CVFHLAA 85
                                      ...5556554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.71u 0.37s 00:00:01.08 Elapsed: 00:00:00.59
# Mc/sec: 1629.44
//
Query:       gi|330507808|ref|YP_004384236.1|  [L=213]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-12   47.4   0.0    2.4e-12   46.9   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    3.6e-12   46.8   0.0    5.9e-12   46.1   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
      1e-09   39.0   0.0    1.6e-09   38.4   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.2e-09   38.7   0.0    1.9e-09   38.0   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    5.8e-09   36.0   0.0      7e-09   35.7   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      1e-06   28.4   0.0    1.5e-06   27.9   0.0    1.2  1  MTS              Methyltransferase small domain
    0.00056   19.5   0.0    0.00082   19.0   0.0    1.2  1  Methyltransf_5   MraW methylase family
     0.0059   16.2   0.0     0.0079   15.8   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
      0.016   14.5   0.0       0.02   14.2   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
       0.02   14.4   0.0      0.032   13.7   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
      0.047   12.9   0.0      0.074   12.2   0.0    1.3  1  Methyltransf_3   O-methyltransferase
      0.071   13.1   0.0        0.1   12.6   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.11   11.8   0.0       0.15   11.3   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase 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 !   46.9   0.0   1.7e-15   2.4e-12       5      98 ..      42     127 ..      38     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.7e-15
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                       ++++D++CG+G+ ++ +a ++ p+++++G D++ +ai++Ar+  q     n++F  gd  + +  l d  +D i+s+
  gi|330507808|ref|YP_004384236.1|  42 KTLIDIACGAGYGSKMIA-QALPDSQIIGADYDLNAINYARSAYQ---APNLRFILGDLMKWD--LGD--YDCIISF 110
                                       689***************.999********************755...6699*********88..666..******* PP

                   Methyltransf_31  82 evlnaladpdkileeie 98 
                                       ++l ++++ + +le+i 
  gi|330507808|ref|YP_004384236.1| 111 DTLEHIPHREITLENIV 127
                                       *************9985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   4.2e-15   5.9e-12       2      89 ..      45     126 ..      44     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 4.2e-15
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhls 78 
                                       +d++cG G  ++++a++l++++++g D++ +++++ar+ +  + +n++f+ gd+ ++++ d  +D+++s+ +l+h++
  gi|330507808|ref|YP_004384236.1|  45 IDIACGAGYGSKMIAQALPDSQIIGADYDLNAINYARSAY--QAPNLRFILGDLMKWDLGD--YDCIISFDTLEHIP 117
                                       69****************99********************..568************9877..******888***99 PP

                                       HHHHHHHHHHH CS
                   Methyltransf_25  79 dedlekalkei 89 
                                       ++++  +l++i
  gi|330507808|ref|YP_004384236.1| 118 HREI--TLENI 126
                                       6654..46666 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.2e-12   1.6e-09       2      92 ..      46     129 ..      45     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.2e-12
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       +i cG G  +++++++lpd++++g D++ +ai        +r+++++ n+++   dl + d g  +D ++++++l+h
  gi|330507808|ref|YP_004384236.1|  46 DIACGAGYGSKMIAQALPDSQIIGADYDLNAI------NYARSAYQAPNLRFILGDLMKWDLG-DYDCIISFDTLEH 115
                                       9*******************************......5555566677899999999988887.************* PP

                   Methyltransf_12  79 lkdirevldnirkl 92 
                                       +++++ +l+ni ++
  gi|330507808|ref|YP_004384236.1| 116 IPHREITLENIVNH 129
                                       **********9987 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.4e-12   1.9e-09       2      85 ..      46     127 ..      45     130 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.4e-12
                                       EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CC CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhved 76 
                                       d++cG+G+ ++ +a++   ++++g D++ +++++a+++++ ++  ++f+ +d+ k  + d  +D+++s+ +l+h++ 
  gi|330507808|ref|YP_004384236.1|  46 DIACGAGYGSKMIAQALpdSQIIGADYDLNAINYARSAYQAPN--LRFILGDLMKWDLGD--YDCIISFDTLEHIPH 118
                                       9*************8889***********************98..99********99999..*************99 PP

                                       HHHHHHHHH CS
                   Methyltransf_11  77 pekalkeia 85 
                                       +e +l++i+
  gi|330507808|ref|YP_004384236.1| 119 REITLENIV 127
                                       999999987 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   5.1e-12     7e-09      19     121 ..      37     139 ..      22     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 5.1e-12
                   Methyltransf_23  19 klraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiaekakkaqkdqfdeqeaae.pqgkfdlIvlrevl 92 
                                       k+ +++ ++di+cG G+ ++ +++     +++g D + +a++ a++a++a++  f   +  + + g +d+I+++++l
  gi|330507808|ref|YP_004384236.1|  37 KDMQPKTLIDIACGAGYGSKMIAQALPdsQIIGADYDLNAINYARSAYQAPNLRFILGDLMKwDLGDYDCIISFDTL 113
                                       4678999***************99977789***************999999999933333334556*********** PP

                   Methyltransf_23  93 ehvpdppellrqiatllkpgGylllsepl 121
                                       eh+p+ + +l +i +++     +l+s+p 
  gi|330507808|ref|YP_004384236.1| 114 EHIPHREITLENIVNHCG---FMLFSTPC 139
                                       **************9886...99999884 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.1e-09   1.5e-06      27     103 ..      36     109 ..      30     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.1e-09
                                       CHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE CS
                               MTS  27 lpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivs 103
                                       l++ + ++++D++cGaG+ + ++a++ p+ ++   d d +A++ a+  ++a +l  +++  d+++    +++d+i+s
  gi|330507808|ref|YP_004384236.1|  36 LKDMQPKTLIDIACGAGYGSKMIAQALPDSQIIGADYDLNAINYARSAYQAPNL--RFILGDLMKWDL-GDYDCIIS 109
                                       555566789*****************************************9996..777888776555.77887775 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     6e-07   0.00082      10      66 ..      30      86 ..      23      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6e-07
                                      HHHHHHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.... CS
                    Methyltransf_5 10 qevvellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLke 66
                                      + +v +l++ + +++iD   Gag  s+++ ++l++ ++ig d D +a++ a++  ++
  gi|330507808|ref|YP_004384236.1| 30 KWAVAVLKDMQPKTLIDIACGAGYGSKMIAQALPDSQIIGADYDLNAINYARSAYQA 86
                                      56789999********************************************97765 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 !   15.8   0.0   5.7e-06    0.0079       3     118 ..      43     174 ..      41     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.7e-06
                   Methyltransf_15   3 vilDlfsGaG..GnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe................. 60 
                                       +++D+ +GaG   ++i+ al  +++i+ +++l+ ++ a      Y  + ++ ++lgd+++                 
  gi|330507808|ref|YP_004384236.1|  43 TLIDIACGAGygSKMIAQALPDSQIIGADYDLNAINYARSA---Y-QAPNLRFILGDLMKwdlgdydciisfdtleh 115
                                       78*******832456666666889*********99998764...5.4568999999999999999999*****9998 PP

                   Methyltransf_15  61 .llaklkleki..kvdlvflSpPwGGpsYkkqekfdlkkklkplkleqllkeslklsknii 118
                                          ++++le+i  +  +++ S P+G p+ +   +++   +  +++ + l++  +++ k++i
  gi|330507808|ref|YP_004384236.1| 116 iPHREITLENIvnHCGFMLFSTPCGAPKINFSPDWSA--HKIEYNADSLYRFLSRYFKRVI 174
                                       75566667776445577888*****999877777766..4445777777777666666665 PP

>> Methyltransf_2  O-methyltransferase 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      0.02      52     132 ..      30     108 ..       4     126 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                       HHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEE..EEE-HHHHHHHHHHS-----TTEEEEES-TTTS--- CS
                    Methyltransf_2  52 kkvleafdleglkslvDvGGGtGalakaivsayPtikvi..vfDlpeVveaAkehlsageeervefvgGdffkdslP 126
                                       k +++  + ++ k+l+D+  G+G   k+i++a P  ++i   +Dl   ++ A++     ++++++f+ Gd++k  l 
  gi|330507808|ref|YP_004384236.1|  30 KWAVAVLKDMQPKTLIDIACGAGYGSKMIAQALPDSQIIgaDYDLNA-INYARSA---YQAPNLRFILGDLMKWDLG 102
                                       44555555556689********************9998722577765.6677766...6889**********99988 PP

                                       --SEEE CS
                    Methyltransf_2 127 eaDail 132
                                       + D i+
  gi|330507808|ref|YP_004384236.1| 103 DYDCII 108
                                       888776 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.3e-05     0.032       3      59 ..      42      95 ..      40      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                                      EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES- CS
                    Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgd 59
                                      +++++i cG G     +A++ Pd +++G +   + ++++ ++ +   + Nlr + gd
  gi|330507808|ref|YP_004384236.1| 42 KTLIDIACGAGYGSKMIAQALPDSQIIGADYDLNAINYARSAYQ---APNLRFILGD 95
                                      5789********9999*****************99999987654...5666666666 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.4e-05     0.074      43      93 ..      36      85 ..      30      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.4e-05
                                      HHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHH CS
                    Methyltransf_3 43 vklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiq 93
                                      +k ++ k  ++i    Gy   ++a+alP D +i+  d d +a + a++ +q
  gi|330507808|ref|YP_004384236.1| 36 LKDMQPKTLIDIACGAGYGSKMIAQALP-DSQIIGADYDLNAINYARSAYQ 85
                                      566788999******************9.89***********999988776 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.3e-05       0.1      21      68 ..      36      81 ..      23      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.3e-05
                   Methyltransf_32 21 akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekae 68
                                       k+ +++t++D+++G gY s ++a+  +    +++g d   + ++ a+
  gi|330507808|ref|YP_004384236.1| 36 LKDMQPKTLIDIACGAGYGSKMIAQ--ALPDSQIIGADYDLNAINYAR 81
                                      4567899**************9999..337899999988776666555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.15      29      91 ..      21      83 ..       7     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                      TTTHHHHHH.HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHH CS
                   Ubie_methyltran 29 lgihrlWkk.fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekk 91
                                      lg+h+l +      +  + ++++++D+a+G+g  + k+  ++    +++++D++ n ++ ++  
  gi|330507808|ref|YP_004384236.1| 21 LGVHHLIRYkWAVAVLKDMQPKTLIDIACGAGYGS-KMIAQALPDSQIIGADYDLNAINYARSA 83
                                      5788888875778889999***********99665.5555566777899999988888777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1357.96
//
Query:       gi|330507809|ref|YP_004384237.1|  [L=51]
Description: hypothetical protein MCON_1821 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.2   0.0      0.032   14.0   0.0    1.1  1  rve_3     Integrase core domain


Domain annotation for each model (and alignments):
>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.8e-06     0.032      39      67 .]       9      38 ..       2      38 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-06
                             rve_3 39 laearekleawred.YNteRPHssLgykTP 67
                                      +++a e +  ++e+ Y ++R Hs+L+y++P
  gi|330507809|ref|YP_004384237.1|  9 FEDAYEYIWHFIEKvYSKKRLHSALDYMSP 38
                                      566666666666544*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 379.05
//
Query:       gi|330507810|ref|YP_004384238.1|  [L=262]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-20   73.2   0.0    2.3e-20   72.9   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.1e-19   70.9   0.2    1.5e-19   70.4   0.2    1.2  1  Methyltransf_11  Methyltransferase domain
    1.4e-19   70.6   0.2    2.1e-19   70.0   0.2    1.3  1  Methyltransf_25  Methyltransferase domain
    1.6e-15   57.3   0.0    2.7e-15   56.6   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    3.4e-15   56.6   0.3    5.4e-15   55.9   0.3    1.3  1  Methyltransf_12  Methyltransferase domain
    4.7e-10   39.2   0.0    8.3e-10   38.4   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    9.7e-10   38.2   0.0    1.4e-09   37.7   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    3.5e-09   36.4   0.1      5e-09   35.9   0.1    1.2  1  MTS              Methyltransferase small domain
    1.6e-07   30.9   0.0    2.4e-07   30.4   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    1.4e-06   28.0   0.0      2e-06   27.6   0.0    1.2  1  NodS             Nodulation protein S (NodS)
    1.7e-06   28.1   0.0    2.9e-06   27.4   0.0    1.4  1  Methyltransf_32  Methyltransferase domain
    4.1e-05   22.8   0.0    6.1e-05   22.3   0.0    1.3  1  DREV             DREV methyltransferase
    0.00045   19.9   0.1    0.00069   19.3   0.1    1.3  1  MetW             Methionine biosynthesis protein MetW
    0.00053   19.5   0.1    0.00076   19.0   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0006   19.7   0.1      0.012   15.4   0.1    2.6  1  Methyltransf_8   Hypothetical methyltransferase
     0.0012   17.8   0.0     0.0015   17.5   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0016   17.7   0.0     0.0061   15.8   0.0    1.7  2  N2227            N2227-like protein
     0.0077   15.9   0.1      0.014   15.1   0.0    1.4  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.021   14.7   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
      0.034   13.4   0.0      0.051   12.8   0.0    1.2  1  DUF43            Branched-chain polyamine synthase A C-termin
      0.046   12.7   0.0      0.071   12.1   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
       0.05   13.9   0.0       0.11   12.8   0.0    1.5  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
      0.054   12.6   0.1      0.093   11.9   0.1    1.3  1  Methyltransf_20  Putative methyltransferase
      0.058   13.1   0.0      0.078   12.6   0.0    1.2  1  TPMT             Thiopurine S-methyltransferase (TPMT)
       0.17   11.0   0.0        9.9    5.2   0.0    2.2  2  Pox_MCEL         mRNA capping enzyme
        0.2   11.4   0.0       0.39   10.4   0.0    1.6  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


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 !   72.9   0.0   3.4e-23   2.3e-20       2     113 ..      45     149 ..      44     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 3.4e-23
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       ++ +++lDlGCGtG+l++ l +e   + +v   D s+e +++A+ +aq+ g++ ++  q di+el   +  + fD +
  gi|330507810|ref|YP_004384238.1|  45 KSSIKILDLGCGTGHLALDLIRE---GYHVSAADVSKELVNFANRKAQEAGFE-LNAVQRDIQELL--YR-DAFDAV 114
                                       6889*****************55...679***********************7.**********99..77.8***** PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedpr 113
                                       ++ +vl ++ d   +l +i ++l++ggi++++ p 
  gi|330507810|ref|YP_004384238.1| 115 VCLDVLEHVGDDRLALANIYQALRSGGIMICAVPA 149
                                       ******************************99887 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.2   2.2e-22   1.5e-19       1      96 []      51     145 ..      51     145 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 2.2e-22
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       Ld+GcGtG la +l + g++v + D+ske+++ a++ka+e+g++++ v+ d+++l ++d  fD+vv+  vl+hv d 
  gi|330507810|ref|YP_004384238.1|  51 LDLGCGTGHLALDLIREGYHVSAADVSKELVNFANRKAQEAGFELNAVQRDIQELLYRD-AFDAVVCLDVLEHVGDD 126
                                       8******************************************999*************.***************** PP

                                       HHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                       + al++i++ L+ gG++++
  gi|330507810|ref|YP_004384238.1| 127 RLALANIYQALRSGGIMIC 145
                                       ****************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.2   3.1e-22   2.1e-19       1      97 []      50     141 ..      50     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 3.1e-22
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       +LdlGcGtG+l+l+l +++  ++v + D+s+e+++ a+++a+e+g++++ vq d+++l + d  fD+vv+  +l+h+
  gi|330507810|ref|YP_004384238.1|  50 ILDLGCGTGHLALDLIREG--YHVSAADVSKELVNFANRKAQEAGFELNAVQRDIQELLYRD-AFDAVVCLDVLEHV 123
                                       8*****************5..**************************************998.9******888***9 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                        d+  + al++i+++L+ gG
  gi|330507810|ref|YP_004384238.1| 124 GDD--RLALANIYQALRSGG 141
                                       955..578***********9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   3.9e-18   2.7e-15       5     161 ..      29     182 ..      22     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 3.9e-18
                   Methyltransf_23   5 reeelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqg 81 
                                       ++  +++ l+r l+ ++++ ++Ld+GcGtG+l+  l ++g++v + D s e+v+ a   +kaq   f  +      +
  gi|330507810|ref|YP_004384238.1|  29 LRLLVKEHLDRSLKGEKSSIKILDLGCGTGHLALDLIREGYHVSAADVSKELVNFA--NRKAQEAGF--ELN----A 97 
                                       55566777888887789999**************9*9**************99998..666666666..222....1 PP

                   Methyltransf_23  82 ............kfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisff 146
                                                    fd +v+ +vlehv d   +l++i++ l+ gG +++ +p+ s+   ++       +++ +h + +
  gi|330507810|ref|YP_004384238.1|  98 vqrdiqellyrdAFDAVVCLDVLEHVGDDRLALANIYQALRSGGIMICAVPALSALYGKR-------DERIGHYRRY 167
                                       222355556666***************************************766522222.......2222566666 PP

                   Methyltransf_23 147 sarslkelleeaGle 161
                                       +++ l +l +  G++
  gi|330507810|ref|YP_004384238.1| 168 DREVLLQLIKSMGFS 182
                                       666666666666665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.3   7.9e-18   5.4e-15       1      98 [.      51     142 ..      51     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 7.9e-18
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++GcGtG+l+  l ++  + ++ + D+s++ ++ a +k ++ +     +++  ++d+ +l  +++fD+vv+++vl+
  gi|330507810|ref|YP_004384238.1|  51 LDLGCGTGHLALDLIRE--GYHVSAADVSKELVNFANRKAQEAGF----ELNAVQRDIQELLYRDAFDAVVCLDVLE 121
                                       8****************..**************777777666665....7777777777777778************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                       h+ d r +l+ni+++L+ gG+
  gi|330507810|ref|YP_004384238.1| 122 HVGDDRLALANIYQALRSGGI 142
                                       ********************7 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.2e-12   8.3e-10      41     151 ..      40     145 ..      26     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.2e-12
                                       HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-E CS
                   Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsf 117
                                        l+++k++ k+lD+ +Gtg la++l   ++e ++v  +D+++++++ +++k++e g+ +++ +q + +eL +  d+f
  gi|330507810|ref|YP_004384238.1|  40 SLKGEKSSIKILDLGCGTGHLALDL---IREGYHVSAADVSKELVNFANRKAQEAGF-ELNAVQRDIQELLYR-DAF 111
                                       467788889*************977...78899*******************99997.7999********886.69* PP

                                       EEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran 118 DvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                       D v     l  v D   aL ++y+ l+ GG++++
  gi|330507810|ref|YP_004384238.1| 112 DAVVCLDVLEHVGDDRLALANIYQALRSGGIMIC 145
                                       *9999999***********************999 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0     2e-12   1.4e-09      64     164 ..      48     145 ..      33     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2e-12
                                       -EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS...-EEEEES-GGG-----SEEEEES-G CS
                              CMAS  64 mtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldler...kvevklldyedldekvdrvvsvgaf 137
                                        ++Ld+GcG G+l+   +++ + +v +  +Ske  + a+++ +e+++e    +++++ l y+   + +d+vv ++++
  gi|330507810|ref|YP_004384238.1|  48 IKILDLGCGTGHLALDLIRE-GYHVSAADVSKELVNFANRKAQEAGFELnavQRDIQELLYR---DAFDAVVCLDVL 120
                                       589*****************.*************************8751113445555555...48********** PP

                                       GGTSGGGHHHHHHHHHHHS-TT-EEEE CS
                              CMAS 138 ehvgkenydtffkklkkllkedGllll 164
                                       ehvg ++++   ++++++l+++G+++ 
  gi|330507810|ref|YP_004384238.1| 121 EHVGDDRLA--LANIYQALRSGGIMIC 145
                                       *******98..699**********985 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.1   7.2e-12     5e-09      28     103 ..      38     116 ..      29     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 7.2e-12
                                       HCC.....TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EE CS
                               MTS  28 pke.....lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfd 99 
                                       + +      s k+lDlGcG+G l++ l +e  +  v + dv+++ +++a++ +++ ++e+++v++d+ e +  + fd
  gi|330507810|ref|YP_004384238.1|  38 DRSlkgekSSIKILDLGCGTGHLALDLIREGYH--VSAADVSKELVNFANRKAQEAGFELNAVQRDIQELLYRDAFD 112
                                       444333245567*****************8887..9***************************************** PP

                                       EEEE CS
                               MTS 100 livs 103
                                       ++v+
  gi|330507810|ref|YP_004384238.1| 113 AVVC 116
                                       **98 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   3.4e-10   2.4e-07      31     128 ..      47     141 ..      38     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.4e-10
                                       S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESSGGG CS
                              TehB  31 pgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderydfilstvvlmf 107
                                         k+ldlgcg g  +l l   gy+v+a d  ++ ++f ++ ++   ++ +++   di+e+   + +d ++   vl  
  gi|330507810|ref|YP_004384238.1|  47 SIKILDLGCGTGHLALDLIREGYHVSAADVSKELVNFANRKAQEAGFE-LNAVQRDIQELLYRDAFDAVVCLDVLEH 122
                                       569******************************999999887777776.*********************9999999 PP

                                       S-GGGHHHHHHHHHHTEEEEE CS
                              TehB 108 leaeripsiienmqectkvgg 128
                                       +  +r++  ++n+ +  + gg
  gi|330507810|ref|YP_004384238.1| 123 VGDDRLA--LANIYQALRSGG 141
                                       8888875..566666666666 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   2.9e-09     2e-06      41     145 ..      44     146 ..      20     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.9e-09
                              NodS  41 qgsiadalevGcaaGalterlapyckrltvvdvveeaiararervkess.hiswivsdvqqfstdekfdlivvaevl 116
                                       ++s  ++l++Gc +G l+  l     +++  dv +e ++ a+++ +e+  +++ ++ d+q++   + fd +v+ +vl
  gi|330507810|ref|YP_004384238.1|  44 EKSSIKILDLGCGTGHLALDLIREGYHVSAADVSKELVNFANRKAQEAGfELNAVQRDIQELLYRDAFDAVVCLDVL 120
                                       4555689********************************99999998754899************************ PP

                              NodS 117 yyiedvaelraavrnlvsllapdgqlvfG 145
                                        +++d    r a+ n+ + l+++g ++  
  gi|330507810|ref|YP_004384238.1| 121 EHVGDD---RLALANIYQALRSGGIMICA 146
                                       999886...78*************99965 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   4.2e-09   2.9e-06      14      89 ..      34     102 ..      27     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.2e-09
                   Methyltransf_32  14 akllkel.akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsi 89 
                                       ++ l+++ + e+++++++D+G+G g+L+  l     e +++v + d+++elv+ a++ a++ g  f  +l+  + +i
  gi|330507810|ref|YP_004384238.1|  34 KEHLDRSlKGEKSSIKILDLGCGTGHLALDLIR---E-GYHVSAADVSKELVNFANRKAQEAG--F--ELNAVQRDI 102
                                       44444444778999*****************99...5.9***********************9..5..444444444 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   8.8e-08   6.1e-05      88     188 ..      40     147 ..      25     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 8.8e-08
                              DREV  88 spasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrd....rlkkkkynvlsal.elqetdv..kldlilc 157
                                       s + ++ + k+ldlG G G+++  +     +v a+++s+++ +    + +  ++++ ++  ++qe  +   +d ++c
  gi|330507810|ref|YP_004384238.1|  40 SLKGEKSSIKILDLGCGTGHLALDLIREGYHVSAADVSKELVNfanrKAQEAGFELNAVQrDIQELLYrdAFDAVVC 116
                                       345567789******************************998722223444566655443147776542259***** PP

                              DREV 158 lnlldrcfdplklledirsalepngrvival 188
                                       l++l+   d    l +i++al++ g +i a+
  gi|330507810|ref|YP_004384238.1| 117 LDVLEHVGDDRLALANIYQALRSGGIMICAV 147
                                       **********99***********99888775 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1     1e-06   0.00069      15     110 ..      48     148 ..      39     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1e-06
                              MetW  15 srvldlGcGdGel.lellkeekqvdgrGleldeegvaecvak..G..lsviqgdldkdlenfedksfdyvvlsqtlq 86 
                                        ++ldlGcG G+l l+l++e  +v++  + ++  + a+  a+  G  l+ +q d+++ l  +  ++fd vv    l 
  gi|330507810|ref|YP_004384238.1|  48 IKILDLGCGTGHLaLDLIREGYHVSAADVSKELVNFANRKAQeaGfeLNAVQRDIQELL--Y-RDAFDAVVCLDVLE 121
                                       589*********989***********999888777765444422533455666665544..4.468*********** PP

                              MetW  87 atrnpkevldel...lrigrraivsfP 110
                                        + + +  l ++   lr g  +i + P
  gi|330507810|ref|YP_004384238.1| 122 HVGDDRLALANIyqaLRSGGIMICAVP 148
                                       999999888765333677777777766 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.1e-06   0.00076     154     257 ..      36     144 ..      32     146 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                              PrmA 154 aleklvkege...evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeeka 227
                                        l++ +k+++   ++lD+G+G+G La+   + g  +v a D+ +  v+ a++ a+  + e +      +ell +  +
  gi|330507810|ref|YP_004384238.1|  36 HLDRSLKGEKssiKILDLGCGTGHLALDLIREG-YHVSAADVSKELVNFANRKAQEAGFELNAVQRDIQELLYRDAF 111
                                       577777777666699************999977.5899**********99999888877776622334666667999 PP

                              PrmA 228 dviva.NILaevl.iel.aedikklvkegglli 257
                                       d +v+  +L +v   +l + +i++++++gg++i
  gi|330507810|ref|YP_004384238.1| 112 DAVVClDVLEHVGdDRLaLANIYQALRSGGIMI 144
                                       999993444444321231345666666666665 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.8e-05     0.012      63     199 ..      37     204 ..      17     221 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                                       HHHHHCTS-TTS-EEEES-TT-HHH.HH--S-..EEEEESS-....S.STT.........EEES-TTS-S--TT-EE CS
                    Methyltransf_8  63 iirklkkkkdnlvvadlGcGeakia.eavrekekvrsfdlva....v.ner.........vvacdlakvPledesvd 124
                                       + r+lk  k+++ + dlGcG  ++a   +re  +v + d+        n +          v  d++++   d + d
  gi|330507810|ref|YP_004384238.1|  37 LDRSLKGEKSSIKILDLGCGTGHLAlDLIREGYHVSAADVSKelvnFaNRKaqeagfelnAVQRDIQELLYRD-AFD 112
                                       55789999*****************777899999988876431111212221111111113444555554444.344 PP

                                       EEEEES---..SS-HHHHHHHHHHHEEEEEEEEEE..EEGG.......G-S.....-HHHHHHHHHCTTEEEEEEE- CS
                    Methyltransf_8 125 vavfclslm..gtnladflkeanrvlkvGGllkva..evks.......rfe.....svklfaraltklGfevkskdl 185
                                        av+cl ++  + + +  l ++++ l+ GG++  a   +++       r+      + +++++ ++++Gf +  ++ 
  gi|330507810|ref|YP_004384238.1| 113 -AVVCLDVLehVGDDRLALANIYQALRSGGIMICAvpALSAlygkrdeRIGhyrryDREVLLQLIKSMGFSICAIRY 188
                                       .6778887622345666788999999999998766222221111111133334444666777777888888888888 PP

                                       -STTEEEEE..EEE-S CS
                    Methyltransf_8 186 snkqfvlfe..fkkve 199
                                        n+  +l++  f+k+ 
  gi|330507810|ref|YP_004384238.1| 189 WNSLGLLMVaiFEKIL 204
                                       8876665543366665 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 !   17.5   0.0   2.2e-06    0.0015     101     217 ..      23     145 ..       7     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.2e-06
                                       HHHHHH....HGGGS..--TT-....EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEE CS
                    Methyltransf_9 101 dwkWdr....vlphls.dlkgr....tildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrah 168
                                       d++W+     v++hl   lkg     +ild+Gcg+G+    ++ eg ++    d  +  l+ f a rk      + +
  gi|330507810|ref|YP_004384238.1|  23 DFRWKNlrllVKEHLDrSLKGEkssiKILDLGCGTGHLALDLIREGYHVS-AADV-SKELVNF-ANRKAQEAGFELN 96 
                                       6677642233567885357765233369***************9997754.3454.4557777.5577777777778 PP

                                       EE---GGGS-T---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEEE CS
                    Methyltransf_9 169 llplgieqlpeleafdtvfsmGvlyhrrsPldhllqlkdqlvkgGelvl 217
                                        +   i++l   +afd+v  + vl h       l ++ ++l++gG ++ 
  gi|330507810|ref|YP_004384238.1|  97 AVQRDIQELLYRDAFDAVVCLDVLEHVGDDRLALANIYQALRSGGIMIC 145
                                       88889*********************9999999999999***9999885 PP

>> N2227  N2227-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.9e-06    0.0061      45      88 ..      37      77 ..      20      85 .. 0.80
   2 ?   -0.9   0.0         1   7.2e+02     186     239 ..     130     184 ..      82     191 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.9e-06
                                      HHHHS-T......T-EEEEET-TT-HHHHHHHHTT-EEEEEE-- CS
                             N2227 45 lkelvpseskerekvkilvPGaGlGrlavelatkgyqvegnEfs 88
                                      l++ +   + e++++kil  G+G+G la++l+++gy+v++ ++s
  gi|330507810|ref|YP_004384238.1| 37 LDRSL---KGEKSSIKILDLGCGTGHLALDLIREGYHVSAADVS 77
                                      33333...468999************************988776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                                       HHHHHHHEEEEEEEEEEE--...--TTTTTTSEEEEE----HHHHHHHHHHS-EEEE CS
                             N2227 186 letiekvlkpgglwiNlGPL...lYhfedltvadevsielsleeilalakkvgfkvl 239
                                       l  i++ l+ gg+ i + P    lY+  d  +          e +l+l+k++gf + 
  gi|330507810|ref|YP_004384238.1| 130 LANIYQALRSGGIMICAVPAlsaLYGKRDERIG--HYRRYDREVLLQLIKSMGFSIC 184
                                       455666666666666666641223444444222..2234556777788888888776 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 !   15.1   0.0   2.1e-05     0.014      20      72 ..      46     104 ..      29     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                                       --SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCH......SHHHHHHH CS
                   MethyltransfD12  20 kgktfvepFaGggaVffeakkqgkkvlinDinedlinlykalikn......nveelike 72 
                                       +  ++ ++ +G+g +++ + ++g++v ++D+ ++l+n+++++ ++       v++ i+e
  gi|330507810|ref|YP_004384238.1|  46 SSIKILDLGCGTGHLALDLIREGYHVSAADVSKELVNFANRKAQEagfelnAVQRDIQE 104
                                       455689999*******************************8777777765544444444 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.1e-05     0.021      16      64 ..      48      94 ..      35     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                   Methyltransf_18 16 srvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagle 64
                                       +++D G+  g+l++ l++eg   +v a+D++++ ++ a++++++ag+e
  gi|330507810|ref|YP_004384238.1| 48 IKILDLGCGTGHLALDLIREGY--HVSAADVSKELVNFANRKAQEAGFE 94
                                      389***************9997..599*****************99986 PP

>> DUF43  Branched-chain polyamine synthase A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.4e-05     0.051      59     114 ..      60     112 ..      46     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.4e-05
                                       HHHHHHT--SEEEEE-S-HHHHHHHHHHHHHHT--EEEE---TTS---TTTSS-BS CS
                             DUF43  59 lalaLtglpkkvvvvDiDeRlikfiervakelglkieaivyDlrkplpeelkekFd 114
                                       lal L +   +v   D+ + l++f +r a+e g++++a++ D+++ l  +   +Fd
  gi|330507810|ref|YP_004384238.1|  60 LALDLIREGYHVSAADVSKELVNFANRKAQEAGFELNAVQRDIQELLYRD---AFD 112
                                       677888888899999*****************************988544...444 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 ?   12.1   0.0    0.0001     0.071     201     243 ..      46      88 ..      34     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                   tRNA_U5-meth_tr 201 skgdllelycGnGnfslalarnfekvlateiakssveaaqyni 243
                                       s+  +l+l cG G ++l l r+  +v a++++k  v++a    
  gi|330507810|ref|YP_004384238.1|  46 SSIKILDLGCGTGHLALDLIREGYHVSAADVSKELVNFANRKA 88 
                                       44579*********************************98665 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00016      0.11      54      90 ..      42      78 ..      27      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                      AdoMet_MTase 54 rseeketsfvdvgcgngllvyvlaaegykgygidlrk 90
                                      + e++   + d+gcg g l   l  egy+    d+ k
  gi|330507810|ref|YP_004384238.1| 42 KGEKSSIKILDLGCGTGHLALDLIREGYHVSAADVSK 78
                                      5567788999*******************99999987 PP

>> Methyltransf_20  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00014     0.093     113     197 ..      25     112 ..       5     122 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                   Methyltransf_20 113 rkvhleellekaver.lkaegrpvrildiaaGhGryvldalekaeer...vesillrdyselnv.eqGraliaekgl 184
                                       r ++l+ l+++ ++r lk e+++++ild+ +G G   ld +++  +      s  l ++++    e+G +l a    
  gi|330507810|ref|YP_004384238.1|  25 RWKNLRLLVKEHLDRsLKGEKSSIKILDLGCGTGHLALDLIREGYHVsaaDVSKELVNFANRKAqEAGFELNAV--Q 99 
                                       6678888999998764889999*****************99876553111223334444433321223332221..2 PP

                   Methyltransf_20 185 ediarfekgdafd 197
                                        di ++   dafd
  gi|330507810|ref|YP_004384238.1| 100 RDIQELLYRDAFD 112
                                       3445555666666 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011     0.078      17     108 ..      24     112 ..      17     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                       T--SS--HHHHHHHHT..T.-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE CS
                              TPMT  17 fhqeevnpllkkflda.lk.akaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepkvkelsgv 91 
                                       f  ++   l+k++ld+ lk +k++ ++l  +CG ++ +  l  +g++v + ++s+  v+ +  +++ ++   el++v
  gi|330507810|ref|YP_004384238.1|  24 FRWKNLRLLVKEHLDRsLKgEKSSIKILDLGCGTGHLALDLIREGYHVSAADVSKELVNFA--NRKAQEAGFELNAV 98 
                                       45556788999999998551567889999**************************999865..55555566666666 PP

                                       --...........-TTT CS
                              TPMT  92 keysageiellcgdvFt 108
                                       ++   +  ell  d+F+
  gi|330507810|ref|YP_004384238.1|  99 QR---DIQELLYRDAFD 112
                                       66...334566666665 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.014       9.9      49      77 ..      31      59 ..      27     115 .. 0.87
   2 ?    3.7   0.0     0.039        27     166     193 ..     127     154 ..     120     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.014
                          Pox_MCEL 49 lLiseyasktkldesnklkvLdldcgkGg 77
                                      lL++e++ +  + e++++k+Ldl+cg G 
  gi|330507810|ref|YP_004384238.1| 31 LLVKEHLDRSLKGEKSSIKILDLGCGTGH 59
                                      789999999999999***********994 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.039
                          Pox_MCEL 166 rtvlrNvaellasGGkvlgTtpdgdels 193
                                       r +l+N+ + l+sGG ++  +p    l 
  gi|330507810|ref|YP_004384238.1| 127 RLALANIYQALRSGGIMICAVPALSALY 154
                                       5689***************999766663 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00056      0.39      73     124 ..      46      94 ..      33     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00056
                                       TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC CS
                              PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle 124
                                          ++L++G+G+G l+     l++e  +v + + +kelv+ a+r+ ++ + e
  gi|330507810|ref|YP_004384238.1|  46 SSIKILDLGCGTGHLAL---DLIREGYHVSAADVSKELVNFANRKAQEAGFE 94 
                                       5679**********985...78899999999999******999998887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1757.96
//
Query:       gi|330507811|ref|YP_004384239.1|  [L=324]
Description: hypothetical protein MCON_1823 [Methanosaeta concilii GP6]
Scores for complete sequence (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  117.0  27.2    1.5e-33  116.7  27.2    1.1  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
       0.85    9.7   3.6        1.3    9.2   0.3    2.6  2  PspB             Phage shock protein B


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 !  116.7  27.2   1.6e-37   1.5e-33       2     301 .]       9     310 ..       8     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 1.6e-37
                   LPG_synthase_TM   2 llglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayligl 78 
                                       +++  ++a+ll+lll+++d+++++++l+ +d  +l+  ++l+ll++++ralr+++ll   + +i+l+ l++++ i +
  gi|330507811|ref|YP_004384239.1|   9 IAAATVTAVLLYLLLSQIDPHDIISTLKGIDASYLAGGFILYLLCNIFRALRFHILL---DQEIKLFPLFNLVCIYN 82 
                                       5566677**************************************************...99*************** PP

                   LPG_synthase_TM  79 fvnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalalll 155
                                       + nn+ P+++ Ge+  +y+lk+ ++ ++ + ++++++ r++d +a++ l+l++++++g  l+    +l+ ++l++++
  gi|330507811|ref|YP_004384239.1|  83 MMNNLAPMRT-GELSYIYMLKKLHNKNAITGASTLILSRIFDFIAIGTLFLASAWMIGDRLGGMKSILIPISLFMIF 158
                                       **********.*************************************************99988877777777777 PP

                   LPG_synthase_TM 156 lavla........lllllllrrrlarlarvlkrlarllarfarklasakrklvlasprrlllafllslliwllealt 224
                                       +++l+        +l ++++ +  +  +++      l++ +++  +s      l++ +  ll+++ s++iw++ +++
  gi|330507811|ref|YP_004384239.1| 159 CLILLlmlfyggeWLSISFSCALDRMGLARNATAIYLISNLKEMVQSMQ---KLRNAKIALLILASSFIIWAANFFV 232
                                       7777644444466555555555555555555555555555555555544...4777899****************** PP

                   LPG_synthase_TM 225 lylllralgvdvslallllillaltlvgalppl.PgGlGvrEaalalllallGvsaaealaaallyrlitlylllll 300
                                       ++l++r++++d+++  ++   ++++l ++lp+  ++GlG+++++ +l++ +lG++  +a++ a+ y +++   +l+l
  gi|330507811|ref|YP_004384239.1| 233 VFLVIRGMHFDIPMPIIVMGSTFTVLSTLLPIYgIAGLGTSQGLWTLVFLPLGIPLDQAIISAFGYYIVQMAYYLVL 309
                                       ***************99999999999999998647***********************************9888887 PP

                   LPG_synthase_TM 301 G 301
                                       G
  gi|330507811|ref|YP_004384239.1| 310 G 310
                                       7 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.3     0.099   8.9e+02       6      22 ..     122     138 ..     118     138 .. 0.86
   2 ?    9.2   0.3   0.00014       1.3       3      29 ..     146     172 ..     144     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.099
                              PspB   6 avpliifvlfVapiWLi 22 
                                       +  ++i +lf+a  W+i
  gi|330507811|ref|YP_004384239.1| 122 FDFIAIGTLFLASAWMI 138
                                       56789**********97 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00014
                              PspB   3 vflavpliifvlfVapiWLiLHYrskk 29 
                                       + +++p+ +f++f +++ L+L+Y   +
  gi|330507811|ref|YP_004384239.1| 146 KSILIPISLFMIFCLILLLMLFYGGEW 172
                                       57899******************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2141.70
//
Query:       gi|330507812|ref|YP_004384240.1|  [L=292]
Description: transposase IS3 family protein integrase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-25   89.8   0.0    2.2e-25   89.1   0.0    1.3  1  rve            Integrase core domain
    2.7e-19   69.1   0.3    1.9e-18   66.3   0.3    2.1  2  HTH_21         HTH-like domain
    3.8e-16   58.6   0.1    9.1e-16   57.4   0.1    1.7  1  rve_3          Integrase core domain
    4.7e-08   33.1   3.6    9.4e-08   32.1   2.4    2.1  2  rve_2          Integrase core domain
    0.00016   21.9   0.3    0.00028   21.1   0.3    1.4  1  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.027   14.6   0.1         12    6.1   0.0    2.4  2  GP3_package    DNA-packaging protein gp3
      0.041   14.1   0.0       0.11   12.7   0.0    1.7  1  HTH_Tnp_Tc3_2  Transposase
      0.049   13.8   0.1       0.17   12.0   0.0    1.9  2  HTH_Tnp_1_2    Helix-turn-helix of insertion element transpos


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.0   9.9e-29   2.2e-25       5     117 ..     127     239 ..     124     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 9.9e-29
                               rve   5 gelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve..pervlsDngseyt 79 
                                       ++ w +D+t+v++      ++l+v++d +sr ++++ ls+++ ++++  +l +a++++ ++    ++++sD+g +y+
  gi|330507812|ref|YP_004384240.1| 127 NQAWASDITYVQLQHE--HIFLAVILDLYSRKCIGWELSRSIRSDLAMSALAKALKNRSKESleGLIHHSDQGVQYA 201
                                       899*********6655..5*****************************************8899************* PP

                               rve  80 skafrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                       sk++ + l+ ++i++s++r+g+p+dn+ +E+f++tlk 
  gi|330507812|ref|YP_004384240.1| 202 SKDYVDCLKAHDIQISMSRKGNPYDNAFAESFIKTLKV 239
                                       ************************************95 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.3   8.5e-22   1.9e-18       6      58 ..      49      99 ..      45     101 .. 0.90
   2 ?   -0.0   0.0      0.45     1e+03      13      33 ..     257     277 ..     248     292 .] 0.66

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 8.5e-22
                            HTH_21  6 llalireifeeskgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgvqrr 58
                                      l ++i+ei  e  + YGyrri+aeL+++g+ +vnhkrV RlMr+++L+++ ++
  gi|330507812|ref|YP_004384240.1| 49 LVNQIQEIALEF-PYYGYRRITAELQNRGY-AVNHKRVLRLMRQEKLLCYKKK 99
                                      7899********.9**************87.5*****************9544 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.45
                            HTH_21  13 ifeeskgrYGyrriwaeLrre 33 
                                       i++    +Y ++r++ +L+ +
  gi|330507812|ref|YP_004384240.1| 257 ICNFIENVYNHKRLHSALNYR 277
                                       555445577788888888854 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1   4.1e-19   9.1e-16       1      67 []     212     279 ..     212     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 4.1e-19
                             rve_3   1 lgielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawred.YNteRPHssLgykTP 67 
                                       ++i++s+++ g P++N+++Esf++tl+ e ++ + ++++++a +++ +++e  YN++R Hs+L+y++P
  gi|330507812|ref|YP_004384240.1| 212 HDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHSALNYRSP 279
                                       689***************************************99999999866*************99 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.4     3e+03      21      33 ..     196     208 ..     184     209 .. 0.74
   2 !   32.1   2.4   4.2e-11   9.4e-08       1      48 [.     231     283 ..     231     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                             rve_2  21 eeleaaiedYIew 33 
                                       + ++ a +dY+++
  gi|330507812|ref|YP_004384240.1| 196 QGVQYASKDYVDC 208
                                       556788999*986 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 4.2e-11
                             rve_2   1 EsfFgsLKtElvygetfktleeleaaiedYIew.YNnkRlk....glsPvqYr 48 
                                       Esf ++LK+E vy  +++t+e +   i ++Ie  YN+kRl+    + sPvq++
  gi|330507812|ref|YP_004384240.1| 231 ESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHsalnYRSPVQFE 283
                                       9******************************988*****988888*******8 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   1.3e-07   0.00028       2     139 ..     128     271 ..     127     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                     DDE_Tnp_IS240   2 kswrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkek.lepeeivtDkasayasalke 76 
                                       ++w+ D Tyv+ + +  +l  ++D  +r  +++ +s     + a  +l kalk+ + ++ e ++    +  + a k 
  gi|330507812|ref|YP_004384240.1| 128 QAWASDITYVQLQHEHIFLAVILDLYSRkCIGWELSRSIRSDLAMSALAKALKNRSkESLEGLIHHSDQGVQYASKD 204
                                       68************************************999************998455555665555555555555 PP

                     DDE_Tnp_IS240  77 lkr...egelfdevshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktl.agfeavknlrkgh 139
                                         +     + + ++s+   +y n   Es  +tlK++  + +  ++++ a + + + +e v+n+++ h
  gi|330507812|ref|YP_004384240.1| 205 YVDclkAHDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNIcNFIENVYNHKRLH 271
                                       44411123556788899999***************************99877625679999999977 PP

>> GP3_package  DNA-packaging protein gp3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0053        12      49      78 ..      19      55 ..      15      63 .. 0.82
   2 ?    6.1   0.0    0.0052        12      51      90 ..     236     275 ..     199     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0053
                                      HHHHT--HHHHHHHGG..SHHH.......HHHHHHHH CS
                       GP3_package 49 alyLgisrstlkeyekrkrefs.......etierikq 78
                                      +l+L++srs  +e+ kr+++f        +++++i++
  gi|330507812|ref|YP_004384240.1| 19 CLALDVSRSGYYEWLKRSEKFTaensessDLVNQIQE 55
                                      899***************9998666666666666555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0052
                                       HHT--HHHHHHHGG..SHHHHHHHHHHHHHHHHHHHHHHT CS
                       GP3_package  51 yLgisrstlkeyekrkrefsetierikqivenqqiegala 90 
                                        L + + +l+eye+ +  f ++ + i+++ +++++  al 
  gi|330507812|ref|YP_004384240.1| 236 TLKVEEVYLNEYETFEDAFRNICNFIENVYNHKRLHSALN 275
                                       6889999*******999****************9999876 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.9e-05      0.11       3      56 ..      52     105 ..      50     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                     HTH_Tnp_Tc3_2   3 rIvrlvrkdPritlreLanelkeeGksvsreTirrrLrkaglkkrkprkkplLs 56 
                                       +I +++ + P+  +r++++el+++G  v ++ + r +r+++l  +k + kp+ +
  gi|330507812|ref|YP_004384240.1|  52 QIQEIALEFPYYGYRRITAELQNRGYAVNHKRVLRLMRQEKLLCYKKKFKPVTT 105
                                       68888889999**********************************999999755 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.7e-05      0.17      33      61 ..      19      48 ..      13      58 .. 0.83
   2 ?   -2.7   0.1       2.7   6.1e+03      55      72 ..     225     243 ..     224     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.7e-05
                                      HHHHTS-HHHHHHHH.H-HHHHHHHHHHHH CS
                       HTH_Tnp_1_2 33 aeevgvsrsTlykWk.kkkeFieyvnelae 61
                                      +  + vsrs +y+W+ + ++F+++ +e ++
  gi|330507812|ref|YP_004384240.1| 19 CLALDVSRSGYYEWLkRSEKFTAENSESSD 48
                                      56789*********9889999999888765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHT.THHHHH CS
                       HTH_Tnp_1_2  55 yvnelaeeflee.eraevy 72 
                                       y n  ae+f+++ +++evy
  gi|330507812|ref|YP_004384240.1| 225 YDNAFAESFIKTlKVEEVY 243
                                       7899999999873557777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2134.85
//
Query:       gi|330507813|ref|YP_004384241.1|  [L=109]
Description: IS3/IS66 family element, Orf1 protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.9e-11   41.8   0.1    1.6e-10   41.1   0.0    1.5  1  HTH_Tnp_1  Transposase
      0.002   17.8   0.0     0.0044   16.8   0.0    1.6  1  HTH_23     Homeodomain-like domain
     0.0046   17.0   0.0     0.0099   16.0   0.0    1.6  1  HTH_28     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.033   14.1   0.3      0.074   12.9   0.3    1.6  1  PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein k
      0.062   13.8   0.1       0.13   12.7   0.0    1.5  2  DUF4733    Domain of unknown function (DUF4733)


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   4.4e-14   1.6e-10       2      74 ..       3      75 ..       2      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 4.4e-14
                         HTH_Tnp_1  2 rrrrrwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyr...egeeaspaefeltaleeenrelkrel 74
                                      ++rrr+++ fK+++++e  e+gk+ +++Ar++g++p+   +W+++     e  +a   +    + +++++el+r+l
  gi|330507813|ref|YP_004384241.1|  3 KTRRRYDRDFKISVLAEL-EAGKPLAQIAREYGIHPSLPCRWKAELAenpE--KAFMGNGNKYKDQAKIAELERLL 75
                                      79***************9.*************************9975332..33333333344466777777765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.2e-06    0.0044       8      40 ..      14      46 ..       2      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                      +++l  l  G++ ++IAre+g++++  +rw+  
  gi|330507813|ref|YP_004384241.1| 14 ISVLAELEAGKPLAQIAREYGIHPSLPCRWKAE 46
                                      567888888***************987777765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.8e-06    0.0099       1      27 [.      12      38 ..      12      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
                            HTH_28  1 qRleiikllaaGhsvreaArelgisrr 27
                                      +++ ++ +l aG++ +++Are+gi+++
  gi|330507813|ref|YP_004384241.1| 12 FKISVLAELEAGKPLAQIAREYGIHPS 38
                                      7999********************997 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.1e-05     0.074       9      28 ..      67      86 ..      61      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                         PKcGMP_CC  9 RIRELEkrlaekdeEIqELr 28
                                      +I+ELE+ l + ++EI  L+
  gi|330507813|ref|YP_004384241.1| 67 KIAELERLLGQAHAEIDLLK 86
                                      9***************9888 PP

>> DUF4733  Domain of unknown function (DUF4733)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.7e-05      0.13      29      67 ..       4      42 ..       1      51 [. 0.88
   2 ?   -2.0   0.0       1.4     5e+03      32      32 ..      91      91 ..      64     106 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                           DUF4733 29 qplrpqravleelsaplelsqplsgllddyGilPkhPrp 67
                                        +r+ r +   + a le  +pl+++  +yGi+P  P +
  gi|330507813|ref|YP_004384241.1|  4 TRRRYDRDFKISVLAELEAGKPLAQIAREYGIHPSLPCR 42
                                      56899999999***********************99976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                           DUF4733 32 r 32
                                       
  gi|330507813|ref|YP_004384241.1| 91 M 91
                                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 933.78
//
Query:       gi|330507814|ref|YP_004384242.1|  [L=1012]
Description: hypothetical protein MCON_1826 [Methanosaeta concilii GP6]
Scores for complete 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   23.9   3.5    4.5e-05   23.0   3.5    1.4  1  Glyco_hydro_26  Glycosyl hydrolase family 26


Domain annotation for each model (and alignments):
>> Glyco_hydro_26  Glycosyl hydrolase family 26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   3.5   2.5e-09   4.5e-05     135     236 ..     341     448 ..     307     465 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.5e-09
                                       HHHHHHHHHHCHCTTT--EEEE-S-STTSSSSTTSTTSTCHHHHHHHHHHHHHHHHHTTS--.....-SEEEEE--B CS
                    Glyco_hydro_26 135 dldkiAeqlqklkeaqvPvlfRplHEaeGeWFWWGakgqerpelykqLyrllyeylvdvkgl.....dnliwvyspe 206
                                       +++  A + ++l+  +v ++f   HE++G+W+ WG+k  e + ++k +   +++++     +     +n  + +  +
  gi|330507814|ref|YP_004384242.1| 341 KMEYFATKCKELD-TEVFIIF--GHEMNGNWYAWGQKPAEYIAKFKTV-AEIFHRIAPRAEMcwipnQNWGYPWGGT 413
                                       5666677777774.4577777..5*************99******987.5688888766554333334556667788 PP

                                       TTSS-TCCC---T.....TT-SEEEEEEEES.CCC CS
                    Glyco_hydro_26 207 asrdvaeefYPGd.....eyvDivGlDvYlddaas 236
                                       +  d  +e+YP       eyvD vGl  Y +d+ +
  gi|330507814|ref|YP_004384242.1| 414 DHGDGYTEYYPSGsgtygEYVDWVGLVFYDKDYDE 448
                                       888********53233448*******999987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1012 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); 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:                         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 0.26s 00:00:00.91 Elapsed: 00:00:00.40
# Mc/sec: 7678.13
//
Query:       gi|330507815|ref|YP_004384243.1|  [L=1241]
Description: beta-propeller repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-64  211.3  69.9    2.3e-11   43.5   3.2    7.8  8  SBBP      Beta-propeller repeat
    7.5e-05   22.5   1.8    0.00034   20.4   1.8    2.1  1  PKD       PKD domain
     0.0013   18.7   3.3        3.5    7.8   0.0    4.8  5  NHL       NHL repeat


Domain annotation for each model (and alignments):
>> SBBP  Beta-propeller repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   2.9   1.5e-12   8.7e-09       2      38 .]     275     310 ..     274     310 .. 0.97
   2 !   39.8   7.2   5.6e-14   3.3e-10       2      38 .]     339     374 ..     338     374 .. 0.98
   3 !   36.3   4.4   6.8e-13   4.1e-09       2      38 .]     403     438 ..     402     438 .. 0.96
   4 !   26.7   3.3   6.6e-10   3.9e-06       1      38 []     466     502 ..     466     502 .. 0.95
   5 !   43.5   3.2   3.9e-15   2.3e-11       2      38 .]     531     566 ..     530     566 .. 0.98
   6 !   33.8   0.2   4.1e-12   2.5e-08       2      38 .]     595     630 ..     594     630 .. 0.94
   7 !   30.1   4.3   5.9e-11   3.5e-07       2      38 .]     659     694 ..     659     694 .. 0.97
   8 ?   -3.3   0.0       1.6   9.3e+03      13      24 ..     791     802 ..     788     802 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.5e-12
                              SBBP   2 WstqlGgpgastygngIavDsnGNiYvtGsTngnnfe 38 
                                       +st+lGg+g+ ++g ++a Ds+GN+YvtG+T ++nf+
  gi|330507815|ref|YP_004384243.1| 275 YSTYLGGSGD-DSGLSLALDSSGNAYVTGYTASTNFP 310
                                       9*********.99***********************7 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 5.6e-14
                              SBBP   2 WstqlGgpgastygngIavDsnGNiYvtGsTngnnfe 38 
                                       +st+lGg+g+ +y++gIavDs GN+YvtG+T ++nf+
  gi|330507815|ref|YP_004384243.1| 339 YSTYLGGGGY-DYAKGIAVDSGGNAYVTGYTASTNFP 374
                                       9*********.99***********************7 PP

  == domain 3  score: 36.3 bits;  conditional E-value: 6.8e-13
                              SBBP   2 WstqlGgpgastygngIavDsnGNiYvtGsTngnnfe 38 
                                       +st+lGg+g  ++g +Ia+D +GN+YvtG+T ++ f+
  gi|330507815|ref|YP_004384243.1| 403 YSTYLGGSGE-DNGESIAIDGSGNAYVTGYTGSASFP 438
                                       9*****9999.*********************99986 PP

  == domain 4  score: 26.7 bits;  conditional E-value: 6.6e-10
                              SBBP   1 qWstqlGgpgastygngIavDsnGNiYvtGsTngnnfe 38 
                                       ++st+lGg+++ + g gIa D ++N+Y+tG T ++nf+
  gi|330507815|ref|YP_004384243.1| 466 VYSTYLGGSSSEY-GLGIALDGSSNAYITGPTYSTNFP 502
                                       59*********77.***********************7 PP

  == domain 5  score: 43.5 bits;  conditional E-value: 3.9e-15
                              SBBP   2 WstqlGgpgastygngIavDsnGNiYvtGsTngnnfe 38 
                                       +st+lGg+ + +++ gIavD+ GN+Y+tG+T +++f+
  gi|330507815|ref|YP_004384243.1| 531 YSTYLGGSFN-DFAEGIAVDRRGNAYITGYTISDDFP 566
                                       9*********.*************************7 PP

  == domain 6  score: 33.8 bits;  conditional E-value: 4.1e-12
                              SBBP   2 WstqlGgpgastygngIavDsnGNiYvtGsTngnnfe 38 
                                       +st lGg+g+  +++gIavDs GN++vtG+T +++f+
  gi|330507815|ref|YP_004384243.1| 595 YSTFLGGSGD-CFAHGIAVDSRGNAFVTGDTSSADFP 630
                                       8888999999.9***********************97 PP

  == domain 7  score: 30.1 bits;  conditional E-value: 5.9e-11
                              SBBP   2 WstqlGgpgastygngIavDsnGNiYvtGsTngnnfe 38 
                                       +st+lGg ++ +y++gIa+D +G  Y tG+T +nnf+
  gi|330507815|ref|YP_004384243.1| 659 FSTYLGGVNY-DYAKGIAIDNFGKTYLTGYTESNNFP 694
                                       69********.99***********************7 PP

  == domain 8  score: -3.3 bits;  conditional E-value: 1.6
                              SBBP  13 tygngIavDsnG 24 
                                       ++++ +a+Ds G
  gi|330507815|ref|YP_004384243.1| 791 YQIKAMATDSKG 802
                                       688999***987 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   1.8   5.7e-08   0.00034      16      69 ..     745     804 ..     735     805 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.7e-08
                                       EEEES..-SS-SEEEEE--SS.....--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EE CS
                               PKD  16 ftaav.pdganvtysWdfgdg.....svvqvlseptvthtYlspGeYeVtvtasnavgsa 69 
                                       ft a+ pdg+ v y++d gdg     + v ++   + +h++ ++G Y+++  a+++ g++
  gi|330507815|ref|YP_004384243.1| 745 FTFASdPDGDQVKYTFDWGDGsttttDLVDSGATASMSHSWINAGVYQIKAMATDSKGAT 804
                                       6666679**************977666666666677789****************99975 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.35   2.1e+03       6      18 ..     289     301 ..     288     301 .. 0.90
   2 !    5.7   0.0    0.0027        16       3      18 ..     350     365 ..     348     365 .. 0.90
   3 ?   -3.6   0.1       2.5   1.5e+04       7      18 ..     418     429 ..     417     429 .. 0.85
   4 ?    1.4   0.0     0.065   3.9e+02       3      18 ..     542     557 ..     540     557 .. 0.86
   5 !    7.8   0.0   0.00059       3.5       2      18 ..     605     621 ..     605     626 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.35
                                       EEEEETTTEEEEE CS
                               NHL   6 GvavdsnGdiyVa 18 
                                       ++a+ds+G+ yV+
  gi|330507815|ref|YP_004384243.1| 289 SLALDSSGNAYVT 301
                                       589********97 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0027
                                       SEEEEEEETTTEEEEE CS
                               NHL   3 yPhGvavdsnGdiyVa 18 
                                       y+ G+avds+G+ yV+
  gi|330507815|ref|YP_004384243.1| 350 YAKGIAVDSGGNAYVT 365
                                       678************7 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.5
                                       EEEETTTEEEEE CS
                               NHL   7 vavdsnGdiyVa 18 
                                       +a+d +G+ yV+
  gi|330507815|ref|YP_004384243.1| 418 IAIDGSGNAYVT 429
                                       899999999997 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.065
                                       SEEEEEEETTTEEEEE CS
                               NHL   3 yPhGvavdsnGdiyVa 18 
                                       +++G+avd  G+ y++
  gi|330507815|ref|YP_004384243.1| 542 FAEGIAVDRRGNAYIT 557
                                       679*****99999986 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.00059
                                       SSEEEEEEETTTEEEEE CS
                               NHL   2 nyPhGvavdsnGdiyVa 18 
                                       +++hG+avds G+ +V+
  gi|330507815|ref|YP_004384243.1| 605 CFAHGIAVDSRGNAFVT 621
                                       899******66655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1241 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:                        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: 0.73u 0.27s 00:00:01.00 Elapsed: 00:00:00.43
# Mc/sec: 8630.62
//
Query:       gi|330507816|ref|YP_004384244.1|  [L=423]
Description: UDP-glucose 6-dehydrogenase [Methanosaeta concilii GP6]
Scores for complete 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  177.3   0.0    4.2e-52  176.5   0.0    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    4.5e-38  129.4   0.0    7.9e-38  128.6   0.0    1.4  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    1.6e-26   92.8   0.0    6.3e-26   90.8   0.0    1.9  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0016   18.9   0.1     0.0049   17.4   0.1    1.9  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0044   16.3   0.0     0.0073   15.6   0.0    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0069   16.3   0.0      0.015   15.2   0.0    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.022   14.3   0.2      0.044   13.4   0.2    1.5  1  DAO             FAD dependent oxidoreductase
      0.024   14.0   0.0      0.046   13.0   0.0    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.024   13.7   0.1      0.045   12.8   0.1    1.4  1  GIDA            Glucose inhibited division protein A
      0.074   13.3   0.4       0.52   10.6   0.1    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
       0.16   12.1   0.4        1.9    8.6   0.0    2.8  3  DpaA_N          Dipicolinate synthase subunit A N-terminal do


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 !  176.5   0.0   2.6e-55   4.2e-52       1     183 [.       1     183 [.       1     187 [. 0.95

  Alignments for each domain:
  == domain 1  score: 176.5 bits;  conditional E-value: 2.6e-55
                                       SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveea 77 
                                       mkisviG GYvGlv+a+++a++gh+v ++ id  + +++ +g+ +iye+gLe l+ k++ ++ l+ +t ++  + ++
  gi|330507816|ref|YP_004384244.1|   1 MKISVIGGGYVGLVSAVCFAQLGHTVGLIEIDIDRASSISRGSPQIYEKGLEALLSKHL-EKSLHVSTAYDA-IPDT 75 
                                       8**********************************************************.799999999987.99** PP

                                       SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHC...EEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE CS
                    UDPG_MGDP_dh_N  78 dvifiaVgTPskkkgkaaDlkyvesaarsiaealkk...gkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvs 151
                                       +++fi+VgTP  + + ++Dl++++sa++s+++ l +   ++vvvvkSTvp+gt+e lv + + e+s++ g +++  +
  gi|330507816|ref|YP_004384244.1|  76 EIFFICVGTPEGD-NGHPDLSMIQSACQSLGRSLIDmdsYHVVVVKSTVPPGTTEGLVVPTVLEHSQRAGDEIGFCM 151
                                       *************.7777*************99865566*********************999999999******** PP

                                       ------TTSHHHHHHS-S-EEEEESSCHHHHH CS
                    UDPG_MGDP_dh_N 152 nPEflregsavkdllnpdrvviGveekkaeaa 183
                                       nPEflreg av+d+++pdr+viG ++++a++ 
  gi|330507816|ref|YP_004384244.1| 152 NPEFLREGRAVEDFMHPDRIVIGSNDSRAGDW 183
                                       **************************998755 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 !  128.6   0.0   4.8e-41   7.9e-38       1      93 [.     201     293 ..     201     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: 128.6 bits;  conditional E-value: 4.8e-41
                      UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaee 77 
                                       ++AE+iK+a+NaflatkIsf+Ne++nlc++lgidv eV+e+vg+d+ri+p+fl++g+G+GGsc+pkD++aL++lae 
  gi|330507816|ref|YP_004384244.1| 201 KSAEMIKYASNAFLATKISFANEIGNLCKRLGIDVYEVMEGVGMDHRISPHFLDAGAGFGGSCFPKDLSALIHLAEG 277
                                       58*************************************************************************** PP

                      UDPG_MGDP_dh  78 lgleaelleavrevNe 93 
                                        + e+ +l++v++vNe
  gi|330507816|ref|YP_004384244.1| 278 MNEEPLILRSVQNVNE 293
                                       ***************8 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.1   3.4e+03      51      78 ..      60      86 ..      41      99 .. 0.68
   2 !   90.8   0.0   3.9e-29   6.3e-26       1     103 [.     316     413 ..     316     415 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.1
                                      BTCCEEES-CHHHHTT-SEEEE-S--GG CS
                    UDPG_MGDP_dh_C 51 ekgvevvdsleealkgadaiviltehde 78
                                      ek+++ v+++++a+ + ++  i++  +e
  gi|330507816|ref|YP_004384244.1| 60 EKSLH-VSTAYDAIPDTEIFFICVGTPE 86
                                      33444.5578999999999999987766 PP

  == domain 2  score: 90.8 bits;  conditional E-value: 3.9e-29
                                       EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--G CS
                    UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehd 77 
                                       a+lGlafK+dtdD+R+S+++ +i +L+e+ga++ +yDP+++++ +++    +++e+++ +++al++ada++++te++
  gi|330507816|ref|YP_004384244.1| 316 AVLGLAFKNDTDDVRQSRSIPVILSLREMGARIAAYDPRANDNMKKM---IHDIEYCSRATDALRDADACLLMTEWP 389
                                       89********************************************9...679************************ PP

                                       GGGGS-HHHHHHCCSS-EEEESSS-C CS
                    UDPG_MGDP_dh_C  78 efkeldlaklkelmkpavvfDgrnvl 103
                                       ef  l  ++  +lmk++v++ gr++l
  gi|330507816|ref|YP_004384244.1| 390 EFGLL--DEEFDLMKNRVIIEGRRIL 413
                                       ****7..67889***********997 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     3e-06    0.0049       1      30 [.       2      31 ..       2      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3e-06
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvver 30
                                      k+ v+GgGy+gl  A  +a+lg+ V ++e 
  gi|330507816|ref|YP_004384244.1|  2 KISVIGGGYVGLVSAVCFAQLGHTVGLIEI 31
                                      578**********************99984 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 !   15.6   0.0   4.5e-06    0.0073     144     173 ..       2      31 ..       1      76 [. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.5e-06
                                       EEEEES-SHHHHHHHHHHHHHT-EEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlvea 173
                                       +i v+GgGy+G++ A  +a+lg+ v l+e 
  gi|330507816|ref|YP_004384244.1|   2 KISVIGGGYVGLVSAVCFAQLGHTVGLIEI 31 
                                       688********************8887763 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.4e-06     0.015       1      44 [.       2      45 ..       2      76 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.4e-06
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44
                                      k+ viG G +G   a  fa+ g++V l++i+ +++ +  +   +
  gi|330507816|ref|YP_004384244.1|  2 KISVIGGGYVGLVSAVCFAQLGHTVGLIEIDIDRASSISRGSPQ 45
                                      689**************************976666554443333 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   2.7e-05     0.044       2      31 ..       3      33 ..       2      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-05
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdi 31
                                      + +iGGG++Gl  A   a+ g  V l+e + i
  gi|330507816|ref|YP_004384244.1|  3 ISVIGGGYVGLVSAVCFAQLGhtVGLIEID-I 33
                                      67*****************999*****987.3 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 ?   13.0   0.0   2.8e-05     0.046      30      69 ..       2      41 ..       1      72 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69
                                      k+ viGgG +Gl ++   ++lg +V +++++++r+  ++ 
  gi|330507816|ref|YP_004384244.1|  2 KISVIGGGYVGLVSAVCFAQLGHTVGLIEIDIDRASSISR 41
                                      789*****************************99988766 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.7e-05     0.045       2      36 ..       3      37 ..       2      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                                      EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkldtia 36
                                      + ViGgG  G+  A+  a+lG+ v Li  ++d+  
  gi|330507816|ref|YP_004384244.1|  3 ISVIGGGYVGLVSAVCFAQLGHTVGLIEIDIDRAS 37
                                      88*************************88888755 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 ?   10.6   0.1   0.00032      0.52       1      28 [.       5      32 ..       5      62 .. 0.88
   2 ?   -0.8   0.0       1.1   1.8e+03      26      36 ..     254     264 ..     245     273 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      ++G+G  Glv A   a+ g+ v l+e  
  gi|330507816|ref|YP_004384244.1|  5 VIGGGYVGLVSAVCFAQLGHTVGLIEID 32
                                      8**********************99975 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                                       -SSSSSSGGG- CS
                     NAD_binding_8  26 ekrdrlGGraa 36 
                                       +++ ++GG + 
  gi|330507816|ref|YP_004384244.1| 254 DAGAGFGGSCF 264
                                       55555555553 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.82   1.3e+03       1      30 [.       2      31 ..       2      50 .. 0.82
   2 ?   -1.4   0.0       1.5   2.4e+03      97     116 .]     220     239 ..     191     239 .. 0.70
   3 ?    8.6   0.0    0.0012       1.9      10      57 ..     333     384 ..     328     387 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.82
                                      EEEEESB-HHHHHHHHHHHHTT-EEEEES- CS
                            DpaA_N  1 kiaviGGDaRqlylarkLaekgakvslygl 30
                                      ki viGG    l+ a  +a+ g++v l+ +
  gi|330507816|ref|YP_004384244.1|  2 KISVIGGGYVGLVSAVCFAQLGHTVGLIEI 31
                                      6899***99999999999999999999877 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                                       --HHHHHHHHHCT-EEEEGG CS
                            DpaA_N  97 ippelkelaeekgielvdlm 116
                                       + +e+ +l+++ gi ++++m
  gi|330507816|ref|YP_004384244.1| 220 FANEIGNLCKRLGIDVYEVM 239
                                       45667788999999999887 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHTT-EEEEES-....TSSS-BTTEEEE-GGGS-GGG-SEEE- CS
                            DpaA_N  10 RqlylarkLaekgakvslygl....eleekiegvekaesleealedadviil 57 
                                       R + ++ +L e+ga++ +y      ++++ i+++e ++  ++al+dad+++l
  gi|330507816|ref|YP_004384244.1| 333 RSIPVILSLREMGARIAAYDPrandNMKKMIHDIEYCSRATDALRDADACLL 384
                                       8888999************777778889999*****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3002.77
//
Query:       gi|330507817|ref|YP_004384245.1|  [L=234]
Description: nucleotidyl transferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-38  131.6   0.0    4.3e-38  131.3   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    4.5e-10   40.1   0.0      5e-10   40.0   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0018   18.1   0.0     0.0026   17.6   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
     0.0061   16.3   0.0      0.071   12.8   0.0    2.1  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


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 !  131.3   0.0   9.5e-42   4.3e-38      10     242 ..       2     224 ..       1     227 [. 0.95

  Alignments for each domain:
  == domain 1  score: 131.3 bits;  conditional E-value: 9.5e-42
                                       -GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BG CS
                   NTP_transferase  10 GtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgt 86 
                                       GtRL P t++++k l+pv++k  +i+++++++  +giee ivv+ + h++ + ++l++g +fgv++++++++e+ g+
  gi|330507817|ref|YP_004384245.1|   2 GTRLGPFTHAIPKELLPVGEK-AVIEHVVEAMKLAGIEE-IVVVVSPHKHGISDYLGSGRRFGVNLTYVVQDEPLGL 76 
                                       9********************.*****************.88888899***************************** PP

                                       GHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEE CS
                   NTP_transferase  87 AdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverf 162
                                       A+Av+ ++ +++ ++    ++vLg++ +  +  + +++  +i+k+a  ++t+g+ +ve+ t+ G+i++++ +r++++
  gi|330507817|ref|YP_004384245.1|  77 ANAVLSGEHVIDGSF----AVVLGDNFFHPKsFLGDLISYHIAKRA--DATLGVADVEDVTRHGIITVQG-DRIKDI 146
                                       ************999....6********9997789***********..9*******************98.6***** PP

                                       ECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHH CS
                   NTP_transferase 163 vEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldsl 238
                                       +EKP  +ka s+l s GiYvf+++ ++ + +  ++  +ge ++td ++ ++e gk+  +   ++     DvGt+++l
  gi|330507817|ref|YP_004384245.1| 147 IEKPMPEKApSSLGSIGIYVFEPDLFDAI-RRTKPGYNGEYQLTDSIKVLIELGKNVIYKKIDGV--HIDVGTPKDL 220
                                       *****999988899***************.77*************************99888885..6********9 PP

                                       HHHH CS
                   NTP_transferase 239 lean 242
                                       + an
  gi|330507817|ref|YP_004384245.1| 221 VWAN 224
                                       8877 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   1.1e-13     5e-10       9     127 ..       2     129 ..       1     194 [. 0.75

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.1e-13
                                       -TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCT..S-EEE-TTSS-SHH CS
                      NTP_transf_3   9 SsRmgg.....dKallplggkpllervldalraagvdevvvvggd..eevlaal...arlg..vrvvededpgkgpl 73 
                                       ++R+g      +K llp+g+k ++e+v++a++ ag++e+vvv+ +  + + ++l   +r+g  +++v++++   g +
  gi|330507817|ref|YP_004384245.1|   2 GTRLGPfthaiPKELLPVGEKAVIEHVVEAMKLAGIEEIVVVVSPhkHGISDYLgsgRRFGvnLTYVVQDE-PLGLA 77 
                                       78999444678*******************************97734445555533345553366677664.59*** PP

                                       HHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE CS
                      NTP_transf_3  74 aslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeger 127
                                        +++++ + +  +  ++v+++D  + +++++  l+  + a++ad++  +++ e 
  gi|330507817|ref|YP_004384245.1|  78 NAVLSGEHVI--DGSFAVVLGDNFFHPKSFLGDLISYHIAKRADATLGVADVED 129
                                       *******988..7999*******************9998888888777666554 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 !   17.6   0.0   5.8e-07    0.0026      27     131 ..      36     140 ..      20     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.8e-07
                                       CEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHH CS
                   Glycos_transf_2  27 pdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklvea 103
                                          ei+vv    + +  + l + ++ + +++++ ++e  G+a+a+  g    +g + ++l +   +++ +l +l+ +
  gi|330507817|ref|YP_004384245.1|  36 GIEEIVVVVSPHKHGISDYLGSGRRFGVNLTYVVQDEPLGLANAVLSGEHVIDGSFAVVLGDNFFHPKSFLGDLISY 112
                                       6667777777788888888888888999************************************************* PP

                                       HHH.TTCEEEEEEEEEECCCCCCCHC-S CS
                   Glycos_transf_2 104 lekdgadvvlgqrprifgetdeiernkr 131
                                         + +ad+ lg  ++ ++ ++ i   ++
  gi|330507817|ref|YP_004384245.1| 113 HIAKRADATLGVADVEDVTRHGIITVQG 140
                                       ***********99999888777666655 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   1.6e-05     0.071      16      59 ..      10      52 ..       1      94 [. 0.85
   2 ?    1.4   0.0     0.052   2.3e+02     175     216 ..     183     224 ..     166     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                                      SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHH CS
                              IspD 16 aglpKqflelkgqtllehtvdallaskavdkivvvvseddteef 59
                                         pK +l +  ++++eh v+a+     +++ivvvvs+++ +  
  gi|330507817|ref|YP_004384245.1| 10 HAIPKELLPVGEKAVIEHVVEAMKL-AGIEEIVVVVSPHKHGIS 52
                                      5689******************987.78*********9985544 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.052
                                       HCT---SSHHHHHHHTT--EEEEE--TTG----SHHHHHHHH CS
                              IspD 175 qegaeitDdaslvekiGlsvkvVeGeednlKittpeDlalAe 216
                                       +  ++ tD ++++ ++G +v   + +   + + tp+Dl+ A+
  gi|330507817|ref|YP_004384245.1| 183 NGEYQLTDSIKVLIELGKNVIYKKIDGVHIDVGTPKDLVWAN 224
                                       444789*************988888889999*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1672.12
//
Query:       gi|330507818|ref|YP_004384246.1|  [L=59]
Description: hypothetical protein MCON_1832 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.08   12.6   0.1      0.091   12.4   0.1    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 ?   12.4   0.1   5.1e-06     0.091       3      39 ..       5      55 ..       3      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-06
                         DDE_Tnp_1  3 krevlivDattvrvpgtk..............edarwgykggkykygyklh 39
                                      +++ +i D t++++ + +               d+rw +kg++ ++gykl+
  gi|330507818|ref|YP_004384246.1|  5 VKRRTIQDTTFIEADQGSskeprgdeaktrrsRDGRWAKKGDETHFGYKLQ 55
                                      677889999****9888899*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 444.22
//
Query:       gi|330507819|ref|YP_004384247.1|  [L=127]
Description: hypothetical protein MCON_1833 [Methanosaeta concilii GP6]
Scores for complete 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   73.4   0.0    1.8e-20   73.2   0.0    1.1  1  Glycos_transf_1  Glycosyl transferases group 1
    1.1e-12   48.6   0.1    1.5e-12   48.1   0.1    1.2  1  Glyco_trans_1_4  Glycosyl transferases group 1
    0.00045   20.5   0.0     0.0006   20.1   0.0    1.2  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.16   10.8   0.0       0.17   10.7   0.0    1.1  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.0   4.1e-24   1.8e-20      73     155 ..       3      84 ..       1      99 [. 0.90

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 4.1e-24
                                       CGGGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHH CS
                   Glycos_transf_1  73 dnviflgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaeala 149
                                       +nv++l  vs+e+l  l+++++ +++++ +E fG+++lEAma g+pv a++ gg+ e+v++getGllv++n  ++la
  gi|330507819|ref|YP_004384247.1|   3 ENVKMLETVSEEKLVDLYSRCKGLICTAVYEDFGMTPLEAMARGKPVMAVDEGGFTETVVNGETGLLVEAN-RDELA 78 
                                       79*********************************************************************.77777 PP

                                       HHHHHH CS
                   Glycos_transf_1 150 eairkl 155
                                         ++ +
  gi|330507819|ref|YP_004384247.1|  79 GTVEAV 84 
                                       766655 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 !   48.1   0.1   3.3e-16   1.5e-12      55     130 ..       3      83 ..       1      88 [. 0.89

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 3.3e-16
                                       .TEEEE---..THHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHH CS
                   Glyco_trans_1_4  55 erveftGfv..edlaellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpeala 125
                                       e+v+++  v  e+l +l+++++ ++++   e fg++ lEama g+pv a d gg+ e+v  ge+gllv++ + ++la
  gi|330507819|ref|YP_004384247.1|   3 ENVKMLETVseEKLVDLYSRCKGLICTAvyEDFGMTPLEAMARGKPVMAVDEGGFTETVvnGETGLLVEA-NRDELA 78 
                                       6899*****8666*************9999*************************99889********74.688888 PP

                                       HHHHH CS
                   Glyco_trans_1_4 126 eailr 130
                                         +++
  gi|330507819|ref|YP_004384247.1|  79 GTVEA 83 
                                       77665 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.3e-07    0.0006       6      60 ..      30      85 ..      16     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.3e-07
                   Glyco_trans_1_2  6 srsespnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryll 60
                                        +e++ +  +Ea+a G ++++ d  g+ e + +g++++l+e + +ela  ++++ 
  gi|330507819|ref|YP_004384247.1| 30 AVYEDFGMTPLEAMARGKPVMAVDEGGFTETVVNGETGLLVEaNRDELAGTVEAVC 85
                                      34499**************************************9999887776543 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.7e-05      0.17     241     320 ..       4      89 ..       1     118 [. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.7e-05
                                       TEEEE----HHHHHHHHHC-SEEEE.....S-H.HHHHHHHHCT--EEESSSS-S-THHHHTTSEEE.-TT-HHHHH CS
                       Epimerase_2 241 nvtlieplgyldflsllknaklvlt.....dSg.GiqeEapslgvpvvnlReeteRpegveagtnvl.vgtdkeeIv 310
                                       nv+++e +  ++++ l +++k ++      d g +   Ea++ g+pv  + +e+   e+v +g+  l v+++++e+ 
  gi|330507819|ref|YP_004384247.1|   4 NVKMLETVSEEKLVDLYSRCKGLICtavyeDFGmTPL-EAMARGKPVMAV-DEGGFTETVVNGETGLlVEANRDELA 78 
                                       7778888888888888888765443233337775556.************.************99999********9 PP

                                       HHHHHHCT-.. CS
                       Epimerase_2 311 aaleklled.k 320
                                        ++e + ++ +
  gi|330507819|ref|YP_004384247.1|  79 GTVEAVCASlR 89 
                                       99999886642 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 906.17
//
Query:       gi|330507820|ref|YP_004384248.1|  [L=252]
Description: ABC transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-23   82.5  33.3    2.7e-23   82.5  33.3    1.6  2  ABC2_membrane    ABC-2 type transporter
     0.0028   16.8  27.4     0.0028   16.8  27.4    1.6  2  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5  33.3     3e-27   2.7e-23       2     209 ..       8     212 ..       7     213 .. 0.93
   2 ?   -1.5   0.2      0.15   1.4e+03     105     123 ..     223     241 ..     221     249 .. 0.64

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 3e-27
                     ABC2_membrane   2 qikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr.pgllffsvlflafsaltsvapvfer 77 
                                       +i+ l + ++++r++ ++lg++w+l++pll+++v+  vf nl   + +  + + ll ++vl++++   ts+++ +++
  gi|330507820|ref|YP_004384248.1|   8 LILRLAWSDLKLRYKGSALGFFWSLLEPLLMLFVLFEVFTNLMRIQVEN-YqLFLLLGIVLWNFLDRGTSLSIWSIV 83 
                                       67899***********************************976333333.25************************* PP

                     ABC2_membrane  78 ergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllisal 154
                                       ++++++++ ++p   l      ++l++ ++ +++ +if++ +  + g+++   ++f++l +l ++++++l++ +sal
  gi|330507820|ref|YP_004384248.1|  84 GKPSMVQKVYFPRDILVISTCIMALMMTMLEFIVFVIFMFAFRAMPGWTI---GYFPILSMLEFFVVLGLSMSLSAL 157
                                       *************888888888889999999999999999999999****...9*********************** PP

                     ABC2_membrane 155 apsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                       +++f+d+++++ +++++ ++ +++++pi+  p+ ++wi  lnP++ ++ ++r ++
  gi|330507820|ref|YP_004384248.1| 158 NVYFRDVQFIWKVIMQIGFFATPILYPITIFPENVRWIVMLNPMALIIIMMRDSI 212
                                       *******************************99******************9875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.15
                     ABC2_membrane 105 lpvsllqalifllivyflv 123
                                       l++ ++ a+++ll+ yf++
  gi|330507820|ref|YP_004384248.1| 223 LLYLAISAVAILLLGYFIF 241
                                       4555666666666666664 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   2.1      0.46   4.1e+03      12      22 ..      36      46 ..      24      71 .. 0.41
   2 !   16.8  27.4   3.1e-07    0.0028     206     344 ..     100     238 ..      89     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.46
                   ABC2_membrane_3 12 iilvlllglif 22
                                      ++++++l+ +f
  gi|330507820|ref|YP_004384248.1| 36 LLMLFVLFEVF 46
                                      22222222111 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.1e-07
                   ABC2_membrane_3 206 wlskilgdflvyllqlllilllafgl.gipfgnlglllllfllfglayialgyllsslfknsetaqilifivillls 281
                                       ++s  ++ +++ +l ++++++++f++ ++p   +g++ +l++l +++++ l++ ls+l    +++q  i+ vi+ ++
  gi|330507820|ref|YP_004384248.1| 100 VISTCIMALMMTMLEFIVFVIFMFAFrAMPGWTIGYFPILSMLEFFVVLGLSMSLSALNVYFRDVQF-IWKVIMQIG 175
                                       45555555555555566677778884333333666666********************888888886.555555355 PP

                   ABC2_membrane_3 282 gffggl.fpledlpsalkwifsiiPffapglgllrlitgdplweillsliilalfavvylllal 344
                                       +f +++ +p+  +p+ ++wi +++P+  ++ ++ + i + ++ e  lsl++la++av+ lll++
  gi|330507820|ref|YP_004384248.1| 176 FFATPIlYPITIFPENVRWIVMLNPMALIIIMMRDSILYRTPPE-PLSLLYLAISAVAILLLGY 238
                                       555555599***************************98884534.47**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1760.16
//
Query:       gi|330507821|ref|YP_004384249.1|  [L=241]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-24   86.2   0.1    2.5e-23   83.1   0.1    2.1  1  ABC_tran         ABC transporter
    6.6e-08   32.7   0.9    0.00087   19.2   0.7    2.3  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    7.6e-05   22.4   0.0    0.00015   21.4   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
    0.00026   20.9   0.3       0.36   10.7   0.2    2.4  2  NTPase_1         NTPase
      0.002   17.9   1.7     0.0052   16.5   0.9    1.6  2  AAA_15           AAA ATPase domain
     0.0021   18.6   2.2     0.0026   18.3   1.3    1.5  1  AAA_23           AAA domain
     0.0028   18.0   0.0      0.004   17.6   0.0    1.2  1  AAA_16           AAA ATPase domain
     0.0036   17.7   0.0      0.016   15.6   0.0    2.0  1  AAA              ATPase family associated with various cellul
     0.0049   16.6   0.0       0.11   12.2   0.0    2.0  2  AAA_30           AAA domain
     0.0065   15.9   0.5      0.025   14.0   0.1    1.9  2  SMC_N            RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.037   13.8   0.3       0.08   12.7   0.1    1.7  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.042   12.9   0.2        2.7    7.0   0.0    2.1  2  T2SSE            Type II/IV secretion system protein
      0.064   13.6   0.0       0.13   12.6   0.0    1.5  1  AAA_19           AAA domain
      0.073   13.3   0.1        0.2   12.0   0.1    1.8  1  AAA_22           AAA domain
       0.12   12.2   0.7       0.58   10.0   0.7    1.9  1  ATPase_2         ATPase domain predominantly from Archaea
       0.13   12.2   0.0       0.64    9.9   0.0    1.9  2  RsgA_GTPase      RsgA GTPase
       0.14   12.1   0.1       0.33   10.9   0.0    1.7  2  NACHT            NACHT domain
       0.17   12.2   0.0       0.35   11.2   0.0    1.5  1  DUF3221          Protein of unknown function (DUF3221)
       0.18   10.6   0.0         14    4.4   0.0    2.0  2  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra


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 !   83.1   0.1   2.7e-26   2.5e-23       1     135 [.      41     172 ..      41     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 2.7e-26
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk+++++++ ge ++i+G+nG+GKSt+lk++a+  +pt+G++++dgk +     ++l+  +g       + p+lt+r
  gi|330507821|ref|YP_004384249.1|  41 LKDINFEVNDGEFIGIIGDNGSGKSTMLKIIANIIRPTKGRVKVDGKMT-----PFLELGVG-------FHPDLTAR 105
                                       79****************************************7775433.....34554544.......45556666 PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       en             e +e+i+++++  gl++++dt++    ++LS G+++r+a   a+ ++p++ll+DE 
  gi|330507821|ref|YP_004384249.1| 106 ENiivygtimgisrkEIRERIDDVIEFAGLEKFQDTKL----KNLSSGMQVRLAFSTAIQTDPDVLLVDEV 172
                                       66666666999999899999******************....****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.7   9.3e-07   0.00087       1      37 [.      53      76 ..      53     131 .. 0.71
   2 !   11.8   0.0   0.00016      0.15     227     297 ..     136     203 ..     112     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.3e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdels 37
                                      + ++iG+NgsGKS+ L+++  +              +
  gi|330507821|ref|YP_004384249.1| 53 FIGIIGDNGSGKSTMLKIIANII-------------R 76
                                      678****************6553.............2 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00016
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       ++ q++ + +lS+G++  la+ ta+  ++   ++ll+DE+ +  + +++ + ++++k+ +++g+ v++++H
  gi|330507821|ref|YP_004384249.1| 136 EKFQDTKLKNLSSGMQVRLAFSTAIQTDP---DVLLVDEVLAVGDMEFQQKCFDVFKRYRNEGVTVLFVSH 203
                                       45566777899****************99...9******98888888888888888888888888888888 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.6e-07   0.00015      15      50 ..      42      79 ..      33      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.6e-07
                            AAA_29 15 htieidlkg..atlltGpsGsGKSTllDAiqalLvpak 50
                                      ++i++++++  ++ ++G++GsGKST+l  i+ ++ p+k
  gi|330507821|ref|YP_004384249.1| 42 KDINFEVNDgeFIGIIGDNGSGKSTMLKIIANIIRPTK 79
                                      66666666656888*************99999888877 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.2   0.00038      0.36       2      37 ..      54      91 ..      53      97 .. 0.83
   2 !    7.9   0.0    0.0028       2.6      92     131 ..     159     201 ..     141     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                                      EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfytee 37
                                      + i G  G+GK+T++k +++ ++     vkv+G +t+ 
  gi|330507821|ref|YP_004384249.1| 54 IGIIGDNGSGKSTMLKIIANIIRPTkgRVKVDGKMTPF 91
                                      56889*************99998553369999999985 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0028
                                       HH.HHH-EEEE--...-STTGGG-HHHHHHHHHHHTTTSEEEEE CS
                          NTPase_1  92 al.seadviviDE...iGkmElkskkfkeaveevLksekpvlav 131
                                       a+ +++dv+++DE   +G mE++ k f    ++  ++++ vl+v
  gi|330507821|ref|YP_004384249.1| 159 AIqTDPDVLLVDEvlaVGDMEFQQKCFD-VFKRYRNEGVTVLFV 201
                                       333799*******5555****9988874.445555555555555 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   0.9   5.5e-06    0.0052      14      46 ..      41      74 ..      37      89 .. 0.76
   2 ?   -1.0   0.0       1.2   1.1e+03     289     310 ..     138     159 ..     106     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.5e-06
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlF 46
                                      lkd+  ++++  +  +iG N+sGKS+ l+++  +
  gi|330507821|ref|YP_004384249.1| 41 LKDINFEVNDGeFIGIIGDNGSGKSTMLKIIANI 74
                                      666444444447999***************9655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                            AAA_15 289 deelplnknGsGvqrllllill 310
                                        ++++l++ +sG+q  l +++ 
  gi|330507821|ref|YP_004384249.1| 138 FQDTKLKNLSSGMQVRLAFSTA 159
                                       4678999999999988888765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.3   2.7e-06    0.0026      11      39 ..      42      71 ..      34      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.7e-06
                            AAA_23 11 rdqeidF...skgltlItGpNGaGKTTildAi 39
                                      +  +i+F   +  +  I+G+NG+GK+T l  i
  gi|330507821|ref|YP_004384249.1| 42 K--DINFevnDGEFIGIIGDNGSGKSTMLKII 71
                                      3..4666665557889************9877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.2e-06     0.004      21     114 ..      50     155 ..      38     209 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.2e-06
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdql.esa............ipysalaqalareellr 83 
                                       +g  e + ++G+ G+GKs++++ +++ ++ ++g + + gk + + e +            i  +  +  ++r+e+ +
  gi|330507821|ref|YP_004384249.1|  50 DG--EFIGIIGDNGSGKSTMLKIIANIIRPTKGRVkVDGKMTPFlELGvgfhpdltarenIIVYGTIMGISRKEIRE 124
                                       44..67889*****************999998888888888888622233334443333333355555555889999 PP

                            AAA_16  84 qlldeaesaeleawrekleealaavpelaga 114
                                        ++d  e a le ++++ +++l+++ +++ a
  gi|330507821|ref|YP_004384249.1| 125 RIDDVIEFAGLEKFQDTKLKNLSSGMQVRLA 155
                                       9999999999999999988888854444443 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 !   15.6   0.0   1.7e-05     0.016       3      86 ..      56     181 ..      54     212 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                                       EESSTTSSHHHHHHHHHHHHTHE...................................EEEEETTTCSSS....... CS
                               AAA   3 lyGppGtGKTllakavakelgve...................................fleisgsellsk....... 37 
                                       ++G  G GK+++ k +a+ +  +                                   ++ is +e+++        
  gi|330507821|ref|YP_004384249.1|  56 IIGDNGSGKSTMLKIIANIIRPTkgrvkvdgkmtpflelgvgfhpdltareniivygtIMGISRKEIRERiddvief 132
                                       6899***************7422233445566777777888888888888999999994444444444335555555 PP

                                       ...........STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHH CS
                               AAA  38 ...........yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervv 86 
                                                      s +++r  f++a +   p +l++DE+ a++  +           +
  gi|330507821|ref|YP_004384249.1| 133 aglekfqdtklKNLSSGMQVRLAFSTAIQTD-PDVLLVDEVLAVGDME----------FQ 181
                                       5555544567666678899999999998887.********98887666..........34 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00012      0.11      20      50 ..      53      83 ..      46      94 .. 0.86
   2 ?    2.4   0.0      0.12   1.1e+02      84     122 ..     158     201 ..     113     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvi 50
                                      +  + G  G+GK+t+lk ++++++  +grv 
  gi|330507821|ref|YP_004384249.1| 53 FIGIIGDNGSGKSTMLKIIANIIRPTKGRVK 83
                                      56789******************99977775 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                            AAA_30  84 arlepg.tllivDEagmv....dtkqlaallkaaekagakvilv 122
                                       ++++++ ++l+vDE+  v     +++  +++k+ +++g++v++v
  gi|330507821|ref|YP_004384249.1| 158 TAIQTDpDVLLVDEVLAVgdmeFQQKCFDVFKRYRNEGVTVLFV 201
                                       45666669******988832222344556888888888888887 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   2.7e-05     0.025      24      44 ..      51      71 ..      35      81 .. 0.81
   2 ?   -0.1   0.0      0.55   5.2e+02     146     198 ..     153     204 ..     117     222 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-05
                                      SSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAi 44
                                       +f  i+G NGSGKs +l  i
  gi|330507821|ref|YP_004384249.1| 51 GEFIGIIGDNGSGKSTMLKII 71
                                      46999***********99766 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.55
                                       HHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N 146 alaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislr 198
                                        la+  Aiq      + l+De+ a  D +  +k  +++k+ +++ + ++ +s+ 
  gi|330507821|ref|YP_004384249.1| 153 RLAFSTAIQ--TDPDVLLVDEVLAVGDMEFQQKCFDVFKRYRNEgVTVLFVSHG 204
                                       333333333..3333557899999999998888888888777654666666665 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   8.5e-05      0.08       1      27 [.      53      79 ..      53     107 .. 0.82
   2 ?   -2.5   0.0       3.7   3.5e+03     105     131 ..     101     127 ..      88     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.5e-05
                               PRK  1 vIgvagsSGaGkttvarklekifgrek 27
                                      +Ig+ g+ G+Gk+t+ + + +i++ +k
  gi|330507821|ref|YP_004384249.1| 53 FIGIIGDNGSGKSTMLKIIANIIRPTK 79
                                      69********************99433 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.7
                               PRK 105 eliegadvlviEGlhalydervaelld 131
                                       +l +  +++v+  + ++  ++++e +d
  gi|330507821|ref|YP_004384249.1| 101 DLTARENIIVYGTIMGISRKEIRERID 127
                                       667778899999999999999988777 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 ?    7.0   0.0    0.0029       2.7     131     160 ..      53      82 ..      18      84 .. 0.85
   2 ?    4.1   0.1     0.022        20     163     208 ..     126     172 ..     109     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0029
                             T2SSE 131 lilvsGgTgsGKttllyallkeinksderi 160
                                        i + G  gsGK+t+l ++ ++i  ++ r+
  gi|330507821|ref|YP_004384249.1|  53 FIGIIGDNGSGKSTMLKIIANIIRPTKGRV 82 
                                       55677999*************999887665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.022
                             T2SSE 163 vEDpvEiq.leganqvqlnakkakvtfadllraaLRlrPDrimvGEi 208
                                       + D +E   le+ + ++l++ + +++++ +  +a+  +PD+++v E+
  gi|330507821|ref|YP_004384249.1| 126 IDDVIEFAgLEKFQDTKLKNLSSGMQVRLAFSTAIQTDPDVLLVDEV 172
                                       6677776525888889999889999*******************997 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   0.00014      0.13      11     115 ..      52     176 ..      43     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelggvkp.......................eeillvaftgrAakelrerlaa 64 
                                       + + +++  G+GK+++lk i +++  ++g+                         + i+  +  g + ke+rer++ 
  gi|330507821|ref|YP_004384249.1|  52 EFIGIIGDNGSGKSTMLKIIANIIRPTKGRVKvdgkmtpflelgvgfhpdltareNIIVYGTIMGISRKEIRERID- 127
                                       67889*************99999988876644699999***************966677789999**********4. PP

                            AAA_19  65 lgaeatTiHrlalldfddlltealelle.....eaeeekklqeee.llivDEfqdvd 115
                                          +   + +l   +f+d++ + l         + + ++ +q    +l+vDE+  v 
  gi|330507821|ref|YP_004384249.1| 128 ---DVIEFAGL--EKFQDTKLKNL---SsgmqvRLAFSTAIQTDPdVLLVDEVLAVG 176
                                       ...44446666..55555442222...22233555566667655569*****97775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00021       0.2       6     101 ..      52     173 ..      48     210 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.........................erpevv....fvtlpsstss 53 
                                        ++ ++G  G+GK+t l+ +++     +   +                         +  e +    ++   s ++ 
  gi|330507821|ref|YP_004384249.1|  52 EFIGIIGDNGSGKSTMLKIIANIIR--PT--KgrvkvdgkmtpflelgvgfhpdltaR--ENIivygTIMGISRKEI 122
                                       67889*************9999863..22..234667778888888888876666431..22201232222222244 PP

                            AAA_22  54 kdllrellralglelkaerlsseellealeqalrarav....ielliiDEaq 101
                                       ++   ++ ++ gle+     +++ l + ++  l    +    + +l++DE+ 
  gi|330507821|ref|YP_004384249.1| 123 RERIDDVIEFAGLEKFQ-DTKLKNLSSGMQVRLAFSTAiqtdPDVLLVDEVL 173
                                       44444445555554444.3333333333333333222234466788888775 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.7   0.00062      0.58      18     137 ..      49     182 ..      33     194 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00062
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie..............eeeekkklek 80 
                                       +  e++ i G  gsGK+++lk i++  +   k ++ ++   + +++    f                   ++k++++
  gi|330507821|ref|YP_004384249.1|  49 NDGEFIGIIGDNGSGKSTMLKIIANIIRP-TKGRVKVDGKMTPFLELGVGFHPdltareniivygtiMGISRKEIRE 124
                                       456788899**********9988887755.55566666665555555555522454444566666555556666777 PP

                          ATPase_2  81 algiavpkaeleeilkeksklvfkaielllekikkkgkk.iiiiiDelqklidlglng 137
                                        + ++++ a le++ ++k k++ + ++  l+  +  ++   ++++De+  ++d+ +++
  gi|330507821|ref|YP_004384249.1| 125 RIDDVIEFAGLEKFQDTKLKNLSSGMQVRLAFSTAIQTDpDVLLVDEVLAVGDMEFQQ 182
                                       7777788777776666888888888887777666666664599999999999998875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00068      0.64      89     121 ..      40      73 ..      16      88 .. 0.80
   2 ?   -0.5   0.0         1   9.8e+02      62      85 ..     182     204 ..     165     220 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00068
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       +l++++ +++d +++ ++G  G GKSt+++ +++
  gi|330507821|ref|YP_004384249.1|  40 ALKDINFEVNDgEFIGIIGDNGSGKSTMLKIIAN 73 
                                       5778888888889999************998876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHTTSEEEE--TT CS
                       RsgA_GTPase  62 eeeleelkeelealgyevllvsak 85 
                                       ++ + ++ +++++ g++vl+vs  
  gi|330507821|ref|YP_004384249.1| 182 QK-CFDVFKRYRNEGVTVLFVSHG 204
                                       33.6678899999*****999865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.8   5.5e+03      23      49 ..       8      33 ..       4      41 .. 0.65
   2 ?   10.9   0.0   0.00035      0.33       4      24 ..      55      75 ..      52      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.8
                                      HHCTS-SCCCC-SEEEEEETTTTTTS- CS
                             NACHT 23 awaegklpqgafklvFflslrelsrsg 49
                                      +w++ + p+++ +  +f +l+el r++
  gi|330507821|ref|YP_004384249.1|  8 LWKTFRIPHEK-RTTIFENLAELVRPN 33
                                      56666677764.677777777766665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00035
                                      EEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqklalaw 24
                                       + G++GsGK+t+l+ +a  +
  gi|330507821|ref|YP_004384249.1| 55 GIIGDNGSGKSTMLKIIANII 75
                                      589************998765 PP

>> DUF3221  Protein of unknown function (DUF3221)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00038      0.35      25      65 ..     116     160 ..     108     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                           DUF3221  25 nlseeeiekykgeaiwv....lidsdkvsnlevGqkVrVwfdgki 65 
                                       + s +ei +  ++ i +    ++++ k++nl++G++Vr  f+  i
  gi|330507821|ref|YP_004384249.1| 116 GISRKEIRERIDDVIEFagleKFQDTKLKNLSSGMQVRLAFSTAI 160
                                       668899999999999999999******************999655 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 ?    4.3   0.0     0.016        15      36      74 ..      45      82 ..      15      89 .. 0.71
   2 ?    4.4   0.0     0.014        14     306     337 ..     166     197 ..     138     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.016
                   T4SS-DNA_transf 36 gllntdGdfehvlvvAptrsgKgvgv.viPnllkwkqsiV 74
                                      ++ ++dG+f  +++++  +sgK++ + +i n++  ++  V
  gi|330507821|ref|YP_004384249.1| 45 NFEVNDGEF--IGIIGDNGSGKSTMLkIIANIIRPTKGRV 82
                                      366788877..***********998757888887777655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.014
                   T4SS-DNA_transf 306 lflLDEfpslGkleileealatiagYgirltl 337
                                        +l DE+  +G +e  ++  ++++ Y+ + ++
  gi|330507821|ref|YP_004384249.1| 166 VLLVDEVLAVGDMEFQQKCFDVFKRYRNEGVT 197
                                       6899**********************866555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 1762.37
//
Query:       gi|330507822|ref|YP_004384250.1|  [L=583]
Description: B12 binding domain/radical SAM domain fusion protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-24   85.0   0.0    1.1e-22   80.3   0.0    2.7  3  B12-binding    B12 binding domain
    2.9e-17   63.5   0.0    1.3e-16   61.5   0.0    2.0  2  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
       0.16   11.1   0.0       0.29   10.3   0.0    1.4  1  Radical_SAM_N  Radical SAM N-terminal
       0.17   12.0   0.0       0.24   11.4   0.0    1.3  1  CbiA           CobQ/CobB/MinD/ParA nucleotide 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 !   80.3   0.0   2.5e-26   1.1e-22      11     120 ..       4     114 ..       2     115 .. 0.94
   2 ?   -1.3   0.0      0.47   2.1e+03      21      48 ..     274     301 ..     273     303 .. 0.88
   3 ?    0.9   0.0     0.096   4.3e+02      33      61 ..     331     359 ..     317     366 .. 0.76

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 2.5e-26
                       B12-binding  11 dlhplGlavlaaalrdagfeVqllganven...edivaairaekpdvvglSalltsqleavkelvellkrirprvkv 84 
                                        l+plGl ++a  l+++g+eV++++a+ven   +++ + +r+ +pd++gl+   t q +a+ e+ve+lkr+  +++v
  gi|330507822|ref|YP_004384250.1|   4 ILPPLGLLYIASTLKREGHEVKVVDADVENlslATVSKTARDYAPDLIGLTM-NTLQSRAAYETVEQLKRAY-DAPV 78 
                                       689***********************************************99.**************99995.58** PP

                       B12-binding  85 vvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                       ++GG+hps++  e+le  + +d vv gege +  ++
  gi|330507822|ref|YP_004384250.1|  79 IAGGPHPSALRGEVLERCPSLDAVVYGEGEATTLEI 114
                                       ***************866999*********998776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.47
                       B12-binding  21 aaalrdagfeVqllganvenedivaair 48 
                                         + +dagf  +++g++  n++++++i+
  gi|330507822|ref|YP_004384250.1| 274 LKMAKDAGFWMIFYGVESGNQRVLDSIK 301
                                       578999**************99999987 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.096
                       B12-binding  33 llganven.edivaairaekpdvvglSall 61 
                                       +lg   e+ +d+++ +r+++pd  g+ +  
  gi|330507822|ref|YP_004384250.1| 331 NLGESRETiKDTIRFARKLDPDYYGFAV-A 359
                                       56555666799***********999976.4 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   2.8e-20   1.3e-16       3     166 ..     182     345 ..     180     346 .. 0.88
   2 ?   -1.5   0.0      0.65   2.9e+03      94     123 ..     378     406 ..     356     416 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 2.8e-20
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHH.HHHHHHHTC... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx... RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggepllypdfve.llerlakla... 74 
                                        +rgC+++C+fC+ +    +e+  r + v+++l+ev++l+   + vke+++  ++ ++++   e l   l++l    
  gi|330507822|ref|YP_004384250.1| 182 ASRGCPFQCTFCSKGI---WERSLRLRKVDSVLAEVEWLRdTFR-VKEIFFQDDTLNVNRGWFEsLCSGLVELGlnk 254
                                       589************8...********************95555.*********99999654440444444443655 PP

                                       CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivg 151
                                       + +++  + +n+ ++d+++l+  +++g+  +  g+e+++ + vl+ +++g t+ e+ +a+++ ++agik   ++++g
  gi|330507822|ref|YP_004384250.1| 255 KVKFKGPFRANEKMVDPDILKMAKDAGFWMIFYGVESGNQR-VLDSIKKGITLRELERAFQITKKAGIKTYASFMIG 330
                                       6677777888888888*************************.*********************************** PP

                                       BTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                       Radical_SAM 152 lpGendeeleellel 166
                                         Ge++e++++++++
  gi|330507822|ref|YP_004384250.1| 331 NLGESRETIKDTIRF 345
                                       *************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.65
                                       HHHHHHTT-SEEEEEEBSSSHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  94 lerllelgvdrvslgleaaddekvlklmnr 123
                                       l+ + e+ ++r+ l  e++ +e+v++lm +
  gi|330507822|ref|YP_004384250.1| 378 LADFEEYDLNRYVLKTESLGPEDVQELM-D 406
                                       5677888899999999999999999988.3 PP

>> Radical_SAM_N  Radical SAM N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   6.5e-05      0.29     161     202 ..      99     137 ..      84     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.5e-05
                     Radical_SAM_N 161 adllvyGmgeraiveiakrlakgeeveelkdirgtavllkke 202
                                        d +vyG ge +++ei k++++g++   l d++g+++ + +e
  gi|330507822|ref|YP_004384250.1|  99 LDAVVYGEGEATTLEILKAFEDGRD---LADVEGICYRQGEE 137
                                       499******************9998...77888999865543 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 ?   11.4   0.0   5.4e-05      0.24      19      55 ..      13     114 ..      10     392 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.4e-05
                                       HHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH......................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................... RF
                              CbiA  19 LaralarrglrVllvDaDpqannlaileglendiep......................................... 54 
                                       +a  l+r+g++V +vDaD++  +la++ ++  d +p                                         
  gi|330507822|ref|YP_004384250.1|  13 IASTLKREGHEVKVVDADVENLSLATVSKTARDYAPdligltmntlqsraayetveqlkraydapviaggphpsalr 89 
                                       68899***************888888999999999977777777776666666666666666666666666665555 PP

                                       ........................C CS
                                       ........................x RF
                              CbiA  55 ........................d 55 
                                                                
  gi|330507822|ref|YP_004384250.1|  90 gevlercpsldavvygegeattleI 114
                                       5555555555555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 3809.77
//
Query:       gi|330507823|ref|YP_004384251.1|  [L=299]
Description: UbiA family prenyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-24   84.7  23.3    2.1e-23   82.9  22.6    2.0  1  UbiA            UbiA prenyltransferase family
  ------ inclusion threshold ------
      0.034   14.2   1.0        1.6    8.9   0.6    2.9  2  YebO            YebO-like protein
      0.096   12.5   0.2       0.16   11.8   0.2    1.2  1  Synaptonemal_3  Synaptonemal complex central element protein 


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9  22.6   3.6e-27   2.1e-23      10     162 ..      46     195 ..      37     283 .. 0.73

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 3.6e-27
                              UbiA  10 alaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllal 86 
                                        +   ++  ++ ++++++ ++l++++++++Nd+ D++ D++++ ++ RP++ G +s ++al+++i+ll ++ll++ +
  gi|330507823|ref|YP_004384251.1|  46 SYNLFNWEMWPRVIFAFIMFCLISGSIYIINDIKDVDRDRLHPKKRFRPIAFGTLSSRTALLVSILLLSISLLIS-F 121
                                       333334445578888888888******************************************************.* PP

                              UbiA  87 llnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaiala 162
                                       ++n ++ ++ ll++++ ++Yt ++lK++ l++ +v+++ f+l +++g  +++  +s++++l+ ++ + +++a+   
  gi|330507823|ref|YP_004384251.1| 122 FVNRPLCYIELLYVFINLLYT-FYLKYFALIDVIVVAVGFVLRAVAGSLVINVYISPWLILCVFL-MSFVLAFGKR 195
                                       *********************.9****************************99986555555444.5555555544 PP

>> YebO  YebO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.6   0.00027       1.6       2      19 ..     108     125 ..     107     127 .. 0.92
   2 ?    2.3   0.0      0.03   1.8e+02      35      47 ..     190     202 ..     182     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00027
                              YebO   2 vlvivvlvgllvwFFvnR 19 
                                       v+++++ + ll++FFvnR
  gi|330507823|ref|YP_004384251.1| 108 VSILLLSISLLISFFVNR 125
                                       7899999**********9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.03
                              YebO  35 leqqkrQnaLLrr 47 
                                       l   krQn+LL++
  gi|330507823|ref|YP_004384251.1| 190 LAFGKRQNELLTA 202
                                       55569******87 PP

>> Synaptonemal_3  Synaptonemal complex central element protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   2.7e-05      0.16      20      46 ..     208     234 ..     192     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                    Synaptonemal_3  20 qlnkdleklteqmedvsvkltwmaydm 46 
                                        l +  ek++e + ++sv +  may +
  gi|330507823|ref|YP_004384251.1| 208 CLSQYTEKMVEGLLNISVSMLLMAYAL 234
                                       488999*******************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2061.74
//
Query:       gi|330507824|ref|YP_004384252.1|  [L=415]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete 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   82.5   0.2    6.2e-23   80.9   0.1    1.9  2  Transposase_20  Transposase IS116/IS110/IS902 family
    6.1e-23   81.4   0.0    1.6e-22   80.1   0.0    1.7  2  DEDD_Tnp_IS110  Transposase
     0.0093   15.6   0.0       0.02   14.5   0.0    1.5  1  SET_assoc       Histone lysine methyltransferase SET associat
  ------ inclusion threshold ------
      0.023   15.0   0.0      0.073   13.4   0.0    1.9  1  Ish1            Putative stress-responsive nuclear envelope p
      0.028   14.4   0.1      0.078   13.0   0.1    1.8  1  Hjc             Archaeal holliday junction resolvase (hjc)
      0.089   12.6   0.1       0.27   11.0   0.0    1.9  2  BING4CT         BING4CT (NUC141) domain
       0.19   12.0   3.9          1    9.7   0.5    2.7  2  DUF4164         Domain of unknown function (DUF4164)


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.1   2.4e-26   6.2e-23       2      87 .]     254     340 ..     253     340 .. 0.95
   2 ?   -2.8   0.0       3.1   8.1e+03      48      78 ..     377     407 ..     372     414 .. 0.66

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 2.4e-26
                    Transposase_20   2 elLesipGiGpvtaaallaei.gdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaair 77 
                                       +l++sipGi++v a+a+laei  d+++f+++++l ++aG++p +n+S++kk++g+++k Gn+ l+ +L eaA+aa++
  gi|330507824|ref|YP_004384252.1| 254 NLIQSIPGISKVSASAILAEIgTDMSQFPDEAHLSSWAGVCPGNNESAGKKKSGKTQK-GNSFLKGTLAEAAWAASK 329
                                       689******************9999***************************999999.*****************7 PP

                    Transposase_20  78 an.pelrayye 87 
                                        + ++  a+y+
  gi|330507824|ref|YP_004384252.1| 330 VKrSTYNAFYQ 340
                                       76699999997 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.1
                    Transposase_20  48 GkkkrrgriskrGnrrlRraLyeaAlaaira 78 
                                       G  + + r +kr  r + r+L  a   ++r+
  gi|330507824|ref|YP_004384252.1| 377 GAEEANERATKRKERSMIRLLEKAGYEVVRT 407
                                       5555567888888888888777777666654 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.0   6.1e-26   1.6e-22       1     152 [.       9     155 ..       9     158 .. 0.91
   2 ?   -3.8   0.0       4.2   1.1e+04      54      74 ..     385     405 ..     384     406 .. 0.80

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 6.1e-26
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvl..ls.ervpndeeglealleklaakagevlvvveatghygallvaflleagitvv 74 
                                       +G+Dv+++k d+c+ +   ++   ++ +++++  ++le+l ++ ++k   +++++e+tg y+++++++  e ++t+v
  gi|330507824|ref|YP_004384252.1|   9 AGMDVHEKKVDVCIAHGPLEKSpkFEiRTFSTMTSDLEDLKSW-LKKYNVTTIGMESTGVYWKPIFNI-MEGEFTIV 83 
                                       69*************98777773333346888899********.9999***************98887.899***** PP

                    DEDD_Tnp_IS110  75 vvnplavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLd 151
                                       + n+   k++      ++KtD  D k IA+llr  g l ++  ++ +++eLr l+r r++lv ++t++knrl+++L+
  gi|330507824|ref|YP_004384252.1|  84 LANAQRLKAIP-----RKKTDIMDCKRIAKLLR-YGLLPNSFIPPREIRELRDLNRTRRKLVGMMTSEKNRLTKVLE 154
                                       ****9999985.....79***************.******************************************8 PP

                    DEDD_Tnp_IS110 152 q 152
                                       +
  gi|330507824|ref|YP_004384252.1| 155 S 155
                                       6 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.2
                    DEDD_Tnp_IS110  54 atghygallvaflleagitvv 74 
                                       at+++ ++++ +l++ag++vv
  gi|330507824|ref|YP_004384252.1| 385 ATKRKERSMIRLLEKAGYEVV 405
                                       567778888999999999986 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 !   14.5   0.0   7.9e-06      0.02       8      37 ..      39      68 ..      34      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.9e-06
                         SET_assoc  8 pvhkvtvedlkkrLkkyeweriledktGyY 37
                                      +++++++edlk  Lkky+++ i ++ tG Y
  gi|330507824|ref|YP_004384252.1| 39 STMTSDLEDLKSWLKKYNVTTIGMESTGVY 68
                                      689999***********************9 PP

>> Ish1  Putative stress-responsive nuclear envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.8e-05     0.073       2      18 ..      39      57 ..      38      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                              Ish1  2 dtWSd..sdLkkWLdshGi 18
                                      +t +   +dLk+WL+++++
  gi|330507824|ref|YP_004384252.1| 39 STMTSdlEDLKSWLKKYNV 57
                                      55555579**********8 PP

>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1     3e-05     0.078       2      26 ..     389     413 ..     388     415 .] 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                                       HHHHHHHHHHHTT-EEEEBSCSSSS CS
                               Hjc   2 yERelvkiLrergfavvRsagSgga 26 
                                       +ER ++++L++ g++vvR ++S  a
  gi|330507824|ref|YP_004384252.1| 389 KERSMIRLLEKAGYEVVRTCTSEIA 413
                                       7*********************866 PP

>> BING4CT  BING4CT (NUC141) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.6   9.3e+03      64      70 ..     176     182 ..     174     190 .. 0.80
   2 ?   11.0   0.0   0.00011      0.27      39      76 ..     368     405 ..     351     407 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.6
                           BING4CT  64 VrsLLeK 70 
                                       +rsLLeK
  gi|330507824|ref|YP_004384252.1| 176 IRSLLEK 182
                                       899**99 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                           BING4CT  39 GsGepnfdaleanpfetkkqrrereVrsLLeKlqpelI 76 
                                         G p  d+  ++ +e +++r+er   +LLeK  +e++
  gi|330507824|ref|YP_004384252.1| 368 KTGAPYQDTGAEEANERATKRKERSMIRLLEKAGYEVV 405
                                       67999***************************988876 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.061   1.6e+02      36      65 ..     133     163 ..     123     182 .. 0.68
   2 ?    9.7   0.5    0.0004         1       9      46 ..     194     240 ..     186     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.061
                           DUF4164  36 eleaei.ealgedrsRLaeeLdqaearaarl 65 
                                         ++++   ++++++RL + L +++ +++++
  gi|330507824|ref|YP_004384252.1| 133 RTRRKLvGMMTSEKNRLTKVLESSNIKLSSV 163
                                       4444433789999999999999888877665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0004
                           DUF4164   9 altrLeaaldsLEkavdrrleaerkr.........deleaeiealge 46 
                                       a   L++++d LEka+d +l+              d l+++i++++e
  gi|330507824|ref|YP_004384252.1| 194 AKGSLKKKVDLLEKALDGKLTDHHRFllkmhmenlDHLARQIAKIDE 240
                                       6779****************988887887777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1155  (0.0644208); expected 358.6 (0.02)
Passed bias filter:                      687  (0.0383178); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2850.21
//
Query:       gi|330507825|ref|YP_004384253.1|  [L=203]
Description: hypothetical protein MCON_1841 [Methanosaeta concilii GP6]
Scores for complete 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   36.7   0.0    4.9e-09   35.8   0.0    1.5  1  PHP_C     PHP-associated
    4.4e-07   30.3   0.0    4.7e-07   30.3   0.0    1.1  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 !   35.8   0.0   5.4e-13   4.9e-09       3      45 ..     125     166 ..     123     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 5.4e-13
                             PHP_C   3 aNrrArrfAeklglpgtgGSDAHrleeVGrayTef.eepiatpd 45 
                                        N+ A  f ++++l+ t+GSDAH+l eVG++ +   +e+i+  +
  gi|330507825|ref|YP_004384253.1| 125 YNDLAYNFGKEYDLAITAGSDAHFLNEVGNGGIITgQENIR--E 166
                                       69*****************************9888555554..3 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   5.2e-11   4.7e-07      15      89 ..       1     108 [.       1     191 [. 0.74

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 5.2e-11
                                       H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
                               PHP  15 lsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse.................. 73 
                                       +++e lv+ ak+++l+ +a+TDh+ ++g++e +  +++++  ++ +iiG e++  ++++                  
  gi|330507825|ref|YP_004384253.1|   1 MKPERLVEHAKKKELDGLAVTDHNTIDGALEVFDIVRDEH-MDFSVIIGEEISTDRGEVlayfinreiepgsfvqvl 76 
                                       5789********************************8877.89********77777776888888888888888888 PP

                                       ..........................E....E CS
                                       ................xxxxxxxxxxxxxxxx RF
                               PHP  74 ................kerpshltllaknqeG 89 
                                                       ++  +h++ l  n  +
  gi|330507825|ref|YP_004384253.1|  77 teirraggisaiphpfDKLRHHAVRLTSNDVE 108
                                       88888888888888885555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1431.17
//
Query:       gi|330507826|ref|YP_004384254.1|  [L=646]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.62u 0.24s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 4680.80
//
Query:       gi|330507827|ref|YP_004384255.1|  [L=490]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-11   42.8   0.0    8.8e-11   41.9   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
    1.8e-10   41.3   0.0    3.9e-10   40.3   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    1.1e-07   31.8   0.0    2.1e-07   30.8   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    4.5e-06   27.3   0.0    9.5e-06   26.2   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    4.3e-05   24.2   0.0    0.00011   22.9   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.015   14.4   0.0      0.027   13.6   0.0    1.3  1  DREV             DREV methyltransferase
      0.033   12.7   0.0       0.05   12.2   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   3.4e-14   8.8e-11      39     164 ..     154     291 ..      92     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 3.4e-14
                   Methyltransf_23  39 vlrengfsvtgvDlspeaveiae....kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvp.dppellrqiatllk 110
                                       ++ren   v+  ++s+e+         k+ ++q+  + ++  ++++  fd++   e++eh++ dp  +l  +++ lk
  gi|330507827|ref|YP_004384255.1| 154 IYRENAERVCPLEISFENPRNHMkeyiKTEFYQFNVE-SDMYPFSDSEFDVVLFCELIEHMQmDPIYALMEMKRVLK 229
                                       3444545666666666644433244445555555555.445566889***************99************* PP

                   Methyltransf_23 111 pgGylllseplasl........kedrllldwlylvpagrhisffsarslkelleeaGlevve 164
                                       p+G+l+l++p+a+         +  + ++++    p grh + ++ ++l +lle  G+++++
  gi|330507827|ref|YP_004384255.1| 230 PNGVLILTTPNANRieniirmiSGSNIYDHYSGYGPYGRHNREYNVHELMTLLEYCGFSIDS 291
                                       ***********998988888875556677777779999********************9976 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   1.5e-13   3.9e-10      18      96 .]     159     236 ..     144     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.5e-13
                                       TSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC.T.SS-TT-EEEEEEES-CCC-.CCHHHHHHHHHHHEEEE CS
                   Methyltransf_11  18 garvvgvDlskemlklakekaseeglkvefvvadaek.l.pfednsfDlvvssevlhhv.edpekalkeiaRvLkpg 91 
                                       ++rv  +++s e  +       +e++k ef + ++e+ + pf d+ fD+v+  e ++h+  dp  al e++RvLkp+
  gi|330507827|ref|YP_004384255.1| 159 AERVCPLEISFENPRNH---M-KEYIKTEFYQFNVESdMyPFSDSEFDVVLFCELIEHMqMDPIYALMEMKRVLKPN 231
                                       45666666666665222...2.222256678999995566*******************99**************** PP

                                       EEEEE CS
                   Methyltransf_11  92 Gllvi 96 
                                       G+l++
  gi|330507827|ref|YP_004384255.1| 232 GVLIL 236
                                       **985 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   8.3e-11   2.1e-07      51     113 ..     177     240 ..     167     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 8.3e-11
                   Methyltransf_31  51 lgldnveFeqgdieelekl.ledekfDlilsnevl.naladpdkileeiervlkpggilliedpr 113
                                       +++   eF q ++e+ ++  ++d+ fD++l  e++ + + dp  +l+e++rvlkp+g+l++++p+
  gi|330507827|ref|YP_004384255.1| 177 KEYIKTEFYQFNVES-DMYpFSDSEFDVVLFCELIeHMQMDPIYALMEMKRVLKPNGVLILTTPN 240
                                       5788899*******9.4455********999999989999************************9 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   3.7e-09   9.5e-06      35      97 .]     173     232 ..     148     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.7e-09
                                       HHHHHHHHHTTTTEEEEESBCCG..BSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  35 eaareraeeeglnvefvqgdaed..lpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                       ++  +    e ++ ef+q ++e+  +pf d++fD+v+ +  ++h++  d   al e++rvLkp+G
  gi|330507827|ref|YP_004384255.1| 173 RNHMK----EYIKTEFYQFNVESdmYPFSDSEFDVVLFCELIEHMQM-DPIYALMEMKRVLKPNG 232
                                       33333....33799*******77668************877***985.66779**********99 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   4.3e-08   0.00011      37      99 .]     173     234 ..     164     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.3e-08
                   Methyltransf_12  37 keklakrennnnnnvelealdlldldggssfDlvvasnvlhhl.kdirevldnirklLkpgGrl 99 
                                       +++++++++    +++++++++   ++ s fD+v+ +++++h+  d+  +l +++++Lkp+G+l
  gi|330507827|ref|YP_004384255.1| 173 RNHMKEYIKTE--FYQFNVESDMYPFSDSEFDVVLFCELIEHMqMDPIYALMEMKRVLKPNGVL 234
                                       56667777655..45555555556666689*************99999**************97 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.1e-05     0.027     128     237 ..     176     291 ..     157     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                              DREV 128 mrdrlkkkkynvlsale.lqetdvkldlilclnlldrc.fdplklledirsalepngrvivalvlPvshyvetntgk 202
                                       m++ +k   y+   + + +  +d ++d++l  +l++ + +dp+  l +++ +l+png  i  l  P  + +e+   +
  gi|330507827|ref|YP_004384255.1| 176 MKEYIKTEFYQFNVESDmYPFSDSEFDVVLFCELIEHMqMDPIYALMEMKRVLKPNGVLI--LTTPNANRIENII-R 249
                                       666666655555555554555799******99999875279***************9655..678*******999.7 PP

                              DREV 203 sekpsellev.kG......rsyeeevarlievlkkagfevea 237
                                       +   s++ +   G      ++ e +v++l+ +l+ +gf +++
  gi|330507827|ref|YP_004384255.1| 250 MISGSNIYDHySGygpygrHNREYNVHELMTLLEYCGFSIDS 291
                                       7777777765234556666778889*************9976 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 ?   12.2   0.0   1.9e-05      0.05     176     223 ..     195     242 ..     188     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                   Methyltransf_29 176 pyPsrsfdlihCsrCridwteedgil.llevdRvlRpgGyfvlsappvy 223
                                       p+  + fd++     +i++ + d i+ l+e++Rvl+p+G ++l++p+++
  gi|330507827|ref|YP_004384255.1| 195 PFSDSEFDVVLFCE-LIEHMQMDPIYaLMEMKRVLKPNGVLILTTPNAN 242
                                       66777788775433.68889999887699***************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3329.13
//
Query:       gi|330507828|ref|YP_004384256.1|  [L=230]
Description: hypothetical protein MCON_1846 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0045   17.0   0.2     0.0056   16.7   0.2    1.1  1  Mucin     Mucin-like glycoprotein
  ------ inclusion threshold ------
       0.17   11.5   0.0       0.25   11.0   0.0    1.2  1  BAR       BAR domain


Domain annotation for each model (and alignments):
>> Mucin  Mucin-like glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   6.3e-07    0.0056       9     109 ..       8     105 ..       1     131 [. 0.65

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.3e-07
                             Mucin   9 alLvlaLcCCasvCvtangeGqsdaavveaaegqskltttttttkppttttttttasttittkttkatttttttttt 85 
                                        +L+++L CCa+         + ++++ ++   ++ +++ ++  +p+t  ++ +ta++ +  k    t+ ++ + t 
  gi|330507828|ref|YP_004384256.1|   8 IILLIVLLCCATLNFSGF---AANSQSGTSLGLNQLKQSESILNTPATNQQANSTATQVQVLKQDSGTNISNMNITL 81 
                                       467888889887654322...23333333333444457777777777888888888888888888888888888888 PP

                             Mucin  86 ttateaPsdavttaeaPtttttra 109
                                         ++   s ++    aP +    +
  gi|330507828|ref|YP_004384256.1|  82 SVSPTYGSAQTVKFTAPKSAWKLE 105
                                       887777777777777777665555 PP

>> BAR  BAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.7e-05      0.25     159     224 ..      87     152 ..      82     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.7e-05
                               BAR 159 lkklktkkskkakdeekaeeelrkAqqkfeesneelkaeLpnllalevefvnqlqafveaqldfhk 224
                                       +++++t k    k+++k+e  l +A++  +esn++l   Lp  ++ +   ++ l  f+++ql +++
  gi|330507828|ref|YP_004384256.1|  87 YGSAQTVKFTAPKSAWKLEGILIMATDGWNESNKQLPNPLPFAIEIRDANLRLLYHFADTQLPYFT 152
                                       678999999998988***********************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1568.88
//
Query:       gi|330507829|ref|YP_004384257.1|  [L=109]
Description: hypothetical protein MCON_1847 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.085   13.0   1.0       0.15   12.2   1.0    1.6  1  CBP_BcsF  Cellulose biosynthesis protein BcsF


Domain annotation for each model (and alignments):
>> CBP_BcsF  Cellulose biosynthesis protein BcsF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.0   8.6e-06      0.15      30      60 .]      28      58 ..       1      58 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.6e-06
                          CBP_BcsF 30 rlsdtlrlrLlpPRylKpaGvlrRnakkkat 60
                                      ++++ + + Ll+ R+ K  G +rR + +k+t
  gi|330507829|ref|YP_004384257.1| 28 KSIEDILMELLKLRAFKVSGRWRRMEVSKKT 58
                                      45555666677*************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 818.63
//
Query:       gi|330507830|ref|YP_004384258.1|  [L=490]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-13   48.1   0.3    2.3e-12   46.9   0.3    1.6  1  MetW             Methionine biosynthesis protein MetW
    1.4e-09   38.4   0.0      3e-09   37.4   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    3.6e-09   37.2   0.0      9e-09   35.9   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    2.9e-08   33.7   0.0    6.9e-08   32.5   0.0    1.7  1  Methyltransf_23  Methyltransferase domain
    5.3e-08   32.8   0.1    1.5e-07   31.4   0.1    1.7  1  Methyltransf_31  Methyltransferase domain
    4.2e-06   27.4   0.1    4.2e-06   27.4   0.1    2.7  2  Methyltransf_12  Methyltransferase domain
     0.0036   17.2   1.6     0.0072   16.2   1.6    1.5  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
  ------ inclusion threshold ------
      0.011   16.1   0.0       0.03   14.7   0.0    1.8  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
      0.018   14.1   0.2      0.038   13.1   0.2    1.5  1  Pox_MCEL         mRNA capping enzyme
      0.019   15.0   0.0      0.019   15.0   0.0    2.8  3  Methyltransf_32  Methyltransferase domain
      0.022   14.8   5.2      0.036   14.0   0.1    2.8  3  PLC-beta_C       PLC-beta C terminal
      0.032   13.6   0.1      0.068   12.6   0.1    1.5  1  TehB             Tellurite resistance protein TehB
      0.043   13.8   0.5       0.14   12.1   0.2    1.8  2  CSN8_PSD8_EIF3K  CSN8/PSMD8/EIF3K family
      0.043   13.7   9.1       0.28   11.0   0.5    3.0  3  ARGLU            Arginine and glutamate-rich 1
       0.08   12.4   1.8       0.14   11.6   1.8    1.4  1  CAP_N            Adenylate cyclase associated (CAP) N termina
       0.23   11.0   1.0         23    4.5   0.1    3.2  3  DUF3201          Protein of unknown function (DUF3201)
       0.27   11.6  10.6        1.4    9.3   2.0    2.3  2  Mobilization_B   Mobilization protein B
       0.33    8.9   3.1        0.8    7.6   0.8    1.7  2  Prominin         Prominin
        9.1    6.0  15.9      0.063   13.1   6.1    2.3  3  Mer2             Mer2


Domain annotation for each model (and alignments):
>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.3   2.4e-15   2.3e-12      13      87 ..     295     368 ..     284     378 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 2.4e-15
                              MetW  13 pgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqa 87 
                                          +vld+GcG Ge+lellk+ ++++g+G+++de+ v  c ++ l+v + d+ + l++ edks+d + + q +  
  gi|330507830|ref|YP_004384258.1| 295 GCKNVLDIGCGRGEFLELLKD-NGISGHGIDIDEDMVRYCRSRDLNVEKLDAVSYLNQLEDKSLDGIFIDQVVEH 368
                                       5568***************98.9**********************************************998865 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   3.2e-12     3e-09       1      79 [.     300     373 ..     300     381 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 3.2e-12
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC.T.SS-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaek.l.pfednsfDlvvssevlhhve 75 
                                       Ld+GcG+G ++e l+++g +  g+D+++ m+++++++  + +      + da + l ++ed+s D +++ +v++h+ 
  gi|330507830|ref|YP_004384258.1| 300 LDIGCGRGEFLELLKDNGISGHGIDIDEDMVRYCRSRDLNVE------KLDAVSyLnQLEDKSLDGIFIDQVVEHL- 369
                                       8*********************************99887776......4444433768******************. PP

                                       CHHH CS
                   Methyltransf_11  76 dpek 79 
                                       dp+ 
  gi|330507830|ref|YP_004384258.1| 370 DPDY 373
                                       4554 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   9.5e-12     9e-09       1      87 [.     299     379 ..     299     383 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 9.5e-12
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vLd+GcG+G++++ l +++   + +g+Di+e+m++++r+r     lnve + +     ++ed+s D +++ ++++hl
  gi|330507830|ref|YP_004384258.1| 299 VLDIGCGRGEFLELLKDNG--ISGHGIDIDEDMVRYCRSRD----LNVEKLDAVSYLNQLEDKSLDGIFIDQVVEHL 369
                                       9***************995..9*****************99....5555544444444679*********666**** PP

                                       SHHHHHHHHH CS
                   Methyltransf_25  78 sdedlekalk 87 
                                       +++ l k+++
  gi|330507830|ref|YP_004384258.1| 370 DPDYLIKMID 379
                                       9888777765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   7.3e-11   6.9e-08      16      96 ..     289     370 ..     270     437 .. 0.64

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 7.3e-11
                   Methyltransf_23  16 llpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaae.pqgkfdlIvlrev 91 
                                       ++++ +  ++vLdiGcG G++le+l++ng s  g+D+++ +v   ++++ ++ +    +   + ++++ d I   +v
  gi|330507830|ref|YP_004384258.1| 289 FVKYFEGCKNVLDIGCGRGEFLELLKDNGISGHGIDIDEDMVRYCRSRDLNVEKLDAVSYLNQlEDKSLDGIFIDQV 365
                                       445555667*******************************9998874333333333222222224456666666666 PP

                   Methyltransf_23  92 lehvp 96 
                                        eh++
  gi|330507830|ref|YP_004384258.1| 366 VEHLD 370
                                       66666 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1   1.5e-10   1.5e-07       5      86 ..     297     369 ..     294     423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.5e-10
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlils 80 
                                       ++vlD+GCG Ge++  l ++    +  +GiDi+e++++++r++        +++e+ d+ + l++ led++ D i+ 
  gi|330507830|ref|YP_004384258.1| 297 KNVLDIGCGRGEFLELLKDNG---ISGHGIDIDEDMVRYCRSR-------DLNVEKLDAVSyLNQ-LEDKSLDGIFI 362
                                       68****************774...5588**************7.......678889999996666.799******** PP

                   Methyltransf_31  81 nevl.na 86 
                                       ++v+ ++
  gi|330507830|ref|YP_004384258.1| 363 DQVVeHL 369
                                       *999522 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.5       3.5   3.3e+03      58      61 ..     169     172 ..     133     218 .. 0.54
   2 !   27.4   0.1   4.5e-09   4.2e-06       1      87 [.     300     379 ..     300     386 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.5
                   Methyltransf_12  58 lldl 61 
                                       ++d+
  gi|330507830|ref|YP_004384258.1| 169 ISDQ 172
                                       2222 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 4.5e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L+iGcG G++l+ l ++  +i+ +g+Di+++++     +  + +++n+++++       ++ + +s D +++ +v++
  gi|330507830|ref|YP_004384258.1| 300 LDIGCGRGEFLELLKDN--GISGHGIDIDEDMV-----RYCRSRDLNVEKLDAVSYL--NQLEDKSLDGIFIDQVVE 367
                                       8****************..**************.....7777777776666666554..444556************ PP

                   Methyltransf_12  78 hl..kdirevld 87 
                                       hl  + + +++d
  gi|330507830|ref|YP_004384258.1| 368 HLdpDYLIKMID 379
                                       *97555556655 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.6   7.7e-06    0.0072      83     158 ..     129     205 ..     111     253 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.7e-06
                                       HHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHC.HHHHHHHHHHHHHHHHHHH-----..-----SSSHHHH CS
                    Apolipoprotein  83 rerlaadaeelqeqlavyaeelrerlerhvealkarla.pyveelrqklaerleelkeslaphaeeveerlssrvee 158
                                        +r+a+   ++ +q+    ++ ++ +++ v +  a+++ ++++++ +++a++   ++++++++ +++++++s++v++
  gi|330507830|ref|YP_004384258.1| 129 DDRIAQSQSAISDQVNDRIAQSQSAISDQVNDRIAQFQsAISDQVNDRIAQSQSSISDQVNDRIAQFQSAISDQVND 205
                                       23334444444444444444444444444444444443334444444444444444444444444444222222222 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.1e-05      0.03      58      89 ..     295     326 ..     244     346 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                      AdoMet_MTase  58 ketsfvdvgcgngllvyvlaaegykgygidlr 89 
                                         +   d+gcg g ++ +l+ +g  g+gid+ 
  gi|330507830|ref|YP_004384258.1| 295 GCKNVLDIGCGRGEFLELLKDNGISGHGIDID 326
                                       556789************************96 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   4.1e-05     0.038      67     108 ..     298     338 ..     285     382 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.1e-05
                          Pox_MCEL  67 kvLdldcgkGgDLeKyekgeIsklvatDiaeesieeckeRYn 108
                                       +vLd++cg+G  Le  +  +Is   ++Di+e+ ++ c+ R  
  gi|330507830|ref|YP_004384258.1| 298 NVLDIGCGRGEFLELLKDNGISGH-GIDIDEDMVRYCRSRDL 338
                                       7*********************98.**************973 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       3.7   3.5e+03      73      93 ..      25      45 ..      10      72 .. 0.48
   2 ?   -0.2   1.8      0.96   9.1e+02      76      93 ..     171     188 ..     119     266 .. 0.57
   3 ?   15.0   0.0     2e-05     0.019      24      78 ..     294     343 ..     283     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.7
                   Methyltransf_32 73 klgkkfnkrlsfaelsieeat 93
                                      k+++++n++++++++s +e++
  gi|330507830|ref|YP_004384258.1| 25 KIRQAVNASTKTEDTSDSETK 45
                                      222333333333333322222 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.96
                   Methyltransf_32  76 kkfnkrlsfaelsieeat 93 
                                        ++n+r+ +++ si+++ 
  gi|330507830|ref|YP_004384258.1| 171 DQVNDRIAQSQSSISDQV 188
                                       222222222222222222 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2e-05
                   Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78 
                                       +g+++v+D+G+G+g     l++    ++++ +gid+ e++v+ ++ r+ +++ k+
  gi|330507830|ref|YP_004384258.1| 294 EGCKNVLDIGCGRGEFLELLKD----NGISGHGIDIDEDMVRYCRSRDLNVE-KL 343
                                       789***********99999999....69*******************99998.44 PP

>> PLC-beta_C  PLC-beta C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       6.1   5.8e+03      38      64 ..      18      45 ..       9      56 .. 0.55
   2 ?   14.0   0.1   3.8e-05     0.036     106     171 ..     114     179 ..     107     183 .. 0.92
   3 ?    1.6   0.1      0.25   2.3e+02     122     156 ..     190     224 ..     185     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.1
                        PLC-beta_C 38 qkllelarekqaael.KkLkeisekekK 64
                                       k++e  + +qa +   k  ++s++e+K
  gi|330507830|ref|YP_004384258.1| 18 RKIKESIKIRQAVNAsTKTEDTSDSETK 45
                                      3444444444433221233445555554 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.8e-05
                        PLC-beta_C 106 vVqvikrleekqkrrqekLeekqaeilqqikeeekqlqeeldeeyeeklkrLpaevkelvkeelke 171
                                       +V +++ ++e   r  +++ + q++i +q++++  q q+ +  + ++++ + ++ +++ v++ +++
  gi|330507830|ref|YP_004384258.1| 114 IVRILNGISERLGRVDDRIAQSQSAISDQVNDRIAQSQSAISDQVNDRIAQFQSAISDQVNDRIAQ 179
                                       588999999***************************************************998765 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.25
                        PLC-beta_C 122 ekLeekqaeilqqikeeekqlqeeldeeyeeklkr 156
                                       +++ + q++i +q++++  q q+++ ++  e++++
  gi|330507830|ref|YP_004384258.1| 190 DRIAQFQSAISDQVNDRIAQSQSKVYSDIGEQVRS 224
                                       56777899999999999999999999999998886 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   7.2e-05     0.068      18     118 ..     282     379 ..     267     398 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.2e-05
                                       --HHHHHHCCCS-S-E.EEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHH.HHHHTT-TTEEEEE--GGG--- CS
                              TehB  18 thsevveavkivkpgk.vldlgcgqgrnslylsllgydvtawdknensiaflee.ikekenlknistalydineakl 92 
                                       t+++ ++ vk  + +k vld+gcg+g     l+ +g     +d +e+ + + ++   + e+l+    a+  +n+++ 
  gi|330507830|ref|YP_004384258.1| 282 TKAKQLKFVKYFEGCKnVLDIGCGRGEFLELLKDNGISGHGIDIDEDMVRYCRSrDLNVEKLD----AVSYLNQLE- 353
                                       5566678899999998689*********99******************999865145777777....333466654. PP

                                       -S-EEEEEEESSGGGS-GGGHHHHHH CS
                              TehB  93 derydfilstvvlmfleaeripsiie 118
                                       d+  d i+   v+  l+++ + ++i+
  gi|330507830|ref|YP_004384258.1| 354 DKSLDGIFIDQVVEHLDPDYLIKMID 379
                                       56666666666677777777666666 PP

>> CSN8_PSD8_EIF3K  CSN8/PSMD8/EIF3K family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.41   3.8e+02      67     107 ..     153     193 ..     146     198 .. 0.76
   2 ?   12.1   0.2   0.00015      0.14      65     112 ..     185     232 ..     176     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.41
                   CSN8_PSD8_EIF3K  67 dlsadltadvagleelvReeiaklvgkaYesIsadvlaelL 107
                                        +s+++ + +a++++++ +++   + ++ +sIs +v  ++ 
  gi|330507830|ref|YP_004384258.1| 153 AISDQVNDRIAQFQSAISDQVNDRIAQSQSSISDQVNDRIA 193
                                       57888889999999999999988888888888887766655 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00015
                   CSN8_PSD8_EIF3K  65 sddlsadltadvagleelvReeiaklvgkaYesIsadvlaelLglssd 112
                                       sd+ ++++ ++ + ++++v ++ia++ +k Y+ I ++v + +L +++d
  gi|330507830|ref|YP_004384258.1| 185 SDQVNDRIAQFQSAISDQVNDRIAQSQSKVYSDIGEQVRSVILAMNKD 232
                                       455666666666667******************************954 PP

>> ARGLU  Arginine and glutamate-rich 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.4       3.4   3.2e+03      66      92 ..      29      55 ..      12      61 .. 0.44
   2 ?    9.6   0.1    0.0008      0.76      18      58 ..     137     177 ..     121     182 .. 0.54
   3 ?   11.0   0.5    0.0003      0.28      19      68 ..     168     217 ..     165     275 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.4
                             ARGLU 66 leeekrkeeeerkkreelerileenkr 92
                                      + ++ +k e+  ++ ++ +++ e ++r
  gi|330507830|ref|YP_004384258.1| 29 AVNASTKTEDTSDSETKGDALHETENR 55
                                      223334444444444444444444444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0008
                             ARGLU  18 eavakrVeeelekrkeeiekeverrveearkkmekqveeel 58 
                                        a+  +V+ ++++ + +i  +v+ r+++ + ++++qv++ +
  gi|330507830|ref|YP_004384258.1| 137 SAISDQVNDRIAQSQSAISDQVNDRIAQFQSAISDQVNDRI 177
                                       34555555555555555555555555555555555555555 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0003
                             ARGLU  19 avakrVeeelekrkeeiekeverrveearkkmekqveeelerereaelee 68 
                                       a+  +V+ ++++ +  i  +v+ r+++ + ++++qv++ + + +++   +
  gi|330507830|ref|YP_004384258.1| 168 AISDQVNDRIAQSQSSISDQVNDRIAQFQSAISDQVNDRIAQSQSKVYSD 217
                                       45566666666666666666666666666666666666666666555443 PP

>> CAP_N  Adenylate cyclase associated (CAP) N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.8   0.00015      0.14       4     127 ..     115     234 ..     112     259 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                       XXXXXXXXXXXXXX..........XXXXXXXXXXXXXXXXXXXXXXXSXH.HHHHHHHHHHHHHHHHHHHHHH.HH- CS
                             CAP_N   4 ikRLEaatsrLEdiaisessssasskasssssaaaaaaaaaakaaaaaaaaksveaFdelisgsvkefvelsk.kig 79 
                                       ++ L+ + +rL  +     +    ++++s+ s + +   a++++a + + +  +++F++ is++v++ ++ s+ +i 
  gi|330507830|ref|YP_004384258.1| 115 VRILNGISERLGRVDD---R---IAQSQSAISDQVNDRIAQSQSAISDQVNDRIAQFQSAISDQVNDRIAQSQsSIS 185
                                       6667778888888832...1...22222222333333334444445555669*************999888873699 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHBE---..HHHHHHHCHHHHHHHH CS
                             CAP_N  80 gevaeqaelvkkafeaqrkfllvaskakkPad.seelqelLkplseaiq 127
                                       ++v++  + +++a+++q +   + s++k  +d  e++ +++  ++++i+
  gi|330507830|ref|YP_004384258.1| 186 DQVNDRIAQFQSAISDQVNDRIAQSQSKVYSDiGEQVRSVILAMNKDIE 234
                                       9*************99988777777777776677777777777766665 PP

>> DUF3201  Protein of unknown function (DUF3201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1       0.3   2.8e+02     114     132 ..     136     154 ..     122     173 .. 0.75
   2 ?    2.0   0.0      0.14   1.3e+02     110     131 ..     163     183 ..     155     188 .. 0.79
   3 ?    4.5   0.1     0.024        23     106     133 ..     189     215 ..     182     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.3
                                       TS---HHHHHHHHTSS-SE CS
                           DUF3201 114 esplseevidrivesdekv 132
                                       +s +s++v dri +s+  +
  gi|330507830|ref|YP_004384258.1| 136 QSAISDQVNDRIAQSQSAI 154
                                       6778888888888876544 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.14
                                       E..TTS---HHHHHHHHTSS-S CS
                           DUF3201 110 nclresplseevidrivesdek 131
                                          ++s +s++v dri +s+  
  gi|330507830|ref|YP_004384258.1| 163 A-QFQSAISDQVNDRIAQSQSS 183
                                       3.6899***********99876 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.024
                                       -EEEE..TTS---HHHHHHHHTSS-SEE CS
                           DUF3201 106 edvynclresplseevidrivesdekvi 133
                                       +d     ++s +s++v dri +s+ kv+
  gi|330507830|ref|YP_004384258.1| 189 NDRIA-QFQSAISDQVNDRIAQSQSKVY 215
                                       45444.6999**************9986 PP

>> Mobilization_B  Mobilization protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.0    0.0015       1.4      10      61 ..     118     170 ..     112     176 .. 0.80
   2 ?    7.1   1.9    0.0071       6.7      22      72 ..     176     224 ..     169     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                    Mobilization_B  10 srginelaeei.eplaqsmatladearqviaevqqaseeqaaewlkaqrqaga 61 
                                         gi e   ++ + +aqs ++++d+  ++ia+ q a  +q  + + + + a +
  gi|330507830|ref|YP_004384258.1| 118 LNGISERLGRVdDRIAQSQSAISDQVNDRIAQSQSAISDQVNDRIAQFQSAIS 170
                                       567777665552579*************************9999998888776 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0071
                    Mobilization_B  22 plaqsmatladearqviaevqqaseeqaaewlkaqrqagaawvelakelre 72 
                                        +aqs ++++d+  ++ia+ q a  +q  + + + +     + ++  ++r+
  gi|330507830|ref|YP_004384258.1| 176 RIAQSQSSISDQVNDRIAQFQSAISDQVNDRIAQSQS--KVYSDIGEQVRS 224
                                       68*************************9998866543..345555555555 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.8   0.00085       0.8     688     748 ..     119     179 ..     107     192 .. 0.86
   2 ?    6.1   3.3    0.0023       2.2     166     233 ..     142     210 ..     135     235 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00085
                          Prominin 688 sdlqesikkllaaveraenflkkngseiinneskklldrileqfeeYidwvieevtenvgk 748
                                       ++++e++ ++ +++ +++  + +++++ i++ ++ ++d ++  + ++ + + ++v++++++
  gi|330507830|ref|YP_004384258.1| 119 NGISERLGRVDDRIAQSQSAISDQVNDRIAQSQSAISDQVNDRIAQFQSAISDQVNDRIAQ 179
                                       5677888889999999999999999999999999999999999999999999999999986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0023
                          Prominin 166 aldegleesketvkrgled.lrtflkdvpqhidhvlvqnyeelekhvsddLddagkhlgldladtlesn 233
                                       ++++++++s++++  +++d + +f + ++++++  + q+ + + ++v d + + ++ + ++++d++ ++
  gi|330507830|ref|YP_004384258.1| 142 QVNDRIAQSQSAISDQVNDrIAQFQSAISDQVNDRIAQSQSSISDQVNDRIAQFQSAISDQVNDRIAQS 210
                                       677778888888877777745678888888887777777888888888888888888877777765443 PP

>> Mer2  Mer2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3       3.1   2.9e+03     103     114 ..      24      35 ..       5      69 .. 0.45
   2 ?   13.1   6.1   6.6e-05     0.063      43     184 ..     108     235 ..     106     239 .. 0.76
   3 ?   -2.5   0.1       4.1   3.9e+03      41      63 ..     455     477 ..     452     478 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.1
                              Mer2 103 skvskavldklk 114
                                        k+++av+  +k
  gi|330507830|ref|YP_004384258.1|  24 IKIRQAVNASTK 35 
                                       222222222222 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.6e-05
                              Mer2  43 rEksskLinvlkenskeLlkvisklnellidlkeeesdnskekeikdlikdLsvkienqlskvskavldklkvkkhk 119
                                       rE  s ++++l+  s++L +v +++ +            + ++ i +    +s ++++ +++ ++a++d+++ +  +
  gi|330507830|ref|YP_004384258.1| 108 REFNSCIVRILNGISERLGRVDDRIAQSQS-----AISDQVNDRIAQSQSAISDQVNDRIAQFQSAISDQVNDRIAQ 179
                                       666777788888888888888888888773.....444578888888888899999999999999999999988888 PP

                              Mer2 120 sntdtksnLtellekkeakileeidkkqtkleksvdttqelllnvnkQledvnevllSlskdlen 184
                                       s+++   ++ + +++ ++ i+++++++  + +  v        ++++Q   v  v+l ++kd+en
  gi|330507830|ref|YP_004384258.1| 180 SQSSISDQVNDRIAQFQSAISDQVNDRIAQSQSKVY------SDIGEQ---VRSVILAMNKDIEN 235
                                       888888888888888888888888887776665554......455555...45578888888876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.1
                              Mer2  41 dLrEksskLinvlkenskeLlkv 63 
                                       +L Ek  +L  ++++n   L ++
  gi|330507830|ref|YP_004384258.1| 455 ELAEKERSLADIINRNTDMLNNM 477
                                       68899999999999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1199  (0.0668749); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 3460.60
//
Query:       gi|330507831|ref|YP_004384259.1|  [L=337]
Description: glycosyl transferase, group 1 family protein [Methanosaeta concilii GP6]
Scores for complete 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-30  103.6   0.0    1.2e-29  103.0   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    1.3e-17   64.5   0.0    1.7e-17   64.1   0.0    1.2  1  Glyco_trans_1_4  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.55   10.2   0.0    1.9  2  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 !  103.0   0.0   2.1e-33   1.2e-29      15     171 ..     164     315 ..     158     316 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 2.1e-33
                                       -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHH CS
                   Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellk 91 
                                       + +i++ +rle  K++dl+i +++ l    ++n+kl iaG+g++++++++la+++++ d+v+flg+vs+++l e ++
  gi|330507831|ref|YP_004384259.1| 164 EDFIFYPSRLESIKRQDLIISSMKYL----QSNIKLKIAGSGSQLESYRSLAKKYKVADKVEFLGYVSDNELLENYS 236
                                       6799********************99....79********************************************* PP

                                       CESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHH CS
                   Glycos_transf_1  92 nadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnnaealaeairklledeelrerlge 167
                                       ++ ++++    E +G v lE++ +++pvi+ n + gp+e v+dg++G++ +p  +e++a+ i+kl +d+ +++++ge
  gi|330507831|ref|YP_004384259.1| 237 KCMCVAYVPFEEDMGYVTLESFLSKKPVITCNdSAGPLEFVEDGVNGYIAEPA-PEEIAASIDKLYQDN-TYKQMGE 311
                                       *9999999999******************************************.**************7.******9 PP

                                       HHHH CS
                   Glycos_transf_1 168 nark 171
                                       ++++
  gi|330507831|ref|YP_004384259.1| 312 KGYR 315
                                       9986 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 !   64.1   0.0   2.8e-21   1.7e-17       4     134 .]     167     303 ..     164     303 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 2.8e-21
                                       EEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT..T-T.TEEEE---TH...HHHHHHH-S CS
                   Glyco_trans_1_4   4 ilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa..gleerveftGfved...laellaaad 74 
                                       i + +rl e +k++dl++  ++ l+ ++++l i+G+g+   e++++la+  +++++vef+G+v+d   l+++ + + 
  gi|330507831|ref|YP_004384259.1| 167 IFYPSRL-ESIKRQDLIISSMKYLQ-SNIKLKIAGSGSqL-ESYRSLAKkyKVADKVEFLGYVSDnelLENYSKCMC 240
                                       7788999.889**************.66********9865.4777777567899*********44456777777778 PP

                                       EEEE--.---SHHHHHHHHTT-EEEE-.TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  75 vfvaPs.egfglkllEamaaglpvVat.dvggiaevv..gengllvppgdpealaeailrLled 134
                                       v+ +P  e +g+++lE++ +++pv++  d +g+ e+v  g+ng++++p  pe++a+ i +L++d
  gi|330507831|ref|YP_004384259.1| 241 VAYVPFeEDMGYVTLESFLSKKPVITCnDSAGPLEFVedGVNGYIAEP-APEEIAASIDKLYQD 303
                                       889999889******************555699**9**9*******87.5************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 ?   10.2   0.0   9.2e-05      0.55       2      26 ..       3      30 ..       2      91 .. 0.76
   2 ?   -0.1   0.0      0.14   8.2e+02     123     152 ..     112     141 ..      26     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 9.2e-05
                    Glyco_transf_4  2 GGverhvleLaraLarrGheVtvv...t 26
                                      GG+e h+  + r+L +r heV+ +    
  gi|330507831|ref|YP_004384259.1|  3 GGAELHCDSIYRELIKREHEVEYIkipY 30
                                      9********************9885433 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.14
                    Glyco_transf_4 123 lralerrllrradrviavSeatadelrery 152
                                       +  + r  l+ ++++ ++S+ + ++l +  
  gi|330507831|ref|YP_004384259.1| 112 IYTMDRICLSESKKIYTNSQNVSNRLWKFN 141
                                       444556668888999999999999998844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2501.09
//
Query:       gi|330507832|ref|YP_004384260.1|  [L=432]
Description: glycosyl transferase, group 1 family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-13   49.5   0.0    5.3e-13   48.9   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    2.1e-09   37.9   0.0    4.2e-09   36.9   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0     6e-17   5.3e-13       2     130 ..     203     330 ..     202     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 6e-17
                                       HHHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEE CS
                   Glycos_transf_1   2 kekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnvifl 78 
                                       +e+ + klg+++k+ +i s g ++ +K++  l+ af+++ ++  pn  l+++G  e++  +  l+  l++++ v+++
  gi|330507832|ref|YP_004384260.1| 203 TEDLKVKLGIDKKEQVITSFGFINAHKRYPILLSAFKRFLRD-YPNSILLLVG--EDLMGIDGLITDLGIGKSVKMT 276
                                       678899**********************************98.**********..********************** PP

                                       ECCHSSSHHHHHHCESEEEEEESS....BSS-HHHHHHHHTT--EEEETTTTHCHH CS
                   Glycos_transf_1  79 gevsredleellknadifvlpsis....EgfGivllEAmaaglpviasnaggpaev 130
                                       g+ + ++++ +l  +d f+++ ++    E  G v l  maag+pvi+sn+g ++e+
  gi|330507832|ref|YP_004384260.1| 277 GYAPFNRIMDYLAVSD-FCVNLRYptagETSGSV-LRIMAAGKPVIVSNVGWFSEI 330
                                       ****99********99.66666777**8888865.78**************99998 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 !   36.9   0.0   4.7e-13   4.2e-09       3     116 ..     218     338 ..     216     356 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 4.7e-13
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---..HHHHHHHT..T-T.TEEEE---..THHHHHHHH- CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgprpeeleelaa..gleerveftGfv..edlaellaaa 73 
                                       vi  +G ++  +k+  +ll a+++ +++ +   l++vG++     ++ l+   g+ ++v++tG+   + + ++la +
  gi|330507832|ref|YP_004384260.1| 218 VITSFGFIN-AHKRYPILLSAFKRFLRDyPnSILLLVGED-LM-GIDGLITdlGIGKSVKMTGYApfNRIMDYLAVS 291
                                       667777674.459*********77775543588*****55.43.45555544799999*******9888******** PP

                                       SEEEE...--.---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE- CS
                   Glyco_trans_1_4  74 dvfva...Ps.egfglkllEamaaglpvVatdvggiaevvgengllv 116
                                       d +v+   P+   ++ ++l  maag+pv++++vg ++e+     l v
  gi|330507832|ref|YP_004384260.1| 292 DFCVNlryPTaGETSGSVLRIMAAGKPVIVSNVGWFSEIPDSCCLKV 338
                                       *****555555469*******************76788444333444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3085.61
//
Query:       gi|330507833|ref|YP_004384261.1|  [L=305]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-15   57.9   0.0    1.9e-15   57.1   0.0    1.4  1  rve           Integrase core domain
    2.5e-06   27.1   0.2    5.9e-06   25.9   0.2    1.6  1  HTH_23        Homeodomain-like domain
    4.2e-06   26.4   0.5    9.8e-05   22.1   0.1    2.9  2  rve_3         Integrase core domain
      7e-05   22.9   7.5    0.00019   21.5   0.7    3.5  3  HTH_21        HTH-like domain
     0.0011   19.0   0.3     0.0011   19.0   0.3    2.0  2  HTH_28        Helix-turn-helix domain
     0.0015   18.5   0.0     0.0029   17.6   0.0    1.5  1  HTH_29        Winged helix-turn helix
     0.0024   17.8   0.2     0.0044   16.9   0.2    1.4  1  HTH_11        HTH domain
     0.0025   18.4   0.3     0.0083   16.7   0.1    2.0  2  HTH_32        Homeodomain-like domain
     0.0036   16.7   0.0     0.0072   15.7   0.0    1.5  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
  ------ inclusion threshold ------
      0.012   15.2   1.3        0.1   12.3   0.1    2.6  3  HTH_33        Winged helix-turn helix
        0.2   11.2   1.8       0.27   10.8   0.4    1.9  2  Sigma70_r4    Sigma-70, region 4


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   1.2e-18   1.9e-15       3     115 ..     130     249 ..     128     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.2e-18
                               rve   3 rpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve.pervlsDngsey 78 
                                       ++ +  ++D+ + +  + g  + ++v++dd+sr++la    +e+++++ + ++++ v++f+++   ++++ D+gse+
  gi|330507833|ref|YP_004384261.1| 130 HSMSAGHIDWHEWD--GTG--VKVCVILDDASRMVLAGGEFTEINTENSILIIDQLVDKFWWLCpLRELILDHGSEF 202
                                       66677888888888..666..99********************9999888888888888888887899********* PP

                               rve  79 tsk..........afrefladlgirvsftrpgrpqdnGkvErfhrtl 115
                                        ++          +f++ l+++gi++ ++r+ +pq+nGk Erf++ +
  gi|330507833|ref|YP_004384261.1| 203 GAHrihddgswnsEFKDHLKKYGIKPILARVKHPQTNGKLERFFGEY 249
                                       ********************************************975 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.2   3.6e-09   5.9e-06      10      49 ..      11      50 ..       5      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 3.6e-09
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryreeGlegl 49
                                      il+  +++ +++eIAr   vs+r v++++k y+e G e++
  gi|330507833|ref|YP_004384261.1| 11 ILRQNRKRVPTKEIARDVKVSQRRVQQIIKEYKETGQEPV 50
                                      77788889****************************9986 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         3   4.8e+03      29      53 ..      18      42 ..      11      44 .. 0.71
   2 !   22.1   0.1     6e-08   9.8e-05       2      63 ..     225     275 ..     224     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3
                             rve_3 29 ellneelfrslaearekleawredY 53
                                      ++ ++e+ r+++  ++ +++ +++Y
  gi|330507833|ref|YP_004384261.1| 18 RVPTKEIARDVKVSQRRVQQIIKEY 42
                                      5556666777888888888888888 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 6e-08
                             rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssLg 63 
                                       gi++ + ++++Pq+Ng+ E+f+g + ++    ++f          ++++++YN  RPH sL+
  gi|330507833|ref|YP_004384261.1| 225 GIKPILARVKHPQTNGKLERFFGEYVKHRPAFHSF----------DEFITWYND-RPHGSLN 275
                                       8999999****************998887777777..........9*******6.9****98 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   2.0       0.2   3.3e+02      28      49 ..      22      41 ..       2      43 .. 0.77
   2 !   21.5   0.7   1.2e-07   0.00019       4      53 ..      64     111 ..      61     122 .. 0.88
   3 ?   -1.1   0.0       1.3   2.2e+03      11      28 ..     192     209 ..     189     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.2
                            HTH_21 28 aeLrreggvrvnhkrVrRlMre 49
                                      +e+ r+  v+v+ +rV+ + +e
  gi|330507833|ref|YP_004384261.1| 22 KEIARD--VKVSQRRVQQIIKE 41
                                      444555..78999999999988 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.2e-07
                            HTH_21   4 dallalireifeeskgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLr 53 
                                       +++ ++ir++++++  r G+r +   +r+++++ ++h+r++   + +GL 
  gi|330507833|ref|YP_004384261.1|  64 EKETEVIRAAHARY--RFGARMLETVIRKQFKICISHNRIHMYLKAAGLA 111
                                       567899******86..8*******************************94 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.3
                            HTH_21  11 reifeeskgrYGyrriwa 28 
                                       re+  ++    G+ ri+ 
  gi|330507833|ref|YP_004384261.1| 192 RELILDHGSEFGAHRIHD 209
                                       7888999999*****985 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.3   6.8e-07    0.0011      13      52 .]      19      59 ..       8      60 .. 0.76
   2 ?   -1.8   0.1       2.2   3.6e+03      42      51 ..     113     122 ..     106     122 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.8e-07
                            HTH_28 13 hsvreaArelgisrrtvyrWikryeegGia.gLvprrrrpr 52
                                      ++ +e+Ar + +s+r+v++ ik y e G +  L  + +rpr
  gi|330507833|ref|YP_004384261.1| 19 VPTKEIARDVKVSQRRVQQIIKEYKETGQEpVLGEKVGRPR 59
                                      4889************************9844444556665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                            HTH_28  42 agLvprrrrp 51 
                                       ++L++++rr+
  gi|330507833|ref|YP_004384261.1| 113 EDLKKQKRRK 122
                                       7889999986 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.8e-06    0.0029       4      58 ..      11      63 ..      10      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.8e-06
                            HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrsgrprnrls 58
                                      +l+  ++ v+ +++iA+ + +s r v+ ++k + e+G +  l  +   grpr+ ++
  gi|330507833|ref|YP_004384261.1| 11 ILRQNRKRVP-TKEIARDVKVSQRRVQQIIKEYKETGQEPVLGeKV--GRPRKPFT 63
                                      5777788898.9****************************998555..99998444 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   2.7e-06    0.0044       4      49 ..       7      53 ..       4      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.7e-06
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIese 49
                                      ++  +L+++r+ ++ +e+A+  +vS r v++ Ik+ +e+g  p+ +e
  gi|330507833|ref|YP_004384261.1|  7 KVRYILRQNRKRVPTKEIARDVKVSQRRVQQIIKEYKETGqEPVLGE 53
                                      66789******************************999997777665 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.76   1.2e+03      44      72 ..      16      38 ..       6      39 .. 0.63
   2 !   16.7   0.1   5.1e-06    0.0083       2      72 ..      35     104 ..      34     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.76
                            HTH_32 44 eprWsprqlaarlaeregvkvShstvyri 72
                                      + r  ++++a+ +      kvS++ v++i
  gi|330507833|ref|YP_004384261.1| 16 RKRVPTKEIARDV------KVSQRRVQQI 38
                                      3366666666644......7888888887 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.1e-06
                            HTH_32   2 vsrwlkRyneeGle.gLkdrprrgrprk.lsdevrariiallreeprWsprqlaarlaeregvkvShstvyri 72 
                                       v+  +k y+e+G e  L ++   grprk +++ + + i+a    + r+++r l   +++++ + +Sh  ++ +
  gi|330507833|ref|YP_004384261.1|  35 VQQIIKEYKETGQEpVLGEK--VGRPRKpFTEKETEVIRAAH-ARYRFGARMLETVIRKQFKICISHNRIHMY 104
                                       678899******99899999..56666537777777777777.455***********8888999***999865 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.4e-06    0.0072      18      51 ..       9      42 ..       8      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.4e-06
                      HTH_Tnp_ISL3 18 ayilelllesrsvkavArqlgvSwtTVwrildry 51
                                      +yil++ +++ + k++Ar++ vS ++V+ i+++y
  gi|330507833|ref|YP_004384261.1|  9 RYILRQNRKRVPTKEIARDVKVSQRRVQQIIKEY 42
                                      7999999999*********************987 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.5   7.4e+03      21      32 ..      29      40 ..      27      42 .. 0.53
   2 ?   12.3   0.1   6.2e-05       0.1       8      36 ..      82     110 ..      76     113 .. 0.92
   3 ?    0.7   0.0      0.25     4e+02      29      49 ..     219     239 ..     215     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.5
                            HTH_33 21 sysvsgvyrlLk 32
                                      ++s+++v ++ k
  gi|330507833|ref|YP_004384261.1| 29 KVSQRRVQQIIK 40
                                      555555555443 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6.2e-05
                            HTH_33   8 arlaqlieerfgvsysvsgvyrlLkrlGf 36 
                                       + l+++i+++f + +s+ +++ +Lk +G+
  gi|330507833|ref|YP_004384261.1|  82 RMLETVIRKQFKICISHNRIHMYLKAAGL 110
                                       67899**********************97 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.25
                            HTH_33  29 rlLkrlGfsyqkPrprapkqd 49 
                                       + Lk+ G+ ++ +r ++p+ +
  gi|330507833|ref|YP_004384261.1| 219 DHLKKYGIKPILARVKHPQTN 239
                                       579**************9865 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   0.00017      0.27      22      43 ..      20      41 ..       9      43 .. 0.87
   2 ?   -2.7   0.0       2.7   4.5e+03       6      16 ..      63      73 ..      63      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                                      -HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4 22 TleEIgerlgiSrerVrqiekr 43
                                      + +EI++   +S+ rV qi+k+
  gi|330507833|ref|YP_004384261.1| 20 PTKEIARDVKVSQRRVQQIIKE 41
                                      679****************985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                      -HHHHHHHHHH CS
                        Sigma70_r4  6 pererevlelr 16
                                      +e+e ev++  
  gi|330507833|ref|YP_004384261.1| 63 TEKETEVIRAA 73
                                      68999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2212.02
//
Query:       gi|330507834|ref|YP_004384262.1|  [L=418]
Description: hypothetical protein MCON_1853 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.8   0.4      0.086   13.6   0.4    1.7  1  DUF2877   Protein of unknown function (DUF2877)


Domain annotation for each model (and alignments):
>> DUF2877  Protein of unknown function (DUF2877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   4.8e-06     0.086      42     100 ..     191     257 ..     162     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.8e-06
                           DUF2877  42 a.......kakkrttdvSaalLkaalegefseellallkalsseeeeel.ekalekllaiGhtSGad 100
                                       a       ++++ ++++Sa++L +a+   ++ +l++ ++  ++++e++   +++++l++iG +SGa 
  gi|330507834|ref|YP_004384262.1| 191 ArvirttgSTADANRAISATWLGSAATTDANLPLTNGASLNAKSAETQSgFNTVATLSNIGMSSGAH 257
                                       223334458889999*******************9955544444444445***************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3005.51
//
Query:       gi|330507835|ref|YP_004384263.1|  [L=491]
Description: hypothetical protein MCON_1854 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3663.87
//
Query:       gi|330507836|ref|YP_004384264.1|  [L=63]
Description: hypothetical protein MCON_1855 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00022   21.4   0.3    0.00027   21.1   0.3    1.1  1  rve_2     Integrase core domain
     0.0032   17.2   0.1      0.004   16.9   0.1    1.1  1  rve_3     Integrase core domain


Domain annotation for each model (and alignments):
>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3     3e-08   0.00027       6      43 ..      19      61 ..      18      63 .] 0.91

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3e-08
                             rve_2  6 sLKtElvygetfktleeleaaiedYIew.YNnkRlk....gls 43
                                      +LK+E vy  ++ t+e +++ +  +Ie  YN kRl+    ++s
  gi|330507836|ref|YP_004384264.1| 19 HLKVEEVYPNEYGTFEDAYENVWHFIEKvYNMKRLHsaldYMS 61
                                      8*************************988*****986666777 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   4.4e-07     0.004      26      65 ..      20      60 ..      15      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.4e-07
                             rve_3 26 lrdellneelfrslaearekleawred.YNteRPHssLgyk 65
                                      l+ e ++ + + ++++a e++  ++e+ YN +R Hs+L+y+
  gi|330507836|ref|YP_004384264.1| 20 LKVEEVYPNEYGTFEDAYENVWHFIEKvYNMKRLHSALDYM 60
                                      6777888888889999999999999866***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 501.20
//
Query:       gi|330507837|ref|YP_004384265.1|  [L=302]
Description: hypothetical protein MCON_1856 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2185.15
//
Query:       gi|330507838|ref|YP_004384266.1|  [L=54]
Description: hypothetical protein MCON_1858, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-06   26.4   0.0      0.075   13.5   0.0    2.0  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 !   13.5   0.0   4.2e-06     0.075       5      21 ..       2      18 ..       1      28 [. 0.77
   2 !   12.8   0.0     7e-06      0.13      76     108 .]      21      51 ..      16      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.2e-06
                   PseudoU_synth_1  5 lvGthdfgsfckqkqek 21
                                      l+G+hdf++f+++k ++
  gi|330507838|ref|YP_004384266.1|  2 LLGEHDFRNFSSAKVDT 18
                                      89********8887766 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7e-06
                   PseudoU_synth_1  76 edvkellnakkrkkiavetapavglvlfhvrYd 108
                                       +++++ll  ++++   ++tapavgl+l++v Y+
  gi|330507838|ref|YP_004384266.1|  21 SWFSDLLRPERNH--GAPTAPAVGLILMNVGYE 51 
                                       6778888777754..59*************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 422.80
//
Query:       gi|330507839|ref|YP_004384267.1|  [L=181]
Description: hypothetical protein MCON_1859 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.2   0.1      0.072   13.0   0.0    1.6  1  HxlR            HxlR-like helix-turn-helix
      0.032   14.1   0.3       0.53   10.2   0.0    2.2  2  B3              B3 DNA binding domain
      0.071   13.5   0.2       0.24   11.7   0.0    1.8  2  DUF2383         Domain of unknown function (DUF2383)
      0.081   13.0   4.6       0.19   11.7   0.4    2.7  2  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
      0.089   13.3   1.2       0.44   11.1   0.3    2.0  2  HisKA_3         Histidine kinase


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 ?   13.0   0.0     2e-05     0.072      15      71 ..      41      96 ..      36     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                      TTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGG CS
                              HxlR 15 lkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrs 71
                                       + ++R  el+r + ++ q++L q L +  q+g++er+    ++ + +Y l++kG  
  gi|330507839|ref|YP_004384267.1| 41 RSSNERADELERMIVDMQQSLLWQLLIRY-QSGFVERVLPLGTGRREKYDLAQKGGR 96
                                      55789***************999988775.68*********************9965 PP

>> B3  B3 DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00015      0.53      50      71 ..      89     108 ..      58     110 .. 0.87
   2 ?    2.0   0.1     0.052   1.8e+02      41      60 ..     131     151 ..     111     158 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                                       EEEEECCTTEEEEETTHHHHHH CS
                                B3  50 kliyrkksgryvltkGWkeFvk 71 
                                        l   +k+gr+++ kGW++F++
  gi|330507839|ref|YP_004384267.1|  89 DL--AQKGGRILFNKGWRDFCR 108
                                       34..78999************7 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.052
                                       ETTSEEEEEEEEEECCTTE.E CS
                                B3  41 desgksWevkliyrkksgr.y 60 
                                       + + + W+ k+ y++ +g+ +
  gi|330507839|ref|YP_004384267.1| 131 SLNERNWQAKYNYKNYGGKkF 151
                                       67889******9966555534 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.7e-05      0.24      34      73 ..      20      59 ..      16      63 .. 0.91
   2 ?   -1.5   0.0      0.86   3.1e+03      40      59 ..     160     179 ..     155     180 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.7e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHCT--------------- CS
                           DUF2383 34 tlleriaeereeaaeeLqseiralggepedggslagklhr 73
                                      ++++r+++er ++++eL++ +r+ ++ +++   + +++++
  gi|330507839|ref|YP_004384267.1| 20 DTFRRCIKERDKRISELEDLLRSSNERADELERMIVDMQQ 59
                                      78**************************999999988877 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.86
                                       HHHHHHHHHHHHHHHHHCT- CS
                           DUF2383  40 aeereeaaeeLqseiralgg 59 
                                        +++ +  +eL++ +++l+g
  gi|330507839|ref|YP_004384267.1| 160 RADKDAVKTELENILKKLNG 179
                                       45555666666666666666 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   5.4e-05      0.19      74     123 ..      11      60 ..       5      65 .. 0.88
   2 ?    1.9   0.4     0.059   2.1e+02      45      60 ..     120     135 ..     114     178 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.4e-05
                    CENP-F_leu_zip  74 dLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekvqmkee 123
                                       +L++l+   ++  + +++  +r+seLe l  s ++   e+E   v m+++
  gi|330507839|ref|YP_004384267.1|  11 QLSSLTVRADTFRRCIKERDKRISELEDLLRSSNERADELERMIVDMQQS 60 
                                       788888999999999999999********999999999999999999876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.059
                    CENP-F_leu_zip  45 leaEtskaevetlkee 60 
                                        + E+s++e+++l+e 
  gi|330507839|ref|YP_004384267.1| 120 FDSENSRKEASSLNER 135
                                       6788899998888775 PP

>> HisKA_3  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00012      0.44      14      67 ..       9      61 ..       8      62 .. 0.88
   2 ?    0.7   0.0      0.21   7.5e+02      30      51 ..     158     179 ..     152     181 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                      HHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHH CS
                           HisKA_3 14 gqsLsaiklqlelakrllekdpekaaeqlreieelarealqevRrllhnLrpaa 67
                                      g +Ls++++++++++r ++++ +k   +l+++ + ++e  +e+ r++ ++++++
  gi|330507839|ref|YP_004384267.1|  9 GKQLSSLTVRADTFRRCIKER-DKRISELEDLLRSSNERADELERMIVDMQQSL 61
                                      679************999655.688899*****************999998765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.21
                                       HTTT-HHHHHHHHHHHHHHHHH CS
                           HisKA_3  30 llekdpekaaeqlreieelare 51 
                                       ++++d+++++++l++i + +++
  gi|330507839|ref|YP_004384267.1| 158 EIRADKDAVKTELENILKKLNG 179
                                       467888899****999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1326.40
//
Query:       gi|330507840|ref|YP_004384268.1|  [L=701]
Description: glycosyl transferase group 2/group 1 fusion protein [Methanosaeta concilii GP6]
Scores for complete 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-23   81.4   1.7    1.5e-22   80.2   1.7    1.6  1  Glycos_transf_2  Glycosyl transferase family 2
    1.5e-22   79.9   0.3    4.5e-22   78.4   0.1    1.9  2  Glycos_transf_1  Glycosyl transferases group 1
      5e-18   65.8   0.0    9.7e-18   64.9   0.0    1.4  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.5e-10   40.9   0.0    8.9e-10   39.1   0.0    2.0  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.6e-07   31.4   0.0    2.6e-07   30.8   0.0    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    3.7e-05   24.0   0.0    9.5e-05   22.7   0.0    1.7  1  Glyco_trans_1_2  Glycosyl transferases group 1
    4.8e-05   23.1   0.9    0.00015   21.5   0.9    1.8  1  Glyco_tranf_2_5  Glycosyltransferase like family
     0.0018   18.3   0.0     0.0071   16.4   0.0    1.9  1  Glyco_transf_4   Glycosyltransferase Family 4
      0.007   15.9   0.0      0.013   15.0   0.0    1.4  1  Glyco_transf_21  Glycosyl transferase family 21
     0.0089   16.5   0.1      0.033   14.7   0.1    2.1  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.73    9.9   3.4        2.7    8.1   0.1    3.2  3  DnaB             DnaB-like helicase N terminal domain


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   1.7   8.9e-26   1.5e-22       1     122 [.       6     124 ..       6     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 8.9e-26
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglr 76 
                                       s++ + yN +++++ + +s+l+   ++   eii+vD+ S+D++v++le+    +p+++vi+++ +  +a+a+n g++
  gi|330507840|ref|YP_004384268.1|   6 SIIAVNYNGKDYIEDFCNSILNTnIDDFTCEIIIVDNLSKDDSVNFLEAN---YPKIKVIKNNIK-NYAKAINLGIK 78 
                                       89999******************8888889********************...89********99.*********** PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECC CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifge 122
                                       +a+g+yi++l++D +++ +wl+ lv+ +++d++ +v+++ + +++e
  gi|330507840|ref|YP_004384268.1|  79 NAKGQYIAILNSDIVVENNWLKGLVDIIDQDEKIGVVQSKMLFSDE 124
                                       *********************************9999987776665 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 ?   -2.3   0.0       1.8   2.9e+03      25      47 ..     259     279 ..     241     283 .. 0.76
   2 !   78.4   0.1   2.8e-25   4.5e-22      11     172 .]     494     667 ..     488     667 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.8
                                       TTTTTHHHHHHHHHCCCCCHCSC CS
                   Glycos_transf_1  25 ekeKgvdllikafallkkqlnpn 47 
                                       e+e  ++ li+a++++ ++  ++
  gi|330507840|ref|YP_004384268.1| 259 EHESLYHSLIQAVKKVAEN--ND 279
                                       5566678899999999875..33 PP

  == domain 2  score: 78.4 bits;  conditional E-value: 2.8e-25
                                       TTTT-EEEEEESS-TTT..TTHHHHHHHHHCCCCC...HCSCEEEEEES.....STTHHHHHHHHHHHCTTCGGGEE CS
                   Glycos_transf_1  11 knekkkiilsvgrleke..Kgvdllikafallkkq...lnpnvklviaG....ngeeekelkklaeelelsdnvifl 78 
                                       + ek+k+ilsv+r+e+   K +  +i+ f +l+k+   +++++kl++aG      ++ ++++k+a+      n+++ 
  gi|330507840|ref|YP_004384268.1| 494 LGEKDKMILSVARFETGgsKKQLEMIETFVDLCKKdkrIKKEWKLILAGgtpkINPYYDKVRKKAKRI---SNIEIA 567
                                       679************9777***************99*************8877667777777776655...559999 PP

                                       ECCHSSSHHHHHHCESEEEEEESS........BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHH CS
                   Glycos_transf_1  79 gevsredleellknadifvlpsis........EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaea 147
                                        ++++ ++++l++na+if + +          E+fG++ +EAm+  +  ++ + gg +e+v++g +G+ + ++  e+
  gi|330507840|ref|YP_004384268.1| 568 TNLNNYEIKQLYSNASIFWHACGLdeidprliEHFGMTTVEAMQNYCVPVVIDGGGQREIVEHGISGFRFTSK--EE 642
                                       9999999*****************************************************************9..** PP

                                       HHHHHHHHHHSHHHHHHHHHHHHHH CS
                   Glycos_transf_1 148 laeairklledeelrerlgenarkr 172
                                       l+ +  kl++d+ lre++ +na++r
  gi|330507840|ref|YP_004384268.1| 643 LKSYTLKLINDDYLREKMAKNAYNR 667
                                       **********************986 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   5.9e-21   9.7e-18       4     227 ..       5     234 ..       3     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 5.9e-21
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksra 78 
                                       ++++ +++n  d++++  +s+l+   ++   e+++v++ s+++ ++++e+   ++p++  +v+ n +   ++ ++ a
  gi|330507840|ref|YP_004384268.1|   5 VSIIAVNYNGKDYIEDFCNSILNTNIDDftCEIIIVDNLSKDDSVNFLEA---NYPKI--KVIKN-N---IKNYAKA 72 
                                       6788899999************987655559***************9987...***96..78733.4...4567889 PP

                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrs....tlvsalgalefaerhlrfla 150
                                       +n +++++k+++++++++D vve + lk l+ ++ +++k+g+v+ ++++  ++    + v  + +++f +  +  + 
  gi|330507840|ref|YP_004384268.1|  73 INLGIKNAKGQYIAILNSDIVVENNWLKGLVDIIdQDEKIGVVQSKMLFSDEEmiesAGVEDAEDFYFSDIGFGDRN 149
                                       ********************************************888665444122155777788877777774444 PP

                   Glyco_tranf_2_3 151 ar..ralg.vltlnGsgslirrevlkelegldplfllt.dDyelglrlrragfrtayvpgaavrev....fpsslka 219
                                       ++  ++++  ++++G+ +l  r++ +e +++d+ fl+  + ++++ r++  g+++ y p ++v++       s+   
  gi|330507840|ref|YP_004384268.1| 150 FAkyNEIReLDYFAGASFLLKRKCADEVGRFDEDFLMYmENVDYSIRCKDLGWKIIYSPNSVVYSKchsiASSTMGN 226
                                       4435666659***********************888888***********************999965556688999 PP

                   Glyco_tranf_2_3 220 yikqrnRw 227
                                       y + rnR 
  gi|330507840|ref|YP_004384268.1| 227 YLRSRNRL 234
                                       *9999997 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 ?   -3.0   0.0       5.7   9.3e+03      33      60 ..     327     352 ..     307     366 .. 0.63
   2 !   39.1   0.0   5.5e-13   8.9e-10       2     134 .]     499     653 ..     498     653 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.7
                                       EEEEES---..HHHHHHHTT-T.TEEEE CS
                   Glyco_trans_1_4  33 rlvivGdgprpeeleelaagleerveft 60 
                                        ++++G+g+ +  + ela+ l++r  +t
  gi|330507840|ref|YP_004384268.1| 327 AFHFAGGGQ-R-YVAELAQILQDRYDIT 352
                                       588889774.3.3443444445555555 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 5.5e-13
                                       EEEEEES---G.G.GTHHHHHHHH.HHHH.H.H.....EEEEEES---......HHHHHHHTT-T.TEEEE---..T CS
                   Glyco_trans_1_4   2 pvilfvGrlee.nvkgvdllleav.pllrkk.d.....vrlvivGdgp..rp..eeleelaagleerveftGfv..e 64 
                                       + il v r+e    k +  ++e +  l + k +     ++l+++G+ p  +p  ++++++a+++ +++e++  +   
  gi|330507840|ref|YP_004384268.1| 499 KMILSVARFETgGSKKQLEMIETFvDLCK-KdKrikkeWKLILAGGTPkiNPyyDKVRKKAKRI-SNIEIATNLnnY 573
                                       67999999944566899999999945555.42245578*******7766444778888888788.69*****99655 PP

                                       HHHHHHHH-SEEEE--..........---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHH CS
                   Glyco_trans_1_4  65 dlaellaaadvfvaPs..........egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeail 129
                                       ++++l+++a++f              e fg++++Eam   +  V+ d gg +e+v  g +g+ +   + e+l    l
  gi|330507840|ref|YP_004384268.1| 574 EIKQLYSNASIFWHACgldeidprliEHFGMTTVEAMQNYCVPVVIDGGGQREIVehGISGFRFT--SKEELKSYTL 648
                                       6***********998888877766777************9999999999*******99****998..7899999999 PP

                                       HHHH- CS
                   Glyco_trans_1_4 130 rLled 134
                                       +L++d
  gi|330507840|ref|YP_004384268.1| 649 KLIND 653
                                       99886 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 !   30.8   0.0   1.6e-10   2.6e-07       1     144 [.      84     238 ..      84     272 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.6e-10
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvlvm....nvanwleelaalffaedhgkdilvreal..grvv 70 
                                       +i++l +D v+  + l+++++ ++ + ++++vq ++l+       +  +e   ++ f++    d+ +++++   +  
  gi|330507840|ref|YP_004384268.1|  84 YIAILNSDIVVENNWLKGLVDIIDqDEKIGVVQSKMLFSdeemIESAGVEDAEDFYFSDIGFGDRNFAKYNeiRELD 160
                                       799*********************559**********9523223344556666666787777788887755113455 PP

                   Glyco_trans_2_3  71 psvGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpes....lvkekspltlraalrQrkRwayG 143
                                        ++G+ ++l r+ ++evg++d d+    E  d ++r+  +G+++++ p s     ++   ++t+  +lr r R +++
  gi|330507840|ref|YP_004384268.1| 161 YFAGASFLLKRKCADEVGRFDEDFLMYMENVDYSIRCKDLGWKIIYSPNSvvysKCHSIASSTMGNYLRSRNRLLLM 237
                                       5********************9999***********************99777777777888999999999997776 PP

                   Glyco_trans_2_3 144 c 144
                                        
  gi|330507840|ref|YP_004384268.1| 238 G 238
                                       4 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   5.9e-08   9.5e-05       9      80 ..     600     670 ..     566     677 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.9e-08
                   Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlae 80 
                                       e + + ++Ea+ + ++ ++ d  g++e+++ g +++ f + eel     +l++++ +r+++a++a++r  ++
  gi|330507840|ref|YP_004384268.1| 600 EHFGMTTVEAMQNYCVPVVIDGGGQREIVEHGISGFRFTSKEELKSYTLKLINDDYLREKMAKNAYNRS-KK 670
                                       7899***********9999999*********************************************94.44 PP

>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.9     9e-08   0.00015      33      88 ..      60     115 ..      52     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9e-08
                   Glyco_tranf_2_5  33 iairna.ksiaeaynkalsasdakykvYlhqDvliinkdfikdlleiFkkdkkiGmi 88 
                                         i+n+ k++a+a n ++++++ +y   l+ D++ ++++++k l++i ++d+kiG++
  gi|330507840|ref|YP_004384268.1|  60 KVIKNNiKNYAKAINLGIKNAKGQYIAILNSDIV-VENNWLKGLVDIIDQDEKIGVV 115
                                       4577778*************************96.6889****************97 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.3e-06    0.0071       1     155 [.     331     476 ..     331     485 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.3e-06
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev.....elvvrvprvplpllkrllrslaflrrlrrllkrek 72 
                                       +GG +r+v eLa+ L++r +++t ++ +d   + +++        + ++ + +p+++ +++++     +  +  ++ 
  gi|330507840|ref|YP_004384268.1| 331 AGGGQRYVAELAQILQDR-YDITYIVNKDISLENYREwfdidLSKCKLKIIKIPFFEERGIYIID-ECMIVHQNENP 405
                                       59****************.*********9999999999997733344444444555555544444.34455566679 PP

                    Glyco_transf_4  73 pDvv...HahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrl.lrradrviavSeata 145
                                       +Dv+    +++ +++ a +l   r l     + +H+++                + + r++ ++r d vi++S++t 
  gi|330507840|ref|YP_004384268.1| 406 FDVIkneSINYDIFINANMLTKVRPLSSLSAFICHFPD----------------KDMGRFFnVDRYDYVITNSNYTT 466
                                       999965555555555666666666777777899*****................4445555589************* PP

                    Glyco_transf_4 146 delrerygvp 155
                                        +l++++g++
  gi|330507840|ref|YP_004384268.1| 467 HWLKQKWGLD 476
                                       *******987 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 !   15.0   0.0   7.8e-06     0.013      22     151 ..      73     212 ..      58     229 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.8e-06
                   Glyco_transf_21  22 llqaleaakydllvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdakglaaal.eaaf...l...ntl.ag 89 
                                       ++ +++ ak +++ i+ sd++v+ + L+ l+  + + +k+g+V+s  + sd++ + +a  e a    +   +++  +
  gi|330507840|ref|YP_004384268.1|  73 INLGIKNAKGQYIAILNSDIVVENNWLKGLVDIIDQdEKIGVVQSKMLFSDEEMIESAGvEDAEdfyFsdiGFGdRN 149
                                       4557889***************************8779***************877776333333224433333677 PP

                   Glyco_transf_21  90 vlqa.klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapia 151
                                       ++++ +  +l+   G+s +l+r+  +++G f +      e    + + ++ G+k++ sp+ ++
  gi|330507840|ref|YP_004384268.1| 150 FAKYnEIRELDYFAGASFLLKRKCADEVGRFDEDFLMYMENVDYSIRCKDLGWKIIYSPNSVV 212
                                       77778999*********************9976333333556666666666666666666655 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 !   14.7   0.1     2e-05     0.033       2      50 ..      13      75 ..      12     123 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgfdr....ilvydndstDgtrailkel.pevkllhvd.........k 50
                                      n +d+++ f+  +l+  +d+    i+++dn s+D++ ++l+++ p++k++++           
  gi|330507840|ref|YP_004384268.1| 13 NGKDYIEDFCNSILNTNIDDftceIIIVDNLSKDDSVNFLEANyPKIKVIKNNiknyakainL 75
                                      7789*********99997655556****************886699**998875444433331 PP

>> DnaB  DnaB-like helicase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       4.5   7.4e+03      90     101 ..      62      73 ..      49      74 .. 0.82
   2 ?    0.6   0.0      0.36   5.8e+02      14      38 ..     117     141 ..     114     144 .. 0.89
   3 ?    8.1   0.1    0.0016       2.7      16      69 ..     235     290 ..     234     306 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.5
                                       -CCCHHHHHHHH CS
                              DnaB  90 saanieeyaeiv 101
                                        ++ni++ya+ +
  gi|330507840|ref|YP_004384268.1|  62 IKNNIKNYAKAI 73 
                                       4579*****988 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.36
                                       HHHHHSTTHHHHHHCC--GGGSSSH CS
                              DnaB  14 galLldpeaidevadilkpedFyep 38 
                                       + +L+++e + e a++ ++edFy +
  gi|330507840|ref|YP_004384268.1| 117 SKMLFSDEEMIESAGVEDAEDFYFS 141
                                       689********************86 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0016
                                       HHHSTTHHHHHHCC--GGGSS.SHHHHHHHHHHHHHHHTT.TS-SHHHHHHHSCSS CS
                              DnaB  16 lLldpeaidevadilkpedFy.epahrliFeailelyekg.epiDlvtvkeelekk 69 
                                       lL+ ++  +++a+ +++ +Fy +++h  ++  +++ ++k  e+ D++tv++ l++ 
  gi|330507840|ref|YP_004384268.1| 235 LLMGKHFPQKLAESIETSHFYiKREHESLYHSLIQAVKKVaENNDTKTVNRTLKEL 290
                                       5677777789999999999994568*****9987777775599*******999764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (701 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4749.92
//
Query:       gi|330507841|ref|YP_004384269.1|  [L=299]
Description: NAD-dependent epimerase/dehydratase [Methanosaeta concilii GP6]
Scores for complete 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-39  134.6   0.0    5.3e-39  134.1   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.2e-38  131.3   0.1    1.9e-37  129.4   0.1    1.9  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.9e-09   35.1   0.0    1.8e-07   30.5   0.0    2.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.3e-06   27.0   0.1    1.2e-05   24.5   0.1    1.9  1  RmlD_sub_bind    RmlD substrate binding domain
    0.00061   19.0   0.3      0.018   14.2   0.1    2.8  2  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
      0.018   14.5   0.0       0.05   13.1   0.0    1.8  1  adh_short        short chain dehydrogenase
      0.047   13.3   0.0        5.8    6.4   0.0    2.2  2  NmrA             NmrA-like family
      0.064   12.4   0.0      0.097   11.8   0.0    1.5  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
       0.07   13.0   0.0        0.2   11.6   0.0    1.7  2  KR               KR domain
      0.071   13.2   0.1       0.35   10.9   0.1    2.2  2  DUF1836          Domain of unknown function (DUF1836)
       0.11   12.8   0.0       0.73   10.1   0.0    2.2  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.1   0.0   3.2e-42   5.3e-39       1     228 [.       3     222 ..       3     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 3.2e-42
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHHH.T-SEEEE--S CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfkee.qpdavihlAa 73 
                                       ilVtG++GfiGs+l++ ll+ g ev++ld+  ++s+t++++     ++v++      +++++ +   +p++++hl+ 
  gi|330507841|ref|YP_004384269.1|   3 ILVTGGAGFIGSNLTEDLLASGEEVVVLDNMHTGSKTNLDDLDgrlKVVQA------SCNQIPRLDlNPEEIYHLGI 73 
                                       8******************************99999988774333333333......34444443349*******99 PP

                                       ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHH CS
                         Epimerase  74 vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlage 150
                                        ++ + + +dp  +  + ++gt+ ++e ar++g+ r++++sSs++Y    + p  e++    +  +  Y  a la+e
  gi|330507841|ref|YP_004384269.1|  74 PSSSPMYKKDPFLVG-EAINGTTAIFELARRTGA-RVIYASSSSLYNGLLP-PHREDM---VIGVTDYYTEARLAIE 144
                                       888888899988855.69****************.************9999.988888...7899************ PP

                                       HHHHHHHHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHH CS
                         Epimerase 151 klveayaaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvl 226
                                       +++e y++ +++n + +r f++yGp  + +++ ++++++++  ++eg+ + +++gdg++ Rdf yv+D+++a+ l++
  gi|330507841|ref|YP_004384269.1| 145 RIAELYKRLFDVNSVGMRFFSVYGPKeRTKKQYANMVTQFLWEMQEGR-SPVIFGDGSQTRDFTYVKDIVRALQLAM 220
                                       **************************888888****************.**************************** PP

                                       HH CS
                         Epimerase 227 eh 228
                                       + 
  gi|330507841|ref|YP_004384269.1| 221 DS 222
                                       98 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.4   0.1   1.2e-40   1.9e-37       1     331 [.       4     294 ..       4     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 1.2e-40
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+l+e Ll+ g ev+++++ ++  + ++++ l        +++lk++++  +   +l     + +p+
  gi|330507841|ref|YP_004384269.1|   4 LVTGGAGFIGSNLTEDLLASGEEVVVLDNMHTG-SKTNLDDL--------DGRLKVVQASCNQIPRL-----DLNPE 66 
                                       9************************99876544.44556555........56899999988775544.....689** PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                       e+y+L+  s  +   ++P  + e+ + Gt+ ++e++r++g    +r++ aS+s +Y  +   p +E+  +  +  Y 
  gi|330507841|ref|YP_004384269.1|  67 EIYHLGIPSSSPMYKKDPFLVGEA-INGTTAIFELARRTG----ARVIYASSSSLYNGLL-PPHREDMVIGVTDYYT 137
                                       **********************99.*************98....69**********5554.79************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-.TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrg.etfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                        a+l+ + i++ y++ +++  v  ++f  ++p+   ++   + +t+++ ++++g+ +v+ +G+++++Rd+++vkD+v
  gi|330507841|ref|YP_004384269.1| 138 EARLAIERIAELYKRLFDVNSVGMRFFSVYGPKERtKKQYANMVTQFLWEMQEGRSPVI-FGDGSQTRDFTYVKDIV 213
                                       ********************************8651567899************97766.9**************** PP

                                       HHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       +a++l++ ++     + +tg+ +s +e++++ +++l   i+ +               ++ ++ ++y+     + +l
  gi|330507841|ref|YP_004384269.1| 214 RALQLAMDSNYHGVLNAGTGKAYSFNEVIRMLNQKLESAIKPKY--------------TENPI-KNYV-----RHTL 270
                                       **********************************9998775431..............22233.2454.....5679 PP

                                       B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeelvre 331
                                       +d+sk +e L +++++++ee++++
  gi|330507841|ref|YP_004384269.1| 271 ADTSKCREILKFEAQFTLEEGISK 294
                                       9********************986 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 !   30.5   0.0   1.1e-10   1.8e-07       1     229 [.       4     220 ..       4     225 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.1e-10
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtGgaGF+G++l + L+  +e  ev vlD  +  ++ +     ++ kv+++  ++ ++l+   e+++    l ++ 
  gi|330507841|ref|YP_004384269.1|   4 LVTGGAGFIGSNLTEDLLASGE--EVVVLDNMHTGSKTNLDDLDGRLKVVQASCNQIPRLDLNPEEIYH---L-GIP 74 
                                       69*******************6..******88887776666666666799**********999888764...3.444 PP

                         3Beta_HSD  78 dvagkltede.imkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                        +  ++++d  +    ++GT  + e ++++g r ++Y Ss +   +      +l  + ++ +    +d y+e +   
  gi|330507841|ref|YP_004384269.1|  75 SSSPMYKKDPfLVGEAINGTTAIFELARRTGAR-VIYASSSSLYNG------LLPPH-REDMVIGVTDYYTEARLAI 143
                                       44445555541356689**************86.69***9887666......33222.2334455678888876555 PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqla......klglalfkigdeevlsdrvYvgNvawa 224
                                       E++  +          +++ + +R   +yG+++++ ++ ++ ++      + g + +  gd +++ d++Yv  ++ a
  gi|330507841|ref|YP_004384269.1| 144 ERI-AELYK----RLFDVNSVGMRFFSVYGPKERTKKQYANMVTqflwemQEGRSPVIFGDGSQTRDFTYVKDIVRA 215
                                       554.44334....2335689***********9987766665554111222577888999***************999 PP

                         3Beta_HSD 225 hilAa 229
                                         lA+
  gi|330507841|ref|YP_004384269.1| 216 LQLAM 220
                                       88885 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   7.6e-09   1.2e-05       1     210 [.       1     228 [.       1     267 [. 0.78

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7.6e-09
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....T--TTSHHHHHHHH.........HHH--SEEEE------H CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre....eldltdaeavaell.........keakpdvvvnaAAytav 64 
                                       m ilvtG+ G +Gs+L++ l ++g ev+ l++     +++l+d +   +++          + +p+ +++++     
  gi|330507841|ref|YP_004384269.1|   1 MSILVTGGAGFIGSNLTEDLLASGEEVVVLDNMhtgsKTNLDDLDGRLKVVqascnqiprLDLNPEEIYHLGIPSSS 77 
                                       88****************************777788877777777766666677788888899**********9999 PP

                                       HHHHHSHHHH.HHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH- CS
                     RmlD_sub_bind  65 DkaEseeeaa.yavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaag 140
                                           +++ +  +a+n  ++ a+ e+a+++ga +i+ S+   ++G    p +ed   +   +Y +++la E+  + ++
  gi|330507841|ref|YP_004384269.1|  78 PMYKKDPFLVgEAIN--GTTAIFELARRTGARVIYASSSSLYNGL-LPPHREDMVIGVTDYYTEARLAIERIAELYK 151
                                       999999766515666..7889***********************9.557999999***************9987754 PP

                                       S....SEEEEEE-SEESS......SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GG CS
                     RmlD_sub_bind 141 k....kalivRtswvyge......kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeeke 205
                                            + + +R+  vyg       +  n+v+++l   +e  +  ++ D  q++  T+++d+ ++l  +++   +   
  gi|330507841|ref|YP_004384269.1| 152 RlfdvNSVGMRFFSVYGPkertkkQYANMVTQFLWEMQEGRSPVIFGDgsQTRDFTYVKDIVRALQLAMDSNYH--- 225
                                       4222367779******9866655455677777777666666666666656899999999999998877776665... PP

                                       G-EEE CS
                     RmlD_sub_bind 206 lagvy 210
                                         gv+
  gi|330507841|ref|YP_004384269.1| 226 --GVL 228
                                       ..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 !   14.2   0.1   1.1e-05     0.018       1      34 [.       5      38 ..       5      73 .. 0.85
   2 ?    1.9   0.0     0.065   1.1e+02     112     142 ..      91     120 ..      81     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                      EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksg 34
                                      +TG+ GF+G+ L e+LL + +ev +   +++ s+
  gi|330507841|ref|YP_004384269.1|  5 VTGGAGFIGSNLTEDLLASGEEVVVLDNMHTGSK 38
                                      7******************997655555666655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.065
                                       HHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS CS
                     NAD_binding_4 112 veGtrevlelakklkklkvllhvST.ayvnge 142
                                       ++Gt  ++ela+++ +   +++ S+ +  ng 
  gi|330507841|ref|YP_004384269.1|  91 INGTTAIFELARRTGAR--VIYASSsSLYNGL 120
                                       67888888888877666..5555543655554 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     3e-05      0.05       3      45 ..       3      45 ..       1      58 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelk 45
                                      +lvtG+++ IG ++ + l+++G +vvv+d+     ++ ++ l 
  gi|330507841|ref|YP_004384269.1|  3 ILVTGGAGFIGSNLTEDLLASGEEVVVLDNMHTGSKTNLDDLD 45
                                      89***************************99887776666655 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0036       5.8       1      28 [.       3      30 ..       3     106 .. 0.86
   2 ?    5.1   0.0    0.0091        15     152     229 ..     180     253 ..     173     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0036
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEE CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvral 28
                                      Ilv+G++G +G+ +++ ll++g +v +l
  gi|330507841|ref|YP_004384269.1|  3 ILVTGGAGFIGSNLTEDLLASGEEVVVL 30
                                      9*********************999887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0091
                                       S-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHTS- CS
                              NmrA 152 laqlkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkigkt 228
                                       +++++  ++++++ + ++ g+g+    +   ++Di ++   +++  ++++g+  + +g+ +s+ne+++++++k++  
  gi|330507841|ref|YP_004384269.1| 180 MVTQFLWEMQEGR-SPVIFGDGSQTRDFT-YVKDIVRALQLAMD--SNYHGVLNAGTGKAYSFNEVIRMLNQKLESA 252
                                       4444666666666.889999999888888.99999999888887..5799*********************999877 PP

                                       E CS
                              NmrA 229 v 229
                                       +
  gi|330507841|ref|YP_004384269.1| 253 I 253
                                       6 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     6e-05     0.097       1      31 [.       3      32 ..       3     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6e-05
                                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES CS
                   Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiiller 31
                                      +lvtG++G iGs+l++ +l++  + +++l++
  gi|330507841|ref|YP_004384269.1|  3 ILVTGGAGFIGSNLTEDLLASGEE-VVVLDN 32
                                      89****************998755.555554 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012       0.2       3      30 ..       3      30 ..       2      59 .. 0.83
   2 ?   -2.8   0.0         3   4.9e+03      81     113 ..     223     257 ..     205     258 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                      EEEETTTSHHHHHHHHHHHHHHS-EEEE CS
                                KR  3 ylitGGlGgLGlelarwlaekgarhlvl 30
                                       l+tGG+G +G  l++ l+++g++ +vl
  gi|330507841|ref|YP_004384269.1|  3 ILVTGGAGFIGSNLTEDLLASGEEVVVL 30
                                      69********************999988 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3
                                       ---EEEE---..------TTT--HHHHHHHHTTTT CS
                                KR  81 pikGvihaAg..vlrdklleemtaedleqvlapKv 113
                                       + +Gv++a    +   + + +m +++le++++pK 
  gi|330507841|ref|YP_004384269.1| 223 NYHGVLNAGTgkAYSFNEVIRMLNQKLESAIKPKY 257
                                       55666655431144567777888888888888886 PP

>> DUF1836  Domain of unknown function (DUF1836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.3   3.8e+03       3      18 ..      55      70 ..      53      79 .. 0.82
   2 ?   10.9   0.1   0.00022      0.35      13      49 ..     238     271 ..     233     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.3
                           DUF1836  3 weelPdldLyldqvve 18
                                       +++P+ldL  +++ +
  gi|330507841|ref|YP_004384269.1| 55 CNQIPRLDLNPEEIYH 70
                                      5789****98888766 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00022
                           DUF1836  13 ldqvvelvnqvleslkrnedkvltktminNYvKkkll 49 
                                        ++v+ ++nq+les  +    ++t++ i+NYv++ l 
  gi|330507841|ref|YP_004384269.1| 238 FNEVIRMLNQKLESAIK---PKYTENPIKNYVRHTLA 271
                                       699**********8777...9************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 ?   10.1   0.0   0.00045      0.73       3      44 ..       5      44 ..       3      66 .. 0.74
   2 ?   -0.0   0.0      0.61   9.9e+02      84     101 ..      96     113 ..      77     191 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00045
                                      EE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH CS
                   Sacchrp_dh_NADP  3 iiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka 44
                                      + G+ G++G+ ++e+l+++++   e++v d  +++ +  ++++
  gi|330507841|ref|YP_004384269.1|  5 VTGGaGFIGSNLTEDLLASGE---EVVVLDNMHTGSKTNLDDL 44
                                      55555**************98...5*****9998877777664 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.61
                                       HHHHHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  84 dvlkaCietgvhyvdtsi 101
                                       ++ +++++tg++++ +s 
  gi|330507841|ref|YP_004384269.1|  96 AIFELARRTGARVIYASS 113
                                       566666666666655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2002.89
//
Query:       gi|330507842|ref|YP_004384270.1|  [L=47]
Description: hypothetical protein MCON_1863 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       160  (0.00892409); expected 358.6 (0.02)
Passed bias filter:                      152  (0.00847788); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 353.45
//
Query:       gi|330507843|ref|YP_004384271.1|  [L=63]
Description: hypothetical protein MCON_1864 [Methanosaeta concilii GP6]
Scores for complete 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-06   25.3   0.0    9.6e-06   25.2   0.0    1.0  1  GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   5.4e-10   9.6e-06     284     331 ..       4      50 ..       1      51 [. 0.91

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.4e-10
                                       ..TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 284 kesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvre 331
                                       ++s++++  +dp++frp+ev  ll d++k++ +Lg+++k+s +e+v++
  gi|330507843|ref|YP_004384271.1|   4 ADSKRIKAAFDPNRFRPAEVPILLSDTTKIE-KLGFNAKCSQKEVVND 50 
                                       567888999*********************9.9***********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 475.45
//
Query:       gi|330507844|ref|YP_004384272.1|  [L=113]
Description: hypothetical protein MCON_1865 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); 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:                         0  (0); expected 0.2 (1e-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 0.20s 00:00:00.54 Elapsed: 00:00:00.33
# Mc/sec: 1013.85
//
Query:       gi|330507845|ref|YP_004384273.1|  [L=550]
Description: glutamine-dependent NAD(+) synthetase [Methanosaeta concilii GP6]
Scores for complete 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-77  257.8   0.0    9.2e-77  257.4   0.0    1.1  1  NAD_synthase   NAD synthase
    2.8e-12   46.5   0.0    6.2e-12   45.4   0.0    1.5  1  CN_hydrolase   Carbon-nitrogen hydrolase
    0.00063   19.5   0.0      0.001   18.8   0.0    1.3  1  Asn_synthase   Asparagine synthase
  ------ inclusion threshold ------
       0.19   10.5   0.0       0.27   10.0   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.4   0.0   2.1e-80   9.2e-77       2     241 ..     269     518 ..     268     519 .. 0.97

  Alignments for each domain:
  == domain 1  score: 257.4 bits;  conditional E-value: 2.1e-80
                                       HHHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE CS
                      NAD_synthase   2 ieelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievkt 78 
                                       +++lv   ++yv+k+g+++v+lGlSGG+DSslvaa+av+alg++nvl++llPs ++ ++++ dalala nlgi++  
  gi|330507845|ref|YP_004384273.1| 269 WRALVLGTRDYVHKCGFSSVLLGLSGGIDSSLVAAIAVQALGPNNVLGVLLPSPYTRQSSIDDALALAANLGIKTIS 345
                                       78899999********************************************************************* PP

                                       ---HHHHHHHHHHHHHHH....-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETT CS
                      NAD_synthase  79 idikpivrafeqelkeak....edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapi 151
                                       i +++i+ +fe el e+     +d++++N++aRiR+++l+a +nk+++++l+Tgn+sEl+vGy+T+yGD+a++la i
  gi|330507845|ref|YP_004384273.1| 346 ILLTDIMGSFELELAEHFagrpKDITEENIQARIRATLLMALSNKYGSILLATGNRSELSVGYCTIYGDMAGGLAVI 422
                                       **********986655545566******************************************************* PP

                                       TTS-HHHHHHHHHHTT.......--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT- CS
                      NAD_synthase 152 aellKtevkeLakeln.......vPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekel 220
                                        +l Kt v+++a++ln       +P++++kkpPsA+L+pgqtD+++L+ +Y  lDeiLk ++++++s+ ++++ ++l
  gi|330507845|ref|YP_004384273.1| 423 SDLPKTMVYRIAEWLNstaskpvIPPSIIKKPPSAELRPGQTDQDSLP-PYPLLDEILKrYIDEHQSRADLLR-AGL 497
                                       ************************************************.*********************999.*** PP

                                       -HHHHHHHHHHHHHTGGGGSS CS
                      NAD_synthase 221 paevvekieklvkksehKrkl 241
                                       ++ +v ++++lvk+ e+Kr +
  gi|330507845|ref|YP_004384273.1| 498 DEVTVDRVISLVKNAEFKRVQ 518
                                       *******************76 PP

>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   1.4e-15   6.2e-12       1     252 [.       2     251 ..       2     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.4e-15
                                       EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBS.....SSHHHHHHHHBHSSSHHHHHHHHHHH CS
                      CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgy.....keeahfleaAeaglgetlallaalar 72 
                                       ++A+ Ql+++  dl++n ++++++i++A   + dL v  El++ gy       +++f+e       + l+ la+ ++
  gi|330507845|ref|YP_004384273.1|   2 KIALLQLNPTIGDLAGNKGLIARAIRRAP--DFDLAVTSELALLGYppcdlLLNEEFVE----RSWQALDELAEELA 72 
                                       69*************************76..899************7666655566665....44489999999999 PP

                                       HHTEEEEEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTE... CS
                      CN_hydrolase  73 kngiavvigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvg... 146
                                       +  +++v+   ++    g  +++n+a l+ +dgk++   +K++L     +   ++e  +f+pg++   ++ ++    
  gi|330507845|ref|YP_004384273.1|  73 DLPPVLVGQAEPNT-SAGERPLFNSAALI-RDGKVTETFQKSMLS----GCDLFHEDRYFQPGKEARLLQIEGQslg 143
                                       99999999999996.44555589998888.899999*******96....6678999999999776333333333334 PP

                                       ......EEEEEEGGGGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCE CS
                      CN_hydrolase 147 ......kiGaaiCyeigfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeq 217
                                              +G +  + +  p  +  l++kga+ +vnls  +p++  + +  +e+     a     +++ +nqvgg  +
  gi|330507845|ref|YP_004384273.1| 144 iligelLLGSSDNERQDRPDPIAELRAKGADAIVNLS-ASPFTAGK-QLLREARLSDLAKKHCLPILSVNQVGG--N 216
                                       557777779999999999999**************44.23333222.22335556667888889**********..* PP

                                       TTEEEE--EEEE-TTS-EEEECCSSSTEEEEEEEE CS
                      CN_hydrolase 218 lilwpvghSaiidpdGrilaglgeeeegvliaeid 252
                                       ++l + g S+++d  Gr++a+   +ee++++a++d
  gi|330507845|ref|YP_004384273.1| 217 DDLIFDGRSCFFDAAGRLIARGRGFEEDIIVADLD 251
                                       **********************************9 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.3e-07     0.001      22      64 ..     290     361 ..     277     376 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.3e-07
                      Asn_synthase  22 alLSGGlDSSliaalaarqsk............................splktFsigfee.kgsdeakyak 64 
                                       + LSGG+DSSl+aa+a + +                               +kt si +++  gs e++ a+
  gi|330507845|ref|YP_004384273.1| 290 LGLSGGIDSSLVAAIAVQALGpnnvlgvllpspytrqssiddalalaanLGIKTISILLTDiMGSFELELAE 361
                                       559*************99887666666666666666666666666666655666666664455555555555 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0     6e-05      0.27       2      32 ..     287     319 ..     286     350 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6e-05
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqg..yevigvfl 32 
                                        v+ +lSgG+DSs++aa+  ++    +v gv l
  gi|330507845|ref|YP_004384273.1| 287 SVLLGLSGGIDSSLVAAIAVQALgpNNVLGVLL 319
                                       5899*********87776655533567777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 4568.87
//
Query:       gi|330507846|ref|YP_004384274.1|  [L=465]
Description: hypothetical protein MCON_1867 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00022   20.9   1.0    0.00052   19.8   0.2    2.0  2  HTH_IclR      IclR helix-turn-helix domain
     0.0011   18.8   0.1     0.0023   17.8   0.1    1.5  1  MarR_2        MarR family
  ------ inclusion threshold ------
      0.028   14.3   0.0      0.057   13.3   0.0    1.5  1  TrmB          Sugar-specific transcriptional regulator TrmB
      0.089   13.0   0.0       0.16   12.2   0.0    1.4  1  BK_channel_a  Calcium-activated BK potassium channel alpha su
       0.15   11.5   0.2        1.3    8.5   0.0    2.2  2  SieB          Super-infection exclusion protein B


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       0.6   2.2e+03      16      30 ..     137     151 ..     136     152 .. 0.89
   2 !   19.8   0.2   1.5e-07   0.00052       8      50 ..     401     443 ..     392     445 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.6
                                       BSS-BHHHHHHHHTS CS
                          HTH_IclR  16 pqeltlselArrtgl 30 
                                       p++++l ++ + +gl
  gi|330507846|ref|YP_004384274.1| 137 PGDMRLGQINASLGL 151
                                       689******999998 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.5e-07
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       ++  l e+++++t +e+  +t  pkS+  ++L +L+++++v++
  gi|330507846|ref|YP_004384274.1| 401 VISTLVEHGGRMTQAEIRYETKTPKSSLTGILISLERRKLVTK 443
                                       6777889**********************************87 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   6.5e-07    0.0023       3      54 ..     394     444 ..     392     449 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.5e-07
                                       --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       lt  +  v+  L  ++gr +t++e+  +++ +ks+++ il  L+++ Lv+++
  gi|330507846|ref|YP_004384274.1| 394 LTHREQAVISTLVEHGGR-MTQAEIRYETKTPKSSLTGILISLERRKLVTKK 444
                                       67788899999*****97.9*****************************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 ?   13.3   0.0   1.6e-05     0.057       6      57 ..     394     447 ..     393     457 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                                       HHHHCCCHCHHHHHH.CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.S CS
                              TrmB   6 LseyEakvYlaLlkl.gpatadeiaeelgvprskvYevLrsLedkGlVerek.g 57 
                                       L+  E  v  +L+++ g++t  ei  e++ p+s+   +L sLe++ lV++++ g
  gi|330507846|ref|YP_004384274.1| 394 LTHREQAVISTLVEHgGRMTQAEIRYETKTPKSSLTGILISLERRKLVTKKEwG 447
                                       67788889999**662679*****************************998844 PP

>> BK_channel_a  Calcium-activated BK potassium channel alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.4e-05      0.16      25      90 ..      33      97 ..      26     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.4e-05
                      BK_channel_a 25 sclcpGistllanLissasikeestkseewlkeYlrgagneiytiklskkfegmtfteaaalifee 90
                                      s++  Gis+l++ L+ s++ +e st+++  l+ Yl+ ag+ + t    + ++g++f +a++  +e+
  gi|330507846|ref|YP_004384274.1| 33 SIFLLGISSLFLLLSLSLGMEEASTQDSLTLNVYLDPAGKALVTGYADN-ISGLNFLAASEYQYEN 97
                                      78899************************************99877655.9999999999887776 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.15   5.5e+02      35      61 ..     209     235 ..     205     240 .. 0.78
   2 ?    8.5   0.0   0.00035       1.3      63      97 ..     379     413 ..     374     419 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.15
                              SieB  35 iglvflisiayllaqvvskllaeikek 61 
                                       i l++l++ a++la+  + ++ + +++
  gi|330507846|ref|YP_004384274.1| 209 ISLILLLAGAFILAIGSVLGVILWRRR 235
                                       78999*******999888777665555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00035
                              SieB  63 kkkreqkkvekklknLteeekavLreflnqgksvl 97 
                                       ++++  ++ e+++++Lt +e+av++++++ g ++ 
  gi|330507846|ref|YP_004384274.1| 379 QRIQLSREMEAVIQTLTHREQAVISTLVEHGGRMT 413
                                       456788999*******************9998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.38
# Mc/sec: 3662.73
//
Query:       gi|330507847|ref|YP_004384275.1|  [L=198]
Description: hypothetical protein MCON_1869 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        1.4    8.9   5.7        6.5    6.8   0.1    3.3  4  Rho_N            Rho termination factor, N-terminal domain


Domain annotation for each model (and alignments):
>> Rho_N  Rho termination factor, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.1   1.8e+03       1      12 [.      53      64 ..      53      65 .. 0.85
   2 ?   -2.3   0.1      0.25   4.4e+03       1      12 [.     125     136 ..     125     137 .. 0.81
   3 ?    3.2   0.1    0.0047        85       1      12 [.     144     155 ..     144     156 .. 0.91
   4 ?    6.8   0.1   0.00036       6.5       4      18 ..     166     180 ..     165     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.1
                                      HHHHS-HHHHHH CS
                             Rho_N  1 eLkektlseLra 12
                                      eL ++tl e ++
  gi|330507847|ref|YP_004384275.1| 53 ELGNMTLGEIKE 64
                                      7899***99987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.25
                                       HHHHS-HHHHHH CS
                             Rho_N   1 eLkektlseLra 12 
                                       eL e++l++ ++
  gi|330507847|ref|YP_004384275.1| 125 ELGEMSLNQILD 136
                                       788999999876 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.0047
                                       HHHHS-HHHHHH CS
                             Rho_N   1 eLkektlseLra 12 
                                       eL+++tl+e r+
  gi|330507847|ref|YP_004384275.1| 144 ELESMTLNEIRD 155
                                       8********997 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.00036
                                       HS-HHHHHHHHHHTT CS
                             Rho_N   4 ektlseLraiAkelg 18 
                                       ++t++eL++ Ak++ 
  gi|330507847|ref|YP_004384275.1| 166 NMTINELVDEAKDMQ 180
                                       8***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1091  (0.0608511); expected 358.6 (0.02)
Passed bias filter:                      733  (0.0408835); 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):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 1558.51
//
Query:       gi|330507848|ref|YP_004384276.1|  [L=234]
Description: hypothetical protein MCON_1870 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.21s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1937.97
//
Query:       gi|330507849|ref|YP_004384277.1|  [L=332]
Description: O-sialoglycoprotein endopeptidase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-82  277.6   0.1    1.6e-82  277.3   0.1    1.0  1  Peptidase_M22   Glycoprotease family
  ------ inclusion threshold ------
      0.034   14.2   0.1       0.16   12.1   0.0    2.2  2  DUF1490         Protein of unknown function (DUF1490)
      0.044   13.5   0.0      0.071   12.8   0.0    1.2  1  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 !  277.3   0.1   2.7e-86   1.6e-82       9     271 .]      35     299 ..      30     299 .. 0.97

  Alignments for each domain:
  == domain 1  score: 277.3 bits;  conditional E-value: 2.7e-86
                                       EEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--EE CS
                     Peptidase_M22   9 sqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnkPlv 85 
                                       ++++++++ GG++P++as++H+e++  ++  +la+a  +  +l+++a+++gPGl+++Lr ++++A++l+l +++Plv
  gi|330507849|ref|YP_004384277.1|  35 KSATYTPARGGIHPREASQHHAEHMRAVVGDVLAQARQRGLKLEGVAFSQGPGLGPCLRTVATAARALSLRFDIPLV 111
                                       556778899******************************************************************** PP

                                       EEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCCHHHHHHH CS
                     Peptidase_M22  86 gVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypggpkiekla 162
                                       gVnh+ ah++ ++ +++ ++P v++vsG ++qv++ ++gry+i+getld+ +g+a+dk+ar +gl +pggpk+e+la
  gi|330507849|ref|YP_004384277.1| 112 GVNHCVAHIEVGKWQSGARDPAVIYVSGANSQVLALRQGRYRIFGETLDISVGNAIDKFARSVGLAHPGGPKVEELA 188
                                       *************9988899********************************************************* PP

                                       CTC.S.......EETTEEE.CHHHHHHHHHHST.THHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXH CS
                     Peptidase_M22 163 keg.kkiefprplkgldfsfsGlktavlkelek.evedlaasfqeavvdhlvekteralklpkakelvilGGvaank 237
                                       +++ ++i +p+++kg+d+sfsGl ta+++++ k + ed+++s+qe+++++lve+tera+++ +++e +++GGv+an+
  gi|330507849|ref|YP_004384277.1| 189 RKAkNYIPLPYTVKGMDLSFSGLSTAATEAAGKhDLEDVCYSLQETAFAMLVEVTERAMAHAEKREAMLVGGVGANA 265
                                       ***888*************************5547****************************************** PP

                                       HHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
                     Peptidase_M22 238 rLrealeeeaeelglkliiPplkyctdnaamiaw 271
                                       rL e+++ ++ e+g++++ Pp +++ dn+ mia+
  gi|330507849|ref|YP_004384277.1| 266 RLGEMMRIMCHERGAEFFLPPRSFMGDNGSMIAY 299
                                       ********************************97 PP

>> DUF1490  Protein of unknown function (DUF1490)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.7e-05      0.16      52      75 ..      49      73 ..      11      76 .. 0.84
   2 ?   -2.8   0.0       1.2   7.2e+03      25      55 ..     186     215 ..     181     225 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.7e-05
                           DUF1490 52 Rkae.eaaEsarLkvaDvvaeArer 75
                                      R+a  + aE++r  v+Dv+a+Ar+r
  gi|330507849|ref|YP_004384277.1| 49 REASqHHAEHMRAVVGDVLAQARQR 73
                                      5554389****************98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                           DUF1490  25 evlrkavakaplreaaVaatalglrgaRkae 55 
                                       e +rka +  pl   +V+ + l++ g  +a 
  gi|330507849|ref|YP_004384277.1| 186 ELARKAKNYIPLP-YTVKGMDLSFSGLSTAA 215
                                       5667777777764.46777777666655544 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.2e-05     0.071     264     334 ..     223     297 ..     197     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                    Carbam_trans_N 264 kdedlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNiklNs..allesglFedvwvqP..aanDsGsAi 334
                                       + ed+  s+q+    ++vev++ ++++ + r   l GGv++N  l    +++ +    + +++P  +++D+Gs i
  gi|330507849|ref|YP_004384277.1| 223 DLEDVCYSLQETAFAMLVEVTERAMAHAEKREAMLVGGVGANARLGEmmRIMCHERGAEFFLPPrsFMGDNGSMI 297
                                       235****************************************99761144555667799999988899999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2560.74
//
Query:       gi|330507850|ref|YP_004384278.1|  [L=475]
Description: phosphoribosylamine--glycine ligase [Methanosaeta concilii GP6]
Scores for complete 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-58  196.0   0.0    7.9e-58  195.4   0.0    1.2  1  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 
    1.2e-24   86.9   0.5    2.3e-24   86.0   0.1    1.8  2  GARS_N       Phosphoribosylglycinamide synthetase, N domain
    2.6e-23   82.1   1.4    4.8e-23   81.2   0.1    2.0  2  GARS_C       Phosphoribosylglycinamide synthetase, C domain
  ------ inclusion threshold ------
      0.031   14.3   0.1       0.45   10.5   0.1    2.2  1  ATP-grasp_3  ATP-grasp domain
      0.042   13.1   0.0       0.42    9.8   0.0    2.1  2  ATPgrasp_ST  Sugar-transfer associated ATP-grasp
      0.098   12.2   0.1       0.25   10.9   0.0    1.6  2  ATP-grasp_2  ATP-grasp domain
       0.12   11.8   0.0       0.81    9.1   0.0    2.2  3  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin


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 !  195.4   0.0   3.1e-61   7.9e-58       2     194 .]     113     330 ..     112     330 .. 0.96

  Alignments for each domain:
  == domain 1  score: 195.4 bits;  conditional E-value: 3.1e-61
                                       BHHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSE....EEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS. CS
                            GARS_A   2 sKsfakdllkkagiptaeyeaftdpeeakeyieeataka....lVvKadglaagKgvivakseeealkavkeilek. 73 
                                       sK+ +kdllkk ++p +  ++f+dp+eakey+++  ++     lVvKadglaagKg iv+++ eea +a++ i+++ 
  gi|330507850|ref|YP_004384278.1| 113 SKCQTKDLLKKLRVPVPPCQNFSDPQEAKEYVQQRCSEEpgrgLVVKADGLAAGKGSIVCATPEEAASAIERIMVSp 189
                                       89******************************99877655677*******************************864 PP

                                       -TTCCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCE..................EEEECECEEE CS
                            GARS_A  74 kkfGeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDk..................gpnTGGmGay 132
                                       + fGeag+++ iE++leG E+ ++al+dg+tv+++++a d+k+++  D+                  +pnTGGmG +
  gi|330507850|ref|YP_004384278.1| 190 RLFGEAGDRIEIEDRLEGRELMFFALSDGHTVQAMQSALDYKQAFSPDEsvairlfnklagnpnqdnNPNTGGMGGF 266
                                       78*************************************************************************** PP

                                       ES-TTS-HHHHHHHHHHTHHHHHHHHHCT.T---EEEEEEEEEEETTE.EEEEEEESS--TTCH CS
                            GARS_A 133 spapvvteellekikeeileptveglkke.gipfkGvLyaglmlvedg.pkvlefnvRfgDpet 194
                                       sp+p++ eel+e+i+++i  ptv g+k+  g++++Gv+y glm++ed  p+vle+nvR gDpe+
  gi|330507850|ref|YP_004384278.1| 267 SPHPWLDEELTERIMKKIALPTVRGFKESsGQEYRGVIYFGLMISEDRePAVLEINVRLGDPEA 330
                                       **************************9862689************7777*************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 !   86.0   0.1   9.1e-28   2.3e-24       2      90 .]       8     111 ..       7     111 .. 0.93
   2 ?   -2.7   0.1       4.1     1e+04      71      90 .]     163     183 ..     160     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 9.1e-28
                                       EEEEEESSHHHHHHHHHHTTSTTESEEEEEE--CGG................TTHHHHHHHHHHCTESEEEE-SHHH CS
                            GARS_N   2 kvLvvGsGGRehalawklaqspkvekvyvapgNagt................edlealvefakeekidlvvvGpeap 62 
                                       +vLvv  GGR +a+a+++a+s +ve+vyvapgNag                  ++++l++f+k+e+idl++vGpe  
  gi|330507850|ref|YP_004384278.1|   8 RVLVVDAGGRGNAIAHAFARSGSVERVYVAPGNAGSemmdkcrlaaiegkvpRSISELLAFVKKERIDLTFVGPEGY 84 
                                       69**********************************888888887777777655678******************** PP

                                       HHTTHHHHHHHHHT-EEES--CCCCHHH CS
                            GARS_N  63 LvaGvadaleeekgikvfGpskeaAqlE 90 
                                       L +G++d ++e+ g +++Gp++eaA lE
  gi|330507850|ref|YP_004384278.1|  85 LSEGIVDIFQED-GQRILGPKREAAVLE 111
                                       *********777.*************99 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.1
                                       HHHHH.T-EEES--CCCCHHH CS
                            GARS_N  71 leeek.gikvfGpskeaAqlE 90 
                                       l++ k  i +  p+++a+ +E
  gi|330507850|ref|YP_004384278.1| 163 LAAGKgSIVCATPEEAASAIE 183
                                       544555788999999999998 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.5   3.8e+03      37      55 ..       4      22 ..       3      32 .. 0.63
   2 !   81.2   0.1   1.9e-26   4.8e-23      10      80 .]     388     473 ..     386     473 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.5
                                      E-SSEEEEEEEEESSHHHH CS
                            GARS_C 37 tsGGRvlavvavgetleeA 55
                                      +sG Rvl v a g   + A
  gi|330507850|ref|YP_004384278.1|  4 MSGNRVLVVDAGGRGNAIA 22
                                      5788999887765433333 PP

  == domain 2  score: 81.2 bits;  conditional E-value: 1.9e-26
                                       TTTSS--ST-EEBS.....TTEEEEESSEE..........EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-TTE CS
                            GARS_C  10 GYPgsyekgkeitg.....egvkvfhagtk..........lvtsGGRvlavvavgetleeArakayeavkkikfegl 71 
                                       GYPg+  ++++i+g      +v v+h+gt+          l+t+GGRv+++va g++l+eArakaye++k+++f+g+
  gi|330507850|ref|YP_004384278.1| 388 GYPGEHYTNMPINGlervdPEVIVYHNGTAwgtdsagnrrLYTTGGRVFTLVARGKSLAEARAKAYENIKRVRFNGM 464
                                       9***********99*****8899******999999999999************************************ PP

                                       E--STTTHH CS
                            GARS_C  72 fyRkDIGar 80 
                                        yRkDIG r
  gi|330507850|ref|YP_004384278.1| 465 RYRKDIGLR 473
                                       *******75 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00018      0.45       3     158 ..     113     325 ..     111     328 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00018
                                       SHHHHHHHHTTT.S---...............-EESS--.SSSEEEEESS-------B--SS--TTE.......... CS
                       ATP-grasp_3   3 dKlktykkLkeagvkvP...........tkleaeeleee.ekklvvKprdGaggesvrvveekeeaeaaieeve... 64 
                                       +K +t + Lk+  v+vP           +++ +++++ee    lvvK    a+g++  v    eea +aie +    
  gi|330507850|ref|YP_004384278.1| 113 SKCQTKDLLKKLRVPVPpcqnfsdpqeaKEYVQQRCSEEpGRGLVVKADGLAAGKGSIVCATPEEAASAIERIMvsp 189
                                       799999***********999999888885555555544437778999888889999999999999999999988889 PP

                                       ..........EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET..........................TEEEEEE CS
                       ATP-grasp_3  65 ..........lvqefieGkplSvsllsdgekvlvlavnrqliekaeke......................fvyaGnv 109
                                                  + + +eG++l   +lsdg++v+ +     + +  + +                          G+ 
  gi|330507850|ref|YP_004384278.1| 190 rlfgeagdriEIEDRLEGRELMFFALSDGHTVQAMQSALDYKQAFSPDesvairlfnklagnpnqdnnpnTGGMGGF 266
                                       99999999966889999999999999999888888777776666555567888888888888888886666666666 PP

                                       ES----H....HHHHHHHHHHHHTTSTT--E..EEEE...EEEESS..SEEEEEEESS- CS
                       ATP-grasp_3 110 tpietel....keevvelaeevvekleglaG..yvGv...Dlvlkd.eepyviEvNPRl 158
                                       +p +  +    ++ + ++a  +v+ +++  G  y Gv    l++++  ep v+E+N Rl
  gi|330507850|ref|YP_004384278.1| 267 SPHPWLDeeltERIMKKIALPTVRGFKESSGqeYRGViyfGLMISEdREPAVLEINVRL 325
                                       66654331122233334455556666643332234442224555554888888888887 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00016      0.42      12      83 ..     103     176 ..      96     187 .. 0.71
   2 ?    0.6   0.0      0.11   2.7e+02     249     266 ..     308     325 ..     291     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00016
                       ATPgrasp_ST  12 praefplvdd.Klkfkelalraglkvpkllgvikeqaeiseleafvkeleeg..vviKpakgsgGkGilvitere 83 
                                       p++e+ ++++ K ++k+l+++  ++vp      + q+  + +++ ++e  +g  +v+K+    +GkG +v++  e
  gi|330507850|ref|YP_004384278.1| 103 PKREAAVLENsKCQTKDLLKKLRVPVPPCQNFSDPQEAKEYVQQRCSEE-PGrgLVVKADGLAAGKGSIVCATPE 176
                                       5566666665489***************444444444344444444443.4466****************98754 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.11
                       ATPgrasp_ST 249 ivldeekgplllElNarp 266
                                       + + e+++p +lE+N r 
  gi|330507850|ref|YP_004384278.1| 308 LMISEDREPAVLEINVRL 325
                                       7899***********885 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       1.8   4.7e+03      48      56 ..      12      20 ..      11      36 .. 0.68
   2 ?   10.9   0.0   9.7e-05      0.25       6      81 ..     116     192 ..     113     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
                                      -SSSTCCCT CS
                       ATP-grasp_2 48 vlaGGRGKa 56
                                      v aGGRG a
  gi|330507850|ref|YP_004384278.1| 12 VDAGGRGNA 20
                                      679****98 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.7e-05
                                       HHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSS....EEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCT.T CS
                       ATP-grasp_2   6 qakeilakygvkvpegevaesaeeaeeaakklgeke....lvvKaQvlaGGRGKagGvklvkskeeakeaakell.g 77 
                                       q+k++l+k  v+vp  +  ++++ea+e +++  ++e    lvvKa  la G+G      +++++eea++a+++++ +
  gi|330507850|ref|YP_004384278.1| 116 QTKDLLKKLRVPVPPCQNFSDPQEAKEYVQQRCSEEpgrgLVVKADGLAAGKGS----IVCATPEEAASAIERIMvS 188
                                       89***********************9988765433223338*****99987753....3556777777777765415 PP

                                       SEEE CS
                       ATP-grasp_2  78 kelv 81 
                                        +l 
  gi|330507850|ref|YP_004384278.1| 189 PRLF 192
                                       5555 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 ?    9.1   0.0   0.00032      0.81       3      72 ..     115     187 ..     113     219 .. 0.78
   2 ?   -0.7   0.0      0.33   8.4e+02       1      22 [.     273     294 ..     273     306 .. 0.82
   3 ?   -3.4   0.0       2.2   5.5e+03     167     180 ..     312     325 ..     295     327 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHTT-BBSSEECSS.BSSHHH..HHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHH CS
                       CPSase_L_D2   3 esakealkkinvpvvpssaap.vetlee..alaiakeigyPviikaafglGGkGmrvarneeelaelvkkala 72 
                                        + k++lkk+ vpv p ++    ++++e  + ++++e g   ++ka     GkG+ v+ + ee a ++++ + 
  gi|330507850|ref|YP_004384278.1| 115 CQTKDLLKKLRVPVPPCQNFSdPQEAKEyvQQRCSEEPGRGLVVKADGLAAGKGSIVCATPEEAASAIERIMV 187
                                       678999********999887433333331134578999*************************9999887654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.33
                                       SHHHHHHHHHHTT-BBSSEECS CS
                       CPSase_L_D2   1 Dkesakealkkinvpvvpssaa 22 
                                       D e  ++++kki  p+v++++ 
  gi|330507850|ref|YP_004384278.1| 273 DEELTERIMKKIALPTVRGFKE 294
                                       66788999***********988 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.2
                                       TTTEEEEEEEESS- CS
                       CPSase_L_D2 167 kskeyyviEvNtRl 180
                                       +++e  v+E+N Rl
  gi|330507850|ref|YP_004384278.1| 312 EDREPAVLEINVRL 325
                                       4778899****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3250.07
//
Query:       gi|330507851|ref|YP_004384279.1|  [L=441]
Description: glutamine synthetase, type I [Methanosaeta concilii GP6]
Scores for complete 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-129  431.2   0.0   2.9e-129  431.0   0.0    1.0  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    9.6e-31  105.4   0.0    1.6e-30  104.6   0.0    1.4  1  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.048   13.5   0.0    1.5  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 !  431.0   0.0  4.8e-133  2.9e-129       2     345 .]     105     437 ..     104     437 .. 0.98

  Alignments for each domain:
  == domain 1  score: 431.0 bits;  conditional E-value: 4.8e-133
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHH CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrrei 78 
                                       ++PR+vl r+l+r++e+G++++vgpElEFflf+k + ++             ++p++ ggyf++ pvd aed+rrei
  gi|330507851|ref|YP_004384279.1| 105 GAPRRVLYRQLERAKEMGFKMNVGPELEFFLFEKGNGGS------------ATTPHDFGGYFDLGPVDLAEDVRREI 169
                                       68*******************************988755............4678899******************* PP

                                       HHHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEE CS
                        Gln-synt_C  79 vealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlS 155
                                       ++al ++g+++eashhEva gQ+Ei++ ++da+k aD+vvtfK+v+k++A ++gl+atFmpKp++g++GsgmHv++S
  gi|330507851|ref|YP_004384279.1| 170 TRALIKMGFTIEASHHEVARGQHEIDFVYDDAIKNADKVVTFKYVTKTIAMRQGLRATFMPKPVYGAAGSGMHVNIS 246
                                       ***************************************************************************** PP

                                       EEECTT.EESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE- CS
                        Gln-synt_C 156 lwdkdg.knlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa 231
                                       l+  +g +n+f+d++++ ++s+lar f+gGl++ha a+ta+++p +nSYkRlv+g+eaPv+++w+  NRs l+Rip 
  gi|330507851|ref|YP_004384279.1| 247 LF--RGlENAFYDPETPLNISDLARFFVGGLIEHASAITAIANPLINSYKRLVSGFEAPVYITWSGPNRSSLIRIPS 321
                                       **..566********************************************************************** PP

                                       TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHC CS
                        Gln-synt_C 232 skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealee 306
                                       +++ ++r+E+R+pd s+NPYL++A++laAgldGi+++++pg+pv+ ++y+l+++er  +gi++lP++l+eAl++le 
  gi|330507851|ref|YP_004384279.1| 322 GRGLSTRLEFRSPDTSCNPYLTFAVILAAGLDGIKRGIDPGDPVDLNVYHLTAAERksLGIQTLPSNLKEALDHLEG 398
                                       *******************************************************9999****************** PP

                                       SHHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 307 dellkevlgeevieaylalkraEleeleeevsdwelery 345
                                       d++++e+lge+v+e+ ++l + E+ee+++ v++we++ry
  gi|330507851|ref|YP_004384279.1| 399 DKVIREALGEHVYENVMRLGMLEWEEYNKFVHPWEIDRY 437
                                       ************************************998 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6   0.0   2.7e-34   1.6e-30       1      83 []      15      98 ..      15      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 2.7e-34
                                      T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-...EEEEE CS
                        Gln-synt_N  1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek..ktarvi 77
                                      +v+f++lqFtDi g +k+v+ipa+++  +al+ g+sFDGSsiegfa+i+eSDm+L+Pdlst+ ++P++ +   + ar+i
  gi|330507851|ref|YP_004384279.1| 15 NVEFLRLQFTDISGIVKNVAIPATQM-GKALKSGISFDGSSIEGFARIQESDMVLRPDLSTFSLLPWSTKDdvNEARLI 92
                                      69************************.*****************************************98889****** PP

                                      EEEE-T CS
                        Gln-synt_N 78 cdvydp 83
                                      cdv+ p
  gi|330507851|ref|YP_004384279.1| 93 CDVHLP 98
                                      ***976 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 ?   13.5   0.0   8.1e-06     0.048       4      49 ..       5      50 ..       2      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.1e-06
                                      .......------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE CS
                      Gln-synt_N_2  4 eavveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGl 49
                                      e++++ ++ek+ve++++ ++d +G+++  a+p +++ + L sGi +
  gi|330507851|ref|YP_004384279.1|  5 EQMLKIIQEKNVEFLRLQFTDISGIVKNVAIPATQMGKALKSGISF 50
                                      56777899***********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3120.76
//
Query:       gi|330507852|ref|YP_004384280.1|  [L=102]
Description: hypothetical protein MCON_1875 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 708.64
//
Query:       gi|330507853|ref|YP_004384281.1|  [L=284]
Description: apurinic-apyrimidinic endonuclease [Methanosaeta concilii GP6]
Scores for complete 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-32  111.9   0.0    3.2e-32  111.7   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.046   12.6   0.0      0.071   12.0   0.0    1.3  1  Dak1          Dak1 domain


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.7   0.0   3.6e-36   3.2e-32       2     210 .]      19     238 ..      18     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 3.6e-36
                                       HHHHHCT-SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkrai 76 
                                       ++a+e G d++++f+ ++++++++   ++ ++ + ++l+e++l+ ++ ++++ ++      r+++  +sv+al +++
  gi|330507853|ref|YP_004384281.1|  19 DRAREKGCDAFQIFTTNPRSWRSKpiAQQSIDLFSSWLKEYDLHPVVSHMPYLPNLASP--RDEVYSRSVQALTDEL 93 
                                       689****************************************9877777766666555..45557779******** PP

                                       HHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHH CS
                      AP_endonuc_2  77 elaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldav 151
                                        +++ LG+p+lv+h G   +  + ++++ +er+ae+l+++++     +v+++lE++ag+ +++g   +++a +++ +
  gi|330507853|ref|YP_004384281.1|  94 VRCRLLGIPYLVTHLG---SNLGAEKKDGRERIAEALKKAIADS-GGDVMVLLENGAGTKNSMGStfKDIASIIESL 166
                                       ****************...99*******************9993.455***************************** PP

                                       TTTT..EEEEEEHHHHHHH..TTTHHHHHHHHHGG.........EEEEEE.EESSTTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 152 dspn..vgvclDtgHllia..eedvddalraladr.........ikhvHikDakgdlgagrdrhvpigeGei 210
                                       +     +gvclDt+Hl++a    +  +al++  +          +k+vH++D  g+lg++ drh+ ig G+i
  gi|330507853|ref|YP_004384281.1| 167 PGQSrsLGVCLDTCHLFAAgyDLRTPRALERTLEEfdccissnrLKLVHLNDCQGTLGSHLDRHEHIGLGQI 238
                                       *99999*************8844444555555555588888899************************9987 PP

>> Dak1  Dak1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.9e-06     0.071     138     184 ..     140     186 ..     125     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.9e-06
                                       HHHHHHHHHHHHHT--HHHHHHHHHHHHTTEEEEEEEEE--B-TTTS CS
                              Dak1 138 vlveKiaGaaAeegasLeevaelaekvaenlrsigvalsactvpgag 184
                                       vl+e  aG + + g +++++a++ e++  + rs+gv+l++c++ +ag
  gi|330507853|ref|YP_004384281.1| 140 VLLENGAGTKNSMGSTFKDIASIIESLPGQSRSLGVCLDTCHLFAAG 186
                                       666778999999******************************98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1918.00
//
Query:       gi|330507854|ref|YP_004384282.1|  [L=130]
Description: response regulator receiver protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-24   85.1   0.3    3.9e-24   85.0   0.3    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 !   85.0   0.3   2.2e-28   3.9e-24       1     111 [.       7     124 ..       7     125 .. 0.93

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 2.2e-28
                                       EEEESSSHHHHHHHHHHHHHTTE.EEEEEESSHHHHHHHHHHHH....ESEEEEESSCSSSEHHHHHHHHHHCT..T CS
                      Response_reg   1 vlivdDdplvrellrqlleeegy.eevaeaedgkealellkeek....vdlillDinmpgmdGlellkeireed..p 70 
                                       +++v+D+   ++ +r++l+++++  +  +a++gkeale l++++    + lillDin+p+++G++ll+ i++e+  +
  gi|330507854|ref|YP_004384282.1|   7 IILVEDNAEDIAFTRRVLKHNELnGNLIVATNGKEALEALQSMNgsdlPELILLDINLPDISGIDLLTLIKKEQrlK 83 
                                       899****************666525778**************99999***********************9999999 PP

                                       TSEEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  71 elpviiltahseeedavealkagaddflsKpfdpeeLlkal 111
                                       ++pv+ilt+ +e++d+++++++ga+ +l+Kp++  +L+  +
  gi|330507854|ref|YP_004384282.1|  84 DIPVVILTGSNEDQDIQKCYDLGASSYLVKPISNGALMLVV 124
                                       *********************************99998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 958.85
//
Query:       gi|330507855|ref|YP_004384283.1|  [L=308]
Description: hypothetical protein MCON_1878 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-25   89.2   0.0    1.2e-24   87.6   0.0    1.7  1  Radical_SAM   Radical SAM superfamily
    1.8e-17   63.4   0.0    3.8e-17   62.4   0.0    1.6  1  Wyosine_form  Wyosine base formation


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0   1.3e-28   1.2e-24       2     167 .]      56     232 ..      55     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 1.3e-28
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilg......................... 53 
                                       ++t  Cn+ C +C+rp +  + +  + + + e+le + ++   + +     g                         
  gi|330507855|ref|YP_004384283.1|  56 TPTLECNHLCLHCWRPID-DPIPGKEPMEPAELLEGILRGQ-QRFIS----Gyggssttdpvrleearepkhmaisl 126
                                       67889***********98.6666666666666666666663.22121....11222355666666666666666666 PP

                                       SSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                       Radical_SAM  54 ggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfee 129
                                       +gep+lyp + e+++  +++   g++ ++++n+t+p     e l+el++++++l+l+a+d+e++++++n  ++ + +
  gi|330507855|ref|YP_004384283.1| 127 MGEPTLYPYLKEFIDLVSRR---GMTSFLVSNATRP-----EVLAELRPTQLYLSLNAPDEERYRQICNpSKDLWPR 195
                                       *******************8...************9.....88888888**************************** PP

                                       HHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 130 vlealeklreagikrvvdrivglpGendeeleellell 167
                                       +le+le+l+e++++ +v+r+++++G+n+e l+++++l+
  gi|330507855|ref|YP_004384283.1| 196 ILESLELLKEHRCR-SVIRMTLVRGQNMEGLDDYARLI 232
                                       **************.9******************9986 PP

>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0   4.2e-21   3.8e-17       2      63 .]     235     295 ..     234     295 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 4.2e-21
                                       HT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                      Wyosine_form   2 aepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                       aepdFvE+Kay+++G sr+rL++ ++P+h+e++  a  l+g ++ Y   a+ + Srv+ll+r
  gi|330507855|ref|YP_004384283.1| 235 AEPDFVELKAYMHLGRSRTRLERTAMPQHSEILALADSLAGLLG-YHPEADVPLSRVALLSR 295
                                       89******************************************.**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2255.58
//
Query:       gi|330507856|ref|YP_004384284.1|  [L=482]
Description: hypothetical protein MCON_1879 [Methanosaeta concilii GP6]
Scores for complete 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   92.3  55.3    1.3e-07   31.6   9.4    6.4  8  Pentapeptide_3  Pentapeptide repeats (9 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.2     4e-10   7.2e-06       6      48 .]      64     107 ..      63     107 .. 0.93
   2 !   31.6   9.4   7.5e-12   1.3e-07       1      47 [.     103     150 ..     103     151 .. 0.97
   3 !   30.3   6.8   1.9e-11   3.3e-07       1      47 [.     114     161 ..     114     162 .. 0.95
   4 !   22.7  10.4   4.5e-09   8.2e-05       1      47 [.     158     204 ..     158     205 .. 0.95
   5 !   11.9   7.1     1e-05      0.19       4      38 ..     193     228 ..     193     235 .. 0.88
   6 !   28.4   3.2   7.4e-11   1.3e-06       4      47 ..     237     281 ..     234     282 .. 0.94
   7 ?   -3.6   0.0      0.75   1.3e+04      33      38 ..     301     306 ..     297     308 .. 0.45
   8 ?   -2.4   0.0      0.32   5.7e+03      14      23 ..     425     434 ..     410     441 .. 0.60

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4e-10
                    Pentapeptide_3   6 FsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsgat 48 
                                       +s++++ +++ F g+++F  a F + +d++g++F ++vdF g++
  gi|330507856|ref|YP_004384284.1|  64 LSQPVRITNSIFLGPVRFAAASFdEPIDLQGCIFRDNVDFFGCR 107
                                       6788999****************88**********99***9995 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 7.5e-12
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       F+g++F g a F g+tF+g a+ +n+ F g a+F  a+F+ d++F+++
  gi|330507856|ref|YP_004384284.1| 103 FFGCRFAGGAGFAGVTFEGQADLRNTYFgGQASFLSAQFSEDASFRNS 150
                                       99**************************88****************98 PP

  == domain 3  score: 30.3 bits;  conditional E-value: 1.9e-11
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       F g++F+g ad+r++ F g asF +a+F ++a+F++++F gd  F ++
  gi|330507856|ref|YP_004384284.1| 114 FAGVTFEGQADLRNTYFGGQASFLSAQFsEDASFRNSQFAGDGIFLNS 161
                                       89**************************88************999776 PP

  == domain 4  score: 22.7 bits;  conditional E-value: 4.5e-09
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                       F +++F +++dF++a F++ asF +a+F +++F +++F g ++F +a
  gi|330507856|ref|YP_004384284.1| 158 FLNSSFARDVDFDFAQFQRLASFADARFVNVSFLETQFGGHTSFLNA 204
                                       6699****************************************776 PP

  == domain 5  score: 11.9 bits;  conditional E-value: 1e-05
                    Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadF.gsadFsgarF 38 
                                       ++F g ++F +a F+g a F  ++F gs+ F++a F
  gi|330507856|ref|YP_004384284.1| 193 TQFGGHTSFLNAEFHGNAAFAATRFvGSVVFREAGF 228
                                       6889999999*******99******99***999977 PP

  == domain 6  score: 28.4 bits;  conditional E-value: 7.4e-11
                    Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       ++F g adF+++ F+++a+F +  F + a F +arF++d++++++
  gi|330507856|ref|YP_004384284.1| 237 SSFGGLADFTNVYFNKTAYFGGVKFtDLAYFVNARFDDDLNMEDS 281
                                       79***********************88***************998 PP

  == domain 7  score: -3.6 bits;  conditional E-value: 0.75
                    Pentapeptide_3  33 FsgarF 38 
                                       + ++ F
  gi|330507856|ref|YP_004384284.1| 301 LNNSDF 306
                                       333333 PP

  == domain 8  score: -2.4 bits;  conditional E-value: 0.32
                    Pentapeptide_3  14 gatFsgaasF 23 
                                       ++ F++a +F
  gi|330507856|ref|YP_004384284.1| 425 RVSFTDALYF 434
                                       4445555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3377.42
//
Query:       gi|330507857|ref|YP_004384285.1|  [L=290]
Description: ATP phosphoribosyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-43  146.9   0.0    7.4e-43  146.3   0.0    1.2  1  HisG      ATP phosphoribosyltransferase
    1.4e-22   79.6   0.1    3.5e-22   78.3   0.1    1.7  1  HisG_C    HisG, C-terminal domain


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.3   0.0   8.2e-47   7.4e-43       1     154 [.      49     202 ..      49     211 .. 0.92

  Alignments for each domain:
  == domain 1  score: 146.3 bits;  conditional E-value: 8.2e-47
                                       -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESE.....EEEEEEEETTSS--SGCGG.TT-.EEEEE CS
                              HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgk.....cklvvavpeesevkslkdlvedkgkriaT 72 
                                       r+++ip yV++g +dlGi G D+++Es++   v+++ dL++gk     +klvvav e+ +++s++    + g r+aT
  gi|330507857|ref|YP_004384285.1|  49 RPQEIPGYVAKGYFDLGISGTDWIMESGA--IVTKVADLNYGKqgpgaVKLVVAVLESLQISSARMI--KPGSRVAT 121
                                       89************************865..6***********99999*********9999987754..4568**** PP

                                       S-HHHHHHHHHHTT-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHHSHH CS
                              HisG  73 sypnlakkyfeekglkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslkkke 149
                                       +ypnl++ yf+++g+ v+i  + G++Ea+++  l D++vDl+etG+TL++ngLk+i+ +les++ L+ankks+++ke
  gi|330507857|ref|YP_004384285.1| 122 EYPNLTRAYFSNLGIPVDIQFSFGATEAKVPE-LTDVVVDLTETGSTLKKNGLKIIDVMLESTSELVANKKSFADKE 197
                                       ******************************99.9***************************************9666 PP

                                       HHHHH CS
                              HisG 150 kieel 154
                                       k +++
  gi|330507857|ref|YP_004384285.1| 198 KHDDI 202
                                       55554 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.1   3.9e-26   3.5e-22       1      73 []     215     287 ..     215     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 3.9e-26
                                       TTTEEEEEEEEEGGGHHHHHHH---SSS-EEEE-.SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEEEE-S- CS
                            HisG_C   1 ArkyvllmynvpkesleevlkilPGlrsPTvspladegwvaVsavveekevaevideLkaaGAsdIlvlpiek 73 
                                       Ar++ ll++nvp+++l++v+++lP+++ PT s+l++ +++a+++vv++++v+ +i+ Lk+ GA+dIl+l i+k
  gi|330507857|ref|YP_004384285.1| 215 ARGKTLLKMNVPEAALDAVISMLPSMKRPTLSKLYSTDYYAIETVVDRSQVNLLIPLLKKSGAEDILELAISK 287
                                       899******************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2224.57
//
Query:       gi|330507858|ref|YP_004384286.1|  [L=286]
Description: hypothetical protein MCON_1883 [Methanosaeta concilii GP6]
Scores for complete 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   40.4   0.0    0.00056   20.1   0.0    2.2  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.3e-06   28.3   0.1      7e-06   26.7   0.1    1.7  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.6e-07    0.0023      27     103 ..      10     130 ..       5     163 .. 0.57
   2 !   20.1   0.0   6.2e-08   0.00056      90     161 ..     183     265 ..     165     268 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.6e-07
                     Metallophos_2  27 gvdaiihaGDl...eeeep.....evleellela....pvlaVrGNnD..........eev.veedvlreaaelgtd 80 
                                       g+d++i++GD+     + p     e++  l++l     ++++V GN+D          +   ++ ++++ +  ++ +
  gi|330507858|ref|YP_004384286.1|  10 GCDQVILLGDIfdfWRVRPenalrESVPLLKRLGeedlKIHYVVGNHDhhlvvqkqesD-FmERTARGDLFPVYSPS 85 
                                       56********655433333323333444444444777***********66666554321.13444555555555555 PP

                     Metallophos_2  81 l...............peeaelelagek.........vlliHgdpl........g 103
                                       l               p          +         vl++Hg++l        +
  gi|330507858|ref|YP_004384286.1|  86 LrwrqtinglnidmlyP----------TyrircchrtVLFTHGHHLagihiftmQ 130
                                       54443333332222222..........0223333344888888865655544442 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.2e-08
                     Metallophos_2  90 agekvlliHgdpl....gvkdalaellkeaeegsd.vvvcGHtHvpeveke.ggvlvvnPGsvgeprdgdpe..... 155
                                       ++ + +++H+++     +  +a+++ +++   g+  ++++G tH+++++++ gg l vn+Gs ++   +  +     
  gi|330507858|ref|YP_004384286.1| 183 QRITTGVFHDHHIasveAQYEAIERFIRDRNLGEIdCFIYGDTHRAGIFQRmGGPLAVNAGSFTRVPGKGSRiktpd 259
                                       455578899997787765556666777775555557**************97899********99844444445555 PP

                     Metallophos_2 156 tyaild 161
                                       ty+ild
  gi|330507858|ref|YP_004384286.1| 260 TYIILD 265
                                       998887 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.1   7.8e-10     7e-06      33     202 ..      10     226 ..       3     228 .. 0.55

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 7.8e-10
                                       TESEEEEESTSSSSS..HHHHHHHHHHHHHHHH...TSEEEEEC-TTS..................CHHHHHHHHHH CS
                       Metallophos  33 kpdlvllaGDlvdrg..dlekellellaalvky...pipvylllGNHe..................gfeeellnkyg 86 
                                       ++d v+l+GD++d     +e++l e +  l ++   + +++ + GNH+                  g   +l++ y 
  gi|330507858|ref|YP_004384286.1|  10 GCDQVILLGDIFDFWrvRPENALRESVPLLKRLgeeDLKIHYVVGNHDhhlvvqkqesdfmertarG---DLFPVYS 83 
                                       789***********9998888666666666666888************8888877777666653332...5555555 PP

                                       HHHHHHHHHEHHHCEEETSEEEEEETTE......EEEEEEESE...CEEE........................... CS
                       Metallophos  87 ylgifsepwrsdaevfnnlplaslgsgs......lkvlllhGg...spel........................... 127
                                        + ++    r+     n+l++  l  ++       +vl+ hG+      +                           
  gi|330507858|ref|YP_004384286.1|  84 PSLRW----RQT---INGLNIDMLYPTYrircchRTVLFTHGHhlaG--Ihiftmqmverirrlygeellpadlemm 151
                                       54444....333...33333333333334446666899999996441..2223333333333344444444433333 PP

                                       .THHHHHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTT...ESEEEEES CS
                       Metallophos 128 .lvsldklgslnleleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkyg...vdlvisGH 200
                                         +  +++ + +++ e    ++  +k ++   +  + +++ H+     ++    +ea+e++ ++ +   +d  i+G+
  gi|330507858|ref|YP_004384286.1| 152 mAYAYESIYRSSYIGEMVSFEERVWKASSLLQRITTGVFHDHH----IASVEAQYEAIERFIRDRNlgeIDCFIYGD 224
                                       3333333333333333333334444442333333333333333....344666777777776666667788888888 PP

                                       SS CS
                       Metallophos 201 tH 202
                                       tH
  gi|330507858|ref|YP_004384286.1| 225 TH 226
                                       88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 2402.45
//
Query:       gi|330507859|ref|YP_004384287.1|  [L=171]
Description: NADH dehydrogenase/NAD(P)H nitroreductase [Methanosaeta concilii GP6]
Scores for complete 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  101.6   3.2    4.2e-15   56.2   0.2    2.0  2  Nitroreductase  Nitroreductase family
    2.3e-09   37.2   0.0    2.1e-08   34.0   0.0    2.2  1  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.4   2.1e-16   1.9e-12       1      57 [.       7      63 ..       7      67 .. 0.89
   2 !   56.2   0.2   4.7e-19   4.2e-15      81     170 .]      63     150 ..      59     150 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 2.1e-16
                                      HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHH CS
                    Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaa 57
                                      +++RrSiR ++++p+pk+  +++++aa++aPsagnl   r+v+v++++ r+ la aa
  gi|330507859|ref|YP_004384287.1|  7 LKSRRSIRRYQSRPIPKDLAKSLIDAAQTAPSAGNLSARRYVLVSNEDMRRLLAAAA 63
                                      589*****************************************8888887666665 PP

  == domain 2  score: 56.2 bits;  conditional E-value: 4.7e-19
                                       HHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S CS
                    Nitroreductase  81 lkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglp 157
                                       ++ q+++++ap+li + a+  +s+ ++++r+  ya++da aa + llLaA+++Glg+c+ g+fd++   vr+ l+l+
  gi|330507859|ref|YP_004384287.1|  63 AYGQEHIEEAPLLIAVCADVKASSVRYGSRGGLYAIQDADAATMCLLLAAHDAGLGACWNGAFDDDM--VREALHLE 137
                                       577999*************************************************************..******** PP

                                       ..SEEEEEEEEE- CS
                    Nitroreductase 158 deeeivvliavGy 170
                                       d+  +v+++++G+
  gi|330507859|ref|YP_004384287.1| 138 DDVLPVAIVSLGW 150
                                       ************8 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   2.3e-12   2.1e-08       1     138 [.       2     156 ..       2     169 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.3e-12
                                       -HHHHHHH--B---B--S---HHHHHHHHH-----S...S----.-EE.E.................-SSSSEEEE- CS
                    TM1586_NiRdase   1 nlyeaiekRhsvRkYkdealeeelleelkeaieeinkesglelq.lvidenkafkskv..aklg..kfkgvpnyial 72 
                                       nl++a++ R+s+R+Y++++++++l++ l +a+++  ++ +l+ +  v  +n++ +  +  a +g  + +++p  ia+
  gi|330507859|ref|YP_004384287.1|   2 NLIDALKSRRSIRRYQSRPIPKDLAKSLIDAAQTAPSAGNLSARrYVLVSNEDMRRLLaaAAYGqeHIEEAPLLIAV 78 
                                       7899*****************************99999877765233444444443331134432156677777777 PP

                                       ---SSHHHHHHHH.....HHHH.......HHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS-- CS
                    TM1586_NiRdase  73 vgekkedleekaG.....Yyge.......qlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyaktk 136
                                       +++ k ++++++G     Y  +       +l+L +  +Glg cW g+  +  ++++++l+++   v++++lG ++++
  gi|330507859|ref|YP_004384287.1|  79 CADVK-ASSVRYGsrgglYAIQdadaatmCLLLAAHDAGLGACWNGAFDDDmVREALHLEDDVLPVAIVSLGWPEES 154
                                       77655.6777777555566555333332258899999*********9877789999*****************9998 PP

                                       -- CS
                    TM1586_NiRdase 137 lv 138
                                         
  gi|330507859|ref|YP_004384287.1| 155 PA 156
                                       75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1233.34
//
Query:       gi|330507860|ref|YP_004384288.1|  [L=515]
Description: histone acetyltransferase, ELP3 family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-27   92.8   0.1    1.6e-26   92.1   0.1    1.4  1  Radical_SAM_C    Radical_SAM C-terminal domain
    8.6e-20   71.8   0.0    1.7e-19   70.8   0.0    1.5  1  Radical_SAM      Radical SAM superfamily
      5e-09   36.4   0.3    1.1e-08   35.3   0.3    1.6  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.6e-06   26.6   0.0    1.1e-05   25.3   0.0    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0034   17.8   0.1     0.0065   16.9   0.1    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.16   12.2   0.7        4.6    7.5   0.1    2.9  2  PCP_red          Proto-chlorophyllide reductase 57 kD subunit


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.1   5.4e-30   1.6e-26       1      81 [.     298     378 ..     298     379 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 5.4e-30
                     Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlrelie 77 
                                       pd +K+yp+lvi+gTeL+++y +gey+pl  +++ +lv +i+e lp  +r++R+++dip++l++ag++++nlr+l++
  gi|330507860|ref|YP_004384288.1| 298 PDYLKIYPTLVIEGTELYRQYLRGEYTPLGDDDAAELVSRIKETLPRYVRLQRVQRDIPSPLIVAGVKKSNLRQLAK 374
                                       89*************************************************************************** PP

                     Radical_SAM_C  78 krlk 81 
                                       krl+
  gi|330507860|ref|YP_004384288.1| 375 KRLE 378
                                       **97 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.0   5.8e-23   1.7e-19       5     157 ..      84     280 ..      80     287 .. 0.93

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 5.8e-23
                                       SEESS-.-TTTSCCTT................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHH CS
                                       xxxxxx.xxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   5 rgCnlr.CsfCarpet................vrregrgrslsveeileevkelkaekgvkevilgggepllypdfv 64 
                                         C+++ C+ C+ +                   +++g   + +v   l++++e+ +  ++ e+i++gg+ + +p  +
  gi|330507860|ref|YP_004384288.1|  84 ARCPHGtCVPCPGGILnlspqsytgkepaalrAEQHGFDPYDQVTARLAQLDEIGHPLDKSELIIMGGTITSRPLGY 160
                                       5677777*****99889**************999999999**************99999**************9999 PP

                                       HHHHHHHHTC............................CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSS CS
                                       xxxxxxxxxx............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  65 ellerlakla............................vpgiritvetngtlpdeeklerllelgvdrvslgleaad 113
                                       + ++  + l+                            v++i +t+et + + +++ +e++l+lg + v+lg++++d
  gi|330507860|ref|YP_004384288.1| 161 QNWFVKRCLQamndfpdgressgwqpfesvaranesalVRNIGTTFETRPDWCRPRDIEEMLRLGATKVELGVQSLD 237
                                       99999999999************************8888888888888888888*********************** PP

                                       HHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 114 dekvlklmnrghtfeevlealeklreagikrvvdrivglpGend 157
                                       ++  l +m+rgh +e+  +a  +lreag+k+ +++++glpG + 
  gi|330507860|ref|YP_004384288.1| 238 ED-LLVRMKRGHKVEDAAQASANLREAGLKVGFHMMPGLPGSSP 280
                                       **.**************************************876 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.3   3.7e-12   1.1e-08      30     117 .]     413     503 ..     387     503 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 3.7e-12
                                       STTCEEEE.EEETTEEEEEEEEEEEETTSTTEEEEEEEEE..........SGGGTTSSHHHHHHHHHHHHHHHTTES CS
                    Acetyltransf_1  30 leaegllv.aeedgeliGfisllkipdekggvayieslaV..........speyrgkGlGsaLlealeerareegik 95 
                                          e++l+  +ed+ l+Gf++l+  +      a +++l+V          +  ++++G+G +L+ea+e+ a e g+ 
  gi|330507860|ref|YP_004384288.1| 413 GAREHFLSfESEDDVLVGFLRLRLSTS-----ARVRELHVygpmvpigkrKDGWQHRGYGARLMEAAERLAQEAGYP 484
                                       333455556888899************.....7777777777777*******************************9 PP

                                       EEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  96 kivlaveedndaairlYeklGF 117
                                        i++    +  +a+++Y++ G+
  gi|330507860|ref|YP_004384288.1| 485 LIEV---TSGIGARGYYRRRGY 503
                                       9988...78********88998 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   3.8e-09   1.1e-05      30     107 ..     416     504 ..     396     510 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.8e-09
                   Acetyltransf_10  30 ealllvaeeggkivGviel.rdgs......hisllfV.....dpeyrgqGigkaLleaveeeaekdgikleltvnas 94 
                                       e++l    e++ +vG+++l  ++s      h++  +V     ++ ++++G+g++L+ea+e+ a+++g+   ++v + 
  gi|330507860|ref|YP_004384288.1| 416 EHFLSFESEDDVLVGFLRLrLSTSarvrelHVYGPMVpigkrKDGWQHRGYGARLMEAAERLAQEAGYP-LIEVTSG 491
                                       444455556688889998843444778888888888866666688******************999998.******* PP

                   Acetyltransf_10  95 pyavpfYeklGFk 107
                                         a+++Y++ G+ 
  gi|330507860|ref|YP_004384288.1| 492 IGARGYYRRRGYD 504
                                       ***********96 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.2e-06    0.0065      34      74 ..     459     503 ..     414     505 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-06
                                       GGGTTSSHHHHHHHHTT.....SEEEEEEEEETHH..HHHHHHHHTTE CS
                    Acetyltransf_7  34 peyrgkGiGraLleaae.....kgiileqlelnae..kaikfYeklGF 74 
                                         ++ +G+G +L+eaae      g+ l+  e++ +   a+++Y++ G+
  gi|330507860|ref|YP_004384288.1| 459 DGWQHRGYGARLMEAAErlaqeAGYPLI--EVT-SgiGARGYYRRRGY 503
                                       369***********83334444564444..332.2358999******9 PP

>> PCP_red  Proto-chlorophyllide reductase 57 kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.094   2.8e+02       2      22 ..     328     353 ..     328     378 .. 0.89
   2 ?    7.5   0.1    0.0015       4.6      19      38 ..     469     488 ..     464     490 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.094
                                       -HHHHHHHTTS....-HHHH.HHHHH CS
                           PCP_red   2 tdeAealLkki....PffvR.kkaRr 22 
                                       +d+A +l  +i    P +vR  +++r
  gi|330507860|ref|YP_004384288.1| 328 DDDAAELVSRIketlPRYVRlQRVQR 353
                                       69999999999999******877766 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHT-SEE-H CS
                           PCP_red  19 kaRraaEklArerGleeVtv 38 
                                       ++  aaE+lA+e+G++ + v
  gi|330507860|ref|YP_004384288.1| 469 RLMEAAERLAQEAGYPLIEV 488
                                       56789**********99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); 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:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 3939.63
//
Query:       gi|330507861|ref|YP_004384289.1|  [L=127]
Description: 30S ribosomal protein S8 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-32  112.9   3.4    1.4e-32  112.7   3.4    1.0  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7   3.4   7.8e-37   1.4e-32       5     137 .]       3     124 ..       1     124 [. 0.98

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 7.8e-37
                                       XXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEEE CS
                     Ribosomal_S8e   5 rdskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlgV 81 
                                       +++k  rkltGgk  l r krk+e gr+++ t +g+ r+k+v+vrgG  k+r lr +   v++p ++++k +kI + 
  gi|330507861|ref|YP_004384289.1|   3 WQGKIGRKLTGGKLILARGKRKFEIGREQSDTTIGEVRIKKVQVRGGREKVRMLRGNMVAVADPVTGMSKMVKIETA 79 
                                       789999*********************************************************************** PP

                                       ECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                     Ribosomal_S8e  82 kknpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                       k+n +n +y+r+++ltKga+i++++++           A++t+rPgqdG +navlL
  gi|330507861|ref|YP_004384289.1|  80 KENRANLHYMRRNILTKGAVIKTEIGD-----------ARITNRPGQDGIINAVLL 124
                                       ***************************...........*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 957.83
//
Query:       gi|330507862|ref|YP_004384290.1|  [L=66]
Description: hypothetical protein MCON_1888 [Methanosaeta concilii GP6]
Scores for complete sequence (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   99.0   0.1    1.5e-28   98.8   0.1    1.0  1  DUF1922   Domain of unknown function (DUF1922)


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 !   98.8   0.1   8.5e-33   1.5e-28       3      66 ..       1      64 [.       1      65 [. 0.99

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 8.5e-33
                                      EEEETTS--EEEETT-SEEEETTTEEEE--SSS-BS--SSHHHHHHHHHHHSS---S-TTSS-T CS
                           DUF1922  3 ifRCdCGRvlYakegaktrkCvCGktikvkerrilkkaedaeeAselVrklqeekyGltafkta 66
                                      +fRC+CGR+lY+ ++aktr+C+CGk+++++++ril++a da++A+e+Vr+lq +++Glt+f++a
  gi|330507862|ref|YP_004384290.1|  1 MFRCSCGRHLYSPDDAKTRTCPCGKRTALSRVRILATAPDARAAGEIVRRLQLGDSGLTGFSQA 64
                                      7*************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 506.68
//
Query:       gi|330507863|ref|YP_004384291.1|  [L=142]
Description: thioesterase superfamily protein [Methanosaeta concilii GP6]
Scores for complete 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-10   38.7   0.0    1.3e-09   38.3   0.0    1.2  1  4HBT      Thioesterase superfamily
     0.0028   17.9   0.0     0.0032   17.8   0.0    1.0  1  4HBT_3    Thioesterase-like superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   1.4e-13   1.3e-09       6      77 ..      52     122 ..      48     124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.4e-13
                                       HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                              4HBT   6 gGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                       gG y al+Dea+++al++   ++ ++++++ s  fl  ++ g  + ++a+v++ gr++a+ve  v++ d+++
  gi|330507863|ref|YP_004384291.1|  52 GGLYSALCDEAMALALFTVLEEEEDIATISESTSFLQGIKKG-CISAQAKVVKKGRRVAFVEGGVTSRDDGT 122
                                       9*****************************************.8***********************99986 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.6e-07    0.0032       3      85 ..      41     133 ..      39     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.6e-07
                                       GGGECTTC..-HHHHHHHHHHHHHHT........-S.SS..EEEEEEE-S---SEEEEEEEEEEE--SS-EEEEEEE CS
                            4HBT_3   3 ppwtpgga.gyGGyvlAlalraaqrtv.......pdprl..hslhvyFlrpgdagpviyhvervrdGrsfstrtvel 69 
                                       p+  +g +   GG+ +Al+ +a+  ++       +  ++   s + +Fl+ ++ g +  ++++v+ Gr+++ ++  +
  gi|330507863|ref|YP_004384291.1|  41 PDMLNGVGwLQGGLYSALCDEAMALALftvleeeE--DIatISESTSFLQGIKKGCISAQAKVVKKGRRVAFVEGGV 115
                                       555556553479************88778898743..45567*******************************9776 PP

                                       ..EETTEEEEEEEEEEE- CS
                            4HBT_3  70 ..sqggrpiftatasfgr 85 
                                         + +g p   ++asf+ 
  gi|330507863|ref|YP_004384291.1| 116 tsRDDGTPLSLTQASFAI 133
                                       325579999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1033.20
//
Query:       gi|330507864|ref|YP_004384292.1|  [L=395]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete 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   0.2    3.4e-24   85.4   0.2    1.4  1  OrfB_IS605      Probable transposase
    8.8e-24   83.2   1.1    2.5e-23   81.8   0.6    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.3e-06   27.8   0.1    2.9e-06   26.7   0.1    1.7  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.032   14.2   0.1    1.8  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.056   13.0   1.5       0.63    9.6   0.0    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.068   12.6   5.1       0.88    9.1   5.1    2.4  1  zf-ribbon_3     zinc-ribbon domain
       0.18   11.4   3.8       0.36   10.4   1.5    2.4  2  RecR            RecR protein
       0.52   10.3   3.7        1.3    9.0   3.7    1.7  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        1.5    9.0   5.1        1.3    9.2   0.7    2.4  2  UPF0547         Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.2   1.7e-27   3.4e-24       5     117 ..     166     275 ..     162     277 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 1.7e-27
                        OrfB_IS605   5 evevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlh 81 
                                       ++++++p  ++++a+g+D+G+  +++ ++++   ++ ++r +k+   +la+ +++l++ + +s+nyk  + k+a+lh
  gi|330507864|ref|YP_004384292.1| 166 ANQEPQPLSETEEAVGLDVGLTSFVVDSVGN---EIENPRCAKQSADKLARLQRRLARAVRGSNNYKSLKYKIAKLH 239
                                       5678899************************...******************************************* PP

                        OrfB_IS605  82 rkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       ++++++r+++lhkl+++ +++ + + ve+L+++++k
  gi|330507864|ref|YP_004384292.1| 240 KRINCQRDDFLHKLSRAYVNNFDIICVEDLDIKGLK 275
                                       *********************************998 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.9   3.9e+03      11      23 ..      39      51 ..      37      54 .. 0.81
   2 !   81.8   0.6   1.3e-26   2.5e-23       1      67 [.     292     358 ..     292     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.9
                    OrfB_Zn_ribbon 11 kakeyGikveevn 23
                                       ake+Gik+++ +
  gi|330507864|ref|YP_004384292.1| 39 DAKEKGIKLKTYD 51
                                      599*****99876 PP

  == domain 2  score: 81.8 bits;  conditional E-value: 1.3e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       ++k+  +l+yka+ +G+k+++v+p++T ++Cs Cgs+ +++ls r+++Cp Cgf++drD+nA++Nil
  gi|330507864|ref|YP_004384292.1| 292 WSKFVFMLSYKAQSAGRKLIKVDPRNTTQRCSACGSIAEKDLSVRVHECPYCGFSCDRDYNASRNIL 358
                                       99****************************************************************7 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.1   1.4e-09   2.9e-06       1      45 [.       1      44 [.       1      46 [. 0.92

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.4e-09
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeee 45
                                      M   +yky + P++  + kla+ ++++R+ YN+ L++ ++a e++
  gi|330507864|ref|YP_004384292.1|  1 M-IISYKYPIFPNKITQWKLAENLDACRWLYNRILQDLNDAKEKG 44
                                      7.899*******************************999987766 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.1   8.2e+03      23      47 ..      53      77 ..      44      84 .. 0.77
   2 ?   14.2   0.1   1.6e-05     0.032      45     110 ..     294     362 ..     282     364 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.1
                                      ..EEEEEEEEEETTCT--HHHHHHH CS
                              HypA 23 arkvtkvkvevGelsgvepeaLefa 47
                                       +k+ ++k+e  +l+ v  ++L+++
  gi|330507864|ref|YP_004384292.1| 53 QNKIPSLKLENPKLNRVYSKVLQMV 77
                                      4688889999999999998888875 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSSS.-EEEEESSSEEEEEE CS
                              HypA  45 efafellaegtvlegaeLeieevpvkvrCreCgkefeleek..alrCpkCgsa.dveivsGeellvksi 110
                                       +f+f l  + + + ++ ++++  + + rC+ Cg+  e++ +    +Cp Cg + d +  + +++l++ +
  gi|330507864|ref|YP_004384292.1| 294 KFVFMLSYKAQSAGRKLIKVDPRNTTQRCSACGSIAEKDLSvrVHECPYCGFScDRDYNASRNILITGM 362
                                       56666667777777777899999**********9999776334669****9665777778888877766 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00032      0.63      11      32 ..     311     332 ..     307     335 .. 0.83
   2 ?    1.1   0.9      0.14   2.8e+02       2       8 ..     339     345 ..     338     356 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00032
                                       CHEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon  11 lveDpergelvCtdCGlVledn 32 
                                       + +Dp +++ +C++CG++ e +
  gi|330507864|ref|YP_004384292.1| 311 IKVDPRNTTQRCSACGSIAEKD 332
                                       67899999*********98876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.14
                                       EETTTTC CS
                      TF_Zn_Ribbon   2 kCPnCgs 8  
                                        CP+Cg 
  gi|330507864|ref|YP_004384292.1| 339 ECPYCGF 345
                                       5999995 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   5.1   0.00044      0.88       2      23 ..     319     344 ..     318     346 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00044
                       zf-ribbon_3   2 tvrCPnCGaplssddnv....CpyCG 23 
                                       t+rC++CG+++++d +v    CpyCG
  gi|330507864|ref|YP_004384292.1| 319 TQRCSACGSIAEKDLSVrvheCPYCG 344
                                       78*******988887777777****9 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.5   0.00018      0.36      13      34 ..     316     343 ..     313     346 .. 0.83
   2 ?    4.0   0.6     0.018        36      15      29 ..     336     350 ..     331     351 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                                       HHH-EE-TTT--EESSS......S-CCC CS
                              RecR  13 kekvrhCsrCgnlteed......lCaIC 34 
                                       +++ ++Cs Cg ++e+d       C+ C
  gi|330507864|ref|YP_004384292.1| 316 RNTTQRCSACGSIAEKDlsvrvhECPYC 343
                                       567899***********66665559999 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.018
                                       H-EE-TTT--EESSS CS
                              RecR  15 kvrhCsrCgnlteed 29 
                                       +v+ C+ Cg  +++d
  gi|330507864|ref|YP_004384292.1| 336 RVHECPYCGFSCDRD 350
                                       89*******999887 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.7   0.00066       1.3       6      31 ..     321     344 ..     321     347 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00066
                    Zn_ribbon_SprT   6 rCtgCgreythhlsirrhnYrCrrCk 31 
                                       rC  Cg+  +  ls+r h   C++C+
  gi|330507864|ref|YP_004384292.1| 321 RCSACGSIAEKDLSVRVHE--CPYCG 344
                                       8******************..****8 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3      0.26   5.2e+02      14      21 ..     319     326 ..     318     326 .. 0.90
   2 ?    9.2   0.7   0.00063       1.3      10      23 ..     333     346 ..     330     347 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.26
                           UPF0547  14 aqfCphCG 21 
                                       +q+C+ CG
  gi|330507864|ref|YP_004384292.1| 319 TQRCSACG 326
                                       699****9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00063
                           UPF0547  10 vPvaaqfCphCGyv 23 
                                       ++v + +Cp+CG++
  gi|330507864|ref|YP_004384292.1| 333 LSVRVHECPYCGFS 346
                                       667789******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3023.61
//
Query:       gi|330507865|ref|YP_004384293.1|  [L=266]
Description: Met10+ like methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-48  164.0   0.0    4.1e-48  163.8   0.0    1.1  1  Met_10           Met-10+ like-protein
    2.6e-07   30.4   0.0    6.9e-07   29.1   0.0    1.6  2  Cons_hypoth95    Conserved hypothetical protein 95
    0.00013   21.6   0.0    0.00021   20.9   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0022   17.2   0.0      0.003   16.7   0.0    1.2  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
     0.0046   17.6   0.0     0.0084   16.8   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   14.8   0.0      0.014   14.4   0.0    1.3  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.022   15.4   0.0      0.055   14.1   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
      0.026   14.2   0.0      0.039   13.6   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.08   14.0   0.0       0.16   13.0   0.0    1.5  1  Methyltransf_24  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.8   0.0   2.1e-51   4.1e-48       2     199 .]      22     220 ..      21     220 .. 0.98

  Alignments for each domain:
  == domain 1  score: 163.8 bits;  conditional E-value: 2.1e-51
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       +f++iGd++il l+ el+ yk +i+ ++ld+  +v+tv++k + +ege Rt +le+laG++++ t+h+E g r++lD
  gi|330507865|ref|YP_004384293.1|  22 RFHVIGDIAILYLDPELDGYKDEIASALLDQCrNVRTVFNKITPLEGERRTSRLELLAGEGNSFTVHREFGFRYHLD 98 
                                       69*****************************99******************************************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                       v++v+f+s+l  Er+r+a +v+ ge  + +fAG+Gpfaip a   ++ rv+a ++ Pe+  +l en + N v++++ 
  gi|330507865|ref|YP_004384293.1|  99 VARVFFNSRLGYERMRVAVQVKAGEEALVLFAGVGPFAIPPAA--RGARVVALEKSPEACSWLAENARENGVAERIA 173
                                       ****************************************997..99****************************** PP

                                       EEES-GGG---..TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 155 pileDgrevir..eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                       +i++D+  ++   +  +dr + ++p+     +d++  +l++gg+ih+
  gi|330507865|ref|YP_004384293.1| 174 VINADAFSMAAllKRRFDRAIVPAPYGMDRIVDALPGMLRRGGIIHF 220
                                       ******9998888*********************************9 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.4   2.8e+03      31      53 ..      58      82 ..      51      85 .. 0.76
   2 !   29.1   0.0   3.4e-10   6.9e-07      42     159 ..     122     229 ..     103     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.4
                                      HHHHHHCCC..HCC-EEEETT-TTS CS
                     Cons_hypoth95 31 alFnilaae..iegarvLDlfaGsG 53
                                      ++Fn + +    ++ + L+l aG G
  gi|330507865|ref|YP_004384293.1| 58 TVFNKITPLegERRTSRLELLAGEG 82
                                      7899999887556667899999988 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 3.4e-10
                                       C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                       g++ L lfaG G  ++  + Rg +++v++ek++ea++ l en +e ++ e++a+++ da++ +  l   k++fd   
  gi|330507865|ref|YP_004384293.1| 122 GEEALVLFAGVGPFAIPPAARG-ARVVALEKSPEACSWLAENARENGVAERIAVINADAFSMAALL---KRRFDRAI 194
                                       556799****************.5899******************************999998777...678***** PP

                                       E--SSSTTCH.HHHHHHHHHTT-EEEEEEEEEEEECCSSS- CS
                     Cons_hypoth95 119 lDPPyakellieevlelleekkllkenalvvvetekekelp 159
                                       +  Py  + +    +++l   ++l++++++ + t k+ + +
  gi|330507865|ref|YP_004384293.1| 195 VPAPYGMDRI----VDALP--GMLRRGGIIHFYTFKKAQQI 229
                                       *****98865....77787..78888888877776665554 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 !   20.9   0.0     1e-07   0.00021       5      67 ..     126     188 ..     123     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1e-07
                   Methyltransf_15   5 lDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkl 67 
                                       l lf+G G  +i  a  + +v+a+e+++e +   ++Na+  gv+++i ++ +d f++ a lk 
  gi|330507865|ref|YP_004384293.1| 126 LVLFAGVGPFAIPPAARGARVVALEKSPEACSWLAENARENGVAERIAVINADAFSMAALLKR 188
                                       5589***************************************************98776664 PP

>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.5e-06     0.003      72     186 ..      72     182 ..      63     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-06
                   Methyltrans_SAM  72 gaasevlvgeldespvvvesglkyqldigrnqnfglfldmrlg....rdwvqenakdknvlnlfaytcgfsvaaiag 144
                                        +  e+l+ge ++  v  e g++y+ld+ r      f++ rlg    r  vq +a + + l lfa    f++   a 
  gi|330507865|ref|YP_004384293.1|  72 TSRLELLAGEGNSFTVHREFGFRYHLDVARV-----FFNSRLGyermRVAVQVKA-GEEALVLFAGVGPFAIPPAAR 142
                                       56789************************95.....4444444110044555554.567899**************9 PP

                   Methyltrans_SAM 145 gaskvvnvdmargslnkgrdnhrlnghdlrrvsflgydifks 186
                                       ga+ vv ++ +  + +   +n r ng   +r++ +  d f  
  gi|330507865|ref|YP_004384293.1| 143 GAR-VVALEKSPEACSWLAENARENGVA-ERIAVINADAFSM 182
                                       995.889999999999999999988864.5666666666655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.2e-06    0.0084       4      70 ..     128     195 ..     125     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.2e-06
                                       ET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBS.SSTTTEEEEEE CS
                   Methyltransf_25   4 lGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlp.fedgsfDlvvs 70 
                                       l +G G +++  a+r+  a+v++++ s+e++   +e+a+e+g+  ++ ++++da ++  + +++fD  ++
  gi|330507865|ref|YP_004384293.1| 128 LFAGVGPFAIPPAARG--ARVVALEKSPEACSWLAENARENGVaeRIAVINADAFSMAaLLKRRFDRAIV 195
                                       5679999999999995..************************************8876368889998877 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.2e-06     0.014     196     273 ..     118     192 ..      68     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.2e-06
                   tRNA_U5-meth_tr 196 evtqeskgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirlsaeeltealkkkrefr 272
                                       +v  ++ ++ l l+ G G f+++ a +  +v+a e +  + +    n  +n + + +i+ + a+ ++ a   kr f 
  gi|330507865|ref|YP_004384293.1| 118 QV--KAGEEALVLFAGVGPFAIPPAARGARVVALEKSPEACSWLAENARENGVAE-RIAVINADAFSMAALLKRRFD 191
                                       33..44567899***************************************9987.789999**************9 PP

                   tRNA_U5-meth_tr 273 r 273
                                       r
  gi|330507865|ref|YP_004384293.1| 192 R 192
                                       8 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.7e-05     0.055       6      64 ..     131     192 ..     127     197 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                                       TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCT.SS-TT-EEE CS
                   Methyltransf_11   6 GtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaekl.pfednsfDl 64 
                                       G G +a + a rgarvv+++ s+e+  +  e+a+e+g+  ++ ++ ada ++  + +  fD 
  gi|330507865|ref|YP_004384293.1| 131 GVGPFAIPPAARGARVVALEKSPEACSWLAENARENGVaeRIAVINADAFSMaALLKRRFDR 192
                                       788888888999*****************999999999999999*****9986788888885 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 ?   13.6   0.0     2e-05     0.039      33      90 ..     143     200 ..     139     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                                       TSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CTCCHHHHCC..EEEEEEEE--C CS
                   Methyltr_RsmB-F  33 kgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDarkidkvlggelfDriLlDaPCs 90 
                                        ++vvA++++ e  + +aen +  gv   + v++aDa  +   l  + fDr+++ aP  
  gi|330507865|ref|YP_004384293.1| 143 GARVVALEKSPEACSWLAENARENGVAeRIAVINADAFSMAALLK-RRFDRAIVPAPYG 200
                                       579**********************985789********966666.7*********965 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.9e-05      0.16      24     103 ..     144     220 ..     109     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.9e-05
                   Methyltransf_24  24 grlvavdhdpgaee...aaalareaglddrvrlikadseealaslaagsiDllfiDgghaaeavledleallprlap 97 
                                        r+va+++ p+  +    a++are+g+++r+ +i+ad+++ +a l+ +++D +++ ++   +   + ++al  +l++
  gi|330507865|ref|YP_004384293.1| 144 ARVVALEKSPE--AcswLAENARENGVAERIAVINADAFSMAALLK-RRFDRAIVPAPYGMD---RIVDALPGMLRR 214
                                       58999999994..23346778888*****************99998.99**99998874333...344555566777 PP

                   Methyltransf_24  98 ggvvlf 103
                                       gg+++f
  gi|330507865|ref|YP_004384293.1| 215 GGIIHF 220
                                       777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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: 00:00:00.45
# Mc/sec: 1792.03
//
Query:       gi|330507866|ref|YP_004384294.1|  [L=416]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete sequence (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   86.2   0.0    2.4e-24   85.4   0.0    1.4  1  Transposase_20  Transposase IS116/IS110/IS902 family
    5.2e-23   81.6   0.0    1.1e-22   80.6   0.0    1.5  1  DEDD_Tnp_IS110  Transposase
  ------ inclusion threshold ------
        1.8    8.9   4.4        5.8    7.3   0.2    2.8  2  DUF4164         Domain of unknown function (DUF4164)


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0     4e-28   2.4e-24       3      86 ..     250     334 ..     248     335 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 4e-28
                    Transposase_20   3 lLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaairan 79 
                                       + +sipG G+v a+a+laeig+ + f++++qlaa++Gl+p+ +qS++k   g+i+k+G++++Rr+L++ A a++r++
  gi|330507866|ref|YP_004384294.1| 250 IAMSIPGTGFVSATAILAEIGNYTDFEKPEQLAAWCGLVPSLYQSAEKTILGGITKQGSKHIRRMLIQVAYAISRTK 326
                                       679*********************************************99************************998 PP

                    Transposase_20  80 .pelrayy 86 
                                        ++l++++
  gi|330507866|ref|YP_004384294.1| 327 dSKLKKFF 334
                                       79999885 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.0   1.8e-26   1.1e-22       1     154 [.       9     153 ..       9     154 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.8e-26
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +GiDv+k+   a+++ ++gk+  ++r++ + e+l ++ ++   + g+ +v++e+tg y+ ++v+ +le +i+++v n
  gi|330507866|ref|YP_004384294.1|   9 CGIDVHKRFLIATILCRDGKK-DTQRFSVTLEDLLKFRDW-VIENGCEQVAIESTGIYW-HPVHSVLEGKIDLIVAN 82 
                                       7*******************9.6779******9*999999.77899*************.56778899********* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdqvf 154
                                        +++k++      ++KtD  D+++IA+l +  g ++p++  +++ +eLr+ltr+re +vk++t++kn++++ Ld+ +
  gi|330507866|ref|YP_004384294.1|  83 SYKIKHT-----PGRKTDVSDSEWIAELCL-NGMIEPSRIFPKDDRELRRLTRAREGYVKQMTQEKNKIHQSLDSAC 153
                                       ******9.....59****************.******************************************9876 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2   0.00098       5.8      33      64 ..     127     158 ..     119     161 .. 0.82
   2 ?    1.8   0.6     0.048   2.9e+02      11      31 ..     224     244 ..     189     254 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00098
                           DUF4164  33 krdeleaeiealgedrsRLaeeLdqaearaar 64 
                                        ++++e  +++++++++++ + Ld+a  ++a+
  gi|330507866|ref|YP_004384294.1| 127 LTRAREGYVKQMTQEKNKIHQSLDSACIKLAS 158
                                       45788999*****************9888776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.048
                           DUF4164  11 trLeaaldsLEkavdrrleae 31 
                                       + +++ +d+L++ + +r++  
  gi|330507866|ref|YP_004384294.1| 224 KSIQERIDELDGEISARIQYR 244
                                       456666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 3098.79
//
Query:       gi|330507867|ref|YP_004384295.1|  [L=206]
Description: hypothetical protein MCON_1894 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1532.24
//
Query:       gi|330507868|ref|YP_004384296.1|  [L=144]
Description: hypothetical protein MCON_1895 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   12.4   0.0      0.066   12.2   0.0    1.0  1  SidC_N    SidC N-terminal domain


Domain annotation for each model (and alignments):
>> SidC_N  SidC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.7e-06     0.066     115     168 ..      57     113 ..      44     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-06
                                       HSSS----HHHHHHHHH-S..SEEEEE---SS-.-S-----..S-SEE----B-GGG CS
                            SidC_N 115 kegfPsypkpleelikese..NlysirLrPkeq.DsflrseavnPvFsvkrkssaee 168
                                       ++++P+y + +ee+  ++e   l  i   P++q Ds+ +s+ ++Pv s++ + ++ +
  gi|330507868|ref|YP_004384296.1|  57 NQAVPQYNAWIEEIFGKNEslMLMPISTVPTRQtDSYFKSQIITPVHSIDASWNQTG 113
                                       799************9999455666777787654***************98877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1086.51
//
Query:       gi|330507869|ref|YP_004384297.1|  [L=75]
Description: hypothetical protein MCON_1896 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 569.64
//
Query:       gi|330507870|ref|YP_004384298.1|  [L=209]
Description: transposase, IS605 OrfB family domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-23   80.7   0.6    1.5e-22   79.3   0.0    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.02   15.1   1.0      0.031   14.5   1.0    1.2  1  OrfB_IS605      Probable transposase
        1.4    9.0   8.0        1.8    8.6   0.1    2.4  2  PriA_CRR        PriA DNA helicase Cys-rich region (CRR) domai
        1.6    8.6   7.3       0.51   10.2   0.3    2.4  2  zf-CCHC_2       Zinc knuckle


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 ?   -1.1   0.1       0.4   1.8e+03      46      46 ..      42      42 ..       8      65 .. 0.60
   2 !   79.3   0.0   3.4e-26   1.5e-22       1      67 [.     111     175 ..     111     176 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.4
                    OrfB_Zn_ribbon 46 t 46
                                      +
  gi|330507870|ref|YP_004384298.1| 42 R 42
                                      0 PP

  == domain 2  score: 79.3 bits;  conditional E-value: 3.4e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       f++lke+l+yka  +G+++++v+payTS+tC++Cg+ + +  +g+ fkC  Cg + d+D+n+a Ni+
  gi|330507870|ref|YP_004384298.1| 111 FYQLKEFLSYKALAAGVPLVLVDPAYTSQTCHQCGEHGIR--NGKSFKCHVCGWSGDADFNGAKNIA 175
                                       899*************************************..************************7 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.0   6.9e-06     0.031      43     106 ..      13      78 ..       2      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.9e-06
                        OrfB_IS605  43 grrlksdykylakeiaelqsklkkskn..ykkasrklarlhrkrsrrrkhllhklathliktlkev 106
                                       g+ +k  +  +a  +a lq+k+ k ++  ++++++ ++rl+ k +r  +   h+++++++ + +e+
  gi|330507870|ref|YP_004384298.1|  13 GKTIKLIKNHYASMRAVLQQKAVKGTRssRRRCRELQQRLSGKEARYQRQINHEISKAIVTRAQEI 78 
                                       566666777788888999988877777789******************************999987 PP

>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   3.6     0.044     2e+02      19      24 ..     141     146 ..     139     147 .. 0.86
   2 ?    8.6   0.1    0.0004       1.8      13      25 ..     151     163 ..     150     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.044
                          PriA_CRR  19 CHyCgy 24 
                                       CH+Cg 
  gi|330507870|ref|YP_004384298.1| 141 CHQCGE 146
                                       *****7 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0004
                          PriA_CRR  13 srnrLrCHyCgyt 25 
                                       ++++ +CH Cg++
  gi|330507870|ref|YP_004384298.1| 151 NGKSFKCHVCGWS 163
                                       67889******85 PP

>> zf-CCHC_2  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.8     0.078   3.5e+02       6      13 ..     141     148 ..     140     148 .. 0.90
   2 ?   10.2   0.3   0.00011      0.51       3      13 ..     154     164 ..     153     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.078
                         zf-CCHC_2   6 ChiCgkkG 13 
                                       Ch Cg +G
  gi|330507870|ref|YP_004384298.1| 141 CHQCGEHG 148
                                       *****998 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00011
                         zf-CCHC_2   3 gYvChiCgkkG 13 
                                       +++Ch+Cg++G
  gi|330507870|ref|YP_004384298.1| 154 SFKCHVCGWSG 164
                                       689******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1131  (0.0630822); expected 358.6 (0.02)
Passed bias filter:                      780  (0.0435049); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1539.00
//
Query:       gi|330507871|ref|YP_004384299.1|  [L=155]
Description: hypothetical protein MCON_1900 [Methanosaeta concilii GP6]
Scores for complete 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   41.4   0.0      2e-10   41.1   0.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    0.00017   21.9   0.0    0.00092   19.6   0.0    1.8  2  Hydrolase       haloacid dehalogenase-like hydrolase
    0.00056   19.9   0.0    0.00099   19.1   0.0    1.4  1  Hydrolase_like  HAD-hyrolase-like
     0.0013   18.5   0.0     0.0025   17.5   0.0    1.4  1  PNK3P           Polynucleotide kinase 3 phosphatase
  ------ inclusion threshold ------
      0.038   14.1   0.0      0.049   13.8   0.0    1.4  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase
       0.14   12.6   0.1       0.22   11.9   0.1    1.7  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 !   41.1   0.0   6.5e-14     2e-10      77     176 ..      20     129 ..       5     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 6.5e-14
                             HAD_2  77 evkpydgvkelLeeLkeagyklgivTsksrea....veekleqlgiesyFd..vivtsedvekk..KPdpeviekal 145
                                       +  +y+++ e+L+ L+e+gy+lg++++ s+e+    v ++le++ i s++d   iv s++  ++  KPd +++ +al
  gi|330507871|ref|YP_004384299.1|  20 QYYLYSDALETLKALRERGYRLGVISNLSEEVtvdeVHSFLEECRIASFIDphLIVLSSEHPENikKPDKRIFDRAL 96 
                                       6789***********************98876111156789999******8554555544433334*********** PP

                             HAD_2 146 eklklkk..eeviyvGDsptDieaakkagikvi 176
                                       ek +l k  +++i+v  ++  i aa+  g ++i
  gi|330507871|ref|YP_004384299.1|  97 EKSGLVKaeNKAIFVTEEHEHILAARSYGWRAI 129
                                       ***997622569*****************9987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.15   4.4e+02       3      15 ..       4      16 ..       3      22 .. 0.86
   2 !   19.6   0.0   3.1e-07   0.00092     115     196 ..      19     111 ..      14     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.15
                                      EEEEESBTTTBCH CS
                                      xxxxxxxxxxxxx RF
                         Hydrolase  3 tvvfDkdGTLttg 15
                                      +++fD++ TL++ 
  gi|330507871|ref|YP_004384299.1|  4 AIFFDLTHTLLEK 16
                                      79********975 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 3.1e-07
                                       HTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHH.HHHHHTT....GGGESEEEEHHCES....STTTSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx....xxxxxxxxxxxxxx....xxxxxxxxxxxx RF
                         Hydrolase 115 dplkvkpeaaeavasLkaagievvlltgdnpetae.raanqlG....ddyfdaviasdiet....vakpspegkvaa 182
                                        +++++ +a e++++L+++g++++++++ ++e    ++ + l     + ++d ++ +  ++    ++kp+++++ +a
  gi|330507871|ref|YP_004384299.1|  19 GQYYLYSDALETLKALRERGYRLGVISNLSEEVTVdEVHSFLEecriASFIDPHLIVLSSEhpenIKKPDKRIFDRA 95 
                                       57789**********************99997666577777776777444433333333333677************ PP

                                       HHHHT..STGGGEEEE CS
                                       xxxxx..xxxxxxxxx RF
                         Hydrolase 183 ireLq..gkpeevamV 196
                                       +++ +     ++ ++V
  gi|330507871|ref|YP_004384299.1|  96 LEKSGlvKAENKAIFV 111
                                       ***9974334556655 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.3e-07   0.00099       3      58 ..      85     142 ..      83     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.3e-07
                                       STTSSHHHHHHHHHH---..GGGEEEEES-TTTHHHHHHHCT-EEEEESS.SSS-TTTH CS
                    Hydrolase_like   3 gKPepemydfalevlgsd..peevlmiGDrlatDiagAnnaGwksvLVlt.Gvtrpedl 58 
                                        KP + ++d+ale+ g+    ++ +++    +  i++A+ +Gw+ +L +  G  +ped 
  gi|330507871|ref|YP_004384299.1|  85 KKPDKRIFDRALEKSGLVkaENKAIFVTEE-HEHILAARSYGWRAILKRNwGECQPEDG 142
                                       7*************987744667*******.****************887788888775 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   8.5e-07    0.0025       4     124 ..       6     111 ..       3     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.5e-07
                             PNK3P   4 aFDlDstliktksgkefakdaddwkllsesvlekLkklkeegykivifsNqggvvekktkkslekfkekieallkel 80 
                                       +FDl +tl+++ +g+          +l++  le+Lk+l e gy + ++sN ++ v+    +++++f+e + ++++ +
  gi|330507871|ref|YP_004384299.1|   6 FFDLTHTLLEKVNGQY---------YLYSDALETLKALRERGYRLGVISNLSEEVT---VDEVHSFLEEC-RIASFI 69 
                                       5777777776655443.........4556689******************888777...79999999986.6999** PP

                             PNK3P  81 dvpllvyaatkkdkyRKPetGmweelkkdleekleidkeksfyv 124
                                       d  l+v+ + + + ++KP++ ++++  ++        ++k ++v
  gi|330507871|ref|YP_004384299.1|  70 DPHLIVLSSEHPENIKKPDKRIFDRALEKSGL--VKAENKAIFV 111
                                       *********************99998887665..2233344555 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.6e-05     0.049       3      66 ..       7      77 ..       5     127 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                                      EESTTTSEE....TTEE-TTHHHHHHHHHHTT-EEEEEE---SS.-HHHHHHHHHHTT--..--GGGEEEH CS
                       Hydrolase_6  3 fDidGvLwr....gdkaipgaaealnalraagkpvvllTNnssk.seeeyakkleklgvd..iteeqvvts 66
                                      fD+  +L++    ++ ++  a e+l+alr++g+++ +++N s + + +e++  le+  +   i++  +v s
  gi|330507871|ref|YP_004384299.1|  7 FDLTHTLLEkvngQYYLYSDALETLKALRERGYRLGVISNLSEEvTVDEVHSFLEECRIAsfIDPHLIVLS 77
                                      6666666644443567899*********************8765144555555566665554555555555 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.3e-05      0.22      61     113 ..       5      50 ..       1     128 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.3e-05
                               HAD  61 llaglseelaaelerfvaevirpklldpgalellaahraaGdrvvvvSgglrp 113
                                       ++ +l+  l + ++  +       +l+ +ale l+a r++G+r+ v+S+  ++
  gi|330507871|ref|YP_004384299.1|   5 IFFDLTHTLLEKVNGQY-------YLYSDALETLKALRERGYRLGVISNLSEE 50 
                                       55555544444554445.......6779********************86655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1088.98
//
Query:       gi|330507872|ref|YP_004384300.1|  [L=84]
Description: hypothetical protein MCON_1901 [Methanosaeta concilii GP6]
Scores for complete 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   0.1    0.00029   20.6   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0013   19.0   0.0     0.0017   18.7   0.0    1.2  1  Rrf2            Transcriptional regulator
     0.0055   16.7   0.0     0.0073   16.3   0.0    1.2  1  HTH_45          Winged helix-turn-helix
     0.0056   16.5   0.0     0.0084   16.0   0.0    1.3  1  TFIIE_alpha     TFIIE alpha subunit
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.019   14.5   0.0    1.2  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.029   14.3   0.0      0.037   13.9   0.0    1.3  1  MarR_2          MarR family
      0.043   14.0   0.1      0.066   13.4   0.1    1.2  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.067   13.0   0.0      0.086   12.6   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
       0.11   12.6   0.0       0.15   12.2   0.0    1.1  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h


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 !   20.6   0.1   1.5e-07   0.00029      18      57 ..      25      65 ..      19      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.5e-07
                                      H.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 18 l.klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      l ++g+++ d++a+ + +p ++v ++L ++ +++lV+ e g
  gi|330507872|ref|YP_004384300.1| 25 LgSKGKMESDKVAKVTHIPAPSVKKILAEMAERDLVREENG 65
                                      4489********************************99865 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.5e-07    0.0017      23      61 ..      28      66 ..      20      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.5e-07
                                      CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                      +++++s+++a+ + i+++ ++kila++++ +lv+ + G 
  gi|330507872|ref|YP_004384300.1| 28 KGKMESDKVAKVTHIPAPSVKKILAEMAERDLVREENGI 66
                                      45699*****************************99997 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.6e-06    0.0073       8      71 ..      21      82 ..      16      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.6e-06
                            HTH_45  8 iadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklke 71
                                      i++IL   s+g+ +  k+ +   +    ++k L  + e++l++++++ + lT  G+e+ ++lk+
  gi|330507872|ref|YP_004384300.1| 21 IVQILG--SKGKMESDKVAKVTHIPAPSVKKILAEMAERDLVREENGIWGLTGAGEEIEKELKK 82
                                      566666..456666667777777888899*****************************999986 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.2e-06    0.0084      11      57 ..      13      60 ..       5      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.2e-06
                                      S-.HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSE CS
                       TFIIE_alpha 11 yg.eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlv 57
                                      +g ++   ++++L +kg++  + +ak ++i  + ++k+L+++ e  lv
  gi|330507872|ref|YP_004384300.1| 13 MGnKQRERIVQILGSKGKMESDKVAKVTHIPAPSVKKILAEMAERDLV 60
                                      4534567899*********************************99998 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 ?   14.5   0.0   9.3e-06     0.019       2      48 .]      15      61 ..      14      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.3e-06
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++ + +I ++L  ++++    +A+ ++++ + v++ l ++ e  l++
  gi|330507872|ref|YP_004384300.1| 15 NKQRERIVQILGSKGKMESDKVAKVTHIPAPSVKKILAEMAERDLVR 61
                                      67889*************************************99986 PP

>> MarR_2  MarR 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     0.037      27      54 ..      36      63 ..       9      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                                      HHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 27 larrlglsksavsrilkrLvaaGLverr 54
                                      +a+ ++++ ++v +il+++ ++ Lv+++
  gi|330507872|ref|YP_004384300.1| 36 VAKVTHIPAPSVKKILAEMAERDLVREE 63
                                      6899*********************998 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 ?   13.4   0.1   3.3e-05     0.066      13      53 ..      21      61 ..      19      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.3e-05
                                      HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      I ++ ++k++ +  ++a++  + ++sV + l ++++  +v 
  gi|330507872|ref|YP_004384300.1| 21 IVQILGSKGKMESDKVAKVTHIPAPSVKKILAEMAERDLVR 61
                                      66778899*****************************9996 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   4.3e-05     0.086      19      50 ..      31      62 ..       8      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.3e-05
                                      -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +    +A+ t++p ++v  +L+ + e+ +v+ 
  gi|330507872|ref|YP_004384300.1| 31 MESDKVAKVTHIPAPSVKKILAEMAERDLVRE 62
                                      666789************************96 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.5e-05      0.15      17      57 ..      20      60 ..      18      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-05
                                      HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                      ++v+ L +kg+  +++ +k t ++  +Vkk+L+ +  + lV
  gi|330507872|ref|YP_004384300.1| 20 RIVQILGSKGKMESDKVAKVTHIPAPSVKKILAEMAERDLV 60
                                      89******************************988777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 606.59
//
Query:       gi|330507873|ref|YP_004384301.1|  [L=323]
Description: phosphoribulokinase/uridine kinase family protein [Methanosaeta concilii GP6]
Scores for complete 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-45  154.6   0.0    4.3e-45  153.9   0.0    1.3  1  PRK             Phosphoribulokinase / Uridine kinase family
     0.0012   19.3   0.2     0.0028   18.2   0.2    1.7  1  AAA_23          AAA domain
  ------ inclusion threshold ------
      0.012   16.1   0.0      0.024   15.2   0.0    1.6  1  AAA_18          AAA domain
      0.013   14.8   0.1      0.035   13.4   0.1    1.7  2  Zeta_toxin      Zeta toxin
      0.014   15.8   0.0      0.025   15.0   0.0    1.5  1  AAA_16          AAA ATPase domain
      0.036   14.1   0.0      0.059   13.4   0.0    1.4  1  TsaE            Threonylcarbamoyl adenosine biosynthesis prot
      0.039   14.5   0.0      0.058   13.9   0.0    1.6  1  ABC_tran        ABC transporter
      0.082   13.0   0.0        0.1   12.7   0.0    1.4  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
      0.091   12.6   0.0       0.21   11.4   0.0    1.5  1  CPT             Chloramphenicol phosphotransferase-like prote
       0.18   11.5   0.1       0.37   10.6   0.1    1.4  1  AAA_29          P-loop containing region of AAA domain
        0.2   11.4   0.0       0.34   10.6   0.0    1.4  1  AAA_30          AAA domain


Domain annotation for each model (and alignments):
>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.9   0.0   2.6e-48   4.3e-45       1     189 [.      16     190 ..      16     195 .. 0.94

  Alignments for each domain:
  == domain 1  score: 153.9 bits;  conditional E-value: 2.6e-48
                               PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllyev 77 
                                       v g+ag+SG+Gktt++r ++ i+g+             +  +   +d+++ +r+++ke++++ l p+an+fdll e 
  gi|330507873|ref|YP_004384301.1|  16 VFGIAGDSGSGKTTISRGIRRILGED------------MVATFSMDDYHSLDRRQRKERNITPLHPDANQFDLLAEH 80 
                                       679*********************33............334556689****************************** PP

                               PRK  78 lkelkegkkvdkpiYsheteeaapdkeeliegadvlviEGlhalydervaelldlkiyvdisidlelarklqRDiae 154
                                       l +l+  +++dkp+Y+h t+e+    +    +a v+++EGlh+ly er+++ +d+ki+vd+s  ++  +k+ RD+ e
  gi|330507873|ref|YP_004384301.1|  81 LEALRRNERIDKPVYDHRTGEISG--TVPFGPAPVIIVEGLHPLYTERLRSQIDFKIFVDPSRSVKRLWKIRRDVGE 155
                                       **********************99..6677899******************************************** PP

                               PRK 155 RGrsleavldsilrrkpdyvnyikpqfseadliiq 189
                                       RG+++ +v+++il r pdy+ y++ q+ +a+++i+
  gi|330507873|ref|YP_004384301.1| 156 RGYETGQVMAEILQREPDYKLYVDIQKIYAQIVIK 190
                                       ********************************997 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   1.7e-06    0.0028      21      50 ..      16      45 ..      15     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
                            AAA_23 21 ltlItGpNGaGKTTildAiklaLygetprl 50
                                      ++ I G+ G+GKTTi + i+ +L+++   +
  gi|330507873|ref|YP_004384301.1| 16 VFGIAGDSGSGKTTISRGIRRILGEDMVAT 45
                                      688********************9976444 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   1.5e-05     0.024       3      55 ..      19      68 ..      18     146 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                            AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrlded 55
                                      ++G +G+GKtt+++ +++ l  g+    +++ +++   +  +  +e ++   +
  gi|330507873|ref|YP_004384301.1| 19 IAGDSGSGKTTISRGIRRIL--GEDMVATFSMDDYHSLDRRQ-RKERNITPLH 68
                                      99**************9998..44443333333333333333.2333333333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.1e-05     0.035      21      59 ..      19      56 ..       3      75 .. 0.82
   2 ?   -1.4   0.0      0.73   1.2e+03     152     188 ..      62      99 ..      53     102 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                        Zeta_toxin 21 lgGqpGAGKselaellkdelerqgnvvrldpDdlRelhP 59
                                      ++G +G+GK+++++ +++ l+ ++ v +++ Dd+ +l +
  gi|330507873|ref|YP_004384301.1| 19 IAGDSGSGKTTISRGIRRILG-EDMVATFSMDDYHSLDR 56
                                      8*******************5.777889999*9988755 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.73
                        Zeta_toxin 152 Rlv.pkeehdeafeglresvealeeekqldrvkikdrd 188
                                       R++ p     ++f+ l+e +eal ++ ++d+ ++  r 
  gi|330507873|ref|YP_004384301.1|  62 RNItPLHPDANQFDLLAEHLEALRRNERIDKPVYDHRT 99 
                                       44404444557888999999999999999976665555 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   1.5e-05     0.025      29      87 ..      19      82 ..       2     132 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                            AAA_16 29 lsGesGvGKsslvrellralekdggiflrgkcdql....esa.......ipysalaqalareellrqlld 87
                                      + G+sG+GK+++ r ++r l +d   +++   d++    +         +p+ + a+++   +ll++ l+
  gi|330507873|ref|YP_004384301.1| 19 IAGDSGSGKTTISRGIRRILGEDM--VATFSMDDYhsldR-RqrkerniTPLHPDANQF---DLLAEHLE 82
                                      78***************9999995..33333333312231.123344456665555555...34444443 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.6e-05     0.059      21      59 ..      16      52 ..       1      93 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                                      EEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEE CS
                              TsaE 21 vilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeY 59
                                      v+ + Gd G+GKTt++rg+ + lg + v   TF++   +
  gi|330507873|ref|YP_004384301.1| 16 VFGIAGDSGSGKTTISRGIRRILGEDMVA--TFSMDDYH 52
                                      46689******************987664..66655555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.5e-05     0.058      14      70 ..      17      73 ..      11     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-05
                                      EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepql 70
                                       +i G++G+GK+t+ + + + l  ++   ++ ++d ++ +++++ +++i  l+ +++ 
  gi|330507873|ref|YP_004384301.1| 17 FGIAGDSGSGKTTISRGIRRILGEDMVA-TFSMDDYHSlDRRQRKERNITPLHPDANQ 73
                                      68*************9999988654433.35555555555566666666666555444 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 ?   12.7   0.0   6.1e-05       0.1       4      55 ..      19      81 ..      16     280 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-05
                                      EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH..............C CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............x RF
                              CbiA  4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep..............d 55
                                      +++ +G+GKTt++ ++ r+l +    V+ + +D   ++++  + +e +i p               
  gi|330507873|ref|YP_004384301.1| 19 IAGDSGSGKTTISRGIRRILGE--DMVATFSMDDYHSLDR-RQRKERNITPlhpdanqfdllaehL 81
                                      5799**************9998..5566665555545554.3333333333666555444444440 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    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       7      55 ..      20      67 ..      14      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                      EE-TTSSHHHHHHHHHHHSSS.-EEEEEHHHHHHHS-GGGGTSTTSEEEE CS
                               CPT  7 nGgsssGKsslaralqevlde.pwlhlgvDafvealppkrqdeadglefe 55
                                       G s sGK++++r ++ +l e     + +D ++   +++rq ++ ++ + 
  gi|330507873|ref|YP_004384301.1| 20 AGDSGSGKTTISRGIRRILGEdMVATFSMDDYHS--LDRRQRKERNITPL 67
                                      6999*************9966155679******9..67777777776543 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00023      0.37      26      38 ..      18      30 ..       6      40 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                            AAA_29 26 lltGpsGsGKSTl 38
                                       ++G+sGsGK+T+
  gi|330507873|ref|YP_004384301.1| 18 GIAGDSGSGKTTI 30
                                      589*********8 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00021      0.34      20      66 ..      16      81 ..       3     119 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                            AAA_30 20 vavltGpAGtGKttalkalreaweaag...................grviglAptgkaAkvLaeel 66
                                      v  + G  G+GKtt+ +++r+++ ++                    +++  l p +++ + Lae+l
  gi|330507873|ref|YP_004384301.1| 16 VFGIAGDSGSGKTTISRGIRRILGEDMvatfsmddyhsldrrqrkeRNITPLHPDANQFDLLAEHL 81
                                      3458899*************9998774455555555555555555555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2113.75
//
Query:       gi|330507874|ref|YP_004384302.1|  [L=309]
Description: HTH-type transcriptional regulatory protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-11   44.0   0.1    3.6e-11   42.9   0.1    1.6  1  HTH_3     Helix-turn-helix
    1.3e-06   28.3   0.4    3.9e-06   26.8   0.1    2.0  2  HTH_19    Helix-turn-helix domain
    2.2e-05   24.7   0.1      6e-05   23.3   0.1    1.7  1  HTH_31    Helix-turn-helix domain
    0.00018   21.4   0.1     0.0005   19.9   0.1    1.7  1  HTH_11    HTH domain
    0.00077   19.2   0.1     0.0023   17.7   0.1    1.8  1  HTH_23    Homeodomain-like domain
     0.0037   17.1   0.1      0.012   15.5   0.1    1.9  1  HTH_25    Helix-turn-helix domain
  ------ inclusion threshold ------
       0.03   14.1   0.7       0.03   14.1   0.7    1.8  2  HTH_38    Helix-turn-helix domain
      0.054   13.3   0.0       0.14   12.0   0.0    1.7  1  HTH_10    HTH DNA binding domain
      0.065   13.5   0.0       0.14   12.5   0.0    1.6  1  NUMOD1    NUMOD1 domain
      0.099   12.8   0.1       0.24   11.6   0.1    1.6  1  HTH_28    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 !   42.9   0.1     2e-14   3.6e-11       1      52 [.     133     184 ..     133     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2e-14
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEH CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsl 52 
                                       ++++R+++g+s+  LA +lGvsr+tis++E  +   s+++++kl++ ++ +l
  gi|330507874|ref|YP_004384302.1| 133 MRQIRLARGISLGALATELGVSRRTISKYEVEDMDTSVDVALKLEEIFNEEL 184
                                       59**********************************************9776 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   2.2e-09   3.9e-06       1      55 [.     130     183 ..     130     188 .. 0.94
   2 ?   -2.1   0.0       2.2   3.9e+03      25      50 ..     271     295 ..     249     299 .. 0.65

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.2e-09
                            HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgid 55 
                                       G+r +++R  +g+++ +la +lg+sr+ is++E + + ++s ++ lk+ e+++ +
  gi|330507874|ref|YP_004384302.1| 130 GDRMRQIRLARGISLGALATELGVSRRTISKYEVEDM-DTSVDVALKLEEIFNEE 183
                                       899********************************99.99999999999999865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                            HTH_19  25 s.rskisaiEngkkdvpsaelllkiae 50 
                                       +  +k+  iE  ++  ++ ++l +i e
  gi|330507874|ref|YP_004384302.1| 271 DgETKLECIE--ETALIEKRELEDIDE 295
                                       4567777888..444777777777766 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   3.3e-08     6e-05       3      35 ..     130     162 ..     130     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.3e-08
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlE 35 
                                       G++ r+ R ++G+s+ ++A  lgvs+ t+s++E
  gi|330507874|ref|YP_004384302.1| 130 GDRMRQIRLARGISLGALATELGVSRRTISKYE 162
                                       89******************************9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   2.8e-07    0.0005       7      35 ..     134     161 ..     132     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.8e-07
                            HTH_11   7 elLleargpisgeeLAeeLnvSrrtvrrd 35 
                                       ++++ arg is   LA eL+vSrrt+ ++
  gi|330507874|ref|YP_004384302.1| 134 RQIRLARG-ISLGALATELGVSRRTISKY 161
                                       56778888.*****************986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.3e-06    0.0023       7      37 ..     132     161 ..     130     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                            HTH_23   7 RlrillllaeGlsvreIAreLgvsrrTvyrw 37 
                                       R+r ++l++ G+s  + A+eLgvsrrT++++
  gi|330507874|ref|YP_004384302.1| 132 RMRQIRLAR-GISLGALATELGVSRRTISKY 161
                                       788899999.******************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 !   15.5   0.1   6.6e-06     0.012       1      36 [.     132     167 ..     132     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.6e-06
                                       HHHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25   1 rLraaRearglsleevaketkIrkdylealEeddfd 36 
                                       r+r+ R+arg+sl ++a e+ ++ +++ + E +d+d
  gi|330507874|ref|YP_004384302.1| 132 RMRQIRLARGISLGALATELGVSRRTISKYEVEDMD 167
                                       68*************************998887765 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       4.4     8e+03       9      17 ..      57      65 ..      55      70 .. 0.50
   2 ?   14.1   0.7   1.7e-05      0.03      14      39 ..     135     160 ..     132     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.4
                            HTH_38  9 eReeIerll 17
                                      eR  +e+ +
  gi|330507874|ref|YP_004384302.1| 57 ERTALEIRR 65
                                      565555543 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.7e-05
                            HTH_38  14 erllaeGlslreIArrLgrspsTIsR 39 
                                       ++ la+G sl + A +Lg+s+ TIs+
  gi|330507874|ref|YP_004384302.1| 135 QIRLARGISLGALATELGVSRRTISK 160
                                       6789********************96 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.7e-05      0.14      22      43 ..     140     161 ..     138     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.7e-05
                            HTH_10  22 RrvtlkeLAkelGIskstlseh 43 
                                       R ++l +LA elG+s+ t+s++
  gi|330507874|ref|YP_004384302.1| 140 RGISLGALATELGVSRRTISKY 161
                                       999***************9975 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.5e-05      0.14      18      36 ..     143     161 ..     142     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.5e-05
                            NUMOD1  18 SireAakyLgishntInky 36 
                                       S+ ++a  Lg+s++tI+ky
  gi|330507874|ref|YP_004384302.1| 143 SLGALATELGVSRRTISKY 161
                                       8999**************9 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00013      0.24       8      30 ..     137     159 ..     136     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                            HTH_28   8 llaaGhsvreaArelgisrrtvy 30 
                                       +la+G s  ++A elg+srrt++
  gi|330507874|ref|YP_004384302.1| 137 RLARGISLGALATELGVSRRTIS 159
                                       689999***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2210.57
//
Query:       gi|330507875|ref|YP_004384303.1|  [L=423]
Description: hypothetical protein MCON_1904 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-41  141.1   0.0    2.4e-41  140.5   0.0    1.3  1  DUF1743          Domain of unknown function (DUF1743)
     0.0036   17.2   0.0     0.0075   16.2   0.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.025   14.6   0.9      0.043   13.8   0.9    1.3  1  zinc-ribbons_6   zinc-ribbons
      0.038   14.0   0.2       0.08   13.0   0.2    1.4  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.051   13.9   0.0      0.097   13.0   0.0    1.4  1  NTP_transf_2     Nucleotidyltransferase domain
       0.13   12.1   0.8       0.23   11.4   0.8    1.4  1  C1_1             Phorbol esters/diacylglycerol binding domain
       0.82    9.7   4.8        1.9    8.5   4.8    1.6  1  Zn_Tnp_IS1595    Transposase 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 !  140.5   0.0   9.2e-45   2.4e-41       1     116 []     135     247 ..     135     247 .. 0.98

  Alignments for each domain:
  == domain 1  score: 140.5 bits;  conditional E-value: 9.2e-45
                                       TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEE CS
                           DUF1743   1 grgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvl 76 
                                       grg+iGA+aa+ga+++  d+tyEl+aYr++++wg +r +d+ +v+ead+ typ+t+d+vD+++ +vv +Ph+ dpvl
  gi|330507875|ref|YP_004384303.1| 135 GRGLIGALAAVGADLP--DWTYELIAYRQRSQWGtPRFIDPATVWEADRLTYPQTWDTVDHHNHRVVFAPHSADPVL 209
                                       89***********666..8********************************************************** PP

                                       EEEEES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                           DUF1743  77 fGirgedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                       fGirg+dp a+++a++ i+s  e++e++++++tnqgtdah
  gi|330507875|ref|YP_004384303.1| 210 FGIRGSDPVAIKRAFETIRS--EPVERYVLYQTNQGTDAH 247
                                       ********************..****************99 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.9e-06    0.0075      15      60 ..     276     329 ..     250     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.9e-06
                                       ETTEEEEEEEETT......EEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEE CS
                   tRNA_anti-codon  15 ggkvifidlrDgt......griqvvlfr..eeatklaenlkeGdvvrvtGrvkr 60 
                                        g+++f++l ++       gri++ +f   ++++++ ++l++Gd ++v+G v+ 
  gi|330507875|ref|YP_004384303.1| 276 AGGHVFLTLHNEGvglnggGRIECAAFEptKNFRNIIKELRPGDELEVFGSVRD 329
                                       58999999999988555556*******************************985 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.9   1.7e-05     0.043      28      64 ..     349     383 ..     343     386 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                                       EEEE-SSS-S---EEEETTEEEE--TTTT----TTSS CS
                    zinc-ribbons_6  28 kealCpeCeqelevlkaCgavdyfCnkcneLiSkkrv 64 
                                         +lCp+C+ ++e   +    +y C++c+   S++++
  gi|330507875|ref|YP_004384303.1| 349 AAPLCPQCHRRMESAGKG--QGYRCRRCKTRSSSREI 383
                                       556666666666655442..35666666665555555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   3.1e-05      0.08      60      96 ..     340     378 ..     321     386 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                                       -EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSSS- CS
                              HypA  60 aeLeieevpvkvrCreCgkefeleek..alrCpkCgsad 96 
                                        +L+ e+v++   C +C++++e++ k   +rC +C++++
  gi|330507875|ref|YP_004384303.1| 340 LHLAPEKVQAAPLCPQCHRRMESAGKgqGYRCRRCKTRS 378
                                       457789999999**********88754588*****9864 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.8e-05     0.097       2      29 ..     306     333 ..     305     335 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHHHHTTTSEEEEEHHHHCTTSC CS
                      NTP_transf_2   2 kklleelkelepvakvvlfGSyarGtal 29 
                                       k +++++kel+p+ ++ +fGS++ Gt++
  gi|330507875|ref|YP_004384303.1| 306 KNFRNIIKELRPGDELEVFGSVRDGTLN 333
                                       6799*********************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 ?   11.4   0.8   9.1e-05      0.23      12      36 ..     351     376 ..     341     378 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.1e-05
                                       -B-TTT-SB--S.SSS-EEEETTT-- CS
                              C1_1  12 tfCkhCgeflwg.kekqglkCswCkl 36 
                                         C +C   ++  +  qg++C+ Ck 
  gi|330507875|ref|YP_004384303.1| 351 PLCPQCHRRMESaGKGQGYRCRRCKT 376
                                       57********888***********96 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.8   0.00076       1.9      19      45 ..     351     376 ..     345     377 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00076
                     Zn_Tnp_IS1595  19 fvCPhCgsr..kayriktrglfqCkeCrk 45 
                                       + CP C+ r  +    k+ + ++C++C++
  gi|330507875|ref|YP_004384303.1| 351 PLCPQCHRRmeS--AGKG-QGYRCRRCKT 376
                                       78*****88533..3444.56******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3175.13
//
Query:       gi|330507876|ref|YP_004384304.1|  [L=311]
Description: manganese-dependent inorganic pyrophosphatase [Methanosaeta concilii GP6]
Scores for complete 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  100.4   0.1    8.9e-29   99.7   0.1    1.4  1  DHH       DHH family
    1.9e-23   83.2   0.4    2.9e-23   82.6   0.4    1.3  1  DHHA2     DHHA2 domain


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.1     1e-32   8.9e-29       1     101 []       4     146 ..       4     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 1e-32
                                       EEEEE-ECSSSHHHHHHHHHHHH.............................................CECS--TCG CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.............................................xxxxxxxxx RF
                               DHH   1 kilivghknpDtDsigSaialan.............................................llvDhneks 32 
                                       ki+++ghk+pDtDs++Sai +an                                             +lvDhne +
  gi|330507876|ref|YP_004384304.1|   4 KIYVIGHKSPDTDSVTSAITYANlknalgmkeavpaaagdinaetkflldhfkvpypekltdatdkkvILVDHNEMA 80 
                                       79*********************7777777777777777777777777777777777777777777777******** PP

                                       GCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  33 qavegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                       qav++   + +++v+i+DHH++g  + t +pi+flnepvg+t +i+a+l+e +++ iske+a+l++++i
  gi|330507876|ref|YP_004384304.1|  81 QAVDN--LNMENIVEIVDHHKIG-GLATGKPIFFLNEPVGATGGIIANLYEMNNVPISKEMAGLMMSAI 146
                                       *****..****************.9*******************************************8 PP

>> DHHA2  DHHA2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.4   3.3e-27   2.9e-23       1     141 [.     182     306 ..     182     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 3.3e-27
                                       HHHHHHHT-STTS-HHHHTTTTEEEEE.ETTEEEEEEEEEES-HHHHHT.THHHHHHHHHHHH.HHT-SEEEEEEE. CS
                             DHHA2   1 kelkkaksdlsglsledllrrDyKeftgeggvkvgiasvpvslsewleekrkgellaalekfaeerkldllvlmttf 77 
                                       +el kaksd+s++s++d+l  D+K+f+  +g k g+++++v++ + le kr +++l++++k++++++ld++vlm+t 
  gi|330507876|ref|YP_004384304.1| 182 MELLKAKSDVSSKSAKDILLGDFKKFD-FSGTKSGVGQIEVMDLKDLEPKR-AAILEEMNKMKDAEGLDMIVLMLT- 255
                                       589************************.*********************66.67*********9999*********. PP

                                       ....ETTT..EEEEEE...STTHHHHHT---B.TEEET...............T---HHHHTHHHHH CS
                             DHHA2  78 eeegdirr..elllaaldaaeklaealekase.eleLeewkegaewrrvykqgnvkasRKqvaPllr 141
                                           d+++  + +l++  ++ ++a+ +eka + +++ +           +  ++v +++Kqv+P l+
  gi|330507876|ref|YP_004384304.1| 256 ----DVMKeaSDILFV--GNAQAAAGFEKAFGgKIQNN----------SIYKEKVLSRKKQVVPPLE 306
                                       ....777769556665..24445555666655336666..........233349***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2438.65
//
Query:       gi|330507877|ref|YP_004384305.1|  [L=211]
Description: thymidylate kinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-37  128.0   0.0    3.8e-37  127.8   0.0    1.0  1  Thymidylate_kin  Thymidylate kinase
    2.5e-05   24.6   0.0    6.8e-05   23.2   0.0    1.7  2  AAA_22           AAA domain
    0.00045   20.5   0.0    0.00066   20.0   0.0    1.4  1  AAA_28           AAA domain
     0.0022   18.5   0.0     0.0063   17.1   0.0    1.8  2  AAA_18           AAA domain
     0.0076   16.0   0.0      0.013   15.3   0.0    1.4  1  AAA_30           AAA domain
      0.009   16.2   0.1      0.037   14.2   0.1    2.0  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.015   14.8   0.0       0.17   11.4   0.0    2.1  2  Ploopntkinase1   P-loop Nucleotide Kinase1
      0.022   14.7   0.1       0.14   12.1   0.1    2.1  2  NACHT            NACHT domain
      0.041   14.3   0.0        0.2   12.1   0.0    2.3  2  AAA_17           AAA domain
        0.1   12.3   0.0       0.14   11.8   0.0    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.11   12.8   0.0       0.11   12.8   0.0    1.3  1  AAA_19           AAA domain
       0.12   11.3   0.0       0.17   10.8   0.0    1.2  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.17   11.5   0.0       0.37   10.4   0.0    1.5  2  SRP54            SRP54-type protein, GTPase 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 !  127.8   0.0   2.8e-40   3.8e-37       1     183 [.       8     200 ..       8     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 2.8e-40
                                       EEESTTSSHHHHHHHHHHHHHHTTE...EEEESSSTTSHHHHHHHHHHH..TCS---HHH...HHHHHHHHHHHTTH CS
                   Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegik..vvltrepggteiGekirelll..keeeleeqt...eallfaadriehle 70 
                                       +EG+DG+GK+t ++ ++++lke   +   ++t ep+++  G+ +r+ +l   + el+      e++lf+ad+++hl+
  gi|330507877|ref|YP_004384305.1|   8 LEGIDGSGKSTAIRHIAAKLKELVPErtLLITAEPSNSAAGRILRSEILreSTGELSFAEhmeELFLFMADHARHLA 84 
                                       6*********************98777899***************999955444443333557************** PP

                                       HHHHHHHHTT-EEEEES-HHHHHHHHHT.TTTTTCH.HHHHHGGGTTS..E-SEEEEEESSHHHHHTSCCTTSSTTT CS
                   Thymidylate_kin  71 ekikpalkqgktvivdRylfSslaYqga.kegvdld.lvlslnedvll..kPdltflldvdpevalkRlakrdelde 143
                                       + i+p+l+ g +v +dRy++S++aYqg+  +g+  d lv+  +   +   +Pd t+l+ +dp+ +++R++ r+   +
  gi|330507877|ref|YP_004384305.1|  85 DTIIPSLEAGAIVLCDRYADSTAAYQGVtLKGIVPDpLVWIREIYRPWnlRPDRTLLFLLDPQLSVQRISSRSG--R 159
                                       ***************************96455554424444444444367************************..9 PP

                                       SHHHHHHHHHHHHHHHHHHHH.TTSTEEEEETTS-HHHHHH CS
                   Thymidylate_kin 144 eeeeqldflrkvrerylelak.ederiliidasksieevhe 183
                                       e++e+++flr+v  ++ +la  e+er++iidas   ++v e
  gi|330507877|ref|YP_004384305.1| 160 EKFERQEFLRQVDGNFRRLASlEPERFVIIDASLDEDAVAE 200
                                       *********************************99998876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   4.9e-08   6.8e-05       6      91 ..       4      85 ..       1      98 [. 0.84
   2 ?   -1.6   0.0       2.2     3e+03      72      98 ..     161     190 ..     138     191 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.9e-08
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdllrellralglelkaerlsseellea 81
                                       ++++ G  G+GK+t +r ++ +l+      e   er  +++ ++++s   + l++e+lr+ + el+      eel+  
  gi|330507877|ref|YP_004384305.1|  4 LLITLEGIDGSGKSTAIRHIAAKLK------ElvpERTLLITAEPSNSAAGRILRSEILRESTGELSF-AEHMEELFLF 75
                                      578999*****************94......23436666667777788899999**************.9999999999 PP

                            AAA_22 82 leqalrarav 91
                                      +++++r+ a+
  gi|330507877|ref|YP_004384305.1| 76 MADHARHLAD 85
                                      9999999988 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                            AAA_22  72 rlsseellealeqalrarav...ielliiD 98 
                                         +++e+l+++  ++r+ a     +++iiD
  gi|330507877|ref|YP_004384305.1| 161 KFERQEFLRQVDGNFRRLASlepERFVIID 190
                                       334666677777777777767766777776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   4.8e-07   0.00066       2     128 ..       6     157 ..       5     195 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.8e-07
                            AAA_28   2 ivitGgestGKTtlleaLaargypvvpEaareileekl.akge.....dalpwvedllafaervleeql..eeeaaa 70 
                                       i + G  ++GK+t ++++aa+  + vpE    i+ e +    +     ++l+++   l fae+++e  l  +++a+ 
  gi|330507877|ref|YP_004384305.1|   6 ITLEGIDGSGKSTAIRHIAAKLKELVPERTLLITAEPSnSAAGrilrsEILRESTGELSFAEHMEELFLfmADHARH 82 
                                       6678889**************99999999999999888533332333333333345666777766655422222222 PP

                            AAA_28  71 .........aankvlfcDrglldtlaYaraygge.aeaelea...aar....ekrydlvfllppapeidddgeRr 128
                                                +a+ +++cDr +  t+aY  +  +  ++ +l+    + r    +   +l fll+p   +++   R 
  gi|330507877|ref|YP_004384305.1|  83 ladtiipslEAGAIVLCDRYADSTAAYQGVTLKGiVPDPLVWireIYRpwnlRPDRTLLFLLDPQLSVQRISSRS 157
                                       3466999999*****************977666546776443123222443455577788888877665555553 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.6e-06    0.0063       1      44 [.       6      43 ..       6      98 .. 0.79
   2 ?   -1.4   0.0       2.3   3.2e+03      52      63 ..     163     174 ..     137     197 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.6e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44
                                      I l G+ G+GK+t  ++++ +l      +++++e+ ll++ +p 
  gi|330507877|ref|YP_004384305.1|  6 ITLEGIDGSGKSTAIRHIAAKL------KELVPERTLLITAEPS 43
                                      899***************9995......7777777777776666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.3
                            AAA_18  52 ldedkldkllda 63 
                                       +++++l ++  +
  gi|330507877|ref|YP_004384305.1| 163 ERQEFLRQVDGN 174
                                       334444444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.2e-06     0.013      20      63 ..       5      52 ..       1      88 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.2e-06
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa.g.grviglA.ptgkaAkv.La 63
                                      + +l+G  G+GK+ta++++++ +++    +++++ A p++ aA + L+
  gi|330507877|ref|YP_004384305.1|  5 LITLEGIDGSGKSTAIRHIAAKLKELvPeRTLLITAePSNSAAGRiLR 52
                                      6789***************99999986436666555478888877444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   2.7e-05     0.037       1      25 [.       5      35 ..       5     178 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg......a 25
                                      l+ l G  GsGKst ++++++kl+      +
  gi|330507877|ref|YP_004384305.1|  5 LITLEGIDGSGKSTAIRHIAAKLKelvperT 35
                                      68899**************999986555542 PP

>> Ploopntkinase1  P-loop Nucleotide Kinase1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.14   1.9e+02      17      40 ..       3      26 ..       1      45 [. 0.80
   2 ?   11.4   0.0   0.00012      0.17     103     157 ..     112     166 ..      85     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.14
                    Ploopntkinase1 17 gelyyvkgsngsgkstvpsylaek 40
                                      g l  + g +gsgkst   ++a k
  gi|330507877|ref|YP_004384305.1|  3 GLLITLEGIDGSGKSTAIRHIAAK 26
                                      566778899*******98887765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00012
                    Ploopntkinase1 103 vlfegiipatllstwieklnrp..arrlvvlfldtpletclsrvdsrnggedfnedl 157
                                       v ++gi+p  l+  wi ++ rp   r+  +l++  + +  + r++sr g e+f+++ 
  gi|330507877|ref|YP_004384305.1| 112 VTLKGIVPDPLV--WIREIYRPwnLRPDRTLLFLLDPQLSVQRISSRSGREKFERQE 166
                                       567899999885..999999984335555555555667789************9864 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0001      0.14       2      27 ..       5      30 ..       4      38 .. 0.87
   2 ?    2.1   0.0      0.12   1.7e+02     115     140 ..      28      52 ..      27      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaeg 27
                                      l+ l+G  GsGK+t ++++a +++e 
  gi|330507877|ref|YP_004384305.1|  5 LITLEGIDGSGKSTAIRHIAAKLKEL 30
                                      5789******************9985 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                                       TTTTT--EEEEEEECCCHHHHCTTSS CS
                             NACHT 115 kkllpeasllltvrpralrdleeqle 140
                                       k+l+pe +ll+t+ p+++  +++ l+
  gi|330507877|ref|YP_004384305.1|  28 KELVPERTLLITAEPSNS-AAGRILR 52 
                                       5799************99.4444444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015       0.2       2      80 ..      10     103 ..       9     169 .. 0.54
   2 ?   -2.2   0.0       3.8   5.3e+03      91     113 ..     170     194 ..     160     199 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                                       E-TTSSHHHHHHHHHHHH.............TEEEEEHHHHHHHHHHTTTS..HSSHHHHCTSHHHHHHHHHHHHHH CS
                            AAA_17   2 GgPGsGKgtqceklveky.............gfthlsaGdllreeakrggl..akardemrklpleekkelqkeaae 63 
                                       G+ GsGK+t++++++ k+             + +   aG +lr+e+ r++    +  ++m++l l   ++ + +a +
  gi|330507877|ref|YP_004384305.1|  10 GIDGSGKSTAIRHIAAKLkelvpertllitaEPSNSAAGRILRSEILRESTgeLSFAEHMEELFLFMADHARHLA-D 85 
                                       899************988666666555555344445669999988877743213455666665444333333333.3 PP

                                       HHHHHH.HSSEEEEEE-S CS
                            AAA_17  64 kiaeea.kkkgvlvdghp 80 
                                       +i     +   vl d ++
  gi|330507877|ref|YP_004384305.1|  86 TIIPSLeAGAIVLCDRYA 103
                                       333322134445555555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.8
                                       SSHHHH..HHHH..SEEEEEE--HH CS
                            AAA_17  91 glpkev..leelkpdaiilleadpe 113
                                       +++ ++  l++l+p+ +++++a+ +
  gi|330507877|ref|YP_004384305.1| 170 QVDGNFrrLASLEPERFVIIDASLD 194
                                       4443332246788888888888755 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.14       3      27 ..       8      29 ..       6      57 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                   Viral_helicase1  3 vhGvpGcGKStlirkllrtsliltv 27
                                        G+ G+GKSt+ir+++ +    ++
  gi|330507877|ref|YP_004384305.1|  8 LEGIDGSGKSTAIRHIAAKL---KE 29
                                      56889************882...22 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.9e-05      0.11      14      60 ..       7      52 ..       1     208 [. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.9e-05
                            AAA_19 14 lvtaGpGtGKTrvlkhivallvelggvkpeeillva..ftgrAakelre 60
                                       + +  G+GK++ ++hi a l+el    pe+ ll++  + + Aa ++  
  gi|330507877|ref|YP_004384305.1|  7 TLEGIDGSGKSTAIRHIAAKLKELV---PERTLLITaePSNSAAGRILR 52
                                      566778***************9998...455555553578899988754 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 ?   10.8   0.0   0.00013      0.17      31      73 ..       5      48 ..       2      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                      EEEEEE-TTSSHHHHHHHHHHHHHCT.T--EEEEEE-------- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrr.GkrvavlavDPsspftG 73
                                       + l G+ G+Gkst++ +++++l++   +r  ++  +Ps + +G
  gi|330507877|ref|YP_004384305.1|  5 LITLEGIDGSGKSTAIRHIAAKLKELvPERTLLITAEPSNSAAG 48
                                      57889******************996257888888888877665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00027      0.37       4      38 ..       6      41 ..       4      57 .. 0.83
   2 ?   -3.6   0.0       5.3   7.2e+03     116     131 ..     184     199 ..     173     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                                      EEEEESTTSSHHHHHHHHHHHHHHT.TS-EEEEEES CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkke.gkkvllvaaD 38
                                      i l G+ G+GK t++  +aa+lk+   +++ll++a 
  gi|330507877|ref|YP_004384305.1|  6 ITLEGIDGSGKSTAIRHIAAKLKELvPERTLLITAE 41
                                      6788*******************9876777777665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.3
                                       EEEEEEETTBHTHHHH CS
                             SRP54 116 evllvldattgqeavk 131
                                       e ++++da++ ++av+
  gi|330507877|ref|YP_004384305.1| 184 ERFVIIDASLDEDAVA 199
                                       5567788888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1311.81
//
Query:       gi|330507878|ref|YP_004384306.1|  [L=210]
Description: hypothetical protein MCON_1908 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-28   99.0   0.0    3.2e-28   98.6   0.0    1.1  1  MAF_flag10     Protein of unknown function DUF115
    0.00027   21.0   0.0    0.00048   20.2   0.0    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 !   98.6   0.0   3.5e-32   3.2e-28      16     168 ..      46     185 ..      29     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 3.5e-32
                        MAF_flag10  16 kellnkfkgnkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevfkeaek 91 
                                       +e +   +g ++a+i+g+ PSL+ +l+ l  +  +a  iaad+a  +Ll +gI+PD+vvs lD+    +  + ea +
  gi|330507878|ref|YP_004384306.1|  46 EERI---RG-RKAVIFGNAPSLDRELDALPPM--DAARIAADGAAAVLLRRGIVPDVVVSdLDG---PFPAILEACQ 113
                                       3333...46.9******************855..8999**************************...7777777777 PP

                        MAF_flag10  92 kgdiplvfasgvnpellkkykgpkiflvtgstqa..lelleeekneilfgGgsvantaldlAvklgfkeIiliGqDl 166
                                       k+ i++v+a+g+n ++l++y +++ +++  ++q+  +  l       +fgG+++++++++lAv+lg+++I l+G+D+
  gi|330507878|ref|YP_004384306.1| 114 KKAIIVVHAHGDNLDALARYVPQLENVIG-TCQCrpSGGL------YNFGGFTDGDRSVFLAVELGASSIELVGFDF 183
                                       77***********************9666.5665333333......89****************************9 PP

                        MAF_flag10 167 ay 168
                                         
  gi|330507878|ref|YP_004384306.1| 184 ED 185
                                       75 PP

>> TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   5.3e-08   0.00048      10      62 ..      76     123 ..      70     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.3e-08
                     TPK_catalytic  10 lrvcaDgGanrlyeeekerlellpdvivGDlDSirpevkefyeskgteivkkp 62 
                                        r++aDg+a  l+     r++++pdv+v DlD   p+++e +++k++ +v+ +
  gi|330507878|ref|YP_004384306.1|  76 ARIAADGAAAVLL-----RRGIVPDVVVSDLDGPFPAILEACQKKAIIVVHAH 123
                                       69***********.....***************************99999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1461.23
//
Query:       gi|330507879|ref|YP_004384307.1|  [L=307]
Description: hypothetical protein MCON_1909 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2212.33
//
Query:       gi|330507880|ref|YP_004384308.1|  [L=286]
Description: hypothetical protein MCON_1911 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.13   10.8  18.0      0.036   12.6   3.5    2.0  2  FUSC          Fusaric acid resistance protein family
        0.5   10.4  43.6       0.68   10.0  18.7    3.8  2  TPR_MLP1_2    TPR/MLP1/MLP2-like protein
        2.3    8.9  37.2        8.9    7.0   5.9    3.8  4  Com_YlbF      Control of competence regulator ComK, YlbF/YmcA
        3.9    6.6  46.8        5.7    6.0  42.8    2.8  2  Taxilin       Myosin-like coiled-coil protein
        4.2    7.8  34.6        0.5   10.8   8.1    4.1  4  CCDC-167      Coiled-coil domain-containing protein 167
        5.5    7.4  40.0        2.4    8.6  14.2    2.6  2  Fez1          Fez1
        8.9    6.6  49.2       0.75   10.1  13.0    3.2  3  OmpH          Outer membrane protein (OmpH-like)


Domain annotation for each model (and alignments):
>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.5   1.4e-05     0.036     186     295 ..       5     120 ..       2     142 .. 0.81
   2 ?    3.9   7.5    0.0059        15     244     326 ..     141     234 ..     126     272 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                              FUSC 186 reaararlaadilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpe....laa 258
                                        e++r +l ++ la+ + rsq+ +e ++++a  + l+ ++ ++++  + l +l+++ +   ae++++++e      +
  gi|330507880|ref|YP_004384308.1|   5 LEEKRGKLRQESLAFKDRRSQLNAEASKWAAKRNELNKATKELIDKAQELKKLRDENNKNVAESKKHRDEfnekTNQ 81 
                                       4678899999*********************************************************9998888888 PP

                              FUSC 259 llaelaaleaaaaaealeaalaalrarlralrrale...a 295
                                       l a++++  +++   + +  ++ lr++++ l+ +++   +
  gi|330507880|ref|YP_004384308.1|  82 LYARIDD-IRKKYNLTGDRSIRDLRREIDHLEFRQQtevL 120
                                       8888888.44467777778888888888877766664443 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0059
                              FUSC 244 rlraeeaaavpelaallaelaal............eaaaaaealeaalaalrarlralrraleadadtaalllarla 308
                                         +++ +   +el++ll+e++al            + a++a+++++++ a  ++++++r++++a+      ++++++
  gi|330507880|ref|YP_004384308.1| 141 SRKEQLE-KNEELRKLLDEAQALrdeaskhhddvtKYAELAQEYHDQMIATFKEADQTRAEADAAHKEFVKAQEAAD 216
                                       3332222.223488888888888777777777777555666666666666666666666666622222222333333 PP

                              FUSC 309 ellaelaqllaslralea 326
                                       e+ +e++++++++r+ e+
  gi|330507880|ref|YP_004384308.1| 217 EQHKEFIRTQREVRDFEK 234
                                       344445555555544443 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 ?    4.6  15.2     0.013        32      63     128 ..      23      88 ..       5      96 .. 0.49
   2 ?   10.0  18.7   0.00027      0.68      10     120 ..     125     244 ..     120     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.013
                        TPR_MLP1_2  63 reelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlneqNklLhdQlEs 128
                                       r++ln   ++ a  ++e+++a++el  + +++++ ++e  k+++e++k++++ ne+ + L+ +++ 
  gi|330507880|ref|YP_004384308.1|  23 RSQLNAEASKWAAKRNELNKATKELIDKAQELKKLRDENNKNVAESKKHRDEFNEKTNQLYARIDD 88 
                                       334444444444444444444444444444444444444444444444444444444444444443 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00027
                        TPR_MLP1_2  10 ikslkeekeeaeaklqklqedlek...qaeiakeaqqkYerelvkhaedvkelqalreel....nelkaeiaelkae 79 
                                        k+l ++++++ a++++ +e+lek    ++++ eaq     e  kh +dv++ ++l +e+      + +e+ + +ae
  gi|330507880|ref|YP_004384308.1| 125 EKQLVDKIASLHAEFKSRKEQLEKneeLRKLLDEAQA-LRDEASKHHDDVTKYAELAQEYhdqmIATFKEADQTRAE 200
                                       4566666677777777766666551115567778877.888***********9999999964444566899999*** PP

                        TPR_MLP1_2  80 aesakaeleeseesweeqkeel...ekelselekriedlneqNk 120
                                       a++a++e+ +++e+ +eq +e+   ++e++++ek i  l+++Nk
  gi|330507880|ref|YP_004384308.1| 201 ADAAHKEFVKAQEAADEQHKEFirtQREVRDFEKVIMGLKKKNK 244
                                       *******************9875558899999999999999997 PP

>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   5.9    0.0035       8.9      36     101 ..      14      87 ..       3      90 .. 0.66
   2 ?   -0.5   0.2      0.75   1.9e+03      27      51 ..      94     118 ..      78     138 .. 0.55
   3 ?    4.6  18.6     0.019        49      19      90 ..     137     216 ..     122     247 .. 0.68
   4 ?    1.7   5.9      0.16     4e+02      25      66 ..     206     254 ..     200     273 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHHHHHHTT....----HHHHH...HHHHHHHHH.HTSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Com_YlbF  36 klikefkklqkelqekqmkg....eelkeeekk...elqelkeel.dknplvkeyleaeqelnellqevnkiia 101
                                       +    fk+++ +l+++++k     +el+++ k+   ++qelk+   ++n++v+e ++ ++e+ne  ++++  i 
  gi|330507880|ref|YP_004384308.1|  14 QESLAFKDRRSQLNAEASKWaakrNELNKATKElidKAQELKKLRdENNKNVAESKKHRDEFNEKTNQLYARID 87 
                                       55556777777776666555555555566555333355555444468889999999999999999888887775 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.75
                                       HHHCSHHHHHHHHHHHHHHHHHHHH CS
                          Com_YlbF  27 aleedeelqklikefkklqkelqek 51 
                                       +l  d  +++l +e+ +l++  q++
  gi|330507880|ref|YP_004384308.1|  94 NLTGDRSIRDLRREIDHLEFRQQTE 118
                                       4455666666666666666633333 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTT...----HHHHHHHHHHHHHH.....HTSHHHHHHHHHHH CS
                          Com_YlbF  19 keykeaeealeedeelqklikefkklqkelqekqmkg...eelkeeekkelqelkeel.....dknplvkeyleaeq 87 
                                        e+k+ +e+le++eel+kl++e ++l++e+++         el +e  +++ +  +e      +++   ke+ +a++
  gi|330507880|ref|YP_004384308.1| 137 AEFKSRKEQLEKNEELRKLLDEAQALRDEASKHHDDVtkyAELAQEYHDQMIATFKEAdqtraEADAAHKEFVKAQE 213
                                       699*************************9977554444443333333333333333333333455555566666665 PP

                                       HHH CS
                          Com_YlbF  88 eln 90 
                                       + +
  gi|330507880|ref|YP_004384308.1| 214 AAD 216
                                       554 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.16
                                       HHHHHCSHHHHHHHHHHHHHHHHHHHHHHTT.......----HHHHHHH CS
                          Com_YlbF  25 eealeedeelqklikefkklqkelqekqmkg.......eelkeeekkel 66 
                                       +e ++++e++ ++ kef + q e+ ++++         +++ke+ +ke+
  gi|330507880|ref|YP_004384308.1| 206 KEFVKAQEAADEQHKEFIRTQREVRDFEKVImglkkknKDIKEDRAKEV 254
                                       4446667777777777777777765544333334322233333333332 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  42.8    0.0022       5.7      43     264 ..      11     247 ..       2     248 .. 0.76
   2 ?    1.6   9.7     0.048   1.2e+02      19     100 ..     175     260 ..     171     271 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0022
                           Taxilin  43 klkkkleqlqkekeqlqaelskaalaksKLekLcRel...qkqnkklkeeskqrareeeekrkelaekfq...akLk 113
                                       kl+++  + + ++ ql ae sk+a+ ++ L+k  +el    ++ kkl++e+++ + e +++r+e +ek +   a + 
  gi|330507880|ref|YP_004384308.1|  11 KLRQESLAFKDRRSQLNAEASKWAAKRNELNKATKELidkAQELKKLRDENNKNVAESKKHRDEFNEKTNqlyARID 87 
                                       4555556678889999*******************9944445667788***************99887651116899 PP

                           Taxilin 114 diqaqieeksernek.lreenae..lteKlkslieqye......lreehfekllktkelelqlaeaKl.qqadallk 180
                                       di+++ +   +r+ + lr+e     +++  + l    e      +  +h e   ++ +le      Kl ++a+al +
  gi|330507880|ref|YP_004384308.1|  88 DIRKKYNLTGDRSIRdLRREIDHleFRQQTEVLSPDKEkqlvdkIASLHAEFKSRKEQLEKNEELRKLlDEAQALRD 164
                                       99999999999998845555444557777777766655443333333344555666666666666676145555566 PP

                           Taxilin 181 eeqekkkrekeyllkeakeltkkvkalketekelkeqlnlYaeKfeefqdtLakSnelFatFkkEmekmtkktkklE 257
                                       e+ + +    +y ++ a+e+++++ a  ++  + ++  +   + f + q++     + F + ++E+ +  k +  l+
  gi|330507880|ref|YP_004384308.1| 165 EASKHHDDVTKY-AELAQEYHDQMIATFKEADQTRAEADAAHKEFVKAQEAADEQHKEFIRTQREVRDFEKVIMGLK 240
                                       666666666666.999************************************************************* PP

                           Taxilin 258 ketnlwk 264
                                       k+++ +k
  gi|330507880|ref|YP_004384308.1| 241 KKNKDIK 247
                                       ***9988 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.048
                           Taxilin  19 kleaLvkkyae.lleerkrlqkqlkklkkkleqlqkekeqlqaelskaalaksK...LekLcRelqkqnkklkeesk 91 
                                       k+++L + y + +++  k+ +++  +++   ++  k +e+  +++++++ ++      ek    l k+nk +ke+  
  gi|330507880|ref|YP_004384308.1| 175 KYAELAQEYHDqMIATFKEADQTRAEADAAHKEFVKAQEAADEQHKEFIRTQREvrdFEKVIMGLKKKNKDIKEDRA 251
                                       67777777665244445555555555555556666666666666666655555445599999999999999999988 PP

                           Taxilin  92 qrareeeek 100
                                       + + + e++
  gi|330507880|ref|YP_004384308.1| 252 KEVAKREAE 260
                                       887766653 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 ?   10.8   8.1   0.00019       0.5      10      70 ..       6      66 ..       2      70 .. 0.74
   2 ?    1.1   0.1       0.2   5.2e+02       7      28 ..      73      94 ..      69      97 .. 0.86
   3 ?    8.9   7.7   0.00076       1.9      12      63 ..     100     154 ..      96     170 .. 0.79
   4 ?   -1.1   0.8      0.94   2.4e+03      30      53 ..     244     268 ..     209     279 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                          CCDC-167 10 eeklascrerLeaverrlrkeelseeeResle..eEeaslkeqleenekeLksLrkeNrksml 70
                                      eek  ++r+  e++ ++ r+ +l  e+ + +   +E+++ +++l ++ +eLk+Lr eN k+++
  gi|330507880|ref|YP_004384308.1|  6 EEKRGKLRQ--ESLAFKDRRSQLNAEASKWAAkrNELNKATKELIDKAQELKKLRDENNKNVA 66
                                      555544444..6777777777777777555546689999999999999*************97 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.2
                          CCDC-167  7 dkleeklascrerLeaverrlr 28
                                      d+ +ek+ +++ r++++ ++++
  gi|330507880|ref|YP_004384308.1| 73 DEFNEKTNQLYARIDDIRKKYN 94
                                      67899***********999876 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00076
                          CCDC-167  12 klascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeLk...sLrk 63 
                                       ++ ++r++++++e+r ++e ls+++ ++l +  asl  + ++  ++L+   +Lrk
  gi|330507880|ref|YP_004384308.1| 100 SIRDLRREIDHLEFRQQTEVLSPDKEKQLVDKIASLHAEFKSRKEQLEkneELRK 154
                                       68899********************999998888888888888888886664444 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.94
                          CCDC-167  30 eelseee.ResleeEeaslkeqlee 53 
                                       + + e++ +e +++E +++ ++ ++
  gi|330507880|ref|YP_004384308.1| 244 KDIKEDRaKEVAKREAEEILTHFRQ 268
                                       3333332244445566666665555 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  14.2   0.00093       2.4      35     146 ..       7     117 ..       2     130 .. 0.80
   2 ?    3.1  18.9     0.043   1.1e+02      53     150 ..     131     245 ..     123     281 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00093
                              Fez1  35 alkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleee 111
                                       + +++lr+ + + +++ ++++   ++   k +el++  +el  k +e + lr++ +k  +e k+ r+e++e++++ +
  gi|330507880|ref|YP_004384308.1|   7 EKRGKLRQESLAFKDRRSQLNAEASKWAAKRNELNKATKELIDKAQELKKLRDENNKNVAESKKHRDEFNEKTNQLY 83 
                                       5689999999999999999999999999***************************************9999665555 PP

                              Fez1 112 eaalesdeakaqrqeaeeleelkreverlraeLke 146
                                         + +  ++k + +  +++++l+re+++l+ + ++
  gi|330507880|ref|YP_004384308.1|  84 ARI-DDIRKKYNLTGDRSIRDLRREIDHLEFRQQT 117
                                       443.3334466666688999999999998765444 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.043
                              Fez1  53 eikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa............... 114
                                       +i +l++++++++++le+  +el++  +ea+ lr++++k ++++++  e ++e + +   ++               
  gi|330507880|ref|YP_004384308.1| 131 KIASLHAEFKSRKEQLEKN-EELRKLLDEAQALRDEASKHHDDVTKYAELAQEYHDQ---MIatfkeadqtraeada 203
                                       4556666666666666553.3566666666666666666666665554433332221...22112222333333333 PP

                              Fez1 115 ......lesdeakaqrqeaeeleelkreverlraeLkeerqk 150
                                             +++++a +q++e  +++++ r+ e++   Lk++++ 
  gi|330507880|ref|YP_004384308.1| 204 ahkefvKAQEAADEQHKEFIRTQREVRDFEKVIMGLKKKNKD 245
                                       333332444444555555555555555556655555554443 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  13.0   0.00029      0.75      12      93 ..      14      85 ..       2      96 .. 0.42
   2 ?    7.7   5.6    0.0016       4.1      26     103 ..      88     164 ..      83     172 .. 0.76
   3 ?    1.7  15.2      0.12   3.1e+02      15      90 ..     181     261 ..     170     275 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                                      HHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH 12 eespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkqqqkaqelqkkqqe 89
                                      +es ++           k+++ +l+a++ +  ++++el+k++k+l +k+++ ++l++++++  ++ ++ + e+++k ++
  gi|330507880|ref|YP_004384308.1| 14 QESLAF-----------KDRRSQLNAEASKWAAKRNELNKATKELiDKAQELKKLRDENNKNVAESKKHRDEFNEKTNQ 81
                                      444444...........55555555555555555555554444432222222223332222222222222444444444 PP

                                      HHHH CS
                              OmpH 90 llkp 93
                                      l+++
  gi|330507880|ref|YP_004384308.1| 82 LYAR 85
                                      4443 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  26 kkfkklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkqqqkaqelqkkqqellkpildkinka 101
                                       + +kk++ + ++  ++l+++++ l+ +++++  +++ke++l +k + l ++++ ++++l+k++  +l+++ld++++ 
  gi|330507880|ref|YP_004384308.1|  88 DIRKKYNLTGDRSIRDLRREIDHLEFRQQTEvLSPDKEKQLVDKIASLHAEFKSRKEQLEKNE--ELRKLLDEAQAL 162
                                       5566666666777788888888887777775449****************9999999999998..666689988876 PP

                                       HH CS
                              OmpH 102 ik 103
                                        +
  gi|330507880|ref|YP_004384308.1| 163 RD 164
                                       55 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHH........HHHHHHHHHHHHHHHHHH CS
                              OmpH  15 pegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkle.keekeqe........lqkkeqelqqkqqqkaqe 82 
                                       +e+ + +    k++ + +ae +a  ke+ k+qe+ +++ k+   ++++e          l+kk++++++    +a+e
  gi|330507880|ref|YP_004384308.1| 181 QEYHDQMIATFKEADQTRAEADAAHKEFVKAQEAADEQHKE-FiRTQREVRdfekvimgLKKKNKDIKE---DRAKE 253
                                       44444444445556788888888888888888888755555.243333333466676666666666666...33456 PP

                                       HHHHHHHH CS
                              OmpH  83 lqkkqqel 90 
                                       ++k+++e+
  gi|330507880|ref|YP_004384308.1| 254 VAKREAEE 261
                                       66666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3165  (0.17653); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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):               7  [number of targets reported over threshold]
# CPU time: 1.16u 0.34s 00:00:01.50 Elapsed: 00:00:00.51
# Mc/sec: 1686.74
//
Query:       gi|330507881|ref|YP_004384309.1|  [L=170]
Description: hypothetical protein MCON_1912 [Methanosaeta concilii GP6]
Scores for complete 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-14   52.7   0.0    7.9e-14   52.1   0.0    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 !   52.1   0.0   4.4e-18   7.9e-14       8     161 ..      18     165 ..      13     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 4.4e-18
                                       HHHHHTH..C..CHCTT-EEE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB-- CS
                           CGI-121   8 aelrkql..lskraeldfafldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgis 82 
                                       ++l++++  l+ r  + +  lda++++s+ h+l A+ +al+a ++ +   k +  Ei+ + s++++I+ al+ +g+s
  gi|330507881|ref|YP_004384309.1|  18 KDLISAIkdLQHRYGCIVQALDADKVVSNRHILFATEKALSAFSQRRNIAKDVGMEIMRYASGERQIERALN-MGVS 93 
                                       55566664455566666789***************************************************9.**** PP

                                       TT-S-EEEEEEESSS--HHHHHHHHHHHS-.SEEE--SHHHHHH--HHHHHHHTT--..TT---SSHHH.HHHHHHH CS
                           CGI-121  83 dkttsllvvkvssseadeeevlkslkevve.gelvpleeeleeltdwkkikkiYklneleeekeeevke.ledlvvs 157
                                       dkt+++ +v  s +         +  + +e   l++++  l+  +  + +k++++++  ++e ++  ++ +edlv++
  gi|330507881|ref|YP_004384309.1|  94 DKTERIALVLASLE------GQCNWPDEIElSRLLKPDG-LGCSCRYNAVKEVFNIS--SAELDSVGEDrIEDLVIE 161
                                       ***********998......3455556666345567888.888899***********..55555555667******* PP

                                       HHHT CS
                           CGI-121 158 aval 161
                                       +val
  gi|330507881|ref|YP_004384309.1| 162 RVAL 165
                                       **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1226.01
//
Query:       gi|330507882|ref|YP_004384310.1|  [L=199]
Description: hypothetical protein MCON_1913 [Methanosaeta concilii GP6]
Scores for complete 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-66  223.8   2.9    1.9e-66  223.6   2.9    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 !  223.6   2.9   1.1e-70   1.9e-66       1     188 []       4     189 ..       4     189 .. 0.99

  Alignments for each domain:
  == domain 1  score: 223.6 bits;  conditional E-value: 1.1e-70
                           DUF2150   1 eFYteeRwqNWlnrvkeedldleedseeleaavllnlqdDvilavlkiikaveeeelskeeAleeleevreivleev 77 
                                       eFYt++Rw NW+n+vk+++++l+e+++++++av+++++dDv+la+lk+i+++e+e +s+eeAl+++e++r+iv++e+
  gi|330507882|ref|YP_004384310.1|   4 EFYTQKRWLNWMNKVKDSNFKLTESDDKNSGAVFIYIMDDVVLACLKVIARFEREIISAEEALDDIEAIRSIVFQEH 80 
                                       7*************************9999*********************************************** PP

                           DUF2150  78 eeddeekeeliesvqtsllvvfaaaeeyieggvakekdieelvkaaaeaeaeedleaaleivaqiGakvidgeklpe 154
                                       e+  e+++ +ies++tsl++vf+++++yi+g++++e++++elv +a++ae++e+l++a+++++q+Ga+vi ge+lpe
  gi|330507882|ref|YP_004384310.1|  81 ESLGEDADLMIESLKTSLAAVFVSSQRYITGSFDRESPLDELVARAVAAEEKENLDEAFDLLSQVGARVIGGENLPE 157
                                       ***************************************************************************** PP

                           DUF2150 155 kvledleyglvaewldgidslaaamsssesveee 188
                                         + +l+y++ ae++dgid+++aam +++s+++e
  gi|330507882|ref|YP_004384310.1| 158 --IGELPYCMTAELMDGIDAISAAMIGDDSYKDE 189
                                       ..79****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1406.06
//
Query:       gi|330507883|ref|YP_004384311.1|  [L=293]
Description: methionine aminopeptidase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-38  132.6   0.0    1.9e-38  132.3   0.0    1.2  1  Peptidase_M24  Metallopeptidase family M24
  ------ inclusion threshold ------
       0.16   10.6   0.0       0.24   10.0   0.0    1.2  1  ILVD_EDD       Dehydratase family


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.3   0.0   2.1e-42   1.9e-38       2     207 ..       8     281 ..       7     283 .. 0.78

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 2.1e-42
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC..SSSB--TTEE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp..ndrvlkegdl 76 
                                       ++rka+ri +++l+++  ++  gv   e+a+++e++  +r  ++ +afp  + ++   +++hytp   d+++ ++ +
  gi|330507883|ref|YP_004384311.1|   8 NYRKAGRILAEVLQEARPKVDVGVPLLEVAEFVEEA--IRSKGGLPAFP--CNISLDRSAAHYTPspKDESVFAENM 80 
                                       79**************988***************99..66667789***..5556666666**885446667788** PP

                                       EEEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCS CS
                     Peptidase_M24  77 vlidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphgl 153
                                       v++d+g+++dgy++D + T+ +G     +++l+ a +++++aa+++v pGv++++i+ a++e ++ +g+ k++ +++
  gi|330507883|ref|YP_004384311.1|  81 VKLDVGVHVDGYIADAAITIDLG----GHEDLVLASRAGLDAALELVGPGVSTADIGGAIEEAITGYGY-KPVYNLT 152
                                       ********************776....2467**************************************.******* PP

                                       EEEESS.SSSEEEEEESS.STTCSSB--TTBEEEEEE...............EEEEETTT................. CS
                     Peptidase_M24 154 GHgvGl.evhdegpsvsr.esndgrkleeGmvftiEp...............giyfapge................. 196
                                       GHg+ +   hd  p v++ + ++g+ l+eG+v++iEp               +iy                      
  gi|330507883|ref|YP_004384311.1| 153 GHGLSRyIAHDQ-PAVPNkRMDKGVILKEGDVIAIEPfatngsgriseapitEIYG---Fggsrpqrlpaaralmke 225
                                       *****9899999.**986344499*************7777665544444443332...133345555555566666 PP

                                       ............................................E.EEEEBEEEEE CS
                     Peptidase_M24 197 ............................................g.gvriedtvlv 207
                                                                                     + + e+tvl+
  gi|330507883|ref|YP_004384311.1| 226 ivesyktlpfarrwlkaeraeyalmhlvrsgavhgypvlwevegAlVSQAEHTVLI 281
                                       66666666666666777777777777777777777777777776346677777766 PP

>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   2.6e-05      0.24      18      86 ..      31     100 ..      19     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 2.6e-05
                          ILVD_EDD  18 vhlkelaeavkegveeaggvpaefntigvsDgiamgeegmr.ysLpsReliadsvetmleaqllDalvli 86 
                                       v+l e+ae v+e+++++gg+pa    i+++   a  +   +  s +  +++  +v +++ ++ +Da+++i
  gi|330507883|ref|YP_004384311.1|  31 VPLLEVAEFVEEAIRSKGGLPAFPCNISLDRSAAHYTPSPKdESVFAENMVKLDVGVHVDGYIADAAITI 100
                                       67899*****************9999999666666665555699999********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2355.75
//
Query:       gi|330507884|ref|YP_004384312.1|  [L=381]
Description: peptidase M24 [Methanosaeta concilii GP6]
Scores for complete 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   0.2    2.7e-42  144.8   0.2    1.1  1  Peptidase_M24    Metallopeptidase family M24
    1.5e-05   25.7   0.0    2.7e-05   24.9   0.0    1.3  1  Creatinase_N     Creatinase/Prolidase N-terminal domain
  ------ inclusion threshold ------
       0.17   11.4   0.0       0.31   10.6   0.0    1.3  1  GTP_cyclohydro2  GTP cyclohydrolase II


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 !  144.8   0.2   4.6e-46   2.7e-42       2     208 ..     149     365 ..     148     366 .. 0.89

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 4.6e-46
                                       HHHHHHHHHHHHHHHHHHHHH...T.T.........CBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTB CS
                     Peptidase_M24   2 lirkaariasaaleavleaik...p.g.........vterelaaeieattlkrhgarglafppivasgenaavlhyt 65 
                                       +i  a+r++++a+++++e i    p g          t +++  +i+   l + g+   a ++iva g+ aa +h++
  gi|330507884|ref|YP_004384312.1| 149 CITTAQRACERAMQRAVELIAcsePrGdtlylqgqpLTAEQIRSAIDIS-LLQDGC--EAADTIVAGGTQAAEPHAR 222
                                       7889************988774443424444444446999999999944.566565..5669**************9 PP

                                       CSSSB--TTEEEEEEEEEEET..TEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHH CS
                     Peptidase_M24  66 pndrvlkegdlvlidagaeyd..gyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevl 140
                                         + +l ++ +++id+ ++ +  +y++D+trTvl G+   e +ely avl+aqea+i a++ G++++e++aa+ +v+
  gi|330507884|ref|YP_004384312.1| 223 G-TGPLPANSPIVIDIYPRSKthRYYADMTRTVLRGEAPGEVKELYHAVLAAQEAGIGAIRSGISGEEVHAAVSAVF 298
                                       9.59**************99999*************8888************************************* PP

                                       HHTTB....CCGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                     Peptidase_M24 141 esagl....akffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                       +++g+    +  f+h++GHgvGl+vh+  ps+s  ++ g+ l+  +v+t+Epg+y  p+ ggvr+ed+++v+
  gi|330507884|ref|YP_004384312.1| 299 QEMGYserdGCGFTHSTGHGVGLDVHEL-PSLS--EG-GEILKSSQVVTVEPGLY-YPDIGGVRLEDLLVVR 365
                                       ***9999999999*************98.**99..45.9****************.99************98 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   4.4e-09   2.7e-05       8     114 ..       8     126 ..       3     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.4e-09
                                       HHHHTT-SEEEEECC....HHHHHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH.TTSEEEEEST.... CS
                      Creatinase_N   8 lmeekgldallvtsp....enlrYltGfatetgsrglalvvtadgalllvdalryteaaeesatveevveydd.... 76 
                                       +++  ++d++l   +    ++++Yl+ f   +g r+++l ++ +++++lv +++  +a++es   +ev++ +d    
  gi|330507884|ref|YP_004384312.1|   8 FLDSSNIDGFLFVGDsisnSDMYYLSHF--LAGDRFAIL-FQ-EKTSILVSSMEKSRAKKES-CADEVLSTRDyhim 79 
                                       67777888888766667779********..899999999.54.455788888**********.8888888888899* PP

                                       ........HSSHHHHHHHHHHHHT..-EEEE-TTSSBHHHHHHHHHHC CS
                      Creatinase_N  77 ........pvealadllkellese..krvgveldaltvafyealkeal 114
                                               p+ a++++lk+ l +    r+gv  + ++ + ++ l  ++
  gi|330507884|ref|YP_004384312.1|  80 eklkscgkPELAYIEALKDFLRDHdvLRLGVAYS-FPIGIFQPLSRHF 126
                                       ********77777777777777766699999887.7888888877665 PP

>> GTP_cyclohydro2  GTP cyclohydrolase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.2e-05      0.31      51     121 ..     148     222 ..     134     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.2e-05
                                       HHS-B--TTTTTHHHHHHHHH.HHH-.EEEEEE-.-TTTTTHHHHHHHHHHHHH..CT--HHHHHHHHT--S--- CS
                   GTP_cyclohydro2  51 Dvlgslrcdcgeqldealeli.aeegrGvlvylr.qegrgigllnklkayalqd..eglDTveanlalglpadar 121
                                       D + +++  c+  +++a+eli  +e rG  +yl+ q     ++ + ++   lqd  e +DT+ a   +  +++ar
  gi|330507884|ref|YP_004384312.1| 148 DCITTAQRACERAMQRAVELIaCSEPRGDTLYLQgQPLTAEQIRSAIDISLLQDgcEAADTIVAGGTQAAEPHAR 222
                                       88899999*************86799********99999999999999999999777999999988888877777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2746.87
//
Query:       gi|330507885|ref|YP_004384313.1|  [L=252]
Description: geranylgeranylglyceryl phosphate synthase [Methanosaeta concilii GP6]
Scores for complete 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-62  209.0   0.0    7.5e-62  208.7   0.0    1.0  1  PcrB            PcrB family
    0.00023   20.7   0.1    0.00037   20.0   0.1    1.3  1  His_biosynth    Histidine biosynthesis protein
    0.00023   20.5   0.4    0.00037   19.8   0.4    1.2  1  DHO_dh          Dihydroorotate dehydrogenase
    0.00037   19.7   1.1      0.084   12.1   0.1    2.3  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
  ------ inclusion threshold ------
       0.01   14.9   0.6      0.067   12.2   0.8    2.0  2  FMN_dh          FMN-dependent dehydrogenase
      0.014   14.8   4.3      0.028   13.7   0.6    2.1  2  ThiG            Thiazole biosynthesis protein ThiG
      0.026   13.6   5.0       0.87    8.6   0.7    2.1  2  Glu_synthase    Conserved region in glutamate synthase
      0.037   13.4   0.5      0.069   12.5   0.5    1.4  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
      0.074   12.0   0.9        0.3   10.0   0.3    1.9  2  IMPDH           IMP dehydrogenase / GMP reductase domain
       0.21   10.7   0.1       0.36   10.0   0.1    1.4  1  IGPS            Indole-3-glycerol phosphate synthase


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 !  208.7   0.0   4.2e-65   7.5e-62       7     217 ..      19     239 ..      13     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 208.7 bits;  conditional E-value: 4.2e-65
                                       S...EEEEE-TTSS-CHHHHHHH...HCTT-SEEEEECST...CHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TT CS
                              PcrB   7 r...hltklDPeeenpdEiveiv...iesgtDavmigGsq...svtldntvrllkkvsriklPivlepsnvegvvry 74 
                                       +   hlt++DP+ ++p+E+ +++    ++gtDa+m+gGs    ++ l ntv  +kkv  ++lP++l+p+ v g+ ++
  gi|330507885|ref|YP_004384313.1|  19 HgagHLTLIDPDSQTPQEAGRMAqaaSQGGTDAIMVGGSVgatGALLHNTVAEIKKV--TDLPVILFPASVAGLCEN 93 
                                       3456**************8554444399***********95556679**********..****************** PP

                                       SSEEEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHHHH CS
                              PcrB  75 aDalFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayallaak 150
                                       aDa+F+msllns  +++++  +a g+  v ++   +e+l+++Y+++eP+++v++v++a+ +++ k+++a +++la k
  gi|330507885|ref|YP_004384313.1|  94 ADAVFFMSLLNSRSPNYLIENQAMGAPLVLRYR--LEALPMAYIIIEPGGTVGYVGDARlIPRKKPELACAYALAGK 168
                                       *********************************..****************************************** PP

                                       HTT-SEEEEE-.TTSSS-H.HHHHHH.HHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHHC CS
                              PcrB 151 llglrliYlEa.sGaledv.eevial.kkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekder 217
                                       +lg+rl+YlEa sGa  +v   ++al kk l +  +ivGGGirs+  A+e v a AD iv+G++ve++++ 
  gi|330507885|ref|YP_004384313.1| 169 YLGMRLVYLEAgSGADSPVpAGMVALtKKLLGDVLIIVGGGIRSGRAAAELVAAgADLIVTGTAVEKSQDV 239
                                       *******************966666615556788899*****************************99854 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   2.1e-07   0.00037      74     115 ..     202     243 ..     174     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.1e-07
                                       SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHH CS
                      His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaavknpelikel 115
                                       + + vGGGIrs  +++el+ agad ++ gta+ k+ ++ + +
  gi|330507885|ref|YP_004384313.1| 202 VLIIVGGGIRSGRAAAELVAAGADLIVTGTAVEKSQDVASFI 243
                                       6799**************************999888876555 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.4   2.1e-07   0.00037     236     279 ..     193     236 ..     187     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.1e-07
                                       HHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHH CS
                            DHO_dh 236 elykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfe 279
                                       +l k+l +++ iI  GGi sg+ a e + aGA l+  +ta+ ++
  gi|330507885|ref|YP_004384313.1| 193 ALTKKLLGDVLIIVGGGIRSGRAAAELVAAGADLIVTGTAVEKS 236
                                       577788889*******************************9654 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 !    6.4   0.1    0.0026       4.7       3      36 ..      39      81 ..      37      83 .. 0.75
   2 !   12.1   0.1   4.7e-05     0.084     135     185 ..     193     242 ..     177     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0026
                                      HHHHHHHHHT-SEEEEES.H........HHHHHHHTT--S-EE CS
                              NanE  3 amakaaeqaGavgirieg.v........edikaikavvdlPii 36
                                       ma+aa+q+G+ +i + g v        + +++ik+v+dlP+i
  gi|330507885|ref|YP_004384313.1| 39 RMAQAASQGGTDAIMVGGsVgatgallhNTVAEIKKVTDLPVI 81
                                      69********999998763233333444678999999999998 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.7e-05
                                       HHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHH CS
                              NanE 135 alvkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrleeiakk 185
                                       al k+l+  ++ +i+ G i +   a++ +  G+d++v G+a+ + +++a+ 
  gi|330507885|ref|YP_004384313.1| 193 ALTKKLLG-DVLIIVGGGIRSGRAAAELVAAGADLIVTGTAVEKSQDVASF 242
                                       55666654.5679999****************************9999874 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.17   3.1e+02     200     221 ..      61      82 ..       9     116 .. 0.70
   2 ?   12.2   0.8   3.7e-05     0.067     266     302 ..     196     232 ..     184     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.17
                                       -TC--HHHHHHHHHHHSSEEEE CS
                            FMN_dh 200 dpsltwddikwlreqtklplvv 221
                                       + +l  ++++++++ t+lp+++
  gi|330507885|ref|YP_004384313.1|  61 TGALLHNTVAEIKKVTDLPVIL 82 
                                       4556667788888888888875 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.7e-05
                                       HHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
                            FMN_dh 266 eavggrievlvDgGirrGsDvlkAlalGAdavllGRp 302
                                       +++ g++ ++v gGir+G  ++  +a GAd+++ G +
  gi|330507885|ref|YP_004384313.1| 196 KKLLGDVLIIVGGGIRSGRAAAELVAAGADLIVTGTA 232
                                       55567999************************99966 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   0.2     0.045        80     137     194 ..      41     100 ..      33     104 .. 0.70
   2 ?   13.7   0.6   1.6e-05     0.028     167     217 ..     191     243 ..     175     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.045
                                       HHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEE....ES---SHHHHHHHH CS
                              ThiG 137 arrleevGcaavmPlaapiGsglGllnkealkiiieeakvPviv....DAGigspsdaaqam 194
                                       a++  + G+ a+m  +  +G+  G l ++++  i + +++Pvi+     AG+ +  da+  m
  gi|330507885|ref|YP_004384313.1|  41 AQAASQGGTDAIMVGG-SVGA-TGALLHNTVAEIKKVTDLPVILfpasVAGLCENADAVFFM 100
                                       5666677899999655.5675.4666667788899999999998433347777777776666 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.6e-05
                                       HHHHHHH-..SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHH CS
                              ThiG 167 lkiiieea..kvPvivDAGigspsdaaqamelGadavllntavaeakdpvamA 217
                                       +  +++++  +v +iv  Gi+s   aa+ +  Gad ++  tav +++d ++  
  gi|330507885|ref|YP_004384313.1| 191 MVALTKKLlgDVLIIVGGGIRSGRAAAELVAAGADLIVTGTAVEKSQDVASFI 243
                                       5555566557999***********************************98765 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 ?    7.0   0.3    0.0015       2.7     216     246 ..      37      67 ..      32      95 .. 0.72
   2 ?    8.6   0.7   0.00049      0.87     269     305 ..     196     232 ..     179     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHTT-SEEEEE-TT---SSEEHH CS
                      Glu_synthase 216 vetiaagvakanadiilidGleGGTGAspks 246
                                       ++ +a  ++++++d+i++ G+ G TGA  ++
  gi|330507885|ref|YP_004384313.1|  37 AGRMAQAASQGGTDAIMVGGSVGATGALLHN 67 
                                       5667777999*****************6543 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00049
                                       TT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHH CS
                      Glu_synthase 269 eglrdrvsliadGglktgadvvkalalGAdavgigta 305
                                       ++l   v +i+ Gg+++g+  +  +a GAd + +gta
  gi|330507885|ref|YP_004384313.1| 196 KKLLGDVLIIVGGGIRSGRAAAELVAAGADLIVTGTA 232
                                       45666799************************99997 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 ?   12.5   0.5   3.8e-05     0.069     166     197 ..     201     233 ..     191     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.8e-05
                                       --EEEEESS--T.TTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 166 dlkievDGGvkl.dnieqiaeagadvlVagsav 197
                                       d+ i v GG++   +++++++agad++V+g+av
  gi|330507885|ref|YP_004384313.1| 201 DVLIIVGGGIRSgRAAAELVAAGADLIVTGTAV 233
                                       7999******873578899************98 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.16   2.9e+02     109     142 ..      41      75 ..      29      89 .. 0.60
   2 ?   10.0   0.3   0.00017       0.3     136     173 ..     192     230 ..     171     246 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.16
                                       HHHHHHTT-SEEEEE-STSSSHHH.HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                             IMPDH 109 vkalveagvdvlvvdsahghsekv.leavkeikkk 142
                                       ++a  + g d+++v  + g +     ++v+eikk 
  gi|330507885|ref|YP_004384313.1|  41 AQAASQGGTDAIMVGGSVGATGALlHNTVAEIKKV 75 
                                       44455556666666666665544313556666654 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00017
                                       HHHHHHHTTT.SEEEEEEE-SHHHHHHHHHTT-SEEEE- CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 136 vkeikkkvee.veviaGnvataegakaLieagadavkvG 173
                                       v+  kk + + + +++G + +  +a++L++agad +  G
  gi|330507885|ref|YP_004384313.1| 192 VALTKKLLGDvLIIVGGGIRSGRAAAELVAAGADLIVTG 230
                                       444555555533444566666666666666666655444 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1    0.0002      0.36     201     254 .]     193     246 ..     189     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0002
                                       HHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHHH CS
                              IGPS 201 eLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekairel 254
                                        L+k++  dvl++   Gi++   + +l ++g++ +  G+++ +++dv+ +i el
  gi|330507885|ref|YP_004384313.1| 193 ALTKKLLGDVLIIVGGGIRSGRAAAELVAAGADLIVTGTAVEKSQDVASFISEL 246
                                       68899999******************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1821.68
//
Query:       gi|330507886|ref|YP_004384314.1|  [L=49]
Description: hypothetical protein MCON_1917 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-05   24.3   4.3    2.5e-05   24.1   4.3    1.2  1  Ribosomal_L40e  Ribosomal L40e family
    0.00036   20.2   4.1    0.00055   19.6   4.1    1.3  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
    0.00097   18.8   2.2     0.0015   18.2   2.2    1.3  1  zinc_ribbon_2   zinc-ribbon domain
     0.0017   18.4   0.5     0.0017   18.4   0.5    1.2  1  DZR             Double zinc ribbon
     0.0099   16.0   2.2      0.012   15.7   2.2    1.3  1  Ribosomal_L37e  Ribosomal protein L37e
  ------ inclusion threshold ------
      0.025   14.7   1.0      0.036   14.1   1.0    1.3  1  UPF0547         Uncharacterised protein family UPF0547


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 !   24.1   4.3   8.5e-09   2.5e-05      16      47 ..      14      42 ..       7      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 8.5e-09
                    Ribosomal_L40e 16 KmiCrkCYArlpprAtnCrkkkCghsnnlrpK 47
                                       +iC +C Ar p++At Cr  kCg  + lr+K
  gi|330507886|ref|YP_004384314.1| 14 LKICMRCNARNPVKATRCR--KCGY-EGLRMK 42
                                      58*****************..9*96.445555 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 !   19.6   4.1   1.8e-07   0.00055       2      25 ..      16      36 ..      16      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.8e-07
                                      B-SSS--B----SSS----SSS-- CS
                    DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCGh 25
                                      iC++C+a++ +k++   RC++CG+
  gi|330507886|ref|YP_004384314.1| 16 ICMRCNARNPVKAT---RCRKCGY 36
                                      8*************...******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 !   18.2   2.2   4.9e-07    0.0015       2      22 ..      17      37 ..      16      38 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.9e-07
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      C +C a ++ +a+ C +CG++
  gi|330507886|ref|YP_004384314.1| 17 CMRCNARNPVKATRCRKCGYE 37
                                      *******************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.5   5.6e-07    0.0017      28      49 .]      14      35 ..       2      44 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.6e-07
                               DZR 28 edrCpsCgekvdpearfCpeCG 49
                                       + C++C++ ++ +a+ C +CG
  gi|330507886|ref|YP_004384314.1| 14 LKICMRCNARNPVKATRCRKCG 35
                                      5678888888888888888887 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   2.2   4.2e-06     0.012      18      46 ..      16      43 ..       8      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.2e-06
                    Ribosomal_L37e 18 lCrrCgkrsyhvqkktCascGypsaklrk 46
                                      +C rC+ r   v+ ++C +cGy   ++++
  gi|330507886|ref|YP_004384314.1| 16 ICMRCNARN-PVKATRCRKCGYEGLRMKS 43
                                      7*****997.79999*******9999986 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.0   1.2e-05     0.036       2      23 ..      16      37 ..      14      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                           UPF0547  2 vCPeCeakvPvaaqfCphCGyv 23
                                       C +C a  Pv a +C+ CGy+
  gi|330507886|ref|YP_004384314.1| 16 ICMRCNARNPVKATRCRKCGYE 37
                                      577999999************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 380.03
//
Query:       gi|330507887|ref|YP_004384315.1|  [L=411]
Description: NAD-dependent malic enzyme [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-30  105.6   0.1      7e-23   81.4   0.1    2.4  2  malic          Malic enzyme, N-terminal domain
      6e-23   81.4   3.7    9.6e-22   77.5   3.5    2.8  2  Malic_M        Malic enzyme, NAD binding domain
    3.7e-05   23.6   0.0    8.8e-05   22.3   0.0    1.6  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
  ------ inclusion threshold ------
      0.013   14.7   0.1      0.026   13.8   0.1    1.6  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      0.018   14.3   0.4      0.048   13.0   0.4    1.7  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.027   13.8   0.1      0.087   12.2   0.0    1.9  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      0.053   12.9   0.8       0.13   11.6   0.8    1.6  1  ThiF           ThiF family


Domain annotation for each model (and alignments):
>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.1   2.7e-26     7e-23       4     116 ..      18     109 ..      15     113 .. 0.91
   2 !   22.5   0.0   3.2e-08   8.1e-05     145     182 .]     111     148 ..     108     148 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 2.7e-26
                                       ECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSBTT CS
                             malic   4 netlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeriLG 80 
                                       + +  + +++++  ++l+++YtP+v+++c+e+++++++++  y+++++                 v+vvtdg+++LG
  gi|330507887|ref|YP_004384315.1|  18 IAVHSKVPCATS--RDLSLAYTPGVAAPCREIERNPDDVY-RYTAKGNL----------------VAVVTDGTAVLG 75 
                                       555666666666..9*************************.********................************ PP

                                       TBS-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEEC CS
                             malic  81 lGdlG.vagvgimvGKlaLytalagidPekvlpvvld 116
                                       lGd+G +a++++m+GK++L++ +agid   ++p+++ 
  gi|330507887|ref|YP_004384315.1|  76 LGDIGaLASIPVMEGKAILFKNFAGID---AFPIAVA 109
                                       ***************************...9999886 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 3.2e-08
                                       HHHHHHHHHHHHHHGCTSEEEE-S--CCHHHHHHHHHC CS
                             malic 145 efvdefveavkelfppkaliqfEDfkaknafeileryr 182
                                       ++ +++v++v+ ++p +++i++ED++a+++fe++er++
  gi|330507887|ref|YP_004384315.1| 111 KDPEDIVRTVAMIEPVFGGINLEDISAPRCFEVEERLK 148
                                       57899******************************986 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.58   1.5e+03     145     168 ..      42      65 ..      39      68 .. 0.87
   2 !   77.5   3.5   3.7e-25   9.6e-22       3     257 ..     162     380 ..     160     381 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.58
                                       SSGGGSSS-HHHHHHHTTT-SEEE CS
                           Malic_M 145 NPtskaEataedvlkwtdgkalva 168
                                        P +++E  ++dv+++t    lva
  gi|330507887|ref|YP_004384315.1|  42 APCREIERNPDDVYRYTAKGNLVA 65 
                                       689999***********9888887 PP

  == domain 2  score: 77.5 bits;  conditional E-value: 3.7e-25
                                       HHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S--- CS
                           Malic_M   3 gTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekle 79 
                                       gTa+vala+l++al++ gk +++ k+ v GaG+ag+ +++ +++     G      +k++ l D++G+++++r +l+
  gi|330507887|ref|YP_004384315.1| 162 GTAVVALAALINALRLVGKDFRDLKVAVSGAGAAGVAVTKFLLSF----G------AKDVILCDSRGVIHKSRPDLN 228
                                       9***********************************999887764....4......57899**************** PP

                                       TTTGGGSBS--SS--S....SHHHHHHHH--SEEEE-SSSSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS-HHH CS
                           Malic_M  80 eekkpfakkkeelkeakdkltLeevvkkvkptvliGlsgvagafteeivremaksterPiilplSNPtskaEataed 156
                                       + k++ a  ++  +    + tL+++++   ++v +Gls vag+ t ++v +ma      +++++ NP    E ++e 
  gi|330507887|ref|YP_004384315.1| 229 PSKQKIAALTNPRNV---TGTLADAIRG--ADVFLGLS-VAGIVTPDMVSSMAGD---AVVFAMANPEP--EIMPEL 294
                                       *****9999988874...479*****97..69*****8.789**********986...59*******75..778886 PP

                                       HHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHHHHTT CS
                           Malic_M 157 vlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseeelkeg 233
                                       +l    g+++va+G          +  +++Q NN++ fPg+  g++ +ra+ i+++m +aa++a+a+lv++ +   +
  gi|330507887|ref|YP_004384315.1| 295 AL--EAGAVVVATG----------RSDYPNQVNNVLGFPGIFRGALDVRASDINEHMKMAASRAIASLVENVTR--E 357
                                       65..5799****98..........56789****************************************88775..5 PP

                                       -SS--GGGHHHHHHHHHHHHHHHH CS
                           Malic_M 234 sllPelseirevslkvavavakaa 257
                                        + P+  + r v  +va ava+aa
  gi|330507887|ref|YP_004384315.1| 358 CIIPSPLD-RRVVPAVAEAVARAA 380
                                       78886544.567778888888877 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 !   22.3   0.0   3.4e-08   8.8e-05      15      75 ..     168     230 ..     156     263 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.4e-08
                                       HHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETT.EE..- CS
                     ELFV_dehydrog  15 vyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpe.Gl..d 75 
                                       ++++ ++l+ ++  ++++ +va+sG G  g ++ ++l + gak v + Ds+Gvi+++   l  +
  gi|330507887|ref|YP_004384315.1| 168 LAALINALRLVGK-DFRDLKVAVSGAGAAGVAVTKFLLSFGAKDVILCDSRGVIHKSRpDLnpS 230
                                       4444445555444.6***************************************9654133453 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 ?   13.8   0.1     1e-05     0.026       2     119 ..     186     323 ..     185     387 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1e-05
                                       SEEEE--SHHHHHHHHHHHHH.TS-EEEEETTHCHHHCSHHH...HCHHHHHHHHHHHHH...............HH CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx...............xx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqa.gakvtlvelegtclnggcll...skallgvaedaeias...............ev 59 
                                       +v+v G+G+AG+a+ ++l      +v+l++++g ++  ++ l   ++++++   ++++                   
  gi|330507887|ref|YP_004384315.1| 186 KVAVSGAGAAGVAVTKFLLSFgAKDVILCDSRGVIHKSRPDLnpsKQKIAALTNPRNVTGtladairgadvflglS- 261
                                       79999***************725679999*********99996644455555555555556666555443332221. PP

                                       HHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC...TCEEEEEESEEEE---E......EE-BCTCTTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx......xxxxxxxxxx RF
                       Pyr_redox_2  60 vkklnqgielllgeevvkidpgkkkvklekkke...gdeekiaydklvlAtGs......sprdlgipGv 119
                                              +  + +   v+   g + v   ++ e     e  ++++++v+AtG        ++ lg pG 
  gi|330507887|ref|YP_004384315.1| 262 -------VAGIVTPDMVSSMAGDAVVFAMANPEpeiMPELALEAGAVVVATGRsdypnqVNNVLGFPGI 323
                                       .......2222222233333444333333333377767789999********42544433334455555 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 ?   13.0   0.4   1.9e-05     0.048      28     128 ..     184     284 ..     171     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                                       --EEEEESTSHHHHHHHHHHHHTT-E.EEEEESSHHHHHHHHH...TTTCECEE...HCHHHHHHHHHHHH-SEEEE CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgak.VtvlDvrparleqles...lgakfvev...lksqeellaeavkeadvvig 97 
                                         kv v G+G aG++  +   ++gak V ++D r    +   +    ++k + +    ++   +la+a++ adv   
  gi|330507887|ref|YP_004384315.1| 184 DLKVAVSGAGAAGVAVTKFLLSFGAKdVILCDSRGVIHKSRPDlnpSKQK-IAAltnPRNVTGTLADAIRGADVF-- 257
                                       569*********************9649999**99888888884434444.444222333344566666666665.. PP

                                       ---BTTSS---SC-HHHHHTS-TTEEEEETT CS
                       AlaDh_PNT_C  98 tvlipGkkaPkLvteemvksMkpgsVivDvA 128
                                            G + + +vt +mv+sM   +V+  +A
  gi|330507887|ref|YP_004384315.1| 258 ----LGLSVAGIVTPDMVSSMAGDAVVFAMA 284
                                       ....56678889999*******999997666 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.94   2.4e+03      40      49 ..      72      81 ..      62      84 .. 0.85
   2 ?   12.2   0.0   3.4e-05     0.087      27      68 ..     175     217 ..     154     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.94
                                      EEES-SHHHH CS
                      2-Hacid_dh_C 40 GiiGlGrIGq 49
                                      +++GlG+IG 
  gi|330507887|ref|YP_004384315.1| 72 AVLGLGDIGA 81
                                      799******6 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.4e-05
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSS CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrs 68 
                                        +l gk+ ++ +v++ G+G+ G av k l +fg+ +vi  d +
  gi|330507887|ref|YP_004384315.1| 175 LRLVGKDFRDLKVAVSGAGAAGVAVTKFLLSFGAkDVILCDSR 217
                                       568899****************************678888876 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8     5e-05      0.13      14      49 ..     180     215 ..     162     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5e-05
                                       HHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  14 ekLrdskvllvGaGglGsellknLalsGvgkltlvD 49 
                                       +  rd kv++ GaG+ G  + k L   G + + l D
  gi|330507887|ref|YP_004384315.1| 180 KDFRDLKVAVSGAGAAGVAVTKFLLSFGAKDVILCD 215
                                       67899**************************99999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3126.76
//
Query:       gi|330507888|ref|YP_004384316.1|  [L=317]
Description: homoisocitrate dehydrogenase [Methanosaeta concilii GP6]
Scores for complete 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-92  308.7   0.0    1.4e-91  307.3   0.0    1.6  1  Iso_dh        Isocitrate/isopropylmalate dehydrogenase
  ------ inclusion threshold ------
       0.16   12.1   0.0       0.28   11.2   0.0    1.4  1  Antirestrict  Antirestriction protein


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 !  307.3   0.0   1.5e-95   1.4e-91       5     348 .]       2     308 ..       1     308 [. 0.96

  Alignments for each domain:
  == domain 1  score: 307.3 bits;  conditional E-value: 1.5e-95
                                       EEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSSSSH CS
                            Iso_dh   5 legdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkekevrp 81 
                                       + gdgiGpevve+al+vl+aa     ++l++ ++++G    ++tge++ e+ le i   d +llga++tp + + r+
  gi|330507888|ref|YP_004384316.1|   2 IAGDGIGPEVVESALEVLRAAG----ASLDLVHFEIGLGRWKRTGEAMDEDDLEEISGCDCILLGAITTPPDPNYRS 74 
                                       89******************99....6799*****************************************999998 PP

                                       HHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEEEEE CS
                            Iso_dh  82 engLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtklys 158
                                           l+Lr+ ldl+an+rp ++                ++d++ivRe+t+g+Y+g e++  ++        ++ +++
  gi|330507888|ref|YP_004384316.1|  75 VL--LRLRRALDLYANIRPFQSH---------------DLDFIIVRENTEGLYSGVEEVGVEE------SRTLRVIT 128
                                       76..99*************9998...............48****************9988774......789***** PP

                                       HHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHHHHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGGSEE CS
                            Iso_dh 159 eeeieriaraafelAlkrgkkkvtlvdKanvlksselwrkiveevaeeeypdielehqlvDsaamqlvkspkqfdVi 235
                                       ++++eria+aa++lA +r   ++t+++K+nvl+s +l+ +++ evae    +i +e++lvD+aa++lv++p++fdV+
  gi|330507888|ref|YP_004384316.1| 129 RRGSERIAEAACDLAARR--RRLTIIHKSNVLRSDRLFLQTCREVAE--RRGILYEDMLVDAAAYNLVTNPQRFDVL 201
                                       ***************998..99***********************99..89************************** PP

                                       EE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT-HHHHH CS
                            Iso_dh 236 vtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLryslgleeaAd 312
                                       vt+NlfGDilSDeaa ++GslGl +Sa+lg k+ a+fE++HGsapdiagk++aNp+++i Saa+m+r  lg+ eaA 
  gi|330507888|ref|YP_004384316.1| 202 VTTNLFGDILSDEAAGVIGSLGLCASANLG-KSRALFEPIHGSAPDIAGKGIANPVGAIRSAAMMMRW-LGELEAAG 276
                                       ******************************.689**********************************.******** PP

                                       HHHHHHHHHHHHTSCCHHHCTTSTCCCHHHHHHHHH CS
                            Iso_dh 313 kiekAvekvleagivTkDlageaakevstsefgdav 348
                                       ++e+Av+k+l ag++T Dl+g      stse++ av
  gi|330507888|ref|YP_004384316.1| 277 RMEEAVKKALSAGVRTPDLGGRC----STSEVTGAV 308
                                       *********************99....999998765 PP

>> Antirestrict  Antirestriction protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.1e-05      0.28      17      53 ..     187     223 ..     181     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                      Antirestrict  17 glymaPesderlrlvvkengfegevSadAaGiivtll 53 
                                       ++y   +  +r+ ++v +n f + +S +AaG+i +l 
  gi|330507888|ref|YP_004384316.1| 187 AAYNLVTNPQRFDVLVTTNLFGDILSDEAAGVIGSLG 223
                                       56666677899********************997764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2386.86
//
Query:       gi|330507889|ref|YP_004384317.1|  [L=275]
Description: hypothetical protein MCON_1921 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2040.76
//
Query:       gi|330507890|ref|YP_004384318.1|  [L=159]
Description: 3-isopropylmalate dehydratase small subunit 1 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.9e-20   72.2   0.1      7e-20   71.7   0.1    1.3  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 !   71.7   0.1   3.9e-24     7e-20      57     123 ..      34      99 ..      11     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 3.9e-24
                                       TEEEEHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT- CS
                       Aconitase_C  57 gekedvvdaaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennlikngl 123
                                       +  ++ +d ++  ++ + +++v++ +nfG+GSSRe+A++al+  G+ av+a SF+rIf++n+i+ gl
  gi|330507890|ref|YP_004384318.1|  34 EHVMEGIDPQFASRVGKGDIIVAG-ENFGSGSSREQAPLALKEAGVAAVVARSFARIFYRNAINVGL 99 
                                       555677778888888899999988.****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1129.40
//
Query:       gi|330507891|ref|YP_004384319.1|  [L=197]
Description: iron-sulfur flavoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-33  116.1   0.0    1.6e-33  115.6   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    4.7e-06   26.4   0.0    5.2e-06   26.3   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.6   0.0   1.8e-37   1.6e-33       3     150 ..       2     153 ..       1     157 [. 0.94

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 1.8e-37
                                       EEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH-SC CS
                           FMN_red   3 ilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaaada 75 
                                       il+isGS+r +  t+ ++ +a+++l+e+g e+el+ ++++ i pc   ++c+k +e  +  +dd+ +l+  i++a++
  gi|330507891|ref|YP_004384319.1|   2 ILGISGSPR-NMATEHILGMALKMLEEKGYETELFAMRGKnISPCrhcDYCLKNKE--CIVKDDMYQLYPLIREAEG 75 
                                       89******7.999********************************99888887774..69***************** PP

                                       EEEEEEECTTCE-HHHHHHHHCHT-...SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEECSEEE CS
                           FMN_red  76 liivtPeYngsysgllKnalDrlsr..trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpraava 149
                                       ++++tP+Yngs+s+++K a+Dr+++   +++++lr Kp++++a+gg+r gg++++ q  + +   +g+i+v+++ + 
  gi|330507891|ref|YP_004384319.1|  76 FVLATPVYNGSMSAQMKIAIDRTRAtlAAEPRSLRRKPGMAIAIGGDRMGGQELAVQQIHTFYiLNGMIPVSGGFFG 152
                                       ***********************99**************************************77999999998776 PP

                                       E CS
                           FMN_red 150 v 150
                                       +
  gi|330507891|ref|YP_004384319.1| 153 A 153
                                       5 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   5.8e-10   5.2e-06       3     132 ..       2     118 ..       1     181 [. 0.77

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 5.8e-10
                                       EEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTTC.HHHHHHH.HHHHHC CS
                      Flavodoxin_2   3 iLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeekp.adveseq.ieklla 77 
                                       iL i ++pr     + +++  +++ le++g  e + + +    +  +++ d+   l ++e + ++ ++ q    +++
  gi|330507891|ref|YP_004384319.1|   2 ILGISGSPRN--MATEHILGMALKMLEEKG-YETELFAMRGKNISPCRHCDYC--LKNKE-CiVKDDMYQlYPLIRE 72 
                                       788999**99..9999**************.9999999998766666654333..34444.77888888888***** PP

                                       SSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEEE CS
                      Flavodoxin_2  78 adaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgkkalviv 132
                                       a+  vl++P+++ +++a++K  iDr  +a  a       e+  + L+ k+ + i+
  gi|330507891|ref|YP_004384319.1|  73 AEGFVLATPVYNGSMSAQMKIAIDRT-RATLAA------EP--RSLRRKPGMAIA 118
                                       *************************6.665555......24..556666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1495.88
//
Query:       gi|330507892|ref|YP_004384320.1|  [L=193]
Description: archaeoflavoprotein AfpA [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-16   59.6   0.0    4.5e-16   59.0   0.0    1.4  1  Flavoprotein  Flavoprotein
  ------ inclusion threshold ------
      0.039   13.2   0.0      0.039   13.2   0.0    1.1  1  DHO_dh        Dihydroorotate dehydrogenase


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0     5e-20   4.5e-16       2     106 ..      11     134 ..      10     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 5e-20
                                       EEEEEE-SSCGGGCH.HHHHHHHHH...TTEEEEEEESCHHHHCCHHGGS..................TCSSHHHHH CS
                      Flavoprotein   2 killgiTGsvaaika.lellekLkk...egievqvvltkaAkkfiskeklklaa..............redpilhie 60 
                                       ki++giTGs + i + +e + +L+k   + ++v+v+++ka++++i+  ++kl +               + p l  +
  gi|330507892|ref|YP_004384320.1|  11 KIAWGITGSGDRITEtVEKMIELQKqydDVVDVRVFVSKAGEQVIK--YYKLFNtlekhfdkvwveinSNSPFLAGQ 85 
                                       89*********999887777777777988*****************..66665556666666666666555555555 PP

                                       H.CTTESEEEEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE CS
                      Flavoprotein  61 l.rrwadllviaPasantlakianGiadnlltlilra..takkpiliaP 106
                                       l  r++++l+ aP + nt+ kia+G+ad+ll++ + +  +a +p++i+P
  gi|330507892|ref|YP_004384320.1|  86 LqVRRYEFLLLAPTTSNTVTKIALGLADSLLSNAAIMsqKAFVPTYIMP 134
                                       5455***************************988855455556777776 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.4e-06     0.039      79     144 ..      25      89 ..      13     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.4e-06
                                       HHHHHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGGES.E.EEEES-SCTCCTSCCCG CS
                            DHO_dh  79 avlekllkrrkeqeekkelginlskakktenavddyvevvrkigpfad.i.lelNvSsPntpglrdlq 144
                                       + +ek+++ +k++ +  ++++++ska+++   v  y ++++++++  d + +e+N  sP  +g+ ++ 
  gi|330507892|ref|YP_004384320.1|  25 ETVEKMIELQKQYDDVVDVRVFVSKAGEQ---VIKYYKLFNTLEKHFDkVwVEINSNSPFLAGQLQVR 89 
                                       5567888899999999************9...999*********555523368999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1369.92
//
Query:       gi|330507893|ref|YP_004384321.1|  [L=131]
Description: sirohydrochlorin cobaltochelatase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-26   92.0   0.0    3.1e-26   91.8   0.0    1.0  1  CbiX            CbiX
      3e-05   23.5   0.0    3.2e-05   23.4   0.0    1.0  1  CbiK            Cobalt chelatase (CbiK)
  ------ inclusion threshold ------
      0.058   12.5   0.0      0.067   12.2   0.0    1.1  1  Ferrochelatase  Ferrochelatase


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.0   5.2e-30   3.1e-26       1     105 [.      11     122 ..      11     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 5.2e-30
                                       -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT CS
                              CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeele 77 
                                       HGS++p  +e ve la+++ ++++  pv++++l++++p+++ +l++++  gvk+iv++Plfl++Gvh+++DIp+el+
  gi|330507893|ref|YP_004384321.1|  11 HGSSLPFNKELVESLAQMIGKNNSSGPVRTAYLNMNQPDIPAGLKSFQGTGVKKIVALPLFLAHGVHTRQDIPHELG 87 
                                       ***************************************************************************** PP

                                       --SSSS-.......TTEEEEE---CCCSCCHHHHH CS
                              CbiX  78 eaeeahp.......kdveieytepLGthplvaevl 105
                                        ++e+         ++ve++++epLG ++ +a++ 
  gi|330507893|ref|YP_004384321.1|  88 VDPEKRRgvlniwgDEVEVICAEPLGVDECIAALA 122
                                       99999999*********************999875 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   5.3e-09   3.2e-05     142     260 ..       4     129 ..       1     131 [] 0.84

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.3e-09
                                       EEEEEEE---SCHHHH.HHHHHHHHHHH.CT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHC CS
                              CbiK 142 ealvfvgHGtehesna.vyaeldkvlke.kdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlvAGdHakn 215
                                         ++ +gHG++ + n+   + l +++ + ++   v  + ++  +P++   +++ +++g+k++  +Pl+l  G H ++
  gi|330507893|ref|YP_004384321.1|   4 VGILVLGHGSSLPFNKeLVESLAQMIGKnNSSGPVRTAYLNmNQPDIPAGLKSFQGTGVKKIVALPLFLAHGVHTRQ 80 
                                       567789*****987761556788888664778899999997468********************************* PP

                                       CCCSS...STTSHHHHHHHTT--EEE.----GGGSHHHHHHHHHHHHHH CS
                              CbiK 216 Dmasd...eedswkealeaaGikvei.ilkgLGeieeirsifikhikea 260
                                       D+ ++   + ++ +  l+  G +ve+   + LG +e i+++ ik+ +e 
  gi|330507893|ref|YP_004384321.1|  81 DIPHElgvDPEKRRGVLNIWGDEVEViCAEPLGVDECIAALAIKRAEES 129
                                       **8765557899999*********9835689********9999998776 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.1e-05     0.067      69     130 ..      16      78 ..       7      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHHHHHHH---EEEEEEESS.SSSBHHHHHHHHHCTT-SEEEEEES-SS--TTT CS
                    Ferrochelatase  69 eitrkqaealekelaergidvkvylamry.wePsiedaleelkadgvervvvlplyPqysast 130
                                         ++++ e l++ +++++ + +v  a+ +  +P i   l+ ++ +gv+++v+lpl+  ++  t
  gi|330507893|ref|YP_004384321.1|  16 PFNKELVESLAQMIGKNNSSGPVRTAYLNmNQPDIPAGLKSFQGTGVKKIVALPLFLAHGVHT 78 
                                       578999**********999******9866267***********************97666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 948.74
//
Query:       gi|330507894|ref|YP_004384322.1|  [L=386]
Description: hypothetical protein MCON_1929 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00018   21.6   0.2    0.00029   20.9   0.2    1.3  1  Mur_ligase_M  Mur ligase middle domain
  ------ inclusion threshold ------
      0.088   13.1   0.0       0.21   11.9   0.0    1.7  1  YqjK          YqjK-like protein


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 !   20.9   0.2   3.2e-08   0.00029       1      68 [.      72     156 ..      72     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.2e-08
                                       EESSS-HHHHHHHHHHHHHCT..EEEEETTC..................SS-THHHHHHHHHHHHHTT-SEEEEE-- CS
                      Mur_ligase_M   1 vTGtnGKTTtteliaaileka..gkvigtvg..................ttnneiglpktlaemekkeaeyavlEvs 57 
                                       vTGt+ KTTt+ l+a il+++  +  ++t g                  t   + ++ ++ +e+  ++ae++++E+s
  gi|330507894|ref|YP_004384322.1|  72 VTGTHSKTTTALLLAMILSRQkrVLSHTTRGleiwsggrpqllkeglsiT---PANVILAAQEALAQGAEALICEIS 145
                                       9*****************999666667777799**********9996433...77788888888899********** PP

                                       HCHHHCTTTCC CS
                      Mur_ligase_M  58 shglgekrleg 68 
                                         g g ++l  
  gi|330507894|ref|YP_004384322.1| 146 LGGTGLAQLGI 156
                                       99988877765 PP

>> YqjK  YqjK-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.3e-05      0.21      15      71 ..      52     108 ..      47     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                              YqjK  15 aaepwekalapvDrgwqtlrslrkhlilvsgllallgvrrPrrllrwlrrglgawst 71 
                                       + +   + + ++D    +++ +++h  + ++ll+++ + r +r+l  + rgl +ws 
  gi|330507894|ref|YP_004384322.1|  52 HHQAAGELMGSIDDDVVKIEVTGTHSKTTTALLLAMILSRQKRVLSHTTRGLEIWSG 108
                                       66778889999999999**************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2873.85
//
Query:       gi|330507895|ref|YP_004384323.1|  [L=369]
Description: putative methanogenesis marker 13 metalloprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-18   64.8   0.0    7.4e-18   64.5   0.0    1.2  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
    0.00046   19.8   0.5      0.001   18.7   0.5    1.6  1  SHOCT           Short C-terminal domain


Domain annotation for each model (and alignments):
>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   8.2e-22   7.4e-18      11     134 ..      26     143 ..      16     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 8.2e-22
                                       TTBTTEEEEEES-HHHHHCCCCHHHCHHSS-HS-EEEE--HHHHSSSSHHHHHHHHHHHHHHC-TSEEEEEE-HHHH CS
                    Oxidored_nitro  11 lgikdalplvhGpqGCatyaralltrhfrepiplastdltekdavfGgeekLkeaikeivkrykpkaIgVittClte 87 
                                         +   ++++hGp GC++ + +ll       + +++t+l+e   vfGg + L   +k++v+ ++p+++++  tC++ 
  gi|330507895|ref|YP_004384323.1|  26 RDLGADVVILHGPSGCCFKHARLLEEDG---VRVLTTALDEAGFVFGGHKPLTALLKKAVELFNPRLMAISGTCSSM 99 
                                       55555689*********99999995554...48******************************************** PP

                                       HTTTTHHHHHHHHHHHHTSSEEEEEE--TTSSSHHHHHHHHHHHHHH CS
                    Oxidored_nitro  88 liGdDieavareaeeelgeipvipvstpgfggsqseGydaalealvr 134
                                       +iGdD+++ + ea+ +    pv+ v++     + ++G  ++lea  +
  gi|330507895|ref|YP_004384323.1| 100 IIGDDLHQAVLEADLDI---PVLEVEVHAGYRDNTKGVIITLEAARD 143
                                       *********99998765...9******99999999999999998765 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.5   1.1e-07     0.001       5      27 ..     137     159 ..     135     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-07
                             SHOCT   5 kLkeLyarGeIteEEFeakKakL 27 
                                       +L + +++G+I+e+EF ++K  L
  gi|330507895|ref|YP_004384323.1| 137 TLEAARDKGIIDEAEFVRQKTLL 159
                                       68999***************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2576.37
//
Query:       gi|330507896|ref|YP_004384324.1|  [L=62]
Description: Preprotein translocase subunit secE [Methanosaeta concilii GP6]
Scores for complete 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   25.6   0.0    9.4e-06   25.5   0.0    1.1  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   5.2e-10   9.4e-06       4      49 ..      12      57 ..       9      62 .] 0.91

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5.2e-10
                                      HHHHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SecE  4 fkevkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfsk 49
                                      ++e ++ lk   +Ptr+E+  +++v ++++ i+g ++f++  +++ 
  gi|330507896|ref|YP_004384324.1| 12 INEYIRVLKLARKPTREEFNMIAKVSMAGIGIIGSIGFVIYALLTE 57
                                      678999**********************************988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 465.32
//
Query:       gi|330507897|ref|YP_004384325.1|  [L=126]
Description: hypothetical protein MCON_1932 [Methanosaeta concilii GP6]
Scores for 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   67.2   1.8    1.3e-18   66.9   1.8    1.1  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 !   66.9   1.8   7.3e-23   1.3e-18       4      80 .]      31     107 ..      29     107 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 7.3e-23
                        Spore_YtfJ   4 gdgtviiPvskvsfGfgaGgsefkskkekepfgggsgaGvsitPvAfLvikkgevkllpvkk...ssldklidlvpd 77 
                                        +g++i+P+++v++GfgaG++ +   ke +p gg++g+G +++P+A+++i++++v++ ++k+   + +d l +++p 
  gi|330507897|ref|YP_004384325.1|  31 VEGKTIVPLMSVGMGFGAGSGTG---KETDPAGGAGGGGLGMKPIAVVIIDQHGVRIERMKEsrdTLVDHLAEAIPR 104
                                       478********************...8889******************************99**999*********9 PP

                        Spore_YtfJ  78 vvd 80 
                                       +v+
  gi|330507897|ref|YP_004384325.1| 105 FVE 107
                                       885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 975.14
//
Query:       gi|330507898|ref|YP_004384326.1|  [L=329]
Description: 2-dehydropantoate 2-reductase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-32  112.9   0.0    2.5e-32  111.7   0.0    1.6  2  ApbA_C     Ketopantoate reductase PanE/ApbA C terminal
    3.7e-25   88.3   0.0    5.3e-25   87.8   0.0    1.2  1  ApbA       Ketopantoate reductase PanE/ApbA
     0.0074   16.8   0.5      0.023   15.2   0.1    1.9  2  Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.085   13.0   0.1       0.42   10.7   0.1    2.1  1  bPH_6      Bacterial PH domain


Domain annotation for each model (and alignments):
>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.7   7.6e+03      43      70 ..      93     120 ..      90     129 .. 0.63
   2 !  111.7   0.0   5.7e-36   2.5e-32       2     125 .]     191     318 ..     190     318 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                            ApbA_C  43 llkEalavaeaegvelseerleeaveav 70 
                                       +++Ea +++ ++g+ +s ++     e++
  gi|330507898|ref|YP_004384326.1|  93 AAREAAELLAEDGIMVSIQNGLGNWETI 120
                                       6788888888888777777644444444 PP

  == domain 2  score: 111.7 bits;  conditional E-value: 5.7e-36
                            ApbA_C   2 irlarweKllinaainpltalldckngellespelralvrallkEalavaeaegvelseerleeaveavlek....t 74 
                                       i++a w K+l+n+++npl+a+l++++g+l e++e+r ++r +++E++ v +a++v+l+ + ++++ + +le+    t
  gi|330507898|ref|YP_004384326.1| 191 IWSALWGKVLYNCSLNPLGAILEVPYGRLGENEETRMIIRGIIEEIFLVCQALKVPLPYKGADDYYRFLLETqlppT 267
                                       8999********************************************************9*********9999999 PP

                            ApbA_C  75 aanrsSMlqDveagrktEidyinGavvklAeklgvetPvnellyellkale 125
                                       +++r SMlqD++a+rktEi+++nGa+ +lA+++ ++tP+n+ll+ l+k +e
  gi|330507898|ref|YP_004384326.1| 268 RDHRASMLQDILAKRKTEIEALNGAISRLARENEIPTPYNDLLTLLIKFKE 318
                                       99*********************************************9876 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.0   1.2e-28   5.3e-25       2     141 ..      10     150 ..       9     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 1.2e-28
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCH.SCCCCS-ESEEEE-SS CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrppealsae.ekselepidlvivtvK 77 
                                       +i GaGaiGs+l++ L+k ++ vt+ +r+ +l a+k++Glr+t+ +ge+ ++p+e    + +    + ++ ++++vK
  gi|330507898|ref|YP_004384326.1|  10 LIYGAGAIGSVLGGFLHKINRSVTFAGRGSHLLAIKEQGLRITGIWGEHLVPPEEIDILSdPLNREKRYSTILLSVK 86 
                                       79********************************************999999988776667677889********** PP

                                       GGGHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE-EEEEEETTEEEECS CS
                              ApbA  78 ayqteealeeikplldpntvvlllqNGlgheeelrealpkprvlggvtthgatregpgevhhag 141
                                       + +te a++e+++ll+++ +++++qNGlg+ e+++  ++++r +g+ + +ga+   pg  + + 
  gi|330507898|ref|YP_004384326.1|  87 SKDTETAAREAAELLAEDGIMVSIQNGLGNWETIARLVGEKRTVGARVIFGAEIPVPGLAKVTV 150
                                       ****************************************************999998877765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   5.2e-06     0.023       3      35 ..      10      42 ..       8      60 .. 0.87
   2 ?   -1.7   0.0         1   4.5e+03      40      63 ..      91     114 ..      80     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.2e-06
                                      EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      ++ G+G ig  l+g+l++++ +Vt   r+++ll
  gi|330507898|ref|YP_004384326.1| 10 LIYGAGAIGSVLGGFLHKINRSVTFAGRGSHLL 42
                                      799****************************99 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHTTEEEECSEEE CS
                         Pyr_redox  40 eeaskilqeklekngievllntkv 63 
                                       e+a+++ +e l + gi v  ++ +
  gi|330507898|ref|YP_004384326.1|  91 ETAAREAAELLAEDGIMVSIQNGL 114
                                       567888888888989888666655 PP

>> bPH_6  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   9.5e-05      0.42       4      38 ..      42      78 ..      41     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.5e-05
                             bPH_6  4 vrvdpdGvevrnlfrtrrlpWsaiagvr..fpegrrl 38
                                      +++ ++G+++ ++ +++++p+++i  ++  +++ +r+
  gi|330507898|ref|YP_004384326.1| 42 LAIKEQGLRITGIWGEHLVPPEEIDILSdpLNREKRY 78
                                      6899*********************999776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2350.03
//
Query:       gi|330507899|ref|YP_004384327.1|  [L=140]
Description: hypothetical protein MCON_1935 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       345  (0.0192426); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 975.82
//
Query:       gi|330507900|ref|YP_004384328.1|  [L=263]
Description: hypothetical protein MCON_1937 [Methanosaeta concilii GP6]
Scores for complete 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   26.2   3.7    6.6e-06   25.9   0.2    2.6  3  HTH_5     Bacterial regulatory protein, arsR family
    0.00028   20.9   0.0    0.00057   19.9   0.0    1.5  1  HTH_20    Helix-turn-helix domain
     0.0011   18.8   0.5     0.0029   17.6   0.3    1.8  2  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.022   15.0   0.1      0.062   13.5   0.1    1.8  1  HTH_34    Winged helix DNA-binding domain
      0.076   13.2   0.0       0.27   11.5   0.0    2.0  1  Rio2_N    Rio2, N-terminal
        0.1   12.2   0.0       0.21   11.2   0.0    1.5  1  DMA       DMRTA motif
       0.53   10.3   4.8        1.1    9.2   0.2    3.3  3  HTH_12    Ribonuclease R winged-helix domain
       0.71   10.1   5.7        1.1    9.5   5.6    1.4  1  MutS_III  MutS domain III


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 ?    0.4   0.0      0.28   6.2e+02      16      27 ..     122     133 ..     119     135 .. 0.89
   2 ?   -3.0   0.1       3.1   6.9e+03       6      13 ..     152     159 ..     151     161 .. 0.83
   3 !   25.9   0.2     3e-09   6.6e-06       2      45 ..     173     216 ..     172     217 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.28
                                       EEHHHHHHHHTS CS
                             HTH_5  16 lcvcelaeelgl 27 
                                       +c++e +++l++
  gi|330507900|ref|YP_004384328.1| 122 RCFSETSRILDK 133
                                       7********987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
                                       HHHHHHTT CS
                             HTH_5   6 kILklLae 13 
                                       +I+ +L+e
  gi|330507900|ref|YP_004384328.1| 152 EIILALSE 159
                                       89999998 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 3e-09
                                       HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5   2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45 
                                       ++R++I+k L+++ ++++ l+  +gl  +++  HL kL ++G++
  gi|330507900|ref|YP_004384328.1| 173 KQRIQIMKVLSSETKTFSALSSLTGLRGGNLLFHLQKLLDCGMI 216
                                       78****************************************87 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.5e-07   0.00057       7      60 ..     170     222 ..     164     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.5e-07
                                       HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20   7 LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                       L+++ R  i++ L + e  t+s+l  + +l+  +l +HL++L + g + ++ e+
  gi|330507900|ref|YP_004384328.1| 170 LSNKQRIQIMKVL-SSETKTFSALSSLTGLRGGNLLFHLQKLLDCGMILQRNER 222
                                       89999********.*********************************9999886 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         4     9e+03       3      20 ..      30      46 ..      29      56 .. 0.59
   2 !   17.6   0.3   1.3e-06    0.0029      10      71 ..     177     240 ..     173     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4
                            HTH_45  3 skleIiadILeaisegea 20
                                      s  + + +IL+ + +++ 
  gi|330507900|ref|YP_004384328.1| 30 SNQQHLESILKGC-RSDF 46
                                      5555566788888.4444 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.3e-06
                            HTH_45  10 dILeaisegeakkTkimykanLsykllnkYLdmLvekgli..kkskekYvlTekGlelleklke 71 
                                       +I++++s++ ++ +++     L   +l   L++L++ g+i  +++ + Y++TekG + l+ l e
  gi|330507900|ref|YP_004384328.1| 177 QIMKVLSSETKTFSALSSLTGLRGGNLLFHLQKLLDCGMIlqRNERGDYMITEKGYKALRGLAE 240
                                       677777788888888888888888889999**********988899***********9998765 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 ?   13.5   0.1   2.8e-05     0.062       2      68 ..     175     234 ..     174     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-05
                            HTH_34   2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGrea 68 
                                       R++++ +L+s+   +f+ l++ +++  gnL  hl+kL + g i        + +r  + iT++G +a
  gi|330507900|ref|YP_004384328.1| 175 RIQIMKVLSSET-KTFSALSSLTGLRGGNLLFHLQKLLDCGMILQ------RNERGDYMITEKGYKA 234
                                       889*****9865.58**********************99998743......3344456666666665 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.27      26      74 ..     188     235 ..     178     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                            Rio2_N  26 ptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyL 74 
                                        ++ ++++++l+ +++  +l++ll+ ++i +++ +   Y +t +Gy +L
  gi|330507900|ref|YP_004384328.1| 188 TFSALSSLTGLRGGNLLFHLQKLLDCGMILQRNERG-DYMITEKGYKAL 235
                                       5678999***********************998654.49******9876 PP

>> DMA  DMRTA motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.4e-05      0.21      15      34 ..      31      50 ..      29      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.4e-05
                               DMA 15 krsvLelvLqrCkGDVvqAI 34
                                      +++ Le++L++C+ D   AI
  gi|330507900|ref|YP_004384328.1| 31 NQQHLESILKGCRSDFSNAI 50
                                      6789***********87776 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.18     4e+02      34      51 ..      11      30 ..       3      36 .. 0.83
   2 ?   -1.3   0.1      0.98   2.2e+03      16      35 ..      81     101 ..      56     116 .. 0.64
   3 ?    9.2   0.2   0.00051       1.1      25      66 .]     198     235 ..     176     235 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.18
                            HTH_12 34 avRyrLrkleerg..ltrrv 51
                                      a+R +L  + e+   +++r 
  gi|330507900|ref|YP_004384328.1| 11 AIRSKLSEMHEDLkrFIERS 30
                                      99*******99866799986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.98
                            HTH_12  16 akeiaeeLkkr.gydigerav 35 
                                       +  +  +++++ + +++e+++
  gi|330507900|ref|YP_004384328.1|  81 SDLLKRNIEQIrDGKVSEESI 101
                                       444555666655777777776 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00051
                            HTH_12  25 krgydigeravRyrLrkleerg.ltrrvgyagreltEkGleeL 66 
                                       +rg ++      ++L+kl + g + +r+ ++   +tEkG + L
  gi|330507900|ref|YP_004384328.1| 198 LRGGNL-----LFHLQKLLDCGmILQRNERGDYMITEKGYKAL 235
                                       454444.....58****9999967799************9865 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   5.6   0.00048       1.1      69     190 ..      11     141 ..       2     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00048
                                       HHHHHHTT--.-HHHHHHHHHTT---HHHHHHHHHHHH..........HHHTTTTT---SSTHHHHHHH.HHHHHHH CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                          MutS_III  69 elrellrrlp.DleRllsrislgkakardlkallealk..........aleelvallekeklaeseees.laellee 133
                                       ++r++l +++ Dl+R + r ++     ++l+++l+ ++          a++e+ + le++++++++ ++  ++l ++
  gi|330507900|ref|YP_004384328.1|  11 AIRSKLSEMHeDLKRFIERSNQ-----QHLESILKGCRsdfsnaiigyATNEIEQGLERNMEKNCHMREaCRSLFSD 82 
                                       57788888777****9999977.....45777888888888888888888899999988888877775524488888 PP

                                       HB-SS--SSGGGS--B-THHHHHHHHHHHHHHHH.HH.THHHHHHHHHHHH.HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxx.xxxxxxxx RF
                          MutS_III 134 aideeplalekegedlraiealeqelfqelleev.ee.alerlrrlaeala.eLDvllSl 190
                                        +++  +++ ++g+++++  +++++ ++ l+e+   +  + ++ +++++l+ ++D+++Sl
  gi|330507900|ref|YP_004384328.1|  83 -LLKRNIEQIRDGKVSEESISKARSKLKGLRENArYDqCVRCFSETSRILDkQVDLMHSL 141
                                       .9999*************999999999999999954435889999999987356777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1228  (0.0684924); expected 358.6 (0.02)
Passed bias filter:                      725  (0.0404373); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1874.55
//
Query:       gi|330507901|ref|YP_004384329.1|  [L=79]
Description: hypothetical protein MCON_1938 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-30  105.2   0.2    1.2e-30  105.1   0.2    1.0  1  MTH865    MTH865-like family


Domain annotation for each model (and alignments):
>> MTH865  MTH865-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.2   6.7e-35   1.2e-30       1      69 [.       6      74 ..       6      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 6.7e-35
                                      HHHHHHHHHHTTSSSTTBHHHHHHHH-TTSS-----BTTB---TTTTGGGS-GGGSB-SHHHHHHHHHH CS
                            MTH865  1 elkeqivealegadFPikspeeLlaalPkGaettceagdvevtagelgkklkdsdFPyksaedladdiv 69
                                      e+++qi +al++a+FPi++peeLlaa+P+Ga+t+c+agdve+tag++gk l+++dFP+ksa+++ad iv
  gi|330507901|ref|YP_004384329.1|  6 EIHAQIEGALKNAKFPINTPEELLAAMPQGAATKCKAGDVELTAGDAGKVLEATDFPFKSAKQVADVIV 74
                                      79******************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 572.43
//
Query:       gi|330507902|ref|YP_004384330.1|  [L=134]
Description: pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   57.2   0.0    1.8e-15   56.9   0.0    1.1  1  Putative_PNPOx   Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.064   13.9   0.0      0.087   13.4   0.0    1.2  1  Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0     2e-19   1.8e-15       1      87 [.       4      90 ..       4      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2e-19
                                      HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEE CS
                    Putative_PNPOx  1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieG 79
                                      +++ +re l+++k   +AT+++ G Pnv+ v+l +  +++++ +a n   ++++nleenp++++l +d+++ ++++i+G
  gi|330507902|ref|YP_004384330.1|  4 MPKDVRETLEKQKPIPIATANKAGVPNVVFVGLLKILDDETLMLADNFFNKTAANLEENPKISILCYDPQTSKSFQIKG 82
                                      56789***************************88888888*************************************** PP

                                      EEEEESCH CS
                    Putative_PNPOx 80 taelvsdg 87
                                       a+++++g
  gi|330507902|ref|YP_004384330.1| 83 SAKVHKEG 90
                                      *****997 PP

>> Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.7e-06     0.087      20      99 ..      15      87 ..       4      88 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.7e-06
                                      GGEEEEEEE-T.TS-EEEEEEE---B-TT...SS-.EEEEEETTSHHHHHHH.H--EEEEEEEETTTTEEEEEEEEEEE CS
                   Pyridox_oxase_2 20 stefqlaTvdeeegkPrvRtvvfRgfleekkeesdvltfttDvrseKvkqlessnaaveavfylketreQfRisGkafv 98
                                      ++ + +aT + ++g P+   vvf g l+  +  ++   + +D   +K++   ++n+++ ++ y ++t++ f i+G+a+v
  gi|330507902|ref|YP_004384330.1| 15 QKPIPIATAN-KAGVPN---VVFVGLLKILD--DE-TLMLADNFFNKTAANLEENPKISILCYDPQTSKSFQIKGSAKV 86
                                      5555666665.355554...56777777654..33.346678888898877779***********************99 PP

                                      E CS
                   Pyridox_oxase_2 99 i 99
                                      +
  gi|330507902|ref|YP_004384330.1| 87 H 87
                                      7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1031.47
//
Query:       gi|330507903|ref|YP_004384331.1|  [L=286]
Description: putative methanogenesis marker protein 8 [Methanosaeta concilii GP6]
Scores for complete 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-95  318.0   5.8    4.1e-95  317.9   5.8    1.0  1  DUF2099       Uncharacterized protein conserved in archaea (D
  ------ inclusion threshold ------
      0.098   12.8   0.5       0.36   11.0   0.2    2.0  2  FrhB_FdhB_N   Coenzyme F420 hydrogenase/dehydrogenase, beta s
       0.11   12.8   0.1       0.42   11.0   0.1    2.0  1  Ribosomal_L5  Ribosomal protein L5


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 !  317.9   5.8   6.8e-99   4.1e-95       1     256 [.       4     259 ..       4     260 .. 0.98

  Alignments for each domain:
  == domain 1  score: 317.9 bits;  conditional E-value: 6.8e-99
                           DUF2099   1 HiiealgkarvvvkdgkvvevgepkikyCPlfkklrgikeitkeaikkniefrikefGlftkkRkleskedfvsfGa 77 
                                       Hiie++++  v+vkdg ++ + +p+i++CPl ++l+g++e ++++++k+++++i+efG++ ++R+les+++ vsfGa
  gi|330507903|ref|YP_004384331.1|   4 HIIEMAKA-LVKVKDGMIEVLIKPTIRHCPLRNDLYGFEEENHKTVEKVLRRHIEEFGMYGPNRVLESDQKPVSFGA 79 
                                       9***9876.******************************************************************** PP

                           DUF2099  78 sEilstalkeglidaavivcdgaGtvivtnpelvqglggrisGlveTePieevierieeeggivldketaeidqveG 154
                                       sEi+++a++egl+daav+vc+gaGtvi+t+pe++q++g++++Gl++TePi+e+++ ++++g+++ldk+ ++idqveG
  gi|330507903|ref|YP_004384331.1|  80 SEIIVDAMTEGLVDAAVVVCEGAGTVIITRPEVLQAVGAHMTGLISTEPIKEIQDGLKQKGCLLLDKQ-CTIDQVEG 155
                                       *****************************************************************998.******** PP

                           DUF2099 155 vkkAiekgykkiavtvae..aedakklrelekeegvkilifavhttgiskeeaeelveaaDlvtacAskeireivkk 229
                                       + +A+e+g++ki+vt++   a++ak+l+el + +gvk ++++vh+tgis eeae+l +++D+v+acAsk++reiv+k
  gi|330507903|ref|YP_004384331.1| 156 YIMAVEAGFRKIVVTITGhkASEAKRLQELGEISGVKPVVVSVHNTGISVEEAETLSDYCDIVWACASKQVREIVGK 232
                                       ****************9866899****************************************************** PP

                           DUF2099 230 kallqvgksvpvfaltekGkelilerl 256
                                       +++lq+g s+pvf++t++Gk+lil+r+
  gi|330507903|ref|YP_004384331.1| 233 RSKLQIGISIPVFGMTQAGKQLILNRA 259
                                       ************************996 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 ?   11.0   0.2   6.1e-05      0.36      22      63 ..      80     115 ..      79     126 .. 0.78
   2 ?   -1.3   0.0      0.43   2.5e+03      54      74 ..     179     199 ..     167     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.1e-05
                       FrhB_FdhB_N  22 tallkylLeegiidgvivvapskdpwrpkpviattkeellaa 63 
                                       ++++  ++ eg++d+++vv ++     + +vi+t +e l +a
  gi|330507903|ref|YP_004384331.1|  80 SEIIVDAMTEGLVDAAVVVCEG-----AGTVIITRPEVL-QA 115
                                       789999**************99.....567777766544.44 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.43
                       FrhB_FdhB_N  54 attkeellaaaGskYtlspnl 74 
                                       a+  +el + +G+k+ ++++ 
  gi|330507903|ref|YP_004384331.1| 179 AKRLQELGEISGVKPVVVSVH 199
                                       566689999999999988775 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   7.1e-05      0.42      10      48 ..     166     199 ..     162     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.1e-05
                                       EEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC-- CS
                      Ribosomal_L5  10 KivinmgvGeagedkkllekaakeLaeItGQkPvvtkak 48 
                                       Kiv+ +   +a+e      k  +eL eI+G kPvv +  
  gi|330507903|ref|YP_004384331.1| 166 KIVVTITGHKASEA-----KRLQELGEISGVKPVVVSVH 199
                                       89997777777776.....8999***********98765 PP



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:                      397  (0.0221429); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2006.01
//
Query:       gi|330507904|ref|YP_004384332.1|  [L=537]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (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  138.3   0.0    2.4e-40  137.2   0.0    1.6  1  DUF4277    Domain of unknown function (DUF4277)
    1.3e-12   47.9   0.1    5.8e-12   45.7   0.1    1.8  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2   0.0   2.7e-44   2.4e-40       3     108 ..      10     115 ..       8     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 2.7e-44
                           DUF4277   3 vksldhlglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfpeffedkplerLlgegve 79 
                                       + sldhlglva+++d+lg++e+ide ipk++++k+s++ ++kal++ngLgf +r+Ly+fp++fe+++lerL+++gv 
  gi|330507904|ref|YP_004384332.1|  10 TLSLDHLGLVAAIFDALGISEVIDESIPKTRNCKLSHSAIIKALVINGLGFAERRLYIFPSYFENLALERLFNPGVV 86 
                                       679************************************************************************** PP

                           DUF4277  80 aehlnddrlgrtLDklyeagvtklfteia 108
                                       +e++n+d++grtLD++ ++g t+lf++ia
  gi|330507904|ref|YP_004384332.1|  87 PEDFNEDVVGRTLDRINKFGSTALFNNIA 115
                                       ****************************8 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.1   6.4e-16   5.8e-12       9     213 ..     131     455 ..     124     456 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 6.4e-16
                         DDE_Tnp_1   9 vDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                       vD t++ v+g                  +d+rw        + + + +++++  g++l v+ ++gn++d k+l++++
  gi|330507904|ref|YP_004384332.1| 131 VDTTSFGVHGDYegldckpameitlghpKDGRW------DLKQFIVSMVTNQC-GIPLFVQAHSGNKSDKKTLIETI 200
                                       666666666666666665554444444444444......55667788888888.9********************** PP

                         DDE_Tnp_1  70 delrpr....kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrn 142
                                       ++++ +     + ++ aD++ +s e+++ l      +i r++  +++ ++   +  +++++ +dr+ il+++ +  +
  gi|330507904|ref|YP_004384332.1| 201 QMFKSNldfsGKNYFAADSALFSSENIRLLG-DSTLWITRVPTTVREVKDLQRRDLEMKTCSDDRYSILETEINYGG 276
                                       **********************999999999.55559****999999888777889999999999999999999999 PP

                         DDE_Tnp_1 143 k............................................................................ 143
                                                                                                                    
  gi|330507904|ref|YP_004384332.1| 277 Idqkwvvvdsremhaskaktfdrrigkeftetrkslkklgyivfaceadarkaadrwisenphftltglsiceiskr 353
                                       9**************************************************************************** PP

                         DDE_Tnp_1 144 ...............................skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrk.f 188
                                                                      + +++  + +v+  n+++l+ e + ++y+ +  +E  F++lk+k f
  gi|330507904|ref|YP_004384332.1| 354 idskrgrpkkgeqlekgyliegevqrneamiANERARLGRFVLASNDKTLDGELMLQYYKGQNAVEKGFRFLKDKsF 430
                                       ***************************************************************************** PP

                         DDE_Tnp_1 189 gldrlryrglnrveaqllllllaln 213
                                       +   +++++ +r+ea  +++ l+l+
  gi|330507904|ref|YP_004384332.1| 431 RVAEVYLKKEERIEALSMIMVLSLL 455
                                       *******************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 3957.20
//
Query:       gi|330507905|ref|YP_004384333.1|  [L=469]
Description: CO dehydrogenase/acetyl-CoA synthase complex subunit beta [Methanosaeta concilii GP6]
Scores for complete 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-57  191.5   0.1    1.4e-56  190.7   0.1    1.4  1  CdhC      CO dehydrogenase/acetyl-CoA synthase complex beta s
  ------ inclusion threshold ------
      0.035   14.0   0.0      0.065   13.1   0.0    1.4  1  MarR_2    MarR family
      0.091   11.3   0.0       0.13   10.8   0.0    1.1  1  DUF1420   Protein of unknown function (DUF1420)


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 !  190.7   0.1   2.3e-60   1.4e-56       2     155 .]       6     159 ..       5     159 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.7 bits;  conditional E-value: 2.3e-60
                              CdhC   2 pvevspafeGeriRkedlyvelggkktkafElvkvkeadevedgkieviGpdideveegsrlplailvevaGkklee 78 
                                        +++sp++eGeriRkedl+ve+gg k+++fEl  ++ +d++edgk+++iGpd+++++egs++p+++ ++v G+k+e+
  gi|330507905|ref|YP_004384333.1|   6 KLDISPMYEGERIRKEDLWVEMGGPKADGFELSIATLMDQIEDGKVNIIGPDLKDIKEGSTIPFGMSFKVGGEKVEK 82 
                                       6899********************99*************************************************** PP

                              CdhC  79 dlEpvlERriHeflnyieGvmHlgqRdiiwvRiskeavekGl.rlkhigevlyaklkeefeaivdkvevtlitdeek 154
                                       dlE+++ERr+H++l+yi G+mHl+qR++iw+R++k+  +kG+ ++++i + +++++k+e+ ++++k+evt++td++k
  gi|330507905|ref|YP_004384333.1|  83 DLESIIERRNHSLLSYISGLMHLNQRYDIWMRLGKSLQKKGVtSWEQIFKPVIELYKAEM-PFIEKMEVTVVTDPAK 158
                                       ******************************************99****************.**************99 PP

                              CdhC 155 v 155
                                       v
  gi|330507905|ref|YP_004384333.1| 159 V 159
                                       7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.1e-05     0.065       9      52 ..     427     469 .]     424     469 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52 
                                       rv+ ++   +g+ +t +++  +l+ls + + ++++ L++ G +e
  gi|330507905|ref|YP_004384333.1| 427 RVISFIEETGGE-FTSSDIRSKLRLSEGQLMQVVEVLQEEGILE 469
                                       788899999986.***************************9875 PP

>> DUF1420  Protein of unknown function (DUF1420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.2e-05      0.13     219     268 ..     309     355 ..     299     360 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.2e-05
                           DUF1420 219 nalglaigaeqfgsllqfsgllsiygilafysflekflesdgvwrkiiii 268
                                       n l ++  a q g   q  g+l+i gil  y f  kfl++dg wr+i+ +
  gi|330507905|ref|YP_004384333.1| 309 NGLPFSTMAGQTGGGKQVVGFLGI-GIL--YYFSSKFLQADGGWRRIVWM 355
                                       777778889999999999999987.776..77889***********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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 0.24s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3593.63
//
Query:       gi|330507906|ref|YP_004384334.1|  [L=67]
Description: hypothetical protein MCON_1943 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 498.43
//
Query:       gi|330507907|ref|YP_004384335.1|  [L=146]
Description: transposase, IS4 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-22   78.1   0.1    5.4e-22   77.6   0.1    1.2  1  DUF772          Transposase domain (DUF772)
  ------ inclusion threshold ------
      0.038   14.4   0.1      0.065   13.6   0.1    1.4  1  Myb_DNA-bind_4  Myb/SANT-like DNA-binding domain


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 !   77.6   0.1     6e-26   5.4e-22       1      72 [.      51     122 ..      51     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 6e-26
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp+++ ++m+kll+lq ++glSd ele+++ +++sfr flg     ++vpd+st + fR+rl++    ++l++e
  gi|330507907|ref|YP_004384335.1|  51 GRPNIDIVIMIKLLVLQRWFGLSDPELERQVADRISFRIFLGT---TEAVPDFSTVWLFRERLIKsgkSKDLWKE 122
                                       9*****************************************5...489***************99887777665 PP

>> Myb_DNA-bind_4  Myb/SANT-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   7.3e-06     0.065      28      57 ..     111     140 ..      94     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-06
                                       ..SS--HHHHHHHHHHHHHHC----HHHHH CS
                    Myb_DNA-bind_4  28 rgkkrnkklWeevaeamaergykrspeqCk 57 
                                        ++ ++k+lW+e +++m+e+gy +++  ++
  gi|330507907|ref|YP_004384335.1| 111 IKSGKSKDLWKELQRQMEEKGYAVKEGSIQ 140
                                       34566677**************98776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1075.13
//
Query:       gi|330507908|ref|YP_004384336.1|  [L=53]
Description: hypothetical protein MCON_1945 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 383.89
//
Query:       gi|330507909|ref|YP_004384337.1|  [L=43]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 320.45
//
Query:       gi|330507910|ref|YP_004384338.1|  [L=240]
Description: hypothetical protein MCON_1947 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0067   16.9   0.0     0.0093   16.5   0.0    1.2  1  Metallophos  Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.022   13.8   0.0      0.028   13.5   0.0    1.1  1  PhoD         PhoD-like phosphatase


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     1e-06    0.0093     104     203 ..      26     128 ..       8     129 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-06
                                       TSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC.HHHHHH..HHHHTTCSEEEEEESSESS.CSSS CS
                       Metallophos 104 nlplaslgsgslkvlllhGgspellvsldklgslnleleapepg.dewlkd..lekrekadwvivlgHsply.rgsg 176
                                       n+p+ +++ +  +++ ++       +++d+l    +   + +++ ++wl +  ++  ++++  i+ +H+p++ +++ 
  gi|330507910|ref|YP_004384338.1|  26 NIPIKVIVLD--DTQRDDDL-----NNPDSL---GYGHASLDNErYDWLVKelDKGQAEGKLMIIAAHIPISvEQAD 92 
                                       4455554444..44444444.....444444...44444444445******9********************94444 PP

                                       CSCCHHHHH.........HHHHHTTESEEEEESSSS CS
                       Metallophos 177 ylfgdeale.........dllkkygvdlvisGHtHv 203
                                         +g + ++         +l +++++ l+i GH H 
  gi|330507910|ref|YP_004384338.1|  93 SMMGWNPAApiseaqlisKLHEYPNLILWIAGHRHL 128
                                       444444444555566666***************995 PP

>> PhoD  PhoD-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.1e-06     0.028     197     301 ..      59     156 ..      29     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-06
                              PhoD 197 eQeqwLkaeLkasrar..WkvlaqqvlmskvdldaelaegalpvnlDawdGypaeRerlletikeakirnvVvLtGD 271
                                       e  +wL +eL + +a+    ++a ++++s  +  a          +      p + ++l++ ++e   + + +++G 
  gi|330507910|ref|YP_004384338.1|  59 ERYDWLVKELDKGQAEgkLMIIAAHIPISVEQ--A-------DSMMGWNPAAPISEAQLISKLHEYP-NLILWIAGH 125
                                       55689999999999987889999999998777..2.......223445578899999******9998.8999***** PP

                              PhoD 272 vHaawandld.ykdpdgeavgvEfvtgsvss 301
                                       +H ++++ l+  +++++e  ++E+ t s+  
  gi|330507910|ref|YP_004384338.1| 126 RHLNIVTALKsPDAARPELGFWEVETASLRD 156
                                       *********53777777999******99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1859.11
//
Query:       gi|330507911|ref|YP_004384339.1|  [L=153]
Description: dCMP deaminase [Methanosaeta concilii GP6]
Scores for complete sequence (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  102.2   2.6    1.6e-29  101.8   2.6    1.2  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    2.5e-18   66.2   1.2    3.3e-18   65.8   1.2    1.1  1  MafB19-deam      MafB19-like deaminase
     0.0013   18.8   2.1     0.0027   17.8   2.0    1.6  2  Bd3614-deam      Bd3614-like deaminase
  ------ inclusion threshold ------
      0.013   15.4   0.8      0.018   15.0   0.8    1.4  1  APOBEC_N         APOBEC-like N-terminal domain
      0.056   13.3   2.4       0.16   11.9   2.4    1.8  1  zf-C3HC4         Zinc finger, C3HC4 type (RING finger)
      0.086   13.0   0.3       0.12   12.5   0.3    1.3  1  APOBEC3          APOBEC3
       0.11   12.5   0.9       0.18   11.9   0.9    1.4  1  NAD1             Novel AID APOBEC clade 1
       0.14   12.3   0.8       0.34   11.1   0.8    1.7  1  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4
        0.2   12.0   0.7       0.38   11.1   0.0    1.9  2  zf-C2H2_jaz      Zinc-finger double-stranded RNA-binding


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 !  101.8   2.6   7.8e-33   1.6e-29       4     100 ..      10     125 ..       7     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 7.8e-33
                                       HHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTG.....................TTB-HHHHHH CS
                   dCMP_cyt_deam_1   4 dekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggs.....................ktiHAEvnAi 59 
                                       de+++e+a+ +ak++ +c + +VGa +vkn++i+ tgyng pag +                     + +HAE+nAi
  gi|330507911|ref|YP_004384339.1|  10 DEYFMEIAIVVAKRS-TCLRNQVGALFVKNKRILTTGYNGAPAGLDhcdvvgcaregvqsgtrhelcRAVHAEQNAI 85 
                                       89*************.************************************************************* PP

                                       HHHHHHTSSCETTEEEEEEE--BHHHHHHHHHHT-SEEEEE CS
                   dCMP_cyt_deam_1  60 lkaaknggsklegatlyvtlePCsmCakaiiqsgikkvvvg 100
                                       ++aa   g+++egatly+t++PC  Cak++i++++ kvv++
  gi|330507911|ref|YP_004384339.1|  86 IQAAMH-GISIEGATLYCTHQPCILCAKMMINARVAKVVYL 125
                                       ****88.99******************************96 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   1.2   1.6e-21   3.3e-18       4     107 ..      10     142 ..       9     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 1.6e-21
                       MafB19-deam   4 ekafrkalaevekatkikedkigavivkdkkviargsn.......................ekelnakataHaEiaa 57 
                                       +++f++++  v k++ +   ++ga+ vk+k+++ +g+n                       ++  +     HaE +a
  gi|330507911|ref|YP_004384339.1|  10 DEYFMEIAIVVAKRSTCLRNQVGALFVKNKRILTTGYNgapagldhcdvvgcaregvqsgtRH--ELCRAVHAEQNA 84 
                                       589**************************************************9999774333..455667****** PP

                       MafB19-deam  58 lqqAakklkskrlddatlyvtlepCdmCagaivqaglkklvygagnpks..........l 107
                                       + qAa  ++s+  ++atly t++pC  Ca+++++a++ k+vy   +p+           +
  gi|330507911|ref|YP_004384339.1|  85 IIQAAMHGISI--EGATLYCTHQPCILCAKMMINARVAKVVYLHCYPDQtaldfleqagI 142
                                       ****8887777..******************************99999856444333333 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.3   2.6e+03      34      47 ..      77      90 ..      73      95 .. 0.78
   2 !   17.8   2.0   1.3e-06    0.0027      76     111 ..      96     124 ..      78     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                       Bd3614-deam 34 vLHAEvnLlapllr 47
                                       +HAE n ++++ +
  gi|330507911|ref|YP_004384339.1| 77 AVHAEQNAIIQAAM 90
                                      57999998887765 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.3e-06
                       Bd3614-deam  76 egarllvtlqcCkmCAalvvaaadapgrevllkvvY 111
                                       ega+l+ t+q+C +CA ++++a +        kvvY
  gi|330507911|ref|YP_004384339.1|  96 EGATLYCTHQPCILCAKMMINARV-------AKVVY 124
                                       79*****************99877.......44555 PP

>> APOBEC_N  APOBEC-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.8   8.9e-06     0.018      46      94 ..      54     116 ..      14     145 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.9e-06
                                       S......................TBCHHHHHHHHHHHHT--.TTEEEEEEEEESS-S-HH....HHHHHHH CS
                          APOBEC_N  46 a......................skHaEelflediedqelrepkkkyeitlYvswsPChessdeCaeklaa 94 
                                                                HaE+  +     q++++  +    tlY++ +PC      Ca+++ +
  gi|330507911|ref|YP_004384339.1|  54 DhcdvvgcaregvqsgtrhelcrAVHAEQNAII----QAAMHGISIEGATLYCTHQPCIL----CAKMMIN 116
                                       0555555555555555555555589***98444....366666788899***********....***9976 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.4   7.9e-05      0.16       4      32 ..      75     117 ..      72     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.9e-05
                                       T-S--SS-E...............E-TTS--B-CHHHHHHHHC CS
                          zf-C3HC4   4 Cleeakepn..............elleCkHsfCskCirkilks 32 
                                       C  + +e+n               +l C+H+ C  C + +++ 
  gi|330507911|ref|YP_004384339.1|  75 CRAVHAEQNaiiqaamhgisiegATLYCTHQPCILCAKMMINA 117
                                       6666666666666667777777789*************99984 PP

>> APOBEC3  APOBEC3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3     6e-05      0.12      30      72 ..      77     116 ..      61     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6e-05
                           APOBEC3  30 kkHAEerfidkirslnldslkqykitcylswsPcpkCaeelve 72 
                                         HAE+ +i + +   ++ +     t+y +  Pc  Ca+ +++
  gi|330507911|ref|YP_004384339.1|  77 AVHAEQNAIIQAAMHGISIEG---ATLYCTHQPCILCAKMMIN 116
                                       57******9998887777666...8**************9998 PP

>> NAD1  Novel AID APOBEC clade 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.9   9.2e-05      0.18      48      91 ..      77     116 ..      57     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.2e-05
                              NAD1  48 kcHaEllflnkikslklldpsqkykvtwylswSPCseCasklae 91 
                                       ++HaE+  + +       +  ++   t+y+++ PC  Ca+ +++
  gi|330507911|ref|YP_004384339.1|  77 AVHAEQNAIIQAAM----HGISIEGATLYCTHQPCILCAKMMIN 116
                                       34999887555533....45578889**************9987 PP

>> SNAD4  Secreted Novel AID/APOBEC-like Deaminase 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.8   0.00017      0.34      21      63 ..      76     117 ..      61     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                             SNAD4  21 ke.haEllflekikseldpsqeyrvtwylswsPCaeCaekiaef 63 
                                       +  haE + + +    ++       t+y +  PC  Ca+ +++ 
  gi|330507911|ref|YP_004384339.1|  76 RAvHAEQNAIIQA--AMHGISIEGATLYCTHQPCILCAKMMINA 117
                                       3359998888777..4554445668**************99875 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       4.8   9.6e+03       2       6 ..     100     104 ..     100     104 .. 0.76
   2 ?   11.1   0.0   0.00019      0.38       4      16 ..     107     119 ..     106     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.8
                                       CBBTT CS
                       zf-C2H2_jaz   2 fYCvl 6  
                                       +YC +
  gi|330507911|ref|YP_004384339.1| 100 LYCTH 104
                                       59*86 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                                       BTTTTBBBSSHHH CS
                       zf-C2H2_jaz   4 CvlCdKyFksena 16 
                                       C+lC+K+++++++
  gi|330507911|ref|YP_004384339.1| 107 CILCAKMMINARV 119
                                       **********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1107.17
//
Query:       gi|330507912|ref|YP_004384340.1|  [L=499]
Description: lysyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.1e-121  406.2   0.0   1.5e-121  405.7   0.0    1.2  1  tRNA-synt_1f  tRNA synthetases class I (K)
    6.5e-06   25.1   0.0     0.0025   16.7   0.0    2.2  2  tRNA-synt_1g  tRNA synthetases class I (M)
     0.0054   16.1   0.0       0.97    8.7   0.0    2.3  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
       0.19   11.3   1.8       0.38   10.3   1.8    1.5  1  TF_Zn_Ribbon  TFIIB zinc-binding


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 !  405.7   0.0  3.4e-125  1.5e-121       2     336 ..       4     328 ..       3     341 .. 0.98

  Alignments for each domain:
  == domain 1  score: 405.7 bits;  conditional E-value: 3.4e-125
                      tRNA-synt_1f   2 aWadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvp 78 
                                       +Wad++aekl         +++ +++++Gi+pSG++HiGn+rev+ta++v+ral +rg ++rli+i+D++D+lR+++
  gi|330507912|ref|YP_004384340.1|   4 HWADVIAEKLE--------GSGPHTIATGITPSGPVHIGNMREVMTAEAVYRALLDRGVQARLIYIADTFDRLRRLY 72 
                                       89999999999........34799***************************************************** PP

                      tRNA-synt_1f  79 enlpekllekylgkpltsiPdpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenrekik 155
                                       ++lpe+ +++++gkpl++iP+p+g+++sya+hf  ++++s+++lgi+ e+++a  lYk+g y++aik+a +++++i+
  gi|330507912|ref|YP_004384340.1|  73 PFLPES-FNEHIGKPLSQIPCPEGCCASYADHFLTPFLKSMERLGIKPEVYRADVLYKEGKYNDAIKTAFSRKDDIA 148
                                       ******.********************************************************************** PP

                      tRNA-synt_1f 156 eilekyrgeereetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeeevdiregngKLqWkvdwamrWaa 232
                                       +il+++ g+   e +sp+ ++c+ cgr +tt+v+ +d ++e++ Y+c +cG +++v++ +g gKL W+vdw++rW +
  gi|330507912|ref|YP_004384340.1| 149 RILKEVSGRAVPEGWSPFDAICKVCGRTNTTHVTGFDLDAETVDYVC-SCGSQGTVSMAGG-GKLVWRVDWPARWPI 223
                                       ***********************************************.**********996.*************** PP

                      tRNA-synt_1f 233 lgVdfEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrfli 308
                                       + V++Ep+GkDha+aGgS+d++++i+ ei+g++aP ++vYe+i+lkg ++m+sS+G v+t++++l+v++pevlr+li
  gi|330507912|ref|YP_004384340.1| 224 FRVTVEPFGKDHATAGGSYDTGKRISeEIYGYPAPFPMVYEWIHLKGVGAMHSSTGIVVTIQEMLDVVPPEVLRYLI 300
                                       ***************************************************************************** PP

                      tRNA-synt_1f 309 lrrkPkkakkldldleilrlvdeYdkle 336
                                       +r+kP+k++++d++l +l+lvdeYd+ +
  gi|330507912|ref|YP_004384340.1| 301 IRNKPEKHIEFDPGLPLLSLVDEYDQRK 328
                                       *************************965 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 !    6.1   0.0    0.0009         4      11      45 ..      28      62 ..      20      66 .. 0.83
   2 !   16.7   0.0   5.5e-07    0.0025     317     361 ..     262     307 ..     254     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0009
                                      SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                      tRNA-synt_1g 11 ngklHlGhllevisaDifaRykrlrgeevlfvcgt 45
                                      +g++H+G+++ev+ a +++R    rg +   +   
  gi|330507912|ref|YP_004384340.1| 28 SGPVHIGNMREVMTAEAVYRALLDRGVQARLIYIA 62
                                      799*****************998888877666555 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.5e-07
                                       EE--EEE--.------------HHHHHHHH-HHHHHHHHHHHS-TT CS
                      tRNA-synt_1g 317 aheyltveg.kKlSkSrgvvvkakealerldadllRYylaaeapek 361
                                       + e++ ++g + + +S g+vv+++e+l+ +++++lRY +++++pek
  gi|330507912|ref|YP_004384340.1| 262 VYEWIHLKGvGAMHSSTGIVVTIQEMLDVVPPEVLRYLIIRNKPEK 307
                                       66899999845799****************************9987 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0     0.003        14      15      59 ..      23      66 ..      11     140 .. 0.71
   2 !    8.7   0.0   0.00022      0.97     246     292 ..     265     312 ..     256     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.003
                                      EEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SH CS
                      tRNA-synt_1e 15 CGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidD 59
                                       G+t    +h+G+ R++++ + + r l ++g + +++  + D  D
  gi|330507912|ref|YP_004384340.1| 23 TGITPSGPVHIGNMREVMTAEAVYRALLDRGVQARLIY-IADTFD 66
                                      69999999*****************9999888776653.444444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00022
                                       -EEETT.BE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE- CS
                      tRNA-synt_1e 246 hlkieg.ekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfk 292
                                       +++++g   m  s + ++ti+++l  + p++lR+l++ ++ +++++f+
  gi|330507912|ref|YP_004384340.1| 265 WIHLKGvGAMHSSTGIVVTIQEMLDVVPPEVLRYLIIRNKPEKHIEFD 312
                                       56666524699999************************9999999985 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.8   8.4e-05      0.38       2      26 ..     169     198 ..     168     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.4e-05
                                       EETTTTCEEC......HEETSTTCEEESSSS CS
                      TF_Zn_Ribbon   2 kCPnCgstnl......veDpergelvCtdCG 26 
                                       +C++Cg tn+       +D+e+ ++vC+ CG
  gi|330507912|ref|YP_004384340.1| 169 ICKVCGRTNTthvtgfDLDAETVDYVCS-CG 198
                                       6********66***9999*********6.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3582.42
//
Query:       gi|330507913|ref|YP_004384341.1|  [L=145]
Description: nucleoside 2-deoxyribosyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (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   63.9   0.0    1.7e-17   63.6   0.0    1.1  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
    1.8e-11   44.3   0.0    2.3e-11   44.0   0.0    1.2  1  Nuc_deoxyri_tr2  Nucleoside 2-deoxyribosyltransferase like
  ------ inclusion threshold ------
      0.055   13.3   0.0      0.089   12.6   0.0    1.3  1  DUF3670          SNF2 Helicase protein


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 !   63.6   0.0   2.9e-21   1.7e-17       1     127 [.      10     117 ..      10     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 2.9e-21
                                       EEEESGGGCSC....CCHHHHHHHHHHHHTTTTEEE-CCTT-TT....--SSHHHHHHHHHHHHHC-SEEEEE--SS CS
                   Nuc_deoxyrib_tr   1 iYLAgplvFrp....dakalaarlkallaengldglaPldneaelelpaeetaraiyeadialirqaDavianldpf 73 
                                       iYL gpl F++    + ++l + l+++la++g++++ P +  ++     + + ++i+ ++++ ++++D+++a+ld+ 
  gi|330507913|ref|YP_004384341.1|  10 IYLSGPL-FSAgeiaWGRELSSFLRERLANAGVQVIWPYELSIN-----QLEPEEIFGENLRALDRCDLMVAILDGP 80 
                                       9******.**73333555666667888888889******77774.....567799*********************8 PP

                                       SSSS--HHHHHHHHHHHHCT-EEEEE-S-GCGHHHHHTSSB.TTS.B-TTSCHC CS
                   Nuc_deoxyrib_tr  74 rgpeaDsGtafEvGyavalgkpvlayttdarelrervealrdadgllvedfglp 127
                                            D+Gta+E+G +  +gk+vl+ +td r+               +e++   
  gi|330507913|ref|YP_004384341.1|  81 L---VDDGTAWEIGRFFLQGKKVLGIRTDIRKA--------------GESERSR 117
                                       8...***************************93..............3344333 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 !   44.0   0.0   3.8e-15   2.3e-11       2     107 ..       8     106 ..       7     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 3.8e-15
                                       EEEEEEE---SSSST-HHHHHHHHH.HTSSS-EEEEE----SS-----HHHHH.....HHHHHHHHHHHH-SEEEEE CS
                   Nuc_deoxyri_tr2   2 ksvFLaGsteseaetdWredlteaL.saipklgvtvfnPqredwdseleedrskkrfreqvewelealekAdvvvfv 77 
                                       ++++L+G+++s +e  W ++l + L ++  ++gv+v+ P++  +++ l       + +e++  +l+al+++d++v++
  gi|330507913|ref|YP_004384341.1|   8 HKIYLSGPLFSAGEIAWGRELSSFLrERLANAGVQVIWPYELSINQ-L-------EPEEIFGENLRALDRCDLMVAI 76 
                                       79***********************88888***********99665.4.......7889****************** PP

                                       E-TT---HHHHHHHHHHTTSS-EEEEE-TT CS
                   Nuc_deoxyri_tr2  78 fdgedsatrslvElglaaakgkkvvlvpkg 107
                                       +dg+ ++  + +E+g +  +gkkv++++++
  gi|330507913|ref|YP_004384341.1|  77 LDGPLVDDGTAWEIGRFFLQGKKVLGIRTD 106
                                       ***77776789***************9987 PP

>> DUF3670  SNF2 Helicase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.5e-05     0.089      12      37 ..      27      49 ..      25      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                           DUF3670 12 eaaefLkeaaeaLeaaGvgVllPrwl 37
                                      e+ +fL+e   +L++aGv+V++P +l
  gi|330507913|ref|YP_004384341.1| 27 ELSSFLRE---RLANAGVQVIWPYEL 49
                                      67789999...9***********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1003.41
//
Query:       gi|330507914|ref|YP_004384342.1|  [L=264]
Description: Ser/Thr protein phosphatase family protein [Methanosaeta concilii GP6]
Scores for complete 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   26.7   0.0    8.2e-06   26.5   0.0    1.2  1  Metallophos    Calcineurin-like phosphoesterase
    0.00033   20.9   0.0    0.00045   20.5   0.0    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   9.1e-10   8.2e-06       2     103 ..      29     156 ..      28     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 9.1e-10
                                       EEEEEESBTB..........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS...HHHHHHHHHHHHHHHH.. CS
                       Metallophos   2 rilvigDlHl..........algggqlddllkllddllreekpdlvllaGDlvdrg...dlekellellaalvky.. 63 
                                       r+l+ +DlHl           + + q +++l+ll+  l+   pd +l++GDl +     +++++ +   ++l ++  
  gi|330507914|ref|YP_004384342.1|  29 RLLIASDLHLglehelwlggVSIPSQTRKILALLKGYLDMTMPDRLLILGDLKHNVpktSWQEKREVP-DFLRQLsa 104
                                       7899****************9999***************************88887666777744444.55555566 PP

                                       TSEEEEEC-TTS.................CHHHHHHHHHHHHHHHHHHHEHHHCEEE CS
                       Metallophos  64 pipvylllGNHe.................gfeeellnkygylgifsepwrsdaevfn 103
                                        ++v ++ GNH+                 g    + + +gy++  +++w  ++ v +
  gi|330507914|ref|YP_004384342.1| 105 QVRVDIVSGNHDsnladmappgvrvhpstG---IVREGRGYFH--GHTWPEEKVVRS 156
                                       8999********888888888776544431...2222222222..555655544444 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 !   20.5   0.0     5e-08   0.00045       2      71 ..      29     120 ..      29     171 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5e-08
                     Metallophos_2   2 klaiiSDlH................snldaleavlealkevgvdaiihaGD....leeeep...........evlee 47 
                                       +l+i SDlH                + +++l+ +   l+ + +d+++ +GD    +    p           ++l++
  gi|330507914|ref|YP_004384342.1|  29 RLLIASDLHlglehelwlggvsipsQTRKILALLKGYLDMTMPDRLLILGDlkhnV----PktswqekrevpDFLRQ 101
                                       689*****************98884334444444445666889********44440....23444444222256666 PP

                     Metallophos_2  48 llelapvlaVrGNnDeevveedvl 71 
                                       l ++ +v +V GN+D     + ++
  gi|330507914|ref|YP_004384342.1| 102 LSAQVRVDIVSGNHD-----SNLA 120
                                       66666**********.....2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1947.27
//
Query:       gi|330507915|ref|YP_004384343.1|  [L=185]
Description: orotate phosphoribosyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-08   34.0   0.0    2.4e-08   33.7   0.0    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0064   16.0   0.0     0.0082   15.6   0.0    1.1  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   2.7e-12   2.4e-08      59     133 ..      91     160 ..      62     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.7e-12
                                       EEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHH CS
                      Pribosyltran  59 rkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeev 133
                                       ++v+++p++ ++++ +     + +++ +g+kV +V+D++++G +ll+a+++++++g e v + +++d+ ++ +ev
  gi|330507915|ref|YP_004384343.1|  91 LIVRKEPKKHGTMSYV-----EGPALEKGSKVAVVEDVVTSGASLLRAIDRIAAAGYEPVQALTILDREEGGREV 160
                                       4444444444444432.....28999*******************************************999887 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.1e-07    0.0082      97     190 ..      90     182 ..      73     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.1e-07
                           UPRTase  97 lglqreeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeef 173
                                       +++ r+e +++  + y   P+  + ++v +++ v+ +G+s+  ai+++    +g e +  l++l  eeg +++ ee 
  gi|330507915|ref|YP_004384343.1|  90 ALIVRKEPKKHGTMSYVEGPALEKGSKVAVVEDVVTSGASLLRAIDRIAA--AGYEPVQALTILDREEGGREVIEER 164
                                       45667777788889999999988999************************..55689***********999998887 PP

                           UPRTase 174 p.kvkvvtaavDeeldek 190
                                         +++      D +ld+k
  gi|330507915|ref|YP_004384343.1| 165 GfSLQALYDRSDLGLDKK 182
                                       667776666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1368.40
//
Query:       gi|330507916|ref|YP_004384344.1|  [L=211]
Description: hypothetical protein MCON_1954 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   15.4   3.1      0.044   14.1   3.1    1.9  1  DUF11     Domain of unknown function DUF11


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.1   2.4e-06     0.044       8      45 ..      34      70 ..      23     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-06
                             DUF11  8 sevrpGdtvtytltvtNtgpasangvvvtDtlPaglay 45
                                      + v+ Gd   +t+t+t +g+++  ++v+t  lP+g ++
  gi|330507916|ref|YP_004384344.1| 34 PSVNLGDSAMVTVTLTYYGNNAT-QAVITPGLPPGIET 70
                                      369*************7776665.********999774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1627.21
//
Query:       gi|330507917|ref|YP_004384345.1|  [L=408]
Description: hypothetical protein MCON_1955 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2762.57
//
Query:       gi|330507918|ref|YP_004384346.1|  [L=329]
Description: Met10+ like methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-61  206.9   0.0    3.6e-61  206.4   0.0    1.2  1  Met_10           Met-10+ like-protein
    0.00033   20.5   0.6     0.0016   18.3   0.0    2.4  3  Trm5_N           tRNA methyltransferase 5 N-terminal domain
     0.0007   19.2   0.0     0.0013   18.3   0.0    1.4  1  MTS              Methyltransferase small domain
     0.0044   17.0   0.0      0.011   15.6   0.0    1.6  2  Methyltransf_18  Methyltransferase domain
      0.006   16.2   0.0     0.0088   15.6   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
      0.032   14.9   0.0      0.071   13.8   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
      0.046   13.4   0.0      0.074   12.7   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.17   10.8   0.0       0.27   10.2   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
        0.2   10.9   0.0       0.27   10.5   0.0    1.1  1  DNA_methylase    C-5 cytosine-specific DNA methylase


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.4   0.0   1.8e-64   3.6e-61       2     199 .]      81     276 ..      80     276 .. 0.98

  Alignments for each domain:
  == domain 1  score: 206.4 bits;  conditional E-value: 1.8e-64
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       +++i Gdv++++++ +l+ ++  i++++l++  +++tvlr+++  eg fR++  e++aG   tet+h+Eng++f+lD
  gi|330507918|ref|YP_004384346.1|  81 GWHIQGDVIVVKIHPRLDSHQDRIARALLNFYpRCHTVLRDYGI-EGPFREPVREIIAGTR-TETVHRENGVTFHLD 155
                                       799*****************************9********998.***************9.*************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                         kv+fs ++ +Er+r+ +l   ge Vvd+fAGiG+f++p+a++s++++vlai+lnP++++yl+ nik N ve++v+
  gi|330507918|ref|YP_004384346.1| 156 ARKVMFSAGNLNERMRMGNL-GRGEYVVDMFAGIGYFSLPMAVHSRPRKVLAIELNPNAYHYLCLNIKKNGVERIVE 231
                                       ****************9886.78****************************************************** PP

                                       EEES-GGG---TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 155 pileDgrevireqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                       p+l+D+++v++e +adrvvm++++ +  +l k + al+ ggv hy
  gi|330507918|ref|YP_004384346.1| 232 PVLGDCAKVTPEGVADRVVMGMVQVTDRYLLKGIGALRSGGVLHY 276
                                       ********************************************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 !   18.3   0.0     8e-07    0.0016      11      44 ..      10      43 ..       4      46 .. 0.86
   2 ?   -2.0   0.0       1.7   3.4e+03      12      27 ..     156     171 ..     155     174 .. 0.87
   3 ?   -2.6   0.2       2.7   5.3e+03       1       6 [.     309     314 ..     309     315 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8e-07
                                      HHHHHHHHTT-B-TTS--EEETTEEEEEB-S--H CS
                            Trm5_N 11 kvRkkLlekglLdrnyKIksdddylyIPvkeepe 44
                                       + k +++ g Ldr++K+    ++++IPv+ +++
  gi|330507918|ref|YP_004384346.1| 10 ATLKMVIAQGFLDRGRKVVEKSGHVEIPVRCNIP 43
                                      67899************************87666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                                       HHHHHHHTT-B-TTS- CS
                            Trm5_N  12 vRkkLlekglLdrnyK 27 
                                       +Rk++ ++g L+ +++
  gi|330507918|ref|YP_004384346.1| 156 ARKVMFSAGNLNERMR 171
                                       7999999****99876 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.7
                                       EEEEEG CS
                            Trm5_N   1 cikVpk 6  
                                       ci+V+k
  gi|330507918|ref|YP_004384346.1| 309 CIRVKK 314
                                       9***99 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   6.7e-07    0.0013      32     103 ..     178     251 ..     153     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.7e-07
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivs 103
                                        + v+D+ +G+G+ ++ +a +s   +v +++ + +A +    n+++n++e  ve v  d+ + ++e+  d +v+
  gi|330507918|ref|YP_004384346.1| 178 GEYVVDMFAGIGYFSLPMAVHSRPRKVLAIELNPNAYHYLCLNIKKNGVEriVEPVLGDCAKVTPEGVADRVVM 251
                                       5569**********************************************99999******9999999999986 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.7   5.3e+03      38      71 ..       8      40 ..       3      51 .. 0.69
   2 !   15.6   0.0   5.6e-06     0.011      15      91 ..     178     253 ..     167     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.7
                   Methyltransf_18 38 akkviasDinegplekakeniekagledkievrl 71
                                      a+  + + i++g l++ ++ +ek+g+  +i vr+
  gi|330507918|ref|YP_004384346.1|  8 APATLKMVIAQGFLDRGRKVVEKSGHV-EIPVRC 40
                                      556666778899999999999988763.455554 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.6e-06
                   Methyltransf_18  15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvviaGm 91 
                                       g+ v+D  +  gy ++ ++ +++ +kv+a+++n+++++    ni+k+g+e  +e +l+d  ++  e+ v   v++Gm
  gi|330507918|ref|YP_004384346.1| 178 GEYVVDMFAGIGYFSLPMAVHSRPRKVLAIELNPNAYHYLCLNIKKNGVERIVEPVLGDCAKVTPEG-VADRVVMGM 253
                                       67788888889999999999****************************************9988655.666667788 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   4.4e-06    0.0088       2      63 ..     179     242 ..     178     275 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.4e-06
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfella 63 
                                       ++++D+f+G G  +  +a +   +kv aie n++       N +  gv+  + +vlgd+ +++ 
  gi|330507918|ref|YP_004384346.1| 179 EYVVDMFAGIGYFSLPMAVHsrPRKVLAIELNPNAYHYLCLNIKKNGVERIVEPVLGDCAKVTP 242
                                       689**************99866689**********************************99654 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.6e-05     0.071       1      76 [.     181     256 ..     181     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       v+d+ +G G ++l +a +    kv+++++++++  +   +++++g+   ve v gd+ ++  ++g  D vv+ g+++
  gi|330507918|ref|YP_004384346.1| 181 VVDMFAGIGYFSLPMAVHSRPRKVLAIELNPNAYHYLCLNIKKNGVerIVEPVLGDCAKVT-PEGVADRVVM-GMVQ 255
                                       899*************99768*************************99999********98.6679999999.4444 PP

                                       G CS
                   Methyltransf_25  76 h 76 
                                       +
  gi|330507918|ref|YP_004384346.1| 256 V 256
                                       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 ?   12.7   0.0   3.7e-05     0.074      40     105 ..     176     242 ..     156     258 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                                       HCC-EEEETT-TTS..HHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHC CS
                     Cons_hypoth95  40 iegarvLDlfaGsG..alglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleall 105
                                       ++g+ v+D+faG G  +l +   SR  +k++++e +++a++ l  n+++ ++e  ++ +  d ++  +
  gi|330507918|ref|YP_004384346.1| 176 GRGEYVVDMFAGIGyfSLPMAVHSRP-RKVLAIELNPNAYHYLCLNIKKNGVERIVEPVLGDCAKVTP 242
                                       78899*********444555566887.99********************9988766666666665555 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00013      0.27     205     251 ..     181     229 ..     168     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                   tRNA_U5-meth_tr 205 llelycGnGnfslalarnf..ekvlateiakssveaaqyniaankidnv 251
                                       +++++ G G fsl++a +   +kvla e+  ++ +    ni++n ++ +
  gi|330507918|ref|YP_004384346.1| 181 VVDMFAGIGYFSLPMAVHSrpRKVLAIELNPNAYHYLCLNIKKNGVERI 229
                                       6789*********999654228**********************99876 PP

>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00014      0.27       3      49 ..     181     236 ..     180     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                                       EEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-.........-SEEEE CS
                     DNA_methylase   3 fidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk........kvsigD 49 
                                       ++d+faGiG f+l ++  +  + v+a+e +++a   ++ n+k        ++++gD
  gi|330507918|ref|YP_004384346.1| 181 VVDMFAGIGYFSLPMAVHSrPRKVLAIELNPNAYHYLCLNIKkngverivEPVLGD 236
                                       79**************999899******************9865555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2736.39
//
Query:       gi|330507919|ref|YP_004384347.1|  [L=108]
Description: hypothetical protein MCON_1958 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 874.55
//
Query:       gi|330507920|ref|YP_004384348.1|  [L=148]
Description: heat shock protein Hsp20 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-11   44.8   3.2    3.6e-10   39.9   3.2    2.1  1  HSP20       Hsp20/alpha crystallin family
    2.5e-07   30.1   0.1    3.5e-07   29.7   0.1    1.2  1  ArsA_HSP20  HSP20-like domain found in ArsA
    6.7e-05   22.9   3.4     0.0017   18.4   1.8    2.2  2  FKBP26_C    FKBP26_C-terminal
    0.00026   21.3   0.1    0.00036   20.9   0.1    1.2  1  PIH1_CS     PIH1 CS-like domain
  ------ inclusion threshold ------
      0.023   15.7   1.2       0.04   14.9   1.2    1.4  1  CS          CS domain
      0.066   13.7   1.5       0.22   12.0   0.8    1.9  2  HMA         Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   3.2   1.2e-13   3.6e-10       1     101 [.      65     147 ..      65     148 .] 0.92

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.2e-13
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslk 77 
                                       d+++e+++f+v +++pg++ke +k++v d++v +k   e               +kF +++ L   +d+d+ kas+k
  gi|330507920|ref|YP_004384348.1|  65 DVMSEKDKFKVFVELPGVEKEKVKLDVADDSVEIKTDDE---------------KKFYKMIYLDSTIDPDSAKASYK 126
                                       67899******************************9999...............689999***************** PP

                                       TTEEEEEEEBSS--..-------- CS
                             HSP20  78 dGvLtvtvpkkepekkkkerkiqi 101
                                       +G+Lt++++kke+    k ++++i
  gi|330507920|ref|YP_004384348.1| 127 NGILTLELDKKEKR---KGKEVKI 147
                                       **********9998...5565555 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 !   29.7   0.1   1.2e-10   3.5e-07       2      62 ..      71     133 ..      70     134 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.2e-10
                        ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkig...nfrRqitLPsvlarkevtsAkfedgvLeIr 62 
                                       d++++ ++LP+v+ke+++l  ++d   Ik +   +f + i L s+++ + + +A++++g L+ +
  gi|330507920|ref|YP_004384348.1|  71 DKFKVFVELPGVEKEKVKLDVADDSVEIKTDdekKFYKMIYLDSTIDPDSA-KASYKNGILTLE 133
                                       8999***************************66666677**********77.*********976 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.8   5.6e-07    0.0017       2      44 ..      70     110 ..      69     114 .. 0.92
   2 ?    4.2   0.0     0.016        47      15      37 ..     115     137 ..     108     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.6e-07
                                       HHHHHHHHHHH-TT--..--EEEEETTEEEEE--TTGGGSTTH CS
                          FKBP26_C   2 kekikelIkryiPnidlekfkieiedktvtIelpeeakFieni 44 
                                       k+k k  +++  P +++ek+k+ ++d +v+I+ ++e kF++ i
  gi|330507920|ref|YP_004384348.1|  70 KDKFKVFVEL--PGVEKEKVKLDVADDSVEIKTDDEKKFYKMI 110
                                       8999999998..***************************9765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.016
                                       T--..--EEEEETTEEEEE--TT CS
                          FKBP26_C  15 nidlekfkieiedktvtIelpee 37 
                                        id + +k +++++++t el+++
  gi|330507920|ref|YP_004384348.1| 115 TIDPDSAKASYKNGILTLELDKK 137
                                       5888999**************98 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   1.2e-07   0.00036      32      92 ..      72     132 ..      55     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.2e-07
                           PIH1_CS  32 elaieielPllksikevklrvgerrleleskk.akyfLslkLpYpvdedkveAkFvkktklL 92 
                                       ++++ +elP++ + ++vkl+v  +++e++++  +k+   + L+ ++d d+++A +++   +L
  gi|330507920|ref|YP_004384348.1|  72 KFKVFVELPGV-EKEKVKLDVADDSVEIKTDDeKKFYKMIYLDSTIDPDSAKASYKNGILTL 132
                                       78999******.7899************888764555559***************8765555 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.2   1.3e-05      0.04       9      76 .]      70     136 ..      68     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                       TTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE...TSCEEEEECEBSS-BETTTEEEEEETTEEEEEEEB CS
                                CS   9 ldeVvvtiyvkkvnikkkdvkvefkerslkvki...gkeklliegeLfgpIdpeesswtieskkveitLkK 76 
                                       +d+ +v +++++v  +k++vk++   +s+++k    +  k+++   L + Idp++++ + ++  + + L+K
  gi|330507920|ref|YP_004384348.1|  70 KDKFKVFVELPGV--EKEKVKLDVADDSVEIKTddeK--KFYKMIYLDSTIDPDSAKASYKNGILTLELDK 136
                                       5778999*****9..*************999985333..555444588*********99999888888887 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.8   7.3e-05      0.22      19      48 ..      75     105 ..      74     118 .. 0.85
   2 ?   -0.0   0.0      0.41   1.2e+03      27      46 ..     119     138 ..     112     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.3e-05
                               HMA  19 vLselpgV..esvkvdlatktvtVegdaestk 48 
                                       v+ elpgV  e+vk+d+a ++v++++d+e+ k
  gi|330507920|ref|YP_004384348.1|  75 VFVELPGVekEKVKLDVADDSVEIKTDDEK-K 105
                                       6669************************98.4 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.41
                               HMA  27 esvkvdlatktvtVegdaes 46 
                                       +s+k +++++ +t e+d  +
  gi|330507920|ref|YP_004384348.1| 119 DSAKASYKNGILTLELDKKE 138
                                       58899999999999987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1272.77
//
Query:       gi|330507921|ref|YP_004384349.1|  [L=581]
Description: glycyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete 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-24   83.6   0.1    2.5e-23   82.0   0.1    1.9  1  HGTP_anticodon  Anticodon binding domain
    1.4e-09   38.2   0.0      5e-09   36.4   0.0    1.8  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
      0.024   14.8   0.7       0.52   10.5   0.1    2.4  2  Zn-ribbon_8     Zinc ribbon domain
       0.11   13.0   0.6        1.4    9.6   0.1    2.6  2  zf-C2H2         Zinc finger, C2H2 type
       0.13   13.2   0.3         29    5.8   0.0    2.6  2  zf-C2H2_4       C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.1   6.9e-27   2.5e-23       1      93 [.     470     560 ..     470     561 .. 0.96

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 6.9e-27
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       +v+v+pl + + el   akk+ eeLr  g+r+++d  ++sig+++r+ d++g+p+ v+++++++e+gtvt+rdrd++
  gi|330507921|ref|YP_004384349.1| 470 EVAVLPLMD-RSELVGPAKKILEELRSRGMRTDYD-TSGSIGRRYRRNDEIGTPYEVTIDYETIEEGTVTIRDRDSM 544
                                       599*****9.777*********************7.8**************************************** PP

                                       EEEEEETTHHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklke 93 
                                       +q+rv++ ++v+kl++
  gi|330507921|ref|YP_004384349.1| 545 SQVRVARWQVVDKLQA 560
                                       *************997 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 !   36.4   0.0   1.4e-12     5e-09      13     177 ..     158     444 ..     150     446 .. 0.62

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.4e-12
                                       E-SSSHHHHHHHHHHHEEEB.GG.SSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  13 LkPtneetfvelirdevlrs.kr.LPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikai 87 
                                       ++P+  +++   +    lr  +  LP+  +qi+  yR+E s  +G++R+reF+q ++++f  + +      d +kai
  gi|330507921|ref|YP_004384349.1| 158 MRPETAQGMFINFPRL-LRYfRGaLPFAAVQIGKSYRNEISPRQGVIRLREFTQAEAEIFIDPRDKTHPRFDEVKAI 233
                                       5666655555444433.6664335****************9566******************766666666667777 PP

                                       HHHHHHTT.SCEEEEEEGTTSC....................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxx....................................................... RF
                      tRNA-synt_2b  88 sriferlglefraiielmsaks....................................................... 109
                                          f +   +++ ++e ms+++                                                       
  gi|330507921|ref|YP_004384349.1| 234 RMKFYSQEAQEKGVEEEMSFGEavergvvahqtlayyvartyqyllavgidpqklrfrqhksdemahyaadcwdaev 310
                                       65555555567889999997777778877777777777777777777777777776666665555555555555555 PP

                                       ..........BTTSEEEEEEEEETT.................................................... CS
                                       ..........xxxxxxxxxxxxxxx.................................................... RF
                      tRNA-synt_2b 110 ..........adykdkkefeavses.................................................... 124
                                                 +                                                                  
  gi|330507921|ref|YP_004384349.1| 311 lldrlgwielV-------------Gvadrtdydlkahttvskvnlsvfvnygqpkkrkktvvkpdfkalgpmfkska 374
                                       55555555551.............03333333333333555555555555666666666666666666677777777 PP

                                       ...............TSEEEEEEEEEEEETHHHHHTTE.EEECT..TSSEEEEEEEEEEEEHHHHHHHHHH CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxx.xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 125 ...............ltkgieigtiqklgtrlserlga.tvlde..nnreksvimicaaigveRllsaile 177
                                                       + +i+ + i +      + l   + ++e   ++e  +++i  ++g+ R+l  il+
  gi|330507921|ref|YP_004384349.1| 375 kavgealralapeqlAGEKIQ-VNIDGETIDIDRSLVSfESVEEevRGEEVVPHVIEPSFGIDRILYSILD 444
                                       777777777777776444443.3333333333333333322232014567777777878888888777776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.066   2.4e+02      23      34 ..      82      93 ..      72      98 .. 0.73
   2 ?   10.5   0.1   0.00014      0.52      18      37 ..     116     135 ..     112     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.066
                       Zn-ribbon_8 23 dapltaCPeCgs 34
                                       +plt C+eC++
  gi|330507921|ref|YP_004384349.1| 82 SDPLTGCKECKE 93
                                      357788999965 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00014
                       Zn-ribbon_8  18 lqsisdapltaCPeCgsevr 37 
                                       + + +++++++CPeCg+e+ 
  gi|330507921|ref|YP_004384349.1| 116 IYRCMQENEITCPECGGELS 135
                                       55566778999*****9875 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00038       1.4       3      20 ..      88     104 ..      88     106 .. 0.95
   2 ?    0.6   0.0      0.26   9.3e+02       2       7 ..     126     131 ..     125     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00038
                                       ETTTTEEESSHHHHHHHH CS
                           zf-C2H2   3 CpdCgksFkrksnLkrHi 20 
                                       C++C++++ r ++L +Hi
  gi|330507921|ref|YP_004384349.1|  88 CKECKEVY-RADHLIKHI 104
                                       ********.********9 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.26
                                       EETTTT CS
                           zf-C2H2   2 kCpdCg 7  
                                       +Cp+Cg
  gi|330507921|ref|YP_004384349.1| 126 TCPECG 131
                                       8****9 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0082        29       3      21 ..      88     105 ..      87     108 .. 0.91
   2 ?    4.7   0.1     0.019        67       2      16 ..     126     140 ..     125     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0082
                         zf-C2H2_4   3 CpiCgksFsskkaLlrHlk 21 
                                       C+ C++++ + ++L +H+ 
  gi|330507921|ref|YP_004384349.1|  88 CKECKEVY-RADHLIKHII 105
                                       ********.********86 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.019
                         zf-C2H2_4   2 kCpiCgksFsskkaL 16 
                                       +Cp Cg+  ss +++
  gi|330507921|ref|YP_004384349.1| 126 TCPECGGELSSVYEF 140
                                       6********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 3263.91
//
Query:       gi|330507922|ref|YP_004384350.1|  [L=221]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (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    7.7  10.2        1.4    8.2   3.2    2.2  2  ThrE      Putative threonine/serine exporter
        8.4    6.7   8.0         21    5.4   0.1    2.3  2  DUF1772   Domain of unknown function (DUF1772)


Domain annotation for each model (and alignments):
>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.6    0.0038        34     163     218 ..      54     129 ..      36     134 .. 0.61
   2 ?    8.2   3.2   0.00016       1.4     129     194 ..     149     214 ..     144     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0038
                              ThrE 163 vaaflasllallavs.l.................glgln...pdaiiigsil..lLvPGlpltnavrDllsgdlvsG 216
                                       + af+a +la+ ++  +                 +   +   +   i+g++l  +++P ++ +nav+ l+ gd +sG
  gi|330507922|ref|YP_004384350.1|  54 TIAFVALALAISLILeWqrlkgkirlpevraqeeH---KvasFVYYITGCLLcvVFLPKMIAVNAVLFLSLGDTISG 127
                                       44444444443332231333444444544433221...143356667777642268899999999999999999999 PP

                              ThrE 217 la 218
                                       la
  gi|330507922|ref|YP_004384350.1| 128 LA 129
                                       87 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00016
                              ThrE 129 dwidflvaflagllggllrlllakrglnsfvleavaaflasllallavslglglnpdaiiigsill 194
                                       +++ ++v+f   ll+g+l + +++ +++ +++ a+aa +a  +a+++   +l++n+++ + +++++
  gi|330507922|ref|YP_004384350.1| 149 SLPIMAVMFSSCLLIGYLVSGITQLSFPVYLAGAAAATIADGVAVIINGNSLDDNFSIPVFSGLVM 214
                                       567899*****************************************9988899998888888765 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0024        21      39      85 ..      55     114 ..      38     146 .. 0.72
   2 ?    3.4   3.5    0.0099        88      40      76 ..     151     188 ..     138     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0024
                           DUF1772  39 fpplallsalafayla...............araasrgarllylaaaallllsivpyTllvm 85 
                                       + ++al+ a++++                  a+   + a+ +y+++++ll+++ +p  ++v+
  gi|330507922|ref|YP_004384350.1|  55 IAFVALALAISLI--LewqrlkgkirlpevrAQEEHKVASFVYYITGCLLCVVFLPKMIAVN 114
                                       3333333333333..14578999999999987777788888887878889988777666665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0099
                           DUF1772  40 pp.lallsalafa.ylaaraasrgarllylaaaalllls 76 
                                       p  +++ s+ +++ yl+ +   + ++ +yla+aa+++++
  gi|330507922|ref|YP_004384350.1| 151 PImAVMFSSCLLIgYLV-SGITQLSFPVYLAGAAAATIA 188
                                       44345555555554888.789999999999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1580.36
//
Query:       gi|330507923|ref|YP_004384351.1|  [L=215]
Description: adenylate kinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-60  204.0   0.0    1.4e-60  203.8   0.0    1.0  1  ADK              Adenylate kinase
    1.3e-28  100.1   0.2    3.9e-28   98.6   0.0    1.7  2  AAA_17           AAA domain
    2.3e-17   62.6   2.4    8.4e-17   60.9   1.8    2.1  2  ADK_lid          Adenylate kinase, active site lid
    1.9e-06   28.5   0.0    3.5e-06   27.6   0.0    1.4  1  AAA_18           AAA domain
    5.4e-05   23.6   0.1      0.048   13.9   0.0    2.2  2  Hydin_ADK        Hydin Adenylate kinase-like domain
    0.00041   20.5   0.0     0.0012   19.0   0.0    1.7  2  AAA_33           AAA domain
     0.0024   17.7   0.0      0.004   16.9   0.0    1.3  1  Cytidylate_kin   Cytidylate kinase
     0.0026   18.2   0.0     0.0046   17.4   0.0    1.5  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.019   14.7   0.0       0.62    9.7   0.0    2.2  1  Thymidylate_kin  Thymidylate kinase
      0.027   14.2   0.0      0.044   13.5   0.0    1.3  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.053   14.0   0.1      0.053   14.0   0.1    1.4  1  ABC_tran         ABC transporter
      0.061   13.3   0.0       0.12   12.4   0.0    1.5  1  Pox_A3L          Poxvirus A3L Protein
      0.067   13.1   0.2       0.14   12.0   0.1    1.6  2  NTPase_1         NTPase
       0.15   11.8   0.3       0.54    9.9   0.0    2.0  3  AAA_24           AAA domain
       0.18   11.8   0.0       0.45   10.5   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)


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 !  203.8   0.0   1.2e-63   1.4e-60       1     150 [.       5     189 ..       5     190 .. 0.99

  Alignments for each domain:
  == domain 1  score: 203.8 bits;  conditional E-value: 1.2e-63
                                       EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgf 77 
                                       llG+Pg+GKGtqa+ +++ky+++h+stGd+lR++v+sgt+lG eak++md+g+lvpd ++++++k++l+k+d k g+
  gi|330507923|ref|YP_004384351.1|   5 LLGPPGSGKGTQAKMIADKYKVTHVSTGDILRENVRSGTPLGVEAKKFMDAGKLVPDALLIDIIKDRLAKDDVKGGW 81 
                                       79*************************************************************************** PP

                                       EEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                               ADK  78 llDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltg................................ 122
                                       +lDGfPRt++qaeal+++l + ++k+d+vl++dvp+e lv+R+tg                                
  gi|330507923|ref|YP_004384351.1|  82 MLDGFPRTMPQAEALDKILPTLGQKIDVVLNIDVPDEELVKRVTGrrmckcgttyhvqfnppkvegkcdacgadlyq 158
                                       ***************************************************************************** PP

                                       ...GSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK 123 ...DneetvkkRletykkqtkplidyykkkg 150
                                          Dneetvk+Rl++y++qt+plidyy+k+g
  gi|330507923|ref|YP_004384351.1| 159 radDNEETVKQRLSAYHAQTQPLIDYYNKRG 189
                                       ****************************987 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.0   3.2e-31   3.9e-28       1     123 [.       6     128 ..       6     132 .. 0.95
   2 ?   -1.3   0.1       2.3   2.7e+03     126     136 .]     158     168 ..     155     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 3.2e-31
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS..HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrggl..akardemrklpleekkelqkeaaekiaeeakkkgvl 75 
                                       lG+PGsGKgtq++ +++ky++th+s+Gd+lre++++g    ++a++ m+ ++l+++  l +++++++a+++ k+g++
  gi|330507923|ref|YP_004384351.1|   6 LGPPGSGKGTQAKMIADKYKVTHVSTGDILRENVRSGTPlgVEAKKFMDAGKLVPDALLIDIIKDRLAKDDVKGGWM 82 
                                       7*********************************999744689999999**************************** PP

                                       EEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHT CS
                            AAA_17  76 vdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdr 123
                                       +dg+pr+  qa++ld++     +++  d+++ +++++ee+++r+  +r
  gi|330507923|ref|YP_004384351.1|  83 LDGFPRTMPQAEALDKILPTLGQKI--DVVLNIDVPDEELVKRVTGRR 128
                                       ******************9999999..****************98875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.3
                                       T-TS-SHHHHH CS
                            AAA_17 126 grdddneesik 136
                                       +r+ddnee++k
  gi|330507923|ref|YP_004384351.1| 158 QRADDNEETVK 168
                                       69999999976 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.1   1.3e+03      25      34 ..     114     123 ..      91     124 .. 0.85
   2 !   60.9   1.8     7e-20   8.4e-17       1      36 []     127     161 ..     127     161 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                                       TTT--.-B-- CS
                           ADK_lid  25 DkCGepLvqR 34 
                                       D++ e+Lv+R
  gi|330507923|ref|YP_004384351.1| 114 DVPDEELVKR 123
                                       889999*999 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 7e-20
                                       EEE-TTT--EEETTTB--SSTTB-TTT--.-B--GG CS
                           ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLvqRsD 36 
                                       Rr+C kCG++Yhv+fnpPkveg+CD CG +L+qR+D
  gi|330507923|ref|YP_004384351.1| 127 RRMC-KCGTTYHVQFNPPKVEGKCDACGADLYQRAD 161
                                       9***.6*****************************9 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   2.9e-09   3.5e-06       1     115 [.       3     129 ..       3     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.9e-09
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssal 71 
                                       I+l G+pG+GK t ak ++++ ++     g++lr++++ + +l  + ++ +   +++ d    d + d l + +   
  gi|330507923|ref|YP_004384351.1|   3 IILLGPPGSGKGTQAKMIADKYKVthvstGDILRENVRSGTPLGVEAKKfMDAGKLVPDALLIDIIKDRLAKDD--- 76 
                                       9*******************976688888999999998877777777776556666666666667777777754... PP

                            AAA_18  72 eegknlvidghlaeleseaakdikk..........vvLtaspeelleRlekRgy 115
                                        +g++  +dg++  + +++a d+              +++++eel +R+  R+ 
  gi|330507923|ref|YP_004384351.1|  77 VKGGW-MLDGFPRTMPQAEALDKILptlgqkidvvLNIDVPDEELVKRVTGRRM 129
                                       45555.**********9999998889*******7777899**********9985 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.1e-05     0.048       2      50 ..       3      50 ..       2      57 .. 0.89
   2 !    7.8   0.0    0.0031       3.7     170     197 ..      58      85 ..      51      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                         Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsvvleAisdgnssaGlrAr 50
                                      ii+ G+P sGK + a  +a kY+   ++  +++ e + +g ++ G+ A+
  gi|330507923|ref|YP_004384351.1|  3 IILLGPPGSGKGTQAKMIADKYKVTHVSTGDILRENVRSG-TPLGVEAK 50
                                      8999*******************************99776.56677776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0031
                         Hydin_ADK 170 vLPedllveIlsERlqlndCyrGvvfDg 197
                                       + P+ ll++I+ +Rl  +d   G ++Dg
  gi|330507923|ref|YP_004384351.1|  58 LVPDALLIDIIKDRLAKDDVKGGWMLDG 85 
                                       67******************99999999 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   9.9e-07    0.0012       2     118 ..       3     127 ..       3     136 .. 0.72
   2 ?   -3.5   0.0       8.6     1e+04     108     116 ..     164     172 ..     156     181 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.9e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrr.rlfg...tdqqsktdytrvldr.....lyqilnelarkalsa 69 
                                       ++l G+pGsGK t a+ ++ k +++++s+ +++r +++     +++ k +  ++ +      l++i++++++ +   
  gi|330507923|ref|YP_004384351.1|   3 IILLGPPGSGKGTQAKMIADKYKVTHVSTGDILReNVRSgtpLGVEAK-KFMDAGKLvpdalLIDIIKDRLA-KDDV 77 
                                       6899**********************9986555527776665333333.23333333211346666666664.4555 PP

                            AAA_33  70 grnvildatnlsrrerarflklarrlgvpvri.vvvetdeetlkeRlakR 118
                                       +++ +ld   ++  + ++++k+++ lg ++ + + +++++e+l +R+  R
  gi|330507923|ref|YP_004384351.1|  78 KGGWMLDGFPRTMPQAEALDKILPTLGQKIDVvLNIDVPDEELVKRVTGR 127
                                       67889998888889999999999999998866256899999999999988 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.6
                            AAA_33 108 eetlkeRla 116
                                       eet k+Rl 
  gi|330507923|ref|YP_004384351.1| 164 EETVKQRLS 172
                                       444444443 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.3e-06     0.004       3      34 ..       5      36 ..       3      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.3e-06
                                      EE-STTSSHHHHHHHHHHHHT-EEEEHHHHHH CS
                    Cytidylate_kin  3 iDGPagsGKssvaralaeklglkyldtgalYR 34
                                      + GP gsGK++ a+++a+k +++ ++tg + R
  gi|330507923|ref|YP_004384351.1|  5 LLGPPGSGKGTQAKMIADKYKVTHVSTGDILR 36
                                      56**************************9988 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.9e-06    0.0046       1      35 [.       3      35 ..       3      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.9e-06
                                      EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
                               AAA  1 vllyGppGtGKTllakavakelgvefleisgsell 35
                                      ++l GppG GK + ak +a + +v    +s  ++l
  gi|330507923|ref|YP_004384351.1|  3 IILLGPPGSGKGTQAKMIADKYKV--THVSTGDIL 35
                                      689******************765..445555555 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00052      0.62       3      65 ..       7      71 ..       7     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00052
                                      ESTTSSHHHHHHHHHHHHHHTTE....EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik...vvltrepggteiGekirelllkeeeleeqteallfaadr 65
                                      G  G+GK tqa+++++++k  + +   +++    +gt++G  +++ +  + +l + ++++ + +dr
  gi|330507923|ref|YP_004384351.1|  7 GPPGSGKGTQAKMIADKYKVTHVStgdILRENVRSGTPLGVEAKKFMD-AGKLVPDALLIDIIKDR 71
                                      5569*************9988877655556666678888887777766.66666666665555555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.7e-05     0.044      36      64 ..       3      31 ..       1      42 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                            RuvB_N 36 vllyGpPGlGkttlakiiakelgvklkit 64
                                      ++l GpPG Gk t ak+ia++ +v+  +t
  gi|330507923|ref|YP_004384351.1|  3 IILLGPPGSGKGTQAKMIADKYKVTHVST 31
                                      799*****************999865443 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.4e-05     0.053      14      45 ..       3      37 ..       1     181 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                                      EEEEESTTSSHHHHHHHHTTSS--...SEEEEEET CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagllkp...teGeilld 45
                                      + ++G+ G+GK t +k++a ++k      G+il +
  gi|330507923|ref|YP_004384351.1|  3 IILLGPPGSGKGTQAKMIADKYKVthvSTGDILRE 37
                                      679*****************999855566777444 PP

>> Pox_A3L  Poxvirus A3L Protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.6e-05      0.12       2      37 ..     136     174 ..     135     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.6e-05
                           Pox_A3L   2 YkveLdppr...rCskCaanlveylkeDretikmilesq 37 
                                       Y+v+ +pp+   +C +C a+l++   + +et+k  l + 
  gi|330507923|ref|YP_004384351.1| 136 YHVQFNPPKvegKCDACGADLYQRADDNEETVKQRLSAY 174
                                       9*******98889*******************9888765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00012      0.14       1      41 [.       2      42 ..       2      51 .. 0.91
   2 ?   -2.8   0.0       4.3   5.1e+03     124     147 ..     105     127 ..      94     139 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                      EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE--- CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreg 41
                                      ++++ GppG+GK T  k ++++ k   v+ g ++ e+vr+g
  gi|330507923|ref|YP_004384351.1|  2 NIILLGPPGSGKGTQAKMIADKYKVTHVSTGDILRENVRSG 42
                                      58999**********************99999999999875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.3
                                       TTSEEEEE--SS--SHHHHHHHT- CS
                          NTPase_1 124 sekpvlavihrrkdlalveeirer 147
                                       ++  v+  i ++ d++lv+++  r
  gi|330507923|ref|YP_004384351.1| 105 QKIDVVLNIDVP-DEELVKRVTGR 127
                                       444555555555.55666665544 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00045      0.54       4      26 ..       2      26 ..       1      42 [. 0.83
   2 ?   -1.4   0.0       1.4   1.6e+03     155     182 ..      98     129 ..      71     140 .. 0.71
   3 ?   -2.6   0.0       3.2   3.8e+03      79     109 ..     150     179 ..     144     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00045
                            AAA_24  4 kiliyGpsgiGKTtlakel..gpkp 26
                                      +i++ Gp+g+GK t+ak++  ++k+
  gi|330507923|ref|YP_004384351.1|  2 NIILLGPPGSGKGTQAKMIadKYKV 26
                                      799**************99665555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                            AAA_24 155 ktanelkeevDlvlranlkred....kvgerv 182
                                       k  + l ++ D+vl +++  e+     +g+r+
  gi|330507923|ref|YP_004384351.1|  98 KILPTLGQKIDVVLNIDVPDEElvkrVTGRRM 129
                                       44566777899999998876666665444444 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.2
                            AAA_24  79 elclaevirqnekaeskedkgdgkGygelae 109
                                       + c a++++++ + ++++ k+++++y + ++
  gi|330507923|ref|YP_004384351.1| 150 DACGADLYQRADD-NEETVKQRLSAYHAQTQ 179
                                       6677788777777.66677777777766555 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   0.00038      0.45       1      23 [.       2      24 ..       2      32 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00038
                                      EEEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal 23
                                      +++L+GppG+gK + a+ +a  +
  gi|330507923|ref|YP_004384351.1|  2 NIILLGPPGSGKGTQAKMIADKY 24
                                      689**********9999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1538.74
//
Query:       gi|330507924|ref|YP_004384352.1|  [L=239]
Description: hypothetical protein MCON_1965 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.36
# Mc/sec: 1982.92
//
Query:       gi|330507925|ref|YP_004384353.1|  [L=224]
Description: uridylate kinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.8e-29  101.4   4.0    6.2e-28   98.0   4.0    1.9  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 !   98.0   4.0   3.5e-32   6.2e-28       1     240 [.       1     200 [.       1     200 [. 0.89

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 3.5e-32
                                       TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC....E..HHHHH CS
                         AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllal..ksglssgelaaglrstleeage 75 
                                       +++V  lGGs+l+  +++sl+++a+ +++l  + +++ vV+Ggg ++++++++  + g s+ +              
  gi|330507925|ref|YP_004384353.1|   1 MILVYSLGGSILAGRDAKSLQEYADALKEL-AKAHQIYVVVGGGRIAREYIEKarALGASEMFC------------- 63 
                                       689**********88889************.9999******************77777777777............. PP

                                       HHHHHHHHHHHHHHHHHHHHTTH.GEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEET CS
                         AA_kinase  76 vatrdalaslgerlvaallaagl.pavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfiglde 151
                                           d++++ +++l++all a++ +a +     +                    ++ ++l   g ++v++g +    
  gi|330507925|ref|YP_004384353.1|  64 ----DLIGIGATKLNSALLIAAFgRAAPQEIPET-------------------YAQAARLACPGRIVVMGGVA---- 113
                                       ....9*****************933333322222...................56677788899*******99.... PP

                                       TTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHH CS
                         AA_kinase 152 egelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaa 226
                                       +g+    ++D +aallAe++gA+klii+t+VdGVy+adp k+p+a+++  +++ e+     +  +  g+  +++p a
  gi|330507925|ref|YP_004384353.1| 114 PGQ----TTDAVAALLAEYVGANKLIIATSVDGVYTADPEKDPKAEKIASMTHGELSRmaAQTDMKAGSRSPVDPLA 186
                                       988....9***************************************************7777788888888***** PP

                                       HHHHHCTT-EEEEE CS
                         AA_kinase 227 laaarrggipvvIt 240
                                       +++++r++ip+ I+
  gi|330507925|ref|YP_004384353.1| 187 AKIIERSRIPTAIV 200
                                       **********9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1693.28
//
Query:       gi|330507926|ref|YP_004384354.1|  [L=295]
Description: hypothetical protein MCON_1966 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-36  122.1   0.1    1.1e-35  121.1   0.1    1.5  1  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor
    9.1e-15   54.9   0.0    1.2e-08   35.3   0.0    2.9  2  CBS           CBS domain
    1.3e-07   31.9   0.1    3.4e-07   30.5   0.0    1.8  2  Rrf2          Transcriptional regulator
    7.4e-07   29.0   0.1    7.6e-06   25.8   0.1    2.3  2  HTH_11        HTH domain
      0.001   19.1   0.0     0.0029   17.6   0.0    1.8  1  HTH_20        Helix-turn-helix domain
     0.0074   16.2   0.0      0.038   13.9   0.0    2.3  1  MarR_2        MarR family
  ------ inclusion threshold ------
      0.038   13.9   0.0        0.3   11.0   0.0    2.3  2  TrmB          Sugar-specific transcriptional regulator TrmB
       0.17   11.6   0.1          1    9.1   0.0    2.3  3  Sigma70_r4_2  Sigma-70, region 4
       0.19   11.5   1.5       0.35   10.7   0.0    2.1  2  HTH_38        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.1   0.1   5.4e-39   1.1e-35       1      77 [.       9      85 ..       9      87 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.1 bits;  conditional E-value: 5.4e-39
                      HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealkiqt 77
                                      +Lt+vq++il+aLi++yr ++ravKgeeiAe+++rn+Gt+RNq+qsLkal+LvegvpGPkGGY+ t +ayeal+++ 
  gi|330507926|ref|YP_004384354.1|  9 DLTPVQRDILTALINIYRVEGRAVKGEEIAELIDRNPGTIRNQMQSLKALNLVEGVPGPKGGYRATGSAYEALNVEA 85
                                      69************************************************************************986 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.9e-06    0.0098       7      56 ..     185     231 ..     178     232 .. 0.84
   2 !   35.3   0.0   5.8e-12   1.2e-08       1      55 [.     239     292 ..     239     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.9e-06
                                       SSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   7 rdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       r+ v +pp +++ ea+++++++gv     V ed    G+v ++D++ra++
  gi|330507926|ref|YP_004384354.1| 185 RRAVRIPPGASMQEAARILVHNGVQEA-LV-EDS-SPGMVNQTDIVRAIA 231
                                       56689**************99998777.77.455.66***********97 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 5.8e-12
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       ++++m+r ++t++ ++t+ ea++++ ++g ++l VV edg l G v+  Dl++ l
  gi|330507926|ref|YP_004384354.1| 239 AREFMSRGFLTIDSEDTIYEAIKMLGKTGSGQL-VVSEDGTLWGFVSPADLIKTL 292
                                       579**********************888899**.**9**************9865 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.7e-10   3.4e-07       8      67 ..      15      73 ..       8      80 .. 0.89
   2 ?   -3.6   0.0       7.4   1.5e+04      24      34 ..     176     186 ..     162     192 .. 0.59

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.7e-10
                                      HHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEE CS
                              Rrf2  8 eyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrL 67
                                      +  l+al+ + + e++  v+ eeiae  + +p  ++  ++ L+  +lv+ v G++GGyr 
  gi|330507926|ref|YP_004384354.1| 15 RDILTALINIYRVEGRA-VKGEEIAELIDRNPGTIRNQMQSLKALNLVEGVPGPKGGYRA 73
                                      556899*********88.****************************************85 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.4
                                       C-B-HHHHHHH CS
                              Rrf2  24 epvsseeiaer 34 
                                        ++++++ia+r
  gi|330507926|ref|YP_004384354.1| 176 PKLAIKKIARR 186
                                       34666777765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   3.8e-09   7.6e-06       8      55 .]      23      72 ..      14      72 .. 0.87
   2 ?    0.5   0.0      0.29   5.9e+02      28      43 ..     252     267 ..     248     282 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.8e-09
                            HTH_11  8 lLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GYr 55
                                       +++ +g  + gee+Ae +++   t+r+ +++L++l   +e++pg+  GYr
  gi|330507926|ref|YP_004384354.1| 23 NIYRVEGRaVKGEEIAELIDRNPGTIRNQMQSLKALN-LVEGVPGPkgGYR 72
                                      355667777***************************9.***********97 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.29
                            HTH_11  28 SrrtvrrdIkaLeelg 43 
                                       S+ t++  Ik L ++g
  gi|330507926|ref|YP_004384354.1| 252 SEDTIYEAIKMLGKTG 267
                                       889*******998887 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.5e-06    0.0029      10      58 ..      12      65 ..       6      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                                      HHHHHHHHHH.....STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 10 PvRrrilraL.....araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      Pv+r+il aL      +++++  +e+ae++d  + t++++++ L    Lve+v 
  gi|330507926|ref|YP_004384354.1| 12 PVQRDILTALiniyrVEGRAVKGEEIAELIDRNPGTIRNQMQSLKALNLVEGVP 65
                                      9************9999999999****************************986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.9e-05     0.038       3      58 ..      10      68 ..       8      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                                      --HHHHHH...HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                            MarR_2  3 ltpaqarv...LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                      ltp q+++   L +++r +gr +   e+a+  +  ++++ +  + L a  Lve +pgp 
  gi|330507926|ref|YP_004384354.1| 10 LTPVQRDIltaLINIYRVEGRAVKGEEIAELIDRNPGTIRNQMQSLKALNLVEGVPGPK 68
                                      5655555411167899*****9*********************************9985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00015       0.3      22      64 ..      31      73 ..       7      83 .. 0.88
   2 ?   -0.4   0.0      0.53   1.1e+03      36      50 ..     253     267 ..     243     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64
                                        + +eiae +++   ++ + ++sL+   lVe ++g +  Yra
  gi|330507926|ref|YP_004384354.1| 31 AVKGEEIAELIDRNPGTIRNQMQSLKALNLVEGVPGPKGGYRA 73
                                      56889******************************99888887 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.53
                                       CHCHHHHHHHHHHCT CS
                              TrmB  36 rskvYevLrsLedkG 50 
                                       + ++Ye+++ L + G
  gi|330507926|ref|YP_004384354.1| 253 EDTIYEAIKMLGKTG 267
                                       468899988888877 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.5     5e+03      11      20 ..      10      19 ..       8      20 .. 0.87
   2 ?    9.1   0.0   0.00052         1      30      48 ..      35      53 ..      31      57 .. 0.92
   3 ?   -1.9   0.0       1.4   2.8e+03      28      38 ..     195     208 ..     193     215 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
                                      S-HHHHHHHH CS
                      Sigma70_r4_2 11 Lperqreifl 20
                                      L++ qr i++
  gi|330507926|ref|YP_004384354.1| 10 LTPVQRDILT 19
                                      8999***997 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00052
                                      HHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 30 kEIAellgisegtVksrls 48
                                      +EIAel++ ++gt++++++
  gi|330507926|ref|YP_004384354.1| 35 EEIAELIDRNPGTIRNQMQ 53
                                      8***************986 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.4
                                       -HHHHHHHH...T- CS
                      Sigma70_r4_2  28 sykEIAell...gi 38 
                                       s +E+A++l   g+
  gi|330507926|ref|YP_004384354.1| 195 SMQEAARILvhnGV 208
                                       88999999965555 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00017      0.35      16      39 ..      25      50 ..      20      53 .. 0.78
   2 ?   -1.8   0.3       1.3   2.7e+03      22      29 ..     179     186 ..     177     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                            HTH_38 16 llaeGlslr..eIArrLgrspsTIsR 39
                                       + eG  ++  eIA +++r+p+TI +
  gi|330507926|ref|YP_004384354.1| 25 YRVEGRAVKgeEIAELIDRNPGTIRN 50
                                      555666666669************87 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                            HTH_38  22 slreIArr 29 
                                        +++IArr
  gi|330507926|ref|YP_004384354.1| 179 AIKKIARR 186
                                       5899***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2155.94
//
Query:       gi|330507927|ref|YP_004384355.1|  [L=378]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.2e-18   65.7   0.0    9.8e-18   65.1   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    1.5e-06   28.6   0.3    3.3e-06   27.5   0.3    1.6  1  SPASM        Iron-sulfur cluster-binding domain
    0.00012   22.4   0.0    0.00019   21.7   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.06   13.5   0.0      0.099   12.8   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 !   65.1   0.0   2.2e-21   9.8e-18       1     166 [.     109     263 ..     109     264 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 2.2e-21
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       +++t+ C++rCs+Ca p    + g    l++  + +++ ++  ++g+  vi+ ggep+ly+++ el+++   +    
  gi|330507927|ref|YP_004384355.1| 109 ISITEECPNRCSHCALP----NSGNRLRLDPNAVQDLISQV-LDMGTSLVIFDGGEPTLYRELPELVRHVDDR---A 177
                                       67999************....57999999999999999999.8*****************************8...8 PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglp 153
                                       i++ +++ ++      +erl+++g+  v+++l+++  e  ++ m+ r + f+e ++a++++  ag+   vd +v+++
  gi|330507927|ref|YP_004384355.1| 178 ISTLFTSGAGFT-LSLAERLKDAGLYAVNVSLDSPLAE-EHDAMRgREGVFSEAMQAVKNALLAGLL--VDLYVVVR 250
                                       999999999997.*************************.7777777******************999..9******* PP

                                       TTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 154 Gendeeleellel 166
                                        en  +le + +l
  gi|330507927|ref|YP_004384355.1| 251 RENLCHLERFHQL 263
                                       ******9988765 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.3   7.3e-10   3.3e-06       1      46 [.     323     362 ..     323     376 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 7.3e-10
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwns 46 
                                       Cfa ++ + +++ G+V+pC    ++y  + + Gni +e+++ Iw+ 
  gi|330507927|ref|YP_004384355.1| 323 CFAARSWMHVTPSGEVYPC----SCY--PESWGNIMKEPMKRIWQR 362
                                       999****************....556..589*************54 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 !   21.7   0.0   4.2e-08   0.00019      12     123 ..     112     216 ..     100     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.2e-08
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdi 88 
                                       ++ C+ +C+ C    + +  +    + ++ + +i ++ +   + +++ GGEP l   +++l elv++v  ++++   
  gi|330507927|ref|YP_004384355.1| 112 TEECPNRCSHCA---LPNSGNRLRLDPNAVQDLISQVLDMGTSLVIFDGGEPTL---YRELPELVRHVDDRAISTLF 182
                                       678999999987...55555566668999999999999****************...99**************7666 PP

                           Fer4_12  89 wlytgytleelskkekeellkeidvlvdGkfeesl 123
                                       ++  g+tl   ++  k+  l  ++v +d +++e+ 
  gi|330507927|ref|YP_004384355.1| 183 TSGAGFTLSLAER-LKDAGLYAVNVSLDSPLAEEH 216
                                       6666777666654.466677788888888887654 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.2e-05     0.099       5      89 ..     112     186 ..     109     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                           Fer4_14   5 lsgCnlsCkgCd.nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeype 80 
                                       +  C+  C  C   ++  + +l +  +++l++q+l      ++  + + + GGeP +y   +el +lv+++ ++   
  gi|330507927|ref|YP_004384355.1| 112 TEECPNRCSHCAlPNSGNRLRLDPNAVQDLISQVL------DMGTSLVIFDGGEPTLY---RELPELVRHVDDRA-- 177
                                       568********964444777999999999998888......4444557899*****9*...67777788887777.. PP

                           Fer4_14  81 kkiwletng 89 
                                       ++  + +++
  gi|330507927|ref|YP_004384355.1| 178 ISTLFTSGA 186
                                       555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2805.32
//
Query:       gi|330507928|ref|YP_004384356.1|  [L=112]
Description: phosphoribosyl-AMP cyclohydrolase [Methanosaeta concilii GP6]
Scores for complete sequence (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  124.2   0.1    1.8e-36  123.8   0.1    1.1  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.1   9.8e-41   1.8e-36       1      74 []      20      93 ..      20      93 .. 0.99

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 9.8e-41
                                      EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
                            PRA-CH  1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74
                                      mlaymn+eal+kt etgka+y+Srsr+k+W KGe+Sg++q v+eir+DcD+Da+ll +eq+g aCHtg++sCFy
  gi|330507928|ref|YP_004384356.1| 20 MLAYMNDEALAKTQETGKAHYWSRSRNKIWLKGESSGHFQLVREIRVDCDEDAILLLIEQEGGACHTGYRSCFY 93
                                      9************************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 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:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 837.23
//
Query:       gi|330507929|ref|YP_004384357.1|  [L=389]
Description: hypothetical protein MCON_1970 [Methanosaeta concilii GP6]
Scores for complete 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-88  296.3   0.0    4.1e-88  295.7   0.0    1.2  1  Nre_N     Archaeal Nre, N-terminal
    1.8e-35  121.2   0.0    2.6e-35  120.7   0.0    1.3  1  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.7   0.0   4.5e-92   4.1e-88       2     269 ..      12     270 ..      12     271 .. 0.96

  Alignments for each domain:
  == domain 1  score: 295.7 bits;  conditional E-value: 4.5e-92
                             Nre_N   2 cglkkcpileklravekakkkisskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwlglslediik 78 
                                       cg++ cpi+++l+++ ++  ki ++++eG +pP+vfVGr+gYP V++gp++p v+      +++   lg+++++ii+
  gi|330507929|ref|YP_004384357.1|  12 CGQPVCPIVRRLEELVSLP-KI-GSRMEGFTPPEVFVGRSGYPLVRAGPVLPSVQ------AEELPHLGMNMDEIIS 80 
                                       9***************965.55.69*************************99764......2333467********* PP

                             Nre_N  79 lrlslvrgekkvkvkkak.edklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkv 154
                                        r+ +vr+e+k++v +a  + klle +q++a+s+ pv  ev++ k+p+++l+fd+vl+P+Gps+el k++++ np +
  gi|330507929|ref|YP_004384357.1|  81 ARMGMVRSETKIRVLEAGePGKLLEACQQIAMSSAPVGAEVSFIKPPRRRLQFDGVLSPTGPSGELAKMEITTNPLI 157
                                       ***************9998999******************************************************* PP

                             Nre_N 155 prkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpei 231
                                       prkv+++v D+ + A+ a++eLy++g+d+++++rlLS+GlLG+  krrlVPTrWsITA dd++gk+lk+e+ d+pe+
  gi|330507929|ref|YP_004384357.1| 158 PRKVDQIVLDRGAPADVAIAELYSAGIDIDHLSRLLSIGLLGN--KRRLVPTRWSITASDDMIGKSLKDEVLDFPEV 232
                                       ******************************************9..******************************** PP

                             Nre_N 232 devevfsgeylgNrflviLaPgkwsfelvEawapgslw 269
                                       + +++fsge lgN+f v+L P+++sfel+E+w p+slw
  gi|330507929|ref|YP_004384357.1| 233 KGYHLFSGEELGNHFEVLLSPRPFSFELIEIWRPHSLW 270
                                       ************************************** PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.0   2.9e-39   2.6e-35       1     110 []     281     389 .]     281     389 .] 0.98

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 2.9e-39
                             Nre_C   1 egyegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleeal 77 
                                       e+++ +k+ys++aG+Yyaarlavle+L++ +rqa+v+ +rei+++Y +P+GvW+vRe +rka++++p++f+ l++a 
  gi|330507929|ref|YP_004384357.1| 281 EDARPKKGYSPLAGGYYAARLAVLEHLSRWGRQAGVLAIREISEDYRIPLGVWVVREVARKAMSSHPTRFDALSSAR 357
                                       567899*********************************************************************** PP

                             Nre_C  78 eevseklklplkkllkkskllkelkkqktLddF 110
                                       e ++ +l++p  ++lkk +ll++  +qk+L++F
  gi|330507929|ref|YP_004384357.1| 358 EVMAGRLHTPEVSWLKKAELLTGS-TQKRLNEF 389
                                       ***********************9.8****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2828.60
//
Query:       gi|330507930|ref|YP_004384358.1|  [L=879]
Description: cation-transporting P-type ATPase [Methanosaeta concilii GP6]
Scores for complete 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-58  195.4  13.8    1.9e-57  193.7   2.8    3.1  3  E1-E2_ATPase     E1-E2 ATPase
    3.6e-44  150.6   3.7    3.6e-44  150.6   3.7    2.8  3  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    1.6e-23   84.1   2.9    4.7e-23   82.6   2.9    1.9  1  Hydrolase        haloacid dehalogenase-like hydrolase
    2.4e-18   66.0   0.0    5.3e-18   64.9   0.0    1.6  1  Cation_ATPase    Cation transport ATPase (P-type)
    1.2e-17   63.3   0.4      4e-17   61.7   0.0    2.1  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    3.9e-06   27.4   0.1      9e-06   26.2   0.1    1.6  1  HAD              haloacid dehalogenase-like hydrolase
    2.8e-05   24.0   1.9    0.00017   21.5   0.8    2.5  3  Hydrolase_3      haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0005       1.3     102     159 ..      35      87 ..      21      88 .. 0.81
   2 !  193.7   2.8   7.3e-61   1.9e-57       2     181 .]     105     296 ..     104     296 .. 0.99
   3 ?   -1.9   0.4       0.8     2e+03     120     154 ..     824     861 ..     800     870 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0005
                                       --------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS CS
                      E1-E2_ATPase 102 eeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaai 159
                                       e+ + k +pl+ ++ k+  ++v+v +++a++ f++     ++++ +++ ++++lva+i
  gi|330507930|ref|YP_004384358.1|  35 ES-TTKPSPLKIFIGKFKDYMVLVLIFAAIISFIAG----ETTNAYVILGIVVLVAII 87 
                                       44.488999999999999999999999999999886....666678888999999876 PP

  == domain 2  score: 193.7 bits;  conditional E-value: 7.3e-61
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-............G CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek............e 65 
                                       + +p+a virdg+  +i+a++lvpGD+v+l+agd+vpaDgri+e ++ +v es+LTGEs+pvek            +
  gi|330507930|ref|YP_004384358.1| 105 MVAPEADVIRDGQMSTIPAADLVPGDVVFLEAGDKVPADGRILEVTSlQVIESSLTGESMPVEKlaqtlpedialaD 181
                                       7899************************************************************************* PP

                                       -TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTS CS
                      E1-E2_ATPase  66 kgdmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgk 142
                                       +++mvf+Gt++ +g+++a+Vtatg  telg+i  l++++ ++++pl+ kl++l+k  +++v++i+++vf++++++g 
  gi|330507930|ref|YP_004384358.1| 182 RKNMVFMGTIISQGNCRAIVTATGLGTELGRISGLMKQE-QAEPPLKIKLQQLAKRQALLVMVISAIVFILMFSRGL 257
                                       **************************************8.9************************************ PP

                                       STTHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 143 slaeallralallvaaiPcaLplavplalalgarrlakk 181
                                       ++++al+ ++al+va iP+aLp +v+lala+g++++akk
  gi|330507930|ref|YP_004384358.1| 258 PVIDALIASIALAVAGIPEALPFIVTLALAFGTQAMAKK 296
                                       *************************************97 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.8
                                       HHHHHHHHHHHHHHHHS-STTTSSTT...HHHHHHHHH CS
                      E1-E2_ATPase 120 kvlvpvvlliallvflialllgksla...eallralal 154
                                          +++++l+++++ +++++ +  +     ++l   + 
  gi|330507930|ref|YP_004384358.1| 824 IAASILAILAVVYIPFMQFIFETRPLsseSWILILTTG 861
                                       33333333333333333333333332466444443332 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   1.4       2.5   6.5e+03     124     139 ..      72      87 ..      52      95 .. 0.57
   2 ?   -0.2   0.4      0.28   7.2e+02     121     142 ..     232     253 ..     185     299 .. 0.57
   3 !  150.6   3.7   1.4e-47   3.6e-44       1     182 []     702     874 ..     702     874 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.5
                   Cation_ATPase_C 124 snkllllaillslllq 139
                                       +n +++l+i++ ++++
  gi|330507930|ref|YP_004384358.1|  72 TNAYVILGIVVLVAII 87 
                                       4555555555555444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.28
                   Cation_ATPase_C 121 glfsnkllllaillslllqvli 142
                                       +l +   ll++++ ++++++++
  gi|330507930|ref|YP_004384358.1| 232 QLAKRQALLVMVISAIVFILMF 253
                                       2223333333333333333332 PP

  == domain 3  score: 150.6 bits;  conditional E-value: 1.4e-47
                   Cation_ATPase_C   1 plplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfg 77 
                                       plpl a qiLwin+v + +pa+ Lalep ++dimkr+Pr++ke++ s+ +++++l++++ +++ tl ++++tl+  +
  gi|330507930|ref|YP_004384358.1| 702 PLPLLAAQILWINVVAEEFPAIGLALEPSHSDIMKRKPRDPKESMPSRPLMIYTLGIAAAIVAGTLGMYIITLQ--S 776
                                       89***********************************************************************9..3 PP

                   Cation_ATPase_C  78 isekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgt 154
                                         +       +ya+t+aF+ l ++ + na+++rs++es+f+ ++   nk ll++i++s+l ++++vy+p+++ +f+t
  gi|330507930|ref|YP_004384358.1| 777 NPD------LSYARTVAFVGLGFFTVYNAYSSRSLQESVFR-MNPLGNKTLLMGIAASILAILAVVYIPFMQFIFET 846
                                       333......357*****************************.88889****************************** PP

                   Cation_ATPase_C 155 aplsleewlialllalvvllvdelvKll 182
                                       +pls e+w+++l  +lvv+l +e++K++
  gi|330507930|ref|YP_004384358.1| 847 RPLSSESWILILTTGLVVVLAAEVMKKI 874
                                       *************************976 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   2.9   1.8e-26   4.7e-23       2     210 .]     313     632 ..     312     632 .. 0.71

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 1.8e-26
                                       SEEEEESBTTTBCHHHHHHHHHHHH.........................CHHHHHHHHHH................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.........................xxxxxxxxxxx................ RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa.........................alalaaaletg................ 37 
                                       ++++ Dk+GTLttge+ ++++  ++                         + +la++l +g                
  gi|330507930|ref|YP_004384358.1| 313 TVICTDKTGTLTTGEMTLREIRTYRkievtgagydpsgqfisqgakleptEEDLARILKIGvhannsaieranggwr 389
                                       5899****************999997788888888888888888888888777777777776666666666677777 PP

                                       .HHCHHHHHHHHHHHHH......HHHHHHHHHETTTE....................HHHHTHHHHHHHH....... CS
                                       .xxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx....................xxxxxxxxxxxxx....... RF
                         Hydrolase  38 .sehpigkalvaaakar......sgaltgfatfigrg....................ayaigkpewltal....... 80 
                                           p   al+ aak+       + + ++f +                         + ++g pe + ++       
  gi|330507930|ref|YP_004384358.1| 390 vVGDPTEGALIVAAKKAgildkiKDSSSRFIE---YPfdsermrmttvdevhkegyiVSMKGAPEVVLSHctktttp 463
                                       76666666664444444354444222233333...114445555555555556667777777777555553332222 PP

                                       .........HCHHHHHHHHHHHHHHCHHHHHH................................TTHHHHHHHHH.H CS
                                       .........xxxxxxxxxxxxxxxxxxxxxxx................................xxxxxxxxxxx.x RF
                         Hydrolase  81 .........dippdlgaaigsaqsqgrtvall................................qaralavftia.d 115
                                                d  + l                                                 ++ + a +t   d
  gi|330507930|ref|YP_004384358.1| 464 ngtktlteeDRRSIL----------------AdaddmaenalrvlalawkpisnndpvevdcieSGLIFAGLTGMmD 524
                                       222222222444444................24455555555556666*******9999999985555555555559 PP

                                       THHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT............GGGESEEEEHHCES...STTTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxx...xxxxxxx RF
                         Hydrolase 116 plkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG............ddyfdaviasdiet...vakpspe 177
                                       p  +++e+ ea++  k agi++v++tgd++ ta+++ ++lG            d+  +  +   i+    +a +  e
  gi|330507930|ref|YP_004384358.1| 525 P--PRKEVPEAIRVSKMAGIRTVMITGDHRLTARAIGKELGigngeviegvqlDRMSSEDLREHIDDvsvFARVTAE 599
                                       9..*****************************************9999988865555444444444469******** PP

                                       HHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 178 gkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       +kv++++ L+++++ vam GDgvnDa+al aA+
  gi|330507930|ref|YP_004384358.1| 600 HKVRIVEALKARGHIVAMTGDGVNDAPALTAAD 632
                                       **********99999****************98 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   2.1e-21   5.3e-18       3      91 .]     376     460 ..     374     460 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 2.1e-21
                     Cation_ATPase   3 cNsaafsensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKG 79 
                                        N++a+  +  ++ + ++G++tE AL+v+a+k+    ++++++  +  e+pF+s+r rm++v +  +++++++ +KG
  gi|330507930|ref|YP_004384358.1| 376 ANNSAI--ERANGGWRVVGDPTEGALIVAAKKA-GILDKIKDSSSRFIEYPFDSERMRMTTVDEV-HKEGYIVSMKG 448
                                       588888..88999********************.8899************************998.7********** PP

                     Cation_ATPase  80 ApeiilkrCthv 91 
                                       Ape++l++Ct++
  gi|330507930|ref|YP_004384358.1| 449 APEVVLSHCTKT 460
                                       *********985 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   1.6e-20     4e-17       4      69 .]       1      65 [.       1      65 [. 0.98
   2 ?   -2.4   0.3       1.5   3.9e+03      38      67 ..     217     247 ..     216     248 .. 0.66

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.6e-20
                   Cation_ATPase_N  4 lsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                      ++ +evl kL+ ++++G+++ +a+erl+++GpN+l+   k+s +++++ +f++ +v++L++aa++s
  gi|330507930|ref|YP_004384358.1|  1 MTTDEVLSKLD-SDQKGISSMQAKERLSQHGPNQLESTTKPSPLKIFIGKFKDYMVLVLIFAAIIS 65
                                      5899******9.9***************************************************98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                   Cation_ATPase_N  38 lkekkkkslwvkllkqftnplvil.Llvaal 67 
                                       +k++  ++ +++ l+q+     +l ++++a+
  gi|330507930|ref|YP_004384358.1| 217 MKQEQAEPPLKIKLQQLAKRQALLvMVISAI 247
                                       5778889999999999965555540444444 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   3.5e-09     9e-06      86     187 ..     523     628 ..     478     629 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.5e-09
                               HAD  86 ldp...galellaahraaGdrvvvvSgglrplvepllaelgadevlat.elevdd........rltgelglegkpvr 150
                                       +dp   ++ e+++  + aG+r+v+++g +r  ++++ +elg    +++ e+ +          +l  +  +++ +v+
  gi|330507930|ref|YP_004384358.1| 523 MDPprkEVPEAIRVSKMAGIRTVMITGDHRLTARAIGKELG----IGNgEVIEGVqldrmsseDLREH--IDDVSVF 593
                                       4555668899999999*************************....88864444434553334433333..4444444 PP

                               HAD 151 g....egkvaalrewlaaegegidleevvay.GDspsDlpll 187
                                            e+kv+ +++ l+a+g+      +va  GD+++D p+l
  gi|330507930|ref|YP_004384358.1| 594 ArvtaEHKVRIVEA-LKARGH------IVAMtGDGVNDAPAL 628
                                       43333355555555.555553......78888********98 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.2   3.1e+03     223     246 ..     441     464 ..     438     467 .. 0.89
   2 ?    0.1   0.0      0.21   5.3e+02      19      66 ..     529     570 ..     525     595 .. 0.77
   3 !   21.5   0.8   6.5e-08   0.00017     195     254 ..     604     664 ..     598     665 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                                       SEEEEETTS-HHHHHHSSEEE--G CS
                       Hydrolase_3 223 glgvAmgnaseevkkaAdyvtksn 246
                                       g+ v m+ a e v ++++++t+ n
  gi|330507930|ref|YP_004384358.1| 441 GYIVSMKGAPEVVLSHCTKTTTPN 464
                                       7889***************99876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE CS
                       Hydrolase_3  19 ktkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali 66 
                                       +  eai+  k +gi  v  TG +  +++ + +elg+       NG +i
  gi|330507930|ref|YP_004384358.1| 529 EVPEAIRVSKMAGIRTVMITGDHRLTARAIGKELGIG------NGEVI 570
                                       566899999**************************88......66666 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 6.5e-08
                                       HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETT.S-HHHHHHSSEEE--GGGTHHHHH CS
                       Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmgn.aseevkkaAdyvtksnnedGVaka 254
                                       +++ l+     v+  GDg ND + L+aa++gvAmg  ++e  k+a+d+v+++ n   ++ a
  gi|330507930|ref|YP_004384358.1| 604 IVEALKARGHIVAMTGDGVNDAPALTAADIGVAMGRtGTEVTKEASDMVIADDNFATIVSA 664
                                       566777777888999*******************962677778889999999887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (879 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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):               7  [number of targets reported over threshold]
# CPU time: 0.77u 0.30s 00:00:01.07 Elapsed: 00:00:00.46
# Mc/sec: 5710.09
//
Query:       gi|330507931|ref|YP_004384359.1|  [L=502]
Description: phenylalanyl-tRNA synthetase subunit alpha [Methanosaeta concilii GP6]
Scores for complete 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-93  311.6   0.0    4.3e-93  311.3   0.0    1.1  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    5.7e-11   42.3   0.0    4.4e-07   29.5   0.0    2.7  3  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    0.00026   20.2   0.5       0.22   10.5   0.0    2.5  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    0.00031   20.7   0.0       0.17   11.9   0.0    2.4  2  HTH_45           Winged helix-turn-helix
  ------ inclusion threshold ------
       0.02   15.2   0.8       0.16   12.3   0.1    2.8  3  PheRS_DBD3       PheRS DNA binding domain 3
        0.1   12.4   0.7         31    4.5   0.1    3.7  3  SinI             Anti-repressor SinI
       0.11   12.3   0.0         11    5.7   0.0    2.2  2  DUF4364          Domain of unknown function (DUF4364)
       0.13   12.7   0.0        3.2    8.3   0.0    2.5  2  HTH_27           Winged helix DNA-binding 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 !  311.3   0.0   1.9e-96   4.3e-93       2     244 ..     230     495 ..     229     496 .. 0.98

  Alignments for each domain:
  == domain 1  score: 311.3 bits;  conditional E-value: 1.9e-96
                                       .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-.. CS
                      tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka.. 76 
                                       +dv+lp++ri +gk+hp+++++++++ei+le+gf e++gp v+++f+nfdaL++pqdhpaR+mqdtFyl+++ ++  
  gi|330507931|ref|YP_004384359.1| 230 YDVSLPADRIFPGKRHPYQRLIDNMREIMLEMGFVEIKGPIVQTSFWNFDALFQPQDHPAREMQDTFYLNSQGDIpd 306
                                       9********************************************************************888887** PP

                                       ..........................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-SEEEE CS
                      tRNA-synt_2d  77 ..........................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathlaeFhq 126
                                                                 v+++ +LRthtt v+i++l e+++pp+k + i+rv+Rr+a+D+th++eF q
  gi|330507931|ref|YP_004384359.1| 307 yarikemhecggsvgstgwggcwspeVARQEVLRTHTTGVTIKYLaEHPRPPVKAFGIDRVYRREAIDSTHTPEFEQ 383
                                       **************************999****************88889*************************** PP

                                       EEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHT CS
                      tRNA-synt_2d 127 veglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevleav 203
                                       +eg+v+de vs+ +l+g+l+e++ k+ g+e +vrfrp yfp+tePs+e +vy+  ++ +w+El+gaG++r+ev++++
  gi|330507931|ref|YP_004384359.1| 384 LEGIVMDESVSFCHLLGILKEFYGKM-GFE-EVRFRPGYFPYTEPSVEPEVYI--DGLGWVELGGAGVFRKEVTAPF 456
                                       **************************.***.**********************..********************** PP

                                       T-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                      tRNA-synt_2d 204 gideevsgfafGlGveRlamlkygieDiRelvendlrflrq 244
                                       gi  + +++a+GlGv R+aml++g++D+R l+++d+++lrq
  gi|330507931|ref|YP_004384359.1| 457 GI--DHPVLAWGLGVSRVAMLRLGLKDLRLLYQSDIEWLRQ 495
                                       **..***********************************98 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 ?   -1.4   0.0      0.56   1.3e+03      14      37 ..      29      52 ..      19      67 .. 0.81
   2 !    9.4   0.0   0.00029      0.65       4      37 ..     233     266 ..     231     295 .. 0.88
   3 !   29.5   0.0     2e-10   4.4e-07      72     209 ..     337     464 ..     329     468 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.56
                   tRNA_synthFbeta 14 elnkeqklrrklrdllagaGlnEv 37
                                      +++ + ++ r+++dlla++Gl +v
  gi|330507931|ref|YP_004384359.1| 29 KRQMKIEAARAAADLLAEQGLIQV 52
                                      456778889999********9887 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00029
                   tRNA_synthFbeta   4 tlPkapttegelnkeqklrrklrdllagaGlnEv 37 
                                       +lP   + +g++++ q+l +++r+++ ++G++E+
  gi|330507931|ref|YP_004384359.1| 233 SLPADRIFPGKRHPYQRLIDNMREIMLEMGFVEI 266
                                       689999999************************8 PP

  == domain 3  score: 29.5 bits;  conditional E-value: 2e-10
                   tRNA_synthFbeta  72 svlRtsLlpglLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlk 147
                                       +vlRt  +   ++ l    ++  + v++F i +v++ +  +++   e ++l ++++ ++           v+f +l 
  gi|330507931|ref|YP_004384359.1| 337 EVLRTHTTGVTIKYL---AEHPRPPVKAFGIDRVYRREaIDSTHTPEFEQLEGIVMDES-----------VSFCHLL 399
                                       566666555554444...457888899***********97889999*************...........******* PP

                   tRNA_synthFbeta 148 givealleslgiekvefepaehpalhpgrsAeikvdgk...evGvlGelhpevleafdlkqrvyv 209
                                       gi++++ +++g+e+v+f+p   p+ +p    e+++dg    e+G +G + +ev + f+++++v +
  gi|330507931|ref|YP_004384359.1| 400 GILKEFYGKMGFEEVRFRPGYFPYTEPSVEPEVYIDGLgwvELGGAGVFRKEVTAPFGIDHPVLA 464
                                       ***********************************996666********************9976 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 !    7.2   0.0     0.001       2.3      27      52 ..     249     274 ..     247     301 .. 0.81
   2 !   10.5   0.0   9.9e-05      0.22      93     119 ..     360     385 ..     359     401 .. 0.93
   3 ?   -3.1   0.1       1.4   3.1e+03     287     305 ..     465     483 ..     464     485 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHTT-EE----SEESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  27 tvtkavrkyleengfieietPiLsks 52 
                                       ++++ +r+++ e gf+ei+ Pi+++s
  gi|330507931|ref|YP_004384359.1| 249 RLIDNMREIMLEMGFVEIKGPIVQTS 274
                                       57889*****************9987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.9e-05
                                       EEEEEEEEE--S--BTTB-S-CEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqie 119
                                       + f i r++R E +++++ + EF q+e
  gi|330507931|ref|YP_004384359.1| 360 KAFGIDRVYRREAIDSTHTP-EFEQLE 385
                                       6799****************.****98 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.4
                                       EEEEHHHHHHHHCT-SSGG CS
                                       xxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 287 lglGldRlvmlllgsesIr 305
                                       +glG++R+ ml lg+++ r
  gi|330507931|ref|YP_004384359.1| 465 WGLGVSRVAMLRLGLKDLR 483
                                       799********99998876 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   7.5e-05      0.17      11      67 ..      12      71 ..      10      76 .. 0.92
   2 !    6.2   0.0    0.0045        10      38      70 ..     148     183 ..     142     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.5e-05
                            HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli...kkskekYvlTekGlelle 67
                                      +L+aiseg + + +i  k  ++ + ++   d L e+gli   k  +e+++lT++G  +++
  gi|330507931|ref|YP_004384359.1| 12 VLKAISEGLSDPQSIAEKRQMKIEAARAAADLLAEQGLIqvdKSVNETFSLTDEGAAYVR 71
                                      6999***********************************88777899********98876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0045
                            HTH_45  38 kYLdmLvekgli...kkskekYvlTekGlelleklk 70 
                                       k L  L ++gl+   k ++  Y +Te G+  + kl+
  gi|330507931|ref|YP_004384359.1| 148 KALAALKSRGLVtssKSKEWRYIITEAGSLAITKLE 183
                                       66899*******886668889*******98877765 PP

>> PheRS_DBD3  PheRS DNA binding domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.1   2.4e+03       3      19 ..       9      23 ..       8      37 .. 0.73
   2 ?   12.3   0.1   6.9e-05      0.16       2      49 ..      75     115 ..      75     125 .. 0.76
   3 ?   -1.9   0.0       1.9   4.2e+03      41      55 ..     438     450 ..     437     453 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                        PheRS_DBD3  3 Earvfaavppeggisqk 19
                                      E+ v +a+ + +g+s  
  gi|330507931|ref|YP_004384359.1|  9 EFLVLKAI-S-EGLSDP 23
                                      999*****.7.557654 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6.9e-05
                        PheRS_DBD3   2 hEarvfaavppeggisqkelkklggdpvakiGfskAmknkWikkdkgd 49 
                                       +E r+  ++   gg+ ++e+    +dp  kiG++   k++W ++ +g+
  gi|330507931|ref|YP_004384359.1|  75 PERRLLLSL-G-GGMHMSEV----KDPALKIGLGWLRKKGWAAI-EGG 115
                                       567777777.4.88*****9....3466***************9.555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.9
                        PheRS_DBD3  41 kWikkdkgdgkvvrk 55 
                                       +W+++  g g v+rk
  gi|330507931|ref|YP_004384359.1| 438 GWVEL-GGAG-VFRK 450
                                       8****.5555.7776 PP

>> SinI  Anti-repressor SinI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.19   4.2e+02       8      18 ..      11      21 ..      10      22 .. 0.95
   2 ?    2.6   0.0     0.055   1.2e+02       7      18 ..     129     140 ..     129     142 .. 0.90
   3 ?    4.5   0.1     0.014        31       3      13 ..     165     175 ..     165     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.19
                                      HHHHHHHHT-- CS
                              SinI  8 LikEAkesGls 18
                                      L+++A+  Gls
  gi|330507931|ref|YP_004384359.1| 11 LVLKAISEGLS 21
                                      9*********8 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.055
                                       HHHHHHHHHT-- CS
                              SinI   7 eLikEAkesGls 18 
                                       eLi+EA+  G+s
  gi|330507931|ref|YP_004384359.1| 129 ELILEALSDGVS 140
                                       8******99998 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHH CS
                              SinI   3 eEWveLikEAk 13 
                                       +EW+++i+EA 
  gi|330507931|ref|YP_004384359.1| 165 KEWRYIITEAG 175
                                       7*********5 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.016        35      39      70 ..      40      70 ..      24      73 .. 0.79
   2 ?    5.7   0.0    0.0049        11      38      74 ..     148     183 ..     147     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.016
                           DUF4364 39 alseLvesglieeeekenktlykiTekGketl 70
                                      a + L e+gli++ +k+ ++++++T++G+  +
  gi|330507931|ref|YP_004384359.1| 40 AADLLAEQGLIQV-DKSVNETFSLTDEGAAYV 70
                                      5566889999998.6699999*******9866 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0049
                           DUF4364  38 qalseLvesglieeeekenktlykiTekGketlelfe 74 
                                       +al+ L + gl+++ +k+++ +y iTe+G+ ++  +e
  gi|330507931|ref|YP_004384359.1| 148 KALAALKSRGLVTS-SKSKEWRYIITEAGSLAITKLE 183
                                       6899*********8.66999*********98887766 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.16   3.6e+02      40      68 .]      42      66 ..       5      66 .. 0.68
   2 ?    8.3   0.0    0.0014       3.2      37      68 .]     148     175 ..     147     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.16
                            HTH_27 40 kkLtekGLvertgdeadrrekrvrlTdkG 68
                                      + L e+GL++  ++     + +++lTd+G
  gi|330507931|ref|YP_004384359.1| 42 DLLAEQGLIQVDKSV----NETFSLTDEG 66
                                      458889999555555....6899999998 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0014
                            HTH_27  37 yslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       ++l +L  +GLv++++++    e r+ +T++G
  gi|330507931|ref|YP_004384359.1| 148 KALAALKSRGLVTSSKSK----EWRYIITEAG 175
                                       7899********777776....9*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3830.87
//
Query:       gi|330507932|ref|YP_004384360.1|  [L=548]
Description: phenylalanyl-tRNA synthetase subunit beta [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-37  127.5   0.0      7e-37  126.9   0.0    1.3  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    8.7e-16   58.0   0.0    2.9e-14   53.1   0.0    2.9  2  B5               tRNA synthetase B5 domain
    6.8e-12   45.4   0.0    1.1e-11   44.7   0.0    1.3  1  B3_4             B3/4 domain
     0.0067   16.6   0.0       0.53   10.5   0.0    2.7  2  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.9   0.0   1.6e-40     7e-37       2     213 ..     348     542 ..     347     543 .. 0.95

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 1.6e-40
                   tRNA_synthFbeta   2 pstlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldkll...eddderkavelanPlsedqsvlR 75 
                                       + +lP+++t+++  ++++ ++ ++r+++ag+G+ E++ +++++e +  +++   +  +   av++++P+se +++lR
  gi|330507932|ref|YP_004384360.1| 348 EARLPQTVTVGR-AHSSEVRKGEIREIMAGLGYLETMPFTLTNELVHFQWMrrsAAPEAAGAVRVLHPISELHTILR 423
                                       6789******99.889**********************************99744447888**************** PP

                   tRNA_synthFbeta  76 tsLlpglLevlarNlargnedvrlFEigkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgivea 152
                                       tsLl++lLe  a N+++ ++  r+F  g+v+  +      + + +la++  ++            +++ ++  +v+a
  gi|330507932|ref|YP_004384360.1| 424 TSLLSSLLEIFALNQHHPLP-QRIFAAGDVVKDK------KTRMNLAAASIHSG-----------ANYSEIRSVVDA 482
                                       ********************.*************......77999999999999...........9*********** PP

                   tRNA_synthFbeta 153 lleslgiekvefepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEld 213
                                       +l+++ + + +++p+++ a+ pgr A++ ++gk++G++Gelhp +l++f+l+q+++++E++
  gi|330507932|ref|YP_004384360.1| 483 VLREMDL-EADIVPTKDRAFMPGRGADLFAEGKRIGCFGELHPLLLRSFGLEQPAVGLEIE 542
                                       *******.***************************************************97 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.089     4e+02       5      51 ..       8      53 ..       4      62 .. 0.71
   2 !   53.1   0.0   6.6e-18   2.9e-14       2      67 .]     276     344 ..     275     344 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.089
                                      HHHHHHHHTS---HHHHHHHHHHTT-E.EE.SSTTCEEEE--TT-TT- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                                B5  5 vekinkllGidlseeeiikiLkrlgcerie.kdkdlllVtvPswRsDl 51
                                      ++ +++l+G   s+e+i   L  +g ++ +  +++ ++V+  + R+Dl
  gi|330507932|ref|YP_004384360.1|  8 YQDMERLIG--ASRETIMSRLAMMGADIGKrAEEEYVDVEFFPDRPDL 53
                                      678899999..699***********98533044445666655557777 PP

  == domain 2  score: 53.1 bits;  conditional E-value: 6.6e-18
                                       EEEHHHHHHHHTS---HHHHHHHHHHTT-E....EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   2 slrvekinkllGidlseeeiikiLkrlgce...riekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                       ++r e++n+l+G dl+ +e +++Lkr+ +    + e+ +d + V+vP++R D+ + +D+ E+ a +yGY
  gi|330507932|ref|YP_004384360.1| 276 KVRTEEANRLIGFDLTGAELAECLKRMRFGavtAGEEMDDIVVVQVPAYRADIMHSWDIFEDAAKAYGY 344
                                       6899*************************86666678888****************************9 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   2.5e-15   1.1e-11      35     130 ..     113     234 ..      94     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.5e-15
                                       --HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEEEEE--TTEEEEBTTS-.EEEE-T................. CS
                              B3_4  35 innvVDitNyvmlelgq.....PlhafDldkiqgdivvrlakegeklvtldgk.erelde................. 88 
                                       i+++  +++ ++  lg+     +++++D++++ ++++      + ++v+ld + e +++e                 
  gi|330507932|ref|YP_004384360.1| 113 IESLMGLQEDLHWGLGRnrrkvAIGVHDISRVRPPFRYFGESPQRRFVPLDYSeEMTMEEilhnhpkgkdyghilkd 189
                                       6677777888888888899999***************88888899*****9773555577***************** PP

                                       ..TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HH CS
                              B3_4  89 ..edlviadsekpv.slagvmggeeskvsedTknvfleaaafdpv 130
                                         ++++i+d+++ v s +++++ge ++v+e+T++ f+ +++ dpv
  gi|330507932|ref|YP_004384360.1| 190 cpVYPLIVDADDRVlSFPPIINGELTSVTEETEDLFIDVTGTDPV 234
                                       ************999****************************94 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 !   10.5   0.0   0.00012      0.53      48      82 ..      34      68 ..       1      69 [. 0.92
   2 ?    3.3   0.0     0.022        96      46      68 ..     307     329 ..     276     337 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                         PhetRS_B1 48 dkkseeviykidipAnryDLLcleglaralkvFlg 82
                                      +k+ ee+++ ++    r+DL + eg+ara++ Flg
  gi|330507932|ref|YP_004384360.1| 34 GKRAEEEYVDVEFFPDRPDLYSSEGVARAMQGFLG 68
                                      577899999**********************9986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.022
                         PhetRS_B1  46 kadkkseeviykidipAnryDLL 68 
                                        ++ ++ + i+ +++pA r D++
  gi|330507932|ref|YP_004384360.1| 307 VTAGEEMDDIVVVQVPAYRADIM 329
                                       456677789999*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3736.63
//
Query:       gi|330507933|ref|YP_004384361.1|  [L=126]
Description: CBS domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-22   78.1   1.9    1.4e-13   51.1   0.3    2.1  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   3.4e-10   6.1e-06       1      52 [.       3      56 ..       3      60 .. 0.84
   2 !   51.1   0.3   7.6e-18   1.4e-13       1      52 [.      71     122 ..      71     125 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.4e-10
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT...BEEEEEEHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedg...klvGivtlrDll 52
                                      V+++m+ ++vtvpp++ + +a++ m+  + ++++V  ++    +++Givt + ++
  gi|330507933|ref|YP_004384361.1|  3 VRELMSYPIVTVPPEAMVLDAIKVMAAQKKGSVLVA-KERllkECLGIVTTSQIF 56
                                      89***********************84444899565.6667877******99987 PP

  == domain 2  score: 51.1 bits;  conditional E-value: 7.6e-18
                                       HHHHSBS.SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS   1 Vgdimtr.dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                       V+dimt+ +++t++ d++  +a+elm+e++++rlPV+ +dg lvGivt +Dll
  gi|330507933|ref|YP_004384361.1|  71 VSDIMTPaPLITIDLDDSTQKAAELMIEHKIRRLPVM-KDGALVGIVTSKDLL 122
                                       89*****8889**************************.89************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 977.04
//
Query:       gi|330507934|ref|YP_004384362.1|  [L=279]
Description: site-specific integrase/recombinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-26   92.4   0.0    3.6e-26   92.0   0.0    1.2  1  Phage_integrase  Phage integrase family
    6.7e-05   23.3   0.3        0.3   11.6   0.0    2.8  3  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    0.00021   21.5   0.1      0.013   15.8   0.0    2.8  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.014   15.7   0.0        2.8    8.3   0.1    2.9  2  Phage_int_SAM_5  Phage integrase SAM-like domain
      0.029   14.5   0.0      0.055   13.6   0.0    1.4  1  UPF0047          Uncharacterised protein family UPF0047


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 !   92.0   0.0     1e-29   3.6e-26       2     171 ..     100     266 ..      99     267 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 1e-29
                                       HHHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHH CS
                   Phage_integrase   2 vltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseeale 78 
                                       ++ ed+v+r++  +++   i++ ++l +l+   lR+sEl +++ +d+dl   ++++  r gKg+++ +vpls+e   
  gi|330507934|ref|YP_004384362.1| 100 YFNEDDVRRIFCVIHN---IKHLAMLNVLFYGCLRASELTAIDDEDIDLGLMTLRI--RDGKGGRSGTVPLSNECIA 171
                                       57899***********...*************************************..******************* PP

                                       HHHHHHHHH.CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHH.HHHHHHHHHHHCTSHHHHHH CS
                   Phage_integrase  79 llkellska.leeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtl.RhsfataLleagvdlrvvqk 153
                                       +lke+l+++     ++++ lf+  rg++  r++++++f  ++ +++++k+   H + Rh+ at ++ +g d+r v++
  gi|330507934|ref|YP_004384362.1| 172 VLKEYLQVRpAIDIDGRKPLFYTDRGRRWDRKDLYRMFIIYKHKSNVQKAGGLHVFsRHTPATLMIANGCDIRIVKE 248
                                       *********988999***************************************999******************** PP

                                       HHT-SSCCHHHHHHCCCH CS
                   Phage_integrase 154 llGHssisttqiYthvak 171
                                       ll H++i+tt +Y+hva+
  gi|330507934|ref|YP_004384362.1| 249 LLRHRDIRTTLRYAHVAD 266
                                       ***************986 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 !   11.6   0.0   8.3e-05       0.3       2      34 ..      17      49 ..      17      54 .. 0.91
   2 !    8.9   0.0   0.00056         2       4      34 ..      53      83 ..      51     103 .. 0.84
   3 ?   -2.1   0.1       1.5   5.5e+03       5      20 ..     255     270 ..     253     274 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.3e-05
                   Phage_int_SAM_4  2 lerfrealrlaglserTiksYlsaikrflrflk 34
                                      l++fr++lr +g +++Ti+sYl  i  +++ +k
  gi|330507934|ref|YP_004384362.1| 17 LDKFRRYLRDHGHRPSTIDSYLMCISKYIQANK 49
                                      689***********************9998766 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00056
                   Phage_int_SAM_4  4 rfrealrlaglserTiksYlsaikrflrflk 34
                                      +f++ l+ ++l+ +Ti++Y++ ik + + l 
  gi|330507934|ref|YP_004384362.1| 53 DFLDGLHNRKLAGSTIDNYITSIKKYHEMLG 83
                                      5778899999999*********999988776 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.5
                   Phage_int_SAM_4   5 frealrlaglserTik 20 
                                        r +lr+a+ +++T +
  gi|330507934|ref|YP_004384362.1| 255 IRTTLRYAHVADKTLR 270
                                       5778999999999976 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 !   15.8   0.0   3.6e-06     0.013       1      80 [.      17      82 ..      17      85 .. 0.90
   2 ?   -3.1   0.0       2.9     1e+04      45      57 ..     251     263 ..     248     270 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.6e-06
                                      HHHHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHH CS
                   Phage_int_SAM_1  1 leqfleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqf 79
                                      l+ f++yL+ + g+ p T+ +Y++ ++++++  ++             v +fl+ l++++l+ +++ +++ ++++++  
  gi|330507934|ref|YP_004384362.1| 17 LDKFRRYLR-DHGHRPSTIDSYLMCISKYIQANKS-------------VPDFLDGLHNRKLAGSTIDNYITSIKKYHEM 81
                                      689*****9.7888********9999888887777.............99**************************998 PP

                                      H CS
                   Phage_int_SAM_1 80 l 80
                                      l
  gi|330507934|ref|YP_004384362.1| 82 L 82
                                      7 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.9
                                       -HHHHHHHHHS-- CS
                   Phage_int_SAM_1  45 ttedvraflaele 57 
                                       +++d+r+ l++ +
  gi|330507934|ref|YP_004384362.1| 251 RHRDIRTTLRYAH 263
                                       5556665555544 PP

>> Phage_int_SAM_5  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00077       2.8      52      81 ..      18      46 ..      14      81 .. 0.87
   2 ?   -2.9   0.0       2.5   8.9e+03      19      36 ..     160     177 ..     154     185 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00077
                                      HHHHHHHHHTS---HHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_5 52 eeFedYLkkkkglsentiskyfkklkavln 81
                                       +F+ YL ++ g+ ++ti +y+ ++ ++++
  gi|330507934|ref|YP_004384362.1| 18 DKFRRYL-RDHGHRPSTIDSYLMCISKYIQ 46
                                      6899999.8999999999999999988875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHTTTS- CS
                   Phage_int_SAM_5  19 kgtlrnykstlkhlkkFl 36 
                                        gt+   ++++  lk++l
  gi|330507934|ref|YP_004384362.1| 160 SGTVPLSNECIAVLKEYL 177
                                       566666777888888887 PP

>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.5e-05     0.055      15      50 ..     219     254 ..     210     274 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                                       .SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHH CS
                           UPF0047  15 vkeGlvlvfsrhttasltinEnadpdvqeDleeale 50 
                                        k G ++vfsrht a l+i + +d ++ ++l ++ +
  gi|330507934|ref|YP_004384362.1| 219 QKAGGLHVFSRHTPATLMIANGCDIRIVKELLRHRD 254
                                       46799*******************999999887644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2119.75
//
Query:       gi|330507935|ref|YP_004384363.1|  [L=113]
Description: hypothetical protein MCON_1979 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0043   16.7   3.0      0.008   15.8   3.0    1.5  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   3.0   4.4e-07     0.008      12      31 ..      65      84 ..      41      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.4e-07
                              SWIM 12 lnkatCsCpefqkngipCkH 31
                                      +  + CsCp+  + + pCkH
  gi|330507935|ref|YP_004384363.1| 65 VTAKGCSCPAATYHHGPCKH 84
                                      55667*************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 886.43
//
Query:       gi|330507936|ref|YP_004384364.1|  [L=101]
Description: hypothetical protein MCON_1981 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0042   16.7   0.3     0.0076   15.9   0.3    1.4  1  HTH_53          Zap  helix turn helix N-terminal domain
  ------ inclusion threshold ------
      0.014   14.6   0.1      0.018   14.2   0.1    1.2  1  Uso1_p115_head  Uso1 / p115 like vesicle tethering protein, h


Domain annotation for each model (and alignments):
>> 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 !   15.9   0.3   8.4e-07    0.0076       9      38 ..      49      78 ..      45      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.4e-07
                            HTH_53  9 iLCAhGGrmaLeeLlgeveLseaqLkevLe 38
                                       L A GG+m  +e +++++Ls+ q  ++L 
  gi|330507936|ref|YP_004384364.1| 49 LLVANGGKMLEKEARQKMHLSKSQFSQLLA 78
                                      689************************997 PP

>> Uso1_p115_head  Uso1 / p115 like vesicle tethering protein, head region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     2e-06     0.018      55     117 ..       6      69 ..       2      91 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-06
                    Uso1_p115_head  55 Aaleclkayltnneelkleflsraiegykesndetssassnllealleldae...laldpykvwFa 117
                                       Aa+ +++a l +n+e++ ++++++ ++++ +  +  + ++ +l all  + +    +   +k+ ++
  gi|330507936|ref|YP_004384364.1|   6 AAMAAMQAHLVENQEIQARLIKQLQTKREPQPMQ--KDRGEILRALLVANGGkmlEKEARQKMHLS 69 
                                       9*********************999999988866..556666666664443333323333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1397  (0.0779185); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 763.83
//
Query:       gi|330507937|ref|YP_004384365.1|  [L=295]
Description: hypothetical protein MCON_1983 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-11   43.0   0.4    2.9e-11   42.6   0.4    1.1  1  P22_CoatProtein  P22 coat protein - gene protein 5


Domain annotation for each model (and alignments):
>> P22_CoatProtein  P22 coat protein - gene protein 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.4   1.6e-15   2.9e-11      15     223 ..      14     227 ..       2     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.6e-15
                                       S-B--B----HHHH..HSEE.E---HHHHH.HTTSEEEEEB------EES.S--TT--B-EE--EEEEE----EEEE CS
                   P22_CoatProtein  15 ealelfenslvlak..avdrqyssefagaqvgssvtiklPadfesrrget.adltgkvqglvelkvtvkvgkqkgvd 88 
                                         le ++ slv+++   ++r+y+ e  + + gs+v+i    d ++ ++ + +d++ + + l+++++t++  + k   
  gi|330507937|ref|YP_004384365.1|  14 RLLENLQKSLVFGQpgVINRDYEGEI-SGK-GSTVKITSIGDITVGNYTKdSDIS-DPEALNDAQATLTATEAK--Y 85 
                                       6799999******9556*****9877.666.8***********998876515555.999999999988876665..7 PP

                                       EEEEGGG..GSSSHHHHHHHHHHHHHHHHHHHHHHHH............HHHHH-SEEEEESS-TTSST..THHHHH CS
                   P22_CoatProtein  89 felssaeralsledlserilkpaieklandieldlln............slaengslvvgkadaspnti..ikkwsd 151
                                       f++s ++  +s +++s+ i+ +a+++ a ++ +d+++            ++ + gs  +g   ++pnt+    +++ 
  gi|330507937|ref|YP_004384365.1|  86 FNFSVDD--VSRAQMSNNIMDAAMRQAAYNL-SDVADqfiagssyvdvaTANKIGSDTAG---KVPNTTpgTTAYDY 156
                                       9999999..999*************999998.5777778888999966444444555555...55555422689*** PP

                                       HHHHHHHHHHCTB--T-EEEEE-HHHHHHHHHHHHSSSSSSHHHHHHHHSTEEESSCTT-SEEEE-TT--EE CS
                   P22_CoatProtein 152 vadaesilkdlgvktdgrsavldpadekklagslagleaageevseayregqirgrvaGfdalmdqnvlsht 223
                                       +++ +  l + +v+++gr +v+ p+  +kla ++ + +a+   + +a+ +g++ +r aGfd+l ++nv  ++
  gi|330507937|ref|YP_004384365.1| 157 LLQMGTKLSEANVQKQGRWVVVPPWFVEKLAADARFTDASASGSTDALLNGSV-KRAAGFDILESNNVPTVA 227
                                       *****************************************************.********9999986554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2202.34
//
Query:       gi|330507938|ref|YP_004384366.1|  [L=83]
Description: hypothetical protein MCON_1985 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 570.78
//
Query:       gi|330507939|ref|YP_004384367.1|  [L=61]
Description: hypothetical protein MCON_1987 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 469.39
//
Query:       gi|330507940|ref|YP_004384368.1|  [L=266]
Description: hypothetical protein MCON_1988 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.068   13.4   2.3       0.19   12.0   2.3    1.7  1  Big_3_5   Bacterial Ig-like domain (group 3)


Domain annotation for each model (and alignments):
>> 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 ?   12.0   2.3     1e-05      0.19      14      73 ..      68     125 ..      66     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1e-05
                                       EE--CCCCTTS--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEEEEE-TTS- CS
                           Big_3_5  14 atVtaasggtptGtVtftdggttlgtavllsanGtAtltvsalaaGthsitAtYsGdany 73 
                                       ++Vt  +g+ p G  t++++gt++  ++++   G+At+++++l   t ++ A  s+  +y
  gi|330507940|ref|YP_004384368.1|  68 VSVTCETGTGPGGALTIVVTGTHILIQMATG--GSATYQIRTLMLATPAVMALLSDVIKY 125
                                       789999999***************8888655..*********999998888866655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2174.00
//
Query:       gi|330507941|ref|YP_004384369.1|  [L=61]
Description: hypothetical protein MCON_1990 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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      0.016   15.2   0.0    1.1  1  DUF5070   Domain of unknown function (DUF5070)


Domain annotation for each model (and alignments):
>> DUF5070  Domain of unknown function (DUF5070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   9.1e-07     0.016      28      57 ..       8      37 ..       3      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.1e-07
                           DUF5070 28 sdckaleielklflkevavvkdrklqrwre 57
                                      + c++le elk fl+++a  kd  l ++  
  gi|330507941|ref|YP_004384369.1|  8 AICFKLESELKDFLEDMADSKDMDLSKYCR 37
                                      56********************99988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 421.83
//
Query:       gi|330507942|ref|YP_004384370.1|  [L=51]
Description: hypothetical protein MCON_1991 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.12   12.0   0.0    1.0  1  SMRP1     Spermatid-specific manchette-related protein 1
       0.15   12.4   0.0       0.19   12.2   0.0    1.1  1  PDZ_4     PDZ domain


Domain annotation for each model (and alignments):
>> SMRP1  Spermatid-specific manchette-related protein 1
   #    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     161     207 ..       2      47 ..       1      49 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                             SMRP1 161 vvvnmlnslsrnqtlpritprcgcleplpgrlpfqgyesacsgrhyc 207
                                       vv+ m+n ls  +++ +i     c++  p + p +gy+ a   +h+c
  gi|330507942|ref|YP_004384370.1|   2 VVLYMVNELSTIKSFWSIFDELICIDGQPIQKPEMGYNEAF-LKHFC 47 
                                       8999*********************************9986.46777 PP

>> PDZ_4  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.1e-05      0.19      17      44 ..       5      32 ..       3      36 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                                      EEEEEE-SSSSSS-TT-EEEEETTEEHH CS
                             PDZ_4 17 yfivdideeklelkvGDellefdgkpvk 44
                                      y + ++++ k+ +++ Del+ +dg+p++
  gi|330507942|ref|YP_004384370.1|  5 YMVNELSTIKSFWSIFDELICIDGQPIQ 32
                                      444556778899***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       183  (0.0102069); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 398.61
//
Query:       gi|330507943|ref|YP_004384371.1|  [L=57]
Description: hypothetical protein MCON_1992 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 429.28
//
Query:       gi|330507944|ref|YP_004384372.1|  [L=74]
Description: hypothetical protein MCON_1993 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 568.50
//
Query:       gi|330507945|ref|YP_004384373.1|  [L=378]
Description: phage/plasmid primase, P4 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-12   45.8   0.1    2.3e-11   44.2   0.1    1.8  1  D5_N      D5 N terminal like
  ------ inclusion threshold ------
      0.019   15.2   0.0      0.068   13.4   0.0    1.9  2  AAA_22    AAA domain
       0.02   14.7   0.1      0.039   13.7   0.0    1.5  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
      0.089   12.6   0.0       0.27   11.0   0.0    1.7  2  AAA_29    P-loop containing region of AAA domain
       0.13   12.9   0.2       0.32   11.6   0.2    1.6  1  SlpA      Surface later protein A domain
       0.17   12.3   0.0       0.34   11.3   0.0    1.5  1  AAA       ATPase family associated with various cellular acti


Domain annotation for each model (and alignments):
>> D5_N  D5 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.1   7.6e-15   2.3e-11      90     147 ..       8      65 ..       2      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 7.6e-15
                              D5_N  90 leideldadplllafaNGvldlktgelrdhepedyltkitpvdydpdadcptfkewld 147
                                        ei ++d+d   ++++NG ++++tg++ +h p++y   ++pv +dpda cp ++++++
  gi|330507945|ref|YP_004384373.1|   8 TEIAKFDSDLSIINMENGLYNWQTGKFLPHTPDYYSVIQIPVRFDPDARCPNIDKMIN 65 
                                       5899*************************************************99886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.3e-05     0.068       5      71 ..      91     156 ..      90     180 .. 0.74
   2 ?   -2.4   0.0       1.7   5.2e+03      42      69 ..     283     314 ..     253     334 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.3e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka...e 71 
                                       +++ v++G+ GtGK++ l  +++ l  +     +++ v   +l+++   s+dl+++l+++ g+  ++   +
  gi|330507945|ref|YP_004384373.1|  91 QKMFVLFGPGGTGKSYFLDVVQRMLGDV-----NCSNVSMQDLAKDRfASSDLYKKLANICGDLDNTamyQ 156
                                       5789*********************876.....3455445566666699********99999765555552 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                            AAA_22  42 vvfvtlpsst...sskdl.lrellralglelk 69 
                                       ++ v++p++t   +   + ++e +++lgl++ 
  gi|330507945|ref|YP_004384373.1| 283 QFVVEVPGETiakNMLAMyFNEYCEILGLPKR 314
                                       33677777774443333335666666665554 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.3e-05     0.039       2      46 ..      94     132 ..      93     154 .. 0.75
   2 ?   -3.0   0.1       1.7   5.1e+03     130     147 ..     185     202 ..     161     238 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkip 46 
                                        vl Gp g+GKS++Ld  + +      + + ++++ + ++++k++
  gi|330507945|ref|YP_004384373.1|  94 FVLFGPGGTGKSYFLDVVQRM------LGDVNCSNVSMQDLAKDR 132
                                       79****************555......455555555555555444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                            AAA_21 130 lsvsepndlqfgkaltdi 147
                                       + + ++++++ ++  +d 
  gi|330507945|ref|YP_004384373.1| 185 FAKPIFSANHLPSSKDDT 202
                                       222222222222222222 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       2.4   7.3e+03       6      11 ..      26      31 ..      25      34 .. 0.84
   2 ?   11.0   0.0     9e-05      0.27      20      46 ..      91     115 ..      78     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.4
                            AAA_29  6 lvNWgt 11
                                      l+NW+t
  gi|330507945|ref|YP_004384373.1| 26 LYNWQT 31
                                      79**97 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9e-05
                            AAA_29  20 dlkgatlltGpsGsGKSTllDAiqalL 46 
                                       +   +++l Gp G+GKS +lD +q +L
  gi|330507945|ref|YP_004384373.1|  91 Q--KMFVLFGPGGTGKSYFLDVVQRML 115
                                       3..5789**************999876 PP

>> SlpA  Surface later protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00011      0.32       8      43 ..     335     368 ..     331     374 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                              SlpA   8 vYdknGkrvkktkklkkgssvktygkkvtIkNgkkY 43 
                                       +Yd++G  ++++   k g+sv ++ ++  I + kk+
  gi|330507945|ref|YP_004384373.1| 335 IYDNKGDHKSNYSAWKDGKSVAVWPDT-MI-DLKKF 368
                                       8*********9999************9.79.58887 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.34       2      37 ..      95     131 ..      94     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                       EEESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSS CS
                               AAA   2 llyGppGtGKTllakavakelg.vefleisgsellsk 37 
                                       +l+Gp GtGK+++   v + lg v++ ++s+ +l ++
  gi|330507945|ref|YP_004384373.1|  95 VLFGPGGTGKSYFLDVVQRMLGdVNCSNVSMQDLAKD 131
                                       69*******************7799999999999954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2793.28
//
Query:       gi|330507946|ref|YP_004384374.1|  [L=118]
Description: hypothetical protein MCON_1996 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.4   0.2       0.15   12.3   0.0    2.0  2  PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
      0.045   14.1   1.0       0.13   12.6   0.0    2.1  3  TPR_20     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> 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 ?   -0.1   0.0      0.12   1.1e+03      45      62 ..      15      32 ..       6      46 .. 0.65
   2 ?   12.3   0.0   1.6e-05      0.15      14      51 ..      69     104 ..      58     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.12
                         PhetRS_B1 45 kkadkkseeviykidipA 62
                                      +++dk s+e   kid  A
  gi|330507946|ref|YP_004384374.1| 15 RNRDKLSDEIRKKIDQDA 32
                                      556666666666776655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.6e-05
                         PhetRS_B1  14 algkelteeeledllfefGlElDeiveeeekkkadkks 51 
                                       +++k+ +++e+ dl+++ G+ +D ++ e+ ++  d++ 
  gi|330507946|ref|YP_004384374.1|  69 LIEKSEKTNEIRDLCVSVGILIDKFQIEQGRT--DDSA 104
                                       567788899*******************9933..3333 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.18   1.6e+03      48      63 ..      12      27 ..       6      34 .. 0.72
   2 ?   -2.9   0.0      0.98   8.7e+03      55      65 ..      49      59 ..      37      63 .. 0.61
   3 ?   12.6   0.0   1.4e-05      0.13      44      73 ..      88     117 ..      69     118 .] 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.18
                            TPR_20 48 ilkrdrkweddaarkq 63
                                        kr+r+   d++rk+
  gi|330507946|ref|YP_004384374.1| 12 AAKRNRDKLSDEIRKK 27
                                      5567777777777776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.98
                            TPR_20 55 weddaarkqll 65
                                      + + + r++ll
  gi|330507946|ref|YP_004384374.1| 49 YLKSEGRQELL 59
                                      44445555554 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 1.4e-05
                            TPR_20  44 qLleilkrdrkweddaarkqllkifealgs 73 
                                        L++ ++ +++ +dd+a+ +l+k+fe lg+
  gi|330507946|ref|YP_004384374.1|  88 ILIDKFQIEQGRTDDSAKAALVKLFEKLGE 117
                                       688889999999****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.36s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 630.30
//
Query:       gi|330507947|ref|YP_004384375.1|  [L=422]
Description: phage terminase, large subunit, PBSx family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-13   50.8   0.0    1.9e-13   50.4   0.0    1.2  1  Terminase_3   Phage terminase large subunit
    1.2e-10   41.4   0.0    2.1e-10   40.6   0.0    1.4  1  Terminase_6   Terminase-like family
    6.2e-05   23.1   0.0    0.00013   22.0   0.0    1.6  1  Terminase_6C  Terminase RNaseH-like domain
    0.00011   22.7   0.2    0.00028   21.3   0.2    1.7  1  Terminase_3C  Terminase RNAseH like domain


Domain annotation for each model (and alignments):
>> Terminase_3  Phage terminase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   4.2e-17   1.9e-13       3     189 ..      21     198 ..      19     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 4.2e-17
                       Terminase_3   3 eikvlvggrgssKsysialkivlkklkekrkalvlRkvkntlkdSvfaeikellselgltklfkilkskieieleng 79 
                                       +i++l+g+  s K+ s+  ki+   l  +  +++       +  S + ++   +++l  +k f++   k+e   ++g
  gi|330507947|ref|YP_004384375.1|  21 RINLLYGSVRSTKTWSVNIKILKDILTLPTGNILF---VGNTGTSLYRNVLTPIKDLVGEKNFELRAGKKEC-EIFG 93 
                                       6889****************************993...3445668888888888888889999998888876.589* PP

                       Terminase_3  80 skflFkglddpaklkSik..nlsdlwlEEasevseedidelvetlrapeqekqiilsfNPvsesnwvykrffkddek 154
                                         +  +g d++ + k i+   l  ++++E  ++ e+  ++l+ +l   +++  ++l+ NP  ++n++y+ ++     
  gi|330507947|ref|YP_004384375.1|  94 RTVWIEGADNTSSYKKIEgeSLLRAYVDEGTTIPENFTNMLLSRLS--DKGACLYLTCNPETPRNYIYRNWIA---- 164
                                       *****************9888999**********************..***********************93.... PP

                       Terminase_3 155 ekdekddvlihkstyrdnefLdeedvkkleelkke 189
                                       ++d + ++ + k t +dn++L+ e++++le+ + +
  gi|330507947|ref|YP_004384375.1| 165 RQD-ELNIKVWKFTLDDNPYLPLEYKRDLEKEYPK 198
                                       233.567899********************97755 PP

>> Terminase_6  Terminase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   4.6e-14   2.1e-10       2     209 ..      25     220 ..      24     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 4.6e-14
                                       EEE-SSS-HHHHHHHHHHHHHHSSSS.-EEEEEESSHHHHHHHHHHHHHHHHTS-TTTS--EEEE-SSEEEETTS-E CS
                       Terminase_6   2 ilggrqsGKTfagarellrhalgrgprnqvflsasktqareeggqfekgigelakeildiefeesaknlvvlsnGas 78 
                                       ++g+ +s KT+ + + +l+++l  +  n+ f++++ t++++ ++     i+ l  e   +e+++++k++ ++  G +
  gi|330507947|ref|YP_004384375.1|  25 LYGSVRSTKTWSVNIKILKDILTLPTGNILFVGNTGTSLYRNVL---TPIKDLVGE-KNFELRAGKKECEIF--GRT 95 
                                       67889999*****************97888888999***99633...334444444.566777788899997..999 PP

                                       EEEES.....SHHHHHTS--SEEEEESGGGSTTHHHHHHHHHHHHCSTT--EEEEEE--.-SSSHHHHHHHHHHCTS CS
                       Terminase_6  79 lhflslese.taggiqGaqidliyfDElteipksqelekvtrlratkgtdtktfattpp.tpdhgvydfvtgwldee 153
                                       + ++++ ++ +  +i G +   +y+DE t ip+ ++++++ +  ++kg     + t++p tp +++y ++    de 
  gi|330507947|ref|YP_004384375.1|  96 VWIEGADNTsSYKKIEGESLLRAYVDEGTTIPE-NFTNMLLSRLSDKGAC--LYLTCNPeTPRNYIYRNWIARQDEL 169
                                       *********999********************7.5999999999999944..488876548*************999 PP

                                       S-EEEEE-GGGSGB-TTSBB-TTHHHHHHHHHTS-HHH..HHHHHS---TTCTCESSX CS
                       Terminase_6 154 gpqsvtkiqavvevtiedakklgedlieeleaeysvee..rarllrGewidtsgsiFq 209
                                             k+++   +t  d++ l  ++++ le+ey++    + r  +G+w++++g++F 
  gi|330507947|ref|YP_004384375.1| 170 ----NIKVWK---FTLDDNPYLPLEYKRDLEKEYPKGTvfYDRFILGNWVAAEGRVFG 220
                                       ....455555...599********************999*****************96 PP

>> Terminase_6C  Terminase RNaseH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0     3e-08   0.00013      86     154 ..     348     419 ..     313     420 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3e-08
                                       SSH..HHHHHHHHHHHHHHHTTSEEEETHHCECCCCCCHCC-EEHCC....HHCHCSGCCTCHHHHHHHHHHT CS
                      Terminase_6C  86 pepaskdkatrvskvkdliesgrlkvdkgaecaksfealegfhtdlg....aerstsaehdDlvdAlsyalla 154
                                       +  a++d+  ++ k++ +i +g+l ++    c+ + +++e +  d +    +e++ ++  d++vdAl+ya+++
  gi|330507947|ref|YP_004384375.1| 348 ARAADNDVLGGIRKIASMIGNGDLIINSE-KCPVLVSEMETYAWDQSaadrGEDKPQKIDDHVVDALRYAVNS 419
                                       3345599999******************8.****************************************985 PP

>> Terminase_3C  Terminase RNAseH like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2   6.3e-08   0.00028      42     154 ..     290     418 ..     266     419 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 6.3e-08
                      Terminase_3C  42 sevikdkthlkevidgdsaevkgiaalksq.....................thrktvrakkaqgsvlqkdrflktf. 96 
                                       ++++kd+++  + + g s    gi ++++                      +     +a+ a   vl ++r++ ++ 
  gi|330507947|ref|YP_004384375.1| 290 ADYSKDMAKFASEQWGYSSGQPGITYGDNTskmyastievdpsaasfilqlQRDGLHKARAADNDVLGGIRKIASMi 366
                                       55555555555555555555555555555555555555555555555544433334444444445555555554431 PP

                      Terminase_3C  97 ..ravlkgeyLdpeaipkleqlisElnkyqykrdkgnrliqkdemrkdphtidAlmyala 154
                                          ++        +++ k+  l+sE ++y++++    r    ++ ++d+h++dAl+ya++
  gi|330507947|ref|YP_004384375.1| 367 gnGDL-------IINSEKCPVLVSEMETYAWDQSAADRGED-KPQKIDDHVVDALRYAVN 418
                                       11233.......3589******************9999999.9***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3117.04
//
Query:       gi|330507948|ref|YP_004384376.1|  [L=518]
Description: portal protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-14   52.8   0.0      5e-14   52.2   0.0    1.2  1  Phage_prot_Gp6  Phage portal protein, SPP1 Gp6-like


Domain annotation for each model (and alignments):
>> Phage_prot_Gp6  Phage portal protein, SPP1 Gp6-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   2.8e-18     5e-14      41     413 ..      68     467 ..      21     469 .. 0.82

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2.8e-18
                    Phage_prot_Gp6  41 nrivlnfakyivdqkagylfgepitltvdddddereeildvlennnfdkkdeellkdasiyGrayelvyvdeeg.ei 116
                                       +++++n++k ++   ++ ++gep++l       e   ++ +++ +++  ++ +++ +   +G a + v + + g e+
  gi|330507948|ref|YP_004384376.1|  68 KKLPMNWFKVVTSVYSDMVVGEPPRLMNPVGQTE---LDGIVNRSDLSVVLYNACNNFIQFGNAILKVRFVGTGsEP 141
                                       799************************9999999...*****************************99998878666 PP

                    Phage_prot_Gp6 117 ..kvkvvdpedafpvyddsierellavvryykdkdektitkvevYtdkevykfekdgggv................n 175
                                          +  vdp   fpv + ++ +e+   v  + + +e   + v    ++ev++    ++                  +
  gi|330507948|ref|YP_004384376.1| 142 gsIIENVDPSIWFPVVNPDNVNEYSCHVLAW-KFKEMVGSSVASLLRTEVHTAGAIDNHLywmngdeidhevelniS 217
                                       88****************6444444444444.556666666666677777775544443378888888888888889 PP

                    Phage_prot_Gp6 176 eeyeseephgfgrvP..liefknnnerlg......dlenvksliDaynkvlsdfaneledfqnailv.ltGmtldde 243
                                       ++y++   h   +vP  l+ +  n ++ +      d++++  l+ ++++ + + +  l+  +++ ++ ++ m ++d 
  gi|330507948|ref|YP_004384376.1| 218 SKYINVPKHIETGVPypLVFVVSNIKKRNdvygisDYDSIENLVKELETRIIKVSSILDIHSRPAMTgPSSMLTTDM 294
                                       9********999999998888889888889****************************9999988775788887777 PP

                    Phage_prot_Gp6 244 dlvk..lkkekaiklks.....lgdgkngdvkfltkeiddealenlldrlekdihqfsmtpnisdenfa..gnaSgv 311
                                       + ++  ++ +      +     ++d+++++  +    +   +  + +drl ++i+ +++      + f+  + aSg 
  gi|330507948|ref|YP_004384376.1| 295 ETGEetMRIN------GrffavNKDEDKPEYITWDGKL--DSSFQEMDRLVSMIYAVTDLNPAAIGDFSggAVASGS 363
                                       7777455554......3344333566666655555555..6777789*********9998777777777889***** PP

                    Phage_prot_Gp6 312 alkykyslleqkaelkerefekalkeliklilellnalde.kdgddvedi.kvkftrnipkndaekadilqklveag 386
                                       al+ ++  ++  +++ +  f + lk+ ik++   l +++  k+++ v ++  + +++++p +d+e   i q+ +++g
  gi|330507948|ref|YP_004384376.1| 364 ALRRLLLRTISHCNRIRVRFDQVLKRAIKAASI-LDVNGRiKNATVV-ELsIISWQDGLPSDDLENSMIEQTRANSG 438
                                       *****************************8765.5555430333333.567899*********************** PP

                    Phage_prot_Gp6 387 ivskktllsklpfvedpe..eelerikee 413
                                       + s+ +++ +l   +  e  ee+erik+e
  gi|330507948|ref|YP_004384376.1| 439 LTSRSSAIMRLDGCTREEadEEMERIKRE 467
                                       ***************96677******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3635.17
//
Query:       gi|330507949|ref|YP_004384377.1|  [L=166]
Description: phage putative head morphogenesis protein domain, SPP1 gp7 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-15   58.1   0.0    1.7e-15   57.8   0.0    1.1  1  Phage_Mu_F  Phage Mu protein F like protein


Domain annotation for each model (and alignments):
>> Phage_Mu_F  Phage Mu protein F like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.0   9.3e-20   1.7e-15      14     112 .]      53     147 ..      41     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 9.3e-20
                        Phage_Mu_F  14 GegeeelakelkkrgqlssrsrlrtiartetlraynaarlaqeaaskevkkekwryvavkdsrtrpeHaaldGkvfk 90 
                                       G+g +++  + +++ +  ++ rl  i+rte  ra+n + +   +a+ + +k+k +++  +d+r +pe+ a+d  v+ 
  gi|330507949|ref|YP_004384377.1|  53 GKGPDAFRAAFEDQYKG-PA-RLDKIYRTEYVRAQNEGIVV--RAKAAGHKYK-MWRCPNDERSCPECVAMDYEVVP 124
                                       66666777777777755.66.******************94..4445555676.*********************** PP

                        Phage_Mu_F  91 vddpfwq.tgappedvnCRCrvi 112
                                       +d++f + +++p+ ++nCRC++i
  gi|330507949|ref|YP_004384377.1| 125 IDEMFSGgVMCPGLHPNCRCVLI 147
                                       ******99************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1294.32
//
Query:       gi|330507950|ref|YP_004384378.1|  [L=411]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 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:                        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 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3042.65
//
Query:       gi|330507951|ref|YP_004384379.1|  [L=275]
Description: hypothetical protein MCON_2004 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-32  111.3   0.0    6.3e-32  111.0   0.0    1.0  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0   0.0   3.5e-36   6.3e-32     310     492 .]      25     216 ..       9     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 3.5e-36
                           DUF2207 310 kndeeldpyEkalldlLfdkseeg.ks...lkeikkyakkskk..kakkfkkalkkwksavkk......kergyfdk 374
                                        +  +ld+yE++++++L+d+s++g  s   +++  k + ks++     ++++a++++   v+k      +  + +++
  gi|330507951|ref|YP_004384379.1|  25 PSAPDLDDYERRVIEFLQDNSRGGaFSapgFEAEVKSLAKSNDtvQLARLRSAMDEILHYVDKdvvsrhAVGRGIRA 101
                                       567899******************888***9998898888888899******************7655544444444 PP

                           DUF2207 375 kgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrteeGaellakwkgF 451
                                        g  ++++  +l l+++ l+++ ++++ +   +l  + +i+++illl++++++  +s+l+gr++e++++++ +w++F
  gi|330507951|ref|YP_004384379.1| 102 LGIGIQTRHLILPLIWGALFIVPFIMGSG---VLGDPVAITAMILLLQSSLAVSAPSTLFGRWKEDYYKEKLEWDAF 175
                                       44444444444444444444443333333...339****************************************** PP

                           DUF2207 452 kkyLeDfsefkerppedlelweryLvYAtalGvadkvakql 492
                                       + +L D++++++++p+dl++w+++L Y+talGv+dkv+k+l
  gi|330507951|ref|YP_004384379.1| 176 RTFLGDYAMIQRYSPSDLNMWKEWLIYGTALGVGDKVEKAL 216
                                       ***************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2108.54
//
Query:       gi|330507952|ref|YP_004384380.1|  [L=537]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-41  140.2   0.0      6e-41  139.2   0.0    1.6  1  DUF4277    Domain of unknown function (DUF4277)
    8.1e-12   45.2   0.2    5.7e-11   42.5   0.2    2.0  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.0   6.7e-45     6e-41       3     109 .]      10     116 ..       8     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 6.7e-45
                           DUF4277   3 vksldhlglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfpeffedkplerLlgegve 79 
                                       + sldhlglva+++d+lg++e+ide ipk++++k+s++ ++ka+++ngLgf +r+Ly+fp++fe+++lerL+++gv 
  gi|330507952|ref|YP_004384380.1|  10 TLSLDHLGLVAAIFDALGISEVIDESIPKTRNCKLSHSAIIKAMVINGLGFAERRLYIFPSYFENLALERLFNPGVV 86 
                                       679************************************************************************** PP

                           DUF4277  80 aehlnddrlgrtLDklyeagvtklfteial 109
                                       +e++n+d++grtLD++ ++g t+lf++ia+
  gi|330507952|ref|YP_004384380.1|  87 PEDFNEDVVGRTLDRINKFGSTALFNNIAM 116
                                       ****************************86 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.2   6.4e-15   5.7e-11       9     213 ..     131     455 ..     124     456 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 6.4e-15
                         DDE_Tnp_1   9 vDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                       vD t++ v+g                  +d+rw        + + + +++++  g++l v+ ++gn++d k+l++++
  gi|330507952|ref|YP_004384380.1| 131 VDTTSFGVHGDYegldcnpameitlghpKDGRW------DLKQFIVSMVTNQC-GIPLFVQAHSGNKSDKKTLIETI 200
                                       666666666666666666554444444444444......55667788888888.9********************** PP

                         DDE_Tnp_1  70 delrpr....kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrn 142
                                       ++++ +     + ++ aD++ +s e+++ l      +i r++  +++ ++      +++++ +dr+ i++++ +  +
  gi|330507952|ref|YP_004384380.1| 201 QMFKSNldfsGKNYFAADSALFSSENIRLLG-DSTLWITRVPTTVREVKDLQRLDLEMKTCSDDRYSIFETEINYGG 276
                                       **********************999999999.55559****888888888666669999999999999999999999 PP

                         DDE_Tnp_1 143 k............................................................................ 143
                                                                                                                    
  gi|330507952|ref|YP_004384380.1| 277 Idqkwvvvdsremhaskaktfdrrigkeftearkslkklgyivfaceadarkaadrwisenphftltglsiceiskr 353
                                       99*************************************************************************** PP

                         DDE_Tnp_1 144 ...............................skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrk.f 188
                                                                      + ++   + +v+  n+++l+ e + ++y+ +  +E  F++lk+k f
  gi|330507952|ref|YP_004384380.1| 354 idskrgrpkkdeqlekgyliegevqrneatiANERSRLGRFVLASNDKTLEGELMLQYYKGQNAVEKGFRFLKDKsF 430
                                       ******************************99999999*************************************** PP

                         DDE_Tnp_1 189 gldrlryrglnrveaqllllllaln 213
                                       +   +++++ +r+ea  +++ l+l+
  gi|330507952|ref|YP_004384380.1| 431 RVAEVYLKKEERIEALSMIMVLSLL 455
                                       *******************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 3882.91
//
Query:       gi|330507953|ref|YP_004384381.1|  [L=356]
Description: hypothetical protein MCON_2005 [Methanosaeta concilii GP6]
Scores for complete 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-30  103.8   0.0    1.4e-29  103.2   0.0    1.2  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   7.8e-34   1.4e-29       3     293 ..      47     346 ..      45     352 .. 0.74

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 7.8e-34
                           DUF2207   3 esydvdatvqedGsldvtEtitydf..dgsrhgiyrdrdlplr....................tydvdgsgnsvrik 57 
                                       +sy++d++   +G+l   E+++y++  +g+++++yr++++pl+                    +             
  gi|330507953|ref|YP_004384381.1|  47 DSYRADLY--LNGTL--AERFDYQVksSGKYRMLYRNWKMPLSsqsldipyieplsilptsgaV------------- 106
                                       67777777..89***..9999999999*************765444444444555555555551............. PP

                           DUF2207  58 irddvtepyykessddg.............................tlstgthtyeisYtvknavtkykdvaelywn 105
                                              py  + ++++                             ++stg+++ e+ +++++ ++ +++ ++ +  
  gi|330507953|ref|YP_004384381.1| 107 -------PYVRDHNGTVqilsasgnrynseiaslalvneaggyypqRFSTGQYQMEYLFRIHPYLECDQELCHWNL- 175
                                       .......444444444444444444445555555566666679999**************************7777. PP

                           DUF2207 106 vigngwdvpienvtitvtlPseaksggdlrawlHgldgsttvkkddgsvtftarnlppgeglevrvlf.pt..n... 176
                                       +++n++  p++++ i ++ P    ++ ++++++H+    + +++++g++++ ++  p++e +ev++l+ p+  n   
  gi|330507953|ref|YP_004384381.1| 176 MLANEH-LPYRQIAIYIHDP----DELIVELFTHP----QLRTQKEGEIWVITGGSPKDELIEVEMLLlPQtaNiie 243
                                       777755.**********999....889********....888999***********************843231223 PP

                           DUF2207 177 .narktsgnkldeilkeeqkntreraarlslallillilllilllllllllliklllwkkygrepkvkevdpeYerd 252
                                        ++r  s+ ++ +            +a++s    +l++l  ++++l++ll+l++ll     gre+++++  p+   +
  gi|330507953|ref|YP_004384381.1| 244 gITREVSNVYQRT-----------ITAQESEGSSLLFVLRFLVAALPMLLILVYLL----IGREKRYTV--PRALST 303
                                       4444444444444...........44444445555555555555555555555544....789999977..444559 PP

                           DUF2207 253 vPedlsPavvgylvkg..dkvdengltAtlldLavkgyitiee 293
                                       +P+   P++v++l+kg   ++d++g++AtlldL+++  i+i++
  gi|330507953|ref|YP_004384381.1| 304 PPSRRRPWQVNMLFKGdaFDFDQDGFYATLLDLHKRDIIRIDT 346
                                       ******************7799*******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 3064.69
//
Query:       gi|330507954|ref|YP_004384382.1|  [L=206]
Description: LemA family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-32  111.2   0.2    4.8e-32  110.9   0.2    1.1  1  LemA        LemA family
     0.0062   16.8   0.2      0.098   12.9   0.1    2.1  2  DUF948      Bacterial protein of unknown function (DUF948)
  ------ inclusion threshold ------
      0.061   13.5   0.0      0.081   13.1   0.0    1.2  1  DUF4330     Domain of unknown function (DUF4330)
      0.065   13.1   0.0      0.097   12.5   0.0    1.3  1  SpoIIIAH    SpoIIIAH-like protein
      0.086   12.7   0.1       0.22   11.4   0.0    1.6  2  EC042_2821  EC042_2821-lke REase
       0.14   12.4   0.1       0.25   11.6   0.1    1.4  1  DUF4381     Domain of unknown function (DUF4381)
       0.42   10.7   3.5       0.59   10.2   0.2    2.4  3  DUF1664     Protein of unknown function (DUF1664)
        1.6    8.1   5.8       0.53    9.7   0.6    2.4  3  DUF3552     Domain of unknown function (DUF3552)


Domain annotation for each model (and alignments):
>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.2   2.1e-35   4.8e-32       2     128 ..      48     173 ..      47     198 .. 0.93

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 2.1e-35
                              LemA   2 wsqidvqlkrRaDlipnLvetvkgyakhEketleevteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLk 78 
                                       +sqi+v++k+R D+i +Lv++++ ya++E++tle++t +R+ + +++  +e  + e++ ++ l+++ +vaE+YPdLk
  gi|330507954|ref|YP_004384382.1|  48 LSQIKVAMKKRLDTIEQLVDSIESYAHFERQTLEKITGMRSGL-QEAGAQELGRVEKESRGVLGNIRLVAESYPDLK 123
                                       69****************************************9.677789*************************** PP

                              LemA  79 anenfleLqeelegtEnriavaRrrYneavreyntkiesfpsnivaklfg 128
                                       +++   + ++ + ++E++ia +R  Yn+ v+e+nt  ++fps+++a  + 
  gi|330507954|ref|YP_004384382.1| 124 TSQATINSMNAIRELEDEIARHRYTYNNIVQEFNTMRDTFPSRWIAASMP 173
                                       ********************************************998664 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   4.4e-05     0.098       6      81 ..      19      94 ..      15     105 .. 0.81
   2 ?    1.9   0.0      0.12   2.7e+02      26      60 ..     127     160 ..     107     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.4e-05
                            DUF948  6 aAiAFvvLviflivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlg 81
                                      +   +++++ + +++ ++l+++ + a at+ +++  +++ l+ +e+l++ ++  +   ++ lek+  + + ++++g
  gi|330507954|ref|YP_004384382.1| 19 ILAVLLLVAGYFVMTYNRLQSLRNGADATLSQIKVAMKKRLDTIEQLVDSIESYAHFERQTLEKITGMRSGLQEAG 94
                                      3333445557999***********************************9999977777777777777777777766 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.12
                            DUF948  26 ktldeaaatieelekqvdpilkevedllakvnell 60 
                                        t++++ ++i+ele+++       ++++++ n++ 
  gi|330507954|ref|YP_004384382.1| 127 ATINSM-NAIRELEDEIARHRYTYNNIVQEFNTMR 160
                                       444444.4688888888888888888888888754 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.6e-05     0.081      19      65 ..      16      63 ..      10     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.6e-05
                           DUF4330 19 llailvilavivgiflkpgts.gsvaqaeaaatkpvevdvvvrglevp 65
                                      ll+il++l++++g f+++ ++ +s+ + ++a+ ++++v +  r  +++
  gi|330507954|ref|YP_004384382.1| 16 LLIILAVLLLVAGYFVMTYNRlQSLRNGADATLSQIKVAMKKRLDTIE 63
                                      7899999999***********999999999999999998887766664 PP

>> SpoIIIAH  SpoIIIAH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.3e-05     0.097       5      47 ..      16      61 ..      13     141 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.3e-05
                                      XXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXX CS
                          SpoIIIAH  5 iitaLalmiavagYlnftedsgk...kaaetaeteqeesekaeigd 47
                                      +++ La+++ vagY+ +t+++ +   + a+++ ++ + + k+ + +
  gi|330507954|ref|YP_004384382.1| 16 LLIILAVLLLVAGYFVMTYNRLQslrNGADATLSQIKVAMKKRLDT 61
                                      7889****************98877744444444444444444444 PP

>> EC042_2821  EC042_2821-lke REase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.1   2.5e+03      76     102 ..      47      72 ..      31      87 .. 0.55
   2 ?   11.4   0.0   9.9e-05      0.22      84     115 ..     126     158 ..     119     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.1
                        EC042_2821  76 dlv.vaidkeadakvkivkelkDpnkth 102
                                       +l  +++    +++  ++++l+D+ +++
  gi|330507954|ref|YP_004384382.1|  47 TLSqIKV--AMKKRLDTIEQLVDSIESY 72 
                                       4442222..2233334556666655555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 9.9e-05
                        EC042_2821  84 ea.dakvkivkelkDpnkthpYtykevikkvne 115
                                       +a  + ++ ++el+D  + h Yty++++++ n 
  gi|330507954|ref|YP_004384382.1| 126 QAtINSMNAIRELEDEIARHRYTYNNIVQEFNT 158
                                       343788999*********************997 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00011      0.25      23      69 ..      16      62 ..      10      87 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                           DUF4381 23 lllaalllllllvlalwllrrrkrnrreAlreLaalradeadakell 69
                                      ll+++++lll+++++++ + r +  r  A + L +++ + +++ +++
  gi|330507954|ref|YP_004384382.1| 16 LLIILAVLLLVAGYFVMTYNRLQSLRNGADATLSQIKVAMKKRLDTI 62
                                      4444555567777777777799999***********93333333333 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.89     2e+03       6      23 ..      17      34 ..      13      38 .. 0.78
   2 ?   10.2   0.2   0.00026      0.59      52     101 ..      46      95 ..      33     119 .. 0.72
   3 ?    0.7   0.0      0.23   5.2e+02      79     106 ..     132     159 ..     101     165 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.89
                           DUF1664  6 livpaavvgavgYgyvww 23
                                      li+ a+++ ++gY+ + +
  gi|330507954|ref|YP_004384382.1| 17 LIILAVLLLVAGYFVMTY 34
                                      56678889999**99976 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00026
                           DUF1664  52 qvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseige 101
                                          ++++ + ++  + i+++ +++++ ++  +++ e++t +r++l+e g 
  gi|330507954|ref|YP_004384382.1|  46 ATLSQIKVAMKKRLDTIEQLVDSIESYAHFERQTLEKITGMRSGLQEAGA 95 
                                       4444555444444456788889999999*****************98874 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.23
                           DUF1664  79 keiskeikeevtevredlseigedvesv 106
                                       +++++e+++e+++ r   ++i ++++++
  gi|330507954|ref|YP_004384382.1| 132 MNAIRELEDEIARHRYTYNNIVQEFNTM 159
                                       3334455555555555555555555555 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.25   5.7e+02       5      24 ..      16      35 ..      13      44 .. 0.63
   2 ?    9.7   0.6   0.00023      0.53     104     160 ..      44     102 ..      35     106 .. 0.81
   3 ?    0.5   0.1      0.15   3.4e+02      26      77 ..      95     146 ..      89     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.25
                           DUF3552  5 laivalvvglvvgylvrkki 24
                                      l+i+ +v+ lv+gy+v   +
  gi|330507954|ref|YP_004384382.1| 16 LLIILAVLLLVAGYFVMTYN 35
                                      45666667777777776554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00023
                           DUF3552 104 keesleekekelkqkeqsleekeeeleelveeqrqeLerisgLtk..eeAkeilleeve 160
                                        +++l++ +  +k++ +++e+  +++e+  + +rq Le+i g+ +  +eA ++ l +ve
  gi|330507954|ref|YP_004384382.1|  44 ADATLSQIKVAMKKRLDTIEQLVDSIESYAHFERQTLEKITGMRSglQEAGAQELGRVE 102
                                       5789999999******************************9997633456555555555 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.15
                           DUF3552  26 ekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreelekelkerr 77 
                                       ++++++ e+e + ++ + +  Ae++ + ++ +a  + +++ +ele+e+ + r
  gi|330507954|ref|YP_004384382.1|  95 AQELGRVEKESRGVLGNIRLVAESYPDLKTSQATINSMNAIRELEDEIARHR 146
                                       6777778888888888888889999999999999999999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1555  (0.086731); expected 358.6 (0.02)
Passed bias filter:                     1124  (0.0626917); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 1593.36
//
Query:       gi|330507955|ref|YP_004384383.1|  [L=627]
Description: cell surface protein [Methanosaeta concilii GP6]
Scores for complete 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-39  133.5  34.4    1.5e-25   89.9  14.8    2.3  2  NosD        Periplasmic copper-binding protein (NosD)
    1.5e-30  106.1  44.1    3.6e-18   65.9  25.1    2.4  2  Beta_helix  Right handed beta helix region
    1.1e-07   31.4  17.8    1.1e-05   24.9   5.4    3.6  3  DUF1565     Protein of unknown function (DUF1565)
    0.00069   19.7   0.1       0.46   10.6   0.0    3.7  4  fn3_PAP     Fn3-like domain from Purple Acid Phosphatase
  ------ inclusion threshold ------
       0.04   13.7   0.0       0.66    9.8   0.0    2.4  2  HECW_N      N-terminal domain of E3 ubiquitin-protein ligase 


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0  11.6   2.3e-19   8.1e-16      73     177 ..     100     202 ..      90     203 .. 0.88
   2 !   89.9  14.8   4.2e-29   1.5e-25      40     240 ..     156     347 ..     156     348 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 2.3e-19
                              NosD  73 iedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesn 148
                                       i++   ++ ++Gi+++s+  n + +N + ++ n+G+ ls + nnti  N i  n n+G +l+nss+n+++gNri +n
  gi|330507955|ref|YP_004384383.1| 100 IKSQSSRRESAGILIQSND-NLIIDNLVHGCGNAGVVLSHAINNTILSNLIEgNGNEGMYLKNSSRNRLEGNRIRDN 175
                                       5555556666898888777.6666***************************************************** PP

                              NosD 149 qkiGilllsssegntiynNyFinnsenvk 177
                                         +G+  l++s++n+i++N + nn+ +++
  gi|330507955|ref|YP_004384383.1| 176 -RYGLR-LEDSHTNEIVGNLLQNNQFEAM 202
                                       .*****.**************99987776 PP

  == domain 2  score: 89.9 bits;  conditional E-value: 4.2e-29
                              NosD  40 gilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsssnntlenNtisnnenyGillsdssn 115
                                       g++l+nss n+++gn+i+++ryG++le+s+ n i +n l++n+ ++++l+ s+ n +e+N + +ne  G  +++s++
  gi|330507955|ref|YP_004384383.1| 156 GMYLKNSSRNRLEGNRIRDNRYGLRLEDSHTNEIVGNLLQNNQfEAMYLQASHSNLIEGNLAEDNEV-GLVMEKSRS 231
                                       689***************************************************************9.********* PP

                              NosD 116 ntisnNtisnnnkGiflens.....ssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsnnneWn 187
                                       n +++N i+ n+kGi+l+++      s++ +g  i++n +       + ++ntiy N++  n+ n+++dg   n+W+
  gi|330507955|ref|YP_004384383.1| 232 NVVARNDIQGNEKGISLTSQessiaVSTKGKGVFISYNATPSGA--ITPSNNTIYLNNL-SNEANAYDDG--LNRWD 303
                                       *******************9544433444456678888444444..44557********.**********..9***8 PP

                              NosD 188 ttktsgtniiggpylgGNyWsdydg..eDadgDGigDtpYeindgv.iDylplvnp 240
                                                       GN +sd++   e   g  i+ t+Y+i++g  iD++p ++p
  gi|330507955|ref|YP_004384383.1| 304 DGL------------IGNNYSDFNDpeEGCRGRTICATSYSIPGGPsIDEHPQASP 347
                                       888............9*******99766688999*********9988*****8876 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 !   54.6  11.0     3e-18   1.1e-14      27     138 ..      87     198 ..      77     200 .. 0.81
   2 !   65.9  25.1     1e-21   3.6e-18       1     153 [.     110     257 ..     110     315 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 3e-18
                                       EE-SSS-.EEES-EEES....-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT CS
                        Beta_helix  27 ylrgssnvvienneian....nsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylny 99 
                                        l   +  +ie+  i +        Gi i++ ++n i +n ++++++ g+ l+ a nn+i  n i+ ng+ G+yl++
  gi|330507955|ref|YP_004384383.1|  87 ILLAKGV-TIEGFAIKSqssrRESAGILIQS-NDNLIIDNLVHGCGNAGVVLSHAINNTILSNLIEGNGNEGMYLKN 161
                                       4444454.88887777777777888888875.999999999999999999999999999999999999999999999 PP

                                       -S--EEES-EEESTT--SEE---TT---EEES-EEES-S CS
                        Beta_helix 100 ssnntienNiidnnagsGividdsssnvtvtnNtitnnk 138
                                       ss+n++e+N+i++n+ +G+ ++ds  ++++ +N + nn 
  gi|330507955|ref|YP_004384383.1| 162 SSRNRLEGNRIRDNR-YGLRLEDSH-TNEIVGNLLQNNQ 198
                                       999999999999999.999999999.9999999999985 PP

  == domain 2  score: 65.9 bits;  conditional E-value: 1e-21
                                       -SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT-- CS
                        Beta_helix   1 sgisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfga 77 
                                       +gi+i +++n  i +n ++++g++G+ l ++ n++i +n i++n+ +G+y+++ss+n +++n+i+dn  +g+ l+++
  gi|330507955|ref|YP_004384383.1| 110 AGILIQSNDN-LIIDNLVHGCGNAGVVLSHAINNTILSNLIEGNGNEGMYLKNSSRNRLEGNRIRDNR-YGLRLEDS 184
                                       59********.*********************************************************.******** PP

                                       S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EE CS
                        Beta_helix  78 snnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtv 153
                                       + n i +n   +n    +yl+ s++n ie+N +++n+  G+v++ s  +++v  N i +n  +Gi ++++ s++ v
  gi|330507955|ref|YP_004384383.1| 185 HTNEIVGNLLQNNQFEAMYLQASHSNLIEGNLAEDNE-VGLVMEKSR-SNVVARNDIQGNE-KGISLTSQESSIAV 257
                                       *************999*********************.*********.888*********8.88888887776655 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0     0.002       7.2      18      41 ..      34      57 ..      32      61 .. 0.93
   2 !   24.9   5.4   3.2e-09   1.1e-05      84     196 ..      77     182 ..      58     201 .. 0.74
   3 !    3.7   5.7    0.0094        34     145     201 ..     202     254 ..     182     315 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.002
                           DUF1565 18 iTkAlllakageviqlapGtYsea 41
                                      i kA+  a +ge+i ++ G Y+e+
  gi|330507955|ref|YP_004384383.1| 34 IQKAIDSAAPGEIILVSSGSYNES 57
                                      78********************97 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 3.2e-09
                           DUF1565  84 ddlsgvqnvtivlaneatiaGvtitNpni.lkgtgvliesasakianNtitgniadGievsiyeaktgaggniisGn 159
                                       +  s+   + i+la+ +ti G+ i+  +   ++ g+li+s    i +N + g+++ G+  s   +++ +  n i Gn
  gi|330507955|ref|YP_004384383.1|  77 QVQSDEGPAIILLAKGVTIEGFAIKSQSSrRESAGILIQSNDNLIIDNLVHGCGNAGVVLSHA-INNTILSNLIEGN 152
                                       34446666788999***********995547899*************************9999.6999999999999 PP

                           DUF1565 160 silfeknGiaisgasaavenkienNiivkNliGvvan 196
                                        +    +G+     +++  n++e N i  N++G+   
  gi|330507955|ref|YP_004384383.1| 153 GN----EGMYL---KNSSRNRLEGNRIRDNRYGLRLE 182
                                       65....45544...44446688888888888887643 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.0094
                           DUF1565 145 yeaktgaggniisGnsilfeknGiaisgasaavenkienNiivkNliGvvanalalD 201
                                       + + +++  n i Gn   +++ G++ ++++      +  N i  N +G+  + ++  
  gi|330507955|ref|YP_004384383.1| 202 M-YLQASHSNLIEGNLAEDNEVGLVMEKSRSN---VVARNDIQGNEKGISLTSQESS 254
                                       2.357888899999999999999988776655...6777888888888876666544 PP

>> fn3_PAP  Fn3-like domain from Purple Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00013      0.46      15      48 ..     460     493 ..     446     507 .. 0.75
   2 ?    3.0   0.0      0.03   1.1e+02      74     115 ..     494     532 ..     486     535 .. 0.73
   3 ?    0.9   0.0      0.13   4.7e+02      17      60 ..     553     596 ..     545     609 .. 0.63
   4 ?    1.1   0.0      0.11   3.9e+02      85     116 ..     596     626 ..     587     627 .] 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                           fn3_PAP  15 eefvtvtvtvsspsdddWvavfsPadfdvsscpa 48 
                                        e +tv+++ + + ++dW++++   ++++ s + 
  gi|330507955|ref|YP_004384383.1| 460 CEKITVSFQGARGGEKDWIGMYRSESSNALSSQS 493
                                       4679******************988888655443 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.03
                           fn3_PAP  74 ylktgsgtlkFrlinqRadysFalfsgGleePvlvavsnkvk 115
                                         +  sg ++F       +y+F+lf+ G   P  +a+sn v+
  gi|330507955|ref|YP_004384383.1| 494 LARRESGAVTFTA-EEAGSYVFKLFATGESIP--LASSNAVE 532
                                       5556677777764.45679*********9999..68888775 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.13
                           fn3_PAP  17 fvtvtvtvssp.sdddWvavfsPadfdvsscpakgeleelpllcs 60 
                                        vtvt   ++p s     ++ sP +fd+ + + +g ++  +++ +
  gi|330507955|ref|YP_004384383.1| 553 TVTVTYWGAAPaSVIGMYGLTSPDKFDSGKRS-TGGKSCGSMVWQ 596
                                       678888888884445667899******98844.444444443333 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.11
                           fn3_PAP  85 rlinqRadysFalfsgGleePvlvavsnkvkF 116
                                       +l     +y F lf + +++P ++a sn v+ 
  gi|330507955|ref|YP_004384383.1| 596 QLPSKPGQYDFRLFGDDVNRP-ILAYSNVVTV 626
                                       555566789******999999.5699999985 PP

>> HECW_N  N-terminal domain of E3 ubiquitin-protein ligase HECW1 and 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00018      0.66      43      67 ..     473     497 ..     432     519 .. 0.67
   2 ?    0.8   0.0      0.11     4e+02      48      83 ..     567     599 ..     561     606 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00018
                            HECW_N  43 daeDWiGlylidetnsenfldyknr 67 
                                       +++DWiG+y+++ +n  ++ +   r
  gi|330507955|ref|YP_004384383.1| 473 GEKDWIGMYRSESSNALSSQSLARR 497
                                       789*******998887665555544 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                            HECW_N  48 iGlylidetnsenfldyknrgvngtrkGqivwkvda 83 
                                       iG+y +   ++   +d+ +r + g   G +vw++  
  gi|330507955|ref|YP_004384383.1| 567 IGMYGLTSPDK---FDSGKRSTGGKSCGSMVWQLPS 599
                                       88887765444...78899*************9855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 4663.37
//
Query:       gi|330507956|ref|YP_004384384.1|  [L=356]
Description: hypothetical protein MCON_2009 [Methanosaeta concilii GP6]
Scores for complete 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-33  113.6  19.5    4.4e-32  111.1  16.2    2.3  2  DUF389     Domain of unknown function (DUF389)
  ------ inclusion threshold ------
        6.7    4.9  13.6         12    4.1  13.6    1.4  1  DUF2070    Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF389  Domain of unknown function (DUF389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.2   0.1     0.009        81      63     100 ..     129     166 ..     115     167 .. 0.86
   2 !  111.1  16.2   4.9e-36   4.4e-32       1     142 []     168     303 ..     168     303 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.009
                            DUF389  63 semlsrtepnlvdllvAlasGaagalallsgnssslvG 100
                                       + +++ t+++ v++++ ++s +++a+ l +++ + ++G
  gi|330507956|ref|YP_004384384.1| 129 EDISTATKLTRVYVVLVILSAIVAAIGLWNNSVAIIIG 166
                                       67889999999******************999999998 PP

  == domain 2  score: 111.1 bits;  conditional E-value: 4.9e-36
                            DUF389   1 MlisPlmgpilaiafglvigdrkllrrglknlliglllallvgflfglllplkvlgeeelptsemlsrtepnlvdll 77 
                                       M+i+Pl+gp +a+++++++gd +l++++lk+ ++gl++a ++++++g++l++      + + +e++srt + l ++l
  gi|330507956|ref|YP_004384384.1| 168 MVIAPLLGPNVALSLAAALGDINLAKNALKTNVVGLAIAAALSIAMGYFLAV------DPTIPEIESRTAVGLDEVL 238
                                       ***********************************************76655......46679************** PP

                            DUF389  78 vAlasGaagalallsgnssslvGvaIaaaLlPPavnaGlglalgewalalgslllllvNivgIvl 142
                                       +Al+sG ag+la++sg  ++l+Gva+a+aLlPP+v++Gl+l++g  +la+g++ll+lvNi+ I+l
  gi|330507956|ref|YP_004384384.1| 239 LALVSGCAGTLAFTSGAPATLIGVAVAVALLPPLVTSGLLLGAGYTTLAYGAFLLFLVNIASINL 303
                                       **************************************************************986 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  13.6    0.0013        12       2     165 ..     125     302 ..     124     351 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0013
                           DUF2070   2 eklskyifrlPswkvsllliillalligllaflssk...lfgillfglpalvaflltlpvlrilggr.......... 65 
                                       e+l+  i ++ ++ +  +++++l+++++++   +++   +      +  +++a ll   v  +l             
  gi|330507956|ref|YP_004384384.1| 125 EELYEDISTATKLTRVYVVLVILSAIVAAIGLWNNSvaiI------IGAMVIAPLLGPNVALSLAAAlgdinlakna 195
                                       5789999999999988888888888877777544443431......3335555555555554444444441211111 PP

                           DUF2070  66 ltykrs.lflalltelivviisllaillsall.............qalvllalvlslalvfalrllvlvavsdesll 128
                                       l+++   l +a++  + +  ++ +                      + vllalv ++a ++a++     ++ +  + 
  gi|330507956|ref|YP_004384384.1| 196 LKTNVVgLAIAAALSIAMGYFLAV-------DptipeiesrtavgLDEVLLALVSGCAGTLAFTSGAPATLIGVAVA 265
                                       544444433333333333333333.......1333334477678888899999999********************* PP

                           DUF2070 129 kavlpaliqpllailllvlyfspesfllllllslifa 165
                                        a+lp l+++ l++ + + ++++  fll+l+ ++ + 
  gi|330507956|ref|YP_004384384.1| 266 VALLPPLVTSGLLLGAGYTTLAYGAFLLFLVNIASIN 302
                                       *****************99966666666555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 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:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2731.74
//
Query:       gi|330507957|ref|YP_004384385.1|  [L=215]
Description: hypothetical protein MCON_2010 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-55  187.3  12.2    2.4e-55  187.1  12.2    1.0  1  MarC       MarC family integral membrane protein
    0.00046   19.9   8.8      0.002   17.8   8.6    1.9  1  TerC       Integral membrane protein TerC family
  ------ inclusion threshold ------
        2.4    8.1   8.6       0.37   10.7   0.2    2.6  3  RseC_MucC  Positive regulator of sigma(E), RseC/MucC
          3    7.5   5.1         14    5.3   0.6    2.7  2  DUF2244    Integral membrane protein (DUF2244)


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 !  187.1  12.2   5.3e-59   2.4e-55       3     201 ..       9     207 ..       7     209 .. 0.97

  Alignments for each domain:
  == domain 1  score: 187.1 bits;  conditional E-value: 5.3e-59
                              MarC   3 aiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgil 79 
                                       +++++f ++++i+np+ +  v+++l+   +  e++ri ++a+++a++i ++f+++G+l+l+lfgi++d+l++aGg+l
  gi|330507957|ref|YP_004384385.1|   9 YFVYVFSTIFVIVNPIEATMVYVTLTIGLPPLEKSRIYKRATLVAFIIAILFAMAGDLVLRLFGITTDSLSVAGGVL 85 
                                       6899************************************************************************* PP

                              MarC  80 lfliaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaali 156
                                       lfl+aidml++ ++++k  ++e ++++++++i+v+PLA+Pl++GPgaittv+vl+ +a+si ek +v+l i+l +++
  gi|330507957|ref|YP_004384385.1|  86 LFLVAIDMLRGVHQQKKVTEEELKDANSREDISVFPLATPLLTGPGAITTVVVLMGSAESIAEKSIVILGIALTYTV 162
                                       *************9999999999999*************************************************** PP

                              MarC 157 tllilllsslilrllgktginaleRlmGllLvalavqlivdGike 201
                                       tl++l+ s+ i r+lg tg+ +l+R+mGl+L a+av++   G  +
  gi|330507957|ref|YP_004384385.1| 163 TLIVLKFSDYIDRVLGITGVMVLNRVMGLILGAVAVNFAAVGAWN 207
                                       **************************************9888765 PP

>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   8.6   4.5e-07     0.002      17     127 ..      29     182 ..      24     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.5e-07
                              TerC  17 viallvkklpeeqqkkalllGilgAlvlRillillavallelf....dlilligglfLlytavkellekrlenklvk 89 
                                       v ++l+  lp+ +++++    +l+A+++ il+ +++  +l+lf    d + ++gg++L+++a+++l+  ++++k+ +
  gi|330507957|ref|YP_004384385.1|  29 VYVTLTIGLPPLEKSRIYKRATLVAFIIAILFAMAGDLVLRLFgittDSLSVAGGVLLFLVAIDMLRGVHQQKKVTE 105
                                       555666679*********************************88888*******************98665566666 PP

                              TerC  90 eekkkkkktkst........................................llavviqielaDlvfs..lDSvlaa 124
                                       ee k+ ++ +++                                        l+++v++i    l fs  +D vl +
  gi|330507957|ref|YP_004384385.1| 106 EELKDANSREDIsvfplatplltgpgaittvvvlmgsaesiaeksivilgiaLTYTVTLI---VLKFSdyIDRVLGI 179
                                       665555555555788888888888888777777777777777777766544433333333...23344334444444 PP

                              TerC 125 vai 127
                                        ++
  gi|330507957|ref|YP_004384385.1| 180 TGV 182
                                       444 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   8.4e-05      0.37      65     117 ..      48     100 ..      40     109 .. 0.85
   2 ?    1.0   0.5     0.084   3.8e+02      80     113 ..     136     169 ..     123     179 .. 0.64
   3 ?   -0.6   3.1      0.27   1.2e+03      61     113 ..     150     200 ..     137     212 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.4e-05
                         RseC_MucC  65 kaallvYllPllllilgallgsallgssellaalgallglvlgflivrllskr 117
                                       +a+l+++++ +l+ ++g l+  +++++++ l+++g++l++++++ ++r + ++
  gi|330507957|ref|YP_004384385.1|  48 RATLVAFIIAILFAMAGDLVLRLFGITTDSLSVAGGVLLFLVAIDMLRGVHQQ 100
                                       688999****************9999**************9999998866655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.084
                         RseC_MucC  80 lgallgsallgssellaalgallglvlgflivrl 113
                                       +++l+gsa +++++ +++lg  l   ++++++++
  gi|330507957|ref|YP_004384385.1| 136 VVVLMGSAESIAEKSIVILGIALTYTVTLIVLKF 169
                                       4444444444567777777777766666666665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.27
                         RseC_MucC  61 ksllkaallvYllPllllilgallgsallgssellaalgallglvlgflivrl 113
                                       + ++ +++l Y + l++l ++  +  +l  + +++ +l  ++gl+lg + v +
  gi|330507957|ref|YP_004384385.1| 150 SIVILGIALTYTVTLIVLKFSDYIDRVL--GITGVMVLNRVMGLILGAVAVNF 200
                                       4456677777777777777777776666..45666666666666666666554 PP

>> DUF2244  Integral membrane protein (DUF2244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3     0.013        58      20      42 ..      50      72 ..      38      92 .. 0.82
   2 ?    5.3   0.6    0.0031        14       7      38 ..     177     208 ..     174     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.013
                           DUF2244 20 alvslvialafllaGawpvlpFa 42
                                      +lv ++ia++f++aG  ++ +F 
  gi|330507957|ref|YP_004384385.1| 50 TLVAFIIAILFAMAGDLVLRLFG 72
                                      7899**********988777775 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0031
                           DUF2244   7 lsprgflllllalalvslvialafllaGawpv 38 
                                       l+ +g+++l  ++ l++ ++a+ f+++Gaw +
  gi|330507957|ref|YP_004384385.1| 177 LGITGVMVLNRVMGLILGAVAVNFAAVGAWNI 208
                                       666789999999******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1657.18
//
Query:       gi|330507958|ref|YP_004384386.1|  [L=891]
Description: DNA polymerase 2 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.1e-107  360.6   0.0   1.5e-107  360.2   0.0    1.1  1  DNA_pol_B       DNA polymerase family B
    3.2e-50  171.2   0.0    4.6e-50  170.6   0.0    1.3  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    9.9e-05   22.4   0.0    0.00024   21.1   0.0    1.6  1  RNase_H_2       RNase_H superfamily
    0.00013   21.7   0.0    0.00024   20.8   0.0    1.4  1  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 !  360.2   0.0  3.3e-111  1.5e-107       6     457 ..     398     854 ..     394     856 .. 0.90

  Alignments for each domain:
  == domain 1  score: 360.2 bits;  conditional E-value: 3.3e-111
                                       HHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS.......-S----BE----EEESS-EEEEEETTHHHHHHHH CS
                         DNA_pol_B   6 vledgqqirveslLlrlakeegfilpdrtekkgkeee......gYqGatVlePkkglydkpvlvlDFaSLYPsiiqa 76 
                                       ++++gq+  ve lLlr ++e ++++p ++++ g ++e      + +G+ Vl P+kgl ++ v++lD++SLYP i++a
  gi|330507958|ref|YP_004384386.1| 398 IVNGGQSGMVENLLLRRFREISRVVPPKPDS-GLSDEryveneELKGGAVLVPEKGLVED-VVILDYKSLYPTIMMA 472
                                       6789**********************84444.4444445555369************876.789************* PP

                                       TT-STTTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHH CS
                         DNA_pol_B  77 hNlcyttlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalld 153
                                       hNlcy+t+v  ++ +k+        ++  +p++  fv+++v  g++p++Lk+ll++R++ k+ +k++++e e++ ld
  gi|330507958|ref|YP_004384386.1| 473 HNLCYSTVVLADSPEKK--------DIITSPSGGSFVSPNVSSGVMPQVLKELLDQRTETKRLMKKASEE-ERRFLD 540
                                       **********9998653........578899999**********************************99.9***** PP

                                       HHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT.....SSGGGT-SS............ CS
                         DNA_pol_B 154 kqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekk..aellskllalpeea.....eee.. 221
                                       ++Q+alK++ Ns+YG+ G+a  rl++lalA+ vT+ GRe++ +tk+++++   + +++ ++ +++e      + +  
  gi|330507958|ref|YP_004384386.1| 541 AKQYALKILLNSFYGYSGYARARLYSLALANAVTSFGRENIIRTKKIIDDIgsVYVIEGRAVFKDELklgapTGKgf 617
                                       *************************************************9953334444666776664554323369 PP

                                       T-EEEEEBSSEEEEE-....S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEETTEEEEEEEEESST CS
                         DNA_pol_B 222 klkviYGDTDSvfiel....kvkdveellkigkelaeevseklfkkplklefekvykkllLisKKkYaglkvektsk 294
                                       +l+v+YGDTDSvf++l    +  ++e++  igk++ae v++  +++p++l fe+   + ++++KK+Ya  ++e+  +
  gi|330507958|ref|YP_004384386.1| 618 DLNVVYGDTDSVFVRLsphnEPVSLEDAGLIGKKIAETVTS-SLPQPMELVFEAFARRGIFLAKKRYALWIFEQMGE 693
                                       ***************966655589999**************.99****************************97766 PP

                                       TS..EEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHH.HHHHTT-S-GGGG-EEEE CS
                         DNA_pol_B 295 an..klliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvl.eeleenkvplekfvlske 368
                                       +   ++ ++G+++vRrd+c l++ + k++lel+lk+     +++e++e ++s++++++  +l +    le+++l+++
  gi|330507958|ref|YP_004384386.1| 694 EWkdRIKVRGMETVRRDWCGLTSGTLKTCLELVLKE----GKVDEAVEHVRSVVVRLQnLDLSQDPGILEELTLTRR 766
                                       55446*******************************....**************9999779999999********** PP

                                       ESS.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTEEEHHHHHHCCSEB-HHHHH CS
                         DNA_pol_B 369 lskepenyksknlphlevakrlkkrneeapevgdrisYvivekkkevkkknllaseraedpeyvleknlpidieyYl 445
                                       ++k++ +yk+k+ ph+++++++++r +++p+vgdr+++vi+  k   kk+++l  +raedpe+vle+n+++d+eyY+
  gi|330507958|ref|YP_004384386.1| 767 YTKSTGSYKNKQ-PHIQLVEKMRERGGKVPTVGDRVPFVIIRGKG-GKKNKTLFVDRAEDPEFVLENNISLDTEYYV 841
                                       ***********9.******************************87.59999************************** PP

                                       H.TTHHHHHHHHT CS
                         DNA_pol_B 446 s.qllkevarlle 457
                                       + q+l++v+r++e
  gi|330507958|ref|YP_004384386.1| 842 NkQILPPVMRIFE 854
                                       ***********98 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.6   0.0     1e-53   4.6e-50       2     337 .]      26     327 ..      25     327 .. 0.87

  Alignments for each domain:
  == domain 1  score: 170.6 bits;  conditional E-value: 1e-53
                                       ECTTSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESS CS
                    DNA_pol_B_exo1   2 teegksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsn 78 
                                       t eg+sv v++ gf+pyfY++a +g+ +    +  ++l+           +ve+ ++ + +gy+kkp+++l++++++
  gi|330507958|ref|YP_004384386.1|  26 TPEGQSVTVKAAGFRPYFYASAIEGCLE----SAADDLKAMG-------LEVEVLERFEPIGYQKKPKKMLQITTND 91 
                                       6799******************977664....4444443222.......3678889999****************** PP

                                       TCHHHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCEETTTC CS
                    DNA_pol_B_exo1  79 pnelkkirkelspleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddliakpkes 155
                                       p+e++ +r+++++l  i  vye+d+ +  rflid+++ g+gw + +  +++ ++++ + +   d    d  +++  +
  gi|330507958|ref|YP_004384386.1|  92 PKEVRNLRERVRSLPGIRAVYETDILFKNRFLIDKSLGGMGWVEAPIPEWTLSQNAGSVQSGRDLPPVDAASIRPVQ 168
                                       ****************************************************9999999999999888888887776 PP

                                       C...S-EEEEEEEEEETEETTSEETTTT..--EEEEEEEE.CCTC.SS.SEEEEEEECCCTSS----EE--SSTCST CS
                    DNA_pol_B_exo1 156 e...pplrvlsFDIeckskkgkfpdaensedpiiqIscvl.dglgekepearklftlrecaseeeedfeltpkpeyp 228
                                           +plr +sFDIec  + g +p+ae+   p+i Is+++  +++    ++ ++++ +e++               p
  gi|330507958|ref|YP_004384386.1| 169 HeanAPLRFMSFDIECLPDHGAMPKAEK--SPVILISMAFePEYQ---GNKDLVLVGKEID--------------CP 226
                                       6677************************..**********65555...5666889999999..............57 PP

                                       TEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCS.CTCEECCCCESEEEE CS
                    DNA_pol_B_exo1 229 gvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrln.kggrskvseigfskq 304
                                       +++   +++E+elL++f  +i++y+Pd+i gYN ++FD+pY+++Rak   + +l++  r+  +g    +++i ++  
  gi|330507958|ref|YP_004384386.1| 227 RPDTRACRNEYELLNQFAAIIRDYNPDIIAGYNSNDFDFPYLQERAK---QQQLDF--RVGrDGSSWYIKKIVNR-- 296
                                       888999*****************************************...555555..33324555555555555.. PP

                                       EECEEEETTSEEEEHHHHHHHHSSSSG-SHHHH CS
                    DNA_pol_B_exo1 305 arekvkisgrihlDlyrvvkrklklpsYkLnav 337
                                         + v+i gr+++Dl+++++ +++l+ Y+L +v
  gi|330507958|ref|YP_004384386.1| 297 --SDVSITGRVVVDLLPIIRSSFSLKQYTLRNV 327
                                       ..9***************************987 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   5.3e-08   0.00024      44     160 ..     236     374 ..     216     379 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.3e-08
                         RNase_H_2  44 ekailelflellekk..kalvtfngksFDvpflkrlfkkyklde......................eefrhiDLlke 96 
                                       e ++l +f+++++++  + +  +n + FD+p+l++++k+ +ld                         +  +DLl +
  gi|330507958|ref|YP_004384386.1| 236 EYELLNQFAAIIRDYnpDIIAGYNSNDFDFPYLQERAKQQQLDFrvgrdgsswyikkivnrsdvsiTGRVVVDLLPI 312
                                       4445556889999995445888***************888888888*9999999999998887777777999***** PP

                         RNase_H_2  97 lrkkkl.esysLksvekelgierreedlsGsqavklyqeylrtgdeellekilaYNedDvr.alat 160
                                       +r++   ++y L +v++el    +  d++ +++ +l+    ++ + e l++ ++Y + D + al  
  gi|330507958|ref|YP_004384386.1| 313 IRSSFSlKQYTLRNVAAELLSMEK-YDVNPQEIEELW---AEESNGEGLKRFISYSRRDSVlALRL 374
                                       *987767999********988777.79****999986...56789999999999998885404444 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 !   20.8   0.0   5.5e-08   0.00024      34     151 ..     233     352 ..     199     393 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.5e-08
                    DNA_pol_B_exo2  34 essekelikkffegvekkkpqlV.sfngrgfDlpvleyralkhgvsapkyfdegded.rekkwnnylsrystrhlDL 108
                                         +e el+++f  +++ ++p ++ ++n++ fD+p l+ ra ++++  +   d ++   ++    + +s   +  +DL
  gi|330507958|ref|YP_004384386.1| 233 CRNEYELLNQFAAIIRDYNPDIIaGYNSNDFDFPYLQERAKQQQLDFRVGRDGSSWYiKKIVNRSDVSITGRVVVDL 309
                                       56799****************9846*****************99998876666664323333334455555558899 PP

                    DNA_pol_B_exo2 109 mdllseygaranakLdelakllglPGKlgvdGskVaelyqegk 151
                                       + ++ +  + ++  L ++a+ l    K++v+ +++ el++e++
  gi|330507958|ref|YP_004384386.1| 310 LPIIRSSFSLKQYTLRNVAAELLSMEKYDVNPQEIEELWAEES 352
                                       8888544466678888888877777899999999999998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (891 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.24s 00:00:00.90 Elapsed: 00:00:00.41
# Mc/sec: 6561.16
//
Query:       gi|330507959|ref|YP_004384387.1|  [L=183]
Description: transcription factor TFIID [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-58  194.8   0.3    1.3e-28   98.8   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
    2.5e-09   37.1   0.0    0.00063   19.8   0.0    2.3  2  DUF3378   Domain of unknown function (DUF3378)


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   0.2   2.9e-31   2.6e-27       2      84 ..       5      85 ..       4      86 .. 0.96
   2 !   98.8   0.0   1.4e-32   1.3e-28       2      84 ..      97     179 ..      96     180 .. 0.96

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 2.9e-31
                                      EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHH CS
                               TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiap 80
                                      ++i+Nvvas++l  e+dL+k++ ++  ++aeY++e+fpglvyr++ p++++liF+sGkvv+tGak++e++r+++ ++a+
  gi|330507959|ref|YP_004384387.1|  5 INIENVVASTKLAEEFDLHKIEAEL--EGAEYNKEKFPGLVYRVKAPRAAFLIFTSGKVVCTGAKNVEDVRTVITNMAQ 81
                                      79*******************8777..**************************************************** PP

                                      HHHH CS
                               TBP 81 ilkk 84
                                       lk 
  gi|330507959|ref|YP_004384387.1| 82 TLKS 85
                                      9986 PP

  == domain 2  score: 98.8 bits;  conditional E-value: 1.4e-32
                                       EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakki 78 
                                       +++qN+vasa+l+ +l+L+++al +  +n+eYepe+fpglvyr++ pkv++liFssGk+v+tG ks+ee++e +k +
  gi|330507959|ref|YP_004384387.1|  97 IHVQNIVASADLKTDLNLNAIALGLGLENIEYEPEQFPGLVYRIKTPKVVVLIFSSGKLVVTGGKSPEECEEGVKIV 173
                                       78********************9988*************************************************99 PP

                                       HHHHHH CS
                               TBP  79 apilkk 84 
                                        + l++
  gi|330507959|ref|YP_004384387.1| 174 REQLEN 179
                                       988876 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.1e-06     0.018      13      56 ..      24      68 ..      14      85 .. 0.79
   2 !   19.8   0.0     7e-08   0.00063      24      59 ..     130     165 ..     125     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-06
                           DUF3378 13 kmkeyyksk.lrskkppyavfaakkndttItaYtSgKVlFQGkna 56
                                      k++ +++    +++k p+ v++ k + +   ++tSgKV+  G++ 
  gi|330507959|ref|YP_004384387.1| 24 KIEAELEGAeYNKEKFPGLVYRVKAPRAAFLIFTSGKVVCTGAKN 68
                                      5555555542456679***********************999765 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 7e-08
                           DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeae 59 
                                        ++ p+ v+++k++++++ ++ SgK+++ G +  +e
  gi|330507959|ref|YP_004384387.1| 130 PEQFPGLVYRIKTPKVVVLIFSSGKLVVTGGKSPEE 165
                                       5789************************99876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1315.13
//
Query:       gi|330507960|ref|YP_004384388.1|  [L=416]
Description: hypothetical protein MCON_2014 [Methanosaeta concilii GP6]
Scores for complete 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-37  126.1   0.1    1.2e-36  125.2   0.1    1.5  1  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
     0.0012   18.6   0.2      0.012   15.3   0.0    2.3  2  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.044   14.4   0.1        0.1   13.2   0.1    1.6  1  ACT_4           ACT domain
       0.16   12.3   0.3       0.39   11.0   0.3    1.6  1  DUF5403         Family of unknown function (DUF5403)


Domain annotation for each model (and alignments):
>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.2   0.1   2.6e-40   1.2e-36       3     100 .]      11     108 ..       9     108 .. 0.99

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 2.6e-40
                                       EEEEEEXXTTSSHHHHHHHHHHHTTXEEEEEEEEXXSSTTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSCCCCEE CS
                    Saccharop_dh_N   3 eveleGhliDsgilnkvldlileaggsfevlefevGkkkkdtSyaelevsaedeevLeeileeltelgaelveeedv 79 
                                        +e+eGhliDs++l++vld+i+++gg+fe+++f++G+kk+dtSy++++v++ed+++L++il+el++lga+l e+ed+
  gi|330507960|ref|YP_004384388.1|  11 DIEMEGHLIDSQMLTRVLDKIMDMGGEFEIKTFRIGEKKNDTSYVQITVTGEDSAHLDRILRELNALGARLLEMEDA 87 
                                       69*************************************************************************** PP

                                       EECESSCTTB--TTB----SS CS
                    Saccharop_dh_N  80 klekaekdgvlpedFYsttnh 100
                                       k+e a+ d+v+p++FYsttnh
  gi|330507960|ref|YP_004384388.1|  88 KTEIAPGDMVVPRGFYSTTNH 108
                                       ********************8 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       0.1   4.5e+02      13      67 ..     205     259 ..     191     265 .. 0.78
   2 !   15.3   0.0   2.7e-06     0.012      69     137 .]     332     401 ..     312     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.1
                                       SEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGS CS
                      TPP_enzyme_M  13 rpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhg 67 
                                       ++++++G      ga+  l++l+++  + v+   ++  v + + +l+  +lg+  
  gi|330507960|ref|YP_004384388.1| 205 KIAVVCGPALVHTGAAPSLAKLIREGYVDVLLAGNAVAVHDIERQLFGTSLGMNC 259
                                       7889999999999999999999998888888888888888877777777888765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHH-SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC....--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  69 kaanealeeaDlvlalGarfddirttgsepefapeakiihididpaeigkny....qvdlaivgdvketleaL 137
                                       +a  ++l+  D  ++lG+ ++ i +++  p +    k i +di+p+++ k        ++++v d++ +l +L
  gi|330507960|ref|YP_004384388.1| 332 DAMGRVLQGVDMTIMLGTMLHSIAVGNLLPSYV---KTICVDINPSTVTKLMdrgsAQAIGLVTDIGIFLPQL 401
                                       555677899*************99988777665...68*********999984443366999***99999887 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.2e-05       0.1      17      71 ..      21      76 ..       9      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                             ACT_4 17 kglLaditqvisee..kanivsvnaktrkkdglaeikitveVkdvehLsrviakLra 71
                                      + +L+++++ i ++  +  i+  ++ ++k + +  ++itv  +d++hL+r+++ L+a
  gi|330507960|ref|YP_004384388.1| 21 SQMLTRVLDKIMDMggEFEIKTFRIGEKK-NDTSYVQITVTGEDSAHLDRILRELNA 76
                                      567899999999996677899******87.66**********************987 PP

>> DUF5403  Family of unknown function (DUF5403)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   8.8e-05      0.39      48      87 ..     117     155 ..     112     160 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.8e-05
                           DUF5403  48 asievetgrvdstvsleDPavlsieyGHlakegarwVpGi 87 
                                       a +ev  +++d  ++l+D +++    GH+ k++ r V G+
  gi|330507960|ref|YP_004384388.1| 117 AWVEVVSNHMDCLIVLHDGKAVCTPIGHIKKGD-RVVIGT 155
                                       5689**************************999.999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2765.31
//
Query:       gi|330507961|ref|YP_004384389.1|  [L=373]
Description: hypothetical protein MCON_2015 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.6e-42  142.7   0.1      9e-42  142.0   0.1    1.3  1  Lig_C       Ligase Pab1020 C-terminal region
    9.8e-13   48.7   0.0    1.7e-12   48.0   0.0    1.4  1  RNA_ligase  RNA ligase
  ------ inclusion threshold ------
      0.064   13.3   0.0       0.16   12.0   0.0    1.7  1  LysM        LysM domain


Domain annotation for each model (and alignments):
>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.0   0.1   1.5e-45     9e-42       1     125 []     247     371 ..     247     371 .. 0.99

  Alignments for each domain:
  == domain 1  score: 142.0 bits;  conditional E-value: 1.5e-45
                                       HHCCSCCGS-STSCHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHH CS
                             Lig_C   1 vafsylfelgrdFlfsRviReafqavefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvrfkdeeni 77 
                                       +afs++++++ dF++sR +Re+fq+ve++es ee+rera+++GesiL p++etik+ +++e++++++++r+k+  ++
  gi|330507961|ref|YP_004384389.1| 247 IAFSHYNDYALDFFLSRAVREGFQSVEWQESVEERRERARRIGESILLPLTETIKNKQQGETIMQRIKIRVKSLATA 323
                                       69*************************************************************************** PP

                                       HHHHHHHHCTT--EEEEEEE..TTEEEEE..EE-HHHHHHHHHHHTT- CS
                             Lig_C  78 eellehLrrlgvkaeveekekedgelvvkfkkiaqsttdkikslLeGg 125
                                       + ++ hLrr+g++a+++++  +d+ +++ ++ki++st+dk+++lL+G+
  gi|330507961|ref|YP_004384389.1| 324 RGFEYHLRRCGIRAIFDQPLPDDDGYTIGITKIIMSTNDKTEALLNGE 371
                                       **********************************************96 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   2.8e-16   1.7e-12       2     159 ..      81     234 ..      80     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 2.8e-16
                                       EEEEEEE-SSEEEEEEEETT.EEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH....ECCEEEEEEEES...SS CS
                        RNA_ligase   2 evvvtEKlDGtnfriylvke.vgvasRsqil.pfgeekfkefkrwaaalrkklkekla..neelilyGElig..hsi 72 
                                        v v+EK++G n+ri   ++ + + +R++++ p          +  +  +  l+e++    ++l+l+ E++g  +++
  gi|330507961|ref|YP_004384389.1|  81 SVAVEEKMNGHNVRITSIDGdIVALTRGGFVcP----------YSTEVATRLLPEDIFeeKPNLVLCAEMVGpeNPY 147
                                       589************999556**********53..........22223333445554468677*********65333 PP

                                       ...TTSS....EEEEEEEEEEECTTBECE--HHHHHHHHHCCT..B..EEEEE.SS.HHHHHCCC..HHHHTC--EE CS
                        RNA_ligase  73 .kygglpk...efyvFdifdirdkeeqrylspdevealakglg..tvpvlyegkfl.aaeellell.lskgnkrEGl 141
                                        + + +p    ++y+Fd++   +k+++      +++++a+++g   + +++e++++ a++ ++e++ +   + rEG+
  gi|330507961|ref|YP_004384389.1| 148 vSLDVYPTdsiDLYLFDVA---QKNQRGTHGVHKTHEIAEDFGlkGTAFFGEFPREtAHKRIKEIViKLGRQGREGV 221
                                       44444555778********...666999999999999999998988999989998877777777754467789**** PP

                                       EEEESSSSBETTEBSEEE CS
                        RNA_ligase 142 VikpeselyknkgraifK 159
                                       V+k+++++      a +K
  gi|330507961|ref|YP_004384389.1| 222 VLKDPENR-----VAPLK 234
                                       ***99885.....55555 PP

>> LysM  LysM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.7e-05      0.16       9      37 ..       3      33 ..       2      34 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHCTCHHHHHHHHC..TCSSCGG--T CS
                              LysM  9 LwsIAkrygitveklleaN..nlsspdkifp 37
                                      L +IA++ gitv++l++++  ++s + +++p
  gi|330507961|ref|YP_004384389.1|  3 LQRIADKLGITVDRLQSLQdtKISESSWPEP 33
                                      899****************999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2591.74
//
Query:       gi|330507962|ref|YP_004384390.1|  [L=259]
Description: CBS domain-containing membrane protein [Methanosaeta concilii GP6]
Scores for 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-38  130.6  10.9    4.6e-12   46.2   0.6    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 !   35.4   0.2     6e-13   1.1e-08       1      55 [.       3      55 ..       3      57 .. 0.90
   2 !   14.5   0.1     2e-06     0.036       8      54 ..      77     120 ..      70     122 .. 0.83
   3 !   39.7   0.0   2.7e-14   4.9e-10       5      55 ..     131     179 ..     127     181 .. 0.89
   4 !   46.2   0.6   2.6e-16   4.6e-12       1      56 [.     201     256 ..     201     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 6e-13
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55
                                      V+dimt++v t++ ++ l+ al++m++ + ++rl+V+ + gk+ Gi+t r ++r+l
  gi|330507962|ref|YP_004384390.1|  3 VKDIMTEPV-TIDKSERLGHALDIMEK-NdLRRLLVT-NKGKIGGIITTRQIARVL 55
                                      89***9888.***************55.55****888.599988*********997 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2e-06
                                       SCEEEETTSBHHHHHHHHHHHTSSEEEE.EETTTBEEEEEEHHHHHHH CS
                               CBS   8 dvvtvppdttleealelmrekgvsrlPV.VdedgklvGivtlrDllra 54 
                                        v+ v  d+++ +a+ l+ +    +++V Vd++ k++G v  r +l++
  gi|330507962|ref|YP_004384390.1|  77 SVIKVLADMDMLDAMLLLQK--T-SVLVaVDGE-KILGWVRPREILEK 120
                                       6899**************55..5.777999655.5**********985 PP

  == domain 3  score: 39.7 bits;  conditional E-value: 2.7e-14
                                       SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       m+ + +t++p++ l  a +++ +++v+rlPVV e g+lvGi+t+ D+++al
  gi|330507962|ref|YP_004384390.1| 131 MRYP-LTANPNDRLVHARRTILDRDVGRLPVV-EAGRLVGILTEGDVAKAL 179
                                       5444.5**************88999*******.9***************98 PP

  == domain 4  score: 46.2 bits;  conditional E-value: 2.6e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+d+mt+dv +v+ dt+lee+  ++ + ++++lPV++  +++ G++t+r +l++l+
  gi|330507962|ref|YP_004384390.1| 201 VSDVMTHDVKYVYTDTPLEEVKSIILSDNIGGLPVLNHREEVAGMITRRSILDYLV 256
                                       89**********************88999*******9999**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1738.88
//
Query:       gi|330507963|ref|YP_004384391.1|  [L=286]
Description: CBS domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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  150.3   7.5    1.1e-12   48.2   0.2    4.2  4  CBS           CBS domain
    0.00043   20.9   0.0        2.1    8.9   0.0    3.3  3  GAF           GAF domain
      0.006   16.9   0.1        1.8    8.8   0.0    3.0  3  GAF_2         GAF domain
  ------ inclusion threshold ------
      0.027   14.4   0.2         31    4.6   0.0    3.9  4  GCV_T_C       Glycine cleavage T-protein C-terminal barrel do
      0.059   12.7   0.0       0.11   11.8   0.0    1.4  1  30K_MP_C_Ter  C-Terminal of 30K viral movement proteins
       0.16   12.6   0.7       0.42   11.2   0.2    2.0  2  Pyr_redox     Pyridine nucleotide-disulphide oxidoreductase


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 !   41.5   0.0   4.5e-14   1.3e-10       1      55 [.       6      59 ..       6      61 .. 0.92
   2 !   48.2   0.2   3.7e-16   1.1e-12       4      55 ..      79     129 ..      76     131 .. 0.93
   3 !   30.0   0.1   1.7e-10   5.1e-07       1      51 [.     138     188 ..     138     191 .. 0.90
   4 !   32.7   0.1   2.5e-11   7.5e-08       1      55 [.     229     282 ..     228     284 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 4.5e-14
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      V+d+m+++v ++  ++++  a +lm ++ ++rlPV+ ++gklvGivt+ D+ + +
  gi|330507963|ref|YP_004384391.1|  6 VKDYMSTPVNVIERNEPIQRARNLMFKYSIGRLPVM-DNGKLVGIVTKYDITNRI 59
                                      89**********************7477799*****.6*************8876 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 3.7e-16
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       +mt++++t+ pd+t+ +a+elm+e+++s+lPV ++dg++vG++t rD +r  
  gi|330507963|ref|YP_004384391.1|  79 VMTEKPITIFPDATMPQAAELMIENDISGLPV-EKDGEIVGVITSRDMVRHF 129
                                       5*******************************.79*************9975 PP

  == domain 3  score: 30.0 bits;  conditional E-value: 1.7e-10
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                       V ++m+++++ v+   t++ +le+m   g+sr +V +++  +vGivt++ l
  gi|330507963|ref|YP_004384391.1| 138 VQELMSKNILNVHRHHTIGHVLEEMNVQGISRALVYEDNRTPVGIVTRSGL 188
                                       789**********************8799999999976667******9865 PP

  == domain 4  score: 32.7 bits;  conditional E-value: 2.5e-11
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55 
                                       ++d+mt+++++++p+t+  ea ++++ek+ + ++PVV +++ +vG+++   ++  +
  gi|330507963|ref|YP_004384391.1| 229 AEDVMTSPILSLTPETNAVEASKTLAEKHiI-GMPVVKDND-VVGYFSADEIIAEI 282
                                       469**********************999988.*****7777.********999765 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.012        37      84     109 ..      28      54 ..      11      69 .. 0.72
   2 !    8.9   0.0   0.00072       2.1      39     119 ..      63     134 ..      52     144 .. 0.74
   3 ?    4.2   0.0     0.021        62      83     106 ..     251     274 ..     158     278 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.012
                                       HTTES.EEEEEEEEETTEEEEEEEEEE CS
                               GAF  84 nmgir.sslvvPlvndgelwGllvlhn 109
                                       n  ++ s   +P++++g+l+G+++ ++
  gi|330507963|ref|YP_004384391.1|  28 NLMFKySIGRLPVMDNGKLVGIVTKYD 54 
                                       55555566789***********99777 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00072
                                       EECCEEEET.TSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSSCS CS
                               GAF  39 asrwlfmkn.grgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsppf 114
                                       a++w +++    +i  qv+ t +p++i    pd    q      +e m  +   ++P+  dge++G+++  +  ++f
  gi|330507963|ref|YP_004384391.1|  63 APEWRRRPIdKVPI--QVVMTEKPITIF---PDATMPQ-----AAELMIENDISGLPVEKDGEIVGVITSRDMVRHF 129
                                       45554444433332..788899999999...9999888.....34456666889***************99966669 PP

                                       HHHHH CS
                               GAF 115 treel 119
                                       +++++
  gi|330507963|ref|YP_004384391.1| 130 SEQDI 134
                                       98886 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.021
                                       HHTTESEEEEEEEEETTEEEEEEE CS
                               GAF  83 enmgirsslvvPlvndgelwGllv 106
                                       +    +  +++P+v d++++G ++
  gi|330507963|ref|YP_004384391.1| 251 KTLAEKHIIGMPVVKDNDVVGYFS 274
                                       334445668************876 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.12   3.7e+02      96     109 ..      38      51 ..      37      61 .. 0.89
   2 !    8.8   0.0   0.00061       1.8      61     124 ..      77     135 ..      60     143 .. 0.70
   3 ?    2.8   0.0     0.046   1.4e+02      68     109 ..     226     274 ..     157     278 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.12
                                       EEE-TTS---EEEE CS
                             GAF_2  96 vPlisegrvvGvln 109
                                       +P++++g++vG+++
  gi|330507963|ref|YP_004384391.1|  38 LPVMDNGKLVGIVT 51 
                                       6**********997 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00061
                                       HHHHHTS-EEES-GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHH CS
                             GAF_2  61 ealrtgrpvilndleedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedle 124
                                       ++++t +p+ +    + + +  ++a+    + + ++P+  +g++vGv++ +++  + f+e+d++
  gi|330507963|ref|YP_004384391.1|  77 QVVMTEKPITIFP--D-ATMP-QAAELMIENDISGLPVEKDGEIVGVIT-SRDMVRHFSEQDIS 135
                                       6777778888633..3.3333.3346667777799***7789*******.6666666*999987 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.046
                                       -EEES-GGG-S-HHHHHHHHHTT--E.......EEEEE-TTS---EEEE CS
                             GAF_2  68 pvilndleedpdkkglpaghaglrsf.......lavPlisegrvvGvln 109
                                       p++ +d+ ++p  +  p+  a  +s        +++P++ ++ vvG ++
  gi|330507963|ref|YP_004384391.1| 226 PFVAEDVMTSPILSLTPETNAVEASKtlaekhiIGMPVVKDNDVVGYFS 274
                                       555555555444444443333332224444555*****99989**9765 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 ?    2.0   0.0     0.069     2e+02      20      34 ..      39      53 ..      32      62 .. 0.84
   2 ?    4.6   0.0      0.01        31      18      33 ..     107     122 ..      96     128 .. 0.87
   3 ?    2.2   0.0     0.059   1.8e+02      19      35 ..     170     187 ..     154     191 .. 0.78
   4 ?   -0.8   0.0      0.49   1.5e+03      18      30 ..     260     272 ..     253     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.069
                           GCV_T_C 20 pilrdgevvGhvTSg 34
                                      p++++g+ vG vT  
  gi|330507963|ref|YP_004384391.1| 39 PVMDNGKLVGIVTKY 53
                                      7999*********76 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.01
                           GCV_T_C  18 gepilrdgevvGhvTS 33 
                                       g p+ +dge+vG +TS
  gi|330507963|ref|YP_004384391.1| 107 GLPVEKDGEIVGVITS 122
                                       568899*********9 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.059
                           GCV_T_C  19 epilr.dgevvGhvTSga 35 
                                       + +++ + ++vG vT+++
  gi|330507963|ref|YP_004384391.1| 170 ALVYEdNRTPVGIVTRSG 187
                                       5678636689*****987 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.49
                           GCV_T_C  18 gepilrdgevvGh 30 
                                       g+p+++d++vvG+
  gi|330507963|ref|YP_004384391.1| 260 GMPVVKDNDVVGY 272
                                       6899999999998 PP

>> 30K_MP_C_Ter  C-Terminal of 30K viral movement proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.7e-05      0.11     192     227 ..     110     145 ..     101     153 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                      30K_MP_C_Ter 192 lekdgevvmildsrdegrmwikddvwaevtehgsks 227
                                       +ekdge+v ++ srd  r +  +d+ + v e  sk 
  gi|330507963|ref|YP_004384391.1| 110 VEKDGEIVGVITSRDMVRHFSEQDISSTVQELMSKN 145
                                       79*****************************99986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00014      0.42      25      68 ..     117     160 ..     111     170 .. 0.87
   2 ?   -3.3   0.0       4.8   1.4e+04      48      62 ..     198     212 ..     189     219 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                       EEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEE CS
                         Pyr_redox  25 VtvversdkllrllDeeaskilqeklekngievllntkveeieg 68 
                                       V v+  +d+++   ++++s+ +qe ++kn  +v+ ++++  + +
  gi|330507963|ref|YP_004384391.1| 117 VGVITSRDMVRHFSEQDISSTVQELMSKNILNVHRHHTIGHVLE 160
                                       779*******************************9999887765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.8
                                       HHHHHTTEEEECSEE CS
                         Pyr_redox  48 eklekngievllntk 62 
                                       + +e ++i++  +++
  gi|330507963|ref|YP_004384391.1| 198 DDMETKNIKMTRKES 212
                                       678888888876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.30s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1985.18
//
Query:       gi|330507964|ref|YP_004384392.1|  [L=305]
Description: CBS domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (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  166.6   5.8    8.4e-15   55.0   0.1    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 !   28.6   0.0   8.2e-11   1.5e-06       5      55 ..      30      81 ..      23      83 .. 0.86
   2 !   55.0   0.1   4.7e-19   8.4e-15       1      53 [.     106     158 ..     106     161 .. 0.96
   3 !   45.9   0.1   3.3e-16   5.9e-12       1      55 [.     169     222 ..     169     224 .. 0.95
   4 !   37.6   0.1   1.2e-13   2.2e-09       2      56 ..     245     298 ..     236     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 8.2e-11
                                      SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT..BEEEEEEHHHHHHHH CS
                               CBS  5 mtrdvvtvppdttleealelmrekgvsrlPVVdedg..klvGivtlrDllral 55
                                       ++dvvtvpp+tt+  a+++m+ +g+srlP+  + g  +l+G vt  D++++l
  gi|330507964|ref|YP_004384392.1| 30 ASPDVVTVPPTTTIMGAIKTMTFYGFSRLPIA-DAGtkRLLGFVTSVDVVDFL 81
                                      588******************8788******9.577678**********9998 PP

  == domain 2  score: 55.0 bits;  conditional E-value: 4.7e-19
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       +++im++++++++++t+l+++l+lm ek+v++lP+Vded ++ Gi+t++D +r
  gi|330507964|ref|YP_004384392.1| 106 IREIMSSKLIYASENTSLHDVLKLMYEKNVGGLPIVDEDSRIKGIITEEDFVR 158
                                       589***********************************************987 PP

  == domain 3  score: 45.9 bits;  conditional E-value: 3.3e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+++m+++vvt+p +tt+e+  +++++kg++r+PVV  dg l G+vt +D++++l
  gi|330507964|ref|YP_004384392.1| 169 VESFMSPNVVTAPAQTTIEKMTRMIIQKGFRRMPVV-QDGVLMGMVTASDIMKYL 222
                                       7899********************99**********.7**999**********98 PP

  == domain 4  score: 37.6 bits;  conditional E-value: 1.2e-13
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       +++  r ++t+   ++l+ a+++m +++++++PV+ + g l Gi+t+rD +ral+
  gi|330507964|ref|YP_004384392.1| 245 KSLIKRSLITIEKKMDLGHAARKMMDNEIGSMPVM-DRGSLAGILTERDFVRALA 298
                                       233444559**************87999*******.6999*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2162.60
//
Query:       gi|330507965|ref|YP_004384393.1|  [L=259]
Description: CBS domain pair protein [Methanosaeta concilii GP6]
Scores for complete 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-44  148.0  12.6    4.6e-12   46.2   0.1    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 !   37.3   0.4   1.5e-13   2.7e-09       1      53 [.       3      55 ..       3      58 .. 0.94
   2 !   28.2   0.2     1e-10   1.9e-06       9      55 ..      72     120 ..      65     121 .. 0.85
   3 !   42.9   0.3   2.8e-15   4.9e-11       1      53 [.     130     181 ..     130     183 .. 0.95
   4 !   46.2   0.1   2.6e-16   4.6e-12       2      53 ..     204     254 ..     203     258 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.5e-13
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT.BEEEEEEHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedg.klvGivtlrDllr 53
                                      V+di +rd+++v  +t l +a +l+r+++v++lPVVd +  +++G++t  D+lr
  gi|330507965|ref|YP_004384393.1|  3 VEDIFSRDPLYVEDSTYLTKARQLIRDNHVRGLPVVD-SRvQVLGVITSQDVLR 55
                                      89***********************9999*******6.5559**********98 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1e-10
                                       CEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHHHH CS
                               CBS   9 vvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllral 55 
                                       v+ v+ dt++ +a+++m +++ + lPVV   ed+ l G+vt  D+++ l
  gi|330507965|ref|YP_004384393.1|  72 VPAVTGDTDVLDAARIMLKEKSNLLPVVesQEDKTLRGVVTIIDIFKHL 120
                                       678999**********998886555***876666699********9987 PP

  == domain 3  score: 42.9 bits;  conditional E-value: 2.8e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       +g+im+++vvt++ d+++ ++ ++m+e+++++lP V  d+k+ Gi+t+ D+l+
  gi|330507965|ref|YP_004384393.1| 130 IGEIMSTKVVTARLDEPVTKVWDRMVERDFTGLPMV-RDEKPMGIITRFDILK 181
                                       689***********************999*******.6888**********98 PP

  == domain 4  score: 46.2 bits;  conditional E-value: 2.6e-16
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       + +m++++ ++ p+++++ea+elm +++v+r+ VV ++g++ Giv ++Dl++
  gi|330507965|ref|YP_004384393.1| 204 EKLMSSPLYSLGPTASVAEAIELMLKHDVGRVSVV-DEGRIMGIVDRSDLIK 254
                                       579********************************.6*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1932.02
//
Query:       gi|330507966|ref|YP_004384394.1|  [L=184]
Description: CBS domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-26   90.6   5.2    2.9e-13   50.0   0.2    2.3  2  CBS              CBS domain
  ------ inclusion threshold ------
      0.024   13.9   0.0      0.025   13.9   0.0    1.1  1  Beta_elim_lyase  Beta-eliminating lyase
        0.1   12.2   0.8       0.33   10.6   0.8    1.9  1  RecR             RecR protein
       0.17   12.0   0.0       0.46   10.6   0.0    1.7  2  DUF1335          Protein of unknown function (DUF1335)


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 !   42.3   1.1   1.7e-14   7.7e-11       1      55 [.       7      60 ..       7      62 .. 0.94
   2 !   50.0   0.2   6.5e-17   2.9e-13       1      53 [.      72     123 ..      72     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.7e-14
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      V+dimtr+v+t++ d ++  a+++m +++v++l +V + +k  Gi+t+rDl+r++
  gi|330507966|ref|YP_004384394.1|  7 VRDIMTRPVITADADLDVLSAAKRMGSANVGSLIIV-SRDKTTGILTERDLVRKV 60
                                      89***********************9999****889.7889***********986 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 6.5e-17
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       V++im+++v  + pd+++++a++lm ++gv rlPV+   gkl Gi+t++Dl++
  gi|330507966|ref|YP_004384394.1|  72 VREIMSSPVTAIEPDASIRDAANLMLRAGVKRLPVI-LKGKLMGIITDTDLVS 123
                                       89*********************************9.69***********985 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.5e-06     0.025     186     241 ..      17      73 ..       7     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-06
                                       HTTSSEEEEESSS.TT--SS-EEEEE-HH....HHHHHHHHHHHHT---SSTHHHHH CS
                   Beta_elim_lyase 186 fsyvDsvtmslkK.dllanvGgvlafrddeledylaerveqrkylggglrqagvlaa 241
                                       ++ +D  ++s+ K  ++anvG+++++++d+    l er  +rk +++g +   +++ 
  gi|330507966|ref|YP_004384394.1|  17 TADADLDVLSAAKrMGSANVGSLIIVSRDKTTGILTERDLVRKVIAQGVDPRNLKVR 73 
                                       56677777776551578*****************************99987766665 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.8   7.3e-05      0.33      19      39 ..     157     184 .]     154     184 .] 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.3e-05
                                       -TTT--EESSS.......S-CCCCSTTS CS
                              RecR  19 CsrCgnlteed.......lCaICsdprR 39 
                                       C++Cg l+++        lC  C+d +R
  gi|330507966|ref|YP_004384394.1| 157 CEVCGQLSDNLenvngelLCWSCRDGNR 184
                                       *********9559999999******998 PP

>> DUF1335  Protein of unknown function (DUF1335)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.63   2.8e+03     101     123 ..      56      78 ..      34      84 .. 0.60
   2 ?   10.6   0.0    0.0001      0.46      14      77 ..     101     165 ..      94     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.63
                           DUF1335 101 klgklfsrsvhPsaksietylsl 123
                                        + k+ ++ v P  +++ +++s 
  gi|330507966|ref|YP_004384394.1|  56 LVRKVIAQGVDPRNLKVREIMSS 78 
                                       34455666666666666666665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0001
                           DUF1335  14 terlsnaavkkkdylivstdfliGlGfsaenvtkklksmesvlrk.hGlkesmvplaeichrlky 77 
                                        +rl+ +  +k   +i  td++ G+ +  +++   l+ m +   + +  + ++  + e+c +l+ 
  gi|330507966|ref|YP_004384394.1| 101 VKRLPVILKGKLMGIITDTDLVSGCSVGLNDILSDLLEMHRENIHfEQPRGTVSGICEVCGQLSD 165
                                       57888888899999999**********************97543403444445557777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 1265.03
//
Query:       gi|330507967|ref|YP_004384395.1|  [L=158]
Description: molybdenum cofactor synthesis domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   97.7   0.0    5.7e-28   97.4   0.0    1.0  1  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   0.0   3.2e-32   5.7e-28       2     144 .]       5     151 ..       4     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 3.2e-32
                                       EEEE-HHHH........TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSST CS
                     MoCF_biosynth   2 vitvGdell........sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptp 70 
                                       v++ +++++        + ++eD +g+++ e+++ +g++  +y ++pD  e i++a++++  +ad+ +++GGtG+t+
  gi|330507967|ref|YP_004384395.1|   5 VVVASTSRYtkfgsvrdPDRAEDLSGKVILEKIRTAGYTG-NYLLIPDGVEPIQRAIKTS--SADAMVICGGTGLTA 78 
                                       566777777777777778999*****************65.599*************555..55************* PP

                                       T--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE.....TTEEEEE-SSHHHHHHHHHHHHHGGH CS
                     MoCF_biosynth  71 dDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsrav.....gktiigLPGspkavkealeeillpal 142
                                        D+t ea ++lfek+l+gf+e+fr  s+k+     v++ a+l ra+     +k+i++LPGsp+a++ ++++il  ++
  gi|330507967|ref|YP_004384395.1|  79 LDLTIEAAEPLFEKTLPGFGEIFRWQSMKE-----VGTRAMLTRATagvfmKKPIFCLPGSPGAARLGMDLIL-AEI 149
                                       *****************************9.....99*************8888******************9.677 PP

                                       HH CS
                     MoCF_biosynth 143 eh 144
                                       eh
  gi|330507967|ref|YP_004384395.1| 150 EH 151
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1230.06
//
Query:       gi|330507968|ref|YP_004384396.1|  [L=345]
Description: hypothetical protein MCON_2022 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-87  293.2   0.0    1.6e-87  293.0   0.0    1.1  1  DUF1786   Putative pyruvate format-lyase activating enzyme (D
  ------ inclusion threshold ------
      0.091   13.2   0.1        7.5    7.0   0.0    2.5  2  FtsA      Cell division protein FtsA


Domain annotation for each model (and alignments):
>> DUF1786  Putative pyruvate format-lyase activating enzyme (DUF1786)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.0   0.0   1.8e-91   1.6e-87       1     251 [.      60     305 ..      60     306 .. 0.98

  Alignments for each domain:
  == domain 1  score: 293.0 bits;  conditional E-value: 1.8e-91
                           DUF1786   1 MGGGavtkavkehlkaGlkvvateeaAltlrddlekvkemGieiveeapeeaekielkDvdlealkealeafglelp 77 
                                       MGGGa+t av+ hl+aGl+v+at++aA t+++dl +v+++G+ i+e+ap++ae +e++D+d+ +l++a++ f+++lp
  gi|330507968|ref|YP_004384396.1|  60 MGGGASTMAVRWHLAAGLRVFATPSAAATINNDLGQVEALGVIIQEDAPASAEIVETGDIDIPSLQRAFQLFDISLP 136
                                       ***************************************************************************** PP

                           DUF1786  78 ekvavavqDHGyspgesnrkfRfelleelleeggkleelvfeeevpeeftRlkavaeslkeeg.kvvvmDtgaaavl 153
                                       + +avavqDHGyspg+ nr++Rfe++   +++gg+l++++f+e  p+e+tR+ av+++l +eg + ++mDtg+aa++
  gi|330507968|ref|YP_004384396.1| 137 KDIAVAVQDHGYSPGKPNRQVRFEHMVAAIRSGGSLDDFTFKEC-PQEMTRMVAVRDTLIKEGfEPFIMDTGPAAIF 212
                                       *****************************************999.**************98999************* PP

                           DUF1786 154 GalldpeveklsgalvvnvGngHtlaalvkegrivgvfEhHTsaltkekleelieklaegeltneevfedgGHGvla 230
                                       Ga ldp++e+  +al++n+Gn+Ht+aa+++egri++vfEhHTs+++ ek++e+ +kl++g+l++ evf+dgGHG + 
  gi|330507968|ref|YP_004384396.1| 213 GAALDPRIED--PALIINFGNSHTIAAILSEGRICAVFEHHTSSMKGEKVREFTQKLCRGTLEEGEVFDDGGHGSYI 287
                                       ********96..**************************************************************555 PP

                           DUF1786 231 aaekeeaeevekvvvtGPrre 251
                                          +   ++v+++++tGPrre
  gi|330507968|ref|YP_004384396.1| 288 GSLP---DGVRSILITGPRRE 305
                                       5555...99**********97 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0   0.00083       7.5       2      23 ..       5      29 ..       4      56 .. 0.75
   2 ?    3.5   0.0      0.01        94       2      46 ..     226     273 ..     225     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00083
                                      EEEE-SSSEEEEEEETTEEEE...E CS
                                      xxxxxxxxxxxxxxxxxxxxx...x RF
                              FtsA  2 lvDiGagktdvavaedgalvh...l 23
                                      +vD+Gag+ d++++++g ++     
  gi|330507968|ref|YP_004384396.1|  5 AVDVGAGTQDILLYQEGVPIEgstK 29
                                      7***************998876642 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.01
                                       EEEE-SSSEEEEEEETTEEEE...EEEES--HHHHHHHHHHHHT--HH CS
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
                              FtsA   2 lvDiGagktdvavaedgalvh...lrvigvggngitkdiakalrtave 46 
                                       ++++G+++t +a++++g++++    ++  ++g+ +++ ++k +r  +e
  gi|330507968|ref|YP_004384396.1| 226 IINFGNSHTIAAILSEGRICAvfeHHTSSMKGEKVREFTQKLCRGTLE 273
                                       799***************998665555555777777766666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2958.18
//
Query:       gi|330507969|ref|YP_004384397.1|  [L=190]
Description: hypothetical protein MCON_2023 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-06   26.7   0.0    4.8e-06   26.1   0.0    1.3  1  Pkinase         Protein kinase domain
    7.9e-06   25.6   0.0    1.2e-05   25.0   0.0    1.2  1  RIO1            RIO1 family
    3.8e-05   23.1   0.0    5.5e-05   22.6   0.0    1.4  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0002   21.4   0.2     0.0063   16.5   0.2    2.2  2  APH             Phosphotransferase enzyme family
     0.0038   16.9   0.1     0.0046   16.6   0.1    1.1  1  WaaY            Lipopolysaccharide core biosynthesis protein 
     0.0047   16.5   0.0       0.66    9.5   0.1    2.5  3  Choline_kinase  Choline/ethanolamine kinase
     0.0071   15.7   0.0      0.008   15.5   0.0    1.2  1  Pkinase_Tyr     Protein tyrosine kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.9e-09   4.8e-06      70     152 ..      64     135 ..      25     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.9e-09
                                       SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSE CS
                           Pkinase  70 kdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlak 146
                                        +++ l +e+++g++l+d+++           ++ +++ e +  lH+ giiH Dl ++N+++  +g++ ++DFGl+ 
  gi|330507969|ref|YP_004384397.1|  64 ISRFELKMEHIRGDKLKDVIN----------PDLSRKVGEMVGRLHQGGIIHGDLTTSNMILV-EGDICLIDFGLSF 129
                                       455556666666666666665..........3677888889999******************9.9**********97 PP

                                       ESSSSC CS
                           Pkinase 147 elesss 152
                                         +s++
  gi|330507969|ref|YP_004384397.1| 130 IERSTE 135
                                       655554 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   4.7e-09   1.2e-05      54     152 ..      40     128 ..      30     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.7e-09
                                       HHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEES CS
                              RIO1  54 waekEfrnLkrleeagvpvPkpielkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHa 130
                                        + +E r+ + ++++gv  P  +++ r  l me i   g    klkdv     + +l ++v  em   +++ g++H+
  gi|330507969|ref|YP_004384397.1|  40 RTIREARITSDARRHGVLTPIICDISRFELKMEHIR--GD---KLKDVI----NPDLSRKVG-EMVGRLHQGGIIHG 106
                                       556888888999999999999999999999999999..54...566666....223334443.46667889****** PP

                                       S-STTSEEEETTEEEE--GTTE CS
                              RIO1 131 DLSeyNvlvdedkvviIDvsQa 152
                                       DL   N+++ e+++ +ID++ +
  gi|330507969|ref|YP_004384397.1| 107 DLTTSNMILVEGDICLIDFGLS 128
                                       ******************9865 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.2e-08   5.5e-05     117     167 ..      81     126 ..      64     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.2e-08
                               Kdo 117 eelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDld 167
                                       +  +  l ++vg ++ +lh+ g+ H+dl   n+ l +++     i+liD+ 
  gi|330507969|ref|YP_004384397.1|  81 DVINPDLSRKVGEMVGRLHQGGIIHGDLTTSNMILVEGD-----ICLIDFG 126
                                       555667789**************************9998.....*****95 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.026        66      39     107 ..      43     100 ..      25     102 .. 0.70
   2 !   16.5   0.2   2.5e-06    0.0063     167     198 ..     102     130 ..      99     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHC CS
                               APH  39 revallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalhq 107
                                       re+++    +++gv +P +++       i +  + +e + g  l +     + p+l +++ge+ ++lhq
  gi|330507969|ref|YP_004384397.1|  43 REARITSDARRHGVLTPIICD-------ISRFELKMEHIRGDKLKD----VINPDLSRKVGEMVGRLHQ 100
                                       666666677777776655666.......222233477777777777....7889999**********98 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.5e-06
                                       EEE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                               APH 167 vllHgDlhpgNllvdpddgrvtGviDfedagl 198
                                       +++HgDl + N+++   +g + ++iDf+++ +
  gi|330507969|ref|YP_004384397.1| 102 GIIHGDLTTSNMILV--EGDI-CLIDFGLSFI 130
                                       79*************..7777.8*****9876 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.8e-06    0.0046     117     179 ..      66     126 ..      37     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-06
                              WaaY 117 vyimiieyiegielvdmpeiddevkakikqsieklhqlgmvsgdphrgnfivkkdevriidls 179
                                        + + +e+i g +l d+  i+ ++  k+ + + +lhq g++ gd    n+i+ ++++ +id+ 
  gi|330507969|ref|YP_004384397.1|  66 RFELKMEHIRGDKLKDV--INPDLSRKVGEMVGRLHQGGIIHGDLTTSNMILVEGDICLIDFG 126
                                       56677899999999996..889999***********************************974 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0075        19      55      81 ..      77     101 ..      43     104 .. 0.83
   2 !    9.5   0.1   0.00026      0.66     149     173 ..     105     127 ..     102     157 .. 0.90
   3 ?   -2.0   0.0      0.84   2.2e+03      31      55 ..     150     174 ..     129     179 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0075
                                       EE--TTGGGCHHHHHHHHHHHHHHTTC CS
                    Choline_kinase  55 rtlstedlrepeiskkiAkklaelHsl 81 
                                       ++   +d+ +p++s+k+++ +++lH+ 
  gi|330507969|ref|YP_004384397.1|  77 DK--LKDVINPDLSRKVGEMVGRLHQG 101
                                       44..4799*****************86 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00026
                                       -S--SGGGEEE.-CTTEEEE--GTT CS
                    Choline_kinase 149 HnDlqegNillnkeekklvlIDFEY 173
                                       H Dl  +N++l   e++++lIDF  
  gi|330507969|ref|YP_004384397.1| 105 HGDLTTSNMIL--VEGDICLIDFGL 127
                                       99*********..9*********65 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.84
                                       HHTTSSS-EEEEETTEEEEE--TCE CS
                    Choline_kinase  31 serglgpklygifenGrieefiesr 55 
                                       s+++   +l+  f+ G +e + +++
  gi|330507969|ref|YP_004384397.1| 150 STHDRPEELIEAFKAGYLEVYPPGE 174
                                       3344444566777777777776665 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.1e-06     0.008     109     167 ..      88     141 ..      32     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-06
                                       HHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEEEETTSSTS CS
                       Pkinase_Tyr 109 alqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddeyvkkeeakl 167
                                       + +v + +  L++  ++H dl++ N++l e++++ i DfGL+       + +++++ ++
  gi|330507969|ref|YP_004384397.1|  88 SRKVGEMVGRLHQGGIIHGDLTTSNMILVEGDICLI-DFGLSFIE----RSTEAQGVDV 141
                                       5666777778999*************9998877755.****9754....3344444445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1458.49
//
Query:       gi|330507970|ref|YP_004384398.1|  [L=89]
Description: DNA-binding protein Alba [Methanosaeta concilii GP6]
Scores for complete 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   59.7   0.2    2.3e-16   59.4   0.2    1.2  1  Alba      Alba
  ------ inclusion threshold ------
       0.05   13.6   0.1      0.077   12.9   0.1    1.4  1  Rpp20     Rpp20 subunit of nuclear RNase MRP and P


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.2   2.5e-20   2.3e-16       2      56 ..       6      58 ..       5      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 2.5e-20
                                      EEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT CS
                              Alba  2 eiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkg 56
                                      +++V++ +p+m+yv+++++++ n++++ V + a+GraIs+Av+vae+ ++rf+++
  gi|330507970|ref|YP_004384398.1|  6 VVFVGN-KPVMNYVLAVVTQF-NSGAKDVRIMARGRAISRAVDVAEVSRSRFLPD 58
                                      799999.**************.******************************875 PP

>> Rpp20  Rpp20 subunit of nuclear RNase MRP and P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   8.6e-06     0.077      58      83 ..      26      51 ..      20      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.6e-06
                             Rpp20 58 elkkeeVfvkatGrAiekalsvgrwf 83
                                      +   ++V + a GrAi +a+ v++  
  gi|330507970|ref|YP_004384398.1| 26 NSGAKDVRIMARGRAISRAVDVAEVS 51
                                      566799****************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 640.51
//
Query:       gi|330507971|ref|YP_004384399.1|  [L=204]
Description: phosphoribosylglycinamide formyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-47  159.0   0.0    1.1e-46  158.8   0.0    1.0  1  Formyl_trans_N  Formyl transferase


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 !  158.8   0.0   6.2e-51   1.1e-46       5     181 .]       7     182 ..       3     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 158.8 bits;  conditional E-value: 6.2e-51
                                       EEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCTT-S CS
                    Formyl_trans_N   5 vlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkelkad 81 
                                       ++ sg g+nl+ +l a ++g l a+v  v+ ++++a  l+ a++++    +++ +  ++r++++++l++ l+ +++d
  gi|330507971|ref|YP_004384399.1|   7 IISSGRGENLRYILLAERDGYLPAQVKIVLADQPDAGALRIAQEFGVRHMYLDPA-GRSREEYDQQLVSHLEGAGVD 82 
                                       7889*******************************99777777666655555554.56778**************** PP

                                       EEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--T CS
                    Formyl_trans_N  82 livlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiia 158
                                       l+vl gym++l++ +v++++++ilniHp+LLP+f+G++a  +ale+G+  tG+tih vde++D+G+i++q  v++  
  gi|330507971|ref|YP_004384399.1|  83 LVVLTGYMRILSPRFVRHYKNRILNIHPALLPSFRGLDAFSQALEHGVMWTGTTIHLVDEDVDHGPIIYQMPVPVKR 159
                                       ***************************************************************************** PP

                                       T--HHHHHHHHHHHHHHHHHHHH CS
                    Formyl_trans_N 159 edtkeeleqrvadaehkalveal 181
                                       +dt e+l++r++ ae +a+++a+
  gi|330507971|ref|YP_004384399.1| 160 NDTHESLKARIQRAEYRAYPRAI 182
                                       ********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1576.65
//
Query:       gi|330507972|ref|YP_004384400.1|  [L=166]
Description: histidine triad (HIT) protein [Methanosaeta concilii GP6]
Scores for complete 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    1.2  1  HIT       HIT domain
      2e-05   24.4   0.0    3.8e-05   23.5   0.0    1.4  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1
    0.00017   22.0   0.0    0.00025   21.5   0.0    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding


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 !   44.2   0.0   4.2e-15   2.5e-11      11      95 ..      45     130 ..      35     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 4.2e-15
                                       E-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSS. CS
                               HIT  11 eddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsva. 86 
                                       + ++ +++l+  p   gh+ v+p kh+s+l   t++e+ +++++++  ++ l+++++ +g+++ in g+ +g  +a 
  gi|330507972|ref|YP_004384400.1|  45 RGKNHFIILNAYPYNNGHMMVVPFKHTSTLAGWTDDERREMMELADLAVELLRRTMRPDGFNLGINMGIVGGAGIAd 121
                                       4567799*****************************************************************98754 PP

                                       S-EEEEEEC CS
                               HIT  87 hlHiHvipr 95 
                                       h+H+H++pr
  gi|330507972|ref|YP_004384400.1| 122 HIHMHIVPR 130
                                       *******98 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   6.4e-09   3.8e-05      10      73 ..      22      87 ..      17     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.4e-09
                                      HHHH-S----..SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHH CS
                          CwfJ_C_1 10 sldsClfCls..npklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirk 73
                                      +++ C fC +  +++ e++li+  g++ ++ l   p ++gH++++p +H+s+l    ++++ e+ +
  gi|330507972|ref|YP_004384400.1| 22 KPEGCIFCSKpgENRDEENLILHRGKNHFIILNAYPYNNGHMMVVPFKHTSTLAGWTDDERREMME 87
                                      6889****873345678899*********************************9999999999865 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 !   21.5   0.0   4.3e-08   0.00025      10     100 ..      34     128 ..      25     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.3e-08
                                       TSS.-B-EEEE-.SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEEEE-- CS
                            DcpS_C  10 gke.pervvyed.ekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdaeelrv 84 
                                       ++  +e+++++  ++  ++  ++p ++ h++v+p ++ ++l   t+++   + e+ + a +++++ +   +++ +++
  gi|330507972|ref|YP_004384400.1|  34 ENRdEENLILHRgKNHFIILNAYPYNNGHMMVVPFKHTSTLAGWTDDERREMMELADLAVELLRRTM---RPDGFNL 107
                                       333255554444488888889****************************999999999999998877...5666666 PP

                                       SCCCT-.....-S-S--EEEE CS
                            DcpS_C  85 gvhyqP.....svyhlHlHvi 100
                                       g+++         +h+H+H++
  gi|330507972|ref|YP_004384400.1| 108 GINMGIvggagIADHIHMHIV 128
                                       66665544558999*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1240.75
//
Query:       gi|330507973|ref|YP_004384401.1|  [L=306]
Description: hypothetical protein MCON_2027 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); 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 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2074.62
//
Query:       gi|330507974|ref|YP_004384402.1|  [L=356]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.3    8.0   9.6        5.3    6.8   9.3    1.9  1  MENTAL    Cholesterol-capturing domain


Domain annotation for each model (and alignments):
>> MENTAL  Cholesterol-capturing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   9.3    0.0003       5.3      47     101 ..     264     321 ..     227     346 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0003
                            MENTAL  47 ktSlFDivllavlRflvLllayallklkhwivvaitTaat...saflvvKvflydlss 101
                                       + S+FD+  la+  +  +l++ya++k+k   + a   +       +++v v+l+ l++
  gi|330507974|ref|YP_004384402.1| 264 SLSFFDLAGLAAATLSSILVIYAIIKMKSSRLEAYRIFKNailVQIFIVQVILFYLTQ 321
                                       67**************************999988765544011455677888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); 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:                         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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2160.83
//
Query:       gi|330507975|ref|YP_004384403.1|  [L=586]
Description: metal ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for 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-38  132.0   0.0      1e-20   74.7   0.0    2.4  2  ABC_tran       ABC transporter
    3.5e-13   49.1   2.4    7.7e-13   48.0   2.4    1.6  1  RLI            Possible Fer4-like domain in RNase L inhibitor
      1e-12   48.0   6.1    9.4e-05   21.9   0.0    4.7  5  SMC_N          RecF/RecN/SMC N terminal domain
    5.4e-10   39.6   9.6     0.0042   16.9   0.6    4.2  4  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    9.8e-08   31.5   3.1    9.8e-08   31.5   3.1    2.3  3  Fer4           4Fe-4S binding domain
    2.3e-06   27.4  11.7    5.8e-06   26.2   1.8    2.3  2  Fer4_6         4Fe-4S binding domain
    6.5e-05   22.6   0.4       0.18   11.6   0.1    2.4  2  AAA_29         P-loop containing region of AAA domain
    0.00011   22.1   0.1       0.32   10.9   0.0    2.3  2  RsgA_GTPase    RsgA GTPase
    0.00012   22.1  15.6     0.0017   18.4   1.2    1.7  2  Fer4_9         4Fe-4S dicluster domain
    0.00015   21.8   0.0       0.69    9.8   0.0    2.3  2  Rad17          Rad17 P-loop domain
    0.00027   21.3   0.7       0.14   12.6   0.0    2.9  2  AAA_16         AAA ATPase domain
    0.00029   21.4   0.4    0.00029   21.4   0.4    2.3  2  Fer4_7         4Fe-4S dicluster domain
    0.00043   20.8   0.4        1.3    9.5   0.0    2.3  2  AAA_23         AAA domain
    0.00058   19.7   0.0        1.3    8.6   0.0    3.2  3  AAA_15         AAA ATPase domain
    0.00072   19.6   6.4     0.0012   19.0   6.4    1.3  1  Fer4_21        4Fe-4S dicluster domain
     0.0043   17.1   1.7     0.0043   17.1   1.7    2.4  2  Fer4_2         4Fe-4S binding domain
     0.0057   16.7   1.0     0.0057   16.7   1.0    2.3  2  Fer4_10        4Fe-4S dicluster domain
     0.0086   15.1   1.1        1.6    7.6   0.1    2.2  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
  ------ inclusion threshold ------
      0.014   16.3   0.4      0.014   16.3   0.4    2.2  1  Fer4_16        4Fe-4S double cluster binding domain
      0.015   15.0   0.7        2.7    7.7   0.1    2.3  2  AAA_24         AAA domain
      0.015   15.5   0.1        8.7    6.7   0.0    2.9  2  SbcCD_C        Putative exonuclease SbcCD, C subunit
      0.023   15.1   0.2        6.2    7.3   0.1    2.4  2  RNA_helicase   RNA helicase
      0.041   13.9   0.5        1.9    8.9   0.1    3.0  2  Cm_res_leader  Chloramphenicol resistance gene leader peptide
      0.049   14.2   0.5      0.049   14.2   0.5    2.2  1  Fer4_17        4Fe-4S dicluster domain
      0.098   13.2  13.0      0.069   13.7   3.0    2.3  2  Fer4_4         4Fe-4S binding domain
       0.13   12.7   0.7         22    5.5   0.1    3.0  2  AAA            ATPase family associated with various cellular
       0.18   11.5   0.9         21    4.7   0.2    2.8  2  AAA_30         AAA domain
        0.2   11.7   1.0         16    5.6   0.0    3.3  3  AAA_14         AAA domain
       0.21   12.1   2.2         66    4.1   0.0    3.4  3  AAA_18         AAA domain
       0.33   11.2   2.1         26    5.0   0.1    3.4  4  AAA_28         AAA domain
       0.47   10.5   1.4         10    6.2   0.2    2.8  2  MMR_HSR1       50S ribosome-binding GTPase
       0.48   10.0   2.9         22    4.5   0.0    3.3  4  AAA_25         AAA domain
        2.4    8.0   4.3         70    3.3   0.2    3.6  4  NTPase_1       NTPase


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 !   54.8   0.0   2.6e-17   1.4e-14      10     134 ..      94     231 ..      93     233 .. 0.76
   2 !   74.7   0.0   1.9e-23     1e-20       8     137 .]     355     475 ..     352     475 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 2.6e-17
                                       TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..........B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..........qeleslrkeigvlpqepqlfpeltv 76 
                                       eg++++++G+nG GKSt +++l+g l+p+ G+    ++ l++          ++      + ++ pq          
  gi|330507975|ref|YP_004384403.1|  94 EGRVTGLLGPNGIGKSTAISILSGILRPNLGKDASWEEALQRfsgsilgdylKKVVDKGIKTSYKPQYVDR------ 164
                                       6999****************************966677777766655555444444444455555555333...... PP

                                       HHH.............HHHTC..HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxx.............xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.............esdee..iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                                       + de+  ++++  +lg+++l d+ +    ssLSgG+ qrva+a+a +k+++++++DE
  gi|330507975|ref|YP_004384403.1| 165 --IpksysgmvsglleKTDERgaLAELTGTLGISKLMDRDI----SSLSGGELQRVAIAAAAAKDADFYFFDE 231
                                       ..133334456778853333366999999999999999999....***************************9 PP

  == domain 2  score: 74.7 bits;  conditional E-value: 1.9e-23
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren..... 79 
                                       +++ge+v+i+G+nG GKSt +k+lag +kpt G+              +++ +i++ pq  + + eltv+       
  gi|330507975|ref|YP_004384403.1| 355 IRRGEVVGILGPNGIGKSTYIKILAGVEKPTTGSF-------------ESQLKISYKPQYLKADTELTVEGMlrglt 418
                                       689*******************************9.............788999999**999999999988899999 PP

                                       ...HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                          +s+   +++l+ +g++ l d+++    s+LSgG+ qrva+ ++l ++++l+llDEp+a
  gi|330507975|ref|YP_004384403.1| 419 hgfDSSYYQAEILRPMGIEPLLDKIL----SELSGGELQRVAITACLSREADLYLLDEPSA 475
                                       9998888899****************....*****************************75 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   2.4   1.4e-15   7.7e-13       1      35 []       1      32 [.       1      32 [. 0.97

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1.4e-15
                                      --EEEES---------TTHHHHHTTSEEEESS--S CS
                               RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrtgkk 35
                                      mr+Ai+++d+C+P+KC+  +c+ fcp   vrtg++
  gi|330507975|ref|YP_004384403.1|  1 MRIAIINRDRCQPRKCSK-ECEYFCPP--VRTGDE 32
                                      9*****************.********..****85 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0098       5.3      20      41 ..      91     112 ..      82     123 .. 0.85
   2 !   21.9   0.0   1.7e-07   9.4e-05     134     203 ..     203     268 ..     143     281 .. 0.84
   3 ?    4.7   0.1     0.032        17      25      41 ..     359     375 ..     341     381 .. 0.79
   4 !   14.0   0.0   4.5e-05     0.025     136     197 ..     446     505 ..     391     521 .. 0.79
   5 ?   -0.8   0.0       1.6   8.5e+02      81     115 ..     549     585 ..     539     586 .] 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0098
                                       EETTSSEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  20 lpfsksftaivGpNGSGKsnll 41 
                                       +p++ ++t ++GpNG GKs  +
  gi|330507975|ref|YP_004384403.1|  91 VPIEGRVTGLLGPNGIGKSTAI 112
                                       5788899************765 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.7e-07
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                                       +++LSgGe + va+a      ++k a +y++Dei   LD +++ + a++l++  k+  ++v+ ++  +l 
  gi|330507975|ref|YP_004384403.1| 203 ISSLSGGELQRVAIA----AAAAKDADFYFFDEISPYLDIHQRINSARILQSLAKDKAVMVVEHDLALLD 268
                                       458*****9988876....5588999***********************************999876665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.032
                                       SEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnll 41 
                                       ++  i+GpNG GKs  +
  gi|330507975|ref|YP_004384403.1| 359 EVVGILGPNGIGKSTYI 375
                                       4678**********865 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 4.5e-05
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivisl 197
                                       +LSgGe + va+   +     + a lyllDe  a+LD +++   a++++  ++s++  ++v+ +
  gi|330507975|ref|YP_004384403.1| 446 ELSGGELQRVAITACL----SREADLYLLDEPSAHLDVEQRMLAAKVMRrfAESTEKTVLVVDH 505
                                       79***98888876664....47889*********************999333344455666655 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 1.6
                                       EEE..EETTEESSSSSSCEEEEEEEETTSEEEEEETT CS
                                       xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  81 itf..dnedkklkiekeevsisrrvkrkgeseyking 115
                                       itf  d+e ++ +++k+e  + r  k++ge  y+i++
  gi|330507975|ref|YP_004384403.1| 549 ITFrrDEETRRPRVNKPESRLDRMQKEQGEYYYQIEE 585
                                       56644666667899****************9999975 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6   7.8e-06    0.0042       1      25 [.      97     121 ..      97     159 .. 0.78
   2 ?    3.1   0.0      0.13        69     232     287 ..     201     253 ..     173     268 .. 0.78
   3 !   10.1   0.4   0.00095      0.52       2      22 ..     361     381 ..     360     396 .. 0.78
   4 !   12.6   0.0   0.00016     0.089     235     303 .]     445     511 ..     411     511 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.8e-06
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarl 25 
                                       +++l GpNg GKS+ + +l+++ r 
  gi|330507975|ref|YP_004384403.1|  97 VTGLLGPNGIGKSTAISILSGILRP 121
                                       699*****************99763 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.13
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                       +++++lS G ++  a+++a + ++   +++++DE+   L+ +     +++l +l++
  gi|330507975|ref|YP_004384403.1| 201 RDISSLSGGELQRVAIAAAAAKDA---DFYFFDEISPYLDIHQRINSARILQSLAK 253
                                       568889999999989999999999...9*******988888777555555555544 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00095
                            AAA_21   2 nvliGpNgsGKSnLLdaldll 22 
                                        ++ GpNg GKS+ +++l ++
  gi|330507975|ref|YP_004384403.1| 361 VGILGPNGIGKSTYIKILAGV 381
                                       689***************765 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00016
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkll...rrllellkelsrngaQviltTHSpllld 303
                                       +elS G ++    +ta+l++    +l+l+DEp ++L+ +     +++++ + e ++    v+++ H+ +l+d
  gi|330507975|ref|YP_004384403.1| 445 SELSGGELQR-VAITACLSREA--DLYLLDEPSAHLDVEQRmlaAKVMRRFAESTE--KTVLVVDHDIYLID 511
                                       5678888777.46667776664..9*************555345666666655555..57777777777765 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       6.6   3.6e+03       2       8 ..       5      11 ..       4      12 .. 0.86
   2 ?   -1.9   0.4       6.5   3.5e+03      13      19 ..      19      25 ..      18      25 .. 0.88
   3 !   31.5   3.1   1.8e-10   9.8e-08       3      24 .]      43      64 ..      41      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.6
                                      EEETTTS CS
                              Fer4  2 videekC 8 
                                      +i+ ++C
  gi|330507975|ref|YP_004384403.1|  5 IINRDRC 11
                                      79***** PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.5
                                      HHHHHST CS
                              Fer4 13 aCvevCP 19
                                      +C+  CP
  gi|330507975|ref|YP_004384403.1| 19 ECEYFCP 25
                                      6*****9 PP

  == domain 3  score: 31.5 bits;  conditional E-value: 1.8e-10
                                      EETTTSSS-THHHHHSTTTEEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                      i e++C+gCG+Cv  CP+gAIt
  gi|330507975|ref|YP_004384403.1| 43 ITENLCVGCGICVRKCPFGAIT 64
                                      7799*****************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 ?    6.3   2.6      0.02        11       2      20 ..       4      25 ..       3      31 .. 0.85
   2 !   26.2   1.8   1.1e-08   5.8e-06       2      24 .]      41      63 ..      40      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.02
                            Fer4_6  2 veidpdkCi..gC.gdCvrvCP 20
                                      + i++d+C    C  +C+  CP
  gi|330507975|ref|YP_004384403.1|  4 AIINRDRCQprKCsKECEYFCP 25
                                      679*****9888*666*****9 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 1.1e-08
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + i +++C+gCg Cvr CP+gai
  gi|330507975|ref|YP_004384403.1| 41 PLITENLCVGCGICVRKCPFGAI 63
                                      66889*****************8 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   0.00033      0.18      20      48 ..      92     121 ..      84     127 .. 0.79
   2 !    8.7   0.0    0.0027       1.4      22      39 ..     357     375 ..     345     383 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                            AAA_29  20 dlkg.atlltGpsGsGKSTllDAiqalLvp 48 
                                         +g +t l Gp+G GKST +  ++ +L p
  gi|330507975|ref|YP_004384403.1|  92 PIEGrVTGLLGPNGIGKSTAISILSGILRP 121
                                       44577999***********99666666665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0027
                            AAA_29  22 kg.atlltGpsGsGKSTll 39 
                                       +g ++ + Gp+G GKST +
  gi|330507975|ref|YP_004384403.1| 357 RGeVVGILGPNGIGKSTYI 375
                                       5558889**********76 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0026       1.4      97     121 ..      93     117 ..      78     128 .. 0.86
   2 !   10.9   0.0   0.00059      0.32      99     133 ..     358     392 ..     333     395 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
                                       CTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallp 121
                                       ++++++ l+G+ G+GKSt i  l +
  gi|330507975|ref|YP_004384403.1|  93 IEGRVTGLLGPNGIGKSTAISILSG 117
                                       68899*************9998876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00059
                                       TSEEEEECSTTSSHHHHHHHHCTT-----S----- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelktgevsek 133
                                       ++++ ++G+ G+GKSt i+ l++ ++  tg+  ++
  gi|330507975|ref|YP_004384403.1| 358 GEVVGILGPNGIGKSTYIKILAGVEKPTTGSFESQ 392
                                       578889****************9988888877665 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   7.2   7.9e-06    0.0043       4      51 .]      15      63 ..       9      63 .. 0.66
   2 !   18.4   1.2   3.2e-06    0.0017       2      27 ..      48      73 ..      47      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.9e-06
                            Fer4_9  4 gCg.aCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      +C  +C++ Cp   + ++     +      e+ C+gCg Cv +Cp gai
  gi|330507975|ref|YP_004384403.1| 15 KCSkECEYFCPPVRTGDETIVFADGKPLITENLCVGCGICVRKCPFGAI 63
                                      353147777766555555555544444444489************9987 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.2e-06
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkar 27
                                      C+gCg Cv++Cp+g+++  + +++++
  gi|330507975|ref|YP_004384403.1| 48 CVGCGICVRKCPFGAITITNLPEEME 73
                                      9**************99999988876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0013      0.69      50      73 ..     100     123 ..      93     131 .. 0.86
   2 !    9.5   0.0    0.0016      0.88      46      68 ..     359     381 ..     346     411 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                             Rad17  50 isGPsGCgkstvvkvLskelgikl 73 
                                       + GP G gkst++ +Ls +l ++l
  gi|330507975|ref|YP_004384403.1| 100 LLGPNGIGKSTAISILSGILRPNL 123
                                       67***************9998765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0016
                             Rad17  46 riLLisGPsGCgkstvvkvLske 68 
                                       +++ i GP G gkst +k+L+  
  gi|330507975|ref|YP_004384403.1| 359 EVVGILGPNGIGKSTYIKILAGV 381
                                       467799**************965 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.023        12      26      60 ..      97     126 ..      90     325 .. 0.70
   2 !   12.6   0.0   0.00025      0.14      23     142 ..     357     504 ..     347     517 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.023
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkc 60 
                                       ++ l G+ G+GKs+ +  l   l+ +      gk 
  gi|330507975|ref|YP_004384403.1|  97 VTGLLGPNGIGKSTAISILSGILRPN-----LGKD 126
                                       56689*********997666444443.....3333 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00025
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqllde..aesaelea 96 
                                       r+e+v + G+ G+GKs+ ++ l+  +ek     ++g +++   +i+y + +++a ++   ++ +l+   +   + ++
  gi|330507975|ref|YP_004384403.1| 357 RGEVVGILGPNGIGKSTYIKILA-GVEKP----TTGSFESQ-LKISYKPqYLKADTE-LTVEGMLRGltH-GFDSSY 425
                                       558999*************8888.79999....77777776.666676655555533.444444444432.225555 PP

                            AAA_16  97 wrekleeala.....................................avpelagaeasrllellkrllallsrderp 136
                                       +++++++ ++                                     ++++l+ +++   + +++r++   +++e+ 
  gi|330507975|ref|YP_004384403.1| 426 YQAEILRPMGieplldkilselsggelqrvaitaclsreadlylldePSAHLDVEQRMLAAKVMRRFA---ESTEK- 498
                                       56656655556666666555555777777777777778888887766666666665555555666665...55455. PP

                            AAA_16 137 lvlvlD 142
                                       +vlv+D
  gi|330507975|ref|YP_004384403.1| 499 TVLVVD 504
                                       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 ?    0.7   1.5       1.5     8e+02      33      49 ..       6      25 ..       1      27 [. 0.73
   2 !   21.4   0.4   5.3e-07   0.00029       2      26 ..      48      72 ..      47      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.5
                            Fer4_7 33 idpekCl..gCga.CvavCP 49
                                      i+ ++C+   C + C+  CP
  gi|330507975|ref|YP_004384403.1|  6 INRDRCQprKCSKeCEYFCP 25
                                      56788864468777999998 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 5.3e-07
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenek 26
                                      C+gCg Cv+ Cp +ai++++  +e 
  gi|330507975|ref|YP_004384403.1| 48 CVGCGICVRKCPFGAITITNLPEEM 72
                                      *****************99764443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0024       1.3      20      40 ..      96     116 ..      84     135 .. 0.87
   2 !    9.1   0.1    0.0032       1.7      21      37 ..     360     376 ..     341     390 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0024
                            AAA_23  20 gltlItGpNGaGKTTildAik 40 
                                        +t + GpNG GK+T +  + 
  gi|330507975|ref|YP_004384403.1|  96 RVTGLLGPNGIGKSTAISILS 116
                                       68999**********997665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0032
                            AAA_23  21 ltlItGpNGaGKTTild 37 
                                       ++ I GpNG GK+T + 
  gi|330507975|ref|YP_004384403.1| 360 VVGILGPNGIGKSTYIK 376
                                       678***********886 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0025       1.3      24      50 ..      96     122 ..      87     170 .. 0.77
   2 ?    4.6   0.0     0.041        22      28      43 ..     363     378 ..     346     411 .. 0.87
   3 ?    2.5   0.0      0.18        96     324     365 ..     465     506 ..     458     510 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0025
                            AAA_15  24 eltvliGkNnsGKSsilealdlFlnnk 50 
                                        +t l G+N++GKS+++ +l  +l  +
  gi|330507975|ref|YP_004384403.1|  96 RVTGLLGPNGIGKSTAISILSGILRPN 122
                                       588999*************98777765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.041
                            AAA_15  28 liGkNnsGKSsileal 43 
                                       + G+N++GKS+ +++l
  gi|330507975|ref|YP_004384403.1| 363 ILGPNGIGKSTYIKIL 378
                                       78***********998 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.18
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                        +++l++EP ahL  ++ +  +k +++ a+++++ v++  H 
  gi|330507975|ref|YP_004384403.1| 465 ADLYLLDEPSAHLDVEQRMLAAKVMRRFAESTEKTVLVVDHD 506
                                       689***************************999777776665 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   6.4   2.2e-06    0.0012       1      58 [.       4      64 ..       4      65 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-06
                           Fer4_21  1 AridedkCi..gCgk.CliaCe..dtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      A+i++d+C   +C k C   C+   t+ + i +++ +   ++e+ CvGC +C+  CP  ++i+
  gi|330507975|ref|YP_004384403.1|  4 AIINRDRCQprKCSKeCEYFCPpvRTGDETIVFADGKP-LITENLCVGCGICVRKCPF-GAIT 64
                                      78999999533565447777763346777777764443.56799*************7.9987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   2.4      0.32   1.8e+02       3      21 ..       4      25 ..       2      26 .. 0.80
   2 !   17.1   1.7   7.9e-06    0.0043       3      21 ..      41      59 ..      39      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.32
                            Fer4_2  3 vvvdtdrC.ig.Cg.aCvsaCP 21
                                      + +++drC  + C+  C   CP
  gi|330507975|ref|YP_004384403.1|  4 AIINRDRCqPRkCSkECEYFCP 25
                                      56899***65679669*999*9 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 7.9e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      + + ++ C+gCg+Cv  CP
  gi|330507975|ref|YP_004384403.1| 41 PLITENLCVGCGICVRKCP 59
                                      6677899************ 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  12.3    0.0011      0.62       2      56 .]       4      59 ..       3      59 .. 0.81
   2 !   16.7   1.0     1e-05    0.0057       3      34 ..      42      73 ..      40      88 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                           Fer4_10  2 vvidddtC..irCg.kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      ++i++d+C   +C  +C  +CP    + g + +   +++  +    C gcg Cv++CP
  gi|330507975|ref|YP_004384403.1|  4 AIINRDRCqpRKCSkECEYFCPP--VRTGDETIVFADGKPLITENLCVGCGICVRKCP 59
                                      6899****77699889*******..556666666666666777788***********9 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1e-05
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgease 34
                                       i ++ C++Cg Cv+ CP+ + +  + +e++e
  gi|330507975|ref|YP_004384403.1| 42 LITENLCVGCGICVRKCPFGAITITNLPEEME 73
                                      678899*************7744444444444 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0029       1.6      30      83 ..      96     147 ..      91     194 .. 0.67
   2 !    6.0   0.1    0.0096       5.2      28      49 ..     357     378 ..     345     383 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0029
                                       EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------ CS
                              MeaB  30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRl 83 
                                       +v Gl G  G Gkst+++ l   lr +  + a  + + + ++  GsilGD l+ 
  gi|330507975|ref|YP_004384403.1|  96 RVTGLLGPNGIGKSTAISILSGILRPNLGKDA--SWEEALQRFSGSILGDYLKK 147
                                       5789******************9998766665..46788899999999997763 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0096
                                       -SEEEEEEE-TTSSHHHHHHHH CS
                              MeaB  28 raqvvGltGvPGaGkstlveal 49 
                                       r +vvG+ G  G Gkst ++ l
  gi|330507975|ref|YP_004384403.1| 357 RGEVVGILGPNGIGKSTYIKIL 378
                                       7899**************9876 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 ?   16.3   0.4   2.5e-05     0.014       2      20 ..      48      66 ..      47      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.5e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++Cg C+  CP +ai+ +
  gi|330507975|ref|YP_004384403.1| 48 CVGCGICVRKCPFGAITIT 66
                                      ****************865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.022        12       5      22 ..      98     115 ..      94     123 .. 0.82
   2 ?    7.7   0.1    0.0049       2.7       4      23 ..     360     381 ..     357     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.022
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                         + Gp+giGK+t ++ l
  gi|330507975|ref|YP_004384403.1|  98 TGLLGPNGIGKSTAISIL 115
                                       6799*********98866 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0049
                            AAA_24   4 kiliyGpsgiGKTtlakel..g 23 
                                        + i Gp+giGK+t +k l   
  gi|330507975|ref|YP_004384403.1| 360 VVGILGPNGIGKSTYIKILagV 381
                                       6789**********99987553 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 ?    6.7   0.0     0.016       8.7      25      47 ..     198     220 ..     179     227 .. 0.78
   2 ?    5.2   0.0     0.047        26      12      47 ..     426     461 ..     422     491 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.016
                           SbcCD_C  25 elsrssgtlSGGekqflaylala 47 
                                        ++r++++lSGGe q +a  a a
  gi|330507975|ref|YP_004384403.1| 198 LMDRDISSLSGGELQRVAIAAAA 220
                                       4899**********765544433 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.047
                           SbcCD_C  12 fevevrdedgkekelsrssgtlSGGekqflaylala 47 
                                       +++e+ ++ g e  l++  ++lSGGe q +a +a +
  gi|330507975|ref|YP_004384403.1| 426 YQAEILRPMGIEPLLDKILSELSGGELQRVAITACL 461
                                       556666777888888899999999999887766654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.044        24       3      20 ..     100     117 ..      99     135 .. 0.81
   2 ?    7.3   0.1     0.011       6.2       3      19 ..     363     379 ..     361     395 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.044
                      RNA_helicase   3 lyGpsgeGKStlakeLak 20 
                                       l Gp+g+GKSt++  L+ 
  gi|330507975|ref|YP_004384403.1| 100 LLGPNGIGKSTAISILSG 117
                                       57**********998765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.011
                      RNA_helicase   3 lyGpsgeGKStlakeLa 19 
                                       + Gp+g+GKSt++k La
  gi|330507975|ref|YP_004384403.1| 363 ILGPNGIGKSTYIKILA 379
                                       78***********9976 PP

>> Cm_res_leader  Chloramphenicol resistance gene leader peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0034       1.9       3      13 ..     279     289 ..     277     291 .. 0.92
   2 ?    1.8   0.1      0.71   3.8e+02       3      10 ..     522     529 ..     520     532 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0034
                     Cm_res_leader   3 GvPGALAvvtR 13 
                                       GvPGA  v+tR
  gi|330507975|ref|YP_004384403.1| 279 GVPGAYGVITR 289
                                       9*********9 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.71
                     Cm_res_leader   3 GvPGALAv 10 
                                       GvPG L v
  gi|330507975|ref|YP_004384403.1| 522 GVPGILGV 529
                                       9****988 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5   9.1e-05     0.049      44      58 ..      46      60 ..      37      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.1e-05
                           Fer4_17 44 slCieCgeCerkCPq 58
                                      +lC++Cg C+rkCP 
  gi|330507975|ref|YP_004384403.1| 46 NLCVGCGICVRKCPF 60
                                      689999999999996 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   2.5     0.099        54       2      15 ..       9      25 ..       8      35 .. 0.80
   2 ?   13.7   3.0   0.00013     0.069       2      17 .]      46      61 ..      45      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.099
                            Fer4_4  2 erCi..gCgs.CvaaCP 15
                                      +rC+   C + C+++CP
  gi|330507975|ref|YP_004384403.1|  9 DRCQprKCSKeCEYFCP 25
                                      67855588866*****9 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00013
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      + C+gCg Cv+ CP+g
  gi|330507975|ref|YP_004384403.1| 46 NLCVGCGICVRKCPFG 61
                                      57************86 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 ?    4.3   0.0     0.092        50       3      22 ..     100     119 ..      98     154 .. 0.82
   2 ?    5.5   0.1      0.04        22       3      20 ..     363     380 ..     361     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.092
                                       EESSTTSSHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel 22 
                                       l Gp G+GK+++++ +   l
  gi|330507975|ref|YP_004384403.1| 100 LLGPNGIGKSTAISILSGIL 119
                                       78**********99887665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.04
                                       EESSTTSSHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavak 20 
                                       + Gp G+GK++ +k +a 
  gi|330507975|ref|YP_004384403.1| 363 ILGPNGIGKSTYIKILAG 380
                                       67************9996 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.062        34      19      42 ..      96     119 ..      92     128 .. 0.83
   2 ?    4.7   0.2     0.039        21      16      42 ..     357     382 ..     348     506 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.062
                            AAA_30  19 rvavltGpAGtGKttalkalreaw 42 
                                       rv+ l Gp G GK+ta++ l  ++
  gi|330507975|ref|YP_004384403.1|  96 RVTGLLGPNGIGKSTAISILSGIL 119
                                       68999************9887666 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.039
                            AAA_30  16 sgdrvavltGpAGtGKttalkalreaw 42 
                                        g  v+ + Gp G GK+t +k l+ + 
  gi|330507975|ref|YP_004384403.1| 357 RG-EVVGILGPNGIGKSTYIKILAGVE 382
                                       44.489999***********9987665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.76   4.1e+02       3      19 ..      96     112 ..      94     123 .. 0.85
   2 ?    1.4   0.0      0.56     3e+02      63      86 ..     222     245 ..     196     260 .. 0.73
   3 ?    5.6   0.0     0.029        16       3      24 ..     359     380 ..     357     416 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.76
                            AAA_14   3 kilvitGaRrvGKTtll 19 
                                       ++  + G+  +GK+t +
  gi|330507975|ref|YP_004384403.1|  96 RVTGLLGPNGIGKSTAI 112
                                       678899*********87 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.56
                            AAA_14  63 ekktylflDEiqevpewekalksl 86 
                                       ++  + f+DEi+ + ++ + ++s 
  gi|330507975|ref|YP_004384403.1| 222 KDADFYFFDEISPYLDIHQRINSA 245
                                       467899*****9998887777764 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.029
                            AAA_14   3 kilvitGaRrvGKTtllkqlik 24 
                                       +++ i G+  +GK+t++k l+ 
  gi|330507975|ref|YP_004384403.1| 359 EVVGILGPNGIGKSTYIKILAG 380
                                       7899************998874 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.12        66       3      33 ..     100     146 ..      99     181 .. 0.73
   2 ?    3.6   0.1      0.17        90       1      19 [.     361     379 ..     361     420 .. 0.88
   3 ?    2.2   0.0      0.47   2.5e+02      31     119 ..     461     571 ..     440     580 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.12
                            AAA_18   3 ltGtpGvGKttlakeLskrl.gf...............gvnlrdvak 33 
                                       l G+ G GK+t    Ls  l  +               g +l+d++k
  gi|330507975|ref|YP_004384403.1| 100 LLGPNGIGKSTAISILSGILrPNlgkdasweealqrfsGSILGDYLK 146
                                       78**************7665433455555555555667444444444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.17
                            AAA_18   1 IlltGtpGvGKttlakeLs 19 
                                       +++ G+ G GK+t  k L+
  gi|330507975|ref|YP_004384403.1| 361 VGILGPNGIGKSTYIKILA 379
                                       6899***********9995 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.47
                            AAA_18  31 vakenglllevdpealdeskrldedkldklldaleenss.............aleegknlvidghlaeleseaakdi 94 
                                       + +e +l+l ++p      ++++++  +k+++ + e+ +             +l ++   v+dg+++ l  +     
  gi|330507975|ref|YP_004384403.1| 461 LSREADLYLLDEPS--AHLDVEQRMLAAKVMRRFAESTEktvlvvdhdiyliDLLSERLMVFDGVPGILGVAHTPLE 535
                                       55667777777777..6777777777777888888876666655555555554444555555555555553322222 PP

                            AAA_18  95 kk...........vvLtaspeelleRlekRgyeeak 119
                                        +           +  + ++e+++ R++k + + ++
  gi|330507975|ref|YP_004384403.1| 536 MRegmnaflkgigITFRRDEETRRPRVNKPESRLDR 571
                                       224666666667777777777777777776655555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.22   1.2e+02       4      20 ..     100     116 ..      99     137 .. 0.84
   2 ?   -2.1   0.0       7.4     4e+03      59      79 ..     210     230 ..     188     234 .. 0.71
   3 ?    5.0   0.1     0.047        26       4      21 ..     363     380 ..     360     392 .. 0.84
   4 ?   -0.5   0.0       2.4   1.3e+03      51      82 ..     475     507 ..     449     518 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.22
                            AAA_28   4 itGgestGKTtlleaLa 20 
                                       ++G+ + GK+t ++ L+
  gi|330507975|ref|YP_004384403.1| 100 LLGPNGIGKSTAISILS 116
                                       68***********9997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.4
                            AAA_28  59 vleeqleeeaaaaankvlfcD 79 
                                        l+  + ++aaa++ +++f+D
  gi|330507975|ref|YP_004384403.1| 210 ELQRVAIAAAAAKDADFYFFD 230
                                       455555556666999999999 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.047
                            AAA_28   4 itGgestGKTtlleaLaa 21 
                                       i+G+ + GK+t ++ La 
  gi|330507975|ref|YP_004384403.1| 363 ILGPNGIGKSTYIKILAG 380
                                       99*************994 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.4
                            AAA_28  51 dllafaervleeql.eeeaaaaankvlfcDrgl 82 
                                         l++++r+l++++ ++ a+ +++ vl++D ++
  gi|330507975|ref|YP_004384403.1| 475 AHLDVEQRMLAAKVmRRFAESTEKTVLVVDHDI 507
                                       456777888887764667777888888888776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.31   1.7e+02       3      21 ..      99     117 ..      97     133 .. 0.84
   2 ?    6.2   0.2     0.019        10       2      22 ..     361     381 ..     360     518 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.31
                                       EEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltg 21 
                                       +++G    GKSt i+ l+g
  gi|330507975|ref|YP_004384403.1|  99 GLLGPNGIGKSTAISILSG 117
                                       789999********99987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.019
                                       EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                       v+i+G    GKSt i+ l g 
  gi|330507975|ref|YP_004384403.1| 361 VGILGPNGIGKSTYIKILAGV 381
                                       89**************99983 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.12        67      32      51 ..      94     113 ..      89     119 .. 0.86
   2 ?   -3.2   0.0       9.4   5.1e+03     130     157 ..     211     238 ..     195     266 .. 0.60
   3 ?    4.5   0.0     0.041        22      28      49 ..     353     374 ..     347     380 .. 0.91
   4 ?    0.1   0.0      0.94   5.1e+02     169     188 ..     486     505 ..     464     506 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.12
                            AAA_25  32 agelallaGapgtGKttlal 51 
                                       +g ++ l G+ g GK+t+ +
  gi|330507975|ref|YP_004384403.1|  94 EGRVTGLLGPNGIGKSTAIS 113
                                       789999***********876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.4
                            AAA_25 130 vdaleaaieevegvrlvviDplsralgg 157
                                       +++++ a+ +++++++  +D +s  l+ 
  gi|330507975|ref|YP_004384403.1| 211 LQRVAIAAAAAKDADFYFFDEISPYLDI 238
                                       4555555555567777777777766665 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.041
                            AAA_25  28 gllpagelallaGapgtGKttl 49 
                                       g++++ge++ + G+ g GK+t 
  gi|330507975|ref|YP_004384403.1| 353 GIIRRGEVVGILGPNGIGKSTY 374
                                       899*****************95 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.94
                            AAA_25 169 vealeriarrtgaavllvhH 188
                                        + ++r+a+ t  +vl+v H
  gi|330507975|ref|YP_004384403.1| 486 AKVMRRFAESTEKTVLVVDH 505
                                       4568999***********99 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.19     1e+02       5      23 ..     101     119 ..      97     123 .. 0.81
   2 ?    0.7   0.0      0.79   4.3e+02      83     135 ..     213     264 ..     189     278 .. 0.73
   3 ?    3.3   0.2      0.13        70       2      19 ..     361     378 ..     360     385 .. 0.83
   4 ?   -2.2   0.0       6.1   3.3e+03      94     122 ..     463     492 ..     448     518 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.19
                                       E--TTSSHHHHHHHHHHHH CS
                          NTPase_1   5 TGppGvGKtTlvkkvlell 23 
                                        Gp G+GK+T ++ ++  l
  gi|330507975|ref|YP_004384403.1| 101 LGPNGIGKSTAISILSGIL 119
                                       59*********98777665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.79
                                       HHHHHHHHHHHHHH-EEEE---ST.TGGG-HHHHHHHHHHHTTTSEEEEE--SS CS
                          NTPase_1  83 elalealrkalseadviviDEiGk.mElkskkfkeaveevLksekpvlavihrr 135
                                       ++a++a   a ++ad +  DEi + +    +  +  + + L+++k v++v h  
  gi|330507975|ref|YP_004384403.1| 213 RVAIAAA--AAKDADFYFFDEISPyLDIHQRINSARILQSLAKDKAVMVVEHDL 264
                                       4444444..4589999******98345555555567999999999887776654 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.13
                                       EEEE--TTSSHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkv 19 
                                       v i Gp G+GK+T +k +
  gi|330507975|ref|YP_004384403.1| 361 VGILGPNGIGKSTYIKIL 378
                                       5688*********99865 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 6.1
                                       HHH-EEEE---.STTGGG-HHHHHHHHHHH CS
                          NTPase_1  94 seadviviDEi.GkmElkskkfkeaveevL 122
                                       +ead++++DE    + ++ + ++ +v + +
  gi|330507975|ref|YP_004384403.1| 463 READLYLLDEPsAHLDVEQRMLAAKVMRRF 492
                                       677888888731345555555444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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):              33  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.43
# Mc/sec: 4057.26
//
Query:       gi|330507976|ref|YP_004384404.1|  [L=144]
Description: hypothetical protein MCON_2030 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.75    9.3   2.8         14    5.1   0.1    2.1  2  L6_membrane  L6 membrane protein


Domain annotation for each model (and alignments):
>> L6_membrane  L6 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1   0.00081        14      78     106 ..      48      76 ..      38      82 .. 0.83
   2 ?    4.4   0.5    0.0014        25     154     172 ..      89     107 ..      78     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.00081
                       L6_membrane  78 cgnrckmllsillavlgvlGalyclvvsa 106
                                         +r +++ ++++a+lgvl+++ c  ++ 
  gi|330507976|ref|YP_004384404.1|  48 KDRRDGIVKTVFAAALGVLAGFACYYIAS 76 
                                       4577889999**************99986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0014
                       L6_membrane 154 ewhltlFsiLllvsllell 172
                                       +wh++l+s++l++sl + +
  gi|330507976|ref|YP_004384404.1|  89 PWHFILLSVILVTSLFQRV 107
                                       7*************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1021.48
//
Query:       gi|330507977|ref|YP_004384405.1|  [L=143]
Description: hypothetical protein MCON_2031 [Methanosaeta concilii GP6]
Scores for complete 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   0.2    6.3e-14   52.3   0.2    1.2  1  PIN_6           PIN domain of ribonuclease
    0.00093   19.2   0.1     0.0012   18.8   0.1    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0028   17.1   0.2     0.0064   15.9   0.1    1.5  1  PIN_5           PINc domain ribonuclease
      0.004   17.7   1.3     0.0056   17.2   1.3    1.2  1  PIN             PIN domain
     0.0076   16.2   4.5      0.012   15.5   4.5    1.3  1  Prok-RING_1     Prokaryotic RING finger family 1
  ------ inclusion threshold ------
      0.028   14.4   2.5      0.041   13.9   2.5    1.3  1  zinc-ribbons_6  zinc-ribbons
       0.04   14.0   6.8       0.11   12.6   6.8    1.8  1  Zn-ribbon_8     Zinc ribbon domain
      0.067   13.2   4.3       0.11   12.5   4.3    1.3  1  DZR             Double zinc ribbon
       0.21   11.8   3.6       0.41   10.9   3.6    1.5  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like


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 !   52.3   0.2   3.1e-17   6.3e-14      22      88 ..      11      75 ..       6      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 3.1e-17
                             PIN_6 22 klyttpeVvaEirdkkarerlellplelevrePspesvkkvtefakktGDlsvLSktDievlALtye 88
                                      +l+t+p+V aE++d +ar+rl++  +e +v++P++ ++k+++++a++tGD+++LS++D+evlA ++e
  gi|330507977|ref|YP_004384405.1| 11 ELITVPAVEAELKDIRARSRLHI--YETRVESPTTIALKAARDAAEQTGDIRSLSAADLEVLAKALE 75
                                      789******************99..89************************************9876 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   6.1e-07    0.0012      38      95 ..      68     134 ..      34     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.1e-07
                                       T--HHHHHHHHHHHHCC.TTTT-EEE.............EEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  38 gvepeaLefafellaegtvlegaeLe.............ieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       +v  +aLe+  +l++++ +l++  L+              +e + + rC+ Cg++fe e     Cp+Cg+ 
  gi|330507977|ref|YP_004384405.1|  68 EVLAKALEYNATLATDDYALQNVALHlglkiepigqpriKKERKYVQRCQGCGQRFEGE----ACPDCGTP 134
                                       45667777777788888889999999999999999999666788999**********76....7****986 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   3.2e-06    0.0064     156     191 ..      63      98 ..      59     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.2e-06
                             PIN_5 156 saeDldvllLAkELdaavvssDeGikkwaeklGlrl 191
                                       sa Dl+vl  A E +a++ ++D  ++++a +lGl++
  gi|330507977|ref|YP_004384405.1|  63 SAADLEVLAKALEYNATLATDDYALQNVALHLGLKI 98 
                                       899*******************************96 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.3   2.8e-06    0.0056      54     120 ..      22      91 ..       9      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.8e-06
                                       HHHHHHHHHHHHHTSEEEEBCHHHHHHHHHHHHHHH....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  54 kaaelvelllllsalkilpidaeiaeeaaeialkyg....llpnDaliaAtAkehgikliatfDedfrrva 120
                                       +++ + +++l   ++++ + ++ +++ a++ a++ g    l+++D+ ++A A+e++++l  t D  + +va
  gi|330507977|ref|YP_004384405.1|  22 LKDIRARSRLHIYETRVESPTTIALKAARDAAEQTGdirsLSAADLEVLAKALEYNATLA-TDDYALQNVA 91 
                                       344444555559999999999999999999999999*********************999.***9998876 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 !   15.5   4.5     6e-06     0.012       4      31 ..     113     136 ..     110     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6e-06
                       Prok-RING_1   4 gkkCpvCgkelkeedDiVvCpeCgtpyH 31 
                                        ++C+ Cg++++ e     Cp+Cgtp  
  gi|330507977|ref|YP_004384405.1| 113 VQRCQGCGQRFEGE----ACPDCGTPAR 136
                                       689***********....9*******65 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.5     2e-05     0.041      12      45 ..     109     141 ..     100     143 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                                       E-SSEEE-TTT--EEEEEEE-SSS-S---EEEET CS
                    zinc-ribbons_6  12 krgeqyhCeaCqedlkkealCpeCeqelevlkaC 45 
                                       +r+   +C+ C ++++ e  Cp+C+ +  + k C
  gi|330507977|ref|YP_004384405.1| 109 ERKYVQRCQGCGQRFEGE-ACPDCGTPARKKKRC 141
                                       4445679********987.5**********9999 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   6.8   5.7e-05      0.11       7      38 ..     115     137 ..     111     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-05
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgsevrr 38 
                                       rC+ Cg++fe          +aCP+Cg ++r+
  gi|330507977|ref|YP_004384405.1| 115 RCQGCGQRFE---------GEACPDCGTPARK 137
                                       8*********.........667******9998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   4.3   5.7e-05      0.11      13      43 ..     114     140 ..     105     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                               DZR  13 rfCseCgtklkavaaedrCpsCgekvdpear 43 
                                       + C+ Cg++ +     ++Cp Cg+++ +++r
  gi|330507977|ref|YP_004384405.1| 114 QRCQGCGQRFE----GEACPDCGTPARKKKR 140
                                       56********9....8*********998865 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   3.6    0.0002      0.41       1      33 [.     106     135 ..     106     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                      NOB1_Zn_bind   1 ikrvkswvlrChaCfkvtkdmtkkFCpkCGnkt 33 
                                       ik+ +++v rC++C + ++    + Cp CG + 
  gi|330507977|ref|YP_004384405.1| 106 IKKERKYVQRCQGCGQRFEG---EACPDCGTPA 135
                                       8999**********997665...55*****875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1037.22
//
Query:       gi|330507978|ref|YP_004384406.1|  [L=205]
Description: phosphoribosyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-23   80.8   0.9    1.1e-22   80.3   0.9    1.1  1  Pribosyltran    Phosphoribosyl transferase domain
    2.6e-05   23.8   0.1    3.5e-05   23.4   0.1    1.3  1  UPRTase         Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.012   15.7   0.1      0.025   14.6   0.1    1.6  2  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
      0.037   14.5   0.1       0.09   13.2   0.1    1.7  1  CBS             CBS domain
      0.037   13.5   0.5       0.11   11.9   0.2    1.7  2  PRTase_2        Phosphoribosyl transferase
      0.056   13.0   0.0       0.18   11.3   0.0    1.9  1  GerE            Bacterial regulatory proteins, luxR family
       0.11   12.4   0.0       0.36   10.8   0.0    1.9  1  Tautomerase     Tautomerase enzyme


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 !   80.3   0.9   4.3e-26   1.1e-22      11     132 ..      71     190 ..      63     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 4.3e-26
                                       EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TT CS
                      Pribosyltran  11 ildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpag 87 
                                       i++a  ++++e+l+ ++ + dvvvgia  G+p+a+ +a+ L ++la+   +k    + ++ a+g+  +  + +d+ +
  gi|330507978|ref|YP_004384406.1|  71 ISEAMTDIIYETLDANESSVDVVVGIALSGLPIASMVANDLAAELAVYTPSKQMIAQENKRAKGNLSS--NFSDVQD 145
                                       6779999***************************************7777776666666666666554..******* PP

                                       SEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHH CS
                      Pribosyltran  88 kkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateee 132
                                       k ++iVDD++++G+Tl++a+e L e+g+ +  iavl+dk+ tee 
  gi|330507978|ref|YP_004384406.1| 146 KDCIIVDDVVTSGQTLEEAVEYLDEHGARINAIAVLIDKKGTEEI 190
                                       ****************************************99875 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   1.4e-08   3.5e-05     117     170 ..     141     191 ..      72     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.4e-08
                           UPRTase 117 kkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrla 170
                                       ++++++  +++D v+ +G+++ +a++ L e+g+   +I  ++vl  ++g +++a
  gi|330507978|ref|YP_004384406.1| 141 SDVQDKDCIIVDDVVTSGQTLEEAVEYLDEHGA---RINAIAVLIDKKGTEEIA 191
                                       3458889***********************997...688888888888887775 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   0.0       1.8   4.5e+03     156     180 ..      52      76 ..      13      79 .. 0.67
   2 ?   14.6   0.1   9.6e-06     0.025      71     114 ..     132     175 ..     108     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.8
                                       TEEEE--HHHHHHHHHHHHHT---T CS
                    Pribosyl_synth 156 kiktvdislllaeairrihngesms 180
                                       k  +vd s +   a r  h  e+m+
  gi|330507978|ref|YP_004384406.1|  52 KDISVDWSAIGRSAFRLNHISEAMT 76 
                                       4456677777777777777777776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9.6e-06
                                       ------.EES--TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EE CS
                    Pribosyl_synth  71 ekpplt.vvGdvgGriaiivddliddvesfvaaaevlkerGayki 114
                                        k  l+    dv+ +  iivdd++   +++ +a e l e+Ga  i
  gi|330507978|ref|YP_004384406.1| 132 AKGNLSsNFSDVQDKDCIIVDDVVTSGQTLEEAVEYLDEHGAR-I 175
                                       5555541468*******************************94.4 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.5e-05      0.09       7      44 ..     146     192 ..     140     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.5e-05
                                       SSCE....EEETTSBHHHHHHHHHHHT..SSEEEE.EETTT..BEEE CS
                               CBS   7 rdvv....tvppdttleealelmrekg..vsrlPV.Vdedg..klvG 44 
                                       +d +    +v+  +tleea+e + e+g  ++++ V +d+ g  ++ G
  gi|330507978|ref|YP_004384406.1| 146 KDCIivddVVTSGQTLEEAVEYLDEHGarINAIAVlIDKKGteEIAG 192
                                       5555556689999**********999999****99569988655777 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.4     1e+03      38      81 ..      74     117 ..      61     135 .. 0.64
   2 ?   11.9   0.2   4.4e-05      0.11     120     160 ..     144     183 ..     134     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.4
                          PRTase_2  38 aLaellaeakkeelpepvlvigfAEtAtaLghgvadaleeealy 81 
                                       a+++ ++e+ +++ ++  +v+g+A     ++  va+ l++e  +
  gi|330507978|ref|YP_004384406.1|  74 AMTDIIYETLDANESSVDVVVGIALSGLPIASMVANDLAAELAV 117
                                       44555554444555666678888888888888888888443333 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.4e-05
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklpr.kryvvvslvd 160
                                       ++k  ++vDD +++G+t+ + ++ l e+  r +   ++ l+d
  gi|330507978|ref|YP_004384406.1| 144 QDKDCIIVDDVVTSGQTLEEAVEYLDEHGARiNA--IAVLID 183
                                       567899********************99888443..444555 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.2e-05      0.18      14      38 ..      15      39 ..      12      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.2e-05
                                      HCTTS-HHHHHHHHTS-HHHHHHHH CS
                              GerE 14 laeGksnkeIAeelniSekTVkvhk 38
                                       aeG+   +I+eeln+S +TV+  +
  gi|330507978|ref|YP_004384406.1| 15 KAEGLVEGQISEELNVSGETVTWLL 39
                                      5899999**************8655 PP

>> Tautomerase  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00014      0.36      10      42 ..      62      94 ..      60      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                      CS-HHHHHHHHHHHHHHHHHHHTS-GGG-EEEE CS
                       Tautomerase 10 grsaeqKaeLaervTealvealgaprsaivVvi 42
                                      grsa ++  + e+ T+++ e+l+a++s++ Vv+
  gi|330507978|ref|YP_004384406.1| 62 GRSAFRLNHISEAMTDIIYETLDANESSVDVVV 94
                                      6777788899*******************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1418.05
//
Query:       gi|330507979|ref|YP_004384407.1|  [L=909]
Description: alanyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete 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-120  402.5   0.0     4e-120  401.9   0.0    1.3  1  tRNA-synt_2c  tRNA synthetases class II (A)
    1.3e-20   74.2   6.4    2.5e-20   73.3   6.4    1.5  1  DHHA1         DHHA1 domain
    2.8e-14   52.9   1.0    6.3e-14   51.8   1.0    1.7  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
     0.0099   15.8   0.6        1.7    8.5   0.1    2.6  3  PhaP_Bmeg     Polyhydroxyalkanoic acid inclusion protein (Pha


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 !  401.9   0.0    9e-124    4e-120       1     550 [.      63     591 ..      63     593 .. 0.94

  Alignments for each domain:
  == domain 1  score: 401.9 bits;  conditional E-value: 9e-124
                                       HHHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTT CS
                      tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVG 77 
                                       e+re++l fFe++gHt++k+++v +++++++++++A++a+f+p++++++  p+++++++sQ+ciR++    Dl++VG
  gi|330507979|ref|YP_004384407.1|  63 EMREHYLGFFEARGHTRIKRYPVAARWRDDIYLTIASIADFQPFVTSGQVPPPANPLTISQPCIRLD----DLDSVG 135
                                       89*****************************************************************....****** PP

                                       TSSS--SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGE CS
                      tRNA-synt_2c  78 ktarHhTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeeri 147
                                       + +rH+T FeM++++ f+     +Y+k+ ++ ++ ell   lg+d+  ++++++++++  +a++  e +vg+ e ++
  gi|330507979|ref|YP_004384407.1| 136 RSGRHLTTFEMMAHHVFNtpdreIYWKDRTVRLCDELLV-GLGMDPLAVTYKENPWAGggNAGPSVEVMVGGLELAT 211
                                       ***************************************.9****************999***************** PP

                                       EEE-HH......HHEEESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEEST....TSHE CS
                      tRNA-synt_2c 148 lrfgek......dnfwemgdtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnree....dgtl 214
                                       l+f ++         +  g+ +++++++++++++g e++++++++ ++++d+++ +++  v   +++e+     +  
  gi|330507979|ref|YP_004384407.1| 212 LVF-MDlvaapaGAVEIKGERYEKMKNYIVDTGYGLERFVWASNGAPTIYDAIFPDLVRQVADLAGVEHnlddPEYA 287
                                       ***.33344444444555666***********************************999999999888866656788 PP

                                       EEEEEEEEEEEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT-- CS
                      tRNA-synt_2c 215 kpLpkksidtGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvv 291
                                       ++ +++++ +Gm +   +  + ++r + + ++++    +++ i +         +e+++++ DH+r+la++l+dG++
  gi|330507979|ref|YP_004384407.1| 288 EIFAQNARLAGMVDLDEY-SMSDLRAKIAGSIGIDPGRLEKAILP---------MERVYAVVDHTRCLAYMLGDGII 354
                                       999*********988766.5899**********************.........899******************** PP

                                       SSSSHHHHHHHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHH CS
                      tRNA-synt_2c 292 psnegrgYvlRrllRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlkl 368
                                       psn++ gY+ R+++Rr++r++k+Lgl+ + la+lv+++++ l+  yp+ +e+ +++++i+++Ee+++a+Tle+G++l
  gi|330507979|ref|YP_004384407.1| 355 PSNVKGGYLSRLVIRRTLRLMKELGLRLP-LADLVQLQISRLD--YPDWEESFATIRDILDQEEQKYAETLEKGMRL 428
                                       *****************************.************9..******************************** PP

                                       HHHHHHHCCC.CSEEXHHHHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXX CS
                      tRNA-synt_2c 369 leelikklkk.kkelsgedafkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvea 444
                                       +++++++  k ++ +++++++ Lydt+G+P+++ +e a + g++v+ ++++++++++++   + ++ekk        
  gi|330507979|ref|YP_004384407.1| 429 VRKTAESYLKkNEPVPLSEMIALYDTHGIPPEIAREAAVQMGAQVELPDNFYSLVAKKHIRAEPEEEKK-------- 497
                                       ****9986554999*********************************************9966655555........ PP

                                       TTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEE CS
                      tRNA-synt_2c 445 lkelkkteeflgyeeleaeakvlallkdkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvq 521
                                          ++ ++e l+ye+            ++ef++ev  + e++ +LdrT +Y+e+GGq +D+G++ek+g+ f+v+dvq
  gi|330507979|ref|YP_004384407.1| 498 -PPIPGKTELLFYEN----------PFEQEFEAEVLDVVEGAAILDRTLLYPEGGGQPADHGTLEKDGQLFQVTDVQ 563
                                       .788999999*****..........6679************************************************ PP

                                       EETTEEEEEXSS.XSXXXTTSEEEEEEXH CS
                      tRNA-synt_2c 522 kakgvvlhkgkleegklkvgdkvkaevde 550
                                       k + vvlhk     g+l +gd+vk++vd 
  gi|330507979|ref|YP_004384407.1| 564 KSGDVVLHKLAEP-GCLAKGDRVKGKVDM 591
                                       **********987.*************96 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   6.4   5.5e-24   2.5e-20       2     138 .]     771     905 ..     770     905 .. 0.87

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 5.5e-24
                                       HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEE CS
                             DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvake 78 
                                       e++ ee+ke +ke+e+lke la++  ++l+++ae+++g  v+v+++  ++d + l  aa  l +  ++ v+++ +k 
  gi|330507979|ref|YP_004384407.1| 771 ERFFEEWKEQQKEIERLKEDLAAARLKTLVSEAETIDGLRVIVQKM-GNADIDELLKAAALLAE--EDCVALLGSKT 844
                                       6789******************************************.*****************..66666555554 PP

                                       ECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHHHHHHHH CS
                             DHHA1  79 egdkvkvsarskkd....gvdagelakeaaaklgggGGGH.dlAaGagipaekleealealeeai 138
                                        g   k++a++ ++    gv+ag ++k+aa+ lgggGGG+  lA+G+g + e+leeal+a +eai
  gi|330507979|ref|YP_004384407.1| 845 -G---KLVAAVGQSglskGVKAGSIIKAAAKVLGGGGGGRpQLAQGGGPDTERLEEALAAGKEAI 905
                                       .4...3333333333469****************************************9988876 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 !   51.8   1.0   1.4e-17   6.3e-14       1      44 []     692     734 ..     692     734 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.4e-17
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +rvv++G+ ++e+C GtHv nTg+Ig +kil+ e++++g+ R++
  gi|330507979|ref|YP_004384407.1| 692 IRVVRVGS-DIEACAGTHVTNTGMIGMIKILRAERVQDGVERVE 734
                                       7******8.*********************************96 PP

>> PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1   0.00039       1.7      16      52 ..     399     435 ..     396     442 .. 0.92
   2 ?   -3.2   0.0       1.6   7.1e+03     112     139 ..     585     612 ..     584     614 .. 0.86
   3 !    4.7   0.1    0.0058        26      11      56 ..     771     816 ..     762     849 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00039
                         PhaP_Bmeg  16 qweeslerfaslskqvEqltLkalkqqqdlvkeltka 52 
                                       +wees+ ++ ++ +q Eq + ++l++   lv+++ ++
  gi|330507979|ref|YP_004384407.1| 399 DWEESFATIRDILDQEEQKYAETLEKGMRLVRKTAES 435
                                       7******************************998875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                         PhaP_Bmeg 112 sKssldllkkaeeqleetvkslieqqkk 139
                                       +K  +d+l +  +  + t + l+ ++ k
  gi|330507979|ref|YP_004384407.1| 585 VKGKVDMLRRLAHARHHTATHLVHDSAK 612
                                       58889********99***9999998876 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0058
                         PhaP_Bmeg  11 dafWdqweeslerfaslskqvEqltLkalkqqqdlvkeltkalsel 56 
                                       + f ++w+e  ++++ l++++  + Lk+l    + +  l+  ++++
  gi|330507979|ref|YP_004384407.1| 771 ERFFEEWKEQQKEIERLKEDLAAARLKTLVSEAETIDGLRVIVQKM 816
                                       5678888888888888888888888888888888887777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (909 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); 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: 0.77u 0.28s 00:00:01.05 Elapsed: 00:00:00.45
# Mc/sec: 6049.57
//
Query:       gi|330507980|ref|YP_004384408.1|  [L=105]
Description: hypothetical protein MCON_2034 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-23   80.9   0.1      7e-23   80.2   0.1    1.3  1  DUF433    Protein of unknown function (DUF433)


Domain annotation for each model (and alignments):
>> DUF433  Protein of unknown function (DUF433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.1   3.9e-27     7e-23       1      56 []      33      88 ..      33      88 .. 0.99

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 3.9e-27
                                      EEE-TTSGGGS-EETTT--BTHHHHHHHHTT--HHHHHHHH.TS-HHHHHHHHT.. CS
                            DUF433  1 ItidpeilgGkPvIrgtRipVetilellaaGesieeiledyPdLtlediqaalaYA 56
                                      Iti+p+i+ GkPvIrgtR++Ve il+lla+G s e ile+yP+L ++di+a l +A
  gi|330507980|ref|YP_004384408.1| 33 ITINPKIMVGKPVIRGTRLTVEYILGLLAHGISMEAILEEYPGLAKDDIYASLLFA 88
                                      9****************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 805.38
//
Query:       gi|330507981|ref|YP_004384409.1|  [L=119]
Description: hypothetical protein MCON_2035 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-22   78.4   0.0    3.6e-22   77.9   0.0    1.2  1  DUF5615   Domain of unknown function (DUF5615)
    3.3e-05   24.0   0.0    3.3e-05   24.0   0.0    1.1  1  Mut7-C    Mut7-C RNAse domain
    0.00013   22.1   0.1    0.00023   21.3   0.1    1.4  1  PIN_10    PIN like domain


Domain annotation for each model (and alignments):
>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.0     6e-26   3.6e-22       1      75 [.       1      75 [.       1      77 [. 0.96

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 6e-26
                           DUF5615  1 mklllDenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDkDFgel.lllggpppgvillr 75
                                      m++l+De++ p++v++lr+++hd+++   ++ +g++De+ile A  e+ri+vT DkDFg++ ++++ p+ g+illr
  gi|330507981|ref|YP_004384409.1|  1 MRFLVDECVGPSVVRWLRDNNHDASSA-FEDCRGWEDERILEKACTEGRIVVTMDKDFGDMiFRMKLPHRGIILLR 75
                                      9**************************.566799***************************999999999*****9 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   5.5e-09   3.3e-05       1      52 [.       1      57 [.       1      99 [. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.5e-09
                            Mut7-C  1 krfllDamlg.klakyLRllGydalyasdv....edeellalaakekrillTrdreL 52
                                      +rfl+D  +g ++ ++LR   +da  a +     ede++l++a++e+ri++T d+++
  gi|330507981|ref|YP_004384409.1|  1 MRFLVDECVGpSVVRWLRDNNHDASSAFEDcrgwEDERILEKACTEGRIVVTMDKDF 57
                                      69*****99967************9766444677********************875 PP

>> PIN_10  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   3.9e-08   0.00023       1      62 [.       1      57 [.       1      60 [. 0.89

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.9e-08
                            PIN_10  1 MkfflDenlppalakaLrelleeeghevvhlrdkfaagtkDeeWiaalaeggwvvltkDrri 62
                                      M+f++De+++p + + Lr      +h++ +   +  +g +De+ ++++  +g +v+t D+++
  gi|330507981|ref|YP_004384409.1|  1 MRFLVDECVGPSVVRWLR----DNNHDASSA-FEDCRGWEDERILEKACTEGRIVVTMDKDF 57
                                      9*****************....888887654.45689**********************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 861.63
//
Query:       gi|330507982|ref|YP_004384410.1|  [L=202]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (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  110.0   0.0    1.7e-31  109.5   0.0    1.2  1  ABC_tran       ABC transporter
      1e-10   41.9   0.0    3.6e-05   23.7   0.0    2.1  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    5.3e-09   35.8   0.0    2.2e-05   24.0   0.0    2.1  2  SMC_N          RecF/RecN/SMC N terminal domain
    0.00012   21.7   0.0    0.00021   21.0   0.0    1.4  1  AAA_29         P-loop containing region of AAA domain
    0.00028   20.9   0.2      0.088   12.7   0.1    2.2  2  NTPase_1       NTPase
    0.00043   20.2   0.1     0.0011   18.8   0.1    1.7  2  RsgA_GTPase    RsgA GTPase
     0.0017   18.1   0.5       0.63    9.7   0.0    2.1  2  AAA_15         AAA ATPase domain
     0.0043   17.3   0.6      0.078   13.3   0.0    2.6  3  AAA_22         AAA domain
      0.006   17.0   0.1     0.0095   16.3   0.1    1.7  1  AAA_16         AAA ATPase domain
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.036   14.2   0.0    1.8  1  AAA_33         AAA domain
      0.016   15.8   0.4       0.25   11.9   0.1    2.2  2  AAA_18         AAA domain
      0.021   14.6   0.0       0.29   10.8   0.0    2.0  2  AAA_24         AAA domain
      0.021   14.6   0.0       0.79    9.4   0.0    2.2  2  IstB_IS21      IstB-like ATP binding protein
      0.025   14.3   0.0      0.085   12.6   0.0    1.8  1  AAA_30         AAA domain
      0.032   13.8   0.0      0.076   12.6   0.0    1.6  2  AAA_25         AAA domain
      0.036   14.6   0.3      0.071   13.6   0.3    1.4  1  AAA_23         AAA domain
      0.042   13.9   0.0       0.14   12.2   0.0    1.9  2  MMR_HSR1       50S ribosome-binding GTPase
      0.043   13.6   0.0      0.059   13.2   0.0    1.1  1  KDGP_aldolase  KDGP aldolase
      0.066   12.4   0.0      0.074   12.2   0.0    1.1  1  G-alpha        G-protein alpha subunit
       0.12   11.5   0.0       0.37    9.9   0.0    1.7  2  NB-ARC         NB-ARC domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   0.0   1.9e-34   1.7e-31       2     136 ..       2     149 ..       1     150 [. 0.92

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 1.9e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpel 74 
                                       k ++l++++ge va++G++G+GKStLl+++  l +pt+G+ ll gkd+++    +  ++ r+e+g+++q+ +l  ++
  gi|330507982|ref|YP_004384410.1|   2 KGIDLEIENGEFVALMGPSGSGKSTLLNIIGCLDRPTSGRFLLLGKDISRtpneELARIRREEMGFIFQTFNLIARI 78 
                                       7899**********************************************988666778899*************** PP

                                       BHHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +v +n           + ++ e+a++ l+ ++++++ ++ +p+++SgG++qrva+aral+++p+++++DEpt
  gi|330507982|ref|YP_004384410.1|  79 SVLQNveipmmlrgvPRGVRRERAMKLLESINVAHR-ADFGPQNISGGERQRVAIARALANDPQIIIADEPT 149
                                       ***************888888888888888885555.47889*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.4e-06    0.0048       1      25 [.      13      37 ..      13      87 .. 0.75
   2 !   23.7   0.0   4.1e-08   3.6e-05     236     301 ..     121     183 ..      95     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.4e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                      + +l Gp gsGKS+LL ++ +l r 
  gi|330507982|ref|YP_004384410.1| 13 FVALMGPSGSGKSTLLNIIGCLDRP 37
                                      57899**************999442 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 4.1e-08
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                       ++S G ++  a++ al+ ++    +++ DEp  +L+ k   +++++l++l+++g  +i++TH+p++
  gi|330507982|ref|YP_004384410.1| 121 NISGGERQRVAIARALANDP---QIIIADEPTGNLDLKNSDEVMKILNQLHEEGRTIIMVTHNPEI 183
                                       55777777767777777777...99***************************************98 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00051      0.46      25      44 ..      12      31 ..       2      38 .. 0.84
   2 !   24.0   0.0   2.5e-08   2.2e-05     122     212 ..     107     194 ..      88     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00051
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                      +f a++Gp GSGKs ll+ i
  gi|330507982|ref|YP_004384410.1| 12 EFVALMGPSGSGKSTLLNII 31
                                      699***********998765 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 2.5e-08
                                       HHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                             SMC_N 122 evsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivisl 197
                                       e  ++ ++a++ ++++SgGe++ va+a  +A    +p  + + De   +LD kn  +v ++l++ +++   +i++++
  gi|330507982|ref|YP_004384410.1| 107 ESINVAHRADFGPQNISGGERQRVAIARALAN---DP-QIIIADEPTGNLDLKNSDEVMKILNQLHEEgRTIIMVTH 179
                                       55566678889999***********9988773...44.47899********************999885678889** PP

                                       SHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxx RF
                             SMC_N 198 reemlekadklvgvt 212
                                       + e++e+++++++++
  gi|330507982|ref|YP_004384410.1| 180 NPEITENCSRVIRLR 194
                                       *********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 !   21.0   0.0   2.3e-07   0.00021      16      39 ..       5      28 ..       1      42 [. 0.82

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.3e-07
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                      ++ei+  +++ l+GpsGsGKSTll
  gi|330507982|ref|YP_004384410.1|  5 DLEIENGEFVALMGPSGSGKSTLL 28
                                      5677755599*************9 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0      0.01       9.1       2      18 ..      14      30 ..      13      36 .. 0.85
   2 !   12.7   0.1   9.8e-05     0.088      68     152 ..     114     198 ..      99     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                                      EEEE--TTSSHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkk 18
                                      v++ Gp+G+GK+Tl++ 
  gi|330507982|ref|YP_004384410.1| 14 VALMGPSGSGKSTLLNI 30
                                      6789**********975 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 9.8e-05
                                       SSEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE--.-STTGGG.-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHH CS
                          NTPase_1  68 eprvgkyvvdvesfeelalealrkalseadviviDE.iGkmElk.skkfkeaveevLksekpvlavihrrk.dlalv 141
                                       ++ +g   +   + +++  ++ r   +++++i+ DE  G++ lk s ++ + ++++ ++++ +++v h+++ +++  
  gi|330507982|ref|YP_004384410.1| 114 RADFGPQNISGGERQRV--AIARALANDPQIIIADEpTGNLDLKnSDEVMKILNQLHEEGRTIIMVTHNPEiTENCS 188
                                       55555555554443443..344444499********88*****835566666677667************9554444 PP

                                       HHHHT-TT-EE CS
                          NTPase_1 142 eeirerkdvkv 152
                                       + ir  +d+++
  gi|330507982|ref|YP_004384410.1| 189 RVIR-LRDGRI 198
                                       4444.446665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.3e-06    0.0011      99     119 ..      10      31 ..       1      40 [. 0.84
   2 ?   -1.6   0.0       2.5   2.2e+03      57      83 ..     153     178 ..     131     192 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-06
                                       T.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinal 119
                                       + ++++l+G+SG GKStL+n +
  gi|330507982|ref|YP_004384410.1|  10 NgEFVALMGPSGSGKSTLLNII 31 
                                       44899***************86 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.5
                                       GG--HHHHHHHHHHHHHHTTSEEEE-- CS
                       RsgA_GTPase  57 Dlleeeeeleelkeelealgyevllvs 83 
                                       Dl +++e + ++ ++l++ g ++++v 
  gi|330507982|ref|YP_004384410.1| 153 DLKNSDE-VMKILNQLHEEGRTIIMVT 178
                                       5555555.6666666666666666654 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0007      0.63      17      45 ..       6      33 ..       2      79 .. 0.81
   2 !    7.1   0.1    0.0044         4     322     368 ..     138     183 ..     127     184 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0007
                            AAA_15 17 veidlsee.ltvliGkNnsGKSsilealdl 45
                                       ei+  +  +  l G+ +sGKS++l+++  
  gi|330507982|ref|YP_004384410.1|  6 LEIE--NGeFVALMGPSGSGKSTLLNIIGC 33
                                      3344..335*****************9965 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0044
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                       +++ i++ +EP  +L  ++  +++k l  l ++++  +i+ TH+p i
  gi|330507982|ref|YP_004384410.1| 138 NDPQIIIADEPTGNLDLKNSDEVMKILNQLHEEGR-TIIMVTHNPEI 183
                                       6899******************************9.9********98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   8.7e-05     0.078       4      23 ..      10      29 ..       7      33 .. 0.88
   2 ?   -0.5   0.0       1.6   1.4e+03     106     134 ..      69      98 ..      55     100 .. 0.63
   3 ?    0.8   0.0      0.62   5.6e+02      91     120 ..     136     170 ..     102     186 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.7e-05
                            AAA_22  4 tagilvvtGesGtGKTtllr 23
                                      +  +++++G+sG+GK+tll+
  gi|330507982|ref|YP_004384410.1| 10 NGEFVALMGPSGSGKSTLLN 29
                                      66799************986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                            AAA_22 106 eealeeLrsllnlsrkgvqliLvGtp.elr 134
                                        + ++ + +++ l+   +++ L G p ++r
  gi|330507982|ref|YP_004384410.1|  69 FQTFNLIARISVLQNVEIPMMLRGVPrGVR 98 
                                       34445554444446799999***9997776 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.62
                            AAA_22  91 v...ielliiDEaqh.lr...seealeeLrsllnlsr 120
                                           ++++i DE    l+   s+e+++ L +l++  +
  gi|330507982|ref|YP_004384410.1| 136 LandPQIIIADEPTGnLDlknSDEVMKILNQLHE--E 170
                                       1235568888886666766554555555555555..4 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.1e-05    0.0095      24      45 ..      11      32 ..       5     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                            AAA_16 24 pelvllsGesGvGKsslvrell 45
                                      +e v l G+sG+GKs+l++ + 
  gi|330507982|ref|YP_004384410.1| 11 GEFVALMGPSGSGKSTLLNIIG 32
                                      4789*************97554 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     4e-05     0.036       2     106 ..      14     178 ..      13     189 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4e-05
                            AAA_33   2 vllvGlpGsGKstlaerl..lkklg...avllssdt......................................... 32 
                                       v l G++GsGKstl+  +  l + +   + ll +d+                                         
  gi|330507982|ref|YP_004384410.1|  14 VALMGPSGSGKSTLLNIIgcLDRPTsgrFLLLGKDIsrtpneelarirreemgfifqtfnliarisvlqnveipmml 90 
                                       6689**********987554555557888888888877777777777777777777777777777776666666666 PP

                            AAA_33  33 ......lrrrlfgtdqqskt.......dytrvldrlyqilnelarkalsagrnvildat..nlsrrerarflklarr 94 
                                             +rr  + +  +s++        +++++   +q++ ++ar  +   + +i+d +  nl+ ++ ++++k++++
  gi|330507982|ref|YP_004384410.1|  91 rgvprgVRRERAMKLLESINvahradfGPQNISGGERQRV-AIARALANDPQIIIADEPtgNLDLKNSDEVMKILNQ 166
                                       6655553332222222222233333333333444455555.555544455555666665556666666666666666 PP

                            AAA_33  95 lgvpvrivvvet 106
                                       l+ + r +++ t
  gi|330507982|ref|YP_004384410.1| 167 LHEEGRTIIMVT 178
                                       665555555554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00027      0.25       1      18 [.      14      31 ..      14      86 .. 0.70
   2 ?    1.8   0.0      0.36   3.3e+02      47      83 ..     147     180 ..     125     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                            AAA_18  1 IlltGtpGvGKttlakeL 18
                                      ++l+G++G+GK+tl + +
  gi|330507982|ref|YP_004384410.1| 14 VALMGPSGSGKSTLLNII 31
                                      689***********9877 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.36
                            AAA_18  47 deskrldedkldklldaleenssaleegknlvidghl 83 
                                       +++  ld ++ d+++++l++     eeg ++++  h 
  gi|330507982|ref|YP_004384410.1| 147 EPTGNLDLKNSDEVMKILNQL---HEEGRTIIMVTHN 180
                                       456778888999999999997...4688888887775 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   0.00032      0.29       5      23 ..      14      39 ..      10      61 .. 0.79
   2 ?    1.7   0.0      0.21   1.8e+02     109     131 ..     158     180 ..     155     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                            AAA_24  5 iliyGpsgiGKTtlakel.......g 23
                                      ++++Gpsg+GK+tl++ +        
  gi|330507982|ref|YP_004384410.1| 14 VALMGPSGSGKSTLLNIIgcldrptS 39
                                      789***********987766554444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.21
                            AAA_24 109 eefrrllkklqelrknvifiahe 131
                                       +e++++l++l+e + ++i++ h 
  gi|330507982|ref|YP_004384410.1| 158 DEVMKILNQLHEEGRTIIMVTHN 180
                                       7999****************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 ?    9.4   0.0   0.00088      0.79      44      67 ..       8      31 ..       5      35 .. 0.86
   2 ?    2.9   0.0     0.087        78     108     148 ..     139     180 ..     120     190 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00088
                         IstB_IS21 44 iekkenivllGpsGvGKshlaial 67
                                      ie+ e ++l+GpsG GKs l   +
  gi|330507982|ref|YP_004384410.1|  8 IENGEFVALMGPSGSGKSTLLNII 31
                                      688899************986655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.087
                         IstB_IS21 108 kvdllilDdlgllpldqaeaellfeviekryerrs..iiitsn 148
                                        ++++i D+  + +ld +++ ++++++++  e     i++t n
  gi|330507982|ref|YP_004384410.1| 139 DPQIIIADE-PTGNLDLKNSDEVMKILNQLHEEGRtiIMVTHN 180
                                       456666666.5678888999999*****999865500455655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.5e-05     0.085      19     109 ..      12     161 ..       5     180 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.5e-05
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g.....grviglAptgkaAkvLaeelgieastiakllkrlk........ 81 
                                        +++l Gp G+GK+t+l+ +  + +   g     g+ i  +p+++ A+  +ee+g+  +t + +  r          
  gi|330507982|ref|YP_004384410.1|  12 EFVALMGPSGSGKSTLLNIIGCLDRPTsGrflllGKDISRTPNEELARIRREEMGFIFQTFNLIA-RISvlqnveip 87 
                                       48999*************99888777744555554445556666666666666665333332222.11112245555 PP

                            AAA_30  82 .............................................grarlepgtllivDE.agmvdtkqlaall 109
                                                                                    +ra  ++ +++i DE +g +d k+ ++++
  gi|330507982|ref|YP_004384410.1|  88 mmlrgvprgvrreramkllesinvahradfgpqnisggerqrvaiARALANDPQIIIADEpTGNLDLKNSDEVM 161
                                       55555556666666666666666666666666666666666665533333333666666644555555555544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.5e-05     0.076      31      50 ..       9      28 ..       4      33 .. 0.90
   2 ?   -2.6   0.0       3.9   3.5e+03     166     175 ..     158     167 ..     121     180 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.5e-05
                            AAA_25 31 pagelallaGapgtGKttla 50
                                        ge+++l+G++g+GK+tl+
  gi|330507982|ref|YP_004384410.1|  9 ENGEFVALMGPSGSGKSTLL 28
                                      679***************97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.9
                            AAA_25 166 galvealeri 175
                                       +++++ l+++
  gi|330507982|ref|YP_004384410.1| 158 DEVMKILNQL 167
                                       3334444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3     8e-05     0.071      18      39 ..      10      31 ..       2      34 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8e-05
                            AAA_23 18 skgltlItGpNGaGKTTildAi 39
                                      +  ++++ Gp G+GK+T+l+ i
  gi|330507982|ref|YP_004384410.1| 10 NGEFVALMGPSGSGKSTLLNII 31
                                      44678999***********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 ?   12.2   0.0   0.00016      0.14       2      19 ..      14      31 ..      13      63 .. 0.91
   2 ?   -1.0   0.0       2.1   1.8e+03      66      66 ..     163     163 ..     121     194 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                      EEEEESTTSSHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                      va++G + +GKStL+n +
  gi|330507982|ref|YP_004384410.1| 14 VALMGPSGSGKSTLLNII 31
                                      89**************76 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.1
                                       H CS
                          MMR_HSR1  66 l 66 
                                       +
  gi|330507982|ref|YP_004384410.1| 163 I 163
                                       1 PP

>> KDGP_aldolase  KDGP aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.6e-05     0.059     135     199 ..      97     165 ..      91     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.6e-05
                                       EEHHHHHHHHHHCT-.-EEEE---TTTTTHHHHHHHHHHHHHC.T-EE..EEBSS--TTTHHHHHHHHH CS
                     KDGP_aldolase 135 vsvetaiallkdmgg.ssvkffpmeGlkrleelaavakaaakk.gltl..ePtGGidldnfeeivqial 199
                                       v  e a++ll+++++ +   f p +    +   +a+a+a a++ ++++  ePtG +dl+n +e+++i  
  gi|330507982|ref|YP_004384410.1|  97 VRRERAMKLLESINVaHRADFGPQNISGGERQRVAIARALANDpQIIIadEPTGNLDLKNSDEVMKILN 165
                                       66688999999998625677877666666667788888877652455568***************9975 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   8.3e-05     0.074      26      90 ..      14     113 ..       7     200 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                                       EEEEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT....... CS
                           G-alpha  26 llllGqseSGKsTilkqlkllykkg.............fseeelatwraviqlnivrsiktilealesleselsesf 89 
                                       + l+G s+SGKsT+l+ + +l +++               +eela +r   +  i + +++i ++   ++ e+   +
  gi|330507982|ref|YP_004384410.1|  14 VALMGPSGSGKSTLLNIIGCLDRPTsgrflllgkdisrTPNEELARIRREEMGFIFQTFNLIARISVLQNVEIPM-M 89 
                                       5799******************99999999999999988888998888888888888888888777666666632.2 PP

                                       .......................H CS
                           G-alpha  90 .......................e 90 
                                                              +
  gi|330507982|ref|YP_004384410.1|  90 lrgvprgvrreramkllesinvaH 113
                                       466764433333333333223320 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00042      0.37      19      39 ..      12      30 ..       5      42 .. 0.84
   2 ?   -0.9   0.0      0.87   7.8e+02      95      95 ..     162     162 ..      71     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00042
                                      CSEEEEEEESTTSSHHHHHHH CS
                            NB-ARC 19 qslvvalvGmgGvGKttlakq 39
                                      +  +val+G  G+GK+tl++ 
  gi|330507982|ref|YP_004384410.1| 12 E--FVALMGPSGSGKSTLLNI 30
                                      4..9**************875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.87
                                       H CS
                            NB-ARC  95 k 95 
                                       k
  gi|330507982|ref|YP_004384410.1| 162 K 162
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1473.81
//
Query:       gi|330507983|ref|YP_004384411.1|  [L=305]
Description: hypothetical protein MCON_2039 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0084   16.0   1.0     0.0084   16.0   1.0    2.3  3  Gram_pos_anchor  LPXTG cell wall anchor motif
  ------ inclusion threshold ------
       0.18   12.1   0.2        1.8    8.9   0.0    2.3  2  Wzz              Chain length determinant protein


Domain annotation for each model (and alignments):
>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   2.2      0.99   8.8e+03      22      32 ..       8      18 ..       4      20 .. 0.61
   2 ?   -3.5   0.1       1.2   1.1e+04      13      22 ..     116     125 ..     116     126 .. 0.79
   3 !   16.0   1.0   9.3e-07    0.0084      15      40 ..     268     293 ..     267     294 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.99
                                      XXXXXXXXXXX CS
                   Gram_pos_anchor 22 aaGllallggl 32
                                      +++ll++ +++
  gi|330507983|ref|YP_004384411.1|  8 ILALLITGLAG 18
                                      56666666665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.2
                                       XXXXXXXXXX CS
                   Gram_pos_anchor  13 Gengniflta 22 
                                       Gen ++++t+
  gi|330507983|ref|YP_004384411.1| 116 GENVSAGTTL 125
                                       8888888887 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 9.3e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor  15 ngnifltaaGllallggllLlvkrRK 40 
                                       n+n++l+a G+l+ll++++ l+++++
  gi|330507983|ref|YP_004384411.1| 268 NNNLLLMAIGALVLLAAGGYLYRKKR 293
                                       799*****************999997 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0002       1.8      15      54 ..       2      41 ..       1      84 [. 0.73
   2 ?    0.7   0.0     0.071   6.4e+02      16      35 ..     270     289 ..     268     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0002
                                      XXXXXXXXXXXXXXXXXXXXXXXXX-EEEEEEEES--CHH CS
                               Wzz 15 rkklIilvtllfallaviyaflatpkYtataqilvpekkq 54
                                      +++lIi+++ll + la++y + ++   +++++ +v  + +
  gi|330507983|ref|YP_004384411.1|  2 KRILIIILALLITGLAGGYEYRMPVNIQSSTTPAVLMPGD 41
                                      5799****************99998888888755555555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.071
                                       XXXXXXXXXXXXXXXXXXXX CS
                               Wzz  16 kklIilvtllfallaviyaf 35 
                                        +l++++ +l++l+a++y++
  gi|330507983|ref|YP_004384411.1| 270 NLLLMAIGALVLLAAGGYLY 289
                                       57889999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.21s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2530.28
//
Query:       gi|330507984|ref|YP_004384412.1|  [L=412]
Description: efflux ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete 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  101.3   0.9    8.7e-29  101.3   0.9    2.4  2  MacB_PCD         MacB-like periplasmic core domain
    2.2e-11   44.0   1.6    2.2e-11   44.0   1.6    3.0  3  FtsX             FtsX-like permease family
  ------ inclusion threshold ------
      0.021   14.1   2.5       0.03   13.5   0.2    2.1  2  Polysacc_synt_3  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.9   1.5e-32   8.7e-29       1     189 [.      24     251 ..      24     256 .. 0.74
   2 ?    1.9   0.9      0.04   2.4e+02       4      21 ..     349     366 ..     346     407 .. 0.85

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 1.5e-32
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlg.nlvtvtpgk..........gsges........lsdpdve 58 
                                       +l++ LGi+iGv a+++++s+gegl + v+sq+s l+ ++++v pg+          g   s        ++d d++
  gi|330507984|ref|YP_004384412.1|  24 TLMSSLGIIIGVLAIVVMLSVGEGLYSGVSSQFSTLDlDVIHVIPGSarfggpdgepG---SrnaaepakFTDKDTK 97 
                                       79999*****************************88534889*9*9888877665551...1444555568999886 PP

                          MacB_PCD  59 alrrevpveavapvv....tvrgggsg.eeevtvvgvdpdyfk.vfglklaeGrffteadlrggpnvvvigeelaer 129
                                        l+  v+v++vap+     ++++++++ +   +++gvdpd  + ++   +a+Gr+++ +d r    ++vig+++ ++
  gi|330507984|ref|YP_004384412.1|  98 VLENVVGVKNVAPQTgasvVISFRNTNsS--GSLTGVDPDKEQdLKEK-VAQGRWLSGSDYR----SIVIGNGISQE 167
                                       6654466******9887643356655433..689**998555514444.7******998877....8********** PP

                          MacB_PCD 130 lf....pvGdtirl......kpftVvGvled.pp....gsgsalg...ddavylp.....lttl......qrrsitv 177
                                        f      G +irl       +ftVvGvle+ ++    g   ++g   d+a+y+         l      +++++ v
  gi|330507984|ref|YP_004384412.1| 168 TFrmkvTPGNKIRLyyrdqpMDFTVVGVLEEeEEsgfgG---GMGdsaDNAMYVThkameE--LldeenyYYQTFQV 239
                                       999*9878********997777******97743254433...3334669******555330..24443335666999 PP

                          MacB_PCD 178 rlkdgadleaaa 189
                                       +++d+++++ + 
  gi|330507984|ref|YP_004384412.1| 240 TVSDPDQVDYII 251
                                       999998887655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.04
                          MacB_PCD   4 tvLGiaiGvaaviaivsl 21 
                                       +++Gi++Gv+   +i+sl
  gi|330507984|ref|YP_004384412.1| 349 SLIGIILGVGTSLLIGSL 366
                                       579**********99998 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.3     0.006        36       9      50 ..      14      55 ..      12      77 .. 0.69
   2 ?   -1.6   1.0      0.66     4e+03      27      46 ..     292     308 ..     275     314 .. 0.57
   3 !   44.0   1.6   3.7e-15   2.2e-11       2      96 .]     318     405 ..     317     405 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.006
                              FtsX  9 alGmkkkqvlllllteillitlvalviGlglgllaaqllsdv 50
                                      +lG+k+ +   l+ + +++i+++a+v+ l +g  +   +s+ 
  gi|330507984|ref|YP_004384412.1| 14 SLGFKSDRFKTLMSSLGIIIGVLAIVVMLSVGEGLYSGVSSQ 55
                                      567777777777777777888888888776665555544444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.66
                              FtsX  27 litlvalviGlglgllaaql 46 
                                        i++++l++G   g+ +a++
  gi|330507984|ref|YP_004384412.1| 292 GIGAISLLVG---GIGIANV 308
                                       3555666666...4444443 PP

  == domain 3  score: 44.0 bits;  conditional E-value: 3.7e-15
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivllll 78 
                                       reig+++alG++  ++++++l+e+ ++++v+++iG++lg+  + l    ++s      l+ si ++++++++++++l
  gi|330507984|ref|YP_004384412.1| 318 REIGTMLALGATVEDIRRQYLLEAGVLGMVSSLIGIILGVGTSLL----IGSL---AGLPSSITPESIVLGVLFGVL 387
                                       8**********************************7777777555....5555...7899***************** PP

                              FtsX  79 lallagllsiskilkkep 96 
                                       ++++ag++++ k++k +p
  gi|330507984|ref|YP_004384412.1| 388 TTTIAGYYPANKAAKLDP 405
                                       **************9987 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1     0.082   4.9e+02     111     147 ..      22      56 ..       8      67 .. 0.73
   2 ?   13.5   0.2     5e-06      0.03     105     205 ..     261     366 ..     254     371 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.082
                   Polysacc_synt_3 111 FkklfkitlvssvvgvivaivlAllglgvwALvigtl 147
                                       Fk+l+  + +++++gv++ +v+  +g g+++ v ++ 
  gi|330507984|ref|YP_004384412.1|  22 FKTLM--SSLGIIIGVLAIVVMLSVGEGLYSGVSSQF 56 
                                       44433..346778889999999999999998777665 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5e-06
                   Polysacc_synt_3 105 lrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslvllwlaskwr.....prlkfslkslk. 175
                                       ++++  ++++++++++s+++++++ i  Al+g g+ +L++g +  + ++++ +    + r     + l   ++ ++ 
  gi|330507984|ref|YP_004384412.1| 261 YHKDEAYDATTARDMLSTLMSTLSMIKYALAGIGAISLLVGGIGIANVMMLTV--KERIReigtmLALGATVEDIRr 335
                                       678899***********************************996555555444..4444443555555555555541 PP

                   Polysacc_synt_3 176 .elfsfglklllsnllnylarnldnlliGkv 205
                                         l++ g+  ++s+l+ ++     +lliG++
  gi|330507984|ref|YP_004384412.1| 336 qYLLEAGVLGMVSSLIGIILGVGTSLLIGSL 366
                                       1689999999999999999999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); 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):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 2915.23
//
Query:       gi|330507985|ref|YP_004384413.1|  [L=107]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 730.09
//
Query:       gi|330507986|ref|YP_004384414.1|  [L=274]
Description: hypothetical protein MCON_2041 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-68  229.7   0.0    3.5e-68  229.5   0.0    1.0  1  DUF166        Domain of unknown function
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.14   11.7   0.0    1.2  1  Peripla_BP_4  Periplasmic binding protein domain


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 !  229.5   0.0   3.8e-72   3.5e-68       2     219 ..       5     255 ..       4     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 229.5 bits;  conditional E-value: 3.8e-72
                            DUF166   2 vltsgeyGervvenilnepdfersl.................ivavvevpe..eldefiedpeelLpe.lkeaDivi 58 
                                       v++sg +G+rvv+n+ n + f++s+                 iva+ve+p+  + ++fi+d+e lLp+ ++++D+vi
  gi|330507986|ref|YP_004384414.1|   5 VYYSGDFGSRVVGNLVNFSGFCISCadactecrnvapdlakdIVALVEMPDpsTYGDFIDDVEPLLPQdIPKVDLVI 81 
                                       89*************************************************************************** PP

                            DUF166  59 aytlhpDlllelaekakekkvkalivpaeapk...aglrkelkekleelgievavpkpfCslee.egkpkideFlee 131
                                        +++hpD+l+ l+ k ke++vka+i ++e+pk    g r++++ek+ elg+e+a+ kpfC+l + ++kp i +Fl+e
  gi|330507986|ref|YP_004384414.1|  82 VINVHPDILYGLLPKFKEAGVKAIIGGSESPKempLGQRRQVEEKAAELGMEAAFAKPFCALAPdPNKPIIAQFLKE 158
                                       *********************************999****************************99*********** PP

                            DUF166 132 ..fGkPelevevk...dgki..kkVeVlrsapCGstwyvakklkGkeveeaeeka..geahqsYpClAsmerdfelk 199
                                         +G+P +e +v+   +gk+     +V+rsapCGstw+vakk+ G e ++ ++++  +eah+sYpC+ smerd el+
  gi|330507986|ref|YP_004384414.1| 159 arIGNPVIEFTVQgsrEGKEviMGANVVRSAPCGSTWFVAKKMLGLETDQPDLREriSEAHHSYPCTGSMERDAELG 235
                                       ************9655444455778***********************977666666******************** PP

                            DUF166 200 etklhkAgyihkeavekAlk 219
                                       +t lh++gyi+++ave +lk
  gi|330507986|ref|YP_004384414.1| 236 DTVLHVGGYIIRDAVEGGLK 255
                                       ***************98876 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 ?   11.7   0.0   1.6e-05      0.14      20     113 ..      36     133 ..      29     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHTTCEEEEE..ECSTT-HHHHHHHHHHHHHTT...-SEEEE--SSHHHHHHHHHHHHHTT-EEEEESTTGC CS
                      Peripla_BP_4  20 leeaakelgaevtvv..gdaendaaeQvaqiedaiakg...vdgiivapvdstalapalkkakaaGIpVvafdsdda 91 
                                       +++ a +l+++ +     ++ ++  + ++ +e ++ +    vd++iv  v+++ l+  l k k+aG++ +   s+ +
  gi|330507986|ref|YP_004384414.1|  36 CRNVAPDLAKDIVALveMPDPSTYGDFIDDVEPLLPQDipkVDLVIVINVHPDILYGLLPKFKEAGVKAIIGGSE-S 111
                                       55566665555555455677777788899999999998888*****************************99999.8 PP

                                       TTT-CEEEEEC-HHHHHHHHHH CS
                      Peripla_BP_4  92 psgerlayvgfdneaaGelqae 113
                                       p++  l    + +e+a+el +e
  gi|330507986|ref|YP_004384414.1| 112 PKEMPLGQRRQVEEKAAELGME 133
                                       8877777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1972.27
//
Query:       gi|330507987|ref|YP_004384415.1|  [L=260]
Description: iron-sulfur cluster-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-11   41.9  14.6    9.4e-07   28.4   3.6    2.9  3  Fer4      4Fe-4S binding domain
    2.5e-07   30.5   2.5    2.5e-07   30.5   2.5    3.1  3  Fer4_6    4Fe-4S binding domain
    1.5e-06   28.2   5.7    1.5e-06   28.2   5.7    1.8  2  Fer4_21   4Fe-4S dicluster domain
    1.6e-06   28.6   6.1    5.7e-06   26.8   6.1    2.0  1  Fer4_7    4Fe-4S dicluster domain
    4.3e-06   27.6   4.7      0.052   14.5   0.2    2.6  2  Fer4_16   4Fe-4S double cluster binding domain
    6.5e-06   26.2   3.8    1.9e-05   24.7   3.8    1.9  1  Fer4_9    4Fe-4S dicluster domain
    2.1e-05   24.6   5.8    2.1e-05   24.6   5.8    2.3  2  Fer4_10   4Fe-4S dicluster domain
    0.00049   20.0   1.6    0.00049   20.0   1.6    3.1  3  Fer4_2    4Fe-4S binding domain
     0.0034   17.8   2.0     0.0034   17.8   2.0    3.2  2  Fer4_4    4Fe-4S binding domain
      0.007   16.9   2.7       0.96   10.0   1.0    2.6  2  Fer4_17   4Fe-4S dicluster domain
     0.0082   16.9  13.3      0.026   15.2   7.9    3.0  2  Fer4_15   4Fe-4S single cluster domain
  ------ inclusion threshold ------
        1.4    9.8   7.7        1.7    9.6   1.6    2.6  2  Fer4_22   4Fe-4S dicluster domain
        1.7    9.1   9.2        2.8    8.4   1.7    2.8  3  Fer4_8    4Fe-4S dicluster domain
        2.4    9.3  18.4       0.92   10.6   5.5    3.3  3  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   3.6   7.4e-10   9.4e-07       1      24 []       7      30 ..       7      30 .. 0.95
   2 !   21.1   0.3   1.5e-07   0.00019       2      24 .]      38      60 ..      37      60 .. 0.92
   3 ?   -2.0   0.2       2.9   3.7e+03      17      20 ..     168     171 ..     166     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.4e-10
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      ++ide++C gCG Cv +C  gAI+
  gi|330507987|ref|YP_004384415.1|  7 IKIDESLCNGCGSCVIACSEGAIE 30
                                      68********************96 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.5e-07
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v+ e+ C g GaC+  CP+gA+t
  gi|330507987|ref|YP_004384415.1| 38 VVRESFCDGLGACIGECPTGALT 60
                                      678999***************86 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.9
                                       HSTT CS
                              Fer4  17 vCPv 20 
                                       +CPv
  gi|330507987|ref|YP_004384415.1| 168 ACPV 171
                                       9**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 !   30.5   2.5   1.9e-10   2.5e-07       1      24 []       6      29 ..       6      29 .. 0.96
   2 !    7.5   0.3    0.0036       4.6       6      24 .]      41      59 ..      38      59 .. 0.83
   3 ?   -2.0   0.4       3.6   4.6e+03      15      20 ..     164     170 ..     162     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.9e-10
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      ++ id+++C+gCg Cv++C egai
  gi|330507987|ref|YP_004384415.1|  6 IIKIDESLCNGCGSCVIACSEGAI 29
                                      689********************8 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0036
                            Fer4_6  6 pdkCigCgdCvrvCPegai 24
                                      ++ C+g g+C+  CP+ga+
  gi|330507987|ref|YP_004384415.1| 41 ESFCDGLGACIGECPTGAL 59
                                      56688889*********97 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.6
                            Fer4_6  15 C.vrvCP 20 
                                       C + +CP
  gi|330507987|ref|YP_004384415.1| 164 CsAFACP 170
                                       6567899 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   5.7   1.2e-09   1.5e-06       2      57 ..       8      59 ..       7      61 .. 0.84
   2 ?   -2.8   0.1       5.5     7e+03      49      53 ..     167     171 ..     161     176 .. 0.66

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.2e-09
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                      +ide+ C gCg+C+iaC++    aie+ + +   v+e+ C G   C+  CP+ +++
  gi|330507987|ref|YP_004384415.1|  8 KIDESLCNGCGSCVIACSE---GAIEMVDGKARVVRESFCDGLGACIGECPT-GAL 59
                                      69****************8...56666555666789***************6.766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.5
                           Fer4_21  49 svCPv 53 
                                         CPv
  gi|330507987|ref|YP_004384415.1| 167 FACPV 171
                                       36888 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   6.1   4.5e-09   5.7e-06       2      52 .]      14      58 ..      13      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 4.5e-09
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C gCg Cv aC+ +aie+ +       +  +++++ C g gaC+ +CPtga
  gi|330507987|ref|YP_004384415.1| 14 CNGCGSCVIACSEGAIEMVDG------KARVVRESFCDGLGACIGECPTGA 58
                                      ******************885......223567889*************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 !   14.2   0.8   4.9e-05     0.062       2      20 ..      14      32 ..      13      42 .. 0.84
   2 !   14.5   0.2   4.1e-05     0.052       1      36 [.      43      81 ..      43     106 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.9e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C +Cg C+ +C ++ai++ 
  gi|330507987|ref|YP_004384415.1| 14 CNGCGSCVIACSEGAIEMV 32
                                      ****************986 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.1e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikek..kekeiearecisy.nta 36
                                      +C + g+C+  CPt+a++ +   ++ ++ ++ ++  ++ 
  gi|330507987|ref|YP_004384415.1| 43 FCDGLGACIGECPTGALTIErrDAEAFDEKAAVEHlQQS 81
                                      69999***********99772233334444444334222 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   3.8   1.5e-08   1.9e-05       2      50 ..      14      58 ..       7      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.5e-08
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      C+gCg+Cv aC  g++++ +++  +  + +    C g gaC+  Cp+ga
  gi|330507987|ref|YP_004384415.1| 14 CNGCGSCVIACSEGAIEMVDGKARVVRESF----CDGLGACIGECPTGA 58
                                      ****************99888888877654....*************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 !   24.6   5.8   1.6e-08   2.1e-05       2      56 .]       7      55 ..       6      55 .. 0.80
   2 ?    0.4   0.2      0.57   7.3e+02      14      23 ..     163     173 ..     161     223 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.6e-08
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                      ++id++ C +Cg Cv aC +        ++++ +++ r+   + C+g gaC+ +CP
  gi|330507987|ref|YP_004384415.1|  7 IKIDESLCNGCGSCVIAC-S------EGAIEMVDGKARVvRESFCDGLGACIGECP 55
                                      789***************.3......455555555555547889***********9 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.57
                           Fer4_10  14 kCvka.CPadl 23 
                                       +C ++ CP+  
  gi|330507987|ref|YP_004384415.1| 163 DCSAFaCPVIS 173
                                       57775599933 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   1.6   3.9e-07   0.00049       3      20 ..       7      24 ..       5      26 .. 0.92
   2 ?    2.6   0.4      0.13   1.7e+02      14      22 .]      48      56 ..      37      56 .. 0.77
   3 ?   -1.4   0.7       2.6   3.3e+03      16      21 ..     164     170 ..     163     171 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.9e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      +++d+  C+gCg+Cv aC
  gi|330507987|ref|YP_004384415.1|  7 IKIDESLCNGCGSCVIAC 24
                                      789*************** PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                            Fer4_2 14 gaCvsaCPa 22
                                      gaC+  CP+
  gi|330507987|ref|YP_004384415.1| 48 GACIGECPT 56
                                      89******7 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.6
                            Fer4_2  16 Cv.saCP 21 
                                       C   aCP
  gi|330507987|ref|YP_004384415.1| 164 CSaFACP 170
                                       64378*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 !   17.8   2.0   2.7e-06    0.0034       3      15 ..      13      25 ..      11      31 .. 0.90
   2 ?    1.4   0.5      0.46   5.8e+02       8      17 .]      48      57 ..      42      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.7e-06
                            Fer4_4  3 rCigCgsCvaaCP 15
                                       C+gCgsCv+aC+
  gi|330507987|ref|YP_004384415.1| 13 LCNGCGSCVIACS 25
                                      5***********7 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.46
                            Fer4_4  8 gsCvaaCPqg 17
                                      g+C+  CP+g
  gi|330507987|ref|YP_004384415.1| 48 GACIGECPTG 57
                                      5899999986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   1.0   0.00075      0.96      44      59 ..      12      27 ..       3      29 .. 0.84
   2 ?    5.6   0.0     0.018        23       1      22 [.      43      64 ..      43      98 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00075
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      slC++Cg C+ +C +g
  gi|330507987|ref|YP_004384415.1| 12 SLCNGCGSCVIACSEG 27
                                      6899999999999875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.018
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnep 22
                                      +C + g+C+ eCp+++ + +++
  gi|330507987|ref|YP_004384415.1| 43 FCDGLGACIGECPTGALTIERR 64
                                      5999999******987744433 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   7.9   2.1e-05     0.026       1      34 [.       7      61 ..       7      98 .. 0.74
   2 ?   -1.8   0.2       4.2   5.4e+03      51      61 ..     161     171 ..     155     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvl.....................l 34
                                      +++D+++C gcg Cv +++e   +  dg+a+v+                     +
  gi|330507987|ref|YP_004384415.1|  7 IKIDESLCNGCGSCVIACSEGAIEMVDGKARVVresfcdglgacigecptgaltI 61
                                      79****************88877777****9996666555555555544444432 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.2
                           Fer4_15  51 aaqeAaraCPv 61 
                                       aa+ +a aCPv
  gi|330507987|ref|YP_004384415.1| 161 AADCSAFACPV 171
                                       57778999**8 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.6    0.0013       1.7      76      94 ..       8      26 ..       2      28 .. 0.84
   2 ?    3.0   0.5      0.15   1.9e+02      77      94 ..      39      56 ..      30      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                           Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                      k++es C GCg C+ ac +
  gi|330507987|ref|YP_004384415.1|  8 KIDESLCNGCGSCVIACSE 26
                                      67899************86 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.15
                           Fer4_22 77 fgesgCvGCgRCieacpv 94
                                      + es C G g Ci  cp+
  gi|330507987|ref|YP_004384415.1| 39 VRESFCDGLGACIGECPT 56
                                      46789***********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 ?    8.4   1.7    0.0022       2.8      50      64 ..      13      27 ..       8      28 .. 0.81
   2 ?    4.7   0.1     0.032        41       5      19 ..      44      58 ..      40     107 .. 0.62
   3 ?   -2.3   0.1       4.9   6.3e+03      14      21 ..     168     175 ..     163     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                            Fer4_8 50 sCttcgaCtevCpvg 64
                                       C++cg+C+ +C +g
  gi|330507987|ref|YP_004384415.1| 13 LCNGCGSCVIACSEG 27
                                      699999999999765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.032
                            Fer4_8  5 CieCgaCqsaCpvlr 19
                                      C + gaC  +Cp+  
  gi|330507987|ref|YP_004384415.1| 44 CDGLGACIGECPTGA 58
                                      444466777776443 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.9
                            Fer4_8  14 aCpvlrrt 21 
                                       aCpv++++
  gi|330507987|ref|YP_004384415.1| 168 ACPVISEF 175
                                       68887764 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   5.5   0.00072      0.92       1      15 []      14      28 ..      14      28 .. 0.97
   2 ?    6.9   0.8     0.011        14       1      15 []      44      58 ..      43      58 .. 0.91
   3 ?   -2.2   0.2       8.9   1.1e+04      10      13 ..     168     171 ..     167     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00072
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg Cv +C +gA
  gi|330507987|ref|YP_004384415.1| 14 CNGCGSCVIACSEGA 28
                                      ***********9998 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+g gaC   CP+gA
  gi|330507987|ref|YP_004384415.1| 44 CDGLGACIGECPTGA 58
                                      78889*********9 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 8.9
                            Fer4_3  10 vCPv 13 
                                       +CPv
  gi|330507987|ref|YP_004384415.1| 168 ACPV 171
                                       7*96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1818.15
//
Query:       gi|330507988|ref|YP_004384416.1|  [L=436]
Description: hydroxylamine reductase [Methanosaeta concilii GP6]
Scores for complete 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-122  407.3   0.0   1.9e-102  343.6   0.0    2.0  2  Prismane  Prismane/CO dehydrogenase family


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   1.3e-22   2.3e-18       1      76 [.       9      90 ..       9      94 .. 0.98
   2 !  343.6   0.0    1e-106  1.9e-102     157     511 .]      84     432 ..      84     432 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 1.3e-22
                                      -EE-SST....CT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHC......HHHHHHHHHCHTSTTTB- CS
                                      xxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxx RF
                          Prismane  1 mfCrqCe....ngpCritknkrGvCGkdadtavardlliavlkgaaahaaharel......adtliakalfktltnvnf 69
                                      mfC+qC+    +++C+++    GvCGk++ +a ++d l++++kg++a+  harel      +d++i+++ f+tltnvnf
  gi|330507988|ref|YP_004384416.1|  9 MFCYQCSqtarGTGCTVK----GVCGKEPIVARLQDNLLFAIKGISAYLYHARELgysdpeVDAFIERGFFSTLTNVNF 83
                                      9*****************....********************************************************* PP

                                      SHHHHHH CS
                                      xxxxxxx RF
                          Prismane 70 ddekklk 76
                                      d e++l+
  gi|330507988|ref|YP_004384416.1| 84 DPEEFLN 90
                                      ****997 PP

  == domain 2  score: 343.6 bits;  conditional E-value: 1e-106
                                       THHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 157 dpldllskalrlGlldlkgmelldeantslfGtPeppltevnlgvldkdkvnIlvsGHdladleelleqtegkglnv 233
                                       dp ++l++a+++G++++++m ll++a+++ fG+P+p  t+v++g++ k+  +I+++GHd+ +l +ll+q+eg+++ v
  gi|330507988|ref|YP_004384416.1|  84 DPEEFLNLAVKAGEMNIRTMKLLKQAHIERFGEPTP--TKVRTGTV-KG-HGIIITGHDMNALDKLLQQVEGTDVFV 156
                                       567899******************************..********.89.9************************** PP

                                       CCCGCCCCCCHHHHHHHHHCCEEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 234 ythgemLpghcctalklkyrhlvgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktrlittsevakpga 310
                                       yth+emLp+h++++l  ky++l+gn+G+aw ++k++f++ + a++ + nC +pp+++    y +r+++t++v  pg+
  gi|330507988|ref|YP_004384416.1| 157 YTHSEMLPAHGYPGLR-KYKNLAGNLGKAWFDQKKLFAQYPMALLGTSNCFLPPREE----YIDRMFSTGPVYLPGV 228
                                       ****************.*************************************777....**************** PP

                                       EEE--CTTCHHHHHHHHHHHHCCHCCTTC.GG.-.................HHHHHTTSS-EEEEE-B---TTCGCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 311 khieeeekadkdaseiiekAielakaree.kkve.................idaiksGtIkgvvlvvGCdnakkgrd 369
                                       khi+       d+se+i++A el++  ++  + e                  +++ +G+Ik+++lv+GCd + k+ d
  gi|330507988|ref|YP_004384416.1| 229 KHID-----GYDYSEVIARARELPELPDApGEYElttgfstsvllshaakiKELVEKGKIKRFFLVGGCDAPLKKSD 300
                                       ****.....99****************884444499999999999999998899*********************** PP

                                       HHHHHHHHCHHTTEEEEEECHHHHHCCCTTTTECGHHHHSTHCEESEEEEESCCCHHHHHHHHHHHHHHTTSSGGGS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 370 yytelakelikrdvlvltaGCakyalnklglgtieaaelagegiPrvLdvGsCvdnyrivvialklaealgvdindL 446
                                       yy e++++l ++dv+vlt++C+k+++n+l+lg+i       egiPr++d+G+C+d+  ++++a +la+ +gv++ndL
  gi|330507988|ref|YP_004384416.1| 301 YYREFVQKL-PQDVVVLTLACGKFRFNDLDLGDI-------EGIPRLIDLGQCNDAIVALEVAGALADLFGVGVNDL 369
                                       *********.************************.......59********************************** PP

                                       SEEEEECC--SHHHHHHHHHHHHTT-.CEEECSS-TTTT-HHHHHHHHCHHHHHHCEEEECHCHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 447 plaalalewyeqKAvailltllalGi.nihlgptlpafgspnvlkvlvedfedriggivtveedpe 511
                                       pl +l+++w+eqKAvail  llalGi  i lgp  p  +++ +lk+lv+++  +i+ i+t++ed++
  gi|330507988|ref|YP_004384416.1| 370 PL-TLVISWMEQKAVAILWSLLALGIkGIWLGPIVPGWINDDMLKILVDQY--DIRLISTPDEDIK 432
                                       **.************************************************..***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2920.15
//
Query:       gi|330507989|ref|YP_004384417.1|  [L=119]
Description: HxlR family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-22   78.6   1.1    2.8e-22   78.4   1.1    1.1  1  HxlR      HxlR-like helix-turn-helix
     0.0017   18.4   0.1     0.0028   17.7   0.1    1.3  1  HTH_20    Helix-turn-helix domain
     0.0038   17.2   0.0     0.0051   16.8   0.0    1.3  1  PadR      Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
       0.01   15.7   0.1      0.023   14.6   0.1    1.7  2  HTH_12    Ribonuclease R winged-helix domain
      0.011   15.8   0.1      0.015   15.5   0.1    1.2  1  HTH_34    Winged helix DNA-binding domain
      0.015   15.2   0.1      0.058   13.3   0.1    1.9  2  MarR_2    MarR family
      0.039   13.8   0.0      0.053   13.3   0.0    1.2  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
      0.049   13.2   0.1       0.11   12.1   0.1    1.6  1  HTH_24    Winged helix-turn-helix DNA-binding
      0.066   13.2   0.2       0.17   11.9   0.2    1.6  1  HTH_45    Winged helix-turn-helix


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 !   78.4   1.1   1.4e-25   2.8e-22       2      87 ..      14     103 ..      13     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.4e-25
                                       HHSTTHHHHHHHHTTS...-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESS.SS-EEEEEE-TCGGGGHH CS
                              HxlR   2 iggkWkllilvellkg...kkRfselkralpkisqkmLaqrLreLeqdglierevype.vPpkveYsltekGrslep 74 
                                       i  kW++lil el kg   ++Rfselk  l +i+qk+L+ rL+eLe++gl+e+++ +e  P k eY+lte G ++ +
  gi|330507989|ref|YP_004384417.1|  14 IARKWTMLILLELYKGvghTRRFSELKGCLAGITQKVLSVRLKELEREGLVEKKMDSEaFPLKSEYTLTESGLEMIE 90 
                                       789************744579********************************9977627***************** PP

                                       HHHHHHHHHHHHH CS
                              HxlR  75 vlqelkkwgeeyl 87 
                                       v++ +k w+ ++ 
  gi|330507989|ref|YP_004384417.1|  91 VIKSIKLWALRWK 103
                                       ********99986 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   0.1   1.4e-06    0.0028      27      55 ..      36      65 ..      21      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
                                      HHHHHHHH.TS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 27 aselaerl.dlskntlsyHLrvLeeagLve 55
                                      +sel+ +l +++++ ls +L++Le+ gLve
  gi|330507989|ref|YP_004384417.1| 36 FSELKGCLaGITQKVLSVRLKELEREGLVE 65
                                      69999***99*******************9 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.5e-06    0.0051      38      71 ..      55      87 ..      37      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.5e-06
                                      HHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                              PadR 38 LkrLekeglveseweesgegpprkyYrlTdaGrr 71
                                      Lk+Le+eglve++++  +  p +  Y+lT+ G +
  gi|330507989|ref|YP_004384417.1| 55 LKELEREGLVEKKMDS-EAFPLKSEYTLTESGLE 87
                                      99***********997.599***********976 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.1e-05     0.023      30      66 .]      46      89 ..      20      89 .. 0.80
   2 ?   -3.7   0.0         6   1.2e+04      34      43 ..      99     108 ..      95     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                            HTH_12 30 igeravRyrLrkleergltrrvgya.......greltEkGleeL 66
                                      i ++ +  rL+ le++gl++++  +         +ltE Gle++
  gi|330507989|ref|YP_004384417.1| 46 ITQKVLSVRLKELEREGLVEKKMDSeafplksEYTLTESGLEMI 89
                                      666777789*************9998899988889******986 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6
                            HTH_12  34 avRyrLrkle 43 
                                       a+R +++ +e
  gi|330507989|ref|YP_004384417.1|  99 ALRWKIKNIE 108
                                       8899988765 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 ?   15.5   0.1   7.4e-06     0.015      16      69 ..      35      89 ..      20      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.4e-06
                            HTH_34 16 dfvelkeal.eatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreaf 69
                                       f+elk +l ++t+  Lsv lk Le  g +e + + +    +  +++T+ G+e  
  gi|330507989|ref|YP_004384417.1| 35 RFSELKGCLaGITQKVLSVRLKELEREGLVEKKMDSEAFPLKSEYTLTESGLEMI 89
                                      7999**998569*******************9999998877889*******9976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.58   1.2e+03      22      31 ..       9      18 ..       4      21 .. 0.84
   2 ?   13.3   0.1   2.9e-05     0.058      32      58 ..      45      71 ..      18      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.58
                                      EEHHHHHHHH CS
                            MarR_2 22 ltvgelarrl 31
                                      ltv+ +ar++
  gi|330507989|ref|YP_004384417.1|  9 LTVKYIARKW 18
                                      89*****986 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.9e-05
                                      TSSHHHHHHHHHHHHHTTSEEEEESSS CS
                            MarR_2 32 glsksavsrilkrLvaaGLverrpgpe 58
                                      g+++  +s +lk+L++ GLve++ ++e
  gi|330507989|ref|YP_004384417.1| 45 GITQKVLSVRLKELEREGLVEKKMDSE 71
                                      899999****************99887 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.7e-05     0.053      38      89 ..      35      91 ..      12      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                           DUF1495 38 kpsnvkGaleGmgkryns.e.ssLielGLveeeeeseglk...lYklteeGieivev 89
                                      + s++kG+l+G  ++  s + + L   GLve++ +se +     Y+lte+G e+ ev
  gi|330507989|ref|YP_004384417.1| 35 RFSELKGCLAGITQKVLSvRlKELEREGLVEKKMDSEAFPlksEYTLTESGLEMIEV 91
                                      35899******9988754142568889***98888777654457********99886 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.5e-05      0.11      28      48 .]      45      65 ..      44      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.5e-05
                            HTH_24 28 glSpstvnrrlkrLeeeGlIk 48
                                      g+++  ++ rlk+Le+eGl++
  gi|330507989|ref|YP_004384417.1| 45 GITQKVLSVRLKELEREGLVE 65
                                      899999*************96 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   8.4e-05      0.17      34      73 ..      49      96 ..      43      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.4e-05
                            HTH_45 34 kllnkYLdmLvekgli........kkskekYvlTekGlelleklkele 73
                                      k+l+  L+ L  +gl+           k++Y+lTe Gle++e +k ++
  gi|330507989|ref|YP_004384417.1| 49 KVLSVRLKELEREGLVekkmdseaFPLKSEYTLTESGLEMIEVIKSIK 96
                                      666677999999999965554432124789************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 772.75
//
Query:       gi|330507990|ref|YP_004384418.1|  [L=350]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-07   30.4   0.5    3.6e-07   30.4   0.5    1.9  2  OrfB_IS605      Probable transposase
    1.4e-05   25.0   0.0    5.7e-05   22.9   0.0    2.1  1  OrfB_Zn_ribbon  Putative transposase DNA-binding 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 ?   -1.7   0.2      0.36   3.2e+03      43      69 ..      93     119 ..      67     137 .. 0.66
   2 !   30.4   0.5   4.1e-11   3.6e-07      10     106 ..     161     255 ..     151     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.36
                        OrfB_IS605  43 grrlksdykylakeiaelqsklkkskn 69 
                                       +  ++++ ++++++  e++ +l +s++
  gi|330507990|ref|YP_004384418.1|  93 SIDYDTRIFAFREKDEEISVTLLRSRQ 119
                                       455666677777777777777777765 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 4.1e-11
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn..ykkasrklarlhrkr 84 
                                       +++    +++g+DlGi ++a++++++     + g+ +k  +  +a  +a lq+k+ k ++  ++++++ ++rl+ k 
  gi|330507990|ref|YP_004384418.1| 161 PEQIHVDTVLGVDLGITDIAVTSEGQ----KFGGKTIKLIKNHYASMRAVLQQKAVKGTRssRRRCRELQQRLSGKE 233
                                       667777899****************9....78999999999***********9998888889*************** PP

                        OrfB_IS605  85 srrrkhllhklathliktlkev 106
                                       +r  +   h+++++++ + +e+
  gi|330507990|ref|YP_004384418.1| 234 ARYQRQINHEISKAIVTRAQEI 255
                                       ****************999987 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 !   22.9   0.0   6.4e-09   5.7e-05       1      29 [.     288     316 ..     288     320 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.4e-09
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSk 29 
                                       f +lke+l+yka  +G+++++v+payTS 
  gi|330507990|ref|YP_004384418.1| 288 FCQLKEFLSYKALAAGVPLVLVDPAYTSR 316
                                       5689************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2525.48
//
Query:       gi|330507991|ref|YP_004384419.1|  [L=72]
Description: hypothetical protein MCON_2048 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 558.67
//
Query:       gi|330507992|ref|YP_004384420.1|  [L=234]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-13   50.8   0.0    3.5e-13   50.1   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    3.5e-11   43.6   0.0    6.1e-11   42.8   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    2.1e-10   40.6   0.0    2.7e-10   40.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    3.9e-10   39.5   0.0    5.5e-10   39.0   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    3.7e-08   34.0   0.0    6.3e-08   33.3   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    9.2e-08   31.7   0.0    1.3e-07   31.2   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.3e-06   26.3   0.0    1.3e-05   25.0   0.0    1.6  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.2e-05   25.3   0.0    1.8e-05   24.7   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
    4.8e-05   23.2   0.0    6.1e-05   22.9   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0011   18.6   0.0     0.0027   17.3   0.0    1.7  1  MetW             Methionine biosynthesis protein MetW
     0.0031   16.8   2.9     0.0047   16.2   2.9    1.2  1  Peptidase_M9     Collagenase
  ------ inclusion threshold ------
      0.036   13.6   0.0      0.049   13.2   0.0    1.3  1  TrmK             tRNA (adenine(22)-N(1))-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 !   50.1   0.0   2.3e-16   3.5e-13       1      97 []      27     122 ..      27     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2.3e-16
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       v+d+GcG  + +  +a+++g  + +g+Dise+++++ar++++++gl  ++e+v+ +  d+ fe+g fD+ +++g+  
  gi|330507992|ref|YP_004384420.1|  27 VIDFGCGCAEPLTLWAEEFG-ITGIGIDISEDFCDRARQKLASSGLsdRIEIVCSNGADYIFEEGAFDAATCIGSTF 102
                                       89*****************8.***************************************************99955 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       ++    ++++l+ ++r+++++G
  gi|330507992|ref|YP_004384420.1| 103 IFG--GWQQTLQVLKRAIRQNG 122
                                       565..68889999999988887 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0   4.1e-14   6.1e-11       2      94 ..      29     124 ..      28     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 4.1e-14
                                       EET-TTSHHHHHHH.HTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   2 dvGcGtGrlaeala.krgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhve 75 
                                       d+GcG    +  +a + g + +g+D+s+ + ++a++k   +gl  ++e+v+++  +  fe++ fD+ ++  + + + 
  gi|330507992|ref|YP_004384420.1|  29 DFGCGCAEPLTLWAeEFGITGIGIDISEDFCDRARQKLASSGLsdRIEIVCSNGADYIFEEGAFDAATCIGSTFIFG 105
                                       99***8888888883666*********************************************************** PP

                                       CHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGll 94 
                                        ++++l+ ++R  +++G+l
  gi|330507992|ref|YP_004384420.1| 106 GWQQTLQVLKRAIRQNGRL 124
                                       *****************97 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   1.8e-13   2.7e-10       2     127 ..      22     145 ..      21     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.8e-13
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDl 77 
                                       ++g+rv+D GCG  e +  +aee   +++ +GiDise+   +Ar+++++ gl+ ++e   ++  +    +e+  fD 
  gi|330507992|ref|YP_004384420.1|  22 EEGKRVIDFGCGCAEPLTLWAEEF--GITGIGIDISEDFCDRARQKLASSGLSdRIEIVCSNGADYI--FEEGAFDA 94 
                                       6799*****************886..5899*********************999*********9966..777***** PP

                   Methyltransf_31  78 ilsnevlnaladpdkileeiervlkpggilliedprllaelp.akveeesk 127
                                        ++ +    +   +++l+ ++r+++++g+l i + ++l+++   +  ++++
  gi|330507992|ref|YP_004384420.1|  95 ATCIGSTFIFGGWQQTLQVLKRAIRQNGRLGIGETHWLSNQVhPEYAQKQT 145
                                       *****99***********************999999777776533333333 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   3.7e-13   5.5e-10      50     167 ..      11     129 ..       3     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.7e-13
                                       HHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG..- CS
                              CMAS  50 KldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyed..l 124
                                       K+  + + l+l++G++++d GcG  + ++  +e++++  +g+ +S++   +a++++++ +l+++ e+  ++  d  +
  gi|330507992|ref|YP_004384420.1|  11 KIIKLGKLLKLEEGKRVIDFGCGCAEPLTLWAEEFGITGIGIDISEDFCDRARQKLASSGLSDRIEIVCSNGADyiF 87 
                                       555666779**********************************************************9988777445 PP

                                       --.--SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEE CS
                              CMAS 125 de.kvdrvvsvgafehvgkenydtffkklkkllkedGllllhti 167
                                       +e  +d+   +g +  +g   +++  ++lk++++++G+l +   
  gi|330507992|ref|YP_004384420.1|  88 EEgAFDAATCIGSTFIFG--GWQQTLQVLKRAIRQNGRLGIGET 129
                                       557*********987776..69999************9976444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   4.2e-11   6.3e-08       2      99 .]      29     124 ..      28     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 4.2e-11
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlh 77 
                                       ++GcG ++ l  ++e+  +i+ +g+Dis++++++a++kla+ +  +  ++e+   + +d   + ++fD+ ++++   
  gi|330507992|ref|YP_004384420.1|  29 DFGCGCAEPLTLWAEE-FGITGIGIDISEDFCDRARQKLASSGLSD--RIEIVCSNGADYIFEeGAFDAATCIGSTF 102
                                       9***************.788889******************99865..77777777776655568***********9 PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        +  ++++l+ ++++++++Grl
  gi|330507992|ref|YP_004384420.1| 103 IFGGWQQTLQVLKRAIRQNGRL 124
                                       ********************97 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   8.6e-11   1.3e-07      42     154 ..      18     129 ..      10     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 8.6e-11
                                       H--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-E CS
                   Ubie_methyltran  42 lvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsf 117
                                       l    +g++v+D  +G ++     +++ g +g  +++Di+e+  + +++kl  +g + +ie +++n+ +  fe+++f
  gi|330507992|ref|YP_004384420.1|  18 LLKLEEGKRVIDFGCGCAEPLTLWAEEFGITG--IGIDISEDFCDRARQKLASSGLSdRIEIVCSNGADYIFEEGAF 92 
                                       55667999*********997777777777766..89********************989****************** PP

                                       EEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE CS
                   Ubie_methyltran 118 DvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlef 154
                                       D  t       +   +++L+ + r ++  Grl + e+
  gi|330507992|ref|YP_004384420.1|  93 DAATCIGSTFIFGGWQQTLQVLKRAIRQNGRLGIGET 129
                                       ***9877777888899999999999999999887776 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 !   25.0   0.0   8.8e-09   1.3e-05      58     145 ..       8      94 ..       5     101 .. 0.89
   2 ?   -2.9   0.0       3.2   4.8e+03     174     195 ..     196     217 ..     194     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 8.8e-09
                                       -HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-G CS
                              PCMT  58 aphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDG 133
                                        p  + ++ +ll+l++g+rv++ G+G+     + a+ +g +g  ++i+ +++++++a+++l  ++l+ ++ +v++ G
  gi|330507992|ref|YP_004384420.1|   8 TPEKIIKLGKLLKLEEGKRVIDFGCGCAEPLTLWAEEFGITG--IGIDISEDFCDRARQKLASSGLSdRIEIVCSNG 82 
                                       56666667789*******************************..*********************9889******** PP

                                       GGTTGGG-SEEE CS
                              PCMT 134 rkGyeekaPYda 145
                                            e+  +da
  gi|330507992|ref|YP_004384420.1|  83 ADYIFEEGAFDA 94 
                                       987777766766 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.2
                                       SBSSSEEEEEEEEETTTEEEEE CS
                              PCMT 174 geeeeQvlklvdkkadgkvvik 195
                                         ++eQv+k+++ ++d++++ +
  gi|330507992|ref|YP_004384420.1| 196 HADYEQVFKHFRADQDDYLQFQ 217
                                       5578999999999999988765 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.2e-08   1.8e-05      13      90 ..      22      99 ..      13     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.2e-08
                   Methyltransf_18 13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdtvviaG 90
                                      e+g+rv+D G+  +  p+ l  e+   + i +Di+e  +++a+++++++gl+d+ie+++s+G + + ee  +d++++ G
  gi|330507992|ref|YP_004384420.1| 22 EEGKRVIDFGCGCAE-PLTLWAEEFGITGIGIDISEDFCDRARQKLASSGLSDRIEIVCSNGADYIFEEGaFDAATCIG 99
                                      6799*******9987.888888999999************************************998654488777665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   4.1e-08   6.1e-05      16     119 ..      18     128 ..       8     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.1e-08
                   Methyltransf_23  16 llpklraggrvLdiGcGtG.illevlrengfsvtgvDlspeaveiae............kakkaqkdqfdeqeaaep 79 
                                       ll kl++g+rv+d+GcG    l+  ++e+g + +g+D+s+   ++a+            +             + ++
  gi|330507992|ref|YP_004384420.1|  18 LL-KLEEGKRVIDFGCGCAePLTLWAEEFGITGIGIDISEDFCDRARqklassglsdriE-------------IVCS 80 
                                       44.4899************6788888999**********988888864444444333333.............4443 PP

                   Methyltransf_23  80 qg........kfdlIvlrevlehvpdppellrqiatllkpgGylllse 119
                                       +g         fd ++++ ++  +  +  +l+ +++ ++ +G+l + e
  gi|330507992|ref|YP_004384420.1|  81 NGadyifeegAFDAATCIGSTFIFGGWQQTLQVLKRAIRQNGRLGIGE 128
                                       334444444499999999999999999999999988888888876655 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.8e-06    0.0027      11      55 ..      21      65 ..      15     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
                              MetW 11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvak 55
                                      +++g rv+d GcG  e l+l +ee +++g G++++e+   ++ +k
  gi|330507992|ref|YP_004384420.1| 21 LEEGKRVIDFGCGCAEPLTLWAEEFGITGIGIDISEDFCDRARQK 65
                                      57899******************************9988877666 PP

>> Peptidase_M9  Collagenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.9   3.1e-06    0.0047     196     274 ..     138     219 ..     126     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.1e-06
                      Peptidase_M9 196 AEyvaystrtksnqaaiseakeeryslskvlettYdsddtriYrygYlavrymlek.hredvdqllallrag..dyk 269
                                        Ey +++t t+++++  + a++e ++l+ + +++Yd++d  i    Y +vr++ ++  ++d +q+++++ra   dy 
  gi|330507992|ref|YP_004384420.1| 138 PEYAQKQTTTHTETELTQFARDEGLELEYIIRASYDDWDRYISDGWYGLVRWLEDNpTHADYEQVFKHFRADqdDYL 214
                                       59*************************************8888999*******555335799********7511565 PP

                      Peptidase_M9 270 eaaal 274
                                       +++++
  gi|330507992|ref|YP_004384420.1| 215 QFQRQ 219
                                       55544 PP

>> TrmK  tRNA (adenine(22)-N(1))-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.3e-05     0.049      22      74 ..      47      99 ..      27     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
                              TrmK 22 svaiagevnegplesAkknvkkskleekievrlgdGlavlekedeidviviaG 74
                                       ++i ++++e   + A++++++s+l+++ie+  ++G + + +e  +d+++  G
  gi|330507992|ref|YP_004384420.1| 47 ITGIGIDISEDFCDRARQKLASSGLSDRIEIVCSNGADYIFEEGAFDAATCIG 99
                                      568999*************************************9999998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1668.73
//
Query:       gi|330507993|ref|YP_004384421.1|  [L=210]
Description: hypothetical protein MCON_2050 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1569.66
//
Query:       gi|330507994|ref|YP_004384422.1|  [L=349]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-69  225.5  21.0    1.3e-10   40.6   0.4    8.0  8  TPR_1            Tetratricopeptide repeat
      4e-56  182.7  18.2    8.4e-08   31.8   0.4    8.2  8  TPR_2            Tetratricopeptide repeat
    3.8e-54  180.1  24.7    5.5e-12   45.2   0.7    7.2  7  TPR_11           TPR repeat
    1.1e-50  165.6  18.3    5.6e-08   32.4   0.3    8.2  8  TPR_8            Tetratricopeptide repeat
    3.6e-44  146.0  12.3    7.2e-06   26.0   0.0    7.5  7  TPR_17           Tetratricopeptide repeat
      4e-43  145.8   3.8    2.4e-12   47.3   1.2    5.0  5  TPR_16           Tetratricopeptide repeat
    9.7e-37  122.5   2.9    5.2e-05   23.7   0.1    7.4  7  TPR_14           Tetratricopeptide repeat
    3.8e-31  107.2   6.4    9.8e-09   35.4   0.2    6.3  5  TPR_12           Tetratricopeptide repeat
    4.4e-23   81.6   6.0    1.2e-06   28.9   0.0    4.9  6  TPR_19           Tetratricopeptide repeat
      4e-21   74.9   0.0    4.6e-06   26.7   0.1    4.5  4  TPR_9            Tetratricopeptide repeat
    1.7e-18   65.9   5.8        0.5   11.1   0.0    7.9  8  TPR_6            Tetratricopeptide repeat
    5.4e-18   63.6   3.0       0.05   13.6   0.0    7.5  8  TPR_7            Tetratricopeptide repeat
    3.1e-17   62.6   0.1    1.2e-05   25.4   0.0    4.3  4  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    2.8e-12   46.1  13.5      0.062   13.2   0.1    6.9  7  TPR_10           Tetratricopeptide repeat
    8.5e-12   45.3   5.4       0.59   10.2   0.0    6.6  6  DUF3856          Domain of Unknown Function (DUF3856)
    6.7e-09   35.7  10.0       0.15   12.1   0.1    6.4  6  MIT              MIT (microtubule interacting and transport) 
    5.2e-08   33.4   0.2       0.05   14.0   0.0    3.9  3  BTAD             Bacterial transcriptional activator domain
    1.9e-07   31.0  14.3       0.57    9.9   0.1    6.0  6  TPR_21           Tetratricopeptide repeat-like domain
    1.8e-06   27.4   4.0    0.00052   19.3   0.8    3.3  4  TPR_15           Tetratricopeptide repeat
    3.2e-05   24.1   6.6       0.39   11.0   0.0    5.6  6  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
    4.3e-05   22.6   3.7       0.57    9.0   0.1    3.9  4  NARP1            NMDA receptor-regulated protein 1
     0.0001   22.3   0.2        0.6   10.2   0.0    3.7  4  SRP_TPR_like     Putative TPR-like repeat
     0.0036   17.7   0.2          2    8.9   0.0    3.0  3  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0069   16.3   0.2         10    6.0   0.0    3.9  3  Wzy_C_2          Virulence factor membrane-bound polymerase, 
     0.0073   15.9   0.8       0.92    9.1   0.0    4.1  4  HTH_Bact         Helix-turn-helix bacterial domain
     0.0075   16.4   0.0         18    5.5   0.0    4.6  5  MAS20            MAS20 protein import receptor
     0.0085   16.1  11.9        2.3    8.3   0.1    5.6  5  TPR_3            Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.014   16.0   1.9         51    4.9   0.0    5.4  5  TPR_4            Tetratricopeptide repeat
      0.018   15.2   2.7        8.3    6.6   0.0    4.6  5  DUF1510          Domain of unknown function (DUF1510)
      0.027   13.7   6.1        3.8    6.6   0.4    4.3  3  FAT              FAT domain
      0.061   13.6   0.4         17    5.7   0.0    3.8  4  TPR_5            Tetratrico peptide repeat
      0.069   13.2   0.3        6.5    6.9   0.0    3.6  4  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
       0.09   12.2   1.6         39    3.8   0.1    4.6  6  SHNi-TPR         SHNi-TPR
        0.2   11.3   0.9         21    4.8   0.1    3.7  4  Lambda_Kil       Bacteriophage lambda Kil protein


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   3.3e-08   1.7e-05       4      34 .]      80     110 ..      77     110 .. 0.93
   2 !   28.2   0.0     2e-09   1.1e-06       3      33 ..     113     143 ..     112     144 .. 0.96
   3 !   29.8   0.1   6.2e-10   3.3e-07       1      33 [.     145     177 ..     145     178 .. 0.97
   4 !   36.9   0.1   3.7e-12   1.9e-09       1      34 []     179     212 ..     179     212 .. 0.97
   5 !   36.5   0.2   4.9e-12   2.6e-09       1      33 [.     213     245 ..     213     246 .. 0.95
   6 !   37.2   0.0   2.9e-12   1.5e-09       3      34 .]     249     280 ..     247     280 .. 0.95
   7 !   40.6   0.4   2.5e-13   1.3e-10       1      33 [.     281     313 ..     281     314 .. 0.95
   8 ?    1.1   0.0      0.78   4.1e+02       2      30 ..     316     344 ..     315     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.3e-08
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +  +G  ++ +gk+deA+ +y+ A+  +P+n
  gi|330507994|ref|YP_004384422.1|  80 WLKKGDDLYDQGKFDEAISCYDNAIGKDPKN 110
                                       7889999**********************97 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 2e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+ n+G+a+++l k deA+ +++kA el+P+
  gi|330507994|ref|YP_004384422.1| 113 AWVNKGAALLELMKSDEAISCFDKATELYPK 143
                                       9*****************************7 PP

  == domain 3  score: 29.8 bits;  conditional E-value: 6.2e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+a++ +G+a+ +l ++deA+ +++ A+ +nP 
  gi|330507994|ref|YP_004384422.1| 145 AEAWNEKGYALNRLDRFDEAIIAFNNAIDINPR 177
                                       89******************************6 PP

  == domain 4  score: 36.9 bits;  conditional E-value: 3.7e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a++++G a+ + gk+deA+++y++A+ ++P++
  gi|330507994|ref|YP_004384422.1| 179 ADAWNGKGIALDNSGKHDEAIQAYDRAIAIRPKF 212
                                       89******************************96 PP

  == domain 5  score: 36.5 bits;  conditional E-value: 4.9e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a a++n+G a+  lgk +eA+++y+kA+++n +
  gi|330507994|ref|YP_004384422.1| 213 AIAWNNKGWALSGLGKKEEAIQAYNKAISINSK 245
                                       68*****************************87 PP

  == domain 6  score: 37.2 bits;  conditional E-value: 2.9e-12
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +++ +Gna+  lgk+deA+++y +A+el+P++
  gi|330507994|ref|YP_004384422.1| 249 SWNCKGNALADLGKHDEAVKAYGRAIELDPKD 280
                                       7*****************************86 PP

  == domain 7  score: 40.6 bits;  conditional E-value: 2.5e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a  ++n+G+a++ l +y+eAle+++kA+e++P+
  gi|330507994|ref|YP_004384422.1| 281 AILWNNKGAAFYGLSRYEEALEAFNKAIEIDPQ 313
                                       568*****************************6 PP

  == domain 8  score: 1.1 bits;  conditional E-value: 0.78
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                        ++  +G ++  l++ +e   ++ kA el
  gi|330507994|ref|YP_004384422.1| 316 LIWHFKGETLKALNRTEESDSAFAKAKEL 344
                                       678899***********999998888776 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     2e-07   0.00011       4      34 .]      80     110 ..      77     110 .. 0.92
   2 !   18.4   0.0   3.1e-06    0.0017       3      33 ..     113     143 ..     112     144 .. 0.95
   3 !   23.6   0.1   6.6e-08   3.5e-05       1      33 [.     145     177 ..     145     178 .. 0.97
   4 !   26.8   0.0   6.1e-09   3.2e-06       1      33 [.     179     211 ..     179     212 .. 0.96
   5 !   28.4   0.1   1.9e-09     1e-06       1      33 [.     213     245 ..     213     246 .. 0.94
   6 !   31.5   0.0   1.9e-10     1e-07       3      34 .]     249     280 ..     247     280 .. 0.95
   7 !   31.8   0.4   1.6e-10   8.4e-08       1      33 [.     281     313 ..     281     314 .. 0.96
   8 ?    6.7   0.1     0.017       9.1       1      30 [.     315     344 ..     315     345 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2e-07
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +   G+ +y +g+++eA+ +++ A+  dP+n
  gi|330507994|ref|YP_004384422.1|  80 WLKKGDDLYDQGKFDEAISCYDNAIGKDPKN 110
                                       8889*********************999987 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.1e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+ n G a+++l + +eA+ +f+kA el+P+
  gi|330507994|ref|YP_004384422.1| 113 AWVNKGAALLELMKSDEAISCFDKATELYPK 143
                                       89****************************7 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 6.6e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       aea+++ G+a+ +l++++eA+ af+ A+ ++P+
  gi|330507994|ref|YP_004384422.1| 145 AEAWNEKGYALNRLDRFDEAIIAFNNAIDINPR 177
                                       89******************************7 PP

  == domain 4  score: 26.8 bits;  conditional E-value: 6.1e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+a++  G a+ ++g+++eA++a+++A+++ P+
  gi|330507994|ref|YP_004384422.1| 179 ADAWNGKGIALDNSGKHDEAIQAYDRAIAIRPK 211
                                       79****************************997 PP

  == domain 5  score: 28.4 bits;  conditional E-value: 1.9e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a++n G+a+  lg+ eeA++a++kA++++ +
  gi|330507994|ref|YP_004384422.1| 213 AIAWNNKGWALSGLGKKEEAIQAYNKAISINSK 245
                                       689***************************976 PP

  == domain 6  score: 31.5 bits;  conditional E-value: 1.9e-10
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                        +++ G+a++ lg+++eA++a+ +A+eldP++
  gi|330507994|ref|YP_004384422.1| 249 SWNCKGNALADLGKHDEAVKAYGRAIELDPKD 280
                                       69****************************86 PP

  == domain 7  score: 31.8 bits;  conditional E-value: 1.6e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a +++n G a y l +yeeAleaf+kA+e+dP+
  gi|330507994|ref|YP_004384422.1| 281 AILWNNKGAAFYGLSRYEEALEAFNKAIEIDPQ 313
                                       679*****************************7 PP

  == domain 8  score: 6.7 bits;  conditional E-value: 0.017
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a +++  G+ + +l++ ee   af kA el
  gi|330507994|ref|YP_004384422.1| 315 ALIWHFKGETLKALNRTEESDSAFAKAKEL 344
                                       678************************887 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.2   5.3e-11   2.8e-08       1      40 [.      84     123 ..      84     124 .. 0.96
   2 !   17.2   0.1   5.7e-06     0.003      11      39 ..     128     156 ..     126     159 .. 0.92
   3 !   23.3   0.2     7e-08   3.7e-05       1      38 [.     152     189 ..     152     192 .. 0.93
   4 !   30.7   0.1   3.6e-10   1.9e-07       7      41 ..     192     226 ..     191     227 .. 0.91
   5 !   31.8   0.4   1.6e-10   8.3e-08       7      42 .]     226     261 ..     222     261 .. 0.96
   6 !   45.2   0.7     1e-14   5.5e-12       1      40 [.     254     293 ..     254     295 .. 0.97
   7 !   24.3   0.1   3.3e-08   1.8e-05       9      38 ..     296     325 ..     294     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 5.3e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       Gd +y+qGk++eAi +Y +A+  dP+n  a+ n G+a+++
  gi|330507994|ref|YP_004384422.1|  84 GDDLYDQGKFDEAISCYDNAIGKDPKNKLAWVNKGAALLE 123
                                       99***********************************986 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.7e-06
                            TPR_11  11 eeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       +eAi ++ kA +l P++aea+++ G+a+ 
  gi|330507994|ref|YP_004384422.1| 128 DEAISCFDKATELYPKSAEAWNEKGYALN 156
                                       8************************9975 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 7e-08
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       G+a+  + +++eAi a+++A++++P +a+a+++ G a+
  gi|330507994|ref|YP_004384422.1| 152 GYALNRLDRFDEAIIAFNNAIDINPRSADAWNGKGIAL 189
                                       78888999*************************99885 PP

  == domain 4  score: 30.7 bits;  conditional E-value: 3.6e-10
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                        Gk +eAi+aY +A++++P++a a++n G a+  +
  gi|330507994|ref|YP_004384422.1| 192 SGKHDEAIQAYDRAIAIRPKFAIAWNNKGWALSGL 226
                                       59**************************9887655 PP

  == domain 5  score: 31.8 bits;  conditional E-value: 1.6e-10
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +Gk eeAi+aY+kA+ +++++++ +++ G+a++ +G
  gi|330507994|ref|YP_004384422.1| 226 LGKKEEAIQAYNKAISINSKDPSSWNCKGNALADLG 261
                                       6899****************************9998 PP

  == domain 6  score: 45.2 bits;  conditional E-value: 1e-14
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       G+a+ ++Gk +eA++aY +A++ldP++a +++n G+a+y 
  gi|330507994|ref|YP_004384422.1| 254 GNALADLGKHDEAVKAYGRAIELDPKDAILWNNKGAAFYG 293
                                       9*************************************96 PP

  == domain 7  score: 24.3 bits;  conditional E-value: 3.3e-08
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       +yeeA+ea++kA+++dP+ a +++  G+++
  gi|330507994|ref|YP_004384422.1| 296 RYEEALEAFNKAIEIDPQEALIWHFKGETL 325
                                       8********************998777665 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00084      0.45       4      33 ..      80     109 ..      78     110 .. 0.84
   2 !   19.2   0.1   1.8e-06   0.00095       3      33 ..     113     143 ..     112     144 .. 0.96
   3 !   24.3   0.0     4e-08   2.1e-05       1      32 [.     145     176 ..     145     178 .. 0.96
   4 !   23.2   0.0   9.2e-08   4.8e-05       1      33 [.     179     211 ..     179     212 .. 0.96
   5 !   32.4   0.3   1.1e-10   5.6e-08       3      34 .]     215     246 ..     213     246 .. 0.95
   6 !   25.5   0.0   1.7e-08   8.8e-06       3      34 .]     249     280 ..     247     280 .. 0.92
   7 !   25.0   0.2   2.5e-08   1.3e-05       3      33 ..     283     313 ..     281     314 .. 0.95
   8 !   11.8   0.0   0.00041      0.22       3      30 ..     317     344 ..     315     344 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00084
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++++g+ + ++g+++eA+++y  a+  dp+
  gi|330507994|ref|YP_004384422.1|  80 WLKKGDDLYDQGKFDEAISCYDNAIGKDPK 109
                                       66677778899*************987777 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++n+g ++l+l + +eA++++ ka+el p+
  gi|330507994|ref|YP_004384422.1| 113 AWVNKGAALLELMKSDEAISCFDKATELYPK 143
                                       7****************************97 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 4e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       aea++ +g+++  l +++eA+ +++ a++++p
  gi|330507994|ref|YP_004384422.1| 145 AEAWNEKGYALNRLDRFDEAIIAFNNAIDINP 176
                                       79*****************************9 PP

  == domain 4  score: 23.2 bits;  conditional E-value: 9.2e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+a++ +g ++++ g+++eA+++y +a+ ++p+
  gi|330507994|ref|YP_004384422.1| 179 ADAWNGKGIALDNSGKHDEAIQAYDRAIAIRPK 211
                                       789****************************98 PP

  == domain 5  score: 32.4 bits;  conditional E-value: 1.1e-10
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a++n+g++++ lg++eeA+++y+ka++++ ++
  gi|330507994|ref|YP_004384422.1| 215 AWNNKGWALSGLGKKEEAIQAYNKAISINSKD 246
                                       8***************************9875 PP

  == domain 6  score: 25.5 bits;  conditional E-value: 1.7e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +++ +g+++ +lg+++eA+++y +a+eldp++
  gi|330507994|ref|YP_004384422.1| 249 SWNCKGNALADLGKHDEAVKAYGRAIELDPKD 280
                                       67779*************************96 PP

  == domain 7  score: 25.0 bits;  conditional E-value: 2.5e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +++n+g +   l +yeeA e+++ka+e+dp+
  gi|330507994|ref|YP_004384422.1| 283 LWNNKGAAFYGLSRYEEALEAFNKAIEIDPQ 313
                                       69****************************7 PP

  == domain 8  score: 11.8 bits;  conditional E-value: 0.00041
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekalel 30 
                                       +++ +g +++ l++ ee+ +++ ka el
  gi|330507994|ref|YP_004384422.1| 317 IWHFKGETLKALNRTEESDSAFAKAKEL 344
                                       79***********************876 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.6e-05    0.0082       1      33 [.      99     131 ..      99     132 .. 0.96
   2 !   22.2   0.1   2.3e-07   0.00012       1      33 [.     133     165 ..     133     166 .. 0.96
   3 !   24.9   0.0   3.1e-08   1.6e-05       2      34 .]     168     200 ..     167     200 .. 0.96
   4 !   26.0   0.0   1.4e-08   7.2e-06       1      34 []     201     234 ..     201     234 .. 0.97
   5 !   23.4   0.1   9.5e-08     5e-05       1      33 [.     235     267 ..     235     268 .. 0.96
   6 !   22.7   0.1   1.6e-07   8.5e-05       2      34 .]     270     302 ..     269     302 .. 0.94
   7 !   12.6   0.0   0.00026      0.14       2      31 ..     304     333 ..     303     336 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y +a+ +dP+n  a+ n++ +ll++ ++++A+
  gi|330507994|ref|YP_004384422.1|  99 CYDNAIGKDPKNKLAWVNKGAALLELMKSDEAI 131
                                       8****************************9997 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 2.3e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       ++ ka el+P++a+a+n+++++l ++ ++++A+
  gi|330507994|ref|YP_004384422.1| 133 CFDKATELYPKSAEAWNEKGYALNRLDRFDEAI 165
                                       799***************************996 PP

  == domain 3  score: 24.9 bits;  conditional E-value: 3.1e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +a++++P +ada+n ++ +l + G++++A+q
  gi|330507994|ref|YP_004384422.1| 168 FNNAIDINPRSADAWNGKGIALDNSGKHDEAIQ 200
                                       789****************************98 PP

  == domain 4  score: 26.0 bits;  conditional E-value: 1.4e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a+++ P+ a a+nn++++l+ +G++++A+q
  gi|330507994|ref|YP_004384422.1| 201 AYDRAIAIRPKFAIAWNNKGWALSGLGKKEEAIQ 234
                                       59******************************98 PP

  == domain 5  score: 23.4 bits;  conditional E-value: 9.5e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y ka+ ++ +++ ++n ++++l+ +G++++A+
  gi|330507994|ref|YP_004384422.1| 235 AYNKAISINSKDPSSWNCKGNALADLGKHDEAV 267
                                       59*****************************97 PP

  == domain 6  score: 22.7 bits;  conditional E-value: 1.6e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y +a+eldP++a ++nn++ +++ + ++++A++
  gi|330507994|ref|YP_004384422.1| 270 YGRAIELDPKDAILWNNKGAAFYGLSRYEEALE 302
                                       88**********************999999975 PP

  == domain 7  score: 12.6 bits;  conditional E-value: 0.00026
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmt 31 
                                       + ka+e+dP  a  ++ ++e+l+ ++++++
  gi|330507994|ref|YP_004384422.1| 304 FNKAIEIDPQEALIWHFKGETLKALNRTEE 333
                                       89**********************999876 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   5.3e-09   2.8e-06       1      46 [.      81     123 ..      81     127 .. 0.95
   2 !   32.3   0.1   2.1e-10   1.1e-07       3      66 ..     117     177 ..     116     179 .. 0.90
   3 !   27.6   0.0   6.6e-09   3.5e-06      19      65 ..     167     210 ..     167     212 .. 0.95
   4 !   36.8   0.0   8.7e-12   4.6e-09       4      67 ..     186     246 ..     184     247 .. 0.92
   5 !   47.3   1.2   4.5e-15   2.4e-12       4      68 .]     254     315 ..     253     315 .. 0.97

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5.3e-09
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalr 46 
                                       l+++++++++g++d+A+  ++ a+ +d   P +  A+ ++g a+l+
  gi|330507994|ref|YP_004384422.1|  81 LKKGDDLYDQGKFDEAISCYDNAIGKD---PKNKLAWVNKGAALLE 123
                                       689************************...*************997 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 2.1e-10
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++ a+l++ + d+A+  ++ a++++   P  aeA++++g a+ r+ r++eA+ +++ a++  p 
  gi|330507994|ref|YP_004384422.1| 117 KGAALLELMKSDEAISCFDKATELY---PKSAEAWNEKGYALNRLDRFDEAIIAFNNAIDINPR 177
                                       5778999999***************...************************888777788886 PP

  == domain 3  score: 27.6 bits;  conditional E-value: 6.6e-09
                            TPR_16  19 aleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       a++ a++ +   P+ a+A++++g a+   g ++eA+++y++a++  p
  gi|330507994|ref|YP_004384422.1| 167 AFNNAIDIN---PRSADAWNGKGIALDNSGKHDEAIQAYDRAIAIRP 210
                                       78999****...******************************99887 PP

  == domain 4  score: 36.8 bits;  conditional E-value: 8.7e-12
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       + a+ ++g+ d+A+ a+++a++ +   P  a A++++g+a+  +g  +eA+++y++a+   +++
  gi|330507994|ref|YP_004384422.1| 186 GIALDNSGKHDEAIQAYDRAIAIR---PKFAIAWNNKGWALSGLGKKEEAIQAYNKAISINSKD 246
                                       678899******************...*****************************98766665 PP

  == domain 5  score: 47.3 bits;  conditional E-value: 4.5e-15
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       ++a++++g+ d+A++a+ +a+++d   P +a  ++++g a++ ++r++eA++++++a++ +p+++
  gi|330507994|ref|YP_004384422.1| 254 GNALADLGKHDEAVKAYGRAIELD---PKDAILWNNKGAAFYGLSRYEEALEAFNKAIEIDPQEA 315
                                       89**********************...***********************************985 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     1e-05    0.0053       4      42 ..      80     118 ..      78     121 .. 0.90
   2 !   14.4   0.0   9.8e-05     0.052       9      42 ..     119     152 ..     117     154 .. 0.87
   3 !   20.8   0.2   8.5e-07   0.00045       2      39 ..     146     183 ..     145     188 .. 0.93
   4 !   20.8   0.1   8.7e-07   0.00046       8      39 ..     186     217 ..     184     222 .. 0.90
   5 !    9.1   0.0    0.0049       2.6       8      37 ..     220     249 ..     218     254 .. 0.84
   6 !   23.7   0.1   9.8e-08   5.2e-05       4      40 ..     250     286 ..     247     290 .. 0.88
   7 !   16.4   0.0   2.3e-05     0.012       9      43 ..     289     323 ..     287     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1e-05
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +l+ ++ l+ +G++deAi +++ a+ ++P++  aw   +
  gi|330507994|ref|YP_004384422.1|  80 WLKKGDDLYDQGKFDEAISCYDNAIGKDPKNKLAWVNKG 118
                                       777788899**************************8765 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 9.8e-05
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeawllla 42 
                                       +all+l + deAi ++++a +l+P++aeaw + +
  gi|330507994|ref|YP_004384422.1| 119 AALLELMKSDEAISCFDKATELYPKSAEAWNEKG 152
                                       678888889*********************7765 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 8.5e-07
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       ea+ + + al +l+++deAi +++ a++ +P +a+aw 
  gi|330507994|ref|YP_004384422.1| 146 EAWNEKGYALNRLDRFDEAIIAFNNAIDINPRSADAWN 183
                                       899999******************************95 PP

  == domain 4  score: 20.8 bits;  conditional E-value: 8.7e-07
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawl 39 
                                       + al ++G++deAi++++ra+a  P++a aw 
  gi|330507994|ref|YP_004384422.1| 186 GIALDNSGKHDEAIQAYDRAIAIRPKFAIAWN 217
                                       578999**********************9995 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.0049
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaea 37 
                                       ++al  lG+ +eAi+++++a++ + +d+  
  gi|330507994|ref|YP_004384422.1| 220 GWALSGLGKKEEAIQAYNKAISINSKDPSS 249
                                       5788899***************98777754 PP

  == domain 6  score: 23.7 bits;  conditional E-value: 9.8e-08
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       + + + al+ lG++deA++++ ra++l+P+da +w  
  gi|330507994|ref|YP_004384422.1| 250 WNCKGNALADLGKHDEAVKAYGRAIELDPKDAILWNN 286
                                       677899**************************99965 PP

  == domain 7  score: 16.4 bits;  conditional E-value: 2.3e-05
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +a++ l +++eA++++++a++ +P++a +w + ++
  gi|330507994|ref|YP_004384422.1| 289 AAFYGLSRYEEALEAFNKAIEIDPQEALIWHFKGE 323
                                       56777889**********************98775 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.4e-06   0.00073       3      77 .]      77     143 ..      75     143 .. 0.81
   2 !   30.7   0.1   5.4e-10   2.8e-07       3      76 ..     145     210 ..     143     211 .. 0.94
   3 !   14.6   0.0   5.8e-05     0.031      45      74 ..     213     242 ..     213     245 .. 0.92
   4 !   35.4   0.2   1.9e-11   9.8e-09       5      76 ..     249     312 ..     247     313 .. 0.93
   5 ?    3.8   0.0      0.14        73       2      32 ..     314     344 ..     313     349 .] 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.4e-06
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       a+ + + ++ l+ +g++deA+++++ a   +     ++ p    +  n g ++++l + +eA++ + +a+++++k
  gi|330507994|ref|YP_004384422.1|  77 ASKWLKKGDDLYDQGKFDEAISCYDNA---I-----GKDPKNKLAWVNKGAALLELMKSDEAISCFDKATELYPK 143
                                       55566899*******************...3.....445666667777777776677***************975 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 5.4e-10
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a a+n+ + +l+rl r+deA+  ++ a++i      p +   a + ++ g++++ +g+++eA++++ +a+ai++
  gi|330507994|ref|YP_004384422.1| 145 AEAWNEKGYALNRLDRFDEAIIAFNNAIDIN-----PRS---ADAWNGKGIALDNSGKHDEAIQAYDRAIAIRP 210
                                       789999*************************.....865...99****************************97 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 5.8e-05
                            TPR_12  45 attlrnLgrlyralgryeeAlelleealai 74 
                                       a++ +n g++++ lg+ eeA++++++a+ i
  gi|330507994|ref|YP_004384422.1| 213 AIAWNNKGWALSGLGKKEEAIQAYNKAISI 242
                                       67899**********************987 PP

  == domain 4  score: 35.4 bits;  conditional E-value: 1.9e-11
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       ++n  +++l+ lg++deA + + +a+e+      p+    a+  +n g +++ l ryeeAle++++a++i++
  gi|330507994|ref|YP_004384422.1| 249 SWNCKGNALADLGKHDEAVKAYGRAIELD-----PK---DAILWNNKGAAFYGLSRYEEALEAFNKAIEIDP 312
                                       68789********************9999.....87...59****************************986 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.14
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekalei 32 
                                        a +++  +++l +l r +e+ + + ka e+
  gi|330507994|ref|YP_004384422.1| 314 EALIWHFKGETLKALNRTEESDSAFAKAKEL 344
                                       5778888999999999999999999999887 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.3e-09   1.2e-06       1      62 [.      87     148 ..      87     153 .. 0.96
   2 !   19.3   0.1   2.4e-06    0.0012       6      56 ..     160     210 ..     157     211 .. 0.93
   3 !   19.5   0.1     2e-06    0.0011       4      59 ..     192     247 ..     191     260 .. 0.92
   4 !   15.6   0.1   3.2e-05     0.017       8      59 ..     230     281 ..     225     289 .. 0.91
   5 !   26.2   0.2   1.6e-08   8.5e-06       3      63 ..     259     319 ..     257     323 .. 0.93
   6 !   14.4   0.0   7.5e-05      0.04       6      44 ..     296     334 ..     291     344 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.3e-09
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       l+++g+++eA++ + +a+ +dpkn  a+ +   all+l   deA+ + d++ e +p++a+++
  gi|330507994|ref|YP_004384422.1|  87 LYDQGKFDEAISCYDNAIGKDPKNKLAWVNKGAALLELMKSDEAISCFDKATELYPKSAEAW 148
                                       789******************************************************98876 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.4e-06
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                       +++eA+ ++ +a++ +p +a+a+ +  +al ++g  deA+++ d++ +  p
  gi|330507994|ref|YP_004384422.1| 160 RFDEAIIAFNNAIDINPRSADAWNGKGIALDNSGKHDEAIQAYDRAIAIRP 210
                                       799****************************************99877655 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 2e-06
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                       +g+++eA++++ +a++  pk a a+ +   al  lg  +eA+++ +++   + +d+
  gi|330507994|ref|YP_004384422.1| 192 SGKHDEAIQAYDRAIAIRPKFAIAWNNKGWALSGLGKKEEAIQAYNKAISINSKDP 247
                                       599*****************************************999988877775 PP

  == domain 4  score: 15.6 bits;  conditional E-value: 3.2e-05
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                       +eA++++ +a++ + k++  +    +al  lg  deA ++  ++ e dp+da
  gi|330507994|ref|YP_004384422.1| 230 EEAIQAYNKAISINSKDPSSWNCKGNALADLGKHDEAVKAYGRAIELDPKDA 281
                                       69********************99*************************986 PP

  == domain 5  score: 26.2 bits;  conditional E-value: 1.6e-08
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryas 63 
                                       + g+++eA++++ +a++ dpk+a ++ +   a + l +++eA ++ +++ e dp++a ++ 
  gi|330507994|ref|YP_004384422.1| 259 DLGKHDEAVKAYGRAIELDPKDAILWNNKGAAFYGLSRYEEALEAFNKAIEIDPQEALIWH 319
                                       679****************************************************887765 PP

  == domain 6  score: 14.4 bits;  conditional E-value: 7.5e-05
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeA 44 
                                       +y+eAl+++ +a++ dp+ a ++    e l al++++e 
  gi|330507994|ref|YP_004384422.1| 296 RYEEALEAFNKAIEIDPQEALIWHFKGETLKALNRTEES 334
                                       89**********************************996 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.18        95      26      62 ..      74     110 ..      68     115 .. 0.87
   2 !   22.9   0.0   1.3e-07   7.1e-05       6      65 ..     122     181 ..     117     182 .. 0.92
   3 !   16.0   0.0     2e-05      0.01       7      63 ..     191     247 ..     185     249 .. 0.90
   4 !   26.7   0.1   8.8e-09   4.6e-06       8      62 ..     260     314 ..     254     318 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.18
                             TPR_9  26 PddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       +++++ ++  G  l+ +G + +A+ + + ++ ++p++
  gi|330507994|ref|YP_004384422.1|  74 SREASKWLKKGDDLYDQGKFDEAISCYDNAIGKDPKN 110
                                       6788999999999*****************9999976 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.3e-07
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       ++  ++++a+ + +    l P+++e + + G +l +l+++ +A+ +++ +++++p  +da
  gi|330507994|ref|YP_004384422.1| 122 LELMKSDEAISCFDKATELYPKSAEAWNEKGYALNRLDRFDEAIIAFNNAIDINPRSADA 181
                                       55667899***********************************************99987 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 2e-05
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       ++ ++++a+++++r +++ P+ +  +   G +l  lG  ++A+++ + +++++ ++p
  gi|330507994|ref|YP_004384422.1| 191 NSGKHDEAIQAYDRAIAIRPKFAIAWNNKGWALSGLGKKEEAIQAYNKAISINSKDP 247
                                       56789*******************************************998877665 PP

  == domain 4  score: 26.7 bits;  conditional E-value: 8.8e-09
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                         ++++a +++ r + l+P+d+ ++   G + + l ++++Al++++ +++++p+ 
  gi|330507994|ref|YP_004384422.1| 260 LGKHDEAVKAYGRAIELDPKDAILWNNKGAAFYGLSRYEEALEAFNKAIEIDPQE 314
                                       56899************************************************86 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0      0.02        11       7      32 ..      84     109 ..      80     110 .. 0.82
   2 !   11.1   0.0   0.00094       0.5       7      33 .]     118     144 ..     113     144 .. 0.85
   3 ?    7.1   0.0     0.018       9.6       7      33 .]     152     178 ..     150     178 .. 0.90
   4 !    8.7   0.0    0.0057         3       8      32 ..     187     211 ..     184     211 .. 0.83
   5 !    8.0   0.0    0.0094       4.9       7      28 ..     220     241 ..     218     245 .. 0.87
   6 !   10.0   0.0    0.0022       1.2       9      32 ..     256     279 ..     253     280 .. 0.86
   7 !    8.6   0.1     0.006       3.2       8      32 ..     289     313 ..     286     314 .. 0.85
   8 ?   -0.9   0.1       6.2   3.3e+03       7      26 ..     322     341 ..     321     344 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       +  ++ +g+ d+A+  +++ i + P+
  gi|330507994|ref|YP_004384422.1|  84 GDDLYDQGKFDEAISCYDNAIGKDPK 109
                                       55567788*************99997 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00094
                                       HHHHHH.HHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   7 alsyrk.lgdtdkAlealerlikeYPdS 33 
                                       + ++++ + ++d+A+  +++  + YP+S
  gi|330507994|ref|YP_004384422.1| 118 GAALLElM-KSDEAISCFDKATELYPKS 144
                                       66777769.*****************98 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPdS 33 
                                       ++++ +l++ d+A+ a+++ i+  P S
  gi|330507994|ref|YP_004384422.1| 152 GYALNRLDRFDEAIIAFNNAIDINPRS 178
                                       67788889****************987 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0057
                                       HHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   8 lsyrklgdtdkAlealerlikeYPd 32 
                                        ++ + g++d+A++a++r i   P+
  gi|330507994|ref|YP_004384422.1| 187 IALDNSGKHDEAIQAYDRAIAIRPK 211
                                       5666657*************99885 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.0094
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       ++++  lg++++A++a+++ i+
  gi|330507994|ref|YP_004384422.1| 220 GWALSGLGKKEEAIQAYNKAIS 241
                                       78888899***********996 PP

  == domain 6  score: 10.0 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                                       ++  lg++d+A++a+ r i+  P+
  gi|330507994|ref|YP_004384422.1| 256 ALADLGKHDEAVKAYGRAIELDPK 279
                                       666789**************9997 PP

  == domain 7  score: 8.6 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   8 lsyrklgdtdkAlealerlikeYPd 32 
                                        +++ l ++++Alea+++ i+  P+
  gi|330507994|ref|YP_004384422.1| 289 AAFYGLSRYEEALEAFNKAIEIDPQ 313
                                       56777789************99886 PP

  == domain 8  score: -0.9 bits;  conditional E-value: 6.2
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerl 26 
                                       ++ +++l++t+++  a+ + 
  gi|330507994|ref|YP_004384422.1| 322 GETLKALNRTEESDSAFAKA 341
                                       56677888999999999886 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00024      0.13      11      34 ..      89     110 ..      84     112 .. 0.88
   2 ?    3.7   0.0      0.14        76       1      28 [.     113     138 ..     113     146 .. 0.82
   3 ?   -0.2   0.0       2.6   1.4e+03       3      20 ..     149     166 ..     147     177 .. 0.76
   4 !    9.7   0.0    0.0017      0.91       3      29 ..     183     209 ..     181     213 .. 0.83
   5 !    8.2   0.0    0.0053       2.8       1      26 [.     215     240 ..     215     249 .. 0.83
   6 !   13.6   0.0   9.6e-05      0.05       6      34 ..     254     280 ..     253     282 .. 0.89
   7 !    7.7   0.1    0.0075       3.9       2      34 ..     284     314 ..     283     316 .. 0.84
   8 ?   -1.4   0.0       6.3   3.3e+03       6      27 ..     322     343 ..     318     349 .] 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                             TPR_7  11 rlGdyeeAielyeqsLaltkdped 34 
                                       ++G+++eAi++y    a+ kdp +
  gi|330507994|ref|YP_004384422.1|  89 DQGKFDEAISCYDN--AIGKDPKN 110
                                       68************..99999976 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.14
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       a++n + +  +l + +eAi+++ +  a+
  gi|330507994|ref|YP_004384422.1| 113 AWVNKGAALLELMKSDEAISCFDK--AT 138
                                       577888888888899*******99..66 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.6
                             TPR_7   3 lnLarlysrlGdyeeAie 20 
                                       +  + +  rl +++eAi 
  gi|330507994|ref|YP_004384422.1| 149 NEKGYALNRLDRFDEAII 166
                                       55667778999*****95 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0017
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLalt 29 
                                       +  + +  + G+++eAi+ y +++a++
  gi|330507994|ref|YP_004384422.1| 183 NGKGIALDNSGKHDEAIQAYDRAIAIR 209
                                       556788999*************77775 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.0053
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsL 26 
                                       a++n + + s lG+ eeAi+ y +++
  gi|330507994|ref|YP_004384422.1| 215 AWNNKGWALSGLGKKEEAIQAYNKAI 240
                                       799*******************9944 PP

  == domain 6  score: 13.6 bits;  conditional E-value: 9.6e-05
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                       +++  +lG+++eA++ y +  a++ dp d
  gi|330507994|ref|YP_004384422.1| 254 GNALADLGKHDEAVKAYGR--AIELDPKD 280
                                       78999**************..88888876 PP

  == domain 7  score: 7.7 bits;  conditional E-value: 0.0075
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       ++n + ++  l +yeeA+e + +  a++ dp++
  gi|330507994|ref|YP_004384422.1| 284 WNNKGAAFYGLSRYEEALEAFNK--AIEIDPQE 314
                                       6888999999*************..77777665 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 6.3
                             TPR_7   6 arlysrlGdyeeAielyeqsLa 27 
                                       +++  +l+++ee  + + ++ +
  gi|330507994|ref|YP_004384422.1| 322 GETLKALNRTEESDSAFAKAKE 343
                                       7788889999998888877544 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   2.3e-08   1.2e-05      18      81 ..      70     136 ..      25     137 .. 0.81
   2 !    8.7   0.0    0.0039       2.1      15      81 ..     140     204 ..     135     205 .. 0.90
   3 !   19.2   0.1   1.9e-06     0.001       3      81 ..     193     272 ..     191     273 .. 0.89
   4 ?    7.3   0.0      0.01       5.3      29      75 ..     287     334 ..     275     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.3e-08
                                       HHH--HHHHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  18 aetespedayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       + ++s e++ +l  +  ly +g++++A+  +++a ++++k++ +++ ++ +ll+L k +eAi++++k
  gi|330507994|ref|YP_004384422.1|  70 RIPKSREASKWLkkGDDLYDQGKFDEAISCYDNAiGKDPKNKLAWVNKGAALLELMKSDEAISCFDK 136
                                       67899999999888**************************************************998 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0039
                                       HH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  15 llaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       l+   ++s+e+   ++++l ++ ++++A+  +++a ++n++s  ++  ++ +l   +k++eAi+a+++
  gi|330507994|ref|YP_004384422.1| 140 LY---PKSAEAWNEKGYALNRLDRFDEAIIAFNNAiDINPRSADAWNGKGIALDNSGKHDEAIQAYDR 204
                                       44...8899999999***********************************999999********9876 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 1.9e-06
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       +++++Ai  ++r+ a  ++ + +   ++ +l  +g+ ++A++ ++ka  +nsk++ ++ +++ +l +L+k++eA++a
  gi|330507994|ref|YP_004384422.1| 193 GKHDEAIQAYDRAIAIRPKFAIAWNNKGWALSGLGKKEEAIQAYNKAiSINSKDPSSWNCKGNALADLGKHDEAVKA 269
                                       578889999999997777777777778999999*******************************************9 PP

                                       H-S CS
                            ANAPC3  79 Lek 81 
                                       +++
  gi|330507994|ref|YP_004384422.1| 270 YGR 272
                                       986 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.01
                                       HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHH CS
                            ANAPC3  29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeA 75 
                                       ++ ++y +++y++A+e ++ka +++++   ++  ++++l +L++ ee 
  gi|330507994|ref|YP_004384422.1| 287 KGAAFYGLSRYEEALEAFNKAiEIDPQEALIWHFKGETLKALNRTEES 334
                                       477889999999999999999999999999999999999999999986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.032        17      12      29 ..      87     104 ..      84     105 .. 0.85
   2 ?   -1.8   0.0       6.3   3.3e+03       9      32 ..     118     141 ..     116     143 .. 0.80
   3 ?    0.6   0.1       1.1   5.5e+02       7      22 ..     150     165 ..     144     174 .. 0.79
   4 !   13.1   0.1   0.00012     0.066       9      32 ..     186     209 ..     179     209 .. 0.94
   5 !    9.8   0.0    0.0014      0.73       6      31 ..     217     242 ..     213     245 .. 0.94
   6 !   13.2   0.1   0.00012     0.062       9      30 ..     254     275 ..     251     276 .. 0.93
   7 ?    6.5   0.2     0.015       7.8       6      31 ..     285     310 ..     285     311 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.032
                            TPR_10  12 lrqrgrydeAealleeal 29 
                                       l+++g++deA   ++ a+
  gi|330507994|ref|YP_004384422.1|  87 LYDQGKFDEAISCYDNAI 104
                                       89********99888776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.3
                            TPR_10   9 analrqrgrydeAealleealair 32 
                                       ++al ++ + deA   +++a +++
  gi|330507994|ref|YP_004384422.1| 118 GAALLELMKSDEAISCFDKATELY 141
                                       788888889999999999887665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.1
                            TPR_10   7 NLanalrqrgrydeAe 22 
                                         + al ++ r+deA 
  gi|330507994|ref|YP_004384422.1| 150 EKGYALNRLDRFDEAI 165
                                       5588999*******96 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 0.00012
                            TPR_10   9 analrqrgrydeAealleealair 32 
                                       ++al + g++deA + +++a+air
  gi|330507994|ref|YP_004384422.1| 186 GIALDNSGKHDEAIQAYDRAIAIR 209
                                       899*******************97 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.0014
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       nN + al+ +g+ +eA + + +a++i
  gi|330507994|ref|YP_004384422.1| 217 NNKGWALSGLGKKEEAIQAYNKAISI 242
                                       999*********************98 PP

  == domain 6  score: 13.2 bits;  conditional E-value: 0.00012
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       +nal ++g++deA++ + +a++
  gi|330507994|ref|YP_004384422.1| 254 GNALADLGKHDEAVKAYGRAIE 275
                                       9*******************98 PP

  == domain 7  score: 6.5 bits;  conditional E-value: 0.015
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       nN ++a + + ry+eA++ + +a++i
  gi|330507994|ref|YP_004384422.1| 285 NNKGAAFYGLSRYEEALEAFNKAIEI 310
                                       8999999****************997 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.017       9.2     103     129 ..     114     140 ..      84     152 .. 0.90
   2 ?    4.7   0.0     0.057        30      78     128 ..     127     173 ..     124     179 .. 0.81
   3 ?    7.1   0.1      0.01       5.4      78     126 ..     161     205 ..     145     209 .. 0.71
   4 !   10.2   0.0    0.0011      0.59     104     127 ..     217     240 ..     210     246 .. 0.87
   5 !    7.4   0.0    0.0081       4.3     106     129 ..     253     276 ..     248     279 .. 0.90
   6 !   10.0   0.2    0.0013      0.67      54      82 ..     280     308 ..     273     345 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 103 vfsravaleelGrkdealkafrmagem 129
                                        +++++al el ++dea+  f +a+e+
  gi|330507994|ref|YP_004384422.1| 114 WVNKGAALLELMKSDEAISCFDKATEL 140
                                       5799********************997 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.057
                                       HHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  78 adkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       +d+a+  f++  el     + W     +++ al+ l r dea+ af+ a +
  gi|330507994|ref|YP_004384422.1| 127 SDEAISCFDKATELYPKSAEAW----NEKGYALNRLDRFDEAIIAFNNAID 173
                                       6778888888888888888877....579999**********999999875 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  78 adkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                        d+a+  fn   +++      W      ++ al++ G++dea++a+  a
  gi|330507994|ref|YP_004384422.1| 161 FDEAIIAFNNAIDINPRSADAW----NGKGIALDNSGKHDEAIQAYDRA 205
                                       4555555666666666666666....468999***********999877 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmag 127
                                        +++ al++lG+k+ea++a+++a 
  gi|330507994|ref|YP_004384422.1| 217 NNKGWALSGLGKKEEAIQAYNKAI 240
                                       689******************986 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0081
                                       HHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 106 ravaleelGrkdealkafrmagem 129
                                       ++ al++lG++dea+ka+  a e+
  gi|330507994|ref|YP_004384422.1| 253 KGNALADLGKHDEAVKAYGRAIEL 276
                                       899***************999885 PP

  == domain 6  score: 10.0 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  54 dalchaglsealaklgrydealesadkal 82 
                                       da+ +     a+ +l ry+eale+ +ka+
  gi|330507994|ref|YP_004384422.1| 280 DAILWNNKGAAFYGLSRYEEALEAFNKAI 308
                                       77777788888888888888877766665 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0072       3.8      17      32 ..      90     105 ..      76     106 .. 0.86
   2 ?    0.5   0.0       1.2   6.5e+02      18      33 ..     125     140 ..     112     150 .. 0.63
   3 !   12.1   0.1   0.00029      0.15      10      31 ..     185     206 ..     183     208 .. 0.91
   4 ?    4.9   0.0     0.051        27      18      31 ..     227     240 ..     217     242 .. 0.91
   5 ?    3.8   0.1      0.11        60      18      33 ..     261     276 ..     256     276 .. 0.89
   6 ?    6.7   0.0     0.014       7.6      25      61 ..     295     332 ..     285     333 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0072
                               MIT  17 agnyeeAlelYkeale 32 
                                       +g+++eA+++Y +a++
  gi|330507994|ref|YP_004384422.1|  90 QGKFDEAISCYDNAIG 105
                                       69************96 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                               MIT  18 gnyeeAlelYkealel 33 
                                        + +eA++++ +a el
  gi|330507994|ref|YP_004384422.1| 125 MKSDEAISCFDKATEL 140
                                       5566666666666554 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00029
                               MIT  10 kAveeDnagnyeeAlelYkeal 31 
                                       k + +Dn+g+ +eA+++Y  a+
  gi|330507994|ref|YP_004384422.1| 185 KGIALDNSGKHDEAIQAYDRAI 206
                                       56899***************98 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.051
                               MIT  18 gnyeeAlelYkeal 31 
                                       g+ eeA+++Y +a+
  gi|330507994|ref|YP_004384422.1| 227 GKKEEAIQAYNKAI 240
                                       789**********9 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.11
                               MIT  18 gnyeeAlelYkealel 33 
                                       g+ +eA+++Y  a+el
  gi|330507994|ref|YP_004384422.1| 261 GKHDEAVKAYGRAIEL 276
                                       899***********96 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.014
                               MIT  25 elYkealelLlqalk.ekneerrellrekieeYleRae 61 
                                       + Y+eale +++a+     e     ++ ++ + l+R e
  gi|330507994|ref|YP_004384422.1| 295 SRYEEALEAFNKAIEiDPQEALIWHFKGETLKALNRTE 332
                                       67888888888888744555666666666666666655 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0     0.001      0.53      54     123 ..     137     206 ..      78     209 .. 0.79
   2 !   12.0   0.0    0.0004      0.21      71     121 ..     188     238 ..     107     246 .. 0.55
   3 !   14.0   0.0   9.5e-05      0.05      71     123 ..     256     308 ..     251     315 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  54 rerleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       +++l  +  ea  +   a+ rl r +ea+   +++++ +P   +++     Al  sG+  eA+++Y+r+ 
  gi|330507994|ref|YP_004384422.1| 137 ATELYPKSAEAWNEKGYALNRLDRFDEAIIAFNNAIDINPRSADAWNGKGIALDNSGKHDEAIQAYDRAI 206
                                       44555555566666666888899999****************************************9975 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0004
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                       a+   G+++ea++ +++++a  P    ++     Al  +G+++eA+++Y++
  gi|330507994|ref|YP_004384422.1| 188 ALDNSGKHDEAIQAYDRAIAIRPKFAIAWNNKGWALSGLGKKEEAIQAYNK 238
                                       333445666667777777777777667777766777777777777777665 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 9.5e-05
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       a++ lG+++ea++ + ++++++P +  l+    +A + + r +eALe+++++ 
  gi|330507994|ref|YP_004384422.1| 256 ALADLGKHDEAVKAYGRAIELDPKDAILWNNKGAAFYGLSRYEEALEAFNKAI 308
                                       7789*********************************************9875 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1    0.0011      0.57     152     180 ..      83     111 ..      76     129 .. 0.85
   2 ?    3.0   0.0      0.14        73     125     176 ..     123     175 ..     118     183 .. 0.74
   3 ?    4.7   0.2     0.042        22     152     174 ..     185     207 ..     178     213 .. 0.86
   4 ?    6.3   0.0     0.013       6.9     151     176 ..     218     243 ..     210     250 .. 0.84
   5 !    9.1   0.1    0.0018      0.96     151     178 ..     252     279 ..     247     289 .. 0.88
   6 ?    3.8   0.1     0.081        42     128     174 ..     296     343 ..     292     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaaleeka 180
                                       +GD l+ qgk+deA + Y++A+ +  +++
  gi|330507994|ref|YP_004384422.1|  83 KGDDLYDQGKFDEAISCYDNAIGKDPKNK 111
                                       8*********************9999887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                            TPR_21 125 aekkydeAlktLeakkeea.faalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                       +  k deA++  ++++e    +a++ + +G +l + +++deA  a+++A++ +
  gi|330507994|ref|YP_004384422.1| 123 ELMKSDEAISCFDKATELYpKSAEAWNEKGYALNRLDRFDEAIIAFNNAIDIN 175
                                       55566777777766555330346667889********************9865 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.042
                            TPR_21 152 rGDilvaqgkldeAraaYqaAla 174
                                       +G +l + gk deA +aY++A+a
  gi|330507994|ref|YP_004384422.1| 185 KGIALDNSGKHDEAIQAYDRAIA 207
                                       77888999*************86 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.013
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaal 176
                                        +G +l+  gk++eA +aY++A++ +
  gi|330507994|ref|YP_004384422.1| 218 NKGWALSGLGKKEEAIQAYNKAISIN 243
                                       58889999**************9755 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.0018
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaalee 178
                                        +G++l+  gk deA +aY +A++   +
  gi|330507994|ref|YP_004384422.1| 252 CKGNALADLGKHDEAVKAYGRAIELDPK 279
                                       79********************987665 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.081
                            TPR_21 128 kydeAlktL.eakkeeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                        y+eAl++  +a + +  +al+   +G+ l a ++++e  +a+ +A +
  gi|330507994|ref|YP_004384422.1| 296 RYEEALEAFnKAIEIDPQEALIWHFKGETLKALNRTEESDSAFAKAKE 343
                                       6999999994455678999************************99975 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.046        24     145     240 ..      76     171 ..      52     180 .. 0.63
   2 ?    3.6   0.1     0.059        31     153     239 ..     118     204 ..     108     212 .. 0.54
   3 !   15.1   0.3   1.8e-05    0.0097     137     242 ..     169     275 ..     150     280 .. 0.83
   4 !   19.3   0.8   9.9e-07   0.00052     157     250 ..     224     317 ..     213     337 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.046
                            TPR_15 145 saafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwg 218
                                       +a  +l  +    ++g+ d+A+ +y +A+ ++p+++ +  +   +l++l + +e   +++ + +++    ++a+ w+
  gi|330507994|ref|YP_004384422.1|  76 EASKWLKKGDDLYDQGKFDEAISCYDNAIGKDPKNKLAWVNKGAALLELMKSDE---AISCFDKATelyPKSAEAWN 149
                                       555566666666677888888888888888888877666655556666666665...44444444444456666666 PP

                            TPR_15 219 plaaAlllLgrpkkALeylrkq 240
                                         + Al +L r ++A   +++ 
  gi|330507994|ref|YP_004384422.1| 150 EKGYALNRLDRFDEAIIAFNNA 171
                                       6666666666666665555555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.059
                            TPR_15 153 aelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgplaaAlll 226
                                       +++ ++  ++d+A+ ++ +A +l p+s+e+ ++  ++l+ l+r +e   ++ a++++     ++a+ w+  + Al  
  gi|330507994|ref|YP_004384422.1| 118 GAALLELMKSDEAISCFDKATELYPKSAEAWNEKGYALNRLDRFDE---AIIAFNNAIdinPRSADAWNGKGIALDN 191
                                       5555566666666666666666666666666666666666666664...5555555544444555555544444444 PP

                            TPR_15 227 LgrpkkALeylrk 239
                                        g+ ++A + + +
  gi|330507994|ref|YP_004384422.1| 192 SGKHDEAIQAYDR 204
                                       4444444444444 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.8e-05
                            TPR_15 137 eeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara.. 210
                                        +  + + +sa  +   + +  + g++d+A+++y +A+a  p+ + + ++  W+l  lg+++e   +++a++++   
  gi|330507994|ref|YP_004384422.1| 169 NNAIDINpRSADAWNGKGIALDNSGKHDEAIQAYDRAIAIRPKFAIAWNNKGWALSGLGKKEE---AIQAYNKAIsi 242
                                       555555557777888888888999***********************************9997...99999999999 PP

                            TPR_15 211 .esdasLwgplaaAlllLgrpkkALeylrkqak 242
                                        ++d+s w+  + Al+ Lg+ ++A + + +  +
  gi|330507994|ref|YP_004384422.1| 243 nSKDPSSWNCKGNALADLGKHDEAVKAYGRAIE 275
                                       99**********************998877655 PP

  == domain 4  score: 19.3 bits;  conditional E-value: 9.9e-07
                            TPR_15 157 rqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgplaaAlllLgrp 230
                                       +  g++++A+++y +A++ + ++ +  +    +l Dlg+ +e   ++ka+ ++     +da Lw+  +aA   L+r+
  gi|330507994|ref|YP_004384422.1| 224 SGLGKKEEAIQAYNKAISINSKDPSSWNCKGNALADLGKHDE---AVKAYGRAIeldPKDAILWNNKGAAFYGLSRY 297
                                       567999************99999999999999*********7...9****98888999******************* PP

                            TPR_15 231 kkALeylrkqakenrkdplw 250
                                       ++ALe ++k  +  ++++l+
  gi|330507994|ref|YP_004384422.1| 298 EEALEAFNKAIEIDPQEALI 317
                                       *********99999988875 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00074      0.39      13      34 ..      82     103 ..      74     107 .. 0.87
   2 ?    7.0   0.0     0.013       6.6      16      37 ..     119     140 ..     107     149 .. 0.84
   3 ?    0.8   0.0       1.1   5.9e+02      19      36 ..     190     207 ..     179     211 .. 0.82
   4 ?    2.3   0.1      0.38     2e+02      18      36 ..     223     241 ..     210     246 .. 0.80
   5 ?   -1.2   0.0       4.7   2.5e+03      14      34 ..     253     273 ..     249     280 .. 0.78
   6 ?   -0.2   0.0       2.3   1.2e+03      22      36 ..     295     309 ..     284     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00074
                         NRBF2_MIT  13 rkadrllaaGkyeeaischkka 34 
                                       +k d l   Gk++eaisc+  a
  gi|330507994|ref|YP_004384422.1|  82 KKGDDLYDQGKFDEAISCYDNA 103
                                       78999*************9877 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                         NRBF2_MIT  16 drllaaGkyeeaischkkaaay 37 
                                         ll   k +eaisc  ka++ 
  gi|330507994|ref|YP_004384422.1| 119 AALLELMKSDEAISCFDKATEL 140
                                       568888999**********986 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.1
                         NRBF2_MIT  19 laaGkyeeaischkkaaa 36 
                                         +Gk++eai  + +a a
  gi|330507994|ref|YP_004384422.1| 190 DNSGKHDEAIQAYDRAIA 207
                                       568*******99998866 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.38
                         NRBF2_MIT  18 llaaGkyeeaischkkaaa 36 
                                       l   Gk eeai  ++ka +
  gi|330507994|ref|YP_004384422.1| 223 LSGLGKKEEAIQAYNKAIS 241
                                       55679***********976 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 4.7
                         NRBF2_MIT  14 kadrllaaGkyeeaischkka 34 
                                       k + l   Gk++ea+  + +a
  gi|330507994|ref|YP_004384422.1| 253 KGNALADLGKHDEAVKAYGRA 273
                                       556677789*****9988776 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 2.3
                         NRBF2_MIT  22 Gkyeeaischkkaaa 36 
                                        +yeea+   +ka +
  gi|330507994|ref|YP_004384422.1| 295 SRYEEALEAFNKAIE 309
                                       68*******999976 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.14        73     186     233 ..     107     152 ..      85     157 .. 0.57
   2 !    7.5   0.0    0.0032       1.7     203     252 ..     156     205 ..     152     211 .. 0.92
   3 !    9.0   0.1    0.0011      0.57     205     271 ..     226     294 ..     221     306 .. 0.83
   4 ?    3.2   0.0     0.062        33     206     254 ..     295     343 ..     289     347 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.14
                                       --SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHH CS
                             NARP1 186 epesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKa 233
                                       +p++ l wv+   A    +l + ++A+++ dka e  p++ e +  K+
  gi|330507994|ref|YP_004384422.1| 107 DPKNKLAWVNKGAALL--ELMKSDEAISCFDKATELYPKSAEAWNEKG 152
                                       3444444444444332..355566777777777777777777776665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0032
                                       HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                       ++l + ++A+   ++ai+ +p + + +  K+  l  +G  ++A+++ ++a
  gi|330507994|ref|YP_004384422.1| 156 NRLDRFDEAIIAFNNAIDINPRSADAWNGKGIALDNSGKHDEAIQAYDRA 205
                                       67788899************************************999987 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0011
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHH.HHH.HHHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyi.Nsk.cakymL 271
                                       lg++e+A++  +kai+ + +    +  K++ l   G  ++A+++  +a +lD +D  + N+k +a y L
  gi|330507994|ref|YP_004384422.1| 226 LGKKEEAIQAYNKAISINSKDPSSWNCKGNALADLGKHDEAVKAYGRAIELDPKDAILwNNKgAAFYGL 294
                                       67899**************************************************87654441444544 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.062
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeeark 254
                                        ++e+Ale  +kaie +p+   ++  K++ lk     ++  ++  +a++
  gi|330507994|ref|YP_004384422.1| 295 SRYEEALEAFNKAIEIDPQEALIWHFKGETLKALNRTEESDSAFAKAKE 343
                                       5677788888888888887777777777777766666666666655555 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         8   4.2e+03      29      73 ..      26      39 ..      23      65 .. 0.67
   2 ?   -0.3   0.0       1.9     1e+03      27      56 ..      71     100 ..      67     103 .. 0.82
   3 !   10.2   0.0    0.0011       0.6      20      69 ..     117     169 ..      99     179 .. 0.85
   4 ?    7.0   0.0     0.011       5.7       4      72 ..     235     308 ..     231     336 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8
                      SRP_TPR_like 29 kyeeaLkllkkgsalsedvrfEkaYvlYklkkykkalkilkkvea 73
                                      ++e aLk+++  s                                
  gi|330507994|ref|YP_004384422.1| 26 RFESALKITDRIS-------------------------------H 39
                                      4555555555444...............................2 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.9
                      SRP_TPR_like  27 lekyeeaLkllkkgsalsedvrfEkaYvlY 56 
                                       + k +ea k+lkkg+ l ++ +f++a   Y
  gi|330507994|ref|YP_004384422.1|  71 IPKSREASKWLKKGDDLYDQGKFDEAISCY 100
                                       567789999999999999999999887766 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0011
                      SRP_TPR_like  20 kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilk 69 
                                       k  al++l k +ea++  +k+      s +   Ek Y+l +l ++ +a   ++
  gi|330507994|ref|YP_004384422.1| 117 KGAALLELMKSDEAISCFDKATelyPKSAEAWNEKGYALNRLDRFDEAIIAFN 169
                                       6789****************9955545888999**************987665 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.011
                      SRP_TPR_like   4 eyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsalsed...vrfEkaYvlYklkkykkalkilkkve 72 
                                       +y+k + +++k  + +  k  al  l+k++ea+k+   + +l+ +   +   k  ++Y l +y++al+ ++k+ 
  gi|330507994|ref|YP_004384422.1| 235 AYNKAISINSKDPSSWncKGNALADLGKHDEAVKAYGRAIELDPKdaiLWNNKGAAFYGLSRYEEALEAFNKAI 308
                                       56666666666555555577888888888888888777665542211134578888999999999998888764 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0038         2      67     121 ..      63     129 ..      47     170 .. 0.82
   2 ?   -1.1   0.0       4.5   2.3e+03      86     123 ..     230     267 ..     218     274 .. 0.83
   3 ?    5.5   0.0     0.042        22      82     123 ..     294     335 ..     250     339 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0038
                                       T............SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
                   Alkyl_sulf_dimr  67 G............gaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                                                    +a+k l+k  + +++g++  a++  ++++ +dp+n+ a   k +al +l +  e
  gi|330507994|ref|YP_004384422.1|  63 DsdeprmripksrEASKWLKKGDDLYDQGKFDEAISCYDNAIGKDPKNKLAWVNKGAALLELMKSDE 129
                                       4455555555555678899******************************999999888888877666 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.5
                                       HHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  86 rwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       + a++  n+++  ++++ +  + k +al  lg++ e+ 
  gi|330507994|ref|YP_004384422.1| 230 EEAIQAYNKAISINSKDPSSWNCKGNALADLGKHDEAV 267
                                       56788889999999999999999999999999988765 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.042
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  82 egdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                          y+ a+e  n++++ dp++a   + k ++l++l + +es 
  gi|330507994|ref|YP_004384422.1| 294 LSRYEEALEAFNKAIEIDPQEALIWHFKGETLKALNRTEESD 335
                                       567999*******************************99985 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.079        42     158     182 ..     126     150 ..      89     154 .. 0.83
   2 ?    6.0   0.0      0.02        10     126     179 ..     195     249 ..     186     256 .. 0.60
   3 ?    0.5   0.0      0.91   4.8e+02     152     181 ..     256     285 ..     253     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.079
                           Wzy_C_2 158 dedeAeqilararalfpeedakwvq 182
                                       + deA    ++a  l+p+++++w++
  gi|330507994|ref|YP_004384422.1| 126 KSDEAISCFDKATELYPKSAEAWNE 150
                                       789********************54 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                           Wzy_C_2 126 laaklalarklihlsPepav.ierlilslallGdedeAeqilararalfpeedak 179
                                        ++ ++++ ++i+  P+ a+  ++  ++l +lG+++eA q + +a+ +  ++  +
  gi|330507994|ref|YP_004384422.1| 195 HDEAIQAYDRAIAIRPKFAIaWNNKGWALSGLGKKEEAIQAYNKAISINSKDPSS 249
                                       4455666666666666655423555667777777777777777766665555555 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.91
                           Wzy_C_2 152 slallGdedeAeqilararalfpeedakwv 181
                                       +la lG++deA + + ra+ l p+++  w+
  gi|330507994|ref|YP_004384422.1| 256 ALADLGKHDEAVKAYGRAIELDPKDAILWN 285
                                       67889**************99999888774 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.8     3e+03       1      15 [.     160     174 ..     160     178 .. 0.86
   2 ?   -0.4   0.0       1.6   8.5e+02       2      15 ..     195     208 ..     194     210 .. 0.88
   3 ?    1.0   0.1      0.63   3.3e+02       3      15 ..     230     242 ..     228     248 .. 0.86
   4 !    9.1   0.0    0.0017      0.92       1      15 [.     296     310 ..     296     315 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.8
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       r++ea+   n Ai i
  gi|330507994|ref|YP_004384422.1| 160 RFDEAIIAFNNAIDI 174
                                       689999999***987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                        +ea++  ++Ai+i
  gi|330507994|ref|YP_004384422.1| 195 HDEAIQAYDRAIAI 208
                                       589*********87 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.63
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   3 eeaLeqvnkAiei 15 
                                       eea++  nkAi i
  gi|330507994|ref|YP_004384422.1| 230 EEAIQAYNKAISI 242
                                       799*******987 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0017
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rYeeaLe  nkAiei
  gi|330507994|ref|YP_004384422.1| 296 RYEEALEAFNKAIEI 310
                                       7************98 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0       0.3   1.6e+02      79     102 ..      81     104 ..      49     111 .. 0.88
   2 ?    5.5   0.0     0.033        18      79     110 ..     115     146 ..     110     149 .. 0.91
   3 ?   -1.8   0.0       5.8   3.1e+03      89     107 ..     159     177 ..     150     180 .. 0.77
   4 ?   -0.5   0.0       2.3   1.2e+03      82     107 ..     254     279 ..     252     285 .. 0.82
   5 ?    1.3   0.0      0.64   3.4e+02      89     109 ..     295     315 ..     286     341 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.3
                             MAS20  79 vqlGEellaqgeeeeaaehlynAl 102
                                       +++G++l  qg+ +ea+++  nA+
  gi|330507994|ref|YP_004384422.1|  81 LKKGDDLYDQGKFDEAISCYDNAI 104
                                       689****************99998 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.033
                             MAS20  79 vqlGEellaqgeeeeaaehlynAlkvcpqPqe 110
                                       v++G  ll+  + +ea++++ +A  ++p+ +e
  gi|330507994|ref|YP_004384422.1| 115 VNKGAALLELMKSDEAISCFDKATELYPKSAE 146
                                       8999999999******************9865 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 5.8
                             MAS20  89 geeeeaaehlynAlkvcpq 107
                                       ++ +ea+ ++ nA+ + p 
  gi|330507994|ref|YP_004384422.1| 159 DRFDEAIIAFNNAIDINPR 177
                                       67899********998776 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.3
                             MAS20  82 GEellaqgeeeeaaehlynAlkvcpq 107
                                       G+ l+  g+++ea+++  +A+ + p+
  gi|330507994|ref|YP_004384422.1| 254 GNALADLGKHDEAVKAYGRAIELDPK 279
                                       7777778*************998776 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.64
                             MAS20  89 geeeeaaehlynAlkvcpqPq 109
                                       +++eea+e++ +A+ + pq +
  gi|330507994|ref|YP_004384422.1| 295 SRYEEALEAFNKAIEIDPQEA 315
                                       6799**********9988865 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0043       2.3      10      25 ..      86     101 ..      84     107 .. 0.85
   2 ?   -0.3   0.0       2.2   1.1e+03      15      25 ..     159     169 ..     152     173 .. 0.81
   3 ?    3.8   0.0      0.11        57      13      33 ..     191     209 ..     188     211 .. 0.80
   4 ?    2.3   0.0      0.33   1.7e+02      11      36 .]     257     280 ..     254     280 .. 0.87
   5 ?    4.9   0.1     0.051        27       8      25 ..     288     305 ..     288     313 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0043
                                       HHHHTT-HHHHHHH.. CS
                             TPR_3  10 efynkkkyqeArelfs 25 
                                       ++y+++k++eA+  ++
  gi|330507994|ref|YP_004384422.1|  86 DLYDQGKFDEAISCYD 101
                                       58**********9987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.2
                                       T-HHHHHHH.. CS
                             TPR_3  15 kkyqeArelfs 25 
                                       ++++eA+ +f 
  gi|330507994|ref|YP_004384422.1| 159 DRFDEAIIAFN 169
                                       799****9965 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.11
                                       HTT-HHHHHHH..HHHHHHH- CS
                             TPR_3  13 nkkkyqeArelfsYallaild 33 
                                       n++k +eA+++++   + +++
  gi|330507994|ref|YP_004384422.1| 191 NSGKHDEAIQAYD--RAIAIR 209
                                       789********77..666665 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.33
                                       HHHTT-HHHHHHH..HHHHHHH-TT- CS
                             TPR_3  11 fynkkkyqeArelfsYallaildken 36 
                                       + + +k +eA+ +  Y+ +  ld+++
  gi|330507994|ref|YP_004384422.1| 257 LADLGKHDEAVKA--YGRAIELDPKD 280
                                       5678999******..99999999987 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.051
                                       HHHHHHTT-HHHHHHH.. CS
                             TPR_3   8 AaefynkkkyqeArelfs 25 
                                       +a+fy   +y+eA+e+f 
  gi|330507994|ref|YP_004384422.1| 288 GAAFYGLSRYEEALEAFN 305
                                       7999999*********64 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0       1.1   5.8e+02      10      20 ..      86      96 ..      83     101 .. 0.86
   2 ?    1.6   0.1       1.1   5.8e+02       8      20 ..     152     164 ..     145     164 .. 0.88
   3 ?    0.2   0.0       3.2   1.7e+03       8      25 ..     186     203 ..     181     204 .. 0.80
   4 ?   -0.6   0.0       5.8   3.1e+03       6      20 ..     218     232 ..     214     236 .. 0.81
   5 ?    4.9   0.0     0.096        51       8      20 ..     254     266 ..     252     270 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1.1
                             TPR_4 10 allalGdldeA 20
                                       l+++G +deA
  gi|330507994|ref|YP_004384422.1| 86 DLYDQGKFDEA 96
                                      6899******9 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 1.1
                             TPR_4   8 ArallalGdldeA 20 
                                       + al +l ++deA
  gi|330507994|ref|YP_004384422.1| 152 GYALNRLDRFDEA 164
                                       6799********9 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 3.2
                             TPR_4   8 ArallalGdldeAralle 25 
                                       + al   G +deA ++ +
  gi|330507994|ref|YP_004384422.1| 186 GIALDNSGKHDEAIQAYD 203
                                       6788889******77665 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 5.8
                             TPR_4   6 aLArallalGdldeA 20 
                                       + ++al  lG  +eA
  gi|330507994|ref|YP_004384422.1| 218 NKGWALSGLGKKEEA 232
                                       568999999998888 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.096
                             TPR_4   8 ArallalGdldeA 20 
                                       + al++lG +deA
  gi|330507994|ref|YP_004384422.1| 254 GNALADLGKHDEA 266
                                       679*********9 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.3   1.7e+03      19      37 ..     139     157 ..     134     180 .. 0.75
   2 ?    0.9   0.1      0.95     5e+02      29      67 ..     162     205 ..     150     229 .. 0.65
   3 ?    0.8   0.0       1.1   5.6e+02      29      54 ..     230     255 ..     224     260 .. 0.87
   4 ?    2.0   0.0      0.44   2.3e+02      29      51 ..     264     286 ..     258     291 .. 0.88
   5 ?    6.6   0.0     0.016       8.3      28      54 ..     297     323 ..     289     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.3
                           DUF1510  19 ssydkgsvDwnEmekavsk 37 
                                       + y k+ + wnE+  a+++
  gi|330507994|ref|YP_004384422.1| 139 ELYPKSAEAWNEKGYALNR 157
                                       5677888888888877764 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.95
                           DUF1510  29 nEmekavskatglsednmivww.....lgnggspqkaigtvssk 67 
                                       +E   a+++a++++  +   w      l n+g++++ai      
  gi|330507994|ref|YP_004384422.1| 162 DEAIIAFNNAIDINPRSADAWNgkgiaLDNSGKHDEAIQAYDRA 205
                                       67777888888888888888852222246777777777665554 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.1
                           DUF1510  29 nEmekavskatglsednmivwwlgng 54 
                                       +E  +a +ka+ +++++   w  + +
  gi|330507994|ref|YP_004384422.1| 230 EEAIQAYNKAISINSKDPSSWNCKGN 255
                                       68899************999988765 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.44
                           DUF1510  29 nEmekavskatglsednmivwwl 51 
                                       +E +ka  +a++l+ ++ i+w  
  gi|330507994|ref|YP_004384422.1| 264 DEAVKAYGRAIELDPKDAILWNN 286
                                       6999*****************75 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.016
                           DUF1510  28 wnEmekavskatglsednmivwwlgng 54 
                                       ++E ++a++ka++++ ++  +w+ + +
  gi|330507994|ref|YP_004384422.1| 297 YEEALEAFNKAIEIDPQEALIWHFKGE 323
                                       89********************99854 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.4    0.0073       3.8     266     291 ..     125     150 ..      74     158 .. 0.88
   2 ?    5.9   0.3     0.012       6.1     265     332 ..     192     276 ..     150     287 .. 0.69
   3 ?    0.3   0.0      0.62   3.3e+02     268     290 ..     297     319 ..     284     343 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0073
                                       ..-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 266 ekieeilqsysaateidpswykawht 291
                                        k++e+ +++ +ate+ p++++aw++
  gi|330507994|ref|YP_004384422.1| 125 MKSDEAISCFDKATELYPKSAEAWNE 150
                                       3599********************86 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                                       ...-SSCCHHHHCCHHCTCCCHSTTCC..CCHH....HHHCCHHHHHHSSSS................S-TCCHHHH CS
                               FAT 265 eekieeilqsysaateidpswykawht..walf....nfevvskeeeqkeeee...............pedlqeyvv 320
                                       + k +e+ q+y +a  i+p+ + aw++  wal      +e+++++ +    ++                +dl +   
  gi|330507994|ref|YP_004384422.1| 192 SGKHDEAIQAYDRAIAIRPKFAIAWNNkgWALSglgkKEEAIQAYNKA---ISinskdpsswnckgnaLADLGK-HD 264
                                       3459999******************99888876222245555555433...11223344455555433334432.34 PP

                                       CCT..CCHHHHT CS
                               FAT 321 pavkgflksisl 332
                                       +avk++ ++i l
  gi|330507994|ref|YP_004384422.1| 265 EAVKAYGRAIEL 276
                                       566666666666 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.62
                                       -SSCCHHHHCCHHCTCCCHSTTC CS
                               FAT 268 ieeilqsysaateidpswykawh 290
                                        ee+l+++ +a eidp+ +  wh
  gi|330507994|ref|YP_004384422.1| 297 YEEALEAFNKAIEIDPQEALIWH 319
                                       57889999999999998888887 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         4   2.1e+03      15      30 ..      91     106 ..      86     148 .. 0.58
   2 ?    5.7   0.0     0.033        17       8      29 ..     186     207 ..     179     210 .. 0.88
   3 ?    1.2   0.0      0.77   4.1e+02      13      29 ..     225     241 ..     213     253 .. 0.79
   4 ?    1.0   0.0      0.94     5e+02      13      29 ..     259     275 ..     247     281 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4
                             TPR_5  15 GhedkavplYrraLae 30 
                                       G+ d+a+  Y +a+ +
  gi|330507994|ref|YP_004384422.1|  91 GKFDEAISCYDNAIGK 106
                                       5556666666666543 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.033
                             TPR_5   8 agarDstGhedkavplYrraLa 29 
                                       + a D  G++d+a++ Y ra+a
  gi|330507994|ref|YP_004384422.1| 186 GIALDNSGKHDEAIQAYDRAIA 207
                                       5688****************87 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.77
                             TPR_5  13 stGhedkavplYrraLa 29 
                                         G++++a++ Y++a+ 
  gi|330507994|ref|YP_004384422.1| 225 GLGKKEEAIQAYNKAIS 241
                                       56899999999999875 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.94
                             TPR_5  13 stGhedkavplYrraLa 29 
                                         G++d+av+ Y ra++
  gi|330507994|ref|YP_004384422.1| 259 DLGKHDEAVKAYGRAIE 275
                                       45777788888877765 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      0.86   4.5e+02      14      35 ..      90     111 ..      87     113 .. 0.90
   2 ?   -1.4   0.0         5   2.7e+03      14      34 ..     192     212 ..     187     213 .. 0.84
   3 ?   -1.1   0.0         4   2.1e+03      14      33 ..     260     279 ..     256     281 .. 0.86
   4 ?    6.9   0.0     0.012       6.5      10      33 ..     290     313 ..     288     315 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.86
                                       HT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenr 35 
                                       +g+++eA  + d  + ++P+n+
  gi|330507994|ref|YP_004384422.1|  90 QGKFDEAISCYDNAIGKDPKNK 111
                                       799*****************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                        g+++eA +  d+ ++i P++
  gi|330507994|ref|YP_004384422.1| 192 SGKHDEAIQAYDRAIAIRPKF 212
                                       588999999999999999975 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       lg+++eA +   + +e++P+
  gi|330507994|ref|YP_004384422.1| 260 LGKHDEAVKAYGRAIELDPK 279
                                       8999*****99999999997 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.012
                                       HHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPe 33 
                                       + y l +Y+eA++  +  +ei+P+
  gi|330507994|ref|YP_004384422.1| 290 AFYGLSRYEEALEAFNKAIEIDPQ 313
                                       66999******************7 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0         3   1.6e+03      15      22 ..      91      98 ..      90     104 .. 0.77
   2 ?   -2.3   0.0       5.9   3.1e+03      15      27 ..     159     171 ..     159     174 .. 0.70
   3 ?    2.6   0.0      0.17        91      15      31 ..     193     209 ..     191     212 .. 0.87
   4 ?   -1.9   0.0       4.4   2.3e+03      18      30 ..     230     242 ..     230     243 .. 0.87
   5 ?   -0.8   0.0         2     1e+03      18      30 ..     264     276 ..     261     276 .. 0.87
   6 ?    3.8   0.1     0.074        39      15      30 ..     295     310 ..     294     311 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3
                          SHNi-TPR 15 enFpqAve 22
                                      ++F++A++
  gi|330507994|ref|YP_004384422.1| 91 GKFDEAIS 98
                                      79****97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.9
                          SHNi-TPR  15 enFpqAveDlrka 27 
                                       ++F++A+  ++ a
  gi|330507994|ref|YP_004384422.1| 159 DRFDEAIIAFNNA 171
                                       59****9666555 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.17
                          SHNi-TPR  15 enFpqAveDlrkaLeLr 31 
                                       ++ ++A++ +++a+++r
  gi|330507994|ref|YP_004384422.1| 193 GKHDEAIQAYDRAIAIR 209
                                       6779************9 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 4.4
                          SHNi-TPR  18 pqAveDlrkaLeL 30 
                                       ++A++ ++ka+ +
  gi|330507994|ref|YP_004384422.1| 230 EEAIQAYNKAISI 242
                                       689******9976 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 2
                          SHNi-TPR  18 pqAveDlrkaLeL 30 
                                       ++Av+ + +a+eL
  gi|330507994|ref|YP_004384422.1| 264 DEAVKAYGRAIEL 276
                                       89********998 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.074
                          SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                       +++++A+e ++ka+e+
  gi|330507994|ref|YP_004384422.1| 295 SRYEEALEAFNKAIEI 310
                                       79***********997 PP

>> Lambda_Kil  Bacteriophage lambda Kil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.38     2e+02      26      37 ..     197     208 ..     191     215 .. 0.83
   2 ?    4.8   0.1     0.039        21      26      37 ..     231     242 ..     229     244 .. 0.92
   3 ?   -0.8   0.0       2.3   1.2e+03      22      35 ..     261     274 ..     257     277 .. 0.78
   4 ?   -2.5   0.0       7.7   4.1e+03      24      37 ..     297     310 ..     296     310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.38
                        Lambda_Kil  26 eAvdayKkavli 37 
                                       eA +ay +a+ i
  gi|330507994|ref|YP_004384422.1| 197 EAIQAYDRAIAI 208
                                       899999999987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.039
                        Lambda_Kil  26 eAvdayKkavli 37 
                                       eA +ay ka++i
  gi|330507994|ref|YP_004384422.1| 231 EAIQAYNKAISI 242
                                       8**********9 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.3
                        Lambda_Kil  22 kMfleAvdayKkav 35 
                                       +   eAv ay +a+
  gi|330507994|ref|YP_004384422.1| 261 GKHDEAVKAYGRAI 274
                                       56679*****9998 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 7.7
                        Lambda_Kil  24 fleAvdayKkavli 37 
                                       + eA +a+ ka+ i
  gi|330507994|ref|YP_004384422.1| 297 YEEALEAFNKAIEI 310
                                       56999999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.73u 0.24s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2063.26
//
Query:       gi|330507995|ref|YP_004384423.1|  [L=229]
Description: hypothetical protein MCON_2053 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-05   24.2   0.0    5.1e-05   23.3   0.0    1.5  1  EVE          EVE domain
     0.0037   16.7   0.2     0.0094   15.4   0.2    1.7  1  CRM1_repeat  Chromosome region maintenance or exportin repeat


Domain annotation for each model (and alignments):
>> EVE  EVE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   5.7e-09   5.1e-05       1     142 [.      11     141 ..      11     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.7e-09
                                       -EEEEEEBHHT......SHHHHHCHHHCEEE-EE-GHHHHHHHCC--TT-EEEEEETSSSS-EEEEEEEEECEEEE- CS
                               EVE   1 ayWllksepde......fsiddlkrkkeegWdgvrnyqarnllramkkGDlvlfYhsgeklqaivgiaeVvseaypd 71 
                                       +yWl ++ pd+      +      r+  ++  g          +a k+GDlvl++ ++ k + i  +++  s+ay  
  gi|330507995|ref|YP_004384423.1|  11 QYWLWVTRPDYyldedgC-----DREDLDPTLGADSDGWWTCNKATKEGDLVLLWRTSPK-KDIRYLIQAESDAYSI 81 
                                       6*********84444444.....55555555555555555555899*********99999.9*******99****96 PP

                                       GGGG-TTSTT--TTTBTTS--E.EEEEEEEEEEEEEEEHHHHTTHGTCTTSHHHHCC.T-SEEEE-HHHHHHH CS
                               EVE  72 etqfdpkskyydpkskkekpwl.rvdvkpvkklkrplslkelkaepelegmkllrkg.rlsvrpvteedweli 142
                                         + d+              w   +d +++ k++++l  k+l+++p + ++  lr + + s+++++ e w+ +
  gi|330507995|ref|YP_004384423.1|  82 ADDNDKG-------------WDyGCDYEVLYKFEQSLHAKDLRQNPYFDEWGPLRCSfQGSNFKISLEYWNKL 141
                                       6444444.............6559******************************************9999876 PP

>> CRM1_repeat  Chromosome region maintenance or exportin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2     1e-06    0.0094      22      32 ..     131     141 ..     130     145 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-06
                                       HHHHHHHHHHH CS
                       CRM1_repeat  22 FKICLEYWnkL 32 
                                       FKI LEYWnkL
  gi|330507995|ref|YP_004384423.1| 131 FKISLEYWNKL 141
                                       9*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1649.91
//
Query:       gi|330507996|ref|YP_004384424.1|  [L=1144]
Description: type III restriction enzyme, res subunit [Methanosaeta concilii GP6]
Scores for complete 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-25   89.1   0.0    6.5e-25   88.1   0.0    1.5  1  ResIII      Type III restriction enzyme, res subunit
    0.00014   21.7   0.0     0.0011   18.7   0.0    2.2  1  DEAD        DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.022   14.3   0.7        1.8    8.1   0.0    3.0  3  HEPN_AbiU2  AbiU2
      0.089   11.7   0.0       0.17   10.8   0.0    1.3  1  ISN1        IMP-specific 5'-nucleotidase


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.0   1.4e-28   6.5e-25       7     170 ..     113     354 ..     106     355 .. 0.88

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 1.4e-28
                                       HHHHHHHHHT...................................TTS..EEEEEESTTSTHHHHH.HHHHHHH-S. CS
                            ResIII   7 yQeeaienlleklks.............................krdk..rglikmaTGtGKTlva.aklierllkk 51 
                                       +Q eaie ++  ++                              +  +  ++ +kmaTG+GKT v+ ++++++++++
  gi|330507996|ref|YP_004384424.1| 113 CQREAIETFIYLYEVrgirtlstitaeflgedsydtalgvnpddD--RwpKYAFKMATGSGKTKVMsLAIVWSYFHS 187
                                       577777777733333455556667777777888888888887434..3559************************** PP

                                       ..........-EEEEESSHHHHHHHHHHGGGGTGG.....GEEEESSS-B--.............-SEEEEEHHHHH CS
                            ResIII  52 gkee......kflflvprkslleqtleefkkflseayke.igkkvsgdkkka......kekdstnkkilvttiqsld 115
                                        +ee       fl+++p++++ e+++e+f + +  +++  i + ++gd +++       ++++t  +i++t+i++l+
  gi|330507996|ref|YP_004384424.1| 188 LREEdsilarDFLIIAPNITVFERLKEDFGDGKVFEADPlIPEAWRGDWNISvvlqdeASGAATGGRIYLTNIHRLY 264
                                       **99*************************888888776689**********99**999999**************** PP

                                       HTH................................HHHTTT-SEEEEETGGGTTS..TTTHHHHHT---........ CS
                            ResIII 116 adseee........................eeeseellrdrfdviiiDEaHrlgak.kswreilekfke........ 159
                                         s+++                        e  +e+  ++r+ ++++DEaH+l +  ++w+ ++e++ +        
  gi|330507996|ref|YP_004384424.1| 265 DTSKRRskslmeshdwlgpavsrsraldtgEALRERVTSHRKIMVLNDEAHHLWDPdSAWNDAIEYVHQtihdrtgg 341
                                       ***888**********************9999999999*****************8559**9999997778889999 PP

                                       ..SEEEEEESS-S CS
                            ResIII 160 ..avllglTATpe 170
                                           +l+++ATp+
  gi|330507996|ref|YP_004384424.1| 342 eiVSQLDFSATPK 354
                                       999*********8 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.5e-07    0.0011      20     172 ..     165     356 ..     160     360 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.5e-07
                                       EESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.ST.SEEEEEET....TSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxx....xxx RF
                              DEAD  20 aaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkky.id.lrvlliig....gva 86 
                                       +++TGsGKT +++++++ + +++    ++  +   li++P     e   +++   k + +d l  +++ g    +v 
  gi|330507996|ref|YP_004384424.1| 165 KMATGSGKTKVMSLAIVWSYFHSlreeDSILARDFLIIAPNITVFERLKEDFGDGKVFeADpLIPEAWRGdwniSVV 241
                                       689**************777776776667777899*****************7766654556555566664544577 PP

                                       HHHHHHHHHTTCSEEEEEHHHHHHHH.............................HCTSSH...CTTEEEEEE.ETH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.............................xxxxxx...xxxxxxxxx.xxx RF
                              DEAD  87 ardqlskldngvdivvgtpgrlddll.............................stgkln...lsqvrflVl.DEa 130
                                        +d+ s    g +i++++  rl d                                    +   +s+ +++Vl DEa
  gi|330507996|ref|YP_004384424.1| 242 LQDEASGAATGGRIYLTNIHRLYDTSkrrskslmeshdwlgpavsrsraldtgeaL----RervTSHRKIMVLnDEA 314
                                       77888888788888888888888876788888899999999999987777544321....25558999999988*** PP

                                       HHHHHT..TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSHH CS
                                       xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 131 drlldq..gfsdfinrilnqlpqitcdgklqrqvivlSATlpkd 172
                                       + l d      d i+ +++++++ t  +  +   + +SAT++++
  gi|330507996|ref|YP_004384424.1| 315 HHLWDPdsAWNDAIEYVHQTIHDRTGGEIVS--QLDFSATPKDN 356
                                       ***998778999*********8777765544..799****9854 PP

>> HEPN_AbiU2  AbiU2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.13   5.6e+02      54      70 ..     257     274 ..     254     283 .. 0.82
   2 ?    2.0   0.0     0.027   1.2e+02      87     125 ..     469     507 ..     443     517 .. 0.85
   3 ?    8.1   0.0   0.00039       1.8     116     146 ..    1085    1120 ..    1069    1141 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.13
                        HEPN_AbiU2  54 llelarlfDkskrs.lsl 70 
                                       l +++rl+D+skr+  sl
  gi|330507996|ref|YP_004384424.1| 257 LTNIHRLYDTSKRRsKSL 274
                                       5689*******9986555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.027
                        HEPN_AbiU2  87 relekardkeadekfpdavekefeellellrklikklkk 125
                                       +++++ + k+ ++ f+++++++++e+l++lrkl  +l +
  gi|330507996|ref|YP_004384424.1| 469 KIKWMGGKKSGIPVFEESEKDIKDEDLRELRKLSRELDQ 507
                                       45699999999**********************998876 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00039
                        HEPN_AbiU2  116 lrklikklkk.....vleklkklRdkviAHrdlkkk 146 
                                        ++ ++++++k     +++k+  +R+++iAH +++ +
  gi|330507996|ref|YP_004384424.1| 1085 IKSKFAGAEKkdildTIDKIYSFRNEYIAHQEKELD 1120
                                        566666666677888***************666544 PP

>> ISN1  IMP-specific 5'-nucleotidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.7e-05      0.17      80     118 ..     611     649 ..     597     654 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.7e-05
                              ISN1  80 kkkekskLklLvPsigkfftkLpleeaflvedkkraiss 118
                                       ++k   +L++LvPsi++ +t++p  e +++ed k++ s+
  gi|330507996|ref|YP_004384424.1| 611 EHKDLNQLDMLVPSISPAYTRIPKLEGLTIEDVKKQFSA 649
                                       4677889****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.45
# Mc/sec: 7581.13
//
Query:       gi|330507997|ref|YP_004384425.1|  [L=687]
Description: DNA methylase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-40  139.7   0.1    3.3e-40  138.2   0.0    1.7  2  N6_N4_Mtase      DNA methylase
     0.0083   15.7   0.0       0.83    9.2   0.0    2.3  2  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.043   13.5   0.0        1.4    8.5   0.0    2.2  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
      0.058   13.2   0.0       0.21   11.4   0.0    2.0  2  N6-adenineMlase  Probable N6-adenine methyltransferase
       0.14   11.7   0.1        2.1    8.0   0.0    2.2  2  Cons_hypoth95    Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2   0.0   9.3e-44   3.3e-40       1     227 [.     102     410 ..     102     414 .. 0.83
   2 ?   -1.7   0.0      0.55     2e+03     117     165 ..     589     649 ..     545     668 .. 0.65

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 9.3e-44
                                       EEEEEE--SSSSSCS............................GCCGCCH.......HHHHHHHHHHHHHHHHHHEE CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy.......................endeqyeeeds.......yeeyleflekvlkevrrvLk 47 
                                       +dli++dpP+ +g d+                       +                  + yl+ ++++l +++++L+
  gi|330507997|ref|YP_004384425.1| 102 IDLIYIDPPFDVGADFtmqvplgdfddvaekdqsllemvA---------YrdmwgngTDSYLNMIYERLVLMHDLLA 169
                                       89**************888888655555555555554443.........05555555679***************** PP

                                       EEEEEEEEE-CCCHHTHHHHHHHHHTT-EEEEEEEEEEESSSTTTSTCCS-B--EEEEEEEESSTT-.......... CS
                       N6_N4_Mtase  48 ddgsifiniddseikkelkaladeifggffllnvivwkkpnsmpesnkdrltsthEyilvfsknkkyl......... 115
                                       ++g i++++d++   + + +l+ e+fg+  +ln ivw+++ s ++ ++ +l +  +yi++++k++ y+         
  gi|330507997|ref|YP_004384425.1| 170 ESGHILVHCDQRVNVY-IRLLLHEVFGEEHFLNEIVWQRT-SAGKTVSGNLPKNSDYIIWCTKSDTYQffgfrgels 244
                                       *************998.**********************9.88888888**************************** PP

                                       ......................................---GGGSSBSS-HHHHHHHHHH................. CS
                       N6_N4_Mtase 116 .....................................lkfnldaikvpyeekdklekrga................. 138
                                                                            + +    +  p++ ++ +e+r +                 
  gi|330507997|ref|YP_004384425.1| 245 demrklynkddgdgrgayttqpiiktsnpgpqttydyTDNRGRVWPCPKKGWRFNESRMHklendnrlvftdvirek 321
                                       ******99999999999999888888888888887774444444444444444444444466666667777788888 PP

                                       ...CHHHCC-B--BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHT CS
                       N6_N4_Mtase 139 ...ytskkkgkkiediWdlseiqsnekkskgdtkkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakel 212
                                          +++++ g ++ +iW  ++i+ n+   +++ ++ +p+qkP++l+ r+I+++tk+gd+v+D+F+GSGtT+++a++l
  gi|330507997|ref|YP_004384425.1| 322 yylQEREELGSQLPNIW--TDISGNALGYSKE-AQGYPTQKPEKLVSRIIEALTKEGDLVADFFCGSGTTGAVAERL 395
                                       88888888899999999..8888888887766.5667**************************************** PP

                                       T-EEEEEESSHHHHH CS
                       N6_N4_Mtase 213 grkfiGieieeeyve 227
                                       gr++i ++  + ++ 
  gi|330507997|ref|YP_004384425.1| 396 GRRWIMCDLGRFAIH 410
                                       ********9877665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.55
                                       ---GGGSSBSS-HHHHHHHHHH............CHHHCC-B--BSEEE-SCCCTTSTTS- CS
                       N6_N4_Mtase 117 kfnldaikvpyeekdklekrga............ytskkkgkkiediWdlseiqsnekksk 165
                                       kf   + +vp +e ++l+ r a             ++ ++gk++e  W++ ++++ ++ ++
  gi|330507997|ref|YP_004384425.1| 589 KFIPSLAEVPSKELAALKDRAAkdgfdfidfwavDFNWQEGKPFEHQWQDYRTRRDRSLKT 649
                                       5555556677777777777776777777777777777788888888884444444443333 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.0    0.0095        34      83     116 ..      88     120 ..      70     129 .. 0.85
   2 !    9.2   0.0   0.00023      0.83      24      77 ..     368     418 ..     361     436 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0095
                                       EEEE-STTTTSTTS-EEEEEE---STTTCHCHHH CS
                               MTS  83 evvasdvleeveekkfdlivsNPPfhagkatela 116
                                       ++v  ++l+++  +k+dli   PPf  g + + +
  gi|330507997|ref|YP_004384425.1|  88 KLVMASLLKDFR-GKIDLIYIDPPFDVGADFTMQ 120
                                       567788899999.*************99986655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00023
                                       HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHH CS
                               MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenlea 77 
                                       +e+l+k + + v+D+ cG G  ga++ +   +    ++d    A++ +++ l +
  gi|330507997|ref|YP_004384425.1| 368 IEALTK-EGDLVADFFCGSGTTGAVAERLGRR--WIMCDLGRFAIHTSRKRLID 418
                                       566666.5667*************99988777..89**********99997755 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 ?    2.4   0.0     0.029   1.1e+02     176     189 ..     100     113 ..      87     140 .. 0.80
   2 ?    8.5   0.0    0.0004       1.4       6      60 ..     361     414 ..     361     432 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.029
                                       TTE.EEEE--S-T. CS
                   MethyltransfD12 176 ieddivYlDPPYnp 189
                                        + d++Y+DPP + 
  gi|330507997|ref|YP_004384425.1| 100 GKIDLIYIDPPFDV 113
                                       5668*******985 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0004
                                       CTTHHHHHCCS-..--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHH CS
                   MethyltransfD12   6 rkllpeIkelipkdkgktfvepFaGggaVffeakkqgkkvlinDinedlinlyka 60 
                                       +kl++ I e + k  g+ +++ F+G+g  +  a + g + +++D+  + i   ++
  gi|330507997|ref|YP_004384425.1| 361 EKLVSRIIEALTK-EGDLVADFFCGSGTTGAVAERLGRRWIMCDLGRFAIHTSRK 414
                                       589*********9.889*************8888899*******98888877664 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.9e-05      0.21      70      99 ..      73     119 ..      66     187 .. 0.75
   2 ?   -2.7   0.0       1.3   4.5e+03      51      77 ..     413     437 ..     407     450 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.9e-05
                   N6-adenineMlase  70 fvfYdlnnpe...elp.......eelkgkfdviviDPPF.......l 99 
                                       ++ Yd++n +   + +       ++++gk+d+i iDPPF       +
  gi|330507997|ref|YP_004384425.1|  73 TRQYDFRNMLiwgDNKlvmasllKDFRGKIDLIYIDPPFdvgadftM 119
                                       68899999997653236676666777*************75555440 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                   N6-adenineMlase  51 kvlLleiDkrFealygeekfvfYdlnn 77 
                                       +  L+++ +r  +  g++ ++ +d+ n
  gi|330507997|ref|YP_004384425.1| 413 RKRLIDLQRRL-QADGQP-YRAFDVYN 437
                                       56799999999.665888.99999877 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00057       2.1     111     127 ..      99     115 ..      69     123 .. 0.78
   2 ?    1.0   0.0     0.082   2.9e+02      43      59 ..     376     392 ..     363     426 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00057
                                       S-EEEEEEE--SSSTTC CS
                     Cons_hypoth95 111 keefdivflDPPyakel 127
                                        +++d++++DPP+  ++
  gi|330507997|ref|YP_004384425.1|  99 RGKIDLIYIDPPFDVGA 115
                                       5689*********8774 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.082
                                       -EEEETT-TTSHHHHHH CS
                     Cons_hypoth95  43 arvLDlfaGsGalglEA 59 
                                         v D f+GsG+ g  A
  gi|330507997|ref|YP_004384425.1| 376 DLVADFFCGSGTTGAVA 392
                                       4577********99644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (687 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 4563.06
//
Query:       gi|330507998|ref|YP_004384426.1|  [L=208]
Description: hypothetical protein MCON_2056 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-13   50.5   0.3    3.7e-13   50.2   0.3    1.1  1  DUF3800   Protein of unknown function (DUF3800)


Domain annotation for each model (and alignments):
>> DUF3800  Protein of unknown function (DUF3800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.3     2e-17   3.7e-13       1     120 []       3     181 ..       3     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 2e-17
                           DUF3800   1 liYiDESGdnklkdgsspyfvlgg.....kkie.eikkleekikelkkky........................... 44 
                                       +i+iDE+G      g++  f++g      k  + ++++++ +ik lk k                            
  gi|330507998|ref|YP_004384426.1|   3 HIFIDEAGV----AGTTQNFIIGFaffsnKNYKlCVDNMKSEIKGLKGKEprelhfhdmspeikmefltclaelkgr 75 
                                       69******9....999999*****88887445577888889999998888999999999999999999999999999 PP

                           DUF3800  45 ....krlleriakflkkn......dlik...........sdeesdesilivldkkkkkekakkel.eil.ld..... 93 
                                           +   e+i+k+++++         +           ++  s e+i +++d+++++++ k++l ++l ++     
  gi|330507998|ref|YP_004384426.1|  76 fgyiHVQKEKIDKEFQNHpdnnliY--NlmlfylienlvKSGYSAEHITVYVDQRSTDRAIKRDLaRYLpMKvnpll 150
                                       9999555555555555544444430..24445556678878889**********99999988888755564467889 PP

                           DUF3800  94 ....esvkfvdSkesrglQlADlvagaifrk 120
                                             vk ++S++srg+Q+AD ++g+++rk
  gi|330507998|ref|YP_004384426.1| 151 kdrrLYVKWERSHNSRGIQCADSICGSVYRK 181
                                       99**************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1491.09
//
Query:       gi|330507999|ref|YP_004384427.1|  [L=80]
Description: hypothetical protein MCON_2057 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   0.1      0.079   12.7   0.0    1.9  2  RHS       RHS protein


Domain annotation for each model (and alignments):
>> RHS  RHS protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.4e-06     0.079      12      32 ..      12      32 ..      11      37 .. 0.86
   2 ?   -0.5   0.1     0.058     1e+03      20      24 ..      63      67 ..      61      71 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-06
                               RHS 12 PeeLtDanGeivWaaeydaWG 32
                                      P  L+    e+vW ++yd +G
  gi|330507999|ref|YP_004384427.1| 12 PHPLCGRKTELVWDGKYDEYG 32
                                      6678889999**********9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.058
                               RHS 20 GeivW 24
                                      G+++W
  gi|330507999|ref|YP_004384427.1| 63 GQTTW 67
                                      66666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 636.35
//
Query:       gi|330508000|ref|YP_004384428.1|  [L=129]
Description: death-on-curing family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-05   25.0   0.2    0.00035   21.4   0.1    2.5  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 !   21.4   0.1   1.9e-08   0.00035      49      97 .]      33      78 ..       4      78 .. 0.86
   2 ?   -0.7   0.0      0.16   2.8e+03      40      76 ..      87     107 ..      79     118 .. 0.51

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.9e-08
                                      HHHHHHHHCHHT-S-HHHHHHHHHHHHHHH--SSS-HHHHHHHHHHHHH CS
                               Fic 49 leelleylnelekeeplekaaalhyefekiHPFaDGNgRtarlllnllL 97
                                      le l++++n   ++e++ kaa+++y ++  HPF DG +Rta+ l +++L
  gi|330508000|ref|YP_004384428.1| 33 LEYLVDSIN--LEAELFRKAAWALY-LADRHPFWDGQKRTAFQLSDFIL 78
                                      455677888..8899999**99776.8899************9998876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.16
                                       -SCCCHHHHHHHHHHHHCHHT-S-HHHHHHHHHHHHH CS
                               Fic  40 appeevpaeleelleylnelekeeplekaaalhyefe 76 
                                       a  ee+ ++l                +k+a +   +e
  gi|330508000|ref|YP_004384428.1|  87 AEDEEIIQAL----------------IKIAEYKCDVE 107
                                       4444444444................44444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 983.74
//
Query:       gi|330508001|ref|YP_004384429.1|  [L=84]
Description: hypothetical protein MCON_2062 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.015   15.4   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   8.2e-07     0.015      10      57 ..      21      68 ..      12      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.2e-07
                   HicB_lk_antitox 10 dsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipe 57
                                      ++ +   + +l G++ +g+tlee  +n k +ie ++   +  g +ip 
  gi|330508001|ref|YP_004384429.1| 21 QELFYGEITELRGVWATGKTLEECGENLKGVIEGWIALRLRLGLAIPP 68
                                      4455556789**************************999999988874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 652.01
//
Query:       gi|330508002|ref|YP_004384430.1|  [L=537]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-41  140.2   0.0      6e-41  139.2   0.0    1.6  1  DUF4277    Domain of unknown function (DUF4277)
    8.1e-12   45.2   0.2    5.7e-11   42.5   0.2    2.0  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.0   6.7e-45     6e-41       3     109 .]      10     116 ..       8     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 6.7e-45
                           DUF4277   3 vksldhlglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfpeffedkplerLlgegve 79 
                                       + sldhlglva+++d+lg++e+ide ipk++++k+s++ ++ka+++ngLgf +r+Ly+fp++fe+++lerL+++gv 
  gi|330508002|ref|YP_004384430.1|  10 TLSLDHLGLVAAIFDALGISEVIDESIPKTRNCKLSHSAIIKAMVINGLGFAERRLYIFPSYFENLALERLFNPGVV 86 
                                       679************************************************************************** PP

                           DUF4277  80 aehlnddrlgrtLDklyeagvtklfteial 109
                                       +e++n+d++grtLD++ ++g t+lf++ia+
  gi|330508002|ref|YP_004384430.1|  87 PEDFNEDVVGRTLDRINKFGSTALFNNIAM 116
                                       ****************************86 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.2   6.4e-15   5.7e-11       9     213 ..     131     455 ..     124     456 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 6.4e-15
                         DDE_Tnp_1   9 vDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                       vD t++ v+g                  +d+rw        + + + +++++  g++l v+ ++gn++d k+l++++
  gi|330508002|ref|YP_004384430.1| 131 VDTTSFGVHGDYegldcnpameitlghpKDGRW------DLKQFIVSMVTNQC-GIPLFVQAHSGNKSDKKTLIETI 200
                                       666666666666666666554444444444444......55667788888888.9********************** PP

                         DDE_Tnp_1  70 delrpr....kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrn 142
                                       ++++ +     + ++ aD++ +s e+++ l      +i r++  +++ ++      +++++ +dr+ i++++ +  +
  gi|330508002|ref|YP_004384430.1| 201 QMFKSNldfsGKNYFAADSALFSSENIRLLG-DSTLWITRVPTTVREVKDLQRLDLEMKTCSDDRYSIFETEINYGG 276
                                       **********************999999999.55559****888888888666669999999999999999999999 PP

                         DDE_Tnp_1 143 k............................................................................ 143
                                                                                                                    
  gi|330508002|ref|YP_004384430.1| 277 Idqkwvvvdsremhaskaktfdrrigkeftearkslkklgyivfaceadarkaadrwisenphftltglsiceiskr 353
                                       99*************************************************************************** PP

                         DDE_Tnp_1 144 ...............................skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrk.f 188
                                                                      + ++   + +v+  n+++l+ e + ++y+ +  +E  F++lk+k f
  gi|330508002|ref|YP_004384430.1| 354 idskrgrpkkdeqlekgyliegevqrneatiANERSRLGRFVLASNDKTLEGELMLQYYKGQNAVEKGFRFLKDKsF 430
                                       ******************************99999999*************************************** PP

                         DDE_Tnp_1 189 gldrlryrglnrveaqllllllaln 213
                                       +   +++++ +r+ea  +++ l+l+
  gi|330508002|ref|YP_004384430.1| 431 RVAEVYLKKEERIEALSMIMVLSLL 455
                                       *******************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.23s 00:00:00.84 Elapsed: 00:00:00.39
# Mc/sec: 4126.60
//
Query:       gi|330508003|ref|YP_004384431.1|  [L=224]
Description: DNA-(apurinic or apyrimidinic site) lyase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-16   60.4   0.0    3.1e-16   59.8   0.0    1.3  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
    0.00042   20.0   0.0     0.0015   18.3   0.0    2.0  2  HHH       Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.037   14.0   0.0       0.07   13.1   0.0    1.4  1  DUF2400   Protein of unknown function (DUF2400)
      0.073   13.7   0.0       0.37   11.4   0.0    2.1  2  HHH_5     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   6.8e-20   3.1e-16       1     108 []      36     181 ..      36     181 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 6.8e-20
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       v++ilsq+tsd +  r++++l++ +g  + e+l+ a+ e+++++ire G+ + Ka +i+e+   +            
  gi|330508003|ref|YP_004384431.1|  36 VMTILSQNTSDINSLRAFANLKRDYG--NYESLLLAPTEEVADCIREGGLANIKALRIQEVLLSIKrdrgamdigfl 110
                                       789**********************9..*********************************99999*********** PP

                                       ...............................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHHT CS
                                       ...............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ...............................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleellep 108
                                                                      g   ++++vD+hv r+ +rl+++ e+ +++k++k+le++++p
  gi|330508003|ref|YP_004384431.1| 111 egmdkdeamsylldlpgvgpktasivllfafG--MPFMPVDTHVFRVSQRLGLVPENLSPEKAQKALERIVPP 181
                                       *****************************555..79*******************************988876 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.9   8.5e+03      21      28 ..      72      79 ..      72      80 .. 0.79
   2 !   18.3   0.0   3.4e-07    0.0015      13      29 ..     122     138 ..     116     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.9
                                      HHHHHHHH CS
                               HHH 21 pktAeaIl 28
                                      +++A++I+
  gi|330508003|ref|YP_004384431.1| 72 EEVADCIR 79
                                      579**997 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3.4e-07
                                       HHTSTT-SHHHHHHHHH CS
                               HHH  13 LlalPGVGpktAeaIls 29 
                                       Ll+lPGVGpktA  +l 
  gi|330508003|ref|YP_004384431.1| 122 LLDLPGVGPKTASIVLL 138
                                       899*********98886 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.6e-05      0.07     173     192 ..     146     165 ..     144     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                           DUF2400 173 iPlDvHvarvarklgllkrk 192
                                       +P+D+Hv+rv+++lgl+ ++
  gi|330508003|ref|YP_004384431.1| 146 MPVDTHVFRVSQRLGLVPEN 165
                                       8***************9655 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.58   2.6e+03      15      22 ..      52      59 ..      35      95 .. 0.56
   2 ?   11.4   0.0   8.2e-05      0.37       3      49 ..     121     134 ..     107     140 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.58
                                      HHHHHTTT CS
                             HHH_5 15 AlallsaG 22
                                      A a l+  
  gi|330508003|ref|YP_004384431.1| 52 AFANLKRD 59
                                      33333333 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8.2e-05
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAe 49 
                                       +Ll+++G+GpktA                                  
  gi|330508003|ref|YP_004384431.1| 121 YLLDLPGVGPKTA---------------------------------S 134
                                       3555555555555.................................4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1566.25
//
Query:       gi|330508004|ref|YP_004384432.1|  [L=414]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-62  209.1  19.7      6e-62  209.1  19.7    3.0  3  DUF4010   Domain of unknown function (DUF4010)
    6.3e-14   52.4  14.0    6.3e-14   52.4  14.0    3.5  3  MgtC      MgtC family


Domain annotation for each model (and alignments):
>> DUF4010  Domain of unknown function (DUF4010)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.8  14.8         2   1.8e+04     128     208 ..      41     117 ..       4     122 .. 0.59
   2 ?    1.1   0.1     0.029   2.6e+02      93     138 ..     113     157 ..     109     161 .. 0.76
   3 !  209.1  19.7   6.7e-66     6e-62       1     210 []     182     388 ..     182     388 .. 0.96

  Alignments for each domain:
  == domain 1  score: -5.8 bits;  conditional E-value: 2
                           DUF4010 128 AlkfallfalilllakaaqeyfGdaglyalaalsGladvdAitlslarlaaegtlsaat...aalaillavlsntlv 201
                                        +    l+ l+  l++ +  ++G+  l+a+ als+++   A+  + a     g+++ ++   a++a +l++l+n   
  gi|330508004|ref|YP_004384432.1|  41 FI----LISLLGALSATLAAHYGS--LFAVGALSSFIILVAVGYASAVSSL-GRIDLTAavaAVVAFVLGMLANDPD 110
                                       33....333333344444444443..6788888888888777554444333.5555444113667778899999888 PP

                           DUF4010 202 Kavlalv 208
                                       K++la++
  gi|330508004|ref|YP_004384432.1| 111 KIALAVS 117
                                       8888876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.029
                           DUF4010  93 lallallvaalllrrrekeeeeeelelenPlelksAlkfallfali 138
                                       +++++l++++ +++ +++ ++   +e  n  +l   lk++++ ++i
  gi|330508004|ref|YP_004384432.1| 113 ALAVSLAIITTWILATRTVTHRY-VEALNEADLLDTLKMGIIALVI 157
                                       45566666666777777777666.8899999999999999999888 PP

  == domain 3  score: 209.1 bits;  conditional E-value: 6.7e-66
                           DUF4010   1 VlisaisfagYvalrllgarrGllltgllGGlvSStAvtlslarrskeepelarllaagillAnavmllrvllivav 77 
                                       +l+s i+++gY+++r+lga+rGl ltg+lGGl+SS Avt sla++sk +p+l +++++++ +A++++++rv +i+a+
  gi|330508004|ref|YP_004384432.1| 182 ILVSLIGYTGYILIRILGAERGLTLTGILGGLASSIAVTTSLAEESKINPQLLSSAVFATAIASSTVFPRVFFIAAI 258
                                       79*************************************************************************** PP

                           DUF4010  78 vnpallvalalpllalallallvaalllrrrekeeeeeelelenPlelksAlkfallfalilllakaaqeyfGdagl 154
                                       vn ++l+ l++pll ++++++++a ++ r+++ +  e  ++++ P+++ +Alk++ lfal+l+++++a  yfGd+g+
  gi|330508004|ref|YP_004384432.1| 259 VNKEVLPDLFIPLLTMTAVGVALAYISHRKSPPQGGE--VKVSDPFRILPALKLGSLFALVLIISRLAGLYFGDTGI 333
                                       ***************9988888888888777777755..7************************************* PP

                           DUF4010 155 yalaalsGladvdAitlslarlaaegtlsaataalaillavlsntlvKavlalviG 210
                                       ya+++lsGl+dvdAitls+a+la+ +tl++++aa+ i+lav++ntlvK+++a+++G
  gi|330508004|ref|YP_004384432.1| 334 YAASILSGLVDVDAITLSMATLAR-STLTPSMAATSITLAVIANTLVKLGMAYLLG 388
                                       ***********************8.***************************9987 PP

>> MgtC  MgtC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4  14.0     7e-18   6.3e-14       2     120 ..      10     134 ..       9     135 .. 0.82
   2 ?    0.7   0.8     0.074   6.6e+02      27      62 ..     204     242 ..     176     265 .. 0.54
   3 ?   -0.7   3.9       0.2   1.8e+03      51      93 ..     366     410 ..     310     413 .. 0.54

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 7e-18
                              MgtC   2 llAlllGlliGleRel...rek...aaGlRTfaLvalgaalfvllslelaesrvaaqvvsgigflgagvilkekega 72 
                                       l+A+l+G+liG eR++   +ek   +aGlRTf+L++l++al++ l+ ++  s  a + +s  ++l+a    +  ++ 
  gi|330508004|ref|YP_004384432.1|  10 LVAMLIGALIGTERQRrlaEEKvrgVAGLRTFILISLLGALSATLAAHY-GSLFAVGALSSFIILVAVGYASAVSSL 85 
                                       79**************544233678********************6665.456666666666666666666566667 PP

                              MgtC  73 kvkglTTaaslwvtaaiGllvgl.glyllavvatvlvllllallreler 120
                                          +lT a+++ v++++G+l+   + ++lav ++++++ +la  +  +r
  gi|330508004|ref|YP_004384432.1|  86 GRIDLTAAVAAVVAFVLGMLANDpDKIALAVSLAIITTWILATRTVTHR 134
                                       99******************996368***************99988776 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.074
                              MgtC  27 faLvalgaalfvllslelae...srvaaqvvsgigflga 62 
                                        +L ++++ l++ +++ ++    s++  q++s  +f +a
  gi|330508004|ref|YP_004384432.1| 204 LTLTGILGGLASSIAVTTSLaeeSKINPQLLSSAVFATA 242
                                       334444444444332222113344444444444444443 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.2
                              MgtC  51 aq..vvsgigflgagvilkekegakvkglTTaaslwvtaaiGllv 93 
                                       a+  ++++i+   + + +++  g++ +g  Taa l+ +a+ G+l 
  gi|330508004|ref|YP_004384432.1| 366 ATsiTLAVIANTLVKLGMAYLLGSREFGNRTAAILLPMALAGILS 410
                                       211211111111122222233344778888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2959.39
//
Query:       gi|330508005|ref|YP_004384433.1|  [L=522]
Description: Na+/solute symporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-52  176.5  33.6    1.3e-51  175.8  33.6    1.4  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 !  175.8  33.6   7.3e-56   1.3e-51       1     406 []      41     455 ..      41     455 .. 0.94

  Alignments for each domain:
  == domain 1  score: 175.8 bits;  conditional E-value: 7.3e-56
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr....nagalTlpd 73 
                                       + +agr+l+ +   l + +s  s+  ++G+aG+++a G   ++ ++ + l + + +l+++ +l     ++g +T+ d
  gi|330508005|ref|YP_004384433.1|  41 FLVAGRNLGFWTFTLLVVSSICSGMTILGVAGLGYATGWPSIWEQIFVPLCAAVCILFFGSKLHavaaKTGYVTMQD 117
                                       789*************************************9999999889999999999***999999********* PP

                               SSF  74 ylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiq 150
                                       y+++Rf + r ++  sa++ + + +++l  + ++  + +  ++ + y+ a++++a++++ Yt++GGl A+     iq
  gi|330508005|ref|YP_004384433.1| 118 YFAHRFYSPRGIRGTSAIIGVFISIIYLVGQYISISMVLSWLFKIPYQWALVIGAVIVMGYTILGGLYAIGMASLIQ 194
                                       **********9999999999999****************************************************** PP

                               SSF 151 avlmlvgalilliivllevGgleslveklkeaapkvvdl....lt.pdslkllrdpltalslwlglvlGvaglphil 222
                                       ++++l+g l++   v+ ++Ggl ++ + l+e++++++ l    ++ p++   +  p+   s+  +l +G+a +ph++
  gi|330508005|ref|YP_004384433.1| 195 GMMILLGVLLVGPAVIDAAGGLTHVNTVLAEMDVNMTHLwypqVHpPYAGYAFMTPMYLVSFFFLLTFGLAAAPHVV 271
                                       *********************************99988866663357777789************************ PP

                               SSF 223 vRflaakdakailkgvlkltivlilvligmisiilfaiklagavp.kavgtevgvsniaypeLvvkllpnllaGlll 298
                                         +laa + +    + l + ++ ++++    + ++ a ++a     ++ + + + +++ ++     ++p ++a l+ 
  gi|330508005|ref|YP_004384433.1| 272 NNVLAAREDRYFKWAPLAAFVIYAVIMYICKITGFAARSMAEEGMiAMPTGVSNPADYSFIVASEYVFPGIFAPLVA 348
                                       *******************99999999999999999999988733333344455567888888899*********** PP

                               SSF 299 avmlAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafa 375
                                        ++l+a+mst + l+l   s ++ D+Y +++ k+ a+ek +  +sr +++  +++ + la+ ++ + +++l+ +a++
  gi|330508005|ref|YP_004384433.1| 349 VIVLSAVMSTTDRLMLTIGSYVSWDIYRQFINKE-ASEKSITLLSRAAIVASTVITLYLAWSNPPELLAWLIWMAIG 424
                                       *********************************9.**************************998888********** PP

                               SSF 376 glasavlavillalfwkrvneqGAlagliiG 406
                                       ++ ++++  +  +l+w r++++GAla++i+G
  gi|330508005|ref|YP_004384433.1| 425 VMLACFVTPLFAGLYWRRATREGALASMILG 455
                                       *****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.53
# Mc/sec: 2954.43
//
Query:       gi|330508006|ref|YP_004384434.1|  [L=415]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete 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   82.5   0.2    6.2e-23   80.9   0.1    1.9  2  Transposase_20  Transposase IS116/IS110/IS902 family
    6.1e-23   81.4   0.0    1.6e-22   80.1   0.0    1.7  2  DEDD_Tnp_IS110  Transposase
     0.0093   15.6   0.0       0.02   14.5   0.0    1.5  1  SET_assoc       Histone lysine methyltransferase SET associat
  ------ inclusion threshold ------
      0.023   15.0   0.0      0.073   13.4   0.0    1.9  1  Ish1            Putative stress-responsive nuclear envelope p
      0.028   14.4   0.1      0.078   13.0   0.1    1.8  1  Hjc             Archaeal holliday junction resolvase (hjc)
      0.089   12.6   0.1       0.27   11.0   0.0    1.9  2  BING4CT         BING4CT (NUC141) domain
       0.19   12.0   3.9          1    9.7   0.5    2.7  2  DUF4164         Domain of unknown function (DUF4164)


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.1   2.4e-26   6.2e-23       2      87 .]     254     340 ..     253     340 .. 0.95
   2 ?   -2.8   0.0       3.1   8.1e+03      48      78 ..     377     407 ..     372     414 .. 0.66

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 2.4e-26
                    Transposase_20   2 elLesipGiGpvtaaallaei.gdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaair 77 
                                       +l++sipGi++v a+a+laei  d+++f+++++l ++aG++p +n+S++kk++g+++k Gn+ l+ +L eaA+aa++
  gi|330508006|ref|YP_004384434.1| 254 NLIQSIPGISKVSASAILAEIgTDMSQFPDEAHLSSWAGVCPGNNESAGKKKSGKTQK-GNSFLKGTLAEAAWAASK 329
                                       689******************9999***************************999999.*****************7 PP

                    Transposase_20  78 an.pelrayye 87 
                                        + ++  a+y+
  gi|330508006|ref|YP_004384434.1| 330 VKrSTYNAFYQ 340
                                       76699999997 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.1
                    Transposase_20  48 GkkkrrgriskrGnrrlRraLyeaAlaaira 78 
                                       G  + + r +kr  r + r+L  a   ++r+
  gi|330508006|ref|YP_004384434.1| 377 GAEEANERATKRKERSMIRLLEKAGYEVVRT 407
                                       5555567888888888888777777666654 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.0   6.1e-26   1.6e-22       1     152 [.       9     155 ..       9     158 .. 0.91
   2 ?   -3.8   0.0       4.2   1.1e+04      54      74 ..     385     405 ..     384     406 .. 0.80

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 6.1e-26
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvl..ls.ervpndeeglealleklaakagevlvvveatghygallvaflleagitvv 74 
                                       +G+Dv+++k d+c+ +   ++   ++ +++++  ++le+l ++ ++k   +++++e+tg y+++++++  e ++t+v
  gi|330508006|ref|YP_004384434.1|   9 AGMDVHEKKVDVCIAHGPLEKSpkFEiRTFSTMTSDLEDLKSW-LKKYNVTTIGMESTGVYWKPIFNI-MEGEFTIV 83 
                                       69*************98777773333346888899********.9999***************98887.899***** PP

                    DEDD_Tnp_IS110  75 vvnplavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLd 151
                                       + n+   k++      ++KtD  D k IA+llr  g l ++  ++ +++eLr l+r r++lv ++t++knrl+++L+
  gi|330508006|ref|YP_004384434.1|  84 LANAQRLKAIP-----RKKTDIMDCKRIAKLLR-YGLLPNSFIPPREIRELRDLNRTRRKLVGMMTSEKNRLTKVLE 154
                                       ****9999985.....79***************.******************************************8 PP

                    DEDD_Tnp_IS110 152 q 152
                                       +
  gi|330508006|ref|YP_004384434.1| 155 S 155
                                       6 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.2
                    DEDD_Tnp_IS110  54 atghygallvaflleagitvv 74 
                                       at+++ ++++ +l++ag++vv
  gi|330508006|ref|YP_004384434.1| 385 ATKRKERSMIRLLEKAGYEVV 405
                                       567778888999999999986 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 !   14.5   0.0   7.9e-06      0.02       8      37 ..      39      68 ..      34      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.9e-06
                         SET_assoc  8 pvhkvtvedlkkrLkkyeweriledktGyY 37
                                      +++++++edlk  Lkky+++ i ++ tG Y
  gi|330508006|ref|YP_004384434.1| 39 STMTSDLEDLKSWLKKYNVTTIGMESTGVY 68
                                      689999***********************9 PP

>> Ish1  Putative stress-responsive nuclear envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.8e-05     0.073       2      18 ..      39      57 ..      38      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                              Ish1  2 dtWSd..sdLkkWLdshGi 18
                                      +t +   +dLk+WL+++++
  gi|330508006|ref|YP_004384434.1| 39 STMTSdlEDLKSWLKKYNV 57
                                      55555579**********8 PP

>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1     3e-05     0.078       2      26 ..     389     413 ..     388     415 .] 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                                       HHHHHHHHHHHTT-EEEEBSCSSSS CS
                               Hjc   2 yERelvkiLrergfavvRsagSgga 26 
                                       +ER ++++L++ g++vvR ++S  a
  gi|330508006|ref|YP_004384434.1| 389 KERSMIRLLEKAGYEVVRTCTSEIA 413
                                       7*********************866 PP

>> BING4CT  BING4CT (NUC141) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.6   9.3e+03      64      70 ..     176     182 ..     174     190 .. 0.80
   2 ?   11.0   0.0   0.00011      0.27      39      76 ..     368     405 ..     351     407 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.6
                           BING4CT  64 VrsLLeK 70 
                                       +rsLLeK
  gi|330508006|ref|YP_004384434.1| 176 IRSLLEK 182
                                       899**99 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                           BING4CT  39 GsGepnfdaleanpfetkkqrrereVrsLLeKlqpelI 76 
                                         G p  d+  ++ +e +++r+er   +LLeK  +e++
  gi|330508006|ref|YP_004384434.1| 368 KTGAPYQDTGAEEANERATKRKERSMIRLLEKAGYEVV 405
                                       67999***************************988876 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.061   1.6e+02      36      65 ..     133     163 ..     123     182 .. 0.68
   2 ?    9.7   0.5    0.0004         1       9      46 ..     194     240 ..     186     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.061
                           DUF4164  36 eleaei.ealgedrsRLaeeLdqaearaarl 65 
                                         ++++   ++++++RL + L +++ +++++
  gi|330508006|ref|YP_004384434.1| 133 RTRRKLvGMMTSEKNRLTKVLESSNIKLSSV 163
                                       4444433789999999999999888877665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0004
                           DUF4164   9 altrLeaaldsLEkavdrrleaerkr.........deleaeiealge 46 
                                       a   L++++d LEka+d +l+              d l+++i++++e
  gi|330508006|ref|YP_004384434.1| 194 AKGSLKKKVDLLEKALDGKLTDHHRFllkmhmenlDHLARQIAKIDE 240
                                       6779****************988887887777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1155  (0.0644208); expected 358.6 (0.02)
Passed bias filter:                      687  (0.0383178); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2876.32
//
Query:       gi|330508007|ref|YP_004384435.1|  [L=395]
Description: transposase, OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-25   88.7   0.8    3.9e-25   87.6   0.8    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.8e-12   46.2   0.1    9.9e-12   45.1   0.1    1.5  1  OrfB_IS605      Probable transposase
      0.005   16.9   0.2      0.011   15.8   0.2    1.6  1  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
  ------ inclusion threshold ------
      0.014   15.5   1.9       0.12   12.5   0.2    2.4  2  zf-HC5HC2H_2    PHD-zinc-finger like domain
      0.049   13.5   1.1       0.12   12.3   0.5    1.9  2  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.052   13.1   2.8        4.7    6.8   0.1    2.4  2  zn-ribbon_14    Zinc-ribbon
      0.058   12.9   0.9       0.12   11.9   0.9    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
      0.061   13.3   1.4       0.15   12.0   1.4    1.7  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        0.1   12.6   0.1        0.2   11.7   0.1    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.13   12.1   1.8       0.32   10.9   1.8    1.5  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.17   12.0   0.0       0.34   11.0   0.0    1.5  1  Exonuc_VII_S    Exonuclease VII small subunit
        2.6    7.8   6.1       0.68    9.7   0.7    2.3  2  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.8   2.6e-28   3.9e-25       1      69 []     302     370 ..     302     370 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 2.6e-28
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       fr+l+ ++eykake+Gi v+++np+yTS+tC++C +++++++ g  f+C++Cg+e ++D ++a+Ni +r
  gi|330508007|ref|YP_004384435.1| 302 FRQLQAFVEYKAKEAGIAVIYINPEYTSQTCPRCNHISRNNRRGVAFRCEKCGYETHADRVGAMNIEHR 370
                                       89****************************************************************765 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.1   6.6e-15   9.9e-12      11     119 ..     173     281 ..     164     282 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 6.6e-15
                        OrfB_IS605  11 pkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrr 87 
                                       + ++ ++  g+D+Gin La+ +t+d + +++ g ++k++    +ke+++lq+   +    +   r l+++  + +r+
  gi|330508007|ref|YP_004384435.1| 173 NIVDASTFMGVDVGINCLAVASTTDKQCKFFAGGEIKNHRNIRSKERRRLQKAGGRYLGTRSSMRTLKKIAGRETRF 249
                                       567788899********************************************999999999*************** PP

                        OrfB_IS605  88 rkhllhklathliktlkevgvetLnvgnmkdi 119
                                       ++ + hk++++l+k   ++gv+ + +++++di
  gi|330508007|ref|YP_004384435.1| 250 MTAVNHKVSKDLVKFATDNGVSAIGMEDLTDI 281
                                       ****************************9987 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 !   15.8   0.2   7.6e-06     0.011       2      30 ..     332     361 ..     331     378 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.6e-06
                          zf-Mss51   2 CPvpkhkqt.apkhvdfeCpdCGiptycse 30 
                                       CP ++h    +++ v+f C +CG+ t+ ++
  gi|330508007|ref|YP_004384435.1| 332 CPRCNHISRnNRRGVAFRCEKCGYETHADR 361
                                       66666654436999*************876 PP

>> zf-HC5HC2H_2  PHD-zinc-finger like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.17   2.6e+02      71      87 ..     152     168 ..     148     209 .. 0.73
   2 ?   12.5   0.2   8.1e-05      0.12      15      82 ..     289     359 ..     280     379 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.17
                      zf-HC5HC2H_2  71 CskkeCktafHvtCala 87 
                                       C +k+ +  fH  Ca +
  gi|330508007|ref|YP_004384435.1| 152 CLHKNGAYFFHLACAKD 168
                                       66666667777777754 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8.1e-05
                      zf-HC5HC2H_2  15 ktsderwvHvlCallvpevsfsnvaerepvdvekikkerlkekCllCkkr.....kGaciqCskkeCktafHv 82 
                                        +++ r+ H + a+ + ++ ++ +a+   + v  i++e ++++C  C++      +G++++C k  C    H+
  gi|330508007|ref|YP_004384435.1| 289 VSTEFRYEHSSWAFRQLQAFVEYKAKEAGIAVIYINPEYTSQTCPRCNHIsrnnrRGVAFRCEK--CGYETHA 359
                                       4567789999999999999999999999999*****************9989999*******99..8888776 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 ?   -3.2   0.0       5.3     8e+03      37      47 ..     160     170 ..     159     174 .. 0.76
   2 ?   12.3   0.5   8.1e-05      0.12      10      41 ..     328     360 ..     324     371 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.3
                                       EE-CCCCTTS- CS
                              C1_1  37 lvHkkChekvp 47 
                                        +H  C++ +p
  gi|330508007|ref|YP_004384435.1| 160 FFHLACAKDIP 170
                                       58999998876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 8.1e-05
                                       S--B-TTT-SB--S.SSS-EEEETTT--EE-CC CS
                              C1_1  10 qptfCkhCgeflwg.kekqglkCswCkllvHkk 41 
                                        +++C  C+ + +   + ++++C+ C++  H +
  gi|330508007|ref|YP_004384435.1| 328 TSQTCPRCNHISRNnRRGVAFRCEKCGYETHAD 360
                                       5789******99999****************86 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3    0.0051       7.7       1      12 [.     330     341 ..     330     342 .. 0.91
   2 ?    6.8   0.1    0.0032       4.7       2       9 ..     349     356 ..     348     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0051
                      zn-ribbon_14   1 gkCerCGylSSq 12 
                                       ++C rC+++S +
  gi|330508007|ref|YP_004384435.1| 330 QTCPRCNHISRN 341
                                       79********98 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0032
                      zn-ribbon_14   2 kCerCGyl 9  
                                       +Ce+CGy 
  gi|330508007|ref|YP_004384435.1| 349 RCEKCGYE 356
                                       7******5 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.9   8.2e-05      0.12       2      27 ..     331     355 ..     330     362 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.2e-05
                                       EETTTTCEECHEETSTTCE.EESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergel.vCtdCGl 27 
                                       +CP C++  + +++ rg   +C++CG+
  gi|330508007|ref|YP_004384435.1| 331 TCPRCNH--ISRNNRRGVAfRCEKCGY 355
                                       7*****9..78999999877******7 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.4    0.0001      0.15      19      45 ..     330     355 ..     312     356 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                     Zn_Tnp_IS1595  19 fvCPhCgsrkayriktrg.lfqCkeCrk 45 
                                       ++CP+C   ++ r ++rg  f+C++C++
  gi|330508007|ref|YP_004384435.1| 330 QTCPRCN--HISRNNRRGvAFRCEKCGY 355
                                       79*****..55555554427******98 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00013       0.2      59      96 ..     318     357 ..     292     369 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                       T-EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSSS- CS
                              HypA  59 gaeLeieevpvkvrCreCgkefeleek..alrCpkCgsad 96 
                                        a++ i+ +  + +C +C++  + +++  a+rC+kCg + 
  gi|330508007|ref|YP_004384435.1| 318 IAVIYINPEYTSQTCPRCNHISRNNRRgvAFRCEKCGYET 357
                                       3577788888999******999977755799*****9864 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 ?   10.9   1.8   0.00021      0.32       4      34 ..     332     360 ..     331     361 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                                       ESTTTSBEEEEECSCCCEEEESSSS-EEESS CS
                    RNA_POL_M_15KD   4 CpkCgNlLlpkedkegknfeCrqCgYeepad 34 
                                       Cp C+   ++++ + g+ f C +CgYe  ad
  gi|330508007|ref|YP_004384435.1| 332 CPRCNH--ISRNNRRGVAFRCEKCGYETHAD 360
                                       999997..8999999988********97665 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 ?   11.0   0.0   0.00023      0.34       7      36 ..       3      32 ..       1      35 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                      Exonuc_VII_S  7 eLeeIvekLEsgelsLeeslklyeeGvkLl 36
                                       +++Iv kL+ ++ +L e+l+ + +G+  +
  gi|330508007|ref|YP_004384435.1|  3 LIKTIVLKLDVPDNDLAELLATFSRGMNYA 32
                                      5789***********************876 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.5      0.43   6.4e+02      17      22 ..     332     337 ..     331     338 .. 0.87
   2 ?    9.7   0.7   0.00045      0.68       1      11 [.     348     358 ..     348     359 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.43
                      Rubredoxin_2  17 CpsCgs 22 
                                       Cp C++
  gi|330508007|ref|YP_004384435.1| 332 CPRCNH 337
                                       ****86 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00045
                      Rubredoxin_2   1 YvCsqCGfesa 11 
                                       ++C++CG+e++
  gi|330508007|ref|YP_004384435.1| 348 FRCEKCGYETH 358
                                       8********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 2882.83
//
Query:       gi|330508008|ref|YP_004384436.1|  [L=272]
Description: inositol-1-monophosphatase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-29  102.5   0.0    3.4e-29  102.2   0.0    1.1  1  Inositol_P  Inositol monophosphatase family
    0.00082   18.9   0.0     0.0012   18.3   0.0    1.2  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0   3.8e-33   3.4e-29      40     265 ..      46     265 ..      14     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 3.8e-33
                                       HHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEETT CS
                        Inositol_P  40 edlvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwivDPiDGTknFvrgipqvaVsigllveg 116
                                         + + +d+a+e ++l++l+ +  +  +l+ee ++       ++d  +  +DP+DGT n ++gip +a si  +  +
  gi|330508008|ref|YP_004384436.1|  46 GTPTKVIDRAAENAVLDVLQSSGMGFLVLSEERGEVRI--GENPD-HFLHLDPLDGTFNAISGIPFYALSI-YISGD 118
                                       457889**************************887655..22455.7***********************9.56678 PP

                                       EEEEEEEEETTTTEEECEETTTEEEETC.EEEEECTTSEGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCHEEEB CS
                        Inositol_P 117 kpvlGviaqPllgqlysaakgkGaflng.eklplsrappiseallvtlfavssrkdtseasllekvesavsaegvrs 192
                                          lG i++ + gq++ a +g+Ga+  + e++ +sr+++ +++++    a+  r++t     + ++  +v++   r 
  gi|330508008|ref|YP_004384436.1| 119 DCRLGYIYDLARGQRFYAEAGRGAYAGSgERICVSRNEDFKNFSIS---AYTIRPNT---GRITGIGNRVRRI--RT 187
                                       899*********************98556*********77777662...23333333...5577787777766..99 PP

                                       ESSHHHHHHHHHHTSTSEEEEEC..EBHHHHHHHHHHHHHTTEEEEESSSC....SSSTTSSEEEEESCHHHHHHHH CS
                        Inositol_P 193 vgssalklaavaeGkadaylefg.rekkWDhAAGeaileeaGGvvtdakge....grlllargiiaanqkelaella 264
                                       +gs+ l++a+va+G +da+++ +  +   D+AAG++i+eeaGG+v d +g+      ++ ++++++++++  +e l+
  gi|330508008|ref|YP_004384436.1| 188 LGSASLEMALVARGMLDAFVDLRgMMRVVDVAAGILIIEEAGGRVSDSDGNqlhmAGDMWQKRCLVGSNGLRHEDLL 264
                                       9*********************99999************************88874555566666666566676666 PP

                                       H CS
                        Inositol_P 265 a 265
                                       +
  gi|330508008|ref|YP_004384436.1| 265 K 265
                                       5 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 !   18.3   0.0   1.4e-07    0.0012      32     116 ..      20     101 ..       7     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.4e-07
                            FBPase  32 lkiisskvrkaelvnllGlagaeNvtGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvaf 108
                                        ++++s++r    +   G+      +G   k +D  a++ + ++l++s++   + SEE+ e+ +    ++  + + +
  gi|330508008|ref|YP_004384436.1|  20 SRAVASSIRDMIGTASGGQMVNMGADGTPTKVIDRAAENAVLDVLQSSGMGFLVLSEERGEVRIG---ENPDHFLHL 93 
                                       455555555433333345555556789999********************************998...56677899* PP

                            FBPase 109 DPlDGSSn 116
                                       DPlDG  n
  gi|330508008|ref|YP_004384436.1|  94 DPLDGTFN 101
                                       *****876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); 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 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1920.00
//
Query:       gi|330508009|ref|YP_004384437.1|  [L=277]
Description: NAD(+)/NADH kinase [Methanosaeta concilii GP6]
Scores for complete 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-58  198.0   0.2    2.2e-58  197.7   0.2    1.1  1  NAD_kinase  ATP-NAD kinase
     0.0018   17.9   0.0     0.0033   17.1   0.0    1.4  1  DAGK_cat    Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
      0.054   13.7   0.1        8.9    6.6   0.0    2.6  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 !  197.7   0.2   3.8e-62   2.2e-58      66     291 ..      48     262 ..       7     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 197.7 bits;  conditional E-value: 3.8e-62
                                       EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEE CS
                        NAD_kinase  66 dtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekre 142
                                       +  ++++++   +vd+i+ +GGDGT+l+  + +++  +P+lg+n+G++gfl ++ep++a e++++ll  ++ v++r+
  gi|330508009|ref|YP_004384437.1|  48 RPPSSVQEMERLKVDFIVSIGGDGTILRTIHKMAD-PVPILGINMGTLGFLVDVEPADALETIKRLLS-GFVVDERS 122
                                       556788999999**********************7.*******************************9.899***** PP

                                       EEEEEEEETTE......EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--E CS
                        NAD_kinase 143 vldavimrskgeediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgpl 219
                                       +l+  + ++ +          + + ne+ + +++++++ie+e+ vd++l+e++++dg+i++t+tGstay++saGgp+
  gi|330508009|ref|YP_004384437.1| 123 RLK-LLLNGVC---------MPRATNEIAFLTASPAKMIEFEILVDGSLMEDFRADGVIIATATGSTAYAMSAGGPI 189
                                       ***.5556666.........47889**************************************************** PP

                                       E-TT---EEEEEESESSS----EEE-TT-EEEEEE-.SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
                        NAD_kinase 220 isPgvlailivpicPhslssrpiVvssssklrirva.srseallaldGseelelspgdevrvtasdkkfklir 291
                                       ++P+v+ai++vp+ P++lssrp V++ +s +++r++  ++eal+++dG++ +++s +d + ++++++++++++
  gi|330508009|ref|YP_004384437.1| 190 VDPRVDAIVLVPMAPFKLSSRPWVMPGNSVIEVRLKlPEKEALVVVDGQSSTNISTKDSIVISKAKTPARFVK 262
                                       ***********************************************************************97 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.5e-07    0.0033      48      92 ..      53      93 ..      41     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.5e-07
                                      HHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-SS CS
                          DAGK_cat 48 akeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlGt 92
                                      ++e+++ +vd+iv +GGDGt+   ++ +++    ++p+  i +Gt
  gi|330508009|ref|YP_004384437.1| 53 VQEMERLKVDFIVSIGGDGTILRTIHKMAD----PVPILGINMGT 93
                                      78999999*******************999....55555556665 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 ?    4.4   0.0    0.0073        43       7      44 ..      52      89 ..      50     142 .. 0.83
   2 ?    6.6   0.0    0.0015       8.9      11      34 ..     162     185 ..     159     202 .. 0.88
   3 ?   -2.1   0.0      0.74   4.4e+03      92     114 ..     227     249 ..     217     255 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0073
                                      HHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEE CS
                              PK_C  7 aveaaeelgakaIvvltesGetArliskyrpkvpiiav 44
                                       v+  e l+++ Iv +   G+  r i k+   vpi+ +
  gi|330508009|ref|YP_004384437.1| 52 SVQEMERLKVDFIVSIGGDGTILRTIHKMADPVPILGI 89
                                      57778999***************************987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0015
                                       HHHHT-SEEEEE-SSSHHHHHHHH CS
                              PK_C  11 aeelgakaIvvltesGetArlisk 34 
                                        e+  a+ ++++t +G+tA  +s 
  gi|330508009|ref|YP_004384437.1| 162 MEDFRADGVIIATATGSTAYAMSA 185
                                       67889999***********99986 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.74
                                       -STSEEEEEE-SSSS..SS--EE CS
                              PK_C  92 kkgdevvvtaGtpkgesgttNtl 114
                                       ++++ +vv+ G ++ + +t + +
  gi|330508009|ref|YP_004384437.1| 227 PEKEALVVVDGQSSTNISTKDSI 249
                                       66778888888877655656655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2029.04
//
Query:       gi|330508010|ref|YP_004384438.1|  [L=352]
Description: ABC transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-40  138.5  16.2    3.2e-40  138.3  16.2    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
    1.5e-32  112.7  25.0    1.8e-32  112.4  15.4    2.7  3  ABC2_membrane    ABC-2 type transporter
    1.2e-10   41.1  13.9    2.2e-10   40.3  13.9    1.4  1  ABC2_membrane_2  ABC-2 family transporter protein
    0.00031   20.3   3.1    0.00031   20.3   3.1    1.8  2  CcmB             CcmB protein
      0.009   16.0   8.6      0.009   16.0   8.6    2.7  3  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.06   13.2   2.1        3.4    7.6   0.4    2.8  2  InaF-motif       TRP-interacting helix


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 !  138.3  16.2   1.1e-43   3.2e-40       2     344 ..      25     344 ..      24     345 .. 0.91

  Alignments for each domain:
  == domain 1  score: 138.3 bits;  conditional E-value: 1.1e-43
                   ABC2_membrane_3   2 sfliitlllPiilvlllglifsnsveddentpiavvdednsslsqqlvealeaspsvelvyevdseeeakkalkngd 78 
                                       +++ ++l+ P++l++l+g+++s +    + +++++vd       + l +++++ ++++ + ++ s+++a+k++ +g 
  gi|330508010|ref|YP_004384438.1|  25 RTIGLILFAPVVLMILFGYALSGEM---TGVQLGLVDGG---GHEPLRDYIASLDDFD-ILYLGSQSDAEKLISEGR 94 
                                       677788999*******999988665...89********8...57889***********.****************** PP

                   ABC2_membrane_3  79 idgilvipkgfskdllkgesatvtvlinssnlnsskailnalns.llqqlnasalvlqseatstsaninvestqlee 154
                                       +dg++vi+              v vl++ss l++s  +  a+++ ++++              t    ++ ++  + 
  gi|330508010|ref|YP_004384438.1|  95 LDGAVVIQPEE-----------VGVLLDSSSLQISERVMAAVQTgVSREVS----------IRTDSYPPIITRYIFG 150
                                       ******97655...........89********************9987753..........3344444555566799 PP

                   ABC2_membrane_3 155 elsnvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll... 227
                                       +   + +++ + ++ ++++f+ ++++a s+++E++ +++e  +vs++s+ +++ + ilg  lv+++q++ +ll+   
  gi|330508010|ref|YP_004384438.1| 151 YDLEMIDTIGPaILGLVAFFFAFIIAAISFLRERTLGTLEKFMVSPLSRVEIVSGYILGFSLVAIIQSATTLLIviy 227
                                       999999999998999999**************************************************877764446 PP

                   ABC2_membrane_3 228 afglgipfgnlgl.llllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsi 303
                                       +fg  +p++++ l ++  +ll g  ++alg ++s + +++  + ++i+ivi++ ++++g+++p++++p++l+ i+ i
  gi|330508010|ref|YP_004384438.1| 228 LFG--VPMKGSPLdAFAIILLLGAGALALGSFVSNFARSEFQVVQFIPIVIIPQIVLCGVFWPVQSVPGFLRPISNI 302
                                       999..****77776*************************************************************** PP

                   ABC2_membrane_3 304 iPffapglgllrli.tgdplweillsliilalfavvylllal 344
                                       +P+++ +++l  ++ +g++l++il++li+l +f+ +++++a 
  gi|330508010|ref|YP_004384438.1| 303 LPLTYASDALRAIMlKGASLYQILPDLIFLGAFFMLMFIAAT 344
                                       *************86888*********************996 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0017       5.1       3      42 ..       9      47 ..       7      61 .. 0.84
   2 !  112.4  15.4   6.2e-36   1.8e-32      52     210 .]     155     317 ..     126     317 .. 0.89
   3 ?   -1.2   0.5      0.37   1.1e+03      60      69 ..     334     343 ..     321     351 .. 0.46

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0017
                     ABC2_membrane  3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgn 42
                                      ++++  r ++q +rd+ ++  + l+ p++l+++fg++ ++
  gi|330508010|ref|YP_004384438.1|  9 VGVVALRVVRQLKRDRRTI-GLILFAPVVLMILFGYALSG 47
                                      57888999********888.99**************9984 PP

  == domain 2  score: 112.4 bits;  conditional E-value: 6.2e-36
                     ABC2_membrane  52 r.....pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv 123
                                       +     p +l+  ++f+a ++++++++++er+ g+le+ +vspl s+ ++v +++l++ +v+++q++  lliv++l+
  gi|330508010|ref|YP_004384438.1| 155 MidtigPAILGLVAFFFA-FIIAAISFLRERTLGTLEKFMVSPL-SRVEIVSGYILGFSLVAIIQSATTLLIVIYLF 229
                                       133455677777777777.9999999******************.******************************** PP

                     ABC2_membrane 124 gldls.rfflflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPlt 199
                                       g++++ + + +++++ll++  a++lg ++s +a+s+ +++q++++v++p ++l+G+f+p++s+p++l+ i+ ++Plt
  gi|330508010|ref|YP_004384438.1| 230 GVPMKgSPLDAFAIILLLGAGALALGSFVSNFARSEFQVVQFIPIVIIPQIVLCGVFWPVQSVPGFLRPISNILPLT 306
                                       ****9777********************************************************************* PP

                     ABC2_membrane 200 yavealrsnlf 210
                                       ya +alr++++
  gi|330508010|ref|YP_004384438.1| 307 YASDALRAIML 317
                                       ********986 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.37
                     ABC2_membrane  60 vlflafsalt 69 
                                       ++f+ +++++
  gi|330508010|ref|YP_004384438.1| 334 AFFMLMFIAA 343
                                       2222222222 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 !   40.3  13.9   7.5e-14   2.2e-10       8     285 ..      17     349 ..      11     350 .. 0.70

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 7.5e-14
                   ABC2_membrane_2   8 frdlvrsrrfllltvllpli.......................dvalaylkdlgsslqseakaikeatlaleyveaa 61 
                                       +r+l r+rr+++l ++ p++                                              + +   y +  
  gi|330508010|ref|YP_004384438.1|  17 VRQLKRDRRTIGLILFAPVVlmilfgyalsgemtgvqlglvdgG---------------------GHEPLRDYIASL 72 
                                       68999************999555555555555543333333330.....................344444444444 PP

                   ABC2_membrane_2  62 sasdeaedtdqdlkv.............................................................. 76 
                                         +d++  ++q+ +                                                               
  gi|330508010|ref|YP_004384438.1|  73 DDFDILYLGSQSDAEklisegrldgavviqpeevgvlldssslqiservmaavqtgvsrevsirtdsyppiitryif 149
                                       444444444444433455555555555777777888888888888899999999999999999999999999***** PP

                   ABC2_membrane_2  77 ..........vstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatv 142
                                                 +++i+ ++  ++a +++a ++ +E++ gTl+  + +P sR ei+ g ++g ++++++  a +ll++ 
  gi|330508010|ref|YP_004384438.1| 150 gydlemidtiGPAILGLVAFFFAFIIAAISFLRERTLGTLEKFMVSPLSRVEIVSGYILGFSLVAIIqSATTLLIV- 225
                                       ***9**99997778888888889999999999********************************555555555555. PP

                   ABC2_membrane_2 143 llalaiilalgivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvael 219
                                             i  +g++++++ l  ++  ++ll++   +lalg ++S +ar s+ +    + ++++ +i+  +v  +v   
  gi|330508010|ref|YP_004384438.1| 226 ------IYLFGVPMKGSPLDAFA-IILLLGA--GALALGSFVSNFAR-SEFQVVQFIPIVIIPQIVLCGVFWPVQ-- 290
                                       ......44556655555443332.2333344..359***********.666777777777777777777765544.. PP

                   ABC2_membrane_2 220 lagpavpqeindflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkr 285
                                        ++p +   ++++ ++l+ t a ++l++ +l+g++   l++    l++l +    +++ ++ ++kr
  gi|330508010|ref|YP_004384438.1| 291 -SVPGF---LRPISNILPLTYASDALRAIMLKGAS---LYQILPDLIFLGAFFMLMFIAATLMLKR 349
                                       .44445...66677777777777777777777775...7788888888888888888888888877 PP

>> CcmB  CcmB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.2   3.5e+03      19      35 ..      25      41 ..      14      49 .. 0.61
   2 !   20.3   3.1     1e-07   0.00031      35     144 ..     147     257 ..     142     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                              CcmB 19 lllgllFfllvvtllpl 35
                                       ++gl+ f+ vv+++ +
  gi|330508010|ref|YP_004384438.1| 25 RTIGLILFAPVVLMILF 41
                                      45566666666655544 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1e-07
                              CcmB  35 lavGPdtallsriapgilWvaallaslLsldrlfaadfedGsLellllapvplellvlaKalAhwlltglplvllap 111
                                       + +G d++++ +i+p+il + a + +++ +   f  ++  G+Le+++++p++   +v + +l   l++ +    +  
  gi|330508010|ref|YP_004384438.1| 147 YIFGYDLEMIDTIGPAILGLVAFFFAFIIAAISFLRERTLGTLEKFMVSPLSRVEIVSGYILGFSLVAIIQSATTLL 223
                                       66899*************999999999999999*************************************9999999 PP

                              CcmB 112 llalllnleaaa..lgllaltLllGtpalsllgav 144
                                       ++  l+++++++  l + a+ LllG+ al+l g +
  gi|330508010|ref|YP_004384438.1| 224 IVIYLFGVPMKGspLDAFAIILLLGAGALAL-GSF 257
                                       9999999999872256789999***999975.444 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.18   5.3e+02      54      75 ..      27      48 ..      18      57 .. 0.60
   2 !   16.0   8.6     3e-06     0.009      59     154 ..     167     257 ..     146     289 .. 0.66
   3 ?   -1.6   0.4      0.74   2.2e+03     106     117 ..     333     344 ..     315     350 .. 0.53

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.18
                   ABC2_membrane_4 54 ftlllllplilgiiasylifrE 75
                                      ++l+l+ p++l i+ +y ++ E
  gi|330508010|ref|YP_004384438.1| 27 IGLILFAPVVLMILFGYALSGE 48
                                      4455555666555555555544 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3e-06
                   ABC2_membrane_4  59 llplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvl 135
                                       +  +   iia++++ rE++ +tl + ++ P sr++++ + +i+ + l+++++ +t+l+   +  l+g v++++++ l
  gi|330508010|ref|YP_004384438.1| 167 VAFFFAFIIAAISFLRERTLGTLEKFMVSPLSRVEIVSG-YILGFSLVAIIQSATTLLI--VIYLFG-VPMKGSP-L 238
                                       4445556799************************99877.5555555555554444433..333444.6677555.5 PP

                   ABC2_membrane_4 136 ellkkclelgllvffavlp 154
                                        ++ ++l+lg++ +++ + 
  gi|330508010|ref|YP_004384438.1| 239 DAFAIILLLGAGALALGSF 257
                                       6666677666666554443 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.74
                   ABC2_membrane_4 106 svllmlvtflit 117
                                        +++ml++ ++t
  gi|330508010|ref|YP_004384438.1| 333 GAFFMLMFIAAT 344
                                       222332222222 PP

>> InaF-motif  TRP-interacting helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.4    0.0011       3.4       5      22 ..     199     216 ..     197     218 .. 0.89
   2 ?    4.0   0.1     0.015        46       7      16 ..     222     231 ..     221     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
                        InaF-motif   5 RlltVvaYllsVSlaAiv 22 
                                       R+  V +Y+l+ Sl+Ai+
  gi|330508010|ref|YP_004384438.1| 199 RVEIVSGYILGFSLVAII 216
                                       777899**********96 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.015
                        InaF-motif   7 ltVvaYllsV 16 
                                       l++v+Yl++V
  gi|330508010|ref|YP_004384438.1| 222 LLIVIYLFGV 231
                                       79*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 2414.99
//
Query:       gi|330508011|ref|YP_004384439.1|  [L=302]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-30  106.0   0.0    4.1e-30  105.1   0.0    1.5  1  ABC_tran    ABC transporter
    2.2e-15   57.2   0.1    2.4e-07   30.9   0.0    2.3  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    1.8e-08   34.5   0.0     0.0038   17.0   0.0    2.1  2  AAA_15      AAA ATPase domain
      1e-05   25.1   0.0    0.00048   19.6   0.0    2.1  1  SMC_N       RecF/RecN/SMC N terminal domain
    9.4e-05   23.0   0.0    0.00019   22.0   0.0    1.5  1  AAA_23      AAA domain
    0.00015   21.4   0.0    0.00035   20.2   0.0    1.5  1  AAA_29      P-loop containing region of AAA domain
    0.00018   21.3   0.0     0.0097   15.6   0.0    2.1  2  AAA_24      AAA domain
     0.0027   17.9   0.0      0.014   15.6   0.0    2.0  1  AAA_33      AAA domain
     0.0059   16.5   0.0      0.011   15.7   0.0    1.4  1  NACHT       NACHT domain
      0.008   16.6   0.0      0.022   15.2   0.0    2.0  1  AAA         ATPase family associated with various cellular ac
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.025   14.6   0.0    1.6  1  TsaE        Threonylcarbamoyl adenosine biosynthesis protein 
      0.031   14.6   0.0      0.092   13.1   0.0    1.9  1  AAA_16      AAA ATPase domain
      0.034   14.4   0.0       0.17   12.1   0.0    2.3  1  AAA_22      AAA domain
       0.04   14.5   0.0      0.081   13.5   0.0    1.6  1  AAA_18      AAA domain
      0.041   13.6   0.0       0.14   11.9   0.0    1.8  2  AAA_30      AAA domain
      0.045   13.7   0.5       0.11   12.3   0.0    1.9  2  ATPase_2    ATPase domain predominantly from Archaea
      0.082   12.9   0.0       0.16   12.0   0.0    1.5  1  AAA_5       AAA domain (dynein-related subfamily)
      0.088   13.1   0.0       0.29   11.5   0.0    1.8  2  AAA_19      AAA domain
        0.1   12.3   0.0       0.16   11.7   0.0    1.3  1  ATP_bind_1  Conserved hypothetical ATP binding protein
       0.13   11.6   0.1        7.8    5.8   0.0    2.4  3  ATPase      KaiC
       0.17   11.1   0.0        3.1    6.9   0.0    2.1  2  DUF815      Protein of unknown function (DUF815)
       0.18   11.7   0.0       0.45   10.4   0.0    1.7  2  NTPase_1    NTPase
        0.2   11.2   0.0        0.6    9.7   0.0    1.7  2  cobW        CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.0   5.2e-33   4.1e-30       1     136 [.      24     166 ..      24     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 5.2e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ +++++ +g ++ ++G+nG+GK+t+++++ +ll+ ++Ge+++ ++++++   e+  ++ig+++q++ l p+ltv+
  gi|330508011|ref|YP_004384439.1|  24 LDGLDVDIPRGVTYCLLGPNGSGKTTFIRAIVRLLRLDSGELRVLDRPVSD--VEEIYSRIGYMTQHKALYPDLTVE 98 
                                       68899*********************************************9..9*********************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en             +++++ie++l+ ++l+e +++ +      LSgG+ qr++la++l+ +p+llllDEpt
  gi|330508011|ref|YP_004384439.1|  99 ENmqfysglygikgqDREDRIEELLRMVDLSEHRKRLA----GALSGGMYQRLSLACTLVHRPELLLLDEPT 166
                                       ************99888999************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0     3e-08   2.3e-05       3      28 ..      38      63 ..      37     124 .. 0.74
   2 !   30.9   0.0   3.1e-10   2.4e-07     234     297 ..     136     196 ..     105     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3e-08
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrd 28
                                      +l GpNgsGK+++++a+  l rld+ 
  gi|330508011|ref|YP_004384439.1| 38 CLLGPNGSGKTTFIRAIVRLLRLDSG 63
                                      699*****************876222 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 3.1e-10
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       a  lS G+ + l l+  l  ++    lll+DEp  g++P+l ++++e + + ++ g  vi+tTH
  gi|330508011|ref|YP_004384439.1| 136 AGALSGGMYQRLSLACTLVHRP---ELLLLDEPTVGIDPRLRKTFWEYFQSMAEAGKTVIITTH 196
                                       4456667655545555555455...9***********************888888********* PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.9e-06    0.0038      19      50 ..      29      61 ..      21     111 .. 0.80
   2 !   15.7   0.0   1.2e-05    0.0097     324     364 ..     157     196 ..     146     197 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.9e-06
                            AAA_15 19 idlseelt.vliGkNnsGKSsilealdlFlnnk 50
                                      +d+   +t +l G+N+sGK+++++a+  +l  +
  gi|330508011|ref|YP_004384439.1| 29 VDIPRGVTyCLLGPNGSGKTTFIRAIVRLLRLD 61
                                      4554554449****************9999866 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.2e-05
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       + +ll++EP + + p + k ++++++++a+ +k  viitTH
  gi|330508011|ref|YP_004384439.1| 157 PELLLLDEPTVGIDPRLRKTFWEYFQSMAEAGK-TVIITTH 196
                                       6799****************************9.9****** PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.2e-07   0.00048      28     204 ..      38     200 ..      26     215 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.2e-07
                                       EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvk 104
                                       +++GpNGSGK+ ++ Ai  +L  +s  +lr  +    ++       v++ +  i +  + k+     ++++++ +++
  gi|330508011|ref|YP_004384439.1|  38 CLLGPNGSGKTTFIRAIVRLLRLDSG-ELRVLDR--PVSD------VEEIYSRIGYMTQHKA---LYPDLTVEENMQ 102
                                       689**************888887666.6765332..2333......3333333433333333...457777777776 PP

                                       TTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 105 rkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                             y i+g++ ++  ++ell+++++s++      +LSgG  +     L +A   v++  l llDe    +D + 
  gi|330508011|ref|YP_004384439.1| 103 FYSG-LYGIKGQD-REDRIEELLRMVDLSEHrkrlagALSGGMYQ----RLSLACTLVHRPELLLLDEPTVGIDPRL 173
                                       6555.79999987.5678999999999998888888889999665....4445556677778999999999999999 PP

                                       HHHHHHHHHHHCTT.SEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N 176 vkkvaellkekskn.aQfivislreemlek 204
                                       +k + e++++  +    +i++++      +
  gi|330508011|ref|YP_004384439.1| 174 RKTFWEYFQSMAEAgKTVIITTHLM---DE 200
                                       9999999999888834445555443...33 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.4e-07   0.00019      11      40 ..      25      55 ..      16      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.4e-07
                            AAA_23 11 rdqeidFskglt.lItGpNGaGKTTildAik 40
                                      ++ ++d  +g+t ++ GpNG+GKTT+++Ai 
  gi|330508011|ref|YP_004384439.1| 25 DGLDVDIPRGVTyCLLGPNGSGKTTFIRAIV 55
                                      66777777776669***************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 !   20.2   0.0   4.5e-07   0.00035      14      46 ..      26      58 ..      22      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.5e-07
                            AAA_29 14 ghtieidlkg.atlltGpsGsGKSTllDAiqalL 46
                                      g +++i  +g ++ l Gp+GsGK+T++ Ai  lL
  gi|330508011|ref|YP_004384439.1| 26 GLDVDIP-RGvTYCLLGPNGSGKTTFIRAIVRLL 58
                                      5667775.677999****************9998 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05    0.0097       2      47 ..      34      76 ..      33     118 .. 0.76
   2 ?    3.7   0.0     0.057        44     107     137 ..     173     203 ..     171     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                            AAA_24  2 klkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie 47
                                      ++ +++ Gp+g+GKTt+++ +   + ++ ++ G  ++ ++ + d+e
  gi|330508011|ref|YP_004384439.1| 34 GVTYCLLGPNGSGKTTFIRAI---VRLLRLDSGELRVLDRPVSDVE 76
                                      5679****************9...6666667777777777777665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.057
                            AAA_24 107 laeefrrllkklqelrknvifiahektrkde 137
                                       l++ f+++ + + e++k+vi++ h+  +   
  gi|330508011|ref|YP_004384439.1| 173 LRKTFWEYFQSMAEAGKTVIITTHLMDEAER 203
                                       78899*******************9987655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-05     0.014       4      91 ..      39     209 ..      37     226 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                            AAA_33   4 lvGlpGsGKstlaerllkklg.....avllssdt........................................... 32 
                                       l G++GsGK+t+++ +++ l        +l+ ++                                           
  gi|330508011|ref|YP_004384439.1|  39 LLGPNGSGKTTFIRAIVRLLRldsgeLRVLDRPVsdveeiysrigymtqhkalypdltveenmqfysglygikgqdr 115
                                       57**************9777676765566777779999999999999988888888888888887777777777777 PP

                            AAA_33  33 .................lrrrlfgtdqqskt..............................dytrvldrlyqilnel 62 
                                                                     +                                  + +rl+++  e+
  gi|330508011|ref|YP_004384439.1| 116 edrieellrmvdlsehrK------------RlagalsggmyqrlslactlvhrpelllldePTVGIDPRLRKTFWEY 180
                                       777775555555554330............13344444444445555666666667777532223556678877888 PP

                            AAA_33  63 arkalsagrnvildatnlsrrerarflkl 91 
                                       ++++++ag++vi+   + +++er +++  
  gi|330508011|ref|YP_004384439.1| 181 FQSMAEAGKTVIITTHLMDEAERCQMVGY 209
                                       88888899999998888888888655544 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.4e-05     0.011       2      25 ..      36      59 ..      35      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                      + +l G++GsGKTt+++ ++++++
  gi|330508011|ref|YP_004384439.1| 36 TYCLLGPNGSGKTTFIRAIVRLLR 59
                                      5699****************9986 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 !   15.2   0.0   2.8e-05     0.022       2      23 ..      38      59 ..      37     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.8e-05
                                      EEESSTTSSHHHHHHHHHHHHT CS
                               AAA  2 llyGppGtGKTllakavakelg 23
                                      +l Gp G GKT++++a+++ l 
  gi|330508011|ref|YP_004384439.1| 38 CLLGPNGSGKTTFIRAIVRLLR 59
                                      899**************99874 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.1e-05     0.025      20      45 ..      35      60 ..      10      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                                      EEEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE 20 dvilLeGdLGaGKTtlvrglakalgv 45
                                       + +L G+ G+GKTt++r++++ l +
  gi|330508011|ref|YP_004384439.1| 35 VTYCLLGPNGSGKTTFIRAIVRLLRL 60
                                      4589*****************99866 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   0.00012     0.092      22      52 ..      32      77 ..      20     203 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekd...............g 52
                                      +r+    l G+ G+GK++ +r++ r l+ d               +
  gi|330508011|ref|YP_004384439.1| 32 PRGVTYCLLGPNGSGKTTFIRAIVRLLRLDsgelrvldrpvsdveE 77
                                      555667799***************9887774433333333333330 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022      0.17       9      38 ..      38      86 ..      33     212 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                            AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaee.....................e 38
                                      ++ G+ G+GKTt +r +++ l  ++   e                      
  gi|330508011|ref|YP_004384439.1| 38 CLLGPNGSGKTTFIRAIVRLLRLDSG--ElrvldrpvsdveeiysrigymT 86
                                      688**************999843222..13355555544444444443332 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0    0.0001     0.081       2      44 ..      38      78 ..      38     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0001
                            AAA_18  2 lltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44
                                      +l G+ G+GKtt+ +++ ++l     ++++   ++++ +v++ 
  gi|330508011|ref|YP_004384439.1| 38 CLLGPNGSGKTTFIRAIVRLL--RLDSGELRVLDRPVSDVEEI 78
                                      799***************998..55555555555555555554 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   0.00018      0.14      21      46 ..      37      62 ..      31      91 .. 0.85
   2 ?   -2.1   0.0       3.5   2.8e+03      27      57 ..     185     214 ..     178     225 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                            AAA_30 21 avltGpAGtGKttalkalreaweaag 46
                                       +l Gp G+GKtt ++a++++++ + 
  gi|330508011|ref|YP_004384439.1| 37 YCLLGPNGSGKTTFIRAIVRLLRLDS 62
                                      5789**************99988664 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.5
                            AAA_30  27 AGtGKttalkalreaweaaggrviglAptgk 57 
                                       A +GKt ++++   + ea+  +++g+   g+
  gi|330508011|ref|YP_004384439.1| 185 AEAGKTVIITT-HLMDEAERCQMVGYMRAGR 214
                                       44667666643.2233333444444444444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015      0.11      23      48 ..      37      63 ..      32      85 .. 0.83
   2 ?   -3.0   0.4       7.3   5.7e+03       3      17 ..     114     128 ..     113     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                          ATPase_2 23 yfiYGpegsGKtaLlkeiienl.edkd 48
                                      y + Gp gsGKt++++ i+  l +d++
  gi|330508011|ref|YP_004384439.1| 37 YCLLGPNGSGKTTFIRAIVRLLrLDSG 63
                                      6778***************99844544 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.3
                          ATPase_2   3 dRekelkeleeiler 17 
                                       dRe  ++el+++++ 
  gi|330508011|ref|YP_004384439.1| 114 DREDRIEELLRMVDL 128
                                       999999999999875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.16       3      24 ..      38      60 ..      36      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                      EEE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5  3 lLvGppGtgKselaerlaaal.n 24
                                      +L+Gp G+gK+++++ + ++l  
  gi|330508011|ref|YP_004384439.1| 38 CLLGPNGSGKTTFIRAIVRLLrL 60
                                      9****************999953 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   0.00037      0.29      12      35 ..      36      59 ..      29      70 .. 0.85
   2 ?   -2.9   0.0       9.7   7.5e+03      22      31 ..     188     197 ..     184     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00037
                            AAA_19 12 vllvtaGpGtGKTrvlkhivallv 35
                                      + +++++ G+GKT+ +++iv+ll 
  gi|330508011|ref|YP_004384439.1| 36 TYCLLGPNGSGKTTFIRAIVRLLR 59
                                      46899***************9886 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.7
                            AAA_19  22 GKTrvlkhiv 31 
                                       GKT ++++ +
  gi|330508011|ref|YP_004384439.1| 188 GKTVIITTHL 197
                                       8998887543 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 ?   11.7   0.0   0.00021      0.16       2      23 ..      40      61 ..      39      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelr 23
                                      +Gp GsGKttf++a++ +l+l 
  gi|330508011|ref|YP_004384439.1| 40 LGPNGSGKTTFIRAIVRLLRLD 61
                                      7*************99988765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0      0.01       7.8      16      35 ..      31      50 ..      22      54 .. 0.88
   2 ?   -2.9   0.0       4.6   3.6e+03      72      95 ..     113     135 ..      96     151 .. 0.71
   3 ?    3.1   0.0     0.066        51     140     170 ..     173     203 ..     161     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.01
                            ATPase 16 ipegrvvlitGepGtGKtif 35
                                      ip+g ++ + G  G+GKt+f
  gi|330508011|ref|YP_004384439.1| 31 IPRGVTYCLLGPNGSGKTTF 50
                                      89****************99 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.6
                            ATPase  72 wdlekleeegklaiidasesaees 95 
                                        d e+  ee +l ++d+se++++ 
  gi|330508011|ref|YP_004384439.1| 113 QDREDRIEE-LLRMVDLSEHRKRL 135
                                       455555555.78889998888765 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.066
                            ATPase 140 aReilrqlvrvlkklgvTailvsekssseea 170
                                       +R+++ + ++ +++ g T i+++   +++e+
  gi|330508011|ref|YP_004384439.1| 173 LRKTFWEYFQSMAEAGKTVIITTHLMDEAER 203
                                       799999****************998777665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0039       3.1      58     111 ..      39      91 ..      34     110 .. 0.70
   2 ?    1.8   0.0      0.14   1.1e+02     196     241 ..     173     218 ..     166     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0039
                            DUF815  58 LwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellrerperfil 111
                                       L G  G+GK + ++a+++ ++ ++  Lr+++     +++++++++ +  + ++  l
  gi|330508011|ref|YP_004384439.1|  39 LLGPNGSGKTTFIRAIVRLLRLDSgeLRVLDRP---VSDVEEIYSRIGYMTQHKAL 91 
                                       89**************99877665558887644...45555556665555555555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.14
                            DUF815 196 dqeeYleiveklakklglelekeeleeeAlewalergsrsgRvArq 241
                                        +++++e  +++a+  ++ + +++l +eA + ++    r+gR+A q
  gi|330508011|ref|YP_004384439.1| 173 LRKTFWEYFQSMAEAGKTVIITTHLMDEAERCQMVGYMRAGRMAAQ 218
                                       5789999999999999999999**********************98 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00057      0.45       4      24 ..      39      59 ..      36      87 .. 0.79
   2 ?   -3.2   0.0       8.5   6.6e+03     113     134 ..     176     197 ..     155     207 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00057
                                      EE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellk 24
                                      + Gp G+GKtT+++ +++ll+
  gi|330508011|ref|YP_004384439.1| 39 LLGPNGSGKTTFIRAIVRLLR 59
                                      679**************9986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.5
                                       HHHHHHHHHHTTTSEEEEE--S CS
                          NTPase_1 113 kfkeaveevLksekpvlavihr 134
                                       +f e  + + + +k v+++ h 
  gi|330508011|ref|YP_004384439.1| 176 TFWEYFQSMAEAGKTVIITTHL 197
                                       5666666677777777777775 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 ?    9.7   0.0   0.00077       0.6       3      22 ..      37      56 ..      35      72 .. 0.83
   2 ?   -1.9   0.0       2.8   2.2e+03      11      25 ..     187     201 ..     182     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00077
                                      EEEEESTTCCHHHHHHHHHC CS
                              cobW  3 tvltGflGsGKTtLlnhlle 22
                                      + l G+ GsGKTt+++++++
  gi|330508011|ref|YP_004384439.1| 37 YCLLGPNGSGKTTFIRAIVR 56
                                      5688************9984 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                                       CCHHHHHHHHHCT-- CS
                              cobW  11 sGKTtLlnhllenra 25 
                                       +GKT ++++ l ++a
  gi|330508011|ref|YP_004384439.1| 187 AGKTVIITTHLMDEA 201
                                       89**99998884433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2029.58
//
Query:       gi|330508012|ref|YP_004384440.1|  [L=371]
Description: hypothetical protein MCON_2075 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00034   20.8   0.0       0.97    9.7   0.0    2.4  2  CARDB        CARDB
     0.0018   18.5   0.0       0.34   11.2   0.0    3.0  3  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
     0.0025   18.1   0.1        3.7    7.9   0.0    2.5  2  DUF11        Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.044   12.6   0.2       0.93    8.2   0.0    2.2  2  BatD         Oxygen tolerance


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1   0.00044         2       2      71 ..      67     136 ..      66     164 .. 0.74
   2 !    9.7   0.0   0.00022      0.97      10      69 ..     238     301 ..     230     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00044
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE- CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtt 71 
                                       p+Lt   +l  s  ++gee  +t+t++N G ++s +++ +  +++ +    ++ ++ +L+ + ++  ++++  
  gi|330508012|ref|YP_004384440.1|  67 PNLTA--SLDRSRIYQGEETALTMTLTNRGRITSFQINEEPAANKREEilaAQREL-ELEKQRTVAQDVSVLL 136
                                       67777..888999*********************9999888888776545444444.5555555555555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00022
                                       EC-SEEETTSE.EEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEE CS
                             CARDB  10 lnpseafvgee.ntitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftw 69 
                                       ++p+++ +g+e n i++ vkN G++ + +  ++l  +  l    +++++p La++e+++  ++ 
  gi|330508012|ref|YP_004384440.1| 238 VTPTSLRPGSEgNVIRIRVKNVGDDRASDLVARLRPESGLYvsvDESPIPTLAPQEEAELLYKL 301
                                       5566666655437899******************98876555779**********999876665 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.025   1.1e+02       3      18 ..      80      95 ..      78     102 .. 0.87
   2 ?   -0.1   0.0      0.25   1.1e+03      60      79 .]     170     189 ..     154     189 .. 0.81
   3 !   11.2   0.0   7.5e-05      0.34       7      74 ..     250     317 ..     243     322 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.025
                       NPCBM_assoc  3 pGetvtltltvtndgt 18
                                      +Ge+++lt+t+tn g+
  gi|330508012|ref|YP_004384440.1| 80 QGEETALTMTLTNRGR 95
                                      8************996 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.25
                       NPCBM_assoc  60 tppagaaaGdyevtakarlt 79 
                                        + ++a +G y++ a++++t
  gi|330508012|ref|YP_004384440.1| 170 EAYENALPGSYRLLAQVNYT 189
                                       556799*********99986 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 7.5e-05
                       NPCBM_assoc   7 vtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGd.yevta 74 
                                       + +++ v+n g++ a+++  +l+  +G   v+v+   +++lap e++e   k+ ++++a +G+ y++++
  gi|330508012|ref|YP_004384440.1| 250 NVIRIRVKNVGDDRASDLVARLRPESGLY-VSVDESPIPTLAPQEEAELLYKLDVSKDALPGKnYQLKI 317
                                       34689999999999999999999999999.9*******************************9788776 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00082       3.7       2      28 ..      70      96 ..      69     141 .. 0.91
   2 !    7.7   0.0   0.00099       4.4       5      82 ..     238     307 ..     236     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00082
                             DUF11  2 tKtvdksevrpGdtvtytltvtNtgpa 28
                                      t + d+s++  G+++  t t+tN+g  
  gi|330508012|ref|YP_004384440.1| 70 TASLDRSRIYQGEETALTMTLTNRGRI 96
                                      5578999*****************975 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00099
                             DUF11   5 vdksevrpGdtvtyt.ltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtr 80 
                                       v+++ +rpG + +++ + v+N g + a+++v + + P++  yvsv  s         +++L++ e+a l +++ v++
  gi|330508012|ref|YP_004384440.1| 238 VTPTSLRPGSEGNVIrIRVKNVGDDRASDLVAR-LRPESGLYVSVDES--------PIPTLAPQEEAELLYKLDVSK 305
                                       678889999999997699*********888887.56888889999999........569***********9999998 PP

                             DUF11  81 ta 82 
                                        a
  gi|330508012|ref|YP_004384440.1| 306 DA 307
                                       76 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00021      0.93     255     305 ..      51     101 ..      49     133 .. 0.67
   2 ?    2.4   0.1     0.012        55     428     450 ..     345     369 ..     299     371 .] 0.62

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00021
                              BatD 255 lPaeglPadFsgavgsfslsaslskdelkvgepltltvtisGtGNlkllql 305
                                       +P e   ad+    g  +l+asl+++++ +ge   lt+t++ +G ++++q+
  gi|330508012|ref|YP_004384440.1|  51 IPPERFSADYYKVYGTPNLTASLDRSRIYQGEETALTMTLTNRGRITSFQI 101
                                       555555666666666666666666666666666666666666666666665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.012
                              BatD 428 fwlllllplllf..vvllllwrkrr 450
                                        w+l +l++l++  +vl++++r+++
  gi|330508012|ref|YP_004384440.1| 345 EWALAILLFLALlaAVLIIFIRRKK 369
                                       4644444444333334444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2779.97
//
Query:       gi|330508013|ref|YP_004384441.1|  [L=198]
Description: hypothetical protein MCON_2076 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-06   27.1   0.9    4.1e-06   27.1   0.9    1.8  3  PEMT      Phospholipid methyltransferase
  ------ inclusion threshold ------
      0.027   14.0   0.1      0.034   13.7   0.1    1.2  1  DUF1295   Protein of unknown function (DUF1295)


Domain annotation for each model (and alignments):
>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.2       1.5   1.3e+04      62      73 ..       7      18 ..       4      23 .. 0.43
   2 ?   -3.4   0.1       1.5   1.3e+04      81      88 ..      52      59 ..      44      68 .. 0.45
   3 !   27.1   0.9   4.6e-10   4.1e-06      15     106 .]      86     180 ..      69     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.5
                              PEMT 62 gflGlaLitgsa 73
                                      ++ ++ L++ s+
  gi|330508013|ref|YP_004384441.1|  7 AMAAYFLVFASV 18
                                      333444444443 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                              PEMT 81 lvllvyli 88
                                      l++l+ +i
  gi|330508013|ref|YP_004384441.1| 52 LIMLLPFI 59
                                      22222222 PP

  == domain 3  score: 27.1 bits;  conditional E-value: 4.6e-10
                              PEMT  15 llvlssiealgefgtfygdfFlelmd.......klvtsGiYrylnnPeyvgstlgflGlaLitgsaaglllallvll 84 
                                       ll  +++  +  f+t + df + + +       +lvt+G+Y +l+nP  ++ +l ++   ++t +++++ + +  ++
  gi|330508013|ref|YP_004384441.1|  86 LL-AAAMLLITLFQTGVLDFLGLEGRprpgrerALVTGGLYCHLRNPLFLFAILFLWTSPIMTMNLLTFNI-MATFY 160
                                       33.345666778888888877655448888888******************************99984433.33334 PP

                              PEMT  85 vylialkfvEephlakiYgkre 106
                                       +yl al   Ee+ l++ +gk++
  gi|330508013|ref|YP_004384441.1| 161 FYLGAL--HEERSLKEEFGKAY 180
                                       444444..5*********9975 PP

>> DUF1295  Protein of unknown function (DUF1295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.8e-06     0.034      85     232 ..      50     184 ..       8     187 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-06
                           DUF1295  85 lsllvvfvlQavllylvalpvllaaaskeeqalkaldviglalwlvgivlealaDqQlsafkkdpankgkvldsGLw 161
                                       l+l++++ +  +llyl    +++a        ++a++++++a++l+ +    + D    + +  p  +  +++ GL+
  gi|330508013|ref|YP_004384441.1|  50 LALIMLLPFIFILLYLPDEVIYIAPW-PAFGLMAAAQLLAAAMLLITLFQTGVLDFLGLEGRPRPGRERALVTGGLY 125
                                       33333333333333333333444433.23337789999***********9999***99999*****9999******* PP

                           DUF1295 162 rysRHPNYfgealiWwglflialealeglealaiagpllltlllvfvsgipllEkkalkkykdkeeyreYq 232
                                          R P +++ +l+ w   +++++ l+      i++      + +f+ g  l E+++lk+    ++y+eY+
  gi|330508013|ref|YP_004384441.1| 126 CHLRNPLFLFAILFLWTSPIMTMNLLTFN----IMA-----TF-YFYLGA-LHEERSLKEEF-GKAYEEYR 184
                                       ********************999986553....333.....11.222233.33333333322.35666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1340.60
//
Query:       gi|330508014|ref|YP_004384442.1|  [L=163]
Description: hypothetical protein MCON_2077 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 1082.11
//
Query:       gi|330508015|ref|YP_004384443.1|  [L=844]
Description: peptidase U32 [Methanosaeta concilii GP6]
Scores for complete 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-95  317.3   0.0    2.7e-74  249.2   0.0    3.1  2  Peptidase_U32  Peptidase family U32
    5.4e-21   75.3   0.0      1e-20   74.3   0.0    1.5  1  DUF3656        Collagenase


Domain annotation for each model (and alignments):
>> Peptidase_U32  Peptidase family U32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.2   0.0   3.1e-78   2.7e-74       3     231 ..      78     311 ..      76     313 .. 0.93
   2 !   63.1   0.0   2.3e-21   2.1e-17       9     228 ..     619     839 ..     614     843 .. 0.80

  Alignments for each domain:
  == domain 1  score: 249.2 bits;  conditional E-value: 3.1e-78
                     Peptidase_U32   3 klrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikaik 79 
                                       +l++yl +l++lg+da+ +qD+g++ lar+ +p+le h+Stq++i+n  ++ + ++ G++rvvlaRE+++eei++  
  gi|330508015|ref|YP_004384443.1|  78 DLAEYLVQLYDLGADAILLQDLGAASLARQLVPDLERHASTQMTIHNLPGALYAAQGGFNRVVLAREVTIEEIERWG 154
                                       5789***********************************************************************99 PP

                     Peptidase_U32  80 ekvp..dvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrldyrlieekekgeeepi...eedekgtyll 151
                                       +k++  ++ lEvfvhGalc++ysG+cllss+++grs+nrg+caqpcr++y l+  +++++ +p+   +  +k  y++
  gi|330508015|ref|YP_004384443.1| 155 QKMEkaGLGLEVFVHGALCYSYSGQCLLSSAIGGRSGNRGMCAQPCRKPYVLMHGRKDEYGRPVglqAVAQKESYII 231
                                       9999889********************************************88777766666551113445555*** PP

                     Peptidase_U32 152 spkdlclieelpelleaGvdslKIeGRmkspeyvatvvrvYreaidallagreevkeelkeeleklanrgltsgfll 228
                                       s++dl+++++l++++   v+slKIeGRmks +yva v+++Yr+a+d +++g ++ ++e +++l+ ++nr++tsg+ll
  gi|330508015|ref|YP_004384443.1| 232 STRDLSVYRHLDKIVRSPVQSLKIEGRMKSHQYVAIVTSIYRRALDGIARGSWSPSKEEERDLALAFNRDFTSGHLL 308
                                       ****************************************************9999*******************99 PP

                     Peptidase_U32 229 grk 231
                                       g k
  gi|330508015|ref|YP_004384443.1| 309 GAK 311
                                       876 PP

  == domain 2  score: 63.1 bits;  conditional E-value: 2.3e-21
                     Peptidase_U32   9 eklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikaikekvp.. 83 
                                         l +++v++++v  +g +  ++e++pe+++   +  n++n+ +++ l+ + +s + l+ Els +++k+ + ++   
  gi|330508015|ref|YP_004384443.1| 619 PLLSQVQVNGIMVENVGPAWAIKEKMPEMPIYGGSGLNVWNHLTAQALAPQ-FSWLTLSPELSSHQLKDAASALRal 694
                                       568899*********************************************.****************999988888 PP

                     Peptidase_U32  84 .....dvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrldyrlieekekgeeepieedekgtyllspkd 155
                                            + +lE  v+G+l v++    + + + +grs ++    q  ++   l  +           de  t+++++ +
  gi|330508015|ref|YP_004384443.1| 695 pgrdgNPKLELVVQGSLEVMVAEDSVPQLA-KGRSSEEFWGLQDFKHIFPLKVD-----------DEGRTHIFNSAE 759
                                       899989****************99887766.66664433333333332222222...........22346******* PP

                     Peptidase_U32 156 lclieelpelleaGvdslKIeGRmkspeyvatvvrvYreaidallagr.......eevkeelkeeleklanrgltsg 225
                                       +cli+ lpe+  +G+d + ++ R ++++y+ +v+ +Y +ai+++++         +e + +lk++++ la +g+t+g
  gi|330508015|ref|YP_004384443.1| 760 TCLIDLLPEICRIGLDGISLDARGRTESYARQVTGAYNQAIERTEKLLatdpaplKEGLLDLKARIQPLALGGITHG 836
                                       ******************************************98776633344433333444444444455577777 PP

                     Peptidase_U32 226 fll 228
                                       ++l
  gi|330508015|ref|YP_004384443.1| 837 HFL 839
                                       776 PP

>> DUF3656  Collagenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   1.2e-24     1e-20       1     106 [.     392     508 ..     392     509 .. 0.80

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1.2e-24
                           DUF3656   1 vyrtsdkklteelekslekseerkipvdlelaakegepl........kltvtde........leeAkkrplteenir 61 
                                       v+ t + +l +++e+ +++ e+  ipvd++l+ + g p+        +              +eeA +rp t e+i+
  gi|330508015|ref|YP_004384443.1| 392 VFLTGSTALARRAEEIAAR-ERASIPVDITLTWEDGFPVaegrldsgE-----LavargesrMEEAVNRPQTPEQIE 462
                                       5677777555555644444.8888*******87888666444334334.....04555699**************** PP

                           DUF3656  62 kqLsklGgtpFeleeieidldgl.fiPvseLnelRRealekLeear 106
                                       +q++k+GgtpF+++++e+d+ g+ f P+++Ln+lRR++l+ Le+a+
  gi|330508015|ref|YP_004384443.1| 463 SQMRKTGGTPFVVRKVEMDYPGGlFSPPGALNQLRRDLLAGLEKAV 508
                                       ********************8555*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (844 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); 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: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.40
# Mc/sec: 6306.05
//
Query:       gi|330508016|ref|YP_004384444.1|  [L=352]
Description: hypothetical protein MCON_2080 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        1.2    8.9   5.1       0.21   11.4   0.9    1.7  2  FA_desaturase  Fatty acid desaturase
        4.7    5.7   9.3         10    4.6   9.2    1.5  1  FapA           Flagellar Assembly Protein A
        6.4    7.6   8.2         20    6.0   3.7    3.0  3  Big_7          Bacterial Ig domain


Domain annotation for each model (and alignments):
>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.9   3.6e-05      0.21      79     177 ..     180     280 ..     168     293 .. 0.75
   2 ?   -1.8   0.3      0.37   2.2e+03     144     177 ..     308     324 ..     285     344 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                     FA_desaturase  79 pdlaplalsrfeglfryllrlllgllvlgwllalvlglwlrrlarrrapsksrrrkwrllawlllllawlglwlall 155
                                        d ap ++ +++g+  + l    g + lg++l ++++++ r ++   + s+  r+   ++ + + ++a+l++++ ++
  gi|330508016|ref|YP_004384444.1| 180 EDKAPPREDKWGGFDLFSLISIIGYFILGLILVKHIPVIFRTVDEEIRTSTLLRTVLGFIIIIASFIALLLVAITVV 256
                                       4555666699999999999999999****999999998999999999999999888888888888888777777777 PP

                     FA_desaturase 156 lllglall..lwlvplllllflla 177
                                       +l+  +++  l++v l+l ++++a
  gi|330508016|ref|YP_004384444.1| 257 GLPIAVVStfLVIVGLMLSGTFVA 280
                                       777766667444444444444444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.37
                     FA_desaturase 144 llawlglwlalllllglalllwlvplllllflla 177
                                       l   l               l+l+p+l +l+ ++
  gi|330508016|ref|YP_004384444.1| 308 LN--L---------------LFLIPYLGGLVSIV 324
                                       11..2...............33444333333332 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   9.2    0.0017        10     195     263 ..      83     151 ..      51     163 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0017
                              FapA 195 GnIkfkG.sViikGnVeegmkVkasgditikGvvesatieAggnItikgGiigkgkskikAggnisakfv 263
                                       G++   G  V ++ +V  g  V  +g i   G v    + Agg++ i  G     ++ i+Ag+ + +  +
  gi|330508016|ref|YP_004384444.1|  83 GDVIAAGgQVYVNSDV-GGKVVAVGGTIDLRGDVGTNLVAAGGQVSILPGRTVGRDALISAGNAVNSGRI 151
                                       4444444466666677.66666677777777777777777777777766665556666666666665555 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.3      0.06   3.6e+02       2      25 ..      41      65 ..      41      71 .. 0.85
   2 ?    6.0   3.7    0.0033        20       3      40 ..      59      96 ..      58     119 .. 0.79
   3 ?    2.2   0.1     0.054   3.2e+02      13      38 ..     150     175 ..     141     189 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.06
                                      EEEEEE--TT--EB.TSEEEEEEEE CS
                             Big_7  2 tvtitsPangatvs.ggtvtisasA 25
                                      t++i++P + + +  g+ v+i+a +
  gi|330508016|ref|YP_004384444.1| 41 TISIVNPVEDDIFAaGNIVNINAPV 65
                                      799***********99999998865 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0033
                                      EEEEE--TT--EBTSEEEEEEEEE-SS-EEEEEEEETT CS
                             Big_7  3 vtitsPangatvsggtvtisasAsddggvskVefyvdg 40
                                      v+i +P + a+v ggtv+i+a +  d+  +  ++yv+ 
  gi|330508016|ref|YP_004384444.1| 59 VNINAPVDSAVVAGGTVNINAPVKGDVIAAGGQVYVNS 96
                                      89******************999888655555666554 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.054
                                       -EBTSEEEEEEEEE-S.S-EEEEEEEE CS
                             Big_7  13 tvsggtvtisasAsdd.ggvskVefyv 38 
                                        ++ gt t+ as  ++ g+  kV+fy 
  gi|330508016|ref|YP_004384444.1| 150 RIN-GTMTVYASDFNNtGSAGKVDFYQ 175
                                       344.5777777766668999*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 2503.59
//
Query:       gi|330508017|ref|YP_004384445.1|  [L=245]
Description: TrmH family RNA methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-29  101.6   0.0    5.4e-29  101.2   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 !  101.2   0.0     3e-33   5.4e-29       2     142 .]       3     158 ..       2     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 3e-33
                                       EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEE CS
                    SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfa 77 
                                       l+vvlve+ ++gN+G++aR++k+fg+++l lv+p++    ++   ++a++a++vl+  + +++l+eal+  + +   
  gi|330508017|ref|YP_004384445.1|   3 LRVVLVEPLYEGNVGSVARAMKNFGFHDLALVNPCKI---EDYGCAMASHARDVLQmSRSFSTLAEALEGANLV--- 73 
                                       89*******************************9887...7777899*********77889*********9999... PP

                                       EEEESTT-SEGCCS................HHH......TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS-- CS
                    SpoU_methylase  78 lvatslkgkslsei................dlk......ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLN 132
                                        v+t++k  + ++                 + +      + val++G+Ed Gl+ ++++l+d +v+Ip+s+e++ +N
  gi|330508017|ref|YP_004384445.1|  74 -VGTTGKRLEHEQHhlrlhlrvpcltpaglA-EklrdkeGMVALLLGREDCGLNSDEISLCDMIVSIPTSEEYPVMN 148
                                       .666653333332212223444444445550.05556669************************************* PP

                                       HHHHHHHHHH CS
                    SpoU_methylase 133 vavAvailly 142
                                       +++++ail+y
  gi|330508017|ref|YP_004384445.1| 149 LSHSAAILFY 158
                                       *******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1984.98
//
Query:       gi|330508018|ref|YP_004384446.1|  [L=474]
Description: hypothetical protein MCON_2082 [Methanosaeta concilii GP6]
Scores for 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-159  531.2   0.0   2.2e-159  531.1   0.0    1.0  1  RtcB      tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  531.1   0.0  1.2e-163  2.2e-159       1     412 []      44     474 .]      44     474 .] 0.98

  Alignments for each domain:
  == domain 1  score: 531.1 bits;  conditional E-value: 1.2e-163
                                       HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvke 73 
                                       q++nva+lpgiv h++amPD+HlG+g+piG+V+a+k   g+i+P++VG+DI CGvrll+ +l+a ++++ +++l+++
  gi|330508018|ref|YP_004384446.1|  44 QVANVATLPGIVGHSMAMPDAHLGYGFPIGGVAAFKeqgGIISPGGVGFDInCGVRLLRSDLQARDVQPLINTLLDA 120
                                       89*************************************************************************** PP

                                       HHHHS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB  74 lekavpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlG 150
                                       l++avp+glgs+++++ ++++l+e + +ga+waveeg+g e+dl+ +ee+g++ +ad+++v  ka++r+r+qlGtlG
  gi|330508018|ref|YP_004384446.1| 121 LFQAVPSGLGSTGRLHATDRQLTESFLRGAEWAVEEGYGVESDLDFCEENGSMPGADPSQVGVKARKRGRPQLGTLG 197
                                       ***************************************************************************** PP

                                       STT-EEEEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 151 sGNHFiEvqlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagse 227
                                       sGNHF+E+q veei++ e+ak++gl +gq++vm+H+GSRg Ghqi++d+l++++ka++k++i++pd++La++p+g++
  gi|330508018|ref|YP_004384446.1| 198 SGNHFLEIQRVEEIYNPEIAKRFGLFKGQITVMIHCGSRGAGHQICTDHLDVLSKAVRKYNIDIPDKQLACAPLGTP 274
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxx RF
                              RtcB 228 egqaYlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAt 300
                                       e+++Y+ am +aanyA+aNR++i++++re++++++ +++    l+l++dvaHN+ak Eeh+ +   e+++VhRKGAt
  gi|330508018|ref|YP_004384446.1| 275 EADHYFGAMVCAANYAWANRHIIAHWTREVFDRYFPGSQ----LQLLYDVAHNVAKIEEHRvEgkkERLYVHRKGAT 347
                                       ***********************************7654....579**************9945789********** PP

                                       E-.............TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCC CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 301 rA.............kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeq 362
                                       rA               gqpv+ipGsmgt+Sy++ G+++a   +fgS++HG+GR+msR++a ++f+++evk+ l++ 
  gi|330508018|ref|YP_004384446.1| 348 RAfgpsrteipaayeGLGQPVLIPGSMGTASYVLCGQDKALdlTFGSACHGSGRVMSRSQALRQFTGKEVKAALNRD 424
                                       ****************************************99*********************************** PP

                                       T-EEEE------------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 363 gigvearkkegvleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                       gi v++++   ++eEap+ YK+  +Vv+++++ g+++ varl p++v kg
  gi|330508018|ref|YP_004384446.1| 425 GIAVRSTSPGMLAEEAPQVYKPSGDVVDVVHNLGIATRVARLVPLGVSKG 474
                                       ***********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 3500.39
//
Query:       gi|330508019|ref|YP_004384447.1|  [L=143]
Description: hypothetical protein MCON_2083 [Methanosaeta concilii GP6]
Scores for complete 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-40  137.9   0.1    2.9e-40  137.7   0.1    1.0  1  Archease  Archease protein family (MTH1598/TM1083)


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   0.1   1.6e-44   2.9e-40       1     138 []       5     143 .]       5     143 .] 0.96

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 1.6e-44
                                       EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S- CS
                          Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvf 77 
                                       +eyl+htADv+++a+G++ ++++++aa alf +m+   +v+ +e+ ++e+eaedledl +++L+e+++lf+te  vf
  gi|330508019|ref|YP_004384447.1|   5 FEYLEHTADVKFRAYGTTPDQMLSNAAAALFGAMISPGQVKVEESWQVELEAEDLEDLAYQWLSEIVFLFETESAVF 81 
                                       9**************************************************************************** PP

                                       ---EE..EE..E-SSSEEEEEEEE----.-TT--------B--S---EEEEETTEEEEEEEEE- CS
                          Archease  78 kevkv..dee.eeeeeleleaeargekfdkekhevqtevKAvTyhelrieeeddgweayvvvDi 138
                                       ++++v  + e ++ ++++l+ae+ ge++d+e+h++ +evKAvT h++ ie+++ +w ++vv+D+
  gi|330508019|ref|YP_004384447.1|  82 SRFQValE-EfQDGKGWKLRAEIGGERMDPERHSFLAEVKAVTRHKFAIEKNE-RWCIQVVLDV 143
                                       ***99653.247789*******************99**************976.9********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1052.83
//
Query:       gi|330508020|ref|YP_004384448.1|  [L=300]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.9e-08   32.8   0.0    1.9e-07   31.6   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
      8e-05   22.9   0.0    0.00014   22.2   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
    0.00032   20.8   0.0    0.00074   19.6   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.048   13.9   2.4        1.2    9.4   0.1    2.6  2  TetR_C_31    Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   4.3e-11   1.9e-07       2     119 ..      75     186 ..      74     211 .. 0.78
   2 ?   -2.8   0.0       1.6   7.2e+03     115     141 ..     264     292 ..     224     295 .. 0.56

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 4.3e-11
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       +++ gCnl C+fC+++   ++e+ g+++  ee+++ + +l ++ g++++ l+  +  + p + e+l  ++++   g+
  gi|330508020|ref|YP_004384448.1|  75 IFFSGCNLSCVFCQNWDI-SQEDLGHEVKAEELAKMMLAL-EDSGCHNINLVTPTHVV-PQILEALVLAREE---GL 145
                                       6899************97.*********************.9**********998777.8888888888887...88 PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlk 119
                                       ++ ++ n +  d   + +ll+  +d +  +++ + d + +k
  gi|330508020|ref|YP_004384448.1| 146 SVPLVYNSGGYDSAEALLLLDGIIDIYMPDAKYGQDGPAQK 186
                                       88888888877644445555545677777777766665555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                                       H...HHHHHHTCTSHHHHHHHHHHHHHHTT CS
                                       x...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 115 e...kvlklmnrghtfeevlealeklreag 141
                                           ++ +l  r  t  e+ +al ++ +ag
  gi|330508020|ref|YP_004384448.1| 264 YqacRYPELS-RAITAREYAQALHLAEKAG 292
                                       2443344444.5555666666666666655 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   3.1e-08   0.00014       9      58 ..      74     123 ..      66     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.1e-08
                           Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltl 58 
                                       ++f+sgCnlsC +C n ++ + + g+e++ e l++++  l+++    + l
  gi|330508020|ref|YP_004384448.1|  74 TIFFSGCNLSCVFCQNWDISQEDLGHEVKAEELAKMMLALEDSGCHNINL 123
                                       79***************************999999999998877766655 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 !   19.6   0.0   1.7e-07   0.00074       2      49 ..      76     121 ..      75     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.7e-07
                           Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiq 49 
                                       f  +sgCnlsC++C n +  +++lg++ + e+l +++  l++s ++  
  gi|330508020|ref|YP_004384448.1|  76 F--FSGCNLSCVFCQNWDISQEDLGHEVKAEELAKMMLALEDSGCHNI 121
                                       4..5***********************999999999988888777544 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 ?    9.4   0.1   0.00026       1.2      76     102 ..     218     242 ..     192     247 .. 0.68
   2 ?    3.5   0.3     0.018        79      25      53 ..     257     283 ..     253     297 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00026
                                       HHHHHHHHHHHHSGTS-HHHHHHHHHH CS
                         TetR_C_31  76 aaldGllldrLagpaadpraevrellr 102
                                        al+Gll+++L++p  +++a+++e++r
  gi|330508020|ref|YP_004384448.1| 218 IALQGLLVRHLVLP--ADAAGTEEVVR 242
                                       589***********..44477777766 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHCCSCHHHHHHHHHHHHHHH CS
                         TetR_C_31  25 lAryelfleaarrPeLraalarlrralre 53 
                                       +A+y    +a r PeL +a++++   +++
  gi|330508020|ref|YP_004384448.1| 257 MAQYHPEYQACRYPELSRAITARE--YAQ 283
                                       688888889*******99999843..333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2313.55
//
Query:       gi|330508021|ref|YP_004384449.1|  [L=116]
Description: hypothetical protein MCON_2088 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-05   24.7   0.1    2.6e-05   24.4   0.1    1.3  1  RHH_8     Ribbon-Helix-Helix transcriptional regulator family
     0.0026   17.7   0.1     0.0041   17.1   0.1    1.4  1  DUF3895   Protein of unknown function (DUF3895)


Domain annotation for each model (and alignments):
>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   2.9e-09   2.6e-05      15      46 ..      26      57 ..      15     113 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.9e-09
                             RHH_8 15 LgqiDlLveeGfYsnRtDlirtairaqLakhd 46
                                      + qi+ Lv+ G Y n +D+ir a+r++La+ +
  gi|330508021|ref|YP_004384449.1| 26 ILQINGLVDAGLYLNPSDFIRDAVREKLAAIK 57
                                      668999**********************9764 PP

>> DUF3895  Protein of unknown function (DUF3895)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   4.6e-07    0.0041       7      63 ..      57     113 ..      50     116 .] 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.6e-07
                           DUF3895   7 aileyvksaelisAkelaeyLvrkgkasnesfstgryKiYgdvCvvLdqlakegvie 63 
                                       +++ey +   +   ke+a y   kg+a     st+    Y  vC+++d l keg++e
  gi|330508021|ref|YP_004384449.1|  57 KVIEYHDVDYETAKKEVAGYFQMKGEAYASDASTDLQLDYELVCKIMDDLEKEGKME 113
                                       577888888888899***************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 847.25
//
Query:       gi|330508022|ref|YP_004384450.1|  [L=500]
Description: type-2 seryl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-55  187.8   0.1    1.5e-55  187.4   0.1    1.2  1  tRNA_bind_4   tRNA-binding domain
    1.2e-07   31.9   0.0    1.9e-07   31.2   0.0    1.3  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 !  187.4   0.1   1.6e-59   1.5e-55       1     160 [.       1     160 [.       1     161 [. 0.98

  Alignments for each domain:
  == domain 1  score: 187.4 bits;  conditional E-value: 1.6e-59
                                       EEEEEEEEEEESS-SCCCHHHHHHHHHHHCCTGGGTTSSTTT.S.SSEEEEEEE-SSEEEEEEEEESSS-HHHHHHH CS
                       tRNA_bind_4   1 lkfelkgklklskdieeaeeeieefieeanktiLkkGvpegkeeegakitewkiegnelkleieSgryvRahdallr 77 
                                       ++f+l+++l+ls+d+ +ae++i++fi++a   iL+kG+peg+   gakitew++ +n+++l i+S+ryvRahdallr
  gi|330508022|ref|YP_004384450.1|   1 MRFHLEASLRLSADAGAAEKAISDFIRDAGP-ILEKGAPEGQ---GAKITEWRLAKNRIDLVIDSDRYVRAHDALLR 73 
                                       89**************************988.*********9...******************************** PP

                                       HHHHHHHHCCCCCS--EEEEEEEEEEEEEE-SS--HH---TTECEEEEETTEEEEEEES--H......HHHHTTHHH CS
                       tRNA_bind_4  78 lkkplaeklGkkyriGvRgikveeyeieiesekelkaekipeveeveveegkitlelkdvde......selkkrvvd 148
                                       l++pl+e+lGk+yriGvRg++v+ +eie+es++e+ a++ip+v+e+++e g+++l+l dv+e      se+++r++d
  gi|330508022|ref|YP_004384450.1|  74 LRRPLSELLGKQYRIGVRGMDVTAFEIEVESDREI-AHRIPYVREMRHEGGRLRLIL-DVGEggtlgqSEIENRIPD 148
                                       **********************************9.9********************.****999999********* PP

                                       HHHHHHHHHHCC CS
                       tRNA_bind_4 149 Riiklveekiek 160
                                       Ri++l+eek+ek
  gi|330508022|ref|YP_004384450.1| 149 RIVSLLEEKLEK 160
                                       *********997 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   2.1e-11   1.9e-07      32     178 ..     321     474 ..     305     475 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.1e-11
                                       BGGSSEEEEE.EEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.SC......... CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                      tRNA-synt_2b  32 skrLPlklyq.iqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlglef......... 98 
                                       + +LP+++++  +t +R+E   ++G+ Rv eFh  + +  +++++  ++ ++l   +++ife+++            
  gi|330508022|ref|YP_004384450.1| 321 NGELPMRVFDrSGTSHRYESGGIHGIERVDEFHRIEIVWLGTKEHTLEEAEKLKGCYKHIFEDILELTwrtawvtpw 397
                                       345****997368*******99********************999******************97333344444443 PP

                                       .EEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEEEEHHHHHHH CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  99 .raiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimicaaigveRllsa 174
                                         a ++ ++  ++ ++ + + ea+ +  +  ie    +  g+++++ + +++    ++ +    +c ++g+eR  sa
  gi|330508022|ref|YP_004384450.1| 398 fMAQEGKTGLSEMTGAGTVDYEAILPYNGNWIEFQNLSVNGEKYPKGFTVKA----QSGEALWSGCSGVGLERWASA 470
                                       33333335555699********************************999988....66667778*********9999 PP

                                       HHHH CS
                                       xxxx RF
                      tRNA-synt_2b 175 ileq 178
                                        l+q
  gi|330508022|ref|YP_004384450.1| 471 FLSQ 474
                                       9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 3619.03
//
Query:       gi|330508023|ref|YP_004384451.1|  [L=76]
Description: hypothetical protein MCON_2090 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 609.91
//
Query:       gi|330508024|ref|YP_004384452.1|  [L=440]
Description: phosphoesterase, RecJ domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-16   58.6   0.0    2.3e-15   57.2   0.0    1.8  1  DHHA1     DHHA1 domain
  ------ inclusion threshold ------
      0.038   14.2   0.1      0.075   13.3   0.1    1.5  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   2.6e-19   2.3e-15      71     138 .]     352     421 ..     297     421 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 2.6e-19
                                       CEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHHH CS
                             DHHA1  71 vivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGagipaekleealealeeai 138
                                        +++  k  +d +k+sar +k     g+d++ ++++aa+++gg+GGGH  A+Ga+ip+++ +e+l++l+e++
  gi|330508024|ref|YP_004384452.1| 352 LVTLNHK--DDMIKISARGNKPliarGLDLSVALRRAAEAVGGNGGGHTIASGASIPPGREDEFLALLDEIL 421
                                       3333333..348********99**********************************************9975 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   8.4e-06     0.075       7      57 ..      24     103 ..      20     147 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.4e-06
                                       ECSSSHHHHHHHHHHHH.............................CECS--TCGGCGCCHHCCCSEEEEEEE-S-- CS
                                       xxxxxxxxxxxxxxxxx.............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH   7 hknpDtDsigSaialan.............................llvDhneksqavegeakeeaedviiiDHHrl 54 
                                       + + D+D+i+Sa ++ +                             + +D+++ + + +    + + +  ++DHHr+
  gi|330508024|ref|YP_004384452.1|  24 ISHNDADGITSAGLICHalmragipfqatlvnrldrsvidgltgpvVFCDMGSGKPDLIS---RVQGECFVLDHHRP 97 
                                       5788*******8888886888888888888888777777777777779999999999987...7778899******9 PP

                                       -S...S CS
                                       xx...x RF
                               DHH  55 ge...e 57 
                                             
  gi|330508024|ref|YP_004384452.1|  98 VGtldC 103
                                       766642 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3167.65
//
Query:       gi|330508025|ref|YP_004384453.1|  [L=151]
Description: 30S ribosomal protein S15P/S13e [Methanosaeta concilii GP6]
Scores for complete 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   85.2   1.1    7.1e-24   83.6   1.1    1.9  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    2.7e-15   56.3   0.5    7.8e-15   54.9   0.4    1.7  2  Ribosomal_S15    Ribosomal protein S15
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.016   15.0   0.0    1.2  1  CCDC66           Coiled-coil domain-containing protein 66


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 !   83.6   1.1   1.2e-27   7.1e-24       1      60 []       1      60 [.       1      60 [. 1.00

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 1.2e-27
                                      X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
                   Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                      Ma+mhsr+ G+S+S  P+ ++ap+W+++skee+e++i+kl+  G++pS+IG++LRDqyGv
  gi|330508025|ref|YP_004384453.1|  1 MAKMHSRKGGSSRSRPPMVTKAPEWSDVSKEELEKTIMKLHDTGMSPSRIGLTLRDQYGV 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 ?   -1.0   0.0      0.36   2.2e+03       3      22 ..      31      50 ..      29      55 .. 0.73
   2 !   54.9   0.4   1.3e-18   7.8e-15      11      80 ..      77     148 ..      69     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.36
                                      HHHHHHSSSTT-TSSHHHHH CS
                     Ribosomal_S15  3 elikefqrhekDtGspevqi 22
                                      e +++   + +DtG ++  i
  gi|330508025|ref|YP_004384453.1| 31 EELEKTIMKLHDTGMSPSRI 50
                                      45677777888999998877 PP

  == domain 2  score: 54.9 bits;  conditional E-value: 1.3e-18
                                       STT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHCTS CS
                     Ribosomal_S15  11 hekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkklieklgl 80 
                                       +++   ++++++ +l++++ ++++h+k nkkD+h++r+L+++++k+r+++kY++   +  +++++  e++++
  gi|330508025|ref|YP_004384453.1|  77 DNNALADIPEDLTNLMRKALHVRKHIKANKKDVHNKRALQLTENKIRRMVKYYHDSGRlaPDWTYSPETAEI 148
                                       555567899***********************************************9999******999987 PP

>> CCDC66  Coiled-coil domain-containing protein 66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.7e-06     0.016      23      81 ..      68     127 ..      57     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-06
                            CCDC66  23 eesqvsylRgqtalLd.aatleererkRrkalEyqnaikkQleEkerikklEkerrrqee 81 
                                        +s + +lR  +al d ++ l + +rk      + +a+kk +++k+ ++  E++ rr+ +
  gi|330508025|ref|YP_004384453.1|  68 GNSITGFLRDNNALADiPEDLTNLMRKALHVRKHIKANKKDVHNKRALQLTENKIRRMVK 127
                                       455689**********8899*********************************9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1033.38
//
Query:       gi|330508026|ref|YP_004384454.1|  [L=224]
Description: hypothetical protein MCON_2093 [Methanosaeta concilii GP6]
Scores for complete 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  162.8   0.0      5e-48  162.5   0.0    1.1  1  DUF116    Protein of unknown function DUF116


Domain annotation for each model (and alignments):
>> DUF116  Protein of unknown function DUF116
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.5   0.0   2.8e-52     5e-48       2     155 .]      60     213 ..      59     213 .. 0.98

  Alignments for each domain:
  == domain 1  score: 162.5 bits;  conditional E-value: 2.8e-52
                            DUF116   2 llkllgrllgldkdklkrvfievnnklvrkkfkkvppekrllllPhClraadCpaklteeglnCkrCgkCkigelkk 78 
                                       ++k l+ + + d++ +++v ++++n +++kkf ++p+ekr++++P+Clr+ +Cpaklt+eg+ C +Cg+C ige+kk
  gi|330508026|ref|YP_004384454.1|  60 VIKSLFWVARADDSMVDDVGVRLRNYINTKKFLETPYEKRFIFMPQCLRSVQCPAKLTPEGIMCIDCGRCGIGEAKK 136
                                       578899999******************************************************************** PP

                            DUF116  79 laeklgykvyivtggtlarkiikekkpkaiigvaCerdltegiqdlkklpvigqlvllekggCinTkvdveeleell 155
                                       +ae+lgy++y+v+g++++++iik+ +p ai+gv C ++++eg++ ++++++++ +v+l+++gC+ T++d+e+++e++
  gi|330508026|ref|YP_004384454.1| 137 YAESLGYRFYVVPGSSFIKRIIKKGRPGAIVGVGCSMEIKEGLDLCHSHGIPARGVPLSTSGCVATSIDWEAFYEAI 213
                                       ************************************************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1609.09
//
Query:       gi|330508027|ref|YP_004384455.1|  [L=58]
Description: ferredoxin [Methanosaeta concilii GP6]
Scores for complete 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-18   63.9  15.9    4.4e-09   35.8   3.6    2.1  2  Fer4          4Fe-4S binding domain
    9.8e-13   47.6  16.9    2.8e-06   27.2   4.3    2.1  2  Fer4_6        4Fe-4S binding domain
    2.7e-12   46.6  29.1    1.1e-08   35.0  16.2    1.8  2  Fer4_10       4Fe-4S dicluster domain
      3e-12   46.5  14.2    3.3e-12   46.4  14.2    1.0  1  Fer4_21       4Fe-4S dicluster domain
    1.2e-11   44.0  15.6    2.5e-06   27.3   3.4    2.1  2  Fer4_2        4Fe-4S binding domain
    3.1e-11   43.3  13.4    4.1e-11   42.9  13.4    1.2  1  Fer4_9        4Fe-4S dicluster domain
    7.1e-10   39.3  13.4    1.4e-09   38.4  13.5    1.4  1  Fer4_7        4Fe-4S dicluster domain
    8.8e-10   39.4  13.8    3.9e-05   24.5   2.0    2.0  2  Fer4_16       4Fe-4S double cluster binding domain
    4.7e-08   33.5  14.8    0.00029   21.3   3.0    2.2  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
    5.1e-07   29.7  16.0    0.00094   19.5   5.9    2.1  2  Fer4_4        4Fe-4S binding domain
    3.7e-05   24.2  17.5     0.0096   16.4   4.7    2.1  2  Fer4_17       4Fe-4S dicluster domain
    4.4e-05   24.1  14.5     0.0059   17.3  14.5    2.4  1  Fer4_15       4Fe-4S single cluster domain
    5.2e-05   23.9  18.0     0.0077   17.1   4.9    2.2  2  Fer4_3        4Fe-4S binding domain
    0.00027   21.3  18.4       0.04   14.4   5.5    2.1  2  Fer4_8        4Fe-4S dicluster domain
    0.00029   20.9   7.5    0.00032   20.8   7.5    1.1  1  Fer4_11       4Fe-4S dicluster domain
     0.0023   18.1   3.8      0.003   17.7   3.8    1.2  1  Furin-like_2  Furin-like repeat, cysteine-rich
     0.0026   18.6   8.6      0.082   13.8   1.4    2.0  2  Fer4_22       4Fe-4S dicluster domain
     0.0065   16.6  15.8       0.07   13.3   4.0    2.0  2  Fer4_18       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.092   12.9   8.7        1.2    9.3   2.9    2.0  2  ETF_QO        Electron transfer flavoprotein-ubiquinone oxido
       0.21   11.7   7.5       0.28   11.3   7.5    1.2  1  Fer4_19       Divergent 4Fe-4S mono-cluster
        5.6    7.1   9.2        6.7    6.8   9.2    1.0  1  Mut7-C        Mut7-C RNAse 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 !   34.4   4.5   1.4e-11   1.2e-08       2      24 .]       4      26 ..       3      26 .. 0.95
   2 !   35.8   3.6   5.2e-12   4.4e-09       2      24 .]      34      56 ..      33      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.4e-11
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v++ + C+ CG+Cve CP +AI+
  gi|330508027|ref|YP_004384455.1|  4 VVNRDECVSCGTCVEECPEEAIS 26
                                      89*******************96 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 5.2e-12
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v+++ekC+ C++Cve+CP +AI+
  gi|330508027|ref|YP_004384455.1| 34 VVNKEKCTECKTCVEACPSEAIS 56
                                      89*******************96 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   4.8   4.5e-09   3.8e-06       2      24 .]       3      25 ..       2      25 .. 0.95
   2 !   27.2   4.3   3.2e-09   2.8e-06       1      24 []      32      55 ..      32      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4.5e-09
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      +++++d C++Cg Cv  CPe ai
  gi|330508027|ref|YP_004384455.1|  3 AVVNRDECVSCGTCVEECPEEAI 25
                                      79*******************98 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 3.2e-09
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      +++++++kC+ C  Cv +CP  ai
  gi|330508027|ref|YP_004384455.1| 32 IAVVNKEKCTECKTCVEACPSEAI 55
                                      689*****************9998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0  16.2   1.3e-11   1.1e-08       3      56 .]       4      51 ..       2      51 .. 0.78
   2 !   22.7   4.9   9.4e-08     8e-05       2      21 ..      33      52 ..      32      58 .] 0.86

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.3e-11
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                      v+++d C+ Cg+Cv+ CP        +++  ++e++ + + ekCt+c  CveaCP
  gi|330508027|ref|YP_004384455.1|  4 VVNRDECVSCGTCVEECPE-------EAISLDDEEIAVvNKEKCTECKTCVEACP 51
                                      7899***************.......333333333333367*************9 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 9.4e-08
                           Fer4_10  2 vvidddtCirCgkCvkaCPa 21
                                      +v+++++C++C++Cv+aCP+
  gi|330508027|ref|YP_004384455.1| 33 AVVNKEKCTECKTCVEACPS 52
                                      68899**************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 !   46.4  14.2   3.8e-15   3.3e-12       1      59 []       3      57 ..       3      57 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 3.8e-15
                           Fer4_21  1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                      A++++d+C++Cg C+  C++   +ai++d+++++ v +++C+ C+ C++ CP +++i+m
  gi|330508027|ref|YP_004384455.1|  3 AVVNRDECVSCGTCVEECPE---EAISLDDEEIAVVNKEKCTECKTCVEACP-SEAISM 57
                                      899****************6...*****************************.699998 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   4.4   7.1e-08   6.1e-05       2      22 .]       2      22 ..       1      22 [. 0.93
   2 !   27.3   3.4   2.9e-09   2.5e-06       2      21 ..      32      51 ..      31      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.1e-08
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      p+vv++d C++Cg+Cv  CP+
  gi|330508027|ref|YP_004384455.1|  2 PAVVNRDECVSCGTCVEECPE 22
                                      5799****************5 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2.9e-09
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                       +vv+ ++C++C++Cv aCP
  gi|330508027|ref|YP_004384455.1| 32 IAVVNKEKCTECKTCVEACP 51
                                      5799**************** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9  13.4   4.8e-14   4.1e-11       1      51 []       9      55 ..       9      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 4.8e-14
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      +C++Cg+Cve Cp ++++ d+ e  + +++    +C++C++CveaCp++ai
  gi|330508027|ref|YP_004384455.1|  9 ECVSCGTCVEECPEEAISLDDEEIAVVNKE----KCTECKTCVEACPSEAI 55
                                      5***********************999876....6*************987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4  13.5   1.7e-12   1.4e-09       2      52 .]      10      54 ..       9      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.7e-12
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C+ Cg Cv+ Cp +ai+ld+e      e ++++ ekC+ C+ Cv++CP++a
  gi|330508027|ref|YP_004384455.1| 10 CVSCGTCVEECPEEAISLDDE------EIAVVNKEKCTECKTCVEACPSEA 54
                                      ******************997......578899***************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 !   24.5   2.0   4.5e-08   3.9e-05       2      24 ..      10      32 ..       9      39 .. 0.79
   2 !   21.1   4.4   5.4e-07   0.00046       1      20 [.      39      58 .]      39      58 .] 0.93

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.5e-08
                           Fer4_16  2 CgtCgkCaevCPtnaikekkeke 24
                                      C++Cg C+e CP++ai+ + e+ 
  gi|330508027|ref|YP_004384455.1| 10 CVSCGTCVEECPEEAISLDDEEI 32
                                      *****************995443 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 5.4e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C++C+ C+e+CP++ai+++
  gi|330508027|ref|YP_004384455.1| 39 KCTECKTCVEACPSEAISME 58
                                      6****************975 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   3.0   3.4e-07   0.00029       1      18 [.       5      22 ..       5      34 .. 0.94
   2 !   18.2   4.0   3.2e-06    0.0027       1      18 [.      35      52 ..      35      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.4e-07
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      V+rd+C++cg+Cve +P+
  gi|330508027|ref|YP_004384455.1|  5 VNRDECVSCGTCVEECPE 22
                                      89***************7 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.2e-06
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      V++++C++c++Cve++P 
  gi|330508027|ref|YP_004384455.1| 35 VNKEKCTECKTCVEACPS 52
                                      89***************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 !   16.1   2.5   1.4e-05     0.012       2      16 ..       8      22 ..       7      29 .. 0.91
   2 !   19.5   5.9   1.1e-06   0.00094       1      16 [.      37      52 ..      37      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      + C+ Cg Cv  CP 
  gi|330508027|ref|YP_004384455.1|  8 DECVSCGTCVEECPE 22
                                      78************5 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.1e-06
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +e+C++C+ Cv aCP+
  gi|330508027|ref|YP_004384455.1| 37 KEKCTECKTCVEACPS 52
                                      69*************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 !   14.4   4.9   4.9e-05     0.042      44      59 ..       8      23 ..       3      25 .. 0.88
   2 !   16.4   4.7   1.1e-05    0.0096      41      59 ..      35      53 ..      22      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.9e-05
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++C++Cg C+++CP++
  gi|330508027|ref|YP_004384455.1|  8 DECVSCGTCVEECPEE 23
                                      68***********986 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.1e-05
                           Fer4_17 41 ekaslCieCgeCerkCPqg 59
                                       + ++C+eC+ C+++CP++
  gi|330508027|ref|YP_004384455.1| 35 VNKEKCTECKTCVEACPSE 53
                                      56789************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 !   17.3  14.5   6.9e-06    0.0059       2      65 ..       4      56 ..       3      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.9e-06
                           Fer4_15  2 vvDrdaCigcglCvaeap.evfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIr 65
                                      vv+rd+C +cg Cv+e+p e + ld++ +a             v++++ ++ +  ++aCP +AI+
  gi|330508027|ref|YP_004384455.1|  4 VVNRDECVSCGTCVEECPeEAISLDDEEIA------------VVNKEKCTECKTCVEACPSEAIS 56
                                      699**************6156666666666............467899999************97 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   5.2   0.00019      0.16       1      15 []      10      24 ..      10      24 .. 0.92
   2 !   17.1   4.9     9e-06    0.0077       1      15 []      40      54 ..      40      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00019
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ Cg+Cve CP+ A
  gi|330508027|ref|YP_004384455.1| 10 CVSCGTCVEECPEEA 24
                                      99**********866 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 9e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct C +Cve+CP+ A
  gi|330508027|ref|YP_004384455.1| 40 CTECKTCVEACPSEA 54
                                      ************876 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   4.8    0.0001     0.088      49      63 ..       8      22 ..       5      25 .. 0.79
   2 !   14.4   5.5   4.7e-05      0.04      49      63 ..      38      52 ..      25      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                            Fer4_8 49 wsCttcgaCtevCpv 63
                                      ++C++cg C+e+Cp+
  gi|330508027|ref|YP_004384455.1|  8 DECVSCGTCVEECPE 22
                                      578888888888887 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.7e-05
                            Fer4_8 49 wsCttcgaCtevCpv 63
                                      ++Ct+c+ C+e+Cp 
  gi|330508027|ref|YP_004384455.1| 38 EKCTECKTCVEACPS 52
                                      578888888888886 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   7.5   3.7e-07   0.00032       9      59 ..       9      55 ..       3      58 .] 0.78

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.7e-07
                           Fer4_11  9 qCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykiv 59
                                      +C  C    Cv+ +p+eai  d+e+ aV+ +++++  e++++veacP +++
  gi|330508027|ref|YP_004384455.1|  9 ECVSC--GTCVEECPEEAISLDDEEIAVV-NKEKCT-ECKTCVEACPSEAI 55
                                      55555..47**************777766.556665.8*********8765 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 !   17.7   3.8   3.5e-06     0.003      23      67 ..       4      48 ..       2      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.5e-06
                      Furin-like_2 23 lleregirqiGvclascpaGyfgvrnkevnrctkckaeecescfs 67
                                      +++r++    G+c+++cp+    +  +e+    k k  ec++c +
  gi|330508027|ref|YP_004384455.1|  4 VVNRDECVSCGTCVEECPEEAISLDDEEIAVVNKEKCTECKTCVE 48
                                      578999******************999998777777777777753 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   1.4   9.6e-05     0.082      77      95 ..       5      23 ..       1      24 [. 0.84
   2 !    9.5   0.9     0.002       1.7      78      94 ..      36      52 ..      28      54 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.6e-05
                           Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                      +++  Cv Cg C+e cp++
  gi|330508027|ref|YP_004384455.1|  5 VNRDECVSCGTCVEECPEE 23
                                      57889***********975 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.002
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                      ++++C+ C  C+eacp+
  gi|330508027|ref|YP_004384455.1| 36 NKEKCTECKTCVEACPS 52
                                      56667777777777765 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   3.8   0.00071       0.6      58      73 ..       7      22 ..       3      29 .. 0.82
   2 !   13.3   4.0   8.3e-05      0.07      50      74 ..      29      53 ..      22      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00071
                           Fer4_18 58 agdcidcescvkvcPt 73
                                        +c++c++cv+ cP 
  gi|330508027|ref|YP_004384455.1|  7 RDECVSCGTCVEECPE 22
                                      6799999999999996 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.3e-05
                           Fer4_18 50 keerkekgagdcidcescvkvcPtg 74
                                       ee +  ++ +c++c++cv+ cP +
  gi|330508027|ref|YP_004384455.1| 29 DEEIAVVNKEKCTECKTCVEACPSE 53
                                      45667778999************75 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 ?    8.4   0.7    0.0027       2.3      69      92 ..       4      27 ..       2      33 .. 0.86
   2 ?    9.3   2.9    0.0014       1.2      65      91 ..      30      56 ..      20      58 .] 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0027
                                      EE-CCC--S--HHHHH-TT--EEE CS
                            ETF_QO 69 qinaqnCvhCktCdikdpsqniew 92
                                      ++n  +Cv C tC    p++ i+ 
  gi|330508027|ref|YP_004384455.1|  4 VVNRDECVSCGTCVEECPEEAISL 27
                                      58999********99999998875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
                                      SEEEEE-CCC--S--HHHHH-TT--EE CS
                            ETF_QO 65 ekklqinaqnCvhCktCdikdpsqnie 91
                                      e+  ++n + C  CktC    ps+ i+
  gi|330508027|ref|YP_004384455.1| 30 EEIAVVNKEKCTECKTCVEACPSEAIS 56
                                      455689***********9888888886 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   7.5   0.00033      0.28      10      61 ..       5      57 ..       2      58 .] 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                           Fer4_19 10 dnrelCihsgnCvkglp.evFdpkrkpwikpdeasteeiievverCPSGALsy 61
                                       nr+ C + g Cv + p e   ++++ +   ++++  e +  ve CPS A+s+
  gi|330508027|ref|YP_004384455.1|  5 VNRDECVSCGTCVEECPeEAISLDDEEIAVVNKEKCTECKTCVEACPSEAISM 57
                                      68999*********8763689999999*********************99985 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   9.2    0.0078       6.7      91     130 ..       8      47 ..       2      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0078
                            Mut7-C  91 srCvaCngeleevekeevkervpekvyeeadeftrCekCr 130
                                       + Cv C + +ee ++e ++ + +e +  +++++t+C++C 
  gi|330508027|ref|YP_004384455.1|   8 DECVSCGTCVEECPEEAISLDDEEIAVVNKEKCTECKTCV 47 
                                       67****************99999999999999*******5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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):              21  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 419.64
//
Query:       gi|330508028|ref|YP_004384456.1|  [L=758]
Description: anaerobic ribonucleoside-triphosphate reductase [Methanosaeta concilii GP6]
Scores for complete 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-159  531.8   0.0   2.6e-159  531.6   0.0    1.0  1  NRDD             Anaerobic ribonucleoside-triphosphate reduct
  ------ inclusion threshold ------
      0.061   13.4   0.1        0.2   11.8   0.1    1.8  2  Cerato-platanin  Cerato-platanin
      0.097   12.8   0.3       0.26   11.4   0.3    1.7  1  DUF2953          Protein of unknown function (DUF2953)
       0.16   11.6   1.1       0.32   10.6   0.0    1.9  2  TackOD1          Thaumarchaeal output domain 1


Domain annotation for each model (and alignments):
>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  531.6   0.0  5.9e-163  2.6e-159       1     561 []     128     754 ..     128     754 .. 0.94

  Alignments for each domain:
  == domain 1  score: 531.6 bits;  conditional E-value: 5.9e-163
                                       .XHTTHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHHHTTSEEETTGGGTTT.S--EEE--SHHHHHH-CTT-SS CS
                              NRDD   1 enanvdskslsglrlklasevskeyalkkllpkevaeaheegdiHiHDldylallttyClgidlkdlleeGlktgng 77 
                                       enan+ +++++++++k a+++ske +l  llp+ +a+ h  gd+HiHDl+y+ +  ++C+++dl+++l +Gl+  +g
  gi|330508028|ref|YP_004384456.1| 128 ENANL-QENAETSHKKKADKISKEQYLL-LLPPYLADRHLAGDLHIHDLEYFGT-RPFCQDWDLRYFLYYGLMP-DG 200
                                       8****.*********************5.************************9.77*************9955.77 PP

                                       S......-B---SHHHHHHHHHHHHHHHHTSSSS-EEETTHHHHHHHHHHHHHHTTSS-GHHHHHHHHHHHHHHHTT CS
                              NRDD  78 v......srppkhietalalavnilqtlqneqaGgqaissfdtylapfvrkdyekklkkltkkeikqamqefvynln 148
                                              + p+k+ e+a+ +av++l+++q+++aGgq++++f+t++ap++++        ++++ei q mq+fvy+++
  gi|330508028|ref|YP_004384456.1| 201 LgtkasvAGPAKKPEVAILHAVKALGSAQTNFAGGQGFYNFLTFIAPYFEN--------RNYEEIVQLMQMFVYEMT 269
                                       7788888******************************************55........6***************** PP

                                       S-S..SSSS---EEEEEE.-HH........................................HHHHHTTTTS-HCH- CS
                              NRDD 149 tlpsrrGaQvpFtninlgldtp.........................tegrfee..kliikallevmleGdgnkgtp 198
                                       +++++rG+Q +F++++l+ ++p                         t+g+fe+  +l +kal+evml+Gd++ g+p
  gi|330508028|ref|YP_004384456.1| 270 QMMVARGGQLVFSSVQLTPGVPklwrdkpavyagrvwdgstpdaplkTYGKFERevRLAFKALMEVMLQGDYW-GKP 345
                                       *************************************************************************.*** PP

                                       ---SEEEEEEEEETETTH..............HHHHHHHHHHTTT--EEE.......EEES--GGGTT-------.. CS
                              NRDD 199 ftFPilifklkedfnleeed.........pnydlfklalevtakrgfpyffnlledlepedekevasmgCRlrld.. 264
                                       f+FP++ ++++ df  e+e+         ++++l+ ++++++a++g+pyf n+l+ +++  e  +++++C +++   
  gi|330508028|ref|YP_004384456.1| 346 FNFPKPEISIEPDFMKEDEEfnaahpdlpTYQELYLQTFKLAAEYGTPYFDNQLPAYRGAGEGISCYQCCAYQFAat 422
                                       *************9555555**********************************98999999*************55 PP

                                       ...-.............S---EEEEEEEEEEHHHHHH..HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.- CS
                              NRDD 265 ...ege...........rlggrgslgvvtiNlprlaleakgdeekffelLdellelakealeerrkilekllakg.l 326
                                          + +           ++ ++gs++vv++N+pr a++a+gd++ +fe L+el++   e+++ +r++++++++++ +
  gi|330508028|ref|YP_004384456.1| 423 fssD-DqfddklrfrdgKHFSMGSWQVVSLNCPRAAYLARGDDDLLFEYLRELMDTSVEIFKVKRQWMNQIINNHrM 498
                                       5431.1345567565555555******************************************************** PP

                                       HHH.HTTSS-G.E.............EEEEEEE-HHHHHHHTTEEEE..-HHHHHHHHHHHHHHHHHHHHHHHHHSS CS
                              NRDD 327 pflmgkgylks.rkkkdeveevlkngtltiGfiGlaEalkaltgkkigeseeakefalkvlkhmrekadelkeetgl 402
                                       pf++++   +  +++  +v+  l+  ++tiG++G++E+++++tgk+++es+ea+++a++++++m+ +a++l+e++g+
  gi|330508028|ref|YP_004384456.1| 499 PFATQQP-RDPiTGEMGSVAVGLDALVYTIGVVGVNEMVQFHTGKQMHESKEAWKLAVRAMTEMEIYARKLSEQHGM 574
                                       **86543.33223566789999******************************************************* PP

                                       -EEEEE---TTHHHHHHHHH....HH...........................HHG-SSSS-TTSSB-HHHHHHHHH CS
                              NRDD 403 nfsleatPaEslsgrfakldk..kkfgeipgv.dke................pyYtNsfhvpvdekislfekiklea 460
                                       +++l +tPaE++++rfa  d   ++f+e  +   k+                +yYtN +h+p ++++++fe+ kle+
  gi|330508028|ref|YP_004384456.1| 575 TIALARTPAETTAQRFAVSDLihEEFRECAERvVKGdldalrrnlhktrdlpVYYTNGTHLPPSADVTIFERAKLEH 651
                                       ********************9879**877766566689999999********************************* PP

                                       HHTGGGTT-S-EEEEBSS--SSHHHHHHHHH.HHHHTT--EEEEE--EEEETT.--..EESSSB-TTT--BE.EEEE CS
                              NRDD 461 efqklttGGailyieldeekknpealeklvk.iakktgigYfsinpkidvCnecgy..kgeiekCpkCgseeevevi 534
                                        f ++++GG+i++++l+e++++p+ l+++   +a++t+igYf+++++++vC  c +   g+ +kCp+Cgse+ v++i
  gi|330508028|ref|YP_004384456.1| 652 VFFPIVDGGNIFHVFLGEATPDPQGLMDFGLrLARETQIGYFTFTKDMTVCLGCSQvsGGLEDKCPNCGSEN-VDHI 727
                                       *****************************888************************9777779******888.**** PP

                                       EESSSSEEEHHHHHHHHHHHSGG---B CS
                              NRDD 535 rRitGYlrpvsswnkgkkaElkdRvkh 561
                                       +RitGYl+ vs wn++k++ElkdR+k+
  gi|330508028|ref|YP_004384456.1| 728 SRITGYLQAVSGWNSAKRQELKDRKKY 754
                                       *************************98 PP

>> Cerato-platanin  Cerato-platanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.2   5.3e+03      77      99 ..     475     497 ..     473     502 .. 0.84
   2 ?   11.8   0.1   4.5e-05       0.2      13      58 ..     696     744 ..     688     755 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
                   Cerato-platanin  77 idaagaGfniakkamdeltngqa 99 
                                       +d++ + f + ++ m+++ n++ 
  gi|330508028|ref|YP_004384456.1| 475 MDTSVEIFKVKRQWMNQIINNHR 497
                                       57888899999*******99875 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4.5e-05
                   Cerato-platanin  13 nrsltv.vscsdGsnGlitky.wptqgavknfpriGGl.saiagwnsan 58 
                                        + +tv + cs+ s Gl  k      ++v  ++ri G+ +a++gwnsa+
  gi|330508028|ref|YP_004384456.1| 696 TKDMTVcLGCSQVSGGLEDKCpNCGSENVDHISRITGYlQAVSGWNSAK 744
                                       566665258***********84444568*******885489******97 PP

>> DUF2953  Protein of unknown function (DUF2953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   5.9e-05      0.26      33      49 ..     346     362 ..     342     366 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.9e-05
                           DUF2953  33 fnikkpeievtPvFnee 49 
                                       fn++kpei+++P+F++e
  gi|330508028|ref|YP_004384456.1| 346 FNFPKPEISIEPDFMKE 362
                                       899***********997 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.3      0.55   2.5e+03     103     122 ..     408     427 ..     405     429 .. 0.80
   2 ?   10.6   0.0   7.2e-05      0.32      68     102 ..     694     728 ..     677     737 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.55
                           TackOD1 103 lihhftCgnvgpeeeflkeg 122
                                        i++++C + +   +f  ++
  gi|330508028|ref|YP_004384456.1| 408 GISCYQCCAYQFAATFSSDD 427
                                       68999999999999987765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 7.2e-05
                           TackOD1  68 elvdrirlCpsCksghlnvrevCpkCkSidieeqe 102
                                       ++ + + +C  C+  +  + + Cp+C+S ++++ +
  gi|330508028|ref|YP_004384456.1| 694 TFTKDMTVCLGCSQVSGGLEDKCPNCGSENVDHIS 728
                                       6788999**********************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (758 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.26s 00:00:00.95 Elapsed: 00:00:00.43
# Mc/sec: 5324.81
//
Query:       gi|330508029|ref|YP_004384457.1|  [L=221]
Description: translocator protein, LysE family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-30  104.9  11.1    4.1e-30  104.7  11.1    1.1  1  LysE      LysE type translocator


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7  11.1   2.3e-34   4.1e-30       2     190 ..      31     213 ..      30     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 2.3e-34
                              LysE   2 slllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlal 78 
                                       +++++pGp +l++++ ++k g+ +g  va+g+++ ++v +ll++ Gla+ ++   +  + + l+Gg+ L+ +g+l++
  gi|330508029|ref|YP_004384457.1|  31 TGAIAPGPTLLATVNSSLKDGWLAGPKVAAGHALIEIVIFLLIVKGLAVTMQ---QYSRSIALMGGLALIAFGILTM 104
                                       6799********************************************9777...8889999*************** PP

                              LysE  79 rdakekkveaeksveaslvkpflkglllslsNPkailfwlsvisallakaeqygdagrlilaaglvvasliwfslla 155
                                       rd+k+ ++ ++ +   s+ +p+l+g+l+s +NP++ ++wls++s+l++ + + g +   i+++g+++a++ w+ l++
  gi|330508029|ref|YP_004384457.1| 105 RDSKSATMASSGDG--SYTNPYLAGFLTSAANPYFWIWWLSIGSVLIVSGLEAGLIVAAIFMIGHWSADFGWYLLVS 179
                                       *******9777777..6*******************************99*************************** PP

                              LysE 156 flaarlsrrlsskkvlriinvvvgvlligfavkll 190
                                        + +r +  ls + ++  i  ++g++li+f+++ l
  gi|330508029|ref|YP_004384457.1| 180 SSLERGRGLLSPENYR-RILGLCGIFLILFGIYYL 213
                                       *******999999877.6779**********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1651.31
//
Query:       gi|330508030|ref|YP_004384458.1|  [L=296]
Description: sodium bile acid symporter family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-07   30.1   9.7    3.6e-07   30.1   9.7    2.3  3  SBF       Sodium Bile acid symporter family


Domain annotation for each model (and alignments):
>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.13   2.3e+03     127     147 ..      15      35 ..      10      46 .. 0.70
   2 !   30.1   9.7     2e-11   3.6e-07       2     149 ..      41     178 ..      40     183 .. 0.83
   3 ?   -0.2   0.2     0.038   6.8e+02      46      72 ..     230     252 ..     195     287 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.13
                               SBF 127 ieeivksvlivviiPliaGil 147
                                       ++ +++svl+ +++P  aG  
  gi|330508030|ref|YP_004384458.1|  15 TSVLILSVLLGLVLPGPAGAT 35 
                                       455678888888888777765 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 2e-11
                               SBF   2 ilLilmmfpmglkveveklkellkrpkalllglvlqwvikPllmfilakillrdlkl.epelavGlilvglapggam 77 
                                       ++L++mm   + +v++ +  +   + k  +lg+++++ +  l + il       ++l +++l+ G ++++++p + +
  gi|330508030|ref|YP_004384458.1|  41 PALMVMMAFSLTEVDLGRDIKSSASLKRGFLGIIINYGL--LSGLILLL----SYSLpDESLRHGFVIMAAVPPAVA 111
                                       678888888888888876666666777789999****99..88888777....4444157899************** PP

                               SBF  78 snvwtylakGdlelsvvlvalstllailltPlllyllaksleqttlkvpieeivksvlivviiPliaGillr 149
                                       ++ +t ++kGd++ls    +ls l+++ll+Pl++yl++++       ++   +++  +++++iP +a  l+r
  gi|330508030|ref|YP_004384458.1| 112 VLPMTRILKGDMSLSFAGEILSYLASLLLMPLIIYLFVHQT-----GISPIYLLQISIVLILIPALASRLVR 178
                                       ****************************************9.....66666666667889999988876666 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.038
                               SBF  46 filakillrdlklepelavGlilvgla 72 
                                       fila+     + l++++a+ l l+g+ 
  gi|330508030|ref|YP_004384458.1| 230 FILAR----SAGLKSSQAISLTLLGSF 252
                                       33333....333444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.42
# Mc/sec: 2092.32
//
Query:       gi|330508031|ref|YP_004384459.1|  [L=194]
Description: integral membrane protein [Methanosaeta concilii GP6]
Scores for complete 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  110.7  14.4    8.2e-32  110.4  14.4    1.1  1  SpoIIM    Stage II sporulation protein M
  ------ inclusion threshold ------
        0.2   11.6   2.3        1.2    9.1   0.1    2.3  2  Ninjurin  Ninjurin


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 !  110.4  14.4   9.2e-36   8.2e-32       1     156 []      20     187 ..      20     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 9.2e-36
                            SpoIIM   1 alllflvgillgallaa......snfaeqis..seskensalslflaifanNlrvalllfllGllllgiptilvlli 69 
                                       +++lf++ +++g+++a+      ++ +e+++      e+++l +++ if++Nl  +++++llGl  lgi++++v   
  gi|330508031|ref|YP_004384459.1|  20 SVFLFALTAVMGYYTAQldpefaASWTEELEmlAWILEQPPLMIMIIIFLKNLLASATAMLLGL-GLGIVPMIVATT 95 
                                       579**************775544222255558889999*************************6.************ PP

                            SpoIIM  70 nGfvlGavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal.....rsrrkalkeakrellklllllv 141
                                       nGf+lG+v++  +e++g+l+++++ilPhgi+elp++++++a+glrlg  l     ++ ++ + e++ ++  ll +++
  gi|330508031|ref|YP_004384459.1|  96 NGFLLGIVGYSAVEQKGWLYLAAGILPHGIIELPVVLLSIAIGLRLGHMLalsllKESSDLSGEMRVAIHFLLRWIM 172
                                       ********888888877*******************************99999965556666667777778888999 PP

                            SpoIIM 142 pllliAaliEafvtp 156
                                       plll+Aa iE+f+tp
  gi|330508031|ref|YP_004384459.1| 173 PLLLLAAAIETFITP 187
                                       9*************8 PP

>> Ninjurin  Ninjurin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3      0.02   1.8e+02      45      94 ..      15      68 ..       4      94 .. 0.64
   2 ?    9.1   0.1   0.00014       1.2      44     103 .]     130     188 ..     122     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.02
                          Ninjurin 45 vLislSllLqvvvgilliliasklnlekekk.er....rlnklnnaatilvfvit 94
                                      + + +S++L  + +++ +++  +l+ e  ++ ++     + +l++  ++++++i 
  gi|330508031|ref|YP_004384459.1| 15 IYVAISVFLFALTAVMGYYT-AQLDPEFAASwTEelemLAWILEQPPLMIMIIIF 68
                                      55788999999999998884.4777776666422122122223333344444444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00014
                          Ninjurin  44 lvLislSllLqvvvgilliliasklnlekekker.rlnklnnaatilvfvitviniviaal 103
                                       +vL+s+ + L + ++++l l++++ +l  e   r ++++l  +++ l ++ ++i+ +i+ +
  gi|330508031|ref|YP_004384459.1| 130 VVLLSIAIGLRLGHMLALSLLKESSDLSGEM--RvAIHFLLRWIMPLLLLAAAIETFITPF 188
                                       89****************9976566665544..3489999999999999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1302.53
//
Query:       gi|330508032|ref|YP_004384460.1|  [L=487]
Description: prolyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-28   99.5   0.0    3.8e-28   98.7   0.0    1.5  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    2.4e-19   69.3   0.1      5e-19   68.2   0.1    1.6  1  HGTP_anticodon  Anticodon binding domain
    1.2e-11   44.7   0.5    1.3e-10   41.4   0.3    2.4  2  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
  ------ inclusion threshold ------
       0.09   12.9   0.0       0.24   11.5   0.0    1.7  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 !   98.7   0.0   8.4e-32   3.8e-28       9     178 ..     117     286 ..     105     287 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 8.4e-32
                                       EEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEE.EEEEEEES.GGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxxx RF
                      tRNA-synt_2b   9 reyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhq.kdgyvfha.easlddslrd 82 
                                        +++L+Pt+e++++ +++ + +rs  ++Pl++yqi   +R+E++ +r+L+R+re++  k+++ +ha  +++ ++++ 
  gi|330508032|ref|YP_004384460.1| 117 VKLALRPTSETAIYPMFKLW-IRShADMPLRIYQIVNTFRYETKHTRPLIRLREITSfKEAHTVHAtWEEAAEQVEV 192
                                       5799**************88.***777*****************9**********8659*******7699******* PP

                                       HHHHHHHHHHHTT.SCEEEEEE.GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  83 likaisriferlglefraiiel.msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreks 158
                                        ik +s++++rl ++f + ++  ++ k + +++++ ++++++  +k++++gt++ lg  ++++ ++t+  e++++k 
  gi|330508032|ref|YP_004384460.1| 193 AIKRYSEFYRRLAIPFLVSRRPsWD-KFPGADYTTAIDVIMP-DGKTLQVGTAHHLGSTFAKTYEITYEAEDGEQKL 267
                                       ***************9877777566.55999***********.9********************************* PP

                                       EEEEEEEEEHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 159 vimicaaigveRllsaileq 178
                                       v  +c++i+ eR ++a++++
  gi|330508032|ref|YP_004384460.1| 268 VNQTCYGIS-ERCIAALISV 286
                                       *********.******9875 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.1   1.1e-22     5e-19       1      91 [.     303     393 ..     303     396 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 1.1e-22
                                       SEEEEESSSS.HHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTT CS
                    HGTP_anticodon   1 qvvviplnek.aeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdt 76 
                                       qvv++p+  + +e+++e++++l + L++agirveld s+e++g k+ +++++g+p++++vG++++ekg+vtv +rd 
  gi|330508032|ref|YP_004384460.1| 303 QVVIVPILLGdKEKVLEVCRDLLRILQQAGIRVELDTSDERPGAKFYKWEMKGVPIRLEVGPRDIEKGVVTVVRRDA 379
                                       89999998777889*************************************************************76 PP

                                       CEEEEEETTHHHHHH CS
                    HGTP_anticodon  77 reqervsldelvekl 91 
                                        e+ +++++ l+++l
  gi|330508032|ref|YP_004384460.1| 380 -EKLTLPREGLAQAL 393
                                       .55688887777665 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 ?    0.5   0.0      0.17   7.4e+02       9      32 ..     174     198 ..     170     227 .. 0.76
   2 !   41.4   0.3   2.8e-14   1.3e-10       2      69 .]     423     487 .]     422     487 .] 0.91

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.17
                                       HTT-EEEEEESS.GHHHHHHHHHHH CS
                         ProRS-C_1   9 ekkgfvlapWcg.eeecEekIkeet 32 
                                       ++ + v a W++  e+ E  Ik  +
  gi|330508032|ref|YP_004384460.1| 174 KEAHTVHATWEEaAEQVEVAIKRYS 198
                                       5667899***995667899999876 PP

  == domain 2  score: 41.4 bits;  conditional E-value: 2.8e-14
                                       HHHHHHHHTT-EEEEEESSGHHHHHHHHHHHS-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                         ProRS-C_1   2 eefkealekkgfvlapWcgeeecEekIkeetgakslcipfdqepseegtkCivcgkpakkwvlfgrsY 69 
                                       +e  ++ e+ g++l+pWc++eec  ++++ + a++l+ p   ++s +   C+vcgk ++k+++++r+Y
  gi|330508032|ref|YP_004384460.1| 423 DEARAQTEA-GVALVPWCEKEECGHQLEDLVEANMLGEPQ--YKSFSPAACAVCGKLTDKRTYMARQY 487
                                       566666666.7****************************8..66889999*****************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 ?   11.5   0.0   5.4e-05      0.24      21      55 ..     428     463 ..     415     469 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.4e-05
                                       TTT-SEEEEE--G.GG-SHHHHHHHSS-EEEEEESS CS
                         ProRS-C_2  21 sekkGvvLvPfne.eiYneefeeeidasvLGeteye 55 
                                       +++ Gv LvP+ e e     +e+ ++a +LGe +y+
  gi|330508032|ref|YP_004384460.1| 428 QTEAGVALVPWCEkEECGHQLEDLVEANMLGEPQYK 463
                                       5678*******772456789*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.23s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3434.62
//
Query:       gi|330508033|ref|YP_004384461.1|  [L=220]
Description: iron sulfur flavoprotein [Methanosaeta concilii GP6]
Scores for complete 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  102.2   0.0      3e-29  101.8   0.0    1.2  1  FMN_red       NADPH-dependent FMN reductase
    7.5e-13   48.6   0.0    9.7e-13   48.3   0.0    1.3  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8   0.0   3.3e-33     3e-29       1     144 [.       1     145 [.       1     154 [. 0.87

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 3.3e-33
                                       -EEEEEES--S.TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--..---HCHGHT.CGGSHHHHHHHHHHHH-S CS
                           FMN_red   1 mkilvisGSlr.kgsntrklaewaaealkeagaevelidladl.ilpcalcdkdlese.gqtsddvaellekiaaad 74 
                                       m+il+i+ S++ ++s+t +l+++a+e + e+gae+el+dl +l i+ c++c   +++  ++++dd++ l+eki  ad
  gi|330508033|ref|YP_004384461.1|   1 MRILGICSSPKgSRSTTLRLVQAALEGAGENGAETELVDLCQLdIKYCNACQTCFKTGkCVHKDDFQGLYEKILMAD 77 
                                       9*********977799********************************555544433359***************** PP

                                       CEEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEE CS
                           FMN_red  75 aliivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvp 144
                                       +li+++P Y+++++++lK+++Dr+    + + l+gK+   +a+gg+     +++  l +++ ++ga v +
  gi|330508033|ref|YP_004384461.1|  78 GLILGSPNYFHTVTAQLKTLIDRMADAVHCQLLTGKYCCSLATGGS--NYDQVTGYLDSLMVNFGAFVTG 145
                                       ************************999999**************87..6666666666666667776665 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   1.1e-16   9.7e-13       1     140 [.       1     126 [.       1     168 [. 0.80

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.1e-16
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCC.HHHHTT.C.HHHHHHH.HH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaak.layeek.p.adveseq.ie 73 
                                       m+iL i ++p++++s++ +l qa++e++ ++g +e + +dL ++ +  +++          +++ + ++ + +   e
  gi|330508033|ref|YP_004384461.1|   1 MRILGICSSPKGSRSTTLRLVQAALEGAGENG-AETELVDLCQLDIKYCNA-----CqTCFKTGkCvHKDDFQGlYE 71 
                                       99******************************.9*********75554443.....12233344454666666677* PP

                                       HHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEEEEESS-GGG CS
                      Flavodoxin_2  74 kllaadaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgkkalvivttGgpees 140
                                       k+l ad ++l++P ++ +v a+lK  iDr + a +++           +L+gk +  ++t G++ + 
  gi|330508033|ref|YP_004384461.1|  72 KILMADGLILGSPNYFHTVTAQLKTLIDRMADAVHCQ-----------LLTGKYCCSLATGGSN-YD 126
                                       *****************************98887755...........6778766555555555.43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1518.71
//
Query:       gi|330508034|ref|YP_004384462.1|  [L=203]
Description: hypothetical protein MCON_2103 [Methanosaeta concilii GP6]
Scores for complete 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-48  162.5   0.0    7.4e-48  162.3   0.0    1.0  1  AMMECR1   AMMECR1
  ------ inclusion threshold ------
       0.24   11.0   0.0       0.38   10.3   0.0    1.3  1  Runt      Runt domain


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 !  162.3   0.0   8.3e-52   7.4e-48       1     166 []      11     182 ..      11     182 .. 0.95

  Alignments for each domain:
  == domain 1  score: 162.3 bits;  conditional E-value: 8.3e-52
                                       HHHHHHHHHHHTTSS-S-H.H---HHHHSEEEEEEEEEEE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS-- CS
                           AMMECR1   1 lklareaieealkeekkle.eeakeelkekaglFVtlkekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRFsp 76 
                                       ++lar+a++++++++++l+ e  ++ +++k+g+FVtl+ ++g+LRGCiG+ +p  pL++++++ A++a+f+DpRF+ 
  gi|330508034|ref|YP_004384462.1|  11 VRLARRALAHYMETKEALDpEGMQPVFSQKRGVFVTLH-EDGDLRGCIGYPRPVLPLGRAIVDSAINAGFRDPRFPG 86 
                                       689**************99899999*************.66************************************ PP

                                       --HHHHTTEEEEEEEE---EE--......GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS- CS
                           AMMECR1  77 vtaeElpeleveVsvLtepepiv......ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKaglr 147
                                       +++ El+++e+eV++Ltep+ ++      +e+++vg++Gli++kg ++++lLPqva e+g d  efl +++ Kagl+
  gi|330508034|ref|YP_004384462.1|  87 LRSGELKRIELEVTILTEPQACTgpkkdlPERIQVGRDGLIVSKGPFTGLLLPQVAIEWGFDSLEFLGQTCVKAGLP 163
                                       **********************5554567888********************************************* PP

                                       TTCCCSTTSEEEEE-EEEE CS
                           AMMECR1 148 pdewkdseikltryevekf 166
                                       +d+w d+++ ++ +e+++f
  gi|330508034|ref|YP_004384462.1| 164 ADAWLDEDTLIEHFEAQIF 182
                                       ****************986 PP

>> Runt  Runt domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   4.2e-05      0.38      78     109 ..      76     108 ..      67     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.2e-05
                              Runt  78 varfnDLrfvG.rsGrgksftltitvatkppqv 109
                                        a f D rf G rsG  k ++l +t+ t+p+  
  gi|330508034|ref|YP_004384462.1|  76 NAGFRDPRFPGlRSGELKRIELEVTILTEPQAC 108
                                       488********9****************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1287.76
//
Query:       gi|330508035|ref|YP_004384463.1|  [L=243]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); 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:                         0  (0); expected 0.2 (1e-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 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1865.81
//
Query:       gi|330508036|ref|YP_004384464.1|  [L=453]
Description: histidyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete 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-62  210.5   2.1    1.5e-46  159.1   0.1    2.1  2  tRNA-synt_His    Histidyl-tRNA synthetase
      3e-17   63.2   0.0    5.1e-17   62.4   0.0    1.4  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
    1.6e-08   34.6   0.0    3.1e-08   33.7   0.0    1.5  1  HGTP_anticodon   Anticodon binding domain
    9.6e-06   24.9   0.3     0.0022   17.1   0.1    3.0  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    3.5e-05   23.4   0.0    0.00083   18.9   0.0    2.1  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
     0.0032   16.9   0.0      0.011   15.2   0.0    1.7  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
  ------ inclusion threshold ------
      0.091   13.1   0.0       0.15   12.3   0.0    1.3  1  CCDC117          Coiled-coil domain-containing protein 117


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 !  159.1   0.1   5.7e-50   1.5e-46       1     223 [.       9     225 ..       9     239 .. 0.94
   2 !   51.2   0.3   4.1e-17   1.1e-13     233     310 .]     269     348 ..     248     348 .. 0.83

  Alignments for each domain:
  == domain 1  score: 159.1 bits;  conditional E-value: 5.7e-50
                                       T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCC.HHHS-EEE-TTSSEEEE-SSSHHHHH CS
                     tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgaged.ldqtfklvDqsgrllglRaDiTpqva 76 
                                       g+rd+lpee++k+++ r+++++++ +wGY++V +P++E+l+ +++++g++  d+++ + D+ gr l+lR+++T+ v 
  gi|330508036|ref|YP_004384464.1|   9 GTRDFLPEEMRKRSQARKAMQEVLCRWGYQEVATPTFEHLELFTEKSGASvIDEIYSFQDKGGRDLALRPELTAPVM 85 
                                       78*********************************************999678************************ PP

                                       HHHHHHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEE CS
                     tRNA-synt_His  77 Riaahrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlg 152
                                       R+    l+  ++plRl+Y+G+++r ++ + gr re+ Q+GaEliG + +++++E + l+ +++ ++ag+ +  + lg
  gi|330508036|ref|YP_004384464.1|  86 RMFVSELQnSPKPLRLYYFGNCFRYERPQKGRFREFWQLGAELIGGARPDSEAEAIALADQLI-RSAGI-RGDIHLG 160
                                       *****9988******************************************************.6****.889**** PP

                                       ETCHHHHHHHHTT--HHHHHHHHHHHHCT-HHHHHHHHHCCTTHHHCCHCC...HCCHCCCHHHHCHCCHC CS
                     tRNA-synt_His 153 hvglvralleaaglsesleeallaalarkdlaelkelaaeaglkealrellkalelygdaevleealeala 223
                                         gl+ra+le+++   ++++a ++++++k++++lkel+++  l++  + ll++++l+g+  +l++ale +a
  gi|330508036|ref|YP_004384464.1| 161 YLGLIRAILERIE--GDKRAAAMRMIDKKERSALKELLED--LDQGDLGLLELIDLKGK-ASLDKALE-IA 225
                                       **********966..999********************97..999******98899655.88999987.33 PP

  == domain 2  score: 51.2 bits;  conditional E-value: 4.1e-17
                                       HHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-SS..-SEEEEEECTTTGGG.T---EEEEEEEE CS
                     tRNA-synt_His 233 deleelaallealakpevrvtlDlaelrgyeYytGlvFaayaegvgq..aiarGGrYdelgaaf.grarpAtGfsld 306
                                        +lee +++++ l++++v++++D+  +rg++Yy+G+vF++yaeg g+  +i +GG+Y el++ f g++ ++tGf l 
  gi|330508036|ref|YP_004384464.1| 269 LHLEEFQETVDLLGAYGVDFQIDFEIVRGLDYYSGTVFEIYAEGLGAqrQICGGGTY-ELSSLFgGKETSSTGFGLG 344
                                       45666666666666667***************************88656********.9*****99********998 PP

                                       HHHH CS
                     tRNA-synt_His 307 leal 310
                                        +++
  gi|330508036|ref|YP_004384464.1| 345 FDRI 348
                                       8775 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 !   62.4   0.0     2e-20   5.1e-17       1     134 [.      64     322 ..      64     357 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 2e-20
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasl 76 
                                       Y ++d+ +r+++L+P+ ++++++++  e  +s k  Pl+ly+++ ++R+E++ ++G  R reF q +++ ++ +   
  gi|330508036|ref|YP_004384464.1|  64 YSFQDKGGRDLALRPELTAPVMRMFVSELQNSpK--PLRLYYFGNCFRYERP-QKG--RFREFWQLGAELIGGAR-- 133
                                       899*************************779989..****************.***..*************9988.. PP

                                       HHHHHHHHHHHHHHHHHTT.SC..........EEEEEEGTTSC.................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxx.................................. RF
                      tRNA-synt_2b  77 ddslrdlikaisriferlglef..........raiielmsaks.................................. 109
                                       +ds ++ i +++++ ++ g+            rai+e                                        
  gi|330508036|ref|YP_004384464.1| 134 PDSEAEAIALADQLIRSAGIRGdihlgylgliRAILER----Iegdkraaamrmidkkersalkelledldqgdlgl 206
                                       9*******************997777777666555555....0334458889999999******************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                      tRNA-synt_2b 110 ............................................................................. 109
                                                                                                                    
  gi|330508036|ref|YP_004384464.1| 207 lelidlkgkasldkaleiagdllltetqeastgiggpkacsepkmqsegrgsarngravssqlhleefqetvdllga 283
                                       ***************************************************************************** PP

                                       ..............BTTSEEEEEEEEETTTSEEEEEEEE CS
                                       ..............xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 110 ..............adykdkkefeavsesltkgieigti 134
                                                     +dy+  ++fe++ e l+++++i   
  gi|330508036|ref|YP_004384464.1| 284 ygvdfqidfeivrgLDYYSGTVFEIYAEGLGAQRQICGG 322
                                       *****************************9999988543 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   1.2e-11   3.1e-08      18      92 ..     374     447 ..     362     449 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.2e-11
                                       HHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHHHH CS
                    HGTP_anticodon  18 akklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelveklk 92 
                                       a ++a  Lr+  + ++ld  ++s+g +++ a  +g + av+vG +el++g + +rd+  +eqe+++l+e+ve l+
  gi|330508036|ref|YP_004384464.1| 374 AARIAVSLRRS-VPTVLDVMGRSMGAQLKAASGAGARHAVIVGREELDSGRLILRDMSGGEQENLTLEEIVERLS 447
                                       55666667766.7889999****************************************************9986 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 !   17.1   0.1   8.5e-07    0.0022      20     122 ..      16     128 ..       8     152 .. 0.72
   2 ?    2.6   0.0     0.022        58     282     298 ..     336     352 ..     324     359 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.5e-07
                                       HHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE.............-E-S-SHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxx RF
                       tRNA-synt_2  20 kvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff.............aLtqspqlyl 83 
                                       + +r rs++ ka++++l + g+ e+ tP++ + +   +     v  +    +f                ++   +  
  gi|330508036|ref|YP_004384464.1|  16 EEMRKRSQARKAMQEVLCRWGYQEVATPTFEHLELFTEKSGASVIDEIY--SFQdkggrdlalrpelTAPVMRMFVS 90 
                                       67899*************************9997444444444433333..22255555443445322334444445 PP

                                       HHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  84 ellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaem 122
                                       el  + +  r + ++++FR E+ ++ r   EF+q+ ae+
  gi|330508036|ref|YP_004384464.1|  91 ELQNSPKPLRLYYFGNCFRYERPQKGRFR-EFWQLGAEL 128
                                       5555556789****************999.*****9997 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.022
                                       -SEEEEEEEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 282 pphgGlglGldRlvmll 298
                                        +  G+glG+dR++ + 
  gi|330508036|ref|YP_004384464.1| 336 TSSTGFGLGFDRIMEIA 352
                                       5678********98765 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 !   18.9   0.0   3.2e-07   0.00083      18     127 ..      20     124 ..       9     133 .. 0.81
   2 ?    2.1   0.0     0.044   1.1e+02     207     226 ..     334     353 ..     320     369 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.2e-07
                                       HHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTS.TTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHH CS
                      tRNA-synt_2d  18 pltkvleeikeiflelgfeevegpevesefynfdaLnv.pqdhpaRdmqdtFylkkpekaveekllLRthttavqir 93 
                                         ++ ++ ++e++ + g++ev+ p         ++L++  ++ +a  +++ + + +++    ++l LR   ta  +r
  gi|330508036|ref|YP_004384464.1|  20 KRSQARKAMQEVLCRWGYQEVATPTF-------EHLELfTEKSGASVIDEIYSF-QDKG--GRDLALRPELTAPVMR 86 
                                       55677889999999999999999876.......555541456677777777777.5555..589*********9999 PP

                                       HH....TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEE CS
                      tRNA-synt_2d  94 tl....ekkkppikiisigrvfRrdavDathlaeFhqv 127
                                       +     +++ +p+++  +g++fR +   + +  eF q+
  gi|330508036|ref|YP_004384464.1|  87 MFvselQNSPKPLRLYYFGNCFRYERPQKGRFREFWQL 124
                                       9888889999****************999999999997 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.044
                                       TTSEEEEEEEEHHHHHHHHH CS
                      tRNA-synt_2d 207 eevsgfafGlGveRlamlky 226
                                       +e+s  +fGlG++R+  + +
  gi|330508036|ref|YP_004384464.1| 334 KETSSTGFGLGFDRIMEIAH 353
                                       678899********987766 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 !   15.2   0.0   4.2e-06     0.011      15     159 ..      18     153 ..      11     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.2e-06
                   tRNA_synthFbeta  15 lnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNla 91 
                                         k+ ++r++++++l+  G++Ev t +f + + + +    +  ++    +   + d+ +lR+ L++ ++    + l+
  gi|330508036|ref|YP_004384464.1|  18 MRKRSQARKAMQEVLCRWGYQEVATPTFEHLELFTEKSGASVIDEIYSFQDKGGRDL-ALRPELTAPVMRMFVSELQ 93 
                                       568999**********************99999998854555555555555555555.79***************99 PP

                   tRNA_synthFbeta  92 rgnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgi 159
                                       ++ + +rl+ +g++f+ +  ++ +++e ++l++ l g +         r+ + +++ +++++l +s gi
  gi|330508036|ref|YP_004384464.1|  94 NSPKPLRLYYFGNCFRYErPQKGRFREFWQLGAELIGGA---------RPDSEAEAIALADQLIRSAGI 153
                                       99999*************99999**************99.........666666666666666666666 PP

>> CCDC117  Coiled-coil domain-containing protein 117
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     6e-05      0.15      74     133 ..      10      69 ..       3      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6e-05
                           CCDC117  74 leellsdklkdslqkkqrkqetaarqaktpvasasfektelssearqaelisslysslea 133
                                       + ++l++ +++ +q ++  qe+ +r   + va+++fe+ el++e++ a++i ++ys++++
  gi|330508036|ref|YP_004384464.1|  10 TRDFLPEEMRKRSQARKAMQEVLCRWGYQEVATPTFEHLELFTEKSGASVIDEIYSFQDK 69 
                                       6799999999999999****************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3169.15
//
Query:       gi|330508037|ref|YP_004384465.1|  [L=427]
Description: ATP-dependent RNA helicase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-50  169.6   0.0    3.1e-49  167.1   0.0    1.9  2  DEAD             DEAD/DEAH box helicase
    4.5e-35  120.4   0.5      1e-34  119.2   0.4    1.7  2  Helicase_C       Helicase conserved C-terminal domain
    1.3e-06   28.5   0.0    2.3e-05   24.5   0.0    2.2  2  ResIII           Type III restriction enzyme, res subunit
    5.2e-05   22.2   0.0     0.0014   17.5   0.0    2.2  2  UTP25            Utp25, U3 small nucleolar RNA-associated SSU
     0.0037   17.0   0.0       0.12   12.1   0.0    2.4  2  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.012   15.6   0.2      0.038   14.0   0.1    1.9  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.04   13.3   0.1      0.091   12.2   0.0    1.6  2  SMC_N            RecF/RecN/SMC N terminal domain
      0.051   12.8   0.1      0.083   12.1   0.1    1.3  1  ERCC3_RAD25_C    ERCC3/RAD25/XPB C-terminal helicase
      0.062   13.2   0.2         10    6.0   0.0    2.5  3  Helicase_RecD    Helicase
      0.098   13.0   0.4        1.1    9.5   0.5    2.3  1  AAA_19           AAA domain
       0.11   12.2   0.6        0.2   11.4   0.1    1.7  2  Phage_integrase  Phage integrase family
       0.12   12.3   0.1       0.32   10.9   0.1    1.7  1  Nuc_rec_co-act   Nuclear receptor coactivator


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 !  167.1   0.0   2.1e-52   3.1e-49       1     173 [.      25     193 ..      25     196 .. 0.96
   2 ?    0.0   0.0      0.42   6.3e+02      65     104 ..     258     301 ..     234     312 .. 0.65

  Alignments for each domain:
  == domain 1  score: 167.1 bits;  conditional E-value: 2.1e-52
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS...TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet...kgktgpkalivePtreLaeqtlnnlkkfkkyi 74 
                                       t+iQ  aip +l+g+d+l+ a+TG+GKT+af++p+lq+++ +    +   p++l+++PtreLa q+ + + +++k++
  gi|330508037|ref|YP_004384465.1|  25 TPIQMLAIPPLLEGKDLLGIAQTGTGKTAAFVLPILQRMSAErraSRPGSPRVLVLAPTRELAAQIGQSFATYGKFL 101
                                       89*************************************98899889999*************************** PP

                                       TSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  75 dlrvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpq 151
                                       + r l+i+ggv++  q++ l++gvdi+v+tpgrl+dl+++g+++l+ v+f+VlDE+dr+ld+gf ++++ri+++lp 
  gi|330508037|ref|YP_004384465.1| 102 RFRQLVIFGGVRQGPQVNMLSRGVDILVATPGRLLDLMNQGYIELKGVEFFVLDEIDRMLDMGFIRDVKRIVSALP- 177
                                       ********************999****************************************************4. PP

                                       HCTTSTTTSEEEEEESSBSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 152 itcdgklqrqvivlSATlpkdv 173
                                             +++  +++SATl+++ 
  gi|330508037|ref|YP_004384465.1| 178 ------EKHSSLFFSATLTRET 193
                                       ......55669*******9765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.42
                                       HHHHHHTTTSTSEEEEEETTSSHHHHHHHH...HTT.CSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx.xxxxxxx RF
                              DEAD  65 nnlkkfkkyidlrvlliiggvaardqlskl...dng.vdivvgt 104
                                       +++ +++++ +++  +i g++++++  +++   ++g ++++v+t
  gi|330508037|ref|YP_004384465.1| 258 DKVAQMLSKNRIQSDAIHGNKSQNQRTKTMerfRSGrIRVLVAT 301
                                       44555555555666677776666666665532234468888887 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.7   8.5e+03      74      82 ..     119     127 ..      76     131 .. 0.73
   2 !  119.2   0.4   6.8e-38     1e-34       2     111 .]     231     339 ..     230     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.7
                                       GGGTSSSTS CS
                        Helicase_C  74 dvaerGidi 82 
                                       ++++rG+di
  gi|330508037|ref|YP_004384465.1| 119 NMLSRGVDI 127
                                       556666665 PP

  == domain 2  score: 119.2 bits;  conditional E-value: 6.8e-38
                                       HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                       k + ll+ll l+e+ +++l+f++t+ r++kv  +l+k+ i++ ++hg+ +qn+r +++e+f++g+++vL+atd+a+r
  gi|330508037|ref|YP_004384465.1| 231 KNSLLLDLL-LKEDMKRVLVFARTKHRADKVAQMLSKNRIQSDAIHGNKSQNQRTKTMERFRSGRIRVLVATDIAAR 306
                                       678899999.99******************777779999************************************** PP

                                       SSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                       Gidi+++++V+n+dlp +++sy++riGRtgRag
  gi|330508037|ref|YP_004384465.1| 307 GIDIDDITHVVNYDLPNEPESYVHRIGRTGRAG 339
                                       *******************************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.5e-08   2.3e-05      30     169 ..      44     189 ..      28     191 .. 0.76
   2 ?    1.5   0.1      0.17   2.5e+02      47     110 ..     237     301 ..     232     320 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.5e-08
                                       EESTTSTHHHHH.HHHHHHH-S..........-EEEEESSHHHHHHHHHHGGGGTGG........GEEEESSS-B-- CS
                            ResIII  30 kmaTGtGKTlva.aklierllkkgkee.....kflflvprkslleqtleefkkflseayke....igkkvsgdkkka 96 
                                        + TGtGKT    + + +r++ +++ +     ++l+l+p+++l  q  + f+ + +  + +     g++ +g + + 
  gi|330508037|ref|YP_004384465.1|  44 IAQTGTGKTAAFvLPILQRMSAERRASrpgspRVLVLAPTRELAAQIGQSFATYGKFLRFRqlviFGGVRQGPQVNM 120
                                       578********95555556665555559************************9999988777776666666666666 PP

                                       .......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT---.SEEEEEESS- CS
                            ResIII  97 kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekfke.avllglTATp 169
                                           s   +ilv+t  +l   +     ++   + +  ++++ DE  r+ ++     +++i+ +++e    l ++AT+
  gi|330508037|ref|YP_004384465.1| 121 ---LSRGVDILVATPGRLLDLM-----NQGYIELKGVEFFVLDEIDRMLDMgfiRDVKRIVSALPEkHSSLFFSATL 189
                                       ...8899999999999999999.....55555556666889999999999833335555555553346778888886 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.17
                                       HH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--........-SEEEEE CS
                            ResIII  47 rllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka.kekdstnkkilvtt 110
                                        ll k++ +++l+++ +k+  ++  + ++k   + ++ +g+k ++++ k  ++ +s  +++lv+t
  gi|330508037|ref|YP_004384465.1| 237 DLLLKEDMKRVLVFARTKHRADKVAQMLSKNRIQSDAIHGNKSQNQRTKTmERFRSGRIRVLVAT 301
                                       5566678889*******999999999999988888776555555554444455666666776665 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 ?    2.3   0.0     0.037        56      75      94 ..      74      93 ..      61     100 .. 0.83
   2 !   17.5   0.0   9.6e-07    0.0014     324     417 ..     240     329 ..     208     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.037
                             UTP25 75 rpkvLillptreaalevvel 94
                                       p+vL+l+ptre a ++ ++
  gi|330508037|ref|YP_004384465.1| 74 SPRVLVLAPTRELAAQIGQS 93
                                      59************998665 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 9.6e-07
                             UTP25 324 kkssskssgiliyipsyfdfvrvrnylkeekvsfaaiseysskkevsraRelFfkgkkkvlLyteRlhffrRykikg 400
                                          +++++++l++  +     +v + l++++++  ai+  +s+++ +++ e F +g+ +vl+ t+ +   r  +i +
  gi|330508037|ref|YP_004384465.1| 240 L--KEDMKRVLVFARTKHRADKVAQMLSKNRIQSDAIHGNKSQNQRTKTMERFRSGRIRVLVATDIAA--RGIDIDD 312
                                       3..478999999999999999********************************************885..99***** PP

                             UTP25 401 vkkvilYklPenpefys 417
                                       + +v+ Y+lP++pe y 
  gi|330508037|ref|YP_004384465.1| 313 ITHVVNYDLPNEPESYV 329
                                       *************9986 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   7.8e-05      0.12      15      67 ..      37      95 ..      25     184 .. 0.71
   2 ?    2.3   0.0     0.083   1.2e+02      43      82 ..     241     286 ..     234     310 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.8e-05
                            AAA_30 15 tsgdrvavltGpAGtGKtta..lkalreaweaag......grviglAptgkaAkvLaeelg 67
                                      +++d   +  +  GtGKt a  l  l+++ +++        rv++lApt + A+++++++ 
  gi|330508037|ref|YP_004384465.1| 37 EGKD--LLGIAQTGTGKTAAfvLPILQRMSAERRasrpgsPRVLVLAPTRELAAQIGQSFA 95
                                      5555..4566789*****7522566666666654588999****************98765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.083
                            AAA_30  43 eaaggrviglAptgkaAkvLaeelg...ieastiakllkrlk...g 82 
                                       +++ +rv+++A t+  A+++a+ l    i+++ i+   ++++    
  gi|330508037|ref|YP_004384465.1| 241 KEDMKRVLVFARTKHRADKVAQMLSknrIQSDAIHGNKSQNQrtkT 286
                                       4556899*******99999997666555788888877776665441 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.5e-05     0.038      24      64 ..     232     272 ..     215     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEE CS
                      Shikimate_DH  24 aelvakhLlakgvkkvvvaNRtlerakelaeelkgeeieal 64 
                                        +l++  Ll++ +k+v+v+ Rt +ra+++a+ l++++i+  
  gi|330508037|ref|YP_004384465.1| 232 NSLLLDLLLKEDMKRVLVFARTKHRADKVAQMLSKNRIQSD 272
                                       5678899**************************99977655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.1e-05     0.091     155     209 ..     145     201 ..     112     211 .. 0.74
   2 ?   -2.7   0.1       2.2   3.2e+03     114     134 ..     251     271 ..     214     281 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.1e-05
                                       CCS--SEEEECTTTTTS-H...HHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                       xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 155 kvkpaplyllDeidaaLDe...knvkkvaellkeksknaQfivislreemlekadklv 209
                                       + k   +++lDeid  LD    + vk++++ l ek+ ++ f+  +l++e+ e a++l+
  gi|330508037|ref|YP_004384465.1| 145 ELKGVEFFVLDEIDRMLDMgfiRDVKRIVSALPEKH-SSLFFSATLTRETGELAQSLL 201
                                       567778************822245555555555555.688999999999999888765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                                       TTEEE-HHHHHHHHHCTT-ST CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 114 ngkevtkkevsellesagisk 134
                                        +++ +  +v+++l++ +i++
  gi|330508037|ref|YP_004384465.1| 251 ARTKHRADKVAQMLSKNRIQS 271
                                       444444455555555555554 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.6e-05     0.083      61     130 ..     245     318 ..     217     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.6e-05
                     ERCC3_RAD25_C  61 DkiivfsDnvfaLkeyakklkkp.....yiyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliq 130
                                        +++vf+   +   ++a++l+k+      i+G+ s+++r+k +++f++  ++++++   ++   iD+ + + ++ 
  gi|330508037|ref|YP_004384465.1| 245 KRVLVFARTKHRADKVAQMLSKNriqsdAIHGNKSQNQRTKTMERFRSG-RIRVLVATDIAARGIDIDDITHVVN 318
                                       4689999999999999998877522222689***************976.899**************99888775 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0067        10       4      48 ..      45      96 ..      43     161 .. 0.82
   2 ?   -3.6   0.0       5.8   8.7e+03     116     154 ..     182     201 ..     170     209 .. 0.52
   3 ?    4.6   0.0     0.017        26      17      83 ..     235     302 ..     231     314 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0067
                     Helicase_RecD  4 AdRGRGKSaalGlalaaliaegk.......snilvtapskenvktlfeflak 48
                                      A+ G+GK+aa  l + + +++++        ++lv ap++e ++++ +++a+
  gi|330508037|ref|YP_004384465.1| 45 AQTGTGKTAAFVLPILQRMSAERrasrpgsPRVLVLAPTRELAAQIGQSFAT 96
                                      899*******9998888877777799999999********999988776655 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.8
                     Helicase_RecD 116 rvvlatTvhGYEGtGrgfslkflkqlkkekkrelrelel 154
                                        ++++                  ++l++e+  el +  l
  gi|330508037|ref|YP_004384465.1| 182 SLFFS------------------ATLTRETG-ELAQSLL 201
                                       44444..................44444444.4555555 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.017
                     Helicase_RecD  17 alaaliaegksnilvtapskenvktlfeflakglealglke.eekkkkaekaelrvrkqrieyiapde 83 
                                       +l  l++e+ +++lv a +k+ ++++ ++l k+  + +  + ++++++++k++ r r+ ri+ +  ++
  gi|330508037|ref|YP_004384465.1| 235 LLDLLLKEDMKRVLVFARTKHRADKVAQMLSKNRIQSDAIHgNKSQNQRTKTMERFRSGRIRVLVATD 302
                                       56678888889******************988765555444366666666666666777777665555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.5   0.00077       1.1       8      65 ..      36      97 ..      28     317 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00077
                            AAA_19  8 lkekvllvtaGpGtGKTrvlkh.ivallvelggvkp...eeillvaftgrAakelrerlaal 65
                                      l+ k ll +a  GtGKT   +  i++ + ++++ +     ++l++a+t+  a ++ ++ a++
  gi|330508037|ref|YP_004384465.1| 36 LEGKDLLGIAQTGTGKTAAFVLpILQRMSAERRASRpgsPRVLVLAPTRELAAQIGQSFATY 97
                                      56667777999******876541555555555444356689********9999998887444 PP

>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00013       0.2      88     168 ..     240     330 ..     220     333 .. 0.73
   2 ?   -3.0   0.1       3.6   5.3e+03     107     139 ..     351     383 ..     338     384 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                       CHCCTTTSBSSBET...........TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHH CS
                   Phage_integrase  88 leeaeksellfask...........rgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqk 153
                                       l+e+ k+ l+fa++            ++++++ ++ +  ++  +     +++++ ++R  +at+ + +g+d++ + +
  gi|330508037|ref|YP_004384465.1| 240 LKEDMKRVLVFARTkhradkvaqmlSKNRIQSDAIHGNKSQNQRTKTM-ERFRSGRIRVLVATDIAARGIDIDDITH 315
                                       566777788888887777764444444555555555544444444333.6*************************** PP

                                       HHT-SSCCHHHHHHC CS
                   Phage_integrase 154 llGHssisttqiYth 168
                                       + ++   +  + Y+h
  gi|330508037|ref|YP_004384465.1| 316 VVNYDLPNEPESYVH 330
                                       999988888888887 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.6
                                       -HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHH CS
                   Phage_integrase 107 srqtvrkafkraveeagiekpltpHtlRhsfat 139
                                        ++++ k ++r+ +e   e + + H+ R  +at
  gi|330508037|ref|YP_004384465.1| 351 EERSFLKDIERLTREKIEEREHKYHSPRAKAAT 383
                                       567788888888888544577778888877776 PP

>> Nuc_rec_co-act  Nuclear receptor coactivator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00021      0.32       9      32 ..     138     161 ..     137     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                    Nuc_rec_co-act   9 LLdQLvslLkntDeigLeEiDraL 32 
                                       L++Q +  Lk+++   L+EiDr+L
  gi|330508037|ref|YP_004384465.1| 138 LMNQGYIELKGVEFFVLDEIDRML 161
                                       89*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3025.30
//
Query:       gi|330508038|ref|YP_004384466.1|  [L=71]
Description: hypothetical protein MCON_2111 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       513  (0.0286129); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 552.68
//
Query:       gi|330508039|ref|YP_004384467.1|  [L=664]
Description: hypothetical protein MCON_2112 [Methanosaeta concilii GP6]
Scores for 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-08   33.5   0.0    7.2e-08   32.7   0.0    1.4  1  MutS_V    MutS domain V
    0.00047   20.0   1.5      0.011   15.6   0.2    2.6  2  GA-like   GA-like domain
  ------ inclusion threshold ------
      0.053   13.3   0.1       0.69    9.7   0.0    2.7  3  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
       0.16   11.6   0.0       0.29   10.8   0.0    1.4  1  SRP54     SRP54-type protein, GTPase domain
       0.22   11.3   0.1       0.44   10.3   0.1    1.4  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 !   32.7   0.0     2e-11   7.2e-08       2     122 ..     480     595 ..     479     626 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2e-11
                                       EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TT CS
                            MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatek 78 
                                       l+ G n +Gk t+l  ++ iv+laq+G  vpa++++++++++++    +  +l+ g  +F + m   a +  +  ++
  gi|330508039|ref|YP_004384467.1| 480 LLSGVNSGGKTTLLDLISQIVILAQMGLPVPADSCRMGLFEQLYYFSKSRGTLSAG--AFETAMRKFAVV--ENEKR 552
                                       789*****************************************988777777665..688888877755..56788 PP

                                       SEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GG CS
                            MutS_V  79 slvilDElGRGtstydGlaialavaeyllekikaktlfatHyhe 122
                                        lv+ DEl   t       i   +++ l +   + ++f  H  e
  gi|330508039|ref|YP_004384467.1| 553 KLVLADELESITEPGASARIIACMLDELNR-RGSAAVFVSHLAE 595
                                       9*******8777666666676667777766.4566667777654 PP

>> GA-like  GA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.035   1.2e+02       7      28 ..     231     250 ..     226     255 .. 0.77
   2 !   15.6   0.2   3.2e-06     0.011       5      33 ..     335     362 ..     332     365 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.035
                           GA-like   7 aLkeAKeaAkaeLkaaGitsdf 28 
                                        L++A eaA + L+aaG+ +df
  gi|330508039|ref|YP_004384467.1| 231 TLAAAVEAA-SKLQAAGV-EDF 250
                                       566666555.78******.887 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.2e-06
                           GA-like   5 keaLkeAKeaAkaeLkaaGitsdfyiekI 33 
                                       +e LkeAKe A +eL+  G+ ++ +++ I
  gi|330508039|ref|YP_004384467.1| 335 QEVLKEAKERAREELDLKGA-EEVWLDEI 362
                                       577*****************.*****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 ?   -2.6   0.0       1.1   3.8e+03     137     203 ..     102     177 ..      84     193 .. 0.58
   2 ?    9.7   0.0   0.00019      0.69       2      22 ..     479     499 ..     478     542 .. 0.76
   3 ?   -0.0   0.0      0.17   6.2e+02     255     297 ..     549     592 ..     544     595 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                            AAA_21 137 dlqfgkaltditsrawsllllldglrke.........rigllnifadyfgfakekrllqrlvrslklveielsdlg 203
                                       +++ ++ + +  sr  + +  ++gl+ e         r + ++ +++ +  a++ + +qrl ++ ++++i l++ +
  gi|330508039|ref|YP_004384467.1| 102 SQELIEENRLAASRSLEVARRMEGLGIEeqlrsirplRERSASRVRERAVAASNAEDFQRLKSRGLDRFIDLHLAE 177
                                       5555555555555555555555555555555555555666666666666666666666666666666666665555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00019
                            AAA_21   2 nvliGpNgsGKSnLLdaldll 22 
                                       ++l G N+ GK++LLd+++ +
  gi|330508039|ref|YP_004384467.1| 479 ALLSGVNSGGKTTLLDLISQI 499
                                       6778**************877 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.17
                            AAA_21 255 lkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTH 297
                                       ++k++l+l DE+E+  +P + +r++  +l+el+r+g+  ++++H
  gi|330508039|ref|YP_004384467.1| 549 NEKRKLVLADELESITEPGASARIIaCMLDELNRRGSAAVFVSH 592
                                       566789999*********99999994555999999********9 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     8e-05      0.29       3      57 ..     478     531 ..     476     559 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8e-05
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTE CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgv 57 
                                       v ll G++  GKTt l  +++++   ++  l v aD  R++ +eQL  + ++ g 
  gi|330508039|ref|YP_004384467.1| 478 VALLSGVNSGGKTTLLDLISQIVILAQM-GLPVPADSCRMGLFEQLYYFSKSRGT 531
                                       789************9988888777655.566889************99998873 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   0.1   0.00012      0.44      24      45 ..     478     499 ..     472     505 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                            AAA_29  24 atlltGpsGsGKSTllDAiqal 45 
                                       + ll+G +  GK+TllD i+ +
  gi|330508039|ref|YP_004384467.1| 478 VALLSGVNSGGKTTLLDLISQI 499
                                       689**************88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (664 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.23s 00:00:00.82 Elapsed: 00:00:00.37
# Mc/sec: 5338.88
//
Query:       gi|330508040|ref|YP_004384468.1|  [L=294]
Description: hypothetical protein MCON_2113 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   12.6   0.0       0.34   11.7   0.0    1.5  1  Methyltransf_25  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 ?   11.7   0.0   1.9e-05      0.34       1      81 [.     150     227 ..     150     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS..SSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp..fedgsfDlvvssgalh 75 
                                       +L+++cG+G  t+al +   + + +++D +   l +a ++   +    +  + da+ lp  f  + f  v+ + ++ 
  gi|330508040|ref|YP_004384468.1| 150 ILEICCGNGLATQALIRL--DLDPMAMDSDRCELCIALKNGLMN--PQRSFVLDARLLPryFSGRPFQTVLGF-MVG 221
                                       8***************98..488999998888888887777332..556666778888766788888888884.445 PP

                                       GSSHHH CS
                   Methyltransf_25  76 hlsded 81 
                                       +++d++
  gi|330508040|ref|YP_004384468.1| 222 LIDDSN 227
                                       555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2157.64
//
Query:       gi|330508041|ref|YP_004384469.1|  [L=130]
Description: hypothetical protein MCON_2115 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00047   20.0   0.2     0.0015   18.4   0.1    1.8  2  TrmB      Sugar-specific transcriptional regulator TrmB
    0.00088   19.4   0.0     0.0015   18.6   0.0    1.5  1  HTH_34    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.036   14.0   0.0    1.5  1  PadR      Transcriptional regulator PadR-like family
      0.024   14.3   0.1      0.038   13.6   0.1    1.4  1  SMC_ScpB  Segregation and condensation complex subunit ScpB


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.11     5e+02      25      37 ..      16      28 ..       7      34 .. 0.78
   2 !   18.4   0.1   3.3e-07    0.0015       1      63 [.      20      89 ..      20      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.11
                                      HCHHCCCTTSSCH CS
                              TrmB 25 adeiaeelgvprs 37
                                        e+ +elg+pr+
  gi|330508041|ref|YP_004384469.1| 16 FVEVLRELGIPRN 28
                                      5689999999997 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.3e-07
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEE CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYr 63
                                      L++lG+  + a++ ++L + ++at +ei   +++ ++ v  ++r L +  +Ve ++ +        k+Yr
  gi|330508041|ref|YP_004384469.1| 20 LRELGIPRNVASMITYLANVEEATSREIEIGSNLRQPEVSIAMRTLRNNNWVEEREIKkdgkgrpMKVYR 89
                                      56777777778888899999***********************************988788888444776 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 !   18.6   0.0   3.4e-07    0.0015       5      62 ..      32      91 ..      30     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.4e-07
                            HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie...vdkefkgkkprtllriT 62
                                      +++yLa v+ea+ +e+    ++ + + s+ +++L +++++e   ++k+ kg+ p+ ++r+T
  gi|330508041|ref|YP_004384469.1| 32 MITYLANVEEATSREIEIGSNLRQPEVSIAMRTLRNNNWVEereIKKDGKGR-PMKVYRLT 91
                                      689*************************************643367777777.*******9 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.9e-06     0.036      37      66 ..      61      91 ..      50      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.9e-06
                                      HHHHHHHTTSEEEEEE-S.TSSS-EEEEEES CS
                              PadR 37 aLkrLekeglvesewees.gegpprkyYrlT 66
                                      a+++L+++++ve+++ ++ g+g+p k+YrlT
  gi|330508041|ref|YP_004384469.1| 61 AMRTLRNNNWVEEREIKKdGKGRPMKVYRLT 91
                                      5789********9998888***********9 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   8.6e-06     0.038      92     144 ..      36      93 ..      10     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.6e-06
                          SMC_ScpB  92 Iaykqpvtraeie...eiRGvnsdsvvrtLlerglieekgrkee.pgrpil.YgtTek 144
                                        a  +  t+ eie   ++R  +++ ++rtL + +++ee++ k+  +grp+  Y++T  
  gi|330508041|ref|YP_004384469.1|  36 LANVEEATSREIEigsNLRQPEVSIAMRTLRNNNWVEEREIKKDgKGRPMKvYRLTIS 93 
                                       444455566666544489999****************99855444****876999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 939.90
//
Query:       gi|330508042|ref|YP_004384470.1|  [L=444]
Description: tryptophanyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete 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-41  141.4   0.0    1.4e-23   83.7   0.0    2.1  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
       0.21   10.4   0.2       0.36    9.6   0.2    1.3  1  Oxysterol_BP  Oxysterol-binding protein


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.0   1.5e-27   1.4e-23       3     177 ..      63     233 ..      60     256 .. 0.88
   2 !   55.8   0.0   4.8e-19   4.3e-15     171     292 ..     300     423 ..     292     424 .. 0.86

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 1.5e-27
                                       HS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHH.HHHHHHHHHHHHHH CS
                      tRNA-synt_1b   3 erplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkr.eevlenaikaqlak 78 
                                        rp++v+sG++PTg+ H G++++++ +++ q++g ++f+ +aD++A  ++    +++  r+   e++  +   ++a 
  gi|330508042|ref|YP_004384470.1|  63 GRPFAVMSGFMPTGRAHFGHMMVMNEIIWHQQQGGDAFAAVADMEAHAVRGI--SWERCRQFgIEEYILS---LIAL 134
                                       799***********************************************99..5666666515677777...**** PP

                                       TCHTTT.EEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHH..CCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS CS
                      tRNA-synt_1b  79 gldpek.aevvlqsewlehlelaellrdlgklgslnrmlqfks..vkkrleegegislgeftYplLqaaDilllkad 152
                                       g++p++ +++++qs+ ++  +la  l   +++ +++ ++ f      + +e+    + +++++p+L ++     k+ 
  gi|330508042|ref|YP_004384470.1| 135 GFQPKEnSHIYFQSKNYDVRNLAFELGIEANFSEVSAIYGFSGetCISHMES-VMAQSADILHPQLEEYGGP--KPV 208
                                       *99987688********************************99444444444.456899***********99..*** PP

                                       EEEEEGGGHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 153 lvpgGsDQkqnielgrdlarrfnkk 177
                                       + p+G DQ+ +i l+rdla r+++ 
  gi|330508042|ref|YP_004384470.1| 209 VIPVGADQDPHIKLTRDLAYRMRRF 233
                                       *********************9875 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 4.8e-19
                                       HHHHHHH...STTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHHHHHT CS
                      tRNA-synt_1b 171 arrfnkk...evfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllklkte 242
                                       + r++ +     f +p +++++++tgl+G+ KmS+S+++s+I L+++++++  ki +a+t  ++    +k l + + 
  gi|330508042|ref|YP_004384470.1| 300 IIRLETEhgeYGFIPPASIYHRFMTGLTGG-KMSSSKPESYIALTEDPKEAAGKIMRAITGGRQslAEQKKLGGEPD 375
                                       555555566689******************.*********************************6666777777777 PP

                                       HHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 243 lsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                        +  ++e l  ++++++ +e+ el ae+++++ ++g++kk++ae ++++l
  gi|330508042|ref|YP_004384470.1| 376 KCT-IYEFLLFHLSEDD-KELLELDAECRSGRRMCGNCKKDVAERIKRFL 423
                                       777.6666666667776.9****************************998 PP

>> Oxysterol_BP  Oxysterol-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2     4e-05      0.36     277     343 ..     375     436 ..     330     440 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 4e-05
                                       -...GGG--HHHHCCT---.TTGGS-TTBGGG-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHCC CS
                      Oxysterol_BP 277 kaeeyygftkfavtlNeieekekslaptDsRlRpDqraleegdideAeeeKkrlEekQRerrkeree 343
                                       ++   y+f  f +++     ++k l   D+ +R   r+  +++ d Ae+ K+ l+e+Q +r+ +re+
  gi|330508042|ref|YP_004384470.1| 375 DKCTIYEFLLFHLSE-----DDKELLELDAECRSGRRMCGNCKKDVAERIKRFLDEHQQAREEARER 436
                                       444567777777776.....4467999*******************************888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3201.56
//
Query:       gi|330508043|ref|YP_004384471.1|  [L=467]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-26   92.2   0.1    4.8e-26   91.8   0.1    1.1  1  Peripla_BP_2  Periplasmic binding protein
     0.0027   17.9   2.1     0.0078   16.4   2.1    1.9  1  Dockerin_1    Dockerin type I domain
  ------ inclusion threshold ------
       0.15   11.6   1.9          7    6.3   0.2    2.7  2  EF-hand_5     EF hand


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.1     8e-30   4.8e-26       7     235 ..     127     381 ..     122     384 .. 0.89

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 8e-30
                                       HHHHHHHHTT-GGGEEEB-GGG--GGGGGGT.....TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHH CS
                      Peripla_BP_2   7 svteillalGatdkvvgvdtttsdpldadklee...aivevgadgeidvEklaalkPDlvilskglgltdedeellk 80 
                                       ++ e+   l  tdkv+gvd + s ++++  ++    ++  ++  +++d+E+ + l PDl++  ++    ++++e+  
  gi|330508043|ref|YP_004384471.1| 127 DNSEMMMILKRTDKVAGVDLAMSKSEKEFPDLVkktSVSGFSPATDPDYEQALSLSPDLLLTFSNK---TAEKEEKM 200
                                       67888888999********9999988886555567888888999**********************...78888889 PP

                                       HHS-EEE----TTS......HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT....-EEEEEEEETTE CS
                      Peripla_BP_2  81 sgiptvivessntg......eslkeqiralgellgledeaeklvaeidsklaaaksaidse...kpkpvlvfggade 148
                                       + +p+v+             +s+++ +  lg + +  ++ae+++ ++ sk++++ks ++++   k+++vl+     e
  gi|330508043|ref|YP_004384471.1| 201 PEVPVVFAGLYYPNlinpenSSFTDAVHKLGYIMQAREQAEEYIDWHISKIDEIKSYTENLaeeKRPKVLIATLPKE 277
                                       *********9999999**********************************************988888888887777 PP

                                       .....EEEE-TTSTTTHHHHTS--EESTTT--....STT-EEE-HHHHHHH--SEEEEEEH...........HHHT- CS
                      Peripla_BP_2 149 ...ggyvvagsnsyigdlldalgieniaaesk....kseyeeisaEqilasdpdvifvsgr...........aeadn 207
                                          +++++a+ ++  ++++  +g+++ia++ +    +s+++e+++E++ +sdpd++++ +            + +  
  gi|330508043|ref|YP_004384471.1| 278 gdnSIFTYAKIDT-LSQMVTLAGGRSIAEDLPayleSSYRIEVDPEWVIKSDPDYMIFITIvltppigydsdDISGI 353
                                       7756666666655.6778888**********************************9988888999****88888888 PP

                                       S--HHHHT-SHHHHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 208 ktgleflkenpllaelpAvkngrVyald 235
                                       ++ l  +k++p++a+l+Avkn++Vy ++
  gi|330508043|ref|YP_004384471.1| 354 SQALLSFKSRPEYANLTAVKNNQVYIIN 381
                                       88888899*****************885 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.1   1.3e-06    0.0078       5      57 ..      48      95 ..      44      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-06
                                      TSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHHHHH CS
                        Dockerin_1  5 NgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallvinyL 57
                                      N Dg+++  D+  ++  +      +s +    aD N DG+v+  D+++v   +
  gi|330508043|ref|YP_004384471.1| 48 NMDGTIDMKDIEYLQEIIA-----GSVNASPLADANFDGKVDENDISQVEMII 95
                                      99********999999999.....777888889***************97655 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1    0.0063        38      10      19 ..      47      56 ..      47      59 .. 0.86
   2 ?    6.3   0.2    0.0012         7       8      18 ..      75      85 ..      74      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0063
                                      SS-SSCE-HH CS
                         EF-hand_5 10 lNgDGkIske 19
                                      +N+DG+I++ 
  gi|330508043|ref|YP_004384471.1| 47 ANMDGTIDMK 56
                                      69******86 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0012
                                      H-SS-SSCE-H CS
                         EF-hand_5  8 iDlNgDGkIsk 18
                                      +D+N DGk++ 
  gi|330508043|ref|YP_004384471.1| 75 ADANFDGKVDE 85
                                      7********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); 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:                         3  (0.000167327); expected 0.2 (1e-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: 3041.52
//
Query:       gi|330508044|ref|YP_004384472.1|  [L=452]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-31  108.6   0.1    4.6e-31  108.2   0.1    1.1  1  Peripla_BP_2  Periplasmic binding protein
    0.00081   19.5   2.9     0.0017   18.5   2.9    1.6  1  Dockerin_1    Dockerin type I 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 !  108.2   0.1   5.1e-35   4.6e-31       1     234 [.     108     372 ..     108     376 .. 0.90

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 5.1e-35
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--.GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsd.pldadkleeaivevgadgeidvEklaalkPDlvilskglgltdede 76 
                                       i++ + +++++ + l  tdkvvgvd ++   p++ +++ +  ++   ++e+d+Ek++ l+PDl+++ ++    ++++
  gi|330508044|ref|YP_004384472.1| 108 IVVEYLDNADLMQILKKTDKVVGVDLAVAKsPAEFPEMSNRTCVGAMHKEPDYEKVLSLDPDLLLVFSNV---TQEK 181
                                       77888999*****************88655055556777799****************************...8888 PP

                                       HHHHHHS-EEE----TTS......HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT....-EEEEEEE CS
                      Peripla_BP_2  77 ellksgiptvivessntg......eslkeqiralgellgledeaeklvaeidsklaaaksaidse...kpkpvlvfg 144
                                       ++  +g+p+++             + +++ +r lg +l+ ++ ae++++++ + l ++ +++ s+    +++vlv +
  gi|330508044|ref|YP_004384472.1| 182 DKNLPGVPVLFAGLYYPDllkpetSAFTDAVRKLGYVLDAQQDAEEYIQWHMNSLNRLVESTGSIpdsERPTVLVAA 258
                                       8888********998877899999*****************************************886666666655 PP

                                       ETTE....EEEE-TTSTTTHHHHTS--EESTTT--....STT-EEE-HHHHHHH--SEEEEEEH............. CS
                      Peripla_BP_2 145 gade..ggyvvagsnsyigdlldalgieniaaesk....kseyeeisaEqilasdpdvifvsgr............. 202
                                       + ++  ++++ ++     + ++d +g++ +a++ +    + +++e+++E++l +dpd+i+                 
  gi|330508044|ref|YP_004384472.1| 259 YPEAdeKTIFTFAQIDTLTSMVDLAGGRTVASDLPdfmkSTYRIEVDPEWVLQEDPDYIVLLVVattysglvldpps 335
                                       544456999999***********************************************98888889********** PP

                                       .....HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 203 .....aeadnktgleflkenpllaelpAvkngrVyal 234
                                            +    k+ le+++++p++a+l+Av+ng+Vy l
  gi|330508044|ref|YP_004384472.1| 336 gydadDPTGMKEALEAFMSRPEYANLKAVQNGDVYIL 372
                                       **98777778999**********************98 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   2.9   1.9e-07    0.0017       5      57 ..      35      82 ..      32      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-07
                                      TSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHHHHH CS
                        Dockerin_1  5 NgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallvinyL 57
                                      N Dgk++  D++ ++  +      ++ s++  aD N DG+v+ +D+++v   +
  gi|330508044|ref|YP_004384472.1| 35 NMDGKIDQEDIATLREIIS-----NNMSPTGLADANLDGEVDLRDIAQVEMII 82
                                      99*****************.....99999*******************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 3385.15
//
Query:       gi|330508045|ref|YP_004384473.1|  [L=447]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-26   94.0   0.0    1.4e-26   93.6   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.026   14.7   1.0      0.052   13.7   1.0    1.5  1  Dockerin_1    Dockerin type I 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 !   93.6   0.0   1.5e-30   1.4e-26       2     237 ..     125     386 ..     124     387 .. 0.90

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 1.5e-30
                                       EE-SHHHHHHHHHTT-GGGEEEB.-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                      Peripla_BP_2   2 aslspsvteillalGatdkvvgv.dtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                       ++++   +eil++lGa++kvvgv dt+++ p+  ++l  +  ++g++ge+dvE++++  PD +++ + +   ++ ++
  gi|330508045|ref|YP_004384473.1| 125 VVYTHQCAEILQLLGAEEKVVGVrDTFAEQPNRFPRLS-KYQSIGSGGEPDVEAVLKTNPDAILAYTWYPSEESLDD 200
                                       7888899**************96589999999999998.99************************999977777888 PP

                                       HHHHHS-EEE----TTS...HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE.. CS
                      Peripla_BP_2  78 llksgiptvivessntg...eslkeqiralgellgledeaeklvaeidsklaaaksaidse.kpkpvlvfggade.. 148
                                       +l + ++++ ++  + g   ++  e++r lg l g  d+ae++ +++d  l+++++ ++++ +++ v v+ ++ +  
  gi|330508045|ref|YP_004384473.1| 201 KLPPEVEVLRFDCECSGqgpDDMRERVRLLGILMGARDRAEEYLQWHDAILDQVEDEVRKIpQNERVRVYLESTPeg 277
                                       88888888888888877********************************************8555555555555569 PP

                                       ......EEEE-TTSTTTHHHHTS--EESTTT--......STT-EEE-HHHHHHH--SEEEEEEH..........HHH CS
                      Peripla_BP_2 149 ....ggyvvagsnsyigdlldalgieniaaesk......kseyeeisaEqilasdpdvifvsgr..........aea 205
                                           ++ + +g+++   +l++ +g+ niaa           ey+ei  E++l+++p+vi+ + +           ++
  gi|330508045|ref|YP_004384473.1| 278 drpmSSRTAIGTGHAAHKLVEMAGGVNIAAGRLpgyedtAFEYGEIETEWVLSQNPEVIVGRAMgpgirpyenvNDS 354
                                       ****************************888888************************************8887666 PP

                                       T-S--HHHHT-SHHHHTSHHHHTT-EEEE-HH CS
                      Peripla_BP_2 206 dnktgleflkenpllaelpAvkngrVyaldss 237
                                            ++++ + p++ e+ Avkn  +y + ++
  gi|330508045|ref|YP_004384473.1| 355 LLESYAQDIRSLPGFDEVRAVKNDGIYIITND 386
                                       677778889999***************98776 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.0   5.8e-06     0.052       5      57 ..      51      98 ..      48     106 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.8e-06
                                      TSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHHHHH CS
                        Dockerin_1  5 NgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallvinyL 57
                                      N D  +n  D++ + + ++     ++++++   D +++G+++  D++lv   +
  gi|330508045|ref|YP_004384473.1| 51 NLDDDINDQDLAYLERIIE-----GTEEPTWLSDADNNGEIDESDISLVQSII 98
                                      8899***************.....9999********************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3117.08
//
Query:       gi|330508046|ref|YP_004384474.1|  [L=90]
Description: hypothetical protein MCON_2123 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-37  128.1   0.7    1.5e-37  127.8   0.7    1.1  1  MC1       Non-histone chromosomal protein MC1


Domain annotation for each model (and alignments):
>> MC1  Non-histone chromosomal protein MC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.8   0.7   8.4e-42   1.5e-37       1      96 []       3      88 ..       3      88 .. 0.99

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 8.4e-42
                               MC1  1 dkrnfalrdedGeeisvfsGkqPrqaaLkaarrletadseeeakeeeirLrekGtkkvhiyegkaeeeeaPddkpdWle 79
                                      +krnfalrd++G+e+++++G++PrqaaLk+a+r+ ++          irLre+Gtkkvhiy+g+++++++P+++p+W++
  gi|330508046|ref|YP_004384474.1|  3 EKRNFALRDASGNEVGIYTGMAPRQAALKVASRGVKD----------IRLRERGTKKVHIYQGNRRKVKKPKNAPAWMP 71
                                      79*********************************99..........******************************** PP

                               MC1 80 dkitkanvskqgiekle 96
                                      dki+k++v+k giekle
  gi|330508046|ref|YP_004384474.1| 72 DKIWKPTVKKIGIEKLE 88
                                      ***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 703.36
//
Query:       gi|330508047|ref|YP_004384475.1|  [L=603]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-32  112.2   0.0    4.5e-32  111.4   0.0    1.4  1  ABC_tran      ABC transporter
    6.7e-18   65.3   9.5    8.6e-18   65.0   9.5    1.1  1  ABC_membrane  ABC transporter transmembrane region
    8.5e-08   31.9   0.2    6.7e-06   25.7   0.2    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
    4.8e-05   23.8   0.7    0.00028   21.3   0.2    2.4  2  AAA_16        AAA ATPase domain
    6.5e-05   22.9   0.3       0.14   11.9   0.0    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0011   18.7   0.0     0.0027   17.4   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
       0.01   16.1   0.0      0.032   14.5   0.0    1.8  1  AAA_22        AAA domain
       0.04   13.8   0.0      0.089   12.7   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
      0.054   12.8   0.0      0.098   11.9   0.0    1.3  1  Zeta_toxin    Zeta toxin
      0.088   12.4   1.1       0.61    9.6   0.4    2.5  2  AAA_25        AAA domain
      0.091   11.5   0.0       0.18   10.6   0.0    1.5  1  ABC_ATPase    Predicted ATPase of the ABC class
      0.099   12.2   0.0       0.22   11.0   0.0    1.5  1  AAA_7         P-loop containing dynein motor region
       0.15   12.1   0.0       0.54   10.3   0.0    1.9  2  MMR_HSR1      50S ribosome-binding GTPase
       0.19   12.2   0.0       0.37   11.3   0.0    1.4  1  AAA_23        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   0.0   3.5e-35   4.5e-32       1     137 []     354     503 ..     354     503 .. 0.89

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 3.5e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+n+s+++k+g++va+vG +G+GKSt++ ll + ++p+eG++ll g+d+++ +l++lr++++ + qe+ lf+++ v+
  gi|330508047|ref|YP_004384475.1| 354 LHNISFEVKPGSTVALVGATGTGKSTVIDLLFRFHDPQEGRVLLGGHDIRSLPLNFLRSQMALVAQESYLFYDT-VE 429
                                       79************************************************************************.99 PP

                                       HH................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +n                +  +++++++  l      +tv+++++  LSgG++qr+a+arallk +++lllDEpt+
  gi|330508047|ref|YP_004384475.1| 430 NNlrlgnpkasheeivraATAANAHQFIVALPE--GYQTVIGERGVLLSGGERQRIAIARALLKGAPILLLDEPTS 503
                                       99*****99666555433333335555544444..569************************************96 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   9.5   6.7e-21   8.6e-18       3     270 ..      22     289 ..      20     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 6.7e-21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   3 liillailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrk 79 
                                       l +l+ +++ +++++  ++ gri+  + d  +  +  +  ++  +l++  +++i++     +    +  +++ +r++
  gi|330508047|ref|YP_004384475.1|  22 LTFLSGLMGSIANIALLFLAGRIIVGIYDGRTLLS--MLDLFSGMLAAIGLRAIAEASIDITAQRSAAMVKSSVRKR 96 
                                       6789999999*******************888888..9999999999999*************************** PP

                                       HHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH.HHHHHHHSHHHHHHHHHHHHHHH CS
                      ABC_membrane  80 lfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgg.livmfylgwkltlvllailplii 155
                                       + +++l +  sf + ++++ l + + + v+ l+  +g  +  +   l++ v + l++++y+    +l+l+a++pl+ 
  gi|330508047|ref|YP_004384475.1|  97 INQHLLDLGPSFVEMRNTSALATTVLDGVEALEAYVGLYVPYMALCLVMPVLLfLGFAIYVDLISALMLMAFVPLVP 173
                                       ****************************************99999888866551689******************** PP

                                       HHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 156 lvsaviakilk.klkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligit 231
                                       l+  +++ + + k+ ++ ++++ ++s+++ Esl+g+ t+k+f   e+  ++ +  +++ +ka ++++ ++   + ++
  gi|330508047|ref|YP_004384475.1| 174 LSLLIFTNLEEwKVGRRAWETYRELSAYFAESLQGLTTLKLFSQAERRGQELHRRSRNLEKALVQSLQLYFGASFVS 250
                                       *******99876899************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHH CS
                      ABC_membrane 232 qllgllsyalalwfGttlvisgelsvgdlvvflslfail 270
                                       ++++ l y+l++ ++++  ++g ls+++lv++l+l +++
  gi|330508047|ref|YP_004384475.1| 251 EVVPVLGYSLTMIVSSFRLSQGSLSMDKLVMVLLLGSLF 289
                                       ****************************88888776655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.2   5.2e-09   6.7e-06      28     213 ..     368     547 ..     353     553 .. 0.63

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.2e-09
                                       EEEESTTSSHHHHHHHHHHHCTT..TTT.TTTCHCCCCCC--BTTCSSTTEEEEEEEE.EETTEESSSSSSC...EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx...xx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGer.sak.klrseklsdlihkskekasvkkaeveitf.dnedkklkiekee...vs 98 
                                       a+vG+ G GKs ++d + F + +  + +  l  +++++l  +  +++ +  a+ + +f d  +++l+  +++    +
  gi|330508047|ref|YP_004384475.1| 368 ALVGATGTGKSTVIDLL-FRFHDPqEGRvLLGGHDIRSLPLNFLRSQMALVAQESYLFyDTVENNLRLGNPKashEE 443
                                       56777777777777755.55554312221345566666655533344444443333332444444333333311133 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                       i r +   +  ++ +       + ++ ++ + g+   lLSgGe++ +a+a        k ap+ llDe  + +D++n
  gi|330508047|ref|YP_004384475.1| 444 IVRAATAANAHQFIVA----LPEGYQTVIGERGV---LLSGGERQRIAIAR----ALLKGAPILLLDEPTSSIDAEN 509
                                       4444444444333332....22445555555555...79*****9888764....4689****************** PP

                                       HHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 176 vkkvaellkeksknaQfivislreemlekadklvgvtk 213
                                        + + + l + + +  +++i++r  +++kad ++ + +
  gi|330508047|ref|YP_004384475.1| 510 EEDIQKALGRLQAQHTVMIIAHRLSTVRKADCILVMEM 547
                                       ******************************98887766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.5   5.7e+03      69      95 ..     201     226 ..     178     258 .. 0.57
   2 !   21.3   0.2   2.2e-07   0.00028      25     107 ..     365     471 ..     353     547 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.5
                            AAA_16  69 ysa.laqalareellrqlldeaesaele 95 
                                       y a  +q l++ +l+ q +++ ++  l 
  gi|330508047|ref|YP_004384475.1| 201 YFAeSLQGLTTLKLFSQAERRGQE--LH 226
                                       323355555555555555555332..22 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.2e-07
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy....sa.laqalareellrqlldeaesaelea 96 
                                       + v l+G+ G+GKs++++ l+r    ++g +l g  d    ++p+    s+  + a +   ++  ++++++  ++ a
  gi|330508047|ref|YP_004384475.1| 365 STVALVGATGTGKSTVIDLLFRFHDPQEGRVLLGGHDIR--SLPLnflrSQmALVAQESYLFYDTVENNLRLGNPKA 439
                                       7899*****************999999999988888877..466655664413322223334444444445545555 PP

                            AAA_16  97 wrekleeala.....................a 107
                                        +e++ +a++                      
  gi|330508047|ref|YP_004384475.1| 440 SHEEIVRAATaanahqfivalpegyqtvigeR 471
                                       55544444444444555444444554444441 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00011      0.14       3      24 ..     368     389 ..     367     411 .. 0.74
   2 !    8.4   0.1    0.0013       1.7     239     273 ..     477     508 ..     434     531 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                            AAA_21   3 vliGpNgsGKSnLLdaldllar 24 
                                       +l+G+ g+GKS+++d+l  +++
  gi|330508047|ref|YP_004384475.1| 368 ALVGATGTGKSTVIDLLFRFHD 389
                                       79***************66644 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0013
                            AAA_21 239 dGtkrllalltallralkkgsllliDEpEngLHPk 273
                                        G ++ +a++ all  +   ++ll+DEp ++++ +
  gi|330508047|ref|YP_004384475.1| 477 GGERQRIAIARALLKGA---PILLLDEPTSSIDAE 508
                                       55555545444555444...***********9974 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 !   17.4   0.0   2.1e-06    0.0027      16      40 ..     358     382 ..     353     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.1e-06
                            AAA_29  16 tieidlkgatlltGpsGsGKSTllD 40 
                                       ++e+++ +++ l+G++G+GKST++D
  gi|330508047|ref|YP_004384475.1| 358 SFEVKPGSTVALVGATGTGKSTVID 382
                                       5777777799**************9 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   2.5e-05     0.032       7      38 ..     366     400 ..     361     468 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee...e 38 
                                        ++++G +GtGK+t++  l++ +d ++       +
  gi|330508047|ref|YP_004384475.1| 366 TVALVGATGTGKSTVIDLLFRFHDPQEGRVLlggH 400
                                       5789******************9865433336664 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.9e-05     0.089      90     120 ..     354     385 ..     335     395 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-05
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinall 120
                                       l++++ ++k  +t++lvG +G GKSt+i+ l 
  gi|330508047|ref|YP_004384475.1| 354 LHNISFEVKPgSTVALVGATGTGKSTVIDLLF 385
                                       6677777887799***************9986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.6e-05     0.098      19      57 ..     367     405 ..     357     428 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.6e-05
                        Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57 
                                       + l+G++G GKs++++ll + +++q++ v l + d+R+l
  gi|330508047|ref|YP_004384475.1| 367 VALVGATGTGKSTVIDLLFRFHDPQEGRVLLGGHDIRSL 405
                                       7799********************************986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.53   6.8e+02      75     102 ..     214     241 ..     212     256 .. 0.76
   2 ?    9.6   0.4   0.00048      0.61      32      50 ..     363     381 ..     349     458 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.53
                            AAA_25  75 lyvsaEdsedelrrRlravgealrddar 102
                                       l+ +aE + +el+rR r + +al +  +
  gi|330508047|ref|YP_004384475.1| 214 LFSQAERRGQELHRRSRNLEKALVQSLQ 241
                                       57799**********9999988843333 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00048
                            AAA_25  32 agelallaGapgtGKttla 50 
                                        g++++l+Ga+gtGK+t+ 
  gi|330508047|ref|YP_004384475.1| 363 PGSTVALVGATGTGKSTVI 381
                                       6999*************85 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00014      0.18     295     352 ..     446     504 ..     438     548 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                                       --EEEE--TTTB---CCC--ST.TEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS- CS
                        ABC_ATPase 295 rsvkgvDispFinnLPegkdtt.kfstedASGStsqAanimealeagakllLiDEDtsA 352
                                       r+ + ++  +Fi +LPeg +t         SG   q  +i++al  ga++lL+DE ts 
  gi|330508047|ref|YP_004384475.1| 446 RAATAANAHQFIVALPEGYQTViGERGVLLSGGERQRIAIARALLKGAPILLLDEPTSS 504
                                       566778999***********9955556678*************************9995 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00017      0.22      30      58 ..     361     389 ..     355     396 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkld 58 
                                       +k +  v lvG tGtGK+++i  l++  d
  gi|330508047|ref|YP_004384475.1| 361 VKPGSTVALVGATGTGKSTVIDLLFRFHD 389
                                       5667899*************998777665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00043      0.54       2      21 ..     367     386 ..     366     454 .. 0.89
   2 ?   -1.7   0.0       2.4   3.1e+03      44      84 ..     491     530 ..     479     551 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00043
                                       EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                       va+vG + +GKSt+i  l++
  gi|330508047|ref|YP_004384475.1| 367 VALVGATGTGKSTVIDLLFR 386
                                       9**************99876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
                                       TTEEEEEEECGGCSS.HHHHHHHHHHHHHHHHCTSEEEEEEE CS
                          MMR_HSR1  44 kgkeielvDtpGlie.gaseekglgkaflaleeadlillvvd 84 
                                       kg +i l+D p   + +a++e++++ka+ +l +a++ ++++ 
  gi|330508047|ref|YP_004384475.1| 491 KGAPILLLDEPT-SSiDAENEEDIQKALGRL-QAQHTVMIIA 530
                                       467777777777.322344444555555443.3344444443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00029      0.37      15      39 ..     357     384 ..     344     386 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                            AAA_23  15 idF..skglt.lItGpNGaGKTTildAi 39 
                                       i F  ++g t +++G +G+GK+T++d +
  gi|330508047|ref|YP_004384475.1| 357 ISFevKPGSTvALVGATGTGKSTVIDLL 384
                                       455446665438*************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); 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: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 3995.23
//
Query:       gi|330508048|ref|YP_004384476.1|  [L=583]
Description: cysteine ABC transporter permease/ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-33  114.0   0.0    1.3e-32  113.2   0.0    1.4  1  ABC_tran       ABC transporter
    1.2e-16   61.1   6.7    1.8e-16   60.7   6.7    1.1  1  ABC_membrane   ABC transporter transmembrane region
    7.7e-08   32.0   0.0    4.1e-06   26.4   0.0    2.2  2  SMC_N          RecF/RecN/SMC N terminal domain
     0.0016   18.8   0.7      0.004   17.5   0.1    2.0  2  AAA_16         AAA ATPase domain
     0.0021   18.0   0.0     0.0044   16.9   0.0    1.5  1  RsgA_GTPase    RsgA GTPase
  ------ inclusion threshold ------
      0.011   15.4   0.1       0.03   14.1   0.1    1.7  1  AAA_29         P-loop containing region of AAA domain
      0.012   14.5   0.0          3    6.6   0.0    2.3  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.021   14.9   0.0      0.051   13.6   0.0    1.7  1  MMR_HSR1       50S ribosome-binding GTPase
      0.025   13.4   0.4      0.047   12.5   0.0    1.5  2  ABC_ATPase     Predicted ATPase of the ABC class
       0.05   13.9   0.0       0.91    9.8   0.0    2.3  2  AAA_22         AAA domain
      0.053   13.2   0.5       0.12   12.0   0.0    2.0  2  AAA_30         AAA domain
       0.06   12.6   0.0       0.12   11.6   0.0    1.4  1  Zeta_toxin     Zeta toxin
      0.084   12.4   0.0       0.22   11.0   0.0    1.7  2  AAA_25         AAA domain
       0.11   11.7   0.0       0.23   10.7   0.0    1.6  1  DUF3666        Ribose-5-phosphate isomerase
       0.12   12.6   0.4        1.5    9.1   0.4    2.4  1  SbcCD_C        Putative exonuclease SbcCD, C subunit
       0.18   11.6   0.6         13    5.4   0.1    2.3  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 


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 !  113.2   0.0   1.1e-35   1.3e-32       1     137 []     363     512 ..     363     512 .. 0.92

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 1.1e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ +sl++ +g++va+vG +GaGKSt+++l+++  +p++G+ill g dl++ ++ +lr+ ++v++q+ +lf+++ +r
  gi|330508048|ref|YP_004384476.1| 363 LSSISLEIPAGSTVALVGTSGAGKSTVINLMLRFWDPEAGRILLGGSDLRRYPMMQLRRLFSVVSQDVFLFSDS-IR 438
                                       5789**********************************************************************.** PP

                                       HH.......HHHTCHHHHHHHSTTGG.......TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.......xxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.......esdeeiekalsklglke.......lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       en       +sd+e+e+++s+ ++++         dt v++++  LSgG++qr+a+arallk +++l+lDE+t+
  gi|330508048|ref|YP_004384476.1| 439 ENirlgrpeASDAEVEEVASRARIHDfiitlpqGYDTLVGERGVRLSGGERQRIAIARALLKGAPILVLDEATS 512
                                       *********7777777777777777766666666699999999*****************************96 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   6.7   1.6e-19   1.8e-16       7     268 ..      28     291 ..      23     297 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1.6e-19
                                       HHHHHHHHHHHHHHHHHHHHHHHHSSTCCHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   7 lailagvlsplfplvlgrildtlldkgdpet..ealnvysllllllglaqfilallqsyllnvtgerlskrlrrklf 81 
                                       la+++++l  +  +  + +   l+  + + t  e+l  y+ ++++lgla++ +++l  yl +v++ r+ ++lr ++f
  gi|330508048|ref|YP_004384476.1|  28 LAVISEILRQVSGIGVAVLGAALFARAVAGTaiEELYPYAAAMIILGLARGTFGYLGPYLSHVAAFRILVDLRDEFF 104
                                       66777777777777777777777777666668889****************************************** PP

                                       HHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane  82 kkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvs 158
                                        +i  +  +   ++++G+l+s   +d++ l+ +++ + g  + ++++ +++l  + +++  l+ +ll++l+l+il+ 
  gi|330508048|ref|YP_004384476.1| 105 WAIEPLAPAKLARRRTGDLVSTAVSDIELLELFFAHTAGPAVVAFIVPIIALTALATINLLLAEALLIFLILLILMP 181
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 159 aviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitqllg 235
                                        +   + ++l ++   + a ++s   ++++g++ + +fg  ++ le+  +++ + +  + + a+  gl++++  +++
  gi|330508048|ref|YP_004384476.1| 182 RLAFWLGTTLGERLRGQQALLNSQELDTIQGMKEILSFGYSRQRLEELSENSATLLALQARQARNIGLQSAAKISIV 258
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHH CS
                      ABC_membrane 236 llsyalalwfGttlvisgelsvgdlvvflslfa 268
                                       ++ ++++l++++ lv ++ l +g l +++ l++
  gi|330508048|ref|YP_004384476.1| 259 SAGTLAVLLCASILVRQNSLAPGFLPITMILAS 291
                                       ******************999997655554444 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.04        44      25      42 ..     374     391 ..     363     402 .. 0.83
   2 !   26.4   0.0   3.6e-09   4.1e-06     135     209 ..     465     552 ..     417     560 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.04
                                       SEEEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlld 42 
                                       s  a+vG  G+GKs +++
  gi|330508048|ref|YP_004384476.1| 374 STVALVGTSGAGKSTVIN 391
                                       45789**********997 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 3.6e-09
                                       T.................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEE CS
                                       x.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e.................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfiv 194
                                                          LSgGe++ +a+a        k ap+ +lDe  + LD++n +++ e l e+++    i+
  gi|330508048|ref|YP_004384476.1| 465 FiitlpqgydtlvgergvRLSGGERQRIAIAR----ALLKGAPILVLDEATSSLDAENERAIKEALMERREGRTTIM 537
                                       45555555556666666679*****9888764....4689************************************* PP

                                       E-SSHHHCCC-SCEE CS
                                       xxxxxxxxxxxxxxx RF
                             SMC_N 195 islreemlekadklv 209
                                       i++r  ++ +ad ++
  gi|330508048|ref|YP_004384476.1| 538 IAHRLSTVVDADWIF 552
                                       *****9999998766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       3.9   4.4e+03      69      69 ..     255     255 ..     198     324 .. 0.50
   2 !   17.5   0.1   3.6e-06     0.004      24     145 ..     373     511 ..     363     539 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.9
                            AAA_16  69 y 69 
                                        
  gi|330508048|ref|YP_004384476.1| 255 I 255
                                       0 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.6e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde....aesaelea 96 
                                       ++ v l+G sG GKs++++  lr +  + g  l g  d      p+ +l ++++  +    l ++         +++
  gi|330508048|ref|YP_004384476.1| 373 GSTVALVGTSGAGKSTVINLMLRFWDPEAGRILLGGSDLR--RYPMMQLRRLFSVVSQDVFLFSDsireNIRLGRPE 447
                                       4789**********************99888887777777..34444455554333333333333222122222222 PP

                            AAA_16  97 wrekleeala......................avpelagaea......srllellkrllallsrderplvlvlDdlq 145
                                       ++++  e++a                                      +r + +++r+l    + +   +lvlD++ 
  gi|330508048|ref|YP_004384476.1| 448 ASDAEVEEVAsrarihdfiitlpqgydtlvgeR--------GvrlsggERQRIAIARAL---LK-G-APILVLDEAT 511
                                       222222222244555555555554444444222........122222244444444444...12.2.2477777665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.9e-06    0.0044      98     120 ..     372     394 ..     357     404 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.9e-06
                                       TTSEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinall 120
                                       +++t++lvG SG+GKSt+in +l
  gi|330508048|ref|YP_004384476.1| 372 AGSTVALVGTSGAGKSTVINLML 394
                                       45899***************876 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   2.7e-05      0.03      20      39 ..     371     390 ..     364     400 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                            AAA_29  20 dlkg.atlltGpsGsGKSTll 39 
                                         +g ++ l+G+sG+GKST++
  gi|330508048|ref|YP_004384476.1| 371 P-AGsTVALVGTSGAGKSTVI 390
                                       4.455899***********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 ?    5.4   0.0    0.0063       7.1     221     255 ..     293     327 ..     286     336 .. 0.85
   2 ?    6.6   0.0    0.0027         3      17      38 ..     375     396 ..     362     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0063
                     TrwB_AAD_bind 221 pllsawldlaikallslpesrerrlWfflDElpaL 255
                                        +ls++  + i++ lsl + + rrl+++lDE pa+
  gi|330508048|ref|YP_004384476.1| 293 VFLSITSVVEISKQLSLTRAAARRLFLLLDEQPAV 327
                                       57777778889999*****************9986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0027
                     TrwB_AAD_bind  17 hilivGttGsGKtqalekllra 38 
                                        +++vGt G+GK+++++ +lr 
  gi|330508048|ref|YP_004384476.1| 375 TVALVGTSGAGKSTVINLMLRF 396
                                       5789*************99985 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.6e-05     0.051       2      21 ..     376     395 ..     375     406 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.6e-05
                                       EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                       va+vG + +GKSt+in +++
  gi|330508048|ref|YP_004384476.1| 376 VALVGTSGAGKSTVINLMLR 395
                                       9***************9976 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.7   1.9e+03     241     262 ..     369     391 ..     367     394 .. 0.82
   2 ?   12.5   0.0   4.2e-05     0.047     292     353 ..     452     514 ..     446     558 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.7
                                       EE-SS.EEEEEE-TTSSHHHHHH CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLe 262
                                        ip G  +++vG+   GKsT ++
  gi|330508048|ref|YP_004384476.1| 369 EIPAGsTVALVGTSGAGKSTVIN 391
                                       58899666799*********876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.2e-05
                                       -TT--EEEE--TTTB---CCC--ST.TEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-H CS
                        ABC_ATPase 292 EdgrsvkgvDispFinnLPegkdtt.kfstedASGStsqAanimealeagakllLiDEDtsAt 353
                                       E     +++ i  Fi +LP+g dt         SG   q  +i++al  ga++l++DE ts  
  gi|330508048|ref|YP_004384476.1| 452 EVEEVASRARIHDFIITLPQGYDTLvGERGVRLSGGERQRIAIARALLKGAPILVLDEATSSL 514
                                       555556778899************955566788**************************9965 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00081      0.91       8      28 ..     376     396 ..     372     424 .. 0.87
   2 ?    1.3   0.0      0.34   3.8e+02      81     105 ..     493     518 ..     457     540 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00081
                            AAA_22   8 lvvtGesGtGKTtllrrlleq 28 
                                       ++++G sG+GK+t+++ +l+ 
  gi|330508048|ref|YP_004384476.1| 376 VALVGTSGAGKSTVINLMLRF 396
                                       689************998875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.34
                            AAA_22  81 aleqalraravielliiDEaqh.lr..s 105
                                       a+++al + a   +l++DEa   l+  +
  gi|330508048|ref|YP_004384476.1| 493 AIARALLKGAP--ILVLDEATSsLDaeN 518
                                       45666666666..*******99885532 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       7.2   8.1e+03      50      67 ..     235     252 ..     224     270 .. 0.58
   2 ?   12.0   0.0   0.00011      0.12      20      50 ..     375     405 ..     370     538 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.2
                            AAA_30  50 iglAptgkaAkvLaeelg 67 
                                        +lA ++++A++++ ++ 
  gi|330508048|ref|YP_004384476.1| 235 TLLALQARQARNIGLQSA 252
                                       577888888888663333 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00011
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrvi 50 
                                       +++l+G  G+GK+t+++ + + w+ + gr++
  gi|330508048|ref|YP_004384476.1| 375 TVALVGTSGAGKSTVINLMLRFWDPEAGRIL 405
                                       5789*******************99954443 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.12      19      57 ..     376     414 ..     371     440 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                        Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57 
                                       + l+G +GAGKs++++l+ +  +++ + + l + dlR++
  gi|330508048|ref|YP_004384476.1| 376 VALVGTSGAGKSTVINLMLRFWDPEAGRILLGGSDLRRY 414
                                       6799*****************999999999999999987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0002      0.22      30      50 ..     370     390 ..     344     423 .. 0.85
   2 ?   -3.5   0.0         6   6.7e+03     141     161 ..     500     520 ..     487     529 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                            AAA_25  30 lpagelallaGapgtGKttla 50 
                                       +pag++++l+G +g+GK+t+ 
  gi|330508048|ref|YP_004384476.1| 370 IPAGSTVALVGTSGAGKSTVI 390
                                       79*****************86 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6
                            AAA_25 141 egvrlvviDplsralggdens 161
                                       +g+  +v+D  ++ l++++++
  gi|330508048|ref|YP_004384476.1| 500 KGAPILVLDEATSSLDAENER 520
                                       367888999988888885554 PP

>> DUF3666  Ribose-5-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00021      0.23      16      44 ..     122     150 ..     121     153 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                                       HHHHHHT-STTHHHHHTTT---HHHHHHH CS
                           DUF3666  16 dLvkgAisGerFqeyFFancqdeeIaayv 44 
                                       dLv +A+s  +  e+FFa+   +++ a++
  gi|330508048|ref|YP_004384476.1| 122 DLVSTAVSDIELLELFFAHTAGPAVVAFI 150
                                       9********************99999998 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.4    0.0013       1.5      65      87 ..     503     525 ..     460     528 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                           SbcCD_C  65 rlvfLDEAFsklDeesiatllel 87 
                                        +++LDEA s+lD+e+ +++ e+
  gi|330508048|ref|YP_004384476.1| 503 PILVLDEATSSLDAENERAIKEA 525
                                       589************98887665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.012        13       3      24 ..     377     398 ..     376     455 .. 0.70
   2 ?    4.3   0.1     0.027        30     200     284 ..     449     528 ..     428     541 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.012
                            AAA_21   3 vliGpNgsGKSnLLdaldllar 24 
                                       +l+G  g+GKS+++ ++  +++
  gi|330508048|ref|YP_004384476.1| 377 ALVGTSGAGKSTVINLMLRFWD 398
                                       79************99988765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.027
                            AAA_21 200 sdlgegeeliasvderlrergvvflengdgqelparel..SdGtkrllalltallralkkgsllliDEpEngLHPkl 274
                                       sd ++ e+ +  ++++    ++++l  g++  +  r +  S G ++ +a++ all  +   ++l++DE  ++L+ + 
  gi|330508048|ref|YP_004384476.1| 449 SDAEVEEVASRARIHD----FIITLPQGYDTLVGERGVrlSGGERQRIAIARALLKGA---PILVLDEATSSLDAEN 518
                                       4444444444444444....77777777777777777777888888877777777666...************9988 PP

                            AAA_21 275 lrrllellke 284
                                        r + e l e
  gi|330508048|ref|YP_004384476.1| 519 ERAIKEALME 528
                                       8887776644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 3688.38
//
Query:       gi|330508049|ref|YP_004384477.1|  [L=222]
Description: membrane protein, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1331.86
//
Query:       gi|330508050|ref|YP_004384478.1|  [L=153]
Description: hypothetical protein MCON_2129 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-18   67.5   0.0      2e-18   66.7   0.0    1.4  1  FmdE      FmdE, Molybdenum formylmethanofuran dehydrogenase o


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.0   1.1e-22     2e-18       1     131 [.      25     142 ..      25     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 1.1e-22
                                       HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-S...TCHHHHHHHHCS--TTTTSEEE--SS-SEEEEE CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetd...sCldDAiqvltgctlGkgnlivmdygkkaltfk 74 
                                       fHGHl+p++vlGy+++++a+k+l  + + +  + +++++++   sCl+D++q+  gctlGk+n+++++ ++    f 
  gi|330508050|ref|YP_004384478.1|  25 FHGHLGPYIVLGYMIGRYARKNLCSD-PFQ-MKAEVFCQDKppqSCLADGVQIGSGCTLGKRNIRIVPSNEIRCHFA 99 
                                       9**********************853.444.8899999999*****************************9999997 PP

                                       ETTT-EEEEEEE-CCTHHHHHHHCCT--.GGGS-HHHHHHHHHHHHHHHHHS.HHHHE CS
                              FmdE  75 krktgkavrlklkeelpelreklakgka.keekeeeeleeeleeaikkilnapeeelf 131
                                         +  + + +  +              a ++e+  +e   ++e++++k++ + +++lf
  gi|330508050|ref|YP_004384478.1| 100 AGE--RELVIIPR------------PIAfTSES-GKEHDLLIEQLAEKMYRMADTDLF 142
                                       532..44444444............22223332.223366788888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1064.60
//
Query:       gi|330508051|ref|YP_004384479.1|  [L=248]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-25   88.5   0.0    7.2e-25   88.1   0.0    1.2  1  ABC_tran  ABC transporter
    3.5e-06   27.1   0.1     0.0018   18.1   0.1    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0012   19.0   1.6      0.084   13.1   1.6    2.3  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
     0.0016   17.9   0.1       0.66    9.4   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
     0.0021   18.6   0.0     0.0032   18.0   0.0    1.2  1  AAA_23    AAA domain
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.024   14.3   0.0    1.3  1  AAA_27    AAA domain
      0.015   15.2   0.5       0.93    9.4   0.5    2.2  1  NTPase_1  NTPase
      0.025   14.3   0.0      0.051   13.3   0.0    1.4  1  AAA_29    P-loop containing region of AAA domain
      0.067   12.9   0.0        0.1   12.3   0.0    1.3  1  AAA_15    AAA ATPase domain
      0.069   13.4   0.0       0.12   12.6   0.0    1.4  1  AAA_28    AAA domain
        0.1   11.5   0.0       0.14   11.1   0.0    1.1  1  DUF4702   Domain of unknown function (DUF4702)


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 !   88.1   0.0   4.4e-28   7.2e-25       2     136 ..      22     170 ..      21     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 4.4e-28
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       k++sl++ +ge v+i G+n aGK+tLl+ + gl+k t G+  + g d+++ +  ++r+++g++ q+  ++p +    
  gi|330508051|ref|YP_004384479.1|  22 KDLSLEVDRGEYVVIGGPNSAGKTTLLESINGLVKITHGRACVCGLDVRR-RGFEVRRRVGYVIQNFYFDPFTPFTA 97 
                                       89************************************************.6777899********55555554333 PP

                                       H...................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n...................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +                    + + +++a++++g+++l+++++     +LSgGq+q+v++a  ++k+p+l++lDEp+
  gi|330508051|ref|YP_004384479.1|  98 QevvmmgrfgrqgllsrpkeSDYDAVQRAIKTVGIEDLAHKTI----GTLSGGQQQKVMIAHNIAKEPDLFMLDEPF 170
                                       345**********999987444445******************....*****************************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 !   18.1   0.1   1.1e-06    0.0018       3      49 ..      35      89 ..      33     100 .. 0.74
   2 !    7.1   0.0    0.0026       4.2     236     281 ..     142     184 ..     112     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl........drdvegltdelsggggirkipsll 49
                                      v+ GpN++GK++LL+ + +l  +          dv++++ e ++++g+ ++ +++
  gi|330508051|ref|YP_004384479.1| 35 VIGGPNSAGKTTLLESINGLVKIthgracvcGLDVRRRGFEVRRRVGYVIQNFYF 89
                                      899***************9977677777777666666666666666665555555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0026
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllel 281
                                        lS G+++    + + +  +k+++l+ +DEp ++L+ ++ + l ++
  gi|330508051|ref|YP_004384479.1| 142 TLSGGQQQK---VMIAHNIAKEPDLFMLDEPFSNLDFRAREFLQDV 184
                                       567777777...66677777888**************887766555 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   1.6   5.2e-05     0.084      26      87 ..     136     184 ..     112     187 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.2e-05
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllel 87 
                                        ++ +gtlSGG++q+++    a    + +       + ++l++LDE Fs+lD + ++ l ++
  gi|330508051|ref|YP_004384479.1| 136 AHKTIGTLSGGQQQKVMI---A----HNI------AKEPDLFMLDEPFSNLDFRAREFLQDV 184
                                       678889999999976542...2....222......34699************9888766665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0026       4.3      26      45 ..      33      52 ..      21      62 .. 0.81
   2 !    9.4   0.0   0.00041      0.66     135     186 ..     141     188 ..      90     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0026
                                      EEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAil 45
                                        +i GpN +GK+ ll++i 
  gi|330508051|ref|YP_004384479.1| 33 YVVIGGPNSAGKTTLLESIN 52
                                      567889************95 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00041
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                        +LSgG+++ v++a  +    +k   l++lDe  ++LD++ ++ + +++k  
  gi|330508051|ref|YP_004384479.1| 141 GTLSGGQQQKVMIAHNI----AKEPDLFMLDEPFSNLDFRAREFLQDVFKGM 188
                                       38******998887554....46667***************99999888754 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     2e-06    0.0032      22      40 ..      34      52 ..      20      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                            AAA_23 22 tlItGpNGaGKTTildAik 40
                                      ++I GpN aGKTT+l+ i 
  gi|330508051|ref|YP_004384479.1| 34 VVIGGPNSAGKTTLLESIN 52
                                      69**************995 PP

>> AAA_27  AAA 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     0.024      19      49 ..      24      54 ..      21      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      l+++ ++ +  +i GpN AGK+t+l++i+ l
  gi|330508051|ref|YP_004384479.1| 24 LSLEVDRGEYVVIGGPNSAGKTTLLESINGL 54
                                      66666788999****************9876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.5   0.00057      0.93       2      49 ..      34      84 ..      33     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00057
                                      EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE-.------EEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfyteevr.eggrrigFki 49
                                      v+i Gp   GKtTl++ +  l+k       v+G+ +++   e  rr+g+ i
  gi|330508051|ref|YP_004384479.1| 34 VVIGGPNSAGKTTLLESINGLVKIThgRACVCGLDVRRRGfEVRRRVGYVI 84
                                      78999999******9999888765421345666655544445566666665 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   3.1e-05     0.051      16      44 ..      25      53 ..      20      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqa 44
                                      ++e+d+ + +++ Gp+ +GK+Tll +i+ 
  gi|330508051|ref|YP_004384479.1| 25 SLEVDRGEYVVIGGPNSAGKTTLLESING 53
                                      57888667999*************98875 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   6.4e-05       0.1      14      48 ..      21      56 ..      20      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.4e-05
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFln 48
                                      +kd +++++   + v+ G+N++GK+++le ++ + +
  gi|330508051|ref|YP_004384479.1| 21 IKDLSLEVDRGeYVVIGGPNSAGKTTLLESINGLVK 56
                                      577777777775888889************986655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.4e-05      0.12       2      26 ..      34      63 ..      33      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.4e-05
                            AAA_28  2 ivitGgestGKTtlleaLa.....argypv 26
                                      +vi G+ s+GKTtlle ++      +g  +
  gi|330508051|ref|YP_004384479.1| 34 VVIGGPNSAGKTTLLESINglvkiTHGRAC 63
                                      7899999********998855555456555 PP

>> DUF4702  Domain of unknown function (DUF4702)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.3e-05      0.14     276     325 ..     163     212 ..     151     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.3e-05
                           DUF4702 276 yCslrePhrtldflaehrlfPalqsvvsqavdklsgarrrdGlPlfPael 325
                                          l eP+  ldf a+  l   ++ +v+q+v  l  a   dGlP  P +l
  gi|330508051|ref|YP_004384479.1| 163 LFMLDEPFSNLDFRAREFLQDVFKGMVQQGVPILMVAHAFDGLPDIPIHL 212
                                       55789***************************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1786.71
//
Query:       gi|330508052|ref|YP_004384480.1|  [L=276]
Description: ABC transporter [Methanosaeta concilii GP6]
Scores for complete 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-47  160.1  40.1    7.9e-47  159.9  40.1    1.0  1  ABC-3     ABC 3 transport family
    5.7e-05   22.3  35.0    5.7e-05   22.3  35.0    2.0  2  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.9  40.1   8.8e-51   7.9e-47       4     257 ..      10     265 ..       7     266 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.9 bits;  conditional E-value: 8.8e-51
                             ABC-3   4 flqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellkrktkl 80 
                                       ++ +al a i+ s+ac++lg+ +     s +g ++sHaa++G al+++lg n  ++ai++++ +a  ++ +++k+k+
  gi|330508052|ref|YP_004384480.1|  10 VVCHALEAMIFASVACSILGVIISRMSLSSIGFTMSHAAFAGAALGMFLGANAQMAAIAFSMGVAALIGPVSEKAKM 86 
                                       6778999*************9999999999*********************************************** PP

                             ABC-3  81 kedtaigivlsvflalglvlvslikk..skvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfde 155
                                       + d+ + +++s ++a++++l+s+++      + +s LfG+++++ +e+++ +a+i  + +l +l f+ke+ +i+f+ 
  gi|330508052|ref|YP_004384480.1|  87 AADATLSVLFSLSMAVAIFLISYMEYmgKGLSASSLLFGDVISLYREEIYALAAICCLSILFVLAFYKEISAIMFNM 163
                                       ************************99656677889****************************************** PP

                             ABC-3 156 elAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllS 232
                                       + A+++g++vkl++++ll +ial+v+++l++vG +L++ ll++Pa++A +++ +++s++ivA l++l+ +++G++  
  gi|330508052|ref|YP_004384480.1| 164 KIAESAGVRVKLVYYVLLFIIALSVALSLNIVGGLLIFVLLVTPASIAGQFCFNVKSMFIVAPLVALLVSAFGVWAG 240
                                       ***************************************************************************** PP

                             ABC-3 233 yyldlatGavivlvatllfllallv 257
                                       + + l+  ++++l++t +f +++++
  gi|330508052|ref|YP_004384480.1| 241 FEFTLPVAPLVALLLTGVFAISVML 265
                                       *********************9986 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2  13.4     0.086   7.7e+02     103     206 ..      18     116 ..      10     121 .. 0.80
   2 !   22.3  35.0   6.3e-09   5.7e-05      80     308 ..      45     261 ..      44     266 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.086
                             FecCD 103 lplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllneealesilfwllGsls.gaswsk 178
                                       +++a++++++l++++   ++ ++ g++      aG a++++l+a +++ ++      ++  +  l+G +s +a++  
  gi|330508052|ref|YP_004384480.1|  18 MIFASVACSILGVIISR-MSLSSIGFTMSHAAFAGAALGMFLGANAQMAAIA-----FSMGVAALIGPVSeKAKMAA 88 
                                       34444455555544444.33588999999999***************99977.....778899999*998799**** PP

                             FecCD 179 vllllvllllllllllllarkldllalg 206
                                        + l+vl+ l+++++++l+++++ +  g
  gi|330508052|ref|YP_004384480.1|  89 DATLSVLFSLSMAVAIFLISYMEYMGKG 116
                                       *********************9999877 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 6.3e-09
                             FecCD  80 ssgaalgavlalllllgslslfalplaaflgallalllvl.llarkrkgasplkliLaGiavsallsaltsllllll 155
                                       s++a +ga+l+++l+  ++++   +++af ++++al+  +   a++ + a+   l    +av+++l + ++++    
  gi|330508052|ref|YP_004384480.1|  45 SHAAFAGAALGMFLG-ANAQM---AAIAFSMGVAALIGPVsEKAKMAADATLSVLFSLSMAVAIFLISYMEYMGK-- 115
                                       678888999999887.44444...444443333333332202233444444444555567777777777777774.. PP

                             FecCD 156 neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvallt 232
                                             s+   l+G++ +   ++++ l+++++l++l++l++++++++++++ ++A+s Gv+v+ v ++ll+++al +
  gi|330508052|ref|YP_004384480.1| 116 ----GLSASSLLFGDVISLYREEIYALAAICCLSILFVLAFYKEISAIMFNMKIAESAGVRVKLVYYVLLFIIALSV 188
                                       ....457889999***999********************************************************** PP

                             FecCD 233 avavalv.GpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiy 308
                                       a++  +v G + Fv L+ P  +      ++  ++ + ++++ l+ ll+  ++ ++ ++++lpv  ++al+ + +f++
  gi|330508052|ref|YP_004384480.1| 189 ALSLNIVgGLLIFVLLVTPASIAG----QFCFNVKSMFIVAPLVALLVSAFGVWAGFEFTLPVAPLVALLLTGVFAI 261
                                       ***977626789*******98884....5555555556666666666777777777788899999999988888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1031  (0.0575046); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2078.79
//
Query:       gi|330508053|ref|YP_004384481.1|  [L=234]
Description: hypothetical protein MCON_2132 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-28   98.7   0.3      5e-28   98.4   0.3    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 !   98.4   0.3   2.8e-32     5e-28       2     173 ..      10     203 ..       9     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 2.8e-32
                            DUF169   2 LaealrlktePVavkfsdekpe..lpekkekieekk....rlCqmvalara.kgktvvf....taetlgCpgGaaal 67 
                                       La+a+++kt+PV+v++sd+ pe  +        ++       C m ++a+     +v++    ++  + C+gG a++
  gi|330508053|ref|YP_004384481.1|  10 LANAVNMKTSPVCVYGSDQVPEnaVR-------SSSfsdcLACNMYQIAEGrITGPVYAgndpSHLFCRCMGGPAWF 79 
                                       7899*****************84322.......222323578888888887644455557865555677******** PP

                            DUF169  68 Gf...........kelpeklksg.......egylk.speaakkfveslprleagevkyvvvapLekaefe..Pdvvv 123
                                       G+                   +g        ++lk ++++a ++ ++++ ++  + +yvv++ +++++++  ++++v
  gi|330508053|ref|YP_004384481.1|  80 GYrgfdprlpglmS-------TGseaakqdGKHLKeNENIACETYKAVGEIKTLG-RYVVMRRCDDFQEDpgVKCIV 148
                                       **666655554431.......334455555555555***************8888.**************9****** PP

                            DUF169 124 ffanpeqlmrLvqlalydrgggrlnvsfpgngaaCadivaypykegepn......i 173
                                       +fa  eq++ L+ la++ + + ++ +s+p+ g+aCa++v+yp++++e++      i
  gi|330508053|ref|YP_004384481.1| 149 CFASGEQIRDLCALAHFGSHNVFNLISVPW-GPACATLVTYPAGMAENAslsqisI 203
                                       ******************************.****************998777552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.19s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 2005.26
//
Query:       gi|330508054|ref|YP_004384482.1|  [L=292]
Description: hypothetical protein MCON_2133 [Methanosaeta concilii GP6]
Scores for complete 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   53.3   1.9    4.3e-14   52.5   1.9    1.4  1  ZnuA      Zinc-uptake complex component A periplasmic


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   1.9   2.4e-18   4.3e-14       1     223 [.      32     261 ..      32     291 .. 0.73

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 2.4e-18
                                       EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT-.---HHHHHH....HHHSSEEEESSTTTSGTHH.HHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx....xxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                              ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsy.eptprdvrk....laeAdllvynglelEtwld.kllasssq 71 
                                       +v+tts+l d + +++Gdrve  ++ +p   pH    + p+ ++     +++A++++      ++ ++  +++++  
  gi|330508054|ref|YP_004384482.1|  32 IVCTTSVLMDPATYIGGDRVEAISIADPTLCPHLQtDIIPNRIQLnmdfIKDANMFMAYNDSNDQRYNmPAINDFMT 108
                                       8********************************7658888888766777**********999998866323344422 PP

                                       CCCEEEEETTTTCCSEBCSSEST.GGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA  72 atrvevidlsegveeeeeeeDpH.iWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireela 147
                                       a++        g  e +  ++p   W  p n + ++ +++  L+++dpan+ +ye+++++y+++ ++++    e+ +
  gi|330508054|ref|YP_004384482.1| 109 ANNY-------GTAEWMTISNPSrGWNTPTNSKLLAAEVEGWLANKDPANKTYYEQRYNDYAKSFDAIEPTESEKKQ 178
                                       2221.......11222233366548*******************************************999888877 PP

                                       TSSGTEGEEEESSSTTHHHHHHTT-EEEEEE..SSSSS...HHHHHHHHHHHHH.....TT-SEEEEETTS-THHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx...xxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxx RF
                              ZnuA 148 eipeekrklvtthdafgylarayglevagia..giste...aaqiaalieeike.....agvkaifveplaspklae 214
                                         + +  ++++++d+++ +    g++v++++  ++       ++ a++++ i++     ++vk+i+ e+++s +la+
  gi|330508054|ref|YP_004384482.1| 179 LNQTQVIVMLWQKDPVQNW---LGMNVVNFFapEF--AlngTKTAARVVDDINAnpekyQNVKYII-ENMQSGELAK 249
                                       555577788899****999...8*****9964444..25596666666666654222235777775.5677777777 PP

                                       HHHH...HHT-E CS
                                       xxxx...xxxxx RF
                              ZnuA 215 tlae...eagvk 223
                                        + e   + g+ 
  gi|330508054|ref|YP_004384482.1| 250 GIEEslkDKGID 261
                                       777744333444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2085.54
//
Query:       gi|330508055|ref|YP_004384483.1|  [L=134]
Description: response regulator receiver domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-25   87.6   0.0    6.8e-25   87.4   0.0    1.1  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.0   3.8e-29   6.8e-25       1     111 [.      21     129 ..      21     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 3.8e-29
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT.TTSEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed.pelpvii 76 
                                       +li++Ddp+++ +  ++l+  gy + +++++g eal  +++++++l+l+Di+mp+mdGl++++ ir++  + +++i+
  gi|330508055|ref|YP_004384483.1|  21 ILIAEDDPANQLVALRMLKTLGY-NADTVDNGLEALIAMESRSYNLVLMDIQMPEMDGLQAARIIRKRWpEGPRIIF 96 
                                       8**********************.*****************************************999945577888 PP

                                       EESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  77 ltahseeedavealkagaddflsKpfdpeeLlkal 111
                                       +t+ ++   + e+++ g d+f+sKp++  +L +a+
  gi|330508055|ref|YP_004384483.1|  97 VTGCTS--RRDECISEGGDGFISKPISLHQLQEAI 129
                                       886665..899*********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 972.37
//
Query:       gi|330508056|ref|YP_004384484.1|  [L=256]
Description: phosphatidylethanolamine N-methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.0    2.5e-24   85.7   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    4.8e-23   81.7   0.0    9.7e-23   80.7   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    3.4e-22   78.9   0.0    6.4e-22   78.0   0.0    1.5  2  Methyltransf_31  Methyltransferase domain
    5.3e-18   65.4   0.0    7.4e-18   64.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.2e-14   54.2   0.0    1.9e-14   53.6   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.1e-11   45.3   0.0      2e-11   44.5   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    2.6e-07   30.4   0.0    4.9e-07   29.4   0.0    1.3  1  MTS              Methyltransferase small domain
    3.5e-06   26.9   0.0    8.6e-06   25.6   0.0    1.6  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    8.6e-06   25.8   0.0    1.6e-05   24.9   0.0    1.4  1  Methyltransf_32  Methyltransferase domain
      2e-05   24.1   0.0    4.6e-05   23.0   0.0    1.5  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.5e-05   24.0   0.0    4.2e-05   23.2   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
     0.0002   21.3   0.0    0.00037   20.5   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
    0.00026   20.7   0.0    0.00035   20.3   0.0    1.1  1  NodS             Nodulation protein S (NodS)
    0.00076   18.8   0.0     0.0017   17.7   0.0    1.6  1  GidB             rRNA small subunit methyltransferase G
     0.0026   17.5   0.0     0.0046   16.7   0.0    1.4  1  UPF0020          Putative RNA methylase family UPF0020
     0.0034   16.7   0.0     0.0045   16.3   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0059   16.0   0.0     0.0085   15.5   0.0    1.2  1  TehB             Tellurite resistance protein TehB
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.015   15.4   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
      0.011   14.8   0.0       0.05   12.7   0.0    1.8  2  RrnaAD           Ribosomal RNA adenine dimethylase
      0.016   14.9   0.0      0.023   14.4   0.0    1.3  1  TPMT             Thiopurine S-methyltransferase (TPMT)
      0.027   13.4   0.1       0.04   12.9   0.1    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.088   12.4   0.0       0.13   11.8   0.0    1.2  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
       0.15   11.7   0.0       0.25   11.0   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F


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 !   85.7   0.0   3.2e-27   2.5e-24       1      95 [.      50     144 ..      50     145 .. 0.99

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 3.2e-27
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       LdvG+G G +a  la+ g +v+gvD+s  m++ a+++a+  gl+v+f++ad e+l f ++sfDl v ++ l +++ p
  gi|330508056|ref|YP_004384484.1|  50 LDVGTGPGFMALILAEMGLDVTGVDISSGMIEKARQNAQSMGLQVDFRHADGEQLSFDSESFDLLVNRHLLWTLPHP 126
                                       8**************************************************************************** PP

                                       HHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                        +a++e+ RvLk gG+++
  gi|330508056|ref|YP_004384484.1| 127 LAAVREWSRVLKDGGRIL 144
                                       ***************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.0   1.2e-25   9.7e-23       1      97 []      49     141 ..      49     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 1.2e-25
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vLd+G+G+G ++l la+ +   +vtgvDis++m+e+ar++a++ gl+v+f+++d e+l+f+++sfDl v ++ l  l
  gi|330508056|ref|YP_004384484.1|  49 VLDVGTGPGFMALILAEMG--LDVTGVDISSGMIEKARQNAQSMGLQVDFRHADGEQLSFDSESFDLLVNRHLLWTL 123
                                       9***************995..*************************************************7555555 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +  +  +a++e++rvLk+gG
  gi|330508056|ref|YP_004384484.1| 124 P--HPLAAVREWSRVLKDGG 141
                                       5..6679************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0   8.2e-25   6.4e-22       5     114 ..      47     155 ..      44     212 .. 0.84
   2 ?   -2.7   0.0       5.8   4.5e+03      49      67 ..     209     228 ..     202     234 .. 0.66

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 8.2e-25
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                       +rvlD+G+G G+ ++ la e+g   +v+G+Dis  +ie+Ar+naq+ gl+ v F+++d e+l+  +  e+fDl++ +
  gi|330508056|ref|YP_004384484.1|  47 KRVLDVGTGPGFMALILA-EMG--LDVTGVDISSGMIEKARQNAQSMGLQ-VDFRHADGEQLS--FDSESFDLLVNR 117
                                       68****************.775..68***********************7.************..999********* PP

                   Methyltransf_31  82 evlnaladpdkileeiervlkpggilliedpr.....l 114
                                        +l +l++p ++ +e +rvlk+gg++l+ d       l
  gi|330508056|ref|YP_004384484.1| 118 HLLWTLPHPLAAVREWSRVLKDGGRILAIDGAwfdpsL 155
                                       ***************************99998333321 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.8
                   Methyltransf_31  49 qklgldnveFeq.gdieele 67 
                                       ++ gl nv+F++ +++++l+
  gi|330508056|ref|YP_004384484.1| 209 EEAGLFNVSFRHlEEVQKLQ 228
                                       45666777777645566555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   9.5e-21   7.4e-18       4     163 ..      28     216 ..      25     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 9.5e-21
                   Methyltransf_23   4 qreeelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae........kakkaqkdqfd 72 
                                       +++  ++ +le +l+  r+ +rvLd+G+G G ++ +l+e g +vtgvD+s+ ++e+a+        + ++ + d   
  gi|330508056|ref|YP_004384484.1|  28 EEKAVWKMELEPFLQ-GRRYKRVLDVGTGPGFMALILAEMGLDVTGVDISSGMIEKARqnaqsmglQVDFRHAD--- 100
                                       556778888888887.8999*************************************97777744433333333... PP

                   Methyltransf_23  73 eqeaaepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllse...plasl.....................k 125
                                        ++ ++++++fdl v+r++l ++p+p +++r   + lk+gG++l  +   ++ sl                     +
  gi|330508056|ref|YP_004384484.1| 101 GEQLSFDSESFDLLVNRHLLWTLPHPLAAVREWSRVLKDGGRILAIDgawFDPSLnaqirrgissaaakicsrkapS 177
                                       337788999***********************************999776454557778888888888888877644 PP

                   Methyltransf_23 126 edrllld.wlylvpagrhisffsarslkelleeaGlevv 163
                                        ++++ld ++ + ++  ++s    + +++ +eeaGl +v
  gi|330508056|ref|YP_004384484.1| 178 LKSKFLDhYQSIKKELPLFSQSKPERICNVFEEAGLFNV 216
                                       444544413444444344455566788888888888766 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   2.4e-17   1.9e-14      33     221 ..      31     221 ..      23     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 2.4e-17
                                       HHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT CS
                   Ubie_methyltran  33 rlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaee 109
                                        +Wk  +e    ++r ++vlDv +G g +a+ l+++     +v+++Di++ m++ +++ ++  g  +++f +a++e+
  gi|330508056|ref|YP_004384484.1|  31 AVWKMELEPFLQGRRYKRVLDVGTGPGFMALILAEM---GLDVTGVDISSGMIEKARQNAQSMGL-QVDFRHADGEQ 103
                                       68*************************999988764...569******************99996.8********** PP

                                       -TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE...E----SHHHHHHHHHHHH.HHH.HHHHHHH CS
                   Ubie_methyltran 110 LpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvle...fskvelpllsqayelyskevlP.vlGklla 182
                                       L f+ +sfD++   + l  ++  l a++e  rvlk GGr++ ++   f    +  ++   +  + ++   ++ +l +
  gi|330508056|ref|YP_004384484.1| 104 LSFDSESFDLLVNRHLLWTLPHPLAAVREWSRVLKDGGRILAIDgawFDPSLNAQIRRGISSAAAKICSrKAPSLKS 180
                                       *******************************************9333333344556666655555555415667888 PP

                                       S-HHHHHHHHHHHHHS--H..HHHHHHHHHTTEEEEEEEEE CS
                   Ubie_methyltran 183 kdldsyryLvesirafPdq..etlkeliedaGfksveyesl 221
                                       k ld y+ +++ +  f +   e + +++e+aG+ +v++++l
  gi|330508056|ref|YP_004384484.1| 181 KFLDHYQSIKKELPLFSQSkpERICNVFEEAGLFNVSFRHL 221
                                       88899999999999888762257889999999999988765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   2.5e-14     2e-11       1      99 []      50     143 ..      50     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 2.5e-14
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       L++G+G G ++  l+e   ++++tgvDis+ +ie+a++  ++ +     +v++++ d ++l+   +sfDl v  ++l
  gi|330508056|ref|YP_004384484.1|  50 LDVGTGPGFMALILAEM--GLDVTGVDISSGMIEKARQNAQSMGL----QVDFRHADGEQLSFDsESFDLLVNRHLL 120
                                       8****************..**************666666666664....66666666555554467*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGrl 99 
                                         l+++ +++++  ++Lk+gGr+
  gi|330508056|ref|YP_004384484.1| 121 WTLPHPLAAVREWSRVLKDGGRI 143
                                       *********************96 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   6.3e-10   4.9e-07      27     102 ..      41     115 ..      37     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 6.3e-10
                                       CHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEEE CS
                               MTS  27 lpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdliv 102
                                       l+ ++ ++vlD+G+G G++++ la++  +  vt vd++   +e a++n+++ +l+v++++ d+ +  ++ ++fdl+v
  gi|330508056|ref|YP_004384484.1|  41 LQGRRYKRVLDVGTGPGFMALILAEMGLD--VTGVDISSGMIEKARQNAQSMGLQVDFRHADGEQlSFDSESFDLLV 115
                                       55667789*****************9877..9******************************987345578888876 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 !   25.6   0.0   1.1e-08   8.6e-06      72     147 ..      44     115 ..      33     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.1e-08
                                       -TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEE CS
                              PCMT  72 kkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaih 147
                                       ++ +rvL+vG+G G+ + +la++  +++   +++ +  ++e+a++n +  +l +v ++++DG++   +   +d ++
  gi|330508056|ref|YP_004384484.1|  44 RRYKRVLDVGTGPGFMALILAEMGLDVT---GVDISSGMIEKARQNAQSMGL-QVDFRHADGEQLSFDSESFDLLV 115
                                       56789*****************976665...***************999988.6********98666666666655 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   2.1e-08   1.6e-05      24      87 ..      44     101 ..      32     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.1e-08
                   Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfael 87 
                                       ++ ++v+DvG G g+++ +la     ++l v+g+d+++ ++eka++ a+ +g  ++ +++ a++
  gi|330508056|ref|YP_004384484.1|  44 RRYKRVLDVGTGPGFMALILAE----MGLDVTGVDISSGMIEKARQNAQSMG--LQVDFRHADG 101
                                       56789****************9....8************************9..5445555444 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   5.9e-08   4.6e-05     158     233 ..      40     117 ..      34     145 .. 0.76
   2 ?   -2.4   0.0       3.1   2.4e+03      11      35 ..     198     222 ..     196     240 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.9e-08
                              PrmA 158 lvkege..evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk..eekadvi 230
                                       ++++++  +vlDvGtG G +a+  a +g  +v++vDi +  ++ a++Na+  +++  ++ ++ +e+l+  +e++d++
  gi|330508056|ref|YP_004384484.1|  40 FLQGRRykRVLDVGTGPGFMALILAEMGL-DVTGVDISSGMIEKARQNAQSMGLQVDFR-HADGEQLSfdSESFDLL 114
                                       555553339*******************7.69******************999999885.55566653447888988 PP

                              PrmA 231 vaN 233
                                       v  
  gi|330508056|ref|YP_004384484.1| 115 VNR 117
                                       865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.1
                              PrmA  11 keaeeavsniLeelgakgvaiedsk 35 
                                       +++ e+++n++ee+g   v++   +
  gi|330508056|ref|YP_004384484.1| 198 QSKPERICNVFEEAGLFNVSFRHLE 222
                                       5677999999999999998886544 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   5.4e-08   4.2e-05      15     101 ..      47     136 ..      41     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.4e-08
                              MetW  15 srvldlGcGdGellellkeekqvdgrGleldeegvaecvak....Glsviqgdldkdlenfedksfdyvvlsqtlqa 87 
                                        rvld+G+G G +  +l+e  ++d  G+++++  + ++ +     Gl+v    +d +   f+++sfd+ v    l +
  gi|330508056|ref|YP_004384484.1|  47 KRVLDVGTGPGFMALILAE-MGLDVTGVDISSGMIEKARQNaqsmGLQVDFRHADGEQLSFDSESFDLLVNRHLLWT 122
                                       69*********99988866.99*********999987655333339**********************998777777 PP

                              MetW  88 trnpkevldellri 101
                                       + +p   ++e  r+
  gi|330508056|ref|YP_004384484.1| 123 LPHPLAAVREWSRV 136
                                       66666666666555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   4.7e-07   0.00037      16      76 ..      47     103 ..      42     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.7e-07
                   Methyltransf_18  16 srvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGle 76 
                                       +rv+D+Gt  g++++ l++ g    v+ +Di++g +eka++n+++ gl  ++++r +dG +
  gi|330508056|ref|YP_004384484.1|  47 KRVLDVGTGPGFMALILAEMGL--DVTGVDISSGMIEKARQNAQSMGL--QVDFRHADGEQ 103
                                       69***************98776..5*********************99..79999999955 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.4e-07   0.00035      35     136 ..      37     137 ..      18     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.4e-07
                              NodS  35 lrlslaqgsiadalevGcaaGalterlapyckrltvvdvveeaiararervkess.hiswivsdvqqfstd.ekfdl 109
                                       l+  l++++   +l+vG   G ++  la +   +t vd+ +  i++ar+  + +  ++ +  +d +q+s d e fdl
  gi|330508056|ref|YP_004384484.1|  37 LEPFLQGRRYKRVLDVGTGPGFMALILAEMGLDVTGVDISSGMIEKARQNAQSMGlQVDFRHADGEQLSFDsESFDL 113
                                       45568899999**************************************9998754899**********87478*** PP

                              NodS 110 ivvaevlyyiedvaelraavrnlvsll 136
                                       +v   +l+ + +     aavr+  ++l
  gi|330508056|ref|YP_004384484.1| 114 LVNRHLLWTLPHP---LAAVREWSRVL 137
                                       **99999877542...24444444444 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.2e-06    0.0017      44     159 ..      40     158 ..      34     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.2e-06
                                       CS-CCC-..EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC.TTTTT-EEE CS
                              GidB  44 llkekrdk.viDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee.kqeeekydv 118
                                       +l+  r k v+DvG+G+G+ +++La +   l +t ++ ++  i+  ++  + ++l+ v + +a+ e+     e++d+
  gi|330508056|ref|YP_004384484.1|  40 FLQGRRYKrVLDVGTGPGFMALILAEMG--LDVTGVDISSGMIEKARQNAQSMGLQ-VDFRHADGEQlSFDSESFDL 113
                                       555566544**********999998665..56678888888888899999999999.99999999998778899*** PP

                                       EEEC-S.....SSHHHHHHHHCCCEEEEEEEEEEESS--HHHHHCC CS
                              GidB 119 vtsRAl.....aslnelteillkllkegglilalKGksaedeleek 159
                                       ++ R l      +l  + e+++  lk+gg+ila+ G++    l+++
  gi|330508056|ref|YP_004384484.1| 114 LVNRHLlwtlpHPLAAVREWSRV-LKDGGRILAIDGAWFDPSLNAQ 158
                                       ****9844444478888899877.999******9999877666655 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.9e-06    0.0046      77     126 ..      68     115 ..      59     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.9e-06
                                       --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEE CS
                           UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdviv 126
                                       l + g+D+ + ++++ar+Na+++g+  +++f+ ad  +L  +++++d++v
  gi|330508056|ref|YP_004384484.1|  68 LDVTGVDISSGMIEKARQNAQSMGL--QVDFRHADGEQLSFDSESFDLLV 115
                                       5689*****************9887..58999999999998888999987 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.8e-06    0.0045      64     113 ..      47      95 ..      18     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.8e-06
                                       -EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS- CS
                              CMAS  64 mtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerk 113
                                       +++Ld+G+G G ++   +e  + +v g+ +S+   ++a+++ ++++l+ +
  gi|330508056|ref|YP_004384484.1|  47 KRVLDVGTGPGFMALILAEM-GLDVTGVDISSGMIEKARQNAQSMGLQVD 95 
                                       68*********999988887.************************98744 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.1e-05    0.0085      33     102 ..      48     117 ..      43     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                                       EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----.S-EEEEEEE CS
                              TehB  33 kvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineakld.erydfilst 102
                                       +vld+g g g  +l l+ +g dvt +d  +  i+  ++ ++   l+ ++ +  d +++++d e +d+++  
  gi|330508056|ref|YP_004384484.1|  48 RVLDVGTGPGFMALILAEMGLDVTGVDISSGMIEKARQNAQSMGLQ-VDFRHADGEQLSFDsESFDLLVNR 117
                                       79**********************************9999999999.999999999999973568887765 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   1.9e-05     0.015      21      86 ..      45     131 ..      23     246 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...HHHTTEEEE..CS-CCCSSHHHHHCHCHHH....... CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...aplpgvtti..qgditdpetiekikealse....... 85 
                                       + k+v+D+g +PG ++  +l ++g    v +vD+ ++   + +++ +++  q d+++ + +++  +  s        
  gi|330508056|ref|YP_004384484.1|  45 RYKRVLDVGTGPG-FMALILAEMG--LDVTGVDISSGmieKARQNAQSMglQVDFRHADGEQLSFDSESFdllvnrh 118
                                       4478********8.8888888887..69******77778777799999999*****999998666533224455555 PP

                                       ............S CS
                              FtsJ  86 ............r 86 
                                                   r
  gi|330508056|ref|YP_004384484.1| 119 llwtlphplaavR 131
                                       5556666666663 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.4e-05      0.05      25      92 ..      34     108 ..      29     125 .. 0.78
   2 ?   -0.5   0.0      0.64     5e+02     187     212 ..     166     192 ..     162     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.4e-05
                                       HH-GG......TTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-CCGHHHHH CS
                            RrnaAD  25 klnle......ekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.kdeklkvvhqDflkfetpe 92 
                                       k++le        + vl++g+G+G++  +La++   v+ + + + +++  +++ +  + ++   h+D+ + ++ +
  gi|330508056|ref|YP_004384484.1|  34 KMELEpflqgrRYKRVLDVGTGPGFMALILAEMGLDVTGVDISSGMIEKARQNAQsMGLQVDFRHADGEQLSFDS 108
                                       555555555556789*********************************999966645556666777777777666 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.64
                                       EEEEEEE-SS-S.--S-HHHHHHHHHH CS
                            RrnaAD 187 alvelerkdedl.pqkdlkkyesvvrk 212
                                       a  ++++++ +  + k l++y+s+ ++
  gi|330508056|ref|YP_004384484.1| 166 AAAKICSRKAPSlKSKFLDHYQSIKKE 192
                                       556788887777799999999998665 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.9e-05     0.023       9      81 ..      17      89 ..       8     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                                      HHHTT--TT--SS--HHHHHHHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTT CS
                              TPMT  9 rweeeqipfhqeevnpllkkfldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanl 81
                                       + ++  +f+ ee     +++ + l+  + +rvl  + G +  +  lAe g +v Gv++s   +ek+ ++a++
  gi|330508056|ref|YP_004384484.1| 17 SYTNGSHGFEEEEKAVWKMELEPFLQGRRYKRVLDVGTGPGFMALILAEMGLDVTGVDISSGMIEKARQNAQS 89
                                      4778888888888777777777778999999***********************************8666655 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 ?   12.9   0.1   5.1e-05      0.04      75     215 ..       6     143 ..       2     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-05
                                       HHHTT----CE-EEETTEEE--SEEHHHHHHHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHH CS
                    Methyltransf_9  75 llralmPWrkGPfslfGvdidteWrsdwkWdrvlphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfl 151
                                        + ++  Wr   ++      + e ++ wk + ++p l   + +++ldvG g G+ +  +++e    v G+d s+  +
  gi|330508056|ref|YP_004384484.1|   6 SISQYWDWRSRSYTNGSHGFEEEEKAVWKME-LEPFLQGRRYKRVLDVGTGPGF-MALILAEMGLDVTGVDISSGMI 80 
                                       6778889999999876666788999999976.9********************7.5567888888999***999888 PP

                                       HHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEE CS
                    Methyltransf_9 152 iqfeavrkllgedqrahllplgieqlpe.leafdtvfsmGvlyhrrsPldhllqlkdqlvkgGel 215
                                        + +   + +g +    +     eql    e+fd +    +l+    Pl  +++    l+ gG +
  gi|330508056|ref|YP_004384484.1|  81 EKARQNAQSMGLQVDFRHA--DGEQLSFdSESFDLLVNRHLLWTLPHPLAAVREWSRVLKDGGRI 143
                                       7777666666665554444..56899877899999999999999999999999999999888876 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 ?   11.8   0.0   0.00017      0.13      15      42 ..      59      86 ..      48     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                                      HHHHHHHCTSEEEEE-S-HHHHHHHCTT CS
                    UDPG_MGDP_dh_N 15 taavlaeighevigvDideekvdklnsg 42
                                      +a++lae+g +v+gvDi++  ++k +++
  gi|330508056|ref|YP_004384484.1| 59 MALILAEMGLDVTGVDISSGMIEKARQN 86
                                      6899*******************99876 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00032      0.25       6      81 ..      43     112 ..      39     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                                       --TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EE CS
                   Methyltr_RsmB-F   6 pqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfD 81 
                                        +  +++lD+ ++PG     +ae+      v+ vd+++  +++  +n + +g++ +   +aD+ + + ++    fD
  gi|330508056|ref|YP_004384484.1|  43 GRRYKRVLDVGTGPGFMALILAEM---GLDVTGVDISSGMIEKARQNAQSMGLQ-VDFRHADGEQLSFDSE--SFD 112
                                       566679*********999999998...6789***********************.9999999999854443..354 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1827.42
//
Query:       gi|330508057|ref|YP_004384485.1|  [L=436]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-17   61.4   0.0    1.6e-16   60.6   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
       0.16   12.2   1.6        0.4   10.9   1.6    1.7  1  Dockerin_1    Dockerin type I 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 !   60.6   0.0   1.8e-20   1.6e-16      41     235 ..     152     369 ..     110     370 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 1.8e-20
                                       S-BSBESSSB-HHHHHHH--SEEEE-GGG............GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHT CS
                      Peripla_BP_2  41 ivevgadgeidvEklaalkPDlvilskgl.........gltdedeellksgiptvivessntgeslkeqiralgell 108
                                       + e  +  ++d+E+++ lk D +     +           +++++++  +++p +  + ++  + l +++r++g l 
  gi|330508057|ref|YP_004384485.1| 152 PDEGAQAENADFERIIMLKTDALQTN--IergssstagRAQKDIFKKNLPDVPLISLNMREL-DVLVKNVRTYGYLI 225
                                       55566778899999999999987532..2235666677888999999999999999999985.************** PP

                                       T-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--...... CS
                      Peripla_BP_2 109 gledeaeklvaeidsklaaaksaidse..kpkpvlvfggadeggyvvagsnsyigdlldalgieniaaesk...... 177
                                       ++e+eae++++++ + +  ++s+++ +   ++p++ f +a e +y   +s+s+ g++l  +g++ni++         
  gi|330508057|ref|YP_004384485.1| 226 DHEKEAEQFIKWYTEYYNLFESRTKDIpeEERPTAFFEYASE-PYNCYASGSNLGQVLVLAGGKNIIDGAVgpddpq 301
                                       *************************99999999999999999.99999******************9987789*999 PP

                                       STT-EEE-HHHHHHH--SEEEEEEH..........HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 178 kseyeeisaEqilasdpdvifvsgr..........aeadnktgleflkenpllaelpAvkngrVyald 235
                                        ++ +  ++E i++++p +if +            + ++ ++  ++++++ +l ++ Avk+++Vy+ld
  gi|330508057|ref|YP_004384485.1| 302 YKGMIAADPEFIVKENPKYIFEAVAswgdggyetdDLSKMTASRDQVLNRSELVNVDAVKENQVYCLD 369
                                       9999*****************7777779****999999999999**********************96 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.6   4.5e-05       0.4      26      55 ..      50      79 ..      30      82 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.5e-05
                                      EBTTSCCCHGGGSTT-SSCESHHHHHHHHH CS
                        Dockerin_1 26 egqssssngkaaDvNgDGrvnalDallvin 55
                                      +  ++++++k aD N DG v+  D+ +v  
  gi|330508057|ref|YP_004384485.1| 50 IAAGKTEPTKLADANYDGDVDEEDIEQVQA 79
                                      3358899*******************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3123.78
//
Query:       gi|330508058|ref|YP_004384486.1|  [L=246]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-26   90.3   0.0    1.6e-25   89.6   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    6.7e-22   78.0   0.0    1.1e-21   77.3   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.1e-17   64.3   0.0    1.4e-17   63.8   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    8.2e-16   58.3   0.0    1.1e-15   57.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    7.9e-15   54.8   0.0      1e-14   54.4   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.3e-11   45.1   0.0    1.9e-11   44.6   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    3.2e-05   23.6   0.0    4.8e-05   23.0   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    0.00012   21.7   0.0    0.00046   19.8   0.0    1.8  1  MTS              Methyltransferase small domain
    0.00014   21.7   0.0    0.00021   21.1   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00088   18.7   0.0     0.0013   18.2   0.0    1.2  1  TehB             Tellurite resistance protein TehB
     0.0072   15.8   0.0     0.0094   15.4   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.013   15.5   0.0       0.02   14.9   0.0    1.4  1  Methyltransf_32  Methyltransferase domain
      0.021   13.9   0.0      0.033   13.3   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.043   12.7   0.0      0.067   12.1   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
        0.1   12.4   0.0       0.19   11.5   0.0    1.6  2  Methyltransf_8   Hypothetical methyltransferase
       0.11   11.6   0.0       0.16   11.0   0.0    1.3  1  DREV             DREV 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 !   89.6   0.0   1.4e-28   1.6e-25       1      96 []      49     144 ..      49     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 1.4e-28
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       LdvG+G G++++ l + g++v+g+D s+ mlk a+++++  ++ + ++++d e lpf d+sfD+vv + vl ++++p
  gi|330508058|ref|YP_004384486.1|  49 LDVGTGPGIVSNLLSELGHDVTGIDASEGMLKKAQSNSEALRNPMHLIQGDGEVLPFDDSSFDAVVNRYVLWTLPQP 125
                                       8***************************************999899******************************* PP

                                       HHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                       eka++e+ RvL+pgG+lvi
  gi|330508058|ref|YP_004384486.1| 126 EKAIAEWQRVLRPGGRLVI 144
                                       *****************96 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0   9.9e-25   1.1e-21       1      97 []      48     140 ..      48     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 9.9e-25
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       +Ld+G+G+G ++  l++ +  ++vtg+D se+ml++a+++ e+ +  ++++qgd e lpf+d+sfD+vv +++l  l
  gi|330508058|ref|YP_004384486.1|  48 ILDVGTGPGIVSNLLSELG--HDVTGIDASEGMLKKAQSNSEALRNPMHLIQGDGEVLPFDDSSFDAVVNRYVLWTL 122
                                       8***************995..********************99888************************9886666 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +  + eka++e+ rvL+pgG
  gi|330508058|ref|YP_004384486.1| 123 P--QPEKAIAEWQRVLRPGG 140
                                       5..677*************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   1.3e-20   1.4e-17       5     119 ..      46     154 ..      43     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.3e-20
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                       lr+lD+G+G G  +  l  elg   +v+GiD se ++++A++n++ l    +++ qgd e l+  + d++fD ++ +
  gi|330508058|ref|YP_004384486.1|  46 LRILDVGTGPGIVSNLLS-ELGH--DVTGIDASEGMLKKAQSNSEALRN-PMHLIQGDGEVLP--FDDSSFDAVVNR 116
                                       79********99999999.8765..799***************997776.6************..************ PP

                   Methyltransf_31  82 evlnaladpdkileeiervlkpggilliedprllaelp 119
                                        vl +l+ p+k++ e +rvl+pgg+l+i d  + +e +
  gi|330508058|ref|YP_004384486.1| 117 YVLWTLPQPEKAIAEWQRVLRPGGRLVIVDGTWFDERD 154
                                       *****************************999666655 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   9.8e-19   1.1e-15      20     124 ..      42     154 ..      16     197 .. 0.71

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 9.8e-19
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeq.....eaaepqgkfdlIvlrev 91 
                                         a+ r+Ld+G+G Gi++++l+e g++vtg+D+s+ + ++a++ + a   +++ +       ++++ +fd +v+r+v
  gi|330508058|ref|YP_004384486.1|  42 GSAPLRILDVGTGPGIVSNLLSELGHDVTGIDASEGMLKKAQSNSEALRNPMHLIqgdgeVLPFDDSSFDAVVNRYV 118
                                       56778******************************99999863333333333222222223333666********** PP

                   Methyltransf_23  92 lehvpdppellrqiatllkpgGylllse...plasl 124
                                       l ++p p+++++  ++ l+pgG+l++ +   +++++
  gi|330508058|ref|YP_004384486.1| 119 LWTLPQPEKAIAEWQRVLRPGGRLVIVDgtwFDERD 154
                                       **************************9966544443 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   9.3e-18     1e-14      17     153 ..      13     146 ..       2     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 9.3e-18
                                       HHHHHH.HHH.HHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHH CS
                   Ubie_methyltran  17 askyDl.mnd.vlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekk 91 
                                       a+ yD  + + + s +  r+W+k +  +  +  + ++lDv +G g ++  ls ++g+  +v+++D +e mLk ++  
  gi|330508058|ref|YP_004384486.1|  13 AKAYDEnVRQvIYSSRERRIWQK-IFSVAIGSAPLRILDVGTGPGIVSNLLS-ELGH--DVTGIDASEGMLKKAQSN 85 
                                       67787523441558889999*86.5567778899*********996665555.4443..799**********99876 PP

                                       HHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran  92 lkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                        +      ++++q+++e Lpf+d sfD v   + l  ++  +ka+ e  rvl+pGGrlv+++
  gi|330508058|ref|YP_004384486.1|  86 SE-ALRNPMHLIQGDGEVLPFDDSSFDAVVNRYVLWTLPQPEKAIAEWQRVLRPGGRLVIVD 146
                                       43.445589**************************************************986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   1.7e-14   1.9e-11       1      99 []      49     142 ..      49     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.7e-14
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++G+G G ++  l e   + ++tg+D s+ ++ ++++  ++  +n  + ++ + + l  +d  ssfD+vv   vl 
  gi|330508058|ref|YP_004384486.1|  49 LDVGTGPGIVSNLLSEL--GHDVTGIDASEGML-KKAQSNSEALRNPMHLIQGDGEVLPFDD--SSFDAVVNRYVLW 120
                                       8****************..**************.5555555555566666666666665555..5************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        l+++++++++  ++L+pgGrl
  gi|330508058|ref|YP_004384486.1| 121 TLPQPEKAIAEWQRVLRPGGRL 142
                                       ********************97 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   4.3e-08   4.8e-05      16     102 ..      47     136 ..      36     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.3e-08
                              MetW  16 rvldlGcGdGellellke....ekqvdg.rGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqa 87 
                                       r+ld+G+G G + +ll e      ++d+ +G+ +++++  e++   +++iqgd   ++  f+d+sfd vv    l +
  gi|330508058|ref|YP_004384486.1|  47 RILDVGTGPGIVSNLLSElghdVTGIDAsEGMLKKAQSNSEALRNPMHLIQGD--GEVLPFDDSSFDAVVNRYVLWT 121
                                       89********988888652111344443357777778888999999*****97..56889***************** PP

                              MetW  88 trnpkevldellrig 102
                                       + +p++ + e  r+ 
  gi|330508058|ref|YP_004384486.1| 122 LPQPEKAIAEWQRVL 136
                                       ******999987773 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.1e-07   0.00046      34     138 ..      47     145 ..      35     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.1e-07
                                       EEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEEEE---STT CS
                               MTS  34 kvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdlivsNPPfha 109
                                       ++lD+G+G G+++  l +   +  vt +d++   l+ a+ n ea +  +++++ d+    +++ +fd++v    +  
  gi|330508058|ref|YP_004384486.1|  47 RILDVGTGPGIVSNLLSELGHD--VTGIDASEGMLKKAQSNSEALRNPMHLIQGDGEVlPFDDSSFDAVVNRYVLW- 120
                                       69***********999998887..9******************************9762677999***99743333. PP

                                       TCHCHHHHHHHHHHHHHHHEEEEEEEEEE CS
                               MTS 110 gkatelavaeeliaeAkeaLkegGeLliV 138
                                           +l   e+ iae +++L++gG+L+iV
  gi|330508058|ref|YP_004384486.1| 121 ----TLPQPEKAIAEWQRVLRPGGRLVIV 145
                                       ....3334677788889999999999988 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.9e-07   0.00021      75     171 ..      46     144 ..      34     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.9e-07
                                       -EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSB CS
                              PCMT  75 arvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaa 151
                                        r+L+vG+G G+ + +l++l ++++   +i+ ++ + ++a+ n ++l  + ++++ gDG+    + + +da++    
  gi|330508058|ref|YP_004384486.1|  46 LRILDVGTGPGIVSNLLSELGHDVT---GIDASEGMLKKAQSNSEALR-NPMHLIQGDGEVLPFDDSSFDAVVNRYV 118
                                       59*************9999866665...***************98875.5799*******99999999***976666 PP

                                       BSS--H......HHHHTEEEEEEEEE CS
                              PCMT 152 apeiPe......alidQLkeGGrlvv 171
                                          +P+      ++ + L +GGrlv+
  gi|330508058|ref|YP_004384486.1| 119 LWTLPQpekaiaEWQRVLRPGGRLVI 144
                                       555554222222688899*****998 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.2e-06    0.0013      30     134 ..      44     146 ..      28     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-06
                                       -S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TT.EEEEE--GGG----S.-EEEEEEESS CS
                              TehB  30 kpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlkn.istalydineaklde.rydfilstvv 104
                                        p ++ld+g g g  s  ls lg+dvt +d  e  ++  ++  + e+l+n ++    d + + +d+  +d ++   v
  gi|330508058|ref|YP_004384486.1|  44 APLRILDVGTGPGIVSNLLSELGHDVTGIDASEGMLKKAQS--NSEALRNpMHLIQGDGEVLPFDDsSFDAVVNRYV 118
                                       6999***************************9999888775..4566654366666777777776526899999888 PP

                                       GGGS-GGGHHHHHHHHHHTEEEEEEEEEEE CS
                              TehB 105 lmfleaeripsiienmqectkvggynliva 134
                                       l  l +    + i++ q+  ++gg  +iv 
  gi|330508058|ref|YP_004384486.1| 119 LWTLPQP--EKAIAEWQRVLRPGGRLVIVD 146
                                       8877543..466888888888888877775 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   0.0   8.4e-06    0.0094     164     208 ..      47      90 ..      40     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.4e-06
                              PrmA 164 evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNk 208
                                       ++lDvGtG Gi +   + Lg+ +v+++D  e  +k a++N e  +
  gi|330508058|ref|YP_004384486.1|  47 RILDVGTGPGIVSNLLSELGH-DVTGIDASEGMLKKAQSNSEALR 90 
                                       69******************7.69****************87533 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   1.8e-05      0.02      24      75 ..      43      90 ..       3     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                   Methyltransf_32 24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75
                                      s++l+++DvG G g  s  l+     +++ v+gida+e + +ka+   e+l+
  gi|330508058|ref|YP_004384486.1| 43 SAPLRILDVGTGPGIVSNLLSE----LGHDVTGIDASEGMLKKAQSNSEALR 90
                                      57889***************99....7******************9999887 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.9e-05     0.033      20      85 ..      34     100 ..      27     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
                                       HHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-C CS
                            RrnaAD  20 neIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.kdeklkvvhqDf 85 
                                       ++I++ +  +  l +l++g+G+Gi ++ L +    v+ +   e ++k  q + + + +++ +++ D+
  gi|330508058|ref|YP_004384486.1|  34 QKIFSVAIGSAPLRILDVGTGPGIVSNLLSELGHDVTGIDASEGMLKKAQSNSEaLRNPMHLIQGDG 100
                                       55666555566789************************************98888888888898885 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 ?   12.1   0.0     6e-05     0.067     115     217 ..      44     144 ..      25     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6e-05
                                       TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES CS
                    Methyltransf_9 115 kgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsmG 190
                                          +ildvG g G     +++e  + v Gid se  l + ++  + l   ++ hl+    e lp   ++fd+v    
  gi|330508058|ref|YP_004384486.1|  44 APLRILDVGTGPGIV-SNLLSELGHDVTGIDASEGMLKKAQSNSEAL--RNPMHLIQGDGEVLPFdDSSFDAVVNRY 117
                                       45579********75.68999999************99887777766..7889999889999*986889******** PP

                                       -GGG-S-HHHHHHHHHCTEEEEEEEEE CS
                    Methyltransf_9 191 vlyhrrsPldhllqlkdqlvkgGelvl 217
                                       vl+    P   + + +  l+ gG lv+
  gi|330508058|ref|YP_004384486.1| 118 VLWTLPQPEKAIAEWQRVLRPGGRLVI 144
                                       *************************97 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.19     107     157 ..      94     145 ..      57     162 .. 0.86
   2 ?   -3.9   0.0       9.1     1e+04     172     191 ..     205     225 ..     203     231 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                                       TEEES-TTS-S--TT-EEEEEEES---SS.-HHHHHHHHHHHEEEEEEEEEE CS
                    Methyltransf_8 107 rvvacdlakvPledesvdvavfclslmgt.nladflkeanrvlkvGGllkva 157
                                       +++  d   +P +d+s d +v    l +  + ++ + e +rvl++GG l + 
  gi|330508058|ref|YP_004384486.1|  94 HLIQGDGEVLPFDDSSFDAVVNRYVLWTLpQPEKAIAEWQRVLRPGGRLVIV 145
                                       5667788889**********988887664266889*************9986 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 9.1
                                       HHHCTTEEE.EEEE--STTEE CS
                    Methyltransf_8 172 altklGfev.kskdlsnkqfv 191
                                        lt+lGf   + +d  n +++
  gi|330508058|ref|YP_004384486.1| 205 MLTRLGFRDvQLRDNLNRKLL 225
                                       578899964044555555544 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00015      0.16      87     135 ..      37      85 ..      23     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                              DREV  87 espasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkk 135
                                       +s a +  + ++ld+G+G G +++ +++  ++v   ++se m ++ +  
  gi|330508058|ref|YP_004384486.1|  37 FSVAIGSAPLRILDVGTGPGIVSNLLSELGHDVTGIDASEGMLKKAQSN 85 
                                       5677788999********************************9987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1760.79
//
Query:       gi|330508059|ref|YP_004384487.1|  [L=422]
Description: major facilitator family transporter [Methanosaeta concilii GP6]
Scores for complete 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-32  112.1  37.0    8.1e-32  110.5  29.9    2.0  2  MFS_1       Major Facilitator Superfamily
    7.4e-10   38.0  19.3    7.4e-10   38.0  19.3    2.8  3  MFS_2       MFS/sugar transport protein
    1.4e-08   34.0  30.7    1.7e-07   30.4  11.8    2.1  2  MFS_1_like  MFS_1 like family
    0.00029   19.7  13.8    0.00029   19.7  13.8    2.2  2  LacY_symp   LacY proton/sugar symporter
  ------ inclusion threshold ------
       0.41    9.0  12.8       0.73    8.2  12.8    1.3  1  MFS_3       Transmembrane secretion effector
       0.44   10.8   2.5        9.6    6.5   0.1    3.0  2  DUF4536     Domain of unknown function (DUF4536)


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 !  110.5  29.9   2.7e-35   8.1e-32       3     344 ..      33     370 ..      31     375 .. 0.84
   2 !   14.0   0.6     6e-06     0.018     104     170 ..     345     411 ..     342     419 .. 0.87

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 2.7e-35
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       l +fl++l+++i+g+++ l++   lg+ ++++gl+l++ a  ++++s+p++++ dr+Gr+r+lll+ +l+a++ l++
  gi|330508059|ref|YP_004384487.1|  33 LFVFLTTLNAGIYGVIFNLYI-LRLGFGEDFLGLILSISATSMGLFSIPAAFVCDRLGRKRTLLLSSVLSAIS-LFF 107
                                       678***************733.577888*********************************************.777 PP

                             MFS_1  80 lfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg...... 149
                                       l+ ++ + ll+++ + +G+++++++ +g +++ + ++keer+  +++ s+ + ++ + g +lgg+l + l       
  gi|330508059|ref|YP_004384487.1| 108 LYNTTTPeLLVLFSLASGMASALGLVTGSTFLLENSTKEERMYLFSMSSLIYTFSLLSGNMLGGFLPDILAdlisaq 184
                                       76688999*************************************99999999999999999996665555566688 PP

                             MFS_1 150 ......Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw.illialllf 219
                                             +r++ y+  ++++ +++    l ++ +++++ +++++        +l   +++++k++v+  + l+ +l++
  gi|330508059|ref|YP_004384487.1| 185 sgsaisYRLTLYVSLVATVASLL---PLAYVAEKNSEENNDIRG-------QLHI-YRSIFKSKVIRqMTLFYCLYG 250
                                       88888888888888888888755...333333333333333333.......4555.889999998875455555555 PP

                             MFS_1 220 ffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallav 296
                                        +g+ + l ++ +y+ +vlg s + ++g+++++++++++ + +l+  l  r+g+ r   +  +l + ++l+++l+++
  gi|330508059|ref|YP_004384487.1| 251 -IGWGTSLPYFNVYFDTVLGAS-ANQIGIIFSVSQVFMILGYFLVPVLTERTGKVRLVAIVQILSIPFLLMFVLTNN 325
                                       .49999****************.8*****************************977777777777777777777777 PP

                             MFS_1 297 tssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfnta 344
                                           +++++++v+  + + +++p+l+++  + + pee+ ++++++ +a
  gi|330508059|ref|YP_004384487.1| 326 L---LIAVVGFVMRYMIMNMANPILNSFKLEIVQPEERSMINSIMWMA 370
                                       7...7777788888889************************9999765 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6e-06
                             MFS_1 104 pagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfll 170
                                       p+ +++  +++ +eer++ ++++ ++    + +g  +ggl+++ +  r +f++ +++++  +v+ ++
  gi|330508059|ref|YP_004384487.1| 345 PILNSFKLEIVQPEERSMINSIMWMACYTFVGIGNYVGGLMMAKGDSRMPFMVTGLFYAATAVFYYI 411
                                       556666678999*************************************************995443 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   6.9   6.2e-05      0.19     226     322 ..      28     125 ..      19     143 .. 0.66
   2 !   38.0  19.3   2.5e-13   7.4e-10      71     343 ..      94     355 ..      94     359 .. 0.81
   3 ?    1.2   0.7     0.036   1.1e+02     129     189 ..     357     412 ..     355     421 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.2e-05
                             MFS_2 226 flillllfllaalalgvlnglllYyltyvlgngsaasvfllvv.tisallgiplwqplakrlgkkntyllgalltiv 301
                                       +++ ll+++l++l  g++  ++ +y+   lg+g+++  + l +  +s+ l+++ ++ ++ rlg+k+t ll+++l ++
  gi|330508059|ref|YP_004384487.1|  28 ARKYLLFVFLTTLNAGIYGVIFNLYILR-LGFGEDFLGLILSIsATSMGLFSIPAAFVCDRLGRKRTLLLSSVLSAI 103
                                       5566777777777777777777777643.666666666666665778888888899*******99888877776666 PP

                             MFS_2 302 llvlvlll.qpsnlllflvllv 322
                                        l++++   +p+ l+lf ++  
  gi|330508059|ref|YP_004384487.1| 104 SLFFLYNTtTPELLVLFSLASG 125
                                       6555555525555555544433 PP

  == domain 2  score: 38.0 bits;  conditional E-value: 2.5e-13
                             MFS_2  71 lllsaiilavsiillftppelsqsakfiwllvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlgg 147
                                       llls ++ a+s+++l+ + +    +++++l+ ++ +++ +  l++ + + l +     ++eR  l+s+ s++ ++  
  gi|330508059|ref|YP_004384487.1|  94 LLLSSVLSAISLFFLYNTTT----PELLVLFSLASGMASALGLVTGSTFLLENST---KEERMYLFSMSSLIYTFSL 163
                                       799***************88....99***9999**********999999888776...89****9999998888766 PP

                             MFS_2 148 vlaailafllvlilgg...lkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevf 221
                                       + +++l + l  il+    ++s   +   ++l  +l+++++ ++  +++ e+ ++   e++  +++l++    +++f
  gi|330508059|ref|YP_004384487.1| 164 LSGNMLGGFLPDILADlisAQSGSAISYRLTLYVSLVATVASLLPLAYVAEKNSE---ENNDIRGQLHI---YRSIF 234
                                       6666666655555555443244444444445555666666666667777777443...45555555555...57788 PP

                             MFS_2 222 rnraflillllfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgal 297
                                       +++  + + l++ l   + g     +  y++ vlg +++++ +++ v  + ++lg +l+++l+ r gk +++++ ++
  gi|330508059|ref|YP_004384487.1| 235 KSKVIRQMTLFYCLYGIGWGTSLPYFNVYFDTVLGaSANQIGIIFSVSQVFMILGYFLVPVLTERTGKVRLVAIVQI 311
                                       8888888888888888889999999999************************************************* PP

                             MFS_2 298 ltivllvlvlllqpsnlllflvllviagfgvgvaallpwsmladvv 343
                                       l i++l++++l   +nll+++v +v+ ++++ +a+ ++ s++ ++v
  gi|330508059|ref|YP_004384487.1| 312 LSIPFLLMFVLT--NNLLIAVVGFVMRYMIMNMANPILNSFKLEIV 355
                                       ****98766655..************************99987776 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.036
                             MFS_2 129 ydeRtsltsvrsflsvlggvlaailafllvlilgglkserkgylifaliialLmllgviiv 189
                                       ++eR+ ++s+ +++ + +  +++ + +l+++       +r  +++++l++a+ +++ + i+
  gi|330508059|ref|YP_004384487.1| 357 PEERSMINSIMWMACYTFVGIGNYVGGLMMAKGD----SRMPFMVTGLFYAATAVFYY-IC 412
                                       5788888888888888888888888888854444....48888888888887655443.34 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 !   10.0  10.7   9.5e-05      0.28     230     373 ..      31     173 ..      23     180 .. 0.85
   2 !   30.4  11.8   5.8e-11   1.7e-07     171     383 ..     183     395 ..     175     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 9.5e-05
                        MFS_1_like 230 fllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhv.klliiallayilrfl 305
                                        ll++++     gi++  ++lY+  lg+ + +lG ++ + + +   + + a  + ++lG   +ll+ ++l+ i  f+
  gi|330508059|ref|YP_004384487.1|  31 YLLFVFLTTLNAGIYGVIFNLYILRLGFGEDFLGLILSISATSMGLFSIPAAFVCDRLGRKrTLLLSSVLSAISLFF 107
                                       5788889999999999999********************9988777778899999****861577777888888888 PP

                        MFS_1_like 306 lyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGll 373
                                       ly+++  + l++++ + +g++ +l  +++ ++  +  +k+ +  + ++ s + + +   +G+++GG+l
  gi|330508059|ref|YP_004384487.1| 108 LYNTT-TPELLVLFSLASGMASALGLVTGSTFLLENSTKEERMYLFSMSSLI-YTFSLLSGNMLGGFL 173
                                       99876.68889999999*****************999999998888876655.7899999******98 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 5.8e-11
                        MFS_1_like 171 hysvnllpysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienF 247
                                         s + + y+  lyv ++  v+sll ++ + e++ e++ +++  l+    i+k + +  + l+ ++ g+ wg    +
  gi|330508059|ref|YP_004384487.1| 183 AQSGSAISYRLTLYVSLVATVASLLPLAYVAEKNSEENNDIRGQLHIYRSIFKSKVIRQMTLFYCLYGIGWGTSLPY 259
                                       445555669999**************9******************9999**************************** PP

                        MFS_1_like 248 lflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLh 323
                                       +++Y+   lgas   +G++  +  v  i  +f+   l+e++G v+l+ i  ++ i  +l+  +++n+ ++++  v+ 
  gi|330508059|ref|YP_004384487.1| 260 FNVYFdTVLGASANQIGIIFSVSQVFMILGYFLVPVLTERTGKVRLVAIVQILSIPFLLMFVLTNNLLIAVVGFVMR 336
                                       *****7789**************************************998888877777777778888888888888 PP

                        MFS_1_like 324 gisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                        + + +   ++ ++  +i+ ++ ++ + +++ ++++ +  ++G+++GGl+    ++++ F
  gi|330508059|ref|YP_004384487.1| 337 YMIMNMANPILNSFKLEIVQPEERSMINSIMWMACYTF-VGIGNYVGGLMMAKGDSRMPF 395
                                       8999999999999999***************9998887.789******999766666655 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.4   4.6     0.009        27       9      95 ..      31     111 ..      22     180 .. 0.66
   2 !   19.7  13.8   9.8e-08   0.00029      11     163 ..     241     387 ..     231     418 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.009
                         LacY_symp   9 fylfalffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllv 85 
                                       + lf +   +   i++++f+l+ +     lg+ +  +G++ s+      lf      + d+lG k+ ll   s +l 
  gi|330508059|ref|YP_004384487.1|  31 YLLFVFLTTLNAGIYGVIFNLYILR----LGFGEDFLGLILSISATSMGLFSIPAAFVCDRLGRKRTLLL--SSVLS 101
                                       5555555555555555555555544....46677778999988777777888888999999999999875..34444 PP

                         LacY_symp  86 lfapfliyvf 95 
                                        ++ f++y  
  gi|330508059|ref|YP_004384487.1| 102 AISLFFLYNT 111
                                       4444444432 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 9.8e-08
                         LacY_symp  11 lfalffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvlf 87 
                                       +++lf+ +y   +++  p+f v+++ vlg s  ++Gi+fsv ++f il   l  +++++ G   +    ++++ +l 
  gi|330508059|ref|YP_004384487.1| 241 QMTLFYCLYGIGWGTSLPYFNVYFDTVLGASANQIGIIFSVSQVFMILGYFLVPVLTERTGK-VR---LVAIVQILS 313
                                       445566655555***********************************************994.33...456777888 PP

                         LacY_symp  88 apfliyvfepllqlnilvGalvGgvflGlvysagagaieayiekvsrask.feyGkarvfGclGya.lcaslaGilf 162
                                        pfl+     +l  n+l+ a+vG v   ++ +   ++++++   + +  +      +  + c  +  ++  + G+++
  gi|330508059|ref|YP_004384487.1| 314 IPFLLMF---VLTNNLLI-AVVGFVMRYMIMNMANPILNSFKLEIVQPEErSMINSIMWMACYTFVgIGNYVGGLMM 386
                                       8998753...46666655.7899999999999999999999655554444033334444456555336666666665 PP

                         LacY_symp 163 s 163
                                       +
  gi|330508059|ref|YP_004384487.1| 387 A 387
                                       4 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  12.8   0.00024      0.73      56     315 ..      72     334 ..      62     341 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00024
                             MFS_3  56 LPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelv 132
                                         + l+si+a  + D + r++ ll   +l a++     ++ +++ ++p ll+ ++l  g+ +al   + +  + e  
  gi|330508059|ref|YP_004384487.1|  72 TSMGLFSIPAAFVCDRLGRKRTLLLSSVLSAIS-----LFFLYNTTTPELLVLFSLASGMASALGLVTGSTFLLENS 143
                                       45779******************9988877654.....445688999****************************** PP

                             MFS_3 133 krrdvpaAvaLnsvginiaRsvGPAlgG........vlvaavGaalafavna.lsylalivallrwkrevrksslpr 200
                                       ++++      ++s+ +  +   G  lgG        ++ a  G+a+++ ++  +s +a ++ ll     ++k+s  +
  gi|330508059|ref|YP_004384487.1| 144 TKEERMYLFSMSSLIYTFSLLSGNMLGGflpdiladLISAQSGSAISYRLTLyVSLVATVASLLPLAYVAEKNSEEN 220
                                       ****999***********999999999943333333356788******99853788899999999999999999999 PP

                             MFS_3 201 EkllealraglRftaasreikavlvRaalFglsasavlaLLPlvardqldgdalvyGillgalGvGAilgalllsrL 277
                                       + +++ l+  +R    s+ i+++ +   l+g+   + l    +     l++ a   Gi+++   v  ilg  l++ L
  gi|330508059|ref|YP_004384487.1| 221 NDIRGQLH-IYRSIFKSKVIRQMTLFYCLYGIGWGTSLPYFNVYFDTVLGASANQIGIIFSVSQVFMILGYFLVPVL 296
                                       99999997.5899999************************************************************* PP

                             MFS_3 278 RerlsserlvllaavalAlvllslalasslwvavlvll 315
                                        er ++ rlv++  +     ll+  l+++l +av+ ++
  gi|330508059|ref|YP_004384487.1| 297 TERTGKVRLVAIVQILSIPFLLMFVLTNNLLIAVVGFV 334
                                       ******************9**********999998766 PP

>> DUF4536  Domain of unknown function (DUF4536)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0032       9.6       9      46 ..     128     164 ..     126     165 .. 0.92
   2 ?    2.9   0.5     0.046   1.4e+02       8      20 ..     369     381 ..     368     408 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0032
                           DUF4536   9 SGsGLigaGvYvyvqarrrlklggkfgmltiaqvafal 46 
                                       S++GL+    +++  + +  ++++ f+m++++ ++ +l
  gi|330508059|ref|YP_004384487.1| 128 SALGLVTGSTFLLENSTKE-ERMYLFSMSSLIYTFSLL 164
                                       99****************9.99**********998877 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.046
                           DUF4536   8 vSGsGLigaGvYv 20 
                                        ++ +++g+G Yv
  gi|330508059|ref|YP_004384487.1| 369 MACYTFVGIGNYV 381
                                       67999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.25s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3036.14
//
Query:       gi|330508060|ref|YP_004384488.1|  [L=517]
Description: oligopeptide ABC transporter solute-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-94  315.2   0.0    7.5e-94  314.8   0.0    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.8   0.0   4.2e-98   7.5e-94       1     369 [.      73     432 ..      73     439 .. 0.94

  Alignments for each domain:
  == domain 1  score: 314.8 bits;  conditional E-value: 4.2e-98
                                       SEEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTE CS
                         SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddyt 77 
                                       ++ p LA+s w+vs+Dg+t+tf+LR+gv F+DGtp++Ae+ + s+er+ +    +++ + +     +++v+a+d+yt
  gi|330508060|ref|YP_004384488.1|  73 KLSPMLAQS-WDVSEDGRTWTFHLREGVSFHDGTPFNAEAAKLSLERTFRRSAEYSSIKAF----PVESVTAPDEYT 144
                                       578******.7**********************************************9999....7*********** PP

                                       EEEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTTSCSSSSE CS
                         SBP_bac_5  78 vrftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgggkpkldr 154
                                       +++t+++p+a++  +l++ +  i     + ++ +++d+  +p+gtGP+k+++++p ++++ +r++dYw g+k+k+++
  gi|330508060|ref|YP_004384488.1| 145 LVITTSRPFAPLAGYLSKDATEIL----AASSFDSNDEVVEPIGTGPFKFDSWVPKESMTGVRFEDYW-GSKAKVEK 216
                                       **********99999999888888....799999**********************************.******** PP

                                       EEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS CS
                         SBP_bac_5 155 iefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyAi 231
                                       ++f+ +p++ +r  +l++Ge+d++  ++p+ +++l e+++ kv  ++  g+v +l +N ++pp+dd+ vRqA+s+Ai
  gi|330508060|ref|YP_004384488.1| 217 VVFSNVPEEKTRESMLRAGEVDIIGTISPALAKKLAEDSSFKVYEQEEMGRVRHLLLNVANPPLDDVLVRQAISMAI 293
                                       *******************************************7777899*************************** PP

                                       -HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETC...EEEEEEEEET CS
                         SBP_bac_5 232 DreeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrek...klkltlllas 305
                                       Dr+ i + +leg  + a +++++++++++++ +++   ydpe+A +lL+eaG+ d+d++g+ +k    lkl l++++
  gi|330508060|ref|YP_004384488.1| 294 DRDLICDSLLEGMDQTASAPFSSNLYWSNDNLETP--SYDPEEAIALLEEAGWSDSDNDGIMDKdgeDLKLSLFTYP 368
                                       *******************************9998..67************************9************* PP

                                       TSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECT.TSTTHHHHHHH CS
                         SBP_bac_5 306 gspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgad.ypdpdnflnpf 369
                                       + p    iae++++ql ++Gi++e+  +d  ++  e++k g++d++l + ++  + dpd+  ++f
  gi|330508060|ref|YP_004384488.1| 369 SRPELPSIAEALKDQLGQVGIDIEITILDD-SAVREQAKGGKVDIYLVSVNTLlNRDPDTWASYF 432
                                       ****************************98.8888************988877334444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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 0.24s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3894.59
//
Query:       gi|330508061|ref|YP_004384489.1|  [L=315]
Description: oligopeptide ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete 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  153.2  10.0    6.3e-45  153.2  10.0    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.1   0.5    0.0039        69      19      84 ..       5     102 ..       2     116 .. 0.80
   2 !  153.2  10.0   3.5e-49   6.3e-45       1     183 [.     119     309 ..     119     311 .. 0.99

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0039
                      BPD_transp_1  19 llrpliivllslPsfvlail.lvlvf...............................vilsilghlilpviilllls 63 
                                       +lr++  ++l++ ++ ++++ l+++f                                ++   ++l l+++  +l +
  gi|330508061|ref|YP_004384489.1|   5 ILRRIAAAILTISVLTVFVFaLLYLFpgdpaerilqtrmngelptsrdtvevlkkemGLDAPPYQLYLSWASGVLHG 81 
                                       67777777777777775555255556889999999999999999999999999999777777778888899999999 PP

                      BPD_transp_1  64 aapyvrlirraalrslpkdlv 84 
                                        ++y +++rr ++ +l+++l+
  gi|330508061|ref|YP_004384489.1|  82 DLGYSYVTRRPVITILSESLR 102
                                       999999999999998888875 PP

  == domain 2  score: 153.2 bits;  conditional E-value: 3.5e-49
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.........vilsilghlilpviillllsaapyv 68 
                                       g+ lG+laa +  +++d++l+ l i++ s+P +v a++l+l+f         +  s+l+++ +p++ l++ +aa ++
  gi|330508061|ref|YP_004384489.1| 119 GLALGFLAAWKEDSWIDDMLSYLAILGISVPGYVTAFVLILIFaiglhllpvAGRSGLYSMLMPAASLSFGGAAMLM 195
                                       789************************************************************************** PP

                      BPD_transp_1  69 rlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleai 145
                                       r++r+++l++  +d+v aa+a+G+++ ++f+ ++++n+lpp++t l+l +ggl+ggav++e +++wpG+g+ll+++ 
  gi|330508061|ref|YP_004384489.1| 196 RMTRYDILEESRQDYVLAAKAKGLGEARVFFGHIFRNSLPPLVTYLGLELGGLFGGAVIVENIFAWPGIGRLLVDSV 272
                                       ***************************************************************************** PP

                      BPD_transp_1 146 lgydyseisnggvlalviavlllnlvadilqrlldprv 183
                                       ++ d+++ + ++vl ++++++l+n+++d+l++++dpr+
  gi|330508061|ref|YP_004384489.1| 273 QSGDVPLVQ-ASVLLIGVIFILINIIVDLLYTYIDPRI 309
                                       *********.***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2233.35
//
Query:       gi|330508062|ref|YP_004384490.1|  [L=284]
Description: oligopeptide ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-31  110.0   3.4    1.1e-31  110.0   3.4    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne
    3.9e-06   26.7   0.2    3.9e-06   26.7   0.2    3.2  4  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   1.5      0.36   3.3e+03     141     141 ..      36      36 ..      16      93 .. 0.50
   2 !  110.0   3.4   1.2e-35   1.1e-31       1     183 [.      95     277 ..      95     279 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.36
                      BPD_transp_1 141 l 141
                                       l
  gi|330508062|ref|YP_004384490.1|  36 L 36 
                                       1 PP

  == domain 2  score: 110.0 bits;  conditional E-value: 1.2e-35
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g+ lG++a+ +++++ d+l+ ++i++ l +P +vla++lv      + lg ++   +++l+++++  y+r+ir+ ++
  gi|330508062|ref|YP_004384490.1|  95 GTALGMMAG-YFGGTADRLICRIIDFELVFPDIVLALVLV------GTLGPGVPNlILALSIVGWSKYARVIRSTVI 164
                                       689******.******************************......*********9********************* PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       ++ +k++ve aralGas+  i+ +++lPn++ p+i+ + l +ggll   + l+f+g    lg    +++lg+++ ++
  gi|330508062|ref|YP_004384490.1| 165 SVKEKGFVESARALGASESYIMGRHILPNTIAPLIPMITLGLGGLLLSVSGLSFIG----LGVEAGTPELGMMIKNG 237
                                       ********************************************************....***************** PP

                      BPD_transp_1 154 s..........nggvlalviavlllnlvadilqrlldprv 183
                                                   ++++ ++++v  ++l+ d l + ldpr 
  gi|330508062|ref|YP_004384490.1| 238 FgvfpghphlvLVPSALIIVCVTGFTLIGDGLRDQLDPRK 277
                                       **************************************96 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 !   26.7   0.2   4.3e-10   3.9e-06      13      45 ..      14      48 ..      11      59 .. 0.84
   2 ?   -1.8   1.0      0.36   3.2e+03      19      29 ..      80      90 ..      78     105 .. 0.73
   3 ?   -0.6   0.7      0.15   1.4e+03      22      36 ..     126     140 ..     126     151 .. 0.83
   4 ?   -2.7   0.0       0.7   6.3e+03      21      36 ..     254     269 ..     252     276 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4.3e-10
                            OppC_N 13 NklAvvglvilllllliaifaPliaPydp..qdli 45
                                      Nk  ++g +i+ ++l+ia+faPliaP+dp   dl+
  gi|330508062|ref|YP_004384490.1| 14 NKKILIGSAIIGTVLIIALFAPLIAPHDPeaIDLR 48
                                      77789***********************9775553 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.36
                            OppC_N 19 glvilllllli 29
                                      +l+i +++lli
  gi|330508062|ref|YP_004384490.1| 80 SLFIAAVVLLI 90
                                      77777777776 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.15
                            OppC_N  22 illlllliaifaPli 36 
                                       i+l+l+l+  ++P +
  gi|330508062|ref|YP_004384490.1| 126 IVLALVLVGTLGPGV 140
                                       788899999999987 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 0.7
                            OppC_N  21 villlllliaifaPli 36 
                                        i++ ++ + ++++ +
  gi|330508062|ref|YP_004384490.1| 254 LIIVCVTGFTLIGDGL 269
                                       5777777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2065.34
//
Query:       gi|330508063|ref|YP_004384491.1|  [L=555]
Description: polymorphic outer membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-05   24.0  45.3       0.37   11.4   0.0   10.0 11  Chlam_PMP  Chlamydia polymorphic membrane protein (Chlamydia_
  ------ inclusion threshold ------
      0.021   14.7   0.2        5.6    6.9   0.1    3.5  2  DUF3797    Domain of unknown function (DUF3797)
        0.1   12.9   0.2        1.3    9.3   0.0    2.9  3  PLDc       Phospholipase D Active site motif


Domain annotation for each model (and alignments):
>> Chlam_PMP  Chlamydia polymorphic membrane protein (Chlamydia_PMP) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.7       2.4   1.5e+04       6      27 ..     162     173 ..     159     174 .. 0.75
   2 ?   -3.7   0.2         3   1.8e+04       4       9 ..     185     190 ..     183     190 .. 0.82
   3 ?    1.0   0.4      0.13   7.6e+02       2       9 ..     208     215 ..     207     224 .. 0.75
   4 !    5.1   0.6    0.0063        38       1      28 []     256     273 ..     256     273 .. 0.91
   5 !    8.5   0.6   0.00049       2.9       2      27 ..     282     296 ..     281     296 .. 0.84
   6 !    4.6   0.0    0.0086        52      17      27 ..     352     362 ..     324     363 .. 0.88
   7 ?   -2.4   0.2       1.5   8.8e+03       7      25 ..     377     385 ..     374     386 .. 0.70
   8 ?    2.0   0.0     0.058   3.5e+02      17      26 ..     440     449 ..     398     450 .. 0.83
   9 !   10.7   0.0    0.0001      0.62       1      27 [.     458     475 ..     458     476 .. 0.89
  10 !   11.4   0.0   6.1e-05      0.37       2      27 ..     487     503 ..     486     504 .. 0.92
  11 !    7.7   1.9   0.00089       5.3       2      28 .]     512     528 ..     511     528 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.4
                         Chlam_PMP   6 nNtatvsstptpaaggGGAIya 27 
                                       nN a           +G  Iy+
  gi|330508063|ref|YP_004384491.1| 162 NNIA----------YNGSSIYN 173
                                       6777..........78888887 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3
                         Chlam_PMP   4 FsnNta 9  
                                       ++nN a
  gi|330508063|ref|YP_004384491.1| 185 VTNNFA 190
                                       79**98 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.13
                         Chlam_PMP   2 itFsnNta 9  
                                        tFs N a
  gi|330508063|ref|YP_004384491.1| 208 STFSQNIA 215
                                       69*****9 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.0063
                         Chlam_PMP   1 sitFsnNtatvsstptpaaggGGAIyae 28 
                                       ++t+s+N +            GGAI +e
  gi|330508063|ref|YP_004384491.1| 256 NCTISYNRG----------DTGGAISNE 273
                                       689******..........******986 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.00049
                         Chlam_PMP   2 itFsnNtatvsstptpaaggGGAIya 27 
                                       ++F++N +           +GGAIya
  gi|330508063|ref|YP_004384491.1| 282 TSFESNRG-----------SGGAIYA 296
                                       67888887...........******8 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.0086
                         Chlam_PMP  17 paaggGGAIya 27 
                                       +++g GG+Iya
  gi|330508063|ref|YP_004384491.1| 352 ETCGTGGGIYA 362
                                       67899*****9 PP

  == domain 7  score: -2.4 bits;  conditional E-value: 1.5
                         Chlam_PMP   7 NtatvsstptpaaggGGAI 25 
                                       N+a           +GG+I
  gi|330508063|ref|YP_004384491.1| 377 NKA----------FYGGGI 385
                                       566..........577777 PP

  == domain 8  score: 2.0 bits;  conditional E-value: 0.058
                         Chlam_PMP  17 paaggGGAIy 26 
                                       + +g+GG+I+
  gi|330508063|ref|YP_004384491.1| 440 TIGGDGGGIF 449
                                       55899****9 PP

  == domain 9  score: 10.7 bits;  conditional E-value: 0.0001
                         Chlam_PMP   1 sitFsnNtatvsstptpaaggGGAIya 27 
                                       ++t++ N a         a +GGAIy 
  gi|330508063|ref|YP_004384491.1| 458 DVTIERNYA---------ARKGGAIYI 475
                                       589999999.........********5 PP

  == domain 10  score: 11.4 bits;  conditional E-value: 6.1e-05
                         Chlam_PMP   2 itFsnNtatvsstptpaaggGGAIya 27 
                                       +t+ +N+a           +GGAIy+
  gi|330508063|ref|YP_004384491.1| 487 VTIIDNQA---------KEKGGAIYN 503
                                       7999****.........********8 PP

  == domain 11  score: 7.7 bits;  conditional E-value: 0.00089
                         Chlam_PMP   2 itFsnNtatvsstptpaaggGGAIyae 28 
                                        ++snN a          + GG+I+ e
  gi|330508063|ref|YP_004384491.1| 512 AIISNNCA----------KEGGGIFIE 528
                                       789*****..........******975 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1   0.00093       5.6      23      40 ..     195     212 ..     192     215 .. 0.89
   2 ?    3.6   0.0     0.011        63      24      39 ..     270     285 ..     267     291 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00093
                           DUF3797  23 kvlNsegkviieddtfyr 40 
                                        v N +gk+i+e+ tf +
  gi|330508063|ref|YP_004384491.1| 195 TVVNEGGKLIVENSTFSQ 212
                                       589*************75 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.011
                           DUF3797  24 vlNsegkviieddtfy 39 
                                       + N +g +ii+  +f 
  gi|330508063|ref|YP_004384491.1| 270 ISNEGGSLIIDSTSFE 285
                                       89**********9995 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.56   3.3e+03       9      15 ..     105     111 ..     104     116 .. 0.88
   2 ?    9.3   0.0   0.00022       1.3       4      22 ..     147     170 ..     145     170 .. 0.87
   3 ?   -3.1   0.0       1.8   1.1e+04       7      14 ..     485     492 ..     481     493 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.56
                                       EEEETTT CS
                              PLDc   9 ivivDdr 15 
                                       +vi+D+r
  gi|330508063|ref|YP_004384491.1| 105 MVIIDGR 111
                                       79***98 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00022
                                       EE---EEEETTT.....EEEEE-- CS
                              PLDc   4 thHqKivivDdr.....vafvGga 22 
                                       ++H K++i+Dd      +a+ G++
  gi|330508063|ref|YP_004384491.1| 147 LNHGKMLILDDCllgnnIAYNGSS 170
                                       79*********9999999998885 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.8
                                       --EEEETT CS
                              PLDc   7 qKivivDd 14 
                                        K  i+D+
  gi|330508063|ref|YP_004384491.1| 485 GKVTIIDN 492
                                       58888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 4133.18
//
Query:       gi|330508064|ref|YP_004384492.1|  [L=216]
Description: hypothetical protein MCON_2151 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-14   54.5   0.3    1.7e-14   54.0   0.3    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 !   54.0   0.3   9.4e-19   1.7e-14     108     236 ..       9     156 ..       8     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 9.4e-19
                                       TT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--..... CS
                      Peripla_BP_2 108 lgledeaeklvaeidsklaaaksaidse..kpkpvlvfggadeggyvvagsnsyigdlldalgieniaaesk..... 177
                                       +++e++a++++a++++++ ++k   d++   +kp ++f +++  g+++++ +s+  + l  +g++n+++        
  gi|330508064|ref|YP_004384492.1|   9 FDEEEKARDFAAWHQETYNRIKRISDQIpeEDKPEVLFNSHEL-GTKYTAGGSRYDQSLKLAGARNLIDKIVkedsp 84 
                                       799*************************988888888888888.55566666777778889******8777679999 PP

                                       ..STT-EEE-HHHHHHH--SEEEEEEH...........HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-H CS
                      Peripla_BP_2 178 ..kseyeeisaEqilasdpdvifvsgr...........aeadnktgleflkenpllaelpAvkngrVyalds 236
                                         ++ + ++ +E++ +++p++if s             + + + + ++++ ++++++el A+kng+Vy++d+
  gi|330508064|ref|YP_004384492.1|  85 fyGKTSVDVEPEWVMEQNPEYIFTSYLnpnsnagfeteDVSGAAESVQAISNQTEFSELDAIKNGNVYYIDN 156
                                       *************************99*********99999****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1686.78
//
Query:       gi|330508065|ref|YP_004384493.1|  [L=352]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete 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   75.4   0.0    4.8e-21   74.6   0.0    1.4  1  DUF772       Transposase domain (DUF772)
    1.5e-15   57.4   4.6      5e-15   55.7   4.6    1.9  1  DDE_Tnp_1    Transposase DDE domain
      3e-05   23.8   0.3    0.00012   21.8   0.3    1.9  1  DDE_Tnp_4    DDE superfamily endonuclease
    3.1e-05   24.2   0.4    5.3e-05   23.4   0.4    1.4  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
      0.052   13.9   0.1       0.12   12.8   0.1    1.6  1  EnY2         Transcription factor e(y)2


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 !   74.6   0.0   1.3e-24   4.8e-21       1      72 [.      51     122 ..      51     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.3e-24
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp+++ ++m+k+l+lq ++glSd ele+++ +++sfr flg     + +pd+st + fR+rl+e    e+l++e
  gi|330508065|ref|YP_004384493.1|  51 GRPNIDIVIMVKALVLQSWFGLSDPELERQVTDRISFRIFLGT---TEVIPDFSTVWLFRERLIEcgrYEDLWKE 122
                                       9*****************************************5...389****************9999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   4.6   1.4e-18     5e-15      20     214 .]     177     340 ..     133     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.4e-18
                         DDE_Tnp_1  20 k............................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkql 68 
                                       +                             ++ w +kg k+++gyk hi++dt+ +li ++++t+++ hds++    
  gi|330508065|ref|YP_004384493.1| 177 PdfdkdllnisnnivssnakpkrlddgpiNEGTWAKKGSKSFFGYKGHILIDTEYHLIRKIETTTASLHDSQVDLG- 252
                                       0555555555555555555556666666677889999**********************************99777. PP

                         DDE_Tnp_1  69 ldelrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnksk 145
                                       +++l++      +aD+GY++a++  + +                            ++k+ r++ l  ++++rnk  
  gi|330508065|ref|YP_004384493.1| 253 INGLPR------YADKGYSGAKTQGYDA---------------------------AMKKAARGHKLGIKDILRNK-- 294
                                       777887......*******888877777...........................89******************.. PP

                         DDE_Tnp_1 146 kekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                              +++r+R+qiEr F+ +kr  + +++++ + +r+ +++++  +++n+
  gi|330508065|ref|YP_004384493.1| 295 -----------------------RISRKRSQIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNI 340
                                       .......................******************999************************7 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   3.4e-08   0.00012      77     130 ..     257     313 ..     195     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.4e-08
                         DDE_Tnp_4  77 vilaDkgFklse..kl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgr 130
                                          aDkg+ +++   +   ++k  ++++l  ++  +n++i++ r  +Er+++ +k+ 
  gi|330508065|ref|YP_004384493.1| 257 PRYADKGYSGAKtqGYdAAMKKAARGHKLGIKDILRNKRISRKRSQIERCFAVMKRA 313
                                       3469*****99954333455555********************************65 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 !   23.4   0.4   1.5e-08   5.3e-05      74     124 ..     294     343 ..     265     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.5e-08
                       DDE_Tnp_1_6  74 kaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                       k+  +kR+ ++E+ fa +kr++++  + ++ ++++ ++f++  +++N+++l
  gi|330508065|ref|YP_004384493.1| 294 KRISRKRS-QIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNIEQL 343
                                       45556665.***************************************997 PP

>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.3e-05      0.12       5      31 ..     107     133 ..     106     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       HHHHHHTTHHHHHHHHHHHHHHHTTHH CS
                              EnY2   5 qqkLvesGererlkelLrerLeesGWr 31 
                                       +++L+e G +e+l + L+++L+e G+ 
  gi|330508065|ref|YP_004384493.1| 107 RERLIECGRYEDLWKELQNQLDEKGFA 133
                                       589**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2725.04
//
Query:       gi|330508066|ref|YP_004384494.1|  [L=249]
Description: hypothetical protein MCON_2153 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.14   12.4   0.2       0.14   12.4   0.2    2.2  3  Dockerin_1  Dockerin type I domain


Domain annotation for each model (and alignments):
>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1      0.88   1.6e+04      35      39 ..      22      26 ..      17      30 .. 0.49
   2 ?   11.4   2.0   1.6e-05      0.28       5      58 .]      35      83 ..      32      83 .. 0.90
   3 ?   12.4   0.2   7.7e-06      0.14       2      42 ..      62      97 ..      61     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.88
                                      GGGST CS
                        Dockerin_1 35 kaaDv 39
                                      +a+Dv
  gi|330508066|ref|YP_004384494.1| 22 DALDV 26
                                      33333 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 1.6e-05
                                      TSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHHHHHT CS
                        Dockerin_1  5 NgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallvinyLl 58
                                      N D  ++  D++ ++  +      +s + ++ aD N D +v+  D++++ + ++
  gi|330508066|ref|YP_004384494.1| 35 NLDDIIDEEDIAYVKDIMK-----GSAETTELADANYDQEVDEEDIAQIERIIN 83
                                      7799999999999999999.....9999999*****************998776 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 7.7e-06
                                      TETTSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-S CS
                        Dockerin_1  2 gDVNgDgkVnalDalliinylnqregqssssngkaaDvNgD 42
                                      +D N D++V+  D++ i + +n     +++s  ++ D+ gD
  gi|330508066|ref|YP_004384494.1| 62 ADANYDQEVDEEDIAQIERIIN-----GTESSLTFIDIFGD 97
                                      699*******************.....77778888887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1913.71
//
Query:       gi|330508067|ref|YP_004384495.1|  [L=66]
Description: hypothetical protein MCON_2154 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-16   59.0   0.5    4.5e-16   58.9   0.5    1.0  1  CooT      CO dehydrogenase accessory protein CooT
  ------ inclusion threshold ------
      0.082   12.8   0.0      0.084   12.8   0.0    1.1  1  DUF3197   Protein of unknown function (DUF3197)


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 !   58.9   0.5   5.1e-20   4.5e-16       1      61 []       1      63 [.       1      63 [. 0.97

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 5.1e-20
                              CooT  1 MCeanvyllkngk.eeelvmedVdkiepeedgvvltdifGeekeve.gkIkeidLvehkiile 61
                                      MCe++vyll++++ +++++++d++  + +e++v+l+d fG+ + ve ++I+e++ +++++il+
  gi|330508067|ref|YP_004384495.1|  1 MCEFTVYLLGDNQkDRQMMAKDILVARRKEGKVLLMDAFGSITPVEnATIEEVNTLSQEMILK 63
                                      *********888879**********************************************95 PP

>> DUF3197  Protein of unknown function (DUF3197)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.4e-06     0.084      14      64 ..       3      53 ..       1      65 [. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.4e-06
                                      T-EEEEEEC-SSSCTS--EEEEEE.-SS-EEEEEEEESTTS.TTHHHHHHHH CS
                           DUF3197 14 eakvvlvtdrqdqRekAryaalle.aakealltedaFGpafGpeGeraLael 64
                                      e +v+l+ d q  R+     +l+    + ++l++daFG    p  +++++e+
  gi|330508067|ref|YP_004384495.1|  3 EFTVYLLGDNQKDRQMMAKDILVArRKEGKVLLMDAFGSIT-PVENATIEEV 53
                                      66899******99998777777762666799*******854.4444455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 497.39
//
Query:       gi|330508068|ref|YP_004384496.1|  [L=261]
Description: CobQ/CobB/MinD/ParA nucleotide binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   74.9   0.0    9.8e-21   74.1   0.0    1.4  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    5.4e-14   52.5   0.0    1.6e-13   51.0   0.0    1.8  2  AAA_31         AAA domain
      4e-12   46.0   0.0    2.2e-11   43.5   0.0    2.0  2  ArsA_ATPase    Anion-transporting ATPase
    1.1e-10   41.4   0.0    3.9e-07   29.8   0.0    2.1  2  CBP_BcsQ       Cellulose biosynthesis protein BcsQ
    9.1e-10   38.4   0.1    1.2e-08   34.7   0.1    2.2  1  Fer4_NifH      4Fe-4S iron sulfur cluster binding proteins, N
    1.1e-08   34.9   0.1      4e-08   33.0   0.0    1.9  2  ParA           NUBPL iron-transfer P-loop NTPase
    9.1e-06   26.2   0.0    1.3e-05   25.6   0.0    1.3  1  AAA_16         AAA ATPase domain
    1.6e-05   24.0   0.2    3.8e-05   22.8   0.0    1.6  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
    4.8e-05   23.2   0.0     0.0011   18.7   0.1    2.2  2  CLP1_P         mRNA cleavage and polyadenylation factor CLP1 
    0.00025   20.8   0.0    0.00045   19.9   0.0    1.4  1  SRP54          SRP54-type protein, GTPase domain
    0.00043   20.1   0.0    0.00065   19.5   0.0    1.4  1  AAA_24         AAA domain
     0.0012   18.8   0.0     0.0018   18.2   0.0    1.4  1  NTPase_1       NTPase
     0.0024   17.8   0.0     0.0059   16.5   0.0    1.6  1  MobB           Molybdopterin guanine dinucleotide synthesis p
     0.0038   17.0   0.0      0.006   16.3   0.0    1.4  1  AAA_30         AAA domain
     0.0052   16.6   0.0      0.013   15.3   0.0    1.6  2  ATP_bind_1     Conserved hypothetical ATP binding protein
     0.0059   17.1   0.1      0.016   15.7   0.1    1.7  1  AAA_18         AAA domain
  ------ inclusion threshold ------
       0.01   15.1   0.0      0.018   14.4   0.0    1.4  1  CTP_synth_N    CTP synthase N-terminus
      0.016   14.5   0.0      0.026   13.8   0.0    1.3  1  VirC1          VirC1 protein
      0.018   15.0   0.0      0.032   14.1   0.0    1.3  1  APS_kinase     Adenylylsulphate kinase
      0.021   13.9   0.3       0.19   10.8   0.1    2.0  2  LpxK           Tetraacyldisaccharide-1-P 4'-kinase
      0.025   14.1   0.0       0.04   13.4   0.0    1.3  1  AAA_7          P-loop containing dynein motor region
      0.027   14.1   0.0      0.084   12.4   0.0    1.8  2  AAA_25         AAA domain
       0.03   14.2   0.0      0.051   13.5   0.0    1.3  1  NACHT          NACHT domain
      0.031   13.5   0.0      0.072   12.4   0.0    1.6  1  MipZ           ATPase MipZ
       0.04   14.2   0.1      0.099   12.9   0.0    1.7  1  AAA_28         AAA domain
      0.043   13.0   0.0      0.062   12.5   0.0    1.3  1  NB-ARC         NB-ARC domain
      0.051   13.5   0.1       0.66    9.9   0.0    2.1  2  RsgA_GTPase    RsgA GTPase
      0.058   13.0   0.8       0.21   11.2   0.0    2.1  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.077   12.4   0.0       0.12   11.8   0.0    1.3  1  KTI12          Chromatin associated protein KTI12
      0.098   11.5   0.0       0.14   11.1   0.0    1.2  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
       0.12   12.7   0.0       0.23   11.7   0.0    1.6  1  AAA_22         AAA domain
       0.16   12.0   0.0       0.29   11.1   0.0    1.4  1  AAA_5          AAA domain (dynein-related subfamily)
       0.18   12.0   0.1        1.3    9.2   0.1    2.1  2  AAA_33         AAA domain
        0.2   11.4   0.3       0.56    9.9   0.1    1.8  2  PduV-EutP      Ethanolamine utilisation - propanediol utilisa


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 !   74.1   0.0   1.9e-23   9.8e-21       2     126 ..       4     235 ..       3     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 1.9e-23
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       +i s+kGGvGKTt++ nLar+lar+g+rVl++D+Dp +n++++l     d+                          
  gi|330508068|ref|YP_004384496.1|   4 IIFSGKGGVGKTTILSNLARLLARDGYRVLVIDCDPSMNLAMSLGIPLSDVVSlakdsshlwerlgpqaeeqehgeh 80 
                                       689**************************************98666666666688899999**************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|330508068|ref|YP_004384496.1|  81 glecteedldefiipaadgvklivmgtipfggagclcapislvrllvnylasgpeehdfifvdsqagveifgrglas 157
                                       ***************************************************************************** PP

                                       .................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE- CS
                                       .................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 .................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgvipr 114
                                                         +k +l+l+ +lg      +k   vv+n+v+ +  e ll+   e      + +++ ++++
  gi|330508068|ref|YP_004384496.1| 158 efdlsfviteptpksleVAKHGLKLAGDLG------VKRQIVVVNKVEVD--EDLLMAKRELDGN--AQQIM-SVSY 223
                                       *******88888888877777778888888......5689**********..8888887777653..55555.8*** PP

                                       -CCHCCCCHHTS CS
                                       xxxxxxxxxxxx RF
                              CbiA 115 deavaeaparge 126
                                       d +v+ea+++g 
  gi|330508068|ref|YP_004384496.1| 224 DREVVEADKKGA 235
                                       *********997 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0     3e-16   1.6e-13       7     126 ..       6     145 ..       1     186 [. 0.63
   2 ?   -1.4   0.0       3.5   1.9e+03      74     106 ..     194     227 ..     171     235 .. 0.74

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 3e-16
                            AAA_31   7 anqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne......iektlyev............... 62 
                                          KGGvGKTT   nla  la+ g++vL++D+Dp  n++++lgi  ++       +++   +               
  gi|330508068|ref|YP_004384496.1|   6 FSGKGGVGKTTILSNLARLLARDGYRVLVIDCDPSMNLAMSLGIPLSDvvslakDSSH---Lwerlgpqaeeqehge 79 
                                       567****************************************987774443321223...2333444433333333 PP

                            AAA_31  63 ..l.ieeknikeaiiktkvenldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcp 126
                                         l ++e++++e ii +      ++ ++i + +a        +  + l ++l +  +e+D+i++D +
  gi|330508068|ref|YP_004384496.1|  80 hgLeCTEEDLDEFIIPAADGVKLIVMGTIPFGGAGCL-CAPISLVRLLVNYLASGPEEHDFIFVDSQ 145
                                       3322355555555553332222333344444444333.33333345567777777777777777766 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.5
                            AAA_31  74 iktk.venldlipssidLaeaeielvelekkeei 106
                                       + +k   + dl+ ++ +L +  +++++++  +e+
  gi|330508068|ref|YP_004384496.1| 194 VVNKvEVDEDLLMAKRELDGNAQQIMSVSYDREV 227
                                       3334144559999999999988888888777665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   4.1e-14   2.2e-11       1      59 [.       1      59 [.       1      92 [. 0.83
   2 ?    0.2   0.0      0.66   3.5e+02     231     249 ..     184     202 ..     161     250 .. 0.67

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 4.1e-14
                                      -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEET CS
                       ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvk 59
                                      +k i+++GKGGVGKtt+ + +a  l++ g++vl+i  DP  +l+ s+   l+  +   k
  gi|330508068|ref|YP_004384496.1|  1 MKRIIFSGKGGVGKTTILSNLARLLARDGYRVLVIDCDPSMNLAMSLGIPLSDVVSLAK 59
                                      789****************************************9998877666665555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.66
                                       HHTT-EEEEEEEEEE-TTC CS
                       ArsA_ATPase 231 kkygikvdavivNkllpee 249
                                         +g+k + v+vNk+  +e
  gi|330508068|ref|YP_004384496.1| 184 GDLGVKRQIVVVNKVEVDE 202
                                       5678888888888873333 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   7.4e-10   3.9e-07       1      59 [.       1      58 [.       1      69 [. 0.90
   2 !   10.0   0.0    0.0008      0.42     107     232 ..     128     256 ..      70     258 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 7.4e-10
                          CBP_BcsQ  1 mkvlalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqregwa 59
                                      mk + ++G +GGvG+t++l+ La+ l + g++vlviD  p+  L+++  +++++  ++a
  gi|330508068|ref|YP_004384496.1|  1 MKRIIFSG-KGGVGKTTILSNLARLLARDGYRVLVIDCDPSMNLAMSLGIPLSDVVSLA 58
                                      77788888.8**************************************99998877666 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0008
                          CBP_BcsQ 107 aalkelkeqyrwillDlpagasaltrellaladlvllvvepdanchvrLhqqalpaaellLiNqfea...asqlqqD 180
                                       + l++  e++++i++D +ag +   r l +  dl++ ++ep   + +  +++ l+ a  l + +  +   + ++ +D
  gi|330508068|ref|YP_004384496.1| 128 NYLASGPEEHDFIFVDSQAGVEIFGRGLASEFDLSFVITEPTPKS-LEVAKHGLKLAGDLGVKRQIVvvnKVEVDED 203
                                       444444489*******************************98775.556666676666666665433111356899* PP

                          CBP_BcsQ 181 llqlWlqslrrllPl.vihrDealaEalaakqPlgeyrpdslaaeevktLanw 232
                                       ll+  ++   + + +  +  D  ++Ea    + l +y+p+s   +++  + ++
  gi|330508068|ref|YP_004384496.1| 204 LLMAKRELDGNAQQImSVSYDREVVEADKKGALLLDYAPHSSSLRDIVRVEQF 256
                                       ******999777665489***********99***********99999877665 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 !   34.7   0.1   2.3e-11   1.2e-08       2      85 ..       3      86 ..       2     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.3e-11
                         Fer4_NifH  2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgav.edvkve.dvvkkGy 78
                                      +i + GkGG+Gk+t ++nl+  la++g +vl++ CDP  + +  +  g   + v+ ++++  +  e +  + +   +G 
  gi|330508068|ref|YP_004384496.1|  3 RIIFSGKGGVGKTTILSNLARLLARDGYRVLVIDCDPSMNLA--MSLGIPLSDVVSLAKDSSHLwERLGPQaEEQEHGE 79
                                      68899********************************98766..33456666777777777666677754413455666 PP

                         Fer4_NifH 79 ggvkcve 85
                                      +g++c+e
  gi|330508068|ref|YP_004384496.1| 80 HGLECTE 86
                                      6666666 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   7.5e-11     4e-08       7      41 ..       4      38 ..       1      50 [. 0.93
   2 ?   -0.7   0.0       1.5     8e+02     140     173 ..     163     196 ..     138     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 7.5e-11
                              ParA  7 avlSgKGGVGKStvavnlAlaLakkglkvgllDaD 41
                                      ++ SgKGGVGK+t+ +nlA  La+ g++v ++D D
  gi|330508068|ref|YP_004384496.1|  4 IIFSGKGGVGKTTILSNLARLLARDGYRVLVIDCD 38
                                      689******************************99 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                              ParA 140 viVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                        ++t p   +l+++k +++++ ++ vk   vv N
  gi|330508068|ref|YP_004384496.1| 163 FVITEPTPKSLEVAKHGLKLAGDLGVKRQIVVVN 196
                                       5778888888888888888888777776666555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.5e-08   1.3e-05      27     104 ..       4      87 ..       2     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.5e-08
                            AAA_16  27 vllsGesGvGKsslvrellralekdggiflrgkcdql.....esaipysa.laqalareellrqlldeaesaeleaw 97 
                                       +++sG  GvGK++++  l+r l +dg  +l  +cd +     + +ip+s  +  a + ++l + l+ +ae++e++++
  gi|330508068|ref|YP_004384496.1|   4 IIFSGKGGVGKTTILSNLARLLARDGYRVLVIDCDPSmnlamSLGIPLSDvVSLAKDSSHLWERLGPQAEEQEHGEH 80 
                                       6899*********************9999*******95554444488877566666667777777777666666665 PP

                            AAA_16  98 rekleea 104
                                         +++e+
  gi|330508068|ref|YP_004384496.1|  81 GLECTEE 87 
                                       5554443 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   7.3e-08   3.8e-05      31      70 ..       3      42 ..       1      63 [. 0.90
   2 ?   -1.8   0.0       2.3   1.2e+03     170     189 ..     191     211 ..     158     227 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.3e-08
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                      ++ + G  G+Gk t++++l+  l+r G+rv v+  DPs +
  gi|330508068|ref|YP_004384496.1|  3 RIIFSGKGGVGKTTILSNLARLLARDGYRVLVIDCDPSMN 42
                                      77889********************************975 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.3
                                       SEEEEE---.HHHHHHHHHHH CS
                              MeaB 170 DiivvnkaD.kkeaekaarel 189
                                        i+vvnk +  ++   a+rel
  gi|330508068|ref|YP_004384496.1| 191 QIVVVNKVEvDEDLLMAKREL 211
                                       368888877544555555555 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 !   18.7   0.1   2.2e-06    0.0011       1      35 [.       8      42 ..       8      64 .. 0.89
   2 ?    2.2   0.0      0.26   1.4e+02       9      33 ..     121     147 ..     120     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-06
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqs 35
                                      G+  +GK+T+  +L+  ++r g++++++D+D+  +
  gi|330508068|ref|YP_004384496.1|  8 GKGGVGKTTILSNLARLLARDGYRVLVIDCDPSMN 42
                                      66789**************************9875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.26
                            CLP1_P   9 TlarlLlNyalrkgr..kpvyvDlDvG 33 
                                       +l+rlL+Ny+++  +    ++vD   G
  gi|330508068|ref|YP_004384496.1| 121 SLVRLLVNYLASGPEehDFIFVDSQAG 147
                                       799*******98654226668887766 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.5e-07   0.00045       3      38 ..       3      38 ..       1      44 [. 0.94

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.5e-07
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                       i++ G  G+GKTt l+ La+ll ++g++vl++ +D
  gi|330508068|ref|YP_004384496.1|  3 RIIFSGKGGVGKTTILSNLARLLARDGYRVLVIDCD 38
                                      68999****************************998 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.2e-06   0.00065       3      36 ..       2      42 ..       1     100 [. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-06
                            AAA_24  3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlk 36
                                      ++i+  G+ g+GKTt++++l       g+++l+id++ +++
  gi|330508068|ref|YP_004384496.1|  2 KRIIFSGKGGVGKTTILSNLarllardGYRVLVIDCDPSMN 42
                                      578889*******************************9886 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.4e-06    0.0018       1      35 [.       3      37 ..       3     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.4e-06
                                      EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEE CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyt 35
                                      +++ +G+ GvGKtT+++++++ll+++g++v  + +
  gi|330508068|ref|YP_004384496.1|  3 RIIFSGKGGVGKTTILSNLARLLARDGYRVLVIDC 37
                                      58899***********************9965555 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.1e-05    0.0059       2      33 ..       4      35 ..       3      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgti 33
                                      + + gk g GKTt+l++l + l++ g+rv +i
  gi|330508068|ref|YP_004384496.1|  4 IIFSGKGGVGKTTILSNLARLLARDGYRVLVI 35
                                      56889************************988 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.1e-05     0.006      22      52 ..       5      35 ..       2     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                            AAA_30 22 vltGpAGtGKttalkalreaweaaggrvigl 52
                                      +  G  G GKtt+l+ l+++++++g+rv+++
  gi|330508068|ref|YP_004384496.1|  5 IFSGKGGVGKTTILSNLARLLARDGYRVLVI 35
                                      67899**********************9986 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.5e-05     0.013       2      55 ..       7      59 ..       6      72 .. 0.81
   2 ?   -2.0   0.0       4.9   2.6e+03     159     177 ..     191     209 ..     190     244 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-05
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitled 55
                                       G  G+GKtt+ ++l+ +l   g++v v+  DP  + l+ +  +   ++++l++
  gi|330508068|ref|YP_004384496.1|  7 SGKGGVGKTTILSNLARLLARDGYRVLVIDCDPSMN-LAMSLGIPLSDVVSLAK 59
                                      5899*****************************876.66666666666666665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.9
                        ATP_bind_1 159 hvvvlnkfDllkek.lekel 177
                                       ++vv+nk+++ +e+ l  + 
  gi|330508068|ref|YP_004384496.1| 191 QIVVVNKVEV-DEDlLMAKR 209
                                       5888888888.545432222 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   3.1e-05     0.016       1      25 [.       4      37 ..       4      67 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.1e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.........g 25
                                      I+ +G+ GvGKtt+  +L+++l+           
  gi|330508068|ref|YP_004384496.1|  4 IIFSGKGGVGKTTILSNLARLLARdgyrvlvidC 37
                                      899****************998656555554441 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.3e-05     0.018      11      46 ..      10      45 ..       2      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                                      TTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSS CS
                       CTP_synth_N 11 SglGkGiiaaslgallksrglkvtlikiDPYlnvda 46
                                       g+Gk  i + l++ll + g++v +i +DP +n+  
  gi|330508068|ref|YP_004384496.1| 10 GGVGKTTILSNLARLLARDGYRVLVIDCDPSMNLAM 45
                                      589*****************************9865 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.9e-05     0.026       7      41 ..       6      40 ..       1      46 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-05
                             VirC1  7 cslkGGaGkttalmglcsalasdgkrvalfeaden 41
                                       s kGG Gktt l  l   la dg rv + ++d  
  gi|330508068|ref|YP_004384496.1|  6 FSGKGGVGKTTILSNLARLLARDGYRVLVIDCDPS 40
                                      367**************************999975 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     6e-05     0.032       5      40 ..       4      39 ..       2      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6e-05
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                      + ++G  g GK+ti  +l++ L ++g++v ++d d 
  gi|330508068|ref|YP_004384496.1|  4 IIFSGKGGVGKTTILSNLARLLARDGYRVLVIDCDP 39
                                      789******************************985 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00036      0.19      46      71 ..      10      35 ..       8      36 .. 0.96
   2 ?    0.9   0.0      0.36   1.9e+02      34      62 ..      99     127 ..      90     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                                      S-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK 46 GGtGKTPlvialvkllqarglkvgvl 71
                                      GG GKT +   l++ll++ g++v v+
  gi|330508068|ref|YP_004384496.1| 10 GGVGKTTILSNLARLLARDGYRVLVI 35
                                      9**********************998 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.36
                                       SS-EEEEEESBSS-HSHHHHHHHHHHHTT CS
                              LpxK  34 pvpVivVGNitvGGtGKTPlvialvkllq 62 
                                       +v+ iv G i  GG+G   + i lv+ll+
  gi|330508068|ref|YP_004384496.1|  99 GVKLIVMGTIPFGGAGCLCAPISLVRLLV 127
                                       6999************8888888887775 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.6e-05      0.04      34      70 ..       2      38 ..       1      47 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.6e-05
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfs 70
                                      k +++ G+ G+GKt+i+++l + l ++ y +l+i + 
  gi|330508068|ref|YP_004384496.1|  2 KRIIFSGKGGVGKTTILSNLARLLARDGYRVLVIDCD 38
                                      6799***************************999876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016     0.084      35      59 ..       3      27 ..       1      42 [. 0.84
   2 ?   -2.4   0.0       5.6     3e+03      56      85 ..     174     204 ..     171     241 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                            AAA_25 35 lallaGapgtGKttlaldlalavat 59
                                       +++ G +g+GKtt++++la  +a+
  gi|330508068|ref|YP_004384496.1|  3 RIIFSGKGGVGKTTILSNLARLLAR 27
                                      57999***************98884 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.6
                            AAA_25  56 ava.tGkpwlgpvapeqgkVlyvsaEdsede 85 
                                       +va  G +++g++ +++  V++   E +ed 
  gi|330508068|ref|YP_004384496.1| 174 EVAkHGLKLAGDLGVKRQIVVVNKVEVDEDL 204
                                       5666677777766666666777777766653 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.7e-05     0.051       2      28 ..       3      29 ..       2      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.7e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegk 28
                                       +i  G+ G+GKTt l  la+++a++ 
  gi|330508068|ref|YP_004384496.1|  3 RIIFSGKGGVGKTTILSNLARLLARDG 29
                                      58999******************9976 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014     0.072       7      38 ..       7      38 ..       2      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                      -SSTTSSHHHHHHHHHHHHHTTT--EEEEE-- CS
                              MipZ  7 nekGGsGksttavhvavaLlkkGarvaaidld 38
                                        kGG Gk+t+   +a  L++ G rv +id d
  gi|330508068|ref|YP_004384496.1|  7 SGKGGVGKTTILSNLARLLARDGYRVLVIDCD 38
                                      469***************************99 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00019     0.099       1      26 [.       3      32 ..       3      36 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00019
                            AAA_28  1 kivitGgestGKTtlleaLa...ar.gypv 26
                                      +i+++G  + GKTt+l++La   ar gy+v
  gi|330508068|ref|YP_004384496.1|  3 RIIFSGKGGVGKTTILSNLArllARdGYRV 32
                                      799*****************6553369887 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012     0.062      23      79 ..       4      71 ..       1     102 [. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                      EEEEESTTSSHHHHHHHHCCSHCCCCCCBT.EEEEE................EEESXXHHHHHHHXXHHHHHCC CS
                            NB-ARC 23 valvGmgGvGKttlakqilnksdevegrFd.svawv................vvsktdkseeiletilkeLsls 79
                                      + ++G+gGvGKtt++++  +     +  +   v+ +                vvs   +s++++e    +L+ +
  gi|330508068|ref|YP_004384496.1|  4 IIFSGKGGVGKTTILSNLARL--LARDGYRvLVIDCdpsmnlamslgiplsdVVSLAKDSSHLWE----RLGPQ 71
                                      5689************99887..444466633444477777777777777777777777777776....44444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0013      0.66     101     120 ..       3      22 ..       1      32 [. 0.87
   2 ?    1.5   0.0      0.46   2.4e+02      46      81 ..     187     227 ..     152     240 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                                       EEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinall 120
                                        +++ G+ GvGK+t++ +l+
  gi|330508068|ref|YP_004384496.1|   3 RIIFSGKGGVGKTTILSNLA 22 
                                       579*************9986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.46
                                       T-.EEEEEEE-GGG--HHH....HHHHHHHHHHHTTSEEEE CS
                       RsgA_GTPase  46 gi.epvivlnKiDlleeee....eleelkeelealgyevll 81 
                                       g+ + ++v+nK+++ e+      el+  ++++ ++ y+  +
  gi|330508068|ref|YP_004384496.1| 187 GVkRQIVVVNKVEVDEDLLmakrELDGNAQQIMSVSYDREV 227
                                       55234556677655554443222444444555555555444 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 ?   11.2   0.0   0.00039      0.21       3      35 ..       4      38 ..       2      45 .. 0.87
   2 ?   -0.3   0.2       1.3   6.8e+02     143     152 ..     191     200 ..     111     223 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                                      EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS CS
                              cobW  3 tvltGflGsGKTtLlnhll..enraglklavivNe 35
                                      ++++G  G GKTt+l++l     r+g+++ vi  +
  gi|330508068|ref|YP_004384496.1|  4 IIFSGKGGVGKTTILSNLArlLARDGYRVLVIDCD 38
                                      6889999***********98889999999999665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.3
                                       SEEEEE-HHH CS
                              cobW 143 dllvlnKtDl 152
                                        ++v+nK+++
  gi|330508068|ref|YP_004384496.1| 191 QIVVVNKVEV 200
                                       3344444443 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00023      0.12       2      39 ..       2      40 ..       1      47 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                                      .EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-.THH CS
                             KTI12  2 pLvvltGlPssGKstrakeLakaleeekrsvvvid.des 39
                                        ++++G   +GK+t+ ++La+ l+  +++v vid d s
  gi|330508068|ref|YP_004384496.1|  2 KRIIFSGKGGVGKTTILSNLARLLARDGYRVLVIDcDPS 40
                                      5699******************************94545 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 ?   11.1   0.0   0.00026      0.14      17      51 ..       3      37 ..       1      44 [. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                     TrwB_AAD_bind 17 hilivGttGsGKtqalekllrairargdraivlDl 51
                                       i++ G  G GKt+ l++l r + + g r++v+D 
  gi|330508068|ref|YP_004384496.1|  3 RIIFSGKGGVGKTTILSNLARLLARDGYRVLVIDC 37
                                      68899*****************************7 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   0.00044      0.23       8      53 ..       4      43 ..       2     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00044
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstss 53
                                      ++  G  G+GKTt l +l++ l ++      + +v+ +++  s+++
  gi|330508068|ref|YP_004384496.1|  4 IIFSGKGGVGKTTILSNLARLLARD------GYRVLVIDCDPSMNL 43
                                      5678999**************9765......999999999988854 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00055      0.29       2      36 ..       4      41 ..       3      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00055
                                      EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal...nreveyvqltrdt 36
                                      ++  G+ G+gK+++   la++l   + +v+++ +  ++
  gi|330508068|ref|YP_004384496.1|  4 IIFSGKGGVGKTTILSNLARLLardGYRVLVIDCDPSM 41
                                      5788******************9888888888877766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0024       1.3       2      25 ..       4      29 ..       4      38 .. 0.80
   2 ?   -0.5   0.0       2.4   1.3e+03      89     105 ..     180     196 ..     169     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0024
                            AAA_33  2 vllvGlpGsGKstlaerllkklg..a 25
                                      +++ G  G+GK+t + +l++ l+  +
  gi|330508068|ref|YP_004384496.1|  4 IIFSGKGGVGKTTILSNLARLLArdG 29
                                      6899**************98766552 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.4
                            AAA_33  89 lklarrlgvpvrivvve 105
                                       lkla +lgv++ ivvv+
  gi|330508068|ref|YP_004384496.1| 180 LKLAGDLGVKRQIVVVN 196
                                       6899999***9999974 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0011      0.56       1      22 [.       1      22 [.       1      27 [. 0.90
   2 ?   -2.0   0.0       5.1   2.7e+03      93     106 ..     192     202 ..     167     225 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                         PduV-EutP  1 mkkilliGkvgsGKttLtqalk 22
                                      mk+i++ Gk g+GKtt+  +l 
  gi|330508068|ref|YP_004384496.1|  1 MKRIIFSGKGGVGKTTILSNLA 22
                                      9***************988775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.1
                         PduV-EutP  93 iGiitkidlaedee 106
                                       i ++ k+++    e
  gi|330508068|ref|YP_004384496.1| 192 IVVVNKVEVD---E 202
                                       3334444333...4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 1753.07
//
Query:       gi|330508069|ref|YP_004384497.1|  [L=237]
Description: hypothetical protein MCON_2156 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-26   93.0   0.0    3.8e-26   92.8   0.0    1.0  1  DUF4198   Domain of unknown function (DUF4198)
    0.00046   20.2   0.0    0.00085   19.3   0.0    1.5  1  bMG3      Bacterial alpha-2-macroglobulin MG3 domain


Domain annotation for each model (and alignments):
>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.0   4.3e-30   3.8e-26       2     213 .]      11     214 ..      10     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 4.3e-30
                           DUF4198   2 qAHelwllpsstvvsggewvtvdlafghdpfeadheplklekl..kvlapdg.ektdlgkylstfdvallkpekegt 75 
                                       q+He+wl+ s+   +++  v++ l++gh ++++d +  ++ ++   v+ pdg   + + + +++ + +++k+e++g 
  gi|330508069|ref|YP_004384497.1|  11 QGHEIWLERSK--IEND-DVELSLVYGH-NMRQD-GVADISRFlpFVFLPDGiRGEAVLSAGDDRHSMKFKAENAGH 82 
                                       89****99988..5555.8*********.****9.99999988789******8566666677777777778899*** PP

                           DUF4198  76 yklaaakkpgdwkeygdpklakevp.aeaae.lkvvkysqyaktfvtvgkpsetwdkpvglglEivPlthpydlkag 150
                                       y + + +  ++w++++d+    + p ++ ++ + +  y+q+akt+++vg++s+   +p+   lEivP + p+  ++g
  gi|330508069|ref|YP_004384497.1|  83 YIAFVDMGTTVWSQTKDGY--NQGPkFQFKDvIYAGAYNQMAKTIISVGNGSDYIGRPLHGILEIVP-KEPF-CRSG 155
                                       *****9999*****88877..6666444444699*************************999*****.9999.669* PP

                           DUF4198 151 eelevqvlldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGlwlleaehed 213
                                       +e+e+ vl++ kPla a+++++ ++    + ++   ++td++Gv+ ++++  G  ++ ++h+d
  gi|330508069|ref|YP_004384497.1| 156 QEIELSVLYEEKPLAFADIKAVSKK----EGREIGSARTDENGVARIPIDVDGECMFLVRHAD 214
                                       *********************9754....444444459**********************986 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 !   19.3   0.0   9.5e-08   0.00085      20      59 ..     161     201 ..     151     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.5e-08
                              bMG3  20 tsLdsgkPvagaeVrlld.kkgevlaegtTDaqGvarfaal 59 
                                       + L + kP+a a+++ ++ k+g+++++++TD++Gvar++ +
  gi|330508069|ref|YP_004384497.1| 161 SVLYEEKPLAFADIKAVSkKEGREIGSARTDENGVARIPID 201
                                       5677899*******9887699****************9855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1887.75
//
Query:       gi|330508070|ref|YP_004384498.1|  [L=313]
Description: nucleoside recognition domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   19.1  21.3      0.061   13.6   3.5    3.4  3  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 !   13.6   3.5   3.4e-06     0.061       5      94 ..      16      96 ..      13     106 .. 0.78
   2 ?    2.4   0.0      0.01   1.8e+02      30      69 ..     110     163 ..     102     176 .. 0.69
   3 !   10.6   6.1   2.8e-05      0.51       2      98 ..     181     267 ..     180     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.4e-06
                              Gate  5 gpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtl.gtlytsalgellqgfdtp 82
                                      + i++++++l +++++ +l+ +i+ l +p+++     l+  ++ +++++++   +++ t+ +++         +g  t+
  gi|330508070|ref|YP_004384498.1| 16 MSIVFIMLFLTGLMNELGLFYKISYLAKPLISFSH--LPAVSASTFVVSLG-SALAANTMiARM-------KDEGSLTE 84
                                      5799*****************************77..99999999999999.333333331333.......47788888 PP

                              Gate 83 ksalafllfvll 94
                                      ++a+ + ++++ 
  gi|330508070|ref|YP_004384498.1| 85 RQAFFCAIMNSV 96
                                      888877777665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.01
                              Gate  30 llepvfaplgqeldwkatvslltgfaakevvvgtlgtly.................t 69 
                                       ++ pv+  +       a+v+l tg++ k  +v +lg+ y                 t
  gi|330508070|ref|YP_004384498.1| 110 FVVPVLGLFA--GGIYAIVALSTGII-KLFIVVILGRAYlpegsdaskdadipenkT 163
                                       5566666655..788899********.888888889998777666555444444444 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 2.8e-05
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                       l++  +++++++l+ +ls++++l+ i  l  p+ + +    + +++v+l+  +a+  +++ +lg +        ++g
  gi|330508070|ref|YP_004384498.1| 181 LRISSLFFIMTFLVLYLSEKGILQSINAL--PIAQIFR--VPPETIVPLTIYVASPKAGITLLGPMI-------SNG 246
                                       6778899********************99..*****99..***********************9996.......999 PP

                              Gate  79 fdtpksalafllfvllyt.pc 98 
                                         ++++al++l+++++ + p 
  gi|330508070|ref|YP_004384498.1| 247 SISEVKALIVLMLGSMFMlPF 267
                                       999999887777766655233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2216.98
//
Query:       gi|330508071|ref|YP_004384499.1|  [L=420]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for 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-24   84.7   0.0    9.4e-24   84.3   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
       0.51   10.6   2.7       0.96    9.7   2.7    1.5  1  Dockerin_1    Dockerin type I 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 !   84.3   0.0   1.1e-27   9.4e-24       1     233 [.     118     365 ..     118     369 .. 0.92

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 1.1e-27
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....TS-BSBESSSB-HHHHHHH--SEEEE-GGG....GG CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..aivevgadgeidvEklaalkPDlvilskgl.gltde 74 
                                       i++l+ + +e + ++ a dk+vgv+ + +  +  d  +e  + ++vg+ +e+d+E+++ l PD+vi++ +  ++ + 
  gi|330508071|ref|YP_004384499.1| 118 IVVLNLACAESVRGIKAQDKIVGVGSSLVEGANRDFFPEmiDLPTVGKWSEPDIEAIISLNPDIVIADLRTpDPEKL 194
                                       89********************************99999********************************888899 PP

                                       GHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.....-EEEEEEEETT CS
                      Peripla_BP_2  75 deellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse....kpkpvlvfggad 147
                                       +++l+  gi +v + ++   +    +i+alg +l+++d a++l ++  +  + ++++++s+     p+ ++++++++
  gi|330508071|ref|YP_004384499.1| 195 EDKLEGTGITVVRMGFTYP-DYSSSEIMALGYILDRKDDARELNSFAGKYSDLIEERLSSIaeseRPRVYPIYYTSA 270
                                       9999999***********9.99999************************************9988888888888888 PP

                                       E..EEEE-TTSTTTHHHHTS--EESTTT--...STT-EEE-HHHHHHH--SEEEEEEH.......HHHT-S--HHHH CS
                      Peripla_BP_2 148 eggyvvagsnsyigdlldalgieniaaesk...kseyeeisaEqilasdpdvifvsgr.......aeadnktglefl 214
                                       +  ++  +++s +  l   +g+enia +     ++ y ++++E+++ ++p++if  ++        ++   +   ++
  gi|330508071|ref|YP_004384499.1| 271 D-LWKTGSNGSIVDMLCGLAGGENIAHDLTggtGGMYPTVDPEWVVGENPQIIFTWSSpggyslaNDSAMRELWTKI 346
                                       7.67766666666666777******999999***********************99999999987777777888899 PP

                                       T-SHHHHTSHHHHTT-EEE CS
                      Peripla_BP_2 215 kenpllaelpAvkngrVya 233
                                        + p+l+++ A+k  rV  
  gi|330508071|ref|YP_004384499.1| 347 VQAPELSRVDAAKDERVHL 365
                                       9************999966 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.7   0.00011      0.96       5      56 ..      41      87 ..      38      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                                      TSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHHHH CS
                        Dockerin_1  5 NgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallviny 56
                                      N D  +n  D++ +   +      ++s  ++  D N DG v+  D+ +v + 
  gi|330508071|ref|YP_004384499.1| 41 NMDDAINESDIAYLEDVIA-----GRSPATELSDANLDGIVDGKDIEQVERL 87
                                      8899********9999999.....888889999***************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2786.97
//
Query:       gi|330508072|ref|YP_004384500.1|  [L=357]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-25   89.9   0.0    4.5e-22   78.8   0.0    2.1  2  Peripla_BP_2     Periplasmic binding protein
  ------ inclusion threshold ------
       0.04   13.7   0.2      0.094   12.5   0.2    1.6  1  T2SS-T3SS_pil_N  Pilus formation protein N terminal region


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 !    9.2   0.0   8.8e-05      0.79       1      55 [.      44      97 ..      44     100 .. 0.94
   2 !   78.8   0.0     5e-26   4.5e-22      91     236 ..     145     303 ..     120     305 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 8.8e-05
                                      EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHH CS
                      Peripla_BP_2  1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEkl 55
                                      i++l+++ +e + alGa+d +vg ++  +  ++ ++l+ + +++g+ ++id+Ek+
  gi|330508072|ref|YP_004384500.1| 44 IIVLNTDAAEAVSALGASDLIVGLAEGIKEDYAFQGLK-ERPSIGTWSDIDFEKI 97
                                      89*********************999999999999998.9*************98 PP

  == domain 2  score: 78.8 bits;  conditional E-value: 5e-26
                                       -TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE...EEEE-TTSTTTHHHHT CS
                      Peripla_BP_2  91 sntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggade.ggyvvagsnsyigdllda 166
                                       ++  e+l +++r lg +lg+ed+ae+l+ ++d+ +a++++ +++++++ v++ g++ + g+++ +g +s  g ll+ 
  gi|330508072|ref|YP_004384500.1| 145 KE--ENLSRELRLLGSILGREDRAEELIDWHDRHVAEVEQGAKNLDRPRVFIEGSSRGlGDITTFGGSSASGMLLEK 219
                                       33..999**************************************77777777766667****************** PP

                                       S--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH................HHHT-S--HHHHT-SHHHHTSHHHH CS
                      Peripla_BP_2 167 lgieniaaeskkseyeeisaEqilasdpdvifvsgr................aeadnktgleflkenpllaelpAvk 227
                                       +g+ n+ +e   ++y ++ +E+++++dp+vi+ ++                 + +   ++  +++++p+++++ Avk
  gi|330508072|ref|YP_004384500.1| 220 AGGSNVMEE--DEAYPKVEWEWVVSQDPEVIIKTDYlkssdglpgwsltssgDVKALEEMRNDILSRPGAQNISAVK 294
                                       *********..8***************************************999999******************** PP

                                       TT-EEEE-H CS
                      Peripla_BP_2 228 ngrVyalds 236
                                       n rVy + +
  gi|330508072|ref|YP_004384500.1| 295 NDRVYVVSA 303
                                       *****9865 PP

>> T2SS-T3SS_pil_N  Pilus formation protein N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.1e-05     0.094       5      50 ..      25      70 ..      22      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.1e-05
                   T2SS-T3SS_pil_N  5 lelevgksrllrlpepvervavgnpkiadvtvlsprevlltGksvG 50
                                      l+++  + r+++lpepv+ ++v n + a+++   + + l++G ++G
  gi|330508072|ref|YP_004384500.1| 25 LTITDSAGRVVTLPEPVQGIIVLNTDAAEAVSALGASDLIVGLAEG 70
                                      67777889**********************9999999999998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2752.62
//
Query:       gi|330508073|ref|YP_004384501.1|  [L=372]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.9e-25   88.4   0.3    7.8e-25   87.8   0.0    1.5  2  DDE_Tnp_1  Transposase DDE domain
     0.0064   15.8   0.2      0.011   15.0   0.2    1.3  1  DDE_Tnp_2  Archaeal putative transposase ISC1217
  ------ inclusion threshold ------
      0.034   13.8   0.3       0.43   10.3   0.0    2.2  2  PRD1_DD    PRD1 phage membrane DNA delivery


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 !   87.8   0.0   1.3e-28   7.8e-25       2     212 ..      55     293 ..      54     295 .. 0.87
   2 ?   -3.2   0.1      0.88   5.3e+03     154     177 ..     299     322 ..     297     322 .. 0.80

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 1.3e-28
                         DDE_Tnp_1   2 skrevlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgk 78 
                                       ++r+vli D+t vr +++ ++ ++ +  +   +g+k+ ++v++ + ++ sv+i++ ++++ k++k    +    kgk
  gi|330508073|ref|YP_004384501.1|  55 QFRDVLIQDSTIVRLHSSLAKLYPAARSKGEAAGLKIAVLVSAVGNTPESVAIHNERTNELKTIKV--GPWI--KGK 127
                                       6899***************8888877755567**********************************..3333..9** PP

                         DDE_Tnp_1  79 lvlaDaGYasaelldtleekgvdyiirlkkntklyrk........................gaeskrrgrlrkhdrn 131
                                       ++l D G+ +++l+ +++e+g++ ++rlk+n++  +                          + +  + +++  +++
  gi|330508073|ref|YP_004384501.1| 128 ILLIDLGFYKYQLFARIAENGGFLVSRLKDNSNPMIIkanrswrgqsidvcgaylqdvlpkLKRQILDVEIEVSFKR 204
                                       *********************************99999997777666666666555555554666677777777777 PP

                         DDE_Tnp_1 132 kiltksqkrrnk........skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnr 200
                                       ++++ +++ +++          + +++++y+tn+ns+ l++e++  ly  Rw iE  Fk+lk+++ ld+l+++++  
  gi|330508073|ref|YP_004384501.1| 205 RAYKGVKRPDTHrfrlvaiyNDEDEKYHTYITNINSDILEPEDIGKLYGARWDIELMFKELKSRYALDALDTKNPLI 281
                                       777777777777999**99988888889************************************************* PP

                         DDE_Tnp_1 201 veaqllllllal 212
                                       +ea ++  +l+l
  gi|330508073|ref|YP_004384501.1| 282 IEALIWVAILTL 293
                                       *****9998877 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.88
                         DDE_Tnp_1 154 vtntnsellsaeevaelyrlRwqi 177
                                       +++  ++  + + ++++ +lRw i
  gi|330508073|ref|YP_004384501.1| 299 TYFNVRKIHPGKNIVRFTQLRWSI 322
                                       5667777788899999999**987 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.8e-06     0.011     244     287 ..     220     267 ..     210     299 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-06
                         DDE_Tnp_2 244 vlddykk.dgrrylfstdln...dtdediittWenrWdievlirelka 287
                                       ++  y++ d++ + + t++n   + +edi   +  rWdie +++elk+
  gi|330508073|ref|YP_004384501.1| 220 LVAIYNDeDEKYHTYITNINsdiLEPEDIGKLYGARWDIELMFKELKS 267
                                       455555515566789***99444479********************96 PP

>> PRD1_DD  PRD1 phage membrane DNA delivery
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.06   3.6e+02      21      31 ..      91     101 ..      88     106 .. 0.89
   2 ?   10.3   0.0   7.1e-05      0.43      11      29 ..     281     299 ..     278     302 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.06
                           PRD1_DD  21 lAvlvsrrsnt 31 
                                       +Avlvs   nt
  gi|330508073|ref|YP_004384501.1|  91 IAVLVSAVGNT 101
                                       8******9999 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 7.1e-05
                           PRD1_DD  11 vltAiiGvAilAvlvsrrs 29 
                                       ++ A+i vAil  lvsrr 
  gi|330508073|ref|YP_004384501.1| 281 IIEALIWVAILTLLVSRRT 299
                                       789**************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.39s 00:00:01.04 Elapsed: 00:00:00.59
# Mc/sec: 1895.46
//
Query:       gi|330508074|ref|YP_004384502.1|  [L=204]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-31  109.1   0.0    1.8e-31  108.9   0.0    1.1  1  DDE_3            DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.021   14.0   0.1      0.028   13.6   0.1    1.3  1  DUF815           Protein of unknown function (DUF815)
       0.09   12.7   0.1        6.4    6.8   0.0    2.2  2  P-mevalo_kinase  Phosphomevalonate kinase


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.9   0.0     3e-35   1.8e-31       2     145 ..      15     164 ..      14     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 3e-35
                             DDE_3   2 vvfiDEsgfqlgt.vrrrawakkGkrer.leeygrrgrvnligaldekgglafvtfeetlnaedfaeflerlletal 76 
                                       ++++DEs+ ql + +r+  +a +G++++ ++ey+r+g  n++ a ++  g+++++++e+++a d+a f+e+++ +++
  gi|330508074|ref|YP_004384502.1|  15 IICMDESPKQLISeTRKPIPASPGRSAKyDYEYKRCGMANIFLACEPLAGKRMIKVTERRTALDWAGFIEEIAAQYE 91 
                                       89***********9************877************************************************ PP

                             DDE_3  77 qakkivlilDnasiHkseslrelveee.....adrlellylPpySPelNpiEivwsklkrellkrrsfksldeL 145
                                       qa+ki l++Dn+++Hk+ s++e++  e     +dr+e++ +P++ ++lN+ Ei  ++l  ++l+ r++++++++
  gi|330508074|ref|YP_004384502.1|  92 QAEKITLVMDNLNTHKAGSFYEKFPPEkakalWDRFEFVHTPKHGSWLNIAEIELNVLWGQCLN-RRIDDIETV 164
                                       **************************99************************************.****99976 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.7e-06     0.028     182     244 ..     123     188 ..      84     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.7e-06
                            DUF815 182 LsdRFGlwlgFykldqeeYleiveklakkl.....glelek.eeleeeAlewalergsrsgRvArqfvk 244
                                       L dRF ++   +++++ ++l+i e  ++ l     + ++++ e++++eA++w+  r++++++v +qf++
  gi|330508074|ref|YP_004384502.1| 123 LWDRFEFV---HTPKHGSWLNIAEIELNVLwgqclNRRIDDiETVRKEAVAWQDIRNNKNAKVNWQFAT 188
                                       55666543...667777778887776644432222445555899***********************86 PP

>> P-mevalo_kinase  Phosphomevalonate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0011       6.4      61     112 ..      65     115 ..      62     117 .. 0.83
   2 ?    3.8   0.0    0.0086        51      54      84 ..     159     189 ..     147     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0011
                   P-mevalo_kinase  61 kemikwgeekrkkdpglFcraaiekieaakkdvliisDiRrktdleyfkeay 112
                                       k mik  e++   d + F++++  ++e+a+ ++ ++ D  +++    f e++
  gi|330508074|ref|YP_004384502.1|  65 KRMIKVTERRTALDWAGFIEEIAAQYEQAE-KITLVMDNLNTHKAGSFYEKF 115
                                       78**********************997766.999999987777766666666 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0086
                   P-mevalo_kinase  54 eykekyRkemikwgeekrkkdpglFcraaie 84 
                                       +  e++Rke + w + + +k++++ ++ a+ 
  gi|330508074|ref|YP_004384502.1| 159 DDIETVRKEAVAWQDIRNNKNAKVNWQFATA 189
                                       56799**********9999999986666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1528.01
//
Query:       gi|330508075|ref|YP_004384503.1|  [L=157]
Description: hypothetical protein MCON_2165 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.6e-15   56.8   0.0    1.6e-14   54.2   0.0    2.0  2  HTH_32      Homeodomain-like domain
    1.5e-13   50.5   0.2    7.5e-13   48.3   0.0    2.0  2  HTH_29      Winged helix-turn helix
    6.7e-07   28.9   0.4     0.0006   19.5   0.0    3.1  3  HTH_23      Homeodomain-like domain
    0.00038   20.5   0.1     0.0073   16.4   0.0    2.2  2  HTH_28      Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.1   0.1      0.025   14.3   0.1    1.5  2  RP-C        Replication protein C N-terminal domain
      0.018   14.7   0.1      0.045   13.4   0.1    1.6  1  PTRF_SDPR   PTRF/SDPR family
      0.042   14.3   0.0      0.046   14.2   0.0    1.2  1  SIMPL       Protein of unknown function (DUF541)
        0.2   11.2   2.5        2.4    7.7   0.2    2.8  3  Sigma70_r4  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.39   8.7e+02      37      55 ..       5      22 ..       1      58 [. 0.66
   2 !   54.2   0.0   7.2e-18   1.6e-14       2      73 .]      65     144 ..      64     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.39
                            HTH_32 37 iiallreeprWsprqlaar 55
                                      i+ l+ ee r +++ +a +
  gi|330508075|ref|YP_004384503.1|  5 IVTLT-EEERKTLSDIASK 22
                                      55555.3335555555543 PP

  == domain 2  score: 54.2 bits;  conditional E-value: 7.2e-18
                            HTH_32   2 vsrwlkRyneeGle.gLkdrprrgrp...rklsdevrariiallreep.....rWsprqlaarlaere.gvkvShst 68 
                                       + r+ kR+ e+Gl+ +L+ r   g +   +k++ + +a++ial ++ep     rWs+r+la++++e    +++Sh+t
  gi|330508075|ref|YP_004384503.1|  65 IDRVKKRFVEGGLDaALDKR--TGNRiyaKKTDGDFEAHLIALSCSEPpegfaRWSLRLLADKVVELNyIDSISHET 139
                                       67999*********555555..663323248***************999***************78875777***** PP

                            HTH_32  69 vyriL 73 
                                       v+riL
  gi|330508075|ref|YP_004384503.1| 140 VRRIL 144
                                       ****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 !   48.3   0.0   3.3e-16   7.5e-13       1      63 []      32     100 ..      32     100 .. 0.93
   2 ?   -0.5   0.0      0.59   1.3e+03      25      35 ..     136     146 ..     130     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 3.3e-16
                            HTH_29   1 RaqallllaeGvs.....tvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrsgrprnrlseeqea 63 
                                       +a++ll +++G +     t  ++ ++l++s+r+++r++krf+egGl+a+ld r +++ ++++ ++++ea
  gi|330508075|ref|YP_004384503.1|  32 NALILLGCDKGDYqtehsTNEEMSRVLQISMRKIDRVKKRFVEGGLDAALDkRTGNRIYAKKTDGDFEA 100
                                       589********99**************************************7777777777****9997 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.59
                            HTH_29  25 srrtvyrwlkr 35 
                                       s  tv+r+lk 
  gi|330508075|ref|YP_004384503.1| 136 SHETVRRILKK 146
                                       55688888875 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.85   1.9e+03      10      24 ..       5      20 ..       3      22 .. 0.79
   2 !   19.5   0.0   2.7e-07    0.0006      19      49 ..      50      80 ..      26      81 .. 0.81
   3 !    6.0   0.1    0.0047        11      29      41 ..     135     147 ..     134     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.85
                            HTH_23 10 illllae.GlsvreIA 24
                                      i+ l  e +++ ++IA
  gi|330508075|ref|YP_004384503.1|  5 IVTLTEEeRKTLSDIA 20
                                      6677777799999999 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.7e-07
                            HTH_23 19 svreIAreLgvsrrTvyrwlkryreeGlegl 49
                                      + +e +r L +s r ++r++kr++e+Gl++ 
  gi|330508075|ref|YP_004384503.1| 50 TNEEMSRVLQISMRKIDRVKKRFVEGGLDAA 80
                                      6778899********************9985 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0047
                            HTH_23  29 vsrrTvyrwlkry 41 
                                       +s+ Tv+r+lk+ 
  gi|330508075|ref|YP_004384503.1| 135 ISHETVRRILKKT 147
                                       89*********84 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.2e-06    0.0073      13      51 ..      48      87 ..      42      88 .. 0.84
   2 ?    1.8   0.0      0.12   2.6e+02      24      35 ..     135     146 ..     134     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.2e-06
                            HTH_28 13 h.svreaArelgisrrtvyrWikryeegGiagLvprrrrp 51
                                      h +  e +r l+is r + r  kr+ egG+++ +++r + 
  gi|330508075|ref|YP_004384503.1| 48 HsTNEEMSRVLQISMRKIDRVKKRFVEGGLDAALDKRTGN 87
                                      54566799**********************9999998765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.12
                            HTH_28  24 isrrtvyrWikr 35 
                                       is++tv+r +k+
  gi|330508075|ref|YP_004384503.1| 135 ISHETVRRILKK 146
                                       899*******98 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 ?   14.3   0.1   1.1e-05     0.025      73     122 ..      50      99 ..      24     106 .. 0.93
   2 ?   -3.1   0.0       2.3   5.2e+03      83      93 ..     135     145 ..     124     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                              RP-C  73 sNaqLsralglsestlrrhlaaLveaGliirrDspngkRyarrdreGeie 122
                                        N+++sr l++s +++ r+ ++ ve Gl +  D  +g R   ++++G+ e
  gi|330508075|ref|YP_004384503.1|  50 TNEEMSRVLQISMRKIDRVKKRFVEGGLDAALDKRTGNRIYAKKTDGDFE 99 
                                       69*******************************************99876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.3
                              RP-C  83 lsestlrrhla 93 
                                       +s++t+rr+l+
  gi|330508075|ref|YP_004384503.1| 135 ISHETVRRILK 145
                                       78889999886 PP

>> PTRF_SDPR  PTRF/SDPR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     2e-05     0.045     135     199 ..      24     154 ..       3     156 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                                       XXXXXXXXXX.XXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......................... CS
                         PTRF_SDPR 135 eteeeelekptidlssdeeeveveeeaeesraerlkrsslkkvdslKkaFs.......................... 185
                                       ++  +++ ++ i l  d   ++ +e++ +   +r+ + s++k+d +Kk F                           
  gi|330508075|ref|YP_004384503.1|  24 KQRSQKILNALILLGCDKG-DYQTEHSTNEEMSRVLQISMRKIDRVKKRFVeggldaaldkrtgnriyakktdgdfe 99 
                                       2333333334566777777.566666777889999***************988888888888888877777777777 PP

                                       .........................................XXXXXXXXXXXXXX CS
                         PTRF_SDPR 186 .........................................kenlektrqniekk 199
                                                                                +  l+ktr+++++k
  gi|330508075|ref|YP_004384503.1| 100 ahlialscseppegfarwslrlladkvvelnyidsishetvRRILKKTRSSLGNK 154
                                       7777777777777777777777777777777777777777777777777777766 PP

>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     2e-05     0.046      22      99 ..       9      72 ..       4     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                             SIMPL 22 vesegkdaaeakaevaekmnavlealkklgikekdiqtsslslkpeysyengknkitgyeasqsltvkfrdldklge.v 99
                                       e+e k++++ +++ +++++++l+al  lg ++ d+qt++ s+          n     e+s+ l+++ r++d++ + +
  gi|330508075|ref|YP_004384503.1|  9 TEEERKTLSDIASKGKQRSQKILNALILLGCDKGDYQTEH-ST----------N----EEMSRVLQISMRKIDRVKKrF 72
                                      46679**********************99*9999999999.44..........2....389999999999999855432 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.05   1.1e+02      12      27 ..       5      20 ..       2      31 .. 0.74
   2 ?   -1.5   0.0      0.83   1.9e+03      22      37 ..      50      65 ..      44      73 .. 0.64
   3 ?    7.7   0.2    0.0011       2.4      32      48 ..     135     151 ..     134     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.05
                                      HHHHHHTTT--HHHHH CS
                        Sigma70_r4 12 vlelrfgeglTleEIg 27
                                      +++l  +e  Tl++I+
  gi|330508075|ref|YP_004384503.1|  5 IVTLTEEERKTLSDIA 20
                                      5666667777777776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.83
                                      -HHHHHHHHTS-HHHH CS
                        Sigma70_r4 22 TleEIgerlgiSrerV 37
                                      T eE +++l+iS   +
  gi|330508075|ref|YP_004384503.1| 50 TNEEMSRVLQISMRKI 65
                                      5567777777775544 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0011
                                       S-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  32 iSrerVrqiekrAlrkL 48 
                                       iS e+Vr+i+k+++  L
  gi|330508075|ref|YP_004384503.1| 135 ISHETVRRILKKTRSSL 151
                                       9***********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); 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:                         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 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1161.72
//
Query:       gi|330508076|ref|YP_004384504.1|  [L=93]
Description: hypothetical protein MCON_2166 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-06   26.6   0.0    5.1e-06   26.2   0.0    1.2  1  DDE_Tnp_IS66  Transposase IS66 family
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.15   12.1   0.0    1.1  1  DUF2593       Protein of unknown function (DUF2593)


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 !   26.2   0.0   5.7e-10   5.1e-06      15      69 ..       2      57 ..       1      60 [. 0.95

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.7e-10
                      DDE_Tnp_IS66 15 lkyadhlPlyRqeeilarl.Gvelsrgtlanwvkraaelleplvealkaallasev 69
                                      lky+d lP ++++++l+rl G++ s++t+ ++++raae ++  ++a+ ++++ +++
  gi|330508076|ref|YP_004384504.1|  2 LKYEDRLPHRKIQDALRRLhGLNTSPATVVDLTRRAAEVVQSEYDAILNKIRCAPI 57
                                      79***********************************************9998776 PP

>> DUF2593  Protein of unknown function (DUF2593)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.7e-05      0.15      57      86 ..      49      78 ..      36      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                           DUF2593 57 lleircafavlrgrnwgrWlylltqiivvl 86
                                      l +irca  +++g+n  rW   ++qi  ++
  gi|330508076|ref|YP_004384504.1| 49 LNKIRCAPIMIQGHNCMRWRETICQIHKAI 78
                                      5579*********************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 672.39
//
Query:       gi|330508077|ref|YP_004384505.1|  [L=58]
Description: hypothetical protein MCON_2167 [Methanosaeta concilii GP6]
Scores for complete 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   19.4   1.1     0.0014   19.0   1.1    1.4  1  zf-IS66   zinc-finger binding domain of transposase IS66


Domain annotation for each model (and alignments):
>> 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 !   19.0   1.1   7.8e-08    0.0014      21      45 ..      18      43 ..       1      44 [. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.8e-08
                           zf-IS66 21 eeldip.PakfrViehirpkyaCpcC 45
                                       + +ip P+ + V+e+ +  y+Cp C
  gi|330508077|ref|YP_004384505.1| 18 VIEEIPkPQPVMVTEYNIANYRCPGC 43
                                      5779999******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 434.07
//
Query:       gi|330508078|ref|YP_004384506.1|  [L=123]
Description: hypothetical protein MCON_2168 [Methanosaeta concilii GP6]
Scores for complete sequence (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  118.4   7.9    1.6e-34  118.2   7.9    1.0  1  DUF2178          Predicted membrane protein (DUF2178)
     0.0028   17.2   0.7     0.0034   16.9   0.7    1.2  1  Intg_mem_TP0381  Integral membrane protein (intg_mem_TP0381)
  ------ inclusion threshold ------
       0.27   10.7   5.5        2.3    7.7   4.7    2.1  2  DUF1576          Protein of unknown function (DUF1576)
       0.35   10.7   0.1       0.35   10.7   0.1    1.9  2  Coat_X           Spore Coat Protein X and V domain


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 !  118.2   7.9   3.6e-38   1.6e-34       1     106 []       1     104 [.       1     104 [. 0.99

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 3.6e-38
                           DUF2178   1 lliivavialvglgiwaaignvllaviavaaGvllaillkkkveevveDERlariaekAsrktlqillfliallgvv 77 
                                       ++iiv ++alvg+ +  a+gn ll++i+++aGv+l++l+k+k++evveDER+++++ekAs+++++i++++++l+gvv
  gi|330508078|ref|YP_004384506.1|   1 MAIIVSMVALVGWFT--AAGNALLVAISITAGVVLLYLCKSKIKEVVEDERDVKVSEKASKLAIEIFAATNILIGVV 75 
                                       68*************..************************************************************ PP

                           DUF2178  78 livlksdfpeytrvgfllafsallllilY 106
                                       li+l+ +++eyt++gf+lafsa+ l+ilY
  gi|330508078|ref|YP_004384506.1|  76 LIALRYRYSEYTNIGFTLAFSASSLMILY 104
                                       ****************************9 PP

>> Intg_mem_TP0381  Integral membrane protein (intg_mem_TP0381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.7   7.6e-07    0.0034       6      93 ..      19     117 ..       3     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.6e-07
                   Intg_mem_TP0381   6 hilfllivillavlllllkrki...........rrkkkakkkrilkvialillileiflllwalaagypnlweslPL 71 
                                       + l+++i i++ v+ll+l++++           + ++ka k  i +++a  +li  +++ l + +++y n+  +l +
  gi|330508078|ref|YP_004384506.1|  19 NALLVAISITAGVVLLYLCKSKikevvederdvKVSEKASKLAIEIFAATNILIGVVLIALRYRYSEYTNIGFTLAF 95 
                                       455667777777777777777779999999887555666666777999999999999999999999*********** PP

                   Intg_mem_TP0381  72 hlCrlaiillaialitkkkklf 93 
                                         ++l+i+  +++ + +kk  +
  gi|330508078|ref|YP_004384506.1|  96 SASSLMILYSLLYGYYNKKYGY 117
                                       *********9999999998765 PP

>> DUF1576  Protein of unknown function (DUF1576)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   4.7   0.00051       2.3      59      93 ..       4      44 ..       2     102 .. 0.76
   2 ?    2.3   0.6     0.023     1e+02      78     107 ..      67      97 ..      58     115 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00051
                           DUF1576 59 iaailtvlg.FsafGknllNiipillGvlLyalvk.....k 93
                                      i ++++++g F a G+ ll  i+i++Gv+L++l+k      
  gi|330508078|ref|YP_004384506.1|  4 IVSMVALVGwFTAAGNALLVAISITAGVVLLYLCKskikeV 44
                                      55666666659*********************999655440 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.023
                           DUF1576  78 iipillGvlLyalvk.kesfkkyilaalfgt 107
                                        + il+Gv+L+al     + +++  +++f++
  gi|330508078|ref|YP_004384506.1|  67 ATNILIGVVLIALRYrYSEYTNIGFTLAFSA 97 
                                       5667888887776552333444444444543 PP

>> Coat_X  Spore Coat Protein X and V domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3      0.33   1.5e+03      38      47 ..      23      32 ..      15      35 .. 0.67
   2 ?   10.7   0.1   7.9e-05      0.35      22      53 ..      44      75 ..      38      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.33
                            Coat_X 38 aalsiqallq 47
                                      +a+si a + 
  gi|330508078|ref|YP_004384506.1| 23 VAISITAGVV 32
                                      5666666655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.9e-05
                            Coat_X 22 iIkdSenVtVtttDtqaalsiqallqtlialv 53
                                      +++d ++V+V+    ++a+ i a++++li +v
  gi|330508078|ref|YP_004384506.1| 44 VVEDERDVKVSEKASKLAIEIFAATNILIGVV 75
                                      79999************************554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 902.70
//
Query:       gi|330508079|ref|YP_004384507.1|  [L=74]
Description: hypothetical protein MCON_2169 [Methanosaeta concilii GP6]
Scores for complete 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   62.6   0.1      3e-17   62.4   0.1    1.1  1  HTH_3           Helix-turn-helix
      2e-09   37.3   0.1    2.4e-09   37.1   0.1    1.1  1  HTH_19          Helix-turn-helix domain
    1.3e-07   31.8   0.0    1.6e-07   31.6   0.0    1.0  1  HTH_31          Helix-turn-helix domain
    2.1e-07   31.3   0.0    2.5e-07   31.1   0.0    1.1  1  HTH_26          Cro/C1-type HTH DNA-binding domain
    0.00029   20.3   0.1     0.0005   19.5   0.1    1.4  1  Sigma70_r4      Sigma-70, region 4
     0.0012   18.8   0.1     0.0021   18.0   0.1    1.5  1  HTH_11          HTH domain
     0.0013   18.4   0.1      0.036   13.8   0.0    2.1  2  Sigma70_r4_2    Sigma-70, region 4
     0.0018   18.2   0.0     0.0037   17.2   0.0    1.5  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0046   16.5   0.0      0.007   15.9   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0079   16.0   0.0      0.011   15.6   0.0    1.3  1  HTH_25          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.024   14.5   0.0    1.4  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.045   13.1   0.0      0.063   12.6   0.0    1.2  1  DUF4941         Domain of unknown function (DUF4941)
      0.058   13.5   0.0       0.07   13.2   0.0    1.1  1  Phage_CI_repr   Bacteriophage CI repressor helix-turn-helix d
      0.066   13.0   0.0       0.12   12.2   0.0    1.5  1  HTH_23          Homeodomain-like domain
      0.066   13.0   0.0        0.1   12.4   0.0    1.3  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.082   12.6   0.0       0.16   11.7   0.0    1.5  1  GntR            Bacterial regulatory proteins, gntR family
      0.097   12.5   0.1       0.37   10.6   0.0    1.9  2  HTH_10          HTH DNA binding domain
       0.13   12.2   0.0       0.23   11.4   0.0    1.4  1  MarR            MarR 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 !   62.4   0.1     3e-20     3e-17       4      55 .]       8      59 ..       5      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 3e-20
                                      HHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHHH CS
                             HTH_3  4 lRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsldel 55
                                      +R  ++l+qeeLA+k+Gv+r+t+ +iE+G+ +Psl+ ++k+ak +gv+++e+
  gi|330508079|ref|YP_004384507.1|  8 YRAINDLTQEELAKKIGVTRQTVLAIEKGKYSPSLDLAFKMAKIFGVKIEEI 59
                                      566689*******************************************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 !   37.1   0.1   2.4e-12   2.4e-09       3      60 ..       4      60 ..       3      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.4e-12
                            HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyll 60
                                      r++ +R  + ltqeela+++g++r    aiE+gk+  ps +l  k a+++g+ +e+++
  gi|330508079|ref|YP_004384507.1|  4 RVRVYRAINDLTQEELAKKIGVTRQTVLAIEKGKY-SPSLDLAFKMAKIFGVKIEEIF 60
                                      889999999*************************9.******************9986 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.6e-10   1.6e-07       5      60 ..       4      58 ..       3      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.6e-10
                            HTH_31  5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpae 60
                                      ++r +R+   L+qee+A+ +gv++ t+  +E G+   ps++   ++a ++g+  +e
  gi|330508079|ref|YP_004384507.1|  4 RVRVYRAINDLTQEELAKKIGVTRQTVLAIEKGKY-SPSLDLAFKMAKIFGVKIEE 58
                                      689999999**************************.6**************97655 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 !   31.1   0.0   2.5e-10   2.5e-07       4      62 ..       7      64 ..       4      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.5e-10
                            HTH_26  4 elmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLleyep 62
                                      +  a +++t+ eLa+++g++++t+  + kgk  ++sld   k ++++g++++++++ye+
  gi|330508079|ref|YP_004384507.1|  7 VYRAINDLTQEELAKKIGVTRQTVLAIEKGK-YSPSLDLAFKMAKIFGVKIEEIFIYED 64
                                      55566789**********************9.6************************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 !   19.5   0.1     5e-07    0.0005      17      42 ..       8      35 ..       4      36 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5e-07
                                      H..TTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4 17 f..geglTleEIgerlgiSrerVrqiek 42
                                      +    +lT+eE++++ g++r +V  iek
  gi|330508079|ref|YP_004384507.1|  8 YraINDLTQEELAKKIGVTRQTVLAIEK 35
                                      33489******************88886 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   2.1e-06    0.0021      14      32 ..      12      30 ..       4      32 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.1e-06
                            HTH_11 14 gpisgeeLAeeLnvSrrtv 32
                                      ++++ eeLA++++v+r+tv
  gi|330508079|ref|YP_004384507.1| 12 NDLTQEELAKKIGVTRQTV 30
                                      679***************9 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   0.0   3.6e-05     0.036      21      43 ..       8      30 ..       7      30 .. 0.94
   2 ?    2.6   0.0      0.11   1.1e+02      18      32 ..      45      59 ..      43      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-05
                                      HHHTS---HHHHHHHHT--HHHH CS
                      Sigma70_r4_2 21 lryleglsykEIAellgisegtV 43
                                       r++++l+++E A+++g++ +tV
  gi|330508079|ref|YP_004384507.1|  8 YRAINDLTQEELAKKIGVTRQTV 30
                                      5899******************9 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                                      HHHHHHTS---HHHH CS
                      Sigma70_r4_2 18 ifllryleglsykEI 32
                                      +f +  ++g +++EI
  gi|330508079|ref|YP_004384507.1| 45 AFKMAKIFGVKIEEI 59
                                      799***********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 !   17.2   0.0   3.7e-06    0.0037      21      38 ..      13      30 ..       2      33 .. 0.87
   2 ?   -2.9   0.0       6.9   6.9e+03      27      37 ..      48      58 ..      47      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-06
                                      EHHHHHHHHHTTSSHHHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretv 38
                                      +ltqeelA  +G+tr+tv
  gi|330508079|ref|YP_004384507.1| 13 DLTQEELAKKIGVTRQTV 30
                                      79***************9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.9
                                      HHHHTTSSHHH CS
                         HTH_Crp_2 27 lAsmlGltret 37
                                      +A + G+  e 
  gi|330508079|ref|YP_004384507.1| 48 MAKIFGVKIEE 58
                                      79999998875 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 !   15.9   0.0     7e-06     0.007      17      36 ..      13      32 ..       7      33 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7e-06
                            HTH_24 17 risqreLAerlglSpstvnr 36
                                      +++q eLA+++g++++tv++
  gi|330508079|ref|YP_004384507.1| 13 DLTQEELAKKIGVTRQTVLA 32
                                      58****************86 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-05     0.011       9      36 ..      12      39 ..       5      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                                      TT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25  9 rglsleevaketkIrkdylealEeddfd 36
                                        l+ ee+ak++ +  +++ a+E+++++
  gi|330508079|ref|YP_004384507.1| 12 NDLTQEELAKKIGVTRQTVLAIEKGKYS 39
                                      689**********************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 ?   14.5   0.0   2.4e-05     0.024      10      32 ..      15      37 ..       8      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgk 32
                                      +q +LA+++gv++q+V    kgk
  gi|330508079|ref|YP_004384507.1| 15 TQEELAKKIGVTRQTVLAIEKGK 37
                                      699*************8876665 PP

>> DUF4941  Domain of unknown function (DUF4941)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.3e-05     0.063     215     245 ..      38      68 ..      32      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                           DUF4941 215 yseskklakkiaeefnlkleicplvdlPvgk 245
                                       ys s +la k+a+ f++k+e++ +++ P +k
  gi|330508079|ref|YP_004384507.1|  38 YSPSLDLAFKMAKIFGVKIEEIFIYEDPQEK 68 
                                       9************************999876 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     7e-05      0.07       5      58 ..       6      60 ..       5      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-05
                                      HHHHHHT-SSCHHHHCCTT--HHHHHHHHHSSS--.HHHHHHHHHHH---HHHHH CS
                     Phage_CI_repr  5 RlmsaygvkmqkeLAdlLgiakssvstwvrRdffP.gdvvvtcaletdtsLewLa 58
                                      R+  a++  +q+eLA+ +g+ +++v    +  + P  d+  ++a+  ++++e++ 
  gi|330508079|ref|YP_004384507.1|  6 RVYRAINDLTQEELAKKIGVTRQTVLAIEKGKYSPsLDLAFKMAKIFGVKIEEIF 60
                                      5667788889**************9766665555669999999999999999875 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.12      17      36 ..      13      32 ..       1      37 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                            HTH_23 17 GlsvreIAreLgvsrrTvyr 36
                                       l+++e A++ gv+r+Tv  
  gi|330508079|ref|YP_004384507.1| 13 DLTQEELAKKIGVTRQTVLA 32
                                      589**************965 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 ?   12.4   0.0    0.0001       0.1      18      35 ..      14      31 ..      12      32 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                     HTH_AsnC-type 18 isyaeLAervGlSestvl 35
                                      ++ +eLA+++G++++tvl
  gi|330508079|ref|YP_004384507.1| 14 LTQEELAKKIGVTRQTVL 31
                                      5789*************8 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.16      18      41 ..       8      30 ..       4      33 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                      S-TTSB---HHHHHHHHTS-HHHH CS
                              GntR 18 lrpGdkLPsereLaaefgVsrttv 41
                                      +r+   L +++eLa+++gV+r+tv
  gi|330508079|ref|YP_004384507.1|  8 YRAINDL-TQEELAKKIGVTRQTV 30
                                      5666679.9**************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 ?   10.6   0.0   0.00037      0.37      25      41 ..      15      31 ..      12      35 .. 0.88
   2 ?   -0.8   0.0       1.4   1.4e+03      28      36 ..      47      55 ..      43      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                            HTH_10 25 tlkeLAkelGIskstls 41
                                      t +eLAk++G++++t++
  gi|330508079|ref|YP_004384507.1| 15 TQEELAKKIGVTRQTVL 31
                                      679************86 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.4
                            HTH_10 28 eLAkelGIs 36
                                      ++Ak++G++
  gi|330508079|ref|YP_004384507.1| 47 KMAKIFGVK 55
                                      589999985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.23      16      34 ..      12      30 ..       5      33 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                      TTEEHHHHHHHHTS-HHHH CS
                              MarR 16 gplsvseLakklgvskstv 34
                                      ++l++ eLakk+gv++ tv
  gi|330508079|ref|YP_004384507.1| 12 NDLTQEELAKKIGVTRQTV 30
                                      459**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 580.82
//
Query:       gi|330508080|ref|YP_004384508.1|  [L=417]
Description: hypothetical protein MCON_2170 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00069   19.9   1.1         26    5.2   0.1    5.3  6  Colicin_E5     Colicin E5 ribonuclease domain
  ------ inclusion threshold ------
      0.027   14.6   1.1        6.2    6.9   0.0    3.9  3  DUF5597        Domain of unknown function (DUF5597)
       0.14   11.9   5.5        1.4    8.7   0.3    3.9  4  DUF1654        Protein of unknown function (DUF1654)
       0.28   11.2   1.7         13    5.9   0.1    3.6  4  CbiN           Cobalt transport protein component CbiN


Domain annotation for each model (and alignments):
>> Colicin_E5  Colicin E5 ribonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.58   2.6e+03      41      67 ..      55      81 ..      47      86 .. 0.77
   2 ?   -0.1   0.0      0.26   1.2e+03      36      66 ..     102     132 ..      97     136 .. 0.83
   3 !    5.2   0.1    0.0058        26      32      68 ..     150     186 ..     148     194 .. 0.91
   4 ?    3.4   0.0     0.022        97      32      67 ..     202     237 ..     200     241 .. 0.91
   5 ?    2.4   0.0     0.043   1.9e+02      32      67 ..     254     289 ..     252     300 .. 0.87
   6 ?    0.3   0.0      0.19   8.6e+02      38      65 ..     366     393 ..     357     396 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.58
                        Colicin_E5 41 anktsDglrrndsAtvYgekdgkYvvv 67
                                      ++++  g + +   +v   kdg+Y++ 
  gi|330508080|ref|YP_004384508.1| 55 WHRSYGGAGSDVGNSVLEVKDGGYIIA 81
                                      5556667888888899999******96 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.26
                        Colicin_E5  36 sddkranktsDglrrndsAtvYgekdgkYvv 66 
                                       + ++++n+t  g   +   +v   +dg Y+ 
  gi|330508080|ref|YP_004384508.1| 102 NGNEKWNRTFGGSDDDSGVSVMQINDGSYIF 132
                                       5678899999999999999999999999995 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0058
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvn 68 
                                       kt+s  ++r+nkt  g + +   +v   kdg+Y++  
  gi|330508080|ref|YP_004384508.1| 150 KTNSDGKERWNKTYGGASYDWGYSVQEIKDGGYIIAG 186
                                       7899999***************************976 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.022
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt s+ ++ +n+t  g + + s ++   kd++Yv+ 
  gi|330508080|ref|YP_004384508.1| 202 KTDSTGNELWNRTFGGPKDDGSHAIRRTKDDGYVIA 237
                                       78999999*****99999999999999*******95 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.043
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt s  ++ +n t  g r +   +v   kdg+Y++ 
  gi|330508080|ref|YP_004384508.1| 254 KTDSAGNELWNITFGGSRDDRGESVQQVKDGGYIIA 289
                                       67888899999999999989999***********96 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 0.19
                        Colicin_E5  38 dkranktsDglrrndsAtvYgekdgkYv 65 
                                        k++++  D  +rn+  +v    dg Y+
  gi|330508080|ref|YP_004384508.1| 366 MKQWDEVFDESGRNEGLSVQQAGDGSYI 393
                                       577888999*************999998 PP

>> DUF5597  Domain of unknown function (DUF5597)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0014       6.2      40      85 ..      92     136 ..      80     145 .. 0.86
   2 ?    0.4   0.0      0.14   6.5e+02      45      84 ..     201     239 ..     188     243 .. 0.79
   3 ?    2.4   0.1     0.035   1.6e+02      55     107 ..     318     371 ..     252     401 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0014
                           DUF5597  40 lgdweltvrygfpqfwdeaapgseepegggliiqlgedefllaGig 85 
                                        ++w ++++   +++w +++ g+++   g+ ++q++++ +++aG  
  gi|330508080|ref|YP_004384508.1|  92 DDAWLVEADQNGNEKW-NRTFGGSDDDSGVSVMQINDGSYIFAGAT 136
                                       5788999999999888.67899999999****************75 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.14
                           DUF5597  45 ltvrygfpqfwdeaapgseepegggliiqlgedefllaGi 84 
                                       ++ + + ++ w +++ g+++  g   i ++++d +++aG 
  gi|330508080|ref|YP_004384508.1| 201 IKTDSTGNELW-NRTFGGPKDDGSHAIRRTKDDGYVIAGF 239
                                       55555555555.5788999999999*************96 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.035
                           DUF5597  55 wde.aapgseepegggliiqlgedefllaGigvrvtfksktekakrvgilrvee 107
                                       w++    g+++ + g    ++ ++ ++laG+g+   + s   k+++vg+ + +e
  gi|330508080|ref|YP_004384508.1| 318 WGRiFSFGDSDYNIGTAAQETTDGGYILAGYGLGAGIYSWLIKNDNVGMKQWDE 371
                                       444344444444445555555555555555554433333333333333333333 PP

>> DUF1654  Protein of unknown function (DUF1654)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2     0.074   3.3e+02      27      60 ..      96     129 ..      91     133 .. 0.86
   2 ?   -1.7   0.1      0.56   2.5e+03      27      40 ..     148     161 ..     145     182 .. 0.68
   3 ?    1.1   0.0     0.074   3.3e+02      15      42 ..     293     322 ..     288     337 .. 0.85
   4 ?    8.7   0.3   0.00031       1.4      30      67 ..     361     399 ..     356     402 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.074
                           DUF1654  27 vlrledeseddWerlleeiaeteevelafrdDgs 60 
                                       ++ +++++++ W+r  +  ++  +v++   +Dgs
  gi|330508080|ref|YP_004384508.1|  96 LVEADQNGNEKWNRTFGGSDDDSGVSVMQINDGS 129
                                       667899999******9999999999999999997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.56
                           DUF1654  27 vlrledeseddWer 40 
                                       +++ ++++++ W++
  gi|330508080|ref|YP_004384508.1| 148 LIKTNSDGKERWNK 161
                                       56777777777775 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.074
                           DUF1654  15 naPaaQkara..avvlrledeseddWerll 42 
                                       naP a k+ +  a ++r ++++  +W+r+ 
  gi|330508080|ref|YP_004384508.1| 293 NAPLANKSLMgdAWLIRTDSNGTMQWGRIF 322
                                       889999986444999***********9986 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.00031
                           DUF1654  30 ledeseddWerlleeiaeteevelafrdDgs.vrirWer 67 
                                        ++ + ++W+++ +e  ++e+++++   Dgs +   W+ 
  gi|330508080|ref|YP_004384508.1| 361 NDNVGMKQWDEVFDESGRNEGLSVQQAGDGSyISTGWTI 399
                                       55667789**********************967788875 PP

>> CbiN  Cobalt transport protein component CbiN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.069   3.1e+02       7      34 ..      32      69 ..      27      78 .. 0.52
   2 ?    5.9   0.1    0.0028        13      22      40 ..     109     127 ..      95     134 .. 0.79
   3 ?   -0.9   0.0      0.37   1.7e+03      22      40 ..     213     231 ..     201     235 .. 0.80
   4 ?   -1.8   0.0      0.69   3.1e+03      23      38 ..     266     281 ..     252     286 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.069
                              CbiN  7 lvvllavvplflv.....kgae.....FgGaDdqaeev 34
                                      l++ll+++ l++      +++e     +gGa +   + 
  gi|330508080|ref|YP_004384508.1| 32 LAILLMLLLLLYTfgtfaPQEEmwhrsYGGAGSDVGNS 69
                                      33333333333335555555556777788886555555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0028
                              CbiN  22 aeFgGaDdqaeevIeeiap 40 
                                         FgG+Dd     +++i+ 
  gi|330508080|ref|YP_004384508.1| 109 RTFGGSDDDSGVSVMQIND 127
                                       34***********999964 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.37
                              CbiN  22 aeFgGaDdqaeevIeeiap 40 
                                         FgG  d ++++I + + 
  gi|330508080|ref|YP_004384508.1| 213 RTFGGPKDDGSHAIRRTKD 231
                                       45************98744 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.69
                              CbiN  23 eFgGaDdqaeevIeei 38 
                                        FgG+ d   e ++++
  gi|330508080|ref|YP_004384508.1| 266 TFGGSRDDRGESVQQV 281
                                       3999955555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2962.26
//
Query:       gi|330508081|ref|YP_004384509.1|  [L=416]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete sequence (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   86.2   0.0    2.4e-24   85.4   0.0    1.4  1  Transposase_20  Transposase IS116/IS110/IS902 family
    5.2e-23   81.6   0.0    1.1e-22   80.6   0.0    1.5  1  DEDD_Tnp_IS110  Transposase
  ------ inclusion threshold ------
        1.8    8.9   4.4        5.8    7.3   0.2    2.8  2  DUF4164         Domain of unknown function (DUF4164)


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0     4e-28   2.4e-24       3      86 ..     250     334 ..     248     335 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 4e-28
                    Transposase_20   3 lLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaairan 79 
                                       + +sipG G+v a+a+laeig+ + f++++qlaa++Gl+p+ +qS++k   g+i+k+G++++Rr+L++ A a++r++
  gi|330508081|ref|YP_004384509.1| 250 IAMSIPGTGFVSATAILAEIGNYTDFEKPEQLAAWCGLVPSLYQSAEKTILGGITKQGSKHIRRMLIQVAYAISRTK 326
                                       679*********************************************99************************998 PP

                    Transposase_20  80 .pelrayy 86 
                                        ++l++++
  gi|330508081|ref|YP_004384509.1| 327 dSKLKKFF 334
                                       79999885 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.0   1.8e-26   1.1e-22       1     154 [.       9     153 ..       9     154 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.8e-26
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +GiDv+k+   a+++ ++gk+  ++r++ + e+l ++ ++   + g+ +v++e+tg y+ ++v+ +le +i+++v n
  gi|330508081|ref|YP_004384509.1|   9 CGIDVHKRFLIATILCRDGKK-DTQRFSVTLEDLLKFRDW-VIENGCEQVAIESTGIYW-HPVHSVLEGKIDLIVAN 82 
                                       7*******************9.6779******9*999999.77899*************.56778899********* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdqvf 154
                                        +++k++      ++KtD  D+++IA+l +  g ++p++  +++ +eLr+ltr+re +vk++t++kn++++ Ld+ +
  gi|330508081|ref|YP_004384509.1|  83 SYKIKHT-----PGRKTDVSDSEWIAELCL-NGMIEPSRIFPKDDRELRRLTRAREGYVKQMTQEKNKIHQSLDSAC 153
                                       ******9.....59****************.******************************************9876 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2   0.00098       5.8      33      64 ..     127     158 ..     119     161 .. 0.82
   2 ?    1.8   0.6     0.048   2.9e+02      11      31 ..     224     244 ..     189     254 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00098
                           DUF4164  33 krdeleaeiealgedrsRLaeeLdqaearaar 64 
                                        ++++e  +++++++++++ + Ld+a  ++a+
  gi|330508081|ref|YP_004384509.1| 127 LTRAREGYVKQMTQEKNKIHQSLDSACIKLAS 158
                                       45788999*****************9888776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.048
                           DUF4164  11 trLeaaldsLEkavdrrleae 31 
                                       + +++ +d+L++ + +r++  
  gi|330508081|ref|YP_004384509.1| 224 KSIQERIDELDGEISARIQYR 244
                                       456666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2833.80
//
Query:       gi|330508082|ref|YP_004384510.1|  [L=446]
Description: cell surface protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   57.8  59.1    2.5e-09   37.2  26.0    4.1  2  Beta_helix       Right handed beta helix region
    4.7e-14   52.2  43.3    4.2e-13   49.1  25.3    3.0  3  NosD             Periplasmic copper-binding protein (NosD)
    5.8e-06   26.3  27.6      0.088   12.6   3.3    4.3  5  Pectate_lyase_3  Pectate lyase superfamily protein
     0.0048   17.0   2.7       0.23   11.6   0.1    3.4  4  Pentapeptide_4   Pentapeptide repeats (9 copies)


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 !   10.3  35.5    0.0001      0.45       2     156 ..      75     357 ..      19     361 .. 0.62
   2 !   37.2  26.0   5.6e-13   2.5e-09       2     137 ..     298     424 ..     297     445 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0001
                                       SEEE-SS-E..EEESEEEES-.......SS-SEEE-SSS-.EEES-EEES.........................-S CS
                        Beta_helix   2 gisingssn.vtiknntisns.......ggyGiylrgssnvvienneian.........................ns 45 
                                       gi+i++++  + ikn+ti+n+        + G+y+++++n+ i ++++++                         ++
  gi|330508082|ref|YP_004384510.1|  75 GIVISNTNAhILIKNCTIENPngkynrrFSKGVYIKNAKNIQINDCRLNGceiflenaetcqikrssapitvsneSR 151
                                       78888877778889999988888888888888888888884444444444444443333333333333333333444 PP

                                       S-SEEE-TT....-S-EEES-EEE---SEEE-TT--S--EEES-EEES-............................ CS
                        Beta_helix  46 gsGiyilgs....snntisnntisdnngggialfgasnnlienneitdn............................ 90 
                                        sG++ l+s    +++ i++++i +   gg+a+f+a n +i+++  ++                             
  gi|330508082|ref|YP_004384510.1| 152 SSGLSNLKSqlksQDCLIEGCKIDN---GGLAFFEATNFIIKDCYLENGpiimehpinftfsnvtllnssldifsps 225
                                       4444444444444555555555542...3355555555555555555555555444444444444444343333333 PP

                                       ..................SS-....................................................SEE- CS
                        Beta_helix  91 ..................ggs....................................................Giyl 97 
                                                         g                                                      Gi+l
  gi|330508082|ref|YP_004384510.1| 226 nvsftgvnliepkinlmfG-LdgypleiknstvnglniyyyknkhgikirnlkagyiwlanctkaelnkteslGIFL 301
                                       3333333333333333330.033333333333333333333333433333333333333355555555556668888 PP

                                       TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES- CS
                        Beta_helix  98 nyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnN 156
                                         s+n +ien+ +++++ +Gi ++ s+ n+ ++n ++ n++ +Gi++ ++s+n+t+++ 
  gi|330508082|ref|YP_004384510.1| 302 LRSNNSVIENSKVNDVG-HGILLSLSE-NCIMENVSLPNSR-KGITIGYGSDNTTLNQS 357
                                       88***************.*********.**99999999887.*********97777665 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 5.6e-13
                                       SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT.-S-EEES-EEE---SEEE-TT.- CS
                        Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgs.snntisnntisdnngggialf.g 76 
                                       gi++ +s+n  i+n+++++  g+Gi l  s+n+++en  + n s  Gi i ++ +n+t+  + i   +   i ++ +
  gi|330508082|ref|YP_004384510.1| 298 GIFLLRSNNSVIENSKVND-VGHGILLSLSENCIMENVSLPN-SRKGITIGYGsDNTTLNQSFIKSET---IGVDiY 369
                                       8999999999*********.5***************888888.9999999988455555555555555...555556 PP

                                       -S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES- CS
                        Beta_helix  77 asnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnn 137
                                       +++n i nn itd    Gi+l+  sn ti  N++ nn+  Gi    s+ ++  ++N+++ n
  gi|330508082|ref|YP_004384510.1| 370 SNRNKITNNLITDSYI-GISLF-GSNSTIMQNTLINNS-IGIDAKVSN-SI--EHNNLSYN 424
                                       8889999999999965.99999.699999999999999.888888888.33..66655544 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   8.9   0.00044         2      11      76 ..      68     140 ..      41     196 .. 0.61
   2 ?    3.1   0.1     0.011        49      21      99 ..     129     213 ..     124     228 .. 0.60
   3 !   49.1  25.3   9.4e-17   4.2e-13       4     181 ..     256     433 ..     243     439 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00044
                              NosD  11 lvsargngiqlens......egsei...snneisnsrdgilldnssnntitgntienlryGihlensesntiedn 76 
                                       ++   gngi+++n+      ++++i   ++++ ++ ++g++++n++n++i +++++ +   i+len+e + i+ +
  gi|330508082|ref|YP_004384510.1|  68 IINHTGNGIVISNTnahiliKNCTIenpNGKYNRRFSKGVYIKNAKNIQINDCRLNGC--EIFLENAETCQIKRS 140
                                       3333566666666655555555555433444444444555777777777777766666..666666666555443 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.011
                              NosD  21 lensegsei.....snneisnsrdgi.....lldnssnntitgntienlryGihlensesntiedntlssnesGial 87 
                                       len+e ++i       +  ++sr++         +s+++ i+g++i n+  G+ + ++ + +i+d+ l++   G ++
  gi|330508082|ref|YP_004384510.1| 129 LENAETCQIkrssaPITVSNESRSSGlsnlkSQLKSQDCLIEGCKIDNG--GLAFFEATNFIIKDCYLEN---GPII 200
                                       5555555555544212222222333333335556777777777777777..9999999999999999887...6666 PP

                              NosD  88 msssnn.tlenNt 99 
                                       m+   n t++n t
  gi|330508082|ref|YP_004384510.1| 201 MEHPINfTFSNVT 213
                                       6666554555444 PP

  == domain 3  score: 49.1 bits;  conditional E-value: 9.4e-17
                              NosD   4 aisgdevlvsargngiqlensegsei.....snneisnsrd.gilldnssnntitgntienlryGihlensesntie 74 
                                       ++ g +++ +++++gi++ n +   i     ++ e++++++ gi+l  s+n  i+++++++  +Gi l+ se++++e
  gi|330508082|ref|YP_004384510.1| 256 TVNGLNIYYYKNKHGIKIRNLKAGYIwlancTKAELNKTESlGIFLLRSNNSVIENSKVNDVGHGILLSLSENCIME 332
                                       44555555555666777777644444444443444444333155777777777777777777777777777777777 PP

                              NosD  75 dntlssnesGialmsssnn.tlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqk 150
                                       +  l ++++Gi++ + s+n tl+++ i++ ++ G+ +  s+ n+i+nN i++++ Gi+l + s++ti++N++ +n +
  gi|330508082|ref|YP_004384510.1| 333 NVSLPNSRKGITIGYGSDNtTLNQSFIKSETI-GVDIY-SNRNKITNNLITDSYIGISLFG-SNSTIMQNTLINN-S 405
                                       77777777777777777775666666666655.66553.4446677777777777777777.4777777777777.6 PP

                              NosD 151 iGilllsssegntiynNyFinnsenvkydgs 181
                                       iGi    +  +n+i  N++  n ++vk dg 
  gi|330508082|ref|YP_004384510.1| 406 IGID---AKVSNSIEHNNLSYNLIDVKRDGI 433
                                       6666...555677777777777777776665 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 !   12.6   3.3     2e-05     0.088     145     210 ..      45     125 ..      20     129 .. 0.67
   2 !    4.8   0.0    0.0049        22     147     208 ..     143     215 ..     127     233 .. 0.71
   3 !    6.2   0.8    0.0018       8.2     157     214 ..     256     321 ..     212     322 .. 0.75
   4 !   12.1   0.8     3e-05      0.13     135     214 ..     252     343 ..     244     344 .. 0.83
   5 !   12.6   7.2     2e-05     0.088     131     211 ..     327     405 ..     324     434 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                                       -TT---SS--E.....EEEES-EEES-SS-SEEES..-EEEEEES-EEE-........S--SEEE-TT-EEEEEEEE CS
                   Pectate_lyase_3 145 hqgifiengsg.....gflndlvfsglgdigiavg..nqqftvrnitfnn........attgievlwgwgwtlknvk 206
                                       + +++  +gsg      +++d+v+ +  + gi ++  n ++ ++n+t++n         + g++++  +++ +++++
  gi|330508082|ref|YP_004384510.1|  45 NADLTKYEGSGtvedpYIIRDIVIINHTGNGIVISntNAHILIKNCTIENpngkynrrFSKGVYIKNAKNIQINDCR 121
                                       3355555566655543334999999989999999656889999*******666666665666666655566666666 PP

                                       EESS CS
                   Pectate_lyase_3 207 innc 210
                                       +n+c
  gi|330508082|ref|YP_004384510.1| 122 LNGC 125
                                       6666 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0049
                                       T---SS--E....EEE......ES-EEES..-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEE CS
                   Pectate_lyase_3 147 gifiengsg....gfl......ndlvfsg..lgdigiav.gnqqftvrnitfnnattgievlwgwgwtlknvkin 208
                                        i+++n s+    + l      +d+ ++g  +++ g+a+    +f++++++ +n    +e     ++t++nv++ 
  gi|330508082|ref|YP_004384510.1| 143 PITVSNESRssglSNLksqlksQDCLIEGckIDNGGLAFfEATNFIIKDCYLENGPIIMEH--PINFTFSNVTLL 215
                                       46666666654442223333567999999999999999999************95554444..577777777664 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0018
                                       EE..ES-EEES-SS-SEEES...-EEEEEES-EEE-....S--SEEE-TT-EEEEEEEEEESSSEEE CS
                   Pectate_lyase_3 157 fl..ndlvfsglgdigiavg...nqqftvrnitfnn....attgievlwgwgwtlknvkinncegGi 214
                                       ++   ++ +++  ++gi+++     ++++ n+t  +     + gi +l++++ +++n k+n+ + Gi
  gi|330508082|ref|YP_004384510.1| 256 TVngLNIYYYK-NKHGIKIRnlkAGYIWLANCTKAElnktESLGIFLLRSNNSVIENSKVNDVGHGI 321
                                       33223555555.7888888557667788888888777777788888888888888888888888887 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 3e-05
                                       SEEE-SSS......---TT---SS--EEEE.....ES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-E CS
                   Pectate_lyase_3 135 femseasg......tkhqgifiengsggfl.....ndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwg 199
                                       +++s+ +g      +++ gi i+n + g++     + ++ ++++  gi + ++++++++n ++n+ + gi ++ +++
  gi|330508082|ref|YP_004384510.1| 252 IKNSTVNGlniyyyKNKHGIKIRNLKAGYIwlancTKAELNKTESLGIFLlRSNNSVIENSKVNDVGHGILLSLSEN 328
                                       4455555555555556669*****99999999777777888899******99********************99999 PP

                                       EEEEEEEEESSSEEE CS
                   Pectate_lyase_3 200 wtlknvkinncegGi 214
                                        +++nv++ n+ +Gi
  gi|330508082|ref|YP_004384510.1| 329 CIMENVSLPNSRKGI 343
                                       *******99999998 PP

  == domain 5  score: 12.6 bits;  conditional E-value: 2e-05
                                       ES-SSEEE-SSS---TT---SS--EEEE.ES-EEES-SS-SEEES-EEEEEES-EEE-S--SEEE-TT-EEEEEEEE CS
                   Pectate_lyase_3 131 envefemseasgtkhqgifiengsggfl.ndlvfsglgdigiavgnqqftvrnitfnnattgievlwgwgwtlknvk 206
                                       en+++e+ +   ++ +gi+i +gs ++  n ++++  + ig+ + ++   ++n+ ++++  gi++  +++ +++n  
  gi|330508082|ref|YP_004384510.1| 327 ENCIMENVSLP-NSRKGITIGYGSDNTTlNQSFIKS-ETIGVDIYSNRNKITNNLITDSYIGISLFGSNSTIMQNTL 401
                                       56766676666.7889*********88857777777.*******555555555556666999999944446665555 PP

                                       EESSS CS
                   Pectate_lyase_3 207 innce 211
                                       inn  
  gi|330508082|ref|YP_004384510.1| 402 INN-S 405
                                       554.3 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.018        80      21      62 ..      85     136 ..      81     142 .. 0.56
   2 !   11.6   0.1   5.2e-05      0.23       5      63 ..     166     234 ..     164     242 .. 0.83
   3 ?   -3.5   0.0       2.8   1.3e+04       5      14 ..     328     337 ..     327     339 .. 0.57
   4 ?   -2.6   0.0       1.4   6.5e+03      33      53 ..     390     412 ..     376     422 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.018
                    Pentapeptide_4  21 arlrdcnFtecrl.........snvn...FdecnlsdvdfaevdlkrasFsgcn 62 
                                       + +++c++++++          +       ++ +++d+++++++++  + + c+
  gi|330508082|ref|YP_004384510.1|  85 ILIKNCTIENPNGkynrrfskgV--YiknAKNIQINDCRLNGCEIFLENAETCQ 136
                                       55777888877776555555331..12234555666666666665555555554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.2e-05
                    Pentapeptide_4   5 rcsfnncklsn..vnFsea...rlrdcnFtecrl.....snvnFdecnlsdvdfaevdlkrasFsgcnl 63 
                                       +c  ++ck +n  + F ea    ++dc +++ ++      n +F++ +l ++++   ++ ++sF+g+nl
  gi|330508082|ref|YP_004384510.1| 166 DCLIEGCKIDNggLAFFEAtnfIIKDCYLENGPIimehpINFTFSNVTLLNSSLDIFSPSNVSFTGVNL 234
                                       677778888774455555566689999999999999*999999************************99 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.8
                    Pentapeptide_4   5 rcsfnnckls 14 
                                       +c ++n+ l 
  gi|330508082|ref|YP_004384510.1| 328 NCIMENVSLP 337
                                       6666666654 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1.4
                    Pentapeptide_4  33 l..snvnFdecnlsdvdfaevdl 53 
                                       +  +++ +++++++++   +++ 
  gi|330508082|ref|YP_004384510.1| 390 FgsNSTIMQNTLINNSIGIDAKV 412
                                       25577888888888887666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2990.09
//
Query:       gi|330508083|ref|YP_004384511.1|  [L=309]
Description: hypothetical protein MCON_2173 [Methanosaeta concilii GP6]
Scores for complete 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  128.8   0.3    1.7e-37  127.9   0.3    1.4  1  PatG_C    PatG C-terminal
    2.3e-32  111.7   0.1    1.2e-30  106.2   0.1    2.2  1  PatG_D    PatG Domain
  ------ inclusion threshold ------
      0.011   16.2   0.1      0.022   15.2   0.1    1.5  1  ZapA      Cell division protein ZapA


Domain annotation for each model (and alignments):
>> PatG_C  PatG C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.9   0.3   2.9e-41   1.7e-37       1     115 []     195     306 ..     195     306 .. 0.98

  Alignments for each domain:
  == domain 1  score: 127.9 bits;  conditional E-value: 2.9e-41
                            PatG_C   1 ekqeeeftkairevLdrvlqelrNlGatdedRAlNylatrapdiyretaelileslsLdsveveksplsradsdcvd 77 
                                       ekqee+f++a++e++dr+lq+++N+Gatde+RAlNyla+r+p iy+++ae++++++sL++ve+++s+ls+  +++v+
  gi|330508083|ref|YP_004384511.1| 195 EKQEEKFRAAANELFDRILQMADNTGATDEHRALNYLAVRYPAIYANAAEEFERNFSLTGVEARPSRLSGE-RKIVS 270
                                       5899******************************************************************9.***** PP

                            PatG_C  78 VkltftnkenssraekkyrvtvDVseelPflvtkvqsy 115
                                       V++++tn+  ++++++k++v+vDVsee+Pf+vtk+ +y
  gi|330508083|ref|YP_004384511.1| 271 VIFSYTNR--ETDVTEKFFVRVDVSEEFPFMVTKMAPY 306
                                       *******9..9************************998 PP

>> PatG_D  PatG Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.1   1.9e-34   1.2e-30       1      99 [.      54     245 ..      54     258 .. 0.93

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 1.9e-34
                            PatG_D   1 lvYviGrieadFpnearekefvqalaraktanpedqqalakvLsnrenrylaralsWiLtiegipiYvllPn..... 72 
                                       +vY++G+ie++F ++a+e+efvqa++ra+t + +dqqa+++vLs++enryl+r+l+W+L ieg+  Y+llP+     
  gi|330508083|ref|YP_004384511.1|  54 YVYALGKIEPRFRSMAVEREFVQATGRAETTGLTDQQAFYSVLSKKENRYLVRDLCWTLAIEGVAAYILLPKdpldf 130
                                       8**************************************************************************** PP

                            PatG_D  73 .......................................................................kpfale 78 
                                                                                                               ++a+e
  gi|330508083|ref|YP_004384511.1| 131 drlvesvkpqqdkagidvvvgskgpvalpemcaglqvpivgfdqlfsfnreefirsiprpesipekqeekfRAAANE 207
                                       ***********************************************************************999*** PP

                            PatG_D  79 lfarliealdnqedteesra.................d 99 
                                       lf+r+++++dn+++t+e+ra                 +
  gi|330508083|ref|YP_004384511.1| 208 LFDRILQMADNTGATDEHRAlnylavrypaiyanaaeE 245
                                       *******************9777766655555554441 PP

>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   3.8e-06     0.022      13      53 ..     192     232 ..     191     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.8e-06
                              ZapA  13 aceegeeeylreaaklvdekikeireaggnlseerllvmaa 53 
                                       +++e +ee  r+aa+++ ++i ++ +++g  +e r+l   a
  gi|330508083|ref|YP_004384511.1| 192 SIPEKQEEKFRAAANELFDRILQMADNTGATDEHRALNYLA 232
                                       5899**************************9*999986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2172.06
//
Query:       gi|330508084|ref|YP_004384512.1|  [L=212]
Description: hypothetical protein MCON_2175 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-12   46.2   0.0    5.6e-12   45.6   0.0    1.2  1  DDE_5      DDE superfamily endonuclease
    6.3e-05   22.4   0.9     0.0051   16.1   0.9    2.1  1  DDE_Tnp_2  Archaeal putative transposase ISC1217
  ------ inclusion threshold ------
        1.2    9.4   7.6        2.3    8.5   7.4    1.6  1  Mlp        Mlp lipoprotein family


Domain annotation for each model (and alignments):
>> DDE_5  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   9.3e-16   5.6e-12       4     186 ..      30     205 ..      27     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 9.3e-16
                             DDE_5   4 ealtradrrrglllylrgllldggrksvepmaarl...ehdg.shqalqrflsrspwddaklrrrlarlvl.pll.a 74 
                                       + +t+ +  + ++ ++ +l  + + k+v ++  ++   + +  s+ ++  f+s+++wd+ ++ +r  +l +  l+ +
  gi|330508084|ref|YP_004384512.1|  30 DLFTKPSYGS-FRDLCGALSVCDKSKTVSNLCDTMadcSKGKkSRSSYNWFFSDANWDENEVAQRKVDLFIdSLClK 105
                                       5555444444.67777777777777***********9955555999*****************99999999655514 PP

                             DDE_5  75 peaav.laiDdTgfpkdGkasvgvarqycgalgkadncqvavslglatervsapldwrlylpeswaqdlsarrrrag 150
                                       + + + l+iDdT   k G ++ gv+++y++++   + ++ +v+  + ++  ++p +   y++              +
  gi|330508084|ref|YP_004384512.1| 106 KNDKIlLIIDDTYNEKEGNQTDGVGKFYDHSKEAYIWGNNFVTSVVQSKGLFIPHKAKMYIK--------------N 168
                                       555559************************************99999999999999999999..............3 PP

                             DDE_5 151 vpddvtaktkpeial.elldraraagvplqvvvaDag 186
                                       +++   +ktk eia  e+++ ++  +  + ++v+D++
  gi|330508084|ref|YP_004384512.1| 169 DDENENFKTKMEIAFeEIIKPLVVPKSIDLYIVFDSW 205
                                       3455589999999985566667666666667888877 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.9   8.5e-07    0.0051     146     197 ..     156     209 ..      90     212 .] 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.5e-07
                         DDE_Tnp_2 146 pyiprkvaeilkerGeksefktkiellle.ileilkeefnva.avvfdsWyvns 197
                                        +ip+k +  +k+  e+ +fktk+e++ e i++ l     +   +vfdsW++ s
  gi|330508084|ref|YP_004384512.1| 156 LFIPHKAKMYIKNDDENENFKTKMEIAFEeIIKPLVVPKSIDlYIVFDSWWFLS 209
                                       3799999999***************98752777776655554279*****9765 PP

>> Mlp  Mlp lipoprotein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.4   0.00038       2.3      42     122 ..      54     131 ..      45     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00038
                               Mlp  42 ytiekltneiqgcsddnkskcnnfldWLktdiqkqkelaqafkkvykFLesk.kekdksfdtyiKseldckkgkdka 117
                                        t+  l + + +cs+++ks     ++W   d +   e   a++kv+ F++s   +k+ +++  i +  + k+g+ ++
  gi|330508084|ref|YP_004384512.1|  54 KTVSNLCDTMADCSKGKKS--RSSYNWFFSDANWD-ENEVAQRKVDLFIDSLcLKKNDKILLIIDDTYNEKEGN-QT 126
                                       59999**************..889****9887755.5556789********98667777888999999999996.34 PP

                               Mlp 118 nkqkn 122
                                       +  ++
  gi|330508084|ref|YP_004384512.1| 127 DGVGK 131
                                       44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1536.77
//
Query:       gi|330508085|ref|YP_004384513.1|  [L=411]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-26   93.1   0.0    2.2e-26   92.4   0.0    1.4  1  rve           Integrase core domain
    1.6e-05   24.6   0.0    8.1e-05   22.3   0.0    2.3  3  rve_3         Integrase core domain
     0.0012   18.9   0.0     0.0037   17.3   0.0    2.0  1  HTH_7         Helix-turn-helix domain of resolvase
     0.0039   17.2   0.1      0.088   12.8   0.0    2.5  2  HTH_29        Winged helix-turn helix
  ------ inclusion threshold ------
      0.016   14.2   0.0      0.024   13.6   0.0    1.2  1  TnsD          Tn7-like transposition protein D
       0.05   13.6   0.1       0.15   12.0   0.1    1.8  1  HTH_11        HTH domain
        0.1   12.4   0.0       0.24   11.2   0.0    1.6  1  HTH_IclR      IclR helix-turn-helix domain
       0.12   12.1   0.2       0.39   10.5   0.0    2.0  2  HTH_38        Helix-turn-helix domain
       0.13   11.8   0.1       0.33   10.5   0.1    1.6  1  Sigma70_r4    Sigma-70, region 4
       0.15   12.1   0.0       0.54   10.3   0.0    2.0  1  HTH_Mga       M protein trans-acting positive regulator (MGA)
       0.16   12.1   0.0       0.44   10.6   0.0    1.7  1  HTH_3         Helix-turn-helix
       0.16   11.7   0.0        0.3   10.8   0.0    1.4  1  Sigma70_r4_2  Sigma-70, region 4
       0.17   12.3   0.0       0.53   10.8   0.0    1.9  1  HTH_40        Helix-turn-helix domain
        0.2   12.1   0.0       0.36   11.3   0.0    1.4  1  GcrA          GcrA cell cycle regulator


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.0   1.7e-29   2.2e-26       2     118 ..     111     240 ..     110     241 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 1.7e-29
                               rve   2 trpgelwqvDvt...vvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDng 75 
                                       t+pg + qvD+    +++i + ++k+y++++v+ +sr+ +ae++ +  d  t+++++ +a+ +fgg  p+++l+Dn 
  gi|330508085|ref|YP_004384513.1| 111 TKPGVQAQVDWAecgYIDIDGEKRKLYCFTMVLGYSRMRYAEFTLRI-DVYTLIQCHINAFGYFGGY-PQELLYDNI 185
                                       79**********777777777777*********************99.******************9.********* PP

                               rve  76 seytsk............afrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                       ++++ k            +f++f +++g+ ++++rp+rpq++Gk+Er+++ +k++
  gi|330508085|ref|YP_004384513.1| 186 TQIVKKrapkssdstwnsHFQDFFEHYGFIPRLCRPYRPQTKGKIERTVGFVKKD 240
                                       ****99********************************************99976 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.5   3.2e+03      36      53 ..     195     212 ..     186     215 .. 0.78
   2 !   22.3   0.0   6.3e-08   8.1e-05       7      54 ..     218     265 ..     212     267 .. 0.92
   3 ?   -2.8   0.0       4.5   5.8e+03      19      40 ..     277     298 ..     272     307 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.5
                             rve_3  36 frslaearekleawredY 53 
                                       ++s ++ +++ ++++e+Y
  gi|330508085|ref|YP_004384513.1| 195 KSSDSTWNSHFQDFFEHY 212
                                       6677888999999**999 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 6.3e-08
                             rve_3   7 yiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYN 54 
                                       + +p++Pq+ g++E+  g +++ +     f+s+++++++l++w+ + N
  gi|330508085|ref|YP_004384513.1| 218 LCRPYRPQTKGKIERTVGFVKKDFFMGGRFTSFTDLNSQLQKWLSRVN 265
                                       679****************************************98755 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.5
                             rve_3  19 vEsfngtlrdellneelfrsla 40 
                                       +E+f +   +++ n++++ + +
  gi|330508085|ref|YP_004384513.1| 277 IERFKQEGLQKIGNAPSYHNRR 298
                                       7888887777777777755444 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 !   17.3   0.0   2.9e-06    0.0037      13      44 ..       6      37 ..       1      38 [. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.9e-06
                                      GGGSSTTTT--STTTSSSS---SSSS--SS-- CS
                             HTH_7 13 rvvkLleeGisiskIAkevnisRsTvYRylad 44
                                      +++ L +e  siskIA++++ sR Tv +yl+ 
  gi|330508085|ref|YP_004384513.1|  6 TLRDLFNEELSISKIARQTGHSRVTVRKYLNS 37
                                      6677888889********************97 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   6.9e-05     0.088       9      54 ..      12      51 ..       9      58 .. 0.75
   2 ?    1.4   0.1      0.25   3.3e+02      33      50 ..     277     294 ..     277     303 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.9e-05
                            HTH_29  9 aeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrpr 54
                                      +e++s +s iA+++g sr tv+++l+          l+++rs+ p+
  gi|330508085|ref|YP_004384513.1| 12 NEELS-ISKIARQTGHSRVTVRKYLNS-----QVPPLPQKRSKKPS 51
                                      68897.*******************98.....33455555555555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.25
                            HTH_29  33 lkrfeegGlaalldrrrs 50 
                                       ++rf ++Gl+++ + ++ 
  gi|330508085|ref|YP_004384513.1| 277 IERFKQEGLQKIGNAPSY 294
                                       79******9888776543 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.9e-05     0.024     191     269 ..       7      78 ..       4     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                              TnsD 191 lkeLveeeglslkeiAkelgvdiktVlryakklgllkekkkqkkesrelsskdrekkrkewleliksypdlgktelr 267
                                       l+ L++ e+ls+ +iA++ g +  tV++y++++    ++k +kk s+      ++ +r+  ++ +k++p +  ++ r
  gi|330508085|ref|YP_004384513.1|   7 LRDLFN-EELSISKIARQTGHSRVTVRKYLNSQVPPLPQKRSKKPSK------LDGHREYIIDRLKEFPLSASRIYR 76 
                                       789999.************************9997776655555543......588888888888888855555555 PP

                              TnsD 268 kl 269
                                       + 
  gi|330508085|ref|YP_004384513.1|  77 EI 78 
                                       55 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00012      0.15      14      36 ..      13      35 ..       5      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                            HTH_11 14 gpisgeeLAeeLnvSrrtvrrdI 36
                                      + +s++++A++++ Sr tvr+++
  gi|330508085|ref|YP_004384513.1| 13 EELSISKIARQTGHSRVTVRKYL 35
                                      349******************98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00019      0.24      17      41 ..      13      37 ..      12      37 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                      SS-BHHHHHHHHTS-HHHHHHHHHH CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqt 41
                                      +el++s +Ar+tg ++ tv+ +L++
  gi|330508085|ref|YP_004384513.1| 13 EELSISKIARQTGHSRVTVRKYLNS 37
                                      789*******************985 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0003      0.39      13      39 ..       7      33 ..       2      36 .. 0.88
   2 ?   -3.0   0.1       4.9   6.3e+03      35      41 ..      72      78 ..      70      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                            HTH_38 13 IerllaeGlslreIArrLgrspsTIsR 39
                                      + +l +e ls+++IAr+ g s+ T+ +
  gi|330508085|ref|YP_004384513.1|  7 LRDLFNEELSISKIARQTGHSRVTVRK 33
                                      56899*****************99976 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.9
                            HTH_38 35 sTIsREl 41
                                      s I+RE+
  gi|330508085|ref|YP_004384513.1| 72 SRIYREI 78
                                      5599*98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00026      0.33      13      39 ..       5      33 ..       2      36 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
                                      HHHHH..TTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 13 lelrf..geglTleEIgerlgiSrerVrq 39
                                      l+lr    e+l+ + I+++ g Sr +Vr 
  gi|330508085|ref|YP_004384513.1|  5 LTLRDlfNEELSISKIARQTGHSRVTVRK 33
                                      5566666********************96 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00042      0.54      18      42 ..      12      36 ..       7      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00042
                           HTH_Mga 18 eksltldelakeLglseltlqsdis 42
                                      +++l+++++a ++g s++t++++++
  gi|330508085|ref|YP_004384513.1| 12 NEELSISKIARQTGHSRVTVRKYLN 36
                                      5799*******************96 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00034      0.44      10      36 ..      15      41 ..       7      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                                      HHHHHHHHHHTSSHHHHHHHHTTSSCS CS
                             HTH_3 10 lsqeeLAeklGvsrstisriEnGernP 36
                                      ls+ ++A+ +G sr t++++ n +  P
  gi|330508085|ref|YP_004384513.1| 15 LSISKIARQTGHSRVTVRKYLNSQVPP 41
                                      78899*****************97655 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00023       0.3      25      47 ..      13      35 ..       5      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                                      S---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 25 eglsykEIAellgisegtVksrl 47
                                      e+ls+  IA+++g s +tV+++l
  gi|330508085|ref|YP_004384513.1| 13 EELSISKIARQTGHSRVTVRKYL 35
                                      79*******************98 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00041      0.53       7      34 ..       9      36 ..       5      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00041
                            HTH_40  7 elleeglsieeIAkerglkesTIegHLa 34
                                      +l++e lsi +IA++ g ++ T+ ++L 
  gi|330508085|ref|YP_004384513.1|  9 DLFNEELSISKIARQTGHSRVTVRKYLN 36
                                      799**********************996 PP

>> GcrA  GcrA cell cycle regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00028      0.36       8      36 ..       4      31 ..       1      37 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                              GcrA  8 velLkklwleGlSasqiaaqlggvsRnAV 36
                                        +L++l++e lS+s+ia+q g  sR  V
  gi|330508085|ref|YP_004384513.1|  4 FLTLRDLFNEELSISKIARQTG-HSRVTV 31
                                      568*****************99.777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2969.59
//
Query:       gi|330508086|ref|YP_004384514.1|  [L=257]
Description: IstB helper protein [Methanosaeta concilii GP6]
Scores for complete 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-65  220.3   0.0    2.2e-65  219.7   0.0    1.3  1  IstB_IS21     IstB-like ATP binding protein
    2.5e-08   34.0   0.0    3.7e-08   33.5   0.0    1.2  1  Bac_DnaA      Bacterial dnaA  protein
    8.9e-07   29.4   0.0    1.6e-06   28.6   0.0    1.4  1  AAA           ATPase family associated with various cellular 
    0.00021   20.8   0.0    0.00035   20.1   0.0    1.3  1  PhoH          PhoH-like protein
     0.0005   19.8   0.0    0.00084   19.1   0.0    1.4  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
    0.00061   20.1   0.2       0.44   10.8   0.0    2.5  2  AAA_22        AAA domain
    0.00063   20.2   0.0     0.0021   18.4   0.0    1.7  1  AAA_16        AAA ATPase domain
    0.00067   19.4   0.0     0.0013   18.5   0.0    1.4  1  AAA_30        AAA domain
     0.0018   18.5   0.0     0.0033   17.7   0.0    1.4  1  AAA_28        AAA domain
     0.0076   16.3   0.0       0.02   14.9   0.0    1.7  2  AAA_14        AAA domain
  ------ inclusion threshold ------
      0.012   15.2   0.2       0.17   11.4   0.0    2.1  2  AAA_25        AAA domain
      0.016   15.0   0.1      0.056   13.2   0.0    2.1  2  AAA_24        AAA domain
      0.022   14.8   0.2      0.089   12.8   0.3    2.0  2  AAA_5         AAA domain (dynein-related subfamily)
      0.022   14.2   0.0       0.04   13.4   0.0    1.4  1  KTI12         Chromatin associated protein KTI12
      0.023   15.3   0.2      0.064   13.8   0.2    2.0  1  AAA_18        AAA domain
      0.027   14.8   0.3       0.42   10.9   0.1    2.4  2  AAA_19        AAA domain
      0.035   14.0   0.5        6.2    6.7   0.0    2.4  2  NTPase_1      NTPase
      0.054   13.0   0.0        0.1   12.1   0.0    1.6  1  AAA_7         P-loop containing dynein motor region
      0.055   13.5   0.1       0.27   11.3   0.1    1.9  2  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
       0.13   11.2   0.0       0.26   10.2   0.0    1.4  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.13   12.2   0.0        3.9    7.5   0.0    2.2  2  ResIII        Type III restriction enzyme, res subunit
       0.14   11.5   0.0       0.21   10.9   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.16   11.9   0.4          1    9.3   0.1    2.3  2  NACHT         NACHT domain
       0.17   11.6   0.2        1.8    8.3   0.0    2.3  2  AAA_11        AAA domain


Domain annotation for each model (and alignments):
>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.7   0.0     3e-68   2.2e-65       2     178 .]      57     233 ..      56     233 .. 0.99

  Alignments for each domain:
  == domain 1  score: 219.7 bits;  conditional E-value: 3e-68
                         IstB_IS21   2 rrletrlrlaklpaqktledidfraarsldkrkvkeLatlsfiekkenivllGpsGvGKshlaialgveavraglsv 78 
                                       r+l+ r+r+a +p++k l+d+df++++sldk  ++e+a+l+fi+++en+vllGp+GvGK+hlaialg eavrag++v
  gi|330508086|ref|YP_004384514.1|  57 RSLALRTRKAGFPMEKRLDDFDFEFQPSLDKSVINEIASLKFIHNAENVVLLGPPGVGKTHLAIALGIEAVRAGFRV 133
                                       89999************************************************************************ PP

                         IstB_IS21  79 lfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpfaewd 155
                                        f  +++L+e+l++a+r+ +l++++++l +++l+i+D++g+lp+d+  a+ +f+++++ryer+sii tsn++ +ew+
  gi|330508086|ref|YP_004384514.1| 134 QFANASALIERLAKADREKRLEEMIRELSRFQLIIIDEMGYLPFDDFGAHCFFQLVSRRYERASIIFTSNKSYGEWG 210
                                       ***************************************************************************** PP

                         IstB_IS21 156 evlgdatlatAilDRlvHhahvv 178
                                       ++++d+++a AilDR++Hh++ v
  gi|330508086|ref|YP_004384514.1| 211 DIFKDHVIAAAILDRILHHCTTV 233
                                       ********************875 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   4.9e-11   3.7e-08      34     140 ..     102     205 ..      84     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 4.9e-11
                                       S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-SEEEEE-GGGGT CS
                          Bac_DnaA  34 ynPlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkvDvLliDDiqfla 110
                                          +++ g+ G+GktHL   i+  +++     rv + +a   +++l+ka r+k++ee+ ++l +  +++iD++ +l 
  gi|330508086|ref|YP_004384514.1| 102 AENVVLLGPPGVGKTHLA--IALGIEAVRAGFRVQFANASALIERLAKADREKRLEEMIRELSRFQLIIIDEMGYLP 176
                                       4557889**********5..55556666789********************************************** PP

                                       T-HHHHHHHHHHHHHHHTTT-EEEEEESS- CS
                          Bac_DnaA 111 gkektqeelfhtfnalleegkqvvlssDrs 140
                                         +   + +f+++   +e +  ++++s++s
  gi|330508086|ref|YP_004384514.1| 177 FDDFGAHCFFQLVSRRYERA-SIIFTSNKS 205
                                       ************99999876.588888876 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 !   28.6   0.0   2.1e-09   1.6e-06       1      68 [.     105     173 ..     105     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.1e-09
                                       EEEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS.STTHHHHHHHHHHHHHHHTSTSEEEEEETGG CS
                               AAA   1 vllyGppGtGKTllakavakel...gvefleisgsellsk.yvgesekkirelfkeakekakpsilfiDEid 68 
                                       v+l GppG+GKT la a+  e+   g+++   ++s l++     ++ek+++e+++e+++      ++iDE+ 
  gi|330508086|ref|YP_004384514.1| 105 VVLLGPPGVGKTHLAIALGIEAvraGFRVQFANASALIERlAKADREKRLEEMIRELSRF---QLIIIDEMG 173
                                       6899***************99655589999999999996625567899999999887655...69*****96 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.7e-07   0.00035      13      47 ..      96     130 ..      88     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.7e-07
                                       HHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTT CS
                              PhoH  13 lealkkndivfaiGpaGtGKtylavalavealkkk 47 
                                       l+ +++ + v+ +Gp G GKt+la+al++ea++++
  gi|330508086|ref|YP_004384514.1|  96 LKFIHNAENVVLLGPPGVGKTHLAIALGIEAVRAG 130
                                       5678899999*********************9986 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 !   19.1   0.0   1.1e-06   0.00084      31      94 ..     100     173 ..      72     178 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiake...lgvklkitsgPv.l......ekagdlaalltnleekdvlfideih 94 
                                       ++ + v+l GpPG+Gkt la  +  e    g +++ + + + +      ++++ l  ++ +l++ +++ ide+ 
  gi|330508086|ref|YP_004384514.1| 100 HNAENVVLLGPPGVGKTHLAIALGIEavrAGFRVQFANASAlIerlakaDREKRLEEMIRELSRFQLIIIDEMG 173
                                       56678999************877655211344444444433132222224567799999999999999999985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00059      0.44       5      23 ..     102     120 ..      99     138 .. 0.85
   2 ?    6.7   0.0     0.011       8.1      80     105 ..     152     176 ..     134     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00059
                            AAA_22   5 agilvvtGesGtGKTtllr 23 
                                       a  +v+ G++G+GKT+l+ 
  gi|330508086|ref|YP_004384514.1| 102 AENVVLLGPPGVGKTHLAI 120
                                       66789***********985 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                            AAA_22  80 ealeqalraravielliiDEaqhlrs 105
                                       ++le+ +r+ ++ +l+iiDE+ +l +
  gi|330508086|ref|YP_004384514.1| 152 KRLEEMIRELSRFQLIIIDEMGYL-P 176
                                       667777777777899******999.5 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.9e-06    0.0021      24     106 ..     102     173 ..      91     197 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.9e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                        e+v+l G++GvGK+ l+ +l  ++ ++g+ +  +++           l++ la+    ++ l+e   +el++++  
  gi|330508086|ref|YP_004384514.1| 102 AENVVLLGPPGVGKTHLAIALGIEAVRAGFRVQFANASA---------LIERLAK-ADREKRLEE-MIRELSRFQLI 167
                                       489***************999988888874444444444.........4666645.444444444.24467777776 PP

                            AAA_16 101 leeala 106
                                       + ++++
  gi|330508086|ref|YP_004384514.1| 168 IIDEMG 173
                                       666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.7e-06    0.0013      20     105 ..     104     180 ..      93     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-06
                            AAA_30  20 vavltGpAGtGKttalkal.reaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivD 95 
                                        +vl Gp+G GKt++  al  ea+ +ag+rv  +A  ++  ++La     +a++ ++l +  ++   l++ +l+i+D
  gi|330508086|ref|YP_004384514.1| 104 NVVLLGPPGVGKTHLAIALgIEAV-RAGFRVQ-FANASALIERLA-----KADREKRLEEMIRE---LSRFQLIIID 170
                                       58999*********9999945555.5788886.677777778887.....55666666655554...5566****** PP

                            AAA_30  96 Eagmvdtkql 105
                                       E+g + ++++
  gi|330508086|ref|YP_004384514.1| 171 EMGYLPFDDF 180
                                       ***9965554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.5e-06    0.0033       1      61 [.     104     170 ..     104     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.5e-06
                            AAA_28   1 kivitGgestGKTtlleaLa....argypvvpEaareileekl.akgedalpwv.edllafaervle 61 
                                       ++v++G+++ GKT l+ aL     + g++v    a  ++e ++ a++e+ l++  ++l +f+  +++
  gi|330508086|ref|YP_004384514.1| 104 NVVLLGPPGVGKTHLAIALGieavRAGFRVQFANASALIERLAkADREKRLEEMiRELSRFQLIIID 170
                                       59******************865444**999555555555555499999999999999999987765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       5.4   4.1e+03      47      71 ..      19      44 ..       3      50 .. 0.58
   2 !   14.9   0.0   2.7e-05      0.02       4      90 ..     104     196 ..     101     212 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.4
                            AAA_14 47 adpekllelilek.lkeekktylflD 71
                                       ++e++l+ +le  +ke+k t+ +lD
  gi|330508086|ref|YP_004384514.1| 19 GTFESVLDNYLEIaAKEKKSTIEILD 44
                                      34556667777763344444555555 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.7e-05
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd.....kkladpekllelileklkeekktylflDEiqe 75 
                                        +v+ G+  vGKT l+  l  e     +  + +++ + +      +k++ +++l+e+i+e+   ++ +++++DE+ +
  gi|330508086|ref|YP_004384514.1| 104 NVVLLGPPGVGKTHLAIALGIEAV---RAGFRVQFANASAlierlAKADREKRLEEMIREL---SRFQLIIIDEMGY 174
                                       689****************99999...7777788877776333323333333677777776...36789*****999 PP

                            AAA_14  76 v.......pewekalkslvdeg 90 
                                       +        ++++ + + +++ 
  gi|330508086|ref|YP_004384514.1| 175 LpfddfgaHCFFQLVSRRYERA 196
                                       8666666666666666666654 PP

>> AAA_25  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      0.17      31      57 ..     100     126 ..      78     135 .. 0.85
   2 ?    1.2   0.0      0.32   2.4e+02     131     150 ..     152     171 ..     141     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                            AAA_25  31 pagelallaGapgtGKttlaldlalav 57 
                                          e ++l G+pg+GKt la+ l+++ 
  gi|330508086|ref|YP_004384514.1| 100 HNAENVVLLGPPGVGKTHLAIALGIEA 126
                                       5567789***************98865 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.32
                            AAA_25 131 daleaaieevegvrlvviDp 150
                                       ++le+ i+e  + +l++iD 
  gi|330508086|ref|YP_004384514.1| 152 KRLEEMIRELSRFQLIIIDE 171
                                       578899999999*******6 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       9.7   7.2e+03     145     165 ..      28      48 ..      20      58 .. 0.63
   2 ?   13.2   0.0   7.4e-05     0.056       3      22 ..     103     122 ..     101     235 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.7
                            AAA_24 145 ytrlepklgkktanelkeevD 165
                                       y  ++ k++k t + l + vD
  gi|330508086|ref|YP_004384514.1|  28 YLEIAAKEKKSTIEILDYLVD 48 
                                       556666666666666666666 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.4e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                        ++++ Gp+g+GKT+la  l
  gi|330508086|ref|YP_004384514.1| 103 ENVVLLGPPGVGKTHLAIAL 122
                                       589*************9888 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   0.00012     0.089       1      16 [.     104     119 ..     104     172 .. 0.90
   2 ?   -1.7   0.0       3.6   2.7e+03     112     136 ..     194     224 ..     179     226 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                                       EEEEE--SSSSHHHHH CS
                             AAA_5   1 dvlLvGppGtgKsela 16 
                                       +v+L+GppG+gK+ la
  gi|330508086|ref|YP_004384514.1| 104 NVVLLGPPGVGKTHLA 119
                                       69***********998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.6
                                       ..-EEEEEESS--.......-TT-TTHHHHT CS
                             AAA_5 112 erfrviatanpld......rslnelspalrs 136
                                       er ++i+t+n+ +      ++ + + +a+++
  gi|330508086|ref|YP_004384514.1| 194 ERASIIFTSNKSYgewgdiFKDHVIAAAILD 224
                                       3478999999988555555555555555555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.4e-05      0.04       4      82 ..     105     175 ..     104     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.4e-05
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHHHHHHHTT.SEEEE-S-- CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslrsavkrdLskekvVIvDsln 80 
                                       vvl G P +GK+ +a  L  +    + +v+  +  +l  e+   +++ +e     +  +++ r+Ls+ +++I+D++ 
  gi|330508086|ref|YP_004384514.1| 105 VVLLGPPGVGKTHLAIALGIEAVRAGFRVQFANASALI-ER--LAKADRE-----KRLEEMIRELSRFQLIIIDEMG 173
                                       89****************************99887777.33..3345555.....555677799************9 PP

                                       -S CS
                             KTI12  81 yi 82 
                                       y 
  gi|330508086|ref|YP_004384514.1| 174 YL 175
                                       96 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   8.6e-05     0.064       1      30 [.     105     135 ..     105     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.6e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..gvnlrd 30 
                                       ++l G+pGvGKt la +L  +  +  g+++++
  gi|330508086|ref|YP_004384514.1| 105 VVLLGPPGVGKTHLAIALGIEA-VraGFRVQF 135
                                       789************9994432.232444443 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00057      0.42       7      26 ..      99     118 ..      91     138 .. 0.81
   2 ?    1.0   0.0      0.67     5e+02      89     111 ..     156     172 ..     133     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00057
                            AAA_19   7 alkekvllvtaGpGtGKTrv 26 
                                        +++++++++++pG GKT++
  gi|330508086|ref|YP_004384514.1|  99 IHNAENVVLLGPPGVGKTHL 118
                                       57899*************97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.67
                            AAA_19  89 elleeaeeekklqeee.llivDEf 111
                                       e+       ++l +++ l+i+DE+
  gi|330508086|ref|YP_004384514.1| 156 EM------IREL-SRFqLIIIDEM 172
                                       22......3346.45559*****8 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0082       6.2       2      28 ..     105     131 ..     104     138 .. 0.73
   2 ?    5.3   0.1     0.023        17      86     107 ..     155     175 ..     144     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0082
                                       EEEE--TTSSHHHHHHHHHHHH...GG CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgv 28 
                                       v++ GppGvGKt l   +  +  + g+
  gi|330508086|ref|YP_004384514.1| 105 VVLLGPPGVGKTHLAIALGIEAVRAGF 131
                                       8899********997655444445555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHH-EEEE---STT CS
                          NTPase_1  86 lealrkalseadviviDEiGkm 107
                                        e++r +ls+ ++i+iDE G +
  gi|330508086|ref|YP_004384514.1| 155 EEMIR-ELSRFQLIIIDEMGYL 175
                                       44555.47899*********76 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   0.00014       0.1      24      71 ..      93     140 ..      83     225 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                             AAA_7  24 yllelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsa 71 
                                       +   ++++n  +v+l Gp G+GKt ++  l  +  +  + + + n sa
  gi|330508086|ref|YP_004384514.1|  93 IASLKFIHNAENVVLLGPPGVGKTHLAIALGIEAVRAGFRVQFANASA 140
                                       55567899****************998885444444666666665555 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   0.1   0.00036      0.27       9      32 ..     112     135 ..     109     162 .. 0.93
   2 ?   -0.6   0.0       1.7   1.3e+03      78     110 ..     139     170 ..     135     180 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
                                       TSSHHHHHHHHHHHHHHTT--EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   9 GvGKTtlaanLaralarrglrVll 32 
                                       GvGKT la++L++   r+g+rV+ 
  gi|330508086|ref|YP_004384514.1| 112 GVGKTHLAIALGIEAVRAGFRVQF 135
                                       9*********************86 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                                       EEEEEEESS...-TTCHHHHHHHHHHCTS-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  78 gvvlnrvdgeneetllkealeelkqrygvpvlg 110
                                       + ++ r  + ++e++l+e+++el  r+ + +++
  gi|330508086|ref|YP_004384514.1| 139 SALIERLAKADREKRLEEMIRELS-RFQLIIID 170
                                       567788888888999999998875.56444444 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 ?   10.2   0.0   0.00035      0.26      27      61 ..     100     134 ..      82     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00035
                                       S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EE CS
                              MeaB  27 GraqvvGltGvPGaGkstlvealglelrrrGkrva 61 
                                        +a+ v l G PG+Gk  l  alg+e +r+G rv 
  gi|330508086|ref|YP_004384514.1| 100 HNAENVVLLGPPGVGKTHLAIALGIEAVRAGFRVQ 134
                                       5789999**************************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 ?    7.5   0.0    0.0052       3.9      10      50 ..      88     128 ..      79     156 .. 0.71
   2 ?    3.3   0.0       0.1        75     111     141 ..     142     172 ..     128     201 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0052
                                       HHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                            ResIII  10 eaienlleklkskrdkrglikmaTGtGKTlvaaklierllk 50 
                                       ++i+++++   +++ +++++  + G+GKT +a++l  +  +
  gi|330508086|ref|YP_004384514.1|  88 SVINEIASLKFIHNAENVVLLGPPGVGKTHLAIALGIEAVR 128
                                       4555555333339999****************877555444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.1
                                       HHHHHHTH........HHHTTT-SEEEEETG CS
                            ResIII 111 iqsldadseeeeeeseellrdrfdviiiDEa 141
                                       i++l ++ +e++ e+   + +rf++iiiDE 
  gi|330508086|ref|YP_004384514.1| 142 IERLAKADREKRLEEMIRELSRFQLIIIDEM 172
                                       344444444445555556677889******7 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.21      23      42 ..     103     122 ..      92     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                      Mg_chelatase  23 HnlllvGppGsGKtmlakrl 42 
                                        n++l+GppG GKt la +l
  gi|330508086|ref|YP_004384514.1| 103 ENVVLLGPPGVGKTHLAIAL 122
                                       589*************9776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.97   7.3e+02      87     132 ..      25      66 ..      15      99 .. 0.78
   2 ?    9.3   0.1    0.0014         1       3      20 ..     105     122 ..     103     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.97
                                       EE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCH CS
                             NACHT  87 lDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpral 132
                                       lD + e+++    kek+++ + L  l+ ++l ++ s  l++r+r+ 
  gi|330508086|ref|YP_004384514.1|  25 LDNYLEIAA----KEKKSTIEILDYLVDRELRSKESRSLALRTRKA 66 
                                       444444444....678899999999999999999999999998876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
                                       EEEEC-TTTCHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqkl 20 
                                       v+l G++G+GKT+L+  l
  gi|330508086|ref|YP_004384514.1| 105 VVLLGPPGVGKTHLAIAL 122
                                       89************9655 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0025       1.8      11      37 ..      97     122 ..      84     154 .. 0.75
   2 ?    1.1   0.1      0.37   2.8e+02     211     226 ..     158     172 ..     145     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0025
                            AAA_11  11 ksalseseitliqGPPGtgKTktivel 37 
                                       k++ + ++ +++ GPPG gKT+  ++l
  gi|330508086|ref|YP_004384514.1|  97 KFIHNAEN-VVLLGPPGVGKTHLAIAL 122
                                       44444454.8999********987665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.37
                            AAA_11 211 leklakkfdvviIDEA 226
                                       +++l  +f+++iIDE 
  gi|330508086|ref|YP_004384514.1| 158 IRELS-RFQLIIIDEM 172
                                       34443.9********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 1760.82
//
Query:       gi|330508087|ref|YP_004384515.1|  [L=184]
Description: hypothetical protein MCON_2179 [Methanosaeta concilii GP6]
Scores for complete 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-06   25.3   0.8    1.2e-05   25.0   0.8    1.1  1  DDE_Tnp_1  Transposase DDE domain
    1.3e-05   24.6   1.0    1.7e-05   24.2   1.0    1.1  1  DDE_Tnp_2  Archaeal putative transposase ISC1217
  ------ inclusion threshold ------
      0.014   15.4   0.3      0.031   14.2   0.1    1.6  2  SeqA       SeqA protein C-terminal domain
      0.073   12.2   0.1        0.1   11.7   0.1    1.2  1  Colicin_M  Colicin M


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 !   25.0   0.8   2.8e-09   1.2e-05     124     212 ..      12     119 ..       2     121 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.8e-09
                         DDE_Tnp_1 124 rlrkhdrnkiltksqkrrnk....................skkekgdvyyvtntnsellsaeevaelyrlRwqiErv 180
                                       ++ k + + +++ + k++++                    + k + ++ y+ +tn  +ls +e+  +y  Rw iE+ 
  gi|330508087|ref|YP_004384515.1|  12 IEDKFFIKTTVSVRGKKKTYyafekkviidkvgevklvisKRKKDSTTKYIISTNG-SLSLKEILSIYEDRWDIETA 87 
                                       44444444444444444444555555555555555566433333334445555555.7999**************** PP

                         DDE_Tnp_1 181 Fkwlkrkfgldrlryrglnrveaqllllllal 212
                                       +++  +k+g+   ++r++  +e+++ +++ ++
  gi|330508087|ref|YP_004384515.1|  88 HREANQKLGFKDYQLRDKHSIERFIQMVFSVW 119
                                       **************************998766 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.0   3.7e-09   1.7e-05     240     306 ..      46     113 ..      21     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.7e-09
                         DDE_Tnp_2 240 ikllvlddykkdgrrylfstdlndtdediittWenrWdievlirel.kalGledssflkrvrnkGfll 306
                                       +kl + +  k+   +y+ st+  ++  +i + +e rWdie  +re  + lG++d  +  +   + f+ 
  gi|330508087|ref|YP_004384515.1|  46 VKLVISKRKKDSTTKYIISTNGSLSLKEILSIYEDRWDIETAHREAnQKLGFKDYQLRDKHSIERFIQ 113
                                       444445556778899*****************************983579999887776666666665 PP

>> SeqA  SeqA protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   6.9e-06     0.031      31      88 ..      11      73 ..       3      79 .. 0.84
   2 ?   -2.6   0.0       1.1     5e+03      14      26 ..     103     115 ..      93     120 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.9e-06
                              SeqA 31 radpeaFakatekvkGrtRvYfakdeetllasgks.....tkpkqipetpfWVitNnntarKr 88
                                      +++++ F k+t +v+G++++Y+a +++ ++++  +     +k k+ ++t + + tN + + K+
  gi|330508087|ref|YP_004384515.1| 11 QIEDKFFIKTTVSVRGKKKTYYAFEKKVIIDKVGEvklviSKRKKDSTTKYIISTNGSLSLKE 73
                                      566788999999****************99887776888889999999999999998766665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                              SeqA  14 eekkavnrFlliL 26 
                                       ++k++++rF+ + 
  gi|330508087|ref|YP_004384515.1| 103 RDKHSIERFIQMV 115
                                       5677899998765 PP

>> Colicin_M  Colicin M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.2e-05       0.1     167     233 ..      15      89 ..       3      96 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                         Colicin_M 167 avvGettvst...ktsyatGddsvitriylGtitlki.......eGkltisasGsvsysGvvkayddkydanasshr 233
                                           +ttvs+   k +y++ +++vi    +G++ l i       + k  is++Gs+s + ++  y+d++d+++ +hr
  gi|330508087|ref|YP_004384515.1|  15 KFFIKTTVSVrgkKKTYYAFEKKVIIDK-VGEVKLVIskrkkdsTTKYIISTNGSLSLKEILSIYEDRWDIET-AHR 89 
                                       5555566664222567888888887653.566665442222222678899********************986.466 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1413.92
//
Query:       gi|330508088|ref|YP_004384516.1|  [L=374]
Description: hypothetical protein MCON_2180 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      6e-07   29.7   0.2         21    5.5   0.0    6.4  7  Colicin_E5   Colicin E5 ribonuclease domain
     0.0072   16.9   0.1        1.4    9.5   0.0    2.9  2  Caskin1-CID  Caskin1 CASK-interaction domain
  ------ inclusion threshold ------
      0.011   15.6  13.8        8.1    6.3   0.0    6.2  6  DUF2064      Uncharacterized protein conserved in bacteria (D


Domain annotation for each model (and alignments):
>> Colicin_E5  Colicin E5 ribonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.0    0.0086        51      34      67 ..      21      54 ..      13      61 .. 0.88
   2 ?   -1.6   0.0      0.58   3.4e+03      32      66 ..      71     105 ..      66     110 .. 0.70
   3 ?    2.1   0.0     0.039   2.4e+02      32      67 ..     122     157 ..     120     160 .. 0.91
   4 ?    3.1   0.0      0.02   1.2e+02      33      68 ..     175     211 ..     173     215 .. 0.78
   5 ?    1.6   0.0     0.059   3.5e+02      39      67 ..     234     262 ..     226     267 .. 0.86
   6 !    5.5   0.0    0.0035        21      32      68 ..     279     315 ..     277     322 .. 0.91
   7 ?    3.1   0.0      0.02   1.2e+02      53      66 ..     351     364 ..     331     367 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0086
                        Colicin_E5 34 kssddkranktsDglrrndsAtvYgekdgkYvvv 67
                                      +++ ++ +nkt  g + +   +v   +dg+Y++ 
  gi|330508088|ref|YP_004384516.1| 21 SAQPEEEWNKTFGGSGSDVGNSVIEAEDGGYIIA 54
                                      5667889*************************96 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.58
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvv 66 
                                       kt s+  + +n+t  g++ +   +v    dg ++v
  gi|330508088|ref|YP_004384516.1|  71 KTDSKGFEEWNRTYGGTGDDIGRSVMNVGDGYFIV 105
                                       55566667788888888888777887777555554 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.039
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt s+ +k ++kt  g   +   t+   +dg+Y+v 
  gi|330508088|ref|YP_004384516.1| 122 KTDSEGNKVWDKTFGGPDFDWGNTAQQTEDGGYIVA 157
                                       788999999****999999999************96 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.02
                        Colicin_E5  33 tkssddkranktsDglrrndsAt.vYgekdgkYvvvn 68 
                                       t  + ++ +nkt  g++ + + + v  +kdg+Yv+v 
  gi|330508088|ref|YP_004384516.1| 175 TDLNGNEMWNKTFGGINLDAAFSmVQSSKDGGYVIVG 211
                                       555668889999999999887653778899*****95 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.059
                        Colicin_E5  39 kranktsDglrrndsAtvYgekdgkYvvv 67 
                                       +++n+t  g   ++  +v    dg+Y++ 
  gi|330508088|ref|YP_004384516.1| 234 EQWNRTFGGADIDEGRSVQQADDGGYIIA 262
                                       57899999999****************96 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.0035
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvn 68 
                                       kt s  ++ +n+t  g + +d  +v   +dg+Y+v  
  gi|330508088|ref|YP_004384516.1| 279 KTDSDGNEEWNRTFGGSEWDDGFSVATVEDGGYLVTG 315
                                       78889999**************************975 PP

  == domain 7  score: 3.1 bits;  conditional E-value: 0.02
                        Colicin_E5  53 sAtvYgekdgkYvv 66 
                                        A++Y  kdg+Y++
  gi|330508088|ref|YP_004384516.1| 351 GASIYRTKDGGYII 364
                                       69***********8 PP

>> Caskin1-CID  Caskin1 CASK-interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00024       1.4      24      50 ..     105     131 ..      92     135 .. 0.91
   2 ?    4.0   0.0     0.013        75      23      37 ..     209     223 ..     199     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00024
                       Caskin1-CID  24 vasaRssgsgqssghaLHagaeGvkll 50 
                                       v+s+Rs gsg+     + + +eG k++
  gi|330508088|ref|YP_004384516.1| 105 VGSTRSHGSGDFDLWLIKTDSEGNKVW 131
                                       89*********999999*********9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.013
                       Caskin1-CID  23 svasaRssgsgqssg 37 
                                        v+s+Rs g+g+s  
  gi|330508088|ref|YP_004384516.1| 209 IVGSTRSYGGGESDV 223
                                       59*********9975 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 ?    3.9   0.1    0.0076        45      95     108 ..      45      58 ..      38      68 .. 0.85
   2 ?    2.1   0.2     0.027   1.6e+02      96     107 ..     149     160 ..     145     172 .. 0.85
   3 ?    6.3   0.0    0.0014       8.1      95     108 ..     201     214 ..     191     223 .. 0.81
   4 ?    2.8   0.1     0.016        98      95     108 ..     253     266 ..     247     275 .. 0.81
   5 ?    3.4   0.0     0.011        63      95     108 ..     305     318 ..     299     330 .. 0.81
   6 ?    0.8   0.1     0.067     4e+02      96     107 ..     357     368 ..     349     373 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0076
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        aeDGGY++ G + 
  gi|330508088|ref|YP_004384516.1|  45 EAEDGGYIIAGWTD 58 
                                       59********9984 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.027
                                       BTTSSEEEEEEE CS
                           DUF2064  96 aeDGGYyllGlk 107
                                       +eDGGY++ G +
  gi|330508088|ref|YP_004384516.1| 149 TEDGGYIVAGTT 160
                                       79******9987 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0014
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        ++DGGY+++G ++
  gi|330508088|ref|YP_004384516.1| 201 SSKDGGYVIVGSTR 214
                                       579********995 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.016
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        a DGGY++ G +k
  gi|330508088|ref|YP_004384516.1| 253 QADDGGYIIAGKTK 266
                                       699******99885 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.011
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        +eDGGY + G ++
  gi|330508088|ref|YP_004384516.1| 305 TVEDGGYLVTGSTH 318
                                       579********996 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 0.067
                                       BTTSSEEEEEEE CS
                           DUF2064  96 aeDGGYyllGlk 107
                                       ++DGGY++ G++
  gi|330508088|ref|YP_004384516.1| 357 TKDGGYIIGGFE 368
                                       78*****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); 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):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.20s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2819.02
//
Query:       gi|330508089|ref|YP_004384517.1|  [L=306]
Description: hypothetical protein MCON_2181 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-38  131.3   0.4    2.1e-38  130.8   0.4    1.2  1  PatG_C    PatG C-terminal
    1.2e-29  103.0   0.0    5.1e-29  100.9   0.0    1.8  1  PatG_D    PatG Domain
  ------ inclusion threshold ------
       0.12   12.8   0.2       0.25   11.8   0.2    1.4  1  ZapA      Cell division protein ZapA


Domain annotation for each model (and alignments):
>> PatG_C  PatG C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.8   0.4   3.5e-42   2.1e-38       1     115 []     192     303 ..     192     303 .. 0.98

  Alignments for each domain:
  == domain 1  score: 130.8 bits;  conditional E-value: 3.5e-42
                            PatG_C   1 ekqeeeftkairevLdrvlqelrNlGatdedRAlNylatrapdiyretaelileslsLdsveveksplsradsdcvd 77 
                                       ekqee+f+++++e++dr+lq+++N+Ga+de+RAlNyla+r+p iy+++ae++++++sL++vev++s+ls+a +++v+
  gi|330508089|ref|YP_004384517.1| 192 EKQEEKFRATANELFDRILQMADNTGANDEHRALNYLAVRYPAIYAKAAEEFEHNFSLTGVEVRPSRLSGA-RKIVS 267
                                       5899*******************************************************************.***** PP

                            PatG_C  78 VkltftnkenssraekkyrvtvDVseelPflvtkvqsy 115
                                       V++++tn+  ++++++k++v+vDVsee+Pf+vtk+ +y
  gi|330508089|ref|YP_004384517.1| 268 VIFSYTNR--ETDVTEKFFVRVDVSEEFPFMVTKMAPY 303
                                       *******9..9************************998 PP

>> PatG_D  PatG Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.0   8.5e-33   5.1e-29       1      99 [.      51     243 ..      51     256 .. 0.93

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 8.5e-33
                            PatG_D   1 lvYviGrieadFpnearekefvqalaraktanpedqqalakvLsnrenrylaralsWiLtiegipiYvllPn..... 72 
                                       +vY +Grie++Fpn+++e+ef qa++ra+ta++ d+qa++ vLs++enryl+r+l+W+Ltie++   +llP+     
  gi|330508089|ref|YP_004384517.1|  51 YVYSLGRIEPRFPNMSAEREFAQAMGRAETAGMIDPQAFYFVLSKKENRYLVRELCWVLTIESVAACILLPKdpldl 127
                                       8**************************************************************************** PP

                            PatG_D  73 .......................................................................kpfale 78 
                                                                                                               + a+e
  gi|330508089|ref|YP_004384517.1| 128 dllvesvrpmsakadidvviglmgpvappemcsglqvplvgfdqlfsfdrnafiksiprpesipekqeekfRATANE 204
                                       ***********************************************************************999*** PP

                            PatG_D  79 lfarliealdnqedteesra..................d 99 
                                       lf+r+++++dn+++++e+ra                  +
  gi|330508089|ref|YP_004384517.1| 205 LFDRILQMADNTGANDEHRAlnylavrypaiyakaaeeF 243
                                       *******************98877777666666655544 PP

>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   4.2e-05      0.25      13      53 ..     189     229 ..     188     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.2e-05
                              ZapA  13 aceegeeeylreaaklvdekikeireaggnlseerllvmaa 53 
                                       +++e +ee  r+ a+++ ++i ++ +++g  +e r+l   a
  gi|330508089|ref|YP_004384517.1| 189 SIPEKQEEKFRATANELFDRILQMADNTGANDEHRALNYLA 229
                                       5899*************************989999886555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        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 0.20s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2516.90
//
Query:       gi|330508090|ref|YP_004384518.1|  [L=381]
Description: hypothetical protein MCON_2182 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   5.0         24    4.8   0.0    4.0  5  DUF2064        Uncharacterized protein conserved in bacteria 
       0.21   11.9   1.2         13    6.3   0.1    3.5  3  Kelch_6        Kelch motif
        0.7   10.5  15.4          8    7.1   0.1    5.6  7  PQQ_3          PQQ-like domain
       0.77    9.3   3.2         27    4.3   0.0    3.5  4  Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like


Domain annotation for each model (and alignments):
>> DUF2064  Uncharacterized protein conserved in bacteria (DUF2064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.01        46      95     108 ..      45      58 ..      38      68 .. 0.85
   2 ?   -3.7   0.0       2.2   9.7e+03     100     116 ..     101     116 ..     101     117 .. 0.70
   3 ?   -2.9   0.0       1.3   5.6e+03      96     108 ..     149     161 ..     144     168 .. 0.72
   4 ?    3.0   0.1     0.019        85      96     107 ..     251     262 ..     246     274 .. 0.83
   5 ?    4.8   0.0    0.0053        24      95     107 ..     350     362 ..     345     373 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.01
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        aeDGGY++ G + 
  gi|330508090|ref|YP_004384518.1|  45 EAEDGGYIIAGWTD 58 
                                       59********9984 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.2
                                       SEEEEEEEG-G...GGG CS
                           DUF2064 100 GYyllGlkkrlapaelF 116
                                       GY ++G ++  + +e F
  gi|330508090|ref|YP_004384518.1| 101 GYFIVGSTR-SHGSEDF 116
                                       9*****995.5444555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.3
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       ++DG Y++ G k+
  gi|330508090|ref|YP_004384518.1| 149 TKDGDYIIGGSKH 161
                                       6899999888885 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.019
                                       BTTSSEEEEEEE CS
                           DUF2064  96 aeDGGYyllGlk 107
                                       + DGG++l+G +
  gi|330508090|ref|YP_004384518.1| 251 TRDGGFILVGRT 262
                                       78********87 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.0053
                                       EBTTSSEEEEEEE CS
                           DUF2064  95 paeDGGYyllGlk 107
                                        ++DGGY++lG  
  gi|330508090|ref|YP_004384518.1| 350 QVKDGGYVILGAV 362
                                       579********86 PP

>> Kelch_6  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0028        13      15      42 ..      51      79 ..      38      83 .. 0.90
   2 ?    2.1   0.0     0.057   2.6e+02      15      31 ..     154     171 ..     154     179 .. 0.82
   3 ?   -2.1   0.1       1.2   5.4e+03      15      31 ..     204     221 ..     204     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0028
                           Kelch_6 15 YifGGytds.spylnkvwvydpetksWeq 42
                                      Yi+ G+tds ++ +n+vw+   ++k +e+
  gi|330508090|ref|YP_004384518.1| 51 YIIAGWTDSfGMGQNDVWLTKTDSKGFEE 79
                                      9******************9999998886 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.057
                           Kelch_6  15 YifGGytds.spylnkvw 31 
                                       Yi+GG++++ ++ +++++
  gi|330508090|ref|YP_004384518.1| 154 YIIGGSKHQsDEDVDDWL 171
                                       9******99877777765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.2
                           Kelch_6  15 YifGGytds.spylnkvw 31 
                                       Y+  G+t+s ++   ++w
  gi|330508090|ref|YP_004384518.1| 204 YVTAGQTNSyGSGNIDIW 221
                                       888999997766666666 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.14   6.2e+02       3      27 ..      26      55 ..      25      55 .. 0.77
   2 ?    5.2   0.2    0.0071        32       5      29 ..      80     108 ..      78     116 .. 0.80
   3 ?   -1.5   0.1       0.9     4e+03       1      13 [.     127     139 ..     127     171 .. 0.70
   4 ?    3.6   0.1     0.022     1e+02       1      17 [.     178     194 ..     178     212 .. 0.69
   5 ?    7.1   0.1    0.0018         8       1      27 [.     229     260 ..     229     267 .. 0.81
   6 ?   -2.5   0.1       1.8     8e+03       5      21 ..     285     296 ..     281     313 .. 0.48
   7 ?   -2.1   0.0       1.4   6.4e+03      13      28 ..     344     361 ..     326     364 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.14
                             PQQ_3  3 vlWsvqlpg...pvnssp..avdgglvyvg 27
                                      + W+++++g   +v+ s+  a dgg++ +g
  gi|330508090|ref|YP_004384518.1| 26 EEWNKTFGGsgsDVGNSVieAEDGGYIIAG 55
                                      569999987566777777899999999876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0071
                             PQQ_3   5 Wsv...qlpgpvnssp.avdgglvyvgtg 29 
                                       W++   ++++++++s+  v++g+  vg++
  gi|330508090|ref|YP_004384518.1|  80 WNRtygGTGDDIGRSVmNVGDGYFIVGST 108
                                       77745567779997777**********97 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.9
                             PQQ_3   1 GevlWsvqlpgpv 13 
                                       G  +W ++++gp+
  gi|330508090|ref|YP_004384518.1| 127 GNKVWDKTFGGPG 139
                                       5567777777765 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.022
                             PQQ_3   1 GevlWsvqlpgpvnssp 17 
                                       G+++W+++l++ ++ + 
  gi|330508090|ref|YP_004384518.1| 178 GQEKWNRTLGDTGYETI 194
                                       99*****9998776555 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.0018
                             PQQ_3   1 GevlWsvqlpgpvnssp......avdgglvyvg 27 
                                       G++lW+++l++p+ s        + dgg + vg
  gi|330508090|ref|YP_004384518.1| 229 GDELWNRTLGSPG-SDIcnsikqTRDGGFILVG 260
                                       99*******9865.5555555999999999988 PP

  == domain 6  score: -2.5 bits;  conditional E-value: 1.8
                             PQQ_3   5 Wsvqlpgpvnsspavdg 21 
                                       W + ++gp       d+
  gi|330508090|ref|YP_004384518.1| 285 WDKVFGGP-----EWDE 296
                                       54444443.....3333 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 1.4
                             PQQ_3  13 vnssp..avdgglvyvgt 28 
                                       + ss   + dgg+v  g+
  gi|330508090|ref|YP_004384518.1| 344 IASSIrqVKDGGYVILGA 361
                                       444445444788888775 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 ?    4.3   0.0    0.0059        27     105     128 ..     111     134 ..     106     138 .. 0.91
   2 ?   -0.7   0.1      0.22   9.8e+02     106     133 ..     163     190 ..     160     211 .. 0.73
   3 ?   -1.7   0.1      0.45     2e+03      81      97 ..     219     235 ..     177     240 .. 0.63
   4 ?    2.9   0.0     0.016        72     103     127 ..     265     287 ..     261     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0059
                     Pyrid_ox_like 105 egkddpnltlikvtpeeaeyWdsk 128
                                       +g +d +l lik + e  ++Wd +
  gi|330508090|ref|YP_004384518.1| 111 HGSEDFDLWLIKTDSEGNKVWDKT 134
                                       699*******************86 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.22
                     Pyrid_ox_like 106 gkddpnltlikvtpeeaeyWdsksgklv 133
                                       + +d +  lik++ +  e W+ + g + 
  gi|330508090|ref|YP_004384518.1| 163 SDEDVDDWLIKIDSNGQEKWNRTLGDTG 190
                                       6677777899999999999998766554 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.45
                     Pyrid_ox_like  81 taevvedrakieelWsp 97 
                                        + +v+  +  +elW+ 
  gi|330508090|ref|YP_004384518.1| 219 DIWIVKTDSNGDELWNR 235
                                       33445555555666665 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.016
                     Pyrid_ox_like 103 fpegkddpnltlikvtpeeaeyWds 127
                                       +  g+  p+l l+kv+ +  + Wd 
  gi|330508090|ref|YP_004384518.1| 265 Y--GTGKPDLWLMKVDSNGNKLWDK 287
                                       4..7778****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3037.60
//
Query:       gi|330508091|ref|YP_004384519.1|  [L=310]
Description: hypothetical protein MCON_2183 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-38  129.5   0.5    1.1e-37  128.6   0.3    1.6  2  PatG_C    PatG C-terminal
    6.2e-32  110.3   0.1    3.1e-30  104.9   0.1    2.2  1  PatG_D    PatG Domain
  ------ inclusion threshold ------
       0.02   15.3   0.1      0.042   14.3   0.1    1.5  1  ZapA      Cell division protein ZapA


Domain annotation for each model (and alignments):
>> PatG_C  PatG C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.75   4.5e+03      42      72 ..      69     101 ..      66     111 .. 0.63
   2 !  128.6   0.3   1.8e-41   1.1e-37       1     115 []     196     307 ..     196     307 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.75
                            PatG_C  42 pdiyretael..ileslsLdsveveksplsrad 72 
                                       + ++re+a++  ++e+  L++ ++ +s ls+++
  gi|330508091|ref|YP_004384519.1|  69 MAVEREFAQAtgRAETTGLTDQQAFYSVLSKKE 101
                                       566666665511456667888888888888774 PP

  == domain 2  score: 128.6 bits;  conditional E-value: 1.8e-41
                            PatG_C   1 ekqeeeftkairevLdrvlqelrNlGatdedRAlNylatrapdiyretaelileslsLdsveveksplsradsdcvd 77 
                                       ekqee+f+ a++e++dr+lq+++N+Gatde+RAlNyla+r+p iy+++ae++++++sL++ve+++s+ls+a +++v+
  gi|330508091|ref|YP_004384519.1| 196 EKQEEKFRTAANELFDRILQMADNTGATDEHRALNYLAVRYPAIYAKAAEEFEHNFSLTGVEARPSRLSGA-RKIVS 271
                                       5899*******************************************************************.***** PP

                            PatG_C  78 VkltftnkenssraekkyrvtvDVseelPflvtkvqsy 115
                                       V++++tn+  ++++++ky+v+vDVsee+Pflvtk  +y
  gi|330508091|ref|YP_004384519.1| 272 VIFSYTNR--ETDVTEKYFVRVDVSEEFPFLVTKTAPY 307
                                       *******9..9***********************9987 PP

>> PatG_D  PatG Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.9   0.1   5.1e-34   3.1e-30       1      99 [.      55     247 ..      55     259 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 5.1e-34
                            PatG_D   1 lvYviGrieadFpnearekefvqalaraktanpedqqalakvLsnrenrylaralsWiLtiegipiYvllPn..... 72 
                                       +vY++G+i+++F ++a+e+ef qa++ra+t + +dqqa+++vLs++enryl+r+l+W+Ltieg+  Y+llP+     
  gi|330508091|ref|YP_004384519.1|  55 YVYALGKIDPRFRSMAVEREFAQATGRAETTGLTDQQAFYSVLSKKENRYLVRDLCWTLTIEGVAAYILLPKdpldf 131
                                       8**************************************************************************** PP

                            PatG_D  73 .......................................................................kpfale 78 
                                                                                                                +a+e
  gi|330508091|ref|YP_004384519.1| 132 drlvesvkpqqdkagmdvvvglkgpvappemcsglqvplvgfdqlfsfnrdafiksiprpesipekqeekfRTAANE 208
                                       ***********************************************************************999*** PP

                            PatG_D  79 lfarliealdnqedteesra..................d 99 
                                       lf+r+++++dn+++t+e+ra                  +
  gi|330508091|ref|YP_004384519.1| 209 LFDRILQMADNTGATDEHRAlnylavrypaiyakaaeeF 247
                                       *******************97777666655555554433 PP

>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   7.1e-06     0.042      13      53 ..     193     233 ..     192     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.1e-06
                              ZapA  13 aceegeeeylreaaklvdekikeireaggnlseerllvmaa 53 
                                       +++e +ee  r aa+++ ++i ++ +++g  +e r+l   a
  gi|330508091|ref|YP_004384519.1| 193 SIPEKQEEKFRTAANELFDRILQMADNTGATDEHRALNYLA 233
                                       5899**************************9*999986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 2522.28
//
Query:       gi|330508092|ref|YP_004384520.1|  [L=391]
Description: hypothetical protein MCON_2184 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0014   18.4   1.6         12    5.6   0.0    4.5  5  DUF4166        Domain of unknown function (DUF4166)
     0.0018   18.5   5.5       0.75   10.1   0.5    4.8  5  Colicin_E5     Colicin E5 ribonuclease domain
  ------ inclusion threshold ------
      0.015   15.7   9.3        1.1    9.9   0.2    5.1  5  PQQ_3          PQQ-like domain
      0.078   13.2   0.1        7.7    6.8   0.0    3.5  5  DUF4263        Domain of unknown function (DUF4263)
        0.1   11.9   0.6         81    2.6   0.0    4.1  4  mRNA_decap_C   mRNA-decapping enzyme C-terminus
        2.1    8.2   9.6         23    4.9   0.0    4.7  6  DUF2064        Uncharacterized protein conserved in bacteria 
        3.4    8.1  10.4        2.6    8.5   0.0    4.6  5  Inhibitor_I42  Chagasin family peptidase inhibitor I42


Domain annotation for each model (and alignments):
>> DUF4166  Domain of unknown function (DUF4166)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0047        12      64      81 ..      72      87 ..      63     116 .. 0.83
   2 ?    0.1   0.0      0.24     6e+02      65      81 ..     125     139 ..     114     145 .. 0.79
   3 ?    3.1   0.0     0.028        72      63      91 ..     175     200 ..     162     210 .. 0.68
   4 ?   -1.5   0.0      0.73   1.9e+03      64      81 ..     280     295 ..     270     311 .. 0.77
   5 ?    3.9   0.0     0.015        40      64      87 ..     332     353 ..     322     363 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0047
                           DUF4166 64 rdesgretltwtRtfefp 81
                                      +d++g+e   w+Rtf++p
  gi|330508092|ref|YP_004384520.1| 72 TDSKGNE--LWNRTFGGP 87
                                      6899***..*******99 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.24
                           DUF4166  65 desgretltwtRtfefp 81 
                                       +++g +   w Rtf+ p
  gi|330508092|ref|YP_004384520.1| 125 NSKGDK--EWDRTFGKP 139
                                       455666..7*****998 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.028
                           DUF4166  63 erdesgretltwtRtfefpgktrtfdstm 91 
                                       ++d++g +   w Rtf+ +      +s++
  gi|330508092|ref|YP_004384520.1| 175 KTDSNGTK--MWDRTFGKS-GNDAGRSVK 200
                                       47888999..*******99.445555555 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.73
                           DUF4166  64 rdesgretltwtRtfefp 81 
                                       +d++g+e   w+ tf+++
  gi|330508092|ref|YP_004384520.1| 280 TDSKGNE--EWNKTFGGS 295
                                       5889999..9*****998 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.015
                           DUF4166  64 rdesgretltwtRtfefpgktrtf 87 
                                       +d++g e   w+Rtf+  g    f
  gi|330508092|ref|YP_004384520.1| 332 TDQNGIE--QWNRTFGSTGTSGAF 353
                                       6899999..*******99766666 PP

>> Colicin_E5  Colicin E5 ribonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.9   2.3e+03      35      69 ..      22      56 ..      15      59 .. 0.80
   2 ?   -0.7   0.0       0.7   1.8e+03      32      66 ..      71     105 ..      70     109 .. 0.82
   3 ?    1.7   0.1      0.13   3.2e+02      32      66 ..     175     209 ..     173     211 .. 0.84
   4 !   10.1   0.5   0.00029      0.75      17      70 ..     211     265 ..     208     274 .. 0.91
   5 ?    4.4   0.0     0.018        47      32      68 ..     279     315 ..     271     320 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.9
                        Colicin_E5 35 ssddkranktsDglrrndsAtvYgekdgkYvvvnd 69
                                      ++ ++ +nkt  g + +   ++   kd +Y++v  
  gi|330508092|ref|YP_004384520.1| 22 AQPKEEWNKTYGGPGDESGFAIQEIKDYGYIIVGK 56
                                      56678899999998888888888889999999865 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.7
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvv 66 
                                       kt s+ ++ +n+t  g r +   ++   +d++Y++
  gi|330508092|ref|YP_004384520.1|  71 KTDSKGNELWNRTFGGPRDDIGYSIQETSDSGYII 105
                                       67888889999888887777788999999999998 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.13
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvv 66 
                                       kt s+  k +++t    + +   +v   kdg+Yv+
  gi|330508092|ref|YP_004384520.1| 175 KTDSNGTKMWDRTFGKSGNDAGRSVKQTKDGGYVI 209
                                       67777788888888888999999***********9 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00029
                        Colicin_E5  17 GWte.eevrdvvskgaktkssddkranktsDglrrndsAtvYgekdgkYvvvndr 70 
                                       GWte +++++ +    kt  s  + +nkt+ g + + + ++   kdg+Y+v+ d 
  gi|330508092|ref|YP_004384520.1| 211 GWTElKDIDKAYVWIIKTDPSGTELWNKTIGGSSWDGARSIQETKDGGYIVIGDT 265
                                       9999678999999999************************************986 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.018
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvn 68 
                                       kt s+ ++ +nkt  g   +   +v   +dg+Y++  
  gi|330508092|ref|YP_004384520.1| 279 KTDSKGNEEWNKTFGGSDVDWGMSVQQARDGGYIIAG 315
                                       789999****************************975 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.1   5.5e+03       3      15 ..      26      39 ..      25      55 .. 0.73
   2 ?    2.3   0.0       0.1   2.6e+02       1      16 [.      76      94 ..      76     111 .. 0.71
   3 ?    9.9   0.2   0.00041       1.1       1      29 [.     232     265 ..     232     275 .. 0.88
   4 ?    3.9   0.5     0.032        83       1      27 [.     284     315 ..     284     325 .. 0.88
   5 ?    0.8   0.0      0.31   7.9e+02       3      30 ..     338     370 ..     338     372 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.1
                             PQQ_3  3 vlWsvqlpgpvn.s 15
                                      + W+++ +gp+  s
  gi|330508092|ref|YP_004384520.1| 26 EEWNKTYGGPGDeS 39
                                      56999999987634 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.1
                             PQQ_3  1 GevlWsvqlpg...pvnss 16
                                      G +lW+++++g   ++++s
  gi|330508092|ref|YP_004384520.1| 76 GNELWNRTFGGprdDIGYS 94
                                      889******9955555555 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00041
                             PQQ_3   1 GevlWsvqlpgpvnssp.....avdgglvyvgtg 29 
                                       G++lW+++++g  + ++     + dgg++++g++
  gi|330508092|ref|YP_004384520.1| 232 GTELWNKTIGGSSWDGArsiqeTKDGGYIVIGDT 265
                                       99*********99999998898889******997 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.032
                             PQQ_3   1 GevlWsvqlpg.pvnssp....avdgglvyvg 27 
                                       G + W+++++g +v  ++    a dgg++ +g
  gi|330508092|ref|YP_004384520.1| 284 GNEEWNKTFGGsDVDWGMsvqqARDGGYIIAG 315
                                       6778*****999999888889999****9987 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.31
                             PQQ_3   3 vlWsvqlpgpvnssp.....avdgglvyvgtgd 30 
                                       ++W++++++ ++s++     a d+ ++  g++d
  gi|330508092|ref|YP_004384520.1| 338 EQWNRTFGSTGTSGAflaqeADDDEYIMLGDTD 370
                                       58*******999999888777777777777765 PP

>> DUF4263  Domain of unknown function (DUF4263)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.003       7.7      93     132 ..      23      62 ..      14      83 .. 0.77
   2 ?   -1.8   0.0       1.3   3.4e+03      95     128 ..      77     110 ..      64     120 .. 0.60
   3 ?    0.0   0.0      0.35   9.1e+02      85     132 ..     119     166 ..     116     184 .. 0.74
   4 ?   -0.1   0.0      0.38   9.7e+02     106     134 ..     244     273 ..     213     289 .. 0.66
   5 ?   -0.2   0.0      0.42   1.1e+03      86     130 ..     276     321 ..     269     338 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.003
                           DUF4263  93 ekgeeladlrntseleeglgikainpkgiliiGrreelee 132
                                       + +ee++++     +e+g+ i++i+ +g++i+G+++++ +
  gi|330508092|ref|YP_004384520.1|  23 QPKEEWNKTYGGPGDESGFAIQEIKDYGYIIVGKTDSFGT 62 
                                       33788888888888999******************77755 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                           DUF4263  95 geeladlrntseleegl..gikainpkgiliiGrre 128
                                        e ++  r ++ +++ +  +i++++ +g++i+G +e
  gi|330508092|ref|YP_004384520.1|  77 NELWN--RTFGGPRDDIgySIQETSDSGYIIAGLTE 110
                                       44444..44444444443478888999999999884 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.35
                           DUF4263  85 lllldknkekgeeladlrntseleegl..gikainpkgiliiGrreelee 132
                                       ++l++ n++  +e+   r ++++ + +  +i++++ +g++++G ++++++
  gi|330508092|ref|YP_004384520.1| 119 IWLIKANSKGDKEWD--RTFGKPSDDIcwSIQETSDHGYILLGDTKSYNA 166
                                       667777777788888..5566666666669999**********9977665 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.38
                           DUF4263 106 eleeglgikainpkgiliiGrr.eeleeke 134
                                       + +   +i++++  g+++iG + ++  + +
  gi|330508092|ref|YP_004384520.1| 244 SWDGARSIQETKDGGYIVIGDTrQKDANDQ 273
                                       4444457888888899****9965555533 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.42
                           DUF4263  86 llldknkekgeeladlrntseleeglgikainpkgiliiGrr.eel 130
                                       +l++  ++  ee++++   s+ + g++ ++ +  g++i+G + ++ 
  gi|330508092|ref|YP_004384520.1| 276 WLIKTDSKGNEEWNKTFGGSDVDWGMSVQQARDGGYIIAGETrSYG 321
                                       4454344448888888888888889999999999******995554 PP

>> mRNA_decap_C  mRNA-decapping enzyme C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.063   1.6e+02      14      21 ..      67      74 ..      67      75 .. 0.89
   2 ?    2.6   0.0     0.031        81      14      22 ..     171     179 ..     171     181 .. 0.92
   3 ?   -1.2   0.0       0.5   1.3e+03      12      22 ..     221     231 ..     216     231 .. 0.74
   4 ?    1.7   0.0     0.063   1.6e+02      14      21 ..     275     282 ..     275     283 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.063
                      mRNA_decap_C 14 iHLIknDs 21
                                      i LIk+Ds
  gi|330508092|ref|YP_004384520.1| 67 IWLIKTDS 74
                                      89*****9 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.031
                      mRNA_decap_C  14 iHLIknDss 22 
                                       i LIk+Ds+
  gi|330508092|ref|YP_004384520.1| 171 IWLIKTDSN 179
                                       89*****97 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.5
                      mRNA_decap_C  12 tLiHLIknDss 22 
                                       + +  Ik+D+s
  gi|330508092|ref|YP_004384520.1| 221 AYVWIIKTDPS 231
                                       66788999975 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.063
                      mRNA_decap_C  14 iHLIknDs 21 
                                       i LIk+Ds
  gi|330508092|ref|YP_004384520.1| 275 IWLIKTDS 282
                                       89*****9 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 ?   -3.9   0.0       4.5   1.2e+04      97     107 ..      47      57 ..      41      62 .. 0.77
   2 ?   -1.2   0.1      0.68   1.7e+03      96     108 ..      98     110 ..      92     115 .. 0.83
   3 ?   -0.9   0.0      0.54   1.4e+03      96     108 ..     150     162 ..     144     172 .. 0.76
   4 ?    3.1   0.0     0.031        79      96     108 ..     202     214 ..     194     222 .. 0.82
   5 ?    4.9   0.0    0.0088        23      96     108 ..     254     266 ..     248     276 .. 0.79
   6 ?    2.0   0.2     0.066   1.7e+02      95     108 ..     305     318 ..     298     326 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.5
                                       TTSSEEEEEEE CS
                           DUF2064  97 eDGGYyllGlk 107
                                       +D GY+++G +
  gi|330508092|ref|YP_004384520.1|  47 KDYGYIIVGKT 57 
                                       67899999977 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.68
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       ++D GY++ Gl++
  gi|330508092|ref|YP_004384520.1|  98 TSDSGYIIAGLTE 110
                                       689********95 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.54
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       ++D GY+llG +k
  gi|330508092|ref|YP_004384520.1| 150 TSDHGYILLGDTK 162
                                       5799******885 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.031
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       ++DGGY++ G ++
  gi|330508092|ref|YP_004384520.1| 202 TKDGGYVIAGWTE 214
                                       68********994 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.0088
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       ++DGGY+++G ++
  gi|330508092|ref|YP_004384520.1| 254 TKDGGYIVIGDTR 266
                                       78********886 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.066
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        a DGGY++ G ++
  gi|330508092|ref|YP_004384520.1| 305 QARDGGYIIAGETR 318
                                       699******99774 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 ?   -0.9   0.0      0.85   2.2e+03      45      65 ..      58      77 ..      35      84 .. 0.78
   2 ?    8.5   0.0     0.001       2.6      37      67 ..     101     131 ..      80     143 .. 0.77
   3 ?   -1.0   0.0      0.92   2.3e+03      21      60 ..     144     188 ..     136     201 .. 0.48
   4 ?    1.1   1.5      0.21   5.4e+02      37      65 ..     309     337 ..     234     352 .. 0.82
   5 ?    0.1   0.0      0.44   1.1e+03      36      60 ..     360     384 ..     339     387 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.85
                                      CESTTSSEEEEEEEEESSSEE CS
                     Inhibitor_I42 45 delvGaggthvwtfkalkpGe 65
                                      d   G+g  ++w +k  ++G+
  gi|330508092|ref|YP_004384520.1| 58 D-SFGTGKDDIWLIKTDSKGN 77
                                      3.78999999**999999998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.001
                                       TTCECCECCESTTSSEEEEEEEEESSSEEEE CS
                     Inhibitor_I42  37 eeyipdesdelvGaggthvwtfkalkpGett 67 
                                       ++yi    +e  Gagg+++w +ka+++G+ +
  gi|330508092|ref|YP_004384520.1| 101 SGYIIAGLTESYGAGGKDIWLIKANSKGDKE 131
                                       555555445599****************975 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.92
                                       EEEEEE--TTTEEE-T..TTCECCECCE...STTSSEEEEEEEEE CS
                     Inhibitor_I42  21 sWtvdasdseglklls..eeyipdesde...lvGaggthvwtfka 60 
                                        W+++++++ g  ll+  ++y + + d       + gt+ w  + 
  gi|330508092|ref|YP_004384520.1| 144 CWSIQETSDHGYILLGdtKSYNAGDFDIwliKTDSNGTKMWDRTF 188
                                       566666644444444412222222222244444444555555544 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.21
                                       TTCECCECCESTTSSEEEEEEEEESSSEE CS
                     Inhibitor_I42  37 eeyipdesdelvGaggthvwtfkalkpGe 65 
                                        +yi   ++   G+gg + w +k  + G 
  gi|330508092|ref|YP_004384520.1| 309 GGYIIAGETRSYGTGGSDAWVIKTDQNGI 337
                                       45555555558999999999999998885 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 0.44
                                       TTTCECCECCESTTSSEEEEEEEEE CS
                     Inhibitor_I42  36 seeyipdesdelvGaggthvwtfka 60 
                                       ++eyi   ++   G+gg +++ +k 
  gi|330508092|ref|YP_004384520.1| 360 DDEYIMLGDTDSYGSGGFDIFMVKM 384
                                       3667766666699*******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3017.05
//
Query:       gi|330508093|ref|YP_004384521.1|  [L=306]
Description: hypothetical protein MCON_2185 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-38  130.1   0.3      6e-38  129.4   0.3    1.4  1  PatG_C    PatG C-terminal
    2.8e-35  121.1   0.1    2.7e-33  114.7   0.1    2.2  1  PatG_D    PatG Domain
  ------ inclusion threshold ------
       0.14   12.6   0.1        0.3   11.5   0.1    1.5  1  ZapA      Cell division protein ZapA


Domain annotation for each model (and alignments):
>> PatG_C  PatG C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.4   0.3     1e-41     6e-38       1     115 []     192     303 ..     192     303 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 1e-41
                            PatG_C   1 ekqeeeftkairevLdrvlqelrNlGatdedRAlNylatrapdiyretaelileslsLdsveveksplsradsdcvd 77 
                                       ekqe++f++a++e++dr+lq+++N+Ga+de+RAlNyla+r+p iy+++ae++++++sL++ve+++s+ls+a +++v+
  gi|330508093|ref|YP_004384521.1| 192 EKQEGKFRAAANELFDRILQMADNTGANDEHRALNYLAVRYPAIYAKAAEEFEHNFSLTGVEARPSRLSGA-RKIVS 267
                                       58999******************************************************************.***** PP

                            PatG_C  78 VkltftnkenssraekkyrvtvDVseelPflvtkvqsy 115
                                       V++++tn+  ++++++ky+v+vDVsee+Pflvtk+ sy
  gi|330508093|ref|YP_004384521.1| 268 VIFSYTNR--ETDVTEKYFVRVDVSEEFPFLVTKMASY 303
                                       *******9..9************************998 PP

>> PatG_D  PatG Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.7   0.1   4.5e-37   2.7e-33       1      99 [.      51     243 ..      51     255 .. 0.93

  Alignments for each domain:
  == domain 1  score: 114.7 bits;  conditional E-value: 4.5e-37
                            PatG_D   1 lvYviGrieadFpnearekefvqalaraktanpedqqalakvLsnrenrylaralsWiLtiegipiYvllPn..... 72 
                                       +vY +Grie++Fpn+++e+ef qa++ra+ta+++d+qa+++vLs++enryl+r+l+W+L ieg+ +Y+llP+     
  gi|330508093|ref|YP_004384521.1|  51 YVYSLGRIEPHFPNMSAEREFAQAMGRAETAGMTDSQAFYSVLSKKENRYLVRDLCWTLAIEGMATYILLPKdpldf 127
                                       8**************************************************************************** PP

                            PatG_D  73 .......................................................................kpfale 78 
                                                                                                               ++a+e
  gi|330508093|ref|YP_004384521.1| 128 drlvesvkpqqdkadidvvvgskgpvalpemcsglqvplvgfdqlfsfdrdafiksiprpesipekqegkfRAAANE 204
                                       ***********************************************************************999*** PP

                            PatG_D  79 lfarliealdnqedteesra..................d 99 
                                       lf+r+++++dn+++++e+ra                  +
  gi|330508093|ref|YP_004384521.1| 205 LFDRILQMADNTGANDEHRAlnylavrypaiyakaaeeF 243
                                       ******************997777666555555544433 PP

>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1     5e-05       0.3      13      53 ..     189     229 ..     188     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5e-05
                              ZapA  13 aceegeeeylreaaklvdekikeireaggnlseerllvmaa 53 
                                       +++e +e   r+aa+++ ++i ++ +++g  +e r+l   a
  gi|330508093|ref|YP_004384521.1| 189 SIPEKQEGKFRAAANELFDRILQMADNTGANDEHRALNYLA 229
                                       58999************************989999986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2175.04
//
Query:       gi|330508094|ref|YP_004384522.1|  [L=395]
Description: hypothetical protein MCON_2186 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-05   25.7   0.6         50    4.3   0.0    6.3  7  Colicin_E5  Colicin E5 ribonuclease domain
    9.5e-05   22.2   9.4        8.3    6.3   0.1    5.8  6  DUF2064     Uncharacterized protein conserved in bacteria (DU
  ------ inclusion threshold ------
      0.015   15.1   0.0          4    7.2   0.0    3.1  4  DUF4166     Domain of unknown function (DUF4166)


Domain annotation for each model (and alignments):
>> Colicin_E5  Colicin E5 ribonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.4   2.4e+03      37      68 ..      23      54 ..      18      58 .. 0.81
   2 ?    2.1   0.0     0.041   2.4e+02      32      67 ..      70     105 ..      68     110 .. 0.87
   3 !    4.3   0.0    0.0085        51      32      67 ..     122     157 ..     120     160 .. 0.91
   4 ?    0.5   0.0      0.13   7.7e+02      33      67 ..     175     209 ..     173     213 .. 0.87
   5 !    4.3   0.0    0.0083        50      32      70 ..     227     265 ..     225     269 .. 0.91
   6 ?    1.8   0.0     0.052   3.1e+02      32      67 ..     279     314 ..     275     328 .. 0.88
   7 ?    2.4   0.1     0.033     2e+02      32      69 ..     341     378 ..     339     386 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.4
                        Colicin_E5 37 ddkranktsDglrrndsAtvYgekdgkYvvvn 68
                                       ++ +nkt  g + +    +   +dg+Y++v 
  gi|330508094|ref|YP_004384522.1| 23 PEEVWNKTFGGSGIDLGSQAQETEDGGYILVG 54
                                      5677899999999999999999999***9985 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.041
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt s+ ++ +n+   g + ++  +v   +dg+Y+ v
  gi|330508094|ref|YP_004384522.1|  70 KTDSNGNELWNRIFGGPKEDNGYSVQKTEDGGYITV 105
                                       678888999999999999999************987 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0085
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt    +k+++kt  g   ++  +v   +dg+Y++ 
  gi|330508094|ref|YP_004384522.1| 122 KTDVAGNKQWDKTFGGRDIDEGRSVLQANDGGYIIA 157
                                       67777899**************************95 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.13
                        Colicin_E5  33 tkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       t  s ++++n+t  g + +   +v   +dg+Y++ 
  gi|330508094|ref|YP_004384522.1| 175 TDPSGKEQWNRTFGGPGYDAGWAVDKTNDGGYIIT 209
                                       66677899999999999999999**********96 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.0083
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvndr 70 
                                       kt+s+  ++++kt  g   +   +v   kdg+Y++v d 
  gi|330508094|ref|YP_004384522.1| 227 KTNSTGITQWEKTFGGSAWDGCRAVRETKDGGYILVGDT 265
                                       688888899***************************986 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.052
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt  s ++++nkt  g + +   ++   +d++Y++ 
  gi|330508094|ref|YP_004384522.1| 279 KTDPSGKEQWNKTYGGSGYDWGFSIQQTNDSGYIIA 314
                                       667778999*************************97 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.033
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvnd 69 
                                       kt s+ ++ +n t  g + + + ++   k+g+Y++   
  gi|330508094|ref|YP_004384522.1| 341 KTDSNGNELWNTTFGGKGTDGAYSIQETKAGGYIIEGS 378
                                       7888999999*9999*****999***********9655 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 !    6.2   0.1    0.0014       8.4      96     108 ..      45      57 ..      42      70 .. 0.84
   2 !    4.7   0.1    0.0042        25      95     108 ..      96     109 ..      87     122 .. 0.83
   3 !    6.3   0.1    0.0014       8.3      95     108 ..     148     161 ..     142     175 .. 0.84
   4 ?    0.9   0.1     0.061   3.7e+02      96     108 ..     201     213 ..     193     227 .. 0.83
   5 !    4.7   0.0    0.0043        26      96     108 ..     254     266 ..     250     279 .. 0.82
   6 ?   -2.5   0.0      0.69   4.2e+03      95     108 ..     305     318 ..     301     323 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0014
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       +eDGGY+l+G ++
  gi|330508094|ref|YP_004384522.1|  45 TEDGGYILVGSTE 57 
                                       69********995 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0042
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        +eDGGY+ +G +k
  gi|330508094|ref|YP_004384522.1|  96 KTEDGGYITVGATK 109
                                       579********996 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0014
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        a+DGGY++ Gl++
  gi|330508094|ref|YP_004384522.1| 148 QANDGGYIIAGLTR 161
                                       699*********97 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.061
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       ++DGGY++ G ++
  gi|330508094|ref|YP_004384522.1| 201 TNDGGYIITGPTE 213
                                       68******99874 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.0043
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       ++DGGY+l+G ++
  gi|330508094|ref|YP_004384522.1| 254 TKDGGYILVGDTQ 266
                                       68********886 PP

  == domain 6  score: -2.5 bits;  conditional E-value: 0.69
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        ++D GY++ G ++
  gi|330508094|ref|YP_004384522.1| 305 QTNDSGYIIAGSTE 318
                                       5789*****99884 PP

>> DUF4166  Domain of unknown function (DUF4166)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0    0.0057        34      64      84 ..      71      89 ..      61     104 .. 0.76
   2 ?    7.2   0.0   0.00068         4      64      96 ..     175     201 ..     128     209 .. 0.89
   3 ?   -3.8   0.0       1.6   9.6e+03      64      81 ..     280     295 ..     274     301 .. 0.80
   4 ?   -1.9   0.0       0.4   2.4e+03      64      84 ..     342     359 ..     332     377 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0057
                           DUF4166 64 rdesgretltwtRtfefpgkt 84
                                      +d++g+e   w+R f++p++ 
  gi|330508094|ref|YP_004384522.1| 71 TDSNGNE--LWNRIFGGPKED 89
                                      6899***..********9443 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00068
                           DUF4166  64 rdesgretltwtRtfefpgktrtfdstmvlagg 96 
                                       +d+sg+e   w+Rtf++p     +d+ +++++ 
  gi|330508094|ref|YP_004384522.1| 175 TDPSGKE--QWNRTFGGP----GYDAGWAVDKT 201
                                       5889999..9********....78888887765 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.6
                           DUF4166  64 rdesgretltwtRtfefp 81 
                                       +d+sg+e   w+ t++++
  gi|330508094|ref|YP_004384522.1| 280 TDPSGKE--QWNKTYGGS 295
                                       6888999..999999987 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.4
                           DUF4166  64 rdesgretltwtRtfefpgkt 84 
                                       +d++g+e   w+ tf+++g t
  gi|330508094|ref|YP_004384522.1| 342 TDSNGNE--LWNTTFGGKG-T 359
                                       5899999..******9993.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 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:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 3104.12
//
Query:       gi|330508095|ref|YP_004384523.1|  [L=537]
Description: hypothetical protein MCON_2188 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-17   63.5  52.2    1.9e-16   60.0  27.1    3.1  3  NosD        Periplasmic copper-binding protein (NosD)
    2.1e-16   60.2  60.7    5.4e-07   29.6  32.1    4.8  3  Beta_helix  Right handed beta helix region


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2  12.5   0.00014       1.3      92     166 ..      69     142 ..      60     165 .. 0.77
   2 !    2.8   1.4    0.0068        61      51     131 ..     192     268 ..     145     283 .. 0.76
   3 !   60.0  27.1   2.2e-20   1.9e-16       2     226 ..     283     505 ..     281     533 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00014
                              NosD  92 nntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiyn 166
                                       nn + n ++++n+++ il+++++  ++++N +  ++ +Gi ++++++ +++++r++++ +  +  +ss+e+ +i+n
  gi|330508095|ref|YP_004384523.1|  69 NNHIGNGIVIRNTDAYILIKNCTMANLTGNYYGlYDVNGINIDDAKNVRVENCRLSGS-GSSLS-VSSAENIQITN 142
                                       4567788888888888999999999999999977999999999999999999999999.88888.77788877775 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0068
                              NosD  51 itgntienl..ryGihlensesntiedntlssnesGialmsssnn.tlenNtisnnenyGillsdssnntisnNtis 124
                                        +++ i+++  +y i+l + +++++e++ +++   G ++  +  n  ++n+t+ n +     +++ssn+t++n t  
  gi|330508095|ref|YP_004384523.1| 192 SQNCLIKDCksAYEIVLLSPKNCIVENCYVKD---GWLMAFTPINtSFTNSTVVNATM---EMDFSSNTTLENMTL- 261
                                       45566666666899999999999999999999...55666666554688888888866...899999998888776. PP

                              NosD 125 nnnkGif 131
                                        + kGi 
  gi|330508095|ref|YP_004384523.1| 262 VDLKGIN 268
                                       4555555 PP

  == domain 3  score: 60.0 bits;  conditional E-value: 2.2e-20
                              NosD   2 nnaisgdevlvsargngiqlensegsei.....snneisnsrdgi.lldnssnntitgntienlryGihlensesnt 72 
                                       n++  g++++ +  ++g++len +   i      +++i+ +++g  ++ ns++ ti+g++    ++ i l  s+++ 
  gi|330508095|ref|YP_004384523.1| 283 NSTANGEKIYYYHDQKGLHLENLTAGYIwlvdcPETRIEGVEAGGiFAINSNSSTIEGSK----ANQIILAFSKDVL 355
                                       4556677777777999999999977777777877888888888776999*********74....4679********* PP

                              NosD  73 iedntlssne..sGialmsssnn.tlenNtisnnen........yGillsdssnntisnNtis.nnnkGiflensss 137
                                       i++ntl++++  ++i l+  + n tl  N+i+++e+         Gi  s+s++n+  +N+i  ++++Gi+  +  +
  gi|330508095|ref|YP_004384523.1| 356 ITNNTLRGSSarEAIKLDTGTSNiTLYHNIITKSERyfgenlfaSGIDASQSDGNNTFENNIItDSGYGIQAGG--N 430
                                       *******999999****9999888******************999**999999866555555449999999887..9 PP

                              NosD 138 ntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydgeD 214
                                       nt+tgN+i++n  + i    s+++n++++N+Fi n ++++ ++  n ++ ++              GN+W++y+g  
  gi|330508095|ref|YP_004384523.1| 431 NTFTGNTIANN-IVSIK--VSGNNNRVTQNNFIYNGVDAEQSSYMNISFANN-----------IWDGNFWATYKGVE 493
                                       ***********.78887..66779************9999999886666333...........369*********** PP

                              NosD 215 adgDGigDtpYe 226
                                       +d+ G+g tpY 
  gi|330508095|ref|YP_004384523.1| 494 KDKTGLGSTPYV 505
                                       ***********2 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 !   29.0  16.8     9e-11   8.1e-07       1     155 [.      74     243 ..      39     246 .. 0.68
   2 !   15.6   0.3   1.2e-06     0.011      33     121 ..     194     294 ..     187     310 .. 0.65
   3 !   29.6  32.1     6e-11   5.4e-07      24     158 .]     326     459 ..     313     481 .. 0.47

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 9e-11
                                       -SEEE-SS-E..EEESEEEES-........SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE--- CS
                        Beta_helix   1 sgisingssn.vtiknntisns........ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnn 68 
                                       +gi+i++++  + ikn+t  n           +Gi +++++nv++en+++++ s                      +
  gi|330508095|ref|YP_004384523.1|  74 NGIVIRNTDAyILIKNCTMANLtgnyyglyDVNGINIDDAKNVRVENCRLSG-S----------------------G 127
                                       3455555555455555555555555555555555555555555555555555.5......................5 PP

                                       .................SEEE-TT--S--EEES-EEES-.SS-SEE-TT-S--EE..........ES-EEESTT.-- CS
                        Beta_helix  69 .................gggialfgasnnlienneitdn.ggsGiylnyssnnti..........enNiidnna.gs 116
                                                        g  i+++g +n lien++ ++   +  i+l+ s+++t           +n+ i++++ ++
  gi|330508095|ref|YP_004384523.1| 128 sslsvssaeniqitnyrGKNIMFNGVKNGLIENCNSEHIlVQEKIELMPSPRVTTdfmpetsvpsQNCLIKDCKsAY 204
                                       5555555555555555556799*****************84447888854443333344444455*********999 PP

                                       SEE---TT---EEES-EEES-SSEEEE-TT-SS.--EEES CS
                        Beta_helix 117 GividdsssnvtvtnNtitnnkgaGiavvgsss.nvtvrn 155
                                        iv+ + + n+ v+n+ +++    +++ +++s  n tv+n
  gi|330508095|ref|YP_004384523.1| 205 EIVLLSPK-NCIVENCYVKDGWLMAFTPINTSFtNSTVVN 243
                                       99999999.************9999999998886777776 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.2e-06
                                       -.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---.................SEEE-TT--S--EEES-EEES-SS CS
                        Beta_helix  33 nvvienneiannsgsGiyilgssnntisnntisdnn.................gggialfgasnnlienneitdngg 92 
                                       n++i++++ a+     i +l+ +n++++n+++ d++                 +  + ++ +sn+++en +  d + 
  gi|330508095|ref|YP_004384523.1| 194 NCLIKDCKSAY----EIVLLSPKNCIVENCYVKDGWlmaftpintsftnstvvNATMEMDFSSNTTLENMTLVDLK- 265
                                       44444444444....6777777888888888887777766666666666667777777888888888888888885. PP

                                       -SEE-TT....-S--EEES-EEESTT--SEE-- CS
                        Beta_helix  93 sGiylny....ssnntienNiidnnagsGivid 121
                                        Gi+l +    s++ +++n+++++ +   i+++
  gi|330508095|ref|YP_004384523.1| 266 -GINLGGfspeSYSPVVKNSTANGEK---IYYY 294
                                       .5666656666888888888886655...3333 PP

  == domain 3  score: 29.6 bits;  conditional E-value: 6e-11
                                       -SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---.SEEE-TT.--S--EEES-EEES-SS-..... CS
                        Beta_helix  24 yGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnn.gggialf.gasnnlienneitdnggs..... 93 
                                        Gi++ +s++ +ie+++ ++     i +  s+++ i+nnt +++    +i+l+ g+sn +++ n it+ +++     
  gi|330508095|ref|YP_004384523.1| 326 GGIFAINSNSSTIEGSKANQ-----IILAFSKDVLITNNTLRGSSaREAIKLDtGTSNITLYHNIITKSERYfgenl 397
                                       55555555553333333333.....4444455555555555555444445555555555555555555544444444 PP

                                       ...SEE-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E. CS
                        Beta_helix  94 ...Giyln.yssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNti 158
                                          Gi  + +  nnt+enNii++ + +Gi+   ++   t+t+Nti nn +++i+v g+++   v++N++
  gi|330508095|ref|YP_004384523.1| 398 fasGIDASqSDGNNTFENNIITDSG-YGIQAGGNN---TFTGNTIANN-IVSIKVSGNNN--RVTQNNF 459
                                       4445555533444555555554444.555444444...3455555555.35554444444..3333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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 0.25s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 4032.59
//
Query:       gi|330508096|ref|YP_004384524.1|  [L=93]
Description: hypothetical protein MCON_2189 [Methanosaeta concilii GP6]
Scores for 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-09   35.1   0.1    1.4e-08   34.5   0.1    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
      4e-08   32.9   0.1    7.4e-08   32.1   0.0    1.5  1  HTH_IclR         IclR helix-turn-helix domain
      4e-08   33.0   0.1    6.6e-08   32.3   0.1    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
    6.8e-07   29.3   0.0    1.1e-06   28.5   0.0    1.5  1  HTH_20           Helix-turn-helix domain
    4.1e-06   26.6   0.0    6.4e-06   26.0   0.0    1.3  1  MarR_2           MarR family
      9e-06   25.6   0.1    1.2e-05   25.2   0.1    1.2  1  PadR             Transcriptional regulator PadR-like family
     0.0002   20.9   0.1    0.00036   20.0   0.1    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00049   19.8   0.0    0.00062   19.5   0.0    1.3  1  RP-C             Replication protein C N-terminal domain
     0.0005   19.8   0.1    0.00077   19.2   0.1    1.5  1  DUF1495          Winged helix DNA-binding domain (DUF1495)
      0.001   19.0   0.1     0.0013   18.6   0.1    1.2  1  HTH_45           Winged helix-turn-helix
     0.0015   18.8   0.0     0.0019   18.5   0.0    1.3  1  DUF2513          Hypothetical protein (DUF2513)
     0.0017   18.4   0.1     0.0046   17.0   0.1    1.8  2  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
     0.0018   18.8   0.1     0.0026   18.2   0.1    1.3  1  HTH_27           Winged helix DNA-binding domain
     0.0028   17.6   0.2     0.0072   16.3   0.1    1.8  2  HTH_35           Winged helix-turn-helix DNA-binding
     0.0031   17.3   0.1     0.0045   16.8   0.1    1.2  1  HxlR             HxlR-like helix-turn-helix
     0.0098   16.1   0.1      0.013   15.7   0.1    1.3  1  Rio2_N           Rio2, N-terminal
  ------ inclusion threshold ------
      0.013   15.6   0.1      0.017   15.2   0.1    1.2  1  Sulfolobus_pRN   Sulfolobus plasmid regulatory protein
      0.015   15.2   0.0      0.023   14.6   0.0    1.4  1  HTH_43           Winged helix-turn helix
       0.02   15.0   0.0      0.027   14.6   0.0    1.3  1  FUR              Ferric uptake regulator family
      0.025   15.0   0.0      0.035   14.6   0.0    1.3  1  HTH_40           Helix-turn-helix domain
      0.035   14.5   0.1       0.13   12.7   0.0    1.9  2  HTH_26           Cro/C1-type HTH DNA-binding domain
      0.055   13.2   0.0      0.079   12.7   0.0    1.2  1  DUF4364          Domain of unknown function (DUF4364)
      0.065   13.6   0.1      0.096   13.1   0.1    1.4  1  Rrf2             Transcriptional regulator
      0.068   13.5   0.3      0.095   13.1   0.3    1.3  1  Penicillinase_R  Penicillinase repressor
      0.088   12.6   0.0      0.094   12.5   0.0    1.2  1  DUF742           Protein of unknown function (DUF742)
       0.11   12.4   0.1       0.19   11.6   0.1    1.6  1  DUF3116          Protein of unknown function (DUF3116)


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1     2e-11   1.4e-08      18      58 ..      30      70 ..      27      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2e-11
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      l++ ++t++e+++ +g+p+s++Y+ L+ L+++GlV +e++ 
  gi|330508096|ref|YP_004384524.1| 30 LSSRRMTVTELSRTSGLPKSTIYDNLSVLVKAGLVVKEDKI 70
                                      57889******************************999865 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 !   32.1   0.0   1.1e-10   7.4e-08      17      51 ..      33      67 ..      25      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.1e-10
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      +++t++el+r +glpkSt +  L+ Lv+ G+v ++
  gi|330508096|ref|YP_004384524.1| 33 RRMTVTELSRTSGLPKSTIYDNLSVLVKAGLVVKE 67
                                      78******************************875 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 !   32.3   0.1   9.5e-11   6.6e-08       3      45 ..      22      64 ..      20      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 9.5e-11
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +R  I++ L+++ ++v+el++  gl++st+   L++L +aGLV
  gi|330508096|ref|YP_004384524.1| 22 KRTTIIRNLSSRRMTVTELSRTSGLPKSTIYDNLSVLVKAGLV 64
                                      7999**************************************9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.7e-09   1.1e-06      12      56 ..      23      66 ..       8      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.7e-09
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      R  i r L + + +t++el ++ +l+k+t++++L vL++agLv  
  gi|330508096|ref|YP_004384524.1| 23 RTTIIRNL-SSRRMTVTELSRTSGLPKSTIYDNLSVLVKAGLVVK 66
                                      66799999.99*******************************865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   9.3e-09   6.4e-06      15      54 ..      31      67 ..      21      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 9.3e-09
                                      HCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 15 grrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                           r++tv+el r+ gl+ks++   l  Lv+aGLv+++
  gi|330508096|ref|YP_004384524.1| 31 SS---RRMTVTELSRTSGLPKSTIYDNLSVLVKAGLVVKE 67
                                      33...459*****************************998 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   1.7e-08   1.2e-05      29      73 ..      46      86 ..      25      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.7e-08
                                      TTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                              PadR 29 lseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                      l ++++Y++L+ L k glv++e + +    +  yY+lT++G+r  
  gi|330508096|ref|YP_004384524.1| 46 LPKSTIYDNLSVLVKAGLVVKEDKIN----QWVYYELTKKGHRLA 86
                                      5699******************9996....99*********9865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   5.3e-07   0.00036      17      47 ..      34      64 ..      25      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.3e-07
                            HTH_24 17 risqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      r++ +eL++ +gl++st+   l  L+++Gl+
  gi|330508096|ref|YP_004384524.1| 34 RMTVTELSRTSGLPKSTIYDNLSVLVKAGLV 64
                                      8****************************98 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 !   19.5   0.0     9e-07   0.00062      75     116 ..      38      79 ..      18      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9e-07
                              RP-C  75 aqLsralglsestlrrhlaaLveaGliirrDspngkRyarrd 116
                                       ++Lsr  gl++st+  +l+ Lv+aGl++  D  n+  y    
  gi|330508096|ref|YP_004384524.1|  38 TELSRTSGLPKSTIYDNLSVLVKAGLVVKEDKINQWVYYELT 79 
                                       589****************************99986665555 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 !   19.2   0.1   1.1e-06   0.00077      52      89 ..      51      88 ..      17      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.1e-06
                           DUF1495 52 rynsessLielGLveeeeeseglklYklteeGieivev 89
                                       y++ s L++ GLv +e++ ++  +Y+lt++G +++e 
  gi|330508096|ref|YP_004384524.1| 51 IYDNLSVLVKAGLVVKEDKINQWVYYELTKKGHRLAEA 88
                                      5899999*******99999999*************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 !   18.6   0.1     2e-06    0.0013      11      70 ..      26      90 ..      23      93 .] 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2e-06
                            HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli.....kkskekYvlTekGlelleklk 70
                                      I +++s+ + + T++   + L  +++   L+ Lv+ gl+      ++   Y+lT+kG +l e +k
  gi|330508096|ref|YP_004384524.1| 26 IIRNLSSRRMTVTELSRTSGLPKSTIYDNLSVLVKAGLVvkedkINQWVYYELTKKGHRLAEAIK 90
                                      777888999999**************************9654433344679*********99887 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.7e-06    0.0019      29      87 ..      38      91 ..      15      93 .] 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.7e-06
                           DUF2513 29 eklsaidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtweGhdFLdsiRd 87
                                      ++ls+  g +k +i+  l++l++agL+  e+k     i ++v+++Lt +Gh + ++i+ 
  gi|330508096|ref|YP_004384524.1| 38 TELSRTSGLPKSTIYDNLSVLVKAGLVVKEDK-----INQWVYYELTKKGHRLAEAIKA 91
                                      33448889999***************986654.....34589*************9986 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.7   2.5e+03      28      32 ..      10      14 ..       1      30 [. 0.53
   2 !   17.0   0.1   6.7e-06    0.0046      24      57 ..      31      64 ..      24      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.7
                                      BEHHH CS
                             HTH_9 28 ltlre 32
                                      l+++ 
  gi|330508096|ref|YP_004384524.1| 10 LSSKA 14
                                      33333 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 6.7e-06
                                      HHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9 24 rkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                      ++ r t++el+++++L+++ + + L+vL++ +lV
  gi|330508096|ref|YP_004384524.1| 31 SSRRMTVTELSRTSGLPKSTIYDNLSVLVKAGLV 64
                                      55689*************************9998 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 !   18.2   0.1   3.8e-06    0.0026       8      68 .]      26      82 ..      23      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.8e-06
                            HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +++++    rr++ ++l+++  + +s+i  +l+ L+++GLv+++ +      + ++lT kG
  gi|330508096|ref|YP_004384524.1| 26 IIRNLS--SRRMTVTELSRTSGLPKSTIYDNLSVLVKAGLVVKEDKI--NQWVYYELTKKG 82
                                      566777..99*******************************666554..334899999888 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 !   16.3   0.1     1e-05    0.0072       5      35 ..      24      54 ..      21      65 .. 0.88
   2 ?   -2.0   0.0       5.4   3.7e+03      10      20 ..      77      87 ..      74      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                            HTH_35  5 adIiAaLrkrgttLaalsreaglssstlsna 35
                                        Ii +L  r++t+++lsr++gl +st+   
  gi|330508096|ref|YP_004384524.1| 24 TTIIRNLSSRRMTVTELSRTSGLPKSTIYDN 54
                                      67999*********************98665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.4
                            HTH_35 10 aLrkrgttLaa 20
                                      +L k+g  La+
  gi|330508096|ref|YP_004384524.1| 77 ELTKKGHRLAE 87
                                      67888888875 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   6.5e-06    0.0045       9      77 ..      25      90 ..      21      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.5e-06
                                      HHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHH CS
                              HxlR  9 lilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlq 77
                                       i+++l + ++  +el+r+  +++++++  +L  L + gl+ +e  +++ + v Y+lt+kG+ l+++++
  gi|330508096|ref|YP_004384524.1| 25 TIIRNLSSRRMTVTELSRTS-GLPKSTIYDNLSVLVKAGLVVKE--DKINQWVYYELTKKGHRLAEAIK 90
                                      689999999999*****998.9******************9776..56777899**********99987 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.9e-05     0.013      26      71 ..      36      83 ..      20      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-05
                            Rio2_N 26 ptelieeisrlkeeevkkrlsrllkaklisr..ktakydGYkLtyeGy 71
                                       +++++++s+l ++ + + ls l+ka+l+++  k  ++  Y+Lt +G+
  gi|330508096|ref|YP_004384524.1| 36 TVTELSRTSGLPKSTIYDNLSVLVKAGLVVKedKINQWVYYELTKKGH 83
                                      567899*************************76566888899999997 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   2.4e-05     0.017       8      51 ..      24      67 ..      17      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-05
                    Sulfolobus_pRN  8 ekillilsrrcatleeleektGiekeellvyltrlykrGlisrk 51
                                        i+  ls r +t+ el   +G++k ++   l+ l k Gl+ ++
  gi|330508096|ref|YP_004384524.1| 24 TTIIRNLSSRRMTVTELSRTSGLPKSTIYDNLSVLVKAGLVVKE 67
                                      568889**********************************9864 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.3e-05     0.023       8      71 ..      22      82 ..      15      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-05
                                      HHHHHHHHHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE--TTS-S--EEEEEE-T CS
                            HTH_43  8 RrlylaylideeeanvpklieltgmPRRtlqDtlkalaeldielefvqegernnaGyyrisdWG 71
                                      +r  ++  +++++ +v +l ++ g+P+ t+ D l+ l + ++ ++   e + n+  yy++++ G
  gi|330508096|ref|YP_004384524.1| 22 KRTTIIRNLSSRRMTVTELSRTSGLPKSTIYDNLSVLVKAGLVVK---EDKINQWVYYELTKKG 82
                                      56666777888899***********************99998877...5667777788877766 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     4e-05     0.027      38      77 ..      44      83 ..      23      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-05
                                      TT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSSS CS
                               FUR 38 peislaTVYrtLklleeaglvkelefedgesryelakkeh 77
                                      + +  +T+Y +L +l +aglv + +  ++  +yel+kk h
  gi|330508096|ref|YP_004384524.1| 44 SGLPKSTIYDNLSVLVKAGLVVKEDKINQWVYYELTKKGH 83
                                      556679***************9999999999999997544 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     5e-05     0.035       7      49 ..      29      74 ..      23      93 .] 0.71

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5e-05
                            HTH_40  7 elleeglsieeIAkerglkesTIegHLaelieeg...eeidlerlv 49
                                      +l    +++ e ++  gl +sTI++ L  l+++g   +e ++++ v
  gi|330508096|ref|YP_004384524.1| 29 NLSSRRMTVTELSRTSGLPKSTIYDNLSVLVKAGlvvKEDKINQWV 74
                                      5567789**************************9555334444444 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 ?   -0.5   0.0       2.6   1.8e+03       5      21 ..       9      25 ..       1      30 [. 0.48
   2 ?   12.7   0.0   0.00018      0.13       7      29 ..      31      53 ..      25      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.6
                            HTH_26  5 lmadrgitkseLargtg 21
                                      ++  + +++  L+++t 
  gi|330508096|ref|YP_004384524.1|  9 ALSSKALKVPALSKRTT 25
                                      23333334444456655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00018
                            HTH_26  7 adrgitkseLargtgisaatlsr 29
                                        r++t++eL+r +g+ ++t++ 
  gi|330508096|ref|YP_004384524.1| 31 SSRRMTVTELSRTSGLPKSTIYD 53
                                      679*****************997 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011     0.079      38      74 ..      53      90 ..      49      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                           DUF4364 38 qalseLvesglieee.ekenktlykiTekGketlelfe 74
                                      + ls Lv++gl+ +e + ++  +y++T+kG + +e ++
  gi|330508096|ref|YP_004384524.1| 53 DNLSVLVKAGLVVKEdKINQWVYYELTKKGHRLAEAIK 90
                                      56899********996779999*********9998765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00014     0.096      19      56 ..      29      65 ..      12      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                                      HSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 19 keeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      + ++++ ++++e+++  ++++s +   l+ L kaglv 
  gi|330508096|ref|YP_004384524.1| 29 NLSSRR-MTVTELSRTSGLPKSTIYDNLSVLVKAGLVV 65
                                      445555.*****************************95 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   0.00014     0.095      24      70 ..      37      83 ..      22      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                                      HHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXX CS
                   Penicillinase_R 24 veeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseee 70
                                      v+el++++ l +sT+   l+ Lvk gl+ +e + ++ +Y+ l+++ +
  gi|330508096|ref|YP_004384524.1| 37 VTELSRTSGLPKSTIYDNLSVLVKAGLVVKEDKINQWVYYELTKKGH 83
                                      68999**********************************98888765 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014     0.094      40      89 ..      19      68 ..       2      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                            DUF742 40 rlqpehrailrLcreplsVaelaAelklPvgvvrvLlsdLldaglltvra 89
                                      +l++  + i +L +++++V el+ +  lP +++   ls L++agl++ + 
  gi|330508096|ref|YP_004384524.1| 19 ALSKRTTIIRNLSSRRMTVTELSRTSGLPKSTIYDNLSVLVKAGLVVKED 68
                                      455556666789999*****************************998665 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00027      0.19      56      84 ..      63      90 ..      15      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                           DUF3116 56 yilRkeekannkkrYelTekGellykelk 84
                                       ++++++ +n+  +YelT+kG+ l + +k
  gi|330508096|ref|YP_004384524.1| 63 LVVKEDK-INQWVYYELTKKGHRLAEAIK 90
                                      5555555.7999***********998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 0.59u 0.38s 00:00:00.97 Elapsed: 00:00:00.58
# Mc/sec: 480.87
//
Query:       gi|330508097|ref|YP_004384525.1|  [L=119]
Description: hypothetical protein MCON_2190 [Methanosaeta concilii GP6]
Scores for complete 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    3.6e-32  111.5   0.0    1.0  1  DUF1670       Protein of unknown function (DUF1670)
      0.001   18.8   0.0        2.4    8.0   0.0    3.1  3  HTH_23        Homeodomain-like domain
     0.0014   18.3   0.1       0.19   11.4   0.0    2.7  3  Sigma70_r4_2  Sigma-70, region 4
      0.004   16.7   0.0        3.4    7.3   0.0    3.3  4  HTH_24        Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.018   15.1   0.0         14    5.8   0.0    3.0  3  HTH_29        Winged helix-turn helix
      0.054   13.2   0.0       0.09   12.5   0.0    1.3  1  PsbH          Photosystem II 10 kDa phosphoprotein


Domain annotation for each model (and alignments):
>> DUF1670  Protein of unknown function (DUF1670)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   0.0   1.2e-35   3.6e-32     115     219 ..       2     103 ..       1     104 [. 0.97

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 1.2e-35
                           DUF1670 115 lgvstrtvskqvkeyqeeegivlptrGaikDiGpavsHKkkivrlylkgyetteiarrtnHseeaidRYikafekvk 191
                                        gvs  t+ k++k+yq e+g++lp+ G+i+DiGp+++  + i+ ++l+g   ++iar t+H+e ++dRYikaf+kv+
  gi|330508097|ref|YP_004384525.1|   2 TGVSAGTIGKNIKAYQTEQGVILPYWGTIRDIGPSMT--QVIIAKFLRGIPAPHIARTTQHTEGTCDRYIKAFKKVR 76 
                                       689********************************99..68************************************ PP

                           DUF1670 192 lLkekkleseeirlitglseklveeYle 219
                                       +L+ k +++ ei+ i+++se+lv+eY+ 
  gi|330508097|ref|YP_004384525.1|  77 MLNGK-MKPLEIARILEMSERLVKEYIV 103
                                       ***99.********************85 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.011        34      27      45 ..       2      21 ..       1      24 [. 0.82
   2 !    8.0   0.0   0.00081       2.4      10      42 ..      41      73 ..      39      81 .. 0.90
   3 ?    3.1   0.0     0.029        86      20      35 ..      84      99 ..      73     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.011
                            HTH_23 27 LgvsrrTvyrwlkryre.eG 45
                                       gvs  T+ + +k+y+   G
  gi|330508097|ref|YP_004384525.1|  2 TGVSAGTIGKNIKAYQTeQG 21
                                      59*************75255 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00081
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryr 42
                                      i+  +++G++ + IAr    ++ T +r++k+++
  gi|330508097|ref|YP_004384525.1| 41 IIAKFLRGIPAPHIARTTQHTEGTCDRYIKAFK 73
                                      7888889************************95 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.029
                            HTH_23 20 vreIAreLgvsrrTvy 35
                                      + eIAr+L +s+r v 
  gi|330508097|ref|YP_004384525.1| 84 PLEIARILEMSERLVK 99
                                      569********99775 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.61   1.8e+03      36      47 ..       2      13 ..       1      14 [. 0.82
   2 ?    3.7   0.0     0.016        49      17      48 ..      39      70 ..      38      74 .. 0.88
   3 !   11.4   0.0   6.5e-05      0.19      31      47 ..      86     102 ..      80     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.61
                                      HT--HHHHHHHH CS
                      Sigma70_r4_2 36 lgisegtVksrl 47
                                      +g+s gt+ +++
  gi|330508097|ref|YP_004384525.1|  2 TGVSAGTIGKNI 13
                                      79*****98776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.016
                                      HHHHHHHTS---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 17 eifllryleglsykEIAellgisegtVksrls 48
                                      ++++ ++l g +   IA+ +  +egt++++++
  gi|330508097|ref|YP_004384525.1| 39 QVIIAKFLRGIPAPHIARTTQHTEGTCDRYIK 70
                                      578888899999999*************9986 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 6.5e-05
                                       HHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2  31 EIAellgisegtVksrl 47 
                                       EIA++l++se+ Vk ++
  gi|330508097|ref|YP_004384525.1|  86 EIARILEMSERLVKEYI 102
                                       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 ?   -0.3   0.0      0.27     8e+02      27      39 ..       2      14 ..       1      19 [. 0.83
   2 ?   -2.2   0.0       1.1   3.3e+03      16      26 ..      35      45 ..      34      46 .. 0.83
   3 !    4.9   0.0    0.0066        20      20      42 ..      51      73 ..      47      74 .. 0.83
   4 !    7.3   0.0    0.0011       3.4      15      38 ..      79     102 ..      77     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.27
                            HTH_24 27 lglSpstvnrrlk 39
                                      +g+S +t+ + +k
  gi|330508097|ref|YP_004384525.1|  2 TGVSAGTIGKNIK 14
                                      89*****988887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                            HTH_24 16 prisqreLAer 26
                                      p+++q  +A+ 
  gi|330508097|ref|YP_004384525.1| 35 PSMTQVIIAKF 45
                                      78999999986 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0066
                            HTH_24 20 qreLAerlglSpstvnrrlkrLe 42
                                         +A+ +  + +t+ r++k ++
  gi|330508097|ref|YP_004384525.1| 51 APHIARTTQHTEGTCDRYIKAFK 73
                                      5569999*************986 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0011
                            HTH_24  15 nprisqreLAerlglSpstvnrrl 38 
                                       n+++   e+A+ l +S   v++++
  gi|330508097|ref|YP_004384525.1|  79 NGKMKPLEIARILEMSERLVKEYI 102
                                       89999*************999987 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.12   3.6e+02      21      39 ..       1      19 [.       1      23 [. 0.92
   2 ?    4.8   0.0    0.0097        29      10      38 ..      47      74 ..      39      80 .. 0.83
   3 ?    5.8   0.0    0.0047        14       6      39 ..      76     108 ..      75     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.12
                            HTH_29 21 llglsrrtvyrwlkrfeeg 39
                                      ++g+s  t+ + +k+++++
  gi|330508097|ref|YP_004384525.1|  1 MTGVSAGTIGKNIKAYQTE 19
                                      79**************987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0097
                            HTH_29 10 eGvstvsqiAkllglsrrtvyrwlkrfee 38
                                      +G +    iA+ ++ ++ t +r++k+f +
  gi|330508097|ref|YP_004384525.1| 47 RGIP-APHIARTTQHTEGTCDRYIKAFKK 74
                                      5666.6779*****************975 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0047
                            HTH_29   6 lllaeGvstvsqiAkllglsrrtvyrwlkrfeeg 39 
                                       ++l+  ++ + +iA++l +s+r v  ++ + +e 
  gi|330508097|ref|YP_004384525.1|  76 RMLNGKMK-PLEIARILEMSERLVKEYIVLIDEQ 108
                                       56666676.889**********999988888776 PP

>> PsbH  Photosystem II 10 kDa phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     3e-05      0.09       4      25 ..       9      30 ..       7      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                              PsbH  4 lGdlLkplnseyGkvaPGWGtt 25
                                      +G+ +k+   e+G + P WGt 
  gi|330508097|ref|YP_004384525.1|  9 IGKNIKAYQTEQGVILPYWGTI 30
                                      7999*****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 881.10
//
Query:       gi|330508098|ref|YP_004384526.1|  [L=54]
Description: hypothetical protein MCON_2193 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-21   75.1   0.2    5.3e-21   75.0   0.2    1.0  1  DUF1670   Protein of unknown function (DUF1670)


Domain annotation for each model (and alignments):
>> DUF1670  Protein of unknown function (DUF1670)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.2   2.9e-25   5.3e-21     136     187 ..       2      53 ..       1      54 [] 0.97

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 2.9e-25
                           DUF1670 136 vlptrGaikDiGpavsHKkkivrlylkgyetteiarrtnHseeaidRYikaf 187
                                       v+ptr  i+DiGp+vsHK +i++l+lkgye tei++rt+H++e+i+RYi  f
  gi|330508098|ref|YP_004384526.1|   2 VVPTRDEIQDIGPTVSHKMNIIKLFLKGYEHTEIEQRTRHTGESIKRYISGF 53 
                                       9************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 413.47
//
Query:       gi|330508099|ref|YP_004384527.1|  [L=311]
Description: oligopeptide ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-25   89.6   0.1    3.3e-25   89.2   0.1    1.2  1  ABC_tran      ABC transporter
    1.6e-15   57.3   0.2    3.4e-15   56.3   0.2    1.6  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    6.2e-05   22.5   0.0    9.9e-05   21.9   0.0    1.3  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0011   19.0   0.0     0.0015   18.6   0.0    1.2  1  ResIII        Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.019   14.2   0.0      0.025   13.8   0.0    1.1  1  DUF2075       Uncharacterized conserved protein (DUF2075)
      0.037   13.8   0.1       0.42   10.4   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
       0.04   13.3   0.0       0.34   10.3   0.0    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.071   12.8   0.0      0.095   12.3   0.0    1.3  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
       0.13   11.8   0.0       0.23   11.0   0.0    1.3  1  AAA_7         P-loop containing dynein motor region
       0.15   11.8   0.0       0.33   10.8   0.0    1.4  1  SAM_3         SAM domain (Sterile alpha motif)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   0.1   1.8e-28   3.3e-25       2     136 ..      24     180 ..      23     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 1.8e-28
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke....qeleslrkeigvlpqe..pq 69 
                                       + v+l++k +e+++++Ge+G+GK+ L + +++ll      eG+i ++g+dl +    + ++   +ei+++ q+  ++
  gi|330508099|ref|YP_004384527.1|  24 NSVDLQIKDNERLGLIGETGCGKTVLGMSIIRLLPSsagVEGQIIYNGQDLLHlteeEMRQLRGREIAMILQNptTS 100
                                       789******************************98888899************999777888889********8889 PP

                                       S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEE CS
                                       xxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  70 lfpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllll 132
                                       l+p l+v+++              e+++++ ++l+   ++e +++++++ p++LSgG+k+rv++a+ l+++p+++++
  gi|330508099|ref|YP_004384527.1| 101 LNPVLKVGDQiaevislhkglgkkEAKARAVQMLEAAMIPE-AERRADQYPHELSGGMKERVMIAMGLASHPSFVIA 176
                                       9*********************9989999999999999999.99999****************************** PP

                                       ESTT CS
                                       xxxx RF
                          ABC_tran 133 DEpt 136
                                       DEpt
  gi|330508099|ref|YP_004384527.1| 177 DEPT 180
                                       ***9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.2   1.9e-18   3.4e-15       1      65 []     230     289 ..     230     289 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.9e-18
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       +E++++++++++p+HPYT++ +rs+p+       l+ i g+ psl + ++GC+F+pRCp+a+e C
  gi|330508099|ref|YP_004384527.1| 230 LEEASAETILNDPQHPYTQGFIRSLPSR-----GLHPISGSSPSLIDPPSGCRFHPRCPYAMEVC 289
                                       699***********************98.....46789*************************99 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   5.5e-08   9.9e-05      28     200 ..      37     212 ..      21     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.5e-08
                                       EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCH...CCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrse...klsdlihk.skekasvkkaeveitfdnedkklkiekeevsis 100
                                        ++G+ G+GK+ l  +i  +L  ++   +  +   + +dl+h  ++e +++   e++++++n+  +    ++ +++ 
  gi|330508099|ref|YP_004384527.1|  37 GLIGETGCGKTVLGMSIIRLLPSSAG--VEGQiiyNGQDLLHLtEEEMRQLRGREIAMILQNPTTS---LNPVLKVG 108
                                       589**************999985544..544411266999999566667777789***99999998...45555555 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDeid 168
                                        ++ +  + +  + +ke+ k+   ++le a+i +          +LSgG k  v++a+ +A +     ++++ De  
  gi|330508099|ref|YP_004384527.1| 109 DQIAEVISLHKGLGKKEA-KARAVQMLEAAMIPEAerradqyphELSGGMKERVMIAMGLASH----PSFVIADEPT 180
                                       555555544334433333.3334455666666555566666666***************9987....47******** PP

                                       TTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 169 aaLDeknvkkvaellkeksknaQfivislree 200
                                         LD++  +++++l++  ++   +++i+++  
  gi|330508099|ref|YP_004384527.1| 181 KGLDARTKAEIVNLIRDMTTGRSMLMITHDLA 212
                                       ********************999999999755 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   8.4e-07    0.0015      10      83 ..      21      91 ..      12     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8.4e-07
                                      HHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG... CS
                            ResIII 10 eaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayk 83
                                      +a++++  ++  k+++r+ +  +TG+GKT++ +++i+ l ++++  +  ++ ++++ll  t+ee++++   + +
  gi|330508099|ref|YP_004384527.1| 21 KAVNSVDLQI--KDNERLGLIGETGCGKTVLGMSIIRLLPSSAGV-EGQIIYNGQDLLHLTEEEMRQLRGREIA 91
                                      5666676666..6999999*********************99887.6677899999999999999887776643 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.4e-05     0.025       8     103 ..      40     148 ..      38     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                           DUF2075   8 GvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsef....... 77 
                                       G++G GKtv++++++  l   ++   +  ++ N++ +l+l e+  ++ +++++   ++++++  n++ +        
  gi|330508099|ref|YP_004384527.1|  40 GETGCGKTVLGMSIIRLL--PSSAGVEGQIIYNGQDLLHLTEEEMRQLRGREIAMILQNPTTSLNPVLKVgdqiaev 114
                                       99***************9..55555555555555555555555556666999*********9999999778878888 PP

                           DUF2075  78 ........kkaeekkeepkedvvivDEAhrlltk 103
                                               kk+++ ++ ++++ + + EA r  ++
  gi|330508099|ref|YP_004384527.1| 115 islhkglgKKEAKARAVQMLEAAMIPEAERRADQ 148
                                       8877777767777777777777777777777664 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 ?    1.3   0.1      0.14   2.5e+02       3      18 ..      37      52 ..      36      74 .. 0.81
   2 ?   10.4   0.0   0.00023      0.42     227     299 ..     143     211 ..      77     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.14
                            AAA_21  3 vliGpNgsGKSnLLda 18
                                      +liG  g+GK+ L   
  gi|330508099|ref|YP_004384527.1| 37 GLIGETGCGKTVLGMS 52
                                      69*********98654 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00023
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       +++ +  ++elS G+k+   ++++ l+ ++  s+++ DEp  gL+ +  ++++ l+++ ++ g   ++ TH+ 
  gi|330508099|ref|YP_004384527.1| 143 ERRADQYPHELSGGMKER-VMIAMGLASHP--SFVIADEPTKGLDARTKAEIVNLIRDMTT-GRSMLMITHDL 211
                                       566677889999999999.56666665565..9***********************99999.89999999985 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00019      0.34      16      51 ..      27      62 ..      14      91 .. 0.81
   2 ?    0.4   0.0      0.19   3.5e+02     174     198 ..     142     166 ..     129     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                      Mg_chelatase 16 eiaaaGgHnlllvGppGsGKtmlakrlpsllpplse 51
                                      ++ +  +  l l+G  G+GKt+l   +  llp+   
  gi|330508099|ref|YP_004384527.1| 27 DLQIKDNERLGLIGETGCGKTVLGMSIIRLLPSSAG 62
                                      555566677889********************8765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.19
                      Mg_chelatase 174 sekeierYlsklsgplldRidlqve 198
                                       +e++ ++Y + lsg + +R+ + + 
  gi|330508099|ref|YP_004384527.1| 142 AERRADQYPHELSGGMKERVMIAMG 166
                                       4677899************998875 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 ?   12.3   0.0   5.3e-05     0.095      15      88 ..      34     146 ..      25     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.3e-05
                                       -EEEEEESTTSSHHHHHHHHHHHSSTS...S.EEEEEE...................................ESEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx...x.xxxxxx...................................xxxx RF
                       ATP-synt_ab  15 qrtlipgafgvGktvisqslskqsnsd...d.aiiyvg...................................iGer 52 
                                       +r++++g+ g+Gktv+  s+++   s+   +  iiy g                                   +G +
  gi|330508099|ref|YP_004384527.1|  34 ERLGLIGETGCGKTVLGMSIIRLLPSSagvEgQIIYNGqdllhlteeemrqlrgreiamilqnpttslnpvlkVGDQ 110
                                       6899****************999877777755999999999999999999999999999999999999998886666 PP

                                       HHHHHHHHHHCHHSSGGGGEEEEEEETTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  53 gnevaevleefpegtimkrtvlvantsnepvaarea 88 
                                         ev ++ + + ++++ +r v ++  +  p a+r a
  gi|330508099|ref|YP_004384527.1| 111 IAEVISLHKGLGKKEAKARAVQMLEAAMIPEAERRA 146
                                       666666666666666666666666666666666655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013      0.23      26      59 ..      26      59 ..      19      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikdllkkldk 59
                                      ++l +k +  + l+G+tG+GKtv+ +++++ l++
  gi|330508099|ref|YP_004384527.1| 26 VDLQIKDNERLGLIGETGCGKTVLGMSIIRLLPS 59
                                      577889999999************9999988875 PP

>> SAM_3  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018      0.33      35      55 ..      69      88 ..      65      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                             SAM_3 35 lsGaqLfsLskeeLeqicgaa 55
                                      ++G++L++L+ ee++q+ g +
  gi|330508099|ref|YP_004384527.1| 69 YNGQDLLHLTEEEMRQLRG-R 88
                                      8***************999.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2029.52
//
Query:       gi|330508100|ref|YP_004384528.1|  [L=266]
Description: oligopeptide ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-33  114.4   0.0    7.5e-33  113.9   0.0    1.2  1  ABC_tran     ABC transporter
    1.3e-05   24.8   0.0    2.3e-05   24.0   0.0    1.5  1  SMC_N        RecF/RecN/SMC N terminal domain
    5.6e-05   23.1   0.3       0.34   10.7   0.0    2.5  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00095   19.6   0.0     0.0014   19.1   0.0    1.4  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
       0.01   16.1   0.4      0.029   14.7   0.4    1.9  1  AAA_22       AAA domain
      0.013   15.5   0.1      0.034   14.1   0.0    1.7  2  AAA_5        AAA domain (dynein-related subfamily)
      0.034   13.9   0.0      0.056   13.2   0.0    1.3  1  PRK          Phosphoribulokinase / Uridine kinase family
      0.057   12.7   0.0       0.14   11.5   0.0    1.6  2  Zeta_toxin   Zeta toxin
      0.064   13.2   0.0       0.11   12.4   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
       0.08   12.6   0.0        0.2   11.3   0.0    1.3  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
      0.084   13.3   0.0       0.18   12.2   0.0    1.8  1  AAA          ATPase family associated with various cellular a
       0.11   12.6   0.0       0.31   11.1   0.0    1.9  1  MMR_HSR1     50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   0.0     5e-36   7.5e-33       2     137 .]      27     180 ..      26     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 5e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       + vs+++ +ge++++vGe+G+GK+t+ +ll++l +pt+G+i +d++d+++   +e+++lr ++++++q+  ++l+p+
  gi|330508100|ref|YP_004384528.1|  27 DSVSFHIDQGETLGLVGESGCGKTTVGRLLLRLIEPTSGSIIFDSRDITRlnrKEMRKLRPRMQMIFQDpeSSLNPR 103
                                       78************************************************999999*************9999**** PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       ++++e+             ++ e  +++l+ ++ ++l+ +++++ p++LSgGq qrv+lar+l+ +p+++++DEpta
  gi|330508100|ref|YP_004384528.1| 104 MRIGESiaepfrlklhgkmTKIEIRDRVLELVDVVGLNPEHINRFPHQLSGGQNQRVVLARILAINPEFIVADEPTA 180
                                       ***********99998865444447889999999999999**999******************************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 !   24.0   0.0   1.5e-08   2.3e-05      28     215 ..      40     227 ..      17     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.5e-08
                                       EEEESTTSSHHHHHHHHHHHCTT.TTTT.TTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE....SSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGersakk.lrseklsdlihkskekasvkkaeveitfdnedkk....lkiekeevsi 99 
                                        +vG+ G+GK+ +   +l ++  +s +  + s+++++l   ++++ +  + +++++f++++++    ++i ++  + 
  gi|330508100|ref|YP_004384528.1|  40 GLVGESGCGKTTVGRLLLRLIEPTSGSIiFDSRDITRL---NRKEMRKLRPRMQMIFQDPESSlnprMRIGESIAEP 113
                                       58999999999999988777665555321344444444...456788889999****99988867767778888888 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHC.TT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevselles.agiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                        r + +++ ++++i ++  +  +v  l ++  +  +++LSgG+ + v la ++Ai+      + + De  a LD + 
  gi|330508100|ref|YP_004384528.1| 114 FRLKLHGKMTKIEIRDRVLELVDVVGLNPEhINRFPHQLSGGQNQRVVLARILAINP----EFIVADEPTASLDVSV 186
                                       8888888889999999999999998875441445589*****************974....499**********999 PP

                                       HHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEEEEE CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 176 vkkvaellkekskn..aQfivislreemlekadklvgvtkve 215
                                        +++ +l+   + +    ++ is++ e++++++  + v+k e
  gi|330508100|ref|YP_004384528.1| 187 QAQILRLMMDLKRKfcLTMLFISHDMEVVRHMSDRIAVMK-E 227
                                       88888887755555347899************99999987.4 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 !   10.0   0.1   0.00037      0.55       3      63 ..      40      96 ..      39     148 .. 0.71
   2 !   10.7   0.0   0.00023      0.34     251     302 ..     165     215 ..     149     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie 63
                                      +l+G  g+GK+++ ++l  l     + +++ ++++++  +r  +++ +   p++ + f+++
  gi|330508100|ref|YP_004384528.1| 40 GLVGESGCGKTTVGRLLLRLI----EPTSGSIIFDSRDITRLNRKEMRKLRPRMQMIFQDP 96
                                      69***************8884....344455555555555555555555555555555555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00023
                            AAA_21 251 llralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                       +l+ ++   +++ DEp ++L+ ++++ +l+l+ +l+r      ++ +H+ +++
  gi|330508100|ref|YP_004384528.1| 165 ILAINP--EFIVADEPTASLDVSVQAQILRLMMDLKRkFCLTMLFISHDMEVV 215
                                       444444..78888*******************555554889999999998775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.2e-07    0.0014      23     120 ..      35     149 ..      21     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.2e-07
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekd.g.giflrgkcdqlesa.....ipysa.laqalareellrqlldeaes 91 
                                       ++e + l+GesG+GK+++ r llr +e + g +if + + ++l ++     +p+ + + q   +++l   +     +
  gi|330508100|ref|YP_004384528.1|  35 QGETLGLVGESGCGKTTVGRLLLRLIEPTsGsIIFDSRDITRLNRKemrklRPRMQmIFQDP-ESSLNPRMRI--GE 108
                                       4578889****************999988533555222222222222333444433233333.3233333322..23 PP

                            AAA_16  92 aeleawrekleeala............avpelagaeasrll 120
                                       + +e++r kl++ ++            +v  l +++ +r+ 
  gi|330508100|ref|YP_004384528.1| 109 SIAEPFRLKLHGKMTkieirdrvlelvDVVGLNPEHINRFP 149
                                       35666666666666666666666655555555555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   1.9e-05     0.029      10      30 ..      41      61 ..      33     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                            AAA_22 10 vtGesGtGKTtllrrlleqld 30
                                      ++GesG+GKTt+ r ll+  +
  gi|330508100|ref|YP_004384528.1| 41 LVGESGCGKTTVGRLLLRLIE 61
                                      89**************99864 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   2.3e-05     0.034       4      37 ..      41      75 ..      38      95 .. 0.84
   2 ?   -2.6   0.0       3.3   4.9e+03      16      45 ..     215     249 ..     212     255 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                                      EE--SSSSHHHHHHHGGGGB.S--EEEEE--TT-- CS
                             AAA_5  4 LvGppGtgKselaerlaaal.nreveyvqltrdtt 37
                                      LvG++G+gK+++ + l++++  ++  ++  +rd+t
  gi|330508100|ref|YP_004384528.1| 41 LVGESGCGKTTVGRLLLRLIePTSGSIIFDSRDIT 75
                                      9******************9877666666666665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.3
                                       HHHGGGGB.....S--EEEEE--TT--HHHHH--B CS
                             AAA_5  16 aerlaaal.....nreveyvqltrdtteedlkgrr 45 
                                       +++++ ++     +r + +vq tr+ +++d +g+r
  gi|330508100|ref|YP_004384528.1| 215 VRHMSDRIavmkeGRITDVVQQTRYSRASDATGER 249
                                       55666665555566666667777777766666655 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   0.0   3.7e-05     0.056       3      46 ..      40      82 ..      38     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-05
                               PRK  3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraek 46
                                      g+ g+SG+Gkttv r l  +++  +  +   +   ++rl+r e+
  gi|330508100|ref|YP_004384528.1| 40 GLVGESGCGKTTVGRLLLRLIE-PTSGSIIFDSRDITRLNRKEM 82
                                      899*************999998.444444446666777777666 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.1e-05      0.14      21      68 ..      41      96 ..      34     106 .. 0.76
   2 ?   -3.6   0.0       3.9   5.8e+03     165     181 ..     217     233 ..     208     246 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.1e-05
                        Zeta_toxin 21 lgGqpGAGKselaellkdele........rqgnvvrldpDdlRelhPeyeeilkad 68
                                      l+G +G+GK+++ +ll + +e          +++ rl++ ++R+l P+ + i+++ 
  gi|330508100|ref|YP_004384528.1| 41 LVGESGCGKTTVGRLLLRLIEptsgsiifDSRDITRLNRKEMRKLRPRMQMIFQDP 96
                                      78**********99999998855555555566677788888888888877777654 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.9
                        Zeta_toxin 165 glresvealeeekqldr 181
                                       ++++ ++ ++e   +d 
  gi|330508100|ref|YP_004384528.1| 217 HMSDRIAVMKEGRITDV 233
                                       33333333333332222 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.5e-05      0.11      77     119 ..      13      56 ..       4      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.5e-05
                                       SEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  77 yevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                       y+  l+s++ ++++++++ ++++ +t  lvG+SG GK+t+   l
  gi|330508100|ref|YP_004384528.1|  13 YSSGLISKQCSRAVDSVSFHIDQgETLGLVGESGCGKTTVGRLL 56 
                                       55667888889999*******9989**************86655 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013       0.2       4      37 ..      25      59 ..      23      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                      HHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHHHH CS
                                      xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  4 vlDal.fpivqGqrtlipgafgvGktvisqslskq 37
                                      ++D++ f i qG++++++g++g+Gkt++ + l++ 
  gi|330508100|ref|YP_004384528.1| 25 AVDSVsFHIDQGETLGLVGESGCGKTTVGRLLLRL 59
                                      5554437899*****************98777665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.18       3      51 ..      41      94 ..      39     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                      EESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSSSTTHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel..........gvefleisgsellskyvgesekkirelfk 51
                                      l+G  G+GKT++ + + + +          ++++ +++ +e++     +   +++++f+
  gi|330508100|ref|YP_004384528.1| 41 LVGESGCGKTTVGRLLLRLIeptsgsiifdSRDITRLNRKEMR-----KLRPRMQMIFQ 94
                                      89**************999744433233323445555555555.....44455555555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00021      0.31       2      57 ..      39     145 ..      38     234 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                                       EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE.ETTEE............................. CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk.lkgke............................. 47 
                                        ++vG +  GK+t+ + l++  +   +++ +  rdi++ + k +  ++                             
  gi|330508100|ref|YP_004384528.1|  39 LGLVGESGCGKTTVGRLLLRLiEPTSGSIIFDSRDITRLNRKeM--RKlrprmqmifqdpesslnprmrigesiaep 113
                                       589****************9755666777788887766655521..1133456677777778888888888888999 PP

                                       ..................EEEEECGGC....S CS
                          MMR_HSR1  48 ..................ielvDtpGl....i 57 
                                                         +elvD++Gl    i
  gi|330508100|ref|YP_004384528.1| 114 frlklhgkmtkieirdrvLELVDVVGLnpehI 145
                                       99999999999999999999****99633331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1691.75
//
Query:       gi|330508101|ref|YP_004384529.1|  [L=526]
Description: hypothetical protein MCON_2195 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00024   21.3   0.0      0.067   13.5   0.0    3.2  3  DUF11         Domain of unknown function DUF11
     0.0059   16.8   0.1        8.2    6.6   0.0    3.2  3  Top6b_C       Type 2 DNA topoisomerase 6 subunit B C-terminal
     0.0087   16.3   0.0         13    6.1   0.0    3.2  3  CARDB         CARDB
  ------ inclusion threshold ------
      0.026   14.7   0.0        6.2    7.0   0.0    2.4  2  Cupredoxin_1  Cupredoxin-like domain
       0.09   12.2   0.0       0.43    9.9   0.0    2.0  2  TRAP_beta     Translocon-associated protein beta (TRAPB)


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 ?    3.1   0.0     0.032   1.2e+02       6      36 ..     119     149 ..     117     160 .. 0.84
   2 ?   -0.3   0.0      0.38   1.3e+03      23      74 ..     252     293 ..     237     300 .. 0.66
   3 !   13.5   0.0   1.9e-05     0.067       3      78 ..     340     406 ..     338     410 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.032
                             DUF11   6 dksevrpGdtvtytltvtNtgpasangvvvt 36 
                                       d+   r G+ ++  l v N+g+++a+++++t
  gi|330508101|ref|YP_004384529.1| 119 DNDIYRGGEDIKMLLSVENRGAVDAEDLKIT 149
                                       5555677999999************999987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.38
                             DUF11  23 tNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsf 74 
                                       +N+g+++   v ++D   +g ++ s+ +       ++++  Le+g+++t+s+
  gi|330508101|ref|YP_004384529.1| 252 SNYGNRTF-SVDLSD--STGKEFHSNETL------QWKI-VLEPGQTKTVSY 293
                                       56666666.666666..555555555554......4554.678888888876 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 1.9e-05
                             DUF11   3 KtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrv 78 
                                       ++ ++++v++G++v   l + N+g+++a  ++   ++P+g +++s+   +        +  L +ge+a  ++++rv
  gi|330508101|ref|YP_004384529.1| 340 RSISPKRVKAGEEVMISLELENRGNRKA-VLTMAEMVPQGAELISGELNE--------SFMLSPGEKAARKIRLRV 406
                                       788899**********************.9*****************992........235899999998888887 PP

>> Top6b_C  Type 2 DNA topoisomerase 6 subunit B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.8     1e+04      35      60 ..      34      59 ..      31      78 .. 0.63
   2 !    6.6   0.0    0.0023       8.2      74      94 ..     276     296 ..     223     302 .. 0.88
   3 !    6.2   0.0    0.0031        11      25      59 ..     348     381 ..     339     390 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.8
                                      EEE---------EEE--EES------ CS
                           Top6b_C 35 lkvkNfsdkkeefelheilpaeieea 60
                                      l+++ ++ + ++f+l e l + +e +
  gi|330508101|ref|YP_004384529.1| 34 LTLEDYTLTLADFSLEEKLMVLVELQ 59
                                      67778888888888887554444333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0023
                                       EE-EEE---TT-EEEE----S CS
                           Top6b_C  74 dlkWelsvsageskvleYsvd 94 
                                        l+W++ +++g++k+++Y ++
  gi|330508101|ref|YP_004384529.1| 276 TLQWKIVLEPGQTKTVSYCIK 296
                                       579***************986 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0031
                                       --SSS-EEEEEEE---------EEE--EES----- CS
                           Top6b_C  25 eengdgvevslkvkNfsdkkeefelheilpaeiee 59 
                                       +  g++v +sl+++N +++k+ +++ e++p+ +e 
  gi|330508101|ref|YP_004384529.1| 348 KA-GEEVMISLELENRGNRKAVLTMAEMVPQGAEL 381
                                       43.47899*********************987665 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0041        15      17      61 ..     125     170 ..     111     188 .. 0.86
   2 ?   -0.6   0.0      0.46   1.6e+03      51      72 ..     278     298 ..     236     304 .. 0.70
   3 !    6.1   0.0    0.0038        13       9      48 ..     341     380 ..     334     414 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0041
                                       TTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.EEEEESEE-CTE CS
                             CARDB  17 vgeentitvtvkNqGtaasgatkvalyldgelv.gtvtvpsLaage 61 
                                        ge++++ ++v+N G  ++++ k+++  +       ++++sL ag+
  gi|330508101|ref|YP_004384529.1| 125 GGEDIKMLLSVENRGAVDAEDLKITVDSSPPIFsRRFNISSLLAGS 170
                                       689999*******************999988777888999998887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.46
                                       EEEESEE-CTEEEEEEEEEE-S CS
                             CARDB  51 tvtvpsLaagesttvsftwtte 72 
                                       ++++  L++g+++tvs+ ++++
  gi|330508101|ref|YP_004384529.1| 278 QWKI-VLEPGQTKTVSYCIKPI 298
                                       3444.68999999998877775 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0038
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEE CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgel 48 
                                       +++p+ + +gee+ i+++++N G+ ++  t ++++  g +
  gi|330508101|ref|YP_004384529.1| 341 SISPKRVKAGEEVMISLELENRGNRKAVLTMAEMVPQGAE 380
                                       678999*******************998888777666655 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0072        26      45      79 ..     257     292 ..     249     300 .. 0.89
   2 ?    7.0   0.0    0.0017       6.2      29      80 ..     339     402 ..     324     405 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0072
                      Cupredoxin_1  45 vklkiknkdktpeefesed.lgeekvlapgktttit 79 
                                        ++ ++  d+t +ef s++ l+ + vl+pg+t+t+ 
  gi|330508101|ref|YP_004384529.1| 257 RTFSVDLSDSTGKEFHSNEtLQWKIVLEPGQTKTVS 292
                                       57899999**********99************9975 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0017
                      Cupredoxin_1  29 dggfePskievkagekvklkiknkdkt............peefesedlgeekvlapgktttiti 80 
                                       + +++P+++++ ++  ++l+++n++++             +e+ s +l+e+  l pg+++  +i
  gi|330508101|ref|YP_004384529.1| 339 KRSISPKRVKAGEEVMISLELENRGNRkavltmaemvpqGAELISGELNESFMLSPGEKAARKI 402
                                       46789****99999999**********9999998888655999999999999999999876555 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.41   1.5e+03      29      60 ..     121     152 ..     117     165 .. 0.81
   2 ?    9.9   0.0   0.00012      0.43      22     114 ..     338     426 ..     329     453 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.41
                         TRAP_beta  29 rllvegedltveytiyNvGssaAldVslvDds 60 
                                       ++  +ged+ + +++ N G   A d++++ ds
  gi|330508101|ref|YP_004384529.1| 121 DIYRGGEDIKMLLSVENRGAVDAEDLKITVDS 152
                                       56678999999999*********999998666 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00012
                         TRAP_beta  22 vkKkilnrllvegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvvepkksg 98 
                                       +k +i  + +++ge++ +++++ N G+ +A+   l+   + ++  e++sg+l+ ++  l pge+   ++ ++   + 
  gi|330508101|ref|YP_004384529.1| 338 AKRSISPKRVKAGEEVMISLELENRGNRKAV---LTMAEMVPQGAELISGELNESF-MLSPGEKAARKIRLRVMDPD 410
                                       5778999999******************997...55555666666*********99.6******************* PP

                         TRAP_beta  99 sfngtaavvtYresek 114
                                        +++ +++v Yr+   
  gi|330508101|ref|YP_004384529.1| 411 GISIPSSMVRYRDVRG 426
                                       ***********87654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 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:                        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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3531.64
//
Query:       gi|330508102|ref|YP_004384530.1|  [L=371]
Description: hypothetical protein MCON_2197 [Methanosaeta concilii GP6]
Scores for complete 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   18.0   1.3       0.25   11.5   0.0    3.3  3  Cupredoxin_1   Cupredoxin-like domain
  ------ inclusion threshold ------
      0.092   12.6   1.8       0.18   11.7   1.8    1.6  1  SspB           Stringent starvation protein B
       0.16   11.3   0.1       0.28   10.5   0.1    1.5  1  Sarcoglycan_1  Sarcoglycan complex subunit protein


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 !   11.5   0.0   4.1e-05      0.25      38      90 ..      56     111 ..      37     121 .. 0.88
   2 ?    2.5   0.1     0.026   1.6e+02      44      87 ..     152     198 ..     146     211 .. 0.70
   3 ?    0.3   0.0      0.12   7.3e+02      40      73 ..     233     264 ..     213     268 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.1e-05
                      Cupredoxin_1  38 evkagekvklkiknkdktp...eefesedlgeekvlapgktttitiaplkpGeYef 90 
                                        +k+g +v + i+n+d++    + f   +l  +k + +g+ ++i+  pl++G+++f
  gi|330508102|ref|YP_004384530.1|  56 SAKEGIPVHVYITNNDNEKldvSLFIDSELIDRKSISSGADQKIDSYPLEKGSHTF 111
                                       689***************655366666669999********************999 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.026
                      Cupredoxin_1  44 kvklkiknkdktp.eefesed..lgeekvlapgktttitiaplkpGe 87 
                                       +++++++n+ ++  e f   d  ++++k++ +++++++   +lk+G 
  gi|330508102|ref|YP_004384530.1| 152 EITVNLVNENSRElEAFLYADgsFEKSKKVGKESSAELGTIKLKEGI 198
                                       68999999999998888888855555666666666666555666665 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.12
                      Cupredoxin_1  40 kagekvklkiknkdktpeefesedlgeekvlapg 73 
                                       ++g  v+++ kn ++ +e ++s d +e++ ++ +
  gi|330508102|ref|YP_004384530.1| 233 PKG--VSFEAKNASSGAEDLSSGDSDEKTSIKDE 264
                                       555..69999**********99999999988865 PP

>> SspB  Stringent starvation protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.8     3e-05      0.18      81     156 ..     216     290 ..     180     311 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3e-05
                                       EEEEEEEEGGGEEEEEETTTTEEEE-.--BGGGCHT.TSXXSSCXXXXXXXX..........XXXXXXXXXXXXXXX CS
                              SspB  81 vpeklvvPfaavlafydpevgfglqFeeaeeaeeeeeeeeaeeeeeaaeeea...keeeeeaeeaedeeapkekkrp 154
                                       + +kl+v  + v+ fy+p+   g+ Fe++++++ +e+ ++ ++ +e+++ ++   ++e++ +e ++d+e++++++++
  gi|330508102|ref|YP_004384530.1| 216 KTKKLMVKRDEVVIFYAPK---GVSFEAKNASSGAEDLSSGDS-DEKTSIKDeqiDKEDPVDEPDDDSENSSKTDST 288
                                       6789**************6...999977666666554444433.333333334553333333333333333333333 PP

                                       XX CS
                              SspB 155 gl 156
                                       ++
  gi|330508102|ref|YP_004384530.1| 289 SA 290
                                       33 PP

>> Sarcoglycan_1  Sarcoglycan complex subunit protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   4.8e-05      0.28     141     197 ..     191     248 ..     119     261 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.8e-05
                     Sarcoglycan_1 141 tvgldkgvkkLrvk.svetprirseadedLklesdtrlslrgnegvrieakageieat 197
                                       t++l++g+++L+v+ +   +ri+ e  ++L ++ d+ + + +++gv +eak+ +  a+
  gi|330508102|ref|YP_004384530.1| 191 TIKLKEGIHNLSVRwQDDDTRIEYEKTKKLMVKRDEVVIFYAPKGVSFEAKNASSGAE 248
                                       7889999*******99999********************************9987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2477.25
//
Query:       gi|330508103|ref|YP_004384531.1|  [L=120]
Description: hypothetical protein MCON_2198 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.38   10.9   2.5        1.3    9.2   2.5    1.8  1  YtpI             YtpI-like protein
       0.44   10.0   1.8       0.82    9.1   0.1    1.9  3  DUF3087          Protein of unknown function (DUF3087)
        1.1    9.3   4.7        2.2    8.4   0.4    2.2  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.5   0.00022       1.3       6      53 ..      16      74 ..      12     101 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00022
                              YtpI  6 lslvlyvyykvkaf...rtkdplekkllsakasialGlflilfginqlll........l 53
                                      l+lv y++ k + f   r  ++ e ++++a  +i+ Glfl+l g  ++l          
  gi|330508103|ref|YP_004384531.1| 16 LALVYYLIHKKQMFmleRGIEKKEDRYVRAERRIINGLFLTLAGFSMILApqlasiagI 74
                                      67888999998887333666677778****************99998887554444441 PP

>> DUF3087  Protein of unknown function (DUF3087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1     0.075   4.5e+02      76     127 ..      16      31 ..       3      33 .. 0.59
   2 ?    0.2   0.0     0.078   4.7e+02     113     128 ..      17      32 ..      10      40 .. 0.78
   3 ?    9.1   0.1   0.00014      0.82       8      64 ..      39      95 ..      33     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.075
                           DUF3087  76 maevvYvWrLKqllnkiyrklkkvkaaakegdenAlkilrFyyqglkqlyqL 127
                                       +                                    +l +y   +kq++ L
  gi|330508103|ref|YP_004384531.1|  16 L------------------------------------ALVYYLIHKKQMFML 31 
                                       3....................................455555555666655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.078
                           DUF3087 113 ilrFyyqglkqlyqLd 128
                                       +l +y   +kq++ L+
  gi|330508103|ref|YP_004384531.1|  17 ALVYYLIHKKQMFMLE 32 
                                       5778888888888886 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00014
                           DUF3087  8 kerYrkklnrvivalvallavlsllfstllialfgeeevsnfhlnllGvvlalvlta 64
                                       +rY +  +r+i +l ++la +s++++  l ++ g e   +f l l+ ++l ++ +a
  gi|330508103|ref|YP_004384531.1| 39 EDRYVRAERRIINGLFLTLAGFSMILAPQLASIAGIEAQLSFDLLLVSMILLCAGLA 95
                                      579*****************************9998887778777777766555444 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 ?    8.4   0.4   0.00037       2.2      22      39 ..       3      20 ..       2      31 .. 0.94
   2 ?    2.7   0.3     0.023   1.4e+02      12      36 ..      74      98 ..      68      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00037
                   Proton_antipo_N 22 salmllvvtfvsllvhlY 39
                                      +a+mllvv +v +l ++Y
  gi|330508103|ref|YP_004384531.1|  3 TAIMLLVVEGVPFLALVY 20
                                      89*************999 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.023
                   Proton_antipo_N 12 ieigfllDklsalmllvvtfvsllv 36
                                      ie ++ +D l + m+l+  ++++l+
  gi|330508103|ref|YP_004384531.1| 74 IEAQLSFDLLLVSMILLCAGLAMLI 98
                                      7788999**********99999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 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:                        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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 879.33
//
Query:       gi|330508104|ref|YP_004384532.1|  [L=66]
Description: hypothetical protein MCON_2199 [Methanosaeta concilii GP6]
Scores for complete 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-08   31.9   0.1    1.2e-07   31.6   0.1    1.1  1  PUA       PUA domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.1   6.5e-12   1.2e-07       2      47 ..      12      57 ..      11      58 .. 0.97

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 6.5e-12
                                      EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEE CS
                               PUA  2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelv 47
                                      +vv+ d Av ++++g  L++  v+ ++  +e g+ V ivd+++++v
  gi|330508104|ref|YP_004384532.1| 12 KVVISDAAVPFVARGGRLFPGQVIATDPGIENGEDVLIVDRKERPV 57
                                      79***************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       162  (0.00903564); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 480.88
//
Query:       gi|330508105|ref|YP_004384533.1|  [L=367]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-27   96.0   0.5    5.5e-27   94.9   0.5    1.5  1  Peripla_BP_2     Periplasmic binding protein
  ------ inclusion threshold ------
       0.12   12.1   0.4       0.23   11.2   0.1    1.6  2  T2SS-T3SS_pil_N  Pilus formation protein N terminal region


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   0.5   6.1e-31   5.5e-27       1     235 [.      49     311 ..      49     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 6.1e-31
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH-........-SEEEE-GGG CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalk........PDlvilskgl 69 
                                       ++++s++ +e +++lGa+dkvvg++ t+++   +  +++ + +vg+ + +d+E++ a          PD+v+  +++
  gi|330508105|ref|YP_004384533.1|  49 VIVTSSDAAEAVVMLGAADKVVGISDTVKNKGYYFPDLKGKQSVGKWNALDYEMIGAIAsdgedaivPDIVVIGYSY 125
                                       799**********************99999888866666*************999765444444444********** PP

                                       ....GGGHHHHH.....HHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEE CS
                      Peripla_BP_2  70 .gltdedeellk.....sgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpv 140
                                        +    ++ l++     ++i+ v+ e+++  ++ +++i++lg++lg+e++a ++++++d+k+ ++k+a+d  + +++
  gi|330508105|ref|YP_004384533.1| 126 pDKSYGIYGLEEglepfENIKAVALEFTKP-QNMTREIEVLGQILGKEEQASDYISWYDEKINSVKDAVDGMNLPEA 201
                                       866666666666444445899999999999.*****************************************66666 PP

                                       EEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH............... CS
                      Peripla_BP_2 141 lvfggadeggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr............... 202
                                        v  ++ +g+++  g +s + ++l  +++ nia++  +++y ++++E++++++p++i+v+ +               
  gi|330508105|ref|YP_004384533.1| 202 YVEWSSSGGDISTLGPGSAFDQVLKVAKGYNIASAL-EESYPKVDWEWVVTENPEIIIVRQTqpaghteigwesaps 277
                                       666667778***************************.**************************************** PP

                                       .HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 203 .aeadnktgleflkenpllaelpAvkngrVyald 235
                                        ++++ ++ + +l+ + +++++ A+k+ r+y +d
  gi|330508105|ref|YP_004384533.1| 278 qEASKLQAAKNELLDRSGASGTSAAKSDRIYFID 311
                                       *******************************986 PP

>> T2SS-T3SS_pil_N  Pilus formation protein N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   2.6e-05      0.23       5      36 ..      30      61 ..      26      71 .. 0.88
   2 ?   -3.9   0.0       1.4   1.2e+04      24      36 ..     249     261 ..     248     265 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.6e-05
                   T2SS-T3SS_pil_N  5 lelevgksrllrlpepvervavgnpkiadvtv 36
                                      l+++  + r +++++p+erv+v   + a+++v
  gi|330508105|ref|YP_004384533.1| 30 LTITDSAGREVTFNQPIERVIVTSSDAAEAVV 61
                                      67788899*********************998 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.4
                   T2SS-T3SS_pil_N  24 vavgnpkiadvtv 36 
                                       v+  np+i+ v+ 
  gi|330508105|ref|YP_004384533.1| 249 VVTENPEIIIVRQ 261
                                       5667999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2770.97
//
Query:       gi|330508106|ref|YP_004384534.1|  [L=1239]
Description: CobN/magnesium chelatase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
          0 1173.6   0.0          0 1173.4   0.0    1.0  1  CobN-Mg_chel  CobN/Magnesium Chelatase
  ------ inclusion threshold ------
       0.26   11.6   2.4         24    5.4   0.3    2.7  2  HalX          HalX domain


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 ! 1173.4   0.0         0         0       2    1088 ..     101    1187 ..     100    1188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1173.4 bits;  conditional E-value: 0
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel    2 aYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilf 76  
                                        +Y   gg++N+knll+y++++ l+ ++ ++epp+e+ ++g+yhp++++ f++++eylewy   + ++++ vg++f
  gi|330508106|ref|YP_004384534.1|  101 RYALFGGRKNFKNLLKYACNQALK-TSFQLEPPEEILWQGLYHPRSETAFATVDEYLEWY---QGKERSWVGLIF 171 
                                        79999******************7.77789*****************************8...688999****** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel   77 yrahllagntavidaliraleerglnvlpvfvssl...d...seaqealeelftkegeekvdalinttsfalvkg 145 
                                        +r+++ +++++v+da i +le++ ++vlp+f+ ++   d    ++ e ++++f    + +v+a++n++ +  +++
  gi|330508106|ref|YP_004384534.1|  172 SRTSWANEDLKVVDAAILELEKE-FDVLPAFCFGMgdsDlgaWSSVEVAKRFF----SGRVEAIVNLQPIFRSRN 241 
                                        *********************98.**********9965255455556666777....579*******97766544 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                      CobN-Mg_chel  146 paeeeeeeaeeealkelnvPvlqa.ilssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeee.ee 218 
                                        ++   e   + + +k+lnvP++++ +++++++eeW+++ +Gls+ ++ +sva+pE++G+iep++i++++++e + 
  gi|330508106|ref|YP_004384534.1|  242 SD---E---ALQTMKALNVPIFHPaVVYHKTEEEWKDDVHGLSSSEVGWSVAMPEFEGVIEPLMIGATSRSEmDG 310 
                                        42...2...23347*****************************************************99777799 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  219 tevekyepipervervadlaarwarLrrkpnaekkvaiilanypp..gegrlgnavgLdvpaSlvnlLkalkeeG 291 
                                        +++ek++piperv+++a+++++w++L++kp +e++va+il+n+p+   e+++g ++++d+++S++++++++ ++G
  gi|330508106|ref|YP_004384534.1|  311 AQIEKHVPIPERVSKLARRVKKWVALKNKPVSERRVAFILHNNPCasVEASVGGGAHIDTLESVARIMDRMVQAG 385 
                                        *********************************************8889************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxx.xxxxx...xxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  292 YdveelpesgdeLiellleggt.ndpew...eelkv.....gaaallpaeeYeewfeeLpeelreeveerWgepp 357 
                                        Y++++ p++g+eLie+++++++ ++++w   e         ga+all++eeY++wf+ L++ +r++++e+Wg+pp
  gi|330508106|ref|YP_004384534.1|  386 YSLQSPPKTGKELIETIMARKAiSEFRWtsiE---EiikrgGALALLSEEEYRQWFDLLSPVVRDQMIEAWGRPP 457 
                                        ***888****************99****5552...334556********************************** PP

                                        xx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  358 ge...mveeeksgekklvipglqlGnvfvgvQParg...yeedps..klyhdpdlpPthqYlAfYlWlreefgad 424 
                                        ge    +   +  ++k+vi+g+++Gn +v+ QP+rg    ++d +  k++hdp++pPthqYlA+Y+++++ fgad
  gi|330508106|ref|YP_004384534.1|  458 GEekdGIPAAMLYQGKIVITGVEYGNALVCTQPKRGcagSRCDGQvcKILHDPQVPPTHQYLATYRYIESCFGAD 532 
                                        *9999566677889**********************77767776678**************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  425 avvHvGkHGtlEwlPGKqvglseecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelyge 499 
                                         +vHvG+HG+lE+lPGK+vgls++cyPdi++gd+PhlY+Y+ +np EGt+AKRRsyA+++dH++ +mt++elyge
  gi|330508106|ref|YP_004384534.1|  533 LIVHVGTHGNLEFLPGKSVGLSADCYPDIAIGDMPHLYIYNSDNPPEGTIAKRRSYATLVDHMQVVMTDSELYGE 607 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  500 laeLeelideYeeaesldperlkalreqilelveelnldkdlgleeakeeeeeefeellekldgyleelkeaqir 574 
                                        l+eLe+ i+eY++a  ++  r++al++ il+l+e+ nl  +++l+ +  ++ ++fee+le+ ++ +++l ++qi+
  gi|330508106|ref|YP_004384534.1|  608 LKELEDRISEYRRAVLSEGGRAHALEHIILNLLEKSNLAGEINLK-RLIASGASFEEILERAHDKISQLYNTQIP 681 
                                        **************999999**********************877.566799*********************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxx.xxxxxxxxx RF
                      CobN-Mg_chel  575 dglhilGeapegeqlvdlvvailrleneegesltealaealgldlde.......leeksekelrt.agdaleale 641 
                                        dg+hi+Ge p+g+++++++ ailr+e +       a a  lg ++++       l     + +r+ ++d   ++e
  gi|330508106|ref|YP_004384534.1|  682 DGMHIFGELPAGKRREEMIRAILRAEVR------GAAALLLGREVTAniedlreLDGLGGDLVRAiIADRRGKIE 750 
                                        ***********************66544......33333333333331111221333333333321233344557 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  642 eeaeelveelleeeaeeeeaeaeeleeeeeeeee.....eteeEitallraLdGeyippgpsGdptrgraevLPT 711 
                                         ++++ +++llee++  +e+ a  l +++ e  e     e ++E+++llr++++++i+pgpsG + +g+ e+LPT
  gi|330508106|ref|YP_004384534.1|  751 GQEKSSISRLLEERSIGKESPALDLLRDRIE--ElswriEESREMESLLRGFSAGFIEPGPSGLMSKGKIEILPT 823 
                                        7777777777776555444444333333333..1458987779******************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  712 GrNfysvDpraiPteaAwevGkklaeellerylqehgeyPekvglslwgtetmrteGediAqiLallGvrPvwda 786 
                                        GrNf+s+Dp+a+PteaAw vG++la++lle+y +e+g++Pe+vg+ +++ + m  +Ge+++q+++l+Gv Pvw++
  gi|330508106|ref|YP_004384534.1|  824 GRNFFSLDPSAVPTEAAWMVGRRLADSLLEKYEKEQGRLPENVGMFWMAGDVMYADGEQMSQMFHLIGVMPVWKG 898 
                                        *************************************************************************77 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  787 agrvvdlelipleeLgRPRiDVtvriSGffRDafpnlielldkavelvaeldEpeedNfvrkhvleeeaeleeke 861 
                                         g+++++e+ipleeLgRPRiD tvr+SG+ RD f n+ie++d+a+  va+ldEp+++Nf+ kh le+        
  gi|330508106|ref|YP_004384534.1|  899 -GKLKGYEVIPLEELGRPRIDLTVRVSGITRDCFYNCIEIMDQAICEVAALDEPQDMNFLHKHDLENG------- 965 
                                        .**************************************************************99874....... PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  862 eaeeratyRvFgskpGaYgagvqeliessnWedeedLaeaYlnwssyaYgkgaegeeaeeafearLkrvdvvvqn 936 
                                             ++ R+F s+pG+Yg+gv+ ++ +s+W+ ++dL ++++ w++yaYgkg+ gee+++ + ++Lk+vdv++++
  gi|330508106|ref|YP_004384534.1|  966 -----SHHRIFASRPGTYGNGVNLAVYASAWKADKDLSDVFIYWNGYAYGKGVFGEESQDGLIKQLKSVDVTFNK 1035
                                        .....678******************************************************************* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  937 qdsrehdlldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvrtlkeeiarelrsrvlNPkWiegmmrh 1011
                                        ++++e dl+ +++y+ ++GG+taa+r++sg+++eay+gd+++ ++++vrtl++e++r++r+++lNPkWi+gm+rh
  gi|330508106|ref|YP_004384534.1| 1036 TTTDEKDLFGCCCYFGNQGGMTAAAREVSGHHVEAYYGDTRDADRVEVRTLSDEVRRVVRTKLLNPKWIAGMKRH 1110
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 1012 GykGafelaatvdnlfgwdatadvvddwvyeevaetYvlDeevrefleekNpwAlreiaerLlEaarrglWease 1086
                                        GykGa +++++v  ++gw+at++ vddw+++++a+t+v Dee+r+f++e+NpwA++e+ +rLlEa++rglW+a+ 
  gi|330508106|ref|YP_004384534.1| 1111 GYKGAGDISKRVGRVYGWEATTQEVDDWIFDDIARTFVMDEENRKFFQENNPWAMEEMSRRLLEAEQRGLWKADP 1185
                                        *************************************************************************99 PP

                                        xx RF
                      CobN-Mg_chel 1087 et 1088
                                        e 
  gi|330508106|ref|YP_004384534.1| 1186 EV 1187
                                        85 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0031        28      33      51 ..     601     622 ..     588     634 .. 0.75
   2 ?    5.4   0.3    0.0026        24      33      56 ..     769     792 ..     768     802 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0031
                              HalX  33 dseeYqeLe...arleelraql 51 
                                       dse Y+eL+   +r+ e+r+ +
  gi|330508106|ref|YP_004384534.1| 601 DSELYGELKeleDRISEYRRAV 622
                                       566565555555*******987 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0026
                              HalX  33 dseeYqeLearleelraqldetld 56 
                                       +s + + L++r+eel  +++e  +
  gi|330508106|ref|YP_004384534.1| 769 ESPALDLLRDRIEELSWRIEESRE 792
                                       6788888*************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.82u 0.33s 00:00:01.14 Elapsed: 00:00:00.47
# Mc/sec: 7889.19
//
Query:       gi|330508107|ref|YP_004384535.1|  [L=137]
Description: hypothetical protein MCON_2204 [Methanosaeta concilii GP6]
Scores for complete 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   33.7   0.0    3.4e-08   33.3   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   1.9e-12   3.4e-08     167     234 ..       5      80 ..       1      83 [. 0.81

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.9e-12
                                       S--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH.........HHHT-S--HHH.HT-SHHHHTSHHHHTT-EEE CS
                      Peripla_BP_2 167 lgieniaaeskkseyeeisaEqilasdpdvifvsgr.........aeadnktglef.lkenpllaelpAvkngrVya 233
                                        g++nia +   +ey +++ E+il+++pdvi+              +++++++l + l+e+p++++l A+kn+rV  
  gi|330508107|ref|YP_004384535.1|   5 TGGRNIAGD--LDEYPKLDSEWILKENPDVIIKLLApgggkagwnSTKEADQILNGyLEERPGWSNLDAAKNNRVHL 79 
                                       689999888..7********************9999999**55555555555555434578**************76 PP

                                       E CS
                      Peripla_BP_2 234 l 234
                                       l
  gi|330508107|ref|YP_004384535.1|  80 L 80 
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1021.06
//
Query:       gi|330508108|ref|YP_004384536.1|  [L=106]
Description: hypothetical protein MCON_2205 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-08   34.6   0.1    2.7e-08   33.6   0.0    1.5  2  MarR        MarR family
    5.5e-06   25.8   0.0    8.8e-06   25.2   0.0    1.3  1  HTH_24      Winged helix-turn-helix DNA-binding
    1.6e-05   24.7   0.0    4.3e-05   23.3   0.0    1.7  2  MarR_2      MarR family
    3.8e-05   23.5   0.0      6e-05   22.9   0.0    1.3  1  TrmB        Sugar-specific transcriptional regulator TrmB
     0.0013   18.7   0.0      0.003   17.5   0.0    1.6  2  HTH_29      Winged helix-turn helix
     0.0034   17.1   0.0      0.007   16.1   0.0    1.6  2  PheRS_DBD1  PheRS DNA binding domain 1
     0.0089   15.8   0.0      0.015   15.1   0.0    1.3  1  HTH_IclR    IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.017   14.8   0.0    1.4  1  GntR        Bacterial regulatory proteins, gntR family
      0.013   15.7   0.2      0.035   14.3   0.0    1.7  2  PaaX        PaaX-like protein
      0.015   15.5   0.0      0.047   13.9   0.0    1.9  2  HTH_34      Winged helix DNA-binding domain
      0.028   14.1   0.1      0.051   13.3   0.1    1.4  1  HTH_41      Helix-turn-helix domain
      0.035   13.4   0.0      0.044   13.1   0.0    1.1  1  EAP30       EAP30/Vps36 family
      0.072   13.0   0.0       0.11   12.5   0.0    1.3  1  HTH_11      HTH domain
      0.087   12.8   0.0       0.11   12.5   0.0    1.3  1  HTH_Crp_2   Crp-like helix-turn-helix domain
      0.097   11.7   0.0       0.11   11.5   0.0    1.1  1  Ter         DNA replication terminus site-binding protein (Te


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       4.2     5e+03      29      39 ..      12      22 ..      10      23 .. 0.79
   2 !   33.6   0.0   2.2e-11   2.7e-08       5      59 .]      27      81 ..      24      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.2
                                      S-HHHHHHHHH CS
                              MarR 29 vskstvtrvld 39
                                      ++k+t+ r+++
  gi|330508108|ref|YP_004384536.1| 12 IQKATLVRTAK 22
                                      78899999877 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 2.2e-11
                                      HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTSE CS
                              MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRev 59
                                      ++++ ++++e ++l+v eLak++g s++ +  +++rLe++Gli+ +ks ++ R+v
  gi|330508108|ref|YP_004384536.1| 27 EWDLYEKISEAPSLNVYELAKRMGWSTGKTRGAVKRLEEEGLIKIEKSIRNGRAV 81
                                      6777789*****************************************9999987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   7.4e-09   8.8e-06      13      48 .]      35      70 ..      29      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 7.4e-09
                            HTH_24 13 qknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       + p+++  eLA+r g S + ++  +krLeeeGlIk
  gi|330508108|ref|YP_004384536.1| 35 SEAPSLNVYELAKRMGWSTGKTRGAVKRLEEEGLIK 70
                                      677888888**************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.5   1.8e+03      45      59 ..      12      26 ..       9      27 .. 0.76
   2 !   23.3   0.0   3.6e-08   4.3e-05      13      62 .]      33      80 ..      24      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.5
                                      HHHTTSEEEEESSSS CS
                            MarR_2 45 LvaaGLverrpgpeD 59
                                       ++a Lv++ ++++D
  gi|330508108|ref|YP_004384536.1| 12 IQKATLVRTAKAEDD 26
                                      578889999888776 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 3.6e-08
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkRa 62
                                       +  +p   l+v ela+r+g s + +  ++krL++ GL+  +++ + +Ra
  gi|330508108|ref|YP_004384536.1| 33 KISEAPS--LNVYELAKRMGWSTGKTRGAVKRLEEEGLIKIEKSIRNGRA 80
                                      4777887..********************************999988886 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     5e-08     6e-05       8      58 ..      25      75 ..      24      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5e-08
                                      HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      + E + Y ++ +  +++++e+a++ g +  k   ++++Le+ Gl+++ek+ 
  gi|330508108|ref|YP_004384536.1| 25 DDEWDLYEKISEAPSLNVYELAKRMGWSTGKTRGAVKRLEEEGLIKIEKSI 75
                                      578999******************************************975 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.4   5.2e+03      20      31 ..       3      14 ..       3      15 .. 0.77
   2 !   17.5   0.0   2.5e-06     0.003      13      55 ..      39      82 ..      28      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.4
                            HTH_29 20 kllglsrrtvyr 31
                                      k+ gl+++++++
  gi|330508108|ref|YP_004384536.1|  3 KRIGLHMQSIQK 14
                                      567999999975 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.5e-06
                            HTH_29 13 s.tvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprn 55
                                      s +v ++Ak++g s  + + ++kr ee+Gl ++ ++ r+gr  +
  gi|330508108|ref|YP_004384536.1| 39 SlNVYELAKRMGWSTGKTRGAVKRLEEEGLIKIEKSIRNGRAVD 82
                                      47899************************999988888888655 PP

>> PheRS_DBD1  PheRS DNA binding domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.5     3e+03      41      59 .]      11      28 ..       9      28 .. 0.73
   2 !   16.1   0.0   5.9e-06     0.007      12      54 ..      33      74 ..      22      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.5
                        PheRS_DBD1 41 SLqalgelIkaeqrsskrw 59
                                      S+q +  l+ +++ +   w
  gi|330508108|ref|YP_004384536.1| 11 SIQKAT-LVRTAKAEDDEW 28
                                      788877.888888776666 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5.9e-06
                        PheRS_DBD1 12 rLekkgevdslelAaelgvdHqkvVGavKSLqalgelIkaeqr 54
                                      ++++  +++ +elA+++g++  k  GavK L+  g lIk e++
  gi|330508108|ref|YP_004384536.1| 33 KISEAPSLNVYELAKRMGWSTGKTRGAVKRLEEEG-LIKIEKS 74
                                      56666678999************************.****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 !   15.1   0.0   1.2e-05     0.015      14      49 ..      36      70 ..      32      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                                      TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      eap  l++ elA+r g++  ++++ ++ L+e+G+++
  gi|330508108|ref|YP_004384536.1| 36 EAPS-LNVYELAKRMGWSTGKTRGAVKRLEEEGLIK 70
                                      4444.8999************************986 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.4e-05     0.017      24      58 ..      40      73 ..      32      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                                      ---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              GntR 24 LPsereLaaefgVsrttvReALrrLeaeglverrq 58
                                      L  + eLa+++g s+   R A +rLe+egl+ +++
  gi|330508108|ref|YP_004384536.1| 40 L-NVYELAKRMGWSTGKTRGAVKRLEEEGLIKIEK 73
                                      5.678**************************9875 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.2   2.6e+03      36      48 ..      14      21 ..       1      23 [. 0.44
   2 ?   14.3   0.0   2.9e-05     0.035      25      60 ..      41      76 ..      30      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.2
                              PaaX 36 seslvRaalsRla 48
                                      +++     l R a
  gi|330508108|ref|YP_004384536.1| 14 KAT-----LVRTA 21
                                      233.....44443 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.9e-05
                              PaaX 25 sLirllaelGiseslvRaalsRlakaGwlvrekegr 60
                                      +  +l + +G s +  R a+ Rl+++G+++ ek  r
  gi|330508108|ref|YP_004384536.1| 41 NVYELAKRMGWSTGKTRGAVKRLEEEGLIKIEKSIR 76
                                      5568999**********************9888655 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.7   3.2e+03      33      51 ..       7      25 ..       4      32 .. 0.73
   2 ?   13.9   0.0   3.9e-05     0.047      15      63 ..      40      88 ..      30     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.7
                            HTH_34 33 vhlkkLekagYievdkefk 51
                                       h++ ++ka  +   k+ +
  gi|330508108|ref|YP_004384536.1|  7 LHMQSIQKATLVRTAKAED 25
                                      6888888888888777765 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.9e-05
                            HTH_34 15 adfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTp 63
                                       +  el + ++ ++g+    +k Le+ g i+++k+ ++++   l++ Tp
  gi|330508108|ref|YP_004384536.1| 40 LNVYELAKRMGWSTGKTRGAVKRLEEEGLIKIEKSIRNGRAVDLVTATP 88
                                      566788899999999999**********************999999987 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.3e-05     0.051       9      45 ..      42      78 ..      40      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-05
                            HTH_41  9 IeelakeleLSvGlvQkALklLeddkaislerrGrlG 45
                                      + elak ++ S G    A+k Le+++ i++e+  r+G
  gi|330508108|ref|YP_004384536.1| 42 VYELAKRMGWSTGKTRGAVKRLEEEGLIKIEKSIRNG 78
                                      679***************************9887777 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.7e-05     0.044     161     234 ..      13      71 ..       5      73 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                             EAP30 161 ggkkvvrSvptelntdqvevlevakrlvsllaekssgggvtaselaeeeenlgwsvarakeaLeelereGllwv 234
                                       ++ ++vr+   e+++ +     + +++     ++     +++ ela++   +gws++ ++ a+++le+eGl+ +
  gi|330508108|ref|YP_004384536.1|  13 QKATLVRTAKAEDDEWD-----LYEKI-----SEA--PSLNVYELAKR---MGWSTGKTRGAVKRLEEEGLIKI 71 
                                       45566666665555544.....44444.....122..3699****888...*******************9966 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.2e-05      0.11       8      49 ..      33      74 ..      29      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.2e-05
                            HTH_11  8 lLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIese 49
                                       + ea + ++  eLA++++ S+   r  +k+Lee g ++Ie++
  gi|330508108|ref|YP_004384536.1| 33 KISEAPS-LNVYELAKRMGWSTGKTRGAVKRLEEEGlIKIEKS 74
                                      5544554.999*************************9999975 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   9.4e-05      0.11      21      57 ..      39      75 ..       8      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.4e-05
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrri 57
                                      +l+  elA ++G +   +  + ++L++egli+ ++ i
  gi|330508108|ref|YP_004384536.1| 39 SLNVYELAKRMGWSTGKTRGAVKRLEEEGLIKIEKSI 75
                                      57888**************************954324 PP

>> Ter  DNA replication terminus site-binding protein (Ter protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.4e-05      0.11     167     207 ..      57      96 ..      39     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.4e-05
                               Ter 167 KqiikkltreevleqLekslkapravapytreqwqekveqe 207
                                       + ++k+l+ e  l ++eks +++rav+  t+  wq +++ e
  gi|330508108|ref|YP_004384536.1|  57 RGAVKRLEEEG-LIKIEKSIRNGRAVDLVTATPWQDMLTPE 96 
                                       44677776655.568*********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 797.14
//
Query:       gi|330508109|ref|YP_004384537.1|  [L=64]
Description: hypothetical protein MCON_2206 [Methanosaeta concilii GP6]
Scores for complete 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   16.5   0.0     0.0066   16.2   0.0    1.0  1  DUF4364       Domain of unknown function (DUF4364)
     0.0069   16.4   0.0     0.0078   16.3   0.0    1.0  1  S10_plectin   Plectin/S10 domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.013   15.5   0.0    1.1  1  HTH_45        Winged helix-turn-helix
      0.035   14.6   0.0      0.045   14.2   0.0    1.2  1  HTH_27        Winged helix DNA-binding domain
       0.05   13.7   0.1       0.05   13.7   0.1    1.1  1  Replic_Relax  Replication-relaxation
      0.058   13.3   0.0      0.079   12.9   0.0    1.2  1  TrmB          Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.2e-06    0.0066      36      74 ..      23      61 ..      21      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-06
                           DUF4364 36 lqqalseLvesglieeeekenktlykiTekGketlelfe 74
                                      +++al +Lv++g++  + ++n+ +y++Te G e  ++++
  gi|330508109|ref|YP_004384537.1| 23 VKKALGKLVSKGYVARHPTRNEMTYQLTELGIEECRQMK 61
                                      789****************************99887776 PP

>> S10_plectin  Plectin/S10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.6e-06    0.0078      23      77 ..       3      60 ..       1      62 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.6e-06
                                      --SS----SSS.---HH..HHHHHHHHCCCCTSEEEEEETTEEEEEE-HHHHHHHHHH CS
                       S10_plectin 23 kdfelkkheel.nvpnl..qvikalqSLksrgyvkeqfaWrhyYytLtneGieylrey 77
                                      k  +l++h  + + pnl  +v kal  L s+gyv ++ + + + y Lt+ Gie  r++
  gi|330508109|ref|YP_004384537.1|  3 KAAHLPEHVLVrRFPNLghRVKKALGKLVSKGYVARHPTRNEMTYQLTELGIEECRQM 60
                                      56678888888888998556899******************************99985 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   4.2e-06     0.013      35      71 ..      22      62 ..      18      64 .] 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.2e-06
                            HTH_45 35 llnkYLdmLvekgli....kkskekYvlTekGlelleklke 71
                                      +++k L +Lv+kg++    + ++ +Y+lTe G e  +++ke
  gi|330508109|ref|YP_004384537.1| 22 RVKKALGKLVSKGYVarhpTRNEMTYQLTELGIEECRQMKE 62
                                      678999*********999999************99999886 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-05     0.045      36      68 .]      23      53 ..      18      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                            HTH_27 36 s.yslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      + ++l kL+ kG+v r +    r e++++lT+ G
  gi|330508109|ref|YP_004384537.1| 23 VkKALGKLVSKGYVARHPT---RNEMTYQLTELG 53
                                      5599**********44433...355******987 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.7e-05      0.05      23      69 ..      20      57 ..       2      64 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                      Replic_Relax 23 hratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarll 69
                                      ++ ++ ++L +L ++g+++r+  r        +++ Y+Lt++G +  
  gi|330508109|ref|YP_004384537.1| 20 GH-RVKKALGKLVSKGYVARHPTR--------NEMTYQLTELGIEEC 57
                                      34.5999*************7777........489********9877 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.6e-05     0.079      38      63 ..      22      48 ..      20      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                                      CHHHHHHHHHHCTSEEEESST.TTEEE CS
                              TrmB 38 kvYevLrsLedkGlVerekgr.pklYr 63
                                      +v ++L +L++kG+V r + r  + Y+
  gi|330508109|ref|YP_004384537.1| 22 RVKKALGKLVSKGYVARHPTRnEMTYQ 48
                                      799**************9966466776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 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:                        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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 480.30
//
Query:       gi|330508110|ref|YP_004384538.1|  [L=305]
Description: hypothetical protein MCON_2207 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.078   12.9   0.0       0.11   12.4   0.0    1.2  1  DUF1275   Protein of unknown function (DUF1275)


Domain annotation for each model (and alignments):
>> DUF1275  Protein of unknown function (DUF1275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.3e-06      0.11      24     116 ..      21     126 ..      14     145 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-06
                           DUF1275  24 fvsaqTGNtvllglalaegnakaalaalvsllaFvlGaalagllarrg.....grrrrlvllle.allllaaallvp 94 
                                       + s  TG  +++ l   + ++  +   l ++++F++G++++ + +          +r + +++  a+++++  l++p
  gi|330508110|ref|YP_004384538.1|  21 YRSSITGLYIYILLPEQQLKWFLLTLILSAVILFLIGILIFYITKSLSkrvlgEEKRNVDIIFAgAIIVALSQLFGP 97 
                                       557789999999888666778777788999************88765456675334444444442666666666666 PP

                           DUF1275  95 agsvsp........lalallafamGlqnal 116
                                        +   +        + ++ l+f++   n +
  gi|330508110|ref|YP_004384538.1|  98 LFGA-SyplilgpdASNYKLSFSSMYYNIT 126
                                       5443.2466666666777777766555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2214.09
//
Query:       gi|330508111|ref|YP_004384539.1|  [L=176]
Description: hypothetical protein MCON_2208 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-07   30.4   3.6    3.4e-07   29.8   3.6    1.3  1  zinc_ribbon_2   zinc-ribbon domain
    3.6e-05   23.0   2.6    5.4e-05   22.5   2.6    1.3  1  zf-ribbon_3     zinc-ribbon domain
    0.00047   20.1   1.0    0.00071   19.6   1.0    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
       0.13   13.0   3.6        0.2   12.4   3.6    1.3  1  zinc_ribbon_15  zinc-ribbon family
       0.23   11.3   5.8        1.2    9.0   5.8    2.1  2  HscB_4_cys      Co-chaperone HscB tetracysteine metal binding


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 !   29.8   3.6   9.4e-11   3.4e-07       1      23 []       3      25 ..       3      25 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 9.4e-11
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGtpl 23
                                      +C++CG e q++++FC  CG++l
  gi|330508111|ref|YP_004384539.1|  3 YCWKCGSEYQEGSNFCQSCGYNL 25
                                      8*******************987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   2.6   1.5e-08   5.4e-05       4      26 .]       3      25 ..       1      25 [. 0.93

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.5e-08
                       zf-ribbon_3  4 rCPnCGa.plssddnvCpyCGtkl 26
                                      +C++CG+   +++ n+C +CG+ l
  gi|330508111|ref|YP_004384539.1|  3 YCWKCGSeY-QEGSNFCQSCGYNL 25
                                      8******88.***********986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.0     2e-07   0.00071       1      22 [.       4      25 ..       2      42 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2e-07
                               DZR  1 CpqCgeelppdarfCseCgtkl 22
                                      C +Cg+e +++++fC+ Cg +l
  gi|330508111|ref|YP_004384539.1|  4 CWKCGSEYQEGSNFCQSCGYNL 25
                                      6666666666666666666665 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.6   5.5e-05       0.2      67      86 .]       3      22 ..       1      22 [. 0.95

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.5e-05
                    zinc_ribbon_15 67 eCknCgkeveeefkyCpkCg 86
                                      +C++Cg+e +e +++C +Cg
  gi|330508111|ref|YP_004384539.1|  3 YCWKCGSEYQEGSNFCQSCG 22
                                      8******************9 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.8   0.00035       1.2       1      23 [.       2      21 ..       2      22 .. 0.74
   2 ?    0.6   0.5      0.14     5e+02       3      14 ..      18      29 ..      17      34 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00035
                                      -B-SSS--B--SS-S---B-TTT CS
                        HscB_4_cys  1 PrCWnCGgpgapgrgdefFCpqC 23
                                      P CW+CG+    g     FC  C
  gi|330508111|ref|YP_004384539.1|  2 PYCWKCGSEYQEGS---NFCQSC 21
                                      89*****9776554...477666 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.14
                                      -SSS--B--SS- CS
                        HscB_4_cys  3 CWnCGgpgapgr 14
                                      C +CG  ++++ 
  gi|330508111|ref|YP_004384539.1| 18 CQSCGYNLGAAS 29
                                      778998766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1177.49
//
Query:       gi|330508112|ref|YP_004384540.1|  [L=450]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-25   89.8   0.0    3.3e-25   89.0   0.0    1.4  1  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
      0.014   14.7   0.3      0.021   14.1   0.3    1.3  1  DDE_Tnp_2    Archaeal putative transposase ISC1217
      0.019   13.3   0.0       0.03   12.6   0.0    1.2  1  DDE_Tnp_1_4  Transposase DDE domain group 1
      0.075   13.0   1.0        1.4    8.9   0.1    2.8  3  Tudor_FRX1   Fragile X mental retardation Tudor 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 !   89.0   0.0   7.3e-29   3.3e-25       2     212 ..     133     371 ..     132     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 7.3e-29
                         DDE_Tnp_1   2 skrevlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkq..lldelrprk 76 
                                       s+r+v i D+t +r +++ +d+++     k  +g+k+  ++++    + s+ i p n++d+k+lk   ++      k
  gi|330508112|ref|YP_004384540.1| 133 SFRDVMIQDSTIIRLHKSLADKWPATRSRKVAAGVKVAFLTSAIANSPKSISILPENTNDVKTLKIgpWV------K 203
                                       6899***************9999988899999********************************995555......7 PP

                         DDE_Tnp_1  77 gklvlaDaGYasaelldtleekgvdyiirlkkntklyrk.............gaeskrrgrlrkhdrnkiltksqkr 140
                                       + ++l D G+ +++l+ ++ e+g+++++rlk+n++ ++              + +++++ +l+k d    ++ + ++
  gi|330508112|ref|YP_004384540.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVgtnqvrntrgvdlNGKHLKDIKLEKSDDIFDVNVEVSF 280
                                       789************************************99777666666663444444444444444444444444 PP

                         DDE_Tnp_1 141 rnk...................skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrgl 198
                                       +++                    +++++++ y+tn++s+ l a+eva+ y+ Rw++E +Fk+lk+++ ld   ++++
  gi|330508112|ref|YP_004384540.1| 281 DRRsyrgeskkdnkifrlvaiyNTEAEEHHFYLTNISSDILNASEVAAVYSGRWEVELIFKELKSRYALDQITTKSP 357
                                       4447777777777799999999999**************************************************** PP

                         DDE_Tnp_1 199 nrveaqllllllal 212
                                        ++ea ++  +l+l
  gi|330508112|ref|YP_004384540.1| 358 YAIEALIWVSILTL 371
                                       *******9998876 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   4.6e-06     0.021     219     288 ..     274     346 ..     202     384 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                         DDE_Tnp_2 219 rhvpvaelPeGeylveyl.dtvikllvlddykkdgrrylfstdln...dtdediittWenrWdievlirelkal 288
                                        +v+v+ + + +y  e   d+ i  lv +   + +  +++ t++    + + ++ + +  rW++e +++elk+ 
  gi|330508112|ref|YP_004384540.1| 274 VNVEVS-FDRRSYRGESKkDNKIFRLVAIYNTEAEEHHFYLTNISsdiLNASEVAAVYSGRWEVELIFKELKSR 346
                                       445543.7777888887767777767777777888999**999973335799********************73 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.6e-06      0.03     217     368 ..     204     372 ..     197     399 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.6e-06
                       DDE_Tnp_1_4 217 kilvRgDSafarpellkwceergvdYviglaknsrlealiaelvekakteaaekkek................erey 277
                                       +i++  D +f + +l++ + e+g ++v +l++n++     ++ v +++  + + k+                 e+++
  gi|330508112|ref|YP_004384540.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVGTNQVRNTRGVDLNGKHLkdikleksddifdvnvEVSF 280
                                       578889999**********************999877766666666666666654436799999999**99999999 PP

                       DDE_Tnp_1_4 278 refayqaesWskerrVvakaerpaeglnlrfvvTsla..klspeelyeqlYcaRGemEnrIKeakldlaadrtsshs 352
                                        +  y+ es + ++   + a +++e  +++f +T+++   l+++e+   +Y  R e+E  +Ke k+  a+d++ ++s
  gi|330508112|ref|YP_004384540.1| 281 DRRSYRGESKKDNKIFRLVAIYNTEAEEHHFYLTNISsdILNASEVA-AVYSGRWEVELIFKELKSRYALDQITTKS 356
                                       99999999855444333334455556667999****99888999999.9*************************999 PP

                       DDE_Tnp_1_4 353 faaNqlrlllsalAyn 368
                                         a ++ +++s l   
  gi|330508112|ref|YP_004384540.1| 357 PYAIEALIWVSILTLL 372
                                       9999988888887654 PP

>> Tudor_FRX1  Fragile X mental retardation Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00031       1.4      17      36 ..      22      41 ..      18      44 .. 0.88
   2 ?    1.1   0.0     0.085   3.8e+02      18      31 ..     269     282 ..     257     291 .. 0.89
   3 ?   -2.6   0.0       1.2   5.4e+03      13      36 ..     313     337 ..     311     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00031
                        Tudor_FRX1 17 vkdvhedsltvaFennWqpe 36
                                       kd+ e++lt +Fe +W  +
  gi|330508112|ref|YP_004384540.1| 22 EKDIVEQELTRMFESKWIRD 41
                                      59***************765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.085
                        Tudor_FRX1  18 kdvhedsltvaFen 31 
                                        d+++ ++ v+F+ 
  gi|330508112|ref|YP_004384540.1| 269 DDIFDVNVEVSFDR 282
                                       59**********96 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.2
                        Tudor_FRX1  13 ykafvkdvhed.sltvaFennWqpe 36 
                                       +  +  d+++  ++ +++   W  e
  gi|330508112|ref|YP_004384540.1| 313 LTNISSDILNAsEVAAVYSGRWEVE 337
                                       5566778888526888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2935.97
//
Query:       gi|330508113|ref|YP_004384541.1|  [L=104]
Description: hypothetical protein MCON_2210 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       415  (0.0231469); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 713.00
//
Query:       gi|330508114|ref|YP_004384542.1|  [L=350]
Description: IS66 family element, transposase [Methanosaeta concilii GP6]
Scores for complete 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-49  166.4   0.0    1.1e-48  166.2   0.0    1.1  1  DDE_Tnp_IS66     Transposase IS66 family
    8.7e-06   26.0   4.7    2.7e-05   24.4   4.7    1.8  1  zf-IS66          zinc-finger binding domain of transposase IS
     0.0031   17.8   0.0     0.0079   16.4   0.0    1.7  2  DDE_Tnp_IS240    DDE domain
  ------ inclusion threshold ------
       0.11   11.3   0.0        2.5    6.8   0.0    2.2  2  Transposase_mut  Transposase, Mutator family


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 !  166.2   0.0   2.4e-52   1.1e-48       2     280 ..      61     320 ..      60     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: 166.2 bits;  conditional E-value: 2.4e-52
                      DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtl 77 
                                       + +g++++A ++vlky+d lP +++++++ rl  +++s++t+ ++++raa++++p ++a+ +++++++++ +DET++
  gi|330508114|ref|YP_004384542.1|  61 GKFGNNVIALATVLKYEDRLPHRKIHDAMMRLyRLKISPATILDLTRRAADAIQPEYDAILRKIRRAPILYVDETGI 137
                                       57999************************************************************************ PP

                      DDE_Tnp_IS66  78 rvlkpgrgkgkksylWvyvtdkrkpavlfeyspsRggevaealLag.fkGvlvsDgyagYnklaeeqvthalCwaHl 153
                                       r       +g+ +++W++ t      ++f + +sRg++v  ++L+  fkG++v+Dg+++Y +++    + + CwaHl
  gi|330508114|ref|YP_004384542.1| 138 R------VQGEMCWIWAFTTPS---ETFFVIRKSRGMKVLMEVLTRrFKGIIVCDGWKPYARFT---NRIQRCWAHL 202
                                       *......89***********88...9*****************9999***************96...77799***** PP

                      DDE_Tnp_IS66 154 rRkfvdaeeakkksqaaaealarigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpksklgka 230
                                       +R+ +d+ e+ +   +a    + +++ly++  +a e  ++   ++r +  +   ++l++w+++        +k++k+
  gi|330508114|ref|YP_004384542.1| 203 LRESKDIAEKFE---EAIPLHNALKELYDLLTKALE--NDPPPEVRMTLWELAREALRHWISK----EYSIEKVRKF 270
                                       ********9754...555555568888887777743..3445555555556677888888875....568899**** PP

                      DDE_Tnp_IS66 231 iryllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                       i ++ +  e  ++f+ +++v+++NN+aERa+Rp v+ RK+ +++++++G 
  gi|330508114|ref|YP_004384542.1| 271 IGKINNGFEYWFTFIINPGVEPTNNRAERALRPHVVLRKILGTLRNDKGT 320
                                       ***********************************************996 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   4.7   6.1e-09   2.7e-05       3      45 ..       3      46 ..       2      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6.1e-09
                           zf-IS66  3 tCpcCGg.llkpigedrvreeldip.PakfrViehirpkyaCpcC 45
                                       Cp+CG+ l +p   d    + +ip P+ + V+e+ +  y+CpcC
  gi|330508114|ref|YP_004384542.1|  3 RCPDCGAeLGSPFRID-SKIVEEIPePQPIMVTEYKIAHYKCPCC 46
                                      6******778888888.8899****999999************99 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.8e-06    0.0079       6      94 ..     132     213 ..     129     257 .. 0.80
   2 ?   -1.9   0.0      0.82   3.7e+03      71     104 ..     251     283 ..     206     287 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.8e-06
                     DDE_Tnp_IS240   6 vDETyvkikGkwaYlyravDkegrildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkelkreg. 81 
                                       vDET ++++G+ +++++      ++  f+++k R++k    +l++ +k        iv D+ + ya+  ++++r   
  gi|330508114|ref|YP_004384542.1| 132 VDETGIRVQGEMCWIWAFTTPS-ET-FFVIRKSRGMKVLMEVLTRRFKGI------IVCDGWKPYARFTNRIQRCWa 200
                                       9***************876554.44.38899*******999999999999......999999999999999998655 PP

                     DDE_Tnp_IS240  82 elfdevshvqvky 94 
                                       +l++e + ++ k 
  gi|330508114|ref|YP_004384542.1| 201 HLLRESKDIAEKF 213
                                       6666666666665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.82
                     DDE_Tnp_IS240  71 asalkelkregelfdevshvqvkylnnriEsdhr 104
                                        +al++   +    ++v++   k  nn  E ++ 
  gi|330508114|ref|YP_004384542.1| 251 REALRHWISKEYSIEKVRKFIGKI-NNGFEYWFT 283
                                       344444444333445666666666.666666665 PP

>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.014        63     115     175 ..      80     140 ..      67     145 .. 0.77
   2 ?    6.8   0.0   0.00057       2.5     221     285 ..     161     229 ..     153     288 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.014
                   Transposase_mut 115 vstrkveklveelygeksvSksevSaitkeldeaveafreRsLeek.eypllflDalylkvR 175
                                       +  rk+++ + +ly   ++S++++  +t +  +a++   +  L +  + p+l++D + ++v 
  gi|330508114|ref|YP_004384542.1|  80 LPHRKIHDAMMRLYR-LKISPATILDLTRRAADAIQPEYDAILRKIrRAPILYVDETGIRVQ 140
                                       5679***********.88***********999999865555555431357888887777665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00057
                   Transposase_mut 221 knrGlkgvelvvsDahkGLvkais...avfpeaavQrCrvHllrnllakvpkkkad.kvaealksiyka 285
                                       k+rG+k    v +  +kG+    +    +      QrC  Hllr++ + ++k +++  +++alk +y+ 
  gi|330508114|ref|YP_004384542.1| 161 KSRGMKVLMEVLTRRFKGIIVCDGwkpYARFTNRIQRCWAHLLRESKDIAEKFEEAiPLHNALKELYDL 229
                                       55555555555555555554322110112234568***********99998866551578899999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2473.90
//
Query:       gi|330508115|ref|YP_004384543.1|  [L=170]
Description: hypothetical protein MCON_2212 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1190.96
//
Query:       gi|330508116|ref|YP_004384544.1|  [L=173]
Description: hypothetical protein MCON_2214 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0062   16.1   0.2      0.008   15.8   0.2    1.1  1  DUF5087   Domain of unknown function (DUF5087)


Domain annotation for each model (and alignments):
>> DUF5087  Domain of unknown function (DUF5087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   4.5e-07     0.008      37     104 ..      46     114 ..      33     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.5e-07
                           DUF5087  37 kyvktnlkkilkyllkniNtlelekicttlllisneleyeeklvil.hDiilfledlskllfiisalfn 104
                                        ++  n  +il  l +ni +le+++ +t + l+ +  e+++ ++i+ hD +l+ ++ + + +++ al +
  gi|330508116|ref|YP_004384544.1|  46 LFISGNYSRILSRLNRNITELEVRRAFTSFQLMTILEENHHSILIVeHDPLLYEDSQEMVGYLAQALKQ 114
                                       6999**************************99999998888877766***************9999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1285.53
//
Query:       gi|330508117|ref|YP_004384545.1|  [L=245]
Description: ABC transporter [Methanosaeta concilii GP6]
Scores for complete 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-25   88.0  14.9    5.7e-25   88.0  14.9    2.0  2  ABC2_membrane    ABC-2 type transporter
    2.7e-05   23.4  24.4    2.7e-05   23.4  24.4    1.6  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
        0.6    9.4   1.1        1.1    8.6   1.1    1.3  1  DUF4820          Domain of unknown function (DUF4820)
        1.6    9.3   5.8       0.46   11.1   1.8    2.2  2  PAP2_C           PAP2 superfamily C-terminal


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 !   88.0  14.9   1.3e-28   5.7e-25       5     201 ..       6     204 ..       3     213 .. 0.93
   2 ?   -2.1   6.2      0.46   2.1e+03     131     150 ..     219     238 ..     205     244 .. 0.67

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 1.3e-28
                     ABC2_membrane   5 allkreflqrwrdpslgllwrliqplllalvfgtvfgn.lg.nsedglnr..pgllffsvlflafsaltsvapvfer 77 
                                        +l+ ++   +r++  +ll+ l++pll+++ fg   g+ ++ n +++l++  pg+++ ++++++f+++ +  +v   
  gi|330508117|ref|YP_004384545.1|   6 SILWSDLTALKRRWPRYLLTTLMSPLLYLVAFGWGLGRgIDmNGTSYLDFviPGIIALTAMTTSFNGAGTRLNVDRL 82 
                                       68999999*****************************876576777776678*******************888888 PP

                     ABC2_membrane  78 ergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv.gldlsrfflflllllltalaasslgllisa 153
                                         +++++ l +p+  l++++l+k+l+ +++++l +++fll+++++  +++++  + f+l lll+ l++ +lg+l + 
  gi|330508117|ref|YP_004384545.1|  83 YFKSFDECLMAPV-ELPSILLGKALIGVVRGILSSVAFLLVAFLIArHIHIT--LPFVLGLLLSCLTFAFLGVLAAL 156
                                       99***********.******************************97788885..*********************** PP

                     ABC2_membrane 154 lapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltya 201
                                       la+s+ed+++++sl+l+p+++l+G f++++++p  l+   y++Plt+ 
  gi|330508117|ref|YP_004384545.1| 157 LARSHEDMATFGSLILMPMTFLGGTFFSVSQVPFGLKMALYALPLTHS 204
                                       **********************************************97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.46
                     ABC2_membrane 131 flflllllltalaasslgll 150
                                       +  +l+l+l++l++++ g++
  gi|330508117|ref|YP_004384545.1| 219 WSSFLVLFLFFLLFLGGGMM 238
                                       44566666666666666665 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 !   23.4  24.4     6e-09   2.7e-05     195     340 ..      90     233 ..      43     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 6e-09
                   ABC2_membrane_3 195 qlvsgvsplqywlskilgdflvyllqlllilllafglgipfg..nlglllllfllfglayialgyllsslfknseta 269
                                        l+++v   +++l+k l+ ++ ++l+++ +ll+af   i       + ++l +ll +l++++lg l   l +++e++
  gi|330508117|ref|YP_004384545.1|  90 CLMAPVELPSILLGKALIGVVRGILSSVAFLLVAFL--IARHihITLPFVLGLLLSCLTFAFLGVLAALLARSHEDM 164
                                       468999999******************999997555..333331456788*************************** PP

                   ABC2_membrane_3 270 qilifivilllsgffgglfp.ledlpsalkwifsiiPffapglgllrlitgdplweillsliilalfavvyl 340
                                        ++ +++++ ++ f+gg+f+ ++++p +lk +++ +P+++ +l+l   +  +pl   + s+++l+lf++++l
  gi|330508117|ref|YP_004384545.1| 165 ATFGSLILM-PMTFLGGTFFsVSQVPFGLKMALYALPLTHSSLFLRAAALDQPL--PWSSFLVLFLFFLLFL 233
                                       *********.77777777655************************999997744..5899999999999997 PP

>> DUF4820  Domain of unknown function (DUF4820)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.1   0.00025       1.1      53      72 ..     210     229 ..     201     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00025
                           DUF4820  53 appLvRPLPWilFLpalilL 72 
                                       a+ L  PLPW  FL++ +++
  gi|330508117|ref|YP_004384545.1| 210 AAALDQPLPWSSFLVLFLFF 229
                                       57899*********998875 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.8    0.0001      0.46      31      71 ..     109     149 ..      99     153 .. 0.89
   2 ?   -3.1   0.1       2.6   1.2e+04      34      39 ..     225     230 ..     215     240 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                            PAP2_C  31 ilkvillllallglfliiasrkHYtvDVllglyittlvfll 71 
                                       +++ il  +a+l ++++ia + H t+  +lgl++++l+f++
  gi|330508117|ref|YP_004384545.1| 109 VVRGILSSVAFLLVAFLIARHIHITLPFVLGLLLSCLTFAF 149
                                       578899999*****************************965 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.6
                            PAP2_C  34 villll 39 
                                       ++l++l
  gi|330508117|ref|YP_004384545.1| 225 LFLFFL 230
                                       222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1752.31
//
Query:       gi|330508118|ref|YP_004384546.1|  [L=286]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (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  119.9   0.0    1.6e-34  119.4   0.0    1.2  1  ABC_tran  ABC transporter
    1.6e-15   57.8   0.2    5.1e-08   33.1   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00013   22.6   0.0    0.00017   22.2   0.0    1.2  1  AAA_23    AAA domain
    0.00049   19.9   0.0       0.65    9.6   0.0    2.1  2  AAA_15    AAA ATPase domain
     0.0053   16.2   0.0      0.018   14.5   0.0    1.7  1  SMC_N     RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.022   14.7   0.0    1.3  1  Rad17     Rad17 P-loop domain
      0.027   14.9   0.0      0.099   13.1   0.0    2.0  1  AAA       ATPase family associated with various cellular acti
      0.028   14.6   0.0      0.052   13.8   0.0    1.5  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
      0.066   13.0   0.1       0.11   12.2   0.1    1.3  1  AAA_29    P-loop containing region of AAA domain
       0.12   12.0   0.0       0.18   11.4   0.0    1.2  1  SRP54     SRP54-type protein, GTPase domain
       0.14   11.1   0.0       0.22   10.5   0.0    1.3  1  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.16   11.7   0.2       0.26   11.0   0.2    1.6  1  AAA_30    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   0.0   1.1e-37   1.6e-34       1     136 [.      20     163 ..      20     164 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 1.1e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       ++n++l++ +ge+ +++G+nGaGK+t +++l+ l+kp +G+i+++g d+ + + +++++e+gv++q+ +l+++lt++
  gi|330508118|ref|YP_004384546.1|  20 VDNLNLEVGQGELFGFLGPNGAGKTTTIRILTTLTKPSSGRIRINGIDVAK-DPSRVKSEFGVVQQHLSLNRDLTIG 95 
                                       589************************************************.89999******************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en             e++e+i+++l+ +gl++  d+ +     s+SgG+k+r ++aral+ +pkll+lDEpt
  gi|330508118|ref|YP_004384546.1|  96 ENlelharlhhlqsrERKERIAELLDYVGLSDHSDQLI----DSVSGGMKRRAMIARALIHRPKLLFLDEPT 163
                                       ************99999999************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   4.6e-08   6.8e-05       2      96 ..      33     116 ..      32     131 .. 0.84
   2 !   33.1   0.0   3.4e-11   5.1e-08     234     297 ..     133     193 ..     126     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.6e-08
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                        ++ GpNg+GK++ +++l  l              ++ ++ r+ ++ +d   + ++++ e+  +++q+   +  l++
  gi|330508118|ref|YP_004384546.1|  33 FGFLGPNGAGKTTTIRILTTL--------------TKPSSGRIRINGIDVAKDPSRVKSEFG-VVQQHLSLNRDLTI 94 
                                       5789**************766..............8899***********************.************** PP

                            AAA_21  79 ersqv....eeklssvetlles 96 
                                       +++        +l+s+e+++++
  gi|330508118|ref|YP_004384546.1|  95 GENLElharLHHLQSRERKERI 116
                                       **99985555555555555555 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 3.4e-11
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       ++++S G+kr  a+++  l  ++  +ll++DEp  gL+ +  rr+++l+++ + +g+ v+ltTH
  gi|330508118|ref|YP_004384546.1| 133 IDSVSGGMKRR-AMIARALIHRP--KLLFLDEPTVGLDAQTRRRVWDLIRRMNLEGTTVFLTTH 193
                                       6789*******.99999999888..7***********************9998899******** 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   1.1e-07   0.00017      13     114 ..      23     122 ..       6     173 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.1e-07
                            AAA_23  13 qeidFsk.gltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese.gkvkayveltfenkdgryt 87 
                                        +++ ++  l+ + GpNGaGKTT ++ ++  +   ++r  r +g +  k+  +++se g v++ ++l+   + g   
  gi|330508118|ref|YP_004384546.1|  23 LNLEVGQgELFGFLGPNGAGKTTTIRILTTLTKPSSGR-IRINGIDVAKDPSRVKSEfGVVQQHLSLNRDLTIG--- 95 
                                       4555544269****************999766655444.45568888888888888843333335555433334... PP

                            AAA_23  88 rsiererelskkkgkttkkaklellei 114
                                       +++e    l   +++++k+ + ell+ 
  gi|330508118|ref|YP_004384546.1|  96 ENLELHARLHHLQSRERKERIAELLDY 122
                                       356666666666666666666666666 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00044      0.65      27      50 ..      34      57 ..      20     101 .. 0.71
   2 !    8.1   0.0    0.0013         2     288     364 ..     127     193 ..     103     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00044
                            AAA_15 27 vliGkNnsGKSsilealdlFlnnk 50
                                       + G+N++GK++ +++l  + + +
  gi|330508118|ref|YP_004384546.1| 34 GFLGPNGAGKTTTIRILTTLTKPS 57
                                      588**************9999988 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0013
                            AAA_15 288 ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       d  ++ ++ ++ G++r   ++  +++           ++l+++EP + L  q  + +++l++++  ++   v++tTH
  gi|330508118|ref|YP_004384546.1| 127 DHSDQLIDSVSGGMKRRAMIARALIHRP---------KLLFLDEPTVGLDAQTRRRVWDLIRRMNLEGT-TVFLTTH 193
                                       5666667777777777777765554443.........67*************************99997.9****** PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.2e-05     0.018      29     210 ..      35     206 ..       3     213 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                                       EEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  29 ivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkr 105
                                        +GpNG+GK+  +  +  +L + s+  +r + ++ + +   ++ +++++ v+ +++ + + +  e+ e+  + +  +
  gi|330508118|ref|YP_004384546.1|  35 FLGPNGAGKTTTIRIL-TTLTKPSSGRIRINGID-VAKD-PSRVKSEFGVVQQHLSLNRDLTIGENLELHARLHHLQ 108
                                       6799*****9999866.89999999899988775.5554.7888888899998876665553333344444444444 PP

                                       TSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 106 kgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvael 182
                                       + e     +++ ++  ++  l  +++  +++ SgG k  +++a       +++  l +lDe    LD++ +++v +l
  gi|330508118|ref|YP_004384546.1| 109 SRE----RKERIAELLDYVGLSDHSDQLIDSVSGGMKRRAMIARA----LIHRPKLLFLDEPTVGLDAQTRRRVWDL 177
                                       333....234445556666666666666779****9876555433....2244457789****************** PP

                                       HHHHCTT.SEEEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 183 lkekskn.aQfivislreemlekadklvg 210
                                       +++ + + + ++ +++  e  e   + vg
  gi|330508118|ref|YP_004384546.1| 178 IRRMNLEgTTVFLTTHYIEEAEALCQRVG 206
                                       *9766443778888776666665555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.5e-05     0.022      39      99 ..      24      85 ..      11     120 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                             Rad17 39 vLesrkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvsl.kepdnqksdfkglteke 99
                                       Le  + ++    GP G gk+t++++L+    ++  r  +n++ + k+p+  ks+f  +++++
  gi|330508118|ref|YP_004384546.1| 24 NLEVGQGELFGFLGPNGAGKTTTIRILTTLTKPSSgRIRINGIDVaKDPSRVKSEFG-VVQQH 85
                                      5565656677788**************998877652678999987355666666664.44443 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.6e-05     0.099       3      38 ..      35     122 ..      33     206 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-05
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................ 37 
                                       + Gp G GKT++++ + + ++  +  ++i+g ++ ++                                        
  gi|330508118|ref|YP_004384546.1|  35 FLGPNGAGKTTTIRILTTLTKpsSGRIRINGIDVAKDpsrvksefgvvqqhlslnrdltigenlelharlhhlqsre 111
                                       68**************9999744556888888888446666666666666666666665555555555555555555 PP

                                       ..........S CS
                               AAA  38 ..........y 38 
                                                 y
  gi|330508118|ref|YP_004384546.1| 112 rkeriaelldY 122
                                       55555555551 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.5e-05     0.052      62      89 ..     152     179 ..     126     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                       ++++l+fLDE   +lD+++++++ +l++
  gi|330508118|ref|YP_004384546.1| 152 HRPKLLFLDEPTVGLDAQTRRRVWDLIR 179
                                       689*********************9987 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   7.5e-05      0.11      24      55 ..      32      64 ..      18      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-05
                            AAA_29 24 atlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                       + + Gp+G+GK+T +  +++l  p++ ++r N
  gi|330508118|ref|YP_004384546.1| 32 LFGFLGPNGAGKTTTIRILTTLTKPSSgRIRIN 64
                                      66789***********99999999988888877 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   0.0   0.00012      0.18       6      38 ..      35      67 ..      31      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      ++G++GaGKTtt+  L  l k +  ++ +   D
  gi|330508118|ref|YP_004384546.1| 35 FLGPNGAGKTTTIRILTTLTKPSSGRIRINGID 67
                                      79***********99998888776666666555 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 ?   10.5   0.0   0.00015      0.22      15      66 ..      16      67 ..       5      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                                      HHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 15 akellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                       k+++++l  + G+ +  G+ G  GaGk t++  l++  +    r+ +  +D
  gi|330508118|ref|YP_004384546.1| 16 RKKVVDNLNLEVGQGELFGFLGPNGAGKTTTIRILTTLTKPSSGRIRINGID 67
                                      5788999999***********************9999888887788775554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00017      0.26      21      49 ..      33      61 ..      24     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                            AAA_30 21 avltGpAGtGKttalkalreaweaaggrv 49
                                          Gp G+GKtt+++ l+ + + + gr+
  gi|330508118|ref|YP_004384546.1| 33 FGFLGPNGAGKTTTIRILTTLTKPSSGRI 61
                                      5567**************99988875454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2054.77
//
Query:       gi|330508119|ref|YP_004384547.1|  [L=661]
Description: magnesium-chelatase subunit ChlD [Methanosaeta concilii GP6]
Scores for complete 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-23   81.4   0.2    9.8e-23   79.8   0.2    1.9  1  AAA_lid_2        AAA lid domain
    1.1e-14   55.0   0.0    6.1e-14   52.6   0.0    2.2  2  VWA_2            von Willebrand factor type A domain
    3.2e-10   40.1   0.0    2.2e-06   27.7   0.0    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
    3.4e-09   37.2   0.0    9.1e-09   35.8   0.0    1.7  1  VWA              von Willebrand factor type A domain
    8.2e-08   31.9   0.1    6.2e-07   29.0   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.3e-05   24.5   0.2    0.00059   19.0   0.1    2.9  2  MCM              MCM P-loop domain
     0.0035   18.0   0.6      0.017   15.8   0.6    2.3  1  Mg_chelatase_C   Magnesium chelatase, subunit ChlI C-terminal
     0.0039   16.9   0.0       0.19   11.4   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
     0.0041   17.5   0.4      0.034   14.5   0.1    2.7  2  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.028   14.3   0.0        2.9    7.8   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
      0.031   14.6   0.0       0.17   12.1   0.0    2.3  1  AAA_22           AAA domain
      0.088   12.7   0.0       0.34   10.8   0.0    2.1  1  VWA_3            von Willebrand factor type A domain
       0.16   12.1   1.7       0.25   11.5   1.7    1.3  1  DDHD             DDHD domain
        1.1    9.3   6.5         13    5.8   4.9    2.4  2  Peptidase_S49_N  Peptidase family S49 N-terminal
        1.3    8.8   7.9        2.3    8.0   7.9    1.3  1  RR_TM4-6         Ryanodine Receptor TM 4-6
        2.8    6.6   5.8          4    6.1   5.8    1.1  1  Presenilin       Presenilin
        4.4    8.3   5.9        9.2    7.3   5.9    1.5  1  DUF4834          Domain of unknown function (DUF4834)
        9.5    4.2   6.7         13    3.7   6.7    1.1  1  Hid1             High-temperature-induced dauer-formation pro


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 !   79.8   0.2   9.9e-26   9.8e-23       2      72 ..     249     319 ..     248     320 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 9.9e-26
                         AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegetteeivee 72 
                                       + +a+++i lgv ++Ra+++++r+A+++Aa++gr++V++eDvk+a +l+LaHR+r +p+++++ ++e++e+
  gi|330508119|ref|YP_004384547.1| 249 RLIASTCIDLGVKTHRAEIVITRTAKTIAAFDGRTEVNQEDVKKAMELALAHRMRSRPFEPPTLNKERLEK 319
                                       56899*********************************************************999998875 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       3.1   3.1e+03      46      88 ..     262     300 ..     220     315 .. 0.54
   2 !   52.6   0.0   6.1e-17   6.1e-14       1     106 [.     462     568 ..     462     569 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.1
                             VWA_2  46 sdgpevlipltkdkakilnalrnleakgggtnlaaaLqlarka 88 
                                        +++e++i+ t   ++i ++  ++e   ++ ++ +a++la ++
  gi|330508119|ref|YP_004384547.1| 262 THRAEIVITRTA--KTIAAFDGRTE--VNQEDVKKAMELALAH 300
                                       444444444442..22222222222..2566777777777665 PP

  == domain 2  score: 52.6 bits;  conditional E-value: 6.1e-17
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallk.slp.gdrvglvtfsd.gpevlipltkdkakilnalrnleakgg 74 
                                       ++fv+D SgSm+++    +r+e ak av +ll  s++ +d++g ++f++ ++e+++p++++ +  l +lr+l + gg
  gi|330508119|ref|YP_004384547.1| 462 VLFVVDASGSMGAN----QRMESAKGAVLSLLMdSYQkRDKIGMIAFKGkEAEIILPPCTSVDLALGRLRELPT-GG 533
                                       79***********9....6*********8877646655***********88**********************7.7* PP

                             VWA_2  75 gtnlaaaLqlarkalkkrr...kgekrvivlitDg 106
                                       +t l a+L+   ++l+ +    +  k  +vli+Dg
  gi|330508119|ref|YP_004384547.1| 534 KTPLSAGLSRGLQLLQGELrkdEESKLMMVLISDG 568
                                       ********999999976656667888899999999 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00098      0.98       2      24 ..      17      39 ..      16      50 .. 0.89
   2 !   27.7   0.0   2.2e-09   2.2e-06      25     138 .]      77     184 ..      70     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00098
                                      EEEE--SSSSHHHHHHHGGGGBS CS
                             AAA_5  2 vlLvGppGtgKselaerlaaaln 24
                                      vl+ G++Gt+Ks+ +++la +l+
  gi|330508119|ref|YP_004384547.1| 17 VLIRGDKGTAKSTAVRSLADLLE 39
                                      8999***************9984 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 2.2e-09
                                       --EEEEE--TT--HHHHH--B--.............--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE.. CS
                             AAA_5  25 reveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllle 97 
                                       +++ +v l+ + te+ ++g+++++    +g ++l++++l   a +  il++DEv+ ++++v+++Ll         +e
  gi|330508119|ref|YP_004384547.1|  77 KKTPVVDLPLGATEDRVVGSLNVEraikEGIKALEPGILA--AANRGILYIDEVNLLDDHVADVLLDAAAMGVNIVE 151
                                       5666777888899**********99999***********9..55667******************887777776666 PP

                                       -SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5  98 eggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                         g  v ++++     f +++t+np +    e+ p+l++Rf
  gi|330508119|ref|YP_004384547.1| 152 REGVSVAHPSK-----FILVGTMNPEE---GEIRPQLLDRF 184
                                       65555555554.....*********99...78899999999 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 !   35.8   0.0   9.1e-12   9.1e-09       2     137 ..     462     599 ..     462     612 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 9.1e-12
                                       EEEEEE-STTS.CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS.EEEEEETTSHCHHHHHHHHHHTGSGGGG CS
                               VWA   2 ivfvlDgSgsm.geenfekvkefikklveklevgpegtrvglvqfsse.vktefslndysskeellsalnnlkysgg 76 
                                       + fv+D+Sgsm  ++++e++k ++ +l+ + +  ++++++g++ f ++ ++++ +  +  s + +l  l++l   +g
  gi|330508119|ref|YP_004384547.1| 462 VLFVVDASGSMgANQRMESAKGAVLSLLMDSY--QKRDKIGMIAFKGKeAEIILPPCT--SVDLALGRLREL--PTG 532
                                       68*********5567899******99998888..9**********9776999999988..6699*******8..666 PP

                                       SSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.......HTHHHHHHHHGCTEEEEEE CS
                               VWA  77 gttntgkalkyaleklfkssagaRenakkviilltdGksndg.......dpkeaaneakeqgikvfav 137
                                       g+t + ++l+ +l+ l+ + ++  e+ k +++l++dG+ n+g       ++   ++++k+ gi ++++
  gi|330508119|ref|YP_004384547.1| 533 GKTPLSAGLSRGLQLLQGELRK-DEESKLMMVLISDGRANEGmggkikdELMAISERIKHLGIHTIVI 599
                                       6666**********77777777.55799999********99889*88888888888888888888887 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.6   1.6e+03      25      50 ..      17      42 ..      15      46 .. 0.87
   2 !   29.0   0.0   6.2e-10   6.2e-07      93     158 ..     106     171 ..      96     180 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.6
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllppls 50
                                      +l+ G  G+ K+   + l+ ll  ++
  gi|330508119|ref|YP_004384547.1| 17 VLIRGDKGTAKSTAVRSLADLLETIQ 42
                                      6899**************99997665 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 6.2e-10
                      Mg_chelatase  93 ggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                       g +  +pG ++ a++G+L++DE+  ++ +v +vL +    g   ++r   +v +p++f lv +mNp
  gi|330508119|ref|YP_004384547.1| 106 GIKALEPGILAAANRGILYIDEVNLLDDHVADVLLDAAAMGVNIVEREGVSVAHPSKFILVGTMNP 171
                                       667899***********************************************************9 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.11   1.1e+02      60      82 ..      17      39 ..      11      46 .. 0.85
   2 !   19.0   0.1     6e-07   0.00059     100     192 ..      98     178 ..      60     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                                      EEEEESSTSTHHHHHHHHHHHSS CS
                               MCM 60 vllvgdpgtaKsqlLkyveklap 82
                                      vl+ gd gtaKs+ ++++++l++
  gi|330508119|ref|YP_004384547.1| 17 VLIRGDKGTAKSTAVRSLADLLE 39
                                      8999*********9998887765 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 6e-07
                                       EEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSS CS
                               MCM 100 avvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkag 176
                                        v r  ++g  +le G l  a++G+++iDe++  +++  ++l++a       + + G+ +  +++  ++  +np++g
  gi|330508119|ref|YP_004384547.1|  98 NVERAIKEGIKALEPGILAAANRGILYIDEVNLLDDHVADVLLDAAAMGVNIVEREGVSVAHPSKFILVGTMNPEEG 174
                                       566777777789*********************************99999999*********************998 PP

                                       SCCTTS-HHHHSSSSH CS
                               MCM 177 rydkkksvaeninlsa 192
                                       +              +
  gi|330508119|ref|YP_004384547.1| 175 EI------------RP 178
                                       63............34 PP

>> Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.6   1.7e-05     0.017      16      91 ..     219     295 ..     196     297 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                    Mg_chelatase_C  16 eiqkeRfakenaelsgeelrevceldeeaeelleeaierlgl.saRaydrilkvArTiADLegseeieeehlaeAlq 91 
                                       e q+e ++ +++  ++++l + ++++++  +l+ + + +lg+ + Ra   i + A+TiA  +g++e+++e++++A++
  gi|330508119|ref|YP_004384547.1| 219 EWQQEQVDMKQKISRARQLLSQVSMSDDFLRLIASTCIDLGVkTHRAEIVITRTAKTIAAFDGRTEVNQEDVKKAME 295
                                       44444443334445556777778888888888888777777637899999*************************97 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.075        75      24      59 ..      16      52 ..       5      62 .. 0.72
   2 !   11.4   0.0   0.00019      0.19      80     140 ..     106     168 ..      68     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.075
                                      -EEEECSTTSSHHHHHHHHHHHSTT.TTS-EEEEETT CS
                   Sigma54_activat 24 svlitGesGtGKellaraiheaskr.kekpfvavnca 59
                                       vli+G++Gt K++  r++ +  +  + ++   +nc 
  gi|330508119|ref|YP_004384547.1| 16 GVLIRGDKGTAKSTAVRSLADLLETiQVASDCPFNCN 52
                                      59************99998874433144455566665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00019
                                       TTSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHH..HHHSEEESBTSSSEEE--EEEEEE CS
                   Sigma54_activat  80 GAekekkGlfekadgGtlfLDeigelplelQekLlrv..lqegevervGsskeikvdvriiaa 140
                                       G ++ + G + +a+ G+l++De++ l+ ++   Ll +  +  + ver G s  ++ ++ ++ +
  gi|330508119|ref|YP_004384547.1| 106 GIKALEPGILAAANRGILYIDEVNLLDDHVADVLLDAaaMGVNIVEREGVSVAHPSKFILVGT 168
                                       5566678*********************99999997511455567777777776666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.4e-05     0.034      21     155 ..      11     140 ..       3     152 .. 0.54
   2 ?   -1.9   0.0       3.9   3.9e+03      51      88 ..     404     441 ..     395     499 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleaw 97 
                                        +r + vl++G++G+ Ks+ vr+l++ l ++ + +++     +  + p          e+ +    ++++s++  a 
  gi|330508119|ref|YP_004384547.1|  11 NPRIGGVLIRGDKGTAKSTAVRSLAD-LLET-IQVASDCPFNCNPENP----------EDMCDLCYQKSQSNQITAV 75 
                                       456689*******************5.6666.6666665555522222..........1222222222222222222 PP

                            AAA_16  98 rekleeala.....avpelagaea........srllellkrll.allsrderplvlvlDdlqwadeaslql.l 155
                                        +k   ++        +      +        +++ e +k+l    l+   r  +l +D++  +d++ +++ l
  gi|330508119|ref|YP_004384547.1|  76 EKKT-PVVDlplgaTED------RvvgslnveRAIKEGIKALEpGILAAANR-GILYIDEVNLLDDHVADVlL 140
                                       2211.111111212112......12222335566666666666655665333.78888888888888777744 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.9
                            AAA_16  51 dggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                       ++g +lr+k  q +++i+ +a ++a+a  + +r   ++
  gi|330508119|ref|YP_004384547.1| 404 NRGRYLRQKMPQEGKDIAIDATIRAAAPYQRIRSGPNA 441
                                       45666666666666666666655555565666655444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.048        48       2      25 ..      17      40 ..      16      55 .. 0.88
   2 ?    7.8   0.0    0.0029       2.9      65     116 ..     122     175 ..     103     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.048
                             AAA_3  2 vllegvPGlaktllvkalakaldl 25
                                      vl++g  G+ak ++v++la+ l++
  gi|330508119|ref|YP_004384547.1| 17 VLIRGDKGTAKSTAVRSLADLLET 40
                                      7999***************99875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0029
                             AAA_3  65 llladeinrappktqsallea..meerqvtvegethklpepflvlatqnPieqe 116
                                       +l  de+n    ++   ll+a  m  + v  eg + + p++f+++ t nP e e
  gi|330508119|ref|YP_004384547.1| 122 ILYIDEVNLLDDHVADVLLDAaaMGVNIVEREGVSVAHPSKFILVGTMNPEEGE 175
                                       7889***************853388899999999****************8755 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   0.00017      0.17       9     130 ..      18     168 ..      15     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...sskdllrellralglelka............ 70 
                                       ++ G +Gt K+t +r l++ l         +  +v  ++p  +   +++d++    ++ ++++ +            
  gi|330508119|ref|YP_004384547.1|  18 LIRGDKGTAKSTAVRSLADLL---------ETIQVASDCPFNCnpeNPEDMCDLCYQKSQSNQITavekktpvvdlp 85 
                                       788******************.........77777777777776777888888888888887777888899999999 PP

                            AAA_22  71 .............erlsseellealeqalraravielliiDEaqhlr.s..eealeeLrsllnl.......srkgvq 124
                                                     +   +e ++ale  + a+a +++l iDE+  l+ +  + +l    + +n+         ++ +
  gi|330508119|ref|YP_004384547.1|  86 lgatedrvvgslnVERAIKEGIKALEPGILAAANRGILYIDEVNLLDdHvaDVLLDAAAMGVNIveregvsVAHPSK 162
                                       9989999998888777888888899999999988************7635455555556667767777777788888 PP

                            AAA_22 125 liLvGt 130
                                       +iLvGt
  gi|330508119|ref|YP_004384547.1| 163 FILVGT 168
                                       888887 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 ?   10.8   0.0   0.00035      0.34       3     138 ..     462     604 ..     460     626 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                             VWA_3   3 vvivvDvsssmsaen...klvkdaLsvalrqLptndkiavllfgtkprplf.pgsravsaaelqealqkikelelsl 75 
                                       v +vvD+s sm a++    +  + Ls+++ + +++dki  ++f  k  + + p   +v     + al  + el+   
  gi|330508119|ref|YP_004384547.1| 462 VLFVVDASGSMGANQrmeSAKGAVLSLLMDSYQKRDKIGMIAFKGKEAEIIlPPCTSV-----DLALGRLRELPT-G 532
                                       789***********9996666778**************99999876555553655444.....478888888888.8 PP

                             VWA_3  76 gasnlegaLkealrqp.....akpgevrsvilltDgss.aqgeervsdlisrar...ekirfhalglgssls 138
                                       g ++l + L + l+       +  ++    +l++Dg +   +  ++ d++ +     +++ +h++ ++s+++
  gi|330508119|ref|YP_004384547.1| 533 GKTPLSAGLSRGLQLLqgelrKDEESKLMMVLISDGRAnEGMGGKIKDELMAISeriKHLGIHTIVIDSEVV 604
                                       888888888888864444554566777788999999974444444444443322224888899988888765 PP

>> DDHD  DDHD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.7   0.00025      0.25      89     170 ..     277     377 ..     176     438 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                              DDHD  89 elkesltsigaalkqkvsglvssls.....a....llnrslelaeeesaslaessksherasesskasqeskaaess 156
                                        + ++ t+++++ ++k  +l+   +          l+++ le ++++++ + +++ ++ +++++++++ ++ ++++ 
  gi|330508119|ref|YP_004384547.1| 277 AAFDGRTEVNQEDVKKAMELALAHRmrsrpFepptLNKERLEKSMSQKQHEHQHQDQKPEQQKKNEQQPQEPSEQKD 353
                                       33344444444444444443333333333303332222223323322222222222222222222222222222222 PP

                              DDHD 157 tasssaksskaee...........k 170
                                       t +++a  + +e+           +
  gi|330508119|ref|YP_004384547.1| 354 TDQKQA-AKPQERifeigtpidvrA 377
                                       222222.122222445555444440 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.9     0.013        13      42     108 ..     313     376 ..     284     388 .. 0.54
   2 ?    2.2   0.0      0.17   1.7e+02      92     112 ..     457     477 ..     434     500 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.013
                   Peptidase_S49_N  42 evtkLneeykelkeeleealldeeelkaaekkekkeekeekkaekkkakeeeekkrvfvldFkGdik 108
                                       + ++L+++ ++ ++e +++  + e++k+ e++ ++ + +++ ++k+   +++ ++r+f +    d++
  gi|330508119|ref|YP_004384547.1| 313 NKERLEKSMSQKQHEHQHQDQKPEQQKKNEQQPQEPSEQKDTDQKQ---AAKPQERIFEIGTPIDVR 376
                                       4444444444444444444444444444433333333333333322...255667777665555555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.17
                   Peptidase_S49_N  92 eeekkrvfvldFkGdikAsev 112
                                       +++   +fv+d +G++ A++ 
  gi|330508119|ref|YP_004384547.1| 457 KTSAVVLFVVDASGSMGANQR 477
                                       5677889**********9864 PP

>> RR_TM4-6  Ryanodine Receptor TM 4-6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   7.9    0.0023       2.3      67     135 ..     295     361 ..     258     377 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0023
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX........ CS
                          RR_TM4-6  67 eagLgDlseteaeesptpelkkklaeeeeaeeekeeeeepeaeaeekadaengekeekekekeeeekes 135
                                       e  L   + + + e+p +  k++l++++++++++++++++++e+++k++++ +e +e++ + ++++ ++
  gi|330508119|ref|YP_004384547.1| 295 ELALAHRMRSRPFEPP-TLNKERLEKSMSQKQHEHQHQDQKPEQQKKNEQQPQEPSEQKDT-DQKQAAK 361
                                       4444444444444443.55566666666666666666666666655555444443332222.2222222 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.8     0.004         4     261     305 ..     317     358 ..     251     399 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.004
                        Presenilin 261 sseksaqsseseeeseeesseaessaeesseekeseessesseee 305
                                        +++++q   +++e++++ ++ e++++++++++e +e++++++++
  gi|330508119|ref|YP_004384547.1| 317 LEKSMSQ---KQHEHQHQDQKPEQQKKNEQQPQEPSEQKDTDQKQ 358
                                       1111111...11111111111111111111111111111111111 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   5.9    0.0093       9.2      37      86 ..     319     368 ..     274     371 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0093
                           DUF4834  37 kss.ksaqkqfgnstnsnqqksqsrsetkeegeiieeersekeakrkkiFe 86 
                                       ks+ +++++++++ ++ +qqk+ ++++ +e  e +++++++  +++ +iFe
  gi|330508119|ref|YP_004384547.1| 319 KSMsQKQHEHQHQDQKPEQQKK-NEQQPQEPSEQKDTDQKQAAKPQERIFE 368
                                       2221222222222222222222.2222222223333333333334448996 PP

>> Hid1  High-temperature-induced dauer-formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   6.7     0.013        13     593     680 ..     274     359 ..     225     377 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.013
                              Hid1 593 dsideeeeenssessrieesrsesrspslsevpelksslaitddeskaereksatessssqavsqlremsekarake 669
                                       + i+  + +++ +++ ++++++ +   ++ + p +  +l ++  e++++++++++++++++ ++  ++ +e+++++ 
  gi|330508119|ref|YP_004384547.1| 274 KTIAAFDGRTEVNQEDVKKAMELALAHRMRSRPFEPPTLNKERLEKSMSQKQHEHQHQDQKPEQ--QKKNEQQPQEP 348
                                       3333334444444444555555666666666666677777777777777777777666666555..22222222222 PP

                              Hid1 670 saesteesrqe 680
                                       s+++++ ++q+
  gi|330508119|ref|YP_004384547.1| 349 SEQKDTDQKQA 359
                                       22222222221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (661 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2291  (0.127782); expected 358.6 (0.02)
Passed bias filter:                     1051  (0.0586201); expected 358.6 (0.02)
Passed Vit filter:                       194  (0.0108205); 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: 0.96u 0.29s 00:00:01.25 Elapsed: 00:00:00.47
# Mc/sec: 4259.98
//
Query:       gi|330508120|ref|YP_004384548.1|  [L=366]
Description: iron chelate uptake ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete 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-94  314.2  35.3    9.4e-94  313.9  35.3    1.1  1  FecCD     FecCD transport family
  ------ inclusion threshold ------
       0.58   10.4   0.1       0.58   10.4   0.1    3.5  4  MWFE      NADH-ubiquinone oxidoreductase MWFE subunit


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 !  313.9  35.3   1.1e-97   9.4e-94       4     312 .]      45     360 ..      36     360 .. 0.96

  Alignments for each domain:
  == domain 1  score: 313.9 bits;  conditional E-value: 1.1e-97
                             FecCD   4 lllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLad 73 
                                       ll  ++ + g+++is+ +v++ +l+k        + ++++iv+ lrl r+l++++ G++La+aGa++Q++++NpLa+
  gi|330508120|ref|YP_004384548.1|  45 LLAGYAATRGSADISVMDVYSTILAKFfpqyfqtTWFSDTIVWGLRLHRILMGIVGGIGLAIAGAVMQGILKNPLAS 121
                                       445556788999***********99999988877777888************************************* PP

                             FecCD  74 PsilGissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsalts 149
                                       P +lGiss+a++ga++a++++  +  +++ ++  af++ lla++ v+ la k kg +p+++iLaGia+s+l+sa+ts
  gi|330508120|ref|YP_004384548.1| 122 PFTLGISSAASFGAAMAIIMGaGFMGGEWLIIGNAFVFTLLAAGAVYGLA-KYKGVTPETMILAGIAISYLFSAMTS 197
                                       *********************888899999********************.************************** PP

                             FecCD 150 llllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrlllll 226
                                       +l+++ ++e++++++fw +Gsl++ sw+kv+++ ++++++l++l++ + +++++  gdetAkslGvnver+r++ ++
  gi|330508120|ref|YP_004384548.1| 198 FLQYIGHAEQVQEVVFWSMGSLGRSSWDKVWIVTAVIAICLPYLIIKSWDINAMGAGDETAKSLGVNVERTRVISMM 274
                                       ***************************************************************************** PP

                             FecCD 227 lvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGa 303
                                       lv+++ta++++++G+igF+GL++Phi r+ +g dhr llp+sal+Gallll ad+lar++l+p+ lpvgi+ta++G+
  gi|330508120|ref|YP_004384548.1| 275 LVSFITASVICFTGTIGFIGLVAPHITRMAIGGDHRFLLPASALVGALLLLGADTLARTILAPVILPVGIMTAFLGV 351
                                       ***************************************************************************** PP

                             FecCD 304 pffiylllr 312
                                       pff+yl++r
  gi|330508120|ref|YP_004384548.1| 352 PFFVYLFMR 360
                                       ******997 PP

>> MWFE  NADH-ubiquinone oxidoreductase MWFE subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.5      0.34   3.1e+03      13      25 ..     136     148 ..     135     156 .. 0.71
   2 ?   -2.2   0.1      0.55     5e+03       5      25 ..     181     202 ..     178     209 .. 0.50
   3 ?   -2.4   0.1      0.62   5.6e+03      12      33 ..     287     308 ..     279     310 .. 0.78
   4 ?   10.4   0.1   6.5e-05      0.58       5      27 ..     339     361 ..     337     364 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.34
                              MWFE  13 amfgitgaglski 25 
                                       am  i+gag+ + 
  gi|330508120|ref|YP_004384548.1| 136 AMAIIMGAGFMGG 148
                                       7888888887665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.55
                              MWFE   5 LlpygI.miamfgitgaglski 25 
                                       ++  gI +   f ++   l++i
  gi|330508120|ref|YP_004384548.1| 181 MILAGIaISYLFSAMTSFLQYI 202
                                       4444443444454444444444 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.62
                              MWFE  12 iamfgitgaglskirklqnggk 33 
                                       ++ +g+ g +  +i++++ gg 
  gi|330508120|ref|YP_004384548.1| 287 TGTIGFIGLVAPHITRMAIGGD 308
                                       5677888999999999998875 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 6.5e-05
                              MWFE   5 LlpygImiamfgitgaglskirk 27 
                                       +lp+gIm+a++g++ +++  +r+
  gi|330508120|ref|YP_004384548.1| 339 ILPVGIMTAFLGVPFFVYLFMRR 361
                                       79************999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2703.64
//
Query:       gi|330508121|ref|YP_004384549.1|  [L=105]
Description: hypothetical protein MCON_2220 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 785.74
//
Query:       gi|330508122|ref|YP_004384550.1|  [L=288]
Description: methyltransferase domain family [Methanosaeta concilii GP6]
Scores for complete 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-21   75.2   0.0    8.3e-21   74.5   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    4.7e-20   72.0   0.0    7.6e-20   71.4   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    5.8e-20   71.6   0.0    1.5e-19   70.3   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    9.8e-14   51.5   0.0    1.3e-13   51.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.8e-13   51.1   0.0    2.8e-13   50.4   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.7e-12   47.2   0.0    2.3e-12   46.7   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00014   21.3   0.0     0.0002   20.8   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00096   18.2   0.0     0.0015   17.6   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
  ------ inclusion threshold ------
      0.011   15.3   0.1      0.075   12.6   0.1    2.1  1  MetW             Methionine biosynthesis protein MetW
      0.021   14.4   0.0      0.033   13.8   0.0    1.2  1  NodS             Nodulation protein S (NodS)
      0.022   14.0   0.0      0.033   13.4   0.0    1.2  1  NNMT_PNMT_TEMT   NNMT/PNMT/TEMT family
      0.066   12.7   0.0        3.7    7.0   0.0    2.1  2  CheR             CheR methyltransferase, SAM binding domain
      0.096   12.5   0.0       0.29   11.0   0.0    1.8  2  Methyltransf_8   Hypothetical methyltransferase
       0.16   10.5   0.0       0.34    9.4   0.0    1.4  2  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
       0.19   11.2   0.0       0.32   10.5   0.0    1.3  1  MTS              Methyltransferase small domain
       0.25   10.7   0.1       0.39   10.1   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


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 !   74.5   0.0   7.4e-24   8.3e-21       1      97 []      79     179 ..      79     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 7.4e-24
                                       EEEET-TTSHHHHHHHCTS....TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl....gkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga 73 
                                       vLd+GcG+G+l++a+++ +    +  +++g+D+s++ml +ar r +  ++++ f+qg++++lpf d+sfD vvssg+
  gi|330508122|ref|YP_004384550.1|  79 VLDAGCGNGELLIAALEMGmakeNGPRFIGMDFSANMLGRARFRTS-GDPRAAFLQGSITSLPFVDQSFDWVVSSGV 154
                                       9***********99999977754369****************9996.458*************************99 PP

                                       GGG.SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  74 lhh.lsdedlekalkeiarvLkpgG 97 
                                       l +  s++ +++al+e+ rvL+pgG
  gi|330508122|ref|YP_004384550.1| 155 LTClASPQSMAEALQEFNRVLRPGG 179
                                       6664889999**************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   6.8e-23   7.6e-20       1      96 []      80     183 ..      80     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 6.8e-23
                                       EEET-TTSHHHHHHH......HTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-C CS
                   Methyltransf_11   1 LdvGcGtGrlaeala......krgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevl 71 
                                       Ld+GcG+G l+ a        ++g r +g+D+s++ml +a+ ++s+++ +  f+++++++lpf d+sfD vvss vl
  gi|330508122|ref|YP_004384550.1|  80 LDAGCGNGELLIAALemgmakENGPRFIGMDFSANMLGRARFRTSGDP-RAAFLQGSITSLPFVDQSFDWVVSSGVL 155
                                       8*******9999988465655555*****************9999999.689************************* PP

                                       CC-...CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  72 hhv...edpekalkeiaRvLkpgGllvi 96 
                                       + +   + +++al+e+ RvL+pgG lv+
  gi|330508122|ref|YP_004384550.1| 156 TCLaspQSMAEALQEFNRVLRPGGGLVV 183
                                       ***999899***************8875 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   1.4e-22   1.5e-19       4     113 ..      76     187 ..      73     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.4e-22
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkae....vvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfD 76 
                                       g  vlD+GCG+Gel++++  e+g+ +e    ++G D+s++++ +Ar +++  g  ++ F qg+i++l+  + d++fD
  gi|330508122|ref|YP_004384550.1|  76 GGMVLDAGCGNGELLIAAL-EMGMAKEngprFIGMDFSANMLGRARFRTS--GDPRAAFLQGSITSLP--FVDQSFD 147
                                       6679***************.88875556778****************854..7779************..9****** PP

                   Methyltransf_31  77 lilsnevlnaladpdk...ileeiervlkpggilliedpr 113
                                        ++s +vl +la+p++   +l+e  rvl+pgg l+++ ++
  gi|330508122|ref|YP_004384550.1| 148 WVVSSGVLTCLASPQSmaeALQEFNRVLRPGGGLVVDFFN 187
                                       ********77777665111678*************99777 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   1.1e-16   1.3e-13      16     164 ..      69     228 ..      17     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.1e-16
                   Methyltransf_23  16 llpklraggrvLdiGcGtGillevl......rengfsvtgvDlspeaveiae....kakkaqkdqfdeqeaaepqgk 82 
                                       ++    +gg vLd GcG G+ll  +      +eng  ++g+D s ++ ++a+    +++ a + q    + ++ +++
  gi|330508122|ref|YP_004384550.1|  69 AFSFAGSGGMVLDAGCGNGELLIAAlemgmaKENGPRFIGMDFSANMLGRARfrtsGDPRAAFLQGSITSLPFVDQS 145
                                       2223567779**********98777666777889*****************9988866666666666778888889* PP

                   Methyltransf_23  83 fdlIvlrevlehvpd...ppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhi..sffsarslkel 154
                                       fd +v++ vl  + +   ++e+l+ +++ l+pgG l++  +++ ++ + + +   yl+ + r +   + s +++ ++
  gi|330508122|ref|YP_004384550.1| 146 FDWVVSSGVLTCLASpqsMAEALQEFNRVLRPGGGLVVDFFNRLSHYTLARK---YLFGE-RIVppEYLSFSEFQNQ 218
                                       **********9998622266*********************98654333333...33433.34445999******** PP

                   Methyltransf_23 155 leeaGlevve 164
                                       le+aG+++ e
  gi|330508122|ref|YP_004384550.1| 219 LENAGFQIEE 228
                                       *******976 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   2.5e-16   2.8e-13       1      99 []      80     181 ..      80     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2.5e-16
                   Methyltransf_12   1 LeiGcGtGsllrallekl....pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas 73 
                                       L+ GcG+G+ll a le       + +++g+D+s++++ +a+ +++   +  + +  ++ l   d+    sfD vv+s
  gi|330508122|ref|YP_004384550.1|  80 LDAGCGNGELLIAALEMGmakeNGPRFIGMDFSANMLGRARFRTSGDPRAAFLQGSITSLPFVDQ----SFDWVVSS 152
                                       89**************999**99**************9999999999986666666666665555....******** PP

                   Methyltransf_12  74 nvlhhl...kdirevldnirklLkpgGrl 99 
                                       +vl +l   + ++e+l+++ ++L+pgG l
  gi|330508122|ref|YP_004384550.1| 153 GVLTCLaspQSMAEALQEFNRVLRPGGGL 181
                                       ******9999999**************65 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   2.1e-15   2.3e-12      45     166 ..      73     198 ..      55     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 2.1e-15
                                       S--TTEEEEES-TT-HHHHHHHHH..HHHHH.EEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EE CS
                   Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsds..vgekg.kvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfD 118
                                         +g  vlD  +G g+l ++ +++  ++e+g + +++D+++nmL  g+++ + +g  +  flq++   Lpf d+sfD
  gi|330508122|ref|YP_004384550.1|  73 AGSGGMVLDAGCGNGELLIAALEMgmAKENGpRFIGMDFSANML--GRARFRTSGDPRAAFLQGSITSLPFVDQSFD 147
                                       456779**********98877665114444579**********9..8899999************************ PP

                                       EEEEES-GGG-...S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHH CS
                   Ubie_methyltran 119 vvtvsfGlrnv...tDklkaLkeayrvlkpGGrlvvlefskvelpllsqay 166
                                        v  s  l  +     + +aL+e  rvl+pGG lvv  f +    +l   y
  gi|330508122|ref|YP_004384550.1| 148 WVVSSGVLTCLaspQSMAEALQEFNRVLRPGGGLVVDFFNRLSHYTLARKY 198
                                       98544333333111567889***************9999998888887777 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.7e-07    0.0002      63     215 ..      76     229 ..      72     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.7e-07
                                       T-EEEEES-TTSHHHHHH.....HHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEE CS
                              CMAS  63 GmtlLdiGcGWGslvrra.....verydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsv 134
                                       G  +Ld GcG G+l++ a     +++ + + +g+ +S++   +a+ r      +   + +++    +d+ +d vvs 
  gi|330508122|ref|YP_004384550.1|  76 GGMVLDAGCGNGELLIAAlemgmAKENGPRFIGMDFSANMLGRARFRTSGDPRAAFLQGSITSLPFVDQSFDWVVSS 152
                                       7889*********99876222226678999*********99888877777777777777888999999********* PP

                                       S-GGGT.SGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTTCCCHHHHHHTSTTS---BHHHHHHHHHHTT- CS
                              CMAS 135 gafehv.gkenydtffkklkkllkedGllllhtitslhkkelaerglklkfidkeiFPgGelpsieeieeeiseagf 210
                                       g++  +   ++ ++  ++++++l+++G l++    +l++ +la +        + i P  +l s +e +++ ++agf
  gi|330508122|ref|YP_004384550.1| 153 GVLTCLaSPQSMAEALQEFNRVLRPGGGLVVDFFNRLSHYTLARKY----LFGERIVPPEYL-SFSEFQNQLENAGF 224
                                       ***9984568999***********************9999999332....346677787777.67889999999999 PP

                                       EEEEE CS
                              CMAS 211 tvvdv 215
                                       ++++ 
  gi|330508122|ref|YP_004384550.1| 225 QIEEH 229
                                       99875 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 !   17.6   0.0   1.3e-06    0.0015     117     218 ..      77     184 ..      72     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                                       -EEEEET-TTSHHH.....HHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEE CS
                    Methyltransf_9 117 rtildvGcgnGyhl.....wrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvf 187
                                        ++ld GcgnG  l     + m+ e+    +G+d s   l    a  + +  d ra  l  +i  lp   ++fd v 
  gi|330508122|ref|YP_004384550.1|  77 GMVLDAGCGNGELLiaaleMGMAKENGPRFIGMDFSANMLGR--ARFRTS-GDPRAAFLQGSITSLPFvDQSFDWVV 150
                                       579********8872222245788888999****99988864..445556.5677778889******95679***** PP

                                       EES-GGG-S-H...HHHHHHHHCTEEEEEEEEEE CS
                    Methyltransf_9 188 smGvlyhrrsP...ldhllqlkdqlvkgGelvle 218
                                       s Gvl    sP    + l++++  l+ gG lv++
  gi|330508122|ref|YP_004384550.1| 151 SSGVLTCLASPqsmAEALQEFNRVLRPGGGLVVD 184
                                       *****999998332467777788999***99986 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   6.7e-05     0.075      14     111 ..      76     187 ..      67     234 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.7e-05
                              MetW  14 gsrvldlGcGdGellel.....lkeekqvdgrGleldeegvaecvakG.....lsviqgdldkdlenfedksfdyvv 80 
                                       g  vld GcG+Gell       +++e++ +  G++ +++ + ++  +       + +qg + +    f d+sfd+vv
  gi|330508122|ref|YP_004384550.1|  76 GGMVLDAGCGNGELLIAalemgMAKENGPRFIGMDFSANMLGRARFRTsgdprAAFLQGSITS--LPFVDQSFDWVV 150
                                       678**********98542122234556667778888888888777665112223344444432..358899999999 PP

                              MetW  81 lsqtlqatrnpkev...ldel...lrigrraivsfPn 111
                                        s  l  +  p+++   l+e    lr g   +v f n
  gi|330508122|ref|YP_004384550.1| 151 SSGVLTCLASPQSMaeaLQEFnrvLRPGGGLVVDFFN 187
                                       9988887777765422255541114445555665554 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.9e-05     0.033      46     143 ..      78     182 ..      52     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                              NodS  46 dalevGcaaG.....alterlap.yckrltvvdvveeaiararervkesshiswivsdvqqfs.tdekfdlivvaev 115
                                        +l+ Gc  G     al   +a     r+  +d   + + rar r+   +  ++++  ++ +   d+ fd +v + v
  gi|330508122|ref|YP_004384550.1|  78 MVLDAGCGNGelliaALEMGMAKeNGPRFIGMDFSANMLGRARFRTSGDPRAAFLQGSITSLPfVDQSFDWVVSSGV 154
                                       5677777776222212222223213457778899999999********************99736999********* PP

                              NodS 116 lyyiedvaelraavrnlvsllapdgqlv 143
                                       l  +   + +  a++++ ++l+p+g lv
  gi|330508122|ref|YP_004384550.1| 155 LTCLASPQSMAEALQEFNRVLRPGGGLV 182
                                       *************************998 PP

>> NNMT_PNMT_TEMT  NNMT/PNMT/TEMT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     3e-05     0.033     155     238 ..     142     230 ..     130     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                                       SS..EEEEEEESSHHHH-SSHHHHHHHHHHHHTTEEEEEEEEEEEECS......-SEEEETTEEEE---B-HHHHHH CS
                    NNMT_PNMT_TEMT 155 lpkkadvvvtifcleaacedleeylralrnlasllkpGGhlvlggvle......eseynvGekkfsllalekeevle 225
                                       + + +d vv+   l + + + ++  +al++  ++l+pGG lv+    +      + +y +Ge+     +l+  e ++
  gi|330508122|ref|YP_004384550.1| 142 VDQSFDWVVSSGVLTCLA-SPQSMAEALQEFNRVLRPGGGLVVDFFNRlshytlARKYLFGERIVPPEYLSFSEFQN 217
                                       556788888887776654.4578899****************854433001111456889999999999******** PP

                                       HHHHTTEEEEEEE CS
                    NNMT_PNMT_TEMT 226 alkkaglkveelk 238
                                        l++ag+++ee  
  gi|330508122|ref|YP_004384550.1| 218 QLENAGFQIEEHL 230
                                       *********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 ?    3.6   0.0     0.036        41      34      81 ..      78     120 ..      56     130 .. 0.75
   2 ?    7.0   0.0    0.0033       3.7     133     173 ..     142     183 ..     129     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.036
                                       EEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHHHH CS
                              CheR  34 riwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlekAk 81 
                                        ++ agc++Ge    l +++ e+  ++++   + ++ D ++++l +A+
  gi|330508122|ref|YP_004384550.1|  78 MVLDAGCGNGE----LLIAALEMGMAKEN-GPRFIGMDFSANMLGRAR 120
                                       6899******8....55555554444444.67899*********9998 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0033
                                       GG--EEEEEE-SSGGGC-C.HHHHHHHHHHHCCEEEEEEEEE CS
                              CheR 133 vlgklDvifcrnvliYfde.etqekvlerfaeklkpgglLll 173
                                       v +++D +++  vl  + + ++ ++ l++f++ l+pgg L++
  gi|330508122|ref|YP_004384550.1| 142 VDQSFDWVVSSGVLTCLASpQSMAEALQEFNRVLRPGGGLVV 183
                                       5689**********98875156789***************98 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.4   2.7e+03      75      86 ..      78      89 ..      74      99 .. 0.78
   2 ?   11.0   0.0   0.00026      0.29     113     156 ..     136     183 ..     127     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.4
                                      -EEEES-TT-HH CS
                    Methyltransf_8 75 vvadlGcGeaki 86
                                      +v d GcG+  +
  gi|330508122|ref|YP_004384550.1| 78 MVLDAGCGNGEL 89
                                      689****99776 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00026
                                       TTS-S--TT-EEEEEE.....ES---SS-HHHHHHHHHHHEEEEEEEEE CS
                    Methyltransf_8 113 lakvPledesvdvavf.....clslmgtnladflkeanrvlkvGGllkv 156
                                       ++ +P  d+s d +v      cl+   + +a+ l+e nrvl++GG l v
  gi|330508122|ref|YP_004384550.1| 136 ITSLPFVDQSFDWVVSsgvltCLA-SPQSMAEALQEFNRVLRPGGGLVV 183
                                       678999999999887522111443.2468999*************9977 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 ?   -2.8   0.0       1.5   1.7e+03     113     128 ..      71      86 ..      51      98 .. 0.73
   2 ?    9.4   0.0   0.00031      0.34     175     216 ..     139     182 ..     128     190 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.5
                   Methyltransf_29 113 aaggkvrtvlDvGCgv 128
                                       ++ g+  +vlD GCg 
  gi|330508122|ref|YP_004384550.1|  71 SFAGSGGMVLDAGCGN 86 
                                       455666789*****96 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00031
                   Methyltransf_29 175 lpyPsrsfdlihCsrCridwt..eedgilllevdRvlRpgGyfv 216
                                       lp+  +sfd +  s  +      ++ +  l e +RvlRpgG +v
  gi|330508122|ref|YP_004384550.1| 139 LPFVDQSFDWVVSSGVLTCLAspQSMAEALQEFNRVLRPGGGLV 182
                                       56666666666655444333300333445666666666666444 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00028      0.32      32     137 ..      76     183 ..      66     204 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00028
                                       CSEEEEET-TTSHHHHHHHHHTTC.E..EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST.TS-EEEEEE- CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeae..vtlvdvdarAlesakenleankle.vevvasdvleeve.ekkfdlivsN 104
                                        g vlD GcG+G l +a++++    e    ++  d+ A  + ++ +++++   + +++ ++++    +++fd++vs 
  gi|330508122|ref|YP_004384550.1|  76 GGMVLDAGCGNGELLIAALEMGMAKEngPRFIGMDFSANMLGRARFRTSGDPrAAFLQGSITSLPFvDQSFDWVVSS 152
                                       5779********99888777654444347788888888888888887777666888888888754348999999987 PP

                                       --STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                               MTS 105 PPfhagkatelavaeeliaeAkeaLkegGeLli 137
                                         +        + + e ++e +++L++gG L++
  gi|330508122|ref|YP_004384550.1| 153 GVLTCLAS--PQSMAEALQEFNRVLRPGGGLVV 183
                                       65444333..45555556677777777777765 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00034      0.39     162     186 ..      76     100 ..      70     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00034
                              PrmA 162 geevlDvGtGSGiLaiaaakLgakk 186
                                       g  vlD G+G G L iaa+ +g +k
  gi|330508122|ref|YP_004384550.1|  76 GGMVLDAGCGNGELLIAALEMGMAK 100
                                       5679*****************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2086.48
//
Query:       gi|330508123|ref|YP_004384551.1|  [L=808]
Description: two-component hybrid sensor and regulator [Methanosaeta concilii GP6]
Scores for complete 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-30  103.4   0.0    1.9e-29  102.5   0.0    1.5  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    2.8e-28   98.3   2.7    3.4e-28   98.1   1.1    2.1  2  Response_reg   Response regulator receiver domain
    1.1e-18   67.1   3.5    2.1e-18   66.1   0.2    2.9  2  HisKA          His Kinase A (phospho-acceptor) domain
  ------ inclusion threshold ------
       0.17   11.8   0.8       0.59   10.2   0.8    1.7  2  DUF1043        Protein of unknown function (DUF1043)
       0.28   11.6  17.3        4.1    7.9   5.6    2.9  3  MerC           MerC mercury resistance protein
       0.29   10.8   7.7       0.44   10.2   7.7    1.2  1  DUF745         Protein of unknown function (DUF745)


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 !  102.5   0.0   6.2e-33   1.9e-29       2     109 ..     533     645 ..     532     648 .. 0.93

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 6.2e-33
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE.....TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTST CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikase.....ddlvisveDnGiGipkedlkklfekfsq.ddstkrggg 72 
                                       d++rLrqi+ n+++Navkf t++ge+++ ++ ++      ++++ v D+GiGip e+++ lf++f q +  t+r++g
  gi|330508123|ref|YP_004384551.1| 533 DPTRLRQILVNILGNAVKF-TSSGEVRILVSGRDlggreHEIHFAVMDTGIGIPAEKMNCLFQSFCQvEPCTTRRYG 608
                                       899****************.99999999988733455559************************************* PP

                                       SSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  73 gtGlGlsivkklvelmgGeiwvesepgrGttftftlp 109
                                       g GlGl+i+k+lvelm+G+iw ese+g+G+tf+ft++
  gi|330508123|ref|YP_004384551.1| 609 GAGLGLAISKRLVELMDGSIWAESEEGKGSTFHFTIK 645
                                       **********************************997 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.2   9.5e+03      56      79 ..     442     466 ..     440     478 .. 0.72
   2 !   98.1   1.1   1.1e-31   3.4e-28       1     111 [.     675     785 ..     675     786 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.2
                                       SEHHHHHHHHHHCT.TTSEEEEEES CS
                      Response_reg  56 mdGlellkeireed.pelpviilta 79 
                                       ++G+ l + +++e+ +++++i  ++
  gi|330508123|ref|YP_004384551.1| 442 LTGILLGTDLNREQrDHMEIIRSSG 466
                                       6799999999555548899987665 PP

  == domain 2  score: 98.1 bits;  conditional E-value: 1.1e-31
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTT.SEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpe.lpvii 76 
                                       +l+++D+ +++++++++l + gy + ++a++g e+l  l+++++d+il+Di+mp+mdGl+++++ire+ p+ +++i+
  gi|330508123|ref|YP_004384551.1| 675 ILVAEDNIINQKVIKKMLHKLGY-RADVAANGLEVLVALDRQDYDVILMDIQMPEMDGLDAARKIRETRPTlPKIIA 750
                                       89*********************.*****************************************999977467*** PP

                                       EESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  77 ltahseeedavealkagaddflsKpfdpeeLlkal 111
                                       +ta + e d++++++ g+d+++sKp++ eeL+++l
  gi|330508123|ref|YP_004384551.1| 751 ITAFAMEGDKEKCIDSGMDGYISKPVNLEELRAIL 785
                                       *******************************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 ?    0.2   0.4      0.26   7.7e+02      27      56 ..     351     376 ..     344     380 .. 0.83
   2 !   66.1   0.2   7.1e-22   2.1e-18       1      67 []     420     485 ..     420     485 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.26
                                       HHC..T-HSSCHHHHHHHHHHHHHHHHHHH CS
                             HisKA  27 Lkregklteelkeyletiesearrldhlve 56 
                                       Lk+    +e+l +  +++e+e+rrl++ +e
  gi|330508123|ref|YP_004384551.1| 351 LKE----NERLFQTSKRAEEEVRRLNQHLE 376
                                       555....699999999*********98766 PP

  == domain 2  score: 66.1 bits;  conditional E-value: 7.1e-22
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       ++++fla+++HE+rtPL+a++g + +L  + +l+ e+++  e+i+s+++ l+++++d+Ld+s+i++g
  gi|330508123|ref|YP_004384551.1| 420 AKSEFLANMSHEIRTPLNAVIGLTGILLGT-DLNREQRDHMEIIRSSGDALLAIINDILDFSKIDSG 485
                                       589***********************9553.69********************************97 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.8    0.0002      0.59       6      63 ..     335     391 ..     332     423 .. 0.87
   2 ?   -1.4   0.1      0.73   2.2e+03      17      43 ..     391     417 ..     388     433 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                           DUF1043   6 vvGiiiGalilrltnsklkkqkklekelekakaeleeqkqeledHfaqsaelLetlae 63 
                                        vG iiG++++r   +  k++++l ++ ++a++e+ + +q+le+  +    +L+  ++
  gi|330508123|ref|YP_004384551.1| 335 SVGGIIGLIVIRQIVAL-KENERLFQTSKRAEEEVRRLNQHLESRVMDRTAMLKAANR 391
                                       59**********98776.**************************99999999986554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.73
                           DUF1043  17 rltnsklkkqkklekelekakaeleeq 43 
                                       r +++ + + kk+e++l ++k++ e  
  gi|330508123|ref|YP_004384551.1| 391 RKLEEDILERKKIEEDLRRSKEAAEAA 417
                                       667777888899999999999887655 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   5.3    0.0024         7      19     107 ..      19     126 ..      14     161 .. 0.63
   2 ?    7.9   5.6    0.0014       4.1      24     106 ..     164     254 ..     145     261 .. 0.71
   3 ?   -3.8   0.0       5.7   1.7e+04      70      84 ..     438     452 ..     426     473 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0024
                              MerC  19 Pvllallpllglsf.lasel...lhqvllilvvaigllalvvgyrrhrktsv.lvlgalGllillvalflg...... 84 
                                        +++++l +++ s+ l++el      +l+ilv  ++ lal++++rr   +   + l+++ l++ lva+ lg      
  gi|330508123|ref|YP_004384551.1|  19 LAFIVALCSISFSIhLKDELqitASDMLAILVDSLATLALFYAARRSSVYGRqVRLAWTVLALALVAHTLGdiaway 95 
                                       445555666677776777778888999*****************887766541557777777888888888555544 PP

                              MerC  85 ................teaeetllfgslwqvltvlGaal 107
                                                                  ++  l ++G++l
  gi|330508123|ref|YP_004384551.1|  96 teivldqppfpsvadwL--------FLIHYPLLIAGILL 126
                                       44444443333333330........33333333333333 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0014
                              MerC  24 llpllglsf.lasellhqvllilvvaigllalvvgyrrhrktsvlvlgalGllillvalflgteaeetl........ 91 
                                       + ++ g++f +++  +   +l l+++++l+ l++   r +++ +++l+++G +++++a ++   a+++l        
  gi|330508123|ref|YP_004384551.1| 164 IESSAGAIFrTQALSVAYPVLGLMLLLALVELLLRRIRFQQMGPVLLLVMGTIVMIIADLIL--AYQSLnniydsgg 238
                                       44566777755677799999**************************************9999..4444446665544 PP

                              MerC  92 ..lfgslwqvltvlGaa 106
                                         ++g++++  +++G+a
  gi|330508123|ref|YP_004384551.1| 239 iwDVGWIMA-YSMIGLA 254
                                       422333332.2333333 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 5.7
                              MerC  70 galGllillvalflg 84 
                                       +++Gl+ +l+++ l+
  gi|330508123|ref|YP_004384551.1| 438 AVIGLTGILLGTDLN 452
                                       445555555555544 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   7.7   0.00015      0.44     111     176 ..     356     421 ..     346     427 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                            DUF745 111 allkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektkkaAykAacAA 176
                                       +l++++k + e++++++++ ++ ++++t++l+aA++++ee   + k+  +dl++ k+aA+ A+ A 
  gi|330508123|ref|YP_004384551.1| 356 RLFQTSKRAEEEVRRLNQHLESRVMDRTAMLKAANRKLEEDILERKKIEEDLRRSKEAAEAATNAK 421
                                       678889999999***************************9999999**************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (808 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1340  (0.0747392); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.86u 0.30s 00:00:01.15 Elapsed: 00:00:00.47
# Mc/sec: 5182.15
//
Query:       gi|330508124|ref|YP_004384552.1|  [L=280]
Description: hypothetical protein MCON_2224 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1941.37
//
Query:       gi|330508125|ref|YP_004384553.1|  [L=237]
Description: hypothetical protein MCON_2225 [Methanosaeta concilii GP6]
Scores for complete 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-49  167.3   0.0    4.1e-49  167.0   0.0    1.0  1  Diphthami_syn_2  Diphthamide synthase


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.0   0.0   2.3e-53   4.1e-49       3     217 ..      21     231 ..      19     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 2.3e-53
                   Diphthami_syn_2   3 vavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLk 78 
                                       ++v + GGkD +l+ yka++e   v++L s  +  +     h +n +l+ +++e++Gipli+ e +   e+e   +k
  gi|330508125|ref|YP_004384553.1|  21 AVVSWTGGKDGCLSCYKAMQEgWRVNYLLSFRNISRI--GSHDINPELILAQSEAIGIPLIHREFTS-YEQE---FK 91 
                                       5678*****************99******98765555..89********************999883.3333...33 PP

                   Diphthami_syn_2  79 gtlkkld.....veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldes 150
                                        t+  l+     ++++v+G i+   +k+ ++r+C  l l ++ PLW++d++++l+ei   +feviv++vk   ++++
  gi|330508125|ref|YP_004384553.1|  92 RTILDLRangekIDGAVFGHIQ--THKKLVDRICTSLNLDLLLPLWQQDSRKILKEITGLGFEVIVISVKDGLMGRE 166
                                       3333333333459999999996..699************************************************** PP

                   Diphthami_syn_2 151 lLGrridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyldiera 217
                                       +LGrrid ++ ++lk+l    +id++ge+Ge++t+v D+P+fkkr+ +   e+   e +++l+i+ +
  gi|330508125|ref|YP_004384553.1| 167 WLGRRIDEEFSEDLKDL--DQSIDPCGENGEFHTIVTDGPIFKKRIILSGSEAVLREGYWFLNIKEF 231
                                       *****************..78*******************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1850.00
//
Query:       gi|330508126|ref|YP_004384554.1|  [L=300]
Description: hypothetical protein MCON_2227 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2340.43
//
Query:       gi|330508127|ref|YP_004384555.1|  [L=724]
Description: hypothetical protein MCON_2230 [Methanosaeta concilii GP6]
Scores for complete 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   33.5   0.0    1.6e-05   24.8   0.0    2.6  2  PLDc_2    PLD-like domain
  ------ inclusion threshold ------
        0.8   10.0   4.3         23    5.4   1.8    2.9  2  PLDc      Phospholipase D Active site motif


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0013        12      21     100 ..      83     186 ..      77     195 .. 0.68
   2 !   24.8   0.0   1.8e-09   1.6e-05       6     125 ..     395     534 ..     390     540 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0013
                            PLDc_2  21 sdreildallkaakrgvkvrilldskkd............dagavdeaslkelkellleagvevrvfet.....ll. 79 
                                        d++i+  +l++ ++g  vrill +  +            d++   +a  +e+k+l +     +          +  
  gi|330508127|ref|YP_004384555.1|  83 KDQTIIGLILRLMQSGITVRILLWMPMKasiiaglgphmsDHNYISDAVSNECKRLSRDDPSAIDR--GivaldMRv 157
                                       6788999999999*********98855588999999999966666666666666663333333332..122332113 PP

                            PLDc_2  80 .....gslHaKlylid...gktvivGSsN 100
                                            ++ H+K+++i+    ++++ G++ 
  gi|330508127|ref|YP_004384555.1| 158 appvsSTHHQKMIVIRvgnINVAYCGGMD 186
                                       3445578899*****87444477778775 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.8e-09
                            PLDc_2   6 ksAkksidiatyyfvsdrei...ldallk.aakrgvkvrilldskkd.....dagavdeaslkelkellleagvevr 73 
                                       + A++ i i  +yf ++  +   l++ +k +++++  v ++l++++d     ++ a++ a    ++ l  + + +  
  gi|330508127|ref|YP_004384555.1| 395 QAAEELILIFDQYF-FSGPLarlLNHRIKsDKEKKLCVILILPPYADehtleEHHARKLALDDLIEGL-SKDQSQ-S 468
                                       56777888888888.56655333443344377888888888999888555554444444444444444.333333.3 PP

                            PLDc_2  74 vfet.....ll........gslHaKlylidgktvivGSsNltkrgldlnlElnvviedk.elakel 125
                                       +fe+     l+          +HaK+ + d + ++ GS+Nl++r+++ ++El   + d   ++k++
  gi|330508127|ref|YP_004384555.1| 469 IFERvavydLWhpnrvpggIYCHAKVQMYDLSLLVCGSANLNRRSFTCDTELDCAVLDDdLVIKHY 534
                                       333233443114566778778*******************************98887772444555 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.8    0.0026        23       4      24 ..     164     187 ..     163     191 .. 0.70
   2 ?    3.8   0.0    0.0082        73       6      28 .]     491     513 ..     486     513 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0026
                                       EE---EEEETTT.....EEEEE---S CS
                              PLDc   4 thHqKivivDdr.....vafvGgaNL 24 
                                       thHqK++++  r     va+ Gg++L
  gi|330508127|ref|YP_004384555.1| 164 THHQKMIVI--RvgninVAYCGGMDL 187
                                       8*******9..444666666666666 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0082
                                       ---EEEETTTEEEEE---SSHHH CS
                              PLDc   6 HqKivivDdrvafvGgaNLcdgr 28 
                                       H+K  + D  + + G+aNL++++
  gi|330508127|ref|YP_004384555.1| 491 HAKVQMYDLSLLVCGSANLNRRS 513
                                       66666666667778*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (724 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.25s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 5448.88
//
Query:       gi|330508128|ref|YP_004384556.1|  [L=307]
Description: carbamate kinase [Methanosaeta concilii GP6]
Scores for 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-26   93.1   0.0    2.8e-26   92.6   0.0    1.1  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   0.0   1.6e-30   2.8e-26       3     241 .]       5     289 ..       4     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 1.6e-30
                                       EEEEE-TTCCC.CTCC.....HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH....TCCCCCHHHC....E. CS
                         AA_kinase   3 vVvKlGGsslt.dkee.....aslrrlaeqiaalkesgnklvvVhGggsftdgllal....ksglssgelaaglrst 69 
                                       +V+++GG++l  d+ +         ++a+ ++ l+ +g+ +v+VhG+g+++ ++l +    k  ++++ l+++  +t
  gi|330508128|ref|YP_004384556.1|   5 TVLAFGGNALLlDPHNpatqeRTAAAFARAVRMLMDRGEGMVLVHGNGPQVGMILLRieatKDCIPPETLDIMVAET 81 
                                       69******888899999***999**********************************88888888888888888899 PP

                                       .HHHHHHHHHHHHHHHHHHHHHHHHHTTH................GEEEE-GGGTCEECCCE..............H CS
                         AA_kinase  70 leeagevatrdalaslgerlvaallaagl................pavglsaaaldateagr............deg 118
                                       +   g ++ r +   + er  aall++ l                p + +  a  ++ ++g+             ++
  gi|330508128|ref|YP_004384556.1|  82 QGSIGYLLCRSMRNEIPEREIAALLTQVLvdpddpgfaspfkpvgPYYAMEEAEGLVKSQGWrmletagkgwrrVVP 158
                                       9999999999999999999999999999999999888887777776666666666666666699999999******* PP

                                       HHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE........EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCES CS
                         AA_kinase 119 sdgnvesvdaeaieelleagvvpvltgfigldeege........lgrgssDtiaallAealgAdkliiltdVdGVyd 187
                                       s+++ e ++  +i++ + +g++++ +g++g+++  +         +++++D +a+ lA a +A++ +iltdV++V +
  gi|330508128|ref|YP_004384556.1| 159 SPRPQEIIELHTIMDAVGHGHLIIAGGGGGIPVIRDecgglhgiEAVIDKDLTACKLAMATRAERFVILTDVPHVST 235
                                       ***************************9988888888666777777******************************* PP

                                       STTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 188 adpkkvpdarllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvvItn 241
                                         ++     r++ +++++ a+    ++e+  g+m +k++aa+ +a+r +  + Itn
  gi|330508128|ref|YP_004384556.1| 236 GFGSTS--ERRIGRMKASRARRllAQGEFPPGSMGPKVEAAAIFAERTDLSALITN 289
                                       ***998..6***************************************9*999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 2517.60
//
Query:       gi|330508129|ref|YP_004384557.1|  [L=458]
Description: hypothetical protein MCON_2234 [Methanosaeta concilii GP6]
Scores for complete 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   18.6   0.0     0.0021   17.8   0.0    1.4  1  Thymidylate_kin  Thymidylate kinase
     0.0059   16.2   0.0      0.023   14.3   0.0    1.9  2  cobW             CobW/HypB/UreG, nucleotide-binding 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 !   17.8   0.0   2.3e-07    0.0021       6      74 ..     136     201 ..     135     248 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-07
                                       TSSHHHHHHHHHHHHHHTTE..EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHH CS
                   Thymidylate_kin   6 GaGKttqaellkerlkeegik.vvltrepggteiGekirelllkeeeleeqteallfaadriehleekik 74 
                                       GaGK+++++++++ ++++g+k vv++++    ++G+++r+++++   l+++ +a l   +r e+ e+ i 
  gi|330508129|ref|YP_004384557.1| 136 GAGKSQVVRYIADIIPQAGLKaVVVRHPM---PYGDLARQAVQRFSSLADLNAADLTIEER-EEYERHID 201
                                       9********************77777775...5**********888888888888888888.55555543 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 ?   -1.6   0.0      0.19   1.7e+03       9      26 ..     135     154 ..     129     162 .. 0.71
   2 !   14.3   0.0   2.5e-06     0.023     110     176 ..     238     301 ..     222     302 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.19
                                       TTCCHHHHHHHHH..CT--S CS
                              cobW   9 lGsGKTtLlnhll..enrag 26 
                                        G+GK+ +++ +     +ag
  gi|330508129|ref|YP_004384557.1| 135 TGAGKSQVVRYIAdiIPQAG 154
                                       59******999875433444 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.5e-06
                                       CCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHHTTS-EE CS
                              cobW 110 ltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerlrqlnpeakvl 176
                                       ++ d  ++v Da  l   +e +   +e  + aadl+v+nK++ + ee ++ ++++ +++lnp+a v+
  gi|330508129|ref|YP_004384557.1| 238 FKPDLWITVADA--LRPGHEISYYPGETNFLAADLIVINKANSAAEE-DIITIQANASRLNPKAGVV 301
                                       566888999999..434444555678999***************999.5699**********99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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 0.25s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 3621.08
//
Query:       gi|330508130|ref|YP_004384558.1|  [L=100]
Description: alkylhydroperoxidase-like protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-13   50.9   0.2    1.3e-13   50.8   0.2    1.1  1  CMD       Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
      0.077   13.0   0.0      0.091   12.7   0.0    1.0  1  Big_10    Bacterial Ig domain


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 !   50.8   0.2   1.4e-17   1.3e-13       4      71 ..      20      86 ..      17     100 .] 0.89

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.4e-17
                                      HHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHH CS
                               CMD  4 lraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaaya 71
                                        a++ lr+ +++ +g+L+ k++ ++ la ++a +c+ Cv +H + A++aGv++ee  e++a++    
  gi|330508130|ref|YP_004384558.1| 20 NSAFASLRNEIMK-DGALSSKDKAIVGLACAVAIRCDTCVEFHKKVAKMAGVSKEEMLEAAAIGGLVR 86
                                      5799********9.**********************************************99976655 PP

>> Big_10  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     1e-05     0.091      71     130 ..      19      78 ..      11      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
                            Big_10  71 ktssftTvapaktvsatltpedgstvGvgqpisikFdkpvedkaavekalkvttspaveg 130
                                        +s+f  ++ + +  ++l+ +d + vG + +++i+ d+ ve +++v k   v+ ++  e 
  gi|330508130|ref|YP_004384558.1|  19 VNSAFASLRNEIMKDGALSSKDKAIVGLACAVAIRCDTCVEFHKKVAKMAGVSKEEMLEA 78 
                                       578999999999999**********************************99999987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 760.52
//
Query:       gi|330508131|ref|YP_004384559.1|  [L=681]
Description: formate dehydrogenase subunit alpha [Methanosaeta concilii GP6]
Scores for complete 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-89  299.7   0.0    4.3e-89  299.4   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    3.2e-27   94.8   0.0    8.1e-27   93.4   0.0    1.7  1  Molydop_binding  Molydopterin dinucleotide binding domain
    3.4e-13   49.4   0.4    6.7e-13   48.4   0.4    1.5  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.4   0.0   7.2e-93   4.3e-89       1     431 [.      60     482 ..      60     483 .. 0.93

  Alignments for each domain:
  == domain 1  score: 299.4 bits;  conditional E-value: 7.2e-93
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rl yP++R       +F ++sWdeAlel+a+ l +  + ygp++  +   ++ +++e+ ++++k+++llg++   ++
  gi|330508131|ref|YP_004384559.1|  60 RLVYPLKR---S-GSDFIPISWDEALELVAQGLARNLERYGPKSLGF-LVSSRCNNEENYLMQKMARLLGSP---NV 128
                                       9*******...7.456**************************99985.5556666****************7...77 PP

                                       ECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HC CS
                     Molybdopterin  78 dwyadlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryael 154
                                       d++a+l+++ ++  +g+++  + +++n+l dlens+ i+++G+N  e +pi+ +r   +a+ ++a viv +pr +++
  gi|330508131|ref|YP_004384559.1| 129 DNCARLCHSPTVMGLGASFG-AGAMTNNLLDLENSKCIFAIGTNFTEAHPIV-SRWVEKAKDNGAVVIVADPRITST 203
                                       88999998777766666544.5567778999*********************.89999999988***********97 PP

                                       GGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHH CS
                     Molybdopterin 155 lkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarna 231
                                       +  ad +l ++pg+d +l+ +m++vi++e+++d +f+ ++t+g++e+++ l+v + ee+++k++  ++ + + ar +
  gi|330508131|ref|YP_004384559.1| 204 TWMADIHLRLNPGSDIDLLRGMMKVIVDEGLEDADFISSRTTGFQELKESLSVFSIEEAAEKTGLDVAEIVKAARVY 280
                                       778************************************************************************** PP

                                       HHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT.. CS
                     Molybdopterin 232 aktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslke.. 306
                                       ak    s+ ++ +g++++ +g++++++ +++al++g++g+pg+g+  ++Gq++++g +++vg +p  ++ ++     
  gi|330508131|ref|YP_004384559.1| 281 AKSSA-SALLYSMGITQHVSGTDNVMTCATIALICGQIGRPGAGVWPMRGQNNVQG-NCDVGGMPEFYPGYRRSVdp 355
                                       ****9.99999*********************************************.99999998888876655458 PP

                                       ..HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHH CS
                     Molybdopterin 307 ..ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstal 381
                                          +++ aa++  +l++ p+ +++ +++++ ++ +k+ly+ g++p+v +a+ n++ +ale+ld++vv ++++t ta+
  gi|330508131|ref|YP_004384559.1| 356 ktIEFFRAAWNATDLPLGPGLTSTDMNDAAIDGRLKALYITGEDPIVCDANVNKTRRALESLDFLVVQEIFMTPTAK 432
                                       777888899******************************************************************** PP

                                       TSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                     Molybdopterin 382 yaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                       +aD+iLPaa+w Ek++ yt++e+r+q +++a++ppgeak+  +I++++a+
  gi|330508131|ref|YP_004384559.1| 433 MADVILPAAAWAEKSGSYTSMERRVQWIDRAIEPPGEAKEGVWIICEIAR 482
                                       ************************************************97 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4   0.0   1.4e-30   8.1e-27       2     109 ..     571     672 ..     570     674 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 1.4e-30
                                       EEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEE CS
                   Molydop_binding   2 rLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmp 77 
                                        L tgr + +++ + +t+++++l+++e+  +ve+np dA+ l i++G++V v++rrG++e+rak+++rv+ G++fmp
  gi|330508131|ref|YP_004384559.1| 571 LLSTGRIVLHYNGGSMTMRSPSLQERESeLYVEVNPVDASNLKIAEGEMVAVKTRRGEAEARAKISDRVMSGMAFMP 647
                                       699************999999999999999*********************************************** PP

                                       SSHCC.....S-GHCTS--SCSTTT--CSTT- CS
                   Molydop_binding  78 fgwweagekggnaNaltddatdplsgtpefks 109
                                       f++         +N lt+da+dp+s++pe+k 
  gi|330508131|ref|YP_004384559.1| 648 FHYHG-------TNLLTSDALDPVSRIPEYKM 672
                                       ***88.......******************96 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.4   1.1e-16   6.7e-13       2      55 .]       4      57 ..       3      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.1e-16
                                      EEEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCCCB CS
                    Molybdop_Fe4S4  2 kvvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllervyn 55
                                      k + ++CpyC vgCgl ++v++gk + ++   dhp+  g lC+KG+++le ++n
  gi|330508131|ref|YP_004384559.1|  4 KLIASLCPYCAVGCGLFIQVEKGKATGIKYMIDHPTCVGALCPKGNSVLELLNN 57
                                      6788**********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 4859.01
//
Query:       gi|330508132|ref|YP_004384560.1|  [L=194]
Description: hypothetical protein MCON_2239 [Methanosaeta concilii GP6]
Scores for complete 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   28.1   0.1    2.4e-06   27.6   0.1    1.3  1  Mrr_cat    Restriction endonuclease
     0.0051   16.4   0.0     0.0083   15.7   0.0    1.4  1  AHJR-like  REase_AHJR-like
     0.0083   16.6   0.1      0.013   15.9   0.1    1.5  1  NERD       Nuclease-related domain
  ------ inclusion threshold ------
      0.022   14.8   0.1      0.035   14.1   0.1    1.4  1  Hjc        Archaeal holliday junction resolvase (hjc)


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   5.3e-10   2.4e-06       4      78 ..      46     118 ..      43     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.3e-10
                                       T-TTCHHHHHHHHHHHHSSS...EEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS. CS
                           Mrr_cat   4 mspkeFeklvaellealGyk...eveltgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqeligalkkrg 77 
                                       + ++ Fekl a ++e++++    +   t +++  + D+ia++ +    +ilv++K++++   +  +++l+ a+++++
  gi|330508132|ref|YP_004384560.1|  46 VIWQNFEKLTAYIFEQNDFLveiNAVKTHKRKRRQYDVIARRMD---STILVECKKWSGH--RSRLSALRRAIEQHK 117
                                       6699***************976666688889999******9855...89********987..677888888887765 PP

                                       . CS
                           Mrr_cat  78 a 78 
                                        
  gi|330508132|ref|YP_004384560.1| 118 E 118
                                       4 PP

>> AHJR-like  REase_AHJR-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    0.0083      44      84 ..      80     118 ..      75     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-06
                         AHJR-like  44 rpDliarkdeeaviiEvksrrssaseqyLqelakaveqhpg 84 
                                       + D+iar+ + ++ +E k+ +    ++ L++l++a+eqh++
  gi|330508132|ref|YP_004384560.1|  80 QYDVIARRMDSTILVECKKWS--GHRSRLSALRRAIEQHKE 118
                                       67***************9875..55678***********97 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     3e-06     0.013       4      57 ..      50     103 ..      47     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3e-06
                              NERD   4 egEravakeLkelkedeylvlhdvrlrpgtg.eiDhlvispkgifviEvKnwsG.w 57 
                                       + E+ +a+  +  ++d  + ++ v+ +++++ + D+++   +  +++E+K wsG +
  gi|330508132|ref|YP_004384560.1|  50 NFEKLTAYIFE--QNDFLVEINAVKTHKRKRrQYDVIARRMDSTILVECKKWSGhR 103
                                       57889999999..8888899999999777446*********************942 PP

>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   7.7e-06     0.035      11      60 ..      60     115 ..      50     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.7e-06
                                       HHTT-EEEEBSCSSSSSS.SS-SEEEEETTEEEEEEEEEESSSEEEE.....EHHH CS
                               Hjc  11 rergfavvRsagSggatk.plpDviAirgdvvlviEvKsskkeriyl.....kkeq 60 
                                       ++++f v   a    ++k  + DviA r d  +++E+K+ +++r  l       eq
  gi|330508132|ref|YP_004384560.1|  60 EQNDFLVEINAVKTHKRKrRQYDVIARRMDSTILVECKKWSGHRSRLsalrrAIEQ 115
                                       5555555444444445455999*****************99998888555543344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); 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 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1397.12
//
Query:       gi|330508133|ref|YP_004384561.1|  [L=161]
Description: hypothetical protein MCON_2240 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-12   48.1  42.3    9.1e-06   26.2  21.8    2.7  3  Stig1     Stigma-specific protein, Stig1


Domain annotation for each model (and alignments):
>> Stig1  Stigma-specific protein, Stig1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2     0.013   2.3e+02      96     112 ..      34      50 ..      22      52 .. 0.79
   2 !   26.2  21.8   5.1e-10   9.1e-06      76     137 ..      42      97 ..      30     100 .. 0.91
   3 !   25.2  14.3     1e-09   1.9e-05      74     121 ..     103     150 ..      97     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.013
                             Stig1  96 kCkfsetCCkgkCvnls 112
                                        C  +   C+g+C+n++
  gi|330508133|ref|YP_004384561.1|  34 VCPDDMFPCNGTCINIT 50 
                                       56777778999999975 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 5.1e-10
                             Stig1  76 CkkkCvdvltdkenCgaCkkkCkfsetCCkgkCvnlsldkrhCGkCnnkCkkgelCvyGlCs 137
                                       C+  C+++++       C+ +C  +   C+g+C +ls+d+++CG+C+n C+ g +C  G+C 
  gi|330508133|ref|YP_004384561.1|  42 CNGTCINITS------PCNMSCLDGMFPCNGTCFDLSTDTQNCGSCGNVCSLGMVCIKGVCT 97 
                                       8888888875......6********************************************6 PP

  == domain 3  score: 25.2 bits;  conditional E-value: 1e-09
                             Stig1  74 tCCkkkCvdvltdkenCgaCkkkCkfsetCCkgkCvnlsldkrhCGkC 121
                                       + C++kC d++ d  nCgaC++ C  + +C +g+C ++s +    G+C
  gi|330508133|ref|YP_004384561.1| 103 DVCNEKCTDTSIDPLNCGACGNICPANAICIDGSCSDMSPQICIDGDC 150
                                       679********************************9998776666776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1230.57
//
Query:       gi|330508134|ref|YP_004384562.1|  [L=99]
Description: hypothetical protein MCON_2241 [Methanosaeta concilii GP6]
Scores for 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-25   86.8   0.1    7.9e-25   86.6   0.1    1.0  1  Thiamine_BP  Thiamine-binding protein


Domain annotation for each model (and alignments):
>> Thiamine_BP  Thiamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.1   4.4e-29   7.9e-25       1      91 [.       4      94 ..       4      95 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 4.4e-29
                                      EEEEEEECSSSSSGHHHHHHHHHHHHHTTSSEEEEETTEEEEEEE.HHHHHHHHHHHHHHHHCTTSSEEEEEEEEEEES CS
                       Thiamine_BP  1 veisviPlgtegesvskyVakvvevlkesglkyeltpmgTtiege.ldevmevvkkahealfeaGakRvstvikiddrr 78
                                      +e+s++P+g  g+s  +y+++++ +l e ++++  +pm+T +eg+ l+e++++ +ka+++l+++G+kR++t+i+id r 
  gi|330508134|ref|YP_004384562.1|  4 AEFSMVPMGS-GTSAGDYIKAIHHILGEAEVNFIPGPMSTAVEGKsLQELFDLMEKANDKLVQMGVKRIITTIRIDMRL 81
                                      69******98.******************************************************************** PP

                                      SS---HHHHHHHH CS
                       Thiamine_BP 79 dkeqtleeKvksv 91
                                      dke +++ K+++v
  gi|330508134|ref|YP_004384562.1| 82 DKEISMQSKLSRV 94
                                      **********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 00:00:00.40
# Mc/sec: 742.01
//
Query:       gi|330508135|ref|YP_004384563.1|  [L=154]
Description: hypothetical protein MCON_2243 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-31  108.7   0.0    2.1e-31  108.4   0.0    1.1  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.4   0.0   1.2e-35   2.1e-31       1     114 [.      35     150 ..      35     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 1.2e-35
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGG...TTS..THHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhn...aegpdnadaHlk 73 
                                       dit+ev++ ++++++k G +++f++ +t ++t+ E+ ++++ +Dl +ale+++p++ +Y+hn   ++g  n+++H++
  gi|330508135|ref|YP_004384563.1|  35 DITDEVQKSLESTSLKAGAMVIFVPGATGAVTTIEY-EDGLVADLGDALERIAPQNiDYSHNlrwHDG--NGHSHIR 108
                                       8**********************************9.*************************887778..******* PP

                                       HHHH-SEEEEEEETTEE---TTEEEEEEESS-S.SEEEEEEE CS
                           UPF0047  74 ssllgssltipvedgklalGtwqsiylveldgp.reRkvvvq 114
                                       +sl+g+sl +p+   +l lGtwq+i+++eld++ r+Rk+v+q
  gi|330508135|ref|YP_004384563.1| 109 ASLIGPSLIVPFAARRLILGTWQQIVFLELDNRkRHRKLVLQ 150
                                       *******************************55599***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 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:                        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 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1144.24
//
Query:       gi|330508136|ref|YP_004384564.1|  [L=185]
Description: extracellular nuclease [Methanosaeta concilii GP6]
Scores for complete 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   40.7   0.0    3.6e-10   40.3   0.0    1.2  1  SNase     Staphylococcal nuclease homologue
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.41   10.5   0.0    1.8  2  DoxA      TQO small subunit DoxA


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 !   40.3   0.0     4e-14   3.6e-10       1      85 [.      56     140 ..      56     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 4e-14
                                       EEEETTEE-STSSBTTTTTSTTHHHHHHHHHHHHHHCSSEEEEE-S.SBSTTSEEEEEEEET.TEEHHHHHHHTTSS CS
                             SNase   1 kvrLvgidaPetakpkktvqpfgkeAkeflkklvlqkkvvvleldk.kkDkygrllayvyln.kknineeLvkeGlA 75 
                                       ++rL++ daPe    ++ + + g++A++++ + ++ + v+++++d   +D+ygr +a  yl+ ++n+n+ Lv  G A
  gi|330508136|ref|YP_004384564.1|  56 RIRLADLDAPELY--GERACKEGEWARDYTYSWLMDNIVTLDIDDVnGQDEYGRWIAVCYLEdGRNFNKMLVDSGNA 130
                                       79***********..5555666*************9999999999999**************9************** PP

                                       EE---BTTST CS
                             SNase  76 rvyevyekne 85 
                                       ++  ++++++
  gi|330508136|ref|YP_004384564.1| 131 TIKDFRSNEF 140
                                       *777776554 PP

>> DoxA  TQO small subunit DoxA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.15   1.3e+03      18      45 ..      41      69 ..      28      73 .. 0.57
   2 ?   10.5   0.0   4.6e-05      0.41      28      78 ..      89     141 ..      82     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.15
                              DoxA 18 leitga..klaengtLvleitrveGpdvYg 45
                                      +ei +   ++ +++t  +++++ + p+ Yg
  gi|330508136|ref|YP_004384564.1| 41 VEIDEHdgRI-QEDTIRIRLADLDAPELYG 69
                                      3443333344.5556666666666666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 4.6e-05
                              DoxA  28 ngtLvleitrveGpdvYgafvikiellnst..gkvvlelnqeeLaslpssnIk 78 
                                       ++  +l+i +v+G d Yg ++    l +    +k++++  +  + ++ s++ +
  gi|330508136|ref|YP_004384564.1|  89 DNIVTLDIDDVNGQDEYGRWIAVCYLEDGRnfNKMLVDSGNATIKDFRSNEFD 141
                                       67789*****************9999987656777878888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1382.14
//
Query:       gi|330508137|ref|YP_004384565.1|  [L=792]
Description: cation-transporting P-type ATPase [Methanosaeta concilii GP6]
Scores for complete 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-42  143.2   2.4    6.2e-42  143.2   2.4    3.3  4  E1-E2_ATPase     E1-E2 ATPase
    1.5e-15   58.0   0.3    4.9e-15   56.4   0.0    1.9  2  Hydrolase        haloacid dehalogenase-like hydrolase
    1.2e-12   47.9  14.3    1.2e-12   47.9  14.3    1.9  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    1.3e-07   31.2   0.1      3e-07   30.0   0.1    1.7  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
  ------ inclusion threshold ------
      0.051   13.3   0.3       0.86    9.3   0.6    2.4  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
      0.084   11.9   0.0        0.2   10.7   0.0    1.6  1  Dak1_2           Dihydroxyacetone kinase family


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.6         2   6.1e+03     117     145 ..      23      51 ..      17      64 .. 0.51
   2 !  143.2   2.4   2.1e-45   6.2e-42       6     181 .]      87     275 ..      83     275 .. 0.96
   3 ?   -1.4   0.1      0.48   1.4e+03      27      42 ..     569     584 ..     566     593 .. 0.87
   4 ?   -1.1   1.1      0.37   1.1e+03     121     145 ..     724     748 ..     695     773 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHHHHHHS-STTTSSTT CS
                      E1-E2_ATPase 117 klgkvlvpvvlliallvflialllgksla 145
                                        + ++++ +  l++l++ ++++ lg+ + 
  gi|330508137|ref|YP_004384565.1|  23 LILRQFSGIFNLLLLAASAVTFALGEVID 51 
                                       44455555555555555555544444444 PP

  == domain 2  score: 143.2 bits;  conditional E-value: 2.1e-45
                                       EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-..........G-TTEE- CS
                      E1-E2_ATPase   6 takvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek..........ekgdmvf 71 
                                       + +v+rdg+ +e+++ e+vpGDi+ l++gd+vpaD+++   ++  vde   TGEs pv+k          + ++++ 
  gi|330508137|ref|YP_004384565.1|  87 SITVRRDGKDQEVPVVEIVPGDILNLESGDIVPADAIVRRAHNlLVDETTFTGESIPVSKqaadssmqeaDDEHRLL 163
                                       6799***************************************************************9999****** PP

                                       TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT... CS
                      E1-E2_ATPase  72 sGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla... 145
                                       +G v+v+g+a a Vt+tg++t+++ ia+ ++e  +++++l+k +d+++ ++  + ++ +l+++l+++l++++ +   
  gi|330508137|ref|YP_004384565.1| 164 QGVVIVRGNALALVTETGNKTRFAAIAKTASEV-QAESELTKGIDRISTFILRTTIITLLFIILANVLIEGKSTdip 239
                                       *********************************.99**************999999999999999999988888899 PP

                                       HHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 146 eallralallvaaiPcaLplavplalalgarrlakk 181
                                       + l++a+al+v++iP+aLpl+++ +l+ ga +lak+
  gi|330508137|ref|YP_004384565.1| 240 QLLIFAIALAVSVIPEALPLVLTFSLSRGALQLAKR 275
                                       99999*****************************96 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.48
                                       SEEEEETT-B--SEEE CS
                      E1-E2_ATPase  27 DivllkagdrvpaDgr 42 
                                       Divl+k+  rv +Dg+
  gi|330508137|ref|YP_004384565.1| 569 DIVLVKNDLRVIVDGI 584
                                       9*************97 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHHHHHHS-STTTSSTT CS
                      E1-E2_ATPase 121 vlvpvvlliallvflialllgksla 145
                                       + +p+v+li++l+f+i+l l   ++
  gi|330508137|ref|YP_004384565.1| 724 WPAPIVVLISALAFVITLALPLIPQ 748
                                       4567888888888888877665555 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.91   2.7e+03      11      46 ..     135     190 ..     132     251 .. 0.58
   2 !   56.4   0.0   1.6e-18   4.9e-15       1     209 [.     291     551 ..     291     552 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.91
                                       TTBCHH..HHHHHHHHHH..................CHHHHHHHHHHHHCHHHHHH CS
                                       xxxxxx..xxxxxxxxxx..................xxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  11 TLttge..psvedvivsa..................alalaaaletgsehpigkal 46 
                                       T  tge  p+ +++ +s                     ala ++etg+++ +++  
  gi|330508137|ref|YP_004384565.1| 135 TTFTGEsiPVSKQAADSSmqeaddehrllqgvvivrGNALALVTETGNKTRFAAIA 190
                                       55555555555555555544444444444444444455666666666322222222 PP

  == domain 2  score: 56.4 bits;  conditional E-value: 1.6e-18
                                       SSEEEEESBTTTBCHHHHHHHHHHHH.......CHHHHHHHHHH....HHCHHHHHHHHHHHHH.HHHHHHHHHETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxx....xxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa.......alalaaaletg....sehpigkalvaaakar.sgaltgfatfig 65 
                                       +++++ Dk+GT+t+ +  ++   +++        l la+  ++g    s+ p+ +a  +a   + + +l+ f+ +++
  gi|330508137|ref|YP_004384565.1| 291 VNLLCTDKTGTITENR--LVYQGNYLdpdsrfhPLLLARLAAHGleerSPEPFDRAADEALTPEqRKELEAFRILQE 365
                                       6899*********666..333222225677777444555555556677******99977777665777788888777 PP

                                       TE....................HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH......TTHHHHHHHHH CS
                                       xx....................xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxx RF
                         Hydrolase  66 rg....................ayaigkpewltal..dippdlgaaigsaqsqgrtvall......qaralavftia 114
                                       +                     ++ +g+pe++ ++     + lg+   +++ +gr v  +        r  + + + 
  gi|330508137|ref|YP_004384565.1| 366 EAfdpalrsngaivslkdglqlHIRRGSPEYFFDQglVNRDRLGSWLAEEENHGRRVLGVsyddgsGPRFAGFVSFV 442
                                       77888888888999999*******************999999999999********9999887665449******** PP

                                       HTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT................GGGESEEEEHHCES..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxx..... RF
                         Hydrolase 115 dplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG................ddyfdaviasdiet..... 170
                                       d+  +k+ + e++   ++ ++ + ++tgd  + ae++ +++G                                   
  gi|330508137|ref|YP_004384565.1| 443 DN--LKDTTIETIDLARELNVAITIITGDALKVAEAVGREAGlvsssdeviraaeflaL----------PAQeqhkr 507
                                       **..**************************************88888666553332221..........11133445 PP

                                       ......STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 171 ......vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                             +a   pe+k+++i +L+++   v + G g+nDa+al+aA
  gi|330508137|ref|YP_004384565.1| 508 igkirvFARTTPEQKLQLIAQLKEQY-TVGFLGEGINDAPALKAA 551
                                       6666668999************7665.7****************9 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       2.2   6.6e+03     145     145 ..     227     227 ..     193     254 .. 0.53
   2 !   47.9  14.3     4e-16   1.2e-12       1     180 [.     621     781 ..     621     782 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.2
                   Cation_ATPase_C 145 v 145
                                        
  gi|330508137|ref|YP_004384565.1| 227 A 227
                                       1 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 4e-16
                   Cation_ATPase_C   1 plplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrri.liqgllqalvtllvffltlllf 76 
                                       +lp+ + q+L++nL++D+   +a+a++  +++  +r +        + + l  i ++ gl+++++ +++f+l +   
  gi|330508137|ref|YP_004384565.1| 621 FLPMLPKQLLLLNLLSDFP-MMAIAFDRVSAKEVSRAQS------YDFRSLYIIfITLGLVSTVFDFIYFALFYR-- 688
                                       58***************76.**********999999665......6777777777*************9955554.. PP

                   Cation_ATPase_C  77 gisekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglf.snkllllaillslllqvlivyvpglnavf 152
                                        is++         qt +Fi+ v+++++ ++++rs    ++++++     ++++l+ +l++++++++ ++p  +a+f
  gi|330508137|ref|YP_004384565.1| 689 -ISPEV-------LQTNWFIASVITELLLMVSIRS----MLPIEKAGwPAPIVVLISALAFVITLALPLIPQTAALF 753
                                       .66655.......9*********************....7776666668999************************* PP

                   Cation_ATPase_C 153 gtaplsleewlialllalvvllvdelvK 180
                                       +++ ++l +++++++la+++l+ +e+vK
  gi|330508137|ref|YP_004384565.1| 754 EFTMPTLDHLALIMGLAVLYLIATEVVK 781
                                       **************************99 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   9.9e-11     3e-07      28      68 ..       3      42 ..       1      43 [. 0.95

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 9.9e-11
                   Cation_ATPase_N 28 erlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalv 68
                                      er+++yGpN+l ++ +  l++++l+qf+  + +lLl+a++v
  gi|330508137|ref|YP_004384565.1|  3 ERQSQYGPNAL-PQTRHRLIRLILRQFSGIFNLLLLAASAV 42
                                      8**********.999999********************998 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.7     5e+03      44      69 ..     358     382 ..     354     388 .. 0.72
   2 ?    1.3   0.0     0.079   2.4e+02      81     164 ..     446     532 ..     442     537 .. 0.69
   3 ?    9.3   0.6   0.00029      0.86     208     248 ..     537     577 ..     520     584 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.7
                                       HHHHHHHHCCCCSEEEEGGGTEEECT CS
                       Hydrolase_3  44 avlpvleelgldlpvialNGalidde 69 
                                       ++ ++l+e  +d p++ +NGa++  +
  gi|330508137|ref|YP_004384565.1| 358 EAFRILQEEAFD-PALRSNGAIVSLK 382
                                       566677777777.9999*****9433 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.079
                                       HHHHHHHHHHHHHTTCEEEEEESSEEEESTT..THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEE..EES-HHHH CS
                       Hydrolase_3  81 kedvkeiikllkennveillytedkvyvlnk.eksekkkkeeektkkkkeeidseeeledeeiakil..ilkdkekl 154
                                       k++  e i+l++e nv i + t d + v ++  ++   +++ +++ +  e     ++++++ i ki     +++e+ 
  gi|330508137|ref|YP_004384565.1| 446 KDTTIETIDLARELNVAITIITGDALKVAEAvGREAGLVSSSDEVIRAAEFLALPAQEQHKRIGKIRvfARTTPEQK 522
                                       45666778888888888888888888888876556666666666666666667777777777777776667777777 PP

                                       HHHHHHHHHH CS
                       Hydrolase_3 155 delekelksk 164
                                        +l+++lk++
  gi|330508137|ref|YP_004384565.1| 523 LQLIAQLKEQ 532
                                       7777777776 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00029
                                       EEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGG CS
                       Hydrolase_3 208 afGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnne 248
                                         G g ND + L+aa +++ +++a + + + Ad v  +n+ 
  gi|330508137|ref|YP_004384565.1| 537 FLGEGINDAPALKAAHVSMVVQSAADVARETADIVLVKNDL 577
                                       4699*******************************999975 PP

>> Dak1_2  Dihydroxyacetone kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.7e-05       0.2     208     263 ..      79     139 ..      63     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.7e-05
                            Dak1_2 208 a.....vktgevtyAvrdtkidggeikkgdllgiadgkivvvgkdleeaakkllkkllded 263
                                       +     v++ +v++  +d ++  +ei +gd+l++  g+iv +++ +++a + l+++    +
  gi|330508137|ref|YP_004384565.1|  79 KlksyfVRSITVRRDGKDQEVPVVEIVPGDILNLESGDIVPADAIVRRAHNLLVDETTFTG 139
                                       133355***********************************99999999998888775544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (792 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.44
# Mc/sec: 5414.85
//
Query:       gi|330508138|ref|YP_004384566.1|  [L=1127]
Description: S-layer-related duplication domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.1e-190  630.9  20.3    1.8e-96  322.2   6.3    2.3  2  S-layer          S-layer protein
    2.8e-10   39.9   4.6    1.4e-06   28.1   0.1    3.8  4  PEGA             PEGA domain
    3.9e-08   33.2   8.2    5.5e-05   23.1   0.5    3.7  3  CarbopepD_reg_2  CarboxypepD_reg-like domain
    2.3e-05   24.6  21.0    0.00017   21.8   0.1    4.7  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0012   18.9   0.5      0.015   15.4   0.2    2.8  2  Transglut_C      Transglutaminase family, C-terminal ig like 
  ------ inclusion threshold ------
      0.036   13.9   0.1       0.51   10.2   0.0    2.6  2  A2M              Alpha-2-macroglobulin family
        6.9    6.6  25.1         18    5.2  25.1    1.6  1  TFIIA            Transcription factor IIA, alpha/beta subunit


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 !  314.3   6.0   1.7e-97   4.4e-94       5     258 .]     269     521 ..     266     521 .. 0.98
   2 !  322.2   6.3  6.9e-100   1.8e-96       5     258 .]     547     802 ..     544     802 .. 0.98

  Alignments for each domain:
  == domain 1  score: 314.3 bits;  conditional E-value: 1.7e-97
                           S-layer   5 eeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfa 81 
                                       +++ ++twt+++Fsgf+yd+++++++E+lt++le  ++r++e+g++ Yst+p+ ++fef++wg+Yevigf+aekYfa
  gi|330508138|ref|YP_004384566.1| 269 KSPYKYTWTPKTFSGFFYDLENEVGTERLTVDLEP-NERSLETGKISYSTKPEATDFEFDDWGEYEVIGFMAEKYFA 344
                                       567899**************************986.9**************************************** PP

                           S-layer  82 gydnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskviss 158
                                       gy+ s+  +dd sl++d++L++vl+d+deekt+++gs+l LeegYel+ikqiD+dg+kv++ L+kdg+e+dskvi++
  gi|330508138|ref|YP_004384566.1| 345 GYKASDLINDDRSLINDGQLRRVLVDSDEEKTVTTGSVLPLEEGYELRIKQIDIDGNKVYMALAKDGDEIDSKVIDP 421
                                       **99999********************************************************************** PP

                           S-layer 159 ska.dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvseneiemen 234
                                       s+  +sty ye ++++ +d  +i  h+++vf +te+ lv+i+g+fqisd++ ++e+gd++gkmevksvs++ +emen
  gi|330508138|ref|YP_004384566.1| 422 SNLdSSTYNYEVEVAG-EDTSLILAHISNVFASTESALVTIDGLFQISDTYASVEDGDKYGKMEVKSVSDEGVEMEN 497
                                       88799***********.6799999***************************************************** PP

                           S-layer 235 ddsitLsrdktieimddlkfkvaD 258
                                       +ds+tL+r++t+ei++d++f vaD
  gi|330508138|ref|YP_004384566.1| 498 EDSLTLRRGSTVEIFGDVSFLVAD 521
                                       ***********************8 PP

  == domain 2  score: 322.2 bits;  conditional E-value: 6.9e-100
                           S-layer   5 eeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfa 81 
                                       +e++e+tw++ nF+gfyydidd++++E++t++++  ++++ieeg+l+Yst++++++fef++wg+Y+vigf+a+kYfa
  gi|330508138|ref|YP_004384566.1| 547 SETSEFTWNPYNFEGFYYDIDDDVGTENMTMRIS--GGSKIEEGDLEYSTKSQPVKFEFSDWGKYDVIGFMADKYFA 621
                                       67899***************************76..79*************************************** PP

                           S-layer  82 gydnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskviss 158
                                       gy++++e +d++s++ +++L++vl+d+d+++t+ sgs+l+LeegYel+ikq+D++g+kv+l L+kdg+evdskv+++
  gi|330508138|ref|YP_004384566.1| 622 GYNDETEFTDEASIIGEGQLRRVLTDSDDSRTIASGSVLSLEEGYELRIKQVDLNGNKVYLALAKDGDEVDSKVVTP 698
                                       **99999********************************************************************** PP

                           S-layer 159 ska....dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvseneie 231
                                       s++    +s+y+y+ d+g+e+dv++i  hv++vfr+te++l+++++ifqisd++ ++eeg+ +gkm+v+s++ + i+
  gi|330508138|ref|YP_004384566.1| 699 SNDptdgSSNYLYKIDMGGEKDVPLISAHVESVFRSTESDLATVDAIFQISDSPESVEEGEMHGKMKVDSLDYDGIT 775
                                       9999*99********************************************************************** PP

                           S-layer 232 menddsitLsrdktieimddlkfkvaD 258
                                       ++nd +i+Lsr+k+++imd+l+++vaD
  gi|330508138|ref|YP_004384566.1| 776 LTNDGTISLSRGKDVDIMDNLRIQVAD 802
                                       **************************9 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.5   6.3e+03      43      60 ..     387     404 ..     385     406 .. 0.82
   2 ?   -3.2   0.0       3.2   8.3e+03      43      60 ..     664     681 ..     662     683 .. 0.79
   3 !   11.1   0.3   0.00011      0.27       8      58 ..     843     898 ..     838     908 .. 0.73
   4 !   28.1   0.1   5.4e-10   1.4e-06       8      63 ..     942    1003 ..     940    1008 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.5
                              PEGA  43 eGYedlektvtvtagetv 60 
                                       eGYe   k+++++ ++++
  gi|330508138|ref|YP_004384566.1| 387 EGYELRIKQIDIDGNKVY 404
                                       899999999999988776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.2
                              PEGA  43 eGYedlektvtvtagetv 60 
                                       eGYe   k+v+++ ++++
  gi|330508138|ref|YP_004384566.1| 664 EGYELRIKQVDLNGNKVY 681
                                       899999999999877765 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00011
                              PEGA   8 SnpeGatVyidGkylGkTPvt..ls.leaGnyslrv..ekeGYedlektvtvtage 58 
                                       S  +G  ++idG+++G T  t  +s +++ + +++v   k GY d+++++ v+  e
  gi|330508138|ref|YP_004384566.1| 843 SALSGVAISIDGNTIGTTDSTgsISyIPKSTGTVKVvaRKTGYNDATADMVVRTVE 898
                                       6668999*********8876533555665555555511799*******99998544 PP

  == domain 4  score: 28.1 bits;  conditional E-value: 5.4e-10
                              PEGA    8 SnpeGatVyidGkylGkTP....vtls.leaGnyslrvekeGYedlektvtvt.agetvkln 63  
                                        +  +Ga++ +d +++G+T      t++   +G++sl+vekeGY+ ++++++vt a e++ l+
  gi|330508138|ref|YP_004384566.1|  942 TPVAGAQILLDDNEIGNTSsqgtFTYAvNLTGEHSLKVEKEGYSSASRKIMVTsALEVMDLT 1003
                                        5578************886222256665569**********************777776665 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 !   12.6   0.6   4.1e-05      0.11       9      71 ..     840     901 ..     825     918 .. 0.79
   2 !   23.1   0.5   2.1e-08   5.5e-05       4      81 ..     934    1009 ..     934    1016 .. 0.85
   3 ?   -1.7   0.0       1.1   2.9e+03      56      83 ..    1040    1067 ..    1024    1070 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                   CarbopepD_reg_2   9 etkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektld 71 
                                       ++  +l g+ +++ g++ gt Td+ G+ +   +  g++++v++  Gy+ ++  + v + ++ +
  gi|330508138|ref|YP_004384566.1| 840 SGTSALSGVAISIDGNTIGT-TDSTGSISYIPKSTGTVKVVARKTGYNDATADMVVRTVEEAS 901
                                       45579*************97.9*****99988999**************99999887655443 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 2.1e-08
                   CarbopepD_reg_2    4 tVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillke 78  
                                        tV++  +++p++ga++++ +++ g  T ++G+F+      g++ L+v+  Gy ++++k+ v++  ++  +++l e
  gi|330508138|ref|YP_004384566.1|  934 TVTEGINQTPVAGAQILLDDNEIGN-TSSQGTFTYAVNLTGEHSLKVEKEGYSSASRKIMVTSALEVM-DLTLPE 1006
                                        578888999**********999996.6799******9999*********************9886654.556666 PP

                   CarbopepD_reg_2   79 eal 81  
                                        +a+
  gi|330508138|ref|YP_004384566.1| 1007 TAN 1009
                                        554 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.1
                   CarbopepD_reg_2   56 ktqekkvtvskektldvnillkeealel 83  
                                          ++k vtv+ +++ +v+++  ++++ l
  gi|330508138|ref|YP_004384566.1| 1040 LAESKDVTVEAGENSTVQFSYNPDETGL 1067
                                        5578889999888888888888777665 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   1.2       5.7   1.5e+04       8      29 ..     198     219 ..     195     230 .. 0.57
   2 !   10.2   6.0   0.00028      0.71       1      77 [.     824     903 ..     824     914 .. 0.70
   3 !   21.8   0.1   6.5e-08   0.00017       5      72 ..     934     996 ..     932    1005 .. 0.76
   4 ?    0.6   0.0      0.26   6.8e+02      62      79 ..    1041    1058 ..    1024    1071 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.7
                   CarboxypepD_reg   8 dasgapiagatVtvtnadtgtv 29 
                                        +   + ag  V++t+++ +++
  gi|330508138|ref|YP_004384566.1| 198 TPPEDVAAGTVVSATDSAADAS 219
                                       5556677888888886543332 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00028
                   CarboxypepD_reg   1 tisGrVtda.sgapi.......agatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtl 69 
                                       t+sG V+d+    ++       +g+++++       ++  ttd++G+ +     +gt +v+++++Gy  at   v+ 
  gi|330508138|ref|YP_004384566.1| 824 TVSGAVVDKaAQIAVrsgtsalSGVAISID-----GNTIGTTDSTGSISYIPKSTGTVKVVARKTGYNDATADMVVR 895
                                       688888886345544666666699999999.....5666789****999766666****************955544 PP

                   CarboxypepD_reg  70 tagqtttl 77 
                                       t++++++l
  gi|330508138|ref|YP_004384566.1| 896 TVEEASQL 903
                                       44444443 PP

  == domain 3  score: 21.8 bits;  conditional E-value: 6.5e-08
                   CarboxypepD_reg   5 rVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltag 72 
                                       +Vt   + +p+aga++ + +     +    t ++G+f+ +   +g++s++v+++Gy +a+r+ + +t  
  gi|330508138|ref|YP_004384566.1| 934 TVTEGiNQTPVAGAQILLDD-----NEIGNTSSQGTFTYAVNLTGEHSLKVEKEGYSSASRK-IMVTSA 996
                                       688877899**********3.....4555677889999874455****************86.777733 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.26
                   CarboxypepD_reg   62 atreevtltagqtttldi 79  
                                        a++++vt++ag+++t+++
  gi|330508138|ref|YP_004384566.1| 1041 AESKDVTVEAGENSTVQF 1058
                                        45689*********9987 PP

>> Transglut_C  Transglutaminase family, C-terminal ig like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.61   1.6e+03      52      78 ..     291     317 ..     288     328 .. 0.82
   2 !   15.4   0.2   5.9e-06     0.015       3      85 ..    1000    1071 ..     999    1085 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.61
                                       EEEEEEEEEEE-TTEEEEEEEEE-HHS CS
                       Transglut_C  52 efkkksleltLePkeeksvrlkilpsk 78 
                                       e+ ++ l+++LeP+e    + ki++s 
  gi|330508138|ref|YP_004384566.1| 291 EVGTERLTVDLEPNERSLETGKISYST 317
                                       67789999*******999999999986 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 5.9e-06
                                        EEEEESSCEBTTSEEEEEEEEEE-SSS-BEEEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE-HH CS
                       Transglut_C    3 lkievlesavlgqdltvsvllkNplseelkdvklnlcaqtveynGvlaaefkkksleltLePkeeksvrlkilps 77  
                                        ++++++e+a+ +q++++s++++N+ se   +++lnl ++              +s+ +t+e++e  +v+++  p 
  gi|330508138|ref|YP_004384566.1| 1000 MDLTLPETANAKQSMKISAVVHNKGSEV-DTITLNLMVND----------TLAESKDVTVEAGENSTVQFSYNPD 1063
                                        899*********************9988.****9995543..........3457888888888888888888888 PP

                                        SHEEECCE CS
                       Transglut_C   78 kyGerkll 85  
                                        ++G +++ 
  gi|330508138|ref|YP_004384566.1| 1064 ETGLHRFS 1071
                                        88887765 PP

>> A2M  Alpha-2-macroglobulin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.28   7.1e+02      35      77 ..     896     936 ..     888     939 .. 0.70
   2 ?   10.2   0.0    0.0002      0.51      41      88 ..     983    1030 ..     974    1034 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.28
                                       EEETTTEEEEEEEEEEEE--SEEEEEE--SEEETTSEEEEEEE CS
                               A2M  35 alsedkglgvaeplevrvfkpffvdlnlPysvrrgeqveikav 77 
                                       +++e  +l  a++  ++v+    + ln P  v  ge++ i+++
  gi|330508138|ref|YP_004384566.1| 896 TVEEASQLTAAQR--ANVTLANQLILNAPAEVSAGENFLITVT 936
                                       5555555555555..4555555566899*********999875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0002
                                        EEEEEEEEEEEE--SE.EEEEE--SEEETTSEEEEEEEEEE-SSS-EEE CS
                               A2M   41 glgvaeplevrvfkpf.fvdlnlPysvrrgeqveikavvfNyldkeikv 88  
                                        g+  a++ ++ v+  + ++dl+lP+++    +++i+avv+N  ++  ++
  gi|330508138|ref|YP_004384566.1|  983 GYSSASR-KIMVTSALeVMDLTLPETANAKQSMKISAVVHNKGSEVDTI 1030
                                        6666777.666666662569*********************98776555 PP

>> TFIIA  Transcription factor IIA, alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  25.1     0.007        18     198     358 ..      63     262 ..      15     267 .. 0.31

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.007
                             TFIIA 198 q................qqqqqqqqqqqqqq.qvqqqqqeesqqaqqasqe...qvagsqvessqtdgaedaleees 254
                                       +                +       +  q++ q+++ + ++  qa++a      +v++sqv+ss   ++e+++++++
  gi|330508138|ref|YP_004384566.1|  63 NiglkplgsksstptgaA-------ASDQSAaQASSASAAPATQAATA--PaaaTVTTSQVSSSAPAQPESSSQNAP 130
                                       122222222111111110.......11111101111111111111111..011122333333333333333333333 PP

                             TFIIA 255 pv.legelsaeeeagaqkeelsreeidri.reealkakelekeskkkkr.aeessla.................... 308
                                       p+      s++e++g+     ++   ++i    ++++  +++++   ++ ++    +                    
  gi|330508138|ref|YP_004384566.1| 131 PAeQTSSASQQESSGSA----TTPASNDIiTPDQISQDTIAADASTDSAaTT----Paeaassgtssggsasevvtp 199
                                       33211111111111111....1111111111111111111111111111000....011111223334444455555 PP

                             TFIIA 309 .....dlseilqlDGagddsde........eeeeeesdedsdsessddedeqveEDplNSdDD 358
                                            + + +   D a+d s+e        ++++e  +e++++++++ e e++eE+ + ++D 
  gi|330508138|ref|YP_004384566.1| 200 pedvaAGTVVSATDSAADASTEaaenvtdeQSTDELTAENESQNETETESEEAEEEEIEEGDN 262
                                       555556677778888888888766544443333333333333333333555588888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1564  (0.087233); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 1.11u 0.32s 00:00:01.43 Elapsed: 00:00:00.45
# Mc/sec: 7582.76
//
Query:       gi|330508139|ref|YP_004384567.1|  [L=349]
Description: daunorubicin resistance ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete 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  117.1   0.0    1.4e-33  116.4   0.0    1.4  1  ABC_tran     ABC transporter
      3e-08   33.9   0.2     0.0029   17.5   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    6.3e-08   33.2   0.0    1.1e-07   32.5   0.0    1.4  1  DUF4162      Domain of unknown function (DUF4162)
    4.7e-06   27.2   0.0    7.2e-05   23.4   0.0    2.1  2  AAA_23       AAA domain
    9.5e-05   22.1   0.1    0.00019   21.1   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00046   20.0   0.0      0.024   14.3   0.0    2.2  2  AAA_15       AAA ATPase domain
     0.0028   17.1   0.0      0.022   14.2   0.0    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.067   12.3   0.0      0.083   12.0   0.0    1.2  1  G-alpha      G-protein alpha subunit
      0.071   13.0   0.0       0.14   12.1   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.092   12.5   0.1       0.42   10.3   0.0    1.9  2  FdtA         WxcM-like, C-terminal


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   7.6e-37   1.4e-33       1     136 [.      40     183 ..      40     184 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 7.6e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       ++n++l++++ge+ +++G nGaGKSt++k+l+ +l+pt+Ge ++ g d+ + e++++r++igv++q+p l+  lt r
  gi|330508139|ref|YP_004384567.1|  40 VDNIDLQIRKGELFGLLGANGAGKSTIIKMLTTMLTPTSGEARVWGYDIVR-ERNEVRSSIGVVFQDPALDGMLTGR 115
                                       589************************************************.9************************ PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en              ++++i+++l+ ++lke++dt++    + +SgG+k+r+++ar l+ +p +l+lDEpt
  gi|330508139|ref|YP_004384567.1| 116 ENldfhgrmygmnaaLRKARIADVLELVDLKEKADTKM----QDYSGGMKRRLEIARGLMHRPHVLFLDEPT 183
                                       ***********999888999************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.3   2.1e-05     0.038       2      22 ..      53      73 ..      52      95 .. 0.81
   2 !   17.5   0.0   1.6e-06    0.0029     230     298 ..     149     215 ..     108     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       +l G+Ng+GKS++++ l  +
  gi|330508139|ref|YP_004384567.1| 53 FGLLGANGAGKSTIIKMLTTM 73
                                      689*************99544 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.6e-06
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell...kelsrngaQviltTHS 298
                                        ++ + + S G+kr l ++  l  ++    +l++DEp  gL+ +  r ++e +   +++   ++  iltTH 
  gi|330508139|ref|YP_004384567.1| 149 ADTKMQDYSGGMKRRLEIARGLMHRP---HVLFLDEPTIGLDAQTRRYIWEYIgrmNKE--MNVTMILTTHY 215
                                       55667788999999998888888888...79*******************999854444..45********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 !   32.5   0.0   6.1e-11   1.1e-07       3      81 .]     240     326 ..     239     326 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 6.1e-11
                                       HHHHHTTS-SSEEEEE....--..-----..---EEEE-TTS-EEEEE--.-----------.----EEEEEEEE-- CS
                           DUF4162   3 leeiKrsygknrieve....ad..aeelleepgveeveeeggelelkled.eeaanellkal.tsgveirsFeeeeP 71 
                                       +e +K+ +g+++i++     +d  + +l++ + +++++ ++g+++l++++ ++   e+  ++ ++++ i+s+ +++P
  gi|330508139|ref|YP_004384567.1| 240 PESLKDTIGSDTITLMtdsgGDalVRSLQSFSWIKSISSDNGSIKLHVDHaQSRIAEVVLEAsRNNAVITSVGLHKP 316
                                       6789**********886765224344444555599999999********7666666666666489999********* PP

                                       -HHHHHHHHH CS
                           DUF4162  72 sLndIFiekv 81 
                                       +L+d+Fi+++
  gi|330508139|ref|YP_004384567.1| 317 TLEDVFIKYT 326
                                       *******986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0     4e-08   7.2e-05      15      49 ..      43      80 ..      33     154 .. 0.83
   2 ?    1.8   0.0      0.17     3e+02      56     107 ..     276     340 ..     255     346 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4e-08
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAiklaLygetpr 49
                                      id+   +  l+ + G NGaGK+Ti+  ++ +L+  +++
  gi|330508139|ref|YP_004384567.1| 43 IDLqirKGELFGLLGANGAGKSTIIKMLTTMLTPTSGE 80
                                      6667766689**********************975544 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.17
                            AAA_23  56 rgfeksdveiesegkvkayveltfenkdgry.............trsiererelskkkgkttkka 107
                                        ++ +++++++ ++ +++++e+ +e  ++               +++i+++ +++k++g + ++a
  gi|330508139|ref|YP_004384567.1| 276 ISSDNGSIKLHVDHAQSRIAEVVLEASRNNAvitsvglhkptleDVFIKYTGKKIKENGGKDRGA 340
                                       45667777777777777888888888777668999999999999999999999999999887776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1     1e-07   0.00019      17      50 ..      45      78 ..      39      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++i+  + + l G++G+GKST++  ++++L+p++
  gi|330508139|ref|YP_004384567.1| 45 LQIRKGELFGLLGANGAGKSTIIKMLTTMLTPTS 78
                                      55654447889*********************87 PP

>> AAA_15  AAA ATPase 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     0.024      23      50 ..      49      77 ..      39     157 .. 0.82
   2 ?    3.8   0.0     0.022        39     322     364 ..     172     214 ..     139     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                            AAA_15 23 ee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      +  l  l G+N++GKS+i+++l  +l+ +
  gi|330508139|ref|YP_004384567.1| 49 KGeLFGLLGANGAGKSTIIKMLTTMLTPT 77
                                      33577899***************999866 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.022
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                        ++++l+++EP + L  q  + +++++ ++ ++ +   i+tTH
  gi|330508139|ref|YP_004384567.1| 172 HRPHVLFLDEPTIGLDAQTRRYIWEYIGRMNKEMNVTMILTTH 214
                                       4689*******************************9******* PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.2e-05     0.022      28     206 ..      54     220 ..      37     232 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                       EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsisrrv 103
                                        ++G+NG+GKs ++  +  +L  +s  + r   + d++ +    ++  + ++ ++f+++  + + + +e++    r+
  gi|330508139|ref|YP_004384567.1|  54 GLLGANGAGKSTIIKMLTTMLTPTSG-EARVWGY-DIVRE----RNEVRSSIGVVFQDPALDgMLTGRENLDFHGRM 124
                                       589***************9**97777.6666554.66665....666778999999998877345555556666666 PP

                                       ETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 104 krkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkva 180
                                       +  +      + + +   e+ +l e+a+ +++  SgG k  + +a      + +p+ l+ lDe    LD++ ++ + 
  gi|330508139|ref|YP_004384567.1| 125 YGMNA--ALRKARIADVLELVDLKEKADTKMQDYSGGMKRRLEIARG---LMHRPHVLF-LDEPTIGLDAQTRRYIW 195
                                       65554..33344455556777777788888889****9997777755...567787775.8**************** PP

                                       HHHHHHCTTSEEEEE-SSHHHCCC-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 181 ellkeksknaQfivislreemlekad 206
                                       e++ + +k++ + +i  +++ +e+ad
  gi|330508139|ref|YP_004384567.1| 196 EYIGRMNKEMNVTMIL-TTHYMEEAD 220
                                       ****999998876664.444555555 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   4.7e-05     0.083      28      51 ..      55      89 ..      40     250 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.7e-05
                                      EEESTTSSHHHHHHHHHHHCS--...........- CS
                           G-alpha 28 llGqseSGKsTilkqlkllykkg...........f 51
                                      llG+++ GKsTi+k l ++ +++           +
  gi|330508139|ref|YP_004384567.1| 55 LLGANGAGKSTIIKMLTTMLTPTsgearvwgydiV 89
                                      8******************9999444444444431 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   7.7e-05      0.14      88     123 ..      38      74 ..      12      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                        +++++  ++++ ++  l+G  G+GKSt+i++l+  l
  gi|330508139|ref|YP_004384567.1|  38 IAVDNIDLQIRKgELFGLLGANGAGKSTIIKMLTTML 74 
                                       56677777777769999**************998765 PP

>> FdtA  WxcM-like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00024      0.42      77     123 ..     176     225 ..     169     231 .. 0.84
   2 ?   -1.0   0.0      0.72   1.3e+03      62      86 ..     280     305 ..     276     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
                                       EEEE-STTEEEEE..-TT-EEEEE---TT.-EEEEEESS---GGGEE--H CS
                              FdtA  77 eilldspskglyi..pkmiWrelinfsed.avllvlasesydeedYirdy 123
                                        ++ld+p+ gl      +iW+ + +++++  v ++l+ ++ +e+dY+ d 
  gi|330508139|ref|YP_004384567.1| 176 VLFLDEPTIGLDAqtRRYIWEYIGRMNKEmNVTMILTTHYMEEADYLCDR 225
                                       578999999996511579*********9989***************9886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.72
                                       ES-EEEEEE-SS-E.EEEEE-STTEE CS
                              FdtA  62 sGsvevllddgkkk.keilldspskg 86 
                                       +Gs+++++d ++++  e++l+ +++ 
  gi|330508139|ref|YP_004384567.1| 280 NGSIKLHVDHAQSRiAEVVLEASRNN 305
                                       6999*****99998788999887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2501.16
//
Query:       gi|330508140|ref|YP_004384568.1|  [L=261]
Description: ABC transporter [Methanosaeta concilii GP6]
Scores for 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  125.4  23.9    3.1e-36  124.8  23.9    1.3  1  ABC2_membrane    ABC-2 type transporter
    3.8e-15   55.9  30.3    3.8e-15   55.9  30.3    1.4  1  ABC2_membrane_3  ABC-2 family transporter protein
    9.5e-08   31.7  18.3    1.2e-07   31.3  18.3    1.2  1  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.8  23.9   5.2e-40   3.1e-36       2     209 ..      12     225 ..      11     226 .. 0.93

  Alignments for each domain:
  == domain 1  score: 124.8 bits;  conditional E-value: 5.2e-40
                     ABC2_membrane   2 qikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg...nsedglnr.....pgllffsvlflafsalts 70 
                                        i+ ++ re+l+++r +s + + ++++p++++ ++g  f n+g      +g+n+     pg++++++lf a  ++++
  gi|330508140|ref|YP_004384568.1|  12 AIYSIWLREMLRFFRLKSRL-FGSVASPFFFLAFLGIGFNNIGripGIPEGVNYmsfltPGIIGMTLLFSA--TFAG 85 
                                       68899************999.********************886665555555577799************..**** PP

                     ABC2_membrane  71 vapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rf.flflllllltalaa 144
                                       ++++++re g+l++ +vsp+ s+ a+vl+++++ l+ ++lqali++l  ++l g+ +   ++ +l l++++l+a ++
  gi|330508140|ref|YP_004384568.1|  86 LSVLWDREFGFLKEIMVSPV-SRIAIVLGRTAGGLTTGILQALIIMLSGILL-GMGIPsiQGlILSLVFMILIATTF 160
                                       ********************.**************************88887.7766656456************** PP

                     ABC2_membrane 145 sslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                       ++lgl++++ ++++  +s++++++++pl++lsG+++p+d+ p+ ++ +ay+nPlty+v++lr+ l
  gi|330508140|ref|YP_004384568.1| 161 IGLGLAFASKMEDMSGFSLIMNFLIFPLFFLSGALYPLDQFPEIIKILAYFNPLTYGVDGLRYCL 225
                                       *****************************************99*******************975 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9  30.3   6.3e-19   3.8e-15     157     345 .]      62     253 ..      46     253 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 6.3e-19
                   ABC2_membrane_3 157 snvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill..lafgl 231
                                        n+ sfl + i+ + ++++a+f+  s++ ++e + ++ ++vs+vs+++++l++  g ++ ++lq+l+i+l  +++g 
  gi|330508140|ref|YP_004384568.1|  62 VNYMSFLTPGIIGMTLLFSATFAGLSVLWDREFGFLKEIMVSPVSRIAIVLGRTAGGLTTGILQALIIMLsgILLGM 138
                                       5889999997777788899999999***********999******************************98889996 PP

                   ABC2_membrane_3 232 gipfg.nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPff 307
                                       gip   +l+l l++++l + ++i lg+++ s + +++  ++++ ++i++l++++g+l+pl+++p+++k++++++P++
  gi|330508140|ref|YP_004384568.1| 139 GIPSIqGLILSLVFMILIATTFIGLGLAFASKMEDMSGFSLIMNFLIFPLFFLSGALYPLDQFPEIIKILAYFNPLT 215
                                       677778999999999999999999999999999999999999*********************************** PP

                   ABC2_membrane_3 308 apglgllrlitgdplweillsliilalfavvylllall 345
                                       +  +gl   + g + ++ l+++++l + ++++l l+++
  gi|330508140|ref|YP_004384568.1| 216 YGVDGLRYCLIGISAFSPLTDFAVLGVCCAAMLFLGAY 253
                                       ******9999999999999********99999999875 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 !   31.3  18.3     2e-11   1.2e-07      81     286 ..      69     258 ..      11     260 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2e-11
                   ABC2_membrane_2  81 mavlipvi...aalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalg 153
                                       + ++i++     a+f+  ++  ++e g lk  + +PvsR +i+lg   ggl+ g++  ++++l + ll       + 
  gi|330508140|ref|YP_004384568.1|  69 TPGIIGMTllfSATFAGLSVLWDREFGFLKEIMVSPVSRIAIVLGRTAGGLTTGILqALIIMLSGILL-------GM 138
                                       34444444444778888899999******************************999999999999655.......44 PP

                   ABC2_membrane_2 154 ivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqein 230
                                         ++++ l+l +v+ +l+++  +f++lgl+++s + + +   +++ +l++ l ++ +++ly++ + +        i 
  gi|330508140|ref|YP_004384568.1| 139 GIPSIQGLILSLVFMILIAT--TFIGLGLAFASKMEDMSGFSLIMNFLIFPL-FFLSGALYPLDQFPE-------II 205
                                       45677777777777777777..78*********9997777777777776666.888999988554444.......44 PP

                   ABC2_membrane_2 231 dflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkrk 286
                                        +l +++p  +   +l+  l g +    +s  t +++l + +a++l lg++lF++ 
  gi|330508140|ref|YP_004384568.1| 206 KILAYFNPLTYGVDGLRYCLIGIS---AFSPLTDFAVLGVCCAAMLFLGAYLFETT 258
                                       446666666665555666666664...7899**********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1959.37
//
Query:       gi|330508141|ref|YP_004384569.1|  [L=206]
Description: hypothetical protein MCON_2252 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   14.4   0.0      0.078   13.5   0.0    1.4  1  SNase     Staphylococcal nuclease homologue
       0.14   12.0   0.0       0.22   11.4   0.0    1.3  1  DUF3636   Protein of unknown function (DUF3636)


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 ?   13.5   0.0   8.7e-06     0.078       2      79 ..      60     141 ..      59     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.7e-06
                                       EEETTEE-STSSBTTTTTSTTHHHHHHHHHHHHHHCSSEEEEE-S...SBSTTSEEEEEEEET.......TEEHHHH CS
                             SNase   2 vrLvgidaPetakpkktvqpfgkeAkeflkklvlqkkvvvleldk...kkDkygrllayvyln.......kkninee 68 
                                       vrL++i aP t        p gk A++ +  l++ + v ++++++    + + g+++  +yl        +  +n  
  gi|330508141|ref|YP_004384569.1|  60 VRLADIAAPSTV------TPQGKAARKAADLLLKDQIVYIDIDENstlGRNEWGQMVCVIYLIdsryrpiWPPVNRM 130
                                       9*********99......88899999999999997777777777787888999********99999***999***** PP

                                       HHHTTSSEE-- CS
                             SNase  69 LvkeGlArvye 79 
                                       Lv +G A ++e
  gi|330508141|ref|YP_004384569.1| 131 LVDDGHADLAE 141
                                       *******9776 PP

>> DUF3636  Protein of unknown function (DUF3636)
   #    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     109     146 ..       2      39 ..       1      41 [. 0.95

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHHHSHHHHHHHHH-SSHHHHHHHHHH CS
                           DUF3636 109 elrleaLrvLtafarspfgslalashdsaigRlvrvLs 146
                                       +l+l++L++++ + ++ f   ala  d a+gR+v+v+s
  gi|330508141|ref|YP_004384569.1|   2 NLKLAILSIMIIVIFEAFNPGALAVPDEAVGRIVSVIS 39 
                                       799*********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1556.78
//
Query:       gi|330508142|ref|YP_004384570.1|  [L=355]
Description: endonuclease/exonuclease/phosphatase family protein [Methanosaeta concilii GP6]
Scores for complete 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-08   32.1   0.0    6.5e-07   29.1   0.0    2.2  1  Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   3.6e-11   6.5e-07       1     211 [.       8     288 ..       8     302 .. 0.63

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.6e-11
                                       EEEEESTG.....CHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHH.........TTCEEEEECC CS
                                       xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxx RF
                     Exo_endo_phos   1 ltwNvngq.....aspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllal.........ggflgassts 63 
                                       +t+N+++       sp    + r+  l+  l + daD+l+LQE+  +++ +    l +         +         
  gi|330508142|ref|YP_004384570.1|   8 ATFNLMSLddrpdRSPS--LDERIPVLRPQLIRLDADILCLQEICAQHERNGRPRLEAldrllegtpY--------- 73 
                                       69999999777663332..33566667777778899*******9999987765555447777664331......... PP

                                       H.........ECSSSTTSSEEEEEECSTE...............EEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE. CS
                                       x.........xxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                     Exo_endo_phos  64 p.........tgggggggnggavlsrfpl...............tslfrrtfiefndlvaalrreplaakleqlni. 115
                                                 + g++  ++ +++lsrf +                 +++  +                         
  gi|330508142|ref|YP_004384570.1|  74 EsfnrastvdRDGNYLSHHNLVILSRFDImeqhqyqheyapspsYKKVTALP-----------------------Ee 127
                                       0223344677888899999999999999965433333332222222222222.......................23 PP

                                       ..........................................................CCCHHGHHHHHHHHHHHHH CS
                                       ..........................................................xxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos 116 ..........................................................ashrdhdlvrdlqllalll 134
                                                                                                     +   ++ + l    l
  gi|330508142|ref|YP_004384570.1| 128 leareiswerpilhakvrlpngavldvinlhlksrrptniqghklsertwktafgwaeGVFISSMKRIGQALETRIL 204
                                       33333555566667777777779999999999999999999999999999999999666666666666666666667 PP

                                       HHHHHHHHTTSEEEEEEE-SSSTSGGGBSCGHHHHHHCTTTHH.......SSCESCETTTTTTTTTTTEB-BEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos 135 qvealnadrgapvivaGDfNarpsdddsrvlrtrglalapapv.......glyllgggptptyvtraggsrlDrila 204
                                           + ++r+a + v+GDfN   ++ +   +r   + +  +            + +   +++   ++ g  lD+il+
  gi|330508142|ref|YP_004384570.1| 205 IDNLFDDNRCALIAVCGDFNEEFDEVSIEAIRGDVENTGNMDLamrvmvpTERNIPEPARYSLLHNGKGKMLDHILV 281
                                       777888888888999******66666666666444433333313333445555555555555555555555599999 PP

                                       ECHHHCC CS
                                       xxxxxxx RF
                     Exo_endo_phos 205 spalalf 211
                                       s ++  f
  gi|330508142|ref|YP_004384570.1| 282 SRTMLAF 288
                                       9844444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2831.43
//
Query:       gi|330508143|ref|YP_004384571.1|  [L=172]
Description: NUDIX family hydrolase [Methanosaeta concilii GP6]
Scores for complete 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-13   48.7   0.5    1.2e-12   48.0   0.5    1.3  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.5   6.6e-17   1.2e-12      12     130 ..      15     146 ..       2     147 .. 0.67

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 6.6e-17
                                       ETTSEEEEEEES.....SSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEE........EEEEEEEEEEEE CS
                             NUDIX  12 nekgevLlvrrs.....kkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaell........ellgrlhylapy 74 
                                       +++ evLlv+       +k+  g W++ +G  e++E+p +AArRE++EEtG+e+e +        +  g++      
  gi|330508143|ref|YP_004384571.1|  15 DSHLEVLLVHPGgplwaGKDE-GaWSISKGLFEENESPLDAARREFKEETGFEVEGIfielgrikQPSGKIVF---- 86 
                                       333449999977667634444.36***************************9885555544444433332222.... PP

                                       EEEEEE.........EEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHHH CS
                             NUDIX  75 dgpygd.........eheilyvfl.eevegelepndenevsevrwvpleellkeklaaesrkllpw 130
                                                      ++ ++  f  e +      ++ +e++ + w+++e + ++k+++++ +++++
  gi|330508143|ref|YP_004384571.1|  87 -----AwavekdldeRRIVSNNFMlEWPRRSGIMREFPEIDRAGWFDVESA-RKKIHKGQQDFIDR 146
                                       .....12223333323444433333555555566688**************.99999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1365.00
//
Query:       gi|330508144|ref|YP_004384572.1|  [L=234]
Description: hypothetical protein MCON_2254 [Methanosaeta concilii GP6]
Scores for complete 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-87  293.0   0.2    1.9e-87  292.8   0.2    1.0  1  4HFCP_synth  4-HFC-P synthase


Domain annotation for each model (and alignments):
>> 4HFCP_synth  4-HFC-P synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.8   0.2     1e-91   1.9e-87       1     227 [.       3     228 ..       3     229 .. 0.99

  Alignments for each domain:
  == domain 1  score: 292.8 bits;  conditional E-value: 1e-91
                                       EEE--SSHHHHHHHHHHT-SEEEE--GGG-TT----HHHHHHHHHHS-TTSEEEEEEEEE-S-HHHHHHHHHHHHHT CS
                       4HFCP_synth   1 LLvSvrnleEaelalaggadiiDvKnPaeGsLGalfpevireivevvpgsvpvSaaiGdlpekpgtvslaalgaaaa 77 
                                       LLvS++n+eEa++alaggadi+DvKnP+eGsLGa+fp+vir+++++++g+vpvSa+iGd+++kpgt+slaalgaa++
  gi|330508144|ref|YP_004384572.1|   3 LLVSPMNMEEAHAALAGGADILDVKNPKEGSLGANFPWVIRSVADLARGKVPVSATIGDMEFKPGTASLAALGAASS 79 
                                       8**************************************************************************** PP

                                       T-SEEEEEE-S--SHHHHHHHHHHHHHHHHHH-TTSEEEEEEETTGGGTT---GGGHHHHHHHHT-SEEEEE-SS-S CS
                       4HFCP_synth  78 gvdyvKvGlaglkkeeealealkavvkavkeedkekkvvavlyaDaervasvsplellelaaeagaagvmlDTadKd 154
                                       g+dyvK Gl g+k++++a e+lka+v+avk+ d++kkvva++y+D+ rv+s+sp+ l+++a eaga++vm+DTa+Kd
  gi|330508144|ref|YP_004384572.1|  80 GADYVKAGLLGVKTCDQAEEMLKAIVRAVKDLDPKKKVVASGYSDYLRVGSISPMLLPAAASEAGADVVMVDTAIKD 156
                                       ***************************************************************************** PP

                                       S--HHHHS-HHHHHHHHHHHHHTT-EEEE-SS--GGGHHHHHHTT-SEEEESGGGBTTSSTTSSB-HHHHHHH CS
                       4HFCP_synth 155 gkslldflseeelaefveeareaglltaLAGslkledlpaLkklkpdilGvRgavCeegdRngkidaelvekl 227
                                       gk ++df+ e++la+f+e  ++++l++aLAGs+ + +l++L +l+pdi+GvRg+vC +gdR++++++elv k+
  gi|330508144|ref|YP_004384572.1| 157 GKPTFDFMGEKDLADFIELGHSNDLEVALAGSIGFPHLETLLRLQPDIIGVRGIVC-GGDRRSAVKEELVVKV 228
                                       ********************************************************.*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1811.05
//
Query:       gi|330508145|ref|YP_004384573.1|  [L=229]
Description: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase-like protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-21   75.9   0.0    4.8e-21   75.3   0.0    1.3  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 !   75.3   0.0   2.7e-25   4.8e-21       3     228 ..       4     223 ..       2     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 2.7e-25
                                       EEEEEEETTEEEEECTTCS........TCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH CS
                      His_biosynth   3 ipalDlkdGkvVrlvkGdr........fqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaee 71 
                                       i++ D+ +G vV+  +G+r        f++  ++ dp+ +    +e    +++v+Dld ++ gr++n +l++ei ++
  gi|330508145|ref|YP_004384573.1|   4 IFVFDILNGAVVHALRGERsrykpvaeFSQVIESSDPLLI---MDELRPVQVYVADLDMIM-GRGNNMELIQEISKR 76 
                                       8899***************555555554444555555555...45668899******9886.*************** PP

                                       -SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEE CS
                      His_biosynth  72 vfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgld 148
                                         ++ + + G ++ +d++ l  + +   ++gt++++  +li+e++    + + ++++D+ +  +v+ +  + + + +
  gi|330508145|ref|YP_004384573.1|  77 --AKTMADTGASRSSDLDLLPPSVI--PVLGTETAS-ISLIEEVSG---QRRTIASLDMSKR-RVLSRD-KAMADRS 143
                                       ..9************9987777643..467887764.457777776...7899*****9998.666555.5566*** PP

                                       HHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHT CS
                      His_biosynth 149 avelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalye 225
                                       ++e++++l++  ++ +++ + dr Gt++G d e++++ +++ ++p+i +GGv++  dl++l++ g+++++v++a ++
  gi|330508145|ref|YP_004384573.1| 144 PLEVLEELNHIDLEGVIIMELDRIGTCAGLDGEFLEKARARSRHPLILGGGVKDEMDLEALEKVGFSGALVATAVHN 220
                                       ****************************************************************************9 PP

                                       TSS CS
                      His_biosynth 226 gel 228
                                       g +
  gi|330508145|ref|YP_004384573.1| 221 GMI 223
                                       986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1751.51
//
Query:       gi|330508146|ref|YP_004384574.1|  [L=365]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-21   76.0   0.1    4.4e-21   74.6   0.1    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.8e-21   76.6   0.0    3.7e-21   75.6   0.0    1.4  1  OrfB_IS605      Probable transposase
    1.1e-07   31.2   0.7      3e-07   29.8   0.7    1.7  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0065   16.5   0.4      0.011   15.7   0.4    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.043   12.7   0.1      0.064   12.1   0.1    1.1  1  Pestivirus_E2   Pestivirus envelope glycoprotein E2
       0.11   12.1   0.8       0.45   10.1   0.1    2.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.14   11.8   0.9       0.25   11.0   0.9    1.4  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.26   10.7   0.9        1.4    8.4   0.9    2.1  1  zf-ribbon_3     zinc-ribbon domain
       0.41   10.6   2.9       0.34   10.8   0.3    2.0  2  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.44   10.2   5.1        5.7    6.6   0.1    2.8  3  RecR            RecR protein


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 !   74.6   0.1   2.5e-24   4.4e-21       1      68 [.     282     349 ..     282     350 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 2.5e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       +  l +  +yka  +G  v++v+p++TSk Cs+Cg   +++ls+r+++C++Cg++ drD+nAaiNil+
  gi|330508146|ref|YP_004384574.1| 282 WTMLVTLTSYKAASAGSVVVLVDPRNTSKMCSRCGTLIEKSLSDRVHNCTQCGLSRDRDWNAAINILR 349
                                       556667779*********************************************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.0   2.1e-24   3.7e-21       4     117 ..     157     268 ..     154     270 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 2.1e-24
                        OrfB_IS605   4 veveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       ve e+  lp+ k + ++giD+G++ +at ++++   ++ ++r++++++ +la+++++l++  k++  +kka + + r
  gi|330508146|ref|YP_004384574.1| 157 VETEDVpLPPWKDGAVVGIDVGLESFATFSNGE---TIANPRFFREEEHELARAQRKLSKAPKGTPDRKKALKVVER 230
                                       5544334999999********************...***************************************** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       +h++++++r +++h+++++l+++   ++ e+Ln+++m+
  gi|330508146|ref|YP_004384574.1| 231 VHERIANKRYEFAHQVSHNLVDRFGLIAFEDLNIKGMV 268
                                       *************************************7 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.7   1.7e-10     3e-07      15      47 .]       3      35 ..       2      35 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.7e-10
                    HTH_OrfB_IS605 15 eQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                       Q +k++rt   +R+ YN+ La+rk+a+e+egk
  gi|330508146|ref|YP_004384574.1|  3 SQITKMERTPNLCRWTYNQTLAYRKNAWENEGK 35
                                      7*****************************998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.4   6.3e-06     0.011      10      44 ..     307     343 ..     303     346 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.3e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + +++Cs+Cgt +++  +   ++C +Cg + d +++ 
  gi|330508146|ref|YP_004384574.1| 307 NTSKMCSRCGTLIEKSLSdrVHNCTQCGLSRDRDWNA 343
                                       6789********99777799********999998886 PP

>> Pestivirus_E2  Pestivirus envelope glycoprotein E2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.6e-05     0.064     125     184 ..     274     334 ..     247     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
                                       EEESS-CT--EEEEEEEE-SSS--EEEEEEE.EE-S-B---TT---EEEETTEEEEEEE-S CS
                     Pestivirus_E2 125 fqmvcpigwtgtvsctsfnmdtlattvvrty.rrskpfphrqgcitqknlgedlhncilgg 184
                                        + +  ++wt  v+ ts++  +  + vv    r +  +  r g + +k l + +hnc   g
  gi|330508146|ref|YP_004384574.1| 274 AKSISDVAWTMLVTLTSYKAASAGSVVVLVDpRNTSKMCSRCGTLIEKSLSDRVHNCTQCG 334
                                       5668899************99988888776526677899******************8765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00025      0.45      11      31 ..     301     321 ..     297     326 .. 0.84
   2 ?   -0.4   0.1      0.46   8.2e+02      22      27 ..     330     335 ..     328     338 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                                       CHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon  11 lveDpergelvCtdCGlVled 31 
                                       +++Dp ++   C++CG+++e 
  gi|330508146|ref|YP_004384574.1| 301 VLVDPRNTSKMCSRCGTLIEK 321
                                       68999*9999*********96 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.46
                                       ESSSSB CS
                      TF_Zn_Ribbon  22 CtdCGl 27 
                                       Ct CGl
  gi|330508146|ref|YP_004384574.1| 330 CTQCGL 335
                                       9***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 ?   11.0   0.9   0.00014      0.25       6      29 ..     312     335 ..     307     336 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                     zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCgl 29 
                                       C+rCG+  e++  ++   C +Cgl
  gi|330508146|ref|YP_004384574.1| 312 CSRCGTLIEKSLSDRVHNCTQCGL 335
                                       **********************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 ?    8.4   0.9    0.0008       1.4       5      24 ..     312     335 ..     309     336 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0008
                       zf-ribbon_3   5 CPnCGa.p...lssddnvCpyCGt 24 
                                       C++CG+ +   ls+++ +C+ CG 
  gi|330508146|ref|YP_004384574.1| 312 CSRCGTlIeksLSDRVHNCTQCGL 335
                                       9999975555578999******95 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       0.9   1.6e+03      37      45 ..     267     275 ..     265     278 .. 0.82
   2 ?   10.8   0.3   0.00019      0.34      10      37 ..     308     336 ..     304     340 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.9
                                       EE-CCCCTT CS
                              C1_1  37 lvHkkChek 45 
                                        vH++C+ k
  gi|330508146|ref|YP_004384574.1| 267 MVHNHCLAK 275
                                       59****876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00019
                                       S--B-TTT-SB--S.SSS-EEEETTT--E CS
                              C1_1  10 qptfCkhCgeflwg.kekqglkCswCkll 37 
                                        ++ C+ Cg ++++ ++ +   C++C+l+
  gi|330508146|ref|YP_004384574.1| 308 TSKMCSRCGTLIEKsLSDRVHNCTQCGLS 336
                                       5789********999***********975 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.8     5e+03       6      16 ..      61      71 ..      61      72 .. 0.87
   2 ?    6.6   0.1    0.0032       5.7      13      28 ..     306     321 ..     301     323 .. 0.77
   3 ?    5.7   0.4    0.0063        11      12      28 ..     323     339 ..     321     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.8
                                      HHHHHHHHHH- CS
                              RecR  6 aeaLqeakekv 16
                                      a++Lq++ e+v
  gi|330508146|ref|YP_004384574.1| 61 AQTLQNVQERV 71
                                      7899**99987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0032
                                       HHH-EE-TTT--EESS CS
                              RecR  13 kekvrhCsrCgnltee 28 
                                       +++ + CsrCg+l e+
  gi|330508146|ref|YP_004384574.1| 306 RNTSKMCSRCGTLIEK 321
                                       667799******9776 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0063
                                       HHHH-EE-TTT--EESS CS
                              RecR  12 akekvrhCsrCgnltee 28 
                                       + ++v+ C +Cg   ++
  gi|330508146|ref|YP_004384574.1| 323 LSDRVHNCTQCGLSRDR 339
                                       679********976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2763.40
//
Query:       gi|330508147|ref|YP_004384575.1|  [L=417]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete 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   88.4   0.1    5.4e-25   87.5   0.1    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family
    3.9e-20   72.3   0.0      7e-20   71.5   0.0    1.4  1  DEDD_Tnp_IS110  Transposase
  ------ inclusion threshold ------
      0.041   14.2   1.2      0.081   13.2   0.1    2.0  2  Init_tRNA_PT    Rit1 DUSP-like domain


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.1     9e-29   5.4e-25       2      83 ..     249     330 ..     248     336 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 9e-29
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaaira 78 
                                       +++ s+pG+G++ aa+++ae+gd r f+sa+++a+y+G++p+++qS++k r g+i+k G++++Rr+L+e A a++r+
  gi|330508147|ref|YP_004384575.1| 249 KIILSVPGVGFISAATIIAEMGDYRDFPSADKMAKYFGIVPSVYQSAGKLRTGKITKTGSKHMRRILVEVAKAISRT 325
                                       6899***********************************************************************99 PP

                    Transposase_20  79 npelr 83 
                                       ++ +r
  gi|330508147|ref|YP_004384575.1| 326 KKNSR 330
                                       75554 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   1.2e-23     7e-20       1     153 [.       9     152 ..       9     154 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1.2e-23
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G D++ d   a++i+++g +l +er++++++gl a+ ++   ++++ + +ve+tg ++++++++ le +++ ++ n
  gi|330508147|ref|YP_004384575.1|   9 CGADIHRDFLIATMISRSGLKL-QERFNMNQDGLLAFRSW-IINHRCQRLAVESTGGFWYPIFTI-LEGHVEFILAN 82 
                                       799************9999885.678**************.889****************88876.7899******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdqv 153
                                       ++++++++     ++KtD++D++ IA + +  + ++p++  +++y++Lr++tr+re+lv+ r++ kn++++ L   
  gi|330508147|ref|YP_004384575.1|  83 AYQIRNIE-----HKKTDKLDSERIAIYCL-NNLITPSRIYPKDYRDLRSITRARETLVNARSKIKNQIHQSLSAC 152
                                       *****995.....89***************.****************************************99765 PP

>> Init_tRNA_PT  Rit1 DUSP-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.2     7e+03      17      44 ..     124     153 ..     119     160 .. 0.50
   2 ?   13.2   0.1   1.4e-05     0.081      10      80 ..     304     378 ..     296     389 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                      Init_tRNA_PT  17 Lrtalpkivdfvrkrlsedkk..kkilvac 44 
                                       Lr++ +  ++ v++r++ +++  +++ ++c
  gi|330508147|ref|YP_004384575.1| 124 LRSITRARETLVNARSKIKNQihQSLSACC 153
                                       555544444444444433332334455554 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.4e-05
                      Init_tRNA_PT  10 gKkgsknLrtalpkivdfvrkrlsedkk....kkilvacetGkdlsvgvaLailcklfddakls...eeqsesnitK 79 
                                        K+gsk++r +l ++ ++++++ ++++     ++il+ c + +   v++a  +lc ++   +l    e+ +e+++tK
  gi|330508147|ref|YP_004384575.1| 304 TKTGSKHMRRILVEVAKAISRTKKNSRLmrffQRILARCGKKNIATVALARKVLCIIY---HLLmnhENYQEPEVTK 377
                                       49*****************99966655599**99******999999999888888888...2222235666777777 PP

                      Init_tRNA_PT  80 d 80 
                                       +
  gi|330508147|ref|YP_004384575.1| 378 T 378
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3051.67
//
Query:       gi|330508148|ref|YP_004384576.1|  [L=45]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       159  (0.00886831); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 351.33
//
Query:       gi|330508149|ref|YP_004384577.1|  [L=320]
Description: putative methanogenesis marker protein 2 [Methanosaeta concilii GP6]
Scores for complete 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-19   68.1   0.0    1.6e-18   67.3   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain
    2.6e-15   56.9   0.0    4.8e-15   56.0   0.0    1.5  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.0   1.8e-22   1.6e-18      46     153 ..     195     299 ..     160     301 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 1.8e-22
                                       HHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHG CS
                            AIRS_C  46 tliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdelesplemllsensGrllvavppe 122
                                        ++ ++r+l ++ glv+a +D+++ GLlg+la++++ s+vga++d+d++ + +   + l  +l  + G ++v+  ++
  gi|330508149|ref|YP_004384577.1| 195 QQLGAMRELGES-GLVRAGKDISNPGLLGTLAMLMETSKVGAVVDVDAIVVPEG--LTLAGWLQMYPGMGFVVTTRP 268
                                       478899999997.**********************************5555555..69**********999998888 PP

                                       GH.HHHHHHHHHTTCCCEEEEEEEEESSSEEE CS
                            AIRS_C 123 ea.davlaileeeglpeaavIGevtakeelsv 153
                                       e+ ++vl++++++gl +a+vIG+vt++++l +
  gi|330508149|ref|YP_004384577.1| 269 ENqEKVLEVFTRRGL-TARVIGRVTDERRLII 299
                                       887************.7*********998755 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 !   56.0   0.0   5.4e-19   4.8e-15       1      92 [.      42     145 ..      42     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 5.4e-19
                                       SSSEE........EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC...HHHHHHHHHHHHH CS
                              AIRS   1 dDaav........vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp...wleevvrglaeaa 66 
                                       +Daav        ++++d+  ++++ ++ +  G+ +v vn+ D+aamG+ P+a++++l+ +   + ++v++g+++++
  gi|330508149|ref|YP_004384577.1|  42 EDAAViddgdevmLFAADGIWSKLMDADPEWSGYCSVLVNVHDIAAMGGWPVAMVDVLSAGdpeISRRVLEGMKKGI 118
                                       689955555555699**********9998999*******************************999*********** PP

                                       HHTT-EEEEEEEEEESS.EEEEEEEEE CS
                              AIRS  67 eelgvplvgGdtsfsne.ptisvtavG 92 
                                       e+l vp++gG+++ ++    + v+++G
  gi|330508149|ref|YP_004384577.1| 119 EKLRVPIIGGHLHPDTPySALDVAILG 145
                                       ************998654566777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2427.32
//
Query:       gi|330508150|ref|YP_004384578.1|  [L=153]
Description: hypothetical protein MCON_2263 [Methanosaeta concilii GP6]
Scores for complete 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   0.4    7.2e-19   68.2   0.4    1.1  1  DUF296    Plants and Prokaryotes Conserved (PCC) domain
  ------ inclusion threshold ------
       0.16   12.3   0.0       0.29   11.5   0.0    1.4  2  SepA      Multidrug Resistance efflux pump


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 !   68.2   0.4     8e-23   7.2e-19       4     105 ..      24     132 ..      21     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 8e-23
                                       EEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE.EEECTTT......EE-S-EEEEEEEEEEEE..TT..E CS
                            DUF296   4 vlrlepGediveaieefarkrgiraacvlsaiGavsnvt.rladgee......kllgrfeilslsGtilp..dg..l 69 
                                       +++le+G +i+ +i++++r+++ira+++ ++iGa+++++ +++d+ +      ++++++e+ s+sG+i+   ++  +
  gi|330508150|ref|YP_004384578.1|  24 LATLEHGAEIIGQITRVIRENDIRAGHL-NVIGALDQAEiGYYDQVShsyqgiQINEPVELASCSGNISLlaGQpyA 99 
                                       6789***********************9.**************9999999999899**************953389* PP

                                       EEEEEEEETTSEEEEEEEEEE.EEEEEEEEEEEEE- CS
                            DUF296  70 HlhvslagedgqvvgGhlaegplvaattvevvvaef 105
                                       H+h++l+g +g+v++Ghl +g  +  + +e++v+e+
  gi|330508150|ref|YP_004384578.1| 100 HVHAVLSGMKGKVWAGHLTSG-RI--FAAELYVQEL 132
                                       ********99*********99.55..6777777776 PP

>> SepA  Multidrug Resistance efflux pump
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.3e-05      0.29      71     126 ..      33      88 ..      16     101 .. 0.88
   2 ?   -3.5   0.0       1.4   1.2e+04     123     137 ..     122     136 ..     118     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.3e-05
                              SepA  71 imdelkrilpenkffhgwyfhiisvsistivfyfgvhinyqhirinffvvlaiisa 126
                                       i+ ++ r++ en +  g+   i ++  + i +y  v   yq i+in  v la  s 
  gi|330508150|ref|YP_004384578.1|  33 IIGQITRVIRENDIRAGHLNVIGALDQAEIGYYDQVSHSYQGIQINEPVELASCSG 88 
                                       788999************99999***********************9999997764 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.4
                              SepA 123 iisalyyltelfypd 137
                                       i +a  y+ el+ pd
  gi|330508150|ref|YP_004384578.1| 122 IFAAELYVQELVGPD 136
                                       567778888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1171.54
//
Query:       gi|330508151|ref|YP_004384579.1|  [L=1136]
Description: DNA polymerase II, large subunit DP2 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
          0 1248.8   0.0          0 1246.5   0.0    1.8  2  PolC_DP2        DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
      0.038   13.3   2.9      0.072   12.4   2.9    1.3  1  NOA36           NOA36 protein
      0.042   13.9  21.2      0.089   12.8   0.6    3.0  2  DZR             Double zinc ribbon
      0.058   13.4   0.1      0.058   13.4   0.1    3.1  2  HypA            Hydrogenase/urease nickel incorporation, meta
        1.8    8.1  28.3       0.34   10.4   3.5    5.2  5  zf-ribbon_3     zinc-ribbon domain
        2.5    8.2   5.7         51    3.9   0.0    4.2  4  CpXC            CpXC protein
        3.2    7.8  16.2        4.2    7.4   0.1    2.8  2  zinc-ribbons_6  zinc-ribbons
        5.9    6.8  14.1       0.97    9.3   0.2    3.9  3  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger


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 ! 1246.5   0.0         0         0       1     864 []       5     886 ..       5     886 .. 0.98
   2 ?   -0.2   0.1     0.076   1.7e+02     617     654 ..    1051    1092 ..    1018    1130 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1246.5 bits;  conditional E-value: 0
                          PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirele.kelsreevalkiakei 76 
                                       +Yf+ l+++l++a++ia+ ar++g dp+++vEiplA dla+Rvekl+gi+g+aerir+ e + lsree+al+i+ ++
  gi|330508151|ref|YP_004384579.1|   5 DYFQLLQDGLDDAMAIAKMARRRGRDPTTDVEIPLAVDLAERVEKLIGIQGIAERIRHHEaEGLSREEAALAIGIDF 81 
                                       6***********************************************************7789************* PP

                          PolC_DP2  77 aegkvgeaeskeeavdkavrtalalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaD 153
                                       aeg++g+ +sk e+v++a+rt++alltegvvaAP+eGia+v+++knddgteylkvyyaGPiRsaGGtaqalsvLvaD
  gi|330508151|ref|YP_004384579.1|  82 AEGRLGAGASKIESVESAIRTSVALLTEGVVAAPMEGIARVDLGKNDDGTEYLKVYYAGPIRSAGGTAQALSVLVAD 158
                                       ***************************************************************************** PP

                          PolC_DP2 154 yvrkklgldrykpreeeieRyveEielYervaslqyspsdeeirlivknipveidGeatedeevsgyrdlervetnr 230
                                       yvr+++g++ +kpr ee+eRyveEi lY+rva+lqyspsd+eir+iv+n+p++idGe+te+eevsgyrdl+r+etnr
  gi|330508151|ref|YP_004384579.1| 159 YVRRSVGIAPWKPRPEEVERYVEEIGLYKRVAGLQYSPSDDEIRTIVRNCPICIDGEPTEEEEVSGYRDLDRIETNR 235
                                       ***************************************************************************** PP

                          PolC_DP2 231 vRGGmllvlaeGialkakKikkkvkklklegWewleelikaekeekkeeeeekkevkpkekylrdliaGRpvlshps 307
                                       vRGG++lv aeGialk +K+kk+v+kl+++gWewl++l+++    kk+  ++      + k+lrdliaGRpv+shps
  gi|330508151|ref|YP_004384579.1| 236 VRGGIALVSAEGIALKRPKLKKHVSKLGISGWEWLDSLASG----KKDGGDS------TPKFLRDLIAGRPVFSHPS 302
                                       ***************************************99....4444443......479**************** PP

                          PolC_DP2 308 rkGGfRLrYGRsrntglatagihPatmelldeflavGtqlkverPgKaaavvpvdsiegPtvklknGdvvriddvee 384
                                       r+GGfRLrYGR+rntgla+agi+Pa+m ll ef+a+Gtq+kve+PgKaaav+pv+siegPtv+l nGdvvr d+ ++
  gi|330508151|ref|YP_004384579.1| 303 RPGGFRLRYGRARNTGLAAAGINPASMLLLGEFMAAGTQIKVEQPGKAAAVAPVSSIEGPTVRLLNGDVVRFDSDQD 379
                                       ****************************************************************************9 PP

                          PolC_DP2 385 al...............eikkeveeildlGeiLvayGeflennhpLvpasyveewwiqelekaaakkeaeekpsaee 446
                                       +l               ++k +v++ildlGeiL++yGeflenn+pL+pasy++eww++el ka+ + + +e+++ ee
  gi|330508151|ref|YP_004384579.1| 380 ILewmpisckdpktiqiALKAHVSRILDLGEILISYGEFLENNRPLAPASYAFEWWAAELLKAGGDPSGKESMDGEE 456
                                       9999***********999*********************************************************** PP

                          PolC_DP2 447 alelseeldvpLhPkytylwhdisveelekLaeavaekkkleeeklvleleeevkeiLekllvehkvkeekivieea 523
                                       a++ls+e++vpLhP++t+lwhd+s e+++ L+e+ a+k++le+++l+l+l  e+ke Le+llv hkv++++i+ie+ 
  gi|330508151|ref|YP_004384579.1| 457 AIALSREYSVPLHPAHTHLWHDLSIEDYDLLREVAASKGILESGRLILPL--EAKESLETLLVLHKVRDGRIIIEDP 531
                                       ***************************************9999******9..678********************** PP

                          PolC_DP2 524 lallkslgldleeeklekeeek.............dalelvnelsglevrekaptrigaRmGRPeKskeRkmkpavh 587
                                       l++l +lg+d+e  +l+++ e+             + l+ vn+++g+ vr++aptrigaRmGRPeKs++R m+p++h
  gi|330508151|ref|YP_004384579.1| 532 LPFLLCLGIDWEGGSLKRRAEEaggepggvdqaedSILARVNRFTGIVVRARAPTRIGARMGRPEKSDKRLMRPPPH 608
                                       ************9999777444678888999999899**************************************** PP

                          PolC_DP2 588 vLfpigeaggkrrsvkeaakk.....kgeieveiarrkCkkCgketlearCeeCgekteeklvCkkceeeveeekce 659
                                       vLfp ge+ggk rs++eaak+     +g i+v+i+rr Ck+Cgke++ ++Ce Cg++te+k vC+kc+  +  ekc+
  gi|330508151|ref|YP_004384579.1| 609 VLFPAGEEGGKGRSIQEAAKHstnssSGIINVQIERRVCKSCGKEGFAFNCE-CGSHTEKKRVCPKCNIPA-PEKCP 683
                                       ********************6678888899**********************.***************988.678** PP

                          PolC_DP2 660 kcekeakavkkkkidlkellekaleklgereekleelkgvkgltskekipEpleKgilRakhdvsvfkdgtvRyDmt 736
                                       kc++e++av++++id+k+l+ +ale+lge  +++e+lkgv gl+s++k+pEpleKgilRakh++ +fkdgtvRyD+t
  gi|330508151|ref|YP_004384579.1| 684 KCGQETNAVADMQIDVKKLYFQALESLGE--REPESLKGVLGLFSRDKTPEPLEKGILRAKHGINIFKDGTVRYDLT 758
                                       *****************************..56******************************************** PP

                          PolC_DP2 737 dlplthfrpkeigvsveklrelGYteDieGkplesedqivelkvqDivlsedaaeyllkvakfvDdlLeklyglerf 813
                                       dlplthfrp+eig+s e l++lGY  D++G+pl+++dq++el++qDivls+da+eyllkv+ fvD+lL+k+y+le+f
  gi|330508151|ref|YP_004384579.1| 759 DLPLTHFRPDEIGTSPEVLQSLGYGVDMHGDPLTRPDQVCELRIQDIVLSRDAGEYLLKVSWFVDELLAKFYHLEPF 835
                                       ***************************************************************************** PP

                          PolC_DP2 814 YnvekkedLiGklviglaPHtsagvlgRiiGftkasvgyahPyfHaakRRn 864
                                       Yn+++ +dLiGkl++glaPHtsagvl+R+iG++ as+g++hP+fHaakRRn
  gi|330508151|ref|YP_004384579.1| 836 YNAQTPQDLIGKLMVGLAPHTSAGVLCRLIGYSPASAGFGHPFFHAAKRRN 886
                                       **************************************************9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.076
                          PolC_DP2  617 arrkCkkCgke....tlearCeeCgekteeklvCkkceeeve 654 
                                        ++ +C kCg++     l+ +C++Cg ++  +++  ++++  e
  gi|330508151|ref|YP_004384579.1| 1051 QKVRCVKCGAKyrrpPLKETCPKCGGRMILTVHEGSVRKYLE 1092
                                        566788887652222467788888888777555555544333 PP

>> NOA36  NOA36 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.9   3.2e-05     0.072     170     237 ..     642     706 ..     625     720 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                             NOA36 170 aetfkcvscnrlgqysclrckacycedhvrrkgfkyeknkaip..cpkcgyetqetkdlslstrslkfgr 237
                                        e   c+sc + g         c c  h+ +k    + n + p  cpkcg et+   d+ + +++l f  
  gi|330508151|ref|YP_004384579.1| 642 IERRVCKSCGKEGFA-----FNCECGSHTEKKRVCPKCNIPAPekCPKCGQETNAVADMQIDVKKLYFQA 706
                                       456668888777753.....3578999999888766666555444****************999988865 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8  14.3     0.027        59       1      38 [.     647     689 ..     639     694 .. 0.82
   2 ?   12.8   0.6     4e-05     0.089      10      37 ..    1050    1077 ..    1045    1082 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.027
                               DZR   1 CpqCgee..........lppdarfCseCgtklkavaaedrCpsCgekv 38 
                                       C++Cg+e          +++++r+C++C+ + +     ++Cp+Cg+++
  gi|330508151|ref|YP_004384579.1| 647 CKSCGKEgfafncecgsHTEKKRVCPKCNIPAP-----EKCPKCGQET 689
                                       888888888888888878888889999998885.....8999998875 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4e-05
                               DZR   10 pdarfCseCgtklkavaaedrCpsCgek 37  
                                        +++  C +Cg+k ++++ +++Cp+Cg  
  gi|330508151|ref|YP_004384579.1| 1050 KQKVRCVKCGAKYRRPPLKETCPKCGGR 1077
                                        5666799999999998899999999865 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 ?   -1.0  10.1      0.78   1.8e+03      71     108 ..     657     700 ..     624     703 .. 0.62
   2 ?   13.4   0.1   2.6e-05     0.058      68      98 ..    1050    1080 ..    1011    1092 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.78
                                       EEETTTS-EEECHHHHH...............S-TTTSSS-EEEEESSSEEEE CS
                              HypA  71 vrCreCgkefeleekal...............rCpkCgsadveivsGeellvk 108
                                       + C eCg++       +               +CpkCg++ ++ v+  ++ vk
  gi|330508151|ref|YP_004384579.1| 657 FNC-ECGSH-------TekkrvcpkcnipapeKCPKCGQE-TNAVADMQIDVK 700
                                       334.24444.......044444556677777799999995.455555555555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.6e-05
                                        --EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA   68 pvkvrCreCgkefeleekalrCpkCgsadve 98  
                                        + kvrC +Cg++++    +++CpkCg++ + 
  gi|330508151|ref|YP_004384579.1| 1050 KQKVRCVKCGAKYRRPPLKETCPKCGGRMIL 1080
                                        6789*********97754689*****98653 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.6      0.68   1.5e+03      17      22 ..     206     211 ..     204     211 .. 0.63
   2 ?    3.3   0.0     0.026        59      13      24 ..     641     652 ..     638     653 .. 0.78
   3 ?    5.3   1.3    0.0062        14       7      22 ..     660     674 ..     660     677 .. 0.90
   4 ?    4.5   0.4     0.011        24      18      24 ..     681     687 ..     680     689 .. 0.55
   5 ?   10.4   3.5   0.00015      0.34       1      25 [.    1051    1077 ..    1051    1078 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.68
                       zf-ribbon_3  17 nvCpyC 22 
                                       ++Cp C
  gi|330508151|ref|YP_004384579.1| 206 RNCPIC 211
                                       466666 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.026
                       zf-ribbon_3  13 ssddnvCpyCGt 24 
                                       + + +vC++CG+
  gi|330508151|ref|YP_004384579.1| 641 QIERRVCKSCGK 652
                                       566689*****7 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0062
                       zf-ribbon_3   7 nCGaplssddnvCpyC 22 
                                       +CG++ ++  +vCp+C
  gi|330508151|ref|YP_004384579.1| 660 ECGSH-TEKKRVCPKC 674
                                       5****.********** PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.011
                       zf-ribbon_3  18 vCpyCGt 24 
                                       +Cp+CG+
  gi|330508151|ref|YP_004384579.1| 681 KCPKCGQ 687
                                       4555554 PP

  == domain 5  score: 10.4 bits;  conditional E-value: 0.00015
                       zf-ribbon_3    1 stvrCPnCGa.p.lssddnvCpyCGtk 25  
                                        ++vrC +CGa     +   +Cp+CG++
  gi|330508151|ref|YP_004384579.1| 1051 QKVRCVKCGAkYrRPPLKETCPKCGGR 1077
                                        589*******768899*********97 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   1.3      0.55   1.2e+03      28      47 ..     635     654 ..     626     675 .. 0.69
   2 ?    3.9   0.0     0.023        51       3      20 ..     682     699 ..     680     719 .. 0.66
   3 ?    1.0   0.0      0.19   4.2e+02      16      47 ..    1031    1062 ..    1023    1065 .. 0.83
   4 ?    1.3   0.0      0.15   3.5e+02      39      50 ..    1070    1081 ..    1067    1107 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.55
                              CpXC  28 eklldgslfeatCpkCgata 47 
                                         +++ ++ + +C +Cg+++
  gi|330508151|ref|YP_004384579.1| 635 SGIINVQIERRVCKSCGKEG 654
                                       56888889999999999875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.023
                              CpXC   3 CpaCgkefeaeiwtsida 20 
                                       Cp+Cg+e++a +   id+
  gi|330508151|ref|YP_004384579.1| 682 CPKCGQETNAVADMQIDV 699
                                       555555555544444444 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.19
                              CpXC   16 tsidadedpelkeklldgslfeatCpkCgata 47  
                                        ++i+    p+l  +l + s ++++C kCga+ 
  gi|330508151|ref|YP_004384579.1| 1031 RVINSHFLPDLIGNLHAFSKQKVRCVKCGAKY 1062
                                        5677777888888888889999*******975 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.15
                              CpXC   39 tCpkCgatakle 50  
                                        tCpkCg +  l+
  gi|330508151|ref|YP_004384579.1| 1070 TCPKCGGRMILT 1081
                                        899999877665 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5  11.7      0.14   3.1e+02       3      47 ..     647     687 ..     642     694 .. 0.81
   2 ?    7.4   0.1    0.0019       4.2      14      39 ..    1050    1078 ..    1040    1088 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.14
                                       -SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S--.-EEEETTE CS
                    zinc-ribbons_6   3 CpeCqqelekrgeqyhCeaCqedlkkealCpeCeqel.evlkaCga 47 
                                       C++C +e    g  ++Ce C ++ +k+ +Cp+C+ +  e++ +Cg 
  gi|330508151|ref|YP_004384579.1| 647 CKSCGKE----GFAFNCE-CGSHTEKKRVCPKCNIPApEKCPKCGQ 687
                                       5566554....5678896.999************987589999997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0019
                                        SSEEE-TTT--EEEE...EEE-SSS-S-- CS
                    zinc-ribbons_6   14 geqyhCeaCqedlkk...ealCpeCeqel 39  
                                        +++++C +C +++++   + +Cp+C+ ++
  gi|330508151|ref|YP_004384579.1| 1050 KQKVRCVKCGAKYRRpplKETCPKCGGRM 1078
                                        5789*******9986333678****9765 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 ?    0.3   0.7      0.27   6.1e+02       2       8 ..     669     675 ..     668     677 .. 0.84
   2 ?    3.0   2.1     0.039        88       2       9 ..     680     687 ..     679     689 .. 0.85
   3 ?    9.3   0.2   0.00043      0.97       2      13 ..    1069    1080 ..    1068    1082 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.27
                                       EE-SSS- CS
                    zf-C4_Topoisom   2 ekCPkCg 8  
                                       + CPkC+
  gi|330508151|ref|YP_004384579.1| 669 RVCPKCN 675
                                       68****8 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.039
                                       EE-SSS-- CS
                    zf-C4_Topoisom   2 ekCPkCgg 9  
                                       ekCPkCg+
  gi|330508151|ref|YP_004384579.1| 680 EKCPKCGQ 687
                                       79*****6 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00043
                                        EE-SSS--EEEE CS
                    zf-C4_Topoisom    2 ekCPkCggdLvl 13  
                                        e+CPkCgg ++l
  gi|330508151|ref|YP_004384579.1| 1069 ETCPKCGGRMIL 1080
                                        89*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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):               8  [number of targets reported over threshold]
# CPU time: 0.82u 0.30s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 7025.90
//
Query:       gi|330508152|ref|YP_004384580.1|  [L=134]
Description: hypothetical protein MCON_2265 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-16   59.3   0.1    4.1e-16   58.8   0.1    1.2  1  Polbeta   Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.1   2.3e-20   4.1e-16       4      93 .]      11     103 ..       8     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 2.3e-20
                                       TTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH......SSSEEEEEETTTS-HH CS
                           Polbeta   4 keilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaeledi.....klgkkvDlvdlneappl 75 
                                         il   +ei+lay+FGS++k +  +  DiDla+ l ++++ +e+++++ ++++      +++ ++D+ +ln ap +
  gi|330508152|ref|YP_004384580.1|  11 GFILDGFDEIDLAYVFGSFLKRDDFH--DIDLAIHLCREKSPYERFKFSGKVARDleegvEPRMEFDVRILNYAPVY 85 
                                       55788889************999986..******9988856666555555555544555999*************** PP

                                       HHHHHHHS-EEEES-SHH CS
                           Polbeta  76 llyeilkegkllyskdee 93 
                                       ++ye++++g++++++d+e
  gi|330508152|ref|YP_004384580.1|  86 FQYEVISNGIVVLERDQE 103
                                       ***************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 984.27
//
Query:       gi|330508153|ref|YP_004384581.1|  [L=171]
Description: hypothetical protein MCON_2266 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   0.6       0.67   10.3   0.1    2.2  2  SSV1_ORF_D-335  ORF D-335-like protein


Domain annotation for each model (and alignments):
>> SSV1_ORF_D-335  ORF D-335-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   3.7e-05      0.67       8      21 ..      24      37 ..      21      73 .. 0.83
   2 ?   -0.1   0.0     0.064   1.1e+03      16      30 ..     141     153 ..     117     163 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3.7e-05
                    SSV1_ORF_D-335  8 iiRerkgkYYVYkl 21
                                       i++r+ kYYVY  
  gi|330508153|ref|YP_004384581.1| 24 EIKQRGTKYYVYHS 37
                                      699*********75 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.064
                    SSV1_ORF_D-335  16 YYVYklEkenGevke 30 
                                       Y  Y +E +n + k 
  gi|330508153|ref|YP_004384581.1| 141 Y--YNIESINPNLKP 153
                                       4..689999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1242.67
//
Query:       gi|330508154|ref|YP_004384582.1|  [L=109]
Description: IS3/IS66 family element, Orf1 protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.9e-11   41.8   0.1    1.6e-10   41.1   0.0    1.5  1  HTH_Tnp_1  Transposase
      0.002   17.8   0.0     0.0044   16.8   0.0    1.6  1  HTH_23     Homeodomain-like domain
     0.0046   17.0   0.0     0.0099   16.0   0.0    1.6  1  HTH_28     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.033   14.1   0.3      0.074   12.9   0.3    1.6  1  PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein k
      0.062   13.8   0.1       0.13   12.7   0.0    1.5  2  DUF4733    Domain of unknown function (DUF4733)


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   4.4e-14   1.6e-10       2      74 ..       3      75 ..       2      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 4.4e-14
                         HTH_Tnp_1  2 rrrrrwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyr...egeeaspaefeltaleeenrelkrel 74
                                      ++rrr+++ fK+++++e  e+gk+ +++Ar++g++p+   +W+++     e  +a   +    + +++++el+r+l
  gi|330508154|ref|YP_004384582.1|  3 KTRRRYDRDFKISVLAEL-EAGKPLAQIAREYGIHPSLPCRWKAELAenpE--KAFMGNGNKYKDQAKIAELERLL 75
                                      79***************9.*************************9975332..33333333344466777777765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.2e-06    0.0044       8      40 ..      14      46 ..       2      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                      +++l  l  G++ ++IAre+g++++  +rw+  
  gi|330508154|ref|YP_004384582.1| 14 ISVLAELEAGKPLAQIAREYGIHPSLPCRWKAE 46
                                      567888888***************987777765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.8e-06    0.0099       1      27 [.      12      38 ..      12      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
                            HTH_28  1 qRleiikllaaGhsvreaArelgisrr 27
                                      +++ ++ +l aG++ +++Are+gi+++
  gi|330508154|ref|YP_004384582.1| 12 FKISVLAELEAGKPLAQIAREYGIHPS 38
                                      7999********************997 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.1e-05     0.074       9      28 ..      67      86 ..      61      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                         PKcGMP_CC  9 RIRELEkrlaekdeEIqELr 28
                                      +I+ELE+ l + ++EI  L+
  gi|330508154|ref|YP_004384582.1| 67 KIAELERLLGQAHAEIDLLK 86
                                      9***************9888 PP

>> DUF4733  Domain of unknown function (DUF4733)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.7e-05      0.13      29      67 ..       4      42 ..       1      51 [. 0.88
   2 ?   -2.0   0.0       1.4     5e+03      32      32 ..      91      91 ..      64     106 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                           DUF4733 29 qplrpqravleelsaplelsqplsgllddyGilPkhPrp 67
                                        +r+ r +   + a le  +pl+++  +yGi+P  P +
  gi|330508154|ref|YP_004384582.1|  4 TRRRYDRDFKISVLAELEAGKPLAQIAREYGIHPSLPCR 42
                                      56899999999***********************99976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                           DUF4733 32 r 32
                                       
  gi|330508154|ref|YP_004384582.1| 91 M 91
                                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 873.23
//
Query:       gi|330508155|ref|YP_004384583.1|  [L=292]
Description: transposase IS3 family protein integrase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-25   89.8   0.0    2.2e-25   89.1   0.0    1.3  1  rve            Integrase core domain
    2.7e-19   69.1   0.3    1.9e-18   66.3   0.3    2.1  2  HTH_21         HTH-like domain
    3.8e-16   58.6   0.1    9.1e-16   57.4   0.1    1.7  1  rve_3          Integrase core domain
    4.7e-08   33.1   3.6    9.4e-08   32.1   2.4    2.1  2  rve_2          Integrase core domain
    0.00016   21.9   0.3    0.00028   21.1   0.3    1.4  1  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.027   14.6   0.1         12    6.1   0.0    2.4  2  GP3_package    DNA-packaging protein gp3
      0.041   14.1   0.0       0.11   12.7   0.0    1.7  1  HTH_Tnp_Tc3_2  Transposase
      0.049   13.8   0.1       0.17   12.0   0.0    1.9  2  HTH_Tnp_1_2    Helix-turn-helix of insertion element transpos


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.0   9.9e-29   2.2e-25       5     117 ..     127     239 ..     124     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 9.9e-29
                               rve   5 gelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve..pervlsDngseyt 79 
                                       ++ w +D+t+v++      ++l+v++d +sr ++++ ls+++ ++++  +l +a++++ ++    ++++sD+g +y+
  gi|330508155|ref|YP_004384583.1| 127 NQAWASDITYVQLQHE--HIFLAVILDLYSRKCIGWELSRSIRSDLAMSALAKALKNRSKESleGLIHHSDQGVQYA 201
                                       899*********6655..5*****************************************8899************* PP

                               rve  80 skafrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                       sk++ + l+ ++i++s++r+g+p+dn+ +E+f++tlk 
  gi|330508155|ref|YP_004384583.1| 202 SKDYVDCLKAHDIQISMSRKGNPYDNAFAESFIKTLKV 239
                                       ************************************95 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.3   8.5e-22   1.9e-18       6      58 ..      49      99 ..      45     101 .. 0.90
   2 ?   -0.0   0.0      0.45     1e+03      13      33 ..     257     277 ..     248     292 .] 0.66

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 8.5e-22
                            HTH_21  6 llalireifeeskgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgvqrr 58
                                      l ++i+ei  e  + YGyrri+aeL+++g+ +vnhkrV RlMr+++L+++ ++
  gi|330508155|ref|YP_004384583.1| 49 LVNQIQEIALEF-PYYGYRRITAELQNRGY-AVNHKRVLRLMRQEKLLCYKKK 99
                                      7899********.9**************87.5*****************9544 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.45
                            HTH_21  13 ifeeskgrYGyrriwaeLrre 33 
                                       i++    +Y ++r++ +L+ +
  gi|330508155|ref|YP_004384583.1| 257 ICNFIENVYNHKRLHSALNYR 277
                                       555445577788888888854 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1   4.1e-19   9.1e-16       1      67 []     212     279 ..     212     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 4.1e-19
                             rve_3   1 lgielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawred.YNteRPHssLgykTP 67 
                                       ++i++s+++ g P++N+++Esf++tl+ e ++ + ++++++a +++ +++e  YN++R Hs+L+y++P
  gi|330508155|ref|YP_004384583.1| 212 HDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHSALNYRSP 279
                                       689***************************************99999999866*************99 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.4     3e+03      21      33 ..     196     208 ..     184     209 .. 0.74
   2 !   32.1   2.4   4.2e-11   9.4e-08       1      48 [.     231     283 ..     231     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                             rve_2  21 eeleaaiedYIew 33 
                                       + ++ a +dY+++
  gi|330508155|ref|YP_004384583.1| 196 QGVQYASKDYVDC 208
                                       556788999*986 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 4.2e-11
                             rve_2   1 EsfFgsLKtElvygetfktleeleaaiedYIew.YNnkRlk....glsPvqYr 48 
                                       Esf ++LK+E vy  +++t+e +   i ++Ie  YN+kRl+    + sPvq++
  gi|330508155|ref|YP_004384583.1| 231 ESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHsalnYRSPVQFE 283
                                       9******************************988*****988888*******8 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   1.3e-07   0.00028       2     139 ..     128     271 ..     127     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                     DDE_Tnp_IS240   2 kswrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkek.lepeeivtDkasayasalke 76 
                                       ++w+ D Tyv+ + +  +l  ++D  +r  +++ +s     + a  +l kalk+ + ++ e ++    +  + a k 
  gi|330508155|ref|YP_004384583.1| 128 QAWASDITYVQLQHEHIFLAVILDLYSRkCIGWELSRSIRSDLAMSALAKALKNRSkESLEGLIHHSDQGVQYASKD 204
                                       68************************************999************998455555665555555555555 PP

                     DDE_Tnp_IS240  77 lkr...egelfdevshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktl.agfeavknlrkgh 139
                                         +     + + ++s+   +y n   Es  +tlK++  + +  ++++ a + + + +e v+n+++ h
  gi|330508155|ref|YP_004384583.1| 205 YVDclkAHDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNIcNFIENVYNHKRLH 271
                                       44411123556788899999***************************99877625679999999977 PP

>> GP3_package  DNA-packaging protein gp3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0053        12      49      78 ..      19      55 ..      15      63 .. 0.82
   2 ?    6.1   0.0    0.0052        12      51      90 ..     236     275 ..     199     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0053
                                      HHHHT--HHHHHHHGG..SHHH.......HHHHHHHH CS
                       GP3_package 49 alyLgisrstlkeyekrkrefs.......etierikq 78
                                      +l+L++srs  +e+ kr+++f        +++++i++
  gi|330508155|ref|YP_004384583.1| 19 CLALDVSRSGYYEWLKRSEKFTaensessDLVNQIQE 55
                                      899***************9998666666666666555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0052
                                       HHT--HHHHHHHGG..SHHHHHHHHHHHHHHHHHHHHHHT CS
                       GP3_package  51 yLgisrstlkeyekrkrefsetierikqivenqqiegala 90 
                                        L + + +l+eye+ +  f ++ + i+++ +++++  al 
  gi|330508155|ref|YP_004384583.1| 236 TLKVEEVYLNEYETFEDAFRNICNFIENVYNHKRLHSALN 275
                                       6889999*******999****************9999876 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.9e-05      0.11       3      56 ..      52     105 ..      50     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                     HTH_Tnp_Tc3_2   3 rIvrlvrkdPritlreLanelkeeGksvsreTirrrLrkaglkkrkprkkplLs 56 
                                       +I +++ + P+  +r++++el+++G  v ++ + r +r+++l  +k + kp+ +
  gi|330508155|ref|YP_004384583.1|  52 QIQEIALEFPYYGYRRITAELQNRGYAVNHKRVLRLMRQEKLLCYKKKFKPVTT 105
                                       68888889999**********************************999999755 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.7e-05      0.17      33      61 ..      19      48 ..      13      58 .. 0.83
   2 ?   -2.7   0.1       2.7   6.1e+03      55      72 ..     225     243 ..     224     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.7e-05
                                      HHHHTS-HHHHHHHH.H-HHHHHHHHHHHH CS
                       HTH_Tnp_1_2 33 aeevgvsrsTlykWk.kkkeFieyvnelae 61
                                      +  + vsrs +y+W+ + ++F+++ +e ++
  gi|330508155|ref|YP_004384583.1| 19 CLALDVSRSGYYEWLkRSEKFTAENSESSD 48
                                      56789*********9889999999888765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHT.THHHHH CS
                       HTH_Tnp_1_2  55 yvnelaeeflee.eraevy 72 
                                       y n  ae+f+++ +++evy
  gi|330508155|ref|YP_004384583.1| 225 YDNAFAESFIKTlKVEEVY 243
                                       7899999999873557777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         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: 2092.98
//
Query:       gi|330508156|ref|YP_004384584.1|  [L=282]
Description: transposase, IS4 family, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-20   73.4   0.1    3.3e-20   72.6   0.1    1.3  1  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
      0.032   14.3   0.2        1.4    8.9   0.0    2.2  2  DDE_Tnp_1_3  Transposase DDE domain
      0.056   11.7   0.3       0.25    9.6   0.3    1.8  1  DDE_Tnp_1_4  Transposase DDE domain group 1


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 !   72.6   0.1   5.6e-24   3.3e-20      23     212 ..       2     219 ..       1     221 [. 0.88

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 5.6e-24
                         DDE_Tnp_1  23 arwgykggk.ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDaGYasaelldtleek 98 
                                       a +gy++++ +++ +++++++++ +gl++ ++  pg+v d+k+l   l el++ +gk+++ D+G++s+e++ +l++ 
  gi|330508156|ref|YP_004384584.1|   2 AEKGYNKDRiHIPQINIVLLCSADTGLPTMIRPLPGSVKDIKTLSNSLLELDI-RGKVLILDRGFFSEEIFNFLDKL 77 
                                       56899*9999************************************999***9.*********************** PP

                         DDE_Tnp_1  99 gvdyiirlkkntklyrk......................................gaeskrrgrlrkhdrnkiltks 137
                                        ++y+i+++ n+++y+                                       +++ ++++   +++++  l ++
  gi|330508156|ref|YP_004384584.1|  78 EISYLIPARRNSHYYEErihlnehfryhkrlircgckklgnkylylfedqvlmleERDTLYDKLDAGRITKVELHEE 154
                                       *****************888887777777766666666665555555555555554777777788888888888888 PP

                         DDE_Tnp_1 138 qkrrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                        k+ ++          ++ +++ ++  +e  el ++R  +E  F + k++++ drl++++ + v+ ++++ +l+l
  gi|330508156|ref|YP_004384584.1| 155 MKKSGR----------ILIISNRKMNEQEAYELFKRRESVEKMFDTYKSTLSADRLYLHDDESVFGHVFIAFLSL 219
                                       888888..........9999999************************************************9987 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 ?    8.9   0.0   0.00023       1.4      65     117 ..      36      91 ..      22     118 .. 0.76
   2 ?    3.0   0.3     0.016        93      88     144 ..     142     194 ..     124     203 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00023
                       DDE_Tnp_1_3  65 pgnvdDrepv..eelakellgk.lfaDkgyiskklaeelleegielitklrknmkk 117
                                       pg v+D +++  + l  ++ gk l+ D+g+ s+++++ l + +i+ +   r+n + 
  gi|330508156|ref|YP_004384584.1|  36 PGSVKDIKTLsnSLLELDIRGKvLILDRGFFSEEIFNFLDKLEISYLIPARRNSHY 91 
                                       78889988886445667899984578******************999999888653 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.016
                       DDE_Tnp_1_3  88 Dkgyisk.klaeelleegielitklrknmkkkllslldkllLrkrslietvndelkni 144
                                       D g i+k +l ee++++g  li + rk   +++       l+++r  +e ++d+ k +
  gi|330508156|ref|YP_004384584.1| 142 DAGRITKvELHEEMKKSGRILIISNRKMNEQEA-----YELFKRRESVEKMFDTYKST 194
                                       566676646888888887777776665333333.....34778889999999988865 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3   4.1e-05      0.25     223     357 ..      62     209 ..      37     250 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 4.1e-05
                       DDE_Tnp_1_4 223 DSafarpellkwceergvdYviglaknsrlealiaelvekakteaaekkek.................ereyrefay 282
                                       D +f ++e+++++++ +++Y+i  ++ns+  ++  +l e+ + +++  +                     e r++ y
  gi|330508156|ref|YP_004384584.1|  62 DRGFFSEEIFNFLDKLEISYLIPARRNSHYYEERIHLNEHFRYHKRLIRCGckklgnkylylfedqvlMLEERDTLY 138
                                       55666666666666666666666666666666555555555544444433344555444444432111111111111 PP

                       DDE_Tnp_1_4 283 qaesWskerrVvakaerpaeglnl.rfvvTslaklspeelyeqlYcaRGemEnrIKeakldlaadrtsshsfaaNq 357
                                            + +   ++k+e ++e  +  r+ + s +k++++e y +l+++R  +E ++ + k+ l adr+ +h+ ++  
  gi|330508156|ref|YP_004384584.1| 139 ----DKLDAGRITKVELHEEMKKSgRILIISNRKMNEQEAY-ELFKRRESVEKMFDTYKSTLSADRLYLHDDESVF 209
                                       ....112222378888887777777777666666*******.*************************999866544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2036.01
//
Query:       gi|330508157|ref|YP_004384585.1|  [L=333]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-25   88.1   0.0    8.2e-25   86.9   0.0    1.7  1  Transposase_20  Transposase IS116/IS110/IS902 family
    1.1e-05   25.3   1.2    3.9e-05   23.6   0.3    2.2  2  DEDD_Tnp_IS110  Transposase
     0.0041   16.9   0.1       0.01   15.7   0.1    1.6  1  YfkB            YfkB-like domain
  ------ inclusion threshold ------
       0.15   13.1   1.3        2.8    9.0   1.0    2.6  2  DUF2018         Domain of unknown function (DUF2018)


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.0   1.8e-28   8.2e-25       2      86 ..     143     228 ..     142     229 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 1.8e-28
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaai.r 77 
                                       ++++sipGi ++  +++l+eig+ r f++++qla+++Gl+p en+S++kkr+ +i+krG++++R +L+eaA++++  
  gi|330508157|ref|YP_004384585.1| 143 AIVMSIPGIAFISGSVILSEIGNYRDFQTPEQLAKWCGLNPGENESAGKKRKCGITKRGSKYIRVVLVEAAQTIAnM 219
                                       589********************************************************************999955 PP

                    Transposase_20  78 anpelrayy 86 
                                       +n  l ++y
  gi|330508157|ref|YP_004384585.1| 220 KNTGLSRFY 228
                                       569999898 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.3   8.6e-09   3.9e-05     110     151 ..       3      44 ..       1      46 [. 0.91
   2 ?   -0.8   0.0      0.28   1.3e+03      27      70 ..     216     260 ..     204     265 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8.6e-09
                    DEDD_Tnp_IS110 110 grlrplklddeayaeLrqltrqredlvkertrlknrlralLd 151
                                       ++++ +++ +++ +eLr+ltr+r+ +vk+rt++knr+++ L 
  gi|330508157|ref|YP_004384585.1|   3 NQIKRSRVFSDEDRELRNLTRARSGYVKTRTQFKNRIHKYLS 44 
                                       6788888899999**************************996 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.28
                    DEDD_Tnp_IS110  27 vpn.deeglealleklaakagevlvvveatghygallvaflleag 70 
                                       ++n +  gl+++ ++l++k+++   +v    +   l++++l +++
  gi|330508157|ref|YP_004384585.1| 216 IANmKNTGLSRFYKRLSKKKEHNVAIVAVARKLICLIYHLLINQE 260
                                       444145688888888666666666666666666666777776665 PP

>> YfkB  YfkB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.2e-06      0.01      91     150 ..     211     271 ..     199     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.2e-06
                              YfkB  91 gdeealgnikeekledvfekwke.sklakslnchcpavkclGpnvlvknayykevdfkkrk 150
                                         +++++n+k++ l+  +++ ++ ++ +  +     ++ cl   +l+++ +y+evd +krk
  gi|330508157|ref|YP_004384585.1| 211 EAAQTIANMKNTGLSRFYKRLSKkKEHNVAIVAVARKLICLIYHLLINQEFYQEVDCRKRK 271
                                       56789***************9873567788999999**********************998 PP

>> DUF2018  Domain of unknown function (DUF2018)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.16   7.4e+02      46      78 ..      34      66 ..      25      68 .. 0.89
   2 ?    9.0   1.0   0.00063       2.8      44      73 ..     117     146 ..      88     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.16
                                      HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2018 46 kvekeikslilenkdeveakkkdlyIesmgnIL 78
                                      ++ ++i++++ +n  ++++ ++d++ +s  +I+
  gi|330508157|ref|YP_004384585.1| 34 QFKNRIHKYLSSNGIKLSSSMDDIFCKSGTHII 66
                                      477899999999**************9999887 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00063
                                       -HHHHHHHHHCCCHHHHHHHHHHHHHHHHH CS
                           DUF2018  44 lekvekeikslilenkdeveakkkdlyIes 73 
                                       +++ve++i+++ l+  +++++k+kdl+I +
  gi|330508157|ref|YP_004384585.1| 117 MDNVESKIEKTSLNILKKIQNKSKDLAIVM 146
                                       448************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1193  (0.0665402); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2504.84
//
Query:       gi|330508158|ref|YP_004384586.1|  [L=628]
Description: DNA polymerase I [Methanosaeta concilii GP6]
Scores for complete 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-74  250.4   0.0      6e-74  249.3   0.0    1.5  1  DNA_pol_A       DNA polymerase family A
     0.0003   20.5   0.0    0.00062   19.5   0.0    1.5  1  DNA_pol_A_exo1  3'-5' exonuclease


Domain annotation for each model (and alignments):
>> DNA_pol_A  DNA polymerase family A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.3   0.0   6.7e-78     6e-74      57     373 ..     289     625 ..     269     628 .] 0.90

  Alignments for each domain:
  == domain 1  score: 249.3 bits;  conditional E-value: 6.7e-78
                                       BTTTCCHHHHHT.S..CHHHHHHHHHHHHHHHHHTTTTGGGCCBTTTSEE--EEESSSSSSSS-EEESS-GGGS-TT CS
                         DNA_pol_A  57 ystdeevLekla.k.hplaklileyrelsklkstyvdallklinkktgrihtsfnqtvtatGrlsssepnlqnipir 131
                                        +t++evL++la +   +a+ +++yr+ls     ++++ l+ +++ +gr+h+++ q  ++tGr+ss++pn+q+ip r
  gi|330508158|ref|YP_004384586.1| 289 ANTKAEVLKSLAaAgCSFAEALMRYRHLSYN-LLFLNKWLEKVHPLDGRVHPQYFQIPSSTGRISSRHPNAQQIPRR 364
                                       56*********953789***********755.56799999999999******************************* PP

                                       SCCHHHHHHTBCG.TTCCEEEEEEETTHHHHHHHHHCT.HHHHHHHHTTH-HHHHHHHHHCTS.GGGHHHHHHHHHH CS
                         DNA_pol_A 132 teegrriRkafvaeegghvllsaDysqiELRilAhlsgdeklieafkegeDiHsktAsevfgvpveevtkeqRrqaK 208
                                        +++  iR++f +  g+  +++aD s iELRi+A +sgde+++eaf +g D+H+ tAs++ g+p eevt++qR+ aK
  gi|330508158|ref|YP_004384586.1| 365 GDDAPAIRRLFRPAAGK-RYVKADLSNIELRIMARISGDEAMQEAFIKGIDLHRLTASRISGTPFEEVTDSQRQAAK 440
                                       **************965.5********************************************************** PP

                                       HHHHHHHTT--HHHHHHHH......TSSHHHHHHHHHHHHHHSHHHH................HHHHHHHHHCCCE. CS
                         DNA_pol_A 209 ainfGiiYGagakgLaeql......giseeeAkefiekyferypgvk................syleetleeakek. 262
                                       a+nf +iYG +ak+L+ ++      +i  +e++e +e++f +ypgv+                ++ + +  +++   
  gi|330508158|ref|YP_004384586.1| 441 AMNFLLIYGGSAKSLQWRIlsdygeFICLDETEERLERFFCSYPGVRewqkmqlsqmsytmqhHFHNCVRGFFSLPl 517
                                       ****************9997766555*********************999999999999998655555666666667 PP

                                       CCEEETTCSEEEECTTT-CCHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEETTEEEEEEE CS
                         DNA_pol_A 263 gyvetllgrrrylpeiksknaalrekaeraavNapiQGsAaDiiklamikieealkeeklkarlllqvHDElvfevp 339
                                         ++t+lgrrr  p++ +  +a     + +  N+p+QG++aD+ikl+m +++e+l++e+  ar++ ++HDE+++evp
  gi|330508158|ref|YP_004384586.1| 518 TATRTILGRRRIWPRFGAGITAS----KFQMYNTPCQGTGADLIKLVMAEVYEKLSDEE--ARIIGSIHDEIILEVP 588
                                       8899*********9998666444....5689************************9995..9*************** PP

                                       CCCHHHHHHHHHHHHHHHHH...SSS--EEEEEEESS CS
                         DNA_pol_A 340 eeeveevaelvkeamesave...ldvplkvevkvGkn 373
                                       e+++ee a+ +ke+me++ +     vp+k+e+kv +n
  gi|330508158|ref|YP_004384586.1| 589 EDRAEEYAARLKEIMERIGSemlYPVPVKAEAKVMRN 625
                                       ***************9999887669999999998777 PP

>> DNA_pol_A_exo1  3'-5' exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   6.9e-08   0.00062      60     137 ..      72     173 ..      16     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.9e-08
                                       TTTT-.....HGHHHHHHHT-TTSEEEESSHHHHHHHHHHH..HTS--SSEEEHHHHHHHTTHSTT........... CS
                    DNA_pol_A_exo1  60 lgddv.....alealkrlledenitkvghnakfDlevlard..fgielenlfdtmlaayvldyers........... 118
                                       + d +     +++ l+ lle+  i+k +h+ kf l ++      + + +++fd+mla++++                
  gi|330508158|ref|YP_004384586.1|  72 IADRPelkesIIGDLAGLLENGRIKKTLHDSKFVLSFIRARagRKLNFCSIFDVMLASQICWSGYYyltpsgnpknp 148
                                       33333446669**************************999955566779************88887888999***** PP

                                       .......SSHHHHHHHHHSB---GHC CS
                    DNA_pol_A_exo1 119 .......hsLdsLaekylgdleldke 137
                                              hsL+sLae+ lg ++ld e
  gi|330508158|ref|YP_004384586.1| 149 wtkrlvdHSLASLAERHLG-IILDEE 173
                                       *******************.888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 4054.53
//
Query:       gi|330508159|ref|YP_004384587.1|  [L=101]
Description: hypothetical protein MCON_2272 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-18   65.4   0.0      6e-18   65.0   0.0    1.2  1  DUF4258     Domain of unknown function (DUF4258)
  ------ inclusion threshold ------
      0.055   13.8   0.0      0.088   13.2   0.0    1.4  1  BrnT_toxin  Ribonuclease toxin, BrnT, of type II toxin-antito


Domain annotation for each model (and alignments):
>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0   6.7e-22     6e-18       1      63 []      17      86 ..      17      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 6.7e-22
                           DUF4258  1 fsaHArermaeRgIseedieevlenGeiieeys........lvlgktsegrplhvvvapdedpvvviTvyr 63
                                      ++ HA +rm+eRgIs+ed+ ++++ G iie+y+        l++g+  + r  h+vva++e+++++iTvy+
  gi|330508159|ref|YP_004384587.1| 17 ITFHAHRRMDERGISTEDLVNLILDGSIIEDYPdsrpcpsaLIAGR-AGWRYCHAVVALCENHLRIITVYW 86
                                      689************************************9877777.777999*****************7 PP

>> BrnT_toxin  Ribonuclease toxin, BrnT, of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.8e-06     0.088       8      71 ..      23      84 ..       4      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.8e-06
                        BrnT_toxin  8 snlkkHgvsfeeaeevfedplalevedrredegEeRfiaiGtidgrllvvvftereekiRiISa 71
                                      + ++++g+s e+ + ++ d  ++e + +  +      ++ G  + r++ +v++  e+++RiI++
  gi|330508159|ref|YP_004384587.1| 23 RRMDERGISTEDLVNLILDGSIIEDYPD--SRPCPSALIAGRAGWRYCHAVVALCENHLRIITV 84
                                      56899**************999976666..556788888999999*****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 716.51
//
Query:       gi|330508160|ref|YP_004384588.1|  [L=85]
Description: hypothetical protein MCON_2273 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.7   0.0      0.027   14.6   0.0    1.1  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito


Domain annotation for each model (and alignments):
>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.5e-06     0.027       5      62 ..       7      64 ..       4      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-06
                    MqsA_antitoxin  5 vCgkaelvrdtrdvpytykgektvikavtgdfCarCGegvldeeeedrlseellefrk 62
                                       Cg++ l r++ +         +vik+v +  C  C e++l+ e+++++ + +++fr+
  gi|330508160|ref|YP_004384588.1|  7 NCGRGRLHRGKTEYLTRVDDGVLVIKNVPALICDICDEAYLTPESSREIDKIVKDFRE 64
                                      59999999998888777788889***************************99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 625.85
//
Query:       gi|330508161|ref|YP_004384589.1|  [L=77]
Description: hypothetical protein MCON_2275 [Methanosaeta concilii GP6]
Scores for complete 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   22.3   0.0    0.00012   22.2   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   6.7e-09   0.00012       9      57 ..      12      60 ..       5      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.7e-09
                   HicB_lk_antitox  9 edsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipe 57
                                      ed+   v+vP+lpG++ +g+t+eea +    +ie ++   +  g+ ip 
  gi|330508161|ref|YP_004384589.1| 12 EDEPIFVSVPELPGAWATGKTVEEARKRLIGVIEEWILLGVRLGHPIPP 60
                                      5667789*****************************9888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 586.66
//
Query:       gi|330508162|ref|YP_004384590.1|  [L=58]
Description: hypothetical protein MCON_2276 [Methanosaeta concilii GP6]
Scores for complete 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   17.9   0.0     0.0026   17.7   0.0    1.1  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.5e-07    0.0026       8      58 .]       1      49 [.       1      49 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-07
                                      HHHTT-EEEEEET.TEEEEE-TTSS-EEEEE.S-SSS--CCCHHHHHHHCC- CS
                        HicA_toxin  8 LeklGfevvrqkG.SHvrfkhpdkrgivtvppHpgkelkpgtlksIlkqaGl 58
                                      +++lGf      G +H ++++   r++++ p H ++e+++ +l  Il++ G+
  gi|330508162|ref|YP_004384590.1|  1 MKSLGFSGPY-AGpDHAFMVRGFARIRIPNP-H-KQEIGISLLVEILREGGI 49
                                      6889999999.5549******7777666666.4.8*************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       180  (0.0100396); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 463.64
//
Query:       gi|330508163|ref|YP_004384591.1|  [L=63]
Description: hypothetical protein MCON_2277 [Methanosaeta concilii GP6]
Scores for complete 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   31.0   0.0    2.5e-07   30.9   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   1.4e-11   2.5e-07      16      60 ..      11      55 ..       6      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.4e-11
                   HicB_lk_antitox 16 vvPdlpGcfsagdtleeaianakeaielhlegliedgeeipepss 60
                                      vvP+lpGc   g+t e a+++ k a++l+le++ + g++ip p++
  gi|330508163|ref|YP_004384591.1| 11 VVPELPGCSAFGETEERALQEVKIAMKLWLETAKKIGRSIPVPQK 55
                                      89***************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 524.60
//
Query:       gi|330508164|ref|YP_004384592.1|  [L=378]
Description: aspartate aminotransferase [Methanosaeta concilii GP6]
Scores for complete 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-56  191.0   0.0    3.7e-56  190.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.1e-06   27.5   0.0    4.2e-06   25.6   0.0    1.7  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    4.8e-06   25.8   0.0    7.4e-06   25.2   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    1.5e-05   24.5   0.0    2.1e-05   24.0   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
       0.15   12.4   0.1       0.62   10.4   0.0    2.0  2  Radical_SAM      Radical SAM superfamily
       0.23    9.5   0.0       0.32    9.1   0.0    1.1  1  Flu_PA           Influenza RNA-dependent RNA polymerase subun


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 !  190.9   0.0   1.2e-59   3.7e-56       2     362 ..      30     371 ..      29     372 .. 0.93

  Alignments for each domain:
  == domain 1  score: 190.9 bits;  conditional E-value: 1.2e-59
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dvi L ++e+++d    ++ +v++a+++  +   +l+ y+++ g  el+ea+++ + + +++ +k+e +vvv+sG++
  gi|330508164|ref|YP_004384592.1|  30 DVIHLEVGEPDFD----VPLAVKEATRK--ALDLGLTHYTHSLGDLELREAICRHYEKTYGVFIKPE-QVVVTSGTS 99 
                                       89***********....*********99..55566888*****************************.********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                        +  +++  l l++g+e++++dp y+ y n +   gg  vr+p+y++++f+  +ea+ e +++      +t+ il++
  gi|330508164|ref|YP_004384592.1| 100 PAMMLVFSSL-LERGQEVVLSDPGYSCYPNFISFLGGVPVRVPVYEKDGFQPRAEAIRERIRD------QTRAILIN 169
                                       ***9999999.9***************************************************......89****** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGy 232
                                       sp+NPtG ++++e  +++       + ++++De+Y g+v++ ++    ++ +e  ++ ++++++sK ++++G+R+Gy
  gi|330508164|ref|YP_004384592.1| 170 SPSNPTGNLLSEENMKAI----AGLGPYIISDEIYHGLVYEGKE----HSILEFTDHAFVLNGYSKLYAMTGLRLGY 238
                                       ******************....55799**************775....8888888899******************* PP

                                       EEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSS CS
                     Aminotran_1_2 233 ilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgm 306
                                       +++ +++v+ ++k++++f +  ssl+q+a  aal+ +     ++ em++ +++rrk+++ +L+e g+ ++ ++ +++
  gi|330508164|ref|YP_004384592.1| 239 LIAPERFVRPIQKMQQNFFIcaSSLAQRAGIAALEETGP---DVAEMKRIYNQRRKFMVRRLREMGFGITVEPtGAF 312
                                       ****************999999*************9885...9**********************999998887999 PP

                                       EEEEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 307 flltdlsae..takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                       +++   +++  +  +l+  +le+ +v vtpg  f+   +g lR+++ + ++e++   +++
  gi|330508164|ref|YP_004384592.1| 313 YVFANARHLsgDSYALAFDILEKAHVGVTPGIDFGPngEGYLRFSY-ANSREKIADGLDR 371
                                       9999999996666666667***********999999**********.7777777766666 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.4e-09   4.2e-06      71     154 ..      92     179 ..      78     190 .. 0.77
   2 ?   -1.0   0.0      0.16   4.9e+02      71     121 ..     257     306 ..     243     318 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.4e-09
                                       EEESSHHH.HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST....TSHHHHHHHCCTTEEEEE CS
                   Cys_Met_Meta_PP  71 lavssGma.AiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt....sdleelekaikentklvy 142
                                       ++v+sG++ A+++++ +ll+ G+e+v+sd  Y++  ++++ +   + ++v ++++      +e++++ i+++t++++
  gi|330508164|ref|YP_004384592.1|  92 VVVTSGTSpAMMLVFSSLLERGQEVVLSDPGYSCYPNFISFL-GGVPVRVPVYEKdgfqPRAEAIRERIRDQTRAIL 167
                                       56777776478888899***************9988888765.4555555555552233467899999********* PP

                                       EESS-TTTT--- CS
                   Cys_Met_Meta_PP 143 lEtptnpllkvv 154
                                       + +p+np+ +++
  gi|330508164|ref|YP_004384592.1| 168 INSPSNPTGNLL 179
                                       *******97765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.16
                                       EEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEE CS
                   Cys_Met_Meta_PP  71 lavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkf 121
                                       ++++s   A+ a i al ++G ++  ++ +Y+  ++++ + l+++g  +++
  gi|330508164|ref|YP_004384592.1| 257 FICAS-SLAQRAGIAALEETGPDVAEMKRIYNQRRKFMVRRLREMGFGITV 306
                                       33444.44566899999999************9999999999997766654 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.5e-09   7.4e-06      62     164 ..      90     187 ..      72     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.5e-09
                                       GGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBE.GGGHHHH-- CS
                       Aminotran_5  62 eeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeld.ldeleklln 137
                                       e++++tsGt+ a+ lv  sl   l++g+e+v+++ ++ +  + +  l    g+ v+v   +++g     +++++ ++
  gi|330508164|ref|YP_004384592.1|  90 EQVVVTSGTSPAMMLVFSSL---LERGQEVVLSDPGYSCYPNFISFLG---GVPVRVPVYEKDGFQPrAEAIRERIR 160
                                       78******************...*****************97788886...999988888888865438999***** PP

                                       TTEEEEEEESBETTTTEB--HHHHHHH CS
                       Aminotran_5 138 ektklvaithvsnvtGtiqpveeigkl 164
                                       ++t+++ i+  sn tG++   e+++++
  gi|330508164|ref|YP_004384592.1| 161 DQTRAILINSPSNPTGNLLSEENMKAI 187
                                       *****************9888877765 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 !   24.0   0.0   7.1e-09   2.1e-05      27     117 ..      78     168 ..      67     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7.1e-09
                                       HHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-T.TTSSB-GG CS
                   DegT_DnrJ_EryC1  27 eFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdp.dtynidpa 102
                                       ++Ek    +++ + ++ +s  + A++l+ + l +++g+eV+    ++    n ++ lg +pv v v + d +++ ++
  gi|330508164|ref|YP_004384592.1|  78 HYEKTYGVFIKPEQVVVTSGTSPAMMLVFSSL-LERGQEVVLSDPGYSCYPNFISFLGGVPVRVPVYEkDGFQPRAE 153
                                       67777777777777765555555777777665.666*****************************9651669***** PP

                                       GCGGG--TTEEEEEE CS
                   DegT_DnrJ_EryC1 103 aieaaitertkaIlp 117
                                       ai++ i  +t+aIl+
  gi|330508164|ref|YP_004384592.1| 154 AIRERIRDQTRAILI 168
                                       *************96 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00021      0.62      33      75 ..      16      73 ..      11     120 .. 0.74
   2 ?   -2.2   0.0       1.5   4.6e+03     124     147 ..     284     306 ..     272     313 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                                      HHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC................C CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................x RF
                       Radical_SAM 33 eileevkelkaekgvkevilgggepllypdfvellerlakla................v 75
                                      e+le ++el +++gv++++l  gep+++ +++++ + +++l+                +
  gi|330508164|ref|YP_004384592.1| 16 EVLERAREL-ERQGVDVIHLEVGEPDFDVPLAVKEATRKALDlglthythslgdlelrE 73
                                      899******.9****************99999999998888655544444444444440 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                                       TSHHHHHHHHHHHHHHTTSETEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 124 ghtfeevlealeklreagikrvvd 147
                                       +  +++++  +++lre g+  +++
  gi|330508164|ref|YP_004384592.1| 284 RIYNQRRKFMVRRLREMGFG-ITV 306
                                       36778888888999999888.554 PP

>> Flu_PA  Influenza RNA-dependent RNA polymerase subunit PA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00011      0.32     383     431 ..     249     298 ..     241     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00011
                                       XXTHHHHHHHHHTSBXSSBXS.XXSXXXXXXSXXXHHHHHHHHHHHHHHS CS
                            Flu_PA 383 lakWvqaefnlaseLtdkrwv.elaeigpdvaevedvaserrkyfesevs 431
                                       + k  q+ f  as L+++  +  l+e gpdvae+  + ++rrk+++  ++
  gi|330508164|ref|YP_004384592.1| 249 IQKMQQNFFICASSLAQRAGIaALEETGPDVAEMKRIYNQRRKFMVRRLR 298
                                       556678888999***998876369*********************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2692.98
//
Query:       gi|330508165|ref|YP_004384593.1|  [L=381]
Description: putative glutamate--cysteine ligase [Methanosaeta concilii GP6]
Scores for complete 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  134.5   0.0    5.9e-39  134.1   0.0    1.1  1  GCS2          Glutamate-cysteine ligase family 2(GCS2)
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.077   12.4   0.0    2.0  2  GCS           Glutamate-cysteine ligase
      0.018   15.4   0.0       0.13   12.6   0.0    2.1  1  AdoMet_MTase  Predicted AdoMet-dependent methyltransferase


Domain annotation for each model (and alignments):
>> GCS2  Glutamate-cysteine ligase family 2(GCS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.1   0.0   9.9e-43   5.9e-39      13     280 ..      33     286 ..      11     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 9.9e-43
                                       TTTEE-S-HHHHHCCCTTT-S.SSEEEE-SSTTEEEEE--SBSSHHHHHHHHHHHHHHHHHHHHHTT-EEE--SB-S CS
                              GCS2  13 atgdlrgwseiledeaiiglseggsvvkelpegqvElstapleslaeaaeeisadleelrsvadelGlellglGthP 89 
                                       + +++   ++++e e++ g     +v kel+++++El +a   +l +++e++   l+el ++ +   +++lglG+hP
  gi|330508165|ref|YP_004384593.1|  33 IIERI---NGRVEHEVAFGGI---RVSKELQKHVLELIPASPGNLGRLEENLFSGLQELFRATK-NEYQFLGLGMHP 102
                                       22222...2445555555544...9************************************998.78********** PP

                                       S---------------THHHHHGG..G.G-S--B-EEEEEEE-SSHHHHH..HHHHHHHTTHHHHHHHH--B-EETT CS
                              GCS2  90 falrsedevtpkaryrrmleymdrvGvlgrqmmvaglhvqvnidssseed.VevlrlvrallPvllAlsAnSPfleG 165
                                         l  +++ ++ +  + +++++dr++ ++++ ++++++ q+ni++ +e++ V +++++r l+P+l+A+ A+SPf+eG
  gi|330508165|ref|YP_004384593.1| 103 -LLTLDQTTYWDHDEQDYYQAYDRLFGIKQHGWLNIQALQINIPYRDEQElVGMFNKIRSLMPYLVAVTASSPFVEG 178
                                       .***********************9999*****************99999*************************** PP

                                       EE-S-SB-GGGCCTTSTT-CS----SSHHH.HHHHHHHHTTSTT-SSGG.G--BSEEEETTTT.EEEEEEEE--... CS
                              GCS2 166 rdtgyaStRariftqtpqagelplafedgaaferyaryaldvpvidvrrfrlwldirpsslpgttlelrihdttlfP 242
                                       ++++y ++R  ++++ +q  ++p ++ ++++ er      +v + +    +++ +++ +  +  + e++++++ +  
  gi|330508165|ref|YP_004384593.1| 179 QVNSYMDSR-LVYYRRNQ-SQIPQICRNVIP-ERLEGIRDYVEINR----NIYRELKKQHAQILCHEWVNSRGEI-- 246
                                       *********.99999999.9*********97.99998888888777....78888888865557**********9.. PP

                                       SSHHHHHHHHHHHHHHHHHHHHH------GGGGTT...HH CS
                              GCS2 243 evrlrallearlldaqpadrldalpaavlvalldd..eae 280
                                       +++ r++le++++d+q++  +d +  a+++all+   e+e
  gi|330508165|ref|YP_004384593.1| 247 VRFTRRCLEIKAIDEQECLHSDMAICAFIMALLRTdlELE 286
                                       ********************************99744454 PP

>> GCS  Glutamate-cysteine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05     0.077      14      57 ..     139     182 ..     134     193 .. 0.90
   2 ?    0.1   0.0     0.069   4.1e+02     307     324 ..     321     338 ..     251     366 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                               GCS  14 cLQvtfqaknieearllYdqlaplaPillalsaaspiykGllad 57 
                                       +LQ+ +  ++ +e   +++++  l P l+a++a+sp++ G + +
  gi|330508165|ref|YP_004384593.1| 139 ALQINIPYRDEQELVGMFNKIRSLMPYLVAVTASSPFVEGQVNS 182
                                       79999999********************************8864 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.069
                               GCS 307 etrkklekylkliskras 324
                                       +++++ ++yl li+kr++
  gi|330508165|ref|YP_004384593.1| 321 NATREEQRYLPLIEKRIE 338
                                       333444556666666654 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.2e-05      0.13       8      56 ..     221     285 ..     216     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                      AdoMet_MTase   8 ndlykelkqkyakrlvenw................vestdplkfvfedlaiaaylivlwkktrse 56 
                                       +++y+elk+++a+ l ++w                 ++ d +  ++ d+ai a+++ l + +   
  gi|330508165|ref|YP_004384593.1| 221 RNIYRELKKQHAQILCHEWvnsrgeivrftrrcleIKAIDEQECLHSDMAICAFIMALLRTDLEL 285
                                       579****************99999999988887666678999**************999876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2946.40
//
Query:       gi|330508166|ref|YP_004384594.1|  [L=163]
Description: hypothetical protein MCON_2281 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-08   33.6   0.1    9.5e-08   32.6   0.1    1.6  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 !   32.6   0.1   5.3e-12   9.5e-08       2      84 ..      13     106 ..      12     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 5.3e-12
                          CxxCxxCC   2 CkeC...gaCCkelkvklteedlerlkaaevaeeeeeskkiak....adgrCvfldeetklCkiYeeRpkicrlfpa 71 
                                       C++C   g CC e+++ l ++ ++ l + +v+ +  e   +++    +dg Cv++++   +C+i+  +p++c + p+
  gi|330508166|ref|YP_004384594.1|  13 CDDChlaGGCCFEARPPLSQKRIDILMENGVSADAIEFVGYKRlrlrQDGFCVLFRDG--KCSIHDIKPETCVAGPF 87 
                                       889877789**********************8888888888779999********999..8**************** PP

                          CxxCxxCC  72 s......ekeellaraetC 84 
                                       +        + +l+r++ C
  gi|330508166|ref|YP_004384594.1|  88 TfdieddMLQIFLKRESIC 106
                                       9887766556666677666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1219.55
//
Query:       gi|330508167|ref|YP_004384595.1|  [L=342]
Description: RimK domain-containing protein ATP-grasp [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-12   45.5   0.0    1.6e-11   44.1   0.0    1.7  1  RimK             RimK-like ATP-grasp domain
    1.5e-07   31.2   0.0    2.4e-07   30.5   0.0    1.3  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    1.5e-07   31.6   0.0    2.6e-07   30.9   0.0    1.3  1  ATP-grasp_3      ATP-grasp domain
     0.0001   22.4   0.0    0.00025   21.1   0.0    1.6  1  R2K_3            ATP-grasp domain, R2K clade family 3
    0.00072   19.4   0.0     0.0024   17.7   0.1    1.9  2  R2K_2            ATP-grasp domain, R2K clade family 2
     0.0072   15.5   0.0      0.081   12.0   0.0    2.0  2  TTL              Tubulin-tyrosine ligase family
  ------ inclusion threshold ------
      0.011   15.1   0.0       0.85    8.8   0.0    2.2  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
        0.1   12.2   0.0       0.14   11.7   0.0    1.3  1  ATP-grasp        ATP-grasp domain
       0.11   12.7   0.0       0.18   12.0   0.0    1.3  1  ARA70            Nuclear coactivator


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 !   44.1   0.0   8.2e-15   1.6e-11       3     185 ..      91     284 ..      89     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 8.2e-15
                                       -HHHHHHHHHHTT-----EEEESS-S....-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH...G CS
                              RimK   3 dKlkslklLakakikvpntalardee....daekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea...l 72 
                                       dK+     L k+++ +p+t++ ++ e    +a++l ++  l++P+v+K+  +s+ ++v    + ++l +v +    l
  gi|330508167|ref|YP_004384595.1|  91 DKINMYMHLQKEGVSMPKTRFLKKRElddqQARQLFDE--LGSPLVLKEPSTSFSVRVEKVSDVEELLKVAKRffkL 165
                                       89999999************987665211155555555..58*****************999999999997769999 PP

                                       GG--EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TT.TT-E....EEE-...---HHHHHHHHHHHHH CS
                              RimK  73 keailvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlh.rGgv....aekl...qlseeekelAikaaka 141
                                          i+vqeyie     d Rv v++++   a r +     F+      G +    +e +   q+ +e  +l  +aa a
  gi|330508167|ref|YP_004384595.1| 166 SDWIVVQEYIESR--FDWRVGVINGQLLYACRYIIPSETFKIQASvNGHIvycdVESVpadQVPPEVIDLGKQAAGA 240
                                       99********975..79***************998888898654413433122233332237888999********* PP

                                       CT-SEEEEEEEEETTEEEEEEEESS--SHHHHHHHT--HHHHHH CS
                              RimK 142 melvvaGvDllrakrgllvlEvnsspglekiektlgidiakkli 185
                                       ++  + GvD+ +++  l+v+Evn +p le+ e +   ++  ++i
  gi|330508167|ref|YP_004384595.1| 241 IGKGLYGVDIKESNGKLFVIEVNDNPSLEGGEDEHYPEMFGQII 284
                                       *****************************998776666666666 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.2e-10   2.4e-07       3     177 ..     100     267 ..      98     280 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.2e-10
                                       HHTT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-SCEEEEE CS
                   Dala_Dala_lig_C   3 kaaGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkydekvlvEe 79 
                                       ++ G+ +++  +l+k+e   ++    +++ +elg p++ K   +  Sv v+kv+ +eel +  ++ fk    ++v e
  gi|330508167|ref|YP_004384595.1| 100 QKEGVSMPKTRFLKKRELDDQQ---ARQLFDELGSPLVLKEPSTSFSVRVEKVSDVEELLKVAKRFFKLSDWIVVQE 173
                                       6788888888899998888888...99************************************************** PP

                                       --ESE.EEEEEEEETSSCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEE CS
                   Dala_Dala_lig_C  80 aiegr.eievavlgneklevsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGla 155
                                       +ie r +  v+v++    + + + + +  ++ ++++a   ++ + ++v+    ++v  ++ +l ++a  a++ +Gl 
  gi|330508167|ref|YP_004384595.1| 174 YIESRfDWRVGVIN---GQLLYACRYIIPSETFKIQASVNGHIVYCDVESVPADQVPPEVIDLGKQAAGAIG-KGLY 246
                                       **6554*******9...8888899999999999*****9989999999999999***************995.9*** PP

                                       EEEEEEETTTEEEEEEEESS-- CS
                   Dala_Dala_lig_C 156 RvDfflteegeivlnEvNtlPG 177
                                        vD+  +++g++++ EvN  P 
  gi|330508167|ref|YP_004384595.1| 247 GVDIK-ESNGKLFVIEVNDNPS 267
                                       ***86.569*********9995 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   1.3e-10   2.6e-07       1     155 [.      89     263 ..      89     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.3e-10
                                       HTSHHHHHHHHTTT.S---...............-EESS--.........SSSEEEEESS-------B--SS--TTE CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvP...........tkleaeeleee.........ekklvvKprdGaggesvrvveekeeae 57 
                                       ++dK+++y  L+++gv +P           +         +          ++lv+K  + + +  v +v + ee+ 
  gi|330508167|ref|YP_004384595.1|  89 CADKINMYMHLQKEGVSMPktrflkkreldD---------QqarqlfdelGSPLVLKEPSTSFSVRVEKVSDVEELL 156
                                       89*****************886666533322.........24444466679*******************9998887 PP

                                       .............EEEE---SE.EEEEEEEE.SSSEEEEEEEEEEEET............TEEEE.EEES----HHH CS
                       ATP-grasp_3  58 aaieeve......lvqefieGk.plSvsllsdgekvlvlavnrqliekaeke........fvyaG.nvtpietelke 118
                                       +  +         +vqe+ie++ +  v ++  +    +l  +r +i  ++ +        +vy+  +++p++ +   
  gi|330508167|ref|YP_004384595.1| 157 KVAKRFFklsdwiVVQEYIESRfDWRVGVINGQ----LLYACRYIIPSETFKiqasvnghIVYCDvESVPAD-QVPP 228
                                       6655544677888********956888888855....99999999977666689888888888862344444.7799 PP

                                       HHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEE CS
                       ATP-grasp_3 119 evvelaeevvekleglaGyvGvDlvlkdeepyviEvN 155
                                       ev++l +++  ++   +G+ GvD+  +++++ viEvN
  gi|330508167|ref|YP_004384595.1| 229 EVIDLGKQAAGAI--GKGLYGVDIKESNGKLFVIEVN 263
                                       9************..79*******************9 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 !   21.1   0.0   1.3e-07   0.00025      29     184 ..      93     265 ..      69     270 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                             R2K_3  29 eavaraarkhgwreapadylpelhflgrdvrqlsrlvel.eaeeepvFvkprgdklfggvV..lrefeelralaakl 102
                                        ++ + ++k+g++ + +++l++      +++++ + ++l +++ +p+ +k++ +  f+ +V  + ++eel + a+++
  gi|330508167|ref|YP_004384595.1|  93 INMYMHLQKEGVSMPKTRFLKKR-----ELDDQ-QARQLfDELGSPLVLKEPSTS-FSVRVekVSDVEELLKVAKRF 162
                                       45555566777777755555554.....66665.666666777999988866666.566663446888888777776 PP

                             R2K_3 103 e..dtevlvsevvrfsaEwRvFvvdGevvaasrYr...................kanddpdl..epdlaafaeavra 156
                                          +  ++v e+++    wRv v++G+++ a+rY                    + ++ p +  +p++  + ++++ 
  gi|330508167|ref|YP_004384595.1| 163 FklSDWIVVQEYIESRFDWRVGVINGQLLYACRYIipsetfkiqasvnghivycDVESVPADqvPPEVIDLGKQAAG 239
                                       6778889999************************9999999888888877777766666666777777777776666 PP

                             R2K_3 157 lvgappfyvlDvavtadGrwkVVEvndg 184
                                       +      y +D+  + +G++ V+Evnd 
  gi|330508167|ref|YP_004384595.1| 240 AI-GKGLYGVDIKES-NGKLFVIEVNDN 265
                                       66.4999*****666.9*********96 PP

>> R2K_2  ATP-grasp domain, R2K clade family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         3     6e+03      20      55 ..      52      86 ..      42      94 .. 0.73
   2 !   17.7   0.1   1.2e-06    0.0024      37     130 ..     149     265 ..     112     271 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3
                             R2K_2 20 pvFvkpasdaksftgavvedgedlpglgsldedlpv 55
                                      ++F++ ++d    t+ v ++ ++++g+  +d+++++
  gi|330508167|ref|YP_004384595.1| 52 ALFIRADTD-PMNTTYVAARMAEMYGVPVIDDPTSI 86
                                      478888888.77777788888888888777777766 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.2e-06
                             R2K_2  37 vedgedlpgl..gsldedlpvlvsevvsfasEyRlfvldgeiitvsrYagegrl.dpdp.................. 92 
                                       v d e+l ++     + + +++v+e+++ +  +R+ v++g+++ ++rY   ++  ++++                  
  gi|330508167|ref|YP_004384595.1| 149 VSDVEELLKVakRFFKLSDWIVVQEYIESRFDWRVGVINGQLLYACRYIIPSETfKIQAsvnghivycdvesvpadq 225
                                       445566666643334566789***************************98888753333557777777788888888 PP

                             R2K_2  93 ...evaeeavaalksalpsayvlDvgvtedgetalvEandg 130
                                          ev++   +a++   +  y +D+ +++ g++ ++E+nd 
  gi|330508167|ref|YP_004384595.1| 226 vppEVIDLGKQAAGAIGKGLYGVDIKESN-GKLFVIEVNDN 265
                                       88866666666666666789999996655.5********96 PP

>> TTL  Tubulin-tyrosine ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.087   1.7e+02      51     110 ..     116     176 ..      73     177 .. 0.62
   2 !   12.0   0.0   4.1e-05     0.081     239     283 ..     245     289 ..     243     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.087
                                       THHHHHHHTTTS--S-B----SS---XX------BSSTHHHHHH.HH..S.SS-EEEEB--S CS
                               TTL  51 padlaefveeaekeesntwIvKpsasarGkgirvfnkledikki.vsqsq.keplvvqkYie 110
                                       + d ++ ++ +++  s  +++K ++ + +  +  ++++e+++k+ +   + ++ +vvq+Yie
  gi|330508167|ref|YP_004384595.1| 116 ELDDQQARQLFDELGS-PLVLKEPSTSFSVRVEKVSDVEELLKVaKRFFKlSDWIVVQEYIE 176
                                       3344445555544444.7788888888888888888888888886334440455678***98 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXX CS
                               TTL 239 lyGvDilidenlkpwLlEvNasPdl.ksttkldaelkeeliddvln 283
                                       lyGvDi  ++n k +++EvN +P+l   ++++++e++ ++i+ +++
  gi|330508167|ref|YP_004384595.1| 245 LYGVDI-KESNGKLFVIEVNDNPSLeGGEDEHYPEMFGQIISHLVS 289
                                       799997.58999*************778999***********9998 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 ?    4.0   0.0     0.012        25      12      71 ..      82     141 ..      76     176 .. 0.85
   2 ?    8.8   0.0   0.00043      0.85     226     269 ..     228     269 ..     224     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.012
                       ATPgrasp_ST  12 praefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgs 71 
                                       + + + + +dK++++  ++++g+++pk+    k + + ++++++  el + +v+K+  +s
  gi|330508167|ref|YP_004384595.1|  82 DPTSIRICADKINMYMHLQKEGVSMPKTRFLKKRELDDQQARQLFDELGSPLVLKEPSTS 141
                                       567778999******99**********999999998889999999998666888876665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00043
                       ATPgrasp_ST 226 eevlelaakaaeklpglgylGwDivldeekgplllElNarpgla 269
                                       +ev++l ++aa    g g+ G+Di   + k + ++E+N++p+l+
  gi|330508167|ref|YP_004384595.1| 228 PEVIDLGKQAAG-AIGKGLYGVDIKESNGK-LFVIEVNDNPSLE 269
                                       578999999999.999********966666.**********996 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.9e-05      0.14       2      73 ..     100     176 ..      99     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.9e-05
                                       HTTT--B-EEEEECCHH....HHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCE.EEEE--- CS
                         ATP-grasp   2 eklglpvprflaveske....eleeaaeelglpvvvKarrlgydGkGqsvvrseedleqalealkeekv.ivEefvp 73 
                                       +k g+++p+  +++++e    +++++++elg p+v+K++  +++ + ++v   ee l+ a + +k   + +v e+++
  gi|330508167|ref|YP_004384595.1| 100 QKEGVSMPKTRFLKKRElddqQARQLFDELGSPLVLKEPSTSFSVRVEKVSDVEELLKVAKRFFKLSDWiVVQEYIE 176
                                       6788888888888887766779999******************9997776655555555555554444404556664 PP

>> ARA70  Nuclear coactivator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.2e-05      0.18      80     120 ..     120     174 ..      91     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.2e-05
                             ARA70  80 qklks...........sslsssfsielekvsdlelldeeem...dLsdwLvtpgt 120
                                       q++ +           ++ s+sfs+ +ekvsd+e l +      +Lsdw+v  + 
  gi|330508167|ref|YP_004384595.1| 120 QQARQlfdelgsplvlKEPSTSFSVRVEKVSDVEELLKVAKrffKLSDWIVVQEY 174
                                       4444477777778888999**************98877777799******97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2384.79
//
Query:       gi|330508168|ref|YP_004384596.1|  [L=218]
Description: hypothetical protein MCON_2283 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-08   34.4   0.1    2.8e-08   33.6   0.1    1.5  1  RLAN       RimK-like ATPgrasp N-terminal domain
  ------ inclusion threshold ------
       0.13   12.5   0.4       0.42   10.8   0.1    1.9  2  Lipocalin  Lipocalin / cytosolic fatty-acid binding protein f


Domain annotation for each model (and alignments):
>> RLAN  RimK-like ATPgrasp N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.1   3.1e-12   2.8e-08      20     148 ..      27     207 ..      15     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3.1e-12
                              RLAN  20 NLcrsyrYqseGYYvSLlAearghkviPsvstindlsrksllrlrleel............................ 68 
                                       N  +sy Y+ e YY+    e  g   +Ps +++ d    +++  +++ +                            
  gi|330508168|ref|YP_004384596.1|  27 N--ESYFYKTEPYYAIVKSENEGIITTPSSRDVLDAYIVPICLEKAKLAgisvcdwtvsyqfvplpaiiyglnyfst 101
                                       4..7999****************************996666655555448999999********************* PP

                              RLAN  69 .........esklqktlkskskenrlelsv..............vFGetee..kelkslarklfeefriPilkvele 120
                                                +++++k++k+ +++ r+++                +FG++ +  +e++++a+k+++ f++P++++ + 
  gi|330508168|ref|YP_004384596.1| 102 pseyflvndHDEAKKVVKHITNHGRYPFCYqkiadtsavtrcvsIFGRSLNccEEVAEIAEKIYQVFKLPLVEIVMV 178
                                       *******9966666666655555555555566677777777788***9654339*******************9998 PP

                              RLAN 121 rkdgk.wkiesikalslkeldeaeeslfa 148
                                       +++++ ++++s+ ++++++l+++e+++++
  gi|330508168|ref|YP_004384596.1| 179 KDNSGtYNLSSLAPVKYSQLSKEEKEMLQ 207
                                       7655449******************9987 PP

>> Lipocalin  Lipocalin / cytosolic fatty-acid binding protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.2   1.8e+03      62      97 ..      20      46 ..       3      56 .. 0.51
   2 ?   10.8   0.1   4.7e-05      0.42      75     141 ..     114     179 ..     100     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.2
                                      STTEEEEEEEESTTEEEEEEEEEESSSEEEEEEEEE CS
                         Lipocalin 62 epgklgvefdeyldgrkvkvlttdydnylilylkke 97
                                      ++ ++ v+        + +  +t+   y+i+++++e
  gi|330508168|ref|YP_004384596.1| 20 DDSQYIVN--------ESYFYKTEP-YYAIVKSENE 46
                                      44444443........333333333.4444444444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.7e-05
                                       TEEEEEEEEEESSSEEEEEEEEEETTEEEEEEEEEESSSSEEHHHHHHHHHHHHHTTETGGGEEEEE CS
                         Lipocalin  75 dgrkvkvlttdydnylilylkkekegkttlvaellsrdpelspelleefkkflkelgideenivrly 141
                                        ++ vk +t ++  y ++y+k  +++  t+ +++++r+++  +e+ e  +k+ +  +++ ++iv + 
  gi|330508168|ref|YP_004384596.1| 114 AKKVVKHITNHG-RYPFCYQKIADTSAVTRCVSIFGRSLNCCEEVAEIAEKIYQVFKLPLVEIVMVK 179
                                       455777777788.999*******7788**************************99999999999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1486.20
//
Query:       gi|330508169|ref|YP_004384597.1|  [L=710]
Description: hypothetical protein MCON_2284 [Methanosaeta concilii GP6]
Scores for complete 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-76  254.8   0.0    5.7e-76  254.0   0.0    1.4  1  Thioredox_DsbH   Protein of unknown function, DUF255
    1.6e-10   41.0   0.0      3e-10   40.1   0.0    1.5  1  Thioredoxin_7    Thioredoxin-like
    9.5e-08   31.7   0.4     0.0021   17.3   0.0    2.3  2  GlcNAc_2-epim    N-acylglucosamine 2-epimerase (GlcNAc 2-epim
    4.9e-06   25.8   0.2      0.066   12.3   0.0    2.4  2  Glyco_hydro_88   Glycosyl Hydrolase Family 88
    0.00032   20.3   2.0     0.0049   16.4   2.1    2.1  1  Glyco_hydro_9    Glycosyl hydrolase family 9
      0.004   16.7   0.1       0.58    9.6   0.1    3.0  3  C5-epim_C        D-glucuronyl C5-epimerase C-terminus
     0.0073   15.9   1.5        2.4    7.6   0.1    2.4  2  Glyco_hydro_76   Glycosyl hydrolase family 76
  ------ inclusion threshold ------
      0.018   13.6   0.0       0.05   12.2   0.0    1.7  1  LANC_like        Lanthionine synthetase C-like protein
      0.028   12.9   0.4        1.7    7.0   0.0    2.1  2  Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127


Domain annotation for each model (and alignments):
>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.0   0.0   2.9e-79   5.7e-76       1     162 [.      18     179 ..      18     180 .. 0.99

  Alignments for each domain:
  == domain 1  score: 254.0 bits;  conditional E-value: 2.9e-79
                    Thioredox_DsbH   1 knrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvk 77 
                                       +nrl +ekspYllqha npvdWypwgeea+e+a++edkpi+ls+Gys+chWChvm++esfed++va+lln+sf+++k
  gi|330508169|ref|YP_004384597.1|  18 QNRLCKEKSPYLLQHACNPVDWYPWGEEAFEAARREDKPIFLSVGYSTCHWCHVMAHESFEDPNVARLLNQSFICIK 94 
                                       69*************************************************************************** PP

                    Thioredox_DsbH  78 vDreerPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleee 154
                                       vDreerPd+d+iym+a+ a++g+ggWPl+v++tpd+kpff++tY+pk+ ++g +g++e++ +++e+w+++re+l ++
  gi|330508169|ref|YP_004384597.1|  95 VDREERPDIDQIYMAAAIAVSGRGGWPLTVMMTPDKKPFFAATYIPKKGHMGLTGLMELIAQVKEMWDNDRESLMSS 171
                                       ***************************************************************************** PP

                    Thioredox_DsbH 155 aeelleal 162
                                       a+ ++++l
  gi|330508169|ref|YP_004384597.1| 172 ANIIVDHL 179
                                       *9999887 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   1.5e-13     3e-10       1      82 [.      38     127 ..      38     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.5e-13
                                       ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.........- CS
                     Thioredoxin_7   1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdani........le 69 
                                       +w+ + +ea+++a+++ kp+++ +g s+c+ C++++ +  +d++v+++l++ f++ +vd +er + i        ++
  gi|330508169|ref|YP_004384597.1|  38 DWYPWGEEAFEAARREDKPIFLSVGYSTCHWCHVMAHESFEDPNVARLLNQSFICIKVDREERPD-IdqiymaaaIA 113
                                       7*************************************99999****9************99987.32334444433 PP

                                       TT---.SSEEEEE- CS
                     Thioredoxin_7  70 ldeqg.vPvvafld 82 
                                       + ++g  P  ++++
  gi|330508169|ref|YP_004384597.1| 114 VSGRGgWPLTVMMT 127
                                       33322366666665 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 !   17.3   0.0   1.1e-06    0.0021      77     128 ..     293     345 ..     263     354 .. 0.86
   2 !   12.2   0.1     4e-05     0.081      33     131 ..     457     553 ..     448     607 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-06
                                       -EEHHHHHHHHHHHHHHHT.TT-TTHHHHHHHHHHHHHHHTEETTTTEE--EE CS
                     GlcNAc_2-epim  77 skdaYdhaFvllalasala.ageeeakdlldetlavlekhlweekaglvkees 128
                                       +k +Yd+a  ++a+a+a++ +geee+++ ++e+l+ + +++ +++ g++  e+
  gi|330508169|ref|YP_004384597.1| 293 EKMLYDQALLAMAYAEAYQaTGEEEYAQTVREILEYILRDMTSPEGGFYSAED 345
                                       5779************7751699999******************999987664 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4e-05
                                       HHHTT-TTHHHHHHHHHHHTTTTTB-TTTSSB-SEEETTEEEE--EEHHHHHHHHHHHHHHHTTT.-TTHHHHHHHH CS
                     GlcNAc_2-epim  33 aaqlgrpgwldlvehGlkflekvlrdaehggyfsalrdggvldaskdaYdhaFvllalasalaag.eeeakdlldet 108
                                       a++l  p+ +++++ +++fl +v+r   +g  +++ r+g   d ++++ d+aF +  l + ++a  + ++ +++ ++
  gi|330508169|ref|YP_004384597.1| 457 AGALQDPDLATAASRAADFLLEVMRT-PEGRLMHRYRQGA--DIQANLDDYAFLIWGLIELYEATfDVKYLKAAVHL 530
                                       34466778999*************95.5599999999999..666667788999999999666551677899999** PP

                                       HHHHHHHTEETTTTEE--EE-TT CS
                     GlcNAc_2-epim 109 lavlekhlweekaglvkeesdke 131
                                        ++++kh+w+ +ag++  ++d  
  gi|330508169|ref|YP_004384597.1| 531 NEIMDKHFWDGEAGGFFFTADDG 553
                                       *************9998887664 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   3.3e-05     0.066      69     119 ..     294     343 ..     242     429 .. 0.78
   2 !   11.2   0.1   7.1e-05      0.14      88     173 ..     460     546 ..     447     555 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                                       TTSGGGTGHHHHHHHHHHHH-THHHHHHHHHHHHHHHHCS-B.TTS.B.SB CS
                    Glyco_hydro_88  69 elelDdidigllllllyeltkderykeaaeeladyvlakpprtseGgfwhk 119
                                       ++  D++ +++ ++  y+ t++e+y ++++e+ +y+l+++ +  eGgf  +
  gi|330508169|ref|YP_004384597.1| 294 KMLYDQALLAMAYAEAYQATGEEEYAQTVREILEYILRDMTS-PEGGFYSA 343
                                       4566888889999999*********************99999.88999873 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 7.1e-05
                                       H-THHHHHHHHHHHHHHHHCS-B.TTS.B.S..BTTSTTEEETHHHHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHH CS
                    Glyco_hydro_88  88 tkderykeaaeeladyvlakpprtseGgfwh..kkkepeqlWlDgLfMaipllaklskvtgepkyldeaikqfllta 162
                                        +d++   aa ++ad++l +  rt eG ++h   +  + q+ lD+    i  l++l++ t + kyl +a++  ++++
  gi|330508169|ref|YP_004384597.1| 460 LQDPDLATAASRAADFLL-EVMRTPEGRLMHryRQGADIQANLDDYAFLIWGLIELYEATFDVKYLKAAVHLNEIMD 535
                                       5789999999*****888.7778899*****888888999999*99999999************************* PP

                                       HHHBETTTSEB CS
                    Glyco_hydro_88 163 rhlfdpetGly 173
                                       +h  d e+G +
  gi|330508169|ref|YP_004384597.1| 536 KHFWDGEAGGF 546
                                       ***99999965 PP

>> Glyco_hydro_9  Glycosyl hydrolase family 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.1   2.5e-06    0.0049      78     252 ..     309     545 ..     294     567 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.5e-06
                                       HHHHTT-HHHHHHHHHHHHHHHHHT.ETCTTEEEEEES-HHHHHT.......--.........S-GGG--....... CS
                     Glyco_hydro_9  78 ayeaagdleeildeikwgldyllkm.htkdgvlyvqvGdgdaDhk.......lW.........gppedmdt...... 131
                                       ay+a+g+ ee+ ++++  l+y+l+  ++ +g +y   + +daD +        W         g      +      
  gi|330508169|ref|YP_004384597.1| 309 AYQATGE-EEYAQTVREILEYILRDmTSPEGGFY---SAEDADSEgeegkfyTWtavelkeslG------Eedfrll 375
                                       5555555.44566666666666654233355555...223333333344444453333222220......0233333 PP

                                       ......................................................---EEEEETTC--HHHHHHHHHH CS
                     Glyco_hydro_9 132 ......................................................prpvykvdesnpgtdaaaetAAa 154
                                                                                             ++ v+ +++++  td  + + Aa
  gi|330508169|ref|YP_004384597.1| 376 irlfdvyesgnyegernilrqrssfsdaasvlkipeeelyhrssdmisrlylarEKRVHPLKDDKILTDWNGLMIAA 452
                                       33344444444444444444444444455555555555555566666666666656667778888899********* PP

                                       HHHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHH-.-..TT--TGTTTTTTS--.SS.......HHHHHHHHHHHHHH CS
                     Glyco_hydro_9 155 lAaasrvfkksdpayAaklleaAkklyafadkyr.ky.adsiaeaagggfYns.sd.......kDellwAaawlyka 221
                                       lA a+ +++  dp+ A+   +aA  l +++++ + ++ ++          Y +  d          l+w+ ++ly+a
  gi|330508169|ref|YP_004384597.1| 453 LARAAGALQ--DPDLATAASRAADFLLEVMRTPEgRLmHR----------YRQgADiqanlddYAFLIWGLIELYEA 517
                                       *****9995..*******************7555533233..........332222222311244799********* PP

                                       H--HHHHHHHHHCC.TTSST...BTTB-HHH CS
                     Glyco_hydro_9 222 tkeasylddaksyyskeaasssfsWdnkvag 252
                                       t + +yl++a +  ++     ++ Wd ++ g
  gi|330508169|ref|YP_004384597.1| 518 TFDVKYLKAAVH-LNEIM--DKHFWDGEAGG 545
                                       *8889***9975.43333..34588886655 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 ?   -1.6   0.0       0.8   1.6e+03      35      92 ..     239     289 ..     236     290 .. 0.77
   2 !    9.6   0.1   0.00029      0.58      30      72 ..     298     342 ..     295     358 .. 0.81
   3 ?    3.0   0.0     0.031        62      37      64 ..     510     537 ..     503     553 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.8
                         C5-epim_C  35 isvllrAYeltgdekYlkaakkalksfkipvekGGvlktledkkiwyeeYptspksyv 92 
                                       i  llr ++ t++   l++ak  l+ +++    GG+ +++      ++ Y+t+p+ +v
  gi|330508169|ref|YP_004384597.1| 239 ILFLLRCWKRTKNILPLEMAKTTLQGMRM----GGIYDHVGF---GFHRYSTDPEWFV 289
                                       67789999999999999999999998765....777777766...4677777777766 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00029
                         C5-epim_C  30 aqgqaisvllrAYeltgdekYlkaakkalksfk..ipvekGGvlk 72 
                                       +q+ ++ ++++AY++tg+e+Y ++ ++ l++++  +++ +GG+ +
  gi|330508169|ref|YP_004384597.1| 298 DQALLAMAYAEAYQATGEEEYAQTVREILEYILrdMTSPEGGFYS 342
                                       5889999*********************99986224566788765 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.031
                         C5-epim_C  37 vllrAYeltgdekYlkaakkalksfkip 64 
                                        l++ Ye+t d kYlkaa ++ ++++  
  gi|330508169|ref|YP_004384597.1| 510 GLIELYEATFDVKYLKAAVHLNEIMDKH 537
                                       57888*************9988887765 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 !    7.6   0.1    0.0012       2.4     219     258 ..     297     336 ..     282     360 .. 0.84
   2 !    7.0   0.1    0.0018       3.7     161     258 ..     451     541 ..     443     555 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHCEEC CS
                    Glyco_hydro_76 219 YnqGtylsgaaylynaTgdekWldrvkgllnatlstffpd 258
                                       Y q+++  + a  y+aTg+e++ + v+++l+ +l+ +++ 
  gi|330508169|ref|YP_004384597.1| 297 YDQALLAMAYAEAYQATGEEEYAQTVREILEYILRDMTSP 336
                                       8899999999999*****************9997776655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHH--CHHHHHHHHHHHHHHHHSCSBTTTS-B-SEEETTTCCEEEE---HHHHHHHHHHHHHHHHHHH-- CS
                    Glyco_hydro_76 161 qlaarLarytgnetYlewAekvwdWvedvgliddedwlvyDgasvednctdinklqwtYnqGtylsgaaylynaTgd 237
                                        + ar a + ++  +++ A++  d++ +v  +++ +++ + + ++     di+ +     +++++ g + ly+aT d
  gi|330508169|ref|YP_004384597.1| 451 AALARAAGALQDPDLATAASRAADFLLEV--MRTPEGRLMHRYRQGA---DIQANL--DDYAFLIWGLIELYEATFD 520
                                       44455555556666666677777776664..3566666666653322...333332..2357788888888888888 PP

                                       HHHHHHHHHHHHHHHHHCEEC CS
                    Glyco_hydro_76 238 ekWldrvkgllnatlstffpd 258
                                        k+l+ +  l + + ++f+++
  gi|330508169|ref|YP_004384597.1| 521 VKYLKAAVHLNEIMDKHFWDG 541
                                       888888888888888888876 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 ?   12.2   0.0   2.5e-05      0.05      14      57 ..     302     342 ..     299     369 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHCCH.-S--STTT CS
                         LANC_like  14 iallllelykvtknekylklahkylekikkelselglesisffs 57 
                                       +a++++e+y++t++e+y ++++++le+i + + +   +  +f+s
  gi|330508169|ref|YP_004384597.1| 302 LAMAYAEAYQATGEEEYAQTVREILEYILRDMTS---PEGGFYS 342
                                       689****************************999...7777776 PP

>> Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1    0.0073        14     180     206 ..     302     328 ..     285     367 .. 0.70
   2 ?    7.0   0.0   0.00087       1.7     129     207 ..     448     534 ..     430     568 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0073
                                       HHHHHHHHHHHHT-CHHHHHHHHCCHH CS
                   Glyco_hydro_127 180 ieealvklyelTgdkrYldlAkrfide 206
                                       + +a+++ y++Tg+++Y ++ + + + 
  gi|330508169|ref|YP_004384597.1| 302 LAMAYAEAYQATGEEEYAQTVREILEY 328
                                       567777777777777777766655544 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00087
                                       HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHCCS-CCHHHHHTTT........HHCTHHHHHHHHHHHHT-CHHH CS
                   Glyco_hydro_127 129 kliegavayyqatgkeklldvatrladyleevleklgdeqlqkalvp........ehggieealvklyelTgdkrYl 197
                                        +i+++  +  a ++  l ++a r+ad+l ev+++++   + ++           +   +  +l++lye+T d +Yl
  gi|330508169|ref|YP_004384597.1| 448 LMIAALARAAGALQDPDLATAASRAADFLLEVMRTPEGRLMHRYRQGadiqanldDYAFLIWGLIELYEATFDVKYL 524
                                       57788888888889999999999999999999998887777665443222222323333446899************ PP

                                       HHHHHCCHHC CS
                   Glyco_hydro_127 198 dlAkrfider 207
                                       + A  +++  
  gi|330508169|ref|YP_004384597.1| 525 KAAVHLNEIM 534
                                       ***9887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (710 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); 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:                         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 0.29s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 4608.30
//
Query:       gi|330508170|ref|YP_004384598.1|  [L=295]
Description: hypothetical protein MCON_2286 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2042.89
//
Query:       gi|330508171|ref|YP_004384599.1|  [L=191]
Description: GPR1/FUN34/YaaH family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-41  141.8  21.6    2.5e-41  141.6  21.6    1.0  1  Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
  ------ inclusion threshold ------
      0.027   14.0   5.9      0.022   14.2   4.3    1.6  1  DUF2938          Protein of unknown function (DUF2938)


Domain annotation for each model (and alignments):
>> Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6  21.6   2.8e-45   2.5e-41      16     201 ..       9     187 ..       5     191 .] 0.94

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 2.8e-45
                   Gpr1_Fun34_YaaH  16 kfaNPaPlgllafalttfvlslvnlgargitepnvvvglalfyGGlvqllaGiwefavgntFgatalssYGgFwlsy 92 
                                       + aNPaPlgll+f++tt +l+++n+g  ++++  +++++ +fyGG++q++aGi+e+   ntFg+ta++sYG Fwl++
  gi|330508171|ref|YP_004384599.1|   9 NTANPAPLGLLGFGMTTVLLNIHNAGYYELNT--MILAMGIFYGGMAQIIAGIMEWKKNNTFGTTAFTSYGLFWLTL 83 
                                       78**************************9998..9****************************************95 PP

                   Gpr1_Fun34_YaaH  93 .aailipgfgilaaYeedeeelnnalglyllgwfiftfllllatlrstvalfllfffldltflllaigeltgsakvl 168
                                        +++l+p++g  +a        + a++ y+++w +ftf++++ tlr + al ++f++l++ f+lla+ ++ gsa + 
  gi|330508171|ref|YP_004384599.1|  84 vGLLLMPSLGLGTAT------SKVAFAAYFFMWGLFTFVMFIGTLRINRALQVVFLTLTILFFLLAARDYFGSAAIG 154
                                       489999*****9998......4889**************************************************** PP

                   Gpr1_Fun34_YaaH 169 kAggvfgiiaaflawYnalaglatkensyftlp 201
                                       + +g+ gii+++ a Y+ala+++++    ++lp
  gi|330508171|ref|YP_004384599.1| 155 TLAGYEGIICGLSAIYAALAQVLNEVYKKVVLP 187
                                       ***********************8876666665 PP

>> DUF2938  Protein of unknown function (DUF2938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   4.3   2.4e-06     0.022      68     139 ..      44     118 ..      38     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-06
                           DUF2938  68 liGilfaallvllvg.aeWlaePtllpalv..vgivtvvapflllqPalGaGlaasrtpkpakarlkslvahtvf 139
                                       ++Gi ++ +  +++g  eW ++ t+  +     g+   +   lll+P+lG+G a+s++  +a   +  l + ++f
  gi|330508171|ref|YP_004384599.1|  44 AMGIFYGGMAQIIAGiMEWKKNNTFGTTAFtsYGLFWLTLVGLLLMPSLGLGTATSKVAFAAYFFMWGLFTFVMF 118
                                       78****876655554289******97654312688888888899*************998888877777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1432.77
//
Query:       gi|330508172|ref|YP_004384600.1|  [L=132]
Description: hypothetical protein MCON_2291 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-39  133.5   0.0    4.2e-39  133.3   0.0    1.0  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.3   0.0   2.4e-43   4.2e-39       1     114 [.      14     126 ..      14     127 .. 0.97

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 2.4e-43
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGGTTS..THHHHHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhnaegpdnadaHlkssl 76 
                                       dit++v  a++e+g++eG++ vf+ htt++lt+nE+ dp +++D++++l++l+pe+  Y h+ +++ na+aHl+++l
  gi|330508172|ref|YP_004384600.1|  14 DITSNVILALHEEGIEEGIAFVFTLHTTTALTVNEA-DPPLMKDIQNLLQRLAPENgGYLHD-HHDGNAHAHLRATL 88 
                                       79*********************************9.************************9.5557********** PP

                                       H-SEEEEEEETTEE---TTEEEEEEESS-SSEEEEEEE CS
                           UPF0047  77 lgssltipvedgklalGtwqsiylveldgpreRkvvvq 114
                                       +g+s+tipv +gk +lGtwq+i+++e+dgpr+R+++++
  gi|330508172|ref|YP_004384600.1|  89 IGNSITIPVAEGKPKLGTWQRILFFEFDGPRRRRIYIK 126
                                       ***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1023.37
//
Query:       gi|330508173|ref|YP_004384601.1|  [L=288]
Description: branched-chain amino acid aminotransferase [Methanosaeta concilii GP6]
Scores for complete 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  184.7   0.0    2.6e-54  184.4   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 !  184.4   0.0   1.4e-58   2.6e-54       1     223 []      30     256 ..      30     256 .. 0.94

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 1.4e-58
                       Aminotran_4   1 glfEtmrvyngeiffldeHleRLrksaellglelpfdeeelrkileelleannsengrlrllvsrgggglg.aatse 76 
                                       g+fE++r+y g++f+l++H+ RL  sa++++l +p+++ee+  +++++l++nn + +++r++v+rg g+lg ++ ++
  gi|330508173|ref|YP_004384601.1|  30 GVFEGIRAYGGRVFRLEDHVRRLFDSAQAIMLCIPLSQEEMALAIRDTLRKNNLRDAYVRPIVTRGYGDLGlDPLKC 106
                                       8**************************9999*****************************************77777 PP

                       Aminotran_4  77 psvavyvsalppgpeseke....lplvtssdvrrdapsplpgaKtlnyldnvlarreakergadevllvdedgnvtE 149
                                        +  v+++a ++g+ +       l+++  s++r  +    p++K+lnyl+n+la+ ea+ +g +e++++d++g+++E
  gi|330508173|ref|YP_004384601.1| 107 RKPTVIIVAVEWGAMYGSLyevgLTAISVSVRRNAPDALPPNIKSLNYLNNILAKIEANVKGGNEAIILDSQGRISE 183
                                       7777777777777777777779988888888999999999************************************* PP

                       Aminotran_4 150 gstsNvfivkggelitPplssgiLpGitrrallelakalgleveereitlkdleeadeafltntlrgvlpvrsi 223
                                       gs  N+f++k+++++tP   +  L+Gitr+a++ela++ g+ev+e+++ l dl   de+f+t+t+++v pv++i
  gi|330508173|ref|YP_004384601.1| 184 GSGDNIFVIKNKKVYTPHTLN-NLKGITREAVFELAEKNGIEVIETDLGLFDLYTGDEVFVTGTAAEVAPVTKI 256
                                       *****************5545.6*************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2180.14
//
Query:       gi|330508174|ref|YP_004384602.1|  [L=136]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-32  112.3   0.3    1.9e-32  112.0   0.3    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 !  112.0   0.3     1e-36   1.9e-32       3     138 ..       3     131 ..       1     133 [. 0.93

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 1e-36
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHH CS
                     DMRL_synthase   3 riaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphf 79 
                                       ++++Vv++fn++it ++    +++++ +g+  +   vv+VPG+f++p+a+kk++ + + +dav+++G+vi+Get h+
  gi|330508174|ref|YP_004384602.1|   3 KLGFVVSEFNRDITYQMELLGREHAQFLGA--DVAAVVYVPGVFDMPIAVKKMLCR-EDIDAVVTIGCVIQGETAHD 76 
                                       899**************************7..599*******************95.447***************** PP

                                       HHHHHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHHHHHHH CS
                     DMRL_synthase  80 eyvaeavskglmrvsldtgvPvifgvltvd.teeqaleraggkagnkGeeaaeaaleman 138
                                       e+v+++++++lm++sl+ ++Pv+ g+  ++ ++++a++r+     ++ ++a+eaa+++++
  gi|330508174|ref|YP_004384602.1|  77 EVVVNHAARKLMDLSLECNKPVTLGITGPKmSRADAQKRV-----DYSKRAVEAAVKLLQ 131
                                       ******************************9999999999.....788888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1043.74
//
Query:       gi|330508175|ref|YP_004384603.1|  [L=378]
Description: aspartate aminotransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-58  199.0   0.0    1.5e-58  198.7   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    0.00013   21.4   0.0     0.0002   20.8   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00031   19.4   0.0    0.00056   18.6   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0015   18.6   0.0     0.0071   16.4   0.0    1.9  2  Rsbr_N           Rsbr N terminal
     0.0029   16.6   0.0     0.0047   15.9   0.0    1.2  1  Aminotran_5      Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.7   0.0   4.3e-62   1.5e-58       2     363 .]      30     373 ..      30     373 .. 0.93

  Alignments for each domain:
  == domain 1  score: 198.7 bits;  conditional E-value: 4.3e-62
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       d+i++g++e+++d    t++++++a     +   + + y p+ g pel++a+a+ l+r++ +  ++e  v+v++Ga+
  gi|330508175|ref|YP_004384603.1|  30 DIIDMGVGEPDFD----TPKHIVEAGCN--SIRMGETHYAPTGGIPELRQAIAEKLNRENLIHSTAE-DVIVTPGAK 99 
                                       589**********....*********88..88888999*****************************.********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                        +  a+i++l l+ g+e ++  p++ sy++ +  +gg vv  +        +d++ + + ++e  + ++kt++i+++
  gi|330508175|ref|YP_004384603.1| 100 MAVFAAIQAL-LQEGEECILIGPSWVSYEPSVAFAGGSVVWGE--------VDADFMPRNIAE--KISPKTRMIIIN 165
                                       **********.*****************************999........777777777777..445599****** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH..HGGSTTSTTEEEEEESSSTTSSGGG-E CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavat..ranveeepnllivgslsKafGlaGeRv 230
                                       sp+NPtG+v+ ++ le++ dla  + l++++De+Y++  ++++ +++   ++++ee+  +++ +++sKa++++G+R+
  gi|330508175|ref|YP_004384603.1| 166 SPSNPTGAVFERPVLEEIRDLAIDHDLFVISDEIYEKIIYDHE-HISMgsLPGMEER--TVTINGFSKAYAMTGWRL 239
                                       ****************************************955.4444457777776..67**************** PP

                                       EEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCS CS
                     Aminotran_1_2 231 Gyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsg 305
                                       Gy++g ++  +++ +l ++  s  ++ +q+a + al+ +++   +++ m++++ +rr+ l+++L++lg+++  + ++
  gi|330508175|ref|YP_004384603.1| 240 GYLTGPKETMKWVIRLLSHSVSqaTTFVQRAGVVALQGPED---DVDMMVAEFRARRDLLVAGLKSLGIPCSVPGGA 313
                                       *****999999999999999999*****************7...9******************************** PP

                                       SEEEEEETHHCHHHHHHH.HHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 306 mflltdlsaetakelskk.Lleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                       ++++ d+s     +l+ + Ll+e  ++ tpg+ f+   +  +R+++ +++++ +++++e++
  gi|330508175|ref|YP_004384603.1| 314 FYVFPDVSGFGGGDLFTErLLKEALIAATPGSAFGPggRDYVRLSY-ATSQNRIRQALERI 373
                                       *********9555555555*****************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 !   20.8   0.0   5.6e-08    0.0002      39     144 ..      90     197 ..      76     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.6e-08
                                       SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEE CS
                   DegT_DnrJ_EryC1  39 khaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaI 115
                                       + +i +  +  A+  a++al  ++g+e+I    ++v+   +v+ +g  +v  +vd+d     p +i+++i ++t+ I
  gi|330508175|ref|YP_004384603.1|  90 EDVIVTPGAKMAVFAAIQALL-QEGEECILIGPSWVSYEPSVAFAGGSVVWGEVDAD---FMPRNIAEKISPKTRMI 162
                                       556666777788888999974.559******************************54...5699************* PP

                                       E...EB-GGGB---...HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 116 l...pVhlyGqvad...mdalkaiaakhglkvieD 144
                                       +   p +  G+v++   +++++++a +h+l vi+D
  gi|330508175|ref|YP_004384603.1| 163 IinsPSNPTGAVFErpvLEEIRDLAIDHDLFVISD 197
                                       945557899**9965569***************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 !   18.6   0.0   1.6e-07   0.00056      67     173 ..      89     197 ..      75     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-07
                                       -SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTS...SHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEE CS
                   Cys_Met_Meta_PP  67 geaalavssGmaAiaaailallkaGdeivvsddl...Yggtqrllkkvlkklgievkfvdtsdleelekaikentkl 140
                                       +e +++++    A++aai+all++G+e ++       Y+++ ++    +   +++++f+      +++++i+++t++
  gi|330508175|ref|YP_004384603.1|  89 AEDVIVTPGAKMAVFAAIQALLQEGEECILIGPSwvsYEPSVAFAGGSVVWGEVDADFMP----RNIAEKISPKTRM 161
                                       5677777778899**************887665311277777777777777777777665....589999******* PP

                                       EEEESS-TTTT----...HHHHHHHHHHTT-EEEEE CS
                   Cys_Met_Meta_PP 141 vylEtptnpllkvvD...iekiaklakkagvlvvvD 173
                                       + + +p+np+  v     +e+i +la ++++ v+ D
  gi|330508175|ref|YP_004384603.1| 162 IIINSPSNPTGAVFErpvLEEIRDLAIDHDLFVISD 197
                                       **********98865443677777777777777666 PP

>> Rsbr_N  Rsbr N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.5   1.8e+03      77     100 ..      65      87 ..      53      95 .. 0.73
   2 !   16.4   0.0     2e-06    0.0071      13      93 ..     180     258 ..     174     271 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHHHHHHHH..T--TT CS
                            Rsbr_N  77 tkgLqefrkvvlellseeddvvke 100
                                       t g+ e+r+++ e+l+ e+ ++++
  gi|330508175|ref|YP_004384603.1|  65 TGGIPELRQAIAEKLNREN-LIHS 87 
                                       7799999999999999976.4443 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2e-06
                                       HHHHHHHHTTSSS-.--HHHHHHHHHHHHHHHHH-SS.-SSTTHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHH CS
                            Rsbr_N  13 lkelkelrkeeslqtisdevyektskefvdlilssveegneeleekleefaerlvqlGwpLkyltkgLqefrkvvle 89 
                                       l+e+++l+ +++l +isde+yek+  ++ ++ + s+  g ee + +++ f++    +Gw L ylt   +e  k v++
  gi|330508175|ref|YP_004384603.1| 180 LEEIRDLAIDHDLFVISDEIYEKIIYDHEHISMGSLP-GMEERTVTINGFSKAYAMTGWRLGYLTG-PKETMKWVIR 254
                                       67899999999*************************9.6677779*******************94.4455555555 PP

                                       HHHH CS
                            Rsbr_N  90 llse 93 
                                       lls+
  gi|330508175|ref|YP_004384603.1| 255 LLSH 258
                                       5554 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.3e-06    0.0047      54     175 ..      83     197 ..      64     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-06
                                       HHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGG CS
                       Aminotran_5  54 elinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldld 130
                                       +li+ +  e++i+t G+  a+ +++++l   l++g+e ++      +   p ++     g  v++ ++d++      
  gi|330508175|ref|YP_004384603.1|  83 NLIHSTA-EDVIVTPGAKMAVFAAIQAL---LQEGEECILIGPSWVSYE-PSVAF---AGGSVVWGEVDADFMP--R 149
                                       6777775.9*******************...999999888877666666.66555...599*******887665..5 PP

                                       GHHHH--TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE CS
                       Aminotran_5 131 elekllnektklvaithvsnvtGtiqp...veeigklakkkgalvlvD 175
                                       ++++++++kt++++i+  sn tG +++   +eei +la +++ +v+ D
  gi|330508175|ref|YP_004384603.1| 150 NIAEKISPKTRMIIINSPSNPTGAVFErpvLEEIRDLAIDHDLFVISD 197
                                       ************************886334567777777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2978.14
//
Query:       gi|330508176|ref|YP_004384604.1|  [L=185]
Description: hypothetical protein MCON_2298 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   12.4   0.1       0.07   12.4   0.1    2.0  2  7TM_GPCR_Srz  Serpentine type 7TM GPCR chemoreceptor Srz
        2.3    7.2   7.6        4.7    6.1   7.6    1.7  1  PalH          PalH/RIM21


Domain annotation for each model (and alignments):
>> 7TM_GPCR_Srz  Serpentine type 7TM GPCR chemoreceptor Srz
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   7.8e-06      0.07     159     216 ..      11      68 ..       3      93 .. 0.83
   2 ?   -0.1   0.8     0.054   4.8e+02      55      86 ..     131     161 ..     117     175 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.8e-06
                      7TM_GPCR_Srz 159 evetikvvylilfiilnillflsallYipImisirKlshLaSaqqnkpqkYIfwQtil 216
                                       +++++ +++  +  +l  l+f+s  l+i  + s+rK s ++   + +   ++++ ++ 
  gi|330508176|ref|YP_004384604.1|  11 SWTNFFMLTGSVAATLIGLIFVSVSLHIDFIASVRKDSDMNTMARQTFGDFLMILSFA 68 
                                       378888888899999999********************99988888887777776654 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.054
                      7TM_GPCR_Srz  55 vilivllilillleskksliililllllllil 86 
                                       ++++v ++ i +l+  ++++ +i+l++++l++
  gi|330508176|ref|YP_004384604.1| 131 FAIVV-FLAIGILHGDTRYLDWIVLVVIWLMI 161
                                       22222.22222222234555555555555444 PP

>> PalH  PalH/RIM21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   7.6   0.00052       4.7     247     313 ..     118     185 .]       7     185 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00052
                              PalH 247 ketilllilnllvillpvvffildis.nadvaewkeliiwvlkllitvivWewierieklerkeekeg 313
                                       + +  lli n +++ + v + i +   +     w  l++  l + +t+++W ++ ++  ++r++e++g
  gi|330508176|ref|YP_004384604.1| 118 QMLGRLLIPNTVCFAIVVFLAIGILHgDTRYLDWIVLVVIWLMISSTINAWDLMLQVADMKREKEQQG 185
                                       333456667777775444444444445888899*******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1481.88
//
Query:       gi|330508177|ref|YP_004384605.1|  [L=247]
Description: metallo-beta-lactamase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-30  106.0   0.9    2.1e-30  105.7   0.9    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    7.1e-15   55.5   0.4      1e-14   55.1   0.4    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0033   17.3   0.2     0.0086   16.0   0.2    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.9   3.6e-34   2.1e-30       2     200 ..      50     221 ..      49     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 3.6e-34
                                       EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyla 78 
                                       r+L+D +pdlr q l        +++++++d+V++thaHyDH+ag+ ++ + +  ++++ya k +++++ + +   +
  gi|330508177|ref|YP_004384605.1|  50 RVLVDSSPDLRWQ-LL-------KKDIASVDGVIWTHAHYDHYAGFGDFHRVQS-HVDVYALKNTMDYILNYLY--F 115
                                       8*********999.32.......45899***********************765.5*************99965..4 PP

                                       CHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S.---HHHHHHH CS
                     Lactamase_B_2  79 leeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg.yipeeigerl 154
                                       l +     +h++ +g++fe++  g+++t++ ++h   +        t+G+ri++g k v+ + Dt+ ++pee  e++
  gi|330508177|ref|YP_004384605.1| 116 LAPV----RHDVIAGQPFEIA--GMQFTLFNVNHPPIE--------TVGVRIDNGSKVVVITSDTKmEVPEESLELM 178
                                       4555....679999******9..899****99999888........*******9999999999**97788******* PP

                                       CT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 155 ggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                       ++adl+l d+   ++  +     H+t +ea+e+a++lg+krl+l+H
  gi|330508177|ref|YP_004384605.1| 179 RDADLMLADAI--TPPGYT-ISKHMTADEAMELAERLGTKRLILTH 221
                                       *******9955..454433.689*********************** PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.4   1.7e-18     1e-14       3     197 .]      34     221 ..      32     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1.7e-18
                                       CCSSEEEEEE..ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEH CS
                       Lactamase_B   3 pdpvnsylie..gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavae 77 
                                       +++ +s+l+e   ++g +L+D+  + +++++       ++++  vd vi TH+H+DH++g g++ +    + ++  +
  gi|330508177|ref|YP_004384605.1|  34 RRMRFSILLEsdEEDGRVLVDSSPDLRWQLL-------KKDIASVDGVIWTHAHYDHYAGFGDFHRVQSHVDVYALK 103
                                       5678999***9788****************6.......89************************************* PP

                                       HHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSS CS
                       Lactamase_B  78 eapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDalla 154
                                        +  ++ +++++ a+             +dv      ++ag+  +l  + +p+   +++++++g++ v++t D+  +
  gi|330508177|ref|YP_004384605.1| 104 NTMDYILNYLYFLAPV-----------RHDVIAGQPFEIAGMQFTLFNVNHPPIETVGVRIDNGSKVVVITSDTKME 169
                                       **********665555...........567888888888888888888888888999999***************** PP

                                       HHCCCCCC.............TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 155 getgridl............tlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                        ++++++l            t+ g +  ++  a+++++    +++l +++l+++H
  gi|330508177|ref|YP_004384605.1| 170 VPEESLELmrdadlmladaiTPPGYTISKHMTADEAMEL---AERLGTKRLILTH 221
                                       ********9999999997777777777777777777754...4477777777776 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.4e-06    0.0086       9     163 .]      39     221 ..      38     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                     Lactamase_B_3   9 sfllet.a.garilvDPfkanlgyeppa...eeaDlvlisqaledHahletl.kqlaenvkvlee............ 67 
                                       s+lle+ + + r+lvD     l ++  +    ++D v+ ++a+ dH++   +  ++++ v+v +             
  gi|330508177|ref|YP_004384605.1|  39 SILLESdEeDGRVLVDSSP-DLRWQLLKkdiASVDGVIWTHAHYDHYAGFGDfHRVQSHVDVYALkntmdyilnyly 114
                                       677887423699****764.4444444444599**************976541445334433333445555555666 PP

                     Lactamase_B_3  68 ...........geslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvl 133
                                                  g+ +e++g++++ ++ +h      ++ e +g +++ +   ++   ++  e  +e+l+ + ++D++l
  gi|330508177|ref|YP_004384605.1| 115 flapvrhdviaGQPFEIAGMQFTLFNVNH------PPIETVGVRIDNGSKVVVITSDTKMEVPEESLELMRDADLML 185
                                       66666555554555666666666666666......5567799999999999999*********************** PP

                     Lactamase_B_3 134 tPvgg......pltlgqeealelakrLkpklvlPmh 163
                                       +  +       ++ + ++ea+ela+rL  k  + +h
  gi|330508177|ref|YP_004384605.1| 186 ADAITppgytiSKHMTADEAMELAERLGTKRLILTH 221
                                       *9999998888889999**********988887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1815.92
//
Query:       gi|330508178|ref|YP_004384606.1|  [L=430]
Description: ATPase [Methanosaeta concilii GP6]
Scores for complete sequence (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    2.7e-34  118.5   0.0    1.6  1  AAA           ATPase family associated with various cellular 
    1.9e-11   43.6   0.0    4.8e-11   42.3   0.0    1.7  1  AAA_lid_3     AAA+ lid domain
    2.3e-05   24.7   0.3      0.021   15.1   0.1    3.7  3  AAA_22        AAA domain
    0.00084   19.9   0.0     0.0029   18.1   0.0    2.1  1  AAA_18        AAA domain
     0.0009   19.3   0.0     0.0038   17.2   0.0    2.2  1  AAA_5         AAA domain (dynein-related subfamily)
     0.0047   17.2   0.2      0.019   15.2   0.0    2.1  3  AAA_28        AAA domain
     0.0051   17.2   0.4       0.11   12.9   0.4    2.8  1  AAA_16        AAA ATPase domain
     0.0051   16.0   0.0      0.053   12.7   0.0    2.3  3  DUF815        Protein of unknown function (DUF815)
     0.0092   16.1   0.0      0.099   12.7   0.0    2.4  2  AAA_2         AAA domain (Cdc48 subfamily)
  ------ inclusion threshold ------
      0.027   14.6   0.1      0.087   13.0   0.1    2.0  1  AAA_33        AAA domain
      0.027   13.8   0.0      0.062   12.7   0.0    1.6  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.08   12.5   0.0       0.17   11.4   0.0    1.5  1  AAA_7         P-loop containing dynein motor region
       0.08   12.7   0.0       0.14   11.9   0.0    1.4  1  AAA_11        AAA domain
      0.096   12.8   0.0        0.3   11.2   0.0    1.9  1  MMR_HSR1      50S ribosome-binding 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 !  118.5   0.0   2.1e-37   2.7e-34       1     131 [.     219     347 ..     219     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 2.1e-37
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       +l++GppGtGKT++a+a+ + ++ +++e+ +s ++s+y+ge++k+i ++f+ ak+ + p+il+iDE+d +ak+r+++
  gi|330508178|ref|YP_004384606.1| 219 LLFVGPPGTGKTSTARALSSWFSLPIVEVRLSMITSQYLGETSKNIDKVFELAKRLS-PCILLIDEFDFVAKTRTSD 294
                                       69******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieie 131
                                       e++  +r+vn+Ll+++d+ +  e+ v++++atn+p+ ld a   +Rfd++++++
  gi|330508178|ref|YP_004384606.1| 295 EHGAMKRAVNTLLKAIDEINLVEHGVLLLAATNHPQLLDYAAW-RRFDKVLNFP 347
                                       *******************************************.7*****9998 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   3.8e-14   4.8e-11       1      43 [.     368     410 ..     368     412 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 3.8e-14
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                                       +vd + LA++T+GySG Dl  ++reA+l+Al +++k + ++d+
  gi|330508178|ref|YP_004384606.1| 368 NVDTATLAKMTDGYSGSDLRLVIREAVLNALLENRKGLCQQDL 410
                                       7999********************************9999997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.5   1.9e+03      37      80 ..     115     168 ..      98     190 .. 0.65
   2 !   15.1   0.1   1.7e-05     0.021       8      40 ..     219     242 ..     216     331 .. 0.88
   3 ?    0.6   0.0      0.47   6.1e+02      40      71 ..     341     379 ..     320     419 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.5
                            AAA_22  37 e..........erpevvfvtlpsstsskdl.lrellralglelkaerlsseelle 80 
                                       +           + +v + ++++++++ +  ++++   +++ +k+  ++ +ell+
  gi|330508178|ref|YP_004384606.1| 115 NpalayfyenyDSMGVSYSEAKNGNKPLSAdREWIDARIKELCKD-QKEADELLK 168
                                       245555554444555667888888855555599999999998888.666666654 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.7e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerp 40 
                                       l+ +G++GtGKT ++r l +++         + 
  gi|330508178|ref|YP_004384606.1| 219 LLFVGPPGTGKTSTARALSSWF---------SL 242
                                       6789****************99.........44 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.47
                            AAA_22  40 pevvfvtlpsstsskdllrellralglelka.......e 71 
                                       ++v+ + lp ++++k +l ++l+ ++ + ++        
  gi|330508178|ref|YP_004384606.1| 341 DKVLNFPLPDQETRKRILDKILEPINANVDTatlakmtD 379
                                       556688888899999999999988887766644444441 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.3e-06    0.0029       3     110 ..     221     357 ..     219     375 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.3e-06
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.......aldeskr 51 
                                         G+pG+GKt+ a++Ls+   +                      +++ ++ak   +++   +e        +++++ 
  gi|330508178|ref|YP_004384606.1| 221 FVGPPGTGKTSTARALSSWFSLpivevrlsmitsqylgetsknIDKVFELAKRLSPCILLIDEfdfvaktRTSDEHG 297
                                       68**************8875557777777778888888888886667777776666666666677788776666666 PP

                            AAA_18  52 ldedkldklldaleenssaleegknlvidghlaele.seaakdikk..vvLtaspeelleRl 110
                                       + +  ++ ll+a++e++  l e+++l++       + ++aa+++        ++++e ++R+
  gi|330508178|ref|YP_004384606.1| 298 AMKRAVNTLLKAIDEIN--LVEHGVLLLAATNHPQLlDYAAWRRFDkvLNFPLPDQETRKRI 357
                                       66666688888888876..5888888887766555524444443334444455556666666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     3e-06    0.0038       2      36 ..     219     253 ..     218     340 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3e-06
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdt 36 
                                       +l vGppGtgK++ a+ l++ +  ++++v l+  t
  gi|330508178|ref|YP_004384606.1| 219 LLFVGPPGTGKTSTARALSSWFSLPIVEVRLSMIT 253
                                       799******************99998888887533 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.8   7.5e+03     132     146 ..     144     158 ..     130     161 .. 0.75
   2 !   15.2   0.0   1.5e-05     0.019       3      42 ..     220     260 ..     218     277 .. 0.71
   3 ?   -3.3   0.0       7.4   9.5e+03      96     118 ..     327     350 ..     320     355 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.8
                            AAA_28 132 eereaiderlrealr 146
                                       ++re+id+r++e+++
  gi|330508178|ref|YP_004384606.1| 144 ADREWIDARIKELCK 158
                                       578999999998876 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.5e-05
                            AAA_28   3 vitGgestGKTtlleaLaar.gypvvpEaareileeklakg 42 
                                        ++G+++tGKT++++aL++    p+v+    +i+++ l ++
  gi|330508178|ref|YP_004384606.1| 220 LFVGPPGTGKTSTARALSSWfSLPIVEVRLSMITSQYLGET 260
                                       699***************98667766655555555555554 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 7.4
                            AAA_28  96 aeaeleaaarekrydlvfllp.pa 118
                                        +++l + a+ +r d+v+ +p p+
  gi|330508178|ref|YP_004384606.1| 327 NHPQLLDYAAWRRFDKVLNFPlPD 350
                                       567788888888899998887445 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   0.4   8.7e-05      0.11      27      45 ..     219     237 ..     205     419 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.7e-05
                            AAA_16  27 vllsGesGvGKsslvrell 45 
                                       +l++G++G+GK+s +r+l 
  gi|330508178|ref|YP_004384606.1| 219 LLFVGPPGTGKTSTARALS 237
                                       899************9987 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.7   3.5e+03      22      42 ..      58      78 ..      44      83 .. 0.72
   2 !   12.7   0.0   4.1e-05     0.053      55     123 ..     218     291 ..     165     336 .. 0.72
   3 ?    0.2   0.0      0.26   3.3e+02     185     222 ..     339     376 ..     334     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.7
                            DUF815 22 vdevklddLvgidkqkealve 42
                                      v + +++++ gid+ k+a+++
  gi|330508178|ref|YP_004384606.1| 58 VTSSDVQKIYGIDNVKAAIKD 78
                                      456678899999999998876 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.1e-05
                            DUF815  55 nvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellrerper...filfvDDLsFeeeee 123
                                       ++L++G  GtGK s+ +al + ++     +rl  ++ + l e +k ++++ e ++r   +il++D   F ++ +
  gi|330508178|ref|YP_004384606.1| 218 KLLFVGPPGTGKTSTARALSSWFSLPIveVRLSMITSQYLGETSKNIDKVFELAKRlspCILLIDEFDFVAKTR 291
                                       6799*****************999887679999999999999888888776655553338*****999966543 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.26
                            DUF815 185 RFGlwlgFykldqeeYleiveklakklglelekeelee 222
                                       RF  +l F  +dqe+  +i++k+++  + ++++++l +
  gi|330508178|ref|YP_004384606.1| 339 RFDKVLNFPLPDQETRKRILDKILEPINANVDTATLAK 376
                                       9999**********************999999988766 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.67   8.6e+02      42      80 ..     155     198 ..     128     207 .. 0.75
   2 !   12.7   0.0   7.8e-05     0.099       3     106 ..     216     313 ..     214     320 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.67
                                       G---.----THHHHHHHHHTTT-HHHHTTSEEEEE....TGGG- CS
                             AAA_2  42 elle.eeevehlvsrligappgyvgaeegGivllD....EidKi 80 
                                       el + ++e+++l++   +++p +v+   +G +l D    Ei+K 
  gi|330508178|ref|YP_004384606.1| 155 ELCKdQKEADELLKLAYIKAPEDVRDSISGLILTDdqktEIEKT 198
                                       44444678888888888888888888888888888666667775 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.8e-05
                                       ---EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG CS
                             AAA_2   3 iisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidK 79 
                                       i+++l++gp g+Gkt +a+al++  ++       +++ +  +   +     s+ i +     ++    i+l+DE d 
  gi|330508178|ref|YP_004384606.1| 216 IGKLLFVGPPGTGKTSTARALSSWFSL------PIVEVRLSMITSQYLGETSKNIDKVFELAKRLSPCILLIDEFDF 286
                                       7899*******************9996......33333333332222333344444444444455567********* PP

                                       -------------HHHHHHHHHHHH-- CS
                             AAA_2  80 ihpkessgadvSregVqrdLLqilegg 106
                                       ++++++s +    +  ++ LL+ +++ 
  gi|330508178|ref|YP_004384606.1| 287 VAKTRTSDEHGAMKRAVNTLLKAIDEI 313
                                       **9855555555556667888888875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   6.8e-05     0.087       3      21 ..     220     238 ..     219     382 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.8e-05
                            AAA_33   3 llvGlpGsGKstlaerllk 21 
                                       l+vG+pG+GK+  a+ l  
  gi|330508178|ref|YP_004384606.1| 220 LFVGPPGTGKTSTARALSS 238
                                       89*************9853 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   4.8e-05     0.062      24      45 ..     218     239 ..     205     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlpsl 45 
                                       +ll+vGppG+GKt  a++l+s 
  gi|330508178|ref|YP_004384606.1| 218 KLLFVGPPGTGKTSTARALSSW 239
                                       69***************99875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.17      35      58 ..     218     241 ..     204     274 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                             AAA_7  35 pvllvGptGtGKtviikdllkkld 58 
                                       ++l+vGp GtGKt++++ l + ++
  gi|330508178|ref|YP_004384606.1| 218 KLLFVGPPGTGKTSTARALSSWFS 241
                                       68*************998776555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.14      12      39 ..     200     238 ..     187     281 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                            AAA_11  12 salsese...........itliqGPPGtgKTktivells 39 
                                       +al+++e             l+ GPPGtgKT+t  +l s
  gi|330508178|ref|YP_004384606.1| 200 KALENREylrqiglfeigKLLFVGPPGTGKTSTARALSS 238
                                       45555555555556666678999********99877755 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   0.00024       0.3       2      45 ..     219     272 ..     218     344 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                                       EEEEESTTSSHHHHHHHHHT.........S.TEEESSSTTSSSSEEEEEEEETT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg.........e.kaivsdkpgtTrdinegrvklkg 45 
                                        ++vG p +GK++  +al+          +   i+s++ g T + + + ++l +
  gi|330508178|ref|YP_004384606.1| 219 LLFVGPPGTGKTSTARALSSwfslpivevRlSMITSQYLGETSKNIDKVFELAK 272
                                       579***************97777777754446799*******999888777443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 2964.13
//
Query:       gi|330508179|ref|YP_004384607.1|  [L=417]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete 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   88.4   0.1    5.4e-25   87.5   0.1    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family
    3.7e-21   75.6   0.0    6.6e-21   74.8   0.0    1.4  1  DEDD_Tnp_IS110  Transposase
  ------ inclusion threshold ------
      0.036   14.4   1.0      0.081   13.2   0.1    2.0  2  Init_tRNA_PT    Rit1 DUSP-like domain


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.1     9e-29   5.4e-25       2      83 ..     249     330 ..     248     336 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 9e-29
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaaira 78 
                                       +++ s+pG+G++ aa+++ae+gd r f+sa+++a+y+G++p+++qS++k r g+i+k G++++Rr+L+e A a++r+
  gi|330508179|ref|YP_004384607.1| 249 KIILSVPGVGFISAATIIAEMGDYRDFPSADKMAKYFGIVPSVYQSAGKLRTGKITKTGSKHMRRILVEVAKAISRT 325
                                       6899***********************************************************************99 PP

                    Transposase_20  79 npelr 83 
                                       ++ +r
  gi|330508179|ref|YP_004384607.1| 326 KKNSR 330
                                       75554 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0   1.1e-24   6.6e-21       1     153 [.       9     152 ..       9     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.1e-24
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G D++kd   a++i+++g +l +er++++++gl a+ ++   ++++ + +ve+tg ++++++++ le +++ ++ n
  gi|330508179|ref|YP_004384607.1|   9 CGADIHKDFLIATMISRSGLKL-QERFNMNQDGLLAFRSW-IINHRCQRLAVESTGGFWYPIFTI-LEGHVEFILAN 82 
                                       79*************9999885.668**************.889****************88876.7899******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdqv 153
                                       ++++++++     ++KtD++D++ IA + +  + ++p++  +++y++Lr++tr+re+lv+ r++ kn++++ L   
  gi|330508179|ref|YP_004384607.1|  83 AYQIRNIE-----HKKTDKLDSERIAIYCL-NNLITPSRIYPKDYRDLRSITRARETLVNARSKIKNQIHQSLSTC 152
                                       *****995.....89***************.****************************************99765 PP

>> Init_tRNA_PT  Rit1 DUSP-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.2   7.1e+03      26      43 ..     133     152 ..     119     162 .. 0.47
   2 ?   13.2   0.1   1.4e-05     0.081      10      80 ..     304     378 ..     296     389 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                      Init_tRNA_PT  26 dfvrkrlsedkk..kkilva 43 
                                       + v++r++ +++  +++  +
  gi|330508179|ref|YP_004384607.1| 133 TLVNARSKIKNQihQSLSTC 152
                                       33333333322222333333 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.4e-05
                      Init_tRNA_PT  10 gKkgsknLrtalpkivdfvrkrlsedkk....kkilvacetGkdlsvgvaLailcklfddakls...eeqsesnitK 79 
                                        K+gsk++r +l ++ ++++++ ++++     ++il+ c + +   v++a  +lc ++   +l    e+ +e+++tK
  gi|330508179|ref|YP_004384607.1| 304 TKTGSKHMRRILVEVAKAISRTKKNSRLmrffQRILARCGKKNIATVALARKVLCIIY---HLLmnhENYQEPEVTK 377
                                       49*****************99966655599**99******999999999888888888...2222235666777777 PP

                      Init_tRNA_PT  80 d 80 
                                       +
  gi|330508179|ref|YP_004384607.1| 378 T 378
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2930.82
//
Query:       gi|330508180|ref|YP_004384608.1|  [L=528]
Description: Na+/solute symporter [Methanosaeta concilii GP6]
Scores for complete 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-58  198.3  38.9    2.5e-58  197.9  38.9    1.2  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.9  38.9   1.4e-62   2.5e-58       1     406 []      34     451 ..      34     451 .. 0.85

  Alignments for each domain:
  == domain 1  score: 197.9 bits;  conditional E-value: 1.4e-62
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllel.galllvlllllllaerlr....nagalTlp 72 
                                       y +agr+  ++ +++s +a+ is + +vG  G + + G++ ++l + ++ +++ +++++ ++r r    n++a+T+p
  gi|330508180|ref|YP_004384608.1|  34 YLVAGRKAHPYIMAMSYGATFISTSAIVGFGGNAGLFGMGLLWLTFfNIFVGIFIAFVFYGKRTRkighNLNAMTFP 110
                                       899****************************************997255556666666667777799********** PP

                               SSF  73 dylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdti 149
                                       ++l kRf+++    y+s ++++l + l+ +v l+g+a+++e++l +++++a+l+  +++a Y++ GGl+ v+ytd  
  gi|330508180|ref|YP_004384608.1| 111 ELLGKRFDSRF-VQYFSGVVIFLGMPLYAAVVLIGAARFMETTLAIDFHVALLIYSVIIAAYVIWGGLRGVMYTDAF 186
                                       *********99.99*************************************************************** PP

                               SSF 150 qavlmlvgalilliivllevGgleslveklkeaapkvvdl...........ltpdslkllrdpltalslwlglvlGv 215
                                       q+++m +g  +ll+++  ++Gg+  + + l+++a  v ++           +   +       +++++l  g+++Gv
  gi|330508180|ref|YP_004384608.1| 187 QGTIMFFGMAFLLFMTYAHLGGITVAHQALTNMAHLVPENlalmghtgwteMPTLGSTWWWTLVSTIVL--GVGIGV 261
                                       ***********************9999999999988844436667666544334444445555555555..889999 PP

                               SSF 216 aglphilvRflaakdakailkgvlkltivlilvligmisiilfa.iklagavp..kavgt.evgvsniaypeLvvkl 288
                                         +p  +vRf+++k+++++++g l++ +v+il++ g ++  ++a  ++++++   ++++t + g+++ ++p  +++ 
  gi|330508180|ref|YP_004384608.1| 262 LAMPQLAVRFMTVKSSRELHRGTLIG-GVFILFMTG-VAFTVGAlSNVFFFNTqgDIAITvAKGNADSIIPIYINAA 336
                                       999**********************9.677888888.44444441334444445566665167899*********** PP

                               SSF 289 lpnllaGlllavmlAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkg 365
                                       +p+++  l++   lAa mst +s++    sa+ +D+Y+ i +k+  +  ++ +++ i+ +v+++    l    +++ 
  gi|330508180|ref|YP_004384608.1| 337 MPEWFVYLFMLTLLAAAMSTSSSQFHTQGSAIGRDIYETISHKKGGSSIMVTRAGIIVAMVIAV---TLGYILPDNI 410
                                       ********************************************99998888888887777654...3444444443 PP

                               SSF 366 vlklvelafaglasavlavillalfwkrvneqGAlagliiG 406
                                       ++   ++ f+  asa+l++   al+wk +++ GA+agl++G
  gi|330508180|ref|YP_004384608.1| 411 IARGTAIFFGLCASAFLPMYTAALYWKGATKAGAIAGLLTG 451
                                       8999999999*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1062  (0.0592336); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 3592.91
//
Query:       gi|330508181|ref|YP_004384609.1|  [L=406]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-21   75.6   0.1    4.3e-21   74.6   0.1    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.8e-20   72.0   0.0      1e-19   70.9   0.0    1.4  1  OrfB_IS605      Probable transposase
    3.2e-18   64.9   0.7    6.6e-18   63.9   0.7    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.4   0.3      0.023   14.7   0.3    1.3  1  DZR             Double zinc ribbon
      0.016   14.1   0.1      0.026   13.4   0.1    1.2  1  Pestivirus_E2   Pestivirus envelope glycoprotein E2
      0.039   13.5   0.0      0.068   12.7   0.0    1.4  1  OpuAC           Substrate binding domain of ABC-type glycine 
       0.14   12.7   0.8       0.82   10.3   0.2    2.4  2  FeoB_Cyto       FeoB cytosolic helical domain
       0.51   10.0   3.5         11    5.7   0.3    3.0  3  RecR            RecR protein


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 !   74.6   0.1   1.9e-24   4.3e-21       1      68 [.     315     382 ..     315     383 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.9e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++ l +  +yka  +G  v++v+p++TSk Cs+Cg  ++++ls+r+++C++Cg+++drD+nAaiNil+
  gi|330508181|ref|YP_004384609.1| 315 WNMLVTLTSYKAASAGSMVVLVDPRNTSKMCSRCGILVQKDLSERVHNCTQCGLSMDRDWNAAINILR 382
                                       667777889*********************************************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.0   4.5e-23     1e-19      10     117 ..     197     301 ..     186     303 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 4.5e-23
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +p+ k ++ +g+D+G++ +at++++    ++ ++r++++++ +la+ +++l++  k++  +kka + + r+h+++++
  gi|330508181|ref|YP_004384609.1| 197 KPPWKDGSLVGVDVGLESFATLSNGV---KIANPRFFREEEHELARVQRKLSKAPKGTPERKKALKVVERVHERIAN 270
                                       556678899*****************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r +++h ++++l++++  ++ e+Ln+++m+
  gi|330508181|ref|YP_004384609.1| 271 KRYEFAHRISNQLVNRYGLIAFEDLNIKGMM 301
                                       ******************************8 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.7   2.9e-21   6.6e-18       1      47 []      25      70 ..      23      70 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 2.9e-21
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkayk+r+yPT+ Q++k++rt++ +R+ YN  L+ rk a+e egk
  gi|330508181|ref|YP_004384609.1| 25 M-LKAYKFRIYPTKSQRTKMERTLDLCRWTYNETLEIRKTAWEDEGK 70
                                      5.*****************************************9997 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3     1e-05     0.023      10      44 ..     340     376 ..     336     379 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + +++Cs+Cg  +++  +   ++C +Cg ++d +++ 
  gi|330508181|ref|YP_004384609.1| 340 NTSKMCSRCGILVQKDLSerVHNCTQCGLSMDRDWNA 376
                                       6789********997766899***********99986 PP

>> Pestivirus_E2  Pestivirus envelope glycoprotein E2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.2e-05     0.026     126     184 ..     308     367 ..     293     375 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                       EESS-CT--EEEEEEEE-SSS--EEEEEEE.EE-S-B---TT---EEEETTEEEEEEE-S CS
                     Pestivirus_E2 126 qmvcpigwtgtvsctsfnmdtlattvvrty.rrskpfphrqgcitqknlgedlhncilgg 184
                                       + +  ++w   v+ ts++  +  + vv    r +  +  r g++ qk+l e +hnc   g
  gi|330508181|ref|YP_004384609.1| 308 KSIGDVAWNMLVTLTSYKAASAGSMVVLVDpRNTSKMCSRCGILVQKDLSERVHNCTQCG 367
                                       5677899***********99998888876526677899******************8765 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 ?   12.7   0.0     3e-05     0.068     115     215 ..     260     359 ..     244     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                                       TEEEEEHHCCHSTTSHHCCHHHHHHHHHHT-TTCEEEGSCEEEEHH..HHHHHHHTTCSSEEEEETTSTHHHHTTEE CS
                             OpuAC 115 lelgakgeflgrpdgwgcekvtegllkaYgldkvelvegseaamda..elyaaykrgepvvvyawtPdwaikkydlv 189
                                       + +++  ++ +    ++ ++++++l++ Ygl  +e++  + ++m++   l++++ +  +++  + t   a ++  +v
  gi|330508181|ref|YP_004384609.1| 260 VVERVHERIANKRYEFA-HRISNQLVNRYGLIAFEDL--NIKGMMHnhNLAKSIGDVAWNMLVTLTSYKAASAGSMV 333
                                       55666777777777888.999**********667776..999***999***************************** PP

                                       E-B-TTSTS-SSEEEEEEEEHHHHHH CS
                             OpuAC 190 vLedpkglfppaynvvpvvrkefaek 215
                                       vL dp++++  +++  ++v+k++ e+
  gi|330508181|ref|YP_004384609.1| 334 VLVDPRNTSKMCSRCGILVQKDLSER 359
                                       **********************9987 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.2   9.5e+03      47      67 ..      87     107 ..      75     115 .. 0.60
   2 ?   10.3   0.2   0.00036      0.82      68      90 ..     262     284 ..     231     285 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.2
                         FeoB_Cyto  47 edpelraeveearkeleaelg 67 
                                       ++pel++   ++ +++ ++ +
  gi|330508181|ref|YP_004384609.1|  87 NKPELKEVFSQVLQNVHERVD 107
                                       446667666777666666554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00036
                         FeoB_Cyto  68 edledvIvdarykfiegilrevv 90 
                                       e + + I+++ry+f+++i+++ v
  gi|330508181|ref|YP_004384609.1| 262 ERVHERIANKRYEFAHRISNQLV 284
                                       67899**************9987 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.2   2.7e+03       5      16 ..      95     106 ..      93     107 .. 0.85
   2 ?    4.5   0.1     0.011        26      13      29 ..     339     355 ..     334     356 .. 0.74
   3 ?    5.7   0.3    0.0048        11      11      26 ..     355     370 ..     354     374 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHH- CS
                              RecR   5 LaeaLqeakekv 16 
                                       +++ Lq+++e+v
  gi|330508181|ref|YP_004384609.1|  95 FSQVLQNVHERV 106
                                       899999999987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
                                       HHH-EE-TTT--EESSS CS
                              RecR  13 kekvrhCsrCgnlteed 29 
                                       +++ + CsrCg l  +d
  gi|330508181|ref|YP_004384609.1| 339 RNTSKMCSRCGILVQKD 355
                                       667799*****986665 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0048
                                       HHHHH-EE-TTT--EE CS
                              RecR  11 eakekvrhCsrCgnlt 26 
                                       ++ e+v+ C +Cg   
  gi|330508181|ref|YP_004384609.1| 355 DLSERVHNCTQCGLSM 370
                                       6889********9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); 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):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2735.39
//
Query:       gi|330508182|ref|YP_004384610.1|  [L=333]
Description: hypothetical protein MCON_2313 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-06   26.9   0.1       0.14   12.2   0.0    3.3  3  Nitroreductase  Nitroreductase family
    1.3e-05   24.8   0.0    3.7e-05   23.4   0.0    1.7  2  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   1.5e-05      0.14      18      44 ..      13      39 ..       7      50 .. 0.85
   2 !    9.7   0.0   8.9e-05       0.8     101     145 ..      49      93 ..      40     108 .. 0.79
   3 ?    0.8   0.0      0.05   4.4e+02     112     157 ..     250     298 ..     240     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHHHHTS--GGG---EEEEEE CS
                    Nitroreductase 18 eelekileaarraPsagnlqpwrfvvv 44
                                      e++  +l+ a  aPs  n+qpwrf v 
  gi|330508182|ref|YP_004384610.1| 13 EKMTFLLNYAILAPSIYNTQPWRFNVS 39
                                      66777999****************886 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 8.9e-05
                                       TS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGG CS
                    Nitroreductase 101 dkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfde 145
                                       +  +  aa+++ r++++++g a++nl++aA  +G+   +   + e
  gi|330508182|ref|YP_004384610.1|  49 ESRWLEAADGNKREMHISIGNALENLIIAADHFGYNHTISYVPGE 93 
                                       556677899999**********************98766655555 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.05
                                       HHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHH...HHHHHHT-S CS
                    Nitroreductase 112 yryalldagaaaqnllLaAtalGlgscpiggfdeaae...evrkllglp 157
                                       ++++ + ag   +++ L   +++l  +p+++  +a e   ev+ llg +
  gi|330508182|ref|YP_004384610.1| 250 DPESQVRAGQLFERIRLLSSSANLSLQPMNQALQAVEtesEVNGLLGEK 298
                                       5788999999999999999***********9997776666888888755 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   4.2e-09   3.7e-05     156     192 ..      11      51 ..       6      78 .. 0.74
   2 ?   -2.9   0.0      0.47   4.2e+03      70     100 ..     241     273 ..     222     274 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.2e-09
                                       S-HHHHHHHHHHHTS--GGG----EEE.E-SSEE........ CS
                    TM1586_NiRdase 156 lpewfkeileaarlAPsAlNqqpwrfelkdddeiki.....k 192
                                        +e++  +l+ a+lAPs  N+qpwrf+++d ++i +     +
  gi|330508182|ref|YP_004384610.1|  11 SEEKMTFLLNYAILAPSIYNTQPWRFNVSD-GSIMVmadesR 51 
                                       4789999********************666.78888444440 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.47
                                       EE----SS..HHHHHHHHHHHHHHHHHHHHTT- CS
                    TM1586_NiRdase  70 ialvgekk..edleekaGYygeqlvLkltalGl 100
                                       + ++ ++    +++++aG + e++ L+ ++++l
  gi|330508182|ref|YP_004384610.1| 241 LGFITSQMndPESQVRAGQLFERIRLLSSSANL 273
                                       444443332267889999999999888777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.54
# Mc/sec: 1850.88
//
Query:       gi|330508183|ref|YP_004384611.1|  [L=223]
Description: hypothetical protein MCON_2317 [Methanosaeta concilii GP6]
Scores for complete 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  118.8   0.0    2.8e-34  118.5   0.0    1.1  1  LUD_dom   LUD domain


Domain annotation for each model (and alignments):
>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.5   0.0   1.6e-38   2.8e-34       2     189 .]      33     217 ..      32     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 1.6e-38
                           LUD_dom   2 eefienleangaevyyaktaeealelilellkeksvvseggstdlgeiglapalhsgreevldlfeekl...trear 75 
                                       + +i+++e++g++v++  ++++al++i+el++++s v+ g st+l eig++++++sg++e+ d+    +   ++++r
  gi|330508183|ref|YP_004384611.1|  33 ASTIKAIEKRGVRVVRLPDGNQALAKIKELIPPGSEVMNGSSTTLIEIGFQELMDSGEHEWKDMKLMVTgenDAQKR 109
                                       5789***********************************************************9888779999**** PP

                           LUD_dom  76 eelrekfltadvgitganfaiAetGtlvlvdnegnr.raltflpkvhivvvginkivpdledavkrlkt..aprnat 149
                                        ++r+k  t+d++++g+n aiA tG+lv +d +g r  a  ++  + ++v+g+nkivp+l+da++r+++   p +  
  gi|330508183|ref|YP_004384611.1| 110 AKIRRKTVTSDYFLSGVN-AIAMTGELVGCDATGSRvGAWPYGAGNLLLVAGTNKIVPSLDDALRRIREytFPLEDL 185
                                       ******************.**************************************************55555555 PP

                           LUD_dom 150 rlqkktpyvsfisgpsrtadielvlvygvhgpkrihvilv 189
                                       r        ++   ps+++    +l+     p+r++++l+
  gi|330508183|ref|YP_004384611.1| 186 R------SRNVYGVPSKIGKCV-ILANES-QPGRVTLLLI 217
                                       5......455555788888855.554444.6888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1749.19
//
Query:       gi|330508184|ref|YP_004384612.1|  [L=169]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-15   54.8  49.5    4.4e-09   36.5  16.4    3.2  3  DUF308    Short repeat of unknown function (DUF308)


Domain annotation for each model (and alignments):
>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5  16.4   2.5e-13   4.4e-09       2      72 ..      15      81 ..      14      82 .. 0.88
   2 !   16.0  11.0   6.5e-07     0.012      23      72 ..      94     136 ..      88     137 .. 0.84
   3 !   20.7  14.4   2.2e-08   0.00039       1      46 [.     123     168 ..     123     169 .] 0.96

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.5e-13
                            DUF308  2 lGillivlGilalllPvaallalvllfGilllvsGivqiiaafaarkknrggrwlglllGilyliaGllll 72
                                       G+ ++++Gi+++l+P +++++lv ++G+++++ G++ +++ +  +  +     ++ l+Gil +iaG++++
  gi|330508184|ref|YP_004384612.1| 15 QGLAALIIGIYLILYPIMTTIYLVQVLGWYWIFVGLLTLATILMDKTDWM----WRALSGILGIIAGMVVI 81
                                      699************************************88884444333....8899**********987 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 6.5e-07
                            DUF308  23 alvllfGilllvsGivqiiaafaarkknrggrwlglllGilyliaGllll 72 
                                       +lv+++Gil++++G+++++ a+  r+     +w   ++G+l++i+Gll++
  gi|330508184|ref|YP_004384612.1|  94 TLVIVVGILAICFGALSLFWAM--RE-----GWGAAIMGALSMIFGLLII 136
                                       89****************7444..44.....344459***********97 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 2.2e-08
                            DUF308   1 llGillivlGilalllPvaallalvllfGilllvsGivqiiaafaa 46 
                                       ++G l++++G+l++  P++ +++l++l+++l++v+G + i+ af+ 
  gi|330508184|ref|YP_004384612.1| 123 IMGALSMIFGLLIIGSPFVGIAILIYLLAVLAIVGGMATIYLAFQL 168
                                       79******************************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 1313.06
//
Query:       gi|330508185|ref|YP_004384613.1|  [L=391]
Description: GTP-binding/TGS domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-33  115.0   0.0      4e-33  114.3   0.0    1.3  1  MMR_HSR1_C     GTPase of unknown function C-terminal
    9.3e-19   67.6   0.0    9.8e-18   64.3   0.0    2.4  3  MMR_HSR1       50S ribosome-binding GTPase
    7.2e-13   48.4   0.0    2.3e-12   46.8   0.0    1.9  2  TGS            TGS domain
    3.3e-08   33.2   0.1    1.2e-06   28.2   0.0    2.5  2  FeoB_N         Ferrous iron transport protein B
  ------ inclusion threshold ------
       0.06   12.9   0.1        2.4    7.7   0.0    2.8  3  GTP_EFTU       Elongation factor Tu GTP binding domain
       0.11   12.7   0.1        2.9    8.2   0.0    2.4  2  YchF-GTPase_C  Protein of unknown function (DUF933)
       0.24   11.4   2.1          2    8.4   0.2    2.4  2  DUF2786        Protein of unknown function (DUF2786)


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 !  114.3   0.0   1.6e-36     4e-33       1     112 []     219     322 ..     219     322 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 1.6e-36
                        MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLeki 77 
                                       a+NK+D+ a+ en++kl + ++ +  v+pvs+aaE+aLr a+k+gli+Y+pgd df+ik+d    l+ +qk+ Leki
  gi|330508185|ref|YP_004384613.1| 219 AANKMDV-APPENVKKLLALKE-EV-VIPVSGAAEIALRMAEKAGLISYRPGDPDFQIKGD----LNPAQKTGLEKI 288
                                       89*****.***********977.45.9**********************************....************ PP

                        MMR_HSR1_C  78 rdlvlkrygsTGVqealnaavfelldlivVYPVed 112
                                       r  ++k+yg+TGVqe++n+a+felld+iv YPVed
  gi|330508185|ref|YP_004384613.1| 289 RA-LMKQYGGTGVQECINRAIFELLDYIVLYPVED 322
                                       **.99****************************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   3.8e-21   9.8e-18       2      87 ..       4     123 ..       3     156 .. 0.81
   2 ?    0.3   0.0      0.28   7.3e+02      90     114 .]     187     222 ..     145     222 .. 0.67
   3 ?   -2.3   0.0       1.8   4.5e+03      65      88 ..     346     370 ..     312     387 .. 0.55

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 3.8e-21
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.......................EEEEECGG CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.......................ielvDtpG 55 
                                       v+++G+pN+GKSt+++a t  ++ ++++p+tT+d n+g   ++  +                       iel+D++G
  gi|330508185|ref|YP_004384613.1|   4 VGLAGKPNSGKSTFFKAATLVEVDIANYPFTTIDANHGVSYVR-VPcpckdlgiekgcgrckdgvrfiaIELIDVAG 79 
                                       89************************************77643.2245555666677777777888888******** PP

                                       CSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT...........T CS
                          MMR_HSR1  56 liegaseekglgkaflalee.adlillvvdas...........e 87 
                                       l+ +a+ +kglg++fl+  + a+++++v+das           +
  gi|330508185|ref|YP_004384613.1|  80 LVPDAHLGKGLGNEFLDALRvAEAVIHVLDASggtdaegnpvgT 123
                                       9999*************99978********99666555544443 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.28
                                       SHHHHHHHHHHHHH...........TTSEEEEEEES CS
                          MMR_HSR1  90 lkpldeeleellee...........akkplilvlnk 114
                                       l++++++l +++ e             kp+il++nk
  gi|330508185|ref|YP_004384613.1| 187 LTEMKKDLGSWNAEdvkmfaillrrYSKPMILAANK 222
                                       444444554444444444444444689999999998 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHCT.SEEEEEEETTTT CS
                          MMR_HSR1  65 glgkaflaleea.dlillvvdasee 88 
                                           af+ + +  + +l+ +da+++
  gi|330508185|ref|YP_004384613.1| 346 ARDLAFRVHSDIgESFLFAIDARTK 370
                                       3344555556644778888887732 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.7   6.9e+03      25      38 ..      85      98 ..      84      98 .. 0.86
   2 !   46.8   0.0   8.9e-16   2.3e-12       3      59 ..     332     388 ..     326     389 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.7
                                      HHSTTHHHHEEEEE CS
                               TGS 25 kIhrslakkfiyAl 38
                                      +++++l+++f+ Al
  gi|330508185|ref|YP_004384613.1| 85 HLGKGLGNEFLDAL 98
                                      7899******9885 PP

  == domain 2  score: 46.8 bits;  conditional E-value: 8.9e-16
                                       EEETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                               TGS   3 vytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                       v +Pd+ +  ++rg+t++D+A ++h++++++f+ A+     +r g +h+L+dgdv++Iv
  gi|330508185|ref|YP_004384613.1| 332 VILPDAFL--MKRGSTARDLAFRVHSDIGESFLFAIDARtkMRLGEKHELKDGDVIKIV 388
                                       56677777..9*****************************9*****************9 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   4.6e-10   1.2e-06       2      41 ..       3      42 ..       2      49 .. 0.92
   2 ?    2.2   0.0     0.045   1.1e+02     100     124 ..     208     232 ..     194     252 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 4.6e-10
                                      EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEE CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegk 41
                                      +v l+G+pn+Gk+t+f a t ++ +++N+p +t++ ++g 
  gi|330508185|ref|YP_004384613.1|  3 SVGLAGKPNSGKSTFFKAATLVEVDIANYPFTTIDANHGV 42
                                      5789*******************************99986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.045
                                       HHHHTTSSEEEEEETHHHHHHTTEE CS
                            FeoB_N 100 qllelgvpvvlalnmideaekkgie 124
                                        l   ++p++la n++d+a  ++++
  gi|330508185|ref|YP_004384613.1| 208 LLRRYSKPMILAANKMDVAPPENVK 232
                                       5667789***********9877765 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.21   5.3e+02       4      21 ..       2      19 ..       1      32 [. 0.81
   2 ?    0.9   0.0      0.11   2.8e+02      86     108 ..      93     115 ..      72     121 .. 0.89
   3 ?    7.7   0.0   0.00093       2.4     116     147 ..     207     242 ..     199     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.21
                                      EEEEEEESTTSSHHHHHH CS
                          GTP_EFTU  4 rnigiighvDhGKtTLtd 21
                                      + +g++g  ++GK+T+  
  gi|330508185|ref|YP_004384613.1|  2 LSVGLAGKPNSGKSTFFK 19
                                      578999*********975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.11
                                       HHHHHHHT-SEEEEEEETTTBST CS
                          GTP_EFTU  86 evirglrvlDgavlvvdaveGve 108
                                       e   +lrv++ ++ v+da+ G  
  gi|330508185|ref|YP_004384613.1|  93 EFLDALRVAEAVIHVLDASGGTD 115
                                       67789*************99976 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00093
                                       HHHHHTTTEEEEEEESCGST....HHHHHHHHHHHH CS
                          GTP_EFTU 116 rlalkegvpiivfiNKmDrl....kaelkeiveevk 147
                                        l++++  p+i++ NKmD +     ++l  ++eev 
  gi|330508185|ref|YP_004384613.1| 207 ILLRRYSKPMILAANKMDVAppenVKKLLALKEEVV 242
                                       57889999**********998666555555666555 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0011       2.9      15      41 ..     338     364 ..     336     370 .. 0.89
   2 ?    2.0   0.1     0.093   2.4e+02      66      81 ..     372     387 ..     364     389 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0011
                     YchF-GTPase_C  15 WtikkgttapqaAgviHsDfekgFira 41 
                                       + +k+g+ta + A  +HsD+ + F+ a
  gi|330508185|ref|YP_004384613.1| 338 FLMKRGSTARDLAFRVHSDIGESFLFA 364
                                       6789*******************9866 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.093
                     YchF-GTPase_C  66 legkdyvvqdgDiilf 81 
                                       + g ++ ++dgD+i +
  gi|330508185|ref|YP_004384613.1| 372 RLGEKHELKDGDVIKI 387
                                       4588899******975 PP

>> DUF2786  Protein of unknown function (DUF2786)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2   0.00078         2       6      31 ..     231     258 ..     229     258 .. 0.88
   2 ?    2.1   0.1     0.074   1.9e+02      27      36 ..     286     295 ..     285     296 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00078
                           DUF2786   6 IrKLLalAes..stneaEAeaAlakAqe 31 
                                       ++KLLal e    +  + Ae Al++A++
  gi|330508185|ref|YP_004384613.1| 231 VKKLLALKEEvvIPVSGAAEIALRMAEK 258
                                       89********7445************86 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.074
                           DUF2786  27 akAqeLmary 36 
                                       +k + Lm++y
  gi|330508185|ref|YP_004384613.1| 286 EKIRALMKQY 295
                                       4555666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2698.19
//
Query:       gi|330508186|ref|YP_004384614.1|  [L=288]
Description: coenzyme F420 hydrogenase subunit beta [Methanosaeta concilii GP6]
Scores for complete 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-40  136.5   0.0    8.5e-40  136.1   0.0    1.2  1  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    7.2e-20   70.9   0.2    1.3e-19   70.1   0.2    1.4  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su


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 !  136.1   0.0   9.5e-44   8.5e-40       2     154 ..     104     257 ..     103     258 .. 0.96

  Alignments for each domain:
  == domain 1  score: 136.1 bits;  conditional E-value: 9.5e-44
                       FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqk.....kklkekilltiglfCggnfspealrk..lleelgvdpedvkklefrgkgkfr 71 
                                       +k+++vGtPCqi++lrk+q      +  +eki+l++glfC++nf+++ l++  ++ + g+dp++v ++e+ +kg fr
  gi|330508186|ref|YP_004384614.1| 104 EKIGFVGTPCQIQGLRKVQLleepyQIGQEKIALLVGLFCMENFDYDLLMNglVKGRFGLDPKNVARFEI-KKGMFR 179
                                       79*****************8889987889***********************9999**************.79**** PP

                       FrhB_FdhB_C  72 velkd..ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveage 146
                                       v  k+  + e++l+e++++  ++C  C+d+ +elADisvG+v      g + +g+stvl+rt+kge+l+++a++ag 
  gi|330508186|ref|YP_004384614.1| 180 VIDKQgkVDEVKLEETDQYNFKGCGPCFDFASELADISVGSV------G-SGDGWSTVLTRTDKGEKLYSDALAAGV 249
                                       *9999997799999****************************......8.9************************** PP

                       FrhB_FdhB_C 147 leleelde 154
                                       l++++++e
  gi|330508186|ref|YP_004384614.1| 250 LQEKAVSE 257
                                       ****9987 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.2   1.4e-23   1.3e-19      14      77 ..      33      95 ..      22      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.4e-23
                       FrhB_FdhB_N 14 kaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYtlspnlklL 77
                                       aq+GG++tall  +Le+g+id++iv++++ d+wr++ +++tt++e++aaaG+kYt+ + ++ L
  gi|330508186|ref|YP_004384614.1| 33 LAQDGGVATALLVFALESGMIDCAIVTDKD-DEWRTVSRVVTTADEIRAAAGTKYTINNSVNSL 95
                                      49****************************.89***********************88776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2008.67
//
Query:       gi|330508187|ref|YP_004384615.1|  [L=341]
Description: putative H4MPT-linked C1 transfer pathway protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-21   75.9   0.1      8e-21   74.6   0.1    1.7  2  Hydantoinase_A  Hydantoinase/oxoprolinase
     0.0004   19.1   0.0      0.018   13.7   0.0    2.2  2  MutL            MutL protein
  ------ inclusion threshold ------
      0.045   12.5   0.2          1    8.0   0.1    2.2  2  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.59   3.5e+03      82      97 ..       3      18 ..       2      24 .. 0.78
   2 !   74.6   0.1   1.3e-24     8e-21       3     274 ..      51     315 ..      49     334 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.59
                    Hydantoinase_A 82 ItfDmGGTstDvslik 97
                                      +++D+GG  t+++  +
  gi|330508187|ref|YP_004384615.1|  3 LGLDIGGANTKAASAD 18
                                      689****999998766 PP

  == domain 2  score: 74.6 bits;  conditional E-value: 1.3e-24
                    Hydantoinase_A   3 etavvnAylspilreylesvekslekrgak...............arlmvmqsdGglvsadearkkpvetilSGPaa 64 
                                       +++v++++l+++++++ e+ve++++ +  +               +++   + + g++++ + +  +++++++++ a
  gi|330508187|ref|YP_004384615.1|  51 VAVVITGELADCFSSKREGVESIMAVACRAfscpvyfwghdgfarNDIINPTNSTGIIDMINTTD-ILHVAAANWSA 126
                                       789********************999887799999999999998844444444445666666666.48********* PP

                    Hydantoinase_A  65 GvvgaaatsklagekkvItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsil.vvdeggkl 140
                                       +++ +a+   + g+  ++++DmG+T+tD+++i+  ++         + k+++ +l+  ++++ G +++ +     + 
  gi|330508187|ref|YP_004384615.1| 127 SAALLAR---EIGD--CLFVDMGSTTTDLIPIR-ARP--------LAAKTDFLRLARGELVYMGLLRTgLACILPVA 189
                                       ****999...7777..*****************.777........6899*******************999999999 PP

                    Hydantoinase_A 141 rvgpesagadpgpacyrkGgteltvTDanlvLGrlqpedfls.gpdgdqkldvelarraf.eelakelnlk...vee 212
                                       r+++  +  +p+         +++++Da lvLG ++ + +++ ++dg+ k +++ +rr + + +a+  + +   +  
  gi|330508187|ref|YP_004384615.1| 190 RIRGHYVPLAPEL--------FAIIADARLVLGHIDLDRYACdTADGKDKGRHSSLRRLArSVCADLEEIGecgALA 258
                                       9999999999999........***************************************67777766555444445 PP

                    Hydantoinase_A 213 vAegilsvavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppya 274
                                       +Ae++     ++ ++a+     er ++++ l  v+ +G G+ ++a++a+ lg+++++  +  
  gi|330508187|ref|YP_004384615.1| 259 IAEQA----CTEQKKALVAA-MERQAERQGLERVAAAGIGEWLIAEAANTLGMECILLSELY 315
                                       55554....44444444444.466799999999***********************987654 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.2   0.0    0.0045        27     249     269 ..       2      20 ..       1      37 [. 0.78
   2 !   13.7   0.0     3e-06     0.018     223     264 ..     115     153 ..      93     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0045
                              MutL 249 llvvDvGGaTTdvhsvaegsp 269
                                       +l++D+GGa T   s+  +s+
  gi|330508187|ref|YP_004384615.1|   2 ILGLDIGGANTKAASA--DSK 20 
                                       589************9..333 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3e-06
                              MutL 223 eimpTPaAvlka.vellaeeeekglgdllvvDvGGaTTdvhsv 264
                                       +i   +aA  +a + lla+    ++gd+l vD+G++TTd++ +
  gi|330508187|ref|YP_004384615.1| 115 DILHVAAANWSAsAALLAR----EIGDCLFVDMGSTTTDLIPI 153
                                       5555566655551455566....79**************9877 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 ?    2.3   0.0    0.0092        55      62      84 ..      35      57 ..      31      95 .. 0.90
   2 ?    8.0   0.1   0.00017         1     234     301 ..     246     311 ..     241     326 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.0092
                                      HHHHHHHHHHHC-TSEEEEEE-H CS
                    Oxidored_nitro 62 LkeaikeivkrykpkaIgVittC 84
                                      L++ +k i +++kp+a++V+ t+
  gi|330508187|ref|YP_004384615.1| 35 LEKVLKRINAEQKPEAVAVVITG 57
                                      8999***************9886 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEE CS
                    Oxidored_nitro 234 aflrelakllgkevaperiaeerarlldaladyheylagkrvaiygdpdrvvalarllkelGmevvaa 301
                                       a l+e++++   ++a++  +e++++l++a++   e+ +  rva +g ++  + +a++ + lGme +++
  gi|330508187|ref|YP_004384615.1| 246 ADLEEIGECGALAIAEQACTEQKKALVAAMERQAERQGLERVAAAGIGE--WLIAEAANTLGMECILL 311
                                       568999999999999*****************9999999*******986..7778999999**99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2447.45
//
Query:       gi|330508188|ref|YP_004384616.1|  [L=411]
Description: transposase, IS4 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-15   55.8   0.0    6.9e-15   55.1   0.0    1.3  1  DDE_5      DDE superfamily endonuclease
    1.5e-12   47.4   6.5    4.9e-11   42.4   6.4    2.3  1  DDE_Tnp_2  Archaeal putative transposase ISC1217
    9.9e-08   31.9   0.9    1.4e-07   31.4   0.9    1.2  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.034   14.1   0.1      0.084   12.8   0.1    1.6  1  SeqA       SeqA protein C-terminal domain
       0.12   11.4   0.3        0.2   10.7   0.3    1.3  1  Colicin_M  Colicin M


Domain annotation for each model (and alignments):
>> DDE_5  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   1.9e-18   6.9e-15       2     214 ..      18     222 ..      17     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1.9e-18
                             DDE_5   2 llealtradrrrglllylrgllldggrksvepmaarl...ehdg.shqalqrflsrspwddaklrrrlarlvl.pll 73 
                                       +++ +t+ + r+ ++ ++ +l  + + k+v ++  ++   + +  s+ ++  f+s+++wd+ ++ +r  +l +  l+
  gi|330508188|ref|YP_004384616.1|  18 FRDLFTKPSYRS-FRDLCGALSVCDKSKTVSNLCDTMadcSKGKkSRSSYNWFFSDANWDENEVAQRKVDLFIdSLC 93 
                                       889999999999.*****999999999***********995555599******************999999997777 PP

                             DDE_5  74 apeaav..laiDdTgfpkdGkasvgvarqycgalgkadncqvavslglatervsapldwrlylpeswaqdlsarrrr 148
                                        +e+    l+iDdT   k G ++ gv+++y++++   + ++ +v+  + ++  ++p +   y++             
  gi|330508188|ref|YP_004384616.1|  94 LKENDKllLIIDDTYNEKEGNQTDGVGKFYDHSKEAYIWGNNFVTSVVQSKGLFIPHKAKMYIK------------- 157
                                       77666679************************************99999999999999999999............. PP

                             DDE_5 149 agvpddvtaktkpeial.elldraraagvplqvvvaDagYgdaaalrqglrelglhyvvrvrsdral 214
                                        ++++   +ktk eia  e+++ ++  +  + ++v+D++  +++ +      lg ++v +++sd+++
  gi|330508188|ref|YP_004384616.1| 158 -NDDENENFKTKMEIAFeEIIKPLVVPKSIDLYIVFDSWWFSSDLF-SKCLKLGHNIVCQIKSDKKV 222
                                       .3456669********96677888888888889*******9*****.888889***********987 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   6.4   1.4e-14   4.9e-11     147     306 ..     147     340 ..      92     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.4e-14
                         DDE_Tnp_2 147 yiprkvaeilkerGeksefktkiellle.ileilkeefnva.avvfdsWyvnskl....lk..gnvvgelksnarv. 214
                                       +ip+k +  +k+  e+ +fktk+e++ e i++ l     +   +vfdsW+++s l    lk   n+v ++ks+++v 
  gi|330508188|ref|YP_004384616.1| 147 FIPHKAKMYIKNDDENENFKTKMEIAFEeIIKPLVVPKSIDlYIVFDSWWFSSDLfskcLKlgHNIVCQIKSDKKVg 223
                                       799999999***************98752777776655554279******997552222433369**********95 PP

                         DDE_Tnp_2 215 ve...................gerhvpvaelPeGeylveyl...dtvikllvldd..ykkdgrrylfstdlndtded 267
                                       ++                    +  v v    +  y  e     d+v ++++++    k+   +y+ st+  ++  +
  gi|330508188|ref|YP_004384616.1| 224 INkdmyfqvrdlanqiedkffIKTTVSVRGKKKTYYAFEKKviiDKVGEVKLVISkrKKDSTTKYIISTNGSLSLKE 300
                                       559****************999999999999999999886555688877776665115667789************* PP

                         DDE_Tnp_2 268 iittWenrWdievlirel.kalGledssflkrvrnkGfll 306
                                       i + +e rWdie  +re  + lG++d  +  +   + f+ 
  gi|330508188|ref|YP_004384616.1| 301 ILSIYEDRWDIETAHREAnQKLGFKDYQLRDKHSIERFIQ 340
                                       ****************983469998877766666666665 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.9     4e-11   1.4e-07      78     212 ..     188     346 ..     154     348 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4e-11
                         DDE_Tnp_1  78 klvlaDaGYasaelldtleekgvdyiirlkkntklyrk.....gaeskrrgrlrkhdrnkiltksqkrrnk...... 143
                                        +++ D++ +s +l+ ++ + g + + ++k+++k+ +         ++ ++++ k + + +++ + k++++      
  gi|330508188|ref|YP_004384616.1| 188 LYIVFDSWWFSSDLFSKCLKLGHNIVCQIKSDKKVGINkdmyfQVRDLANQIEDKFFIKTTVSVRGKKKTYyafekk 264
                                       5899*******************************99999**9888899**************************** PP

                         DDE_Tnp_1 144 ..............skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqll 206
                                                     + k + ++ y+ +tn  +ls +e+  +y  Rw iE+ +++  +k+g+   ++r++  +e+++ 
  gi|330508188|ref|YP_004384616.1| 265 viidkvgevklvisKRKKDSTTKYIISTNG-SLSLKEILSIYEDRWDIETAHREANQKLGFKDYQLRDKHSIERFIQ 340
                                       ************755555555555555555.899******************************************* PP

                         DDE_Tnp_1 207 llllal 212
                                       +++ ++
  gi|330508188|ref|YP_004384616.1| 341 MVFSVW 346
                                       998765 PP

>> SeqA  SeqA protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.4e-05     0.084      30      88 ..     237     300 ..     217     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                              SeqA  30 yradpeaFakatekvkGrtRvYfakdeetllasgks.....tkpkqipetpfWVitNnntarKr 88 
                                        +++++ F k+t +v+G++++Y+a +++ ++++  +     +k k+ ++t + + tN + + K+
  gi|330508188|ref|YP_004384616.1| 237 NQIEDKFFIKTTVSVRGKKKTYYAFEKKVIIDKVGEvklviSKRKKDSTTKYIISTNGSLSLKE 300
                                       466778899999*****************99887776888889999999999999998766665 PP

>> Colicin_M  Colicin M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   5.6e-05       0.2     155     233 ..     230     316 ..     209     322 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.6e-05
                         Colicin_M 155 ekindlkdiiksavvGettvst...ktsyatGddsvitriylGtitlki.......eGkltisasGsvsysGvvkay 221
                                        ++ dl + i+     +ttvs+   k +y++ +++vi    +G++ l i       + k  is++Gs+s + ++  y
  gi|330508188|ref|YP_004384616.1| 230 FQVRDLANQIEDKFFIKTTVSVrgkKKTYYAFEKKVIIDK-VGEVKLVIskrkkdsTTKYIISTNGSLSLKEILSIY 305
                                       4677777778777777888876333678999898888653.566666442222222678899*************** PP

                         Colicin_M 222 ddkydanasshr 233
                                       +d++d+++ +hr
  gi|330508188|ref|YP_004384616.1| 306 EDRWDIET-AHR 316
                                       *****986.466 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3100.02
//
Query:       gi|330508189|ref|YP_004384617.1|  [L=144]
Description: flavoprotein [Methanosaeta concilii GP6]
Scores for complete 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   42.8   0.0    7.3e-11   42.4   0.0    1.2  1  Flavodoxin_1  Flavodoxin
    3.6e-10   40.3   0.0      4e-10   40.1   0.0    1.1  1  Flavodoxin_5  Flavodoxin domain
    9.5e-05   22.1   0.0    0.00014   21.6   0.0    1.2  1  Flavodoxin_3  Flavodoxin domain
    0.00045   20.0   0.3      0.051   13.3   0.3    2.1  1  FMN_red       NADPH-dependent FMN reductase


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 !   42.4   0.0   1.6e-14   7.3e-11       1     139 [.       6     131 ..       6     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.6e-14
                                       EEEETSSSHHHHHHHHHHHHHHH.TTTEEEEEEEEGTTSC.GGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHHHH CS
                      Flavodoxin_1   1 ilYgSetGnteklAkqlaeelge.hgfnadvvslsdydes.lseieeealllvvtsTfgnGdppengesffqdllel 75 
                                       i+Y+S+ G+t+ +A+++a ++++ +g+    v l+++ ++ ++++ + + ++++ sT++   +  ++  f  +    
  gi|330508189|ref|YP_004384617.1|   6 IIYASQSGKTKRMAEAIANGAKSvEGV---DVLLKNVFQAkPDDVLDADAVVLGGSTYNSKLIK-TMDPFLAQ---- 74 
                                       89********************84444...4445555555589*************99966555.44433333.... PP

                                       HCHHGCCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEESSSEEEETTST.HGHHHH CS
                      Flavodoxin_1  76 kgdeledgdlsgvrfavfglGdsayenFcaagkkldekleelGaerllkllegdednq.egqeea 139
                                           le+ dl  +    +++G++++++  + +  l ++++  G++++ +++++ + ++ e++e +
  gi|330508189|ref|YP_004384617.1|  75 ----LEKLDL--KGKVGVAFGSYGWSG--EGVPILIDRMKSFGMSVIEPGTTAVQLPTkEDLERC 131
                                       ....343334..4556899********..********************9999999987777766 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   8.9e-14     4e-10       2      80 ..       6      87 ..       5     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 8.9e-14
                      Flavodoxin_5  2 ilYsSrdGqTkkiaeriaeelree.gelvdved.vekesedlesydavvigasvyygkllpelakFvekh.reaLstkp 77
                                      i+Y+S+ G+Tk+ ae+ia+  ++  g +v +++  +++ +d+ ++davv+g+s y++kl ++++ F+ +  + +L+ k 
  gi|330508189|ref|YP_004384617.1|  6 IIYASQSGKTKRMAEAIANGAKSVeGVDVLLKNvFQAKPDDVLDADAVVLGGSTYNSKLIKTMDPFLAQLeKLDLKGKV 84
                                      9******************999767777777784446677**************************9985244566665 PP

                      Flavodoxin_5 78 val 80
                                       ++
  gi|330508189|ref|YP_004384617.1| 85 GVA 87
                                      555 PP

>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0     3e-08   0.00014       1      67 [.       5      76 ..       5      97 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3e-08
                      Flavodoxin_3  1 lilysSltGNTkkvAeaikealeeekeivsi.keakek....veeadvvfvGfwvdkgtadeealkfletlk 67
                                      +i+y S++G Tk +Aeai++ +++ + +  + k++ ++    v +ad v++G  ++ ++  + +  fl++l+
  gi|330508189|ref|YP_004384617.1|  5 AIIYASQSGKTKRMAEAIANGAKSVEGVDVLlKNVFQAkpddVLDADAVVLGGSTYNSKLIKTMDPFLAQLE 76
                                      59****************9988884443322122222134459999*********************99875 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.3   1.1e-05     0.051       1      46 [.       2      45 ..       2     124 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                                      -EEEEEES--STT-HHHHHHHHHHCCT-T..T-CEEEEETTTS.--. CS
                           FMN_red  1 mkilvisGSlrkgsntrklaewaaealkea.gaevelidladlilpc 46
                                      +ki++i++S +  ++t+++ae++a+ +k   g++v l ++ +  +p+
  gi|330508189|ref|YP_004384617.1|  2 PKIAIIYASQS--GKTKRMAEAIANGAKSVeGVDVLLKNVFQA-KPD 45
                                      599******97..**************7645566644444442.443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1071.13
//
Query:       gi|330508190|ref|YP_004384618.1|  [L=274]
Description: phosphate binding protein [Methanosaeta concilii GP6]
Scores for 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-38  132.7   3.3    8.1e-38  130.7   3.3    1.7  1  PBP_like_2  PBP superfamily domain
    3.1e-21   75.4   0.1    4.2e-21   75.0   0.1    1.2  1  PBP_like    PBP superfamily domain
    0.00013   21.8   0.1       0.27   11.0   0.1    2.1  2  SBP_bac_11  Bacterial extracellular solute-binding protein
    0.00086   19.3   0.6     0.0025   17.8   0.6    1.7  1  SBP_bac_1   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.7   3.3   1.8e-41   8.1e-38      12     279 ..      28     258 ..      23     261 .. 0.89

  Alignments for each domain:
  == domain 1  score: 130.7 bits;  conditional E-value: 1.8e-41
                        PBP_like_2  12 ifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangaggliqv 88 
                                       +++aGstt+ p+ +  a+ f+ ++++++v+++++G+g g+k +++g   +a+++r +t++e +    + g  ++ + 
  gi|330508190|ref|YP_004384618.1|  28 VRVAGSTTVLPLAEGGAEVFNAEQSDYRVTVTGGGTGVGMKNIAEGNSEIAMASREVTDEERE----KFG-DKFQEN 99 
                                       89**********************************************************993....344.8899** PP

                        PBP_like_2  89 pvaigaialvvnkd...npln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqgpwt 161
                                        +++++i+++v+++    +++ ls+e++++I++g+I nW + l +p d+ I v+ r+ gsgt+++f + ++  + ++
  gi|330508190|ref|YP_004384618.1| 100 LIGYDGIVIAVSREiydAGVTsLSKEQVEEIYAGEIDNWEE-LDGP-DEEILVIGREQGSGTRDTFNEEIMGDKSAE 174
                                       **************99988889******************9.7777.************************998888 PP

                        PBP_like_2 162 asgigasg..segvasavsn.ngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplawsl 235
                                       + g+++    + ++++a+++ + aigy+ ++y ++                           +  +++     ++ +
  gi|330508190|ref|YP_004384618.1| 175 TPGVSTVAgsNAEIKTALTGsDQAIGYLGYSYVQDD-------------------------SVGTISL-----DG-I 220
                                       878776666777888888777999999999888844.........................2233333.....45.9 PP

                        PBP_like_2 236 qpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyll 279
                                        p+ee+i+dg+y l r +y+++y++        a+a++F+d++l
  gi|330508190|ref|YP_004384618.1| 221 LPTEETIKDGSYELARELYFYTYDEA------TAGAQSFIDFML 258
                                       99**********************87......**********98 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.1   9.3e-25   4.2e-21       1     191 [.      44     256 ..      44     258 .. 0.74

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 9.3e-25
                                       HHHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCC.CCEEEEEEEEEEEE-CC-HCHCCCCH CS
                          PBP_like   1 aeelaeknpgvrvavanvGsggGlkalrageadiagshlldketeeynap.alrkaldgievvlvnlarreqglvva 76 
                                       ae ++++++++rv+v++ G+g G+k++++g  +ia++++  +++e+ ++  +++++l g + +++ + r   +  v 
  gi|330508190|ref|YP_004384618.1|  44 AEVFNAEQSDYRVTVTGGGTGVGMKNIAEGNSEIAMASREVTDEEREKFGdKFQENLIGYDGIVIAVSREIYDAGVT 120
                                       5789999********************************77777777765245666777777777766665544444 PP

                                       CCHHH........S--BGGGC..-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCCE CS
                          PBP_like  77 kgnpk........kitnwkdl..adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVaag 143
                                       +  +         +i nw++l  +d+++ +++Re+GSGtrd f+e++ +   + ++ +g++++a s+ ++++a    
  gi|330508190|ref|YP_004384618.1| 121 SLSKEqveeiyagEIDNWEELdgPDEEILVIGREQGSGTRDTFNEEIMGD--KSAETPGVSTVAGSNAEIKTALTGS 195
                                       44444235555556*********************************776..7899********************* PP

                                       TTCCE................C.CCGG-HCCCCCCECTTCE-EEEEEEEECTCCCSHHHHHHHHH CS
                          PBP_like 144 radvg................v.gieavaeelkgldfvplaeerydlvvrkealddpevqaflef 191
                                       ++++g                + gi ++ e++k++++ +la+e y++ + ++       q+f++f
  gi|330508190|ref|YP_004384618.1| 196 DQAIGylgysyvqddsvgtisLdGILPTEETIKDGSY-ELARELYFYTYDEAT---AGAQSFIDF 256
                                       *****55555555555555443355555555555554.355566666666664...456666666 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0002      0.91       2     106 ..      29     148 ..      28     201 .. 0.77
   2 !   11.0   0.1     6e-05      0.27     204     229 ..     246     271 ..     226     272 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0002
                                       EEEE-SSTHHHHHHHHHHH.HHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEE CS
                        SBP_bac_11   2 tvaaagslaaalrelaaaF.eahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavpla 77 
                                       +va ++++ +  +  a+ F +++++ +v+v++gg g  ++ ia+g+    +++as   +++ +++ ++++ +++ + 
  gi|330508190|ref|YP_004384618.1|  29 RVAGSTTVLPLAEGGAEVFnAEQSDYRVTVTGGGTGVGMKNIAEGN--SEIAMASR-EVTDEEREKFGDKFQENLIG 102
                                       677777777777788999*777899********************4..44566664.46788889999988899999 PP

                                       EEEEEEEESTT-.................TT---SHHHHHHSS--E CS
                        SBP_bac_11  78 ssplviavpkgn.................pkkikgwadLlkpglkl 106
                                       +  +viav ++                  +  i++w++L +p+ ++
  gi|330508190|ref|YP_004384618.1| 103 YDGIVIAVSREIydagvtslskeqveeiyAGEIDNWEELDGPDEEI 148
                                       999********95555555554444444224799999999986544 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6e-05
                                       --HHHHHHHHHTTSHHHHHHHHHTT- CS
                        SBP_bac_11 204 kreaAraFlafLrspeaqailrkyGf 229
                                         + A+ F++f++++++++++++yGf
  gi|330508190|ref|YP_004384618.1| 246 ATAGAQSFIDFMLGSKGRDVATEYGF 271
                                       45789********************9 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.6   5.5e-07    0.0025      17     313 ..      42     262 ..      29     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.5e-07
                                       H....HHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHH.....HHHHT..TSBECCHHHHHHTT CS
                         SBP_bac_1  17 a....fekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwia.....rlaka..glllpldpyvkayl 82 
                                            f++e  ++ V+++ +g+g ++      ia G+ +  +++  ++ ++     ++ ++    l+  d +v+a  
  gi|330508190|ref|YP_004384618.1|  42 GgaevFNAEQSDYRVTVTGGGTGVGMK----NIAEGNSE--IAMA-SREVTdeereKFGDKfqENLIGYDGIVIAVS 111
                                       233469999******************....******55..5555.5555556678888888888************ PP

                                       ECTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCE CS
                         SBP_bac_1  83 apgvkdaadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkkpiggargg 159
                                        ++++ +  +ls+++++ i+++                       ++d   +W+el  +++++   g+         
  gi|330508190|ref|YP_004384618.1| 112 REIYDAGVTSLSKEQVEEIYAG-----------------------EID---NWEELDGPDEEILVIGREQ------- 155
                                       *******************994.......................234...**************99999....... PP

                                       EHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCS CS
                         SBP_bac_1 160 sasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaa 236
                                        +sgt + f ++++                                 + +++e +g+++   ++a+ +++++  + a
  gi|330508190|ref|YP_004384618.1| 156 -GSGTRDTFNEEIM---------------------------------GDKSAETPGVSTVAGSNAEIKTALTGSDQA 198
                                       .4444444432222.................................233355666666666666666666633333 PP

                                       EEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE.EEEEEEEEBTTCSTHHHHHHHHHHHTSHH CS
                         SBP_bac_1 237 maivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi.lgayglaipkgsknpeaAkkFldfllspe 312
                                       +++ g ++          +++ + + ++++     +lP++++ k+g+   a  l  ++     ++A+ F+df+l+++
  gi|330508190|ref|YP_004384618.1| 199 IGYLGYSY---------VQDDSVGTISLDG-----ILPTEETIKDGSyELARELYFYTYDEATAGAQSFIDFMLGSK 261
                                       33333333.........3444555555544.....89***********99999*********************998 PP

                                       H CS
                         SBP_bac_1 313 a 313
                                       +
  gi|330508190|ref|YP_004384618.1| 262 G 262
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2044.66
//
Query:       gi|330508191|ref|YP_004384619.1|  [L=153]
Description: hypothetical protein MCON_2325 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1139.57
//
Query:       gi|330508192|ref|YP_004384620.1|  [L=970]
Description: ATP-dependent RNA helicase [Methanosaeta concilii GP6]
Scores for complete 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-35  122.5   0.0    3.4e-34  118.1   0.0    2.4  2  DEAD        DEAD/DEAH box helicase
    3.4e-35  121.6   0.0    6.8e-35  120.6   0.0    1.6  1  DEAD_assoc  DEAD/H associated
    7.4e-24   84.2   0.0    2.1e-21   76.3   0.0    3.2  3  Helicase_C  Helicase conserved C-terminal domain
    2.5e-06   27.6   0.0    1.1e-05   25.5   0.0    2.0  1  ResIII      Type III restriction enzyme, res subunit
    0.00035   19.4   0.0    0.00074   18.3   0.0    1.5  1  SNF2_N      SNF2 family N-terminal domain
    0.00057   20.2   0.1       0.52   10.7   0.2    3.1  2  AAA_19      AAA domain
  ------ inclusion threshold ------
      0.032   14.0   2.7      0.085   12.6   2.7    1.7  1  YdjO        Cold-inducible protein YdjO
      0.048   13.3   0.7        1.5    8.6   0.0    3.3  3  Crp         Bacterial regulatory proteins, crp family
      0.071   12.7   0.1        0.8    9.2   0.0    2.6  3  AAA_25      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 !  118.1   0.0   1.7e-37   3.4e-34       3     170 ..      26     229 ..      24     236 .. 0.90
   2 ?    1.4   0.0      0.12   2.4e+02      43      81 ..     291     329 ..     279     357 .. 0.72

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 1.7e-37
                                       HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS..TTSTS.............................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx.............................. RF
                              DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet..kgktg.............................. 47 
                                        Q++aip+il+g++vl+ a+TG+GKT+a+++p+++++++   k  ++                              
  gi|330508192|ref|YP_004384620.1|  26 PQEKAIPTILEGENVLLIAPTGTGKTEAASLPIFHQILSGegK--SNntpkhgrekkkasrtmdsdgmqssamesgg 100
                                       59********************************999988552..33447777888889999999999999999999 PP

                                       ........-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH..HC CS
                                       ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                              DEAD  48 ........pkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngvdivvgtpgrlddll..st 114
                                                +a++++P+r+L +++l+++  +++ ++++v +  g+++++d +++  + +di+++tp+ l+ +l  ++
  gi|330508192|ref|YP_004384620.1| 101 mdsngikgIRAVYITPLRALNRDMLRRFHDWGESLGISVAVRHGDTSQSDRRRQSLSPPDILITTPETLQVMLtgKR 177
                                       99999999*******************************9999999998888887677*************997777 PP

                                       TSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 115 gklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                        +lnls vr++V+DE++++ +++++ +++ +l++l +i  d +     i lSAT+ 
  gi|330508192|ref|YP_004384620.1| 178 LRLNLSTVRTVVVDEVHEMASSKRGSQLSVLLERLVEIAGDFQ----RIGLSATVG 229
                                       7799*******************************98888866....*******86 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.12
                                       TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                       ++ + +k+li + tr+ ae   +++++++++i++   ++
  gi|330508192|ref|YP_004384620.1| 291 DEVRDKKCLIFVNTRQAAEVLGSRFRQLGEPIGVHHGSL 329
                                       456778************************998544433 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.0   3.4e-38   6.8e-35       1     189 [.     641     810 ..     641     812 .. 0.94

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 3.4e-38
                        DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldel 77 
                                       +P+++ ++vE   ++      +++ +fG++ n++l++++++ ls+rfg++v++++++++i+l+lp++  + +++++l
  gi|330508192|ref|YP_004384620.1| 641 VPNESLVVVEGGGEG-----AIINCCFGHKTNDTLGRVITSILSARFGSSVALQIDPYRIELTLPKALLA-EEIEKL 711
                                       799999999999875.....5*****************************************99754444.6799** PP

                        DEAD_assoc  78 lellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavre 154
                                       +e l+pd ++ +le  l++++l+++++ +vA+++++l+r+ +        qr+++a+Ll+v++   ++p+++ea+re
  gi|330508192|ref|YP_004384620.1| 712 IEDLDPDYVQPILEMTLKNTSLLRWKMIHVARKFGALSRDVDY-------QRVSMAKLLAVFE---GTPMYREALRE 778
                                       *****************************************99.......*************...*********** PP

                        DEAD_assoc 155 vledqlDlerlaellrriaageirvvevetprpSp 189
                                       + +d lD+er++++l ri++g++ +++   ++ Sp
  gi|330508192|ref|YP_004384620.1| 779 IYHDRLDIERTRMVLVRIRDGSMAMTT---SSLSP 810
                                       **********************99886...66776 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 ?    3.0   0.0     0.061   1.2e+02      37      57 ..     133     153 ..     107     170 .. 0.75
   2 !   76.3   0.0   1.1e-24   2.1e-21      10     108 ..     289     387 ..     280     389 .. 0.90
   3 ?    0.2   0.0      0.48   9.5e+02       4      31 ..     830     857 ..     827     933 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.061
                                       HHTTSTEEEESTTSTHHHHHH CS
                        Helicase_C  37 ekkgikvavlhgelpqneree 57 
                                       e+ gi+vav hg+++q++r++
  gi|330508192|ref|YP_004384620.1| 133 ESLGISVAVRHGDTSQSDRRR 153
                                       3449**************986 PP

  == domain 2  score: 76.3 bits;  conditional E-value: 1.1e-24
                                       HHHTTTTSEEEEEESSHHHHHHHHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTST CS
                        Helicase_C  10 lkleeeggkilifvntidrlekvklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidip 83 
                                       +  e++++k+lifvnt++ +   ++l +++   g  + v+hg+l+ + r e+ e+f++ge + Li+t+ +e Gidi 
  gi|330508192|ref|YP_004384620.1| 289 IRDEVRDKKCLIFVNTRQAA---EVLGSRFrqlGEPIGVHHGSLSREARVEAEEAFKAGELQGLICTSSMELGIDIG 362
                                       467899************99...55644445569******************************************* PP

                                       TESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  84 kvnlVinfdlprnvtsyiqriGRtg 108
                                       +v++Vi+++ pr+v+++ qr+GR+g
  gi|330508192|ref|YP_004384620.1| 363 DVDHVIQYSSPREVSRMLQRVGRAG 387
                                       ************************8 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.48
                                       HHHHHHHHHTTTTSEEEEEESSHHHHHH CS
                        Helicase_C   4 eallellkleeeggkilifvntidrlek 31 
                                       +a+++llk++  ++++l+f+ ++++ ++
  gi|330508192|ref|YP_004384620.1| 830 AAVIKLLKNRIMKDRVLLFCVNCKKWKS 857
                                       6788999999999******999986533 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 !   25.5   0.0   5.6e-09   1.1e-05       7     169 ..      26     228 ..       9     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5.6e-09
                                       HHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S................................ CS
                            ResIII   7 yQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkee........................... 55 
                                        Qe+ai  +l      + +++l+ ++TGtGKT  a + +  ++l+ ++++                           
  gi|330508192|ref|YP_004384620.1|  26 PQEKAIPTIL------EGENVLLIAPTGTGKTEAAsLPIFHQILSGEGKSnntpkhgrekkkasrtmdsdgmqssam 96 
                                       4555555555......456899************978888888876666699************************* PP

                                       .............-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.........-SEEEEEHHHHHHT CS
                            ResIII  56 .............kflflvprkslleqtleefkkflseaykeigkkvsgdkkka..kekdstnkkilvttiqsldad 117
                                                    +++ + p ++l   +l++f ++ ++       + +gd+ ++  ++++ +  +il+tt ++l+  
  gi|330508192|ref|YP_004384620.1|  97 esggmdsngikgiRAVYITPLRALNRDMLRRFHDWGESLGI-SVAVRHGDTSQSdrRRQSLSPPDILITTPETLQVM 172
                                       ********************************999998753.3444445544445556689999************* PP

                                       H........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT---SEEEEEESS- CS
                            ResIII 118 seeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekfkeavllglTATp 169
                                       +   + ++ +l  ++   +++DE+H ++++k         ++++e   ++ ++gl+AT 
  gi|330508192|ref|YP_004384620.1| 173 L---TGKRLRLNLSTVRTVVVDEVHEMASSKrgsqlsvLLERLVEIAGDFQRIGLSATV 228
                                       *...999999999999*************8655555555556677777799*******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 !   18.3   0.0   3.7e-07   0.00074     104     203 ..     116     212 ..      28     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.7e-07
                                       -H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-S CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 104 Pa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewk 179
                                       P  +l +   + ++ + +s  + v v +g+++++       ++ l   d++itt ++l+  + l  kr  l+    +
  gi|330508192|ref|YP_004384620.1| 116 PLrALNRDMLRRFHDWGESLGISVAVRHGDTSQSD----RRRQSLSPPDILITTPETLQ--VMLTGKRLRLNLSTVR 186
                                       555555666678999**************974444....4788999*************..55679999999999** PP

                                       EEEES-GGGT--TT..SHHHHHHHH- CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxx RF
                            SNF2_N 180 rvvlDEghtlknst..skaaeavskL 203
                                        vv+DE h + +s+  s+++  +++L
  gi|330508192|ref|YP_004384620.1| 187 TVVVDEVHEMASSKrgSQLSVLLERL 212
                                       *************6235555555555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.2   0.00026      0.52       1      31 [.      27      58 ..      27     219 .. 0.78
   2 ?    5.4   0.0     0.011        22      36      84 ..     291     335 ..     281     369 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                            AAA_19  1 qreave.alkekvllvtaGpGtGKTrvlkhiv 31
                                      q++a+   l+ +++l++a+ GtGKT+     +
  gi|330508192|ref|YP_004384620.1| 27 QEKAIPtILEGENVLLIAPTGTGKTEAASLPI 58
                                      889996699****************9766555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
                            AAA_19  36 elggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddll 84 
                                       ++  v  +++l+   t++Aa+ l  r ++lg+++   H+   l  + ++
  gi|330508192|ref|YP_004384620.1| 291 DE--VRDKKCLIFVNTRQAAEVLGSRFRQLGEPIGVHHGS--LSREARV 335
                                       33..44589************************9999976..5444444 PP

>> YdjO  Cold-inducible protein YdjO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.7   4.3e-05     0.085      26      53 ..     852     881 ..     849     884 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.3e-05
                              YdjO  26 CngW..mRdnFsfeeePtCplCkseMvkev 53 
                                       C+ W  mR+  ++ ++P CplC+s+Mv   
  gi|330508192|ref|YP_004384620.1| 852 CKKWksMRQVERVPDRPECPLCGSRMVAAL 881
                                       8888889999999*************9865 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.29   5.8e+02      15      23 ..     230     238 ..     229     239 .. 0.90
   2 ?   -1.0   0.2       0.7   1.4e+03      19      28 ..     376     385 ..     374     387 .. 0.81
   3 ?    8.6   0.0   0.00073       1.5      13      29 ..     931     947 ..     931     948 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.29
                                       -HHHHHHHH CS
                               Crp  15 TrETVSRlL 23 
                                       ++ETV RlL
  gi|330508192|ref|YP_004384620.1| 230 SPETVARLL 238
                                       68*****98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.7
                                       HHHHHHHHHH CS
                               Crp  19 VSRlLtrLre 28 
                                       VSR+L r  +
  gi|330508192|ref|YP_004384620.1| 376 VSRMLQRVGR 385
                                       9****99766 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00073
                                       TS-HHHHHHHHHHHHHT CS
                               Crp  13 GlTrETVSRlLtrLrek 29 
                                       Gl +ET+ R+ ++L+++
  gi|330508192|ref|YP_004384620.1| 931 GLGPETAARVIGKLQKD 947
                                       8899***********96 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0004       0.8      13      51 ..      18      55 ..       8      76 .. 0.81
   2 ?   -2.4   0.0       1.5     3e+03      88     157 ..     126     199 ..     121     222 .. 0.47
   3 ?   -0.7   0.0      0.46   9.1e+02      89     139 ..     244     295 ..     239     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0004
                            AAA_25 13 adlaapppprrwlvkgllpagelallaGapgtGKttlal 51
                                       ++  p  p+++ ++ +l +ge +ll++++gtGKt +a+
  gi|330508192|ref|YP_004384620.1| 18 QGIIEPTLPQEKAIPTIL-EGENVLLIAPTGTGKTEAAS 55
                                      557777788999999998.8***************8875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                            AAA_25  88 rRlravgeal............rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDpls 152
                                       rR++ +ge l            + d+r + l+ +   ++ ++++++ +  lt++   l+  ++    vr vv+D + 
  gi|330508192|ref|YP_004384620.1| 126 RRFHDWGESLgisvavrhgdtsQSDRRRQSLSPP---DILITTPETLQVMLTGKR--LR--LNL-STVRTVVVDEVH 194
                                       6666666666555555444433222222222221...222222222222233331..22..222.336777777776 PP

                            AAA_25 153 ralgg 157
                                       ++ + 
  gi|330508192|ref|YP_004384620.1| 195 EMASS 199
                                       66655 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.46
                            AAA_25  89 Rlravgealrddarllvldlagv.eslpLfakdrggtlltadvdaleaaiee 139
                                        +r v++++++ ++ +v++ + + ++  L+++   +++l+a+++++++++++
  gi|330508192|ref|YP_004384620.1| 244 GYRIVCADVERASNYQVVSPQPKgGDYSLASTLECDPRLAAQIRWIRDEVRD 295
                                       5677899999999******99999*****999999999********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (970 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.79u 0.28s 00:00:01.07 Elapsed: 00:00:00.46
# Mc/sec: 6307.73
//
Query:       gi|330508193|ref|YP_004384621.1|  [L=406]
Description: transposase [Methanosaeta concilii GP6]
Scores for 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-76  255.6   1.2    9.9e-76  254.6   0.6    1.7  2  DDE_Tnp_ISL3  Transposase
    3.3e-14   52.0   0.1    6.3e-14   51.1   0.1    1.5  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
    1.9e-10   41.2   6.3      5e-10   39.9   6.3    1.7  1  zf-ISL3       zinc-finger of transposase IS204/IS1001/IS1096/


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 ?   -1.1   0.0      0.21   1.3e+03     185     211 ..     121     147 ..     102     150 .. 0.81
   2 !  254.6   0.6   1.7e-79   9.9e-76       1     240 []     159     393 ..     159     393 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.21
                      DDE_Tnp_ISL3 185 efkklaktlknhreeIlnyfdsrlsng 211
                                        +  +a+++++h ++I +++++++  +
  gi|330508193|ref|YP_004384621.1| 121 TVTAIAEMIDEHDTRIWRVLQHYVAEA 147
                                       567789999999999999999987766 PP

  == domain 2  score: 254.6 bits;  conditional E-value: 1.7e-79
                      DDE_Tnp_ISL3   1 lgiDEislkkghkyvtvvvdllvdggrlldilpgRkketlkafleslsek..erekveavvmDmsaayksavkealP 75 
                                       +g+DE+s  kghkyv+v++dl  d++r++++++g++++t+ +f ++l+++    e++e +++Dms+a++s +++ +P
  gi|330508193|ref|YP_004384621.1| 159 IGVDETSRAKGHKYVSVFIDL--DESRVIHVCEGKDASTIGSFKDDLEQHngSSENIENFCCDMSPAFISGIENSFP 233
                                       8********************..************************8888899*********************** PP

                      DDE_Tnp_ISL3  76 nAkivvDrFHvvklanealdevRrreqkelreekrkklkrsrrlllknpenlteeqkqrldelleaspelekaYelk 152
                                       nA+i++D+FHv+kl+nea+d+vRr+eq++        lkr+r+++lknpenlt +q + l  l +   ++ +aY++k
  gi|330508193|ref|YP_004384621.1| 234 NASITFDKFHVMKLMNEAVDKVRREEQSHNA-----LLKRTRYIWLKNPENLTANQNKMLTPLKSIRLKTMRAYNIK 305
                                       ****************************865.....6***********************99*************** PP

                      DDE_Tnp_ISL3 153 eelrevfrkkdkeearkalkewiekaersglkefkklaktlknhreeIlnyfdsrlsngpvEgiNnkikaikrrayG 229
                                        +lr+++ ++ +++a+ +lk+w+ +a++s+l+++ ++ak++knh+++++ny+++++ ng++Eg+N+ i+a+k +a+G
  gi|330508193|ref|YP_004384621.1| 306 LALRDFWSYEYRKSAEDYLKRWYYWATHSRLDPVIECAKMIKNHWNGVTNYIKTKIDNGILEGTNSLIQAAKDSARG 382
                                       ********99*******************************************99********************** PP

                      DDE_Tnp_ISL3 230 frnfenfrlri 240
                                       fr+++nf+++i
  gi|330508193|ref|YP_004384621.1| 383 FRSTKNFITII 393
                                       ********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 !   51.1   0.1   1.1e-17   6.3e-14       2      52 .]      95     144 ..      94     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.1e-17
                      HTH_Tnp_ISL3   2 elPwarrrsriTlrleayilelllesrsvkavArqlgvSwtTVwrildryv 52 
                                       ++Pwar++s++Tl+++  i+ +++ + +v+a+A++ + ++t++wr+l +yv
  gi|330508193|ref|YP_004384621.1|  95 KVPWARKGSGFTLLMDSLIVLMAQYM-TVTAIAEMIDEHDTRIWRVLQHYV 144
                                       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 !   39.9   6.3   8.4e-14     5e-10       5      47 .]      47      89 ..      44      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 8.4e-14
                           zf-ISL3  5 CPnCgsktvvkhgkkerrvrhlpiggkrvyLrlrkrRyrCkeC 47
                                      C +Cg++   +h++ er++rhl+++++++y+++r++R  C +C
  gi|330508193|ref|YP_004384621.1| 47 CAKCGNPGCSVHDTIERTWRHLNFFQFKTYIHCRVPRTICEDC 89
                                      *******99*********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2870.79
//
Query:       gi|330508194|ref|YP_004384622.1|  [L=191]
Description: acylphosphatase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-18   67.3   0.0    2.3e-18   66.3   0.0    1.5  1  Acylphosphatase  Acylphosphatase
     0.0044   17.1   0.1     0.0062   16.6   0.1    1.5  1  DUF1115          Protein of unknown function (DUF1115)
  ------ inclusion threshold ------
      0.053   13.6   0.2      0.089   12.9   0.2    1.3  1  Mis12            Mis12 protein
       0.38   10.1   3.2       0.62    9.4   3.2    1.3  1  DUF3552          Domain of unknown function (DUF3552)


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 !   66.3   0.0   5.2e-22   2.3e-18       5      84 ..       2      81 ..       1      82 [. 0.97

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 5.2e-22
                   Acylphosphatase  5 vtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkdF 83
                                      ++G+VQ+vg+R+ v ++A++lgl+G+v+N++dg V + aeg++e++ek+ +++k +   + v+e+e e +e+ + + +F
  gi|330508194|ref|YP_004384622.1|  2 ISGKVQRVGYRAKVVSAAQNLGLTGFVQNRPDGHVLLIAEGSRENLEKLASAIKIKDLLIDVHEIESEFSEASGAYPTF 80
                                      89*********************************************************************99999888 PP

                   Acylphosphatase 84 e 84
                                      +
  gi|330508194|ref|YP_004384622.1| 81 R 81
                                      6 PP

>> DUF1115  Protein of unknown function (DUF1115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.4e-06    0.0062      13      55 ..      11      54 ..       4     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-06
                           DUF1115 13 hrfkvdknAkqlsltGvvllgpk.fnlvvveGgekaikkYkklm 55
                                       r+kv   A+ l+ltG+v   p+   l+++eG++++++k  + +
  gi|330508194|ref|YP_004384622.1| 11 YRAKVVSAAQNLGLTGFVQNRPDgHVLLIAEGSRENLEKLASAI 54
                                      589*************999995525899********99988777 PP

>> Mis12  Mis12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2     2e-05     0.089      31      83 ..     131     182 ..     110     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                                       HHHHHH........TTSTHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Mis12  31 avekvLdkkleedeeeekaaeesteeieeGtakletlleasvDknfdkfElyv 83 
                                        ++++Ldk+++  ++++++ +++++ i   ++kl++ ++ ++D++fd+ E y+
  gi|330508194|ref|YP_004384622.1| 131 KMDQMLDKQDQMLDKQDQMLDKQDSTI-GEIQKLRSDMKCHLDRRFDRIEGYL 182
                                       577777655555555555554444444.459*******************996 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.2   0.00014      0.62      83     138 ..     132     187 ..     126     189 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00014
                           DUF3552  83 lekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrq 138
                                       +++ l +++++Ld++++ l+k+++++ e +k  +  + +l+++ +++e  ++ q++
  gi|330508194|ref|YP_004384622.1| 132 MDQMLDKQDQMLDKQDQMLDKQDSTIGEIQKLRSDMKCHLDRRFDRIEGYLNVQKE 187
                                       56667777788888888888888888777776666667777777777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1425.91
//
Query:       gi|330508195|ref|YP_004384623.1|  [L=84]
Description: hypothetical protein MCON_2330 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 649.83
//
Query:       gi|330508196|ref|YP_004384624.1|  [L=443]
Description: phenylacetate-coenzyme A ligase [Methanosaeta concilii GP6]
Scores for complete 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   95.2   0.4    6.3e-27   93.7   0.4    1.8  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    7.7e-17   61.0   0.0    5.5e-16   58.2   0.0    1.9  1  AMP-binding      AMP-binding enzyme
  ------ inclusion threshold ------
       0.01   14.9   0.0      0.019   14.0   0.0    1.4  1  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 !   93.7   0.4   1.1e-30   6.3e-27       1      96 []     333     430 ..     333     430 .. 0.97

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 1.1e-30
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEET.TEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtreg.elDelevkvEvke.gfsdelkelealekkiakklksklgvsvkve 75 
                                       G+nvfPsqie+vl +i+e+++++q+vv+r++ +lDe++++vE+k+ +f+ el++l++++k  ++klks+l+v+ ++e
  gi|330508196|ref|YP_004384624.1| 333 GINVFPSQIEDVLVSIPEIGNYFQVVVDRKKhGLDEISIQVELKDeAFTGELADLARIRKITEDKLKSVLNVRSRIE 409
                                       99***************************9747************78899*************************** PP

                                       EE-TT-S---------EEE-S CS
                   AMP-binding_C_2  76 lvepgtlprsegKakrviDkR 96 
                                       lve+g++pr+ gK+k+v+D R
  gi|330508196|ref|YP_004384624.1| 410 LVEKGSIPRTAGKSKKVVDLR 430
                                       *******************98 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   9.2e-20   5.5e-16     158     422 ..      82     331 ..      18     332 .. 0.76

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 9.2e-20
                                       TTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC...SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EE CS
                       AMP-binding 158 pddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr...fklkeddvvlsilplahifglilelllallsGatv 231
                                        d+++ +  +SGTTGkP  V ++ r + +    ++  ++    +++++d +   + + + +g  l++ + + + +++
  gi|330508196|ref|YP_004384624.1|  82 LDEVVRVHASSGTTGKPTVVGYTARDIETWSDLMA--RDfvmAGVRKGDIFQNAVNYGFFTGG-LGVHYGIERMGAM 155
                                       5666677779****************955433332..22233557779**************8.6776666666668 PP

                                       EE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHH CS
                       AMP-binding 232 vllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralf 307
                                        ++++   ++  + le + +++vtv++++P+ + +l+e ++a        d  +lr+  +g+ep s e+ +++++ +
  gi|330508196|ref|YP_004384624.1| 156 AVPSGVGNTN--RQLEIMMDFGVTVLHCTPSYALYLAEtAKANG----VVDKLKLRIGCFGAEPWSDEARKELEEAL 226
                                       8888888855..558*********************99555444....226667999889***************** PP

                                       TCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-T..TEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-H CS
                       AMP-binding 308 geevlegYGlTEttgvvtvlpleedkkklgsvGkplp..gvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkp 382
                                         + +++YGl+E+ g  + ++++e+       G  ++  +  ++i+D + ++p+++ge+Gel+v +           
  gi|330508196|ref|YP_004384624.1| 227 NIKAYDSYGLSEMMGPGVAFECQEQ------NGLHIWedHFLIEILDNN-EQPCAPGEPGELVVTS----------- 285
                                       99**************984554444......366665348999****99.9*************75........... PP

                                       HHHHHHEEETCCEEEEEEEEEEETTS.........EEEEEEECCCEEEE CS
                       AMP-binding 383 eataeafdsegrwlrTGDlgrldedG.........yleivgRkkdlikl 422
                                        +t+ea+      ++TGD+ ++ e+            +++gR++d++++
  gi|330508196|ref|YP_004384624.1| 286 -LTKEAMP-LI-RYHTGDVTYIMEEKcscgrtsrkLHRFLGRADDMLIV 331
                                       .5777773.22.6888888885433234446666557788888888776 PP

>> LuxE  Acyl-protein synthetase, LuxE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.2e-06     0.019     266     360 ..     230     327 ..     216     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-06
                              LuxE 266 vvdiygfteqvelntpdfkdelkrkrvysdviir..deetlkvvgdGkvGlleyvdalstsyPafvvltddlGviee 340
                                         d yg++e ++   ++  +e +  ++  d ++    +++ +++++G +G l   + + ++ P     t d+  i e
  gi|330508196|ref|YP_004384624.1| 230 AYDSYGLSEMMGPGVAFECQEQNGLHIWEDHFLIeiLDNNEQPCAPGEPGELVVTSLTKEAMPLIRYHTGDVTYIME 306
                                       46899******9999998889999999888665535677889***********************99*****97777 PP

                              LuxE 341 slcegqkaG.klvkvlrrvkk 360
                                        +c ++++  kl + l+r++ 
  gi|330508196|ref|YP_004384624.1| 307 EKCSCGRTSrKLHRFLGRADD 327
                                       7****9987255678999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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 0.22s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 3521.17
//
Query:       gi|330508197|ref|YP_004384625.1|  [L=92]
Description: hypothetical protein MCON_2334 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-23   80.7   0.2    6.3e-23   80.6   0.2    1.0  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.014   15.2   0.0    1.3  1  HxlR      HxlR-like 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 !   80.6   0.2     7e-27   6.3e-23       1      75 [.       2      78 ..       2      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 7e-27
                            HTH_45  1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli...kkskekYvlTekGlelleklkeleel 75
                                      +R + eIi++IL+++  ++a+kTk++y+anL++++++ YL+ L++++li   +  +  Y++TekG++l++ +++++++
  gi|330508197|ref|YP_004384625.1|  2 KRNRNEIISEILRIC-IKGARKTKVVYQANLNFRTADPYLQLLIKNDLIvssQGPHVVYKTTEKGMNLMKAIDQVHST 78
                                      8**************.*********************************774458899***************99875 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.5e-06     0.014      53      87 ..      49      83 ..      11      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-06
                                      EESSSS-EEEEEE-TCGGGGHHHHHHHHHHHHHHH CS
                              HxlR 53 vypevPpkveYsltekGrslepvlqelkkwgeeyl 87
                                      ++++++p+v Y+ tekG +l++++++++   +ey 
  gi|330508197|ref|YP_004384625.1| 49 IVSSQGPHVVYKTTEKGMNLMKAIDQVHSTLAEYQ 83
                                      46788999******************998877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 668.71
//
Query:       gi|330508198|ref|YP_004384626.1|  [L=299]
Description: dihydroorotate dehydrogenase, catalytic subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-62  210.9   0.0    2.6e-62  210.7   0.0    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
    3.2e-12   46.2   0.0    2.1e-06   27.1   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
    1.2e-05   24.9   4.4    2.7e-05   23.7   4.4    1.7  1  NMO           Nitronate monooxygenase
    0.00013   21.5   0.1    0.00026   20.5   0.1    1.5  1  His_biosynth  Histidine biosynthesis protein
    0.00045   19.3   0.5     0.0012   18.0   0.6    1.6  2  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.008   15.4   0.2      0.022   14.0   0.2    1.7  1  DUF561        Protein of unknown function (DUF561)
  ------ inclusion threshold ------
      0.026   13.7   0.0      0.047   12.9   0.0    1.3  1  IGPS          Indole-3-glycerol phosphate synthase
      0.089   12.2   0.3       0.21   11.0   0.1    1.6  2  PcrB          PcrB family
        0.1   11.6   0.5       0.33    9.9   0.3    1.8  2  FMN_dh        FMN-dependent dehydrogenase
       0.15   11.5   0.3       0.48    9.8   0.1    1.9  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
        0.2   10.5   0.4         15    4.4   0.0    2.3  2  Trp_syntA     Tryptophan synthase alpha chain


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 !  210.7   0.0   1.6e-65   2.6e-62       2     295 .]       4     281 ..       3     281 .. 0.93

  Alignments for each domain:
  == domain 1  score: 210.7 bits;  conditional E-value: 1.6e-65
                                       G-EEETTEEESSSEEE-TTSSTTSSSHH.HHHCTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-H CS
                            DHO_dh   2 latkvlglkfknpiglAaGfdkegeeil.kllklgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGl 77 
                                       l+++  gl++knp++lAaG+ + + + l +   +g+g + ++s++  p+ G+p P ++++  +  ++N++Gl+n+  
  gi|330508198|ref|YP_004384626.1|   4 LSVHAGGLDLKNPVLLAAGILGTTGASLcRASRAGAGGVVTKSIGSVPRAGHPGPCIVHVDCG--LINAMGLPNPSY 78 
                                       6788889*************998776551666777****************************..************ PP

                                       HHHHHHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGGESEEEEES-SCTCC.TSCCCGCHHHHHHHH CS
                            DHO_dh  78 davlekllkrrkeqeekkelginlskakktenavddyvevvrkigpfadilelNvSsPntp.glrdlqekeelkail 153
                                       +   +++ + rk       +++++s+  ++   +++++++ r+++  ad+lelN+S+P++  ++ +l++ ++l + +
  gi|330508198|ref|YP_004384626.1|  79 KDFQAEIDAARKG-----GVPVIASIFASS---AEEFAQISRNLD--ADALELNLSCPHAEkYGSELGRYPDLVESV 145
                                       ********99977.....699********9...*********998..8************99*************** PP

                                       HHHHHHHHSSEEEEEE-SSSSHHHHHHHHHHHH.HHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHH CS
                            DHO_dh 154 lkvvkevskvpvlvKlaPdltdeekkdiadvll.elkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdi 229
                                       + +vk++s+vpv+vKl+P+ +d+ +   a++   ++ + +i+    t++ +aid+++  ++  n++GGlsG+a+k++
  gi|330508198|ref|YP_004384626.1| 146 TGAVKAASSVPVWVKLTPNTADILELGLAAQRGgADAVVAIN----TLKAMAIDIETGYPILGNRFGGLSGRAIKPV 218
                                       *********************999999998877677776666....788888************************* PP

                                       HHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
                            DHO_dh 230 alkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                                       a++ +++l++rl+  ip+IgvGGi+s eDa+e+i+aGAs++qv+tal  +g+ i+++i  +l + L
  gi|330508198|ref|YP_004384626.1| 219 AVRAVYDLASRLE--IPVIGVGGISSWEDAVEMIMAGASAIQVGTAL-LQGYGIFEEIASGLSAYL 281
                                       *************..********************************.9***********998765 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.3e-09   2.1e-06      67     156 ..     103     184 ..      87     186 .. 0.87
   2 !   17.1   0.0   1.4e-06    0.0023     169     225 ..     217     272 ..     210     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.3e-09
                                       HHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HHHH CS
                               Dus  67 llaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenalel 143
                                        + e+A++  +l+ad+ +lN+ CP      +++G+ L r pdlv+++  av+ a ++Pv vk          ++lel
  gi|330508198|ref|YP_004384626.1| 103 SAEEFAQISRNLDADALELNLSCPHA----EKYGSELGRYPDLVESVTGAVKAASSVPVWVKLTPNTA----DILEL 171
                                       56799*******************75....689****************************9865544....67788 PP

                                       HHHHHHCT-SEEE CS
                               Dus 144 akiveaaGaqalt 156
                                       + ++++ Ga+a++
  gi|330508198|ref|YP_004384626.1| 172 GLAAQRGGADAVV 184
                                       8888888888775 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.4e-06
                                       G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH CS
                               Dus 169 tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae 225
                                       ++  +a++++  +++ipvi+ G+I ++eda +++   Ga ++ +g + l+   +f+e
  gi|330508198|ref|YP_004384626.1| 217 PVAVRAVYDLASRLEIPVIGVGGISSWEDAVEMIMA-GASAIQVGTALLQGYGIFEE 272
                                       566789***************************999.********999998777765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   4.4   1.7e-08   2.7e-05     132     226 ..     175     264 ..      71     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.7e-08
                               NMO 132 lkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgv 208
                                        +++g+ +++ i + k++ + ++ G  +l   G   GG  G ++++    ++ v   ++ ++iPvi  GGi   ++ 
  gi|330508198|ref|YP_004384626.1| 175 AQRGGADAVVAINTLKAMAIDIETGYPIL---GNRFGGLSG-RAIK-PVAVRAVYDLASRLEIPVIGVGGISSWEDA 246
                                       45666666777777777777777777665...999999999.6664.345666777788899*************** PP

                               NMO 209 aaaLalGAsgvqigtrfL 226
                                         ++ +GAs++q+gt++L
  gi|330508198|ref|YP_004384626.1| 247 VEMIMAGASAIQVGTALL 264
                                       ****************99 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   1.6e-07   0.00026      60     116 ..     218     274 ..     210     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHH CS
                      His_biosynth  60 anldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikela 116
                                       +   +v  +a++++ipv   GGI+s ed+ e++ aga+ + +gta ++   +++e+a
  gi|330508198|ref|YP_004384626.1| 218 VAVRAVYDLASRLEIPVIGVGGISSWEDAVEMIMAGASAIQVGTALLQGYGIFEEIA 274
                                       556778888888888888888888888888888888888888888888777777776 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         1   1.6e+03      53      67 ..      86     100 ..      80     167 .. 0.72
   2 !   18.0   0.6   7.2e-07    0.0012     194     239 ..     218     263 ..     211     279 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1
                                       HHHHTTSEEEE-SSS CS
                                       xxxxxxxxxxxxxxx RF
                             IMPDH  53 alareGgigvihknl 67 
                                         ar+Gg+ vi    
  gi|330508198|ref|YP_004384626.1|  86 DAARKGGVPVIASIF 100
                                       557777777776543 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 7.2e-07
                                       HHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 194 tAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsll 239
                                        Av +v++ a++ ++pvi  GGi++ +d v  + aGa+a+ +G  l
  gi|330508198|ref|YP_004384626.1| 218 VAVRAVYDLASRLEIPVIGVGGISSWEDAVEMIMAGASAIQVGTAL 263
                                       589999*************************************876 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2   1.3e-05     0.022     174     219 ..     219     265 ..     211     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                            DUF561 174 tlastyeiskkvslPvicasGlsdvtvpla.lslgasGiGigsavsk 219
                                       ++ ++y +++++++Pvi   G+s+    +  + +gas i +g a+ +
  gi|330508198|ref|YP_004384626.1| 219 AVRAVYDLASRLEIPVIGVGGISSWEDAVEmIMAGASAIQVGTALLQ 265
                                       56799******************99877752578********98765 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.9e-05     0.047     148     243 ..     169     265 ..     154     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE-CHHHHHHCHCC-.TTSEEEEESSS-SHHH CS
                              IGPS 148 eelaeaakslglevLvEvhdeeeleralklgakiiGvNnRnLktlevdlntteeLaklvp.kdvllvaeSGiktred 223
                                        el  aa++ g +++v +++ + +++ ++ g +i+G     L    ++   ++ + +l+   ++ ++   Gi++ ed
  gi|330508198|ref|YP_004384626.1| 169 LELGLAAQRGGADAVVAINTLKAMAIDIETGYPILGNRFGGLSGRAIKPVAVRAVYDLASrLEIPVIGVGGISSWED 245
                                       56778899999999999999999999999999999866666766665555555555544423499************ PP

                                       HHHHCCTT-SEEEESHHHHC CS
                              IGPS 224 veklkeegvnafLvGeslmr 243
                                       + ++  +g++a+ vG++l++
  gi|330508198|ref|YP_004384626.1| 246 AVEMIMAGASAIQVGTALLQ 265
                                       ******************87 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.7   2.8e+03      11      35 ..     160     184 ..     158     194 .. 0.78
   2 ?   11.0   0.1   0.00013      0.21     169     212 ..     221     264 ..     209     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.7
                                       EE-TTSS-CHHHHHHHHCTT-SEEE CS
                              PcrB  11 klDPeeenpdEiveiviesgtDavm 35 
                                       kl P+   + E   ++ ++g+Dav+
  gi|330508198|ref|YP_004384626.1| 160 KLTPNTADILELGLAAQRGGADAVV 184
                                       6778888777877788899999986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHH CS
                              PcrB 169 eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvve 212
                                        +v +l  +le   +i  GGi s E+A e++ a A +i vG+++ 
  gi|330508198|ref|YP_004384626.1| 221 RAVYDLASRLEI-PVIGVGGISSWEDAVEMIMAgASAIQVGTALL 264
                                       455666666654.4555689*********************9975 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.61     1e+03      81     106 ..      85     109 ..      71     130 .. 0.76
   2 ?    9.9   0.3    0.0002      0.33     262     309 ..     224     269 ..     209     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.61
                                       HHHHHHHTS-EEEETT-SS-HHHHHH CS
                            FMN_dh  81 araaakagipfvlstvastsleevaa 106
                                         aa+k g+p++ s +as s ee a+
  gi|330508198|ref|YP_004384626.1|  85 IDAARKGGVPVIASIFAS-SAEEFAQ 109
                                       468999999999999966.4555555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0002
                                       HHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHH CS
                            FMN_dh 262 peiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaa 309
                                        +++ ++  +i+v+  gGi++ +D++  +  GA+a+ +G ++l g  +
  gi|330508198|ref|YP_004384626.1| 224 YDLASRL--EIPVIGVGGISSWEDAVEMIMAGASAIQVGTALLQGYGI 269
                                       3333333..588999999999999999999999999999988877655 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.5   2.4e+03      83     114 ..      85     113 ..      82     122 .. 0.53
   2 ?    9.8   0.1   0.00029      0.48     129     168 ..     221     260 ..     214     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                                       HHHHHHTT--EEEEEE--SHHHHHHHHHHHHH CS
                      G3P_antiterm  83 ikkakklglltiqrlfliDssalekalkqiek 114
                                       i +a+k g+ +i  +f    + + +     ++
  gi|330508198|ref|YP_004384626.1|  85 IDAARKGGVPVIASIFASSAEEFAQ---ISRN 113
                                       5566666666666666544333333...3333 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00029
                                       HHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                      G3P_antiterm 129 kvikeikkelkipiiaGGLietkedveealkaGaiavsts 168
                                       + + ++ ++l+ip+i  G i++ ed  e++ aGa+a+ ++
  gi|330508198|ref|YP_004384626.1| 221 RAVYDLASRLEIPVIGVGGISSWEDAVEMIMAGASAIQVG 260
                                       5566788899**************************9876 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0089        15      20      46 ..     148     174 ..     141     195 .. 0.85
   2 ?    4.1   0.1     0.011        18     192     231 ..     225     265 ..     209     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0089
                                       SS-HHHHHHHHHHHHHCT-SSEEEE-- CS
                         Trp_syntA  20 dpdleqsleilkalekagadviElGlp 46 
                                         ++++s+ +  +l+ + ad++ElGl+
  gi|330508198|ref|YP_004384626.1| 148 AVKAASSVPVWVKLTPNTADILELGLA 174
                                       5567889999999************97 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.011
                                       HHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHH CS
                         Trp_syntA 192 rlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvk 231
                                        l +  + Pv    Gis+ e++ +++ ++a+++ vG al++
  gi|330508198|ref|YP_004384626.1| 225 DLASRLEIPVIGVGGISSWEDAVEMImAGASAIQVGTALLQ 265
                                       555666778765569**9999888887**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2218.37
//
Query:       gi|330508199|ref|YP_004384627.1|  [L=256]
Description: oxidoreductase FAD/NAD [Methanosaeta concilii GP6]
Scores for complete 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   36.4   2.4      7e-09   35.3   2.4    1.6  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
    3.2e-05   24.5   0.0    6.8e-05   23.5   0.0    1.5  1  NAD_binding_1    Oxidoreductase NAD-binding domain
  ------ inclusion threshold ------
       0.13   12.3   1.0       0.28   11.2   1.0    1.5  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   2.4   1.2e-12     7e-09       1      41 [.     201     235 ..     201     236 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.2e-12
                                       ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       +++ +C+ G+C++C+++ +g       rvC++GPv++ad++
  gi|330508199|ref|YP_004384627.1| 201 NRYFKCAEGICGSCCLDPDG------LRVCVEGPVIRADRL 235
                                       5899**************65......9***********987 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.1e-08   6.8e-05       2     107 ..      96     185 ..      95     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.1e-08
                                       EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHH CS
                     NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvq 78 
                                       i+gG+G aP+  + ++++++     +v+ + G+r   d+++ +++++l     g+ ++v++    ++g++g +grv 
  gi|330508199|ref|YP_004384627.1|  96 IGGGVGTAPLAFLGEQAMNA---GMEVTSLIGYRCCSDMIFLKRFQRL-----GK-TIVTT----DDGSSGIRGRVA 159
                                       9********99888888886...789**********************.....54.56666....6677788***** PP

                                       HHHHHHHHHHSSTTEEEEEECSHHHHHHH CS
                     NAD_binding_1  79 dalleellslkkeethvyvCGppgMikav 107
                                       + l e l+   ++ +++y+CGp+ M+ +v
  gi|330508199|ref|YP_004384627.1| 160 AGL-EALDL--DDYDQIYLCGPELMMWDV 185
                                       999.66666..9*************9765 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   4.7e-05      0.28      43      66 ..     197     220 ..     169     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.7e-05
                            Fer2_3  43 dptlafrasCregiCGscavainG 66 
                                       +  ++ + +C egiCGsc +  +G
  gi|330508199|ref|YP_004384627.1| 197 QACINRYFKCAEGICGSCCLDPDG 220
                                       344555689*********988777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1888.39
//
Query:       gi|330508200|ref|YP_004384628.1|  [L=243]
Description: fumarylacetoacetate hydrolase family protein [Methanosaeta concilii GP6]
Scores for complete 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  234.0   0.0    1.7e-69  233.8   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 !  233.8   0.0   9.7e-74   1.7e-69       1     218 []      44     238 ..      44     238 .. 0.96

  Alignments for each domain:
  == domain 1  score: 233.8 bits;  conditional E-value: 9.7e-74
                                       .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T-- CS
                     FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevls 77 
                                       ki+c+glny+eh+re++   ++ p+     ep++flk+++++  pg +i +P +s+++dyE+ELavvigk+ r++ +
  gi|330508200|ref|YP_004384628.1|  44 KIICVGLNYVEHARELK---MKLPE-----EPIIFLKPPTAALSPGGEIIYPPSSRQVDYEGELAVVIGKRGRNI-P 111
                                       69*************97...56777.....788******************************************.9 PP

                                       HHHHHTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGG CS
                     FAA_hydrolase  78 veeAedaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntk 154
                                       ++eAe +i+Gyt +nDv+aRdlq+++    +w+++ksfdtf+p+Gpwi   +++ dp+ +++++rvnge+vq+snt+
  gi|330508200|ref|YP_004384628.1| 112 ADEAEGHILGYTCFNDVTARDLQQRDT---QWTRAKSFDTFAPFGPWI---ASI-DPSGVDIETRVNGETVQKSNTS 181
                                       ***************************...******************...556.5689****************** PP

                                       GTTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE. CS
                     FAA_hydrolase 155 dmifspaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrVa 218
                                       d+if++++li+ +s ++tL+pGd+i+tGTp+gvg+       l+ gD veveieg+G l+n V+
  gi|330508200|ref|YP_004384628.1| 182 DLIFGVPRLIEFISGIMTLQPGDVIATGTPPGVGQ-------LHRGDLVEVEIEGIGVLKNSVV 238
                                       ********************************994.......*******************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1889.27
//
Query:       gi|330508201|ref|YP_004384629.1|  [L=432]
Description: erythromycin esterase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-52  177.4   0.0    7.5e-52  177.3   0.0    1.1  1  Erythro_esteras  Erythromycin esterase
  ------ inclusion threshold ------
      0.074   13.0   0.2       0.18   11.7   0.2    1.8  1  Cofac_haem_bdg   Haem-binding uptake, Tiki superfamily, ChaN


Domain annotation for each model (and alignments):
>> Erythro_esteras  Erythromycin esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.3   0.0   8.3e-56   7.5e-52       1     297 [.      77     387 ..      77     431 .. 0.83

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 8.3e-56
                                       HHHC---EEEEEEEHHHHHHHHHHHHHS-S-GGGT......S-CCC-CHHHHHHHHHHHHHHHSTT-SS--EEEEEE CS
                   Erythro_esteras   1 veehGfrtvalEadwpdalrvdryvrggtgdaeea...krfptwmWrneevlelveWlReyNagrpkkervrfyGlD 74 
                                       ve+hGf ++a+E+++p ++ vd+y+ g   d  ++    +f+ ++ r ++++elveW+ReyN+++++ ++++fyG+D
  gi|330508201|ref|YP_004384629.1|  77 VENHGFVAIAIESSFPRGRLVDQYIAGLGPDSFDDileLGFSHGFGRLDANRELVEWMREYNSDPSHVHKLHFYGFD 153
                                       89***********************888866666688868************************************* PP

                                       -S.--......-HHHHHHHHHHHHCHCCCCHHHHHHHCCHGGC.S................TSSCCCCCHHHHHHHH CS
                   Erythro_esteras  75 lq.sl......resldavldyLakvdpelagaareryaclapl.adp........raar..saeaaelrscedevva 133
                                        + ++      ++ +  vld+L ++dp   ++ r+r++++    +d            +   + +    ++++ev  
  gi|330508201|ref|YP_004384629.1| 154 SPtEMlasdspKQLIYFVLDFLGTIDPVQGEEHRQRIEPFLGQeSDWdnpdslidP--AksIGRSPNAIALRAEVED 228
                                       **8889*99966666*********************99995554222434555542..0454556688899999999 PP

                                       HHHHCCHGGG.....GGTSHHHHHHHHHHHHHHHHHHHC....CSSSSSCHHHHHHHHHHHHHHHHHHHH....HHS CS
                   Erythro_esteras 134 llkellakreeyaaedgeaeeffsaeqnarlvknaeryyra..gdeeswnlrllalRDrhMaenleallehe..arg 206
                                       l++ell +r+e  a +  + ++ +a ++a l+++ + y++   g++ ++++rll++RD++Maenl  + ++e  +rg
  gi|330508201|ref|YP_004384629.1| 229 LYEELLVRRPELVAGSD-PARYQEAVHYAALARQQLSYHAElaGNSLDRTSRLLGIRDAMMAENLAYITSREgsQRG 304
                                       9***9999998888555.789**********************99999**********************77**99* PP

                                       SEEEEEEHHHHSSS-STTTT-S......S-HHHHHHHHHGGGEEEEEEEEEEEEEEEC-.......EEEE----TTS CS
                   Erythro_esteras 207 kivvwAHNsHigdaratdmgke....rglnaGqllrerlgdeyvaiGftfgtgtvaaasewgepmevmtvrppppgs 279
                                       +++ +AHN+H+++ ra+   ++    + + aG++l + +g+ y++iG+++g               + ++++p++ +
  gi|330508201|ref|YP_004384629.1| 305 RVMAFAHNRHLQRGRAEWQYTDdlysW-WPAGSHLDQIMGSGYAVIGTAVGVS------------SSNGIGKPEEST 368
                                       ************555544433322336.*************************............899********* PP

                                       HHHHHHCSS-SEEEEEG.- CS
                   Erythro_esteras 280 lEallhaagppdflldl.r 297
                                       lEa+l aa  p+ l+++ +
  gi|330508201|ref|YP_004384629.1| 369 LEARLTAAPGPARLIPTcK 387
                                       *******998888888753 PP

>> Cofac_haem_bdg  Haem-binding uptake, Tiki superfamily, ChaN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2     2e-05      0.18     141     208 ..     253     319 ..      50     321 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHHHHHT-TTTHHHHHHHHHHHHHHHHHHHHHHHH-SS.E......EEEEEEHHHH-TTT CS
                    Cofac_haem_bdg 141 eeyraaleevlaehhcgeakeealerfveaQvlwDetMAesiaaalkarnpgk.lvvviaGsgHveygl 208
                                         y a+ +++l+ h   e   ++l+r  +   ++D++MAe++a    ++ +++ +v+ +a + H+++g 
  gi|330508201|ref|YP_004384629.1| 253 VHYAALARQQLSYHA--ELAGNSLDRTSRLLGIRDAMMAENLAYITSREGSQRgRVMAFAHNRHLQRGR 319
                                       233333344444443..6999999******************986665566446**********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3303.07
//
Query:       gi|330508202|ref|YP_004384630.1|  [L=421]
Description: alkaline phosphatase family protein [Methanosaeta concilii GP6]
Scores for complete 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-103  344.5   2.6    5.2e-95  318.8   1.3    2.1  2  Alk_phosphatase  Alkaline phosphatase
    5.4e-10   39.1   0.0    1.2e-09   37.9   0.0    1.5  2  Metalloenzyme    Metalloenzyme superfamily
    1.5e-05   24.6   0.1    0.00078   18.9   0.1    2.6  1  Sulfatase        Sulfatase
  ------ inclusion threshold ------
      0.013   15.1   0.1      0.051   13.3   0.1    2.0  2  HTH_41           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.8   1.3   1.2e-98   5.2e-95       1     319 [.      35     346 ..      35     356 .. 0.94
   2 !   25.1   0.0   1.8e-09   7.9e-06     375     414 ..     379     419 ..     361     421 .] 0.87

  Alignments for each domain:
  == domain 1  score: 318.8 bits;  conditional E-value: 1.2e-98
                                       -SEEEEEEETT-SHHHHHHHHHHHCHCTCSSSTTS.TTGGG-SEEEEEESSECSTTSSGHHHHHHHHHHSSBTBTT- CS
                   Alk_phosphatase   1 aknvilligDGmgvstvtaaRslkeqakdklgeetllamdrfplvglsktyavdkqvtDSaataTAyacgvktynga 77 
                                       aknvilligDGmg +++t aR+ k + + +     +l md ++ +g+ kt + ++ vtDSa ++ A+a+g kt+ng+
  gi|330508202|ref|YP_004384630.1|  35 AKNVILLIGDGMGFPQLTLARIDKAGGNVTQYGSVELFMDGMEQTGMVKTSSANSLVTDSAPASSAMATGEKTNNGV 111
                                       7***********************9999999999******************************************* PP

                                       BSB-TTS......T-B---HHHHHHHTT-EEEEEEEEETTSHHHHTTTTTBSSTTSSSHHHSTCCCHHTTS-SHHHH CS
                   Alk_phosphatase  78 igvdaaa......gkevksvleaAkkaGkstGlVtTtritdAtPaalvahvesRkwkedaavpaealeegkkdiaeq 148
                                       i+ + aa      g++++++le+A + G stGl+tTtrit+AtPaa++ahv++R+++              ++ia+q
  gi|330508202|ref|YP_004384630.1| 112 ISQNSAAiqgkrdGENLTTILEMAEDSGLSTGLITTTRITHATPAAFYAHVDNRDNE--------------SEIADQ 174
                                       ****9999****999***************************************443..............5678** PP

                                       HHHCST-SEEEEESCGGGSBCSBCTS.....STCCT.SBHHHHHCCTTCEEE-SHHHHHHHCTSTSSCEEEESSSSS CS
                   Alk_phosphatase 149 likakkidvllGGGrkeffpaeyatd.....GerkdGrnlieeakkkgyqyvsdrkeLlkakeenvkplLGLFadgd 220
                                       l++   ++v+lGGG ++f   e  td     G+r d r+l +e++++gy +v + +++ k++++ ++ lLGLF+ ++
  gi|330508202|ref|YP_004384630.1| 175 LLAS-GVEVILGGGLQYF-TGENDTDplgnyGKRGDERDLLNEFESQGYALVYNGSSFQKVDSNTTERLLGLFDSSH 249
                                       ***9.*************.545555567888********************************************** PP

                                       CS-CCCSCT..CCE--HHHHHHHHHHHHTTSTT-EEEEEEETCHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHCHHC CS
                   Alk_phosphatase 221 lkveldrde..atdPsLkemtevAiklLsknekGFFLlVEGsrIDhaaHendavgalsEvvefdeAvkaalefakke 295
                                       ++++l+r +  + dPsL+emt++Ai +Ls+n+kGFFL+VEG+rIDha+He ++ + + ++++fdeAvk a++fa+ +
  gi|330508202|ref|YP_004384630.1| 250 MQYDLERLSgvERDPSLAEMTRKAISILSRNPKGFFLMVEGGRIDHAGHERNISKNIADTLAFDEAVKVATDFASLK 326
                                       *******8733567*************************************************************** PP

                                       TTEEEEEEESSEESEEEESTTSTT CS
                   Alk_phosphatase 296 ketlvvvTaDHshvfsfggyttrg 319
                                       +etlv+vTaDH+     gg+++++
  gi|330508202|ref|YP_004384630.1| 327 NETLVIVTADHEC----GGLVLQP 346
                                       ***********98....7776665 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.8e-09
                                       .SSHTEE-SSEEEEEESTTGGGG.SCEEECCHHHHHHHHHC CS
                   Alk_phosphatase 375 ltseeHtgedvavfAygpkaelv.rGvqeqteiakvlaaal 414
                                       +++ +Ht++dv+++A gp ae+v +Gv+++t+i+++++ a 
  gi|330508202|ref|YP_004384630.1| 379 MEEATHTAVDVPIMASGPGAEKVsKGVIDNTRIFEIMKEAF 419
                                       6889****************99956************9885 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.59   2.6e+03       2      13 ..      37      48 ..      36     111 .. 0.79
   2 !   37.9   0.0   2.6e-13   1.2e-09     107     221 ..     251     401 ..     215     416 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.59
                                      EEEEEEETTBB- CS
                                      xxxxxxxxxxxx RF
                     Metalloenzyme  2 kvvlvvlDGlGe 13
                                      +v+l++ DG+G 
  gi|330508202|ref|YP_004384630.1| 37 NVILLIGDGMGF 48
                                      678888888884 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 2.6e-13
                                       -SHH......STT--HHHHHHHHHHHH.CC.-S.EEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-.TT CS
                                       xxxx......xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                     Metalloenzyme 107 tfdl......qpemkavevaekaldailsgkfd.lvvvniknaDmvGHtgdleatiaaieaaDeavkeildaie.qv 175
                                       ++dl      +++ +  e+++ka++ +  +    +++v     D +GH++++++ ia   a+Deavk  +d  + ++
  gi|330508202|ref|YP_004384630.1| 251 QYDLerlsgvERDPSLAEMTRKAISILSRNPKGfFLMVEGGRIDHAGHERNISKNIADTLAFDEAVKVATDFASlKN 327
                                       444444444488889999999**99996665558999**********************************987245 PP

                                       TEEEEEE-SSB--TTTSS......................................-----EEEEEESTT----S- CS
                                       xxxxxxxxxxxxxxxxxxxxx..............................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 176 dgilvvtADHgnaedmvkrdk..............................qplTsHtlepVPilivgkglapdkv 221
                                       +++++vtADH +   + + ++                                   Ht+  VPi+  g+g ++  v
  gi|330508202|ref|YP_004384630.1| 328 ETLVIVTADHECGGLVLQPENldvyeagginplfasgttktqgprydfiteMEEATHTAVDVPIMASGPGAEK--V 401
                                       567789************999**************************999866778*************9765..3 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.7e-07   0.00078       1     287 [.      36     370 ..      36     390 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-07
                                       EEEEEEEESSE-TT............GSGGGTTTSCSSHHHHHHHHTSEEESSEE.-SSSSHHHHHHHHHHSS-HHH CS
                         Sulfatase   1 pnvvliladdlgag............dlglyggktattpnldrlaeeglrftnfy.saaplcspsraalltgryphn 64 
                                       +nv+l+++d +g++            +++ yg       ++d + + g++ t+   s  + ++p+ +a+ tg   +n
  gi|330508202|ref|YP_004384630.1|  36 KNVILLIGDGMGFPqltlaridkaggNVTQYGSVEL---FMDGMEQTGMVKTSSAnSLVTDSAPASSAMATGEKTNN 109
                                       69************9999988777777777776555...45777766655555443777789************999 PP

                                       HTHSSCCSTTT.HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC........................CT CS
                         Sulfatase  65 sgvasntevgg.gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk........................nr 116
                                         + +n+ + + +  +++ +t++e+  + G  t++i  +  ++    ++y                         ++
  gi|330508202|ref|YP_004384630.1| 110 GVISQNSAAIQgKRDGENLTTILEMAEDSGLSTGLITTTRITHATPAAFYAhvdnrdneseiadqllasgvevilGG 186
                                       8888888777789999****************************999999899999999999999996666666666 PP

                                       TTSEEEETSSSCHHTCCCCCCCCCECTCCCTTTTCSHHHHHHHHHHHHH..........HCCC.TSSEEEEEEE-TT CS
                         Sulfatase 117 gfdrflgfptgsaalkdpekseyngevlrvppeggysddrlldealefl..........larn.dkpfflylatlap 182
                                       g ++f g           ++ ++ g     ++ ++++ ++ll+e++ +           ++ + +    l   + ++
  gi|330508202|ref|YP_004384630.1| 187 GLQYFTG----------ENDTDPLG-----NYGKRGDERDLLNEFESQGyalvyngssfQKVDsNTTERLLGLFDSS 248
                                       6666666..........22222222.....12233333333333332222222333333444444444444446666 PP

                                       SSSTCTCGGHTCCGSTTTTCCCCCCH.............................HHHHHHHHHHHHHHHHHHHHHH CS
                         Sulfatase 183 Happeapdeyakkyatffddgseaar.............................qlleaylnsveyvDdligrvla 230
                                       H   +  ++  +   ++++++ e +r                             +   + +++++  D++++    
  gi|330508202|ref|YP_004384630.1| 249 HM-QYDLERLSGV--ERDPSLAEMTRkaisilsrnpkgfflmveggridhagherNISKNIADTLAF-DEAVKV-AT 320
                                       64.3333333333..3333333333344445555555666666666666666664555666666666.777754.44 PP

                                       HHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHC CS
                         Sulfatase 231 aLeenglldntlvvftSDhgasleesngplrggkganayeggtrvPllvwwpgekap 287
                                       ++  + l+++tlv++t+Dh      ++ +l++++  + ye g   Pl+  +  + + 
  gi|330508202|ref|YP_004384630.1| 321 DF--ASLKNETLVIVTADHEC----GGLVLQPENL-DVYEAGGINPLFASGTTKTQG 370
                                       44..47788888888888855....3356666666.666666666666666655555 PP

>> HTH_41  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         1   4.5e+03      30      39 ..      76      85 ..      73      86 .. 0.83
   2 ?   13.3   0.1   1.1e-05     0.051       3      23 ..     125     145 ..     123     147 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1
                            HTH_41 30 Leddkaisle 39
                                      +e+ ++++++
  gi|330508202|ref|YP_004384630.1| 76 MEQTGMVKTS 85
                                      99*****987 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.1e-05
                            HTH_41   3 GdRlktIeelakeleLSvGlv 23 
                                       G+ l tI e+a++++LS Gl+
  gi|330508202|ref|YP_004384630.1| 125 GENLTTILEMAEDSGLSTGLI 145
                                       999*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2904.34
//
Query:       gi|330508203|ref|YP_004384631.1|  [L=722]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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  204.5  23.7    1.3e-10   40.6   0.3    7.9  8  TPR_1            Tetratricopeptide repeat
    3.7e-52  170.3  17.9    2.9e-08   33.2   0.2    7.8  8  TPR_2            Tetratricopeptide repeat
    8.5e-51  169.4  35.9    8.9e-11   41.3   0.2    8.3  8  TPR_11           TPR repeat
    2.1e-41  136.6  14.4    3.5e-05   23.7   0.0    8.1  7  TPR_8            Tetratricopeptide repeat
    7.7e-30  101.1  18.8    5.3e-05   23.3   0.0    9.0  8  TPR_17           Tetratricopeptide repeat
      7e-29  100.2   8.8    8.1e-09   36.0   0.1    5.6  6  TPR_16           Tetratricopeptide repeat
    7.8e-26   90.2   9.0      4e-07   30.2   0.0    5.9  6  TPR_12           Tetratricopeptide repeat
    1.7e-25   87.5   9.7     0.0023   18.6   0.1    8.1  7  TPR_14           Tetratricopeptide repeat
    8.6e-23   80.6  16.4    7.8e-08   32.7   0.1    5.7  5  TPR_19           Tetratricopeptide repeat
    4.4e-18   65.2   0.8    0.00019   21.5   0.0    5.8  6  TPR_9            Tetratricopeptide repeat
      1e-16   59.6   3.6       0.11   12.6   0.0    7.3  7  TPR_7            Tetratricopeptide repeat
    1.1e-14   54.0   8.2       0.43   11.3   0.1    7.9  7  TPR_6            Tetratricopeptide repeat
    2.7e-11   43.6   9.2      0.001   19.3   1.7    4.4  4  ANAPC3           Anaphase-promoting complex, cyclosome, subun
      1e-10   41.1  16.5     0.0019   18.0   0.1    7.2  7  TPR_10           Tetratricopeptide repeat
    1.5e-10   41.0  16.6      0.038   14.1   0.0    7.0  6  MIT              MIT (microtubule interacting and transport) 
    8.7e-10   38.1   8.8     0.0067   15.4   0.1    5.3  6  NARP1            NMDA receptor-regulated protein 1
      4e-07   30.0  16.2      0.027   14.2   1.0    5.4  5  TPR_21           Tetratricopeptide repeat-like domain
    1.3e-06   28.3   4.6       0.12   12.5   0.1    6.4  7  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    6.6e-06   26.2   5.5        1.2    9.2   0.4    5.6  5  DUF3856          Domain of Unknown Function (DUF3856)
    6.9e-06   25.9  16.3       0.12   12.4   0.0    7.1  7  TPR_3            Tetratricopeptide repeat
     0.0006   19.2   1.2         54    3.4   0.0    6.0  6  SHNi-TPR         SHNi-TPR
    0.00074   18.8   3.1        3.2    6.9   0.2    4.3  5  TPR_15           Tetratricopeptide repeat
     0.0012   18.8   8.0     0.0046   17.0   1.1    2.8  2  DZR              Double zinc ribbon
     0.0015   18.2   5.8     0.0015   18.2   5.8    2.9  2  zinc_ribbon_2    zinc-ribbon domain
     0.0026   17.2   0.2        3.5    6.9   0.0    3.0  3  TPR_MalT         MalT-like TPR region
      0.004   17.6   0.0        5.7    7.4   0.0    2.9  2  BTAD             Bacterial transcriptional activator domain
     0.0075   16.8   0.8         81    4.3   0.0    4.6  4  TPR_4            Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.024   14.6   1.9        1.1    9.3   0.5    3.2  2  SRP_TPR_like     Putative TPR-like repeat
      0.036   14.0   6.4      0.071   13.0   0.1    3.0  3  Nudix_N_2        Nudix N-terminal
      0.064   13.0   2.2       0.58   10.0   0.1    3.6  3  PPTA             Protein prenyltransferase alpha subunit repe
      0.087   13.0   0.1        4.4    7.6   0.0    2.6  2  Vps36_ESCRT-II   Vacuolar protein sorting protein 36 Vps36
       0.15   11.7   0.1       0.15   11.7   0.1    2.6  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.22    9.3   3.1      0.097   10.5   0.1    1.7  2  PolC_DP2         DNA polymerase II large subunit DP2
       0.37   10.4  18.4        2.6    7.7   0.0    6.6  6  HTH_Bact         Helix-turn-helix bacterial domain
       0.38   11.0   4.1        2.5    8.4   0.3    2.7  2  IBR              IBR domain, a half RING-finger domain
       0.68   10.0   5.2       0.24   11.4   0.2    2.5  2  HypA             Hydrogenase/urease nickel incorporation, met
        1.2    9.2   7.0         25    5.0   0.1    4.9  5  ANAPC5           Anaphase-promoting complex subunit 5
        2.4    8.3   5.0        8.9    6.5   0.2    4.1  4  DUF1510          Domain of unknown function (DUF1510)
          3    8.2  12.1         13    6.2   0.2    4.4  4  TPR_20           Tetratricopeptide repeat
        4.1    7.8   7.1          5    7.6   0.1    2.9  2  DnaJ_CXXCXGXG    DnaJ central domain
        6.3    7.6   9.5        3.7    8.4   0.5    3.6  3  zinc_ribbon_15   zinc-ribbon family
        7.1    6.1   6.1         17    4.8   0.0    3.2  3  zf-TFIIB         Transcription factor zinc-finger
        9.1    6.4   8.9       0.66   10.0   0.4    2.8  2  zinc-ribbons_6   zinc-ribbons


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 !   40.6   0.3   3.1e-13   1.3e-10       1      32 [.     210     241 ..     210     242 .. 0.99
   2 !   35.1   0.0   1.7e-11   6.9e-09       3      34 .]     246     277 ..     244     277 .. 0.95
   3 !   19.2   0.6   1.8e-06   0.00075       9      33 ..     287     311 ..     287     312 .. 0.96
   4 !   28.1   0.0   2.9e-09   1.2e-06       3      32 ..     315     344 ..     313     346 .. 0.95
   5 !   33.4   0.0   6.1e-11   2.5e-08       1      34 []     347     380 ..     347     380 .. 0.95
   6 !   22.6   2.0   1.5e-07   6.4e-05       1      34 []     381     414 ..     381     414 .. 0.96
   7 ?   -0.7   0.0       3.4   1.4e+03      16      24 ..     432     440 ..     423     442 .. 0.72
   8 !   35.5   0.0   1.3e-11   5.3e-09       5      33 ..     440     468 ..     436     469 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 3.1e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+a+ n+G a++k+gk++eA+++yekA+++nP
  gi|330508203|ref|YP_004384631.1| 210 ADAWRNKGIALHKQGKFNEAVAAYEKAIQINP 241
                                       89*****************************9 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 1.7e-11
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++ ++G+++  lg+yd+A+ +y++A+e+nP++
  gi|330508203|ref|YP_004384631.1| 246 SWSGKGAVLDDLGQYDQAIRAYDQAIEINPQD 277
                                       79****************************86 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 1.8e-06
                                       HHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   9 nayfklgkydeAleyyekALelnPn 33 
                                       n+y+++ kydeA+ + + A+++nP+
  gi|330508203|ref|YP_004384631.1| 287 NLYHYQAKYDEAIVALDMAIKINPQ 311
                                       79**********************7 PP

  == domain 4  score: 28.1 bits;  conditional E-value: 2.9e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                       a++ +G ++   gky eA+e+y+kA+el+P
  gi|330508203|ref|YP_004384631.1| 315 AWNIKGGILTGRGKYGEAIEAYDKAIELDP 344
                                       9****************************9 PP

  == domain 5  score: 33.4 bits;  conditional E-value: 6.1e-11
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a +++n+G+a+   g+ydeA+ ++++A+e++ +n
  gi|330508203|ref|YP_004384631.1| 347 ASIWNNRGAAFVGEGNYDEAVRAFNRAIEIDQQN 380
                                       678****************************987 PP

  == domain 6  score: 22.6 bits;  conditional E-value: 1.5e-07
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+ ++ +  a+fk+ kydeAl + +kA+el+Pn+
  gi|330508203|ref|YP_004384631.1| 381 AYYWNAKCTALFKQTKYDEALNAVNKAIELDPNY 414
                                       678*****************************97 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 3.4
                                       -HHHHHHHH CS
                             TPR_1  16 kydeAleyy 24 
                                       + +eA++++
  gi|330508203|ref|YP_004384631.1| 432 NTEEAVDCF 440
                                       457888888 PP

  == domain 8  score: 35.5 bits;  conditional E-value: 1.3e-11
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   5 ynlGnayfklgkydeAleyyekALelnPn 33 
                                       +++G+ ++++gkydeA+ +y+kA+el+P+
  gi|330508203|ref|YP_004384631.1| 440 FGKGVSFHQQGKYDEAILAYNKAIELDPT 468
                                       789*************************7 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.2     7e-11   2.9e-08       1      33 [.     210     242 ..     210     243 .. 0.96
   2 !   26.8   0.0   7.6e-09   3.2e-06       4      34 .]     247     277 ..     244     277 .. 0.94
   3 !   12.0   0.2   0.00043      0.18       9      33 ..     287     311 ..     287     312 .. 0.94
   4 !   23.9   0.0   6.7e-08   2.8e-05       2      34 .]     314     346 ..     313     346 .. 0.92
   5 !   26.9   0.0   7.2e-09     3e-06       1      34 []     347     380 ..     347     380 .. 0.94
   6 !   25.1   1.1   2.8e-08   1.2e-05       1      34 []     381     414 ..     381     414 .. 0.96
   7 ?    0.2   0.0       2.6   1.1e+03      16      26 ..     432     442 ..     424     445 .. 0.71
   8 !   28.4   0.0   2.4e-09     1e-06       4      33 ..     439     468 ..     436     469 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 7e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+a+ n G a+ k+g+++eA++a+ekA++++P 
  gi|330508203|ref|YP_004384631.1| 210 ADAWRNKGIALHKQGKFNEAVAAYEKAIQINPL 242
                                       79*****************************95 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 7.6e-09
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +   G ++  lg+y++A++a+++A+e++P++
  gi|330508203|ref|YP_004384631.1| 247 WSGKGAVLDDLGQYDQAIRAYDQAIEINPQD 277
                                       8899*************************86 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00043
                             TPR_2   9 layyklgdyeeAleafekAleldPn 33 
                                       ++y ++ +y+eA+ a++ A++++P+
  gi|330508203|ref|YP_004384631.1| 287 NLYHYQAKYDEAIVALDMAIKINPQ 311
                                       5799********************7 PP

  == domain 4  score: 23.9 bits;  conditional E-value: 6.7e-08
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        a++  G ++  +g+y eA+ea++kA+eldP n
  gi|330508203|ref|YP_004384631.1| 314 GAWNIKGGILTGRGKYGEAIEAYDKAIELDPLN 346
                                       58999999***********************65 PP

  == domain 5  score: 26.9 bits;  conditional E-value: 7.2e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a +++n+G a    g+y+eA++af++A+e+d +n
  gi|330508203|ref|YP_004384631.1| 347 ASIWNNRGAAFVGEGNYDEAVRAFNRAIEIDQQN 380
                                       568***************************9876 PP

  == domain 6  score: 25.1 bits;  conditional E-value: 2.8e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+++++   a++k+ +y+eAl+a +kA+eldPn+
  gi|330508203|ref|YP_004384631.1| 381 AYYWNAKCTALFKQTKYDEALNAVNKAIELDPNY 414
                                       689*****************************96 PP

  == domain 7  score: 0.2 bits;  conditional E-value: 2.6
                             TPR_2  16 dyeeAleafek 26 
                                       + eeA+++f k
  gi|330508203|ref|YP_004384631.1| 432 NTEEAVDCFGK 442
                                       559*****987 PP

  == domain 8  score: 28.4 bits;  conditional E-value: 2.4e-09
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                       ++  G +  ++g+y+eA+ a++kA+eldP+
  gi|330508203|ref|YP_004384631.1| 439 CFGKGVSFHQQGKYDEAILAYNKAIELDPT 468
                                       7889*************************8 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00067      0.28      18      42 .]     200     224 ..     190     224 .. 0.90
   2 !   27.3   0.1   5.2e-09   2.2e-06       3      37 ..     219     253 ..     217     255 .. 0.86
   3 !   31.8   0.9   1.9e-10     8e-08       6      36 ..     256     286 ..     251     286 .. 0.92
   4 !   18.2   0.4   3.6e-06    0.0015       2      32 ..     287     317 ..     287     321 .. 0.94
   5 !   41.3   0.2   2.1e-13   8.9e-11       4      39 ..     323     358 ..     320     361 .. 0.90
   6 !   22.0   1.4   2.3e-07   9.6e-05       5      32 ..     358     385 ..     356     387 .. 0.89
   7 !   17.7   0.6   5.1e-06    0.0021       3      27 ..     390     414 ..     389     419 .. 0.92
   8 !   31.2   0.0     3e-10   1.2e-07       3      26 ..     445     468 ..     443     469 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00067
                            TPR_11  18 kkAlkldPdnaeayynLGlayykqG 42 
                                       ++ ++ + ++a+a+ n G a++kqG
  gi|330508203|ref|YP_004384631.1| 200 NRSIETNAQDADAWRNKGIALHKQG 224
                                       578999******************9 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 5.2e-09
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       a+++qGk++eA++aY+kA++++P + + +++ G++
  gi|330508203|ref|YP_004384631.1| 219 ALHKQGKFNEAVAAYEKAIQINPLDSSSWSGKGAV 253
                                       899********************887777777765 PP

  == domain 3  score: 31.8 bits;  conditional E-value: 1.9e-10
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                       ++G+y++Ai aY +A++++P++a+ + n Gl
  gi|330508203|ref|YP_004384631.1| 256 DLGQYDQAIRAYDQAIEINPQDADSFANKGL 286
                                       79***********************999885 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 3.6e-06
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayy 32 
                                       ++y+ q ky+eAi a+  A+k++P+ a a++
  gi|330508203|ref|YP_004384631.1| 287 NLYHYQAKYDEAIVALDMAIKINPQLAGAWN 317
                                       78999*********************99986 PP

  == domain 5  score: 41.3 bits;  conditional E-value: 2.1e-13
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       ++ +Gky eAieaY kA++ldP na++++n+G+a+ 
  gi|330508203|ref|YP_004384631.1| 323 LTGRGKYGEAIEAYDKAIELDPLNASIWNNRGAAFV 358
                                       6669******************************96 PP

  == domain 6  score: 22.0 bits;  conditional E-value: 2.3e-07
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayy 32 
                                       +  G+y+eA+ a+++A+++d++na  ++
  gi|330508203|ref|YP_004384631.1| 358 VGEGNYDEAVRAFNRAIEIDQQNAYYWN 385
                                       557*********************9987 PP

  == domain 7  score: 17.7 bits;  conditional E-value: 5.1e-06
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdn 27 
                                       a+++q ky+eA++a +kA++ldP++
  gi|330508203|ref|YP_004384631.1| 390 ALFKQTKYDEALNAVNKAIELDPNY 414
                                       689999******************8 PP

  == domain 8  score: 31.2 bits;  conditional E-value: 3e-10
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPd 26 
                                        +++qGky+eAi aY+kA++ldP+
  gi|330508203|ref|YP_004384631.1| 445 SFHQQGKYDEAILAYNKAIELDPT 468
                                       599********************7 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   9.8e-08   4.1e-05       1      32 [.     210     241 ..     210     241 .. 0.95
   2 !   23.7   0.0   8.4e-08   3.5e-05       3      34 .]     246     277 ..     244     277 .. 0.92
   3 !   11.7   0.3   0.00058      0.24       1      33 [.     278     311 ..     278     312 .. 0.93
   4 !   22.1   0.0   2.7e-07   0.00011       2      32 ..     314     344 ..     313     344 .. 0.96
   5 !   22.0   0.0   2.8e-07   0.00012       1      34 []     347     380 ..     347     380 .. 0.95
   6 !   13.2   0.5   0.00019      0.08       4      34 .]     384     414 ..     381     414 .. 0.84
   7 !   23.0   0.0   1.3e-07   5.6e-05       4      33 ..     439     468 ..     439     469 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 9.8e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+a+ n+g +++k+g+++eA+++yeka++++p
  gi|330508203|ref|YP_004384631.1| 210 ADAWRNKGIALHKQGKFNEAVAAYEKAIQINP 241
                                       678999************************98 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 8.4e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++  +g ++++lg+y++A+ +y +a+e++p++
  gi|330508203|ref|YP_004384631.1| 246 SWSGKGAVLDDLGQYDQAIRAYDQAIEINPQD 277
                                       67789999**********************86 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00058
                                       CCHHHHHH.HHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlg.siylklgdyeeAkeyyekaleldpd 33 
                                       a++  n+g ++y+ + +y+eA+ ++  a++++p+
  gi|330508203|ref|YP_004384631.1| 278 ADSFANKGlNLYHYQAKYDEAIVALDMAIKINPQ 311
                                       577889999***********************97 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 2.7e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                        a++ +g i+   g+y eA+e+y ka+eldp
  gi|330508203|ref|YP_004384631.1| 314 GAWNIKGGILTGRGKYGEAIEAYDKAIELDP 344
                                       69****************************9 PP

  == domain 5  score: 22.0 bits;  conditional E-value: 2.8e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a++++n g +    g+y+eA+ ++++a+e+d++n
  gi|330508203|ref|YP_004384631.1| 347 ASIWNNRGAAFVGEGNYDEAVRAFNRAIEIDQQN 380
                                       679****************************986 PP

  == domain 6  score: 13.2 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++ +  +++k+ +y+eA  + +ka+eldp++
  gi|330508203|ref|YP_004384631.1| 384 WNAKCTALFKQTKYDEALNAVNKAIELDPNY 414
                                       555556889999*****************95 PP

  == domain 7  score: 23.0 bits;  conditional E-value: 1.3e-07
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++ +g   +++g+y+eA+ +y+ka+eldp+
  gi|330508203|ref|YP_004384631.1| 439 CFGKGVSFHQQGKYDEAILAYNKAIELDPT 468
                                       67789999********************95 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   7.5e-06    0.0031       3      33 ..     200     230 ..     198     231 .. 0.93
   2 !   22.6   0.0   2.1e-07   8.7e-05       1      33 [.     232     264 ..     232     265 .. 0.96
   3 !   16.5   0.6   1.9e-05    0.0078       1      33 [.     266     299 ..     266     299 .. 0.91
   4 ?    7.6   0.0     0.013       5.4       5      34 .]     305     334 ..     301     334 .. 0.94
   5 !   23.3   0.0   1.3e-07   5.3e-05       1      33 [.     335     367 ..     335     368 .. 0.95
   6 !    8.2   1.0    0.0083       3.5       2      33 ..     370     401 ..     369     402 .. 0.91
   7 ?    5.3   0.0     0.073        30       4      31 ..     406     433 ..     404     437 .. 0.83
   8 ?    4.2   0.0      0.16        68       1      11 [.     458     468 ..     458     471 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.5e-06
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtAr 33 
                                        +++e +  +ada+ n++ +l+k+G++ +A+
  gi|330508203|ref|YP_004384631.1| 200 NRSIETNAQDADAWRNKGIALHKQGKFNEAV 230
                                       699************************9996 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 2.1e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y+ka++++P ++ ++  ++ +l  +G++++A+
  gi|330508203|ref|YP_004384631.1| 232 AYEKAIQINPLDSSSWSGKGAVLDDLGQYDQAI 264
                                       5*******************************7 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.9e-05
                            TPR_17   1 lylkaleldPnnadaynnLAe.lllknGdlmtAr 33 
                                       +y +a+e++P +ad++ n++  l++ + ++++A+
  gi|330508203|ref|YP_004384631.1| 266 AYDQAIEINPQDADSFANKGLnLYHYQAKYDEAI 299
                                       59*******************8888999999985 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.013
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmtArq 34 
                                       a++++P  a a+n ++ +l  +G++++A++
  gi|330508203|ref|YP_004384631.1| 305 AIKINPQLAGAWNIKGGILTGRGKYGEAIE 334
                                       9**************************986 PP

  == domain 5  score: 23.3 bits;  conditional E-value: 1.3e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y ka+eldP na  +nn++ ++   G++++A+
  gi|330508203|ref|YP_004384631.1| 335 AYDKAIELDPLNASIWNNRGAAFVGEGNYDEAV 367
                                       59***************************9996 PP

  == domain 6  score: 8.2 bits;  conditional E-value: 0.0083
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + +a+e+d  na+ +n + ++l k+ ++++A+
  gi|330508203|ref|YP_004384631.1| 370 FNRAIEIDQQNAYYWNAKCTALFKQTKYDEAL 401
                                       89***************999999999999985 PP

  == domain 7  score: 5.3 bits;  conditional E-value: 0.073
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmt 31 
                                       ka+eldPn+  a + +  +l+k+G++ t
  gi|330508203|ref|YP_004384631.1| 406 KAIELDPNYKAAQTTKTLILRKLGNFNT 433
                                       9********9999999999999997654 PP

  == domain 8  score: 4.2 bits;  conditional E-value: 0.16
                            TPR_17   1 lylkaleldPn 11 
                                       +y ka+eldP+
  gi|330508203|ref|YP_004384631.1| 458 AYNKAIELDPT 468
                                       59********8 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.7e-05    0.0069      27      67 ..     206     243 ..     196     245 .. 0.87
   2 !   23.9   0.6   1.2e-07   4.9e-05       6      66 ..     253     311 ..     248     313 .. 0.90
   3 !   26.1   0.1   2.4e-08     1e-05       9      67 ..     291     346 ..     287     347 .. 0.94
   4 !   36.0   0.1     2e-11   8.1e-09       9      67 ..     325     380 ..     319     381 .. 0.92
   5 !    9.3   0.1    0.0042       1.7       5      36 ..     389     417 ..     385     429 .. 0.90
   6 !   14.0   0.0   0.00015     0.062      38      65 ..     440     467 ..     440     469 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.7e-05
                            TPR_16  27 dpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +    ++a+A+ ++g a+ +qg + eA+a+y++a++  p +
  gi|330508203|ref|YP_004384631.1| 206 N---AQDADAWRNKGIALHKQGKFNEAVAAYEKAIQINPLD 243
                                       5...789***************************9988865 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.2e-07
                            TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaal.rqgrlaeAaalyraalraapd 66 
                                        + ++g+yd+A++a+++a++ +   P++a++  ++g+ ++  q  ++eA+ +++ a++  p+
  gi|330508203|ref|YP_004384631.1| 253 VLDDLGQYDQAIRAYDQAIEIN---PQDADSFANKGLNLYhYQAKYDEAIVALDMAIKINPQ 311
                                       56799*****************...**********999995579******999999999987 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 2.4e-08
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++ +yd+A+ al+ a+k +   P+ a A++ +g ++  +g + eA+++y++a++ +p +
  gi|330508203|ref|YP_004384631.1| 291 YQAKYDEAIVALDMAIKIN---PQLAGAWNIKGGILTGRGKYGEAIEAYDKAIELDPLN 346
                                       7889***************...********************************99965 PP

  == domain 4  score: 36.0 bits;  conditional E-value: 2e-11
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                        +g+y +A++a++ a+++d   P++a  ++++g a+   g+++eA+ ++++a++ + ++
  gi|330508203|ref|YP_004384631.1| 325 GRGKYGEAIEAYDKAIELD---PLNASIWNNRGAAFVGEGNYDEAVRAFNRAIEIDQQN 380
                                       68*****************...*****************************99998876 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.0042
                            TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeA 36 
                                       +a++++ +yd+A++a + a+++d   P   +A
  gi|330508203|ref|YP_004384631.1| 389 TALFKQTKYDEALNAVNKAIELD---PNYKAA 417
                                       589********************...876665 PP

  == domain 6  score: 14.0 bits;  conditional E-value: 0.00015
                            TPR_16  38 lllgdaalrqgrlaeAaalyraalraap 65 
                                       +++g+++ +qg ++eA+ +y++a++ +p
  gi|330508203|ref|YP_004384631.1| 440 FGKGVSFHQQGKYDEAILAYNKAIELDP 467
                                       689********************99998 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   2.7e-06    0.0011      32      74 ..     199     239 ..     191     241 .. 0.83
   2 !   21.2   0.3   6.2e-07   0.00026       4      74 ..     245     308 ..     242     311 .. 0.89
   3 !   30.2   0.0   9.6e-10     4e-07       2      77 .]     312     379 ..     311     379 .. 0.91
   4 !   22.0   0.2   3.6e-07   0.00015       3      75 ..     347     411 ..     345     413 .. 0.79
   5 ?    7.2   0.1     0.014         6       9      33 ..     387     411 ..     377     437 .. 0.76
   6 !   13.6   0.0   0.00015     0.061      49      75 ..     440     466 ..     415     468 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.7e-06
                            TPR_12  32 iarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       i r++  +++++ a + rn g++++++g++ eA++++e+a++i
  gi|330508203|ref|YP_004384631.1| 199 INRSI--ETNAQDADAWRNKGIALHKQGKFNEAVAAYEKAIQI 239
                                       45556..6778999999**********************9987 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 6.2e-07
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrl.yralgryeeAlelleealai 74 
                                       ++++  +avl  lg+yd+A++ +++a+ei      p+    a +  n g   y+++ +y+eA+ +l  a++i
  gi|330508203|ref|YP_004384631.1| 245 SSWSGKGAVLDDLGQYDQAIRAYDQAIEIN-----PQD---ADSFANKGLNlYHYQAKYDEAIVALDMAIKI 308
                                       567889***********************9.....875...999*****9966799*******999999987 PP

  == domain 3  score: 30.2 bits;  conditional E-value: 9.6e-10
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       +a a+n  + +l+ +g+y eA+e ++ka+e+      p   l a++ +n g ++   g+y+eA++++++a++i+++
  gi|330508203|ref|YP_004384631.1| 312 LAGAWNIKGGILTGRGKYGEAIEAYDKAIELD-----P---LNASIWNNRGAAFVGEGNYDEAVRAFNRAIEIDQQ 379
                                       56788559********************8888.....5...56******************************975 PP

  == domain 4  score: 22.0 bits;  conditional E-value: 3.6e-07
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a+++nn++a+    g+ydeA + +++a+ei ++    ++ +      +  ++++++ +y+eAl++ ++a++++
  gi|330508203|ref|YP_004384631.1| 347 ASIWNNRGAAFVGEGNYDEAVRAFNRAIEIDQQN--AYY-WN-----AKCTALFKQTKYDEALNAVNKAIELD 411
                                       78999**************************876..543.32.....22233556669999999999999986 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.014
                            TPR_12   9 laavlrrlgrydeAlellekaleia 33 
                                         ++l+++ +ydeAl   +ka+e+ 
  gi|330508203|ref|YP_004384631.1| 387 KCTALFKQTKYDEALNAVNKAIELD 411
                                       6677888888888888888888875 PP

  == domain 6  score: 13.6 bits;  conditional E-value: 0.00015
                            TPR_12  49 rnLgrlyralgryeeAlelleealaia 75 
                                       ++ g  ++++g+y+eA+ ++++a++++
  gi|330508203|ref|YP_004384631.1| 440 FGKGVSFHQQGKYDEAILAYNKAIELD 466
                                       566888999999999999999999986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   9.9e-05     0.041       2      35 ..     211     244 ..     210     250 .. 0.90
   2 !   18.6   0.1   5.5e-06    0.0023       8      35 ..     251     278 ..     244     284 .. 0.90
   3 !    9.0   0.0    0.0068       2.8      11      38 ..     289     316 ..     286     320 .. 0.88
   4 !   14.2   0.0   0.00014     0.058       7      39 ..     319     351 ..     313     355 .. 0.84
   5 !   13.9   0.1   0.00018     0.076       7      38 ..     353     384 ..     350     391 .. 0.87
   6 ?    6.7   0.0     0.036        15      16      38 ..     396     418 ..     389     422 .. 0.88
   7 !    9.9   0.0    0.0033       1.4      11      33 ..     446     468 ..     441     477 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.9e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPdda 35 
                                       +a++  + al  +G++ eA+a++++a++ +P d 
  gi|330508203|ref|YP_004384631.1| 211 DAWRNKGIALHKQGKFNEAVAAYEKAIQINPLDS 244
                                       7899999************************775 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 5.5e-06
                            TPR_14   8 aeallalGdpdeAiallrralalaPdda 35 
                                       +++l  lG++d+Ai+++++a++ +P+da
  gi|330508203|ref|YP_004384631.1| 251 GAVLDDLGQYDQAIRAYDQAIEINPQDA 278
                                       789999*******************997 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0068
                            TPR_14  11 llalGdpdeAiallrralalaPddaeaw 38 
                                       +  + ++deAi +l+ a++ +P+ a aw
  gi|330508203|ref|YP_004384631.1| 289 YHYQAKYDEAIVALDMAIKINPQLAGAW 316
                                       556789*****************99999 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 0.00014
                            TPR_14   7 laeallalGdpdeAiallrralalaPddaeawl 39 
                                        + +l  +G++ eAi+++++a++l+P +a +w 
  gi|330508203|ref|YP_004384631.1| 319 KGGILTGRGKYGEAIEAYDKAIELDPLNASIWN 351
                                       56778889*********************9995 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 0.00018
                            TPR_14   7 laeallalGdpdeAiallrralalaPddaeaw 38 
                                       +++a+   G++deA+++++ra++ + ++a +w
  gi|330508203|ref|YP_004384631.1| 353 RGAAFVGEGNYDEAVRAFNRAIEIDQQNAYYW 384
                                       67888899****************99999888 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.036
                            TPR_14  16 dpdeAiallrralalaPddaeaw 38 
                                       ++deA+++ ++a++l+P+  +a+
  gi|330508203|ref|YP_004384631.1| 396 KYDEALNAVNKAIELDPNYKAAQ 418
                                       58****************99887 PP

  == domain 7  score: 9.9 bits;  conditional E-value: 0.0033
                            TPR_14  11 llalGdpdeAiallrralalaPd 33 
                                       + ++G++deAi ++++a++l+P+
  gi|330508203|ref|YP_004384631.1| 446 FHQQGKYDEAILAYNKAIELDPT 468
                                       5689******************7 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.6e-05     0.019       9      59 ..     191     245 ..     188     253 .. 0.84
   2 !   20.4   1.8   1.3e-06   0.00053       5      57 ..     258     311 ..     256     320 .. 0.92
   3 !   32.7   0.1   1.9e-10   7.8e-08       3      64 ..     325     386 ..     323     388 .. 0.96
   4 !   11.9   0.1   0.00059      0.25       1      41 [.     391     431 ..     391     436 .. 0.88
   5 ?    6.8   0.1     0.023       9.7       3      23 ..     448     468 ..     446     480 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.6e-05
                            TPR_19   9 eAlalleq...alqedpknaearllLAeallalgqldeAealLdalpeedpdd.a 59 
                                       +A++ le+    ++ ++++a+a+ +  +al ++g ++eA a+ +++ + +p d +
  gi|330508203|ref|YP_004384631.1| 191 NAIENLEEinrSIETNAQDADAWRNKGIALHKQGKFNEAVAAYEKAIQINPLDsS 245
                                       6888888855555889*****************************9999999844 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 1.3e-06
                            TPR_19   5 gdyaeAlalleqalqedpknaearllL.AeallalgqldeAealLdalpeedpd 57 
                                       g+y++A++++ qa++ +p++a+  ++   +++  +  +deA+ +Ld + + +p+
  gi|330508203|ref|YP_004384631.1| 258 GQYDQAIRAYDQAIEINPQDADSFANKgLNLYHYQAKYDEAIVALDMAIKINPQ 311
                                       9************************99999******************999997 PP

  == domain 3  score: 32.7 bits;  conditional E-value: 1.9e-10
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL 64 
                                        +g+y eA++++ +a++ dp na ++ +   a +  g++deA ++ +++ e d+++a+y+++
  gi|330508203|ref|YP_004384631.1| 325 GRGKYGEAIEAYDKAIELDPLNASIWNNRGAAFVGEGNYDEAVRAFNRAIEIDQQNAYYWNA 386
                                       68*********************************************************976 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00059
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgql 41 
                                       l+++ +y+eAl++  +a++ dp++ +a+     +l +lg++
  gi|330508203|ref|YP_004384631.1| 391 LFKQTKYDEALNAVNKAIELDPNYKAAQTTKTLILRKLGNF 431
                                       68899*********************998877777777776 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.023
                            TPR_19   3 aegdyaeAlalleqalqedpk 23 
                                       ++g+y+eA+ ++ +a++ dp 
  gi|330508203|ref|YP_004384631.1| 448 QQGKYDEAILAYNKAIELDPT 468
                                       788888888888888888884 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   4.5e-07   0.00019      17      60 ..     198     241 ..     192     246 .. 0.91
   2 !   13.5   0.3   0.00015     0.062      17      65 ..     232     280 ..     231     284 .. 0.93
   3 !   14.4   0.0   7.6e-05     0.032       4      60 ..     288     344 ..     286     356 .. 0.91
   4 !   17.1   0.1   1.1e-05    0.0045      13      61 ..     331     379 ..     328     382 .. 0.93
   5 !   10.7   0.0     0.001      0.44       7      70 ..     359     422 ..     353     425 .. 0.89
   6 ?    2.5   0.0      0.39   1.6e+02      35      60 ..     442     467 ..     390     480 .. 0.56

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.5e-07
                             TPR_9  17 vverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                        ++r +  + +d++ +r  G++l+++G +++A+a+ e +++++p
  gi|330508203|ref|YP_004384631.1| 198 EINRSIETNAQDADAWRNKGIALHKQGKFNEAVAAYEKAIQINP 241
                                       589999***********************************999 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00015
                             TPR_9  17 vverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       ++e  ++++P d + +   G +l  lG++ +A+++ +++++++p+++d 
  gi|330508203|ref|YP_004384631.1| 232 AYEKAIQINPLDSSSWSGKGAVLDDLGQYDQAIRAYDQAIEINPQDADS 280
                                       678889999************************************9986 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 7.6e-05
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       ++  + ++++a+ ++++ + ++P+ ++ +   G +l  +G + +A+++ + +++l+p
  gi|330508203|ref|YP_004384631.1| 288 LYHYQAKYDEAIVALDMAIKINPQLAGAWNIKGGILTGRGKYGEAIEAYDKAIELDP 344
                                       566677899***********************************************9 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 1.1e-05
                             TPR_9  13 ralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       +a+++++  + l+P  ++ +  RG + +  G++ +A+++++++++++ +
  gi|330508203|ref|YP_004384631.1| 331 EAIEAYDKAIELDPLNASIWNNRGAAFVGEGNYDEAVRAFNRAIEIDQQ 379
                                       799*****************************************98865 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.001
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeaira 70 
                                        e ++++a ++ +r + ++ + ++ +     +l+++  + +Al++ + +++l+p+  +a + + 
  gi|330508203|ref|YP_004384631.1| 359 GEGNYDEAVRAFNRAIEIDQQNAYYWNAKCTALFKQTKYDEALNAVNKAIELDPNYKAAQTTKT 422
                                       678899************************************************8777777665 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.39
                             TPR_9  35 RGlllaqlGclsaAladLeaylalap 60 
                                        G+  +q+G + +A+ + + +++l+p
  gi|330508203|ref|YP_004384631.1| 442 KGVSFHQQGKYDEAILAYNKAIELDP 467
                                       34445555555555555555555555 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0017       0.7       2      26 ..     213     237 ..     212     245 .. 0.83
   2 !   12.6   0.0   0.00026      0.11       6      34 ..     251     277 ..     246     280 .. 0.77
   3 ?    0.5   0.0       1.9   8.1e+02       7      19 ..     287     299 ..     287     310 .. 0.87
   4 !    8.7   0.0    0.0046       1.9       8      35 ..     322     347 ..     315     348 .. 0.83
   5 !    9.9   0.0    0.0019      0.78       2      33 ..     350     379 ..     349     382 .. 0.83
   6 ?   -1.4   0.0       7.4   3.1e+03       9      31 ..     391     411 ..     389     413 .. 0.71
   7 !   10.4   0.0    0.0013      0.55       6      32 ..     443     467 ..     439     472 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0017
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsL 26 
                                       + n + + +++G++ eA+  ye+++
  gi|330508203|ref|YP_004384631.1| 213 WRNKGIALHKQGKFNEAVAAYEKAI 237
                                       6688999****************44 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00026
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                       + +  +lG+y++Ai+ y q  a++  p+d
  gi|330508203|ref|YP_004384631.1| 251 GAVLDDLGQYDQAIRAYDQ--AIEINPQD 277
                                       567789*************..66544444 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.9
                             TPR_7   7 rlysrlGdyeeAi 19 
                                       +ly+ + +y+eAi
  gi|330508203|ref|YP_004384631.1| 287 NLYHYQAKYDEAI 299
                                       58999*******9 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0046
                             TPR_7   8 lysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +   +G+y eAie y +  a++ dp++a
  gi|330508203|ref|YP_004384631.1| 322 ILTGRGKYGEAIEAYDK--AIELDPLNA 347
                                       66678************..999999886 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.0019
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       ++n + +++ +G+y+eA++ + +  a++ d++
  gi|330508203|ref|YP_004384631.1| 350 WNNRGAAFVGEGNYDEAVRAFNR--AIEIDQQ 379
                                       689999*****************..6655554 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 7.4
                             TPR_7   9 ysrlGdyeeAielyeqsLaltkd 31 
                                        +++ +y+eA+    +  a++ d
  gi|330508203|ref|YP_004384631.1| 391 LFKQTKYDEALNAVNK--AIELD 411
                                       5778899999987777..55555 PP

  == domain 7  score: 10.4 bits;  conditional E-value: 0.0013
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdp 32 
                                       ++ ++++G+y+eAi  y +  a++ dp
  gi|330508203|ref|YP_004384631.1| 443 GVSFHQQGKYDEAILAYNK--AIELDP 467
                                       77899**************..776666 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0029       1.2       6      31 ..     216     241 ..     211     243 .. 0.87
   2 !   11.3   0.1     0.001      0.43      12      32 ..     256     276 ..     250     277 .. 0.87
   3 ?    5.5   0.0     0.073        30       9      32 ..     287     311 ..     279     311 .. 0.80
   4 ?    3.6   0.0       0.3   1.2e+02      14      31 ..     327     344 ..     314     346 .. 0.86
   5 ?    7.2   0.0     0.021       8.9       9      28 ..     356     375 ..     352     377 .. 0.80
   6 ?    3.4   0.1      0.34   1.4e+02       9      32 ..     390     413 ..     389     414 .. 0.90
   7 !    9.9   0.0    0.0029       1.2       6      31 ..     442     467 ..     438     468 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                        + ++ k+g+  +A++a+e+ i+  P
  gi|330508203|ref|YP_004384631.1| 216 KGIALHKQGKFNEAVAAYEKAIQINP 241
                                       57889999**************9888 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  12 klgdtdkAlealerlikeYPd 32 
                                        lg++d+A++a+++ i+  P+
  gi|330508203|ref|YP_004384631.1| 256 DLGQYDQAIRAYDQAIEINPQ 276
                                       479**************9997 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.073
                                       HHHH.HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   9 syrk.lgdtdkAlealerlikeYPd 32 
                                        ++  + ++d+A+ al+  ik  P+
  gi|330508203|ref|YP_004384631.1| 287 NLYHyQAKYDEAIVALDMAIKINPQ 311
                                       5555577**************9995 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHH-T CS
                             TPR_6  14 gdtdkAlealerlikeYP 31 
                                       g++ +A+ea+++ i+  P
  gi|330508203|ref|YP_004384631.1| 327 GKYGEAIEAYDKAIELDP 344
                                       6899**********9877 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   9 syrklgdtdkAlealerlik 28 
                                       ++   g++d+A++a++r i+
  gi|330508203|ref|YP_004384631.1| 356 AFVGEGNYDEAVRAFNRAIE 375
                                       555568***********997 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                                       +++k++++d+Al a ++ i+  P+
  gi|330508203|ref|YP_004384631.1| 390 ALFKQTKYDEALNAVNKAIELDPN 413
                                       789999********9999999997 PP

  == domain 7  score: 9.9 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                        + s+ ++g++d+A+ a+++ i+  P
  gi|330508203|ref|YP_004384631.1| 442 KGVSFHQQGKYDEAILAYNKAIELDP 467
                                       58999999**************9888 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 !   13.9   0.0   0.00012     0.049      29      80 ..     216     268 ..     190     270 .. 0.83
   2 !    9.2   0.0    0.0033       1.4      36      81 ..     292     338 ..     274     339 .. 0.90
   3 !   19.3   1.7   2.4e-06     0.001       3      81 ..     361     442 ..     359     443 .. 0.83
   4 ?    2.0   0.1      0.59   2.5e+02      67      81 ..     447     461 ..     442     462 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00012
                                       HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       ++ +l ++g++++A   ++ka ++n+ +  ++  ++ +l +L++y++Ai+a++
  gi|330508203|ref|YP_004384631.1| 216 KGIALHKQGKFNEAVAAYEKAiQINPLDSSSWSGKGAVLDDLGQYDQAIRAYD 268
                                       567899********************************************987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0033
                                       TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       + +y++A+  l+ a k+n++  g++ +++  l   +ky eAi a++k
  gi|330508203|ref|YP_004384631.1| 292 QAKYDEAIVALDMAiKINPQLAGAWNIKGGILTGRGKYGEAIEAYDK 338
                                       779****************************************9987 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 2.4e-06
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-H..HHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkky..eeAi 76 
                                       +ny++A+  ++r+ + ++++++   +++ +l+++ +y++A++ ++ka +l+++ +++  ++   l kL+++  eeA+
  gi|330508203|ref|YP_004384631.1| 361 GNYDEAVRAFNRAIEIDQQNAYYWNAKCTALFKQTKYDEALNAVNKAiELDPNYKAAQTTKTLILRKLGNFntEEAV 437
                                       69************6666666666668999*****************999999999999999999999764226888 PP

                                       HHH-S CS
                            ANAPC3  77 aaLek 81 
                                       ++++k
  gi|330508203|ref|YP_004384631.1| 438 DCFGK 442
                                       88876 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.59
                                       HHTT-HHHHHHHH-S CS
                            ANAPC3  67 lkLkkyeeAiaaLek 81 
                                        +++ky+eAi a+ k
  gi|330508203|ref|YP_004384631.1| 447 HQQGKYDEAILAYNK 461
                                       478999999987765 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   4.5e-06    0.0019       7      31 ..     215     239 ..     211     240 .. 0.94
   2 !    8.2   0.1    0.0054       2.2       9      31 ..     251     273 ..     250     274 .. 0.94
   3 ?    1.2   0.1      0.86   3.6e+02      10      31 ..     287     308 ..     287     309 .. 0.85
   4 ?    7.0   0.0     0.013       5.4       9      30 ..     320     341 ..     319     342 .. 0.91
   5 ?    6.5   0.2      0.02       8.2       6      31 ..     351     376 ..     347     382 .. 0.84
   6 ?    0.1   0.0         2   8.4e+02      11      30 ..     390     409 ..     389     410 .. 0.82
   7 ?    4.6   0.0     0.075        31      13      30 ..     447     464 ..     443     465 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.5e-06
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N ++al+++g+++eA+a +e+a++i
  gi|330508203|ref|YP_004384631.1| 215 NKGIALHKQGKFNEAVAAYEKAIQI 239
                                       669********************98 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0054
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       +++l ++g+yd+A + +++a++i
  gi|330508203|ref|YP_004384631.1| 251 GAVLDDLGQYDQAIRAYDQAIEI 273
                                       78999****************98 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.86
                            TPR_10  10 nalrqrgrydeAealleealai 31 
                                       n+++ + +ydeA   l+ a+ i
  gi|330508203|ref|YP_004384631.1| 287 NLYHYQAKYDEAIVALDMAIKI 308
                                       689*********9888877765 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.013
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       + +l+ rg+y eA + +++a++
  gi|330508203|ref|YP_004384631.1| 320 GGILTGRGKYGEAIEAYDKAIE 341
                                       568999**************98 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.02
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       nN ++a    g+ydeA++ + +a++i
  gi|330508203|ref|YP_004384631.1| 351 NNRGAAFVGEGNYDEAVRAFNRAIEI 376
                                       7888888888**************99 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 2
                            TPR_10  11 alrqrgrydeAealleeala 30 
                                       al+++ +ydeA++   +a++
  gi|330508203|ref|YP_004384631.1| 390 ALFKQTKYDEALNAVNKAIE 409
                                       6788889*****99888886 PP

  == domain 7  score: 4.6 bits;  conditional E-value: 0.075
                            TPR_10  13 rqrgrydeAealleeala 30 
                                       +q+g+ydeA   + +a++
  gi|330508203|ref|YP_004384631.1| 447 HQQGKYDEAILAYNKAIE 464
                                       89*******999999987 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3     0.034        14      10      32 ..     216     238 ..     207     239 .. 0.87
   2 !   10.7   0.0   0.00099      0.41      11      32 ..     251     272 ..     247     273 .. 0.89
   3 !    8.3   0.2    0.0057       2.4      17      33 ..     326     342 ..     325     342 .. 0.92
   4 ?    4.2   0.0      0.11        44      17      32 ..     360     375 ..     359     381 .. 0.90
   5 ?    3.5   0.2      0.18        75       2      17 ..     398     413 ..     397     420 .. 0.81
   6 !   14.1   0.0   9.1e-05     0.038       2      33 ..     434     465 ..     433     482 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.034
                               MIT  10 kAveeDnagnyeeAlelYkeale 32 
                                       k + + ++g++ eA+ +Y++a++
  gi|330508203|ref|YP_004384631.1| 216 KGIALHKQGKFNEAVAAYEKAIQ 238
                                       67778899*************98 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00099
                               MIT  11 AveeDnagnyeeAlelYkeale 32 
                                        + +D  g+y+ A+++Y +a+e
  gi|330508203|ref|YP_004384631.1| 251 GAVLDDLGQYDQAIRAYDQAIE 272
                                       5678999**************8 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0057
                               MIT  17 agnyeeAlelYkealel 33 
                                       +g+y eA+e+Y +a+el
  gi|330508203|ref|YP_004384631.1| 326 RGKYGEAIEAYDKAIEL 342
                                       59*************96 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.11
                               MIT  17 agnyeeAlelYkeale 32 
                                       +gny+eA++++  a+e
  gi|330508203|ref|YP_004384631.1| 360 EGNYDEAVRAFNRAIE 375
                                       69*********99998 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.18
                               MIT   2 dkAlelvkkAveeDna 17 
                                       d+Al+ v+kA+e+D +
  gi|330508203|ref|YP_004384631.1| 398 DEALNAVNKAIELDPN 413
                                       89************74 PP

  == domain 6  score: 14.1 bits;  conditional E-value: 9.1e-05
                               MIT   2 dkAlelvkkAveeDnagnyeeAlelYkealel 33 
                                       ++A++++ k v   ++g+y+eA+ +Y +a+el
  gi|330508203|ref|YP_004384631.1| 434 EEAVDCFGKGVSFHQQGKYDEAILAYNKAIEL 465
                                       6899999***********************96 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1    0.0097       4.1      12      69 ..     184     241 ..     173     249 .. 0.65
   2 ?    4.3   0.0     0.036        15     202     236 ..     254     288 ..     251     292 .. 0.88
   3 !   15.4   0.1   1.6e-05    0.0067     202     256 ..     289     343 ..     286     358 .. 0.94
   4 !   12.4   0.1   0.00013     0.054     207     267 ..     328     389 ..     325     394 .. 0.91
   5 !   12.6   0.3   0.00011     0.047     204     247 ..     393     438 ..     371     452 .. 0.74
   6 ?   -1.3   0.0       1.8   7.6e+02     203     226 ..     447     470 ..     444     479 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0097
                                       HHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-T CS
                             NARP1  12 qiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernp 69 
                                       +i +++g++ e le+++++ ++         +k+  l k g+++eA a+ye+ ++ np
  gi|330508203|ref|YP_004384631.1| 184 TIWRDKGNAIENLEEINRSIETNAQDADAWRNKGIALHKQGKFNEAVAAYEKAIQINP 241
                                       5666677776777777665444444444445667777777777777777777777776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.036
                                       HHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHH CS
                             NARP1 202 ydklgsrekAleyidkaiehtptlvelyltKaril 236
                                        d lg++++A++  d+aie +p+  + + +K+  l
  gi|330508203|ref|YP_004384631.1| 254 LDDLGQYDQAIRAYDQAIEINPQDADSFANKGLNL 288
                                       5889*************************998655 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.6e-05
                                       HHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 202 ydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       y +  ++++A+  +d ai+ +p+l   + +K+ il   G   +A+e+ ++a +lD
  gi|330508203|ref|YP_004384631.1| 289 YHYQAKYDEAIVALDMAIKINPQLAGAWNIKGGILTGRGKYGEAIEAYDKAIELD 343
                                       778899************************************************9 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00013
                                       -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-H.HHHHHHH CS
                             NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDR.yiNskca 267
                                       ++ +A+e  dkaie +p    ++ +++  +   G+ ++A+++ ++a ++D++   y N+kc+
  gi|330508203|ref|YP_004384631.1| 328 KYGEAIEAYDKAIELDPLNASIWNNRGAAFVGEGNYDEAVRAFNRAIEIDQQNAyYWNAKCT 389
                                       6779***********************************************9972579**97 PP

  == domain 5  score: 12.6 bits;  conditional E-value: 0.00011
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HH..HHHH CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlk..kAae 247
                                       k  ++++Al+ ++kaie +p+    ++tK  il++ G+++  +A++
  gi|330508203|ref|YP_004384631.1| 393 KQTKYDEALNAVNKAIELDPNYKAAQTTKTLILRKLGNFNteEAVD 438
                                       345688*******************************986114555 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 1.8
                                       HHHT-SHHHHHHHHHHHHH-TT-H CS
                             NARP1 203 dklgsrekAleyidkaiehtptlv 226
                                        + g++++A+   +kaie +ptl+
  gi|330508203|ref|YP_004384631.1| 447 HQQGKYDEAILAYNKAIELDPTLT 470
                                       5678999***************86 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.3   0.00075      0.31     132     174 ..     195     238 ..     184     246 .. 0.79
   2 ?    4.3   0.2     0.068        28     152     180 ..     250     278 ..     243     288 .. 0.86
   3 !   14.2   1.0   6.5e-05     0.027      91     174 ..     259     341 ..     258     352 .. 0.80
   4 ?    4.0   0.1     0.088        37     146     180 ..     347     381 ..     344     394 .. 0.82
   5 ?    3.6   0.0      0.11        46     156     176 ..     446     466 ..     441     479 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00075
                            TPR_21 132 AlktL.eakkeeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                        l+++  + +++a +a +   +G +l +qgk++eA aaY++A++
  gi|330508203|ref|YP_004384631.1| 195 NLEEInRSIETNAQDADAWRNKGIALHKQGKFNEAVAAYEKAIQ 238
                                       455553346778889999999*********************97 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.068
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaaleeka 180
                                       +G +l   g+ d+A  aY++A++ + ++a
  gi|330508203|ref|YP_004384631.1| 250 KGAVLDDLGQYDQAIRAYDQAIEINPQDA 278
                                       8999*****************99777665 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 6.5e-05
                            TPR_21  91 dlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLe.akkeeafaalvaelrGDilvaqgkldeAr 166
                                       ++++A  ++++++e ++++  ++ a+  L +++  + kydeA+ +L+ a k +   a + +++G il+ +gk  eA 
  gi|330508203|ref|YP_004384631.1| 259 QYDQAIRAYDQAIEINPQD-ADSFANKGL-NLYHYQAKYDEAIVALDmAIKINPQLAGAWNIKGGILTGRGKYGEAI 333
                                       5667777777777766655.566676666.5778899*********72456688899999***************** PP

                            TPR_21 167 aaYqaAla 174
                                       +aY++A++
  gi|330508203|ref|YP_004384631.1| 334 EAYDKAIE 341
                                       ******97 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.088
                            TPR_21 146 alvaelrGDilvaqgkldeAraaYqaAlaaleeka 180
                                       a++ + rG ++v +g+ deA  a+++A++  +++a
  gi|330508203|ref|YP_004384631.1| 347 ASIWNNRGAAFVGEGNYDEAVRAFNRAIEIDQQNA 381
                                       5566789*********************9888774 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.11
                            TPR_21 156 lvaqgkldeAraaYqaAlaal 176
                                       + +qgk deA  aY++A++  
  gi|330508203|ref|YP_004384631.1| 446 FHQQGKYDEAILAYNKAIELD 466
                                       679**************9865 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 ?    0.5   0.0       1.6   6.5e+02       9      33 ..     218     242 ..     217     246 .. 0.88
   2 ?    4.8   0.0     0.072        30      14      34 ..     257     277 ..     256     280 .. 0.93
   3 ?   -0.8   0.0         4   1.7e+03      16      33 ..     294     311 ..     291     315 .. 0.90
   4 ?   -0.2   0.0       2.6   1.1e+03      15      35 ..     327     347 ..     325     349 .. 0.91
   5 ?    3.7   0.0      0.16        66      15      34 ..     361     380 ..     355     381 .. 0.92
   6 !   12.5   0.1   0.00029      0.12      10      47 ..     390     427 ..     388     429 .. 0.91
   7 ?   -1.9   0.0       9.1   3.8e+03      12      23 ..     602     613 ..     601     616 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.6
                                       HHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPe 33 
                                       ++  k+g+++eA    +  ++i P 
  gi|330508203|ref|YP_004384631.1| 218 IALHKQGKFNEAVAAYEKAIQINPL 242
                                       7888**************9999995 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.072
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                       lg+Y++A r  d+ +ei P+ 
  gi|330508203|ref|YP_004384631.1| 257 LGQYDQAIRAYDQAIEINPQD 277
                                       79*****************86 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 4
                                       -HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPe 33 
                                       +Y+eA   +d+ ++i P+
  gi|330508203|ref|YP_004384631.1| 294 KYDEAIVALDMAIKINPQ 311
                                       7**************997 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.6
                                       T-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenr 35 
                                       g+Y eA +  d  +e++P n 
  gi|330508203|ref|YP_004384631.1| 327 GKYGEAIEAYDKAIELDPLNA 347
                                       78****************995 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.16
                                       T-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPen 34 
                                       g+Y+eA r  ++ +ei+ +n
  gi|330508203|ref|YP_004384631.1| 361 GNYDEAVRAFNRAIEIDQQN 380
                                       8***************9888 PP

  == domain 6  score: 12.5 bits;  conditional E-value: 0.00029
                                       HHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHH CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPenrQaqsLkeliedk 47 
                                       + +k+ +Y+eA++ v+  +e++P+ + aq+ k+li +k
  gi|330508203|ref|YP_004384631.1| 390 ALFKQTKYDEALNAVNKAIELDPNYKAAQTTKTLILRK 427
                                       6789*************************999988666 PP

  == domain 7  score: -1.9 bits;  conditional E-value: 9.1
                                       HHHT-HHHHHHH CS
                        Fis1_TPR_C  12 yklgeYseArry 23 
                                        + g+Ys +r  
  gi|330508203|ref|YP_004384631.1| 602 VRTGNYSSSRVR 613
                                       699****99965 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.13        53      86     127 ..     200     237 ..     191     240 .. 0.72
   2 ?    3.5   0.0      0.17        69     106     129 ..     250     273 ..     244     286 .. 0.86
   3 ?    6.5   0.1      0.02       8.2     104     129 ..     351     376 ..     320     381 .. 0.78
   4 !    9.2   0.4    0.0028       1.2      68     129 ..     360     410 ..     334     424 .. 0.74
   5 ?    7.1   0.1     0.013       5.4      62     129 ..     388     465 ..     377     477 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.13
                                       HHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  86 nrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       nr  e + ++   W     +++ al++ G+ +ea+ a+++a 
  gi|330508203|ref|YP_004384631.1| 200 NRSIETNAQDADAW----RNKGIALHKQGKFNEAVAAYEKAI 237
                                       55555555555555....589999999999999999998886 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.17
                                       HHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 106 ravaleelGrkdealkafrmagem 129
                                       +++ l++lG++d+a++a+ +a e+
  gi|330508203|ref|YP_004384631.1| 250 KGAVLDDLGQYDQAIRAYDQAIEI 273
                                       788899999999999999999886 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.02
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmagem 129
                                        +r++a+ + G++dea++af+ a e+
  gi|330508203|ref|YP_004384631.1| 351 NNRGAAFVGEGNYDEAVRAFNRAIEI 376
                                       58999999999999999999999985 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0028
                                       TT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  68 lgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                        g+y       d+a+r fnr  e++q++   W a    +++al +  ++deal+a ++a e+
  gi|330508203|ref|YP_004384631.1| 360 EGNY-------DEAVRAFNRAIEIDQQNAYYWNA----KCTALFKQTKYDEALNAVNKAIEL 410
                                       4444.......45677799999999999999965....778888889999999999988886 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.013
                                       HHHHHHTT-HHHHHHHHHHHHH....HHHHH--...TTSTHHHHHH.HH..HHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  62 sealaklgrydealesadkalr....yfnrrGe...leqdeGklWi.aa..vfsravaleelGrkdealkafrmage 128
                                       + al k  +ydeal++++ka++    y   +     + +  G+     a   f ++v++++ G++dea+ a+++a e
  gi|330508203|ref|YP_004384631.1| 388 CTALFKQTKYDEALNAVNKAIEldpnYKAAQTTktlILRKLGNFNTeEAvdCFGKGVSFHQQGKYDEAILAYNKAIE 464
                                       56677777777777777777651111211111111111222332221221147899999999999999999999988 PP

                                       H CS
                           DUF3856 129 m 129
                                       +
  gi|330508203|ref|YP_004384631.1| 465 L 465
                                       6 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2      0.12        50      10      26 ..     219     233 ..     217     237 .. 0.87
   2 !    8.1   0.0    0.0065       2.7      13      35 ..     256     276 ..     246     277 .. 0.81
   3 ?    1.8   0.2      0.59   2.4e+02      11      30 ..     289     306 ..     288     311 .. 0.78
   4 ?    2.8   0.0      0.29   1.2e+02      15      31 ..     327     341 ..     326     346 .. 0.72
   5 ?    1.3   0.0      0.83   3.5e+02      15      33 ..     361     377 ..     354     380 .. 0.73
   6 ?   -0.4   0.2       2.9   1.2e+03      12      23 ..     392     403 ..     390     403 .. 0.80
   7 !   12.4   0.0   0.00029      0.12       9      27 ..     444     460 ..     440     468 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.12
                                       HHHHTT-HHHHHHH..H CS
                             TPR_3  10 efynkkkyqeArelfsY 26 
                                       +++ ++k++eA+ +  Y
  gi|330508203|ref|YP_004384631.1| 219 ALHKQGKFNEAVAA--Y 233
                                       79**********99..6 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0065
                                       HTT-HHHHHHH..HHHHHHH-TT CS
                             TPR_3  13 nkkkyqeArelfsYallaildke 35 
                                       + ++y++A+ +++  ++  + ++
  gi|330508203|ref|YP_004384631.1| 256 DLGQYDQAIRAYD--QAIEINPQ 276
                                       579********77..99888776 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.59
                                       HHHTT-HHHHHHH..HHHHH CS
                             TPR_3  11 fynkkkyqeArelfsYalla 30 
                                       ++ + ky+eA+ +++   + 
  gi|330508203|ref|YP_004384631.1| 289 YHYQAKYDEAIVALD--MAI 306
                                       67788******9988..665 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.29
                                       T-HHHHHHH..HHHHHH CS
                             TPR_3  15 kkyqeArelfsYallai 31 
                                       +ky eA+e+++   +  
  gi|330508203|ref|YP_004384631.1| 327 GKYGEAIEAYD--KAIE 341
                                       79999999976..5555 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.83
                                       T-HHHHHHH..HHHHHHH- CS
                             TPR_3  15 kkyqeArelfsYallaild 33 
                                       ++y+eA+ +f    +  +d
  gi|330508203|ref|YP_004384631.1| 361 GNYDEAVRAFN--RAIEID 377
                                       9******9954..655555 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 2.9
                                       HHTT-HHHHHHH CS
                             TPR_3  12 ynkkkyqeArel 23 
                                       + + ky+eA+++
  gi|330508203|ref|YP_004384631.1| 392 FKQTKYDEALNA 403
                                       66779****986 PP

  == domain 7  score: 12.4 bits;  conditional E-value: 0.00029
                                       HHHHHTT-HHHHHHH..HH CS
                             TPR_3   9 aefynkkkyqeArelfsYa 27 
                                        +f++++ky+eA+ +  Y 
  gi|330508203|ref|YP_004384631.1| 444 VSFHQQGKYDEAILA--YN 460
                                       68***********99..54 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.13        54      14      30 ..     223     239 ..     222     240 .. 0.92
   2 ?    0.4   0.0       1.1   4.5e+02      16      30 ..     259     273 ..     258     274 .. 0.88
   3 ?    2.2   0.0      0.29   1.2e+02      15      30 ..     327     342 ..     325     342 .. 0.92
   4 ?    3.0   0.0      0.17        69      15      33 ..     361     379 ..     358     381 .. 0.89
   5 ?    0.6   0.0      0.93   3.9e+02      14      30 ..     449     465 ..     446     469 .. 0.92
   6 ?   -0.7   0.0       2.5     1e+03       5      12 ..     589     596 ..     588     600 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       +++F++Av  ++ka+++
  gi|330508203|ref|YP_004384631.1| 223 QGKFNEAVAAYEKAIQI 239
                                       589***********997 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                          SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                       +++qA+  ++ a+e+
  gi|330508203|ref|YP_004384631.1| 259 QYDQAIRAYDQAIEI 273
                                       8*****999999987 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.29
                          SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                       +++ +A+e ++ka+eL
  gi|330508203|ref|YP_004384631.1| 327 GKYGEAIEAYDKAIEL 342
                                       79************98 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.17
                          SHNi-TPR  15 enFpqAveDlrkaLeLreq 33 
                                       +n+++Av  +++a+e+ +q
  gi|330508203|ref|YP_004384631.1| 361 GNYDEAVRAFNRAIEIDQQ 379
                                       6**************9766 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.93
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A+  ++ka+eL
  gi|330508203|ref|YP_004384631.1| 449 QGKYDEAILAYNKAIEL 465
                                       689***********998 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 2.5
                          SHNi-TPR   5 dlLGEisl 12 
                                       ++LG+isl
  gi|330508203|ref|YP_004384631.1| 589 ITLGDISL 596
                                       58*****9 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.23        94     134     180 ..     197     244 ..     185     246 .. 0.77
   2 !    6.6   0.1    0.0094       3.9     131     181 ..     228     279 ..     215     317 .. 0.78
   3 ?    6.0   0.1     0.014         6     147     238 ..     314     405 ..     305     409 .. 0.84
   4 !    6.9   0.2    0.0077       3.2     143     183 ..     378     418 ..     361     432 .. 0.86
   5 ?   -0.6   0.0       1.5   6.1e+02     157     178 ..     447     468 ..     443     475 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.23
                            TPR_15 134 ksleeeea.aeqsaafllaraelyrqegqtdaAlrdyreAlalapdss 180
                                       +++ +  +  +q+a  +   + +  ++g+ ++A+ +y++A++ +p +s
  gi|330508203|ref|YP_004384631.1| 197 EEINRSIEtNAQDADAWRNKGIALHKQGKFNEAVAAYEKAIQINPLDS 244
                                       4444333314489999999999999****************9999776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0094
                            TPR_15 131 ellksleeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsse 181
                                       e ++  e+  + +  ++  ++  +++  + gq d+A+r+y +A++ +p++++
  gi|330508203|ref|YP_004384631.1| 228 EAVAAYEKAIQINpLDSSSWSGKGAVLDDLGQYDQAIRAYDQAIEINPQDAD 279
                                       5555555556655567888999999999999999999999999999999875 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.014
                            TPR_15 147 afllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgpl 220
                                         + + + + + +g+  +A+++y +A++l+p ++++ ++   + +  g+++e   +++a++++    +++a +w++ 
  gi|330508203|ref|YP_004384631.1| 314 GAWNIKGGILTGRGKYGEAIEAYDKAIELDPLNASIWNNRGAAFVGEGNYDE---AVRAFNRAIeidQQNAYYWNAK 387
                                       5677777788899999999999999999999999999999999999999997...7777777667779999999999 PP

                            TPR_15 221 aaAlllLgrpkkALeylr 238
                                        +Al +  ++++AL+ ++
  gi|330508203|ref|YP_004384631.1| 388 CTALFKQTKYDEALNAVN 405
                                       999999999999997655 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0077
                            TPR_15 143 eqsaafllaraelyrqegqtdaAlrdyreAlalapdsselr 183
                                       +q+a+++ a   +  ++ + d+Al+++ +A++l+p+ ++++
  gi|330508203|ref|YP_004384631.1| 378 QQNAYYWNAKCTALFKQTKYDEALNAVNKAIELDPNYKAAQ 418
                                       5899*******************************977665 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 1.5
                            TPR_15 157 rqegqtdaAlrdyreAlalapd 178
                                        q+g+ d+A+ +y +A++l+p+
  gi|330508203|ref|YP_004384631.1| 447 HQQGKYDEAILAYNKAIELDPT 468
                                       589****************997 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.1   1.1e-05    0.0046       1      27 [.     116     140 ..     116     177 .. 0.79
   2 ?    4.0   1.0      0.12        51       1      24 [.     506     542 ..     506     554 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-05
                               DZR   1 CpqCgeelppdarfCseCgtklkavaa 27 
                                       Cp+Cg+e  +d +fCs+Cg++l++  a
  gi|330508203|ref|YP_004384631.1| 116 CPKCGAE--DDGKFCSQCGSPLSQIDA 140
                                       *****99..999**********97665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.12
                               DZR   1 CpqCgee.............lppdarfCseCgtklka 24 
                                       Cp C+               +++++ +C++C +kl+ 
  gi|330508203|ref|YP_004384631.1| 506 CPACKMGrlivtdrkkllglMTQHDVTCNKCYSKLPD 542
                                       5566555556666666666677888889999888874 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   5.8   3.6e-06    0.0015       1      23 []     115     135 ..     115     135 .. 0.97
   2 ?    2.3   0.4      0.35   1.5e+02       2      14 ..     533     545 ..     532     546 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.6e-06
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                                       +Cp+CGae  d+ kFC++CG+pl
  gi|330508203|ref|YP_004384631.1| 115 KCPKCGAE--DDGKFCSQCGSPL 135
                                       8*******..***********97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.35
                     zinc_ribbon_2   2 CpnCGaelqdnak 14 
                                       C +C  +l+d+  
  gi|330508203|ref|YP_004384631.1| 533 CNKCYSKLPDTKE 545
                                       *********9865 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0083       3.5      46     111 ..     216     275 ..     207     282 .. 0.82
   2 ?   -0.9   0.0         2   8.2e+02      85     109 ..     318     342 ..     284     348 .. 0.77
   3 ?    6.5   0.0     0.011       4.7      45     102 ..     352     410 ..     318     431 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0083
                          TPR_MalT  46 lGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlat 111
                                        G a + qG++++A++a+++a+++      l+ + ++  + + +l   G+ ++A++ y qa++  +
  gi|330508203|ref|YP_004384631.1| 216 KGIALHKQGKFNEAVAAYEKAIQIN----PLDSSSWS--GKGAVLDDLGQYDQAIRAYDQAIEINP 275
                                       58999***********999998765....66666666..559999999999999999999998655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                          TPR_MalT  85 qqaeilvaqGrLheAletyeqalql 109
                                         + il+ +G+  eA+e y +a++l
  gi|330508203|ref|YP_004384631.1| 318 IKGGILTGRGKYGEAIEAYDKAIEL 342
                                       3478999**************9987 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.011
                          TPR_MalT  45 vlGeasllqGdleaAlqalqeaeklarqadsl.hvallallqqaeilvaqGrLheAlet 102
                                       + G a++ +G+ ++A++a++ a+++ +q  ++ ++  +al +q++   a +   +A+e+
  gi|330508203|ref|YP_004384631.1| 352 NRGAAFVGEGNYDEAVRAFNRAIEIDQQNAYYwNAKCTALFKQTKYDEALNAVNKAIEL 410
                                       55889999****************98777777355699999999998888888888775 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.021       8.9      70     122 ..     218     270 ..     186     279 .. 0.76
   2 ?    7.4   0.0     0.014       5.7      74     123 ..     325     374 ..     310     380 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.021
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  70 eaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        a+ + G+ +ea+a +e++++ +Pl+  ++    + l  +G+  +A+++Y+++
  gi|330508203|ref|YP_004384631.1| 218 IALHKQGKFNEAVAAYEKAIQINPLDSSSWSGKGAVLDDLGQYDQAIRAYDQA 270
                                       35566788888888888999999999988888888888888888888888876 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.014
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                         G++ ea++ ++++++++Pl+   +    +A    G+  eA ++++r+ 
  gi|330508203|ref|YP_004384631.1| 325 GRGKYGEAIEAYDKAIELDPLNASIWNNRGAAFVGEGNYDEAVRAFNRAI 374
                                       568999****************************************9986 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.19        81       3      25 ..     212     234 ..     210     235 .. 0.87
   2 ?    3.8   0.0      0.28   1.2e+02       7      26 .]     250     269 ..     245     269 .. 0.83
   3 ?    2.6   0.0      0.67   2.8e+02       6      24 ..     352     370 ..     349     372 .. 0.84
   4 ?   -0.5   0.0         7   2.9e+03      11      20 ..     446     455 ..     440     455 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.19
                             TPR_4   3 allaLArallalGdldeAralle 25 
                                       a  + + al+ +G + eA a+ e
  gi|330508203|ref|YP_004384631.1| 212 AWRNKGIALHKQGKFNEAVAAYE 234
                                       667889*************9987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.28
                             TPR_4   7 LArallalGdldeAraller 26 
                                        + +l +lG++d+A ++ ++
  gi|330508203|ref|YP_004384631.1| 250 KGAVLDDLGQYDQAIRAYDQ 269
                                       578999********888765 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.67
                             TPR_4   6 aLArallalGdldeArall 24 
                                       +++ a    G++deA +++
  gi|330508203|ref|YP_004384631.1| 352 NRGAAFVGEGNYDEAVRAF 370
                                       678888899******9976 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 7
                             TPR_4  11 llalGdldeA 20 
                                        +++G +deA
  gi|330508203|ref|YP_004384631.1| 446 FHQQGKYDEA 455
                                       699******9 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 ?    3.1   0.0      0.22        91      15      66 ..     211     265 ..     193     306 .. 0.73
   2 ?    9.3   0.5    0.0026       1.1      13      60 ..     380     430 ..     332     464 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.22
                      SRP_TPR_like  15 elkkfkvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalk 66 
                                          + k +al k +k++ea+ + +k+     l+++    k  vl  l +y +a +
  gi|330508203|ref|YP_004384631.1| 211 DAWRNKGIALHKQGKFNEAVAAYEKAIqinPLDSSSWSGKGAVLDDLGQYDQAIR 265
                                       34456999***********999998763334455555666666666666666665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0026
                      SRP_TPR_like  13 gkelkkfkvvaliklekyeeaLkllkkgsalsed...vrfEkaYvlYklkk 60 
                                       ++ + + k +al k  ky+eaL++++k+ +l+ +    +  k+ +l kl +
  gi|330508203|ref|YP_004384631.1| 380 NAYYWNAKCTALFKQTKYDEALNAVNKAIELDPNykaAQTTKTLILRKLGN 430
                                       333445599999999999999999998875543300023344445555544 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.18        73      20      29 ..     111     120 ..     102     121 .. 0.84
   2 ?   13.0   0.1   0.00017     0.071       1      11 [.     126     136 ..     126     140 .. 0.91
   3 ?   -1.9   0.3       7.8   3.3e+03      24      29 ..     505     510 ..     504     511 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.18
                                       S-EEEETTTT CS
                         Nudix_N_2  20 reRlvCpaCg 29 
                                        +Rl Cp+Cg
  gi|330508203|ref|YP_004384631.1| 111 TTRLKCPKCG 120
                                       5799999999 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00017
                                       -B-TTT--B-E CS
                         Nudix_N_2   1 kFCsqCGtpve 11 
                                       kFCsqCG+p++
  gi|330508203|ref|YP_004384631.1| 126 KFCSQCGSPLS 136
                                       9********97 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 7.8
                                       EETTTT CS
                         Nudix_N_2  24 vCpaCg 29 
                                        CpaC 
  gi|330508203|ref|YP_004384631.1| 505 ACPACK 510
                                       589986 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       3.3   1.4e+03       6      20 ..     234     248 ..     234     248 .. 0.90
   2 ?   10.0   0.1    0.0014      0.58       7      22 ..     338     353 ..     337     353 .. 0.94
   3 ?   -0.9   0.0       3.8   1.6e+03       2      13 ..     401     412 ..     400     413 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.3
                                       HHHHHH-TT-CHHHH CS
                              PPTA   6 ekliekdpkNYsaWn 20 
                                       ek+i+ +p + s W+
  gi|330508203|ref|YP_004384631.1| 234 EKAIQINPLDSSSWS 248
                                       699******999995 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0014
                                       HHHHH-TT-CHHHHHH CS
                              PPTA   7 kliekdpkNYsaWnyR 22 
                                       k+ie+dp N s+Wn R
  gi|330508203|ref|YP_004384631.1| 338 KAIELDPLNASIWNNR 353
                                       89************99 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.8
                                       HHHHHHHHHH-T CS
                              PPTA   2 Leltekliekdp 13 
                                       L+ ++k+ie+dp
  gi|330508203|ref|YP_004384631.1| 401 LNAVNKAIELDP 412
                                       56689******9 PP

>> Vps36_ESCRT-II  Vacuolar protein sorting protein 36 Vps36
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.45   1.9e+02       9      40 ..     580     612 ..     574     616 .. 0.85
   2 ?    7.6   0.0     0.011       4.4      34      70 ..     635     667 ..     628     685 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.45
                    Vps36_ESCRT-II   9 vLeenEsiilvqdnVglYegde.KilnrqnGrl 40 
                                       +L++nE  i++  +++l+e+++ ++ n+++ r+
  gi|330508203|ref|YP_004384631.1| 580 ILKRNETAIITLGDISLFENRSvRTGNYSSSRV 612
                                       699****************99988888877665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.011
                    Vps36_ESCRT-II  34 nrqnGrlyLTthriiyvdsadpkkeslslelklvesv 70 
                                       +  +G+l+LT++ri+++      ++s+ + lk++ s+
  gi|330508203|ref|YP_004384631.1| 635 EIDRGTLTLTNRRIVFL----GGSHSSDILLKKIISI 667
                                       6789************8....4444566777777776 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 ?    2.6   0.1      0.26   1.1e+02       6      11 ..     116     121 ..     106     122 .. 0.77
   2 ?   11.7   0.1   0.00037      0.15       4      17 ..     126     139 ..     124     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.26
                     zf-NADH-PPase   6 CgrCGa 11 
                                       C++CGa
  gi|330508203|ref|YP_004384631.1| 116 CPKCGA 121
                                       666665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00037
                     zf-NADH-PPase   4 rFCgrCGaptepae 17 
                                       +FC++CG+p  + +
  gi|330508203|ref|YP_004384631.1| 126 KFCSQCGSPLSQID 139
                                       5********98876 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 ?   10.5   0.1   0.00023     0.097     602     647 ..      94     152 ..      69     207 .. 0.58
   2 ?   -2.0   0.4       1.4   5.7e+02     609     655 ..     494     542 ..     472     560 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00023
                          PolC_DP2 602 vkeaakk...kgeieveiarrkCkkCgketlearCeeCgekteeklvC..........k 647
                                       v++a ++    ++ie++ +r kC+kCg+e   + C++Cg+  ++  +           +
  gi|330508203|ref|YP_004384631.1|  94 VAQAEEMarmLTRIETSTTRLKCPKCGAEDDGKFCSQCGSPLSQIDALaknepitdmlE 152
                                       3344332344677888999999*****************99888655534444443331 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                          PolC_DP2 609 kgeieveiarrkCkkCgketl..earCeeCgekteeklvCkkceeevee 655
                                       +++++  i+   C++C++  l  + r +  g  t++ ++C+kc ++  +
  gi|330508203|ref|YP_004384631.1| 494 ETNTHNVIEFDACPACKMGRLivTDRKKLLGLMTQHDVTCNKCYSKLPD 542
                                       4555666888999999987651145566689999999******987763 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 ?    3.7   0.1      0.11        45       1      15 [.     259     273 ..     259     279 .. 0.90
   2 ?   -0.6   0.0       2.4     1e+03       1      15 [.     294     308 ..     294     313 .. 0.88
   3 ?    0.4   0.0       1.2   4.9e+02       1      15 [.     328     342 ..     328     347 .. 0.91
   4 ?    2.9   0.1       0.2        84       2      16 ..     363     377 ..     362     383 .. 0.87
   5 ?    7.7   0.0    0.0061       2.6       1      15 [.     396     410 ..     396     414 .. 0.93
   6 ?    3.0   0.1      0.19        79       1      15 [.     451     465 ..     451     466 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.11
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y++a+   ++Aiei
  gi|330508203|ref|YP_004384631.1| 259 QYDQAIRAYDQAIEI 273
                                       7*************8 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.4
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y+ea+   + Ai+i
  gi|330508203|ref|YP_004384631.1| 294 KYDEAIVALDMAIKI 308
                                       6************98 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.2
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y ea+e  +kAie+
  gi|330508203|ref|YP_004384631.1| 328 KYGEAIEAYDKAIEL 342
                                       599**********95 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAieiS 16 
                                       Y+ea    n+Aiei 
  gi|330508203|ref|YP_004384631.1| 363 YDEAVRAFNRAIEID 377
                                       *************85 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0061
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y+eaL+ vnkAie+
  gi|330508203|ref|YP_004384631.1| 396 KYDEALNAVNKAIEL 410
                                       6************96 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.19
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y+ea+   nkAie+
  gi|330508203|ref|YP_004384631.1| 451 KYDEAILAYNKAIEL 465
                                       6************95 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3     0.006       2.5      35      55 ..     110     134 ..      89     137 .. 0.71
   2 ?    2.9   0.4      0.31   1.3e+02      18      45 ..     503     537 ..     484     540 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.006
                               IBR  35 gcksvtCskCg....fefCfnCkke 55 
                                       ++++++C+kCg     +fC++C+++
  gi|330508203|ref|YP_004384631.1| 110 STTRLKCPKCGaeddGKFCSQCGSP 134
                                       3455889999844445799999876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.31
                               IBR  18 lkwCprpdCe..aiiekseg.......cksvtCskCg 45 
                                       +  Cp   C+  ++i  + +       +++vtC+kC 
  gi|330508203|ref|YP_004384631.1| 503 FDACP--ACKmgRLIVTDRKkllglmtQHDVTCNKCY 537
                                       67799..67743455444444566664455******6 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00058      0.24      57      98 ..     100     137 ..      84     145 .. 0.71
   2 ?   -0.9   0.8         4   1.6e+03      89     100 ..     506     517 ..     485     547 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00058
                                       TTT-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA  57 legaeLeieevpvkvrCreCgkefeleekalrCpkCgsadve 98 
                                       +++   +ie+   +++C +Cg+e + +     C +Cgs   +
  gi|330508203|ref|YP_004384631.1| 100 MARMLTRIETSTTRLKCPKCGAEDDGK----FCSQCGSPLSQ 137
                                       33344459*************665543....5*****97655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4
                                       -TTTSSS-EEEE CS
                              HypA  89 CpkCgsadveiv 100
                                       Cp+C+  ++ ++
  gi|330508203|ref|YP_004384631.1| 506 CPACKMGRLIVT 517
                                       555544333322 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       5.6   2.4e+03      54      70 ..     223     239 ..     215     241 .. 0.83
   2 ?    2.4   0.0      0.38   1.6e+02      53      77 ..     256     280 ..     251     292 .. 0.85
   3 ?    5.0   0.1      0.06        25      55      75 ..     361     381 ..     354     394 .. 0.90
   4 ?   -0.6   0.0       3.4   1.4e+03      55      70 ..     395     410 ..     384     435 .. 0.78
   5 ?   -0.9   0.0       4.1   1.7e+03      53      70 ..     448     465 ..     439     466 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 5.6
                            ANAPC5  54 fghneeAvkaleeairl 70 
                                        g+ +eAv+a e ai++
  gi|330508203|ref|YP_004384631.1| 223 QGKFNEAVAAYEKAIQI 239
                                       48889*********997 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.38
                            ANAPC5  53 dfghneeAvkaleeairlArenkDk 77 
                                       d+g++++A++a   ai++  + +D+
  gi|330508203|ref|YP_004384631.1| 256 DLGQYDQAIRAYDQAIEINPQDADS 280
                                       789**************99888875 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.06
                            ANAPC5  55 ghneeAvkaleeairlArenk 75 
                                       g+++eAv+a++ ai++ ++n+
  gi|330508203|ref|YP_004384631.1| 361 GNYDEAVRAFNRAIEIDQQNA 381
                                       899***************986 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 3.4
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                        +++eA++a++ ai+l
  gi|330508203|ref|YP_004384631.1| 395 TKYDEALNAVNKAIEL 410
                                       4689999999999987 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 4.1
                            ANAPC5  53 dfghneeAvkaleeairl 70 
                                       + g+++eA+ a + ai+l
  gi|330508203|ref|YP_004384631.1| 448 QQGKYDEAILAYNKAIEL 465
                                       44999********99976 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         5   2.1e+03      28      50 ..     226     248 ..     221     253 .. 0.85
   2 ?   -1.4   0.0       6.4   2.7e+03      28      50 ..     329     351 ..     322     358 .. 0.85
   3 ?    6.5   0.2     0.021       8.9      24      51 ..     359     386 ..     350     396 .. 0.90
   4 ?   -1.0   0.0       4.9     2e+03      26      44 ..     395     413 ..     389     419 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5
                           DUF1510  28 wnEmekavskatglsednmivww 50 
                                       +nE + a +ka++++  ++  w 
  gi|330508203|ref|YP_004384631.1| 226 FNEAVAAYEKAIQINPLDSSSWS 248
                                       89************999988875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.4
                           DUF1510  28 wnEmekavskatglsednmivww 50 
                                       + E  +a  ka++l+  n  +w 
  gi|330508203|ref|YP_004384631.1| 329 YGEAIEAYDKAIELDPLNASIWN 351
                                       779999**********9999996 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.021
                           DUF1510  24 gsvDwnEmekavskatglsednmivwwl 51 
                                       g  +++E ++a+++a++++++n ++w  
  gi|330508203|ref|YP_004384631.1| 359 GEGNYDEAVRAFNRAIEIDQQNAYYWNA 386
                                       5679**********************86 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 4.9
                           DUF1510  26 vDwnEmekavskatglsed 44 
                                       + ++E ++av+ka++l+ +
  gi|330508203|ref|YP_004384631.1| 395 TKYDEALNAVNKAIELDPN 413
                                       5689**********99865 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.032        13       6      44 ..     194     232 ..     190     243 .. 0.90
   2 ?    3.5   0.4      0.21        89       6      52 ..     262     309 ..     259     314 .. 0.82
   3 ?    1.2   0.0       1.1   4.7e+02       7      53 ..     332     378 ..     328     383 .. 0.88
   4 ?    2.6   0.4      0.43   1.8e+02      10      65 ..     369     424 ..     363     432 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.032
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                       ++l+e+ + +++n +d da  +   al+++g+  eA+++
  gi|330508203|ref|YP_004384631.1| 194 ENLEEINRSIETNAQDADAWRNKGIALHKQGKFNEAVAA 232
                                       57899*******************************975 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.21
                            TPR_20   6 pelaeleaalaanpddldarldlAl.allaagryeeAleqLleilkrd 52 
                                       + +++ ++a++ np+d d   +  l +++ + +y+eA+ +L + +k +
  gi|330508203|ref|YP_004384631.1| 262 QAIRAYDQAIEINPQDADSFANKGLnLYHYQAKYDEAIVALDMAIKIN 309
                                       5789999**********9988888626778999****99998877766 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.1
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                                        +++ ++a++ +p +  +  +   a + +g+y+eA+ ++ + ++ d+
  gi|330508203|ref|YP_004384631.1| 332 AIEAYDKAIELDPLNASIWNNRGAAFVGEGNYDEAVRAFNRAIEIDQ 378
                                       68889999999*************************99988888776 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.43
                            TPR_20  10 eleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqll 65 
                                       ++ +a++ + ++     +  +al+++ +y+eAl++  + ++ d +++  +  k+l+
  gi|330508203|ref|YP_004384631.1| 369 AFNRAIEIDQQNAYYWNAKCTALFKQTKYDEALNAVNKAIELDPNYKAAQTTKTLI 424
                                       5556666666665555566678999********************98877777764 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.3      0.56   2.4e+02      37      63 ..     109     131 ..      93     134 .. 0.63
   2 ?    7.6   0.1     0.012         5      15      48 ..     504     537 ..     492     542 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.56
                     DnaJ_CXXCXGXG  37 vqqsqstCpeCeGtGkvikekdkCkkC 63 
                                       +++++ +Cp+C+ +       + C++C
  gi|330508203|ref|YP_004384631.1| 109 TSTTRLKCPKCGAEDD----GKFCSQC 131
                                       3345568999988766....3457777 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
                     DnaJ_CXXCXGXG  15 ktCktCk.GsGvvreeqkt.lgpfvqqsqstCpeCe 48 
                                       + C++Ck G+  v++++ + lg ++ q   tC++C 
  gi|330508203|ref|YP_004384631.1| 504 DACPACKmGRLIVTDRK-KlLGLMT-QHDVTCNKCY 537
                                       57****93333444444.4355555.6799*****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 ?    8.4   0.5    0.0088       3.7      60      86 .]     108     132 ..      88     132 .. 0.68
   2 ?   -0.6   0.0       5.7   2.4e+03      29      54 ..     374     398 ..     367     418 .. 0.79
   3 ?    1.7   1.0       1.1   4.5e+02      37      61 ..     530     554 ..     505     567 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0088
                    zinc_ribbon_15  60 kessekkeCknCgkeveeefkyCpkCg 86 
                                       ++s++  +C++Cg+  e++ k+C++Cg
  gi|330508203|ref|YP_004384631.1| 108 ETSTTRLKCPKCGA--EDDGKFCSQCG 132
                                       23334899****97..68899*****9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 5.7
                    zinc_ribbon_15  29 fkwkkkkpylacskCkslleaskelg 54 
                                       ++++++++y+   kC +l+++ k + 
  gi|330508203|ref|YP_004384631.1| 374 IEIDQQNAYYWNAKCTALFKQTK-YD 398
                                       6788889999999*****99987.33 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 1.1
                    zinc_ribbon_15  37 ylacskCkslleaskelgkeiekke 61 
                                        ++c+kC s+l++ ke  ++ e+++
  gi|330508203|ref|YP_004384631.1| 530 DVTCNKCYSKLPDTKEFMRTWEAHK 554
                                       4788999999998888777776665 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.8      0.25     1e+02       1       8 [.     115     122 ..     115     123 .. 0.84
   2 ?   -1.7   0.1       4.4   1.8e+03       2      12 ..     128     138 ..     128     143 .. 0.81
   3 ?    4.8   0.0     0.041        17      15      26 ..     499     510 ..     488     519 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.25
                          zf-TFIIB   1 kCPkCqde 8  
                                       kCPkC++e
  gi|330508203|ref|YP_004384631.1| 115 KCPKCGAE 122
                                       7****975 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.4
                          zf-TFIIB   2 CPkCqdelees 12 
                                       C  C+++l ++
  gi|330508203|ref|YP_004384631.1| 128 CSQCGSPLSQI 138
                                       88899998876 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.041
                          zf-TFIIB  15 ggveidyCpqCr 26 
                                       + +e+d Cp+C+
  gi|330508203|ref|YP_004384631.1| 499 NVIEFDACPACK 510
                                       44999*****95 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4    0.0016      0.66      10      44 ..     107     140 ..     101     145 .. 0.84
   2 ?    0.0   1.0       2.1   8.6e+02       3      25 ..     506     539 ..     504     545 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0016
                                       -EE-SSEEE-TTT--EEEEEEE-SSS-S---EEEE CS
                    zinc-ribbons_6  10 lekrgeqyhCeaCqedlkkealCpeCeqelevlka 44 
                                       +e+++++++C +C ++ +  ++C +C+++l+ + a
  gi|330508203|ref|YP_004384631.1| 107 IETSTTRLKCPKCGAE-DDGKFCSQCGSPLSQIDA 140
                                       56778999*****998.5678*********99876 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.1
                                       -SSS-S--E.E-S..........SEEE-TTT--E CS
                    zinc-ribbons_6   3 CpeCqqele.krg..........eqyhCeaCqed 25 
                                       Cp+C+      ++          + ++C++C ++
  gi|330508203|ref|YP_004384631.1| 506 CPACKMGRLiVTDrkkllglmtqHDVTCNKCYSK 539
                                       6666543221111245555555556667777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (722 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); 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):              43  [number of targets reported over threshold]
# CPU time: 0.88u 0.29s 00:00:01.17 Elapsed: 00:00:00.52
# Mc/sec: 4194.75
//
Query:       gi|330508204|ref|YP_004384632.1|  [L=71]
Description: hypothetical protein MCON_2341 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.36   10.8   3.8       0.41   10.6   3.8    1.1  1  RseC_MucC  Positive regulator of sigma(E), RseC/MucC
        1.5    8.6   8.2       0.35   10.6   1.2    2.1  2  DUF4190    Domain of unknown function (DUF4190)


Domain annotation for each model (and alignments):
>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.8   4.5e-05      0.41      64     120 ..       9      69 ..       4      71 .] 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.5e-05
                         RseC_MucC  64 lkaallvYllPllllilgallgsall....gssellaalgallglvlgflivrllskrlkk 120
                                            l+Y++P l+l + al++ +++    ++se  +++++ +++++  l  ++ls   kk
  gi|330508204|ref|YP_004384632.1|   9 AAWFTLLYAIPALILGVLALFFGVASiwllMDSEYGSFFLGSVITIILALASYRLSPYYKK 69 
                                       4556799****99887777766666666789999999999999998888888888766555 PP

>> DUF4190  Domain of unknown function (DUF4190)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.2   3.9e-05      0.35      10      31 ..       8      28 ..       4      29 .. 0.83
   2 ?    4.5   6.0    0.0033        29       2      16 ..      17      36 ..      16      62 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.9e-05
                           DUF4190 10 ilgllfliitgivavilGhvAl 31
                                      ++ +++ ++ +i+a+ilG++Al
  gi|330508204|ref|YP_004384632.1|  8 LAAWFT-LLYAIPALILGVLAL 28
                                      566777.6************97 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0033
                           DUF4190  2 AiasLvlgilgllf.....l 16
                                      Ai +L+lg+l l+f      
  gi|330508204|ref|YP_004384632.1| 17 AIPALILGVLALFFgvasiW 36
                                      88899999999888554440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 550.04
//
Query:       gi|330508205|ref|YP_004384633.1|  [L=112]
Description: hypothetical protein MCON_2342 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0025   18.1   0.0     0.0045   17.3   0.0    1.6  1  HTH_Tnp_1  Transposase
  ------ inclusion threshold ------
      0.038   13.8   0.1      0.045   13.6   0.1    1.1  1  BBP1_C     Spindle pole body component BBP1, C-terminal


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     5e-07    0.0045      21      73 ..       3      56 ..       1      72 [. 0.69

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5e-07
                         HTH_Tnp_1 21 epgksvsevArrhgvspnqLykWrrqyr...egeeaspaefeltaleeenrelkre 73
                                      e++k+ +++Ar++g++p+   +Wr +     e   +s  +    + e  ++el+r+
  gi|330508205|ref|YP_004384633.1|  3 EADKPLAQIAREYGIHPSLPCRWRDELAenpERANSSNGN--RCKYETMIAELERL 56
                                      788999*******************997443333333333..33444444444444 PP

>> BBP1_C  Spindle pole body component BBP1, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     5e-06     0.045     124     183 ..      34      90 ..      16      98 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-06
                            BBP1_C 124 eleekreidkikYesrikdLerqllereneikdtssssnafstseyrkkeelsskdenqs 183
                                       e  +  + ++ kYe+ i++Ler l + +    +++  ++++++   +++  ++++d+n+ 
  gi|330508205|ref|YP_004384633.1|  34 ERANSSNGNRCKYETMIAELERLLGQAH-A--ENELLKKSVRHDPKESQGGKTKTDTNRR 90 
                                       5556677899***********9776664.4..5666666666666666666667777744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 846.48
//
Query:       gi|330508206|ref|YP_004384634.1|  [L=306]
Description: hypothetical protein MCON_2343 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        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 0.20s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2335.50
//
Query:       gi|330508207|ref|YP_004384635.1|  [L=199]
Description: hypothetical protein MCON_2346 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1511.89
//
Query:       gi|330508208|ref|YP_004384636.1|  [L=151]
Description: hypothetical protein MCON_2347 [Methanosaeta concilii GP6]
Scores for complete 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   94.8   0.0    4.2e-27   94.5   0.0    1.1  1  DUF123    Domain of unknown function DUF123


Domain annotation for each model (and alignments):
>> DUF123  Domain of unknown function DUF123
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.0   2.4e-31   4.2e-27       1      94 []      31     123 ..      31     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 2.4e-31
                            DUF123   1 ielkkgvylYvGsalgsgglasRvkrHaslskkkekklhWhiDyLleseeaelaevvv.aseerlEcalaeal.eae 75 
                                       i++++g+y+Y+Gsa g+gg  +Rv+rH++  ++++++++WhiDyLl+  +a l ev++ +++++lEc++ae + e+ 
  gi|330508208|ref|YP_004384636.1|  31 IDFAPGCYAYTGSARGPGGC-KRVDRHIEILRGTRNTRRWHIDYLLA--QAGLVEVFItRTSRDLECSIAEMVgERL 104
                                       5799***************9.*************************5..55677777746*************5555 PP

                            DUF123  76 apvagfGasDckcesHLlk 94 
                                        p++gfG+sDc+c sHL++
  gi|330508208|ref|YP_004384636.1| 105 VPIKGFGSSDCRCISHLHY 123
                                       6****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1144.47
//
Query:       gi|330508209|ref|YP_004384637.1|  [L=1143]
Description: hypothetical protein MCON_2348 [Methanosaeta concilii GP6]
Scores for complete 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   40.7   0.0        4.5    7.6   0.0    6.7  6  DUF11        Domain of unknown function DUF11
    2.7e-09   37.2   2.7       0.67   10.3   0.0    6.4  7  CARDB        CARDB
  ------ inclusion threshold ------
      0.021   14.8   0.0       0.42   10.6   0.0    2.8  2  AGS_C        Adenylyl/Guanylyl and SMODS C-terminal sensor do
       0.14   12.4   2.5         57    4.1   0.0    5.4  7  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.79   3.5e+03      23      38 ..      90     105 ..      86     152 .. 0.63
   2 !    6.2   0.0    0.0027        12       4      36 ..     221     253 ..     218     254 .. 0.94
   3 ?    3.1   0.0     0.026   1.2e+02      10      39 ..     323     352 ..     318     411 .. 0.74
   4 !    6.3   0.1    0.0027        12       6      36 ..     417     447 ..     412     482 .. 0.87
   5 !    7.6   0.0     0.001       4.5       9      36 ..     517     544 ..     503     572 .. 0.93
   6 !    7.5   0.0    0.0011       5.1       5      40 ..     611     716 ..     607     768 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.79
                             DUF11  23 tNtgpasangvvvtDt 38 
                                        N+g +++ +++vtD 
  gi|330508209|ref|YP_004384637.1|  90 ENNGITKLHRIKVTDR 105
                                       5666666666666663 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0027
                             DUF11   4 tvdksevrpGdtvtytltvtNtgpasangvvvt 36 
                                       +v++s+  +G++++y   +tN g++ +++v++t
  gi|330508209|ref|YP_004384637.1| 221 SVNRSACLAGEAISYRCLATNIGQDELSDVRIT 253
                                       799999***********************9986 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.026
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtDtl 39 
                                       v  G++ +  +   N+g +++++++v D  
  gi|330508209|ref|YP_004384637.1| 323 VHRGENASILIRIENSGEDNLTDLKVDDGF 352
                                       677999999999***************966 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0027
                             DUF11   6 dksevrpGdtvtytltvtNtgpasangvvvt 36 
                                       ++++  pG+  ++t ++ Ntg+ ++ +v+++
  gi|330508209|ref|YP_004384637.1| 417 TQVATYPGEPAEVTWILENTGQETLFNVTLQ 447
                                       455788********************99986 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.001
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvt 36 
                                       e++pGd+ +    vtN+g + + +vv+t
  gi|330508209|ref|YP_004384637.1| 517 EAAPGDEAEISCLVTNSGEDRLREVVLT 544
                                       799***********************97 PP

  == domain 6  score: 7.5 bits;  conditional E-value: 0.0011
                             DUF11   5 vdksevrpGdtvtytltvtNtgpasa.ngvvvtDtl......................................... 39 
                                        ++s+v+pG+t + t tv N g +++ +  v++  l                                         
  gi|330508209|ref|YP_004384637.1| 611 ASPSAVAPGGTSSITCTVANMGSVPLySIFVISESLgplgsidilspkhqktitakksisrggedtitaegftmdrs 687
                                       57789********************9566677777777777777776666666666666666666666555555555 PP

                             DUF11  40 ............................P 40 
                                                                   P
  gi|330508209|ref|YP_004384637.1| 688 svrgeynlnlaliegasaegsvkpsddyP 716
                                       55555555555555555555555444442 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.087   3.9e+02       4      72 ..      65     130 ..      62     159 .. 0.76
   2 ?   -2.5   0.0       1.4   6.1e+03       9      40 ..     221     252 ..     216     255 .. 0.82
   3 !   10.3   0.0   0.00015      0.67      12      79 ..     320     382 ..     313     397 .. 0.79
   4 !    6.6   0.1     0.002       8.9       4      68 ..     410     469 ..     407     483 .. 0.77
   5 !    5.2   0.0    0.0057        25      13      67 ..     516     566 ..     505     589 .. 0.72
   6 !    6.8   0.0    0.0018       8.2       9      40 ..     610     641 ..     605     698 .. 0.67
   7 ?   -3.1   0.0       2.2   9.9e+03       8      28 ..     859     879 ..     853     880 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.087
                                       EEE..EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S CS
                             CARDB   4 Ltv.tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtte 72 
                                       L + ++ ++  ++++ + n  +v+++N+G  +   +kv+   d++  +  t+++L++ge++  s++  +e
  gi|330508209|ref|YP_004384637.1|  65 LRIaSSDVSLLAVVNSSPNLSQVHLENNGITKLHRIKVT---DRDR-SLGTLSELDPGEKKVLSISGRAE 130
                                       555556666667777788888999999999998877764...4444.44588999999999988887665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEE CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkv 40 
                                       ++n s+  +ge+++ ++  +N G+++  ++++
  gi|330508209|ref|YP_004384637.1| 221 SVNRSACLAGEAISYRCLATNIGQDELSDVRI 252
                                       67888899999************998877765 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00015
                                       -SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEE CS
                             CARDB  12 pseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevt 79 
                                       p+ ++ ge+ +i + ++N+G+++ ++ kv    d+   + + +p+Laage +tv+ + t+  ++  ++
  gi|330508209|ref|YP_004384637.1| 320 PELVHRGENASILIRIENSGEDNLTDLKV----DDGFGEVARIPALAAGEAKTVQQNRTIL-HSLPYE 382
                                       5667889****************987766....555556679************9999886.554444 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.002
                                       EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEE CS
                             CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsft 68 
                                       L+++++++  ++++ge  ++t  ++N+G+++   ++v+l  +g+     ++p++ +g s+   + 
  gi|330508209|ref|YP_004384637.1| 410 LEIQSESTQVATYPGEPAEVTWILENTGQETL--FNVTLQGNGTD---CILPQMLPGRSVRMAAI 469
                                       899************************99865..55666666655...67777777777766655 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.0057
                                       SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEE CS
                             CARDB  13 seafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsf 67 
                                        ea +g+e +i++ v+N+G++  +++   l+ldg + +  ++  L++ge + v++
  gi|330508209|ref|YP_004384637.1| 516 IEAAPGDEAEISCLVTNSGEDRLREV--VLTLDGAKLS--SLGDLEPGEFRVVQA 566
                                       57899***************998765..5566776644..666777776666555 PP

  == domain 6  score: 6.8 bits;  conditional E-value: 0.0018
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEE CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkv 40 
                                       +++ps++ +g +++it+tv+N G+   +++ v
  gi|330508209|ref|YP_004384637.1| 610 SASPSAVAPGGTSSITCTVANMGSVPLYSIFV 641
                                       568999*****************987777654 PP

  == domain 7  score: -3.1 bits;  conditional E-value: 2.2
                                       EEEC-SEEETTSEEEEEEEEE CS
                             CARDB   8 ntlnpseafvgeentitvtvk 28 
                                       ++++ps++ ++e++++tv++k
  gi|330508209|ref|YP_004384637.1| 859 VNAQPSQPAAEEDVKVTVHIK 879
                                       567889999999999999986 PP

>> AGS_C  Adenylyl/Guanylyl and SMODS C-terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.4e-05      0.42      22      86 ..     381     448 ..     365     454 .. 0.71
   2 ?    0.1   0.0      0.16   7.3e+02      63      84 ..     955     976 ..     946     996 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.4e-05
                             AGS_C  22 ikcevkqngf..srslreylsssellekgksLkFkiknttsvp.epykvkWkvrNtGeeAerandlrg 86 
                                       +++ v+ ++    + +++  +   ++++  +++ + ++ +++p ep++v W+  NtG+e+  + +l+g
  gi|330508209|ref|YP_004384637.1| 381 YEVMVSARDEvgGEVYSSQSQTIAVMNSSLEIQSESTQVATYPgEPAEVTWILENTGQETLFNVTLQG 448
                                       44443333322456777777777888888888888888888889***************977766666 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.16
                             AGS_C  63 epykvkWkvrNtGeeAerandl 84 
                                        py ++W  +N   +A+r+++ 
  gi|330508209|ref|YP_004384637.1| 955 GPYLIHWSTVNVAPDAKREEST 976
                                       6899************998765 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 ?   -0.5   0.0      0.34   1.5e+03       3      27 ..     229     253 ..     228     256 .. 0.88
   2 ?   -3.2   0.0       2.4   1.1e+04       2      26 ..     324     348 ..     323     349 .. 0.86
   3 ?   -1.8   0.0      0.83   3.7e+03      41      56 ..     355     370 ..     353     375 .. 0.85
   4 ?    0.4   0.0      0.18   7.9e+02       3      26 ..     423     446 ..     421     449 .. 0.91
   5 ?    4.1   0.0     0.013        57       2      29 ..     519     546 ..     518     547 .. 0.93
   6 ?    1.0   0.0      0.12   5.2e+02       2      24 ..     617     639 ..     616     645 .. 0.87
   7 ?   -3.0   0.1         2   9.1e+03      48      63 ..     867     882 ..     860     886 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.34
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvsls 27 
                                       +Ge  +++  +tn g++ +++v+++
  gi|330508209|ref|YP_004384637.1| 229 AGEAISYRCLATNIGQDELSDVRIT 253
                                       5888899999************997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.4
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvsl 26 
                                        +Ge  ++ + + n+g++ +t++++
  gi|330508209|ref|YP_004384637.1| 324 HRGENASILIRIENSGEDNLTDLKV 348
                                       578899999999******9999987 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.83
                       NPCBM_assoc  41 pasaaslapGetveat 56 
                                       +a++++la+Ge+ +++
  gi|330508209|ref|YP_004384637.1| 355 VARIPALAAGEAKTVQ 370
                                       68999******99987 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.18
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvsl 26 
                                       pGe+ ++t  + n+g++++ nv l
  gi|330508209|ref|YP_004384637.1| 423 PGEPAEVTWILENTGQETLFNVTL 446
                                       89****************999987 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.013
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslsls 29 
                                        pG++ ++   vtn+g++ +++v l+l+
  gi|330508209|ref|YP_004384637.1| 519 APGDEAEISCLVTNSGEDRLREVVLTLD 546
                                       69**********************9986 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.12
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnv 24 
                                        pG t ++t tv+n g+ ++ ++
  gi|330508209|ref|YP_004384637.1| 617 APGGTSSITCTVANMGSVPLYSI 639
                                       6999*************998665 PP

  == domain 7  score: -3.0 bits;  conditional E-value: 2
                       NPCBM_assoc  48 apGetveatvkVtppa 63 
                                       a+ e v++tv +++p+
  gi|330508209|ref|YP_004384637.1| 867 AAEEDVKVTVHIKSPS 882
                                       5677888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.42
# Mc/sec: 8162.39
//
Query:       gi|330508210|ref|YP_004384638.1|  [L=118]
Description: hypothetical protein MCON_2349 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.069   13.4   0.9        0.1   12.9   0.9    1.4  1  Syntaxin-18_N  SNARE-complex protein Syntaxin-18 N-terminus
      0.078   13.1   8.1      0.098   12.7   8.1    1.2  1  DivIVA         DivIVA protein
       0.39   10.2   5.1       0.43   10.0   5.1    1.1  1  FIN1           Filaments in between nuclei protein-1
        0.4   10.8   9.5       0.48   10.5   9.5    1.1  1  UPF0242        Uncharacterised protein family (UPF0242) N-ter


Domain annotation for each model (and alignments):
>> Syntaxin-18_N  SNARE-complex protein Syntaxin-18 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.9   2.3e-05       0.1      17      66 ..      27      83 ..      10      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                     Syntaxin-18_N 17 sssskseekeakkrkkkrlkkskekd.......eFikeAkeilkhItkLrkfLleir 66
                                      +++ +++e  ++k+ + r+k+ ++++       +F++eA +i+   ++L ++ +e++
  gi|330508210|ref|YP_004384638.1| 27 REEREKSEALSQKEIELRRKSVETRSvnaelaeSFWQEAENIRDECRELMRLFMEHK 83
                                      334444444555555555566666667777788******************999996 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   8.1   2.2e-05     0.098      28     119 ..       6     102 ..       6     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                            DivIVA  28 dqvakdyeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekive. 103
                                       d va+++e++ +e+eel++  +e +ek +  ++ e +L++  v + +   e+ ++  +eae+i +e ++  +  +e 
  gi|330508210|ref|YP_004384638.1|   6 DLVARSIEDMAQEVEELQALAREEREKSEALSQKEIELRRKSVETRSVNAELAESFWQEAENIRDECRELMRLFMEh 82 
                                       5699**************************************************************99877655544 PP

                                       ....XXXXXXXXXXXXXXXX CS
                            DivIVA 104 ....eaeeeakkiaeeieel 119
                                              +   +i+++ie+l
  gi|330508210|ref|YP_004384638.1|  83 klraAEVQHRIDIHDQIESL 102
                                       44322223334455555555 PP

>> FIN1  Filaments in between nuclei protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.1   9.6e-05      0.43     166     237 ..      19      93 ..       4     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 9.6e-05
                              FIN1 166 eedvnkltksntklnselakegks.kksetrkksvkfelped..deeeeikkelkdikklleellerqdelesrl 237
                                        e++++l + + +  ++l++++++ ++++   +sv+ el e+  +e e+i++e ++++ l  e   r  e+ +r+
  gi|330508210|ref|YP_004384638.1|  19 VEELQALAREEREKSEALSQKEIElRRKSVETRSVNAELAESfwQEAENIRDECRELMRLFMEHKLRAAEVQHRI 93 
                                       346777788888888888888888899999***********9434559***************999999999998 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 ?   10.5   9.5   0.00011      0.48      81     167 ..       6     104 ..       1     111 [. 0.64

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                           UPF0242  81 d......eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaia.e...dfeelkleleeqLaek 147
                                       d      e+++++ e+l+ l  ee+e  e l++ke el+r   e  +++ +l ++  +   ++ +  +el     e 
  gi|330508210|ref|YP_004384638.1|   6 DlvarsiEDMAQEVEELQALAREEREKSEALSQKEIELRRKSVETRSVNAELAESFwQeaeNIRDECRELMRLFMEH 82 
                                       333434589999999*************************9999876665554432121224444434444444455 PP

                           UPF0242 148 qellqeyqet..ieeqrsvlek 167
                                       +++  e q+   i++q ++l+ 
  gi|330508210|ref|YP_004384638.1|  83 KLRAAEVQHRidIHDQIESLDD 104
                                       6666666554115666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1927  (0.10748); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 1030.64
//
Query:       gi|330508211|ref|YP_004384639.1|  [L=192]
Description: glutamine amidotransferase subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-53  180.4   0.0    3.5e-53  180.3   0.0    1.0  1  SNO            SNO glutamine amidotransferase family
    2.2e-09   37.2   0.0      3e-09   36.8   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    0.00033   20.4   0.0    0.00043   20.0   0.0    1.1  1  Peptidase_S51  Peptidase family S51
  ------ inclusion threshold ------
      0.095   11.8   0.0       0.14   11.2   0.0    1.2  1  BPL_N          Biotin-protein ligase, N terminal


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 !  180.3   0.0   7.8e-57   3.5e-53       1     187 [.       6     191 ..       6     192 .] 0.95

  Alignments for each domain:
  == domain 1  score: 180.3 bits;  conditional E-value: 7.8e-57
                                       EESSSSSHHHHHHHHHHTT..SEEEEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEET CS
                               SNO   1 vlalqGaveehveaikkcl..aenktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtC 75 
                                       vlalqG+v ehv+a+++ +  ++ + v+++ ++a + al++PGGest++ + ++  gl  +l + +  + +++l tC
  gi|330508211|ref|YP_004384639.1|   6 VLALQGDVSEHVDALQRIGegIDVLEVRKPGQIASCSALVLPGGESTTIVQQLNSSGLAGELEAAATTG-LPILATC 81 
                                       8****************97224569**********************************9998888877.******* PP

                                       HHHHHHCCEETTB.SS-SS--CCEEEETTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTCEEEEECT CS
                               SNO  76 aGlillskelene.lvktlellkvkvkrnafGrqvdsfekeldfknliekftavfiraPvieeilddeavkvlyeld 151
                                       aGl+l+s+e+e++ +v+ l+l+++k+ rnafG q +sfe++ld+++++ ++ avfiraPv+ e++    v+vl +  
  gi|330508211|ref|YP_004384639.1|  82 AGLVLISREIEGDnHVQPLGLMDIKISRNAFGPQRESFEADLDVEDMDRPYRAVFIRAPVVSEVG--RDVQVLAKVG 156
                                       ***********98799*************************************************..889******* PP

                                       TEEEEEEETTEEEESS-GGGSTTHCHHHHHHHHHHC CS
                               SNO 152 geivvakqkkilatsfhPelaeddirvhdyfveevv 187
                                       g  v+++ k++l+++fhPel++d +r+h++f+++++
  gi|330508211|ref|YP_004384639.1| 157 GLPVAVREKNLLGLAFHPELTDD-MRFHQLFLKMLE 191
                                       *99******************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 !   36.8   0.0   6.6e-13     3e-09      25     116 ..      27     108 ..      12     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 6.6e-13
                          GATase_3  25 vrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvege 101
                                       ++v  v+ k  ++++ + +++lpGg++t+  ++l   sgl+ ++++aa++g p+l+ C+Gl + ++eie ++     
  gi|330508211|ref|YP_004384639.1|  27 IDVLEVR-KPGQIAS-CSALVLPGGESTTIVQQLNS-SGLAGELEAAATTGLPILATCAGLVLISREIEGDN----- 95 
                                       4555566.6667755.************98777665.5******************************9987..... PP

                          GATase_3 102 ageveglglLdiete 116
                                          v+ lgl+di++ 
  gi|330508211|ref|YP_004384639.1|  96 --HVQPLGLMDIKIS 108
                                       ..5799999999875 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   9.5e-08   0.00043      63     138 ..      27      96 ..       9     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.5e-08
                                       EEE--TTTS-HHHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GGGTT CS
                     Peptidase_S51  63 vdeLelskdpeeeieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesiettsy 138
                                       +d+Le+   ++ +    +++  ++++ GG+   ++++l++ gl+  l+ a   gl++  + AG + ++++ie ++ 
  gi|330508211|ref|YP_004384639.1|  27 IDVLEVR--KPGQ----IASCSALVLPGGESTTIVQQLNSSGLAGELEAAATTGLPILATCAGLVLISREIEGDNH 96 
                                       5555544..2333....44488999************************************************993 PP

>> BPL_N  Biotin-protein ligase, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.1e-05      0.14      48     100 ..      39      92 ..      33     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                             BPL_N  48 stcallVlPgGaDlpYvrelngegnr.kikeyVekGGkylGlCAGaYygskrve 100
                                       ++c++lVlPgG  +  v++ln++g + ++++  ++G   l+ CAG    s+++e
  gi|330508211|ref|YP_004384639.1|  39 ASCSALVLPGGESTTIVQQLNSSGLAgELEAAATTGLPILATCAGLVLISREIE 92 
                                       58*******************998653788888888889999998776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1565.55
//
Query:       gi|330508212|ref|YP_004384640.1|  [L=297]
Description: pyridoxine biosynthesis protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   3.9e-101  337.1   8.3     6e-101  336.5   8.3    1.3  1  SOR_SNZ       SOR/SNZ family
    3.7e-11   42.8   6.6    1.4e-07   31.1   0.8    2.5  2  ThiG          Thiazole biosynthesis protein ThiG
    2.6e-05   23.5   0.4      0.015   14.4   0.0    2.3  2  Dus           Dihydrouridine synthase (Dus)
    4.2e-05   22.8   2.2     0.0046   16.2   0.0    2.8  3  NanE          Putative N-acetylmannosamine-6-phosphate epimer
     0.0019   17.4   0.1      0.012   14.7   0.0    2.0  2  IGPS          Indole-3-glycerol phosphate synthase
     0.0027   17.7   0.0     0.0063   16.6   0.0    1.5  1  TetR_C_27     Tetracyclin repressor-like, C-terminal domain
     0.0046   16.4   0.6     0.0046   16.4   0.6    2.3  2  NMO           Nitronate monooxygenase
     0.0051   16.3   0.4      0.016   14.6   0.1    1.9  2  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.046   12.9   0.1       0.32   10.1   0.0    2.2  2  DUF561        Protein of unknown function (DUF561)
      0.064   12.6   1.7       0.44    9.9   0.1    2.3  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 !  336.5   8.3  3.3e-104    6e-101       3     207 .]      12     215 ..      10     215 .. 0.99

  Alignments for each domain:
  == domain 1  score: 336.5 bits;  conditional E-value: 3.3e-104
                                       HHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEET CS
                           SOR_SNZ   3 kvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvri 79 
                                        +k+g+a+m+kgGvimdv+++eqa iaeeaGavavmal+ vpadirk ggvarm+dp +i++i+eav+ipvmak+ri
  gi|330508212|ref|YP_004384640.1|  12 LLKRGFAKMQKGGVIMDVTTPEQAIIAEEAGAVAVMALHAVPADIRKMGGVARMADPLVIESIIEAVTIPVMAKARI 88 
                                       589************************************************************************** PP

                                       T-HHHHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHH CS
                           SOR_SNZ  80 GhfveaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveav 156
                                       Ghfveaqilealgvd++Desevltpade +hi+k+kf++pfvcGarnlgea rri+eGaamirtkGeagtGdv++av
  gi|330508212|ref|YP_004384640.1|  89 GHFVEAQILEALGVDMVDESEVLTPADE-FHIEKTKFTIPFVCGARNLGEACRRIKEGAAMIRTKGEAGTGDVSQAV 164
                                       ***************************7.8*********************************************** PP

                                       HHHHHHHHHHHHHTTS-HHHHHHHHHHHHGGGHHHHHHHHHTTS-S---T. CS
                           SOR_SNZ 157 rhvrkikeeirklkslseeelvalakelkaplelvkevaelgrlpvvnfaa 207
                                        h+r+i  +ir+lk +++ +l+++a+e++a+l+lv+e+a+++rlpvvnfaa
  gi|330508212|ref|YP_004384640.1| 165 LHMRMILGQIRSLKGMDDLQLMKVAREIEADLDLVRECAQMQRLPVVNFAA 215
                                       *************************************************98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.6   7.9e-06     0.014     139     201 ..      37     105 ..       3     148 .. 0.78
   2 !   31.1   0.8   7.8e-11   1.4e-07     173     225 ..     205     259 ..     190     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.9e-06
                                       HHHHTT-SEBEEBSSS......TTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEE CS
                              ThiG 139 rleevGcaavmPlaap......iGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadav 201
                                         ee+G+ avm l a       +G    ++++ +++ iie +++Pv+  A ig+  +a     lG+d v
  gi|330508212|ref|YP_004384640.1|  37 IAEEAGAVAVMALHAVpadirkMGGVARMADPLVIESIIEAVTIPVMAKARIGHFVEAQILEALGVDMV 105
                                       3489*******99763233222466666778999***********************999999999987 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 7.8e-11
                                       H-SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                              ThiG 173 eakvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklave 225
                                         ++Pv+  A  G+ +p daa  m+lGad+v++ + + +++ p amAra+  av+
  gi|330508212|ref|YP_004384640.1| 205 MQRLPVVNFAagGVATPADAALMMQLGADGVFVGSGIFKSESPEAMARAIVEAVH 259
                                       4478888544349***************************************997 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0012       2.1      95     133 ..      56      90 ..      28     105 .. 0.75
   2 !   14.4   0.0   8.5e-06     0.015     166     224 ..     190     251 ..     162     278 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0012
                                       TTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESES CS
                               Dus  95 trggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigi 133
                                       +r+++G a +++p ++++i++    av iPv +k rig 
  gi|330508212|ref|YP_004384640.1|  56 IRKMGGVARMADPLVIESIIE----AVTIPVMAKARIGH 90 
                                       677888888888888888876....46788888888875 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 8.5e-06
                                       T-CG--CHHHHHHHHH-S..S-EEEESS--SHHHHHHHHHHH--SEEEESCHHC..CSTTHHH CS
                               Dus 166 yegtadweaIkevkqavs..ipviaNGdIkdaedaqaileetGadgvmigrgal..gnPwlfa 224
                                       +e++ad++ ++e  q  +  ++ +a G++ ++ da  +++  Gadgv +g g    + P  +a
  gi|330508212|ref|YP_004384640.1| 190 REIEADLDLVRECAQMQRlpVVNFAAGGVATPADAALMMQL-GADGVFVGSGIFksESPEAMA 251
                                       6789999999999887772255579**********999998.********9975114566665 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   0.1     0.081   1.5e+02      98     171 ..      28      47 ..       7      56 .. 0.66
   2 !    4.7   0.6    0.0084        15      98     170 ..      28     105 ..      18     119 .. 0.51
   3 !   16.2   0.0   2.6e-06    0.0046     129     180 ..     191     245 ..     184     260 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.081
                                       E-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-.SS--HHHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEE CS
                              NanE  98 DistleeglvakklGvdivGttlsGytkeeekaepDfalvkalseaglkviaeGrintPekakkaieiGvdavv 171
                                       D                                                      + tPe+a  a e G++av+
  gi|330508212|ref|YP_004384640.1|  28 D------------------------------------------------------VTTPEQAIIAEEAGAVAVM 47 
                                       3......................................................4567777777777766665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0084
                                       E-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-......SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--S CS
                              NanE  98 DistleeglvakklGvdivGttlsGytkeeek.....aepDfalvkalsea.glkviaeGrintPekakkaieiGvd 168
                                       D+ t e++++a+++G+  v  +l     + +k        D  +++++ ea  + v+a  ri    +a+    +Gvd
  gi|330508212|ref|YP_004384640.1|  28 DVTTPEQAIIAEEAGAVAVM-ALHAVPADIRKmggvaRMADPLVIESIIEAvTIPVMAKARIGHFVEAQILEALGVD 103
                                       55555555555555544442.23333333332233333444455555554423445555555555555555555555 PP

                                       EE CS
                              NanE 169 av 170
                                       +v
  gi|330508212|ref|YP_004384640.1| 104 MV 105
                                       54 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 2.6e-06
                                       .SS--HHHHHHHHHTT.--..EEEES---SHHHHHHHHTT--SEEEE-HHHH-HH CS
                              NanE 129 kaepDfalvkalseag.lk..viaeGrintPekakkaieiGvdavvvGsaitrle 180
                                       + e D++lv++  + + l     a G + tP+ a+ ++++G+d v vGs i + e
  gi|330508212|ref|YP_004384640.1| 191 EIEADLDLVRECAQMQrLPvvNFAAGGVATPADAALMMQLGADGVFVGSGIFKSE 245
                                       5689999999887654244225699************************998754 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.18   3.3e+02      61      88 ..      22      49 ..      18     104 .. 0.80
   2 !   14.7   0.0     7e-06     0.012     191     253 ..     191     253 ..     187     254 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.18
                                      TEESBSS--HHHHHHHHTTT.-SEEEEE CS
                              IGPS 61 kgliredfdpaeiAkkyeeagAsaiSVL 88
                                      kg + +d+  +e+A   eeagA a+  L
  gi|330508212|ref|YP_004384640.1| 22 KGGVIMDVTTPEQAIIAEEAGAVAVMAL 49
                                      7888889999999999999999887544 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 7e-06
                                       TTEE-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHH CS
                              IGPS 191 tlevdlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekaire 253
                                       ++e dl+ ++e a++ +  v+  a  G++t++d+  + + g++++ vG+ + ++e+ e++ r+
  gi|330508212|ref|YP_004384640.1| 191 EIEADLDLVRECAQMQRLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSESPEAMARA 253
                                       5788999999999999999***********************************999988775 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 !   16.6   0.0   3.5e-06    0.0063      61      95 ..     238     272 ..     232     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.5e-06
                                       HCT-STT--HHHHHHHHHHHSGGGTSHHHHHHHGG CS
                         TetR_C_27  61 aaGeFkaadpeaaaravfdatarfhhPalaaewsd 95 
                                        +G Fk++ pea+ara+++a+ ++ +Pa++a+ s+
  gi|330508212|ref|YP_004384640.1| 238 GSGIFKSESPEAMARAIVEAVHHYDDPAHLAKVSK 272
                                       689***************************99876 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.7     0.036        64     182     198 ..      68      84 ..      19     100 .. 0.78
   2 !   16.4   0.6   2.6e-06    0.0046     179     228 ..     193     244 ..     178     285 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.036
                               NMO 182 faLvpqvldavdiPviA 198
                                         +++++ +av iPv+A
  gi|330508212|ref|YP_004384640.1|  68 PLVIESIIEAVTIPVMA 84 
                                       56899***********9 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.6e-06
                               NMO 179 kglfaLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrfLlt 228
                                       +  + Lv + ++   +Pv+  AaGG+ +  + a ++ lGA gv +g+     
  gi|330508212|ref|YP_004384640.1| 193 EADLDLVRECAQMQRLPVVnfAAGGVATPADAALMMQLGADGVFVGSGIFKS 244
                                       566778888888888***877*************************986543 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.48   8.6e+02      64      97 ..      70     103 ..      50     109 .. 0.69
   2 !   14.6   0.1   9.2e-06     0.016      56     108 ..     190     244 ..     142     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.48
                                       HHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-S CS
                      His_biosynth  64 lveeiaeevfipvqvGGGIrsledveelleagad 97 
                                       ++e i+e+v+ipv+    I ++ +++ l  +g+d
  gi|330508212|ref|YP_004384640.1|  70 VIESIIEAVTIPVMAKARIGHFVEAQILEALGVD 103
                                       6777777777777766666655555555555555 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9.2e-06
                                       TTHHHHHHHHHHHHHH-SSEE..EEESSSSSHHHHHHHHHCT-SEEEESHHHHH- CS
                      His_biosynth  56 egreanldlveeiaeevfipv..qvGGGIrsledveelleagadkviigtaavkn 108
                                       ++ ea+ldlv+e a+  ++pv     GG+ +  d++ ++++gad v +g+  +k+
  gi|330508212|ref|YP_004384640.1| 190 REIEADLDLVRECAQMQRLPVvnFAAGGVATPADAALMMQLGADGVFVGSGIFKS 244
                                       5566777888888887777773346788888888888888888888888876654 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.23   4.1e+02      59     149 ..      77     105 ..      62     122 .. 0.59
   2 ?   10.1   0.0   0.00018      0.32     170     232 ..     191     256 ..     122     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.23
                            DUF561  59 vsniPiCvsaveakllleavkaGadlveiGnfdslYeqgrklsseeilalvkevrkLlPktdlsvtiPyiLkle.eq 134
                                       +                                                               vtiP + k     
  gi|330508212|ref|YP_004384640.1|  77 A---------------------------------------------------------------VTIPVMAKARiGH 90 
                                       3...............................................................4555444433122 PP

                            DUF561 135 vkLakkLeslgvdli 149
                                          a+ Le+lgvd++
  gi|330508212|ref|YP_004384640.1|  91 FVEAQILEALGVDMV 105
                                       333555555555555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00018
                            DUF561 170 kslstlastyeiskkvslPvi..casGlsd.vtvplalslgasGiGigsavsklndeeemvallse 232
                                       ++   l  + e ++  +lPv+  +a G+++   + l ++lga G+ +gs + k ++ e+m  ++ e
  gi|330508212|ref|YP_004384640.1| 191 EIEADLDLVRECAQMQRLPVVnfAAGGVATpADAALMMQLGADGVFVGSGIFKSESPEAMARAIVE 256
                                       44446777788889999**9855788987625689999**********************988866 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2     0.076   1.4e+02     104     157 ..      30      86 ..      24     105 .. 0.77
   2 ?    9.9   0.1   0.00025      0.44     137     181 .]     194     241 ..     184     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.076
                          TMP-TENI 104 hsleeaeeaealgadYigvGpifpTdtKkda...eplgleglkelaealeiPvvaiG 157
                                        ++e+a  ae++ga  +++ +  p d +k+    ++++   ++ + ea++iPv+a +
  gi|330508212|ref|YP_004384640.1|  30 TTPEQAIIAEEAGAVAVMALHAVPADIRKMGgvaRMADPLVIESIIEAVTIPVMAKA 86 
                                       6788999999999988888888899999987444555666789999******99955 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00025
                          TMP-TENI 137 lgleglkelaealeiPvv..aiGGi.tlenvaevleagadgvavvsai 181
                                       ++l++++e+a++ ++Pvv  a GG+ t++++a +++ gadgv v s+i
  gi|330508212|ref|YP_004384640.1| 194 ADLDLVRECAQMQRLPVVnfAAGGVaTPADAALMMQLGADGVFVGSGI 241
                                       57889999999999888555888875799***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2236.79
//
Query:       gi|330508213|ref|YP_004384641.1|  [L=1216]
Description: WD40-like beta propeller repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-13   50.4  15.4     0.0014   18.0   0.1    6.6  6  DUF5050          Domain of unknown function (DUF5050)
    2.3e-11   43.3  62.8      0.068   13.1   0.7   18.7 18  PD40             WD40-like Beta Propeller Repeat
    1.9e-09   36.8  12.4       0.14   10.9   0.1    8.5  8  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
      3e-05   22.9   7.3        1.2    7.7   0.0    7.0  7  Pectate_lyase22  Oligogalacturonate lyase
  ------ inclusion threshold ------
       0.37   10.8   2.8    2.8e+02    1.6   0.1    6.0  6  Kelch_4          Galactose oxidase, central domain
       0.62    9.8  25.6        5.5    6.8   0.1   10.1 12  DUF2606          Protein of unknown function (DUF2606)
        3.3    7.8   5.9       0.48   10.4   2.0    1.7  2  TraW_N           Sex factor F TraW protein N terminal


Domain annotation for each model (and alignments):
>> DUF5050  Domain of unknown function (DUF5050)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   5.4e-07    0.0014     103     244 ..     128     274 ..     110     278 .. 0.80
   2 !   11.0   1.0   7.2e-05      0.19     141     257 ..     333     454 ..     328     464 .. 0.75
   3 !    5.6   0.0    0.0032       8.3     105     205 ..     463     570 ..     444     585 .. 0.68
   4 !   12.4   0.3   2.7e-05      0.07     102     258 ..     604     762 ..     584     788 .. 0.81
   5 ?    0.4   0.0      0.12   3.1e+02     102     141 ..     847     885 ..     818     945 .. 0.56
   6 !    6.3   0.1    0.0019         5     184     250 ..    1108    1177 ..    1002    1209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.4e-07
                                       EETTEEEEEEESSSS-EEEEEEETTS---EEEES...S----SEEETTEEEEE-T.TT--EEEEETTTTEEEEEE-. CS
                           DUF5050 103 lvgnwiYYqhydekdglklykikidgkektklsd...eaieplsvkdgwiYytgesedhslykldtdgksiskvse. 175
                                       ++gn + + + d k +++++  ++  +++ ++s+   e+i+p + +d ++   + s d  +y +d++++++s vs  
  gi|330508213|ref|YP_004384641.1| 128 ISGNRVVWAD-DRKGTYQIHLLDLSSRNEVEISSakgEQIRPKISDDRIVWMDERSGDFDIYMYDISTGKESAVSTg 203
                                       6677777773.556666788888888888888552225888888889999999999999*********999999984 PP

                                       .S-EEEEEEEETTEEEEEG.GGTT-EEEE-SSS---EE-S-S-EEE.EEEETTEEEEEE-SSS-E.EEEEET CS
                           DUF5050 176 .enlyllvvegdyiYyidl.sknyaLyrvklsgsekevltedkvdn.yNvtgnwiYyqkesdeekalyrikl 244
                                        ++  +++v+ d + + d  + +  ++ ++ls+++++++++  +++   v+g++i y +++++ + ly i++
  gi|330508213|ref|YP_004384641.1| 204 pGDQSFPSVSKDIVAWADNrTGESDIAFMDLSSGKETTINKSGIQTdPRVYGRYIAYLNNHTDIN-LYDIET 274
                                       4456669999999988887477889***************9999997889*******99999999.999987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 7.2e-05
                                       -SEEETTEEEEE-T.TT--EEEEETTTTEEEEEE-S-EEE..EEEEETTEEEEEGG.GTT-EEEE-SSS---EE-S- CS
                           DUF5050 141 plsvkdgwiYytgesedhslykldtdgksiskvseenlyl..lvvegdyiYyidls.knyaLyrvklsgsekevlte 214
                                       p + +d ++   + + + ++y +++ ++++++++e+ + +  + ++++++ ++d+s  n ++   +ls++e++ +t 
  gi|330508213|ref|YP_004384641.1| 333 PSISEDSVVWTDNRDGNFNVYLFNITTGKETQITEDSFDHssPDISNKNLIWTDMSlGNLQIFLRNLSTKETKQVTI 409
                                       455556666666666677*****************998776799***999999**5368889999999999988888 PP

                                       S-EEE.EEE.E.TTEEEEEE-SSS-E.EEEEETTS---EEEEES-E CS
                           DUF5050 215 dkvdn.yNv.t.gnwiYyqkesdeekalyrikldGsekeklaegnv 257
                                       d+ d+ y + + +n+i+    s+ e+ +y ++  + +++ ++  ++
  gi|330508213|ref|YP_004384641.1| 410 DQSDHrYGMiDgNNIIWIDARSGGEQ-IYLYDIITGQEKQITAAQS 454
                                       88877666534257778888877777.9999887777777766554 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0032
                                       TTEEEEEEE.SSSS-EEEEEEETTS---EEEESS...----SEEETTEEEEE-T.TT--EEEEETTTTEEEEEE-.. CS
                           DUF5050 105 gnwiYYqhy.dekdglklykikidgkektklsde...aieplsvkdgwiYytgesedhslykldtdgksiskvse.. 175
                                       ++ i +++  + +d+ +ly  ++   e+t + ++   +++p +  d+++   g + +  +y++d+++++++ v    
  gi|330508213|ref|YP_004384641.1| 463 QDRIVWIDSrSGEDKWDLYLYNLTTGEETAICTNparQAQPWIWGDNVVWADGRNGNWDIYAYDLATNTERAVVIdt 539
                                       45555554325677788888888888899996651225667778899999999988889999998886655554401 PP

                                       S-EEEEEEEETTEEEEEG.GGTT-EEEE-SS CS
                           DUF5050 176 enlyllvvegdyiYyidl.sknyaLyrvkls 205
                                        n   +vv g+y+ ++d+ + n  +y  +l 
  gi|330508213|ref|YP_004384641.1| 540 ANQGNPVVHGNYLAWLDVrQGNSDIYLFDLR 570
                                       455559******9999994456667766665 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 2.7e-05
                                       EEETTEEEEEEESSSS-EEEEEEETTS---EEEESS----SEEETTEEEEE-T.TT-.-EEEEETTTTEEEEEE-S- CS
                           DUF5050 102 slvgnwiYYqhydekdglklykikidgkektklsdeaieplsvkdgwiYytgesedh.slykldtdgksiskvseen 177
                                        +++n+i ++  d++dg++  k++   ++   l   ++ + s+++  + ++++ +++ ++y +d  ++s++ +++++
  gi|330508213|ref|YP_004384641.1| 604 IISDNKIVWM--DNSDGYSQIKMRYINSDPLLLL--EADYPSTNGSLLVWSDNRRGNwNIYGFDFFTRSEKPITKGD 676
                                       5789999999..8999997666666555555555..5556677788888888888778****************998 PP

                                       EEE..EEEEETTEEEEEG.GGTT-EEEE-SSS---EE-S-S-E..EEEEEETTEEEEEE-SSS-E.EEEEETTS--- CS
                           DUF5050 178 lyl..lvvegdyiYyidl.sknyaLyrvklsgsekevltedkv..dnyNvtgnwiYyqkesdeekalyrikldGsek 249
                                       +    + ++gd + y d  s +  +y++++ ++ ++ + + k    +  ++g+ +  q +s+ + ++y+ +l + ++
  gi|330508213|ref|YP_004384641.1| 677 YDQlyPKASGDIVVYSDYrSGDSDIYMTNIATGVESPVATGKRdqMWPSISGDLVVWQDNSSGNWDIYMKELSTDKT 753
                                       8765599**********9677889*******9999888666651145789**************99*********** PP

                                       EEEEES-EE CS
                           DUF5050 250 eklaegnvs 258
                                       + +++g+ +
  gi|330508213|ref|YP_004384641.1| 754 TPIYKGSGQ 762
                                       *99999754 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.12
                                       EEETTEEEEEEESSSS-EEEEEEETTS---EEEESS---- CS
                           DUF5050 102 slvgnwiYYqhydekdglklykikidgkektklsdeaiep 141
                                       +++gn+i Y++  + +++++ k ++   +++ ++  + + 
  gi|330508213|ref|YP_004384641.1| 847 VVSGNYIAYVD-GSGEDTSIRKLDLASWKDELVQAGPGQA 885
                                       56666666664.3345555666666666666665544333 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.0019
                                        EETTEEEEEG.GGTT-EEEE-SSS---EE-S-S-EEEEE..EETTEEEEEE-SSS-E.EEEEETTS---E CS
                           DUF5050  184 egdyiYyidl.sknyaLyrvklsgsekevltedkvdnyN..vtgnwiYyqkesdeekalyrikldGseke 250 
                                        +g ++ + d  + n  +y ++l++s++  +t+d++d +N  v++ +i  q + + + ++y ++ +   ++
  gi|330508213|ref|YP_004384641.1| 1108 DGRTVVWQDNrNGNWDIYAYDLNTSKEMQITTDSADQINpdVENGVIVWQDKRNGDWDIYVYDQNVGRET 1177
                                        4444433333245566777777777777777777766664455555555555555555666666555544 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.026        66      24      38 .]      50      63 ..      48      63 .. 0.91
   2 ?    2.5   0.0     0.056   1.4e+02      20      38 .]      88     105 ..      84     105 .. 0.94
   3 ?    3.2   0.0     0.034        86      20      36 ..     130     145 ..     114     147 .. 0.82
   4 !    5.6   0.1     0.006        15      14      38 .]     168     189 ..     157     189 .. 0.77
   5 ?    2.5   0.2     0.056   1.4e+02       4      19 ..     200     215 ..     198     229 .. 0.75
   6 !   13.1   0.7   2.7e-05     0.068       4      37 ..     323     353 ..     322     354 .. 0.96
   7 ?   -1.4   0.1      0.98   2.5e+03      19      37 ..     420     437 ..     420     438 .. 0.90
   8 ?    1.8   0.0     0.099   2.5e+02      20      37 ..     507     523 ..     507     524 .. 0.85
   9 ?    2.6   0.0     0.055   1.4e+02      20      37 ..     549     565 ..     549     566 .. 0.95
  10 !    6.7   0.1    0.0028       7.3      19      37 ..     643     660 ..     640     660 .. 0.94
  11 ?    3.1   0.2     0.038        97      20      38 .]     686     703 ..     684     703 .. 0.89
  12 ?    1.1   0.3      0.16     4e+02      12      38 .]     722     745 ..     712     745 .. 0.64
  13 ?    3.2   0.1     0.036        92      20      38 .]     770     787 ..     758     787 .. 0.87
  14 ?    2.1   0.0      0.08     2e+02      21      38 .]     936     952 ..     935     952 .. 0.87
  15 ?    1.8   0.1     0.097   2.5e+02      20      37 ..    1066    1082 ..    1066    1084 .. 0.92
  16 !   11.4   0.1     9e-05      0.23      19      37 ..    1108    1125 ..    1105    1126 .. 0.94
  17 ?    2.7   0.1     0.048   1.2e+02      23      38 .]    1154    1168 ..    1151    1168 .. 0.87
  18 !    6.4   0.2    0.0036       9.1      22      38 .]    1195    1210 ..    1194    1210 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.026
                                      EEEEECT.TCEEEEE CS
                              PD40 24 aFsSdRgsGkpdIyv 38
                                      a+s +R+ G++dI++
  gi|330508213|ref|YP_004384641.1| 50 AWSDNRS-GNYDIFM 63
                                      8999***.*****96 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.056
                                       SSEEEEEEECT.TCEEEEE CS
                              PD40  20 GkrlaFsSdRgsGkpdIyv 38 
                                       G r+++   R+ G+ dIy+
  gi|330508213|ref|YP_004384641.1|  88 GERIVWQDMRS-GNGDIYM 105
                                       889********.******7 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.034
                                       SSEEEEEEECT.TCEEE CS
                              PD40  20 GkrlaFsSdRgsGkpdI 36 
                                       G+r +++ dR+ G+++I
  gi|330508213|ref|YP_004384641.1| 130 GNRVVWADDRK-GTYQI 145
                                       899********.****9 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.006
                                       EEE-TTSSEEEEEEECT.TCEEEEE CS
                              PD40  14 PsfSPDGkrlaFsSdRgsGkpdIyv 38 
                                       P +S D   +++  +R+ G++dIy+
  gi|330508213|ref|YP_004384641.1| 168 PKISDDR--IVWMDERS-GDFDIYM 189
                                       5566665..********.******7 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.056
                                       --SSSS.EEEEEE-TT CS
                              PD40   4 ltntpgnegaPsfSPD 19 
                                       + ++pg+   Ps+S+D
  gi|330508213|ref|YP_004384641.1| 200 VSTGPGDQSFPSVSKD 215
                                       6799***********9 PP

  == domain 6  score: 13.1 bits;  conditional E-value: 2.7e-05
                                       --SSSS.EEEEEE-TTSSEEEEEEECT.TCEEEE CS
                              PD40   4 ltntpgnegaPsfSPDGkrlaFsSdRgsGkpdIy 37 
                                       +t++p+n ++Ps+S D    +++ +R+ G++++y
  gi|330508213|ref|YP_004384641.1| 323 ITSGPFNHTNPSISEDS--VVWTDNRD-GNFNVY 353
                                       8***************9..********.****99 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 0.98
                                       TSSEEEEEEECT.TCEEEE CS
                              PD40  19 DGkrlaFsSdRgsGkpdIy 37 
                                       DG+ +++   R+ G+ +Iy
  gi|330508213|ref|YP_004384641.1| 420 DGNNIIWIDARS-GGEQIY 437
                                       9*******9999.998888 PP

  == domain 8  score: 1.8 bits;  conditional E-value: 0.099
                                       SSEEEEEEECT.TCEEEE CS
                              PD40  20 GkrlaFsSdRgsGkpdIy 37 
                                       G   +++  R+ G++dIy
  gi|330508213|ref|YP_004384641.1| 507 GDNVVWADGRN-GNWDIY 523
                                       566789999**.*****9 PP

  == domain 9  score: 2.6 bits;  conditional E-value: 0.055
                                       SSEEEEEEECT.TCEEEE CS
                              PD40  20 GkrlaFsSdRgsGkpdIy 37 
                                       G++la+   R+ G++dIy
  gi|330508213|ref|YP_004384641.1| 549 GNYLAWLDVRQ-GNSDIY 565
                                       899********.*****9 PP

  == domain 10  score: 6.7 bits;  conditional E-value: 0.0028
                                       TSSEEEEEEECT.TCEEEE CS
                              PD40  19 DGkrlaFsSdRgsGkpdIy 37 
                                       +G+ l++s +R  G+++Iy
  gi|330508213|ref|YP_004384641.1| 643 NGSLLVWSDNRR-GNWNIY 660
                                       79*********9.*****9 PP

  == domain 11  score: 3.1 bits;  conditional E-value: 0.038
                                       SSEEEEEEECT.TCEEEEE CS
                              PD40  20 GkrlaFsSdRgsGkpdIyv 38 
                                       G   ++s +R+ G++dIy+
  gi|330508213|ref|YP_004384641.1| 686 GDIVVYSDYRS-GDSDIYM 703
                                       67789******.******7 PP

  == domain 12  score: 1.1 bits;  conditional E-value: 0.16
                                       EEEEE-TTSSEEEEEEECT.TCEEEEE CS
                              PD40  12 gaPsfSPDGkrlaFsSdRgsGkpdIyv 38 
                                       ++Ps+S  G   ++  + + G++dIy+
  gi|330508213|ref|YP_004384641.1| 722 MWPSIS--GDLVVWQDNSS-GNWDIYM 745
                                       555555..44566666655.9999996 PP

  == domain 13  score: 3.2 bits;  conditional E-value: 0.036
                                       SSEEEEEEECT.TCEEEEE CS
                              PD40  20 GkrlaFsSdRgsGkpdIyv 38 
                                       G   ++  +R+ G++dIyv
  gi|330508213|ref|YP_004384641.1| 770 GDLVVWQDSRN-GDFDIYV 787
                                       556788889**.******8 PP

  == domain 14  score: 2.1 bits;  conditional E-value: 0.08
                                       SEEEEEEECT.TCEEEEE CS
                              PD40  21 krlaFsSdRgsGkpdIyv 38 
                                        + a+  +R+ G+pd+yv
  gi|330508213|ref|YP_004384641.1| 936 YYVAWMDNRT-GDPDVYV 952
                                       5779999***.******8 PP

  == domain 15  score: 1.8 bits;  conditional E-value: 0.097
                                        SSEEEEEEECT.TCEEEE CS
                              PD40   20 GkrlaFsSdRgsGkpdIy 37  
                                        G +l+F  ++  G++dI+
  gi|330508213|ref|YP_004384641.1| 1066 GDYLVFQNNKA-GSWDIF 1082
                                        889********.****98 PP

  == domain 16  score: 11.4 bits;  conditional E-value: 9e-05
                                        TSSEEEEEEECT.TCEEEE CS
                              PD40   19 DGkrlaFsSdRgsGkpdIy 37  
                                        DG++ ++  +R+ G++dIy
  gi|330508213|ref|YP_004384641.1| 1108 DGRTVVWQDNRN-GNWDIY 1125
                                        ************.*****9 PP

  == domain 17  score: 2.7 bits;  conditional E-value: 0.048
                                        EEEEEECT.TCEEEEE CS
                              PD40   23 laFsSdRgsGkpdIyv 38  
                                        +++   R+ G++dIyv
  gi|330508213|ref|YP_004384641.1| 1154 IVWQDKRN-GDWDIYV 1168
                                        78888899.******8 PP

  == domain 18  score: 6.4 bits;  conditional E-value: 0.0036
                                        EEEEEEECT.TCEEEEE CS
                              PD40   22 rlaFsSdRgsGkpdIyv 38  
                                        r++++ dR+ G+ dIy+
  gi|330508213|ref|YP_004384641.1| 1195 RIVWTDDRS-GDKDIYI 1210
                                        8********.******7 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.026        65     231     279 ..      71     119 ..      45     128 .. 0.73
   2 ?    2.4   0.1     0.021        54      63      84 ..     350     371 ..     347     386 .. 0.80
   3 !    7.8   0.1   0.00048       1.2     227     278 ..     402     451 ..     377     454 .. 0.79
   4 ?   -0.5   0.0      0.16   4.1e+02      62      82 ..     477     497 ..     451     505 .. 0.71
   5 ?   -0.3   0.0      0.13   3.4e+02      26      81 ..     481     538 ..     477     550 .. 0.44
   6 ?    3.2   0.0     0.012        30     200     272 ..     552     654 ..     545     692 .. 0.68
   7 !   10.9   0.1   5.3e-05      0.14      20      87 ..     738     806 ..     728     814 .. 0.81
   8 !    6.6   0.2    0.0011       2.8      62      93 ..    1121    1156 ..    1083    1159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.026
                                       SS-SSS-S-EEE-.TTTSSEEEEEEETTSSEEEEEEESSS-C.EEESS-S CS
                           DPPIV_N 231 dgWvelhdevhfl.krdesgflwisekdGfkHLylfdldgkseikqlTsG 279
                                       + Wv ++  ++++   ++++++w+  ++G   +y++d+ +k+ ++++T  
  gi|330508213|ref|YP_004384641.1|  71 ERWVCIDPFFQISpAVSGERIVWQDMRSGNGDIYMYDVINKT-ESAITTA 119
                                       567755555555555778899999999999999999999999.7777765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.021
                                       TEEEEESTTTSEEEECES-STT CS
                           DPPIV_N  63 nnLyvrelatgkeiqlTsdgsa 84 
                                        n+y+ ++ tgke+q+T+d  +
  gi|330508213|ref|YP_004384641.1| 350 FNVYLFNITTGKETQITEDSFD 371
                                       699***************9833 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00048
                                       EEESSS-S.SS-S-EEE-TTTSSEEEEEEETTSSEEEEEEESSS-C.EEESS- CS
                           DPPIV_N 227 eetsdgWv.elhdevhflkrdesgflwisekdGfkHLylfdldgkseikqlTs 278
                                       +et+++ + + ++ + ++  d+++++wi +++G +++yl+d  +++ +kq+T 
  gi|330508213|ref|YP_004384641.1| 402 KETKQVTIdQSDHRYGMI--DGNNIIWIDARSGGEQIYLYDIITGQ-EKQITA 451
                                       555555554455666666..9************************9.899985 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.16
                                       TTEEEEESTTTSEEEECES-S CS
                           DPPIV_N  62 nnnLyvrelatgkeiqlTsdg 82 
                                       +++Ly+ +l tg+e+++ ++ 
  gi|330508213|ref|YP_004384641.1| 477 KWDLYLYNLTTGEETAICTNP 497
                                       689999999999999997765 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 0.13
                                       EEEETTTEECEEEETT.TT.BSEEEEESSTTEEEEEE....TTEEEEESTTTSEEEECES- CS
                           DPPIV_N  26 yiydletneveelspg.eeklqlakwSPagdklafvr....nnnLyvrelatgkeiqlTsd 81 
                                       y+y+l t+e ++++ +  +++q   w   gd++++      n+++y  +lat++e++++ d
  gi|330508213|ref|YP_004384641.1| 481 YLYNLTTGEETAICTNpARQAQPWIW---GDNVVWADgrngNWDIYAYDLATNTERAVVID 538
                                       44444444444444442222222222...22222221111155666666666666666555 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.012
                                       EEEEETTSTEEEEEEEETTTCCEEEEE..........EEESSS-SSS-S-EEE-TTTSSEEEEEEETTSSEEEEEEE CS
                           DPPIV_N 200 vqwlnRsqnrlkvvlvdaetgravvkl..........eetsdgWvelhdevhflkrdesgflwisekdGfkHLylfd 266
                                       + wl+  q +++++l+d+++g  v++            + ++  +++ ++ +++  ++++++w+ ++dG++++ +  
  gi|330508213|ref|YP_004384641.1| 552 LAWLDVRQGNSDIYLFDLRKGVEVPVAtlptqqtpndGKGDPYQIKPYHSSKII--SDNKIVWMDNSDGYSQIKMRY 626
                                       678888899999999999888777777777777775555555666888888888..889999999999999988766 PP

                                       SSS-C....................... CS
                           DPPIV_N 267 ldgks......................e 272
                                        ++                         
  gi|330508213|ref|YP_004384641.1| 627 INSDPlllleadypstngsllvwsdnrR 654
                                       6655555555555544444444444440 PP

  == domain 7  score: 10.9 bits;  conditional E-value: 5.3e-05
                                       EETTEEEEEETTTEECEEEETTTT.BSEEEEESS..TTEEEEEETTEEEEESTTTSEEEECES-STTTEE CS
                           DPPIV_N  20 sytaeyyiydletneveelspgeeklqlakwSPa..gdklafvrnnnLyvrelatgkeiqlTsdgsagif 87 
                                       s+  + y+++l+t++++++ +g+++++++ +S +    + +   + ++yv++l +g+e++lT dg ++++
  gi|330508213|ref|YP_004384641.1| 738 SGNWDIYMKELSTDKTTPIYKGSGQQMYPAISGDlvVWQDSRNGDFDIYVKDLVNGTETKLTGDG-DQLY 806
                                       4455678999**********************875444455566779******************.5565 PP

  == domain 8  score: 6.6 bits;  conditional E-value: 0.0011
                                        TTEEEEESTTTSEEEECES-S....TTTEEESB--H CS
                           DPPIV_N   62 nnnLyvrelatgkeiqlTsdg....sagifnGvadW 93  
                                        n+++y  +l t+ke q+T+d     + ++ nGv  W
  gi|330508213|ref|YP_004384641.1| 1121 NWDIYAYDLNTSKEMQITTDSadqiNPDVENGVIVW 1156
                                        79*****************99444444444776655 PP

>> Pectate_lyase22  Oligogalacturonate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.04     1e+02      46      82 ..     129     165 ..     122     173 .. 0.91
   2 ?    0.6   0.0     0.067   1.7e+02      51     132 ..     176     259 ..     170     275 .. 0.74
   3 !    5.1   0.1     0.003       7.8      50      83 ..     340     373 ..     328     422 .. 0.80
   4 ?   -1.9   0.0      0.38   9.9e+02      49      81 ..     509     544 ..     506     625 .. 0.65
   5 ?    2.0   0.0     0.025        65      45      83 ..     642     680 ..     637     694 .. 0.90
   6 ?    0.7   0.0     0.062   1.6e+02      47      85 ..     728     766 ..     720     799 .. 0.79
   7 !    7.7   0.0   0.00048       1.2      43      82 ..    1105    1144 ..    1097    1160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.04
                   Pectate_lyase22  46 dgskllfggafdgprnyylldlntqqavqltegkgdn 82 
                                        g++++++ +  g+++ +lldl +++ v+++  kg++
  gi|330508213|ref|YP_004384641.1| 129 SGNRVVWADDRKGTYQIHLLDLSSRNEVEISSAKGEQ 165
                                       588999*************************999985 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.067
                   Pectate_lyase22  51 lfggafdgprnyylldlntqqavqltegkgdntfggflssdddalfyvkn.ernlmrvdletleetviyq..vdeew 124
                                       ++  +  g+++ y+ d+ t +   ++ g gd++f   +s d  a    +  e ++  +dl++ +et+i +  ++ + 
  gi|330508213|ref|YP_004384641.1| 176 VWMDERSGDFDIYMYDISTGKESAVSTGPGDQSFPS-VSKDIVAWADNRTgESDIAFMDLSSGKETTINKsgIQTDP 251
                                       55566779999*********************9975.5666666555443245677788888888888753366777 PP

                   Pectate_lyase22 125 vgygtwva 132
                                       + yg ++a
  gi|330508213|ref|YP_004384641.1| 252 RVYGRYIA 259
                                       77887776 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.003
                   Pectate_lyase22  50 llfggafdgprnyylldlntqqavqltegkgdnt 83 
                                       ++++ + dg++n yl+++ t + +q+te   d +
  gi|330508213|ref|YP_004384641.1| 340 VVWTDNRDGNFNVYLFNITTGKETQITEDSFDHS 373
                                       5677889*********************988765 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.38
                   Pectate_lyase22  49 kllfggafdgprnyylldlnt..qqavql.tegkgd 81 
                                       +++++   +g+++ y  dl t  ++av + t  +g+
  gi|330508213|ref|YP_004384641.1| 509 NVVWADGRNGNWDIYAYDLATntERAVVIdTANQGN 544
                                       566666777888888888754114444431333343 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.025
                   Pectate_lyase22  45 rdgskllfggafdgprnyylldlntqqavqltegkgdnt 83 
                                        +gs l+++ +  g++n y +d+ t+    +t+g  d+ 
  gi|330508213|ref|YP_004384641.1| 642 TNGSLLVWSDNRRGNWNIYGFDFFTRSEKPITKGDYDQL 680
                                       689999**************************9998875 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 0.062
                   Pectate_lyase22  47 gskllfggafdgprnyylldlntqqavqltegkgdntfg 85 
                                       g+ +++  +  g+++ y+ +l t +++ + +g g++ + 
  gi|330508213|ref|YP_004384641.1| 728 GDLVVWQDNSSGNWDIYMKELSTDKTTPIYKGSGQQMYP 766
                                       55667777889***********************98764 PP

  == domain 7  score: 7.7 bits;  conditional E-value: 0.00048
                   Pectate_lyase22   43 ftrdgskllfggafdgprnyylldlntqqavqltegkgdn 82  
                                         + dg+ +++  + +g+++ y  dlnt + +q+t    d+
  gi|330508213|ref|YP_004384641.1| 1105 ASTDGRTVVWQDNRNGNWDIYAYDLNTSKEMQITTDSADQ 1144
                                        5789******************************988875 PP

>> Kelch_4  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         1   2.7e+03      30      41 ..      60      73 ..      59      84 .. 0.81
   2 ?    0.4   0.0      0.26   6.6e+02      30      40 ..     186     196 ..     185     204 .. 0.87
   3 ?   -0.0   0.0      0.36   9.3e+02      31      44 ..     352     365 ..     350     376 .. 0.77
   4 ?    0.4   0.0      0.27   6.8e+02      30      40 ..     479     489 ..     479     493 .. 0.93
   5 ?    1.6   0.1      0.11   2.8e+02      30      40 ..     521     531 ..     520     534 .. 0.95
   6 ?   -2.4   0.0         2   5.2e+03      29      37 ..     562     570 ..     562     573 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1
                           Kelch_4 30 dlylldlstn..tW 41
                                      d++ +dl+t+  +W
  gi|330508213|ref|YP_004384641.1| 60 DIFMYDLETGleRW 73
                                      99*******96666 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.26
                           Kelch_4  30 dlylldlstnt 40 
                                       d+y +d+st++
  gi|330508213|ref|YP_004384641.1| 186 DIYMYDISTGK 196
                                       99*******97 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.36
                           Kelch_4  31 lylldlstntWrrl 44 
                                       +yl++++t++ +++
  gi|330508213|ref|YP_004384641.1| 352 VYLFNITTGKETQI 365
                                       7********97777 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.27
                           Kelch_4  30 dlylldlstnt 40 
                                       dlyl++l+t++
  gi|330508213|ref|YP_004384641.1| 479 DLYLYNLTTGE 489
                                       9********96 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.11
                           Kelch_4  30 dlylldlstnt 40 
                                       d+y++dl+tnt
  gi|330508213|ref|YP_004384641.1| 521 DIYAYDLATNT 531
                                       89********8 PP

  == domain 6  score: -2.4 bits;  conditional E-value: 2
                           Kelch_4  29 ndlylldls 37 
                                       +d+yl+dl 
  gi|330508213|ref|YP_004384641.1| 562 SDIYLFDLR 570
                                       79*****96 PP

>> DUF2606  Protein of unknown function (DUF2606)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.028        71      87     111 ..      46      70 ..      19      77 .. 0.82
   2 ?    1.2   0.0      0.12     3e+02      89     106 ..     132     149 ..     108     171 .. 0.80
   3 ?    0.9   0.0      0.14   3.5e+02      62     107 ..     146     192 ..     142     202 .. 0.74
   4 ?    6.8   0.1    0.0021       5.5      87     129 ..     337     377 ..     333     378 .. 0.88
   5 ?    0.8   0.0      0.15   3.7e+02      87     124 ..     379     414 ..     378     420 .. 0.81
   6 ?   -1.4   0.1      0.74   1.9e+03      89     114 ..     509     533 ..     507     544 .. 0.70
   7 ?   -0.7   0.0      0.45   1.1e+03      90     105 ..     773     788 ..     743     801 .. 0.79
   8 ?   -0.8   0.0      0.45   1.2e+03      86     114 ..     889     918 ..     879     925 .. 0.84
   9 ?   -3.3   0.0       2.8   7.2e+03      81     103 ..     928     951 ..     922     954 .. 0.77
  10 ?    2.1   0.2      0.06   1.5e+02      88     127 ..    1110    1147 ..    1096    1150 .. 0.80
  11 ?    2.1   0.4     0.058   1.5e+02      86     106 ..    1150    1170 ..    1139    1182 .. 0.83
  12 ?   -1.8   0.0      0.93   2.4e+03      86     104 ..    1192    1210 ..    1180    1214 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.028
                           DUF2606  87 eGdvkwdtvrkGdyivaltknetsv 111
                                       e  v w + r G+y +++ + et +
  gi|330508213|ref|YP_004384641.1|  46 EYVVAWSDNRSGNYDIFMYDLETGL 70 
                                       55689**************999965 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                           DUF2606  89 dvkwdtvrkGdyivaltk 106
                                        v+w + rkG y + l +
  gi|330508213|ref|YP_004384641.1| 132 RVVWADDRKGTYQIHLLD 149
                                       599*********998854 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.14
                           DUF2606  62 ilvkdessde.ePskeiGiilGktdkeGdvkwdtvrkGdyivaltkn 107
                                        l+   s +e e s   G+ +     +  ++w + r Gd+ +++ + 
  gi|330508213|ref|YP_004384641.1| 146 HLLDLSSRNEvEISSAKGEQIRPKISDDRIVWMDERSGDFDIYMYDI 192
                                       55555554443778888999988888999***********9987655 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0021
                           DUF2606  87 eGdvkwdtvrkGdyivaltknetsvthqivliedkddtkkilv 129
                                       e  v+w + r G++ v+l +  t   ++  ++ed  d+  + +
  gi|330508213|ref|YP_004384641.1| 337 EDSVVWTDNRDGNFNVYLFNITT--GKETQITEDSFDHSSPDI 377
                                       5689***************9999..778888999999998877 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.15
                           DUF2606  87 eGdvkwdtvrkGdyivaltknetsvthqivliedkddt 124
                                       + +++w +   G+  ++l +  t  t+q+++  d+ d+
  gi|330508213|ref|YP_004384641.1| 379 NKNLIWTDMSLGNLQIFLRNLSTKETKQVTI--DQSDH 414
                                       56799******************99998865..44444 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 0.74
                           DUF2606  89 dvkwdtvrkGdyivaltknetsvthq 114
                                       +v+w ++r+G++ ++  +  t  t +
  gi|330508213|ref|YP_004384641.1| 509 NVVWADGRNGNWDIYAYDLAT-NTER 533
                                       699********9887666555.3333 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 0.45
                           DUF2606  90 vkwdtvrkGdyivalt 105
                                       v+w+++r+Gd+ +++ 
  gi|330508213|ref|YP_004384641.1| 773 VVWQDSRNGDFDIYVK 788
                                       79********988754 PP

  == domain 8  score: -0.8 bits;  conditional E-value: 0.45
                           DUF2606  86 keGdvkwdtvrkGd.yivaltknetsvthq 114
                                        + +++w ++  G+  +va++ ++tsv  +
  gi|330508213|ref|YP_004384641.1| 889 MDKKLVWINTHSGKpRSVAVAAGQTSVISK 918
                                       567899*******9569********99876 PP

  == domain 9  score: -3.3 bits;  conditional E-value: 2.8
                           DUF2606  81 lGktdkeG.dvkwdtvrkGdyiva 103
                                       +G  d+ G  v w + r+Gd  v+
  gi|330508213|ref|YP_004384641.1| 928 VGGNDQVGyYVAWMDNRTGDPDVY 951
                                       667777773489*******97665 PP

  == domain 10  score: 2.1 bits;  conditional E-value: 0.06
                           DUF2606   88 GdvkwdtvrkGdyivaltknetsvthqivliedkddtkki 127 
                                          v+w++ r+G++ ++  + +t  ++++ ++ d  d+  +
  gi|330508213|ref|YP_004384641.1| 1110 RTVVWQDNRNGNWDIYAYDLNT--SKEMQITTDSADQINP 1147
                                        3699***********9999999..6788888888777655 PP

  == domain 11  score: 2.1 bits;  conditional E-value: 0.058
                           DUF2606   86 keGdvkwdtvrkGdyivaltk 106 
                                        ++G ++w++ r+Gd+ +++ +
  gi|330508213|ref|YP_004384641.1| 1150 ENGVIVWQDKRNGDWDIYVYD 1170
                                        89************9887654 PP

  == domain 12  score: -1.8 bits;  conditional E-value: 0.93
                           DUF2606   86 keGdvkwdtvrkGdyival 104 
                                        + G ++w + r Gd  +++
  gi|330508213|ref|YP_004384641.1| 1192 RTGRIVWTDDRSGDKDIYI 1210
                                        5689999999999877665 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 ?   10.4   2.0   0.00019      0.48       1      21 [.       6      26 ..       6      27 .. 0.94
   2 ?   -3.4   0.1       4.1   1.1e+04      23      28 ..     833     838 ..     833     838 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00019
                            TraW_N  1 illaLaallllapaAyAkdLG 21
                                      +ll ++a+llla+aA ++d+G
  gi|330508213|ref|YP_004384641.1|  6 RLLIITAALLLAGAASGADFG 26
                                      68899***************9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.1
                            TraW_N  23 iGpvfP 28 
                                       +G+++P
  gi|330508213|ref|YP_004384641.1| 833 WGKTYP 838
                                       8****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.84u 0.26s 00:00:01.10 Elapsed: 00:00:00.42
# Mc/sec: 8729.11
//
Query:       gi|330508214|ref|YP_004384642.1|  [L=298]
Description: hypothetical protein MCON_2353 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-12   46.6   9.8    2.5e-06   27.5   7.3    3.4  3  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
      0.064   12.3   0.0       0.11   11.6   0.0    1.3  1  DUF4855         Domain of unknown function (DUF4855)
       0.13   11.9   0.2       0.13   11.9   0.2    2.0  2  DUF4131         Domain of unknown function (DUF4131)
       0.95    9.5  12.2        1.3    9.0   8.0    3.0  3  Ion_trans_2     Ion channel


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.9     2e-09   8.8e-06      12      48 .]      14      51 ..      10      51 .. 0.93
   2 !   27.5   7.3   5.6e-10   2.5e-06       1      47 [.      36      83 ..      36      84 .. 0.95
   3 !    9.1   0.0   0.00031       1.4       4      39 ..      83     118 ..      81     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2e-09
                    Pentapeptide_3 12 FrgatFsgaasFsnadF.gsadFsgarFtgdvdFsgat 48
                                       r+++F g ++F n+ F +  d+sg++F ++++Fs at
  gi|330508214|ref|YP_004384642.1| 14 IRNSVFLGRVNFINSIFrEPLDLSGSTFRQEASFSSAT 51
                                      689**************99***************9986 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 5.6e-10
                    Pentapeptide_3  1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47
                                      +sg++F++ a+F+ atF  ++sF +a+F ++a F+g+ F +++d s+a
  gi|330508214|ref|YP_004384642.1| 36 LSGSTFRQEASFSSATFLAMVSFASAHFqEDALFDGTAFMKTADCSAA 83
                                      589*************************99**************9987 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00031
                    Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadF.gsadFsgarFt 39 
                                       a+F++  +F ga  +++ + s+a++ g  ++++a F+
  gi|330508214|ref|YP_004384642.1|  83 ASFQREITFAGASINKM-RLSRAQIsGQLSLQNAEFN 118
                                       67888889999999999.9999999889999999997 PP

>> DUF4855  Domain of unknown function (DUF4855)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.4e-05      0.11      11      59 ..      41      89 ..      35     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                           DUF4855 11 erattdwtkeeflpyvaYvdkdgkkdwlFDsfLfLelsdgkgedgskaf 59
                                       r+++++++  fl +v++  ++ ++d lFD+  f++++d +  +++++ 
  gi|330508214|ref|YP_004384642.1| 41 FRQEASFSSATFLAMVSFASAHFQEDALFDGTAFMKTADCSAASFQREI 89
                                      555578999*****************************98887776433 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   2.9e-05      0.13      13      51 ..     189     224 ..     179     245 .. 0.76
   2 ?   -2.4   0.9      0.72   3.2e+03      34      43 ..     281     290 ..     267     296 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.9e-05
                           DUF4131  13 llllllllllllrrrprrrvllllllllllallgfalra 51 
                                       +l+ + + + +   rpr++v+l+++++ll+a+l+++   
  gi|330508214|ref|YP_004384642.1| 189 GLAWISCGYGV---RPRYTVFLSCFFILLFAFLYWQGMG 224
                                       55566666666...9********************9765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.72
                           DUF4131  34 llllllllla 43 
                                       + lll+l+l+
  gi|330508214|ref|YP_004384642.1| 281 GWLLLALFLV 290
                                       2222222222 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.26   1.2e+03      20      37 ..      42      59 ..      19      60 .. 0.75
   2 ?   -0.4   0.4      0.26   1.2e+03      40      63 ..     196     216 ..     194     231 .. 0.54
   3 ?    9.0   8.0   0.00029       1.3       5      78 ..     211     297 ..     202     298 .] 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.26
                                      .T---HHHHHHHHHHHHT CS
                       Ion_trans_2 20 wekwsfldalYfsfvtlt 37
                                       ++ sf++a + ++v++ 
  gi|330508214|ref|YP_004384642.1| 42 RQEASFSSATFLAMVSFA 59
                                      456699999999999985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.26
                                       ----SSTT.-----HHHHHHHHHHH CS
                       Ion_trans_2  40 GYGdivpe.tdagrlftivyillGl 63 
                                       GYG + p+ t +   +++++ill  
  gi|330508214|ref|YP_004384642.1| 196 GYG-VRPRyTVF---LSCFFILLFA 216
                                       666.55653333...3333333332 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00029
                                       HTCHHHHHHHHT..................T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHH CS
                       Ion_trans_2   5 lvlifgaviysl..............eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfa 67 
                                       ++l+f++++                 + + e+ +fld lYfs +++t       +p++ + r++++++ +lG +l+a
  gi|330508214|ref|YP_004384642.1| 211 FILLFAFLYWQGmgivveplngseylQGQNEELTFLDNLYFSAMVFTAKTQVKWYPVGVY-RYLATLEFILGWLLLA 286
                                       333333333333777778889999963337899**************9999999999888.**************** PP

                                       HHHHHHHHHHH CS
                       Ion_trans_2  68 lflavlgkvlt 78 
                                       lfl  lg+ ++
  gi|330508214|ref|YP_004384642.1| 287 LFLVSLGRTMI 297
                                       ****9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); 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:                         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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2133.51
//
Query:       gi|330508215|ref|YP_004384643.1|  [L=400]
Description: phosphoglycerate kinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.5e-111  373.0   0.2   1.7e-111  372.8   0.2    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 !  372.8   0.2  9.4e-116  1.7e-111       1     377 [.       1     381 [.       1     382 [. 0.93

  Alignments for each domain:
  == domain 1  score: 372.8 bits;  conditional E-value: 9.4e-116
                                       GGGS--TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHH CS
                               PGK   1 vkdldlkgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLse 77 
                                       ++d++l++krvlvRvDfN+p++ +g+i dd+ri+++l+T+++l  ++++vvl++H++r  g+k+ ++++++a+  ++
  gi|330508215|ref|YP_004384643.1|   1 MEDVKLDNKRVLVRVDFNSPMDPSGNILDDKRIKSHLDTLRAL--EDCRVVLMAHQSRA-GKKDYTTMEAHARSATR 74 
                                       689****************************************..89***********8.899************** PP

                                       HHTT-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H.......HHHHHHHHT-SEEEE--GGGTTS- CS
                               PGK  78 llgkeVkfvedvvgeeveeaiaelkegevllLeNvrfykeEeknde.......elakklasladvyVnDAFgtahra 147
                                       ll ++V++++d++g++++eai++l +gevllLeN+rfy+eE+ n++       +++k+la l+d+++nDAF+++hr+
  gi|330508215|ref|YP_004384643.1|  75 LLRRDVAYIDDIFGSHAREAIRSLMPGEVLLLENTRFYAEENMNRTpadhaksHMVKRLAPLFDLFINDAFAVSHRS 151
                                       *****************************************9875556666556*********************** PP

                                       -TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHHHHHH CS
                               PGK 148 haStvgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgmantFlk 222
                                       h+S+vg+++vl+++aGllm+kE++al+k l+  e+p ++ lGG+k +d ikvien+l++   dk+++ G++a +Fl 
  gi|330508215|ref|YP_004384643.1| 152 HCSVVGFTEVLPSIAGLLMDKEITALDKGLKGDEHPTIYSLGGTKADDSIKVIENVLRRGgaDKILTSGVVATVFLM 228
                                       ***********99*********************************************9888*************** PP

                                       HTT-B-T...TSS--G....GGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EEEEE-HH CS
                               PGK 223 aqgleig...kslvee....dklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipedemalDigpk 292
                                       a+g+++g   +++ve+    +++ +a++ll+++    +ki +pvDv+++k+    e+  v+v+a+++d  + Dig +
  gi|330508215|ref|YP_004384643.1| 229 AAGINVGeanRKFVEDqeylEQIPVAAKLLAEYP---DKIAMPVDVALNKN---GERIDVAVSALSNDLPIADIGLE 299
                                       *******443344455444446999999999998...89**********83...2234568999************* PP

                                       HHHHHHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSSH CS
                               PGK 293 tielfaeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGGg 369
                                       ti  +++++k+a++ v+nGp+G+fe ekf+ GT +++ka ae+ +  +si+GGg+s+aa+e+lgl++k+shvS GGg
  gi|330508215|ref|YP_004384643.1| 300 TIVDYSKELKDARVTVMNGPAGIFEQEKFKLGTSELLKASAES-D--YSIAGGGHSVAAIEQLGLESKFSHVSMGGG 373
                                       ******************************************7.4..9***************************** PP

                                       HHHHHHCT CS
                               PGK 370 AsLelLeg 377
                                       As+++L+g
  gi|330508215|ref|YP_004384643.1| 374 ASITYLSG 381
                                       ******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3011.47
//
Query:       gi|330508216|ref|YP_004384644.1|  [L=312]
Description: phosphoesterase, RecJ domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-12   47.5   0.0    2.6e-12   46.9   0.0    1.3  1  DHH       DHH family
    4.2e-09   36.9   3.2    1.3e-08   35.4   3.4    1.8  2  DHHA1     DHHA1 domain


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   2.9e-16   2.6e-12       2     101 .]      18     150 ..      17     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 2.9e-16
                                       EEEE-ECSSSHHHHHHHHHHHH.......................................CECS--TCGGCGCCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxxx RF
                               DHH   2 ilivghknpDtDsigSaialan.......................................llvDhneksqavegea 39 
                                       +l ++h+n D D+igSa+ala                                        ++vD++ + q      
  gi|330508216|ref|YP_004384644.1|  18 VLYLCHRNADPDAIGSAFALAGafggtvgaiddlsrigealsdiigahilidpseegwdliVVVDTSVQLQLG---- 90 
                                       56679*****************999999998888888888888888888888888888866688887777766.... PP

                                       CCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  40 keeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                       + +  +   iDHH+ +  +++    ++++ p+ staeiv+++l++++ ++s+e+a  l++gi
  gi|330508216|ref|YP_004384644.1|  91 RIQLARYGLIDHHQDE-GLTHK-AEFYIQRPAKSTAEIVWKILKDNGRQPSREMALGLMAGI 150
                                       45888999*******8.44444.568999***************************999998 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.2     1e+04      29      59 ..      10      34 ..       4      38 .. 0.66
   2 !   35.4   3.4   1.4e-12   1.3e-08      49     122 ..     205     292 ..     156     311 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.2
                                      HHHHTCEEECTCEEEEEECHCCHHHHHHHHH CS
                             DHHA1 29 ellekaeevkgvkvlvaevgeewdagalgia 59
                                      +++++      ++vl+     ++d++a+g+a
  gi|330508216|ref|YP_004384644.1| 10 SIVSR-----YKNVLYLCH-RNADPDAIGSA 34
                                      45554.....556666666.88999999887 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 1.4e-12
                                       CCHHH.HHHHHHHHHHHT........HGBT.TCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCE CS
                             DHHA1  49 eewda.galgiaadklks........klkk.pvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggG 111
                                       +++++ g   iaa++++s         ++  + ++fva+  gd+v++sars+++    g++++ ++ ++ ++ gg G
  gi|330508216|ref|YP_004384644.1| 205 AKIERrGEWLIAASRINSfegssaaaLIDLgADVAFVAGRHGDRVRISARSSRKaanaGLNLNQILGDIGRAHGGDG 281
                                       4444445556666666665555444333455899******************99*********************** PP

                                       EEETCEEEEEE CS
                             DHHA1 112 GGHdlAaGagi 122
                                       GGH  Aa +  
  gi|330508216|ref|YP_004384644.1| 282 GGHSSAASFDA 292
                                       ***99997555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2365.02
//
Query:       gi|330508217|ref|YP_004384645.1|  [L=211]
Description: hypothetical protein MCON_2357 [Methanosaeta concilii GP6]
Scores for complete sequence (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   70.3   0.0    1.8e-19   69.8   0.0    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00036   20.0   0.0     0.0005   19.6   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
     0.0029   17.1   0.0     0.0048   16.4   0.0    1.4  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 !   69.8   0.0   3.1e-23   1.8e-19      16     151 ..      10     185 ..       2     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 3.1e-23
                                       EETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE..................... CS
                      Pribosyltran  16 arlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes............. 79 
                                        +++a +l+ + g+  vv + +rgGv++++++a++L++p++ +  +k   +gs e a  ++ e              
  gi|330508217|ref|YP_004384645.1|  10 GKALAGALDGFIGQDSVVYALPRGGVVLGYEVARHLDAPMDLLITRKIGYPGSRECAVCAISEDgemicdslgasrl 86 
                                       5677778888788899***************************************9998888889************ PP

                                       ..........................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHH CS
                      Pribosyltran  80 ..........................rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpate 130
                                                                 r++ +  gk  ++VDD+++tG T+l a+  Lk++ p+++ +av+v  ++ +
  gi|330508217|ref|YP_004384645.1|  87 dpawlgvraeeemeeanrrrraylegRPPLNAGGKVAIVVDDGMATGLTVLLAIMVLKKQHPKSIVVAVPVSSMEAA 163
                                       ***************************************************************************** PP

                                       HHHHHH-TTS......EEEEEE CS
                      Pribosyltran 131 eevdknakrvfsls.pdnfvav 151
                                       e+ + +a++++ l  p +f  v
  gi|330508217|ref|YP_004384645.1| 164 EKIRREADELVALDvPPDFCSV 185
                                       **********999988877655 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   8.3e-08    0.0005     120     174 ..     119     171 ..      91     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.3e-08
                           UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefp 174
                                         + ++++D  +aTG ++  ai +Lk+++   ++I+v+  ++s e+++++ +e  
  gi|330508217|ref|YP_004384645.1| 119 GGKVAIVVDDGMATGLTVLLAIMVLKKQH--PKSIVVAVPVSSMEAAEKIRREAD 171
                                       66789**********************54..689****99****99999988766 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   8.1e-07    0.0048     121     173 ..     120     172 ..      96     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.1e-07
                          PRTase_2 121 akelvLvDDEistGktalnliralqeklprkryvvvslvdwrseedeaafaal 173
                                        k  ++vDD ++tG t+l  i  l++++p++ +v v +  +  +e+ ++ a+ 
  gi|330508217|ref|YP_004384645.1| 120 GKVAIVVDDGMATGLTVLLAIMVLKKQHPKSIVVAVPVSSMEAAEKIRREADE 172
                                       456689************************99999999888888865555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1482.54
//
Query:       gi|330508218|ref|YP_004384646.1|  [L=823]
Description: hypothetical protein MCON_2358 [Methanosaeta concilii GP6]
Scores for complete sequence (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   25.0   0.0    2.4e-05   23.9   0.0    1.4  1  CHAT           CHAT domain
    0.00091   18.5   0.0     0.0015   17.8   0.0    1.2  1  Peptidase_C25  Peptidase family C25


Domain annotation for each model (and alignments):
>> CHAT  CHAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.7e-09   2.4e-05     137     271 ..     671     803 ..     661     813 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.7e-09
                                       xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx RF
                              CHAT 137 sals.rryrvvHfatHgvfnanpplqsglvlsaenseedglLtaeeilelnldg...aelVvLsACqtglgevidge 209
                                       + l+ ++ ++++f +Hg  +   +  ++l   +++   +++++++ + ++n +      lV+++ C+t      d e
  gi|330508218|ref|YP_004384646.1| 671 NNLKsPKSHLIYFYCHGGIS--TNNIPYLQVGDGTG--NDFIDGSNLNAFNIEWiepKPLVFINGCHTT---ALDPE 740
                                       44566899*********999..77788999976666..557777777776555555678**********...5599* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                              CHAT 210 gvlgLaralllaGarsviaslwpVddeatalLmkrfyqnlla.glskaeALreaqlkllsgkr 271
                                         + L+  ++++G+  vi++   + +  ++ ++++   ++l+ + s+ +A r a+lkll++ +
  gi|330508218|ref|YP_004384646.1| 741 MAINLVADFVRSGSAGVIGTETTIFEPLACSFAEACLGHFLKdKSSIGDAIRMARLKLLKEYN 803
                                       ******************************************9999************99865 PP

>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.7e-07    0.0015     240     353 ..     679     801 ..     660     814 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-07
                                       SEEEEES-EETTEE...........TTTTEEHHHHHT---TT..--EEEEEESSSTT-TTSSS-..-HHHHHHHSTT CS
                     Peptidase_C25 240 lfvnytGHGsetaw...........adeslstndisaltntn..klpiaitaaCltgafdeetkr.sfgeklvlnan 302
                                       +++ ++ HG+ +             +++ ++ ++++a++       p+++ ++C+t+a+ ++++  ++  ++v   +
  gi|330508218|ref|YP_004384646.1| 679 HLIYFYCHGGISTNnipylqvgdgtGNDFIDGSNLNAFNIEWiePKPLVFINGCHTTAL-DPEMAiNLVADFV---R 751
                                       55666677777654455555544444444544444433332244679************.6665568888888...9 PP

                                       SSEEEEEEESS---SS--SHHHHHHHHHHHHHHH...T-S-SS-HHHHHHH CS
                     Peptidase_C25 303 gGavayigatrlgysgvndrlsraffealfadaartlGealllaknellet 353
                                        G  ++ig+  ++++     + +a +++ + d+  ++G+a+++a+ +ll++
  gi|330508218|ref|YP_004384646.1| 752 SGSAGVIGTETTIFEPLACSFAEACLGHFLKDKS-SIGDAIRMARLKLLKE 801
                                       ******************************9999.5*********999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (823 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 5226.84
//
Query:       gi|330508219|ref|YP_004384647.1|  [L=136]
Description: hypothetical protein MCON_2359 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.05   13.8   0.9       0.05   13.8   0.9    2.0  2  DUF3180   Protein of unknown function (DUF3180)
       0.21   11.8   2.1       0.39   11.0   2.2    1.5  1  DUF2304   Uncharacterized conserved protein (DUF2304)


Domain annotation for each model (and alignments):
>> DUF3180  Protein of unknown function (DUF3180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.9   5.5e-06      0.05      78     122 ..      12      56 ..       8      58 .. 0.72
   2 ?    1.1   0.1     0.045   4.1e+02      78      97 ..      64      83 ..      62      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-06
                           DUF3180  78 lvGAllaGvyaGllvyll.ragelpaaaedllaavvavlaavalvv 122
                                       l+GAll+G  +G  vyl+ r+ + +++ +dl  a+++v+++ a+++
  gi|330508219|ref|YP_004384647.1|  12 LIGALLFGTIIGWYVYLInRYRKGDVQLSDLA-ALIGVIGGSAVLA 56 
                                       89****************66666666666665.5556665555443 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.045
                           DUF3180 78 lvGAllaGvyaGllvyllra 97
                                      l+GA   G+ +G++ y+l+ 
  gi|330508219|ref|YP_004384647.1| 64 LFGAYGIGLAIGFFSYFLSL 83
                                      7899999*****99999954 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.2   4.3e-05      0.39       6      76 ..      17      86 ..       6      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.3e-05
                           DUF2304  6 liivsvllllliirlvrkkklkleysllwlllalilivlslfpqiltvlanllGvgrgtnllfllgivfll 76
                                      l+  ++   +++i+++rk  ++l++  + + ++ + +vl+lf +    l  + G+g ++ ++ +++ ++++
  gi|330508219|ref|YP_004384647.1| 17 LFGTIIGWYVYLINRYRKGDVQLSDLAALIGVIGGSAVLALFDRE-GGLFGAYGIGLAIGFFSYFLSLIVM 86
                                      344456667899******************************843.4444566666666666665555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 974.07
//
Query:       gi|330508220|ref|YP_004384648.1|  [L=96]
Description: hypothetical protein MCON_2360 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.67   10.4   2.7        3.2    8.2   1.7    2.0  2  FUN14     FUN14 family


Domain annotation for each model (and alignments):
>> FUN14  FUN14 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.7   0.00018       3.2       1      33 [.       9      43 ..       9      55 .. 0.76
   2 ?    1.2   0.0     0.028   4.9e+02      21      43 ..      57      79 ..      49      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00018
                                      xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                             FUN14  1 igiGaviGlvtGfalkkvgKlaa..iavGggllll 33
                                      +giG++ G+ +G +  k+ + ++  ia+G + l++
  gi|330508220|ref|YP_004384648.1|  9 MGIGLIWGWWIGSLSGKITRPLFdgIAAGAATLMF 43
                                      589*****************998334444444444 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.028
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                             FUN14 21 laaiavGggllllqilasqgyik 43
                                      ++++++Gg  l l ++ ++++i+
  gi|330508220|ref|YP_004384648.1| 57 VLFFCAGGLTLYLHLAWRRELID 79
                                      78899999999999999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 705.48
//
Query:       gi|330508221|ref|YP_004384649.1|  [L=176]
Description: hypothetical protein MCON_2361 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1246.07
//
Query:       gi|330508222|ref|YP_004384650.1|  [L=298]
Description: hypothetical protein MCON_2362 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.04   13.4   0.0      0.076   12.5   0.0    1.4  1  FAP206        Domain of unknown function
       0.08   13.1   5.1       0.16   12.2   5.1    1.4  1  ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transpor
       0.12   11.2   0.1       0.13   11.0   0.1    1.1  1  DUF2207       Predicted membrane protein (DUF2207)
       0.47   10.7   4.4       0.95    9.7   4.4    1.4  1  DUF3784       Domain of unknown function (DUF3784)
        2.6    8.1   5.0        5.2    7.1   0.4    2.3  2  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.1e-05     0.076      64     110 ..      40      86 ..      35      89 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                            FAP206  64 lrilledveksaeeveellkrfeaeleklketvksktavpkeqVyPk 110
                                       +++l+ +v++s++++e++   f   l++lk+ +k++ + p  +++P+
  gi|330508222|ref|YP_004384650.1|  40 VKFLNPKVITSENKIEVMGPAFLISLAELKKAIKNRYKTPGRNIFPE 86 
                                       678999****************************************6 PP

>> ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   5.1   4.5e-05      0.16       8      48 ..     225     263 ..     222     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.5e-05
                      ATPase_gene1   8 GielvapillggllGyw..LDkkfgtspwfliiglllGlaaGf 48 
                                       G +++++ l+++l+G +  +++++    +f+ii++++G+a+++
  gi|330508222|ref|YP_004384650.1| 225 GNTMAVISLICLLIGAFslIERRL----FFFIILFICGVALAV 263
                                       779**************9899988....9***********985 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   3.7e-05      0.13     326     431 ..     169     265 ..      59     276 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.7e-05
                           DUF2207 326 Lfdkseegkslkeikkyakkskkkakkfkkalkkwksavkkkergyfdkk.gkkklkklsalglgliilglililla 401
                                         d+++ +  +++  +   ++k + ++++ ++k+++  v+++  + ++++ g k+ +  ++ +++     li++l++
  gi|330508222|ref|YP_004384650.1| 169 TDDGAQFD--FENPSDVMGTDKRLEESMSINMKSIMLIVERVDDNTIQTTsGLKHVFLGNTMAVIS----LICLLIG 239
                                       44333333..55555555556669999**************4444444440333333333333333....3333333 PP

                           DUF2207 402 llllvlllvfllilllillliaiivlllfs 431
                                       +++    l+   ++++i+l+i+ ++l++++
  gi|330508222|ref|YP_004384650.1| 240 AFS----LIERRLFFFIILFICGVALAVAR 265
                                       333....44444444444444444444443 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.4   0.00026      0.95      45      84 ..     223     262 ..     221     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00026
                           DUF3784  45 fmgivllligilflllgllsaiesealliialiviiiivi 84 
                                       f g+ + +i++++ll+g++s ie+  ++ i+l+++ +++ 
  gi|330508222|ref|YP_004384650.1| 223 FLGNTMAVISLICLLIGAFSLIERRLFFFIILFICGVALA 262
                                       789****************888888888876666666554 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 ?    7.1   0.4    0.0015       5.2      10      25 ..     223     238 ..     220     244 .. 0.87
   2 ?    2.6   0.4     0.038   1.4e+02      19      35 ..     249     266 ..     247     276 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0015
                            OppC_N  10 FkrNklAvvglvilll 25 
                                       F+ N +Av++l+ ll+
  gi|330508222|ref|YP_004384650.1| 223 FLGNTMAVISLICLLI 238
                                       889**********996 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.038
                            OppC_N  19 glvilllllliaif.aPl 35 
                                        ++i+l++  +a+  a +
  gi|330508222|ref|YP_004384650.1| 249 FFFIILFICGVALAvARY 266
                                       578888888888662344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); 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:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2150.57
//
Query:       gi|330508223|ref|YP_004384651.1|  [L=293]
Description: SPFH domain/band 7 family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-27   95.8   1.4      4e-27   95.4   1.4    1.1  1  Band_7    SPFH domain / Band 7 family
  ------ inclusion threshold ------
      0.041   13.6   0.1      0.067   12.9   0.1    1.3  1  Band_7_1  SPFH domain-Band 7 family
      0.076   13.2   7.8       0.04   14.1   5.8    1.5  2  IFT20     Intraflagellar transport complex B, subunit 20
       0.11   12.1   0.1       0.16   11.6   0.1    1.3  1  AMMECR1   AMMECR1


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 !   95.4   1.4   8.8e-31     4e-27       2     178 .]      51     230 ..      50     232 .. 0.94

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 8.8e-31
                            Band_7   2 iieegevgvvvrfGklsr.vlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrv.pddap 76 
                                       ii++g+vgv  rfG +s+ vl pG+ ++ P ++sv+++++++q+++ ++   ++t++gl++++d++v +++ p +ap
  gi|330508223|ref|YP_004384651.1|  51 IIPAGHVGVQDRFGVVSDtVLSPGFNLKDP-LTSVHQMNTQTQQIEYKQVTGTLTREGLEINLDSSVLWHLdPAKAP 126
                                       89****************************.9*****************88899*****************999999 PP

                            Band_7  77 klvaaveresanldnlirrvlesalrevisemtleellsnr.eelaeelknelneqlrkyGvevldvritdidpppe 152
                                        ++++v  + +++d+ +++ + + lr+ i ++t+e+++ n+  e++++++++l+ +l++ G+ +++v ++ i +p e
  gi|330508223|ref|YP_004384651.1| 127 DIFRSV--RGDYVDTKLTPSFMGLLRAEIKKYTAEDIYTNKsTEIQADVEKQLKMELDRTGIIIERVWLRGIFLPTE 201
                                       999999..******************************9966*********************************** PP

                            Band_7 153 vaqalaakqaaeaea...qaeiaraeaea 178
                                       ++ a+  kq+ +++a   q  i+++e+ea
  gi|330508223|ref|YP_004384651.1| 202 LQVAITTKQQKQQQAqqmQFTIQQSEKEA 230
                                       ***************87766666666654 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 ?   12.9   0.1   1.5e-05     0.067     160     208 ..     163     211 ..     137     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                          Band_7_1 160 aakseelaeklkealkeelaeyGlelekleienislpeevekaldkras 208
                                       + ks+e+ + ++++lk el++ G+ +e++ ++ i lp e++ a++++ +
  gi|330508223|ref|YP_004384651.1| 163 TNKSTEIQADVEKQLKMELDRTGIIIERVWLRGIFLPTELQVAITTKQQ 211
                                       456789999**********************************998876 PP

>> IFT20  Intraflagellar transport complex B, subunit 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.5   1.1e+04      48      60 ..      86      98 ..      83     108 .. 0.60
   2 ?   14.1   5.8     9e-06      0.04      29     105 ..     160     240 ..     149     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.5
                             IFT20 48 vleelakkvekeK 60
                                      +++++ +++e ++
  gi|330508223|ref|YP_004384651.1| 86 QMNTQTQQIEYKQ 98
                                      4555566665554 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 9e-06
                             IFT20  29 keFvkkinefqklvkeliev.leelakkvekeKlkAigarnllk...seakqreaeqqqlqaliaekkaeleRlrve 101
                                       + +++k +e q+ v++ +++ l++ +  +e+  l+ i   + l+   + ++q++++ qq+q +i++ ++e eRl +e
  gi|330508223|ref|YP_004384651.1| 160 DIYTNKSTEIQADVEKQLKMeLDRTGIIIERVWLRGIFLPTELQvaiTTKQQKQQQAQQMQFTIQQSEKEAERLVIE 236
                                       5588999999998888777659999999**********9999984334566677778889999************99 PP

                             IFT20 102 lesL 105
                                        + +
  gi|330508223|ref|YP_004384651.1| 237 AKGI 240
                                       8765 PP

>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.6e-05      0.16     100     138 ..     174     217 ..     140     238 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.6e-05
                                       GGG..--TTT-EEEEEETTEEEEE-T...HHHHHTT--HHHHHH CS
                           AMMECR1 100 led..levgkhGliiekgsrsatlLP...qvaveqgwdkeefla 138
                                       +++  +e+ + G+iie+   ++++LP   qva  ++ +k+++ +
  gi|330508223|ref|YP_004384651.1| 174 EKQlkMELDRTGIIIERVWLRGIFLPtelQVAITTKQQKQQQAQ 217
                                       233459999*****************544455555554444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1767  (0.0985554); expected 358.6 (0.02)
Passed bias filter:                      919  (0.0512577); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 1986.98
//
Query:       gi|330508224|ref|YP_004384652.1|  [L=150]
Description: transposase, IS200-like MITE [Methanosaeta concilii GP6]
Scores for complete 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-29  100.0   0.0    1.1e-28   99.7   0.0    1.1  1  Y1_Tnp    Transposase IS200 like


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.0   6.2e-33   1.1e-28       2     121 .]      12     132 ..      11     132 .. 0.93

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 6.2e-33
                            Y1_Tnp   2 snlkyhivlvtkyRrkvltge.veerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgassr 77 
                                       +++ yh+v+ +kyRrk+l++    + +k +++ei e++ +++ ++ ++ DHvH++v + p++s+sk+++ +k+ ++r
  gi|330508224|ref|YP_004384652.1|  12 YKIRYHMVFSIKYRRKLLQDIdRINYIKFVCSEIGERYYFDFDAIGTDGDHVHIFVGAAPRYSPSKVMQIVKSITAR 88 
                                       7899*****************55566666779********************************************* PP

                            Y1_Tnp  78 linkefpelkkkklkkeslWqrgYfvstvgea.sletvkrYIenq 121
                                        ++k++pe+kk+ l+++++W++g +v tvg+   ++t+++Y+e+q
  gi|330508224|ref|YP_004384652.1|  89 EFFKKYPEVKKQ-LWGGEFWSDGGYVGTVGDGvMADTIRNYVETQ 132
                                       ********9988.56688************877**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1078.37
//
Query:       gi|330508225|ref|YP_004384653.1|  [L=314]
Description: transposase, IS4 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-23   81.4   0.0    6.3e-23   80.6   0.0    1.4  1  DUF772       Transposase domain (DUF772)
      3e-17   63.0   0.7    6.5e-17   61.9   0.7    1.6  1  DDE_Tnp_1    Transposase DDE domain
    4.6e-06   26.4   0.3    1.6e-05   24.6   0.0    1.9  2  DDE_Tnp_4    DDE superfamily endonuclease
    1.9e-05   24.7   0.1    4.9e-05   23.4   0.1    1.6  1  DDE_Tnp_1_3  Transposase DDE domain
  ------ inclusion threshold ------
      0.055   14.1   0.0       0.23   12.1   0.0    1.9  2  DUF3502      Domain of unknown function (DUF3502)
        0.1   12.4   0.1       0.29   11.0   0.1    1.8  1  DUF5315      Disordered region of unknown function (DUF5315)


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 !   80.6   0.0   2.1e-26   6.3e-23       1      72 [.      51     122 ..      51     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 2.1e-26
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp++++ +mlk l++q+ly+lSd++le+++ +++sfr flg     ++vpd +t+++fR+rl+e   ++++++e
  gi|330508225|ref|YP_004384653.1|  51 GRPNLDVIVMLKSLFIQQLYSLSDEQLEREIADRISFRVFLGT---TETVPDSTTIWKFRERLAEtgaDQKIWAE 122
                                       9*****************************************5...489****************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 !   61.9   0.7   2.2e-20   6.5e-17       9     213 ..     140     301 ..     132     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 2.2e-20
                         DDE_Tnp_1   9 vDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                        Dat+++    +                +d+ w +kg k+++gyklh a+d + gli ++++t++nvhds++  +  
  gi|330508225|ref|YP_004384653.1| 140 QDATFITSDPGHakadtprgdeaktrrsKDGAWAKKGTKSFFGYKLHDAMDEKFGLIRRIEVTAANVHDSQVDLA-- 214
                                       5777777555557777778888888888999***************************************98555.. PP

                         DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskk 146
                                       +     +g + +aD+GY++a++  + +                            +rk+ r+++l+ +++ rnk   
  gi|330508225|ref|YP_004384653.1| 215 E-----EGEVRYADKGYSGAKTKGYDA---------------------------AMRKATRGHPLSYKDEMRNK--- 256
                                       6.....9***********888877766...........................79******************... PP

                         DDE_Tnp_1 147 ekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllaln 213
                                                             +++++R+ +Er+ +++k +++ +++ + + +rv+ +++++ +++n
  gi|330508225|ref|YP_004384653.1| 257 ----------------------RISSKRSPVERFYAFIKCVCKAGHVAVTTVARVRVKMMITGIVFN 301
                                       ......................***************************************999988 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.38   1.1e+03      55      95 ..     116     151 ..     113     171 .. 0.63
   2 !   24.6   0.0   5.4e-09   1.6e-05      71     128 ..     211     273 ..     186     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.38
                         DDE_Tnp_4  55 Dkeilens.gllkalkeavkpgdvilaDkgFklsekllvpyk 95 
                                       D++i+++  + l+a+k  +k ++ i+ D+ F +s+    p +
  gi|330508225|ref|YP_004384653.1| 116 DQKIWAEMqRQLDAMK--LKVQKGIMQDATFITSD----PGH 151
                                       6777766546677766..45558889999998888....333 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 5.4e-09
                         DDE_Tnp_4  71 a..vkpgdvilaDkgFklse..kl.lvpykkkkkkqlseeevefnraiasarihvErvigrlk 128
                                           ++g+v  aDkg+ +++   +   + k +++++ls +++ +n++i+s r  vEr+ + +k
  gi|330508225|ref|YP_004384653.1| 211 VdlAEEGEVRYADKGYSGAKtkGYdAAMRKATRGHPLSYKDEMRNKRISSKRSPVERFYAFIK 273
                                       1445688999********99432223444449***************************9999 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 !   23.4   0.1   1.6e-08   4.9e-05      33     149 ..     173     280 ..     161     285 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.6e-08
                       DDE_Tnp_1_3  33 akrGkssmGWfyGfkLhliindk.GeilavkltpgnvdDrepveelakellgklfaDkgyiskklaeelleegieli 108
                                       a   k  +  f+G+kLh  +++k G i ++++t++nv+D +   +la+e  +  +aDkgy + k        + ++ 
  gi|330508225|ref|YP_004384653.1| 173 A---KKGTKSFFGYKLHDAMDEKfGLIRRIEVTAANVHDSQV--DLAEE-GEVRYADKGYSGAKTK----GYDAAMR 239
                                       3...4444559******9999883556679*********875..36666.4566******876532....2344455 PP

                       DDE_Tnp_1_3 109 tklrknmkkkllslldkllLrkrslietvndelknisqieh 149
                                         +r +  +   ++ +k + +krs +e  +  +k +++  h
  gi|330508225|ref|YP_004384653.1| 240 KATRGHPLSYKDEMRNKRISSKRSPVERFYAFIKCVCKAGH 280
                                       55555555555666666667777777777777776666655 PP

>> DUF3502  Domain of unknown function (DUF3502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.8e-05      0.23     100     127 ..     101     129 ..      81     131 .. 0.87
   2 ?   -0.9   0.0      0.79   2.4e+03      35      96 ..     237     299 ..     205     310 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.8e-05
                           DUF3502 100 etlpkfneklkaaGid.kviaelqkQlda 127
                                       +t+ kf+e+l + G d k+ ae+q+Qlda
  gi|330508225|ref|YP_004384653.1| 101 TTIWKFRERLAETGADqKIWAEMQRQLDA 129
                                       67889*********9758**********8 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.79
                           DUF3502  35 firyllegepedkwekvkefneeakaspalgF.tfDsspvkteiaalsnvveeykkaletGlv 96 
                                        +r+ ++g+p +  +++++   ++k sp+  F +f +   k+   a+++v    +k + tG+v
  gi|330508225|ref|YP_004384653.1| 237 AMRKATRGHPLSYKDEMRNKRISSKRSPVERFyAFIKCVCKAGHVAVTTVARVRVKMMITGIV 299
                                       344444555555555566665667777777762344444555566666666666666666655 PP

>> DUF5315  Disordered region of unknown function (DUF5315)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   9.8e-05      0.29      12      36 ..     115     141 ..     107     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.8e-05
                           DUF5315  12 rqDalWaeid.tLddVklsAeeg.kkt 36 
                                          ++Wae++ +Ld  kl  ++g +++
  gi|330508225|ref|YP_004384653.1| 115 ADQKIWAEMQrQLDAMKLKVQKGiMQD 141
                                       56799*************999985544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); 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:                         6  (0.000334653); expected 0.2 (1e-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 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2313.50
//
Query:       gi|330508226|ref|YP_004384654.1|  [L=379]
Description: hypothetical protein MCON_2370 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2846.69
//
Query:       gi|330508227|ref|YP_004384655.1|  [L=215]
Description: hypothetical protein MCON_2371 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0016   18.5   5.6      0.096   12.8   0.2    2.3  2  F_actin_bind    F-actin binding
  ------ inclusion threshold ------
      0.011   15.6   1.0      0.011   15.6   1.0    2.1  2  YkuI_C          EAL-domain associated signalling protein doma
      0.022   14.9   3.4      0.022   14.9   3.4    3.2  3  DivIVA          DivIVA protein
      0.028   13.7  10.3      0.016   14.6   6.1    1.9  2  CorA            CorA-like Mg2+ transporter protein
      0.032   14.7  20.3      0.082   13.4  11.9    2.5  2  T3SSipB         Type III cell invasion protein SipB
      0.049   13.9   1.2      0.049   13.9   1.2    3.5  4  HalX            HalX domain
      0.064   13.3   9.2      0.062   13.3   1.4    2.2  2  DUF1664         Protein of unknown function (DUF1664)
       0.13   12.4  24.5      0.056   13.6   6.2    2.1  2  UPF0242         Uncharacterised protein family (UPF0242) N-te
       0.19   11.8  10.8      0.035   14.1   2.1    2.3  2  Laminin_II      Laminin Domain II
       0.21   12.1   3.6        3.2    8.3   0.2    2.8  3  NPV_P10         Nucleopolyhedrovirus P10 protein
       0.23   11.8  12.2         17    5.8  12.2    2.7  1  Syntaxin_2      Syntaxin-like protein
       0.25   11.6  21.1       0.15   12.3   2.7    3.3  3  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
       0.33    9.4   9.4        1.4    7.4   9.4    1.8  1  FUSC            Fusaric acid resistance protein family
        0.4   11.0   4.0        5.2    7.4   0.2    2.9  2  DUF948          Bacterial protein of unknown function (DUF948
       0.42   11.0  26.7        0.6   10.5   7.4    2.7  2  DUF4200         Domain of unknown function (DUF4200)
       0.49   10.5  13.7       0.36   10.9   2.8    2.2  2  DUF848          Gammaherpesvirus protein of unknown function 
       0.51    9.5  15.0       0.87    8.8   5.3    2.1  2  TMPIT           TMPIT-like protein
       0.53   11.0  13.7       0.27   12.0   3.1    2.7  2  Occludin_ELL    Occludin homology domain
       0.57   10.8   6.3    2.5e+02    2.3   6.3    3.0  1  YtxH            YtxH-like protein
       0.61   10.3   8.8        0.7   10.1   2.3    2.6  2  OrfB_IS605      Probable transposase
       0.84   10.0   9.2        1.3    9.4   2.4    2.4  2  DUF2935         Domain of unknown function (DUF2935)
        1.4    9.3  13.6        1.7    9.0   4.5    3.4  3  CCDC-167        Coiled-coil domain-containing protein 167
        1.7    8.8  13.9       0.65   10.1   1.0    2.9  2  DUF148          Domain of unknown function DUF148
          2    8.4  11.6        6.1    6.8   1.5    3.2  4  Prefoldin       Prefoldin subunit
        2.5    7.1  19.9        1.3    8.1   8.5    2.0  2  Atg14           Vacuolar sorting 38 and autophagy-related sub
        3.6    7.4   9.0        9.5    6.1   0.8    3.2  3  Synaptobrevin   Synaptobrevin
        5.8    6.1  21.4        1.1    8.5   9.1    2.1  2  DUF3450         Protein of unknown function (DUF3450)
        7.9    6.9  10.7          1    9.8   0.9    2.1  2  DUF3280         Protein of unknown function (DUF2380)


Domain annotation for each model (and alignments):
>> F_actin_bind  F-actin binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   1.1    0.0047         3      30     102 ..      42     111 ..      27     114 .. 0.75
   2 !   12.8   0.2   0.00015     0.096       5      56 ..     127     175 ..     123     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0047
                      F_actin_bind  30 qesaqllqlldkvenlhssCsgyvdsipphakFaFrellsrLesqsreLrsavgsknssenekllqdlqstvk 102
                                       q ++ql+  +   ++l+++C++ v + + +   +  el+s+L ++ +++r  +  +n  + e+ ++dl   ++
  gi|330508227|ref|YP_004384655.1|  42 QATEQLIDTAQDFKKLRDECNKNVAQSKRKWD-ECNELVSQLYQKIDSIRKQH--SNHRAGERSITDLRREID 111
                                       34566777778888899999988776554444.799**************665..477777888888877765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00015
                      F_actin_bind   5 kesiLelvelleaalsnlkesvsssqesaqllqlldkvenlhssCsgyvdsi 56 
                                        +++++ + +l+a+++  ke++  ++   ++ +lld+ ++l+++ s+y d++
  gi|330508227|ref|YP_004384655.1| 127 EKQLVNKIAALQAEFNGRKEELEKTE---EMKKLLDEAQSLRDQASSYHDKV 175
                                       67899999*************66666...667******************94 PP

>> YkuI_C  EAL-domain associated signalling protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   1.0   1.7e-05     0.011       2      70 ..      48     116 ..      47     119 .. 0.92
   2 ?    2.5   1.1      0.18   1.2e+02      22      68 ..     140     186 ..     122     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                            YkuI_C   2 verdllkdklkkefhqfiayekkklealyelseklkkrlkellkklkkaedydelllklakeldevafr 70 
                                       +++ +  +kl++e+++ +a+ k+k ++  el  +l+++++++ k+  +++  +  +++l +e+d + fr
  gi|330508227|ref|YP_004384655.1|  48 IDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQKIDSIRKQHSNHRAGERSITDLRREIDYLEFR 116
                                       566666679*******************************************************99998 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.18
                            YkuI_C  22 ekkklealyelseklkkrlkellkklkkaedydelllklakeldeva 68 
                                       e +  ++ +e +e++kk l+e+ +  ++a++y++ ++++a+  +e+ 
  gi|330508227|ref|YP_004384655.1| 140 EFNGRKEELEKTEEMKKLLDEAQSLRDQASSYHDKVINFAEMAQECH 186
                                       55556677889999999999999999999999999999888777765 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   3.6       0.6   3.8e+02      36     112 ..      53      82 ..       7     114 .. 0.56
   2 ?    3.3   0.6      0.13        83      35      67 ..     128     160 ..     108     161 .. 0.89
   3 ?   14.9   3.4   3.4e-05     0.022      32      87 ..     152     207 ..     148     214 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.6
                                       HHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  36 allkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeakki 112
                                       ++ k ++e +++v                                               +++++  +e +e + ++
  gi|330508227|ref|YP_004384655.1|  53 DFKKLRDECNKNV-----------------------------------------------AQSKRKWDECNELVSQL 82 
                                       2222222222222...............................................22222233334444444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXX CS
                            DivIVA  35 eallkeneelkekvkeleeklkeykeleetLkk 67 
                                       ++l+++ ++l+++ +  +e+l++ +e+++ L +
  gi|330508227|ref|YP_004384655.1| 128 KQLVNKIAALQAEFNGRKEELEKTEEMKKLLDE 160
                                       68999999999999999*****99999988765 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  32 kdyeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkea 87 
                                       +++++ll+e ++l+++ +  ++k+ +++e+ ++  + ++++ + a++++a+a + +
  gi|330508227|ref|YP_004384655.1| 152 EEMKKLLDEAQSLRDQASSYHDKVINFAEMAQECHDQMISNFKEADQTRAEADAAQ 207
                                       799************************************************98765 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.31     2e+02     186     228 ..      25      67 ..      14      69 .. 0.78
   2 ?   14.6   6.1   2.4e-05     0.016     121     217 ..      73     177 ..      66     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.31
                              CorA 186 lddedkeylrdlldelerllemlealrerleslqdtyssllse 228
                                       +  +++      ++el+++ e+l  +++   +l+d+++ ++++
  gi|330508227|ref|YP_004384655.1|  25 EQNAEASKWAARRNELNQATEQLIDTAQDFKKLRDECNKNVAQ 67 
                                       4555555567778999999999999999999999999998876 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.4e-05
                              CorA 121 drlfellekleeeldeledeledstkkeilrelaqlrrrlvkl.....rralapnrevlk..rlla.....kaddkl 185
                                       d+++el+++l +++d + ++   s+++   r++++lrr++ +l      ++l+p +e     ++ a     ++++++
  gi|330508227|ref|YP_004384655.1|  73 DECNELVSQLYQKIDSIRKQH--SNHRAGERSITDLRREIDYLefrqqTEVLSPDKEKQLvnKIAAlqaefNGRKEE 147
                                       8899****************9..9999999*************8888845555543322233333333222233333 PP

                              CorA 186 lddedkeylrdlldelerllemlealrerles 217
                                       l+++  e ++ llde+++l ++++++++++ +
  gi|330508227|ref|YP_004384655.1| 148 LEKT--EEMKKLLDEAQSLRDQASSYHDKVIN 177
                                       3333..35999999999999999999999865 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4  11.9   0.00013     0.082      29     147 ..      32     178 ..      24     182 .. 0.92
   2 ?    6.6   1.5     0.016        10      53      86 ..     180     213 ..     171     215 .] 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                                       HHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH................. CS
                           T3SSipB  29 awkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqk................. 88 
                                        w a  +  ++a ++l d  q+  +  +++ +++ ++  k d+ +  + ++ +k+d + k                 
  gi|330508227|ref|YP_004384655.1|  32 KWAARRNELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQKIDSIRKqhsnhragersitdlrr 108
                                       5888888889999999999999999999************************************************* PP

                                       .........HHTT---------CHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTX CS
                           T3SSipB  89 .........rlkeLaPdePekakleaaeqQagaa..adalqadealqKkldaasklsekakakekevDdi 147
                                                + + L+Pd+ ++   + a  Qa+    ++ l++ e ++K ld a+ l+++a + + +v ++
  gi|330508227|ref|YP_004384655.1| 109 eidylefrqQTEVLSPDKEKQLVNKIAALQAEFNgrKEELEKTEEMKKLLDEAQSLRDQASSYHDKVINF 178
                                       *******998899*9999998889999999998899************************9998887665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           T3SSipB  53 seakgatddleaaiekadqaksaadaatkkvdea 86 
                                       + a+++ d++    ++adq  ++adaa++   +a
  gi|330508227|ref|YP_004384655.1| 180 EMAQECHDQMISNFKEADQTRAEADAAQREFLKA 213
                                       67899**********************9876555 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       2.6   1.7e+03      43      65 ..      36      55 ..      24      62 .. 0.59
   2 ?   -0.7   0.1         3   1.9e+03      41      56 ..      83      98 ..      74     116 .. 0.53
   3 ?   13.9   1.2   7.7e-05     0.049      14      56 ..     129     173 ..     128     188 .. 0.86
   4 ?   -1.5   0.2       5.2   3.3e+03      52      65 ..     197     211 ..     194     214 .. 0.50

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.6
                              HalX 43 rleelraqldetldelddaddfe 65
                                      r +el +  ++++d    a+df 
  gi|330508227|ref|YP_004384655.1| 36 RRNELNQATEQLIDT---AQDFK 55
                                      555555555555555...44443 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3
                              HalX 41 earleelraqldetld 56
                                       + ++++r q++   +
  gi|330508227|ref|YP_004384655.1| 83 YQKIDSIRKQHSNHRA 98
                                      5555555555444333 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 7.7e-05
                              HalX  14 aLasKravLeaeks..eaeLadseeYqeLearleelraqldetld 56 
                                       +L++K a+L+ae     +eL+ +ee   L ++ ++lr+q++   d
  gi|330508227|ref|YP_004384655.1| 129 QLVNKIAALQAEFNgrKEELEKTEEMKKLLDEAQSLRDQASSYHD 173
                                       599*********964479*********************987665 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 5.2
                              HalX  52 detldeldd.addfe 65 
                                       d+t +e d+ +++f+
  gi|330508227|ref|YP_004384655.1| 197 DQTRAEADAaQREFL 211
                                       444444444455555 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.4   9.6e-05     0.062      42     108 ..      39     105 ..      33     117 .. 0.81
   2 ?    4.3   1.4      0.06        38      62     114 ..     128     179 ..     116     198 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.6e-05
                           DUF1664  42 avesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                        +++ ++ql +  ++ ++ +++ ++++++  +k de++e+ +++ ++++++r++ s+ +   +s+ +
  gi|330508227|ref|YP_004384655.1|  39 ELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQKIDSIRKQHSNHRAGERSITD 105
                                       5677888999999999999999999999999999999999999999999999999988777666654 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.06
                           DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       ++L ++i+ ++++ +  ke  +++ ee++++ ++ ++++++ +s ++ v +++
  gi|330508227|ref|YP_004384655.1| 128 KQLVNKIAALQAEFNGRKEELEKT-EEMKKLLDEAQSLRDQASSYHDKVINFA 179
                                       556666666666666665555554.3455555555555555555555554433 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 ?   13.6   6.2   8.7e-05     0.056     104     186 ..      15     110 ..       1     113 [. 0.70
   2 ?    4.9  10.4      0.04        25      77     164 ..     121     210 ..     113     215 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.7e-05
                           UPF0242 104 e..........ldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvlek..r 168
                                       +          ++a  ++ + +++e +q  e+l ++a+df++l+ e ++++a+ + + +e +e ++++ + +++  +
  gi|330508227|ref|YP_004384655.1|  15 KslglkdgpreQNAEASKWAARRNELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQKIDSirK 91 
                                       4444444453355555555556666668888************************************9999986324 PP

                           UPF0242 169 qdqieq.LeskVrDlnyEi 186
                                       q  +++  e  + Dl  Ei
  gi|330508227|ref|YP_004384655.1|  92 QHSNHRaGERSITDLRREI 110
                                       4444331467788887777 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.04
                           UPF0242  77 lteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae...dfeelkleleeqLaekqel 150
                                       + + d + k+  +++  lq+e + +keel+ k+ee+++l  e q+L+ +++       +f+e+ +e  +q+    + 
  gi|330508227|ref|YP_004384655.1| 121 VLSPD-KEKQLVNKIAALQAEFNGRKEELE-KTEEMKKLLDEAQSLRDQASSYHDkviNFAEMAQECHDQMISNFKE 195
                                       44444.45677789999***********97.68899***********999987767889999999999987666555 PP

                           UPF0242 151 lqeyqeti.eeqrsv 164
                                        ++ +++    qr+ 
  gi|330508227|ref|YP_004384655.1| 196 ADQTRAEAdAAQREF 210
                                       555444431445555 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.1   5.5e-05     0.035      28      99 ..      39     110 ..      24     118 .. 0.74
   2 ?    2.6   1.6      0.19   1.2e+02      18      74 ..     133     188 ..     121     209 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHHHH CS
                        Laminin_II  28 ntkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseikelI 99 
                                       ++++  +++ ++++  +++ ++ nk +++ +r+  + ++l+ qL +k+ +++++++++ +  ++i  ++  I
  gi|330508227|ref|YP_004384655.1|  39 ELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQKIDSIRKQHSNHRAGERSITDLRREI 110
                                       344455555555566666666889999999999999999999999999999999998888677776666554 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.19
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGG CS
                        Laminin_II  18 qlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldk 74 
                                       ++a+l+++ +  ke+l++ ++  ++  ++++++  +  +  ++v +  + a++  d+
  gi|330508227|ref|YP_004384655.1| 133 KIAALQAEFNGRKEELEKTEEM-KKLLDEAQSLRDQASSYHDKVINFAEMAQECHDQ 188
                                       4455555555566666555544.5555555555555555556666655555444443 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4      0.18   1.2e+02      27      62 ..      54      90 ..      36      93 .. 0.71
   2 ?    2.4   0.0      0.35   2.2e+02      13      45 ..      79     111 ..      73     123 .. 0.68
   3 ?    8.3   0.2    0.0051       3.2      15      47 ..     129     161 ..     125     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.18
                           NPV_P10 27 vddvqenl.pdvtelnekLdaqsaqLaeletkvenIq 62
                                       ++++++  ++v + + k d+ ++ + +l +k+++I 
  gi|330508227|ref|YP_004384655.1| 54 FKKLRDECnKNVAQSKRKWDECNELVSQLYQKIDSIR 90
                                      4555555425788888899999999999999999886 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.35
                           NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLd 45 
                                       ++++ +k+d++ +q  + ++  + +t+l  ++d
  gi|330508227|ref|YP_004384655.1|  79 VSQLYQKIDSIRKQHSNHRAGERSITDLRREID 111
                                       556666777777777666666666666666666 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0051
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaq 47 
                                       ++ +k+ alq++ +  +e+l++++e+++ Ld+ 
  gi|330508227|ref|YP_004384655.1| 129 QLVNKIAALQAEFNGRKEELEKTEEMKKLLDEA 161
                                       6778**********************9999863 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  12.2     0.027        17      14      74 ..      39     101 ..      32     215 .] 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.027
                        Syntaxin_2  14 tleklvkq.Lgtkkdteelreklhelieeinelikktnellkklsqldnsssds....qqklqkek 74 
                                       +l++ ++q + t++d ++lr+++++++ + ++   ++nel+++l q ++s  ++    +   + e+
  gi|330508227|ref|YP_004384655.1|  39 ELNQATEQlIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQKIDSIRKQhsnhR---AGER 101
                                       57777777799*********************************999888766543330...3344 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 ?   12.2   3.4   0.00025      0.16      34     103 ..      19      88 ..       2      90 .. 0.79
   2 ?   12.3   2.7   0.00023      0.15      33      89 ..      39      99 ..      34     110 .. 0.73
   3 ?    3.8   8.3       0.1        66      37      97 ..     126     189 ..     111     215 .] 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                      Seryl_tRNA_N  34 ldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekllla 103
                                       l +  re ++e+ +  a+rNel+++ +++++  +d ++l++e +++ ++ k++ +e +el ++l +++ +
  gi|330508227|ref|YP_004384655.1|  19 LKDGPREQNAEASKWAARRNELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQKIDS 88 
                                       5566678888888889999999999999999988888888888888888888888888888888777655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00023
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHH CS
                      Seryl_tRNA_N 33 eldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleae 89
                                      el+++ ++l+ +++++++ r e++k++++ k+k     e  ++l ++++++ ++ ++  a 
  gi|330508227|ref|YP_004384655.1| 39 ELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWdecnELVSQLYQKIDSIRKQHSNHRAG 99
                                      6888999999999*****************9987555555555555555555555555554 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHHHCCCCCCTT...S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  37 krrelqveleelqaerNelskeIgkakkkk...edaeeliaevkelkeelkaleaelkeleael 97 
                                       k ++l +++ +lqae N   +e +k  + k   ++a++l++++++  +++ +  +  +e  +++
  gi|330508227|ref|YP_004384655.1| 126 KEKQLVNKIAALQAEFNGRKEELEKTEEMKkllDEAQSLRDQASSYHDKVINFAEMAQECHDQM 189
                                       4566666777777777777777766666555566666666666666666666666555555554 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   9.4    0.0022       1.4     192     327 ..      11     154 ..       3     215 .] 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0022
                              FUSC 192 rlaadilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpe....laallaela 264
                                       +l ++ l+l +      +e ++++ar + l++++ ++++  + + +l+++ +   a++++ ++e    +++l ++++
  gi|330508227|ref|YP_004384655.1|  11 ELGQKSLGLKDGPREQNAEASKWAARRNELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWDEcnelVSQLYQKID 87 
                                       556666777777777889**********************************************7777777777777 PP

                              FUSC 265 al.eaaaaaealeaalaalrarlralrrale...adadtaalllarlaellaelaqllaslraleaa 327
                                       ++ +++  + a e  ++ lr++++ l+ +++   ++ d +  l+   a l ae+    ++l++ e+ 
  gi|330508227|ref|YP_004384655.1|  88 SIrKQHSNHRAGERSITDLRREIDYLEFRQQtevLSPDKEKQLVNKIAALQAEFNGRKEELEKTEEM 154
                                       7797788888889999999999988887777778455555555555555544444444444444433 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0082       5.2      26      70 ..      45      89 ..      33     107 .. 0.49
   2 ?    4.0   0.4     0.091        58      46      79 ..     151     184 ..      98     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0082
                            DUF948 26 ktldeaaatieelekqvdpilkevedllakvnelledvneklekv 70
                                      + l  +a+  ++l+++ ++ + ++++  ++ nel++++ +k++++
  gi|330508227|ref|YP_004384655.1| 45 EQLIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQKIDSI 89
                                      222223333333444444444444444444444555555555554 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.091
                            DUF948  46 lkevedllakvnelledvneklekvdplteavad 79 
                                       ++e+++ll++++ l ++ ++  +kv ++ e +++
  gi|330508227|ref|YP_004384655.1| 151 TEEMKKLLDEAQSLRDQASSYHDKVINFAEMAQE 184
                                       5667777777777666666666666666666665 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.4   0.00094       0.6      25      91 ..      29      95 ..       3     117 .. 0.65
   2 ?    6.1  11.0     0.022        14       8      82 ..     134     210 ..     127     215 .] 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00094
                           DUF4200 25 leealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeiet 91
                                         + + r++el+++ ++l ++++ f+k   e++++ a+  +k +e ++l  +  ++i  ++++ ++
  gi|330508227|ref|YP_004384655.1| 29 EASKWAARRNELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQKIDSIRKQHSN 95
                                      4444556777777777777777777777777777777777777777777777777777666666554 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.022
                           DUF4200   8 mfevqealeakkeeiqr..leealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaei 82 
                                       +  +q + +  kee+++   +++l ++ + l+++ +   +++++f ++ +e+ ++ +   k+a++ r + +  ++e 
  gi|330508227|ref|YP_004384655.1| 134 IAALQAEFNGRKEELEKteEMKKLLDEAQSLRDQASSYHDKVINFAEMAQECHDQMISNFKEADQTRAEADAAQREF 210
                                       67789999999999996447889999************************************999999988877775 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 ?   10.9   2.8   0.00057      0.36      51     129 ..      29     107 ..      22     117 .. 0.88
   2 ?    5.1   3.4     0.034        22      53     111 ..     125     182 ..     115     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00057
                            DUF848  51 qlkrtkeikalveavdteieakkkelslLkklnrkkvarveeLtdkvlelkeevsleldsleeaqeeyqegessets 127
                                       ++++ ++ ++ ++++++++ ++ +++++L+    k+va+     d+  el  ++ +++ds+ ++ ++   ge s t+
  gi|330508227|ref|YP_004384655.1|  29 EASKWAARRNELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQKIDSIRKQHSNHRAGERSITD 105
                                       56677788999999*****************999****************************999999988888877 PP

                            DUF848 128 ip 129
                                       ++
  gi|330508227|ref|YP_004384655.1| 106 LR 107
                                       75 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.034
                            DUF848  53 krtkeikalveavdteieakkkelslLkklnrkkvarveeLtdkvlelkeevsleldsl 111
                                        ++k++ +++ a++ e++ +k el++  +  +k +++++ L+d+    ++ v    +  
  gi|330508227|ref|YP_004384655.1| 125 DKEKQLVNKIAALQAEFNGRKEELEKT-EEMKKLLDEAQSLRDQASSYHDKVINFAEMA 182
                                       578889999999999999999999994.4446778999999999988888775544444 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   5.3    0.0014      0.87       5      76 ..      38     111 ..      28     144 .. 0.72
   2 ?    6.8   1.7    0.0053       3.4       2      57 ..     152     207 ..     151     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelk 76 
                                       +el++ +++l +ta+ +k+  +e++k   + +++ +++++ +++l +++++++k+ +  +  e+ +++l++e++
  gi|330508227|ref|YP_004384655.1|  38 NELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQKIDSIRKQHSnhRAGERSITDLRREID 111
                                       67788888888888888888888888888888888888888888888888888775533444556666666665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0053
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklk 57 
                                       ee+++l +e+++l+++a++y+ k+ + +++ ++c  ++ ++ k++ + +++ +  +
  gi|330508227|ref|YP_004384655.1| 152 EEMKKLLDEAQSLRDQASSYHDKVINFAEMAQECHDQMISNFKEADQTRAEADAAQ 207
                                       799***********************************999999999888877666 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.1   0.00042      0.27      23      90 ..      39     111 ..      24     118 .. 0.80
   2 ?    3.9   3.0      0.14        87      26      82 ..     129     185 ..     125     213 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00042
                      Occludin_ELL  23 eYkelhaeleevskkfseLerelkelkegsk....eykkieeeilqeykklkk.dpeyqekkkrceyLkekLs 90 
                                       e ++  ++l +++++f++L++e+++   +sk    e ++++++++q+  +++k ++++++ ++ +++L+++ +
  gi|330508227|ref|YP_004384655.1|  39 ELNQATEQLIDTAQDFKKLRDECNKNVAQSKrkwdECNELVSQLYQKIDSIRKqHSNHRAGERSITDLRREID 111
                                       666778899999********88888777776656688888888888888887768889998999999998766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.14
                      Occludin_ELL  26 elhaeleevskkfseLerelkelkegsk...eykkieeeilqeykklkkdpeyqekkkrc 82 
                                       +l +++++++++f+  ++el++ +e +k   e +++ ++  ++y+++    ++ e+ ++c
  gi|330508227|ref|YP_004384655.1| 129 QLVNKIAALQAEFNGRKEELEKTEEMKKlldEAQSLRDQ-ASSYHDK--VINFAEMAQEC 185
                                       566777777777777777777777777767666666666.6666665..45555555555 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   6.3      0.38   2.5e+02      41      41 ..     148     148 ..      34     207 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.38
                              YtxH  41 a 41 
                                       +
  gi|330508227|ref|YP_004384655.1| 148 L 148
                                       0 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.3    0.0011       0.7      44      93 ..      45      95 ..      26     107 .. 0.87
   2 ?    3.7   0.3      0.11        67      50      90 ..     127     167 ..     121     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                        OrfB_IS605 44 rrlksdykylakeiaelqsklkkskn.ykkasrklarlhrkrsrrrkhllh 93
                                       +l  + + ++k ++e+ + +++sk+ + ++ + ++ l++k+  +rk + +
  gi|330508227|ref|YP_004384655.1| 45 EQLIDTAQDFKKLRDECNKNVAQSKRkWDECNELVSQLYQKIDSIRKQHSN 95
                                      678889999***************999*****************9986654 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                        OrfB_IS605  50 ykylakeiaelqsklkksknykkasrklarlhrkrsrrrkh 90 
                                       +k+l ++ia lq   ++ k   + ++++++l ++ +  r+ 
  gi|330508227|ref|YP_004384655.1| 127 EKQLVNKIAALQAEFNGRKEELEKTEEMKKLLDEAQSLRDQ 167
                                       67788999999999999999999999999999887777764 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.5     0.062        40      23      54 ..      38      69 ..      28     110 .. 0.69
   2 ?    9.4   2.4     0.002       1.3      22      93 ..     120     186 ..     110     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.062
                           DUF2935 23 alldpkekdlikeakefkkeFekllaeavels 54
                                      + l++  ++li++a++fkk  ++  +++ + +
  gi|330508227|ref|YP_004384655.1| 38 NELNQATEQLIDTAQDFKKLRDECNKNVAQSK 69
                                      56788888999999999988888888775543 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.002
                           DUF2935  22 ealldpkekdlikeakefkkeFekllaeavelseglvrasseleeavakLneealkltreliqFkkellekv 93 
                                       e l + kek+l+++  +++ eF+   +e ++ +       ++l ++ ++L ++a ++ +++i+F++  +e +
  gi|330508227|ref|YP_004384655.1| 120 EVLSPDKEKQLVNKIAALQAEFNGRKEELEKTE-----EMKKLLDEAQSLRDQASSYHDKVINFAEMAQECH 186
                                       55667899****************999999974.....44799999******************99887755 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 ?    4.6   0.4     0.065        42      41      71 ..      37      67 ..      14      70 .. 0.82
   2 ?   -0.6   0.1       2.8   1.8e+03       8      27 ..      74      93 ..      69     101 .. 0.62
   3 ?    9.0   4.5    0.0027       1.7      10      60 ..     100     150 ..      97     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.065
                          CCDC-167 41 eeEeaslkeqleenekeLksLrkeNrksmll 71
                                       +E+++ +eql +  +  k+Lr e  k+++ 
  gi|330508227|ref|YP_004384655.1| 37 RNELNQATEQLIDTAQDFKKLRDECNKNVAQ 67
                                      38999999*******************9986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.8
                          CCDC-167  8 kleeklascrerLeaverrl 27
                                      + +e +++++++++++ ++ 
  gi|330508227|ref|YP_004384655.1| 74 ECNELVSQLYQKIDSIRKQH 93
                                      55666666666666665554 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0027
                          CCDC-167  10 eeklascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeLks 60 
                                       e +++++r++++ +e+r ++e ls+++ ++l +  a+l+ + +   +eL++
  gi|330508227|ref|YP_004384655.1| 100 ERSITDLRREIDYLEFRQQTEVLSPDKEKQLVNKIAALQAEFNGRKEELEK 150
                                       77899**********************888887777777777777777763 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   4.3     0.093        60      21      58 ..      27      68 ..      22     111 .. 0.49
   2 ?   10.1   1.0     0.001      0.65      18      67 ..     148     198 ..     140     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.093
                            DUF148 21 eeqleawaeky....gvtdeykefeakvkaqkeevkknvtav 58
                                      +++ ++wa++     + t+++ +  ++ k+ ++e +knv++ 
  gi|330508227|ref|YP_004384655.1| 27 NAEASKWAARRnelnQATEQLIDTAQDFKKLRDECNKNVAQS 68
                                      555555554443333444444444444444444444444432 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.001
                            DUF148  18 aeieeqleawaeky.gvtdeykefeakvkaqkeevkknvtavisnLssvqe 67 
                                        e+ e+++++  +  ++ d+ + ++ kv +  e +++ ++++isn++++++
  gi|330508227|ref|YP_004384655.1| 148 LEKTEEMKKLLDEAqSLRDQASSYHDKVINFAEMAQECHDQMISNFKEADQ 198
                                       567777777776555********************************9986 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.68   4.3e+02       7      32 ..      32      57 ..      27      60 .. 0.55
   2 ?    6.8   1.5    0.0096       6.1      74     120 .]      39      85 ..      35      85 .. 0.94
   3 ?    5.7   0.3     0.021        13      82     113 ..      61      92 ..      52      99 .. 0.79
   4 ?    6.6   1.0     0.011       7.1       4      35 ..     133     165 ..     130     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.68
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  7 slqaelaqlkeaieelektletlktl 32
                                      + +a++++l++a e l +t +  k+l
  gi|330508227|ref|YP_004384655.1| 32 KWAARRNELNQATEQLIDTAQDFKKL 57
                                      55566666666666665555555554 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0096
                                       EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  74 sleeAiellkkkleelekqlekleeeleklkdqittleanlaqlyqk 120
                                       +l++A+e l +  ++ +k ++++++++++ k++ ++ ++ ++qlyqk
  gi|330508227|ref|YP_004384655.1|  39 ELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQK 85 
                                       57899999999*********************************996 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  82 lkkkleelekqlekleeeleklkdqittlean 113
                                       ++k++++ ++  ++++e + +l+++i++++++
  gi|330508227|ref|YP_004384655.1|  61 CNKNVAQSKRKWDECNELVSQLYQKIDSIRKQ 92 
                                       78888888888888888888888888888776 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.. CS
                         Prefoldin   4 eleslqaelaqlkeaieelektletlktlkk.e 35 
                                       ++++lqae++  ke++e+ e+ ++ l++ +  +
  gi|330508227|ref|YP_004384655.1| 133 KIAALQAEFNGRKEELEKTEEMKKLLDEAQSlR 165
                                       78999************9999999999998753 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   8.5     0.002       1.3      37     131 ..       8      99 ..       1     125 [. 0.77
   2 ?    4.7   4.5     0.022        14      88     156 ..     125     191 ..     104     208 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.002
                             Atg14  37 ekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkk 113
                                       ++ +l++k   +  g++   ++++++ + +a+ +el + +++l +  q  k+ +++ +k +++ k+k  ++++ +++
  gi|330508227|ref|YP_004384655.1|   8 KRGELGQKSLGLKDGPR---EQNAEASKWAARRNELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQ 81 
                                       55555555555545555...888888888899999999999999999999999999********************* PP

                             Atg14 114 Rrsdleslqneleerrkk 131
                                        +++++s++++ ++ r+ 
  gi|330508227|ref|YP_004384655.1|  82 LYQKIDSIRKQHSNHRAG 99 
                                       ****99*99999888863 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.022
                             Atg14  88 dklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikrieqklsslssktle 156
                                       dk +ql  +i++ ++++ +++++l ++++++++l +e ++ r +q +++ d++++ +++ +++++++++
  gi|330508227|ref|YP_004384655.1| 125 DKEKQLVNKIAALQAEFNGRKEEL-EKTEEMKKLLDEAQSLR-DQASSYHDKVINFAEMAQECHDQMIS 191
                                       444555556666666666666666.45555555555554443.45556666666666666666665555 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.8     0.015       9.5      34      62 ..      38      66 ..      29      75 .. 0.83
   2 ?    4.9   1.0     0.035        22      27      53 ..     148     174 ..     133     190 .. 0.86
   3 ?   -1.0   0.0       2.4   1.5e+03       7      26 ..     177     196 ..     172     207 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                                      HHHCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                     Synaptobrevin 34 deLvdktenLqssaqqFkkqarklkrkmw 62
                                      +eL++ te+L ++aq+Fkk   + ++++ 
  gi|330508227|ref|YP_004384655.1| 38 NELNQATEQLIDTAQDFKKLRDECNKNVA 66
                                      689***************98877777665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.035
                                       HCCCCCHHHHCCCCHHHHHHHHHHHHH CS
                     Synaptobrevin  27 lergekldeLvdktenLqssaqqFkkq 53 
                                       le+ e++ +L d+++ L+++a++++ +
  gi|330508227|ref|YP_004384655.1| 148 LEKTEEMKKLLDEAQSLRDQASSYHDK 174
                                       788899999999999999999999876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.4
                                       HHHHHHHCCCCHHCCHHHHC CS
                     Synaptobrevin   7 kikaevdevkdimkeNidkv 26 
                                       +  +  +e +d m++N++++
  gi|330508227|ref|YP_004384655.1| 177 NFAEMAQECHDQMISNFKEA 196
                                       55566678888999998876 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   9.1    0.0017       1.1      19     101 ..      24     106 ..      15     139 .. 0.85
   2 ?    1.1   7.4      0.31     2e+02      22     101 ..     128     206 ..     122     215 .] 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0017
                           DUF3450  19 dqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeie 95 
                                       ++ ++ea+k+ a + + ++  ++l d +q+ ++   + ++ +++ + + ++ ++lv+++ q+i+s+++q ++ ++ e
  gi|330508227|ref|YP_004384655.1|  24 REQNAEASKWAARRNELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQKIDSIRKQHSNHRAGE 100
                                       66678999*******************************************************************99 PP

                           DUF3450  96 relvpl 101
                                       r+++ l
  gi|330508227|ref|YP_004384655.1| 101 RSITDL 106
                                       999875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.31
                           DUF3450  22 lkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierel 98 
                                       ++  +k+ a +a+ + ++++l+ +++e+++ + ++++  ++++ y +++ +  + +++  +++  + +e++++++e 
  gi|330508227|ref|YP_004384655.1| 128 KQLVNKIAALQAEFNGRKEELE-KTEEMKKLLDEAQSLRDQASSYHDKVINFAEMAQECHDQMISNFKEADQTRAEA 203
                                       5566777777777777777774.466677777777777777777888888888888888888888888888888776 PP

                           DUF3450  99 vpl 101
                                          
  gi|330508227|ref|YP_004384655.1| 204 DAA 206
                                       655 PP

>> DUF3280  Protein of unknown function (DUF2380)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.9    0.0016         1      10      77 ..      19      86 ..      16      91 .. 0.87
   2 ?    1.9   3.1      0.45   2.9e+02       2      81 ..     133     208 ..     132     215 .] 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                           DUF3280 10 liDtsaepadqtaeearRlaavteqlreaLaesgryevvdlapaaaeiekesnlrkCngceadiArkl 77
                                      l+D  +e + +  + a+R ++++++ ++ ++++++++ ++ +++++ ++++++  +Cn+   ++ +k+
  gi|330508227|ref|YP_004384655.1| 19 LKDGPREQNAEASKWAARRNELNQATEQLIDTAQDFKKLRDECNKNVAQSKRKWDECNELVSQLYQKI 86
                                      6777777777788999****************************999989999*****9988876665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.45
                           DUF3280   2 kvavldfeliDtsaepadqtaeearRlaavteqlreaLaesgryevvdlapaaaeiekesnlrkCngceadiArklg 78 
                                       k+a l  e++  ++e +  ++ee ++l   +++lr++ ++    +v++ a+ a+e  +++ ++++++++++ A++  
  gi|330508227|ref|YP_004384655.1| 133 KIAALQAEFNGRKEELE--KTEEMKKLLDEAQSLRDQASSYH-DKVINFAEMAQEC-HDQMISNFKEADQTRAEADA 205
                                       8999999**99999999..89999999999999999977666.7899999999988.55678888888888887766 PP

                           DUF3280  79 Adl 81 
                                       A++
  gi|330508227|ref|YP_004384655.1| 206 AQR 208
                                       655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2150  (0.119917); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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):              28  [number of targets reported over threshold]
# CPU time: 0.77u 0.28s 00:00:01.05 Elapsed: 00:00:00.44
# Mc/sec: 1471.35
//
Query:       gi|330508228|ref|YP_004384656.1|  [L=511]
Description: beta-ribofuranosylaminobenzene 5'-phosphate synthase family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-29  101.1   0.0    8.1e-29  100.5   0.0    1.2  1  DUF98           p-hydroxybenzoic acid synthase
    8.8e-07   29.2   0.0    3.4e-06   27.3   0.0    2.0  2  GHMP_kinases_C  GHMP kinases C terminal
      2e-05   24.5   0.0    3.8e-05   23.6   0.0    1.5  1  UTRA            UTRA domain
  ------ inclusion threshold ------
      0.019   15.2   0.0      0.043   14.1   0.0    1.7  1  GHMP_kinases_N  GHMP kinases N terminal 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 !  100.5   0.0   1.8e-32   8.1e-29       1     143 [.      30     181 ..      29     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 1.8e-32
                                       HH--S-HHHHHHHHHSS-EEEEEEEEEEEE--HHHHHHHTS-TT-EEEEEEEEEEE..TTEEEEEEEEEEEGGGS-H CS
                             DUF98   1 LlgDGsvTrhlelltqekveveliemeaeeseeeeapkeveelkkpllrRqVwlra..ngqklayAeSwwneeelek 75 
                                       L +DGsvT  le+lt++++e+e++++e+++++++ a++ + + ++ +++R+V l+   +g++l+yA+S+++ ++le+
  gi|330508228|ref|YP_004384656.1|  30 LGTDGSVTSLLEILTGSPIEIETLAQEIIPADQAVAKELNLNPGEDVNYRVVKLKKagTGETLIYAVSHTPLKRLED 106
                                       568***************************************************99899****************** PP

                                       HHHH....SSS-HHHHHHHTT--BEEEEEEEEEEE--.HHHHHHT..SS-EEEEEEEEEEETTEEEEEEEEEEEG CS
                             DUF98  76 ylke....kdqpiwksLtkerlelfReirglalgead.eLeeafg..ekgpfwsRhYrlfhkgkpltvirEvFsp 143
                                       ++++    +d+pi+ +L+k+++e++Rei+     +ad +L + f+   k   + R+Y+++++g+pl+ i E+F+ 
  gi|330508228|ref|YP_004384656.1| 107 SFRDdltrADIPIGVILKKHKIESRREINSAGFLQADrKLGQIFNifPKELALQRNYKIIRQGEPLIAIEETFPY 181
                                       ***999999**********************99999989*****9655777899*******************97 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 ?   -3.1   0.0       2.3     1e+04      70      79 ..     243     252 ..     234     264 .. 0.55
   2 !   27.3   0.0   7.6e-10   3.4e-06       2      71 ..     410     478 ..     409     491 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.3
                    GHMP_kinases_C  70 deaeqvaral 79 
                                       d+a+++a+a+
  gi|330508228|ref|YP_004384656.1| 243 DRAKAAAQAV 252
                                       4444444444 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 7.6e-10
                    GHMP_kinases_C   2 lealergdlellgellnlsqrs.elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkde 71 
                                       l+ + ++dl+++g ++n+ q+   ++ ++   +p +++l e+++++G  +a+   +++Gptv+++++++ +
  gi|330508228|ref|YP_004384656.1| 410 LPSVVEEDLDEFGAAINRIQEIgFKRIEIMLQHPLVRSLMEEMRAAG--SACAGLSSFGPTVYVITDTQTR 478
                                       6778899****************9999********************..*****************76655 PP

>> UTRA  UTRA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   8.4e-09   3.8e-05       6     111 ..      48     156 ..      44     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8.4e-09
                                       EEEEEEEEEEEE--HHHHHHHTS-TTSEE.EEEEEEEEE.TTEEEEEEEEEEEGGGTTTCHHHHHH..CS-HHHHHH CS
                              UTRA   6 pktevlsleevpasaeiaeaLglpagepv.lrieRlrla.dgepvaleesylpaslvpdlleedle..egslyayle 78 
                                        + e+l  e +pa++++a++L+l++ge+v +r++ l  a  ge ++++ s+ p+++++d   +dl+  + ++  +l+
  gi|330508228|ref|YP_004384656.1|  48 IEIETLAQEIIPADQAVAKELNLNPGEDVnYRVVKLKKAgTGETLIYAVSHTPLKRLEDSFRDDLTraDIPIGVILK 124
                                       57899***********************8799999999977************************976666677776 PP

                                       HHHTTSEEEEEEEEEEEE-..-HHHHHHHTSTTT- CS
                              UTRA  79 erlgvpitraeetiearla..daeeaelLgisags 111
                                       +   ++i + +e+ +a ++  d++  ++++i + +
  gi|330508228|ref|YP_004384656.1| 125 K---HKIESRREINSAGFLqaDRKLGQIFNIFPKE 156
                                       6...7777777777776651145555555555555 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 ?   14.1   0.0   9.5e-06     0.043       2      66 .]     263     323 ..     262     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.5e-06
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHH..HHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeakl..aleaerlaqggngsggDvaasvyGg 66 
                                       ++++ +  ++ GLG ++ l  a+ +A+++l+       k     e+ r + +g +sg+  aa+ +Gg
  gi|330508228|ref|YP_004384656.1| 263 LTLRENYKMHVGLGRGTQLGIAAGKAICELYH------KEvgVREIARTINRGGTSGIGTAAFDMGG 323
                                       678889999**********************5......4423445556666799*********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3417.74
//
Query:       gi|330508229|ref|YP_004384657.1|  [L=590]
Description: TrkA-C domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-60  203.9  53.6      1e-47  162.8  23.3    1.9  2  CitMHS         Citrate transporter
    1.3e-19   70.6  36.0    3.7e-16   59.2  17.0    2.2  2  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    2.3e-12   46.6   0.0    1.2e-06   28.3   0.0    2.5  2  TrkA_C         TrkA-C domain


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.8  23.3   1.7e-51     1e-47       1     300 []      16     536 ..      16     536 .. 0.86
   2 !   55.4  22.3     9e-19   5.4e-15      14     168 ..     421     586 ..     404     589 .. 0.73

  Alignments for each domain:
  == domain 1  score: 162.8 bits;  conditional E-value: 1.7e-51
                                       xxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   1 lvllileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd 73 
                                       ++++i+++ r d+va+++l++     v+   +a+sg+a p++++++++ ii++   e+ l++++ +++ +  ++  +
  gi|330508229|ref|YP_004384657.1|  16 FAFFIWGRWRYDLVAMMALLTSviagVVPWSQAFSGFAHPAVITVAAVLIISRCFLESDLIEFIFRHISKSNRS-VN 91 
                                       689*************87777799*********************************************76665.66 PP

                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  74 .llvllvlltallsafvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaarpglsl 148
                                          + l  l+alls+f++n+g++++++p+ +++ ++ ++++p+ +l+ la+++ +gg++t+iGtp            
  gi|330508229|ref|YP_004384657.1|  92 sQALSLTGLVALLSGFMNNVGALALLMPLSIRISRS-GGSSPSlYLMTLAFGSLLGGLITLIGTP------------ 155
                                       68899******************************8.8888888*********************............ PP

                                       xxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                            CitMHS 149 pnlll.....................lalllvgllplvllfmfgvalalpvnapkvkkqkaiieaiarsllpv.... 200
                                       pn+++                     l++++vgl+++ l++                          ++l p+    
  gi|330508229|ref|YP_004384657.1| 156 PNIIIstfradnlgqpftmfdftpvgLGVAFVGLVFISLIG--------------------------WRLTPIrqgq 206
                                       ************************99999************..........................4444445555 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|330508229|ref|YP_004384657.1| 207 asgeeefevenyytevripqtsmtsgksihellsaagsdiqllglwreqqclpdlngseallpddiliiktnvdald 283
                                       55555555555555555555555555555555555555668888888888888888888888888888888888888 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|330508229|ref|YP_004384657.1| 284 kllksanlelvgskeagaiqseriglmevvvmnssllagksansicmrrhygvnliavaghdskslkrlsqiifhpg 360
                                       88888888889999999999999999999999999999999999999999999999999999999999999999999 PP

                                       .................................................................xxxxxxx..... RF
                            CitMHS 201 .................................................................atillla..... 207
                                                                                                        at+++l+     
  gi|330508229|ref|YP_004384657.1| 361 dvlllqgsadslpgivellgclplaerslklgqaknmilplvifalaiigsalgllpvevafvgaATVMVLIgiltl 437
                                       9999999**99999999999999999999999999999998888888888888888888777776444444488999 PP

                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 208 ...ykkveWsvlllfaGvfllvgaleqtGilealadll.ga.g..gplvalalvlgliallsafisnvavaalmapi 277
                                          y++++Ws+++l+++++++++ale +G +e+la+ l +  g  + +v+l+++l+ +++l+++++n+a+a+lmapi
  gi|330508229|ref|YP_004384657.1| 438 qeaYESIDWSIIILLGAMIPVSQALESSGGAELLAGNLlQVfGqfPAAVILTVLLVWTMVLTNVVNNAAAAVLMAPI 514
                                       *****************************9999997774448445666666777777888***************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 278 algmapalgllspsplalalavg 300
                                       a+ +a ++g  sp+p+++++a+g
  gi|330508229|ref|YP_004384657.1| 515 AYDTALVIG-ASPDPFLMTIAIG 536
                                       ******999.99********998 PP

  == domain 2  score: 55.4 bits;  conditional E-value: 9e-19
                                       xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxx RF
                            CitMHS  14 vallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd.llvl.lvlltal 84 
                                       + + +++++    +lt++ea++ i+++ii+ll++++ +++ale++G+++ la  ll+++g  ++ +++  l + t++
  gi|330508229|ref|YP_004384657.1| 421 AFVGAATVMvligILTLQEAYESIDWSIIILLGAMIPVSQALESSGGAELLAGNLLQVFGQFPAaVILTvLLVWTMV 497
                                       33322333345689999999999999999999999999999999999999999999999999887544458888999 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                            CitMHS  85 lsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnlll........ 153
                                       l+ +v+n +++++m+pi+ + a  ++ +p  +l+ +a++a+    ltpiG               n l+        
  gi|330508229|ref|YP_004384657.1| 498 LTNVVNNAAAAVLMAPIAYDTALVIGASPDPFLMTIAIGASCAF-LTPIGHQ------------SNTLVmgpggykf 561
                                       99999999999999999999999877777779999999999998.9999988............5555555555555 PP

                                       .........xxxxxxxx.xxxxxxx RF
                            CitMHS 154 .........lalllvgl.lplvllf 168
                                                l ++++++ +pl+l f
  gi|330508229|ref|YP_004384657.1| 562 gdywhmglpLSIIVTAVaIPLILWF 586
                                       5555555544444442226666655 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2  11.0   3.4e-07     0.002     266     462 ..       2     196 ..       1     201 [. 0.81
   2 !   59.2  17.0   6.2e-20   3.7e-16     273     468 ..     397     589 ..     376     590 .] 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.4e-07
                     Na_sulph_symp 266 tarekallilfvlllllWifgeslnidattvaivvlvillllrvldWkDivkqktaWntllllgglialakllersg 342
                                        + + a+ i++ ++  + i g         va+++l + ++  v+ W     +  a   ++  ++++ +++   +s 
  gi|330508229|ref|YP_004384657.1|   2 DSDQAAIFIIISIAFAFFIWGRWR---YDLVAMMALLTSVIAGVVPWS-QAFSGFAHPAVITVAAVLIISRCFLESD 74 
                                       566778888888888888887754...5689*****************.6667789999999999999********* PP

                     Na_sulph_symp 343 liewlgnklttslsglspavaiiiilslfvlvhylfaSatAttaallpillavaqaipgappllvalllalatslag 419
                                       lie++   +++s   +      +  l+ +v++   f  ++   a l+p+ + ++ +  g  p l  ++la+ + l+g
  gi|330508229|ref|YP_004384657.1|  75 LIEFIFRHISKSNRSVNS-Q--ALSLTGLVALLSGFMNNVGALALLMPLSIRISRSG-GSSPSLYLMTLAFGSLLGG 147
                                       ******999999883222.2..23355667778899*******************99.888999999********** PP

                     Na_sulph_symp 420 fllpyatgpnpivfgagy......lkvkdywrlGfilsiigllillllg 462
                                       +++ ++t+pn i+  +        + + d+  +G+ ++++gl+ + l+g
  gi|330508229|ref|YP_004384657.1| 148 LITLIGTPPNIIISTFRAdnlgqpFTMFDFTPVGLGVAFVGLVFISLIG 196
                                       ************9766431122224566888888888888888888877 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 6.2e-20
                     Na_sulph_symp 273 lilfvlllllWifgeslnidattvaivvlv.illllrvldWkDivkqktaWntllllgglialakllersgliewlg 348
                                       +il +++  l i g+ l++    va+v+ + +++l+ +l+ +    +   W +++llg++i +++ le sg  e l+
  gi|330508229|ref|YP_004384657.1| 397 MILPLVIFALAIIGSALGLLPVEVAFVGAAtVMVLIGILTLQ-EAYESIDWSIIILLGAMIPVSQALESSGGAELLA 472
                                       4555556666778888888888899998762678899*****.677899**************************** PP

                     Na_sulph_symp 349 nklttslsglspavaiiiilslfvlvhylfaSatAttaallpillavaqaipgappllvalllalatslagfllpya 425
                                         l +      pa++i+ +l+++ +v +    ++A  + ++pi    a +i ga p  + +++a+  s a fl+p++
  gi|330508229|ref|YP_004384657.1| 473 GNLLQVFG-QFPAAVILTVLLVWTMVLTNVVNNAAAAVLMAPIAYDTALVI-GASPDPFLMTIAIGASCA-FLTPIG 546
                                       99999888.6788888888889999999***********************.9999999999*******9.****** PP

                     Na_sulph_symp 426 tgpnpivfgagylkvkdywrlGfilsiigllillllgalwwkl 468
                                          n +v g g  k  dyw +G++lsii  ++ + l+ ++w l
  gi|330508229|ref|YP_004384657.1| 547 HQSNTLVMGPGGYKFGDYWHMGLPLSIIVTAVAIPLILWFWPL 589
                                       *****************************************75 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.3e-06    0.0079       2      67 ..     220     287 ..     219     290 .. 0.89
   2 !   28.3   0.0     2e-10   1.2e-06       1      69 [.     309     379 ..     309     380 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-06
                                       EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       +ev++p  s   Gk++ el   a  ++ ++++ R+ + l+  +g+  L ++D+l++ ++ ++l++l +
  gi|330508229|ref|YP_004384657.1| 220 TEVRIPQTSMTSGKSIHELLSAAGsDIQLLGLWREqQCLPDLNGSEALLPDDILIIKTNVDALDKLLK 287
                                       599***************8777779*******999666777777********************9976 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 2e-10
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEE.E-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvai.rRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                       l+ev+v ++s l+Gk+   + +r++ gv+++a+  ++ + +   +  ++++GDvll+ gs ++l  + ell
  gi|330508229|ref|YP_004384657.1| 309 LMEVVVMNSSLLAGKSANSICMRRHyGVNLIAVaGHDSKSLKRLSQIIFHPGDVLLLQGSADSLPGIVELL 379
                                       69*******************************768889999999*****************998777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3734.56
//
Query:       gi|330508230|ref|YP_004384658.1|  [L=998]
Description: two-component hybrid sensor and regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-42  144.5   0.0    4.1e-17   62.4   0.0    3.4  3  PAS_4         PAS fold
    1.6e-40  137.6   0.1    1.1e-15   57.8   0.0    3.6  3  PAS_9         PAS domain
    1.6e-39  134.4   0.1    9.6e-18   64.2   0.0    3.7  3  PAS           PAS fold
    1.1e-36  125.4   0.3    4.8e-26   91.1   0.0    3.1  3  Response_reg  Response regulator receiver domain
    1.4e-30  106.1   0.0    3.5e-30  104.8   0.0    1.7  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    6.1e-20   71.0   0.2    4.5e-19   68.2   0.0    2.6  2  HisKA         His Kinase A (phospho-acceptor) domain
      4e-18   65.0   0.5    8.4e-06   25.7   0.1    4.0  4  PAS_8         PAS domain
    1.7e-16   60.3   0.1      5e-13   49.2   0.0    3.5  3  PAS_3         PAS fold
    6.6e-09   35.6   0.6     0.0025   17.5   0.0    3.3  3  PAS_12        UPF0242 C-terminal PAS-like domain
    1.4e-07   31.7   0.0     0.0041   17.3   0.0    4.0  3  PAS_7         PAS fold
    1.7e-05   25.3   0.0          3    8.5   0.0    4.1  4  PAS_10        PAS domain
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.054   13.4   0.0    1.8  1  HATPase_c_5   GHKL domain
      0.082   13.0   0.0        7.2    6.7   0.0    2.6  2  MLTR_LBD      MmyB-like transcription regulator ligand bindin


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 !   62.4   0.0     3e-20   4.1e-17       4     108 ..     103     206 ..     101     208 .. 0.95
   2 !   40.5   0.0   1.9e-13   2.6e-10       2     107 ..     250     356 ..     249     359 .. 0.94
   3 !   37.7   0.0   1.4e-12     2e-09       2     109 ..     372     481 ..     371     482 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 3e-20
                             PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerh 80 
                                       lp++l+ +++d+r+l++N+++a ++g++  e++G++  ++lpee  + + + ++rvl+gee+i+  +++   ++ ++
  gi|330508230|ref|YP_004384658.1| 103 LPFMLVHISSDQRYLFVNQSYANWLGLDSSEMVGRHISDILPEEIYQTYLPLIQRVLSGEEVISCITFPSG-DRLKY 178
                                       79999999***************************************************999998887777.***** PP

                             PAS_4  81 yelrllPlrdesGevigvlvisrDiTer 108
                                        +++l+P +desG +i++++++ DiT+ 
  gi|330508230|ref|YP_004384658.1| 179 QDITLIPQLDESGSTIAYFAVIKDITDH 206
                                       **************************85 PP

  == domain 2  score: 40.5 bits;  conditional E-value: 1.9e-13
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlae.llpeedaarleralrrvlegeepiefleelll.pg 76 
                                       +s++d+++v++++ r + +Naa+++l+ +p e+llG+ +++  ++ e a+++ +  ++v  +++    +e++   pg
  gi|330508230|ref|YP_004384658.1| 250 NSISDPIFVINREHRLVLVNAAFCRLMSLPKEDLLGEEVHDfCFSREMADDHWQRNEEVFNSRRETVVEEIHSYsPG 326
                                       799*************************************96677779999999999*****999999999999*** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTe 107
                                       ++ ++++  +P+ d++G+   +++i+rDiT+
  gi|330508230|ref|YP_004384658.1| 327 APATVLIKRIPIIDSDGK-WLIVGIIRDITD 356
                                       ******************.9**********7 PP

  == domain 3  score: 37.7 bits;  conditional E-value: 1.4e-12
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlae.llpeedaarleralrrvlegeepiefleelll.pg 76 
                                       +++   +++ d +g+++y+N++a+ l+g+  ee++Gk  ae ++pe   +   r +  +++ +  ++ + + +  +g
  gi|330508230|ref|YP_004384658.1| 372 EQVHNTVIATDLEGNIIYWNKSAETLLGWKSEEAMGKNIAEtVVPEWGLDKMNRVISDLIKDRGNWDGEFYFKKkDG 448
                                       6777778999******************************846666699999999********************** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +++++   ++ +rd +Ge ig++++++D+Ter+
  gi|330508230|ref|YP_004384658.1| 449 STVPFHQCFSSIRDGRGELIGLVGVAVDLTERK 481
                                       ********************************8 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.7e-10   2.4e-07       6     104 .]     107     205 ..     102     205 .. 0.87
   2 !   44.7   0.0   8.9e-15   1.2e-11       2     104 .]     254     356 ..     253     356 .. 0.95
   3 !   57.8   0.0   7.8e-19   1.1e-15       5     104 .]     378     479 ..     375     479 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.7e-10
                             PAS_9   6 i..dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvl. 79 
                                       +  + +d r l++N++ +++lG ++ e++g++i+d++  ++e  ++   ++++   + +ev   ++ ++g ++ ++ 
  gi|330508230|ref|YP_004384658.1| 107 LvhISSDQRYLFVNQSYANWLGLDSSEMVGRHISDIL--PEEIYQTYLPLIQRVL-SGEEVISCITFPSGDRLKYQd 180
                                       336679999****************************..6666666666666666.899999999999999999999 PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                       +t++p  d++g  +++ ++++Dit+
  gi|330508230|ref|YP_004384658.1| 181 ITLIPQLDESGSTIAYFAVIKDITD 205
                                       ************************6 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 8.9e-15
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgrkkerevevvlirknget 75 
                                       d+i+++n ++r++ +N a++rl+   +e++lg  ++d++   + ++++ +r ++++++ r  e  ve ++ ++ g +
  gi|330508230|ref|YP_004384658.1| 254 DPIFVINREHRLVLVNAAFCRLMSLPKEDLLGEEVHDFCfsrEMADDHWQRNEEVFNSRR--ETVVEEIHSYSPGAP 328
                                       7899999***************9999**********************************..999999999999*** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                         vl++ +p++d+dg+   i++i+rDit+
  gi|330508230|ref|YP_004384658.1| 329 ATVLIKRIPIIDSDGKWL-IVGIIRDITD 356
                                       ***********9988866.89*******6 PP

  == domain 3  score: 57.8 bits;  conditional E-value: 7.8e-19
                             PAS_9   5 li.dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkngetfwv 78 
                                       +i ++ +g+i+y+N++a++llG ++ee +gk+i +++  ++ + +++++++ ++ k    +++e  + +k+g+t+++
  gi|330508230|ref|YP_004384658.1| 378 VIaTDLEGNIIYWNKSAETLLGWKSEEAMGKNIAETV-VPEWGLDKMNRVISDLIKdrGNWDGEFYFKKKDGSTVPF 453
                                       444889*******************************.777777777777777777787****************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                       + ++s ++d+ gel+g++++ +D+te
  gi|330508230|ref|YP_004384658.1| 454 HQCFSSIRDGRGELIGLVGVAVDLTE 479
                                       *************************8 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.5e-07   0.00034      14     113 .]     107     203 ..      99     203 .. 0.92
   2 !   45.3   0.1   5.4e-15   7.4e-12       4     113 .]     246     354 ..     243     354 .. 0.93
   3 !   64.2   0.0     7e-21   9.6e-18       6     111 ..     370     475 ..     367     477 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.5e-07
                                       EEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEE CS
                               PAS  14 ifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihle 90 
                                        + +  d r l+vN++++  lGl+ +e++g++++d ++ee   +++  l q+ ++gee  + +i+f+    r ++ +
  gi|330508230|ref|YP_004384658.1| 107 LVHISSDQRYLFVNQSYANWLGLDSSEMVGRHISDILPEEIY-QTYLPLIQRVLSGEEVIS-CITFPS-GDRLKYQD 180
                                       5567789999****************************9986.599999999999999988.9*****.******** PP

                                       EEEEEEEETTEEEEEEEEEEEES CS
                               PAS  91 vraspvrdaggeilgflgvlrdi 113
                                       ++  p +d++g  + ++ v++di
  gi|330508230|ref|YP_004384658.1| 181 ITLIPQLDESGSTIAYFAVIKDI 203
                                       ********************998 PP

  == domain 2  score: 45.3 bits;  conditional E-value: 5.4e-15
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       + i++s+ dpifv+++ +r ++vNaa+++l  l+ e++lg+ + d+ +     e+a+  +q+ e+  +sr + + ++
  gi|330508230|ref|YP_004384658.1| 246 DMIINSISDPIFVINREHRLVLVNAAFCRLMSLPKEDLLGEEVHDFCFSR---EMADDHWQRNEEVFNSRRETVVEE 319
                                       569*********************************************75...699999998888888888888888 PP

                                       C...TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 l...rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                             g p  +++ + p++d +g++  ++g++rdi
  gi|330508230|ref|YP_004384658.1| 320 IhsySPGAPATVLIKRIPIIDSDGKW-LIVGIIRDI 354
                                       89999*********************.********8 PP

  == domain 3  score: 64.2 bits;  conditional E-value: 7e-21
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEEC CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfkl 81 
                                       +le+ ++ ++++D  g+i+y+N++ae+llG++ ee++gk++ + +++e    ++++ ++ l++++ ++ + e  fk+
  gi|330508230|ref|YP_004384658.1| 370 LLEQVHNTVIATDLEGNIIYWNKSAETLLGWKSEEAMGKNIAETVVPEWGLdKMNRVISDLIKDRGNWDG-EFYFKK 445
                                       7999******************************************997779****************88.777888 PP

                                       TTSSEEEEEEEEEEEEETTEEEEEEEEEEE CS
                               PAS  82 rdgrpihlevraspvrdaggeilgflgvlr 111
                                       +dg++++++++ s++rd+ ge++g++gv+ 
  gi|330508230|ref|YP_004384658.1| 446 KDGSTVPFHQCFSSIRDGRGELIGLVGVAV 475
                                       8*************************9975 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.3   4.6e+03      21      79 ..     584     643 ..     561     655 .. 0.60
   2 !   31.1   0.0   1.5e-10   2.1e-07       1     110 [.     747     847 ..     746     849 .. 0.83
   3 !   91.1   0.0   3.5e-29   4.8e-26       1     110 [.     877     987 ..     877     989 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.3
                                       TTEEEEEEESSHHHHHHHHHHHHESEEEEE.SSCSSSEHHHHHHHHHHCTTTSEEEEEES CS
                      Response_reg  21 egyeevaeaedgkealellkeekvdlillD.inmpgmdGlellkeireedpelpviilta 79 
                                        ++  + +a++g ++   ++++ + +i+ D  ++ ++ G  l + ++ +d+   v+ ++a
  gi|330508230|ref|YP_004384658.1| 584 LDLVGINAANKGLNLAYSIDKSVPEMIVGDpSKLKQVLGNLLSNAVKFTDKGEVVVTVSA 643
                                       444455666666666666677777777766334666666666666655554444555554 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 1.5e-10
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       v+ivd++ + r l++q+++  g+     ++++ ea++ +++  vd+ +lD ++ + +Glel++ei++  +++p ++l
  gi|330508230|ref|YP_004384658.1| 747 VIIVDNETTRRILCKQICD-WGM-IPLITSSAWEAIQCIQRGGVDIAILDTDLLDNSGLELAEEIQRCMRTMPLLLL 821
                                       6777777777777777776.999.77799************************************************ PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlka 110
                                       t++++          + + +l+Kp++p++L+ a
  gi|330508230|ref|YP_004384658.1| 822 TTRGK-------QVPDGYSHLTKPLKPTQLHRA 847
                                       *9987.......234455667777777777665 PP

  == domain 3  score: 91.1 bits;  conditional E-value: 3.5e-29
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpvi 75 
                                       +l+++Dd   + + +++l++ gy + ++a +g+e+l  l+++++d++l+D++mp+mdGle+++ ir++   ++l++i
  gi|330508230|ref|YP_004384658.1| 877 ILLAEDDMPSQWVAQKMLKRLGY-RADTACNGSEVLLALEQHDFDVVLMDWRMPEMDGLEATRIIRQRWpkSQLKII 952
                                       89*********************.*******************************************997788**** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpeeLlka 110
                                       +lta++   d++++l+ag+d+++sKp+++e+L   
  gi|330508230|ref|YP_004384658.1| 953 ALTAYALPGDMEKCLEAGMDGYISKPLRKEDLARE 987
                                       *******************************9876 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 !  104.8   0.0   2.6e-33   3.5e-30       1     109 [.     612     724 ..     612     727 .. 0.94

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 2.6e-33
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE....TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTST CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikase....ddlvisveDnGiGipkedlkklfekfsq.ddstkrggg 72 
                                       gd+++L+q++ nl++Navkf t++ge+ v+++a+e    + ++++v+D+GiGip++ +k+lf +fsq + st+r +g
  gi|330508230|ref|YP_004384658.1| 612 GDPSKLKQVLGNLLSNAVKF-TDKGEVVVTVSAQEvdgdNVIQFEVRDTGIGIPQNRMKLLFLPFSQmEPSTSRLYG 687
                                       7999****************.***********955665678888********************************* PP

                                       SSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  73 gtGlGlsivkklvelmgGeiwvesepgrGttftftlp 109
                                       gtGlGl+i+k+lve+m+G+iw es++g G++f+ft++
  gi|330508230|ref|YP_004384658.1| 688 GTGLGLAISKRLVEMMKGRIWAESSEGTGSSFHFTIR 724
                                       **********************************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 ?   -1.6   0.0       2.1   2.9e+03      33      48 ..     237     252 ..     220     263 .. 0.75
   2 !   68.2   0.0   3.3e-22   4.5e-19       2      66 ..     501     564 ..     500     565 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.1
                                       -HSSCHHHHHHHHHHH CS
                             HisKA  33 lteelkeyletiesea 48 
                                       + e+ ++yl+ i++++
  gi|330508230|ref|YP_004384658.1| 237 ALERSRDYLDMIINSI 252
                                       4577888888887765 PP

  == domain 2  score: 68.2 bits;  conditional E-value: 3.3e-22
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       +++fla+++HE+rtP++ai+g++++L +e +lt+e+++ +e+ie +++ l+ +++d+Ld+s++e+
  gi|330508230|ref|YP_004384658.1| 501 KSDFLANMSHEIRTPMNAIIGMTSLLLEE-PLTPEQRDCIEVIETNGDALLTVINDILDFSKMEN 564
                                       79***********************9775.9********************************97 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00017      0.23      11      56 ..     102     147 ..     102     159 .. 0.75
   2 !   25.7   0.1   6.1e-09   8.4e-06       2      53 ..     244     292 ..     243     311 .. 0.76
   3 !   22.9   0.0   4.4e-08   6.1e-05       3      55 ..     366     417 ..     364     430 .. 0.80
   4 ?   -3.1   0.0       6.5     9e+03      28      38 ..     891     904 ..     888     936 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                             PAS_8  11 pdgiavvd..lgdrivdvNqaalellGysadlkgellgqllpvlrpll 56 
                                       p + ++v    ++r ++vNq+++  lG++  +++++ + + + l++++
  gi|330508230|ref|YP_004384658.1| 102 PLPFMLVHisSDQRYLFVNQSYANWLGLD--SSEMVGRHISDILPEEI 147
                                       56788888777789*************88..77777766666665555 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 6.1e-09
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlr 53 
                                       +l  +++s++d+i+v+++  r+v vN a+++l  ++ +dl+ge+++    ++ 
  gi|330508230|ref|YP_004384658.1| 244 YLDMIINSISDPIFVINREHRLVLVNAAFCRLMSLPkEDLLGEEVH----DFC 292
                                       56779************6669*************997777776663....333 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 4.4e-08
                             PAS_8   3 lra.lfesspdgiavvd.lgdrivdvNqaalellGysadlkgellgqllpvlrpl 55 
                                       ++a l+e++++ ++ +d +g+ i+++N++a+ llG++  + ++   ++ + + p+
  gi|330508230|ref|YP_004384658.1| 366 FQAdLLEQVHNTVIATDlEGN-IIYWNKSAETLLGWK--SEEAMGKNIAETVVPE 417
                                       55559************6666.**************9..7777666666666655 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 6.5
                             PAS_8  28 qaalellGys...a 38 
                                       q++l+ lGy+   a
  gi|330508230|ref|YP_004384658.1| 891 QKMLKRLGYRadtA 904
                                       77888889884331 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0093        13       2      52 ..     117     165 ..     116     169 .. 0.80
   2 ?    0.3   0.0      0.63   8.6e+02       3      32 ..     267     294 ..     265     315 .. 0.81
   3 !   49.2   0.0   3.6e-16     5e-13       1      89 []     387     474 ..     387     474 .. 0.98

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0093
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepy 52 
                                       ++v++++ ++lG++++e+ g+  ++ d++  e  + +   +q++l++ e++
  gi|330508230|ref|YP_004384658.1| 117 LFVNQSYANWLGLDSSEMVGR--HISDILPEEIYQTYLPLIQRVLSGEEVI 165
                                       79*******************..7777776666777777888888776665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.63
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhp 32 
                                        v++++++++ + +e+llg   ++ d++  
  gi|330508230|ref|YP_004384658.1| 267 LVNAAFCRLMSLPKEDLLGE--EVHDFCFS 294
                                       689****************9..77777754 PP

  == domain 3  score: 49.2 bits;  conditional E-value: 3.6e-16
                             PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwveararvir 76 
                                       iiy++++ e +lG+ +ee +gk  ++++ v pe  ++++++ + +++k+++ ++ge+ +++kdG+++ ++ + + ir
  gi|330508230|ref|YP_004384658.1| 387 IIYWNKSAETLLGWKSEEAMGK--NIAETVVPEWgLDKMNRVISDLIKDRGNWDGEFYFKKKDGSTVPFHQCFSSIR 461
                                       69********************..***************************************************** PP

                             PAS_3  77 dengkpvrvigva 89 
                                       d  g+ + ++gva
  gi|330508230|ref|YP_004384658.1| 462 DGRGELIGLVGVA 474
                                       ***********96 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 !   10.3   0.0   0.00029      0.41      59      97 ..     106     145 ..      99     164 .. 0.83
   2 ?    4.0   0.1     0.026        36      31      91 ..     227     287 ..     219     318 .. 0.75
   3 !   17.5   0.0   1.8e-06    0.0025      60     141 ..     378     463 ..     364     469 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                            PAS_12  59 ilvysqkenkllfaNaqirallGwssdkfl.qdfseivqe 97 
                                       +lv+   +++ lf+N+   ++lG+ s +++ ++ s+i+ e
  gi|330508230|ref|YP_004384658.1| 106 MLVHISSDQRYLFVNQSYANWLGLDSSEMVgRHISDILPE 145
                                       6788889*****************8777663678888866 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.026
                            PAS_12  31 rfrdlsldnyaldl.RrLfDsLrsEnlgailvysqkenkllfaNaqirallGwssdkflqdf 91 
                                       r ++l l n+al+  R   D + +  +  i+v  ++e++l+ +Na + +l+ + ++++l ++
  gi|330508230|ref|YP_004384658.1| 227 RTKELELANSALERsRDYLDMIINSISDPIFV-INREHRLVLVNAAFCRLMSLPKEDLLGEE 287
                                       67899999999985266777777777777766.578******************99998654 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 1.8e-06
                            PAS_12  60 lvysqkenkllfaNaqirallGwssdkfl.qdfseivqe..gleeWkralakl.sskteskirlvlKtKagqevlln 132
                                       ++ +  e  +++ N+  ++llGw s++ + ++ +e v +  gl++ +r ++ l + + + ++++ +K K g  v+++
  gi|330508230|ref|YP_004384658.1| 378 VIATDLEGNIIYWNKSAETLLGWKSEEAMgKNIAETVVPewGLDKMNRVISDLiKDRGNWDGEFYFKKKDGSTVPFH 454
                                       566778999**************8877552666665543369********98725567889**************** PP

                            PAS_12 133 cllgiipsG 141
                                        +   i  G
  gi|330508230|ref|YP_004384658.1| 455 QCFSSIRDG 463
                                       999888766 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     0.026        36      10      45 ..     109     143 ..     106     152 .. 0.90
   2 !   17.3   0.0     3e-06    0.0041       1      54 [.     249     301 ..     249     362 .. 0.72
   3 ?    4.8   0.0     0.022        31       1      43 [.     371     412 ..     371     418 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.026
                             PAS_7  10 vfDadlrLvawNrrylelldlpeelvqvgvpleell 45 
                                        +++d+r +++N+ y + l+l ++ + vg++++++l
  gi|330508230|ref|YP_004384658.1| 109 HISSDQRYLFVNQSYANWLGLDSSEM-VGRHISDIL 143
                                       5789******************9999.9****9997 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3e-06
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergef 54 
                                       ++++s+ i v+++++rLv++N  +++l++lp+e +  g ++++++  +    ++
  gi|330508230|ref|YP_004384658.1| 249 INSISDPIFVINREHRLVLVNAAFCRLMSLPKEDL-LGEEVHDFCFSREMADDH 301
                                       6899999*************************998.777777766554443333 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.022
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvplee 43 
                                       le++++ ++  D +++++ wN+    ll++ +e + +g++++e
  gi|330508230|ref|YP_004384658.1| 371 LEQVHNTVIATDLEGNIIYWNKSAETLLGWKSEEA-MGKNIAE 412
                                       78999999********************9987766.6666655 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0022         3      13      75 ..     108     171 ..     101     203 .. 0.75
   2 ?    3.6   0.0      0.07        97       1     105 [.     245     357 ..     245     358 .. 0.66
   3 !    7.7   0.0    0.0037       5.2       4     106 .]     370     478 ..     368     478 .. 0.77
   4 ?   -1.1   0.0         2   2.8e+03      33      56 ..     838     861 ..     834     870 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0022
                            PAS_10  13 tflDdnlqirrFtpaakklfklip.advGrpladihpkkavknveeviealrtgekdevevvvp 75 
                                       + + ++ + ++ ++++++ + l + + vGr+++di p+++++    +i+++ +ge++ + +  p
  gi|330508230|ref|YP_004384658.1| 108 VHISSDQRYLFVNQSYANWLGLDSsEMVGRHISDILPEEIYQTYLPLIQRVLSGEEVISCITFP 171
                                       5555566666666666666666541569*************************99876655555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.07
                            PAS_10   1 lnnlLnstpieltflDdnlqirrFtpaakklfklipad.vGrpladi..hpk...kavknveeviealrtgekdeve 71 
                                       l++++ns+   +  ++++ ++   + a  +l++l ++d +G+++ d+  + +   +  ++ eev+++ r++  +e +
  gi|330508230|ref|YP_004384658.1| 245 LDMIINSISDPIFVINREHRLVLVNAAFCRLMSLPKEDlLGEEVHDFcfSREmadDHWQRNEEVFNSRRETVVEEIH 321
                                       6788899999999999999999999999999999999945******9442221113333334444444444444444 PP

                            PAS_10  72 vvvpkngkwvlvrylpyrdedge..iaGvvetfvDi 105
                                        + p    +vl++  p+ d dg+  i G++  ++Di
  gi|330508230|ref|YP_004384658.1| 322 SYSPGAPATVLIKRIPIIDSDGKwlIVGIIRDITDI 357
                                       444455667888888999999984456666666666 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0037
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfkli.padvGrpladi.hpkkavknveeviealrtgek.devevvvp.k 76 
                                       lL+++   ++  D + +i++++++a++l+  + ++ +G ++a+  +p+  ++++++vi +l++ +     e++ + k
  gi|330508230|ref|YP_004384658.1| 370 LLEQVHNTVIATDLEGNIIYWNKSAETLLGWKsEEAMGKNIAETvVPEWGLDKMNRVISDLIKDRGnWDGEFYFKkK 446
                                       677788888899999********99988887616789****97626889**********999877632334444435 PP

                            PAS_10  77 ngkw..vlvrylpyrdedgeiaGvvetfvDit 106
                                       +g +  + +  + +rd  ge  G+v + vD+t
  gi|330508230|ref|YP_004384658.1| 447 DGSTvpFHQCFSSIRDGRGELIGLVGVAVDLT 478
                                       54443388889999999999999999999975 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2
                            PAS_10  33 klipadvGrpladihpkkavknve 56 
                                       +l+p+++ r l+di p++++k+++
  gi|330508230|ref|YP_004384658.1| 838 PLKPTQLHRALSDILPNSSEKEIR 861
                                       58999***********99988876 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   3.9e-05     0.054       5      92 ..     616     714 ..     613     724 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.9e-05
                       HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg..............ekkklesskskkeeh 67 
                                        l  +lgnlL NA+   +k e    +++++++e +++ +i++e   +g               ++  +s+++  +  
  gi|330508230|ref|YP_004384658.1| 616 KLKQVLGNLLSNAVKFTDKGE---VVVTVSAQEVDGDNVIQFEVRDTGigipqnrmkllflpFSQMEPSTSRLYGGT 689
                                       67889*********9988865...89********99999999988777778876664444431144448899999** PP

                       HATPase_c_5  68 GiGlksireivkkykgnlsieaedg 92 
                                       G+Gl   +++v+  kg ++ e ++g
  gi|330508230|ref|YP_004384658.1| 690 GLGLAISKRLVEMMKGRIWAESSEG 714
                                       ******************9998876 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 ?    6.7   0.0    0.0052       7.2      15      43 ..     254     282 ..     242     324 .. 0.76
   2 ?    3.3   0.0     0.056        77       8      56 ..     370     416 ..     367     429 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0052
                          MLTR_LBD  15 vPAlVldrrwdvlaaNraaraLlgdpaal 43 
                                        P +V++r   ++  N+a+ +L++ p++ 
  gi|330508230|ref|YP_004384658.1| 254 DPIFVINREHRLVLVNAAFCRLMSLPKED 282
                                       499********************996543 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.056
                          MLTR_LBD   8 lLdalepvPAlVldrrwdvlaaNraaraLlgdpaalpeperNllrlvfl 56 
                                       lL+++ ++ ++ +d   +++ +N+ a+ Llg  ++ ++ ++N++ +v  
  gi|330508230|ref|YP_004384658.1| 370 LLEQV-HNTVIATDLEGNIIYWNKSAETLLGW-KSEEAMGKNIAETVVP 416
                                       56666.7788999999***************9.6777778888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (998 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); 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: 0.82u 0.29s 00:00:01.10 Elapsed: 00:00:00.47
# Mc/sec: 6421.85
//
Query:       gi|330508231|ref|YP_004384659.1|  [L=336]
Description: hypothetical protein MCON_2376 [Methanosaeta concilii GP6]
Scores for complete 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-39  133.2   0.7    7.3e-39  132.7   0.7    1.2  1  DUF1722   Protein of unknown function (DUF1722)
      1e-30  106.6   0.0      2e-30  105.6   0.0    1.5  1  DUF523    Protein of unknown function (DUF523)
  ------ inclusion threshold ------
      0.026   14.3   0.4      0.052   13.4   0.4    1.5  1  DUF3283   Protein of unknown function (DUF3283)


Domain annotation for each model (and alignments):
>> DUF1722  Protein of unknown function (DUF1722)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.7   0.7   1.2e-42   7.3e-39       1     117 []     191     307 ..     191     307 .. 1.00

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 1.2e-42
                           DUF1722   1 KyllmahsqkeyrelgrlvanakkepleelaeeYeellmealskpatrkkhinvlqhilgyfkkklsaeekqellel 77 
                                       K+ll ahsqke + lg++van++ +++++l+ eY+e+l  al +p+++++ +nvl+h lgyf+++ls++ek+ +l++
  gi|330508231|ref|YP_004384659.1| 191 KLLLAAHSQKEAKVLGNIVANREGKDISKLLGEYHEHLAMALMRPPRYTSKANVLMHSLGYFSHELSSAEKAFFLQS 267
                                       9**************************************************************************** PP

                           DUF1722  78 iekYregkvplsvpltlLkhyarkydneylleqtylnpyP 117
                                       iekY+++k+p+s+pl++L+++++++d+eyl+eqt+++p+P
  gi|330508231|ref|YP_004384659.1| 268 IEKYKQKKLPFSAPLSILQSWIARFDEEYLKEQTFFEPFP 307
                                       ***************************************9 PP

>> DUF523  Protein of unknown function (DUF523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.6   0.0   3.3e-34     2e-30       1     137 []       9     149 ..       9     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 3.3e-34
                            DUF523   1 ilvSaCLlgekvrydgkakksevleeelkelvkeelvpvCPEvaggLptPRepael.....akr.vlkkegedvtea 71 
                                       i++S+C+ ++++rydg++ +s+++ + lk ++  +++pvC E+++gL++PR+++++     + r ++ ++g dvt++
  gi|330508231|ref|YP_004384659.1|   9 IVISRCIEFDHCRYDGSMITSDFVAA-LKPHA--HFIPVCAEMEIGLGVPRSSIRIvsvkgELRlIQPATGLDVTDR 82 
                                       89******************999887.99999..**************************988989*********** PP

                            DUF523  72 lekgaeealeelkeeeikgailkekSPSCGveki..Y...dgtfskklvegeGvfaallkeegievpseee 137
                                       ++++++++l +l+  +i+g+ilk +SPSCG+++i  Y   dg   +++++++G+f  ++ ++++++++e+e
  gi|330508231|ref|YP_004384659.1|  83 MVSFSRSFLCSLS--GIDGFILKFRSPSCGMKDIkvYssqDGP--STATKAAGFFGGAVVKSFPDLAIEDE 149
                                       *********8888..8******************999544333..455999***************99986 PP

>> DUF3283  Protein of unknown function (DUF3283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   8.7e-06     0.052      45      60 ..     257     272 ..     251     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.7e-06
                           DUF3283  45 deaekalfeqsvekYk 60 
                                       + aeka+f qs+ekYk
  gi|330508231|ref|YP_004384659.1| 257 SSAEKAFFLQSIEKYK 272
                                       569************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2302.90
//
Query:       gi|330508232|ref|YP_004384660.1|  [L=245]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete 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-45  152.7   0.3    8.9e-45  152.7   0.3    1.4  2  DUF2807   Putative auto-transporter adhesin, head GIN domain


Domain annotation for each model (and alignments):
>> DUF2807  Putative auto-transporter adhesin, head GIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.7   0.3     5e-49   8.9e-45       1     181 []      47     227 ..      47     227 .. 0.98
   2 ?   -3.4   0.1      0.39   6.9e+03     169     175 ..     234     240 ..     229     243 .. 0.47

  Alignments for each domain:
  == domain 1  score: 152.7 bits;  conditional E-value: 5e-49
                                       S-SEEEEECCEEEEEEE-SS-EEEEEEEHHHHCCEEEEEETTEEEEEE-.TTTTSSB.EEEEEEES--SEEEEECCE CS
                           DUF2807   1 dfdeievsgsidvevtqgdeqsvviegdenllekvevevedgtLkirle.kefestktlkvtvtvpnleelelsgsg 76 
                                       df++i + g  dv++ q ++  ++ie+++n++++++++v++g+L+i++    +++ +++k+  + p le++++sgsg
  gi|330508232|ref|YP_004384660.1|  47 DFSSIDLAGIGDVYLVQEEK-HLRIEAEDNIIQYMKTDVSGGKLTIYQRaDCINPHEPIKIFASTPVLESISISGSG 122
                                       79***************888.9***************************66677777******************** PP

                                       EEEE-S-EEEEEEEEEEECSEEEEEEEEEEEEEEEEECCEEEEEEEEEEEEEEEEECCEEEEEEEEEEEEEEEEEEC CS
                           DUF2807  77 sievegtlkadklelniagsgditlkldaeelsveasgsgdielsGtadrlevsvaGsGeleardlkasevevevaG 153
                                       +i + +++++d+l+l ++gsg+++l++ +++l++++sgsgd  l+G +++ ++ ++GsG+++++dl ++  +v+++G
  gi|330508232|ref|YP_004384660.1| 123 RIISRSPIESDALSLGMSGSGSMELNILCQDLRATISGSGDALLKGVTKDSDIMISGSGTMHGYDLMTDRSDVTISG 199
                                       ***************************************************************************** PP

                                       CEEEEEEEEEEEEEEEECCEEEEEES-- CS
                           DUF2807 154 sgdaevnaseslkasisgsGdvrykGnP 181
                                       sg a+vna ++l+a isgsG+v+ykGnP
  gi|330508232|ref|YP_004384660.1| 200 SGMAQVNAMDELNALISGSGSVYYKGNP 227
                                       ***************************9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.39
                                       EECCEEE CS
                           DUF2807 169 isgsGdv 175
                                       +sgsG+v
  gi|330508232|ref|YP_004384660.1| 234 VSGSGKV 240
                                       3444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); 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:                         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: 00:00:00.42
# Mc/sec: 1771.73
//
Query:       gi|330508233|ref|YP_004384661.1|  [L=298]
Description: hypothetical protein MCON_2378 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2326.78
//
Query:       gi|330508234|ref|YP_004384662.1|  [L=463]
Description: FAD dependent oxidoreductase [Methanosaeta concilii GP6]
Scores for 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   58.1   0.1    4.9e-07   29.3   0.0    3.2  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    9.4e-14   51.3   0.9    1.1e-06   28.1   0.1    2.5  3  FAD_binding_2  FAD binding domain
      4e-13   49.2   0.0    2.9e-05   23.4   0.0    3.0  2  GIDA           Glucose inhibited division protein A
    4.7e-11   42.0   0.0    1.2e-07   30.9   0.0    2.2  2  HI0933_like    HI0933-like protein
    2.2e-09   37.4   0.6    9.1e-07   28.8   0.6    2.4  1  DAO            FAD dependent oxidoreductase
    1.9e-06   27.3   0.0    3.1e-06   26.7   0.0    1.3  1  FAD_binding_3  FAD binding domain
    3.2e-06   27.3   0.0    1.1e-05   25.5   0.1    2.0  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    2.9e-05   23.6   0.3    0.00011   21.7   0.2    1.9  2  FAD_oxidored   FAD dependent oxidoreductase
    3.8e-05   23.1   0.1    8.3e-05   21.9   0.1    1.5  1  Thi4           Thi4 family
    0.00011   21.6   0.0    0.00018   20.9   0.0    1.3  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    0.00012   21.3   0.1    0.00017   20.8   0.1    1.2  1  Lycopene_cycl  Lycopene cyclase protein
     0.0003   21.3   0.0       0.18   12.4   0.0    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.017   15.1   0.0       0.47   10.4   0.0    2.2  2  NAD_binding_9  FAD-NAD(P)-binding
      0.025   14.0   0.0       0.69    9.2   0.0    2.1  2  GMC_oxred_N    GMC oxidoreductase
      0.098   11.9   0.0       0.31   10.3   0.0    1.8  3  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   4.1e-10   4.9e-07       2      43 ..       3      44 ..       2      98 .. 0.81
   2 !   15.4   0.0     7e-06    0.0084     174     239 ..     136     203 ..      78     225 .. 0.87
   3 !   10.0   0.0   0.00031      0.37     236     284 ..     391     437 ..     387     444 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 4.1e-10
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggclls 43
                                      dv+++G+GpAGl aal+l+++ akv+++++++ +  + c+++
  gi|330508234|ref|YP_004384662.1|  3 DVIIVGAGPAGLFAALELSRSDAKVLVIDQGKDIRDRNCPMK 44
                                      8***************************95544444444443 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 7e-06
                                       SSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE-S-EEE CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 174 rdrll.raldkelsaaleealekeGvevklgtsvkeidgngekle.vvledgeeidadlvvvavGvrp 239
                                       ++r + +   +e+ aa +  le++Gv ++l++++++++ +ge+ +   l dg+e++a+ +++a G+  
  gi|330508234|ref|YP_004384662.1| 136 NQRHMgSDRTPEIIAAFKMDLERRGVVFRLNCRAEDLIVEGERCTgIRLADGTEEKASRILLAPGRIG 203
                                       55566666779999999*************************8889*****************99865 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00031
                                       -EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 236 GvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggp 284
                                       Gv ++++l+  +  ++   +++i+vd + +++ +g+y++GD ag  +g+
  gi|330508234|ref|YP_004384662.1| 391 GVNADSTLV-YAPEIKF-YARKIEVDGSFQSSLKGLYVAGDGAGLSRGI 437
                                       666666666.6666776.7899*******************99444433 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   8.9e-10   1.1e-06       1      33 [.       3      35 ..       3      38 .. 0.95
   2 !   21.4   0.0   9.4e-08   0.00011     135     209 ..     140     209 ..      88     222 .. 0.82
   3 ?   -3.4   0.0       3.2   3.8e+03     384     404 ..     413     432 ..     410     443 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 8.9e-10
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      Dvi++G+G AGL AAle+++  +kv+v+++++ 
  gi|330508234|ref|YP_004384662.1|  3 DVIIVGAGPAGLFAALELSRSDAKVLVIDQGKD 35
                                      9*****************************975 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 9.4e-08
                                       ....HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..... CS
                     FAD_binding_2 135 etlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallke 209
                                       +     ++++a++   ++++gv f+ +++a++Live++r+tG+ ++   +g+e++  a +++la g +g++++  
  gi|330508234|ref|YP_004384662.1| 140 MGSDRTPEIIAAFKMDLERRGVVFRLNCRAEDLIVEGERCTGIRLA---DGTEEK--ASRILLAPGRIGAQWISI 209
                                       44446799*************************************9...666664..899*********977654 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.2
                                       ESTTEEESSBTEEE-STCEES CS
                     FAD_binding_2 384 vldadgqpipGLYAaGevaag 404
                                       v+++ ++ ++GLY aG  a g
  gi|330508234|ref|YP_004384662.1| 413 VDGSFQSSLKGLYVAGDGA-G 432
                                       4444456899***999877.4 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.4e-08   2.9e-05       1     162 [.       3     213 ..       3     222 .. 0.72
   2 !   20.9   0.0   1.3e-07   0.00016     300     390 ..     361     457 ..     343     459 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.4e-08
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE..................................ES-GGGTT--SSSSE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..................................thkldtiaelsCnps 43 
                                       dvi++G+G AG+ AAl+++r+ akvl i                                      d +++l   p+
  gi|330508234|ref|YP_004384662.1|   3 DVIIVGAGPAGLFAALELSRSDAKVLVIdqgkdirdrncpmkdrghcfhcypcqimcgvggaGAFSDGLLNL--HPT 77 
                                       7***************************99999999999999999999999999999999877777888888..899 PP

                                       EE-T....THHHHHHHHHHHT-SHHH......HHHHHEEEEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTT CS
                              GIDA  44 iggi....akgllvrEidalggliik......aadkagiqfrilNrskGpavralraqvdrelyskevteklenepn 110
                                       igg+    ak++  r id++++   +      ++++++  ++ l r+k  a +a  + ++++++ ++ t ++ +  +
  gi|330508234|ref|YP_004384662.1|  78 IGGDleslAKSEAWRLIDEVDSAFLRygapnmVIESSEYDKEQL-RRKAAAAGARFVPINQRHMGSDRTPEIIAAFK 153
                                       99999999999999989998888776222222344445455555.55555555555556555555555544444444 PP

                                       EEEEES........-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEE CS
                              GIDA 111 leiiee........eveeliveekkvkgvvtedgetikakavviatGtflkgkihigeke 162
                                       +++ ++        ++e+live ++++g++++dg++ ka+ + +a G   +++i i  ++
  gi|330508234|ref|YP_004384662.1| 154 MDLERRgvvfrlncRAEDLIVEGERCTGIRLADGTEEKASRILLAPGRIGAQWISILLDR 213
                                       444433111111115566667669999999999999999999999998777877776655 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1.3e-07
                                       EEEET----S-HHHHHHHHTTSTT-TT--EEE--EEEEEEEE-GGGB-..T.TSBB.....SSSBTEEE-CGGGTB. CS
                              GIDA 300 iylvgfstslpeevqkevlrsipGLenaeivrpGyaieydyvdprqll..n.tLet.....kkvkgLflAGqinGt. 367
                                       +++  +s  lp+   + v+  i+GLe ++ + pG+  + + v +++++  + ++e+     ++ kgL++AG+  G  
  gi|330508234|ref|YP_004384662.1| 361 VTPGDISMALPH---RIVMDIIEGLEILNQIIPGVNADSTLVYAPEIKfyArKIEVdgsfqSSLKGLYVAGDGAGLs 434
                                       566677777777...4578999*******************999998766446776222223589***********9 PP

                                       -SHHHHHHHHHHHHHHHHHHHCT CS
                              GIDA 368 eGYeEaaaqGllAGinaarkakg 390
                                        G + aaa+G+lAG+ +  +++g
  gi|330508234|ref|YP_004384662.1| 435 RGIVSAAATGILAGRGILSDLNG 457
                                       9*************988777665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   9.6e-11   1.2e-07       2      35 ..       3      36 ..       2      49 .. 0.93
   2 !    9.1   0.0    0.0004      0.48     105     163 ..     142     200 ..     107     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 9.6e-11
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35
                                      dvi++G+G+AGl+aA+++++ +++Vl+++++k +
  gi|330508234|ref|YP_004384662.1|  3 DVIIVGAGPAGLFAALELSRSDAKVLVIDQGKDI 36
                                      8*****************************9976 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0004
                                       T.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 105 sdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       sd+  +i+ a++  l+++gv +rl+++ +++  e ++   +++ +++e +a++++lA G
  gi|330508234|ref|YP_004384662.1| 142 SDRTPEIIAAFKMDLERRGVVFRLNCRAEDLIVEGERCTGIRLADGTEEKASRILLAPG 200
                                       446889*************************************9*************87 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.6   7.6e-10   9.1e-07       1     268 [.       3     265 ..       3     286 .. 0.50

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 7.6e-10
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSS.........................TTSSGGGSSEEEEESSSST CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdi.........................agsgaSgrnsgllhsglry 50 
                                       dv+i+G+G +Gl++A+eL+r    V+++++g++                         +g ga   + gll  +   
  gi|330508234|ref|YP_004384662.1|   3 DVIIVGAGPAGLFAALELSRSDakVLVIDQGKDirdrncpmkdrghcfhcypcqimcgVG-GAGAFSDGLLNLHPTI 78 
                                       9*****************998789*******88444444444444444444444443322.3333333333221111 PP

                                       HHSTHHHHHHHH.HHHHHHHHHHHHHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEE.....EHHHH CS
                               DAO  51 lpeaselarlsl.ealeelreleeelgididyrrtGllslaadeeelealdkllallleagldaell.....daeev 121
                                            +l  l++ ea+++++e+++                                 l++g+++ ++     d+e++
  gi|330508234|ref|YP_004384662.1|  79 G---GDLESLAKsEAWRLIDEVDSAF-------------------------------LRYGAPNMVIesseyDKEQL 121
                                       1...1333444434444444444432...............................22333222220000033333 PP

                                       HHHSTTSTTTSEEEEET....TEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEE CS
                               DAO 122 relepalpgllgalfyp....dtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgendaad 194
                                       r+++      +ga f+p    + g   + + +aa+  ++e++Gv +++++++++l  e+++ +g+ r ++g++++a 
  gi|330508234|ref|YP_004384662.1| 122 RRKAA----AAGARFVPinqrHMGSDRTPEIIAAFKMDLERRGVVFRLNCRAEDLIVEGERCTGI-RLADGTEEKAS 193
                                       33332....12332222000011222457799999999****************98888999999.44446665568 PP

                                       EEEE--G....GGHHHHHTTCTT.TSEEEEEEEEEEEEEECCTHSTGSG.CSEEEEE.EEETTTTEEEEEETTSEEE CS
                               DAO 195 avVnaaG....awsdllgllkel.dlpispvrgqvlvlkplseklvspa.ailpvpe.tdddgrgvyvtprkdgrvl 264
                                        + +a G     w        +l d+  +++++ +  l+   +  + p    +p+   ++d++++ +vt+r d+ v+
  gi|330508234|ref|YP_004384662.1| 194 RILLAPGrigaQWI------SILlDR--YAIKARYGPLDVGVR-IEVPSiIMDPITRiNRDPKFH-IVTRRYDDFVR 260
                                       89999994222222......222221..333333322211111.112221333333323443333.44444456555 PP

                                       .EEES CS
                               DAO 265 .vGgt 268
                                        ++++
  gi|330508234|ref|YP_004384662.1| 261 tFCTN 265
                                       33655 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   2.6e-09   3.1e-06       2      47 ..       2      52 ..       1      68 [. 0.76

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.6e-09
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.....S--EEEH CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.....radglnq 47
                                      +dV+IVGaGpaGl +al+Ls+   +v+++++ ++  +       r++ +++
  gi|330508234|ref|YP_004384662.1|  2 VDVIIVGAGPAGLFAALELSRSDAKVLVIDQGKDIRDRNcpmkdRGHCFHC 52
                                      79****************************866543332334456666666 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.1   9.3e-09   1.1e-05       1      31 [.       6      36 ..       6      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 9.3e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31
                                      IvGaG +Gl aA +L++ +++vl+++++ ++
  gi|330508234|ref|YP_004384662.1|  6 IVGAGPAGLFAALELSRSDAKVLVIDQGKDI 36
                                      9**************************9887 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   9.5e-08   0.00011       1      31 [.       3      33 ..       3      36 .. 0.95
   2 ?   -0.6   0.0      0.53   6.3e+02      95     129 ..     154     188 ..     118     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 9.5e-08
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      Dv++vG+gpaG+ AA+   r++akvl++++ 
  gi|330508234|ref|YP_004384662.1|  3 DVIIVGAGPAGLFAALELSRSDAKVLVIDQG 33
                                      9***************************986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.53
                      FAD_oxidored  95 emlaeagvtvllntrlvevekegkriesvtveske 129
                                         l++ gv   ln+r+++ ++eg+r++++++++ +
  gi|330508234|ref|YP_004384662.1| 154 MDLERRGVVFRLNCRAEDLIVEGERCTGIRLADGT 188
                                       33466799999************9*****997643 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   6.9e-08   8.3e-05      18      49 ..       2      32 ..       1      35 [. 0.94

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 6.9e-08
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailer 49
                                       Dv+ivGaG++GL aa  l+++ d kv+++++
  gi|330508234|ref|YP_004384662.1|  2 VDVIIVGAGPAGLFAALELSRS-DAKVLVIDQ 32
                                      69********************.******986 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.5e-07   0.00018       1      31 [.       5      34 ..       5      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.5e-07
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      iI+GaGPaGl aa+el +++  ++l++++g+
  gi|330508234|ref|YP_004384662.1|  5 IIVGAGPAGLFAALELSRSDA-KVLVIDQGK 34
                                      8********************.7*****995 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.4e-07   0.00017       1      36 [.       3      36 ..       3      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.4e-07
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      Dv+++GaGpAgl  A +l  ++ + kv++i+ ++++
  gi|330508234|ref|YP_004384662.1|  3 DVIIVGAGPAGLFAALEL--SRSDAKVLVIDQGKDI 36
                                      9*****************..************9987 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00015      0.18       2      36 ..       4      39 ..       3      44 .. 0.91
   2 ?    6.2   0.0     0.012        15      40      80 ..     146     186 ..     133     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.T CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.r 36
                                      v++vG+G  gl +A +l++  +kV v++ ++ ++ r
  gi|330508234|ref|YP_004384662.1|  4 VIIVGAGPAGLFAALELSRSDAKVLVIDQGKDIRdR 39
                                      89***************************9999855 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEET CS
                         Pyr_redox  40 eeaskilqeklekngievllntkveeiegsedgvesvklkd 80 
                                       +e+ ++++  le++g+ ++ln ++e +  +++  ++++l+d
  gi|330508234|ref|YP_004384662.1| 146 PEIIAAFKMDLERRGVVFRLNCRAEDLIVEGERCTGIRLAD 186
                                       678889999******************99998899999876 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00039      0.47       2      33 ..       6      32 ..       5      49 .. 0.82
   2 ?    2.4   0.0      0.12   1.4e+02     118     154 ..     163     200 ..     142     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00039
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdp 33
                                      ivGaGp+Gl ++ +L ++     + ++ ++d+
  gi|330508234|ref|YP_004384662.1|  6 IVGAGPAGLFAALELSRS-----DAKVLVIDQ 32
                                      9**************999.....467777776 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                     NAD_binding_9 118 evhraevvdleeradgq.avlladgaslaadaVvLAlG 154
                                         ++ +++dl  ++++   ++ladg++ +a ++ LA G
  gi|330508234|ref|YP_004384662.1| 163 FRLNCRAEDLIVEGERCtGIRLADGTEEKASRILLAPG 200
                                       4456688888888877537*****************99 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.064        76       1      42 [.       2      43 ..       2      51 .. 0.83
   2 ?    9.2   0.0   0.00058      0.69     198     239 ..     151     190 ..     125     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.064
                       GMC_oxred_N  1 vdelveggGsagsvvAaRLsedpstsvlvleaggreknrl.im 42
                                      vd +++g+G ag   A  Ls  + ++vlv++ g + ++r+  m
  gi|330508234|ref|YP_004384662.1|  2 VDVIIVGAGPAGLFAALELSRSD-AKVLVIDQGKDIRDRNcPM 43
                                      588***********999999876.6899999999888877544 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00058
                       GMC_oxred_N 198 wLrpalerpnleiltgakaekiilegrkkravGVeasdkkgt 239
                                        ++  ler ++++  +++ae +i+e  ++r++G++  d  ++
  gi|330508234|ref|YP_004384662.1| 151 AFKMDLERRGVVFRLNCRAEDLIVE--GERCTGIRLADGTEE 190
                                       566678899****************..********9998887 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00026      0.31      30      62 ..       3      35 ..       1      46 [. 0.90
   2 ?   -3.3   0.0       3.6   4.4e+03     165     185 ..     306     326 ..     287     333 .. 0.79
   3 ?   -3.7   0.0       4.9   5.9e+03     165     190 ..     392     417 ..     389     422 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00026
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                       v+++G+G aGl A+   ++ +akV v+D  ++
  gi|330508234|ref|YP_004384662.1|  3 DVIIVGAGPAGLFAALELSRSDAKVLVIDQGKD 35
                                      599**************************8765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.6
                                       SHHHHHHHHHHHHHHHHHHHC CS
                       AlaDh_PNT_C 165 vprtasalltnntlpyleell 185
                                        p++ ++++ +++ ++++++ 
  gi|330508234|ref|YP_004384662.1| 306 RPVENTTAYGMSIAKLVTTIG 326
                                       578889999999999998884 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.9
                                       SHHHHHHHHHHHHHHHHHHHCHHHTC CS
                       AlaDh_PNT_C 165 vprtasalltnntlpyleelladkgl 190
                                       v ++++ +++ ++  y++++  d+ +
  gi|330508234|ref|YP_004384662.1| 392 VNADSTLVYAPEIKFYARKIEVDGSF 417
                                       56789999999999999999666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3241.90
//
Query:       gi|330508235|ref|YP_004384663.1|  [L=358]
Description: major facilitator family transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-42  146.0  72.1    9.4e-36  123.5  43.0    2.0  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.78    8.5  31.0      0.059   12.2  13.5    2.4  2  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5  43.0     1e-39   9.4e-36      16     351 ..       3     316 ..       1     318 [. 0.91
   2 !   36.2  21.0   3.5e-13   3.2e-09      43     169 ..     225     349 ..     225     356 .. 0.90

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 1e-39
                             MFS_1  16 gpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfasslw.lllv 90 
                                       +++ p +l ++lg+s  ++ ll ++ +l ++++++++G+l+d+ G r  + +++ll++ g ++l+l+ s+++ ++l 
  gi|330508235|ref|YP_004384663.1|   3 MALQP-LLITTLGYSYVQAALLPVMHSLISSLLQPVFGSLADKRGFRVSVAVSILLSGCGiAVLGLL-SNHYlAMLG 77 
                                       44445.889***************************************************5555556.88888**** PP

                             MFS_1  91 lrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvl 167
                                       + +++++ga+++ p+++  +a ++  ++rgr ++++ +g +lG +lgp+l+g++++++g +a+ ++l ++ + a++l
  gi|330508235|ref|YP_004384663.1|  78 CVAIASVGAATFHPGALCKVASIAVLSNRGRLTSFFIVGGNLGHALGPILAGIVITAGGLSAITWLLIPAVIGALLL 154
                                       ***************************************************************99999999999777 PP

                             MFS_1 168 fllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsgll 244
                                         l  p +++ +   +++e    +g+ +++p         v++ l++++ l ++++ g++t+lp+y     g++ ll
  gi|330508235|ref|YP_004384663.1| 155 --LIRPIPDTCPVAARQAES---DGEENWKP---------VIL-LFTGSTLRSWVTVGTMTFLPTY-LVLNGYP-LL 214
                                       ..999999999999999999...46666666.........554.99999999**************.*******.** PP

                             MFS_1 245 laglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsl 321
                                       +a+++++ + l+g++++l +g++sdr+gr++  + + l+ + a+++++l++ +    l +++++++Gf+l   f+  
  gi|330508235|ref|YP_004384663.1| 215 EATFFISSMLLAGVVGQLAGGYFSDRVGRKPVVIATTLCSIPAFAAILLTNDA----LQIFAILCFGFFLWASFSVT 287
                                       ****************************9999999999999999999999999....9999*******99999**** PP

                             MFS_1 322 lalasdlappeeagtasglfntagslggal 351
                                       +a+a +l+p ++ g +sglf+ +   +g l
  gi|330508235|ref|YP_004384663.1| 288 IAMAHELMP-SKIGLISGLFMGIAMGAGGL 316
                                       ********8.***********555555555 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 3.5e-13
                             MFS_1  43 lgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeer 119
                                       l+ +v++l +G++sdr+Gr++v++++ l+++ +++++l+ ++  l +++ +  G++  a+f++ +a++ ++ p  + 
  gi|330508235|ref|YP_004384663.1| 225 LAGVVGQLAGGYFSDRVGRKPVVIATTLCSIPAFAAILL-TNDALQIFAILCFGFFLWASFSVTIAMAHELMPS-KI 299
                                       57799****************************444444.9999*****************************9.99 PP

                             MFS_1 120 graigllsagfslGailgpllggllasslgWravfyilaivsllafvlfl 169
                                       g+  gl+++ +  +  lg  +++++a+++g +a+  ++ ++ lla++lf 
  gi|330508235|ref|YP_004384663.1| 300 GLISGLFMGIAMGAGGLGVSVSSAIADQFGLTATLSVFPFLILLAALLFS 349
                                       999999999888888******************************99654 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   9.3    0.0089        80      65     183 ..      37     153 ..      13     162 .. 0.84
   2 ?   12.2  13.5   6.6e-06     0.059      48     184 ..     216     348 ..     197     353 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.0089
                                       HHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHH CS
                          Sugar_tr  65 fagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvs 141
                                       ++g l+d+ G + s +++++l+  g+++ ++    n++ +++ +  ++ +g+ ++   +   ++ iA  + Rg+l+s
  gi|330508235|ref|YP_004384663.1|  37 VFGSLADKRGFRVSVAVSILLSGCGIAVLGLLS--NHYLAMLGCVAIASVGAATFHPGALCKVASIAVLSNRGRLTS 111
                                       7899**********************9999999..799999999********************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHTSS-..TTHHHHHHHCCHHHHHH CS
                          Sugar_tr 142 lyqlaitfGilvaaifglglnktsn..adgwrillglqlvpall 183
                                       ++ ++  +G  ++ i+  ++ + ++  a +w  ll  +++ all
  gi|330508235|ref|YP_004384663.1| 112 FFIVGGNLGHALGPILAGIVITAGGlsAITW--LLIPAVIGALL 153
                                       ****************999999999444444..33333333333 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.6e-06
                                       HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                          Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                        +++ s++l+ +++G+l +g+++dr+GRk++ ++++++++ + + + +++      ++++  +  G+++ +   ++ 
  gi|330508235|ref|YP_004384663.1| 216 ATFFISSMLLAGVVGQLAGGYFSDRVGRKPVVIATTLCSIPAFAAILLTN---DALQIFAI-LCFGFFLWASFSVTI 288
                                       5899**************************99888877765544444444...23333333.444555555555555 PP

                                       HHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHH CS
                          Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpalll 184
                                         + E+ p k+  + + +   a+ +G l  +++ ++ ++++ + +  ++ +l l+ all+
  gi|330508235|ref|YP_004384663.1| 289 AMAHELMPSKIGLISGLFMGIAMGAGGLGVSVSSAIADQFGLTATLSVFPFLILLAALLF 348
                                       557777777776555555555555555555555555555555555555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2540.01
//
Query:       gi|330508236|ref|YP_004384664.1|  [L=345]
Description: hypothetical protein MCON_2382 [Methanosaeta concilii GP6]
Scores for 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   77.4   0.0    7.5e-14   51.9   0.0    2.2  2  FmdE      FmdE, Molybdenum formylmethanofuran dehydrogenase o


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.7e-09   4.8e-05      11      88 ..      31     120 ..      28     145 .. 0.77
   2 !   51.9   0.0   4.2e-18   7.5e-14       1      86 [.     173     275 ..     173     306 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.7e-09
                                       HHHHHHHHHHHCC....-TTSSSEEEEES-S..........TCHHHHHHHHCS--TTTTSEEE--...SS-SEEEEE CS
                              FmdE  11 lGyrmakaalkelgpkeeegdeelvaivetd..........sCldDAiqvltgctlGkgnlivmd...ygkkaltfk 74 
                                       lG  ++++a+ elg +  +gd ++ a+++            +Cl DA++ + gct+Gk nl+      +    + f 
  gi|330508236|ref|YP_004384664.1|  31 LGTNATNYAMTELGFE--KGDVNVLALTNAGypvidgqttdMCL-DAVVEVSGCTPGKENLVNILsapWKPLWFGFF 104
                                       799999*******984..46778888888779999999998886.9************9998765333666667999 PP

                                       ETTT-EEEEEEE-..C CS
                              FmdE  75 krktgkavrlklk..e 88 
                                       +++tg+av +k++   
  gi|330508236|ref|YP_004384664.1| 105 NKNTGEAVYMKMNadA 120
                                       99******99999331 PP

  == domain 2  score: 51.9 bits;  conditional E-value: 4.2e-18
                                       HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--............ CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetdsCldDAiqvltgctlGkgnlivmd............ 65 
                                       +H+HlCpg+ +G+  a+++ kel+++++ + + + +i+  ++C+dD +q++++ct+Gk  ++v+             
  gi|330508236|ref|YP_004384664.1| 173 LHDHLCPGVSSGFLLARYMEKELPIDDPAN-QSYKVIACPNWCKDDYFQIAWDCTPGKSGIFVKCltedetsaltek 248
                                       5************************98887.***************************8888877433333333333 PP

                                       .SS-SEE.EEEET.....TT-EEEEEEE CS
                              FmdE  66 .ygkkal.tfkkr.....ktgkavrlkl 86 
                                         g+ ++  f+ r     k+g+++ l +
  gi|330508236|ref|YP_004384664.1| 249 yNGTRVAgIFI-RwdassKSGDGLVLGF 275
                                       23333332222.2355555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2555.94
//
Query:       gi|330508237|ref|YP_004384665.1|  [L=189]
Description: FMN-binding protein [Methanosaeta concilii GP6]
Scores for complete 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   69.8   0.0    3.4e-19   69.4   0.0    1.1  1  Flavin_Reduct  Flavin reductase like domain
    0.00014   21.7   0.0    0.00026   20.8   0.0    1.3  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 !   69.4   0.0   3.8e-23   3.4e-19       4     137 ..      12     145 ..       8     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 3.8e-23
                                       S-EE-EEEEE.EETTEEEEEEESSEEEEETTT.TEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS... CS
                     Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldP.plvafslrlpsstadalkeagefvinllsesqealadafsqksg 79 
                                       ++ pv++++t  +++ +++a+ s +t++ l P   v+++  l+++t+++++++gefvin+  +  e+++  +++  +
  gi|330508237|ref|YP_004384665.1|  12 MPLPVVLLSTISQDGVRNAAPWSCVTPV-LRPlDEVLIASWLKRDTLENIRQTGEFVINVPRAGMEDAVMTCAKSFP 87 
                                       688*******999**************9.999999***************************************887 PP

                                       SCCCCCCCCCCCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEEST CS
                     Flavin_Reduct  80 prtddksifagltwees.ptgapallgalasleCqvvgsvelgdhelfigeVvavkvgd 137
                                         ++d+++ agl  ++s ++++p ++g+la+ eC+v +++   +  l++g+Vv+ + +d
  gi|330508237|ref|YP_004384665.1|  88 -PEVDELKEAGLVARPSvKVKPPGIEGCLAWAECTVEEEIAREKYVLIVGRVVHLEADD 145
                                       .9***************99***********************************99887 PP

>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.9e-08   0.00026       3     121 ..      17     149 ..      17     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.9e-08
                                       EEEEEE-TT.-EEEEEEEEEE....SSSEEEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEEE CS
                            DUF447   3 vivtTksek.rpnaaPiGviv....kgdkvvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfdse 74 
                                       v+++T s++ ++naaP   ++      d+v+++ + +  TleN++++ge+vinv +  ++ a +++ +    ++d+ 
  gi|330508237|ref|YP_004384665.1|  17 VLLSTISQDgVRNAAPWSCVTpvlrPLDEVLIASWLKRDTLENIRQTGEFVINVPRAGMEDAVMTCAKSFPPEVDEL 93 
                                       67889999999999998766655558899999999999****************86555444444444433333333 PP

                                       TTTC.TT..........EETT-SEEEEEEEEEECTCECCEEEEEEEEEEEEETTB-- CS
                            DUF447  75 tkpa.kia.........vlksaeawveveveevegdsealelelepvkeeileervk 121
                                       ++++   a          ++++ aw+e++vee+  +++ + +  ++v+ e  ++++ 
  gi|330508237|ref|YP_004384665.1|  94 KEAGlV-ArpsvkvkppGIEGCLAWAECTVEEEIAREKYVLIVGRVVHLEADDRFFS 149
                                       332111.1122334489****************999999999999999888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1362.24
//
Query:       gi|330508238|ref|YP_004384666.1|  [L=249]
Description: carbon monoxide dehydrogenase accessory protein [Methanosaeta concilii GP6]
Scores for complete 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   47.3   0.0    3.4e-12   46.5   0.0    1.4  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    6.2e-09   35.7   0.5    4.6e-07   29.5   0.1    2.9  3  ParA             NUBPL iron-transfer P-loop NTPase
    1.9e-08   34.4   0.0    5.4e-08   33.0   0.0    1.7  1  AAA_31           AAA domain
    2.3e-07   30.3   0.2    4.5e-07   29.4   0.2    1.4  1  ArsA_ATPase      Anion-transporting ATPase
      3e-06   26.9   3.6    3.1e-05   23.6   0.1    2.4  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
      4e-05   23.5   0.0      8e-05   22.6   0.0    1.5  1  APS_kinase       Adenylylsulphate kinase
    4.5e-05   23.3   0.0      0.001   18.9   0.0    2.2  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
    8.1e-05   22.0   0.1     0.0021   17.4   0.1    2.1  2  MipZ             ATPase MipZ
    0.00014   22.1   0.1      0.051   13.8   0.0    2.4  2  TrkA_N           TrkA-N domain
    0.00019   20.8   0.1    0.00064   19.1   0.1    1.8  2  Zeta_toxin       Zeta toxin
    0.00025   20.6   0.0      0.011   15.3   0.0    2.1  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
    0.00052   20.2   0.0      0.001   19.2   0.0    1.6  1  DUF87            Helicase HerA, central domain
     0.0019   17.9   0.0     0.0059   16.3   0.0    1.8  2  SRP54            SRP54-type protein, GTPase domain
     0.0019   17.9   0.1      0.004   16.9   0.0    1.6  2  AAA_24           AAA domain
     0.0032   17.0   0.0     0.0049   16.3   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
     0.0046   15.9   0.0      0.044   12.7   0.0    2.0  2  AAA_10           AAA-like domain
      0.007   16.9   0.0     0.0098   16.4   0.0    1.4  1  ABC_tran         ABC transporter
  ------ inclusion threshold ------
      0.015   14.7   0.1      0.036   13.4   0.1    1.5  1  ATPase           KaiC
       0.02   13.9   0.3      0.045   12.7   0.1    1.6  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.021   13.8   0.0      0.031   13.2   0.0    1.2  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.027   14.1   0.2      0.084   12.4   0.0    1.8  2  AAA_25           AAA domain
      0.027   14.6   0.0      0.057   13.6   0.0    1.6  2  AAA_33           AAA domain
      0.027   14.5   0.0      0.033   14.2   0.0    1.1  1  DUF1995          Domain of unknown function (DUF1995)
      0.036   13.3   0.1      0.091   12.0   0.0    1.6  2  KAP_NTPase       KAP family P-loop domain
      0.043   13.6   0.2        3.8    7.3   0.1    2.3  2  AAA_26           AAA domain
       0.05   14.1   0.0        0.1   13.1   0.0    1.5  1  AAA_18           AAA domain
       0.15   12.5   0.0       0.31   11.5   0.0    1.6  1  RNA_helicase     RNA helicase
       0.16   11.7   0.0       0.34   10.6   0.0    1.5  1  Thymidylate_kin  Thymidylate 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 !   46.5   0.0   5.2e-15   3.4e-12       3     126 ..       4     231 ..       2     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 5.2e-15
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep......................... 54 
                                       ++ +kGG+GK+t++a +ar +a rg +Vl+vD+D    n   l++  +  +p                         
  gi|330508238|ref|YP_004384666.1|   4 VICGKGGSGKSTVSALIAREMASRGEKVLVVDTDES--NFG-LYKQLGLPQPrdfmdslggkkglgerlmkfmrseg 77 
                                       6789****************************9988..544.4444444444667999******************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|330508238|ref|YP_004384666.1|  78 keklsilqefsiddipqelivgedgiklvaigkihdygegcacpmgalarefieklkadgmqvivdtdagiehfgrg 154
                                       ***************************************************************************** PP

                                       .................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE- CS
                                       .................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 .................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgvipr 114
                                                        +  +l+e ++++g k +   k++ ++lnr +++   ++l ++l +     g +v+g++p+
  gi|330508238|ref|YP_004384666.1| 155 veagsdrivvvidpsfeS-VQLSEKISEMGAKIN---KPVCFILNRMNED--AAEL-SSLVD-----GKKVIGSVPF 219
                                       ***999999999998853.455777777777765...89********999..4444.44445.....99******** PP

                                       -CCHCCCCHHTS CS
                                       xxxxxxxxxxxx RF
                              CbiA 115 deavaeaparge 126
                                       d +v +a  +g 
  gi|330508238|ref|YP_004384666.1| 220 DRDVFQACLKGS 231
                                       ****99988776 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   7.2e-10   4.6e-07       7      42 ..       3      38 ..       1      60 [. 0.88
   2 ?    1.7   0.0      0.23   1.5e+02     136     175 ..     159     198 ..      92     206 .. 0.88
   3 ?    1.2   0.0      0.31     2e+02     202     233 ..     210     241 ..     198     248 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 7.2e-10
                              ParA  7 avlSgKGGVGKStvavnlAlaLakkglkvgllDaDi 42
                                       v+ gKGG GKStv++ +A ++a++g kv ++D+D 
  gi|330508238|ref|YP_004384666.1|  3 FVICGKGGSGKSTVSALIAREMASRGEKVLVVDTDE 38
                                      5899******************************95 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.23
                              ParA 136 lagaviVttpqevaladvkkaiemfkkvkvkvlGvveNms 175
                                        + +v+V  p   +++  +k  em  k++ +v  +++ m+
  gi|330508238|ref|YP_004384666.1| 159 SDRIVVVIDPSFESVQLSEKISEMGAKINKPVCFILNRMN 198
                                       5678999999999999999*********999999998886 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.31
                              ParA 202 gvpllgeipldpeireasdegkplvlkepese 233
                                       g +++g++p+d ++ +a+ +g+++ + ++ +e
  gi|330508238|ref|YP_004384666.1| 210 GKKVIGSVPFDRDVFQACLKGSQVPQLAEMKE 241
                                       45899*************99998766554444 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   8.4e-11   5.4e-08       9     155 ..       7     174 ..       3     192 .. 0.59

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 8.4e-11
                            AAA_31   9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt..glgiekne...........iektlyevlieeknikea 72 
                                        KGG GK+T s  +a  +a++g+kvL+vD D  +n     +lg+ + +           + ++l++ + +e + k  
  gi|330508238|ref|YP_004384666.1|   7 GKGGSGKSTVSALIAREMASRGEKVLVVDTDE-SNFGLykQLGLPQPRdfmdslggkkgLGERLMKFMRSEGKEKLS 82 
                                       6******************************6.45444233333222234444443333455666665433333333 PP

                            AAA_31  73 iiktkvenldlipssidLaeaeielvelekk..........eeil.kellekvkdeYDyiiiDcpPsLglltenaLv 138
                                       i  ++  ++d ip ++ + e  i+lv + k             +l +e++ek+k +   +i+D+   ++ + +   +
  gi|330508238|ref|YP_004384666.1|  83 IL-QE-FSIDDIPQELIVGEDGIKLVAIGKIhdygegcacpMGALaREFIEKLKADGMQVIVDTDAGIEHFGRGVEA 157
                                       33.22.23344555555555555555555553333334443222447778888888888888888888888888888 PP

                            AAA_31 139 asdsviipvqaeayale 155
                                        sd +++++++++ +++
  gi|330508238|ref|YP_004384666.1| 158 GSDRIVVVIDPSFESVQ 174
                                       88888888888555543 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.2     7e-10   4.5e-07       4      38 ..       3      37 ..       1      40 [. 0.93

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 7e-10
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      +++ GKGG GK+tvsa +a +++  g+kvl++ tD
  gi|330508238|ref|YP_004384666.1|  3 FVICGKGGSGKSTVSALIAREMASRGEKVLVVDTD 37
                                      4679******************************9 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 !   23.6   0.1   4.9e-08   3.1e-05       1      37 [.       1      37 [.       1      42 [. 0.93
   2 ?    3.9   0.7     0.047        30      77     235 ..      99     244 ..      67     248 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.9e-08
                         Fer4_NifH  1 rkiaiyGkGGiGksttsqnlsaalaemgkkvlivGCD 37
                                      +k+ i GkGG+Gkst s+ ++  +a++g+kvl+v  D
  gi|330508238|ref|YP_004384666.1|  1 MKFVICGKGGSGKSTVSALIAREMASRGEKVLVVDTD 37
                                      57899****************************9887 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.047
                         Fer4_NifH  77 GyggvkcvesGG.PepGvGCaGrgvitaielleelgayddlDfvlyDvLGDvvCGGfalPiredkaqevyivtsgel 152
                                       G  g+k v  G   + G GCa      a e++e+l a   +  v+ D   D     f+  ++   ++++++v +  +
  gi|330508238|ref|YP_004384666.1|  99 GEDGIKLVAIGKiHDYGEGCACPMGALAREFIEKLKADG-M-QVIVD--TDAGIEHFGRGVE-AGSDRIVVVIDPSF 170
                                       556667666665235677777766666777777766522.2.22223..4555556666666.45677777777777 PP

                         Fer4_NifH 153 malyaanniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyap 229
                                       +++  + +i++   k +k   v     i n r ++++   ++ +++  g kv+  vP d +v +a l+   v + a+
  gi|330508238|ref|YP_004384666.1| 171 ESVQLSEKISEMGAKINKP--V---CFILN-R-MNEDAAELSSLVD--GKKVIGSVPFDRDVFQACLKGSQVPQLAE 238
                                       7777777777655555443..2...45777.5.4555555666665..68999999999999999999999999988 PP

                         Fer4_NifH 230 eseqak 235
                                        +e+ +
  gi|330508238|ref|YP_004384666.1| 239 MKEIVD 244
                                       887665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.3e-07     8e-05       6      51 ..       4      49 ..       1      55 [. 0.93

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.3e-07
                                      EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--S CS
                        APS_kinase  6 wltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgf 51
                                       + G  gsGKst++  +++++ ++g +v ++d d+  +gL+k+Lg 
  gi|330508238|ref|YP_004384666.1|  4 VICGKGGSGKSTVSALIAREMASRGEKVLVVDTDESNFGLYKQLGL 49
                                      57899***************************************97 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 !   18.9   0.0   1.6e-06     0.001       1      31 [.       7      37 ..       7      48 .. 0.94
   2 ?    2.2   0.0       0.2   1.3e+02      86     119 ..     124     153 ..     117     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.6e-06
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlD 31
                                      G+  sGKST+++l++ +++++g+k+++vD+D
  gi|330508238|ref|YP_004384666.1|  7 GKGGSGKSTVSALIAREMASRGEKVLVVDTD 37
                                      6778**************************9 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.2
                            CLP1_P  86 elareveekleenkkakasgliIntpGwvkglga 119
                                       +lare+ ekl+++       +i++t+  ++ +g+
  gi|330508238|ref|YP_004384666.1| 124 ALAREFIEKLKAD----GMQVIVDTDAGIEHFGR 153
                                       6788888777775....99999999998888775 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   3.3e-06    0.0021       8      39 ..       7      38 ..       2      48 .. 0.90
   2 ?    2.7   0.0       0.1        65      92     155 ..     129     192 ..     118     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.3e-06
                                      SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                              MipZ  8 ekGGsGksttavhvavaLlkkGarvaaidldl 39
                                       kGGsGkst++  +a  ++++G +v ++d d 
  gi|330508238|ref|YP_004384666.1|  7 GKGGSGKSTVSALIAREMASRGEKVLVVDTDE 38
                                      59***************************996 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.1
                                       HHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEESSHHHHCCCEEE-SSS--EEEE-HH CS
                              MipZ  92 lvadleaeldfividtPGsdsalsrlahsladtlvtPlndsfvdfdllgkvdpetlkvkrpsly 155
                                        +++l+a+   +++dt    ++  r + + +d +v  ++ sf  + l  k+     k+++p  +
  gi|330508238|ref|YP_004384666.1| 129 FIEKLKADGMQVIVDTDAGIEHFGRGVEAGSDRIVVVIDPSFESVQLSEKISEMGAKINKPVCF 192
                                       5666777777899****999***************************99999999999998765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0     8e-05     0.051       1      39 [.       3      46 ..       3      51 .. 0.85
   2 ?    5.9   0.0     0.023        15       6      63 ..     122     182 ..     119     187 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8e-05
                                      EEEES-SHHHHHHHHHHHHTT.....EEEEEEESSHHHHHHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLsegg.....kdvvvidkdeerveelre 39
                                      ++i+G G  G+s +  L +++     ++v+v+d+de+++  +++
  gi|330508238|ref|YP_004384666.1|  3 FVICGKGGSGKSTVSALIAREmasrgEKVLVVDTDESNFGLYKQ 46
                                      79**********9999999777999988********98766655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.023
                                       -SHHHHHHHHHHHHTTEEEEEEESSH..HHHHHHHHTTSE..EEES-TTSHHHHHHTTGGGE CS
                            TrkA_N   6 lGrvGrslaeeLseggkdvvvidkde..erveelreegle..vvvgdatdeevLeeagieka 63 
                                       +G ++r+ +e+L+++g+  v++d+d   e++ +  e g +  vvv d++ e+v  + +i+++
  gi|330508238|ref|YP_004384666.1| 122 MGALAREFIEKLKADGM-QVIVDTDAgiEHFGRGVEAGSDriVVVIDPSFESVQLSEKISEM 182
                                       89999*********886.89999998444455555666334688888888888888888876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1     1e-06   0.00064      20      53 ..       4      38 ..       2      40 .. 0.93
   2 ?   -2.2   0.0       3.2     2e+03      33     101 ..     126     143 ..     121     148 .. 0.46

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                        Zeta_toxin 20 llgGqpGAGKselaellkdele.rqgnvvrldpDd 53
                                      ++ G  G+GKs++++l+++e++ r+++v+++d+D+
  gi|330508238|ref|YP_004384666.1|  4 VICGKGGSGKSTVSALIAREMAsRGEKVLVVDTDE 38
                                      688*******************99999******97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
                        Zeta_toxin  33 aellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdaselvekllqeaiengyniive 101
                                       a+++                                                   ++++   g+ +iv+
  gi|330508238|ref|YP_004384666.1| 126 AREF---------------------------------------------------IEKLKADGMQVIVD 143
                                       3333...................................................33333333333333 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.7e-05     0.011      10      42 ..       8      40 ..       2      56 .. 0.92
   2 ?    3.4   0.0      0.07        45     106     151 ..     127     172 ..      88     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                          CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDlspdn 42
                                      +GG G+++++a +a+ + + ge+vlv+D+  +n
  gi|330508238|ref|YP_004384666.1|  8 KGGSGKSTVSALIAREMASRGEKVLVVDTDESN 40
                                      6***************************99888 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.07
                          CBP_BcsQ 106 laalkelkeqyrwillDlpagasaltrellaladlvllvvepdanc 151
                                        +++++lk++   +++D  ag ++  r + a +d+ + v+ p   +
  gi|330508238|ref|YP_004384666.1| 127 REFIEKLKADGMQVIVDTDAGIEHFGRGVEAGSDRIVVVIDPSFES 172
                                       5678999999999***************************998765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.6e-06     0.001      26      61 ..       3      37 ..       1      95 [. 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-06
                             DUF87 26 lAilgsTGsGKSntvavLleellekkgatililDpH 61
                                      + i g+ GsGKS+  a++ +e++ ++g ++l++D +
  gi|330508238|ref|YP_004384666.1|  3 FVICGKGGSGKSTVSALIAREMA-SRGEKVLVVDTD 37
                                      6799*******************.99********76 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   9.2e-06    0.0059       4      48 ..       3      47 ..       1      54 [. 0.93
   2 ?   -2.4   0.0       4.8   3.1e+03      71      91 ..     125     144 ..     116     154 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.2e-06
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHH CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQL 48
                                      ++++G  G+GK t  a +a+ + ++g+kvl+v +D    + ++QL
  gi|330508238|ref|YP_004384666.1|  3 FVICGKGGSGKSTVSALIAREMASRGEKVLVVDTDESNFGLYKQL 47
                                      6899*******************************9999999998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHHTTSSEEEEEE CS
                             SRP54  71 vakeavekakeekidvvlvDT 91 
                                       +a+e +ek k+++++ v+vDT
  gi|330508238|ref|YP_004384666.1| 125 LAREFIEKLKADGMQ-VIVDT 144
                                       566777777877765.56777 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.3e-06     0.004       4      35 ..       2      40 ..       1      81 [. 0.90
   2 ?   -2.6   0.0         6   3.8e+03      28      36 ..     141     149 ..     126     174 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.3e-06
                            AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtekGl 35
                                      k++i G+ g+GK+t+ + +       g+k+l++dt+++ 
  gi|330508238|ref|YP_004384666.1|  2 KFVICGKGGSGKSTVSALIaremasrGEKVLVVDTDESN 40
                                      89************999999999*************975 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6
                            AAA_24  28 fidtekGlk 36 
                                       ++dt++G  
  gi|330508238|ref|YP_004384666.1| 141 IVDTDAGIE 149
                                       445555443 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.7e-06    0.0049       5      41 ..       4      40 ..       1      75 [. 0.93

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.7e-06
                                      EEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                             KTI12  5 vltGlPssGKstrakeLakaleeekrsvvviddeslg 41
                                      v++G   sGKst+++ +a+++++++ +v v+d++  +
  gi|330508238|ref|YP_004384666.1|  4 VICGKGGSGKSTVSALIAREMASRGEKVLVVDTDESN 40
                                      89******************************88765 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   6.9e-05     0.044      25      60 ..       4      39 ..       1      59 [. 0.86
   2 ?    1.0   0.0      0.25   1.6e+02      52      76 ..     163     187 ..     154     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-05
                            AAA_10 25 liiGdlGnGKSvlakllvlyisllggkaliiDpkke 60
                                      +i G+ G GKS ++ l+   ++ +g+k+l++D  + 
  gi|330508238|ref|YP_004384666.1|  4 VICGKGGSGKSTVSALIAREMASRGEKVLVVDTDES 39
                                      799*****************************8665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.25
                            AAA_10  52 aliiDpkkerekfketlpeiakkin 76 
                                       +++iDp  e  +  e++ e+  kin
  gi|330508238|ref|YP_004384666.1| 163 VVVIDPSFESVQLSEKISEMGAKIN 187
                                       789**************99887776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.5e-05    0.0098      14      47 ..       3      36 ..       1      98 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-05
                                      EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagllkpteGeilldgk 47
                                       +i G+ G+GKSt+ +l+a+++    +++l+ ++
  gi|330508238|ref|YP_004384666.1|  3 FVICGKGGSGKSTVSALIAREMASRGEKVLVVDT 36
                                      689******************9998888876544 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.6e-05     0.036      23      66 ..       4      46 ..       2      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.6e-05
                            ATPase 23 litGepGtGKtifalqFlikgaekygepgvfvtveepaedlren 66
                                       i+G+ G+GK+++++  + + a++ ge+++ v ++e++  l+++
  gi|330508238|ref|YP_004384666.1|  4 VICGKGGSGKSTVSALIAREMASR-GEKVLVVDTDESNFGLYKQ 46
                                      69*************999999999.***********99888876 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 ?   12.7   0.1     7e-05     0.045      34      68 ..       5      39 ..       2      42 .. 0.90
   2 ?   -2.8   0.0       3.8   2.5e+03     132     132 ..     148     148 ..     119     171 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7e-05
                                      EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--- CS
                              MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavlavDPs 68
                                      + G  G+Gkst+   ++ e+++rG++v v+  D s
  gi|330508238|ref|YP_004384666.1|  5 ICGKGGSGKSTVSALIAREMASRGEKVLVVDTDES 39
                                      67999******9999999***********998866 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.8
                                       S CS
                              MeaB 132 v 132
                                       +
  gi|330508238|ref|YP_004384666.1| 148 I 148
                                       2 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   4.8e-05     0.031      17      52 ..       2      37 ..       1      48 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.8e-05
                     TrwB_AAD_bind 17 hilivGttGsGKtqalekllrairargdraivlDlt 52
                                      +++i G  GsGK+++   + r++ +rg++++v+D+ 
  gi|330508238|ref|YP_004384666.1|  2 KFVICGKGGSGKSTVSALIAREMASRGEKVLVVDTD 37
                                      5899******************************85 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013     0.084      37      85 ..       4      42 ..       2      48 .. 0.83
   2 ?   -1.4   0.0       2.3   1.5e+03     127     151 ..     145     169 ..     127     186 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                            AAA_25 37 llaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsede 85
                                      +++G +g+GK+t+   +a ++a +G+           kVl+v++++s+ +
  gi|330508238|ref|YP_004384666.1|  4 VICGKGGSGKSTVSALIAREMAsRGE-----------KVLVVDTDESNFG 42
                                      689*******************7776...........7888888887755 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.3
                            AAA_25 127 tadvdaleaaieevegvrlvviDpl 151
                                       +a +++  + +e+  +  +vviDp 
  gi|330508238|ref|YP_004384666.1| 145 DAGIEHFGRGVEAGSDRIVVVIDPS 169
                                       5566777777777677789999985 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   8.9e-05     0.057       3      39 ..       4      45 ..       3     106 .. 0.77
   2 ?   -2.6   0.0       8.8   5.6e+03      60      76 ..     127     143 ..     118     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.9e-05
                            AAA_33  3 llvGlpGsGKstlaerllkklg.....avllssdtlrrrlfg 39
                                      +++G  GsGKst++  ++++ +     + ++++d+  + l++
  gi|330508238|ref|YP_004384666.1|  4 VICGKGGSGKSTVSALIAREMAsrgekVLVVDTDESNFGLYK 45
                                      78*************998888788888888999984444443 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.8
                            AAA_33  60 nelarkalsagrnvild 76 
                                       +e+++k  + g +vi+d
  gi|330508238|ref|YP_004384666.1| 127 REFIEKLKADGMQVIVD 143
                                       57888888999999997 PP

>> DUF1995  Domain of unknown function (DUF1995)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.1e-05     0.033      60     127 ..      25     205 ..      11     228 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-05
                           DUF1995  60 lgsgrrvkivfpdageaalarr....................................................... 81 
                                       + +g++v +v  d++   l+++                                                       
  gi|330508238|ref|YP_004384666.1|  25 ASRGEKVLVVDTDESNFGLYKQlglpqprdfmdslggkkglgerlmkfmrsegkeklsilqefsiddipqelivged 101
                                       44555677777777777777777777777777777777777777777777777777777777777777777777777 PP

                           DUF1995  82 .........................................................eddvfvvvaPspseleavea 101
                                                                                                 d+++vv+ Ps++ ++  e+
  gi|330508238|ref|YP_004384666.1| 102 giklvaigkihdygegcacpmgalarefieklkadgmqvivdtdagiehfgrgveagSDRIVVVIDPSFESVQLSEK 178
                                       77777777777777777777777766677766666666666666655555556766424****************** PP

                           DUF1995 102 laeaag..drpvvllNprledvdevglg 127
                                       ++e  +  ++pv ++ +r+++++ ++l 
  gi|330508238|ref|YP_004384666.1| 179 ISEMGAkiNKPVCFILNRMNEDA-AELS 205
                                       **9988777*****999999865.5555 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 ?   12.0   0.0   0.00014     0.091      23      59 ..       3      37 ..       1      47 [. 0.90
   2 ?   -1.7   0.0       2.1   1.4e+03     169     180 ..     156     167 ..     123     168 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                        KAP_NTPase 23 vgLygkWGsGKssllnkledelkefakpvrflfaefn 59
                                      +++ gk GsGKs++ +++ +e+ ++   +++l+++ +
  gi|330508238|ref|YP_004384666.1|  3 FVICGKGGSGKSTVSALIAREMASR--GEKVLVVDTD 37
                                      6788999******************..9999999987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                        KAP_NTPase 169 dalqkrlVvviD 180
                                       +a + r+VvviD
  gi|330508238|ref|YP_004384666.1| 156 EAGSDRIVVVID 167
                                       4577899***99 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1     0.006       3.8       9      32 ..       8      31 ..       3      34 .. 0.85
   2 ?    4.4   0.0     0.045        29     157     194 ..     187     223 ..     125     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.006
                            AAA_26  9 dtgvGKTvvslgLvralkrkgvkv 32
                                        g+GK++vs++++r + ++g kv
  gi|330508238|ref|YP_004384666.1|  8 KGGSGKSTVSALIAREMASRGEKV 31
                                      568***************9*9998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.045
                            AAA_26 157 vrvlGvilNkvrnpenvetlekksgipvlGvvPylpdl 194
                                       ++ +  ilN++ n+++ e  +   g +v+G+vP ++d+
  gi|330508238|ref|YP_004384666.1| 187 NKPVCFILNRM-NEDAAELSSLVDGKKVIGSVPFDRDV 223
                                       44666789995.55667777777889*******99986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00016       0.1       2      25 ..       4      28 ..       4      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf.g 25
                                      +++G+ G+GK+t++  +++++++ g
  gi|330508238|ref|YP_004384666.1|  4 VICGKGGSGKSTVSALIAREMASrG 28
                                      59***************99985553 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   0.00048      0.31       2      26 ..       4      28 ..       3      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00048
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                      +++G+ g GKSt++  +a++++++ 
  gi|330508238|ref|YP_004384666.1|  4 VICGKGGSGKSTVSALIAREMASRG 28
                                      79******************99554 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00053      0.34       4      29 ..       8      35 ..       5      45 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00053
                                      STTSSHHHHHHHHHHHHHHTTE...EEE CS
                   Thymidylate_kin  4 lDGaGKttqaellkerlkeegik..vvl 29
                                        G+GK+t+++l+++ + ++g+k  vv 
  gi|330508238|ref|YP_004384666.1|  8 KGGSGKSTVSALIAREMASRGEKvlVVD 35
                                      569******************9953333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 1817.90
//
Query:       gi|330508239|ref|YP_004384667.1|  [L=512]
Description: family 5 extracellular solute-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-74  250.0   0.3    4.4e-74  249.7   0.3    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.7   0.3   2.4e-78   4.4e-74       2     365 ..      70     418 ..      69     430 .. 0.88

  Alignments for each domain:
  == domain 1  score: 249.7 bits;  conditional E-value: 2.4e-78
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       ++paLAes we ++    ytfkLR++v ++DG+ + A+Dvvf++++++++++ + +++       ik++eavddytv
  gi|330508239|ref|YP_004384667.1|  70 IIPALAES-WE-MEGDDAYTFKLREDVLWHDGERFAADDVVFTIDYIKEHPYIWVSSDI------IKTAEAVDDYTV 138
                                       79******.68.555566************************************99776......59********** PP

                                       EEEESSETTTTTTHCHHHHHHHGCCHTCTCTTT.TTGTTTSE-BSSSEEEEEEETTT.EEEEEE-TTSTTTSCSSSS CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiakkaaekeddk.dkdtnekpvgtGPYklkefkpgq.kivlernpdYwgggkpkld 153
                                       r+ l++p+a+fl+l+a + + ++++ +e  dd+ +  ++ ++vgtGP++l+++++ q +  +++++dY+  g pk++
  gi|330508239|ref|YP_004384667.1| 139 RISLNQPYAPFLELVAGTLPILPEHIYEGVDDPaEFREDSALVGTGPFQLVDYDQSQgSYLYQAFDDYY-LGSPKVK 214
                                       ***********************9766666665155678899*************987888*******9.******* PP

                                       EEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHH CS
                         SBP_bac_5 154 riefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyA 230
                                       +++f  + + +  aaal++G++  +a++pp+ +e lk++  + +   s   ++t +++N+kk+p++d r+RqAl yA
  gi|330508239|ref|YP_004384667.1| 215 QLKFVKV-NLEMSAAALEKGDV-NAANVPPEVVENLKDEGFTVM--LSSHDSITKIMVNHKKEPLSDSRFRQALYYA 287
                                       *******.999999999*****.999*********988877777..8999999999********************* PP

                                       S-HHHHHHHCTTTSSEEESSS.STTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETC..EEEEEEEEE CS
                         SBP_bac_5 231 iDreeivkavlegyatpansl.lppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrek..klkltllla 304
                                       iDr+++v+++ +gy++ a    ++    +++ + +p+  +ydp+k ++l++e Gy ++dg +++ +  +     l +
  gi|330508239|ref|YP_004384667.1| 288 IDRQALVDNAARGYGVLASPGlFAVDNHWYNSDVEPY--DYDPAKTEELMEELGYSKVDG-YFSVDgsPV---KLEM 358
                                       *****************99995665555555555554..79*****************74.666665433...3444 PP

                                       TTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHH CS
                         SBP_bac_5 305 sgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnf 365
                                         ++ ++++ eli qql+++G+ ++++tvd+ +t ++ v++++fd++l + g+  +dp+  
  gi|330508239|ref|YP_004384667.1| 359 LVTSINERAGELIRQQLEDAGFMISLRTVDS-KTLDSMVTEWKFDLALNSHGGMGADPEIL 418
                                       5567899************************.*********************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3213.49
//
Query:       gi|330508240|ref|YP_004384668.1|  [L=290]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-28   99.3   0.0    5.1e-28   98.3   0.0    1.5  2  ABC_tran      ABC transporter
    5.5e-14   52.7   0.2    5.9e-08   32.9   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.3e-05   23.5   0.0      6e-05   22.7   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00039   20.2   0.0       0.75    9.4   0.0    2.1  2  AAA_15        AAA ATPase domain
    0.00061   18.6   0.0       0.15   10.6   0.0    2.1  2  AAA_13        AAA domain
      0.002   18.7   0.0     0.0039   17.7   0.0    1.6  2  AAA_23        AAA domain
     0.0028   17.6   0.0     0.0042   17.0   0.0    1.3  1  Rad17         Rad17 P-loop domain
  ------ inclusion threshold ------
      0.029   14.3   0.0       0.05   13.5   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.061   12.7   0.1        1.2    8.5   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.084   12.9   0.0        2.9    7.9   0.0    2.3  2  AAA_14        AAA domain
      0.088   13.2   0.1       0.45   10.9   0.1    2.2  1  AAA           ATPase family associated with various cellular 
        0.1   13.0   0.0       0.14   12.5   0.0    1.5  1  AAA_16        AAA ATPase domain
       0.12   12.8   0.0       0.29   11.6   0.0    1.7  1  RNA_helicase  RNA helicase
       0.12   12.4   0.0       0.46   10.6   0.0    2.0  2  MMR_HSR1      50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.0     4e-31   5.1e-28       1     136 [.      35     179 ..      35     180 .. 0.93
   2 ?   -2.8   0.0       6.6   8.4e+03      38      46 ..     227     235 ..     194     249 .. 0.61

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 4e-31
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-T.TSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfp.eltv 76 
                                       l++v++k++ege+++++G+nGaGKStL+k+l+ l  p eGe  ++g d+ + e +++r+++g+++ +++ f+ +l+ 
  gi|330508240|ref|YP_004384668.1|  35 LDRVNIKVQEGEVYGLLGPNGAGKSTLIKILCTLILPSEGEAYVNGYDVVK-EGQQARESLGFVTTDERSFYwRLSG 110
                                       789**********************************************99.99*************5555516679 PP

                                       HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ren               +++ e++l+ ++lk+ +d++     +s+S G+kq +a+ar ll++p +l++DEpt
  gi|330508240|ref|YP_004384668.1| 111 RENlqffatlynlpqsVVRSRTEELLDVVRLKHRADEPF----YSYSAGMKQQMAIARGLLNDPAVLFMDEPT 179
                                       999********9997767777************999998....*****************************9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.6
                                       SEEEEEETT CS
                                       xxxxxxxxx RF
                          ABC_tran  38 teGeilldg 46 
                                       +eG+i+ +g
  gi|330508240|ref|YP_004384668.1| 227 DEGKIKANG 235
                                       344444444 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 !   17.7   0.4   1.9e-06    0.0024       2      19 ..      48      65 ..      47      93 .. 0.86
   2 !   32.9   0.0   4.6e-11   5.9e-08     226     298 ..     141     212 ..      98     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
                            AAA_21  2 nvliGpNgsGKSnLLdal 19
                                       +l GpNg+GKS+L+++l
  gi|330508240|ref|YP_004384668.1| 48 YGLLGPNGAGKSTLIKIL 65
                                      5799*************9 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 4.6e-11
                            AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell..kelsrngaQviltTHS 298
                                        +++ + p+++ S G+k+  a++  ll ++   ++l+ DEp  +L+P + r l +++  k+ +++g  ++++TH+
  gi|330508240|ref|YP_004384668.1| 141 LKHRADEPFYSYSAGMKQQMAIARGLLNDP---AVLFMDEPTRSLDPGAARNLRKFIkeKIVAEKGKTIFISTHQ 212
                                       46788899***********99999999988...************************99888889*********8 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   4.7e-08     6e-05      11      50 ..      34      73 ..      33      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.7e-08
                            AAA_29 11 tfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      t+d+  i++++ +++ l Gp+G+GKSTl+  + +l++p++
  gi|330508240|ref|YP_004384668.1| 34 TLDRVNIKVQEGEVYGLLGPNGAGKSTLIKILCTLILPSE 73
                                      5677788888666999*********************998 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00058      0.75      18      47 ..      39      69 ..      34      98 .. 0.79
   2 !    8.8   0.0    0.0009       1.1     322     364 ..     168     211 ..     153     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00058
                            AAA_15 18 eidlsee.ltvliGkNnsGKSsilealdlFl 47
                                       i+++e  +  l G+N++GKS+++++l  ++
  gi|330508240|ref|YP_004384668.1| 39 NIKVQEGeVYGLLGPNGAGKSTLIKILCTLI 69
                                      5555555577799*************97665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0009
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnkt.QviitTH 364
                                       +++++l+++EP  +L p a + l k +ke +  +k+  ++i+TH
  gi|330508240|ref|YP_004384668.1| 168 NDPAVLFMDEPTRSLDPGAARNLRKFIKEKIVAEKGkTIFISTH 211
                                       6899***********************984444444399***** PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0031         4      23      48 ..      52      77 ..      34      94 .. 0.80
   2 !   10.6   0.0   0.00012      0.15     526     572 ..     169     214 ..     161     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0031
                            AAA_13 23 GwNGaGKTtLSrllrslelgetepkf 48
                                      G NGaGK+tL ++l  l l +  +++
  gi|330508240|ref|YP_004384668.1| 52 GPNGAGKSTLIKILCTLILPSEGEAY 77
                                      89********9999887666555555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00012
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnle 572
                                          + ++D P  SLD ++      +ik+++  ++k k +fi+TH l+
  gi|330508240|ref|YP_004384668.1| 169 DPAVLFMDEPTRSLDPGAARNLRKFIKEKI-VAEKGKTIFISTHQLD 214
                                       567999***********************9.69999********986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.1e-06    0.0039      20      41 ..      46      67 ..      33     147 .. 0.89
   2 ?   -2.4   0.0       4.4   5.6e+03     117     135 ..     190     208 ..     175     233 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.1e-06
                            AAA_23 20 gltlItGpNGaGKTTildAikl 41
                                       ++ + GpNGaGK+T++  ++ 
  gi|330508240|ref|YP_004384668.1| 46 EVYGLLGPNGAGKSTLIKILCT 67
                                      577899***********99996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.4
                            AAA_23 117 leqfisellgskkiilnli 135
                                       l++fi+e++  +k    +i
  gi|330508240|ref|YP_004384668.1| 190 LRKFIKEKIVAEKGKTIFI 208
                                       4444444444333322222 PP

>> Rad17  Rad17 P-loop 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    0.0042      25     103 ..      25     105 ..      21     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.3e-06
                             Rad17  25 kkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgik.lrewlnpvslkepdnqksdfkgltekes 100
                                       ++  +++ + l+   ++ ++ ++  + GP G gkst +k+L     ++  + ++n+  + +   q  + +g + +++
  gi|330508240|ref|YP_004384668.1|  25 RSGNRDILTTLDRVNIKVQEGEVYGLLGPNGAGKSTLIKILCTLILPSeGEAYVNGYDVVKEGQQARESLGFVTTDE 101
                                       55556788888888888888889999***************9866555156799**999999999999999887765 PP

                             Rad17 101 r.fl 103
                                       r f 
  gi|330508240|ref|YP_004384668.1| 102 RsFY 105
                                       4154 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   3.9e-05      0.05      91     120 ..      36      66 ..      25     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-05
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinall 120
                                       ++++ ++++ ++  l+G+ G+GKStLi+ l 
  gi|330508240|ref|YP_004384668.1|  36 DRVNIKVQEgEVYGLLGPNGAGKSTLIKILC 66 
                                       55565666659999*************9886 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00095       1.2      26      42 ..      47      63 ..      34      73 .. 0.80
   2 ?    2.0   0.0     0.095   1.2e+02     160     198 ..     171     212 ..     156     231 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00095
                                      EEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlld 42
                                      +  ++GpNG+GKs l+ 
  gi|330508240|ref|YP_004384668.1| 47 VYGLLGPNGAGKSTLIK 63
                                      66799********9987 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.095
                                       SEEEECTTTTTS-HHHHHHHHHHHHHH...CTTSEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx RF
                             SMC_N 160 plyllDeidaaLDeknvkkvaellkek...sknaQfivislr 198
                                       ++ ++De    LD    +++ +++kek   +k   +++ +++
  gi|330508240|ref|YP_004384668.1| 171 AVLFMDEPTRSLDPGAARNLRKFIKEKivaEKGKTIFISTHQ 212
                                       45679********************87221233444444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0023       2.9       3      40 ..      46      82 ..      44     110 .. 0.79
   2 ?    3.0   0.0     0.078     1e+02      62     101 ..     164     211 ..     111     229 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0023
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldd 40
                                      +++ + G+  +GK+tl+k l   l+ ++e   y+n  d
  gi|330508240|ref|YP_004384668.1| 46 EVYGLLGPNGAGKSTLIKILCT-LILPSEGEAYVNGYD 82
                                      68899************98874.444888888887655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.078
                            AAA_14  62 e...ekktylflDEiqev..pewekalkslvdeg...knldvivtGSn 101
                                       +   ++  +lf+DE  ++  p++ + l+++++e+   ++++ i+   +
  gi|330508240|ref|YP_004384668.1| 164 RgllNDPAVLFMDEPTRSldPGAARNLRKFIKEKivaEKGKTIFISTH 211
                                       134456788999999888776666666666665533345555555554 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   0.1   0.00035      0.45       3      22 ..      50      69 ..      48     218 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                                      EESSTTSSHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel 22
                                      l Gp G GK++l+k +++ +
  gi|330508240|ref|YP_004384668.1| 50 LLGPNGAGKSTLIKILCTLI 69
                                      78***************985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.14      12      55 ..      31      78 ..      22     219 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                            AAA_16 12 Llsalervrsgrp..elvllsGesGvGKsslvrellralekd..ggif 55
                                      +l++l+rv+      e+  l G+ G GKs+l++ l + +  +  ++++
  gi|330508240|ref|YP_004384668.1| 31 ILTTLDRVNIKVQegEVYGLLGPNGAGKSTLIKILCTLILPSegEAYV 78
                                      55556655554444588899************9999988887431333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00022      0.29       3      24 ..      50      71 ..      48     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                      RNA_helicase  3 lyGpsgeGKStlakeLakallk 24
                                      l Gp+g GKStl+k L++ +l 
  gi|330508240|ref|YP_004384668.1| 50 LLGPNGAGKSTLIKILCTLILP 71
                                      67***************99883 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00036      0.46       3      21 ..      49      67 ..      47     164 .. 0.78
   2 ?   -0.9   0.0       1.3   1.6e+03      24      57 ..     196     226 ..     186     249 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00036
                                      EEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltg 21
                                      +++G   +GKStLi+ l+ 
  gi|330508240|ref|YP_004384668.1| 49 GLLGPNGAGKSTLIKILCT 67
                                      789*************995 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                                       EEESSSTTSSSSEEEEEEEETTEEEEEEECGGCS CS
                          MMR_HSR1  24 aivsdkpgtTrdinegrvklkgkeielvDtpGli 57 
                                        ++ +++g+T+ i ++++++     el+D + ++
  gi|330508240|ref|YP_004384668.1| 196 EKIVAEKGKTIFISTHQLDE---AEELCDRVAIL 226
                                       46667889999999998872...34677766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1936.90
//
Query:       gi|330508241|ref|YP_004384669.1|  [L=268]
Description: ABC transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-19   69.2  24.7    3.1e-19   69.2  24.7    1.6  2  ABC2_membrane    ABC-2 type transporter
    1.7e-11   43.8  27.3    1.7e-11   43.8  27.3    1.7  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
        2.3    8.0   5.0        8.7    6.1   0.1    2.5  2  DUF3481          C-terminal domain of neuropilin glycoprotein


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 !   69.2  24.7   5.3e-23   3.1e-19      14     209 ..      20     221 ..       6     222 .. 0.83
   2 ?   -2.3   0.2      0.39   2.4e+03     105     120 ..     234     249 ..     224     257 .. 0.47

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 5.3e-23
                     ABC2_membrane  14 rwrdpslgllwrliqplllalvfgtvfgnlg.nsedglnr.............pgllffsvlflafsaltsvapvfe 76 
                                       ++ d +l    rl+++l+ +l + ++   +g   ++   +             +g+ f   l++++ +++++ +  e
  gi|330508241|ref|YP_004384669.1|  20 YKFDFFL----RLFFMLFNILTYYFIAKLIGdGAAK---YlepyggdyfsfvlIGMAFSGYLMISLRSFSES-VRDE 88 
                                       4444444....4555555555555554443322222...233467777777888888888888886666666.9999 PP

                     ABC2_membrane  77 rergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rfflflllllltalaasslglli 151
                                       + +g+le +lv+p+ s+s++++ + l++++++ + +l++l+i ++l g+d++  +++ +ll+l+lt++++ss+g+l 
  gi|330508241|ref|YP_004384669.1|  89 QMMGTLEAMLVTPT-STSSIIALSSLWNFIFASFRVLLYLVIGILL-GVDMTqaNVGGALLILVLTIICFSSIGILS 163
                                       99************.******************************9.*****9888999****************** PP

                     ABC2_membrane 152 salapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                       +++ + f+ +  + +l++    l++G+++pi+  p+wlq i++++P+ty v+++r++l
  gi|330508241|ref|YP_004384669.1| 164 ASFIMVFKRGDPINMLLMGTSELFGGVLFPIEVFPSWLQSISHILPITYSVNGMRHAL 221
                                       *******************************************************987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.39
                     ABC2_membrane 105 lpvsllqalifllivy 120
                                       l+  +l+++++l +++
  gi|330508241|ref|YP_004384669.1| 234 LLSLVLFSIVLLPLSL 249
                                       3333333333333333 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   3.1      0.58   3.5e+03     233     251 ..      22      41 ..       6      47 .. 0.54
   2 !   43.8  27.3   2.9e-15   1.7e-11     163     344 ..      60     249 ..      41     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.58
                   ABC2_membrane_3 233 ipfg.nlglllllfllfgla 251
                                       ++f+  l+++l+++l ++++
  gi|330508241|ref|YP_004384669.1|  22 FDFFlRLFFMLFNILTYYFI 41 
                                       44444556666666666665 PP

  == domain 2  score: 43.8 bits;  conditional E-value: 2.9e-15
                   ABC2_membrane_3 163 lvgliliilifitasfiav.....siveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afglg 232
                                       +++++li ++f ++++i+      s+  E   +++e +lv++ s+++++  + l+ f+ + + +ll+l++  ++g+ 
  gi|330508241|ref|YP_004384669.1|  60 YFSFVLIGMAFSGYLMISLrsfseSVRDEQMMGTLEAMLVTPTSTSSIIALSSLWNFIFASFRVLLYLVIgiLLGVD 136
                                       33344444433333333332222266677777999********************************9966699977 PP

                   ABC2_membrane_3 233 ipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffap 309
                                       ++  n+g +ll ++l +++++++g l  s++   + +  + ++++ +  +f g+lfp+e +ps+l+ i+ i+P+++ 
  gi|330508241|ref|YP_004384669.1| 137 MTQANVGGALLILVLTIICFSSIGILSASFIMVFKRGDPINMLLMGTSELFGGVLFPIEVFPSWLQSISHILPITYS 213
                                       8888**************************77777777766666664556666669999999*************** PP

                   ABC2_membrane_3 310 glgllrli.tgdplweillsliilalfavvylllal 344
                                        +g+   + +g+++ e+++ l+ l+lf++v+l l+l
  gi|330508241|ref|YP_004384669.1| 214 VNGMRHALlQGYSIGELAPELLSLVLFSIVLLPLSL 249
                                       *******65999*******************99887 PP

>> DUF3481  C-terminal domain of neuropilin glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0015       8.7       5      40 ..      86     127 ..      82     132 .. 0.85
   2 ?    3.0   1.2     0.014        81      15      30 ..     148     163 ..     134     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0015
                           DUF3481   5 kegsllktldPilit......iiamsalGvllGaicGvvlyc 40 
                                       ++++++ tl+ +l+t      iia+s+l  ++ a   v+ly 
  gi|330508241|ref|YP_004384669.1|  86 RDEQMMGTLEAMLVTptstssIIALSSLWNFIFASFRVLLYL 127
                                       678999*******987777889******99999999999995 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.014
                           DUF3481  15 PilitiiamsalGvll 30 
                                        +++tii  s++G+l 
  gi|330508241|ref|YP_004384669.1| 148 ILVLTIICFSSIGILS 163
                                       4678*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1787.90
//
Query:       gi|330508242|ref|YP_004384670.1|  [L=58]
Description: F420H2 dehydrogenase subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-13   48.7   0.1    8.2e-13   48.6   0.1    1.0  1  FpoO      F420H2 dehydrogenase subunit FpoO


Domain annotation for each model (and alignments):
>> FpoO  F420H2 dehydrogenase subunit FpoO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.1   4.6e-17   8.2e-13       1      50 [.       1      48 [.       1      57 [. 0.91

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 4.6e-17
                              FpoO  1 madcdlcgvsiPtviPvrvfkPrlelsyPeGvwkGlcekclkaakktyde 50
                                      madcdlc+++ Pt+ P++  +P  +l+yPeG +kG+c+ cl+  +k  +e
  gi|330508242|ref|YP_004384670.1|  1 MADCDLCTRARPTLYPIK--APVHNLTYPEGAYKGVCDICLEHLEKGWQE 48
                                      9***************99..6999******************99888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 472.39
//
Query:       gi|330508243|ref|YP_004384671.1|  [L=133]
Description: tRNA/helicase-type nucleic acid-binding protein [Methanosaeta concilii GP6]
Scores for complete 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   24.8   0.0    3.6e-05   23.7   0.0    1.6  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.017   15.3   0.0      0.026   14.7   0.0    1.2  1  tRNA_anti_2      OB-fold nucleic acid binding domain
       0.11   12.1   0.0       0.18   11.4   0.0    1.4  1  SelB-wing_3      Elongation factor SelB, winged helix
       0.14   11.8   0.0       0.35   10.5   0.0    1.6  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 !   23.7   0.0   8.1e-09   3.6e-05       2      71 ..      56     123 ..      55     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 8.1e-09
                                       EEEEEEEEEE.EEEETTEEEEEEEETTEEEEEEEET.HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEE CS
                   tRNA_anti-codon   2 tvaGrvtsis.drsggkvifidlrDgtgriqvvlfr.eeatklaenlkeGdvvrvtGrvkrrpggelelkve 71 
                                       t+ Gr+ts + +rs     +++l+ ++  + v++   ++a++l  +l++++ vr+tG++++++g+  elkv+
  gi|330508243|ref|YP_004384671.1|  56 TLDGRITSAEnTRS---GGNLILNLDSTAMPVFIPAsSGAKELSAQLQKDTRVRITGTINSYQGK-DELKVS 123
                                       788******64444...467777777888888888888*************************99.777765 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 ?   14.7   0.0   5.7e-06     0.026      20      85 ..      53     118 ..      46     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-06
                       tRNA_anti_2  20 kavwvrGeisnlkr.kasghvYftLkDekakisavifr.sraaklkftledGmkVlvkgrlsvYeprG 85 
                                       + +++ G i++ ++ ++ g + ++L   + ++ + i + s a++l+++l+++++V ++g+++ Y+ + 
  gi|330508243|ref|YP_004384671.1|  53 PLITLDGRITSAENtRSGGNLILNLD--STAMPVFIPAsSGAKELSAQLQKDTRVRITGTINSYQGKD 118
                                       568899******86355779999998..5568888888566799********************9875 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 ?   11.4   0.0   4.1e-05      0.18       7      30 ..     109     132 ..     104     133 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.1e-05
                                       S-BBHHHHHHHHT--HHHHHHHHH CS
                       SelB-wing_3   7 geitaaefRdllgtSRKyaiplLE 30 
                                       g+i+  + +d l +SRK  ++lLE
  gi|330508243|ref|YP_004384671.1| 109 GTINSYQGKDELKVSRKADVQLLE 132
                                       56666688***************9 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   7.7e-05      0.35      33      96 ..      12      91 ..       3     123 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.7e-05
                           DUF4131 33 llllllllllallgfalrapqpnandlsqlles.......gqeviveGvvaslpeltgsgtrfvleverv......... 95
                                      ++++ll+++l++l +a++a +p+++  +   +        +  +++ G+++s  +++  g  ++l+ ++          
  gi|330508243|ref|YP_004384671.1| 12 IVVVLLFMALGSLAAAFWAFSPEESYTPASGDMgsgensrSPLITLDGRITSAENTRSGG-NLILNLDSTampvfipas 89
                                      567888888888888888888888555554444558888999999*****8877666554.477766554445555444 PP

                           DUF4131 96 .l 96
                                       +
  gi|330508243|ref|YP_004384671.1| 90 sG 91
                                      41 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1017.28
//
Query:       gi|330508244|ref|YP_004384672.1|  [L=252]
Description: hypothetical protein MCON_2393 [Methanosaeta concilii GP6]
Scores for complete 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  255.1   0.0    6.5e-76  254.9   0.0    1.1  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr


Domain annotation for each model (and alignments):
>> SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.9   0.0   3.6e-80   6.5e-76       1     234 [.       3     247 ..       3     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 254.9 bits;  conditional E-value: 3.6e-80
                                       EEEEESSTSSSSHHHHHHHHHHHH-........TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TT CS
                   SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsia........pdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpg 69 
                                       itLl+DFG  + y+++mkgvils+          +++ vDi+Hdip++dvr++af+L +++++fp+gt+h+avVDpg
  gi|330508244|ref|YP_004384672.1|   3 ITLLSDFG--SFYPAQMKGVILSRLqgksgniaGKITFVDIAHDIPAQDVRAGAFALLSTVRFFPPGTIHIAVVDPG 77 
                                       9*******..************98766666666899***************************************** PP

                                       TTSS--EEEEEETTSEEEEESSSTTHHHH...SEEEEEEGSSCC.--TS-HHHHTHHHHHHHHHCT--GGGCSEEES CS
                   SAM_adeno_trans  70 vgterralvveakggyfvgPDNGlltlal...lleeaveieeee.ssatFhgrDvFapvaarlaagvsleelgeeld 142
                                       vgt+rr+lvve++g++f gPDNGll +a+   +   a+ei+ +  +s+tFhgrDvFap+aa +aag+++++lg++++
  gi|330508244|ref|YP_004384672.1|  78 VGTARRSLVVESGGQMFAGPDNGLLIPAArslGRPVAYEITPHPgASSTFHGRDVFAPAAALIAAGQPPASLGPRVR 154
                                       *****************************86644789***9666999****************************** PP

                                       GGGS-SSS.....E.CSCEEEEEEEE-TTS-EEEEEE...EHHHHHTTCEEEEEEESSGGGSTTTSEEEEE-TTSEE CS
                   SAM_adeno_trans 143 peelvrle.....e.derlegevlyvDrFGNvitniskelleelekerkvaklkkvetyaevaegellalvnssgll 213
                                       p +l   +     + ++ le++++yvDrFGN+i+n+++  ++++  + + ++lk+++tyae ++ e+l++++s+g+ 
  gi|330508244|ref|YP_004384672.1| 155 PVDL---DfgeakKtAHGLEATIIYVDRFGNLILNLQRLPAQDMMLK-G-VRLKRARTYAEGRRIEPLITLGSHGFA 226
                                       9555...4444533578899****************96666666443.3.357788********************* PP

                                       EEEETTC-HHHHHT--TT-EE CS
                   SAM_adeno_trans 214 eiavnkgsaaellglkvgdev 234
                                       eia+n+g+a+e++ lk++d++
  gi|330508244|ref|YP_004384672.1| 227 EIAINQGNASEAFCLKAQDRI 247
                                       *******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 2144.42
//
Query:       gi|330508245|ref|YP_004384673.1|  [L=321]
Description: 5,10-methylenetetrahydromethanopterin reductase [Methanosaeta concilii GP6]
Scores for complete 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-60  205.2   0.0    1.9e-60  204.9   0.0    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.9   0.0   1.1e-64   1.9e-60      28     314 .]      18     296 ..      10     296 .. 0.95

  Alignments for each domain:
  == domain 1  score: 204.9 bits;  conditional E-value: 1.1e-64
                    Bac_luciferase  28 laraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfglg 104
                                       +a++aE++Gf  +w+++h+++    +d +t+la+l+  T++i lgt+vt++ytr+ a++A ++a++++lsgGR++lg
  gi|330508245|ref|YP_004384673.1|  18 MAKLAEDAGFGNIWITDHYNN----RDVWTTLAVLSLLTNKISLGTGVTNPYTRNAAITASSIASINELSGGRAILG 90 
                                       69******************9....**************************************************** PP

                    Bac_luciferase 105 lgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyvaaaspaglel 181
                                       +g g  a+  +++G+d+d+++ r rE+v ++r+ +++e v+ +G f +  ga+ +  + ++ iP+y++a +p++lel
  gi|330508245|ref|YP_004384673.1|  91 IGPGDKATF-DKMGIDWDKPLSRVRETVLAIRAFLAKEQVSQAG-F-K--GAQMSFTT-SK-IPIYIGAQGPKMLEL 160
                                       ****99887.999**********************999998888.3.3..44444444.44.9************** PP

                    Bac_luciferase 182 aarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraea...raliagldfyalds 255
                                       a+ + dg+l++ ++p++ + +++ +raga++agr p+d++v++ +++++++++++A        a+i  +   +  +
  gi|330508245|ref|YP_004384673.1| 161 AGAISDGVLINASHPDDFKFAVPMIRAGAEKAGRKPEDVQVCAYASFSADKDPAKAVNASkivVAFIVAGSPENVLE 237
                                       **********************************************************9988889998888999999 PP

                    Bac_luciferase 256 egagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvde 314
                                       ++   ++ea++i+++ ++ +++ga+d v++++ +a+ + G p+++++r++++ ++gv++
  gi|330508245|ref|YP_004384673.1| 238 RHGIGMDEAKAISDAISRFDFKGAMDGVTPRMTEAFSISGAPADCRARIDELLSTGVTQ 296
                                       9999999*************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2463.91
//
Query:       gi|330508246|ref|YP_004384674.1|  [L=184]
Description: nicotinamide-nucleotide adenylyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-15   57.6   0.0    2.3e-15   57.0   0.0    1.2  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.034   13.4   0.0        1.8    7.7   0.0    2.1  2  HIGH_NTase1      HIGH Nucleotidyl Transferase
      0.052   13.2   0.0       0.49   10.1   0.0    2.0  2  Citrate_ly_lig   Citrate lyase ligase C-terminal domain
      0.056   13.3   0.0      0.089   12.7   0.0    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 !   57.0   0.0   5.1e-19   2.3e-15       1     142 [.       4     133 ..       4     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 5.1e-19
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       l+ G+F+p HlGH ++le+++++++e +++ + s+++++   ++++++ eR+em+ +a  + e+ + +  ++ +++ 
  gi|330508246|ref|YP_004384674.1|   4 LYIGRFQPYHLGHQAVLEEIAREVDE-IVIVIGSAQESHGP-ENPFTSGERMEMIYAALGKGELRKRCIVTTLQDIN 78 
                                       689***********************.9999********77.****************9999966666555555333 PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                       ++       +v   +++        ++ +++n++lv++ ++e   +v+ ++ +++  +S++ ir+
  gi|330508246|ref|YP_004384674.1|  79 RN---S--LWVSHLQSMVPC-----FDLVYSNNPLVIRLFSEAGVEVKKPPLYQRDVYSGSAIRA 133
                                       33...3..788888888876.....9***************99999*9***************97 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0004       1.8      10      36 ..       9      34 ..       5      38 .. 0.79
   2 ?    3.8   0.0     0.006        27     201     237 ..     123     156 ..     106     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0004
                       HIGH_NTase1 10 YNPfHnGHlyhlekakeltgadvviav 36
                                      + P+H GH+  le++ ++++ ++vi++
  gi|330508246|ref|YP_004384674.1|  9 FQPYHLGHQAVLEEIAREVD-EIVIVI 34
                                      78**************9954.566665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.006
                       HIGH_NTase1 201 eeiaSAtaiRkalkeekkleelkklvPestleilkee 237
                                       +++ S +aiR +++e+    + ++lvP +++ +++e 
  gi|330508246|ref|YP_004384674.1| 123 RDVYSGSAIRALMRER---GDWERLVPPAVAGFIQEI 156
                                       5789*********655...67999***9999988765 PP

>> Citrate_ly_lig  Citrate lyase ligase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00011      0.49       9      63 ..      10      71 ..       6      88 .. 0.78
   2 ?    1.1   0.0     0.061   2.7e+02     147     174 ..     120     145 ..      92     153 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
                    Citrate_ly_lig  9 nPftlGhryLvekaakendvvhlfvvkedksl.....fsyeerlklvkk..Gikdlknvtlh 63
                                       P+ lGh+ ++e+ a+e d + + + + ++s+     f+  er++++ +  G  +l++ +++
  gi|330508246|ref|YP_004384674.1| 10 QPYHLGHQAVLEEIAREVDEIVIVIGSAQESHgpenpFTSGERMEMIYAalGKGELRKRCIV 71
                                      69**********************99998886444447778999999652255556665555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.061
                    Citrate_ly_lig 147 ekeeelisaskvrkllkek.nleklaelv 174
                                        ++ ++ s s++r+l++e+ ++e+   lv
  gi|330508246|ref|YP_004384674.1| 120 LYQRDVYSGSAIRALMRERgDWER---LV 145
                                       4678899*********98625554...44 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05     0.089      11      33 ..       5      27 ..       3      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                           FAD_syn 11 tlGnFDGvHlGHqallkkaveaa 33
                                       +G F   HlGHqa+l+++ ++ 
  gi|330508246|ref|YP_004384674.1|  5 YIGRFQPYHLGHQAVLEEIAREV 27
                                      69**************9987664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1511.15
//
Query:       gi|330508247|ref|YP_004384675.1|  [L=537]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-41  140.2   0.0      6e-41  139.2   0.0    1.6  1  DUF4277    Domain of unknown function (DUF4277)
    8.1e-12   45.2   0.2    5.7e-11   42.5   0.2    2.0  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.0   6.7e-45     6e-41       3     109 .]      10     116 ..       8     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 6.7e-45
                           DUF4277   3 vksldhlglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfpeffedkplerLlgegve 79 
                                       + sldhlglva+++d+lg++e+ide ipk++++k+s++ ++ka+++ngLgf +r+Ly+fp++fe+++lerL+++gv 
  gi|330508247|ref|YP_004384675.1|  10 TLSLDHLGLVAAIFDALGISEVIDESIPKTRNCKLSHSAIIKAMVINGLGFAERRLYIFPSYFENLALERLFNPGVV 86 
                                       679************************************************************************** PP

                           DUF4277  80 aehlnddrlgrtLDklyeagvtklfteial 109
                                       +e++n+d++grtLD++ ++g t+lf++ia+
  gi|330508247|ref|YP_004384675.1|  87 PEDFNEDVVGRTLDRINKFGSTALFNNIAM 116
                                       ****************************86 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.2   6.4e-15   5.7e-11       9     213 ..     131     455 ..     124     456 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 6.4e-15
                         DDE_Tnp_1   9 vDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                       vD t++ v+g                  +d+rw        + + + +++++  g++l v+ ++gn++d k+l++++
  gi|330508247|ref|YP_004384675.1| 131 VDTTSFGVHGDYegldcnpameitlghpKDGRW------DLKQFIVSMVTNQC-GIPLFVQAHSGNKSDKKTLIETI 200
                                       666666666666666666554444444444444......55667788888888.9********************** PP

                         DDE_Tnp_1  70 delrpr....kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrn 142
                                       ++++ +     + ++ aD++ +s e+++ l      +i r++  +++ ++      +++++ +dr+ i++++ +  +
  gi|330508247|ref|YP_004384675.1| 201 QMFKSNldfsGKNYFAADSALFSSENIRLLG-DSTLWITRVPTTVREVKDLQRLDLEMKTCSDDRYSIFETEINYGG 276
                                       **********************999999999.55559****888888888666669999999999999999999999 PP

                         DDE_Tnp_1 143 k............................................................................ 143
                                                                                                                    
  gi|330508247|ref|YP_004384675.1| 277 Idqkwvvvdsremhaskaktfdrrigkeftearkslkklgyivfaceadarkaadrwisenphftltglsiceiskr 353
                                       99*************************************************************************** PP

                         DDE_Tnp_1 144 ...............................skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrk.f 188
                                                                      + ++   + +v+  n+++l+ e + ++y+ +  +E  F++lk+k f
  gi|330508247|ref|YP_004384675.1| 354 idskrgrpkkdeqlekgyliegevqrneatiANERSRLGRFVLASNDKTLEGELMLQYYKGQNAVEKGFRFLKDKsF 430
                                       ******************************99999999*************************************** PP

                         DDE_Tnp_1 189 gldrlryrglnrveaqllllllaln 213
                                       +   +++++ +r+ea  +++ l+l+
  gi|330508247|ref|YP_004384675.1| 431 RVAEVYLKKEERIEALSMIMVLSLL 455
                                       *******************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); 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: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 3595.04
//
Query:       gi|330508248|ref|YP_004384676.1|  [L=243]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1749.36
//
Query:       gi|330508249|ref|YP_004384677.1|  [L=124]
Description: hypothetical protein MCON_2398 [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.4    1.5e-06   28.3   0.4    2.2  1  DUF333    Domain of unknown function (DUF333)


Domain annotation for each model (and alignments):
>> DUF333  Domain of unknown function (DUF333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.4   8.5e-11   1.5e-06       4      48 .]      81     116 ..      79     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 8.5e-11
                            DUF333   4 NPAsvyCvkqGGkleiakdadGgqvgyCqlpdGkrceEwaLyrgd 48 
                                       +PA+++C++ G  +     ++    g+C++p G++c++w+++rgd
  gi|330508249|ref|YP_004384677.1|  81 DPAEAFCIQRGNLY-----NN----GICTFPGGSSCDAWDFMRGD 116
                                       68888888888655.....34....9*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 943.68
//
Query:       gi|330508250|ref|YP_004384678.1|  [L=439]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-25   87.4   0.0    1.3e-24   86.3   0.0    1.6  1  Transposase_20  Transposase IS116/IS110/IS902 family
    9.3e-23   80.8   0.2    3.7e-22   78.9   0.0    2.0  2  DEDD_Tnp_IS110  Transposase
     0.0059   16.4   0.1      0.015   15.1   0.1    1.7  1  YfkB            YfkB-like domain
  ------ inclusion threshold ------
       0.12   11.3   0.1       0.79    8.6   0.0    2.1  2  UPF0261         Uncharacterised protein family (UPF0261)


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0     3e-28   1.3e-24       2      86 ..     249     334 ..     248     335 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 3e-28
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaai.r 77 
                                       ++++sipGi ++  +++l+eig+ r f++++qla+++Gl+p en+S++kkr+ +i+krG++++R +L+eaA++++  
  gi|330508250|ref|YP_004384678.1| 249 AIVMSIPGIAFISGSVILSEIGNYRDFQTPEQLAKWCGLNPGENESAGKKRKCGITKRGSKYIRVVLVEAAQTIAnM 325
                                       589********************************************************************999955 PP

                    Transposase_20  78 anpelrayy 86 
                                       +n  l ++y
  gi|330508250|ref|YP_004384678.1| 326 KNTGLSRFY 334
                                       569999888 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   8.3e-26   3.7e-22       1     151 [.       9     150 ..       9     152 .. 0.93
   2 ?   -1.5   0.0      0.46     2e+03      28      70 ..     323     366 ..     312     370 .. 0.63

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 8.3e-26
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G Dv+kd ++a+++  ++   ++e++ +++++l+++ ++ +a+ ++ +v++eatg y+ +++ + l++ i+++v n
  gi|330508250|ref|YP_004384678.1|   9 CGADVHKDLIVATITG-DEVPSIRENFGTTKSELDRFRNW-LADNKCEQVAFEATGVYWIPIYDV-LSRTIDTIVAN 82 
                                       799******9999984.66666778999999999999999.88999*************999998.6789******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLd 151
                                       pl++k +      ++K+D+kD+k IA l +  ++++ +++ +++ +eLr+ltr+r+ +vk+rt++knr+++ L 
  gi|330508250|ref|YP_004384678.1|  83 PLQIKSIP-----NDKSDSKDSKRIATLCL-NNQIKRSRVFSDEDRELRNLTRARSGYVKTRTQFKNRIHKYLS 150
                                       ******95.....8****************.****************************************996 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.46
                    DEDD_Tnp_IS110  28 pn.deeglealleklaakagevlvvveatghygallvaflleag 70 
                                       +n +  gl+++ ++l++k+++   +v    +   l++++l +++
  gi|330508250|ref|YP_004384678.1| 323 ANmKNTGLSRFYKRLSKKKEHNVAIVAVARKLICLIYHLLINQE 366
                                       44144678888888666666666666666666666666766665 PP

>> YfkB  YfkB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.4e-06     0.015      91     150 ..     317     377 ..     306     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-06
                              YfkB  91 gdeealgnikeekledvfekwke.sklakslnchcpavkclGpnvlvknayykevdfkkrk 150
                                         +++++n+k++ l+  +++ ++ ++ +  +     ++ cl   +l+++ +y+evd +krk
  gi|330508250|ref|YP_004384678.1| 317 EAAQTIANMKNTGLSRFYKRLSKkKEHNVAIVAVARKLICLIYHLLINQEFYQEVDCRKRK 377
                                       56789***************9873567788999999**********************998 PP

>> UPF0261  Uncharacterised protein family (UPF0261)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00018      0.79     195     224 ..      34      63 ..      30      64 .. 0.96
   2 ?   -0.4   0.1     0.096   4.3e+02     156     192 ..     311     347 ..     307     356 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00018
                           UPF0261 195 fGvttpavdairelLeeegyevlvFhAtGt 224
                                       fG+t+   d+ r+ L+++++e ++F AtG+
  gi|330508250|ref|YP_004384678.1|  34 FGTTKSELDRFRNWLADNKCEQVAFEATGV 63 
                                       9****************************6 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.096
                           UPF0261 156 lrkvLsnAaaaiaGmakaeekskeekeeeeekplvai 192
                                       +r vL +Aa+ ia m ++  ++  ++ ++++ + vai
  gi|330508250|ref|YP_004384678.1| 311 IRVVLVEAAQTIANMKNTGLSRFYKRLSKKKEHNVAI 347
                                       6889*************99999988877777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:01.16
# Mc/sec: 1145.59
//
Query:       gi|330508251|ref|YP_004384679.1|  [L=369]
Description: hypothetical protein MCON_2401 [Methanosaeta concilii GP6]
Scores for 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   25.0   0.0    6.3e-05   23.4   0.0    1.8  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 !   23.4   0.0   3.5e-09   6.3e-05      48     103 ..     166     212 ..     118     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.5e-09
                    Transglut_core  48 e.tgkGncedfaslfvallRalGipaRvvtgylsgeeekeqsvasedaHawvevyle 103
                                         +g+G+c dfa l++al  ++G  +R++   +           + + Ha++evyl 
  gi|330508251|ref|YP_004384679.1| 166 GcAGAGDCDDFAILMAALVESIGGTTRIILANNN----------TTGGHAYAEVYLG 212
                                       24677************************87765..........6799*******92 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2520.35
//
Query:       gi|330508252|ref|YP_004384680.1|  [L=224]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   78.1  10.5    2.4e-07   30.4   0.1    4.8  4  TPR_2         Tetratricopeptide repeat
    9.6e-21   72.7  12.8    3.2e-09   36.2   0.1    4.6  5  TPR_1         Tetratricopeptide repeat
    4.7e-19   67.8   1.4    1.8e-06   27.5   0.1    3.6  3  TPR_11        TPR repeat
    8.3e-16   56.8   9.8    6.4e-06   26.0   0.1    4.9  4  TPR_8         Tetratricopeptide repeat
    2.7e-15   55.6   7.7    2.8e-06   27.3   0.1    4.6  4  TPR_17        Tetratricopeptide repeat
    1.9e-14   54.0   1.4      3e-08   34.2   0.1    3.1  3  TPR_16        Tetratricopeptide repeat
    2.5e-13   50.3   8.3    3.9e-07   30.5   0.8    3.1  4  TPR_19        Tetratricopeptide repeat
    1.8e-12   47.0   3.3     0.0021   18.7   0.0    3.7  3  TPR_14        Tetratricopeptide repeat
    2.7e-12   46.6   0.3      4e-07   30.1   0.0    2.5  2  TPR_9         Tetratricopeptide repeat
    7.7e-10   38.9   8.5    0.00028   21.1   0.2    4.0  3  TPR_12        Tetratricopeptide repeat
    6.4e-08   32.7   8.6    0.00028   21.0   0.6    2.9  3  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    8.8e-08   31.7   1.3      0.041   13.9   0.3    3.7  3  TPR_7         Tetratricopeptide repeat
    3.5e-06   26.7   6.6      0.092   12.6   0.1    3.9  4  TPR_10        Tetratricopeptide repeat
    8.9e-05   21.6   1.0       0.15   11.0   0.0    2.8  3  NARP1         NMDA receptor-regulated protein 1
    0.00075   19.5   0.4        1.1    9.4   0.0    3.3  3  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
     0.0012   19.2   1.5        1.7    9.5   0.0    3.0  2  TPR_4         Tetratricopeptide repeat
     0.0019   18.2   0.3     0.0046   17.0   0.2    1.8  1  SRP_TPR_like  Putative TPR-like repeat
     0.0069   16.4   2.5       0.42   10.7   0.2    2.5  2  ANAPC5        Anaphase-promoting complex subunit 5
  ------ inclusion threshold ------
      0.013   16.1   7.6        2.7    8.8   0.0    4.4  4  TPR_6         Tetratricopeptide repeat
      0.016   14.4   1.8       0.12   11.6   0.3    2.1  2  FAT           FAT domain
       0.02   14.9   1.0          5    7.2   0.0    2.9  3  DUF3856       Domain of Unknown Function (DUF3856)
      0.034   13.5   3.5        3.2    7.0   0.7    2.6  2  TPR_MalT      MalT-like TPR region
      0.048   13.9   1.3        3.3    8.0   0.2    3.2  3  NRBF2_MIT     MIT domain of nuclear receptor-binding factor 2
      0.071   12.1   1.0       0.44    9.5   0.1    2.0  2  ChAPs         ChAPs (Chs5p-Arf1p-binding proteins)
      0.089   12.4   0.1         21    4.8   0.0    2.7  2  HTH_Bact      Helix-turn-helix bacterial domain
       0.12   12.4   1.9         19    5.3   0.1    3.4  3  TPR_3         Tetratricopeptide repeat
       0.12   12.5   4.9        7.7    6.7   0.1    3.1  3  MIT           MIT (microtubule interacting and transport) dom
        1.7    8.8   5.6        1.4    9.1   0.1    3.0  3  HEPN          HEPN domain


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   2.3e-09   1.5e-06       2      33 ..      88     119 ..      87     120 .. 0.94
   2 !   19.4   0.0   1.2e-06   0.00078       1      33 [.     121     153 ..     121     154 .. 0.95
   3 !   30.4   0.1   3.7e-10   2.4e-07       1      32 [.     155     186 ..     155     188 .. 0.96
   4 ?    2.5   2.4      0.32     2e+02      18      34 .]     201     217 ..     189     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.3e-09
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +++   G++++++++yeeAl+af+++++ +P+
  gi|330508252|ref|YP_004384680.1|  88 KVWQKKGQVLLNQNRYEEALQAFDQSIQMNPR 119
                                       68999**************************7 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.2e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       ae ++  G + +++ ++e+Al++fe A++l+P 
  gi|330508252|ref|YP_004384680.1| 121 AENWNDKGVVQIAAYNFEDALKCFEVAIALEPS 153
                                       688****************************96 PP

  == domain 3  score: 30.4 bits;  conditional E-value: 3.7e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       a a++n ++++y+lg+y+eA+  +++A++l+P
  gi|330508252|ref|YP_004384680.1| 155 ATAWNNKAQILYALGRYDEAILTCDQAIQLEP 186
                                       679***************************99 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.32
                             TPR_2  18 eeAleafekAleldPnn 34 
                                       +eA +af kA el+ +n
  gi|330508252|ref|YP_004384680.1| 201 KEAQKAFAKAKELAQKN 217
                                       69999999999998765 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   8.1e-10   5.2e-07       2      33 ..      88     119 ..      87     120 .. 0.95
   2 !   12.4   0.0   0.00017      0.11       4      34 .]     124     154 ..     121     154 .. 0.87
   3 !   36.2   0.1     5e-12   3.2e-09       1      32 [.     155     186 ..     155     188 .. 0.96
   4 ?   -2.7   0.0       9.7   6.2e+03       1      25 [.     189     194 ..     189     198 .. 0.59
   5 ?    0.7   1.1      0.83   5.3e+02      19      34 .]     202     217 ..     201     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 8.1e-10
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                       k++  +G++++++++y+eAl+++++ ++ nP 
  gi|330508252|ref|YP_004384680.1|  88 KVWQKKGQVLLNQNRYEEALQAFDQSIQMNPR 119
                                       78999**************************6 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++ +G++     ++++Al+++e A+ l+P++
  gi|330508252|ref|YP_004384680.1| 124 WNDKGVVQIAAYNFEDALKCFEVAIALEPSF 154
                                       7888888888889****************86 PP

  == domain 3  score: 36.2 bits;  conditional E-value: 5e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a a++n++++++ lg+ydeA+  +++A++l+P
  gi|330508252|ref|YP_004384680.1| 155 ATAWNNKAQILYALGRYDEAILTCDQAIQLEP 186
                                       679***************************99 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 9.7
                                       HHHHHHHHHHHHHTT-HHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyye 25 
                                       a+a+y                    
  gi|330508252|ref|YP_004384680.1| 189 AEAWY-------------------T 194
                                       56666...................4 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.83
                                       HHHHHHHHHHHHSTTH CS
                             TPR_1  19 eAleyyekALelnPnn 34 
                                       eA +++ kA el  +n
  gi|330508252|ref|YP_004384680.1| 202 EAQKAFAKAKELAQKN 217
                                       8999999**9998876 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0     2e-07   0.00013       1      38 [.      94     131 ..      94     133 .. 0.93
   2 !   23.3   0.1   5.8e-08   3.7e-05      10      42 .]     137     169 ..     136     169 .. 0.97
   3 !   27.5   0.1   2.8e-09   1.8e-06       2      32 ..     163     193 ..     162     199 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2e-07
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       G+++  q++yeeA++a+ + ++ +P +ae ++  G+++
  gi|330508252|ref|YP_004384680.1|  94 GQVLLNQNRYEEALQAFDQSIQMNPRSAENWNDKGVVQ 131
                                       889999***********************999999875 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 5.8e-08
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +e+A+++++ A++l P++a+a++n ++++y++G
  gi|330508252|ref|YP_004384680.1| 137 FEDALKCFEVAIALEPSFATAWNNKAQILYALG 169
                                       89*****************************98 PP

  == domain 3  score: 27.5 bits;  conditional E-value: 2.8e-09
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayy 32 
                                       +++y++G+y+eAi    +A++l P +aea+y
  gi|330508252|ref|YP_004384680.1| 163 QILYALGRYDEAILTCDQAIQLEPMSAEAWY 193
                                       79****************************9 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   3.9e-08   2.5e-05       2      32 ..      88     118 ..      87     120 .. 0.95
   2 ?    5.3   0.0     0.042        27       1      33 [.     121     153 ..     121     154 .. 0.88
   3 !   26.0   0.1     1e-08   6.4e-06       1      32 [.     155     186 ..     155     186 .. 0.96
   4 ?    2.4   2.2      0.36   2.3e+02      18      33 ..     201     216 ..     189     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.9e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ++++++g+++l++++yeeA +++ + ++++p
  gi|330508252|ref|YP_004384680.1|  88 KVWQKKGQVLLNQNRYEEALQAFDQSIQMNP 118
                                       89****************************9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.042
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ae ++ +g + +   ++e A +++e a+ l+p+
  gi|330508252|ref|YP_004384680.1| 121 AENWNDKGVVQIAAYNFEDALKCFEVAIALEPS 153
                                       5778899999999999*************9996 PP

  == domain 3  score: 26.0 bits;  conditional E-value: 1e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a a++n+++i+  lg+y+eA+ ++ +a++l+p
  gi|330508252|ref|YP_004384680.1| 155 ATAWNNKAQILYALGRYDEAILTCDQAIQLEP 186
                                       679***************************98 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHHH CS
                             TPR_8  18 eeAkeyyekaleldpd 33 
                                       +eA++++ ka el+++
  gi|330508252|ref|YP_004384680.1| 201 KEAQKAFAKAKELAQK 216
                                       4788888888888776 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.2   0.00024      0.16      12      34 .]      86     108 ..      82     108 .. 0.91
   2 !   11.6   0.0   0.00046      0.29       2      33 ..     110     141 ..     109     142 .. 0.87
   3 !   27.3   0.1   4.4e-09   2.8e-06       1      33 [.     143     175 ..     143     175 .. 0.96
   4 ?    6.1   0.0     0.027        17       2      25 ..     178     201 ..     177     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                            TPR_17  12 nadaynnLAelllknGdlmtArq 34 
                                       + ++++ ++++ll+++++++A+q
  gi|330508252|ref|YP_004384680.1|  86 DYKVWQKKGQVLLNQNRYEEALQ 108
                                       789******************97 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00046
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + ++++ +P +a+ +n +++++  + ++++A+
  gi|330508252|ref|YP_004384680.1| 110 FDQSIQMNPRSAENWNDKGVVQIAAYNFEDAL 141
                                       789*****************998887777775 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 4.4e-09
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +++ a++l+P+ a a+nn+A++l+ +G++++A+
  gi|330508252|ref|YP_004384680.1| 143 CFEVAIALEPSFATAWNNKAQILYALGRYDEAI 175
                                       7899***************************96 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.027
                            TPR_17   2 ylkaleldPnnadaynnLAelllk 25 
                                       + +a++l+P +a+a++ +  +l k
  gi|330508252|ref|YP_004384680.1| 178 CDQAIQLEPMSAEAWYTKSLILGK 201
                                       789*************99988864 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   5.3e-06    0.0034       3      43 ..      93     130 ..      92     134 .. 0.87
   2 !   34.2   0.1   4.7e-11     3e-08      12      62 ..     136     183 ..     126     189 .. 0.91
   3 ?   -0.2   0.1       2.6   1.7e+03      23      38 ..     181     193 ..     179     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.3e-06
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgda 43 
                                       +++ +l++++y++A+ a+++ + ++   P+ ae ++ +g++
  gi|330508252|ref|YP_004384680.1|  93 KGQVLLNQNRYEEALQAFDQSIQMN---PRSAENWNDKGVV 130
                                       68999********************...8888888877776 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 4.7e-11
                            TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       +++dA++ +e a+++    P  a A+++++++++++gr++eA+  ++ a++
  gi|330508252|ref|YP_004384680.1| 136 NFEDALKCFEVAIALE---PSFATAWNNKAQILYALGRYDEAILTCDQAIQ 183
                                       8***************...************************99998875 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.6
                            TPR_16  23 alkrdpssPdaaeAll 38 
                                       a+ +    P  aeA++
  gi|330508252|ref|YP_004384680.1| 181 AIQLE---PMSAEAWY 193
                                       66666...88888887 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00023      0.15      33      58 ..      95     120 ..      83     128 .. 0.71
   2 !   24.4   0.2   4.8e-08   3.1e-05       1      57 [.      97     153 ..      97     158 .. 0.92
   3 !   30.5   0.8   6.2e-10   3.9e-07       2      62 ..     132     192 ..     131     198 .. 0.92
   4 ?   -0.4   0.3       2.7   1.7e+03       9      25 ..     202     218 ..     200     221 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                            TPR_19  33 eallalgqldeAealLdalpeedpdd 58 
                                       ++ll++++++eA ++ d+  +++p +
  gi|330508252|ref|YP_004384680.1|  95 QVLLNQNRYEEALQAFDQSIQMNPRS 120
                                       67777777777777777777777665 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 4.8e-08
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       ll +++y+eAl+++ q +q +p +ae + +   +++a+ ++++A ++ + + + +p 
  gi|330508252|ref|YP_004384680.1|  97 LLNQNRYEEALQAFDQSIQMNPRSAENWNDKGVVQIAAYNFEDALKCFEVAIALEPS 153
                                       67799*******************************************999888776 PP

  == domain 3  score: 30.5 bits;  conditional E-value: 6.2e-10
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       +a+ ++++Al+ +e a++ +p  a a+ + A++l+alg++deA+ ++d++ + +p +a+++
  gi|330508252|ref|YP_004384680.1| 132 IAAYNFEDALKCFEVAIALEPSFATAWNNKAQILYALGRYDEAILTCDQAIQLEPMSAEAW 192
                                       67889**********************************************9999987765 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.7
                            TPR_19   9 eAlalleqalqedpkna 25 
                                       eA++++++a + + kn+
  gi|330508252|ref|YP_004384680.1| 202 EAQKAFAKAKELAQKNQ 218
                                       45555555555555444 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   3.3e-06    0.0021       3      38 ..      89     124 ..      88     130 .. 0.92
   2 !   14.8   0.0   5.8e-05     0.037       8      44 .]     128     164 ..     122     164 .. 0.88
   3 !   15.2   0.1   4.4e-05     0.028       8      39 ..     162     193 ..     161     198 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.3e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       ++++ +++ll++ +++eA++++++ ++ +P +ae w
  gi|330508252|ref|YP_004384680.1|  89 VWQKKGQVLLNQNRYEEALQAFDQSIQMNPRSAENW 124
                                       69999***************************9987 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5.8e-05
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawlllaql 44 
                                       + +  a+ ++++A+++++ a+al P++a+aw   aq+
  gi|330508252|ref|YP_004384680.1| 128 GVVQIAAYNFEDALKCFEVAIALEPSFATAWNNKAQI 164
                                       55778899***********************999985 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 4.4e-05
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawl 39 
                                       a++l+alG++deAi  +++a++l P +aeaw+
  gi|330508252|ref|YP_004384680.1| 162 AQILYALGRYDEAILTCDQAIQLEPMSAEAWY 193
                                       899**********************9999996 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   6.3e-10     4e-07       4      61 ..      96     153 ..      94     157 .. 0.94
   2 !   21.7   0.1   2.6e-07   0.00017       7      64 ..     133     190 ..     130     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 6.3e-10
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       ++++++++e+al++ +  ++++P+++e + d G+++    +++ Al+++e ++al+p+
  gi|330508252|ref|YP_004384680.1|  96 VLLNQNRYEEALQAFDQSIQMNPRSAENWNDKGVVQIAAYNFEDALKCFEVAIALEPS 153
                                       6899****************************************************97 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.6e-07
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                        + ++e al++ e  ++l P  +  +   +++l+ lG++ +A+   +++++l+p  ++
  gi|330508252|ref|YP_004384680.1| 133 AAYNFEDALKCFEVAIALEPSFATAWNNKAQILYALGRYDEAILTCDQAIQLEPMSAE 190
                                       67789**************************************999999999995555 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1     2e-05     0.013       9      73 ..      93     149 ..      88     151 .. 0.81
   2 !   21.1   0.2   4.4e-07   0.00028       3      32 ..     155     184 ..     153     185 .. 0.93
   3 ?    4.5   0.3     0.069        44      21      39 ..     202     220 ..     197     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-05
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                        ++vl+ + ry+eAl+ +++++++      p     a+  ++ g ++ a+ ++e+Al+ +e a+a
  gi|330508252|ref|YP_004384680.1|  93 KGQVLLNQNRYEEALQAFDQSIQMN-----PR---SAENWNDKGVVQIAAYNFEDALKCFEVAIA 149
                                       7899999999999999999998888.....65...477888888888888888888888888876 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 4.4e-07
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                       ata+nn a++l++lgrydeA+  +++a+++
  gi|330508252|ref|YP_004384680.1| 155 ATAWNNKAQILYALGRYDEAILTCDQAIQL 184
                                       89************************9986 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.069
                            TPR_12  21 eAlellekaleiarrllGp 39 
                                       eA++ + ka e+a++ +G 
  gi|330508252|ref|YP_004384680.1| 202 EAQKAFAKAKELAQKNQGA 220
                                       9*************99885 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.4e-05    0.0087      29      80 ..      93     145 ..      65     147 .. 0.86
   2 !   21.0   0.6   4.4e-07   0.00028       3      63 ..     135     196 ..     133     201 .. 0.94
   3 !   13.0   0.2   0.00014     0.089       4      57 ..     170     221 ..     169     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       ++++l+++++y++A++ ++++ + n++s + +  ++ ++++  ++e+A++++e
  gi|330508252|ref|YP_004384680.1|  93 KGQVLLNQNRYEEALQAFDQSiQMNPRSAENWNDKGVVQIAAYNFEDALKCFE 145
                                       59************************************************998 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 4.4e-07
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfA 63 
                                       +n+++A+ ++e + a e+  + +   +A+ ly +g+y++A+  +++a +l++ s +++y++ 
  gi|330508252|ref|YP_004384680.1| 135 YNFEDALKCFEVAIALEPSFATAWNNKAQILYALGRYDEAILTCDQAiQLEPMSAEAWYTKS 196
                                       799********************************************************875 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00014
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-..HHHHHHHHHCTSHHHC-HH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngq..ykrAyellrkaklnskslg 57 
                                       +y++Ai+ ++ + + e+ s+e+ y ++l l +  q  + +A el++k+    +   
  gi|330508252|ref|YP_004384680.1| 170 RYDEAILTCDQAIQLEPMSAEAWYTKSLILGKEAQkaFAKAKELAQKN----QGAS 221
                                       8********************999966666665555566666666555....5554 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0023       1.5       6      28 ..      94     116 ..      90     123 .. 0.86
   2 ?    5.6   0.0     0.029        19      14      32 ..     136     152 ..     124     156 .. 0.81
   3 !   13.9   0.3   6.3e-05     0.041       1      28 [.     157     184 ..     157     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0023
                             TPR_7   6 arlysrlGdyeeAielyeqsLal 28 
                                       +++  ++++yeeA++ + qs+++
  gi|330508252|ref|YP_004384680.1|  94 GQVLLNQNRYEEALQAFDQSIQM 116
                                       788999*************8766 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.029
                             TPR_7  14 dyeeAielyeqsLaltkdp 32 
                                       ++e+A++++e   a++ +p
  gi|330508252|ref|YP_004384680.1| 136 NFEDALKCFEV--AIALEP 152
                                       79*********..555555 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 6.3e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       a++n a++  +lG+y+eAi  + q+++l
  gi|330508252|ref|YP_004384680.1| 157 AWNNKAQILYALGRYDEAILTCDQAIQL 184
                                       799*********************6555 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00014     0.092       9      31 ..      94     116 ..      93     117 .. 0.93
   2 ?    3.6   0.0       0.1        65       9      31 ..     128     150 ..     125     151 .. 0.84
   3 !   12.0   0.2   0.00023      0.15       2      30 ..     155     183 ..     154     184 .. 0.82
   4 ?   -1.7   0.1       4.8   3.1e+03      21      34 ..     189     202 ..     188     216 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + +l +++ry+eA++ +++++++
  gi|330508252|ref|YP_004384680.1|  94 GQVLLNQNRYEEALQAFDQSIQM 116
                                       67999***************997 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.1
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       +++  + +++++A++ +e a+a+
  gi|330508252|ref|YP_004384680.1| 128 GVVQIAAYNFEDALKCFEVAIAL 150
                                       67777899**********99985 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00023
                            TPR_10   2 AsslnNLanalrqrgrydeAealleeala 30 
                                       A++ nN a +l+++grydeA   +++a++
  gi|330508252|ref|YP_004384680.1| 155 ATAWNNKAQILYALGRYDEAILTCDQAIQ 183
                                       56669***************876666665 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.8
                            TPR_10  21 Aealleealairrr 34 
                                       Aea++ ++l + ++
  gi|330508252|ref|YP_004384680.1| 189 AEAWYTKSLILGKE 202
                                       66666666655444 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.1    0.0083       5.3      39      73 ..      88     122 ..      76     131 .. 0.84
   2 !   11.0   0.0   0.00023      0.15     208     254 ..     137     183 ..     131     184 .. 0.91
   3 !   10.0   0.1   0.00045      0.29     202     240 ..     165     203 ..     162     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0083
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CH CS
                             NARP1  39 avketkaelllkLgrkeeAeatyeaLlernpensk 73 
                                       +v ++k+++ll+ +r+eeA +++ + +++np + +
  gi|330508252|ref|YP_004384680.1|  88 KVWQKKGQVLLNQNRYEEALQAFDQSIQMNPRSAE 122
                                       567999*********************99997654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00023
                                       SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1 208 rekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeeark 254
                                        e Al++ + ai+ +p++   + +Ka+il   G  ++A+ + ++a +
  gi|330508252|ref|YP_004384680.1| 137 FEDALKCFEVAIALEPSFATAWNNKAQILYALGRYDEAILTCDQAIQ 183
                                       568************************************99999865 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00045
                                       HHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT CS
                             NARP1 202 ydklgsrekAleyidkaiehtptlvelyltKarilkhaG 240
                                          lg++++A+ + d+ai+ +p + e ++tK+ il +  
  gi|330508252|ref|YP_004384680.1| 165 LYALGRYDEAILTCDQAIQLEPMSAEAWYTKSLILGKEA 203
                                       556899****************************96643 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.11        69      14      33 ..     100     119 ..      97     122 .. 0.88
   2 ?    2.7   0.0      0.21   1.3e+02      16      35 ..     136     155 ..     133     159 .. 0.90
   3 !    9.4   0.0    0.0016       1.1      12      33 ..     166     187 ..     165     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.11
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       + +Y+eA++  d+ +++ P+
  gi|330508252|ref|YP_004384680.1| 100 QNRYEEALQAFDQSIQMNPR 119
                                       679************99996 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.21
                                       -HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPenr 35 
                                       ++++A+++ +  +++EP++ 
  gi|330508252|ref|YP_004384680.1| 136 NFEDALKCFEVAIALEPSFA 155
                                       899**************985 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0016
                                       HHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPe 33 
                                       y lg+Y+eA   +d+ +++EP 
  gi|330508252|ref|YP_004384680.1| 166 YALGRYDEAILTCDQAIQLEPM 187
                                       679******************6 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0084       5.4       8      26 .]      94     112 ..      93     112 .. 0.91
   2 !    9.5   0.0    0.0027       1.7       5      20 ..     159     174 ..     155     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0084
                             TPR_4   8 ArallalGdldeAraller 26 
                                       +++ll + +++eA++++++
  gi|330508252|ref|YP_004384680.1|  94 GQVLLNQNRYEEALQAFDQ 112
                                       789***********99886 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0027
                             TPR_4   5 laLArallalGdldeA 20 
                                        + A+ l+alG++deA
  gi|330508252|ref|YP_004384680.1| 159 NNKAQILYALGRYDEA 174
                                       5789***********9 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 !   17.0   0.2   7.2e-06    0.0046      20      95 ..      93     175 ..      72     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.2e-06
                      SRP_TPR_like  20 kvvaliklekyeeaLkllkkgsal...sedvrfEkaYvlYklkkykkalkilkkveaee....kvkvlksqvlYrlg 89 
                                       k   l++ ++yeeaL++ ++  ++   s +   +k  v     ++++alk ++ + a e     +   k+q+lY lg
  gi|330508252|ref|YP_004384680.1|  93 KGQVLLNQNRYEEALQAFDQSIQMnprSAENWNDKGVVQIAAYNFEDALKCFEVAIALEpsfaTAWNNKAQILYALG 169
                                       677899***********99877551115677789999**************998877664222344569******** PP

                      SRP_TPR_like  90 syekAY 95 
                                        y++A 
  gi|330508252|ref|YP_004384680.1| 170 RYDEAI 175
                                       ***995 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.2   0.00066      0.42      12      70 ..     101     184 ..      95     192 .. 0.89
   2 ?    5.5   0.1     0.028        18      58      80 ..     201     223 ..     190     224 .] 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00066
                            ANAPC5  12 kdYqqaldsLhryFDyvlsqnessq.............................kksyqyalLnlaslhadfghnee 59 
                                       ++Y++al    + FD ++++n +s+                             + s+ +a  n a + +++g ++e
  gi|330508252|ref|YP_004384680.1| 101 NRYEEAL----QAFDQSIQMNPRSAenwndkgvvqiaaynfedalkcfevaialEPSFATAWNNKAQILYALGRYDE 173
                                       4555554....689999999999999999***********************9999********************* PP

                            ANAPC5  60 Avkaleeairl 70 
                                       A+ +   ai+l
  gi|330508252|ref|YP_004384680.1| 174 AILTCDQAIQL 184
                                       ********987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.028
                            ANAPC5  58 eeAvkaleeairlArenkDkscL 80 
                                       +eA ka+  a +lA++n+  scL
  gi|330508252|ref|YP_004384680.1| 201 KEAQKAFAKAKELAQKNQGASCL 223
                                       79********************9 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0043       2.7       7      33 .]      94     120 ..      90     120 .. 0.87
   2 ?    1.9   0.0      0.67   4.3e+02       9      31 ..     130     152 ..     127     153 .. 0.78
   3 ?    6.1   0.1     0.032        20       7      31 ..     162     186 ..     160     186 .. 0.86
   4 ?   -0.3   0.1       3.4   2.2e+03      13      24 ..     204     215 ..     192     216 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0043
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPdS 33 
                                       ++ +++++++++Al+a+++ i+  P S
  gi|330508252|ref|YP_004384680.1|  94 GQVLLNQNRYEEALQAFDQSIQMNPRS 120
                                       88899999**********999888876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   9 syrklgdtdkAlealerlikeYP 31 
                                        ++++ + ++Al+ +e  i   P
  gi|330508252|ref|YP_004384680.1| 130 VQIAAYNFEDALKCFEVAIALEP 152
                                       566656999*******9998766 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       a+ +++lg++d+A+ + ++ i+  P
  gi|330508252|ref|YP_004384680.1| 162 AQILYALGRYDEAILTCDQAIQLEP 186
                                       88999999******99999998655 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHHH CS
                             TPR_6  13 lgdtdkAleale 24 
                                       ++  +kA+e+ +
  gi|330508252|ref|YP_004384680.1| 204 QKAFAKAKELAQ 215
                                       445566666665 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00018      0.12     232     297 ..      73     137 ..      53     139 .. 0.79
   2 ?    3.3   0.1     0.061        39     252     291 ..     128     160 ..     125     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                       ...........HH.HHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC.....CCHHHH CS
                               FAT 232 keptnleeftkll.arcylkkGewqealqkldwseekieeilqsysaateidpswykawht.....walfnf 297
                                       k+ +++ e++++   ++  kkG+ + + ++        ee+lq++ ++ +++p+++++w+       a +nf
  gi|330508252|ref|YP_004384680.1|  73 KSYKTVGEIRDEYdYKVWQKKGQVLLNQNR-------YEEALQAFDQSIQMNPRSAENWNDkgvvqIAAYNF 137
                                       567788888888888888888887777777.......9*********************8755555666666 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.061
                                       CCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 252 Gewqealqkldwseekieeilqsysaateidpswykawht 291
                                       G  q+a ++       +e++l+++  a  + ps + aw++
  gi|330508252|ref|YP_004384680.1| 128 GVVQIAAYN-------FEDALKCFEVAIALEPSFATAWNN 160
                                       555555566.......99********************98 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0078         5      62     102 ..      94     134 ..      80     150 .. 0.82
   2 ?    5.1   0.0     0.034        22      57      82 ..     157     182 ..     143     186 .. 0.78
   3 ?   -0.7   0.0       2.1   1.3e+03     116     135 ..     200     219 ..     187     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0078
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHH CS
                           DUF3856  62 sealaklgrydealesadkalryfnrrGeleqdeGklWiaa 102
                                        + l++  ry+eal++ d++++   r  e  +d+G   iaa
  gi|330508252|ref|YP_004384680.1|  94 GQVLLNQNRYEEALQAFDQSIQMNPRSAENWNDKGVVQIAA 134
                                       556677789************99999999999999999987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  57 chaglsealaklgrydealesadkal 82 
                                       ++   ++ l  lgrydea+ + d+a+
  gi|330508252|ref|YP_004384680.1| 157 AWNNKAQILYALGRYDEAILTCDQAI 182
                                       45556677788888888888888886 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHHHH--S CS
                           DUF3856 116 kdealkafrmagemiaerkG 135
                                        +ea kaf +a+e+ +  +G
  gi|330508252|ref|YP_004384680.1| 200 GKEAQKAFAKAKELAQKNQG 219
                                       57899999999998887776 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0074       4.7     128     154 ..      93     119 ..      88     135 .. 0.84
   2 ?    7.0   0.7    0.0051       3.2      82     116 ..     157     191 ..     127     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0074
                          TPR_MalT 128 ladllyEwndLeeAeqhlqeGielleq 154
                                        +++l+ +n+ eeA q+ +++i++  +
  gi|330508252|ref|YP_004384680.1|  93 KGQVLLNQNRYEEALQAFDQSIQMNPR 119
                                       699*******************99755 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0051
                          TPR_MalT  82 allqqaeilvaqGrLheAletyeqalqlateqglq 116
                                       a    a+il a Gr +eA+ t+ qa+ql +++ ++
  gi|330508252|ref|YP_004384680.1| 157 AWNNKAQILYALGRYDEAILTCDQAIQLEPMSAEA 191
                                       33456899999999999999999999998877665 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      0.72   4.6e+02      13      31 ..      92     110 ..      88     118 .. 0.81
   2 ?    1.8   0.0      0.45   2.9e+02      18      35 ..     131     148 ..     116     153 .. 0.82
   3 ?    8.0   0.2    0.0051       3.3       9      33 ..     156     180 ..     148     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.72
                         NRBF2_MIT  13 rkadrllaaGkyeeaisch 31 
                                       +k + ll   +yeea+   
  gi|330508252|ref|YP_004384680.1|  92 KKGQVLLNQNRYEEALQAF 110
                                       67788999999***98765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.45
                         NRBF2_MIT  18 llaaGkyeeaischkkaa 35 
                                        +aa  +e+a+ c + a 
  gi|330508252|ref|YP_004384680.1| 131 QIAAYNFEDALKCFEVAI 148
                                       57999********98775 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0051
                         NRBF2_MIT   9 hqqsrkadrllaaGkyeeaischkk 33 
                                          + ka+ l a G+y+eai    +
  gi|330508252|ref|YP_004384680.1| 156 TAWNNKAQILYALGRYDEAILTCDQ 180
                                       566899*************954443 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00068      0.44     230     289 ..      83     142 ..      71     147 .. 0.90
   2 ?    4.3   0.2     0.026        17     253     291 ..     140     178 ..     133     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00068
                                       SS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHH CS
                             ChAPs 230 eekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienALl 289
                                       +e d+++ + + + ll+++++e Al++ ++++++ P   + W     v i+  ++e+AL 
  gi|330508252|ref|YP_004384680.1|  83 DEYDYKVWQKKGQVLLNQNRYEEALQAFDQSIQMNPRSAENWNDKGVVQIAAYNFEDALK 142
                                       4567888899999********************************************996 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                             ChAPs 253 AlevakravksaPsefktWalLvkvYikledienALltL 291
                                       Al++ + a+ + Ps  + W   +++  +l+ +++A+lt 
  gi|330508252|ref|YP_004384680.1| 140 ALKCFEVAIALEPSFATAWNNKAQILYALGRYDEAILTC 178
                                       899999*****************************9986 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 ?    4.8   0.0     0.033        21       1      15 [.     102     116 ..     102     122 .. 0.89
   2 ?    4.7   0.0     0.036        23       1      14 [.     170     183 ..     170     187 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.033
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rYeeaL+  ++ i++
  gi|330508252|ref|YP_004384680.1| 102 RYEEALQAFDQSIQM 116
                                       7***********986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.036
                                       -HHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAie 14 
                                       rY+ea+   ++Ai+
  gi|330508252|ref|YP_004384680.1| 170 RYDEAILTCDQAIQ 183
                                       7************8 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1      0.03        19      13      29 ..      99     113 ..      87     117 .. 0.88
   2 ?   -0.7   0.0       2.3   1.5e+03      16      34 ..     136     152 ..     136     153 .. 0.83
   3 ?    4.3   0.1     0.066        42      10      21 ..     164     175 ..     162     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.03
                                       HTT-HHHHHHH..HHHH CS
                             TPR_3  13 nkkkyqeArelfsYall 29 
                                       n+ +y+eA+++f+  ++
  gi|330508252|ref|YP_004384680.1|  99 NQNRYEEALQAFD--QS 113
                                       789********98..65 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.3
                                       -HHHHHHH..HHHHHHH-T CS
                             TPR_3  16 kyqeArelfsYallaildk 34 
                                       ++++A+    ++++ +l++
  gi|330508252|ref|YP_004384680.1| 136 NFEDALKC--FEVAIALEP 152
                                       5899****..77**99975 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.066
                                       HHHHTT-HHHHH CS
                             TPR_3  10 efynkkkyqeAr 21 
                                        +y  ++y+eA+
  gi|330508252|ref|YP_004384680.1| 164 ILYALGRYDEAI 175
                                       589********8 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.012       7.7      12      32 ..      95     115 ..      91     128 .. 0.81
   2 ?    0.9   0.0      0.76   4.9e+02      17      31 ..     134     148 ..     119     153 .. 0.76
   3 ?    5.5   0.4     0.027        17      22      64 ..     166     214 ..     153     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                               MIT  12 veeDnagnyeeAlelYkeale 32 
                                         + n++ yeeAl+++ ++++
  gi|330508252|ref|YP_004384680.1|  95 QVLLNQNRYEEALQAFDQSIQ 115
                                       556688899999999998886 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.76
                               MIT  17 agnyeeAlelYkeal 31 
                                       a n+e+Al++++ a+
  gi|330508252|ref|YP_004384680.1| 134 AYNFEDALKCFEVAI 148
                                       567888888877776 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.027
                               MIT  22 eAlelYkealelLlqalk.e..kne...errellrekieeYleRaeeLk 64 
                                        Al  Y ea+  + qa++ e  ++e   ++   l +++++  ++a+eL 
  gi|330508252|ref|YP_004384680.1| 166 YALGRYDEAILTCDQAIQlEpmSAEawyTKSLILGKEAQKAFAKAKELA 214
                                       59999*************9886666898888888888999999999886 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.88   5.6e+02      16      36 ..      95     115 ..      91     117 .. 0.87
   2 ?    9.1   0.1    0.0021       1.4      11      37 ..     158     184 ..     154     185 .. 0.89
   3 ?   -1.7   0.1       4.7     3e+03       7      19 ..     202     214 ..     190     220 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.88
                                       HHHHHTT-HHHHHHHHHHHHH CS
                              HEPN  16 ellleegdydlacfhaqqaae 36 
                                       ++ll++++y+ a+ +  q+++
  gi|330508252|ref|YP_004384680.1|  95 QVLLNQNRYEEALQAFDQSIQ 115
                                       7899***********999987 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              HEPN  11 dleaAellleegdydlacfhaqqaaek 37 
                                         ++A+ l+  g+yd a+  + qa+++
  gi|330508252|ref|YP_004384680.1| 158 WNNKAQILYALGRYDEAILTCDQAIQL 184
                                       5689********************996 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.7
                                       HHHHHHHHHHHHH CS
                              HEPN   7 rAeedleaAelll 19 
                                       +A++ +++A++l 
  gi|330508252|ref|YP_004384680.1| 202 EAQKAFAKAKELA 214
                                       4555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1514.66
//
Query:       gi|330508253|ref|YP_004384681.1|  [L=247]
Description: hypothetical protein MCON_2404 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   0.0        0.8   10.0   0.0    2.6  3  DUF4352   Domain of unknown function (DUF4352)


Domain annotation for each model (and alignments):
>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0     0.076   1.4e+03      99     114 ..      92     106 ..      46     114 .. 0.69
   2 ?    1.2   0.0     0.023   4.2e+02      19      43 ..     110     133 ..     104     134 .. 0.76
   3 ?   10.0   0.0   4.5e-05       0.8      34      75 ..     143     184 ..     137     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.076
                                       EEEEESTT-CGEEEEE CS
                           DUF4352  99 lvFdvpkgkkkleLey 114
                                       ++F+vp+++  ++L+ 
  gi|330508253|ref|YP_004384681.1|  92 VYFVVPRDSL-FKLIT 106
                                       7899999987.77776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.023
                                       EEEEEEETTS-CEETT-.SEEEEEE CS
                           DUF4352  19 veytksvgkneylqpdaggeflivd 43 
                                       v + ++   n + +p+ag+efl+++
  gi|330508253|ref|YP_004384681.1| 110 V-GGRPININWWATPKAGNEFLLIR 133
                                       5.556666688999********985 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 4.5e-05
                                       T-.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEE CS
                           DUF4352  34 daggeflivdvtvkNkgkealtvnssqfkLkdgdgkeydadl 75 
                                       +++++  +v+v+ +N+g +++ +++ +f L d+ g  y+a++
  gi|330508253|ref|YP_004384681.1| 143 NPDEQGIVVQVRGQNNGTQDVVFSPENFVLLDQWGWPYSATI 184
                                       45678899***********************99888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1778.52
//
Query:       gi|330508254|ref|YP_004384682.1|  [L=243]
Description: hypothetical protein MCON_2406 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.055   14.2   3.2      0.061   14.1   3.2    1.1  1  PRCC        Mitotic checkpoint regulator, MAD2B-interacting
          1    7.6  13.2        1.2    7.4  13.2    1.0  1  Atrophin-1  Atrophin-1 family


Domain annotation for each model (and alignments):
>> PRCC  Mitotic checkpoint regulator, MAD2B-interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.2   6.9e-06     0.061       1      96 [.      20     134 ..      20     186 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.9e-06
                              PRCC   1 dfFSl.............esasassssaaaksaptisyeplvssap..eaeeseeedppetepepasqpeaenadle 62 
                                       ++F+l              ++ a++ ++ a++a+t +++p+ +++    +++ ++++  ++++++++q++  +++++
  gi|330508254|ref|YP_004384682.1|  20 SLFGLaigqntydaypgaPTSVATQIPTPAPTAETQTTIPSQVQTTvpASNQMQPTSIVAPSAAQQQQTAVMTTPVV 96 
                                       68888888888888887733334444444444444444444433322246666666666666666666666666666 PP

                              PRCC  63 akkaakssea...mvpepteqdp.vkensknypgyyll 96 
                                       ++++a ++     + p++t+q++  ++++++ p    +
  gi|330508254|ref|YP_004384682.1|  97 SSSSATATAVysaQAPPATQQNVlLTYDVQTAPPSAVY 134
                                       66555554448889999999999866666666554444 PP

>> Atrophin-1  Atrophin-1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  13.2   0.00013       1.2     183     262 ..      37     119 ..      24     172 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00013
                        Atrophin-1 183 sepsaptavasaaptp.satslpsqvsppvts.pplqslssaspltliqstatlhpqrlpsphsp.lqeltqpapps 256
                                       +++s +t++ ++apt+ + t++psqv  +v+  + +q+ s ++p++  q+ +++ ++ ++s  s+  +++ + + p 
  gi|330508254|ref|YP_004384682.1|  37 APTSVATQIPTPAPTAeTQTTIPSQVQTTVPAsNQMQPTSIVAPSAAQQQQTAVMTTPVVSSSSAtATAVYSAQAPP 113
                                       34445577777777775556789988775543133478888888666655555554444444444033333333332 PP

                        Atrophin-1 257 qvsaqs 262
                                       ++ ++ 
  gi|330508254|ref|YP_004384682.1| 114 ATQQNV 119
                                       222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1651.86
//
Query:       gi|330508255|ref|YP_004384683.1|  [L=245]
Description: hypothetical protein MCON_2407 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1741.60
//
Query:       gi|330508256|ref|YP_004384684.1|  [L=800]
Description: hypothetical protein MCON_2409 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-06   27.3   0.0    1.9e-05   25.0   0.0    2.1  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 !   25.0   0.0   1.1e-09   1.9e-05      13     102 ..     121     214 ..     111     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.1e-09
                    Transglut_core  13 dplekakaiyewvr......knveysaprrtpgsrd....aeavletgk.......GncedfaslfvallRalGipa 72 
                                       +  ++++ iy++++      k  +y+   ++p++ d    a+++l++g        G+c dfa l++al  ++G  +
  gi|330508256|ref|YP_004384684.1| 121 KTIDQIVSIYDYLKngdeskKGWGYV---SDPRGIDdfmfANQTLRNGErancvggGDCDDFAILMSALVESIGGTT 194
                                       44589999999999776666666666...55555556779******77778999999******************** PP

                    Transglut_core  73 RvvtgylsgeeekeqsvasedaHawvevyl 102
                                       R++   +           s + Ha++evyl
  gi|330508256|ref|YP_004384684.1| 195 RIILARNN----------STGGHAYTEVYL 214
                                       ***88765..........6799*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (800 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 5269.06
//
Query:       gi|330508257|ref|YP_004384685.1|  [L=713]
Description: hypothetical protein MCON_2410 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-05   24.9   2.9         10    5.9   0.0    6.2  6  DUF4166         Domain of unknown function (DUF4166)
    3.6e-05   24.2   0.0    7.1e-05   23.2   0.0    1.5  1  Transglut_core  Transglutaminase-like superfamily
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.21   11.1   0.0    1.4  1  DUF553          Transglutaminase-like domain


Domain annotation for each model (and alignments):
>> DUF4166  Domain of unknown function (DUF4166)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0017        10      62     105 ..     393     437 ..     388     440 .. 0.69
   2 ?    2.3   0.0     0.021   1.2e+02      64     105 ..     447     489 ..     444     497 .. 0.75
   3 !    4.2   0.0    0.0055        33      64     104 ..     499     540 ..     495     548 .. 0.76
   4 ?    2.9   0.0     0.014        81      64      84 ..     551     568 ..     545     596 .. 0.72
   5 ?    2.0   0.0     0.026   1.5e+02      64      83 ..     603     620 ..     599     642 .. 0.81
   6 ?    0.3   0.0     0.086   5.1e+02      64      81 ..     655     670 ..     651     685 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0017
                           DUF4166  62 aerdesgretltwtRtfefpgktrtfdstmvlaggkg....lvEylGa 105
                                       +++d++g+    w+Rtf+++++ + ++ +++ +gg       +E++Ga
  gi|330508257|ref|YP_004384685.1| 393 TKTDDQGNR--LWERTFGGEEFDEGYSVQQTSDGG-YiitgFTESFGA 437
                                       456899999..9********665555555555555.335556666665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.021
                           DUF4166  64 rdesgretltwtRtfefpgktrtfdstmvlaggkg....lvEylGa 105
                                       +d++g++   w+R f+++ ++ +  s+++ ++g       +E++Ga
  gi|330508257|ref|YP_004384685.1| 447 TDDHGNK--LWERIFGGE-EPDEGYSVQQTSDGGYiitgYTESFGA 489
                                       5899999..*********.777777777777775555555666666 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.0055
                           DUF4166  64 rdesgretltwtRtfefpgktrtfdstmvlaggkg...lvEylG 104
                                       +d+ g++   w+Rtf++++  + ++ +++l+gg      +E++G
  gi|330508257|ref|YP_004384685.1| 499 TDDYGNK--LWERTFGGEEPDEGMSVQQTLDGGYIvtaYTESFG 540
                                       5889999..*********88888888888887743444556666 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.014
                           DUF4166  64 rdesgretltwtRtfefpgkt 84 
                                       +d++g++   w+Rtf+++ ++
  gi|330508257|ref|YP_004384685.1| 551 TDDQGNK--LWERTFGGE-EP 568
                                       5899999..*******99.44 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.026
                           DUF4166  64 rdesgretltwtRtfefpgk 83 
                                       ++++g++   w+Rtf++++ 
  gi|330508257|ref|YP_004384685.1| 603 TNDEGSK--LWERTFGGAKG 620
                                       4788999..*******9844 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 0.086
                           DUF4166  64 rdesgretltwtRtfefp 81 
                                       +d+sg++   w+Rtf+++
  gi|330508257|ref|YP_004384685.1| 655 TDASGNK--LWERTFGGA 670
                                       5788999..9*****987 PP

>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.2e-08   7.1e-05      16     103 ..     125     216 ..     114     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.2e-08
                    Transglut_core  16 ekakaiyewvr......knveysaprrtpgsrd....aeavle.......tgkGncedfaslfvallRalGipaRvv 75 
                                       ++++ iye+++            ++ ++p++ d    a+++++       +g+G+c dfa l++al  ++G  +R++
  gi|330508257|ref|YP_004384685.1| 125 DQIASIYEYLKngddskRGW---SYVPDPRGIDyfmyANETIKigkevgcAGAGDCDDFAILMAALVESVGGTTRII 198
                                       67777777777444332222...333555555566667777774444444566************************ PP

                    Transglut_core  76 tgylsgeeekeqsvasedaHawvevyle 103
                                          +           + + Ha++evyl 
  gi|330508257|ref|YP_004384685.1| 199 LAHNN----------TTGGHAYAEVYLG 216
                                       77654..........6899*******93 PP

>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.4e-05      0.21      73     151 ..     172     245 ..     149     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.4e-05
                            DUF553  73 tkkgiCrDYaiLTaalLlnlniskvylvsvtfenskvgHaavavkidgtyfvlDqklpiikideylkkllkkvkiit 149
                                         +g C D+aiL aal    + +   ++  +  n++ gHa + v   +   +  q++ + +i ++lk+  +  ki+t
  gi|330508257|ref|YP_004384685.1| 172 AGAGDCDDFAILMAALVESVGGTTRIILAHN--NTTGGHAYAEVYLGQ---IGEQNSLVEDIIKWLKSNSDTDKIYT 243
                                       56788**********8888888886666555..88999***9998765...67888888888888888888888888 PP

                            DUF553 150 ev 151
                                       ++
  gi|330508257|ref|YP_004384685.1| 244 HI 245
                                       77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.24s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 5339.53
//
Query:       gi|330508258|ref|YP_004384686.1|  [L=812]
Description: hypothetical protein MCON_2411 [Methanosaeta concilii GP6]
Scores for complete 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   30.6   0.1         19    5.7   0.0    6.5  7  Colicin_E5      Colicin E5 ribonuclease domain
    1.3e-06   28.8   0.0    3.1e-05   24.4   0.0    2.3  2  Transglut_core  Transglutaminase-like superfamily
    0.00054   20.5   0.4        0.3   11.5   0.0    3.8  4  DERM            Dermatopontin
  ------ inclusion threshold ------
        1.2    8.9  11.3         63    3.4   0.0    6.0  7  DUF2064         Uncharacterized protein conserved in bacteria


Domain annotation for each model (and alignments):
>> Colicin_E5  Colicin E5 ribonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.2   1.4e+04      40      66 ..     437     463 ..     431     465 .. 0.79
   2 ?    2.6   0.0     0.037   1.6e+02      32      70 ..     481     519 ..     478     522 .. 0.90
   3 ?   -0.1   0.0      0.27   1.2e+03      32      67 ..     533     568 ..     532     571 .. 0.86
   4 ?    4.0   0.0     0.014        61      32      67 ..     596     631 ..     594     636 .. 0.91
   5 ?    3.9   0.0     0.015        68      32      67 ..     648     683 ..     646     688 .. 0.90
   6 !    5.7   0.0    0.0042        19      32      70 ..     701     739 ..     699     742 .. 0.92
   7 ?    4.0   0.0     0.014        63      32      67 ..     753     788 ..     751     793 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.2
                        Colicin_E5  40 ranktsDglrrndsAtvYgekdgkYvv 66 
                                        + kt  g + +   +v    d++Y++
  gi|330508258|ref|YP_004384686.1| 437 TWSKTFGGAENDWGMSVQQTLDSGYII 463
                                       567788888888888999999999998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.037
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvndr 70 
                                       kt+ + +k +++t  g + ++  +v    dg+Y+++ + 
  gi|330508258|ref|YP_004384686.1| 481 KTNDHGNKLWDRTFGGAECDEGDSVQQTLDGGYIIMGNT 519
                                       67788899999************************9775 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.27
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt  + +k +++t  g   +   +v   +dg+Y++ 
  gi|330508258|ref|YP_004384686.1| 533 KTDDHGNKLWDRTFGGADWDWGSSVQQTSDGGYIIT 568
                                       5667778889999999999999************96 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.014
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt  + +k +++t  g ++++  +v    dg+Y+++
  gi|330508258|ref|YP_004384686.1| 596 KTDDQGNKLWDRTFGGAGHDEGNSVQQTLDGGYIIM 631
                                       6777889999************************97 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.015
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt  + +k +++t  g   +d  +v    dg+Y++ 
  gi|330508258|ref|YP_004384686.1| 648 KTDDQGNKLWDRTFGGAYGDDGSSVQQTFDGGYIIT 683
                                       67778899999***********************96 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.0042
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvndr 70 
                                       kt ++ +k +++t  g   +d  +v    dg+Y+++ + 
  gi|330508258|ref|YP_004384686.1| 701 KTDAEGNKLWDRTFGGAYGDDGSSVQQTLDGGYIIMGNT 739
                                       7889999****************************9775 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.014
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt  + ++ +++t  g ++++  +v    dg+Y+++
  gi|330508258|ref|YP_004384686.1| 753 KTDDQGNRLWDRTFGGAGHDEGNSVQQTLDGGYIIM 788
                                       677788999*************************97 PP

>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0     7e-09   3.1e-05      14     102 ..     122     214 ..     113     221 .. 0.81
   2 ?    1.9   0.0     0.068   3.1e+02      11      42 ..     219     249 ..     215     258 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 7e-09
                    Transglut_core  14 plekakaiyewvr......knveysaprrtpgsrd....aeavletgk.......GncedfaslfvallRalGipaR 73 
                                         ++++ iy++++      k  +y+   ++p++ d    a+++l++g        G+c dfa l++al  ++G  +R
  gi|330508258|ref|YP_004384686.1| 122 TIDQIVSIYDYLKngdeskKGWGYV---SDPRGIDdfmfANQTLRNGErancvggGDCDDFAILMSALVESIGGTTR 195
                                       4589999999999776666666666...55555556779******77778999999********************* PP

                    Transglut_core  74 vvtgylsgeeekeqsvasedaHawvevyl 102
                                       ++   +           s + Ha++evyl
  gi|330508258|ref|YP_004384686.1| 196 IILARNN----------STGGHAYAEVYL 214
                                       **88765..........6799*******9 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.068
                    Transglut_core  11 akdplekakaiyewvrknveysaprrtpgsrd 42 
                                        +d+  +++ai +w+r++ + + + +t+ + d
  gi|330508258|ref|YP_004384686.1| 219 NSDSGNQVEAIIDWLREKLDAD-KIYTHIDTD 249
                                       5677799************999.555555554 PP

>> DERM  Dermatopontin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.58   2.6e+03      19      61 ..     323     366 ..     315     375 .. 0.84
   2 !   11.5   0.0   6.8e-05       0.3       1     135 [.     447     576 ..     430     597 .. 0.72
   3 ?    3.7   0.0     0.018        80      30     142 ..     589     698 ..     585     714 .. 0.77
   4 ?    2.5   0.0     0.042   1.9e+02      50     135 ..     660     744 ..     644     800 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.58
                              DERM  19 gvssefsnskeDRr.wsfeCsdvgavnsiterswseyvnsydqe 61 
                                       ++++e  + +eD++ ++f  +d  a++ i+e++w+   ++yd++
  gi|330508258|ref|YP_004384686.1| 323 TWTAEARDPEEDQMlYRFYLNDEPATKWINEDMWTWTAEDYDAG 366
                                       6888999999999889**99999989999999999999999864 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.8e-05
                              DERM   1 NnfdeplsftCpsgqgltgvssefsnskeDRrwsfeCsdvgavnsiterswseyvnsydqeftftcpnnqyltgves 77 
                                       N+++ +++ t +sg ++tg++s f   ++   w ++ +d g  n+  +r++++ + +  +++++t + ++++ g + 
  gi|330508258|ref|YP_004384686.1| 447 NDWGMSVQQTLDSGYIITGWTSSFGAGYN-GLWLIKTNDHG--NKLWDRTFGGAECDEGDSVQQTLDGGYIIMGNTE 520
                                       56677777777777777777777777775.67777777765..6777777777777777777777777777777777 PP

                              DERM  78 ehsnskeDRrwkfqCartngatlsnCsttgylnsfdetlsftapskrvitGvqsdfsn 135
                                       ++ ++++D  w +++ +   ++l + ++ g   ++ ++++ t++ +++itG + +f++
  gi|330508258|ref|YP_004384686.1| 521 SFGAGNND-LWLIKTDDHG-NKLWDRTFGGADWDWGSSVQQTSDGGYIITGSTFSFDE 576
                                       77777777.6777777654.56666677777777777888888888888886666665 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.018
                              DERM  30 DRr.wsfeCsdvgavnsiterswseyvnsydqeftftcpnnqyltgvesehsnskeDRrwkfqCartngatlsnCst 105
                                       DR  w ++ +d g  n+  +r++++  ++  +++++t + ++++ g + ++ ++++D  w +++ +   ++l + ++
  gi|330508258|ref|YP_004384686.1| 589 DRDlWLIKTDDQG--NKLWDRTFGGAGHDEGNSVQQTLDGGYIIMGYTESFGAGSSD-LWLIKTDDQG-NKLWDRTF 661
                                       6654666666644..777777788888888888889999999999998888888888.7888888865.56777777 PP

                              DERM 106 tgylnsfdetlsftapskrvitGvqsdfsnskeDRrw 142
                                        g   +  ++++ t + +++itG +s+f+++     w
  gi|330508258|ref|YP_004384686.1| 662 GGAYGDDGSSVQQTFDGGYIITGGTSSFDEAGDGDLW 698
                                       7777888888999999999999999999986654455 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.042
                              DERM  50 swseyvnsydqeftftcpnnqyltgvesehsnskeDRrwkfqCartngatlsnCsttgylnsfdetlsftapskrvi 126
                                       ++++ + +  +++++t + ++++tg +s+++++     w +++     ++l + ++ g   +  ++++ t + +++i
  gi|330508258|ref|YP_004384686.1| 660 TFGGAYGDDGSSVQQTFDGGYIITGGTSSFDEAGDGDLWLIKTDAEG-NKLWDRTFGGAYGDDGSSVQQTLDGGYII 735
                                       55555555556666666666666666666655544445555554432.34444445555555555555555555555 PP

                              DERM 127 tGvqsdfsn 135
                                        G + +f +
  gi|330508258|ref|YP_004384686.1| 736 MGNTESFGA 744
                                       555555554 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 ?   -3.2   0.0       1.6   7.3e+03      26      52 ..     408     434 ..     399     440 .. 0.76
   2 ?    1.3   0.0     0.062   2.8e+02      96     108 ..     508     520 ..     504     529 .. 0.83
   3 ?   -0.4   0.0      0.21   9.4e+02      96     107 ..     560     571 ..     557     579 .. 0.83
   4 ?    3.2   0.1     0.016        72      96     108 ..     623     635 ..     614     644 .. 0.84
   5 ?   -0.7   0.1      0.27   1.2e+03      96     108 ..     675     687 ..     672     694 .. 0.80
   6 ?    1.3   0.0     0.062   2.8e+02      96     108 ..     728     740 ..     724     749 .. 0.83
   7 ?    3.4   0.0     0.014        63      96     108 ..     780     792 ..     771     801 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.6
                                       HHHHHH-TTSEEEE--SSSHHHHHHHH CS
                           DUF2064  26 aeqlalakglevlpQqggdlgeRlara 52 
                                       +++ a++++ +v  + ++d+++R+   
  gi|330508258|ref|YP_004384686.1| 408 EDDRAVPEESSVAMDVTADVDDRIVSE 434
                                       444588899999999999999998665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.062
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       + DGGY+++G ++
  gi|330508258|ref|YP_004384686.1| 508 TLDGGYIIMGNTE 520
                                       57********885 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.21
                                       BTTSSEEEEEEE CS
                           DUF2064  96 aeDGGYyllGlk 107
                                       ++DGGY++ G +
  gi|330508258|ref|YP_004384686.1| 560 TSDGGYIITGST 571
                                       68******9987 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.016
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       + DGGY+++G+++
  gi|330508258|ref|YP_004384686.1| 623 TLDGGYIIMGYTE 635
                                       57*********96 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 0.27
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       + DGGY++ G ++
  gi|330508258|ref|YP_004384686.1| 675 TFDGGYIITGGTS 687
                                       57******99885 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.062
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       + DGGY+++G ++
  gi|330508258|ref|YP_004384686.1| 728 TLDGGYIIMGNTE 740
                                       57********885 PP

  == domain 7  score: 3.4 bits;  conditional E-value: 0.014
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       + DGGY+++G+++
  gi|330508258|ref|YP_004384686.1| 780 TLDGGYIIMGYTE 792
                                       57*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (812 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 5461.86
//
Query:       gi|330508259|ref|YP_004384687.1|  [L=802]
Description: hypothetical protein MCON_2412 [Methanosaeta concilii GP6]
Scores for complete sequence (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   28.8   0.0    3.6e-05   24.2   0.0    2.3  2  Transglut_core  Transglutaminase-like superfamily
    4.1e-05   23.8   1.9         75    3.7   0.0    6.5  7  Colicin_E5      Colicin E5 ribonuclease domain
    0.00023   21.7   0.0       0.41   11.1   0.0    3.7  4  DERM            Dermatopontin


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   6.1e-09   3.6e-05      13     102 ..     121     214 ..     112     219 .. 0.81
   2 ?    2.1   0.0     0.044   2.6e+02      11      42 ..     219     249 ..     215     258 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 6.1e-09
                    Transglut_core  13 dplekakaiyewvr......knveysaprrtpgsrd....aeavletgk.......GncedfaslfvallRalGipa 72 
                                       +  ++++ iy++++      k  +y+   ++p++ d    a+++l++g        G+c dfa l++al  ++G  +
  gi|330508259|ref|YP_004384687.1| 121 KTIDQIVSIYDYLKngdeskKGWGYV---SDPRGIDdfmfANQTLRNGErancvggGDCDDFAILMSALVESIGGTT 194
                                       44589999999999776666666666...55555556779******77778999999******************** PP

                    Transglut_core  73 RvvtgylsgeeekeqsvasedaHawvevyl 102
                                       R++   +           s + Ha++evyl
  gi|330508259|ref|YP_004384687.1| 195 RIILARNN----------STGGHAYTEVYL 214
                                       ***88765..........6799*******9 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.044
                    Transglut_core  11 akdplekakaiyewvrknveysaprrtpgsrd 42 
                                        +d+ ++++ai +w++++ + + + +t+ + d
  gi|330508259|ref|YP_004384687.1| 219 NSDSGDQVEAIIDWLKEKLDAD-KIYTHIDTD 249
                                       56778*************9999.555555554 PP

>> Colicin_E5  Colicin E5 ribonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.017     1e+02      36      67 ..     435     466 ..     417     472 .. 0.84
   2 ?   -2.4   0.0      0.99   5.9e+03      38      68 ..     489     519 ..     483     523 .. 0.76
   3 ?    2.8   0.0     0.024   1.4e+02      32      67 ..     535     570 ..     533     574 .. 0.91
   4 ?    2.5   0.0      0.03   1.8e+02      32      67 ..     587     622 ..     585     627 .. 0.90
   5 ?   -0.2   0.0      0.21   1.2e+03      34      68 ..     641     675 ..     638     679 .. 0.85
   6 ?    3.7   0.0     0.013        75      32      68 ..     691     727 ..     689     731 .. 0.89
   7 ?    2.3   0.0     0.034     2e+02      32      68 ..     743     779 ..     741     783 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.017
                        Colicin_E5  36 sddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       s+ k + kt  g + +d  +v    dg+Y++ 
  gi|330508259|ref|YP_004384687.1| 435 SEAKTWSKTYGGEEFDDGTSVQQTLDGGYIIT 466
                                       67789999**********************96 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.99
                        Colicin_E5  38 dkranktsDglrrndsAtvYgekdgkYvvvn 68 
                                       +k +++t  g + +   +v    dg+Y++  
  gi|330508259|ref|YP_004384687.1| 489 NKLWERTFGGEEFDVGESVHQTLDGGYIITG 519
                                       666777777777788889999999***9975 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.024
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt  + +k +++t  g + ++  +v    dg+Y++ 
  gi|330508259|ref|YP_004384687.1| 535 KTDDQGNKLWERTFGGAHYDEVSSVQQTFDGGYIIT 570
                                       6777889999************************96 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.03
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt  + +k +++t  g + ++  +v    dg+Y++ 
  gi|330508259|ref|YP_004384687.1| 587 KTDDQGNKLWERTFGGAHYDEGESVHQTLDGGYIIT 622
                                       6777889999************************97 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.21
                        Colicin_E5  34 kssddkranktsDglrrndsAtvYgekdgkYvvvn 68 
                                        ++ +  ++kt  gl+ +   +v    dg+Y++  
  gi|330508259|ref|YP_004384687.1| 641 DAEGNDLWDKTFGGLESDWGYSVQQTLDGGYIITG 675
                                       5666778999999*******************976 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.013
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvn 68 
                                       kt  + +k +++t  g + ++  +v   +dg+Y++  
  gi|330508259|ref|YP_004384687.1| 691 KTDDQGNKIWGRTFGGAEDDEGKSVQQTHDGGYIITG 727
                                       677888999*************************976 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.034
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvn 68 
                                       kt ++  k +++t  g + ++  +v   +dg+Y++  
  gi|330508259|ref|YP_004384687.1| 743 KTDEQGSKLWDRTFGGAEDDEGKSVQQTHDGGYIITG 779
                                       566677788999999*******************976 PP

>> DERM  Dermatopontin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.42   2.5e+03      19      60 ..     323     365 ..     313     373 .. 0.83
   2 ?    3.9   0.0     0.012        70      44     139 ..     489     582 ..     479     588 .. 0.81
   3 !    4.7   0.0    0.0067        40      49     139 ..     598     686 ..     583     693 .. 0.77
   4 !   11.1   0.0   6.9e-05      0.41       9     139 ..     665     790 ..     658     796 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.42
                              DERM  19 gvssefsnskeDRr.wsfeCsdvgavnsiterswseyvnsydq 60 
                                       ++++e  + +eD++ ++f  +d  a++ i+e++w+   ++yd+
  gi|330508259|ref|YP_004384687.1| 323 TWTAEARDPEEDQMlYRFYLNDEPATKWINEDMWTWTAEDYDS 365
                                       6889999999999889**9999998999999999999999986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.012
                              DERM  44 nsiterswseyvnsydqeftftcpnnqyltgvesehsnskeDRrwkfqCartngatlsnCsttgylnsfdetlsfta 120
                                       n+  er++++++ ++ +++++t + ++++tg + ++ ++++D  w +++ +   ++l + ++ g   +  ++++ t 
  gi|330508259|ref|YP_004384687.1| 489 NKLWERTFGGEEFDVGESVHQTLDGGYIITGSTDSFGEGSRD-LWLIKTDDQG-NKLWERTFGGAHYDEVSSVQQTF 563
                                       556677888888899999999999999999999999999998.8999999866.46666666666666677788899 PP

                              DERM 121 pskrvitGvqsdfsnskeD 139
                                       + +++itG +s+f + + D
  gi|330508259|ref|YP_004384687.1| 564 DGGYIITGGTSSFGAGDMD 582
                                       99*********99988877 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0067
                              DERM  49 rswseyvnsydqeftftcpnnqyltgvesehsnskeDRrwkfqCartngatlsnCsttgylnsfdetlsftapskrv 125
                                       r++++   +  +++++t + ++++tg + ++ ++++D  w ++    +g+ l + ++ g ++++  +++ t + +++
  gi|330508259|ref|YP_004384687.1| 598 RTFGGAHYDEGESVHQTLDGGYIITGSTESFGEGSND-LWLIKADA-EGNDLWDKTFGGLESDWGYSVQQTLDGGYI 672
                                       5555555555577788888888888888888888887.78887655.4467888889999999999*********** PP

                              DERM 126 itGvqsdfsnskeD 139
                                       itG +s+f + ++D
  gi|330508259|ref|YP_004384687.1| 673 ITGETSSFGEGERD 686
                                       *******9998888 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 6.9e-05
                              DERM   9 ftCpsgqgltgvssefsnskeDRrwsfeCsdvgavnsiterswseyvnsydqeftftcpnnqyltgvesehsnskeD 85 
                                        t + g ++tg +s f + + D  w ++ +d g  n+i  r++++ +++  +++++t + ++++tg +s++ ++++D
  gi|330508259|ref|YP_004384687.1| 665 QTLDGGYIITGETSSFGEGERD-LWLIKTDDQG--NKIWGRTFGGAEDDEGKSVQQTHDGGYIITGETSSFGEGERD 738
                                       5556677888889999998886.7999999875..9999999********************************999 PP

                              DERM  86 RrwkfqCartngatlsnCsttgylnsfdetlsftapskrvitGvqsdfsnskeD 139
                                         w +++ +    +l + ++ g + +  ++++ t + +++itG +s+f + + D
  gi|330508259|ref|YP_004384687.1| 739 -LWLIKTDEQG-SKLWDRTFGGAEDDEGKSVQQTHDGGYIITGETSSFGEGEGD 790
                                       .8999998865.899999999*************************99887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (802 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 5571.39
//
Query:       gi|330508260|ref|YP_004384688.1|  [L=714]
Description: hypothetical protein MCON_2413 [Methanosaeta concilii GP6]
Scores for complete 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    1.6e-05   25.3   0.0    1.8  2  Transglut_core  Transglutaminase-like superfamily
     0.0074   16.8   0.3        7.9    6.9   0.0    3.2  5  DERM            Dermatopontin


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 !   25.3   0.0   1.8e-09   1.6e-05      13     102 ..     121     214 ..     111     234 .. 0.80
   2 ?   -1.6   0.0       0.4   3.6e+03      11      41 ..     219     248 ..     215     256 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.8e-09
                    Transglut_core  13 dplekakaiyewvr......knveysaprrtpgsrd....aeavletgk.......GncedfaslfvallRalGipa 72 
                                       +  ++++ iy++++      k  +y+   ++p++ d    a+++l++g        G+c dfa l++al  ++G  +
  gi|330508260|ref|YP_004384688.1| 121 KTIDQIVSIYDYLKngdeskKGWGYV---SDPRGIDdfmfANQTLRNGErancvggGDCDDFAILMSALVESIGGTT 194
                                       44589999999999776666666666...55555556779******77778999999******************** PP

                    Transglut_core  73 RvvtgylsgeeekeqsvasedaHawvevyl 102
                                       R++   +           s + Ha++evyl
  gi|330508260|ref|YP_004384688.1| 195 RIILARNN----------STGGHAYAEVYL 214
                                       ***88765..........6799*******9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.4
                    Transglut_core  11 akdplekakaiyewvrknveysaprrtpgsr 41 
                                        +d+  +++ai  w++++ + + + +t+ + 
  gi|330508260|ref|YP_004384688.1| 219 NSDSGGQVEAIVGWLKEKLDAD-KIYTHIDT 248
                                       566678999*******999999.55555544 PP

>> DERM  Dermatopontin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.01        91      45     133 ..     351     436 ..     332     443 .. 0.65
   2 !    6.9   0.0   0.00089       7.9       1     139 [.     361     494 ..     361     500 .. 0.86
   3 !    6.9   0.0   0.00092       8.2      44     139 ..     453     546 ..     414     562 .. 0.81
   4 !    4.8   0.0    0.0039        35      44     137 ..     505     596 ..     495     616 .. 0.78
   5 ?   -0.4   0.0      0.16   1.5e+03      48     128 ..     613     691 ..     598     699 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.01
                              DERM  45 siterswseyvnsydqeftftcpnnqyltgvesehsnskeDRrwkfqCartngatlsnCsttgylnsfdetlsftap 121
                                       s++++ +  ++n++  ++++t + ++++tg + ++ ++k D  w +++ +   + l + ++ g   ++  +++ t +
  gi|330508260|ref|YP_004384688.1| 351 SWSKT-FCREENNIGWSVQQTLDGGYIITGYTGSFRAGKYD-LWLIKTDDQG-NGLWERTFGGANYHYSYSVQQTLD 424
                                       33332.23347888888888888888888888888888888.7888887755.344444556666666667777777 PP

                              DERM 122 skrvitGvqsdf 133
                                        +++itG + +f
  gi|330508260|ref|YP_004384688.1| 425 GGYIITGSTYSF 436
                                       788888766555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00089
                              DERM   1 NnfdeplsftCpsgqgltgvssefsnskeDRrwsfeCsdvgavnsiterswseyvnsydqeftftcpnnqyltgves 77 
                                       Nn++ +++ t + g ++tg ++ f   k D  w ++ +d g  n   er++++   +y  ++++t + ++++tg + 
  gi|330508260|ref|YP_004384688.1| 361 NNIGWSVQQTLDGGYIITGYTGSFRAGKYD-LWLIKTDDQG--NGLWERTFGGANYHYSYSVQQTLDGGYIITGSTY 434
                                       666667777778889999999999999997.8999999976..88888999999999*****************999 PP

                              DERM  78 ehsnskeDRrwkfqCartngatlsnCsttgylnsfdetlsftapskrvitGvqsdfsnskeD 139
                                       ++ ++++D  w +++ +   ++l + ++ g + ++  +++ t + +++itG + +f + ++D
  gi|330508260|ref|YP_004384688.1| 435 SFGAGSSD-LWLIKTDDQG-NRLWERTFGGAEYDWGMSVQQTLDGGYIITGSTYSFGAGSRD 494
                                       99999999.8****99866.6788888999999******************88888777776 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.00092
                              DERM  44 nsiterswseyvnsydqeftftcpnnqyltgvesehsnskeDRrwkfqCartngatlsnCsttgylnsfdetlsfta 120
                                       n+  er++++ + ++  ++++t + ++++tg + ++ ++++D  w +++ +   ++l + ++ g + ++ ++++ t 
  gi|330508260|ref|YP_004384688.1| 453 NRLWERTFGGAEYDWGMSVQQTLDGGYIITGSTYSFGAGSRD-LWLIKTDDQG-NRLWDRTFGGEEHDWGTSVQQTL 527
                                       667778888999999999999999999999966666666666.8999999866.68888889999************ PP

                              DERM 121 pskrvitGvqsdfsnskeD 139
                                       + +++itG + +f + ++D
  gi|330508260|ref|YP_004384688.1| 528 DGGYIITGSTYSFGAGSRD 546
                                       ********88888776665 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.0039
                              DERM  44 nsiterswseyvnsydqeftftcpnnqyltgvesehsnskeDRrwkfqCartngatlsnCsttgylnsfdetlsfta 120
                                       n+  +r+++++++++ +++++t + ++++tg + ++ ++++D  w +++ +   ++l + ++ g + ++ e+++ + 
  gi|330508260|ref|YP_004384688.1| 505 NRLWDRTFGGEEHDWGTSVQQTLDGGYIITGSTYSFGAGSRD-LWLIKTDNQG-NRLWDRTFGGEEDDVGESVQQAH 579
                                       56667889999999999*******999999966666666666.8999988755.68888889999999999999999 PP

                              DERM 121 pskrvitGvqsdfsnsk 137
                                       + +++itG + +f + +
  gi|330508260|ref|YP_004384688.1| 580 DGGYIITGSTYSFGAGS 596
                                       99999999877776644 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 0.16
                              DERM  48 erswseyvnsydqeftftcpnnqyltgvesehsnskeDRrwkfqCartngatlsnCsttgylnsfdetlsftapskr 124
                                       er++++++++   ++++t + ++++tg + ++  +++D  w +++ +   +++ + ++ g + +  ++++ t + ++
  gi|330508260|ref|YP_004384688.1| 613 ERTFGGEESDKGYSVQQTLDGEYIITGYTGSFGTGNSD-LWLIKTDDEG-NKIWDRTFGGAEYDDGKSVQQTLDGGY 687
                                       55555666666666666666666666666666666666.5666655543.344444455555555555555556666 PP

                              DERM 125 vitG 128
                                       +itG
  gi|330508260|ref|YP_004384688.1| 688 IITG 691
                                       6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (714 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 5062.37
//
Query:       gi|330508261|ref|YP_004384689.1|  [L=207]
Description: hypothetical protein MCON_2414 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-17   64.8   0.2      2e-17   63.9   0.2    1.4  1  AAA_17    AAA domain
    2.2e-10   41.2   0.0    3.3e-10   40.6   0.0    1.2  1  AAA_18    AAA domain
    1.6e-06   28.3   0.0    2.4e-06   27.7   0.0    1.3  1  AAA_33    AAA domain
      0.004   17.3   0.0     0.0073   16.4   0.0    1.4  1  ADK       Adenylate kinase
  ------ inclusion threshold ------
      0.032   13.8   0.0      0.046   13.4   0.0    1.2  1  SRP54     SRP54-type protein, GTPase 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 !   63.9   0.2   5.5e-21     2e-17       1     133 [.      11     135 ..      11     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 5.5e-21
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC.TSHHHHHHHHHHHHHHHHHHHHHSSE... CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr.klpleekkelqkeaaekiaeeakkkg... 73 
                                       +G+PGsGKg+++ k+++++g++++ +Gd++r+ea+r gl+++++++   ++  ++k+  + +a+k  ++a+k+g   
  gi|330508261|ref|YP_004384689.1|  11 VGLPGSGKGEAS-KIARELGLSVVVMGDVIRQEAARLGLEPTDQNLGrIGNALREKDGPEAIARKTLKMARKTGrdl 86 
                                       7*********99.**************************88887776366777788888888888888774433344 PP

                                       EEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH.TTST-TS-SHH CS
                            AAA_17  74 vlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd.rtrgrdddnee 133
                                       v+vdg  +         g ++e++++   d + l+e+++    e rl + ++rgr+dd  e
  gi|330508261|ref|YP_004384689.1|  87 VVVDGLRS---------GAEAEFFRSQ-ADEFYLIEVQAA--AEARLGRlEKRGRPDDPKE 135
                                       89999875.........5566666664.788999999886..7788888899*****9876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   9.2e-14   3.3e-10       1     124 [.       8     143 ..       8     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 9.2e-14
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssal 71 
                                       I+  G pG+GK + +k  ++++ +     g+++r+ a+  gl+ ++++   + + +r++++  + + ++l+ +++  
  gi|330508261|ref|YP_004384689.1|   8 IGFVGLPGSGKGEASKIARELG-LsvvvmGDVIRQEAARLGLEPTDQNLgRIGNALREKDGPEAIARKTLKMARK-- 81 
                                       7899**************9985.556999*************999999998888888888888889999999876.. PP

                            AAA_18  72 eegknlvidghlaeleseaakdikk....vvLtaspeelleRlekRgyeeakik.....ene 124
                                       +  + +v+dg+++  e e ++        + ++a  e +l RlekRg+ ++ ++     +n 
  gi|330508261|ref|YP_004384689.1|  82 TGRDLVVVDGLRSGAEAEFFRSQADefylIEVQAAAEARLGRLEKRGRPDDPKEwgevrGNA 143
                                       778888**********998888777999*******************766544466555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   6.8e-10   2.4e-06       3     127 ..       9     135 ..       7     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 6.8e-10
                            AAA_33   3 llvGlpGsGKstlaerllkklg.avllssdtlrrrlfg.....tdqqskt..dytrvldrlyqilnelarkalsagr 71 
                                        +vGlpGsGK   ++ ++++lg  v++  d++r+  +      tdq+  +  +  r +d   +i +++++ a++ gr
  gi|330508261|ref|YP_004384689.1|   9 GFVGLPGSGKGEASK-IARELGlSVVVMGDVIRQEAARlglepTDQNLGRigNALREKDGPEAIARKTLKMARKTGR 84 
                                       59********99877.89*****6666666655544443222266663332244444444677999999999***** PP

                            AAA_33  72 nvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrse 127
                                       ++++  +++s +e + f++ a     ++ ++ v++  e    Rl+kR ++ dd+ e
  gi|330508261|ref|YP_004384689.1|  85 DLVVVDGLRSGAEAEFFRSQAD----EFYLIEVQAAAEARLGRLEKRGRP-DDPKE 135
                                       ******************9998....899********************7.55555 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     2e-06    0.0073       2      36 ..      11      44 ..      10      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2e-06
                                      EESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  2 lGaPgaGKGtqaeklvkkyglahlstGdllRaevk 36
                                      +G Pg+GKG  a+k+++++gl  +  Gd++R+e +
  gi|330508261|ref|YP_004384689.1| 11 VGLPGSGKG-EASKIARELGLSVVVMGDVIRQEAA 44
                                      8********.6899*****************9975 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.3e-05     0.046       3      90 ..       7      90 ..       5     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSST.THHHHHHHHHHHTTEEEEE.SSTTSCHHHHHHHHHHHH CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRa.aAveQLktlaeklgvpvik.kkeeadpaavakeaveka 79
                                      +i +vGl G+GK   ++K+a+ l   g +v +v  D+ R  aA   L+   ++lg ++ +  +e++ p a+a++++++a
  gi|330508261|ref|YP_004384689.1|  7 IIGFVGLPGSGKGE-ASKIAREL---GLSV-VVMGDVIRQeAARLGLEPTDQNLG-RIGNaLREKDGPEAIARKTLKMA 79
                                      7889********75.67888544...5555.667899997255567888888888.44444666778************ PP

                                      HHTTSSEEEEE CS
                             SRP54 80 keekidvvlvD 90
                                      ++ + d+v+vD
  gi|330508261|ref|YP_004384689.1| 80 RKTGRDLVVVD 90
                                      **********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 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:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1407.20
//
Query:       gi|330508262|ref|YP_004384690.1|  [L=278]
Description: anaerobic ribonucleoside-triphosphate reductase activating protein [Methanosaeta concilii GP6]
Scores for complete 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-14   52.1   0.1    2.3e-13   50.9   0.1    1.6  1  Radical_SAM  Radical SAM superfamily
    1.3e-08   35.2   0.0    3.4e-08   33.8   0.0    1.7  1  Fer4_12      4Fe-4S single cluster domain
     0.0023   18.1   0.3      0.029   14.5   0.3    2.2  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.1   3.8e-17   2.3e-13       1     153 [.      22     195 ..      22     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 3.8e-17
                                       EEEESEESS--TTTSCCTT........................HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEE CS
                                       xxxxxxxxxxxxxxxxxxx........................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpet........................vrregrgrslsveeileevkelkaekg.vkevil 52 
                                       vv++rgC+lrC++C+++                              +  ++l + ++++   +++ ++  v+ ++l
  gi|330508262|ref|YP_004384690.1|  22 VVFLRGCPLRCPHCHNHALqtgesdiefhalasrivcrtkglhTPAIKLRANLHQISLEDASIRAS-SRPfVEAFVL 97 
                                       689**************99***********************966666777777777777777774.4445****** PP

                                       ESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHH.HHHHHHTCTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       Radical_SAM  53 gggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelg.vdrvslgleaadde.kvlklmnrghtf 127
                                       +ggepl + +    l+ la+    ++   +et+g+   ++ l++lle g vd v ++l+++ +e  ++  ++ g+  
  gi|330508262|ref|YP_004384690.1|  98 SGGEPLQQLKACHRLFGLARS--LELASGLETSGFY--PDRLKTLLEGGiVDKVFIDLKTVLNEpAYQMATGIGGVA 170
                                       *********************..7************..69*******99***************9999999999*** PP

                                       HHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 128 eevlealeklreagikrvvdrivglp 153
                                        +v e+le+++e g+     r++++p
  gi|330508262|ref|YP_004384690.1| 171 ARVRESLEICHEFGVA-FDARCTVFP 195
                                       *************987.666666666 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   5.7e-12   3.4e-08       7      83 ..      20     120 ..      16     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 5.7e-12
                           Fer4_12   7 rlslfvsgCnlsCkgCfnketwsfk..........................sgkeftkelleeiiedlkkesieglt 57 
                                        l++f+ gC+l+C+ C+n +++  +                          + +  +  l++  i+  + + +e ++
  gi|330508262|ref|YP_004384690.1|  20 ALVVFLRGCPLRCPHCHNHALQTGEsdiefhalasrivcrtkglhtpaiklRANLHQISLEDASIRASSRPFVEAFV 96 
                                       579*******************77777777788888888888888888887778888999999999999******** PP

                           Fer4_12  58 llGGEPllpenaeallelvkevkeek 83 
                                       l+GGEPl   + +a+ +l+   ++  
  gi|330508262|ref|YP_004384690.1|  97 LSGGEPLQ--QLKACHRLFGLARSLE 120
                                       ********..8888888876666555 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.3   4.8e-06     0.029       3      70 ..      23     112 ..      21     131 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.8e-06
                           Fer4_14   3 vrlsgCnlsCkgCdnketwks.........................elgkpqteel.leqilkdlkkseikiqglvl 53 
                                       v l gC+l C+ C n++ +                           +l     +   +++ +  ++ + ++ +  vl
  gi|330508262|ref|YP_004384690.1|  23 VFLRGCPLRCPHCHNHALQTGesdiefhalasrivcrtkglhtpaiKLRANLHQISlEDASI-RASSRPFVEA-FVL 97 
                                       5569*******888665444355666677777777777766666664443333333033444.4555555455.9** PP

                           Fer4_14  54 tGGePLhyenkkellkl 70 
                                       +GGePL  ++ k++ +l
  gi|330508262|ref|YP_004384690.1|  98 SGGEPL--QQLKACHRL 112
                                       ******..556655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1966.60
//
Query:       gi|330508263|ref|YP_004384691.1|  [L=424]
Description: hypothetical protein MCON_2416 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.097   12.2   0.2       0.16   11.5   0.2    1.3  1  VirArc_Nuclease  Viral/Archaeal nuclease
        0.2   10.7   2.4          8    5.4   0.7    2.2  2  Pox_F11          Poxvirus F11 protein
       0.29    9.8   1.1       0.85    8.2   0.0    2.1  2  Tweety           Tweety
        1.5    8.0  12.6       0.53    9.5   3.3    3.2  4  DUF4763          Domain of unknown function (DUF4763)
        1.6    8.9  12.0          6    7.1   3.9    3.4  3  Fib_alpha        Fibrinogen alpha/beta chain family
        4.1    6.7  15.4       0.67    9.2   3.1    2.4  2  FAM76            FAM76 protein


Domain annotation for each model (and alignments):
>> VirArc_Nuclease  Viral/Archaeal nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   5.4e-05      0.16      99     179 ..     173     257 ..     168     265 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.4e-05
                   VirArc_Nuclease  99 fteeqskkrygeaiyailstkvevakelevlGrtifihyadredklklisalrilnlekqgk.....ikkeeiefaa 170
                                       +  ++  + +g+ ++ai s k +va e + +G t+ +++ d e++++ ++a+++    ++ k      k+e+i+ ++
  gi|330508263|ref|YP_004384691.1| 173 WYSKELAEELGKGLVAIDSLKKKVAGEEALIGSTA-ARLRDHEERIRNLAASELGRRTEELKksleeKKREKIQTEE 248
                                       55666678899*********************997.899*************9976555544233345556666666 PP

                   VirArc_Nuclease 171 ksryyiipl 179
                                       + r  i pl
  gi|330508263|ref|YP_004384691.1| 249 ELRSLISPL 257
                                       666666665 PP

>> Pox_F11  Poxvirus F11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0032       9.6     255     338 ..      86     167 ..      34     198 .. 0.73
   2 ?    5.4   0.7    0.0027         8     293     351 ..     325     383 ..     240     410 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0032
                           Pox_F11 255 vyadmiklseeivdeilk.rlekaadsaladvkavrkaksklrGerslaaAlkskeaivEeiladvalleegtlktt 330
                                       v  +m  l+ e +d   k +l+ a++   a vk ++++      ++   aA+  k   +E i +d+ ++ ++ ++ +
  gi|330508263|ref|YP_004384691.1|  86 VVKQMESLE-EKIDPPRKmDLQSASEHHWALVKGLERTVTTFGRAQRYVAAIFPKS--LESINSDLGQISRTLVELE 159
                                       344666666.6677654427999***************999887888999999999..************9998877 PP

                           Pox_F11 331 sllqrlar 338
                                        ++ +  +
  gi|330508263|ref|YP_004384691.1| 160 EMIDKRRK 167
                                       66654443 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0027
                           Pox_F11 293 sklrGerslaaAlkskeaivEeiladvalleegtlkttsllqrlardkkvlykrvseLv 351
                                       ++l G+rsl+ A +++ ++ Eei +   +l+e+  +   l   + +dkk l k  + L 
  gi|330508263|ref|YP_004384691.1| 325 DQLIGKRSLELARSRHFSLAEEIKSLEGQLKESSKEALQLKDTISQDKKALIKLEAALE 383
                                       6899*********************************************9998777775 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00028      0.85      89     168 ..     117     196 ..     114     225 .. 0.81
   2 ?   -0.7   0.2      0.14   4.2e+02     110     150 ..     345     385 ..     319     418 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00028
                            Tweety  89 dGvlqltyslrkanhtlagikklv.seteesleekleeeLtkleeifakrtdlletlrlvqeqveevvqqlselpfl 164
                                        G+ + +++  +a++ +a+i  +  ++++++l  +++++L++lee+++kr +l e +   +e +ee+ + l ++  l
  gi|330508263|ref|YP_004384691.1| 117 KGLERTVTTFGRAQRYVAAIFPKSlESINSDL-GQISRTLVELEEMIDKRRKLSEEIWYSKELAEELGKGLVAIDSL 192
                                       68999999999999999999765505555555.57999***************************999999999988 PP

                            Tweety 165 kkkd 168
                                       kkk 
  gi|330508263|ref|YP_004384691.1| 193 KKKV 196
                                       7664 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.14
                            Tweety 110 klvseteesleekleeeLtkleeifakrtdlletlrlvqeq 150
                                       + ++++e +l+e+ +e L+  ++i + ++ l++   ++++ 
  gi|330508263|ref|YP_004384691.1| 345 EEIKSLEGQLKESSKEALQLKDTISQDKKALIKLEAALEQS 385
                                       45555555555555555444444444444444433333333 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.43   1.3e+03      47      78 ..      37      68 ..      16      76 .. 0.74
   2 ?    3.4   0.0     0.013        40     115     164 ..     150     199 ..     131     202 .. 0.62
   3 ?   -1.9   0.2      0.56   1.7e+03     150     155 ..     235     240 ..     206     278 .. 0.55
   4 ?    9.5   3.3   0.00018      0.53     103     153 ..     334     384 ..     282     390 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.43
                           DUF4763 47 eeldLdeiydelekiKqrvlelrskLalnvpe 78
                                       e  L+eiy  le   + +++  s+La   p+
  gi|330508263|ref|YP_004384691.1| 37 WEKSLSEIYRHLEDQAKELSLDVSRLASAEPD 68
                                      45679999999999999998888888877665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.013
                           DUF4763 115 qlaelqqhlkasrkslkelreslcqekkrlrklqkrlneldsfkrklehe 164
                                       q+++    l+++ ++ ++l e++  +k+ +++l k l ++ds k+k++ e
  gi|330508263|ref|YP_004384691.1| 150 QISRTLVELEEMIDKRRKLSEEIWYSKELAEELGKGLVAIDSLKKKVAGE 199
                                       45555555555555556666666666666666666666666666666655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.56
                           DUF4763 150 rlneld 155
                                       +l+e +
  gi|330508263|ref|YP_004384691.1| 235 SLEEKK 240
                                       111111 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00018
                           DUF4763 103 leLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlne 153
                                          + ++  L  ++++l+ +lk+s k+  +l++ ++q+kk+l kl++ l++
  gi|330508263|ref|YP_004384691.1| 334 ELARSRHFSLAEEIKSLEGQLKESSKEALQLKDTISQDKKALIKLEAALEQ 384
                                       445778899*************************************99987 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 ?    4.4   0.7     0.013        39      42     122 ..     139     221 ..     131     246 .. 0.72
   2 ?    2.5   0.2      0.05   1.5e+02      83     119 ..     207     245 ..     174     274 .. 0.48
   3 ?    7.1   3.9     0.002         6      30     129 ..     293     400 ..     284     402 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.013
                                       CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHH CS
                         Fib_alpha  42 neleeisnstkeaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrlketidaqesnirvLqnvlesne 115
                                       ++le+i++   +++++ +e+++++ ++ k +++    +++ +++ k l   i  lk+++  +e  i      l++ e
  gi|330508263|ref|YP_004384691.1| 139 KSLESINSDLGQISRTLVELEEMIDKRRKLSEEIwysKELAEELGKGLV-AIDSLKKKVAGEEALIGSTAARLRDHE 214
                                       5677777777777777777777777777777752333555555555565.677788888888888888888888888 PP

                                       HHHHHHH CS
                         Fib_alpha 116 qkiqkLe 122
                                       ++i +L 
  gi|330508263|ref|YP_004384691.1| 215 ERIRNLA 221
                                       8888775 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.05
                                       HHHHHHCCCHHHHHHHCCH.HHHHHHHHHHHHH.HHHHH CS
                         Fib_alpha  83 skeleeeilrlketidaqe.snirvLqnvlesn.eqkiq 119
                                       + +l+++ +r+++   ++  ++ ++L++ le++ ++kiq
  gi|330508263|ref|YP_004384691.1| 207 AARLRDHEERIRNLAASELgRRTEELKKSLEEKkREKIQ 245
                                       333333333333333333333333333333322022222 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.002
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHH...HCCCHHHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.....dnvikksskele...eeilrlketid 98 
                                       ++++  +le+l+ +l+++  + ++ e++  +i++ + ++  + + +      + ik+++ +l+   +e l+lk+ti+
  gi|330508263|ref|YP_004384691.1| 293 DNEIAGSLEELRAHLATLGLKDRKKEKVLDHIDQLIGKRSLELARSrhfslAEEIKSLEGQLKessKEALQLKDTIS 369
                                       56788899************************999988877666533334555555555555411137788999999 PP

                                       CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  99 aqesnirvLqnvlesneqkiqkLeqdidqke 129
                                       +  + + +L   le+ ++++  Le+ + +k+
  gi|330508263|ref|YP_004384691.1| 370 QDKKALIKLEAALEQSRKDLLILEERMGSKQ 400
                                       9999999999999999999988888776665 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.1   0.00023      0.67     207     298 ..     175     267 ..      84     269 .. 0.80
   2 ?    3.1   4.6     0.017        51     223     267 ..     342     386 ..     283     419 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00023
                             FAM76 207 kksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaell.ekekelreklkelekeakekiekle 282
                                       +k+l  +    lva+  Lk+++a  +  + +    l + +  i +l a +l +  +el++ l+e ++e  ++ e+l+
  gi|330508263|ref|YP_004384691.1| 175 SKELAEELGKGLVAIDSLKKKVAGEEALIGSTAARLRDHEERIRNLAASELgRRTEELKKSLEEKKREKIQTEEELR 251
                                       336677778889*********************************9986651677788999999999999999**** PP

                             FAM76 283 kkirellkevaelskk 298
                                       + i+ l+k + +++k+
  gi|330508263|ref|YP_004384691.1| 252 SLISPLTKALGRITKQ 267
                                       ********99999987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.017
                             FAM76 223 qLkeeiaslkkqleqkdqellekdkkitelkaellekekelrekl 267
                                        L eei+sl+ ql++  +e l+ + +i++ k  l++ e+ l++  
  gi|330508263|ref|YP_004384691.1| 342 SLAEEIKSLEGQLKESSKEALQLKDTISQDKKALIKLEAALEQSR 386
                                       355666666666666666666666666666665555555443322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1755  (0.0978861); expected 358.6 (0.02)
Passed bias filter:                      763  (0.0425568); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.46
# Mc/sec: 2781.91
//
Query:       gi|330508264|ref|YP_004384692.1|  [L=769]
Description: putative Ski2-type helicase [Methanosaeta concilii GP6]
Scores for complete 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-24   85.2   0.0    8.2e-24   84.3   0.0    1.4  1  DEAD             DEAD/DEAH box helicase
    5.1e-10   39.6   0.0      1e-09   38.7   0.0    1.4  1  ResIII           Type III restriction enzyme, res subunit
    2.2e-08   34.4   0.0    1.5e-07   31.8   0.0    2.4  2  Helicase_C       Helicase conserved C-terminal domain
    4.8e-08   33.5   0.4    4.8e-08   33.5   0.4    2.2  2  HHH_5            Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.025   14.7   0.2       0.43   10.8   0.0    2.6  2  DUF2508          Protein of unknown function (DUF2508)
      0.084   12.8   0.0       0.96    9.5   0.0    2.5  2  HHH              Helix-hairpin-helix motif
      0.085   12.7   0.0       0.38   10.6   0.0    2.1  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda


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 !   84.3   0.0   3.2e-27   8.2e-24       2     170 ..      29     185 ..      28     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 3.2e-27
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       + Qa+a++  l +g+++l+a +T+sGKT  + +++l++ +     + ++ l+++P+r+La + ++ +++fk+   l 
  gi|330508264|ref|YP_004384692.1|  29 PPQAQAVERGLlEGKNMLLALATASGKTFLAELAMLKAAL-----QSKRSLYIVPLRALAAEKFDSFQRFKD---LG 97 
                                       679999999887************************8884.....57799********************99...66 PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                       v++ i+  + +++ ++l  + +i+++t ++ d+l+++g   ++++ +lV+DE++ l d g++++++  +++l++ ++
  gi|330508264|ref|YP_004384692.1|  98 VSVGISTGDFDKKDERL-GRNQIIIATSEKADSLMRNGASWIRDLAVLVIDEIHLLNDVGRGPTLEMTITKLRRSNS 173
                                       77667877888999999.88***************999999*******************************65544 PP

                                       TSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxx RF
                              DEAD 155 dgklqrqvivlSATlp 170
                                          lq  +i lSAT+ 
  gi|330508264|ref|YP_004384692.1| 174 G--LQ--IIGLSATVA 185
                                       3..34..*******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 !   38.7   0.0   3.9e-13     1e-09       3     169 ..      26     184 ..      25     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 3.9e-13
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       el++ Q++a+e+ l      + k++l+++aT +GKT++a +++ ++ l++   ++ l +vp ++l     + f++f+
  gi|330508264|ref|YP_004384692.1|  26 ELYPPQAQAVERGLL-----EGKNMLLALATASGKTFLAeLAMLKAALQS---KRSLYIVPLRALAAEKFDSFQRFK 94 
                                       578999999999983.....4689***************65555555554...599********************* PP

                                       GG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....T.... CS
                            ResIII  79 seaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...k.... 148
                                       +  +    ++ +gd +k+  ++   ++i+++t +++d+ +      +         v++iDE H l++         
  gi|330508264|ref|YP_004384692.1|  95 DLGV--SVGISTGDFDKK-DERLGRNQIIIATSEKADSLM-----RNGASWIRDLAVLVIDEIHLLNDVgrgPtlem 163
                                       9998..889999999999.88999****************.....33344444445************865515556 PP

                                       TTHHHHHT---SEEEEEESS- CS
                            ResIII 149 swreilekfkeavllglTATp 169
                                       +++++ ++++   ++gl+AT 
  gi|330508264|ref|YP_004384692.1| 164 TITKLRRSNSGLQIIGLSATV 184
                                       88888888899*********7 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.7   4.3e+03      11      54 ..      65     111 ..      56     130 .. 0.58
   2 !   31.8   0.0   5.7e-11   1.5e-07      12     111 .]     245     383 ..     231     383 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.7
                                       HHTTTTSEEEEEESSHH.HHHHHHHHHHHT...TSTEEEESTTSTHHH CS
                        Helicase_C  11 kleeeggkilifvntid.rlekvklllekk...gikvavlhgelpqne 54 
                                       k   + +++l +v+ +   +ek++ + +++   g++v + +g+  +++
  gi|330508264|ref|YP_004384692.1|  65 KAALQSKRSLYIVPLRAlAAEKFDSF-QRFkdlGVSVGISTGDFDKKD 111
                                       55667777777777777544444444.222345666666666655554 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 5.7e-11
                                       HTTTTSEEEEEESSHHHHHH....HHHH.....................HHHT.........TSTEEEESTTSTHHH CS
                        Helicase_C  12 leeeggkilifvntidrlek....vkll.....................lekk.........gikvavlhgelpqne 54 
                                       + +++ +ilif n+++++e     +                           +         +  +a +h+ l  ++
  gi|330508264|ref|YP_004384692.1| 245 TLSQDAQILIFENSRKNAEAaaikL--SnlippdpkaetlsesilatgeS--EtchrlascvSRGIAFHHAGLLPDQ 317
                                       4477888999999999664444331..12234444444444444455430..1444556677899999********* PP

                                       HHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSH.........HHHHHHHTTSSSTT CS
                        Helicase_C  55 reeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnv.........tsyiqriGRtgRag 111
                                       r+ + + f++++++v+ +t  ++ G+++p  +++i     +++          +y q++GR+gR g
  gi|330508264|ref|YP_004384692.1| 318 RRLVEQGFRENRIKVIASTPTLAAGLNLPARRVLIKSYRRYEYgsgmvpipvIEYRQMAGRAGRPG 383
                                       *****************************99999977777665556677777************75 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       5.7   1.5e+04      11      31 ..      42      63 ..      42      67 .. 0.70
   2 !   33.5   0.4   1.9e-11   4.8e-08       3      56 ..     658     709 ..     656     710 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.7
                                      -HHHHHHHHTT.T--SHHHHHH CS
                             HHH_5 11 GpktAlallsa.Giesvedlaa 31
                                      G+ + lal+ a G +++++la 
  gi|330508264|ref|YP_004384692.1| 42 GKNMLLALATAsGKTFLAELAM 63
                                      5666777777767778888886 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 1.9e-11
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                       +Ll+++G+G+++A++l+  Gi+  e+l++ d+ e+a++  +G+k Ae+++l+l 
  gi|330508264|ref|YP_004384692.1| 658 SLLDLKGVGRVRARKLHQSGITNREKLKSTDPVEIARL--LGPKIAEKVLLQLA 709
                                       69************************************..***********995 PP

>> DUF2508  Protein of unknown function (DUF2508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.26   6.7e+02      16      35 ..      55      74 ..      44      76 .. 0.88
   2 ?   10.8   0.0   0.00017      0.43      50      67 ..     569     586 ..     520     589 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.26
                           DUF2508 16 eeLleeIektkeelesaksl 35
                                      + +l+e++++k +l+s++sl
  gi|330508264|ref|YP_004384692.1| 55 KTFLAELAMLKAALQSKRSL 74
                                      6789*************997 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00017
                           DUF2508  50 lklaeakYeFLlreAkkr 67 
                                       +  +e  Y++LlreAk+ 
  gi|330508264|ref|YP_004384692.1| 569 ELFNEENYDYLLREAKTS 586
                                       3467889*********86 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00037      0.96      13      28 ..     659     674 ..     658     676 .. 0.90
   2 ?   -0.0   0.0      0.38   9.6e+02      20      28 ..     697     705 ..     696     706 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00037
                                       HHTSTT-SHHHHHHHH CS
                               HHH  13 LlalPGVGpktAeaIl 28 
                                       Ll+l+GVG+ +A++ +
  gi|330508264|ref|YP_004384692.1| 659 LLDLKGVGRVRARKLH 674
                                       99***********987 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.38
                                       SHHHHHHHH CS
                               HHH  20 GpktAeaIl 28 
                                       Gpk Ae++l
  gi|330508264|ref|YP_004384692.1| 697 GPKIAEKVL 705
                                       9******98 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 ?   -3.2   0.0       3.1   7.8e+03      33      46 ..     627     640 ..     616     642 .. 0.79
   2 ?   10.6   0.0   0.00015      0.38       8      30 ..     664     686 ..     659     695 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.1
                   DNA_pol_lambd_f  33 akLtreqqiGlkyy 46 
                                       a+L+++ ++G+ y 
  gi|330508264|ref|YP_004384692.1| 627 AELSKHLDLGITYR 640
                                       67999999999885 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00015
                   DNA_pol_lambd_f   8 GVGpktAkkwyakGirtledlra 30 
                                       GVG+++A+k+++ Gi++ e l+ 
  gi|330508264|ref|YP_004384692.1| 664 GVGRVRARKLHQSGITNREKLKS 686
                                       9****************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (769 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 5229.85
//
Query:       gi|330508265|ref|YP_004384693.1|  [L=383]
Description: aminotransferase [Methanosaeta concilii GP6]
Scores for complete 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-61  206.9   0.0    5.5e-61  206.8   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.8   0.0     3e-65   5.5e-61       2     363 .]      30     378 ..      29     378 .. 0.97

  Alignments for each domain:
  == domain 1  score: 206.8 bits;  conditional E-value: 3e-65
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dvi+L++++++      t++++++a k+ a+  +++++y+ ++g  ++++a+a+++++   ++l+++ +v+++ G++
  gi|330508265|ref|YP_004384693.1|  30 DVIDLSVGDPDLP----TPDHIVQALKQ-AANDSSNHQYPSYEGKLAFRNAVADWYKKTFDIDLDPKNEVLTLIGSK 101
                                       89**********9....***********.****************************999***************** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       ++i+ ++ ++ +npgd+ lvpdp y+ y ++   +gge   +pl  e++f  dl+a+ +++++      + k+++++
  gi|330508265|ref|YP_004384693.1| 102 EGIAHAPLAF-INPGDVALVPDPAYPVYATATAFAGGEPAIMPLLRENGFLPDLDAIPADVAR------RAKIMFLN 171
                                       **********.****************************************************......99****** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvG 231
                                        p+NP G+ a+++   +l+d a+ +n++++ D  Y++ +++  +  + +++++ + +  +   slsK ++++G+R+G
  gi|330508265|ref|YP_004384693.1| 172 YPNNPIGATASEKFFGELVDYARDHNIIIMHDNPYSEIYYDGNRSLS-ILEIDGAKEvAVEFHSLSKTYNMTGWRIG 247
                                       *****************************************776555.88888888877899*************** PP

                                       EEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 232 yilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                        ++gna+v+  + k+++++ s    ++q a   als ++++   ++e r+ +q+r + l+++L++++l   ++ +++
  gi|330508265|ref|YP_004384693.1| 248 SVVGNADVLAGIGKVKSNIDSgtFGAVQDAGIVALSSPKEV---VDEIRKVYQQRIEILYKALKDIDLVLEKPRATL 321
                                       *********************999***************96...********************************* PP

                                       EEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 307 flltdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                       +l+  ++ +   + + kLle+ g++ tpg  f++  +g  R+++ +  ++ +ee++++l
  gi|330508265|ref|YP_004384693.1| 322 YLWAWVKGS-SIDYAAKLLERTGIVATPGLGFGKygEGYMRFSI-TRETKRVEEAARRL 378
                                       ****99999.899999****************************.***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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 0.22s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2895.06
//
Query:       gi|330508266|ref|YP_004384694.1|  [L=950]
Description: leucyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete 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-57  195.0   0.0    1.2e-41  142.7   0.0    3.0  2  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    2.1e-22   79.4   0.0      6e-10   38.4   0.1    3.0  3  tRNA-synt_1g   tRNA synthetases class I (M)
    1.1e-21   77.4   0.0    2.1e-21   76.5   0.0    1.5  1  Anticodon_1    Anticodon-binding domain of tRNA
    4.1e-08   32.9   0.0    9.4e-08   31.8   0.0    1.5  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    2.7e-07   30.2   0.0     0.0004   19.8   0.0    2.6  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.032   13.2   0.0      0.052   12.5   0.0    1.3  1  tRNA-synt_1f   tRNA synthetases class I (K)
      0.037   13.0   0.0      0.066   12.2   0.0    1.3  1  tRNA-synt_1d   tRNA synthetases class I (R)
      0.076   13.4   0.1        0.2   12.0   0.1    1.7  1  CPSase_L_D3    Carbamoyl-phosphate synthetase large chain, ol
       0.14   11.7   0.0        0.3   10.6   0.0    1.5  1  Prenyltransf   Putative undecaprenyl diphosphate synthase


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 !  142.7   0.0   6.2e-45   1.2e-41       2     305 ..      14     323 ..      13     332 .. 0.88
   2 !   46.7   0.0   6.9e-16   1.4e-12     319     601 ..     390     667 ..     363     668 .. 0.85

  Alignments for each domain:
  == domain 1  score: 142.7 bits;  conditional E-value: 6.2e-45
                       tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlai.. 76 
                                       ++  Wee+ +f++e    +e+++f l+++ Py +G+lH Gh  + t+ d   rykrm+G++vl+ +G+   G +i  
  gi|330508266|ref|YP_004384694.1|  14 WQRIWEENAIFEPE---PDERQKFLLTIPYPYLNGNLHAGHTRTFTIGDAYARYKRMRGYNVLFPMGFHATGTPIvg 87 
                                       7889**********...88899****************************************************933 PP

                       tRNA-synt_1  77 ..eakvekklgakek.kerkklgreefr..ekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfv 148
                                         e   +k   + +  +  + + +ee    +   +++ ++  + + +++ +G s+D+ re  T d+ +++ +++ f+
  gi|330508266|ref|YP_004384694.1|  88 lsELIANKDPLIWGVyTRLHGIPEEELAslNTPEKIVLYFRRQAKAAMQSIGYSIDWRREFTTTDPAYSKFIEWQFG 164
                                       3233333332222321345667777765226778999**************************************** PP

                       tRNA-synt_1 149 rladkgliyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeld 225
                                        l + + + +g+++v w+++ k ++ + ++ + +    + +   ++  +++  +  aT +PeT++g t + +np + 
  gi|330508266|ref|YP_004384694.1| 165 ILRNLDYVVKGSHPVRWCPHDKNPVEDHDILKGEDATIMDFALIKFRMGDA-IMPCATLRPETVFGVTNLWLNPSVT 240
                                       ******************************776666554444444444555.6799********************* PP

                       tRNA-synt_1 226 yv...itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahd 299
                                       yv   i++e++i+ +   ++l+  +       ++ g eL+gk+v++pl++ ++ ++   +vd ++G+G+V   Pah 
  gi|330508266|ref|YP_004384694.1| 241 YVmarINDENWIVSKEAYEKLTYTDRAVAWGAEIPGIELIGKRVTNPLTGAEVLVLPAGFVDPDNGSGIVMSVPAHA 317
                                       ****9****************9999999999********************************************** PP

                       tRNA-synt_1 300 edDyev 305
                                       + Dy +
  gi|330508266|ref|YP_004384694.1| 318 PYDYLA 323
                                       ****65 PP

  == domain 2  score: 46.7 bits;  conditional E-value: 6.9e-16
                       tRNA-synt_1 319 edgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..ladaalk 393
                                       ++g+l+ +++ ++g+ v + ++ ++++l ++g      +++ +  +c  +   +i+++ +qWf + ++   +  +l 
  gi|330508266|ref|YP_004384694.1| 390 HNGVLKPNTGRYAGVAVSKIKDLLLRDLIDRGIAEIFYEFSETPVICRCGTRCVIMMVRDQWFLEYSNpeWKGRVLW 466
                                       5899************************************999999999999*************998779999*** PP

                       tRNA-synt_1 394 avekvqfvpkskekryaswleniqdWciSRqrwWGhripl...fvsketeevvvreelkelvagreeeeaekkalek 467
                                        +++++++p  ++ ++++ +   +d +  R +  G+++p    +  ++ ++ ++     ++ a+ ++   ++  l  
  gi|330508266|ref|YP_004384694.1| 467 CLSRMNIIPPEFRVEFENKIDWLKDKACARRKGLGTHLPWdkeWLIESLGDSTI-YMAYYILAKYVNAGMKIDSLPP 542
                                       ***************************************644477777666555.2344445555555556666666 PP

                       tRNA-synt_1 468 eakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgs 544
                                       e+ + +      +  + d   v    g+   ++++     +++++  +p d+ ++G D +   +   +   +a++ +
  gi|330508266|ref|YP_004384694.1| 543 EFFEYI------FMDNGDAAAVANLTGLPEQTVQQ----IHDDFAYWYPVDLRTSGKDLVANHLLFFLYHHVAIFPE 609
                                       666666......44444555554456777776666....4789*******************************999 PP

                       tRNA-synt_1 545 ePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                       + + k + v+g+v   eG+KmSKs+g  +   + + + gad+ Rl+++ +++ ++d+++
  gi|330508266|ref|YP_004384694.1| 610 QLWpKAIAVNGFVS-LEGQKMSKSKGPLLTLRQAVAENGADVTRLYILgNAEGTADVDW 667
                                       95538899****96.68*******************************99999999987 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     3e-13     6e-10       2      53 ..      35      86 ..      34      95 .. 0.95
   2 ?   -0.8   0.0      0.24   4.8e+02      48     134 ..     107     193 ..     104     198 .. 0.79
   3 !   37.0   0.0     8e-13   1.6e-09     286     371 ..     585     672 ..     555     687 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 3e-13
                                      EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHH CS
                      tRNA-synt_1g  2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpie 53
                                      l+t + pY ng+lH Gh ++  ++D++aRykr+rg++vlf  g  + Gtpi 
  gi|330508266|ref|YP_004384694.1| 35 LLTIPYPYLNGNLHAGHTRTFTIGDAYARYKRMRGYNVLFPMGFHATGTPIV 86
                                      789***********************************************95 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.24
                                       -SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE CS
                      tRNA-synt_1g  48 hGtpielkAekegvtpeelvekvheeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqly 122
                                       hG+p e  A+    tpe++v  ++++ k+ +++++ s d     +tt+ + +++ +  f  l + +++ +++  + +
  gi|330508266|ref|YP_004384694.1| 107 HGIPEEELASL--NTPEKIVLYFRRQAKAAMQSIGYSIDwrREFTTTDPAYSKFIEWQFGILRNLDYVVKGSHPVRW 181
                                       55555555544..489999999999999999998877773333468889999999999******************* PP

                                       ETTTTEEE-GGG CS
                      tRNA-synt_1g 123 cpkderflpdry 134
                                       cp+d++   d  
  gi|330508266|ref|YP_004384694.1| 182 CPHDKNPVEDHD 193
                                       ***999887765 PP

  == domain 3  score: 37.0 bits;  conditional E-value: 8e-13
                                       EEEEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-T CS
                      tRNA-synt_1g 286 hfigkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeape 360
                                          gkd +  H +f+     +   e   pk++++++++ +eg+K+SkS+g + + ++a+ +  ad+ R y++ +a+ 
  gi|330508266|ref|YP_004384694.1| 585 RTSGKDLVANHLLFFLYHHVAifPEQLWPKAIAVNGFVSLEGQKMSKSKGPLLTLRQAVAENGADVTRLYILGNAEG 661
                                       4469***********9999998767779************************************************* PP

                                       TS-EEE-HHHH CS
                      tRNA-synt_1g 361 kkDldfswedf 371
                                       + D+d++ + +
  gi|330508266|ref|YP_004384694.1| 662 TADVDWRNDGV 672
                                       *****988765 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   1.1e-24   2.1e-21       1     138 [.     705     830 ..     705     841 .. 0.81

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.1e-24
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       drw+ls+l++ + ++tea+ee + ++a+++++++++ dl +wy +   +              + l+ vl++++r++
  gi|330508266|ref|YP_004384694.1| 705 DRWMLSRLQRRIVQATEAMEEIQTRRALQSAFYLLMGDL-RWYQRRGGK--------------NQLRAVLSAWVRMM 766
                                       9**************************************.999776432..............349*********** PP

                       Anticodon_1  78 aPfmPfitEelwqreeeelgkkesimlaewpekaeel...ekele.....eeevellkeivkairklrs 138
                                       +Pf+P+i+Eelw     +  ++   +laewp ++e l   ++e +     e+ ++ ++eiv++ + + +
  gi|330508266|ref|YP_004384694.1| 767 SPFIPHICEELW----ASGLGEGYASLAEWPVADESLidlKAE-KaedllERTLNDVQEIVNVTGTKPA 830
                                       ************....66667788899****955455554222.1335777777777888877766554 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 !   31.8   0.0   4.7e-11   9.4e-08      24     126 ..     218     321 ..     205     329 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 4.7e-11
                     tRNA-synt_1_2  24 evfttrpdtlfGvtfvalapehplveklaekkkelaafieevkkksesereletkekeGv.ftglkaihPitgekip 99 
                                          t rp+t+fGvt + l p+   v +  ++++ + +  +  k + + ++ +  +e  G+   g  +++P+tg ++ 
  gi|330508266|ref|YP_004384694.1| 218 PCATLRPETVFGVTNLWLNPSVTYVMARINDENWIVSKEAYEKLTYTDRAVAWGAEIPGIeLIGKRVTNPLTGAEVL 294
                                       55689****************999888766666665555555555555566778999***889************** PP

                     tRNA-synt_1_2 100 iwvanyvlmeygtgavmavPahdqrDf 126
                                       +  a +v  + g+g vm+vPah   D+
  gi|330508266|ref|YP_004384694.1| 295 VLPAGFVDPDNGSGIVMSVPAHAPYDY 321
                                       **********************98887 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0012       2.4      21      50 ..      45      74 ..      36      80 .. 0.92
   2 !   19.8   0.0     2e-07    0.0004     207     282 ..     581     657 ..     573     676 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                                      S--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvqf 50
                                       + h Gh+R++ + D  +r+ +++gY+v f
  gi|330508266|ref|YP_004384694.1| 45 GNLHAGHTRTFTIGDAYARYKRMRGYNVLF 74
                                      578*************************88 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2e-07
                                       SEEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                      tRNA-synt_1e 207 eidihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                                        +d+ + G+DL+  h    l  + a f  + + k    ng++++eg+kmsks + ++t+++++ +  + + Rl++l 
  gi|330508266|ref|YP_004384694.1| 581 PVDLRTSGKDLVANHLLFFLYHHVAIFPeQLWPKAIAVNGFVSLEGQKMSKSKGPLLTLRQAVAENGADVTRLYILG 657
                                       5799999**********9********98577899999*********************************9998875 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 ?   12.5   0.0   2.6e-05     0.052     235     340 ..     582     690 ..     577     711 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                      tRNA-synt_1f 235 VdfEpaGkDhaaaGgSvdvsskiaeilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrflilrr 311
                                       Vd+  +GkD++a+   + +++++a + +   P+ +  + +   +g+kms+SkG  ltl++++     +v r++il  
  gi|330508266|ref|YP_004384694.1| 582 VDLRTSGKDLVANHLLFFLYHHVAIFPEQLWPKAIAVNGFVSLEGQKMSKSKGPLLTLRQAVAENGADVTRLYILG- 657
                                       6666777777776667777777776666777877777666666667***************************998. PP

                      tRNA-synt_1f 312 kPkkakkldldle....ilrlvdeYdklerkyf 340
                                       + +   ++d + +      + +d +++l r+++
  gi|330508266|ref|YP_004384694.1| 658 NAEGTADVDWRNDgveaTHAHLDRFYNLAREIM 690
                                       666666666543211112334566666666665 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 ?   12.2   0.0   3.3e-05     0.066      14      61 ..      26      73 ..      15      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.3e-05
                                      ---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEE CS
                      tRNA-synt_1d 14 kksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvi 61
                                      ++  e++k ++    P +  ++h+Gh r+  iGda +r   + Gy+v+
  gi|330508266|ref|YP_004384694.1| 26 PEPDERQKFLLTIPYPYLNGNLHAGHTRTFTIGDAYARYKRMRGYNVL 73
                                      566788999999999999****************************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 ?   12.0   0.1   9.8e-05       0.2       6      56 ..     677     728 ..     673     748 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.8e-05
                       CPSase_L_D3   6 ptdeRifaiaealrrglsveeiheltkidpwFLekle.elvelekelkkkkk 56 
                                       ++ +R++ +a+ + ++ s++e +e t id+w L++l+ ++v++ +++++ ++
  gi|330508266|ref|YP_004384694.1| 677 AHLDRFYNLAREIMADGSIDESAEKTLIDRWMLSRLQrRIVQATEAMEEIQT 728
                                       5668999******9999*******************7369999999888764 PP

>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015       0.3     168     203 ..     581     614 ..     529     622 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                                       S-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG CS
                      Prenyltransf 168 dpDlliRtsGeeRlSnFllwqlayselyfldvlWPd 203
                                       ++Dl  RtsG+  + n ll+ l ++  +f ++lWP+
  gi|330508266|ref|YP_004384694.1| 581 PVDL--RTSGKDLVANHLLFFLYHHVAIFPEQLWPK 614
                                       5664..***************88888*********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (950 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 6339.89
//
Query:       gi|330508267|ref|YP_004384695.1|  [L=90]
Description: hypothetical protein MCON_2420 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.009   16.1   0.2       0.01   15.9   0.2    1.1  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
  ------ inclusion threshold ------
       0.11   12.7   0.2       0.17   12.0   0.2    1.3  1  4PPT_N          4'-phosphopantetheinyl transferase N-terminal


Domain annotation for each model (and alignments):
>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   1.2e-06      0.01       5      60 ..       9      64 ..       6      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-06
                    MqsA_antitoxin  5 vCgkaelvrdtrdvpytykgektvikavtgdfCarCGegvldeeeedrlseellef 60
                                      +C  +++ ++++d+    + e +vik+vt   C  CGe  ++ e ++++ +  +ef
  gi|330508267|ref|YP_004384695.1|  9 CCKIGKMREGRHDFMARIEDEIIVIKDVTVLICDTCGEIEYTLEVSREIDRIRKEF 64
                                      799999999******************************99999888877766665 PP

>> 4PPT_N  4'-phosphopantetheinyl transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   1.9e-05      0.17       6      28 ..      53      75 ..      48      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
                            4PPT_N  6 irkavakRkaeFlaGRicAraal 28
                                      +++ +++ ++eFlaGR+ Ar + 
  gi|330508267|ref|YP_004384695.1| 53 VSREIDRIRKEFLAGRLRARPLA 75
                                      57788999***********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 690.10
//
Query:       gi|330508268|ref|YP_004384696.1|  [L=142]
Description: hypothetical protein MCON_2421 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   15.1   0.0       0.03   14.2   0.0    1.5  1  DUF4411   Domain of unknown function (DUF4411)
      0.017   15.6   0.0      0.024   15.1   0.0    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> DUF4411  Domain of unknown function (DUF4411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.4e-06      0.03      72     126 ..      64     118 ..      46     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-06
                           DUF4411  72 dlavveevgkvakwv.ivesekyskaakkefl.svaDpfliAaAlaknatvVTkEvk 126
                                       + +++e++ ++  +   + s++y  +  + ++   aD  +i++A +++a v T++ +
  gi|330508268|ref|YP_004384696.1|  64 NIRYLEQINEIYVTKnEIISDEYLGS--NAWKfGFADSSIILCARNNSACVLTQDYP 118
                                       34567777777777666666666664..5788899*******************987 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.7e-06     0.024      15     114 ..      17     117 ..      11     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-06
                                       SHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHHHHHHHHHHH. CS
                               PIN  15 eekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidaeiaeeaaeialkyg. 89 
                                       e++ + + + l++  e ++++ +l+E+++ + +  s+++ ++el++++++ l++++ + ++++     + + ++++ 
  gi|330508268|ref|YP_004384696.1|  17 EVHYDILMQYLNHTKERIITPGILSEAWNLIDNDISNKKDKKELFDSNIRyLEQINEIYVTKNEIISDEYLGSNAWk 93 
                                       55666666677777999999999**********99999999999999999999999999888888887778888889 PP

                                       SBHHHHHHHHHHHHHT-EEE.ESST CS
                               PIN  90 llpnDaliaAtAkehgikliatfDe 114
                                        + +D  i+ +A+ + + ++ t D 
  gi|330508268|ref|YP_004384696.1|  94 FGFADSSIILCARNNSACVL-TQDY 117
                                       **************999666.*996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1037.37
//
Query:       gi|330508269|ref|YP_004384697.1|  [L=75]
Description: hypothetical protein MCON_2422 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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       0.12   12.6   0.0    1.1  1  Prok-E2_C  Prokaryotic E2 family C


Domain annotation for each model (and alignments):
>> Prok-E2_C  Prokaryotic E2 family C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.5e-06      0.12      38      93 ..       8      63 ..       3      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.5e-06
                         Prok-E2_C 38 eeakklakalerlaksinedvtiarrgksalsiclvvgvtrpelrcpkfflgsdgw 93
                                       +akk  ++ +++ k i e ++++r g+    iclv    +   +  k ++ s+g 
  gi|330508269|ref|YP_004384697.1|  8 MAAKKYFQDTKSIIKFIFETISVKRDGDNWEVICLVQDLFEDAGKEFKVIVDSEGA 63
                                      5799999*****************************88776666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 597.00
//
Query:       gi|330508270|ref|YP_004384698.1|  [L=101]
Description: hypothetical protein MCON_2423 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-05   23.1   0.0    8.9e-05   22.6   0.0    1.3  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.9e-09   8.9e-05       9      57 ..      36      84 ..      28      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.9e-09
                   HicB_lk_antitox  9 edsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipe 57
                                      + + +   vP+l+G++ +g+tle+  ++ +e+ie ++   +  g+ ip+
  gi|330508270|ref|YP_004384698.1| 36 DPEPFYGEVPELEGVWATGKTLEDCRRELQEVIEGWIALKLRFGHPIPA 84
                                      445566689*****************************99999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 719.12
//
Query:       gi|330508271|ref|YP_004384699.1|  [L=41]
Description: hypothetical protein MCON_2424 [Methanosaeta concilii GP6]
Scores for complete 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     0.0013   18.8   0.0    1.1  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     7e-08    0.0013      34      58 .]       8      32 ..       2      32 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7e-08
                                      EEEE.S-SSS--CCCHHHHHHHCC- CS
                        HicA_toxin 34 vtvppHpgkelkpgtlksIlkqaGl 58
                                      v +p+ +g ++++ +l++Ilk+aG+
  gi|330508271|ref|YP_004384699.1|  8 VRIPNPHGSDISTALLQKILKRAGI 32
                                      5677777*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 312.86
//
Query:       gi|330508272|ref|YP_004384700.1|  [L=82]
Description: hypothetical protein MCON_2425 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-06   26.0   0.8      9e-06   25.8   0.8    1.1  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
      0.002   17.9   1.7      0.019   14.7   0.2    2.2  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
     0.0031   17.3   2.2       0.39   10.6   0.1    2.4  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
     0.0056   16.7   5.1      0.021   14.8   3.0    2.7  3  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
  ------ inclusion threshold ------
       0.02   14.7   2.1      0.045   13.6   0.1    2.2  2  Rad50_zn_hook   Rad50 zinc hook motif
      0.036   14.0   3.2       0.97    9.5   0.2    2.8  2  YhfH            YhfH-like protein
      0.037   14.1   0.2      0.085   12.9   0.2    1.6  1  DZR             Double zinc ribbon
       0.11   12.1   0.5         10    5.8   0.0    2.2  2  zf-C2H2_12      Zinc-finger C2H2-type
       0.12   12.4   2.8        3.7    7.7   0.1    2.7  3  zf-ACC          Acetyl-coA carboxylase zinc finger domain
       0.17   12.1   3.2       0.86    9.8   0.0    2.7  2  Zn-ribbon_8     Zinc ribbon domain
       0.19   11.7   2.6        4.2    7.4   0.2    2.2  2  ADK_lid         Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.8   5.6e-09     9e-06       2      68 ..       8      72 ..       7      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.6e-09
                    MqsA_antitoxin  2 kCpvCgkaelvrdtrdvpytykgektvikavtgdfCarCGegvldeeeedrlseellefrkkvnael 68
                                      kCpvCg+ +l++++ + ++   g +t + +v ++ C rCGe ++++e  +++ +   ++++k  ae 
  gi|330508272|ref|YP_004384700.1|  8 KCPVCGG-DLIEKQVEKVL-RGGVNTAVLKVCAEVCLRCGERLYSQETVRKFEQIRSKLERKETAEF 72
                                      8****97.56666555554.5788999999**********************999999999877765 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   1.2e-05     0.019       2      15 ..       7      20 ..       6      23 .. 0.90
   2 ?    2.5   0.1     0.079   1.3e+02       2      18 ..      39      55 ..      38      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                      EE-SSS--EEEEEE CS
                    zf-C4_Topoisom  2 ekCPkCggdLvlkr 15
                                      ekCP CggdL++k+
  gi|330508272|ref|YP_004384700.1|  7 EKCPVCGGDLIEKQ 20
                                      79**********98 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.079
                                      EE-SSS--EEEEEE-SS CS
                    zf-C4_Topoisom  2 ekCPkCggdLvlkrgkk 18
                                      e C  Cg+ L  +++ +
  gi|330508272|ref|YP_004384700.1| 39 EVCLRCGERLYSQETVR 55
                                      67999*****9998876 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00024      0.39       2      10 ..       7      15 ..       6      23 .. 0.78
   2 !    6.4   0.2    0.0049         8       2       8 ..      39      45 ..      38      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                                      SB-TTT--B CS
                      zf-FPG_IleRS  2 epCpRCwry 10
                                      e+Cp+C++ 
  gi|330508272|ref|YP_004384700.1|  7 EKCPVCGGD 15
                                      9******86 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0049
                                      SB-TTT- CS
                      zf-FPG_IleRS  2 epCpRCw 8 
                                      e+C RC+
  gi|330508272|ref|YP_004384700.1| 39 EVCLRCG 45
                                      89****9 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   3.0   1.3e-05     0.021       1      19 [.       8      26 ..       8      50 .. 0.69
   2 ?   -0.0   0.2      0.58   9.4e+02       2      10 ..      41      49 ..      40      55 .. 0.70
   3 ?    0.3   0.0      0.45   7.3e+02       7      13 ..      62      68 ..      61      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                    DNA_ligase_ZBD  1 hCPvCGsavvReegeaiyR 19
                                      +CPvCG  ++ ++ e ++R
  gi|330508272|ref|YP_004384700.1|  8 KCPVCGGDLIEKQVEKVLR 26
                                      6**********99554444 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.58
                    DNA_ligase_ZBD  2 CPvCGsavv 10
                                      C  CG  + 
  gi|330508272|ref|YP_004384700.1| 41 CLRCGERLY 49
                                      666887765 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.45
                    DNA_ligase_ZBD  7 savvRee 13
                                      s+++R+e
  gi|330508272|ref|YP_004384700.1| 62 SKLERKE 68
                                      89***98 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.8e-05     0.045      21      39 ..       8      26 ..       6      27 .. 0.89
   2 ?    0.3   0.2       0.4   6.4e+02      40      49 ..      59      68 ..      50      74 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                                      E-TTT--EE-HHHHHHHHH CS
                     Rad50_zn_hook 21 cCPlCgReldeehrseLik 39
                                      +CP+Cg +l e+  +++++
  gi|330508272|ref|YP_004384700.1|  8 KCPVCGGDLIEKQVEKVLR 26
                                      9********9999999876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.4
                                      HHHHHHHHHH CS
                     Rad50_zn_hook 40 elqsklerlp 49
                                      +++skler++
  gi|330508272|ref|YP_004384700.1| 59 QIRSKLERKE 68
                                      4555555554 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00059      0.97      11      27 ..       4      20 ..       1      22 [. 0.78
   2 ?    4.4   0.3     0.022        36      15      26 ..      40      51 ..      34      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00059
                              YhfH 11 LPkKkCteCGkeieEqa 27
                                      +P  kC+ CG ++ E++
  gi|330508272|ref|YP_004384700.1|  4 IPFEKCPVCGGDLIEKQ 20
                                      67789*******77764 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.022
                              YhfH 15 kCteCGkeieEq 26
                                      +C  CG+ +  q
  gi|330508272|ref|YP_004384700.1| 40 VCLRCGERLYSQ 51
                                      6999**988665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   5.2e-05     0.085      14      40 ..       8      50 ..       2      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                               DZR 14 fCseCgtklkavaa................edrCpsCgekvdp 40
                                       C+ Cg +l + +                 +++C +Cge + +
  gi|330508272|ref|YP_004384700.1|  8 KCPVCGGDLIEKQVekvlrggvntavlkvcAEVCLRCGERLYS 50
                                      69******98555489999**********999*****998654 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 ?    5.8   0.0    0.0062        10      25      40 ..       9      24 ..       7      27 .. 0.90
   2 ?    4.7   0.1     0.014        23      24      35 ..      40      51 ..      36      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0062
                        zf-C2H2_12 25 CmvCgeslaslklsti 40
                                      C vCg+ l + +++++
  gi|330508272|ref|YP_004384700.1|  9 CPVCGGDLIEKQVEKV 24
                                      99***********998 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.014
                        zf-C2H2_12 24 vCmvCgeslasl 35
                                      vC+ Cge l+s 
  gi|330508272|ref|YP_004384700.1| 40 VCLRCGERLYSQ 51
                                      8********986 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0023       3.7       3      18 ..       8      23 ..       6      26 .. 0.90
   2 ?   -2.1   0.0       2.6   4.2e+03      20      23 ..      34      37 ..      34      39 .. 0.76
   3 ?    4.7   0.1      0.02        33       4      15 ..      41      52 ..      40      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0023
                            zf-ACC  3 KCpsCgemlykkeLer 18
                                      KCp Cg  l  k++e+
  gi|330508272|ref|YP_004384700.1|  8 KCPVCGGDLIEKQVEK 23
                                      9*******99999997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                            zf-ACC 20 lyVC 23
                                      l+VC
  gi|330508272|ref|YP_004384700.1| 34 LKVC 37
                                      6899 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.02
                            zf-ACC  4 CpsCgemlykke 15
                                      C +Cge ly +e
  gi|330508272|ref|YP_004384700.1| 41 CLRCGERLYSQE 52
                                      889******988 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00053      0.86      25      39 ..       5      20 ..       1      21 [. 0.76
   2 ?    1.9   0.4      0.15   2.5e+02       8      14 ..      41      47 ..      32      56 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00053
                       Zn-ribbon_8 25 pltaCPeCgs.evrrv 39
                                      p ++CP Cg+   +++
  gi|330508272|ref|YP_004384700.1|  5 PFEKCPVCGGdLIEKQ 20
                                      5678******777776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.15
                       Zn-ribbon_8  8 CeeCghe 14
                                      C +Cg++
  gi|330508272|ref|YP_004384700.1| 41 CLRCGER 47
                                      5666643 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0026       4.2      23      33 ..       8      18 ..       6      20 .. 0.87
   2 ?    4.4   0.2     0.023        37      22      32 ..      39      49 ..      36      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0026
                                      B-TTT--.-B- CS
                           ADK_lid 23 lCDkCGepLvq 33
                                      +C +CG++L+ 
  gi|330508272|ref|YP_004384700.1|  8 KCPVCGGDLIE 18
                                      8********95 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.023
                                      TB-TTT--.-B CS
                           ADK_lid 22 glCDkCGepLv 32
                                       +C  CGe L+
  gi|330508272|ref|YP_004384700.1| 39 EVCLRCGERLY 49
                                      58999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1125  (0.0627475); expected 358.6 (0.02)
Passed bias filter:                      734  (0.0409393); 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):              11  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 634.06
//
Query:       gi|330508273|ref|YP_004384701.1|  [L=109]
Description: hypothetical protein MCON_2426 [Methanosaeta concilii GP6]
Scores for complete 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-10   39.5   0.0    1.3e-09   38.3   0.0    1.6  2  DUF4258   Domain of unknown function (DUF4258)


Domain annotation for each model (and alignments):
>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.25   4.4e+03      16      26 ..       9      19 ..       8      21 .. 0.79
   2 !   38.3   0.0   7.4e-14   1.3e-09       1      63 []      23      95 ..      23      95 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.25
                           DUF4258 16 eedieevlenG 26
                                       +di+e+++ G
  gi|330508273|ref|YP_004384701.1|  9 LADILEAIQLG 19
                                      589**999866 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 7.4e-14
                           DUF4258  1 fsaHArermaeRgIseedieevlenGeiieeys........lvlgktsegrplhvvvapdedpv..vviTvyr 63
                                      +++HA e+  +++++ ++i  + ++G +ieey         l++g+t  g+p+h v+a+ e +   v+iTvyr
  gi|330508273|ref|YP_004384701.1| 23 ITDHAYEEANADELKFDEIYFSALHGVVIEEYAddspypsvLIFGQTFAGDPVHSVWAYSELNGwaVLITVYR 95
                                      79***********************************************************9989*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 845.58
//
Query:       gi|330508274|ref|YP_004384702.1|  [L=381]
Description: hypothetical protein MCON_2427 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.5    9.5   6.3         13    6.4   4.8    2.8  2  CrtC      CrtC N-terminal lipocalin domain


Domain annotation for each model (and alignments):
>> CrtC  CrtC N-terminal lipocalin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.8   0.00072        13       2     164 ..      68     224 ..      67     225 .. 0.57
   2 ?   -1.0   0.0      0.14   2.5e+03      94     107 ..     305     318 ..     268     372 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00072
                                       EEEEEEEEEE-TT--EEEEEEEEEEE----S.SS--EEEEEEEEEE-TTTSS-EEEEEEEEESS-TTTEEE-S.SEE CS
                              CrtC   2 EwWYltGnLedeegreyGfqltffrsalepaawateqlymahaavtdveagkflseervargglglagaeekp.fkv 77 
                                       EwWY++G+  d   ++  f+ltf+ s  ++    + q +  ++ +   ++g+       ++ g+g  g +++p f++
  gi|330508274|ref|YP_004384702.1|  68 EWWYFNGRDGD---TH--FMLTFLLSDPDN--LTAYQRIQVQVILL--QNGQIPILGSHQSRGFG--GDRNSPmFDI 133
                                       78888876422...34..777777733333..44444444444444..56665554444444344..5555565776 PP

                                       EETTEEEEE.TS...-EEEE....EE-SSEEEEEEEE--S--EE-TBTTEEE-SSSTT-EEEEEEEEEEEEEEEEEE CS
                              CrtC  78 rlddWqlks.ssellparlr....asaegfsldLtlsstkppvlqgdnGysrkgaepeqasyYySqprlavkGtltl 149
                                         + +   + +    ++r +    a++e f+ dL ++++  p    +  + + ++   ++ +Y  +p  +v+G++t+
  gi|330508274|ref|YP_004384702.1| 134 DKNGFYSDQeG--RIHIRGEvedeATSELFRWDLVYEAAADPWYAIPTQTKTGQSGWMKWLVY--MPSANVTGSFTI 206
                                       66665554431..22222222222445677778888888777776443333333233344455..9**********9 PP

                                       ...EEEEEEEEEEEEEEE CS
                              CrtC 150 ...kvsVtGeaWlDhews 164
                                          +v++ G+ + Dh w+
  gi|330508274|ref|YP_004384702.1| 207 gnrTVDIDGTGYHDHIWG 224
                                       999999***********7 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.14
                                       EEEEE-SSEEEEEE CS
                              CrtC  94 rlrasaegfsldLt 107
                                       +++a+++++sl+L 
  gi|330508274|ref|YP_004384702.1| 305 NISADNGDWSLELA 318
                                       33344445555332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2853.01
//
Query:       gi|330508275|ref|YP_004384703.1|  [L=133]
Description: hypothetical protein MCON_2429 [Methanosaeta concilii GP6]
Scores for complete 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-40  136.3   0.9    7.5e-40  136.1   0.9    1.0  1  LDcluster4       SLOG cluster4 family
    1.9e-10   40.9   0.0    2.9e-10   40.3   0.0    1.3  1  Lysine_decarbox  Possible lysine decarboxylase
    0.00039   19.7   1.9      0.017   14.4   0.9    2.0  2  DNA_processg_A   DNA recombination-mediator protein A


Domain annotation for each model (and alignments):
>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.1   0.9   1.3e-43   7.5e-40      21     141 ..       1     117 [.       1     127 [. 0.91

  Alignments for each domain:
  == domain 1  score: 136.1 bits;  conditional E-value: 1.3e-43
                        LDcluster4  21 laeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdiiiyTGlglagRnlilvlss 97 
                                       +aeelGrl+A eg++l++Gg +Gvmeaa+kGa e gG++vGilp+  +++++n+yv i ++TG+ +a Rn i+v+ss
  gi|330508275|ref|YP_004384703.1|   1 MAEELGRLLAAEGHTLICGGLGGVMEAACKGAAESGGTVVGILPG--DRKDANPYVGISVATGMSHA-RNAIIVRSS 74 
                                       59*******************************************..56668999**********99.********* PP

                        LDcluster4  98 dvviaiggrsGTlsEialaleegkpvivlkgtdellseiiekke 141
                                       d+via++g++GTlsEialal+ +k vi l  ++++  ++ +k  
  gi|330508275|ref|YP_004384703.1|  75 DAVIALPGEYGTLSEIALALKMNKAVISLG-SWDIAGTLRAKDP 117
                                       *****************************9.7766666655554 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   4.8e-14   2.9e-10       1      74 [.      25      95 ..      25     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 4.8e-14
                                      HHHHHHHHHHTTS-EEEEEECCHHHHHCCTTT-SEEEEESSHHHHHHHHHHHESEEEE-S-SHHHHHHHHHHHH CS
                   Lysine_decarbox  1 meavakgaleaggrviGiipkillaeeapneevnelvivedmeeRkealveladafvilPGGiGTleElleilt 74
                                      mea+ kga+e+gg+v+Gi p     ++ +n++v+  v +   + R++ +v+ +da+++lPG +GTl E+  +l 
  gi|330508275|ref|YP_004384703.1| 25 MEAACKGAAESGGTVVGILPGD---RKDANPYVGISVATGMSHARNAIIVRSSDAVIALPGEYGTLSEIALALK 95
                                      9*****************6655...55678**************************************976665 PP

>> DNA_processg_A  DNA recombination-mediator protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.9   2.8e-06     0.017      61     125 ..       2      66 ..       1      70 [. 0.87
   2 !    6.1   0.1   0.00098       5.9     144     184 ..      64     102 ..      53     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-06
                    DNA_processg_A  61 akklakelaeagitivSGlAlGiDaaahraaleaggktvavlgtgldkiyPkenrklleeiaeeg 125
                                       a++l + la +g+t + G+  G+ +aa ++a e+gg+ v++l++  +   P    ++++ + + +
  gi|330508275|ref|YP_004384703.1|   2 AEELGRLLAAEGHTLICGGLGGVMEAACKGAAESGGTVVGILPGDRKDANPYVGISVATGMSHAR 66 
                                       7889999************************************9999998887777777766555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00098
                    DNA_processg_A 144 peRnriiaglseavlvveaaekSGalitaelAlelgrevfa 184
                                        +Rn ii+  s+av+ +  + + G+l  + lAl++++ v+ 
  gi|330508275|ref|YP_004384703.1|  64 HARNAIIVRSSDAVIAL--PGEYGTLSEIALALKMNKAVIS 102
                                       68**********98765..6678**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1009.58
//
Query:       gi|330508276|ref|YP_004384704.1|  [L=147]
Description: hypothetical protein MCON_2431 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1258.16
//
Query:       gi|330508277|ref|YP_004384705.1|  [L=351]
Description: chromosome segregation and condensation protein ScpB [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-37  128.7   0.4    2.7e-37  127.9   0.1    1.5  2  SMC_ScpB  Segregation and condensation complex subunit ScpB
     0.0021   17.6   0.5       0.71    9.5   0.0    3.0  2  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.049   13.7   0.6        0.6   10.2   0.0    2.8  2  HTH_20    Helix-turn-helix domain
      0.062   13.2   1.3        1.8    8.5   0.4    3.1  2  MarR      MarR family
       0.21   11.3   1.9        1.1    8.9   0.2    3.0  4  GntR      Bacterial regulatory proteins, gntR family


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 !  127.9   0.1   7.5e-41   2.7e-37       2     153 ..       9     152 ..       8     156 .. 0.97
   2 ?   -3.5   0.0       1.9   6.9e+03      27      41 ..     257     271 ..     236     277 .. 0.55

  Alignments for each domain:
  == domain 1  score: 127.9 bits;  conditional E-value: 7.5e-41
                          SMC_ScpB   2 iiEAiLfvageplsleeLakilelskeeveealeeLkeeyeeedrglelvevaggyrlvtkpelaevvkklvkekkk 78 
                                       +iEA+Lf+ag+ ls +eLa+i +ls + +eea  +L++ey+++++g+e++++++gy++++++ la  v +++++   
  gi|330508277|ref|YP_004384705.1|   9 VIEAALFAAGRTLSPRELADISGLSLQMAEEAARDLAQEYASRSSGIEIKSIGDGYSMQVRSMLAGRVLSFAPK--- 82 
                                       79************************************************************************... PP

                          SMC_ScpB  79 trLsqaaletLaiIaykqpvtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglks 153
                                        +++   ++tLaiIaykqp+ ++e+ +iRG +s+++v++L +rgli+ ++    + r+ l++tT  F +yfg++s
  gi|330508277|ref|YP_004384705.1|  83 -EIEAPLIRTLAIIAYKQPIKQSELVQIRGNKSYEHVKELEKRGLINAVK----HSRTKLLTTTPGFADYFGITS 152
                                       .9************************************************....5699***************98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.9
                          SMC_ScpB  27 keeveealeeLkeey 41 
                                        +ev+++l++++++ 
  gi|330508277|ref|YP_004384705.1| 257 AAEVDRLLKRFRKRA 271
                                       555666666665554 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 !    9.5   0.0    0.0002      0.71      15      34 ..      17      37 ..      10      47 .. 0.77
   2 !    5.2   0.1    0.0043        16      36      47 ..     116     127 ..     115     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0002
                            HTH_24 15 npr.isqreLAerlglSpstv 34
                                       +r +s reLA+ +glS++  
  gi|330508277|ref|YP_004384705.1| 17 AGRtLSPRELADISGLSLQMA 37
                                      56669************9865 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0043
                            HTH_24  36 rrlkrLeeeGlI 47 
                                       +++k+Le+ GlI
  gi|330508277|ref|YP_004384705.1| 116 EHVKELEKRGLI 127
                                       69*********9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.21   7.5e+02       8      37 ..       3      33 ..       1      44 [. 0.80
   2 ?   10.2   0.0   0.00017       0.6      33      61 .]     106     134 ..     100     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.21
                                      S-HHHHHHHHHH.STCTTB-HHHHHHHHTS- CS
                            HTH_20  8 ahPvRrrilraL.araegltaselaerldls 37
                                      ++   + i++aL a ++ l++ ela+  +ls
  gi|330508277|ref|YP_004384705.1|  3 DSSAKAVIEAALfAAGRTLSPRELADISGLS 33
                                      5567778999999999999999999876655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00017
                                       HHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  33 rldlskntlsyHLrvLeeagLvevvregr 61 
                                       +++++ n  + H+++Le+ gL+  v+++r
  gi|330508277|ref|YP_004384705.1| 106 LVQIRGNKSYEHVKELEKRGLINAVKHSR 134
                                       557888999***************99986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.35   1.3e+03      18      43 ..      21      46 ..      17      47 .. 0.83
   2 ?    8.5   0.4   0.00051       1.8       4      48 ..      87     128 ..      84     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.35
                                      EEHHHHHHHHTS-HHHHHHHHHHHHH CS
                              MarR 18 lsvseLakklgvskstvtrvldrLek 43
                                      ls  eLa+ +g+s  ++ ++++ L +
  gi|330508277|ref|YP_004384705.1| 21 LSPRELADISGLSLQMAEEAARDLAQ 46
                                      6778*********9999888888876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00051
                                       HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR   4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                                       + +++L+i+++++p+++seL   +  +ks+  + +++Lek+Gli+
  gi|330508277|ref|YP_004384705.1|  87 PLIRTLAIIAYKQPIKQSELVQ-IRGNKSY--EHVKELEKRGLIN 128
                                       6688999999999999999985.4445554..8999999999997 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2   0.00031       1.1      13      51 ..      10      47 ..       7      50 .. 0.92
   2 ?   -2.9   0.0       1.6   5.6e+03      46      62 ..     119     135 ..     118     136 .. 0.79
   3 ?   -3.0   0.0       1.6   5.8e+03      41      56 ..     158     171 ..     155     177 .. 0.65
   4 ?   -1.5   0.0      0.57     2e+03      45      59 ..     199     213 ..     197     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00031
                                      HHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHT CS
                              GntR 13 IlsgelrpGdkLPsereLaaefgVsrttvReALrrLeae 51
                                      I +  +++G +L s reLa+  g s +   eA r L++e
  gi|330508277|ref|YP_004384705.1| 10 IEAALFAAGRTL-SPRELADISGLSLQMAEEAARDLAQE 47
                                      777889******.***********************997 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.6
                                       HHHHHTTSEEEETTCEE CS
                              GntR  46 rrLeaeglverrqgrGt 62 
                                       ++Le +gl+ + + + t
  gi|330508277|ref|YP_004384705.1| 119 KELEKRGLINAVKHSRT 135
                                       68999999998877665 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHTTSEEE CS
                              GntR  41 vReALrrLeaeglver 56 
                                       vR+AL  L+ ++lv +
  gi|330508277|ref|YP_004384705.1| 158 VRKAL--LQNKKLVGV 171
                                       67776..666666655 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.57
                                       HHHHHHTTSEEEETT CS
                              GntR  45 LrrLeaeglverrqg 59 
                                       L+rLe+ +l+++ +g
  gi|330508277|ref|YP_004384705.1| 199 LSRLEEIDLLIIAPG 213
                                       89********99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 2522.74
//
Query:       gi|330508278|ref|YP_004384706.1|  [L=1149]
Description: helicase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-19   67.3   0.0    2.7e-18   65.8   0.0    1.9  1  DUF3883        Domain of unknown function (DUF3883)
    9.1e-16   58.2   0.0    3.3e-15   56.4   0.0    2.1  1  Helicase_C     Helicase conserved C-terminal domain
    9.6e-16   57.4   0.0    2.1e-15   56.3   0.0    1.5  1  SNF2_N         SNF2 family N-terminal domain
      2e-11   44.2   0.2    5.6e-11   42.7   0.0    1.9  2  ResIII         Type III restriction enzyme, res subunit
    1.7e-07   31.2   0.0    3.6e-07   30.1   0.0    1.5  1  DEAD           DEAD/DEAH box helicase
    1.7e-05   25.2   0.0     0.0012   19.3   0.0    2.9  1  AAA            ATPase family associated with various cellular
    0.00028   20.3   0.0    0.00058   19.2   0.0    1.4  1  DUF2075        Uncharacterized conserved protein (DUF2075)
     0.0027   16.7   0.0     0.0099   14.8   0.0    1.8  1  AAA_34         P-loop containing NTP hydrolase pore-1
     0.0027   17.6   0.0      0.008   16.1   0.0    1.8  1  Helicase_RecD  Helicase
     0.0029   17.6   0.0     0.0062   16.5   0.0    1.5  1  Flavi_DEAD     Flavivirus DEAD domain
  ------ inclusion threshold ------
          9    7.2   5.8        9.1    7.2   0.4    3.1  2  Histone_HNS    H-NS histone family


Domain annotation for each model (and alignments):
>> DUF3883  Domain of unknown function (DUF3883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   1.6e-21   2.7e-18       2      91 ..    1027    1120 ..    1026    1121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 1.6e-21
                           DUF3883    2 Eklvlealkekekeegvewvnedve.dglgYDiesvd......kedgeerfIEVKttakgkkdfelsrnElefaq 69  
                                        E+++++a+ ++e+++g  w +e+ve d+ g+D+ s++      ++  e rfIEVK++a g  ++ l++nE+++a+
  gi|330508278|ref|YP_004384706.1| 1027 ERIAVQAVIAYEEARG--WKVESVEqDSRGFDLISRRphpedpQTAVEVRFIEVKGRA-GVGEIALTSNEYRTAE 1098
                                        99*************9..******9999********877665544555**********.9*************** PP

                           DUF3883   70 ekgdkYwlyrVfnagkepkvki 91  
                                        + +++Ywly+Vfn+ ++p+++ 
  gi|330508278|ref|YP_004384706.1| 1099 RLKNDYWLYVVFNCASKPEIHS 1120
                                        ******************9986 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 !   56.4   0.0     2e-18   3.3e-15       4     111 .]     478     603 ..     475     603 .. 0.83

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2e-18
                                       HHHHHHH....HHTTTTSEEEEEESSHHHHHHHHHH............HHHT.TSTEEEESTTSTHHHHHHHHHHHH CS
                        Helicase_C   4 eallell....kleeeggkilifvntidrlekvkll............lekk.gikvavlhgelpqnereeileqfn 63 
                                       ++l+e l     +   + k l+f++ +d+l   ++l            l+ + g++v+ +hg ++  +r+ + ++ n
  gi|330508278|ref|YP_004384706.1| 478 QRLKEVLkeqgVFADPKMKLLLFTEHKDTL---EYLagdgkdgrplgkLR-EwGLSVTQIHGGMKIGDRDTAGTRIN 550
                                       55555554444456678899**********...67766666666655333.36*****************9999999 PP

                                       .....TTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  64 .....kgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                            k++++v+ at +a++Gi+++ + ++in+d+p+n+ ++ qr+GR++R+g
  gi|330508278|ref|YP_004384706.1| 551 aerifKEDCQVMAATEAAGEGINLQFCWFMINYDIPWNPMRLEQRMGRIHRYG 603
                                       77777889*******************************************86 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 !   56.3   0.0   1.3e-18   2.1e-15      59     250 ..     125     301 ..     121     394 .. 0.73

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.3e-18
                                       EE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE--SSHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  59 iLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlvyggqkkm 135
                                       +LaD++G+GKT+++  li++++              l + +Liv+Pa+l  qW++e++   ++   +vl  +  +  
  gi|330508278|ref|YP_004384706.1| 125 LLADDPGAGKTIMAGLLIKELKIR-----------GLIKRILIVSPANLTFQWQREMQDKFKEH-FEVLRSDILR-- 187
                                       7******************55543...........34455********************9987.7788877743.. PP

                                       ----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH--......-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx RF
                            SNF2_N 136 kkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLs......ts 206
                                           +  ++ ++++ ++ +t+   +s        ++ l + +w+ v++DE+h++    +  ++++ +L       t+
  gi|330508278|ref|YP_004384706.1| 188 ---ANYGSNPWQEKNQI-VTSMPWVSIIE---DAKESLLRSHWDLVIVDEAHKMSAYSQDHKTMAYQLGealsdrTD 257
                                       ...34445556666665.57776666444...4679999***************9985444444444433333779* PP

                                       -EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 207 nrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpie 250
                                       + +++t+TP + + +++   l +L  +++ + ++ ++ + r  +
  gi|330508278|ref|YP_004384706.1| 258 HFLLMTATPHKGDPANFSLFLRLLDKDVYADIKSLEEAMRRHEA 301
                                       *******************************9998888777554 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 !   42.7   0.0   3.4e-14   5.6e-11       3     170 ..     103     267 ..     101     268 .. 0.76
   2 ?   -2.9   0.3       3.7     6e+03     118     145 ..     973    1003 ..     916    1006 .. 0.64

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 3.4e-14
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       ++ ++Q ea+ +   kl    + r+l++   G+GKT++a  li++l+  g ++++l++ p  +l+ q+++e+++ ++
  gi|330508278|ref|YP_004384706.1| 103 DPLPHQLEAVYDYFLKL---PRIRFLLADDPGAGKTIMAGLLIKELKIRGLIKRILIVSP-ANLTFQWQREMQDKFK 175
                                       56799999999999888...488*************************999877766655.68******99999999 PP

                                       G....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T......TT CS
                            ResIII  80 eaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk......sw 150
                                       e+++    ++   ++ +  +  ++k+ +vt+   ++ ++     ++e+llr++ d++i+DEaH+++a +      ++
  gi|330508278|ref|YP_004384706.1| 176 EHFEVLRSDILRANYGS--NPWQEKNQIVTSMPWVSIIE----DAKESLLRSHWDLVIVDEAHKMSAYSqdhktmAY 246
                                       99877444444444444..34666677778887777777....789********************98344455433 PP

                                       HHHHHT---..SEEEEEESS-S CS
                            ResIII 151 reilekfke..avllglTATpe 170
                                       + + e++++     l +TATp 
  gi|330508278|ref|YP_004384706.1| 247 Q-LGEALSDrtDHFLLMTATPH 267
                                       3.344443333677778***96 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.7
                                        H.............HHHTTT-SEEEEETGGGTT CS
                            ResIII  118 seee.....eeeseellrdrfdviiiDEaHrlg 145 
                                        +  +      e + + l++++++ i D  H+ +
  gi|330508278|ref|YP_004384706.1|  973 I--DdlnerLERRRKELKQEHNLSISDIQHHGR 1003
                                        3..123333455556666677788888888876 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   2.2e-10   3.6e-07      18     172 ..     125     270 ..     108     274 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.2e-10
                                       EEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.ST.SEEEEEETTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxx RF
                              DEAD  18 lvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.id.lrvlliiggvaardqls 92 
                                       l+a + G+GKT ++ + + +  ++  g  + ++liv+P   L+ q  ++++  +k+  + lr   i+    a+   +
  gi|330508278|ref|YP_004384706.1| 125 LLADDPGAGKTIMAGLLIKELKIR--GLIK-RILIVSPA-NLTFQWQREMQDKFKEhFEvLRSD-ILR---ANYGSN 193
                                       677788*******99988755543..5555.88888885.799999999987777524422222.222...222233 PP

                                       HHHTTCSEEEEEHHHHHHHH..HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  93 kldngvdivvgtpgrlddll..stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSA 167
                                         +++ +iv + p  +++++   +++l  s+  ++++DEa++++   +s++ ++++ ql ++ +d   +  +++++A
  gi|330508278|ref|YP_004384706.1| 194 PWQEKNQIVTSMP--WVSIIedAKESLLRSHWDLVIVDEAHKMSA--YSQDHKTMAYQLGEALSDRTDH--FLLMTA 264
                                       3345567777777..677674445667799*************98..8***********9999998855..****** PP

                                       SBS.HH CS
                                       xxx.xx RF
                              DEAD 168 Tlp.kd 172
                                       T++  d
  gi|330508278|ref|YP_004384706.1| 265 TPHkGD 270
                                       **9555 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   0.0   7.3e-07    0.0012       2     122 ..     125     275 ..     124     285 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.3e-07
                                       EEESSTTSSHHHHHHHHHHHHTHE............................EEEEETTTCSSS...........ST CS
                               AAA   2 llyGppGtGKTllakavakelgve............................fleisgsellsk...........yv 39 
                                       ll   pG GKT++a  ++kel+++                             +e+  s++l              +
  gi|330508278|ref|YP_004384706.1| 125 LLADDPGAGKTIMAGLLIKELKIRglikrilivspanltfqwqremqdkfkeHFEVLRSDIL-RanygsnpwqekNQ 200
                                       56668****************97766667665555655555555555555554444444444.14678887666677 PP

                                       THHHHHHHHHHHHHHHTS..TS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGG CS
                               AAA  40 gesekkirelfkeakeka..kp.silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpd 113
                                         +++    ++++ake+   ++   +++DE++++   +     +++++++ qL ++l++ ++      ++++t +p+
  gi|330508278|ref|YP_004384706.1| 201 IVTSMPWVSIIEDAKESLlrSHwDLVIVDEAHKMSAYS-----QDHKTMAYQLGEALSDRTD-----HFLLMTATPH 267
                                       77778888899999998899667***********6666.....9999*************99.....4777777777 PP

                                       GSTHHHHST CS
                               AAA 114 kldpallrg 122
                                       k dpa   +
  gi|330508278|ref|YP_004384706.1| 268 KGDPANF-S 275
                                       8787776.4 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.5e-07   0.00058       9     110 ..     129     242 ..     124     261 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.5e-07
                           DUF2075   9 vaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakke......ekkkkkeafeklssfinnlsef. 77 
                                       ++G+GKt+++  l+ el  + ++  + +l+v+ + +    +++++ k            ++++ + +   n+ +e+ 
  gi|330508278|ref|YP_004384706.1| 129 DPGAGKTIMAGLLIKEL--KIRGLIKRILIVSPANLTfQWQREMQDKFkehfevL----RSDILRANYGSNPWQEKn 199
                                       7****************..888888888888876655345555544443322330....333333333334444335 PP

                           DUF2075  78 ............kkaeekkeepkedvvivDEAhrlltksdqaekq 110
                                                   ++a+e+  + + d+vivDEAh++   s+   ++
  gi|330508278|ref|YP_004384706.1| 200 qivtsmpwvsiiEDAKESLLRSHWDLVIVDEAHKMSAYSQD--HK 242
                                       5566666679999**********************993333..22 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 !   14.8   0.0   6.1e-06    0.0099      57     201 ..     118     251 ..      80     280 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.1e-06
                            AAA_34  57 dgkRaGfllGDgaGvGkgrqiagiilenllqgrkkavwvsvsedLkeDaerDlkdigaseievvalnklkegkkike 133
                                       +  R  fll D+ G Gk+   + +i e  ++g  k + + + ++L+   +r+++d  +++ ev + + l+++   + 
  gi|330508278|ref|YP_004384706.1| 118 KLPRIRFLLADDPGAGKTIMAGLLIKELKIRGLIKRILIVSPANLTFQWQREMQDKFKEHFEVLRSDILRANYGSNP 194
                                       445899*************99999*******************************9999999988777766544433 PP

                            AAA_34 134 seelkeGvlFvtYstliseskkkkksrleqlveWlgedfdGvivfDEchkaknlakseekkatktgka 201
                                        +e ++ v  + + + i+++k+   s        l +++d +++ DE+hk+    +++++ a + g+a
  gi|330508278|ref|YP_004384706.1| 195 WQEKNQIVTSMPWVSIIEDAKE---SL-------LRSHWD-LVIVDEAHKMSAYSQDHKTMAYQLGEA 251
                                       4444444555555555555444...22.......345666.777789999888888777766666655 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.9e-06     0.008       4     101 ..     128     233 ..     125     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.9e-06
                     Helicase_RecD   4 AdRGRGKSaalGlalaaliaegk.snilvtapskenvktlfeflakglealglke..........eekkkkaekael 69 
                                        d+G GK+ ++Gl++++l  +g  ++il+++p + + +   e+  k  e+ ++ +          ++ ++   k+++
  gi|330508278|ref|YP_004384706.1| 128 DDPGAGKTIMAGLLIKELKIRGLiKRILIVSPANLTFQWQREMQDKFKEHFEVLRsdilranygsNPWQE---KNQI 201
                                       589***************9999989*******99888776666665555555555556766644333333...3335 PP

                     Helicase_RecD  70 rvrkqrieyiapdellklkeqadllvvDEAAa 101
                                        ++   +  i+  +   l++++dl++vDEA  
  gi|330508278|ref|YP_004384706.1| 202 VTSMPWVSIIEDAKESLLRSHWDLVIVDEAHK 233
                                       5556666666666666666788*******965 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.8e-06    0.0062      11     137 ..     128     267 ..     121     275 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.8e-06
                                       --TTS-TTTTHHHHHHHHHHHTT..--EEEEESSHHHH...HHHHHHTTTS-EEE--------......-----SEE CS
                        Flavi_DEAD  11 lhPGaGktrkvlpelvkeaierr..lrtlvLaPtrvvl...aemeealkglevryktsavkee......ktgrelvd 76 
                                         PGaGkt      l+ke   r   +r l+++P+       +em++ +k+     +++ ++++      + ++++v+
  gi|330508278|ref|YP_004384706.1| 128 DDPGAGKTIMA-GLLIKELKIRGliKRILIVSPANLTFqwqREMQDKFKEHFEVLRSDILRANygsnpwQEKNQIVT 203
                                       56999998543.23344433333225788899988775222588888776533333333222211111278899*** PP

                                       EEEHHHHHHHHHHT------SEEEEETTT--SHHHHHHHHHHHHHHH...TTS-EEEEEESS-T CS
                        Flavi_DEAD  77 vmchatftkrllspvrkknyeliimDeahflDPasiaarGyletkae...egeaalilltatPP 137
                                        m    +++   ++  +  ++l+i+Deah +   s   + ++ ++ e    ++  ++l+tatP 
  gi|330508278|ref|YP_004384706.1| 204 SMPWVSIIEDAKESLLRSHWDLVIVDEAHKMSAYSQDHKTMAYQLGEalsDRTDHFLLMTATPH 267
                                       ********************************9999998887765441115667899*****95 PP

>> Histone_HNS  H-NS histone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.4    0.0056       9.1       2      38 ..     451     490 ..     450     518 .. 0.85
   2 ?    1.5   0.1      0.33   5.3e+02      13      55 ..     946     989 ..     934    1010 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0056
                                       XXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXX-- CS
                       Histone_HNS   2 Lkalieelekqeea...leaeerkealaeirelaaeyGlt 38 
                                       Lk++i +l+k +++   le++e + +l++++e+++e+G+ 
  gi|330508278|ref|YP_004384706.1| 451 LKEEIFQLDKLIDQarlLEQREVESKLQRLKEVLKEQGVF 490
                                       677788888888887768********************75 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.33
                                       XXXX.XXXXXXXXXXXXXXXXXXXX----SSS-----EEEEE.. CS
                       Histone_HNS  13 eeal.eaeerkealaeirelaaeyGltleelaaeakkakkkkak 55 
                                       +++l e++er e  + i + +++ +  +++l +  ++++k+ ++
  gi|330508278|ref|YP_004384706.1| 946 LSELmEKRERGETAQPIAASIKSTDDRIDDLNERLERRRKELKQ 989
                                       55633889999999999999999999999997776666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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):              11  [number of targets reported over threshold]
# CPU time: 0.93u 0.33s 00:00:01.26 Elapsed: 00:00:00.51
# Mc/sec: 6836.38
//
Query:       gi|330508279|ref|YP_004384707.1|  [L=191]
Description: hypothetical protein MCON_2434 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-11   43.0   0.0    5.1e-11   42.1   0.0    1.4  1  UPF0175   Uncharacterised protein family (UPF0175)
  ------ inclusion threshold ------
       0.14   12.2   0.0        0.3   11.2   0.0    1.5  1  HemN_C    HemN C-terminal domain
       0.14   12.2   0.1       0.46   10.5   0.0    1.9  2  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   8.5e-15   5.1e-11      12      62 ..     141     190 ..     133     191 .] 0.92

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 8.5e-15
                           UPF0175  12 teeelerelrialAvklYeegrlSlgkAaelaglsrveflelLarrgipli 62 
                                       +++el+ + r+  A++l++++++S++kAae+agl+ vef  lL++++i ++
  gi|330508279|ref|YP_004384707.1| 141 KWDELKPR-RKDFAISLFRRNKVSFSKAAEIAGLTPVEFDILLKNKNIRWR 190
                                       68999999.99*************************************986 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     5e-05       0.3      29      65 ..      58      93 ..      50      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5e-05
                            HemN_C 29 rfgldleellaaaleklqeqGLLeldggrlrltprGr 65
                                      +fg  ++e+l ++le l++ G+++  g+++rlt+ G+
  gi|330508279|ref|YP_004384707.1| 58 LFGP-YSETLDNVLESLIRLGYVQTIGSNFRLTKSGL 93
                                      6777.79999************************995 PP

>> HTH_45  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   7.8e-05      0.46      35      70 ..      65     100 ..      62     107 .. 0.89
   2 ?   -1.6   0.0      0.46   2.8e+03      35      49 ..     111     125 ..     109     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.8e-05
                            HTH_45  35 llnkYLdmLvekglikkskekYvlTekGlelleklk 70 
                                       +l++ L+ L+  g++++ +++++lT+ Gl+ +++lk
  gi|330508279|ref|YP_004384707.1|  65 TLDNVLESLIRLGYVQTIGSNFRLTKSGLNAYSSLK 100
                                       67889*************************999887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.46
                            HTH_45  35 llnkYLdmLvekgli 49 
                                        ++++L+ L +++++
  gi|330508279|ref|YP_004384707.1| 111 DFKRFLNDLNDEEVL 125
                                       588999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1369.57
//
Query:       gi|330508280|ref|YP_004384708.1|  [L=193]
Description: hypothetical protein MCON_2435 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-05   23.8   0.0    6.3e-05   22.7   0.0    1.6  1  DUF3368   Domain of unknown function (DUF3368)
  ------ inclusion threshold ------
      0.039   14.0   0.5      0.076   13.0   0.5    1.5  1  RSV_NS2   Respiratory synctial virus non-structural protein N


Domain annotation for each model (and alignments):
>> DUF3368  Domain of unknown function (DUF3368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   7.1e-09   6.3e-05       1      41 [.     145     187 ..     145     188 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.1e-09
                           DUF3368   1 vtGTLGiLllAKqrGlIps..vkplldaLiqaGfrispklyae 41 
                                       +tGT+G++ ++ q+G  ++  +k ++ +++++ fris+kl+ e
  gi|330508280|ref|YP_004384708.1| 145 FTGTIGLIKRLCQKGWFSEddIKLIISDIKNSTFRISDKLIGE 187
                                       69**************************************965 PP

>> RSV_NS2  Respiratory synctial virus non-structural protein NS2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   8.5e-06     0.076      34      85 ..      30      81 ..       4      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.5e-06
                           RSV_NS2 34 iithkfiylinnecivrklderqatftflvnye.mkllhkvgstkykkyteyn 85
                                      +   ++  l+  +c+ r+  er +  t+ +ny+ +++++k g  ky +  +y 
  gi|330508280|ref|YP_004384708.1| 30 VCRNEY-ILVTTDCVQRETSERFSRETIDINYKnINVFRKTGDKKYDQALDYL 81
                                      333444.478999*******************638999********9988885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1580.67
//
Query:       gi|330508281|ref|YP_004384709.1|  [L=357]
Description: hypothetical protein MCON_2436 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2818.64
//
Query:       gi|330508282|ref|YP_004384710.1|  [L=987]
Description: hypothetical protein MCON_2437 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-23   80.5   1.9    2.2e-22   79.0   1.9    1.8  1  DUF1156          Protein of unknown function (DUF1156)
     0.0018   18.0   0.0     0.0062   16.2   0.0    1.7  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
      0.009   15.7   0.0       0.81    9.3   0.0    2.7  2  UPF0020          Putative RNA methylase family UPF0020


Domain annotation for each model (and alignments):
>> DUF1156  Protein of unknown function (DUF1156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   1.9   3.6e-26   2.2e-22       2      53 ..      16      67 ..      15      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 3.6e-26
                           DUF1156  2 lPldkinaesakEksirhghlstLhlWWaRrPLaaaRAvifaqLvpdpssel 53
                                      lP++ki+a + +Ek irhgh+stLh+WWaRrPLaa+RAvi a+L pdp+ e 
  gi|330508282|ref|YP_004384710.1| 16 LPIKKISAHARREKPIRHGHISTLHIWWARRPLAACRAVICAALWPDPAQED 67
                                      8**********************************************98744 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     1e-06    0.0062      24      64 ..     147     187 ..     140     219 .. 0.84
   2 ?   -1.7   0.0      0.32   1.9e+03     155     188 ..     513     546 ..     480     557 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-06
                                       EEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCH CS
                   MethyltransfD12  24 fvepFaGggaVffeakkqgkkvlinDinedlinlykalikn 64 
                                       +v+pFaGgg++ +ea++ g ++ ++D+n+  + l+k +++ 
  gi|330508282|ref|YP_004384710.1| 147 VVDPFAGGGSIPLEALRVGADAFASDLNPVAVLLNKVVLEY 187
                                       79****************************99999966654 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.32
                                       HHHHHCCEEEC-CHHHHTT--TTE.EEEE--S-T CS
                   MethyltransfD12 155 eklknakiecgdfdavllkakieddivYlDPPYn 188
                                        + +n  +++++  +  +  +++++++  DPPY 
  gi|330508282|ref|YP_004384710.1| 513 INCNNSGHTNCNSVTPCQLIDDSAQAFVTDPPYY 546
                                       4455555555555555555568888888999996 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00014      0.81      32      54 ..     147     169 ..     126     197 .. 0.82
   2 ?    3.2   0.0      0.01        63     113     157 ..     529     571 ..     504     584 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00014
                                       EEETT-TTSHHHHHHHHHHTT-- CS
                           UPF0020  32 llDPmCGsGtilIEaallgania 54 
                                        +DP+ G+G+i++Ea  +ga++ 
  gi|330508282|ref|YP_004384710.1| 147 VVDPFAGGGSIPLEALRVGADAF 169
                                       47*************87777665 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.01
                                       GG--STTS---EEEE----------HHHHHHHHHHHHHHHHHH-T CS
                           UPF0020 113 akLrlkegevdvivtnpPYGerlgskkalekLYseflrelkrvlr 157
                                       ++L   +++  + vt+pPY +++  +   + +Y  + r l  v++
  gi|330508282|ref|YP_004384710.1| 529 CQLI--DDSAQAFVTDPPYYDAIAYATLSDFFYVWLKRMLRDVFS 571
                                       3444..5688999*******9998877666666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (987 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.41
# Mc/sec: 7186.70
//
Query:       gi|330508283|ref|YP_004384711.1|  [L=138]
Description: hypothetical protein MCON_2438 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.5   0.0      0.025   14.3   0.0    1.1  1  DUF4423   Domain of unknown function (DUF4423)
       0.11   12.6   0.2         17    5.5   0.0    2.5  3  HemN_C    HemN C-terminal domain
       0.15   11.7   0.1       0.24   11.1   0.1    1.3  1  GntR      Bacterial regulatory proteins, gntR family
       0.16   12.0   0.0       0.21   11.6   0.0    1.1  1  DUF758    Domain of unknown function (DUF758)


Domain annotation for each model (and alignments):
>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.6e-06     0.025       6      78 ..       4      76 ..       1     102 [. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.6e-06
                           DUF4423  6 kirkLdeeefe.yfssWyypvirellplkdf.kadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrq 78
                                      +i+++d + f+ +f + + + i + + + +f    p+ l++     +sa  ++kal++L++lgll ++  ++ ++
  gi|330508283|ref|YP_004384711.1|  4 EIEEIDMQHFAgLFGDSHLSWIIAQIVADPFqVYRPKDLEELAE--ASAPSTRKALRILTRLGLLIRNDTDRQHP 76
                                      67777888888777777666666666666664578999999999..******************99998865544 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0042        19      19      34 ..       6      33 ..       5      48 .. 0.69
   2 ?    5.5   0.0    0.0038        17      25      55 ..      41      70 ..      38      73 .. 0.81
   3 ?   -3.5   0.0       2.5   1.1e+04      27      40 ..     113     126 ..     112     129 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0042
                            HemN_C 19 eGldlaafeqrfgld............l 34
                                      e++d+++f+ +fg +             
  gi|330508283|ref|YP_004384711.1|  6 EEIDMQHFAGLFGDShlswiiaqivadP 33
                                      79************97666655544442 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0038
                            HemN_C 25 afeqrfgldleellaaaleklqeqGLLeldg 55
                                      ++e++ + + +++ ++al+ l++ GLL  ++
  gi|330508283|ref|YP_004384711.1| 41 DLEELAEAS-APSTRKALRILTRLGLLIRND 70
                                      667777777.777899***********8877 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.5
                            HemN_C  27 eqrfgldleellaa 40 
                                       ++++  dl++++++
  gi|330508283|ref|YP_004384711.1| 113 AEYYDSDLRDRYES 126
                                       67777888888765 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   5.4e-05      0.24      29      58 ..      41      70 ..      38      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.4e-05
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              GntR 29 eLaaefgVsrttvReALrrLeaeglverrq 58
                                      +L +  + s+++ R+ALr L++ gl++r++
  gi|330508283|ref|YP_004384711.1| 41 DLEELAEASAPSTRKALRILTRLGLLIRND 70
                                      5677778999****************9975 PP

>> DUF758  Domain of unknown function (DUF758)
   #    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      57     119 ..      53     114 ..      40     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                            DUF758  57 vKniiKvvvKvgvllrnkqlsaeelallekfrkklrtlamtlisfyevdftfdkavLadlLke 119
                                       ++++++++ ++g+l+rn++ ++   ++++ + +k ++la+tl+s+  vd ++  + + d + e
  gi|330508283|ref|YP_004384711.1|  53 TRKALRILTRLGLLIRNDTDRQHPSYKAN-LDSKKKHLALTLLSYSVVDDSIGTDCMDDPIAE 114
                                       67899**************9999999998.99999**************99999999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1049.40
//
Query:       gi|330508284|ref|YP_004384712.1|  [L=1047]
Description: hypothetical protein MCON_2440 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-22   76.7   0.0    6.6e-18   63.9   0.0    3.1  3  DUF499          Protein of unknown function (DUF499)
  ------ inclusion threshold ------
      0.033   14.1   0.1       0.15   12.1   0.0    2.1  3  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> DUF499  Protein of unknown function (DUF499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   7.3e-22   6.6e-18      51     272 ..     156     385 ..     150     466 .. 0.81
   2 !    5.9   0.0   0.00025       2.3     465     693 ..     549     769 ..     527     792 .. 0.72
   3 !    3.1   0.0    0.0018        16     788     839 ..     799     848 ..     790     857 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 7.3e-22
                            DUF499  51 kTlWGylayeL...grYeiveksDrnetaPdieelrkllqgek.vliLiDEIadyvdnllrSgledkkdYaeevsaF 123
                                       kT WG +a++L     +++ve++Dr+  aP  +++r+ l   +  liL+DE+++yv     Sgl d+      + +F
  gi|330508284|ref|YP_004384712.1| 156 KTPWGEIAFQLsgtQGFDLVEEHDRQRIAPGGDVIRSFLPKDRpCLILMDELMNYVSRNRDSGLSDQ------LYNF 226
                                       899********433369**********************88888************97777766655......69** PP

                            DUF499 124 ldnLakAle.vsevalvitipaekreGeakaeeeYkrevvrailealrrvageiykPvrrneelvevlkkRiFsevd 199
                                       ++nL++  +  ++v+lv++ip  + e +      Y     ++  + + + +  ++  ++++ e  +++++R+F+   
  gi|330508284|ref|YP_004384712.1| 227 IQNLTNVASgEDKVVLVVSIPGSQMEMNEADFSDY-----NSFKKIMDKHGKAVM--ISAEAETSQIIRRRLFEWSP 296
                                       ******9998999********97777766666777.....455555556655555..6689************9866 PP

                            DUF499 200 edekkkelkkl................ret.aevreifgdesdlekeleetYPFHPeylevLreiierl.dlqrTRd 258
                                       e++  +    l                     +v   f    + e+  e +YPFHP+ l+v ++  + l   qrTR 
  gi|330508284|ref|YP_004384712.1| 297 EEISPDGTILLgneakktckayatwvkA-HrNQVPGWFPVD-HAEEMFEAAYPFHPMVLSVFETKWQALpRFQRTRG 371
                                       6666555555555666666666655421.213333334322.23455566*******************9******* PP

                            DUF499 259 lirItrivvrklld 272
                                       ++r+  + v k+ +
  gi|330508284|ref|YP_004384712.1| 372 ILRLLALWVSKVYQ 385
                                       ***99888877654 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.00025
                            DUF499 465 vevFdkkavivlkyaaeipkEllDnkeykLvvlvkkdvsk.....eeleklifkegggeRtyaNtvvvvapvkekle 536
                                        +vF++ ++i   +  e+  +++D++ + L+vl  +         e +e + + +g+++Rty+  ++   + +++  
  gi|330508284|ref|YP_004384712.1| 549 FRVFNEGNIIKPVFFPENSSDIPDTPALTLIVLSPDHRRPdsrtiELIESMTKDHGASSRTYKSALI--WSLVDNDA 623
                                       5899999***88899999***************8654221111226678888888********9765..56666666 PP

                            DUF499 537 sllellarlvAaeeikeelrelygeYakevlkiqknkveskkekaledllnqilslfrkVaYpvlgkereeveevea 613
                                       sl        A e+i+ e ++l       + + q+ +v++k+ ka+ dl + + ++++  a   + +    ++ +  
  gi|330508284|ref|YP_004384712.1| 624 SLTSEARNALAWEKIHFESEQLH------LNERQNREVNEKIGKAKRDLKEAVWRSYKNLALLGKDNRIYLMDLGLI 694
                                       67677777889999987755554......577788889999999999999999999999988744444334555544 PP

                            DUF499 614 teS.dksivekVesaLkekekiveeldfeelkdilkdnlgidilpg.rkikvgelinviltnpkaP.mirekaliea 687
                                         S  ++iv++    Lk+k+ i+ ++      ++l +  ++   p    ++   +++ + + p  P +++++a++ea
  gi|330508284|ref|YP_004384712.1| 695 HSSaARTIVDLYLLQLKQKDIITSSISP----NFLVK--NWP--PAfSIWSTRSVRDAFFASPLYPrLLNQQAVKEA 763
                                       4332577888877888888887776653....34444..233..555566666777777777777645667777777 PP

                            DUF499 688 ikeavk 693
                                       i ++v+
  gi|330508284|ref|YP_004384712.1| 764 ISKGVS 769
                                       777776 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.0018
                            DUF499 788 kvlrelliekrEeilksefelkVkrrsvelkpgekveveveiepikdyeeei 839
                                       ++ +e++i k+  +  +  ++ V ++++ +kpg++v++  ++++++d  +e+
  gi|330508284|ref|YP_004384712.1| 799 EISEEWFIAKEPPKRSGPCTIVVTPEQISIKPGDEVQF--SAKVMNDRGQEV 848
                                       67899*********9999****************9877..566777776666 PP

>> Ribosomal_S24e  Ribosomal protein S24e
   #    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      27      53 ..      73      99 ..      63     103 .. 0.88
   2 ?   -2.8   0.0      0.73   6.6e+03       8      21 ..     531     544 ..     527     547 .. 0.80
   3 ?   -4.1   0.0       1.8   1.6e+04      31      50 ..     903     922 ..     902     924 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                                      S-CTTEEEEEEEE-SSSSEEEEEEEEE CS
                    Ribosomal_S24e 27 vdpdlvvvfgfrthfGggkttGfakiY 53
                                      ++ ++  vf++ t+fGggkt++  + Y
  gi|330508284|ref|YP_004384712.1| 73 IKTETSAVFNMATQFGGGKTHALTLLY 99
                                      5778899**************999988 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.73
                                       SS-S--HHHHHHHH CS
                    Ribosomal_S24e   8 gkatpskteirekl 21 
                                       +ka ++k+ei e l
  gi|330508284|ref|YP_004384712.1| 531 RKASVPKQEIDECL 544
                                       599*******9866 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 1.8
                                       TEEEEEEEE-SSSSEEEEEE CS
                    Ribosomal_S24e  31 lvvvfgfrthfGggkttGfa 50 
                                        +vv   + h G g+t+ f+
  gi|330508284|ref|YP_004384712.1| 903 RIVVSPQDAHIGPGRTQTFV 922
                                       689999999******99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1047 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.81u 0.31s 00:00:01.12 Elapsed: 00:00:00.46
# Mc/sec: 6847.90
//
Query:       gi|330508285|ref|YP_004384713.1|  [L=232]
Description: chromosome segregation and condensation protein ScpA [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-18   66.0   0.3    1.8e-16   60.8   0.3    2.6  1  SMC_ScpA        Segregation and condensation protein ScpA
  ------ inclusion threshold ------
      0.057   14.1   0.1      0.078   13.7   0.1    1.2  1  NAM-associated  No apical meristem-associated C-terminal doma
       0.19   11.3   1.9       0.16   11.6   0.5    1.5  2  Snf7            Snf7


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 !   60.8   0.3     3e-20   1.8e-16       1     239 [.      25     229 ..      25     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 3e-20
                                       HHHHHHHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXXXXXXXXXXXXXXXXX CS
                          SMC_ScpA   1 LiiakeldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqveeeedeeleleelrdk 77 
                                       L+ ++ +d++d+++a  t++fl+yi  l +k +l + +  l+ as l+++K++s+   ++v++ee +e elee+ ++
  gi|330508285|ref|YP_004384713.1|  25 LARRGDIDPWDIDIARTTEKFLQYIDSL-EKRDLRIPARTLLYASILLRMKSDSMEGQKEVADEE-PEPELEEVGEE 99 
                                       567899**********************.**********************************55.5569*****99 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          SMC_ScpA  78 LiarLleYrkykeeaklfkeleaerlksfskarsdleefikevee.vavkieksvfklieafnkllkrakivalaek 153
                                         +              + +     ++  +k++++lee+i+e+++ ++v+  k       a   +  r+    ++ek
  gi|330508285|ref|YP_004384713.1| 100 VWEEE--------RESTLPRPP---VRRRTKRPVTLEELISELKKaEMVGRRK-------A---MRDRW--PSTEEK 153
                                       86642........223333333...44446999**********9944444322.......2...33466..455664 PP

                                       XX...HHHHHHHHHHHH...............HHH...TS-EEGGGSSTT...--HHHHHHHHHHHHHHHHTT-EEE CS
                          SMC_ScpA 154 qiseleisieeqleellaqleqflqarlkevLldl...rswvdlseLladnkledkkelvgvFlAlLeLiknqaval 227
                                           l++s++e  ee +     fl      +L d+   ++ + + ++         ++ v+ ++ lL + + + v l
  gi|330508285|ref|YP_004384713.1| 154 ---ALDLSHDEGIEERIR----FLGP----ILDDMfmeKKTITFLDINSR--DGLNEDGVTNYVSLLFMAQRKQVWL 217
                                       ...7899*******9994....7654....55555543468888887776..677899******************* PP

                                       EESSTTS-EEEE CS
                          SMC_ScpA 228 eQeeflddLqvs 239
                                       eQee ++dL+v+
  gi|330508285|ref|YP_004384713.1| 218 EQEEIFGDLFVK 229
                                       *********995 PP

>> NAM-associated  No apical meristem-associated C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.3e-05     0.078      15     126 ..      42     155 ..      36     191 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                    NAM-associated  15 epKWkdqydelkkk...............rkpkssassspatsssestdeedssesssesseesaadsestsssrlk 76 
                                        +K+ ++ d+l+k+                + ks++++++++  +        +e+++e +e+++   e++++s+l+
  gi|330508285|ref|YP_004384713.1|  42 TEKFLQYIDSLEKRdlripartllyasilLRMKSDSMEGQKEVAD--------EEPEPELEEVGEEVWEEERESTLP 110
                                       566766666666666766666666665555555555555555555........6666777788888888999999** PP

                    NAM-associated  77 RPiGkkkaKekrkeaskdeealeklasaqkkiakk..skekkeeae.leekkl 126
                                       RP  ++++K+  +         e+l s+ kk +++  +k+++ ++  +eek l
  gi|330508285|ref|YP_004384713.1| 111 RPPVRRRTKRPVTL--------EELISELKKAEMVgrRKAMRDRWPsTEEKAL 155
                                       *********99994........4444444444444213333322333344444 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   2.6e-05      0.16     128     169 ..      75     113 ..      64     117 .. 0.86
   2 ?   -3.7   0.0       1.3   7.9e+03     147     158 ..     125     136 ..     123     146 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.6e-05
                                       HHHHTT-GGTTHHHHHHHHHHHHHHHHHCSH.HHHHHHHTXX CS
                              Snf7 128 srslddadeedEeeleaeLdaLeqelgdeelldesvklpevP 169
                                       s+s++  +e+ +ee e eL+++ +e+++ee    + +lp  P
  gi|330508285|ref|YP_004384713.1|  75 SDSMEGQKEVADEEPEPELEEVGEEVWEEE---RESTLPRPP 113
                                       7888777***********************...699999887 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.3
                                       HHHHHHHHHCSH CS
                              Snf7 147 daLeqelgdeel 158
                                       ++L +el++ e+
  gi|330508285|ref|YP_004384713.1| 125 EELISELKKAEM 136
                                       455555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1862.48
//
Query:       gi|330508286|ref|YP_004384714.1|  [L=1171]
Description: chromosome segregation protein SMC [Methanosaeta concilii GP6]
Scores for complete 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-68  228.0   1.1    1.1e-67  227.7   1.1    1.2  1  SMC_N          RecF/RecN/SMC N terminal domain
      3e-29  101.7   0.0    1.5e-28   99.5   0.0    2.2  2  SMC_hinge      SMC proteins Flexible Hinge Domain
    4.5e-18   66.1   0.3    8.1e-14   52.1   0.0    3.9  1  AAA_15         AAA ATPase domain
    2.9e-14   54.0   4.7    2.9e-14   54.0   4.7    6.5  1  AAA_23         AAA domain
    4.9e-10   39.7   4.5    0.00018   21.4   0.0    3.4  4  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    3.7e-07   29.8   0.0    8.2e-07   28.7   0.0    1.6  1  AAA_29         P-loop containing region of AAA domain
    0.00028   20.5   7.3    0.00028   20.5   7.3    6.0  5  PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subun
     0.0081   15.7  72.5       0.87    9.1  10.8    5.2  5  MscS_porin     Mechanosensitive ion channel porin domain
     0.0092   16.7   2.2     0.0092   16.7   2.2    7.1  7  DUF4472        Domain of unknown function (DUF4472)
  ------ inclusion threshold ------
      0.022   14.4   0.6      0.022   14.4   0.6    5.1  5  TMCO5          TMCO5 family
      0.022   13.7  90.0     0.0054   15.7   8.6    6.3  6  Spc7           Spc7 kinetochore protein
      0.028   15.0  55.8      0.052   14.2   2.1   10.2  8  SlyX           SlyX
      0.072   13.0   3.5        9.4    6.2   0.3    3.9  2  HetR_C         Heterocyst differentiation regulator C-termina
       0.12   12.6   0.0       0.12   12.6   0.0    9.9  9  XhlA           Haemolysin XhlA
       0.71   10.1   8.6        7.9    6.8   0.0    4.2  3  AAA_22         AAA domain
        1.1    9.6   0.0        1.1    9.6   0.0    4.6  3  AAA_16         AAA ATPase domain
        1.4    9.4   0.0        1.4    9.4   0.0    4.7  3  ABC_tran       ABC transporter
        1.7    8.2  74.5      0.014   15.0   3.9    5.4  4  Filament       Intermediate filament protein
          3    7.6  17.2        1.1    9.0   1.1    4.4  4  DUF3287        Protein of unknown function (DUF3287)


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 !  227.7   1.1   1.2e-70   1.1e-67       1     219 [.       2    1163 ..       2    1164 .. 1.00

  Alignments for each domain:
  == domain 1  score: 227.7 bits;  conditional E-value: 1.2e-70
                                        EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N    1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvk 75  
                                        ++k++e++nFks+ gk++ +p+++ f  ++GpNGSGKsn++dA+lF L  +s++++r+e+l dli++ +++++ +
  gi|330508286|ref|YP_004384714.1|    2 YIKEVELKNFKSF-GKSIRVPLKNDFVTVTGPNGSGKSNIVDALLFALCLSSSRAMRAERLPDLIYRGDNGKNPD 75  
                                        79***********.5************************************************************ PP

                                        EEEEEEEEEETTEESSSSSSCEEEEEEEETTSE...EEEEETTEEE-HHHHHHHHHCTT-STT............ CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                             SMC_N   76 kaeveitfdnedkklkiekeevsisrrvkrkge...seykingkevtkkevsellesagiske............ 135 
                                        +a+v + +dn++++++ +++ +++sr++k + +   s+y +ngk++ ++e+ +ll++agi++e            
  gi|330508286|ref|YP_004384714.1|   76 FAQVIVRLDNTSRHFPLDQDTIEVSRKIKINRDkyaSSYSFNGKSCGQAELLDLLAKAGITPEsynivmqgdvtr 150 
                                        ****************************99988889*************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508286|ref|YP_004384714.1|  151 iiemtaverrkiideiagvaefdekkkkaleeldvvrervervdvileevggqldrlraerdkahsyqahkdelk 225 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508286|ref|YP_004384714.1|  226 rqeaflllarlkeasgeleslnqeisslqgkndeiklradedrselavqeeklqnlgqeithkgedeqievkrri 300 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508286|ref|YP_004384714.1|  301 eelkgelaretskiqmaekalndldrqqnasfiqlgnlsgeeevlaekirdasirkaslegeledqndllqevee 375 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508286|ref|YP_004384714.1|  376 sltredaqfsalreelerargtreeakarlgdllrerdrlldatrrgslereelsgaikeamdalagsdheaeql 450 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508286|ref|YP_004384714.1|  451 keelaglnsramelekdrddlesarlrlrreiaeaeremnklqsefartdsrikaaedkggfsravdairtalkn 525 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508286|ref|YP_004384714.1|  526 gmlpglygtvaelgnvqsrfsvalevaagarmqsivaatdedaaraieylkrsqigratflplnkldrgspsvkp 600 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508286|ref|YP_004384714.1|  601 nyegivdyafrlidfdpkfqgafwyvfrdtlvveslnharalmgryrmvtlegdlversgamtgghyrtrmkfaa 675 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508286|ref|YP_004384714.1|  676 eegkkllelserianadaergkllerldrmeeqishitreveelnrsiskktfqademagskprleksisekrer 750 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508286|ref|YP_004384714.1|  751 lvqmeseflsykgrldalegeireseatlasmnetigrieadlsgsaipelnrkadaakseirrlqdriaeidae 825 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508286|ref|YP_004384714.1|  826 ilkdkireegiiekqkeisskkellesekaeaaeqkeaamtmiqslnleldgmksreaeievelhglkgvrvell 900 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508286|ref|YP_004384714.1|  901 ektitmqraidrmeremdriqarldaslsardviqmrveglrreieqsgvdstqeppdsntvaekiraltqfmrd 975 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508286|ref|YP_004384714.1|  976 lepvnmlaideydhvltrydflalrrttlreereaiidklerydqmkkeaflssfneinknfknifqelsrgegd 1050
                                        *************************************************************************** PP

                                        .............................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHH CS
                                        .............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  136 .............................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvae 181 
                                                                     ++SgGek+L+al+++f+iq+++pap+y +Deid+ LD +nv++va+
  gi|330508286|ref|YP_004384714.1| 1051 lilenpedplsggmtikarpagkpfhrleAMSGGEKSLTALSFIFSIQMFRPAPFYAMDEIDMFLDGANVERVAK 1125
                                        *************************************************************************** PP

                                        HHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETTEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  182 llkeksknaQfivislreemlekadklvgvtkvengvs 219 
                                        l+k+ s +aQfiv+slr+ m+ +++ ++gvt++en+++
  gi|330508286|ref|YP_004384714.1| 1126 LIKKISAQAQFIVVSLRKPMILQSKFTLGVTMQENNIT 1163
                                        *********************************99987 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       3.1   2.9e+03      39      73 ..     315     347 ..     311     358 .. 0.81
   2 !   99.5   0.0   1.6e-31   1.5e-28       2     116 ..     529     642 ..     528     643 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                         SMC_hinge  39 etakkiieflkkknagratflpldrikqknkadga 73 
                                       + a+k+++ l ++   +a+f+ l +++ +++  ++
  gi|330508286|ref|YP_004384714.1| 315 QMAEKALNDLDRQ--QNASFIQLGNLSGEEEVLAE 347
                                       789999*999999..79****99999988776655 PP

  == domain 2  score: 99.5 bits;  conditional E-value: 1.6e-31
                         SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkns 78 
                                       +g++G++a+l +v++++ +A+e+a+g+r+q++v  ++e+a ++ie+lk+ + gratflpl++++  +++ ++n ++ 
  gi|330508286|ref|YP_004384714.1| 529 PGLYGTVAELGNVQSRFSVALEVAAGARMQSIVAATDEDAARAIEYLKRSQIGRATFLPLNKLDRGSPSVKPNYEG- 604
                                       799**********************************************************************999. PP

                         SMC_hinge  79 gavplidlvevddelrkalryllgdtlvvdsldeAeel 116
                                        + +++ l+++d++++ a+ y+++dtlvv+sl +A++l
  gi|330508286|ref|YP_004384714.1| 605 IVDYAFRLIDFDPKFQGAFWYVFRDTLVVESLNHARAL 642
                                       9**********************************987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   8.6e-17   8.1e-14       1     256 [.       1     377 [.       1     436 [. 0.69

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 8.6e-17
                            AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn...................... 54 
                                       M+Ik++++kNF+s+ + + ++l++++ ++ G+N+sGKS+i++al + l  +++                        
  gi|330508286|ref|YP_004384714.1|   1 MYIKEVELKNFKSFGKsIRVPLKNDFVTVTGPNGSGKSNIVDALLFALCLSSSRAmraerlpdliyrgdngknpdfa 77 
                                       **************999***************************776666644448999*****************9 PP

                            AAA_15  55 ...kkvikiekedleifeniseskdikIdvef............................................. 83 
                                          +  +++  ++  +++ i+ s++ikI+                                                
  gi|330508286|ref|YP_004384714.1|  78 qviVRLDNTSRHFPLDQDTIEVSRKIKINRDKyassysfngkscgqaelldllakagitpesynivmqgdvtriiem 154
                                       99977788888888888899999999998655588889999999999999999999999999999999999999999 PP

                            AAA_15  84 .....................................................aek.ekakeyektlkskekkkadl 106
                                                                                            +++ +ka +y +++k++ k+++ +
  gi|330508286|ref|YP_004384714.1| 155 taverrkiideiagvaefdekkkkaleeldvvrervervdvileevggqldrlRAErDKAHSY-QAHKDELKRQEAF 230
                                       999999999999999988888888888888888999999999988888888773332444444.4444444444555 PP

                            AAA_15 107 llkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkke 183
                                       ll    ++ +  +++ ++++++ + +++ i++  ++++ el + +e+ +++ +e + +  +++ ++ +++ee + +e
  gi|330508286|ref|YP_004384714.1| 231 LLLARLKEASGELESLNQEISSLQGKNDEIKLRADEDRSELAVQEEKLQNLGQEITHKGEDEQIEVKRRIEELK-GE 306
                                       66666666777777888888888888888888888888888888777777777777666444444444333333.22 PP

                            AAA_15 184 eelknvlksaiiklllisakRnvsdedsekkssllgklkekilee.alqekl......eeelteklkeiqeklkeid 253
                                                a +++++ +a++  +d d ++ + ++++l +   ee  l+ek       + +l+ +l++ ++ l+e +
  gi|330508286|ref|YP_004384714.1| 307 L--------ARETSKIQMAEKALNDLDRQQ-NASFIQLGNLSGEEeVLAEKIrdasirKASLEGELEDQNDLLQEVE 374
                                       2........333355555555555544444.3333333333332202222223333332233333333333333333 PP

                            AAA_15 254 kkl 256
                                       + l
  gi|330508286|ref|YP_004384714.1| 375 ESL 377
                                       333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   4.7   3.1e-17   2.9e-14       2     199 ..       6     285 ..       5     286 .. 0.70

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 3.1e-17
                            AAA_23   2 Lkienfrsf.rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvel 77 
                                       ++++nf+sf +   + +++ ++ +tGpNG+GK+ i+dA+ +aL   ++r  r ++     + +  +++gk++ ++++
  gi|330508286|ref|YP_004384714.1|   6 VELKNFKSFgKSIRVPLKNDFVTVTGPNGSGKSNIVDALLFALCLSSSRAMRAER---LPDLIYRGDNGKNPDFAQV 79 
                                       79*******55578*******************************9999998653...4455556666777778777 PP

                            AAA_23  78 tfenkdgry.......trsiererelskkkgkttkkaklelleideleqfise........llgskkiilnlilflg 139
                                        ++ +++ +       t +++r+++ +++k  + +  ++++++ +el +++ +        ++  + +  ++i + +
  gi|330508286|ref|YP_004384714.1|  80 IVRLDNTSRhfpldqdTIEVSRKIKINRDKYASSYSFNGKSCGQAELLDLLAKagitpesyNIVMQGDVTRIIEMTA 156
                                       76666666667778554555555555666665566666666666666666666666666776777777888888888 PP

                            AAA_23 140 qer............feefelkdkke................................................... 153
                                        er            f   ++k+kk                                                    
  gi|330508286|ref|YP_004384714.1| 157 VERrkiideiagvaeF---DEKKKKAleeldvvrervervdvileevggqldrlraerdkahsyqahkdelkrqeaf 230
                                       8886666666663332...3333333666888888888888888888888887777777777777777777788788 PP

                            AAA_23 154 ....rleelekeleeledekkllekl.....eqekekekeleeleeeleeilkel 199
                                           rl+e++ ele l++e++ l+ +     +++ e + el   ee+l+++ +e+
  gi|330508286|ref|YP_004384714.1| 231 lllaRLKEASGELESLNQEISSLQGKndeikLRADEDRSELAVQEEKLQNLGQEI 285
                                       8888777777777777777777777666665666777778888888888887776 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.9e-07   0.00018       2      26 ..      27      57 ..      26     127 .. 0.65
   2 ?   -2.0   0.2       2.5   2.4e+03      66      91 ..     277     304 ..     228     417 .. 0.55
   3 ?   -3.0   0.0       5.1   4.8e+03      97     178 ..     407     485 ..     397     511 .. 0.67
   4 !   18.5   0.1   1.5e-06    0.0014     206     296 ..    1033    1140 ..     933    1140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.9e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl......d 26
                                        ++GpNgsGKSn+ dal ++  l      +
  gi|330508286|ref|YP_004384714.1| 27 VTVTGPNGSGKSNIVDALLFALCLsssramR 57
                                      5789**************8875435554440 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                            AAA_21  66 lsqgvryryglrlersqv..eeklssve 91 
                                        +q+   +  ++ e++q+  ++++ +++
  gi|330508286|ref|YP_004384714.1| 277 KLQNLGQEITHKGEDEQIevKRRIEELK 304
                                       3344444444444444442222222222 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.1
                            AAA_21  97 gllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifa 173
                                        ll+ ++ l +  +  + +r++ +g+  +   +l  s+ +++q ++ l  + sra +l+++ d+l   ++++l++ +
  gi|330508286|ref|YP_004384714.1| 407 DLLRERDRLLDATRRGSLEREELSGAIKEAMDALAGSDHEAEQLKEELAGLNSRAMELEKDRDDL---ESARLRLRR 480
                                       56666777777777777777777777778888888888888888888888888888887777777...444444444 PP

                            AAA_21 174 dyfgf 178
                                       + +  
  gi|330508286|ref|YP_004384714.1| 481 EIAEA 485
                                       44433 PP

  == domain 4  score: 18.5 bits;  conditional E-value: 1.5e-06
                            AAA_21  206 eeliasvderlrer................gvvflengdgqelparel.SdGtkrl..lalltallralkkgsll 261 
                                        ++++++++++++ r                g+++  ++ g+++   e+ S G k+l  l ++ ++   ++  +++
  gi|330508286|ref|YP_004384714.1| 1033 INKNFKNIFQELSRgegdlilenpedplsgGMTIKARPAGKPFHRLEAmSGGEKSLtaLSFIFSIQMFRPA-PFY 1106
                                        2333333333333355666666666666667777777777777544444*******644888888888888.*** PP

                            AAA_21  262 liDEpEngLHPkllrrllellkelsrngaQviltT 296 
                                        + DE++ +L+ + ++r+++l+k+ s+  aQ+i+++
  gi|330508286|ref|YP_004384714.1| 1107 AMDEIDMFLDGANVERVAKLIKKISA-QAQFIVVS 1140
                                        *********************99999.9****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 !   28.7   0.0   8.7e-10   8.2e-07       2      49 ..       4      51 ..       3      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 8.7e-10
                            AAA_29  2 krlqlvNWgtfdg.htieidlkg.atlltGpsGsGKSTllDAiqalLvpa 49
                                      k+++l N  +f +  +++++  + ++ +tGp+GsGKS ++DA+ + L+ +
  gi|330508286|ref|YP_004384714.1|  4 KEVELKNFKSFGKsIRVPLK--NdFVTVTGPNGSGKSNIVDALLFALCLS 51
                                      67899999999986666666..449******************9998755 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 ?   -3.8  10.3         9   8.5e+03      80     133 ..     247     308 ..     197     360 .. 0.63
   2 !   20.5   7.3     3e-07   0.00028      15     133 ..     359     497 ..     346     502 .. 0.87
   3 !    5.9   3.4    0.0091       8.6      79     135 ..     710     768 ..     679     793 .. 0.83
   4 ?   -0.6   0.7      0.96     9e+02      95     138 ..     777     818 ..     762     846 .. 0.68
   5 ?   -0.7   0.2         1   9.4e+02      19      42 ..    1004    1028 ..     963    1045 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 9
                     PI3K_P85_iSH2  80 ehEieklqenleqlksrlke.......lhsskekLeedlkqqkeeer.eleReinalkpell 133
                                       ++Ei++lq  ++++k r +e        +++ ++L +++  + e+e+ e+ R+i +lk el 
  gi|330508286|ref|YP_004384714.1| 247 NQEISSLQGKNDEIKLRADEdrselavQEEKLQNLGQEITHKGEDEQiEVKRRIEELKGELA 308
                                       66666666666666655443211111134445555566776666666677777777776664 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3e-07
                     PI3K_P85_iSH2  15 lseklrevskqlqekskeydqlkeeynkiseeiqlkr.qaleaFneaikmFeeqiklqekfskea............ 78 
                                       l  +l++ +++lqe ++++ +   ++++++ee++  r +  ea      +++e  +l +   +              
  gi|330508286|ref|YP_004384714.1| 359 LEGELEDQNDLLQEVEESLTREDAQFSALREELERARgTREEAKARLGDLLRERDRLLDATRRGSlereelsgaike 435
                                       566899999*************************9997888999999999999999999888888666666666666 PP

                     PI3K_P85_iSH2  79 .......qehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpell 133
                                              ++hE e+l+e l+ l+sr  el++ +++Le +      e  e eRe+n+l++e  
  gi|330508286|ref|YP_004384714.1| 436 amdalagSDHEAEQLKEELAGLNSRAMELEKDRDDLESARLRLRREIAEAEREMNKLQSEFA 497
                                       66666555*****************************9999999999***********9975 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0091
                     PI3K_P85_iSH2  79 q..ehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqL 135
                                       +   +E+e+l+ ++++ + + +e+  sk +Le+++ ++ e+  ++e e  + k  l  L
  gi|330508286|ref|YP_004384714.1| 710 ShiTREVEELNRSISKKTFQADEMAGSKPRLEKSISEKRERLVQMESEFLSYKGRLDAL 768
                                       134789999*************************************9999999777665 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.96
                     PI3K_P85_iSH2  95 srlkelhsskekLeedlkqqkeeereleReinalkpellqLqkr 138
                                       + l +++++  ++e dl        el+R+  a+k+e+ +Lq r
  gi|330508286|ref|YP_004384714.1| 777 ATLASMNETIGRIEADLSGS--AIPELNRKADAAKSEIRRLQDR 818
                                       55566666666666666543..4557889999999999888865 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 1
                     PI3K_P85_iSH2   19 lrevskqlqekskeydqlk.eeynk 42  
                                        lre  + + +k + ydq+k e++ +
  gi|330508286|ref|YP_004384714.1| 1004 LREEREAIIDKLERYDQMKkEAFLS 1028
                                        4444444444444555432133333 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1  19.1    0.0036       3.4      15     185 ..     159     334 ..     153     351 .. 0.86
   2 !    8.6  19.1    0.0013       1.2      71     199 ..     347     481 ..     334     498 .. 0.71
   3 ?    2.0   7.0      0.13   1.2e+02      56     126 ..     433     507 ..     408     530 .. 0.67
   4 ?    4.9   1.8     0.018        17      93     158 ..     680     756 ..     674     762 .. 0.54
   5 !    9.1  10.8   0.00092      0.87      41     208 ..     760     925 ..     753     931 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0036
                        MscS_porin  15 qkallqdLeqalnlLdkidkskkkaeelqkaiddaPkelrelqqeleal..qkkkeeaskeilaklslee...Leqr 86 
                                       + ++++++    ++ +k++k  ++++  ++++++    l+e+  +l++l  + +k+++++++ ++l+ +e   L  r
  gi|330508286|ref|YP_004384714.1| 159 RRKIIDEIAGVAEFDEKKKKALEELDVVRERVERVDVILEEVGGQLDRLraERDKAHSYQAHKDELKRQEaflLLAR 235
                                       56667777777778899999999**************************98677777777777777777666699** PP

                        MscS_porin  87 llqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaalea 163
                                       l+++s +l++l++++++l+ +  e+  r ++ +++l+   ++lq + ++++ + ++++   + +   l+ ela  ++
  gi|330508286|ref|YP_004384714.1| 236 LKEASGELESLNQEISSLQGKNDEIKLRADEDRSELAVQEEKLQNLGQEITHKGEDEQIEVKRRIEELKGELARETS 312
                                       **************************************************7775666688889999*********** PP

                        MscS_porin 164 qieeleqellsnnnrqeLlklq 185
                                       +i++ e++l   + +q+ + +q
  gi|330508286|ref|YP_004384714.1| 313 KIQMAEKALNDLDRQQNASFIQ 334
                                       ************9999887666 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
                        MscS_porin  71 skeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqei...rnrLnstaaage 144
                                        k ++a++  + Le +l+++++ lqe++e l+ +++q+ +l+  +era+ +  ea+ rl ++   r+rL +   +g+
  gi|330508286|ref|YP_004384714.1| 347 EKIRDASIRKASLEGELEDQNDLLQEVEESLTREDAQFSALREELERARGTREEAKARLGDLlreRDRLLDATRRGS 423
                                       455677788899**************************************************887666644445555 PP

                        MscS_porin 145 ....alsqaqrtalqaelaaleaqieeleqellsnnnrqeLlklqrdllklriqqleqe 199
                                           +ls a + a  a la  + + e+l+ el++ n r   l++ rd l+    +l +e
  gi|330508286|ref|YP_004384714.1| 424 lereELSGAIKEAMDA-LAGSDHEAEQLKEELAGLNSRAMELEKDRDDLESARLRLRRE 481
                                       3444555555555554.455577888888888887777655555555444444444444 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.13
                        MscS_porin  56 lqqeleal..qkkkeeaskeilaklsle..eLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltear 126
                                       +++  +al  ++ ++e+ ke+la l ++  eLe+  ++ +s+ ++l++++a+++ + ++lq+  +r  +++ +a 
  gi|330508286|ref|YP_004384714.1| 433 IKEAMDALagSDHEAEQLKEELAGLNSRamELEKDRDDLESARLRLRREIAEAEREMNKLQSEFARTDSRIKAAE 507
                                       444444444445666666666666665533677777777777777777777777777777777777777777664 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.018
                        MscS_porin  93 qlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrL..........nstaaage.alsqaqrtalqael 158
                                       +l+el+e++a+++++  +l  r++r  +q++   ++ +e+++ +          ++++++ e  +s+ +  + q+e+
  gi|330508286|ref|YP_004384714.1| 680 KLLELSERIANADAERGKLLERLDRMEEQISHITREVEELNRSIskktfqademAGSKPRLEkSISEKRERLVQMES 756
                                       56677777777777777777777777777777777777776655322221111122222222555555555555555 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.00092
                        MscS_porin  41 elqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrper 117
                                        ++ ++d    e+re ++ l+++ +++    +++l+   + eL+++ ++++s+  +lq ++a++++++ +   r e 
  gi|330508286|ref|YP_004384714.1| 760 SYKGRLDALEGEIRESEATLASM-NETIGRIEADLSGSAIPELNRKADAAKSEIRRLQDRIAEIDAEILKDKIREEG 835
                                       69999999999************.9999999********************************************** PP

                        MscS_porin 118 aqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaaleaqieeleqellsn.nnrqeLlklqrdllklri 193
                                       + +++ e + + + ++++ ++  a++++ + +  ++l+ el   +++ +e e el +   +r eLl++    ++  i
  gi|330508286|ref|YP_004384714.1| 836 IIEKQKEISSKKELLESEKAEA-AEQKEAAMTMIQSLNLELDGMKSREAEIEVELHGLkGVRVELLEKTIT-MQRAI 910
                                       ***********99999954444.5666999999999*********99999999999962588899888765.67789 PP

                        MscS_porin 194 qqleqelqaLqelln 208
                                       ++ e+e++ +q++l+
  gi|330508286|ref|YP_004384714.1| 911 DRMEREMDRIQARLD 925
                                       999999999998886 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   4.5       3.2     3e+03      44      91 ..     236     283 ..     204     291 .. 0.46
   2 ?    2.9   9.5      0.19   1.8e+02      14     107 .]     291     391 ..     290     391 .. 0.95
   3 !   16.7   2.2   9.7e-06    0.0092      29      90 ..     446     507 ..     423     512 .. 0.92
   4 ?   -0.4   3.7       2.1     2e+03      35      79 ..     679     723 ..     670     751 .. 0.65
   5 ?    1.0   0.3      0.76   7.2e+02      26      70 ..     740     784 ..     736     797 .. 0.83
   6 ?    4.6   9.0     0.056        53      21     107 .]     803     889 ..     798     889 .. 0.89
   7 ?   -2.3   0.1       7.9   7.5e+03      48      92 ..     998    1043 ..     997    1047 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.2
                           DUF4472  44 vlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalek 91 
                                       + e + e e +++ei+sl+ + +e++  ++e + e++v ++++q+l +
  gi|330508286|ref|YP_004384714.1| 236 LKEASGELESLNQEISSLQGKNDEIKLRADEDRSELAVQEEKLQNLGQ 283
                                       223333333344444444444444444444444444444444444443 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                           DUF4472  14 dlqietnklreqheaekfelknkvlalenrvlelelerek.......aaeeiqslrerlaeleeekkeleeeyvvlk 83 
                                       d qie ++  e+++ e    ++k+ ++e+ + +l+ +++        +  e++ l+e+ + +   k +le e+   +
  gi|330508286|ref|YP_004384714.1| 291 DEQIEVKRRIEELKGELARETSKIQMAEKALNDLDRQQNAsfiqlgnLSGEEEVLAEKIRDASIRKASLEGELEDQN 367
                                       78**********************************999999999999999999*********************99 PP

                           DUF4472  84 knyqalekefekekkkqqelsleL 107
                                         +q++e+ +++e ++   l +eL
  gi|330508286|ref|YP_004384714.1| 368 DLLQEVEESLTREDAQFSALREEL 391
                                       999**********99999998887 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 9.7e-06
                           DUF4472  29 ekfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqale 90 
                                       e  +lk ++  l++r +ele +r+ +++++  lr++ ae+e+e ++l+ e++ ++++++a e
  gi|330508286|ref|YP_004384714.1| 446 EAEQLKEELAGLNSRAMELEKDRDDLESARLRLRREIAEAEREMNKLQSEFARTDSRIKAAE 507
                                       55589***********************************************9999998876 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.1
                           DUF4472  35 nkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeey 79 
                                        k+l+l +r+ + ++er k+ e  + ++e+   + +e +el+   
  gi|330508286|ref|YP_004384714.1| 679 KKLLELSERIANADAERGKLLERLDRMEEQISHITREVEELNRSI 723
                                       688999999999999999966555555555555555555554433 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.76
                           DUF4472  26 heaekfelknkvlalenrvlelelerekaaeeiqslrerlaelee 70 
                                       +e+ + e   ++ + e++ l+ + + + ++ ei++ ++ la ++e
  gi|330508286|ref|YP_004384714.1| 740 LEKSISEKRERLVQMESEFLSYKGRLDALEGEIRESEATLASMNE 784
                                       678888999999999999999999999999999999998888776 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.056
                           DUF4472  21 klreqheaekfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekek 97 
                                       +    +++e+  l+ ++ + + ++l  ++++e   e++++++++ + le+ek e++e+  +  + +q+l+ e++  k
  gi|330508286|ref|YP_004384714.1| 803 RKADAAKSEIRRLQDRIAEIDAEILKDKIREEGIIEKQKEISSKKELLESEKAEAAEQKEAAMTMIQSLNLELDGMK 879
                                       555566778888889999999999999999999******************************************** PP

                           DUF4472  98 kkqqelsleL 107
                                       +++ e++ eL
  gi|330508286|ref|YP_004384714.1| 880 SREAEIEVEL 889
                                       ***9999997 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 7.9
                           DUF4472   48 elerekaaeeiqslrerlaeleeekke.leeeyvvlkknyqaleke 92  
                                         l+r +++ee++++ ++l+  ++ kke +   +  ++kn++++ +e
  gi|330508286|ref|YP_004384714.1|  998 ALRRTTLREEREAIIDKLERYDQMKKEaFLSSFNEINKNFKNIFQE 1043
                                        5677888888888888888888776651456777777777776555 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8  20.4         2   1.9e+03      22     145 ..     232     355 ..     216     404 .. 0.75
   2 ?   14.4   0.6   2.3e-05     0.022       3      53 ..     459     509 ..     457     525 .. 0.90
   3 ?    5.7   1.6      0.01       9.5      59     143 ..     674     760 ..     647     789 .. 0.71
   4 ?   -0.7  15.6      0.89   8.4e+02      22     138 ..     801     921 ..     797     947 .. 0.78
   5 ?   -1.0   0.2       1.1   1.1e+03       8      99 ..     913    1008 ..     910    1039 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2
                             TMCO5  22 lLrkiqekeetiqslereitkldsller..eedeeenfsenekedalkeLele.taklekkneiLlkevveLqkkis 95 
                                       lL +++e+ ++ +sl++ei  l+  +++     +e+++    +e++l++L +e t k e +     + + eL++++ 
  gi|330508286|ref|YP_004384714.1| 232 LLARLKEASGELESLNQEISSLQGKNDEikLRADEDRSELAVQEEKLQNLGQEiTHKGEDEQIEVKRRIEELKGELA 308
                                       7899***************99876665521234455677789***********445555555667889********* PP

                             TMCO5  96 rkeskqddleketlkqkleelkvklqkseescaeqekelakveedyqsva 145
                                       r++sk +  ek +l++   + ++   ++ +   e+e   +k+ +  +s+ 
  gi|330508286|ref|YP_004384714.1| 309 RETSKIQMAEK-ALNDLDRQQNASFIQLGNLSGEEEVLAEKIRD--ASIR 355
                                       ***75555555.88888888888888888888887887788887..5555 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.3e-05
                             TMCO5   3 sLnmdlekdlqrldeaNqslLrkiqekeetiqslereitkldsllereede 53 
                                       s  m+lekd   l+ a   l r+i e+e ++++l++e++++ds  ++ ed+
  gi|330508286|ref|YP_004384714.1| 459 SRAMELEKDRDDLESARLRLRREIAEAEREMNKLQSEFARTDSRIKAAEDK 509
                                       5679**************************************999988876 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.01
                             TMCO5  59 enekedalkeLeletaklekkneiLlkevveLqkkisrkeskqddleketlkqk..leelkvklqkseescaeqeke 133
                                       + e+ ++l eL +  a  + +   Ll+ +  ++++is+ +++ ++l+++  k++   +e+     ++e+s  e+ + 
  gi|330508286|ref|YP_004384714.1| 674 AAEEGKKLLELSERIANADAERGKLLERLDRMEEQISHITREVEELNRSISKKTfqADEMAGSKPRLEKSISEKRER 750
                                       55566666677777677777777777777777777777776555777655554411344555556678888889999 PP

                             TMCO5 134 lakveedyqs 143
                                       l+++e+++ s
  gi|330508286|ref|YP_004384714.1| 751 LVQMESEFLS 760
                                       9999998866 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.89
                             TMCO5  22 lLrkiqekeetiqslereitkldsllereedeeenfsenekedalke..LeletaklekkneiLlkevveLqkkisr 96 
                                       l rk ++++++i++l++ i+++d    +    ee  +e++ke + k+  Le e a   +++e+ +  + +L+ +++ 
  gi|330508286|ref|YP_004384714.1| 801 LNRKADAAKSEIRRLQDRIAEIDAEILKDKIREEGIIEKQKEISSKKelLESEKAEAAEQKEAAMTMIQSLNLELDG 877
                                       558999****************976555555555777788887777679**************************99 PP

                             TMCO5  97 keskqddlek..etlkqkleelkvklqkseescaeqekelakve 138
                                        +s++ ++e   + lk    el  k   ++ +  + e+e+ +++
  gi|330508286|ref|YP_004384714.1| 878 MKSREAEIEVelHGLKGVRVELLEKTITMQRAIDRMEREMDRIQ 921
                                       88777655551155666666666666666677777777777765 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 1.1
                             TMCO5    8 lekdlqrldeaNqslLrkiqekeetiqslereitk..ldsllereedeeenfsenekedalkeLel.etaklekk 79  
                                        +e+++ r++ + ++ L   +  +  ++ l+rei +  +ds++e  + +     +   ++++++Le  + + +++ 
  gi|330508286|ref|YP_004384714.1|  913 MEREMDRIQARLDASLSARDVIQMRVEGLRREIEQsgVDSTQEPPDSNTVAEKIRALTQFMRDLEPvNMLAIDEY 987 
                                        566666666666777777777777888899999882234444444444444445566788888885245566666 PP

                             TMCO5   80 neiLlk.evveLqkkisrkes 99  
                                        +++L++ + + L++ + r+e+
  gi|330508286|ref|YP_004384714.1|  988 DHVLTRyDFLALRRTTLREER 1008
                                        666665355555555555553 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  18.4     0.026        24     145     276 ..     173     304 ..     159     312 .. 0.90
   2 ?    1.7  15.9       0.1        95     145     232 ..     237     331 ..     226     353 .. 0.47
   3 ?    1.7  14.4       0.1        98     154     254 ..     334     437 ..     300     441 .. 0.70
   4 ?   15.7   8.6   5.7e-06    0.0054     155     242 ..     426     509 ..     423     524 .. 0.90
   5 ?   12.7   8.7   4.5e-05     0.042     144     279 ..     684     823 ..     679     829 .. 0.85
   6 ?    1.8  12.8     0.093        87     142     267 ..     834     955 ..     826     975 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.026
                              Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkke 221
                                       +e+ ++  e+ +++ ++ e +d +l+e+  + ++l++e +k  + ++  ++++++e   l  +l+e++ e+e++++e
  gi|330508286|ref|YP_004384714.1| 173 DEKKKKALEELDVVRERVERVDVILEEVGGQLDRLRAERDKAHSYQAHKDELKRQEAFLLLARLKEASGELESLNQE 249
                                       5777777889999*******************************999999***999999****************** PP

                              Spc7 222 laelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevk 276
                                       +++lq + +e++ + +e +++ +  ee++++  + +  + + ++ ev+r  ee+k
  gi|330508286|ref|YP_004384714.1| 250 ISSLQGKNDEIKLRADEDRSELAVQEEKLQNLGQEITHKGEDEQIEVKRRIEELK 304
                                       ***************9999999999999999999999999999999999877765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.1
                              Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles......id.keeLeelreelaelkae 214
                                       +e   +le+ ++++++ + + de++ + +e ++el  + eklq+  +e++       i+ k ++eel+ ela+  ++
  gi|330508286|ref|YP_004384714.1| 237 KEASGELESLNQEISSLQGKNDEIKLRADEDRSELAVQEEKLQNLGQEITHkgedeqIEvKRRIEELKGELARETSK 313
                                       34444444444444444444444444444444444444444444333333311112244455555555555555555 PP

                              Spc7 215 ieekkkelaelqeqleel 232
                                       i+  +k l++l +q +++
  gi|330508286|ref|YP_004384714.1| 314 IQMAEKALNDLDRQQNAS 331
                                       555555555555554444 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.1
                              Spc7 154 dkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkkelaelqe 227
                                       +  +L+ +ee l e   + + +ka+le ele++++  +e+e+    + ++  +lreel+++  + ee k++l +l +
  gi|330508286|ref|YP_004384714.1| 334 QLGNLSGEEEVLAEKIRDASIRKASLEGELEDQNDLLQEVEEsltREDAQFSALREELERARGTREEAKARLGDLLR 410
                                       44567777777777777777788888888877777666665543345778888888888888888888888888888 PP

                              Spc7 228 qleeleekieelkeqkseleeeiaeae 254
                                       ++++l ++    + +++el  +i+ea 
  gi|330508286|ref|YP_004384714.1| 411 ERDRLLDATRRGSLEREELSGAIKEAM 437
                                       888888888888888888888888875 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 5.7e-06
                              Spc7 155 kelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqlee 231
                                       +e+L+   +e++++l   ++e ++l+eel+ l+++a ele+ d+++Le++r +l++   ei+e ++e+++lq++ ++
  gi|330508286|ref|YP_004384714.1| 426 REELSGAIKEAMDALAGSDHEAEQLKEELAGLNSRAMELEK-DRDDLESARLRLRR---EIAEAEREMNKLQSEFAR 498
                                       68899999******************************998.***********987...566666************ PP

                              Spc7 232 leekieelkeq 242
                                        +++i++++++
  gi|330508286|ref|YP_004384714.1| 499 TDSRIKAAEDK 509
                                       *****998765 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 4.5e-05
                              Spc7 144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid...keeLeelreelaelkaeiee 217
                                       l+e++++ ++++ +L ++ + ++e    +++e +el++ + k   +a+e++ ++   ++++ e re+l++ ++e  +
  gi|330508286|ref|YP_004384714.1| 684 LSERIANADAERGKLLERLDRMEEQISHITREVEELNRSISKKTFQADEMAGSKprlEKSISEKRERLVQMESEFLS 760
                                       667777778888888888888888888888888888888888888899998877445689***************** PP

                              Spc7 218 kkkelaelqeqleeleekieelkeqkseleeeia.eaervleeckgwsesevsrlkeevkale 279
                                        k +l+ l+ ++ e+e+++++++e + ++e++++ +a   l+++ +  +se++rl+++  +++
  gi|330508286|ref|YP_004384714.1| 761 YKGRLDALEGEIRESEATLASMNETIGRIEADLSgSAIPELNRKADAAKSEIRRLQDRIAEID 823
                                       *********************************9334567778888899********998886 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.093
                              Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieek 218
                                       eg+ e+ +++ + kelLe++++e+ e +++  +  ++l+ el+ ++++++e+e ++   L+ +r el e   +++  
  gi|330508286|ref|YP_004384714.1| 834 EGIIEKQKEISSKKELLESEKAEAAEQKEAAMTMIQSLNLELDGMKSREAEIE-VELHGLKGVRVELLEKTITMQ-- 907
                                       567788899999999999999999999999999999*******9999999965.678888888888888877777.. PP

                              Spc7 219 kkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsese 267
                                        + +++++++++++++++++  + ++ ++ +++  +r +e+    s++e
  gi|330508286|ref|YP_004384714.1| 908 -RAIDRMEREMDRIQARLDASLSARDVIQMRVEGLRREIEQSGVDSTQE 955
                                       .9*******************9999999999999999999888888877 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.2       1.3   1.2e+03      20      47 ..     244     271 ..     234     293 .. 0.52
   2 ?   -0.5   4.6         2   1.9e+03      17      43 ..     298     324 ..     268     344 .. 0.57
   3 ?    6.5   3.2     0.014        13       7      51 ..     358     402 ..     345     413 .. 0.70
   4 ?    2.9   0.2      0.18   1.7e+02      19      55 ..     433     469 ..     429     476 .. 0.83
   5 ?    8.5   1.2    0.0033       3.2       3      55 ..     452     504 ..     450     519 .. 0.64
   6 ?   14.2   2.1   5.5e-05     0.052       3      53 ..     700     750 ..     698     757 .. 0.87
   7 ?    4.0   1.1      0.08        76       4      33 ..     764     793 ..     761     842 .. 0.69
   8 ?    7.6   0.8    0.0064       6.1      19      49 ..     896     926 ..     878     957 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                              SlyX  20 eeLndvvaeqqqqidrlqrqlrllaerl 47 
                                       e+Ln+++   q + d+++ + ++ + +l
  gi|330508286|ref|YP_004384714.1| 244 ESLNQEISSLQGKNDEIKLRADEDRSEL 271
                                       5555555555555555444333333333 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX  17 dtieeLndvvaeqqqqidrlqrqlrll 43 
                                       + ieeL  ++a+   +i+  ++ l+ l
  gi|330508286|ref|YP_004384714.1| 298 RRIEELKGELARETSKIQMAEKALNDL 324
                                       334555555555555555555555554 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXX CS
                              SlyX   7 eLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkele 51 
                                        LE +l  q d+++e  + +++ + q ++l+++l++ +   +e++
  gi|330508286|ref|YP_004384714.1| 358 SLEGELEDQNDLLQEVEESLTREDAQFSALREELERARGTREEAK 402
                                       577777777777777777777777777777777777666655555 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX  19 ieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                       i+e  d++a  +++ ++l+++l+ l+ r  ele++  
  gi|330508286|ref|YP_004384714.1| 433 IKEAMDALAGSDHEAEQLKEELAGLNSRAMELEKDRD 469
                                       5556688999999****************99998765 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0033
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                       e l  L ++ + +e+  ++L  +  + +++i++ +r++++l+ +++  +++ +
  gi|330508286|ref|YP_004384714.1| 452 EELAGLNSRAMELEKDRDDLESARLRLRREIAEAEREMNKLQSEFARTDSRIK 504
                                       56666777777777777777777777777777777777777776654444433 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                       erl+++E+++++  + +eeLn+ + +   q d++     +l++ ++e +e+
  gi|330508286|ref|YP_004384714.1| 700 ERLDRMEEQISHITREVEELNRSISKKTFQADEMAGSKPRLEKSISEKRER 750
                                       8********************************998888888877776665 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.08
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   4 rleeLEiklafqedtieeLndvvaeqqqqi 33 
                                       rl++LE ++   e t+ ++n+++ + + ++
  gi|330508286|ref|YP_004384714.1| 764 RLDALEGEIRESEATLASMNETIGRIEADL 793
                                       889999999999999999999887766543 PP

  == domain 8  score: 7.6 bits;  conditional E-value: 0.0064
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHT-XX CS
                              SlyX  19 ieeLndvvaeqqqqidrlqrqlrllaerlke 49 
                                         eL +  +  q+ idr++r++++++ rl +
  gi|330508286|ref|YP_004384714.1| 896 RVELLEKTITMQRAIDRMEREMDRIQARLDA 926
                                       556666777899****************944 PP

>> HetR_C  Heterocyst differentiation regulator C-terminal Hood domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3      0.01       9.4      24      54 ..     170     200 ..     151     220 .. 0.78
   2 ?    4.6   0.2     0.033        31      24      66 ..     689     731 ..     669     735 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                            HetR_C  24 aerkpkvlrvleeldippekleqaleeldei 54 
                                       ae  +k  ++leeld+  e++e+    l+e+
  gi|330508286|ref|YP_004384714.1| 170 AEFDEKKKKALEELDVVRERVERVDVILEEV 200
                                       7888889999*********999876666555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.033
                            HetR_C  24 aerkpkvlrvleeldippekleqaleeldeiirewadkyhqeg 66 
                                       a+  ++  ++le ld  +e++++   e++e+ r+ + k  q +
  gi|330508286|ref|YP_004384714.1| 689 ANADAERGKLLERLDRMEEQISHITREVEELNRSISKKTFQAD 731
                                       5556666689*********************999988877765 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.3       0.8   7.5e+02      22      44 ..     185     207 ..     164     217 .. 0.53
   2 ?    1.0   2.0      0.54   5.1e+02       6      44 ..     243     281 ..     232     287 .. 0.72
   3 ?    2.1   1.7      0.25   2.3e+02      17      50 ..     295     330 ..     285     333 .. 0.84
   4 ?   -0.6   0.2       1.7   1.6e+03       9      42 ..     359     392 ..     357     396 .. 0.88
   5 ?    2.5   2.3      0.18   1.7e+02       2      46 ..     450     494 ..     449     496 .. 0.93
   6 ?    2.8   1.0      0.15   1.4e+02       2      25 ..     698     721 ..     679     733 .. 0.67
   7 ?   12.6   0.0   0.00013      0.12       2      47 ..     747     792 ..     746     794 .. 0.95
   8 ?    8.0   0.4    0.0036       3.4      20      46 ..     798     824 ..     791     827 .. 0.88
   9 ?    2.1   0.5      0.25   2.3e+02       2      33 ..     899     930 ..     898     944 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.8
                              XhlA  22 kleekaaeaeekiknleedlkkl 44 
                                        + e+ ++++  ++++  +l++l
  gi|330508286|ref|YP_004384714.1| 185 VVRERVERVDVILEEVGGQLDRL 207
                                       44444444444444444444443 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.54
                              XhlA   6 lerietkldnleervdkleekaaeaeekiknleedlkkl 44 
                                       le +++++ +l+ + d+++++a+e ++++   ee+l +l
  gi|330508286|ref|YP_004384714.1| 243 LESLNQEISSLQGKNDEIKLRADEDRSELAVQEEKLQNL 281
                                       566666677777777788888888888888888888777 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.25
                              XhlA  17 ee..rvdkleekaaeaeekiknleedlkklesnqkW 50 
                                       e   r+++l+   a+  +ki+ +e+ l++l  +q+ 
  gi|330508286|ref|YP_004384714.1| 295 EVkrRIEELKGELARETSKIQMAEKALNDLDRQQNA 330
                                       44559*************************999875 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.7
                              XhlA   9 ietkldnleervdkleekaaeaeekiknleedlk 42 
                                       +e++l++ ++ ++++ee  ++ +++   l e+l+
  gi|330508286|ref|YP_004384714.1| 359 LEGELEDQNDLLQEVEESLTREDAQFSALREELE 392
                                       78999999999999******99999999999986 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.18
                              XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                       +ke+l+ ++++  +le++ d+le    + + +i ++e +++kl+s
  gi|330508286|ref|YP_004384714.1| 450 LKEELAGLNSRAMELEKDRDDLESARLRLRREIAEAEREMNKLQS 494
                                       6899999999*******77************************97 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.15
                              XhlA   2 ikerlerietkldnleervdklee 25 
                                       ++erl r+e+++  +  +v++l++
  gi|330508286|ref|YP_004384714.1| 698 LLERLDRMEEQISHITREVEELNR 721
                                       456666666666666666666655 PP

  == domain 7  score: 12.6 bits;  conditional E-value: 0.00013
                              XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleedlkklesn 47 
                                        +erl+++e++  +++ r+d le   +e e+ + +++e++ ++e+ 
  gi|330508286|ref|YP_004384714.1| 747 KRERLVQMESEFLSYKGRLDALEGEIRESEATLASMNETIGRIEAD 792
                                       58*****************************************986 PP

  == domain 8  score: 8.0 bits;  conditional E-value: 0.0036
                              XhlA  20 vdkleekaaeaeekiknleedlkkles 46 
                                       + +l++ka+ a+++i  l+++++++ +
  gi|330508286|ref|YP_004384714.1| 798 IPELNRKADAAKSEIRRLQDRIAEIDA 824
                                       7799*********************87 PP

  == domain 9  score: 2.1 bits;  conditional E-value: 0.25
                              XhlA   2 ikerlerietkldnleervdkleekaaeaeek 33 
                                       ++e+  ++++ +d +e ++d+++ + +  ++ 
  gi|330508286|ref|YP_004384714.1| 899 LLEKTITMQRAIDRMEREMDRIQARLDASLSA 930
                                       67888999999999999999998887776665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0083       7.9       6      37 ..      25      56 ..      22     198 .. 0.77
   2 ?   -0.8   1.4       1.7   1.6e+03      91      91 ..     358     358 ..     273     417 .. 0.50
   3 ?    5.2   0.4     0.026        24      53     105 ..     930     992 ..     900    1015 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0083
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee 37
                                       +++vtG+ G+GK+  +  ll  l+  ++ ++
  gi|330508286|ref|YP_004384714.1| 25 DFVTVTGPNGSGKSNIVDALLFALCLSSSRAM 56
                                      5889**********999998877766655555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                            AAA_22  91 v 91 
                                        
  gi|330508286|ref|YP_004384714.1| 358 S 358
                                       1 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.026
                            AAA_22  53 skdllrellralglelka..........erlsseellealeqalraravielliiDEaqh.lrs 105
                                        +d+ ++ ++ l +e +             ++  e ++al+q +r+   + +l iDE +h l +
  gi|330508286|ref|YP_004384714.1| 930 ARDVIQMRVEGLRREIEQsgvdstqeppDSNTVAEKIRALTQFMRDLEPVNMLAIDEYDHvL-T 992
                                       3444444444444333334444444444448888889999999999999***********55.3 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0012       1.1      26      50 ..      26      50 ..      15      86 .. 0.86
   2 ?   -3.0   1.0       8.7   8.2e+03     110     110 ..     800     800 ..     710     884 .. 0.56
   3 ?   -0.9   0.3         2   1.9e+03     117     145 ..     960     988 ..     894    1041 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                            AAA_16 26 lvllsGesGvGKsslvrellralek 50
                                       v ++G+ G+GKs +v++ll al+ 
  gi|330508286|ref|YP_004384714.1| 26 FVTVTGPNGSGKSNIVDALLFALCL 50
                                      588**************99977765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.7
                            AAA_16 110 e 110
                                       e
  gi|330508286|ref|YP_004384714.1| 800 E 800
                                       1 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2
                            AAA_16 117 srllellkrllallsrderplvlvlDdlq 145
                                       + ++e++++l ++++  e+   l +D+ +
  gi|330508286|ref|YP_004384714.1| 960 NTVAEKIRALTQFMRDLEPVNMLAIDEYD 988
                                       44444444444554444432333344333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0015       1.4      13      32 ..      26      45 ..      20      63 .. 0.90
   2 ?   -2.1   3.2       5.5   5.2e+03      49     111 ..     250     340 ..     230     359 .. 0.44
   3 ?   -0.2   1.6       1.4   1.4e+03      79      80 ..    1007    1018 ..     700    1110 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                                      EEEEEESTTSSHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlklla 32
                                       v ++G+nG+GKS ++ +l+
  gi|330508286|ref|YP_004384714.1| 26 FVTVTGPNGSGKSNIVDALL 45
                                      68899**********99885 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.5
                                       GGG.......B-HHHCCHCEEEE-SS...--S-TTSBHHHH..................HHHTC...HHHHHHHSTT CS
                                       xxx.......xxxxxxxxxxxxxxxx...xxxxxxxxxxxx..................xxxxx...xxxxxxxxxx RF
                          ABC_tran  49 lke.......qeleslrkeigvlpqe...pqlfpeltvren..................esdee...iekalsklgl 94 
                                       +++       ++l+  + +++   qe   ++l +e+t + +                   ++++   +ekal+ l+ 
  gi|330508286|ref|YP_004384714.1| 250 ISSlqgkndeIKLRADEDRSELAVQEeklQNLGQEITHKGEdeqievkrrieelkgelaRETSKiqmAEKALNDLDR 326
                                       44444444442222222333333333113333333332222344434444555566555222222224444444444 PP

                                       GGTTCBGESTTSGGS-H CS
                                       xxxxxxxxxxxxxxxxx RF
                          ABC_tran  95 kelkdtvvksspssLSg 111
                                       ++ +++ +  +  +LSg
  gi|330508286|ref|YP_004384714.1| 327 QQ-NASFI--QLGNLSG 340
                                       44.22222..3466665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.4
                                        H..........H CS
                                        x..........x RF
                          ABC_tran   79 n..........e 80  
                                        +          +
  gi|330508286|ref|YP_004384714.1| 1007 EreaiidklerY 1018
                                        233333333332 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  10.5    0.0017       1.6     193     278 ..     296     384 ..     284     394 .. 0.85
   2 ?    0.9   7.3      0.29   2.8e+02     199     280 ..     435     498 ..     410     509 .. 0.50
   3 ?   15.0   3.9   1.5e-05     0.014     201     282 ..     699     783 ..     689     787 .. 0.88
   4 ?    9.6  11.1   0.00067      0.63       3     134 ..     809     946 ..     796     972 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0017
                                       XXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHH CS
                          Filament 193 ykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlael...eerleaeleklqeklse 266
                                        k+++eel+ + ++++++++ a++ +++l rq ++  i+l +l ++++ l ++++++   ++ le ele+ ++ l+e
  gi|330508286|ref|YP_004384714.1| 296 VKRRIEELKGELARETSKIQMAEKALNDLDRQQNASFIQLGNLSGEEEVLAEKIRDAsirKASLEGELEDQNDLLQE 372
                                       5789****************************************************8333466789*********** PP

                                       HHHHHHHHHHHH CS
                          Filament 267 leeelaeireem 278
                                       +ee l++  ++ 
  gi|330508286|ref|YP_004384714.1| 373 VEESLTREDAQF 384
                                       ***998765555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.29
                                       XXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 199 elqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeir 275
                                       e+ +a + +++++++ kee++ l+ +  +le + ++l++++  l++++ae+                  e+e+++++
  gi|330508286|ref|YP_004384714.1| 435 EAMDALAGSDHEAEQLKEELAGLNSRAMELEKDRDDLESARLRLRREIAEA------------------EREMNKLQ 493
                                       333333333444444444444444444444444444444444444444444..................44444444 PP

                                       HHHHH CS
                          Filament 276 eemar 280
                                       +e ar
  gi|330508286|ref|YP_004384714.1| 494 SEFAR 498
                                       44333 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 1.5e-05
                                       XXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 201 qeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleer...leaeleklqeklseleeelaei 274
                                        e  ++ +e++++  +e++el+r+i +++ + +++ ++k  le++++e  er   +e+e  +++  l++le e++e 
  gi|330508286|ref|YP_004384714.1| 699 LERLDRMEEQISHITREVEELNRSISKKTFQADEMAGSKPRLEKSISEKRERlvqMESEFLSYKGRLDALEGEIRES 775
                                       56778899*****************************************99833346778899************99 PP

                                       HHHHHHHH CS
                          Filament 275 reemarql 282
                                        +++a ++
  gi|330508286|ref|YP_004384714.1| 776 EATLASMN 783
                                       98888765 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00067
                                       XXXXXXXXXXXXXX...X..XXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament   3 keelqeLNdrlAsY...i..dkVra...LEqenkeLeakieeleekksaevsklkelyekeleelrkqldeltkera 71 
                                       k+e+++L dr+A     i  dk+r    +E + ke+ +k e le + +ae ++ ke+  + +++l  +ld +++ +a
  gi|330508286|ref|YP_004384714.1| 809 KSEIRRLQDRIAEIdaeIlkDKIREegiIE-KQKEISSKKELLESE-KAEAAEQKEAAMTMIQSLNLELDGMKSREA 883
                                       667777777777532221236777433233.445667776666665.677777888888889999999999999999 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  72 rlqleldnlreeledlrkkyekelnkreevEaelkalrkdldeatlarvdLekkvesLkeela 134
                                        +++el+ l+    +l +k  + ++  + +E+e+  ++  ld+   ar  ++++ve L+ e++
  gi|330508286|ref|YP_004384714.1| 884 EIEVELHGLKGVRVELLEKTITMQRAIDRMEREMDRIQARLDASLSARDVIQMRVEGLRREIE 946
                                       999999999988888888888888888889999999999999888888888999998888886 PP

>> DUF3287  Protein of unknown function (DUF3287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.1    0.0011       1.1      28      99 ..     426     496 ..     409     502 .. 0.86
   2 ?    5.3   0.3     0.016        15      68      97 ..     692     721 ..     673     732 .. 0.88
   3 ?    2.3   0.5      0.14   1.3e+02      71      97 ..     896     922 ..     884     929 .. 0.87
   4 ?   -2.0   0.1         3   2.8e+03      35      90 ..     966    1017 ..     950    1024 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                           DUF3287  28 rdFerasvkfphaafkylppkdkeealdfidkvvekHrrlcderqklgkkrqtleaRiarveRklrelesep 99 
                                       r+   + +k  ++a+   +++++e+  + +  +  +   l  +r  l   r +l + ia+ eR++ +l+se 
  gi|330508286|ref|YP_004384714.1| 426 REELSGAIKEAMDAL-AGSDHEAEQLKEELAGLNSRAMELEKDRDDLESARLRLRREIAEAEREMNKLQSEF 496
                                       555667899999999.8889999999999999999999999*****************************96 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                           DUF3287  68 cderqklgkkrqtleaRiarveRklreles 97 
                                         er kl+ +++++e  i ++ R++ el+ 
  gi|330508286|ref|YP_004384714.1| 692 DAERGKLLERLDRMEEQISHITREVEELNR 721
                                       5699***********************995 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.14
                           DUF3287  71 rqklgkkrqtleaRiarveRklreles 97 
                                       r +l+ k  t+++ i r+eR++  +++
  gi|330508286|ref|YP_004384714.1| 896 RVELLEKTITMQRAIDRMEREMDRIQA 922
                                       778999999*************98765 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 3
                           DUF3287   35 vkfphaafkylppkdkeealdfidkvvekHrrlcderqklgkkrqtleaRiarveR 90  
                                        ++++ + ++ l p +   + +  d v ++   l+++r  l+  r+ +   i ++eR
  gi|330508286|ref|YP_004384714.1|  966 IRALTQFMRDLEPVNMLAIDE-YDHVLTRYDFLALRRTTLREEREAI---IDKLER 1017
                                        667777776666666554444.4889999999999999999999988...555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1734  (0.0967148); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                       138  (0.00769703); expected 17.9 (0.001)
Passed Fwd filter:                        95  (0.00529868); 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: 2.38u 0.38s 00:00:02.76 Elapsed: 00:00:00.63
# Mc/sec: 5588.00
//
Query:       gi|330508287|ref|YP_004384715.1|  [L=409]
Description: putative methanogenesis marker protein 10 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.2e-14   52.5   5.1      4e-12   46.8   5.1    2.6  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   5.1   2.2e-16     4e-12       7     164 ..      17     195 ..      13     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 2.2e-16
                                       ESS--TTTSCCTT.......................HHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGG CS
                                       xxxxxxxxxxxxx.......................xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                       Radical_SAM   7 CnlrCsfCarpet.......................vrregrgrslsveeileevkelk.aekgvkevilgggepll 59 
                                       C++ Cs+C+++                           +eg++ ++++ ++l ev +    ++  k+ i+ggg+ + 
  gi|330508287|ref|YP_004384715.1|  17 CRGFCSYCYFKGVkkvppfgckncmpfkkgcdycarAIMEGYPGFKPMNDVLFEVAQRCmGSMPDKVTISGGGDLSC 93 
                                       666666666666666666666666666666666666669****************888778999************* PP

                                       STTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  60 ypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealek 136
                                       ypd+  l+++  +     i++ +++  +  d++ +++l ++gv+ vs+++ ++++e  +++ ++ + +e  le+l++
  gi|330508287|ref|YP_004384715.1|  94 YPDLLPLARMVGQG-IVPISLGYTSGKGFRDKDDAAKLIDAGVNEVSFTVFSTNPE-LRRKYMGDKHPEVALENLKT 168
                                       ****9999999998.4888888888777777*************************.66666699************ PP

                                       HHHTTSETEEEEEEEBTTTSH.HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                       Radical_SAM 137 lreagikrvvdrivglpGend.eeleell 164
                                       +  + ++ v+   v++pG+nd +ele++ 
  gi|330508287|ref|YP_004384715.1| 169 FCHS-CE-VYCAAVIIPGVNDgHELEKTC 195
                                       ****.**.*************66677665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2976.99
//
Query:       gi|330508288|ref|YP_004384716.1|  [L=389]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      6e-13   49.5   0.0    2.3e-12   47.6   0.0    1.9  2  Radical_SAM  Radical SAM superfamily
    1.2e-06   28.9   0.2    3.1e-06   27.6   0.2    1.7  1  SPASM        Iron-sulfur cluster-binding domain
    0.00056   20.2   0.0     0.0029   17.9   0.0    2.0  2  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.028   14.5   0.0      0.075   13.2   0.0    1.8  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   5.2e-16   2.3e-12       1     145 [.      15     157 ..      15     171 .. 0.78
   2 ?   -1.7   0.1      0.71   3.2e+03       3      13 ..     313     323 ..     312     335 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 5.2e-16
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS......TTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly......pdfvellerla 71 
                                       +++t gC+ +Cs+C+ +e     +r  + +v ei+e ++ ++  ++  +++++ggepll       + + +l +   
  gi|330508288|ref|YP_004384716.1|  15 IIPTLGCPSKCSYCWSSEV--GSPRMTIETVGEIVEWLRDFR--DDPVTFTFHGGEPLLAgadyyrAALPMLKR--- 84 
                                       57999************85..777777777777777777775..459***********9986555433333333... PP

                                       HTC..CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.. CS
                                       xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       Radical_SAM  72 kla..vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.. 144
                                         +  +   ++++ tn  l+++e +e l+e +   +  +l+ + +    +l +  + +e+++++ e+++++g+ +  
  gi|330508288|ref|YP_004384716.1|  85 --EleHLSPNFALQTNLWLLTPELAEVLAEHE-IPIGSSLDGPQEL--NDLQRSSGYYEKTMAGYELAKKHGLQVqf 156
                                       ..23445788********************99.9999999999996..444445689**************998433 PP

                                       E CS
                                       x RF
                       Radical_SAM 145 v 145
                                       +
  gi|330508288|ref|YP_004384716.1| 157 I 157
                                       2 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.71
                                       EESEESS--TT CS
                                       xxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsf 13 
                                       ++r C+++C++
  gi|330508288|ref|YP_004384716.1| 313 HLRYCRGGCPY 323
                                       6899*****99 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.2   6.9e-10   3.1e-06       4      68 .]     250     312 ..     244     312 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 6.9e-10
                             SPASM   4 psrslfInsdGdVvpCcvdkktyvee.lklGnirees.leeIwnseeyqefrkskkfplielCrnCp 68 
                                       + +++++ +dG ++pC   ++ +  + +++Gn+r+ +  +++  s++  ++r ++k+     C+ C+
  gi|330508288|ref|YP_004384716.1| 250 MENTFAVGPDGSIYPC---YRFVGMPeYVMGNVRDRPsQADLAASPAGVRMR-QFKEYVDVNCKGCK 312
                                       67899***********...44555558******8776377999***999999.788888888***95 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 !   17.9   0.0   6.5e-07    0.0029      12      69 ..      18      73 ..       8     134 .. 0.69
   2 ?   -0.7   0.1      0.34   1.5e+03      16      23 ..     305     312 ..     293     366 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.5e-07
                           Fer4_12 12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi..egltllGGEPllpena 69
                                      + gC+ +C++C   e+ s++   e+      ei+e l + ++    +t+ GGEPll   +
  gi|330508288|ref|YP_004384716.1| 18 TLGCPSKCSYCWSSEVGSPRMTIETV----GEIVEWLRDFRDdpVTFTFHGGEPLLAGAD 73
                                      569********988888887665555....55555555433323789999*****95433 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.34
                           Fer4_12  16 nlsCkgCf 23 
                                       +++CkgC 
  gi|330508288|ref|YP_004384716.1| 305 DVNCKGCK 312
                                       55666664 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.7e-05     0.075       6      61 ..      19      70 ..      14     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                           Fer4_14  6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhy 61
                                       gC+ +C  C  +e   s   +++t  ++++ l+d+ ++ +     ++ GGePL+ 
  gi|330508288|ref|YP_004384716.1| 19 LGCPSKCSYCWSSE-VGSPRMTIETVGEIVEWLRDFRDDPV---TFTFHGGEPLLA 70
                                      69********9999.44444455556666677777777777...689*******64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2858.51
//
Query:       gi|330508289|ref|YP_004384717.1|  [L=151]
Description: hypothetical protein MCON_2445 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-55  184.8   0.5    7.9e-55  184.6   0.5    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 !  184.6   0.5   4.4e-59   7.9e-55       1     140 [.       8     144 ..       8     145 .. 0.99

  Alignments for each domain:
  == domain 1  score: 184.6 bits;  conditional E-value: 4.4e-59
                                       EHHHHHHHHHHHHTTT-SEEEEEE-TTTTHHHHHHHHHHTTT..SEEEEEETT-GGG-EEEEEETTEEEEEEE-.-S CS
                           DUF2124   1 kglsgllrefkelvkesekivfvGspgvCtpfaellayaiRdlekelvfvpdldlekarklevtdvGmqleeeaeee 77 
                                       kgl+g+l+ f++lvk+++ki+fvGspg+Ctpfa +l+y +R+  ke++f+p ld ekarkl++t+ Gm+l+e++ + 
  gi|330508289|ref|YP_004384717.1|   8 KGLGGMLNGFRDLVKDDQKIIFVGSPGFCTPFALFLGYPVRE--KEMAFIPGLDSEKARKLVATESGMELGEKC-SF 81 
                                       8*****************************************..9*****************************.** PP

                                       -EEEEEEEGGGGSTTTS--HHHHHHHHHHHEEEEEEEEEETTHHHHTTHHHHS--SEEEEEEE CS
                           DUF2124  78 kadvvvllGGlampkikveaedvkeliekiekkkviGvcfmsifekagWldkidFdliidakl 140
                                       +ad+vv+lGG+ampki+v+ae+++++++k++ kk+iGvcfmsifekagW+++++Fd++++  +
  gi|330508289|ref|YP_004384717.1|  82 EADAVVVLGGMAMPKIGVKAEEMADFLAKMKYKKLIGVCFMSIFEKAGWCQALKFDSVMNIII 144
                                       ***********************************************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1321.91
//
Query:       gi|330508290|ref|YP_004384718.1|  [L=154]
Description: transposase, IS200 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-33  114.0   1.0      5e-33  113.8   1.0    1.1  1  Y1_Tnp    Transposase IS200 like


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8   1.0   2.8e-37     5e-33       3     120 ..      12     129 ..      10     130 .. 0.96

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 2.8e-37
                            Y1_Tnp   3 nlkyhivlvtkyRrkvltge.veerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgassrl 78 
                                       +++yhivlv+kyR+k++ ++ v+++++ ++++i+ +++ ki+++e+ +DHvHl++e++ ++s+s++v+ lkg  s++
  gi|330508290|ref|YP_004384718.1|  12 QITYHIVLVPKYRYKIFYDKrVKKDCELVLSKICMEQGYKIHAMEIVDDHVHLFLEFRLSYSLSRVVQFLKGGISYR 88 
                                       789************************************************************************** PP

                            Y1_Tnp  79 inkefpelkkkklkkeslWqrgYfvstvgeasletvkrYIen 120
                                       ++k +pelkk+++  +slW+ g f  +vg+++++t+++YI++
  gi|330508290|ref|YP_004384718.1|  89 MFKLHPELKKRYWG-GSLWSSGKFFRSVGNVTADTIQHYIKE 129
                                       *********88655.88***********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1114.77
//
Query:       gi|330508291|ref|YP_004384719.1|  [L=352]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete 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   75.4   0.0    4.8e-21   74.6   0.0    1.4  1  DUF772       Transposase domain (DUF772)
    1.5e-15   57.5   4.6      5e-15   55.7   4.6    1.9  1  DDE_Tnp_1    Transposase DDE domain
    2.9e-05   23.8   0.3    0.00012   21.8   0.3    1.9  1  DDE_Tnp_4    DDE superfamily endonuclease
    3.1e-05   24.2   0.4    5.3e-05   23.4   0.4    1.4  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
      0.052   13.9   0.1       0.12   12.8   0.1    1.6  1  EnY2         Transcription factor e(y)2


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 !   74.6   0.0   1.3e-24   4.8e-21       1      72 [.      51     122 ..      51     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.3e-24
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp+++ ++m+k+l+lq ++glSd ele+++ +++sfr flg     + +pd+st + fR+rl+e    e+l++e
  gi|330508291|ref|YP_004384719.1|  51 GRPNIDIVIMVKALVLQSWFGLSDPELERQVTDRISFRIFLGT---TEVIPDFSTVWLFRERLIEcgrYEDLWKE 122
                                       9*****************************************5...389****************9999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   4.6   1.4e-18     5e-15      20     214 .]     177     340 ..     133     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.4e-18
                         DDE_Tnp_1  20 k............................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkql 68 
                                       +                             ++ w +kg k+++gyk hi++dt+ +li ++++t+++ hds++    
  gi|330508291|ref|YP_004384719.1| 177 PdfdkdllnisnnivssnakpkrlddgpiNEGTWAKKGSKSFFGYKGHILIDTEYHLIRKIETTTASLHDSQVDLG- 252
                                       0555555555555555555556666666677889999**********************************99777. PP

                         DDE_Tnp_1  69 ldelrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnksk 145
                                       +++l++      +aD+GY++a++  + +                            ++k+ r++ l  ++++rnk  
  gi|330508291|ref|YP_004384719.1| 253 INGLPR------YADKGYSGAKTQGYDA---------------------------AMKKAARGHKLGIKDILRNK-- 294
                                       777887......*******888877777...........................89******************.. PP

                         DDE_Tnp_1 146 kekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                              +++r+R+qiEr F+ +kr  + +++++ + +r+ +++++  +++n+
  gi|330508291|ref|YP_004384719.1| 295 -----------------------RISRKRSQIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNI 340
                                       .......................******************999************************7 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   3.4e-08   0.00012      77     130 ..     257     313 ..     195     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.4e-08
                         DDE_Tnp_4  77 vilaDkgFklse..kl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgr 130
                                          aDkg+ +++   +   ++k  ++++l  ++  +n++i++ r  +Er+++ +k+ 
  gi|330508291|ref|YP_004384719.1| 257 PRYADKGYSGAKtqGYdAAMKKAARGHKLGIKDILRNKRISRKRSQIERCFAVMKRA 313
                                       3469*****99954333455555********************************65 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 !   23.4   0.4   1.5e-08   5.3e-05      74     124 ..     294     343 ..     265     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.5e-08
                       DDE_Tnp_1_6  74 kaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                       k+  +kR+ ++E+ fa +kr++++  + ++ ++++ ++f++  +++N+++l
  gi|330508291|ref|YP_004384719.1| 294 KRISRKRS-QIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNIEQL 343
                                       45556665.***************************************997 PP

>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.3e-05      0.12       5      31 ..     107     133 ..     106     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       HHHHHHTTHHHHHHHHHHHHHHHTTHH CS
                              EnY2   5 qqkLvesGererlkelLrerLeesGWr 31 
                                       +++L+e G +e+l + L+++L+e G+ 
  gi|330508291|ref|YP_004384719.1| 107 RERLIECGRYEDLWKELQNQLDEKGFA 133
                                       589**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2666.79
//
Query:       gi|330508292|ref|YP_004384720.1|  [L=302]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete 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-23   80.1   0.2    2.9e-22   78.4   0.0    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.6e-07   30.9   0.5    2.6e-07   30.9   0.5    1.7  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.029   14.4   0.1      0.064   13.3   0.1    1.5  1  DZR             Double zinc ribbon
      0.078   13.0   0.0        0.2   11.7   0.0    1.8  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.14   12.0   0.6       0.27   11.1   0.6    1.4  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.59   10.2   3.8        9.2    6.4   0.1    2.2  2  DUF4337         Domain of unknown function (DUF4337)


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 ?   -1.9   0.1       1.1   3.3e+03      45      45 ..     134     134 ..     102     157 .. 0.60
   2 !   78.4   0.0   9.5e-26   2.9e-22       1      67 [.     204     268 ..     204     269 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                    OrfB_Zn_ribbon  45 r 45 
                                        
  gi|330508292|ref|YP_004384720.1| 134 S 134
                                       0 PP

  == domain 2  score: 78.4 bits;  conditional E-value: 9.5e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       f++lke+l yka  +G+++++v+payTS+tC++Cg+ + +  +g+ fkCp Cg + d+D+n+a Ni+
  gi|330508292|ref|YP_004384720.1| 204 FYQLKEFLGYKALAAGVPLVLVDPAYTSQTCHQCGEHGIR--NGKSFKCPVCGWSGDADFNGAKNIA 268
                                       899*************************************..************************7 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       1.2   3.6e+03      46      70 ..      12      44 ..       7      53 .. 0.65
   2 !   30.9   0.5   8.9e-11   2.6e-07       7     106 ..      75     171 ..      66     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                        OrfB_IS605 46 lksdykylakeiaelqsklkkskn........y 70
                                      ++++ ++l+++  e++ +l +s++        y
  gi|330508292|ref|YP_004384720.1| 12 YDTRIFALREKDEEVSVTLLRSRQriklvlgdY 44
                                      566677888888888888888875444444444 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 8.9e-11
                        OrfB_IS605   7 evelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn..ykkasrklarlh 81 
                                       e  +++    +++g+DlGi ++a++++++     + g+ +k  +  +a  +a lq+k+ k ++  ++++++ ++rl+
  gi|330508292|ref|YP_004384720.1|  75 EA-PEQIHVDTVLGVDLGITDIAVTSEGQ----KFGGKTIKLIKNHYASMRAVLQQKAVKGTRssRRRCRELQQRLS 146
                                       33.667777899****************9....78999999999***********9998888889************ PP

                        OrfB_IS605  82 rkrsrrrkhllhklathliktlkev 106
                                        k +r  +   h+++++++ + +e+
  gi|330508292|ref|YP_004384720.1| 147 GKEARYQRQINHEISKAIVTRAQEI 171
                                       *******************999987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.1e-05     0.064      28      49 .]     231     254 ..     211     265 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                               DZR  28 edrCpsCgek.vdpearf.CpeCG 49 
                                       +++C +Cge  + ++++f Cp CG
  gi|330508292|ref|YP_004384720.1| 231 SQTCHQCGEHgIRNGKSFkCPVCG 254
                                       566666666666666666666666 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.7e-05       0.2      67      95 ..     228     256 ..     158     267 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.7e-05
                                       E--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  67 vpvkvrCreCgkefeleekalrCpkCgsa 95 
                                          + +C++Cg+++  + k+++Cp Cg +
  gi|330508292|ref|YP_004384720.1| 228 AYTSQTCHQCGEHGIRNGKSFKCPVCGWS 256
                                       456779*****9998777789*****965 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 ?   11.1   0.6     9e-05      0.27      25      43 ..     233     253 ..     225     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9e-05
                                       E-HHHHHHHHH..TT-B-TTT CS
                        zf-C3HC4_3  25 lCeeCaekllk..rkkkCpiC 43 
                                       +C++C e+  +  ++ kCp+C
  gi|330508292|ref|YP_004384720.1| 233 TCHQCGEHGIRngKSFKCPVC 253
                                       8*******99999******** PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.1     0.011        32      46     105 ..     110     173 ..     107     184 .. 0.76
   2 ?    6.4   0.1    0.0031       9.2      25      47 ..     187     209 ..     175     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.011
                           DUF4337  46 ksikehlaeleleqlelllkakaeelaaavdkkiakykkkiarykke.....kkeikkkAkelea 105
                                       k ik+h a++ +  l+ ++ ++++  +++ ++ +++++ k ary+++     +k+i ++A+e+ a
  gi|330508292|ref|YP_004384720.1| 110 KLIKNHYASM-RAVLQQKAVKGTRSSRRRCRELQQRLSGKEARYQRQinheiSKAIVTRAQEIPA 173
                                       5578888888.44444444444999999999***************9877777777778888765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0031
                           DUF4337  25 aqteailaqaeasdqWafYQAks 47 
                                       ++++a  ++ ++++ WafYQ k+
  gi|330508292|ref|YP_004384720.1| 187 VNQKAGKNHRRKVNGWAFYQLKE 209
                                       567888899***********885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2168.22
//
Query:       gi|330508293|ref|YP_004384721.1|  [L=307]
Description: putative molybdenum cofactor biosynthesis protein A [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-23   84.4   0.0    2.7e-23   83.2   0.0    1.6  2  Radical_SAM  Radical SAM superfamily
    9.7e-15   54.6   0.0    1.8e-14   53.8   0.0    1.4  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    8.2e-05   22.7   0.0    0.00019   21.6   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
    0.00021   21.6   0.0    0.00038   20.7   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 !   83.2   0.0   5.9e-27   2.7e-23       3     166 ..      16     170 ..      14     171 .. 0.96
   2 ?   -2.7   0.0       1.4   6.5e+03     110     138 ..     267     282 ..     259     287 .. 0.57

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 5.9e-27
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                        t+ Cnl+C++C+         +g +++ ++++ ++k++ ae g + v l+ggepll++d+  +++r+ +     + 
  gi|330508293|ref|YP_004384721.1|  16 LTPRCNLKCIYCHHEG---ELLPGGEIPGDMVVSIAKAA-AELGMRSVKLTGGEPLLRKDLDLIIARIPQS----LD 84 
                                       699************7...8*******************.8********************9999999996....9* PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGe 155
                                       i+++tng+l+  e +e+l+++g+drv+++l+++ + ++ ++++  ++++e+vl+++++ rea++ +++ + v+l+  
  gi|330508293|ref|YP_004384721.1|  85 ISITTNGILL-AERAEALARAGLDRVNVSLDSLQPNRYCQITGgSPGDLEKVLAGIDASREADLLPIKLNFVVLK-R 159
                                       **********.*********************************99****************************9.9 PP

                                       SHHHHHHHHHH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 156 ndeeleellel 166
                                       n++e+ e++++
  gi|330508293|ref|YP_004384721.1| 160 NESEVPEMIDF 170
                                       99999999998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                                       BSSSHHHHHHHHTCTSHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 110 eaaddekvlklmnrghtfeevlealeklr 138
                                       ++              ++e+v+e+l+ ++
  gi|330508293|ref|YP_004384721.1| 267 DS-------------CDPERVKELLRVAN 282
                                       33.............44555555555554 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 !   53.8   0.0   3.9e-18   1.8e-14      38     122 ..     204     285 ..     177     290 .. 0.72

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 3.9e-18
                                       EEEE-..-SST-SSEEEEETTT--EEEEE-TTTS-.-GGG--EEEE-TTSEEESSSS-SS-.EEHHHHHHTT--HHH CS
                       Mob_synth_C  38 lleak..ketkgpakrykikdgkgeiglIapvsep.FCasCnRlRltadGklktCLfaeee.idlrdllregaseee 110
                                        ++++   ++++ +k+y +++++  +++++p++++ FCa+C+RlR+t+dGk+k+CL ++++ +++ +      + e+
  gi|330508293|ref|YP_004384721.1| 204 ARADSilIREMHRRKKYFLDGAE--VEVVRPMDNTeFCAHCTRLRVTSDGKIKPCLLRSDNlVKIDS-C----DPER 273
                                       4333322466999******8888..9********99***********************98444432.2....2234 PP

                                       HHHHHHHHHHT- CS
                       Mob_synth_C 111 Lkelikealark 122
                                       +kel++ a +r+
  gi|330508293|ref|YP_004384721.1| 274 VKELLRVANSRR 285
                                       555555555555 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 !   21.6   0.0   4.2e-08   0.00019       6      94 ..      18      96 ..      14     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.2e-08
                           Fer4_14  6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw 84
                                       +Cnl+C  C ++ +     g +   +++++i   + + e  ++ + ltGGePL+    k+l+ ++ r+ ++    +i 
  gi|330508293|ref|YP_004384721.1| 18 PRCNLKCIYCHHEGELLP--GGEIPGDMVVSIA--KAAAELGMRSVKLTGGEPLLR---KDLDLIIARIPQSL---DIS 86
                                      68*********9994433..3333445566777..5555556688*********55...88999999999988...9** PP

                           Fer4_14 85 letngtleie 94
                                      + tng l  e
  gi|330508293|ref|YP_004384721.1| 87 ITTNGILLAE 96
                                      ****988654 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   8.5e-08   0.00038      12      98 ..      17      96 ..       8     116 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 8.5e-08
                           Fer4_12 12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwl 90
                                      + +Cnl+C +C+ +    +    e++ ++   i + +++   + + l+GGEPll   +++l  ++ ++ +       + 
  gi|330508293|ref|YP_004384721.1| 17 TPRCNLKCIYCHHEGELLPG--GEIPGDMVVSIAKAAAELGMRSVKLTGGEPLL---RKDLDLIIARIPQSLD--ISIT 88
                                      678*********77766665..55666788889999999999************...6666666666666554..4556 PP

                           Fer4_12 91 ytgytlee 98
                                      ++g  l e
  gi|330508293|ref|YP_004384721.1| 89 TNGILLAE 96
                                      66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2027.79
//
Query:       gi|330508294|ref|YP_004384722.1|  [L=130]
Description: hypothetical protein MCON_2450 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.2   9.2      0.029   14.0   9.2    1.1  1  DUF998           Protein of unknown function (DUF998)
      0.031   13.8  12.1       0.04   13.4  12.1    1.1  1  5TM-5TMR_LYT     5TMR of 5TMR-LYT
      0.098   11.7   8.9       0.12   11.4   8.9    1.1  1  PHO4             Phosphate transporter family
       0.16   12.4  11.3        9.8    6.7   1.1    2.3  2  DUF202           Domain of unknown function (DUF202)
       0.32   10.7  13.0       0.76    9.5  13.0    1.5  1  Cation_efflux    Cation efflux family
       0.34   10.4   9.1      0.088   12.3   1.4    2.3  2  DUF1129          Protein of unknown function (DUF1129)
       0.37   10.0   9.8       0.49    9.6   9.8    1.2  1  Peptidase_U4     Sporulation factor SpoIIGA
       0.84    9.9   9.1        1.6    9.0   9.0    1.5  1  GtrA             GtrA-like protein
        1.3    8.5  17.8        3.7    7.0  17.8    1.6  1  ABC2_membrane_5  ABC-2 family transporter protein
        1.5    7.0   9.8        1.8    6.8   9.8    1.1  1  DUF2070          Predicted membrane protein (DUF2070)
        2.7    8.7  15.3        2.3    8.9  12.2    2.2  1  Phage_holin_4_2  Mycobacterial 4 TMS phage holin, superfamily
        5.2    7.5  15.4         11    6.5   5.4    2.1  2  MgtE             Divalent cation transporter


Domain annotation for each model (and alignments):
>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   9.2   1.9e-05     0.029      48     156 ..      18     122 ..       8     130 .] 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                            DUF998  48 llgllvlalavgllraargragragrlllavaglglvlagvfptdpgggspslsglvHglasavaflalavavllla 124
                                       ll++ ++ala+gl+   r   g ++++ l++a++++vl++ f +    gs     ++ +l+s++a l la+    + 
  gi|330508294|ref|YP_004384722.1|  18 LLAVVMMALALGLIQLFRYGPGLPASITLILAAIAFVLSASFFERYEVGSI----MWSMLVSIIATLILALLSGGII 90 
                                       456666669999999977777777777777788887777766666554432....4778888888888888888666 PP

                            DUF998 125 saarrrawallrlvggvallllvaalvwllaa 156
                                        a+ ++ +++  l++g a+ +++a++++  ++
  gi|330508294|ref|YP_004384722.1|  91 YAFSENSHPWEELLSGFAICIIIAMTLLSYLK 122
                                       67889999999999999999999999888777 PP

>> 5TM-5TMR_LYT  5TMR of 5TMR-LYT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4  12.1   2.7e-05      0.04      58     161 ..      16     121 ..       9     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-05
                      5TM-5TMR_LYT  58 gGplvGliagliaglhRyllgGftalacgistilagllaGlihrklkrrr...kkltvlvalligllveilqmllil 131
                                        G l  ++ +l  gl  ++  G   l+++i+ ila++++ l  +++ r++     +++lv ++ +l++ +l  ++i 
  gi|330508294|ref|YP_004384722.1|  16 SGLLAVVMMALALGLIQLFRYG-PGLPASITLILAAIAFVLSASFFERYEvgsIMWSMLVSIIATLILALLSGGIIY 91 
                                       4555555666666666666668.8999999999999999999999999999989999999***************** PP

                      5TM-5TMR_LYT 132 llakpfdqalalvktialPmilvnslgtal 161
                                       ++++  +   +l++  a+ +i++ +l ++l
  gi|330508294|ref|YP_004384722.1|  92 AFSENSHPWEELLSGFAICIIIAMTLLSYL 121
                                       ***********************9997765 PP

>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   8.9   8.1e-05      0.12      64     170 ..      19     118 ..       4     125 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.1e-05
                              PHO4  64 lgmlaallgaavwlllatvlglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllv 140
                                       l++++++l+ ++ +l+    glP+S   +l+ a i++ l a   +  +  +++ i+ s+++s +  +i+a l   ++
  gi|330508294|ref|YP_004384722.1|  19 LAVVMMALALGLIQLFRYGPGLPASI--TLILAAIAFVLSA---SFFERYEVGSIMWSMLVSIIATLILALLSGGII 90 
                                       34444445556666777777888875..6899999999995...455666788888888888888888888888888 PP

                              PHO4 141 krlilvkeklknalralpvlvlvtiailal 170
                                        ++   ++++ ++  +  + ++++ia+ +l
  gi|330508294|ref|YP_004384722.1|  91 YAF--SENSHPWEELLSGFAICIIIAMTLL 118
                                       888..4445555555555444444444444 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   8.2     0.011        16      17      52 ..      20      57 ..      13      88 .. 0.79
   2 ?    6.7   1.1    0.0065       9.8      16      57 ..      79     120 ..      70     126 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                            DUF202 17 slalialglallrffl..tgepsalgkilglilivlgi 52
                                      +++++al+l+l+++f+  +g p++++ il++i++vl++
  gi|330508294|ref|YP_004384722.1| 20 AVVMMALALGLIQLFRygPGLPASITLILAAIAFVLSA 57
                                      67899********9986666666666666655555544 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0065
                            DUF202  16 tslalialglallrffltgepsalgkilgli.livlgiltllv 57 
                                       t+++++  g  +++f +++++ +   + g++ +i++++ +l++
  gi|330508294|ref|YP_004384722.1|  79 TLILALLSGGIIYAF-SENSHPWEELLSGFAiCIIIAMTLLSY 120
                                       455555555555555.455555534555655477777777766 PP

>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5  13.0   0.00051      0.76      71     197 ..      12     127 ..       7     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00051
                     Cation_efflux  71 alvsgllllglavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDa 147
                                       a+  + ll ++++ l l  iq +    ++  +a+++l++a++++v++    ++ r          + ++++++l+ +
  gi|330508294|ref|YP_004384722.1|  12 AFLASGLLAVVMMALALGLIQLFR--YGPGLPASITLILAAIAFVLSAS--FFERY--------EVGSIMWSMLVSI 76 
                                       666677777777777777776555..78888999999999999999887..44443........3667888888887 PP

                     Cation_efflux 148 l.tslgvlvsalvillfnlksgplaDpvaslligliilysalkllkeslse 197
                                       + t + +l+s  +i+ f ++s+p+ + + +++i++ii+++ l+ lk sl e
  gi|330508294|ref|YP_004384722.1|  77 IaTLILALLSGGIIYAFSENSHPWEELLSGFAICIIIAMTLLSYLKRSLGE 127
                                       7577889999999****99999**********************9999876 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.4   5.9e-05     0.088     147     204 ..      10      66 ..       4      68 .. 0.74
   2 ?    2.5   1.3     0.057        85      86     119 ..      76     113 ..      67     123 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                           DUF1129 147 wkrllilllllvvwlvlftlvallpaviNpvLpplvliiigviafvvryylkkkyniq 204
                                       +k +l++ ll vv+++l + +  l +   p Lp+ +++i+++iafv+   +  +y++ 
  gi|330508294|ref|YP_004384722.1|  10 LKAFLASGLLAVVMMALALGLIQLFR-YGPGLPASITLILAAIAFVLSASFFERYEVG 66 
                                       55666666666666666666555554.38******************99888888875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.057
                           DUF1129  86 Llllalfallf.gilalfskkkqtas...iGlitlllv 119
                                        + + ++all+ gi+++fs++++  +   +G+   +++
  gi|330508294|ref|YP_004384722.1|  76 IIATLILALLSgGIIYAFSENSHPWEellSGFAICIII 113
                                       33333334443246666666665555445444444444 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   9.8   0.00033      0.49      36     139 ..      18     123 ..       3     129 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00033
                      Peptidase_U4  36 llaAllGalyvvlvlflpklesillsillkilvsllmvlia..fgpkslk....eflkalllfylvsfllgGilfal 106
                                       lla ++ al   l+ ++      l   ++ il +++ vl a  f+  ++      +l  ++  ++++ l gGi++a+
  gi|330508294|ref|YP_004384722.1|  18 LLAVVMMALALGLIQLFR-YGPGLPASITLILAAIAFVLSAsfFERYEVGsimwSMLVSIIATLILALLSGGIIYAF 93 
                                       444455555555555553.4556666666666666666665556666666333355555566666666677777777 PP

                      Peptidase_U4 107 sylllksknllvlllgalvaylllkllvkiikk 139
                                       s +    + +  ll g+ +++++   l++++k+
  gi|330508294|ref|YP_004384722.1|  94 SENS---HPWEELLSGFAICIIIAMTLLSYLKR 123
                                       7733...34777776666666666666666654 PP

>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   9.0     0.001       1.6       2     110 ..      13     121 ..      12     125 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.001
                              GtrA   2 FlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakllkqflkFvlvsllgllln 78 
                                       Fl+ G+l++++ +++l l+  l+  ++ l   i  i+a+ ++F+l+  + F++ e +++++ +l  +++ l+ +ll+
  gi|330508294|ref|YP_004384722.1|  13 FLASGLLAVVMMALALGLIQ-LFRYGPGLPASITLILAA-IAFVLSASF-FERYEVGSIMWSMLVSIIATLILALLS 86 
                                       99999999988877777776.667777777777777765.489999887.999999999999999999999999999 PP

                              GtrA  79 llilwllveklgleall...aklvgiivalvlnyv 110
                                        +i++++ e  +  + l    ++  ii++++l+y+
  gi|330508294|ref|YP_004384722.1|  87 GGIIYAFSENSHPWEELlsgFAICIIIAMTLLSYL 121
                                       99999999887776666343233333333467775 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  17.8    0.0025       3.7      89     199 ..      14     121 ..       3     124 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0025
                   ABC2_membrane_5  89 liliailitlllliiavlikgnvtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaif 165
                                       l    + +++++     l  g +++      + +++ ++l+++a+vl   f   +e g i+  +++ +i+ l+ a++
  gi|330508294|ref|YP_004384722.1|  14 LASGLLAVVMMA-----LALGLIQLFRYGPGLPASITLILAAIAFVLSASFFERYEVGSIMWSMLVSIIATLILALL 85 
                                       332222222222.....233334444567888889999999999999999999999999988888888888888888 PP

                   ABC2_membrane_5 166 slsklelslidlsny..illiillviillliivSyf 199
                                       s   + ++ ++   +  +l  +++ ii++++++Sy+
  gi|330508294|ref|YP_004384722.1|  86 SGGIIYAFSENSHPWeeLLSGFAICIIIAMTLLSYL 121
                                       865554444444444668888888888889999986 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   9.8    0.0012       1.8      81     172 ..      19     121 ..       2     128 .. 0.35

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0012
                           DUF2070  81 ivviisllaillsall.....qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly.... 148
                                       ++v+++ la+ l  l+        ++  ++ ++a+v++ +++  + v++    +++l+++i +l+++ll+  +    
  gi|330508294|ref|YP_004384722.1|  19 LAVVMMALALGLIQLFrygpgLPASITLILAAIAFVLSASFFERYEVGSI--MWSMLVSIIATLILALLSGGIiyaf 93 
                                       22222222222222222332222222222222333333333333222222..1112222222222222221112333 PP

                           DUF2070 149 ....fspesfllllllslifalavylfi 172
                                            ++e  l  +++++i+a+ ++ ++
  gi|330508294|ref|YP_004384722.1|  94 sensHPWEELLSGFAICIIIAMTLLSYL 121
                                       5555445555555555555555555544 PP

>> Phage_holin_4_2  Mycobacterial 4 TMS phage holin, superfamily IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  12.2    0.0016       2.3      52     102 ..      18      81 ..       5      85 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                   Phage_holin_4_2  52 llslpltiltl..........Gl...ftlvinalmlllaaalvsgfevdgfwsallgaliisvv 102
                                       ll++ ++ l l          Gl   +tl++ a+ ++l a++++ +ev ++++ +l+++i +++
  gi|330508294|ref|YP_004384722.1|  18 LLAVVMMALALgliqlfrygpGLpasITLILAAIAFVLSASFFERYEVGSIMWSMLVSIIATLI 81 
                                       2333333333311222334444455599***************99***************9987 PP

>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   5.4     0.007        11      32      85 ..       5      60 ..       1      72 [. 0.59
   2 ?    6.3   4.0    0.0079        12      36      85 ..      68     117 ..      60     126 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.007
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-...CTSHHHHHHHHHHHHHHHHHH CS
                              MgtE 32 lkkvllkelrvvlllgvilgllifllalllgw..slllalvvglalvlvllaaall 85
                                      +++++lk +++  ll+v++++l++ l+ l+     l +++++ la ++++l+a+++
  gi|330508294|ref|YP_004384722.1|  5 FDNYILKAFLASGLLAVVMMALALGLIQLFRYgpGLPASITLILAAIAFVLSASFF 60
                                      56778888888666666655555555333333356666666677777777777776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0079
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHHHHHHHHHHH CS
                              MgtE  36 llkelrvvlllgvilgllifllalllgwslllalvvglalvlvllaaall 85 
                                       ++ +++v ++  +il+ll + +++ ++++++ +  +   +++++++a++l
  gi|330508294|ref|YP_004384722.1|  68 IMWSMLVSIIATLILALLSGGIIYAFSENSHPWEELLSGFAICIIIAMTL 117
                                       67788999999999999999999999995555553222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1230  (0.0686039); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 876.42
//
Query:       gi|330508295|ref|YP_004384723.1|  [L=126]
Description: histidine-containing phosphotransfer protein [Methanosaeta concilii GP6]
Scores for complete 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-13   48.8   1.2    9.6e-13   48.2   1.2    1.3  1  Hpt       Hpt domain
  ------ inclusion threshold ------
      0.099   12.7   0.2       0.16   12.1   0.2    1.3  1  XkdW      XkdW protein


Domain annotation for each model (and alignments):
>> Hpt  Hpt domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   1.2   1.1e-16   9.6e-13       5      82 ..      38     114 ..      34     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.1e-16
                                       HHHHHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHCTSCHHHHHHHHHHHHHHHH CS
                               Hpt   5 lfleeaeelleqleqaldqedlqelaraaHtLKGsagmlGltelaelahelEdlldragelelepellealkallea 81 
                                       lfle +++ ++++ +a++ +d +el+ aaH+LK+s++++G+++l+el +elE  ++r++ ++  +e++e l++++ +
  gi|330508295|ref|YP_004384723.1|  38 LFLEHSPQKIAAILKAVENGDAKELQTAAHSLKSSSAYVGAMRLSELSRELEI-MGRSQVMDGAEEKAEKLNREYKQ 113
                                       7***************************************************9.66899999999998877666665 PP

                                       H CS
                               Hpt  82 l 82 
                                       +
  gi|330508295|ref|YP_004384723.1| 114 V 114
                                       4 PP

>> XkdW  XkdW protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.8e-05      0.16      44     102 ..      58     118 ..      41     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
                                       -HHHHHHHHHHHHHS----XXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXX CS
                              XkdW  44 tekelktwWeelqsnpayepPvqldllaqelskeklarkql....eelnktlgnelsklklel 102
                                         kel+t+   l+s++ay   ++l+ l++el    + r q+    ee++++l +e +++ +el
  gi|330508295|ref|YP_004384723.1|  58 DAKELQTAAHSLKSSSAYVGAMRLSELSRELEI--MGRSQVmdgaEEKAEKLNREYKQVMMEL 118
                                       579***************************965..6666643333899999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1017  (0.0567237); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 939.17
//
Query:       gi|330508296|ref|YP_004384724.1|  [L=200]
Description: hypothetical protein MCON_2452 [Methanosaeta concilii GP6]
Scores for complete 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-54  183.5   0.1    2.7e-54  183.3   0.1    1.0  1  DUF2284   Predicted metal-binding protein (DUF2284)


Domain annotation for each model (and alignments):
>> DUF2284  Predicted metal-binding protein (DUF2284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.3   0.1   1.5e-58   2.7e-54       2     164 .]      22     199 ..      21     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 1.5e-58
                           DUF2284   2 lidaedivveervrlkCekgCknYgknlsCPPavptveefrkilkeYkkallvqtkaeledeedd...keemkevke 75 
                                        i+++ ivv+++vrlkC++gC+ Ygk+l+CPP++p++ee+r++++eYk+a+l ++ ae+ + +d    ++ +++ ++
  gi|330508296|ref|YP_004384724.1|  22 PISTDLIVVADWVRLKCRYGCRAYGKHLCCPPFAPSPEEMRRVVSEYKTAILARFLAEPGPGNDPrhiHHYLWDSIN 98 
                                       699*********************************************************99999999********* PP

                           DUF2284  76 elekillelekeafeagypkalalsagsCtlCetCayeegep............CrhpekarpsmealGidvfktae 140
                                       +l++++++le +af  gy+kal+++a +CtlCetC+ ee ++            Crh++++rpsme++G+dvfkt+e
  gi|330508296|ref|YP_004384724.1|  99 NLHDTVYQLETRAFLLGYYKALGFYALPCTLCETCVGEEMQEsgekmnpldvlkCRHKDRMRPSMEGCGVDVFKTLE 175
                                       ***************************************87789********************************* PP

                           DUF2284 141 kaglelevgkeeketvslvglvLl 164
                                       +ag++ +v+++++e+v l+g+vLl
  gi|330508296|ref|YP_004384724.1| 176 NAGYSPQVIRSYSERVVLFGMVLL 199
                                       **********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1362.88
//
Query:       gi|330508297|ref|YP_004384725.1|  [L=314]
Description: universal stress protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-38  131.5   1.4    3.4e-18   66.5   0.5    3.9  2  Usp             Universal stress protein family
  ------ inclusion threshold ------
       0.08   13.0   0.0       0.14   12.2   0.0    1.3  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 !   57.3   0.0   2.7e-19   2.4e-15       1     141 []       1     169 [.       1     169 [. 0.92
   2 !   66.5   0.5   3.8e-22   3.4e-18       3     141 .]     190     310 ..     189     310 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 2.7e-19
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH....... CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada....... 70 
                                       m++++l+++D+s +s k +e+  e   +r  e++ll+v+d+++++    + ++     +e + + +e+++       
  gi|330508297|ref|YP_004384725.1|   1 MFEKVLIPTDFSRYSSKMAEYVTEIPGTR--EVVLLNVLDASNPKLLEKSGWSYDAIISEAAFRLNEEAKllasitc 75 
                                       99**************************9..7********999998888888887777777777777777888**** PP

                                       .......................HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBH CS
                               Usp  71 .......................akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGS 124
                                                                 +  ++  +    v +g ++++i ++a ee+++li++G+ g++ l+++llGS
  gi|330508297|ref|YP_004384725.1|  76 knevslmvkpilkvivepmsgadGINLNPPEPRQDADFVYGGTVGDAIQKTAWEENVSLIIMGAEGKGMLEGILLGS 152
                                       ********************997777777777778889*************************************** PP

                                       HHHHHHHHTSSEEEEEE CS
                               Usp 125 vseyvlrhapcpVlvVr 141
                                       vs  vlr+ + ++l++r
  gi|330508297|ref|YP_004384725.1| 153 VSTEVLRQGETDLLIIR 169
                                       **************997 PP

  == domain 2  score: 66.5 bits;  conditional E-value: 3.8e-22
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                        rIlV +D s +++ A+  A el  ++  e+ l+hvi+ ++   +++++    ++ le+ ++               
  gi|330508297|ref|YP_004384725.1| 190 SRILVTTDLSAAAEDAIVLAGELEGTK--EILLAHVISKEEEFGRAAEKLNLMRQDLEQPGR--------------- 249
                                       69*********************9998..7***********999999999999988888775............... PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                         v+v+++ g+pa+ ile+a+++d++l++  s g+++++++ lGS+s  v+r+++ pVlvVr
  gi|330508297|ref|YP_004384725.1| 250 -MVTVHILKGKPADQILELAKKHDVSLLIFSSQGKGWIKQMRLGSTSFDVARRSDRPVLVVR 310
                                       .79**********************************************************8 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.6e-05      0.14      52      99 ..     234     283 ..     212     294 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHHTT..--EEEEESSHHHHHHHHHHHCTECEEEEE---S CS
                    DNA_photolyase  52 lesLadLdeeLrelg..irLvvrrgdpadvlpelakelgasavvanreye 99 
                                       +e L+ ++++L++ g  ++ ++++g+pad + elak++++s ++++ + +
  gi|330508297|ref|YP_004384725.1| 234 AEKLNLMRQDLEQPGrmVTVHILKGKPADQILELAKKHDVSLLIFSSQGK 283
                                       68899999***99998899999*********************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2282.05
//
Query:       gi|330508298|ref|YP_004384726.1|  [L=726]
Description: hypothetical protein MCON_2454 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-31  107.1   0.0    1.5e-30  105.7   0.0    1.8  1  VIT       Vault protein inter-alpha-trypsin domain
    4.4e-19   69.4   0.0    7.3e-19   68.7   0.0    1.3  1  VWA       von Willebrand factor type A domain
    4.5e-16   59.2   0.0    7.3e-16   58.5   0.0    1.3  1  VWA_3     von Willebrand factor type A domain
    1.1e-12   48.5   0.0      2e-12   47.7   0.0    1.4  1  VWA_2     von Willebrand factor type A domain
    0.00028   20.7   0.0    0.00097   19.0   0.0    1.9  2  VIT_2     Vault protein inter-alpha-trypsin domain
    0.00045   19.7   0.0    0.00085   18.8   0.0    1.4  1  VWA_CoxE  VWA domain containing CoxE-like protein
    0.00088   19.4   0.1      0.027   14.6   0.0    2.6  2  DUF2201   VWA-like domain (DUF2201)
     0.0057   16.3   0.0      0.011   15.5   0.0    1.4  1  CobT_C    Cobalamin biosynthesis protein CobT VWA domain


Domain annotation for each model (and alignments):
>> VIT  Vault protein inter-alpha-trypsin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.0   6.7e-34   1.5e-30       2     111 .]      45     154 ..      44     154 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 6.7e-34
                               VIT   2 ksvsvevkivdrvarvtvtqtfvNpsseakeakYvfplpegaavsgfemeiggkvikgevkekeearkeyeeavaqg 78 
                                       k ++v+++i+d+va+++v q fvN+++++ e++Y fplpegaavs+f m+++gk ++ge+ e +ear +y++ v++ 
  gi|330508298|ref|YP_004384726.1|  45 KYHHVDIQIKDQVATTRVDQVFVNDNPWTAEGTYIFPLPEGAAVSDFVMWVDGKAVHGEILEADEARTIYDDVVRRM 121
                                       678************************************************************************** PP

                               VIT  79 ktaglleqeepdvftvsvgnippgeevtveltY 111
                                       k+++lle    +  ++sv +ippgee ++el+Y
  gi|330508298|ref|YP_004384726.1| 122 KDPALLEYVGRKALKASVFPIPPGEERKIELEY 154
                                       ********************************9 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.0   3.3e-22   7.3e-19       1     160 [.     277     429 ..     277     442 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 3.3e-22
                                       EEEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHC.HHHHHHHHHHTGSGGGG CS
                               VWA   1 DivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndys.skeellsalnnlkysgg 76 
                                       Di++vlD+Sgsm++e+++++ke++  ++++l+   + +r+++v+f+++++   +  +   + ++ ++ l++l  +  
  gi|330508298|ref|YP_004384726.1| 277 DIILVLDTSGSMQGEKMDQAKEAARYVLDHLN---PLDRFAIVSFATTTRSFSPSLEPAaQADKGKDFLDRL--EAM 348
                                       9*******************************...*****************88888555778888999987..667 PP

                                       SSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.....HTHHHHHHHHGCTEEEEEEEESSSHHHHHH CS
                               VWA  77 gttntgkalkyaleklfkssagaRenakkviilltdGksndg.....dpkeaaneakeqgikvfavGvgnadekelL 148
                                       g+t+++ a+ +a+  +   + +     +  +i+ltdG +++g      +++++++   +++++f++Gvg++++++lL
  gi|330508298|ref|YP_004384726.1| 349 GSTDINRAMIEAVGLAE--EVR-----PTTLIFLTDGLPTEGvtvtgAILDNVAREAPDNVRIFSFGVGDDVDTDLL 418
                                       7788********99333..333.....579*********99999***9999999999999***************** PP

                                       HHHSSSSCHHCE CS
                               VWA 149 nkiasepgeghv 160
                                        +i+ ++g g  
  gi|330508298|ref|YP_004384726.1| 419 DQISMDNG-GAS 429
                                       ***99998.433 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 !   58.5   0.0   3.3e-19   7.3e-16       1     151 [.     276     427 ..     276     430 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 3.3e-19
                             VWA_3   1 gevvivvDvsssmsaen.klvkdaLsvalrqLptndkiavllfgtkprplfpgsravsaaelqealqkikelelslg 76 
                                       +++++v+D+s sm++e+ + +k+a + +l  L++ d++a+++f t++r+ +p    +   + ++ +++++ le+ +g
  gi|330508298|ref|YP_004384726.1| 276 KDIILVLDTSGSMQGEKmDQAKEAARYVLDHLNPLDRFAIVSFATTTRSFSPSLEPAA--QADKGKDFLDRLEA-MG 349
                                       58****************************************************9988..788899********.** PP

                             VWA_3  77 asnlegaLkealrqpakpgevrsvilltDgssaqge...ervsdlisr.arekirfhalglgsslsaamlqaLAeas 149
                                        ++  +a+ ea+   a   ++ ++i ltDg +++g      + d++ r a+ ++r++++g g+++++++l++++   
  gi|330508298|ref|YP_004384726.1| 350 STDINRAMIEAVGL-AEEVRPTTLIFLTDGLPTEGVtvtGAILDNVAReAPDNVRIFSFGVGDDVDTDLLDQISMDN 425
                                       ************96.57789************88543337899999974669********************99877 PP

                             VWA_3 150 gG 151
                                       gG
  gi|330508298|ref|YP_004384726.1| 426 GG 427
                                       77 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 !   47.7   0.0     9e-16     2e-12       1     106 [.     278     378 ..     278     379 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 9e-16
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslp.gdrvglvtfsdgpevlipl...tkdkakilnalrnleakg 73 
                                       +++vlDtSgSm+++     ++++ak+a++ +l++l+  dr+++v+f+++ + ++p        +k +++l++lea+ 
  gi|330508298|ref|YP_004384726.1| 278 IILVLDTSGSMQGE-----KMDQAKEAARYVLDHLNpLDRFAIVSFATTTRSFSPSlepAAQADKGKDFLDRLEAM- 348
                                       689**********9.....8*************9955***********999888743325999************8. PP

                             VWA_2  74 ggtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                       g t+++ a+  a  + ++ r   + +++++tDg
  gi|330508298|ref|YP_004384726.1| 349 GSTDINRAMIEAVGLAEEVR---PTTLIFLTDG 378
                                       *****************998...*********9 PP

>> VIT_2  Vault protein inter-alpha-trypsin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.3e-07   0.00097      24      74 ..      54     104 ..      39     108 .. 0.85
   2 ?   -3.5   0.0       4.5     1e+04      47      53 ..     165     172 ..     159     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.3e-07
                             VIT_2  24 lgaslgvtasltYyNdqeqpvegvFvyPldekttvvgfeaeiagRvisvqi 74 
                                           + ++  + ++Nd++   eg +++Pl e+  v++f   + g+ + ++i
  gi|330508298|ref|YP_004384726.1|  54 KDQVATTRVDQVFVNDNPWTAEGTYIFPLPEGAAVSDFVMWVDGKAVHGEI 104
                                       55567788999**********************************999887 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.5
                             VIT_2  47 v.FvyPld 53 
                                       v ++yPl 
  gi|330508298|ref|YP_004384726.1| 165 VhYIYPLS 172
                                       349***96 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 !   18.8   0.0   3.8e-07   0.00085      57     178 ..     276     396 ..     263     404 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.8e-07
                          VWA_CoxE  57 prelvllvDvSgSmaaysaifla.llhAllqqlp...rtevfaFdtrlvdlTral...rerD.paeaLarvsaaved 125
                                       + +++l++D SgSm+      ++  ++ +l+ l+   r  ++ F t + + ++ l   +++D  ++ L+r++     
  gi|330508298|ref|YP_004384726.1| 276 K-DIILVLDTSGSMQGEKMDQAKeAARYVLDHLNpldRFAIVSFATTTRSFSPSLepaAQADkGKDFLDRLE----- 346
                                       4.89**********98333322212333445544677******************43323331345566666..... PP

                          VWA_CoxE 126 lgGgTrigaalaeflelvtrpaLsrravvvlvsDglergdreellaelarlvr 178
                                         G T+i++a+ e+  l + ++  r ++++ ++Dgl ++ +    a l+++ r
  gi|330508298|ref|YP_004384726.1| 347 AMGSTDINRAMIEAVGLAE-EV--RPTTLIFLTDGLPTEGVTVTGAILDNVAR 396
                                       89*************9999.66..69*********999888776666666655 PP

>> DUF2201  VWA-like domain (DUF2201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.2e-05     0.027       1      89 [.     278     379 ..     278     401 .. 0.78
   2 ?    1.7   0.0      0.12   2.6e+02      52      72 ..     509     529 ..     497     536 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                           DUF2201   1 lvlavDtSgSikdkelarfaaeiadilrrl..eaevhvvavdeevqsvq.rlep...aeklael..qltggGGTdlv 69 
                                       ++l++DtSgS++ +++ + +    ++l +l    +  +v + ++ +s    lep   a+k +++  +l+  G Td+ 
  gi|330508298|ref|YP_004384726.1| 278 IILVLDTSGSMQGEKMDQAKEAARYVLDHLnpLDRFAIVSFATTTRSFSpSLEPaaqADKGKDFldRLEAMGSTDIN 354
                                       5799*************************97445699****999999763577765544444433468999****86 PP

                           DUF2201  70 .pvlEav...aklrPdaavvLTD.l 89 
                                        +++Eav   ++ rP++ + LTD l
  gi|330508298|ref|YP_004384726.1| 355 rAMIEAVglaEEVRPTTLIFLTDgL 379
                                       24556642226889********955 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.12
                           DUF2201  52 aeklaelqltggGGTdlvpvl 72 
                                       + + ++l+++++GG d++p l
  gi|330508298|ref|YP_004384726.1| 509 SYTYEDLSFRKEGGDDFIPRL 529
                                       556899************987 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 !   15.5   0.0   4.7e-06     0.011      13      74 ..     276     336 ..     266     357 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.7e-06
                            CobT_C  13 avvtllldlsGsmrGrkitlalasadiladalerinvkveilGfttrawkGsqdreallkaG 74 
                                         + l+ld sGsm+G k+  a  +a  + d l+ ++    i+ f+t +   s++ e   +a 
  gi|330508298|ref|YP_004384726.1| 276 KDIILVLDTSGSMQGEKMDQAKEAARYVLDHLNPLDR-FAIVSFATTTRSFSPSLEPAAQAD 336
                                       335689*******************999999998874.566777776677777777655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (726 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 5169.60
//
Query:       gi|330508299|ref|YP_004384727.1|  [L=300]
Description: putative arsenical pump-driving ATPase [Methanosaeta concilii GP6]
Scores for complete 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-70  237.8   0.0    1.7e-70  237.7   0.0    1.0  1  ArsA_ATPase  Anion-transporting ATPase
    5.9e-10   39.3   0.0    1.8e-09   37.7   0.0    1.7  2  AAA_31       AAA domain
    4.7e-08   33.1   0.0    7.1e-08   32.6   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    6.5e-08   32.3   0.5     0.0074   15.8   0.2    2.2  2  ParA         NUBPL iron-transfer P-loop NTPase
  ------ inclusion threshold ------
      0.042   13.3   0.1       0.15   11.5   0.0    1.8  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.7   0.0   4.7e-74   1.7e-70       1     304 [.       1     293 [.       1     294 [. 0.93

  Alignments for each domain:
  == domain 1  score: 237.7 bits;  conditional E-value: 4.7e-74
                                       -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHH CS
                       ArsA_ATPase   1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeak 77 
                                       +k+i v+GKGGVGK+ +saat+++ sekg ++l+ s DPAhslsD+fd +lg +p k+ke L+a E d  +e +   
  gi|330508299|ref|YP_004384727.1|   1 MKLIYVAGKGGVGKSVCSAATGIWASEKGLETLVFSMDPAHSLSDIFDIDLGSQPNKIKEHLFAYEPDLAEESRSFF 77 
                                       799************************************************************************** PP

                                       CCHHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHH CS
                       ArsA_ATPase  78 qevqkeeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevlekllek 154
                                       ++ ++ ++al+gl e+ +v  e  as+PG+ e++ +++l++ + +++yd vv+D+aPT   l ll+lp++   +++k
  gi|330508299|ref|YP_004384727.1|  78 RRYKNMITALFGLFEV-EVKPEDFASMPGVSELIFMDKLNDIYVQKKYDLVVIDSAPTAMVLPLLQLPSITTGFVTK 153
                                       ************6665.5666666777************************************************** PP

                                       HHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHH CS
                       ArsA_ATPase 155 lvklkeklsplakqlvkllglggvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLk 231
                                       ++ +++k   ++++l    g+g+    + l+e++++  + +++++ ltdp+++s+++V+ipEk +++E++R+i+ ++
  gi|330508299|ref|YP_004384727.1| 154 VLGIRNKWIGVLNMLES--GFGD----SILKEVRAMRLKAETMRNALTDPKTASITVVTIPEKAAVEESRRLIETVQ 224
                                       ******99999999933..5555....45667777888888888********************************* PP

                                       HTT-EEEEEEEEEE-TTCSSSTSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHHHHHHHHHC CS
                       ArsA_ATPase 232 kygikvdavivNkllpeeeqenCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekleklselly 304
                                       + g++v a+++N+++ e     C+f++++ + q  y+++i++ ++d+ +v lp + +Ev+G ++l++++e ly
  gi|330508299|ref|YP_004384727.1| 225 SHGVNVSAIVINHVIGECP---CQFCQEKMASQTSYIQDIRNRYHDKDIVILPDYGGEVKG-DRLNRVAEDLY 293
                                       ***************9865...68************************************9.78999999998 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   5.1e-13   1.8e-09       8     131 ..       7     137 ..       1     146 [. 0.83
   2 ?   -1.2   0.0      0.47   1.7e+03     143     166 ..     202     225 ..     189     273 .. 0.66

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 5.1e-13
                            AAA_31   8 nqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevli.eeknikeaiiktkvenldl 83 
                                         KGGvGK+  s + + + +++g  +L+  +Dp  +++  ++i+  +  +++ e l+  e +++e   +   +  ++
  gi|330508299|ref|YP_004384727.1|   7 AGKGGVGKSVCSAATGIWASEKGLETLVFSMDPAHSLSDIFDIDLGSQPNKIKEHLFaYEPDLAEESRSFFRRYKNM 83 
                                       46******************************************999999999998657777777777443444599 PP

                            AAA_31  84 ipssidLaeaeielvelekk....eeilkellekv..kdeYDyiiiDcpPsLgl 131
                                       i +   L e+e++  ++ +     e i+ ++l+++  +++YD+++iD  P+  +
  gi|330508299|ref|YP_004384727.1|  84 ITALFGLFEVEVKPEDFASMpgvsELIFMDKLNDIyvQKKYDLVVIDSAPTAMV 137
                                       9******999998877777666678889999987533899**********8655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.47
                            AAA_31 143 viipvqaeayaleGleqllktiee 166
                                       + +++ +e+ a+e  ++l++t+++
  gi|330508299|ref|YP_004384727.1| 202 ITVVTIPEKAAVEESRRLIETVQS 225
                                       445555666666666666666654 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 !   32.6   0.0     2e-11   7.1e-08       2      87 ..       4     241 ..       3     273 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2e-11
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       + +++kGGvGK++ +a+ ++  +++gl++l++ +Dp  +++ i++ + + + +                        
  gi|330508299|ref|YP_004384727.1|   4 IYVAGKGGVGKSVCSAATGIWASEKGLETLVFSMDPAHSLSDIFDIDLGSQPNkikehlfayepdlaeesrsffrry 80 
                                       5689**************************************95555555555666899999999999********* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|330508299|ref|YP_004384727.1|  81 knmitalfglfevevkpedfasmpgvselifmdklndiyvqkkydlvvidsaptamvlpllqlpsittgfvtkvlgi 157
                                       ******************99999999999999999999999999999999999999999999999999999999999 PP

                                       .........................................................CCHCCCHHHHHHCHCHHHH. CS
                                       .........................................................xxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 .........................................................dlkrllellealgkkkalll 74 
                                                                                                   rl+e++++ g      +
  gi|330508299|ref|YP_004384727.1| 158 rnkwigvlnmlesgfgdsilkevramrlkaetmrnaltdpktasitvvtipekaaveESRRLIETVQSHG------V 228
                                       9999999999999999999999999999999999999999999998888888885554444444444444......6 PP

                                       .EEEEEEEEESS. CS
                                       xxxxxxxxxxxxx RF
                              CbiA  75 kiagvvlnrvdge 87 
                                       ++  +v+n v ge
  gi|330508299|ref|YP_004384727.1| 229 NVSAIVINHVIGE 241
                                       6888888887665 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.9e-06     0.014       8      41 ..       5      38 ..       1      67 [. 0.80
   2 !   15.8   0.2   2.1e-06    0.0074     135     187 ..     198     249 ..     185     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.9e-06
                              ParA  8 vlSgKGGVGKStvavnlAlaLakkglkvgllDaD 41
                                       ++gKGGVGKS +++   +  ++kgl++ ++ +D
  gi|330508299|ref|YP_004384727.1|  5 YVAGKGGVGKSVCSAATGIWASEKGLETLVFSMD 38
                                      468**********************999998888 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.1e-06
                              ParA 135 plagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekte 187
                                       ++a + +Vt p+++a+++ ++ ie +++  v+v ++v N  +  cp c+ ++e
  gi|330508299|ref|YP_004384727.1| 198 KTASITVVTIPEKAAVEESRRLIETVQSHGVNVSAIVINHVIGECP-CQFCQE 249
                                       5567889********************************9998888.333333 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.2e-05      0.15       3      40 ..       4      41 ..       2      57 .. 0.90
   2 ?   -1.1   0.0      0.29     1e+03     164     182 ..     218     236 ..     193     280 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.2e-05
                         Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPka 40
                                      i + GkGG+Gks+ s+ + +  +e+g   l+   DP +
  gi|330508299|ref|YP_004384727.1|  4 IYVAGKGGVGKSVCSAATGIWASEKGLETLVFSMDPAH 41
                                      5678********************************76 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.29
                         Fer4_NifH 164 giekyaksggvrlgGliin 182
                                        + +  +s+gv+++ ++in
  gi|330508299|ref|YP_004384727.1| 218 RLIETVQSHGVNVSAIVIN 236
                                       4445556777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2200.06
//
Query:       gi|330508300|ref|YP_004384728.1|  [L=139]
Description: hypothetical protein MCON_2457 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.055   14.1   0.0       0.26   11.9   0.0    1.9  2  Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.5e-05      0.26      54      92 ..      55      96 ..      13      98 .. 0.73
   2 ?   -0.1   0.0     0.077   1.4e+03      17      31 ..     116     129 ..     108     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.5e-05
                   Pur_ac_phosph_N 54 tnyksgyshkatltgLepgttYyYrvgddeg...gwSevysf 92
                                       +++s+++  a++++L+ + +Y+Y +g+ ++    ++++  f
  gi|330508300|ref|YP_004384728.1| 55 GSTTSNIQVGALAKDLQSQCRYCYECGACGEpkiYTTPWDDF 96
                                      6678899999****************9987666666666666 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.077
                   Pur_ac_phosph_N  17 tvsWitpektkksvv 31 
                                       +++W+t + + ++ v
  gi|330508300|ref|YP_004384728.1| 116 MINWNTGTMD-QEPV 129
                                       799**99974.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1104.74
//
Query:       gi|330508301|ref|YP_004384729.1|  [L=138]
Description: hypothetical protein MCON_2459 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        6.9    6.5  11.9       0.47   10.3   1.7    2.3  2  TB        TB domain


Domain annotation for each model (and alignments):
>> TB  TB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   3.3     0.017   3.1e+02      25      34 ..      72      81 ..      66      90 .. 0.73
   2 ?   10.3   1.7   2.6e-05      0.47      25      43 ..      91     109 ..      88     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.017
                                TB 25 spCelCParg 34
                                      + C+ CP+  
  gi|330508301|ref|YP_004384729.1| 72 QSCQICPQCP 81
                                      5688888754 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 2.6e-05
                                TB  25 spCelCPargseefkelCp 43 
                                       ++C  CP++++e +k+l+p
  gi|330508301|ref|YP_004384729.1|  91 PECPTCPSPSEELYKQLMP 109
                                       57***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1052.87
//
Query:       gi|330508302|ref|YP_004384730.1|  [L=633]
Description: phosphoadenosine phosphosulfate reductase [Methanosaeta concilii GP6]
Scores for complete 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-37  126.9   0.0    1.3e-36  126.3   0.0    1.3  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
    0.00062   20.3  12.7     0.0023   18.5  12.7    2.1  1  Fer4_7         4Fe-4S dicluster domain
     0.0087   16.5  10.0        2.1    8.9   0.2    4.0  4  Fer4_8         4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   15.4   2.2      0.012   15.4   2.2    3.1  4  Fer4           4Fe-4S binding domain
      0.086   12.9   0.2        0.3   11.1   0.2    1.9  1  OTT_1508_deam  OTT_1508-like deaminase
       0.14   11.6   0.0       0.14   11.6   0.0    2.2  2  QueC           Queuosine biosynthesis protein QueC
       0.21   11.7  16.4      0.041   14.0  12.4    2.0  2  Fer4_10        4Fe-4S dicluster domain
       0.24   11.5  24.3      0.055   13.6   3.3    3.0  3  Fer4_6         4Fe-4S binding domain
        1.5    9.8  13.2         17    6.5  13.2    2.6  1  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 !  126.3   0.0   6.5e-40   1.3e-36       3     173 ..     241     412 ..     239     413 .. 0.97

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 6.5e-40
                                       EEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHH CS
                       PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslye 79 
                                        +s+sgGkdsl+ l+La+k ++ + v+f++tg efpet+e+v++l ++ +lrl+  + + ++ ++ + ++ + ++y+
  gi|330508302|ref|YP_004384730.1| 241 NISFSGGKDSLASLILARKLMPRIDVLFINTGLEFPETVEYVQKLCSNNKLRLHEIRGDSDFFKQAESFGPPAKDYR 317
                                       68*************************************************************************** PP

                                       CHHHHHHTHHHHHHHHHCT..TECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT-- CS
                       PAPS_reduct  80 eaaeriaKveplkkaLekl..dedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilrenip 154
                                       + +++  K+ p++  L +   +  +++ G R +es++r++++ ve++   + +  + P+ nW   +v  yi  ++  
  gi|330508302|ref|YP_004384730.1| 318 W-CCKTNKLGPMTSFLAGQypRGCVTIEGRRVYESFNRSSIKAVERNPYVPGQTMLSPIRNWRALEVMLYIHWNGEV 393
                                       *.**************9876888999*************************************************** PP

                                       B-CCCCTT-SS--BCTTB- CS
                       PAPS_reduct 155 ynpLydqgfrsiGcvpctg 173
                                       +npLyd+ +++iGc+ c++
  gi|330508302|ref|YP_004384730.1| 394 LNPLYDEDYERIGCWLCPA 412
                                       ****************985 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5  12.7   1.2e-06    0.0023       2      48 ..     579     617 ..     578     619 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavC 48 
                                       C++Cg C ++C+ +ai+l++         +++++e+C +Cg+C + C
  gi|330508302|ref|YP_004384730.1| 579 CTKCGICIRNCSRGAITLEDT--------IVVNQERCNHCGKCDRGC 617
                                       ******************775........99************9999 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.095   1.9e+02       7      34 ..      17      50 ..      14      76 .. 0.81
   2 ?   -1.8   0.0       2.3   4.5e+03      17      34 ..     428     445 ..     405     456 .. 0.62
   3 !    8.9   0.2    0.0011       2.1       3      16 ..     577     590 ..     550     602 .. 0.79
   4 !    8.1   1.3    0.0018       3.6       3      18 ..     605     620 ..     603     629 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.095
                            Fer4_8  7 eCgaCq.....saCpvlrrtk.khlldargeaae 34
                                       C  C+     + C +++r++ + +l+++g++  
  gi|330508302|ref|YP_004384730.1| 17 WCRKCNlpllsEDCSLCHRSGfRIPLSPPGDVRL 50
                                      4777777778889********9999999999876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.3
                            Fer4_8  17 vlrrtkkhlldargeaae 34 
                                       +++r++ +l+d rg++  
  gi|330508302|ref|YP_004384730.1| 428 LYSRWNSFLHDWRGKNDL 445
                                       788888888988888765 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0011
                            Fer4_8   3 ekCieCgaCqsaCp 16 
                                       + C++Cg C  +C 
  gi|330508302|ref|YP_004384730.1| 577 QMCTKCGICIRNCS 590
                                       56777777777773 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0018
                            Fer4_8   3 ekCieCgaCqsaCpvl 18 
                                       e+C++Cg C   C ++
  gi|330508302|ref|YP_004384730.1| 605 ERCNHCGKCDRGCIAI 620
                                       6899999998888655 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.2       6.9   1.4e+04       6      11 ..      28      33 ..      27      34 .. 0.70
   2 ?   -3.1   0.9       4.1   8.1e+03       9      14 ..     405     410 ..     405     410 .. 0.89
   3 ?   15.4   2.2   6.1e-06     0.012       7      24 .]     578     595 ..     572     595 .. 0.90
   4 ?    9.8   4.4   0.00036      0.72       1      14 [.     600     613 ..     600     617 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.9
                                      TTSSS- CS
                              Fer4  6 ekCigC 11
                                      e+C  C
  gi|330508302|ref|YP_004384730.1| 28 EDCSLC 33
                                      677777 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.1
                                       SS-THH CS
                              Fer4   9 igCGaC 14 
                                       igC +C
  gi|330508302|ref|YP_004384730.1| 405 IGCWLC 410
                                       899999 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 6.1e-06
                                       TSSS-THHHHHSTTTEEE CS
                              Fer4   7 kCigCGaCvevCPvgAIt 24 
                                       +C++CG+C+  C  gAIt
  gi|330508302|ref|YP_004384730.1| 578 MCTKCGICIRNCSRGAIT 595
                                       8***************97 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00036
                                       EEEETTTSSS-THH CS
                              Fer4   1 vvideekCigCGaC 14 
                                       +v+++e+C +CG+C
  gi|330508302|ref|YP_004384730.1| 600 IVVNQERCNHCGKC 613
                                       69************ PP

>> OTT_1508_deam  OTT_1508-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00015       0.3      32      61 ..     407     433 ..     404     434 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                     OTT_1508_deam  32 CylCelylrahgkatlkvreshgklydkWr 61 
                                       C+lC   l++ ++   +++esh +ly++W+
  gi|330508302|ref|YP_004384730.1| 407 CWLCPASLQS-EFS--RLKESHPNLYSRWN 433
                                       ********84.334..56***********6 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     7e-05      0.14       5      58 ..     243     296 ..     240     308 .. 0.88
   2 ?   -5.0   5.1       8.6   1.7e+04     188     197 ..     605     614 ..     574     624 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7e-05
                                       E--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEE CS
                              QueC   5 llSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehki 58 
                                        +SGG DS + l+la+k + ++ +l ++ g    +++e+++k++++ +++ h+i
  gi|330508302|ref|YP_004384730.1| 243 SFSGGKDSLASLILARKLMPRIDVLFINTGLEFPETVEYVQKLCSNNKLRLHEI 296
                                       59*******************************************999955543 PP

  == domain 2  score: -5.0 bits;  conditional E-value: 8.6
                                       -BTTTTSSSH CS
                              QueC 188 eegkaCgeCd 197
                                       e+ ++Cg+Cd
  gi|330508302|ref|YP_004384730.1| 605 ERCNHCGKCD 614
                                       4556777776 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.7   0.1         9   1.8e+04      19      21 ..     410     412 ..     404     416 .. 0.60
   2 ?   14.0  12.4   2.1e-05     0.041       3      55 ..     573     617 ..     571     618 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.7 bits;  conditional E-value: 9
                           Fer4_10  19 CPa 21 
                                       CPa
  gi|330508302|ref|YP_004384730.1| 410 CPA 412
                                       554 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.1e-05
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       ++ ++ C++Cg C + C +       +g+++ e+++ ++ e+C +cg+C + C
  gi|330508302|ref|YP_004384730.1| 573 ILRAQMCTKCGICIRNC-S-------RGAITLEDTIVVNQERCNHCGKCDRGC 617
                                       667889***********.5.......9**********************9988 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   2.2         9   1.8e+04       8      15 ..      20      33 ..      18      35 .. 0.52
   2 ?   13.6   3.3   2.8e-05     0.055       7      24 .]     577     594 ..     575     594 .. 0.92
   3 ?   12.1   3.5   7.9e-05      0.16       2      15 ..     600     613 ..     599     620 .. 0.88

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 9
                            Fer4_6  8 kCi......gCgdC 15
                                      kC+      +C  C
  gi|330508302|ref|YP_004384730.1| 20 KCNlpllseDCSLC 33
                                      45544444456666 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.8e-05
                            Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                       + C+ Cg C+r+C  gai
  gi|330508302|ref|YP_004384730.1| 577 QMCTKCGICIRNCSRGAI 594
                                       68************9998 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 7.9e-05
                            Fer4_6   2 veidpdkCigCgdC 15 
                                       +++++++C++Cg+C
  gi|330508302|ref|YP_004384730.1| 600 IVVNQERCNHCGKC 613
                                       89************ 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 ?    6.5  13.2    0.0084        17       2      33 ..     579     610 ..     578     628 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0084
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy 33 
                                       C++Cg C+  C  +ai+ +   ++++++c   
  gi|330508302|ref|YP_004384730.1| 579 CTKCGICIRNCSRGAITLEDTIVVNQERCNHC 610
                                       *******************9999999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); 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:                        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: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 4503.84
//
Query:       gi|330508303|ref|YP_004384731.1|  [L=64]
Description: cold shock DNA binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-19   68.2   0.6    4.3e-19   68.1   0.6    1.0  1  CSD       'Cold-shock' DNA-binding domain
  ------ inclusion threshold ------
      0.037   13.7   1.4       0.06   13.0   1.4    1.5  1  OB_RNB    Ribonuclease B OB domain
       0.06   13.7   0.2      0.069   13.5   0.2    1.2  1  S1        S1 RNA binding domain


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.6   7.2e-23   4.3e-19       2      65 ..       3      63 ..       2      64 .] 0.97

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 7.2e-23
                                      EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                               CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                       GtVk fn+ k+fGFI+ +dg+ d FvH + +  d   +++eg++V+Fevveg+kgp+A  Vtk
  gi|330508303|ref|YP_004384731.1|  3 SGTVKFFNRTKRFGFIAGDDGK-DYFVHATGLMPDV--TITEGDKVSFEVVEGEKGPKADRVTK 63
                                      7********************9.*************..************************97 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.4     1e-05      0.06       8      48 ..      13      55 ..       4      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                                      SS-EEEEECT.TEEEEE-HHHHT...TS-TT-EEEEEEEESSSE CS
                            OB_RNB  8 kGFGFlipdegkeDifippeqmk...kamhGDrVlvritkgdrr 48
                                      k FGF+  d+ ++D+f++++ +    ++  GD+V  ++ +g+++
  gi|330508303|ref|YP_004384731.1| 13 KRFGFIAGDD-GKDYFVHATGLMpdvTITEGDKVSFEVVEGEKG 55
                                      66*******8.********9985333788999999999886655 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   1.2e-05     0.069      15      67 ..      12      56 ..       1      63 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                                      EETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTT CS
                                S1 15 vtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdr 67
                                        ++G++   + g + fv+a  l+       pd ++++Gd+v ++v + +k  
  gi|330508303|ref|YP_004384731.1| 12 TKRFGFIAGDD-GKDYFVHATGLM-------PDVTITEGDKVSFEVVEGEKGP 56
                                      34599998888.************.......99***************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 478.18
//
Query:       gi|330508304|ref|YP_004384732.1|  [L=713]
Description: S1 RNA binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-59  201.1   1.6      2e-59  200.4   1.6    1.4  1  Tex_N       Tex-like protein N-terminal domain
    9.1e-45  152.2   0.0    2.2e-44  150.9   0.0    1.7  1  Tex_YqgF    Tex protein YqgF-like domain
    4.2e-28   97.4   0.0    8.6e-28   96.4   0.0    1.6  1  HHH_3       Helix-hairpin-helix motif
      4e-22   78.9   0.1    3.5e-21   75.9   0.0    2.5  2  HHH_9       HHH domain
    1.5e-19   70.1   1.8    1.5e-19   70.1   1.8    1.9  2  S1          S1 RNA binding domain
    4.9e-08   33.3   0.0    1.1e-07   32.1   0.0    1.6  1  HHH_7       Helix-hairpin-helix motif
    1.1e-07   31.8   0.3    6.2e-07   29.3   0.0    2.5  3  YqgF        Holliday-junction resolvase-like of SPT6
    6.4e-05   22.6   0.0    0.00056   19.6   0.1    2.6  2  HHH         Helix-hairpin-helix motif
      0.001   19.3   0.0     0.0049   17.1   0.0    2.2  1  HHH_6       Helix-hairpin-helix motif
     0.0025   17.3   0.1       0.01   15.3   0.0    2.0  2  T2SSK       Type II secretion system (T2SS), protein K
     0.0046   17.5   0.2       0.22   12.2   0.0    3.4  2  HHH_5       Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.028   14.4   0.0      0.058   13.4   0.0    1.4  1  PsbU        Photosystem II 12 kDa extrinsic protein (PsbU)
       0.39   11.1   7.2        2.5    8.5   0.0    4.7  5  E3_binding  e3 binding domain


Domain annotation for each model (and alignments):
>> Tex_N  Tex-like protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.4   1.6   1.4e-62     2e-59       1     181 [.       9     194 ..       9     195 .. 0.97

  Alignments for each domain:
  == domain 1  score: 200.4 bits;  conditional E-value: 1.4e-62
                             Tex_N   1 iaeelslkekqveavveLldegatvPFIARYRkeatggldeeqlreieerleylrelekrkeevlksieeqgkltee 77 
                                       ia+elsl+++ v av eLld+gat+PFIARYRkeatg lde+++ +i+++l++ r +++r+ ++++s+++q++lt e
  gi|330508304|ref|YP_004384732.1|   9 IASELSLDRRAVGAVSELLDSGATLPFIARYRKEATGDLDEVAIGKIRDSLNRSRLMDERRIAIIRSLARQNQLTAE 85 
                                       799************************************************************************** PP

                             Tex_N  78 LkkkieaaktleeledlylpYkpkrkTkatiArekGLeplAelileqk..sl.aeeeaakyvn..kevksaeealeg 149
                                       +++k+++a +l+eled+ylp++pkr+T+a++A+e+GLe lA++il+q+  +  +eeeaa y++  k+v+s+ ea++g
  gi|330508304|ref|YP_004384732.1|  86 IEEKLSKAVSLAELEDIYLPFRPKRRTRAMVAKERGLETLARIILAQDerERdPEEEAALYIDpeKGVSSVYEAIQG 162
                                       **********************************************998844469********************** PP

                             Tex_N 150 ardIiaeeisedaelrkklrellkkegvivsk 181
                                       a+dIiae ised ++r++lr+l+++ gv++s+
  gi|330508304|ref|YP_004384732.1| 163 AMDIIAECISEDIRARSELRSLFWSAGVLESR 194
                                       ****************************9986 PP

>> Tex_YqgF  Tex protein YqgF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.9   0.0   1.6e-47   2.2e-44       2     126 .]     320     442 ..     319     442 .. 0.97

  Alignments for each domain:
  == domain 1  score: 150.9 bits;  conditional E-value: 1.6e-47
                                       -EEEEE--STT-EEEEEE-TTS-EEEEEEE--STTT--HHHHHHHHHHHHHHTT--EEEEESSTTHHHHHHHHHHHH CS
                          Tex_YqgF   2 vvlglDPgyrtGcKlavvdetgkvletaviyphepkkkveeakkklkklvkkykveliaiGnGtasreteklvaeli 78 
                                        vl++DPg+rtGcKl+v+d  g++++++viyphep++k++ea +k+++++++ +ve+ia+GnGta+rete+++++l 
  gi|330508304|ref|YP_004384732.1| 320 CVLAVDPGFRTGCKLVVLDPLGRLIKSDVIYPHEPHNKTREAGSKVARICQENDVEVIAVGNGTAGRETESFLRRLN 396
                                       79************************************************************************986 PP

                                       HHGGG--EEEEE--TTHHHHHHSHHHHHH-TTS-HHHHHHHHHHHHHH CS
                          Tex_YqgF  79 keeelkvkyvivsEaGaSvYSaselaaeEfpdldvslrgavsiarrlq 126
                                           +++++v v+E+GaSvYS+s  a++Efpd d ++rgavsi+rrlq
  gi|330508304|ref|YP_004384732.1| 397 L--PRSISIVPVNESGASVYSTSARARSEFPDQDATVRGAVSIGRRLQ 442
                                       4..4689****************************************9 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.0   6.2e-31   8.6e-28       1      65 []     482     546 ..     482     546 .. 0.99

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 6.2e-31
                             HHH_3   1 vnavgvdiNtAsaeeLqklpGlgpklAknIvayReknGpfksreeLlkvkglgpktfeqlagflr 65 
                                       vn+vgvd+N As e+L++++GlgpklA+++v+yR+++Gpf+sr +Ll v++lgpk+feq+agflr
  gi|330508304|ref|YP_004384732.1| 482 VNQVGVDVNAASIELLARVSGLGPKLAEAVVRYRNEHGPFRSRRDLLAVPRLGPKAFEQAAGFLR 546
                                       79*************************************************************97 PP

>> HHH_9  HHH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2       1.6   2.2e+03      42      69 ..     112     139 ..      67     140 .. 0.64
   2 !   75.9   0.0   2.5e-24   3.5e-21       1      70 []     552     623 ..     552     623 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.6
                             HHH_9  42 kkklaeeevgeptleDIleeLakPgrDp 69 
                                       + +++++e g++tl  I+ +  + +rDp
  gi|330508304|ref|YP_004384732.1| 112 TRAMVAKERGLETLARIILAQDERERDP 139
                                       3445556778888888888877777776 PP

  == domain 2  score: 75.9 bits;  conditional E-value: 2.5e-24
                             HHH_9   1 npLDnTavHPEsYalakkllkklgldlkeligeeallkkldkkklaee..evgeptleDIleeLakPgrDpR 70 
                                       npLD+TavHPE Y+++++++k+lg++++el+++e+ll+ l+ + ++++  +vg+ tl+DIl+eL +PgrDpR
  gi|330508304|ref|YP_004384732.1| 552 NPLDRTAVHPERYPIVERMAKDLGVSISELVENERLLSGLSLEDYMNQegGVGLCTLQDILNELFRPGRDPR 623
                                       9****************************************9999876456********************9 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.5     1e+04      38      63 ..     355     379 ..     352     383 .. 0.79
   2 !   70.1   1.8   1.1e-22   1.5e-19       4      75 .]     643     713 .]     641     713 .] 0.97

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.5
                                       SSSCEESCHHHCEETTEEEEEEEEEE CS
                                S1  38 srdarvedpdevlkvGdevkvkvlkv 63 
                                       +++ ++e +++v ++ +e +v+v+ v
  gi|330508304|ref|YP_004384732.1| 355 HNK-TREAGSKVARICQENDVEVIAV 379
                                       455.7888889999999999999887 PP

  == domain 2  score: 70.1 bits;  conditional E-value: 1.1e-22
                                       TTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1   4 kgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                                       +g  v G+Vt+vt +GafV++g +++g+v++sel+    v++p++v++v ++v vkvl+vd +r+ri+ls+k
  gi|330508304|ref|YP_004384732.1| 643 VGMSVPGIVTNVTSFGAFVDVGVHQDGLVHKSELAKS-YVPVPGDVVRVRQKVMVKVLDVDLERKRISLSMK 713
                                       6889********************************9.9*******************************97 PP

>> HHH_7  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0     8e-11   1.1e-07      10     103 ..     460     547 ..     453     548 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 8e-11
                                       TTGGGS-HHHHHHHHHHHHHHHHHHH-EEHHHHCT-HHHHGGGGGSTT--HHHHHHHHHHHHHC-S----TTHHHHT CS
                             HHH_7  10 PlqellskeellkaletalvdivnlvgvdvnkavankyeaallkyiaGlGprkatdllkklkrlnerlearsqlitk 86 
                                        +q+ + +  l + l+  +   vn+vgvdvn a     + +ll  ++GlGp+ a+ +++  ++  +++ +r +l++ 
  gi|330508304|ref|YP_004384732.1| 460 QYQHDVDPSSLGRSLDDVVAACVNQVGVDVNAA-----SIELLARVSGLGPKLAEAVVRY-RNEHGPFRSRRDLLAV 530
                                       689****************************99.....5679*************99986.67789*********** PP

                                       TSS-HHHHHHHCCCEE- CS
                             HHH_7  87 qilskkvflncagflki 103
                                         l++k f  +agfl i
  gi|330508304|ref|YP_004384732.1| 531 PRLGPKAFEQAAGFLRI 547
                                       ***************98 PP

>> YqgF  Holliday-junction resolvase-like of SPT6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.4     6e+03     120     138 ..     273     293 ..     269     311 .. 0.67
   2 !   29.3   0.0   4.5e-10   6.2e-07      97     147 ..     399     449 ..     353     452 .. 0.93
   3 ?   -1.8   0.0       1.8   2.5e+03      14      33 ..     470     489 ..     468     499 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.4
                                       HHSTT-..-HHHHHHHHHHHH CS
                              YqgF 120 aefrdk..PpllkyavalaRk 138
                                       + fr +  P+l   ++++aR+
  gi|330508304|ref|YP_004384732.1| 273 DSFRRLlaPSLETETISIARQ 293
                                       556553337777888888875 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 4.5e-10
                                       -B--EEE---TTHHHHHTSHHHHHHSTT--HHHHHHHHHHHHHH-HHHHHH CS
                              YqgF  97 stvgvilvddevailYqnskkaeaefrdkPpllkyavalaRkiqdPLleya 147
                                        ++ ++ v++  a  Y  s +a  ef+d+ + ++ av++ R++qdPL e  
  gi|330508304|ref|YP_004384732.1| 399 RSISIVPVNESGASVYSTSARARSEFPDQDATVRGAVSIGRRLQDPLAELV 449
                                       5799999****************************************9976 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.8
                                       T--TTS-EEEEEE-TTS-EE CS
                              YqgF  14 kgrsddaiicvlvngeGevv 33 
                                        grs d ++++ vn++G  v
  gi|330508304|ref|YP_004384732.1| 470 LGRSLDDVVAACVNQVGVDV 489
                                       5899999********99655 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   0.1   4.1e-07   0.00056       5      30 .]     489     514 ..     487     514 .. 0.92
   2 ?   -1.2   0.0       1.7   2.4e+03       7      22 ..     521     536 ..     517     539 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.1e-07
                                       HHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   5 lipasreeLlalPGVGpktAeaIlsy 30 
                                       +++as+e L+ ++G Gpk Aea+  y
  gi|330508304|ref|YP_004384732.1| 489 VNAASIELLARVSGLGPKLAEAVVRY 514
                                       799********************876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                                       TSSHHHHHTSTT-SHH CS
                               HHH   7 pasreeLlalPGVGpk 22 
                                        +sr +Lla+P  Gpk
  gi|330508304|ref|YP_004384732.1| 521 FRSRRDLLAVPRLGPK 536
                                       67899******77776 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.6e-06    0.0049      25      61 ..     494     529 ..     472     543 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.6e-06
                             HHH_6  25 irlGLaaikglgeaaaerivaeRekegpfksledlar 61 
                                       i l La + glg + ae++v+ R+++gpf+s +dl+ 
  gi|330508304|ref|YP_004384732.1| 494 IEL-LARVSGLGPKLAEAVVRYRNEHGPFRSRRDLLA 529
                                       555.99****************************986 PP

>> T2SSK  Type II secretion system (T2SS), protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.9   2.6e+03      23      41 ..     120     138 ..     117     147 .. 0.83
   2 !   15.3   0.0   7.4e-06      0.01     170     233 ..     472     535 ..     465     547 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.9
                             T2SSK  23 lgaealarqiLredaredk 41 
                                       +g e+lar iL++d re++
  gi|330508304|ref|YP_004384732.1| 120 RGLETLARIILAQDERERD 138
                                       799***********87765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 7.4e-06
                             T2SSK 170 arLrPyvtvlpektkiNiNtasaevLaAlveglslsqaqrllaaRpea.gfrsvadflaasalsg 233
                                       + L  +v++   ++ +++N as e+La +   l  + a++++  R+e  +frs  d+la + l+ 
  gi|330508304|ref|YP_004384732.1| 472 RSLDDVVAACVNQVGVDVNAASIELLARVSG-LGPKLAEAVVRYRNEHgPFRSRRDLLAVPRLGP 535
                                       567788999999**************77655.9************8888*********9988776 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00016      0.22      33      52 ..     493     512 ..     468     514 .. 0.63
   2 ?    0.9   0.0      0.51     7e+02       2      13 ..     525     536 ..     522     542 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                       -HHHHHTSTTS-HHHHHHHH CS
                             HHH_5  33 dveeLakipGiGkktAerii 52 
                                       ++e La++ G+G+k+Ae ++
  gi|330508304|ref|YP_004384732.1| 493 SIELLARVSGLGPKLAEAVV 512
                                       45557777777777777654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.51
                                       HHHHTSTT--HH CS
                             HHH_5   2 eeLlsvsGiGpk 13 
                                       ++Ll v+ +Gpk
  gi|330508304|ref|YP_004384732.1| 525 RDLLAVPRLGPK 536
                                       578888888887 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 ?   13.4   0.0   4.2e-05     0.058      14      58 ..     486     534 ..     474     543 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.2e-05
                                       SEETTTS-GGGGGGSTTTTTHHHHHHH....HS---SSGGGGGG-TT-- CS
                              PsbU  14 kvDlnnanvrafrqlrGlyPtlakkiv....knaPYdsvedvlniPgLs 58 
                                        vD+n a++    ++ Gl P+la+ +v    +++P+ s  d+l +P L 
  gi|330508304|ref|YP_004384732.1| 486 GVDVNAASIELLARVSGLGPKLAEAVVryrnEHGPFRSRRDLLAVPRLG 534
                                       49*************************4433469************986 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.2   7.2e+03       8      16 ..      74      82 ..      73      85 .. 0.85
   2 ?   -3.2   0.2       8.3   1.2e+04       7      17 ..     291     301 ..     291     302 .. 0.86
   3 ?    1.9   0.0      0.22     3e+02      26      35 ..     339     348 ..     338     348 .. 0.92
   4 ?    0.7   0.0      0.52   7.2e+02       7      29 ..     365     386 ..     365     390 .. 0.79
   5 ?    8.5   0.0    0.0018       2.5       4      21 ..     564     581 ..     564     582 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.2
                                      HHHHHHCT- CS
                        E3_binding  8 RklAkelGi 16
                                      R lA+++ +
  gi|330508304|ref|YP_004384732.1| 74 RSLARQNQL 82
                                      89****976 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.3
                                       HHHHHHHCT-- CS
                        E3_binding   7 aRklAkelGid 17 
                                       aR  A+e+ i+
  gi|330508304|ref|YP_004384732.1| 291 ARQRAEEKAIE 301
                                       8999****995 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.22
                                       TTTBE-HHHH CS
                        E3_binding  26 pgGRItkeDV 35 
                                       p GR++k DV
  gi|330508304|ref|YP_004384732.1| 339 PLGRLIKSDV 348
                                       78*******9 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.52
                                       HHHHHHHCT--TTTS---CTTTB CS
                        E3_binding   7 aRklAkelGidLsdvkGtGpgGR 29 
                                       + ++ +e+ ++  +v G G  GR
  gi|330508304|ref|YP_004384732.1| 365 VARICQENDVEVIAV-GNGTAGR 386
                                       56999*****66666.8888888 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0018
                                       -HHHHHHHHHCT--TTTS CS
                        E3_binding   4 sPaaRklAkelGidLsdv 21 
                                       +P + ++Ak+lG+++s++
  gi|330508304|ref|YP_004384732.1| 564 YPIVERMAKDLGVSISEL 581
                                       699**********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        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: 00:00:00.43
# Mc/sec: 4957.04
//
Query:       gi|330508305|ref|YP_004384733.1|  [L=219]
Description: orotidine 5'-phosphate decarboxylase [Methanosaeta concilii GP6]
Scores for complete 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-37  128.1   0.0    4.7e-37  127.8   0.0    1.1  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil
  ------ inclusion threshold ------
      0.017   14.5   0.6      0.017   14.5   0.6    2.0  2  ThiG       Thiazole biosynthesis protein ThiG
      0.041   13.2   0.1      0.078   12.3   0.1    1.5  1  TMP-TENI   Thiamine monophosphate synthase
       0.14   12.1   0.0       0.25   11.3   0.0    1.3  1  RST        RCD1-SRO-TAF4 (RST) plant domain


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.8   0.0     1e-40   4.7e-37       2     224 ..       6     207 ..       5     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 1e-40
                                       EEEEEE-SSSHHHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHHS CS
                         OMPdecase   2 nLclalDvatarelleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqata 78 
                                        L+lalDv +++++lel +++ ++++ +K++y+l+ + g       +++++ +   ++++D+K+aD +nt +++++ 
  gi|330508305|ref|YP_004384733.1|   6 SLILALDVLSRDKALELTEQLVDHFDAIKVGYPLILHAG-----LGIVEEISSIS-PVIADLKIADTPNTNRLICE- 75 
                                       59*************************************.....*********96.*******************9. PP

                                       TCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEE CS
                         OMPdecase  79 gsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGf 155
                                         a   ++ad+++++a++Gk+s+ a+a+ ae++g + l+++++ms++g++++        ++e++++ + e++  G+
  gi|330508305|ref|YP_004384733.1|  76 --AVLGAGADAIIAQAFPGKDSLVACADCAESFG-ADLFVVTEMSHPGAEQFMA-----PLAERMARLAVESGASGV 144
                                       ..778****************************8.9******************.....8888888888888999** PP

                                       ECCCHTH.HHHHH...TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 156 vaqetln.ateed...addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                       va +t++ +++ +     d +++ pg+g+ qgg ++        ++  +agad++ivGR++++++dpv++a++
  gi|330508305|ref|YP_004384733.1| 145 VAPATRPeRIRMIrsiIGDKLIISPGVGA-QGGSAG--------EA-LQAGADYLIVGRSVYGSADPVAQAKE 207
                                       *****995323323345566666666665.333333........33.3479*******************997 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.13   5.7e+02     176     190 ..      37      51 ..      21      90 .. 0.77
   2 ?   14.5   0.6   3.7e-06     0.017     162     228 ..     149     216 ..     107     219 .] 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.13
                                       S-BEEES---SHHHH CS
                              ThiG 176 vPvivDAGigspsda 190
                                        P+i+ AG+g  +++
  gi|330508305|ref|YP_004384733.1|  37 YPLILHAGLGIVEEI 51 
                                       588888888876665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.7e-06
                                       S-HHHHHHHHHH-SS-BEEES---SH.HHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHH CS
                              ThiG 162 lnkealkiiieeakvPvivDAGigsp.sdaaqamelGadavllntavaeakdpvamArafklaveaGr 228
                                       + +e +++i++ +   +i+  G+g     a +a++ Gad +++  +v  ++dpva A+ +++ ve  r
  gi|330508305|ref|YP_004384733.1| 149 TRPERIRMIRSIIGDKLIISPGVGAQgGSAGEALQAGADYLIVGRSVYGSADPVAQAKELAAQVEQSR 216
                                       5678899999999999********7626788*****************************99998766 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.7e-05     0.078      67     126 ..     134     195 ..     124     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                          TMP-TENI  67 dlalavgadgvHlgq.ddlpvaearellgpdliiGlSvhslee.aeeaealgadYigvGpif 126
                                       +la + ga gv     +   ++ +r ++g++lii   v  +   a ea ++gadY+ vG   
  gi|330508305|ref|YP_004384733.1| 134 RLAVESGASGVVAPAtRPERIRMIRSIIGDKLIISPGVGAQGGsAGEALQAGADYLIVGRSV 195
                                       67777788887776645568999***********9999999888***************855 PP

>> RST  RCD1-SRO-TAF4 (RST) plant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.6e-05      0.25      41      59 ..     149     167 ..     148     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.6e-05
                               RST  41 sreefvrklRsivGDklLk 59 
                                       +r e +r +Rsi+GDkl++
  gi|330508305|ref|YP_004384733.1| 149 TRPERIRMIRSIIGDKLII 167
                                       577889**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 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:                        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 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1606.36
//
Query:       gi|330508306|ref|YP_004384734.1|  [L=144]
Description: hypothetical protein MCON_2466 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1019.70
//
Query:       gi|330508307|ref|YP_004384735.1|  [L=123]
Description: hypothetical protein MCON_2467 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       482  (0.0268838); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 901.46
//
Query:       gi|330508308|ref|YP_004384736.1|  [L=464]
Description: transposase, IS4 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-20   74.0   1.2    1.8e-20   73.5   0.1    1.8  2  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
      0.093   11.0   0.2       0.37    9.0   0.2    1.8  1  DDE_Tnp_1_4  Transposase DDE domain group 1


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 ?   -1.8   0.1      0.22     2e+03     107     143 ..      25      67 ..       7     133 .. 0.61
   2 !   73.5   0.1     2e-24   1.8e-20      23     212 ..     184     401 ..     151     403 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.22
                         DDE_Tnp_1 107 kkntklyrk......gaeskrrgrlrkhdrnkiltksqkrrnk 143
                                        kn k+ +k      + +++r + +   +++ ++++ q+++ +
  gi|330508308|ref|YP_004384736.1|  25 DKNIKKAIKtskylgRLDRERGMVESHENQESQRSEAQSTDVR 67 
                                       4555555555555554555555555555555555555555555 PP

  == domain 2  score: 73.5 bits;  conditional E-value: 2e-24
                         DDE_Tnp_1  23 arwgykggk.ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDaGYasaelldtleek 98 
                                       a +gy++++ y++ +++++++++ +gl++ ++  pg+v d+k+l   l el++ +gk+++ D+G++s+e++ +l++ 
  gi|330508308|ref|YP_004384736.1| 184 AEKGYNKDRiYIPQINIVLLCSADTGLPTMIRPLPGSVKDIKTLSNSLLELDI-RGKVLILDRGFFSEEIFNFLDKL 259
                                       6789**9999************************************999***9.*********************** PP

                         DDE_Tnp_1  99 gvdyiirlkkntklyrk......................................gaeskrrgrlrkhdrnkiltks 137
                                        ++y+i+++ n+++y+                                       +++ ++++   +++++  l ++
  gi|330508308|ref|YP_004384736.1| 260 EISYLIPARRNSHYYEErihlnehfryhkrlircgckklgnkylylfedqvlmleERDTLYDKLDAGRITKVELHEE 336
                                       *****************888887777777766666666665555555555555554777777788888888888888 PP

                         DDE_Tnp_1 138 qkrrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                        k+ ++          ++ +++ ++  +e  el ++R  +E  F + k++++ drl++++ + v+ ++++ +l+l
  gi|330508308|ref|YP_004384736.1| 337 MKKSGR----------ILIISNRKMNEKEAYELFKRRESVEKMFDTYKSTLSADRLYLHDDESVFGHVFIAFLSL 401
                                       888888..........9999999************************************************9987 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2   4.1e-05      0.37     294     394 ..     328     428 ..     219     433 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 4.1e-05
                       DDE_Tnp_1_4 294 vakaerpaeglnl.rfvvTslaklspeelyeqlYcaRGemEnrIKeakldlaadrtsshsfaaNqlrlllsalAynL 369
                                       ++k+e ++e  +  r+ + s +k++++e y +l+++R  +E ++ + k+ l adr+ +h+ ++    +++++l    
  gi|330508308|ref|YP_004384736.1| 328 ITKVELHEEMKKSgRILIISNRKMNEKEAY-ELFKRRESVEKMFDTYKSTLSADRLYLHDDESVFGHVFIAFLSLYA 403
                                       78888877777777777666666*******.**************************99988776666666666555 PP

                       DDE_Tnp_1_4 370 laalrelalaktelakaevktlrlk 394
                                          l  l  ++ + +k++++ l +k
  gi|330508308|ref|YP_004384736.1| 404 YCKLELLLKKAGANKKMTPDDLLFK 428
                                       5555555555555666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 3318.93
//
Query:       gi|330508309|ref|YP_004384737.1|  [L=104]
Description: hypothetical protein MCON_2471 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.022   15.1   0.2      0.045   14.1   0.2    1.6  1  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   2.5e-06     0.045       4      50 ..      23      85 ..      20      95 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-06
                   Lar_restr_allev  4 kpCPfCggravlersq.rvvaeigq............cvyCadCga.......stpwfkiaedeaea 50
                                      + CP C++++  + ++ +   ei +             ++C +Cg+       +    + + +e ea
  gi|330508309|ref|YP_004384737.1| 23 QACPICKEQNWAIPDNiYELREIKYkelknlkitplvEIICLNCGYtilmnamV----SGIYKEGEA 85
                                      67*****9997765540334444449999*****************98855332....333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 702.68
//
Query:       gi|330508310|ref|YP_004384738.1|  [L=194]
Description: hypothetical protein MCON_2474 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.3   0.3        6.9    6.7   0.0    2.2  2  Thg1      tRNAHis guanylyltransferase


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 ?    5.7   0.0   0.00081        14      43      80 ..      80     121 ..      66     134 .. 0.69
   2 ?    6.7   0.0   0.00039       6.9      61      92 ..     154     185 ..     145     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00081
                              Thg1  43 eralklmneaakelvkef....edivlaYgqSDEislvlske 80 
                                        ++ + mn+ a +l+ +f    e+i l Y++ +E+   +++ 
  gi|330508310|ref|YP_004384738.1|  80 ISIEDFMNANAMNLLMKFysgfENINLTYTNAEEFLNNFQSL 121
                                       346789999999988776432247**********96555554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00039
                              Thg1  61 edivlaYgqSDEislvlsketklynrraqklv 92 
                                       + i++  ++SDEi   + +e k+y+r ++k +
  gi|330508310|ref|YP_004384738.1| 154 NYIIICSTESDEIVAFIMRELKVYSRGESKTA 185
                                       4578899*******99999*******999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1484.80
//
Query:       gi|330508311|ref|YP_004384739.1|  [L=547]
Description: hypothetical protein MCON_2475 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-11   42.9   4.9        0.1   13.5   0.0    6.6  6  WD40             WD domain, G-beta repeat
    7.7e-11   42.2   0.0       0.29   11.5   0.0    5.6  5  ANAPC4_WD40      Anaphase-promoting complex subunit 4 WD40 do
    4.2e-07   29.6   0.3      0.028   13.8   0.0    5.0  6  Nbas_N           Neuroblastoma-amplified sequence, N terminal
    1.1e-05   25.1   0.0      0.058   13.0   0.0    2.7  3  PQQ_2            PQQ-like domain
    2.3e-05   24.2   4.9        2.2    8.3   0.0    5.3  6  PD40             WD40-like Beta Propeller Repeat
      7e-05   23.3   0.0    0.00013   22.4   0.0    1.5  1  Glucosaminidase  Mannosyl-glycoprotein endo-beta-N-acetylgluc
     0.0033   16.4   0.1        2.7    6.9   0.0    4.2  5  Ge1_WD40         WD40 region of Ge1, enhancer of mRNA-decappi
  ------ inclusion threshold ------
      0.027   13.7   0.1        6.7    5.8   0.0    3.4  4  RAB3GAP2_N       Rab3 GTPase-activating protein regulatory su
      0.075   13.0   0.3         69    3.6   0.0    3.7  3  PQQ              PQQ enzyme repeat
       0.18   11.4   0.0        9.1    5.9   0.0    2.4  2  Pep_deformylase  Polypeptide deformylase


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   5.8e-05       0.1      12      38 .]     257     283 ..     244     283 .. 0.78
   2 ?    2.2   0.0      0.21   3.7e+02      15      27 ..     302     314 ..     290     327 .. 0.79
   3 !   11.5   0.1   0.00025      0.44      18      38 .]     346     366 ..     325     366 .. 0.85
   4 !    6.5   0.0    0.0091        16      17      38 .]     387     409 ..     375     409 .. 0.86
   5 ?    3.2   0.0       0.1   1.8e+02      16      33 ..     474     494 ..     447     496 .. 0.81
   6 ?    0.8   0.0       0.6   1.1e+03      15      37 ..     523     545 ..     513     545 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.8e-05
                                       SEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40  12 svtslafspdgawlasGsdDgtvriWd 38 
                                       +v+s+afspdg+ la++s+ g + iWd
  gi|330508311|ref|YP_004384739.1| 257 GVWSVAFSPDGNKLAASSYEGPLLIWD 283
                                       4**************999877777776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.21
                                       EEEEETTSSEEEE CS
                              WD40  15 slafspdgawlas 27 
                                        lafspdg+ la+
  gi|330508311|ref|YP_004384739.1| 302 RLAFSPDGSKLAA 314
                                       589*******975 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00025
                                       EETTSSEEEEEETTSEEEEEE CS
                              WD40  18 fspdgawlasGsdDgtvriWd 38 
                                       f p+g+ l++++ D+t++iWd
  gi|330508311|ref|YP_004384739.1| 346 FRPSGTELVTSDGDNTIYIWD 366
                                       8999*****9966*******9 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0091
                                       EEETTSSEEEEE.ETTSEEEEEE CS
                              WD40  17 afspdgawlasG.sdDgtvriWd 38 
                                       a s dg+ la++  d +tv iWd
  gi|330508311|ref|YP_004384739.1| 387 AISLDGSKLAACnYDERTVSIWD 409
                                       56669999**99779*******9 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.1
                                       EEEETTSSEEEE...EETTSE CS
                              WD40  16 lafspdgawlas...GsdDgt 33 
                                       lafspdg+ la+   Gs D+ 
  gi|330508311|ref|YP_004384739.1| 474 LAFSPDGSKLAAvtvGSFDKI 494
                                       57*******975444777875 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 0.6
                                       EEEEETTSSEEEEEETTSEEEEE CS
                              WD40  15 slafspdgawlasGsdDgtvriW 37 
                                       ++afs d++ la G  Dg v iW
  gi|330508311|ref|YP_004384739.1| 523 AIAFSLDSSKLAIGQNDGYVPIW 545
                                       789999********66**99999 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00021      0.38      18      78 ..     230     295 ..     220     298 .. 0.81
   2 ?    5.6   0.0     0.011        19      44      75 ..     303     336 ..     301     342 .. 0.83
   3 !    5.8   0.0    0.0091        16      45      81 ..     345     381 ..     343     430 .. 0.91
   4 !   11.5   0.0   0.00016      0.29      29      81 ..     449     513 ..     419     525 .. 0.76
   5 ?   -0.5   0.0      0.86   1.5e+03      44      65 ..     524     545 ..     519     547 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                       ANAPC4_WD40  18 ellvfRlngqrvwtl.....eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsv 78 
                                       +++++ ++ ++++ +      ++++ + v s+a++pdg+ La +  +g + + d+ sg+ +++l++
  gi|330508311|ref|YP_004384739.1| 230 NVQAHPVSEEKIVAGtllqqLNCSQYRGVWSVAFSPDGNKLAASSYEGPLLIWDIASGTELQTLET 295
                                       5556666666666666666667888999*******************************9998876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                       ANAPC4_WD40  44 LaWkpdgklLavay..sdgevrlldaesgkvvhs 75 
                                       La++pdg+ La ++  s g++ ++d++sg+ ++ 
  gi|330508311|ref|YP_004384739.1| 303 LAFSPDGSKLAAVTigSMGRILIYDVNSGEKLQW 336
                                       89******99987644789**********98765 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0091
                       ANAPC4_WD40  45 aWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                       a++p+g+ L+ +  d+++ + d+  g+ +++l ++++
  gi|330508311|ref|YP_004384739.1| 345 AFRPSGTELVTSDGDNTIYIWDVIRGTNLETLYTETN 381
                                       689***********************99999887766 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00016
                       ANAPC4_WD40  29 vwtl..........eedkedsevrsLaWkpdgklLavaysdg..evrlldaesgkvvhslsvkse 81 
                                       +w++           +d+++s+ + La++pdg+ La ++  +  ++ ++d++sg+ +  l+ +s+
  gi|330508311|ref|YP_004384739.1| 449 IWDVksgtklrefnLKDNSGSRLSPLAFSPDGSKLAAVTVGSfdKILIYDVNSGEKLLDLKLNST 513
                                       566666666666666899***************999877554449**********9998888776 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.86
                       ANAPC4_WD40  44 LaWkpdgklLavaysdgevrll 65 
                                       +a++ d + La++ +dg v + 
  gi|330508311|ref|YP_004384739.1| 524 IAFSLDSSKLAIGQNDGYVPIW 545
                                       789999999********99875 PP

>> Nbas_N  Neuroblastoma-amplified sequence, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   1.5e-05     0.028     229     260 ..     255     286 ..     246     300 .. 0.87
   2 !    6.0   0.0    0.0037       6.6     233     260 ..     301     330 ..     291     341 .. 0.82
   3 ?   -0.2   0.0      0.27   4.9e+02     233     259 ..     384     411 ..     374     428 .. 0.78
   4 ?   -0.5   0.0      0.34     6e+02     237     272 ..     430     466 ..     425     473 .. 0.77
   5 ?    0.6   0.0      0.16   2.8e+02     232     260 ..     471     501 ..     443     512 .. 0.74
   6 ?    0.6   0.0      0.16   2.8e+02     215     258 ..     504     547 .]     492     547 .] 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                            Nbas_N 229 kdgvfkmslspdgtllavihfsgklsiwdips 260
                                         gv+ +++spdg +la+  + g l iwdi s
  gi|330508311|ref|YP_004384739.1| 255 YRGVWSVAFSPDGNKLAASSYEGPLLIWDIAS 286
                                       579***************************98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0037
                            Nbas_N 233 fkmslspdgtllavihf..sgklsiwdips 260
                                       f++++spdg++la++ +   g++ i+d+ s
  gi|330508311|ref|YP_004384739.1| 301 FRLAFSPDGSKLAAVTIgsMGRILIYDVNS 330
                                       99***********98762269999999988 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.27
                            Nbas_N 233 fkmslspdgtllavihfsgk.lsiwdip 259
                                       +  ++s dg++la+  +  + +siwd  
  gi|330508311|ref|YP_004384739.1| 384 MAQAISLDGSKLAACNYDERtVSIWDTT 411
                                       5567999********99875489**975 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.34
                            Nbas_N 237 lspdgtllavih.fsgklsiwdipslkqrgeweqeeq 272
                                       +s dg++la    +  ++siwd+ s  +  e++ +++
  gi|330508311|ref|YP_004384739.1| 430 FSIDGSKLALHSmLRDEISIWDVKSGTKLREFNLKDN 466
                                       68899999975425789******99877777776655 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.16
                            Nbas_N 232 vfkmslspdgtllavihfs..gklsiwdips 260
                                       +  +++spdg++la++      k+ i+d+ s
  gi|330508311|ref|YP_004384739.1| 471 LSPLAFSPDGSKLAAVTVGsfDKILIYDVNS 501
                                       556789*******999764124677777766 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 0.16
                            Nbas_N 215 kllslklysrkaeekdgvfkmslspdgtllavihfsgklsiwdi 258
                                       kll+lkl s  ++  +g + +++s d ++la+ +  g + iw++
  gi|330508311|ref|YP_004384739.1| 504 KLLDLKLNSTLKQLLNGPYAIAFSLDSSKLAIGQNDGYVPIWAV 547
                                       789999************************************86 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00042      0.76     173     234 ..     267     334 ..     235     337 .. 0.84
   2 !   13.0   0.0   3.2e-05     0.058     157     235 ..     375     459 ..     345     461 .. 0.81
   3 ?   -3.2   0.0       2.8     5e+03     132     150 ..     492     510 ..     473     519 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00042
                             PQQ_2 173 egtVyassgqgrllaldlatgrrl.w.ske.issinglpildgdllyvvsa...gelialdratGavl 234
                                       ++++ ass++g ll +d+a+g +l   ++  + ++     +dg  l  v+    g+++ +d+++G++l
  gi|330508311|ref|YP_004384739.1| 267 GNKLAASSYEGPLLIWDIASGTELqTlETYdFYGFRLAFSPDGSKLAAVTIgsmGRILIYDVNSGEKL 334
                                       5599******************6654455558888888************559************975 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.2e-05
                             PQQ_2 157 selsrvgdisgrpvvaeg.tVyassgqgrllal.dlatgrrl.w.ske.issinglpildgdllyvvsa..gelial 226
                                       + + +++++ ++ ++ +g ++ a+++++r++++ d+++g +l   +   ++ + +    dg  l ++s   +e+  +
  gi|330508311|ref|YP_004384739.1| 375 TLYTETNRTMAQAISLDGsKLAACNYDERTVSIwDTTNGVKLqEiELNhPADFAA-FSIDGSKLALHSMlrDEISIW 450
                                       4445788888888888888**********99999*****9665457777999999.999*********67******* PP

                             PQQ_2 227 dratGavlW 235
                                       d+++G++l+
  gi|330508311|ref|YP_004384739.1| 451 DVKSGTKLR 459
                                       *****9875 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.8
                             PQQ_2 132 gklvaldpkdGkvlWerel 150
                                        k+ ++d+ +G++l + +l
  gi|330508311|ref|YP_004384739.1| 492 DKILIYDVNSGEKLLDLKL 510
                                       3555566666666555554 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0012       2.2      15      29 ..     262     276 ..     260     283 .. 0.83
   2 !    6.4   0.1    0.0049       8.8      15      24 ..     304     313 ..     296     313 .. 0.88
   3 ?   -3.1   0.0       4.7   8.4e+03      16      24 ..     388     396 ..     387     396 .. 0.83
   4 ?   -1.8   0.0       1.9   3.4e+03      14      24 ..     428     438 ..     423     438 .. 0.84
   5 !    6.0   0.0    0.0066        12      15      24 ..     475     484 ..     474     484 .. 0.92
   6 ?    0.1   0.0      0.47   8.4e+02       2      24 ..     515     534 ..     514     535 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                                       EE-TTSSEEEEEEEC CS
                              PD40  15 sfSPDGkrlaFsSdR 29 
                                       +fSPDG++la sS+ 
  gi|330508311|ref|YP_004384739.1| 262 AFSPDGNKLAASSYE 276
                                       8********977774 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0049
                                       EE-TTSSEEE CS
                              PD40  15 sfSPDGkrla 24 
                                       +fSPDG++la
  gi|330508311|ref|YP_004384739.1| 304 AFSPDGSKLA 313
                                       8*******97 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4.7
                                       E-TTSSEEE CS
                              PD40  16 fSPDGkrla 24 
                                       +S DG++la
  gi|330508311|ref|YP_004384739.1| 388 ISLDGSKLA 396
                                       788***997 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 1.9
                                       EEE-TTSSEEE CS
                              PD40  14 PsfSPDGkrla 24 
                                        +fS DG++la
  gi|330508311|ref|YP_004384739.1| 428 AAFSIDGSKLA 438
                                       68999***997 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.0066
                                       EE-TTSSEEE CS
                              PD40  15 sfSPDGkrla 24 
                                       +fSPDG++la
  gi|330508311|ref|YP_004384739.1| 475 AFSPDGSKLA 484
                                       7*******97 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 0.47
                                       EE--SSSS.EEEEEE-TTSSEEE CS
                              PD40   2 krltntpgnegaPsfSPDGkrla 24 
                                       k+l+n+p    a++fS D ++la
  gi|330508311|ref|YP_004384739.1| 515 KQLLNGPY---AIAFSLDSSKLA 534
                                       67777777...899999999987 PP

>> Glucosaminidase  Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   7.4e-08   0.00013       5      86 ..      98     206 ..      94     207 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.4e-08
                                       HHHHHHCT.-HHHHHHHHHHHHTTTTC...HHHHHCT-TSE.B.........HCTE-SSHHHHHHHH.SHHHH.... CS
                   Glucosaminidase   5 leaakkygippsvalaqaalEsgwgts...rlakeqnNlfGik.........kfrkydsveesirah.kllss.... 64 
                                       + a++  +++p++++a a+lE g+gt    +  +e++N fG            f   ds+ + ++   +++ +    
  gi|330508311|ref|YP_004384739.1|  98 IVAGQSNNVNPAFLVATACLEGGFGTLgwaASHPECHNTFGYGipngstspdDFNCMDSWCAMVQKVaSVIAHgtny 174
                                       66788899*****************6633355677******533344455552333333333333332233333333 PP

                                       ...........HCCHECECTHCCHHHHHHHHCT CS
                   Glucosaminidase  65 ...........skkyatdpaYaekliaiikklk 86 
                                                  + kya dp+ a+++++++++l+
  gi|330508311|ref|YP_004384739.1| 175 ysqgrytisqvRAKYAADPN-ADSIASLMNELY 206
                                       22344444333333887777.999999999875 PP

>> Ge1_WD40  WD40 region of Ge1, enhancer of mRNA-decapping protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0015       2.7     183     216 ..     251     284 ..     214     292 .. 0.73
   2 ?   -0.7   0.0       0.3   5.4e+02     194     218 ..     304     330 ..     301     356 .. 0.73
   3 ?   -2.9   0.0       1.4   2.5e+03     194     218 ..     345     369 ..     340     400 .. 0.64
   4 ?    2.4   0.0     0.035        64     162     207 ..     442     488 ..     433     506 .. 0.70
   5 ?    0.0   0.0      0.18   3.2e+02     194     216 ..     525     547 .]     508     547 .] 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0015
                          Ge1_WD40 183 kieehsliveaafspdGtalatasedGevkffqv 216
                                       + ++   + + afspdG  la++s +G +  + +
  gi|330508311|ref|YP_004384739.1| 251 NCSQYRGVWSVAFSPDGNKLAASSYEGPLLIWDI 284
                                       33344458999****************9988877 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.3
                          Ge1_WD40 194 afspdGtalatas..edGevkffqvyl 218
                                       afspdG  la+ +  + G +  + v+ 
  gi|330508311|ref|YP_004384739.1| 304 AFSPDGSKLAAVTigSMGRILIYDVNS 330
                                       799999999976511456666666654 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.4
                          Ge1_WD40 194 afspdGtalatasedGevkffqvyl 218
                                       af p Gt l t+  d ++  + v  
  gi|330508311|ref|YP_004384739.1| 345 AFRPSGTELVTSDGDNTIYIWDVIR 369
                                       5677777777777777777776643 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.035
                          Ge1_WD40 162 miaskygsgelsve.eieegllkieehsliveaafspdGtalatase 207
                                       m++ + +++++++  +++e  lk ++ s ++  afspdG  la+ + 
  gi|330508311|ref|YP_004384739.1| 442 MLRDEISIWDVKSGtKLREFNLKDNSGSRLSPLAFSPDGSKLAAVTV 488
                                       56666666666543044455666666789999********9997654 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 0.18
                          Ge1_WD40 194 afspdGtalatasedGevkffqv 216
                                       afs d   la+  +dG+v  + v
  gi|330508311|ref|YP_004384739.1| 525 AFSLDSSKLAIGQNDGYVPIWAV 547
                                       89****************98865 PP

>> RAB3GAP2_N  Rab3 GTPase-activating protein regulatory subunit N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.095   1.7e+02     241     336 ..     185     284 ..     151     292 .. 0.54
   2 ?    5.8   0.0    0.0038       6.7     311     339 ..     301     331 ..     290     335 .. 0.86
   3 ?   -1.7   0.0      0.73   1.3e+03     381     409 ..     437     465 ..     436     471 .. 0.85
   4 ?    1.7   0.0     0.067   1.2e+02     303     339 ..     463     502 ..     453     505 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.095
                        RAB3GAP2_N 241 ssqpllsdvasavaskltsal..fslakswlGgssk.sseeqqtkkeekkkpkvepaaplsl.rfgL.kDskReges 312
                                        + + ++d   + ++ l ++l  fs+  +  + s++ ++++++t ++ +++p +e++  + + +  L +   R + s
  gi|330508311|ref|YP_004384739.1| 185 VRAKYAADPNADSIASLMNELytFSINHKLASLSTSiAADQTPT-TNVQAHPVSEEKIVAGTlLQQLnCSQYRGVWS 260
                                       44444444444444445555534555555555555544444444.55566665554444443033442356799999 PP

                        RAB3GAP2_N 313 ivlsPsgrlaavtDsLgRVlLlDv 336
                                       ++ sP+g+ +a++   g  l++D+
  gi|330508311|ref|YP_004384739.1| 261 VAFSPDGNKLAASSYEGPLLIWDI 284
                                       ******655554444555555555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0038
                        RAB3GAP2_N 311 esivlsPs.grlaavt.DsLgRVlLlDvqag 339
                                        +++ sP+  +laavt  s+gR+l+ Dv+ g
  gi|330508311|ref|YP_004384739.1| 301 FRLAFSPDgSKLAAVTiGSMGRILIYDVNSG 331
                                       67999***7779999978**********987 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.73
                        RAB3GAP2_N 381 LvIYaprrgilEvWsmqngpRvaafnvgk 409
                                       L++++  r  + +W +++g+++  fn + 
  gi|330508311|ref|YP_004384739.1| 437 LALHSMLRDEISIWDVKSGTKLREFNLKD 465
                                       77888889999**********99998765 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.067
                        RAB3GAP2_N 303 LkDskReges.ivlsPs.grlaavt.DsLgRVlLlDvqag 339
                                       LkD   + +s ++ sP+  +laavt  s++++l+ Dv+ g
  gi|330508311|ref|YP_004384739.1| 463 LKDNSGSRLSpLAFSPDgSKLAAVTvGSFDKILIYDVNSG 502
                                       55555444444999***66799998679********9976 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.038        69      10      23 ..     321     334 ..     315     334 .. 0.90
   2 ?    0.5   0.0      0.38   6.8e+02      16      35 ..     451     470 ..     447     472 .. 0.90
   3 ?    3.6   0.0     0.041        73       3      23 ..     486     505 ..     485     505 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.038
                                       SEEEEEETTTCCEE CS
                               PQQ  10 GylyAlDadTGkvl 23 
                                       G+++ +D+++G++l
  gi|330508311|ref|YP_004384739.1| 321 GRILIYDVNSGEKL 334
                                       8**********986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.38
                                       ETTTCCEEEEEESSSCGSSE CS
                               PQQ  16 DadTGkvlWrfktggpvlsl 35 
                                       D+++G++l +f+++++  s+
  gi|330508311|ref|YP_004384739.1| 451 DVKSGTKLREFNLKDNSGSR 470
                                       99************998875 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.041
                                       EEEEETTSEEEEEETTTCCEE CS
                               PQQ   3 vylgsadGylyAlDadTGkvl 23 
                                       v +gs+d +++ +D+++G++l
  gi|330508311|ref|YP_004384739.1| 486 VTVGSFD-KILIYDVNSGEKL 505
                                       6789999.9*********986 PP

>> Pep_deformylase  Polypeptide deformylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0051       9.1      42      71 ..     308     337 ..     291     361 .. 0.83
   2 ?    2.7   0.0     0.047        85      42      69 ..     479     506 ..     463     524 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0051
                                       T-SEEEGGGGT--BSEEEEECCSS-ETT.. CS
                   Pep_deformylase  42 kgvgLAApQigvnkrlfvielpseeeeeee 71 
                                       +g +LAA+ ig   r+ +++++s+e++++ 
  gi|330508311|ref|YP_004384739.1| 308 DGSKLAAVTIGSMGRILIYDVNSGEKLQWI 337
                                       6899*********************98765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.047
                                       T-SEEEGGGGT--BSEEEEECCSS-ETT CS
                   Pep_deformylase  42 kgvgLAApQigvnkrlfvielpseeeee 69 
                                       +g +LAA+ +g   ++ +++++s+e++ 
  gi|330508311|ref|YP_004384739.1| 479 DGSKLAAVTVGSFDKILIYDVNSGEKLL 506
                                       6899*******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 3750.85
//
Query:       gi|330508312|ref|YP_004384740.1|  [L=69]
Description: IS3/IS66 family element, Orf1 protein [Methanosaeta concilii GP6]
Scores for complete 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   40.4   0.1    2.9e-10   40.3   0.1    1.1  1  HTH_Tnp_1      Transposase
    6.6e-05   22.6   0.5    9.2e-05   22.1   0.5    1.3  1  HTH_23         Homeodomain-like domain
  ------ inclusion threshold ------
      0.052   13.6   0.0      0.068   13.2   0.0    1.2  1  HTH_29         Winged helix-turn helix
      0.064   13.4   0.1        0.1   12.8   0.1    1.3  1  HTH_28         Helix-turn-helix domain
      0.067   13.2   0.0      0.072   13.1   0.0    1.1  1  HTH_Tnp_IS630  Transposase


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.1     8e-14   2.9e-10       2      49 ..       3      49 ..       2      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 8e-14
                         HTH_Tnp_1  2 rrrrrwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyre 49
                                      ++rrr+++ fK+ +++e  e+gk+ +++Ar++ ++ + L +Wrr+  e
  gi|330508312|ref|YP_004384740.1|  3 KTRRRYDRDFKILVLAEL-EAGKPLAQIAREYSIHLSLLCRWRRELDE 49
                                      79***************9.**************************853 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.5   2.6e-08   9.2e-05       8      41 ..      14      47 ..       1      55 [. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.6e-08
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrwlkry 41
                                      +++l  l  G++ ++IAre+ ++ + ++rw++  
  gi|330508312|ref|YP_004384740.1| 14 ILVLAELEAGKPLAQIAREYSIHLSLLCRWRREL 47
                                      445555666**********************986 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.9e-05     0.068       2      38 ..      14      49 ..      13      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                            HTH_29  2 aqallllaeGvstvsqiAkllglsrrtvyrwlkrfee 38
                                      +++l+ l+ G +  +qiA+ + ++ +  +rw++  +e
  gi|330508312|ref|YP_004384740.1| 14 ILVLAELEAGKP-LAQIAREYSIHLSLLCRWRRELDE 49
                                      789999*****9.*******************98776 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.8e-05       0.1       1      38 [.      12      49 ..      12      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                            HTH_28  1 qRleiikllaaGhsvreaArelgisrrtvyrWikryee 38
                                      +++ ++ +l aG++ +++Are+ i+ + + rW++ ++e
  gi|330508312|ref|YP_004384740.1| 12 FKILVLAELEAGKPLAQIAREYSIHLSLLCRWRRELDE 49
                                      6888999**********************999998765 PP

>> HTH_Tnp_IS630  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     2e-05     0.072       3      46 ..       8      51 ..       6      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                     HTH_Tnp_IS630  3 ydldlrlkvidyiesGggitkaskvfkvgratvyrWlkreelaa 46
                                      yd+d+++ v++ +e+G+ + ++ + + +  + + rW +  +  +
  gi|330508312|ref|YP_004384740.1|  8 YDRDFKILVLAELEAGKPLAQIAREYSIHLSLLCRWRRELDENP 51
                                      9***********************************76655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 483.37
//
Query:       gi|330508313|ref|YP_004384741.1|  [L=280]
Description: glutamine cyclotransferase [Methanosaeta concilii GP6]
Scores for complete 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-98  326.7   0.0    1.1e-97  326.4   0.0    1.0  1  Glu_cyclase_2  Glutamine cyclotransferase


Domain annotation for each model (and alignments):
>> Glu_cyclase_2  Glutamine cyclotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.4   0.0  6.2e-102   1.1e-97       4     251 .]      23     273 ..      19     273 .. 0.93

  Alignments for each domain:
  == domain 1  score: 326.4 bits;  conditional E-value: 6.2e-102
                     Glu_cyclase_2   4 alalallaaaeaaea.k.aasaaeelkvevvaeyphdpeaftqGLefedgelyestGlegksslrkvdletgkvlke 78 
                                       a+ +a++a+a++ +  + ++s+ +++++++v++yphdp+aftqGLe++dg lye+tG +g+sslr+vd++tg+v++ 
  gi|330508313|ref|YP_004384741.1|  23 AALTAGSASADKVDIdSfTSSSIKTYSYRIVNSYPHDPNAFTQGLEYDDGLLYEGTGGYGQSSLRRVDIQTGRVVDI 99 
                                       333444444445554557999******************************************************** PP

                     Glu_cyclase_2  79 aeldeelFgEGitvlgdklyqltwkegvafvydaetleeigrvsyegeGWGlttdgkrlvmsdGsstltfldpktfa 155
                                       ++l++e+F+EGi+ ++d+++qltw++ ++fv+d+e+l+++g++sy++eGWG+t+d +rl+msdGs++l+fldp++++
  gi|330508313|ref|YP_004384741.1| 100 VHLEDEFFAEGIAIWKDRIIQLTWRSYQGFVWDKENLTRTGSFSYRREGWGITSDASRLIMSDGSDALYFLDPNDYS 176
                                       ***************************************************************************** PP

                     Glu_cyclase_2 156 etksvevtkdgkevsklNELeyvkgeiyaNvwqtdrilridpatGkvtgvidlsalreeaek.aakedVlNGiAydp 231
                                        ++s++vt+dg++v+ lNELey++g+iyaN+w ++ i++i+p+tG+vtg idls++++e +  +   dVlNGiAydp
  gi|330508313|ref|YP_004384741.1| 177 LQGSIRVTADGEPVKGLNELEYINGMIYANLWPSTWIAIISPDTGEVTGRIDLSGIMDEGDIpKRWVDVLNGIAYDP 253
                                       *********************************************************9998834445********** PP

                     Glu_cyclase_2 232 etdrlfvTGKlWpklfevkl 251
                                       ++drlfvTGKlWp+lfe++l
  gi|330508313|ref|YP_004384741.1| 254 SEDRLFVTGKLWPSLFEIEL 273
                                       ******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2040.34
//
Query:       gi|330508314|ref|YP_004384742.1|  [L=251]
Description: rhomboid family protein [Methanosaeta concilii GP6]
Scores for complete sequence (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  116.4  19.4    1.1e-33  116.4  19.4    1.6  2  Rhomboid  Rhomboid family
    1.1e-05   25.9   0.2    1.1e-05   25.9   0.2    2.4  3  DUF1751   Eukaryotic integral membrane protein (DUF1751)


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.25   2.2e+03      86      94 ..      74      82 ..      55     101 .. 0.48
   2 !  116.4  19.4   1.2e-37   1.1e-33       5     148 ..     102     245 ..      98     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.25
                                      HHHHHHCCC CS
                          Rhomboid 86 llvlvprnr 94
                                      +++lv+   
  gi|330508314|ref|YP_004384742.1| 74 ICILVFLLS 82
                                      111111111 PP

  == domain 2  score: 116.4 bits;  conditional E-value: 1.2e-37
                                       C-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S...-EESSHHHHHH CS
                          Rhomboid   5 gelwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaesesplvGaSGaifg 81 
                                       ++ w++lt+mf+H+++ Hl+fNml+l++fG +lerr+G  +fl +y+lsg++++l++ ++++ s+  +vGaSGa+fg
  gi|330508314|ref|YP_004384742.1| 102 ERPWTILTHMFVHFSFDHLFFNMLFLFFFGMELERRVGGRKFLQIYILSGIVAALAQTAVTSGSMVGMVGASGALFG 178
                                       678************************************************************************** PP

                                       HHHHHHHHHHCCCCGS----HC.....CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHHHHHHHHHHCCH CS
                          Rhomboid  82 llgallvlvprnrkllrkliia..llllllfillnlvlgllpraggvsnlAHlgGllaGlllgllllrr 148
                                        lg+l++  p+ r ll+++i++    ++++f+l++++++   +a++++++AH++Gl +Gl++g ++ ++
  gi|330508314|ref|YP_004384742.1| 179 ALGCLAIIAPEIRVLLFFVIPMsiRWAVVVFALIDFLFMG--SADNIAHMAHIAGLFVGLAFGQMMKNQ 245
                                       **********************665566666666666665..5557****************9998776 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   0.2       1.1   9.8e+03      61      70 ..      73      82 ..      63      90 .. 0.51
   2 !   25.9   0.2   1.2e-09   1.1e-05       1      65 [.      97     161 ..      97     179 .. 0.90
   3 ?    0.8   0.5     0.081   7.2e+02      49      85 ..     194     231 ..     189     241 .. 0.45

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                           DUF1751 61 lvvlltllly 70
                                      l+++l +ll+
  gi|330508314|ref|YP_004384742.1| 73 LICILVFLLS 82
                                      3333333333 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.2e-09
                           DUF1751   1 PgallpypwtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvll 65 
                                       P+ ++  pwt+lt++fv  ++ ++ +++l l+++g  lEr  g + +l+  ++ +++++l  +++
  gi|330508314|ref|YP_004384742.1|  97 PHFVVERPWTILTHMFVHFSFDHLFFNMLFLFFFGMELERRVGGRKFLQIYILSGIVAALAQTAV 161
                                       788899*************************************9999998888888888876655 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.081
                           DUF1751  49 kFilvvnvitnllvvlltlllylvtksee.lll.vpisG 85 
                                        F+++  +i   +vv++ l+ +l++ s + +   ++i+G
  gi|330508314|ref|YP_004384742.1| 194 LFFVIPMSIRWAVVVFA-LIDFLFMGSADnIAHmAHIAG 231
                                       45555555544433333.333333333330222244544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1733.57
//
Query:       gi|330508315|ref|YP_004384743.1|  [L=161]
Description: hypothetical protein MCON_2481 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-21   77.8   0.0    1.4e-21   77.5   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 !   77.5   0.0     8e-26   1.4e-21       1     146 [.      22     153 ..      22     154 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 8e-26
                               NYN   1 rvavfiDgenlpvpakgkevdyrklleeirskgelvraraygnwedeeqnkfqdalsstgi.kvkhkplkkrggsgk 76 
                                       r+++++Dg n+    k+ ++d++++++ ++ +g+++  ++++n+++   +k+ +a +++g+ +v             
  gi|330508315|ref|YP_004384743.1|  22 RIGLLVDGPNMLR--KEFQMDLEEIRDILKDYGDIKMGKVFLNQYA--SEKLVEAVENQGFePVICT---------- 84 
                                       799**********..6668************************444..48999********888444.......... PP

                               NYN  77 kavDvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaadefisl 146
                                        +vDv++av+ ++++y++ +dt+ Lv++D+D+ p++ k++e+gk++++++ae +  s +L+++ad++i+l
  gi|330508315|ref|YP_004384743.1|  85 SDVDVRMAVEGVDMIYNPVIDTLALVTRDADLKPVLMKAMEHGKETIIFGAE-PGFSVALRNSADYVIVL 153
                                       67****************99******************************65.99************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1145.44
//
Query:       gi|330508316|ref|YP_004384744.1|  [L=268]
Description: deoxyribonuclease [Methanosaeta concilii GP6]
Scores for complete 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-66  222.4   0.1      7e-66  222.2   0.1    1.0  1  TatD_DNase    TatD related DNase
  ------ inclusion threshold ------
      0.073   12.8   0.1        1.3    8.7   0.0    2.4  2  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.2   0.1   7.9e-70     7e-66       1     255 []      21     266 ..      21     266 .. 0.95

  Alignments for each domain:
  == domain 1  score: 222.2 bits;  conditional E-value: 7.9e-70
                                       EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHH CS
                        TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleel 77 
                                       iD+HcHld+k f++dre+++e+a++agv ++++ g++  ++++ lelak+y+  + a+lG+ Pn++d +++  ++ +
  gi|330508316|ref|YP_004384744.1|  21 IDSHCHLDFKHFNKDREAVMENARKAGVVRMINSGVDYSTNSKSLELAKNYDF-ISATLGLSPNSIDGKNDPEIKMI 96 
                                       8***************************************************9.*************9988888888 PP

                                       HHHHHCCCTSEEEEEEEEEET-.CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEE CS
                        TatD_DNase  78 kelanvkhskvvaiGeiGLDyy.sreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvv 153
                                        +  + + s++v+iGe GLDyy  ++   +e+q e+F++ +++A+ l+lplviH+r+ae+  l+++k ++    kvv
  gi|330508316|ref|YP_004384744.1|  97 LDQIESNASQAVGIGEAGLDYYhTKDAPSRERQAEIFKKVIAIAESLNLPLVIHSRDAEQPALDMVKHLD----KVV 169
                                       777799***************735666778**************************************84....79* PP

                                       ETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHH CS
                        TatD_DNase 154 lHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvvek 230
                                       +H++sg+  ++k++ ++gyyisl+ +++ +   +++ l+++v ld lL+ETD+P+l+p   r+ rnepanv  +v+ 
  gi|330508316|ref|YP_004384744.1| 170 FHCYSGTLPTMKEAQDRGYYISLATNVCRS--GHHQILARNVSLDHLLVETDSPFLSP---RKGRNEPANVLDSVRL 241
                                       ****************************94..4566667*******************...789************* PP

                                       HHHHHTS-HHHHHHHHHHHHHHHHH CS
                        TatD_DNase 231 laelkaltleelaeitaeNakrlfk 255
                                       +a++k+l+++e+a++ta+N+kr+++
  gi|330508316|ref|YP_004384744.1| 242 IARIKGLEPQEVAAQTATNTKRIYN 266
                                       **********************996 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       0.4   3.5e+03       1       9 [.      21      29 ..      21      57 .. 0.62
   2 ?    8.7   0.0   0.00015       1.3     132     290 ..     134     266 ..      97     267 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.4
                                      EEEEEEE.. CS
                      Amidohydro_2  1 iDvHaHllp 9 
                                      iD H+Hl  
  gi|330508316|ref|YP_004384744.1| 21 IDSHCHLDF 29
                                      899999633 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHT-EEEEE....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHH CS
                      Amidohydro_2 132 rpifealeelglpvdihtGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrpn 208
                                        ++ +++e l+lp+ ih               +r    ++l+ + +k+  l+ v+ H+  +   l+++ e+ +r+  
  gi|330508316|ref|YP_004384744.1| 134 KKVIAIAESLNLPLVIH---------------SRDAEQPALD-M-VKH--LDKVVFHCYSG--TLPTMKEAQDRG-- 187
                                       56666777777777777...............2222222222.1.222..44455566555..233333332222.. PP

                                       CCEEECCGHHHSSEEECCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHH.......SSHHHHH CS
                      Amidohydro_2 209 vyvklsglytellyfdspladppalarlieavgpdrilfGsDyPhptleaepealalldlval.......lsdeere 278
                                       +y  +s          + + +  +   l   v  d++l  +D P+ +++  + + a++ +  +       l ++e++
  gi|330508316|ref|YP_004384744.1| 188 YY--ISL--------ATNVCRSGHHQILARNVSLDHLLVETDSPFLSPRKGRNEPANVLDSVRliarikgLEPQEVA 254
                                       34..222........56677777788888999999999999999999999999999888777789999999999999 PP

                                       HHHTHHHHHHCT CS
                      Amidohydro_2 279 kilggNAarlyg 290
                                       +   +N  r+y+
  gi|330508316|ref|YP_004384744.1| 255 AQTATNTKRIYN 266
                                       999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1986.21
//
Query:       gi|330508317|ref|YP_004384745.1|  [L=518]
Description: (R)-citramalate synthase [Methanosaeta concilii GP6]
Scores for complete 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-84  282.1   3.4    4.6e-84  282.1   3.4    1.7  2  HMGL-like   HMGL-like
    1.4e-30  105.9   3.4      3e-30  104.8   3.4    1.6  1  LeuA_dimer  LeuA allosteric (dimerisation) domain


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.1   3.4   5.1e-88   4.6e-84       1     264 []      19     277 ..      19     277 .. 0.99
   2 ?   -2.2   0.0      0.27   2.4e+03     118     132 ..     357     371 ..     329     431 .. 0.58

  Alignments for each domain:
  == domain 1  score: 282.1 bits;  conditional E-value: 5.1e-88
                                       B-EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHH CS
                         HMGL-like   1 kvkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekd 77 
                                       kv+i+dttLRDGeq+++++l+++ek++ia++Ld++gv++iE+gfp++s+++f++vr+ia+++ +a++++l r ++kd
  gi|330508317|ref|YP_004384745.1|  19 KVRIFDTTLRDGEQTPGVSLTTDEKIQIARQLDKLGVNVIEAGFPVSSKGEFDSVRQIARSGLQAQVCGLSRIVKKD 95 
                                       699************************************************************************** PP

                                       HHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHH CS
                         HMGL-like  78 ikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevvea 154
                                        +a  +    a ++ vhvf +ts++++ + +k++ +e+++ a + v+++++ g  + +s++da+rt++efl ++ +a
  gi|330508317|ref|YP_004384745.1|  96 AQACLD----ADVDLVHVFSPTSDIQIAHTIKMSHDEIVEGAMRTVELVKDNGRTCLFSAMDATRTSPEFLHRIFKA 168
                                       ******....******************************************************************* PP

                                       HHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSB CS
                         HMGL-like 155 aeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGera 231
                                       +ee+ +++ini+DtvGv+ P+++++l++ + + v   + + vHcHnd+GlAvan+laAveaGa++v ++vnGlGera
  gi|330508317|ref|YP_004384745.1| 169 VEEVHCDIINIPDTVGVAVPSSFYRLVKDICDDVH--MVVDVHCHNDFGLAVANSLAAVEAGAREVQVCVNGLGERA 243
                                       ***********************************..**************************************** PP

                                       BB-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 232 Gnaaleelvaalealg.vdtgldlqklrsiaalv 264
                                       Gna l e+v+ l+    ++t ++++ l ++a+++
  gi|330508317|ref|YP_004384745.1| 244 GNANLAEVVMGLHSIYnAKTSIKTEYLVETARMI 277
                                       *************9877************99986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHTT-E CS
                         HMGL-like 118 kaeeavkaarslgkd 132
                                       + +e+++++++lg++
  gi|330508317|ref|YP_004384745.1| 357 QLQEILERIKELGDK 371
                                       344444444444444 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   3.4   3.4e-34     3e-30       7     132 ..     383     509 ..     374     510 .. 0.90

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 3.4e-34
                                       XXXXXXXXXXXXX--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH..T-EEEEE CS
                        LeuA_dimer   7 lealvkdelleaeerlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv..dikLldY 81 
                                       + ++v   + ++++ + l++++v++g+  ++tatvk+ v  g+ek+ + +G+GpvdA++nA++ +l++  +i+L d+
  gi|330508317|ref|YP_004384745.1| 383 IADVVIGDVAKESQAVVLKEVSVMTGNIITPTATVKAMV-RGKEKVLANTGVGPVDAAVNAVQGLLDSdtSIHLCDF 458
                                       34444455556779*************************.99**************************6666***** PP

                                       EEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHH CS
                        LeuA_dimer  82 svhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrl 132
                                       +++ai++g+da+aev + +e d g++vs++++++div+AS++Al+sa+nrl
  gi|330508317|ref|YP_004384745.1| 459 RIEAISGGADALAEVVIGVEDDRGRRVSARSAREDIVMASVEALVSAINRL 509
                                       ********************888999***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); 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: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3591.50
//
Query:       gi|330508318|ref|YP_004384746.1|  [L=485]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-69  226.7  20.4    1.9e-09   37.0   0.3   13.5 14  TPR_1         Tetratricopeptide repeat
    4.6e-62  205.4  13.9    2.3e-07   30.4   0.3   11.3 11  TPR_11        TPR repeat
    2.3e-60  195.9  19.0    3.7e-07   29.8   0.4   13.1 13  TPR_2         Tetratricopeptide repeat
    4.2e-52  170.0  14.9    1.3e-05   25.0   0.2   12.4 13  TPR_8         Tetratricopeptide repeat
    1.4e-44  147.3  20.0     0.0026   18.0   0.0   12.2 12  TPR_17        Tetratricopeptide repeat
    1.7e-43  147.0  14.7    4.1e-09   36.9   0.4    7.7  8  TPR_16        Tetratricopeptide repeat
    5.3e-36  120.2  14.5     0.0013   19.4   0.4   11.4 11  TPR_14        Tetratricopeptide repeat
    4.5e-30  103.6   8.8    0.00032   20.8   0.7    8.3  8  TPR_9         Tetratricopeptide repeat
    6.6e-26   90.4  22.9    1.6e-06   28.3   0.1    9.5 10  TPR_12        Tetratricopeptide repeat
    3.7e-21   75.4  18.8    5.7e-06   26.7   0.0    8.3 12  TPR_19        Tetratricopeptide repeat
      1e-17   63.5   6.5      0.095   13.4   0.0    9.5  9  TPR_6         Tetratricopeptide repeat
    5.8e-15   56.0   6.5      0.002   18.5   0.0    5.1  5  BTAD          Bacterial transcriptional activator domain
    5.7e-14   52.1   8.6     0.0017   18.6   0.0    5.4  7  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
      7e-10   38.2  12.9      0.019   15.0   0.6    7.7  7  TPR_7         Tetratricopeptide repeat
    1.4e-09   38.2  14.7        0.8    9.8   0.0    8.6  9  DUF3856       Domain of Unknown Function (DUF3856)
      9e-09   34.8   1.8       0.36    9.7   0.0    4.9  7  NARP1         NMDA receptor-regulated protein 1
    1.4e-08   34.7   1.0       0.91    9.6   0.0    6.2  6  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
    7.4e-08   32.0   3.6       0.28   10.4   0.0    5.2  5  FAT           FAT domain
    2.5e-06   27.5   0.0      0.011   15.7   0.0    3.8  4  SRP_TPR_like  Putative TPR-like repeat
    8.9e-06   25.4  25.8      0.049   13.5   0.6    8.5  9  TPR_10        Tetratricopeptide repeat
     0.0067   15.7  15.4       0.55    9.4   0.2    4.6  5  TPR_15        Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.01   15.9   7.0        9.7    6.3   0.1    6.5  6  MIT           MIT (microtubule interacting and transport) dom
      0.012   15.2   4.7        4.1    7.1   0.0    5.6  5  HTH_Bact      Helix-turn-helix bacterial domain
      0.013   15.8   5.0        6.9    7.1   0.2    4.3  5  TPR_20        Tetratricopeptide repeat
      0.026   14.8   0.3         21    5.6   0.0    4.5  3  PPR           PPR repeat
      0.049   12.5   0.0       0.35    9.7   0.0    2.1  2  DUF5588       Family of unknown function (DUF5588)


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.2e-05     0.029       2      34 .]      44      76 ..      43      76 .. 0.86
   2 !   20.3   0.0   4.9e-07   0.00034       1      33 [.      77     109 ..      77     110 .. 0.94
   3 !   25.4   0.1   1.2e-08   8.3e-06       1      33 [.     111     143 ..     111     144 .. 0.95
   4 ?    3.9   0.0     0.074        51       1      23 [.     145     167 ..     145     177 .. 0.87
   5 !   16.2   0.0     1e-05    0.0069       2      32 ..     180     210 ..     179     212 .. 0.94
   6 !   23.1   0.2   6.4e-08   4.4e-05       2      32 ..     214     244 ..     213     246 .. 0.96
   7 !    8.5   0.0    0.0026       1.8       1      32 [.     247     278 ..     247     280 .. 0.96
   8 !   30.4   0.0   3.2e-10   2.2e-07       1      34 []     281     314 ..     281     314 .. 0.97
   9 !   29.1   0.0   8.5e-10   5.8e-07       2      33 ..     316     347 ..     315     348 .. 0.97
  10 !    7.2   0.6     0.007       4.8       5      19 ..     353     367 ..     351     367 .. 0.92
  11 !   37.0   0.3   2.7e-12   1.9e-09       1      34 []     383     416 ..     383     416 .. 0.95
  12 ?   -1.9   0.0         5   3.4e+03       4      10 ..     420     426 ..     418     426 .. 0.84
  13 !    9.1   0.0    0.0018       1.2      19      33 ..     436     450 ..     431     451 .. 0.87
  14 ?    2.5   0.0      0.21   1.4e+02       2      20 ..     453     471 ..     452     478 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-05
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                      + +  +G  ++++  ++ Al++y+k +el+ +n
  gi|330508318|ref|YP_004384746.1| 44 NYWLEKGDEFLRNSTFEIALDCYNKSIELDSTN 76
                                      678888888888888999************987 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4.9e-07
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a ++  +G a+  l++y eAl +y++ ++l+P+
  gi|330508318|ref|YP_004384746.1|  77 ASIWIKKGRALVGLNRYSEALFAYNESIRLDPQ 109
                                       568999**************************7 PP

  == domain 3  score: 25.4 bits;  conditional E-value: 1.2e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a a+y +G+a+ +lg y+e ++++++A+ ++P+
  gi|330508318|ref|YP_004384746.1| 111 AMAWYSKGLALANLGLYNESIAAFDEAIVIQPE 143
                                       679***************************996 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.074
                                       HHHHHHHHHHHHHTT-HHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAley 23 
                                       a ++  +G  + ++g ++e l++
  gi|330508318|ref|YP_004384746.1| 145 ALSWLSKGISLANMGLFNESLQA 167
                                       5689***************9987 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       +++ n+G+++ +l + de ++ +++A +l+ 
  gi|330508318|ref|YP_004384746.1| 180 DVWLNRGLVLAELDRDDESVDSFRRAAQLDK 210
                                       79***************************96 PP

  == domain 6  score: 23.1 bits;  conditional E-value: 6.4e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       +a+ nlG+a++++g+  +Al++ye   elnP
  gi|330508318|ref|YP_004384746.1| 214 EAWLNLGLALMSKGNNSDALAAYENLTELNP 244
                                       79****************************9 PP

  == domain 7  score: 8.5 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+a+  +G a++ lg+  e  e + +A  ++P
  gi|330508318|ref|YP_004384746.1| 247 ANAWIKKGEALLTLGRAAESSESFYRATMIDP 278
                                       79**************************9999 PP

  == domain 8  score: 30.4 bits;  conditional E-value: 3.2e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a+y++++a++  g+y+e +e+y++ +el+P n
  gi|330508318|ref|YP_004384746.1| 281 ADAWYGRAMALRLSGRYNESIEAYNRTVELEPGN 314
                                       89******************************87 PP

  == domain 9  score: 29.1 bits;  conditional E-value: 8.5e-10
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                       +a+++l+  + ++++y+e le +++A+e++P+
  gi|330508318|ref|YP_004384746.1| 316 DAWNGLAISHVEMERYNESLEWFDRAIEIDPD 347
                                       8******************************8 PP

  == domain 10  score: 7.2 bits;  conditional E-value: 0.007
                                       HHHHHHHHHTT-HHH CS
                             TPR_1   5 ynlGnayfklgkyde 19 
                                       yn+++a+ klg+y e
  gi|330508318|ref|YP_004384746.1| 353 YNKALALNKLGNYSE 367
                                       9************86 PP

  == domain 11  score: 37.0 bits;  conditional E-value: 2.7e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a +++nlG+a+ +l++yd A+e+y++A+eln ++
  gi|330508318|ref|YP_004384746.1| 383 AVCWNNLGLALARLEQYDSAIEAYDRAVELNSSY 416
                                       679****************************876 PP

  == domain 12  score: -1.9 bits;  conditional E-value: 5
                                       HHHHHHH CS
                             TPR_1   4 lynlGna 10 
                                       ++n+G a
  gi|330508318|ref|YP_004384746.1| 420 WNNRGIA 426
                                       9****86 PP

  == domain 13  score: 9.1 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHSTT CS
                             TPR_1  19 eAleyyekALelnPn 33 
                                        Al+ +++A++++P 
  gi|330508318|ref|YP_004384746.1| 436 GALQSFDRAIQIDPR 450
                                       59************6 PP

  == domain 14  score: 2.5 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHTT-HHHH CS
                             TPR_1   2 kalynlGnayfklgkydeA 20 
                                       +a+ n++na+    +  eA
  gi|330508318|ref|YP_004384746.1| 453 EAWVNKANALDMADRGPEA 471
                                       8********9876665555 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.5e-06     0.001       1      38 [.      50      87 ..      50      90 .. 0.88
   2 !   30.4   0.3   3.3e-10   2.3e-07       1      42 []      84     125 ..      84     125 .. 0.97
   3 !   11.1   0.0   0.00036      0.25       8      42 .]     125     159 ..     123     159 .. 0.92
   4 !   24.1   0.0     3e-08   2.1e-05       1      42 []     186     227 ..     186     227 .. 0.94
   5 !   27.2   0.4   3.3e-09   2.2e-06       1      42 []     220     261 ..     220     261 .. 0.97
   6 !   11.5   0.0   0.00027      0.18       1      37 [.     254     290 ..     254     292 .. 0.91
   7 !   22.2   0.0   1.2e-07   8.4e-05       3      40 ..     290     327 ..     289     329 .. 0.91
   8 !   24.7   0.0   1.9e-08   1.3e-05       5      42 .]     326     363 ..     324     363 .. 0.94
   9 !    8.3   0.0    0.0026       1.8       3      41 ..     358     396 ..     357     397 .. 0.94
  10 !   29.8   0.1     5e-10   3.4e-07       1      38 [.     390     427 ..     390     430 .. 0.94
  11 !   17.0   0.0   5.2e-06    0.0036      11      38 ..     435     462 ..     432     463 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                                      Gd++     +e A+ +Y+k ++ld++na+++ + G a+
  gi|330508318|ref|YP_004384746.1| 50 GDEFLRNSTFEIALDCYNKSIELDSTNASIWIKKGRAL 87
                                      777777788899*******************9999876 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 3.3e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+a++ +++y eA+ aY++ ++ldP++a a+y  Gla++++G
  gi|330508318|ref|YP_004384746.1|  84 GRALVGLNRYSEALFAYNESIRLDPQQAMAWYSKGLALANLG 125
                                       889999*********************************998 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00036
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G y+e+i+a+ +A+ + P+ a  ++  G  ++++G
  gi|330508318|ref|YP_004384746.1| 125 GLYNESIAAFDEAIVIQPEVALSWLSKGISLANMG 159
                                       77*********************999999998887 PP

  == domain 4  score: 24.1 bits;  conditional E-value: 3e-08
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G ++ e+ + +e++ ++++A +ld ++ ea++nLGla++ +G
  gi|330508318|ref|YP_004384746.1| 186 GLVLAELDRDDESVDSFRRAAQLDKSSEEAWLNLGLALMSKG 227
                                       6788899999****************************9887 PP

  == domain 5  score: 27.2 bits;  conditional E-value: 3.3e-09
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G a++++G++ +A++aY++  +l+P na+a+ + G+a++ +G
  gi|330508318|ref|YP_004384746.1| 220 GLALMSKGNNSDALAAYENLTELNPINANAWIKKGEALLTLG 261
                                       889***********************************9987 PP

  == domain 6  score: 11.5 bits;  conditional E-value: 0.00027
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       G a+  +G+  e+ e++ +A  +dP na+a+y+++ a
  gi|330508318|ref|YP_004384746.1| 254 GEALLTLGRAAESSESFYRATMIDPINADAWYGRAMA 290
                                       7788889999**********************99855 PP

  == domain 7  score: 22.2 bits;  conditional E-value: 1.2e-07
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       a++  G+y+e+ieaY++ ++l P n +a+++L+  + +
  gi|330508318|ref|YP_004384746.1| 290 ALRLSGRYNESIEAYNRTVELEPGNSDAWNGLAISHVE 327
                                       57889***************************988765 PP

  == domain 8  score: 24.7 bits;  conditional E-value: 1.9e-08
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +e  +y+e++e++ +A+++dPd   + yn +la+ k+G
  gi|330508318|ref|YP_004384746.1| 326 VEMERYNESLEWFDRAIEIDPDEIGFQYNKALALNKLG 363
                                       57789****************************99998 PP

  == domain 9  score: 8.3 bits;  conditional E-value: 0.0026
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       a+ ++G+y e ++++++ ++  Pd a  ++nLGla++++
  gi|330508318|ref|YP_004384746.1| 358 ALNKLGNYSEEVAVLNRTVEQHPDCAVCWNNLGLALARL 396
                                       67899******************************9875 PP

  == domain 10  score: 29.8 bits;  conditional E-value: 5e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       G a+  + +y+ AieaY +A++l++++ e ++n+G a+
  gi|330508318|ref|YP_004384746.1| 390 GLALARLEQYDSAIEAYDRAVELNSSYMEPWNNRGIAM 427
                                       77899999***************************997 PP

  == domain 11  score: 17.0 bits;  conditional E-value: 5.2e-06
                            TPR_11  11 eeAieaYkkAlkldPdnaeayynLGlay 38 
                                        +A++++ +A+++dP ++ea+ n ++a+
  gi|330508318|ref|YP_004384746.1| 435 AGALQSFDRAIQIDPRSVEAWVNKANAL 462
                                       68*********************99985 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0033       2.3       3      34 .]      45      76 ..      43      76 .. 0.80
   2 !   22.3   0.0   1.3e-07   9.2e-05       2      33 ..      78     109 ..      77     110 .. 0.94
   3 !   20.9   0.1   3.6e-07   0.00025       1      33 [.     111     143 ..     111     144 .. 0.95
   4 ?    3.3   0.0      0.16   1.1e+02       2      31 ..     146     175 ..     145     178 .. 0.86
   5 !   17.3   0.0   5.3e-06    0.0037       2      32 ..     180     210 ..     179     212 .. 0.94
   6 !   22.8   0.1   8.7e-08     6e-05       2      32 ..     214     244 ..     213     246 .. 0.96
   7 ?    6.5   0.0     0.015        10       1      32 [.     247     278 ..     247     280 .. 0.92
   8 !   27.3   0.1   3.2e-09   2.2e-06       1      34 []     281     314 ..     281     314 .. 0.97
   9 !   25.3   0.0   1.4e-08   9.7e-06       2      33 ..     316     347 ..     315     348 .. 0.96
  10 ?    0.8   0.1         1     7e+02      24      31 ..     353     360 ..     351     368 .. 0.56
  11 !   29.8   0.4   5.3e-10   3.7e-07       3      32 ..     385     414 ..     383     416 .. 0.93
  12 !    8.4   0.0    0.0038       2.6      16      33 ..     433     450 ..     418     451 .. 0.88
  13 ?    2.2   0.1      0.37   2.6e+02       2      23 ..     453     474 ..     452     481 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0033
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                                      ++ + G+  +++  +e Al++++k++eld +n
  gi|330508318|ref|YP_004384746.1| 45 YWLEKGDEFLRNSTFEIALDCYNKSIELDSTN 76
                                      67777777777777899************886 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.3e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                        ++   G+a+  l++y eAl a++++++ldP+
  gi|330508318|ref|YP_004384746.1|  78 SIWIKKGRALVGLNRYSEALFAYNESIRLDPQ 109
                                       6899***************************6 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 3.6e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a+y  Gla+++lg y+e ++af++A+ + P+
  gi|330508318|ref|YP_004384746.1| 111 AMAWYSKGLALANLGLYNESIAAFDEAIVIQPE 143
                                       569**************************9996 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.16
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                         +   G +++++g ++e l+a++ A + d
  gi|330508318|ref|YP_004384746.1| 146 LSWLSKGISLANMGLFNESLQAMDMAASMD 175
                                       578899****************99988777 PP

  == domain 5  score: 17.3 bits;  conditional E-value: 5.3e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       +++ n+Gl++++l++ +e ++ f++A +ld 
  gi|330508318|ref|YP_004384746.1| 180 DVWLNRGLVLAELDRDDESVDSFRRAAQLDK 210
                                       68***************************97 PP

  == domain 6  score: 22.8 bits;  conditional E-value: 8.7e-08
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       ea+ nlGla++ +g+  +Al+a+e   el+P
  gi|330508318|ref|YP_004384746.1| 214 EAWLNLGLALMSKGNNSDALAAYENLTELNP 244
                                       89****************************9 PP

  == domain 7  score: 6.5 bits;  conditional E-value: 0.015
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       a a+   G+a++ lg+ +e  e f +A  +dP
  gi|330508318|ref|YP_004384746.1| 247 ANAWIKKGEALLTLGRAAESSESFYRATMIDP 278
                                       689*******************9999999988 PP

  == domain 8  score: 27.3 bits;  conditional E-value: 3.2e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+a+y +++a++ +g+y+e +ea+++ +el+P+n
  gi|330508318|ref|YP_004384746.1| 281 ADAWYGRAMALRLSGRYNESIEAYNRTVELEPGN 314
                                       79******************************87 PP

  == domain 9  score: 25.3 bits;  conditional E-value: 1.4e-08
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +a++ l+ ++ ++ +y+e le+f++A+e+dP+
  gi|330508318|ref|YP_004384746.1| 316 DAWNGLAISHVEMERYNESLEWFDRAIEIDPD 347
                                       79*****************************8 PP

  == domain 10  score: 0.8 bits;  conditional E-value: 1
                             TPR_2  24 fekAleld 31 
                                       ++kAl+l+
  gi|330508318|ref|YP_004384746.1| 353 YNKALALN 360
                                       55555555 PP

  == domain 11  score: 29.8 bits;  conditional E-value: 5.3e-10
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                       +++nlGla+++l +y+ A+ea+++A+el+ 
  gi|330508318|ref|YP_004384746.1| 385 CWNNLGLALARLEQYDSAIEAYDRAVELNS 414
                                       8***************************96 PP

  == domain 12  score: 8.4 bits;  conditional E-value: 0.0038
                             TPR_2  16 dyeeAleafekAleldPn 33 
                                       d + Al+ f++A+++dP+
  gi|330508318|ref|YP_004384746.1| 433 DVAGALQSFDRAIQIDPR 450
                                       6689*************7 PP

  == domain 13  score: 2.2 bits;  conditional E-value: 0.37
                             TPR_2   2 ealynlGlayyklgdyeeAlea 23 
                                       ea+ n ++a+  +++  eA ea
  gi|330508318|ref|YP_004384746.1| 453 EAWVNKANALDMADRGPEAQEA 474
                                       89**********9999999887 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0082       5.7       1      33 [.      43      75 ..      43      76 .. 0.90
   2 !   20.1   0.0   7.1e-07   0.00049       1      33 [.      77     109 ..      77     110 .. 0.96
   3 !   18.0   0.1   3.5e-06    0.0024       3      32 ..     113     142 ..     111     144 .. 0.93
   4 ?    0.5   0.0       1.4   9.7e+02       3      31 ..     147     175 ..     145     177 .. 0.82
   5 !   13.8   0.0   7.3e-05      0.05       2      32 ..     180     210 ..     179     212 .. 0.94
   6 !   19.2   0.1   1.4e-06   0.00096       2      33 ..     214     245 ..     213     246 .. 0.95
   7 !   15.9   0.0   1.6e-05     0.011       1      33 [.     247     279 ..     247     280 .. 0.95
   8 !   18.4   0.0   2.5e-06    0.0017       1      33 [.     281     313 ..     281     314 .. 0.95
   9 !   18.6   0.0   2.2e-06    0.0015       2      33 ..     316     347 ..     315     348 .. 0.95
  10 !    7.8   0.0    0.0064       4.4       4      26 ..     352     374 ..     349     382 .. 0.86
  11 !   25.0   0.2   1.9e-08   1.3e-05       3      33 ..     385     415 ..     383     416 .. 0.93
  12 ?    2.0   0.0      0.45   3.1e+02      20      32 ..     437     449 ..     432     451 .. 0.85
  13 ?   -1.7   0.0       6.7   4.6e+03       2      11 ..     453     462 ..     452     463 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0082
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      a +++ +g+  l    +e A  +y+k +eld +
  gi|330508318|ref|YP_004384746.1| 43 ANYWLEKGDEFLRNSTFEIALDCYNKSIELDST 75
                                      5689999999999999**************986 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 7.1e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+++ ++g+++  l++y eA  +y++ ++ldp+
  gi|330508318|ref|YP_004384746.1|  77 ASIWIKKGRALVGLNRYSEALFAYNESIRLDPQ 109
                                       679*****************************7 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 3.5e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+y +g+++ +lg y+e+++++ +a+ ++p
  gi|330508318|ref|YP_004384746.1| 113 AWYSKGLALANLGLYNESIAAFDEAIVIQP 142
                                       8************************98877 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                                       +++ +g  + ++g ++e+ +++  a ++d
  gi|330508318|ref|YP_004384746.1| 147 SWLSKGISLANMGLFNESLQAMDMAASMD 175
                                       68899999999999999999987776666 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 7.3e-05
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ++++n g+++ +l + +e++ ++++a +ld+
  gi|330508318|ref|YP_004384746.1| 180 DVWLNRGLVLAELDRDDESVDSFRRAAQLDK 210
                                       79***************************98 PP

  == domain 6  score: 19.2 bits;  conditional E-value: 1.4e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ea++nlg++++++g+   A ++ye  +el+p 
  gi|330508318|ref|YP_004384746.1| 214 EAWLNLGLALMSKGNNSDALAAYENLTELNPI 245
                                       79****************************95 PP

  == domain 7  score: 15.9 bits;  conditional E-value: 1.6e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a a+ ++g ++l+lg+  e+ e++ +a+ +dp 
  gi|330508318|ref|YP_004384746.1| 247 ANAWIKKGEALLTLGRAAESSESFYRATMIDPI 279
                                       679****************************95 PP

  == domain 8  score: 18.4 bits;  conditional E-value: 2.5e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+a+y  +++++  g+y+e++e+y++ +el+p 
  gi|330508318|ref|YP_004384746.1| 281 ADAWYGRAMALRLSGRYNESIEAYNRTVELEPG 313
                                       78****************************996 PP

  == domain 9  score: 18.6 bits;  conditional E-value: 2.2e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a++ l+  + ++++y+e+ e++ +a+e+dpd
  gi|330508318|ref|YP_004384746.1| 316 DAWNGLAISHVEMERYNESLEWFDRAIEIDPD 347
                                       79*****************************8 PP

  == domain 10  score: 7.8 bits;  conditional E-value: 0.0064
                                       HHHHHHHHHHTT-HHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyek 26 
                                        yn+++++ klg+y e ++++++
  gi|330508318|ref|YP_004384746.1| 352 QYNKALALNKLGNYSEEVAVLNR 374
                                       69**************9999887 PP

  == domain 11  score: 25.0 bits;  conditional E-value: 1.9e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        ++nlg+++  l++y++A+e+y +a+el+ +
  gi|330508318|ref|YP_004384746.1| 385 CWNNLGLALARLEQYDSAIEAYDRAVELNSS 415
                                       69**************************975 PP

  == domain 12  score: 2.0 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHH CS
                             TPR_8  20 Akeyyekaleldp 32 
                                       A +++ +a+++dp
  gi|330508318|ref|YP_004384746.1| 437 ALQSFDRAIQIDP 449
                                       889*********9 PP

  == domain 13  score: -1.7 bits;  conditional E-value: 6.7
                                       CHHHHHHHHH CS
                             TPR_8   2 eayynlgsiy 11 
                                       ea++n+++++
  gi|330508318|ref|YP_004384746.1| 453 EAWVNKANAL 462
                                       89*****986 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-05    0.0088       1      33 [.      65      97 ..      65      98 .. 0.94
   2 !   16.3   0.3   1.3e-05    0.0091       1      31 [.      99     129 ..      99     132 .. 0.90
   3 ?    2.7   0.0       0.3   2.1e+02       2      27 ..     134     159 ..     133     169 .. 0.86
   4 !    7.8   0.0    0.0069       4.8       5      31 ..     171     197 ..     167     200 .. 0.85
   5 !   12.1   0.1   0.00028      0.19       2      33 ..     202     233 ..     201     234 .. 0.92
   6 !   16.6   0.1   1.1e-05    0.0075       1      30 [.     235     264 ..     235     267 .. 0.93
   7 !   12.5   0.0   0.00021      0.15       8      33 ..     276     301 ..     270     302 .. 0.90
   8 !   12.8   0.0   0.00018      0.12       2      23 ..     304     325 ..     303     336 .. 0.82
   9 !   11.1   0.0   0.00059      0.41       2      30 ..     338     366 ..     337     370 .. 0.92
  10 !   14.8   0.1   3.9e-05     0.027       4      34 .]     374     404 ..     372     404 .. 0.92
  11 !    8.4   0.0    0.0044         3       1      22 [.     405     426 ..     405     429 .. 0.92
  12 !   18.0   0.0   3.7e-06    0.0026       2      31 ..     441     473 ..     440     476 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                            TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      +y k++eld +na  +  ++++l  ++++ +A+
  gi|330508318|ref|YP_004384746.1| 65 CYNKSIELDSTNASIWIKKGRALVGLNRYSEAL 97
                                      8**********************9999998885 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.3e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                       +y ++++ldP  a a++ ++ +l+++G + +
  gi|330508318|ref|YP_004384746.1|  99 AYNESIRLDPQQAMAWYSKGLALANLGLYNE 129
                                       599***********************97765 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.3
                            TPR_17   2 ylkaleldPnnadaynnLAelllknG 27 
                                       + +a+ + P  a ++  ++  l++ G
  gi|330508318|ref|YP_004384746.1| 134 FDEAIVIQPEVALSWLSKGISLANMG 159
                                       789*******************9988 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0069
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmt 31 
                                       a+  d n +d++ n++ +l+++ + ++
  gi|330508318|ref|YP_004384746.1| 171 AASMDGNLSDVWLNRGLVLAELDRDDE 197
                                       56678899************9987765 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 0.00028
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +++a++ld+++ +a+ nL+ +l ++G+  +A+
  gi|330508318|ref|YP_004384746.1| 202 FRRAAQLDKSSEEAWLNLGLALMSKGNNSDAL 233
                                       789***********************988876 PP

  == domain 6  score: 16.6 bits;  conditional E-value: 1.1e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlm 30 
                                       +y++  el+P na+a+  ++e+ll +G+ +
  gi|330508318|ref|YP_004384746.1| 235 AYENLTELNPINANAWIKKGEALLTLGRAA 264
                                       59************************9976 PP

  == domain 7  score: 12.5 bits;  conditional E-value: 0.00021
                            TPR_17   8 ldPnnadaynnLAelllknGdlmtAr 33 
                                       +dP nada++ +A +l+  G++ + +
  gi|330508318|ref|YP_004384746.1| 276 IDPINADAWYGRAMALRLSGRYNESI 301
                                       69*******************98865 PP

  == domain 8  score: 12.8 bits;  conditional E-value: 0.00018
                            TPR_17   2 ylkaleldPnnadaynnLAell 23 
                                       y + +el+P n+da+n LA  +
  gi|330508318|ref|YP_004384746.1| 304 YNRTVELEPGNSDAWNGLAISH 325
                                       999***************9766 PP

  == domain 9  score: 11.1 bits;  conditional E-value: 0.00059
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlm 30 
                                       + +a+e+dP+   + +n+A +l k+G++ 
  gi|330508318|ref|YP_004384746.1| 338 FDRAIEIDPDEIGFQYNKALALNKLGNYS 366
                                       78************************986 PP

  == domain 10  score: 14.8 bits;  conditional E-value: 3.9e-05
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +e++P+ a+ +nnL+ +l+++ +++ A++
  gi|330508318|ref|YP_004384746.1| 374 RTVEQHPDCAVCWNNLGLALARLEQYDSAIE 404
                                       67899**********************9986 PP

  == domain 11  score: 8.4 bits;  conditional E-value: 0.0044
                            TPR_17   1 lylkaleldPnnadaynnLAel 22 
                                       +y +a+el+ ++ +++nn++ +
  gi|330508318|ref|YP_004384746.1| 405 AYDRAVELNSSYMEPWNNRGIA 426
                                       59*****************976 PP

  == domain 12  score: 18.0 bits;  conditional E-value: 3.7e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknG...dlmt 31 
                                       + +a+++dP +++a+ n+A++l ++    + ++
  gi|330508318|ref|YP_004384746.1| 441 FDRAIQIDPRSVEAWVNKANALDMADrgpEAQE 473
                                       789*******************97662244555 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       3.3   2.3e+03       1      27 [.      47      73 ..      47      80 .. 0.84
   2 !   36.9   0.4     6e-12   4.1e-09       2      65 ..      82     142 ..      81     145 .. 0.95
   3 !   10.4   0.0    0.0012      0.82       3      64 ..     151     209 ..     149     213 .. 0.84
   4 !   30.1   0.1   8.4e-10   5.8e-07       1      58 [.     217     272 ..     217     278 .. 0.92
   5 !   13.4   0.3   0.00013      0.09      31      59 ..     278     306 ..     276     306 .. 0.93
   6 !   31.0   0.0   4.3e-10     3e-07       1      67 [.     285     348 ..     285     349 .. 0.95
   7 !   30.1   0.2     8e-10   5.5e-07       1      63 [.     353     412 ..     353     416 .. 0.94
   8 !   10.0   0.4    0.0016       1.1      12      53 ..     433     471 ..     432     479 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.3
                            TPR_16  1 lalaraalragdyddAaaaleaalkrd 27
                                      l++++++lr+  ++ A+  ++  +++d
  gi|330508318|ref|YP_004384746.1| 47 LEKGDEFLRNSTFEIALDCYNKSIELD 73
                                      568999************999888777 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 6e-12
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +++ra++ +++y +A+ a+++ +++d   P+ a A++ +g+a++ +g + e +a++++a+   p
  gi|330508318|ref|YP_004384746.1|  82 KKGRALVGLNRYSEALFAYNESIRLD---PQQAMAWYSKGLALANLGLYNESIAAFDEAIVIQP 142
                                       689***********************...*****************************987666 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0012
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                       ++ ++++ g + + + a + a  +d       + +l++g++++++ r +e ++ +r+a++ +
  gi|330508318|ref|YP_004384746.1| 151 KGISLANMGLFNESLQAMDMAASMD---GNLSDVWLNRGLVLAELDRDDESVDSFRRAAQLD 209
                                       6778888888888999999999999...56667*************************9765 PP

  == domain 4  score: 30.1 bits;  conditional E-value: 8.4e-10
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyr 58 
                                       l+l++a++  g+  dA+aa+e +++++   P +a A+  +g+a+l +gr ae    +yr
  gi|330508318|ref|YP_004384746.1| 217 LNLGLALMSKGNNSDALAAYENLTELN---PINANAWIKKGEALLTLGRAAESSeSFYR 272
                                       689************************...*********************98755554 PP

  == domain 5  score: 13.4 bits;  conditional E-value: 0.00013
                            TPR_16  31 PdaaeAllllgdaalrqgrlaeAaalyra 59 
                                       P +a+A+++++ a+   gr+ e +++y++
  gi|330508318|ref|YP_004384746.1| 278 PINADAWYGRAMALRLSGRYNESIEAYNR 306
                                       889*********************99986 PP

  == domain 6  score: 31.0 bits;  conditional E-value: 4.3e-10
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       + +a+a++ +g+y + ++a+++++++    P + +A+++l+ ++ +  r+ e ++++++a++ +pd+
  gi|330508318|ref|YP_004384746.1| 285 YGRAMALRLSGRYNESIEAYNRTVELE---PGNSDAWNGLAISHVEMERYNESLEWFDRAIEIDPDE 348
                                       5678899999*****************...***********************************96 PP

  == domain 7  score: 30.1 bits;  conditional E-value: 8e-10
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       +++a+a+ ++g+y + +a+l+++++++   Pd+a  +++lg+a++r+  ++ A+++y++a++ 
  gi|330508318|ref|YP_004384746.1| 353 YNKALALNKLGNYSEEVAVLNRTVEQH---PDCAVCWNNLGLALARLEQYDSAIEAYDRAVEL 412
                                       6889999999*****************...*****************************9976 PP

  == domain 8  score: 10.0 bits;  conditional E-value: 0.0016
                            TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeA 53 
                                       d + A+  +++a+  d   P+ +eA+ ++++a+  + r +eA
  gi|330508318|ref|YP_004384746.1| 433 DVAGALQSFDRAIQID---PRSVEAWVNKANALDMADRGPEA 471
                                       6789************...*************9988665555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.011       7.7       3      43 ..      45      85 ..      43      86 .. 0.91
   2 !   13.3   0.1   0.00017      0.12       4      39 ..      80     115 ..      77     119 .. 0.91
   3 !   11.6   0.1   0.00061      0.42       3      39 ..     113     149 ..     111     154 .. 0.91
   4 !   19.4   0.4   1.9e-06    0.0013       3      42 ..     181     220 ..     179     222 .. 0.94
   5 !   18.4   0.1   3.8e-06    0.0026       2      43 ..     214     255 ..     213     256 .. 0.95
   6 !   11.8   0.2    0.0005      0.34       2      40 ..     248     286 ..     247     288 .. 0.93
   7 !   19.0   0.1   2.4e-06    0.0017       2      42 ..     282     322 ..     281     324 .. 0.95
   8 !   11.7   0.0   0.00055      0.38       2      41 ..     316     355 ..     315     358 .. 0.89
   9 !    9.1   0.0    0.0036       2.5       8      42 ..     356     390 ..     349     392 .. 0.89
  10 !   15.3   0.2   3.9e-05     0.027       7      34 ..     389     416 ..     385     431 .. 0.85
  11 !   12.8   0.0   0.00024      0.16      16      42 ..     433     459 ..     423     462 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.011
                            TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43
                                       +l+ ++ +l++  ++ A++++++ ++l+ ++a +w+  ++
  gi|330508318|ref|YP_004384746.1| 45 YWLEKGDEFLRNSTFEIALDCYNKSIELDSTNASIWIKKGR 85
                                      6889999999**************************99887 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00017
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       + + ++al  l ++ eA+ ++++ ++l+P++a aw+
  gi|330508318|ref|YP_004384746.1|  80 WIKKGRALVGLNRYSEALFAYNESIRLDPQQAMAWY 115
                                       777899*****************************7 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00061
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       a++  + al++lG + e+ia++++a+  +P+ a  wl
  gi|330508318|ref|YP_004384746.1| 113 AWYSKGLALANLGLYNESIAAFDEAIVIQPEVALSWL 149
                                       89999*************************9887775 PP

  == domain 4  score: 19.4 bits;  conditional E-value: 1.9e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       ++l ++ +l++l++ de+++ +rra +l+ +++eawl l+
  gi|330508318|ref|YP_004384746.1| 181 VWLNRGLVLAELDRDDESVDSFRRAAQLDKSSEEAWLNLG 220
                                       7999*********************************997 PP

  == domain 5  score: 18.4 bits;  conditional E-value: 3.8e-06
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       ea+l l+ al+  G+  +A+a+++ + +l+P +a aw+  ++
  gi|330508318|ref|YP_004384746.1| 214 EAWLNLGLALMSKGNNSDALAAYENLTELNPINANAWIKKGE 255
                                       89***********************************98776 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 0.0005
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       +a+ + +eall+lG+ +e+ + + ra   +P +a+aw+ 
  gi|330508318|ref|YP_004384746.1| 248 NAWIKKGEALLTLGRAAESSESFYRATMIDPINADAWYG 286
                                       7999*********************************86 PP

  == domain 7  score: 19.0 bits;  conditional E-value: 2.4e-06
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +a++ +a al+ +G++ e+i++++r ++l P++ +aw  la
  gi|330508318|ref|YP_004384746.1| 282 DAWYGRAMALRLSGRYNESIEAYNRTVELEPGNSDAWNGLA 322
                                       79***********************************8887 PP

  == domain 8  score: 11.7 bits;  conditional E-value: 0.00055
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       +a+  la  + + +++ e+++ ++ra++ +Pd+  +++  
  gi|330508318|ref|YP_004384746.1| 316 DAWNGLAISHVEMERYNESLEWFDRAIEIDPDEIGFQYNK 355
                                       68999***************************98877655 PP

  == domain 9  score: 9.1 bits;  conditional E-value: 0.0036
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                                       a al  lG++ e +a+l+r ++++Pd a+ w  l+
  gi|330508318|ref|YP_004384746.1| 356 ALALNKLGNYSEEVAVLNRTVEQHPDCAVCWNNLG 390
                                       78999***********************9997765 PP

  == domain 10  score: 15.3 bits;  conditional E-value: 3.9e-05
                            TPR_14   7 laeallalGdpdeAiallrralalaPdd 34 
                                       l+ al++l+++d Ai++++ra++l+ + 
  gi|330508318|ref|YP_004384746.1| 389 LGLALARLEQYDSAIEAYDRAVELNSSY 416
                                       899*******************998554 PP

  == domain 11  score: 12.8 bits;  conditional E-value: 0.00024
                            TPR_14  16 dpdeAiallrralalaPddaeawllla 42 
                                       d ++A++ ++ra++ +P + eaw   a
  gi|330508318|ref|YP_004384746.1| 433 DVAGALQSFDRAIQIDPRSVEAWVNKA 459
                                       7899*******************9877 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   5.7e-05      0.04       6      52 ..      54     100 ..      53     105 .. 0.93
   2 !   18.2   0.1   2.9e-06     0.002      11      60 ..      93     142 ..      92     146 .. 0.92
   3 ?    6.7   0.0     0.012       8.1      17      60 ..     133     176 ..     131     181 .. 0.87
   4 !   10.7   0.4   0.00066      0.46      14      64 ..     164     214 ..     155     217 .. 0.85
   5 !   16.0   0.0   1.4e-05    0.0098       4      65 ..     222     283 ..     219     283 .. 0.92
   6 !    9.3   0.0    0.0018       1.2      21      65 ..     273     317 ..     271     319 .. 0.92
   7 !   16.9   0.0   7.6e-06    0.0052       4      61 ..     324     381 ..     321     385 .. 0.93
   8 !   20.8   0.7   4.7e-07   0.00032       4      63 ..     392     452 ..     389     476 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-05
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladL 52 
                                       +r+  +e al +++  + l++  ++ +   G++l+ l+++s+Al++ 
  gi|330508318|ref|YP_004384746.1|  54 LRNSTFEIALDCYNKSIELDSTNASIWIKKGRALVGLNRYSEALFAY 100
                                       57888999***********************************9876 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.9e-06
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       +++al +++  + l+P+++  ++  Gl+la lG +++ +a+++ ++ ++p
  gi|330508318|ref|YP_004384746.1|  93 YSEALFAYNESIRLDPQQAMAWYSKGLALANLGLYNESIAAFDEAIVIQP 142
                                       678999999**********************************9998777 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.012
                             TPR_9  17 vverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       + +  ++++P+ +  ++  G+ la +G +++ l++++ ++++++
  gi|330508318|ref|YP_004384746.1| 133 AFDEAIVIQPEVALSWLSKGISLANMGLFNESLQAMDMAASMDG 176
                                       66778999****************************99888775 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00066
                             TPR_9  14 alavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                        l++ ++   ++ +  + ++ RGl+la+l++  + ++ + ++++l+ + ++
  gi|330508318|ref|YP_004384746.1| 164 SLQAMDMAASMDGNLSDVWLNRGLVLAELDRDDESVDSFRRAAQLDKSSEE 214
                                       577788888888888889*************************99877665 PP

  == domain 5  score: 16.0 bits;  conditional E-value: 1.4e-05
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       +++++ +++ ala++e l  l+P  +  +   G +l  lG+ ++  + + ++  ++p ++da
  gi|330508318|ref|YP_004384746.1| 222 ALMSKGNNSDALAAYENLTELNPINANAWIKKGEALLTLGRAAESSESFYRATMIDPINADA 283
                                       56788999*****************************************9999999988876 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.0018
                             TPR_9  21 llllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                         +++P  ++ ++ R+++l  +G++++ +++ ++ ++l+p + da
  gi|330508318|ref|YP_004384746.1| 273 ATMIDPINADAWYGRAMALRLSGRYNESIEAYNRTVELEPGNSDA 317
                                       56789999********************************88876 PP

  == domain 7  score: 16.9 bits;  conditional E-value: 7.6e-06
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                        + + e++ + l+  +r + ++Pd+++  +  +l+l +lG++s+++a L++ +++ pd
  gi|330508318|ref|YP_004384746.1| 324 SHVEMERYNESLEWFDRAIEIDPDEIGFQYNKALALNKLGNYSEEVAVLNRTVEQHPD 381
                                       57788999999********************************************998 PP

  == domain 8  score: 20.8 bits;  conditional E-value: 4.7e-07
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGllla.qlGclsaAladLeaylalapdap 63 
                                       +++r e+++ a+++++r + l++   e +  RG++ +   +++++Al+ ++++++++p   
  gi|330508318|ref|YP_004384746.1| 392 ALARLEQYDSAIEAYDRAVELNSSYMEPWNNRGIAMVlGYEDVAGALQSFDRAIQIDPRSV 452
                                       67999*****************************876389******************654 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00011     0.075      26      76 ..      59     108 ..      41     109 .. 0.83
   2 !    8.7   0.2    0.0029         2       2      52 ..     110     159 ..     109     174 .. 0.78
   3 !    8.8   0.0    0.0029         2      44      75 ..     178     209 ..     143     211 .. 0.62
   4 !   10.2   0.2     0.001      0.69       4      52 ..     180     220 ..     177     236 .. 0.69
   5 !   10.2   0.7    0.0011      0.73       4      74 ..     214     276 ..     211     279 .. 0.78
   6 !   14.2   0.9   5.8e-05      0.04       3      73 ..     247     309 ..     246     311 .. 0.79
   7 !   28.3   0.1   2.4e-09   1.6e-06       3      76 ..     281     346 ..     279     347 .. 0.92
   8 !   19.7   0.0   1.2e-06    0.0008       4      53 ..     316     364 ..     313     377 .. 0.80
   9 !   25.5   0.8   1.8e-08   1.2e-05       9      74 ..     355     412 ..     352     415 .. 0.78
  10 ?    0.7   0.1      0.92   6.3e+02      22      47 ..     437     461 ..     421     478 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                            TPR_12  26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +e al+ ++++ + d+   a++ +  gr++  l+ry eAl +++e++++++
  gi|330508318|ref|YP_004384746.1|  59 FEIALDCYNKSIELDS-TNASIWIKKGRALVGLNRYSEALFAYNESIRLDP 108
                                       5556666666666666.3599**************************9976 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0029
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLg 52 
                                        a a++  +++l+ lg y e+++ +++a+ i+ + +    ++   ++l n+g
  gi|330508318|ref|YP_004384746.1| 110 QAMAWYSKGLALANLGLYNESIAAFDEAIVIQpEVA--LSWLSKGISLANMG 159
                                       5788999*********************98874444..34555666555555 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0029
                            TPR_12  44 tattlrnLgrlyralgryeeAlelleealaia 75 
                                       ++ +  n g ++ +l+r +e ++ +++a +++
  gi|330508318|ref|YP_004384746.1| 178 LSDVWLNRGLVLAELDRDDESVDSFRRAAQLD 209
                                       55556666666666666666666666666555 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.001
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLg 52 
                                        ++ n+++vl++l r de+ + +++a ++ +++ ++       +  nLg
  gi|330508318|ref|YP_004384746.1| 180 DVWLNRGLVLAELDRDDESVDSFRRAAQLDKSS-EE-------AWLNLG 220
                                       567899********************9998555.22.......233333 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.0011
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        a+ nl+++l+  g+  +Al+ +e   e+        +p  a++ +  g++++ lgr +e  e + +a+ i
  gi|330508318|ref|YP_004384746.1| 214 EAWLNLGLALMSKGNNSDALAAYENLTEL--------NPINANAWIKKGEALLTLGRAAESSESFYRATMI 276
                                       57889**********99999999999444........5667788888888888888888887777777655 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 5.8e-05
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       a+a+ + +++l+ lgr +e+ e + +a    + +     p  a + ++ ++++r++gry e +e+++++++
  gi|330508318|ref|YP_004384746.1| 247 ANAWIKKGEALLTLGRAAESSESFYRA----TMI----DPINADAWYGRAMALRLSGRYNESIEAYNRTVE 309
                                       567778888888888888888888888....233....567888999999999999999999999999877 PP

  == domain 7  score: 28.3 bits;  conditional E-value: 2.4e-09
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a a++ +a++lr  gry e++e +++ +e+    +G  +   + + ++L++ + +++ry e le++ +a++i++
  gi|330508318|ref|YP_004384746.1| 281 ADAWYGRAMALRLSGRYNESIEAYNRTVELE---PG--N---SDAWNGLAISHVEMERYNESLEWFDRAIEIDP 346
                                       678999*********************9999...44..3...679**************************975 PP

  == domain 8  score: 19.7 bits;  conditional E-value: 1.2e-06
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgr 53 
                                        a+n la  + +++ry e+le++++a+ei   ++  +  ++ a +l+ Lg 
  gi|330508318|ref|YP_004384746.1| 316 DAWNGLAISHVEMERYNESLEWFDRAIEIDpDEI--GFQYNKALALNKLGN 364
                                       58989*************************6666..666667777777664 PP

  == domain 9  score: 25.5 bits;  conditional E-value: 1.8e-08
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        a++l++lg+      + e++  + r +  ++hp+ a + +nLg ++ +l++y+ A+e++ +a+++
  gi|330508318|ref|YP_004384746.1| 355 KALALNKLGN------YSEEVAVLNRTV--EQHPDCAVCWNNLGLALARLEQYDSAIEAYDRAVEL 412
                                       5556666666......444444444556..89999****************************997 PP

  == domain 10  score: 0.7 bits;  conditional E-value: 0.92
                            TPR_12  22 Alellekaleia.rrllGpdhpltatt 47 
                                       Al+ +++a++i  r++  + + + a++
  gi|330508318|ref|YP_004384746.1| 437 ALQSFDRAIQIDpRSV--EAWVNKANA 461
                                       4444444444443333..333333333 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00061      0.42      10      59 ..      62     111 ..      53     124 .. 0.86
   2 !    9.7   0.2    0.0018       1.2       5      51 ..      91     137 ..      87     148 .. 0.90
   3 ?   -0.5   0.1       2.7   1.8e+03      21      62 ..     141     182 ..     124     192 .. 0.69
   4 ?    1.1   0.2      0.83   5.7e+02       9      60 ..     163     214 ..     155     219 .. 0.66
   5 !    8.8   0.3    0.0033       2.3      14      46 ..     202     234 ..     196     235 .. 0.91
   6 !   15.5   0.1   2.8e-05     0.019       1      46 [.     223     268 ..     223     278 .. 0.89
   7 !   14.4   0.0   6.1e-05     0.042      17      64 ..     273     320 ..     268     323 .. 0.84
   8 !   26.7   0.0   8.3e-09   5.7e-06       4      58 ..     294     348 ..     291     359 .. 0.91
   9 !   17.1   0.0   8.4e-06    0.0058       2      60 ..     326     384 ..     325     396 .. 0.93
  10 ?    7.2   0.1      0.01       7.1      12      54 ..     370     412 ..     359     419 .. 0.84
  11 ?    3.6   0.1      0.14        94       5      24 ..     397     416 ..     393     427 .. 0.80
  12 !   15.0   0.3   3.8e-05     0.026       4      46 ..     431     473 ..     428     479 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00061
                            TPR_19  10 AlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                       Al+ + + ++ d  na +++   +al+ l+++ eA  + ++  + dp++a
  gi|330508318|ref|YP_004384746.1|  62 ALDCYNKSIELDSTNASIWIKKGRALVGLNRYSEALFAYNESIRLDPQQA 111
                                       77888899999****************************99999999943 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0018
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                       ++y eAl ++ + +  dp++a a++    al +lg ++e +a+ d++
  gi|330508318|ref|YP_004384746.1|  91 NRYSEALFAYNESIRLDPQQAMAWYSKGLALANLGLYNESIAAFDEA 137
                                       689***********************************999998876 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.7
                            TPR_19  21 dpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                        p+ a  +l   + l ++g ++e  +++d +  +d + ++++
  gi|330508318|ref|YP_004384746.1| 141 QPEVALSWLSKGISLANMGLFNESLQAMDMAASMDGNLSDVW 182
                                       555555555556667788889999999999888888866665 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.83
                            TPR_19   9 eAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                       e l+++  a + d + ++++l+   +l +l + de  +   ++ + d+ +++
  gi|330508318|ref|YP_004384746.1| 163 ESLQAMDMAASMDGNLSDVWLNRGLVLAELDRDDESVDSFRRAAQLDKSSEE 214
                                       5556666666667777777777777777777777777777777776666544 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0033
                            TPR_19  14 leqalqedpknaearllLAeallalgqldeAea 46 
                                       +++a q d  ++ea+l+L  al++ g+  +A a
  gi|330508318|ref|YP_004384746.1| 202 FRRAAQLDKSSEEAWLNLGLALMSKGNNSDALA 234
                                       899***************************987 PP

  == domain 6  score: 15.5 bits;  conditional E-value: 2.8e-05
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                       l+  g+  +Ala++e++ + +p na+a++   eall lg+ +e  +
  gi|330508318|ref|YP_004384746.1| 223 LMSKGNNSDALAAYENLTELNPINANAWIKKGEALLTLGRAAESSE 268
                                       56779999********************************999776 PP

  == domain 7  score: 14.4 bits;  conditional E-value: 6.1e-05
                            TPR_19  17 alqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL 64 
                                       a   dp na+a+++ A al  +g+++e +++ ++  e +p ++++++ 
  gi|330508318|ref|YP_004384746.1| 273 ATMIDPINADAWYGRAMALRLSGRYNESIEAYNRTVELEPGNSDAWNG 320
                                       55679999**********************999999999998877754 PP

  == domain 8  score: 26.7 bits;  conditional E-value: 8.3e-09
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       +g+y e ++++ +  + +p+n++a+ +LA+ ++++ +++e  +  d++ e dpd+
  gi|330508318|ref|YP_004384746.1| 294 SGRYNESIEAYNRTVELEPGNSDAWNGLAISHVEMERYNESLEWFDRAIEIDPDE 348
                                       79****************************************************4 PP

  == domain 9  score: 17.1 bits;  conditional E-value: 8.4e-06
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                       +++++y e l+ + +a++ dp+    +++ A al +lg++ e  a+L++  e+ pd+a 
  gi|330508318|ref|YP_004384746.1| 326 VEMERYNESLEWFDRAIEIDPDEIGFQYNKALALNKLGNYSEEVAVLNRTVEQHPDCAV 384
                                       5899****************************************************765 PP

  == domain 10  score: 7.2 bits;  conditional E-value: 0.01
                            TPR_19  12 alleqalqedpknaearllLAeallalgqldeAealLdalpee 54 
                                       a l +  ++ p+ a  + +L  al  l q+d A+++ d++ e 
  gi|330508318|ref|YP_004384746.1| 370 AVLNRTVEQHPDCAVCWNNLGLALARLEQYDSAIEAYDRAVEL 412
                                       6788888999999999999999999999999999999998775 PP

  == domain 11  score: 3.6 bits;  conditional E-value: 0.14
                            TPR_19   5 gdyaeAlalleqalqedpkn 24 
                                       ++y++A++++ +a + +  +
  gi|330508318|ref|YP_004384746.1| 397 EQYDSAIEAYDRAVELNSSY 416
                                       69999999999999988765 PP

  == domain 12  score: 15.0 bits;  conditional E-value: 3.8e-05
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                        +d a Al+ + +a+q dp + ea+ + A+al  + +  eA++
  gi|330508318|ref|YP_004384746.1| 431 YEDVAGALQSFDRAIQIDPRSVEAWVNKANALDMADRGPEAQE 473
                                       5799************************************998 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       2.5   1.7e+03       7      31 ..      84     108 ..      81     109 .. 0.81
   2 ?    3.9   0.0      0.15     1e+02       2      31 ..     113     142 ..     112     143 .. 0.88
   3 ?    3.5   0.0      0.19   1.3e+02       1      27 [.     180     206 ..     180     211 .. 0.90
   4 !   13.4   0.0   0.00014     0.095       1      31 [.     214     244 ..     214     244 .. 0.93
   5 !   13.0   0.0   0.00018      0.12       1      32 [.     282     313 ..     282     314 .. 0.91
   6 ?    0.1   0.0       2.4   1.6e+03       6      32 ..     321     347 ..     320     348 .. 0.90
   7 !    8.0   0.0    0.0069       4.8       3      32 ..     352     381 ..     352     381 .. 0.96
   8 !    9.4   0.1    0.0026       1.8       5      28 ..     388     411 ..     388     414 .. 0.90
   9 ?    3.2   0.0      0.23   1.6e+02       7      33 .]     426     451 ..     422     451 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       ++++  l+++++Al a+++ i+  P
  gi|330508318|ref|YP_004384746.1|  84 GRALVGLNRYSEALFAYNESIRLDP 108
                                       78888889******99998777666 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYP 31 
                                       A y  +l++ +lg + ++++a+++ i   P
  gi|330508318|ref|YP_004384746.1| 113 AWYSKGLALANLGLYNESIAAFDEAIVIQP 142
                                       678889*****99**********9997666 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerli 27 
                                       d+ ++++l + +l++ d++++ ++r  
  gi|330508318|ref|YP_004384746.1| 180 DVWLNRGLVLAELDRDDESVDSFRRAA 206
                                       67899********9999*******976 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                       +A ++l+l++ + g+ ++Al+a+e+l +  P
  gi|330508318|ref|YP_004384746.1| 214 EAWLNLGLALMSKGNNSDALAAYENLTELNP 244
                                       799*********88************99776 PP

  == domain 5  score: 13.0 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       dA y +a+++r  g++ +++ea++r ++  P+
  gi|330508318|ref|YP_004384746.1| 282 DAWYGRAMALRLSGRYNESIEAYNRTVELEPG 313
                                       79**********77***********9998885 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                       la s+ ++ ++ ++le ++r i+  Pd
  gi|330508318|ref|YP_004384746.1| 321 LAISHVEMERYNESLEWFDRAIEIDPD 347
                                       799999988******99***9999998 PP

  == domain 7  score: 8.0 bits;  conditional E-value: 0.0069
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPd 32 
                                       +y+ al++ klg++++ ++ l+r ++++Pd
  gi|330508318|ref|YP_004384746.1| 352 QYNKALALNKLGNYSEEVAVLNRTVEQHPD 381
                                       5999******9******************8 PP

  == domain 8  score: 9.4 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                       +l+l++ +l ++d A+ea++r ++
  gi|330508318|ref|YP_004384746.1| 388 NLGLALARLEQYDSAIEAYDRAVE 411
                                       58999**988***********987 PP

  == domain 9  score: 3.2 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPdS 33 
                                       a+ +    d + Al+ ++r i+  P S
  gi|330508318|ref|YP_004384746.1| 426 AMVLGYE-DVAGALQSFDRAIQIDPRS 451
                                       4444445.999************9987 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.055        38      69     122 ..      84     137 ..      60     140 .. 0.84
   2 !   18.5   0.0     3e-06     0.002      72     124 ..     189     241 ..     179     244 .. 0.92
   3 !   16.7   0.2   1.1e-05    0.0077      68     124 ..     253     309 ..     245     311 .. 0.93
   4 !    9.7   0.0    0.0015       1.1      76     138 ..     295     357 ..     295     359 .. 0.94
   5 !   14.7   0.2   4.7e-05     0.032      69     124 ..     356     411 ..     316     415 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.055
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  69 aeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        +a++ l+r++eal  +++ ++++P +  ++    +Ala +G  +e +++++++
  gi|330508318|ref|YP_004384746.1|  84 GRALVGLNRYSEALFAYNESIRLDPQQAMAWYSKGLALANLGLYNESIAAFDEA 137
                                       567888999999999999999999999999999999999999999999998875 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 3e-06
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  72 elrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       +++l r +e ++  +++++++   E+++  l +Al+  G++++AL++Ye+l +
  gi|330508318|ref|YP_004384746.1| 189 LAELDRDDESVDSFRRAAQLDKSSEEAWLNLGLALMSKGNNSDALAAYENLTE 241
                                       5689999******************************************9865 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  68 laeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                         ea+l+lGra+e  +   +++  +P + +++     Al+ sGr +e +e+Y+r+++
  gi|330508318|ref|YP_004384746.1| 253 KGEALLTLGRAAESSESFYRATMIDPINADAWYGRAMALRLSGRYNESIEAYNRTVE 309
                                       5799*************************************************9876 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0015
                                       T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH CS
                              BTAD  76 GraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepgpel 138
                                       Gr++e ++ +++ v+++P + +++  l      ++r +e Le ++r+ ++  +e+g +  ++l
  gi|330508318|ref|YP_004384746.1| 295 GRYNESIEAYNRTVELEPGNSDAWNGLAISHVEMERYNESLEWFDRAIEIDPDEIGFQYNKAL 357
                                       8999*********************************************99999998766665 PP

  == domain 5  score: 14.7 bits;  conditional E-value: 4.7e-05
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  69 aeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       a a+ +lG ++e +a l++ v++hP     +  l +Alar+++   A+e+Y+r+++
  gi|330508318|ref|YP_004384746.1| 356 ALALNKLGNYSEEVAVLNRTVEQHPDCAVCWNNLGLALARLEQYDSAIEAYDRAVE 411
                                       5577899*********************************************9976 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   8.1e-06    0.0056      20      80 ..      38     101 ..      25     103 .. 0.89
   2 ?    5.4   0.1     0.032        22      50      81 ..     105     136 ..     100     137 .. 0.87
   3 ?    6.0   0.1      0.02        14      15      74 ..     205     265 ..     199     273 .. 0.85
   4 !   11.9   0.0    0.0003      0.21      28      80 ..     284     339 ..     274     341 .. 0.88
   5 !   18.6   0.0   2.4e-06    0.0017       3      80 ..     295     373 ..     293     375 .. 0.95
   6 !   15.0   0.4   3.1e-05     0.022       5      81 ..     331     408 ..     330     409 .. 0.88
   7 ?    5.7   0.1     0.025        17      29      54 ..     389     415 ..     375     419 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.1e-06
                                       H--HHHHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  20 tespedayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +e + + y+l  +  +++n+ ++ A++ ++k+ +l+s++  +++ ++++l+ L++y eA+ a+ 
  gi|330508318|ref|YP_004384746.1|  38 SEEYTANYWLekGDEFLRNSTFEIALDCYNKSiELDSTNASIWIKKGRALVGLNRYSEALFAYN 101
                                       456667788777999********************************************99876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.032
                                       SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  50 klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +l+++   ++y ++ +l  L+ y+e iaa+++
  gi|330508318|ref|YP_004384746.1| 105 RLDPQQAMAWYSKGLALANLGLYNESIAAFDE 136
                                       67889999*********************987 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.02
                                       HH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHH CS
                            ANAPC3  15 llaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyee 74 
                                       + + ++ s+e+ + l+l+l + g+   A+  ++++ +ln+ + ++++ ++++ll L++  e
  gi|330508318|ref|YP_004384746.1| 205 AAQLDKSSEEAWLNLGLALMSKGNNSDALAAYENLtELNPINANAWIKKGEALLTLGRAAE 265
                                       555566677777779****************************************999777 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.0003
                                       HH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  28 ll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       ++  A +l l+g+y++ +e ++++ +l++ +  ++  +A + +++++y+e +  ++
  gi|330508318|ref|YP_004384746.1| 284 WYgrAMALRLSGRYNESIEAYNRTvELEPGNSDAWNGLAISHVEMERYNESLEWFD 339
                                       4444999*******************************************987665 PP

  == domain 5  score: 18.6 bits;  conditional E-value: 2.4e-06
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       ++y++ i  ++r ++ e+ ++++   lA ++ ++++y++ +e++++a ++++  +g  y +A +l kL++y e +a+
  gi|330508318|ref|YP_004384746.1| 295 GRYNESIEAYNRTVELEPGNSDAWNGLAISHVEMERYNESLEWFDRAiEIDPDEIGFQYNKALALNKLGNYSEEVAV 371
                                       58999999****************************************************************98888 PP

                                       H- CS
                            ANAPC3  79 Le 80 
                                       L 
  gi|330508318|ref|YP_004384746.1| 372 LN 373
                                       86 PP

  == domain 6  score: 15.0 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       y++ + +++r+ + +++     y +Al+l ++g+y +   +l+++ ++ +    c+  ++ +l  L++y+ Ai a++
  gi|330508318|ref|YP_004384746.1| 331 YNESLEWFDRAIEIDPDEIGFQYNKALALNKLGNYSEEVAVLNRTvEQHPDCAVCWNNLGLALARLEQYDSAIEAYD 407
                                       7888899999998888888889999********************777777778888888999**********9987 PP

                                       S CS
                            ANAPC3  81 k 81 
                                       +
  gi|330508318|ref|YP_004384746.1| 408 R 408
                                       6 PP

  == domain 7  score: 5.7 bits;  conditional E-value: 0.025
                                       HHHHHHHTT-HHHHHHHHHCT.SHHHC CS
                            ANAPC3  29 lAlclylngqykrAyellrka.klnsk 54 
                                       l+l+l +++qy++A+e +++a +lns+
  gi|330508318|ref|YP_004384746.1| 389 LGLALARLEQYDSAIEAYDRAvELNSS 415
                                       789999999999999999999777765 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0         2   1.4e+03       6      24 ..      84     102 ..      82     111 .. 0.74
   2 ?   -0.1   0.0       1.8   1.3e+03       3      28 ..     115     138 ..     113     145 .. 0.75
   3 ?    3.1   0.1      0.17   1.1e+02       2      33 ..     182     213 ..     181     215 .. 0.86
   4 !    8.9   0.1    0.0025       1.7       1      24 [.     215     238 ..     215     245 .. 0.90
   5 ?    3.0   0.0      0.18   1.2e+02       6      34 ..     288     314 ..     283     316 .. 0.80
   6 !    8.1   0.0    0.0042       2.9       1      31 [.     317     347 ..     317     350 .. 0.84
   7 !   15.0   0.6   2.8e-05     0.019       1      28 [.     385     412 ..     385     416 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2
                             TPR_7   6 arlysrlGdyeeAielyeq 24 
                                       +r+ + l++y+eA+  y +
  gi|330508318|ref|YP_004384746.1|  84 GRALVGLNRYSEALFAYNE 102
                                       7888899******866666 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLal 28 
                                       +  + +  +lG y e i  + +  a+
  gi|330508318|ref|YP_004384746.1| 115 YSKGLALANLGLYNESIAAFDE--AI 138
                                       5667788899999999999988..55 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.17
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       +ln + +  +l + +e ++ ++++ +l+k+ e
  gi|330508318|ref|YP_004384746.1| 182 WLNRGLVLAELDRDDESVDSFRRAAQLDKSSE 213
                                       6889999999*************999988765 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0025
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeq 24 
                                       a+lnL+ +  + G+ ++A+  ye 
  gi|330508318|ref|YP_004384746.1| 215 AWLNLGLALMSKGNNSDALAAYEN 238
                                       79********************98 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.18
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                       a + +  G+y e ie y +   ++ +p++
  gi|330508318|ref|YP_004384746.1| 288 AMALRLSGRYNESIEAYNR--TVELEPGN 314
                                       6677889**********99..88877765 PP

  == domain 6  score: 8.1 bits;  conditional E-value: 0.0042
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       a++ La  ++++ +y e +e + ++++++ d
  gi|330508318|ref|YP_004384746.1| 317 AWNGLAISHVEMERYNESLEWFDRAIEIDPD 347
                                       6899********************5555544 PP

  == domain 7  score: 15.0 bits;  conditional E-value: 2.8e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       +++nL+ +  rl +y+ Aie y ++ +l
  gi|330508318|ref|YP_004384746.1| 385 CWNNLGLALARLEQYDSAIEAYDRAVEL 412
                                       79**********************5544 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0012       0.8      77     125 ..      58     102 ..      41     106 .. 0.84
   2 ?    3.7   0.2     0.088        60     104     126 ..     115     137 ..     107     181 .. 0.63
   3 ?    3.8   0.1     0.082        56     102     127 ..     181     206 ..     145     214 .. 0.67
   4 ?    2.9   0.1      0.15     1e+02      79     129 ..     196     242 ..     190     247 .. 0.82
   5 ?    2.8   0.1      0.16   1.1e+02      80     127 ..     231     274 ..     213     283 .. 0.70
   6 ?    3.5   0.0     0.098        67     103     129 ..     284     310 ..     279     312 .. 0.89
   7 !    7.4   0.0    0.0064       4.4      63     128 ..     316     377 ..     311     381 .. 0.81
   8 !    7.6   0.1    0.0055       3.8      55      83 ..     383     411 ..     381     443 .. 0.91
   9 ?   -1.5   0.0       3.4   2.3e+03      82     124 ..     438     476 ..     430     481 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                           DUF3856  77 sadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrm 125
                                       + + al  +n+  el++ + ++Wi    ++++al +l r++eal a++ 
  gi|330508318|ref|YP_004384746.1|  58 TFEIALDCYNKSIELDSTNASIWI----KKGRALVGLNRYSEALFAYNE 102
                                       35789******************9....69**************99976 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.088
                                       HHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrma 126
                                       +s++ al++lG ++e++ af  a
  gi|330508318|ref|YP_004384746.1| 115 YSKGLALANLGLYNESIAAFDEA 137
                                       45555555555555555555444 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.082
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmag 127
                                       + ++r+  l+el r de++++fr a+
  gi|330508318|ref|YP_004384746.1| 181 VWLNRGLVLAELDRDDESVDSFRRAA 206
                                       33577888888888888888888776 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.15
                                       HHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  79 dkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                       d+++  f r  +l++   + W+    + + al + G++++al a++  +e+
  gi|330508318|ref|YP_004384746.1| 196 DESVDSFRRAAQLDKSSEEAWL----NLGLALMSKGNNSDALAAYENLTEL 242
                                       6677788888899988888886....56999***********999988775 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.16
                                       HHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  80 kalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                        al  ++   el+  + + Wi    +++ al  lGr +e+ ++f  a+
  gi|330508318|ref|YP_004384746.1| 231 DALAAYENLTELNPINANAWI----KKGEALLTLGRAAESSESFYRAT 274
                                       455556666666666677776....58889999999988888887664 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.098
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 103 vfsravaleelGrkdealkafrmagem 129
                                        + ra+al   Gr++e+++a++ ++e+
  gi|330508318|ref|YP_004384746.1| 284 WYGRAMALRLSGRYNESIEAYNRTVEL 310
                                       5789*****************999885 PP

  == domain 7  score: 7.4 bits;  conditional E-value: 0.0064
                                       HHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  63 ealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       +a+ +l   +  +e  +++l++f+r  e++ de    i   +++a al++lG+++e +  ++ ++e
  gi|330508318|ref|YP_004384746.1| 316 DAWNGLAISHVEMERYNESLEWFDRAIEIDPDE----IGFQYNKALALNKLGNYSEEVAVLNRTVE 377
                                       555666666666677778899999*99***999....78889************999988887766 PP

  == domain 8  score: 7.6 bits;  conditional E-value: 0.0055
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  55 alchaglsealaklgrydealesadkalr 83 
                                       a+c+  l  ala+l +yd+a+e+ d+a++
  gi|330508318|ref|YP_004384746.1| 383 AVCWNNLGLALARLEQYDSAIEAYDRAVE 411
                                       89**********************99975 PP

  == domain 9  score: -1.5 bits;  conditional E-value: 3.4
                                       HHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                           DUF3856  82 lryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafr 124
                                       l+ f+r  +++    +    a +++a al+   r  ea +a +
  gi|330508318|ref|YP_004384746.1| 438 LQSFDRAIQIDPRSVE----AWVNKANALDMADRGPEAQEARE 476
                                       5555555544444444....44678888888888887766544 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.98   6.8e+02     209     248 ..      60      99 ..      41     111 .. 0.61
   2 !    9.3   0.0    0.0007      0.48     183     263 ..     104     184 ..      88     198 .. 0.84
   3 ?   -0.0   0.0      0.46   3.1e+02      48      74 ..     223     249 ..     178     292 .. 0.58
   4 ?    0.0   0.1      0.44     3e+02      15      63 ..     224     272 ..     210     319 .. 0.59
   5 !    9.7   0.0   0.00053      0.36     198     251 ..     321     374 ..     302     378 .. 0.90
   6 ?    0.3   0.0      0.36   2.5e+02     184     230 ..     377     421 ..     373     430 .. 0.79
   7 !    9.2   0.0   0.00073       0.5     207     255 ..     433     481 ..     420     484 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.98
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
                             NARP1 209 ekAleyidkaiehtptlvelyltKarilkhaGdlkkAaev 248
                                       e Al++ +k ie + t   +++ K+r l      ++A  +
  gi|330508318|ref|YP_004384746.1|  60 EIALDCYNKSIELDSTNASIWIKKGRALVGLNRYSEALFA 99 
                                       4677777777777777777777777765554444555444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0007
                                       S----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT..T CS
                             NARP1 183 sekepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD..l 257
                                        + +p++a+ w    lA    +lg +++++   d+ai  +p++   +l K+  l  +G +++  ++m+ a ++D  l
  gi|330508318|ref|YP_004384746.1| 104 IRLDPQQAMAWYSKGLAL--ANLGLYNESIAAFDEAIVIQPEVALSWLSKGISLANMGLFNESLQAMDMAASMDgnL 178
                                       556777888887777774..789999************************************************333 PP

                                       T-HHHH CS
                             NARP1 258 aDRyiN 263
                                        D ++N
  gi|330508318|ref|YP_004384746.1| 179 SDVWLN 184
                                       566666 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.46
                                       HHHTT-HHHHHHHHHHHHHH-TT-CHH CS
                             NARP1  48 llkLgrkeeAeatyeaLlernpenskY 74 
                                       l+  g++++A a+ye+L e np n + 
  gi|330508318|ref|YP_004384746.1| 223 LMSKGNNSDALAAYENLTELNPINANA 249
                                       333345555555555555555544433 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.44
                                       HHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                             NARP1  15 eeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyea 63 
                                         +g++ +Al+  e+  +    + +   +k+e ll Lgr +e+++ + +
  gi|330508318|ref|YP_004384746.1| 224 MSKGNNSDALAAYENLTELNPINANAWIKKGEALLTLGRAAESSESFYR 272
                                       4555556666665554443333333444567777777777666555443 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.00053
                                       HHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                             NARP1 198 lAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmee 251
                                       lA  + ++++++++le  d+aie +p  + ++++Ka  l + G+ ++ ++v+++
  gi|330508318|ref|YP_004384746.1| 321 LAISHVEMERYNESLEWFDRAIEIDPDEIGFQYNKALALNKLGNYSEEVAVLNR 374
                                       5666778999***********************************999988875 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 0.36
                                       ----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHH CS
                             NARP1 184 ekepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyl 230
                                       e++p  a++w +  lA    +l++++ A+e  d+a+e + + +e + 
  gi|330508318|ref|YP_004384746.1| 377 EQHPDCAVCWNNLGLA--LARLEQYDSAIEAYDRAVELNSSYMEPWN 421
                                       5667777888887777..57999999999999999999998888665 PP

  == domain 7  score: 9.2 bits;  conditional E-value: 0.00073
                                       -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                       ++  Al+  d+ai+ +p +ve +++Ka+ l  a    +A e+ e+a+ l
  gi|330508318|ref|YP_004384746.1| 433 DVAGALQSFDRAIQIDPRSVEAWVNKANALDMADRGPEAQEAREKAKML 481
                                       56689*************************9999999999999999877 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 ?   -1.8   0.0       4.8   3.3e+03      13      33 ..      89     109 ..      86     111 .. 0.75
   2 ?   -0.0   0.0       1.4   9.4e+02       8      33 ..     118     143 ..     114     145 .. 0.85
   3 ?    5.7   0.0     0.022        15      13      37 ..     293     317 ..     282     319 .. 0.83
   4 !    9.6   0.0    0.0013      0.91       7      33 ..     321     347 ..     321     349 .. 0.96
   5 ?    5.9   0.0     0.019        13       5      34 ..     353     382 ..     350     383 .. 0.87
   6 ?    4.5   0.1     0.053        37       6      29 ..     388     411 ..     384     418 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.8
                                       HHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPe 33 
                                        l +YseA+   +  ++++P+
  gi|330508318|ref|YP_004384746.1|  89 GLNRYSEALFAYNESIRLDPQ 109
                                       588999999877777777775 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.4
                                       HHHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C   8 AlGhyklgeYseArryvdalLeiEPe 33 
                                        l+ + lg Y+e+    d  + i+Pe
  gi|330508318|ref|YP_004384746.1| 118 GLALANLGLYNESIAAFDEAIVIQPE 143
                                       578899999****9999999999997 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.022
                                       HHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQa 37 
                                         g+Y+e+ +  ++  e+EP+n+ a
  gi|330508318|ref|YP_004384746.1| 293 LSGRYNESIEAYNRTVELEPGNSDA 317
                                       5699******************987 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0013
                                       HHHHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C   7 lAlGhyklgeYseArryvdalLeiEPe 33 
                                       lA+ h  + +Y+e+++  d+ +ei+P+
  gi|330508318|ref|YP_004384746.1| 321 LAISHVEMERYNESLEWFDRAIEIDPD 347
                                       89************************8 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C   5 YylAlGhyklgeYseArryvdalLeiEPen 34 
                                       Y  Al+  klg+Yse    +++  e +P++
  gi|330508318|ref|YP_004384746.1| 353 YNKALALNKLGNYSEEVAVLNRTVEQHPDC 382
                                       888***********9999998888888876 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.053
                                       HHHHHHHHHT-HHHHHHHHHHHHH CS
                        Fis1_TPR_C   6 ylAlGhyklgeYseArryvdalLe 29 
                                        l l+ ++l +Y+ A +  d+  e
  gi|330508318|ref|YP_004384746.1| 388 NLGLALARLEQYDSAIEAYDRAVE 411
                                       6899***********999998776 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.071        49     245     296 ..      77     123 ..      64     136 .. 0.82
   2 !   10.4   0.0    0.0004      0.28     245     296 ..     179     223 ..     163     230 .. 0.87
   3 ?    2.8   0.0     0.078        54     233     290 ..     235     285 ..     224     291 .. 0.81
   4 ?    4.8   0.1     0.019        13     145     290 ..     279     421 ..     272     427 .. 0.70
   5 !    7.7   0.0    0.0026       1.8     266     310 ..     432     476 ..     425     483 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.071
                                       HHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC..CCHHH CS
                               FAT 245 arcylkkGewqealqkldwseekieeilqsysaateidpswykawht..walfn 296
                                       a +  kkG  +  l++        +e+l +y ++ ++dp+++ aw++  +al+n
  gi|330508318|ref|YP_004384746.1|  77 ASIWIKKGRALVGLNR-------YSEALFAYNESIRLDPQQAMAWYSkgLALAN 123
                                       6777899999999999.......89********************997755555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0004
                                       HHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHH CS
                               FAT 245 arcylkkGewqealqkldwseekieeilqsysaateidpswykawhtwalfn 296
                                       + + l +G  +++l +        +e ++s+++a+++d+s+++aw +++l+ 
  gi|330508318|ref|YP_004384746.1| 179 SDVWLNRGLVLAELDR-------DDESVDSFRRAAQLDKSSEEAWLNLGLAL 223
                                       5667788888888888.......799*********************99985 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.078
                                       ..........HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTC CS
                               FAT 233 eptnleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykawh 290
                                         +nl e++   a +  kkGe +  l++       + e  +s+++at idp  ++aw+
  gi|330508318|ref|YP_004384746.1| 235 AYENLTELNPINANAWIKKGEALLTLGR-------AAESSESFYRATMIDPINADAWY 285
                                       4577778877778999999999999999.......89999999999999999999996 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.019
                                       -STTCCCCCCCCHCHHHHCCSTTHHCCCCCHCTT........TT.TSSCCCHHH..HHHHCCHHHHHSSCC..HHHH CS
                               FAT 145 vkaemwlkfanlarksgrlslAekaLkelleedp...eewlprappevvyaylK..ylwssgeqkealqkL..reft 214
                                       ++a++w   a   r sgr++ +++a ++  e +p   + w+  a ++v +++    ++w +  ++    ++  +++ 
  gi|330508318|ref|YP_004384746.1| 279 INADAWYGRAMALRLSGRYNESIEAYNRTVELEPgnsDAWNGLAISHVEMERYNesLEWFDRAIEIDPDEIgfQYNK 355
                                       45688888888888888888888888888888888878888877777777765422444444444444444223333 PP

                                       CCTSSCCCSS-SS---............HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTC CS
                               FAT 215 sellekkeelqsgleaqkeptnleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykawh 290
                                          l+k +++++++++    +   e++   a c + +G  +++l++        + + ++y +a+e++ s  + w+
  gi|330508318|ref|YP_004384746.1| 356 ALALNKLGNYSEEVAVL---NRTVEQHPDCAVCWNNLGLALARLEQ-------YDSAIEAYDRAVELNSSYMEPWN 421
                                       33345555777777765...55566677779999999999999999.......89999999999999999988887 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0026
                                       ..-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHHHHHSSSS CS
                               FAT 266 ekieeilqsysaateidpswykawhtwalfnfevvskeeeqkeee 310
                                       e++ ++lqs+ +a +idp++ +aw + a + + + +  e q+ +e
  gi|330508318|ref|YP_004384746.1| 432 EDVAGALQSFDRAIQIDPRSVEAWVNKANALDMADRGPEAQEARE 476
                                       567899*******************99988887777766665554 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 ?    5.6   0.0     0.022        15       4      43 ..      65     106 ..      59     147 .. 0.69
   2 ?    0.1   0.0       1.1   7.8e+02      20      45 ..     151     176 ..     140     213 .. 0.68
   3 !   15.7   0.0   1.7e-05     0.011       3      73 ..     302     377 ..     300     403 .. 0.81
   4 ?   -1.2   0.0       2.9     2e+03      23      45 ..     392     414 ..     377     418 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.022
                      SRP_TPR_like   4 eyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsal 43 
                                       +y+k ++l++++ + +  k  al+ l++y+eaL + ++   l
  gi|330508318|ref|YP_004384746.1|  65 CYNKSIELDSTNASIWikKGRALVGLNRYSEALFAYNESIRL 106
                                       566666666666655577889************988876644 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                      SRP_TPR_like  20 kvvaliklekyeeaLkllkkgsalse 45 
                                       k ++l +++ ++e+L++++ + ++++
  gi|330508318|ref|YP_004384746.1| 151 KGISLANMGLFNESLQAMDMAASMDG 176
                                       7789999999***9999987775543 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.7e-05
                      SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsalsed...vrfEkaYvlYklkkykkalkilkkvea 73 
                                       e+y++ ++le  + + +   +++ +++e+y+e+L++ + + +++ d    ++ ka +l kl +y + + +l+++ +
  gi|330508318|ref|YP_004384746.1| 302 EAYNRTVELEPGNSDAWngLAISHVEMERYNESLEWFDRAIEIDPDeigFQYNKALALNKLGNYSEEVAVLNRTVE 377
                                       5677777777777776644578899************99987776533368********************98654 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 2.9
                      SRP_TPR_like  23 aliklekyeeaLkllkkgsalse 45 
                                       al +le+y+ a+++ + + +l++
  gi|330508318|ref|YP_004384746.1| 392 ALARLEQYDSAIEAYDRAVELNS 414
                                       78899999999998887766655 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       4.1   2.8e+03       9      22 ..      84      97 ..      84     106 .. 0.82
   2 ?    2.4   0.0      0.22   1.5e+02       9      31 ..     118     140 ..     116     141 .. 0.90
   3 ?   -2.1   0.0       5.8     4e+03       9      28 ..     152     171 ..     152     174 .. 0.78
   4 ?    1.8   0.1      0.35   2.4e+02       7      30 ..     184     207 ..     183     210 .. 0.90
   5 ?    4.6   0.4     0.044        30       7      26 ..     218     237 ..     217     239 .. 0.95
   6 ?    3.0   0.2      0.14        96       9      30 ..     288     309 ..     287     310 .. 0.89
   7 !   10.3   0.0   0.00076      0.52       6      31 ..     319     344 ..     318     344 .. 0.95
   8 ?   -0.1   0.1       1.3   9.3e+02       7      24 ..     354     371 ..     351     377 .. 0.70
   9 !   13.5   0.6   7.1e-05     0.049       4      31 ..     385     412 ..     382     413 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.1
                            TPR_10  9 analrqrgrydeAe 22
                                      ++al  ++ry eA+
  gi|330508318|ref|YP_004384746.1| 84 GRALVGLNRYSEAL 97
                                      67888999**9997 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.22
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al ++g y+e+ a ++ea+ i
  gi|330508318|ref|YP_004384746.1| 118 GLALANLGLYNESIAAFDEAIVI 140
                                       7899****************965 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.8
                            TPR_10   9 analrqrgrydeAealleea 28 
                                       ++ l ++g ++e+++ ++ a
  gi|330508318|ref|YP_004384746.1| 152 GISLANMGLFNESLQAMDMA 171
                                       67789999999999987765 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.35
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N + +l ++ r de+++ +++a +
  gi|330508318|ref|YP_004384746.1| 184 NRGLVLAELDRDDESVDSFRRAAQ 207
                                       7799****************9987 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.044
                            TPR_10   7 NLanalrqrgrydeAealle 26 
                                       NL+ al + g+  +A+a +e
  gi|330508318|ref|YP_004384746.1| 218 NLGLALMSKGNNSDALAAYE 237
                                       9****************998 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.14
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       a+alr  gry+e+ + + ++++
  gi|330508318|ref|YP_004384746.1| 288 AMALRLSGRYNESIEAYNRTVE 309
                                       89***********999988876 PP

  == domain 7  score: 10.3 bits;  conditional E-value: 0.00076
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       n La+ + ++ ry+e+++++++a++i
  gi|330508318|ref|YP_004384746.1| 319 NGLAISHVEMERYNESLEWFDRAIEI 344
                                       679*********************97 PP

  == domain 8  score: -0.1 bits;  conditional E-value: 1.3
                            TPR_10   7 NLanalrqrgrydeAeal 24 
                                       N a al ++g+y e +a 
  gi|330508318|ref|YP_004384746.1| 354 NKALALNKLGNYSEEVAV 371
                                       667888888888886665 PP

  == domain 9  score: 13.5 bits;  conditional E-value: 7.1e-05
                            TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                                       + nNL+ al ++ +yd A + +++a+++
  gi|330508318|ref|YP_004384746.1| 385 CWNNLGLALARLEQYDSAIEAYDRAVEL 412
                                       55***********************985 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.6   1.1e+03     212     240 ..      75     103 ..      61     123 .. 0.60
   2 ?    5.2   2.5     0.015        10     152     263 ..     185     262 ..     143     275 .. 0.61
   3 !    8.4   0.0    0.0016       1.1     147     198 ..     282     333 ..     279     346 .. 0.89
   4 !    9.4   0.2    0.0008      0.55     155     245 ..     324     414 ..     317     447 .. 0.82
   5 ?    2.4   0.3      0.11        75     228     274 ..     432     478 ..     411     481 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.6
                            TPR_15 212 sdasLwgplaaAlllLgrpkkALeylrkq 240
                                       ++as+w   + Al+ L+r+++AL  ++  
  gi|330508318|ref|YP_004384746.1|  75 TNASIWIKKGRALVGLNRYSEALFAYNES 103
                                       45555555555666666666666444433 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
                            TPR_15 152 raelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgplaaAll 225
                                       r+                                   +l +l+r++e    +  ++++a   +s+++ w+ l+ Al+
  gi|330508318|ref|YP_004384746.1| 185 RGL----------------------------------VLAELDRDDE---SVDSFRRAAqldKSSEEAWLNLGLALM 224
                                       333..................................4555555564...566666666665666666777777777 PP

                            TPR_15 226 lLgrpkkALeylrkqakenrkdplwllaYADaleqagr 263
                                         g+++ AL+ +++ ++ n+ ++   ++  +al + gr
  gi|330508318|ref|YP_004384746.1| 225 SKGNNSDALAAYENLTELNPINANAWIKKGEALLTLGR 262
                                       77777777777776666666555444444444444444 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0016
                            TPR_15 147 afllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrrae 198
                                         ++ ra + r  g+ ++++++y + ++l+p++s++ ++l    ++++r++e
  gi|330508318|ref|YP_004384746.1| 282 DAWYGRAMALRLSGRYNESIEAYNRTVELEPGNSDAWNGLAISHVEMERYNE 333
                                       57999***********************************999999999997 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0008
                            TPR_15 155 lyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgplaaAlllLgrpk 231
                                       ++ +  + +++l+ + +A++ +pd+  ++ +   +l+ lg++ e  ++l +  +++   a+ w+ l+ Al++L++++
  gi|330508318|ref|YP_004384746.1| 324 SHVEMERYNESLEWFDRAIEIDPDEIGFQYNKALALNKLGNYSEEVAVLNRTVEQHPDCAVCWNNLGLALARLEQYD 400
                                       56667778899*********************************999999999999********************* PP

                            TPR_15 232 kALeylrkqakenr 245
                                        A e + +  + n+
  gi|330508318|ref|YP_004384746.1| 401 SAIEAYDRAVELNS 414
                                       ****9998766544 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.11
                            TPR_15 228 grpkkALeylrkqakenrkdplwllaYADaleqagradeAwrlRrqv 274
                                       ++ + AL+ + +  +  ++++   +  A al++a+r  eA++ R ++
  gi|330508318|ref|YP_004384746.1| 432 EDVAGALQSFDRAIQIDPRSVEAWVNKANALDMADRGPEAQEAREKA 478
                                       566789************************************99887 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.54   3.7e+02      19      33 ..      58      72 ..      52      72 .. 0.85
   2 ?    2.0   0.1      0.32   2.2e+02      18      32 ..      91     105 ..      90     106 .. 0.88
   3 ?   -0.4   0.1       1.7   1.2e+03      23      39 ..     111     127 ..     107     141 .. 0.46
   4 ?   -0.5   0.0       1.9   1.3e+03      17      32 ..     294     309 ..     287     310 .. 0.80
   5 ?    1.6   0.0      0.43     3e+02      25      44 ..     329     353 ..     328     373 .. 0.66
   6 ?    6.3   0.1     0.014       9.7      18      33 ..     397     412 ..     390     423 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.54
                               MIT 19 nyeeAlelYkealel 33
                                       +e Al++Y +++el
  gi|330508318|ref|YP_004384746.1| 58 TFEIALDCYNKSIEL 72
                                      6889*********96 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.32
                               MIT  18 gnyeeAlelYkeale 32 
                                       + y+eAl +Y e+++
  gi|330508318|ref|YP_004384746.1|  91 NRYSEALFAYNESIR 105
                                       57**********997 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.7
                               MIT  23 AlelYkealelLlqalk 39 
                                       A+ +Y+++l l +++l 
  gi|330508318|ref|YP_004384746.1| 111 AMAWYSKGLALANLGLY 127
                                       44444444444333332 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.9
                               MIT  17 agnyeeAlelYkeale 32 
                                       +g y e +e+Y   +e
  gi|330508318|ref|YP_004384746.1| 294 SGRYNESIEAYNRTVE 309
                                       689********98776 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.43
                               MIT  25 elYkealelLlqalk.ekne....e 44 
                                       e Y e+le +  a+    +e     
  gi|330508318|ref|YP_004384746.1| 329 ERYNESLEWFDRAIEiDPDEigfqY 353
                                       7899999999999974466555533 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.014
                               MIT  18 gnyeeAlelYkealel 33 
                                       ++y+ A+e+Y  a+el
  gi|330508318|ref|YP_004384746.1| 397 EQYDSAIEAYDRAVEL 412
                                       79************98 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.6   1.8e+03      30      47 ..     115     132 ..     113     140 .. 0.66
   2 ?    0.2   0.1      0.84   5.8e+02       1      14 [.     296     309 ..     296     311 .. 0.90
   3 ?    7.1   0.0     0.006       4.1       1      46 [.     330     369 ..     330     372 .. 0.72
   4 ?    2.3   0.1      0.19   1.3e+02       1      15 [.     398     412 ..     398     415 .. 0.92
   5 ?   -3.1   0.0       8.8   6.1e+03       5      15 ..     437     447 ..     435     448 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.6
                                       HHHHHHHHHTT--HHHHH CS
                          HTH_Bact  30 YqkgecleklgfseeeIk 47 
                                       Y kg  l  lg  +e+I+
  gi|330508318|ref|YP_004384746.1| 115 YSKGLALANLGLYNESIA 132
                                       667777777776666665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.84
                                       -HHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAie 14 
                                       rY+e++e  n+ +e
  gi|330508318|ref|YP_004384746.1| 296 RYNESIEAYNRTVE 309
                                       7*********9998 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.006
                                       -HHHHHHHHHHHHHHHHHTTB-TTHHHHHHHHHHHHHHTT--HHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiSirinsMsLlGQLyYqkgecleklgfseeeI 46 
                                       rY+e+Le  ++Aiei         +G ++Y k+  l klg+ +ee+
  gi|330508318|ref|YP_004384746.1| 330 RYNESLEWFDRAIEIDPDE-----IG-FQYNKALALNKLGNYSEEV 369
                                       7999999999999986544.....44.6677777777777666665 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.19
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y++a+e  ++A+e+
  gi|330508318|ref|YP_004384746.1| 398 QYDSAIEAYDRAVEL 412
                                       7************96 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 8.8
                                       HHHHHHHHHHH CS
                          HTH_Bact   5 aLeqvnkAiei 15 
                                       aL+  ++Ai+i
  gi|330508318|ref|YP_004384746.1| 437 ALQSFDRAIQI 447
                                       899999**987 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2      0.01       6.9       4      43 ..     195     234 ..     192     258 .. 0.89
   2 ?    1.7   0.0      0.47   3.3e+02      13      44 ..     272     303 ..     261     317 .. 0.82
   3 ?    3.0   0.0      0.19   1.3e+02       5      50 ..     298     343 ..     295     356 .. 0.86
   4 ?    5.5   0.0      0.03        21       6      53 ..     333     380 ..     328     411 .. 0.87
   5 ?   -1.2   0.2       3.7   2.6e+03       7      41 ..     437     471 ..     433     474 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.01
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAle 43 
                                       d+++++++++a++ +++  +a l+l lal+++g++ +Al+
  gi|330508318|ref|YP_004384746.1| 195 DDESVDSFRRAAQLDKSSEEAWLNLGLALMSKGNNSDALA 234
                                       77899999*****************************996 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.47
                            TPR_20  13 aalaanpddldarldlAlallaagryeeAleq 44 
                                       +a   +p + da +  A al   gry e++e+
  gi|330508318|ref|YP_004384746.1| 272 RATMIDPINADAWYGRAMALRLSGRYNESIEA 303
                                       55567999********************9986 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.19
                            TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                       ++++++  ++++ +p + da   lA   ++ +ry e+le + + ++
  gi|330508318|ref|YP_004384746.1| 298 NESIEAYNRTVELEPGNSDAWNGLAISHVEMERYNESLEWFDRAIE 343
                                       5789999999**************************9987655555 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.03
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                                       ++l+ +++a++ +pd++  +++ Alal++ g+y e ++ L + ++++ 
  gi|330508318|ref|YP_004384746.1| 333 ESLEWFDRAIEIDPDEIGFQYNKALALNKLGNYSEEVAVLNRTVEQHP 380
                                       677788999***********************9998888888887765 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 3.7
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeA 41 
                                        l+++++a++ +p  ++a ++ A+al +a r  eA
  gi|330508318|ref|YP_004384746.1| 437 ALQSFDRAIQIDPRSVEAWVNKANALDMADRGPEA 471
                                       6889999999********99999999888777666 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         7   4.8e+03       9      25 ..     120     136 ..     120     138 .. 0.86
   2 ?    3.4   0.0      0.16   1.1e+02       2      27 ..     317     342 ..     316     345 .. 0.89
   3 ?    5.6   0.0     0.031        21       1      28 [.     384     411 ..     384     414 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 7
                               PPR   9 gycknGkleeAlelfke 25 
                                       +++  G++ e +  f+e
  gi|330508318|ref|YP_004384746.1| 120 ALANLGLYNESIAAFDE 136
                                       6788999**99999998 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.16
                               PPR   2 tynslIsgycknGkleeAlelfkeMk 27 
                                       ++n l  +++   ++ e le+f++ +
  gi|330508318|ref|YP_004384746.1| 317 AWNGLAISHVEMERYNESLEWFDRAI 342
                                       6999999***************9865 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.031
                               PPR   1 vtynslIsgycknGkleeAlelfkeMke 28 
                                       v++n l  ++++  +++ A+e +++ +e
  gi|330508318|ref|YP_004384746.1| 384 VCWNNLGLALARLEQYDSAIEAYDRAVE 411
                                       79*******************9998766 PP

>> DUF5588  Family of unknown function (DUF5588)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.53   3.7e+02      55     108 ..      49      97 ..      40     107 .. 0.82
   2 ?    9.7   0.0    0.0005      0.35     126     179 ..     215     267 ..     167     277 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.53
                           DUF5588  55 kgdlayrrqeyqkalqeyssiseklsstnfamkrdvqegqarclahlgrhaeal 108
                                       kgd   r+  ++ al+ y   s +l stn ++   +++g  r l+ l r++eal
  gi|330508318|ref|YP_004384746.1|  49 KGDEFLRNSTFEIALDCYNK-SIELDSTNASIW--IKKG--RALVGLNRYSEAL 97 
                                       78888999999999999975.556999998874..5555..6699999999998 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0005
                           DUF5588 126 tvlylqlaicsslqnlektilclqklislhpfnpwswgklaeaylslgpalsas 179
                                       + l l la++s  +n   ++   + l  l p+n  +w k  ea l+lg a  +s
  gi|330508318|ref|YP_004384746.1| 215 AWLNLGLALMSKGNNS-DALAAYENLTELNPINANAWIKKGEALLTLGRAAESS 267
                                       4577888988876665.578899*************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.79u 0.28s 00:00:01.07 Elapsed: 00:00:00.53
# Mc/sec: 2739.83
//
Query:       gi|330508319|ref|YP_004384747.1|  [L=135]
Description: CopG family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-33  113.8   1.5    4.3e-33  113.3   1.5    1.2  1  NikR_C           NikR C terminal nickel binding domain
    8.7e-08   31.8   0.1    2.2e-07   30.6   0.0    1.6  2  RHH_1            Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.038   14.1   0.0      0.067   13.3   0.0    1.4  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.3   1.5   7.2e-37   4.3e-33       1      77 []      53     129 ..      53     129 .. 0.99

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 7.2e-37
                                       EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEEE CS
                            NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltli 77 
                                       vGviti+ydh+qr+l+++lt+iqh++  +i+sslhvhld+d cLev+vl+G++ e+++ ae+++alkgVkhvklt++
  gi|330508319|ref|YP_004384747.1|  53 VGVITILYDHSQRGLMDNLTEIQHDFGSIIQSSLHVHLDQDICLEVVVLRGDGPEVRKAAESMMALKGVKHVKLTTT 129
                                       7**************************************************************************86 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   3.6e-11   2.2e-07       1      37 [.       2      39 ..       2      40 .. 0.97
   2 ?   -2.6   0.0         1   6.2e+03       4       9 ..      88      93 ..      86      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.6e-11
                                      EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                      r+ i+l+e+ll ++de++  rg +SrSe +R+A+r+y+
  gi|330508319|ref|YP_004384747.1|  2 RIGISLPENLLNKFDEIIMNRGySSRSEGVRDAIRNYI 39
                                      899*********************************97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1
                                      EEEEHH CS
                             RHH_1  4 irldee 9 
                                      ++ld++
  gi|330508319|ref|YP_004384747.1| 88 VHLDQD 93
                                      899998 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.1e-05     0.067      91     117 ..       2      29 ..       1      34 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                   HicB_lk_antitox  91 riNitlpervlkriDaavkaag.esRSg 117
                                       ri i+lpe++l++ D+++ ++g +sRS 
  gi|330508319|ref|YP_004384747.1|   2 RIGISLPENLLNKFDEIIMNRGySSRSE 29 
                                       899******************9669996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 799.66
//
Query:       gi|330508320|ref|YP_004384748.1|  [L=287]
Description: hypothetical protein MCON_2487 [Methanosaeta concilii GP6]
Scores for complete 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-05   23.6   0.0    0.00021   22.0   0.0    2.0  1  Methyltransf_25  Methyltransferase domain
     0.0029   17.4   0.0     0.0052   16.6   0.0    1.6  1  Methyltransf_31  Methyltransferase domain
     0.0041   17.8   0.0     0.0095   16.6   0.0    1.9  1  Methyltransf_11  Methyltransferase domain
      0.006   16.4   0.0      0.011   15.5   0.0    1.4  1  Met_10           Met-10+ like-protein
     0.0062   16.4   0.0     0.0082   16.0   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
     0.0091   15.3   0.0      0.015   14.6   0.0    1.3  1  GidB             rRNA small subunit methyltransferase G
  ------ inclusion threshold ------
      0.018   15.7   0.0      0.054   14.3   0.0    2.0  1  Methyltransf_12  Methyltransferase domain
      0.034   13.5   0.0      0.085   12.2   0.0    1.6  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
       0.11   12.4   0.0       0.18   11.7   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
       0.13   11.8   0.0       0.22   11.0   0.0    1.4  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.2e-07   0.00021       2      57 ..      66     120 ..      65     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.2e-07
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaed 57 
                                       Ld+G+GtG +++ l++       +++D+s+  l++   +a+eegl n+ +++++ +d
  gi|330508320|ref|YP_004384748.1|  66 LDIGAGTGAFAIPLSHLT--TATVALDPSAYHLQILTGKAREEGLtNIAIIEKEWKD 120
                                       9**************996..9************************999998877765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.9e-06    0.0052       2      65 ..      60     120 ..      59     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.9e-06
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee 65 
                                       ++g ++lD+G+GtG++++ l ++       v +D s+  ++  + +a++ gl+n+   + ++ +
  gi|330508320|ref|YP_004384748.1|  60 KSGSTLLDIGAGTGAFAIPLSHLT---TATVALDPSAYHLQILTGKAREEGLTNIAIIEKEWKD 120
                                       7899*****************753...23699*************************9988877 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.3e-06    0.0095       1      49 [.      66     115 ..      66     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.3e-06
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETT CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvv 49 
                                       Ld+G+GtG++a +l +  + +v++D+s++ l++   ka+eegl ++ +++
  gi|330508320|ref|YP_004384748.1|  66 LDIGAGTGAFAIPLSHLTTATVALDPSAYHLQILTGKAREEGLtNIAIIE 115
                                       8**************999****************9999999987555544 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.9e-06     0.011      92     139 ..      53      96 ..      47     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.9e-06
                                       HHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHH CS
                            Met_10  92 erlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvky 139
                                       +r+++ ++ g + +d+ AG G faip+++++ a     + l+P+++++
  gi|330508320|ref|YP_004384748.1|  53 NRIISFIKSGSTLLDIGAGTGAFAIPLSHLTTAT----VALDPSAYHL 96 
                                       69**************************866554....7788888875 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   4.6e-06    0.0082      11      62 ..      50     110 ..      39     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.6e-06
                   Methyltransf_23  11 dklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........k 62 
                                       + l+r+    ++g+ +LdiG+GtG ++  l+   +  ++ D+s    +i+          +
  gi|330508320|ref|YP_004384748.1|  50 EVLNRIISFIKSGSTLLDIGAGTGAFAIPLSHLTTATVALDPSAYHLQILTgkareegltN 110
                                       55667776678999*****************************876666655555555551 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.3e-06     0.015      42     109 ..      56     120 ..      51     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.3e-06
                                       GGCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC CS
                              GidB  42 lellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee 109
                                       ++++k+   +++D+G+G G  +ipL+ +      + l+++    + L+   +e +l+n++i+e++  +
  gi|330508320|ref|YP_004384748.1|  56 ISFIKSGS-TLLDIGAGTGAFAIPLSHLTTAT--VALDPSAYHLQILTGKAREEGLTNIAIIEKEWKD 120
                                       56777777.7***************9776554..479*************************998766 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     3e-05     0.054       1      47 [.      66     110 ..      66     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennn 47 
                                       L+iG+GtG+++ +l     ++  +++D+s+  ++    k ++++  n
  gi|330508320|ref|YP_004384748.1|  66 LDIGAGTGAFAIPLSHL--TTATVALDPSAYHLQILTGKAREEGLTN 110
                                       8****************..************9966666655555544 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.7e-05     0.085      45     104 ..      59     115 ..      50     122 .. 0.87
   2 ?   -3.1   0.0       2.2     4e+03     154     181 ..     152     179 ..     149     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.7e-05
                                       S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE CS
                   Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflq 104
                                        k+g+++lD+ +Gtg +a+ ls+   ++   v lD ++  L++   k++eeg +ni  + 
  gi|330508320|ref|YP_004384748.1|  59 IKSGSTLLDIGAGTGAFAIPLSHLTTAT---VALDPSAYHLQILTGKAREEGLTNIAIIE 115
                                       6899******************987765...678999*****************998765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.2
                                       E----SHHHHHHHHHHHH.HHHHHHHHH CS
                   Ubie_methyltran 154 fskvelpllsqayelyskevlPvlGkll 181
                                       +s++e+     ay+l+  e+  +l +++
  gi|330508320|ref|YP_004384748.1| 152 ISRPEVDYALAAYSLFDEEIEGFLARMI 179
                                       6899999999999999999888888886 PP

>> Methyltransf_18  Methyltransferase 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       5      65 ..      52     110 ..      49     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                   Methyltransf_18   5 LkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagled 65 
                                       L++i+s++++gs+++DiG+  g  +i l   + ++  +a D ++  l+    +++++gl++
  gi|330508320|ref|YP_004384748.1|  52 LNRIISFIKSGSTLLDIGAGTGAFAIPLS--HLTTATVALDPSAYHLQILTGKAREEGLTN 110
                                       899***********************998..566678999999999988888888888765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013      0.22      32      94 ..      62     123 ..      50     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve 94 
                                         ++lD+G+G+G+ ++ l + +     +++d +a+ l++ +  +++++l  + +++++  ++ +
  gi|330508320|ref|YP_004384748.1|  62 GSTLLDIGAGTGAFAIPLSHLTTA--TVALDPSAYHLQILTGKAREEGLTnIAIIEKEWKDARP 123
                                       4569**************998877..7999********99999999999887777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2104.46
//
Query:       gi|330508321|ref|YP_004384749.1|  [L=243]
Description: hypothetical protein MCON_2490 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-11   43.8   1.3    4.8e-11   43.4   1.3    1.2  1  DUF4198   Domain of unknown function (DUF4198)


Domain annotation for each model (and alignments):
>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   1.3   2.7e-15   4.8e-11       1     211 [.       3     201 ..       3     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2.7e-15
                           DUF4198   1 aqAHelwllpsstvvsggewvtvdlafghdpfeadheplk.leklkvlapdgektdlgkylstfdvallkpekegty 76 
                                       a+AH +w + ++  v+ ge+ ++ + +gh   ++++ +l+ +e+ ++++pdg+k++l  ++ + +++    ++ g +
  gi|330508321|ref|YP_004384749.1|   3 ASAHGVWAEVKDL-VEVGESQDAYVFYGH-ANDPAGFALPaMESSYLMTPDGQKITLNTNKVEGEWVPGYGWT-GDF 76 
                                       89*****888665.55556**********.777767888889999*******999999999999998855554.444 PP

                           DUF4198  77 klaa..akkpgdwkeygdpklakevpaeaaelkvvkysqyaktfvtvgkpsetwdkpvglglEivPlthpydlkage 151
                                        ++   a+ pg ++ +  ++     p +  +     +++ a++++++g++s++  k  gl++Ei   +  y++k  e
  gi|330508321|ref|YP_004384749.1|  77 GVSPvvAYWPGNYVYVAPRA-----PSYSNK-TLRLTYSAAEAVINAGNDSSASFK-SGLPMEISSQKPLYQIKNKE 146
                                       444433566****9976666.....866666.68899999**********665555.7******************* PP

                           DUF4198 152 elevqvlldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGlwlleaeh 211
                                       +++++v +  + +      ++y  + + +a++ +k  t+++  + +++ + G+w++++ +
  gi|330508321|ref|YP_004384749.1| 147 NVTFTVKYLDQQVN-----ATYSAYPQMTATKVQKGFTNDKDSFVINFNQTGMWVVNCYY 201
                                       ********977766.....555555555666655559*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1698.57
//
Query:       gi|330508322|ref|YP_004384750.1|  [L=85]
Description: hypothetical protein MCON_2492 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0014   18.9   0.0     0.0018   18.5   0.0    1.1  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0034   17.4   0.0     0.0038   17.2   0.0    1.1  1  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
  ------ inclusion threshold ------
      0.064   13.6   0.0      0.068   13.5   0.0    1.1  1  DUF4198          Domain of unknown function (DUF4198)
       0.11   12.5   0.0       0.16   12.0   0.0    1.2  1  Big_1            Bacterial Ig-like domain (group 1)


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     4e-07    0.0018      10      63 ..      24      78 ..      19      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4e-07
                   CarboxypepD_reg 10 sgapiagatVtvtnadtgtvastttdadGafrlrglpp...gtysvtvsapGyatat 63
                                      +g+p a a+V v+  ++   ++ +td++G fr++ lp    g+   ++s +G +++ 
  gi|330508322|ref|YP_004384750.1| 24 DGEPAADASVQVF-LNGALYSQNQTDSTGFFRMA-LPGtgaGDWMFVISGDGHDEVI 78
                                      8************.566678889*********97.6666779999999999988765 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 !   17.2   0.0   8.5e-07    0.0038      23      79 ..      23      75 ..      10      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.5e-07
                              bMG3 23 dsgkPvagaeVrlldkkgevlaegtTDaqGvarfaallargkegaapylvsArkded 79
                                      d+g+P+a+a+V++   +g++  + +TD++G  r+a +   g+++ + ++v+  +++d
  gi|330508322|ref|YP_004384750.1| 23 DDGEPAADASVQVF-LNGALYSQNQTDSTGFFRMALP---GTGAGDWMFVISGDGHD 75
                                      89**********98.59******************99...66677777777665554 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.5e-05     0.068     160     208 ..      24      68 ..       7      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                           DUF4198 160 dGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpk..aGlwlle 208
                                       dG+P+a+a+v+v+  g+ y++++      td+ G +  +lp   aG w++ 
  gi|330508322|ref|YP_004384750.1|  24 DGEPAADASVQVFLNGALYSQNQ------TDSTGFFRMALPGtgAGDWMFV 68 
                                       9***********99987665554......7899999999985337778875 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.5e-05      0.16      17      58 ..      24      63 ..      13      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.5e-05
                             Big_1 17 ngnpvagatVtfsvsggalsassgtTdanGkatvtltstkag 58
                                      +g p a+a+V +  +g+    s+ +Td+ G +++ l +t ag
  gi|330508322|ref|YP_004384750.1| 24 DGEPAADASVQVFLNGALY--SQNQTDSTGFFRMALPGTGAG 63
                                      799**********999666..89************9999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 695.76
//
Query:       gi|330508323|ref|YP_004384751.1|  [L=248]
Description: hypothetical protein MCON_2493 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-16   60.3   0.1    7.2e-16   59.2   0.0    1.6  2  DUF4198   Domain of unknown function (DUF4198)


Domain annotation for each model (and alignments):
>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.0     4e-20   7.2e-16       1     211 [.       3     207 ..       3     209 .. 0.75
   2 ?   -1.5   0.0      0.15   2.6e+03      82     119 ..     210     246 ..     205     247 .. 0.50

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 4e-20
                           DUF4198   1 aqAHelwllpsstvvsggewvtvdlafgh.dpfeadheplk.leklkvlapdgektdlgkylstfdvallkpekegt 75 
                                       a++H++wl+  +    g+ +  + + +gh d+  +   + + +e+  +lapdg+ktdl   + t d+       +g 
  gi|330508323|ref|YP_004384751.1|   3 ASGHSVWLESRDQADVGD-SDRLYALYGHlDDVTG--ITSPaIESAFLLAPDGQKTDLD--MNTGDWL------PGY 68 
                                       789****99888777777.9*********444444..333357788*******999998..4444422......455 PP

                           DUF4198  76 yklaaakk......pgdwkeygdpk.lakevpaeaae.lkvvkysqyaktfvtvgkpsetwdkpvglglEivPlthp 144
                                         + +a++      pgd+ +   +     +  ++ +        ++ ak  ++vg++s++ +  +gl + i P + p
  gi|330508323|ref|YP_004384751.1|  69 GWIGYAYSdmtyssPGDYLFAIARTpSVYDPSWHGSGpSNPRLGYSVAKMAINVGNESNKTSWDTGLAFDINPDKAP 145
                                       555554443333357777775554431222225555544466689999*********88666677************ PP

                           DUF4198 145 ydlkageelevqvlldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGlwlleaeh 211
                                       y+++age++++   ++G+P+  a+ ++++ ++   ++++    +t++dG + +++++ Glw ++a++
  gi|330508323|ref|YP_004384751.1| 146 YAIHAGENVTFLAKYNGQPVN-ATFSAFPNNAMALTQTG----STGSDGSFMVNFSQGGLWQVSASY 207
                                       *********************.******98864444444....7********************997 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.15
                           DUF4198  82 kkpgdwkeygdpk....lakevpaeaaelkvvkysqyaktfv 119
                                       ++p++w+ +++ +    + +     + +  +++ys+y+ ++v
  gi|330508323|ref|YP_004384751.1| 210 NEPATWTATMESAghykVGD---MVPYN--TTRYSTYMMVYV 246
                                       55777777666663222222...22233..555666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1881.50
//
Query:       gi|330508324|ref|YP_004384752.1|  [L=256]
Description: hypothetical protein MCON_2494 [Methanosaeta concilii GP6]
Scores for complete 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   77.0   0.0    3.5e-21   76.6   0.0    1.2  1  DUF4198   Domain of unknown function (DUF4198)


Domain annotation for each model (and alignments):
>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   1.9e-25   3.5e-21       1     211 [.      12     214 ..      12     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 1.9e-25
                           DUF4198   1 aqAHelwllpsstvvsggewvtvdlafghdpfeadheplk.lekl.kvlapdg.ektdlg..kylstfdvallkpek 72 
                                       a+AH+l+ +  +++ + + + ++ +a+gh    ad   ++ l  l ++++pdg e  +l   +y + ++  + + ++
  gi|330508324|ref|YP_004384752.1|  12 AAAHSLYAEFPQDTGPDS-QTEFWIAYGH-GGSAD-SQIEsL-PLaRLISPDGsE-SELFfePYQDGLK-GSVAFDD 82 
                                       79*****77777666555.8*********.66666.455533.33399*****43.3333444444444.5556688 PP

                           DUF4198  73 egtyklaaakkpgdwkeygdpklakevpaeaaelkvvkysqyaktfvtvgkpse.twdkpvglglEivPlthpydlk 148
                                       +g y l ++++    ++  dp+         a+ k + +++y  +++  +++++ +w++  g+glEivP ++py+lk
  gi|330508324|ref|YP_004384752.1|  83 PGCYILDLQMD----TTLFDPA------SFGAAGKKSLVEKYGRVLMPYQSGEGyDWSS--GKGLEIVPEADPYQLK 147
                                       ********777....4457888......44444589999*********99995446666..**************** PP

                           DUF4198 149 ageelevqvlldGkPlagaeveveyggt...ryrdapdeikv.ktdadGvvtftlpkaGlwlleaeh 211
                                       +ge+++ +vl+dGkP++g    +++++      +++++e ++    +dG+++f+  +aGlw+l+ e 
  gi|330508324|ref|YP_004384752.1| 148 SGEDFRARVLYDGKPVPGSYSAIITRSPedvLVVQHAQESEIsGESEDGIISFATGRAGLWVLAFEA 214
                                       *****************96666666555477445555555556999*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1873.72
//
Query:       gi|330508325|ref|YP_004384753.1|  [L=209]
Description: CbiM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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  158.5  21.9    2.2e-46  158.3  21.9    1.0  1  CbiM      Cobalt uptake substrate-specific transmembrane regi
  ------ inclusion threshold ------
        7.8    6.3   9.7        7.3    6.4   0.2    2.3  2  PAP2      PAP2 superfamily


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 !  158.3  21.9   2.4e-50   2.2e-46       1     207 []       3     197 ..       3     197 .. 0.96

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 2.4e-50
                              CbiM   1 HipdgiLspavllaayavalallalalrrlrkeldearvpllallaafifaaqminipipggtslHllgavlaaiLl 77 
                                       Hi+dg+L++a+l+a+++ +l+ll++++r++r e    ++p+++l++a++f+a+++++pi g+ts+Hl++++la+iLl
  gi|330508325|ref|YP_004384753.1|   3 HISDGVLPLAMLAAGFLFTLILLVFSMRNIRIE----EIPKVSLITAALFVASLVHFPI-GPTSVHLIMNGLAGILL 74 
                                       *********************************....**********************.***************** PP

                              CbiM  78 GpwaaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaal 154
                                       G   af+ v+v+l+lqa++f++GG+++LG+N++n++v+++l+  l+ +  +r ++s   +a+ ++la+ l+v+ ++l
  gi|330508325|ref|YP_004384753.1|  75 G-RRAFIGVFVALTLQAVFFQHGGLSVLGVNAFNIGVPALLAWQLFEK--RRGLESPHLEAVFGALAGGLAVLTSVL 148
                                       *.*************************************999996666..5566888999999999*********** PP

                              CbiM 155 lvalelalsgleaslsltaalaamllvhlpvgilEgviTaaivkalkkvrpel 207
                                       lv+lel++ g++    + +   +++ +hlpv+i+E+++ +a++ +l kv+pe+
  gi|330508325|ref|YP_004384753.1| 149 LVSLELLALGEA----FNEISLLVIGAHLPVIIIEALVVGAAAGFLLKVKPEM 197
                                       *********996....***********************************96 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   4.6     0.011        99      63     128 ..      14      83 ..      12      91 .. 0.77
   2 ?    6.4   0.2   0.00081       7.3      90     128 ..     154     192 ..     104     199 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.011
                              PAP2  63 fafalalllalllrrkrkkig....lvllalillllavlvalsRlylgvHflsDvlaGlliGialaalay 128
                                        a+ ++++l+ll+ ++r+ +     +v l++ +l++a lv +      vH  +  laG+l+G   ++ ++
  gi|330508325|ref|YP_004384753.1|  14 LAAGFLFTLILLVFSMRNIRIeeipKVSLITAALFVASLVHFPIGPTSVHLIMNGLAGILLGRRAFIGVF 83 
                                       455555555555555555533689999999999*****************************88777665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00081
                              PAP2  90 illllavlvalsRlylgvHflsDvlaGlliGialaalay 128
                                       +l+l  ++  +s l++g+H +  ++ +l++G+a ++l++
  gi|330508325|ref|YP_004384753.1| 154 LLALGEAFNEISLLVIGAHLPVIIIEALVVGAAAGFLLK 192
                                       4444455666899********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1500.10
//
Query:       gi|330508326|ref|YP_004384754.1|  [L=105]
Description: hypothetical protein MCON_2496 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-05   23.9   0.1    4.6e-05   23.6   0.1    1.2  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    0.00017   21.5   0.0    0.00022   21.2   0.0    1.2  1  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
     0.0004   20.8   0.0     0.0005   20.5   0.0    1.2  1  DUF4198          Domain of unknown function (DUF4198)
     0.0009   19.2   0.0     0.0012   18.8   0.0    1.2  1  Big_1            Bacterial Ig-like domain (group 1)
  ------ inclusion threshold ------
      0.013   16.2   0.0      0.017   15.8   0.0    1.2  1  TTR-52           Transthyretin-like family
      0.023   14.9   0.0      0.031   14.5   0.0    1.2  1  Big_3_5          Bacterial Ig-like domain (group 3)
      0.058   13.3   0.1       0.07   13.0   0.1    1.2  1  DUF1416          Protein of unknown function (DUF1416)
       0.11   12.8   0.1       0.22   11.8   0.1    1.5  2  Big_6            Bacterial Ig domain


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1     2e-08   4.6e-05       6      60 ..      35      90 ..      30     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2e-08
                   CarboxypepD_reg  6 VtdasgapiagatVtvtnadtgtvastttdadGafrlrglpp...gtysvtvsapGya 60
                                      V   +g p a+a+V ++ +++   a+ +tda+G+f+++ lp    g+ s +v+  G  
  gi|330508326|ref|YP_004384754.1| 35 VFYDDGSPAANAEVKLY-QEGALFAENVTDATGRFTFT-LPGkgtGDWSYEVEGGGHT 90
                                      67789************.56667899***********9.7777667777777776655 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 !   21.2   0.0   9.6e-08   0.00022      23      61 ..      38      75 ..      27      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 9.6e-08
                              bMG3 23 dsgkPvagaeVrlldkkgevlaegtTDaqGvarfaalla 61
                                      d+g P+a+aeV+l++ +g++ ae  TDa+G+ +f+ + +
  gi|330508326|ref|YP_004384754.1| 38 DDGSPAANAEVKLYQ-EGALFAENVTDATGRFTFTLPGK 75
                                      89***********96.69****************98844 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.2e-07    0.0005     155     203 ..      34      76 ..      18      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.2e-07
                           DUF4198 155 vqvlldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaG 203
                                       ++++ dG P+a+aev++  +g+    a++     tda G++tftlp +G
  gi|330508326|ref|YP_004384754.1|  34 FVFYDDGSPAANAEVKLYQEGA--LFAEN----VTDATGRFTFTLPGKG 76 
                                       556679**********976653..44444....7************998 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 !   18.8   0.0   5.3e-07    0.0012       6      54 ..      28      74 ..      26      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.3e-07
                             Big_1  6 tntltatvkDangnpvagatVtfsvsggalsassgtTdanGkatvtlts 54
                                      ++tl   v   +g p a+a+V++   g+    ++ +Tda G++t+tl +
  gi|330508326|ref|YP_004384754.1| 28 QITLDLFVFYDDGSPAANAEVKLYQEGALF--AENVTDATGRFTFTLPG 74
                                      789999999***************988555..89************966 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   7.5e-06     0.017       8      44 ..      40      71 ..      38      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.5e-06
                                      T-GGSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEE CS
                            TTR-52  8 gkpaknvkVkLwekdtldpddlldetkTdedGnFels 44
                                      g+pa+n++VkL+++       l++e+ Td++G+F+ +
  gi|330508326|ref|YP_004384754.1| 40 GSPAANAEVKLYQEGA-----LFAENVTDATGRFTFT 71
                                      79***********865.....*************987 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 ?   14.5   0.0   1.4e-05     0.031       6      63 ..      25      82 ..      20      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                                      TTSEEEEEEE--CCCC.TTS--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEE CS
                           Big_3_5  6 agqtvtltatVtaasg.gtptGtVtftdggttlgtavllsanGtAtltvsalaaGthsi 63
                                      +gq++tl   V   +g ++++  V+++++g+ ++++v+ + +G  t+t+++  +G  s+
  gi|330508326|ref|YP_004384754.1| 25 VGQQITLDLFVFYDDGsPAANAEVKLYQEGALFAENVTDA-TGRFTFTLPGKGTGDWSY 82
                                      6999999999987777689*****************9876.9*******9988887555 PP

>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   3.1e-05      0.07      17      62 ..      26      71 ..      14      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                           DUF1416 17 ekeaviqGkvtr.dgepvggayvRLLdssgeFtaevvtsaeGefrFf 62
                                       +++ +   v   dg+p ++a v+L + +g   ae vt a+G+f F 
  gi|330508326|ref|YP_004384754.1| 26 GQQITLDLFVFYdDGSPAANAEVKLYQ-EGALFAENVTDATGRFTFT 71
                                      556666666665599*********986.577779999*******985 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   9.7e-05      0.22      19      56 ..      40      76 ..      39      94 .. 0.85
   2 ?   -2.4   0.0       2.7     6e+03      19      27 ..      88      96 ..      78     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.7e-05
                             Big_6 19 GkaeagatVtvkdadgtvlgtgtadadGeFsvtlepaq 56
                                      G+  a+a+V++  ++g+++++ + da+G+F++tl+ + 
  gi|330508326|ref|YP_004384754.1| 40 GSPAANAEVKLY-QEGALFAENVTDATGRFTFTLPGKG 76
                                      666789999999.699******************7654 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.7
                             Big_6 19 GkaeagatV 27
                                      G++e g+ +
  gi|330508326|ref|YP_004384754.1| 88 GHTEKGSII 96
                                      788888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 816.24
//
Query:       gi|330508327|ref|YP_004384755.1|  [L=140]
Description: hypothetical protein MCON_2497 [Methanosaeta concilii GP6]
Scores for complete 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   20.4   0.1    0.00056   19.9   0.1    1.2  1  Big_1            Bacterial Ig-like domain (group 1)
     0.0006   20.0   0.0    0.00078   19.7   0.0    1.2  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0025   17.8   0.0     0.0034   17.4   0.0    1.3  1  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
     0.0089   16.0   0.1      0.048   13.7   0.0    1.9  2  CarbopepD_reg_2  CarboxypepD_reg-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 !   19.9   0.1   1.2e-07   0.00056       3      48 ..      27      70 ..      27      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.2e-07
                             Big_1  3 GvdtntltatvkDangnpvagatVtfsvsggalsassgtTdanGka 48
                                      G + n++++t+   +g+p  g+++ ++++g ++   +g+Td++G +
  gi|330508327|ref|YP_004384755.1| 27 GYQVNEIQVTALYDDGTPAGGVEIEVQSDGKTI--EKGVTDDEGAY 70
                                      6678**************************999..79*******76 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.7e-07   0.00078       9      63 ..      40      93 ..      32     108 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.7e-07
                   CarboxypepD_reg  9 asgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtv.sapGyatat 63
                                       +g+p  g++++v+ +d++t    +td++Ga+ lr    gt ++++ s++  + a+
  gi|330508327|ref|YP_004384755.1| 40 DDGTPAGGVEIEVQ-SDGKTIEKGVTDDEGAYVLR-PSKGTGDLRFvSYSAGHKAE 93
                                      59************.599999************98.55577777764444444444 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 !   17.4   0.0   7.7e-07    0.0034      17      60 ..      33      76 ..      19     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.7e-07
                              bMG3 17 vwvtsL.dsgkPvagaeVrlldkkgevlaegtTDaqGvarfaall 60
                                      + vt+L d+g P+ g+e+++   +g+++ +g TD++G + + + +
  gi|330508327|ref|YP_004384755.1| 33 IQVTALyDDGTPAGGVEIEVQ-SDGKTIEKGVTDDEGAYVLRPSK 76
                                      567776589**********85.68*************99998873 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.17   7.7e+02      52      63 ..      25      36 ..      22      41 .. 0.86
   2 !   13.7   0.0   1.1e-05     0.048      12      68 ..      43     102 ..      37     113 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.17
                   CarbopepD_reg_2 52 yvGyktqekkvt 63
                                      ++Gy+  e++vt
  gi|330508327|ref|YP_004384755.1| 25 MMGYQVNEIQVT 36
                                      89*****99998 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.1e-05
                   CarbopepD_reg_2  12 eplpgatVyvkg...tkkgtvTdenGnFelknlpagkytLvv.syvGyktqekkvtvskek 68 
                                       +p  g+ + v++   t  + vTd++G + l+ + +g+  L++ sy   +++e ++++++++
  gi|330508327|ref|YP_004384755.1|  43 TPAGGVEIEVQSdgkTIEKGVTDDEGAYVLR-PSKGTGDLRFvSYSAGHKAELELDLEQKE 102
                                       46777766665422245889**********7.88899999852555555566777776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1151.43
//
Query:       gi|330508328|ref|YP_004384756.1|  [L=249]
Description: cobalt ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-40  136.8  10.7    9.9e-40  136.5  10.7    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 !  136.5  10.7   5.5e-44   9.9e-40       3     212 ..      14     220 ..      13     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: 136.5 bits;  conditional E-value: 5.5e-44
                                       CCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---.HHHHHHHCCCHCHHHHHHHHHHE..... CS
                              CbiQ   3 svlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp.rvlaqalilpllflllgllillfqlitt 78 
                                       s+lhr+++r kli lf+ll+ +v+a ++  +l   ++ +ll+l+++lp +  ++++ +p+lfll+ l+il +   + 
  gi|330508328|ref|YP_004384756.1|  14 SPLHRWETRAKLISLFMLLISIVIAGGIGQALAGLIVSMLLVLISGLPlSHVLRFMKWPFLFLLPLLVILPI-TAGG 89 
                                       789*************************99977777777788888888899*********************.4555 PP

                                       ..EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHH CS
                              CbiQ  79 egefvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLle 155
                                          f + ++    + ++Gl+ g+l+++R +++ +l+l+++ T p++  +++l++lg+P +l+ i+l ayR+ifl+++
  gi|330508328|ref|YP_004384756.1|  90 DNLFSYHILT---VSRQGLQLGVLFMIRGIAAALLALIMVGTAPFNVNINALRSLGMPGPLTQIFLFAYRYIFLFYD 163
                                       5555566666...**************************************************************** PP

                                       HHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS.. CS
                              CbiQ 156 evqrikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg.s 212
                                        +q+++++ ++ ++++++  +rs+r l+  +a+l++r+++r+e+v  Am +RGY+g  
  gi|330508328|ref|YP_004384756.1| 164 DLQTMRRSLASKGFEMRS-SARSARILAVSVAMLLIRSYERSEDVFNAMLSRGYQGrL 220
                                       ****************55.55559********************************44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2007.14
//
Query:       gi|330508329|ref|YP_004384757.1|  [L=276]
Description: cobalt ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-31  108.5   0.0    5.4e-31  107.9   0.0    1.3  1  ABC_tran     ABC transporter
    3.9e-16   59.7   0.0    3.3e-10   40.3   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    9.8e-09   35.0   0.0    1.9e-08   34.0   0.0    1.4  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00042   20.0   0.1    0.00076   19.2   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00073   20.0   0.1     0.0015   19.0   0.1    1.5  1  AAA_16       AAA ATPase domain
     0.0011   18.9   0.1     0.0047   16.8   0.1    1.9  2  RsgA_GTPase  RsgA GTPase
     0.0021   18.6   0.0     0.0026   18.3   0.0    1.3  1  AAA_23       AAA domain
     0.0024   16.6   0.0       0.52    8.9   0.0    2.0  2  AAA_13       AAA domain
      0.007   16.1   0.0       0.57    9.9   0.0    2.2  2  IstB_IS21    IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.011   16.1   0.1       0.17   12.2   0.1    2.2  1  AAA_22       AAA domain
      0.034   13.7   0.3      0.086   12.4   0.3    1.9  1  AAA_25       AAA domain
       0.06   12.9   0.0      0.096   12.3   0.0    1.4  1  AAA_27       AAA domain
      0.066   12.9   0.0        1.3    8.6   0.0    2.0  2  AAA_15       AAA ATPase domain
      0.071   13.3   0.0       0.25   11.5   0.0    1.9  1  AAA_33       AAA domain
       0.15   11.8   0.0       0.23   11.2   0.0    1.3  1  AAA_24       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   4.5e-34   5.4e-31       1     137 []      23     168 ..      23     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 4.5e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpelt 75 
                                       l++vs++l ege +ai+G+nGaGKStLl  l gll+  +G++++++k++ +++l+++r+++g+++q+  +qlf    
  gi|330508329|ref|YP_004384757.1|  23 LNQVSFSLAEGESLAILGPNGAGKSTLLLHLNGLLR-GQGKVRIRNKEIGDESLRWVRSQVGMVFQDpdDQLFMSR- 97 
                                       799********************************9.59****************************544555444. PP

                                       HHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       ++e              e de+++ al+ +gl++ +++v     ++LS Gq++r a a +l  +p++l+lDEpt+
  gi|330508329|ref|YP_004384757.1|  98 LEEDvafgptnmelsqkEVDERVQWALKCVGLSDQAAKVP----HHLSFGQRKRAAFATVLSMRPPVLVLDEPTS 168
                                       66669*********99999999************888887....*****************************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 !   17.3   0.0   2.8e-06    0.0033       3      40 ..      37      68 ..      35     105 .. 0.74
   2 !   40.3   0.0   2.8e-13   3.3e-10     234     301 ..     137     201 ..     131     202 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.8e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggg 40
                                      ++ GpNg+GKS+LL  l +l r      g + ++ +++
  gi|330508329|ref|YP_004384757.1| 37 AILGPNGAGKSTLLLHLNGLLR------GQGKVRIRNK 68
                                      799**************99964......3333333333 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 2.8e-13
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                       +++lS G+++ +a++t l  ++   ++l++DEp ++L+P+   + + l++e +rng+ +i +TH+  l
  gi|330508329|ref|YP_004384757.1| 137 PHHLSFGQRKRAAFATVLSMRP---PVLVLDEPTSNLDPRSRMEMVSLIREQQRNGTAIITATHDVNL 201
                                       689****************999...***************************************9877 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   1.6e-11   1.9e-08      26     198 ..      35     197 ..      18     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.6e-11
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrr 102
                                         ai+GpNG+GKs ll  +  +L  + +  +r++++       +e+ +  + +v ++f+++d++l +++ e  +   
  gi|330508329|ref|YP_004384757.1|  35 SLAILGPNGAGKSTLLLHLNGLLRGQGKVRIRNKEIG------DESLRWVRSQVGMVFQDPDDQLFMSRLEEDVAFG 105
                                       568*************999888876666667766654......467789999************9999988888888 PP

                                       EETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                         + + s+ +++++     +   l  +a   ++ LS G+++ +a a ++++    + p+ +lDe  ++LD + + ++
  gi|330508329|ref|YP_004384757.1| 106 PTNMELSQKEVDERVQWALKCVGLSDQAAKVPHHLSFGQRKRAAFATVLSM----RPPVLVLDEPTSNLDPRSRMEM 178
                                       888888889999988888888888888888899***********9999876....469******************* PP

                                       HHHHHHHCTTSEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 180 aellkeksknaQfivislr 198
                                       ++l++e++ n   i+++ +
  gi|330508329|ref|YP_004384757.1| 179 VSLIREQQRNGTAIITATH 197
                                       ******9999777776544 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 !   19.2   0.1   6.4e-07   0.00076      15      49 ..      26      60 ..      19      67 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.4e-07
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                       ++++ + ++  + Gp+G+GKSTll  ++ lL ++
  gi|330508329|ref|YP_004384757.1| 26 VSFSLAEGESLAILGPNGAGKSTLLLHLNGLLRGQ 60
                                      45555544499*************96666666655 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   0.1   1.2e-06    0.0015      23     165 ..      32     188 ..      20     193 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-06
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipy....salaqalareellrqllde...... 88 
                                       ++e++ + G+ G GKs+l+ +l   l+++g  + +r k    es  +     +  + +   ++l+   l+e      
  gi|330508329|ref|YP_004384757.1|  32 EGESLAILGPNGAGKSTLLLHLNGLLRGQG-KVrIRNKEIGDESL-RWvrsqVGMVFQDPDDQLFMSRLEEdvafgp 106
                                       3489*******************9999994.33244444444111.1122222222222233555555554444444 PP

                            AAA_16  89 .......aesaeleawrekleealaavpelagaea..srllellkrllallsrderplvlvlDdlq.wadeaslqll 155
                                              +e +e+ +w+ k+ +   ++++++  ++  +r +++++  l   s   rp vlvlD+    +d+ s++ +
  gi|330508329|ref|YP_004384757.1| 107 tnmelsqKEVDERVQWALKCVGLSDQAAKVPHHLSfgQRKRAAFATVL---S--MRPPVLVLDEPTsNLDPRSRMEM 178
                                       434443333334444444444433344444443334444444444444...2..45899999986668888888888 PP

                            AAA_16 156 aaLlrllesk 165
                                        +L r+++++
  gi|330508329|ref|YP_004384757.1| 179 VSLIREQQRN 188
                                       8888887765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1     4e-06    0.0047      74     121 ..       6      55 ..       1      74 [. 0.74
   2 ?   -0.2   0.0       0.7   8.4e+02      20      63 ..     191     236 ..     180     276 .] 0.64

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4e-06
                                       HTTSEEEE--TTTH.TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  74 algyevllvsaktk.egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       a+++e l  s +++ ++l++++  l++ +  +++G+ G+GKStL+ +l++
  gi|330508329|ref|YP_004384757.1|   6 AIEVENLSYSYSDGtRALNQVSFSLAEgESLAILGPNGAGKSTLLLHLNG 55 
                                       45555555555544367788888998889***************999887 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.7
                                       EEEEESTTTT--HHHHHHHHHHHHHTT-..EEEEEEE-GGG--HHH CS
                       RsgA_GTPase  20 livvslkepelslnlldrfLvlaeekgi..epvivlnKiDlleeee 63 
                                        i++++++ +l + l dr+L+l  +  +  +++ ++++ Dl+++  
  gi|330508329|ref|YP_004384757.1| 191 AIITATHDVNLVPLLADRVLLLNRSIVAegSVHQIMSRRDLMDDLG 236
                                       5888888899999999999998776554225556778888877765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.2e-06    0.0026      21      46 ..      35      60 ..      15     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.2e-06
                            AAA_23 21 ltlItGpNGaGKTTildAiklaLyge 46
                                        +I GpNGaGK+T+l  +   L g+
  gi|330508329|ref|YP_004384757.1| 35 SLAILGPNGAGKSTLLLHLNGLLRGQ 60
                                      568************98888777664 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0     0.004       4.7      21      53 ..      38      70 ..      36     101 .. 0.78
   2 !    8.9   0.0   0.00043      0.52     527     574 ..     158     202 ..     149     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.004
                            AAA_13 21 iYGwNGaGKTtLSrllrslelgetepkfangsi 53
                                      i G NGaGK+tL   l+ l +g+ + +  n +i
  gi|330508329|ref|YP_004384757.1| 38 ILGPNGAGKSTLLLHLNGLLRGQGKVRIRNKEI 70
                                      77**********988888877766655555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00043
                            AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleff 574
                                         + v+D P S LD  s +  +sli+++     +   ++  TH +++ 
  gi|330508329|ref|YP_004384757.1| 158 PPVLVLDEPTSNLDPRSRMEMVSLIREQQ---RNGTAIITATHDVNLV 202
                                       6799************************8...89999******99875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00048      0.57      35      64 ..      20      50 ..       6      62 .. 0.84
   2 ?    4.0   0.0      0.03        35     106     151 ..     155     199 ..     127     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00048
                         IstB_IS21 35 vkeLatlsf.iekkenivllGpsGvGKshla 64
                                      +++L + sf +++ e++++lGp G+GKs l 
  gi|330508329|ref|YP_004384757.1| 20 TRALNQVSFsLAEGESLAILGPNGAGKSTLL 50
                                      56788888867889**************885 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.03
                         IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpf 151
                                        +++ +l+lD+  + +ld  ++ ++  +i ++  + + iit+   +
  gi|330508329|ref|YP_004384757.1| 155 SMRPPVLVLDEP-TSNLDPRSRMEMVSLIREQQRNGTAIITATHDV 199
                                       35779*****96.689****************99999999997665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.17       6      34 ..      34      62 ..      31     204 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeak 34
                                       +l++ G+ G+GK+tll  l   l  + k
  gi|330508329|ref|YP_004384757.1| 34 ESLAILGPNGAGKSTLLLHLNGLLRGQGK 62
                                      5799*************999888754333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   7.2e-05     0.086      30      53 ..      30      53 ..      24     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.2e-05
                            AAA_25 30 lpagelallaGapgtGKttlaldl 53
                                      l++ge  ++ G+ g+GK+tl+l+l
  gi|330508329|ref|YP_004384757.1| 30 LAEGESLAILGPNGAGKSTLLLHL 53
                                      5789999***************98 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     8e-05     0.096      19      52 ..      26      59 ..      19      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8e-05
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdllfG 52
                                      ++fs +e +   i+GpN AGKst+l  ++ ll G
  gi|330508329|ref|YP_004384757.1| 26 VSFSLAEGESLAILGPNGAGKSTLLLHLNGLLRG 59
                                      55665555556699**********9998888866 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0011       1.3      26      50 ..      36      60 ..      21     103 .. 0.78
   2 ?    2.4   0.0     0.087     1e+02     326     365 ..     160     198 ..     147     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                            AAA_15 26 tvliGkNnsGKSsilealdlFlnnk 50
                                        + G+N++GKS++l  l+ +l  +
  gi|330508329|ref|YP_004384757.1| 36 LAILGPNGAGKSTLLLHLNGLLRGQ 60
                                      5789***********9999888866 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.087
                            AAA_15 326 illiEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +l+++EP  +L p   ++++ l++e  +++   +i  TH 
  gi|330508329|ref|YP_004384757.1| 160 VLVLDEPTSNLDPRSRMEMVSLIREQQRNGT-AIITATHD 198
                                       799**********************999996.99999*97 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021      0.25       5      97 ..      39     187 ..      36     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                            AAA_33   5 vGlpGsGKstlaerl...lkklgavllssdt.............................................. 32 
                                        G++G+GKstl+ +l   l+ +g v+++  +                                              
  gi|330508329|ref|YP_004384757.1|  39 LGPNGAGKSTLLLHLnglLRGQGKVRIRNKEigdeslrwvrsqvgmvfqdpddqlfmsrleedvafgptnmelsqke 115
                                       6**********988755588888999999999999999888888888888888887777777777777777666666 PP

                            AAA_33  33 ......lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvil.dat..nlsrrerarflklarrlgv 97 
                                             +  +++g  +q  + + ++++  +++  ++a  +ls + +v++ d +  nl++r r+++++l r++  
  gi|330508329|ref|YP_004384757.1| 116 vdervqWALKCVGLSDQAAKVPHHLSFGQRKRA-AFA-TVLSMRPPVLVlDEPtsNLDPRSRMEMVSLIREQQR 187
                                       665555444444444444445555555555554.455.577888775544766678889999999988887765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00019      0.23       4      37 ..      35      74 ..      32      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                            AAA_24  4 kiliyGpsgiGKTtlakel......gpkplfidtekGlks 37
                                      +++i Gp+g+GK+tl+++l      + k+ + + e G  s
  gi|330508329|ref|YP_004384757.1| 35 SLAILGPNGAGKSTLLLHLngllrgQGKVRIRNKEIGDES 74
                                      689**************99777666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2200.74
//
Query:       gi|330508330|ref|YP_004384758.1|  [L=246]
Description: hypothetical protein MCON_2500 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
        1.1    9.4   8.8        1.2    9.2   7.0    2.1  2  DivIVA      DivIVA protein
        4.2    7.5  16.2          4    7.5   2.4    2.1  2  TPR_MLP1_2  TPR/MLP1/MLP2-like protein


Domain annotation for each model (and alignments):
>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2     0.065   5.8e+02      86     109 ..      75     104 ..      73     114 .. 0.56
   2 ?    9.2   7.0   0.00014       1.2      38     120 ..      98     182 ..      88     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.065
                                       XXXXXXXXXXXXXXXXXX......XXXXXX CS
                            DivIVA  86 eaeliikeAekkaekive......eaeeea 109
                                       +a+++++eA  ++++ v+       a++ea
  gi|330508330|ref|YP_004384758.1|  75 QAKNLMDEAARAKDESVAarneslSARDEA 104
                                       677777777777777665344444333333 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  38 lkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeael..iikeAekkaekiveeaeeeakki 112
                                       l+ ++e k+   e+++ l+e++e+e++++  lv a++ a+   +na +   l  +++eA  k  ++ +e e +a + 
  gi|330508330|ref|YP_004384758.1|  98 LSARDEAKAAYGEAKSLLAEMNEAEKNIQSQLVKAESWADVSATNAVRAGGLfnMTDEACRKTLALSKEVEGNASRT 174
                                       456678899999**********************************9987652256666666666665555555555 PP

                                       XXXXXXXX CS
                            DivIVA 113 aeeieelk 120
                                       ++ +e+ +
  gi|330508330|ref|YP_004384758.1| 175 ESMMEQAR 182
                                       55555444 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.2    0.0018        16       2      53 ..      82     133 ..      73     146 .. 0.66
   2 ?    7.5   2.4   0.00044         4      10      87 ..     164     241 ..     157     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0018
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkha 53 
                                       e +++++e  ++++e+ +a+++++++  + ++  ++++ea+++ +++lvk +
  gi|330508330|ref|YP_004384758.1|  82 EAARAKDESVAARNESLSARDEAKAAYGEAKSLLAEMNEAEKNIQSQLVKAE 133
                                       4556666666777777777777777777777777777777777777777654 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00044
                        TPR_MLP1_2  10 ikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakae 86 
                                        k+++ ++++ e+ ++++++  ++ a++a +a ++  r  ++h+e++   ++    +n+++  ++e++ + ++ ++ 
  gi|330508330|ref|YP_004384758.1| 164 SKEVEGNASRTESMMEQARDYANASAKSAGQAIESQNRTYLLHNETAVIFSQSSVVYNNMTLLAKEMQINSDKIRTW 240
                                       5788889999**************************************99999999999999999999888887765 PP

                        TPR_MLP1_2  87 l 87 
                                       +
  gi|330508330|ref|YP_004384758.1| 241 M 241
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1217  (0.0678789); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1724.80
//
Query:       gi|330508331|ref|YP_004384759.1|  [L=308]
Description: hypothetical protein MCON_2503 [Methanosaeta concilii GP6]
Scores for complete 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-18   67.1   0.0    3.9e-18   66.6   0.0    1.1  1  DUF4198   Domain of unknown function (DUF4198)
  ------ inclusion threshold ------
      0.022   14.8   0.1      0.041   13.9   0.1    1.4  1  bMG3      Bacterial alpha-2-macroglobulin MG3 domain


Domain annotation for each model (and alignments):
>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0   4.3e-22   3.9e-18       2     200 ..      40     256 ..      39     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 4.3e-22
                           DUF4198   2 qAHelwllpsstvvsggewvtvdlafghdpfeadheplkleklkvlapdg........ektdlgkylstfdvallkp 70 
                                        AH +++ p s   + g++  + +a gh+    +  p  l++l+v+ +dg        ek d+    ++ ++ +++ 
  gi|330508331|ref|YP_004384759.1|  40 DAHQIFVRPISGFANLGDTAMLPVAAGHNTSSTE-MPEGLTNLTVIRQDGgvidhilnEKSDTM---GNWPIFSFDV 112
                                       599***999999999999**********555554.555599*********99886554455555...5556666666 PP

                           DUF4198  71 ekegtyklaaakkpgdwke.........ygdpk........lakevp..aeaae..lkvvkysqyaktfvtvgkpse 126
                                       e++g+y+++  +  g w+          y +++        +    +  + ++     +    +y k+f+   + + 
  gi|330508331|ref|YP_004384759.1| 113 EHPGLYVITSYNGGGAWTHiitnppaigYWEAGivdeidfdA--INKtgWAKDWyvERSYPLHTYGKSFIAGPESDY 187
                                       88********9999*****76555555544444666665431..222222222253446666667799998887755 PP

                           DUF4198 127 .twdkpvglglEivPlthpydlkageelevqvlldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlp 200
                                         ++kpvg+ lEi+Plt+ +++  ++++e+qvl++G+P +++e  + + g     +  +i  +tda+G++ ++l+
  gi|330508331|ref|YP_004384759.1| 188 sIASKPVGQILEIIPLTNITEVG-NGDFEFQVLYQGQPFSDLELIAQKVG-----DDTKIRGTTDAEGKAMLNLS 256
                                       68999*****************6.566****************9996554.....33333339******988775 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.6e-06     0.041      22      90 ..     219     284 ..     210     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-06
                              bMG3  22 LdsgkPvagaeVrlldkkgevlaegtTDaqGvarfaallargkegaapylvsArkdedlaflkldwerg 90 
                                       L +g+P ++ e+   +  +++  +gtTDa+G a ++     ++++ +  +v+A +  d+ ++++++ + 
  gi|330508331|ref|YP_004384759.1| 219 LYQGQPFSDLELIAQKVGDDTKIRGTTDAEGKAMLNLS---STDELSEWVVVADTLMDTRVVEVRDAPR 284
                                       7899********9999999999**************99...678***********99999999976555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2155.19
//
Query:       gi|330508332|ref|YP_004384760.1|  [L=263]
Description: hypothetical protein MCON_2504 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.23   10.9   0.3       0.42   10.1   0.3    1.3  1  Humanin   Humanin family


Domain annotation for each model (and alignments):
>> Humanin  Humanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   2.3e-05      0.42       6      15 ..     148     157 ..     147     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 2.3e-05
                           Humanin   6 FSCLLLsisE 15 
                                       F+CLL+++s 
  gi|330508332|ref|YP_004384760.1| 148 FNCLLFPTSQ 157
                                       9*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 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 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1949.89
//
Query:       gi|330508333|ref|YP_004384761.1|  [L=210]
Description: ribonuclease HII [Methanosaeta concilii GP6]
Scores for complete sequence (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  149.2   0.2    1.4e-43  149.0   0.2    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 !  149.0   0.2     8e-48   1.4e-43       1     197 [.       4     201 ..       4     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 149.0 bits;  conditional E-value: 8e-48
                                       EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHHSEEEEEEE-HHHHH...HHTTTS CS
                         RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklikkkiekrklvaeeiky..asenei 75 
                                       +G DEaG+Gpv+G+++va+ ++++er   l  lgvkDSK Ls+ kre La++i +  + +++     +   +    +
  gi|330508333|ref|YP_004384761.1|   4 MGADEAGKGPVIGSMFVAGLVIDEERFFDLAVLGVKDSKMLSPAKREALARKITTIATDQYILEVRAEVidELRLVM 80 
                                       79****************************************************44444444433333333666779 PP

                                       -HHHHHHHHHHHHHHHHHHTCEECCECCCE--SSHHHHHHHHHHHHCCEEEEETTGGGT-HHHHHHHHHHHHHHHHH CS
                         RNase_HII  76 nlneikaaltlaviklleklgvkvdeilvdgvttpeslkkkleqiikikvtvekkadekyllvaaASiiAkverdee 152
                                       + n+i + ++++v  +l+++++ +d+ +v++ + ++ + ++ ++   + +++e+kad+++ +v+aASi+Akv+rd  
  gi|330508333|ref|YP_004384761.1|  81 TMNDIMVRSFSQVVGRLHADRAILDAADVNAERFAQAVRNHSKTS--MDLIAEHKADQRHHVVSAASILAKVRRDRS 155
                                       9*****************************555555555555555..559*************************** PP

                                       HHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHH CS
                         RNase_HII 153 lellkrkpgtldkgsGyasdektrallkkgats..klpdivrlsfkt 197
                                       ++ l++++ + ++gsGy+ d  t a+l +++ +   lp ++r+s++t
  gi|330508333|ref|YP_004384761.1| 156 MRELENEM-HCKIGSGYPHDRDTIAFLSEWVREnkDLPPCARHSWTT 201
                                       ***99999.6*********************99889*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1557.70
//
Query:       gi|330508334|ref|YP_004384762.1|  [L=381]
Description: soluble hydrogenase small subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-41  141.4   0.0    4.3e-41  141.1   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
     0.0014   18.0   0.1      0.013   14.9   0.0    2.0  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.033   14.1   0.1        1.1    9.1   0.0    2.6  3  YjeF_N           YjeF-related protein N-terminus


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 !  141.1   0.0   7.2e-45   4.3e-41       2     342 ..       7     330 ..       6     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 7.2e-45
                                       EEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHH CS
                       Aminotran_5   2 yldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlva 78 
                                       +l+ +++ ++ ++Vl+a+++           +++h++ e+ +++ e+ e ++e++++++ +  i t ++t ++ +++
  gi|330508334|ref|YP_004384762.1|   7 LLMIPGPVKVAPRVLRAMSKP----------MISHRSGEFGAIYSECAELLKEFFQTKN-QIAIMTGSGTLGMDAAV 72 
                                       588899999999999999998..........99*************************7.88888888888****** PP

                                       HHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB CS
                       Aminotran_5  79 lslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGti 155
                                        ++   + ++d+iv+ ++++ +++    e+ +r g  v  +++d++   dld++e++l+e +k+va+ h++++ G  
  gi|330508334|ref|YP_004384762.1|  73 AGI---IGHEDKIVTISNGKFGER--FTEIGERYGKCV-PVKFDWGMPFDLDRVEAALEEGAKAVAMVHNETSVGLT 143
                                       ***...9*****************..*****9999777.99************************************ PP

                                       --HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSE CS
                       Aminotran_5 156 qpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemv 231
                                       +p +e+g+lakk++a+++vD+ +++g  ++ ++++++D++  +++K l  P+G+ v++v++++ e++  l  + ++ 
  gi|330508334|ref|YP_004384762.1| 144 NPAKEVGRLAKKYDAVFIVDGISSIGGNEFLTDEWNIDIAITGSQKaLAVPPGLAVVSVSPRAEERF--LAQSASYY 218
                                       **********************************************9999*****************..88888889 PP

                                       EEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES..-B-CT CS
                       Aminotran_5 232 eevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlyg.pdkaer 307
                                       ++ + + ++ +++p +    Tp v+ + ++++al + +e g++a +++++++ae ++++ k+l+   + +  ++ + 
  gi|330508334|ref|YP_004384762.1| 219 ADLKAHLKSARKSPAQTPF-TPAVPLFFAMQEALHMAAEEGFAARRERAAKQAESVRSAAKALGIELFPQtNENSHY 294
                                       9999999999999998886.******************************************998888552234445 PP

                                       CBSEEEEEE.TTCSHHHHHHHHHHTTEEEEEE-TTT CS
                       Aminotran_5 308 rasivsfnf.kgvhaedvatlLdeegIavrsGhhca 342
                                       +++++++++ +gv+ ++++  ++++g+ v++G++ +
  gi|330508334|ref|YP_004384762.1| 295 SNTVTAMKMpEGVSDDKLRGGMKKKGVIVSGGQEQL 330
                                       56777888888999999***************9987 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.1e-06     0.013      28     150 ..      43     169 ..      22     172 .. 0.79
   2 ?    0.7   0.0     0.044   2.6e+02     238     302 ..     256     321 ..     246     325 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-06
                                       HHHHHHHHHT-SEEEEESSHHHHHHHHHHHTT.TTTT-EEEEESSS.-THHHHHHHHTT-EEEEE-B-TTTSSB-GG CS
                   DegT_DnrJ_EryC1  28 FEkafaaylgvkhaiavssGtaAlhlaLralg.vgpgdeVIvpslt.FvatanavlelgakpvfvDvdpdtynidpa 102
                                        ++ ++++ ++k+ ia+ +G+ +l +   + g +g++d++++ s++ F      + e   k v+v  d   +  d +
  gi|330508334|ref|YP_004384762.1|  43 CAELLKEFFQTKNQIAIMTGSGTLGMDAAVAGiIGHEDKIVTISNGkFGERFTEIGERYGKCVPVKFD-WGMPFDLD 118
                                       55667888887777777777766666666655157999999999973555677888888899999998.67889*** PP

                                       GCGGG--TTEEEEEEB-...GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1 103 aieaaitertkaIlpVh...lyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                       ++eaa++e  ka+ +Vh    +G  +  +++ ++a+k++ ++i D   ++G
  gi|330508334|ref|YP_004384762.1| 119 RVEAALEEGAKAVAMVHnetSVGLTNPAKEVGRLAKKYDAVFIVDGISSIG 169
                                       *****************4444788899*****************9887777 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSS.EEESCEEEEEHCCHHHCHHHHHHHHHHCCE CS
                   DegT_DnrJ_EryC1 238 delvarRreiaelykeeLaelegtaelttpketkk.hawhlyavlveeeaevkrdelvealkeegi 302
                                       +e  a Rre a+   e ++++ + + +++ ++t++ + +  ++  ++  + v+ d+l   +k++g+
  gi|330508334|ref|YP_004384762.1| 256 EEGFAARRERAAKQAESVRSAAKALGIELFPQTNEnSHYSNTVTAMKMPEGVSDDKLRGGMKKKGV 321
                                       555667777777778888888888888888888852334444444444444999999999999887 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 ?    9.1   0.0   0.00018       1.1      11      47 ..      42      75 ..      40      96 .. 0.90
   2 ?    1.5   0.0     0.042   2.5e+02      80     120 ..     129     176 ..     112     202 .. 0.66
   3 ?   -1.4   0.0      0.31   1.8e+03      66      96 ..     265     295 ..     250     315 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00018
                            YjeF_N 11 avaevlrallgnspaekkvlvlvGsgnnGgdglaaAr 47
                                      ++ae+l++ +   + ++++ +++Gsg  G d+ +a+ 
  gi|330508334|ref|YP_004384762.1| 42 ECAELLKEFF---QTKNQIAIMTGSGTLGMDAAVAGI 75
                                      689999****...9********************995 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.042
                            YjeF_N  80 kaggkvveekpeedleekls.......apvdlviDAllGiglrgelre 120
                                       ka   v+ e+++   + + +        ++  ++D++  ig ++ l +
  gi|330508334|ref|YP_004384762.1| 129 KAVAMVHNETSVGLTNPAKEvgrlakkYDAVFIVDGISSIGGNEFLTD 176
                                       444444444444444444446666655667789*******99987666 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.31
                            YjeF_N  66 kldedaeralellkkaggkvveekpeedlee 96 
                                          ++ae   +++k++g++++ +++e+++ +
  gi|330508334|ref|YP_004384762.1| 265 RAAKQAESVRSAAKALGIELFPQTNENSHYS 295
                                       4555555555666666666666666665543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2627.17
//
Query:       gi|330508335|ref|YP_004384763.1|  [L=450]
Description: pyridoxal-phosphate dependent TrpB-like enzyme [Methanosaeta concilii GP6]
Scores for complete 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-39  134.7   0.0    4.9e-39  134.5   0.0    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.5   0.0   2.8e-43   4.9e-39       4     293 ..      75     412 ..      72     413 .. 0.82

  Alignments for each domain:
  == domain 1  score: 134.5 bits;  conditional E-value: 2.8e-43
                                       CSSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   4 gigpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllar.lkegtgaktvveassGNhgralAaaaall 77 
                                         +pTPl r+ +l+k+l++p  +++K+E+  p gS+K ++a    ++  keg   +  +e+++G++g al++a  l+
  gi|330508335|ref|YP_004384763.1|  75 LWRPTPLYRAASLEKALKTPakIYYKYEGVSPAGSHKPNTAIPQAYYnMKEG-IERLATETGAGQWGSALSLATCLF 150
                                       579***************************************8888868888.9999999999************** PP

                                       T-EEEEEEETTS-...HHHHHHHHHTT-EEEEE..................CCHHHHHHHHHHHHHHHSTTCEE--T CS
                              PALP  78 Glkvtivvpadas...pekvallrllGaevvev..................ggdydeavaaaaelaaegegaylvsq 133
                                       Gl++t+++ +++    p+++ ++r +Gae+  +                  +g+   a + a e aa+ ++ ++ s 
  gi|330508335|ref|YP_004384763.1| 151 GLQCTVYMVRSSFdskPYRKSAMRVWGAECLSSpsdrtnfgrqirekmpdtPGSLGIAISEAVEDAAS-HDNTNYSL 226
                                       *******9998887779****************55555555555544444444455555554455555.33333333 PP

                                       TT.SHHHHHHHHTHHHHHHHHTT...TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT-EEEEEEECTTCGGTTCC CS
                              PALP 134 fd.nptviegygtiglEileqlg...gkpdavvvpvGgGgliaGiaaglke....rrpdvrvigvepegsdalarsl 202
                                       ++   +v + ++  g+E+++q++   + pd+++ ++GgG+++ G+++++      ++ d r+++ ep+ +++l+++l
  gi|330508335|ref|YP_004384763.1| 227 GSvLNHVLLHQTIEGQELKKQFDmteDYPDVMFGCCGGGSNFPGMVFPFIPdklkDKKDLRMVACEPTACPTLTEGL 303
                                       32133455557777*****8888888*************************98765666****************** PP

                                       ...S..S.SS..B.........SSS.CCSTCS.....CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B CS
                              PALP 203 ...ragrrvtvpvs........dtiadglavg.....spselafelldrlvdeivtvsdeealeamrllarregivv 263
                                          + g+   + +         d i +g+++g      +++l   l+++ + e+ ++ + e++ea+ l+ar+egi++
  gi|330508335|ref|YP_004384763.1| 304 fayDYGDTAGMAPVimmytlghDFIPPGIHAGglryhGDAPLLSNLVHDGLIEATALQQTEVFEAATLFARTEGIIP 380
                                       55555555555555********7777777777777779999************************************ PP

                                       -HHHHHHHHHH..HHHHHHCCTTCEEEEEEE- CS
                              PALP 264 epssaaalaal..klreagelkegdrvvvilt 293
                                        p sa+a+  +  +++++++ +e++++ + l+
  gi|330508335|ref|YP_004384763.1| 381 APESAHAIKPAidEALNCRKTGEEKVIFISLS 412
                                       ********9999************66666565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3273.06
//
Query:       gi|330508336|ref|YP_004384764.1|  [L=374]
Description: NAD(+)/NADH kinase [Methanosaeta concilii GP6]
Scores for 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  162.5   0.0    1.0  1  NAD_kinase  ATP-NAD kinase
    4.6e-05   23.0   0.0     0.0001   21.9   0.0    1.6  1  DAGK_cat    Diacylglycerol kinase catalytic domain
     0.0019   18.1   0.0     0.0037   17.2   0.0    1.5  1  DeoRC       DeoR C terminal sensor domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.5   0.0   2.1e-51   1.2e-47       1     286 [.       7     362 ..       7     367 .. 0.94

  Alignments for each domain:
  == domain 1  score: 162.5 bits;  conditional E-value: 2.1e-51
                                       .EEEEESSC........................GGTCSHHHHHHHHHHHCT-...EEEEECCGGCCSSSTT--HHHH CS
                        NAD_kinase   1 kvgivvnpi........................kkeaieraeevarwLldals.rvlevtveeklgeslaeaaefrs 52 
                                       ++g++vnpi                        ++ a era+ ++++L++  +  +l++t ++++ges  e+ + ++
  gi|330508336|ref|YP_004384764.1|   7 RIGFLVNPIagmggpvglkgtdglaeeaiamgaRPRAMERARACLDLLSKE-RdAILFFTASGSMGESCLEECGLDY 82 
                                       69***************************8777777778888888888777.469********************** PP

                                       TTTT--.......EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SE..EGGGHHHH CS
                        NAD_kinase  53 evisvlkkvkttddtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltef..epeaaael 127
                                       +v++ +  v +++dt++  +af d+gvdli++ GGDGTa+dva +    + P+l+++aGvk+++++f  +p+aaa l
  gi|330508336|ref|YP_004384764.1|  83 KVVYSALPVTSSRDTIRTCQAFLDEGVDLILFCGGDGTARDVAGIAG--STPILAIPAGVKMHSGVFaaSPQAAADL 157
                                       ***********************************************..9*************************** PP

                                       HHHHHHT-SEEEEEEEEE...............................EEEEETTE..........EEEEEEESSE CS
                        NAD_kinase 128 lekllegeirvekrevld...............................avimrskgee....diadiviensvlne 169
                                         ++l+ge ++ + e++d                                 i+ s++e     +ia +++e  ++++
  gi|330508336|ref|YP_004384764.1| 158 VIRFLNGELNLRDTEIVDvdeelyragilqtklyalaktpylpvlvaerKRIYSSDQEDefkdQIALFASEF-MRDG 233
                                       *******************************************99999989999999888886666666555.5*** PP

                                       EEEEESSSSS-EE..EEEEETTEEEEEEEESEE.......................EEE-TGGGGTHHHHTT--EE- CS
                        NAD_kinase 170 vviirgpgstlie..lelyvdtelleadqldgl.......................ivstPtGstayslsaGgplis 221
                                         +i+g g+t +     l+++++ll++d+++++                       i+++P+G +++ l++G++++s
  gi|330508336|ref|YP_004384764.1| 234 SAYIIGAGTTTSRiaDILGLEKTLLGVDVVKDGrlmitdaseqdllelldretrvmIIISPIGAQGFILGRGNQQLS 310
                                       *************9888*************9999******************************************* PP

                                       TT---EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSE CS
                        NAD_kinase 222 PgvlailivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkk 286
                                        +v +         +  +++i++s++ kl      ++  ll+++G+e+l+ s+ +  +v+++++ 
  gi|330508336|ref|YP_004384764.1| 311 AEVIR--------RVGIDKLIIISTPHKLA-----EIPYLLVDTGDEDLDESLAGKRQVVTGYRI 362
                                       *****........*****************.....*************************99985 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.7e-08    0.0001      32      91 ..      85     139 ..      71     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-08
                                       EEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-S CS
                          DAGK_cat  32 elelieteepgdakelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlG 91 
                                        +++  ++++ d  + ++   +egvdli+ +GGDGt++ v++         +p+  iP+G
  gi|330508336|ref|YP_004384764.1|  85 VYSALPVTSSRDTIRTCQAFLDEGVDLILFCGGDGTARDVAGIAGS-----TPILAIPAG 139
                                       45666667788888899999999*****************976666.....777778888 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.1e-07    0.0037       4      42 ..     217     255 ..     214     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.1e-07
                             DeoRC   4 eeKrrIAkaAaeliedgdtifldaGtTtlelaraLaekk 42 
                                       e K +IA  A e+ +dg++ +++aGtTt  +a+ L  +k
  gi|330508336|ref|YP_004384764.1| 217 EFKDQIALFASEFMRDGSAYIIGAGTTTSRIADILGLEK 255
                                       5699****************************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2831.08
//
Query:       gi|330508337|ref|YP_004384765.1|  [L=231]
Description: V-type ATP synthase subunit D [Methanosaeta concilii GP6]
Scores for complete 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  177.7  10.5      3e-52  177.3  10.5    1.1  1  ATP-synt_D  ATP synthase subunit D


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.3  10.5   1.7e-56     3e-52       2     195 ..      14     205 ..      13     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 1.7e-56
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-.. CS
                        ATP-synt_D   2 LirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvkla 78 
                                       Li+lkkr+k+aq ghslLk+Krd L++ef+e+l+++k+ r+el e+l  a++ l++a+a +g  +i s++ + +k  
  gi|330508337|ref|YP_004384765.1|  14 LIALKKRMKVAQTGHSLLKMKRDGLMIEFFEVLNKAKTVRKELVEALLIAEQRLQMAMAIEGTVAIGSVAYSLQK-- 88 
                                       89*****************************************************************99995555.. PP

                                       TSS-SEEEEEEBTTSEEEEEEE-...S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  79 kvvkvelktenvaGVkvpvfeleee.ksdstelygllrtgaqldeavealrellellvelasletslelLdeeikkt 154
                                        + +++l+++n++GV vp++e e   k+  ++ yg+++t+a +dea++a++ ll++++ +a++et++++L e i  t
  gi|330508337|ref|YP_004384765.1|  89 -EPTIQLESRNIMGVVVPKIEAEAVqKKMYERGYGVIGTSAAIDEAADAYEVLLDKIILAAEVETAMIRLVEDIDST 164
                                       .699****************9877653334457******************************************** PP

                                       HHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 155 nrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvk 195
                                       +rRvNaLe +v+P l+ tik+I+++L+E+er + + +k++k
  gi|330508337|ref|YP_004384765.1| 165 KRRVNALEFKVVPDLKLTIKFISMALEEMERDNLVKMKMLK 205
                                       ***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1585.64
//
Query:       gi|330508338|ref|YP_004384766.1|  [L=461]
Description: V-type ATP synthase subunit B [Methanosaeta concilii GP6]
Scores for complete 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-60  204.0   0.0    3.1e-60  203.5   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    8.2e-12   45.5   0.6    8.2e-12   45.5   0.6    1.9  2  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
  ------ inclusion threshold ------
       0.24   11.6   0.9       0.42   10.8   0.4    1.8  2  HAS-barrel     HAS barrel domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.5   0.0   5.1e-64   3.1e-60       1     213 []     129     347 ..     129     347 .. 0.98

  Alignments for each domain:
  == domain 1  score: 203.5 bits;  conditional E-value: 5.1e-64
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrt 72 
                                       Gi+++D   ++v+Gq++ i++++g++++ ++ ++++q+++     + a+i++++G  ++e++++l +f+++++++r 
  gi|330508338|ref|YP_004384766.1| 129 GISTIDGTNTLVRGQKLPIFSGAGLPHNDLALQIARQAKALgeaeSfAVIFCAMGITNEEAQHFLADFERTGALERA 205
                                       899**********************************8655888768****************************** PP

                                       EEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  73 vlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklasl 148
                                       v+++n +++p+++r++++++g+t+AEy++   +++vl+i++++++++e+lr+++++ +e+p+++gyp+y++++la  
  gi|330508338|ref|YP_004384766.1| 206 VVFLNLADDPAVERILTPRLGLTTAEYLAFdLDMHVLIIYTDMTNYCESLRQMGAAREEVPGRRGYPGYMYTDLACQ 282
                                       ****************************9879********************************************* PP

                                       HTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 149 yERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       yERag ++ ++Gs+t++++++++g+D+++p+++   +it+g+i ++++l++++++P++++  S+S
  gi|330508338|ref|YP_004384766.1| 283 YERAGIIKGKKGSITQFPILTMPGDDITHPIPDLSGYITEGQILISRELHRKGIYPPVDIRPSLS 347
                                       ***************************************************************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 !   45.5   0.6   1.4e-15   8.2e-12       1      69 []       8      72 ..       8      72 .. 0.98
   2 ?   -3.7   0.0         3   1.8e+04      53      64 ..     133     144 ..     129     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1.4e-15
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      i++++Gp++ ve+ +    g+ +++e++   +g+l +g++l  ++d V+++++++t Gls+ + V +TG
  gi|330508338|ref|YP_004384766.1|  8 ITEISGPLIFVEKTEP--VGYMELVEIR--TGGDLKRGQVLDSSDDIVVIQIFEGTGGLSKDSAVSFTG 72
                                      89**************..**********..999***********************************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3
                                       SS-STTBBTTSE CS
                     ATP-synt_ab_N  53 mgstdGlsrGte 64 
                                       +++t  l+rG++
  gi|330508338|ref|YP_004384766.1| 133 IDGTNTLVRGQK 144
                                       688999999985 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   7.1e-05      0.42       2      83 ..       2      67 ..       1      89 [. 0.77
   2 ?   -3.8   0.0       2.5   1.5e+04       5      21 ..     128     144 ..     128     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.1e-05
                        HAS-barrel  2 Gevigests.sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalat 79
                                       +++ + t  s+++++ve +++v++ e+Vei++  g+   G+v+d +                        d++v++++
  gi|330508338|ref|YP_004384766.1|  2 TKEYKTITEiSGPLIFVEKTEPVGYMELVEIRTG-GDLKRGQVLDSSD-----------------------DIVVIQIF 56
                                      6789999999**********************99.9999999999888.......................77777777 PP

                        HAS-barrel 80 edt.......g 83
                                      e+t        
  gi|330508338|ref|YP_004384766.1| 57 EGTgglskdsA 67
                                      77766665551 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.5
                        HAS-barrel   5 igestssslifrvegsk 21 
                                       +g st++++ + v+g+k
  gi|330508338|ref|YP_004384766.1| 128 TGISTIDGTNTLVRGQK 144
                                       68899999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3846.10
//
Query:       gi|330508339|ref|YP_004384767.1|  [L=576]
Description: V-type ATP synthase subunit A [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-92  307.4   0.0    6.5e-92  307.0   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    1.3e-41  141.2   0.1    2.6e-41  140.3   0.1    1.5  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    1.9e-09   37.9   0.8    6.3e-09   36.2   0.8    2.0  1  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
  ------ inclusion threshold ------
      0.019   14.9   0.7      0.089   12.8   0.1    2.1  2  RnfC_N           RnfC Barrel sandwich hybrid domain
      0.079   13.2   0.0       0.16   12.2   0.0    1.4  1  AAA_22           AAA domain
       0.12   12.6   0.4       0.49   10.6   0.1    2.1  2  Peptidase_M23    Peptidase family M23


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.0   0.0   2.2e-95   6.5e-92       1     213 []     208     429 ..     208     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 307.0 bits;  conditional E-value: 2.2e-95
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imk 70 
                                       G+rv+D +f++++G++ +ipg+fg+Gktv++q+lsk+++ d +++yvg+Gergne+a++l+efpe      g+ +m+
  gi|330508339|ref|YP_004384767.1| 208 GQRVIDGFFSLAKGGTAAIPGGFGTGKTVMQQTLSKWADVD-IVVYVGCGERGNEMADLLHEFPElqdprtGRpLME 283
                                       9************************************9888.***********************988865338*** PP

                                       GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  71 rtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                       r+++ antsn+pvaareas+ytg+t++Ey+rd+g++vl+ ads+srwaeA+re++ rl+emp+++gypaylga+la 
  gi|330508339|ref|YP_004384767.1| 284 RSIVYANTSNMPVAAREASVYTGMTTSEYYRDMGYDVLMTADSTSRWAEAMREMGSRLEEMPGEEGYPAYLGARLAD 360
                                       ***************************************************************************** PP

                                       HHTTSEEE...TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 148 lyERagka...pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       +yERag+a   +  +Gsv+iv avspaggDf++pvt++tl+++++f+ Ld+kl+qr+hfP+in+l S+S
  gi|330508339|ref|YP_004384767.1| 361 FYERAGRAevlNGGQGSVSIVGAVSPAGGDFTEPVTQNTLRMVKVFWALDSKLTQRRHFPSINWLDSYS 429
                                       ********8887789*****************************************************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 !  140.3   0.1   8.6e-45   2.6e-41       1     121 []      83     199 ..      83     199 .. 0.96

  Alignments for each domain:
  == domain 1  score: 140.3 bits;  conditional E-value: 8.6e-45
                                       EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEE.EE CS
                   ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegk.vk 76 
                                       yDGiqrpL k+ae+sg+fi+rG+ v+ +d++kkwefk  vk+gd+v++g+ +G+vqe+ li+hkimvpp+++g  +k
  gi|330508339|ref|YP_004384767.1|  83 YDGIQRPLPKLAEASGDFISRGLFVDGIDHKKKWEFKSVVKKGDTVKPGQAIGEVQEQLLIKHKIMVPPNLKGGaIK 159
                                       9*********************************************************************9765599 PP

                                       EE--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
                   ATP-synt_ab_Xtn  77 eiaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                       ei  +g++tv++tia++++++    +l +++kwPvr++rpv+ekl
  gi|330508339|ref|YP_004384767.1| 160 EIY-DGNFTVDETIAVLDDGT----KLFMMHKWPVRQARPVTEKL 199
                                       999.**************776....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 !   36.2   0.8   2.1e-12   6.3e-09       1      69 []       6      67 ..       6      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 2.1e-12
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      i +v Gp+v++ + +     +y+++ v+  e  ++l+ ++++++++k +++v+++t G+++G++Vk TG
  gi|330508339|ref|YP_004384767.1|  6 IKRVAGPLVQATGLK---ASMYDLVLVG--E--EGLMSEVIGISGNKHIIQVYEDTGGVRPGEPVKETG 67
                                      679********5555...5*********..8..9**********************************8 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.34     1e+03      28      70 ..       7      51 ..       2      58 .. 0.78
   2 ?   12.8   0.1     3e-05     0.089      43      69 ..     119     147 ..     112     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.34
                            RnfC_N 28 kelvlplsqhiGapakp..lvkvgdkVlkGqkiaeaegfvsapvh 70
                                      k++  pl q  G +a++  lv vg++ l+ ++i+ +++    +v+
  gi|330508339|ref|YP_004384767.1|  7 KRVAGPLVQATGLKASMydLVLVGEEGLMSEVIGISGNKHIIQVY 51
                                      677889999999999875589999999999999988775566666 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3e-05
                            RnfC_N  43 kplvkvgdkVlkGqkiaeaeg..fvsapv 69 
                                       k +vk+gd+V+ Gq i+e ++  +++ ++
  gi|330508339|ref|YP_004384767.1| 119 KSVVKKGDTVKPGQAIGEVQEqlLIKHKI 147
                                       789***************98755555555 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   5.4e-05      0.16       6      63 ..     222     272 ..     219     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.4e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellra 63 
                                       g  ++ G  GtGKT+  ++l +++d         + vv+v + + + + +dll+e+ + 
  gi|330508339|ref|YP_004384767.1| 222 GTAAIPGGFGTGKTVMQQTLSKWAD--------VDIVVYVGCGERGnEMADLLHEFPEL 272
                                       6678999*****************7........88888****99998888999887654 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         2     6e+03      33      64 ..      35      64 ..      26      68 .. 0.68
   2 ?   10.6   0.1   0.00017      0.49      56      74 ..     121     139 ..     109     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2
                                      TEEEEEEEECTCEEEEEEEESEESS-TTEEE- CS
                     Peptidase_M23 33 yGnvviidhgdgystlyahlskisvkegqkVk 64
                                      + +v+ i  +++++++y       v++g+ Vk
  gi|330508339|ref|YP_004384767.1| 35 MSEVIGISGNKHIIQVYEDTGG--VRPGEPVK 64
                                      4777888888888888877666..77777776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00017
                                       SS-TTEEE-TTCEEEEEBS CS
                     Peptidase_M23  56 svkegqkVkaGqvIGtvgs 74 
                                        vk+g++Vk Gq IG+v +
  gi|330508339|ref|YP_004384767.1| 121 VVKKGDTVKPGQAIGEVQE 139
                                       39**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4013.64
//
Query:       gi|330508340|ref|YP_004384768.1|  [L=99]
Description: V-type ATP synthase subunit F [Methanosaeta concilii GP6]
Scores for complete 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   50.9   0.1    1.7e-13   50.7   0.1    1.0  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.1   9.4e-18   1.7e-13       1      88 [.       3      90 ..       3      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 9.4e-18
                                      EEEEESHHHHHHHHHTTCEEEE.CSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCS.SSSEEEEESCSC CS
                        ATP-synt_F  1 iavIGdedtvtgfrlaGvgeve.vtdeeeieealkelleredigiilitekiaeeirelideykee.alPaileIPske 77
                                      ia++G +++v+gf laGv++ + +++e+e+ +++ ++++++++gi+++++  +++++++++e  +e  +P+ ++I +++
  gi|330508340|ref|YP_004384768.1|  3 IAFVGGSESVLGFNLAGVKKSYaANTEDEMVSKIGDVMADSSVGILVLKQSDYNKLPKRLQEQLSEsIKPTMITIGTEQ 81
                                      89******************99666699*****************************8888777776********7666 PP

                                      CGGSHHCHHHH CS
                        ATP-synt_F 78 gpydeekdsvr 88
                                      ++    +++++
  gi|330508340|ref|YP_004384768.1| 82 STE--MREKIK 90
                                      633..355555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 643.24
//
Query:       gi|330508341|ref|YP_004384769.1|  [L=337]
Description: V-type ATP synthase subunit C [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-72  244.6   0.2    2.1e-72  244.5   0.2    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.5   0.2   1.2e-76   2.1e-72       1     335 [.       6     332 ..       6     333 .. 0.91

  Alignments for each domain:
  == domain 1  score: 244.5 bits;  conditional E-value: 1.2e-76
                                       HHHHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H CS
                    vATP-synt_AC39   1 leArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapg 77 
                                       +++rvram+++l+++e y ++  ++ +++++ryL+et Y++++   + ++++++ ie+a  +++a++f+kl e + +
  gi|330508341|ref|YP_004384769.1|   6 ITGRVRAMKTKLIPAEMYPRM-MNMEMSEIARYLEETQYKEEIDALAKDYSGVDLIEHATFDNMAKTFRKLAEVSID 81 
                                       579******************.555*****************7777799************************9999 PP

                                       .HHHHHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SSSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHHH CS
                    vATP-synt_AC39  78 psrefldyllyrydidNvklllrgklsgdldleeleeklhplgelsaldldklieaksveelyeallgtpyakylee 154
                                       ++  ++  +l+r+d++N+k+llrgk+s +++  e++++l+p+gels+++l++l++++s++++++a+ gt ya++l++
  gi|330508341|ref|YP_004384769.1|  82 EPSFLILEYLRRWDVWNIKTLLRGKFS-GASDTEIMKYLVPAGELSPEHLEELAKKDSIQDIISAFDGTDYASALAQ 157
                                       95499999*******************.57779***************************************99998 PP

                                       HHCC...--SHHHHHHHHHHHHHHHHHHH.HHTSS..-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T... CS
                    vATP-synt_AC39 155 aldeleetgdleiienaLdkayledllkf.ckklg..getaeilreilgfeiDlrniniilrskkygelskedrkkl 228
                                           ++  ++l+ +enaLdk y+ ++ ++   +l+  g     l +++++eiD++n+ +++r+ k+g +  + +++ 
  gi|330508341|ref|YP_004384769.1| 158 ----YDG-KNLASLENALDKLYYFRMERAvGGTLSvgGGL---LLKYVRREIDIKNLITLFRMNKAGID-AAVIQEN 225
                                       ....666.889******************64444443667...**********************8843.4448888 PP

                                       --SS-S--HHHHHHHHTT-G.....GG.GGSSTSSTTGGGTT-.-S.HHHHHHHHHHHHHHHHHT.TTSSSTSTHHH CS
                    vATP-synt_AC39 229 lipggslypeglealaeaedveellaalkyteygelleealee.agslksledaldealvkllkk.afrqqfsvgvf 303
                                       lipgg+l+ ++l+++a +  + e+l+ l+ +++++ +++++ +  ++ + +e +l+++l++++   + ++++s+ ++
  gi|330508341|ref|YP_004384769.1| 226 LIPGGKLH-DELSRMAGQ-PFGEFLRGLEGYPFWSSISDIATSdLDAVSRVEARLKAYLIRYAWAlSNYHPLSILPV 300
                                       *******9.567779988.8********8888888888776664444****************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHT--SHHHHG CS
                    vATP-synt_AC39 304 yaYlklkeqEirnlrwIaegiaqglpkekIre 335
                                       ++Y+  ke+E+ n+r I++g+++glp+e I+e
  gi|330508341|ref|YP_004384769.1| 301 LGYMVSKETEVSNIRKIVRGKEAGLPSELIEE 332
                                       ******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); 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 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2429.80
//
Query:       gi|330508342|ref|YP_004384770.1|  [L=182]
Description: V-type ATP synthase subunit E [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-16   58.4  15.0    5.5e-14   52.1  15.0    2.0  1  vATP-synt_E   ATP synthase (E/31 kDa) subunit
  ------ inclusion threshold ------
       0.39   11.2  11.5       0.43   11.0  10.4    1.6  2  V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
          1    8.4   5.6        1.5    7.8   5.6    1.3  1  Atg14         Vacuolar sorting 38 and autophagy-related subun
        1.8    8.2   8.1       0.26   11.0   0.7    2.3  3  tRNA_bind_2   Possible tRNA binding domain


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1  15.0   1.2e-17   5.5e-14       6     199 .]      14     181 ..       9     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.2e-17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       vATP-synt_E   6 AeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevfeeae 82 
                                        ++k+ +I ++a+ e++ +++++ e++ e + ++  +    +e+  +++iS+a ++ +++ L++ +++le+++ ++ 
  gi|330508342|ref|YP_004384770.1|  14 SKDKVAQITSEADLEAARILNEARERAAEIKSRKESEVGHAIEAIERREISSANLEVKRSELNVHKDLLEKARTKLL 90 
                                       689**************************9999999***************************************** PP

                                       HHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEESSEBTT CS
                       vATP-synt_E  83 kkLaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveealdkaaeeykaktkkktvevagdeedfled 159
                                       +k+++++++        + ++++ l+     ++ v+++k+D+  +++    +a +y ++                 d
  gi|330508342|ref|YP_004384770.1|  91 EKISNLPKKD------NEAMLKKMLEPYDLKDMKVYSNKRDEAFLSS----LAPNYGGN----------------LD 141
                                       ********99......6677777888888999**************9....57777774................79 PP

                                       SSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                       vATP-synt_E 160 vlGGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                       ++GGvv+e+ dg  + + + e +   v+++ ++e++k LF
  gi|330508342|ref|YP_004384770.1| 142 IIGGVVVESGDGALRYDLSYETLAREVFNNRMKEVSKVLF 181
                                       ***************************************9 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0  10.4   9.6e-05      0.43      25      88 ..      15      78 ..       2      95 .. 0.80
   2 ?   -1.7   0.0      0.89     4e+03      45      61 ..     100     116 ..      81     128 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.6e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2 25 rkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqavrkrae 88
                                      + + ++  ++A+ eAaril+eA ++a +++++ e e+ + +++i+ +  + a+ e+++ + + +
  gi|330508342|ref|YP_004384770.1| 15 KDKVAQITSEADLEAARILNEARERAAEIKSRKESEVGHAIEAIERREISSANLEVKRSELNVH 78
                                      4455666789**************************************999*999998765554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.89
                                       HHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2  45 eAeakakalqaeyeqel 61 
                                       + ea +k++ + y+ + 
  gi|330508342|ref|YP_004384770.1| 100 DNEAMLKKMLEPYDLKD 116
                                       44555566655555555 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   5.6   0.00034       1.5      67     142 ..      25      99 ..       4     126 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00034
                             Atg14  67 akleelksliadlrerlqelkd.klsqlkkeie.ekkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaik 141
                                       a+le  ++l +  rer +e+k  k s+   +ie + ++++++ + ++  +rs+l+ +++ le++r+k+++k+++  k
  gi|330508342|ref|YP_004384770.1|  25 ADLEAARILNEA-RERAAEIKSrKESEVGHAIEaIERREISSANLEV--KRSELNVHKDLLEKARTKLLEKISNLPK 98 
                                       444555554443.3344444430344444555425788888888887..5999999999999999999999998766 PP

                             Atg14 142 r 142
                                       +
  gi|330508342|ref|YP_004384770.1|  99 K 99 
                                       4 PP

>> tRNA_bind_2  Possible tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.7     0.049   2.2e+02     149     200 ..      32      86 ..       8      95 .. 0.71
   2 ?   11.0   0.7   5.7e-05      0.26      45      74 ..      94     123 ..      80     126 .. 0.76
   3 ?   -3.6   0.0       1.7   7.4e+03      87      99 ..     163     175 ..     161     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.049
                                       HH-HHHHHHHHH-XXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       tRNA_bind_2 149 alreilekaieeelpkekeee...kaaeaeeeeakekelkpleesleeeLeeaak 200
                                       +l+e  e+a e +  ke+e+    +a e++e ++++ e+k+ e +++++L e+a+
  gi|330508342|ref|YP_004384770.1|  32 ILNEARERAAEIKSRKESEVGhaiEAIERREISSANLEVKRSELNVHKDLLEKAR 86 
                                       5677777777777777777665444555555556666778888888888887775 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.7e-05
                                       -----------------HHHHHHHHHHHHS CS
                       tRNA_bind_2  45 seekkeltkeeldellspfDlkRLesYann 74 
                                       s+ +k+ +++ l+++l+p+Dlk ++ Y+n+
  gi|330508342|ref|YP_004384770.1|  94 SNLPKKDNEAMLKKMLEPYDLKDMKVYSNK 123
                                       44566778999*****************97 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.7
                                       HHHHHHHH--SST CS
                       tRNA_bind_2  87 tlaklyFsgrlke 99 
                                       tla+  F++r+ke
  gi|330508342|ref|YP_004384770.1| 163 TLAREVFNNRMKE 175
                                       6888888888884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1174  (0.0654805); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1325.54
//
Query:       gi|330508343|ref|YP_004384771.1|  [L=88]
Description: ATP synthase C subunit, lipid binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-11   44.3  12.3    1.7e-11   44.3  12.3    2.0  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 !    2.7   0.4    0.0088   1.6e+02      42      56 ..       1      15 [.       1      16 [. 0.86
   2 !   44.3  12.3   9.3e-16   1.7e-11       2      60 .]      17      75 ..      16      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0088
                                      HHHHHHHHHHHHHHH CS
                        ATP-synt_C 42 ilafaeaialygLiv 56
                                      ++++a a  lygLi 
  gi|330508343|ref|YP_004384771.1|  1 MVVVADAGILYGLIA 15
                                      57899999*****95 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 9.3e-16
                                      HHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_C  2 gaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60
                                      gagla+Gl+++g+G+g   +g+a ++ va+ p   +k l ++ ++e++ ++gL v+lil
  gi|330508343|ref|YP_004384771.1| 17 GAGLATGLAGIGAGVGEQGIGAAVVGVVAEEPGFLGKGLFLMLLPETLIIFGLAVSLIL 75
                                      9********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 686.06
//
Query:       gi|330508344|ref|YP_004384772.1|  [L=677]
Description: V-type ATP synthase subunit I [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-33  115.5   3.9    3.5e-20   71.6   0.0    2.2  2  V_ATPase_I  V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
       0.11   11.9   0.1        3.8    6.9   0.0    2.2  2  FliD_C      Flagellar hook-associated protein 2 C-terminus


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 !   71.6   0.0   3.9e-24   3.5e-20     217     573 ..     185     536 ..     158     557 .. 0.75
   2 !   43.3   2.4   1.4e-15   1.2e-11     716     811 ..     566     668 ..     560     670 .. 0.69

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 3.9e-24
                        V_ATPase_I 217 eqlkekikkicesfgaklyelpeseeereeklkeveeriedlekvleqteealkevleeiakeleewklkvkk..ek 291
                                        +  + ++ + +  g +  ++p+ e + ++++++++ +i+ le  l      l++ l +++k++e+++l        
  gi|330508344|ref|YP_004384772.1| 185 AEKASEVSAVLSEHGFSEMSVPKLEGSVDSAIASLNGSIKSLEGELAP----LHKKLVDVKKQYEDLMLATDEylSM 257
                                       444556666777777777777777777777777777777766655544....4555555566666655555541135 PP

                        V_ATPase_I 292 aiyhtLnlfnldvtkkvliaegWvpkeeleeiqkalkeateessssvpsilneietk.....etpPTyfrtnkftea 363
                                       ++ +t   +++ +t++ ++ +gWvp+++  ++++ l++a    + +v+ i ++   +     e+ PT +   ++ + 
  gi|330508344|ref|YP_004384772.1| 258 QVSKTESPLRFAETDNAFVIDGWVPSDQYGRLKSELESAA-GGKLDVQLIADKEADDlvkggEDVPTKMDNPSIVKP 333
                                       67777788889999************************98.455778888777665333355888************ PP

                        V_ATPase_I 364 fQeivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvlkekklkkkkkdeilemlfsgRYiil 440
                                       +  i   ++i++Y+E  p+l+  + FP +F++  GD+G G+++ll+   l l +k++++    e ++ l++   i++
  gi|330508344|ref|YP_004384772.1| 334 YELITRLFAIPEYKEFDPSLLIFVFFPIMFGMILGDVGYGIVILLI---LTLLKKRFRT----EGWQQLIN---IVM 400
                                       *****************************************99975...6667777776....56777776...799 PP

                        V_ATPase_I 441 lmGlfsiYtGliYNdifskslnlfgSswevkeka..veeeelk...........kekkeekvYpfGlDpaWklaene 504
                                       + G++s+  G+ Y +if+ +l l++ +  + +++  +     +           +    ++  p+G+ p  +la+n+
  gi|330508344|ref|YP_004384772.1| 401 IAGVWSVIFGIFYGEIFG-PLGLWNYMVGMLSHHemI-----ElqemglffgegTFGPLGRLGPLGIFPLYRLATNA 471
                                       9****************8.555554333331111112.....1223446777766677788889************* PP

                        V_ATPase_I 505 llflnSlKmKlsvilGviqMlfgvllslvNalyfkkkldiilefiPqllfllsifgYlvlliiyKWlvd 573
                                       +l l    + +s  +Gvi+ ++g +l +   l+  +k + ++e +P +lf + + + l  l++   ++ 
  gi|330508344|ref|YP_004384772.1| 472 VLLL----IGVSLFIGVIHCSVGSILGIKTELNYGEKRHAYFERLPVMLFQVFFAVALLGLVMGQMIMV 536
                                       *987....678**************************************98777666666665555554 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 1.4e-15
                        V_ATPase_I 716 ciSnTASYLRLWALSLAHaqLseVlwemvlkkal......lksksvlgvillvilfavfavltvavLllmeglsafL 786
                                        +Sn  SYLRL A+ LA   L+    +  +  ++       + +s+   il +i+ ++ +v+  ++ +l+  ls f+
  gi|330508344|ref|YP_004384772.1| 566 YVSNLISYLRLLAIGLASVGLAYAANQLSFYVIMpmlsggAT-NSADFSILAIIVGIMVLVAVHFINILLGILSPFM 641
                                       79*************998888765544444333333333222.23333344444555555555677788999***** PP

                        V_ATPase_I 787 HaLRLhWVEfqsKFyk..gdGykFepf 811
                                       H LRLh VE+ +KFy+  g G++++pf
  gi|330508344|ref|YP_004384772.1| 642 HPLRLHYVEMFTKFYSahGGGVEYSPF 668
                                       ***************822567999999 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1    0.0084        76     152     213 ..      65     125 ..      56     129 .. 0.84
   2 ?    6.9   0.0   0.00042       3.8     150     221 ..     162     248 ..     158     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.0084
                                       HHHHHHTTTSS.......SXSHHHHHHHHHHHHHSTT.SHHHHHHHHXXXXHHHHHHHHHHH CS
                            FliD_C 152 sveelFsgstsqektvtsdsglatrlenllksyvkssngtlqtasknltkqikdldkkiedl 213
                                       sv+  +  + ++ ++++ +s + ++++nll+++ +   +++ +++  ++ +ik+++++i +l
  gi|330508344|ref|YP_004384772.1|  65 SVTRYLDIKNKAPEKTYPESQVLSEMDNLLNNVGGDV-TATYERIVAIEAEIKSKQDQIRAL 125
                                       566666666777789999************9877666.999*****************9876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00042
                                       HHHHHHHHTTT...............SS.......SXSHHHHHHHHHHHHHSTT.SHHHHHHHHXXXXHHHHHHHHH CS
                            FliD_C 150 pssveelFsgs...............tsqektvtsdsglatrlenllksyvkssngtlqtasknltkqikdldkkie 211
                                       +s v+e+F+g+                s+ ++v s+ g+ ++    l+  v+s   +l++++k+l+ ++  l kk  
  gi|330508344|ref|YP_004384772.1| 162 VSPVNEIFTGTaknatyvavfvpaekASEVSAVLSEHGFSEMSVPKLEGSVDSAIASLNGSIKSLEGELAPLHKKLV 238
                                       5678888888888888888888887766678999********9999*****9999********************** PP

                                       HHHHCHHHHH CS
                            FliD_C 212 dldkrletle 221
                                       d++k++e+l+
  gi|330508344|ref|YP_004384772.1| 239 DVKKQYEDLM 248
                                       **99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (677 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1256  (0.0700541); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.46
# Mc/sec: 4394.92
//
Query:       gi|330508345|ref|YP_004384773.1|  [L=108]
Description: V-type ATP synthase subunit H [Methanosaeta concilii GP6]
Scores for complete 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   29.4  12.8      1e-06   29.1  12.8    1.0  1  V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
     0.0016   18.5  15.8     0.0024   17.9  15.7    1.4  1  ATP-synt_B    ATP synthase B/B' CF(0)
     0.0017   18.9  10.4     0.0021   18.6  10.4    1.1  1  V-ATPase_G    Vacuolar (H+)-ATPase G subunit
  ------ inclusion threshold ------
      0.014   15.8   4.6      0.022   15.2   2.6    2.0  2  BMFP          Membrane fusogenic activity
       0.24   10.9   4.5       0.12   11.9   1.2    1.8  2  UPF0556       Uncharacterised protein family UPF0556
       0.86    9.5  10.8       0.78    9.7   9.8    1.4  2  RRF           Ribosome recycling factor


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 !   29.1  12.8   3.4e-10     1e-06       1     101 [.       1     101 [.       1     103 [. 0.97

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.4e-10
                                       XXXXHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2   1 dessrllkeLaerEaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararae 77 
                                       ++   +l+++++ Ea+  + + +A +e e++++aA  eA  +++ Ae +a+   ++  ++ +  v++ ++ + + ++
  gi|330508345|ref|YP_004384773.1|   1 MARDEILSKIKSAEAQSRAAVQQALEEKEKKIAAATTEAMNLVKSAEIDAQDYYDKSVAKAESDVKAKKQSIIQSGD 77 
                                       566789*********************************************************************** PP

                                       HHHHHHHHHHHCSHHHHHHHHHHH CS
                      V-ATPase_G_2  78 aeaqavrkraearlqqAvelilka 101
                                       +++ +++ +a+a+l++Ave  lk+
  gi|330508345|ref|YP_004384773.1|  78 KNVASMSGSASAKLDKAVEYLLKE 101
                                       **********************98 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  15.7   8.1e-07    0.0024      32      99 ..       3      71 ..       2      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.1e-07
                        ATP-synt_B 32 eekIadeiaeAe.errkeaaallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkes 99
                                      +++I ++i++Ae ++r+  +++l+e+e++ + A  eA +++k+A+ +a+   ++ +a+ae +++  k+s
  gi|330508345|ref|YP_004384773.1|  3 RDEILSKIKSAEaQSRAAVQQALEEKEKKIAAATTEAMNLVKSAEIDAQDYYDKSVAKAESDVKAKKQS 71
                                      57899******94478999******************************99999999999888765543 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 !   18.6  10.4   6.9e-07    0.0021      11     100 ..      12     101 ..       3     104 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.9e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHHHHHHH CS
                        V-ATPase_G  11 qAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgseeelekkieketeekikelkesvk 87 
                                       +AE + +  v++A ++k+k++  A +eA + +++     +  + ++ a++ ++ ++ +++i +  ++++++++ s++
  gi|330508345|ref|YP_004384773.1|  12 SAEAQSRAAVQQALEEKEKKIAAATTEAMNLVKSAEIDAQDYYDKSVAKAESDVKAKKQSIIQSGDKNVASMSGSAS 88 
                                       79*************************************************************************** PP

                                       HHHHHHHHHHHHH CS
                        V-ATPase_G  88 knkeavvkellkl 100
                                       ++ ++ v+ llk 
  gi|330508345|ref|YP_004384773.1|  89 AKLDKAVEYLLKE 101
                                       **********985 PP

>> BMFP  Membrane fusogenic activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   2.6   7.5e-06     0.022       8      55 ..       4      52 ..       2      67 .. 0.91
   2 ?    1.0   0.1      0.21   6.2e+02      20      44 ..      67      92 ..      52     106 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.5e-06
                              BMFP  8 ddlakkvgdalpaaag.vreeieknvravlqealsklDLVtREEFdvqr 55
                                      d++  k+++a +++ + v++ +e++ +++++++ + ++LV+  E d+q 
  gi|330508345|ref|YP_004384773.1|  4 DEILSKIKSAEAQSRAaVQQALEEKEKKIAAATTEAMNLVKSAEIDAQD 52
                                      788999999999988889*****************************95 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.21
                              BMFP 20 aaag.vreeieknvravlqealsklD 44
                                      a ++ + +  +knv ++  +a +klD
  gi|330508345|ref|YP_004384773.1| 67 AKKQsIIQSGDKNVASMSGSASAKLD 92
                                      33333444444555555555555554 PP

>> UPF0556  Uncharacterised protein family UPF0556
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.14   4.1e+02      96     117 ..       9      30 ..       5      42 .. 0.64
   2 ?   11.9   1.2   3.9e-05      0.12      91     143 ..      42      95 ..      34      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.14
                           UPF0556  96 kieyaeaysqaavegqsdvklk 117
                                       ki+ aea s+aav++  + k k
  gi|330508345|ref|YP_004384773.1|   9 KIKSAEAQSRAAVQQALEEKEK 30 
                                       7788888888887765444333 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.9e-05
                           UPF0556  91 evkgakieyaeaysqaavegqsdvklkeee.fevtetavthrdGkfkaelsklv 143
                                        vk a+i+    y ++ ++++sdvk k++   + +++ v+   G+ +a+l k v
  gi|330508345|ref|YP_004384773.1|  42 LVKSAEIDAQDYYDKSVAKAESDVKAKKQSiIQSGDKNVASMSGSASAKLDKAV 95 
                                       589**********************98765167899************999865 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   9.8   0.00026      0.78      91     161 ..       3      72 ..       2      73 .. 0.89
   2 ?   -2.9   0.0         2   5.8e+03     133     145 ..      89     101 ..      77     106 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00026
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               RRF  91 rkelvkeakkaaekakvairniRrdankklkklekkiseDdvkkaekeiqkltdkyikeidellkakekel 161
                                       r+e+  ++k+a  + + a++++ ++ +kk+ ++  + + + vk+ae + q+  dk ++++++ +kak++++
  gi|330508345|ref|YP_004384773.1|   3 RDEILSKIKSAEAQSRAAVQQALEEKEKKIAAATTE-AMNLVKSAEIDAQDYYDKSVAKAESDVKAKKQSI 72 
                                       889999999999999999999999999999877664.3499****************************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHH CS
                               RRF 133 kkaekeiqkltdk 145
                                        k++k ++ l ++
  gi|330508345|ref|YP_004384773.1|  89 AKLDKAVEYLLKE 101
                                       3444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2167  (0.120866); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 790.72
//
Query:       gi|330508346|ref|YP_004384774.1|  [L=312]
Description: fructose-1,6-bisphosphatase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-37  128.3   0.0    3.3e-37  127.8   0.0    1.1  1  FBPase    Fructose-1-6-bisphosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> 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 !  127.8   0.0   1.9e-41   3.3e-37      16     188 ..      23     181 ..       8     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 1.9e-41
                            FBPase  16 natgeltallsalklalkiisskvrkaelvnllGlagaeNvtGdeqkklDvladeiliealkaseevkvlvSEEeee 92 
                                         + el+ l+  ++   k is k++ ++      lag +Nv G++q +lD ++d+il+++l++s+ v   +SEE+e+
  gi|330508346|ref|YP_004384774.1|  23 GIEVELRRLIWQIAVVGKYISAKIHESN----RKLAGFKNVYGEDQLALDRISDDILKNMLRNSGFVREYASEEQED 95 
                                       3456899********************9....677899*************************************** PP

                            FBPase  93 livlerekegkyvvafDPlDGSSnidtnvsvGtifsiyrkksedeettidvlqpGke.qvAAgyvvYGsstmlVltl 168
                                       +i + ++ + +y+v  DP+DGSS +dtn+++Gti++i+r     +     +  +Gk+ +vAA y+ YG+  +++++ 
  gi|330508346|ref|YP_004384774.1|  96 IITI-GQGQEQYIVTADPVDGSSLVDTNLAIGTIIGIHR-----N----SIFDCGKNsMVAALYITYGPLITMIYSA 162
                                       ****.888899****************************.....2....2456775439****************** PP

                            FBPase 169 gaGvngFtlDpslgefiltk 188
                                       g+Gv++F+lD+ +ge++l++
  gi|330508346|ref|YP_004384774.1| 163 GKGVHEFVLDR-EGEYVLSE 181
                                       *********76.79999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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: 2124.55
//
Query:       gi|330508347|ref|YP_004384775.1|  [L=464]
Description: hypothetical protein MCON_2526 [Methanosaeta concilii GP6]
Scores for complete 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   60.6   0.0    2.1e-16   60.3   0.0    1.1  1  F_bP_aldolase   Fructose-bisphosphate aldolase class-II
      1e-06   27.7   0.0    1.5e-06   27.2   0.0    1.1  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 !   60.3   0.0   2.3e-20   2.1e-16      12     240 ..      86     361 ..      75     401 .. 0.81

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 2.3e-20
                                       HHT--EEEEE-..-SHHHHHHHHHHHHHHTS.-EEEEE-HHHHHHHH-HHHHHHHHHHHHHHHHT...-EEEEEE-- CS
                     F_bP_aldolase  12 eegyavgafnv..tnletvkavleaaeeaks.PvIlqlsegaaakyaggaealaelvraaaeaykkasvpvalhlDH 85 
                                         g+ v+a+n+  ++++ ++av++a  + ++ PvI +++++++ ++++  + +a  v aaa + +  + pv l+ DH
  gi|330508347|ref|YP_004384775.1|  86 VSGFTVPAINIrgITYHVAQAVFRASMKGNVgPVIFEIARSEIGYTKQRPREYACAVLAAAIKSG-WRGPVFLQGDH 161
                                       57899******5556789*******9886655***********9888866666666666666555.699******** PP

                                       --G................HHHHHHHHHHS-SEEEE--TTS..........-HHHHHHHHHHHHHHHHHTT.....- CS
                     F_bP_aldolase  86 gak................leglkkaieagfsSvMiDgSel..........pleeNialtkevverahalg.....v 131
                                        +                  + +++ai+agf  + iD S+l          +   N  l++e+++++++l+     v
  gi|330508347|ref|YP_004384775.1| 162 FQInakkfaadgeketqsvKDLIREAIQAGFYNIDIDTSTLvdlskatikdQQRLNYTLAAELTALIRDLEpegitV 238
                                       8877889********9998899999999999999888886666666666657778999999999999997666677* PP

                                       EEEEE-----------TT-TTTS--HHHHHHHHHHHH.....-EEEE--SS---SS--SS........--THHHHHH CS
                     F_bP_aldolase 132 svEaElGriggeedgvvaeeklyTdpeeaeefveetg.....vdalAvaiGnvHGvykpk....pk..Ldferlkei 197
                                       sv +E+G++gg+++ v   e+l T ++   e +++ g     +  + v  G++HG  + +    +k  +dfe+l+++
  gi|330508347|ref|YP_004384775.1| 239 SVGGEIGEVGGKNSTV---EELQTFMDGYLEELKKRGpalkgISKISVQTGTTHGGVPLAdgtvAKvkIDFEVLEKL 312
                                       *************988...46777777777777666667779*************9865555562256********* PP

                                       HHHH......--SEE-SGTTS-HHHHHHHHHTTEEEEEE-HHHHHHHHH CS
                     F_bP_aldolase 198 qkav......vplVlHGgsgvpdeeirkaiklGvvKiNidtdlrlaytk 240
                                       ++ +         V HG+s +pde + +  + G + i ++t +++ +++
  gi|330508347|ref|YP_004384775.1| 313 SETAraeyglSGAVQHGASTLPDEAFDRFPATGTAEIHLATGFQNIIYD 361
                                       **99988554445*************************99999987665 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 !   27.2   0.0   1.7e-10   1.5e-06      55     186 ..     129     258 ..     122     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.7e-10
                                       TTTT--HHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGGTTS.-HHHHHHHHHHHHHHHHTTT--EEEE---B--S CS
                    Tagatose_6_P_K  55 GYtGmtpadFrefvleiaeevglpkerlilGGDHLGPnawkkl.paeeAmakaeelvaayvaagfkKiHlDasmsca 130
                                       GYt  +p++++  vl+ a + g  +  ++l GDH   na k   + e+  ++ ++l+++ ++agf  i +D+s  + 
  gi|330508347|ref|YP_004384775.1| 129 GYTKQRPREYACAVLAAAIKSGW-RGPVFLQGDHFQINAKKFAaDGEKETQSVKDLIREAIQAGFYNIDIDTSTLVD 204
                                       9***************9999997.578*******99888765414567788999********************999 PP

                                       SS-SB--HHHHHHHHHHHHHHHHHT---------EEEEE----------------- CS
                    Tagatose_6_P_K 131 ddpaplsdevvaeRaarLakvaeeaaeeakaekpvYviGtevPvPGGaeeeleele 186
                                         +a+++d++  +   +La+   + +++ + e ++  +G e+   GG+++++eel+
  gi|330508347|ref|YP_004384775.1| 205 LSKATIKDQQRLN--YTLAAELTALIRDLEPEGITVSVGGEIGEVGGKNSTVEELQ 258
                                       9999999876443..34455555556666677888899*********999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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 0.26s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 3473.89
//
Query:       gi|330508348|ref|YP_004384776.1|  [L=371]
Description: thermophile-specific fructose-1,6-bisphosphatase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.3e-181  603.5   0.0   1.5e-181  603.4   0.0    1.0  1  FBPase_3       Fructose-1,6-bisphosphatase
  ------ inclusion threshold ------
      0.081   12.8   0.0       0.22   11.4   0.0    1.7  1  Biotin_lipoyl  Biotin-requiring enzyme


Domain annotation for each model (and alignments):
>> FBPase_3  Fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  603.4   0.0  1.7e-185  1.5e-181       1     360 [.       3     367 ..       3     368 .. 0.99

  Alignments for each domain:
  == domain 1  score: 603.4 bits;  conditional E-value: 1.7e-185
                          FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafk 77 
                                       k+t+s+ikaDvG+++Gh++vh+el++++ee+leeakk+g+l+d++v+++GDD+el+m+h+ g d  ++h+law++f+
  gi|330508348|ref|YP_004384776.1|   3 KITISLIKADVGGYPGHCSVHPELIKTAEEKLEEAKKSGCLVDYRVMACGDDLELLMSHRTGCDCGDIHGLAWETFE 79 
                                       89*************************************************************************** PP

                          FBPase_3  78 eatevakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGl 154
                                       +ate+ak lklyg GqDlL+dafsGn+kG+GPgvae+e++eR++ep++ f++Dktepgafnlp++k+fadpfntaGl
  gi|330508348|ref|YP_004384776.1|  80 AATETAKGLKLYGYGQDLLADAFSGNIKGMGPGVAEMEITERTAEPIIAFMMDKTEPGAFNLPIFKMFADPFNTAGL 156
                                       ***************************************************************************** PP

                          FBPase_3 155 vidpklheGfkfevlDvieekkillsapeelydllallgakeryvikrvysk.....kdeeiaavvsterlsliaGk 226
                                       +idp++h+Gf+fev+D+ e+kk+l+++pee+yd+lal+gak+ryvikrv+ k      ++e++av+ste+l ++aGk
  gi|330508348|ref|YP_004384776.1| 157 IIDPSFHHGFTFEVWDILEHKKVLMNCPEEMYDMLALIGAKSRYVIKRVFAKpgskiPQSEPVAVISTEKLYQTAGK 233
                                       ****************************************************988877899**************** PP

                          FBPase_3 227 YvGkDDPvaivRaqsglPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklv 303
                                       YvGkDDPva+vR+qsglPa+gevlepf++ hlv+GwmrGshngplmP+s+++a+ptrfdgpprv+a gfql+egk+v
  gi|330508348|ref|YP_004384776.1| 234 YVGKDDPVALVRSQSGLPALGEVLEPFSIGHLVSGWMRGSHNGPLMPCSFDTAHPTRFDGPPRVIAAGFQLAEGKFV 310
                                       ***************************************************************************** PP

                          FBPase_3 304 gpvDlfddpafdeaRekaaeiadelRrqGpfephrlpeeeleYttlpevleklkerf 360
                                       gpvDlf+d afd++R+++ ei+d++R++Gpfephrlp+ee+eYttlp+v++ l++rf
  gi|330508348|ref|YP_004384776.1| 311 GPVDLFNDLAFDRVRQRCLEITDYMRAHGPFEPHRLPMEEMEYTTLPHVMDCLRDRF 367
                                       ********************************************************9 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    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       9      41 ..     195     227 ..     191     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.5e-05
                                       EEEEEE.ECSESSSTTCEE-TTSEEEEEECTTE CS
                     Biotin_lipoyl   9 GesveegvvevlvkvGdkVkagqvlaeveamKm 41 
                                       G   ++ + +v+ k+G+k+ + +++a++++ K+
  gi|330508348|ref|YP_004384776.1| 195 GAKSRYVIKRVFAKPGSKIPQSEPVAVISTEKL 227
                                       5555656899*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.40
# Mc/sec: 2788.09
//
Query:       gi|330508349|ref|YP_004384777.1|  [L=293]
Description: hypothetical protein MCON_2529 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.095   12.3   0.0       0.14   11.7   0.0    1.2  1  GCIP      Grap2 and cyclin-D-interacting


Domain annotation for each model (and alignments):
>> GCIP  Grap2 and cyclin-D-interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.9e-06      0.14     115     187 ..      23      87 ..      20     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.9e-06
                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....S------------------TTS--HHHHHHHHHHHHHHH CS
                              GCIP 115 dNktAilraieevlglvkDaleEmkelleeedeeedededdldddedeergnqdrklseeekevikavlkllk 187
                                       +Nk  il++ ++  +l k+ale++++l+e+  ++ d+++ ++ + ++         +s+ee+e+i+  + ++k
  gi|330508349|ref|YP_004384777.1|  23 NNKHKILKDFQSPEDLFKEALEDIEKLKEKLYSKPDQIDSFVRENPQG--------FSAEELEIISSWQHFVK 87 
                                       79999*************************878888999999998666........9**********999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); 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 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2060.92
//
Query:       gi|330508350|ref|YP_004384778.1|  [L=216]
Description: hypothetical protein MCON_2531 [Methanosaeta concilii GP6]
Scores for 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-17   61.5   0.4    1.3e-16   60.9   0.4    1.3  1  TerB            Tellurite resistance protein TerB
      2e-08   34.0   2.8    0.00031   20.3   0.4    2.1  2  DUF533          Protein of unknown function (DUF533)
    1.4e-07   32.1   2.9      2e-07   31.6   2.9    1.3  1  zinc_ribbon_15  zinc-ribbon family
     0.0028   16.6   0.1      0.011   14.6   0.1    1.8  2  DUF2600         Protein of unknown function (DUF2600)
  ------ inclusion threshold ------
          2    8.0   5.5        1.2    8.7   0.3    2.6  3  TF_Zn_Ribbon    TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> TerB  Tellurite resistance protein TerB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.4   3.5e-20   1.3e-16      15     140 ..      85     208 ..      75     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 3.5e-20
                              TerB  15 gaektdaakeafalalaallaevakaDgqvsesErqafrellksrfglspeeakallelfeeaeeeavdleqftral 91 
                                        a+k+++ k +f+ a++ +++ ++ aD+++ esE+q + ++  +  g  p ++ +l+++  ++++++ ++++  + +
  gi|330508350|ref|YP_004384778.1|  85 AAKKQKF-KAEFHKAILKVMVTMMLADEKIEESEKQLISRVYINLAG-HPLDEVDLIQEMYQVKNSKLSMQELLKSM 159
                                       2333333.337*******************************88887.7788888999******************* PP

                              TerB  92 krklspeqrraliealweiAlADGeldeaEdavlrrvaelLglspadfi 140
                                         +l++  ++ +i+a +  A ADG++d +E+++l++ a +L++sp+  +
  gi|330508350|ref|YP_004384778.1| 160 TPSLNDYGKEMVIKAAFLTASADGKIDSEEKRLLTELASALEMSPSHLN 208
                                       *********************************************9876 PP

>> DUF533  Protein of unknown function (DUF533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   3.4e-06     0.012      61     117 ..      88     142 ..      35     162 .. 0.76
   2 !   20.3   0.4   8.8e-08   0.00031      64     117 ..     161     214 ..     137     216 .] 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.4e-06
                            DUF533  61 pkfqeeeeekaelllrAmiaAAkADGhideeErqrIlqeleelgldaeekalledeL 117
                                       ++  + + e+++++l+ m++   AD +i+e+E+q I +   +l+ ++ ++  l +e+
  gi|330508350|ref|YP_004384778.1|  88 KQ--KFKAEFHKAILKVMVTMMLADEKIEESEKQLISRVYINLAGHPLDEVDLIQEM 142
                                       22..4678999*************************998887777776666666666 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 8.8e-08
                            DUF533  64 qeeeeekaelllrAmiaAAkADGhideeErqrIlqeleelgldaeekalledeL 117
                                       ++ ++  +e++++A    A ADG+id eE++ +++  ++l+++++  + + +e+
  gi|330508350|ref|YP_004384778.1| 161 PSLNDYGKEMVIKAAFLTASADGKIDSEEKRLLTELASALEMSPSHLNAVIQEM 214
                                       24778889999*******************************999999888887 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   2.9   5.7e-11     2e-07       2      62 ..      30      90 ..      29     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 5.7e-11
                    zinc_ribbon_15  2 lCpkCgklskaelvkkkkvlklffipvfkwkkkkpylacskCkslleaskelgkeiekkes 62
                                       Cp+C++  ++e ++ ++v++l+fip+++++  + y+ c+ Ck +++ +  + +   kk++
  gi|330508350|ref|YP_004384778.1| 30 FCPSCNEFRDYEQKRCRRVFTLYFIPIIPLDILQEYVECKICKCTYKLEALQYDPAAKKQK 90
                                      7**********************************************99866666655554 PP

>> DUF2600  Protein of unknown function (DUF2600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.15   5.4e+02     199     231 ..      33      65 ..      22      67 .. 0.80
   2 !   14.6   0.1   3.1e-06     0.011     275     315 ..      91     131 ..      72     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.15
                           DUF2600 199 alaaepdlteedaekikeaYfpwicglhiLLdy 231
                                       ++   +d+++++ +++ + Yf  i  l iL +y
  gi|330508350|ref|YP_004384778.1|  33 SCNEFRDYEQKRCRRVFTLYFIPIIPLDILQEY 65 
                                       5555567999999***********99*999887 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.1e-06
                           DUF2600 275 pdkkfhrlvvegLlalYlsdekvkqkelkklakrllkaggl 315
                                        +++fh+++++ ++++ l+dek++++e + +++  ++ +g 
  gi|330508350|ref|YP_004384778.1|  91 FKAEFHKAILKVMVTMMLADEKIEESEKQLISRVYINLAGH 131
                                       3679*******************999999999988887775 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3   0.00034       1.2       9      25 ..      17      34 ..      16      41 .. 0.85
   2 ?    1.1   0.2      0.08   2.9e+02      24      40 ..      72      88 ..      67      91 .. 0.58
   3 ?   -3.2   0.0       1.8   6.4e+03      31      42 ..     106     117 ..     103     118 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00034
                                      EE.CHEETSTTCEEESSS CS
                      TF_Zn_Ribbon  9 tn.lveDpergelvCtdC 25
                                      t+ ++++   g+++C++C
  gi|330508350|ref|YP_004384778.1| 17 TRgITYNSGKGTFFCPSC 34
                                      444899************ PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.08
                                      SSSBEEEECCCCCCCHH CS
                      TF_Zn_Ribbon 24 dCGlVlednsidegpew 40
                                      +C++ le  ++d+   +
  gi|330508350|ref|YP_004384778.1| 72 KCTYKLEALQYDPAAKK 88
                                      46666666666665555 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.8
                                       ECCCCCCCHHHH CS
                      TF_Zn_Ribbon  31 dnsidegpewre 42 
                                        + +de++e+ e
  gi|330508350|ref|YP_004384778.1| 106 MMLADEKIEESE 117
                                       566788887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1041  (0.0580624); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1579.01
//
Query:       gi|330508351|ref|YP_004384779.1|  [L=440]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-133  428.0  28.8    1.8e-11   43.3   0.1   12.2 12  TPR_1            Tetratricopeptide repeat
   2.9e-110  359.7  55.0    3.4e-12   45.9   0.3   11.1 11  TPR_11           TPR repeat
     5e-110  351.0  29.2    1.8e-09   37.0   0.1   12.3 12  TPR_2            Tetratricopeptide repeat
    1.4e-95  313.6  39.1    3.3e-16   59.6   1.9    7.1  8  TPR_16           Tetratricopeptide repeat
    2.9e-90  289.1  21.0    7.6e-07   28.9   0.0   12.1 12  TPR_8            Tetratricopeptide repeat
    1.9e-80  259.7  18.5    8.1e-06   25.9   0.1   12.1 12  TPR_17           Tetratricopeptide repeat
    1.5e-63  206.0  36.0    1.1e-05   25.9   0.9   11.2 11  TPR_14           Tetratricopeptide repeat
    5.7e-53  177.1  18.4    3.1e-08   33.8   0.1    9.3  9  TPR_12           Tetratricopeptide repeat
    9.2e-50  163.1  17.0    0.00021   21.1   0.0   11.3 11  TPR_7            Tetratricopeptide repeat
    2.5e-39  133.6  37.4    1.6e-08   35.0   1.8    7.3  7  TPR_19           Tetratricopeptide repeat
    8.4e-37  123.4  14.3      0.046   14.4   0.1   11.4 11  TPR_6            Tetratricopeptide repeat
    2.9e-33  113.9   5.0    0.00016   21.8   0.5    6.2  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    3.9e-31  106.0  35.4       0.05   13.5   0.2   11.7 12  TPR_10           Tetratricopeptide repeat
    2.1e-28   98.1  47.2      0.015   15.4   0.8   11.2 11  MIT              MIT (microtubule interacting and transport) 
    4.6e-26   90.8  21.5    1.7e-05   24.9   0.8    6.7  9  TPR_9            Tetratricopeptide repeat
    1.9e-22   78.8  27.0      0.028   14.4   0.0   11.2 11  TPR_3            Tetratricopeptide repeat
    3.9e-17   62.3  20.1     0.0022   17.0   0.2    5.7  6  NARP1            NMDA receptor-regulated protein 1
    6.9e-16   57.2   5.4         14    6.6   0.0   10.1  9  TPR_4            Tetratricopeptide repeat
    7.1e-15   54.1   3.8         25    5.4   0.0   10.8 11  PPR              PPR repeat
    5.9e-13   48.7  16.0     0.0027   17.0   0.5    8.3  8  TPR_15           Tetratricopeptide repeat
      2e-12   47.2  48.6      0.021   14.6   2.1    9.7 11  TPR_21           Tetratricopeptide repeat-like domain
    4.6e-12   46.2  13.5        4.6    7.3   0.1   10.1  8  DUF3856          Domain of Unknown Function (DUF3856)
      5e-12   45.7   8.5         33    4.6   0.0   10.6 11  ANAPC5           Anaphase-promoting complex subunit 5
    6.8e-11   42.8  10.9      0.013   16.0   0.6    5.6  8  BTAD             Bacterial transcriptional activator domain
    3.1e-10   39.8  16.6        4.8    7.1   0.0    9.1  9  Imm31            Immunity protein 31
    9.7e-07   28.5   1.2       0.27   10.6   0.0    4.1  5  Coatomer_E       Coatomer epsilon subunit
    3.1e-05   23.9   0.0        1.4    9.0   0.0    4.8  5  DUF627           Protein of unknown function (DUF627)
    3.3e-05   23.9   0.2        3.1    7.8   0.0    5.0  3  SRP_TPR_like     Putative TPR-like repeat
    6.6e-05   23.5   0.1         53    4.6   0.0    6.4  5  DUF4326          Domain of unknown function (DUF4326)
    8.1e-05   22.6  17.0       0.73    9.7   0.0    6.2  7  Wzy_C_2          Virulence factor membrane-bound polymerase, 
    0.00034   20.2  27.3         21    4.6   0.1    9.7  9  4HB_MCP_1        Four helix bundle sensory module for signal 
     0.0014   18.4  14.7        1.9    8.1   0.2    8.0  8  RPN7             26S proteasome subunit RPN7
     0.0019   18.2  10.5         17    5.6   0.0    7.7  7  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
     0.0025   18.0  12.0    1.1e+02    3.1   0.0    8.8  9  PPR_2            PPR repeat family
     0.0027   18.3   0.8         19    5.9   0.0    4.0  4  Adeno_VII        Adenoviral core protein VII
     0.0048   17.2   8.2         52    4.1   0.0    6.5  7  PHP              PHP domain
     0.0052   17.1  20.9          4    7.9   0.7    6.5  8  TPR_20           Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.013   16.2   0.1         40    4.9   0.0    3.9  4  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
      0.017   14.8   0.0         85    3.1   0.0    5.1  4  PPTA             Protein prenyltransferase alpha subunit repe
      0.053   13.2   0.3         10    5.7   0.0    2.7  2  FSH1             Serine hydrolase (FSH1)
      0.098   13.4   0.4    1.4e+02    3.3   0.0    4.8  5  TetR_C_15        Tetracyclin repressor-like, C-terminal domai
       0.17   11.4  15.8         96    2.6   0.0    7.7  9  SHNi-TPR         SHNi-TPR
       0.24   12.1   0.3    6.5e+02    1.0   0.0    5.1  5  Mif2_N           Kinetochore CENP-C fungal homologue, Mif2, N
        1.2    9.6  17.3         69    4.0   0.2    7.2  7  DUF2799          Protein of unknown function (DUF2799)
        2.1    8.2  20.2      3e+02    1.3   0.0    9.7 12  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 !   35.2   0.1   1.7e-11   6.9e-09       4      33 ..      27      56 ..      25      57 .. 0.96
   2 !   43.3   0.0   4.7e-14   1.9e-11       1      34 []      58      91 ..      58      91 .. 0.97
   3 !   42.9   0.2   6.2e-14   2.5e-11       1      34 []      92     125 ..      92     125 .. 0.97
   4 !   36.3   0.2   7.7e-12   3.1e-09       1      32 [.     126     157 ..     126     157 .. 0.97
   5 !   34.9   0.1   2.1e-11   8.3e-09       1      34 []     160     193 ..     160     193 .. 0.94
   6 !   42.4   0.0     9e-14   3.6e-11       2      34 .]     195     227 ..     194     227 .. 0.96
   7 !   39.3   0.0   8.6e-13   3.4e-10       1      34 []     228     261 ..     228     261 .. 0.96
   8 !   38.8   0.0   1.2e-12   4.8e-10       1      34 []     262     295 ..     262     295 .. 0.95
   9 !   43.3   0.1   4.6e-14   1.8e-11       1      34 []     296     329 ..     296     329 .. 0.97
  10 !   41.1   0.2   2.3e-13   9.1e-11       1      33 [.     330     362 ..     330     363 .. 0.96
  11 !   31.4   0.0   2.7e-10   1.1e-07       1      33 [.     364     396 ..     364     397 .. 0.93
  12 !   10.3   0.1    0.0012      0.48       1      16 [.     398     413 ..     398     415 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.7e-11
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  4 lynlGnayfklgkydeAleyyekALelnPn 33
                                      ++  G+a+  +gkydeA+++y++A++l+P+
  gi|330508351|ref|YP_004384779.1| 27 WFYQGVALADQGKYDEAIKAYDEAIRLDPT 56
                                      9999*************************7 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 4.7e-14
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a a+ n+G+a+  +gk+deA+e+y++A++l+P++
  gi|330508351|ref|YP_004384779.1| 58 AAAWSNKGVAFADQGKHDEAIEAYDEAIRLDPTD 91
                                      78******************************86 PP

  == domain 3  score: 42.9 bits;  conditional E-value: 6.2e-14
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a+ n+G+ +  +gkydeA+e+y++A++l+P++
  gi|330508351|ref|YP_004384779.1|  92 AAAWGNKGASLADQGKYDEAIEAYDEAIRLDPTD 125
                                       78******************************86 PP

  == domain 4  score: 36.3 bits;  conditional E-value: 7.7e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a a++n+Gn + k++kyde +++y++A+ lnP
  gi|330508351|ref|YP_004384779.1| 126 AIAWFNKGNSLNKQKKYDESIKAYDEAIGLNP 157
                                       68*****************************9 PP

  == domain 5  score: 34.9 bits;  conditional E-value: 2.1e-11
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+ + ++G  +  +gkydeA+e+y++A++l+P n
  gi|330508351|ref|YP_004384779.1| 160 AEPWIGKGKSLADQGKYDEAIEAYDEAIRLDPAN 193
                                       67799***************************65 PP

  == domain 6  score: 42.4 bits;  conditional E-value: 9e-14
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        a+ n+G+ +  +gkydeA+e+y++A++l+P++
  gi|330508351|ref|YP_004384779.1| 195 AAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTD 227
                                       69*****************************86 PP

  == domain 7  score: 39.3 bits;  conditional E-value: 8.6e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a ++ n+G+ +  +gk+deA+e+y++A++l+P++
  gi|330508351|ref|YP_004384779.1| 228 AAVWGNKGVSLADQGKHDEAIEAYDEAIRLDPTD 261
                                       679*****************************86 PP

  == domain 8  score: 38.8 bits;  conditional E-value: 1.2e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a ++ n+G+ +  +gkydeA+e+y++A++l+P n
  gi|330508351|ref|YP_004384779.1| 262 AAVWGNKGVSLVDQGKYDEAIEAYDEAIRLDPAN 295
                                       679*****************************65 PP

  == domain 9  score: 43.3 bits;  conditional E-value: 4.6e-14
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a+ n+G+ +  +gkydeA+e+y++A++l+P++
  gi|330508351|ref|YP_004384779.1| 296 AAAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTD 329
                                       78******************************86 PP

  == domain 10  score: 41.1 bits;  conditional E-value: 2.3e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a a++n+Gn + k++kyde +++y++A++lnP+
  gi|330508351|ref|YP_004384779.1| 330 ATAWFNKGNSLNKQKKYDESIKAYDEAIRLNPD 362
                                       679*****************************8 PP

  == domain 11  score: 31.4 bits;  conditional E-value: 2.7e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+ + ++Gn +  +gk+deA+++y++A++l+ +
  gi|330508351|ref|YP_004384779.1| 364 AEPWIGKGNSLDDQGKHDEAIQAYDEAIRLDST 396
                                       67799**************************87 PP

  == domain 12  score: 10.3 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHTT- CS
                             TPR_1   1 akalynlGnayfklgk 16 
                                       a+a+yn+G++++++++
  gi|330508351|ref|YP_004384779.1| 398 ANAWYNKGVVLHNQNR 413
                                       79************98 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.4   2.5e-14     1e-11       3      42 .]      33      72 ..      31      72 .. 0.96
   2 !   39.7   0.4   7.3e-13   2.9e-10       3      42 .]      67     106 ..      65     106 .. 0.95
   3 !   44.2   0.6   2.8e-14   1.1e-11       3      40 ..     101     138 ..      99     139 .. 0.91
   4 !   22.3   0.3   1.9e-07   7.5e-05       1      36 [.     133     168 ..     133     171 .. 0.91
   5 !   42.1   0.9   1.2e-13   4.8e-11       1      42 []     167     208 ..     167     208 .. 0.97
   6 !   40.0   0.2   5.7e-13   2.3e-10       4      42 .]     204     242 ..     201     242 .. 0.94
   7 !   33.1   0.0   8.3e-11   3.3e-08       4      36 ..     238     270 ..     235     273 .. 0.90
   8 !   42.8   0.8   7.5e-14     3e-11       4      42 .]     272     310 ..     269     310 .. 0.95
   9 !   45.9   0.3   8.5e-15   3.4e-12       4      41 ..     306     343 ..     303     344 .. 0.92
  10 !   31.4   0.3   2.8e-10   1.1e-07       1      36 [.     337     372 ..     337     374 .. 0.93
  11 !   45.3   0.3   1.3e-14   5.1e-12       1      41 [.     371     411 ..     371     412 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 2.5e-14
                            TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      a+ +qGky+eAi+aY +A++ldP+ a a++n G+a++ qG
  gi|330508351|ref|YP_004384779.1| 33 ALADQGKYDEAIKAYDEAIRLDPTIAAAWSNKGVAFADQG 72
                                      789***********************************99 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 7.3e-13
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       a+ +qGk +eAieaY +A++ldP++a a+ n G+ ++ qG
  gi|330508351|ref|YP_004384779.1|  67 AFADQGKHDEAIEAYDEAIRLDPTDAAAWGNKGASLADQG 106
                                       899********************************99998 PP

  == domain 3  score: 44.2 bits;  conditional E-value: 2.8e-14
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                        + +qGky+eAieaY +A++ldP++a a++n G+ + k
  gi|330508351|ref|YP_004384779.1| 101 SLADQGKYDEAIEAYDEAIRLDPTDAIAWFNKGNSLNK 138
                                       5789*****************************98766 PP

  == domain 4  score: 22.3 bits;  conditional E-value: 1.9e-07
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                       G+ + +q ky+e+i+aY +A+ l+P  ae + + G+
  gi|330508351|ref|YP_004384779.1| 133 GNSLNKQKKYDESIKAYDEAIGLNPVLAEPWIGKGK 168
                                       999**********************99999888776 PP

  == domain 5  score: 42.1 bits;  conditional E-value: 1.2e-13
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+ + +qGky+eAieaY +A++ldP n+ a+ n G+ ++ qG
  gi|330508351|ref|YP_004384779.1| 167 GKSLADQGKYDEAIEAYDEAIRLDPANVAAWGNKGVSLADQG 208
                                       88999********************************99998 PP

  == domain 6  score: 40.0 bits;  conditional E-value: 5.7e-13
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       + +qGky+eAieaY +A++ldP++a ++ n G+ ++ qG
  gi|330508351|ref|YP_004384779.1| 204 LADQGKYDEAIEAYDEAIRLDPTDAAVWGNKGVSLADQG 242
                                       679******************************999998 PP

  == domain 7  score: 33.1 bits;  conditional E-value: 8.3e-11
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                       + +qGk +eAieaY +A++ldP++a ++ n G+
  gi|330508351|ref|YP_004384779.1| 238 LADQGKHDEAIEAYDEAIRLDPTDAAVWGNKGV 270
                                       679***********************9988886 PP

  == domain 8  score: 42.8 bits;  conditional E-value: 7.5e-14
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +++qGky+eAieaY +A++ldP na a+ n G+ ++ qG
  gi|330508351|ref|YP_004384779.1| 272 LVDQGKYDEAIEAYDEAIRLDPANAAAWGNKGVSLADQG 310
                                       79********************************99998 PP

  == domain 9  score: 45.9 bits;  conditional E-value: 8.5e-15
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       + +qGky+eAieaY +A++ldP++a+a++n G+ + kq
  gi|330508351|ref|YP_004384779.1| 306 LADQGKYDEAIEAYDEAIRLDPTDATAWFNKGNSLNKQ 343
                                       679*****************************988766 PP

  == domain 10  score: 31.4 bits;  conditional E-value: 2.8e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                       G+ + +q ky+e+i+aY +A++l+Pd ae + + G+
  gi|330508351|ref|YP_004384779.1| 337 GNSLNKQKKYDESIKAYDEAIRLNPDLAEPWIGKGN 372
                                       999**************************9988776 PP

  == domain 11  score: 45.3 bits;  conditional E-value: 1.3e-14
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       G+ + +qGk +eAi+aY +A++ld+++a+a+yn G+++++q
  gi|330508351|ref|YP_004384779.1| 371 GNSLDDQGKHDEAIQAYDEAIRLDSTDANAWYNKGVVLHNQ 411
                                       777889*********************************98 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.1   4.5e-12   1.8e-09       3      33 ..      26      56 ..      24      57 .. 0.95
   2 !   34.2   0.1   3.4e-11   1.4e-08       1      34 []      58      91 ..      58      91 .. 0.97
   3 !   35.8   0.2   1.1e-11   4.4e-09       1      34 []      92     125 ..      92     125 .. 0.96
   4 !   23.5   0.1   9.4e-08   3.7e-05       1      32 [.     126     157 ..     126     157 .. 0.97
   5 !   33.3   0.1   6.9e-11   2.8e-08       1      34 []     160     193 ..     160     193 .. 0.95
   6 !   35.6   0.0   1.3e-11   5.1e-09       2      34 .]     195     227 ..     194     227 .. 0.96
   7 !   32.3   0.0   1.4e-10   5.7e-08       1      34 []     228     261 ..     228     261 .. 0.96
   8 !   33.0   0.0   8.7e-11   3.5e-08       1      34 []     262     295 ..     262     295 .. 0.95
   9 !   36.4   0.1   6.8e-12   2.7e-09       1      34 []     296     329 ..     296     329 .. 0.96
  10 !   29.9   0.1   8.1e-10   3.2e-07       1      33 [.     330     362 ..     330     363 .. 0.96
  11 !   25.4   0.0   2.2e-08   8.9e-06       1      34 []     364     397 ..     364     397 .. 0.94
  12 ?    6.2   0.1     0.033        13       1      30 [.     398     426 ..     398     428 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 4.5e-12
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPn 33
                                       ++++G a++ +g+y+eA++a+++A++ldP+
  gi|330508351|ref|YP_004384779.1| 26 DWFYQGVALADQGKYDEAIKAYDEAIRLDPT 56
                                      6*****************************7 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 3.4e-11
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      a a+ n G a + +g+++eA+ea+++A++ldP++
  gi|330508351|ref|YP_004384779.1| 58 AAAWSNKGVAFADQGKHDEAIEAYDEAIRLDPTD 91
                                      689*****************************97 PP

  == domain 3  score: 35.8 bits;  conditional E-value: 1.1e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a a+ n G +++ +g+y+eA+ea+++A++ldP++
  gi|330508351|ref|YP_004384779.1|  92 AAAWGNKGASLADQGKYDEAIEAYDEAIRLDPTD 125
                                       689*****************************97 PP

  == domain 4  score: 23.5 bits;  conditional E-value: 9.4e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       a a++n G+++ k+++y+e ++a+++A+ l+P
  gi|330508351|ref|YP_004384779.1| 126 AIAWFNKGNSLNKQKKYDESIKAYDEAIGLNP 157
                                       689*************************9998 PP

  == domain 5  score: 33.3 bits;  conditional E-value: 6.9e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ae +   G++++ +g+y+eA+ea+++A++ldP n
  gi|330508351|ref|YP_004384779.1| 160 AEPWIGKGKSLADQGKYDEAIEAYDEAIRLDPAN 193
                                       67899***************************86 PP

  == domain 6  score: 35.6 bits;  conditional E-value: 1.3e-11
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        a+ n G +++ +g+y+eA+ea+++A++ldP++
  gi|330508351|ref|YP_004384779.1| 195 AAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTD 227
                                       699****************************97 PP

  == domain 7  score: 32.3 bits;  conditional E-value: 1.4e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a ++ n G +++ +g+++eA+ea+++A++ldP++
  gi|330508351|ref|YP_004384779.1| 228 AAVWGNKGVSLADQGKHDEAIEAYDEAIRLDPTD 261
                                       6799****************************97 PP

  == domain 8  score: 33.0 bits;  conditional E-value: 8.7e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a ++ n G ++  +g+y+eA+ea+++A++ldP n
  gi|330508351|ref|YP_004384779.1| 262 AAVWGNKGVSLVDQGKYDEAIEAYDEAIRLDPAN 295
                                       6799****************************86 PP

  == domain 9  score: 36.4 bits;  conditional E-value: 6.8e-12
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a a+ n G +++ +g+y+eA+ea+++A++ldP++
  gi|330508351|ref|YP_004384779.1| 296 AAAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTD 329
                                       689*****************************97 PP

  == domain 10  score: 29.9 bits;  conditional E-value: 8.1e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a++n G+++ k+++y+e ++a+++A++l+P+
  gi|330508351|ref|YP_004384779.1| 330 ATAWFNKGNSLNKQKKYDESIKAYDEAIRLNPD 362
                                       679*****************************8 PP

  == domain 11  score: 25.4 bits;  conditional E-value: 2.2e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ae +   G+++  +g+++eA++a+++A++ld ++
  gi|330508351|ref|YP_004384779.1| 364 AEPWIGKGNSLDDQGKHDEAIQAYDEAIRLDSTD 397
                                       67899*************************9875 PP

  == domain 12  score: 6.2 bits;  conditional E-value: 0.033
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a a+yn G ++ ++++    +eaf kA el
  gi|330508351|ref|YP_004384779.1| 398 ANAWYNKGVVLHNQNR-PGSHEAFAKAREL 426
                                       689*********5555.5566666666666 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   2.3   1.2e-16   4.8e-14       4      68 .]      31      92 ..      30      92 .. 0.96
   2 !   46.9   0.0   7.9e-15   3.1e-12       3      65 ..      98     157 ..      97     159 .. 0.95
   3 !   59.6   1.8   8.8e-19   3.5e-16       3      68 .]     166     228 ..     164     228 .. 0.96
   4 !   52.6   0.4   1.3e-16   5.4e-14       6      68 .]     203     262 ..     200     262 .. 0.96
   5 !   59.6   1.9   8.4e-19   3.3e-16       4      68 .]     269     330 ..     267     330 .. 0.96
   6 !   47.4   0.1   5.4e-15   2.2e-12       7      66 ..     306     362 ..     305     364 .. 0.96
   7 !   41.1   0.0   5.3e-13   2.1e-10       2      67 ..     335     397 ..     334     398 .. 0.94
   8 !   27.5   0.1   9.1e-09   3.6e-06       3      50 ..     370     414 ..     368     429 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.2e-16
                            TPR_16  4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68
                                      + a++++g+yd+A++a+++a+++d   P  a+A+ ++g+a++ qg ++eA+++y++a+r +p ++
  gi|330508351|ref|YP_004384779.1| 31 GVALADQGKYDEAIKAYDEAIRLD---PTIAAAWSNKGVAFADQGKHDEAIEAYDEAIRLDPTDA 92
                                      6799********************...***********************************985 PP

  == domain 2  score: 46.9 bits;  conditional E-value: 7.9e-15
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       ++ +++++g+yd+A++a+++a+++d   P +a A++++g+++ +q+ ++e + +y++a++  p
  gi|330508351|ref|YP_004384779.1|  98 KGASLADQGKYDEAIEAYDEAIRLD---PTDAIAWFNKGNSLNKQKKYDESIKAYDEAIGLNP 157
                                       57899********************...******************************98876 PP

  == domain 3  score: 59.6 bits;  conditional E-value: 8.8e-19
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       ++++++++g+yd+A++a+++a+++d   P++++A+ ++g++++ qg ++eA+++y++a+r +p ++
  gi|330508351|ref|YP_004384779.1| 166 KGKSLADQGKYDEAIEAYDEAIRLD---PANVAAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTDA 228
                                       6899*********************...***********************************985 PP

  == domain 4  score: 52.6 bits;  conditional E-value: 1.3e-16
                            TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       +++++g+yd+A++a+++a+++d   P +a+ + ++g++++ qg ++eA+++y++a+r +p ++
  gi|330508351|ref|YP_004384779.1| 203 SLADQGKYDEAIEAYDEAIRLD---PTDAAVWGNKGVSLADQGKHDEAIEAYDEAIRLDPTDA 262
                                       799*******************...***********************************985 PP

  == domain 5  score: 59.6 bits;  conditional E-value: 8.4e-19
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       + +++++g+yd+A++a+++a+++d   P++a+A+ ++g++++ qg ++eA+++y++a+r +p ++
  gi|330508351|ref|YP_004384779.1| 269 GVSLVDQGKYDEAIEAYDEAIRLD---PANAAAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTDA 330
                                       6789********************...***********************************985 PP

  == domain 6  score: 47.4 bits;  conditional E-value: 5.4e-15
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++++g+yd+A++a+++a+++d   P +a A++++g+++ +q+ ++e + +y++a+r  pd
  gi|330508351|ref|YP_004384779.1| 306 LADQGKYDEAIEAYDEAIRLD---PTDATAWFNKGNSLNKQKKYDESIKAYDEAIRLNPD 362
                                       79*******************...********************************9998 PP

  == domain 7  score: 41.1 bits;  conditional E-value: 5.3e-13
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++++++ ++++yd+ ++a+++a++++   Pd ae + ++g+++  qg ++eA+++y++a+r ++ +
  gi|330508351|ref|YP_004384779.1| 335 NKGNSLNKQKKYDESIKAYDEAIRLN---PDLAEPWIGKGNSLDDQGKHDEAIQAYDEAIRLDSTD 397
                                       67888999******************...*******************************999876 PP

  == domain 8  score: 27.5 bits;  conditional E-value: 9.1e-09
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrl 50 
                                       +++++ ++g+ d+A+ a+++a+++d   + +a A++++g+++  q+r 
  gi|330508351|ref|YP_004384779.1| 370 KGNSLDDQGKHDEAIQAYDEAIRLD---STDANAWYNKGVVLHNQNRP 414
                                       6999*********************...99999**********99775 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.8e-07   0.00019       8      33 ..      31      56 ..      27      57 .. 0.91
   2 !   26.9   0.0   8.4e-09   3.3e-06       1      34 []      58      91 ..      58      91 .. 0.94
   3 !   27.4   0.1   5.4e-09   2.2e-06       1      34 []      92     125 ..      92     125 .. 0.95
   4 !   24.9   0.1   3.6e-08   1.4e-05       3      32 ..     128     157 ..     126     158 .. 0.96
   5 !   26.0   0.1   1.5e-08   6.2e-06       2      34 .]     161     193 ..     160     193 .. 0.93
   6 !   28.2   0.0     3e-09   1.2e-06       3      34 .]     196     227 ..     194     227 .. 0.95
   7 !   26.7   0.0   9.6e-09   3.8e-06       2      34 .]     229     261 ..     228     261 .. 0.94
   8 !   28.9   0.0   1.9e-09   7.6e-07       2      34 .]     263     295 ..     262     295 .. 0.95
   9 !   28.8   0.0     2e-09   7.9e-07       1      34 []     296     329 ..     296     329 .. 0.95
  10 !   28.5   0.1   2.5e-09     1e-06       1      33 [.     330     362 ..     330     363 .. 0.96
  11 !   21.4   0.0   4.8e-07   0.00019       2      33 ..     365     396 ..     364     397 .. 0.91
  12 ?    4.0   0.0      0.18        73       1      16 [.     398     413 ..     398     422 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.8e-07
                                      HHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  8 gsiylklgdyeeAkeyyekaleldpd 33
                                      g ++ ++g+y+eA+++y +a++ldp+
  gi|330508351|ref|YP_004384779.1| 31 GVALADQGKYDEAIKAYDEAIRLDPT 56
                                      78899*******************96 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 8.4e-09
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      a a+ n+g +  ++g+++eA+e+y +a++ldp++
  gi|330508351|ref|YP_004384779.1| 58 AAAWSNKGVAFADQGKHDEAIEAYDEAIRLDPTD 91
                                      569*****************************75 PP

  == domain 3  score: 27.4 bits;  conditional E-value: 5.4e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a a+ n+g  + ++g+y+eA+e+y +a++ldp++
  gi|330508351|ref|YP_004384779.1|  92 AAAWGNKGASLADQGKYDEAIEAYDEAIRLDPTD 125
                                       579*****************************75 PP

  == domain 4  score: 24.9 bits;  conditional E-value: 3.6e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a++n+g+ + k+++y+e++++y +a+ l+p
  gi|330508351|ref|YP_004384779.1| 128 AWFNKGNSLNKQKKYDESIKAYDEAIGLNP 157
                                       8****************************9 PP

  == domain 5  score: 26.0 bits;  conditional E-value: 1.5e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       e +  +g+ + ++g+y+eA+e+y +a++ldp+n
  gi|330508351|ref|YP_004384779.1| 161 EPWIGKGKSLADQGKYDEAIEAYDEAIRLDPAN 193
                                       679999*************************86 PP

  == domain 6  score: 28.2 bits;  conditional E-value: 3e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+ n+g  + ++g+y+eA+e+y +a++ldp++
  gi|330508351|ref|YP_004384779.1| 196 AWGNKGVSLADQGKYDEAIEAYDEAIRLDPTD 227
                                       8*****************************75 PP

  == domain 7  score: 26.7 bits;  conditional E-value: 9.6e-09
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        ++ n+g  + ++g+++eA+e+y +a++ldp++
  gi|330508351|ref|YP_004384779.1| 229 AVWGNKGVSLADQGKHDEAIEAYDEAIRLDPTD 261
                                       68*****************************75 PP

  == domain 8  score: 28.9 bits;  conditional E-value: 1.9e-09
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        ++ n+g  + ++g+y+eA+e+y +a++ldp+n
  gi|330508351|ref|YP_004384779.1| 263 AVWGNKGVSLVDQGKYDEAIEAYDEAIRLDPAN 295
                                       68*****************************86 PP

  == domain 9  score: 28.8 bits;  conditional E-value: 2e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a a+ n+g  + ++g+y+eA+e+y +a++ldp++
  gi|330508351|ref|YP_004384779.1| 296 AAAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTD 329
                                       579*****************************75 PP

  == domain 10  score: 28.5 bits;  conditional E-value: 2.5e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a a++n+g+ + k+++y+e++++y +a++l+pd
  gi|330508351|ref|YP_004384779.1| 330 ATAWFNKGNSLNKQKKYDESIKAYDEAIRLNPD 362
                                       679*****************************7 PP

  == domain 11  score: 21.4 bits;  conditional E-value: 4.8e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       e +  +g+ ++++g+++eA+++y +a++ld +
  gi|330508351|ref|YP_004384779.1| 365 EPWIGKGNSLDDQGKHDEAIQAYDEAIRLDST 396
                                       67999************************976 PP

  == domain 12  score: 4.0 bits;  conditional E-value: 0.18
                                       CCHHHHHHHHHHHTT- CS
                             TPR_8   1 aeayynlgsiylklgd 16 
                                       a a+yn+g +++++++
  gi|330508351|ref|YP_004384779.1| 398 ANAWYNKGVVLHNQNR 413
                                       689********99987 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.023       9.3      16      34 .]      27      45 ..      25      45 .. 0.94
   2 !   22.7   0.0     2e-07   8.1e-05       1      34 []      46      79 ..      46      79 .. 0.96
   3 !   25.9   0.1     2e-08   8.1e-06       1      34 []      80     113 ..      80     113 .. 0.96
   4 !   25.4   0.1   2.8e-08   1.1e-05       1      33 [.     114     146 ..     114     147 .. 0.94
   5 !   12.7   0.0   0.00033      0.13       1      34 []     148     181 ..     148     181 .. 0.96
   6 !   23.8   0.0   9.4e-08   3.7e-05       1      34 []     182     215 ..     182     215 .. 0.96
   7 !   25.5   0.0   2.6e-08     1e-05       1      34 []     216     249 ..     216     249 .. 0.96
   8 !   24.4   0.0   5.9e-08   2.3e-05       1      34 []     250     283 ..     250     283 .. 0.96
   9 !   24.9   0.1   4.2e-08   1.7e-05       1      34 []     284     317 ..     284     317 .. 0.96
  10 !   25.5   0.1   2.7e-08   1.1e-05       1      33 [.     318     350 ..     318     351 .. 0.94
  11 !   20.4   0.0   1.1e-06   0.00044       1      34 []     352     385 ..     352     385 .. 0.97
  12 !   23.1   0.1   1.6e-07   6.3e-05       1      29 [.     386     414 ..     386     424 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.023
                            TPR_17 16 ynnLAelllknGdlmtArq 34
                                      +++ +++l+ +G++++A++
  gi|330508351|ref|YP_004384779.1| 27 WFYQGVALADQGKYDEAIK 45
                                      99***************85 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 2e-07
                            TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtArq 34
                                      +y +a++ldP+ a a+ n++++++ +G++++A++
  gi|330508351|ref|YP_004384779.1| 46 AYDEAIRLDPTIAAAWSNKGVAFADQGKHDEAIE 79
                                      599*****************************86 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 2e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++ldP++a a+ n++  l+ +G++++A++
  gi|330508351|ref|YP_004384779.1|  80 AYDEAIRLDPTDAAAWGNKGASLADQGKYDEAIE 113
                                       599*****************************86 PP

  == domain 4  score: 25.4 bits;  conditional E-value: 2.8e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y +a++ldP++a a++n+++ l k++++++ +
  gi|330508351|ref|YP_004384779.1| 114 AYDEAIRLDPTDAIAWFNKGNSLNKQKKYDESI 146
                                       599**************************9876 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 0.00033
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a+ l+P  a+++  +++ l+ +G++++A++
  gi|330508351|ref|YP_004384779.1| 148 AYDEAIGLNPVLAEPWIGKGKSLADQGKYDEAIE 181
                                       599*****************************86 PP

  == domain 6  score: 23.8 bits;  conditional E-value: 9.4e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++ldP n+ a+ n+++ l+ +G++++A++
  gi|330508351|ref|YP_004384779.1| 182 AYDEAIRLDPANVAAWGNKGVSLADQGKYDEAIE 215
                                       599*****************************86 PP

  == domain 7  score: 25.5 bits;  conditional E-value: 2.6e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++ldP++a ++ n+++ l+ +G++++A++
  gi|330508351|ref|YP_004384779.1| 216 AYDEAIRLDPTDAAVWGNKGVSLADQGKHDEAIE 249
                                       599*****************************86 PP

  == domain 8  score: 24.4 bits;  conditional E-value: 5.9e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++ldP++a ++ n+++ l  +G++++A++
  gi|330508351|ref|YP_004384779.1| 250 AYDEAIRLDPTDAAVWGNKGVSLVDQGKYDEAIE 283
                                       599*****************************86 PP

  == domain 9  score: 24.9 bits;  conditional E-value: 4.2e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++ldP na a+ n+++ l+ +G++++A++
  gi|330508351|ref|YP_004384779.1| 284 AYDEAIRLDPANAAAWGNKGVSLADQGKYDEAIE 317
                                       599*****************************86 PP

  == domain 10  score: 25.5 bits;  conditional E-value: 2.7e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y +a++ldP++a a++n+++ l k++++++ +
  gi|330508351|ref|YP_004384779.1| 318 AYDEAIRLDPTDATAWFNKGNSLNKQKKYDESI 350
                                       599**************************9876 PP

  == domain 11  score: 20.4 bits;  conditional E-value: 1.1e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++l+P+ a+++  +++ l  +G++++A+q
  gi|330508351|ref|YP_004384779.1| 352 AYDEAIRLNPDLAEPWIGKGNSLDDQGKHDEAIQ 385
                                       599*****************************98 PP

  == domain 12  score: 23.1 bits;  conditional E-value: 1.6e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdl 29 
                                       +y +a++ld ++a+a++n++++l++++++
  gi|330508351|ref|YP_004384779.1| 386 AYDEAIRLDSTDANAWYNKGVVLHNQNRP 414
                                       599***********************986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.4   1.1e-07   4.3e-05       3      39 ..      26      62 ..      24      67 .. 0.90
   2 !   25.9   0.9   2.7e-08   1.1e-05       4      41 ..      61      98 ..      59     101 .. 0.87
   3 !   23.6   0.1   1.4e-07   5.5e-05      10      41 ..     101     132 ..      98     135 .. 0.91
   4 ?    5.2   0.0      0.11        45      11      36 ..     136     161 ..     133     169 .. 0.79
   5 !   24.0   0.1   1.1e-07   4.4e-05       7      41 ..     166     200 ..     160     203 .. 0.88
   6 !   23.5   0.1   1.6e-07   6.2e-05      11      41 ..     204     234 ..     200     237 .. 0.91
   7 !   23.7   0.1   1.4e-07   5.4e-05      11      41 ..     238     268 ..     234     271 .. 0.91
   8 !   22.9   0.2   2.3e-07   9.3e-05      11      41 ..     272     302 ..     268     305 .. 0.90
   9 !   25.2   0.1   4.3e-08   1.7e-05      11      41 ..     306     336 ..     302     339 .. 0.92
  10 !   13.4   0.0   0.00027      0.11      11      40 ..     340     369 ..     336     373 .. 0.87
  11 !   17.3   0.0   1.5e-05    0.0061      11      42 ..     374     405 ..     367     407 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.1e-07
                            TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawl 39
                                       +   + al+ +G++deAi+++++a++l+P+ a+aw 
  gi|330508351|ref|YP_004384779.1| 26 DWFYQGVALADQGKYDEAIKAYDEAIRLDPTIAAAWS 62
                                      5788899****************************95 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 2.7e-08
                            TPR_14  4 llalaeallalGdpdeAiallrralalaPddaeawlll 41
                                      +   + a++ +G++deAi+++++a++l+P+da+aw   
  gi|330508351|ref|YP_004384779.1| 61 WSNKGVAFADQGKHDEAIEAYDEAIRLDPTDAAAWGNK 98
                                      555677999**************************865 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 1.4e-07
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawlll 41 
                                        l+ +G++deAi+++++a++l+P+da aw+  
  gi|330508351|ref|YP_004384779.1| 101 SLADQGKYDEAIEAYDEAIRLDPTDAIAWFNK 132
                                       6899*************************976 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.11
                            TPR_14  11 llalGdpdeAiallrralalaPddae 36 
                                       l  + ++de+i+++++a+ l+P  ae
  gi|330508351|ref|YP_004384779.1| 136 LNKQKKYDESIKAYDEAIGLNPVLAE 161
                                       667889************99995555 PP

  == domain 5  score: 24.0 bits;  conditional E-value: 1.1e-07
                            TPR_14   7 laeallalGdpdeAiallrralalaPddaeawlll 41 
                                        ++ l+ +G++deAi+++++a++l+P++ +aw   
  gi|330508351|ref|YP_004384779.1| 166 KGKSLADQGKYDEAIEAYDEAIRLDPANVAAWGNK 200
                                       577899**************************765 PP

  == domain 6  score: 23.5 bits;  conditional E-value: 1.6e-07
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawlll 41 
                                       l+ +G++deAi+++++a++l+P+da++w   
  gi|330508351|ref|YP_004384779.1| 204 LADQGKYDEAIEAYDEAIRLDPTDAAVWGNK 234
                                       7899************************765 PP

  == domain 7  score: 23.7 bits;  conditional E-value: 1.4e-07
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawlll 41 
                                       l+ +G++deAi+++++a++l+P+da++w   
  gi|330508351|ref|YP_004384779.1| 238 LADQGKHDEAIEAYDEAIRLDPTDAAVWGNK 268
                                       7899************************765 PP

  == domain 8  score: 22.9 bits;  conditional E-value: 2.3e-07
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawlll 41 
                                       l  +G++deAi+++++a++l+P++a+aw   
  gi|330508351|ref|YP_004384779.1| 272 LVDQGKYDEAIEAYDEAIRLDPANAAAWGNK 302
                                       6789************************765 PP

  == domain 9  score: 25.2 bits;  conditional E-value: 4.3e-08
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawlll 41 
                                       l+ +G++deAi+++++a++l+P+da+aw+  
  gi|330508351|ref|YP_004384779.1| 306 LADQGKYDEAIEAYDEAIRLDPTDATAWFNK 336
                                       7899************************976 PP

  == domain 10  score: 13.4 bits;  conditional E-value: 0.00027
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawll 40 
                                       l  + ++de+i+++++a++l+Pd ae w+ 
  gi|330508351|ref|YP_004384779.1| 340 LNKQKKYDESIKAYDEAIRLNPDLAEPWIG 369
                                       667889******************999975 PP

  == domain 11  score: 17.3 bits;  conditional E-value: 1.5e-05
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawllla 42 
                                       l  +G++deAi+++++a++l+ +da aw+  +
  gi|330508351|ref|YP_004384779.1| 374 LDDQGKHDEAIQAYDEAIRLDSTDANAWYNKG 405
                                       6789************************8765 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.8   2.7e-10   1.1e-07      10      75 ..      31      88 ..      27      90 .. 0.92
   2 !   18.0   0.2   6.5e-06    0.0026       3      32 ..      92     121 ..      90     122 .. 0.89
   3 !   27.7   0.0     6e-09   2.4e-06       3      75 ..     126     190 ..     124     192 .. 0.92
   4 !   28.9   0.2   2.7e-09   1.1e-06       6      75 ..     163     224 ..     158     226 .. 0.88
   5 !   33.7   0.1   8.4e-11   3.4e-08       4      75 ..     195     258 ..     192     260 .. 0.92
   6 !   33.7   0.0   8.2e-11   3.3e-08       3      75 ..     228     292 ..     226     294 .. 0.93
   7 !   33.8   0.1   7.8e-11   3.1e-08       3      75 ..     262     326 ..     260     327 .. 0.92
   8 !   31.2   0.0   5.1e-10     2e-07       3      74 ..     330     393 ..     328     395 .. 0.93
   9 ?    2.1   0.0      0.62   2.5e+02       3      33 ..     398     427 ..     396     434 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.7e-10
                            TPR_12 10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75
                                      +++l+ +g+ydeA++ +++a+++      p+    a++  n g ++  +g+++eA+e++ ea++++
  gi|330508351|ref|YP_004384779.1| 31 GVALADQGKYDEAIKAYDEAIRLD-----PT---IAAAWSNKGVAFADQGKHDEAIEAYDEAIRLD 88
                                      8899****************7777.....64...*****************************986 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 6.5e-06
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                       a+a+ n +a l+ +g+ydeA+e +++a+++
  gi|330508351|ref|YP_004384779.1|  92 AAAWGNKGASLADQGKYDEAIEAYDEAIRL 121
                                       7899999*****************999875 PP

  == domain 3  score: 27.7 bits;  conditional E-value: 6e-09
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a+a+ n ++ l+++++yde+++ +++a   +     + +p +a+  ++ g  +  +g+y+eA+e++ ea++++
  gi|330508351|ref|YP_004384779.1| 126 AIAWFNKGNSLNKQKKYDESIKAYDEA---I-----GLNPVLAEPWIGKGKSLADQGKYDEAIEAYDEAIRLD 190
                                       67888**********************...3.....56889*****************************987 PP

  == domain 4  score: 28.9 bits;  conditional E-value: 2.7e-09
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +   +  l+ +g+ydeA+e +++a+++      p     +++  n g  +  +g+y+eA+e++ ea++++
  gi|330508351|ref|YP_004384779.1| 163 WIGKGKSLADQGKYDEAIEAYDEAIRLD-----PA---NVAAWGNKGVSLADQGKYDEAIEAYDEAIRLD 224
                                       55678899****************7766.....65...599**************************986 PP

  == domain 5  score: 33.7 bits;  conditional E-value: 8.4e-11
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +a+ n ++ l+ +g+ydeA+e +++a+++      p+    a++  n g  +  +g+++eA+e++ ea++++
  gi|330508351|ref|YP_004384779.1| 195 AAWGNKGVSLADQGKYDEAIEAYDEAIRLD-----PT---DAAVWGNKGVSLADQGKHDEAIEAYDEAIRLD 258
                                       57889*********************8887.....86...599**************************986 PP

  == domain 6  score: 33.7 bits;  conditional E-value: 8.2e-11
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a+++ n ++ l+ +g++deA+e +++a+++      p+    a++  n g  +  +g+y+eA+e++ ea++++
  gi|330508351|ref|YP_004384779.1| 228 AAVWGNKGVSLADQGKHDEAIEAYDEAIRLD-----PT---DAAVWGNKGVSLVDQGKYDEAIEAYDEAIRLD 292
                                       78999**********************8887.....86...599**************************987 PP

  == domain 7  score: 33.8 bits;  conditional E-value: 7.8e-11
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a+++ n ++ l  +g+ydeA+e +++a+++      p     a++  n g  +  +g+y+eA+e++ ea++++
  gi|330508351|ref|YP_004384779.1| 262 AAVWGNKGVSLVDQGKYDEAIEAYDEAIRLD-----PA---NAAAWGNKGVSLADQGKYDEAIEAYDEAIRLD 326
                                       78999**********************6666.....64...6****************************985 PP

  == domain 8  score: 31.2 bits;  conditional E-value: 5.1e-10
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       ata+ n ++ l+++++yde+++ +++a+++      pd   +a+  ++ g  ++ +g+++eA++++ ea+++
  gi|330508351|ref|YP_004384779.1| 330 ATAWFNKGNSLNKQKKYDESIKAYDEAIRLN-----PD---LAEPWIGKGNSLDDQGKHDEAIQAYDEAIRL 393
                                       78999**********************6666.....76...9***************************997 PP

  == domain 9  score: 2.1 bits;  conditional E-value: 0.62
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleia 33 
                                       a+a++n ++vl+ + r   + e + ka+e+ 
  gi|330508351|ref|YP_004384779.1| 398 ANAWYNKGVVLHNQNR-PGSHEAFAKARELN 427
                                       78999******99988.88888888888875 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   7.3e-06    0.0029       4      35 ..      29      58 ..      27      59 .. 0.90
   2 !   21.1   0.0   5.4e-07   0.00021       1      35 [.      60      92 ..      60      93 .. 0.94
   3 !   18.0   0.1   5.2e-06    0.0021       1      35 [.      94     126 ..      94     127 .. 0.90
   4 ?    2.7   0.0       0.4   1.6e+02       1      26 [.     128     153 ..     128     157 .. 0.82
   5 !   14.5   0.1   6.5e-05     0.026       9      34 ..     170     193 ..     166     195 .. 0.86
   6 !   19.8   0.1   1.4e-06   0.00056       1      35 [.     196     228 ..     196     229 .. 0.93
   7 !   16.4   0.0   1.7e-05    0.0068       2      35 ..     231     262 ..     230     263 .. 0.91
   8 !   18.3   0.0   4.1e-06    0.0016       2      35 ..     265     296 ..     264     297 .. 0.90
   9 !   20.2   0.0     1e-06   0.00041       1      36 []     298     331 ..     298     331 .. 0.93
  10 ?    5.2   0.0     0.061        24       1      33 [.     332     362 ..     332     366 .. 0.80
  11 !   10.3   0.0    0.0015       0.6       7      34 ..     372     397 ..     370     412 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.3e-06
                             TPR_7  4 nLarlysrlGdyeeAielyeqsLaltkdpeda 35
                                      + +++  ++G+y+eAi+ y +  a++ dp++a
  gi|330508351|ref|YP_004384779.1| 29 YQGVALADQGKYDEAIKAYDE--AIRLDPTIA 58
                                      66999****************..****99876 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 5.4e-07
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35
                                      a++n ++++ ++G+++eAie y +  a++ dp+da
  gi|330508351|ref|YP_004384779.1| 60 AWSNKGVAFADQGKHDEAIEAYDE--AIRLDPTDA 92
                                      7899********************..******987 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 5.2e-06
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       a+ n +    ++G+y+eAie y +  a++ dp+da
  gi|330508351|ref|YP_004384779.1|  94 AWGNKGASLADQGKYDEAIEAYDE--AIRLDPTDA 126
                                       5778888999**************..***999986 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.4
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsL 26 
                                       a++n ++   ++ +y+e i+ y +++
  gi|330508351|ref|YP_004384779.1| 128 AWFNKGNSLNKQKKYDESIKAYDEAI 153
                                       6788889999999*********9954 PP

  == domain 5  score: 14.5 bits;  conditional E-value: 6.5e-05
                             TPR_7   9 ysrlGdyeeAielyeqsLaltkdped 34 
                                         ++G+y+eAie y +  a++ dp +
  gi|330508351|ref|YP_004384779.1| 170 LADQGKYDEAIEAYDE--AIRLDPAN 193
                                       568*************..99999976 PP

  == domain 6  score: 19.8 bits;  conditional E-value: 1.4e-06
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       a+ n ++   ++G+y+eAie y +  a++ dp+da
  gi|330508351|ref|YP_004384779.1| 196 AWGNKGVSLADQGKYDEAIEAYDE--AIRLDPTDA 228
                                       68899999****************..******987 PP

  == domain 7  score: 16.4 bits;  conditional E-value: 1.7e-05
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       + n ++   ++G+++eAie y +  a++ dp+da
  gi|330508351|ref|YP_004384779.1| 231 WGNKGVSLADQGKHDEAIEAYDE--AIRLDPTDA 262
                                       678899999**************..******987 PP

  == domain 8  score: 18.3 bits;  conditional E-value: 4.1e-06
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       + n ++  +++G+y+eAie y +  a++ dp +a
  gi|330508351|ref|YP_004384779.1| 265 WGNKGVSLVDQGKYDEAIEAYDE--AIRLDPANA 296
                                       67889999***************..999999775 PP

  == domain 9  score: 20.2 bits;  conditional E-value: 1e-06
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpedae 36 
                                       a+ n ++   ++G+y+eAie y +  a++ dp+da+
  gi|330508351|ref|YP_004384779.1| 298 AWGNKGVSLADQGKYDEAIEAYDE--AIRLDPTDAT 331
                                       68899999****************..******9975 PP

  == domain 10  score: 5.2 bits;  conditional E-value: 0.061
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       a++n ++   ++ +y+e i+ y +  a++  p+
  gi|330508351|ref|YP_004384779.1| 332 AWFNKGNSLNKQKKYDESIKAYDE--AIRLNPD 362
                                       6788899999999***********..6665554 PP

  == domain 11  score: 10.3 bits;  conditional E-value: 0.0015
                             TPR_7   7 rlysrlGdyeeAielyeqsLaltkdped 34 
                                       +   ++G+++eAi+ y +  a++ d +d
  gi|330508351|ref|YP_004384779.1| 372 NSLDDQGKHDEAIQAYDE--AIRLDSTD 397
                                       66789*************..66655544 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   2.5   1.7e-08   6.8e-06       1      62 [.      34      95 ..      34     100 .. 0.95
   2 !   19.4   0.4   2.9e-06    0.0011       1      51 [.     102     152 ..     102     160 .. 0.92
   3 !   35.0   1.8   3.9e-11   1.6e-08       1      62 [.     170     231 ..     170     235 .. 0.96
   4 !   31.5   1.7   4.6e-10   1.8e-07       1      62 [.     204     265 ..     204     268 .. 0.97
   5 !   30.8   2.8   7.5e-10     3e-07       1      61 [.     238     298 ..     238     300 .. 0.94
   6 !   25.2   0.5   4.4e-08   1.7e-05       1      57 [.     306     362 ..     306     367 .. 0.95
   7 !   15.3   0.0   5.2e-05     0.021       3      40 ..     376     413 ..     376     416 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.7e-08
                            TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62
                                      l ++g+y+eA++++ +a+  dp  a+a+ +   a   +g  deA+++ d++ + dp da+++
  gi|330508351|ref|YP_004384779.1| 34 LADQGKYDEAIKAYDEAIRLDPTIAAAWSNKGVAFADQGKHDEAIEAYDEAIRLDPTDAAAW 95
                                      679******************************************************97766 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 2.9e-06
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                       l ++g+y+eA++++ +a+  dp +a a+ +  + l +++ +de +++ d++
  gi|330508351|ref|YP_004384779.1| 102 LADQGKYDEAIEAYDEAIRLDPTDAIAWFNKGNSLNKQKKYDESIKAYDEA 152
                                       679****************************************99988876 PP

  == domain 3  score: 35.0 bits;  conditional E-value: 3.9e-11
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       l ++g+y+eA++++ +a+  dp n +a+ +    l  +g +deA+++ d++ + dp da+++
  gi|330508351|ref|YP_004384779.1| 170 LADQGKYDEAIEAYDEAIRLDPANVAAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTDAAVW 231
                                       679*******************************************************9987 PP

  == domain 4  score: 31.5 bits;  conditional E-value: 4.6e-10
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       l ++g+y+eA++++ +a+  dp +a+++ +    l  +g  deA+++ d++ + dp da+++
  gi|330508351|ref|YP_004384779.1| 204 LADQGKYDEAIEAYDEAIRLDPTDAAVWGNKGVSLADQGKHDEAIEAYDEAIRLDPTDAAVW 265
                                       679*******************************************************9987 PP

  == domain 5  score: 30.8 bits;  conditional E-value: 7.5e-10
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       l ++g+++eA++++ +a+  dp +a+++ +    l+ +g +deA+++ d++ + dp +a++
  gi|330508351|ref|YP_004384779.1| 238 LADQGKHDEAIEAYDEAIRLDPTDAAVWGNKGVSLVDQGKYDEAIEAYDEAIRLDPANAAA 298
                                       679*****************************************************98665 PP

  == domain 6  score: 25.2 bits;  conditional E-value: 4.4e-08
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       l ++g+y+eA++++ +a+  dp +a a+ +  + l +++ +de +++ d++ + +pd
  gi|330508351|ref|YP_004384779.1| 306 LADQGKYDEAIEAYDEAIRLDPTDATAWFNKGNSLNKQKKYDESIKAYDEAIRLNPD 362
                                       679**************************************************9999 PP

  == domain 7  score: 15.3 bits;  conditional E-value: 5.2e-05
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgq 40 
                                       ++g+++eA++++ +a+  d  +a+a+++   +l ++++
  gi|330508351|ref|YP_004384779.1| 376 DQGKHDEAIQAYDEAIRLDSTDANAWYNKGVVLHNQNR 413
                                       69**************************9999999998 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   0.00012     0.046       4      31 ..      28      55 ..      27      56 .. 0.93
   2 !   11.2   0.0    0.0011      0.45       7      32 ..      65      90 ..      60      91 .. 0.88
   3 !   11.1   0.1    0.0013      0.52       8      32 ..     100     124 ..      97     125 .. 0.85
   4 ?    7.7   0.0     0.015         6       2      28 ..     128     154 ..     127     157 .. 0.89
   5 !   11.8   0.1   0.00075       0.3       7      31 ..     167     191 ..     165     193 .. 0.89
   6 !   12.0   0.0   0.00064      0.26       7      32 ..     201     226 ..     199     227 .. 0.89
   7 !   10.9   0.0    0.0015      0.59       7      32 ..     235     260 ..     233     261 .. 0.89
   8 !   10.9   0.0    0.0014      0.57       7      31 ..     269     293 ..     267     295 .. 0.88
   9 !   12.0   0.0   0.00064      0.26       7      32 ..     303     328 ..     301     329 .. 0.89
  10 !   12.3   0.0   0.00052      0.21       2      32 ..     332     362 ..     331     363 .. 0.95
  11 ?    7.1   0.0     0.023       9.3       7      28 ..     371     392 ..     369     395 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00012
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  4 yklalsyrklgdtdkAlealerlikeYP 31
                                      ++++ ++  +g++d+A++a+++ i+  P
  gi|330508351|ref|YP_004384779.1| 28 FYQGVALADQGKYDEAIKAYDEAIRLDP 55
                                      899*********************9887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0011
                                      HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  7 alsyrklgdtdkAlealerlikeYPd 32
                                      + ++  +g++d+A+ea+++ i+  P+
  gi|330508351|ref|YP_004384779.1| 65 GVAFADQGKHDEAIEAYDEAIRLDPT 90
                                      7788889**************99885 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   8 lsyrklgdtdkAlealerlikeYPd 32 
                                        s+  +g++d+A+ea+++ i+  P+
  gi|330508351|ref|YP_004384779.1| 100 ASLADQGKYDEAIEAYDEAIRLDPT 124
                                       5667799*************99885 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                       A ++ + s+ k++++d++++a+++ i 
  gi|330508351|ref|YP_004384779.1| 128 AWFNKGNSLNKQKKYDESIKAYDEAIG 154
                                       78999*****************99885 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 0.00075
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       ++s+  +g++d+A+ea+++ i+  P
  gi|330508351|ref|YP_004384779.1| 167 GKSLADQGKYDEAIEAYDEAIRLDP 191
                                       7889999**************9887 PP

  == domain 6  score: 12.0 bits;  conditional E-value: 0.00064
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + s+  +g++d+A+ea+++ i+  P+
  gi|330508351|ref|YP_004384779.1| 201 GVSLADQGKYDEAIEAYDEAIRLDPT 226
                                       7788999**************99885 PP

  == domain 7  score: 10.9 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + s+  +g++d+A+ea+++ i+  P+
  gi|330508351|ref|YP_004384779.1| 235 GVSLADQGKHDEAIEAYDEAIRLDPT 260
                                       7788899**************99885 PP

  == domain 8  score: 10.9 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       + s+  +g++d+A+ea+++ i+  P
  gi|330508351|ref|YP_004384779.1| 269 GVSLVDQGKYDEAIEAYDEAIRLDP 293
                                       77888999*************9887 PP

  == domain 9  score: 12.0 bits;  conditional E-value: 0.00064
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + s+  +g++d+A+ea+++ i+  P+
  gi|330508351|ref|YP_004384779.1| 303 GVSLADQGKYDEAIEAYDEAIRLDPT 328
                                       7788999**************99885 PP

  == domain 10  score: 12.3 bits;  conditional E-value: 0.00052
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       A ++ + s+ k++++d++++a+++ i+  Pd
  gi|330508351|ref|YP_004384779.1| 332 AWFNKGNSLNKQKKYDESIKAYDEAIRLNPD 362
                                       88999***********************998 PP

  == domain 11  score: 7.1 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       + s+  +g++d+A++a+++ i+
  gi|330508351|ref|YP_004384779.1| 371 GNSLDDQGKHDEAIQAYDEAIR 392
                                       66778899**********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 !   21.8   0.5     4e-07   0.00016      17      81 ..      18      83 ..       5      84 .. 0.88
   2 !   18.6   0.0   4.2e-06    0.0017      30      81 ..      99     151 ..      85     152 .. 0.90
   3 !   21.2   0.0   6.4e-07   0.00026      30      81 ..     167     219 ..     163     220 .. 0.94
   4 !   20.6   0.0   9.9e-07    0.0004      26      81 ..     229     287 ..     223     288 .. 0.89
   5 !   20.9   0.0   7.5e-07    0.0003      29      81 ..     302     355 ..     291     356 .. 0.89
   6 ?    7.0   0.0     0.017       6.7      32      69 ..     373     411 ..     367     427 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4e-07
                                      .HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3 17 aaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                      a+ ++ +ed ++ + +l  +g+y++A++ +++a +l+++  +++  ++ +  +++k++eAi a+++
  gi|330508351|ref|YP_004384779.1| 18 AQCQQTEEDWFYQGVALADQGKYDEAIKAYDEAiRLDPTIAAAWSNKGVAFADQGKHDEAIEAYDE 83
                                      345999******************************99999*********************9986 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 4.2e-06
                                       HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       + +l  +g+y++A+e +++a +l++++  +++ ++ +l k+kky+e i+a+++
  gi|330508351|ref|YP_004384779.1|  99 GASLADQGKYDEAIEAYDEAiRLDPTDAIAWFNKGNSLNKQKKYDESIKAYDE 151
                                       667889*******************************************9986 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 6.4e-07
                                       HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +++l  +g+y++A+e +++a +l++ + +++  ++ +l +++ky+eAi a+++
  gi|330508351|ref|YP_004384779.1| 167 GKSLADQGKYDEAIEAYDEAiRLDPANVAAWGNKGVSLADQGKYDEAIEAYDE 219
                                       678899*******************************************9986 PP

  == domain 4  score: 20.6 bits;  conditional E-value: 9.9e-07
                                       HHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  26 ayl..lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       a +  ++ +l  +g++++A+e +++a +l++++ +++  ++ +l++++ky+eAi a+++
  gi|330508351|ref|YP_004384779.1| 229 AVWgnKGVSLADQGKHDEAIEAYDEAiRLDPTDAAVWGNKGVSLVDQGKYDEAIEAYDE 287
                                       555445778999*******************************************9986 PP

  == domain 5  score: 20.9 bits;  conditional E-value: 7.5e-07
                                       HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++ +l  +g+y++A+e +++a +l++++  +++ ++ +l k+kky+e i+a+++
  gi|330508351|ref|YP_004384779.1| 302 KGVSLADQGKYDEAIEAYDEAiRLDPTDATAWFNKGNSLNKQKKYDESIKAYDE 355
                                       5778999*******************************************9986 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.017
                                       HHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHT CS
                            ANAPC3  32 clylngqykrAyellrka.klnskslgcrylfAqcllkL 69 
                                       +l  +g++++A++ +++a +l+s++ +++y ++ +l  +
  gi|330508351|ref|YP_004384779.1| 373 SLDDQGKHDEAIQAYDEAiRLDSTDANAWYNKGVVLHNQ 411
                                       667899999999999999999999999999888777665 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   0.00013      0.05       9      30 ..      31      52 ..      31      53 .. 0.94
   2 !   12.5   0.1   0.00026       0.1       6      30 ..      62      86 ..      57      87 .. 0.88
   3 !   12.7   0.3   0.00022     0.086       7      30 ..      97     120 ..      92     121 .. 0.90
   4 ?    6.0   0.0     0.029        12       8      29 ..     132     153 ..     131     155 .. 0.91
   5 !   10.8   0.2   0.00091      0.36      12      30 ..     170     188 ..     167     189 .. 0.90
   6 !   12.9   0.1    0.0002     0.079       7      30 ..     199     222 ..     198     223 .. 0.90
   7 !   12.2   0.1   0.00031      0.12       7      30 ..     233     256 ..     232     257 .. 0.90
   8 !   11.4   0.0   0.00056      0.22       9      30 ..     269     290 ..     266     291 .. 0.89
   9 !   13.0   0.2   0.00018     0.071       7      30 ..     301     324 ..     296     325 .. 0.90
  10 ?    7.4   0.0      0.01       4.1       8      31 ..     336     359 ..     335     360 .. 0.91
  11 !   10.7   0.1   0.00098      0.39       9      30 ..     371     392 ..     371     393 .. 0.92
  12 ?   -1.9   0.0       8.8   3.5e+03       7      18 ..     403     414 ..     402     422 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00013
                            TPR_10  9 analrqrgrydeAealleeala 30
                                      ++al ++g+ydeA + ++ea++
  gi|330508351|ref|YP_004384779.1| 31 GVALADQGKYDEAIKAYDEAIR 52
                                      789*****************97 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00026
                            TPR_10  6 nNLanalrqrgrydeAealleeala 30
                                      +N ++a  ++g++deA + ++ea++
  gi|330508351|ref|YP_004384779.1| 62 SNKGVAFADQGKHDEAIEAYDEAIR 86
                                      788999*****************97 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00022
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N ++ l ++g+ydeA + ++ea++
  gi|330508351|ref|YP_004384779.1|  97 NKGASLADQGKYDEAIEAYDEAIR 120
                                       668899****************97 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.029
                            TPR_10   8 LanalrqrgrydeAealleeal 29 
                                        +n l ++++yde+ + ++ea+
  gi|330508351|ref|YP_004384779.1| 132 KGNSLNKQKKYDESIKAYDEAI 153
                                       5899*****************8 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.00091
                            TPR_10  12 lrqrgrydeAealleeala 30 
                                       l ++g+ydeA + ++ea++
  gi|330508351|ref|YP_004384779.1| 170 LADQGKYDEAIEAYDEAIR 188
                                       899**************97 PP

  == domain 6  score: 12.9 bits;  conditional E-value: 0.0002
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N ++ l ++g+ydeA + ++ea++
  gi|330508351|ref|YP_004384779.1| 199 NKGVSLADQGKYDEAIEAYDEAIR 222
                                       558899****************97 PP

  == domain 7  score: 12.2 bits;  conditional E-value: 0.00031
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N ++ l ++g++deA + ++ea++
  gi|330508351|ref|YP_004384779.1| 233 NKGVSLADQGKHDEAIEAYDEAIR 256
                                       558899****************97 PP

  == domain 8  score: 11.4 bits;  conditional E-value: 0.00056
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       ++ l ++g+ydeA + ++ea++
  gi|330508351|ref|YP_004384779.1| 269 GVSLVDQGKYDEAIEAYDEAIR 290
                                       78899***************97 PP

  == domain 9  score: 13.0 bits;  conditional E-value: 0.00018
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N ++ l ++g+ydeA + ++ea++
  gi|330508351|ref|YP_004384779.1| 301 NKGVSLADQGKYDEAIEAYDEAIR 324
                                       66899*****************97 PP

  == domain 10  score: 7.4 bits;  conditional E-value: 0.01
                            TPR_10   8 LanalrqrgrydeAealleealai 31 
                                        +n l ++++yde+ + ++ea+++
  gi|330508351|ref|YP_004384779.1| 336 KGNSLNKQKKYDESIKAYDEAIRL 359
                                       5899*****************985 PP

  == domain 11  score: 10.7 bits;  conditional E-value: 0.00098
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       +n l ++g++deA + ++ea++
  gi|330508351|ref|YP_004384779.1| 371 GNSLDDQGKHDEAIQAYDEAIR 392
                                       68899***************97 PP

  == domain 12  score: -1.9 bits;  conditional E-value: 8.8
                            TPR_10   7 NLanalrqrgry 18 
                                       N +++l++++r 
  gi|330508351|ref|YP_004384779.1| 403 NKGVVLHNQNRP 414
                                       56999****996 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 !   11.5   0.5   0.00059      0.24      11      33 ..      31      53 ..      28      53 .. 0.86
   2 !   10.0   0.3    0.0018      0.73       7      33 ..      61      87 ..      57      87 .. 0.86
   3 !   13.3   0.7   0.00017     0.067       4      33 ..      92     121 ..      90     121 .. 0.84
   4 !    9.5   0.1    0.0025      0.98       4      33 ..     126     155 ..     124     161 .. 0.90
   5 !   11.4   0.2   0.00065      0.26      16      33 ..     172     189 ..     164     189 .. 0.85
   6 !   14.2   0.2   8.5e-05     0.034       9      33 ..     199     223 ..     195     223 .. 0.90
   7 !   10.6   0.1    0.0011      0.45       9      33 ..     233     257 ..     227     257 .. 0.89
   8 !   11.9   0.1   0.00044      0.18      10      33 ..     268     291 ..     261     291 .. 0.83
   9 !   15.4   0.8   3.7e-05     0.015       4      33 ..     296     325 ..     294     325 .. 0.90
  10 !    7.9   0.1    0.0082       3.3       4      33 ..     330     359 ..     328     359 .. 0.83
  11 !   10.4   0.0    0.0013      0.52      13      33 ..     373     393 ..     367     393 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00059
                               MIT 11 AveeDnagnyeeAlelYkealel 33
                                       v +  +g+y+eA+++Y ea++l
  gi|330508351|ref|YP_004384779.1| 31 GVALADQGKYDEAIKAYDEAIRL 53
                                      5777789*************975 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0018
                               MIT  7 lvkkAveeDnagnyeeAlelYkealel 33
                                        +k v    +g+ +eA+e+Y ea++l
  gi|330508351|ref|YP_004384779.1| 61 WSNKGVAFADQGKHDEAIEAYDEAIRL 87
                                      56889999999*************975 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 0.00017
                               MIT   4 AlelvkkAveeDnagnyeeAlelYkealel 33 
                                       A +  +k + +  +g+y+eA+e+Y ea++l
  gi|330508351|ref|YP_004384779.1|  92 AAAWGNKGASLADQGKYDEAIEAYDEAIRL 121
                                       56667888888899*************975 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0025
                               MIT   4 AlelvkkAveeDnagnyeeAlelYkealel 33 
                                       A++ ++k   + ++++y+e +++Y ea++l
  gi|330508351|ref|YP_004384779.1| 126 AIAWFNKGNSLNKQKKYDESIKAYDEAIGL 155
                                       888889999999***************985 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 0.00065
                               MIT  16 nagnyeeAlelYkealel 33 
                                        +g+y+eA+e+Y ea++l
  gi|330508351|ref|YP_004384779.1| 172 DQGKYDEAIEAYDEAIRL 189
                                       679************975 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 8.5e-05
                               MIT   9 kkAveeDnagnyeeAlelYkealel 33 
                                       +k v +  +g+y+eA+e+Y ea++l
  gi|330508351|ref|YP_004384779.1| 199 NKGVSLADQGKYDEAIEAYDEAIRL 223
                                       78999999**************975 PP

  == domain 7  score: 10.6 bits;  conditional E-value: 0.0011
                               MIT   9 kkAveeDnagnyeeAlelYkealel 33 
                                       +k v +  +g+ +eA+e+Y ea++l
  gi|330508351|ref|YP_004384779.1| 233 NKGVSLADQGKHDEAIEAYDEAIRL 257
                                       78999999**************975 PP

  == domain 8  score: 11.9 bits;  conditional E-value: 0.00044
                               MIT  10 kAveeDnagnyeeAlelYkealel 33 
                                       k v +  +g+y+eA+e+Y ea++l
  gi|330508351|ref|YP_004384779.1| 268 KGVSLVDQGKYDEAIEAYDEAIRL 291
                                       66666678*************975 PP

  == domain 9  score: 15.4 bits;  conditional E-value: 3.7e-05
                               MIT   4 AlelvkkAveeDnagnyeeAlelYkealel 33 
                                       A +  +k v +  +g+y+eA+e+Y ea++l
  gi|330508351|ref|YP_004384779.1| 296 AAAWGNKGVSLADQGKYDEAIEAYDEAIRL 325
                                       7778899********************975 PP

  == domain 10  score: 7.9 bits;  conditional E-value: 0.0082
                               MIT   4 AlelvkkAveeDnagnyeeAlelYkealel 33 
                                       A + ++k   + ++++y+e +++Y ea++l
  gi|330508351|ref|YP_004384779.1| 330 ATAWFNKGNSLNKQKKYDESIKAYDEAIRL 359
                                       55666777788899*************975 PP

  == domain 11  score: 10.4 bits;  conditional E-value: 0.0013
                               MIT  13 eeDnagnyeeAlelYkealel 33 
                                        +D +g+ +eA+++Y ea++l
  gi|330508351|ref|YP_004384779.1| 373 SLDDQGKHDEAIQAYDEAIRL 393
                                       689***************975 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.021       8.2      30      61 ..      25      56 ..      11      65 .. 0.86
   2 !   19.2   1.7   2.4e-06   0.00097       5      65 ..      34      94 ..      29      94 .. 0.94
   3 !   24.9   0.8   4.3e-08   1.7e-05       6      65 ..      69     128 ..      64     132 .. 0.93
   4 !   10.4   0.1    0.0014      0.56       8      63 ..     139     194 ..     134     196 .. 0.92
   5 !   22.0   0.6   3.4e-07   0.00013       6      64 ..     171     229 ..     167     231 .. 0.94
   6 !   22.8   0.5   1.9e-07   7.7e-05       6      65 ..     239     298 ..     234     299 .. 0.94
   7 !   23.6   0.4   1.1e-07   4.3e-05       7      65 ..     274     332 ..     267     334 .. 0.95
   8 !   13.2   0.1   0.00019     0.074       6      61 ..     307     362 ..     302     365 .. 0.92
   9 !   10.6   0.0    0.0012      0.49       8      44 ..     377     413 ..     372     416 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.021
                             TPR_9 30 eerrdRGlllaqlGclsaAladLeaylalapd 61
                                      e+++  G++la +G + +A+++ + +++l+p 
  gi|330508351|ref|YP_004384779.1| 25 EDWFYQGVALADQGKYDEAIKAYDEAIRLDPT 56
                                      57888899999999999999999999999995 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.4e-06
                             TPR_9  5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                                      ++ + ++++a+++++  + l+P  +  +   G++ a +G   +A+++ + +++l+p +++a
  gi|330508351|ref|YP_004384779.1| 34 LADQGKYDEAIKAYDEAIRLDPTIAAAWSNKGVAFADQGKHDEAIEAYDEAIRLDPTDAAA 94
                                      577899**************************************************99875 PP

  == domain 3  score: 24.9 bits;  conditional E-value: 4.3e-08
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       + + ++++a+++++  + l+P d+  +   G  la +G + +A+++ + +++l+p ++ a
  gi|330508351|ref|YP_004384779.1|  69 ADQGKHDEAIEAYDEAIRLDPTDAAAWGNKGASLADQGKYDEAIEAYDEAIRLDPTDAIA 128
                                       67889**************************************************99865 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0014
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       ++++++ +++++  + l+P  +e +   G  la +G + +A+++ + +++l+p++ 
  gi|330508351|ref|YP_004384779.1| 139 QKKYDESIKAYDEAIGLNPVLAEPWIGKGKSLADQGKYDEAIEAYDEAIRLDPANV 194
                                       678899999********************************************765 PP

  == domain 5  score: 22.0 bits;  conditional E-value: 3.4e-07
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       + + ++++a+++++  + l+P  +  +   G+ la +G + +A+++ + +++l+p +++
  gi|330508351|ref|YP_004384779.1| 171 ADQGKYDEAIEAYDEAIRLDPANVAAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTDAA 229
                                       678899*************************************************8875 PP

  == domain 6  score: 22.8 bits;  conditional E-value: 1.9e-07
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       + + ++++a+++++  + l+P d+  +   G+ l+ +G + +A+++ + +++l+p++++a
  gi|330508351|ref|YP_004384779.1| 239 ADQGKHDEAIEAYDEAIRLDPTDAAVWGNKGVSLVDQGKYDEAIEAYDEAIRLDPANAAA 298
                                       678899*************************************************88765 PP

  == domain 7  score: 23.6 bits;  conditional E-value: 1.1e-07
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                        + ++++a+++++  + l+P  +  +   G+ la +G + +A+++ + +++l+p +++a
  gi|330508351|ref|YP_004384779.1| 274 DQGKYDEAIEAYDEAIRLDPANAAAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTDATA 332
                                       67899*************************************************99987 PP

  == domain 8  score: 13.2 bits;  conditional E-value: 0.00019
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       + + ++++a+++++  + l+P d+  ++  G  l ++  + + +++ + +++l+pd
  gi|330508351|ref|YP_004384779.1| 307 ADQGKYDEAIEAYDEAIRLDPTDATAWFNKGNSLNKQKKYDESIKAYDEAIRLNPD 362
                                       678899****************************************9999999997 PP

  == domain 9  score: 10.6 bits;  conditional E-value: 0.0012
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGc 44 
                                       + ++++a+++++  + l++ d+  ++  G++l+ +++
  gi|330508351|ref|YP_004384779.1| 377 QGKHDEAIQAYDEAIRLDSTDANAWYNKGVVLHNQNR 413
                                       56899***************************99876 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.4    0.0016      0.63       8      25 ..      31      48 ..      25      54 .. 0.85
   2 ?    7.0   0.0     0.015         6      10      25 ..      67      82 ..      65      90 .. 0.89
   3 !   14.4   0.0     7e-05     0.028       8      25 ..      99     116 ..      99     124 .. 0.92
   4 ?   -0.0   0.1       2.3   9.3e+02      14      25 ..     139     150 ..     138     157 .. 0.63
   5 !   13.0   0.1   0.00019     0.075       9      25 ..     168     184 ..     166     193 .. 0.85
   6 !   12.2   0.0   0.00034      0.13      10      25 ..     203     218 ..     201     226 .. 0.88
   7 ?    5.5   0.0     0.043        17      10      25 ..     237     252 ..     235     260 .. 0.88
   8 !   10.1   0.0    0.0016      0.63      13      25 ..     274     286 ..     270     295 .. 0.86
   9 !   12.2   0.0   0.00034      0.13      10      25 ..     305     320 ..     303     328 .. 0.88
  10 ?   -0.5   0.3       3.4   1.4e+03      14      25 ..     343     354 ..     342     359 .. 0.73
  11 ?    2.3   0.1      0.43   1.7e+02      14      25 ..     377     388 ..     376     395 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0016
                                      HHHHHHTT-HHHHHHH.. CS
                             TPR_3  8 AaefynkkkyqeArelfs 25
                                      + ++ +++ky+eA+ +++
  gi|330508351|ref|YP_004384779.1| 31 GVALADQGKYDEAIKAYD 48
                                      678999**********77 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.015
                                      HHHHTT-HHHHHHH.. CS
                             TPR_3 10 efynkkkyqeArelfs 25
                                      +f +++k +eA+e+++
  gi|330508351|ref|YP_004384779.1| 67 AFADQGKHDEAIEAYD 82
                                      799***********77 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 7e-05
                                       HHHHHHTT-HHHHHHH.. CS
                             TPR_3   8 AaefynkkkyqeArelfs 25 
                                       +a++ +++ky+eA+e+++
  gi|330508351|ref|YP_004384779.1|  99 GASLADQGKYDEAIEAYD 116
                                       7999************87 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 2.3
                                       TT-HHHHHHH.. CS
                             TPR_3  14 kkkyqeArelfs 25 
                                       +kky+e + +++
  gi|330508351|ref|YP_004384779.1| 139 QKKYDESIKAYD 150
                                       566666555544 PP

  == domain 5  score: 13.0 bits;  conditional E-value: 0.00019
                                       HHHHHTT-HHHHHHH.. CS
                             TPR_3   9 aefynkkkyqeArelfs 25 
                                        ++ +++ky+eA+e+++
  gi|330508351|ref|YP_004384779.1| 168 KSLADQGKYDEAIEAYD 184
                                       68899**********77 PP

  == domain 6  score: 12.2 bits;  conditional E-value: 0.00034
                                       HHHHTT-HHHHHHH.. CS
                             TPR_3  10 efynkkkyqeArelfs 25 
                                       ++ +++ky+eA+e+++
  gi|330508351|ref|YP_004384779.1| 203 SLADQGKYDEAIEAYD 218
                                       6889**********87 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.043
                                       HHHHTT-HHHHHHH.. CS
                             TPR_3  10 efynkkkyqeArelfs 25 
                                       ++ +++k +eA+e+++
  gi|330508351|ref|YP_004384779.1| 237 SLADQGKHDEAIEAYD 252
                                       6789**********77 PP

  == domain 8  score: 10.1 bits;  conditional E-value: 0.0016
                                       HTT-HHHHHHH.. CS
                             TPR_3  13 nkkkyqeArelfs 25 
                                       +++ky+eA+e+++
  gi|330508351|ref|YP_004384779.1| 274 DQGKYDEAIEAYD 286
                                       69*********77 PP

  == domain 9  score: 12.2 bits;  conditional E-value: 0.00034
                                       HHHHTT-HHHHHHH.. CS
                             TPR_3  10 efynkkkyqeArelfs 25 
                                       ++ +++ky+eA+e+++
  gi|330508351|ref|YP_004384779.1| 305 SLADQGKYDEAIEAYD 320
                                       6889**********87 PP

  == domain 10  score: -0.5 bits;  conditional E-value: 3.4
                                       TT-HHHHHHH.. CS
                             TPR_3  14 kkkyqeArelfs 25 
                                       +kky+e + +++
  gi|330508351|ref|YP_004384779.1| 343 QKKYDESIKAYD 354
                                       788888777754 PP

  == domain 11  score: 2.3 bits;  conditional E-value: 0.43
                                       TT-HHHHHHH.. CS
                             TPR_3  14 kkkyqeArelfs 25 
                                       ++k +eA+++++
  gi|330508351|ref|YP_004384779.1| 377 QGKHDEAIQAYD 388
                                       889999999976 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.6   9.3e-06    0.0037     204     259 ..      36      91 ..      26      93 .. 0.93
   2 !   12.2   0.4   0.00015      0.06     205     259 ..      71     125 ..      68     128 .. 0.94
   3 !   14.5   0.2   3.1e-05     0.012     202     258 ..     136     192 ..     105     193 .. 0.92
   4 !   13.4   0.1   6.9e-05     0.027     205     259 ..     207     261 ..     202     267 .. 0.94
   5 !   11.4   0.2   0.00027      0.11     206     259 ..     276     329 ..     271     337 .. 0.95
   6 !   17.0   0.2   5.5e-06    0.0022     203     259 ..     341     397 ..     332     412 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.3e-06
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                         g++++A++  d+ai+ +pt+   + +K+  +  +G  ++A+e+ +ea +lD  D
  gi|330508351|ref|YP_004384779.1|  36 DQGKYDEAIKAYDEAIRLDPTIAAAWSNKGVAFADQGKHDEAIEAYDEAIRLDPTD 91 
                                       56899************************************************887 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00015
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                        g+ ++A+e  d+ai+ +pt    + +K+  l  +G  ++A+e+ +ea +lD  D
  gi|330508351|ref|YP_004384779.1|  71 QGKHDEAIEAYDEAIRLDPTDAAAWGNKGASLADQGKYDEAIEAYDEAIRLDPTD 125
                                       57889***********************************************888 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.1e-05
                                       HHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT CS
                             NARP1 202 ydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDla 258
                                        +k ++++++++  d+ai  +p l e ++ K++ l  +G  ++A+e+ +ea +lD a
  gi|330508351|ref|YP_004384779.1| 136 LNKQKKYDESIKAYDEAIGLNPVLAEPWIGKGKSLADQGKYDEAIEAYDEAIRLDPA 192
                                       5788999***********************************************965 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 6.9e-05
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                        g++++A+e  d+ai+ +pt   ++ +K+  l  +G  ++A+e+ +ea +lD  D
  gi|330508351|ref|YP_004384779.1| 207 QGKYDEAIEAYDEAIRLDPTDAAVWGNKGVSLADQGKHDEAIEAYDEAIRLDPTD 261
                                       5789************************************************988 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 0.00027
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                       g++++A+e  d+ai+ +p     + +K+  l  +G  ++A+e+ +ea +lD  D
  gi|330508351|ref|YP_004384779.1| 276 GKYDEAIEAYDEAIRLDPANAAAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTD 329
                                       6899***********************************************888 PP

  == domain 6  score: 17.0 bits;  conditional E-value: 5.5e-06
                                       HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                       +k ++++++++  d+ai+ +p l e ++ K++ l  +G  ++A+++ +ea +lD  D
  gi|330508351|ref|YP_004384779.1| 341 NKQKKYDESIKAYDEAIRLNPDLAEPWIGKGNSLDDQGKHDEAIQAYDEAIRLDSTD 397
                                       778899************************************************998 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.11        44       7      20 ..      30      43 ..      28      44 .. 0.91
   2 ?    6.6   0.0     0.036        14       1      24 [.      58      81 ..      58      83 .. 0.86
   3 ?    6.5   0.1      0.04        16       2      24 ..      93     115 ..      92     117 .. 0.83
   4 ?    4.3   0.0       0.2        81       6      24 ..     165     183 ..     160     185 .. 0.78
   5 ?    6.2   0.0     0.051        20       2      24 ..     195     217 ..     194     219 .. 0.82
   6 ?    6.3   0.0     0.047        19       4      24 ..     231     251 ..     228     253 .. 0.79
   7 ?    3.8   0.0      0.28   1.1e+02       4      24 ..     265     285 ..     262     287 .. 0.78
   8 ?    6.6   0.0     0.035        14       2      24 ..     297     319 ..     296     321 .. 0.83
   9 ?    2.6   0.0      0.73   2.9e+02       6      24 ..     369     387 ..     364     389 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.11
                             TPR_4  7 LArallalGdldeA 20
                                      ++ al+++G +deA
  gi|330508351|ref|YP_004384779.1| 30 QGVALADQGKYDEA 43
                                      589**********9 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.036
                             TPR_4  1 arallaLArallalGdldeArall 24
                                      a+a ++ + a +++G +deA ++ 
  gi|330508351|ref|YP_004384779.1| 58 AAAWSNKGVAFADQGKHDEAIEAY 81
                                      6789999*************7665 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.04
                             TPR_4   2 rallaLArallalGdldeArall 24 
                                       +a  + +  l+++G +deA ++ 
  gi|330508351|ref|YP_004384779.1|  93 AAWGNKGASLADQGKYDEAIEAY 115
                                       67889999***********7665 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.2
                             TPR_4   6 aLArallalGdldeArall 24 
                                       + +  l+++G +deA ++ 
  gi|330508351|ref|YP_004384779.1| 165 GKGKSLADQGKYDEAIEAY 183
                                       567789*********7665 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.051
                             TPR_4   2 rallaLArallalGdldeArall 24 
                                       +a  + +  l+++G +deA ++ 
  gi|330508351|ref|YP_004384779.1| 195 AAWGNKGVSLADQGKYDEAIEAY 217
                                       56778899***********7665 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.047
                             TPR_4   4 llaLArallalGdldeArall 24 
                                         + +  l+++G +deA ++ 
  gi|330508351|ref|YP_004384779.1| 231 WGNKGVSLADQGKHDEAIEAY 251
                                       5677999**********7665 PP

  == domain 7  score: 3.8 bits;  conditional E-value: 0.28
                             TPR_4   4 llaLArallalGdldeArall 24 
                                         + +  l ++G +deA ++ 
  gi|330508351|ref|YP_004384779.1| 265 WGNKGVSLVDQGKYDEAIEAY 285
                                       5677899**********7665 PP

  == domain 8  score: 6.6 bits;  conditional E-value: 0.035
                             TPR_4   2 rallaLArallalGdldeArall 24 
                                       +a  + +  l+++G +deA ++ 
  gi|330508351|ref|YP_004384779.1| 297 AAWGNKGVSLADQGKYDEAIEAY 319
                                       67889999***********7665 PP

  == domain 9  score: 2.6 bits;  conditional E-value: 0.73
                             TPR_4   6 aLArallalGdldeArall 24 
                                       + +  l ++G +deA ++ 
  gi|330508351|ref|YP_004384779.1| 369 GKGNSLDDQGKHDEAIQAY 387
                                       56778999*******7665 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.084        33       9      28 ..      33      52 ..      32      54 .. 0.85
   2 ?    5.0   0.0     0.082        33       9      28 ..      67      86 ..      66      88 .. 0.86
   3 ?    5.2   0.0     0.075        30      10      28 ..     102     120 ..     100     122 .. 0.84
   4 ?   -0.6   0.0       5.2   2.1e+03       9      25 ..     135     151 ..     134     156 .. 0.81
   5 ?    5.4   0.0     0.062        25       9      28 ..     169     188 ..     168     190 .. 0.84
   6 ?    4.9   0.0     0.093        37      10      28 ..     204     222 ..     203     224 .. 0.84
   7 ?    4.1   0.0      0.17        67      10      28 ..     238     256 ..     237     258 .. 0.83
   8 ?    4.5   0.0      0.12        47      11      28 ..     273     290 ..     271     292 .. 0.83
   9 ?    4.9   0.0     0.093        37      10      28 ..     306     324 ..     305     326 .. 0.84
  10 ?    0.2   0.0         3   1.2e+03       9      28 ..     339     358 ..     338     360 .. 0.82
  11 ?    1.3   0.0       1.3   5.3e+02      14      28 ..     378     392 ..     376     394 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.084
                               PPR  9 gycknGkleeAlelfkeMke 28
                                      +++  Gk++eA++ ++e ++
  gi|330508351|ref|YP_004384779.1| 33 ALADQGKYDEAIKAYDEAIR 52
                                      57889**********99765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.082
                               PPR  9 gycknGkleeAlelfkeMke 28
                                      +++  Gk++eA+e ++e ++
  gi|330508351|ref|YP_004384779.1| 67 AFADQGKHDEAIEAYDEAIR 86
                                      68889**********99765 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.075
                               PPR  10 ycknGkleeAlelfkeMke 28 
                                       ++  Gk++eA+e ++e ++
  gi|330508351|ref|YP_004384779.1| 102 LADQGKYDEAIEAYDEAIR 120
                                       6779**********99765 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 5.2
                               PPR   9 gycknGkleeAlelfke 25 
                                       ++ k  k++e ++ ++e
  gi|330508351|ref|YP_004384779.1| 135 SLNKQKKYDESIKAYDE 151
                                       6778999***9999998 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.062
                               PPR   9 gycknGkleeAlelfkeMke 28 
                                       +++  Gk++eA+e ++e ++
  gi|330508351|ref|YP_004384779.1| 169 SLADQGKYDEAIEAYDEAIR 188
                                       67889**********99765 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.093
                               PPR  10 ycknGkleeAlelfkeMke 28 
                                       ++  Gk++eA+e ++e ++
  gi|330508351|ref|YP_004384779.1| 204 LADQGKYDEAIEAYDEAIR 222
                                       6678**********99765 PP

  == domain 7  score: 4.1 bits;  conditional E-value: 0.17
                               PPR  10 ycknGkleeAlelfkeMke 28 
                                       ++  Gk++eA+e ++e ++
  gi|330508351|ref|YP_004384779.1| 238 LADQGKHDEAIEAYDEAIR 256
                                       5678**********99765 PP

  == domain 8  score: 4.5 bits;  conditional E-value: 0.12
                               PPR  11 cknGkleeAlelfkeMke 28 
                                       +  Gk++eA+e ++e ++
  gi|330508351|ref|YP_004384779.1| 273 VDQGKYDEAIEAYDEAIR 290
                                       668**********99765 PP

  == domain 9  score: 4.9 bits;  conditional E-value: 0.093
                               PPR  10 ycknGkleeAlelfkeMke 28 
                                       ++  Gk++eA+e ++e ++
  gi|330508351|ref|YP_004384779.1| 306 LADQGKYDEAIEAYDEAIR 324
                                       6678**********99765 PP

  == domain 10  score: 0.2 bits;  conditional E-value: 3
                               PPR   9 gycknGkleeAlelfkeMke 28 
                                       ++ k  k++e ++ ++e ++
  gi|330508351|ref|YP_004384779.1| 339 SLNKQKKYDESIKAYDEAIR 358
                                       6779999******9999766 PP

  == domain 11  score: 1.3 bits;  conditional E-value: 1.3
                               PPR  14 GkleeAlelfkeMke 28 
                                       Gk++eA++ ++e ++
  gi|330508351|ref|YP_004384779.1| 378 GKHDEAIQAYDEAIR 392
                                       99******9999665 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0073       2.9     133     178 ..      11      56 ..       3      64 .. 0.85
   2 ?    6.4   0.1     0.011       4.4     149     181 ..      61      93 ..      57      95 .. 0.83
   3 !    6.7   0.1    0.0091       3.6     145     180 ..      91     126 ..      90     164 .. 0.83
   4 !    8.1   0.1    0.0035       1.4     149     215 ..     163     229 ..     130     232 .. 0.76
   5 !   17.0   0.5   6.8e-06    0.0027     137     224 ..     218     299 ..     203     301 .. 0.81
   6 !    7.9   0.1    0.0039       1.6     145     204 ..     261     317 ..     261     327 .. 0.79
   7 !    7.0   0.2    0.0072       2.9     152     218 ..     302     365 ..     294     368 .. 0.63
   8 ?    5.0   0.1      0.03        12     130     181 ..     347     399 ..     334     402 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0073
                            TPR_15 133 lksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapd 178
                                       l  l   ++ +q +  +++ + +  ++g+ d+A+++y eA++l+p+
  gi|330508351|ref|YP_004384779.1|  11 LLALLTSAQCQQTEEDWFYQGVALADQGKYDEAIKAYDEAIRLDPT 56 
                                       4445566788999999****************************97 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                            TPR_15 149 llaraelyrqegqtdaAlrdyreAlalapdsse 181
                                       ++  + +  ++g++d+A+++y eA++l+p++++
  gi|330508351|ref|YP_004384779.1|  61 WSNKGVAFADQGKHDEAIEAYDEAIRLDPTDAA 93 
                                       66666666789******************9875 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0091
                            TPR_15 145 saafllaraelyrqegqtdaAlrdyreAlalapdss 180
                                       +aa +   +++  ++g+ d+A+++y eA++l+p+++
  gi|330508351|ref|YP_004384779.1|  91 DAAAWGNKGASLADQGKYDEAIEAYDEAIRLDPTDA 126
                                       6788999999999********************975 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0035
                            TPR_15 149 llaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdas 215
                                       ++  +++  ++g+ d+A+++y eA++l+p++ ++  +    l D g+++e   +++a+ ++     +da+
  gi|330508351|ref|YP_004384779.1| 163 WIGKGKSLADQGKYDEAIEAYDEAIRLDPANVAAWGNKGVSLADQGKYDE---AIEAYDEAIrldPTDAA 229
                                       55566777888999999999999999999998888777778888888886...77777666544445555 PP

  == domain 5  score: 17.0 bits;  conditional E-value: 6.8e-06
                            TPR_15 137 eeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraes 212
                                        e  ++   +aa++   + +  ++g++d+A+++y eA++l+p+++++  +    l+D g+++e   +++a+ ++   
  gi|330508351|ref|YP_004384779.1| 218 DEAIRLDpTDAAVWGNKGVSLADQGKHDEAIEAYDEAIRLDPTDAAVWGNKGVSLVDQGKYDE---AIEAYDEA--- 288
                                       455555568999************************************99999*********7...99888876... PP

                            TPR_15 213 dasLwgplaaAl 224
                                         +L+++ aaA+
  gi|330508351|ref|YP_004384779.1| 289 -IRLDPANAAAW 299
                                       .45555555554 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.0039
                            TPR_15 145 saafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellk 204
                                       +aa++   + +  ++g+ d+A+++y eA++l+p+++++  +    l D g+++e   +++
  gi|330508351|ref|YP_004384779.1| 261 DAAVWGNKGVSLVDQGKYDEAIEAYDEAIRLDPANAAAWGNKGVSLADQGKYDE---AIE 317
                                       57888888899999********************99887666666777776665...555 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.0072
                            TPR_15 152 raelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwg 218
                                        + +  ++g+ d+A+++y eA++l+p+++++  +    l+  ++++e    +ka+ ++ + +++L +
  gi|330508351|ref|YP_004384779.1| 302 KGVSLADQGKYDEAIEAYDEAIRLDPTDATAWFNKGNSLNKQKKYDE---SIKAYDEAIRLNPDLAE 365
                                       55566778888889999999999998887765555555554444443...66666666666666555 PP

  == domain 8  score: 5.0 bits;  conditional E-value: 0.03
                            TPR_15 130 aellksleeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsse 181
                                       +e +k   e  +++ + a  ++  +++  ++g++d+A+++y eA++l+ ++++
  gi|330508351|ref|YP_004384779.1| 347 DESIKAYDEAIRLNpDLAEPWIGKGNSLDDQGKHDEAIQAYDEAIRLDSTDAN 399
                                       555666566666664556678888889999****************9998765 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3      0.01       4.2     153     174 ..      31      52 ..      25      57 .. 0.89
   2 !   11.4   4.6   0.00048      0.19     123     175 ..      34      87 ..      33      94 .. 0.84
   3 !    8.4   0.6    0.0039       1.5     150     175 ..      96     121 ..      88     130 .. 0.85
   4 ?    6.1   1.6     0.021       8.2     124     173 ..     103     153 ..     102     160 .. 0.69
   5 ?    7.1   2.0      0.01       4.1     152     176 ..     166     190 ..     136     200 .. 0.76
   6 !   10.1   3.8    0.0012      0.49     123     175 ..     170     223 ..     168     229 .. 0.85
   7 !   14.6   2.1   5.2e-05     0.021     123     175 ..     204     257 ..     200     264 .. 0.89
   8 !   13.3   2.0   0.00012      0.05     123     179 ..     238     295 ..     238     304 .. 0.88
   9 !   13.0   2.3   0.00016     0.064     123     176 ..     272     326 ..     271     335 .. 0.86
  10 !    7.6   1.4    0.0069       2.8     123     174 ..     306     358 ..     305     368 .. 0.77
  11 !    8.0   0.2    0.0052       2.1     152     179 ..     370     397 ..     368     407 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.01
                            TPR_21 153 GDilvaqgkldeAraaYqaAla 174
                                       G +l+ qgk deA +aY++A++
  gi|330508351|ref|YP_004384779.1|  31 GVALADQGKYDEAIKAYDEAIR 52 
                                       77899***************86 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00048
                            TPR_21 123 llaekkydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       l++++kydeA+k+ +++ + +   a++   +G +++ qgk deA +aY++A++ 
  gi|330508351|ref|YP_004384779.1|  34 LADQGKYDEAIKAYDEAiRLDPTIAAAWSNKGVAFADQGKHDEAIEAYDEAIRL 87 
                                       689***********6651556677778889*********************975 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0039
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAlaa 175
                                         +G  l+ qgk deA +aY++A++ 
  gi|330508351|ref|YP_004384779.1|  96 GNKGASLADQGKYDEAIEAYDEAIRL 121
                                       679999*****************975 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.021
                            TPR_21 124 laekkydeAlktL.eakkeeafaalvaelrGDilvaqgkldeAraaYqaAl 173
                                       ++++kydeA+++  ea + +  +a +   +G+ l +q+k de  +aY++A+
  gi|330508351|ref|YP_004384779.1| 103 ADQGKYDEAIEAYdEAIRLDPTDAIAWFNKGNSLNKQKKYDESIKAYDEAI 153
                                       677777777777733344556666666677888888888888888887776 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.01
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaal 176
                                       +G  l+ qgk deA +aY++A++  
  gi|330508351|ref|YP_004384779.1| 166 KGKSLADQGKYDEAIEAYDEAIRLD 190
                                       8999*****************9865 PP

  == domain 6  score: 10.1 bits;  conditional E-value: 0.0012
                            TPR_21 123 llaekkydeAlktLea.kkeeafaalvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       l++++kydeA+++ ++  + +  ++++   +G  l+ qgk deA +aY++A++ 
  gi|330508351|ref|YP_004384779.1| 170 LADQGKYDEAIEAYDEaIRLDPANVAAWGNKGVSLADQGKYDEAIEAYDEAIRL 223
                                       789**********9651566778888899**********************975 PP

  == domain 7  score: 14.6 bits;  conditional E-value: 5.2e-05
                            TPR_21 123 llaekkydeAlktL.eakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       l++++kydeA+++  ea + +  +a+v   +G  l+ qgk deA +aY++A++ 
  gi|330508351|ref|YP_004384779.1| 204 LADQGKYDEAIEAYdEAIRLDPTDAAVWGNKGVSLADQGKHDEAIEAYDEAIRL 257
                                       689***********455677999****************************975 PP

  == domain 8  score: 13.3 bits;  conditional E-value: 0.00012
                            TPR_21 123 llaekkydeAlktL.eakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaaleek 179
                                       l++++k+deA+++  ea + +  +a+v   +G  lv qgk deA +aY++A++   ++
  gi|330508351|ref|YP_004384779.1| 238 LADQGKHDEAIEAYdEAIRLDPTDAAVWGNKGVSLVDQGKYDEAIEAYDEAIRLDPAN 295
                                       5899*********9455677999****************************9876655 PP

  == domain 9  score: 13.0 bits;  conditional E-value: 0.00016
                            TPR_21 123 llaekkydeAlktL.eakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                       l++++kydeA+++  ea + +  +a++   +G  l+ qgk deA +aY++A++  
  gi|330508351|ref|YP_004384779.1| 272 LVDQGKYDEAIEAYdEAIRLDPANAAAWGNKGVSLADQGKYDEAIEAYDEAIRLD 326
                                       689**********944556788899999***********************9865 PP

  == domain 10  score: 7.6 bits;  conditional E-value: 0.0069
                            TPR_21 123 llaekkydeAlktL.eakkeeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       l++++kydeA+++  ea + +  +a +   +G+ l +q+k de  +aY++A++
  gi|330508351|ref|YP_004384779.1| 306 LADQGKYDEAIEAYdEAIRLDPTDATAWFNKGNSLNKQKKYDESIKAYDEAIR 358
                                       57888999998888334556677777778899999999999999999999886 PP

  == domain 11  score: 8.0 bits;  conditional E-value: 0.0052
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaaleek 179
                                       +G+ l  qgk deA +aY++A++  +++
  gi|330508351|ref|YP_004384779.1| 370 KGNSLDDQGKHDEAIQAYDEAIRLDSTD 397
                                       7889999**************9866655 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.046        18     104     126 ..      28      50 ..      17      54 .. 0.86
   2 ?    6.1   0.0     0.027        11     101     126 ..      59      84 ..      55      87 .. 0.85
   3 ?    6.1   0.4     0.028        11      71      83 ..     108     120 ..      82     190 .. 0.52
   4 ?    5.3   0.1     0.048        19     100     126 ..     194     220 ..     168     224 .. 0.79
   5 ?    4.4   0.0     0.093        37     104     126 ..     232     254 ..     226     259 .. 0.84
   6 ?    6.9   0.1     0.016       6.3      51     126 ..     258     322 ..     252     325 .. 0.67
   7 ?    3.1   0.1      0.22        89      45      81 ..     320     356 ..     303     359 .. 0.52
   8 ?    7.3   0.1     0.012       4.6      47     126 ..     322     390 ..     320     395 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.046
                                       HHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrma 126
                                       f ++val++ G++dea+ka+  a
  gi|330508351|ref|YP_004384779.1|  28 FYQGVALADQGKYDEAIKAYDEA 50 
                                       56899999999999999999877 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 101 aavfsravaleelGrkdealkafrma 126
                                       aa  +++va+++ G++dea++a+  a
  gi|330508351|ref|YP_004384779.1|  59 AAWSNKGVAFADQGKHDEAIEAYDEA 84 
                                       456789****************9877 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHHHH CS
                           DUF3856  71 ydealesadkalr 83 
                                       ydea+e+ d+a+r
  gi|330508351|ref|YP_004384779.1| 108 YDEAIEAYDEAIR 120
                                       4444444444332 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.048
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 100 iaavfsravaleelGrkdealkafrma 126
                                       +aa  +++v+l++ G++dea++a+  a
  gi|330508351|ref|YP_004384779.1| 194 VAAWGNKGVSLADQGKYDEAIEAYDEA 220
                                       566678999999999999999999876 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.093
                                       HHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrma 126
                                        +++v+l++ G++dea++a+  a
  gi|330508351|ref|YP_004384779.1| 232 GNKGVSLADQGKHDEAIEAYDEA 254
                                       4899**************99877 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  51 eGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       +  da ++     +l+  g+ydea+e+ d+a+r       l+ ++   W     +++v+l++ G++dea++a+  a
  gi|330508351|ref|YP_004384779.1| 258 DPTDAAVWGNKGVSLVDQGKYDEAIEAYDEAIR-------LDPANAAAW----GNKGVSLADQGKYDEAIEAYDEA 322
                                       555666666666777777777777777777775.......455555555....57888888888888888888765 PP

  == domain 7  score: 3.1 bits;  conditional E-value: 0.22
                                       TS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  45 eeafdheGfdalchaglsealaklgrydealesadka 81 
                                       +ea   +  da ++    ++l k ++yde++++ d+a
  gi|330508351|ref|YP_004384779.1| 320 DEAIRLDPTDATAWFNKGNSLNKQKKYDESIKAYDEA 356
                                       3344444445555555555555555555555555555 PP

  == domain 8  score: 7.3 bits;  conditional E-value: 0.012
                                       ---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                           DUF3856  47 afdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkaf 123
                                       a   +  da ++    ++l k ++yde++++ d+a+r       l+ d  + Wi     ++ +l++ G++dea++a+
  gi|330508351|ref|YP_004384779.1| 322 AIRLDPTDATAWFNKGNSLNKQKKYDESIKAYDEAIR-------LNPDLAEPWIG----KGNSLDDQGKHDEAIQAY 387
                                       5556667888888888888899999999999999986.......78888889985....999*************99 PP

                                       HHH CS
                           DUF3856 124 rma 126
                                         a
  gi|330508351|ref|YP_004384779.1| 388 DEA 390
                                       877 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.082        33      53      70 ..      36      53 ..      27      60 .. 0.89
   2 ?    4.0   0.0      0.13        53      51      70 ..      68      87 ..      58      91 .. 0.85
   3 ?    3.9   0.0      0.14        55      53      70 ..     104     121 ..      97     124 .. 0.88
   4 ?   -0.3   0.0       2.9   1.1e+03      55      69 ..     140     154 ..     126     156 .. 0.77
   5 ?    3.8   0.0      0.15        59      54      70 ..     173     189 ..     169     194 .. 0.88
   6 ?    4.0   0.0      0.13        53      53      70 ..     206     223 ..     199     227 .. 0.88
   7 ?    3.3   0.0      0.22        87      53      70 ..     240     257 ..     233     261 .. 0.88
   8 ?    3.9   0.0      0.14        56      55      70 ..     276     291 ..     269     298 .. 0.87
   9 ?    4.0   0.0      0.13        50      53      70 ..     308     325 ..     301     331 .. 0.88
  10 ?    2.1   0.0      0.53   2.1e+02      55      70 ..     344     359 ..     330     363 .. 0.81
  11 ?    3.0   0.0      0.26     1e+02      55      70 ..     378     393 ..     374     400 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.082
                            ANAPC5 53 dfghneeAvkaleeairl 70
                                      d g+++eA+ka  eairl
  gi|330508351|ref|YP_004384779.1| 36 DQGKYDEAIKAYDEAIRL 53
                                      5699************97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.13
                            ANAPC5 51 hadfghneeAvkaleeairl 70
                                       ad g+++eA++a  eairl
  gi|330508351|ref|YP_004384779.1| 68 FADQGKHDEAIEAYDEAIRL 87
                                      566799************97 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.14
                            ANAPC5  53 dfghneeAvkaleeairl 70 
                                       d g+++eA++a  eairl
  gi|330508351|ref|YP_004384779.1| 104 DQGKYDEAIEAYDEAIRL 121
                                       5599************97 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.9
                            ANAPC5  55 ghneeAvkaleeair 69 
                                        +++e++ka  eai 
  gi|330508351|ref|YP_004384779.1| 140 KKYDESIKAYDEAIG 154
                                       68999*******996 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.15
                            ANAPC5  54 fghneeAvkaleeairl 70 
                                        g+++eA++a  eairl
  gi|330508351|ref|YP_004384779.1| 173 QGKYDEAIEAYDEAIRL 189
                                       589************97 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.13
                            ANAPC5  53 dfghneeAvkaleeairl 70 
                                       d g+++eA++a  eairl
  gi|330508351|ref|YP_004384779.1| 206 DQGKYDEAIEAYDEAIRL 223
                                       5699************97 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.22
                            ANAPC5  53 dfghneeAvkaleeairl 70 
                                       d g+++eA++a  eairl
  gi|330508351|ref|YP_004384779.1| 240 DQGKHDEAIEAYDEAIRL 257
                                       55899***********97 PP

  == domain 8  score: 3.9 bits;  conditional E-value: 0.14
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                       g+++eA++a  eairl
  gi|330508351|ref|YP_004384779.1| 276 GKYDEAIEAYDEAIRL 291
                                       89************98 PP

  == domain 9  score: 4.0 bits;  conditional E-value: 0.13
                            ANAPC5  53 dfghneeAvkaleeairl 70 
                                       d g+++eA++a  eairl
  gi|330508351|ref|YP_004384779.1| 308 DQGKYDEAIEAYDEAIRL 325
                                       5699************97 PP

  == domain 10  score: 2.1 bits;  conditional E-value: 0.53
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                        +++e++ka  eairl
  gi|330508351|ref|YP_004384779.1| 344 KKYDESIKAYDEAIRL 359
                                       6899**********97 PP

  == domain 11  score: 3.0 bits;  conditional E-value: 0.26
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                       g+++eA++a  eairl
  gi|330508351|ref|YP_004384779.1| 378 GKHDEAIQAYDEAIRL 393
                                       789***********98 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.52   2.1e+02     104     124 ..      32      52 ..      16      56 .. 0.78
   2 !   16.0   0.6   3.2e-05     0.013      36     124 ..      29     120 ..      28     124 .. 0.78
   3 ?    0.9   0.0       1.5   5.8e+02     103     123 ..     167     187 ..     138     190 .. 0.66
   4 !   14.1   0.2   0.00012     0.049      53     124 ..     185     256 ..     166     261 .. 0.80
   5 !   11.1   0.0     0.001      0.41      74     124 ..     240     290 ..     232     291 .. 0.93
   6 !   11.6   0.1   0.00069      0.27      73     124 ..     273     324 ..     267     329 .. 0.93
   7 ?    0.5   0.0       1.8   7.3e+02     106     124 ..     374     392 ..     324     399 .. 0.76
   8 ?    0.4   0.0         2     8e+02     109     124 ..     377     392 ..     368     426 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.52
                                       HHHHHTT-HHHHHHHHHHHHH CS
                              BTAD 104 rAlarsGrqaeALevYerlrr 124
                                        Ala +G+  eA+++Y+++ r
  gi|330508351|ref|YP_004384779.1|  32 VALADQGKYDEAIKAYDEAIR 52 
                                       589999999999999998765 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.2e-05
                                       --SSTTGGGTT...STTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHT CS
                              BTAD  36 wrGpaladlea...gewleaererleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlars 109
                                       ++G alad  +      + +e+ rl+    +a      a +  G+++ea++ ++++++++P++ +++    + la +
  gi|330508351|ref|YP_004384779.1|  29 YQGVALADQGKydeAIKAYDEAIRLDPTIAAAWSNKGVAFADQGKHDEAIEAYDEAIRLDPTDAAAWGNKGASLADQ 105
                                       56666666444333334455666777777777777777888999********************************* PP

                                       T-HHHHHHHHHHHHH CS
                              BTAD 110 GrqaeALevYerlrr 124
                                       G+  eA+e+Y+++ r
  gi|330508351|ref|YP_004384779.1| 106 GKYDEAIEAYDEAIR 120
                                       **********99865 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.5
                                       HHHHHHTT-HHHHHHHHHHHH CS
                              BTAD 103 mrAlarsGrqaeALevYerlr 123
                                        + la +G+  eA+e+Y+++ 
  gi|330508351|ref|YP_004384779.1| 167 GKSLADQGKYDEAIEAYDEAI 187
                                       456777788888888887765 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  53 ererleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       e+ rl+   ++a       ++  G+++ea++ ++++++++P++ + +      la +G+  eA+e+Y+++ r
  gi|330508351|ref|YP_004384779.1| 185 EAIRLDPANVAAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTDAAVWGNKGVSLADQGKHDEAIEAYDEAIR 256
                                       555556666666666666677889999999999999999999999999999999999999999999998765 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.001
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                         G+++ea++ ++++++++P++ + +      l  +G+  eA+e+Y+++ r
  gi|330508351|ref|YP_004384779.1| 240 DQGKHDEAIEAYDEAIRLDPTDAAVWGNKGVSLVDQGKYDEAIEAYDEAIR 290
                                       679*******************************************99865 PP

  == domain 6  score: 11.6 bits;  conditional E-value: 0.00069
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       +  G+++ea++ ++++++++P + +++      la +G+  eA+e+Y+++ r
  gi|330508351|ref|YP_004384779.1| 273 VDQGKYDEAIEAYDEAIRLDPANAAAWGNKGVSLADQGKYDEAIEAYDEAIR 324
                                       56799******************************************99865 PP

  == domain 7  score: 0.5 bits;  conditional E-value: 1.8
                                       HHHTT-HHHHHHHHHHHHH CS
                              BTAD 106 larsGrqaeALevYerlrr 124
                                       l  +G+  eA+++Y+++ r
  gi|330508351|ref|YP_004384779.1| 374 LDDQGKHDEAIQAYDEAIR 392
                                       4455666666666666544 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 2
                                       TT-HHHHHHHHHHHHH CS
                              BTAD 109 sGrqaeALevYerlrr 124
                                       +G+  eA+++Y+++ r
  gi|330508351|ref|YP_004384779.1| 377 QGKHDEAIQAYDEAIR 392
                                       3444444444444433 PP

>> Imm31  Immunity protein 31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.61   2.4e+02      31      48 ..      32      49 ..      29      56 .. 0.83
   2 ?    0.8   0.0       1.1   4.4e+02      15      48 ..      54      83 ..      49      87 .. 0.73
   3 ?    6.0   0.1     0.027        11      14      48 ..      87     117 ..      82     125 .. 0.81
   4 ?    4.0   0.0      0.11        46      30      48 ..     167     185 ..     155     190 .. 0.88
   5 ?    4.8   0.0     0.064        26      19      48 ..     194     219 ..     185     223 .. 0.76
   6 ?    6.3   0.0     0.021       8.3      14      48 ..     223     253 ..     218     257 .. 0.83
   7 ?    7.1   0.0     0.012       4.8      14      48 ..     257     287 ..     253     292 .. 0.83
   8 ?    6.5   0.0     0.018       7.3      14      48 ..     291     321 ..     287     330 .. 0.83
   9 ?    6.4   0.0      0.02       8.1      30      48 ..     371     389 ..     362     410 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.61
                             Imm31 31 rseddqGefeyavfiyad 48
                                       +  dqG+++ a+ +y +
  gi|330508351|ref|YP_004384779.1| 32 VALADQGKYDEAIKAYDE 49
                                      5668***********964 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.1
                             Imm31 15 dailaelhGerGvvlGrseddqGefeyavfiyad 48
                                      d+ +a  + ++Gv       dqG+++ a+ +y +
  gi|330508351|ref|YP_004384779.1| 54 DPTIAAAWSNKGVA----FADQGKHDEAIEAYDE 83
                                      55666666666654....4799***999999964 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.027
                             Imm31  14 tdailaelhGerGvvlGrseddqGefeyavfiyad 48 
                                        d+  a  +G++G+    s  dqG+++ a+ +y +
  gi|330508351|ref|YP_004384779.1|  87 LDPTDAAAWGNKGA----SLADQGKYDEAIEAYDE 117
                                       56777888999876....678***********964 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.11
                             Imm31  30 GrseddqGefeyavfiyad 48 
                                       G+s  dqG+++ a+ +y +
  gi|330508351|ref|YP_004384779.1| 167 GKSLADQGKYDEAIEAYDE 185
                                       8999************964 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.064
                             Imm31  19 aelhGerGvvlGrseddqGefeyavfiyad 48 
                                          +G++Gv    s  dqG+++ a+ +y +
  gi|330508351|ref|YP_004384779.1| 194 VAAWGNKGV----SLADQGKYDEAIEAYDE 219
                                       556777765....778***********964 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.021
                             Imm31  14 tdailaelhGerGvvlGrseddqGefeyavfiyad 48 
                                        d+  a ++G++Gv    s  dqG+++ a+ +y +
  gi|330508351|ref|YP_004384779.1| 223 LDPTDAAVWGNKGV----SLADQGKHDEAIEAYDE 253
                                       57888999***987....6689********99964 PP

  == domain 7  score: 7.1 bits;  conditional E-value: 0.012
                             Imm31  14 tdailaelhGerGvvlGrseddqGefeyavfiyad 48 
                                        d+  a ++G++Gv    s  dqG+++ a+ +y +
  gi|330508351|ref|YP_004384779.1| 257 LDPTDAAVWGNKGV----SLVDQGKYDEAIEAYDE 287
                                       57888999***987....668***********964 PP

  == domain 8  score: 6.5 bits;  conditional E-value: 0.018
                             Imm31  14 tdailaelhGerGvvlGrseddqGefeyavfiyad 48 
                                        d+  a  +G++Gv    s  dqG+++ a+ +y +
  gi|330508351|ref|YP_004384779.1| 291 LDPANAAAWGNKGV----SLADQGKYDEAIEAYDE 321
                                       57888889999987....668***********964 PP

  == domain 9  score: 6.4 bits;  conditional E-value: 0.02
                             Imm31  30 GrseddqGefeyavfiyad 48 
                                       G s ddqG+++ a+++y +
  gi|330508351|ref|YP_004384779.1| 371 GNSLDDQGKHDEAIQAYDE 389
                                       8899*************65 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.013         5     205     258 ..      28      81 ..      16      92 .. 0.85
   2 ?   -1.8   0.0         4   1.6e+03     214     245 ..     105     136 ..      82     151 .. 0.69
   3 !   10.6   0.0   0.00067      0.27     169     258 ..     159     251 ..     148     261 .. 0.81
   4 ?    6.7   0.0     0.011       4.3     206     260 ..     267     321 ..     250     354 .. 0.79
   5 ?   -1.0   0.1       2.3   9.3e+02     215     251 ..     378     414 ..     375     431 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.013
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHH CS
                        Coatomer_E 205 ngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsern 258
                                         + v+   +g+y+eA +   ea+  d+  + + +N  va  + gk +e++e +
  gi|330508351|ref|YP_004384779.1|  28 FYQGVALADQGKYDEAIKAYDEAIRLDPTIAAAWSNKGVAFADQGKHDEAIEAY 81 
                                       5577788889**************************************998865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4
                                       TT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHH CS
                        Coatomer_E 214 lgryeeAeslLkeaLdkdakdeetLiNlvvaa 245
                                       +g+y+eA +   ea+  d+ d+ +  N   + 
  gi|330508351|ref|YP_004384779.1| 105 QGKYDEAIEAYDEAIRLDPTDAIAWFNKGNSL 136
                                       67788888888888888877776666654444 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00067
                                       HHHHHH...HHHH-TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHH CS
                        Coatomer_E 169 LAqawv...klavggekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlv 242
                                       LA+ w+   k+ +  +k+ +A   ++e     + + +    k v    +g+y+eA +   ea+  d+ d+ +  N  
  gi|330508351|ref|YP_004384779.1| 159 LAEPWIgkgKSLADQGKYDEAIEAYDEAIRLDPANVAAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTDAAVWGNKG 235
                                       66666633334555688999999999987775666666666777777899*************************** PP

                                       HHHHHTT--HHHHHHH CS
                        Coatomer_E 243 vaaqhlgkdaevsern 258
                                       v+  + gk +e++e +
  gi|330508351|ref|YP_004384779.1| 236 VSLADQGKHDEAIEAY 251
                                       **********998765 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.011
                                       HHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHHH CS
                        Coatomer_E 206 gkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernls 260
                                        k v  + +g+y+eA +   ea+  d+ ++ +  N  v+  + gk +e++e + +
  gi|330508351|ref|YP_004384779.1| 267 NKGVSLVDQGKYDEAIEAYDEAIRLDPANAAAWGNKGVSLADQGKYDEAIEAYDE 321
                                       46677788999**********************************9999887655 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 2.3
                                       T-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-- CS
                        Coatomer_E 215 gryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkd 251
                                       g+++eA +   ea+  d+ d+++  N  v+ ++ +++
  gi|330508351|ref|YP_004384779.1| 378 GKHDEAIQAYDEAIRLDSTDANAWYNKGVVLHNQNRP 414
                                       788999999**************99998888777766 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       9.2   3.7e+03       8      27 ..      71      90 ..      67     104 .. 0.66
   2 !    7.8   0.0    0.0082       3.3      62     102 ..     111     151 ..     107     157 .. 0.91
   3 ?   -1.9   0.0       8.5   3.4e+03       7      26 ..     240     259 ..     236     277 .. 0.69
   4 !    9.0   0.0    0.0035       1.4      62     103 ..     315     356 ..     311     360 .. 0.91
   5 ?   -1.7   0.0       7.1   2.8e+03      62      81 ..     383     402 ..     376     411 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.2
                            DUF627  8 rgnhikALeiiedlisrhge 27
                                      +g h +A+e  +++i+    
  gi|330508351|ref|YP_004384779.1| 71 QGKHDEAIEAYDEAIRLDPT 90
                                      66666777666666654444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0082
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakr 102
                                       ++e++ ea +l    A   f+ ++ l+++++Y +++k   +
  gi|330508351|ref|YP_004384779.1| 111 AIEAYDEAIRLDPTDAIAWFNKGNSLNKQKKYDESIKAYDE 151
                                       8*********************************9987655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 8.5
                            DUF627   7 argnhikALeiiedlisrhg 26 
                                       ++g h +A+e  +++i+   
  gi|330508351|ref|YP_004384779.1| 240 DQGKHDEAIEAYDEAIRLDP 259
                                       56777777777777665444 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0035
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakra 103
                                       ++e++ ea +l    A+  f+ ++ l+++++Y +++k   +a
  gi|330508351|ref|YP_004384779.1| 315 AIEAYDEAIRLDPTDATAWFNKGNSLNKQKKYDESIKAYDEA 356
                                       8**********************************9976665 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 7.1
                            DUF627  62 svecfseavelsrfyArsLf 81 
                                       +++++ ea +l +  A+  +
  gi|330508351|ref|YP_004384779.1| 383 AIQAYDEAIRLDSTDANAWY 402
                                       67777777777766666555 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   0.1       0.1        41       3      66 ..      79     147 ..      18     156 .. 0.67
   2 ?    2.8   0.0      0.28   1.1e+02       3      40 ..     181     220 ..     179     233 .. 0.89
   3 !    7.8   0.0    0.0079       3.1       3      67 ..     283     352 ..     247     358 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.1
                      SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalk 66 
                                       e+y++ +rl+ +    +  k  +l   +ky+ea+++ +++     ++    f k   l k kky ++ k
  gi|330508351|ref|YP_004384779.1|  79 EAYDEAIRLDPTDAAAWgnKGASLADQGKYDEAIEAYDEAIrldPTDAIAWFNKGNSLNKQKKYDESIK 147
                                       455555555555555555566666667777777777766652223334455677777777777777666 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.28
                      SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkg 40 
                                       e+y++ +rl+ +++  +  k v+l   +ky+ea+++ +++
  gi|330508351|ref|YP_004384779.1| 181 EAYDEAIRLDPANVAAWgnKGVSLADQGKYDEAIEAYDEA 220
                                       7899999999999999999**************9988765 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0079
                      SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalki 67 
                                       e+y++ +rl+ ++   +  k v+l   +ky+ea+++ +++     ++    f k   l k kky ++ k 
  gi|330508351|ref|YP_004384779.1| 283 EAYDEAIRLDPANAAAWgnKGVSLADQGKYDEAIEAYDEAIrldPTDATAWFNKGNSLNKQKKYDESIKA 352
                                       6788888888887777777999999999999999998887644455677889999999999999998876 PP

>> DUF4326  Domain of unknown function (DUF4326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0       1.1   4.6e+02      20      47 ..      60      87 ..      43      94 .. 0.83
   2 ?    2.3   0.0      0.71   2.8e+02      20      48 ..      94     122 ..      73     152 .. 0.72
   3 ?    4.6   0.0      0.13        53      20      45 ..     230     255 ..     140     277 .. 0.75
   4 ?    0.2   0.0       3.3   1.3e+03      20      47 ..     264     291 ..     258     298 .. 0.81
   5 ?    3.7   0.0      0.26     1e+02      20      60 ..     298     338 ..     290     413 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.1
                           DUF4326 20 klgNpFvvgqelgereevvekyreylee 47
                                       + N  v +++ g+++e++e+y e ++ 
  gi|330508351|ref|YP_004384779.1| 60 AWSNKGVAFADQGKHDEAIEAYDEAIRL 87
                                      5888888999999*********998875 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.71
                           DUF4326  20 klgNpFvvgqelgereevvekyreyleer 48 
                                        +gN     ++ g+ +e++e+y e ++ +
  gi|330508351|ref|YP_004384779.1|  94 AWGNKGASLADQGKYDEAIEAYDEAIRLD 122
                                       5999888777789999******9999877 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.13
                           DUF4326  20 klgNpFvvgqelgereevvekyreyl 45 
                                        +gN  v  ++ g+++e++e+y e +
  gi|330508351|ref|YP_004384779.1| 230 VWGNKGVSLADQGKHDEAIEAYDEAI 255
                                       46666666555566666666666665 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 3.3
                           DUF4326  20 klgNpFvvgqelgereevvekyreylee 47 
                                        +gN  v   + g+ +e++e+y e ++ 
  gi|330508351|ref|YP_004384779.1| 264 VWGNKGVSLVDQGKYDEAIEAYDEAIRL 291
                                       588988777777999*******998875 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.26
                           DUF4326  20 klgNpFvvgqelgereevvekyreyleeraekdeelkaale 60 
                                        +gN  v  ++ g+ +e++e+y e ++ +  +++   ++ +
  gi|330508351|ref|YP_004384779.1| 298 AWGNKGVSLADQGKYDEAIEAYDEAIRLDPTDATAWFNKGN 338
                                       58888888788789999999999998877444443333333 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2     0.003       1.2     117     180 ..      31      95 ..      22     101 .. 0.87
   2 ?    0.7   0.0       1.1   4.4e+02     152     180 ..     101     129 ..      97     136 .. 0.85
   3 ?    1.4   0.1      0.64   2.5e+02     152     180 ..     169     197 ..     137     205 .. 0.89
   4 !    9.7   0.0    0.0018      0.73     121     180 ..     205     265 ..     199     271 .. 0.89
   5 !    8.6   0.1     0.004       1.6     122     180 ..     240     299 ..     235     303 .. 0.88
   6 !    7.4   0.2    0.0095       3.8     121     180 ..     273     333 ..     266     341 .. 0.84
   7 ?    0.8   0.1      0.99   3.9e+02     152     180 ..     373     401 ..     338     405 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.003
                           Wzy_C_2 117 gllplspenlaaklalarklihlsPepa.vierlilslallGdedeAeqilararalfpeedakw 180
                                       g++ +++ ++++ ++++ ++i+l P+ a   ++  ++ a +G++deA   +++a+ l p ++a+w
  gi|330508351|ref|YP_004384779.1|  31 GVALADQGKYDEAIKAYDEAIRLDPTIAaAWSNKGVAFADQGKHDEAIEAYDEAIRLDPTDAAAW 95 
                                       5666789999***************965168999****************************999 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.1
                           Wzy_C_2 152 slallGdedeAeqilararalfpeedakw 180
                                       sla +G+ deA   +++a+ l p ++ +w
  gi|330508351|ref|YP_004384779.1| 101 SLADQGKYDEAIEAYDEAIRLDPTDAIAW 129
                                       788899*******9999999988888888 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.64
                           Wzy_C_2 152 slallGdedeAeqilararalfpeedakw 180
                                       sla +G+ deA   +++a+ l p++ a+w
  gi|330508351|ref|YP_004384779.1| 169 SLADQGKYDEAIEAYDEAIRLDPANVAAW 197
                                       78899**************9999999999 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0018
                           Wzy_C_2 121 lspenlaaklalarklihlsPe.pavierlilslallGdedeAeqilararalfpeedakw 180
                                       +++ ++++ ++++ ++i+l P+ +av  +  +sla +G++deA   +++a+ l p ++a w
  gi|330508351|ref|YP_004384779.1| 205 ADQGKYDEAIEAYDEAIRLDPTdAAVWGNKGVSLADQGKHDEAIEAYDEAIRLDPTDAAVW 265
                                       5788999**************8346889***********************9999998888 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.004
                           Wzy_C_2 122 spenlaaklalarklihlsPe.pavierlilslallGdedeAeqilararalfpeedakw 180
                                       ++ + ++ ++++ ++i+l P+ +av  +  +sl+ +G+ deA   +++a+ l p+++a+w
  gi|330508351|ref|YP_004384779.1| 240 DQGKHDEAIEAYDEAIRLDPTdAAVWGNKGVSLVDQGKYDEAIEAYDEAIRLDPANAAAW 299
                                       567778999999********834688999****************************999 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.0095
                           Wzy_C_2 121 lspenlaaklalarklihlsPepa.vierlilslallGdedeAeqilararalfpeedakw 180
                                       +++ ++++ ++++ ++i+l P  a    +  +sla +G+ deA   +++a+ l p ++ +w
  gi|330508351|ref|YP_004384779.1| 273 VDQGKYDEAIEAYDEAIRLDPANAaAWGNKGVSLADQGKYDEAIEAYDEAIRLDPTDATAW 333
                                       56788999999999999999976515789999******************99999999999 PP

  == domain 7  score: 0.8 bits;  conditional E-value: 0.99
                           Wzy_C_2 152 slallGdedeAeqilararalfpeedakw 180
                                       sl  +G++deA q +++a+ l   ++ +w
  gi|330508351|ref|YP_004384779.1| 373 SLDDQGKHDEAIQAYDEAIRLDSTDANAW 401
                                       66679***********9998766666666 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 ?    4.6   0.1     0.053        21     129     149 ..      32      52 ..      30      64 .. 0.85
   2 ?    3.6   0.0      0.11        42     126     149 ..      63      86 ..      59      94 .. 0.84
   3 ?    4.5   0.1     0.056        22     130     156 ..     101     127 ..      96     153 .. 0.80
   4 ?    3.2   0.0      0.14        57     131     151 ..     170     190 ..     168     197 .. 0.84
   5 ?    4.0   0.0     0.078        31     129     149 ..     202     222 ..     198     230 .. 0.84
   6 ?    2.6   0.0      0.21        85     129     149 ..     236     256 ..     232     264 .. 0.84
   7 ?    4.0   0.0      0.08        32     129     149 ..     270     290 ..     266     298 .. 0.82
   8 ?    4.6   0.1     0.052        21     129     151 ..     304     326 ..     300     344 .. 0.79
   9 ?    0.4   0.0         1   4.1e+02     134     154 ..     377     397 ..     373     423 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.053
                         4HB_MCP_1 129 lelakegkkdeAyqlyetegr 149
                                       ++la +gk+deA+++y++ +r
  gi|330508351|ref|YP_004384779.1|  32 VALADQGKYDEAIKAYDEAIR 52 
                                       689**************9886 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.11
                         4HB_MCP_1 126 kkvlelakegkkdeAyqlyetegr 149
                                       +k +++a +gk+deA+++y++ +r
  gi|330508351|ref|YP_004384779.1|  63 NKGVAFADQGKHDEAIEAYDEAIR 86 
                                       66789**************99886 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.056
                         4HB_MCP_1 130 elakegkkdeAyqlyetegrparekli 156
                                        la +gk+deA+++y++ +r    ++i
  gi|330508351|ref|YP_004384779.1| 101 SLADQGKYDEAIEAYDEAIRLDPTDAI 127
                                       6999************99986665555 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.14
                         4HB_MCP_1 131 lakegkkdeAyqlyetegrpa 151
                                       la +gk+deA+++y++ +r  
  gi|330508351|ref|YP_004384779.1| 170 LADQGKYDEAIEAYDEAIRLD 190
                                       899************998755 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.078
                         4HB_MCP_1 129 lelakegkkdeAyqlyetegr 149
                                       + la +gk+deA+++y++ +r
  gi|330508351|ref|YP_004384779.1| 202 VSLADQGKYDEAIEAYDEAIR 222
                                       6799************99886 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.21
                         4HB_MCP_1 129 lelakegkkdeAyqlyetegr 149
                                       + la +gk+deA+++y++ +r
  gi|330508351|ref|YP_004384779.1| 236 VSLADQGKHDEAIEAYDEAIR 256
                                       6799************99886 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.08
                         4HB_MCP_1 129 lelakegkkdeAyqlyetegr 149
                                       + l+ +gk+deA+++y++ +r
  gi|330508351|ref|YP_004384779.1| 270 VSLVDQGKYDEAIEAYDEAIR 290
                                       6799*************9987 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.052
                         4HB_MCP_1 129 lelakegkkdeAyqlyetegrpa 151
                                       + la +gk+deA+++y++ +r  
  gi|330508351|ref|YP_004384779.1| 304 VSLADQGKYDEAIEAYDEAIRLD 326
                                       6799*************998744 PP

  == domain 9  score: 0.4 bits;  conditional E-value: 1
                         4HB_MCP_1 134 egkkdeAyqlyetegrparek 154
                                       +gk+deA+q+y++ +r    +
  gi|330508351|ref|YP_004384779.1| 377 QGKHDEAIQAYDEAIRLDSTD 397
                                       799999999999988755544 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.2    0.0049       1.9      20      63 ..      41      85 ..      33      93 .. 0.80
   2 ?    2.3   0.0       0.3   1.2e+02      38      63 ..      94     119 ..      90     131 .. 0.82
   3 ?    2.3   0.1      0.29   1.2e+02      39      63 ..     163     187 ..     131     195 .. 0.77
   4 ?    1.4   0.0      0.58   2.3e+02      42      63 ..     200     221 ..     194     231 .. 0.79
   5 ?    0.8   0.0      0.84   3.4e+02      45      63 ..     237     255 ..     228     265 .. 0.79
   6 ?    0.4   0.0       1.1   4.5e+02      46      63 ..     272     289 ..     262     293 .. 0.79
   7 ?    2.5   0.1      0.26     1e+02      37      63 ..     297     323 ..     279     336 .. 0.80
   8 ?    0.6   0.0         1     4e+02      47      63 ..     375     392 ..     336     403 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0049
                                      HHHHHHHH.HTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7 20 daelkdak.enlgkeeirrakldlaehYlkigdleeAlkaysrir 63
                                      d+ +k +      +  i++a+ +++  +++ g+++eA++ay +++
  gi|330508351|ref|YP_004384779.1| 41 DEAIKAYDeAIRLDPTIAAAWSNKGVAFADQGKHDEAIEAYDEAI 85
                                      555666553445677899***********************9964 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  38 akldlaehYlkigdleeAlkaysrir 63 
                                       a+ +++   ++ g+++eA++ay +++
  gi|330508351|ref|YP_004384779.1|  94 AWGNKGASLADQGKYDEAIEAYDEAI 119
                                       566778888999**********9954 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  39 kldlaehYlkigdleeAlkaysrir 63 
                                       +  +++  ++ g+++eA++ay +++
  gi|330508351|ref|YP_004384779.1| 163 WIGKGKSLADQGKYDEAIEAYDEAI 187
                                       55678888999**********9964 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.58
                                       HHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  42 laehYlkigdleeAlkaysrir 63 
                                       ++   ++ g+++eA++ay +++
  gi|330508351|ref|YP_004384779.1| 200 KGVSLADQGKYDEAIEAYDEAI 221
                                       56666788**********9964 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.84
                                       HHHHCT-HHHHHHHHHTCC CS
                              RPN7  45 hYlkigdleeAlkaysrir 63 
                                         ++ g+++eA++ay +++
  gi|330508351|ref|YP_004384779.1| 237 SLADQGKHDEAIEAYDEAI 255
                                       567889*********9964 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1.1
                                       HHHCT-HHHHHHHHHTCC CS
                              RPN7  46 YlkigdleeAlkaysrir 63 
                                        ++ g+++eA++ay +++
  gi|330508351|ref|YP_004384779.1| 272 LVDQGKYDEAIEAYDEAI 289
                                       56789*********9964 PP

  == domain 7  score: 2.5 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  37 rakldlaehYlkigdleeAlkaysrir 63 
                                       +a+ +++   ++ g+++eA++ay +++
  gi|330508351|ref|YP_004384779.1| 297 AAWGNKGVSLADQGKYDEAIEAYDEAI 323
                                       5667788888999**********9953 PP

  == domain 8  score: 0.6 bits;  conditional E-value: 1
                                       HHCT-HHHHHHHHHT.CC CS
                              RPN7  47 lkigdleeAlkaysr.ir 63 
                                        + g+++eA++ay + ir
  gi|330508351|ref|YP_004384779.1| 375 DDQGKHDEAIQAYDEaIR 392
                                       56799999***9999444 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.043        17       5      33 ..      28      56 ..      25      60 .. 0.91
   2 ?    0.3   0.0       1.9   7.7e+02      14      33 ..     105     124 ..     103     126 .. 0.89
   3 ?    2.8   0.0      0.32   1.3e+02      14      34 ..     173     193 ..     171     196 .. 0.92
   4 ?    0.6   0.0       1.6   6.3e+02      14      33 ..     207     226 ..     202     229 .. 0.89
   5 ?    3.4   0.0       0.2        79      14      35 ..     275     296 ..     272     299 .. 0.91
   6 ?    0.8   0.0       1.3   5.2e+02      14      33 ..     309     328 ..     304     332 .. 0.88
   7 ?    0.7   0.1       1.4   5.7e+02      13      33 ..     342     362 ..     340     364 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.043
                                      HHHHHHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  5 YylAlGhyklgeYseArryvdalLeiEPe 33
                                      +y  ++ + +g+Y+eA +  d  ++++P 
  gi|330508351|ref|YP_004384779.1| 28 FYQGVALADQGKYDEAIKAYDEAIRLDPT 56
                                      89999********************9996 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.9
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       +g+Y+eA +  d  ++++P 
  gi|330508351|ref|YP_004384779.1| 105 QGKYDEAIEAYDEAIRLDPT 124
                                       589**********9999996 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.32
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                       +g+Y+eA +  d  ++++P n
  gi|330508351|ref|YP_004384779.1| 173 QGKYDEAIEAYDEAIRLDPAN 193
                                       589****************99 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.6
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       +g+Y+eA +  d  ++++P 
  gi|330508351|ref|YP_004384779.1| 207 QGKYDEAIEAYDEAIRLDPT 226
                                       689***********999996 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.2
                                       HT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenr 35 
                                       +g+Y+eA +  d  ++++P n 
  gi|330508351|ref|YP_004384779.1| 275 QGKYDEAIEAYDEAIRLDPANA 296
                                       589*****************96 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 1.3
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       +g+Y+eA +  d  ++++P 
  gi|330508351|ref|YP_004384779.1| 309 QGKYDEAIEAYDEAIRLDPT 328
                                       689*************9997 PP

  == domain 7  score: 0.7 bits;  conditional E-value: 1.4
                                       HHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPe 33 
                                       k+++Y+e+ +  d  +++ P+
  gi|330508351|ref|YP_004384779.1| 342 KQKKYDESIKAYDEAIRLNPD 362
                                       8999****9999999999987 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.28   1.1e+02      13      28 ..      34      49 ..      32      52 .. 0.88
   2 ?    1.4   0.0      0.94   3.7e+02      12      28 ..      67      83 ..      66      86 .. 0.88
   3 ?    1.8   0.0       0.7   2.8e+02      13      28 ..     102     117 ..     100     120 .. 0.87
   4 ?    1.9   0.0      0.64   2.6e+02      13      28 ..     170     185 ..     168     188 .. 0.87
   5 ?    1.5   0.0      0.86   3.4e+02      14      28 ..     205     219 ..     203     222 .. 0.87
   6 ?    0.4   0.0       1.9   7.6e+02      14      28 ..     239     253 ..     237     256 .. 0.86
   7 ?    1.7   0.0      0.75     3e+02      13      28 ..     272     287 ..     271     290 .. 0.87
   8 ?    1.6   0.0      0.79   3.2e+02      14      28 ..     307     321 ..     305     326 .. 0.86
   9 ?   -0.7   0.0       4.2   1.7e+03      16      28 ..     377     389 ..     374     393 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.28
                             PPR_2 13 lckkgkveeAfklfne 28
                                      l+ +gk++eA+k ++e
  gi|330508351|ref|YP_004384779.1| 34 LADQGKYDEAIKAYDE 49
                                      6789**********98 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.94
                             PPR_2 12 glckkgkveeAfklfne 28
                                      +++ +gk +eA++ ++e
  gi|330508351|ref|YP_004384779.1| 67 AFADQGKHDEAIEAYDE 83
                                      57889********9998 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.7
                             PPR_2  13 lckkgkveeAfklfne 28 
                                       l+ +gk++eA++ ++e
  gi|330508351|ref|YP_004384779.1| 102 LADQGKYDEAIEAYDE 117
                                       6679********9998 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.64
                             PPR_2  13 lckkgkveeAfklfne 28 
                                       l+ +gk++eA++ ++e
  gi|330508351|ref|YP_004384779.1| 170 LADQGKYDEAIEAYDE 185
                                       6789********9998 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.86
                             PPR_2  14 ckkgkveeAfklfne 28 
                                       + +gk++eA++ ++e
  gi|330508351|ref|YP_004384779.1| 205 ADQGKYDEAIEAYDE 219
                                       679********9998 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1.9
                             PPR_2  14 ckkgkveeAfklfne 28 
                                       + +gk +eA++ ++e
  gi|330508351|ref|YP_004384779.1| 239 ADQGKHDEAIEAYDE 253
                                       679********9998 PP

  == domain 7  score: 1.7 bits;  conditional E-value: 0.75
                             PPR_2  13 lckkgkveeAfklfne 28 
                                       l+ +gk++eA++ ++e
  gi|330508351|ref|YP_004384779.1| 272 LVDQGKYDEAIEAYDE 287
                                       5679********9998 PP

  == domain 8  score: 1.6 bits;  conditional E-value: 0.79
                             PPR_2  14 ckkgkveeAfklfne 28 
                                       + +gk++eA++ ++e
  gi|330508351|ref|YP_004384779.1| 307 ADQGKYDEAIEAYDE 321
                                       679********9998 PP

  == domain 9  score: -0.7 bits;  conditional E-value: 4.2
                             PPR_2  16 kgkveeAfklfne 28 
                                       +gk +eA++ ++e
  gi|330508351|ref|YP_004384779.1| 377 QGKHDEAIQAYDE 389
                                       7999****99998 PP

>> Adeno_VII  Adenoviral core protein VII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.21        86      31      69 ..      82     120 ..      46     142 .. 0.80
   2 ?    2.9   0.0      0.41   1.6e+02      32      74 ..     185     226 ..     177     232 .. 0.80
   3 ?    3.9   0.0      0.19        77       5      68 ..     223     289 ..     220     309 .. 0.63
   4 ?    5.9   0.0     0.049        19       3      71 ..     255     325 ..     253     347 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.21
                         Adeno_VII  31 kqpvrvrgyyraqwGahkrgltartslddaidavveear 69 
                                        + +r+ +   a wG++  +l+ +   d+ai+a  e  r
  gi|330508351|ref|YP_004384779.1|  82 DEAIRLDPTDAAAWGNKGASLADQGKYDEAIEAYDEAIR 120
                                       567899999999****99999999999999999765544 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.41
                         Adeno_VII  32 qpvrvrgyyraqwGahkrgltartslddaidavveearnytpt 74 
                                       + +r+ +   a wG++  +l+ +   d+ai+a  e      pt
  gi|330508351|ref|YP_004384779.1| 185 EAIRLDPANVAAWGNKGVSLADQGKYDEAIEAYDEA-IRLDPT 226
                                       5688999999*****9999999********997554.445555 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.19
                         Adeno_VII   5 vspsdntGwGlrftskmfatakk....rsdkqpvrvrgyyraqwGahkrgltartslddaidavveea 68 
                                       + p+d + wG +   ++   +k      +  + +r+ +   a wG++  +l  +   d+ai+a  e  
  gi|330508351|ref|YP_004384779.1| 223 LDPTDAAVWGNK-GVSLADQGKHdeaiEAYDEAIRLDPTDAAVWGNKGVSLVDQGKYDEAIEAYDEAI 289
                                       556666667666.3333333333111123456788888888888887777788888888888765544 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.049
                         Adeno_VII   3 ilvspsdntGwGlrftskmfatakk...rsdkqpvrvrgyyraqwGahkrgltartslddaidavveearny 71 
                                       i + p+d + wG +  s +  +       +  + +r+ +   a wG++  +l+ +   d+ai+a  e  r  
  gi|330508351|ref|YP_004384779.1| 255 IRLDPTDAAVWGNKGVSLVDQGKYDeaiEAYDEAIRLDPANAAAWGNKGVSLADQGKYDEAIEAYDEAIR-L 325
                                       556788888888874444444333211134567899***********999999999******99765544.4 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.89   3.5e+02      26      50 ..      26      50 ..      14      57 .. 0.85
   2 ?    3.0   0.1      0.28   1.1e+02      24      50 ..      58      84 ..      48      88 .. 0.91
   3 ?    2.0   0.0      0.56   2.2e+02      23      50 ..      91     118 ..      89     124 .. 0.92
   4 ?    2.6   0.0      0.38   1.5e+02      23      50 ..     193     220 ..     182     226 .. 0.92
   5 ?   -0.3   0.0       2.9   1.2e+03      24      50 ..     228     254 ..     225     258 .. 0.91
   6 ?    0.9   0.0       1.3     5e+02      24      50 ..     262     288 ..     259     293 .. 0.91
   7 ?    4.1   0.0      0.13        52      23      50 ..     295     322 ..     293     328 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.89
                                      HCT-SEEEEEEEEBTTHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP 26 elglkaiaiTDhgnlfgyvefykaa 50
                                      ++ ++ +a+ D+g +++++++y +a
  gi|330508351|ref|YP_004384779.1| 26 DWFYQGVALADQGKYDEAIKAYDEA 50
                                      566789****************998 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.28
                                      HHHCT-SEEEEEEEEBTTHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP 24 akelglkaiaiTDhgnlfgyvefykaa 50
                                      a+++  k +a+ D+g  ++++e+y +a
  gi|330508351|ref|YP_004384779.1| 58 AAAWSNKGVAFADQGKHDEAIEAYDEA 84
                                      7899999*****************998 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.56
                                       HHHHCT-SEEEEEEEEBTTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  23 kakelglkaiaiTDhgnlfgyvefykaa 50 
                                        a+++g k   + D+g +++++e+y +a
  gi|330508351|ref|YP_004384779.1|  91 DAAAWGNKGASLADQGKYDEAIEAYDEA 118
                                       5999*********************998 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.38
                                       HHHHCT-SEEEEEEEEBTTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  23 kakelglkaiaiTDhgnlfgyvefykaa 50 
                                        ++++g k + + D+g +++++e+y +a
  gi|330508351|ref|YP_004384779.1| 193 NVAAWGNKGVSLADQGKYDEAIEAYDEA 220
                                       5789*********************998 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 2.9
                                       HHHCT-SEEEEEEEEBTTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  24 akelglkaiaiTDhgnlfgyvefykaa 50 
                                       a+ +g k + + D+g  ++++e+y +a
  gi|330508351|ref|YP_004384779.1| 228 AAVWGNKGVSLADQGKHDEAIEAYDEA 254
                                       788999******************998 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 1.3
                                       HHHCT-SEEEEEEEEBTTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  24 akelglkaiaiTDhgnlfgyvefykaa 50 
                                       a+ +g k + + D+g +++++e+y +a
  gi|330508351|ref|YP_004384779.1| 262 AAVWGNKGVSLVDQGKYDEAIEAYDEA 288
                                       788999******************998 PP

  == domain 7  score: 4.1 bits;  conditional E-value: 0.13
                                       HHHHCT-SEEEEEEEEBTTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  23 kakelglkaiaiTDhgnlfgyvefykaa 50 
                                        a+++g k + + D+g +++++e+y +a
  gi|330508351|ref|YP_004384779.1| 295 NAAAWGNKGVSLADQGKYDEAIEAYDEA 322
                                       699**********************998 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       7.9   3.1e+03      30      45 ..      32      47 ..      23      60 .. 0.79
   2 !    7.9   0.7    0.0099         4       3      49 ..      73     119 ..      71     126 .. 0.87
   3 ?    1.3   0.0       1.1   4.4e+02       9      43 ..     113     147 ..     112     152 .. 0.90
   4 ?    6.6   0.1     0.024       9.4       6      50 ..     178     222 ..     173     236 .. 0.87
   5 ?    6.1   0.2     0.034        14       3      50 ..     243     290 ..     241     298 .. 0.87
   6 ?    4.1   0.4      0.15        58       7      44 ..     281     318 ..     279     325 .. 0.90
   7 ?    5.6   0.1     0.049        20       6      44 ..     314     352 ..     309     365 .. 0.87
   8 ?   -0.4   0.1       3.8   1.5e+03       3      37 ..     379     413 ..     377     423 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 7.9
                            TPR_20 30 lallaagryeeAleqL 45
                                       al+ +g+y+eA+++ 
  gi|330508351|ref|YP_004384779.1| 32 VALADQGKYDEAIKAY 47
                                      5788999999999875 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0099
                            TPR_20   3 adapelaeleaalaanpddldarldlAlallaagryeeAleqLleil 49 
                                       ++++ +++ ++a+  +p+d +a  +    l+ +g+y+eA+e+  e +
  gi|330508351|ref|YP_004384779.1|  73 KHDEAIEAYDEAIRLDPTDAAAWGNKGASLADQGKYDEAIEAYDEAI 119
                                       5788999*********************************9865555 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 1.1
                            TPR_20   9 aeleaalaanpddldarldlAlallaagryeeAle 43 
                                       ++ ++a+  +p+d  a ++  + l+++++y+e+++
  gi|330508351|ref|YP_004384779.1| 113 EAYDEAIRLDPTDAIAWFNKGNSLNKQKKYDESIK 147
                                       677899999**********************9886 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.024
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                       + +++ ++a+  +p++++a  +    l+ +g+y+eA+e+  e ++
  gi|330508351|ref|YP_004384779.1| 178 EAIEAYDEAIRLDPANVAAWGNKGVSLADQGKYDEAIEAYDEAIR 222
                                       6789999******************************98666665 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.034
                            TPR_20   3 adapelaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                       ++++ +++ ++a+  +p+d +   +    l+ +g+y+eA+e+  e ++
  gi|330508351|ref|YP_004384779.1| 243 KHDEAIEAYDEAIRLDPTDAAVWGNKGVSLVDQGKYDEAIEAYDEAIR 290
                                       5788999*********************************98666655 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.15
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                        +++ ++a+  +p++ +a  +    l+ +g+y+eA+e+
  gi|330508351|ref|YP_004384779.1| 281 AIEAYDEAIRLDPANAAAWGNKGVSLADQGKYDEAIEA 318
                                       68899999***************************996 PP

  == domain 7  score: 5.6 bits;  conditional E-value: 0.049
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                       + +++ ++a+  +p+d  a ++  + l+++++y+e++++
  gi|330508351|ref|YP_004384779.1| 314 EAIEAYDEAIRLDPTDATAWFNKGNSLNKQKKYDESIKA 352
                                       6789999****************************9876 PP

  == domain 8  score: -0.4 bits;  conditional E-value: 3.8
                            TPR_20   3 adapelaeleaalaanpddldarldlAlallaagr 37 
                                       ++++ +++ ++a+  + +d +a ++   +l+ ++r
  gi|330508351|ref|YP_004384779.1| 379 KHDEAIQAYDEAIRLDSTDANAWYNKGVVLHNQNR 413
                                       56788999999999999999999999999988876 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 ?    4.9   0.0       0.1        40      84     121 ..      33      70 ..      28      74 .. 0.90
   2 ?   -0.1   0.0       3.7   1.5e+03      84     110 ..     135     161 ..      76     179 .. 0.74
   3 ?    3.7   0.0      0.24        96      76     121 ..     196     240 ..     169     243 .. 0.79
   4 ?    1.2   0.0       1.5   5.9e+02      73     121 ..     261     308 ..     242     312 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.1
                                       HHHCHTT-SEEEE--SSGGGHHHHHHHHHTTSEEEE-- CS
                   DXP_reductoisom  84 elaeeeeadvvvaaivGaaGLkptlaaikagkriaLAN 121
                                       +la + + d  ++a   a+ L pt+aa+ ++k +a A 
  gi|330508351|ref|YP_004384779.1|  33 ALADQGKYDEAIKAYDEAIRLDPTIAAAWSNKGVAFAD 70 
                                       57788899999************************995 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.7
                                       HHHCHTT-SEEEE--SSGGGHHHHHHH CS
                   DXP_reductoisom  84 elaeeeeadvvvaaivGaaGLkptlaa 110
                                       +l ++++ d  ++a   a+GL+p la 
  gi|330508351|ref|YP_004384779.1| 135 SLNKQKKYDESIKAYDEAIGLNPVLAE 161
                                       566778888889999999999999885 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.24
                                       EESHHHHHHHHCHTT-SEEEE--SSGGGHHHHHHHHHTTSEEEE-- CS
                   DXP_reductoisom  76 lvGeealkelaeeeeadvvvaaivGaaGLkptlaaikagkriaLAN 121
                                       + G++++ +la + + d  + a   a+ L pt aa+  +k + LA 
  gi|330508351|ref|YP_004384779.1| 196 AWGNKGV-SLADQGKYDEAIEAYDEAIRLDPTDAAVWGNKGVSLAD 240
                                       4566654.6888899****************************996 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 1.5
                                       SEEEESHHHHHHHHCHTT-SEEEE--SSGGGHHHHHHHHHTTSEEEE-- CS
                   DXP_reductoisom  73 tevlvGeealkelaeeeeadvvvaaivGaaGLkptlaaikagkriaLAN 121
                                          + G++++ +l+ + + d  + a   a+ L p+ aa+  +k + LA 
  gi|330508351|ref|YP_004384779.1| 261 DAAVWGNKGV-SLVDQGKYDEAIEAYDEAIRLDPANAAAWGNKGVSLAD 308
                                       4556677776.46677899999999999999999999999999999985 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       9.1   3.6e+03       7      19 ..      83      95 ..      82      96 .. 0.85
   2 ?    2.4   0.0      0.35   1.4e+02       7      19 ..     185     197 ..     184     199 .. 0.90
   3 ?    3.1   0.0      0.21        85       7      19 ..     287     299 ..     286     301 .. 0.90
   4 ?    1.7   0.0      0.59   2.4e+02       7      20 ..     321     334 ..     320     335 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 9.1
                                      HHHHH-TT-CHHH CS
                              PPTA  7 kliekdpkNYsaW 19
                                      ++i++dp +  aW
  gi|330508351|ref|YP_004384779.1| 83 EAIRLDPTDAAAW 95
                                      799****988888 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.35
                                       HHHHH-TT-CHHH CS
                              PPTA   7 kliekdpkNYsaW 19 
                                       ++i++dp N  aW
  gi|330508351|ref|YP_004384779.1| 185 EAIRLDPANVAAW 197
                                       79*******9999 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.21
                                       HHHHH-TT-CHHH CS
                              PPTA   7 kliekdpkNYsaW 19 
                                       ++i++dp N  aW
  gi|330508351|ref|YP_004384779.1| 287 EAIRLDPANAAAW 299
                                       79*********** PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.59
                                       HHHHH-TT-CHHHH CS
                              PPTA   7 kliekdpkNYsaWn 20 
                                       ++i++dp + +aW+
  gi|330508351|ref|YP_004384779.1| 321 EAIRLDPTDATAWF 334
                                       79***********7 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0      0.05        20      64      96 ..     120     152 ..      74     158 .. 0.85
   2 ?    5.7   0.0     0.025        10      64      98 ..     324     358 ..     301     365 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.05
                              FSH1  64 seeeeesraWfrkkdekneyegleesldavkdy 96 
                                         + +++ aWf+k +  n+ ++++es++a  ++
  gi|330508351|ref|YP_004384779.1| 120 RLDPTDAIAWFNKGNSLNKQKKYDESIKAYDEA 152
                                       56788999*******************987665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.025
                              FSH1  64 seeeeesraWfrkkdekneyegleesldavkdyik 98 
                                         + +++ aWf+k +  n+ ++++es++a  ++i+
  gi|330508351|ref|YP_004384779.1| 324 RLDPTDATAWFNKGNSLNKQKKYDESIKAYDEAIR 358
                                       56788999********************9888776 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.85   3.4e+02       7      50 ..      41      84 ..      40      90 .. 0.81
   2 ?   -0.6   0.0       5.4   2.2e+03       7      37 ..     177     207 ..     173     223 .. 0.74
   3 ?   -0.6   0.0       5.8   2.3e+03       7      50 ..     211     254 ..     209     259 .. 0.77
   4 ?   -0.4   0.0       4.9   1.9e+03       7      37 ..     279     309 ..     278     325 .. 0.73
   5 ?    3.3   0.0      0.34   1.4e+02       7      52 ..     347     392 ..     346     393 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.85
                         TetR_C_15  7 dalvdallaahrenpalrrvlleeapslgelelvealeqriaea 50
                                      d+ + a+ +a r +p + ++++    +   +  ++++ +  +ea
  gi|330508351|ref|YP_004384779.1| 41 DEAIKAYDEAIRLDPTIAAAWSNKGVAFADQGKHDEAIEAYDEA 84
                                      78899****************99988888886666666666655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 5.4
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgel 37 
                                       d+ ++a+ +a r +pa  +++     sl  +
  gi|330508351|ref|YP_004384779.1| 177 DEAIEAYDEAIRLDPANVAAWGNKGVSLADQ 207
                                       6889999999999999988886666555555 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 5.8
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgelelvealeqriaea 50 
                                       d+ ++a+ +a r +p   +v+     sl  +  ++++ +  +ea
  gi|330508351|ref|YP_004384779.1| 211 DEAIEAYDEAIRLDPTDAAVWGNKGVSLADQGKHDEAIEAYDEA 254
                                       67899999999999999999988888888886666666666555 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 4.9
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgel 37 
                                       d+ ++a+ +a r +pa  +++     sl  +
  gi|330508351|ref|YP_004384779.1| 279 DEAIEAYDEAIRLDPANAAAWGNKGVSLADQ 309
                                       68899999*****999999987666555555 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.34
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgelelvealeqriaeala 52 
                                       d+ + a+ +a r np+l + + +   sl+ +  ++++ q  +ea++
  gi|330508351|ref|YP_004384779.1| 347 DESIKAYDEAIRLNPDLAEPWIGKGNSLDDQGKHDEAIQAYDEAIR 392
                                       67799**************************999999988888875 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.33   1.3e+02      14      30 ..      37      53 ..      36      53 .. 0.87
   2 ?   -2.2   0.0       7.6     3e+03      16      29 ..      73      86 ..      71      87 .. 0.75
   3 ?    2.3   0.0       0.3   1.2e+02      14      30 ..     105     121 ..     104     121 .. 0.87
   4 ?    2.3   0.0       0.3   1.2e+02      14      30 ..     173     189 ..     172     189 .. 0.87
   5 ?    2.6   0.0      0.24        96      14      30 ..     207     223 ..     202     223 .. 0.86
   6 ?   -2.1   0.0         7   2.8e+03      16      29 ..     243     256 ..     240     257 .. 0.77
   7 ?    2.5   0.0      0.24        97      14      30 ..     275     291 ..     271     291 .. 0.88
   8 ?    2.6   0.0      0.24        96      14      30 ..     309     325 ..     304     325 .. 0.86
   9 ?   -2.2   0.0       7.2   2.9e+03      16      29 ..     379     392 ..     377     393 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.33
                          SHNi-TPR 14 nenFpqAveDlrkaLeL 30
                                      ++++++A++ +++a+ L
  gi|330508351|ref|YP_004384779.1| 37 QGKYDEAIKAYDEAIRL 53
                                      579*********99865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.6
                          SHNi-TPR 16 nFpqAveDlrkaLe 29
                                      + ++A+e +++a+ 
  gi|330508351|ref|YP_004384779.1| 73 KHDEAIEAYDEAIR 86
                                      56899999999875 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.3
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A+e +++a+ L
  gi|330508351|ref|YP_004384779.1| 105 QGKYDEAIEAYDEAIRL 121
                                       579*********99865 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.3
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A+e +++a+ L
  gi|330508351|ref|YP_004384779.1| 173 QGKYDEAIEAYDEAIRL 189
                                       579*********99865 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.24
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A+e +++a+ L
  gi|330508351|ref|YP_004384779.1| 207 QGKYDEAIEAYDEAIRL 223
                                       589*********99865 PP

  == domain 6  score: -2.1 bits;  conditional E-value: 7
                          SHNi-TPR  16 nFpqAveDlrkaLe 29 
                                       + ++A+e +++a+ 
  gi|330508351|ref|YP_004384779.1| 243 KHDEAIEAYDEAIR 256
                                       66899999999875 PP

  == domain 7  score: 2.5 bits;  conditional E-value: 0.24
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A+e +++a+ L
  gi|330508351|ref|YP_004384779.1| 275 QGKYDEAIEAYDEAIRL 291
                                       689*********99865 PP

  == domain 8  score: 2.6 bits;  conditional E-value: 0.24
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A+e +++a+ L
  gi|330508351|ref|YP_004384779.1| 309 QGKYDEAIEAYDEAIRL 325
                                       589*********99865 PP

  == domain 9  score: -2.2 bits;  conditional E-value: 7.2
                          SHNi-TPR  16 nFpqAveDlrkaLe 29 
                                       + ++A++ +++a+ 
  gi|330508351|ref|YP_004384779.1| 379 KHDEAIQAYDEAIR 392
                                       66899999999976 PP

>> Mif2_N  Kinetochore CENP-C fungal homologue, Mif2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       3.2   1.3e+03      12      23 ..      31      42 ..      30      43 .. 0.94
   2 ?    0.9   0.0       1.8   7.1e+02      12      23 ..     201     212 ..     193     218 .. 0.90
   3 ?    0.2   0.0         3   1.2e+03      12      23 ..     235     246 ..     230     252 .. 0.91
   4 ?   -0.8   0.0         6   2.4e+03      12      23 ..     269     280 ..     265     285 .. 0.92
   5 ?    1.0   0.0       1.6   6.5e+02      12      23 ..     303     314 ..     300     352 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 3.2
                            Mif2_N 12 GvtlkdtgvrDe 23
                                      Gv l+d+g++De
  gi|330508351|ref|YP_004384779.1| 31 GVALADQGKYDE 42
                                      9**********9 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.8
                            Mif2_N  12 GvtlkdtgvrDe 23 
                                       Gv l+d+g++De
  gi|330508351|ref|YP_004384779.1| 201 GVSLADQGKYDE 212
                                       9**********9 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 3
                            Mif2_N  12 GvtlkdtgvrDe 23 
                                       Gv l+d+g+ De
  gi|330508351|ref|YP_004384779.1| 235 GVSLADQGKHDE 246
                                       9**********9 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 6
                            Mif2_N  12 GvtlkdtgvrDe 23 
                                       Gv l d+g++De
  gi|330508351|ref|YP_004384779.1| 269 GVSLVDQGKYDE 280
                                       9**********9 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 1.6
                            Mif2_N  12 GvtlkdtgvrDe 23 
                                       Gv l+d+g++De
  gi|330508351|ref|YP_004384779.1| 303 GVSLADQGKYDE 314
                                       9**********9 PP

>> DUF2799  Protein of unknown function (DUF2799)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.18        73       1      26 [.      26      51 ..      26      57 .. 0.92
   2 ?    4.0   0.2      0.17        69       2      27 ..      61      86 ..      60      99 .. 0.84
   3 ?    1.1   0.1       1.4   5.5e+02       2      27 ..      95     120 ..      94     150 .. 0.85
   4 ?   -0.4   0.0       4.1   1.6e+03       2      26 ..     163     187 ..     162     195 .. 0.87
   5 ?    1.3   0.0       1.1   4.6e+02       2      26 ..     197     221 ..     196     227 .. 0.90
   6 ?    1.8   0.1      0.83   3.3e+02       2      27 ..     231     256 ..     230     266 .. 0.89
   7 ?    2.7   0.2      0.44   1.7e+02       2      37 ..     299     332 ..     298     357 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.18
                           DUF2799  1 dWqqiGyedgaaGktasrleelakac 26
                                      dW   G++ + +Gk  + ++ + +a+
  gi|330508351|ref|YP_004384779.1| 26 DWFYQGVALADQGKYDEAIKAYDEAI 51
                                      8******************9999876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.17
                           DUF2799  2 WqqiGyedgaaGktasrleelakaca 27
                                      W++ G++ + +Gk+ + +e + +a++
  gi|330508351|ref|YP_004384779.1| 61 WSNKGVAFADQGKHDEAIEAYDEAIR 86
                                      *********************99876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.4
                           DUF2799   2 WqqiGyedgaaGktasrleelakaca 27 
                                       W + G + + +Gk  + +e + +a++
  gi|330508351|ref|YP_004384779.1|  95 WGNKGASLADQGKYDEAIEAYDEAIR 120
                                       99999999999*99999999999865 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 4.1
                           DUF2799   2 WqqiGyedgaaGktasrleelakac 26 
                                       W   G + + +Gk  + +e + +a+
  gi|330508351|ref|YP_004384779.1| 163 WIGKGKSLADQGKYDEAIEAYDEAI 187
                                       8889999999***999999999876 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 1.1
                           DUF2799   2 WqqiGyedgaaGktasrleelakac 26 
                                       W + G++ + +Gk  + +e + +a+
  gi|330508351|ref|YP_004384779.1| 197 WGNKGVSLADQGKYDEAIEAYDEAI 221
                                       9999**************9999876 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.83
                           DUF2799   2 WqqiGyedgaaGktasrleelakaca 27 
                                       W + G++ + +Gk+ + +e + +a++
  gi|330508351|ref|YP_004384779.1| 231 WGNKGVSLADQGKHDEAIEAYDEAIR 256
                                       9999***************9999865 PP

  == domain 7  score: 2.7 bits;  conditional E-value: 0.44
                           DUF2799   2 WqqiGyedgaaGktasrleelakacakagvkpdaaa 37 
                                       W + G++ + +Gk  + +e + +a++     +da+a
  gi|330508351|ref|YP_004384779.1| 299 WGNKGVSLADQGKYDEAIEAYDEAIRLD--PTDATA 332
                                       9999****************99987643..334444 PP

>> Sda  Sporulation inhibitor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       3.2   1.3e+03      10      20 ..      44      54 ..      41      54 .. 0.89
   2 ?    1.3   0.0      0.74     3e+02      10      20 ..      78      88 ..      74      91 .. 0.89
   3 ?    1.1   0.0      0.85   3.4e+02      10      20 ..     112     122 ..     109     125 .. 0.90
   4 ?   -1.9   0.0       7.4     3e+03      10      20 ..     146     156 ..     146     156 .. 0.88
   5 ?    0.9   0.0      0.96   3.8e+02      10      20 ..     180     190 ..     177     191 .. 0.90
   6 ?    1.1   0.0      0.85   3.4e+02      10      20 ..     214     224 ..     211     227 .. 0.90
   7 ?    1.3   0.0      0.74     3e+02      10      20 ..     248     258 ..     244     261 .. 0.89
   8 ?    0.9   0.0      0.96   3.8e+02      10      20 ..     282     292 ..     279     293 .. 0.90
   9 ?    1.1   0.0      0.85   3.4e+02      10      20 ..     316     326 ..     313     329 .. 0.90
  10 ?    0.0   0.0       1.8   7.1e+02      10      20 ..     350     360 ..     349     362 .. 0.90
  11 ?   -0.3   0.0       2.3   9.2e+02      10      20 ..     384     394 ..     380     397 .. 0.87
  12 ?    0.2   0.2       1.7   6.6e+02      11      21 ..     418     428 ..     418     430 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.2
                               Sda 10 ieaYekAleln 20
                                      i+aY++A+ l+
  gi|330508351|ref|YP_004384779.1| 44 IKAYDEAIRLD 54
                                      89******986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.74
                               Sda 10 ieaYekAleln 20
                                      ieaY++A+ l+
  gi|330508351|ref|YP_004384779.1| 78 IEAYDEAIRLD 88
                                      9*******997 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.85
                               Sda  10 ieaYekAleln 20 
                                       ieaY++A+ l+
  gi|330508351|ref|YP_004384779.1| 112 IEAYDEAIRLD 122
                                       9*******997 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 7.4
                               Sda  10 ieaYekAleln 20 
                                       i+aY++A+ ln
  gi|330508351|ref|YP_004384779.1| 146 IKAYDEAIGLN 156
                                       89*****9886 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.96
                               Sda  10 ieaYekAleln 20 
                                       ieaY++A+ l+
  gi|330508351|ref|YP_004384779.1| 180 IEAYDEAIRLD 190
                                       9*******986 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.85
                               Sda  10 ieaYekAleln 20 
                                       ieaY++A+ l+
  gi|330508351|ref|YP_004384779.1| 214 IEAYDEAIRLD 224
                                       9*******997 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.74
                               Sda  10 ieaYekAleln 20 
                                       ieaY++A+ l+
  gi|330508351|ref|YP_004384779.1| 248 IEAYDEAIRLD 258
                                       9*******997 PP

  == domain 8  score: 0.9 bits;  conditional E-value: 0.96
                               Sda  10 ieaYekAleln 20 
                                       ieaY++A+ l+
  gi|330508351|ref|YP_004384779.1| 282 IEAYDEAIRLD 292
                                       9*******986 PP

  == domain 9  score: 1.1 bits;  conditional E-value: 0.85
                               Sda  10 ieaYekAleln 20 
                                       ieaY++A+ l+
  gi|330508351|ref|YP_004384779.1| 316 IEAYDEAIRLD 326
                                       9*******997 PP

  == domain 10  score: 0.0 bits;  conditional E-value: 1.8
                               Sda  10 ieaYekAleln 20 
                                       i+aY++A+ ln
  gi|330508351|ref|YP_004384779.1| 350 IKAYDEAIRLN 360
                                       89******998 PP

  == domain 11  score: -0.3 bits;  conditional E-value: 2.3
                               Sda  10 ieaYekAleln 20 
                                       i+aY++A+ l+
  gi|330508351|ref|YP_004384779.1| 384 IQAYDEAIRLD 394
                                       89******997 PP

  == domain 12  score: 0.2 bits;  conditional E-value: 1.7
                               Sda  11 eaYekAlelnL 21 
                                       ea+ kA+eln 
  gi|330508351|ref|YP_004384779.1| 418 EAFAKARELNA 428
                                       89*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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):              45  [number of targets reported over threshold]
# CPU time: 0.97u 0.31s 00:00:01.28 Elapsed: 00:00:00.64
# Mc/sec: 2085.47
//
Query:       gi|330508352|ref|YP_004384780.1|  [L=166]
Description: hypothetical protein MCON_2534 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00084   18.9   0.3     0.0011   18.6   0.3    1.1  1  Allexi_40kDa    Allexivirus 40kDa protein
     0.0023   18.0   3.1     0.0059   16.6   0.9    2.0  2  DUF4446         Protein of unknown function (DUF4446)
     0.0029   16.3   4.9     0.0037   16.0   4.9    1.1  1  AAA_13          AAA domain
     0.0041   17.3   5.1      0.005   17.0   5.1    1.1  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
  ------ inclusion threshold ------
       0.03   14.0   8.8      0.067   12.9   8.8    1.6  1  SHE3            SWI5-dependent HO expression protein 3
      0.035   14.5   2.0      0.043   14.1   2.0    1.1  1  Vfa1            AAA-ATPase Vps4-associated protein 1
      0.035   14.2   1.6      0.035   14.2   1.6    1.7  2  Ntox15          Novel toxin 15
      0.037   14.4   1.1      0.065   13.7   0.5    1.7  2  DUF4094         Domain of unknown function (DUF4094)
      0.055   14.0   5.5      0.051   14.1   4.2    1.6  1  APG6_N          Apg6 coiled-coil region
       0.07   13.6   5.7       0.28   11.7   1.5    2.4  2  ZapB            Cell division protein ZapB
      0.093   13.4   1.6       0.17   12.5   0.9    1.9  2  SlyX            SlyX
        0.1   12.2   9.1       0.16   11.5   4.1    2.0  2  Filament        Intermediate filament protein
       0.11   11.1   0.6       0.14   10.8   0.6    1.1  1  Carboxyl_trans  Carboxyl transferase domain
       0.12   12.5   5.8       0.32   11.1   5.6    1.9  1  Mod_r           Modifier of rudimentary (Mod(r)) protein
       0.12   12.2   7.9      0.097   12.5   3.0    2.1  2  Mt_ATP-synt_D   ATP synthase D chain, mitochondrial (ATP5H)
       0.15   11.4   5.3       0.26   10.6   0.7    2.2  2  DUF4407         Domain of unknown function (DUF4407)
       0.16   12.4   4.5       0.35   11.3   2.7    2.3  2  LPP             Lipoprotein leucine-zipper
        0.2   10.4   5.2       0.22   10.3   5.2    1.1  1  O-antigen_lig   O-antigen ligase like membrane protein
       0.21   12.1   4.2        0.2   12.2   1.8    1.9  2  DUF16           Protein of unknown function DUF16
       0.23   11.8   4.8       0.37   11.1   2.3    2.0  2  DUF641          Plant protein of unknown function (DUF641)
       0.49    9.4   5.3       0.79    8.7   3.5    1.8  2  Atg14           Vacuolar sorting 38 and autophagy-related sub
       0.57   10.0   7.9       0.11   12.2   3.5    2.1  2  DivIC           Septum formation initiator
       0.63    9.9   6.5        4.5    7.1   0.5    2.4  2  LemA            LemA family
       0.76    9.8   9.8        3.2    7.8   8.1    2.0  2  FlxA            FlxA-like protein
        1.4    9.7   8.4          5    7.9   1.3    2.2  2  Occludin_ELL    Occludin homology domain
        1.7    9.2   7.2       0.61   10.6   1.1    2.7  3  Fungal_TACC     Fungal Transforming acidic coiled-coil (TACC)
        7.8    7.3   9.1         10    6.9   0.1    3.3  4  FliD_N          Flagellar hook-associated protein 2 N-terminu


Domain annotation for each model (and alignments):
>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   1.6e-06    0.0011      73     171 ..      30     127 ..      17     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-06
                      Allexi_40kDa  73 llsqttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelsssetsesegPs 149
                                         s +   +++ + + +++++ + ++s++++++l++++++++k   + +si+ +l++  +++d+++ se +++  P 
  gi|330508352|ref|YP_004384780.1|  30 YASYQGDYNKMDQLSSEISQDKQAIASLNETISLEEKEIDQRK--AERDSIKAQLDAWEMRMDKMTPSEYNQNVDPY 104
                                       45666677888888899999999***********999999999..5689**************************** PP

                      Allexi_40kDa 150 ssptkassaeaaased.Lpiyqa 171
                                       ++  ++ ++  ++ ++ ++ y+a
  gi|330508352|ref|YP_004384780.1| 105 NALVSQYNSLRDPYNElVNKYNA 127
                                       *9999988888887775667776 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.9   8.9e-06    0.0059       2      78 ..      15      92 ..      14     106 .. 0.90
   2 ?    1.0   0.0      0.55   3.7e+02      49      85 ..      99     135 ..      91     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.9e-06
                           DUF4446  2 iilvlavlvvillillivllvklkklkkkykklmkgk.dgksleellkekleeveelkeeseelekeieeleeklkks 78
                                      +i ++av+++i ++ +     +++k+++  +++ ++k   +sl+e+++ + +e+++ k+e +++++++++ e +++k+
  gi|330508352|ref|YP_004384780.1| 15 LIGIIAVIIIIDILQYASYQGDYNKMDQLSSEISQDKqAIASLNETISLEEKEIDQRKAERDSIKAQLDAWEMRMDKM 92
                                      567888889999999999999**********9999775889*****************************99999876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.55
                           DUF4446  49 ekleeveelkeeseelekeieeleeklkkslqkvglv 85 
                                       ++++ +++l ++ ++l++ ++el +k ++ ++k++l 
  gi|330508352|ref|YP_004384780.1|  99 QNVDPYNALVSQYNSLRDPYNELVNKYNADIEKYNLQ 135
                                       5666667777777777777777777777777777665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   4.9   5.6e-06    0.0037     281     400 ..      33     144 ..      29     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.6e-06
                            AAA_13 281 feekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfk.sve 356
                                       ++ +++++++l +++ ++k +++++l++ +  +      e+++++ kae + +++qL++++ ++++    p++ + +
  gi|330508352|ref|YP_004384780.1|  33 YQGDYNKMDQLSSEISQDK-QAIASLNETISLE------EKEIDQRKAERDSIKAQLDAWEMRMDKMT--PSEyNQN 100
                                       6667777777777777775.5667776666655......45677888888999999999999887544..6654677 PP

                            AAA_13 357 lesvkakiesikklvaeineliakhNekvanleeekeeakkkle 400
                                       ++ ++a +++ ++l +  nel++k+N+ +++++ ++  ++ k+ 
  gi|330508352|ref|YP_004384780.1| 101 VDPYNALVSQYNSLRDPYNELVNKYNADIEKYNLQRDIINIKID 144
                                       89999999999999999999999999999998887777776665 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 !   17.0   5.1   7.5e-06     0.005      33     175 ..       4     149 ..       1     156 [. 0.70

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.5e-06
                           UPF0242  33 Ws...llsiGlllaaaGsLlllllllkwe.kalkekl..ekskleekeaklteldeglktkeealeelqeeeeeLke 103
                                       W+    l + +l+ +++ ++++ +l + + +   +k+   +s+++++++ + +l+e ++ +e+++ ++++e +  k 
  gi|330508352|ref|YP_004384780.1|   4 WQemqKLNLKILIGIIAVIIIIDILQYASyQGDYNKMdqLSSEISQDKQAIASLNETISLEEKEIDQRKAERDSIKA 80 
                                       5444467777788888888666544433202222333556899********************************** PP

                           UPF0242 104 eldakeeelerlk..eenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqieqL 175
                                       +lda e  + +++  e nq++    +a + +++ l+  ++e +++ +  +++y+     qr  ++ + d+ ++L
  gi|330508352|ref|YP_004384780.1|  81 QLDAWEMRMDKMTpsEYNQNVD-PYNALVSQYNSLRDPYNELVNKYNADIEKYN----LQRDIINIKIDEYNEL 149
                                       *****99999997334566665.6677777888888887777776666666654....3555555555555555 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 ?   12.9   8.8    0.0001     0.067      72     148 ..      65     144 ..      37     155 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHH CS
                              SHE3  72 ekelselkesveelklekkqlkkrlenssase.teleeelerlkvqYdalvdsqkeYkehYqqeiee..Lkeslekl 145
                                       eke+ + k + +++k++ ++ ++r+++ + se +++ + ++ l  qY++l d  +e  ++Y+ +ie+  L++ + + 
  gi|330508352|ref|YP_004384780.1|  65 EKEIDQRKAERDSIKAQLDAWEMRMDKMTPSEyNQNVDPYNALVSQYNSLRDPYNELVNKYNADIEKynLQRDIINI 141
                                       45555555555555555555555555554444244455555566666666666666666666655542244545444 PP

                                       HHH CS
                              SHE3 146 kle 148
                                       k +
  gi|330508352|ref|YP_004384780.1| 142 KID 144
                                       444 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 ?   14.1   2.0   6.5e-05     0.043      65     168 ..      40     155 ..      27     164 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.5e-05
                              Vfa1  65 kkeleeeiekvkkeyeekqkkkkekekkkkekd...........kkdkdkkkekekdkkkekekeeekkkelkkaee 130
                                        ++l++ei++ k+ + + +++ + +ek+ ++++           + +   +k + ++ +++ ++++++ +++++  +
  gi|330508352|ref|YP_004384780.1|  40 MDQLSSEISQDKQAIASLNETISLEEKEIDQRKaerdsikaqldAWEMRMDKMTPSEYNQNVDPYNALVSQYNSLRD 116
                                       34444444444444444444433333322111111111111111222233333333333333338888888888888 PP

                              Vfa1 131 elee...keeprvkkykLhkefyqsRlerkrqaeaakenee 168
                                         +e   k +  ++ky+L++++ +  +++++  e ak+ ++
  gi|330508352|ref|YP_004384780.1| 117 PYNElvnKYNADIEKYNLQRDIINIKIDEYN--ELAKKPRQ 155
                                       887788889999****************974..44444444 PP

>> Ntox15  Novel toxin 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2      0.96   6.4e+02      29      74 ..      33      74 ..      26      86 .. 0.45
   2 ?   14.2   1.6   5.3e-05     0.035       6      75 ..      77     148 ..      72     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.96
                            Ntox15 29 nrdkYkqqkraseaaaerrqakarqerevreelekkiveklvrdlk 74
                                       +  Y++  + s++ ++ +qa      + + +le+k +++++    
  gi|330508352|ref|YP_004384780.1| 33 YQGDYNKMDQLSSEISQDKQAI--ASLNETISLEEKEIDQRK--AE 74
                                      4444555554444445444433..333344455555555333..33 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.3e-05
                            Ntox15   6 eFrrQLkeQeeglnkltvdeylknrdkYkqqkraseaaaerrq..akarqerevreelekkiveklvrdlke 75 
                                         ++QL + e  + k+t++ey +n d Y++   + ++   + +   ++ +  + + +l++ i++   +++ e
  gi|330508352|ref|YP_004384780.1|  77 SIKAQLDAWEMRMDKMTPSEYNQNVDPYNALVSQYNSLRDPYNelVNKYNADIEKYNLQRDIINIKIDEYNE 148
                                       5689************************99877766554443310233444555667888888888888876 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   9.7e-05     0.065      54      87 ..      39      73 ..      25      74 .. 0.80
   2 ?   -1.9   0.0       7.1   4.7e+03      61      73 ..     122     136 ..      85     147 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.7e-05
                           DUF4094 54 skdilg.evskthkaiqtLdktissLemeLaaara 87
                                      + d l+ e+s+ ++ai +L+ tis  e e+   +a
  gi|330508352|ref|YP_004384780.1| 39 KMDQLSsEISQDKQAIASLNETISLEEKEIDQRKA 73
                                      3455666******************9999998876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.1
                           DUF4094  61 vskthkaiq..tLdk 73 
                                       v+k + +i+  +L++
  gi|330508352|ref|YP_004384780.1| 122 VNKYNADIEkyNLQR 136
                                       333333444333444 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   4.2   7.7e-05     0.051      28     129 ..      30     128 ..      25     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.7e-05
                            APG6_N  28 YeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeeleale.eeeerfwr 103
                                       Y ++    +k ++      +e+ + ++ ++ l+++ +  ++e+++ ++er++++a+l a e   +++   e ++ + 
  gi|330508352|ref|YP_004384780.1|  30 YASYQGDYNKMDQL----SSEISQDKQAIASLNETISLEEKEIDQRKAERDSIKAQLDAWEMRMDKMTpSEYNQNVD 102
                                       55555555555444....4599999*************************************999998356688999 PP

                            APG6_N 104 eynelqlelleleeeldsleaqyeha 129
                                        yn+l  + ++l +  + l ++y+ +
  gi|330508352|ref|YP_004384780.1| 103 PYNALVSQYNSLRDPYNELVNKYNAD 128
                                       9*************999999999876 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.5   0.00042      0.28      19      64 ..      39      84 ..      31      92 .. 0.85
   2 ?    3.6   0.1      0.14        90      13      41 ..     104     132 ..      96     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00042
                              ZapB 19 titlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64
                                      ++++L+ ei++ k+  ++l+e +   e+e++q k+er ++++ l++
  gi|330508352|ref|YP_004384780.1| 39 KMDQLSSEISQDKQAIASLNETISLEEKEIDQRKAERDSIKAQLDA 84
                                      7889999**************9999999999999999888888764 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.14
                              ZapB  13 iqkaidtitlLqmeieeLkeeneelkeen 41 
                                       +++++ ++ +L+  + eL  + ++  e+ 
  gi|330508352|ref|YP_004384780.1| 104 YNALVSQYNSLRDPYNELVNKYNADIEKY 132
                                       67778888888888888877776655544 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.9   0.00026      0.17       4      52 ..      39      87 ..      37     103 .. 0.85
   2 ?   -2.0   0.0       8.9   5.9e+03      23      47 ..     119     143 ..     114     159 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00026
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                              SlyX  4 rleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelee 52
                                      ++++L ++++   ++i +Ln+++   +++id+ +++ + ++ +l + e 
  gi|330508352|ref|YP_004384780.1| 39 KMDQLSSEISQDKQAIASLNETISLEEKEIDQRKAERDSIKAQLDAWEM 87
                                      678899999999************************9999999966554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.9
                                       HHHHHHHHHHHHHHHHHHHHHHHT- CS
                              SlyX  23 ndvvaeqqqqidrlqrqlrllaerl 47 
                                       n+ v + + +i++   q + ++ ++
  gi|330508352|ref|YP_004384780.1| 119 NELVNKYNADIEKYNLQRDIINIKI 143
                                       5666666677776665555554444 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.1   0.00024      0.16     196     264 ..      39     108 ..      31     113 .. 0.70
   2 ?    4.3   0.3     0.039        26     169     213 ..     109     152 ..      98     159 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                                       XXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHH CS
                          Filament 196 kleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaele.erleaeleklqekl 264
                                       k+++l+++++++++a+ s +e i+   ++i+++++e +s+k+q +++e ++  +   +++++++ +++ +
  gi|330508352|ref|YP_004384780.1|  39 KMDQLSSEISQDKQAIASLNETISLEEKEIDQRKAERDSIKAQLDAWEMRMDKMTpSEYNQNVDPYNALV 108
                                       7778888888888888888888888888888888888888888888888777654245555565555555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.039
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 169 eilkeiraqyeelaeknreeaeewykskleelqeaaeknsealrs 213
                                       +  + +r+ y+el++k+++++e+ y+ + + ++ ++++ +e +++
  gi|330508352|ref|YP_004384780.1| 109 SQYNSLRDPYNELVNKYNADIEK-YNLQRDIINIKIDEYNELAKK 152
                                       55577888899999999999886.666666666666666666555 PP

>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.6    0.0002      0.14     206     267 ..      48     110 ..      43     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                                       SSHHHHHHHHHHHHTTS-SSTTSGG.SS----ECSSGSSSH..HCS-CTTTS---HHHHHHCE CS
                    Carboxyl_trans 206 eddeealelirkllsylPkkasnnr.esaPivetadepdrdlieivPdnakkpyDvreviarl 267
                                       ++d++a++++ + +s   k+ ++ + e + i ++ d+++ ++++++P++ ++  D+++ +   
  gi|330508352|ref|YP_004384780.1|  48 SQDKQAIASLNETISLEEKEIDQRKaERDSIKAQLDAWEMRMDKMTPSEYNQNVDPYNALVSQ 110
                                       789***************99999887899999********999*************9876554 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 ?   11.1   5.6   0.00048      0.32      16     103 ..      48     137 ..      36     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00048
                             Mod_r  16 eklealvktlpevkqlkeekeellaeneslaeknlsl.epeleelr.selqekleelkelekefeekeqeldellqk 90 
                                       ++ ++ + +l+e+ +l+e+  + ++++++  +++l+  e ++++   se ++  + +++l ++++ +   ++el++k
  gi|330508352|ref|YP_004384780.1|  48 SQDKQAIASLNETISLEEKEIDQRKAERDSIKAQLDAwEMRMDKMTpSEYNQNVDPYNALVSQYNSLRDPYNELVNK 124
                                       44455566788999999999999999999999999998888887653888889999999999999999999999999 PP

                             Mod_r  91 fspdallarLqta 103
                                       ++ d  + +Lq  
  gi|330508352|ref|YP_004384780.1| 125 YNADIEKYNLQRD 137
                                       9999888888865 PP

>> Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.0   0.00015     0.097      71     147 ..      29     105 ..      19     109 .. 0.86
   2 ?    3.2   0.4       0.1        70      65     105 ..     108     149 ..      94     157 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                       HHHH-------.-TTTTHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXXXXXXXX CS
                     Mt_ATP-synt_D  71 kYealkipype.dkyteevdaeekevkkeikefkeeskkrieelekeleklksllpfeemtmedfaeafPetaldki 146
                                       +Y +++  y + d+ ++e+  + k++ ++ +e ++  +k+i++ + e + +k+ l+  em m+++     ++ +d+ 
  gi|330508352|ref|YP_004384780.1|  29 QYASYQGDYNKmDQLSSEIS-QDKQAIASLNETISLEEKEIDQRKAERDSIKAQLDAWEMRMDKMTPSEYNQNVDPY 104
                                       67777777877678888886.56788899**********************************99888777777776 PP

                                       X CS
                     Mt_ATP-synt_D 147 n 147
                                       n
  gi|330508352|ref|YP_004384780.1| 105 N 105
                                       6 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.1
                                       HHHHHHHHHH-------..-TTTTHHHH...HHHHHHHHCHHHHHH CS
                     Mt_ATP-synt_D  65 VdeFekkYealkipype..dkyteevda...eekevkkeikefkee 105
                                       V     +Y++l  py e  +ky++ +++   + + ++ +i+e++e 
  gi|330508352|ref|YP_004384780.1| 108 V----SQYNSLRDPYNElvNKYNADIEKynlQRDIINIKIDEYNEL 149
                                       3....35666777766655555544443111444445555555554 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.1     0.037        25     133     164 ..      38      69 ..      27      73 .. 0.68
   2 ?   10.6   0.7   0.00039      0.26     105     168 ..      65     130 ..      63     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.037
                           DUF4407 133 aelaeleaqiaalqaeidaaearldalraeaq 164
                                       +++++l ++i++ +++i++++++++ +++e +
  gi|330508352|ref|YP_004384780.1|  38 NKMDQLSSEISQDKQAIASLNETISLEEKEID 69 
                                       56777777777777777777777777776665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00039
                           DUF4407 105 ekeIdaelaeeqq..eeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeld 168
                                       ekeId+++ae+++  ++ ++ + ++++   +e++++ +  +al ++++++++ +++l +++++ ++
  gi|330508352|ref|YP_004384780.1|  65 EKEIDQRKAERDSikAQLDAWEMRMDKMTPSEYNQNVDPYNALVSQYNSLRDPYNELVNKYNADIE 130
                                       68899998888761144445555555559999***************************9998876 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.7   0.00052      0.35       1      36 [.      39      74 ..      39      86 .. 0.83
   2 ?    0.1   0.0       1.7   1.1e+03       9      31 ..     111     130 ..     101     148 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00052
                               LPP  1 kldeLssqVsqLkskvdqlssdvnsakaaaqaakeE 36
                                      k+d+Lss++sq k+ +++l++ ++  ++++++ k+E
  gi|330508352|ref|YP_004384780.1| 39 KMDQLSSEISQDKQAIASLNETISLEEKEIDQRKAE 74
                                      8********************977666666665554 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.7
                               LPP   9 VsqLkskvdqlssdvnsakaaaq 31 
                                        ++L +  ++l   vn+ +a+++
  gi|330508352|ref|YP_004384780.1| 111 YNSLRDPYNEL---VNKYNADIE 130
                                       33333333333...555555544 PP

>> O-antigen_lig  O-antigen ligase like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   5.2   0.00034      0.22     237     322 ..       5     106 ..       1     154 [. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00034
                     O-antigen_lig 237 lkkkklkkkklllaiillvligillaiypyspiyrrkelkekeieiksekk.........eeeeikne......... 295
                                       +  +kl+ k l ++ii++++i+ +l + +y+  y++++  + ei +++++          ee+ei++          
  gi|330508352|ref|YP_004384780.1|   5 QEMQKLNLKIL-IGIIAVIIIIDILQYASYQGDYNKMDQLSSEISQDKQAIaslnetislEEKEIDQRkaerdsika 80 
                                       55689999998.99999999999999999999998888777777765554489999999988888888788888444 PP

                     O-antigen_lig 296 ........ikenykseglkeavleqyeyandkqfs 322
                                               ++         +   ++y+++ d++++
  gi|330508352|ref|YP_004384780.1|  81 qldawemrMD---------KMTPSEYNQNVDPYNA 106
                                       4444444422.........2222333333333332 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.8    0.0003       0.2      48     102 ..      38      92 ..       5      94 .. 0.89
   2 ?    0.2   0.0       1.6     1e+03      43      64 ..     122     143 ..      96     157 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0003
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHH CS
                             DUF16  48 eqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsi 102
                                       +++++l  ++++  + i  l++++   ++e+++ +   ++i   L++ + R+D++
  gi|330508352|ref|YP_004384780.1|  38 NKMDQLSSEISQDKQAIASLNETISLEEKEIDQRKAERDSIKAQLDAWEMRMDKM 92 
                                       6889999999999999999999999999999999999999999999999999998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.6
                                       HH...HHHHHHHHHHHHHHHHH CS
                             DUF16  43 vdklgeqinkleqkvekqgeki 64 
                                       v+k +  i+k + + +  + ki
  gi|330508352|ref|YP_004384780.1| 122 VNKYNADIEKYNLQRDIINIKI 143
                                       2222222222222222222223 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 ?   11.1   2.3   0.00056      0.37      72     124 ..      39      91 ..      29      95 .. 0.87
   2 ?    1.5   0.1      0.51   3.4e+02      77     122 ..     105     150 ..      87     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00056
                            DUF641  72 eeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkk 124
                                       +  +l++ei + ++++++++ t++  e+e++++++e +++k++L++ e++  k
  gi|330508352|ref|YP_004384780.1|  39 KMDQLSSEISQDKQAIASLNETISLEEKEIDQRKAERDSIKAQLDAWEMRMDK 91 
                                       567899***************************************99888766 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.51
                            DUF641  77 eaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksn 122
                                       +a + +  sl ++y+  v+k +a++++ + + + ++ k++e ++  
  gi|330508352|ref|YP_004384780.1| 105 NALVSQYNSLRDPYNELVNKYNADIEKYNLQRDIINIKIDEYNELA 150
                                       5556667788889999999999999998888888888887777655 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.5    0.0012      0.79      89     127 ..      39      84 ..      28     100 .. 0.70
   2 ?    0.2   0.0      0.48   3.2e+02     226     249 ..     106     129 ..      99     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                             Atg14  89 klsqlkkeieekkkklaklsdklk.......kRrsdleslqnelee 127
                                       k++ql +ei + k+ +a+l+++++       +R+++ +s++ +l +
  gi|330508352|ref|YP_004384780.1|  39 KMDQLSSEISQDKQAIASLNETISleekeidQRKAERDSIKAQLDA 84 
                                       5667777777777777777777777777777777777777776654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.48
                             Atg14 226 aLvshyLsirLPaeltlphscqpi 249
                                       aLvs+y s+r P++ ++   +  i
  gi|330508352|ref|YP_004384780.1| 106 ALVSQYNSLRDPYNELVNKYNADI 129
                                       688999999999988777666544 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.5   0.00017      0.11       4      60 ..      27      81 ..      22      87 .. 0.86
   2 ?   -1.4   0.1       3.1     2e+03      31      31 ..     127     127 ..     104     152 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                                      XXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                             DivIC  4 lfllllifgkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieer 60
                                      ++++++++g+++   + ql +ei + ++ +a+l++++   e+e+++ k ++d i+++
  gi|330508352|ref|YP_004384780.1| 27 ILQYASYQGDYNK--MDQLSSEISQDKQAIASLNETISLEEKEIDQRKAERDSIKAQ 81
                                      5778888777665..568999************************999899998765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.1
                                       H CS
                             DivIC  31 a 31 
                                       a
  gi|330508352|ref|YP_004384780.1| 127 A 127
                                       2 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.5     0.019        13      48     118 ..      41     111 ..      27     114 .. 0.68
   2 ?    7.1   0.5    0.0068       4.5     101     127 ..     115     139 ..     109     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.019
                              LemA  48 esveekaeaenqlssalsrllavaEnYPdLkanenfleLqeelegtEnria.vaRrrYneavreyntkiesf 118
                                       +++++ +++++q  ++l++ + + E+  d + +++  +++++l   E r+  ++ ++Yn++v+ yn+ ++++
  gi|330508352|ref|YP_004384780.1|  41 DQLSSEISQDKQAIASLNETISLEEKEIDQR-KAERDSIKAQLDAWEMRMDkMTPSEYNQNVDPYNALVSQY 111
                                       5555555555555556666666666655533.3445678899999999996256799*********999876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0068
                              LemA 101 RrrYneavreyntkiesfpsnivaklf 127
                                       R  Yne v++yn+ ie++  n+   ++
  gi|330508352|ref|YP_004384780.1| 115 RDPYNELVNKYNADIEKY--NLQRDII 139
                                       899************986..4445555 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   8.1    0.0048       3.2      11      65 ..      32      89 ..      27     101 .. 0.87
   2 ?    1.8   0.0      0.35   2.3e+02      19      59 ..     104     144 ..      91     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0048
                              FlxA 11 sssgsasqiasLqkQiknlqkqLkelses...deltkeekkkqqqliqaQIqqlqaQI 65
                                      s +g  +++ +L  +i++ ++ + +l e+   +e+  +++k+ ++ i+aQ+++ ++ +
  gi|330508352|ref|YP_004384780.1| 32 SYQGDYNKMDQLSSEISQDKQAIASLNETislEEKEIDQRKAERDSIKAQLDAWEMRM 89
                                      5677788999******************999*******************99877665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.35
                              FlxA  19 iasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIq 59 
                                        ++L  Q+++l +  +el ++ + + e  + q++ i  +I+
  gi|330508352|ref|YP_004384780.1| 104 YNALVSQYNSLRDPYNELVNKYNADIEKYNLQRDIINIKID 144
                                       56788999999999999999988888878889999988886 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.3    0.0076         5      20      70 ..      29      79 ..      28      93 .. 0.63
   2 ?    5.9   1.0     0.032        21      16      74 ..      96     154 ..      93     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0076
                      Occludin_ELL 20 eYkeYkelhaeleevskkfseLerelkelkegsk.eykkieeeilqeykklk 70
                                      +Y++Y+  +++++++s+++s+ ++ + +l+e+ + e+k+i ++   e  ++k
  gi|330508352|ref|YP_004384780.1| 29 QYASYQGDYNKMDQLSSEISQDKQAIASLNETISlEEKEIDQR-KAERDSIK 79
                                      5777777777777777777777777777777766666666555.44444444 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.032
                      Occludin_ELL  16 eFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpe 74 
                                       e+n++ + Y++l ++ +++++  +eL ++ ++  e+ +  ++i++  ++ey++l k+p+
  gi|330508352|ref|YP_004384780.1|  96 EYNQNVDPYNALVSQYNSLRDPYNELVNKYNADIEKYNLQRDIINIKIDEYNELAKKPR 154
                                       8999999***********************99999999555555555999999998875 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.1   0.00093      0.61      31      68 ..      32      68 ..      26      73 .. 0.86
   2 ?   -0.1   0.3         2   1.3e+03      50      64 ..      71      85 ..      65     124 .. 0.68
   3 ?    0.9   0.2      0.94   6.2e+02      34      55 ..     123     144 ..     106     155 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00093
                       Fungal_TACC 31 gyeakyqkkldklelenkslkqeieqLkkqleaerkEK 68
                                      +y+  y +k+d+l+ e ++ kq i +L++++++e+kE 
  gi|330508352|ref|YP_004384780.1| 32 SYQGDY-NKMDQLSSEISQDKQAIASLNETISLEEKEI 68
                                      565555.589************************9995 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2
                       Fungal_TACC 50 lkqeieqLkkqleae 64
                                       k e +++k ql+a 
  gi|330508352|ref|YP_004384780.1| 71 RKAERDSIKAQLDAW 85
                                      455556666666543 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.94
                       Fungal_TACC  34 akyqkkldklelenkslkqeie 55 
                                       +ky+ +++k +l+++  +  i+
  gi|330508352|ref|YP_004384780.1| 123 NKYNADIEKYNLQRDIINIKID 144
                                       6888888888888776655554 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.61   4.1e+02      17      44 ..      34      61 ..      24      63 .. 0.73
   2 ?    2.9   1.0      0.28   1.8e+02      10      38 ..      58      86 ..      50      94 .. 0.86
   3 ?    2.2   0.0      0.46     3e+02      23      54 ..      97     121 ..      86     127 .. 0.44
   4 ?    6.9   0.1     0.015        10      10      43 ..     119     152 ..     114     155 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.61
                                      XXXXXXXXXXXXXXXXXHHHHHHHHHHH CS
                            FliD_N 17 rakldkleqkktklewkqsayrelnskl 44
                                      +  ++k++q  +++++ ++a+ +ln  +
  gi|330508352|ref|YP_004384780.1| 34 QGDYNKMDQLSSEISQDKQAIASLNETI 61
                                      3377888888888888888888888765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.28
                                      XXXXXXXXXXXXXXXXXXXXXXXXHHHHH CS
                            FliD_N 10 kqlmkaerakldkleqkktklewkqsayr 38
                                      ++ ++ e++++d+ +++  +++++ +a++
  gi|330508352|ref|YP_004384780.1| 58 NETISLEEKEIDQRKAERDSIKAQLDAWE 86
                                      56789999*******************97 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.46
                                       XXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHH CS
                            FliD_N  23 leqkktklewkqsayrelnsklsnlksalsal 54 
                                       ++q         + y++l s+ ++l++ +++l
  gi|330508352|ref|YP_004384780.1|  97 YNQ-------NVDPYNALVSQYNSLRDPYNEL 121
                                       333.......3344444444444444433322 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.015
                                       XXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHH CS
                            FliD_N  10 kqlmkaerakldkleqkktklewkqsayrelnsk 43 
                                       ++l++ ++a ++k++ +   ++ k+++y+el +k
  gi|330508352|ref|YP_004384780.1| 119 NELVNKYNADIEKYNLQRDIINIKIDEYNELAKK 152
                                       6799999***********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2045  (0.114061); expected 358.6 (0.02)
Passed bias filter:                      965  (0.0538234); expected 358.6 (0.02)
Passed Vit filter:                       140  (0.00780858); 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):              27  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 1071.21
//
Query:       gi|330508353|ref|YP_004384781.1|  [L=235]
Description: lipoprotein-releasing system ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-32  111.7   0.0    5.3e-32  111.2   0.0    1.2  1  ABC_tran     ABC transporter
    7.1e-09   35.4   0.0    2.4e-05   23.9   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    7.3e-06   26.5   0.1    1.3e-05   25.7   0.1    1.4  1  AAA_16       AAA ATPase domain
     0.0001   22.0   0.1     0.0002   21.0   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00029   21.1   0.5     0.0027   18.0   0.5    2.4  1  AAA_22       AAA domain
    0.00037   20.4   2.8       0.11   12.3   0.6    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0013   18.7   0.4      0.003   17.5   0.1    1.7  2  RsgA_GTPase  RsgA GTPase
     0.0061   17.1   0.1      0.015   15.8   0.1    1.6  2  AAA_23       AAA domain
     0.0072   15.0   0.0      0.029   13.0   0.0    1.8  2  AAA_13       AAA domain
  ------ inclusion threshold ------
      0.011   15.7   0.4       0.65    9.9   0.1    2.2  2  NTPase_1     NTPase
      0.013   15.1   0.0       0.28   10.7   0.0    2.2  2  AAA_25       AAA domain
      0.022   15.0   0.0      0.035   14.4   0.0    1.3  1  PIN_4        PIN domain
      0.034   13.7   0.1       0.11   12.1   0.0    1.8  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.04   13.6   0.0      0.086   12.6   0.0    1.7  1  AAA_30       AAA domain
      0.061   12.4   0.3       0.13   11.3   0.1    1.6  2  T2SSE        Type II/IV secretion system protein
      0.065   13.1   0.0       0.14   12.1   0.0    1.5  2  Rad17        Rad17 P-loop domain
      0.071   13.0   0.2       0.38   10.6   0.2    2.0  1  ATPase_2     ATPase domain predominantly from Archaea
        0.1   11.9   0.3        6.9    5.9   0.0    2.2  2  ATPase       KaiC
       0.11   12.8   0.2       0.32   11.2   0.0    1.9  3  AAA_28       AAA domain
       0.15   11.9   0.1       0.91    9.4   0.1    2.0  2  NACHT        NACHT domain
       0.18   11.9   0.2       0.67   10.1   0.1    2.0  2  MMR_HSR1     50S ribosome-binding GTPase
       0.33   11.5   1.8       0.63   10.6   1.7    1.9  1  AAA_18       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   0.0   6.5e-35   5.3e-32       1     136 [.      22     170 ..      22     171 .. 0.94

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 6.5e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l++v+l++ ege + i+G++G+GKStLl++l  l kp  Gei+l+g+++++    ++ +  +ke+g+++q ++l pe
  gi|330508353|ref|YP_004384781.1|  22 LDDVDLTILEGEFLSITGPSGSGKSTLLNMLGLLDKPSGGEIWLKGREVSQssslERSRLRNKELGFIFQYHHLLPE 98 
                                       799***********************************************999988899999*************** PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        t+ en             +++ + e++l+++gl+e  +++     s+LSgGq qrva+aral+++p++++ DEpt
  gi|330508353|ref|YP_004384781.1|  99 FTALENvmipqliagedkkAARHRSEELLREMGLVERLNHKP----SELSGGQSQRVAVARALANRPSIVIGDEPT 170
                                       **************998776677799*******999666665....*****************************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 !    9.7   0.0   0.00064      0.52      23      42 ..      31      50 ..      21      56 .. 0.85
   2 !   23.9   0.0   2.9e-08   2.4e-05     122     212 ..     122     216 ..      65     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00064
                                      TSSEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 23 sksftaivGpNGSGKsnlld 42
                                      + +f +i+Gp GSGKs ll+
  gi|330508353|ref|YP_004384781.1| 31 EGEFLSITGPSGSGKSTLLN 50
                                      567999**********9986 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 2.9e-08
                                       HHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SE CS
                                       xxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                             SMC_N 122 evsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQ 191
                                         +ell+++g+ +       +LSgG+ + va+a  +A    ++ ++++ De   +LD k  + v ell++ + +  Q
  gi|330508353|ref|YP_004384781.1| 122 RSEELLREMGLVERlnhkpsELSGGQSQRVAVARALA----NRPSIVIGDEPTGNLDTKSSEMVYELLRKLNREiKQ 194
                                       34444444443322555555*********99998876....56689999********************88777544 PP

                                       .EEEE-SSHHHCCC-SCEEEEE CS
                                       .xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 192 .fivislreemlekadklvgvt 212
                                        fi ++++ +m +k d+++++ 
  gi|330508353|ref|YP_004384781.1| 195 tFILVTHDMNMAQKTDRILRLV 216
                                       4899*************99875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   1.6e-08   1.3e-05      22     141 ..      32     200 ..      12     216 .. 0.63

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.6e-08
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesa.................ipysalaqalare 79 
                                       g  e + ++G+sG+GKs+l+++l   l k   g i+l+g+ ++ +s+                  ++++  +al++ 
  gi|330508353|ref|YP_004384781.1|  32 G--EFLSITGPSGSGKSTLLNMLG-LLDKPsgGEIWLKGREVSQSSSlersrlrnkelgfifqyHHLLPEFTALEN- 104
                                       3..7899*************9999.677775434557777777755556666666666666443333665666634. PP

                            AAA_16  80 ellrqlldeaesaeleawrekleeala.....................................avpelagaeasrl 119
                                         + ql + ++++++++ +e+l+++++                                     ++++l+ ++++ +
  gi|330508353|ref|YP_004384781.1| 105 VMIPQLIAGEDKKAARHRSEELLREMGlverlnhkpselsggqsqrvavaralanrpsivigdePTGNLDTKSSEMV 181
                                       89999999888888888888888888899999886666666666555555555555554444333333333333333 PP

                            AAA_16 120 lellkrllallsrderplvlvl 141
                                       +ell++l + +++   +++lv 
  gi|330508353|ref|YP_004384781.1| 182 YELLRKLNREIKQ---TFILVT 200
                                       3333333333332...355555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   2.4e-07    0.0002      17      39 ..      27      49 ..      21      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.4e-07
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTll 39
                                      ++i  +g +  +tGpsGsGKSTll
  gi|330508353|ref|YP_004384781.1| 27 LTIL-EGeFLSITGPSGSGKSTLL 49
                                      5554.344889************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.5   3.3e-06    0.0027       6      29 ..      33      56 ..      29     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.3e-06
                            AAA_22  6 gilvvtGesGtGKTtllrrlleql 29
                                       +l +tG+sG+GK+tll++l   +
  gi|330508353|ref|YP_004384781.1| 33 EFLSITGPSGSGKSTLLNMLGLLD 56
                                      6899**************998765 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.6   0.00014      0.11       4      22 ..      37      55 ..      34      71 .. 0.82
   2 !    8.7   0.1    0.0016       1.3     131     299 ..      69     203 ..      61     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                            AAA_21  4 liGpNgsGKSnLLdaldll 22
                                      ++Gp gsGKS+LL  l ll
  gi|330508353|ref|YP_004384781.1| 37 ITGPSGSGKSTLLNMLGLL 55
                                      99***********999888 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0016
                            AAA_21 131 svsepndlqfgkaltditsrawsllllldglrke...rigllnifadyfgfakekrllqrlvrslklveielsdlge 204
                                       +vs++++l++++++++   +++++ +ll ++      +i++l +  d     ++ + l r ++ + + + ++s l  
  gi|330508353|ref|YP_004384781.1|  69 EVSQSSSLERSRLRNKELGFIFQYHHLLPEFTALenvMIPQLIAGEDKKAARHRSEELLREMGLVERLNHKPSEL-- 143
                                       566666666666666666666666666666665555566666666666655555555555555555555555555.. PP

                            AAA_21 205 geeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllel 281
                                                                        S G+ +  a++ al+ ++   s+++ DEp  +L+ k  + ++el
  gi|330508353|ref|YP_004384781.1| 144 ---------------------------------SGGQSQRVAVARALANRP---SIVIGDEPTGNLDTKSSEMVYEL 184
                                       .................................999999989999999999...9********************** PP

                            AAA_21 282 lkelsrngaQv.iltTHSp 299
                                       l++l+r+  Q  il+TH+ 
  gi|330508353|ref|YP_004384781.1| 185 LRKLNREIKQTfILVTHDM 203
                                       *99999888888*****96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.7e-06     0.003      96     120 ..      29      53 ..      16      79 .. 0.84
   2 ?   -1.6   0.0       2.8   2.2e+03     113     113 ..     177     177 ..     118     217 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.7e-06
                                       HCTTSEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinall 120
                                        l++++  + G+SG GKStL+n+l 
  gi|330508353|ref|YP_004384781.1|  29 ILEGEFLSITGPSGSGKSTLLNMLG 53 
                                       57889999**************985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.8
                                       H CS
                       RsgA_GTPase 113 S 113
                                       S
  gi|330508353|ref|YP_004384781.1| 177 S 177
                                       1 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      23      39 ..      36      52 ..      21      55 .. 0.84
   2 ?   -2.2   0.0         6   4.9e+03     125     130 ..     185     190 ..     133     221 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                            AAA_23 23 lItGpNGaGKTTildAi 39
                                       ItGp G+GK+T+l+ +
  gi|330508353|ref|YP_004384781.1| 36 SITGPSGSGKSTLLNML 52
                                      6*************977 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6
                            AAA_23 125 lgskki 130
                                       l + ++
  gi|330508353|ref|YP_004384781.1| 185 LRKLNR 190
                                       111111 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.31   2.5e+02      23      41 ..      39      57 ..      36     152 .. 0.77
   2 !   13.0   0.0   3.5e-05     0.029     526     577 ..     160     209 ..     149     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.31
                            AAA_13 23 GwNGaGKTtLSrllrslel 41
                                      G  G+GK+tL ++l  l +
  gi|330508353|ref|YP_004384781.1| 39 GPSGSGKSTLLNMLGLLDK 57
                                      7789*****9999877744 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.5e-05
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiL.THnleffkev 577
                                          iv+ D P   LD++s+ +v+ l+++      ++kQ fiL TH ++  ++ 
  gi|330508353|ref|YP_004384781.1| 160 RPSIVIGDEPTGNLDTKSSEMVYELLRKLN---REIKQTFILvTHDMNMAQKT 209
                                       6789999**********************7...9******988**99876665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00079      0.65       3      17 ..      36      50 ..      34      61 .. 0.88
   2 ?    4.0   0.0     0.052        42      88     154 ..     153     222 ..     119     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00079
                                      EEE--TTSSHHHHHH CS
                          NTPase_1  3 fiTGppGvGKtTlvk 17
                                       iTGp+G+GK+Tl++
  gi|330508353|ref|YP_004384781.1| 36 SITGPSGSGKSTLLN 50
                                      69***********97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.052
                                       HHHHHHHHH-EEEE--.-STTGGG-HHHHHHHHHHHT..TTSEEEEE--SS--SHHHHHHHT-TT-EEEE CS
                          NTPase_1  88 alrkalseadviviDE.iGkmElkskkfkeaveevLk..sekpvlavihrrkdlalveeirerkdvkvfe 154
                                       + r   +++ +++ DE  G++  ks ++  ++ + L+   ++ ++ v h  +  + +++i +  d+++++
  gi|330508353|ref|YP_004384781.1| 153 VARALANRPSIVIGDEpTGNLDTKSSEMVYELLRKLNreIKQTFILVTHDMNMAQKTDRILRLVDGRIVS 222
                                       333334788899999978*********9999999998655677888889888888899998888888764 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00034      0.28      30      52 ..      29      51 ..      24      72 .. 0.85
   2 ?    1.8   0.0      0.19   1.5e+02     164     188 ..     177     201 ..     162     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00034
                            AAA_25 30 lpagelallaGapgtGKttlald 52
                                      + +ge+  ++G++g+GK+tl+  
  gi|330508353|ref|YP_004384781.1| 29 ILEGEFLSITGPSGSGKSTLLNM 51
                                      6799****************855 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.19
                            AAA_25 164 dvgalvealeriarrtgaavllvhH 188
                                         ++++e l+++ r+ + +++lv H
  gi|330508353|ref|YP_004384781.1| 177 SSEMVYELLRKLNREIKQTFILVTH 201
                                       34899999****************9 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.3e-05     0.035      14     120 ..      95     209 ..      87     212 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-05
                             PIN_4  14 alksfkeehdvviPitVleELdklKkgsserelarlarqanrlldelleke...sgrlkvqtsaeelpeee...... 81 
                                       +l +f    +v+iP+ +  E  k  +++s +el r++  + rl ++  e +   s+r+ v ++ ++ p+        
  gi|330508353|ref|YP_004384781.1|  95 LLPEFTALENVMIPQLIAGEDKKAARHRS-EELLREMGLVERLNHKPSELSggqSQRVAVARALANRPS-Ivigdep 169
                                       55566566679999999999555555554.555555555555444443333222566666555444443.1345555 PP

                             PIN_4  82 ..seseknDnrIlavalelkeekpdrkvvLvskDinlrikA 120
                                         + ++k  +++ +   +l++e+ +++ +Lv+ D+n+  k 
  gi|330508353|ref|YP_004384781.1| 170 tgNLDTKSSEMVYELLRKLNREI-KQTFILVTHDMNMAQKT 209
                                       44225688899999999999999.89***********9996 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.11       4      20 ..      36      52 ..      33      89 .. 0.87
   2 ?   -0.8   0.0       1.2   9.8e+02      89     121 ..     168     203 ..     118     225 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                      EEEESTTCCHHHHHHHH CS
                              cobW  4 vltGflGsGKTtLlnhl 20
                                       +tG+ GsGK+tLln l
  gi|330508353|ref|YP_004384781.1| 36 SITGPSGSGKSTLLNML 52
                                      69************986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                       EECTTTTHHHH.HTT..SHHHHHCCCECEEEEEEET CS
                              cobW  89 EttGlaePapv.aft..eeelksdltldavvavvDa 121
                                       E tG+++ + + ++    ++l+++++ +++++  D 
  gi|330508353|ref|YP_004384781.1| 168 EPTGNLDTKSSeMVYelLRKLNREIKQTFILVTHDM 203
                                       666666666664322344444444444444444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011     0.086      20      53 ..      34      67 ..      25     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglA 53
                                      +  +tGp G+GK+t+l+ l  + + +gg++ +  
  gi|330508353|ref|YP_004384781.1| 34 FLSITGPSGSGKSTLLNMLGLLDKPSGGEIWLKG 67
                                      6789*************99888888887776655 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 ?   11.3   0.1   0.00016      0.13     132     149 ..      35      52 ..      24      62 .. 0.84
   2 ?   -2.1   0.0         2   1.6e+03     140     140 ..     172     172 ..     102     217 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                             T2SSE 132 ilvsGgTgsGKttllyal 149
                                       + ++G+ gsGK+tll++l
  gi|330508353|ref|YP_004384781.1|  35 LSITGPSGSGKSTLLNML 52 
                                       459************975 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
                             T2SSE 140 s 140
                                        
  gi|330508353|ref|YP_004384781.1| 172 N 172
                                       1 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00017      0.14      46      66 ..      33      53 ..      20      89 .. 0.83
   2 ?   -2.8   0.0         6   4.9e+03     137     171 ..     164     199 ..     154     211 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                             Rad17 46 riLLisGPsGCgkstvvkvLs 66
                                      + L i+GPsG gkst +++L 
  gi|330508353|ref|YP_004384781.1| 33 EFLSITGPSGSGKSTLLNMLG 53
                                      3899************99985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6
                             Rad17 137 lvedlP..nkfyrdsdalrevirkylrssealplilv 171
                                       ++ d P  n   ++s+ + e++rk  r  +  ++ilv
  gi|330508353|ref|YP_004384781.1| 164 VIGDEPtgNLDTKSSEMVYELLRKLNREIKQ-TFILV 199
                                       5555554444444556666666665544333.34444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00047      0.38      21      39 ..      33      51 ..      27     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                          ATPase_2 21 eiyfiYGpegsGKtaLlke 39
                                      e++ i+Gp gsGK++Ll+ 
  gi|330508353|ref|YP_004384781.1| 33 EFLSITGPSGSGKSTLLNM 51
                                      6778************985 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0085       6.9      16      35 ..      29      48 ..      19      51 .. 0.86
   2 ?    3.9   0.1     0.035        29     142     190 ..     179     225 ..     162     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0085
                            ATPase 16 ipegrvvlitGepGtGKtif 35
                                      i eg+   itG +G+GK+++
  gi|330508353|ref|YP_004384781.1| 29 ILEGEFLSITGPSGSGKSTL 48
                                      789999***********987 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.035
                            ATPase 142 eilrqlvrvl.kklgvTailvsekssseeaaggygveefivdgvivLdlk 190
                                       e + +l+r l +++++T ilv+     + a ++ ++   +vdg iv + +
  gi|330508353|ref|YP_004384781.1| 179 EMVYELLRKLnREIKQTFILVTHD--MNMAQKTDRILR-LVDGRIVSEMR 225
                                       5677888888889999****9994..445667777888.89998876655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00039      0.32       4      20 ..      37      53 ..      35      95 .. 0.81
   2 ?   -2.6   0.0       7.2   5.8e+03     132     160 ..     118     147 ..     113     150 .. 0.66
   3 ?   -3.0   0.0       9.1   7.4e+03     137     157 ..     181     200 ..     174     211 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                            AAA_28  4 itGgestGKTtlleaLa 20
                                      itG++++GK+tll+ L 
  gi|330508353|ref|YP_004384781.1| 37 ITGPSGSGKSTLLNMLG 53
                                      9*************996 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.2
                            AAA_28 132 eereaiderlre..alrelgipviivpsgdv 160
                                       ++r +++e+lre  ++++l+++  ++ sg  
  gi|330508353|ref|YP_004384781.1| 118 AARHRSEELLREmgLVERLNHKPSEL-SGGQ 147
                                       56777778888766677788777777.6555 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 9.1
                            AAA_28 137 iderlrealrelgipviivps 157
                                       ++e+lr++ re+   +i v +
  gi|330508353|ref|YP_004384781.1| 181 VYELLRKLNREIKQTFILV-T 200
                                       5566666666666666655.4 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0011      0.91       4      20 ..      36      52 ..      33      57 .. 0.86
   2 ?   -0.1   0.0      0.97   7.9e+02      97     133 ..     173     207 ..     146     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                                      EEEC-TTTCHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqkl 20
                                       ++G++GsGK+tLl  l
  gi|330508353|ref|YP_004384781.1| 36 SITGPSGSGKSTLLNML 52
                                      699**********9865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.97
                                       TCH.........HHHHHCTTTTT--EEEEEEECCCHH CS
                             NACHT  97 lgqkekqpvrtlLselirkkllpeasllltvrpralr 133
                                       l+ k  + v +lL++l r+  ++++ +l+t   +  +
  gi|330508353|ref|YP_004384781.1| 173 LDTKSSEMVYELLRKLNRE--IKQTFILVTHDMNMAQ 207
                                       4445667788888888888..8888888887655555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00082      0.67       3      19 ..      36      52 ..      34      79 .. 0.90
   2 ?   -0.9   0.0       2.1   1.7e+03      32      33 ..     199     200 ..     150     227 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00082
                                      EEEESTTSSHHHHHHHH CS
                          MMR_HSR1  3 aivGrpNvGKStLinal 19
                                       i G + +GKStL+n l
  gi|330508353|ref|YP_004384781.1| 36 SITGPSGSGKSTLLNML 52
                                      699************87 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.1
                                       SS CS
                          MMR_HSR1  32 tT 33 
                                       +T
  gi|330508353|ref|YP_004384781.1| 199 VT 200
                                       22 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.7   0.00077      0.63       3      18 ..      37      52 ..      36     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00077
                            AAA_18  3 ltGtpGvGKttlakeL 18
                                      +tG++G+GK+tl + L
  gi|330508353|ref|YP_004384781.1| 37 ITGPSGSGKSTLLNML 52
                                      8***********9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 1727.22
//
Query:       gi|330508354|ref|YP_004384782.1|  [L=386]
Description: ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete 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   60.3   2.5    1.9e-16   60.3   2.5    3.0  3  FtsX         FtsX-like permease family
    1.4e-10   41.9   0.1    2.3e-10   41.2   0.1    1.3  1  MacB_PCD     MacB-like periplasmic core domain
  ------ inclusion threshold ------
      0.016   14.4   2.7      0.035   13.4   1.1    1.9  2  Lung_7-TM_R  Lung seven transmembrane receptor


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 ?    0.6   0.1      0.14   8.2e+02      69      84 ..      18      33 ..       9      49 .. 0.52
   2 ?    1.6   0.7     0.066     4e+02      61      91 ..     249     279 ..     219     281 .. 0.76
   3 !   60.3   2.5   3.1e-20   1.9e-16       2      96 .]     281     379 ..     280     379 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.14
                              FtsX 69 vliiivlllllallag 84
                                      vl+ ++ + l +++++
  gi|330508354|ref|YP_004384782.1| 18 VLFPVLAVALAVMVIA 33
                                      3333333333333332 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.066
                              FtsX  61 kisidlitvliiivlllllallagllsiski 91 
                                       + ++ ++ +l+i+v++ + ++ +++  is+ 
  gi|330508354|ref|YP_004384782.1| 249 QRFFTYLFYLLIFVISGFGVVNTMIMTISRR 279
                                       5567777888888888888888888877775 PP

  == domain 3  score: 60.3 bits;  conditional E-value: 3.1e-20
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs....selkisidlitvliiiv 74 
                                       reigil a+G+++++++++++ e+l+++ +++++G++l+++aa+l+ ++  ++       s+++i +++++++ +++
  gi|330508354|ref|YP_004384782.1| 281 REIGILMAIGANRGSIIKIFMAESLILGPPSAALGCLLAYVAAKLIEAFPIEIPAEvyaaSRMSILLSPEIFAYAVA 357
                                       9********************************************999999994434446***************** PP

                              FtsX  75 lllllallagllsiskilkkep 96 
                                       +++++ l+agl++++k+++++p
  gi|330508354|ref|YP_004384782.1| 358 FAMMVDLAAGLYPAYKASRMDP 379
                                       ********************98 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.1   3.8e-14   2.3e-10       5     181 ..      22     213 ..      19     226 .. 0.70

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 3.8e-14
                          MacB_PCD   5 vLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsd.pdvealrr...evp.veavapvv... 73 
                                       vL++a++v+++ a+++l+e+ ++ + s+  +++  +tv p++g  e  ++  ++++l+      + veav+p++   
  gi|330508354|ref|YP_004384782.1|  22 VLAVALAVMVIAAMMGLMESYREEIISSTVENSPYLTVEPKEG--E--DYiHLYKTLSSviwGYSgVEAVSPRLlgm 94 
                                       89*************************9776666788888752..1..221222233223343456******98887 PP

                          MacB_PCD  74 .tvrgggsgeeevtvvgvdpdyfk.vfgl..klaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl....kp 141
                                        +++++++  ++v+++g dp + + ++g+  +l+ G   +++dl+ +++++++g++lae+l  + Gd   l    ++
  gi|330508354|ref|YP_004384782.1|  95 aAAKYREQV-KGVSIIGIDPLLEDpLLGVqsDLVWG---DFNDLAFKKHSAIVGAKLAEDLKlKPGDGFYLvrkgVS 167
                                       645666642.3499*****85544688884233445...44666779999**********99*99*******99966 PP

                          MacB_PCD 142 ftVvGv..ledppgsgsalgddavylplttlqrrs........itvrlkd 181
                                       ++V+    +   +g+  + +++ vylpl+t+qr +        i ++++d
  gi|330508354|ref|YP_004384782.1| 168 LKVTPAgyI--RTGT--GADESLVYLPLETAQRLMgegdvvseIGIKTSD 213
                                       666655114..2243..346789****99986655555555556666665 PP

>> Lung_7-TM_R  Lung seven transmembrane receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.062   3.7e+02     151     181 ..      19      49 ..       7      76 .. 0.72
   2 ?   13.4   1.1   5.8e-06     0.035     127     178 ..     253     304 ..     243     331 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.062
                       Lung_7-TM_R 151 lkkvlllglllfvlaevlelvresseesess 181
                                       l+ vl ++l+++v+a++++l++ ++ee+ ss
  gi|330508354|ref|YP_004384782.1|  19 LFPVLAVALAVMVIAAMMGLMESYREEIISS 49 
                                       4446667777777777777777777666555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.8e-06
                       Lung_7-TM_R 127 tlsrlliliislGygivkpkLgdllkkvlllglllfvlaevlelvressees 178
                                       t+++ l++ + +G+g+v++++ ++ ++   +g+l+ + a+  ++++ +  es
  gi|330508354|ref|YP_004384782.1| 253 TYLFYLLIFVISGFGVVNTMIMTISRRTREIGILMAIGANRGSIIKIFMAES 304
                                       678889999999********************************99887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3073.63
//
Query:       gi|330508355|ref|YP_004384783.1|  [L=388]
Description: ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-13   48.8  14.1    1.3e-11   44.8   2.4    3.2  3  FtsX             FtsX-like permease family
    4.2e-12   46.8   3.2    4.2e-12   46.8   3.2    1.5  2  MacB_PCD         MacB-like periplasmic core domain
     0.0023   17.1   1.6     0.0023   17.1   1.6    1.5  2  ABC2_membrane_3  ABC-2 family transporter protein


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 !    8.6   0.8   0.00041       2.5      25      68 ..      24      68 ..      22      68 .. 0.84
   2 ?    2.1   0.1     0.046   2.7e+02      58      83 ..     256     281 ..     223     282 .. 0.68
   3 !   44.8   2.4   2.1e-15   1.3e-11       2      96 .]     286     382 ..     285     382 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00041
                              FtsX 25 illitlvalviG.lglgllaaqllsdvllssvfsselkisidlit 68
                                      +l+it+v+++++  +l +++ + +sd++l +vf+s ++i i++i+
  gi|330508355|ref|YP_004384783.1| 24 ALAITAVGMAVAvSLLIIAVQNGFSDYMLDIVFKSLPHIIIKPID 68
                                      58999****99955666666677******************9985 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.046
                              FtsX  58 selkisidlitvliiivlllllalla 83 
                                        +  i++ li+v+++++++ ++ +l+
  gi|330508355|ref|YP_004384783.1| 256 ASNMITLLLIMVIATFGIASIMNMLV 281
                                       45556777777777777777776665 PP

  == domain 3  score: 44.8 bits;  conditional E-value: 2.1e-15
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs..selkisidlitvliiivll 76 
                                       reig+l a G+ + ++++++l+e+ l++l ++++G++ +l++a  l ++  ++  +    l++ +++ +++++ +++
  gi|330508355|ref|YP_004384783.1| 286 REIGMLMAAGADSSHIRKIFLLESGLLGLMGALLGCAMSLVLAIRLRSLQIEMPTGgmVDLPVILSYQDMVTLSLIA 362
                                       9*****************************************99988777777555789****************** PP

                              FtsX  77 lllallagllsiskilkkep 96 
                                       l+l l+ag++++  ++k +p
  gi|330508355|ref|YP_004384783.1| 363 LILSLAAGIYPAHIASKLDP 382
                                       ****************9987 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   3.2   7.1e-16   4.2e-12       2     192 ..      24     230 ..      23     232 .. 0.68
   2 ?   -6.2   3.0         3   1.8e+04       2      20 ..     263     281 ..     262     283 .. 0.70

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 7.1e-16
                          MacB_PCD   2 lltvLGiaiGvaaviaivslgeglqasvlsq.isdlgnlvtvtpgkgsgeslsdpdve.alrr...evp.veavapv 72 
                                       +l++ ++  +va+  +i+++ +g+++++l+  +++   l ++ +++ +ge+   ++++  + +    ++ v++v+pv
  gi|330508355|ref|YP_004384783.1|  24 ALAITAVGMAVAVSLLIIAVQNGFSDYMLDIvFKS---LPHIIIKPIDGEN-YLNLYQnVI-DgvwGLEgVVGVSPV 95 
                                       89****************************84443...4466666522233.223333212.12333556999***9 PP

                          MacB_PCD  73 v..tvrgggsg...eeevtvvgvdp.dyfkvfgl.klaeGrffteadlrg..gpnvvvigeelaerlf.pvGdtirl 139
                                       +  t++++ ++   +  + + gv p +  k+ ++ +      + + dl++  g + +++g++lae+l  ++Gdt+  
  gi|330508355|ref|YP_004384783.1|  96 LaaTATFTHEDkvaN--AAMLGVLPfEADKISKIsE---S--MVQGDLNSiiGGKKILLGRSLAEKLDmKLGDTVHA 165
                                       876333333222333..5678855323444555532...2..55556665557777**********88*******99 PP

                          MacB_PCD 140 .......kpftVvGvled.ppgsgsalgddavylplttlqrrs........itvrlkdgadleaaaael 192
                                               ++tV+G++++ +    ++ ++   y++l+t+q+          i ++l+d ++++a+a ++
  gi|330508355|ref|YP_004384783.1| 166 dfpdardLNLTVSGIFDTgY----ASVDEKTSYVSLETAQVFLnegnvvtqIDIKLNDIDQAQAVAGQI 230
                                       99**99999******95433....455777788887777443344555555*************99888 PP

  == domain 2  score: -6.2 bits;  conditional E-value: 3
                          MacB_PCD   2 lltvLGiaiGvaaviaivs 20 
                                       ll ++  ++G+a+++ +++
  gi|330508355|ref|YP_004384783.1| 263 LLIMVIATFGIASIMNMLV 281
                                       5677777888888876665 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 ?   -4.0   0.2      0.99   5.9e+03     274     286 ..      34      39 ..      21      63 .. 0.46
   2 !   17.1   1.6   3.8e-07    0.0023      98     236 ..     197     341 ..      95     372 .. 0.64

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 0.99
                   ABC2_membrane_3 274 fivilllsgffgg 286
                                       ++v+l       +
  gi|330508355|ref|YP_004384783.1|  34 VAVSL-------L 39 
                                       11111.......1 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.8e-07
                   ABC2_membrane_3  98 satvtvlinssnlnsskailnalnsllqqlnasalvlqseatstsaninvestqleeel..snvasf....lvg.li 167
                                         t++v++n+ n+  +++i   ln++ q+++          +++s+ ++v+  q ++++  ++ a+     +++ l+
  gi|330508355|ref|YP_004384783.1| 197 LETAQVFLNEGNV--VTQIDIKLNDIDQAQA-------VAGQISSDRYEVQVWQESNPEivESLAYEkasnMITlLL 264
                                       3444444444432..3445555555444433.......456778888888887775555545555546666555699 PP

                   ABC2_membrane_3 168 liilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afgl.......gipf 235
                                       +++++++++++i++++v Ek++ i +l+  +g + + +    +l ++l++l  +ll +++  ++++       ++p 
  gi|330508355|ref|YP_004384783.1| 265 IMVIATFGIASIMNMLVLEKTREIGMLM-AAGADSSHIRKIFLLESGLLGLMGALLGCAMslVLAIrlrslqiEMPT 340
                                       9999********************9887.677777664444444444444444444444222333333555554444 PP

                   ABC2_membrane_3 236 g 236
                                       g
  gi|330508355|ref|YP_004384783.1| 341 G 341
                                       3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.21s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3045.76
//
Query:       gi|330508356|ref|YP_004384784.1|  [L=115]
Description: hypothetical protein MCON_2539 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   14.1   0.0      0.041   13.9   0.0    1.1  1  Wzt_C     Wzt C-terminal domain


Domain annotation for each model (and alignments):
>> Wzt_C  Wzt C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.3e-06     0.041      75     125 ..      24      71 ..      12      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-06
                             Wzt_C  75 feleelkagervevefefklpLapGeYlltvaledrdgeeneiydwlddal 125
                                       +++++l +g+  ++e++ +  L+pG Y l + l +++g+    +d+ ++++
  gi|330508356|ref|YP_004384784.1|  24 KKTPVLLKGDDETIEVSWNKTLNPGIYQLKIQLLGTEGD---LIDFTERVI 71 
                                       3378899***********559************999998...888877765 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:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 835.71
//
Query:       gi|330508357|ref|YP_004384785.1|  [L=206]
Description: hypothetical protein MCON_2540 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1548.48
//
Query:       gi|330508358|ref|YP_004384786.1|  [L=216]
Description: HTH DNA binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-20   70.8   0.1    9.9e-20   70.1   0.1    1.3  1  HTH_10    HTH DNA binding domain
  ------ inclusion threshold ------
      0.035   14.0   0.0       0.06   13.2   0.0    1.4  1  MarR_2    MarR family
      0.054   13.1   0.1       0.11   12.0   0.1    1.4  1  HTH_CodY  CodY helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.1   1.7e-23   9.9e-20       1      52 [.     158     209 ..     158     210 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.7e-23
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT +q+ +l +A + GY+dyPRr+++++LA++lGI ks++ ehLrkae ++i
  gi|330508358|ref|YP_004384786.1| 158 LTNRQRDILIKAKKGGYYDYPRRINADQLAERLGIGKSATVEHLRKAEGRII 209
                                       9*************************************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     1e-05      0.06      20      46 ..     173     205 ..     148     207 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                                       S......EEEHHHHHHHHTSSHHHHHHHHHHHH CS
                            MarR_2  20 r......dltvgelarrlglsksavsrilkrLv 46 
                                       +      ++++ +la+rlg+ ksa+  +l++++
  gi|330508358|ref|YP_004384786.1| 173 GyydyprRINADQLAERLGIGKSATVEHLRKAE 205
                                       155555589*********************997 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.9e-05      0.11       4      30 ..     180     206 ..     179     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
                          HTH_CodY   4 rLtaskiaDriGitrsvivnaLrkLes 30 
                                       r+ a ++a+r+Gi +s  v  Lrk e 
  gi|330508358|ref|YP_004384786.1| 180 RINADQLAERLGIGKSATVEHLRKAEG 206
                                       678999******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1695.60
//
Query:       gi|330508359|ref|YP_004384787.1|  [L=81]
Description: hypothetical protein MCON_2543 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.3   0.1       0.19   11.7   0.1    1.3  1  DUF2633   Protein of unknown function (DUF2633)


Domain annotation for each model (and alignments):
>> DUF2633  Protein of unknown function (DUF2633)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.1e-05      0.19       8      29 ..      15      36 ..       4      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.1e-05
                           DUF2633  8 rlTrivLliSFLflFGRllYsa 29
                                      +l  ++LliS L+l  R+ Ys+
  gi|330508359|ref|YP_004384787.1| 15 KLSGLLLLISMLILLSRYGYSS 36
                                      566689**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 682.90
//
Query:       gi|330508360|ref|YP_004384788.1|  [L=70]
Description: Helix-turn-helix protein [Methanosaeta concilii GP6]
Scores for complete 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   57.7   0.2    9.8e-16   57.6   0.2    1.0  1  HTH_3           Helix-turn-helix
    2.6e-09   37.3   0.0    3.3e-09   37.0   0.0    1.0  1  HTH_31          Helix-turn-helix domain
    2.2e-08   34.0   0.1    2.5e-08   33.8   0.1    1.0  1  HTH_19          Helix-turn-helix domain
    7.9e-07   29.4   0.0      9e-07   29.2   0.0    1.0  1  HTH_26          Cro/C1-type HTH DNA-binding domain
    0.00065   19.6   0.1    0.00096   19.1   0.1    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00076   19.3   0.1     0.0012   18.7   0.1    1.3  1  HTH_25          Helix-turn-helix domain
     0.0048   16.4   0.3      0.007   15.9   0.3    1.3  1  Sigma70_r4      Sigma-70, region 4
  ------ inclusion threshold ------
      0.024   14.4   0.4      0.024   14.4   0.4    1.5  2  HTH_38          Helix-turn-helix domain
      0.053   13.5   0.0      0.065   13.2   0.0    1.4  1  HTH_37          Helix-turn-helix domain
      0.055   13.3   0.0       0.13   12.1   0.0    1.7  1  MerR            MerR family regulatory protein
       0.12   12.5   0.0       0.13   12.3   0.0    1.1  1  Phage_CI_repr   Bacteriophage CI repressor helix-turn-helix d
       0.13   12.3   0.0       0.14   12.3   0.0    1.1  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
       0.15   11.9   0.8       0.16   11.8   0.1    1.4  2  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 !   57.6   0.2   7.1e-19   9.8e-16       1      55 []       7      61 ..       7      61 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 7.1e-19
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsldel 55
                                      +kelR  +gl+qeeLA+++Gv r ti  +E+G+ nPsl+ + k+a aL+ s+de+
  gi|330508360|ref|YP_004384788.1|  7 IKELRARHGLTQEELARMVGVRRETILFLEKGKYNPSLKLACKIALALQASIDEI 61
                                      8***************************************************996 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   2.4e-12   3.3e-09       5      60 ..       6      60 ..       3      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 2.4e-12
                            HTH_31  5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpae 60
                                      + ++lR+r+GL+qee+A+ +gv + t+  lE G+  +ps+    ++a al+++ +e
  gi|330508360|ref|YP_004384788.1|  6 HIKELRARHGLTQEELARMVGVRRETILFLEKGKY-NPSLKLACKIALALQASIDE 60
                                      6789*******************************.6*************999877 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   1.8e-11   2.5e-08       4      60 ..       7      62 ..       6      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.8e-11
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyll 60
                                      +ke+R   gltqeela+++g++r  i  +E+gk+ +ps +l  kia al  ++++++
  gi|330508360|ref|YP_004384788.1|  7 IKELRARHGLTQEELARMVGVRRETILFLEKGKY-NPSLKLACKIALALQASIDEIF 62
                                      89*******************************9.************9999988887 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 !   29.2   0.0   6.5e-10     9e-07       1      62 [.       6      66 ..       6      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 6.5e-10
                            HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLleyep 62
                                      +++el a +g+t+ eLar++g+ + t+  l kgk  ++sl+   ki+ aL+ ++++++++e 
  gi|330508360|ref|YP_004384788.1|  6 HIKELRARHGLTQEELARMVGVRRETILFLEKGK-YNPSLKLACKIALALQASIDEIFIFEE 66
                                      689******************************9.6***********************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 !   19.1   0.1     7e-07   0.00096      21      38 ..      15      32 ..       3      33 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7e-07
                                      EHHHHHHHHHTTSSHHHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretv 38
                                       ltqeelA+m+G++ret+
  gi|330508360|ref|YP_004384788.1| 15 GLTQEELARMVGVRRETI 32
                                      59**************97 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   8.6e-07    0.0012       3      36 ..       8      41 ..       6      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.6e-07
                                      HHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25  3 raaRearglsleevaketkIrkdylealEeddfd 36
                                      ++ R + gl+ ee+a+   +r +++  lE+++++
  gi|330508360|ref|YP_004384788.1|  8 KELRARHGLTQEELARMVGVRRETILFLEKGKYN 41
                                      789****************************996 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3     5e-06     0.007      14      37 ..       9      32 ..       4      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5e-06
                                      HHHHTTT--HHHHHHHHTS-HHHH CS
                        Sigma70_r4 14 elrfgeglTleEIgerlgiSrerV 37
                                      elr  +glT+eE++++ g+ re++
  gi|330508360|ref|YP_004384788.1|  9 ELRARHGLTQEELARMVGVRRETI 32
                                      577789****************98 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.4   1.7e-05     0.024      10      37 ..       4      32 ..       3      33 .. 0.92
   2 ?   -3.4   0.0       6.4   8.8e+03      25      30 ..      49      54 ..      46      57 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                            HTH_38 10 ReeIerlla.eGlslreIArrLgrspsTI 37
                                      R +I  l+a  Gl++ e Ar +g+ + TI
  gi|330508360|ref|YP_004384788.1|  4 RTHIKELRArHGLTQEELARMVGVRRETI 32
                                      899****96599****************9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.4
                            HTH_38 25 eIArrL 30
                                      +IA  L
  gi|330508360|ref|YP_004384788.1| 49 KIALAL 54
                                      787666 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.7e-05     0.065      22      55 ..       6      39 ..       1      58 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.7e-05
                                      HHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT- CS
                            HTH_37 22 aiaeliekrelsqseaaqllgiaqPkvsrllrgk 55
                                       i+el+++ +l+q+e+a++ g+ +  +  l++gk
  gi|330508360|ref|YP_004384788.1|  6 HIKELRARHGLTQEELARMVGVRRETILFLEKGK 39
                                      49********************998888888877 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.4e-05      0.13       4      21 ..      20      37 ..       6      39 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.4e-05
                                      HHHHHHTTTHHHHHHHHH CS
                              MerR  4 evAeltGvsprtLRyYEr 21
                                      e+A+++Gv   t+ ++E+
  gi|330508360|ref|YP_004384788.1| 20 ELARMVGVRRETILFLEK 37
                                      89**************97 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.7e-05      0.13      14      58 ..      17      62 ..       6      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.7e-05
                                      SCHHHHCCTT--HHHHHHHHHSSS--.HHHHHHHHHHH---HHHHH CS
                     Phage_CI_repr 14 mqkeLAdlLgiakssvstwvrRdffP.gdvvvtcaletdtsLewLa 58
                                      +q+eLA   g+ + ++  + +  ++P  ++  ++al++++s++++ 
  gi|330508360|ref|YP_004384788.1| 17 TQEELARMVGVRRETILFLEKGKYNPsLKLACKIALALQASIDEIF 62
                                      466***********************99**************9875 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.14      72     113 ..       5      46 ..       1      59 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                    MqsA_antitoxin  72 afiarvrkkleldqreaaeifGgGvnafsryekGkvrpplal 113
                                       ++i+++r + +l+q+e+a++ G+  ++    ekGk +p+l l
  gi|330508360|ref|YP_004384788.1|   5 THIKELRARHGLTQEELARMVGVRRETILFLEKGKYNPSLKL 46 
                                       68999*********************************9877 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00012      0.16       5      34 ..       2      32 ..       1      38 [. 0.87
   2 ?   -3.0   0.0       5.2   7.1e+03      12      21 ..      51      59 ..      46      61 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                            HTH_23  5 reRlrillllae.GlsvreIAreLgvsrrTv 34
                                      + R +i  l a+ Gl+++e Ar+ gv r T+
  gi|330508360|ref|YP_004384788.1|  2 VLRTHIKELRARhGLTQEELARMVGVRRETI 32
                                      6677888888889*************99998 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.2
                            HTH_23 12 lllaeGlsvr 21
                                       l++  +s+ 
  gi|330508360|ref|YP_004384788.1| 51 ALAL-QASID 59
                                      3333.25555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 587.70
//
Query:       gi|330508361|ref|YP_004384789.1|  [L=127]
Description: hypothetical protein MCON_2545 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00039   20.2   5.3    0.00049   19.8   5.3    1.0  1  TerC             Integral membrane protein TerC family
  ------ inclusion threshold ------
      0.017   14.1  11.4      0.045   12.7  11.4    1.6  1  MFS_1            Major Facilitator Superfamily
      0.024   14.3   0.1      0.046   13.4   0.1    1.5  1  DUF716           Family of unknown function (DUF716)
      0.031   14.1   0.0      0.051   13.5   0.0    1.3  1  XPB_DRD          Xeroderma pigmentosum group B helicase damag
      0.089   12.4   0.1       0.11   12.1   0.1    1.1  1  DUF533           Protein of unknown function (DUF533)
       0.12   12.7   4.5       0.14   12.6   1.6    1.9  2  DUF805           Protein of unknown function (DUF805)
        5.3    7.4   9.0         16    5.9   4.0    2.2  2  DUF3040          Protein of unknown function (DUF3040)
        5.5    6.6   8.6       0.63    9.7   2.6    1.9  2  DUF4131          Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   5.3   2.2e-07   0.00049      42     145 ..      10     118 ..       6     121 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.2e-07
                              TerC  42 lvlRillillavallelf..dlilligglf.Llytavkellekr.lenklvkeekkkkkktkst.......llavvi 107
                                       ++l ++li+++v l ++    ++l++gg+  L  tav+     + +e++   ++ +       +       +  +++
  gi|330508361|ref|YP_004384789.1|  10 MLLGAALIFAGVLLTQAGydAFFLVAGGVAaLATTAVRRWQRGNePEKDERTNKIRA------FglayswlVSIIIV 80 
                                       667778899999998885677888888875155566665543332222222222222......13455665667788 PP

                              TerC 108 qielaDlvfslDSvlaavaitsdlfivitavilsilvl 145
                                       +i++   ++ + S+ a+ a++  ++i+  + i+s+ vl
  gi|330508361|ref|YP_004384789.1|  81 LIIFCATIMGFISIDAITALSITIYIMTGSAIVSLAVL 118
                                       999*******************************9987 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  11.4     2e-05     0.045     131     230 ..       7     101 ..       5     119 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                             MFS_1 131 slGailg..pllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallk 205
                                       s+G++lg   +++g+l++++g+ a f+++++v++la   +  + + ++pe+   + k +           a+++  +
  gi|330508361|ref|YP_004384789.1|   7 SAGMLLGaaLIFAGVLLTQAGYDAFFLVAGGVAALATTAVRRWQRGNEPEKDERTNKIR-----------AFGLAYS 72 
                                       445555433569************************88777777666666666666555...........2333332 PP

                             MFS_1 206 dpvlw.....illialllfffgfsg...lltll 230
                                           w     i+li+++ + +gf +   +++l+
  gi|330508361|ref|YP_004384789.1|  73 ----WlvsiiIVLIIFCATIMGFISidaITALS 101
                                       ....33322234444444444444434322222 PP

>> DUF716  Family of unknown function (DUF716)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     2e-05     0.046      57     136 ..       5      85 ..       1      87 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                            DUF716  57 sfllelvrsvllilqGtWflqmGfiLytpslipkgClldeeegegsvkcdse.....esehrakalvnlqFswhlaa 128
                                       +f + ++ +++li+ G+ + q+G+  +      +g +   ++ +   +++       +++++ +    l++sw++ +
  gi|330508361|ref|YP_004384789.1|   5 RFSAGMLLGAALIFAGVLLTQAGYDAFFL---VAGGVAALAT-TAVRRWQRGnepekDERTNKIRAFGLAYSWLVSI 77 
                                       78999******************875554...3555444333.23344544333333556667778899******99 PP

                            DUF716 129 vlvfvvvl 136
                                       ++v+++++
  gi|330508361|ref|YP_004384789.1|  78 IIVLIIFC 85 
                                       99999875 PP

>> XPB_DRD  Xeroderma pigmentosum group B helicase damage recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.3e-05     0.051      24      44 ..      56      76 ..      40      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
                                      EEETTTTEEEEEGGGHHHHHH CS
                           XPB_DRD 24 ewDeRvekyRapAlrYrdlve 44
                                      e DeR++k Ra +l+Y  lv+
  gi|330508361|ref|YP_004384789.1| 56 EKDERTNKIRAFGLAYSWLVS 76
                                      78***************9997 PP

>> DUF533  Protein of unknown function (DUF533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   4.8e-05      0.11       5      56 ..       9      58 ..       5      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.8e-05
                            DUF533  5 gaaaggl...lglllGskkgrklgkkalklGglAalGglAykayqnwqanqqeaa 56
                                      g+++g++   +g+ll++++   + +  l +Gg+Aal++ A++ +q+ +  ++e++
  gi|330508361|ref|YP_004384789.1|  9 GMLLGAAlifAGVLLTQAG---YDAFFLVAGGVAALATTAVRRWQRGN--EPEKD 58
                                      5555554567999999999...99999******************544..44333 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.24   5.4e+02      40      63 ..      25      49 ..       5      54 .. 0.44
   2 ?   12.6   1.6     6e-05      0.14      12      62 ..      70     121 ..      58     127 .] 0.66

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.24
                            DUF805 40 asalsvvlallllvps.lavtvRRl 63
                                      ++    +++++  v + ++++vRR+
  gi|330508361|ref|YP_004384789.1| 25 QAGYDAFFLVAGGVAAlATTAVRRW 49
                                      2222222222223333355667776 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6e-05
                            DUF805  12 efwwfvlfllllvivlallaavlaa.aavasalsvvlallllvpslavtvRR 62 
                                        + w v ++++l+i++a ++ ++   a+ a ++++ ++    ++slav+ RR
  gi|330508361|ref|YP_004384789.1|  70 AYSWLVSIIIVLIIFCATIMGFISIdAITALSITIYIMTGSAIVSLAVLHRR 121
                                       574444444444444455555544347777778888888999999*****99 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   4.0    0.0071        16      50      81 ..       8      43 ..       2      46 .. 0.66
   2 ?    4.5   0.2     0.019        43      46      82 ..      74     111 ..      51     118 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0071
                           DUF3040 50 llfvaGllllvlGvaaaa....vvlgvvGfvvmlag 81
                                      +++++G++l+++Gv++ +      + v+G v++la 
  gi|330508361|ref|YP_004384789.1|  8 AGMLLGAALIFAGVLLTQagydAFFLVAGGVAALAT 43
                                      566778888888855444477766777777777665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.019
                           DUF3040  46 vlavllfvaGllllvlG.vaaaavvlgvvGfvvmlagv 82 
                                       +++++++++ +++ ++G ++ +a++   + + +m++ +
  gi|330508361|ref|YP_004384789.1|  74 LVSIIIVLIIFCATIMGfISIDAITALSITIYIMTGSA 111
                                       44555555578888888888888555555555555544 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.6    0.0022       4.9      12      56 ..      11      55 ..       5      65 .. 0.59
   2 ?    9.7   2.6   0.00028      0.63       7      61 ..      30     104 ..      24     124 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0022
                           DUF4131 12 lllllllllllllrrrprrrvllllllllllallgfalrapqpna 56
                                      ll+++l+++++ll ++    ++l+++ +++la+  +  +++ ++ 
  gi|330508361|ref|YP_004384789.1| 11 LLGAALIFAGVLLTQAGYDAFFLVAGGVAALATTAVRRWQRGNEP 55
                                      333333333333333777777888888888887777666655554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00028
                           DUF4131   7 lvllalllllllllllllrr....................rprrrvllllllllllallgfalrapqpnandlsq 61 
                                       +++l+++++++l+  ++ r+                    ++++ v +++ l++++a+++ +++ +  +a ++  
  gi|330508361|ref|YP_004384789.1|  30 AFFLVAGGVAALATTAVRRWqrgnepekdertnkirafglAYSWLVSIIIVLIIFCATIMGFISIDAITALSITI 104
                                       44444444444444444333469******99999999999999999************99999888777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1312  (0.0731775); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 1049.68
//
Query:       gi|330508362|ref|YP_004384790.1|  [L=130]
Description: HxlR family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-35  119.1   0.0    7.2e-35  118.7   0.0    1.2  1  HxlR      HxlR-like helix-turn-helix
     0.0016   18.4   0.0     0.0024   17.8   0.0    1.3  1  PadR      Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.017   15.0   0.0    1.2  1  MarR      MarR family
      0.018   15.2   0.0      0.028   14.6   0.0    1.3  1  HTH_34    Winged helix DNA-binding 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 !  118.7   0.0   1.6e-38   7.2e-35       1      88 [.      20     107 ..      20     110 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 1.6e-38
                                       HHHSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHH CS
                              HxlR   1 liggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlq 77 
                                       +iggkWk lil++l +   Rf+el++a+p++ +kmL+++LreLe+dg+i+r++ypevPp+veY++t++G++l pvl+
  gi|330508362|ref|YP_004384790.1|  20 VIGGKWKPLILWALGDAVLRFNELQKAIPGVNTKMLTKQLRELEEDGVIKRTIYPEVPPRVEYRITDFGKTLIPVLE 96 
                                       79*************************************************************************** PP

                                       HHHHHHHHHHH CS
                              HxlR  78 elkkwgeeyle 88 
                                       +l++wg++yl 
  gi|330508362|ref|YP_004384790.1|  97 ALCNWGANYLG 107
                                       ********985 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.4e-07    0.0024      36      71 ..      57      90 ..      40      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.4e-07
                                      HHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                              PadR 36 paLkrLekeglveseweesgegpprkyYrlTdaGrr 71
                                      ++L++Le++g+++++  ++   ppr  Yr+Td G++
  gi|330508362|ref|YP_004384790.1| 57 KQLRELEEDGVIKRTIYPE--VPPRVEYRITDFGKT 90
                                      689*************985..8************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.8e-06     0.017      22      53 ..      42      74 ..      28      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.8e-06
                                      HHHHHH.TS-HHHHHHHHHHHHHTTSEEEEEET CS
                              MarR 22 eLakkl.gvskstvtrvldrLekkGlieRsksp 53
                                      eL+k++ gv++ ++t++l++Le++G i+R+  p
  gi|330508362|ref|YP_004384790.1| 42 ELQKAIpGVNTKMLTKQLRELEEDGVIKRTIYP 74
                                      66666658999******************8655 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   6.2e-06     0.028      15      67 ..      38      90 ..      28     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.2e-06
                            HTH_34 15 adfvelkeal.eatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGre 67
                                        f+el++a+ ++++  L ++l+ Le+ g i++++  +   pr  +riT+ G++
  gi|330508362|ref|YP_004384790.1| 38 LRFNELQKAIpGVNTKMLTKQLRELEEDGVIKRTIYPEVP-PRVEYRITDFGKT 90
                                      57899988875789999******************99999.*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 922.16
//
Query:       gi|330508363|ref|YP_004384791.1|  [L=187]
Description: flavin reductase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-19   70.3   0.0    2.4e-19   69.9   0.0    1.0  1  Flavin_Reduct  Flavin reductase like domain


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.0   1.3e-23   2.4e-19       4     136 ..      12     141 ..       9     160 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.3e-23
                                       S-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...S CS
                     Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgp 80 
                                       ++ pv++v t + ++ ++ + + ++t   ++Pp+++  +++ ++t + ++e++ f +n+ s +  +  d ++  sg 
  gi|330508363|ref|YP_004384791.1|  12 IPMPVVLVGT-QVSGIANFMAVGWCTRANATPPMLVCGIANHHYTPKGIAETKTFSVNIPSSELLDKTDYCGLVSG- 86 
                                       689*******.55666779*********************************************************. PP

                                       CCCCCCCCCCCEEECTCCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEES CS
                     Flavin_Reduct  81 rtddksifagltweesptgapallgalasleCqvvgsvelgdhelfigeVvavkvg 136
                                       +++dks+++++ +++   +ap++ ++++sleC++v+ v+l +  l+ige+v ++ +
  gi|330508363|ref|YP_004384791.1|  87 EKVDKSETFEIFYGSL-KTAPMIRECPVSLECRLVQIVPLPTNSLYIGEIVGAYAD 141
                                       9**************7.9*********************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1481.41
//
Query:       gi|330508364|ref|YP_004384792.1|  [L=272]
Description: nitroreductase/iron-sulfur domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-27   95.8   0.0    3.9e-27   95.4   0.0    1.2  1  Nitroreductase  Nitroreductase family
    2.8e-09   36.6  12.2    0.00012   21.9   1.9    2.4  2  Fer4_6          4Fe-4S binding domain
    7.8e-09   35.0  12.6    7.7e-05   22.3   2.9    2.4  2  Fer4            4Fe-4S binding domain
    1.6e-08   35.0  18.4    3.5e-06   27.5   9.7    2.2  2  Fer4_7          4Fe-4S dicluster domain
    8.8e-08   32.0   0.1      0.022   14.3   0.0    2.9  3  TM1586_NiRdase  Putative TM nitroreductase
    1.4e-07   31.6   8.6    2.5e-07   30.8   8.6    1.4  1  Fer4_9          4Fe-4S dicluster domain
    6.1e-07   29.5  22.0    9.1e-06   25.7  11.7    1.8  2  Fer4_10         4Fe-4S dicluster domain
    2.2e-06   28.5   4.1     0.0045   17.9   0.1    2.4  2  Fer4_16         4Fe-4S double cluster binding domain
    1.1e-05   25.2  14.3    0.00075   19.5   3.3    2.5  2  Fer4_2          4Fe-4S binding domain
    0.00014   22.3  12.7      0.012   16.1  12.9    2.4  1  Fer4_17         4Fe-4S dicluster domain
    0.00018   21.5   8.6      0.085   13.0   0.7    2.3  2  Fer4_21         4Fe-4S dicluster domain
     0.0023   18.4  12.6      0.043   14.3   2.4    2.4  2  Fer4_8          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.021   15.3  10.5      0.053   14.0   0.6    2.3  2  Fer4_4          4Fe-4S binding domain
      0.042   13.0   0.2      0.061   12.5   0.2    1.1  1  Phage_cap_E     Phage major capsid protein E
        1.1    9.8  12.8        2.9    8.5   1.4    2.5  2  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
        7.9    7.7  18.5        3.4    8.8   6.7    2.4  2  Fer4_3          4Fe-4S binding domain
        8.6    6.6  11.9          3    8.1   1.5    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 !   95.4   0.0   3.7e-30   3.9e-27       1     170 []      88     253 ..      88     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 3.7e-30
                                       HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGG CS
                    Nitroreductase   1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrke 77 
                                       +rkRrS+R+++++ vpke++ ++l+ ar+a sagn+qp++ +vv+d+e  +k+a    e+++++  ++   + y+ +
  gi|330508364|ref|YP_004384792.1|  88 LRKRRSVRHYTKDIVPKEKILELLDIARYAASAGNRQPVEWIVVHDQERVKKIAAMTIEWMRTLAGSNHPMSGYVPA 164
                                       58**************************************************************9999988888877 PP

                                       ...HHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHH... CS
                    Nitroreductase  78 ...elklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaae... 148
                                           ++ + +   +gap l+v+          + +++y++a  da +a++ + LaA a+G+g+c+ g++ +aa+   
  gi|330508364|ref|YP_004384792.1| 165 lirGWESGSDVICRGAPHLLVA----------TIPEEYPVAQTDAIIALTHFDLAAPAHGIGTCWAGFVAMAASsyk 231
                                       *9888888889999********..........99************************************9999999 PP

                                       HHHHHHT-S..SEEEEEEEEE- CS
                    Nitroreductase 149 evrkllglpdeeeivvliavGy 170
                                        ++k l +p + +  +++ +G+
  gi|330508364|ref|YP_004384792.1| 232 PLQKELSIPAGRRSAYAMIFGH 253
                                       9********99*********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 !   21.9   1.9   1.2e-07   0.00012       2      24 .]       4      26 ..       3      26 .. 0.91
   2 !   19.5   3.0   6.7e-07   0.00071       7      24 .]      43      60 ..      41      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + +d+d+C+ Cg C +vC +g+i
  gi|330508364|ref|YP_004384792.1|  4 ILVDQDLCTRCGICSTVCIMGII 26
                                      679***************99887 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 6.7e-07
                            Fer4_6  7 dkCigCgdCvrvCPegai 24
                                        Ci+Cg C+++CP  a+
  gi|330508364|ref|YP_004384792.1| 43 GICIQCGHCEAHCPSHAL 60
                                      57************9886 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   2.9   7.3e-08   7.7e-05       2      23 ..       5      26 ..       4      27 .. 0.89
   2 !   17.8   2.3     2e-06    0.0021       5      23 ..      42      60 ..      40      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 7.3e-08
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                       +d+++C++CG+C  vC  g I
  gi|330508364|ref|YP_004384792.1|  5 LVDQDLCTRCGICSTVCIMGII 26
                                      59***************88887 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2e-06
                                      TTTSSS-THHHHHSTTTEE CS
                              Fer4  5 eekCigCGaCvevCPvgAI 23
                                         Ci CG C+  CP  A+
  gi|330508364|ref|YP_004384792.1| 42 AGICIQCGHCEAHCPSHAL 60
                                      567************9997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   9.7   3.3e-09   3.5e-06       2      52 .]      11      59 ..      10      59 .. 0.88
   2 !   20.1   1.4   6.9e-07   0.00073       2      26 ..      45      69 ..      44      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3.3e-09
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C+ Cg C  +C ++ iel +e++ +  ++ + ++  C++Cg+C+a CP+ a
  gi|330508364|ref|YP_004384792.1| 11 CTRCGICSTVCIMGIIELADENSLP--KTNDTNAGICIQCGHCEAHCPSHA 59
                                      ******************9985443..46678899*************976 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.9e-07
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenek 26
                                      Ci+Cg C+a Cp++a+ l+++ +ek
  gi|330508364|ref|YP_004384792.1| 45 CIQCGHCEAHCPSHALILNDRPDEK 69
                                      ****************999987776 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.1     0.008       8.5       6      28 ..      88     110 ..      83     112 .. 0.84
   2 !   11.7   0.4   0.00014      0.15     156     191 ..     103     139 ..      91     152 .. 0.72
   3 !   14.3   0.0   2.1e-05     0.022      88     139 ..     203     261 ..     175     268 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.008
                                       HHH--B---B--S---HHHHHHH CS
                    TM1586_NiRdase   6 iekRhsvRkYkdealeeelleel 28 
                                       ++kR+svR+Y++  +++e++ el
  gi|330508364|ref|YP_004384792.1|  88 LRKRRSVRHYTKDIVPKEKILEL 110
                                       689************99987665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00014
                                       S-HHHHHHHHHHHTS--GGG----EEE.E-SS.EE.. CS
                    TM1586_NiRdase 156 lpewfkeileaarlAPsAlNqqpwrfelkddd.eiki 191
                                        +e++ e+l++ar+A sA N+qp++  ++ d+ ++k 
  gi|330508364|ref|YP_004384792.1| 103 PKEKILELLDIARYAASAGNRQPVEWIVVHDQeRVKK 139
                                       46789999***************99887665424443 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHTT-EEEEES-......-SST...........T-S-EEEEE-BS----.. CS
                    TM1586_NiRdase  88 geqlvLkltalGlgtcWvgg......tykkkkakvelkkgeklvivIalGyaktklv.e 139
                                       + ++ L + a+G+gtcW g+      +yk+ +++++++ g + ++++ +G ++++++  
  gi|330508364|ref|YP_004384792.1| 203 LTHFDLAAPAHGIGTCWAGFvamaasSYKPLQKELSIPAGRRSAYAMIFGHPQHEIYgI 261
                                       567899***********875222222566677889999999999999999999988753 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   8.6   2.3e-10   2.5e-07       2      50 ..      11      59 ..      10      60 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.3e-10
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      Ct+Cg C ++C +g+++  + +   + + +++  Ci+Cg C+++Cp++a
  gi|330508364|ref|YP_004384792.1| 11 CTRCGICSTVCIMGIIELADENSLPKTNDTNAGICIQCGHCEAHCPSHA 59
                                      ********************99999999999999************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 !   25.7  11.7   8.7e-09   9.1e-06       2      56 .]       4      56 ..       3      56 .. 0.93
   2 !   16.7   2.5   5.5e-06    0.0058       6      25 ..      42      69 ..      37      95 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 8.7e-09
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      + +d+d C+rCg C ++C   +   +  +e+s  ++++++ + C++cg C ++CP
  gi|330508364|ref|YP_004384792.1|  4 ILVDQDLCTRCGICSTVC--IMGIIELADENSLPKTNDTNAGICIQCGHCEAHCP 56
                                      56899*************..7788899999999999******************9 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.5e-06
                           Fer4_10  6 ddtCirCgkCvkaCPadl........ts 25
                                      +  Ci+Cg C + CP+++        ++
  gi|330508364|ref|YP_004384792.1| 42 AGICIQCGHCEAHCPSHAlilndrpdEK 69
                                      568*************777776666533 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 !   11.5   0.8   0.00041      0.43       2      25 ..      11      34 ..      10      42 .. 0.80
   2 !   17.9   0.1   4.3e-06    0.0045       2      22 ..      45      65 ..      44     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00041
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekei 25
                                      C++Cg C  vC  + i+   e+++
  gi|330508364|ref|YP_004384792.1| 11 CTRCGICSTVCIMGIIELADENSL 34
                                      9***********999998866655 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 4.3e-06
                           Fer4_16  2 CgtCgkCaevCPtnaikekke 22
                                      C++Cg C   CP++a+  + +
  gi|330508364|ref|YP_004384792.1| 45 CIQCGHCEAHCPSHALILNDR 65
                                      ***************876632 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   3.3   7.1e-07   0.00075       4      20 ..       5      21 ..       3      22 .. 0.94
   2 !   11.0   3.3   0.00035      0.37       7      21 ..      42      56 ..      38      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.1e-07
                            Fer4_2  4 vvdtdrCigCgaCvsaC 20
                                       vd d C++Cg+C ++C
  gi|330508364|ref|YP_004384792.1|  5 LVDQDLCTRCGICSTVC 21
                                      79*************** PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00035
                            Fer4_2  7 tdrCigCgaCvsaCP 21
                                      + +Ci+Cg C   CP
  gi|330508364|ref|YP_004384792.1| 42 AGICIQCGHCEAHCP 56
                                      569*******777** PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1  12.9   1.2e-05     0.012       2      59 ..      11      58 ..      10      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                      C++Cg C  +C ++++   ++++l +           ++++a+ Ci+Cg Ce+ CP++
  gi|330508364|ref|YP_004384792.1| 11 CTRCGICSTVCIMGIIELADENSLPKT----------NDTNAGICIQCGHCEAHCPSH 58
                                      ****************88877777666..........35799**************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 !   12.4   1.9   0.00013      0.14      35      58 ..       5      27 ..       1      32 [. 0.80
   2 !   13.0   0.7   8.1e-05     0.085       7      27 ..      44      62 ..      37      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                           Fer4_21 35 kvvedeCvGCnlCssvCPvedcie 58
                                       v +d C+ C +Cs+vC + + ie
  gi|330508364|ref|YP_004384792.1|  5 LVDQDLCTRCGICSTVCIM-GIIE 27
                                      5779999999999999964.6665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.1e-05
                           Fer4_21  7 kCigCgkCliaCedtshqaie 27
                                       Ci+Cg+C   C+  sh  i 
  gi|330508364|ref|YP_004384792.1| 44 ICIQCGHCEAHCP--SHALIL 62
                                      6***********9..676664 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   3.6    0.0045       4.7      50      64 ..      10      24 ..       7      25 .. 0.73
   2 !   14.3   2.4   4.1e-05     0.043       5      22 ..      45      62 ..      41     106 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0045
                            Fer4_8 50 sCttcgaCtevCpvg 64
                                       Ct cg C++vC +g
  gi|330508364|ref|YP_004384792.1| 10 LCTRCGICSTVCIMG 24
                                      688888888888666 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.1e-05
                            Fer4_8  5 CieCgaCqsaCpvlrrtk 22
                                      Ci+Cg C+++Cp+     
  gi|330508364|ref|YP_004384792.1| 45 CIQCGHCEAHCPSHALIL 62
                                      999999999999654433 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   3.4     0.032        33       1      14 [.       8      21 ..       8      23 .. 0.90
   2 ?   14.0   0.6   5.1e-05     0.053       4      15 ..      45      56 ..      37      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.032
                            Fer4_4  1 qerCigCgsCvaaC 14
                                      q+ C++Cg C  +C
  gi|330508364|ref|YP_004384792.1|  8 QDLCTRCGICSTVC 21
                                      799*****998888 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.1e-05
                            Fer4_4  4 CigCgsCvaaCP 15
                                      Ci+Cg C+a CP
  gi|330508364|ref|YP_004384792.1| 45 CIQCGHCEAHCP 56
                                      ************ PP

>> Phage_cap_E  Phage major capsid protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   5.8e-05     0.061      61     122 ..      89     149 ..      87     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.8e-05
                       Phage_cap_E  61 regrstrsfeppyikekdvitadelqnlrafgespaervqeevarkladlrdkidrteEwmr 122
                                       r++rs+r+++   ++ ++ ++  ++ ++ a    + + v+++v  +++++++ ++ t+Ewmr
  gi|330508364|ref|YP_004384792.1|  89 RKRRSVRHYTKDIVPKEKILELLDIARYAASAG-NRQPVEWIVVHDQERVKKIAAMTIEWMR 149
                                       789999999999999999999999999888777.8899***********************9 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.2     0.017        18       1      16 [.       6      21 ..       6      23 .. 0.95
   2 ?    8.5   1.4    0.0028       2.9       6      18 ..      45      57 ..      41      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.017
                           Fer4_13  1 VDrdtCiacgaCvela 16
                                      VD+d C+ cg+C  ++
  gi|330508364|ref|YP_004384792.1|  6 VDQDLCTRCGICSTVC 21
                                      9***********9998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0028
                           Fer4_13  6 CiacgaCvelaPd 18
                                      Ci cg C + +P 
  gi|330508364|ref|YP_004384792.1| 45 CIQCGHCEAHCPS 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 ?    4.6   3.9     0.074        78       1      11 [.      11      21 ..      11      25 .. 0.91
   2 ?    8.8   6.7    0.0032       3.4       1      15 []      45      59 ..      45      59 .. 0.97

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.074
                            Fer4_3  1 CtgCgaCvevC 11
                                      Ct Cg C  vC
  gi|330508364|ref|YP_004384792.1| 11 CTRCGICSTVC 21
                                      *********** PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0032
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C++Cg C+  CP++A
  gi|330508364|ref|YP_004384792.1| 45 CIQCGHCEAHCPSHA 59
                                      *************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 ?    3.4   3.3     0.081        86      60      75 ..      10      25 ..       6      31 .. 0.88
   2 ?    8.1   1.5    0.0028         3      52      76 ..      36      60 ..      26      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.081
                           Fer4_18 60 dcidcescvkvcPtgi 75
                                       c+ c+ c +vc +gi
  gi|330508364|ref|YP_004384792.1| 10 LCTRCGICSTVCIMGI 25
                                      5***********9997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0028
                           Fer4_18 52 erkekgagdcidcescvkvcPtgid 76
                                      ++++++ag ci+c++c + cP +  
  gi|330508364|ref|YP_004384792.1| 36 KTNDTNAGICIQCGHCEAHCPSHAL 60
                                      455678899************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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):              17  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2155.13
//
Query:       gi|330508365|ref|YP_004384793.1|  [L=253]
Description: carboxymuconolactone decarboxylase [Methanosaeta concilii GP6]
Scores for complete 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  124.2   0.8    2.3e-19   69.2   0.2    2.1  2  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 !   69.2   0.2   1.3e-23   2.3e-19       1      82 [.      25     107 ..      25     110 .. 0.94
   2 !   53.8   0.0   8.6e-19   1.5e-14       1      83 [.     159     242 ..     159     244 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.3e-23
                                       HHHHHHHHHHHHHHCC.GSSTS-HHHHHHHHHHHHHHTT-HHHH.HHHHHHHHHTT--HHHHHHHHHHHHHHHSHHH CS
                               CMD   1 pellraltalrealla.reggLdpkereLialavsaangceyCv.daHtraAleaGvteeeiaevlaqaaayagwpa 75 
                                       p+l+r+l ++ +++++ r+g Ld ++reL+ +a+++a+g +  + ++Ht aAl+ G+ +eei+ev+ q+  yag+pa
  gi|330508365|ref|YP_004384793.1|  25 PDLARYLIEYSFGEIYaRDG-LDNRTRELAVVAALTAMGTAAPQlKVHTHAALHVGCIPEEIREVIIQMCGYAGFPA 100
                                       99**************9999.******************666556******************************** PP

                                       HHHHHHH CS
                               CMD  76 araAlaa 82 
                                        ++A++ 
  gi|330508365|ref|YP_004384793.1| 101 TLNAMKT 107
                                       ****986 PP

  == domain 2  score: 53.8 bits;  conditional E-value: 8.6e-19
                                       HHHHHHHHHHHHHHCC.GSSTS-HHHHHHHHHHHHHHTT-HHHH.HHHHHHHHHTT--HHHHHHHHHHHHHHHSHHH CS
                               CMD   1 pellraltalrealla.reggLdpkereLialavsaangceyCv.daHtraAleaGvteeeiaevlaqaaayagwpa 75 
                                       p++++++ a++ ++++ r g L++++r+++++a++aa g +  + ++H+ +  +aG++e ei e++    +yag+pa
  gi|330508365|ref|YP_004384793.1| 159 PDIAKYVIAFGYGDIYaR-GLLSLRDRQVATIAALAAKGTAPSQlRFHIGGGFRAGLSEAEIVEIMLLISIYAGFPA 234
                                       899*************66.88******************999889******************************** PP

                                       HHHHHHHH CS
                               CMD  76 araAlaaa 83 
                                       a++   a+
  gi|330508365|ref|YP_004384793.1| 235 ALNGILAT 242
                                       **998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1918.73
//
Query:       gi|330508366|ref|YP_004384794.1|  [L=209]
Description: TetR family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-11   42.5   0.0    6.7e-11   41.8   0.0    1.4  1  TetR_N          Bacterial regulatory proteins, tetR family
    3.9e-05   23.6   0.1    0.00015   21.8   0.1    2.0  1  TetR_C_27       Tetracyclin repressor-like, C-terminal domain
    0.00027   21.2   0.5    0.00077   19.7   0.0    2.0  2  TetR_C_24       Tetracyclin repressor-like, C-terminal domain
      0.006   16.7   0.0      0.018   15.1   0.0    1.9  2  TetR_C_29       Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.077   13.1   0.0    2.0  1  TetR_C_4        YsiA-like protein, C-terminal region
      0.054   13.3   0.0      0.088   12.7   0.0    1.4  1  Sigma54_CBD     Sigma-54 factor, core binding domain
      0.074   13.1   0.0       0.15   12.1   0.0    1.5  1  Erp_C           Erp protein C-terminus
      0.081   13.1   0.0       0.16   12.2   0.0    1.7  1  TetR_C_5        QacR-like protein, C-terminal region
       0.09   13.2   0.0       0.24   11.8   0.0    1.7  1  ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin t


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   3.4e-14   6.7e-11       1      45 [.      22      66 ..      22      68 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 3.4e-14
                                      HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHH CS
                            TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLle 45
                                      I++a+ + + e Gy ++++++IAkrAG+s +++ ++F++K +L++
  gi|330508366|ref|YP_004384794.1| 22 IIEATIATLDEIGYVNASLAQIAKRAGISTPLISYHFSDKNDLIN 66
                                      99*****************************************87 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 !   21.8   0.1   7.5e-08   0.00015       2      91 ..      91     184 ..      90     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.5e-08
                                       HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH-H....HHHHHHHHHHHHHHHHHHHHHHHCT-STT--HHHHH CS
                         TetR_C_27   2 eerLrewlaalfeakrrkarddpelFatyvvlieeel....evvekhieeleeqlaeIireGvaaGeFkaadpeaaa 74 
                                       +e+Lr +++a+++ + ++ +++  l +++  + + +     +  ++  + ++  l+++++eG+a+GeF++ d++a+a
  gi|330508366|ref|YP_004384794.1|  91 REKLRIFIEARLAYQGTHSKHNVALIEIVFNARTPDNvpyyKLSDDGEDPVVYALEQLLTEGQASGEFREFDIHAMA 167
                                       5666666666666666666666666666666554332111133444455677789********************** PP

                                       HHHHHHSGGGTSHHHHH CS
                         TetR_C_27  75 ravfdatarfhhPalaa 91 
                                       +a+  a++ ++  +++ 
  gi|330508366|ref|YP_004384794.1| 168 SAIQGAIGEYLADQYLI 184
                                       *********99877654 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 ?   -2.1   0.1       2.3   4.6e+03      52      62 ..      20      30 ..       6      50 .. 0.51
   2 !   19.7   0.0   3.9e-07   0.00077       2      84 ..      88     174 ..      87     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.3
                                      HHHHHHHHHHH CS
                         TetR_C_24 52 erllrdlieeG 62
                                      e+++++ i+  
  gi|330508366|ref|YP_004384794.1| 20 EQIIEATIATL 30
                                      34444444444 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 3.9e-07
                                       SSHHHHHHHHHHHHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHH....HHHHHHHHHHHTTSB-SS-HH CS
                         TetR_C_24   2 gspaerLralvrahveviaeereeaavllrelraLspehreeiralrreyer....llrdlieeGvaagefedldpk 74 
                                        +++e+Lr +++a +++  ++ ++ + l++ + +   ++   + +l ++ e+     l++l++eG+a+gef++ d +
  gi|330508366|ref|YP_004384794.1|  88 STAREKLRIFIEARLAYQGTHSKHNVALIEIVFNARTPDNVPYYKLSDDGEDpvvyALEQLLTEGQASGEFREFDIH 164
                                       6899*****************9999999999988888888888888887665333389******************* PP

                                       HHHHHHHHHH CS
                         TetR_C_24  75 laalailgml 84 
                                        +a ai g++
  gi|330508366|ref|YP_004384794.1| 165 AMASAIQGAI 174
                                       ******9986 PP

>> TetR_C_29  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.9   3.8e+03      19      45 ..      66      92 ..      61     101 .. 0.71
   2 !   15.1   0.0   8.9e-06     0.018      47      82 ..     138     169 ..     107     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.9
                                      -HHHHHHHHHHHHS-TT--TTS--SS- CS
                         TetR_C_29 19 npefvrLvsiEnlhrgrhlkksesire 45
                                      n+ + +L+s+ n    ++lk+ +++re
  gi|330508366|ref|YP_004384794.1| 66 NQTLTTLLSEANAYVTERLKEGSTARE 92
                                      556677888888887787777777766 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.9e-06
                                       THHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHHH CS
                         TetR_C_29  47 nspliekleeilerGqaagvFrpgvdaldlylliss 82 
                                       ++p++ +le++l +Gqa+g Fr+     d++++ s+
  gi|330508366|ref|YP_004384794.1| 138 EDPVVYALEQLLTEGQASGEFRE----FDIHAMASA 169
                                       6799******************9....445544444 PP

>> TetR_C_4  YsiA-like protein, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.9e-05     0.077      12     106 ..      80     177 ..      66     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.9e-05
                                       HHHHHTT-SSHHHHHHHHHHHHHHHH..HC-HHHHHHHH.TTCCGSSHHHHHHHHH.HHHHHHHHHHHHHHHHHHTT CS
                          TetR_C_4  12 ikeeikekesaeeklkllvekhfsql..sadkelaivtq.lelrqsnlelrlkine.vlkgyltlldeiiaeGkekG 84 
                                       + e++ke ++a+ekl++++e  +      +++++a++   ++ r  ++    k+++    + +  l+++++eG+++G
  gi|330508366|ref|YP_004384794.1|  80 VTERLKEGSTAREKLRIFIEARLAYQgtHSKHNVALIEIvFNARTPDNVPYYKLSDdGEDPVVYALEQLLTEGQASG 156
                                       56889999999999999999987654115567788775415678777777788876156788999************ PP

                                       SC-TT--HHHHHHHHHHHHHHH CS
                          TetR_C_4  85 efkeeldvrlarqlifGtldev 106
                                       ef+ e+d++ +   i G++ e 
  gi|330508366|ref|YP_004384794.1| 157 EFR-EFDIHAMASAIQGAIGEY 177
                                       **7.689999999998888775 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 ?   12.7   0.0   4.4e-05     0.088      27      58 ..      17      52 ..      10      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-05
                       Sigma54_CBD 27 eeereiaeylienLdedGYleesleeiaeel....e 58
                                       + ++i+e+ i  Lde GY+++sl++ia+++     
  gi|330508366|ref|YP_004384794.1| 17 ARREQIIEATIATLDEIGYVNASLAQIAKRAgistP 52
                                      67899***********************98766550 PP

>> Erp_C  Erp protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.5e-05      0.15      34      81 ..      50      98 ..      21     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.5e-05
                             Erp_C 34 tgpvy.ddftdgnkaiyktwgdledeedeglgkllkelsdtrdelrtkl 81
                                      + p+   +f+d n+ i +t   l  e +  +   lke s +r++lr  +
  gi|330508366|ref|YP_004384794.1| 50 STPLIsYHFSDKNDLINQTLTTLLSEANAYVTERLKEGSTAREKLRIFI 98
                                      555441469*************************************865 PP

>> TetR_C_5  QacR-like protein, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     8e-05      0.16      67     100 ..     142     175 ..      77     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8e-05
                          TetR_C_5  67 lkayekileeGiqsGefrienvedvskivaslls 100
                                       + a e++l eG  sGefr+ ++++++  ++++++
  gi|330508366|ref|YP_004384794.1| 142 VYALEQLLTEGQASGEFREFDIHAMASAIQGAIG 175
                                       457799******************9988888876 PP

>> ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.24      47      71 ..     142     166 ..     132     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHCT-EESS--HHHH CS
                    ParD_antitoxin  47 lkaLreaLeegeqsGeaepfDldaf 71 
                                       + aL ++L eg+ sGe ++fD+ a 
  gi|330508366|ref|YP_004384794.1| 142 VYALEQLLTEGQASGEFREFDIHAM 166
                                       789******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1449.13
//
Query:       gi|330508367|ref|YP_004384795.1|  [L=360]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2775.45
//
Query:       gi|330508368|ref|YP_004384796.1|  [L=437]
Description: amidohydrolase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-30  105.1   0.0    7.2e-30  104.5   0.0    1.3  1  Amidohydro_1  Amidohydrolase family
    1.4e-12   47.9   3.6    4.5e-08   33.0   2.0    2.4  2  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.041   14.2   0.0       0.11   12.8   0.0    1.7  2  Urease_alpha  Urease alpha-subunit, N-terminal domain


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 !  104.5   0.0   1.2e-33   7.2e-30       1     344 []      90     429 ..      90     429 .. 0.78

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 1.2e-33
                                       EEEE-EEEEEEECETTECSSS...GHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH...HHHHHHHHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga...tledwlvppetaaealesgiktalksGtttvadmgattst...giealleaae 71 
                                       +++PGlID+HvHl  + ++       +++     ++   +    +++l++G+ttv+d g+ +       + l++ + 
  gi|330508368|ref|YP_004384796.1|  90 TLMPGLIDMHVHLGPQTYKANeepGILEMPKLVFDWVRFYPDTRRAFLENGVTTVRDLGNEHGWimeLRRHLRDGSL 166
                                       58***********7554444454433333344467788899999****************77645555555555555 PP

                                       TSSSEEEEEEESSEGGS..................GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCS CS
                      Amidohydro_1  72 elplglrilggkvsldr..................gsaetskasreklkagaaetikgkadgvvk.valapheapaf 129
                                       e   g+r++++++++++                  + ++t ++ r+++k+ a    +++  +vv+  +   +    +
  gi|330508368|ref|YP_004384796.1| 167 E---GPRLFAAGPIFTTpgghpvatfgvdpasdsvRLPSTTEEARRAVKELASGEDRADLIKVVQeRGGPGRDLEPI 240
                                       5...*******************************555555555555555555556666667999555555555679 PP

                                       HHHHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCC..HHTTTHCCEEEHCTCEEEHHHHH CS
                      Amidohydro_1 130 sdeelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaes..lglldeiklilahgvhltpteae 204
                                        +e l++++ ea++++l v++H  +t ++ ed++aa++++ eh     v+++   ++ld    +++++v++tpt   
  gi|330508368|ref|YP_004384796.1| 241 APEVLDAIVTEAHEQGLAVTAHW-GTLEDLEDVLAAGVDGLEHVEARAVLDGwpEDVLDR---LVEQNVPITPT--- 310
                                       9**********************.7788889************77777777655555555...9**********... PP

                                       HHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCG..GHHHHHHHHHHHHHHCCTTTTHCH CS
                      Amidohydro_1 205 llkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnsl..nlleelrlalklqrgllyedeegg 279
                                                +v++   + +i+++ r ++ ++  +G  +++g+D    g  +   + +el l++           ++g
  gi|330508368|ref|YP_004384796.1| 311 --------LSVTDAVLPPQISSQLRLRVGELYAAGGWIVVGSDAPINGVPFgaGVHRELELLV-----------DCG 368
                                       ........345566677888999999999*****99*******44333333333444566666...........9** PP

                                       CHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 280 lslkealrmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGklv 344
                                       l++ ealr+aTi +A+al+ d  +G+ie+G+ ADl vvd+d+l ++   k++ nv++++ +G+ v
  gi|330508368|ref|YP_004384796.1| 369 LTPQEALRAATIEAARALRTD-SIGAIEPGRAADLLVVDGDPLQDI---KDAQNVVMLFRDGRRV 429
                                       *******************95.*****************9966655...5555699999999876 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.5e-06     0.021       1      21 [.      82     102 ..      82     153 .. 0.85
   2 !   33.0   2.0   7.5e-12   4.5e-08     262     473 .]     242     430 ..     193     430 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-06
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHl 21 
                                       +v D++  +++PG++D+H Hl
  gi|330508368|ref|YP_004384796.1|  82 KVLDLTSYTLMPGLIDMHVHL 102
                                       689*****************5 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 7.5e-12
                      Amidohydro_3 262 dealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegv....tesqiervaalqvaagv 334
                                        e+l ++v +a+e+gl v  h  + ++++dvl+a        g++ ++  +    v    +e+ ++r+ + +v +  
  gi|330508368|ref|YP_004384796.1| 242 PEVLDAIVTEAHEQGLAVTAHWGTLEDLEDVLAAG-----VDGLEHVEARA----VldgwPEDVLDRLVEQNVPITP 309
                                       56688888888888888888888888888555432.....33333222222....1244477777777777766655 PP

                      Amidohydro_3 335 qpvfnfedelldsrlgperargs.tpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeelsl 410
                                        +        +d +l p+  +++  +v+el +ag  ++ gsD   +p++   ++ga v r+       l  d  l+ 
  gi|330508368|ref|YP_004384796.1| 310 TLS------VTDAVLPPQISSQLrLRVGELYAAGGWIVVGSD---APING-VPFGAGVHRELE-----LLVDCGLTP 371
                                       522......233445466666668899******999999***...55555.467888877763.....568889*** PP

                      Amidohydro_3 411 eealalyTrgpAkalgledrkGtLevGadADlvvldadpl.dvdppelaearvrltvvdGrvvy 473
                                       +eal++ T ++A+al+ +   G +e+G  ADl v d dpl d++++    ++v++   dGr v+
  gi|330508368|ref|YP_004384796.1| 372 QEALRAATIEAARALRTDSI-GAIEPGRAADLLVVDGDPLqDIKDA----QNVVMLFRDGRRVV 430
                                       *******************8.***************7776156655....56899999998885 PP

>> Urease_alpha  Urease alpha-subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05      0.11      68     108 ..      38      81 ..      26      90 .. 0.84
   2 ?   -2.9   0.0       1.4   8.2e+03      51      73 ..     230     252 ..     188     253 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                      Urease_alpha  68 lvitnavil...DatgivkadigikdgrivaiGkagnpdvmdgv 108
                                       l +tna++l   D   i +a++ ikdg+i+++G  g  d+ +g 
  gi|330508368|ref|YP_004384796.1|  38 LALTNATVLegeDLEPINRAEVLIKDGTIIEVGEEGKIDIPPGA 81 
                                       5689999995556689********************99998776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                      Urease_alpha  51 RdgmgqssaakeeealDlvitna 73 
                                       R g g++ +  + e+lD ++t+a
  gi|330508368|ref|YP_004384796.1| 230 RGGPGRDLEPIAPEVLDAIVTEA 252
                                       44555566666666777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3078.59
//
Query:       gi|330508369|ref|YP_004384797.1|  [L=319]
Description: bifunctional short chain isoprenyl diphosphate synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-65  220.0   0.0    3.2e-65  219.7   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.7   0.0   1.8e-69   3.2e-65       4     225 ..      28     246 ..      25     270 .. 0.93

  Alignments for each domain:
  == domain 1  score: 219.7 bits;  conditional E-value: 1.8e-69
                                       HHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCH CS
                   polyprenyl_synt   4 leealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGn 80 
                                       l+ea+++lv++gGKrlRp ++llaaea +    e   +a +a+ +el+h+++L+hDDimD++++RRG+p++h+++G+
  gi|330508369|ref|YP_004384797.1|  28 LYEASRHLVDSGGKRLRPSMLLLAAEAAG-G--EALALAPAAVSIELVHNFTLIHDDIMDNADVRRGRPAVHKIWGQ 101
                                       7899*************************.2..45789*************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH...STT.HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHH CS
                   polyprenyl_synt  81 klAindgdfllarafellaklf...eks.lellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTay 153
                                       + Ai++gd l+++af++l  +    e + l +++++s++++ ++eGq ld+e e++d ++   ++ey+e++++KT++
  gi|330508369|ref|YP_004384797.1| 102 SGAILAGDTLYSKAFQVLGMTAaspE-RiLGAMNMLSRTCTAICEGQWLDMEFESKDRVT---ENEYMEMIEKKTGV 174
                                       *******************9988644.269*********************999888888...************** PP

                                       HCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHH CS
                   polyprenyl_synt 154 lfalpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkale 225
                                       l+ +++ ++ llagas+e+++al+++g+  G+ FQ+qDD++Dl + +ev gK  g D+ egk tl++++a+ 
  gi|330508369|ref|YP_004384797.1| 175 LYGASAGMGGLLAGASPEVVRALDEFGRLTGMGFQLQDDVIDLLTPEEVSGKRQGGDLIEGKKTLIMIHAFA 246
                                       **********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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 0.22s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2303.41
//
Query:       gi|330508370|ref|YP_004384798.1|  [L=445]
Description: RNA-metabolising metallo-beta-lactamase [Methanosaeta concilii GP6]
Scores for complete sequence (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   34.6   0.4    8.3e-08   32.0   0.1    2.2  2  Lactamase_B_2  Beta-lactamase superfamily domain
      2e-08   34.0   1.1    1.6e-07   31.1   0.1    2.4  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    3.9e-06   27.0   2.5    1.6e-05   25.0   2.3    2.2  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.1   1.4e-11   8.3e-08      30     143 ..      74     175 ..      63     190 .. 0.85
   2 ?   -0.1   0.0     0.096   5.7e+02     175     200 ..     384     409 ..     343     409 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.4e-11
                                       SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEE CS
                     Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleit 106
                                       ++ a+  th+H DH+  +  l++ +   +p++a++ +++ ++++++ +      + +++++++ge+f+++ ++++++
  gi|330508370|ref|YP_004384798.1|  74 KVRAIACTHGHLDHIGAISKLAHKYH--APIIASPFTADLINQEIKSEKIFGV-NNPLKTMNAGERFQVT-PDIDLE 146
                                       799************99999999544..89**************999988888.9**************8.699*** PP

                                       EEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS- CS
                     Lactamase_B_2 107 atparhksgrrldrnagdtlGlriegggkrvyyigDt 143
                                       ++ ++h+           ++  +i +++  ++y+ D 
  gi|330508370|ref|YP_004384798.1| 147 FVRVQHSIVD--------CVFAAIHTPKGIILYANDF 175
                                       ******8766........6666666666666666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.096
                                       HHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 175 hmgHltpeeaveaaadlgakrlvliH 200
                                         gH+  e+ +e++++++++ +++ H
  gi|330508370|ref|YP_004384798.1| 384 VSGHACREDHWELLRMINPEHVIPSH 409
                                       56777789****************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 ?    0.8   0.1     0.082   4.9e+02      32      56 ..      76      99 ..      73     106 .. 0.81
   2 !   31.1   0.1   2.7e-11   1.6e-07       9      54 ..     380     424 ..     373     435 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.082
                             RMMBL 32 rnvilvHGeeeatsalarllkeeeg 56
                                      r ++  HG+ +++ a  +l+  +++
  gi|330508370|ref|YP_004384798.1| 76 RAIACTHGHLDHIGAISKLA-HKYH 99
                                      66999**********99998.6665 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 2.7e-11
                             RMMBL   9 eeidfSgHadknellelirklkprnvilvHGeeeatsalarllkee 54 
                                       +++++SgHa ++++ el+r+++p++vi+ HG  ++  ++   + ee
  gi|330508370|ref|YP_004384798.1| 380 DNVHVSGHACREDHWELLRMINPEHVIPSHGTLRSHGSYLMMA-EE 424
                                       4567***************************887766665555.55 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   2.3   2.7e-09   1.6e-05      43      82 ..      73     112 ..      13     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.7e-09
                                       GGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B  43 kdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                        +v+a+  TH+HlDHiG+  +l++++ +p++a + +a   
  gi|330508370|ref|YP_004384798.1|  73 GKVRAIACTHGHLDHIGAISKLAHKYHAPIIASPFTADLI 112
                                       579***************************9988766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 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:                        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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3020.68
//
Query:       gi|330508371|ref|YP_004384799.1|  [L=365]
Description: isopentenyl-diphosphate delta-isomerase, type 2 [Methanosaeta concilii GP6]
Scores for complete 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   82.8   2.6    4.4e-13   49.0   1.3    2.2  2  FMN_dh          FMN-dependent dehydrogenase
    0.00028   20.0   0.7      0.025   13.6   0.0    2.6  2  IMPDH           IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.035   13.3   0.1      0.073   12.3   0.1    1.5  1  DHO_dh          Dihydroorotate dehydrogenase
      0.047   12.8   6.1       0.76    8.9   3.7    2.7  2  Glu_synthase    Conserved region in glutamate synthase
       0.12   12.8   0.0       0.28   11.6   0.0    1.6  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai


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 !   32.9   0.0   9.7e-12   3.5e-08      28     102 ..      27     102 ..      22     117 .. 0.88
   2 !   49.0   1.3   1.2e-16   4.4e-13     216     342 ..     184     333 ..     141     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 9.7e-12
                                       HGGGGEEE---SSSS-SS-..B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT-SS-HH CS
                            FMN_dh  28 aaferirlrprvlrdvskv..dlsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvlstvastsle 102
                                       ++f+++ l++++l ++ ++  d+s+++lG+kls+P++i+++       ++ +++la aa+++gi ++++++  ++le
  gi|330508371|ref|YP_004384799.1|  27 RSFDDLVLVHKALPEIDEAdiDTSCRFLGRKLSAPLMISAMTGGHPSVKEINVNLALAASELGIAMGVGSQR-AALE 102
                                       689***********998876689999***************88888889*******************9984.4444 PP

  == domain 2  score: 49.0 bits;  conditional E-value: 1.2e-16
                                       SSEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG.........TSSTT---HHHCH............HHHHHHH CS
                            FMN_dh 216 klplvvKGv...ltaedakraveaGvdgivvSNHGG.........RqldgapatidvL............peiveav 268
                                       ++p++vK+    ++ e+a  ++++Gv+ i vS  GG         R  +     ++ +             +ive  
  gi|330508371|ref|YP_004384799.1| 184 SVPIIVKETgagISRETAASLADVGVKMIDVSGQGGlswagvetyRAAEIGDCDLEEMgrlfwswgiptpVSIVECR 260
                                       589****999999***********************99999999977777777777775556666665445556666 PP

                                       ..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHH CS
                            FMN_dh 269 ggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvksvaeld 342
                                          ++v+ +gGir+G Dv+k l lGA++ + + p+l   a++ ++ v r+++   + l+ +m l+G+++  el+
  gi|330508371|ref|YP_004384799.1| 261 SIGLDVISSGGIRSGLDVAKSLSLGASLAGTALPMLKP-ATKDAKAVVRAMSPYLRALRICMFLTGCRRAGELK 333
                                       668********************************877.88999999999999999************998885 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.3     0.004        14       3      56 ..      28      85 ..      26     221 .. 0.74
   2 !   13.6   0.0   7.1e-06     0.025     202     232 ..     258     288 ..     242     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.004
                                      -GGGEEEE---B.-S-GGGSB--EESSTTEEESSSEEE-SST....TT-SHHHHHHHHH CS
                                      xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx RF
                             IMPDH  3 tfddvllvpaks.evlpkevdlktkltkkiklniPlvsaamd....tvtesemAialar 56
                                      +fdd++lv ++  e+  +++d++ ++  + kl+ Pl+ +am     +v e ++  ala 
  gi|330508371|ref|YP_004384799.1| 28 SFDDLVLVHKALpEIDEADIDTSCRFLGR-KLSAPLMISAMTgghpSVKEINVNLALAA 85
                                      79**9999888758888899999999976.9*****99999633335666666666654 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.1e-06
                                       HHCTCT-EEEEES---SHHHHHHHHHTT-SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 202 aakkagvpviaDGGikysgdivkAlaaGada 232
                                        +++ g  vi+ GGi++  d++k+l++Ga+ 
  gi|330508371|ref|YP_004384799.1| 258 ECRSIGLDVISSGGIRSGLDVAKSLSLGASL 288
                                       3577899**********************85 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1     2e-05     0.073     245     270 ..     264     289 ..     254     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                                       S-EEEESS--SHHHHHHHHHHTECEE CS
                            DHO_dh 245 ipiIgvGGiesgeDalekieaGAslv 270
                                       + +I++GGi sg D+   +  GAsl 
  gi|330508371|ref|YP_004384799.1| 264 LDVISSGGIRSGLDVAKSLSLGASLA 289
                                       679*********************85 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 ?    2.5   0.0     0.017        63      63     100 ..      57      95 ..      31     117 .. 0.86
   2 ?    8.9   3.7   0.00021      0.76     201     304 ..     182     293 ..     165     298 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.017
                                       HHHTTEE---B-TTTS-.HHHHHHHHHHHHHHT-B-EET CS
                      Glu_synthase  63 kikkriltsamSyGals.eeahealakamnrlgtksntG 100
                                       k++ ++++sam  G  s +e +  la a+++lg+++  G
  gi|330508371|ref|YP_004384799.1|  57 KLSAPLMISAMTGGHPSvKEINVNLALAASELGIAMGVG 95 
                                       78899*********9984677899**********99887 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00021
                                       -TTSEEEEEEE.-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHHHH.........HHB-.--HHHHHHHHHHHH CS
                      Glu_synthase 201 nkeakvsvKlv.aeagvetiaagvakanadiilidGleGGTGAspkssi.........khaG.lPlelalaevdqtl 266
                                       n ++++ vK + a+   et a+ +a+ ++ +i ++G  G   A  ++ +         ++ G l +  +++  +  +
  gi|330508371|ref|YP_004384799.1| 182 NGSVPIIVKETgAGISRETAAS-LADVGVKMIDVSGQGGLSWAGVETYRaaeigdcdlEEMGrLFWSWGIPTPVSIV 257
                                       3677777775414444444444.777777777777777766555554431111111112233356777777777766 PP

                                       HHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SH CS
                      Glu_synthase 267 keeglrdrvsliadGglktgadvvkalalGAdavgigt 304
                                           +   +++i +Gg+++g dv+k+l lGA   g++ 
  gi|330508371|ref|YP_004384799.1| 258 ECRSIG--LDVISSGGIRSGLDVAKSLSLGASLAGTAL 293
                                       666554..67899******************9877765 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.7e-05      0.28      61      98 ..     179     216 ..     159     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.7e-05
                                       GGGCTT-SEEEE-SCHHHHHHHHHHHHHTTSEEEESSS CS
                    Semialdhyde_dh  61 eeelkevdivflalpagvskelapklaeagvkviDlss 98 
                                       e++  +v i++  ++ag+s+e a++la+ gvk+iD s+
  gi|330508371|ref|YP_004384799.1| 179 EAANGSVPIIVKETGAGISRETAASLADVGVKMIDVSG 216
                                       5566789999999***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2673.51
//
Query:       gi|330508372|ref|YP_004384800.1|  [L=250]
Description: amino acid kinase [Methanosaeta concilii GP6]
Scores for complete 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-40  137.8   0.1    4.8e-40  137.7   0.1    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 !  137.7   0.1   2.7e-44   4.8e-40       1     241 []       1     226 [.       1     226 [. 0.95

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 2.7e-44
                                       TEEEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..H CS
                         AA_kinase   1 krvVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstle 71 
                                       ++ V+K+GGs+ltdk++        ++r+a+++a      ++lv+VhG+gsf++  +++ +gl+++++         
  gi|330508372|ref|YP_004384800.1|   1 MVRVLKIGGSILTDKSCergalpMEIERVAREVASR---PHDLVLVHGAGSFGHIPARQ-YGLPQRFSP-------- 65 
                                       678*****************99999********999...899*****************.********9........ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEE CS
                         AA_kinase  72 eagevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfig 148
                                        +g  +t+++++ l++ +++al++ag+ a ++++ ++++ ++gr       +es  +e i+++le+g+ p+l+g+++
  gi|330508372|ref|YP_004384800.1|  66 -EGLRVTHESVVRLNRLVLEALAKAGVGALPVHPLSCLILSGGR-------IESFATEPIKKMLEDGIMPILHGDVA 134
                                       .677888899*******************************999.......************************** PP

                                       EETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSC.ESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHH CS
                         AA_kinase 149 ldeegelgrgssDtiaallAealgAdkliiltdVdGV.ydadpkkvpdarllpeisvdeaeesaselatgGmkvkhp 224
                                       +d ++  g++s+D++ ++lA al+A+ + +  +VdGV ++  p  + +   lp i+    ++ a+ ++tgGmk k++
  gi|330508372|ref|YP_004384800.1| 135 MDLTQRAGIVSGDQLVSHLARALKAEIVAVGCNVDGVlFSGRPMAEVKRSDLPLIEGAIGGS-AGIDVTGGMKGKLD 210
                                       *************************************9999999996667777777766666.************** PP

                                       HHHHHHHCTT-EEEEEE CS
                         AA_kinase 225 aalaaarrggipvvItn 241
                                       + l++a  g +  +I+n
  gi|330508372|ref|YP_004384800.1| 211 ELLDLADMG-MSSMIFN 226
                                       ********9.9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1901.85
//
Query:       gi|330508373|ref|YP_004384801.1|  [L=317]
Description: mevalonate kinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-21   74.8   0.3    4.6e-21   74.8   0.3    2.2  2  GHMP_kinases_N   GHMP kinases N terminal domain
    1.3e-11   44.7   1.4    2.8e-11   43.6   1.4    1.6  1  GHMP_kinases_C   GHMP kinases C terminal
     0.0042   16.6   0.2       0.01   15.4   0.1    1.7  2  GalKase_gal_bdg  Galactokinase galactose-binding signature


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.6      0.98   5.9e+03      16      32 ..      68      84 ..      67      87 .. 0.76
   2 !   74.8   0.3   7.6e-25   4.6e-21       1      66 []      90     158 ..      90     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.98
                                      HHHHHHHHHHHHHHHHT CS
                    GHMP_kinases_N 16 SSAAlavalvaAllall 32
                                       SAA+a+  v A+l+ l
  gi|330508373|ref|YP_004384801.1| 68 ASAAYATRYVSAVLKEL 84
                                      58999988888888766 PP

  == domain 2  score: 74.8 bits;  conditional E-value: 7.6e-25
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                       ++ i+s+iP++aGLGSSA+++va+vaAl+ +lgl+l  +e a l++++e+++q+g+gs++D a ++yGg
  gi|330508373|ref|YP_004384801.1|  90 RVMIESDIPPAAGLGSSASIVVATVAALNGHLGLELsqKEiAALSYRIEKEVQKGRGSPMDTALATYGG 158
                                       5889*******************************964338***************************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 !   43.6   1.4   4.7e-15   2.8e-11       2      66 ..     220     283 ..     219     299 .. 0.91

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 4.7e-15
                    GHMP_kinases_C   2 lealergdlellgellnlsqrselkavvgilppeleellealselG.algaklsGaGgGptvfalf 66 
                                       ++++++++l+ lgel+  ++   l++ +g+ ++el el+ a+++ G algakl+GaGgG++ +al 
  gi|330508373|ref|YP_004384801.1| 220 APLIREQRLKDLGELMDINHG--LLEALGVGSRELSELVYAARNTGgALGAKLTGAGGGGCMIALP 283
                                       689999***************..899****************99999*****************97 PP

>> GalKase_gal_bdg  Galactokinase galactose-binding signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.7e-06      0.01      13      47 ..       3      37 ..       2      39 .. 0.93
   2 ?   -3.9   0.0       1.7     1e+04      24      32 ..     232     240 ..     231     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-06
                                      EEEEEEEEEEE--S-TTTT-EEEEEEEEEEEEEEE CS
                   GalKase_gal_bdg 13 vasAPGRvnLiGEHtDYngGfVlpmAieqdiyiav 47
                                      +asAPG + L GEH   +g   l  Ai+++  ++v
  gi|330508373|ref|YP_004384801.1|  3 MASAPGKIILFGEHAVVSGTAALGGAIDLRARAIV 37
                                      69***************************998877 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.7
                                       --S-TTTT- CS
                   GalKase_gal_bdg  24 GEHtDYngG 32 
                                       GE +D n+G
  gi|330508373|ref|YP_004384801.1| 232 GELMDINHG 240
                                       999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.18s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2703.33
//
Query:       gi|330508374|ref|YP_004384802.1|  [L=237]
Description: hypothetical protein MCON_2560 [Methanosaeta concilii GP6]
Scores for complete 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-64  215.1   0.0    1.1e-63  214.9   0.0    1.0  1  Memo      Memo-like protein
  ------ inclusion threshold ------
       0.06   12.4   0.0       0.08   12.0   0.0    1.2  1  LigB      Catalytic LigB subunit of aromatic ring-opening dio


Domain annotation for each model (and alignments):
>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.9   0.0   1.3e-67   1.1e-63      38     270 ..      13     234 ..       2     235 .. 0.96

  Alignments for each domain:
  == domain 1  score: 214.9 bits;  conditional E-value: 1.3e-67
                              Memo  38 isPHagyvysgevaakayaelesskvervvilGpsHtilgskvsvlaaseleTPlGdlkvDeelveeLvkkeeiadl 114
                                       ++PHagyvysg++aa +y++l ++  e+ vilGp+H++lgs+v++++ + ++T lG +  D el+  L+   +i+d 
  gi|330508374|ref|YP_004384802.1|  13 VVPHAGYVYSGRIAAMVYSRLPKR--ETYVILGPNHHGLGSPVALSR-DSWRTALGVVTPDLELADLLTG--SIIDH 84 
                                       35********************99..9********************.******************9998..6**** PP

                              Memo 115 detaalaEHSlEvqlpfLkellkekkfkivPilvsaqseetakevgealakvikdes..nlviiSsDlsHygrrFgs 189
                                       de a+++EHS+Evq+pfL++++++  fki+ i +++q+eeta evge +a+++ +      vi+SsD++Hy+     
  gi|330508374|ref|YP_004384802.1|  85 DEAAHQHEHSIEVQIPFLQKRFED--FKILAISMGMQDEETAVEVGEEIARAALKLGrkCTVIASSDFTHYE----- 154
                                       ************************..************************99988877899***********..... PP

                              Memo 190 pqeiaesieDrevikaleelneeelkeylektnnticGekpiavilkalkklgakkakllkYaqssdvtsdtdsvVs 266
                                       p+e+a++  D++vi+a+ +++  +++  +++ n++ cG +pia+++ a++ lga  +kll Y +s+dv++d+++vV+
  gi|330508374|ref|YP_004384802.1| 155 PREVARKV-DSQVIEAILNMDIPQIYSRVYRFNASSCGIGPIAATIAASRLLGASSGKLLCYGTSGDVSGDYSQVVG 230
                                       ********.******************************************************************** PP

                              Memo 267 yasl 270
                                       y+++
  gi|330508374|ref|YP_004384802.1| 231 YGAI 234
                                       *987 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 ?   12.0   0.0     9e-06      0.08     114     195 ..      89     165 ..      69     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9e-06
                              LigB 114 mklDHGtlvPLelmlpdeakvpvikvslntvaypllsferlykLGeAlrkaveeldknvlilgsGglsHqlegdeaa 190
                                        + +H + v + ++ +      ++k+  ++  +++ + e   ++Ge +++a  +l ++  +++s +++H+ + + a 
  gi|330508374|ref|YP_004384802.1|  89 HQHEHSIEVQIPFLQK---RFEDFKILAIS--MGMQDEETAVEVGEEIARAALKLGRKCTVIASSDFTHYEPREVAR 160
                                       5556666666677777...77888998888..789**********************************98777777 PP

                              LigB 191 kadaq 195
                                       k d+q
  gi|330508374|ref|YP_004384802.1| 161 KVDSQ 165
                                       66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1867.99
//
Query:       gi|330508375|ref|YP_004384803.1|  [L=206]
Description: 30S ribosomal protein S2 [Methanosaeta concilii GP6]
Scores for 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-26   91.3   0.5    5.6e-15   55.2   0.4    2.0  2  Ribosomal_S2  Ribosomal protein S2
  ------ inclusion threshold ------
      0.032   13.8   1.6       0.06   12.9   1.4    1.4  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 !   34.6   0.0   1.2e-12   1.1e-08       2      95 ..      23     113 ..      22     120 .. 0.91
   2 !   55.2   0.4   6.3e-19   5.6e-15     148     213 ..     121     186 ..     116     188 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.2e-12
                      Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIygern.gihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaak 77 
                                       L+agvh+G q++  +++m pyIy +r+ g +++d++ t + +r a+k++++   +  +il+v+ ++  ++     ak
  gi|330508375|ref|YP_004384803.1|  23 LAAGVHIGTQQK--TNDMMPYIYRVRSdGLYVLDVQSTDKRIRLAAKFLSKY--DPTNILIVSARQYGQRPALMFAK 95 
                                       89******6665..899******999549********************986..6789********99999999999 PP

                      Ribosomal_S2  78 rangyyvnerWlgGtLTN 95 
                                        +++     r+++ tLTN
  gi|330508375|ref|YP_004384803.1|  96 ATGATANVGRFVPNTLTN 113
                                       99999999********** PP

  == domain 2  score: 55.2 bits;  conditional E-value: 6.3e-19
                      Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladaie 213
                                        Pd+++ +dp  +  av+Ea  +gipvia++Dtn  +++vd +Ip N++  ++++li+ +la+++ 
  gi|330508375|ref|YP_004384803.1| 121 EPDVIIATDPSGDAQAVNEAVDVGIPVIALCDTNNMTSNVDLVIPTNNKGRKALTLIYWLLARQVL 186
                                       59************************************************************9875 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   6.7e-06      0.06      60     105 ..     124     169 ..     120     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.7e-06
                                       EE--SSHHHHHHHHHHHHHTT-EEEEESTTGCTTT-CEEEEEC-HH CS
                      Peripla_BP_4  60 ivapvdstalapalkkakaaGIpVvafdsddapsgerlayvgfdne 105
                                       ++ ++d+++ a+a+++a + GIpV+a    ++ +++++ ++ ++n+
  gi|330508375|ref|YP_004384803.1| 124 VIIATDPSGDAQAVNEAVDVGIPVIALCDTNNMTSNVDLVIPTNNK 169
                                       4667899999****************65554999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1706.17
//
Query:       gi|330508376|ref|YP_004384804.1|  [L=59]
Description: hypothetical protein MCON_2562 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-12   47.1   0.0    2.2e-12   46.7   0.0    1.1  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   1.2e-16   2.2e-12       8      49 .]       7      52 ..       4      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.2e-16
                                      -HHHHHHHHHHHHHHH....HT.......S.S-SSSSTTCHHHHTT-S-- CS
                      RNA_pol_Rpb6  8 trYelvriaakRArQieegesl.......e.tqkpvviAlrEiaegkipi 49
                                      trYe +ri+++RA+Q      +         +++p+ iAl+E+  g ipi
  gi|330508376|ref|YP_004384804.1|  7 TRYERARIVGARALQV----FMgapvlidTnHTDPLEIALEEMRLGVIPI 52
                                      9***************....6666666764467***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 455.16
//
Query:       gi|330508377|ref|YP_004384805.1|  [L=61]
Description: hypothetical protein MCON_2564 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-28   97.9   0.7    3.2e-28   97.8   0.7    1.0  1  RNA_pol_N       RNA polymerases N / 8 kDa subunit
      0.003   17.8   0.1     0.0034   17.6   0.1    1.1  1  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.7   3.5e-32   3.2e-28       2      58 ..       1      56 [.       1      57 [. 0.97

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 3.5e-32
                                      ---SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THHH CS
                         RNA_pol_N  2 iiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdliek 58
                                      +iPVrCF+CG+vi+++weey+e+++++  p++++d+Lg+++yCCrrmll+hv+++++
  gi|330508377|ref|YP_004384805.1|  1 MIPVRCFSCGRVISHVWEEYRERIKTE-PPGKVMDDLGIDKYCCRRMLLSHVEIVDT 56
                                      8***********************998.99************************997 PP

>> Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   3.7e-07    0.0034       4      49 ..       3      52 ..       1      58 [. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.7e-07
                    Chordopox_RPO7  4 plvCstCGrDlse..eryrLlvkkkkLkdvlatv..krkCCrlkLstqie 49
                                      p+ C +CGr +s+  e yr  +k +   +v++ +   + CCr  L   +e
  gi|330508377|ref|YP_004384805.1|  3 PVRCFSCGRVISHvwEEYRERIKTEPPGKVMDDLgiDKYCCRRMLLSHVE 52
                                      678*********95568**************97533899**988777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 443.57
//
Query:       gi|330508378|ref|YP_004384806.1|  [L=132]
Description: 30S ribosomal protein S9 [Methanosaeta concilii GP6]
Scores for complete 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-33  113.9   0.4      7e-33  113.7   0.4    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.4   3.9e-37     7e-33       1     121 []       8     132 .]       8     132 .] 0.95

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 3.9e-37
                                       EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSSS.EEEEEEEESS-HHHHHHHHHHHHHH CS
                      Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllgk.fdvfvkvkgGGlsgqaeAirlgiar 76 
                                       G++K ++Ar+++kegkg +++n+++l+   + + ar k++ep++++g l k +++ v v+gGG++gq++A+r++ia+
  gi|330508378|ref|YP_004384806.1|   8 GKKKAATARATLKEGKGIVRINKVPLDI-HEPRLARLKIQEPVEIAGDLLKgMNIDVVVSGGGIMGQTDAVRTAIAK 83 
                                       89**************************.555999***********999888************************* PP

                                       HHHHHHHHHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                      Ribosomal_S9  77 aLvalekeekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                       ++v+++    ++Lk      +++ll++D R++ErkK+g ++AR+kyq+s+R
  gi|330508378|ref|YP_004384806.1|  84 GIVEWTG--DTALKeayseyDRNLLVSDHRQKERKKFGGPGARSKYQKSYR 132
                                       *****88..588887777889****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1027.19
//
Query:       gi|330508379|ref|YP_004384807.1|  [L=139]
Description: 50S ribosomal protein L13 [Methanosaeta concilii GP6]
Scores for complete 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   0.1    2.4e-09   37.5   0.1    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 !   37.5   0.1   1.3e-13   2.4e-09       4     114 ..       3      99 ..       1     107 [. 0.88

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.3e-13
                                       EEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHH CS
                     Ribosomal_L13   4 viDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakell 80 
                                       v+DA+g vlgrlas  ak L             +G+ v ++naek  +tg+k +  + y +t+  gg ++ ++   +
  gi|330508379|ref|YP_004384807.1|   3 VVDATGLVLGRLASVTAKSLL------------AGEEVNIVNAEKALITGDKEHIFTDYGQTRARGGKERGPY---F 64 
                                       799999999999999998774............7999***************999999999999998887665...7 PP

                                       CCSHHHHHHHHHHCCS-.SSHHHHHHGCTEEEESS CS
                     Ribosomal_L13  81 ekkpeeilekaVkgmLp.knklgrrrlkrLkvyag 114
                                        ++pe+il+++V+gmLp k + gr+ ++rLk+y g
  gi|330508379|ref|YP_004384807.1|  65 PRRPEMILKRTVRGMLPyKMRRGRDAFSRLKIYVG 99 
                                       899**************5667899999******88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1027.84
//
Query:       gi|330508380|ref|YP_004384808.1|  [L=139]
Description: 50S ribosomal protein L18e [Methanosaeta concilii GP6]
Scores for complete sequence (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   50.6   0.4    1.8e-13   50.3   0.4    1.2  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    4.6e-08   33.8   0.1    1.9e-07   31.8   0.1    1.9  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
  ------ inclusion threshold ------
      0.097   13.6   0.0       0.22   12.4   0.0    1.6  1  HHH_9           HHH domain


Domain annotation for each model (and alignments):
>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.4     3e-17   1.8e-13      19     139 ..      26     139 .]       4     139 .] 0.86

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 3e-17
                     Ribosomal_L18  19 senvylklLvklyrfLarRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevP 95 
                                       + n+ +  L+   +  +r t++   + + +rL +  +n +++ ls++ +++++    + ++ v g+v+    l +  
  gi|330508380|ref|YP_004384808.1|  26 T-NPRIVRLIGELKAATRDTGAPLWRDIARRLEKPSRNYAAVNLSKINRHTQS----NDTVLVAGKVLASGNLEH-- 95 
                                       3.44443344444677899*****************************99985....589**********99986.. PP

                     Ribosomal_L18  96 klsvaALrftetararilkaGGeiltlDqLalraPtGkntvLlr 139
                                       +++vaAL+f+++a ++i +aGG ++ +++L  ++P+G+   +lr
  gi|330508380|ref|YP_004384808.1|  96 NVTVAALNFSSQAMSKIQQAGGRCMRIENLMQEHPKGSGIKILR 139
                                       79************************************998886 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 !   31.8   0.1   3.1e-11   1.9e-07      70     127 ..      61     120 ..      38     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3.1e-11
                                       ----EEEGGGTTTTSSS....SE..EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A  70 deaeeidleelaeaglikkkdgv..KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                        + + ++l+++ ++   + +  v  Kvl++g+l+++++v a +fS++A +kI++aGG+++
  gi|330508380|ref|YP_004384808.1|  61 RNYAAVNLSKINRHTQSNDTVLVagKVLASGNLEHNVTVAALNFSSQAMSKIQQAGGRCM 120
                                       3455778888844444444444457********************************995 PP

>> HHH_9  HHH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.8e-05      0.22      30      68 ..      24      62 ..       9      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.8e-05
                             HHH_9 30 ligeeallkkldkkklaeeevgeptleDIleeLakPgrD 68
                                      ++++ + ++ + + k+a+ ++g p  +DI + L+kP r 
  gi|330508380|ref|YP_004384808.1| 24 EKTNPRIVRLIGELKAATRDTGAPLWRDIARRLEKPSRN 62
                                      45566777778888999999****************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1098.45
//
Query:       gi|330508381|ref|YP_004384809.1|  [L=423]
Description: integral membrane protein [Methanosaeta concilii GP6]
Scores for complete 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-66  222.3  40.8    1.1e-65  222.0  40.8    1.0  1  TctA      Tripartite tricarboxylate transporter TctA family


Domain annotation for each model (and alignments):
>> TctA  Tripartite tricarboxylate transporter TctA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.0  40.8     6e-70   1.1e-65       3     408 ..      12     411 ..      10     412 .. 0.94

  Alignments for each domain:
  == domain 1  score: 222.0 bits;  conditional E-value: 6e-70
                              TctA   3 lvllGvllGtliGllPGlhatlavalllpltf.....gldpeaalilllgiyvgaifggsipaillgvPGtpssvat 74 
                                       +v+lG++lG+++Gl PGlh ++++++ll++++     gl p +++ ++l+++++++f ++ipai+lg+P +++++++
  gi|330508381|ref|YP_004384809.1|  12 CVALGFALGIISGLTPGLHLNNFASMLLAISPqllllGLTPFQMASIILAASISQTFFDAIPAIFLGAP-DSETALS 87 
                                       789******************************************************************.9****** PP

                              TctA  75 vldgyplakqGrageAlrlaaigSfiGglvsvllllllapllakvalkfgpaeyfalillglvliailse....... 144
                                       vl+g++l+++Gr+ eA+rl+a+gS+ ++ +++ll+ +l+++++  + + ++ +y+ ++ll+++l++i se       
  gi|330508381|ref|YP_004384809.1|  88 VLPGQRLMLEGRGIEAVRLSALGSAGSIAFALLLVYPLSWIIS--SYYDYLVKYVGVLLLAISLMMIKSErgpwieg 162
                                       *******************************************..999999************************** PP

                              TctA 145 .......ksllkglialllglllgtvgldpnsgtpRftfgsielldgislvpvliGlFgiselltsleskskip.ls 213
                                              k  l + +++l +++lg+++++ +   +     s+  l+   l+p+l+G+Fg+s l+ sl++k +ip ++
  gi|330508381|ref|YP_004384809.1| 163 qgslvhwKYKLIAGMLFLTSGVLGIFAFEHEDLLY-----SPLDLEPQVLLPLLSGIFGASSLILSLTTKVQIPkQT 234
                                       *****************************998555.....555578999******************9998887656 PP

                              TctA 214 lkdlk....kslptilrgsliGtivGilPgvGasiaaflayavakrlskkpekfgkgaiegvaapeaannaaaggal 286
                                        +++k     +++++l g l G++v+++Pgv++s+a+++a   +             a+e++++  ++n+a+a ++l
  gi|330508381|ref|YP_004384809.1| 235 ESKIKmpgpTIAKAVLSGGLGGSLVAWIPGVSPSVASIAARLGSPG----------TAEEFLVSIAGVNSANALFSL 301
                                       67777666558889999**************************775..........699****************** PP

                              TctA 287 iplltlgipgsgvaavllgallihglqpgpeLftenpelvyallasllianvlllvlgllliklfak.llkipkelL 362
                                       ++l+++  p+sg+aa++ ++l++            + +++  ++++++i ++++++ ++++++l+a+ + ++++  L
  gi|330508381|ref|YP_004384809.1| 302 VALYVIDRPRSGAAAAIQQLLTL------------DQNIMAQMMIMAVIVVLASYLATIAAAQLAARsISSLNYPRL 366
                                       *****************998744............5667788*************************666******* PP

                              TctA 363 lpiilvllvigayalnnslfdvlvmlifgvlGlllrrlgvplaplv 408
                                       ++i+lv+l++++ya+++  f+++v+++++++Gl+    g+ +++++
  gi|330508381|ref|YP_004384809.1| 367 CIIVLVFLLAMTYAFTGI-FGLFVFFLSTIVGLIAPVAGIHRIHAM 411
                                       ******************.************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1132  (0.0631379); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3274.05
//
Query:       gi|330508382|ref|YP_004384810.1|  [L=227]
Description: hypothetical protein MCON_2571 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.6   0.2          3    8.0   0.1    2.2  2  SPRY      SPRY domain


Domain annotation for each model (and alignments):
>> SPRY  SPRY domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0    0.0086   1.5e+02      87     106 ..      84     103 ..      80     112 .. 0.79
   2 ?    8.0   0.1   0.00017         3       9      37 ..     197     225 ..     191     227 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.0086
                                       EEEEEEEESTTTSSEEEEEE CS
                              SPRY  87 knlgvaFrnvrgaelfPvvs 106
                                       k++++ +r  + ++l+P+v+
  gi|330508382|ref|YP_004384810.1|  84 KKTNTFYRLSPATPLYPYVY 103
                                       6667777777777******8 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00017
                                       TCCTSSEEEEEEEETTSSSSSTSSSTSST CS
                              SPRY   9 qsaeggsisvGlateqtdlsdksgegddr 37 
                                       +++egg+++vG a+++t++++k+  g+++
  gi|330508382|ref|YP_004384810.1| 197 EKKEGGKVQVGKAKRPTRRKRKEAPGQKE 225
                                       4789*******************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1844.70
//
Query:       gi|330508383|ref|YP_004384811.1|  [L=404]
Description: glucosamine-1-phosphate N-acetyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-35  121.5   0.0    5.4e-35  121.2   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    3.3e-16   60.1   0.2    4.5e-16   59.6   0.2    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    3.3e-15   55.1  20.4      3e-07   29.9   1.3    4.4  4  Hexapep          Bacterial transferase hexapeptide (six repea
    3.9e-05   23.5   0.0    5.9e-05   22.9   0.0    1.2  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    0.00096   18.8  21.6     0.0038   16.9   2.3    4.9  5  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.041   12.0   1.7       0.09   10.9   1.7    1.4  1  DUF4954          Domain of unknown function (DUF4954)
      0.053   13.4   0.0      0.097   12.6   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
      0.079   12.8   0.0       0.13   12.1   0.0    1.2  1  DUF268           Caenorhabditis protein of unknown function, 
      0.086   12.8   0.0       0.18   11.8   0.0    1.5  1  PepSY_2          Peptidase propeptide and YPEB domain
       0.14   11.1   0.6        1.3    7.8   0.2    2.1  2  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 !  121.2   0.0     3e-38   5.4e-35       2     246 ..       3     226 ..       2     228 .. 0.89

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 3e-38
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       a+ILa G+G+R++PLt  ++k ++p++g  +l+++ + r+ ++gi++  v +  + + +v++++++g  +gv++++a
  gi|330508383|ref|YP_004384811.1|   3 AIILAAGEGSRMRPLTAGVPKVMLPIAGR-PLLEHIVLRAKEAGIDR-FVLVVGYGADSVRDHFQDGRSLGVKIEYA 77 
                                       8****************************.*****************.55555699********************* PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       +++e+ gtA+A++ a+ l+ed++     +vL+gD+l +  a++e        aak  +++ + +v+++ +yGv   +
  gi|330508383|ref|YP_004384811.1|  78 HQNEQLGTAHALMAAESLAEDSF-----MVLNGDVLPDIgALKE-------LAAK-GMAVSAIKVDDPGRYGVFLEE 141
                                       *************9999999777.....9*******99433333.......3332.3356668999******98655 PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       + g  ++ vEK + ++ s+la++GiY+f++ ++++l + + +++rge e+td l++a ++  +a ++++     W  
  gi|330508383|ref|YP_004384811.1| 142 D-GIFQSVVEKSEDPP-SNLANAGIYLFKKWIFDEL-RLIPKSTRGEYELTDGLNRAANK--EAIEIVELN--SWLE 211
                                       5.8*************.*******************.89******************776..678877777..5*** PP

                                       XSSHHHHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleanekla 246
                                       +G + ++lean +l+
  gi|330508383|ref|YP_004384811.1| 212 IGRPWDILEANLALL 226
                                       ***********9876 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.2   2.5e-19   4.5e-16       1     111 [.       3     121 ..       3     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 2.5e-19
                                       EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS. CS
                      NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggd..eevlaalarlgvrvvededpg. 69 
                                       a+iLA+G++sRm     g +K +lp++g+plle+++ ++++ag+d+ v+v+g+  ++v++++++ +   v+ e+++ 
  gi|330508383|ref|YP_004384811.1|   3 AIILAAGEGSRMrpltaGVPKVMLPIAGRPLLEHIVLRAKEAGIDRFVLVVGYgaDSVRDHFQDGRSLGVKIEYAHq 79 
                                       79**********6666444*******************************988778999998777544444444431 PP

                                       -SHHHHHHHHHHHH..SSSCEEEEETT-TT--HHHHHHHHHCH CS
                      NTP_transf_3  70 kgplaslaaalraaa.dadavlvlacDmPlltpelverllaaa 111
                                         +l++ +a ++a +  +d ++vl +D+ l +  ++++l+a+ 
  gi|330508383|ref|YP_004384811.1|  80 NEQLGTAHALMAAESlAEDSFMVLNGDV-LPDIGALKELAAKG 121
                                       455555555555422379*********9.77999999999875 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   8.9e-05      0.16      13      36 .]     240     263 ..     233     263 .. 0.91
   2 !   29.9   1.3   1.7e-10     3e-07       2      35 ..     265     298 ..     264     299 .. 0.91
   3 !   18.8   0.9   5.3e-07   0.00095       1      33 [.     299     330 ..     299     333 .. 0.91
   4 !    6.9   0.9    0.0031       5.6       2      24 ..     359     381 ..     358     382 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.9e-05
                                       TEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  13 faviggnVkIGdnvkIgagvvigg 36 
                                       +a++ g + IG+++++ +g++i g
  gi|330508383|ref|YP_004384811.1| 240 GATLKGKISIGRGTVVRSGSYIEG 263
                                       8999*****************976 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 1.7e-10
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       + IG+++ Igp+++i++ + IGdnv+Ig+ v i+
  gi|330508383|ref|YP_004384811.1| 265 VMIGQDSEIGPNCYIRPTCCIGDNVRIGNAVEIK 298
                                       579*************************988886 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 5.3e-07
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvv 33 
                                       +++I ++++Ig+ +++ g+ +IG+++  gag+ 
  gi|330508383|ref|YP_004384811.1| 299 NSTIMNGTKIGHLSYV-GDSIIGERCNFGAGTI 330
                                       579*************.9999*********986 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0031
                                       EEEETTEEE-TTEEEETTEEE-T CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGd 24 
                                       ++ G +v+ g ++ i+++++I  
  gi|330508383|ref|YP_004384811.1| 359 VIMGHGVMTGINTSIYPGTVIEA 381
                                       789*****************976 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   3.3e-08   5.9e-05       1      52 [.       1      54 [.       1      73 [. 0.83

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.3e-08
                                      EEEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE- CS
                              IspD  1 vvvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvs 52
                                      + ++i AAG+G+Rm+   ag+pK  l ++g++lleh v  + +   +d+ v+vv 
  gi|330508383|ref|YP_004384811.1|  1 MQAIILAAGEGSRMRpltAGVPKVMLPIAGRPLLEHIVLRAKE-AGIDRFVLVVG 54
                                      579**********954449*****************9987776.67899888875 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 ?    5.1   0.0     0.011        19      18      32 ..     247     261 ..     240     262 .. 0.87
   2 !   16.9   2.3   2.1e-06    0.0038       1      28 [.     264     293 ..     264     299 .. 0.90
   3 ?    3.6   2.4     0.032        57       4      21 ..     285     309 ..     284     315 .. 0.66
   4 !    7.4   1.3     0.002       3.6       3      15 ..     318     330 ..     317     332 .. 0.88
   5 ?   -1.8   0.3       1.5   2.7e+03      23      33 ..     370     380 ..     358     381 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                                       EEE-TT-EE-TT-EE CS
                         Hexapep_2  18 vslGdncvvgaGvvi 32 
                                       +s+G++ vv +G++i
  gi|330508383|ref|YP_004384811.1| 247 ISIGRGTVVRSGSYI 261
                                       9*************9 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.1e-06
                                       .EEE-TT-EE-TT-EE.S.EEE-TT-EE-T CS
                         Hexapep_2   1 pviIGdnCliGanagi.G.vslGdncvvga 28 
                                       pv IG+++ iG+n++i +   +Gdn+ +g+
  gi|330508383|ref|YP_004384811.1| 264 PVMIGQDSEIGPNCYIrPtCCIGDNVRIGN 293
                                       899**************6479*******98 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.032
                                       E-TT-EE-.....TT-EE..SEEE- CS
                         Hexapep_2   4 IGdnCliG.....anagi..GvslG 21 
                                       IGdn+ iG     +n++i  G+++G
  gi|330508383|ref|YP_004384811.1| 285 IGDNVRIGnaveiKNSTImnGTKIG 309
                                       9999999933333344447888887 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.002
                                       EE-TT-EE-TT-E CS
                         Hexapep_2   3 iIGdnCliGanag 15 
                                       iIG++C++Ga  +
  gi|330508383|ref|YP_004384811.1| 318 IIGERCNFGAGTI 330
                                       8*********876 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 1.5
                                       T-EE-TT-EE- CS
                         Hexapep_2  23 ncvvgaGvvit 33 
                                       n  +++G vi 
  gi|330508383|ref|YP_004384811.1| 370 NTSIYPGTVIE 380
                                       55577777776 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.7     5e-05      0.09     216     261 ..     287     332 ..     248     335 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5e-05
                           DUF4954 216 apveiGegViledfiissGskikdgavisrcfvGqavklkkqfsae 261
                                       + v+iG+ V+++++ i++G+ki + + + ++++G+ ++++ +  ++
  gi|330508383|ref|YP_004384811.1| 287 DNVRIGNAVEIKNSTIMNGTKIGHLSYVGDSIIGERCNFGAGTICS 332
                                       4689999999999999999999999999999999999988776665 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.4e-05     0.097      63     114 ..       3      69 ..       1      98 [. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                                       EEEES---TCCHHHH................HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHH CS
                    NAD_binding_10  63 aVvsalggggkdeeg................aknivdaakeagvkRfvlvsaigvgdevpgefgewnk 114
                                       a++ a+g g++ +                   ++iv  akeag+ Rfvlv + g++ +v ++f++  +
  gi|330508383|ref|YP_004384811.1|   3 AIILAAGEGSRMRPLtagvpkvmlpiagrplLEHIVLRAKEAGIDRFVLVVGYGAD-SVRDHFQDGRS 69 
                                       6677776666632223345556666677777899999******************9.68888877544 PP

>> DUF268  Caenorhabditis protein of unknown function, DUF268
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.1e-05      0.13      21      94 ..      44     118 ..      29     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.1e-05
                            DUF268  21 nGakk.iltveynkleieeefkdrlssilpvefaknwkkyaekfdfaasfssieksglgrygdpldpiGdlrell 94 
                                        G ++ +l v y +  + ++f+d  s   ++e+a++ ++  ++  ++a+ s  e s +   gd+l  iG l+el+
  gi|330508383|ref|YP_004384811.1|  44 AGIDRfVLVVGYGADSVRDHFQDGRSLGVKIEYAHQNEQLGTAHALMAAESLAEDSFMVLNGDVLPDIGALKELA 118
                                       4554438999**************************************************************986 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.18       6      59 ..      85     137 ..      82     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                           PepSY_2   6 lalallaaaAlAgrrdtdspkadwlpreklvakleaqGykvkkievddggcyEv 59 
                                       +a al+aa  lA ++   +   d lp   + + l+a+G+ v+ i+vdd g y v
  gi|330508383|ref|YP_004384811.1|  85 TAHALMAAESLA-EDSFMVLNGDVLPDIGALKELAAKGMAVSAIKVDDPGRYGV 137
                                       677899999999.8888999999999999*******************999976 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.067   1.2e+02     284     310 ..     246     273 ..     236     295 .. 0.47
   2 ?    7.8   0.2   0.00075       1.3     272     344 ..     293     359 ..     282     394 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.067
                        Fucokinase 284 svsvgegsvie.hsslkgnvsigsnsiv 310
                                       ++s+g+g+v+   s ++g+v ig+ s +
  gi|330508383|ref|YP_004384811.1| 246 KISIGRGTVVRsGSYIEGPVMIGQDSEI 273
                                       5555555555422444444444444433 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00075
                        Fucokinase 272 esavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtilqtlslklskekeyv 344
                                       + + + nS + ++ ++g  s++ +s ++++++ g+++i s+l+ +++    +++  + l + +++++++k  v
  gi|330508383|ref|YP_004384811.1| 293 NAVEIKNSTIMNGTKIGHLSYVGDSIIGERCNFGAGTICSNLRHDKG----SIK--SYLKGEKVDSGRRKLGV 359
                                       566789************************************99976....355..35555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2876.46
//
Query:       gi|330508384|ref|YP_004384812.1|  [L=366]
Description: DegT/DnrJ/EryC1/StrS aminotransferase [Methanosaeta concilii GP6]
Scores for 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-129  432.0   0.0   2.3e-129  431.8   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.9e-05   24.1   0.0    4.9e-05   22.8   0.0    1.6  1  Beta_elim_lyase  Beta-eliminating lyase
    2.4e-05   23.5   0.0    3.8e-05   22.8   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
     0.0096   14.5   0.0      0.019   13.5   0.0    1.5  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
       0.05   13.8   0.0       0.13   12.5   0.0    1.6  1  DUF2795          Protein of unknown function (DUF2795)
       0.14   12.2   0.1       0.35   11.0   0.1    1.7  1  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.8   0.0  7.6e-133  2.3e-129       3     360 ..      13     361 ..      11     362 .. 0.97

  Alignments for each domain:
  == domain 1  score: 431.8 bits;  conditional E-value: 7.6e-133
                                       HHHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHH CS
                   DegT_DnrJ_EryC1   3 keeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatana 79 
                                       +eee+eav evl+sg+lt+g++v++FE++f++ylgv+h+iavs+Gt Al laL+ lg++pgdeVI p++tF+atan+
  gi|330508384|ref|YP_004384812.1|  13 GEEEIEAVGEVLRSGMLTQGEKVKNFEEEFSEYLGVEHSIAVSNGTVALDLALKGLGLEPGDEVISPAFTFIATANT 89 
                                       799************************************************************************** PP

                                       HHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTE CS
                   DegT_DnrJ_EryC1  80 vlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgk 156
                                       vl+ g +pvf+Dvdp t+nidp+++ ++it+rt+a++ VhlyGq++d +a+ +i+++ ++ ++eD+A+A+Ga + g+
  gi|330508384|ref|YP_004384812.1|  90 VLYQGSVPVFADVDPRTFNIDPDDLSEKITPRTRAVIGVHLYGQPFDAKAVCQICEDRNIALVEDCAQAHGAMMGGR 166
                                       ***************************************************************************** PP

                                       ECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 157 kvGalgdaavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAiglaq 233
                                       ++G++g +++fSFyptKn+ttGeGG+++tnd++la+++r+lrnhG       +y +   +Gynyr+t+iq Aig  q
  gi|330508384|ref|YP_004384812.1| 167 MAGSFG-TGCFSFYPTKNMTTGEGGMITTNDDALADRMRLLRNHGDT----GKYNHIS-IGYNYRMTNIQGAIGSGQ 237
                                       ******.9*************************************77....8999999.****************** PP

                                       HCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSC CS
                   DegT_DnrJ_EryC1 234 LerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhypn 310
                                       L+rl+ ++a+R e+a+++++ ++  +   ++++ + + +h++ +y+++ve+++ v+r++l+e l+++gi+t vhyp+
  gi|330508384|ref|YP_004384812.1| 238 LKRLEGFIAKRIENADTLNKTIKIDGL--TVPFRTADVRHVYNQYVLRVEDDFPVSREKLMEYLNANGIATAVHYPK 312
                                       *********************987554..4667766667*************99*********************** PP

                                       HGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 311 plhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                                       ++++qp+y++   + ++++p++e++++rv+sLp++p+l+  d++++++++
  gi|330508384|ref|YP_004384812.1| 313 AVYEQPIYQKLG-YGRDRCPVSEDVSRRVMSLPVHPSLSASDLQHIAQTI 361
                                       ***********6.6688*****************************9987 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   1.6e-08   4.9e-05      32     237 ..      33     263 ..      27     313 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.6e-08
                                       HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT. CS
                   Beta_elim_lyase  32 ktvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknkea. 106
                                       ++v+++e+++ e++g e+ + v +Gt A  ++lk l  ++g+evi   pa   f  t + + ++g+ ++ ++ +   
  gi|330508384|ref|YP_004384812.1|  33 EKVKNFEEEFSEYLGVEHSIAVSNGTVALDLALKGLGlEPGDEVIS--PAF-TFIATANTVLYQGSVPVFADVDPRt 106
                                       678999***************************99988******74..554.4555666778888888887766554 PP

                                       TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CH CS
                   Beta_elim_lyase 107 GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivk 183
                                        ++d+++l ++i+++ +     ++i +   + +  Gq+      ++v +i+++++i l+ D A    a+   g  + 
  gi|330508384|ref|YP_004384812.1| 107 FNIDPDDLSEKITPRTR-----AVIGV---HLY--GQPFDA---KAVCQICEDRNIALVEDCAQAHGAM-MGGRMAG 169
                                       89************555.....44444...445..999976...68999**************988887.4444444 PP

                                       HHHTTSSEEEEESSSTT--SS-EEEEE-HH..............................................H CS
                   Beta_elim_lyase 184 emfsyvDsvtmslkKdllanvGgvlafrddel..........................................edy 218
                                       +   ++  +++  +K++++  Gg++ ++dd l                                          e +
  gi|330508384|ref|YP_004384812.1| 170 SFGTGC--FSFYPTKNMTTGEGGMITTNDDALadrmrllrnhgdtgkynhisigynyrmtniqgaigsgqlkrlEGF 244
                                       444554..78888*****************66888888888888888888888888888888888888888888888 PP

                                       HHHHHHHHHHHT---SSTH CS
                   Beta_elim_lyase 219 laerveqrkylggglrqag 237
                                       +a+r+e + +l + ++  g
  gi|330508384|ref|YP_004384812.1| 245 IAKRIENADTLNKTIKIDG 263
                                       8888887777766666555 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.3e-08   3.8e-05      43     183 ..      33     162 ..      20     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.3e-08
                                       HHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE CS
                       Aminotran_5  43 kaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi 119
                                       ++v++ +e++ e +++e     i +s++t a+ l++++l+  l+pgde++  +    a+    + +  +  + v ++
  gi|330508384|ref|YP_004384812.1|  33 EKVKNFEEEFSEYLGVEH---SIAVSNGTVALDLALKGLG--LEPGDEVISPAFTFIATA---NTVLYQGSVPV-FA 100
                                       678889999999999996...7899**************5..9*******9999888777...55554545555.77 PP

                                       EBETT.SCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS CS
                       Aminotran_5 120 pldee.geldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghi 183
                                        +d++  ++d+d+l ++++++t++v+  h     G  ++ +++++++ ++++ ++ D aqa g +
  gi|330508384|ref|YP_004384812.1| 101 DVDPRtFNIDPDDLSEKITPRTRAVIGVHL---YGQPFDAKAVCQICEDRNIALVEDCAQAHGAM 162
                                       78765158******************9995...8**************************98876 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 !   13.5   0.0   6.4e-06     0.019      54     173 ..      35     154 ..      25     165 .. 0.74
   2 ?   -4.3   0.0       1.6   4.8e+03     262     279 ..     294     311 ..     283     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.4e-06
                                       HHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHH..THHH.TTCEEEEESTTS CS
                   Cys_Met_Meta_PP  54 rsvleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrllkk..vlkk.lgievkfvdtsd 126
                                       ++++ee+ ++  g+e+++avs G+ A+++a+  l l+ Gde+++    +  t + + +   ++    ++ + ++  d
  gi|330508384|ref|YP_004384812.1|  35 VKNFEEEFSEYLGVEHSIAVSNGTVALDLALKGLgLEPGDEVISPAFTFIATANTVLYqgSVPVfADVDPRTFNI-D 110
                                       57899***************************996788***********99988654411333324455555555.8 PP

                                       HHHHHHHCCTTEEEEE.EESS-TTTT----HHHHHHHHHHTT-EEEEE CS
                   Cys_Met_Meta_PP 127 leelekaikentklvy.lEtptnpllkvvDiekiaklakkagvlvvvD 173
                                       +++l ++i+++t++v  +   +    +  D +++++++ ++++ +v D
  gi|330508384|ref|YP_004384812.1| 111 PDDLSEKITPRTRAVIgVHLYG----QPFDAKAVCQICEDRNIALVED 154
                                       999*********9984122222....3356666666666666666655 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1.6
                                       HHHHHHHTSTTEEEEE-T CS
                   Cys_Met_Meta_PP 262 kvAefLekhpkvekvyYp 279
                                       k+ e+L+++   ++v Yp
  gi|330508384|ref|YP_004384812.1| 294 KLMEYLNANGIATAVHYP 311
                                       788999999999999999 PP

>> DUF2795  Protein of unknown function (DUF2795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.2e-05      0.13       5      23 ..     287     305 ..     287     316 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                           DUF2795   5 dyPatKdeLveyArrngAp 23 
                                       d+P+++++L+ey++ ng  
  gi|330508384|ref|YP_004384812.1| 287 DFPVSREKLMEYLNANGIA 305
                                       8***************943 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00012      0.35      97     126 ..     294     326 ..     292     327 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                       HHHHHHHHTT--EEEE--...SSHHHHHTTT-E CS
                    Acetyltransf_9  97 raleemreegqplsllfP...ssipiYrrfGye 126
                                       +++e+++++g+  ++ +P   ++ piY+++Gy+
  gi|330508384|ref|YP_004384812.1| 294 KLMEYLNANGIATAVHYPkavYEQPIYQKLGYG 326
                                       789***************999999********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2721.05
//
Query:       gi|330508385|ref|YP_004384813.1|  [L=311]
Description: oxidoreductase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-24   87.4   0.6    3.8e-24   85.8   0.1    2.0  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    9.2e-08   32.4   0.1    1.8e-07   31.5   0.1    1.6  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    9.4e-07   28.4   0.5    3.2e-06   26.6   0.0    2.1  3  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0053   17.3   0.0      0.029   14.9   0.0    2.2  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0089   16.7   0.1      0.021   15.5   0.1    1.6  1  CoA_binding      CoA binding domain
  ------ inclusion threshold ------
      0.011   15.3   0.1       0.02   14.5   0.1    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.036   13.0   0.0      0.058   12.3   0.0    1.2  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
      0.083   13.3   0.1       0.57   10.6   0.0    2.3  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      0.085   13.3   0.1       0.22   11.9   0.0    1.7  1  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase family


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.1   1.9e-27   3.8e-24       2     120 .]       2     115 ..       1     115 [. 0.95
   2 ?   -1.1   0.0       1.7   3.3e+03      55      81 ..     127     151 ..     120     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 1.9e-27
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheel 78 
                                        v++iG+G +g++h+r + e  ++ + v ++dp +e+a+++  s  + ++s+ eella  ++dav+v++p++ h++ 
  gi|330508385|ref|YP_004384813.1|   2 DVGVIGVGAMGKNHVRVYSEL-KGVDTVYVYDPISENAQRA--SDLATVCSSPEELLA--KVDAVSVCVPTRYHFDT 73 
                                       69*************888888.*****************75..7777899********..***************** PP

                                       HHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  79 akaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       a ++++ag++ l+EKP+++tv+ea++l+ l ek++ +v+vg+
  gi|330508385|ref|YP_004384813.1|  74 ASKVINAGVNCLIEKPITMTVQEAERLLGLIEKTDLVVGVGH 115
                                       ****************************************97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                                       HHHHTCTTESEEEE-S-GGGHHHHHHH CS
                      GFO_IDH_MocA  55 eelladpeidavivatpngtheelaka 81 
                                       +++++  ++d+v++  +n t ++++ a
  gi|330508385|ref|YP_004384813.1| 127 KKIAE--RPDYVSIKRHNPTSNRITDA 151
                                       44444..89999999998877777665 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   8.9e-11   1.8e-07       1      73 [.       2      75 ..       2     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 8.9e-11
                                      EEEEE--SHHHHHHHHHH..HHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHH CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnl..lkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevi 73
                                      ++g+iG+G MG+n ++    lk   +v+vy+  +e+++++  + a++++s+eel+a++d+v ++v+   + d+  
  gi|330508385|ref|YP_004384813.1|  2 DVGVIGVGAMGKNHVRVYseLKGVDTVYVYDPISENAQRAS-DLATVCSSPEELLAKVDAVSVCVPTRYHFDTAS 75
                                      59*************99965677899*******99999987.5589********************998887655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.6e-09   3.2e-06      38     102 ..       2      68 ..       1      81 [. 0.88
   2 ?   -1.5   0.1      0.67   1.3e+03      36      47 ..     105     116 ..      93     204 .. 0.68
   3 ?   -2.0   0.0      0.99     2e+03      50      96 ..     185     228 ..     173     233 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.6e-09
                                       EEEEES-SHHHHHHHHHHHHTT-..EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--S CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgm..kviaydrskkkeeeeeelgvelvsleellaesDivslhlplt 102
                                        vG+iG+G++G++  ++ ++++    v++yd+  ++ +++++l   + s eella+ D vs+++p  
  gi|330508385|ref|YP_004384813.1|   2 DVGVIGVGAMGKNHVRVYSELKGvdTVYVYDPISENAQRASDLATVCSSPEELLAKVDAVSVCVPTR 68 
                                       69***************9987655899******999998999888899****************964 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.67
                                       TSEEEEES-SHH CS
                      2-Hacid_dh_C  36 gktvGiiGlGrI 47 
                                       +kt  ++G+G+I
  gi|330508385|ref|YP_004384813.1| 105 EKTDLVVGVGHI 116
                                       566666777766 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.99
                                       HHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEE CS
                      2-Hacid_dh_C  50 avakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivs 96 
                                       +v + ++ f   v+ ++ s+ +++   + +  +v+ ee+  e D+ +
  gi|330508385|ref|YP_004384813.1| 185 NVCEAMAVFSESVVSISASRLSSK---KFRTFYVEAEEFTTEGDFMT 228
                                       566677777777888887777555...33334788888888888876 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.5e-05     0.029       2      81 ..       3      77 ..       2      85 .. 0.85
   2 ?   -2.4   0.0       3.9   7.7e+03      26      47 ..     107     127 ..      97     139 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlse 80
                                      +g+iG G mg+  ++  ++       ++v  ++  e a+ + + +  +v++ + ee++++ d v ++v+++++ +++s+
  gi|330508385|ref|YP_004384813.1|  3 VGVIGVGAMGKNHVRVYSELK-GVDTVYVY-DPISENAQRASDLA--TVCS-SPEELLAKVDAVSVCVPTRYHFDTASK 76
                                      89*************999986.79999955.88888777776665..6888.89999999*************999988 PP

                                      C CS
                     F420_oxidored 81 l 81
                                      +
  gi|330508385|ref|YP_004384813.1| 77 V 77
                                      7 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.9
                                       GCEEEEEESSCCCHHHHHHHHC CS
                     F420_oxidored  26 heivvansrnpekaeelaeelg 47 
                                       +++vv+   + e+ + + ee++
  gi|330508385|ref|YP_004384813.1| 107 TDLVVG-VGHIERFNPIVEEIK 127
                                       445544.556666666655554 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.1e-05     0.021       5      88 ..       2      83 ..       1      86 [. 0.96

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                                      EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHH CS
                       CoA_binding  5 kviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelv 83
                                       v+viG+g +g+  + + +e +++ ++ v++   + + +  +  +v  s +el +k  vd+  ++vP +   +++ +++
  gi|330508385|ref|YP_004384813.1|  2 DVGVIGVGAMGKNHVRVYSELKGVDTVYVYDPISENAQRASDLATVCSSPEELLAK--VDAVSVCVPTRYHFDTASKVI 78
                                      599****************************99999********************..********************* PP

                                      HTT-S CS
                       CoA_binding 84 eagik 88
                                      +ag++
  gi|330508385|ref|YP_004384813.1| 79 NAGVN 83
                                      **996 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   9.8e-06      0.02       7      81 ..       3      78 ..       1      88 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.8e-06
                                      EEEES-SHHHHHHHHHHHH.TT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHT CS
                              IlvN  7 iaviGyGsqGhaqalnlrd.sgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeei 81
                                      + viG G+ G+++ +   +  g+d v+     s+++++A++ +    + +e+ +k d v + +P +++ +  ++ i
  gi|330508385|ref|YP_004384813.1|  3 VGVIGVGAMGKNHVRVYSElKGVDTVYVYDPISENAQRASDLATVCSSPEELLAKVDAVSVCVPTRYHFDTASKVI 78
                                      89************99988579******************************************999877665555 PP

>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.9e-05     0.058     132     204 ..       3      68 ..       2      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
                                       EEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----S CS
                   OCD_Mu_crystall 132 laiiGaGvqaetqlealkavldikevriydrdeeaaekfaenlqefefevsackseeeavegadivvtvTaak 204
                                       +++iG G++ + ++++ +++ ++++v +yd   e+a+++ + +        +c+s+ee  +++d v  + +++
  gi|330508385|ref|YP_004384813.1|   3 VGVIGVGAMGKNHVRVYSELKGVDTVYVYDPISENAQRASDLAT-------VCSSPEELLAKVDAVSVCVPTR 68 
                                       589***************************99999999888776.......7999999999998887777665 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 ?   10.6   0.0   0.00028      0.57       2      92 ..       3      83 ..       2      88 .. 0.85
   2 ?   -0.6   0.0      0.88   1.8e+03      40      72 ..     137     167 ..     115     174 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                                      EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHH CS
                    Semialdhyde_dh  2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvsk 80
                                      v+++G  G++G++ +r+ +e + v+ v+++   +++ ++ ++++         +v +  ee l++vd v  ++p  ++ 
  gi|330508385|ref|YP_004384813.1|  3 VGVIG-VGAMGKNHVRVYSELKGVDTVYVYDPISENAQRASDLA---------TVCSSPEELLAKVDAVSVCVPTRYHF 71
                                      99***.9*********************9998887777777773.........3444346677**************** PP

                                      HHHHHHHHTTSE CS
                    Semialdhyde_dh 81 elapklaeagvk 92
                                      + a k+++agv 
  gi|330508385|ref|YP_004384813.1| 72 DTASKVINAGVN 83
                                      ********9985 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.88
                                       BHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE CS
                    Semialdhyde_dh  40 klaeavkaleegkdlkvedvdeeelkevdivfl 72 
                                        +++++++ + ++d +v +  +  ++++divf 
  gi|330508385|ref|YP_004384813.1| 137 SIKRHNPTSNRITDASVVE--DLMIHDIDIVFN 167
                                       5566666677777777777..556689999995 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 ?   11.9   0.0   0.00011      0.22      32      76 ..      27      67 ..      15      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      EEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S-- CS
                    UDPG_MGDP_dh_C 32 evkiyDPkvkeeaveaeleekgvevvdsleealkgadaivilteh 76
                                       v +yDP  ++++++ +     ++v++s+ee l+++da+ ++++ 
  gi|330508385|ref|YP_004384813.1| 27 TVYVYDPISENAQRASD----LATVCSSPEELLAKVDAVSVCVPT 67
                                      499****9999999884....579***************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2271.05
//
Query:       gi|330508386|ref|YP_004384814.1|  [L=205]
Description: transferase hexapeptide repeat containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   85.1  12.2    2.7e-08   33.2   0.1    3.3  3  Hexapep          Bacterial transferase hexapeptide (six repea
    2.1e-15   56.1  11.2    9.8e-07   28.4   1.3    3.5  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.017   14.8   0.1      0.054   13.1   0.1    1.9  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.089   12.9   1.1       0.16   12.1   1.1    1.4  1  DUF2613          Protein of unknown function (DUF2613)
       0.17   11.6   0.8       0.42   10.4   0.8    1.6  1  zf-CSL           CSL zinc finger


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 !   30.5   0.2   5.4e-11   1.9e-07       4      34 ..      32      62 ..      31      63 .. 0.95
   2 !   33.2   0.1   7.5e-12   2.7e-08       2      35 ..      66      99 ..      65     100 .. 0.93
   3 !   27.3   2.5   5.6e-10     2e-06       2      35 ..     117     150 ..     116     151 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 5.4e-11
                                      EETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep  4 IGsnvlIgpfaviggnVkIGdnvkIgagvvi 34
                                      IG++++I++fa++++  kIG+++ Ig  v+i
  gi|330508386|ref|YP_004384814.1| 32 IGEGTKIWHFAHVRPSSKIGKGCNIGKSVYI 62
                                      9*************************98887 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 7.5e-12
                                      EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35
                                      + +G+nv+I +f+ ++ +VkI d+v +g+ ++ +
  gi|330508386|ref|YP_004384814.1| 66 AEVGDNVKIQNFVSVYKGVKIEDDVFVGPSATFT 99
                                      789**************************99976 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 5.6e-10
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       t+I  ++ Ig++a+i  +++IG+++ Igag+v++
  gi|330508386|ref|YP_004384814.1| 117 TRICRGSSIGANATIVCGITIGEYAMIGAGSVVA 150
                                       78999***************************96 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 !   28.4   1.3   2.7e-10   9.8e-07       3      34 .]      49      82 ..      48      82 .. 0.90
   2 !   10.5   0.0   0.00011      0.39       2      15 ..      84      97 ..      83      99 .. 0.91
   3 !   20.1   3.0   1.1e-07    0.0004       9      32 ..     124     149 ..     117     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.7e-10
                                      EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2  3 iIGdnCliGanagi..GvslGdncvvgaGvvita 34
                                      +IG+ C+iG++ +i  G ++Gdn+++++ v +++
  gi|330508386|ref|YP_004384814.1| 49 KIGKGCNIGKSVYIdiGAEVGDNVKIQNFVSVYK 82
                                      7************666***********9888775 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00011
                                      EEE-TT-EE-TT-E CS
                         Hexapep_2  2 viIGdnCliGanag 15
                                      v+I+d++++G++a+
  gi|330508386|ref|YP_004384814.1| 84 VKIEDDVFVGPSAT 97
                                      9**********986 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 1.1e-07
                                       EE-TT-EE..SEEE-TT-EE-TT-EE CS
                         Hexapep_2   9 liGanagi..GvslGdncvvgaGvvi 32 
                                        iGana+i  G+++G+ + +gaG+v+
  gi|330508386|ref|YP_004384814.1| 124 SIGANATIvcGITIGEYAMIGAGSVV 149
                                       69*****778***************9 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.5e-05     0.054       5      20 ..     188     203 ..     185     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                                       -EEE-TTT--EEEECC CS
                   Desulfoferrod_N   5 evYkCevCGniVeVle 20 
                                        vY+C  CG  Ve+++
  gi|330508386|ref|YP_004384814.1| 188 TVYRCSSCGTDVEIVK 203
                                       69***********985 PP

>> DUF2613  Protein of unknown function (DUF2613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.1   4.4e-05      0.16       4      34 ..     125     154 ..     122     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                           DUF2613   4 gPaaaSaVaGivlGvvavfgvtavvqqdsrP 34 
                                       ++a a +V Gi++G  a +g+++vv + ++P
  gi|330508386|ref|YP_004384814.1| 125 IGANATIVCGITIGEYAMIGAGSVVAE-DVP 154
                                       567789******************985.455 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.8   0.00012      0.42      21      51 ..     171     196 ..     169     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                                       ETTSSEEEEEHHHHHTT....--EEEETTSS CS
                            zf-CSL  21 CRCgdeFelteedleegaegaevvvqCssCS 51 
                                       CRCg + +  + d  ++     +v +CssC 
  gi|330508386|ref|YP_004384814.1| 171 CRCGRRLNTILHDDGSK-----TVYRCSSCG 196
                                       ******99999998886.....9*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 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:                        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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1433.74
//
Query:       gi|330508387|ref|YP_004384815.1|  [L=398]
Description: NDP-N-acetyl-D-galactosaminuronic acid dehydrogenase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-31  107.0   0.0    1.2e-30  106.5   0.0    1.2  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    1.2e-17   63.9   0.0    1.8e-17   63.3   0.0    1.3  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    0.00017   21.8   0.0    0.00067   19.9   0.0    2.0  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0043   17.0   0.0      0.012   15.5   0.0    1.7  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0086   16.5   0.0      0.016   15.6   0.0    1.4  1  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
  ------ inclusion threshold ------
      0.046   13.0   0.5       0.11   11.7   0.0    1.8  2  FAD_binding_3   FAD binding domain
      0.049   13.2   0.0      0.077   12.5   0.0    1.2  1  DUF4147         Domain of unknown function (DUF4147)
       0.05   13.9   0.1       0.12   12.6   0.1    1.7  1  TrkA_N          TrkA-N domain
       0.11   12.4   0.0       0.23   11.4   0.0    1.6  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.5   0.0   6.1e-34   1.2e-30       2     180 ..       9     185 ..       8     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 6.1e-34
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS.--TTHHHHHHHHCHTTTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipi.yepgLeelvkkavesgrlsfttdvekaveea 77 
                                       ki+v+GlG  Gl+ aav+a +g+ v+gvDi++e+ + +n+g  pi +e+gLeel+ ++   + + +t ++e  ++++
  gi|330508387|ref|YP_004384815.1|   9 KIAVVGLGNAGLPLAAVIADRGIAVLGVDINDERCRLINQGTNPIpEEEGLEELIIRHG-GKSFIATPRFED-ARDC 83 
                                       8********************************************55689******999.566677777776.8999 PP

                                       SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE--- CS
                    UDPG_MGDP_dh_N  78 dvifiaVgTPskkkgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvsnPE 154
                                         +++ V+  +++  +++D + + +a+ s++++lkkg++vv++ T p+gt+   vkk+l e+s   + +f ++++PE
  gi|330508387|ref|YP_004384815.1|  84 SSFIVIVPLFVDQ-SNNPDFSIMDKALLSLGRILKKGDLVVLETTFPPGTTSGRVKKLLCECSGLGEGEFFLAYSPE 159
                                       999999**99999.9999*********************************************************** PP

                                       ---TTSHHHHHHS-S-EEEEESSCHH CS
                    UDPG_MGDP_dh_N 155 flregsavkdllnpdrvviGveekka 180
                                       ++  g  +  l + ++v++G++e++ 
  gi|330508387|ref|YP_004384815.1| 160 RIMTGYSISRLREFPKVIGGTDEESG 185
                                       ********************999875 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 !   63.3   0.0     9e-21   1.8e-17       2      92 ..     207     296 ..     206     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 9e-21
                      UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeel 78 
                                        AE+iK+++ ++++++I+++Nel ++c+ lgid  e +e ++++     +++ p+ GvGG+c+p+ +++L++ +e+ 
  gi|330508387|ref|YP_004384815.1| 207 VAEMIKVMEGCYRDVNIALANELYKICQDLGIDFFEAREKACHQFC---HIHLPSTGVGGHCIPVYPWFLIKEMEKR 280
                                       69**************************************998765...89*********************99998 PP

                      UDPG_MGDP_dh  79 gle..aelleavrevN 92 
                                       ++    +ll++ r  N
  gi|330508387|ref|YP_004384815.1| 281 EMFdkCRLLHTSRILN 296
                                       7654577777776666 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 !   19.9   0.0   3.3e-07   0.00067       1     103 [.       9     139 ..       9     144 .. 0.70
   2 ?   -3.2   0.0       4.3   8.6e+03      14      30 ..     345     361 ..     344     377 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.3e-07
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.......................EEE-SSHHHHHH CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.......................akaaesieelva 54 
                                       ki+++GlG+ G ++a  ++++g+ v +++ + e+++ + +                            +e+++++ +
  gi|330508387|ref|YP_004384815.1|   9 KIAVVGLGNAGLPLAAVIADRGIAVLGVDINDERCRLINQGTnpipeeegleeliirhggksfiaTPRFEDARDCSS 85 
                                       79*****************************9998765554478888888888887777766543233344444444 PP

                                       HCSEEEE-SSSHHHHHHHHHS.....HCCC--TT-EEEE-S---HHHHHHHHHH CS
                     NAD_binding_2  55 sldvvitmvkagkavdevieg.....llealkkgdilidgstsspedtrelake 103
                                        + +v ++v ++++ d  i +     l + lkkgd+++  +t  p +t  + k+
  gi|330508387|ref|YP_004384815.1|  86 FIVIVPLFVDQSNNPDFSIMDkallsLGRILKKGDLVVLETTFPPGTTSGRVKK 139
                                       446666677766655544433354446677788888888888888777766665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.3
                                       HHHHHHHTT-EEEEE-S CS
                     NAD_binding_2  14 malnllkagykvavynr 30 
                                       +a+ l ++g +v+v + 
  gi|330508387|ref|YP_004384815.1| 345 LARLLYDKGLDVYVADP 361
                                       78889999999999884 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.9e-06     0.012       1      36 [.       9      44 ..       9      61 .. 0.91
   2 ?   -2.6   0.0       2.2   4.3e+03      14      42 ..     345     376 ..     344     382 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.9e-06
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseeale 36
                                      k+av+G G  G  +aav+a +g+ V  vdi++e+ +
  gi|330508387|ref|YP_004384815.1|  9 KIAVVGLGNAGLPLAAVIADRGIAVLGVDINDERCR 44
                                      69*****************************99875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.2
                                       HHHHHHHTT-EEEEE-S...-HHHHHHHHHHH CS
                           3HCDH_N  14 iaavfasagleVvlvdi...seealekaleki 42 
                                       +a ++  +gl+V + d    ++e ++++ e+i
  gi|330508387|ref|YP_004384815.1| 345 LARLLYDKGLDVYVADPllnNDEVAARGFESI 376
                                       57888999******998776666666666665 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 !   15.6   0.0   8.3e-06     0.016       2      47 ..     325     370 ..     324     385 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.3e-06
                                       EE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCH CS
                    UDPG_MGDP_dh_C   2 ilGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeavea 47 
                                       i G++f++++ ++ +S+ l++++ L ++g +v + DP  ++++v+a
  gi|330508387|ref|YP_004384815.1| 325 IKGITFRAGVREFYHSRNLALARLLYDKGLDVYVADPLLNNDEVAA 370
                                       67**************************************999987 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.5e-05      0.11       2      68 ..       8      69 ..       7     110 .. 0.85
   2 ?   -2.4   0.5         1   2.1e+03     293     303 ..     252     262 ..     252     263 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.5e-05
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEE CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegap 68
                                      +++++VG G aGl la + + +G+ v+ v+     +++ r + +nq t  + ++ Gle+ i+++g +
  gi|330508387|ref|YP_004384815.1|  8 AKIAVVGLGNAGLPLAAVIADRGIAVLGVD-----INDERCRLINQGTNPIPEEEGLEELIIRHGGK 69
                                      5789**********************9887.....66778889999999999999999999988855 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                                       TEEE-STTSHH CS
                     FAD_binding_3 293 aHihpPtgGqG 303
                                       +Hih P++G+G
  gi|330508387|ref|YP_004384815.1| 252 CHIHLPSTGVG 262
                                       8********99 PP

>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.9e-05     0.077      36      93 ..       8      60 ..       2      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                                      -SEEEEEESTTHHHHHHHHH.HHHGEEEEEEETT-----TT-EE.EEE-SSS--HHHHH CS
                           DUF4147 36 krvvvvgaGKAaaamaaaleeealksgvvvvkkghaeekeriev.leaahplPdeesve 93
                                       ++ vvg+G+A +++aa+++    ++g+ v   +   ++er+++  ++++p+P+ee++e
  gi|330508387|ref|YP_004384815.1|  8 AKIAVVGLGNAGLPLAAVIA----DRGIAVLGVD--INDERCRLiNQGTNPIPEEEGLE 60
                                      689*************9999....4899888544..446667773678********986 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   6.2e-05      0.12       1      38 [.      10      47 ..      10      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.2e-05
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelr 38
                                      i+++GlG+ G  la  + ++g+ v+++d ++er++ + 
  gi|330508387|ref|YP_004384815.1| 10 IAVVGLGNAGLPLAAVIADRGIAVLGVDINDERCRLIN 47
                                      79*****************9988***********9764 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.23       1      41 [.       9      49 ..       9      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                      -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHH CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeinee 41
                                      kiav+G G+ G  lA+v+a++g  v     ++e ++ in+ 
  gi|330508387|ref|YP_004384815.1|  9 KIAVVGLGNAGLPLAAVIADRGIAVLGVDINDERCRLINQG 49
                                      7************************9999999999999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2716.08
//
Query:       gi|330508388|ref|YP_004384816.1|  [L=358]
Description: UDP-N-acetylglucosamine 2-epimerase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.4e-102  343.2   0.0   1.6e-102  343.0   0.0    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 !  343.0   0.0  8.7e-107  1.6e-102       2     346 ..      22     349 ..      21     350 .. 0.94

  Alignments for each domain:
  == domain 1  score: 343.0 bits;  conditional E-value: 8.7e-107
                                       HHTTS-..EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSH CS
                       Epimerase_2   2 alkaeselelqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDtn 78 
                                       +++++ + ++++v+tGqH+++em++++f++++i++pdy+l+ +s+s++ +tg++l++ eevl++e pD+v+v GDtn
  gi|330508388|ref|YP_004384816.1|  22 EIRKR-DHKEVIVHTGQHYNYEMDRIFFDQMGIAAPDYHLGIGSGSHGFQTGEMLKKTEEVLQKEVPDAVIVFGDTN 97 
                                       56666.4599******************************************************************* PP

                                       HHHHHHHHHHHTT-EEEEET-----S-TT..SHHHHHHHHHHHT-SEEEESSHHHHHHHHHTT--GGGEEE---HHH CS
                       Epimerase_2  79 etlagalaAfklripvaHveAGlRsfdltegmpeEinRhlidklsdlhfapteearenLlkegeeeerifvvGntvi 155
                                       +tlag laA+k++i+ aH+eAGlRsfd++  mpeEinR+l+d++sdl+++pt++a +nL +eg+  ++++ +G++++
  gi|330508388|ref|YP_004384816.1|  98 STLAGGLAAAKMHIKCAHIEAGLRSFDKR--MPEEINRVLVDHCSDLLLCPTRTAIDNLKREGI-VQNVHLTGDVMV 171
                                       *****************************..*********************************.779********* PP

                                       HHHHHHHHHHH...T-HHHHHH..--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHH CS
                       Epimerase_2 156 Dalllskeeieeklkaseilke..lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrk 230
                                       Da +  ++ +e+   +s+il+   lk  +y+l+t+Hr++n+d+pe+l+ i+ al++l++     vv+p+h  pr +k
  gi|330508388|ref|YP_004384816.1| 172 DAQKDCERIAES---ESHILEAlgLKPWSYYLATVHRASNTDDPENLRAIALALQDLDD-----VVFPCH--PRAEK 238
                                       ***998777774...4699999999********************************98.....6*****..***** PP

                                       HH..HHHHHH-.TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT CS
                       Epimerase_2 231 rl..leeleel.envtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvnlReeteRpegveagtnvlvgt 304
                                        l  +  +++l +++++i+p+gyld+l l knak ++tdSgG+q+Ea++lg+p+++lR++te+ e+v+ g+nvlv  
  gi|330508388|ref|YP_004384816.1| 239 YLkkFGLWDDLeKKIRMIKPVGYLDMLLLEKNAKKIVTDSGGVQKEAYLLGIPCITLRDTTEWIETVNDGWNVLVR- 314
                                       **77667788866**************************************************************6. PP

                                       -HHHHHHHHHHHCT-..--......--TT-SS-HHHHHHHHH CS
                       Epimerase_2 305 dkeeIvaaleklledkkelekmanaknpYgdGkaseriveil 346
                                         e+I +a+++++         +++++++g+G+as  iv+++
  gi|330508388|ref|YP_004384816.1| 315 PGEDIASAIRDFRPR-------HERQDVFGKGRASAMIVDLV 349
                                       5789********955.......445789***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2541.56
//
Query:       gi|330508389|ref|YP_004384817.1|  [L=327]
Description: hypothetical protein MCON_2578 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-10   41.7   0.0    8.4e-10   39.2   0.0    1.9  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.8e-10   41.0   0.1    1.9e-09   37.8   0.0    2.3  3  Glyco_transf_4   Glycosyltransferase Family 4
    1.9e-06   28.0   0.0    0.00022   21.3   0.0    2.2  2  Glyco_trans_4_2  Glycosyl transferase 4-like
    6.1e-06   26.8   0.0    3.2e-05   24.4   0.0    2.0  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0051   16.4   0.0      0.015   14.8   0.0    1.8  2  Glycos_transf_1  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.29   1.1e+03      50      86 ..     114     155 ..      96     159 .. 0.59
   2 !   39.2   0.0   2.3e-13   8.4e-10       4     124 ..     169     294 ..     166     300 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.29
                                       HTT-T.TEEEE---.....THHHHHHHH-SEEEE--...---SHH CS
                   Glyco_trans_1_4  50 aagleerveftGfv.....edlaellaaadvfvaPs...egfglk 86 
                                       +   +e   +   v     ++++e+  + +v+++P+   ++f  k
  gi|330508389|ref|YP_004384817.1| 114 L---AEAADVITTVnepleKKVKEYAPQKKVYIVPNypqRSFCQK 155
                                       2...23333333333234455999999999999998776666555 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 2.3e-13
                                       EEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEE CS
                   Glyco_trans_1_4   4 ilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaadvfv 77 
                                       i+f+Gr+   ++g+  lle + ++ ++  +++ivG+gp  +  l    ++  ++v+ +G+   +++a+ll +a++++
  gi|330508389|ref|YP_004384817.1| 169 IIFIGRV-CTQEGIGKLLELARAIPER--EFWIVGGGPfARYYLW---RK-PANVRNLGWQphDKVAALLGKASLCL 238
                                       89*****.5669*************88..******9997653442...22.368*******9556************ PP

                                       E--.-.........--SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-.HHHH CS
                   Glyco_trans_1_4  78 aPs.e.........gfglkllEamaaglpvVatdvggiaevvgengllvppgd.peal 124
                                       +P  e             kl E++a+g+ vVa+ v  i++   +n ++vp++d + a 
  gi|330508389|ref|YP_004384817.1| 239 IPReEnaltpystdKSVWKLNEYLALGKIVVASGVTMIEK--RKNLVIVPSRDlERAV 294
                                       ***735555555557899***************9955555..5676888988855454 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.26   9.2e+02      13      25 ..      21      33 ..      12      44 .. 0.76
   2 !   37.8   0.0   5.2e-13   1.9e-09      58     164 ..      41     146 ..      22     147 .. 0.88
   3 ?   -0.6   0.0      0.33   1.2e+03     132     152 ..     278     298 ..     247     305 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.26
                    Glyco_transf_4 13 raLarrGheVtvv 25
                                        L+ +GheV v 
  gi|330508389|ref|YP_004384817.1| 21 GTLQSQGHEVIVP 33
                                      5689999999985 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 5.2e-13
                    Glyco_transf_4  58 laflrrlrrllkrekpDvvHahspaalgaallalrr.rlgiplVltvHglyekrllkarlkplsrllralerrllrr 133
                                       ++ +r++++++  +kpDvvH+ + + +++ ++a +r r  ++l++ + +++   + + +l p++++++++er l+ +
  gi|330508389|ref|YP_004384817.1|  41 ISIARQAKKMALDHKPDVVHIFNVPDVIYHGFAGLRgRGYKKLIYDYRSPWGVEFAQTFLAPGKAFAERFERELAEA 117
                                       34567888999999******999999988888888878899***********99999******************** PP

                    Glyco_transf_4 134 adrviavSeatadelrerygvppekitVipn 164
                                       ad +++v e + + ++e y  p +k++++pn
  gi|330508389|ref|YP_004384817.1| 118 ADVITTVNEPLEKKVKE-YA-PQKKVYIVPN 146
                                       *****************.88.88*******9 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.33
                    Glyco_transf_4 132 rradrviavSeatadelrery 152
                                       +r + vi++S+ + + +r+++
  gi|330508389|ref|YP_004384817.1| 278 KRKNLVIVPSRDLERAVRDNL 298
                                       566789999999999999865 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 !    5.2   0.0    0.0056        20       1      29 [.       2      32 ..       2      38 .. 0.77
   2 !   21.3   0.0     6e-08   0.00022      57     136 ..      37     122 ..      31     125 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0056
                   Glyco_trans_4_2  1 killlanlssvht.lrlake.LakrgyeVhv 29
                                      killlan ++  t lr+ ++ L+++g+eV v
  gi|330508389|ref|YP_004384817.1|  2 KILLLANQPERTTrLRMFRGtLQSQGHEVIV 32
                                      8********665436655445********88 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 6e-08
                   Glyco_trans_4_2  57 pleylk.afklkklikkikPDvvhahyakpygllgslaarl.sgvipvv...lsvwGldv...lkfpkksklkklll 125
                                       + ++++ a++ kk+  + kPDvvh++++++++++g +a ++  g+++++    s wG  +   +  p k+ + +  +
  gi|330508389|ref|YP_004384817.1|  37 TRNWISiARQAKKMALDHKPDVVHIFNVPDVIYHG-FAGLRgRGYKKLIydyRSPWGVEFaqtFLAPGKA-FAERFE 111
                                       67889966799*******************98888.7776515689999444456777664322222222.445455 PP

                   Glyco_trans_4_2 126 klalkkatkvi 136
                                       + +++ a++++
  gi|330508389|ref|YP_004384817.1| 112 RELAEAADVIT 122
                                       55555666665 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 !   24.4   0.0     9e-09   3.2e-05      46     159 ..      31     146 ..       6     147 .. 0.73
   2 ?   -0.6   0.0      0.45   1.6e+03     132     149 ..     282     300 ..     278     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 9e-09
                   Glyco_trans_4_4  46 pvprrpspladlaalralrrllrqrrerpdvvhahspt....aglaarlarrrrgiplvvtlh...glllrrg.sga 114
                                        vp   +++++ + +r+++ +    + +pdvvh+++ +     g+a+++ r +   +l+++++   g ++++   ++
  gi|330508389|ref|YP_004384817.1|  31 IVPSF-GTRNWISIARQAKKMA--LDHKPDVVHIFNVPdviyHGFAGLRGR-G-YKKLIYDYRspwGVEFAQTfLAP 102
                                       33333.3567778889999998..9*********99664665777776666.3.34588888722244466667666 PP

                   Glyco_trans_4_4 115 vrrlyralerrllrradavlvvseaeaeelralgvpadrvvvvpn 159
                                        ++++ ++er l+  ad++++v e + +++ ++  p+ +v +vpn
  gi|330508389|ref|YP_004384817.1| 103 GKAFAERFERELAEAADVITTVNEPLEKKVKEYA-PQKKVYIVPN 146
                                       67889************************99995.5689999998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.45
                   Glyco_trans_4_4 132 avlvvseaeaeelra.lgv 149
                                       +v+v+s+++ +++r+ l +
  gi|330508389|ref|YP_004384817.1| 282 LVIVPSRDLERAVRDnLLR 300
                                       79**********9994434 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      0.81   2.9e+03      73      99 ..     122     145 ..     108     148 .. 0.55
   2 !   14.8   0.0   4.3e-06     0.015      13     124 ..     164     273 ..     154     296 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.81
                                       CGGGEEECCHSSSHHHHHHCESEEEEE CS
                   Glycos_transf_1  73 dnviflgevsredleellknadifvlp 99 
                                        +v+      +++++e+  +++++++p
  gi|330508389|ref|YP_004384817.1| 122 TTVNEPL---EKKVKEYAPQKKVYIVP 145
                                       3333333...33466777777777766 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.3e-06
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleel 89 
                                        +k  i+++gr+ ++ g+  l+++++ +     p+  + i+G+g+  +++  +       +nv+ lg ++++++ +l
  gi|330508389|ref|YP_004384817.1| 164 PGKGPIIFIGRVCTQEGIGKLLELARAI-----PEREFWIVGGGPF-ARYYLW----RKPANVRNLGWQPHDKVAAL 230
                                       5666699*******************76.....677******6665.555555....677899************** PP

                                       HHCESEEEEEESS........BSS-HHHHHHHHTT--EEEETT CS
                   Glycos_transf_1  90 lknadifvlpsis........EgfGivllEAmaaglpviasna 124
                                       l +a++ ++p +         +     l E++a+g++v+as +
  gi|330508389|ref|YP_004384817.1| 231 LGKASLCLIPREEnaltpystDKSVWKLNEYLALGKIVVASGV 273
                                       **********9999999999999999*************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2422.68
//
Query:       gi|330508390|ref|YP_004384818.1|  [L=436]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete 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   27.8   0.6    2.7e-05   23.8   0.6    2.1  1  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
      0.088   13.3   4.0       0.13   12.8   1.7    2.4  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.15   12.2   0.6        7.5    6.8   0.1    2.4  2  Zn-ribbon_8      Zinc ribbon domain
       0.21   11.2   0.6         12    5.6   0.1    2.4  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.27   11.3   2.8        1.3    9.1   3.1    1.9  2  DZR              Double zinc ribbon
       0.66   10.0   2.5        7.3    6.7   0.3    2.6  2  YhfH             YhfH-like protein
        6.2    6.4   5.5         77    2.9   5.5    2.4  1  TF_Zn_Ribbon     TFIIB zinc-binding


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 !   23.8   0.6     1e-08   2.7e-05     111     259 ..     188     381 ..     146     393 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1e-08
                      DDE_Tnp_IS66 111 sRggevaealLag.....fkGvlvsDgyagYnklae....eqvthalCwaHlrRkfvdaeeakkksqaaaealar.. 176
                                       s  ++++e +L        + ++v+D y gY+++ +    ++v h++C+ Hl   +v+   +k   ++ +e l++  
  gi|330508390|ref|YP_004384818.1| 188 SKDADTIEGFLRRnldtqKQIFIVTDLYRGYSNVFKrvfgNKVIHQFCLLHLNKLIVNDFPRKT--SIEQELLKYkm 262
                                       55566666666655554445699**********9999***************999887776643..44444444442 PP

                      DDE_Tnp_IS66 177 igklya.............ierearea...........eae.........erlalrqeesrpllaelea.wleeql. 218
                                       ++ +++              e+ +r +           e           + + +r++es+ l+++ ++  l++ + 
  gi|330508390|ref|YP_004384818.1| 263 LNIFFNreleieflstlieEEKMMR-QrsnkeykswiaE-AkhlfydfvrRLELRRRRESKNLEQRTYHeALNNFKf 337
                                       4444445555555555543233332.1233344334331.0333333442555666777788877655504444448 PP

                      DDE_Tnp_IS66 219 ...kkvlpksklgkairyllkrweallrfledgrvpidNNaaER 259
                                          ++ +    ++k ++++ + w++l+ f    + p +NN +E+
  gi|330508390|ref|YP_004384818.1| 338 lkmQSDSFMISVRKRLDKIEELWPNLTAFYFTDNAPATNNPIEN 381
                                       777666677789*******************************9 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.7     5e-05      0.13       8      51 ..      44     118 ..      43     123 .. 0.62
   2 ?   -1.0   0.0      0.99   2.5e+03      14      29 ..     284     299 ..     282     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                   Zn_ribbon_recom   8 CgeCGspmtr......rkrkgkr.......hyYrCstyrrkgk..................k.Csnh...sireekl 49 
                                       C eCG+pm++      +    kr         Y C+++ ++ +                  + C+     ++++e++
  gi|330508390|ref|YP_004384818.1|  44 CPECGHPMSHngfntcQ----KRhlgganvGKYLCGACGKSTEedrdfwiklkadffgivtEiCTRLrlnHVSYEVI 116
                                       **********5543322....22355558889999988766655556666666666665531466544556666666 PP

                   Zn_ribbon_recom  50 ee 51 
                                       e+
  gi|330508390|ref|YP_004384818.1| 117 ES 118
                                       65 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.99
                   Zn_ribbon_recom  14 pmtrrkrkgkrhyYrC 29 
                                       +m r+++++++  ++ 
  gi|330508390|ref|YP_004384818.1| 284 KMMRQRSNKEYKSWIA 299
                                       7999999999988875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0029       7.5      26      35 ..      40      50 ..      25      53 .. 0.60
   2 ?    3.3   0.1     0.036        93       6      17 ..      72      83 ..      71      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                       Zn-ribbon_8 26 lta.CPeCgse 35
                                       ++ CPeCg++
  gi|330508390|ref|YP_004384818.1| 40 VPPlCPECGHP 50
                                      3444****986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.036
                       Zn-ribbon_8  6 YrCeeCghefev 17
                                      Y C +Cg+  e+
  gi|330508390|ref|YP_004384818.1| 72 YLCGACGKSTEE 83
                                      89*****99885 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0046        12       4      14 ..      43      53 ..      43      57 .. 0.86
   2 ?    3.5   0.1     0.021        54       2      15 ..      71      84 ..      70      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0046
                            zf_UBZ  4 lCerCgkeipe 14
                                      lC++Cg+++++
  gi|330508390|ref|YP_004384818.1| 43 LCPECGHPMSH 53
                                      6*******987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.021
                            zf_UBZ  2 tylCerCgkeipes 15
                                       ylC  Cgk+ +e+
  gi|330508390|ref|YP_004384818.1| 71 KYLCGACGKSTEED 84
                                      69*******97765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.9     0.002         5      30      46 ..      43      60 ..      26      63 .. 0.76
   2 ?    9.1   3.1    0.0005       1.3      15      43 ..      44      86 ..      41     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.002
                               DZR 30 rCpsCgek.vdpearfCp 46
                                       Cp+Cg++  ++++++C+
  gi|330508390|ref|YP_004384818.1| 43 LCPECGHPmSHNGFNTCQ 60
                                      688888886666777775 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0005
                               DZR 15 CseCgtklkavaa................edrCpsCgekvdpear 43
                                      C+eCg++++   +                ++ C +Cg++++++  
  gi|330508390|ref|YP_004384818.1| 44 CPECGHPMSH--NgfntcqkrhlgganvgKYLCGACGKSTEEDRD 86
                                      5566655552..123555555555556669999999998877665 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0028       7.3       7      24 ..      35      52 ..      31      61 .. 0.85
   2 ?    2.6   0.1     0.055   1.4e+02      15      26 ..      73      84 ..      67      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0028
                              YhfH  7 FfrnLPkKkCteCGkeie 24
                                      +fr++ +  C+eCG  + 
  gi|330508390|ref|YP_004384818.1| 35 IFRKIVPPLCPECGHPMS 52
                                      799999999*****9986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.055
                              YhfH 15 kCteCGkeieEq 26
                                       C  CGk  eE 
  gi|330508390|ref|YP_004384818.1| 73 LCGACGKSTEED 84
                                      6******99995 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   5.5      0.03        77       3      32 ..      44      84 ..      43      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.03
                                      ETTTTCEEC...........HEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon  3 CPnCgstnl...........veDpergelvCtdCGlVledn 32
                                      CP+Cg+++            +  ++ g ++C++CG   e++
  gi|330508390|ref|YP_004384818.1| 44 CPECGHPMShngfntcqkrhLGGANVGKYLCGACGKSTEED 84
                                      99999987458888888777777999999999999877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3019.68
//
Query:       gi|330508391|ref|YP_004384819.1|  [L=513]
Description: transposase, IS4 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-12   46.4   0.0    1.5e-10   41.1   0.0    2.4  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 !   41.1   0.0   8.5e-15   1.5e-10      25     214 .]     181     454 ..     156     454 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 8.5e-15
                         DDE_Tnp_1  25 wgyk.ggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYasaelldtleek 98 
                                       +gy+  g   + ++l ++vd   g+++ +++ pg+ +d+ +lk +++ ++++  ++ + ++D+G++s++++++l + 
  gi|330508391|ref|YP_004384819.1| 181 YGYNrDGLDLPQINLSLIVDMDLGIPVMYDLYPGSIADVSTLKNTVRKIKAQgvRNYTMIMDRGFFSTDNIEELVAA 257
                                       578867778999***************************************************************** PP

                         DDE_Tnp_1  99 gvdyiirl...kkntklyrk...............................gaeskrrgrlrkhdrnkiltksqkrr 141
                                        +++ii++    kn+k+  +                               +       +l +   +++ +++q+r 
  gi|330508391|ref|YP_004384819.1| 258 DLSFIIPPtstLKNVKEAVSaihssiddpehlklyekeplfvmpvsievgeN-------KLSGYAYYDQKREQQERS 327
                                       ********98877777777777776666666655555666666543333330.......333333333333333333 PP

                         DDE_Tnp_1 142 nk...................................................................skkekgdv 151
                                       ++                                                                           
  gi|330508391|ref|YP_004384819.1| 328 TFykrlydlmevlksknlkhwmnpgevfratakrdakyiewkaidgrfqvalrknavsqainkmgkfvlL------- 397
                                       3355555555555555669999999999999999999999999999999999999876655444433332....... PP

                         DDE_Tnp_1 152 yyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                              + ++s  e   lyr + ++E  F  lk++  l   ++r+    + +l++ ++al l
  gi|330508391|ref|YP_004384819.1| 398 ------YRGEFSWIECLSLYRSKDVVEKGFDVLKNDIELMPANLRTNSSLRGYLFIAFIALIL 454
                                       ......233445566668999999999999999999999999999999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3567.46
//
Query:       gi|330508392|ref|YP_004384820.1|  [L=601]
Description: glucosamine-6-phosphate synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-42  144.9   0.6    1.7e-21   76.4   0.2    2.3  2  SIS       SIS domain
    9.7e-21   74.4   0.0    1.7e-20   73.6   0.0    1.4  1  GATase_6  Glutamine amidotransferase domain
    8.5e-17   61.2   0.0    1.4e-16   60.5   0.0    1.4  1  GATase_7  Glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.015   15.3   0.9        1.9    8.5   0.0    3.3  3  SIS_2     SIS domain


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.2   3.8e-25   1.7e-21       6     130 ..     291     412 ..     286     413 .. 0.96
   2 !   66.7   0.0     4e-22   1.8e-18       8     127 ..     463     580 ..     456     582 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 3.8e-25
                                       SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSE CS
                               SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergak 82 
                                       +r+ ++++Gtsy++++ ++  + + +g +v+ve ase+ +     +++++l++ i++sget+d+++a+++ak  g++
  gi|330508392|ref|YP_004384820.1| 291 ERVTIIACGTSYHAGMLARNLFVRAAGLPVDVEVASEFLSL---QLRPRTLLVGITQSGETADTLLALKKAKTCGGR 364
                                       7999*********************************8887...89******************************* PP

                                       EEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                               SIS  83 iiaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                        +aIT+  gs++ +  d ++ ++ +pe++va+tk++t+q++a+ +la+
  gi|330508392|ref|YP_004384820.1| 365 SLAITNVVGSTVTELVDGTIFTRCGPEIGVAATKTFTSQMVAVILLAI 412
                                       ******************************************999987 PP

  == domain 2  score: 66.7 bits;  conditional E-value: 4e-22
                                       EEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEE CS
                               SIS   8 iyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakii 84 
                                        +++G+ + y+i +e+alk++ei++i++e+++ +elkhg+lali+e+++v+++++ g +   + +++++++rga++i
  gi|330508392|ref|YP_004384820.1| 463 YFFIGRDYLYPISLEGALKMKEIAYIPSEGYAGGELKHGPLALITEKTPVVALATCGKKI--QSNIKEVRARGAEVI 537
                                       59****************************************************999765..55799********** PP

                                       EEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHH CS
                               SIS  85 aITdskgsplareadlalyinaepetlvastksltaqlaalda 127
                                       a++ + +  +a+ a+ ++++++ + +  a + ++ +ql+a+++
  gi|330508392|ref|YP_004384820.1| 538 ALATEGDPDIAKVASKVIELPETRPIYSAVLCTVAVQLLAYYT 580
                                       **********************999988888888888888865 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.0   3.8e-24   1.7e-20      11     133 ..      65     189 ..      47     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 3.8e-24
                          GATase_6  11 edevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall..eelG 85 
                                       +++++++H+R+a++g + +  a+P   ++g++++vhNG i+ny +lre l +  g++f+s++D+evl++l+   + G
  gi|330508392|ref|YP_004384820.1|  65 GEGMGIGHTRWATHGRPSDINAHPH--TSGEIAIVHNGIIENYLDLRELLTE-MGYEFQSETDSEVLAHLIhfYYKG 138
                                       4469*************99989***..*************************.****************99784445 PP

                          GATase_6  86 ......eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafas 133
                                              ++le+++G +a+a++ ++   +++a  r   +pl+++   s + +as
  gi|330508392|ref|YP_004384820.1| 139 dlcaatLKALEKVEGSYAIAVMAASSPYIVCA--RYE-SPLVIGKGSSSVFVAS 189
                                       56666688889**********99999889888..443.8999998888888888 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.0   3.1e-20   1.4e-16      16     122 ..      89     195 ..      72     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 3.1e-20
                          GATase_7  16 mvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.......ewgeealerlnGmfAfaiwde 85 
                                            +g+++iv+nG i Ny +lre L++ g++f++++D+evl++l++        +   +ale+++G++A+a++ +
  gi|330508392|ref|YP_004384820.1|  89 H---TSGEIAIVHNGIIENYLDLRELLTEMGYEFQSETDSEVLAHLIHFyykgdlcAATLKALEKVEGSYAIAVMAA 162
                                       3...4699**************************************9889999999889999*************** PP

                          GATase_7  86 eekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       ++  +++aR    + PL +g+ + +++++aS + all
  gi|330508392|ref|YP_004384820.1| 163 SSPYIVCARY---ESPLVIGKGS-SSVFVASDVPALL 195
                                       *********9...7********7.7********9997 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.027   1.2e+02      37      60 ..     294     318 ..     289     322 .. 0.90
   2 ?    8.5   0.0   0.00043       1.9      90     137 ..     323     369 ..     318     370 .. 0.91
   3 ?    0.0   0.1      0.18     8e+02     123     137 ..     526     540 ..     522     541 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.027
                                       -EEEEESG.GGHHHHHHTSSSTT-B CS
                             SIS_2  37 kvlvfGsG.hSaalaeelaaraggl 60 
                                        ++++G++ h+ +la +l+ ra gl
  gi|330508392|ref|YP_004384820.1| 294 TIIACGTSyHAGMLARNLFVRAAGL 318
                                       5899**977*************998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00043
                                       THHHHHHHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                             SIS_2  90 gyakqilrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                        +a+++l+l +l+p+ +L+ i +sG+ a  + a+++ak++g +  A+t
  gi|330508392|ref|YP_004384820.1| 323 EVASEFLSL-QLRPRTLLVGITQSGETADTLLALKKAKTCGGRSLAIT 369
                                       577888888.9******************************9999988 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.18
                                       HHHHHHHT-EEEEEE CS
                             SIS_2 123 aeaakergmkviAlt 137
                                       ++++++rg++viAl 
  gi|330508392|ref|YP_004384820.1| 526 IKEVRARGAEVIALA 540
                                       7899*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3970.31
//
Query:       gi|330508393|ref|YP_004384821.1|  [L=402]
Description: nucleotidyl transferase [Methanosaeta concilii GP6]
Scores for complete 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-35  122.3   0.0    3.4e-35  121.8   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
      2e-17   62.1  12.7    2.2e-07   30.3   0.3    5.8  7  Hexapep          Bacterial transferase hexapeptide (six repea
    1.9e-14   54.3   0.0    2.8e-14   53.8   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
    1.3e-08   34.4  20.1    4.3e-06   26.4   0.3    5.6  5  Hexapep_2        Hexapeptide repeat of succinyl-transferase
     0.0006   18.9   2.3     0.0065   15.5   0.8    2.1  2  Fucokinase       L-fucokinase
  ------ inclusion threshold ------
      0.016   14.9   0.0      0.037   13.8   0.0    1.6  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
       0.14   10.2   0.4       0.21    9.7   0.4    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 !  121.8   0.0   1.3e-38   3.4e-35       1     231 [.       5     218 ..       5     231 .. 0.93

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 1.3e-38
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       k+vILa G+G R +PLt+t++k ++pv++  + +++++ +la++gie+ i+v+  +++++v +++++g +f+v +++
  gi|330508393|ref|YP_004384821.1|   5 KGVILAAGEGRRCRPLTQTRSKVMLPVGNR-PFMEYVIRALAANGIED-IYVVVGYQKERVMDYFEDGIDFDVAITY 79 
                                       79****************************.*****************.777777999******************* PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       + ++e  gtA+A+++a++++++e+     lv++gD li+   ++av++ ++++   + ++++  ++   +yGv  +d
  gi|330508393|ref|YP_004384821.1|  80 IEQNELLGTAHALLKAEQYVDEEF-----LVVNGDNLID---KRAVNELVSAKG--DNVILAALRRHTGDYGVLIVD 146
                                       ********************9887.....9*********...777777777777..56677777888899******9 PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       + g v++++EKP ++  s ++++G Y f+++v++ l k++  ++rg+ e+ +++ ++++eg++ + ++ k+   W D
  gi|330508393|ref|YP_004384821.1| 147 N-GLVTEIIEKPGRPC-SGILNTGSYKFTPDVFDAL-KQAPISERGSYELPETIMQMIKEGTQIVPLITKG--IWAD 218
                                       8.8***********99.******************9.8899999***************************..7*99 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.7   4.3e+03      23      30 ..     125     132 ..     125     132 .. 0.80
   2 !   12.2   0.1   4.4e-05      0.11      13      34 ..     247     268 ..     236     270 .. 0.84
   3 !   30.3   0.3   8.8e-11   2.2e-07       2      34 ..     254     286 ..     253     288 .. 0.95
   4 !   28.5   0.2   3.2e-10   8.1e-07       2      36 .]     272     306 ..     271     306 .. 0.95
   5 !   20.2   0.4   1.3e-07   0.00034       1      29 [.     289     322 ..     289     325 .. 0.91
   6 !    6.0   0.1     0.004        10       7      27 ..     323     343 ..     322     346 .. 0.59
   7 !    7.1   0.3    0.0018       4.6       2      36 .]     358     392 ..     357     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
                                       -TTEEEET CS
                           Hexapep  23 GdnvkIga 30 
                                       Gdnv+++a
  gi|330508393|ref|YP_004384821.1| 125 GDNVILAA 132
                                       89999876 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.4e-05
                                       TEEEETTEEE-TTEEEETTEEE CS
                           Hexapep  13 faviggnVkIGdnvkIgagvvi 34 
                                       +a+i g+V++G+++++ +g+++
  gi|330508393|ref|YP_004384821.1| 247 GAMIKGPVHLGEGSIVRSGSYL 268
                                       9******************987 PP

  == domain 3  score: 30.3 bits;  conditional E-value: 8.8e-11
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       +++G+++++++++++ g+V IG+++ Ig+++vi
  gi|330508393|ref|YP_004384821.1| 254 VHLGEGSIVRSGSYLVGPVSIGEDCDIGPNAVI 286
                                       789*****************************9 PP

  == domain 4  score: 28.5 bits;  conditional E-value: 3.2e-10
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       + IG+++ Igp+avi++ + +Gd ++Ig+++ +++
  gi|330508393|ref|YP_004384821.1| 272 VSIGEDCDIGPNAVILPSTSVGDSARIGPHSEVRN 306
                                       78*****************************9985 PP

  == domain 5  score: 20.2 bits;  conditional E-value: 1.3e-07
                                       TEEEETTEEE-T.....TEEEETTEEE-TTEEEE CS
                           Hexapep   1 stvIGsnvlIgp.....faviggnVkIGdnvkIg 29 
                                       st +G+ + Igp     ++++++++ IG++++I 
  gi|330508393|ref|YP_004384821.1| 289 STSVGDSARIGPhsevrNSILMNDARIGSGCIIS 322
                                       68899999999999999***************96 PP

  == domain 6  score: 6.0 bits;  conditional E-value: 0.004
                                       TEEE-TTEEEETTEEE-TTEE CS
                           Hexapep   7 nvlIgpfaviggnVkIGdnvk 27 
                                       +++Ig+ +++++ V++  +++
  gi|330508393|ref|YP_004384821.1| 323 DSVIGASCTLRDQVVVETGSC 343
                                       556666666666666666555 PP

  == domain 7  score: 7.1 bits;  conditional E-value: 0.0018
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       +++ ++v +g+ +   +++++G  + I +g+ i+g
  gi|330508393|ref|YP_004384821.1| 358 AILADDVSVGARVLASPGTVVGTKASISSGAAIRG 392
                                       56678999999999999999999999999998876 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 !   53.8   0.0   1.1e-17   2.8e-14       1     123 [.       6     136 ..       6     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.1e-17
                                       EEEEEESS-TTTT...T..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC.TS-EEE-TTSS CS
                      NTP_transf_3   1 aviLAGGrSsRmg...g..dKallplggkpllervldalraagvdevvvvggd..eevlaalarl.gvrvvededpg 69 
                                       +viLA+G+++R     +   K +lp+g++p++e+v++al+a g+++++vv+g+  e v +++++  + +v+    ++
  gi|330508393|ref|YP_004384821.1|   6 GVILAAGEGRRCRpltQtrSKVMLPVGNRPFMEYVIRALAANGIEDIYVVVGYqkERVMDYFEDGiDFDVAITYIEQ 82 
                                       79**********6554245********************************99655677777644434444444445 PP

                                       -SHHHHHHHHHHHH..SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEES CS
                      NTP_transf_3  70 kgplaslaaalraaa.dadavlvlacDmPlltpelverllaaaaasgadvvvpty 123
                                          l++ +a l+a +  ++ +lv+ +D  l+++ +v++l+ a  ++   ++  ++
  gi|330508393|ref|YP_004384821.1|  83 NELLGTAHALLKAEQyVDEEFLVVNGDN-LIDKRAVNELVSAKGDNVILAALRRH 136
                                       66666666666654446899********.89**********96433333333333 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   0.1       0.4     1e+03      21      28 ..     125     132 ..     125     132 .. 0.89
   2 !    7.5   0.0    0.0014       3.5      15      32 ..     249     268 ..     247     269 .. 0.84
   3 !   26.4   0.3   1.7e-09   4.3e-06       1      27 [.     271     299 ..     271     300 .. 0.95
   4 ?    4.5   3.3     0.011        28       3      31 ..     314     343 ..     311     346 .. 0.76
   5 ?    4.2   0.1     0.014        35       6      32 ..     362     390 ..     359     391 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.4
                                       -TT-EE-T CS
                         Hexapep_2  21 Gdncvvga 28 
                                       Gdn++++a
  gi|330508393|ref|YP_004384821.1| 125 GDNVILAA 132
                                       99999997 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0014
                                       EE..SEEE-TT-EE-TT-EE CS
                         Hexapep_2  15 gi..GvslGdncvvgaGvvi 32 
                                        i  +v+lG++++v +G+++
  gi|330508393|ref|YP_004384821.1| 249 MIkgPVHLGEGSIVRSGSYL 268
                                       56745*************97 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 1.7e-09
                                       .EEE-TT-EE-TT-EE..SEEE-TT-EE- CS
                         Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvg 27 
                                       pv+IG++C iG+na+i   +s+Gd + +g
  gi|330508393|ref|YP_004384821.1| 271 PVSIGEDCDIGPNAVIlpSTSVGDSARIG 299
                                       8***************999*****99998 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.011
                                       EE-TT-EE-TT-EES..EEE-TT-EE-TT-E CS
                         Hexapep_2   3 iIGdnCliGanagiG..vslGdncvvgaGvv 31 
                                       +IG  C+i ++++iG   +l+d +vv+ G+ 
  gi|330508393|ref|YP_004384821.1| 314 RIGSGCII-SDSVIGasCTLRDQVVVETGSC 343
                                       57777777.6677766699********9985 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.014
                                       TT-EE-TT-EE..SEEE-TT-EE-TT-EE CS
                         Hexapep_2   6 dnCliGanagi..GvslGdncvvgaGvvi 32 
                                       d++ +Ga+     G+ +G ++ +++G  i
  gi|330508393|ref|YP_004384821.1| 362 DDVSVGARVLAspGTVVGTKASISSGAAI 390
                                       7888999999778***********99876 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.022        57     280     308 ..     249     278 ..     246     283 .. 0.85
   2 !   15.5   0.8   2.5e-06    0.0065     273     332 ..     283     340 ..     279     349 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.022
                        Fucokinase 280 vlessvsvgegsvieh.sslkgnvsigsns 308
                                       ++++ v++gegs++ + s l g+vsig+ +
  gi|330508393|ref|YP_004384821.1| 249 MIKGPVHLGEGSIVRSgSYLVGPVSIGEDC 278
                                       789999********9626677*******99 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.5e-06
                        Fucokinase 273 savvinS.vlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtilqt 332
                                       +av++ S  +  s+++g++s + +s l ++ +igs++i+s+  + +s   ++l+d++++ t
  gi|330508393|ref|YP_004384821.1| 283 NAVILPStSVGDSARIGPHSEVRNSILMNDARIGSGCIISDSVIGAS---CTLRDQVVVET 340
                                       55565441567899******************************987...46888888765 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.4e-05     0.037       4      60 ..       7      64 ..       4     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                                      EEECTTSSCT...T-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHH CS
                              IspD  4 vipAAGsGkR...mkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefe 60
                                      vi AAG+G+R   + + + K  l + +++ +e  ++al+a + ++ i vvv  ++ e+++
  gi|330508393|ref|YP_004384821.1|  7 VILAAGEGRRcrpLTQTRSKVMLPVGNRPFMEYVIRALAA-NGIEDIYVVVGYQK-ERVM 64
                                      899*******44446899********************99.78999999987666.4444 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4   8.3e-05      0.21     208     260 ..     290     338 ..     244     362 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 8.3e-05
                           DUF4954 208 gtinSskeapveiGegViledfiissGskikdgavisrcfvGqavklkkqfsa 260
                                       +++     +  +iG   +++++i+++ ++i  g +is++++G +++l  q  +
  gi|330508393|ref|YP_004384821.1| 290 TSV----GDSARIGPHSEVRNSILMNDARIGSGCIISDSVIGASCTLRDQVVV 338
                                       333....3456899999999999999999999999999999999999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); 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:                         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: 00:00:00.40
# Mc/sec: 2996.12
//
Query:       gi|330508394|ref|YP_004384822.1|  [L=374]
Description: glycosyl transferase, group 1 family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-14   54.4   0.0    2.7e-14   53.7   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.6e-12   47.8   0.1    2.6e-12   47.1   0.1    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    2.1e-10   40.4   0.0    4.4e-10   39.4   0.0    1.5  2  Glycos_transf_1  Glycosyl transferases group 1
    4.6e-08   33.7   0.0    7.5e-08   33.0   0.0    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    8.2e-08   32.5   0.0    1.7e-07   31.5   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.016   15.2   0.1      0.024   14.7   0.1    1.3  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0   9.1e-18   2.7e-14       3     133 ..     203     341 ..     201     342 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 9.1e-18
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---.....HHHHHHHT..T-T.TEEEE---..THHHHHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rp..eeleelaa..gleerveftGfv..edlaellaa 72 
                                       v+++vG+l e++  ++ ++ea+p+l    ++l++vG g   +  + ++++a+  g++erv+ tG v  ++l+++++a
  gi|330508394|ref|YP_004384822.1| 203 VLGYVGSL-EHWVDLETVIEALPRLD---ATLLVVGPGLfTDygDGIKRMAEdlGVAERVVCTGAVpyNELSRYISA 275
                                       799*****.56699************...68*****87554456778877766899**********9999******* PP

                                       -SEEEE--......-.--SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  73 advfvaPs......e.gfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeailrLle 133
                                       +d+ ++P+      e   g k+  ++a+g+pv ++++  +++++g++ + ++  d+e++++++  +l+
  gi|330508394|ref|YP_004384822.1| 276 MDIGLNPLkmmkknEyAAGGKVFNYLACGRPVLSSRMISLEKLLGDEIYYFD--DVESFIAQVNSILS 341
                                       ********9887654789******************9898888899999998..9*******999885 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.1   8.6e-16   2.6e-12      16     169 ..      28     183 ..      24     184 .. 0.69

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 8.6e-16
                    Glyco_transf_4  16 arrGheVtvvtpgddgpleeev...elvvrvprvpl...pllkrllrslaflrrlrrllkrekpDvvHahspaalga 86 
                                       a+  heV+v+ +g ++ +  ++   ++     ++     p+l+  l+ + +++++rr++k+ k+Dv+ + +  + +a
  gi|330508394|ref|YP_004384822.1|  28 AEE-HEVYVLHFGLKRFSNLREretKCQLLKASWIEtqdPSLYYILNFPYHIWKIRRIVKEKKIDVILSTNILPSFA 103
                                       444.999999888777766666666444444444441113444455667789***************7776666655 PP

                    Glyco_transf_4  87 allalrrrlgiplVltvHglye.....krllkarlkplsrllralerrl.lrradrviavSeatadelrerygvppe 157
                                       a       ++ p+V+ + ++ e     +++  a     ++++  + + + lr+a+ vi+v+++++++l+   gv+  
  gi|330508394|ref|YP_004384822.1| 104 A----NF-SRTPIVFDYLDHLEesasiYYPGSALGEIVKYVVSFITK-FnLRHARSVITVTKELKEYLLG-VGVKD- 172
                                       5....33.789999887666666677433333334444444444444.36********************.**986. PP

                    Glyco_transf_4 158 kitVipnGvDle 169
                                        ++VipnGvD+ 
  gi|330508394|ref|YP_004384822.1| 173 -VAVIPNGVDTR 183
                                       .*********95 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 ?   -4.0   0.0       3.1   9.3e+03      21      34 ..      81      94 ..      78      95 .. 0.78
   2 !   39.4   0.0   1.5e-13   4.4e-10      13     167 ..     199     351 ..     191     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.1
                                      ESS-TTTTTHHHHH CS
                   Glycos_transf_1 21 vgrlekeKgvdlli 34
                                      + r++keK +d+++
  gi|330508394|ref|YP_004384822.1| 81 IRRIVKEKKIDVIL 94
                                      67999999998876 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 1.5e-13
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....STTHHHHHHHHHHHCTTCGGGEEECCHSSSH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...ngeeekelkklaeelelsdnviflgevsredl 86 
                                        +  ++ +vg le++ +++++i+a+++l      ++ l+++G     ++ + +k++ae l++ ++v  +g v++++l
  gi|330508394|ref|YP_004384822.1| 199 LGGTVLGYVGSLEHWVDLETVIEALPRL------DATLLVVGpglFTDYGDGIKRMAEDLGVAERVVCTGAVPYNEL 269
                                       5677999*******************87......789*****999889999************************** PP

                                       HHHHHCESEEEEEESS.....BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHS CS
                   Glycos_transf_1  87 eellknadifvlpsis.....EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklled 158
                                         ++++ di + p  +      + G  + +++a+g pv++s +  + +++ d+   + ++ +  e+++++++++l+ 
  gi|330508394|ref|YP_004384822.1| 270 SRYISAMDIGLNPLKMmkkneYAAGGKVFNYLACGRPVLSSRMISLEKLLGDEI--YYFDDV--ESFIAQVNSILSV 342
                                       *************9999***779999***************************9..888877..************9 PP

                                       HHHHHHHHH CS
                   Glycos_transf_1 159 eelrerlge 167
                                       e++ +r++ 
  gi|330508394|ref|YP_004384822.1| 343 EPTTKRFRS 351
                                       999999876 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 !   33.0   0.0   2.5e-11   7.5e-08      35     160 .]      48     179 ..      23     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.5e-11
                   Glyco_trans_4_4  35 leedgvrvhrlpvprrpsplad.....laalralrrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtlhgl 106
                                       ++e ++++    +  +++p        + +++  rr++  ++ ++dv+ + +++ ++aa + r    +p+v+++ ++
  gi|330508394|ref|YP_004384822.1|  48 ERETKCQLLKASWIETQDPSLYyilnfPYHIWKIRRIV--KEKKIDVILSTNILPSFAANFSR----TPIVFDYLDH 118
                                       5566666655544444432222222236689*******..*************7777665555....9*******98 PP

                   Glyco_trans_4_4 107 l......lrrgsgavrrly....ralerrllrradavlvvseaeaeelralgvpadrvvvvpng 160
                                       l      + ++++a++ ++      + ++ lr+a+ v++v+ ++ e+l   gv   +v+v+png
  gi|330508394|ref|YP_004384822.1| 119 LeesasiY-YPGSALGEIVkyvvSFITKFNLRHARSVITVTKELKEYLLGVGVK--DVAVIPNG 179
                                       84444432.3355655555333377799*************************9..8******8 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   5.7e-11   1.7e-07       2      63 ..     279     344 ..     278     365 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 5.7e-11
                   Glyco_trans_1_2   2 vLnpsrs.....espnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekirylla.np 63 
                                       +Lnp        +   +++f ++acG+++l+++  +le+l+  g+e+ +f+d+e+++++++  l+ +p
  gi|330508394|ref|YP_004384822.1| 279 GLNPLKMmkkneYAAGGKVFNYLACGRPVLSSRMISLEKLL--GDEIYYFDDVESFIAQVNSILSvEP 344
                                       66755554444344668***********************9..889****************998544 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1     8e-06     0.024      21     137 ..      28     156 ..       2     158 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8e-06
                   Glyco_trans_4_2  21 akrgyeVhvitpkkgakdeleaegihvhrlkvd...rkg.pleyl....k.afklkklikkikPDvvhahyakpygl 88 
                                       a+  +eV+v+  + ++  +l++   +++ lk +   +++ +l y+      + k+++++k+ k+Dv+   +     +
  gi|330508394|ref|YP_004384822.1|  28 AE-EHEVYVLHFGLKRFSNLRERETKCQLLKASwieTQDpSLYYIlnfpYhIWKIRRIVKEKKIDVILSTN-----I 98 
                                       44.677777666555534444444444444333322222333333222332569*************6665.....5 PP

                   Glyco_trans_4_2  89 lgslaarlsgvipvvlsvwGldvlkfpkksk........lkkl....llklalkkatkvis 137
                                       l s+aa +s+  p+v++    d l++   +         + k+    + k++l++a+ vi+
  gi|330508394|ref|YP_004384822.1|  99 LPSFAANFSR-TPIVFDYL--DHLEESASIYypgsalgeIVKYvvsfITKFNLRHARSVIT 156
                                       55788999*9.****7766..5555544443333333353333577799999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2826.31
//
Query:       gi|330508395|ref|YP_004384823.1|  [L=322]
Description: glycosyl transferase, group 1 family protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   86.7   0.0    1.9e-24   86.2   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    4.8e-22   78.8   0.0    8.4e-22   78.0   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.4e-06   28.4   0.0    2.2e-06   27.8   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    0.00029   21.2   0.1    0.00055   20.3   0.1    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 !   86.2   0.0   4.1e-28   1.9e-24      21     160 ..     163     294 ..     141     305 .. 0.86

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 4.1e-28
                                       ESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEE CS
                   Glycos_transf_1  21 vgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadifv 97 
                                       +gr+ k Kg+d +i a+all     p+++++i+G  +++++ + ++ + e+   v ++g+vsre+l ++++ a +++
  gi|330508395|ref|YP_004384823.1| 163 SGRIIKLKGLDAFIGAAALL-----PEIRFLIVG-LSDQDRGELQSRSTEN---VSLFGYVSREELLAFYQEARVYC 230
                                       59****************87.....89*******.6666777766666665...*********************** PP

                                       EEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH...H CS
                   Glycos_transf_1  98 lpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede...e 160
                                       + s++E+fG++l EAma+g+  +++  g ++evv d+   + v+ ++a+a aeai+k+l ++    
  gi|330508395|ref|YP_004384823.1| 231 QLSYRESFGMALAEAMACGCVPVVTERGAIPEVVGDAG--YYVPYGSAKATAEAIEKALCSKkgiG 294
                                       **********************************9987..******************97775554 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0   1.9e-25   8.4e-22       8     132 ..     164     287 ..     157     289 .. 0.91

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 1.9e-25
                                       S---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE--. CS
                   Glyco_trans_1_4   8 GrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaadvfvaPs. 80 
                                       Gr+  + kg+d ++ a++ll   ++r++ivG ++ ++ el+++     e+v++ G+v  e+l +++++a+v++  s 
  gi|330508395|ref|YP_004384823.1| 164 GRI-IKLKGLDAFIGAAALLP--EIRFLIVGLSDqDRGELQSRST---ENVSLFGYVsrEELLAFYQEARVYCQLSy 234
                                       666.467**************..68******77665579987664...8********9889**************** PP

                                       .---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  81 .egfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeailrLl 132
                                        e+fg++l Eama+g+  V+t+ g+i+evvg++g+ vp g+++a aeai++ l
  gi|330508395|ref|YP_004384823.1| 235 rESFGMALAEAMACGCVPVVTERGAIPEVVGDAGYYVPYGSAKATAEAIEKAL 287
                                       99*********************99***99*******************9876 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0     5e-10   2.2e-06      84     170 .]      59     145 ..      28     145 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 5e-10
                    Glyco_transf_4  84 lgaallalrr...rlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppe 157
                                       + +a++ l +   ++ + +V  +   +e     + +  l rl r +  ++l +ad v+ vSe+t+ e+++  + +p+
  gi|330508395|ref|YP_004384823.1|  59 HSFAAVLLSKllrKRSAVVVGGYDVAFE-PDISYGQYTLGRLKRVYSDFVLGNADIVLPVSEFTKSEVLA--RAKPK 132
                                       3333333333344556666666666664.333445556667778888899********************..5669* PP

                    Glyco_transf_4 158 kitVipnGvDler 170
                                       ++ V+++G+Dl+r
  gi|330508395|ref|YP_004384823.1| 133 RVQVLYPGIDLDR 145
                                       ***********98 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.2e-07   0.00055       5      88 ..     232     310 ..     209     314 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.2e-07
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaeh 81 
                                       +s +es+ + l Ea+acG++ +++++ +++e + +    + + + +  ae+i+++l     +++ ++  r+rv++++
  gi|330508395|ref|YP_004384823.1| 232 LSYRESFGMALAEAMACGCVPVVTERGAIPEVVGDAGYYVPYGSAKATAEAIEKAL-----CSKKGIGSRKRVEERF 303
                                       455699*************8888889******98888889999**********985.....7777777899999999 PP

                   Glyco_trans_1_2  82 tydhrae 88 
                                       ++++r e
  gi|330508395|ref|YP_004384823.1| 304 SLRRREE 310
                                       9999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2240.08
//
Query:       gi|330508396|ref|YP_004384824.1|  [L=328]
Description: glycosyl transferase, group 1 family protein [Methanosaeta concilii GP6]
Scores for complete 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   78.0   0.0    2.4e-21   76.5   0.0    1.7  2  Glyco_trans_1_4  Glycosyl transferases group 1
    5.1e-20   71.7   0.0    8.3e-20   71.0   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
     0.0015   18.8   0.0     0.0083   16.5   0.0    2.0  2  Glyco_trans_1_2  Glycosyl transferases group 1
     0.0025   17.8   0.0      0.015   15.3   0.0    2.2  2  Glyco_transf_4   Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       0.9     4e+03      65      92 ..      18      47 ..       8      85 .. 0.58
   2 !   76.5   0.0   5.4e-25   2.4e-21      13     134 .]     172     293 ..     160     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.9
                                      HHHHHHHH-SEEEE--..---SHHHHHHHH CS
                   Glyco_trans_1_4 65 dlaellaaadvfvaPs..egfglkllEama 92
                                      dl+ l ++ dv v+ +   g  +kl  am 
  gi|330508396|ref|YP_004384824.1| 18 DLDMLSRHYDVEVVSLssLGDAVKLAGAMI 47
                                      566666666666666632244555555553 PP

  == domain 2  score: 76.5 bits;  conditional E-value: 5.4e-25
                                       G.GTHHHHHHHHHHHH.HHEEEEEES.---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE--..--- CS
                   Glyco_trans_1_4  13 nvkgvdllleavpllrkkdvrlvivG.dgp.rpeeleelaagleerveftGfv..edlaellaaadvfvaPs..egf 83 
                                        +kg+d++++ ++ l ++   + +vG  g+  + +l+e a    ++veftGfv  +dl e +++a+vf+  s  eg+
  gi|330508396|ref|YP_004384824.1| 172 VIKGLDVFVQSAKYLPEA--GFKVVGiTGDaLS-RLKEIAP---DNVEFTGFVthDDLIESYQRARVFCQLSmrEGL 242
                                       579*************55..7888883343343.6764443...88********889***************999** PP

                                       SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  84 glkllEamaaglpvVatdvggiaevvgengllvppgdpealaeailrLled 134
                                       +++l Eam +++  V td  gi++++g++g++vp gdp a aeai + l+d
  gi|330508396|ref|YP_004384824.1| 243 PNALCEAMLCECIPVGTDRNGIPRAIGDTGFIVPYGDPRAAAEAIKKALAD 293
                                       ***********************************************9987 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 !   71.0   0.0   1.8e-23   8.3e-20      28     163 ..     174     303 ..     146     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 1.8e-23
                                       TTHHHHHHHHHCCCCCHCSCEEEEEES..STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEEEEESSB CS
                   Glycos_transf_1  28 KgvdllikafallkkqlnpnvklviaG.ngeeekelkklaeelelsdnviflgevsredleellknadifvlpsisE 103
                                       Kg+d+++++++ l     p++ + ++G  g+ + +lk+        dnv+f+g+v ++dl+e +++a +f++ s++E
  gi|330508396|ref|YP_004384824.1| 174 KGLDVFVQSAKYL-----PEAGFKVVGiTGDALSRLKEI-----APDNVEFTGFVTHDDLIESYQRARVFCQLSMRE 240
                                       8889999999977.....667888888777888888888.....68******************************* PP

                                       SS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH.....HHHH CS
                   Glycos_transf_1 104 gfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede.....elre 163
                                       g++ +l EAm + ++ + ++  g++  + d  tG++v+ +++ a+aeai+k+l d+     + re
  gi|330508396|ref|YP_004384824.1| 241 GLPNALCEAMLCECIPVGTDRNGIPRAIGD--TGFIVPYGDPRAAAEAIKKALADRsnrgkKARE 303
                                       ********************9999999976..77*********************8444433333 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 ?   -0.6   0.0      0.41   1.8e+03      20      58 ..     190     229 ..     184     232 .. 0.84
   2 !   16.5   0.0   1.9e-06    0.0083      11      76 ..     242     304 ..     232     314 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.41
                   Glyco_trans_1_2  20 acGafaltdda.egleelftpgkevilfedleelaekiry 58 
                                       ++ ++ +t da + l e+  ++ e+  f ++++l+e  ++
  gi|330508396|ref|YP_004384824.1| 190 GFKVVGITGDAlSRLKEIAPDNVEFTGFVTHDDLIESYQR 229
                                       6677788888899999999999999999999999987665 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.9e-06
                   Glyco_trans_1_2  11 pnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarer 76 
                                       +   l Ea+ c ++ + +d+ g+++ + +   ++ + d+  +ae+i+++la++  r + a   rer
  gi|330508396|ref|YP_004384824.1| 242 LPNALCEAMLCECIPVGTDRNGIPRAIGDTGFIVPYGDPRAAAEAIKKALADRSNRGKKA---RER 304
                                       555678*******************996665666666*************9877766554...444 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.3e-06     0.015     118     166 ..      96     144 ..      33     148 .. 0.82
   2 ?   -0.7   0.0      0.27   1.2e+03      11      36 ..     182     207 ..     178     236 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.3e-06
                    Glyco_transf_4 118 plsrllralerrllrradrviavSeatadelrerygvppekitVipnGv 166
                                        + rl   l + +l+ adrv++v ++++d+ +++ g++  +i  +p G 
  gi|330508396|ref|YP_004384824.1|  96 AQGRLKSILTKIALKYADRVLVVDPSLKDDAIKNAGINGHNIDYLPSGF 144
                                       4556777788888*********************************996 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.27
                    Glyco_transf_4  11 LaraLarrGheVtvvtpgddgpleee 36 
                                        a++L+++G++V+ +t +   +l e 
  gi|330508396|ref|YP_004384824.1| 182 SAKYLPEAGFKVVGITGDALSRLKEI 207
                                       58999*****9999987665555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2405.25
//
Query:       gi|330508397|ref|YP_004384825.1|  [L=346]
Description: family 2 glycosyl transferase [Methanosaeta concilii GP6]
Scores for complete 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   0.0      4e-28   98.3   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    3.3e-12   46.4   0.0    5.2e-12   45.8   0.0    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    1.7e-11   44.5   0.0    7.5e-10   39.1   0.0    2.1  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00014   21.7   0.5    0.00041   20.2   0.5    1.8  1  TPR_2            Tetratricopeptide repeat
     0.0007   20.1   0.1     0.0014   19.1   0.1    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
     0.0088   16.6   0.4      0.059   14.0   0.1    2.4  2  TPR_6            Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.017   15.6   0.1      0.036   14.6   0.1    1.5  1  TPR_19           Tetratricopeptide repeat
       0.02   15.5   0.1       0.04   14.6   0.1    1.5  1  TPR_16           Tetratricopeptide repeat
      0.021   14.8   0.1      0.065   13.3   0.1    1.8  1  TPR_7            Tetratricopeptide repeat
      0.029   14.2   0.5      0.085   12.7   0.2    1.9  2  TPR_1            Tetratricopeptide repeat
        0.1   12.3   0.0       0.25   11.1   0.0    1.7  1  TPR_11           TPR repeat
       0.13   13.1   0.1       0.37   11.7   0.1    1.8  1  TPR_14           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.0   2.7e-31     4e-28       1     116 [.      24     138 ..      24     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 2.7e-31
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-..HHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenv..Gkagalnagl 75 
                                       s+++ptyN e+ + e+les+laq  y ++e iv+DDgStD+t++i+ ++   d+r+++ir++++    ++ ++n +l
  gi|330508397|ref|YP_004384825.1|  24 SIITPTYNHENFISECLESVLAQ-SYANWEQIVIDDGSTDRTAKIVSKFK--DDRIKYIRQDNKGilRLGESYNLAL 97 
                                       8**********************.*************************5..8*********8877789******** PP

                                       HH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEE CS
                   Glycos_transf_2  76 raatgdyilflDaDdepdpdwleklvealekdgadvvlgqr 116
                                       + ++g+yi++l  Dd ++ d+le  ++a+   +a + +g  
  gi|330508397|ref|YP_004384825.1|  98 QISKGEYIAVLEGDDFWPSDKLEIQIDAMRGSDAVLSWGRA 138
                                       *****************************997776665554 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   3.5e-15   5.2e-12       1     111 [.      24     126 ..      24     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 3.5e-15
                   Glyco_tranf_2_2   1 svviplraseerhyieerv..lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddk.ayslaaarN 74 
                                       s++ p +++e+   i e +   + ++y   + e iv+ddgS++ +++ vs+++d + +     +d+k    l+ + N
  gi|330508397|ref|YP_004384825.1|  24 SIITPTYNHENF--ISECLesVLAQSY--ANWEQIVIDDGSTDRTAKIVSKFKDDRIKYI--RQDNKgILRLGESYN 94 
                                       688899999865..***9954444455..8************************997754..4445659******** PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfissDkfekilklitikkl 111
                                       +  + ++++++  l++D+f+ sDk+e ++      ++
  gi|330508397|ref|YP_004384825.1|  95 LALQISKGEYIAVLEGDDFWPSDKLEIQID-----AM 126
                                       **************************8876.....44 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 !   39.1   0.0     5e-13   7.5e-10       4     112 ..      23     126 ..      20     212 .. 0.72
   2 ?    3.5   0.0     0.037        55     180     223 ..     260     309 ..     228     311 .. 0.72

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 5e-13
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       ++++ pt+n e  + e+les+laq+y + e +v++d+s++ t++ +     +++d r++++++++  g+    +++n
  gi|330508397|ref|YP_004384825.1|  23 VSIITPTYNHENFISECLESVLAQSYANWEQIVIDDGSTDRTAKIVS----KFKDDRIKYIRQDN-KGILRLGESYN 94 
                                       899*****************************************887....59999***998866.6776777889* PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqff 112
                                        al++ k+++++++++D+ +  d l+ +  ++
  gi|330508397|ref|YP_004384825.1|  95 LALQISKGEYIAVLEGDDFWPSDKLEIQIDAM 126
                                       ********************999988877776 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.037
                   Glyco_tranf_2_3 180 p.lflltdDyelglrlrragfrtayvpgaa.....vrevfpsslkayikq 223
                                         ++l  +D++++ r+ r    ++y+ g+a      ++  ++sl ++ik+
  gi|330508397|ref|YP_004384825.1| 260 VkASLAHEDNDIAARMDRKTREIDYYLGRAylregKWSDARESLLKAIKE 309
                                       3456777******************9999954444333355667777776 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.5   2.7e-07   0.00041       5      31 ..     284     310 ..     284     312 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.7e-07
                             TPR_2   5 ynlGlayyklgdyeeAleafekAleld 31 
                                       y+lG+ay++ g++ +A+e + kA++ d
  gi|330508397|ref|YP_004384825.1| 284 YYLGRAYLREGKWSDARESLLKAIKED 310
                                       89**********************987 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   9.1e-07    0.0014       2      87 ..      31     117 ..      30     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.1e-07
                   Glyco_tranf_2_4   2 neadiLpeflahhlalgfd..rilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvl 76 
                                       n ++++ e+l+  la  +   + +v+d++stD+t++i+++ ++ ++ +++++ ++  r  e ++ +l +++++++++
  gi|330508397|ref|YP_004384825.1|  31 NHENFISECLESVLAQSYAnwEQIVIDDGSTDRTAKIVSKFKDDRIKYIRQDNKGILRLGESYNLAL-QISKGEYIA 106
                                       88899999999888887752369******************99999999998887666677777555.67899**** PP

                   Glyco_tranf_2_4  77 vvDaDEflvvp 87 
                                       v+  D f  ++
  gi|330508397|ref|YP_004384825.1| 107 VLEGDDFWPSD 117
                                       ***99996555 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.2   4.8e+03       4      12 ..      87      95 ..      85     103 .. 0.77
   2 !   14.0   0.1     4e-05     0.059       4      29 ..     284     309 ..     282     310 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.2
                                      HHHHHHHHH CS
                             TPR_6  4 yklalsyrk 12
                                      ++l++sy  
  gi|330508397|ref|YP_004384825.1| 87 LRLGESYNL 95
                                      899999975 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlike 29 
                                       y+l+++y++ g++++A+e l + ike
  gi|330508397|ref|YP_004384825.1| 284 YYLGRAYLREGKWSDARESLLKAIKE 309
                                       9********99*******99999986 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.4e-05     0.036      21      59 ..     276     313 ..     265     321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-05
                            TPR_19  21 dpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                       d k  e+ ++L +a+l  g + +A++ L ++ +ed   +
  gi|330508397|ref|YP_004384825.1| 276 DRKTREIDYYLGRAYLREGKWSDARESLLKAIKEDNL-P 313
                                       77778999**********************9999977.5 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.7e-05      0.04      22      63 ..     271     309 ..     263     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                            TPR_16  22 aalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       +a ++d     ++e  ++lg+a+lr g + +A++ +++a+++
  gi|330508397|ref|YP_004384825.1| 271 IAARMD---RKTREIDYYLGRAYLREGKWSDARESLLKAIKE 309
                                       577777...7788899*****************766666643 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.3e-05     0.065       4      31 ..     285     310 ..     284     314 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-05
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkd 31 
                                       +L+r+y r+G++++A e + +  a+ +d
  gi|330508397|ref|YP_004384825.1| 285 YLGRAYLREGKWSDARESLLK--AIKED 310
                                       8*****************999..88877 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.7   8.6e+03      23      30 ..      92      99 ..      91     100 .. 0.71
   2 ?   12.7   0.2   5.7e-05     0.085       5      30 ..     284     309 ..     284     310 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.7
                                      HHHHHHHH CS
                             TPR_1 23 yyekALel 30
                                       y+ AL++
  gi|330508397|ref|YP_004384825.1| 92 SYNLALQI 99
                                      68888876 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.7e-05
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   5 ynlGnayfklgkydeAleyyekALel 30 
                                       y lG ay++ gk+ +A e   kA++ 
  gi|330508397|ref|YP_004384825.1| 284 YYLGRAYLREGKWSDARESLLKAIKE 309
                                       89**********************85 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00017      0.25       1      22 [.     287     308 ..     287     311 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlk 22 
                                       G+ay   Gk+ +A e++ kA+k
  gi|330508397|ref|YP_004384825.1| 287 GRAYLREGKWSDARESLLKAIK 308
                                       99*******************8 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00025      0.37       5      31 ..     284     310 ..     280     319 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                            TPR_14   5 lalaeallalGdpdeAiallrralala 31 
                                       + l++a+l+ G++ +A++ l +a++ +
  gi|330508397|ref|YP_004384825.1| 284 YYLGRAYLREGKWSDARESLLKAIKED 310
                                       789********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2529.10
//
Query:       gi|330508398|ref|YP_004384826.1|  [L=486]
Description: lipopolysaccharide O-side chain biosynthesis protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-33  115.4  40.5    2.9e-33  115.4  40.5    2.8  3  Polysacc_synt    Polysaccharide biosynthesis protein
    1.5e-17   64.0  19.3    1.5e-17   64.0  19.3    4.4  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    2.4e-15   56.5  24.2    6.7e-15   55.1  24.2    1.7  1  Polysacc_synt_3  Polysaccharide biosynthesis protein
    1.6e-08   33.6  43.4    1.6e-08   33.6  43.4    1.7  2  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 !  115.4  40.5   6.4e-37   2.9e-33       2     273 ..       8     278 ..       7     279 .. 0.93
   2 ?   -5.4  11.5         4   1.8e+04     100     200 ..     317     420 ..     282     426 .. 0.67
   3 ?   -0.5   3.0      0.14   6.4e+02     141     186 ..     416     459 ..     413     469 .. 0.63

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 6.4e-37
                     Polysacc_synt   2 lkgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslil 78 
                                       +k++i+l++s++i   ++f +lvy++r+lg+e +Gl+++a+a++++ + l+d G++  +vr +a+ r+   ++++++
  gi|330508398|ref|YP_004384826.1|   8 AKNTIFLASSNIIGFVFSFFFLVYTTRYLGTERYGLLSFAIAFASITIFLADIGISSVIVRDVARDRS---KTAIYI 81 
                                       79*****************************************************************8...8***** PP

                     Polysacc_synt  79 lnvllvllvlvllfllllliaaflglpelavlylilalmll.llvgvasfrrglfqglermkyaavsqvveqlsrvi 154
                                        n++l+++vl++++l++     f  +  +++  +++ + l  ++++++  +++ + + e m+y+++ +v+++l+ ++
  gi|330508398|ref|YP_004384826.1|  82 GNSILMKVVLAAITLMSTAAIGFALGYPFSTMKIVMVILLSlIVISFSGIISSVVSAYEIMEYISIGTVIYNLIMLT 158
                                       *****************999998777777776555555555799********************************* PP

                     Polysacc_synt 155 lvliavflfldivaavlgavlaalvggivslavlrkkf.rprfvilslklvrellsfsapltisslaillytyidsi 230
                                       + l+a+  + d+++ + ++++++++++ ++++v  +k+ rpr +i    l++ ++++++p+ +ss+++ +y y+d++
  gi|330508398|ref|YP_004384826.1| 159 FALLAISSGVDVYGFAYVYLFSSFISLGYFALVALRKLpRPRWNID-IDLWKYMIKEAIPFGLSSVFVRVYYYVDTV 234
                                       ***********99999999999999998888888888877888888.****************************** PP

                     Polysacc_synt 231 llglll..gaeavGiYnaayqllvaisgllapivtaalfPvfsel 273
                                       +++ll+   +e+ G Ynaay+++ ++s + +++++ +++P++s++
  gi|330508398|ref|YP_004384826.1| 235 MISLLIlnPNEVMGWYNAAYRMVIILSFIPVTFLG-SIYPIMSKF 278
                                       **9987335566***********************.*******95 PP

  == domain 2  score: -5.4 bits;  conditional E-value: 4
                     Polysacc_synt 100 aflglpelavlylilalmll..llvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgav 174
                                        + ++p++a   ++l + +    l++++s ++ lf+  +r+  +a ++++     +il l+++   + + +a  ++v
  gi|330508398|ref|YP_004384826.1| 317 SLVYGPAFAPSAIALQILIWseALIFINSAFGYLFNSINRQMVVAKQTMLAAGLNIILNLFLIPQYS-YIGASSATV 392
                                       3667777777777777777777799999999999999999988888777777666666666665555.777777777 PP

                     Polysacc_synt 175 laalvggivslavlrkkfr..prfvils 200
                                       + +l + +++l +  k+ +  pr +i+s
  gi|330508398|ref|YP_004384826.1| 393 ATQLFSFLFLLHIASKEGYglPRNMISS 420
                                       7777777766666666653456666665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.14
                     Polysacc_synt 141 aavsqvveqlsrvilvliavflfldivaavlgavlaalvggivsla 186
                                       +++s++++ l+   + ++++++f+  + ++l +v++a++  +++++
  gi|330508398|ref|YP_004384826.1| 416 NMISSLLKILVACLAMVLFIRGFD-HLPVPLLIVISAIIY-FFLII 459
                                       567777777777777777777777.555555555555554.33333 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 ?   -5.4  10.6         4   1.8e+04      34     104 ..      17      58 ..       3     105 .. 0.45
   2 ?   -1.4  19.9      0.48   2.2e+03       2     116 ..     116     239 ..     115     312 .. 0.76
   3 !   64.0  19.3   3.2e-21   1.5e-17       1     143 []     330     463 ..     330     463 .. 0.88

  Alignments for each domain:
  == domain 1  score: -5.4 bits;  conditional E-value: 4
                   Polysacc_synt_C  34 alvigalvklilnllliplfgi..vGaaiatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgiv 104
                                       +++ig+++ + + ++ + ++g+  +G +++                                +++a++ ++++
  gi|330508398|ref|YP_004384826.1|  17 SNIIGFVFSFFFLVYTTRYLGTerYG-LLSF------------------------------AIAFASITIFLA 58 
                                       34444444444444444444444333.2222..............................344444444444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.48
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli.plfgivGaaiatvlallvvavlnlyal 77 
                                       ++++ ls+i++s+s + ss+  +     ++ + +vi  l+ l + ll i     ++G a+  +++ ++++ +    +
  gi|330508398|ref|YP_004384826.1| 116 VMVILLSLIVISFSGIISSVVSAYEIMEYISIGTVIYNLIMLTFALLAIsSGVDVYGFAYVYLFSSFISLGYFALVA 192
                                       578889*******************************************667789***************9996655 PP

                   Polysacc_synt_C  78 rrllgikl.....ellrrll...kpllaalvmgivvylllllllgll 116
                                        r+l  +      +l++ ++    p+ ++ v + v y++  ++++ll
  gi|330508398|ref|YP_004384826.1| 193 LRKLPRPRwnidiDLWKYMIkeaIPFGLSSVFVRVYYYVDTVMISLL 239
                                       55555555555554444444322333333333333444444444444 PP

  == domain 3  score: 64.0 bits;  conditional E-value: 3.2e-21
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyal 77 
                                       +L+il++s  ++++++ +++++++++rq  ++k ++++a +++ilnl+lip+++++Ga+ atv+++l++++++l+++
  gi|330508398|ref|YP_004384826.1| 330 ALQILIWSEALIFINSAFGYLFNSINRQMVVAKQTMLAAGLNIILNLFLIPQYSYIGASSATVATQLFSFLFLLHIA 406
                                       69***********************************************************************8888 PP

                   Polysacc_synt_C  78 rr.llgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllrl 143
                                       ++  +g++ +++ +llk+l+a+l+m++ + ++ +l ++         l  +++ a++Y++l+++lr+
  gi|330508398|ref|YP_004384826.1| 407 SKeGYGLPRNMISSLLKILVACLAMVLFIRGFDHLPVP---------L-LIVISAIIYFFLIIILRV 463
                                       88345565588*****************6644444433.........2.345899*********985 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1  24.2   1.5e-18   6.7e-15       3     291 ..      33     327 ..      32     329 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1.5e-18
                   Polysacc_synt_3   3 ARLLspedFGvvaialvvislanlfvdmGlssaliqkedlteedlstvftfnlvlgllialvlfllapliasfynqp 79 
                                       +R L  e +G++++a+++ s++  ++d+G+ss++++   ++++++      ++++ +++a++++++  +i  +++ p
  gi|330508398|ref|YP_004384826.1|  33 TRYLGTERYGLLSFAIAFASITIFLADIGISSVIVRDVARDRSKTAIYIGNSILMKVVLAAITLMSTAAIGFALGYP 109
                                       59999*******************************99988886666666678999********************* PP

                   Polysacc_synt_3  80 el.vtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslv 155
                                           +++ v+ l+li+ ++s + ++ ++     + +++ t++ +++++ +a+++   g  v+ +++  l+ss++sl 
  gi|330508398|ref|YP_004384826.1| 110 FStMKIVMVILLSLIVISFSGIISSVVSAYEIMEYISIGTVIYNLIMLTFALLAISSGVDVYGFAYVYLFSSFISLG 186
                                       752689999*************9999999999999***************************************998 PP

                   Polysacc_synt_3 156 llwlaskwr...prlkfslkslkelfsfglklllsnllnylarnldnlliGkvl.s.saaLGlYsvakrlaslpvae 227
                                        + l++  +   pr++++++  k +++  + + ls++   ++  +d+++i  ++ + ++ +G Y+ a+r++ +++  
  gi|330508398|ref|YP_004384826.1| 187 YFALVALRKlprPRWNIDIDLWKYMIKEAIPFGLSSVFVRVYYYVDTVMISLLIlNpNEVMGWYNAAYRMVIILS-F 262
                                       776665554444999999999******9999999999999999999999998752326789********997665.5 PP

                   Polysacc_synt_3 228 itsviakVlfPalSrlqddk.kklrelylkvlrlialivlPiavglavvaellvkvllGsqWlea 291
                                       i  ++   ++P++S++   + + l  +y+++++ ++ i++Pi vg+ v+ e lv++++G  + ++
  gi|330508398|ref|YP_004384826.1| 263 IPVTFLGSIYPIMSKFYVSSdQYLGFMYERSFKYLMAIAIPIGVGTTVLGEDLVSLVYGPAFAPS 327
                                       5555556679*****865550567889********************************988776 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.14   6.4e+02     379     403 ..      12      35 ..       2      68 .. 0.49
   2 !   33.6  43.4   3.5e-12   1.6e-08      61     437 ..      76     442 ..      66     457 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.14
                              MurJ 379 vglalatslsaliglvllyvllrkr 403
                                       + la ++ +++++++ +l + + + 
  gi|330508398|ref|YP_004384826.1|  12 IFLASSNIIGFVFSFFFLVYTT-RY 35 
                                       4455555555544444433322.22 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 3.5e-12
                              MurJ  61 tllilvlllvtligilaapllirllatgfdeetlelavsllrillpylllvslsavfgavLnarkkFfapafsPvll 137
                                        ++i++  ++ +  +laa  l++  a gf+      +++++  +l++l+++s+s+++++v  a++     ++  v+ 
  gi|330508398|ref|YP_004384826.1|  76 KTAIYIGNSILMKVVLAAITLMSTAAIGFALGYPFSTMKIVMVILLSLIVISFSGIISSVVSAYEIMEYISIGTVIY 152
                                       55666666777777999999999999999877778899*************************************** PP

                              MurJ 138 NvsvIltllllanklgeeailaLaiGvliGgvlql.lvqlpalkkaglllkprfafrdeglkkflklllptllgvsv 213
                                       N+ +  ++ll+  +     +++ a++ l+  ++ l  + l+al+k   l +pr++      k ++k ++p  l++  
  gi|330508398|ref|YP_004384826.1| 153 NLIMLTFALLAISSGV--DVYGFAYVYLFSSFISLgYFALVALRK---LPRPRWNIDIDLWKYMIKEAIPFGLSSVF 224
                                       ****999999888766..9***********999762344444444...4699***999999**************** PP

                              MurJ 214 sqlnllvdtalAsf..laegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltlll 288
                                         +  +vdt++ s   l+++ v   ++a   + + l+ + v+++  + P +S+ +++ d+  +    + + + ++++
  gi|330508398|ref|YP_004384826.1| 225 VRVYYYVDTVMISLliLNPNEVMGWYNAAYRMVIILSFIPVTFLGSIYPIMSKFYVSSDQY-LGFMYERSFKYLMAI 300
                                       *************98899*****************************************99.889999********* PP

                              MurJ 289 lipvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvln 365
                                       +ip+ +g +vl++ +vsl++   +F +++   +a  + +++ +Li++  +  +  +f + +++   +k +++++ ln
  gi|330508398|ref|YP_004384826.1| 301 AIPIGVGTTVLGEDLVSLVY-GPAFAPSA---IALQILIWSEALIFI--NSAFGYLFNSINRQMVVAKQTMLAAGLN 371
                                       ********************.66788775...455566788899997..5679999********************* PP

                              MurJ 366 illsllllpplgvvglalatslsaliglvllyvllrkrlklteargiktflaklvvllalaavvilllsslt 437
                                       i+l+l+l+p+++++g + at++  l+++++l+ ++ k+  + + ++i   l+  +v+++ +   i ++ +l 
  gi|330508398|ref|YP_004384826.1| 372 IILNLFLIPQYSYIGASSATVATQLFSFLFLLHIASKEGYGLPRNMISSLLKI-LVACLAMVLFIRGFDHLP 442
                                       **************************************666666666555555.555555555666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1088  (0.0606838); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 3323.31
//
Query:       gi|330508399|ref|YP_004384827.1|  [L=165]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-13   48.7   0.0    1.4e-12   47.7   0.0    1.5  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
    5.2e-05   22.9   0.1    9.5e-05   22.0   0.1    1.3  1  Cupin_2          Cupin domain


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 !   47.7   0.0   1.5e-16   1.4e-12       4     150 ..       2     142 ..       1     156 [. 0.82

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.5e-16
                                       STTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEEE CS
                   dTDP_sugar_isom   4 iegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldva 80 
                                       ++g+++   k+f+DeRGff+e  +++  +   ++ ++vq+n+s s  g++R  H +  +++q     vvrG++  +a
  gi|330508399|ref|YP_004384827.1|   2 LPGIVIKPLKRFADERGFFTEIMRKDWKDV--IQDDIVQANMSLSYPGMVRAWHRH--ERGQVDHFLVVRGALKICA 74 
                                       689999999*************99877554..5678******************55..679************9999 PP

                                       EE-BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-.SSEEEEEEEESS---GG..GEEEE-TT-TTTT- CS
                   dTDP_sugar_isom  81 VDlRkgSptfgkwvgveLsaenkrqlyipegfahGflvl.sdeaevlYkvteyyape..sergirwnDpelgi 150
                                        D  +     ++  ++    +n +++ +p  + hGf v+ +++a+++Y v++ y+ +  +e+   wnDp++  
  gi|330508399|ref|YP_004384827.1|  75 YDDDT-----RELDEIISAGDNPQMVRMPGHYWHGFGVVgNEQATLIYFVNRLYDYAspDEERRPWNDPAIVP 142
                                       99544.....466777777899**************7662688********7655443399999*****9864 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   1.1e-08   9.5e-05       7      68 ..      46     116 ..      42     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.1e-08
                                       TTEEEEEECSSSEE.EEEEEEESEEEEE.ECTE....EEEEETTE...EEEE-TT-EEEEEE-SSS-EEEE CS
                           Cupin_2   7 pGesapshrHpged.effyVleGegelt.vdge....eveleaGd...svyfpagtpHrfrNtgdeparll 68 
                                       pG +  +hrH++ +   f V++G +++  +d+     + +++aGd   +v  p + +H+f+  g+e+a l+
  gi|330508399|ref|YP_004384827.1|  46 PGMVRAWHRHERGQvDHFLVVRGALKICaYDDDtrelDEIISAGDnpqMVRMPGHYWHGFGVVGNEQATLI 116
                                       667788****99999****************888889999****96667*****************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1311.56
//
Query:       gi|330508400|ref|YP_004384828.1|  [L=290]
Description: dTDP-4-dehydrorhamnose reductase [Methanosaeta concilii GP6]
Scores for complete 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-71  239.4   0.0    4.9e-71  239.2   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    1.3e-24   87.0   0.0      2e-24   86.4   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.5e-16   59.5   0.1    2.2e-15   56.9   0.1    2.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.6e-11   43.2   0.1    6.8e-10   38.6   0.1    2.6  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    7.6e-11   41.5   0.1    2.7e-10   39.7   0.1    1.9  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    3.4e-10   39.5   0.0      2e-09   37.0   0.0    2.1  2  NAD_binding_4    Male sterility protein
    0.00021   21.2   0.1     0.0061   16.4   0.0    2.5  3  DFP              DNA / pantothenate metabolism flavoprotein


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 !  239.2   0.0   1.9e-74   4.9e-71       1     278 [.       1     282 [.       1     289 [. 0.94

  Alignments for each domain:
  == domain 1  score: 239.2 bits;  conditional E-value: 1.9e-74
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.........T--TTSHHHHHHHHHHH--SEEEE------HHHHH CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre.........eldltdaeavaellkeakpdvvvnaAAytavDkaE 68 
                                       m+i +tG++G+ Gs+La+ + ++g +v++   +         ++dl da+ ++++++ ++pdv+v+ AA t+vD++E
  gi|330508400|ref|YP_004384828.1|   1 MRIFITGGSGLAGSKLAEMALARGEQVYSGYAHnqppygkevKFDLLDANGIRDTIERMRPDVIVHSAALTDVDRCE 77 
                                       89*************************998666689***************************************** PP

                                       HSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEE CS
                     RmlD_sub_bind  69 seeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkali 145
                                        ++++ay++n+e+++++Aeaa+++g+ L+++StDyVFdG++   Y+e++et+P+++YG +Kl+GEq  l+   + +i
  gi|330508400|ref|YP_004384828.1|  78 RKKDLAYRINVEGTRTIAEAARKAGSYLVYISTDYVFDGQR-GLYREEEETNPVSYYGLSKLLGEQFCLD---QGCI 150
                                       ****************************************5.55************************95...568* PP

                                       EEE-SEESS....SSS-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-E CS
                     RmlD_sub_bind 146 vRtswvyge....kgknfvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlaneget 218
                                        Rt ++yg+     + nf+  +l+ +k+ +e++vv Dq+ +PT   +lA+++l+++++ ++     g+yHl++++ +
  gi|330508400|ref|YP_004384828.1| 151 ARTCVIYGSrpasGKVNFALWLLNALKSGKEVRVVTDQFITPTLNSNLAAMVLEAANRNLS-----GIYHLSGAARV 222
                                       *******997886778******************************************996.....*********** PP

                                       EHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHH CS
                     RmlD_sub_bind 219 swlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewreal 278
                                       s+++fA++ +++++ d++ + p ++++    A+RP +S+Ldt+k+++t   ++ +  e+l
  gi|330508400|ref|YP_004384828.1| 223 SRYDFACELARAFDIDRRLIIPSQMSDIGWLARRPMDSSLDTSKASRTLKNRPLNLYESL 282
                                       **********************************************99877776666555 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4   0.0   7.7e-28     2e-24       1     204 [.       3     186 ..       3     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 7.7e-28
                                       EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S--- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavgg 76 
                                       i++tG++G+ Gs l++  l++g +   g +++  + + ++      v+ dl+d++ +++ +++ +pd+++h Aa  +
  gi|330508400|ref|YP_004384828.1|   3 IFITGGSGLAGSKLAEMALARGEQvYSGYAHN--QPPYGK-----EVKFDLLDANGIRDTIERMRPDVIVHSAALTD 72 
                                       79********************9956667776..334343.....369***************************** PP

                                       HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSS.SBSTCSTTS----SSHHHHHHHHHHHH CS
                         Epimerase  77 vaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeq.pkeettltgplkpnspYaaaKlagekl 152
                                       v++   ++   +++n++gt++++eaarkag   l+++s++ v+  +     +ee+t     +p s Y+++Kl+ge+ 
  gi|330508400|ref|YP_004384828.1|  73 VDRCERKKDLAYRINVEGTRTIAEAARKAGS-YLVYISTDYVFDGQRGLyREEEET-----NPVSYYGLSKLLGEQF 143
                                       *******************************.***********9888751255555.....9*************** PP

                                       HHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEET CS
                         Epimerase 153 veayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllg 204
                                       + +       + +i r + +yG r + +   ++   l++ +++gk ev ++ 
  gi|330508400|ref|YP_004384828.1| 144 CLD-------QGCIARTCVIYGSR-PASGKVNFALWLLNALKSGK-EVRVVT 186
                                       **6.......45***********9.55557777788899999999.888776 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 !   56.9   0.1   8.7e-19   2.2e-15       1     164 [.       4     144 ..       4     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 8.7e-19
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       +iTG++G  Gs lae+ l++g +v+         ++++    +           k +k Dl D++ +++ +++++pd
  gi|330508400|ref|YP_004384828.1|   4 FITGGSGLAGSKLAEMALARGEQVYSG-------YAHNQPP-YG----------KEVKFDLLDANGIRDTIERMRPD 62 
                                       69**********************763.......3333322.22..........23789****************** PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        +++ AA   Vd+   k +  +++nv Gt ++ ea+r++g      ++ +St+ v+ + q+  ++E+  ++P s Y+
  gi|330508400|ref|YP_004384828.1|  63 VIVHSAALTDVDRCERKKDLAYRINVEGTRTIAEAARKAGS----YLVYISTDYVF-DGQRGLYREEEETNPVSYYG 134
                                       ***************************************97....5999*******.4456899************* PP

                                       HHHHHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwiv 164
                                        +Kl  ++++
  gi|330508400|ref|YP_004384828.1| 135 LSKLLGEQFC 144
                                       ****999876 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.1   2.6e-13   6.8e-10      61     150 ..      44     145 ..       3     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 2.6e-13
                                       --TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG...... CS
                   Polysacc_synt_2  61 gdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA...... 131
                                        d+ d++ +++++e++++dv++h+AAl  V  +e++   a + Nv gt++++eaa +ag + +v+iStD        
  gi|330508400|ref|YP_004384828.1|  44 FDLLDANGIRDTIERMRPDVIVHSAALTDVDRCERKKDLAYRINVEGTRTIAEAARKAG-SYLVYISTDYVfdgqrg 119
                                       57889999***********************************************9998.789******75222222 PP

                                       .......SS--SHHHHHHHHHHHHHH CS
                   Polysacc_synt_2 132 .......vnPtnvmGatKrlaekllq 150
                                               nP++ +G++K+l e+++ 
  gi|330508400|ref|YP_004384828.1| 120 lyreeeeTNPVSYYGLSKLLGEQFCL 145
                                       22222225788999999998888776 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 !   39.7   0.1   1.1e-13   2.7e-10       3     229 ..       6     206 ..       4     217 .. 0.69

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1.1e-13
                         3Beta_HSD   3 tGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegv..dvvihlaslv 77 
                                       tGg+G  G++l ++ + ++e  +v +   +++p+        +    ++ D++d++ +++ +e +  dv++h a+l+
  gi|330508400|ref|YP_004384828.1|   6 TGGSGLAGSKLAEMALARGE--QVYSGYAHNQPPY-------GK--EVKFDLLDANGIRDTIERMrpDVIVHSAALT 71 
                                       56666666666666555554..4433333333333.......22..36789***********986558********* PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                       dv   + ++d  +++nv+GTr++ ea++kag  +lvY S+ + v++   g+  l    ++e e+++++ y  sK l 
  gi|330508400|ref|YP_004384828.1|  72 DVDRcERKKDLAYRINVEGTRTIAEAARKAG-SYLVYIST-DYVFD---GQRGL---YREEEETNPVSYYGLSKLLG 140
                                       **9979999*********************9.89****98.78899...44333...344456678999******** PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyGe....gdkllvpllkqlaklglalfkigdeevlsdrvYvgNvawahi 226
                                       E++ l        +g     c  R  +iyG     g+  +   l +++k+g++ ++++ ++    ++   N+a + +
  gi|330508400|ref|YP_004384828.1| 141 EQFCLD-------QG-----CIARTCVIYGSrpasGKVNFALWLLNALKSGKE-VRVVTDQF-ITPTLNSNLAAMVL 203
                                       *99885.......23.....677777777752121344455556677777743.34443333.45666777777766 PP

                         3Beta_HSD 227 lAa 229
                                        Aa
  gi|330508400|ref|YP_004384828.1| 204 EAA 206
                                       555 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.28   7.3e+02       1      22 [.       5      26 ..       5      35 .. 0.83
   2 !   37.0   0.0   7.8e-13     2e-09      89     244 ..      62     195 ..      47     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.28
                                      EE-TTSHHHHHHHHHHHHHS-. CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpe 22
                                      +TG++G  G+ L e  L + ++
  gi|330508400|ref|YP_004384828.1|  5 ITGGSGLAGSKLAEMALARGEQ 26
                                      8*********999988877764 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 7.8e-13
                                       -EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH CS
                     NAD_binding_4  89 dviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekld 162
                                       dvi+hsaA +++d+  ++   ++r+NveGtr + e a+k  +   l+++ST yv + ++g                 
  gi|330508400|ref|YP_004384828.1|  62 DVIVHSAALTDVDRCERKkdlAYRINVEGTRTIAEAARKAGS--YLVYISTDYVFDGQRGLY--------------R 122
                                       9*********999844333459***************96644..6******88888888653..............2 PP

                                       --EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST---TTSHHHHHHHHHHHH-EEES-S CS
                     NAD_binding_4 163 ederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGwingsdlgirgllgliakgvlpeil 238
                                       e   +++++    Y  sK l+E+ + +++       +i R  +i+g ++ +G +n   ++++ l+++ + +v+++ +
  gi|330508400|ref|YP_004384828.1| 123 E---EEETNPVSYYGLSKLLGEQFCLDQG-------CIARTCVIYGsRPASGKVNFALWLLNALKSGKEVRVVTDQF 189
                                       3...344455667***********99999.......89999999997888899999999999999988888888877 PP

                                       B---TT CS
                     NAD_binding_4 239 gdkeav 244
                                        ++  +
  gi|330508400|ref|YP_004384828.1| 190 ITPTLN 195
                                       777655 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.4e-06    0.0061      25     100 ..       6      78 ..       1      87 [. 0.79
   2 ?   -1.5   0.0      0.75   1.9e+03      34      52 ..      93     111 ..      89     120 .. 0.85
   3 ?    1.4   0.0     0.094   2.4e+02      24      57 ..     159     193 ..     155     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.4e-06
                                       E----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-E.EEE--SHHHHHHHHHHHHTT-SEEEE---S--EEES-- CS
                               DFP  25 NrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegve.vvkvesaeemleaveealkeadivimaAAvaDyrpkea 100
                                          SG  G +lAe a+arG +V    ++   + p g e   +  +a+ +++++e+     d+++++AA  D    e+
  gi|330508400|ref|YP_004384828.1|   6 TGGSGLAGSKLAEMALARGEQVYSGYAH--NQPPYGKEvKFDLLDANGIRDTIERMR--PDVIVHSAALTDVDRCER 78 
                                       5679******************966665..444554432578999********9985..5***********987665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.75
                                       HHHHHHHHTT-EEEEEE-S CS
                               DFP  34 alAeaaaarGaeVtlvsgp 52 
                                       ++Aeaa+++G    ++s  
  gi|330508400|ref|YP_004384828.1|  93 TIAEAARKAGSYLVYISTD 111
                                       79********999999875 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.094
                                       EE----HHHHHHH.HHHHHTT-EEEEEE-S-SS-- CS
                               DFP  24 sNrSSGkmGyalA.eaaaarGaeVtlvsgpvslet 57 
                                       s ++SGk  +al   +a++ G eV++v+ +  ++t
  gi|330508400|ref|YP_004384828.1| 159 SRPASGKVNFALWlLNALKSGKEVRVVTDQFITPT 193
                                       5678999999996258999********99864443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2076.77
//
Query:       gi|330508401|ref|YP_004384829.1|  [L=333]
Description: dTDP-glucose 4,6-dehydratase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-83  278.4   0.0    1.1e-82  278.1   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    7.1e-61  205.7   0.0    8.8e-61  205.4   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.2e-18   65.3   0.0    5.4e-18   65.0   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.4e-17   63.0   0.0    3.6e-17   62.4   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
    2.7e-13   49.7   0.0    3.1e-12   46.2   0.0    2.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    9.5e-10   38.1   0.1      2e-08   33.7   0.1    2.4  1  NAD_binding_4    Male sterility protein
    2.7e-05   23.7   0.0    7.9e-05   22.2   0.0    1.7  2  adh_short        short chain dehydrogenase
     0.0087   16.0   0.0      0.013   15.4   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.027   14.7   0.0      0.047   14.0   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.066   13.1   0.0       0.12   12.3   0.0    1.4  1  KR               KR domain


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.1   0.0   6.4e-86   1.1e-82       1     331 [.       4     303 ..       4     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 278.1 bits;  conditional E-value: 6.4e-86
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+ GfiGs++++l+l+++ ++  i +++++   ++i++la+    + ++++++++gD+ Dss + +l++++  d
  gi|330508401|ref|YP_004384829.1|   4 LVTGGLGFIGSNFIRLMLNRHDDC-RILNLDAQGFGSNIQNLADY---KDDRRYTFFRGDIADSSLVSSLVEKA--D 74 
                                       9*******************8887.67899999999******974...4578********************99..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        v+n+AA+ hVd+s++ P+ ++  nv G++ LLeair+++  ++vr++q+St+EvYG+  +   tE+  ++P sPY+
  gi|330508401|ref|YP_004384829.1|  75 LVVNFAAETHVDRSISRPDSFLHSNVNGVFCLLEAIRDHN--PSVRYVQISTDEVYGDILRGSSTEDSTLRPSSPYS 149
                                       9*************************************97..79********************************* PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                       a+K++ d +v +y ++ygl a+++++ n+++p++   f++++i++++ r+++g+ +++++G ++++Rdw +v D+++
  gi|330508401|ref|YP_004384829.1| 150 ASKAAGDVFVLAYARTYGLEAMITRCTNNYGPYQ---FPEKLIPKTIIRAKEGL-KIPIYGTGENVRDWIYVTDHCR 222
                                       *********************************6...****************9.78889***************** PP

                                       HHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B CS
                     GDP_Man_Dehyd 232 amwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllg 308
                                       a+ ++l++++        ge +++    e+++l + k i   +            gk + +++++ +rpg++ ++  
  gi|330508401|ref|YP_004384829.1| 223 AVEQVLNRGR-------RGEIYNISAGEERTNLFIAKFILE-M-----------LGKSEDQIEFVEDRPGHDARYSL 280
                                       ********98.......799999999999999999875542.2...........3556678999************* PP

                                       -THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 309 daskakeeLgWkpkvsfeelvre 331
                                       d s++++eLgW+p+ sfee+++ 
  gi|330508401|ref|YP_004384829.1| 281 DSSRIRKELGWRPERSFEEGLQT 303
                                       ********************986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.4   0.0   4.9e-64   8.8e-61       2     240 ..       4     239 ..       3     240 .. 0.96

  Alignments for each domain:
  == domain 1  score: 205.4 bits;  conditional E-value: 4.9e-64
                                       EEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE CS
                         Epimerase   2 lVtGatGfiGsalvkallekg..yevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavih 70 
                                       lVtG+ GfiGs++++ +l+++   ++++ld +  +sn ++l+d       ++ ++d+ d+s +  l++  ++d v++
  gi|330508401|ref|YP_004384829.1|   4 LVTGGLGFIGSNFIRLMLNRHddCRILNLDAQGFGSNIQNLADYkddrryTFFRGDIADSSLVSSLVE--KADLVVN 78 
                                       9******************997777*****************99************************..9****** PP

                                       --S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHH CS
                         Epimerase  71 lAavggvaassedpadfieknlqgtlnlleaarkagvk.rllflsSsevYGkdaeqpkeettltgplkpnspYaaaK 146
                                       +Aa+ +v++s+++p  f+++n++g+  llea+r++++  r++++s++evYG+  +    ++t+++ l+p+spY+a+K
  gi|330508401|ref|YP_004384829.1|  79 FAAETHVDRSISRPDSFLHSNVNGVFCLLEAIRDHNPSvRYVQISTDEVYGDILR---GSSTEDSTLRPSSPYSASK 152
                                       ***********************************9999************8887...455555689********** PP

                                       HHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHH CS
                         Epimerase 147 lageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeail 223
                                       +ag+  v aya++ygl+a+i+r++n+yGp+   ++++++ip+ i +++eg  ++ ++g+g+++Rd++yv D+++a+ 
  gi|330508401|ref|YP_004384829.1| 153 AAGDVFVLAYARTYGLEAMITRCTNNYGPY---QFPEKLIPKTIIRAKEGL-KIPIYGTGENVRDWIYVTDHCRAVE 225
                                       ******************************...9*****************.************************* PP

                                       HHHHHHTT-STTEEEEE CS
                         Epimerase 224 lvlehvdagdkgeiyni 240
                                        vl++   g+ geiyni
  gi|330508401|ref|YP_004384829.1| 226 QVLNR---GRRGEIYNI 239
                                       *****...9999****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 !   65.0   0.0     3e-21   5.4e-18       1     219 [.       4     218 ..       4     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 3e-21
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk.....viegDvtdkdkleealegvdvvih 72 
                                       +vtGg GF+G++ ++ ++++++  + r+l l+ +   ++ ++  + k+     +  gD+ d + ++  +e++d+v+ 
  gi|330508401|ref|YP_004384829.1|   4 LVTGGLGFIGSNFIRLMLNRHD--DCRILNLDAQGFGSNIQNLADYKDdrrytFFRGDIADSSLVSSLVEKADLVVN 78 
                                       69*****************998..555555444332222222222222224559*********************** PP

                         3Beta_HSD  73 laslvdvag.kltedeimkvnvkGTrnvleacvkag..vrvlvYtSsaevvgpnslgeeilngdEeleyeslhqday 146
                                        a+ + v     + d++ + nv+G   +lea ++++  vr  v  S+ ev g+      il+g  ++     ++++y
  gi|330508401|ref|YP_004384829.1|  79 FAAETHVDRsISRPDSFLHSNVNGVFCLLEAIRDHNpsVR-YVQISTDEVYGD------ILRGSSTEDSTLRPSSPY 148
                                       *******8847789*******************9862154.578999999999......999*************** PP

                         3Beta_HSD 147 pesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegd..kllvpllkqlaklglalfkigdeevlsdrvYvg 219
                                       + sKa  + +vl+        g  l     R +  yG+++  ++l p     ak gl++  +g  e++ d++Yv 
  gi|330508401|ref|YP_004384829.1| 149 SASKAAGDVFVLAYAR---TYG--LEAMITRCTNNYGPYQfpEKLIPKTIIRAKEGLKIPIYGTGENVRDWIYVT 218
                                       *******999998776...333..55555588999999975567888888889********************96 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 !   62.4   0.0     2e-20   3.6e-17       1     283 [.       1     306 [.       1     310 [. 0.83

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 2e-20
                                       EEEEEESTTSHHHHHHHHHCTT..TSEEEEEE-TT.....................T--TTSHHHHHHHHHHH--SE CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlae..eglevlaltre.....................eldltdaeavaellkeakpdv 54 
                                       m++lvtG+ G +Gs+ ++++ +  +++ +l l+ +                     + d++d++ v +l+++   d+
  gi|330508401|ref|YP_004384829.1|   1 MNLLVTGGLGFIGSNFIRLMLNrhDDCRILNLDAQgfgsniqnladykddrrytffRGDIADSSLVSSLVEK--ADL 75 
                                       89****************997722556777777779**********************************98..899 PP

                                       EEE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT..-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHH CS
                     RmlD_sub_bind  55 vvnaAAytavDkaEseeeaayavnaeavealAeaaaavg..alLihvStDyVFdGekkrpYeeddetsPlnvYGrtK 129
                                       vvn AA t vD+  s +++  + n+++v  l ea + ++  +  +++StD V+        +ed++  P + Y ++K
  gi|330508401|ref|YP_004384829.1|  76 VVNFAAETHVDRSISRPDSFLHSNVNGVFCLLEAIRDHNpsVRYVQISTDEVYGDILRGSSTEDSTLRPSSPYSASK 152
                                       ***********************************999744677*********98888889**************** PP

                                       HHHHHHHHH....H-SSEEEEEE-SEESS...SSS-HHHHHHHHHHH-SEEEE..ESS-EE--EEHHHHHHHHHHHH CS
                     RmlD_sub_bind 130 laGEqavla....agkkalivRtswvyge...kgknfvktmlrlakereelkv..vaDqlgsPTsardlAevllqll 197
                                       +aG   vla    +g +a+i R +  yg     +k   kt++r ake  ++ +      ++   ++ d  +++ q+l
  gi|330508401|ref|YP_004384829.1| 153 AAGDVFVLAyartYGLEAMITRCTNNYGPyqfPEKLIPKTIIR-AKEGLKIPIygTGENVRDWIYVTDHCRAVEQVL 228
                                       *******99766677899*********9943223445555555.444444444115678888888999999999999 PP

                                       HHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT---.-B CS
                     RmlD_sub_bind 198 ekaaeekelagvyHlanegetswlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgikl.re 273
                                       ++  +     ++y +++ +e + l +A+ il+++g+++ +++ +  ++   p +  ++S Ld+++++++ g+++ r+
  gi|330508401|ref|YP_004384829.1| 229 NRGRR----GEIYNISAGEERTNLFIAKFILEMLGKSEDQIEFV--EDR--PGHDARYS-LDSSRIRKELGWRPeRS 296
                                       98888....99***************************999999..333..44444565.77777777766654278 PP

                                       HHHHHHHHHH CS
                     RmlD_sub_bind 274 wrealkevlk 283
                                       ++e+l+++++
  gi|330508401|ref|YP_004384829.1| 297 FEEGLQTTVE 306
                                       8888888775 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   1.7e-15   3.1e-12       1     267 [.       3     273 ..       3     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.7e-15
                                       EEEETTTSHHHHHHHHHHHHH.B-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.. CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkk.kpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel 76 
                                       +lvtG+ G iGs+++r +l++ +  +i+ l+ + +   +i++ l + +++++++++     gd++d++ +++++e  
  gi|330508401|ref|YP_004384829.1|   3 LLVTGGLGFIGSNFIRLMLNRhDDCRILNLDAQGFG-SNIQN-LADYKDDRRYTFF----RGDIADSSLVSSLVE-- 71 
                                       59**************99988344455555555443.34544.5445555556555....8**************.. PP

                                       T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT.-SEEEEEEEGG..............GSS--SHH CS
                   Polysacc_synt_2  77 kvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieag.vkkvvliStDK..............AvnPtnvm 138
                                       k d+v++ AA  hV    + p + ++ Nv g   ++ea  +++   + v iStD                 +P + +
  gi|330508401|ref|YP_004384829.1|  72 KADLVVNFAAETHVDRSISRPDSFLHSNVNGVFCLLEAIRDHNpSVRYVQISTDEvygdilrgsstedsTLRPSSPY 148
                                       **************************************9988724589*****8622222222222222579***** PP

                                       HHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGT...TSSHHHHHHHHHTTSSEEE..S-TT-EEEEE-HHHHH CS
                   Polysacc_synt_2 139 GatKrlaekllqalakeseekktkfvvvRfGNVlgSr...GSviplFkkqikeggpvtv..TdpemtRyfmtieeav 210
                                        a+K++ + ++ a+a++      + +++R  N  g       +ip+   + keg ++++  T  e +R ++ +++ +
  gi|330508401|ref|YP_004384829.1| 149 SASKAAGDVFVLAYARTY---GLEAMITRCTNNYGPYqfpEKLIPKTIIRAKEGLKIPIygT-GENVRDWIYVTDHC 221
                                       ***************999...677777787777776422268****************9433.467899******** PP

                                       HHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH..........SSSS-EEE----TT CS
                   Polysacc_synt_2 211 qLvlqalalakggeifvldmGepvkivdlakalielsgleekkeedieikitGlRpG 267
                                       + v q l+++++gei+   +Ge  + + +ak ++e+ g++e++     i+++  RpG
  gi|330508401|ref|YP_004384829.1| 222 RAVEQVLNRGRRGEIYNISAGEERTNLFIAKFILEMLGKSEDQ-----IEFVEDRPG 273
                                       **************************************76665.....777777777 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.1   1.1e-11     2e-08       1     205 [.       5     177 ..       5     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.1e-11
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TG+ GF+G+ +++ +L+++++++i  l    + +     + ++l++++          +r ++  GD++++ l   
  gi|330508401|ref|YP_004384829.1|   5 VTGGLGFIGSNFIRLMLNRHDDCRILNL----DAQGFGSNI-QNLADYKD--------DRRYTFFRGDIADSSL--- 65 
                                       7********************8555555....444455566.44444432........56899*******9875... PP

                                       HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                          +  l+e+ d++++ aA +++d+++++   +l  Nv+G+  +le  +  +    ++++ST  v+g+  +      
  gi|330508401|ref|YP_004384829.1|  66 ---VSSLVEKADLVVNFAAETHVDRSISRpdsFLHSNVNGVFCLLEAIRDHNPSVRYVQISTDEVYGDILRG----- 134
                                       ...899*******************88765569****************9999999******7777777743..... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-E CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsi 205
                                                  + ++++    +  Y+ sKa+++  v +++r  gl ++i R+++
  gi|330508401|ref|YP_004384829.1| 135 -----------SSTEDSTLRPSSPYSASKAAGDVFVLAYARTYGLEAMITRCTN 177
                                       ...........4566777778899***************************986 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.4e-08   7.9e-05       3     167 ..       3     166 ..       1     175 [. 0.88
   2 ?   -2.5   0.0       1.7     3e+03     116     136 ..     221     241 ..     218     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.4e-08
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklgk 77 
                                        lvtG+ + IG ++ + ++++  ++ +++  ++     +++l +    ++++++++D++d++ v+ lveka      
  gi|330508401|ref|YP_004384829.1|   3 LLVTGGLGFIGSNFIRLMLNRHDDCRILNLDAQGFGSNIQNLADYkdDRRYTFFRGDIADSSLVSSLVEKA------ 73 
                                       59*******************99999999999999999999999988889*********************...... PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.........HCTTEEEEEEEEGGGTSB-TT CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpaml.........kqssGrIvnvsSvagkvpvag 145
                                        d++vn A+ t      + s ++ ++ ++ N++gvf l +a+ ++           ++  G+I   sS+     +  
  gi|330508401|ref|YP_004384829.1|  74 -DLVVNFAAET----HVDRSISRPDSFLHSNVNGVFCLLEAIRDHNPsvryvqistDEVYGDILRGSSTED-STLRP 144
                                       .9****99993....55667788999***************999833556778889999*****9888876.67777 PP

                                       BHHHHHHHHHHHHHHHHHHHHH CS
                         adh_short 146 vaaYsAsKaavagltrslakel 167
                                        ++YsAsKaa + ++ + a+ +
  gi|330508401|ref|YP_004384829.1| 145 SSPYSASKAAGDVFVLAYARTY 166
                                       899***********99998876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHCTTEEEEEEEE CS
                         adh_short 116 travlpamlkqssGrIvnvsS 136
                                       +rav + + ++++G+I n+s 
  gi|330508401|ref|YP_004384829.1| 221 CRAVEQVLNRGRRGEIYNISA 241
                                       67788888899*****99996 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 !   15.4   0.0     7e-06     0.013       1     108 [.       7     134 ..       7     176 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7e-06
                                       TTTSHHHHHHHHHHHHC-......T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---T CS
                    NAD_binding_10   1 GAtGkvGrllvkellarg......ghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggg 71 
                                       G+ G +G+  ++  l+r+      +++   +  n + la+++++ + + + gd+ d++ + + ++ ad Vv  ++ +
  gi|330508401|ref|YP_004384829.1|   7 GGLGFIGSNFIRLMLNRHddcrilNLDAQGFGSNIQNLADYKDDRRYTFFRGDIADSSLVSSLVEKADLVVNFAAET 83 
                                       78899***********98766666667777888889999999**************************887777666 PP

                                       CCHHHH.............HHHHHHHHHHCT.--EEEEEEETTTTSGCGCH CS
                    NAD_binding_10  72 gkdeeg.............aknivdaakeag.vkRfvlvsaigvgdevpge 108
                                       + d+ +             +  +++a + ++   R+v +s+  v+ ++ + 
  gi|330508401|ref|YP_004384829.1|  84 HVDRSIsrpdsflhsnvngVFCLLEAIRDHNpSVRYVQISTDEVYGDILRG 134
                                       554444455556655545577779999998844699999998888765443 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 ?   14.0   0.0   2.6e-05     0.047       2      80 ..       4      83 ..       3      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                                      EEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSH..HHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP  2 liiGa.GsvGqavaellarhfdvdaeitvadrsk..eklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77
                                      l+ G+ G++G+ +++l+++++d   +i   d +   ++ ++la+ +   r ++   d+++ +  +++l++++dlvvn +
  gi|330508401|ref|YP_004384829.1|  4 LVTGGlGFIGSNFIRLMLNRHDDC-RILNLDAQGfgSNIQNLADYKDDRRYTFFRGDIADSSL-VSSLVEKADLVVNFA 80
                                      566777*********999888763.787777764226778888888****************8.*************98 PP

                                      SGG CS
                   Sacchrp_dh_NADP 78 ppi 80
                                        +
  gi|330508401|ref|YP_004384829.1| 81 AET 83
                                      766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.7e-05      0.12       4      75 ..       4      73 ..       2      84 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                                      EEETTTSHHHHHHHHHHHHHH.S-EEEEE-SS..--HHHHHHHHHHHHT..T-EEEE----TT-HHHHHHHHHHH CS
                                KR  4 litGGlGgLGlelarwlaekg.arhlvllsRsaaadedskaliaeleal..gaevevvaaDvsdkdavealleei 75
                                      l+tGGlG +G  ++r +++++   +++ l  +        ++i++l+++  + + ++++ D++d++ v++l+e++
  gi|330508401|ref|YP_004384829.1|  4 LVTGGLGFIGSNFIRLMLNRHdDCRILNLDAQ-G----FGSNIQNLADYkdDRRYTFFRGDIADSSLVSSLVEKA 73
                                      9******************9944445544444.2....2334555555433668889999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2319.82
//
Query:       gi|330508402|ref|YP_004384830.1|  [L=350]
Description: glucose-1-phosphate thymidylyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-50  171.0   0.0      4e-50  170.7   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    1.7e-07   31.7   0.0    2.5e-07   31.2   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0014   18.3   9.6     0.0047   16.6   0.2    3.9  4  Hexapep          Bacterial transferase hexapeptide (six repea
     0.0026   16.8   0.1     0.0034   16.4   0.1    1.1  1  Fucokinase       L-fucokinase
  ------ inclusion threshold ------
       0.14   11.8   0.0       0.28   10.8   0.0    1.4  1  GGA_N-GAT        GGA N-GAT domain
       0.21    9.7   1.1       0.71    7.9   1.1    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 !  170.7   0.0   1.3e-53     4e-50       1     245 [.       2     232 ..       2     235 .. 0.91

  Alignments for each domain:
  == domain 1  score: 170.7 bits;  conditional E-value: 1.3e-53
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       ka+IL+GGsGtRL+PLt +++k+l+pv++k +++ + l+ ++++g +ei ++l   +++ v e +++++ ++v +++
  gi|330508402|ref|YP_004384830.1|   2 KALILSGGSGTRLRPLTYSQQKQLIPVANK-PVLFYALEDVIEAGADEIGIILG-PNKEQVIETVRSAD-WSVPIKF 75 
                                       799***************************.*****************666666.66677777888776.9****** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       +++ e+kg+A+ +++a+++l++++    v++Lg+++l +  +    k++ + ++   ++++++pv++++++Gv+  +
  gi|330508402|ref|YP_004384830.1|  76 IYQGEPKGLAHTILVAEDFLDEDF----VMYLGDNILRD-GIVSHEKRFHSLGS--SASVLLTPVDDPQRFGVADLN 145
                                       *********************999....89998877655.77777777777777..8******************** PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                        +g ++r+vEKPk ++ s++a  G+Y+f++ +++   k++++++r e eitd+++ ++e+g++  a + +++  W+D
  gi|330508402|ref|YP_004384830.1| 146 PDGSIRRLVEKPKVPP-SNYALVGVYFFTPLIIEAC-KSIKPSWRNELEITDAIQWLIENGHKVDASFVEGW--WKD 218
                                       ****************.*************999999.88**********************99988888995..*** PP

                                       XSSHHHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleanekl 245
                                       +G++++++ean+ +
  gi|330508402|ref|YP_004384830.1| 219 TGKPEDIFEANRLI 232
                                       **********9876 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   8.3e-11   2.5e-07       1      95 [.       3     134 ..       3     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 8.3e-11
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-E....EE-T CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaalarlgvrv....vede 66 
                                       a+iL GG ++R+      + K+l+p+++kp+l ++l+ + +ag+de+ ++ g+  e+v + +++ +++v    +++ 
  gi|330508402|ref|YP_004384830.1|   3 ALILSGGSGTRLRpltysQQKQLIPVANKPVLFYALEDVIEAGADEIGIILGPnkEQVIETVRSADWSVpikfIYQG 79 
                                       79**********6554436*****************************99877567888888877644422316665 PP

                                       TSS-SHHHHHHHHH...........................HHH.SSSCEEEEETT CS
                      NTP_transf_3  67 dpgkgplaslaaal...........................raaadadavlvlacD 95 
                                        + kg +++++ a                            ++++++  vl++++D
  gi|330508402|ref|YP_004384830.1|  80 -EPKGLAHTILVAEdfldedfvmylgdnilrdgivshekrfHSLGSSASVLLTPVD 134
                                       .4689999999999555555555555555555555555544334455556666655 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   1.6e-06    0.0047       2      29 ..     253     279 ..     252     281 .. 0.92
   2 ?    4.5   0.1     0.011        32       2      17 ..     281     296 ..     279     305 .. 0.73
   3 ?    2.0   0.0     0.066     2e+02      22      30 ..     322     330 ..     320     331 .. 0.74
   4 ?   -3.3   0.2       3.1   9.2e+03      21      28 ..     341     348 ..     341     348 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-06
                                       EEEETTEEE-TTEEEETTEEE-TTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIg 29 
                                       +v ++++ I+  +v+ g+++IG++++I 
  gi|330508402|ref|YP_004384830.1| 253 VVMEEGTRIR-RSVVKGPCIIGRDSIIS 279
                                       68899*****.***************95 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
                                       EEEETTEEE-TTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfavig 17 
                                       + IG  + Ig +++i+
  gi|330508402|ref|YP_004384830.1| 281 SYIGPYTSIGIGCQIC 296
                                       5677777777777774 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.066
                                       E-TTEEEET CS
                           Hexapep  22 IGdnvkIga 30 
                                       IG+nv+I +
  gi|330508402|ref|YP_004384830.1| 322 IGRNVRIKE 330
                                       888888865 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 3.1
                                       EE-TTEEE CS
                           Hexapep  21 kIGdnvkI 28 
                                       ++Gdn+ I
  gi|330508402|ref|YP_004384830.1| 341 IVGDNSDI 348
                                       68998755 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.1e-06    0.0034     270     339 ..     251     315 ..     200     338 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-06
                        Fucokinase 270 k....kesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtilqtlslklsk 339
                                       +    +e+  +  Sv+++ + +g++s+i +s +++ +sig ++ + g e+e         d +i+ + ++++ +
  gi|330508402|ref|YP_004384830.1| 251 GrvvmEEGTRIRRSVVKGPCIIGRDSIISDSYIGPYTSIGIGCQICGTEVE---------DSIIMDESRIVNAG 315
                                       023335555566666666666666666666666666666666666665555.........55555555555555 PP

>> GGA_N-GAT  GGA N-GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.5e-05      0.28      17      29 ..     220     232 ..     219     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.5e-05
                         GGA_N-GAT  17 knpeDLqaANrLI 29 
                                       ++peD+ +ANrLI
  gi|330508402|ref|YP_004384830.1| 220 GKPEDIFEANRLI 232
                                       58**********9 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.1   0.00024      0.71     223     258 ..     297     332 ..     246     349 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00024
                           DUF4954 223 gViledfiissGskikdgavisrcfvGqavklkkqf 258
                                       g ++ed+ii+  s+i ++ +++++++G++v++k+  
  gi|330508402|ref|YP_004384830.1| 297 GTEVEDSIIMDESRIVNAGKVVESLIGRNVRIKECD 332
                                       45689**************************98755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 2315.40
//
Query:       gi|330508403|ref|YP_004384831.1|  [L=394]
Description: 2-isopropylmalate synthase 1 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-83  280.5   0.9      2e-83  280.0   0.9    1.2  1  HMGL-like      HMGL-like
      0.003   17.7   0.6       0.97    9.6   0.0    3.0  3  Ribosomal_L50  Ribosomal subunit 39S
  ------ inclusion threshold ------
      0.016   14.6   0.4        2.4    7.4   0.1    2.2  2  MTHFR          Methylenetetrahydrofolate reductase
       0.05   13.8   0.2       0.17   12.2   0.2    1.9  1  DUF1611_N      Domain of unknown function (DUF1611_N) Rossman


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 !  280.0   0.9   4.4e-87     2e-83       2     264 .]      20     276 ..      19     276 .. 0.99

  Alignments for each domain:
  == domain 1  score: 280.0 bits;  conditional E-value: 4.4e-87
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       ++i+d+tLRDGeq +++ ++++ekl ia  Lde+gv++iE+gfp+ s  ++++v+++++ + ka+i al r+++kd+
  gi|330508403|ref|YP_004384831.1|  20 IEICDVTLRDGEQMPGVVFRADEKLDIALRLDEIGVEVIEAGFPVVSAAEMNAVKEVCNLGLKAKISALSRSVKKDV 96 
                                       79*************************************************************************** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       +aa++    +g++++ vfiats+lhlk+kl+++  e+++ a + v++a+++g  v++s+eda+rtd e+l +++++a
  gi|330508403|ref|YP_004384831.1|  97 DAAID----CGVDMISVFIATSDLHLKHKLHMSCPEAIACALQTVEYAKDHGLIVRFSAEDATRTDFETLKKLYKKA 169
                                       *****....******************************************************************** PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                       ee+ a+++++aDtvG+++P+  + +is+l++ +k  +++ +HcH+dlG+A+antla++eaGa+++ +tvnG+Ger+G
  gi|330508403|ref|YP_004384831.1| 170 EEYHADYVSVADTVGIMNPRTTYYMISELRKSIK--TPICMHCHDDLGMALANTLAGAEAGARQLHTTVNGIGERSG 244
                                       **********************************..***************************************** PP

                                       B-BHHHHHHHHHHTT-B----HHHHHHHHHHH CS
                         HMGL-like 233 naaleelvaalealgvdtgldlqklrsiaalv 264
                                       n++leel +al+       +dl+k+ ++++lv
  gi|330508403|ref|YP_004384831.1| 245 NTPLEELLIALRLHYDIESYDLSKIKDLSQLV 276
                                       ***********99988899*********9997 PP

>> Ribosomal_L50  Ribosomal subunit 39S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.52   2.3e+03      42      59 ..     159     176 ..     148     182 .. 0.70
   2 !    9.6   0.0   0.00022      0.97      52      83 ..     257     288 ..     253     299 .. 0.86
   3 !    4.7   0.0    0.0072        32      44      80 ..     338     374 ..     336     388 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.52
                     Ribosomal_L50  42 FaflkrlqqllgheipDy 59 
                                       F+ lk+l+++ + +  Dy
  gi|330508403|ref|YP_004384831.1| 159 FETLKKLYKKAEEYHADY 176
                                       777777777766666665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00022
                     Ribosomal_L50  52 lgheipDykltklhtvkdlveyleevvnpkpk 83 
                                       l+++i  y l+k++++++lv+ ++ v   k k
  gi|330508403|ref|YP_004384831.1| 257 LHYDIESYDLSKIKDLSQLVQTYSDVPVAKNK 288
                                       79*********************888766666 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0072
                     Ribosomal_L50  44 flkrlqqllgheipDykltklhtvkdlveyleevvnp 80 
                                        lk + q +g++++D +l  l+   ++ ++++  +n+
  gi|330508403|ref|YP_004384831.1| 338 ALKYITQRMGYYLKDQELGDLSERVKMCSEYKHAINC 374
                                       5899****************99999999999888875 PP

>> MTHFR  Methylenetetrahydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1   0.00053       2.4     199     269 ..      53     123 ..      36     134 .. 0.84
   2 ?    5.2   0.0    0.0025        11      27      83 ..     160     214 ..     150     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00053
                                       -SS-EEEEE---SSHHHHHHHHHHHT----HHHHCCCTCHCT-HHHHHHHHHHHHHHHHHHHHHCT--EEE CS
                             MTHFR 199 idipiipgimpiksykslkrlaklskvkiPqelldrleeikdddeavkkigielavemvkkllaegvkglH 269
                                       i +++i + +p+ s+++++ +++++++ + +++ +  +++k+d +a  + g++++  +++    +  ++lH
  gi|330508403|ref|YP_004384831.1|  53 IGVEVIEAGFPVVSAAEMNAVKEVCNLGLKAKISALSRSVKKDVDAAIDCGVDMISVFIATSDLHLKHKLH 123
                                       446999999************************99999********9999*99999998876555556666 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHHGGGG-SEEEE---CCCTTHHHHHHHHHHHHHHH-S-EEEEEESTTS- CS
                             MTHFR  27 rnLleridrleevkplfvdvTwgaggstaeltssiakviqqelgleailhlTctdas 83 
                                       ++L +  ++ ee+++++v+v +  g  + ++t ++++ ++++++ + ++h  c d  
  gi|330508403|ref|YP_004384831.1| 160 ETLKKLYKKAEEYHADYVSVADTVGIMNPRTTYYMISELRKSIKTPICMH--CHDDL 214
                                       667777899999************************************99..55555 PP

>> DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   3.7e-05      0.17      15      65 ..      60     108 ..      51     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                         DUF1611_N  15 rgipvvssleealaagaevlviGiapeggklpeswreavkeAleaGldvvs 65 
                                       +g+pvvs  e+   a  ev  +G+ ++  +l+ s++++v++A++ G+d +s
  gi|330508403|ref|YP_004384831.1|  60 AGFPVVSAAEMN--AVKEVCNLGLKAKISALSRSVKKDVDAAIDCGVDMIS 108
                                       789999999966..9999******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2785.93
//
Query:       gi|330508404|ref|YP_004384832.1|  [L=190]
Description: glutamine amidotransferase class-I [Methanosaeta concilii GP6]
Scores for 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   59.8   0.0    3.9e-16   59.4   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
     0.0003   20.6   1.0     0.0015   18.4   0.2    2.3  3  Peptidase_C26  Peptidase C26
      0.002   17.8   0.0     0.0025   17.4   0.0    1.1  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.023   14.5   0.0    1.5  2  SNO            SNO glutamine amidotransferase family
       0.15   11.1   0.0        1.2    8.1   0.0    2.1  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.0   1.1e-19   3.9e-16      13     175 ..      28     180 ..      19     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 1.1e-19
                                       HHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHT CS
                            GATase  13 lvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGICLGmQllaief 88 
                                       + + l ++g+ ++v  i+  +ee    lk++d++++ g   + + + +++e  +++ e + P+LGIC GmQ++a  f
  gi|330508404|ref|YP_004384832.1|  28 VQRILERTGFPCQVCHISLLNEER---LKSCDKVVLCGTALKDNeYLNHLERYTWLKEGDRPVLGICAGMQIIAAIF 101
                                       667778888999999988655555...89*********9888888******************************** PP

                                       TTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEE CS
                            GATase  89 grkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfv 165
                                       g++v +++ k+  g +m     +++ + g  ++++++h H++      ++p+g++ +a +e   + +++ + ++p++
  gi|330508404|ref|YP_004384832.1| 102 GGEVRSRH-KPAIGLEMIEVV-GESDILGPCRKIEVYHLHGLDP----TLPEGFIRLAGTEL--SPEAFSHCSQPIW 170
                                       ********.899999985555.4567777779999999999875....58***999888855..69*********** PP

                                       EESSBTTSTT CS
                            GATase 166 gvQFHPEsts 175
                                       g+ FHPE++ 
  gi|330508404|ref|YP_004384832.1| 171 GLLFHPEVRN 180
                                       *******976 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.58   2.1e+03      52      68 ..      48      64 ..      18      77 .. 0.73
   2 !   18.4   0.2   4.1e-07    0.0015     105     128 ..      84     107 ..      77     125 .. 0.87
   3 ?    0.1   0.0      0.16   5.8e+02     197     216 .]     160     177 ..     124     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.58
                     Peptidase_C26 52 vkaildkldgllltGgq 68
                                       ++ l+++d+++l G +
  gi|330508404|ref|YP_004384832.1| 48 NEERLKSCDKVVLCGTA 64
                                      46678899999999975 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 4.1e-07
                     Peptidase_C26 105 gvPilgiCrGlqllnvalGGtlyq 128
                                       + P+lgiC G+q+++  +GG++ +
  gi|330508404|ref|YP_004384832.1|  84 DRPVLGICAGMQIIAAIFGGEVRS 107
                                       67******************9876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.16
                     Peptidase_C26 197 EaieseeakafvlgvQwHPE 216
                                       Ea+++ +  ++++g+ +HPE
  gi|330508404|ref|YP_004384832.1| 160 EAFSHCS--QPIWGLLFHPE 177
                                       7777777..5799******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 !   17.4   0.0   7.1e-07    0.0025      29      92 ..      44     101 ..      34     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.1e-07
                          GATase_3  29 fvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeei 92 
                                       ++ l++e+l++ +d v+l+G+   ++d+++l+  +   ++ke    ++pvlgiC+G+q+    +
  gi|330508404|ref|YP_004384832.1|  44 ISLLNEERLKS-CDKVVLCGT--ALKDNEYLNHLERYTWLKE---GDRPVLGICAGMQIIAAIF 101
                                       55568899966.********8..5899999999999999998...689**********987655 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.5e-06     0.023      25      88 ..      46     104 ..      23     152 .. 0.73
   2 ?   -3.7   0.0       2.5     9e+03     163     172 ..     170     179 ..     166     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.5e-06
                                       E-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB CS
                               SNO  25 vkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelene 88 
                                       + ++e l+ +d +++ G   ta++   +++    + +  +k+++++vlG CaG+ ++++  ++e
  gi|330508404|ref|YP_004384832.1|  46 LLNEERLKSCDKVVLCG---TALKD--NEYLNHLERYTWLKEGDRPVLGICAGMQIIAAIFGGE 104
                                       55678888888888887...44432..12222223478899****************9988777 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.5
                                       EEESS-GGGS CS
                               SNO 163 latsfhPela 172
                                        ++ fhPe+ 
  gi|330508404|ref|YP_004384832.1| 170 WGLLFHPEVR 179
                                       56779**975 PP

>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00035       1.2      85     105 ..      79      99 ..      25     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00035
                          GATase_5  85 flnredtlaLGiCnGfqlLvk 105
                                       +l++ d  +LGiC G+q+++ 
  gi|330508404|ref|YP_004384832.1|  79 WLKEGDRPVLGICAGMQIIAA 99 
                                       4688999**********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1314.52
//
Query:       gi|330508405|ref|YP_004384833.1|  [L=228]
Description: putative ATP binding protein [Methanosaeta concilii GP6]
Scores for complete 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-62  208.4   0.0    1.1e-61  208.2   0.0    1.0  1  Diphthami_syn_2  Diphthamide synthase


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.2   0.0   5.9e-66   1.1e-61       1     218 [.       1     224 [.       1     225 [. 0.97

  Alignments for each domain:
  == domain 1  score: 208.2 bits;  conditional E-value: 5.9e-66
                   Diphthami_syn_2   1 mkvavlysGGkDsilaLykalkesevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedL 77 
                                       m+  vl+sGGkDs++a ++a ++  v  L++++s+n++symfh++n+  ++ +ae++ ip     t+G++eke edL
  gi|330508405|ref|YP_004384833.1|   1 MRLGVLFSGGKDSVFACWRAQERNTVACLITLLSQNPDSYMFHTPNICHTHFQAEAMHIPQLCRPTQGVKEKELEDL 77 
                                       7888************************************************************************* PP

                   Diphthami_syn_2  78 kgtlkkld....veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldes 150
                                       k  + + +    v+++v+Gaies+yq  r++r+C+ l l  + PLW+ d  ++l+  + e+f+vi+ +v+a+  d s
  gi|330508405|ref|YP_004384833.1|  78 KSAIAEARdcygVQGIVTGAIESIYQAARVQRICHSLDLWCFDPLWQTDQIDYLKTLLIEGFRVIISGVYAYPFDAS 154
                                       ****99988999***************************************************************** PP

                   Diphthami_syn_2 151 lLGrridkklidelkklsekygidkagegGeaetlvlDaPl..fkkrlevkelekkwderrgyldierak 218
                                       +LG  ++ + i  l++l+e+y i+++gegGe+et+vlD+P+  f+kr+e+  +  ++ + rg + ie ++
  gi|330508405|ref|YP_004384833.1| 155 WLGAELTEEKIMRLAQLQERYQINPSGEGGEIETFVLDGPIplFRKRIEILRASGTYANYRGQYIIEEMR 224
                                       ***************************************7444********************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1769.59
//
Query:       gi|330508406|ref|YP_004384834.1|  [L=505]
Description: cobyric acid synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-50  171.3   0.0    3.3e-50  170.4   0.0    1.5  1  GATase_3   CobB/CobQ-like glutamine amidotransferase domain
    1.1e-22   80.8   0.0    8.1e-22   78.0   0.0    2.1  1  AAA_26     AAA domain
    3.6e-21   75.6   0.0      1e-20   74.1   0.0    1.7  2  CbiA       CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00037   20.3   0.0    0.00068   19.5   0.0    1.4  1  GATase     Glutamine amidotransferase class-I
     0.0006   19.7   0.1     0.0053   16.7   0.0    2.2  2  MobB       Molybdopterin guanine dinucleotide synthesis prote
     0.0088   15.9   0.0      0.014   15.2   0.0    1.3  1  SNO        SNO glutamine amidotransferase family
  ------ inclusion threshold ------
      0.022   14.6   0.1        8.1    6.2   0.0    2.3  2  DJ-1_PfpI  DJ-1/PfpI family
      0.034   13.1   0.0       0.22   10.4   0.0    2.2  2  MeaB       Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.07   13.0   0.1       0.57   10.1   0.0    2.1  2  NTPase_1   NTPase
       0.13   11.5   0.2       0.89    8.8   0.0    2.2  2  DUF1611    Domain of unknown function (DUF1611_C) P-loop doma


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 !  170.4   0.0   1.8e-53   3.3e-50       1     195 [.     252     433 ..     252     434 .. 0.93

  Alignments for each domain:
  == domain 1  score: 170.4 bits;  conditional E-value: 1.8e-53
                          GATase_3   1 kiavirlpaisnytdldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggp 77 
                                       +iavirlp+isn+td++pLe+++  ++r+v+  de lg+ +d+vi+pG+k+ti+dl  ++++g++++i+++  +g+p
  gi|330508406|ref|YP_004384834.1| 252 EIAVIRLPRISNFTDFEPLERRA--YIRYVD-LDEPLGH-PDAVIIPGTKNTISDLLEMEKKGMADQIRSL--QGTP 322
                                       69*****************9977..899***.99***88.*****************************96..79** PP

                          GATase_3  78 vlgiCGGlqmLGeeiedpegvegeageveglglLdietefek.ekltgqvegevel......aaegeevkGyEiHsG 147
                                       +lgiCGG+q+LG+ei+d  gve+ +g+++glglL+++t+f + ek+t qv++ v          +g+ev+GyEiH+G
  gi|330508406|ref|YP_004384834.1| 323 ILGICGGYQILGKEIIDC-GVEDTEGSLPGLGLLNATTRFDQyEKRTVQVRKPVTGggpildRISGQEVTGYEIHMG 398
                                       *****************6.8**********************9****999999777***9997789*********** PP

                          GATase_3 148 rtilkekakpllkvkvggnngekdGavkksedgnvlGtYlHglfdnrn 195
                                        t + +   p +++       ++dGav   ++g v+GtYlHg+fdn+n
  gi|330508406|ref|YP_004384834.1| 399 VTASVD---P-AAF-------GDDGAV--ANCGLVIGTYLHGIFDNQN 433
                                       777654...4.446.......79****..67***************97 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0   4.5e-25   8.1e-22       3     191 ..       5     227 ..       3     231 .. 0.83

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 4.5e-25
                            AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie.....................ededselikellgld 58 
                                       i+v gt+ ++GK+++ ++L+r l+++g++v+ fK  +  ++                     + e +e++  +l  +
  gi|330508406|ref|YP_004384834.1|   5 IVVLGTTSHSGKSTLVAALCRLLSDRGYRVAPFKSQNMSLNswvtksgaeigiaqavqaraaRAEPTEFMNPILLKP 81 
                                       89*********************************998888888888887777666666665556777777766666 PP

                            AAA_26  59 qtyelpeplalsaplspelaarqegedid.lekiv....kelekdadivvVEGagglgvp.itee.llnadiaknlg 128
                                       +     + ++l +pl+++ a +    di+ l+++v    +ele+++d++vVEGagg  +  +++    n+++a+ l+
  gi|330508406|ref|YP_004384834.1|  82 KGDRTSQVIVLGKPLADKSAEEYYR-DIEgLKEVVdrsvRELENEYDFIVVEGAGGAAEInLFDRdIANIYVARLLQ 157
                                       6555667777888888777776655.5555888889999*******************7624444588********* PP

                            AAA_26 129 apvilVarggl.gtinqllltiealrqknvr.vlGvilNkvrnp.....envetlekksgipvlGvvPyl 191
                                       ap+ilV+ +++ g ++ l+ t+++l     + v+G+++Nk+r +     + +++le+ +g+pvlGv+Pyl
  gi|330508406|ref|YP_004384834.1| 158 APIILVGDIERgGVFASLYGTVQLLPPDVRPlVRGLVINKFRGDpailgTGLRSLEELTGVPVLGVLPYL 227
                                       *********994589********998754447*********999777777******************97 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.0   5.8e-24     1e-20       1     116 [.       5     228 ..       5     238 .. 0.97
   2 ?   -2.8   0.0       3.5   6.2e+03      91     110 ..     305     325 ..     296     328 .. 0.78

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 5.8e-24
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx...................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep...................... 54 
                                       i++ +t++ +GK+tl+a+L+r+l++rg+rV++++ ++++ n+ +   g e+ i++                      
  gi|330508406|ref|YP_004384834.1|   5 IVVLGTTSHSGKSTLVAALCRLLSDRGYRVAPFKSQNMSLNSWVtKSGAEIGIAQavqaraaraeptefmnpillkp 81 
                                       799***************************************99999****************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|330508406|ref|YP_004384834.1|  82 kgdrtsqvivlgkpladksaeeyyrdieglkevvdrsvreleneydfivvegaggaaeinlfdrdianiyvarllqa 158
                                       ***************************************************************************** PP

                                       ......CCHCCCHHHHHHCHCHHHH.......EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--C CS
                                       ......xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ......dlkrllellealgkkkall.....lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprde 116
                                             d++r ++++++l+++++ll      ++ g+v+n+++g+   + l  +l+ l++ +gvpvlgv+p+ +
  gi|330508406|ref|YP_004384834.1| 159 piilvgDIER-GGVFASLYGTVQLLppdvrPLVRGLVINKFRGD--PAILGTGLRSLEELTGVPVLGVLPYLD 228
                                       **********.**********9999*******************..9**********9988*********976 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.5
                                       TTCHHHHHHHHHHC.TS-EEE CS
                                       xxxxxxxxxxxxxx.xxxxxx RF
                              CbiA  91 tllkealeelkqry.gvpvlg 110
                                       +++k++++++++ + g p+lg
  gi|330508406|ref|YP_004384834.1| 305 EMEKKGMADQIRSLqGTPILG 325
                                       677888998888778999998 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.8e-07   0.00068      40      88 ..     285     337 ..     264     405 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.8e-07
                                       HHSTSEEEEEEESSCTT...TTTHHHHHHHHCT.STS-EEEETHHHHHHHHHT CS
                            GATase  40 lknpdgilvsgGpgspg...vegkieaikeare.nkiPiLGICLGmQllaief 88 
                                       l +pd+++++g  ++ +     +k  ++ ++r+ +++PiLGIC G Q+l++e+
  gi|330508406|ref|YP_004384834.1| 285 LGHPDAVIIPGTKNTISdllEMEKKGMADQIRSlQGTPILGICGGYQILGKEI 337
                                       6789******99999999984455556666666689*************9986 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.9e-06    0.0053       3      39 ..       7      43 ..       5      54 .. 0.85
   2 ?   -0.2   0.0      0.48   8.5e+02      81      98 ..     115     133 ..      97     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.9e-06
                              MobB  3 givgksgsGKTtLleklipelkarglrvgtiKhahhg 39
                                       +  +s sGK tL+  l + l++rg+rv+  K ++ +
  gi|330508406|ref|YP_004384834.1|  7 VLGTTSHSGKSTLVAALCRLLSDRGYRVAPFKSQNMS 43
                                      455679***********************99987755 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.48
                              MobB  81 leellarl.sevDlvlvEG 98 
                                       +++ ++ l +e+D+++vEG
  gi|330508406|ref|YP_004384834.1| 115 VDRSVRELeNEYDFIVVEG 133
                                       455566664669******9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     8e-06     0.014      25     103 ..     279     362 ..     263     376 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8e-06
                                       E-SGGGGCC-SEEEE-SS-HHHHHHH.HHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB.......SS-SS CS
                               SNO  25 vkrkedlaevdaliiPGGestamskl.iertglyedllefvknsekvvlGtCaGlillskelene.......lvktl 93 
                                       v   e l + da+iiPG   t   +l +e+ g+ ++++        ++lG C G  +l ke+            + l
  gi|330508406|ref|YP_004384834.1| 279 VDLDEPLGHPDAVIIPGTKNTISDLLeMEKKGMADQIRSLQG---TPILGICGGYQILGKEIIDCgvedtegSLPGL 352
                                       5556788899********999887776789998888887643...57*************98543222333445566 PP

                                       --CCEEEETT CS
                               SNO  94 ellkvkvkrn 103
                                       +ll+ + + +
  gi|330508406|ref|YP_004384834.1| 353 GLLNATTRFD 362
                                       6666666555 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 ?    5.9   0.0    0.0056        10      36      70 ..      93     134 ..      63     154 .. 0.71
   2 ?    6.2   0.0    0.0045       8.1      61     109 ..     287     335 ..     278     342 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0056
                                       S........TSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--B CS
                         DJ-1_PfpI  36 d........keevkgsrGlkvtvdaslddvkaaeyDalvlpGG 70 
                                       +        +e ++  +Glk +vd+s+ +++++ yD +v+ G 
  gi|330508406|ref|YP_004384834.1|  93 GkpladksaEEYYRDIEGLKEVVDRSVRELENE-YDFIVVEGA 134
                                       45566666566679999************9888.******773 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0045
                                       G-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHH CS
                         DJ-1_PfpI  61 eyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaa 109
                                         Da+++pG ++   +l e ek +   +    +g+++  IC g q+L +
  gi|330508406|ref|YP_004384834.1| 287 HPDAVIIPGTKNTISDLLEMEKKGMADQIRSLQGTPILGICGGYQILGK 335
                                       68********99988888877777666666789*************987 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00013      0.22      38      61 ..      12      35 ..       2      42 .. 0.85
   2 ?   -0.8   0.0      0.33   5.8e+02     208     231 ..     463     486 ..     454     494 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                      TTSSHHHHHHHHHHHHHCTT--EE CS
                              MeaB 38 PGaGkstlvealglelrrrGkrva 61
                                        +Gkstlv al   l +rG+rva
  gi|330508406|ref|YP_004384834.1| 12 SHSGKSTLVAALCRLLSDRGYRVA 35
                                      458********************8 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.33
                                       EEEBCCCTBSHHHHHHHHHHHHHH CS
                              MeaB 208 lktsavegeGidelvdaieehrev 231
                                        ++ a++g G  el+ a+e+h ++
  gi|330508406|ref|YP_004384834.1| 463 HRANAQKGSGYRELALAVESHLDM 486
                                       578999**************9876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00032      0.57       5      38 ..       9      42 ..       5      56 .. 0.85
   2 ?    0.3   0.0      0.32   5.7e+02      71     102 ..     101     132 ..      91     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00032
                                      E--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE CS
                          NTPase_1  5 TGppGvGKtTlvkkvlellkssgvkvgGfyteev 38
                                         + +GK+Tlv  +++ll+++g++v+ f  +++
  gi|330508406|ref|YP_004384834.1|  9 GTTSHSGKSTLVAALCRLLSDRGYRVAPFKSQNM 42
                                      556678********************99988766 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.32
                                       ETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE- CS
                          NTPase_1  71 vgkyvvdvesfeelalealrkalseadviviD 102
                                        ++y+ d+e ++e++ +++r+  +e d iv+ 
  gi|330508406|ref|YP_004384834.1| 101 AEEYYRDIEGLKEVVDRSVRELENEYDFIVVE 132
                                       67899****************99****99986 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 ?    8.8   0.0   0.00049      0.89      13      54 ..       3      44 ..       1      66 [. 0.85
   2 ?   -0.2   0.0      0.28     5e+02      77      98 ..     117     136 ..     112     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00049
                           DUF1611 13 krvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgi 54
                                      + ++v+GT +  GK t   +l + l +rG+++a +    +++
  gi|330508406|ref|YP_004384834.1|  3 RFIVVLGTTSHSGKSTLVAALCRLLSDRGYRVAPFKSQNMSL 44
                                      6799***************************98777766665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.28
                           DUF1611  77 glvkkaaeeeepdlilveGQgs 98 
                                       + v +++  +e d+i+veG g+
  gi|330508406|ref|YP_004384834.1| 117 RSVRELE--NEYDFIVVEGAGG 136
                                       5566666..4559******886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 3581.73
//
Query:       gi|330508407|ref|YP_004384835.1|  [L=185]
Description: iron-sulfur flavoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-22   78.9   0.0      4e-22   78.6   0.0    1.2  1  FMN_red       NADPH-dependent FMN reductase
    2.2e-09   37.3   0.0    2.8e-09   37.0   0.0    1.1  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
       0.14   12.4   0.0       0.23   11.7   0.0    1.4  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 !   78.6   0.0   6.8e-26     4e-22       1     101 [.       1     106 [.       1     159 [. 0.80

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 6.8e-26
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH- CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaaa 73 
                                       mk ++i+GS+rk++nt+ l+ +++e ++eag++++   l+++   +c    +c++++  ++  +ddv +lle +++a
  gi|330508407|ref|YP_004384835.1|   1 MKAIGIVGSPRKNGNTDILVSRVLEGAREAGLDTSKYLLNEMkYSGCqacEYCKSHD--HCRLDDDVTKLLEEMKEA 75 
                                       999**********************************99999999998755666665..479*************** PP

                                       SCEEEEEEECTTCE-HHHHHHHHCHT-.... CS
                           FMN_red  74 daliivtPeYngsysgllKnalDrlsr...t 101
                                       da+++++P+Y+  +sg++K + Dr+      
  gi|330508407|ref|YP_004384835.1|  76 DAVVFGSPIYFSLFSGQFKLMEDRMYSlidA 106
                                       ************************9446553 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   4.6e-13   2.8e-09       1     182 [.       1     161 [.       1     176 [. 0.74

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 4.6e-13
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHC.C..HHHHTTC.HHHHHHH.H CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaa.k..layeekp.adveseq.i 72 
                                       mk   i+++pr+ + ++  l  +++e++++ag  +     L+++    ++     a +  ++++ ++  d +  + +
  gi|330508407|ref|YP_004384835.1|   1 MKAIGIVGSPRK-NGNTDILVSRVLEGAREAG-LDTSKYLLNEMKYSGCQ-----AcEycKSHD-HCrLDDDVTKlL 69 
                                       788889*****9.5999***************.78888899997333333.....233322333.344666666667 PP

                                       HHHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTT.TSEEEEEEEESS-GGGSSTTSSS- CS
                      Flavodoxin_2  73 ekllaadaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLk.gkkalvivttGgpeesyqergleg 148
                                       e++++ada+v+++P+++  ++ ++K   Dr ++   a        +   +L+ gkka+++++     e  +   + +
  gi|330508407|ref|YP_004384835.1|  70 EEMKEADAVVFGSPIYFSLFSGQFKLMEDRMYSLIDAA-------F-VPRLRpGKKAIIVTSQADA-EVEN---Y-A 133
                                       *******************************9987754.......2.3577779999998888555.4433...3.3 PP

                                       S-HHHHHHHHHHHHHHTT-EEEEEEEEESCTCCC CS
                      Flavodoxin_2 149 aamdellpplrgilgfiGikdvepvlvegvagae 182
                                       +a d++      +l+++G+++ +++++ +  g++
  gi|330508407|ref|YP_004384835.1| 134 RAADDFA----LALKMLGFEVADIIRMVD--GIT 161
                                       3444444....799999999999998644..444 PP

>> Flavodoxin_5  Flavodoxin 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      37      62 ..      68      93 ..      51     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.8e-05
                      Flavodoxin_5 37 esedlesydavvigasvyygkllpel 62
                                        e+++++davv+g+++y + +++++
  gi|330508407|ref|YP_004384835.1| 68 LLEEMKEADAVVFGSPIYFSLFSGQF 93
                                      447899*************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1388.68
//
Query:       gi|330508408|ref|YP_004384836.1|  [L=264]
Description: DNA polymerase IV 2 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-15   58.4   0.1    2.1e-15   57.5   0.1    1.5  1  IMS_C     impB/mucB/samB family C-terminal domain
      1e-10   41.8   0.0    2.1e-10   40.8   0.0    1.5  1  IMS       impB/mucB/samB family
    2.1e-06   27.7   0.1    5.9e-06   26.3   0.1    1.8  1  IMS_HHH   IMS family HHH motif
    3.6e-05   24.3   0.1    9.4e-05   22.9   0.1    1.7  1  HHH_5     Helix-hairpin-helix domain
    0.00015   22.0   0.0    0.00036   20.7   0.0    1.6  1  Cdd1      Pathogenicity locus
     0.0069   16.6   0.0       0.02   15.1   0.0    1.7  2  DUF4332   Domain of unknown function (DUF4332)


Domain annotation for each model (and alignments):
>> 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 !   57.5   0.1   6.9e-19   2.1e-15       7     108 ..     160     262 ..     154     264 .] 0.91

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 6.9e-19
                             IMS_C   7 epksissektfpepydesk.lkkelreLaeelarrLrdkglvartitlklrysdfh.asrsatLprptsdtreilea 81 
                                       e+ksi+ e tf ++++++  + + +  Laee++  L + g+  +tit+k+ry +f+ ++r ++L+++t+d +++ + 
  gi|330508408|ref|YP_004384836.1| 160 ETKSIGREVTFERDIKDAApILQMMDGLAEEIHGELIECGFRFKTITVKVRYEHFDtFTRARSLSFSTNDLDILRNN 236
                                       89***********4443335777777***************************8888******************** PP

                             IMS_C  82 alkLlrrlidepglpirligvsasnlv 108
                                        ++L ++  + +++++rl+g+++s l+
  gi|330508408|ref|YP_004384836.1| 237 GKRLVDQFLR-KKKKVRLVGLRVSALS 262
                                       **********.*************998 PP

>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   7.1e-14   2.1e-10      99     149 ..      25      74 ..      13      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 7.1e-14
                                       EEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH---EEEEEESSHHHHHHHH CS
                               IMS  99 EayldltgleelaesegaalakelrkaikeelgltvsiGiasnkllAKlas 149
                                       Eayldl+g++e+ ++  a+la+ + +++ ++ +l++s+G+a+nk+lAK+ s
  gi|330508408|ref|YP_004384836.1|  25 EAYLDLSGRVEDLDQA-ANLARTIMQEVLDREDLSCSVGVAPNKMLAKIGS 74 
                                       9*******99999996.*******************************987 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1     2e-09   5.9e-06       4      32 .]      90     118 ..      87     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2e-09
                           IMS_HHH   4 vkefLwplpitkipGiGgklgekLeklGi 32 
                                        kefL+pl ++kipG+G++++e L +l+i
  gi|330508408|ref|YP_004384836.1|  90 AKEFLSPLGVRKIPGVGPRTEEILLDLDI 118
                                       68********************9877776 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   3.1e-08   9.4e-05       6      47 ..     101     143 ..      97     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.1e-08
                                       TSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS.-HHH CS
                             HHH_5   6 svsGiGpktAlallsaGiesvedlaaadveeLakipGi.Gkkt 47 
                                       +++G+Gp+t   ll+  i+++ +laaad+++La+  Gi Gk++
  gi|330508408|ref|YP_004384836.1| 101 KIPGVGPRTEEILLDLDIRTIGQLAAADPDRLARQLGIlGKRL 143
                                       8********************************9777656665 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.2e-07   0.00036       9      45 ..     100     136 ..      95     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.2e-07
                              Cdd1   9 qdiPniGkalaedlvelGirsveelkgedpeelyekl 45 
                                       ++iP++G+++ e l +l+ir++ +l+  dp++l ++l
  gi|330508408|ref|YP_004384836.1| 100 RKIPGVGPRTEEILLDLDIRTIGQLAAADPDRLARQL 136
                                       78*******************************9987 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.3   6.8e+03      47      58 ..      35      46 ..      31      71 .. 0.65
   2 !   15.1   0.0   6.6e-06      0.02      57     104 ..     101     148 ..      94     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.3
                           DUF4332 47 lklanlAdLari 58
                                       +l ++A+Lar+
  gi|330508408|ref|YP_004384836.1| 35 EDLDQAANLART 46
                                      555666666654 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 6.6e-06
                           DUF4332  57 rikgigeeyaeLLeaaGvdsvaeLaqrnpanLhqklkrlnrskklkrq 104
                                       +i+g+g++  e+L+   ++++ +La   p++L ++l+ l +++  + q
  gi|330508408|ref|YP_004384836.1| 101 KIPGVGPRTEEILLDLDIRTIGQLAAADPDRLARQLGILGKRLYERAQ 148
                                       69*********************************9987776655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1948.04
//
Query:       gi|330508409|ref|YP_004384837.1|  [L=374]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for 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   77.4   0.0    2.1e-21   76.4   0.0    1.5  1  OrfB_IS605      Probable transposase
      1e-21   76.6   0.0    2.6e-21   75.3   0.0    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.5e-19   68.5   2.3    5.3e-19   67.4   2.3    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0032   17.4   0.2     0.0057   16.7   0.2    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.064   12.7   0.6       0.83    9.1   0.1    2.3  2  zf-ribbon_3     zinc-ribbon domain
      0.082   12.6   0.1          2    8.2   0.0    2.3  2  zinc_ribbon_2   zinc-ribbon domain
        0.1   12.1   0.3        2.8    7.5   0.0    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.12   11.9   2.8         11    5.6   0.2    3.1  3  RecR            RecR protein
        0.2   11.3   0.7       0.42   10.3   0.7    1.5  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.0     1e-24   2.1e-21       3     117 ..     165     277 ..     163     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 1e-24
                        OrfB_IS605   3 pveveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        ve+e++  p+ k ++ +g+D+G++ +at+++++   ++ ++r++++++ +la+ +++l++  k++  +kka r + 
  gi|330508409|ref|YP_004384837.1| 165 SVEIEDQlRPPWKDGSLVGVDVGLESFATLSNGE---TIANPRFFREEETELARVQRKLSKAPKGTPERKKALRMVE 238
                                       6899999666779999******************...**************************************** PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       r+h++++++r +++hk++++l+++   ++ e+L ++nm 
  gi|330508409|ref|YP_004384837.1| 239 RVHERIANKRYDFAHKVSRYLVNRFGLIAFEDLSIQNML 277
                                       *************************************97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   1.3e-24   2.6e-21       1      68 [.     291     358 ..     291     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 1.3e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++ l +  +yka  +G  v++v+p++TSk Cs+Cg  ++++ls+r++ Cp+Cg+++drD+nAaiNil+
  gi|330508409|ref|YP_004384837.1| 291 WNMLVTLTSYKAASAGSMVVLVDPRNTSKMCSRCGILVEKTLSDRVHSCPQCGLSLDRDWNAAINILR 358
                                       667777889*********************************************************97 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   2.3   2.7e-22   5.3e-19       1      47 []       1      46 [.       1      46 [. 0.99

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 2.7e-22
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkayk+r+yPT+ Q++k++rt++ +R+ YN+ La+rk+a+e+egk
  gi|330508409|ref|YP_004384837.1|  1 M-LKAYKFRIYPTKSQRTKMERTLDLCRWTYNQTLAYRKDAWEKEGK 46
                                      8.*******************************************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   2.9e-06    0.0057      10      44 ..     316     352 ..     312     355 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.9e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + +++Cs+Cg  ++++ +   + Cp+Cg ++d +++ 
  gi|330508409|ref|YP_004384837.1| 316 NTSKMCSRCGILVEKTLSdrVHSCPQCGLSLDRDWNA 352
                                       6789*********9877799************99986 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      0.13   2.5e+02       5       9 ..     321     325 ..     317     331 .. 0.70
   2 ?    9.1   0.1   0.00042      0.83       4      17 ..     338     351 ..     335     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.13
                       zf-ribbon_3   5 CPnCG 9  
                                       C++CG
  gi|330508409|ref|YP_004384837.1| 321 CSRCG 325
                                       77777 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00042
                       zf-ribbon_3   4 rCPnCGaplssddn 17 
                                       +CP+CG  l+ d+n
  gi|330508409|ref|YP_004384837.1| 338 SCPQCGLSLDRDWN 351
                                       7*****98899998 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.1     2e+02      15      20 ..     320     325 ..     315     328 .. 0.70
   2 ?    8.2   0.0     0.001         2       7      20 ..     330     343 ..     329     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.1
                     zinc_ribbon_2  15 FCpyCG 20 
                                        C++CG
  gi|330508409|ref|YP_004384837.1| 320 MCSRCG 325
                                       577776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.001
                     zinc_ribbon_2   7 aelqdnakFCpyCG 20 
                                       ++l+d++  Cp+CG
  gi|330508409|ref|YP_004384837.1| 330 KTLSDRVHSCPQCG 343
                                       6799*********9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0014       2.8      11      31 ..     310     330 ..     305     335 .. 0.84
   2 ?    2.2   0.0     0.064   1.3e+02      21      29 ..     338     346 ..     337     349 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0014
                                       CHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon  11 lveDpergelvCtdCGlVled 31 
                                       +++Dp ++   C++CG ++e 
  gi|330508409|ref|YP_004384837.1| 310 VLVDPRNTSKMCSRCGILVEK 330
                                       689***999*******99996 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.064
                                       EESSSSBEE CS
                      TF_Zn_Ribbon  21 vCtdCGlVl 29 
                                        C+ CGl l
  gi|330508409|ref|YP_004384837.1| 338 SCPQCGLSL 346
                                       588888765 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.44   8.8e+02       5      16 ..      71      82 ..      69      84 .. 0.89
   2 ?    5.1   0.1    0.0082        16      13      28 ..     315     330 ..     310     332 .. 0.76
   3 ?    5.6   0.2    0.0057        11      12      23 ..     332     343 ..     330     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.44
                                      HHHHHHHHHHH- CS
                              RecR  5 LaeaLqeakekv 16
                                      ++++Lq+a e+v
  gi|330508409|ref|YP_004384837.1| 71 FSQTLQNAQERV 82
                                      89*******998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0082
                                       HHH-EE-TTT--EESS CS
                              RecR  13 kekvrhCsrCgnltee 28 
                                       +++ + CsrCg l e+
  gi|330508409|ref|YP_004384837.1| 315 RNTSKMCSRCGILVEK 330
                                       667799*****99776 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0057
                                       HHHH-EE-TTT- CS
                              RecR  12 akekvrhCsrCg 23 
                                       + ++v+ C++Cg
  gi|330508409|ref|YP_004384837.1| 332 LSDRVHSCPQCG 343
                                       6799*******9 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 ?   10.3   0.7   0.00021      0.42       6      29 ..     321     344 ..     316     345 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                     zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCgl 29 
                                       C+rCG  +e+   ++   Cp+Cgl
  gi|330508409|ref|YP_004384837.1| 321 CSRCGILVEKTLSDRVHSCPQCGL 344
                                       **********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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: 2457.52
//
Query:       gi|330508410|ref|YP_004384838.1|  [L=193]
Description: hypothetical protein MCON_2604 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-34  116.6   0.0      1e-33  116.4   0.0    1.0  1  DUF3786   Domain of unknown function (DUF3786)


Domain annotation for each model (and alignments):
>> DUF3786  Domain of unknown function (DUF3786)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.0   5.8e-38     1e-33      20     174 ..      24     181 ..      13     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 5.8e-38
                           DUF3786  20 tlpflgreyrisypggeisdgedeeeddlnekilllnylleak.g.apptgkwvsfrelpggavyyrafekraekpl 94 
                                       ++++++  y+i++ + e+    +  ++   + +lll+yl+  + + ++p+g+w+s++e  gg+ + ++f +ra++pl
  gi|330508410|ref|YP_004384838.1|  24 IISLFQDRYEIKQAEREVLFLPSRRQAIETVSVLLLHYLIGRSkNgYEPAGEWISIKETYGGKLFCSNFSRRAIRPL 100
                                       6899******************998888889*********876346******************************* PP

                           DUF3786  95 aktfggdpeklkkaaek.lggkpldkgDaayvfealpkipvlllfwegDeeFpasaniLFDksaeeyldaEdlavlg 170
                                       a++f++ pe+l + ++  + g+ l+ +D+a+++e +p + v +lfw++De++pa+a++LFD+   + l++Edl vl 
  gi|330508410|ref|YP_004384838.1| 101 AERFSQSPEELVRTLQDdFAGRMLEGADVAVEVETFPGVIVRILFWRSDEDLPADATMLFDRALAQILTMEDLTVLL 177
                                       *********99999886699**99****************************************************9 PP

                           DUF3786 171 ellv 174
                                       ++l+
  gi|330508410|ref|YP_004384838.1| 178 TILA 181
                                       9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1486.12
//
Query:       gi|330508411|ref|YP_004384839.1|  [L=355]
Description: hypothetical protein MCON_2605 [Methanosaeta concilii GP6]
Scores for complete 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-42  144.6  46.1    4.5e-42  144.4  46.1    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 !  144.4  46.1   2.5e-46   4.5e-42       3     325 ..      12     347 ..      10     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: 144.4 bits;  conditional E-value: 2.5e-46
                   AI-2E_transport   3 lilvllllllalypfiselllplliAlvlayllnpvvk...fL.kkrgvkrvlavllvlllllvll.vllvlllvpl 74 
                                        i+v+l++ll ly  ++ +l ++l+++vl++ll+p++    +L kk+ ++ +l+++lv++l+l+l+  ++ +llv l
  gi|330508411|ref|YP_004384839.1|  12 GIFVFLIILLTLYLTLN-FLTTILLSVVLVFLLKPLYAlffRLtKKKQISSFLSIMLVFILILSLIlGITSALLVEL 87 
                                       6899*************.*****************997443578899999999999999998876515677888999 PP

                   AI-2E_transport  75 liaqltqlvkslp..ayidslqnilnelpslleelen........liqalkqslskilsnilssilnsllsllasll 141
                                          q++  +++++  + i+++ ++ +++        n         +q++ +  ++ ++ + + +   l+ + ++l+
  gi|330508411|ref|YP_004384839.1|  88 SYLQSSGAISDVEidKTINEIDAWSKSFIPAWLY--NsiieialrYAQEISDIPIAFATWVFPILQRELTAFGSNLP 162
                                       9999999999998776777777776666543333..22335444445555555555555555555888999999999 PP

                   AI-2E_transport 142 glilslvlvllllffllldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgv 218
                                        l+ +l++v++++++ll dg+ + +  + l+p++ +  v+++l el++++  ++   + +++++gv+++ig+++lg+
  gi|330508411|ref|YP_004384839.1| 163 ILFAHLIVVVFFTYYLLIDGKVFIDQAVDLVPQEKQGIVRRFLDELYSIYHTLFTVYFSTSMLSGVMAAIGFSLLGI 239
                                       9**************************************************************************** PP

                   AI-2E_transport 219 pyalllailvglanliPyiGavivlipiaiialltggikevlivlivvllvq.liegnilePklmgkrlglhplvil 294
                                       py++l++++v ++ l+P++G+ +v+ipia++ l++g+  ++li+l++ ++v  +i +n+++P+l  ++ ++hp+++l
  gi|330508411|ref|YP_004384839.1| 240 PYPFLMGVVVAVFTLLPLLGPPFVFIPIAVYYLIVGDLFRCLILLVFGTVVLmVIPENVIRPHLAMMSSRIHPILTL 316
                                       *************************************7777777777766651678********************* PP

                   AI-2E_transport 295 lsllaggklfGlvGlilavpltavikailea 325
                                       l+  a + + G++G+i++++l++++ a+++ 
  gi|330508411|ref|YP_004384839.1| 317 LAYTAPIFVIGIIGVIVGPTLYGFLLAVYRS 347
                                       **************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1164  (0.0649228); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 2795.89
//
Query:       gi|330508412|ref|YP_004384840.1|  [L=299]
Description: integral membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-48  163.9  46.9    5.2e-25   88.2  16.0    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
       0.34   10.1  22.0      0.024   13.9  11.5    2.4  2  PUNUT     Purine nucleobase transmembrane transport
       0.88    9.6  14.8       0.11   12.5   1.5    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 !   82.1  22.9   6.8e-27   4.1e-23       2     137 .]       9     143 ..       8     143 .. 0.98
   2 !   88.2  16.0   8.7e-29   5.2e-25       2     135 ..     156     292 ..     155     294 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 6.8e-27
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       l++l+++l +lfw+++f+ +k++l++++p++++f+r +ia+  l+++ l+++ ++ k+ ++d+ +++l +++g+v++
  gi|330508412|ref|YP_004384840.1|   9 LAVLFIILDVLFWGFSFISTKVVLSQIPPVSIAFFRQIIAASTLIMLVLFTRTSF-KIGRRDMGYIVLASFFGIVMY 84 
                                       5799***************************************************.********************* PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllill 137
                                       f+l +++l +t+asnas+i++  P+ftl+  + l++ k+t+k +l ++++ +Gv+l+++
  gi|330508412|ref|YP_004384840.1|  85 FSLENTGLLYTTASNASMIVAALPIFTLFAEAMLFRLKVTWKMILCLIFSTIGVALVVT 143
                                       ********************************************************986 PP

  == domain 2  score: 88.2 bits;  conditional E-value: 8.7e-29
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl...aklslkdwllllllgllgt 75 
                                       +g ll++ a ++w +y++l ++l+++++ l+lt+ +++++ il+++++ ++ +++   +++sl  ++ ll+lg++++
  gi|330508412|ref|YP_004384840.1| 156 FGNLLVMGAIICWVFYTLLNRRLSENYPCLALTAAQSTVSIILFIPLIIPEIERWpaiSEISLPVFANLLFLGVFCS 232
                                       799************************************************99999999****************** PP

                              EamA  76 vlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                        +a+++++ya ++++a+++s +++l+Pv+t+++++l+l+ +l+++q+lg++li+++++ +
  gi|330508412|ref|YP_004384840.1| 233 GFAYIFYIYATRRLGATVVSAFLNLIPVVTVVFGYLILHDTLSWMQVLGMALIMIALYHL 292
                                       *******************************************************99865 PP

>> PUNUT  Purine nucleobase transmembrane transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9  11.5     4e-06     0.024      77     153 ..      71     149 ..      25     203 .. 0.77
   2 ?    1.8   2.3     0.018   1.1e+02     269     308 ..     246     288 ..     229     294 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-06
                             PUNUT  77 lyivlGllvav..dnllyslgllylpvstfslilatqLaFtaifsalinkqkftrfiinsvvlltisaallalssss 151
                                        yivl   +++  +  l   glly  +s +s+i+a+  +Ft +  a++ + k+t  +i+++++ ti+ al+++ + +
  gi|330508412|ref|YP_004384840.1|  71 GYIVLASFFGIvmYFSLENTGLLYTTASNASMIVAALPIFTLFAEAMLFRLKVTWKMILCLIFSTIGVALVVTVDGK 147
                                       4555555555411335789**************************************************99855444 PP

                             PUNUT 152 dk 153
                                         
  gi|330508412|ref|YP_004384840.1| 148 VD 149
                                       33 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.018
                             PUNUT 269 lfsnvistvll..p.vvsvlavilfrdkfsavkgvalllailg 308
                                       l + v+s+ l   p v+ v+  ++++d +s+++++ ++l +++
  gi|330508412|ref|YP_004384840.1| 246 LGATVVSAFLNliPvVTVVFGYLILHDTLSWMQVLGMALIMIA 288
                                       5555666554311314456677788899999999988876665 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   5.2     0.023   1.4e+02      58     116 .]      81     142 ..      44     142 .. 0.75
   2 ?   12.5   1.5   1.9e-05      0.11      58     112 ..     236     289 ..     214     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.023
                           TMEM234  58 Svlffll....lgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialcv 116
                                        v++f l    l  +  s a++i+ +l  +fT+  e +l +  +++k++l +++ ++g+al+v
  gi|330508412|ref|YP_004384840.1|  81 IVMYFSLentgLLYTTASNASMIVAALP-IFTLFAEAMLFRLKVTWKMILCLIFSTIGVALVV 142
                                       4555432111144455577788888875.79*****9999999*****************986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.9e-05
                           TMEM234  58 SvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgi 112
                                        +++ ++ ++   +++++  N +  v+Tv+ ++l+  ++l++ +vlgm+l+++++
  gi|330508412|ref|YP_004384840.1| 236 YIFYIYATRRLGATVVSAFLNLI-PVVTVVFGYLILHDTLSWMQVLGMALIMIAL 289
                                       58999999999999999999966.5789************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2100.55
//
Query:       gi|330508413|ref|YP_004384841.1|  [L=407]
Description: hypothetical protein MCON_2608 [Methanosaeta concilii GP6]
Scores for complete 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    1.7e-15   56.9   0.0    1.9  1  Hydrolase_4    Serine aminopeptidase, S33
    6.4e-11   42.1   0.0    1.1e-05   25.1   0.0    2.1  2  Peptidase_S9   Prolyl oligopeptidase family
      1e-10   41.9   0.0    2.8e-05   24.1   0.0    2.2  2  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
      6e-10   39.1   0.0    5.1e-07   29.5   0.0    2.1  2  DLH            Dienelactone hydrolase family
    8.9e-09   36.3   0.0    1.3e-08   35.7   0.0    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family
    8.3e-05   22.4   0.0    0.00058   19.6   0.0    2.0  1  Abhydrolase_1  alpha/beta hydrolase fold
    0.00014   21.6   0.0     0.0035   17.1   0.0    2.2  2  Abhydrolase_5  Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.014   15.2   0.0       0.98    9.2   0.0    2.3  2  Abhydrolase_2  Phospholipase/Carboxylesterase
      0.047   13.3   0.0      0.078   12.6   0.0    1.3  1  Abhydrolase_8  Alpha/beta hydrolase
      0.072   12.9   0.0       0.46   10.3   0.0    2.0  2  Abhydrolase_3  alpha/beta hydrolase fold
       0.15   12.1   0.0        2.1    8.5   0.0    2.4  2  EF-hand_6      EF-hand domain
       0.15   10.7   0.0       0.24   10.1   0.0    1.3  1  AXE1           Acetyl xylan esterase (AXE1)
       0.17   11.4   0.0        4.7    6.9   0.0    2.3  2  EF-hand_5      EF hand


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   1.3e-18   1.7e-15      12     235 ..      95     371 ..      93     375 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 1.3e-18
                       Hydrolase_4  12 GlaehsgryaelaeaLaaqGfavyalDhrGhGrse....gkrghvpsfddyvdDlaafvekvkeehpel..plfllG 82 
                                       G  e s+ + ++ae+L  +G+av+ ++ rG G ++       +  + +++y  D+++++  ++++ +     ++llG
  gi|330508413|ref|YP_004384841.1|  95 GSDEPSRPFLQIAEHLSSRGIAVLRFNKRGVGLNGtilnASIVANSTYQSYKSDAEKALAILRAQPEVDknDITLLG 171
                                       66677888999************************999766677788999*********999954443347****** PP

                       Hydrolase_4  83 hSmGGliallyllrypdkva.glilsaPalkikakl..k.appllklllkllgkllpklqv................ 139
                                       hS G+++a +++ + ++ ++  + lsaPa +++ +l  + + + l  + +++ + +  l                  
  gi|330508413|ref|YP_004384841.1| 172 HSEGAIVAPRVAREDAE-IRkMVLLSAPAGNLRDNLqfQlLARPLLYAEEVIDSNHDGLLTiteveatmgtpgesla 247
                                       ************99999.66477789***999998855333333334667777777777668888888888888888 PP

                       Hydrolase_4 140 ........................snnlkadslsrdpevvaayeadplv.hgkitvrlllelldamkrleeraakit 191
                                                               s++  + s+  d e + + +  p++  + ++++ +l  + a++++++   +i+
  gi|330508413|ref|YP_004384841.1| 248 plqaiglvmwnstteehqwhsviaSDPRGNISIRGDLEPLIKKQVQPMLsNESVKASPWLASYFALNNTTDIIGDIS 324
                                       89999999999999999999999977777778888888887788888887999****99999*************** PP

                       Hydrolase_4 192 lPllllhGeaDkvvdpeas...relyerlgskdktlklypglyHell 235
                                       + +l+l+Ge+D+ ++  ++   ++ + ++++ d tl +ypgl H+ +
  gi|330508413|ref|YP_004384841.1| 325 ASILILQGENDTQIPLPEAmllEQKLTEVKHPDHTLIIYPGLGHSFH 371
                                       ************999888889999999999**************976 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   8.3e-06     0.011       8     102 ..     108     203 ..     102     228 .. 0.84
   2 !   25.1   0.0   7.7e-09   1.1e-05     111     191 ..     288     373 ..     253     396 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.3e-06
                                       HHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHH.HHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHH CS
                      Peptidase_S9   8 qlladrGyvvvvanirGsggyGeafhdagkrklgqnef.dDfiaaaealakegyvdserlaitGgSyGGyltgaaln 83 
                                       + l++rG++v+  n rG g  G   + ++  +   +++ +D  +a+  l ++  vd++ + + G+S G  ++  ++ 
  gi|330508413|ref|YP_004384841.1| 108 EHLSSRGIAVLRFNKRGVGLNGTILNASIVANSTYQSYkSDAEKALAILRAQPEVDKNDITLLGHSEGAIVAPRVAR 184
                                       5688*********************999977666666626*****************************99999999 PP

                                       H-GGG-SEEEEESE---CC CS
                      Peptidase_S9  84 qrpdlFkaavaevpvvdvl 102
                                       +  ++ k+++ ++p  +++
  gi|330508413|ref|YP_004384841.1| 185 EDAEIRKMVLLSAPAGNLR 203
                                       9999888888888877666 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 7.7e-09
                                       THHHCCCC--TTTCHHHHHHHHHH-CGGG--.....---EEEEEEETT-SSS-THHHHHHHHHHH--S-S.EEEEEE CS
                      Peptidase_S9 111 lteeymewgnpeeneegykelspyspldnvk.....aypplLlihGlaDdrvppaealklvaaLqkkgkn.vlllif 181
                                       ++++++ +  + e+ +   +l++y  l+n +     +++++L+++G++D+++p+ ea+ l ++L++ +++ + l i+
  gi|330508413|ref|YP_004384841.1| 288 IKKQVQPMLSN-ESVKASPWLASYFALNNTTdiigdISASILILQGENDTQIPLPEAMLLEQKLTEVKHPdHTLIIY 363
                                       55566666665.34444669999999999889*********************************988888****** PP

                                       TTS-SSTTSS CS
                      Peptidase_S9 182 pdegHgvgkp 191
                                       p+ gH++  +
  gi|330508413|ref|YP_004384841.1| 364 PGLGHSFHPS 373
                                       *****87644 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0     2e-08   2.8e-05       7      99 ..     150     239 ..     149     273 .. 0.80
   2 !   15.6   0.0   8.4e-06     0.012     111     165 ..     320     372 ..     310     379 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2e-08
                                       HHHHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEEETTE..EE----B-GGG-E CS
                            BAAT_C   7 eeainyllrhpkvkkdkigllGiSkGgelalllasflkkisavvlingsavvvegklvykdeskvlpelklsmeklk 83 
                                       e+a+++l+ +p+v k++i+llG+S G+ +a  +a    +i+ +vl++++a + +++l ++       +l   +e + 
  gi|330508413|ref|YP_004384841.1| 150 EKALAILRAQPEVDKNDITLLGHSEGAIVAPRVAREDAEIRKMVLLSAPAGNLRDNLQFQLL---ARPLLYAEEVID 223
                                       89***************************************************999999855...666666666777 PP

                                       E-TTS-EE-TT-B--T CS
                            BAAT_C  84 vnknglldivdvlall 99 
                                        n +gll i++v a++
  gi|330508413|ref|YP_004384841.1| 224 SNHDGLLTITEVEATM 239
                                       7777777777766555 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 8.4e-06
                                       GGG--SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S---S CS
                            BAAT_C 111 vekakgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGHliep 165
                                       +++++++il+++ge+D  +p  e    ++++L++ +++   +l++Yp+ GH ++p
  gi|330508413|ref|YP_004384841.1| 320 IGDISASILILQGENDTQIPLPEAM-LLEQKLTEVKHP-DHTLIIYPGLGHSFHP 372
                                       57899***************88766.9***********.999999******9987 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0021       2.9      72     123 ..     139     190 ..     129     197 .. 0.87
   2 !   29.5   0.0   3.7e-10   5.1e-07     133     193 ..     313     374 ..     296     387 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0021
                               DLH  72 kvaeekvlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevd 123
                                       + + +  ++d++ a+a l+++pev+++ + + G   G+ +a  +a+e++e+ 
  gi|330508413|ref|YP_004384841.1| 139 NSTYQSYKSDAEKALAILRAQPEVDKNDITLLGHSEGAIVAPRVAREDAEIR 190
                                       555678899************************************9997665 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 3.7e-10
                               DLH 133 pekeleeaakikapilalfgeeDefipadevekleealka.anvdlelkvYpgagHaFands 193
                                       ++++ + + +i+a il+l ge+D+ ip  e+  le++l++ +++d+ l +Ypg gH+F+  +
  gi|330508413|ref|YP_004384841.1| 313 LNNTTDIIGDISASILILQGENDTQIPLPEAMLLEQKLTEvKHPDHTLIIYPGLGHSFHPSK 374
                                       5677788899***************************9874689**************9665 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   9.5e-12   1.3e-08      10     210 ..      97     371 ..      74     378 .. 0.59

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 9.5e-12
                                       ......GCHHHHHHHHCCT.CEEEEE--TTST.......S-GGCS--HHHC.HHH....HHHHCCTT...TTSEEEE CS
                     Abhydrolase_6  10 s..assWlvapLaallaag.vhvlapDlpGhG.......rsdpppldledl.adl....aalldelaa.gggpvvlv 70 
                                       +  ++ +l  ++a+ l+++ ++vl +  +G G        s  +  +++ +   +    +a+l++ ++ + +++ l+
  gi|330508413|ref|YP_004384841.1|  97 DepSRPFL--QIAEHLSSRgIAVLRFNKRGVGlngtilnASIVANSTYQSYkS-DaekaLAILRAQPEvDKNDITLL 170
                                       25567777..8888888888999********9776777655556677755432.22334556666666899****** PP

                                       EETCHHHHHHHHHHCC...EE.EEES-....----TTT......S----TTHHHHHHTT-CCCCH.CCH......S- CS
                     Abhydrolase_6  71 GHSlGGalalaaapla.lvvg.vlldppp..talpagl......laaalelllallallrllawl.sre......pl 130
                                       GHS G+++a ++a+    +++ vll++p   +    ++      la++l +++ ++++ ++ ++l  +e       +
  gi|330508413|ref|YP_004384841.1| 171 GHSEGAIVAPRVAREDaEIRKmVLLSAPAgnL----RDnlqfqlLARPLLYAEEVIDSNHD-GLLtITEveatmgTP 242
                                       ***********444446777799999944221....2223444444445554444444443.333222233333322 PP

                                       HSCCCCHHHC..CCCHCHCCCGHH.......................................HHCCHHC..HTTCC CS
                     Abhydrolase_6 131 prlfladeda..daawrarlarla.......................................allaglg..llpaa 164
                                       + + la++ a   + w+ +  +++                                       + la+ +   ++ +
  gi|330508413|ref|YP_004384841.1| 243 G-ESLAPLQAigLVMWNSTTEEHQwhsviasdprgnisirgdleplikkqvqpmlsnesvkasPWLASYFalNNTTD 318
                                       2.333333323355566666666666666677788888888888888887777777776655522222223233466 PP

                                       HHTT-TTGCEEE.CTT-CHHH....HCHHCCCH...STTEEETCE...SSS-HH CS
                     Abhydrolase_6 165 awadlpvpllvl.ggeDplvp....rllerlla...qagarlpvvlpgaGHlph 210
                                        + d+ +++l+l g++D  +p     lle+ l+    ++ +l +++pg GH++h
  gi|330508413|ref|YP_004384841.1| 319 IIGDISASILILqGENDTQIPlpeaMLLEQKLTevkHPDHTL-IIYPGLGHSFH 371
                                       777777777999888888555222233444444333366666.********887 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   4.2e-07   0.00058      17     251 ..     104     369 ..      93     374 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.2e-07
                                       TTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB........CHHSHHHHHHHHH..HHHHHCTTSSEEEEEETHHH CS
                     Abhydrolase_1  17 aerglapaLakdgfdvillDlrGvgySspapacin.......ddygtasvaddld..rildalgddkltlvGhSmGG 84 
                                        +  +a++L+ +g  v+ ++ rGvg   + ++  +       + y   + ++ l   r++   +   +tl+GhS G 
  gi|330508413|ref|YP_004384841.1| 104 LQ--IAEHLSSRGIAVLRFNKRGVGLNGTILNA-SivanstyQSYKS-DAEKALAilRAQPEVDKNDITLLGHSEGA 176
                                       45..899*******************9999986.4589966555555.477777744446666777799******** PP

                                       HHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHH CS
                     Abhydrolase_1  85 mialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrlvdal 161
                                        +a  +a e +  ++++vll+a  pa  l++  ++q+   p      ++d     + ++ + e+++ +   +l  +l
  gi|330508413|ref|YP_004384841.1| 177 IVAPRVARE-DAEIRKMVLLSA--PAGNLRDNLQFQLLARPLLYAEEVIDSNHDGLLTITEVEATMGTPGESL-APL 249
                                       999999998.556*********..************9999999999998888888888888888887777665.455 PP

                                       HH......................HCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHC.......... CS
                     Abhydrolase_1 162 kf......................pdkskrfpssgsdnasslatgalksieqwpttdsaklllrlre.......... 206
                                                               p       ++++ ++  l    +k +++   + s k   +l +          
  gi|330508413|ref|YP_004384841.1| 250 QAiglvmwnstteehqwhsviasdP-------RGNISIRGDLEPLIKKQVQPMLSNESVKASPWLASyfalnnttdi 319
                                       5557777766666666644443332.......222222222222222333333333333333333333333335556 PP

                                       THHHHSEEEEEEETTCSSSCH.HHHHHHHHC....HTSEEEEEEETCSSS CS
                     Abhydrolase_1 207 lknvlaptlvisgtsDplvpp.kaledlaql....lpkkrlvvisdagHl 251
                                       + +++a +l+++g++D  +p  +a+   ++l     p+++l+++++ gH 
  gi|330508413|ref|YP_004384841.1| 320 IGDISASILILQGENDTQIPLpEAMLLEQKLtevkHPDHTLIIYPGLGHS 369
                                       66666677777777777777744444444445544333677777766665 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.5e-06    0.0035      44     104 ..     150     211 ..     133     239 .. 0.73
   2 ?    2.1   0.0       0.1   1.4e+02      77     127 ..     297     351 ..     288     370 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.5e-06
                     Abhydrolase_5  44 nkaeeiikeapklek..fvvgGhslGGvvasrfaaeeekiegvvflasYPekdelselskkvl 104
                                       +ka  i++++p+++k    + Ghs G +va r+a+e+ +i  +v+l++ P+ +   +l++++l
  gi|330508413|ref|YP_004384841.1| 150 EKALAILRAQPEVDKndITLLGHSEGAIVAPRVAREDAEIRKMVLLSA-PAGNLRDNLQFQLL 211
                                       678889999998876225667***********************9976.66444445555544 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.1
                     Abhydrolase_5  77 eeekiegvvflasYPe....kdelselskkvlsivgteDgvlnvkslekakkflp 127
                                       ++e++++  +lasY +     d + + s  +l + g++D  ++  ++   +++l+
  gi|330508413|ref|YP_004384841.1| 297 SNESVKASPWLASYFAlnntTDIIGDISASILILQGENDTQIPLPEAMLLEQKLT 351
                                       678899999999998642234556788999*********9999888777777766 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.035        48     101     119 ..     160     179 ..     136     193 .. 0.84
   2 ?    9.2   0.0   0.00071      0.98     156     202 ..     324     371 ..     295     376 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.035
                                       T.--GGGEEEEEETHHHHHH CS
                     Abhydrolase_2 101 g.ipssriiigGFSqGaala 119
                                       + +++++i + G S Ga++a
  gi|330508413|ref|YP_004384841.1| 160 PeVDKNDITLLGHSEGAIVA 179
                                       2599**************98 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00071
                                       G-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-.GEEEEEETT--SS-- CS
                     Abhydrolase_2 156 klpilqiHgeeDpvvplalgkaakevlkkllk.kvelksyeglaHsid 202
                                         +il + ge D  +pl  + ++++ l+++ + +++l +y+gl+Hs  
  gi|330508413|ref|YP_004384841.1| 324 SASILILQGENDTQIPLPEAMLLEQKLTEVKHpDHTLIIYPGLGHSFH 371
                                       45788899*************************************976 PP

>> Abhydrolase_8  Alpha/beta hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.7e-05     0.078      99     148 ..     154     203 ..     135     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-05
                     Abhydrolase_8  99 rdlrats.vpgqhlallgHSYGSlvaslAlddaaseVsdvvlyGSPGleae 148
                                         lra+  v ++ ++llgHS G++va + + +  +e+  +vl  +P  ++ 
  gi|330508413|ref|YP_004384841.1| 154 AILRAQPeVDKNDITLLGHSEGAIVAPRVARE-DAEIRKMVLLSAPAGNLR 203
                                       4566776677899**************99988.8999****9999976665 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00033      0.46      50     108 ..     147     214 ..     139     288 .. 0.77
   2 ?    0.2   0.0       0.4   5.6e+02     169     210 ..     327     371 ..     292     372 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00033
                                       HHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---............EEEEEEESE CS
                     Abhydrolase_3  50 edalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepk............vagqvliyP 108
                                        da +al  l++q    ++d++ i+l+G S G+  a  va++ ++  ++             +++q+l  P
  gi|330508413|ref|YP_004384841.1| 147 SDAEKALAILRAQP---EVDKNDITLLGHSEGAIVAPRVAREDAEIRKMVllsapagnlrdnLQFQLLARP 214
                                       58889999999995...8******************99996655532222445555566666666666665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.4
                                       EEEEEETT-TT..HHHHHHHHHHHHH.TT--EEEEEETTEETTGG CS
                     Abhydrolase_3 169 tlvvvaefDpl..rdegeayaerlra.agvevelieyegmvHgfa 210
                                       +l++ +e+D+     e+  + ++l + +  + +li y+g+ H+f+
  gi|330508413|ref|YP_004384841.1| 327 ILILQGENDTQipLPEAMLLEQKLTEvKHPDHTLIIYPGLGHSFH 371
                                       566666666541145666777888873445678999999999997 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.48   6.6e+02      13      21 ..      79      87 ..      77      89 .. 0.89
   2 ?    8.5   0.0    0.0015       2.1       9      27 ..     222     240 ..     220     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.48
                         EF-hand_6 13 gdGkidaeE 21
                                      g+G+id++E
  gi|330508413|ref|YP_004384841.1| 79 GSGTIDMNE 87
                                      89*****99 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0015
                         EF-hand_6   9 fDkdgdGkidaeElrkalr 27 
                                       +D ++dG +++ E+ + + 
  gi|330508413|ref|YP_004384841.1| 222 IDSNHDGLLTITEVEATMG 240
                                       8************998775 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00017      0.24     151     201 ..     142     192 ..     121     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEE CS
                              AXE1 151 yrrvflDavrlveivaslpevDeeRvavlGasqGGalalavaalekrikav 201
                                       y++   Da +++ i+++ pevD++ ++ lG+s G  +a  va  + +i+++
  gi|330508413|ref|YP_004384841.1| 142 YQSYKSDAEKALAILRAQPEVDKNDITLLGHSEGAIVAPRVAREDAEIRKM 192
                                       566667****************************99998888777777765 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.11   1.6e+02      12      20 ..      79      87 ..      79      89 .. 0.90
   2 ?    6.9   0.0    0.0034       4.7       7      20 ..     221     234 ..     220     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.11
                                      -SSCE-HHH CS
                         EF-hand_5 12 gDGkIskeE 20
                                      g+G+I++ E
  gi|330508413|ref|YP_004384841.1| 79 GSGTIDMNE 87
                                      89*****99 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0034
                                       HH-SS-SSCE-HHH CS
                         EF-hand_5   7 aiDlNgDGkIskeE 20 
                                        iD N+DG +++ E
  gi|330508413|ref|YP_004384841.1| 221 VIDSNHDGLLTITE 234
                                       69*********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 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:                        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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2858.01
//
Query:       gi|330508414|ref|YP_004384842.1|  [L=84]
Description: hypothetical protein MCON_2609 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-17   62.7   0.2    3.6e-17   62.6   0.2    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
     0.0048   16.9   0.1     0.0065   16.5   0.1    1.2  1  Sigma70_r1_1     Sigma-70 factor, region 1.1
  ------ inclusion threshold ------
      0.017   15.4   0.0      0.027   14.7   0.0    1.4  1  AglB_L1          Archaeal glycosylation protein B long periph
      0.022   14.6   0.1       0.03   14.2   0.1    1.2  1  PulG             Type II secretory pathway pseudopilin
       0.16   12.4   0.0       0.19   12.1   0.0    1.1  1  Arm-DNA-bind_3   Arm DNA-binding domain


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 !   62.6   0.2     1e-20   3.6e-17       1      65 [.      13      78 ..      13      84 .] 0.91

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1e-20
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeip.epssieell 65
                                      y i+i ++ d +y+v+vP lpGc + gdt+eea+++akeaie+++e+l+ +g +ip e  +ie+++
  gi|330508414|ref|YP_004384842.1| 13 YKITIRPETDGTYTVIVPSLPGCLTFGDTIEEALEMAKEAIEAYIESLAARGIDIPvEEDQIEATI 78
                                      899*****************************************************6677777665 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.8e-06    0.0065      19      64 ..      35      78 ..      33      84 .] 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                                      CEEHHH.HHHHGCCSS--HHHHHHHHHHHHCCT-EEE-SS-...... CS
                      Sigma70_r1_1 19 yLtyeE.indaLpddeldseqiediiemLedmgIdvveeaededell 64
                                       Lt+ + i++aL+   + +e+ie  ie L + gId+  e+++ + ++
  gi|330508414|ref|YP_004384842.1| 35 CLTFGDtIEEALE---MAKEAIEAYIESLAARGIDIPVEEDQIEATI 78
                                      5666444999999...9*******************77777555544 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 ?   14.7   0.0   7.6e-06     0.027      22      87 ..       5      75 ..       2      80 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.6e-06
                                      -TTS-EEEEEEEEE.-BTTEEEEEE---SS............-SSSSEESS-EEEEETTEEEEE---HHHHH CS
                           AglB_L1 22 tnqgrtftYrqeaeadedGefeltvPYstegee......dgetnssveaagpYevtagnvtaeveVpEeaVl 87
                                      +nq rt +Y+ + + ++dG+++++vP    g        ++  ++  ea ++Y  +  +    + V E++++
  gi|330508414|ref|YP_004384842.1|  5 INQMRTLRYKITIRPETDGTYTVIVPSL-PGCLtfgdtiEEALEMAKEAIEAYIESLAARGIDIPVEEDQIE 75
                                      599**********************943.2222344445666677777777777777777777777777776 PP

>> PulG  Type II secretory pathway pseudopilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   8.2e-06      0.03      37      73 ..      43      79 ..      37      84 .] 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.2e-06
                              PulG 37 qEvlnvalmAvqtkqdeLslNGvevtikktqeeisvy 73
                                      +E+l +a+ A+++  ++L+  G+++ ++++q e ++ 
  gi|330508414|ref|YP_004384842.1| 43 EEALEMAKEAIEAYIESLAARGIDIPVEEDQIEATIT 79
                                      79*****************************999886 PP

>> Arm-DNA-bind_3  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.4e-05      0.19      38      72 ..      14      73 ..       6      75 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.4e-05
                    Arm-DNA-bind_3 38 r.......................lGrypavslaeARkkarelraliaq.GiD.Paeekk 72
                                      +                       +G+  +  l++A+++ +++ + +a+ GiD P+ee +
  gi|330508414|ref|YP_004384842.1| 14 KitirpetdgtytvivpslpgcltFGDTIEEALEMAKEAIEAYIESLAArGIDiPVEEDQ 73
                                      44455554444445555555554346655679999999999999998777***9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 654.86
//
Query:       gi|330508415|ref|YP_004384843.1|  [L=349]
Description: Radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-18   67.4   0.1    8.7e-18   65.2   0.1    1.9  2  Radical_SAM  Radical SAM superfamily
      4e-14   53.0   0.3    6.5e-14   52.4   0.3    1.3  1  Fer4_12      4Fe-4S single cluster domain
    2.8e-10   40.1   0.0    5.7e-10   39.1   0.0    1.5  1  Fer2_4       2Fe-2S iron-sulfur cluster binding domain
    4.3e-10   39.7   0.3    9.4e-10   38.7   0.3    1.5  1  Fer4_14      4Fe-4S single cluster domain
     0.0012   18.8   0.1     0.0025   17.8   0.1    1.5  1  Fer2_3       2Fe-2S iron-sulfur cluster binding domain
     0.0046   16.7   0.0     0.0092   15.8   0.0    1.4  1  UBA_4        UBA-like domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.1   2.9e-21   8.7e-18       2     153 ..     114     268 ..     113     286 .. 0.85
   2 ?    1.1   0.0      0.15   4.6e+02      91     142 ..     280     329 ..     224     336 .. 0.54

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 2.9e-21
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                        +t gCnl C+ C++++  +  + g+ l++ee +e + e k+  gv+ + ++gge +l+++      rl ++++p  
  gi|330508415|ref|YP_004384843.1| 114 CFTSGCNLCCPQCQNWRY-AFMDAGELLTPEEAAERMTETKKQCGVERIAISGGECTLNRPWLISFIRLLREQNPIA 189
                                       689**************7.*********************75555******************************** PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHH.....HHHHHHHHHHHHTTSETEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx.....xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtf.....eevlealeklreagikrvvdri 149
                                       ri+v tngt ++e+++++l+ +g++ + ++l+a+   ++ ++++   +++     +  +ea+++l+++  +  v+  
  gi|330508415|ref|YP_004384843.1| 190 RIHVDTNGTILTEDYIDELVGAGMTDIGIDLKALRISTFMEITGlLDEGLatkylQTAWEAVKYLHDS-HPQ-VFLG 264
                                       **********************************9996666665522332455559999999999999.774.4555 PP

                                       EEBT CS
                                       xxxx RF
                       Radical_SAM 150 vglp 153
                                       +g+p
  gi|330508415|ref|YP_004384843.1| 265 IGIP 268
                                       5555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.15
                                       HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  91 eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagi 142
                                        e++er++     ++++ +  + +e +++    +++  + le+  +lr+ g+
  gi|330508415|ref|YP_004384843.1| 280 QEMAERIVSID-PWIQVCVLDYRPE-FRRSDLVRPSHWKMLEVHYILRDCGL 329
                                       34444444444.5555555555555.44444444555666666666666665 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 !   52.4   0.3   2.2e-17   6.5e-14       6      98 ..     110     202 ..     104     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2.2e-17
                           Fer4_12   6 vrlslfvsgCnlsCkgCfnketwsfksgkeft.kelleeiiedlkkesiegltllGGEPllpenaeallelvkevke 81 
                                       + ++ f+sgCnl C+ C n     +++g+  t +e++e++ e  k+  +e + ++GGE  l  n++ l+++++ ++e
  gi|330508415|ref|YP_004384843.1| 110 IEAVCFTSGCNLCCPQCQNWRYAFMDAGELLTpEEAAERMTETKKQCGVERIAISGGECTL--NRPWLISFIRLLRE 184
                                       55789**************************945555555555555667************..************** PP

                           Fer4_12  82 ekp.ekdiwlytgytlee 98 
                                       ++p    ++ ++g++l e
  gi|330508415|ref|YP_004384843.1| 185 QNPiARIHVDTNGTILTE 202
                                       ***999*********987 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   1.9e-13   5.7e-10       4      80 ..       2      76 ..       1      78 [. 0.88

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.9e-13
                            Fer2_4  4 vtltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnvracstpvedGlkvetq 80
                                      +++++DG++++vp G +v +Al + g ++  +  + +   + c +g C  C  +++ge   +ac+ +v++G++++t 
  gi|330508415|ref|YP_004384843.1|  2 TSIEVDGRRIEVPSGFSVKEALEKLGYNITLHPSD-KGLFMPCQVGGCWACALKIDGEA-RPACTAQVQEGMRIRTA 76
                                      789************************99844443.334566999*************9.8**************96 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 !   38.7   0.3   3.1e-13   9.4e-10       5      92 ..     116     200 ..     113     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 3.1e-13
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                       +sgCnl C+ C n     +++g+  t e+  ++++++kk+    + + ++GGe     n + l+ +++ l+e+ p  
  gi|330508415|ref|YP_004384843.1| 116 TSGCNLCCPQCQNWRYAFMDAGELLTPEEAAERMTETKKQCG-VERIAISGGECT--LNRPWLISFIRLLREQNPIA 189
                                       6***********999888899999999999999966665554.566*******98..9******************* PP

                           Fer4_14  82 kiwletngtle 92 
                                       +i++ tngt+ 
  gi|330508415|ref|YP_004384843.1| 190 RIHVDTNGTIL 200
                                       ********986 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 !   17.8   0.1   8.3e-07    0.0025      51      80 ..      42      71 ..      10      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.3e-07
                            Fer2_3 51 sCregiCGscavainGkptlaCtatikdla 80
                                       C+ g C +ca++i+G+ + aCta++++  
  gi|330508415|ref|YP_004384843.1| 42 PCQVGGCWACALKIDGEARPACTAQVQEGM 71
                                      69************************9865 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.1e-06    0.0092       4      24 ..     225     246 ..     224     247 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.1e-06
                             UBA_4   4 iaqFqaiTGa.deekArqlLea 24 
                                       i++F++iTG  de  A+++L+ 
  gi|330508415|ref|YP_004384843.1| 225 ISTFMEITGLlDEGLATKYLQT 246
                                       99*******88*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2832.04
//
Query:       gi|330508416|ref|YP_004384844.1|  [L=91]
Description: hypothetical protein MCON_2611 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.072   12.5   0.1      0.091   12.2   0.1    1.1  1  SEO_C          Sieve element occlusion C-terminus
       0.15   12.2   0.0       0.33   11.1   0.0    1.6  1  Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix do


Domain annotation for each model (and alignments):
>> SEO_C  Sieve element occlusion C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     1e-05     0.091      46     100 ..       5      58 ..       2      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1e-05
                             SEO_C  46 ireftstakkvakaagiqlemvYvgksnkkekvrkiiktieeeklshvlkdltki 100
                                       i++f +++++ ak   + +em+Y  k ++k+ v +ii++ +++k+  + +  t+i
  gi|330508416|ref|YP_004384844.1|   5 IDTFMESVEERAKMQLLAIEMAYNIKIRNKDDVARIIAAKSRDKSDVL-MACTSI 58 
                                       7889999999999888999******************88777775544.466665 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.7e-05      0.33      24      46 ..      53      75 ..      43      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.7e-05
                                      --HHHHHHHHHSSS--HHHHHHH CS
                     Phage_CI_repr 24 iakssvstwvrRdffPgdvvvtc 46
                                      +a  s+stw+ R+ ++g+ v+ +
  gi|330508416|ref|YP_004384844.1| 53 MACTSISTWIARNGISGETVLPI 75
                                      56789*************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 670.96
//
Query:       gi|330508417|ref|YP_004384845.1|  [L=204]
Description: superoxide dismutase (Mn/Fe) [Methanosaeta concilii GP6]
Scores for complete 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-34  115.8   0.9    1.1e-33  115.5   0.2    1.5  2  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do
      1e-29  102.8   0.4    1.8e-29  102.0   0.4    1.4  1  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin
  ------ inclusion threshold ------
      0.033   14.5   2.6        2.5    8.5   0.7    2.4  2  FAM25     FAM25 family


Domain annotation for each model (and alignments):
>> Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.7   9.9e+03      61      75 ..      25      39 ..      16      44 .. 0.60
   2 !  115.5   0.2   1.8e-37   1.1e-33       1     102 []      96     198 ..      96     198 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.7
                                      TTCEEEEEE-SGGGT CS
                          Sod_Fe_C 61 eakplLalDvwehAY 75
                                      +a+ +L  D +  AY
  gi|330508417|ref|YP_004384845.1| 25 QAQLVLHHDKHHAAY 39
                                      445566666666665 PP

  == domain 2  score: 115.5 bits;  conditional E-value: 1.8e-37
                                       --HHHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTH CS
                          Sod_Fe_C   1 psgelaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYy 76 
                                       p+g+laea++++fgs+e+fkkef++aa++++gsGwa L +    ++  i+++++++ ++      l++lDvwehAYy
  gi|330508417|ref|YP_004384845.1|  96 PEGALAEALKKEFGSIERFKKEFTTAAVSTEGSGWAALSWCGMtGRPIIMQIEKHNVNVYPMFRILMVLDVWEHAYY 172
                                       899*************************************8764688899*****9999998999************ PP

                                       HHHTT-HHHHHHHHGGGBBHHHHHHH CS
                          Sod_Fe_C  77 ldyqnkradYieafwnvvnWkeveer 102
                                       ldy+n+ra+++eafwn+vnW+ev++r
  gi|330508417|ref|YP_004384845.1| 173 LDYKNERAKFVEAFWNIVNWDEVNRR 198
                                       ***********************986 PP

>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.4   3.1e-33   1.8e-29       1      82 []       6      87 ..       6      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 3.1e-33
                                      S------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCHHHHCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Sod_Fe_N  1 kyeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekleeakkkleelvlkklekalrnnagghvnHslfwk 79
                                      ky+LpeLpYa +aLePhi++ +l lHhdkHh++Yvn++N++le+l++a+++  ++++k++ k+l+++agghv+Hslfw 
  gi|330508417|ref|YP_004384845.1|  6 KYTLPELPYAGNALEPHITQAQLVLHHDKHHAAYVNGANAILERLDKARESGSDIDMKATLKELSFQAGGHVLHSLFWA 84
                                      6****************************************************************************** PP

                                      TB- CS
                          Sod_Fe_N 80 nls 82
                                      nl+
  gi|330508417|ref|YP_004384845.1| 85 NLA 87
                                      995 PP

>> FAM25  FAM25 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0038        23      19      38 ..      41      60 ..      27      79 .. 0.80
   2 ?    8.5   0.7   0.00042       2.5      16      46 ..      92     122 ..      89     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0038
                             FAM25 19 aGEKAiadalKkAqesgekv 38
                                       G  Ai + l kA+esg  +
  gi|330508417|ref|YP_004384845.1| 41 NGANAILERLDKARESGSDI 60
                                      5999************9754 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00042
                             FAM25  16 aKeaGEKAiadalKkAqesgekvvKevtekv 46 
                                       aK+  E A+a+alKk   s e+  Ke t   
  gi|330508417|ref|YP_004384845.1|  92 AKKEPEGALAEALKKEFGSIERFKKEFTTAA 122
                                       88999*********************88654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1577.10
//
Query:       gi|330508418|ref|YP_004384846.1|  [L=221]
Description: peroxiredoxin [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-30  105.9   0.0    1.8e-30  105.4   0.0    1.2  1  AhpC-TSA    AhpC/TSA family
    1.9e-13   50.0   1.1    3.5e-13   49.2   1.1    1.4  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
    2.4e-12   46.8   0.0    5.9e-12   45.5   0.0    1.6  2  Redoxin     Redoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0     3e-34   1.8e-30       1     123 [.      14     143 ..      14     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 3e-34
                                       TTSB----EEESTTCEEEECHHH.TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvslsdy.kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkf 76 
                                       +gdk+p++e+k+++ + v+l d  +gk++vlf +p+d++pvCtte  a++k+  +f+++++e+ig+svd++++h k+
  gi|330508418|ref|YP_004384846.1|  14 IGDKFPSMEVKTTH-GMVKLPDAySGKWLVLFSHPGDFTPVCTTEFVAFQKMRSDFDKLNCELIGLSVDQVFAHMKW 89 
                                       8**********999.889995555***************************************************** PP

                                       HHH-H.......SSEEEE-TTSHHHHHTT-EETT.TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  77 iekes......lnfpllsDeegkvakaygvlkee.kglalratfvidkegkiry 123
                                        + ++      ++fp+++D  gkva ++g++++     ++ra+f+id+e +ir 
  gi|330508418|ref|YP_004384846.1|  90 TQWIKenlkveITFPIIADDLGKVAMRLGMIHPGkGANTVRAVFIIDPEATIRL 143
                                       ***9999************************999666799************95 PP

>> 1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   1.1   5.8e-17   3.5e-13       1      33 [.     164     200 ..     164     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 5.8e-17
                                       HHHHHHHHT-BB-TTT.T.....BT-EEE---SSHHHH CS
                        1-cysPrx_C   1 ALQladkhgvatPAnWkp.....GdkvivpPpateeda 33 
                                       ALQ++dk++vatPAnW p     Gd vivpPpa+e+ a
  gi|330508418|ref|YP_004384846.1| 164 ALQVVDKNKVATPANW-PnndflGDQVIVPPPADEKAA 200
                                       9***************.99****************965 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   9.9e-16   5.9e-12       3     128 ..      15     142 ..      13     159 .. 0.84
   2 ?   -1.6   0.0      0.32   1.9e+03      70     102 ..     175     206 ..     159     210 .. 0.70

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 9.9e-16
                                       TSBB---ECCEETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH... CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf... 75 
                                       gdk+P+ +    +t    v+l + + gk +v+++ pg f+P+C++e ++++k    + + + + +++++d+      
  gi|330508418|ref|YP_004384846.1|  15 GDKFPSMEV---KTTHGMVKLPDaYSGKWLVLFSHPGDFTPVCTTEFVAFQKMRSDFDKLNCELIGLSVDQVFAhmk 88 
                                       99***9995...456667777777*****************************9999**********9998766566 PP

                                       HHHHHHH...TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEE CS
                           Redoxin  76 vkefwgk...eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvv 128
                                        ++++++    +++fp+++D  ++++  lG+     ++++   +++++id +  ++
  gi|330508418|ref|YP_004384846.1|  89 WTQWIKEnlkVEITFPIIADDLGKVAMRLGMI-HPGKGAN-TVRAVFIIDPEATIR 142
                                       5566666999777*****************66.3344444.9999****9887775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.32
                                       ESSSHHHHHHHHHTT-TSEEEE-TTSHHHHHTT CS
                           Redoxin  70 adndafvkefwgkeglkfpvlsDgsaaftkalG 102
                                       +  + + ++f+g++   +p  +D++aa  ++ G
  gi|330508418|ref|YP_004384846.1| 175 TPANWPNNDFLGDQV-IVPPPADEKAAAGRKTG 206
                                       444455666777655.78888999998888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1730.50
//
Query:       gi|330508419|ref|YP_004384847.1|  [L=162]
Description: Fur family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete 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-31  106.7   0.0      1e-30  106.3   0.0    1.1  1  FUR          Ferric uptake regulator family
  ------ inclusion threshold ------
      0.032   13.6   0.1      0.053   12.9   0.1    1.3  1  RepL         Firmicute plasmid replication protein (RepL)
      0.078   12.9   0.2       0.25   11.3   0.0    1.9  3  HTH_11       HTH domain
       0.11   12.4   0.4        1.3    9.0   0.1    2.2  2  Prok-RING_4  Prokaryotic RING finger family 4


Domain annotation for each model (and alignments):
>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.0   2.3e-34     1e-30       2     114 ..      18     129 ..      17     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 2.3e-34
                                       TTHCHHHHHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSSSE CS
                               FUR   2 aglklTkqRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelakkehh 78 
                                       +g+++T+qR +i +++ +++eh+sa++ y+e+k+++p++slaT+Y t+k+l++ gl++el++ ++++ry+ + +e h
  gi|330508419|ref|YP_004384847.1|  18 SGYRATPQRIAISRYILRNHEHPSAQKTYQEVKKTHPTVSLATIYTTIKILKKTGLICELNLPQSQTRYDPN-TEPH 93 
                                       79**********************************************************************.6*** PP

                                       EEEEETTT--EEEE--HHHHHHHHHHHHHTT-EEEE CS
                               FUR  79 dhlicekCgkviefkddeiekiqeeiaekegfklvs 114
                                       +hl+c +Cg+v++ +d+ ++k+ ++++ k +f+++ 
  gi|330508419|ref|YP_004384847.1|  94 AHLVCLQCGSVTDWMDPIMQKLVKNVSSKANFTVIG 129
                                       ********************************9875 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.2e-05     0.053      56     106 ..      25      75 ..      20      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                              RepL  56 kktrlvyylidnlnsnntliatnRelaee.tgislktvsetlkileeanilk 106
                                       ++  +  y++ n ++     +t  e+ +    +sl+t+ +t+kil++++++ 
  gi|330508419|ref|YP_004384847.1|  25 QRIAISRYILRNHEHPS-AQKTYQEVKKThPTVSLATIYTTIKILKKTGLIC 75 
                                       67778889999977654.457778876641479***************9985 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.1   4.7e+03       6      15 ..      12      21 ..       9      31 .. 0.51
   2 ?   -3.0   0.0       1.7   7.4e+03      23      34 ..      25      36 ..      24      37 .. 0.67
   3 ?   11.3   0.0   5.7e-05      0.25      27      44 ..      56      73 ..      53      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                            HTH_11  6 lelLleargp 15
                                      ++ ++++   
  gi|330508419|ref|YP_004384847.1| 12 IKTFRNSGYR 21
                                      4444333333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                            HTH_11 23 eeLnvSrrtvrr 34
                                      +++ +Sr   r+
  gi|330508419|ref|YP_004384847.1| 25 QRIAISRYILRN 36
                                      567778766666 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 5.7e-05
                            HTH_11 27 vSrrtvrrdIkaLeelgv 44
                                      vS +t++  Ik+L+++g+
  gi|330508419|ref|YP_004384847.1| 56 VSLATIYTTIKILKKTGL 73
                                      899*************94 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 ?    9.0   0.1   0.00028       1.3      10      26 ..      87     103 ..      73     116 .. 0.80
   2 ?    1.3   0.0     0.073   3.3e+02       1      10 [.     138     147 ..     132     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00028
                       Prok-RING_4  10 kailepCgHlvCkeCfd 26 
                                       ++  ep +HlvC +C +
  gi|330508419|ref|YP_004384847.1|  87 DPNTEPHAHLVCLQCGS 103
                                       6667899********65 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.073
                       Prok-RING_4   1 CvlCgeqekk 10 
                                       C lCg++ k+
  gi|330508419|ref|YP_004384847.1| 138 CALCGRRAKD 147
                                       6777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1227.81
//
Query:       gi|330508420|ref|YP_004384848.1|  [L=276]
Description: HtpX protease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-36  125.5   0.0    3.3e-36  124.9   0.0    1.3  1  Peptidase_M48  Peptidase family M48
    0.00054   19.2   0.0    0.00094   18.5   0.0    1.3  1  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
       0.18   12.3   0.0       0.41   11.2   0.0    1.6  1  OsmC           OsmC-like protein


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 !  124.9   0.0   5.5e-40   3.3e-36       3     195 ..      66     276 .]      64     276 .] 0.84

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 5.5e-40
                                       -SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   3 reaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhr 78 
                                       +++el  +ve+la++agl  p++++y+v++p  NAFa+g+  ++  +++t+g+  + l+++ela+V++HEl+H+ +r
  gi|330508420|ref|YP_004384848.1|  66 EAPELFGMVENLAANAGL--PMPRLYIVDNPMPNAFATGRDPKHaAVAVTTGIT-RILNRDELAGVISHELAHVRNR 139
                                       56788889**********..********************98888*********.********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH.....HTT-SHHHHHTT--S---HHHHHHHHHHTTHHHHHHHHHHHHHHHHTTT. CS
                                       xxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  79 hsvvslivsllasillllglal.....lisraeedaagafldalavliglliillflalSRkrEyqADeagvellkr 150
                                       ++++s+i ++la ++ +++ ++     +++  ++  +   + a a+l+ l   +++la+SR rE++AD+ g+++  +
  gi|330508420|ref|YP_004384848.1| 140 DTLISTIAATLAGVITFMANMAqwsliFGGGDDDGPNPLGVLAMAILAPLAATIVQLAISRGREFEADAGGAKISGK 216
                                       *****************9986522111222333333344456777777788888888******************** PP

                                       HHHHHHHHHHHHHHTT--S---HHHH...............HHS-SS--HHHHHHHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 151 akdlvraliklakdlerqdvsaslrs...............ellstHPplleRiqalkel 195
                                       +  l++al+kl ++++ +  +  + +                l+stHP+++eRi++l+++
  gi|330508420|ref|YP_004384848.1| 217 PLSLASALAKLESGNNAVRSDVNPSTahmfivnplkgkavaSLFSTHPSTEERIARLRSM 276
                                       *************9999555544444557777777777777****************986 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.6e-07   0.00094     184     222 ..     113     151 ..     104     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.6e-07
                     Peptidase_M56 184 PadflkklsdeeleyillHElaHlkrkDllvnllvavlq 222
                                        + +++ l+ +el+ ++ HElaH++++D+l+  ++a l 
  gi|330508420|ref|YP_004384848.1| 113 TTGITRILNRDELAGVISHELAHVRNRDTLISTIAATLA 151
                                       5567788999**********************9998775 PP

>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.8e-05      0.41       1      35 [.     170     204 ..     169     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.8e-05
                                       TTXSSB-HHHHHHHHHHHHHHHHHHHHTCCCT--- CS
                              OsmC   1 gdgsgpsPeelllaalasCfaitlravakkkgikl 35 
                                       gd++gp+P   l++a+ + +a+t+  +a  +g ++
  gi|330508420|ref|YP_004384848.1| 170 GDDDGPNPLGVLAMAILAPLAATIVQLAISRGREF 204
                                       7889************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2048.19
//
Query:       gi|330508421|ref|YP_004384849.1|  [L=235]
Description: rhomboid family protein [Methanosaeta concilii GP6]
Scores for complete sequence (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  125.9  16.3    1.3e-36  125.9  16.3    1.9  2  Rhomboid  Rhomboid family
    0.00072   20.1   3.5     0.0065   17.0   0.0    3.0  3  DUF1751   Eukaryotic integral membrane protein (DUF1751)


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.049   4.4e+02     102     123 ..      15      36 ..       1      54 [. 0.75
   2 !  125.9  16.3   1.4e-40   1.3e-36       8     145 ..      72     223 ..      68     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.049
                                       HC...CCCCCCCCCCHHHCTSS CS
                          Rhomboid 102 iallllllfillnlvlgllpra 123
                                       +++++ ++++++n+++ +++ +
  gi|330508421|ref|YP_004384849.1|  15 SFPIVTAVIVAINVLFFIYEIY 36 
                                       3477889999999999988765 PP

  == domain 2  score: 125.9 bits;  conditional E-value: 1.4e-40
                                       THHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S...-EESSHHHHHHHHH CS
                          Rhomboid   8 wrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaesesplvGaSGaifgllg 84 
                                        +++tsmf+Hag+lH+l Nm++l vfG ++e+ lG   +l++yll+gla+s++++++++ s  p vGaSGai+g+l+
  gi|330508421|ref|YP_004384849.1|  72 STFFTSMFIHAGILHILSNMVFLAVFGDNVEDLLGPIPYLIFYLLCGLAASAAQIAADPSSIIPNVGASGAISGVLA 148
                                       589**********************************************************99************** PP

                                       HHHHHHHCCCCGS----HC............CCCCCCCCCCHHHCTSS.....STTTHHHHHHHHHHHHHHHHHH CS
                          Rhomboid  85 allvlvprnrkllrkliia.........llllllfillnlvlgllpra.....ggvsnlAHlgGllaGlllglll 145
                                        +lvl p+   +l+ ++++         ll++ ++++++l+ g+ +       ggv+++AH+gG++aGlll++  
  gi|330508421|ref|YP_004384849.1| 149 GYLVLLPTGTVRLFIFFGFfyritkipaLLFITVWFVIQLFSGVASLGavaegGGVAYWAHIGGFIAGLLLAFAY 223
                                       ******************9*************************99999**********************9875 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2     0.037   3.3e+02      10      35 ..      17      42 ..       9      53 .. 0.63
   2 !   17.0   0.0   7.3e-07    0.0065       9      59 ..      72     122 ..      65     130 .. 0.89
   3 ?   -0.3   0.3      0.18   1.6e+03      49      72 ..     163     186 ..     156     221 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.037
                           DUF1751 10 tlltasfveqnvwkvlvslltlllgg 35
                                       ++ta  v +nv+ ++ ++ +l+  g
  gi|330508421|ref|YP_004384849.1| 17 PIVTAVIVAINVLFFIYEIYILITDG 42
                                      35555555555555555555555444 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 7.3e-07
                           DUF1751   9 wtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitn 59 
                                        t++t++f+ + ++++l +++ l+++g  +E l g   +l+F l+ +++++
  gi|330508421|ref|YP_004384849.1|  72 STFFTSMFIHAGILHILSNMVFLAVFGDNVEDLLGPIPYLIFYLLCGLAAS 122
                                       589*****************************************9988766 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.18
                           DUF1751  49 kFilvvnvitnllvvlltlllylv 72 
                                       +F+ +   it++ ++l+ ++ +++
  gi|330508421|ref|YP_004384849.1| 163 IFFGFFYRITKIPALLFITVWFVI 186
                                       555555555555444444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); 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:                         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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1679.98
//
Query:       gi|330508422|ref|YP_004384850.1|  [L=208]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-44  146.5   5.2    1.7e-09   37.1   0.0    5.2  5  TPR_1            Tetratricopeptide repeat
    3.7e-38  126.6   5.8    1.5e-07   31.0   0.0    5.3  5  TPR_2            Tetratricopeptide repeat
      2e-36  124.4  11.9    3.5e-15   56.4   0.5    3.7  5  TPR_16           Tetratricopeptide repeat
    2.9e-33  113.3  10.3    1.8e-08   33.9   0.0    5.5  6  TPR_11           TPR repeat
    3.8e-30  101.6   2.7    1.1e-06   28.3   0.0    5.9  6  TPR_8            Tetratricopeptide repeat
    1.5e-22   79.9  15.2    2.9e-10   40.5   0.7    3.4  4  TPR_19           Tetratricopeptide repeat
    1.9e-21   74.9   9.2    2.2e-05   24.9   0.3    5.2  5  TPR_14           Tetratricopeptide repeat
      8e-20   70.9   7.4    1.6e-08   34.7   0.7    4.4  3  TPR_12           Tetratricopeptide repeat
    1.1e-18   66.2   7.1    1.2e-05   25.3   0.0    5.9  6  TPR_17           Tetratricopeptide repeat
    5.8e-17   61.6   8.2    3.2e-06   27.2   0.3    4.7  5  TPR_9            Tetratricopeptide repeat
    4.9e-15   55.1   2.2     0.0035   17.9   0.1    5.3  5  TPR_6            Tetratricopeptide repeat
    2.6e-13   49.2   1.4       0.15   12.8   0.2    4.7  4  TPR_4            Tetratricopeptide repeat
    1.6e-11   44.3   1.2    7.4e-08   32.5   0.1    3.0  3  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    1.1e-09   37.9  12.1       0.11   12.4   0.1    5.6  6  TPR_10           Tetratricopeptide repeat
    1.2e-07   31.2   7.9       0.25   11.5   0.0    5.5  5  TPR_7            Tetratricopeptide repeat
    3.9e-06   26.8   3.1     0.0046   17.0   0.0    4.4  5  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    8.5e-06   26.3   1.2      0.017   15.6   0.0    3.1  4  BTAD             Bacterial transcriptional activator domain
    1.4e-05   25.2   2.0        2.7    8.1   0.0    4.5  5  DUF3856          Domain of Unknown Function (DUF3856)
    2.4e-05   24.3   0.0    8.1e-05   22.6   0.0    1.8  2  SRP_TPR_like     Putative TPR-like repeat
    6.4e-05   22.9   2.6        3.6    7.7   0.2    4.2  3  TPR_3            Tetratricopeptide repeat
    8.2e-05   22.9   0.3        2.1    8.7   0.0    3.4  3  TPR_20           Tetratricopeptide repeat
     0.0006   19.1   1.9      0.012   14.9   0.2    2.1  2  TPR_15           Tetratricopeptide repeat
     0.0066   15.4   1.0        2.3    7.0   0.0    2.9  3  NARP1            NMDA receptor-regulated protein 1
  ------ inclusion threshold ------
       0.02   15.3   0.3        1.7    9.1   0.0    2.1  2  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
      0.023   14.5   0.4        9.7    6.1   0.0    3.5  4  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
      0.028   13.4   0.0       0.97    8.4   0.0    2.1  2  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
      0.036   13.8   2.2          5    6.8   0.1    2.4  2  TPR_21           Tetratricopeptide repeat-like domain
      0.058   13.2   0.2         15    5.5   0.0    3.0  3  PPTA             Protein prenyltransferase alpha subunit repe
        0.5   10.3   3.4        4.7    7.1   0.5    3.0  3  Wzy_C_2          Virulence factor membrane-bound polymerase, 


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   6.5e-06     0.004       4      26 ..      24      46 ..      22      53 .. 0.89
   2 !   37.1   0.0   2.8e-12   1.7e-09       1      34 []      55      88 ..      55      88 .. 0.97
   3 !   26.9   0.0   4.6e-09   2.8e-06       2      23 ..      90     111 ..      89     119 .. 0.94
   4 !   35.5   0.0   8.5e-12   5.3e-09       1      33 [.     123     155 ..     123     156 .. 0.97
   5 !   28.6   0.0   1.3e-09   8.1e-07       1      33 [.     157     189 ..     157     190 .. 0.97

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.5e-06
                                      HHHHHHHHHHTT-HHHHHHHHHH CS
                             TPR_1  4 lynlGnayfklgkydeAleyyek 26
                                      +yn+G  + ++g+ydeA++ +++
  gi|330508422|ref|YP_004384850.1| 24 CYNKGIDLAEQGRYDEAIAEFDR 46
                                      8*****************97777 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 2.8e-12
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a+a+yn+G+a+ ++gky+eAl +++++  ++P+n
  gi|330508422|ref|YP_004384850.1| 55 ARAWYNKGVALTQQGKYEEALIAFDRVTDIEPQN 88
                                      89******************************97 PP

  == domain 3  score: 26.9 bits;  conditional E-value: 4.6e-09
                                       HHHHHHHHHHHHTT-HHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAley 23 
                                       +a+yn+G++++ lg+y+eAle+
  gi|330508422|ref|YP_004384850.1|  90 QAWYNRGVVLYILGRYEEALEA 111
                                       79******************97 PP

  == domain 4  score: 35.5 bits;  conditional E-value: 8.5e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+a+ n Gn++f+l+++++A+++y++A+ ++P+
  gi|330508422|ref|YP_004384850.1| 123 ARAWINEGNVLFQLNRHEQAVAAYDRAIGIDPH 155
                                       89******************************7 PP

  == domain 5  score: 28.6 bits;  conditional E-value: 1.3e-09
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+a++n+ n + +  +yd Al   +kA++++P+
  gi|330508422|ref|YP_004384850.1| 157 AQAWCNRCNSLINRSEYDLALSSAQKAIQIDPD 189
                                       79******************************8 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.1e-07   6.7e-05       3      34 .]      23      54 ..      21      54 .. 0.93
   2 !   31.0   0.0   2.4e-10   1.5e-07       1      34 []      55      88 ..      55      88 .. 0.97
   3 !   24.0   0.0   4.2e-08   2.6e-05       2      23 ..      90     111 ..      89     122 .. 0.85
   4 !   27.5   0.0   3.1e-09   1.9e-06       1      33 [.     123     155 ..     123     156 .. 0.96
   5 !   20.7   0.0   4.9e-07    0.0003       1      33 [.     157     189 ..     157     190 .. 0.97

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.1e-07
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                                       +yn G  ++++g+y+eA++ f++ ++ +P++
  gi|330508422|ref|YP_004384850.1| 23 SCYNKGIDLAEQGRYDEAIAEFDRYIQDYPDY 54
                                      58*************************99985 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 2.4e-10
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      a+a+yn G a+ ++g+yeeAl af+++  ++P+n
  gi|330508422|ref|YP_004384850.1| 55 ARAWYNKGVALTQQGKYEEALIAFDRVTDIEPQN 88
                                      78******************************97 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 4.2e-08
                             TPR_2   2 ealynlGlayyklgdyeeAlea 23 
                                       +a+yn+G ++y lg+yeeAlea
  gi|330508422|ref|YP_004384850.1|  90 QAWYNRGVVLYILGRYEEALEA 111
                                       69******************98 PP

  == domain 4  score: 27.5 bits;  conditional E-value: 3.1e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+a+ n G+++++l+++e+A++a+++A+ +dP+
  gi|330508422|ref|YP_004384850.1| 123 ARAWINEGNVLFQLNRHEQAVAAYDRAIGIDPH 155
                                       78***************************9997 PP

  == domain 5  score: 20.7 bits;  conditional E-value: 4.9e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+a++n+ ++++++ +y+ Al   +kA+++dP+
  gi|330508422|ref|YP_004384850.1| 157 AQAWCNRCNSLINRSEYDLALSSAQKAIQIDPD 189
                                       789*****************************7 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.5   5.7e-18   3.5e-15       1      67 [.      25      88 ..      25      89 .. 0.94
   2 !   37.2   0.2   5.4e-12   3.3e-09       9      55 ..      67     111 ..      67     116 .. 0.93
   3 !   23.1   0.2   1.3e-07   8.3e-05      32      67 ..     121     156 ..     118     159 .. 0.93
   4 !   31.3   0.0   3.8e-10   2.3e-07       2      66 ..     128     189 ..     127     191 .. 0.96
   5 ?    6.7   0.0     0.019        12       5      37 ..     165     194 ..     161     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 5.7e-18
                            TPR_16  1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                                      ++++ +++++g+yd+A+a +++++ ++   Pd a+A++++g+a+ +qg ++eA+ ++++  +  p++
  gi|330508422|ref|YP_004384850.1| 25 YNKGIDLAEQGRYDEAIAEFDRYIQDY---PDYARAWYNKGVALTQQGKYEEALIAFDRVTDIEPQN 88
                                      7899***********************...************************9999988877776 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 5.4e-12
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.a 55 
                                       ++g+y++A+ a++++++     P++ +A++++g++++ +gr++eA+ a
  gi|330508422|ref|YP_004384850.1|  67 QQGKYEEALIAFDRVTDIE---PQNSQAWYNRGVVLYILGRYEEALeA 111
                                       79*****************...***********************955 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 1.3e-07
                            TPR_16  32 daaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++a+A+ + g+++++++r++ A+a+y++a++ +p +
  gi|330508422|ref|YP_004384850.1| 121 EDARAWINEGNVLFQLNRHEQAVAAYDRAIGIDPHS 156
                                       689*****************************9987 PP

  == domain 4  score: 31.3 bits;  conditional E-value: 3.8e-10
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++++ ++++++ ++A+aa+++a+  d   P  a+A+ ++ +++  ++++++A+   ++a++ +pd
  gi|330508422|ref|YP_004384850.1| 128 NEGNVLFQLNRHEQAVAAYDRAIGID---PHSAQAWCNRCNSLINRSEYDLALSSAQKAIQIDPD 189
                                       689***********************...************************999999999998 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.019
                            TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAl 37 
                                       ++++++ +yd A+  ++ a+  d   Pd +eA+
  gi|330508422|ref|YP_004384850.1| 165 NSLINRSEYDLALSSAQKAIQID---PDMVEAY 194
                                       67899999***************...9988887 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.4   1.5e+03      13      23 ..      21      31 ..      19      33 .. 0.80
   2 !   30.8   1.4   2.7e-10   1.7e-07       4      42 .]      31      69 ..      28      69 .. 0.96
   3 !   33.9   0.0     3e-11   1.8e-08       3      42 .]      64     103 ..      62     103 .. 0.93
   4 !   10.6   0.0   0.00055      0.34       3      31 ..      98     126 ..      96     129 .. 0.81
   5 !   33.8   0.0   3.3e-11     2e-08       1      34 [.     130     163 ..     130     169 .. 0.96
   6 !   17.4   0.0   4.2e-06    0.0026       6      42 .]     169     205 ..     165     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.4
                            TPR_11 13 AieaYkkAlkl 23
                                       i +Y+k ++l
  gi|330508422|ref|YP_004384850.1| 21 GISCYNKGIDL 31
                                      5889***9987 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 2.7e-10
                            TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      + eqG+y+eAi+++ + ++  Pd+a+a+yn G+a+ +qG
  gi|330508422|ref|YP_004384850.1| 31 LAEQGRYDEAIAEFDRYIQDYPDYARAWYNKGVALTQQG 69
                                      679*********************************999 PP

  == domain 3  score: 33.9 bits;  conditional E-value: 3e-11
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       a+++qGkyeeA+ a+ +  ++ P+n  a+yn+G+++y +G
  gi|330508422|ref|YP_004384850.1|  64 ALTQQGKYEEALIAFDRVTDIEPQNSQAWYNRGVVLYILG 103
                                       899*********************************9665 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00055
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeay 31 
                                       ++y +G+yeeA+ea ++   l+ ++a+a+
  gi|330508422|ref|YP_004384850.1|  98 VLYILGRYEEALEASNRSTMLNGEDARAW 126
                                       79***********9888877777777776 PP

  == domain 5  score: 33.8 bits;  conditional E-value: 3.3e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynL 34 
                                       G++++++++ e+A++aY +A+ +dP +a a++n+
  gi|330508422|ref|YP_004384850.1| 130 GNVLFQLNRHEQAVAAYDRAIGIDPHSAQAWCNR 163
                                       9*******************************97 PP

  == domain 6  score: 17.4 bits;  conditional E-value: 4.2e-06
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                        + +y+ A+ + +kA+++dPd +eay+++ +a++++G
  gi|330508422|ref|YP_004384850.1| 169 NRSEYDLALSSAQKAIQIDPDMVEAYSCREAALMELG 205
                                       577899999999***************9988888776 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.17   1.1e+02      18      32 ..      19      33 ..      17      34 .. 0.88
   2 !    9.4   0.1    0.0021       1.3       4      28 ..      24      48 ..      22      53 .. 0.86
   3 !   27.8   0.0   2.7e-09   1.7e-06       1      34 []      55      88 ..      55      88 .. 0.97
   4 !   18.6   0.0   2.4e-06    0.0015       2      31 ..      90     119 ..      89     122 .. 0.90
   5 !   28.3   0.0   1.8e-09   1.1e-06       1      33 [.     123     155 ..     123     156 .. 0.96
   6 !   11.8   0.0   0.00037      0.23       1      33 [.     157     189 ..     157     190 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.17
                                      HHHHHHHHHHHHHHH CS
                             TPR_8 18 eeAkeyyekaleldp 32
                                      ee +++y+k ++l++
  gi|330508422|ref|YP_004384850.1| 19 EEGISCYNKGIDLAE 33
                                      899*********987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0021
                                      HHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8  4 yynlgsiylklgdyeeAkeyyekal 28
                                      +yn+g  + ++g+y+eA++ + +++
  gi|330508422|ref|YP_004384850.1| 24 CYNKGIDLAEQGRYDEAIAEFDRYI 48
                                      7888877889***********9987 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 2.7e-09
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      a+a+yn+g ++ ++g+yeeA  ++ ++++++p+n
  gi|330508422|ref|YP_004384850.1| 55 ARAWYNKGVALTQQGKYEEALIAFDRVTDIEPQN 88
                                      79******************************86 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 2.4e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                       +a+yn g ++  lg+yeeA e+ ++ + l+
  gi|330508422|ref|YP_004384850.1|  90 QAWYNRGVVLYILGRYEEALEASNRSTMLN 119
                                       89********************99988887 PP

  == domain 5  score: 28.3 bits;  conditional E-value: 1.8e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+a+ n g+++++l+++e+A+++y +a+ +dp 
  gi|330508422|ref|YP_004384850.1| 123 ARAWINEGNVLFQLNRHEQAVAAYDRAIGIDPH 155
                                       79*****************************95 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 0.00037
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+a++n  + +++  +y+ A ++ +ka+++dpd
  gi|330508422|ref|YP_004384850.1| 157 AQAWCNRCNSLINRSEYDLALSSAQKAIQIDPD 189
                                       68999999999*********************8 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.7   4.8e-13   2.9e-10       1      62 [.      31      92 ..      31      93 .. 0.96
   2 !   28.2   0.1   3.3e-09   2.1e-06       2      62 ..      66     126 ..      65     127 .. 0.94
   3 !   20.5   0.3   8.1e-07    0.0005       4      61 ..     102     159 ..      99     161 .. 0.91
   4 !   19.0   0.3   2.4e-06    0.0015       2      57 ..     134     189 ..     127     202 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 4.8e-13
                            TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62
                                      l ++g+y+eA+a + + +q++p++a+a+++   al ++g ++eA  + d++ + +p++++++
  gi|330508422|ref|YP_004384850.1| 31 LAEQGRYDEAIAEFDRYIQDYPDYARAWYNKGVALTQQGKYEEALIAFDRVTDIEPQNSQAW 92
                                      679******************************************************98875 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 3.3e-09
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                        ++g+y+eAl ++ ++ + +p+n+ a+++   +l+ lg+++eA ++ ++    +  dar++
  gi|330508422|ref|YP_004384850.1|  66 TQQGKYEEALIAFDRVTDIEPQNSQAWYNRGVVLYILGRYEEALEASNRSTMLNGEDARAW 126
                                       69*******************************************9999999999888865 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 8.1e-07
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                        g+y+eAl++  +    + ++a+a+++  ++l++l++ ++A a+ d++   dp +a++
  gi|330508422|ref|YP_004384850.1| 102 LGRYEEALEASNRSTMLNGEDARAWINEGNVLFQLNRHEQAVAAYDRAIGIDPHSAQA 159
                                       59999999999999999*******************************9999997765 PP

  == domain 4  score: 19.0 bits;  conditional E-value: 2.4e-06
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       ++ +++++A+a++ +a+  dp++a a+ + ++ l++  ++d A    +++ + dpd
  gi|330508422|ref|YP_004384850.1| 134 FQLNRHEQAVAAYDRAIGIDPHSAQAWCNRCNSLINRSEYDLALSSAQKAIQIDPD 189
                                       66789*****************************************9999999999 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.3   3.5e-08   2.2e-05      11      42 ..      31      62 ..      27      64 .. 0.91
   2 !   18.7   0.0   3.4e-06    0.0021       3      41 ..      57      95 ..      56      97 .. 0.93
   3 !   15.7   0.1   3.1e-05     0.019       2      39 ..      90     127 ..      89     130 .. 0.95
   4 !   18.3   0.1   4.6e-06    0.0028       8      39 ..     130     161 ..     129     164 .. 0.93
   5 !    8.1   0.0    0.0088       5.5      11      38 ..     167     194 ..     163     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.5e-08
                            TPR_14 11 llalGdpdeAiallrralalaPddaeawllla 42
                                      l+++G++deAia ++r+++++Pd a+aw+  +
  gi|330508422|ref|YP_004384850.1| 31 LAEQGRYDEAIAEFDRYIQDYPDYARAWYNKG 62
                                      789*************************9765 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 3.4e-06
                            TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawlll 41
                                      a++  + al ++G+++eA+ +++r+ +  P++ +aw+  
  gi|330508422|ref|YP_004384850.1| 57 AWYNKGVALTQQGKYEEALIAFDRVTDIEPQNSQAWYNR 95
                                      8999999*****************************865 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 3.1e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +a++ ++ +l+ lG+++eA+++ +r   l+ +da+aw+
  gi|330508422|ref|YP_004384850.1|  90 QAWYNRGVVLYILGRYEEALEASNRSTMLNGEDARAWI 127
                                       69***********************************7 PP

  == domain 4  score: 18.3 bits;  conditional E-value: 4.6e-06
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawl 39 
                                       + +l++l ++++A+a+++ra+  +P +a+aw 
  gi|330508422|ref|YP_004384850.1| 130 GNVLFQLNRHEQAVAAYDRAIGIDPHSAQAWC 161
                                       5799**************************95 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0088
                            TPR_14  11 llalGdpdeAiallrralalaPddaeaw 38 
                                       l ++ ++d A+  +++a++ +Pd  ea+
  gi|330508422|ref|YP_004384850.1| 167 LINRSEYDLALSSAQKAIQIDPDMVEAY 194
                                       677889******************9997 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.3     7e-10   4.3e-07       8      74 ..      26      84 ..      21      87 .. 0.89
   2 !   34.7   0.7   2.7e-11   1.6e-08       4      74 ..      90     152 ..      87     154 .. 0.89
   3 ?    5.5   0.0     0.035        22       3      32 ..     157     186 ..     155     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 7e-10
                            TPR_12  8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74
                                      n +  l+++grydeA++ +++ ++        d+p++a++ +n g ++ ++g+yeeAl ++ ++++i
  gi|330508422|ref|YP_004384850.1| 26 NKGIDLAEQGRYDEAIAEFDRYIQ--------DYPDYARAWYNKGVALTQQGKYEEALIAFDRVTDI 84
                                      88999****************944........45557*************************99887 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 2.7e-11
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +a++n+++vl+ lgry+eAle  +++    + l G+     a++ +n g ++++l+r+e+A++++ +a+ i
  gi|330508422|ref|YP_004384850.1|  90 QAWYNRGVVLYILGRYEEALEASNRS----TMLNGE----DARAWINEGNVLFQLNRHEQAVAAYDRAIGI 152
                                       6899**********************....456555....49*************************9866 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.035
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                       a+a+ n+ + l  + +yd Al+  +ka++i
  gi|330508422|ref|YP_004384850.1| 157 AQAWCNRCNSLINRSEYDLALSSAQKAIQI 186
                                       7789999999999999*********99987 PP

>> TPR_17  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   9.1e+02      23      33 ..      31      41 ..      24      42 .. 0.80
   2 !   21.6   0.1   2.9e-07   0.00018       2      33 ..      44      75 ..      43      76 .. 0.93
   3 !   25.3   0.0     2e-08   1.2e-05       2      34 .]      78     110 ..      77     110 .. 0.94
   4 ?    4.5   0.1     0.087        54      10      33 ..     120     143 ..     118     144 .. 0.89
   5 !    9.5   0.1    0.0021       1.3       1      32 [.     145     176 ..     145     178 .. 0.86
   6 ?    3.1   0.0      0.25   1.5e+02       3      16 ..     181     194 ..     180     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.5
                            TPR_17 23 llknGdlmtAr 33
                                      l+++G++++A+
  gi|330508422|ref|YP_004384850.1| 31 LAEQGRYDEAI 41
                                      78999**9998 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2.9e-07
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      + + ++ +P++a a++n++++l ++G++++A+
  gi|330508422|ref|YP_004384850.1| 44 FDRYIQDYPDYARAWYNKGVALTQQGKYEEAL 75
                                      7789999***********************96 PP

  == domain 3  score: 25.3 bits;  conditional E-value: 2e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + ++ +++P n+ a++n++++l+ +G++++A++
  gi|330508422|ref|YP_004384850.1|  78 FDRVTDIEPQNSQAWYNRGVVLYILGRYEEALE 110
                                       789999*************************85 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.087
                            TPR_17  10 PnnadaynnLAelllknGdlmtAr 33 
                                         +a a+ n +++l +++++++A+
  gi|330508422|ref|YP_004384850.1| 120 GEDARAWINEGNVLFQLNRHEQAV 143
                                       5799*****************996 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0021
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y +a+ +dP +a a++n+ + l ++ +++ A
  gi|330508422|ref|YP_004384850.1| 145 AYDRAIGIDPHSAQAWCNRCNSLINRSEYDLA 176
                                       59****************98888887777776 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.25
                            TPR_17   3 lkaleldPnnaday 16 
                                       +ka+++dP+ ++ay
  gi|330508422|ref|YP_004384850.1| 181 QKAIQIDPDMVEAY 194
                                       8*******988887 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.4   0.00048       0.3      35      62 ..      27      54 ..      24      57 .. 0.86
   2 !   26.3   0.6   9.9e-09   6.1e-06       6      65 ..      32      91 ..      31      91 .. 0.95
   3 !   25.5   0.1   1.8e-08   1.1e-05       5      50 ..      65     110 ..      61     111 .. 0.93
   4 !   27.2   0.3   5.2e-09   3.2e-06      10      65 ..     104     159 ..     102     161 .. 0.96
   5 ?    5.6   0.0     0.028        17       5      42 ..     167     204 ..     165     208 .] 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00048
                             TPR_9 35 RGlllaqlGclsaAladLeaylalapda 62
                                       G+ la++G++ +A+a++++y++  pd 
  gi|330508422|ref|YP_004384850.1| 27 KGIDLAEQGRYDEAIAEFDRYIQDYPDY 54
                                      677799*****************99985 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 9.9e-09
                             TPR_9  6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                                      +++ ++++a+a  +r ++  Pd ++ ++  G++l q+G +++Al ++++  +++p++ +a
  gi|330508422|ref|YP_004384850.1| 32 AEQGRYDEAIAEFDRYIQDYPDYARAWYNKGVALTQQGKYEEALIAFDRVTDIEPQNSQA 91
                                      67889**************************************************99876 PP

  == domain 3  score: 25.5 bits;  conditional E-value: 1.8e-08
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAla 50 
                                       + ++ ++e+al + +r+  + P+  + ++ RG++l+ lG++++Al+
  gi|330508422|ref|YP_004384850.1|  65 LTQQGKYEEALIAFDRVTDIEPQNSQAWYNRGVVLYILGRYEEALE 110
                                       47999***************************************97 PP

  == domain 4  score: 27.2 bits;  conditional E-value: 5.2e-09
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       ++e+al++++r  +l+ +d++ +   G +l+ql++ ++A+a+ ++++ ++p+ ++a
  gi|330508422|ref|YP_004384850.1| 104 RYEEALEASNRSTMLNGEDARAWINEGNVLFQLNRHEQAVAAYDRAIGIDPHSAQA 159
                                       799************************************************99887 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.028
                             TPR_9   5 aireedweralavverllllaPddpeer..rdRGlllaql 42 
                                       +i++ +++ al  ++  ++++Pd +e +  r+ +l++  l
  gi|330508422|ref|YP_004384850.1| 167 LINRSEYDLALSSAQKAIQIDPDMVEAYscREAALME--L 204
                                       79999******************98776225555544..4 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   5.7e-06    0.0035      10      32 ..      31      53 ..      23      54 .. 0.85
   2 !   14.7   0.0     6e-05     0.037       2      32 ..      57      87 ..      56      88 .. 0.94
   3 ?    5.6   0.1     0.048        29       1      22 [.      90     111 ..      90     114 .. 0.77
   4 !    9.9   0.0    0.0019       1.2       7      33 .]     130     156 ..     124     156 .. 0.86
   5 ?    2.4   0.0       0.5   3.1e+02      14      32 ..     171     189 ..     159     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.7e-06
                                      HHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6 10 yrklgdtdkAlealerlikeYPd 32
                                      + ++g++d+A++ ++r i++YPd
  gi|330508422|ref|YP_004384850.1| 31 LAEQGRYDEAIAEFDRYIQDYPD 53
                                      56789*****************9 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  2 AlyklalsyrklgdtdkAlealerlikeYPd 32
                                      A y+ + ++ ++g++++Al a++r+ +  P+
  gi|330508422|ref|YP_004384850.1| 57 AWYNKGVALTQQGKYEEALIAFDRVTDIEPQ 87
                                      89************************99887 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.048
                                       HHHHHHH.HHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlykla.lsyrklgdtdkAlea 22 
                                       +A y+++  +y+ lg++++Alea
  gi|330508422|ref|YP_004384850.1|  90 QAWYNRGvVLYI-LGRYEEALEA 111
                                       699****55555.55******97 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPdS 33 
                                       +  +++l+++++A++a++r i   P S
  gi|330508422|ref|YP_004384850.1| 130 GNVLFQLNRHEQAVAAYDRAIGIDPHS 156
                                       66788999************9988876 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHHHHHHH-TT CS
                             TPR_6  14 gdtdkAlealerlikeYPd 32 
                                        ++d Al   ++ i+  Pd
  gi|330508422|ref|YP_004384850.1| 171 SEYDLALSSAQKAIQIDPD 189
                                       48999**********9997 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0    0.0011       0.7       4      26 .]      24      46 ..      22      46 .. 0.85
   2 !    9.4   0.0     0.003       1.9       1      21 [.      55      75 ..      55      80 .. 0.93
   3 !   11.9   0.0   0.00046      0.28       2      22 ..      90     110 ..      89     114 .. 0.91
   4 !   12.8   0.2   0.00024      0.15       1      26 []     123     148 ..     123     148 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0011
                             TPR_4  4 llaLArallalGdldeAraller 26
                                      +++ +  l+++G++deA a ++r
  gi|330508422|ref|YP_004384850.1| 24 CYNKGIDLAEQGRYDEAIAEFDR 46
                                      5788999**********887765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.003
                             TPR_4  1 arallaLArallalGdldeAr 21
                                      ara ++ + al ++G ++eA+
  gi|330508422|ref|YP_004384850.1| 55 ARAWYNKGVALTQQGKYEEAL 75
                                      799*****************7 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00046
                             TPR_4   2 rallaLArallalGdldeAra 22 
                                       +a ++++ +l+ lG+++eA++
  gi|330508422|ref|YP_004384850.1|  90 QAWYNRGVVLYILGRYEEALE 110
                                       6899***************98 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 0.00024
                             TPR_4   1 arallaLArallalGdldeAraller 26 
                                       ara ++ + +l++l ++++A a+ +r
  gi|330508422|ref|YP_004384850.1| 123 ARAWINEGNVLFQLNRHEQAVAAYDR 148
                                       799*******************9876 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 !   17.6   0.1   5.4e-06    0.0033      34      81 ..      32      80 ..      23      81 .. 0.93
   2 !   32.5   0.1   1.2e-10   7.4e-08       1      81 [.      67     148 ..      67     149 .. 0.96
   3 ?    5.9   0.3     0.025        15       3      54 ..     137     189 ..     135     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.4e-06
                                      HHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3 34 ylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                       ++g+y++A+  ++++ + ++   +++y ++ +l +++kyeeA+ a+++
  gi|330508422|ref|YP_004384850.1| 32 AEQGRYDEAIAEFDRYiQDYPDYARAWYNKGVALTQQGKYEEALIAFDR 80
                                      579*****************************************99876 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 1.2e-10
                                       HTT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                            ANAPC3   1 dqnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76 
                                       +q++y++A++ ++r+   e++++++ y  + +ly +g+y++A+e  +++  ln+++ ++++  + +l++L+++e+A+
  gi|330508422|ref|YP_004384850.1|  67 QQGKYEEALIAFDRVTDIEPQNSQAWYNRGVVLYILGRYEEALEASNRStMLNGEDARAWINEGNVLFQLNRHEQAV 143
                                       699*************9999999999999************************************************ PP

                                       HHH-S CS
                            ANAPC3  77 aaLek 81 
                                       aa+++
  gi|330508422|ref|YP_004384850.1| 144 AAYDR 148
                                       *9876 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.025
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnsk 54 
                                       n+++ A+  ++r+   +++s+++    + +l ++++y+ A+  ++ka ++++ 
  gi|330508422|ref|YP_004384850.1| 137 NRHEQAVAAYDRAIGIDPHSAQAWCNRCNSLINRSEYDLALSSAQKAiQIDPD 189
                                       79999*********9999999999999**************999999666554 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00072      0.45       6      27 ..      25      46 ..      22      51 .. 0.84
   2 !   11.3   0.0   0.00041      0.25       7      27 ..      60      80 ..      55      84 .. 0.84
   3 !    7.2   0.1    0.0076       4.7       7      23 ..      94     110 ..      93     111 .. 0.91
   4 !   12.4   0.1   0.00018      0.11       9      29 ..     130     150 ..     128     152 .. 0.94
   5 ?   -0.6   0.0       2.3   1.4e+03      13      31 ..     168     186 ..     165     187 .. 0.82
   6 ?   -0.3   0.1       1.8   1.1e+03      24      36 ..     189     201 ..     175     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00072
                            TPR_10  6 nNLanalrqrgrydeAeallee 27
                                       N ++ l ++grydeA a +++
  gi|330508422|ref|YP_004384850.1| 25 YNKGIDLAEQGRYDEAIAEFDR 46
                                      57899***********998765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00041
                            TPR_10  7 NLanalrqrgrydeAeallee 27
                                      N ++al+q+g+y+eA+  +++
  gi|330508422|ref|YP_004384850.1| 60 NKGVALTQQGKYEEALIAFDR 80
                                      6799***********976665 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0076
                            TPR_10   7 NLanalrqrgrydeAea 23 
                                       N +++l+ +gry+eA++
  gi|330508422|ref|YP_004384850.1|  94 NRGVVLYILGRYEEALE 110
                                       7799***********97 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00018
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       +n+l+q++r+++A+a +++a+
  gi|330508422|ref|YP_004384850.1| 130 GNVLFQLNRHEQAVAAYDRAI 150
                                       89******************9 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 2.3
                            TPR_10  13 rqrgrydeAealleealai 31 
                                        +r +yd A+  +++a++i
  gi|330508422|ref|YP_004384850.1| 168 INRSEYDLALSSAQKAIQI 186
                                       5788999999999999987 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 1.8
                            TPR_10  24 lleealairrrll 36 
                                       ++ ea+++r+++l
  gi|330508422|ref|YP_004384850.1| 189 DMVEAYSCREAAL 201
                                       6779999999887 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.015       9.4       2      22 ..      24      44 ..      23      48 .. 0.80
   2 !   11.5   0.0    0.0004      0.25       1      29 [.      57      83 ..      57      89 .. 0.84
   3 ?    2.5   0.1      0.29   1.8e+02       4      20 ..      94     110 ..      91     111 .. 0.71
   4 !   10.1   0.1    0.0011      0.69       6      28 ..     130     152 ..     125     190 .. 0.87
   5 ?    0.9   0.0      0.96   5.9e+02      15      30 ..     190     206 ..     187     208 .] 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.015
                             TPR_7  2 LlnLarlysrlGdyeeAiely 22
                                      ++n +    ++G+y+eAi  +
  gi|330508422|ref|YP_004384850.1| 24 CYNKGIDLAEQGRYDEAIAEF 44
                                      6777777889********865 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0004
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLalt 29
                                      a++n +++  ++G+yeeA+  + +  +++
  gi|330508422|ref|YP_004384850.1| 57 AWYNKGVALTQQGKYEEALIAFDR--VTD 83
                                      789***************988887..655 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.29
                             TPR_7   4 nLarlysrlGdyeeAie 20 
                                       n +++   lG+yeeA+e
  gi|330508422|ref|YP_004384850.1|  94 NRGVVLYILGRYEEALE 110
                                       555555558******97 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0011
                             TPR_7   6 arlysrlGdyeeAielyeqsLal 28 
                                       +++ ++l+++e+A+  y +++++
  gi|330508422|ref|YP_004384850.1| 130 GNVLFQLNRHEQAVAAYDRAIGI 152
                                       8899***************5444 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.96
                             TPR_7  15 yeeAielyeqsL.altk 30 
                                       + eA ++ e++L +l +
  gi|330508422|ref|YP_004384850.1| 190 MVEAYSCREAALmELGR 206
                                       66999*****8888765 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.9   2.4e+03      14      30 ..      34      50 ..      24      57 .. 0.72
   2 !   17.0   0.0   7.4e-06    0.0046       5      37 ..      59      91 ..      55      98 .. 0.94
   3 ?    1.7   0.1      0.45   2.8e+02       7      23 ..      95     111 ..      92     115 .. 0.76
   4 ?    1.2   0.0      0.65     4e+02      14      37 ..     136     159 ..     133     160 .. 0.90
   5 ?    3.5   0.0      0.12        75      16      37 ..     172     193 ..     168     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.9
                                      HT-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C 14 lgeYseArryvdalLei 30
                                      +g+Y+eA    d+ ++ 
  gi|330508422|ref|YP_004384850.1| 34 QGRYDEAIAEFDRYIQD 50
                                      78999998777776665 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 7.4e-06
                                      HHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  5 YylAlGhyklgeYseArryvdalLeiEPenrQa 37
                                      Y   ++ + +g+Y+eA+   d++  iEP+n+Qa
  gi|330508422|ref|YP_004384850.1| 59 YNKGVALTQQGKYEEALIAFDRVTDIEPQNSQA 91
                                      7778999*************************9 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.45
                                       HHHHHHHHT-HHHHHHH CS
                        Fis1_TPR_C   7 lAlGhyklgeYseArry 23 
                                         +  y lg+Y+eA++ 
  gi|330508422|ref|YP_004384850.1|  95 RGVVLYILGRYEEALEA 111
                                       55666889******986 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.65
                                       HT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQa 37 
                                       l ++++A    d+ + i+P   Qa
  gi|330508422|ref|YP_004384850.1| 136 LNRHEQAVAAYDRAIGIDPHSAQA 159
                                       78999**************99998 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.12
                                       -HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPenrQa 37 
                                       eY+ A+  ++  ++i+P+   a
  gi|330508422|ref|YP_004384850.1| 172 EYDLALSSAQKAIQIDPDMVEA 193
                                       9****************97666 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.7e-05     0.017      59     123 ..      19      82 ..      13      85 .. 0.92
   2 !    9.2   0.0    0.0025       1.6      71     118 ..      64     111 ..      62     121 .. 0.92
   3 ?    6.5   0.0     0.017        11      71     102 ..     132     163 ..     112     179 .. 0.83
   4 ?   -1.3   0.0       4.3   2.7e+03      67     100 ..     169     202 ..     162     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  59 elrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       e+ ++++ + ++ +++ Gr++ea+ae ++ ++ +P   r++     Al ++G+ +eAL +++r+ 
  gi|330508422|ref|YP_004384850.1|  19 EEGISCYNKGID-LAEQGRYDEAIAEFDRYIQDYPDYARAWYNKGVALTQQGKYEEALIAFDRVT 82 
                                       677888888888.899*********************************************9986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0025
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALev 118
                                       a+++ G++eeal   ++ ++ +P + +++      l+ +Gr +eALe+
  gi|330508422|ref|YP_004384850.1|  64 ALTQQGKYEEALIAFDRVTDIEPQNSQAWYNRGVVLYILGRYEEALEA 111
                                       56789*****************************************97 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.017
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrql 102
                                        +++l+r+e+a+a +++++  +P+  ++++  
  gi|330508422|ref|YP_004384850.1| 132 VLFQLNRHEQAVAAYDRAIGIDPHSAQAWCNR 163
                                       56899******************999998865 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 4.3
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHH CS
                              BTAD  67 alaeaelrlGraeealaelealvaehPlrErlhr 100
                                        + e +l+l  a++a++   ++v+++  rE++  
  gi|330508422|ref|YP_004384850.1| 169 NRSEYDLALSSAQKAIQIDPDMVEAYSCREAALM 202
                                       5667777788888888777777777777777655 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.044        27     103     124 ..      24      45 ..      19      50 .. 0.89
   2 !    8.1   0.0    0.0043       2.7     101     128 ..      56      83 ..      48      90 .. 0.88
   3 ?    5.9   0.0     0.021        13      85     125 ..      78     114 ..      74     129 .. 0.70
   4 ?    5.1   0.1     0.036        22      68     125 ..     102     148 ..      94     152 .. 0.64
   5 ?    2.7   0.0      0.19   1.2e+02      55      83 ..     157     185 ..     145     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHTT-HHHHHHHHH CS
                           DUF3856 103 vfsravaleelGrkdealkafr 124
                                        ++++  l+e Gr+dea+ +f 
  gi|330508422|ref|YP_004384850.1|  24 CYNKGIDLAEQGRYDEAIAEFD 45 
                                       5899**************9996 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0043
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 101 aavfsravaleelGrkdealkafrmage 128
                                       +a ++++val + G+++eal af  +++
  gi|330508422|ref|YP_004384850.1|  56 RAWYNKGVALTQQGKYEEALIAFDRVTD 83 
                                       6889******************988765 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.021
                                       HHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                           DUF3856  85 fnrrGeleqdeGklWiaavfsravaleelGrkdealkafrm 125
                                       f+r  ++e ++ + W    ++r+v l  lGr++eal+a + 
  gi|330508422|ref|YP_004384850.1|  78 FDRVTDIEPQNSQAW----YNRGVVLYILGRYEEALEASNR 114
                                       666666666666655....7888888888888888887654 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.036
                                       TT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                           DUF3856  68 lgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrm 125
                                       lgry+ea       l+  nr   l+ ++ + Wi    + +  l +l r+++a+ a+  
  gi|330508422|ref|YP_004384850.1| 102 LGRYEEA-------LEASNRSTMLNGEDARAWI----NEGNVLFQLNRHEQAVAAYDR 148
                                       4555555.......5555777778888888887....456666666666666666655 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  55 alchaglsealaklgrydealesadkalr 83 
                                       a +++  +++l++  +yd al+sa+ka++
  gi|330508422|ref|YP_004384850.1| 157 AQAWCNRCNSLINRSEYDLALSSAQKAIQ 185
                                       5556666788899999********99985 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 !   22.6   0.0   1.3e-07   8.1e-05      17      94 ..      45     142 ..      33     153 .. 0.73
   2 ?   -0.9   0.0       2.6   1.6e+03      20      41 ..     163     184 ..     132     196 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.3e-07
                      SRP_TPR_like  17 kkf.............kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkve...ae 74 
                                       +++             k val + +kyeeaL++ +        +++  + +  vlY l +y++al+  ++ +   +e
  gi|330508422|ref|YP_004384850.1|  45 DRYiqdypdyarawynKGVALTQQGKYEEALIAFDRVTdiePQNSQAWYNRGVVLYILGRYEEALEASNRSTmlnGE 121
                                       444444566666688899**************998776444678999*****************9987765411144 PP

                      SRP_TPR_like  75 e.kvkvlksqvlYrlgsyekA 94 
                                       + ++ + +  vl+ l+ +e+A
  gi|330508422|ref|YP_004384850.1| 122 DaRAWINEGNVLFQLNRHEQA 142
                                       445555566666666666666 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.6
                      SRP_TPR_like  20 kvvaliklekyeeaLkllkkgs 41 
                                       +  +li+   y+ aL+ ++k+ 
  gi|330508422|ref|YP_004384850.1| 163 RCNSLINRSEYDLALSSAQKAI 184
                                       5566777777777777777765 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.026        16       9      22 ..      29      42 ..      20      47 .. 0.81
   2 !    7.7   0.2    0.0058       3.6      13      25 ..      67      79 ..      53      82 .. 0.88
   3 ?    6.6   0.0     0.013       7.9       8      23 ..      96     111 ..      91     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.026
                                      HHHHHTT-HHHHHH CS
                             TPR_3  9 aefynkkkyqeAre 22
                                       ++  +++y+eA+ 
  gi|330508422|ref|YP_004384850.1| 29 IDLAEQGRYDEAIA 42
                                      57889*******85 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0058
                                      HTT-HHHHHHH.. CS
                             TPR_3 13 nkkkyqeArelfs 25
                                      +++ky+eA+ +f+
  gi|330508422|ref|YP_004384850.1| 67 QQGKYEEALIAFD 79
                                      79*********98 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.013
                                       HHHHHHTT-HHHHHHH CS
                             TPR_3   8 AaefynkkkyqeArel 23 
                                       + ++y  ++y+eA+e+
  gi|330508422|ref|YP_004384850.1|  96 GVVLYILGRYEEALEA 111
                                       7799*********997 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0034       2.1       6      42 ..      39      75 ..      34      82 .. 0.91
   2 !    7.4   0.0    0.0088       5.4      18      43 ..      85     110 ..      77     112 .. 0.91
   3 ?    3.1   0.1      0.19   1.2e+02       4      54 ..     139     189 ..     136     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0034
                            TPR_20  6 pelaeleaalaanpddldarldlAlallaagryeeAl 42
                                      + +ae+++ +++ pd   a ++   al ++g+yeeAl
  gi|330508422|ref|YP_004384850.1| 39 EAIAEFDRYIQDYPDYARAWYNKGVALTQQGKYEEAL 75
                                      678999999***************************8 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0088
                            TPR_20  18 npddldarldlAlallaagryeeAle 43 
                                       +p++ +a ++   +l+  gryeeAle
  gi|330508422|ref|YP_004384850.1|  85 EPQNSQAWYNRGVVLYILGRYEEALE 110
                                       8************************8 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.19
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                       +++ +a+ ++a+  +p   +a ++  + l+ +++y+ Al+   + ++ d +
  gi|330508422|ref|YP_004384850.1| 139 HEQAVAAYDRAIGIDPHSAQAWCNRCNSLINRSEYDLALSSAQKAIQIDPD 189
                                       67788999999999************************9999888888766 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.037        23     141     182 ..      50      91 ..      24     111 .. 0.76
   2 !   14.9   0.2   1.9e-05     0.012     138     229 ..     114     206 ..      99     208 .] 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.037
                            TPR_15 141 aaeqsaafllaraelyrqegqtdaAlrdyreAlalapdssel 182
                                       ++ + a+ ++  + + +q+g+ ++Al ++ ++ + +p++s++
  gi|330508422|ref|YP_004384850.1|  50 DYPDYARAWYNKGVALTQQGKYEEALIAFDRVTDIEPQNSQA 91 
                                       366778889999999999999999999999999999999886 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.9e-05
                            TPR_15 138 eeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesd 213
                                       +   ++ ++a+ ++  +++  q +++++A+ +y +A+  +p s+++  +    li++++++    +l+  +++ + d
  gi|330508422|ref|YP_004384850.1| 114 RSTMLNgEDARAWINEGNVLFQLNRHEQAVAAYDRAIGIDPHSAQAWCNRCNSLINRSEYDL---ALSSAQKAIQID 187
                                       33335568999**************************************************7...999999999*** PP

                            TPR_15 214 asLwgpla...aAlllLgr 229
                                       +++ +++    aAl+ Lgr
  gi|330508422|ref|YP_004384850.1| 188 PDMVEAYScreAALMELGR 206
                                       *******755578888887 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0038       2.3      14      73 ..      31      90 ..      21     100 .. 0.86
   2 ?    4.6   0.1      0.02        13      13      68 ..      98     153 ..      87     167 .. 0.79
   3 ?    1.9   0.0      0.13        80     206     231 ..     171     196 ..     162     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0038
                                      HHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CH CS
                             NARP1 14 ieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpensk 73
                                      ++e+g+++eA+++++++ ++  D      +k+  l++ g++eeA  ++ +  +  p+ns+
  gi|330508422|ref|YP_004384850.1| 31 LAEQGRYDEAIAEFDRYIQDYPDYARAWYNKGVALTQQGKYEEALIAFDRVTDIEPQNSQ 90
                                      689999999999999999999999999999999999999999999999999999998876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.02
                                       HHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH- CS
                             NARP1  13 iieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlern 68 
                                       ++   g++eeAle  +++     +      +++++l++L+r+e+A a+y + +   
  gi|330508422|ref|YP_004384850.1|  98 VLYILGRYEEALEASNRSTMLNGEDARAWINEGNVLFQLNRHEQAVAAYDRAIGID 153
                                       55567889999998888777777777777789*****************9877655 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.13
                                       T-SHHHHHHHHHHHHH-TT-HHHHHH CS
                             NARP1 206 gsrekAleyidkaiehtptlvelylt 231
                                        +++ Al+  +kai+ +p +ve y  
  gi|330508422|ref|YP_004384850.1| 171 SEYDLALSSAQKAIQIDPDMVEAYSC 196
                                       57899*****************9976 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1      0.07        43      77     127 ..      63     113 ..      45     123 .. 0.84
   2 ?    9.1   0.0    0.0027       1.7      50     118 ..     133     206 ..     126     208 .] 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.07
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHH CS
                   Alkyl_sulf_dimr  77 kealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRn 127
                                        +  ++g+y+ a+   + +   +p+n++a   +  +l  lg+ +e+  + n
  gi|330508422|ref|YP_004384850.1|  63 VALTQQGKYEEALIAFDRVTDIEPQNSQAWYNRGVVLYILGRYEEALEASN 113
                                       566799************************999999999999988766543 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0027
                                       TS---HHHHH.HHHHHHTT....SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  50 Lnplppeeka.krlvelmG....gaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgy 118
                                       L++l+++e+a + + +++G    +a++ +++ ++ +++ +y +a++ ++++++ dp+  ea + + +al +lg+
  gi|330508422|ref|YP_004384850.1| 133 LFQLNRHEQAvAAYDRAIGidphSAQAWCNRCNSLINRSEYDLALSSAQKAIQIDPDMVEAYSCREAALMELGR 206
                                       6777777666245677788888889999999********************************99999999997 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 ?    3.5   0.1     0.099        61      13      22 ..      54      63 ..      52      64 .. 0.85
   2 ?    6.1   0.0     0.016       9.7       3      22 ..      78      97 ..      77      98 .. 0.92
   3 ?   -1.2   0.0         3   1.8e+03      14      21 ..     123     130 ..     121     131 .. 0.86
   4 ?   -1.2   0.0       2.9   1.8e+03       8      20 ..     151     163 ..     150     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.099
                   DNA_pol_lambd_f 13 tAkkwyakGi 22
                                       A+ wy+kG+
  gi|330508422|ref|YP_004384850.1| 54 YARAWYNKGV 63
                                      69*******7 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
                   DNA_pol_lambd_f  3 FtkvyGVGpktAkkwyakGi 22
                                      F +v+++ p+  + wy++G+
  gi|330508422|ref|YP_004384850.1| 78 FDRVTDIEPQNSQAWYNRGV 97
                                      78999*************97 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3
                   DNA_pol_lambd_f  14 AkkwyakG 21 
                                       A+ w+++G
  gi|330508422|ref|YP_004384850.1| 123 ARAWINEG 130
                                       999**998 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 2.9
                   DNA_pol_lambd_f   8 GVGpktAkkwyak 20 
                                       G+ p+ A+ w ++
  gi|330508422|ref|YP_004384850.1| 151 GIDPHSAQAWCNR 163
                                       777999****986 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.059        36     244     298 ..      65     119 ..      60     128 .. 0.86
   2 ?    8.4   0.0    0.0016      0.97     209     268 ..     132     191 ..     118     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.059
                                       HHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHT----S CS
                             ChAPs 244 llskkkeelAlevakravksaPsefktWalLvkvYikledienALltLNscPmft 298
                                       l ++ k+e Al + +r +++ P +++ W+    v   l+ +e+AL + N   m +
  gi|330508422|ref|YP_004384850.1|  65 LTQQGKYEEALIAFDRVTDIEPQNSQAWYNRGVVLYILGRYEEALEASNRSTMLN 119
                                       567788899999999**************998888889*******9999888865 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0016
                                       HHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-H CS
                             ChAPs 209 vllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsef 268
                                       vl+  ++  +av    +++  ++++a+  + + + l+++++++lAl+ a++a+++ P   
  gi|330508422|ref|YP_004384850.1| 132 VLFQLNRHEQAVAAYDRAIGIDPHSAQAWCNRCNSLINRSEYDLALSSAQKAIQIDPDMV 191
                                       66777777789999999999999999999999**********************999765 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3     0.011       6.7     123     178 ..      31      87 ..      30     100 .. 0.77
   2 ?    6.8   0.1    0.0081         5     127     174 ..     103     151 ..      96     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.011
                            TPR_21 123 llaekkydeAlktLeakkeeaf.aalvaelrGDilvaqgkldeAraaYqaAlaalee 178
                                       l++++ ydeA+++ ++  ++    a++   +G +l++qgk +eA  a+++  +   +
  gi|330508422|ref|YP_004384850.1|  31 LAEQGRYDEAIAEFDRYIQDYPdYARAWYNKGVALTQQGKYEEALIAFDRVTDIEPQ 87 
                                       5799999999999987665543146666789*************9999887665555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0081
                            TPR_21 127 kkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       + y+eAl++ ++++  ++ +a++   +G++l++ ++ ++A aaY++A+ 
  gi|330508422|ref|YP_004384850.1| 103 GRYEEALEASNRSTMlNGEDARAWINEGNVLFQLNRHEQAVAAYDRAIG 151
                                       566666666644433144455555668********************86 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.024        15      11      22 ..      84      95 ..      80      99 .. 0.83
   2 ?    4.3   0.1     0.056        35       8      22 ..     149     163 ..     147     167 .. 0.87
   3 ?   -1.3   0.0       3.3   2.1e+03       5      13 ..     180     188 ..     176     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.024
                                      H-TT-CHHHHHH CS
                              PPTA 11 kdpkNYsaWnyR 22
                                        p+N +aW+ R
  gi|330508422|ref|YP_004384850.1| 84 IEPQNSQAWYNR 95
                                      479*******99 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.056
                                       HHHH-TT-CHHHHHH CS
                              PPTA   8 liekdpkNYsaWnyR 22 
                                       +i  dp + +aW+ R
  gi|330508422|ref|YP_004384850.1| 149 AIGIDPHSAQAWCNR 163
                                       7889*********99 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.3
                                       HHHHHHH-T CS
                              PPTA   5 tekliekdp 13 
                                        +k+i+ dp
  gi|330508422|ref|YP_004384850.1| 180 AQKAIQIDP 188
                                       689*****9 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.5    0.0076       4.7     153     180 ..      31      58 ..      22      64 .. 0.88
   2 ?    1.9   0.1      0.29   1.8e+02     151     180 ..      63      92 ..      59      97 .. 0.89
   3 ?    0.2   0.1         1   6.3e+02     153     180 ..      99     126 ..      90     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0076
                           Wzy_C_2 153 lallGdedeAeqilararalfpeedakw 180
                                       la +G+ deA    +r++  +p+++ +w
  gi|330508422|ref|YP_004384850.1|  31 LAEQGRYDEAIAEFDRYIQDYPDYARAW 58 
                                       5779************************ PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.29
                           Wzy_C_2 151 lslallGdedeAeqilararalfpeedakw 180
                                       ++l ++G+ +eA+   +r+  + p++ ++w
  gi|330508422|ref|YP_004384850.1|  63 VALTQQGKYEEALIAFDRVTDIEPQNSQAW 92 
                                       68999*****************99999999 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1
                           Wzy_C_2 153 lallGdedeAeqilararalfpeedakw 180
                                       l +lG+ +eA+    r   l +e++ +w
  gi|330508422|ref|YP_004384850.1|  99 LYILGRYEEALEASNRSTMLNGEDARAW 126
                                       5579*******99999999999998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1272.61
//
Query:       gi|330508423|ref|YP_004384851.1|  [L=388]
Description: signal recognition particle-docking protein FtsY [Methanosaeta concilii GP6]
Scores for complete 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-72  240.8   0.1    1.4e-71  240.2   0.1    1.3  1  SRP54            SRP54-type protein, GTPase domain
    1.5e-10   41.1   0.9    4.4e-10   39.7   0.9    1.8  1  SRP54_N          SRP54-type protein, helical bundle domain
    2.9e-05   23.9   0.2      5e-05   23.1   0.2    1.3  1  AAA_30           AAA domain
    0.00016   22.1   0.0    0.00033   21.1   0.0    1.5  1  AAA_17           AAA domain
    0.00064   20.2   0.0     0.0015   19.0   0.0    1.7  1  AAA              ATPase family associated with various cellul
      0.001   19.0   0.0     0.0023   17.9   0.0    1.6  1  APS_kinase       Adenylylsulphate kinase
     0.0011   18.2   0.0     0.0018   17.6   0.0    1.3  1  Zeta_toxin       Zeta toxin
     0.0013   18.5   0.1      0.019   14.7   0.0    2.4  2  Thymidylate_kin  Thymidylate kinase
     0.0017   18.5   0.0     0.0031   17.7   0.0    1.4  1  AAA_33           AAA domain
     0.0057   17.0   0.4      0.044   14.2   0.1    2.5  2  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.014   15.5   0.1      0.028   14.4   0.1    1.6  1  ResIII           Type III restriction enzyme, res subunit
      0.016   14.8   0.0       0.03   13.8   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.039   13.0   0.4        1.1    8.3   0.0    2.2  2  T2SSE            Type II/IV secretion system protein
      0.045   14.0   0.1       0.18   12.0   0.1    2.1  2  AAA_28           AAA domain
      0.046   14.0   0.1       0.13   12.5   0.1    1.7  1  AAA_22           AAA domain
      0.047   13.6   0.5        0.3   11.0   0.1    2.1  2  NTPase_1         NTPase
      0.049   13.6   0.0       0.24   11.4   0.0    2.1  2  AAA_5            AAA domain (dynein-related subfamily)
      0.095   12.1   0.0       0.17   11.4   0.0    1.4  1  Arf              ADP-ribosylation factor family
      0.096   12.7   0.1        0.2   11.7   0.1    1.7  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.19   11.8   0.7       0.93    9.6   0.7    2.1  1  MMR_HSR1         50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.2   0.1   1.6e-74   1.4e-71       2     195 ..     190     383 ..     189     384 .. 0.99

  Alignments for each domain:
  == domain 1  score: 240.2 bits;  conditional E-value: 1.6e-74
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                         il+vG++G+GKTt++aK+a++l+++ ++v+l+a DtfRa+A+eQL++++++lg +v+k+k++ dpaav+++a+e 
  gi|330508423|ref|YP_004384851.1| 190 VKILFVGVNGTGKTTSIAKVAKYLMDQSYSVVLAAGDTFRAGAIEQLEVHGNNLGLKVVKHKTGGDPAAVIFDAIEY 266
                                       579************************************************************************** PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                       a++++ dvvl DTaGrl+++ +lm++++ki +v++pd  ++v +a++g++av+ a+ F+e+v i+g iltk D+dak
  gi|330508423|ref|YP_004384851.1| 267 ARAHNKDVVLADTAGRLHTNINLMDQMRKIVRVTTPDLLIFVDEAIAGNDAVERARLFNESVPIDGSILTKTDADAK 343
                                       ***************************************************************************** PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrll 195
                                       gG+a+sia+ +++P+ f+gvG+++ dl +f+pe+lv+rl+
  gi|330508423|ref|YP_004384851.1| 344 GGSAISIAYITGKPVLFLGVGQTYPDLVKFEPEWLVNRLM 383
                                       **************************************98 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.9   4.9e-13   4.4e-10      17      74 ..     107     167 ..      91     170 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 4.9e-13
                                       CGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHH CS
                           SRP54_N  17 kideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkde 74 
                                        + e+dlee ++ le+aL+e+DV+++v+++++ +vk   vg+kk     ++q  ++ ++++
  gi|330508423|ref|YP_004384851.1| 107 ILEEKDLEEPMWALEMALMESDVALPVAEEIVREVKSDLVGKKKkigSDTGQLAEDSLRNA 167
                                       469**************************************77776655777777766665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   5.6e-08     5e-05      22     114 ..     193     299 ..     181     328 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.6e-08
                            AAA_30  22 vltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.............grar 85 
                                       + +G+ GtGKtt+++++++ + ++ ++v+++A     A +++ +l+++++++   + ++k             + ar
  gi|330508423|ref|YP_004384851.1| 193 LFVGVNGTGKTTSIAKVAKYLMDQSYSVVLAAGDTFRAGAIE-QLEVHGNNLGLKVVKHKtggdpaavifdaiEYAR 268
                                       569******************************999999998.7788888887666666678888888888886677 PP

                            AAA_30  86 lepgtllivDEagmv..dtkqlaallkaaek 114
                                        +++++++ D ag +  +++ ++++ k+++ 
  gi|330508423|ref|YP_004384851.1| 269 AHNKDVVLADTAGRLhtNINLMDQMRKIVRV 299
                                       8888999999998884444555555555554 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.7e-07   0.00033       1     109 [.     195     309 ..     195     326 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.7e-07
                                       EE-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTT.TSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH..H CS
                            AAA_17   1 lGgPGsGKgtqceklveky....gfthlsaGdllreeakrg.glakardemrklpleekkelqkeaaekiaeea..k 70 
                                       +G+ G GK+t ++k+++ +       +l aGd +r+ a ++ +   ++  ++ ++++   +  + + ++i+ ++  +
  gi|330508423|ref|YP_004384851.1| 195 VGVNGTGKTTSIAKVAKYLmdqsYSVVLAAGDTFRAGAIEQlEVHGNNLGLKVVKHKTGGDPAAVIFDAIEYARahN 271
                                       79*************986666646678899*****988666444333333344455554455555555553332226 PP

                                       SSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE CS
                            AAA_17  71 kkgvlvdghprikeqagfldglpkevleelkpdaiille 109
                                       k+ vl d+  r+ ++  ++d++  ++++   pd++i+++
  gi|330508423|ref|YP_004384851.1| 272 KDVVLADTAGRLHTNINLMDQMR-KIVRVTTPDLLIFVD 309
                                       77799999999988777666665.6899999*****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 !   19.0   0.0   1.6e-06    0.0015       1      74 [.     192     287 ..     192     322 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.6e-06
                                       EEEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS....................STTHHHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel...gvefleisgsellsk....................yvgesekkirelfkeak 54 
                                       +l++G  GtGKT+ +  vak l   + +++   g +++                      + g+ ++ i + ++ a+
  gi|330508423|ref|YP_004384851.1| 192 ILFVGVNGTGKTTSIAKVAKYLmdqSYSVVLAAGDTFRAGaieqlevhgnnlglkvvkhkTGGDPAAVIFDAIEYAR 268
                                       69*******************86532333333333333334444444444444445555555566666666666666 PP

                                       HTSTSEEEEEETGGGHHHHH CS
                               AAA  55 ekakpsilfiDEidalaksr 74 
                                       +++ + +++ D + +l+++ 
  gi|330508423|ref|YP_004384851.1| 269 AHN-KDVVLADTAGRLHTNI 287
                                       665.5666666666665555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.5e-06    0.0023       2      50 ..     189     237 ..     188     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-06
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT-- CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLg 50 
                                       +v +++ G+ g+GK+t   +++k+L+++ +sv+l  Gd+ R g  ++L 
  gi|330508423|ref|YP_004384851.1| 189 PVKILFVGVNGTGKTTSIAKVAKYLMDQSYSVVLAAGDTFRAGAIEQLE 237
                                       6789*************9***********************99888775 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     2e-06    0.0018      11      56 ..     184     230 ..     174     301 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                        Zeta_toxin  11 psqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe 56 
                                        ++++P+ il +G  G GK++ +++++++l  +  +vv   +D++R+
  gi|330508423|ref|YP_004384851.1| 184 RAKDKPVKILFVGVNGTGKTTSIAKVAKYLMdQSYSVVLAAGDTFRA 230
                                       3459**********************999984555666667899997 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.1e-05     0.019       3      30 ..     196     223 ..     194     244 .. 0.89
   2 ?    0.9   0.0      0.34   3.1e+02     106     137 ..     289     323 ..     280     336 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEE CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvlt 30 
                                       G++G+GKtt +++++++l ++ ++vvl 
  gi|330508423|ref|YP_004384851.1| 196 GVNGTGKTTSIAKVAKYLMDQSYSVVLA 223
                                       9**********************98764 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                                       HHHHHGGGTTS.E-SEEEEEE..SSHHHHHTSCCT CS
                   Thymidylate_kin 106 lvlslnedvll.kPdltflld..vdpevalkRlak 137
                                       l+ ++++ v   +Pdl +++d  +  + a++R++ 
  gi|330508423|ref|YP_004384851.1| 289 LMDQMRKIVRVtTPDLLIFVDeaIAGNDAVERARL 323
                                       5555555554469*******977888888888875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.4e-06    0.0031       2     104 ..     192     308 ..     192     327 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.4e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdtlrr.rlfgtdqqskt......dytrvldrlyqilnelarka 66 
                                       +l+vG++G+GK+t + +++k l      +vl + dt+r  +++  +++  +      + ++  d   + +++ ++ a
  gi|330508423|ref|YP_004384851.1| 192 ILFVGVNGTGKTTSIAKVAKYLMdqsysVVLAAGDTFRAgAIEQLEVHGNNlglkvvKHKTGGD-PAAVIFDAIEYA 267
                                       69****************9998888986677778887775555544444443333322222333.444777999999 PP

                            AAA_33  67 lsagrnvildat....nlsrrerarflklarrlgvpvrivvv 104
                                       ++++++v+l  t     ++ + +++++k++r    p+++++v
  gi|330508423|ref|YP_004384851.1| 268 RAHNKDVVLADTagrlHTNINLMDQMRKIVR-VTTPDLLIFV 308
                                       9999999997775664333466677777776.4446666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.8   4.3e+03      98     127 ..     134     172 ..      92     178 .. 0.61
   2 !   14.2   0.1   4.9e-05     0.044      25      63 ..     190     228 ..     180     311 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.8
                            AAA_16  98 rekleeala........avpelagaea.srllellkrll 127
                                       +e++ ++++         +++++g++a  +l+++l  ll
  gi|330508423|ref|YP_004384851.1| 134 AEEIVREVKsdlvgkkkKIGSDTGQLAeDSLRNALITLL 172
                                       333333333555555555555566655666666666666 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.9e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                         +l++G  G+GK++ + +++++l ++   ++ +  d +
  gi|330508423|ref|YP_004384851.1| 190 VKILFVGVNGTGKTTSIAKVAKYLMDQSYSVVLAAGDTF 228
                                       5689******************99999555555555555 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 ?   14.4   0.1   3.2e-05     0.028      21     140 ..     181     310 ..     135     317 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
                                       .......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS CS
                            ResIII  21 s.....krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgd 92 
                                       +     ++  ++l++   GtGKT  +ak++++l+ + +    ++l+ + +    ++e+++   ++   ++ k ++g 
  gi|330508423|ref|YP_004384851.1| 181 EyirakDKPVKILFVGVNGTGKTTSIAKVAKYLMDQSY---SVVLAAGDTFRAGAIEQLEVHGNNLGLKVVKHKTGG 254
                                       144432444499**********************9877...588888888888888877776666665544444444 PP

                                       -B--.............-SEEEE.EHHHHHHTH........HHHTTT-S.EEEEET CS
                            ResIII  93 kkka......kekdstnkkilvt.tiqsldadseeeeeeseellrdrfd.viiiDE 140
                                          a      +  +++nk+++++ t  +l+ +++  +++++  + ++ d +i++DE
  gi|330508423|ref|YP_004384851.1| 255 DPAAvifdaiEYARAHNKDVVLAdTAGRLHTNINLMDQMRKIVRVTTPDlLIFVDE 310
                                       43334556653344444444444245566666655444444444444444566666 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   3.3e-05      0.03      34      65 ..     190     221 ..     181     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                             AAA_7  34 kpvllvGptGtGKtviikdllkkldkekylsl 65 
                                        ++l+vG  GtGKt+ i ++ k l +++y+++
  gi|330508423|ref|YP_004384851.1| 190 VKILFVGVNGTGKTTSIAKVAKYLMDQSYSVV 221
                                       578*****************999998888765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0012       1.1     117     162 ..     178     222 ..     158     240 .. 0.81
   2 ?    2.9   0.1     0.053        48     161     204 ..     258     306 ..     240     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                             T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivt 162
                                       +++e +r+   +   il+ G  g+GKtt++  + k++ +++  +v+
  gi|330508423|ref|YP_004384851.1| 178 DFDEYIRAK-DKPVKILFVGVNGTGKTTSIAKVAKYLMDQSYSVVL 222
                                       677778877.78899***************9999988877555554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.053
                             T2SSE 161 vtvEDpvEiqleganqvqlnak....kakvtfadllraaLRl.rPDrim 204
                                        ++ D++E+  ++++ v l +     ++++++ d +r+++R   PD ++
  gi|330508423|ref|YP_004384851.1| 258 AVIFDAIEYARAHNKDVVLADTagrlHTNINLMDQMRKIVRVtTPDLLI 306
                                       5678*********99999999889999999***********63699754 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.5   3.1e+03      24      45 ..     131     152 ..     121     169 .. 0.74
   2 ?   12.0   0.1    0.0002      0.18       1      36 [.     191     230 ..     191     285 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.5
                            AAA_28  24 ypvvpEaareileeklakgeda 45 
                                        pv +E++re+ +++  k++++
  gi|330508423|ref|YP_004384851.1| 131 LPVAEEIVREVKSDLVGKKKKI 152
                                       6789999999999998777654 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0002
                            AAA_28   1 kivitGgestGKTtlleaLaar....gypvvpEaareile 36 
                                       ki ++G  +tGKTt +++ a+      y+vv  a+ ++  
  gi|330508423|ref|YP_004384851.1| 191 KILFVGVNGTGKTTSIAKVAKYlmdqSYSVVLAAGDTFRA 230
                                       799****************976666688888666555544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00015      0.13       8     111 ..     192     295 ..     191     312 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.........erlss 75 
                                       ++ +G  GtGKTt+++++++ l          ++ ++v l+++    +++    ++l++ +++          +++ 
  gi|330508423|ref|YP_004384851.1| 192 ILFVGVNGTGKTTSIAKVAKYL---------MDQSYSVVLAAGD---TFRAGAIEQLEVHGNNlglkvvkhkTGGDP 256
                                       5789****************99.........5555555555555...355555555555555555555557756666 PP

                            AAA_22  76 eellealeqalraravielliiDEaqhlrs.....eealee 111
                                        +++    +++ra+ +  +++ D a +l +     ++++++
  gi|330508423|ref|YP_004384851.1| 257 AAVIFDAIEYARAHNK-DVVLADTAGRL-HtninlMDQMRK 295
                                       6666555566666666.67777777777.333223333333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00033       0.3       2      30 ..     192     220 ..     191     253 .. 0.90
   2 ?    0.4   0.0      0.59   5.3e+02      84     132 ..     259     308 ..     229     327 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                                       EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                       ++  G  G+GKtT + kv++ l ++ ++v
  gi|330508423|ref|YP_004384851.1| 192 ILFVGVNGTGKTTSIAKVAKYLMDQSYSV 220
                                       5667999***************9999887 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.59
                                       HHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHHHHHT.TTSEEEEE- CS
                          NTPase_1  84 lalealrkal.seadviviDEiGkmElkskkfkeaveevLk.sekpvlavi 132
                                       ++ +a++ a  +++dv++ D  G++  +++ + ++++++++ + + +l+ +
  gi|330508423|ref|YP_004384851.1| 259 VIFDAIEYARaHNKDVVLADTAGRLHTNINLM-DQMRKIVRvTTPDLLIFV 308
                                       55667777766889999999999998888654.567777774444455544 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 ?   -0.7   0.0       1.4   1.3e+03      77      98 ..     160     181 ..     134     189 .. 0.83
   2 ?   11.4   0.0   0.00026      0.24       2      47 ..     192     238 ..     191     304 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                                       --HHHHHHHHHHHHSSEEE..- CS
                             AAA_5  77 aesevlnsLlslleerrlllee 98 
                                       ae++  n+L++ll++++l+++e
  gi|330508423|ref|YP_004384851.1| 160 AEDSLRNALITLLSKNHLDFDE 181
                                       67788899*******9998766 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00026
                                       EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrrei 47 
                                       +l vG  GtgK++ + ++a+ l  +++ +v+   dt ++  + ++e+
  gi|330508423|ref|YP_004384851.1| 192 ILFVGVNGTGKTTSIAKVAKYLmDQSYSVVLAAGDTFRAGAIEQLEV 238
                                       789*********99999999888999999999888877766666666 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.17       9      36 ..     184     211 ..     177     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                       TT.TTEEEEEEEESTTSSHHHHHHHHHH CS
                               Arf   9 klkkkelrilllGLDnaGKtTilkklkl 36 
                                       + k+k ++il++G  ++GKtT + k+ +
  gi|330508423|ref|YP_004384851.1| 184 RAKDKPVKILFVGVNGTGKTTSIAKVAK 211
                                       567899***************9888655 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 ?   11.7   0.1   0.00022       0.2       9      33 ..     199     223 ..     195     358 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                       TSSHHHHHHHHHHHHHHTT--EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllv 33 
                                       G+GKTt  a+ a++l ++ + V+l 
  gi|330508423|ref|YP_004384851.1| 199 GTGKTTSIAKVAKYLMDQSYSVVLA 223
                                       9*********************986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.7     0.001      0.93       2      84 ..     192     310 ..     191     331 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                                       EEEEESTTSSHHHHHHHHHT....STEEESSSTTSSSSE.EEEEEEETTEE.......................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg....ekaivsdkpgtTrdi.negrvklkgke.......................... 47 
                                       +++vG   +GK+t i +  +    +   v   +g T      ++++++g++                          
  gi|330508423|ref|YP_004384851.1| 192 ILFVGVNGTGKTTSIAKVAKylmdQSYSVVLAAGDTFRAgAIEQLEVHGNNlglkvvkhktggdpaavifdaieyar 268
                                       67788888888888877776444322233333333333322233332233334444444444445555555555555 PP

                                       .....EEEEECGGCSSHHHHHHHHHHHHHHHHC..T.SEEEEEEE CS
                          MMR_HSR1  48 .....ielvDtpGliegaseekglgkaflalee..a.dlillvvd 84 
                                            ++l+Dt+G ++   ++ +l ++++++ +  + dl+++v +
  gi|330508423|ref|YP_004384851.1| 269 ahnkdVVLADTAGRLH---TNINLMDQMRKIVRvtTpDLLIFVDE 310
                                       55555********655...66677777777776543477777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 2548.23
//
Query:       gi|330508424|ref|YP_004384852.1|  [L=151]
Description: prefoldin subunit alpha [Methanosaeta concilii GP6]
Scores for complete 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-22   78.5   3.6    5.3e-22   78.0   3.6    1.2  1  Prefoldin        Prefoldin subunit
     0.0052   16.7   6.5      0.011   15.6   1.8    2.1  2  Prefoldin_2      Prefoldin subunit
  ------ inclusion threshold ------
      0.032   13.8   2.1        3.6    7.2   0.2    2.1  2  Snf7             Snf7
       0.22   11.6   4.9      0.078   13.0   1.8    1.8  2  MCC-bdg_PDZ      PDZ domain of MCC-2 bdg protein for Usher sy
       0.39   11.2   3.4        0.2   12.1   1.1    1.7  2  Snapin_Pallidin  Snapin/Pallidin
        1.9    8.1   4.9        3.3    7.4   0.6    2.4  2  Trimer_CC        Trimerisation motif
        6.6    6.6   7.1        3.1    7.6   1.1    2.1  2  Nsp1_C           Nsp1-like C-terminal region


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 !   78.0   3.6   2.1e-25   5.3e-22       1     116 [.      21     136 ..       8     139 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 2.1e-25
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHH CS
                         Prefoldin   1 lkeeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyvekslee 77 
                                       +++++e +  +l+  + a   le++l++++ l++++ g+e+lvp+g+g+++ +++ ++++v++++Gag+++ek +ee
  gi|330508424|ref|YP_004384852.1|  21 YQAQAEGISHQLGLSQIAAQGLESALAAVDALQEAEVGQEILVPIGSGSFIHGKLASKENVILNVGAGVSIEKRSEE 97 
                                       7899999999******************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  78 Aiellkkkleelekqlekleeeleklkdqittleanlaq 116
                                       Aie+l  +++e+ + ++kl+e l+k+ +++++++ +++q
  gi|330508424|ref|YP_004384852.1|  98 AIEILRTRKNEVLEGSKKLTEVLAKIDQEMQKIQGIMQQ 136
                                       ************************************998 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.025        63       3      44 ..      14      55 ..      12      61 .. 0.88
   2 !   15.6   1.8   4.4e-06     0.011      41     101 ..      75     136 ..      73     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.025
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT CS
                       Prefoldin_2  3 linkfqqlqqqlqqlaqqikqletqlkelelvleelellded 44
                                      l++ ++q+q+q + + +q+   +   + le++l +++ l e 
  gi|330508424|ref|YP_004384852.1| 14 LLAAYEQYQAQAEGISHQLGLSQIAAQGLESALAAVDALQEA 55
                                      68899**************99999999999999999888875 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 4.4e-06
                                       S-TT--EEEEET.TEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  41 ldedtkvyklvG.dvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqk 101
                                       l++ ++v  +vG +v +++  ee++e L +rk+++ + +k+l++ l k+ +e+++++   q+
  gi|330508424|ref|YP_004384852.1|  75 LASKENVILNVGaGVSIEKRSEEAIEILRTRKNEVLEGSKKLTEVLAKIDQEMQKIQGIMQQ 136
                                       6677788888885588999*************************************987775 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0023       5.8      51      90 ..      16      55 ..      11      57 .. 0.93
   2 ?    7.2   0.2    0.0014       3.6      79     114 ..     105     138 ..      91     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0023
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Snf7 51 kryekqldqldnqlanleqvslaienlksnkevlnamkqg 90
                                        ye++ +q+++ + +l   + a+++l+s+ + ++a++++
  gi|330508424|ref|YP_004384852.1| 16 AAYEQYQAQAEGISHQLGLSQIAAQGLESALAAVDALQEA 55
                                      579**********************************987 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHHHHHHHHHHHCTCCHHHHHHHHHHH CS
                              Snf7  79 snkevlnamkqgakamkamnkkvdidkidklmdeie 114
                                       +++evl++ k+ ++++ ++ ++++  ki+ +m++ e
  gi|330508424|ref|YP_004384852.1| 105 RKNEVLEGSKKLTEVLAKIDQEMQ--KIQGIMQQYE 138
                                       468999999999999999999999..9999999876 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 ?   13.0   1.8     3e-05     0.078      13      58 ..      11      56 ..       8      59 .. 0.93
   2 ?   -1.6   0.1       1.1   2.8e+03      25      25 ..     115     115 ..      96     140 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                       MCC-bdg_PDZ 13 nelLsltleerkqqseeLsldlgkaEsnatALvlALeyserlkeay 58
                                       ++L ++ e++++q+e++s +lg     a  L +AL   + l ea+
  gi|330508424|ref|YP_004384852.1| 11 IRRLLAAYEQYQAQAEGISHQLGLSQIAAQGLESALAAVDALQEAE 56
                                      689***********************99999******999999987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                       MCC-bdg_PDZ  25 q 25 
                                       +
  gi|330508424|ref|YP_004384852.1| 115 K 115
                                       2 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.5   6.4e+03      21      26 ..      45      50 ..      25      62 .. 0.54
   2 ?   12.1   1.1   7.8e-05       0.2      36      86 ..      91     141 ..      89     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.5
                   Snapin_Pallidin 21 klkelr 26
                                       l+++ 
  gi|330508424|ref|YP_004384852.1| 45 ALAAVD 50
                                      222222 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 7.8e-05
                   Snapin_Pallidin  36 ldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRa 86 
                                       +++ +e+  e+ ++ ++evl+  k+  + L++i ++m++++ ++q+ + R+
  gi|330508424|ref|YP_004384852.1|  91 IEKRSEEAIEILRTRKNEVLEGSKKLTEVLAKIDQEMQKIQGIMQQYESRL 141
                                       6777777778888888999999**************************998 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3      0.05   1.3e+02      25      39 ..       8      22 ..       7      24 .. 0.82
   2 ?    7.4   0.6    0.0013       3.3      18      42 ..     117     141 ..     102     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.05
                                      HHHHHHHHHHHHHHH CS
                         Trimer_CC 25 EEelrkLqatVQelQ 39
                                      EEe+r+L a   + Q
  gi|330508424|ref|YP_004384852.1|  8 EEEIRRLLAAYEQYQ 22
                                      9******99776666 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0013
                                       XXX--HHHHHHHHHHHHHHHHHHHH CS
                         Trimer_CC  18 sdavSRLEEelrkLqatVQelQkRL 42 
                                       ++++ ++  e++k+q + Q+   RL
  gi|330508424|ref|YP_004384852.1| 117 TEVLAKIDQEMQKIQGIMQQYESRL 141
                                       7899999*************99998 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 ?    2.4   0.6     0.051   1.3e+02      56      98 ..       8      50 ..       6      62 .. 0.79
   2 ?    7.6   1.1    0.0012       3.1      55     102 ..      95     142 ..      93     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.051
                            Nsp1_C 56 gekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyE 98
                                       e+I++L  + ++ +++ + i ++L + +   + Les L+   
  gi|330508424|ref|YP_004384852.1|  8 EEEIRRLLAAYEQYQAQAEGISHQLGLSQIAAQGLESALAAVD 50
                                      5789999999999999999999999888888888888887665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0012
                            Nsp1_C  55 ngekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkele 102
                                       + e I+ L++   e+ + ++k+ + L  i ++ + ++ ++++yE++l+
  gi|330508424|ref|YP_004384852.1|  95 SEEAIEILRTRKNEVLEGSKKLTEVLAKIDQEMQKIQGIMQQYESRLS 142
                                       5689999*************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1336  (0.0745161); expected 358.6 (0.02)
Passed bias filter:                      890  (0.0496402); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1157.68
//
Query:       gi|330508425|ref|YP_004384853.1|  [L=62]
Description: ribosomal LX protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-08   33.6   0.0    4.1e-08   33.4   0.0    1.2  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 !   33.4   0.0   2.3e-12   4.1e-08      68     121 .]       3      59 ..       1      59 [. 0.87

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.3e-12
                                       ..............TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEEE CS
                    Ribosomal_L18A  68 nygiwlryd...srsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekve 121
                                       n+ i  ry+   + +++ +f k + + +e++a + vYs +gs+h +kr  I+I++v+
  gi|330508425|ref|YP_004384853.1|   3 NFEIKGRYKgglIGKTWLPFSKVVDSQNEKNAKNMVYSLMGSQHGLKRGLIKIDEVK 59 
                                       666666776333568999*************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 458.29
//
Query:       gi|330508426|ref|YP_004384854.1|  [L=221]
Description: translation initiation factor eIF-6 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-66  221.0   0.3      1e-65  220.8   0.3    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 !  220.8   0.3   5.8e-70     1e-65       1     197 []       5     199 ..       5     199 .. 0.99

  Alignments for each domain:
  == domain 1  score: 220.8 bits;  conditional E-value: 5.8e-70
                                       .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHH CS
                             eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeele 77 
                                       r++i+gss +Gvfar+t++++l+p  v+ e  + iee L+v++v +  +  ++ Gsl+ +N++g++v+++++ e+l+
  gi|330508426|ref|YP_004384854.1|   5 RIKIAGSSLLGVFARCTDDIVLLPAVVGPEDLAFIEEGLHVKAVCIPAGIGSVTGSLISANKSGFVVSRHAEAEDLK 81 
                                       799************************************************************************** PP

                                       HHHHHHH---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE CS
                             eIF-6  78 klkeslkleverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllv 154
                                        l+e+   +v+rl+++++A+GNvilaND++A+vhp ls +++++i+++L+v+v +gti+g+ktvG+a+v+tnkgllv
  gi|330508426|ref|YP_004384854.1|  82 ILQEH--GKVSRLPTRINAAGNVILANDSAAMVHPGLSTRACRAIEETLEVKVQKGTIGGLKTVGMAGVATNKGLLV 156
                                       ****9..9********************************************************************* PP

                                       -TT--HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                             eIF-6 155 hpkateeeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                       hp+++e+e++ leel++++v++gTvN Gs+lvgsgl+aN+ g+
  gi|330508426|ref|YP_004384854.1| 157 HPRVSEQEMAVLEELFELPVDVGTVNLGSPLVGSGLLANSYGY 199
                                       ****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1627.68
//
Query:       gi|330508427|ref|YP_004384855.1|  [L=88]
Description: 50S ribosomal protein L31e [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-12   47.6   0.1    1.9e-12   47.2   0.1    1.1  1  Ribosomal_L31e  Ribosomal protein L31e
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.21   11.7   0.0    1.3  1  DUF167          Uncharacterised ACR, YggU family COG1872


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.1   2.1e-16   1.9e-12       5      69 ..       6      71 ..       4      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 2.1e-16
                    Ribosomal_L31e  5 reytInihkrihgvgfkkraprAlkeikkfamkemgtp..dvridtrLnkavwakgirnvpyrirvr 69
                                      r ytI     ++ v + +r  rA+ ei+++ +++m+tp  dv+id+ Ln+ +w +g  ++p+r+rvr
  gi|330508427|ref|YP_004384855.1|  6 RVYTIP-LGIVKCVPVYRRSNRAMAEIRNYLARHMKTPaeDVKIDPGLNQVIWRRGDMKPPRRVRVR 71
                                      678888.678999999********************765599************************9 PP

>> DUF167  Uncharacterised ACR, YggU family COG1872
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.4e-05      0.21      39      67 ..      24      52 ..      15      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                                      IIIHHHHHHHHHHHHHS...SEEEE-S-G CS
                            DUF167 39 dGkANkalikfLakalgvpksdveivsGe 67
                                       ++A +++ ++La++++ p  dv+i  G 
  gi|330508427|ref|YP_004384855.1| 24 SNRAMAEIRNYLARHMKTPAEDVKIDPGL 52
                                      689999*******************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 655.69
//
Query:       gi|330508428|ref|YP_004384856.1|  [L=218]
Description: hypothetical protein MCON_2623 [Methanosaeta concilii GP6]
Scores for complete 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    0.00048   19.9   0.0    1.8  2  Asn_synthase     Asparagine synthase
    0.00044   19.8   0.0    0.00062   19.3   0.0    1.3  1  QueC             Queuosine biosynthesis protein QueC
     0.0081   15.7   0.0      0.017   14.6   0.0    1.6  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
      0.018   13.8   0.0      0.026   13.3   0.0    1.4  1  tRNA_Me_trans    tRNA methyl transferase


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.1e-07   0.00048      19      89 ..       2      69 ..       1      79 [. 0.91
   2 ?   -0.3   0.0      0.14   6.5e+02     278     309 ..     152     183 ..     100     215 .. 0.49

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-07
                      Asn_synthase 19 pvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalp 89
                                      +v++l+SGG DSSl a l+  + + ++  +   f   ++d    ake+a++lg + +++v++++ l++al+
  gi|330508428|ref|YP_004384856.1|  2 KVAVLFSGGKDSSLTALLLEPFFE-EIELVNFSF--GHDDSWMRAKEAARELGYPLRRMVFDADVLERALK 69
                                      699********************8.9********..77888899******************998887765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.14
                      Asn_synthase 278 eeileRp.Kegfsapvgewklkgelrelaeell 309
                                       ee+ e+   ++f +++++  lk++  ++  +++
  gi|330508428|ref|YP_004384856.1| 152 EELSEKHpASDFEVGLRYA-LKERHGQMEVDRI 183
                                       2222222233333344444.3333333333333 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.4e-07   0.00062       2      52 ..       3      51 ..       2      82 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.4e-07
                                      EEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT- CS
                              QueC  2 avvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelg 52
                                      + vl+SGG DS+  ++l +  ++e+e+++f++g+        ak+ a+elg
  gi|330508428|ref|YP_004384856.1|  3 VAVLFSGGKDSSLTALLLEPFFEEIELVNFSFGHDD--SWMRAKEAARELG 51
                                      569******************************763..3444555555554 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.8e-06     0.017       1      41 [.       1      41 [.       1      50 [. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.8e-06
                   Diphthami_syn_2  1 mkvavlysGGkDsilaLykalkesevesLvsvisenkesym 41
                                      mkvavl+sGGkDs l        +e + Lv+     ++s+m
  gi|330508428|ref|YP_004384856.1|  1 MKVAVLFSGGKDSSLTALLLEPFFEEIELVNFSFGHDDSWM 41
                                      9************9876554445777778887777777776 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.8e-06     0.026       1      35 [.       1      35 [.       1      84 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.8e-06
                     tRNA_Me_trans  1 kkvvvalSgGVDSsvaaallkeqgyevigvflklw 35
                                      +kv+v++SgG DSs++a+ll+  + e++ v + + 
  gi|330508428|ref|YP_004384856.1|  1 MKVAVLFSGGKDSSLTALLLEPFFEEIELVNFSFG 35
                                      69******************998888877766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1646.02
//
Query:       gi|330508429|ref|YP_004384857.1|  [L=113]
Description: DNA-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-29  102.9  16.6    1.3e-29  102.7  16.6    1.0  1  dsDNA_bind  Double-stranded DNA-binding domain
     0.0014   18.2   3.1     0.0016   18.0   3.1    1.1  1  4HB_MCP_1   Four helix bundle sensory module for signal trans


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 !  102.7  16.6   1.4e-33   1.3e-29       1     110 [.       9     112 ..       9     113 .] 0.91

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 1.4e-33
                                       XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                        dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaq 77 
                                       +r++rl+++q+q+ +s+   +a +q+++qqe  +e++k ai+++iL+peAreR++ ir+++pe ++++e +Li+laq
  gi|330508429|ref|YP_004384857.1|   9 LRRKRLEQIQRQQADSQM--AAVQQEQAQQE--MEAKKAAIMRTILTPEARERMNAIRMTRPEFVSQIEAQLIMLAQ 81 
                                       79**********998877..45566666666..9******************************************* PP

                                       --SS-----HHHHHHHHHHHS---XXXXX..XX CS
                        dsDNA_bind  78 sGqlrskvteeqLkeLLeqvaekkketkivisr 110
                                       sG+lr+ +t+eqLk +L+q + kk++ +i  +r
  gi|330508429|ref|YP_004384857.1|  82 SGRLRGPITDEQLKAILTQAQPKKRDINI--TR 112
                                       ***********************997666..55 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 !   18.0   3.1   1.8e-07    0.0016      63     155 ..      11     108 ..       2     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.8e-07
                         4HB_MCP_1  63 adlleliltkdkaekdellkdieeleaeidkllekyektilteeEkelleefkeqlnaY.revrkkvlelakegkkd 138
                                       ++ le i   ++a+ +  + + e+ ++e++ + +++++tilt+e +e+++++     ++ ++++++++ la++g   
  gi|330508429|ref|YP_004384857.1|  11 RKRLEQIQR-QQADSQMAAVQQEQAQQEMEAKKAAIMRTILTPEARERMNAIRMTRPEFvSQIEAQLIMLAQSGRLR 86 
                                       444444444.3444444445569************************************99*************976 PP

                         4HB_MCP_1 139 .....eAyqlyetegrparekl 155
                                            e+ ++  t+++p+ +++
  gi|330508429|ref|YP_004384857.1|  87 gpitdEQLKAILTQAQPKKRDI 108
                                       6666677777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2519  (0.140499); expected 358.6 (0.02)
Passed bias filter:                      826  (0.0460706); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 877.37
//
Query:       gi|330508430|ref|YP_004384858.1|  [L=155]
Description: 30S ribosomal protein S19e [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-54  183.1   0.0    2.2e-54  182.9   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
  ------ inclusion threshold ------
      0.024   14.5   0.0       0.36   10.7   0.0    2.1  2  RuvB_C          RuvB C-terminal winged helix domain
      0.064   12.9   0.0       0.13   12.0   0.0    1.5  1  GntR            Bacterial regulatory proteins, gntR family
      0.091   12.7   0.0       0.15   12.0   0.0    1.3  1  HTH_12          Ribonuclease R winged-helix domain
       0.13   12.1   0.1       0.21   11.5   0.1    1.3  1  HTH_5           Bacterial regulatory protein, arsR family


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 !  182.9   0.0   6.2e-58   2.2e-54       1     136 [.       3     137 ..       3     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 182.9 bits;  conditional E-value: 6.2e-58
                                       TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS CS
                    Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGg 77 
                                       tv+dVp+++li+a a eLk  gk+++P wa+++Ktg+++e++p+++dW++vR AsilR++y++gpvGv+rlr++YGg
  gi|330508430|ref|YP_004384858.1|   3 TVYDVPPHDLIAATALELKAAGKVQPPVWAEFAKTGVNREMPPTNPDWWFVRSASILRRIYIDGPVGVSRLRTFYGG 79 
                                       79*************************************************************************** PP

                                       -------THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
                    Ribosomal_S19e  78 kkrrgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                                       kkr+gv+   f+k+sgsv+r+ lqqLek+glv+k kk gr++t++Gq++ld ia++va+
  gi|330508430|ref|YP_004384858.1|  80 KKRKGVATGTFAKGSGSVVRESLQQLEKAGLVRKLKK-GRQMTPEGQAFLDGIAHKVAS 137
                                       ********************************98855.******************975 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.078   2.8e+02      13      34 ..      57      78 ..      54      83 .. 0.81
   2 ?   10.7   0.0    0.0001      0.36      50      71 ..     107     128 ..     103     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.078
                                      HHHHHT.TT--B-HHHHHHHTT CS
                            RuvB_C 13 kllkekfkggpvglktlaailg 34
                                      ++l + + +gpvg++ l ++ g
  gi|330508430|ref|YP_004384858.1| 57 SILRRIYIDGPVGVSRLRTFYG 78
                                      57888899******99977665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0001
                                       HTTSEEEETTEEEE-HHHHHHH CS
                            RuvB_C  50 keglIertsrGRilTkkglkyl 71 
                                       k gl+++ ++GR++T++g  +l
  gi|330508430|ref|YP_004384858.1| 107 KAGLVRKLKKGRQMTPEGQAFL 128
                                       679***************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 ?   12.0   0.0   3.6e-05      0.13      37      56 ..      94     113 ..      89     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.6e-05
                                       -HHHHHHHHHHHHHTTSEEE CS
                              GntR  37 srttvReALrrLeaeglver 56 
                                       s ++vRe+L++Le +glv  
  gi|330508430|ref|YP_004384858.1|  94 SGSVVRESLQQLEKAGLVRK 113
                                       6689*************975 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.1e-05      0.15      35      63 ..      98     125 ..      92     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
                            HTH_12  35 vRyrLrkleergltrrvgyagreltEkGl 63 
                                       vR  L+ le+ gl+r+  ++ r++t  G 
  gi|330508430|ref|YP_004384858.1|  98 VRESLQQLEKAGLVRKLKKG-RQMTPEGQ 125
                                       899*************9987.99998876 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 ?   11.5   0.1     6e-05      0.21      29      47 .]      95     113 ..      92     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                                       HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  29 qstvShHLkkLreaGLVek 47 
                                        s v++ L +L++aGLV+k
  gi|330508430|ref|YP_004384858.1|  95 GSVVRESLQQLEKAGLVRK 113
                                       589**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1152.41
//
Query:       gi|330508431|ref|YP_004384859.1|  [L=910]
Description: cation-transporting P-type ATPase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-51  174.9   2.8    1.1e-51  174.9   2.8    2.8  4  E1-E2_ATPase     E1-E2 ATPase
    2.6e-51  173.9   6.3    2.6e-51  173.9   6.3    2.1  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    9.7e-25   88.1   0.9    4.8e-24   85.8   0.9    2.2  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.1e-24   86.4   0.0    2.4e-24   85.3   0.0    1.6  1  Cation_ATPase    Cation transport ATPase (P-type)
    1.8e-17   62.8   0.2    4.6e-17   61.5   0.1    1.9  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    2.1e-06   27.7   0.5    0.00011   22.0   0.5    2.3  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
      2e-05   25.1   0.1    5.5e-05   23.7   0.0    1.8  2  HAD              haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.5   3.7e+03     122     144 ..      65      83 ..      47     109 .. 0.49
   2 !  174.9   2.8   4.4e-55   1.1e-51       4     180 ..     118     313 ..     115     314 .. 0.95
   3 ?   -1.4   0.3      0.56   1.4e+03      94     139 ..     685     732 ..     664     754 .. 0.51
   4 ?   -3.3   0.4       2.1   5.5e+03     120     133 ..     851     864 ..     812     890 .. 0.51

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHS-STTTSST CS
                      E1-E2_ATPase 122 lvpvvlliallvflialllgksl 144
                                       l++v  l+a++ f++     k++
  gi|330508431|ref|YP_004384859.1|  65 LIAVLGLAAVISFMAD----KFI 83 
                                       3333333333333332....222 PP

  == domain 2  score: 174.9 bits;  conditional E-value: 4.4e-55
                                       --EEEEE-TT......S-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-......... CS
                      E1-E2_ATPase   4 pptakvirdg......teeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek......... 64 
                                       +++a+v+rd       +e++i+++e+v+GDi+l++ag +vpaD ri+e+ + e+des+LTGEs+p++k         
  gi|330508431|ref|YP_004384859.1| 118 SAEARVLRDCpetgtcQEMRIKSQEVVVGDIILVEAGAKVPADSRIIEQANlELDESMLTGESVPARKmaealqedl 194
                                       66788887775555555666********************************************************* PP

                                       ...G-TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-S CS
                      E1-E2_ATPase  65 ...ekgdmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflial 138
                                          e  + +f+Gtvv++g++kavV atg+dte+gkia+++++++++ktpl++    l+k l++++l+++ l++++ +
  gi|330508431|ref|YP_004384859.1| 195 itaEMDNIIFAGTVVTQGRCKAVVFATGMDTEMGKIAHQIARTEKAKTPLKRRTLDLSKKLMILALVASSLTLVVGF 271
                                       **99************************************************************************* PP

                                       TTTSSTTHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 139 llgkslaeallralallvaaiPcaLplavplalalgarrlak 180
                                       ++g +l+e +l++la++v+aiP++Lp+a+++ala+g++r+a 
  gi|330508431|ref|YP_004384859.1| 272 WRGFELIELFLFTLAMAVSAIPEGLPAAITVALAVGVSRMAS 313
                                       ****************************************96 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.56
                                       TTTTSTTS--------HHHHHHHHHHHHHHHHH..HHHHHHHHHS-ST CS
                      E1-E2_ATPase  94 lgkiarlveeakskktplqkkldklgkvlvpvv..lliallvfliall 139
                                       ++ i+++vee +    ++ k ++ l+++ +  +  +l+al++++i++l
  gi|330508431|ref|YP_004384859.1| 685 FQSIVNAVEEGRVIFENIRKTVKYLISTNAGEIltILVALVFMAINVL 732
                                       555666666665444444444444433333222002223333333333 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHH CS
                      E1-E2_ATPase 120 kvlvpvvlliallv 133
                                       ++++ ++l +++++
  gi|330508431|ref|YP_004384859.1| 851 AIVASIALQLMATT 864
                                       11222222222222 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       0.8   2.1e+03     124     146 ..     252     273 ..     214     305 .. 0.66
   2 !  173.9   6.3     1e-54   2.6e-51       2     182 .]     732     902 ..     731     902 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.8
                   Cation_ATPase_C 124 snkllllaillslllqvlivyvp 146
                                       s+kl++la+++s  l++++ ++ 
  gi|330508431|ref|YP_004384859.1| 252 SKKLMILALVASS-LTLVVGFWR 273
                                       5666666666666.444444444 PP

  == domain 2  score: 173.9 bits;  conditional E-value: 1e-54
                   Cation_ATPase_C   2 lplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgi 78 
                                       l+++++qiLw+nLvtD+l+ + La+ep+e+d+m++pPr++ke++i+  +++++l++++++a+ tllvf   l   g 
  gi|330508431|ref|YP_004384859.1| 732 LIFTPVQILWVNLVTDGLLVVNLAMEPKEEDVMDQPPRNPKENIINMDIVKNVLFVAAFMAAGTLLVFTRELN--GG 806
                                       68******************************************************************66665..44 PP

                   Cation_ATPase_C  79 sekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgta 155
                                       + ++       aqt+ F+tl+++qifnaln+rs+++s+fk  glfsnk+l++ai++s++lq++ +  p+++ ++gt+
  gi|330508431|ref|YP_004384859.1| 807 DIHR-------AQTLGFTTLAMFQIFNALNCRSEDKSVFK-IGLFSNKYLIGAIVASIALQLMATTLPFFQMALGTV 875
                                       4444.......*****************************.************************************ PP

                   Cation_ATPase_C 156 plsleewlialllalvvllvdelvKll 182
                                        lsl++w+i++++++ v++ del+Kl+
  gi|330508431|ref|YP_004384859.1| 876 ALSLYDWAIIFAVSSTVFIADELRKLI 902
                                       *************************97 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.9   1.9e-27   4.8e-24       1     209 [.     330     658 ..     330     659 .. 0.79

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 1.9e-27
                                       SSEEEEESBTTTBCHHHHHHHHHHHH...........................CHHHHHHHHHH............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx...........................xxxxxxxxxxx............. RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa...........................alalaaaletg............. 37 
                                       i++v+ Dk+GTLtt ++ v +++                              +++l+  l ++             
  gi|330508431|ref|YP_004384859.1| 330 ITAVCTDKTGTLTTNQMTVQKLFLAGrivdvsgvgfqpkgdfeldgvplkaseDKSLSMFLKIAslcndaslkshke 406
                                       789******************99999999999999999999999999998888444444444446666667777777 PP

                                       .......HHCHHHHHH.HHHHHHH..............HHHHHHHHHETTTE.....................HHHH CS
                                       .......xxxxxxxxx.xxxxxxx..............xxxxxxxxxxxxxx.....................xxxx RF
                         Hydrolase  38 .......sehpigkal.vaaakar..............sgaltgfatfigrg.....................ayai 71 
                                                 p   al vaaaka               +                                  a+++
  gi|330508431|ref|YP_004384859.1| 407 eedrweiLGDPTEGALlVAAAKAGldkseleeshprvdE------------IpfdpknrymstfhrtgsaellALLK 471
                                       888899988888888878888877665444333333331............03444445556666666999999999 PP

                                       THHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH..............................TTHHHHHHHHH.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............................xxxxxxxxxxx.... RF
                         Hydrolase  72 gkpewltaldippdlgaaigsaqsqgrtvall..............................qaralavftia.... 114
                                       g pe + ++  +   + ++ ++ ++ ++++l+                              ++ a  +ft      
  gi|330508431|ref|YP_004384859.1| 472 GAPETILDMCSYVLDRGEVKELDQKRKEEFLKassqmaaealrvlalayvtikpeevdefknKGPANLIFTGFsgmi 548
                                       9999999995555555666666666666666688889999999*****************99666666666666767 PP

                                       HTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..............GGGESEEEEHHCES...STTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxx...xxxx RF
                         Hydrolase 115 dplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG..............ddyfdaviasdiet...vakp 174
                                       dp  ++pea   v+  k+agi+v ++tgd++ ta+++a+ +G              dd  d ++++ i     +a +
  gi|330508431|ref|YP_004384859.1| 549 DP--PRPEAIRSVHLCKRAGIKVTMATGDHKITAQAIARDIGiyeegskvltgsdlDDLSDEELDGLIQDtsvFARV 623
                                       99..***************************************9999988888886666655555555557****** PP

                                       SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 175 spegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                       sp++k+++++ Lq k++ vam GDgvnDa+al+aA
  gi|330508431|ref|YP_004384859.1| 624 SPKHKHRIVQSLQRKGHIVAMTGDGVNDAPALKAA 658
                                       **********************************9 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.0   9.2e-28   2.4e-24       2      91 .]     395     484 ..     394     484 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 9.2e-28
                     Cation_ATPase   2 lcNsaaf.sensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyv 77 
                                       lcN+a++ s+++e+d++++lG++tE ALlv+a+k+gld++el+e++++v eipF+ ++++ms+ +++  + +++++ 
  gi|330508431|ref|YP_004384859.1| 395 LCNDASLkSHKEEEDRWEILGDPTEGALLVAAAKAGLDKSELEESHPRVDEIPFDPKNRYMSTFHRT-GSAELLALL 470
                                       8******999********************************************************9.8******** PP

                     Cation_ATPase  78 KGApeiilkrCthv 91 
                                       KGApe il+ C++v
  gi|330508431|ref|YP_004384859.1| 471 KGAPETILDMCSYV 484
                                       ***********986 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.1   1.8e-20   4.6e-17       1      69 []       9      76 ..       9      76 .. 0.99
   2 ?   -3.5   0.0       3.3   8.4e+03      40      66 ..     238     264 ..     237     265 .. 0.73

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1.8e-20
                   Cation_ATPase_N  1 ehalsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                      +hals++ vl+kL+ + ++GL+++eaa+r k +GpNel+e +k s + +l++q++npl+ +L  aa++s
  gi|330508431|ref|YP_004384859.1|  9 WHALSADRVLQKLD-STTRGLSTEEAARRYKAFGPNELEEGEKLSKLDILIEQVKNPLIAVLGLAAVIS 76
                                      9************9.9***************************************************98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.3
                   Cation_ATPase_N  40 ekkkkslwvkllkqftnplvilLlvaa 66 
                                       ek k++l ++ l+  + ++++ L++++
  gi|330508431|ref|YP_004384859.1| 238 EKAKTPLKRRTLDLSKKLMILALVASS 264
                                       567778888888888888888887765 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.026        66      19      54 ..     554     589 ..     549     608 .. 0.85
   2 !   22.0   0.5   4.5e-08   0.00011     195     254 ..     631     691 ..     627     692 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCC CS
                       Hydrolase_3  19 ktkeaikklkekgikvviATGRslravlpvleelgl 54 
                                       ++++ ++ +k +gikv+ ATG +  +++ +++++g+
  gi|330508431|ref|YP_004384859.1| 554 EAIRSVHLCKRAGIKVTMATGDHKITAQAIARDIGI 589
                                       66777888999**********999999999988875 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 4.5e-08
                                       HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEET.TS-HHHHHHSSEEE--GGGTHHHHH CS
                       Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmg.naseevkkaAdyvtksnnedGVaka 254
                                       +++ l+ +   v+  GDg ND + L+aa++g+Amg  +++  k+ Ad++ ++ n  ++++a
  gi|330508431|ref|YP_004384859.1| 631 IVQSLQRKGHIVAMTGDGVNDAPALKAAEIGIAMGiTGTDVTKETADMILTDDNFQSIVNA 691
                                       677788888889999*******************9789*************9999998876 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         4     1e+04      48      77 ..      11      41 ..       5      48 .. 0.75
   2 !   23.7   0.0   2.1e-08   5.5e-05      39     188 .]     498     656 ..     454     656 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4
                               HAD 48 rldraglaelleallagls.eelaaelerfv 77
                                       l+ + + + l+++ +gls ee a++ ++f+
  gi|330508431|ref|YP_004384859.1| 11 ALSADRVLQKLDSTTRGLStEEAARRYKAFG 41
                                      5666778888999999999888877777776 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 2.1e-08
                               HAD  39 llalfrellrldraglaelleallaglseelaaelerfv.....aevirpk....lldp...galellaahraaGdr 103
                                       ++  f ++++++ a++ ++l+ ++   ++e  +e++  +                 +dp   +a + ++ +++aG++
  gi|330508431|ref|YP_004384859.1| 498 KEE-FLKASSQMAAEALRVLALAYVTIKPEEVDEFKNKGpanliF-----TgfsgMIDPprpEAIRSVHLCKRAGIK 568
                                       333.47788888888999999999999999999999999433330.....245552333344*************** PP

                               HAD 104 vvvvSgglrplvepllaelg.....adevlatelevdd..rltgelglegkpvrg....egkvaalrewlaaegegi 169
                                       v++ +g +++ ++++++  g     ++ + +++l+      l+g   +++++v+     ++k + +++ l+++g+  
  gi|330508431|ref|YP_004384859.1| 569 VTMATGDHKITAQAIARDIGiyeegSKVLTGSDLDDLSdeELDGL--IQDTSVFArvspKHKHRIVQS-LQRKGH-- 640
                                       ********************7666666666665554446766666..777777773322333333333.444443.. PP

                               HAD 170 dleevvay.GDspsDlpllr 188
                                           +va  GD+++D p+l+
  gi|330508431|ref|YP_004384859.1| 641 ----IVAMtGDGVNDAPALK 656
                                       ....67777*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (910 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.44
# Mc/sec: 6247.04
//
Query:       gi|330508432|ref|YP_004384860.1|  [L=374]
Description: transposase, Mutator family [Methanosaeta concilii GP6]
Scores for complete 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-105  352.7   1.9   2.6e-105  352.4   1.9    1.0  1  Transposase_mut  Transposase, Mutator family
    4.9e-08   33.3   0.1    1.3e-07   31.9   0.0    1.8  2  MULE             MULE transposase domain
  ------ inclusion threshold ------
      0.016   14.9   0.2      0.041   13.6   0.2    1.7  1  DDE_Tnp_ISL3     Transposase
        0.4   11.3   4.9        3.1    8.5   0.1    3.7  4  DUF5499          Family of unknown function (DUF5499)


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 !  352.4   1.9  5.8e-109  2.6e-105      21     380 ..      13     365 ..       2     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 352.4 bits;  conditional E-value: 5.8e-109
                   Transposase_mut  21 gkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspalleryk 97 
                                       + ++ +k+l+  +l+e+++ e++++++a  yer+++r+ +RnG r+rkl+T +g++el  P+ R+  F++a++er+ 
  gi|330508432|ref|YP_004384860.1|  13 DRKEGMKKLTAGFLNEVMQLEAENQIQARPYERTGKRRAHRNGTRSRKLKTIYGEIELDKPQIREFPFETAVFERFS 89 
                                       4568999********************************************************************** PP

                   Transposase_mut  98 RrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkv 174
                                       R e+ l  +v+e y +Gvstrkvek++ +++  k++S+sevS+i+k+ld+ v+ f +R++e +  p++f+Da y kv
  gi|330508432|ref|YP_004384860.1|  90 RVEDSLRVAVAESYFEGVSTRKVEKVFSKFGL-KNISASEVSRIAKKLDKLVKDFLNRPIEGS-IPYIFVDASYFKV 164
                                       *******************************9.88****************************.************* PP

                   Transposase_mut 175 ReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaa 251
                                       R +gr v+ka l+ ++++ dG+reiL+ +v+dsE+e+ W++ +esLk+rGlkgv+lv+sDahkG+++a++++f +a+
  gi|330508432|ref|YP_004384860.1| 165 RTDGRYVNKALLVVVAIHDDGYREILSATVDDSEDESCWENCFESLKARGLKGVKLVISDAHKGIQAAVQKSFLGAS 241
                                       ***************************************************************************** PP

                   Transposase_mut 252 vQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaedvlaflafpe 328
                                       +Q C vH++r +l+++pkk++++va +lk    a + e   ++l+ +l+   k ++k a+++d+ + d+ ++ +fp+
  gi|330508432|ref|YP_004384860.1| 242 WQMCNVHFMRAVLKNIPKKEKKEVAYMLKD---AIEDEFKMQELAVILD--DKGFKKSADTIDSFRFDLWNYKSFPR 313
                                       ****************************95...6677888889999998..56899********************* PP

                   Transposase_mut 329 qirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                        ++++i++tN+lEr+Nke++Rr+rv g + n++s+lr+ + ++++ +++w++
  gi|330508432|ref|YP_004384860.1| 314 SHWKRIRTTNVLERINKELKRRSRVAGAYSNDQSLLRVAVCIMMDINEDWIT 365
                                       **************************************************86 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0     3e-11   1.3e-07      14      95 ..     172     251 ..     154     252 .. 0.87
   2 ?   -3.6   0.0       3.6   1.6e+04      61      70 ..     351     360 ..     341     364 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3e-11
                              MULE  14 klplltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlCl 90 
                                       +  ll vv+++d g   +l  ++ +se+e+++e  +++l+++    +  k +i+D +k+++ a+++ f +a  ++C 
  gi|330508432|ref|YP_004384860.1| 172 NKALLVVVAIHDDGYREILSATVDDSEDESCWENCFESLKARGL--KGVKLVISDAHKGIQAAVQKSFLGASWQMCN 246
                                       56789999********************************9644..69***************************** PP

                              MULE  91 fHiak 95 
                                        H+++
  gi|330508432|ref|YP_004384860.1| 247 VHFMR 251
                                       ***96 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.6
                              MULE  61 spkviitDke 70 
                                         ++i++D +
  gi|330508432|ref|YP_004384860.1| 351 VAVCIMMDIN 360
                                       4578888865 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   9.1e-06     0.041      23     105 ..     183     268 ..     162     351 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.1e-06
                      DDE_Tnp_ISL3  23 vdg.grlldilpg..RkketlkafleslsekerekveavvmDmsaayksavkealPnAkivvDrFHvvklanealde 96 
                                        dg +++l ++ +   ++++ ++++esl+++  + v+ v+ D ++++++av++ +  A+  + + H+++ + + + +
  gi|330508432|ref|YP_004384860.1| 183 DDGyREILSATVDdsEDESCWENCFESLKARGLKGVKLVISDAHKGIQAAVQKSFLGASWQMCNVHFMRAVLKNIPK 259
                                       3446677666544115667889*******9***************************************99998877 PP

                      DDE_Tnp_ISL3  97 vRrreqkel 105
                                         ++e+  +
  gi|330508432|ref|YP_004384860.1| 260 KEKKEVAYM 268
                                       766666555 PP

>> DUF5499  Family of unknown function (DUF5499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.7   3.1e+03       9      25 ..      37      53 ..      33      68 .. 0.74
   2 ?    8.5   0.1   0.00069       3.1      25      64 ..     113     152 ..      94     187 .. 0.83
   3 ?    1.9   0.0     0.076   3.4e+02      29      54 ..     199     224 ..     179     238 .. 0.78
   4 ?   -1.0   0.3      0.63   2.8e+03      36      61 ..     310     333 ..     276     346 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.7
                           DUF5499  9 dlkvrdydyfgkrkapd 25
                                      +++ r y+  gkr+a  
  gi|330508432|ref|YP_004384860.1| 37 QIQARPYERTGKRRAHR 53
                                      57789999999999864 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00069
                           DUF5499  25 dgvshkdmvenifrsdkwrrmkgidsevkdelnrqlrgev 64 
                                       + v  k  ++ni  s+  r  k +d  vkd lnr + g +
  gi|330508432|ref|YP_004384860.1| 113 EKVFSKFGLKNISASEVSRIAKKLDKLVKDFLNRPIEGSI 152
                                       4556677789*************************99987 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.076
                           DUF5499  29 hkdmvenifrsdkwrrmkgidsevkd 54 
                                        +   en f s k r +kg+   + d
  gi|330508432|ref|YP_004384860.1| 199 DESCWENCFESLKARGLKGVKLVISD 224
                                       556779*************9877666 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.63
                           DUF5499  36 ifrsdkwrrmkgidsevkdelnrqlr 61 
                                        f   +w+r++  +  v + +n++l+
  gi|330508432|ref|YP_004384860.1| 310 SFPRSHWKRIRTTN--VLERINKELK 333
                                       45566788877643..3344444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2739.00
//
Query:       gi|330508433|ref|YP_004384861.1|  [L=561]
Description: Na+/Pi-cotransporter [Methanosaeta concilii GP6]
Scores for complete 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-57  191.4  24.4    2.1e-39  134.8   8.3    2.4  2  Na_Pi_cotrans    Na+/Pi-cotransporter
    0.00019   21.9   5.4     0.0039   17.6   3.0    2.5  2  PhoU             PhoU domain
  ------ inclusion threshold ------
       0.16   11.7   0.0        0.4   10.4   0.0    1.6  1  DUF4116          Domain of unknown function (DUF4116)
        2.9    7.9   8.7       0.51   10.3   0.9    3.4  3  DUF2108          Predicted membrane protein (DUF2108)


Domain annotation for each model (and alignments):
>> Na_Pi_cotrans  Na+/Pi-cotransporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.8   8.3   4.8e-43   2.1e-39       1     138 [.      15     148 ..      15     149 .. 0.98
   2 !   62.3   8.2   1.1e-20   5.1e-17      26     110 ..     164     253 ..     156     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 4.8e-43
                     Na_Pi_cotrans   1 LfLfGmkllsegleklageklkkilekltsnrlkgvlvGllvTallqSSsattvmvvglvnaglltlkqaigvilGa 77 
                                       LfL+G++  se+++++age++++il+++t++ l+g+l+G++vTal+qSS+att+++vglvnag++++ +++g+++Ga
  gi|330508433|ref|YP_004384861.1|  15 LFLYGIENFSEEVRHAAGERFRTILQNATKTSLRGALAGAAVTALVQSSTATTIIAVGLVNAGAISFLASLGLVIGA 91 
                                       8**************************************************************************** PP

                     Na_Pi_cotrans  78 niGttvtaqllslalklsslalllllvgvllllfskkkklkklgeillglgllflglelms 138
                                       n+Gtt+taql+  a+kl+++a+l++++g++l l+   + ++ +g+ ++ +gl+f++l+l+s
  gi|330508433|ref|YP_004384861.1|  92 NVGTTLTAQLV--AFKLTAFAPLIVIAGFMLSLIR--TPYRAYGKPVFYFGLVFYSLNLIS 148
                                       ***********..*****************99995..59*******************998 PP

  == domain 2  score: 62.3 bits;  conditional E-value: 1.1e-20
                     Na_Pi_cotrans  26 ekltsnrlkgvlvGllvTallqSSsattvmvvglvnaglltlkqaigvilGaniGttvtaqllsl.....alklssl 97 
                                        ++t+  l+++++G+++T l+qSSs+tt ++v ++++gl++ +qa++++lGaniGt++t +++sl     a ++++ 
  gi|330508433|ref|YP_004384861.1| 164 LSMTDDILIAIIIGFIITNLFQSSSVTTGLIVVMAQSGLINASQALPILLGANIGTSTTGLVVSLnmntaAKRTATA 240
                                       4799999********************************************************99888865555666 PP

                     Na_Pi_cotrans  98 alllllvgvllll 110
                                        +l+ ++gvll+l
  gi|330508433|ref|YP_004384861.1| 241 QFLFNFLGVLLFL 253
                                       6667777777544 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   3.0   8.6e-07    0.0039       2      87 ..     338     421 ..     337     428 .. 0.74
   2 ?    4.0   0.0     0.015        68       1      83 [.     441     517 ..     441     521 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.6e-07
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERi 78 
                                        +m +i+++++d++le+ +e++t+++ ++  ++d id l+ +i  +++++ +++ +++     +  l r++     +
  gi|330508433|ref|YP_004384861.1| 338 VHMLSICKDIFDNTLEV-AEGNTDMCSRIAHLRDYIDYLRTQIMSAVINLTNRDISVED-AAHVAILARVTDLSALM 412
                                       68***************.57778********************9998888888777765.44444444444444444 PP

                                       HHHHHHHHH CS
                              PhoU  79 gDhavniae 87 
                                       + + +++a+
  gi|330508433|ref|YP_004384861.1| 413 AHQMTSMAR 421
                                       444444444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHH.HHHHHHHHHHHHH.HHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtela.revierddeidrl.ekeiersllealakrqplaedlrellsllriardl 75 
                                       +++ma +++e  ++++ ++ e   e++ +e++++d+ + +      + +l++++ak+++ +        + +i  + 
  gi|330508433|ref|YP_004384861.1| 441 IEEMAALCRENTEQLIGVFPEMP-EYIdKEMRSNDELLRQVlNWHYKTYLIQLVAKSSSGGI-------FSDILFSF 509
                                       689****************8886.99999999999888876455556677777787776655.......77888888 PP

                                       HHHHHHHH CS
                              PhoU  76 ERigDhav 83 
                                       ERig  ++
  gi|330508433|ref|YP_004384861.1| 510 ERIGSIIR 517
                                       88887665 PP

>> DUF4116  Domain of unknown function (DUF4116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0     9e-05       0.4      12      41 ..     459     488 ..     453     492 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9e-05
                           DUF4116  12 ngsalkylseeLknDkeivlkAvkqngtal 41 
                                       +++  +y+++e++++ e++ + ++++ + +
  gi|330508433|ref|YP_004384861.1| 459 FPEMPEYIDKEMRSNDELLRQVLNWHYKTY 488
                                       577889*******************99876 PP

>> DUF2108  Predicted membrane protein (DUF2108)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.9   0.00011      0.51      10      44 ..      50      85 ..      44      89 .. 0.81
   2 ?   -0.3   0.1      0.24   1.1e+03      26      46 ..     105     127 ..      84     128 .. 0.69
   3 ?   -0.6   0.2      0.29   1.3e+03      49      68 ..     274     293 ..     273     304 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                           DUF2108 10 aliGaigvillk.kpldKlimlalleaGlillivak 44
                                      al+Ga++++l++ +    +i+++l++aG i ++++ 
  gi|330508433|ref|YP_004384861.1| 50 ALAGAAVTALVQsSTATTIIAVGLVNAGAISFLASL 85
                                      789998877765156779**************9985 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.24
                           DUF2108  26 Klimla..lleaGlillivakgY 46 
                                       Kl ++a  ++ aG++l ++   Y
  gi|330508433|ref|YP_004384861.1| 105 KLTAFAplIVIAGFMLSLIRTPY 127
                                       77777766889999999887766 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.29
                           DUF2108  49 VaiavallePvstiilllai 68 
                                       Va a  +++  + +i+llai
  gi|330508433|ref|YP_004384861.1| 274 VANAHLIFNSTCAVIFLLAI 293
                                       66666777777888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3951.57
//
Query:       gi|330508434|ref|YP_004384862.1|  [L=428]
Description: sodium:neurotransmitter symporter family protein [Methanosaeta concilii GP6]
Scores for 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-68  229.8  35.2    1.9e-34  119.2  16.0    2.2  2  SNF       Sodium:neurotransmitter symporter family


Domain annotation for each model (and alignments):
>> SNF  Sodium:neurotransmitter symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4  11.5     8e-38   1.4e-33       2     113 ..       2     113 ..       1     125 [. 0.97
   2 !  119.2  16.0   1.1e-38   1.9e-34     181     481 ..     134     426 ..     117     428 .] 0.85

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 8e-38
                               SNF   2 etwskkldfilsvvGfavgLgnvWRFPYlcyknGGGafliPYlilllvaGiPlfflelalGqytreGaitvwrkicP 78 
                                       e+ws++l f+l+++G+avg+gn+WRFP ++ +nGGGa+liPY++++++  +Pl+ le+a+G++ r+  ++++ +   
  gi|330508434|ref|YP_004384862.1|   2 ERWSSRLVFVLAAIGSAVGIGNIWRFPMVVGQNGGGAYLIPYFLAVVCLAVPLMILEMAVGRHWRRNLVASFGRAGK 78 
                                       78*************************************************************************** PP

                               SNF  79 llkgiGyasivvalyvglyYnvilawalfYlfssf 113
                                       +++ +G+ +++++l++  yY vi++w+l Yl+ s+
  gi|330508434|ref|YP_004384862.1|  79 RFEIVGWLICLIVLLILSYYLVIMGWTLAYLLFSL 113
                                       *******************************9997 PP

  == domain 2  score: 119.2 bits;  conditional E-value: 1.1e-38
                               SNF 181 tlcllvawvvvylailkGvkssgkvvyftatfPyvvllvllvrgvlLpGavkgikfyltpdlekllepkvWidaatq 257
                                       ++++l++ ++v+l++  G++   +++     f +++l+ l++  v LpG   g++f+++pd+++l +p+vW +a  q
  gi|330508434|ref|YP_004384862.1| 134 LISVLATGLIVSLGVNMGIERIVSIM---IPFAFLILVALVLFCVSLPGFHPGMDFFIQPDYSMLRRPDVWSAAIGQ 207
                                       44556667899999999998755555...56888******************************************* PP

                               SNF 258 iffslgigfGvlialasYnkfennvyrdallvslinsltsvlaglvvFsvlGfmaeeqgekisevaeeGpgLaFiay 334
                                        ffsl++g+G+li+++++ + + ++ ++al++++ + l  +lag+++Fs++     e           G+ LaF + 
  gi|330508434|ref|YP_004384862.1| 208 AFFSLSVGMGILITYGAHLEDDMDIPQSALIITFSDLLAAMLAGIAIFSLVFTFGLE--------PAAGAELAFTTL 276
                                       *************************************************87333322........3579******** PP

                               SNF 335 pealtklplsplwsvlFFlmlillgldsqfgtvegiitavvDefkvllrrrelltlivavla.....flvglllvte 406
                                       p+a   +p+++++sv FF  l  ++l+s+++++e  ++a++ + k++ +r  +l +i+ v+      +  + l +  
  gi|330508434|ref|YP_004384862.1| 277 PRAFELMPYGQIFSVAFFALLFSAALTSSISMMEMNVAAIMGQTKSSRKRASILLMILLVALgtpsaLSYSSLDLRF 353
                                       *********************************************96666666655555543111102222233456 PP

                               SNF 407 gGiyvltlldkyaaslsllvvvlleaiavawvyglkkflddikemlgfrpllflklcwkfvspllllvlliasiv 481
                                        G  +l+l+d  + +++l +++ll ai+  w+   + +  +++  l+ r l+ l +  k+v p+ ll ++ a i+
  gi|330508434|ref|YP_004384862.1| 354 FGSRILDLMDVSVGTIGLPIAALLVAITFRWLIDDDVLAGQVH--LSERWLRTLSILTKYVIPAALLLITAAMIM 426
                                       79******************************99999998886..677888888889999999999888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1155  (0.0644208); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 2877.47
//
Query:       gi|330508435|ref|YP_004384863.1|  [L=285]
Description: universal stress protein [Methanosaeta concilii GP6]
Scores for complete 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-45  153.9   3.1    1.2e-25   90.6   0.2    2.1  2  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.037   13.8   0.0         16    5.3   0.0    3.1  3  RQC       RQC domain
      0.083   13.1   1.5       0.17   12.1   1.5    1.5  1  GFD1      GFD1 mRNA transport factor


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 !   90.6   0.2     2e-29   1.2e-25       1     141 []       1     135 [.       1     135 [. 0.95
   2 !   64.3   0.2   2.8e-21   1.7e-17       2     141 .]     152     280 ..     151     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 2e-29
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       m++rIl+++D+s +s+++le  +el  ++  +++llhvi  +a + v d+  e++e+ ++ ee+++ +    +a+++
  gi|330508435|ref|YP_004384863.1|   1 MFQRILIPTDFSRYSQNLLECIAELPGEK--TVVLLHVIQRKAVERVWDPTAEVAEAKEKIEEQKRYL----EALRI 71 
                                       9***************************8..8*************99999999999999999988864....68*** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++++++ ++ eg+ a +i +va+ee+a li+vG+rgr+++s+lllGSvs+ vlr  + ++l+ r
  gi|330508435|ref|YP_004384863.1|  72 EVKTRVETIMEGSIAKTIQRVADEENATLIMVGARGRGRISGLLLGSVSRDVLRYGQTDLLIMR 135
                                       ******************************************************9999999865 PP

  == domain 2  score: 64.3 bits;  conditional E-value: 2.8e-21
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       + ++++++D+s+ +k A+     + +++  e+ l++v+++ +s++  da+  ++ + l +  +e +           
  gi|330508435|ref|YP_004384863.1| 152 FTKVICPTDFSDPAKDAILLVKGMKETS--EIGLVYVVSSGESDEQIDAAVRVAGSKLNSIVKEID---------RP 217
                                       579***************9999998886..8*******************************9985.........79 PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       g kv+++v++gd+ +ei  +a++eda+li + s+g ++l+++++GS++   +r a+ pVl+Vr
  gi|330508435|ref|YP_004384863.1| 218 GLKVTTHVKVGDAPHEISSLADNEDASLIAMSSHGAGWLEQMVVGSTTYDTARIANRPVLIVR 280
                                       **************************************************************8 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0027        16       5      31 ..       9      37 ..       7      39 .. 0.77
   2 ?   -0.5   0.0      0.17     1e+03      27     100 ..     108     128 ..      79     138 .. 0.55
   3 ?    4.5   0.0    0.0048        29       5      43 ..     159     197 ..     158     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0027
                                      EE-HHHHHHHHHHHHHT.T.S-SBHHHHH CS
                               RQC  5 vDvteeaqkilscvyrt.g.qrfgaghiv 31
                                       D+++++q++l+c+ ++ g + + + h++
  gi|330508435|ref|YP_004384863.1|  9 TDFSRYSQNLLECIAELpGeKTVVLLHVI 37
                                      59***************851444556665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.17
                                       HHHHHHHHHT---CCCCCTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEE..SSSBEEE-CCGHHHHT.SS CS
                               RQC  27 aghivdvLrGsktkkirqlghdklstfGigkdlskkewrrlirqLiaegyLeedveeygvlkltekarevlk.ge 100
                                        g i                                                      ++l l++ +r+vl+ g+
  gi|330508435|ref|YP_004384863.1| 108 RGRI------------------------------------------------------SGLLLGSVSRDVLRyGQ 128
                                       3333......................................................45555555555555443 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0048
                                       EE-HHHHHHHHHHHHHTTS-SBHHHHHHHHHT---CCCC CS
                               RQC   5 vDvteeaqkilscvyrtgqrfgaghivdvLrGsktkkir 43 
                                        D+++ a++++ +v+ +++   +g +  v  G+++++i 
  gi|330508435|ref|YP_004384863.1| 159 TDFSDPAKDAILLVKGMKETSEIGLVYVVSSGESDEQID 197
                                       59***************9888888887788888888776 PP

>> GFD1  GFD1 mRNA transport factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.5   2.9e-05      0.17       6      17 ..      56      67 ..      52      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
                              GFD1  6 KKKIEEQrkIle 17
                                      K+KIEEQ++ le
  gi|330508435|ref|YP_004384863.1| 56 KEKIEEQKRYLE 67
                                      9*******9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2184.02
//
Query:       gi|330508436|ref|YP_004384864.1|  [L=299]
Description: aspartate carbamoyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-48  162.8   0.0    2.7e-47  160.5   0.0    1.9  2  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    6.2e-30  104.4   0.0    8.2e-30  104.0   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 !  160.5   0.0   3.1e-51   2.7e-47       6     147 ..       1     136 [.       1     137 [. 0.93
   2 ?    0.5   0.0     0.063   5.6e+02      35      75 ..     139     179 ..     136     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 160.5 bits;  conditional E-value: 3.1e-51
                                       GGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTTG CS
                          OTCace_N   6 ledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlssv 82 
                                       ++++skeei+++ldla++l+    + kk++ l+gk+lallF+epStRTr+Sfe+A+krlGg+v++l+ a   + ss+
  gi|330508436|ref|YP_004384864.1|   1 MREFSKEEIDSVLDLAQSLEPLA-RGKKSSMLAGKILALLFFEPSTRTRMSFETAMKRLGGSVINLGPA---EGSSI 73 
                                       5789****************775.5999***************************************66...46888 PP

                                       GSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                          OTCace_N  83 skgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                       skg  Esl+Dt+rv+++y+da+viRhp++ +++   +++ vpv+Nagdg+g+HPtQ+L+Dl+tir
  gi|330508436|ref|YP_004384864.1|  74 SKG--ESLADTVRVIGGYADALVIRHPKEGSARLASQFSPVPVLNAGDGAGHHPTQTLLDLYTIR 136
                                       999..**********************666688778889*************************8 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.063
                                       TTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTT CS
                          OTCace_N  35 kllkgktlallFeepStRTrvSfevAakrlGgkvlslseae 75 
                                       + l++ ++al+   +  RT  S   A +  G++ + +s ++
  gi|330508436|ref|YP_004384864.1| 139 SRLENLHVALVGDLKYGRTVHSLAYALSLYGADITLVSPPT 179
                                       56778888888888889************999998888553 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.0   9.1e-34   8.2e-30       2     156 ..     143     291 ..     142     292 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 9.1e-34
                                       C.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE CS
                            OTCace   2 glkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvyt 77 
                                       +l++a+vGd k++++++sl+++l+ +g+d++lv+P++l++     + +k++ +++g  +  t dl e+++++Dv+y+
  gi|330508436|ref|YP_004384864.1| 143 NLHVALVGDlKYGRTVHSLAYALSLYGADITLVSPPTLRM----PDPIKADLSSKGTIVRETADLGEVIDNVDVLYM 215
                                       789**********************************877....35668889999********************** PP

                                       --SSETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHH CS
                            OTCace  78 dvwvsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhti 150
                                       ++++     +er+    +++k++  y++t e l+  ++++i++H+LP  r +E++ +V+ds ++ +f+q  +++ ++
  gi|330508436|ref|YP_004384864.1| 216 TRIQ-----RERFpdpVEYQKVASsYRITPESLAGSQQNLIIMHPLP--RVDEISPSVDDSSHARYFQQSFYGVPVR 285
                                       ****.....8888788777777777**********************..**************************** PP

                                       HHHHHH CS
                            OTCace 151 kAllvl 156
                                       +All +
  gi|330508436|ref|YP_004384864.1| 286 MALLKM 291
                                       ***976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2158.39
//
Query:       gi|330508437|ref|YP_004384865.1|  [L=167]
Description: aspartate carbamoyltransferase, regulatory subunit [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-34  115.8   1.4    1.1e-33  115.4   1.4    1.2  1  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    3.4e-16   58.9   0.8      6e-16   58.1   0.8    1.4  1  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me
  ------ inclusion threshold ------
      0.024   13.7   0.1      0.029   13.4   0.1    1.1  1  T2SSE     Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> PyrI  Aspartate carbamoyltransferase regulatory chain, allosteric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   1.4   1.8e-37   1.1e-33       1      93 [.      19     110 ..      19     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 1.8e-37
                                       X-----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT- CS
                              PyrI   1 lkvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapna 77 
                                       l+vk+i+nG+ViDHI+ g+al+vlk+L++++ +++++v++++nv+skklgkKdi+k+e++el+eeel+++aliap a
  gi|330508437|ref|YP_004384865.1|  19 LRVKPINNGTVIDHIAGGQALNVLKILGISG-TTGATVSVVMNVESKKLGKKDIVKVEDRELREEELNRIALIAPAA 94 
                                       68****************************8.7777***************************************** PP

                                       EEEEEETTEEEEEE-- CS
                              PyrI  78 tiniIkdgevveKkkv 93 
                                       +iniI++ +v+eK+ v
  gi|330508437|ref|YP_004384865.1|  95 SINIIRNCRVIEKRPV 110
                                       *************976 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 !   58.1   0.8     1e-19     6e-16       1      43 [.     115     158 ..     115     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1e-19
                                       EEESSS--S-TTBGGGT.TS-.-EEEEEETTTTEEEETTT--EE CS
                            PyrI_C   1 eiegvlkCpNpnCItnn.epveskFkvedkekvklkCkYCekei 43 
                                       ei gv++C+NpnCI+n+ ep++s++ v+ k++v l+C YCe+++
  gi|330508437|ref|YP_004384865.1| 115 EIVGVVRCQNPNCISNThEPIKSRMLVKVKNPVLLRCLYCEQPL 158
                                       699**************89**********************986 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.8e-06     0.029     130     188 ..      43      98 ..      28     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-06
                             T2SSE 130 glilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnakkakvtf 188
                                       +++ +sG+Tg   ++++++  k++ k+   iv vED +E++ e+ n+++l a +a++++
  gi|330508437|ref|YP_004384865.1|  43 KILGISGTTGATVSVVMNVESKKLGKK--DIVKVED-RELREEELNRIALIAPAASINI 98 
                                       56669********************99..9******.8********9999887666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1146.39
//
Query:       gi|330508438|ref|YP_004384866.1|  [L=257]
Description: FKBP-type peptidylprolyl isomerase [Methanosaeta concilii GP6]
Scores for complete 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   0.2    1.8e-05   25.0   0.1    2.4  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
    9.9e-07   28.8   0.3    2.4e-06   27.5   0.2    1.7  2  FKBP26_C  FKBP26_C-terminal


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1     2e-09   1.8e-05       5      76 ..       3      86 ..       1     112 [. 0.86
   2 !    4.5   0.0    0.0047        42       8      74 ..     122     195 ..     115     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2e-09
                                      B-TTCEEEEEEEEEETTSSEEEEH..........CC...HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGT CS
                            FKBP_C  5 akegdtVtvhykgkledgkvfdss..........rs...rakplefkvGsgqvikGfeealegmkvGekrtltippela 70
                                      +k+gd+++++y+ ++ dg+ ++++          +s   ++ p  ++vG+gq++kGfe  l+g + G   +++  pe a
  gi|330508438|ref|YP_004384866.1|  3 VKNGDFIRIDYTEFV-DGQAIATTvkdlaeekgiFSeeiQYGPHLVVVGAGQLVKGFESDLVGKEIGYSGRVEMDPENA 80
                                      799***********9.888888886666666666225679*************************************** PP

                                      TTTTTB CS
                            FKBP_C 71 Ygekgl 76
                                      +g ++ 
  gi|330508438|ref|YP_004384866.1| 81 FGLHDP 86
                                      *98765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0047
                                       TCEEEEEEEEEETTSSEEEEHCCHTSEEEEETTSSS.SCHHHHHH.HTTSBTT-EEEEEEEGGGTTTT......T CS
                            FKBP_C   8 gdtVtvhykgkledgkvfdssrsrakplefkvGsgq.vikGfeea.legmkvGekrtltippelaYge......k 74 
                                       g +V+++++  l++++v+ +  +  + +e + ++ + +ik f +  le   ++e + +t+p el+Y +      +
  gi|330508438|ref|YP_004384866.1| 122 GRKVSIDFNHPLAGKTVVYEY-TIRETVEDQTERLKaLIKTFGRVdLEAEIKDEVAVITVPWELNYYKewvmirR 195
                                       667777777777554444444.677777777777555777776543666668899999*******9885555552 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.3   1.2e+04      36      46 ..      32      42 ..      31      46 .. 0.83
   2 !   27.5   0.2   2.7e-10   2.4e-06       2      70 ..     152     215 ..     151     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                                      TTGGGSTTHHH CS
                          FKBP26_C 36 eeakFieniql 46
                                      e+ +F e+iq+
  gi|330508438|ref|YP_004384866.1| 32 EKGIFSEEIQY 42
                                      67789999997 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 2.7e-10
                                       HHHHHHHHHHH-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEE CS
                          FKBP26_C   2 kekikelIkryiPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvde 70 
                                        e +k+lIk    ++d   ++ ei+d++++I++p e  ++++  ++++++A+ i++ + ++++V +++ 
  gi|330508438|ref|YP_004384866.1| 152 TERLKALIKT-FGRVD---LEAEIKDEVAVITVPWELNYYKEWVMIRRGLAEMIIQHL-GMKEVHYIEK 215
                                       5888999998.67888...99*************************************.********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1842.72
//
Query:       gi|330508439|ref|YP_004384867.1|  [L=136]
Description: hypothetical protein MCON_2634 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   15.9   0.2      0.017   15.4   0.2    1.2  1  Tad       Putative Flp pilus-assembly TadE/G-like


Domain annotation for each model (and alignments):
>> Tad  Putative Flp pilus-assembly TadE/G-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.2   9.3e-07     0.017       6      27 ..      12      34 ..       8      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.3e-07
                               Tad  6 lfalallpllllvglav.Dvgra 27
                                      ++a+++l ll++vg+a+ D+g  
  gi|330508439|ref|YP_004384867.1| 12 ILAVLALGLLVAVGAAFeDYGGS 34
                                      89******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1066.12
//
Query:       gi|330508440|ref|YP_004384868.1|  [L=195]
Description: hypothetical protein MCON_2635 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       297  (0.0165653); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1396.42
//
Query:       gi|330508441|ref|YP_004384869.1|  [L=541]
Description: hypothetical protein MCON_2637 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-09   36.4   0.0     0.0036   17.4   0.0    2.9  2  Nitroreductase  Nitroreductase family


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.9e-07     0.011      28     154 ..      91     211 ..      57     218 .. 0.79
   2 !   17.4   0.0     2e-07    0.0036      97     169 ..     455     526 ..     330     527 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.9e-07
                                       HTS--GGG---EEEEEE..-CCCH......HHHHHHHHHHHHHHHTT-SS-GGGGGGHHHHHHHHHHHHSSEEEEE- CS
                    Nitroreductase  28 rraPsagnlqpwrfvvv.qdkelr......yklaeaalelllkaeaqaelaqryrkeelklkaqkalagapvliviv 97 
                                       r  Ps+gnl+p++ +++   +e++      y ++++ ++l l a  ++e++q+            +l   ++l++++
  gi|330508441|ref|YP_004384869.1|  91 RVNPSSGNLHPTECYLLaGGGEELdlspgvYHYQPKDHSLELLAGIREESWQS-----------LHLPSGTILLILT 156
                                       779**************777777788888866666666666666666666665...........3466666666668 PP

                                       --TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHH CS
                    Nitroreductase  98 atldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkll 154
                                       + + + ++k+++ra ry +ld+g+a+     aA  lG+    ++ +  ++  ++++l
  gi|330508441|ref|YP_004384869.1| 157 TIYWRESWKYGARAFRYCMLDLGHALAAAGEAACCLGWTLSLQEELGTDD--LARIL 211
                                       8888***********************99999999999888888887777..77766 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2e-07
                                       ---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S...SEEEEEEEEE CS
                    Nitroreductase  97 vatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglp.deeeivvliavG 169
                                         ++++    +++  y+  + ++g++ q l+L+ +a G+  c ig f ++   v+++lgl   +++ +++++vG
  gi|330508441|ref|YP_004384869.1| 455 ISRFEDPIGEYGPWFYSRLYWECGMIGQALYLSSEATGYRGCGIGCFFDDM--VHRMLGLFdLGYQDLYHFTVG 526
                                       467777778888889999*********************************..******974445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 3043.63
//
Query:       gi|330508442|ref|YP_004384870.1|  [L=417]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete 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   88.4   0.1    5.4e-25   87.5   0.1    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family
    3.7e-21   75.6   0.0    6.6e-21   74.8   0.0    1.4  1  DEDD_Tnp_IS110  Transposase
  ------ inclusion threshold ------
      0.036   14.4   1.0      0.081   13.2   0.1    2.0  2  Init_tRNA_PT    Rit1 DUSP-like domain


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.1     9e-29   5.4e-25       2      83 ..     249     330 ..     248     336 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 9e-29
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaaira 78 
                                       +++ s+pG+G++ aa+++ae+gd r f+sa+++a+y+G++p+++qS++k r g+i+k G++++Rr+L+e A a++r+
  gi|330508442|ref|YP_004384870.1| 249 KIILSVPGVGFISAATIIAEMGDYRDFPSADKMAKYFGIVPSVYQSAGKLRTGKITKTGSKHMRRILVEVAKAISRT 325
                                       6899***********************************************************************99 PP

                    Transposase_20  79 npelr 83 
                                       ++ +r
  gi|330508442|ref|YP_004384870.1| 326 KKNSR 330
                                       75554 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0   1.1e-24   6.6e-21       1     153 [.       9     152 ..       9     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.1e-24
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G D++kd   a++i+++g +l +er++++++gl a+ ++   ++++ + +ve+tg ++++++++ le +++ ++ n
  gi|330508442|ref|YP_004384870.1|   9 CGADIHKDFLIATMISRSGLKL-QERFNMNQDGLLAFRSW-IINHRCQRLAVESTGGFWYPIFTI-LEGHVEFILAN 82 
                                       79*************9999885.668**************.889****************88876.7899******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdqv 153
                                       ++++++++     ++KtD++D++ IA + +  + ++p++  +++y++Lr++tr+re+lv+ r++ kn++++ L   
  gi|330508442|ref|YP_004384870.1|  83 AYQIRNIE-----HKKTDKLDSERIAIYCL-NNLITPSRIYPKDYRDLRSITRARETLVNARSKIKNQIHQSLSTC 152
                                       *****995.....89***************.****************************************99765 PP

>> Init_tRNA_PT  Rit1 DUSP-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.2   7.1e+03      26      43 ..     133     152 ..     119     162 .. 0.47
   2 ?   13.2   0.1   1.4e-05     0.081      10      80 ..     304     378 ..     296     389 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                      Init_tRNA_PT  26 dfvrkrlsedkk..kkilva 43 
                                       + v++r++ +++  +++  +
  gi|330508442|ref|YP_004384870.1| 133 TLVNARSKIKNQihQSLSTC 152
                                       33333333322222333333 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.4e-05
                      Init_tRNA_PT  10 gKkgsknLrtalpkivdfvrkrlsedkk....kkilvacetGkdlsvgvaLailcklfddakls...eeqsesnitK 79 
                                        K+gsk++r +l ++ ++++++ ++++     ++il+ c + +   v++a  +lc ++   +l    e+ +e+++tK
  gi|330508442|ref|YP_004384870.1| 304 TKTGSKHMRRILVEVAKAISRTKKNSRLmrffQRILARCGKKNIATVALARKVLCIIY---HLLmnhENYQEPEVTK 377
                                       49*****************99966655599**99******999999999888888888...2222235666777777 PP

                      Init_tRNA_PT  80 d 80 
                                       +
  gi|330508442|ref|YP_004384870.1| 378 T 378
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); 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: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2894.12
//
Query:       gi|330508443|ref|YP_004384871.1|  [L=272]
Description: prephenate dehydratase [Methanosaeta concilii GP6]
Scores for complete 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   0.0    5.9e-56  189.2   0.0    1.1  1  PDT            Prephenate dehydratase
    3.4e-13   49.1   0.0    7.7e-13   48.0   0.0    1.7  1  ACT            ACT domain
     0.0049   17.4   0.0      0.016   15.8   0.0    1.8  2  ACT_4          ACT domain
  ------ inclusion threshold ------
      0.071   12.8   0.0       0.13   12.0   0.0    1.5  1  PEP-utilizers  PEP-utilising enzyme, mobile 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 !  189.2   0.0   1.3e-59   5.9e-56       1     180 [.       5     179 ..       5     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 189.2 bits;  conditional E-value: 1.3e-59
                                       EEEES-TTSHHHHHHCCCS......EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEE CS
                               PDT   1 vaylGpegtyshqAalkvf.kaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkivg 76 
                                       +++lGpegtys++Aal    + +++ l+ ++ +++v++ave+ge dy++vP+ENs+eG+V+ + DlLl+  ++ ivg
  gi|330508443|ref|YP_004384871.1|   5 IGVLGPEGTYSEKAALIWSeGMPSTVLVYFKDFDGVLQAVEEGELDYGIVPLENSLEGAVTVVNDLLLR-LNVVIVG 80 
                                       789*************88888999*********************************************.88***** PP

                                       EEEEE---EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHH CS
                               PDT  77 EvvlpiehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaa 153
                                       Ev +p++hcL+++  +  +eik ++Shpqal+Qcr+f++eh+p++e +++ st++Aa+   a++  ++aaia + aa
  gi|330508443|ref|YP_004384871.1|  81 EVNVPVRHCLVGQG-E--SEIKIILSHPQALAQCRQFIREHYPGAETRTTGSTSHAARL--AQEFGEMAAIADAGAA 152
                                       **********7665.5..6****************************************..99999*********** PP

                                       HHTT-EEEECS-SS-S--EEEEEEEEE CS
                               PDT 154 elyglkvleeniedkknntTRFlvlak 180
                                       e+ygl+vl+++++d+++n+TRF+v ++
  gi|330508443|ref|YP_004384871.1| 153 ERYGLRVLARDVQDVRENVTRFIVAGR 179
                                       ***********************9876 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   1.7e-16   7.7e-13       2      66 ..     191     256 ..     190     257 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1.7e-16
                                       EEEE.EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT   2 vlrv.gvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                       +l + +++DrPG+L  +++ +a+r iN+++ie+r+s++++++++f +++++++d + vl+al+k+ 
  gi|330508443|ref|YP_004384871.1| 191 SLVIhLAKDRPGALYSILQEFAQRSINLTRIESRPSRRGLGDYYFYIDLEGHQDNSVVLDALEKIR 256
                                       67774566*******************************************************986 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.5   6.8e+03       9      27 ..     157     175 ..     155     177 .. 0.79
   2 !   15.8   0.0   3.5e-06     0.016      13      73 ..     197     256 ..     189     257 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                             ACT_4   9 leveaedrkglLaditqvi 27 
                                       l+v a+d + +  ++t+ i
  gi|330508443|ref|YP_004384871.1| 157 LRVLARDVQDVRENVTRFI 175
                                       7888999988888888765 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.5e-06
                             ACT_4  13 aedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraip 73 
                                       a+dr+g+L +i+q +++  +n++ ++++  +  gl +  + + ++ +++ s v+++L++i+
  gi|330508443|ref|YP_004384871.1| 197 AKDRPGALYSILQEFAQRSINLTRIESRPSR-RGLGDYYFYIDLEGHQDNSVVLDALEKIR 256
                                       79***************************86.99**************9999999999986 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     3e-05      0.13      29      58 ..     124     154 ..     103     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                                       ES--TTHHHHHHHHHHTT.--EEE--SSHH. CS
                     PEP-utilizers  29 terGGmtSHaAivArelg.iPaVvgvgeati 58 
                                       t + G tSHaA +A+e+g + a++ +g+a++
  gi|330508443|ref|YP_004384871.1| 124 TRTTGSTSHAARLAQEFGeMAAIADAGAAER 154
                                       8899*************84566888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1858.80
//
Query:       gi|330508444|ref|YP_004384872.1|  [L=423]
Description: hydroxymethylglutaryl-CoA reductase [Methanosaeta concilii GP6]
Scores for complete 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-111  372.9   5.6   1.9e-111  372.6   5.6    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 !  372.6   5.6  1.1e-115  1.9e-111       3     367 .]      14     376 ..      12     376 .. 0.95

  Alignments for each domain:
  == domain 1  score: 372.6 bits;  conditional E-value: 1.1e-115
                                       HHHHHHHHH...S-HHHHHHHTT----HHHHHHHSSS---------EEEEEEEETTEEEEEEE---STTHHHHHHHH CS
                       HMG-CoA_red   3 eeRrkllee...lteeeleelkeesldeevadkmiEnviGyvqlPlGvagpllingkeylvPmAteEgslvAsasrg 76 
                                       +eR+k+++e      ee++++ e +l  ++a+km+EnviG +q+PlG+a++++i+g+e+l+PmAteE+s++A+as+g
  gi|330508444|ref|YP_004384872.1|  14 NERLKAVAEqvaVGSEEISQV-ERGLVLDQAEKMVENVIGMFQVPLGIATNFVIDGQEVLIPMATEEPSVIAAASNG 89 
                                       689999999444444444443.56788************************************************** PP

                                       HHHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHH.HTHHHHHHHHHHCSHH..CCT-EEEEEEE.EE-... CS
                       HMG-CoA_red  77 akainesgGvkttvlkdgmtraqvvllesvedaaelkkwi.ekkeeleelanaaest..srggglkdiev.vla... 146
                                       a++++ +gG+  t+++  ++raq++ +  ++d+ +++++i  +k+el ++an+ +++  + ggg+kdiev v++   
  gi|330508444|ref|YP_004384872.1|  90 ARMARGGGGF-LTSSTGPVMRAQIQAT-GIDDPFAARQAIlLHKDELMAMANELDPMlvKYGGGVKDIEVyVIDsrl 164
                                       **********.7777778*********.******************************************7777999 PP

                                       SSEEEEEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHH CS
                       HMG-CoA_red 147 grlvvlrlkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeev 223
                                       g++vv +l vd++DAmGaN+vn+++ea+a+ ie++ g++++l+i sNl++ ++a+a+++++ +++        g ev
  gi|330508444|ref|YP_004384872.1| 165 GPMVVTHLIVDCRDAMGANAVNTMAEALAPRIEQIAGGRVYLRIISNLADLRLARAKAVFRAEDI-------GGPEV 234
                                       99***********************************************************9999.......9**** PP

                                       HHHHHHHHHHHHH-HHHH..HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTT.......SEEE...TT CS
                       HMG-CoA_red 224 vekilkasaealvdlnranigtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaa.......leev...ed 290
                                       v+ i+ a + a+vd++ra  +t+nkGi       +Ng++Av+lAtG+D++ave+++h +a+       l+++   +d
  gi|330508444|ref|YP_004384872.1| 235 VDGIILAAELAVVDPYRA--ATHNKGI-------MNGVTAVVLATGNDTRAVEAGAHSYASrtgrymsLTRYernRD 302
                                       ******************..*******.......********************************99666666588 PP

                                       TEEEEEEEEE.----SBSHHHHH-HHHHHH.HHTT---HH...HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHH CS
                       HMG-CoA_red 291 gdlygsvtlPsleVGtvGGgtklppqaell.kllgvkgaknakeLaeiiaavgLAqelsalrALaaeglqkgHmklh 366
                                       gdl+g+++lP ++VG vGG+t+++p a+ + k+l vk+a+   +L++ iaavgL+q+++alrALa+eg+q+gHm+lh
  gi|330508444|ref|YP_004384872.1| 303 GDLVGTIELP-VAVGLVGGATRVHPVAKTAvKILAVKSAD---DLSRKIAAVGLCQNFAALRALASEGIQRGHMSLH 375
                                       88********.*****************************...*********************************9 PP

                                       H CS
                       HMG-CoA_red 367 r 367
                                       +
  gi|330508444|ref|YP_004384872.1| 376 A 376
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3333.92
//
Query:       gi|330508445|ref|YP_004384873.1|  [L=350]
Description: cellulase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.1e-103  346.3   0.6   1.3e-103  346.1   0.6    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
      2e-09   37.4   0.1      3e-09   36.9   0.1    1.3  1  Peptidase_M20  Peptidase family M20/M25/M40
  ------ inclusion threshold ------
      0.094   13.5   0.0       0.81   10.4   0.0    2.2  1  DUF1691        Protein of unknown function (DUF1691)
       0.14   11.8   0.0        1.1    9.0   0.0    2.2  2  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.1   0.6  2.8e-107  1.3e-103       1     292 []      45     336 ..      45     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 346.1 bits;  conditional E-value: 2.8e-107
                                       S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGC CS
                     Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHll 77 
                                       Gnlia+kkg  ++p++mi AH DeiG+mVk+I+e+Gf+rf ++GG+ +++l +qrv i+t++g + GvigskppH++
  gi|330508445|ref|YP_004384873.1|  45 GNLIATKKG--DRPSIMIDAHADEIGLMVKQIDEKGFIRFIRIGGWFDQTLLNQRVIIHTSSGPVVGVIGSKPPHVM 119
                                       9********..****************************************************************** PP

                                       HHHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS- CS
                     Peptidase_M42  78 keeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeeel 154
                                       k+e+rkk +e  ++fiDig ++++e+eelGi +G+++++d+efv ++++ +++ka+D+rag+++++e+lk+ k+++ 
  gi|330508445|ref|YP_004384873.1| 120 KDEDRKKVVEARDMFIDIGCSNQAEVEELGILPGTPISIDREFVPMHGDTVTGKAFDNRAGLVIMIEALKRTKSKS- 195
                                       ************************************************************************9985. PP

                                       SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETT...CCSHHHHH CS
                     Peptidase_M42 155 eatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDas...giyhpklr 226
                                         t+y+va vqEEvGl+Gak++a+ ++pdiaia Dvt+ gd+pg ++k+a   +gkGpv++v D s   +i+ p++ 
  gi|330508445|ref|YP_004384873.1| 196 --TIYAVAAVQEEVGLKGAKVAAFGLDPDIAIASDVTIPGDHPGIEKKDAPieMGKGPVLVVADGSgrgLIATPQVI 270
                                       ..***********************************************9999***********998889******* PP

                                       HHHHHHHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                     Peptidase_M42 227 kkllelAkknnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                       ++l+ +Ak+ +ip+qle+  gg+tDA++i lt++g+pt++is++tryiHspvev++l+d+e +++L
  gi|330508445|ref|YP_004384873.1| 271 EWLVGTAKEFEIPVQLEASDGGTTDATSIYLTRSGIPTGVISVATRYIHSPVEVLNLNDIERAADL 336
                                       *************************************************************99987 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 !   36.9   0.1   6.8e-13     3e-09      28     206 ..     172     342 ..     151     343 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 6.8e-13
                                       TEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEEEESSSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20  28 GklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelhieepgi 104
                                       G      a d+ +g+++++eal++ k +      ti  ++ + EE+g +Gak  + gl  + ++   + +    pgi
  gi|330508445|ref|YP_004384873.1| 172 G-----KAFDNRAGLVIMIEALKRTKSKS-----TIYAVAAVQEEVGLKGAKVAAFGLDPDIAIASDVTIPGDHPGI 238
                                       4.....5899************9977665.....***********88899977777666335555544333233333 PP

                                       TCHSTETEEEE....EEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEE.EESSSBHTHHHH....TTTEEE CS
                                       xxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx....xxxxxx RF
                     Peptidase_M20 105 leagklaigvv....kvevelleggapvtlndsplvkalaeaaeelfgekveli.vsgpggtdarff....agiptv 172
                                        + +   + +      v v   ++g+   +  ++++++l  +a+e+    v+l+   g g+tda  +     gipt 
  gi|330508445|ref|YP_004384873.1| 239 EK-KD--APIEmgkgPVLVVADGSGRGLIAT-PQVIEWLVGTAKEF-EIPVQLEaSDG-GTTDATSIyltrSGIPTG 309
                                       33.22..233255655555545778877777.*************6.87888886778.******999998899*** PP

                                       EEEESSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 173 mifgpgsglaHspnEyvdledlekgikvlarlle 206
                                       +i +     +Hsp E ++l+d+e++++++ar le
  gi|330508445|ref|YP_004384873.1| 310 VISVAT-RYIHSPVEVLNLNDIERAADLMARSLE 342
                                       887766.89********************99875 PP

>> DUF1691  Protein of unknown function (DUF1691)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00018      0.81      14      97 ..      56     211 ..      55     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                           DUF1691  14 Pllvgdsskvgllyvahglarsppl......slleyaaLvgsgvlHivsGlakwlgll................... 65 
                                       P + +d  +++++ +++++ ++ ++      +++ +++L   +++H  sG +  +g++                   
  gi|330508445|ref|YP_004384873.1|  56 PSIMIDAHADEIGLMVKQIDEKGFIrfirigGWFDQTLLNQRVIIHTSSGPV--VGVIgskpphvmkdedrkkvvea 130
                                       788899999**********999988999999*******************99..88888888877777777777777 PP

                           DUF1691  66 .................................................rilkki...kkkkrrrrwliingiaaak 90 
                                                                                        ++   +   +  kr + +++i ++aa++
  gi|330508445|ref|YP_004384873.1| 131 rdmfidigcsnqaeveelgilpgtpisidrefvpmhgdtvtgkafdnraGL---VimiEALKRTKSKSTIYAVAAVQ 204
                                       777777777777777777777777777777777777776666666554422...12334444555555777777777 PP

                           DUF1691  91 aalglaG 97 
                                       +++gl G
  gi|330508445|ref|YP_004384873.1| 205 EEVGLKG 211
                                       7777766 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.097   4.3e+02       1      26 [.      46      69 ..      46      79 .. 0.80
   2 ?    9.0   0.0   0.00023       1.1      20      82 ..     166     216 ..     161     336 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.097
                                      EEEEEESTTCESEEEEEEEE--B-TT CS
                     Peptidase_M28  1 NviatlegkatdevlllgAHyDsvgv 26
                                      N+iat +g+     +++ AH D +g 
  gi|330508445|ref|YP_004384873.1| 46 NLIATKKGDR--PSIMIDAHADEIGL 69
                                      7888887777..58********9875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00023
                                       E--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHH CS
                     Peptidase_M28  20 HyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafa 82 
                                       H D+v    g+    A Dn +g ++++e ++  ++     k ++  ++   EE gl G+k  a
  gi|330508445|ref|YP_004384873.1| 166 HGDTVT---GK----AFDNRAGLVIMIEALKRTKS-----KSTIYAVAAVQEEVGLKGAKVAA 216
                                       556665...45....89**********99998886.....89*****************9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2405.78
//
Query:       gi|330508446|ref|YP_004384874.1|  [L=143]
Description: universal stress protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-33  114.6   5.1    5.5e-33  114.5   5.1    1.0  1  Usp           Universal stress protein family
     0.0045   16.4   0.6     0.0077   15.7   0.4    1.5  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.042   14.2   1.4       0.61   10.5   0.1    2.4  2  Toprim_3      Toprim domain
      0.074   13.0   0.3       0.19   11.7   0.3    1.7  1  DUF3606       Protein of unknown function (DUF3606)
      0.083   13.1   1.8       0.51   10.6   0.3    2.1  2  GAD           GAD domain


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.5   5.1   1.5e-36   5.5e-33       1     141 []       1     143 []       1     143 [] 0.94

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 1.5e-36
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHH CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaa 75 
                                       mykrIl+a+Dgse sk+A++ + elaka ga++i+l+v+ +   +++     + +++ ++  +a+ e++   +k + 
  gi|330508446|ref|YP_004384874.1|   1 MYKRILIATDGSEKSKAAAKEGMELAKALGAQVIALNVVNEVVIASAVRQLGSDRKDVEARLKAAGEKAVeeLKSMG 77 
                                       9****************************************999999888888888887777777776667899999 PP

                                       HCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  76 eaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       + +gv+ ++vv+ g pa++i+++a +e+adliVvGs+g+sg  +ll+GSv+++vl  a++pVlvVr
  gi|330508446|ref|YP_004384874.1|  78 ASAGVNIDTVVRIGAPATAIIDTAGAEKADLIVVGSHGESGATKLLIGSVAQKVLYWATIPVLVVR 143
                                       *****************************************************************8 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 !   15.7   0.4   2.2e-06    0.0077      64     120 ..      10      69 ..       3      90 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.2e-06
                                       S.HHHHHHHHHHHHHHHHHHTBSEEEEEBCC......GBCTTTSGHHHHHHHHHHHHHHHHHHH CS
                      AP_endonuc_2  64 r.reesvdalkraielaaaLGapllvlhpGt......agagpkgseeeawerlaeslneladya 120
                                       + +e+s++a+k+ +ela+aLGa ++ l++ +      a ++ +++++     + ++l++++++a
  gi|330508446|ref|YP_004384874.1|  10 DgSEKSKAAAKEGMELAKALGAQVIALNVVNevviasAVRQLGSDRK----DVEARLKAAGEKA 69 
                                       356789**********************9987766553333333333....3333333333333 PP

>> Toprim_3  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00017      0.61      41      79 ..       2      38 ..       1      62 [. 0.78
   2 ?    3.1   0.2     0.033   1.2e+02      55      78 ..      61      88 ..      39     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                          Toprim_3 41 gkrvviaaDnDaandGreaaeklaerleaagieavllep 79
                                      +kr+ ia D+  +  +++aa++ +e ++a g ++++l  
  gi|330508446|ref|YP_004384874.1|  2 YKRILIATDGSEK--SKAAAKEGMELAKALGAQVIALNV 38
                                      699******9888..9***************99999876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.033
                          Toprim_3 55 d....Greaaeklaerleaagieavlle 78
                                           G++a+e+l +  ++ag+++ +++
  gi|330508446|ref|YP_004384874.1| 61 RlkaaGEKAVEELKSMGASAGVNIDTVV 88
                                      3556688888888888888887776665 PP

>> DUF3606  Protein of unknown function (DUF3606)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   5.4e-05      0.19      36      54 .]      45      63 ..      39      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.4e-05
                           DUF3606 36 raAVraVGnsakkVrayLg 54
                                      + AVr+ G+++k+V+a L+
  gi|330508446|ref|YP_004384874.1| 45 ASAVRQLGSDRKDVEARLK 63
                                      67**************997 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.029     1e+02      21      53 ..      12      44 ..       4      51 .. 0.76
   2 ?   10.6   0.3   0.00014      0.51       8      94 ..      40     122 ..      35     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.029
                                      TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGE CS
                               GAD 21 aklsrkeideleefakelgakglawikvegegl 53
                                      ++ s+ + +e++e+ak lga+ +a   v++  +
  gi|330508446|ref|YP_004384874.1| 12 SEKSKAAAKEGMELAKALGAQVIALNVVNEVVI 44
                                      566788899***********9988777776555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00014
                                       TEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCCS-HHHHHHHHHHCT--TTEEEEEE CS
                               GAD   8 ggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakflteeevkklleavgaeegDillfv 84 
                                       +++v a  v++   +  rk++++  + a e++ + l  ++ + +  +++++++  ++    +++++gae+ D+++ +
  gi|330508446|ref|YP_004384874.1|  40 NEVVIASAVRQ--LGSDRKDVEARLKAAGEKAVEELKSMGASAGVNIDTVVRI--GAPATAIIDTAGAEKADLIVVG 112
                                       56677777777..3667888888889999999999999999999999*****9..999******************* PP

                                       EEEHHHHHHH CS
                               GAD  85 Adkkktvnka 94 
                                       ++ ++ ++k 
  gi|330508446|ref|YP_004384874.1| 113 SHGESGATKL 122
                                       *999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1053.44
//
Query:       gi|330508447|ref|YP_004384875.1|  [L=129]
Description: AIR carboxylase [Methanosaeta concilii GP6]
Scores for 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-45  154.9   0.2    1.1e-45  154.8   0.2    1.0  1  AIRC      AIR carboxylase
  ------ inclusion threshold ------
      0.029   14.1   0.0      0.032   13.9   0.0    1.0  1  Fe-ADH_2  Iron-containing alcohol dehydrogenase


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.8   0.2   1.3e-49   1.1e-45       2     128 ..       4     126 ..       3     129 .] 0.97

  Alignments for each domain:
  == domain 1  score: 154.8 bits;  conditional E-value: 1.3e-49
                                       EEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS CS
                              AIRC   2 VgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttl 78 
                                       +++i GS+sD  ++ ++   lk+ gv++e rv+Sahr+p+el+ y++  ++   +v+Ia+AG +a+Lpgv+as+t+ 
  gi|330508447|ref|YP_004384875.1|   4 IAVISGSKSDQLIVDRILGRLKDEGVSFEHRVLSAHRNPKELEGYVSGTDA---HVFIAVAGLSAALPGVIASQTHR 77 
                                       89********************************************98765...8********************** PP

                                       -EEEEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHT CS
                              AIRC  79 PVigvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqila 128
                                       PVigvPv++ +l gldsllSivqmP+gvpva+v+i++++nAallA++il 
  gi|330508447|ref|YP_004384875.1|  78 PVIGVPVSA-KLGGLDSLLSIVQMPPGVPVACVGIDNGENAALLAIRILE 126
                                       *********.9*************************************96 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.6e-06     0.032      21     118 ..       3      95 ..       1     106 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-06
                          Fe-ADH_2  21 kvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvsak 97 
                                       +++++++++  +++ +++   lk++g++ e +   +++++ +e e     ++ +++ +++av +G    +  +++++
  gi|330508447|ref|YP_004384875.1|   3 DIAVISGSKSDQLIVDRILGRLKDEGVSFEHRV-LSAHRNPKELE---GYVSGTDAHVFIAV-AGLSAALPGVIASQ 74 
                                       689************************999554.55666666665...44555689******.899999******** PP

                          Fe-ADH_2  98 lnvpyvsvpTaaSvDGfaspg 118
                                       +++p++ vp +a   G  s  
  gi|330508447|ref|YP_004384875.1|  75 THRPVIGVPVSAKLGGLDSLL 95 
                                       ***********9888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1008.14
//
Query:       gi|330508448|ref|YP_004384876.1|  [L=94]
Description: chorismate mutase [Methanosaeta concilii GP6]
Scores for complete 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   60.3   4.5      2e-16   60.1   4.5    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 !   60.1   4.5   1.1e-20     2e-16       1      75 []       8      86 ..       8      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.1e-20
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHHHH....S-HHHHHHHHHHHHHHHHHHHH CS
                              CM_2  1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerleega....ldeeaierifreiisasralqk 75
                                      R+ I+e+D++i+eL+ +R  ++k++ e+K++eg+p++dpe+e  vl+r ++ a    ld+ a+++i++ +i++s + q+
  gi|330508448|ref|YP_004384876.1|  8 RSDIEEVDQTIIELIDKRIGITKRIFEVKRREGKPIRDPEQEGRVLRRAMDLAteknLDAGAVKNIYEILIRMSTQKQQ 86
                                      99*************************************************444457******************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 681.47
//
Query:       gi|330508449|ref|YP_004384877.1|  [L=285]
Description: shikimate kinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-12   45.7   2.7    5.6e-12   45.7   2.7    1.8  2  GHMP_kinases_N  GHMP kinases N terminal domain
      0.001   19.4   0.7     0.0027   18.0   0.2    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 ?   -3.3   0.1       1.2   1.1e+04      18      29 ..      14      25 ..      12      42 .. 0.59
   2 !   45.7   2.7   6.2e-16   5.6e-12       2      66 .]      77     145 ..      76     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.2
                                      HHHHHHHHHHHH CS
                    GHMP_kinases_N 18 AAlavalvaAll 29
                                      A+++ a+++   
  gi|330508449|ref|YP_004384877.1| 14 ASIINAVATWKG 25
                                      555555555443 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 6.2e-16
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEH..H.HHHHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallgls..l.eeaklaleaerlaqggngsggDv.aasvyGg 66 
                                       ++++seiP+++GL SS+A+a a+++A l++l+++  l + ak+++ea r+++++ ++  D+  as++Gg
  gi|330508449|ref|YP_004384877.1|  77 VRTSSEIPIASGLKSSSAAANAVILATLDALDVDmdLvSAAKIGVEAAREVGVTITGALDDaLASMLGG 145
                                       7899***************************999433555***********999988888868999987 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 ?   -2.3   0.0      0.67     6e+03      40      56 ..     121     134 ..     112     134 .. 0.85
   2 !   18.0   0.2     3e-07    0.0027      15      82 ..     206     265 ..     198     267 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.67
                    GHMP_kinases_C  40 lealselGalgaklsGa 56 
                                       +ea++e+G   + ++Ga
  gi|330508449|ref|YP_004384877.1| 121 VEAAREVG---VTITGA 134
                                       58889999...888887 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3e-07
                    GHMP_kinases_C  15 ellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralree 82 
                                       ++++l+       +++ l  + e l+ al e Ga g +lsG+  Gp+ +al+ d+++ + +++++r++
  gi|330508449|ref|YP_004384877.1| 206 RAMTLNGL--A--YCAALGLSSEPLILAL-EKGARGTSLSGT--GPSYAALI-DESKMDGLEESWRAL 265
                                       55555555..3..6666666666666665.999*********..********.****99999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2172.66
//
Query:       gi|330508450|ref|YP_004384878.1|  [L=174]
Description: hypothetical protein MCON_2646 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.5   0.0       0.16   11.9   0.0    1.3  1  VHL       VHL beta domain


Domain annotation for each model (and alignments):
>> VHL  VHL beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.1e-06      0.16      25      52 ..      62      89 ..      48      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.1e-06
                               VHL 25 lWidfeGePqsYeelkPgtgrrmttyvg 52
                                      ++i+++ +P +Y++l+ ++ ++m+++ +
  gi|330508450|ref|YP_004384878.1| 62 MFIEYKDSPAAYKDLSSRRVQQMNSFAK 89
                                      79***********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1485.96
//
Query:       gi|330508451|ref|YP_004384879.1|  [L=385]
Description: hypothetical protein MCON_2647 [Methanosaeta concilii GP6]
Scores for 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   32.1   2.4      7e-05   22.6   0.0    2.6  3  DAO             FAD dependent oxidoreductase
    9.8e-08   31.3   0.4    1.4e-06   27.4   0.0    2.0  2  Trp_halogenase  Tryptophan halogenase
    1.7e-07   31.0   3.6    1.1e-06   28.2   3.6    2.0  1  FAD_oxidored    FAD dependent oxidoreductase
    4.4e-06   25.7   1.1    7.6e-06   24.9   1.1    1.3  1  HI0933_like     HI0933-like protein
    1.3e-05   24.6   0.3    0.00066   19.0   0.2    2.3  2  FAD_binding_3   FAD binding domain
    1.5e-05   24.3   0.0    3.5e-05   23.0   0.0    1.7  2  Lycopene_cycl   Lycopene cyclase protein
    2.6e-05   23.5   0.9    2.6e-05   23.5   0.9    2.3  2  GIDA            Glucose inhibited division protein A
    0.00023   20.4   1.1    0.00023   20.4   1.1    1.6  2  FAD_binding_2   FAD binding domain
     0.0012   18.2   0.7     0.0037   16.5   0.3    1.8  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.007   15.7   0.1      0.007   15.7   0.1    1.6  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.051   12.8   1.4       0.37   10.0   0.3    2.5  3  Thi4            Thi4 family
      0.062   12.5   0.1       0.25   10.5   0.1    1.9  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.15   11.5   0.0       0.24   10.8   0.0    1.2  1  Sp38            Zona-pellucida-binding protein (Sp38)


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.3    0.0014       1.9       1      29 [.       4      34 ..       4      43 .. 0.93
   2 !   22.6   0.0   5.1e-08     7e-05     130     213 ..      74     156 ..      43     161 .. 0.73
   3 ?   -1.7   0.0       1.2   1.7e+03     317     347 ..     173     202 ..     161     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0014
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      dv+++G+  +G+ +A  +a+ g  V ll+++
  gi|330508451|ref|YP_004384879.1|  4 DVLVVGASSAGMMAAISAAEGGasVMLLDRN 34
                                      8*****************9988*******98 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 5.1e-08
                                       TTSEEEEETTEEEE.EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH CS
                               DAO 130 gllgalfypdtgqv.dpakltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd 205
                                       +   ++  p  g + d  ++ + +++ ae++Gv +l g ev++l  e g + +v   + g + +a+ v+ a G++s+
  gi|330508451|ref|YP_004384879.1|  74 PSGRGVTIPAKGYFiDRDAFDRHYLHLAEKAGVALLSG-EVRSLHLE-GNGRTV-GLK-GVQIHARVVIDASGVQSG 146
                                       456788899999998***********************.****9554.444555.223.66635588*********9 PP

                                       HH.HTT..CTT CS
                               DAO 206 ll.gll..kel 213
                                       l+ + +  k++
  gi|330508451|ref|YP_004384879.1| 147 LSeK-AglKPM 156
                                       8842.223444 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.2
                                       EEEEEEETEEEEEEEEECTTTHHHHHHHHHH CS
                               DAO 317 pligetpgvkglylatGhsghGltlapatGk 347
                                       p++ge+  +  +++ + + g+  t++pa G 
  gi|330508451|ref|YP_004384879.1| 173 PYLGEEM-FFQYWVGSMAPGWKATFSPAGGD 202
                                       5666632.3378999999**********886 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.6     0.074     1e+02       1      22 [.       4      25 ..       4      36 .. 0.78
   2 !   27.4   0.0   1.1e-09   1.4e-06     142     235 ..      79     164 ..      50     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.074
                                      EEEEE--SHHHHHHHHHHHHHT CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakal 22
                                      ++++vG+ +aG +aA+  a+ +
  gi|330508451|ref|YP_004384879.1|  4 DVLVVGASSAGMMAAISAAEGG 25
                                      699************9766544 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.1e-09
                                       -B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT CS
                    Trp_halogenase 142 lsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqaL 218
                                       ++  + +y +d+  ++++  + ae++Gv  ++g+v + +l+ +gr  +l+   g ++ a+ +iD+sG ++ l e+a 
  gi|330508451|ref|YP_004384879.1|  79 VTIPAKGYFIDRDAFDRHYLHLAEKAGVALLSGEVRSLHLEGNGRTVGLK---GVQIHARVVIDASGVQSGLSEKA- 151
                                       555566899***********************************988886...68999*****************8. PP

                                       ---EEE-TTT----EEE CS
                    Trp_halogenase 219 ktgfedwsdvLltdrAl 235
                                         g + + +  + d A+
  gi|330508451|ref|YP_004384879.1| 152 --GLKPMRH--PEDIAW 164
                                       ..6666555..345555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   3.6   8.3e-10   1.1e-06       1     144 [.       4     142 ..       4     154 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 8.3e-10
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee..qvvtgiareflerlrqrggarl 75 
                                       Dv+VvG+ +aG++AAi+Aa+ Ga+v+L++++    G l   + + ++g+ a +  ++   + ++ le +r    +  
  gi|330508451|ref|YP_004384879.1|   4 DVLVVGASSAGMMAAISAAEGGASVMLLDRNL---GRLHHDANTLFEGMAAVSgiEIKDCLLKKELEGMRILSPS-- 75 
                                       9****************************986...6777777677777653333344444444444444332222.. PP

                      FAD_oxidored  76 kkrskwn......tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                       ++    +      + + +++ + + ++ ++agv +l ++ +++ + eg + + v ++    + +i+A+v+iDA+g
  gi|330508451|ref|YP_004384879.1|  76 GRGV--TipakgyFIDRDAFDRHYLHLAEKAGVALLSGE-VRSLHLEG-NGRTVGLK----GVQIHARVVIDASG 142
                                       1111..122334478888888888888877777776665.45555554.44555553....56788888888876 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   1.1   5.5e-09   7.6e-06       2      32 ..       4      34 ..       3      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 5.5e-09
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                      dv+v+G+  AG+maAisaa+ g++V+ll+++
  gi|330508451|ref|YP_004384879.1|  4 DVLVVGASSAGMMAAISAAEGGASVMLLDRN 34
                                      8****************************87 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   4.8e-07   0.00066       2      33 ..       3      34 ..       2      41 .. 0.93
   2 ?    3.5   0.0     0.026        35     151     185 ..     130     165 ..      97     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.8e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      +dVl+VGa+ aG+m+a   +e G +v+l+++ 
  gi|330508451|ref|YP_004384879.1|  3 CDVLVVGASSAGMMAAISAAEGGASVMLLDRN 34
                                      9*****************************96 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.026
                                       EEEEEEEEEE--GTT-HHHHHHTGG.EEEEEEEEEE CS
                     FAD_binding_3 151 etvrakYlvGaDGgrStvrktlgie.fegeetvyea 185
                                        +++a+ ++ a G++S   +++g++ ++ +e++  a
  gi|330508451|ref|YP_004384879.1| 130 VQIHARVVIDASGVQSGLSEKAGLKpMRHPEDIAWA 165
                                       36***********************88888877333 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   2.6e-08   3.5e-05       1     145 [.       4     147 ..       4     173 .. 0.83
   2 ?   -3.8   0.0       3.5   4.9e+03     257     275 ..     360     378 ..     357     380 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.6e-08
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga..leec.vehsWsgtivylddgkk 74 
                                       Dv+v+Ga  Ag+  A     a+ g +v+l++   + l+    +     +++++  +++c +++  +g+++  + g+ 
  gi|330508451|ref|YP_004384879.1|   4 DVLVVGASSAGMMAAISA--AEGGASVMLLDRNLGRLHHDANTLFEGMAAVSGieIKDClLKKELEGMRILSPSGRG 78 
                                       9**********9877777..99********99988877766655444444444677777257889************ PP

                     Lycopene_cycl  75 illgraYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                       +++  +   + ++ + ++ l+   ++gv ll++ v s + e +  ++ v   g++i+ar+v+da+g+ s+ 
  gi|330508451|ref|YP_004384879.1|  79 VTIPAKGYFIDRDAFDRHYLHLAEKAGVALLSGEVRSLHLEGN-GRT-VGLKGVQIHARVVIDASGVQSGL 147
                                       ***977779***********9999*************999888.445.555689************87764 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.5
                     Lycopene_cycl 257 kvlaiGaaaglvhPaTGYs 275
                                       k l +Ga   +++P T Y 
  gi|330508451|ref|YP_004384879.1| 360 KALYAGALVTMIRPQTPYD 378
                                       5677899999******996 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.9   1.8e-08   2.6e-05       1     150 [.       4     143 ..       4     154 .. 0.71
   2 ?    0.5   0.6      0.19   2.6e+02     356     389 ..     264     297 ..     261     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.8e-08
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEEEEEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvrEidalggliikaadkagiqfril 77 
                                       dv V+G+  AG+ AA+ aa+ Ga+v+L+  +l+++ +   n  + g+a+   v  i+  + l+ k  +  +i   + 
  gi|330508451|ref|YP_004384879.1|   4 DVLVVGASSAGMMAAISAAEGGASVMLLDRNLGRLHHD-ANTLFEGMAA---VSGIEIKDCLLKKELEGMRI---LS 73 
                                       79**************************6666665544.4445555532...33344444455555555555...34 PP

                                       STTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA  78 NrskGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                        + +G  + a    +dr+++ +++ +  e+   + ++++ev +l +e  + +  v  +g +i+a++v+ a+G 
  gi|330508451|ref|YP_004384879.1|  74 PSGRGVTIPAKGYFIDRDAFDRHYLHLAEK-AGVALLSGEVRSLHLEG-NGR-TVGLKGVQIHARVVIDASGV 143
                                       44566666666667*********9987777.99***********9843.222.34456788889999988886 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.19
                                       BTEEE-CGGGTB-SHHHHHHHHHHHHHHHHHHHC CS
                              GIDA 356 kgLflAGqinGteGYeEaaaqGllAGinaarkak 389
                                       + L +AG   G +G   ++  G++ Gi a   + 
  gi|330508451|ref|YP_004384879.1| 264 DSLMVAGGAAGQSGLAYSMRAGTICGIVAGEAVL 297
                                       57999*********99999999999999987765 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   1.1   1.7e-07   0.00023       1      30 [.       4      33 ..       4      42 .. 0.94
   2 ?   -3.1   0.0       2.3   3.1e+03     172     201 ..     111     143 ..      90     159 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.7e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvek 30
                                      Dv+V+G+  AG++AA++aae G++v++++ 
  gi|330508451|ref|YP_004384879.1|  4 DVLVVGASSAGMMAAISAAEGGASVMLLDR 33
                                      9*************************9985 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.3
                                       TEEEEEEEEETTTTCEE.....EEEESEEEE---- CS
                     FAD_binding_2 172 grvtGavvenpesgrev.....rirakavvlatgG 201
                                       g+v+   +e   +gr+v     +i+a+ v++a+g 
  gi|330508451|ref|YP_004384879.1| 111 GEVRSLHLE--GNGRTVglkgvQIHARVVIDASGV 143
                                       566666666..666666666668888888888875 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   2.7e-06    0.0037       2      31 ..       4      35 ..       3      70 .. 0.80
   2 ?   -1.3   0.0      0.73     1e+03     185     239 ..      93     145 ..      84     157 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-06
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEE..T CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve..l 31
                                      dv+v+G+  AG+ aa+ +a+ ga v+l++  l
  gi|330508451|ref|YP_004384879.1|  4 DVLVVGASSAGMMAAISAAEGGASVMLLDrnL 35
                                      89**************************7542 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.73
                                       HHHHHHHHHHHTTEEEEESCEEE.EEEETTEEEEEEETTSCEEEESEEEE-S-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 185 lsaaleealekeGvevklgtsvk.eidgngeklevvledgeeidadlvvvavGvrp 239
                                       + + + +  ek Gv++  g++    ++gng+   +v  +g +i a+ v+ a Gv+ 
  gi|330508451|ref|YP_004384879.1|  93 FDRHYLHLAEKAGVALLSGEVRSlHLEGNGR---TVGLKGVQIHARVVIDASGVQS 145
                                       5667777888889999877655457777776...8888888899999999999875 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 !   15.7   0.1   5.1e-06     0.007      29      66 ..       3      40 ..       1      71 [. 0.87
   2 ?   -3.7   0.8       4.3   5.9e+03      28      52 ..     262     286 ..     255     300 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.1e-06
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHH CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleq 66
                                      + vlv+G+  aG+ A+  a++ ga+V++lD +  rl++
  gi|330508451|ref|YP_004384879.1|  3 CDVLVVGASSAGMMAAISAAEGGASVMLLDRNLGRLHH 40
                                      68******************************988765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.3
                                       --EEEEESTSHHHHHHHHHHHHTT- CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglga 52 
                                        a  l + gG aG++ +a +++ g 
  gi|330508451|ref|YP_004384879.1| 262 VADSLMVAGGAAGQSGLAYSMRAGT 286
                                       4666777788888888887777665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00027      0.37      17      51 ..       2      35 ..       1      38 [. 0.90
   2 ?   -1.4   0.0      0.83   1.1e+03     155     170 ..     130     145 ..     104     154 .. 0.79
   3 ?    0.4   0.0      0.24   3.3e+02     180     227 ..     230     278 ..     204     287 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersv 51
                                      + Dv++vGa s+G+ aa   a+  +  v++l+r++
  gi|330508451|ref|YP_004384879.1|  2 NCDVLVVGASSAGMMAAISAAEG-GASVMLLDRNL 35
                                      68***************999988.99999999886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.83
                                       EEEEEEEEEE--GSSS CS
                              Thi4 155 lvirakvvvdatGhdg 170
                                         i+a+vv+da+G ++
  gi|330508451|ref|YP_004384879.1| 130 VQIHARVVIDASGVQS 145
                                       5689999999999765 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.24
                                       HHHCTTTS-----ECB-HHHHHHHHH.HHECEEETTEEE-THHHHHHHT CS
                              Thi4 180 ikleakiekvkgeksldaekaedaiv.kktrevvpnlyvaGmevaevdg 227
                                        +++++ +++  +k l + ++ d i     + v + l+vaG ++ ++  
  gi|330508451|ref|YP_004384879.1| 230 AQKASQYKNIDRMKVLSVRRGGDPICvMPGEMVADSLMVAGGAAGQSGL 278
                                       4556677899999999999999988624455566889999988766544 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00018      0.25     166     202 ..       4      40 ..       1      60 [. 0.88
   2 ?   -1.0   0.0       0.6   8.3e+02     100     134 ..     109     143 ..      80     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00018
                       Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtrgseieke 202
                                       +v+V+G++  ++ aA+  ++ ga+V +++r+  + ++
  gi|330508451|ref|YP_004384879.1|   4 DVLVVGASSAGMMAAISAAEGGASVMLLDRNLGRLHH 40 
                                       89***************************98765554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.6
                       Pyr_redox_3 100 lfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                       l  eV+s++ e++g +v  +  +++A+ vi A G 
  gi|330508451|ref|YP_004384879.1| 109 LSGEVRSLHLEGNGRTVGLKGVQIHARVVIDASGV 143
                                       45689999999999****************99995 PP

>> Sp38  Zona-pellucida-binding protein (Sp38)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017      0.24      50     108 ..     175     240 ..     166     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                              Sp38  50 lqselfiafqvnpfapgwkdlcnssldtedt.......tnkrllkakdrieeffrkqveilkkkfe 108
                                       l +e+f+++ v  +apgwk+  + +     t       + ++++   dr  ++f+ q    +k+++
  gi|330508451|ref|YP_004384879.1| 175 LGEEMFFQYWVGSMAPGWKATFSPAGGDRATigvfvrgHGQNVQPFFDRFSRLFKAQKASQYKNID 240
                                       568****************99876443333357777777788888888888888888777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.38
# Mc/sec: 3053.87
//
Query:       gi|330508452|ref|YP_004384880.1|  [L=135]
Description: hypothetical protein MCON_2649 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-57  192.4   0.0    2.4e-57  192.2   0.0    1.0  1  DUF1699   Protein of unknown function (DUF1699)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.2   0.0   1.3e-61   2.4e-57       1     129 [.       1     129 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 192.2 bits;  conditional E-value: 1.3e-61
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       m++rvvs+++ei++ln+nek+vHlafr+sn d+l+l+++cp+l++iqvp+Sy+kt+s+++++fl++qgiellegdvw
  gi|330508452|ref|YP_004384880.1|   1 MRLRVVSARNEISNLNPNEKTVHLAFRASNVDFLNLMQRCPRLRMIQVPPSYRKTMSNAIQVFLDMQGIELLEGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfll 129
                                       ghrkd++ey++v++++i++i++l ++g+s +e+a++++k+++l p+lik+++
  gi|330508452|ref|YP_004384880.1|  78 GHRKDLDEYFTVDDTTIDEIRSLAASGASMDEVANQIQKKARLGPELIKYIA 129
                                       **************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 990.14
//
Query:       gi|330508453|ref|YP_004384881.1|  [L=568]
Description: pyruvate carboxylase subunit B [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.3    2.8e-53  180.6   0.3    1.4  1  PYC_OADA         Conserved carboxylase domain
    6.4e-50  170.1   0.0      9e-50  169.7   0.0    1.2  1  HMGL-like        HMGL-like
    8.6e-20   70.4   2.8    1.8e-19   69.3   2.8    1.6  1  Biotin_lipoyl    Biotin-requiring enzyme
    1.4e-10   40.8   1.3    6.2e-05   22.7   0.0    2.9  2  Biotin_lipoyl_2  Biotin-lipoyl like
    0.00031   21.4   0.3        0.9   10.3   0.0    2.6  2  HlyD_3           HlyD family secretion protein
    0.00063   19.0   0.3       0.68    9.1   0.0    2.3  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
     0.0063   16.3   0.1       0.33   10.7   0.0    2.5  2  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
      0.007   16.3   0.2      0.032   14.2   0.2    2.1  1  DUF2118          Uncharacterized protein conserved in archaea
     0.0077   15.1   0.1     0.0077   15.1   0.1    2.6  3  YqfD             Putative stage IV sporulation protein YqfD
  ------ inclusion threshold ------
       0.01   15.7   0.4      0.037   13.9   0.2    2.0  2  GCV_H            Glycine cleavage H-protein
       0.02   14.8   0.3      0.065   13.2   0.2    1.9  2  RnfC_N           RnfC Barrel sandwich hybrid domain
      0.072   13.2   0.1         19    5.4   0.0    2.7  2  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
       0.13   12.2   0.0       0.56   10.2   0.0    2.0  2  ADH_zinc_N       Zinc-binding dehydrogenase
       0.17   11.6   0.8       0.86    9.3   0.1    2.5  3  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin


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 !  180.6   0.3   2.2e-56   2.8e-53       1     196 [.     292     481 ..     292     482 .. 0.89

  Alignments for each domain:
  == domain 1  score: 180.6 bits;  conditional E-value: 2.2e-56
                                       HHCCT--CCHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHTT----STTHHHHHHHHHHHHHHH........TS.TT CS
                          PYC_OADA   1 VykheiPGGqltnlkeqakeqglldkfeevlkeyaevnkllGdivkVTPsSkvvgdlAvfnvlnklteedvleegry 77 
                                       V++++iPGG+l+nl +q++eq ++dk+eevl+e+++v+k+lG++++VTP+S++v ++Av+nv +        ++ ry
  gi|330508453|ref|YP_004384881.1| 292 VLVYQIPGGMLSNLVSQLNEQKAMDKYEEVLAEVPKVRKDLGYPPLVTPTSQIVTTQAVLNVVT--------GD-RY 359
                                       789*************************************************************........75.** PP

                                       SS--HHHHHHHTTSS---SS---HHHHHHHHT.-----S-GGGG---.-HHHHHHHTTTTS..SSHHHHHHHHHSHH CS
                          PYC_OADA  78 kdipdsvvdllkGelGkppggfpeelvkkvlkgeepitsrpadslepedleklrkeleeka..kteedvlsyalypk 152
                                       k +p++v+d++kG +Gk p+ ++++++ kvl +e ++t+rpad+l+p ++e+++k++++    k+eed+l+yalyp+
  gi|330508453|ref|YP_004384881.1| 360 KMVPKEVKDYVKGLYGKSPAMIDPKVRIKVLCDEDAVTVRPADLLPP-EYEEAKKAVDALGlaKKEEDYLTYALYPQ 435
                                       ***********************************************.***********664479************ PP

                                       HHHHHHHHHHHHHHHH....CTTTS.......-SEEEEEETTEEEE. CS
                          PYC_OADA 153 vaekflkfreeygdvs..vlptkvffeglk.vgeeveveveggkyli 196
                                       va kflk  ++ +++    + +    + lk ++  ++ve++g+ yl+
  gi|330508453|ref|YP_004384881.1| 436 VALKFLKGAATEESLVkkDMAS-DLGASLKaEPLALNVEIDGEAYLV 481
                                       *******877655544223333.333444447889999999999984 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.7   0.0     7e-53     9e-50       2     263 ..       4     269 ..       3     270 .. 0.96

  Alignments for each domain:
  == domain 1  score: 169.7 bits;  conditional E-value: 7e-53
                                       -EEEE-TTTHHHHTS.SS---HHHHHHHHHHHHHHT-SEE--........TSGGGT.THHHHHHHS---TT-B.... CS
                         HMGL-like   2 vkivdttLRDGeqal.kaalsveeklaiakaLdeagvdeiEv........gfpaaseddfevvraiakavkka.... 65 
                                       v +++t+ RD++q+l ++++++ ++l+ia+++d++g+ ++Ev        +++ + ed++e++ra++ka++++    
  gi|330508453|ref|YP_004384881.1|   4 VMLTETVFRDAHQSLlATRMRTRDMLPIAEQMDQVGFFSLEVwggatfdsCIRYLNEDPWERLRALKKAMPNTpmqm 80 
                                       7899**********99*********************************************************7777 PP

                                       .......--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-E..TTT CS
                         HMGL-like  66 ..r...ilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkd..vel 135
                                         r   +++++++++++++++v+++ ++g++++++f+a+++              ++++e+ +kaa+++ k+  + +
  gi|330508453|ref|YP_004384881.1|  81 llRgqnLVGYRHYADDLVDRFVKRAAENGVDIFRIFDAVND--------------IRNMERSIKAAKKMDKHvqAGI 143
                                       662557***********************************..............*****************44457 PP

                                       -BTTTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHH CS
                         HMGL-like 136 sledasrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaA 212
                                       s++ ++ ++ e+ a+ + +++e+G+++i i+D+ G++tP++a++li+a+k++v+  +++++H+H + G+A +    +
  gi|330508453|ref|YP_004384881.1| 144 SYTISPVHSNEQFAQFAVQLAELGCDSICIKDMGGLITPKNAYDLIRAIKKEVN--LPVNLHTHCTSGMAQMSYFHG 218
                                       88999*************************************************..********************* PP

                                       HHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT-B----HHHHHHHHHH CS
                         HMGL-like 213 veaGadrvdgtvnGlGeraGnaaleelvaalealgvdtgldlqklrsiaal 263
                                        +aG+d +d++++ l++++  +a+e lvaal+++++dtgldl+ l++i+++
  gi|330508453|ref|YP_004384881.1| 219 CQAGVDILDTAMSPLSGGSSQPATESLVAALKGTPYDTGLDLELLTEIKRY 269
                                       **********************************************99875 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   2.8   1.4e-22   1.8e-19       3      73 .]     502     567 ..     500     567 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 1.4e-22
                                       EEESSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl   3 iksPmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                       +++Pm G++++     ++vk+Gd V++g+++a++eamKme  i a k+G++ ei+vkeG+tv  gd+l+ i
  gi|330508453|ref|YP_004384881.1| 502 VTVPMQGVVIR-----YKVKKGDRVAKGDPVAVLEAMKMEQNILANKDGKIREIYVKEGTTVAPGDVLISI 567
                                       799********.....****************************************************976 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   5.1e-06    0.0065       5      37 ..     502     534 ..     498     542 .. 0.86
   2 !   22.7   0.0   4.8e-08   6.2e-05       5      34 ..     539     568 .]     536     568 .] 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.1e-06
                   Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLaelDsra 37 
                                       ++ p  G+V +  Vk G+rV +Gd  a+l+  +
  gi|330508453|ref|YP_004384881.1| 502 VTVPMQGVVIRYKVKKGDRVAKGDPVAVLEAMK 534
                                       567889*******************99998765 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 4.8e-08
                   Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLaelD 34 
                                       I a  +G++ +++Vk+G  V  GdvL+ ++
  gi|330508453|ref|YP_004384881.1| 539 ILANKDGKIREIYVKEGTTVAPGDVLISIE 568
                                       667779*********************985 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0021       2.7       2      30 ..     502     530 ..     501     535 .. 0.92
   2 !   10.3   0.0   0.00071       0.9       2      30 ..     539     567 ..     538     568 .] 0.93

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0021
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                       +++p +Gvv   +v++g+ v++gd+++ +
  gi|330508453|ref|YP_004384881.1| 502 VTVPMQGVVIRYKVKKGDRVAKGDPVAVL 530
                                       789***********************976 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00071
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                       + A  dG++ e+ v+eg  v++gd+l +i
  gi|330508453|ref|YP_004384881.1| 539 ILANKDGKIREIYVKEGTTVAPGDVLISI 567
                                       77999*********************998 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 !    8.1   0.1    0.0011       1.4     111     139 ..     502     530 ..     488     535 .. 0.72
   2 !    9.1   0.0   0.00053      0.68     108     139 ..     536     567 ..     531     568 .] 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 111 vkapisGvVteknvreGqyvqpgdtlfti 139
                                       v+ p++GvV++ +v +G++v +gd+++ +
  gi|330508453|ref|YP_004384881.1| 502 VTVPMQGVVIRYKVKKGDRVAKGDPVAVL 530
                                       66688888888888888888888877655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00053
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 108 tvtvkapisGvVteknvreGqyvqpgdtlfti 139
                                       + ++ a+ +G + e  v eG +v pgd+l++i
  gi|330508453|ref|YP_004384881.1| 536 EQNILANKDGKIREIYVKEGTTVAPGDVLISI 567
                                       55788999*******************99998 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00025      0.33      76     111 ..     503     538 ..     501     543 .. 0.90
   2 ?    3.1   0.0      0.06        77      80     103 ..     544     567 ..     539     568 .] 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                                       TTTTTTTTEEES----SEE-SEEEEEEE-HHHHGGG CS
                        PTS_EIIA_1  76 tvklkgegFellvkegdkVkagdklvevdleaikka 111
                                       tv ++g + + +vk+gd+V +gd+++ ++  +++++
  gi|330508453|ref|YP_004384881.1| 503 TVPMQGVVIRYKVKKGDRVAKGDPVAVLEAMKMEQN 538
                                       8999*********************99988888776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.06
                                       TTTTEEES----SEE-SEEEEEEE CS
                        PTS_EIIA_1  80 kgegFellvkegdkVkagdklvev 103
                                       +g+  e++vkeg++V  gd l+++
  gi|330508453|ref|YP_004384881.1| 544 DGKIREIYVKEGTTVAPGDVLISI 567
                                       6788899**************986 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   2.5e-05     0.032      85     130 ..     503     547 ..     498     562 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                           DUF2118  85 lipvegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvV 130
                                        +p++gv++   v+ Gdrv +gd++a + + k e   + a ++g++
  gi|330508453|ref|YP_004384881.1| 503 TVPMQGVVIRYKVKKGDRVAKGDPVAVLEAMKMEQN-ILANKDGKI 547
                                       699*****************************9965.446777776 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 ?   -1.0   0.1      0.46   5.8e+02      17      57 ..      99     139 ..      96     147 .. 0.76
   2 ?    0.3   0.5      0.19   2.5e+02     158     217 ..     472     525 ..     470     529 .. 0.55
   3 !   15.1   0.1     6e-06    0.0077     184     221 ..     536     566 ..     529     568 .] 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.46
                              YqfD  17 erflnllarrgIelwdikrkkdgeleakislkdfkklrkia 57 
                                        rf++++a++g++++ i    ++   ++ s+k+ kk+ k +
  gi|330508453|ref|YP_004384881.1|  99 DRFVKRAAENGVDIFRIFDAVNDIRNMERSIKAAKKMDKHV 139
                                       68888999999988888877777777777777777777765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.19
                              YqfD 158 veikGtrlivevvekeeppeieekdepcn.ivAkkdGvItkvivesGeplvkegdtVkkGd 217
                                       vei+G  + v+v+ +    ++ + ++p++ +   ++Gv+ +  v++G         V kGd
  gi|330508453|ref|YP_004384881.1| 472 VEIDGEAYLVKVAPAGMTIQEAQPKAPTDgVTVPMQGVVIRYKVKKGD-------RVAKGD 525
                                       677777777777777744444444444442555666666666666665.......444444 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 6e-06
                              YqfD 184 pcnivAkkdGvItkvivesGeplvkegdtVkkGdvLIs 221
                                        +ni A+kdG I +++v       keg tV +GdvLIs
  gi|330508453|ref|YP_004384881.1| 536 EQNILANKDGKIREIYV-------KEGTTVAPGDVLIS 566
                                       48*************97.......56678999999998 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.6   3.3e+03      77     101 ..     462     486 ..     452     497 .. 0.67
   2 ?   13.9   0.2   2.9e-05     0.037      31      74 ..     508     550 ..     499     556 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.6
                                       GGTT-TTHHHH-TTTTT--EEEEES CS
                             GCV_H  77 kleeepeliNkdpyeegWliklkls 101
                                        l+ ep  +N +  +e++l+k+ ++
  gi|330508453|ref|YP_004384881.1| 462 SLKAEPLALNVEIDGEAYLVKVAPA 486
                                       4666666667776777777776654 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.9e-05
                                       -SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                             GCV_H  31 gdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvev 74 
                                       g v+ ++++ +g++v+kg+++a++E+ K+  ++ a+ +G++ e+
  gi|330508453|ref|YP_004384881.1| 508 GVVIRYKVK-KGDRVAKGDPVAVLEAMKMEQNILANKDGKIREI 550
                                       555556655.79*****************************987 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 ?   -3.4   0.0       7.5   9.6e+03      30      51 ..     337     358 ..     329     360 .. 0.83
   2 ?   13.2   0.2   5.1e-05     0.065      31      81 ..     503     551 ..     485     566 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7.5
                            RnfC_N  30 lvlplsqhiGapakplvkvgdk 51 
                                       lv p sq + ++a + v  gd+
  gi|330508453|ref|YP_004384881.1| 337 LVTPTSQIVTTQAVLNVVTGDR 358
                                       6788899999999888888886 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.1e-05
                            RnfC_N  31 vlplsqhiGapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaie 81 
                                       ++p++   G   +  vk+gd+V kG+ +a  e+  +  ++ a   G++ +i 
  gi|330508453|ref|YP_004384881.1| 503 TVPMQ---GVVIRYKVKKGDRVAKGDPVAVLEAmKMEQNILANKDGKIREIY 551
                                       55554...5666778**************999866799**********9985 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 ?    5.4   0.0     0.015        19      44      69 ..     507     532 ..     501     542 .. 0.88
   2 ?    4.9   0.0      0.02        26      49      68 ..     549     568 .]     536     568 .] 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.015
                                       TTTEEEESS-TT-EEETTEEEEEEEE CS
                         QRPTase_N  44 pglevellvkDGervekgdvlleieG 69 
                                       +g+ + ++vk G+rv+kgd ++ +e+
  gi|330508453|ref|YP_004384881.1| 507 QGVVIRYKVKKGDRVAKGDPVAVLEA 532
                                       588999***************99886 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.02
                                       EESS-TT-EEETTEEEEEEE CS
                         QRPTase_N  49 ellvkDGervekgdvlleie 68 
                                       e++vk+G++v++gdvl+ ie
  gi|330508453|ref|YP_004384881.1| 549 EIYVKEGTTVAPGDVLISIE 568
                                       589*************9986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.8   6.1e+03      63      81 ..      43      60 ..      41      61 .. 0.85
   2 ?   10.2   0.0   0.00043      0.56      44     100 ..      94     153 ..      65     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.8
                                      EESSCSHHHHHHHHHCEEE CS
                        ADH_zinc_N 63 fecvGsgatleaalkllkp 81
                                      +e+ G gat+++++++l++
  gi|330508453|ref|YP_004384881.1| 43 LEVWG-GATFDSCIRYLNE 60
                                      78899.*******999986 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00043
                                       C.HHHHHHHHHTTTSSEEE..EEESSCSHHHHHHHHHCEEEEEEEEECSCTSSEEEEEHH CS
                        ADH_zinc_N  44 a.dlverikeltggegvdv..vfecvGsgatleaalkllkpgGrlvvvGggkgeeefdlr 100
                                       a dlv+r  +   ++gvd+  +f++v++ + +e+++k++k+  + v  G+++  +++  +
  gi|330508453|ref|YP_004384881.1|  94 AdDLVDRFVKRAAENGVDIfrIFDAVNDIRNMERSIKAAKKMDKHVQAGISYTISPVHSN 153
                                       337888888888899****99****************************98887775554 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 ?   -1.5   0.0       1.6     2e+03      34      59 ..     129     156 ..     126     165 .. 0.69
   2 ?    9.3   0.1   0.00067      0.86      34      57 ..     511     534 ..     505     546 .. 0.82
   3 ?   -2.4   0.0         3   3.8e+03      37      53 ..     551     567 ..     549     567 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.6
                                       EEES--TT-EEBTT..SEEEEEEESSSC CS
                            PYNP_C  34 ielhkklGdkVkkG..eplatiYankee 59 
                                       i+  kk+  +V++G   ++  +++n++ 
  gi|330508453|ref|YP_004384881.1| 129 IKAAKKMDKHVQAGisYTISPVHSNEQF 156
                                       5667888899998833467778887765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00067
                                       EEES--TT-EEBTTSEEEEEEESS CS
                            PYNP_C  34 ielhkklGdkVkkGeplatiYank 57 
                                       i+ ++k Gd+V kG+p+a++ a k
  gi|330508453|ref|YP_004384881.1| 511 IRYKVKKGDRVAKGDPVAVLEAMK 534
                                       77899*************986555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3
                                       S--TT-EEBTTSEEEEE CS
                            PYNP_C  37 hkklGdkVkkGeplati 53 
                                        +k G  V  G++l+ i
  gi|330508453|ref|YP_004384881.1| 551 YVKEGTTVAPGDVLISI 567
                                       6799999*****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 3764.49
//
Query:       gi|330508454|ref|YP_004384882.1|  [L=291]
Description: acetylglutamate kinase [Methanosaeta concilii GP6]
Scores for complete 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  141.5   1.3    3.6e-41  141.3   1.3    1.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.3   1.3     2e-45   3.6e-41       2     241 .]      23     267 ..      22     267 .. 0.97

  Alignments for each domain:
  == domain 1  score: 141.3 bits;  conditional E-value: 2e-45
                                       EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHH CS
                         AA_kinase   2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevat 78 
                                       + V K+GGs+++d+    l+++++++  l+  g+++++VhGgg+ + + +++  g ++++   glr+t+ e++ +a+
  gi|330508454|ref|YP_004384882.1|  23 IMVFKIGGSIMSDTAV--LEDFIQDVVLLRYIGIHPIIVHGGGPEISQAMEK-FGKKAEFVG-GLRVTDRETLSIAR 95 
                                       5799**********99..**********************************.*********.************** PP

                                       HHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..............HHHTTTCEEECCHHHHHHHTT-EEEE CS
                         AA_kinase  79 rdalaslgerlvaallaaglpavglsaaaldateagr............degsdgnvesvdaeaieelleagvvpvl 143
                                       +++l+ ++ +lv  + ++g + +gls+++    +a++            d g +g+ve+vd e ++ +  +g++pv+
  gi|330508454|ref|YP_004384882.1|  96 MVLLGHINAELVNLIGKHGGKGIGLSGQDGMFLKAKKkalqmvegkepvDLGFVGDVEKVDPEILMIMAGKGYIPVI 172
                                       *******************************999999**************************************** PP

                                       ESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.CSSS.TTTHH CS
                         AA_kinase 144 tgfigldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.saselatgGm 219
                                       ++++  d++g   ++++Dt+a ++A a++A+k   +tdV+GV   +p+++  a +++e  +++++  +a++ ++gGm
  gi|330508454|ref|YP_004384882.1| 173 SPIA-TDDQGNNFNVNADTAAGAVAIAMRAKKFFSITDVEGVRM-NPDDP--ASVISEFPASDFGRlVAEGIIKGGM 245
                                       **86.99999978*****************************65.56777..8************************ PP

                                       HHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 220 kvkhpaalaaarrggipvvItn 241
                                       ++k++a++ ++r+g+ +++I++
  gi|330508454|ref|YP_004384882.1| 246 IPKVEACVSVVRSGVEKAHIID 267
                                       ********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2063.31
//
Query:       gi|330508455|ref|YP_004384883.1|  [L=157]
Description: FeS cluster assembly scaffold protein NifU [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-46  157.3   0.0    2.5e-46  157.0   0.0    1.1  1  NifU_N    NifU-like N terminal domain
  ------ inclusion threshold ------
      0.024   14.9   0.1      0.042   14.1   0.1    1.4  1  TSCPD     TSCPD domain


Domain annotation for each model (and alignments):
>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.0   0.0   2.7e-50   2.5e-46       2     126 ..      13     132 ..      12     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 157.0 bits;  conditional E-value: 2.7e-50
                                       SCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHHT CS
                            NifU_N   2 ysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelvk 78 
                                       y++ v+dh+ nPrnvGv+e+ d   g g+vg+p+cGD + + i+v++  dri d+kF+tfGCgsaiA+ss++te+ k
  gi|330508455|ref|YP_004384883.1|  13 YNETVMDHFMNPRNVGVIENPD---GYGKVGNPVCGDLMEIFINVKD--DRIDDIKFRTFGCGSAIAVSSMVTEMAK 84 
                                       99********************...8********************9..8*************************** PP

                                       TSBHHHHCCCCHHHHHHHHTCSCSSSCHCSCHHHHHHHHHHHHHHHHC CS
                            NifU_N  79 gktleealkitnkeiaeelgglpkeklhcsvlaedalkaavkkYkakk 126
                                       gk l+ea kit++++a elgglp++klhcs+l++dal+aa+k+Y  k 
  gi|330508455|ref|YP_004384883.1|  85 GKILDEAIKITRDDVAGELGGLPPQKLHCSNLGADALRAAIKDYWVKI 132
                                       ********************************************8775 PP

>> TSCPD  TSCPD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   4.6e-06     0.042       6      51 ..      43      90 ..      39     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                             TSCPD  6 vCs..reieievddkliknvkfvg.GCngnlkgiskLvegmkveevikk 51
                                      vC+  +ei i+v+d+ i ++kf   GC g   ++s++v+ m   ++ ++
  gi|330508455|ref|YP_004384883.1| 43 VCGdlMEIFINVKDDRIDDIKFRTfGC-GSAIAVSSMVTEMAKGKILDE 90
                                      899778888999999*******65388.667799***988876666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1150.04
//
Query:       gi|330508456|ref|YP_004384884.1|  [L=178]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-06   27.1   7.0     0.0035   17.6   0.3    2.2  2  DUF2306          Predicted membrane protein (DUF2306)
    1.1e-05   25.5   6.2    5.5e-05   23.3   6.2    2.0  1  Cytochrom_B561   Eukaryotic cytochrome b561
     0.0002   21.5  11.6      0.002   18.3   3.1    2.3  2  DUF4079          Protein of unknown function (DUF4079)
  ------ inclusion threshold ------
      0.013   15.9  10.7       0.09   13.2   1.3    2.3  2  DUF2231          Predicted membrane protein (DUF2231)
       0.02   15.3   2.2       0.02   15.3   2.2    2.1  2  DUF4199          Protein of unknown function (DUF4199)
       0.18   10.5   1.3       0.25   10.0   1.3    1.1  1  ResB             ResB-like family
       0.25   11.4   8.4       0.32   11.1   0.7    2.6  3  Ferric_reduct    Ferric reductase like transmembrane componen
       0.57   10.3   0.1       0.57   10.3   0.1    2.5  3  GutM             Glucitol operon activator protein (GutM)
       0.69   10.2   6.3        3.6    7.9   5.3    2.2  2  DUF420           Protein of unknown function (DUF420)
       0.89   10.1  14.4       0.51   10.9   1.5    2.9  3  DUF4405          Domain of unknown function (DUF4405)
        1.8    8.6  12.7        1.6    8.8   0.6    2.5  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> DUF2306  Predicted membrane protein (DUF2306)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   3.5   0.00013      0.21      42     127 ..      23     119 ..      16     133 .. 0.70
   2 !   17.6   0.3   2.1e-06    0.0035       7      52 ..     129     173 ..     119     178 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                           DUF2306  42 vllaalsglflsvyatgg......lvlllgflllallwlvftvlalvairrrd.....faaHrawmirsYalalaav 107
                                       +llaa s+l  ++++ +       l+l+   +ll l  l+f+++++v +r  +     ++aHr   i  +al+l+ +
  gi|330508456|ref|YP_004384884.1|  23 ALLAASSSLIAASANELEpiedkiLILFPYHALLVLSGLLFLIAGMVCARYLKgkrwwLKAHRTLGIAGAALTLSGI 99 
                                       5667777776666666656777755566666666666788888887777655445577******************* PP

                           DUF2306 108 tlrlvllvlillvgedfeta 127
                                       t +++++++ +  ++     
  gi|330508456|ref|YP_004384884.1| 100 TVAIYMVSASAGLQPPGGPH 119
                                       *****999888666555544 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.1e-06
                           DUF2306   7 lalvalllGalqlvkrlrakrpklHrlaGrvyvlavllaalsglfl 52 
                                       ++++  +lG +ql kr + +   +Hr+ Gr++++++++ a  g  +
  gi|330508456|ref|YP_004384884.1| 129 MVILTPVLGFIQLKKRDK-RLQTIHRWSGRMTIALMIINAYLGWMM 173
                                       456667899999977655.6789****************9988776 PP

>> Cytochrom_B561  Eukaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   6.2   3.4e-08   5.5e-05       1     132 [.      52     173 ..      52     178 .] 0.86

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.4e-08
                                       HHHHHHHHHHTHHHHHHHTHHHHS-S...-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.T--SS-SHHHHHH CS
                    Cytochrom_B561   1 lHpvlmviGfvllmgeaiLvyrvsstrklskktkkllHlilqllalilavvgllavfksknek.eianlyslHswlG 76 
                                       +H++l++ G+++l++ ++++ r      + k+++   H +l +++ +l++ g+ ++++  +++ + +     H++lG
  gi|330508456|ref|YP_004384884.1|  52 YHALLVLSGLLFLIA-GMVCARY----LKGKRWWLKAHRTLGIAGAALTLSGITVAIYMVSASaGLQPPGGPHAYLG 123
                                       6************98.5666665....267999*******************988877766652789999******* PP

                                       HHHHHHHHHHHHHHHHHHTSS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Cytochrom_B561  77 lvtvilfllqlvlGfvlfllpklskklralllplHvllGlvifvlaivtallGlle 132
                                       +++ ++++l  vlGf+ +       k  ++l+ +H+++G ++  l i++a+lG + 
  gi|330508456|ref|YP_004384884.1| 124 IIVSLMVILTPVLGFIQLK------KRDKRLQTIHRWSGRMTIALMIINAYLGWMM 173
                                       ***************9886......445678999*******************855 PP

>> DUF4079  Protein of unknown function (DUF4079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   3.8    0.0048       7.9      56      97 ..      55      97 ..      17     112 .. 0.72
   2 !   18.3   3.1   1.2e-06     0.002      81     140 ..     116     176 ..      93     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0048
                           DUF4079 56 lllllvvlgaigglvll.ylrrgklfpssHlyaGlavvvLlal 97
                                      ll+l ++l++i+g+v   yl+ ++ +   H   G+a ++L + 
  gi|330508456|ref|YP_004384884.1| 55 LLVLSGLLFLIAGMVCArYLKGKRWWLKAHRTLGIAGAALTLS 97
                                      5566667777777665415555566667788888777777654 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.2e-06
                           DUF4079  81 pssHlyaGlavvvLlalsaalv.peiqkgkstaRtlHialnvlalllfawqaitGlrillk 140
                                        ++H y G++v ++++l  +l   + +k+++++ t+H   + + ++l+++ a  G+ ++++
  gi|330508456|ref|YP_004384884.1| 116 GGPHAYLGIIVSLMVILTPVLGfIQLKKRDKRLQTIHRWSGRMTIALMIINAYLGWMMIQS 176
                                       58*********999999877751444444558************************99986 PP

>> DUF2231  Predicted membrane protein (DUF2231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.2    0.0022       3.6      50      95 ..      61     112 ..      14     115 .. 0.76
   2 ?   13.2   1.3   5.5e-05      0.09      43     101 ..     119     177 ..     113     178 .] 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0022
                           DUF2231  50 llalivaltvW......rfvlrlreeeqvsplylalslvvvvlllvqgwlGa 95 
                                       ll+li+++         r++l++++   +  + l+ls ++v++ +v++  G 
  gi|330508456|ref|YP_004384884.1|  61 LLFLIAGMVCArylkgkRWWLKAHRTLGIAGAALTLSGITVAIYMVSASAGL 112
                                       44555555444678898******************************99996 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.5e-05
                           DUF2231  43 HavggvlllalivaltvWrfvlrlreeeqvsplylalslvvvvlllvqgwlGaeLvyef 101
                                       Ha +g+++++++++  v  f+  ++++++++  +   + ++++l++++++lG+ ++  f
  gi|330508456|ref|YP_004384884.1| 119 HAYLGIIVSLMVILTPVLGFIQLKKRDKRLQTIHRWSGRMTIALMIINAYLGWMMIQSF 177
                                       9999*99999999977888888888888***************************9887 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   1.4       1.8   2.9e+03      75      75 ..      54      54 ..       5      78 .. 0.58
   2 ?   15.3   2.2   1.2e-05      0.02       5      82 ..      95     169 ..      88     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.8
                           DUF4199 75 l 75
                                      +
  gi|330508456|ref|YP_004384884.1| 54 A 54
                                      1 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.2e-05
                           DUF4199   5 ilglvwilifll.ilyllglhqilstg..pllgllallllllvpflvylalkkyrkknlgGfisfgqafgfgflisl 78 
                                        l  ++++i ++   ++l+      +g  ++lg+++ l+++l+p+l++++lk +r+k l+ +i+ + + ++  l+++
  gi|330508456|ref|YP_004384884.1|  95 TLSGITVAIYMVsASAGLQP----PGGphAYLGIIVSLMVILTPVLGFIQLK-KRDKRLQ-TIHRWSGRMTIALMII 165
                                       44455555555333333333....233569**********************.6677745.5999999999999988 PP

                           DUF4199  79 vagl 82 
                                        a l
  gi|330508456|ref|YP_004384884.1| 166 NAYL 169
                                       8766 PP

>> ResB  ResB-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.3   0.00015      0.25     441     472 ..      56      89 ..      53     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00015
                              ResB 441 lvllgalllvlGlvlslyvrhrRvWvrieae..d 472
                                       lvl g l+l++G+v + y++ +R W+++ ++   
  gi|330508456|ref|YP_004384884.1|  56 LVLSGLLFLIAGMVCARYLKGKRWWLKAHRTlgI 89 
                                       799*************************643332 PP

>> Ferric_reduct  Ferric reductase like transmembrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.2     0.032        52      75     122 ..      48      92 ..      16      95 .. 0.63
   2 ?    3.7   1.0     0.037        61      25      47 ..      71      94 ..      47     110 .. 0.54
   3 ?   11.1   0.7    0.0002      0.32       9      50 ..     126     165 ..     119     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.032
                     Ferric_reduct  75 lkkpynllGvlalllliilaitSlkfirrrlsyelFyylHhllyvayl 122
                                       + +py++l vl+ ll++i  ++  +++    + ++++  H++l +a +
  gi|330508456|ref|YP_004384884.1|  48 ILFPYHALLVLSGLLFLIAGMVCARYLK---GKRWWLKAHRTLGIAGA 92 
                                       5555555555555555555555545555...45788888888777655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.037
                     Ferric_reduct 25 ltglsldklll.fHkwlgvlafll 47
                                       + l+  +++l  H+ lg++ ++l
  gi|330508456|ref|YP_004384884.1| 71 ARYLKGKRWWLkAHRTLGIAGAAL 94
                                      233333444444566666555554 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0002
                     Ferric_reduct   9 lplalllalRnnflepltglsldklll.fHkwlgvlafllall 50 
                                       ++l+++l+   ++l ++   + dk l  +H+w g+++++l+++
  gi|330508456|ref|YP_004384884.1| 126 VSLMVILT---PVLGFIQLKKRDKRLQtIHRWSGRMTIALMII 165
                                       56777777...66666666678887777***********9986 PP

>> GutM  Glucitol operon activator protein (GutM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       9.4   1.5e+04      66      73 ..      94     101 ..      91     103 .. 0.78
   2 ?   10.3   0.1   0.00035      0.57       2      39 ..     122     160 ..     121     162 .. 0.88
   3 ?    2.5   0.9      0.09   1.5e+02       5      25 ..     158     178 .]     154     178 .] 0.88

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 9.4
                              GutM  66 rvmkGvTv 73 
                                         ++G+Tv
  gi|330508456|ref|YP_004384884.1|  94 LTLSGITV 101
                                       67899998 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00035
                              GutM   2 lililliawllqillglfQiknfnkalkelrkk.gkvai 39 
                                       l++i+ ++ +l  +lg++Q+k+  k+l+ + +  g++ i
  gi|330508456|ref|YP_004384884.1| 122 LGIIVSLMVILTPVLGFIQLKKRDKRLQTIHRWsGRMTI 160
                                       78999***********************99886567665 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.09
                              GutM   5 illiawllqillglfQiknfn 25 
                                       + +++++++++lg++ i++f+
  gi|330508456|ref|YP_004384884.1| 158 MTIALMIINAYLGWMMIQSFQ 178
                                       67899************9996 PP

>> DUF420  Protein of unknown function (DUF420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.0       0.1   1.6e+02       6      50 ..      54     105 ..      13     113 .. 0.63
   2 ?    7.9   5.3    0.0022       3.6      12     127 ..      60     172 ..      49     174 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.1
                            DUF420   6 avlnalaavllllglvaikk.....gkieaHrklml..lafvlsalFlvlYl 50 
                                       a+l+    ++l++g+v+++         +aHr+l +  +a++ls + +++Y+
  gi|330508456|ref|YP_004384884.1|  54 ALLVLSGLLFLIAGMVCARYlkgkrWWLKAHRTLGIagAALTLSGITVAIYM 105
                                       4444444555666666665322211234666666441134445555555555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0022
                            DUF420  12 aavllllglvaikk.....gkieaHrklml..lafvlsalFlvlYllkhalagetkfggpeeegvirpvYlaiLitH 81 
                                         ++l++g+v+++         +aHr+l +  +a++ls + +++Y++    + +   g         ++Yl i+++ 
  gi|330508456|ref|YP_004384884.1|  60 GLLFLIAGMVCARYlkgkrWWLKAHRTLGIagAALTLSGITVAIYMVSASAGLQPP-G-------GPHAYLGIIVS- 127
                                       55566666666653222113346677764411455555566666666555553322.2.......24567777665. PP

                            DUF420  82 ivLavvvvplvlvtlvlalkgkfekHrkiaritvpiwlyvavtGvv 127
                                        ++ +++ +l +++l    k+  + Hr  +r+t+ ++++ a +G++
  gi|330508456|ref|YP_004384884.1| 128 -LMVILTPVLGFIQLKKRDKRLQTIHRWSGRMTIALMIINAYLGWM 172
                                       .444566666777777777779999*******************97 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2         8   1.3e+04      50      56 ..      20      26 ..      17      33 .. 0.51
   2 ?   10.9   1.5   0.00031      0.51       4      58 ..      54      95 ..      47      97 .. 0.72
   3 ?    8.2   2.4    0.0022       3.6       5      60 ..      93     165 ..      89     171 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8
                           DUF4405 50 lgllfli 56
                                      l++++l+
  gi|330508456|ref|YP_004384884.1| 20 LAIALLA 26
                                      3333333 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00031
                           DUF4405  4 lllllsflvlaiSGillsfavlpsgrgaywaflgl.skhqwrdiHeilgllflilv 58
                                      +ll+ls+l+ +i G++  +               l +k++w + H++lg++  +l 
  gi|330508456|ref|YP_004384884.1| 54 ALLVLSGLLFLIAGMVCARY--------------LkGKRWWLKAHRTLGIAGAALT 95
                                      45666666666666666655..............237888***********99986 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0022
                           DUF4405   5 llllsflvlaiSGillsfavlpsgrgaywa...............flgl..skhqwrdiHeilgllflilvvl 60 
                                       +l+ls++++ai  +  s+ + p+g++++                 f+ l      ++ iH+++g   ++l+++
  gi|330508456|ref|YP_004384884.1|  93 ALTLSGITVAIYMVSASAGLQPPGGPHAYLgiivslmviltpvlgFIQLkkRDKRLQTIHRWSGRMTIALMII 165
                                       45555555555555555555555555444467888888888866666668788899***************98 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 ?    6.6   3.1    0.0048       7.9      44      87 ..      20      74 ..       9      86 .. 0.55
   2 ?    8.8   0.6     0.001       1.6      32      93 ..      82     146 ..      76     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0048
                   Phage_holin_3_6 44 gvlallalllllval.a..........lalaalwlaalivaavllvla.gvlalvg 87
                                      +++alla+ + l+a+ a          l+l ++  a l++ ++l+++a +v+a+  
  gi|330508456|ref|YP_004384884.1| 20 LAIALLAASSSLIAAsAnelepiedkiLIL-FPYHALLVLSGLLFLIAgMVCARYL 74
                                      344444444444444235557777775333.3677777766555555515555443 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.001
                   Phage_holin_3_6  32 ragsgagllgaagvlallalllllvalalala.a..lwlaalivaavllvlagvlalvglkklkk 93 
                                       +a + +g++gaa+ l  +++++ +v + ++l+    + +   i+  ++++l+ vl+++ lkk  k
  gi|330508456|ref|YP_004384884.1|  82 KAHRTLGIAGAALTLSGITVAIYMVSASAGLQpPggPHAYLGIIVSLMVILTPVLGFIQLKKRDK 146
                                       66677888888888888888888888889997668766666677788888888888888775544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1147.14
//
Query:       gi|330508457|ref|YP_004384885.1|  [L=556]
Description: pyruvate flavodoxin/ferredoxin oxidoreductase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-48  165.8   0.1    1.7e-48  165.4   0.1    1.2  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    2.2e-30  106.0   0.0      4e-30  105.2   0.0    1.4  1  POR           Pyruvate ferredoxin/flavodoxin oxidoreductase
    3.5e-07   30.0   1.1    6.8e-07   29.1   1.1    1.5  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    4.4e-05   23.7   0.0    0.00011   22.5   0.0    1.6  1  PFOR_II       Pyruvate:ferredoxin oxidoreductase core domain 


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4   0.1   3.8e-52   1.7e-48       2     228 ..     197     429 ..     196     432 .. 0.85

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 3.8e-52
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       + i+ag++ ++aYP+TPss i++ +a+ ++++++   +vv  esEi+ i ++ G a+aG+raa+ TSg G+ Lm e+
  gi|330508457|ref|YP_004384885.1| 197 GLIRAGLEAYVAYPMTPSSAILDFMANSAEEFGL---KVVHPESEIAVILMAEGFAYAGVRAAVGTSGGGFCLMTEA 270
                                       6799*****************************8...9*************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvi 150
                                       l la+++e+P+ ivv++R++pstgl+++t+q+Dl +++     +++ +v+a++++++a+   ++A+nlA+k+++P++
  gi|330508457|ref|YP_004384885.1| 271 LSLAGMAEIPLAIVVAQRTGPSTGLPTYTAQGDLHFVInagqgEFPRLVIAPGDAEDAYLWSAAALNLAWKYQIPAF 347
                                       ***************************************************************************** PP

                                       EEEEHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXX........SXXXBXXTXXTSSXXEEESBXBXTTSXBXX CS
                             POR_N 151 vlfDgfllshevekvelpdeedelklikekleeyerkey........aldpekpiargtaanpdtglehrekgneae 219
                                       +l+D+++  ++  +++l     + +++++ +  +e+ +y        +++p   + + ++  ++ ++ h+ +g  +e
  gi|330508457|ref|YP_004384885.1| 348 ILSDKIVS-ESQYSLDLGLTG-KAETARPAQLWNEQGDYhryrhsdtGVSPLAYPPQRGQVIKADSYAHDATGITTE 422
                                       *****998.887777775544.2233332222222222222444666777766666666777777888999888888 PP

                                       XXHHHHHHH CS
                             POR_N 220 daaekvvee 228
                                       d  +++++e
  gi|330508457|ref|YP_004384885.1| 423 D--PQITRE 429
                                       8..555555 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.0   8.9e-34     4e-30       1     177 []      12     169 ..      10     169 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 8.9e-34
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       +G+G+  ag   a+ + r Gy+++++ +y+s i+Ggh +s vr+s+e ++  ++ +e dll+al+++t+++h  +lk
  gi|330508457|ref|YP_004384885.1|  12 AGDGINEAGLTAARLMNRLGYRIFMYYDYPSLIKGGHNFSMVRASSE-RIGVCR-DEIDLLIALNQDTVDRHSGRLK 86 
                                       5**********************************************.99****.********************** PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallglplealeeai 154
                                       +g+i+i++++ +  + ++++               +g+++t i+ke g  ++++N ++lGa++++ g++   lee++
  gi|330508457|ref|YP_004384885.1|  87 EGSIFIFDADNVMGEGIAEKS--------------CGISVTGILKEEGAPSVMKNSCILGAFCHAVGIEWTVLEEVL 149
                                       *********887777777755..............5***************************************** PP

                                       HCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 155 kkrfpkkkeviekNlkafragye 177
                                       kk++pkk   +e+Nlk++r+gy+
  gi|330508457|ref|YP_004384885.1| 150 KKHIPKK---LELNLKVARRGYD 169
                                       *****98...************7 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   1.1   1.5e-10   6.8e-07       2     107 ..     189     297 ..     188     317 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.5e-10
                                       EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHH CS
                      TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpG 75 
                                       t+ +a+   L ++g e ++++p + + ++ld ++++    g++vv   +E +++ +A+g+a a   + +++ tsg G
  gi|330508457|ref|YP_004384885.1| 189 TGNQAISLGLIRAGLEAYVAYPMTPSSAILDFMANSAeefGLKVVHPESEIAVILMAEGFAYAG--VRAAVGTSGGG 263
                                       788999999*************************99999*********************9996..8899999**** PP

                                       HHHCHHHHHHHHHHT--EEEEEEE--CCCHH..S CS
                      TPP_enzyme_N  76 atnaltalaeAkvdriPllvlsgdrptslrg..q 107
                                       +  ++ al  A  + iPl +++++r   ++g  +
  gi|330508457|ref|YP_004384885.1| 264 FCLMTEALSLAGMAEIPLAIVVAQRTGPSTGlpT 297
                                       ************************9877777542 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 !   22.5   0.0   2.4e-08   0.00011       8      72 ..     466     521 ..     461     545 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.4e-08
                                       -STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHH CS
                           PFOR_II   8 mGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlve 72 
                                        Gs  g++k+a+d+l  +      +++ +l+PFPe++lk++l++v++++ ++ n++    Gql++
  gi|330508457|ref|YP_004384885.1| 466 WGSNKGVCKEAADSLGLR-----AVQVLVLWPFPENRLKDALRGVERLIAVECNAT----GQLAT 521
                                       566667777777766666.....68999**************************94....55544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3979.26
//
Query:       gi|330508458|ref|YP_004384886.1|  [L=283]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit beta [Methanosaeta concilii GP6]
Scores for complete 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  105.7   0.0    2.8e-30  105.1   0.0    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
      2e-06   27.8   0.1    3.9e-06   26.9   0.1    1.5  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.0   3.1e-34   2.8e-30       2     153 .]      50     197 ..      49     197 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 3.1e-34
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       iGc+               yl+ +++++ +G+++p+A+G+kla+pd +v++++GDG+ l   + +l+ a++rn++it
  gi|330508458|ref|YP_004384886.1|  50 IGCHGK----------IVDYLDvNSFYSIHGRTIPVATGIKLANPDLNVICFSGDGDSLAEgMDHLIFAAKRNIDIT 116
                                       777777..........667888888************************************9*************** PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpa 149
                                       +++++N++yg+t gq   ++p+g + ks+p+g++++p+++  l+ ++Ga+  ar  ++ +e+l+  +kea+ +kg++
  gi|330508458|ref|YP_004384886.1| 117 LILHDNRVYGLTTGQytpTSPTGFRGKSTPEGSIERPLNPLDLMLSAGATfIARGYSHGIEQLQTLFKEAILHKGFS 193
                                       *****************999******************************888878999****************** PP

                                       EEEE CS
                      TPP_enzyme_C 150 liev 153
                                       +++v
  gi|330508458|ref|YP_004384886.1| 194 FVDV 197
                                       **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 !   26.9   0.1   4.4e-10   3.9e-06       1      64 [.     201     265 ..     201     267 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.4e-10
                                       XTTTXSSSXSXXXXX-EEEGGGST---EEHHHHHHHHT----.....-EEEEEEEETTS--HHHHHHT. CS
                        PFO_beta_C   1 CvtFNkvnTfdwYkervykleedgyDpsdlekAlekalewgd.....kiplGifYkeekptyeerleel 64 
                                       Cv++  +n ++ Y+ r+y++e   +D   +++A e +++w       +iplG fY+ + p +++ ++++
  gi|330508458|ref|YP_004384886.1| 201 CVSY--FNMYESYNRRTYSVEG--NDAASFDQAQEIIRRWSYddsesPIPLGKFYQIDAPRFDQAYSQT 265
                                       9***..***************7..7**************976678888***************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.58
# Mc/sec: 1480.42
//
Query:       gi|330508459|ref|YP_004384887.1|  [L=53]
Description: rubredoxin [Methanosaeta concilii GP6]
Scores for complete 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-26   90.3   2.9      6e-26   90.2   2.9    1.0  1  Rubredoxin      Rubredoxin
      7e-05   22.8   0.1    9.6e-05   22.4   0.1    1.2  1  PHD_4           PHD-finger
     0.0008   18.9   2.1       0.18   11.3   0.2    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0049   16.7   3.1       0.59   10.1   0.7    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
     0.0072   16.0   0.4       0.53   10.0   0.0    2.1  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
  ------ inclusion threshold ------
      0.016   15.4   2.7       0.13   12.4   2.7    2.0  1  Zn-ribbon_8     Zinc ribbon domain
       0.02   14.2   4.3      0.038   13.3   0.5    2.1  2  zf-RanBP        Zn-finger in Ran binding protein and others
      0.038   13.7   2.7        1.3    8.8   0.5    2.2  2  A2L_zn_ribbon   A2L zinc ribbon domain
       0.12   12.4   0.1       0.14   12.2   0.1    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.12   12.2   1.8        7.3    6.5   0.4    2.2  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO
       0.21   12.1   1.3         18    6.0   0.1    2.1  2  zf-H2C2_2       Zinc-finger double domain
       0.29   11.1   4.5        1.3    9.0   0.5    2.2  2  Nudix_N_2       Nudix N-terminal
       0.29   11.1   1.6        5.8    6.9   1.6    2.0  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.32   10.8   7.4        2.4    7.9   0.8    2.1  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.37   10.4   2.9        2.4    7.8   0.2    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.41   10.7   4.0        3.1    7.8   3.9    2.0  1  ADK_lid         Adenylate kinase, active site lid
       0.42   11.2   2.9          8    7.1   0.4    2.2  2  zf-C2H2         Zinc finger, C2H2 type
       0.92    9.6   6.2        9.6    6.4   1.1    2.3  2  UPF0547         Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   2.9   6.1e-29     6e-26       1      47 []       3      49 ..       3      49 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 6.1e-29
                                      EEEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                        Rubredoxin  1 kyeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47
                                      ky C+vCgy+Ydp+kGd  +giapgT+FedlPddW+CP+Cgv+ke F
  gi|330508459|ref|YP_004384887.1|  3 KYVCTVCGYIYDPEKGDSASGIAPGTAFEDLPDDWTCPECGVGKELF 49
                                      79******************************************987 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   9.6e-08   9.6e-05      33      67 ..       6      42 ..       2      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.6e-08
                             PHD_4 33 CsvCyeivHpeClkek..egegvvnedlpnsWeCpkC 67
                                      C+vC  i  pe  ++    ++g++ edlp +W Cp+C
  gi|330508459|ref|YP_004384887.1|  6 CTVCGYIYDPEKGDSAsgIAPGTAFEDLPDDWTCPEC 42
                                      **********988877556789*************** PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.2   0.00018      0.18      20      36 ..       4      20 ..       2      24 .. 0.82
   2 !    7.5   0.2    0.0028       2.8       2       8 ..      38      44 ..      37      51 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                      EEESSSSBEEEECCCCC CS
                      TF_Zn_Ribbon 20 lvCtdCGlVlednside 36
                                      +vCt CG++ + +  d+
  gi|330508459|ref|YP_004384887.1|  4 YVCTVCGYIYDPEKGDS 20
                                      89999999988888776 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0028
                                      EETTTTC CS
                      TF_Zn_Ribbon  2 kCPnCgs 8 
                                      +CP+Cg 
  gi|330508459|ref|YP_004384887.1| 38 TCPECGV 44
                                      6999986 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.7    0.0006      0.59       4      14 ..       3      11 ..       2      16 .. 0.80
   2 !    7.3   0.1    0.0043       4.3       4      11 ..      36      43 ..      34      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0006
                    Zn_ribbon_SprT  4 vYrCtgCgrey 14
                                      +Y+Ct Cg  y
  gi|330508459|ref|YP_004384887.1|  3 KYVCTVCG--Y 11
                                      8*******..4 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0043
                    Zn_ribbon_SprT  4 vYrCtgCg 11
                                       ++C+ Cg
  gi|330508459|ref|YP_004384887.1| 36 DWTCPECG 43
                                      59*****9 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.4      0.03        30      44      52 ..       3      11 ..       1      13 [. 0.86
   2 !   10.0   0.0   0.00054      0.53      30      52 ..      20      44 ..      16      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.03
                    zinc_ribbon_10 44 kyrCpkCga 52
                                      ky+C  Cg 
  gi|330508459|ref|YP_004384887.1|  3 KYVCTVCGY 11
                                      7******97 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00054
                    zinc_ribbon_10 30 shnGlapkeeleev..kyrCpkCga 52
                                      s +G ap  ++e++   + Cp+Cg+
  gi|330508459|ref|YP_004384887.1| 20 SASGIAPGTAFEDLpdDWTCPECGV 44
                                      56899999999999889******95 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.7   0.00013      0.13       6      33 ..       4      43 ..       3      48 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                       Zn-ribbon_8  6 YrCeeCghefe...........vlqsisdaplta.CPeCg 33
                                      Y C+ Cg  ++           +  ++ d p+   CPeCg
  gi|330508459|ref|YP_004384887.1|  4 YVCTVCGYIYDpekgdsasgiaPGTAFEDLPDDWtCPECG 43
                                      9**********888777777653333346667777****9 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 ?    2.6   0.2     0.085        84       7      12 ..       6      11 ..       5      12 .. 0.82
   2 ?   13.3   0.5   3.9e-05     0.038       3      12 ..      35      44 ..      33      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.085
                                      -SSS-- CS
                          zf-RanBP  7 CskClv 12
                                      C++C++
  gi|330508459|ref|YP_004384887.1|  6 CTVCGY 11
                                      999997 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.9e-05
                                      SSEE-SSS-- CS
                          zf-RanBP  3 gdWdCskClv 12
                                      +dW+C+ C+v
  gi|330508459|ref|YP_004384887.1| 35 DDWTCPECGV 44
                                      89******97 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.5    0.0013       1.3       1      10 [.       1      10 [.       1      13 [. 0.71
   2 ?    5.2   0.1     0.018        18      23      28 ..      38      43 ..      35      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                     A2L_zn_ribbon  1 snlkvCsvCg 10
                                      ++ +vC+vCg
  gi|330508459|ref|YP_004384887.1|  1 MDKYVCTVCG 10
                                      5677888886 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.018
                     A2L_zn_ribbon 23 vCieCg 28
                                       C+eCg
  gi|330508459|ref|YP_004384887.1| 38 TCPECG 43
                                      599998 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.14      71      94 ..       4      44 ..       2      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                      EEETTTS-EEECHH.HHH................S-TTTSS CS
                              HypA 71 vrCreCgkefelee.kal................rCpkCgs 94
                                      + C++Cg+ ++ e+ +++                +Cp+Cg 
  gi|330508459|ref|YP_004384887.1|  4 YVCTVCGYIYDPEKgDSAsgiapgtafedlpddwTCPECGV 44
                                      68*********88744336899*****************96 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.4    0.0073       7.3      15      25 ..       5      15 ..       1      19 [. 0.81
   2 ?    5.2   0.0     0.019        19      14      20 ..      37      43 ..      31      44 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0073
                         zf-C2H2_3 15 qCkeCgMvYnp 25
                                       C++Cg +Y p
  gi|330508459|ref|YP_004384887.1|  5 VCTVCGYIYDP 15
                                      5********87 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.019
                         zf-C2H2_3 14 sqCkeCg 20
                                       +C+eCg
  gi|330508459|ref|YP_004384887.1| 37 WTCPECG 43
                                      57****9 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.026        25      14      22 ..       3      11 ..       1      14 [. 0.84
   2 ?    6.0   0.1     0.018        18      15      21 ..      37      43 ..      29      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                         zf-H2C2_2 14 pyeCplCdk 22
                                      +y C +C++
  gi|330508459|ref|YP_004384887.1|  3 KYVCTVCGY 11
                                      699****99 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.018
                         zf-H2C2_2 15 yeCplCd 21
                                      ++Cp+C+
  gi|330508459|ref|YP_004384887.1| 37 WTCPECG 43
                                      89****7 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5    0.0013       1.3      23      31 ..       4      12 ..       3      13 .. 0.92
   2 ?    3.7   0.3     0.059        59       3       7 ..      39      43 ..      38      48 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                                      EEETTTTEE CS
                         Nudix_N_2 23 lvCpaCgti 31
                                      +vC+ Cg+i
  gi|330508459|ref|YP_004384887.1|  4 YVCTVCGYI 12
                                      7*******9 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.059
                                      -TTT- CS
                         Nudix_N_2  3 CsqCG 7 
                                      C++CG
  gi|330508459|ref|YP_004384887.1| 39 CPECG 43
                                      66666 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.6    0.0059       5.8      31      54 ..       6      44 ..       4      47 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0059
                    OrfB_Zn_ribbon 31 CseCgsknke...............alsgrtfkCpnCgf 54
                                      C +Cg++ ++               ++ ++ ++Cp+Cg+
  gi|330508459|ref|YP_004384887.1|  6 CTVCGYIYDPekgdsasgiapgtafEDLPDDWTCPECGV 44
                                      777777776666777777777776667778899999986 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.8    0.0025       2.4       1       9 [.       4      12 ..       4      14 .. 0.89
   2 ?    6.7   0.9     0.006         6      15      21 ..      37      43 ..      37      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0025
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      YvC  CG+ 
  gi|330508459|ref|YP_004384887.1|  4 YVCTVCGYI 12
                                      9******96 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.006
                      Rubredoxin_2 15 GrCpsCg 21
                                      + Cp+Cg
  gi|330508459|ref|YP_004384887.1| 37 WTCPECG 43
                                      99****8 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.065        64       1       9 [.       2      10 ..       2      17 .. 0.86
   2 ?    7.8   0.2    0.0025       2.4       1       9 [.      35      43 ..      35      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.065
                            zf_UBZ  1 dtylCerCg 9 
                                      d y+C  Cg
  gi|330508459|ref|YP_004384887.1|  2 DKYVCTVCG 10
                                      68******8 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0025
                            zf_UBZ  1 dtylCerCg 9 
                                      d ++C++Cg
  gi|330508459|ref|YP_004384887.1| 35 DDWTCPECG 43
                                      689*****8 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.9    0.0032       3.1       3      29 ..       5      44 ..       4      49 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0032
                                      E-TTT--EEETT.............T.B--SSTTB-TTT-- CS
                           ADK_lid  3 vCpkCGrsYhvv.............f.npPkveglCDkCGe 29
                                      vC  CG +Y  +             f   P  +  C +CG+
  gi|330508459|ref|YP_004384887.1|  5 VCTVCGYIYDPEkgdsasgiapgtaFeDLP-DDWTCPECGV 44
                                      9********744444444444444443444.9999999996 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.4     0.008         8       1      10 [.       4      13 ..       4      16 .. 0.88
   2 ?    4.7   0.1     0.049        48       2       7 ..      38      43 ..      37      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.008
                                      EEETTTTEEE CS
                           zf-C2H2  1 ykCpdCgksF 10
                                      y+C++Cg+ +
  gi|330508459|ref|YP_004384887.1|  4 YVCTVCGYIY 13
                                      9******876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.049
                                      EETTTT CS
                           zf-C2H2  2 kCpdCg 7 
                                      +Cp+Cg
  gi|330508459|ref|YP_004384887.1| 38 TCPECG 43
                                      8****9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3     0.015        15      16      25 ..       5      14 ..       4      15 .. 0.83
   2 ?    6.4   1.1    0.0096       9.6       2       7 ..      38      43 ..      38      44 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.015
                           UPF0547 16 fCphCGyvFq 25
                                      +C  CGy+++
  gi|330508459|ref|YP_004384887.1|  5 VCTVCGYIYD 14
                                      5999***986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0096
                           UPF0547  2 vCPeCe 7 
                                      +CPeC 
  gi|330508459|ref|YP_004384887.1| 38 TCPECG 43
                                      577774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 336.68
//
Query:       gi|330508460|ref|YP_004384888.1|  [L=174]
Description: ferritin [Methanosaeta concilii GP6]
Scores for complete 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  131.0   2.3    3.6e-38  130.7   2.3    1.1  1  Ferritin       Ferritin-like domain
  ------ inclusion threshold ------
       0.02   15.0   0.2       0.12   12.5   0.0    2.3  2  DUF3906        Protein of unknown function (DUF3906)
      0.073   13.2   0.2        0.1   12.7   0.2    1.3  1  Mad3_BUB1_I_2  Putative Mad3/BUB1 like region 1 protein


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 !  130.7   2.3     6e-42   3.6e-38       2     137 ..       8     139 ..       7     144 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.7 bits;  conditional E-value: 6e-42
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS. CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke. 77 
                                       +aLn q ++el+++y+yl+m+ y++++g++g+a +++ qa ee+ h +kl++++ a G+     +a+  ++eap++ 
  gi|330508460|ref|YP_004384888.1|   8 EALNYQANRELYSSYLYLSMSYYFESIGFRGFASWMRVQAGEELVHTMKLLDYVAASGE-----KAKMLAVEAPQHs 79 
                                       79*********************************************************.....************* PP

                                       CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  78 fgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeehewelealle 137
                                       ++s++++++++ ehe++vt+++++l+++ae+e+D  t+ fl+++++eq+e+e+  + +l+
  gi|330508460|ref|YP_004384888.1|  80 WESPQQAFAHVWEHERAVTRMIHDLVAVAESESDAMTRKFLQWYVDEQVEEEESSDGVLK 139
                                       ****************************************************99888776 PP

>> DUF3906  Protein of unknown function (DUF3906)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.37   2.2e+03      16      28 ..     103     115 ..      88     118 .. 0.77
   2 ?   12.5   0.0   1.9e-05      0.12       9      43 ..     132     166 ..     127     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.37
                           DUF3906  16 svvvvAendeqAF 28 
                                         v vAe++  A 
  gi|330508460|ref|YP_004384888.1| 103 DLVAVAESESDAM 115
                                       5688999999885 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.9e-05
                           DUF3906   9 eleeetvsvvvvAendeqAFrqleielekhylklP 43 
                                       e+++ +++ v++A nd +A r++++el k   k P
  gi|330508460|ref|YP_004384888.1| 132 ESSDGVLKRVLAAGNDPKALRAADEELGKRGFKFP 166
                                       567899999******************99766666 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 ?   12.7   0.2   1.8e-05       0.1      43     109 ..      18      84 ..      10     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                     Mad3_BUB1_I_2  43 kfyyfvYlelsryFlkkgkkeaalfiLqegiknkvydkeilkeelksikklekklseeeakkllkpk 109
                                        +++++Yl +s yF  +g+++ a ++  ++ ++ v+  ++l     s +k +  + e   ++   p+
  gi|330508460|ref|YP_004384888.1|  18 LYSSYLYLSMSYYFESIGFRGFASWMRVQAGEELVHTMKLLDYVAASGEKAKMLAVEAPQHSWESPQ 84 
                                       5889**********************99999999999888876655555554344444455555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.57
# Mc/sec: 914.12
//
Query:       gi|330508461|ref|YP_004384889.1|  [L=145]
Description: hypothetical protein MCON_2662 [Methanosaeta concilii GP6]
Scores for complete 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   81.6   1.3    2.9e-12   45.9   0.0    2.1  2  Lipoprotein_15  Secreted repeat of unknown function


Domain annotation for each model (and alignments):
>> Lipoprotein_15  Secreted repeat of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.2   4.5e-13   8.1e-09       7      46 ..      38      76 ..      34      77 .. 0.95
   2 !   45.9   0.0   1.6e-16   2.9e-12       2      46 ..      94     136 ..      93     137 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 4.5e-13
                    Lipoprotein_15  7 dGtkqvaykGmPLYtFakDkkpgdktGdgvgaCagvWpvv 46
                                       G+ +v+  G  LY++++D+   ++ ++++++Ca++W ++
  gi|330508461|ref|YP_004384889.1| 38 LGSYLVNETGFALYYYQNDSSLDGM-STCNDDCAKMWMPF 76
                                      599**********************.***********986 PP

  == domain 2  score: 45.9 bits;  conditional E-value: 1.6e-16
                    Lipoprotein_15   2 tvtrddGtkqvaykGmPLYtFakDkkpgdktGdgvgaCagvWpvv 46 
                                       t++r+dG+kq++ k +PLY++++D+ pgd+ G+g     + W v+
  gi|330508461|ref|YP_004384889.1|  94 TIERADGSKQTTFKSWPLYLYSRDSSPGDARGNGLE--DDQWRVI 136
                                       89*********************************7..5999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 798.55
//
Query:       gi|330508462|ref|YP_004384890.1|  [L=449]
Description: queuine tRNA-ribosyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.9e-113  378.6   0.0      4e-86  289.3   0.0    2.0  2  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 !   87.4   0.0   5.7e-29     1e-24       2      92 ..      16     110 ..      12     123 .. 0.91
   2 !  289.3   0.0   2.2e-90     4e-86      90     346 ..     181     447 ..     169     449 .] 0.95

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 5.7e-29
                                       TEEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-E CS
                               TGT   2 gaRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpi 78 
                                       +aR+G +++++g+i+tP ++pv+t g+v++l +d+l  +lg++  l+ntyhl+l+pg+el+++ gglh+f+g+++p+
  gi|330508462|ref|YP_004384890.1|  16 NARAGLIKTRRGDIQTPYLVPVATLGSVRALGSDDL-VSLGVSCALANTYHLHLKPGDELIRRLGGLHRFMGFSRPL 91 
                                       59**********************************.599************************************* PP

                                       EEE-SHHHHHHH....E.E CS
                               TGT  79 ltdsggfqvfsl....k.k 92 
                                        tdsggfq fsl    + +
  gi|330508462|ref|YP_004384890.1|  92 FTDSGGFQAFSLgfgrEhN 110
                                       ***********96653134 PP

  == domain 2  score: 289.3 bits;  conditional E-value: 2.2e-90
                                       HEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHHHHHHHH...S CS
                               TGT  90 lkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwldrcleah...q 163
                                       l kit++g+sf+s  dG  ++l++e+s++iq++lgsDiim++d+++++ +++++ +k++ rT+ w+++++++h   q
  gi|330508462|ref|YP_004384890.1| 181 LTKITDQGISFKSMADGAWHFLDAERSMRIQSNLGSDIIMSFDECTSPLSDYDYTKKAMYRTHDWAEESIRYHdksQ 257
                                       4599***********************************************************************99 PP

                                       EEEEEE--TT-HHHHHHHHHHHHHH--SEEEE-SSSSSSHHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHH CS
                               TGT 164 alfgivqGglyedlreesaeelakrdfdgyaigGlsvgeekeellevveavtellpedkprylmGvgtPedlleava 240
                                       a+ gi+qGg +edlr+ s + ++++ fdg+aigG s+g++k+++ +v++ ++++l +d+pr+l G+g  +d+ e+va
  gi|330508462|ref|YP_004384890.1| 258 AIYGIIQGGWFEDLRRTSTDFIVSQPFDGIAIGG-SLGNSKQDMHQVLDWTIPRL-DDRPRHLLGIGEIDDIFECVA 332
                                       9*********************************.99******************.99******************* PP

                                       TT--EEEESHHHHHHHTTEEEE...TTE.......EEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-H CS
                               TGT 241 lGvDmfdcvyptrtarngralt...seg.......elnlknakyaedfspldegCsCytCknytraylhhllktkem 307
                                       +G+D fdcv ptr+ar+g +l    s g       +ln+k+a+++ d  p+d+ CsC+tC +y+rayl+hl+ ++e+
  gi|330508462|ref|YP_004384890.1| 333 RGIDTFDCVSPTRIARRGSLLLspqS-GgsrqnkfRLNIKSARFKGDDLPVDPACSCPTCCTYSRAYLRHLYVSREL 408
                                       **********************5541.356677779************************99*************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                               TGT 308 lgaiLltiHNlhyylelfkriReaIkegtfeefveefar 346
                                          +L+t+HNlh++l+l+++iRe+I+ g+f e+++++++
  gi|330508462|ref|YP_004384890.1| 409 SYFRLATLHNLHFMLRLMESIRESIRCGSFMELRDRWLK 447
                                       ***********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2825.63
//
Query:       gi|330508463|ref|YP_004384891.1|  [L=242]
Description: hypothetical protein MCON_2664 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-37  128.3  12.0    2.9e-37  128.3  12.0    1.4  2  Vut_1     Putative vitamin uptake transporter


Domain annotation for each model (and alignments):
>> Vut_1  Putative vitamin uptake transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1      0.71   1.3e+04      57      59 ..      34      36 ..      22      50 .. 0.43
   2 !  128.3  12.0   1.6e-41   2.9e-37       4     150 .]      58     233 ..      56     233 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.71
                             Vut_1 57 svf 59
                                       +f
  gi|330508463|ref|YP_004384891.1| 34 LFF 36
                                      222 PP

  == domain 2  score: 128.3 bits;  conditional E-value: 1.6e-41
                             Vut_1   4 vllfpltflitdiisevyGkkaarkvvllgflanllalillllalllpa........................eale 56 
                                        ++++ltf+++d+i++  G++aa ++++l++ +nlla+i++++++llpa                        + ++
  gi|330508463|ref|YP_004384891.1|  58 GFIYSLTFTWRDLIHKQLGERAALTTIWLAAGFNLLAAIYFQFVVLLPAqtdwansggqaawtflfgildssgQGWQ 134
                                       79**********************************************999999988888888888888777777** PP

                             Vut_1  57 svfgltprivlasliaylvsqlldvyvfhrlkkltkgkk.lwlrnigStlvsqlvdtlifvtiaflg....eqllei 128
                                       sv++l++rivlas+++ l+++l+d++v+  + +  ++++ +w+r+++S++vs  +d+l+f +iaf+g    + l+++
  gi|330508463|ref|YP_004384891.1| 135 SVLSLQMRIVLASILTALLAELIDTRVYRIWTQGARKSWpQWTRVFASNAVSIPLDSLLFPVIAFMGilgtQGLVQM 211
                                       *******************************988889999*************************99********** PP

                             Vut_1 129 ilsqylikllialldtplvylv 150
                                       i++++++k +i+ll+++++ylv
  gi|330508463|ref|YP_004384891.1| 212 IWTNIIVKAAITLLVFWTIYLV 233
                                       ********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1658.26
//
Query:       gi|330508464|ref|YP_004384892.1|  [L=297]
Description: methyltransferase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-12   47.3   0.0    5.6e-12   46.2   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
      1e-09   37.9   0.0    1.5e-09   37.3   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    5.6e-08   32.3   0.0    8.4e-08   31.7   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G
    2.5e-07   31.4   0.0    5.4e-07   30.3   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    5.3e-07   29.6   0.0      1e-06   28.7   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    1.3e-06   28.2   0.0    2.1e-06   27.6   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    6.8e-06   26.7   0.0    1.3e-05   25.8   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    0.00018   20.7   0.0    0.00024   20.3   0.0    1.2  1  DREV             DREV methyltransferase
    0.00044   19.8   0.0     0.0008   19.0   0.0    1.4  1  MTS              Methyltransferase small domain
     0.0018   17.7   0.0     0.0028   17.0   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.002   18.1   0.0     0.0032   17.4   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
     0.0039   16.6   0.4     0.0081   15.6   0.0    1.7  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0042   16.7   0.0     0.0081   15.8   0.0    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0057   16.4   0.0      0.017   14.9   0.0    1.6  1  Met_10           Met-10+ like-protein
     0.0063   16.2   0.2      0.012   15.3   0.2    1.4  1  DUF995           Protein of unknown function (DUF995)
     0.0067   15.5   0.0      0.011   14.7   0.0    1.3  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
     0.0091   15.8   0.0      0.014   15.1   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)
  ------ inclusion threshold ------
       0.01   15.2   0.0      0.017   14.5   0.0    1.2  1  TehB             Tellurite resistance protein TehB
      0.012   15.0   0.0      0.018   14.4   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.016   14.6   0.0      0.029   13.8   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
      0.017   14.9   0.0      0.027   14.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.022   14.4   0.0      0.032   13.8   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
      0.033   13.8   0.0      0.051   13.1   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.037   14.0   0.0      0.074   13.0   0.0    1.5  1  Methyltransf_32  Methyltransferase domain
       0.04   14.3   0.0      0.075   13.5   0.0    1.4  1  DUF5541          Family of unknown function (DUF5541)
       0.13   11.8   0.0       0.24   11.0   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F


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   8.2e-15   5.6e-12       1      89 [.      69     156 ..      69     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 8.2e-15
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS...SSTTTEEEEEEEST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp...fedgsfDlvvssga 73 
                                       vLd+G+G+G+l++ la++    +vt+v+++++m+  +re+++e g+ n+++vq+  e+++     d  +D+vv+s++
  gi|330508464|ref|YP_004384892.1|  69 VLDIGAGPGTLAIPLAQKA--THVTAVEPADGMCSVMREKMAEYGVeNITIVQKRWEEVDvarDLDPPYDVVVASFS 143
                                       9*****************6..*************************************983334677********99 PP

                                       GGGSSHHHHHHHHHHH CS
                   Methyltransf_25  74 lhhlsdedlekalkei 89 
                                       l +++    ++a++++
  gi|330508464|ref|YP_004384892.1| 144 LGMMDI---RDAIEKM 156
                                       888764...4444444 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   2.2e-12   1.5e-09      14      83 ..      49     120 ..      47     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.2e-12
                                       --HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S CS
                            RrnaAD  14 knkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvvhq 83 
                                       k+++ i++++ +++++ek  vl+ig+G+G l  +La+ a +v+++E    ++ ++++k+     e++++v++
  gi|330508464|ref|YP_004384892.1|  49 KEQNRIERVIWETDITEKSRVLDIGAGPGTLAIPLAQKATHVTAVEPADGMCSVMREKMAeyGVENITIVQK 120
                                       578999*****************************************************988889****997 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   1.2e-10   8.4e-08      48     121 ..      65     140 ..      54     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.2e-10
                                       CC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC....TTTTT-EEEEE CS
                              GidB  48 krdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee....kqeeekydvvt 120
                                       ++++v+D+G+G+G  +ipLa  ++  ++t +e+    ++ ++e ++e ++en++iv++r ee    ++   +ydvv+
  gi|330508464|ref|YP_004384892.1|  65 EKSRVLDIGAGPGTLAIPLA--QKATHVTAVEPADGMCSVMREKMAEYGVENITIVQKRWEEvdvaRDLDPPYDVVV 139
                                       3336**********999997..7888999*********************************777777778888887 PP

                                       E CS
                              GidB 121 s 121
                                       +
  gi|330508464|ref|YP_004384892.1| 140 A 140
                                       5 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   7.9e-10   5.4e-07       1      89 [.      70     156 ..      70     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 7.9e-10
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnv..elealdlldldggssfDlvvasnv 75 
                                       L+iG+G G+l+ +l++k   +++t+v++   ++   +ek+a+++ +n + v  ++e+ d++ + ++  +D+vvas+ 
  gi|330508464|ref|YP_004384892.1|  70 LDIGAGPGTLAIPLAQK--ATHVTAVEPADGMCSVMREKMAEYGVENITIVqkRWEEVDVARDLDP-PYDVVVASFS 143
                                       8****************..************************98887655115666665554444.********** PP

                   Methyltransf_12  76 lhhlkdirevldni 89 
                                       l  + dir++++++
  gi|330508464|ref|YP_004384892.1| 144 LGMM-DIRDAIEKM 156
                                       **98.888888776 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.5e-09     1e-06      20      96 ..      63     148 ..      41     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.5e-09
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqgkfdlIv 87 
                                         +++rvLdiG+G G+l+  l+++ ++vt+v++ + + +  +         ++   qk  +  + a++ +  +d++v
  gi|330508464|ref|YP_004384892.1|  63 ITEKSRVLDIGAGPGTLAIPLAQKATHVTAVEPADGMCSVMRekmaeygveNITIVQKRWEEVDVARDLDPPYDVVV 139
                                       46788****************************9988888889999****988999999998899999999****** PP

                   Methyltransf_23  88 lrevlehvp 96 
                                       ++++l+ ++
  gi|330508464|ref|YP_004384892.1| 140 ASFSLGMMD 148
                                       *****9886 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   3.1e-09   2.1e-06       2      99 ..      64     158 ..      63     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.1e-09
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled...ekf 75 
                                       +++ rvlD+G+G G+l++ la++     +v+ ++    + +++re+ ++ g++n++  q  +ee +  +++    ++
  gi|330508464|ref|YP_004384892.1|  64 TEKSRVLDIGAGPGTLAIPLAQK---ATHVTAVEPADGMCSVMREKMAEYGVENITIVQKRWEEVD--VARdldPPY 135
                                       56789****************76...468***********************************99..5555669** PP

                   Methyltransf_31  76 Dlilsnevlnaladpdkileeier 99 
                                       D++++   l  + d  +++e++++
  gi|330508464|ref|YP_004384892.1| 136 DVVVASFSL-GMMDIRDAIEKMIQ 158
                                       ***996555.66666666666655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.9e-08   1.3e-05       1      76 [.      70     152 ..      70     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.9e-08
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT...-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfedn...sfDlvvssevlhh 73 
                                       Ld+G+G G la +la+++++v++v++++ m  + +ek  e g+ ++++v+ + e++ ++ +    +D+vv+s++l  
  gi|330508464|ref|YP_004384892.1|  70 LDIGAGPGTLAIPLAQKATHVTAVEPADGMCSVMREKMAEYGVeNITIVQKRWEEVDVARDldpPYDVVVASFSLGM 146
                                       8*****************************************9*9*********99766544459*******99988 PP

                                       -...CC CS
                   Methyltransf_11  74 v...ed 76 
                                       +   + 
  gi|330508464|ref|YP_004384892.1| 147 MdirDA 152
                                       833333 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.4e-07   0.00024      84     161 ..      54     138 ..      47     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.4e-07
                              DREV  84 iekespasdqe.dkklldlGaGdGeitkrvaptfeevyate....lsetmrdrlkkkkynvlsale..lqetdvkld 153
                                       ie+  +++d + + ++ld+GaG G ++  +a+   +v a e    + + mr+++   + + +++++  ++e dv  d
  gi|330508464|ref|YP_004384892.1|  54 IERVIWETDITeKSRVLDIGAGPGTLAIPLAQKATHVTAVEpadgMCSVMREKMAEYGVENITIVQkrWEEVDVARD 130
                                       677788888651569***********************999333345667777777777779988778999999888 PP

                              DREV 154 lilclnll 161
                                       l   ++++
  gi|330508464|ref|YP_004384892.1| 131 LDPPYDVV 138
                                       76555554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.2e-06    0.0008      31     126 ..      65     161 ..      57     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-06
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-..STTTTSTTS-EEEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevvas..dvleeveekkfdli 101
                                       ++ +vlD+G+G G l++ la++  +  vt+v+       + +e +++ ++e    v+ +++  dv  +++   +d++
  gi|330508464|ref|YP_004384892.1|  65 EKSRVLDIGAGPGTLAIPLAQKATH--VTAVEPADGMCSVMREKMAEYGVEnitiVQKRWEevDVARDLD-PPYDVV 138
                                       4678*****************9988..7777777777777777777777777556455554114555555.889999 PP

                                       EE---STTTCHCHHHHHHHHHHHHH CS
                               MTS 102 vsNPPfhagkatelavaeeliaeAk 126
                                       v    f  g     +++e++i+++ 
  gi|330508464|ref|YP_004384892.1| 139 VAS--FSLGMMDIRDAIEKMIQASS 161
                                       874..66666666677777776665 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     4e-06    0.0028      47     137 ..      65     154 ..      44     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4e-06
                                       -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-...T-EEEE CS
                   Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed...dsfDvv 120
                                       + ++vlD+ +G g la+ l++++ +   v+ ++  + m +v ++k+ e g+ ni  +q   ee++        +Dvv
  gi|330508464|ref|YP_004384892.1|  65 EKSRVLDIGAGPGTLAIPLAQKATH---VTAVEPADGMCSVMREKMAEYGVENITIVQKRWEEVDVARdldPPYDVV 138
                                       5579***************988765...666667779**************************99875122579999 PP

                                       EEES-GGG-S-HHHHHH CS
                   Ubie_methyltran 121 tvsfGlrnvtDklkaLk 137
                                         sf l  + D+  a++
  gi|330508464|ref|YP_004384892.1| 139 VASFSLG-MMDIRDAIE 154
                                       9999774.445555544 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.7e-06    0.0032      12      68 ..      63     116 ..      51     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.7e-06
                   Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkie 68 
                                       ++++srv+DiG+  g l+i l+  +ka++v+a++ ++g ++  +e+++++g+e+ i+
  gi|330508464|ref|YP_004384892.1|  63 ITEKSRVLDIGAGPGTLAIPLA--QKATHVTAVEPADGMCSVMREKMAEYGVEN-IT 116
                                       67899****************9..58899**********************976.33 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       4.7   3.2e+03      93     105 ..       6      18 ..       3      22 .. 0.84
   2 !   15.6   0.0   1.2e-05    0.0081     157     233 ..      61     141 ..      52     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.7
                              PrmA  93 eeedWaeewkkyy 105
                                       ++ dW e wk++ 
  gi|330508464|ref|YP_004384892.1|   6 KDIDWNEIWKSQM 18 
                                       689******9986 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.2e-05
                              PrmA 157 klvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk.....eekad 228
                                       + + e+++vlD+G+G G Lai  a+  a +v+av   +   +v +e ++  +ve+   v+   e ++     + ++d
  gi|330508464|ref|YP_004384892.1|  61 TDITEKSRVLDIGAGPGTLAIPLAQ-KATHVTAVEPADGMCSVMREKMAEYGVENITIVQKRWEEVDvardlDPPYD 136
                                       45678889*************9776.7999******9999***************877876666664445667899* PP

                              PrmA 229 vivaN 233
                                       v+va 
  gi|330508464|ref|YP_004384892.1| 137 VVVAS 141
                                       ***96 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.2e-05    0.0081      39     117 ..      62     138 ..      51     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                                       C.HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EE CS
                     Cons_hypoth95  39 e.iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeef 114
                                       +  e++rvLD+ aG G+l++  l  +a ++++ve  + ++++++e+++e ++e+   ++++++ e+++     ++++
  gi|330508464|ref|YP_004384892.1|  62 DiTEKSRVLDIGAGPGTLAI-PLAQKATHVTAVEPADGMCSVMREKMAEYGVEN--ITIVQKRWEEVDVARDLDPPY 135
                                       4357899*************.59999*************************998..666666666666654445555 PP

                                       EEE CS
                     Cons_hypoth95 115 div 117
                                       d+v
  gi|330508464|ref|YP_004384892.1| 136 DVV 138
                                       554 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   2.4e-05     0.017      86     151 ..      51     114 ..      36     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                                       GGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TT CS
                            Met_10  86 kleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvek 151
                                       ++  Er    + + e  +V+d+ AG G +aip+a+  ka  v a++        ++e ++   ve+
  gi|330508464|ref|YP_004384892.1|  51 QNRIERVIWETDITEKSRVLDIGAGPGTLAIPLAQ--KATHVTAVEPADGMCSVMREKMAEYGVEN 114
                                       233333333344778889****************9..********977777777777666666655 PP

>> DUF995  Protein of unknown function (DUF995)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.7e-05     0.012      16      69 ..     235     288 ..     222     291 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                            DUF995  16 kkaakarpltaaelealYsdktwlWkdGagyfskeerrfiAwtsekkkksyaeG 69 
                                       + +a+a + +++++ + Y +k+ +W++Ga  ++ ++ r+  w ++++++s + G
  gi|330508464|ref|YP_004384892.1| 235 APQARADTKEQKAVLRDYLEKAMKWEEGAFVLNGSSIRVKIWWEKQEDSSCGYG 288
                                       4566788889999*************************************9988 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 !   14.7   0.0   1.6e-05     0.011     191     264 ..      57     128 ..      46     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                   tRNA_U5-meth_tr 191 leWalevtqeskgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirlsaeeltea 264
                                       + W +++t++s   +l++  G G ++++la++ ++v a e a    ++ +  +a+  ++n+ i++   ee+  a
  gi|330508464|ref|YP_004384892.1|  57 VIWETDITEKS--RVLDIGAGPGTLAIPLAQKATHVTAVEPADGMCSVMREKMAEYGVENITIVQKRWEEVDVA 128
                                       55888888765..589************************************************9999987655 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.1e-05     0.014       6     115 ..      46     147 ..      42     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                            DUF938   6 aaernrepilevLksylakttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlkpPle 82 
                                        +++ ++ i  v+ ++  ++++rvL+i++G G  A+ +A++  ++   + ++++ + + ++  ++e +++n++    
  gi|330508464|ref|YP_004384892.1|  46 MCKKEQNRIERVIWETDITEKSRVLDIGAGPGTLAIPLAQKATHV--TAVEPADGMCSVMREKMAEYGVENITI--- 117
                                       57778888888888776666669****************987655..577888888888999*********975... PP

                            DUF938  83 ldvtaevapvereappapasidailsinllHis 115
                                       ++  +e  +v r+    + ++d+++++  l ++
  gi|330508464|ref|YP_004384892.1| 118 VQKRWEEVDVARDL---DPPYDVVVASFSLGMM 147
                                       55566666666664...5555555554444433 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.5e-05     0.017      22     119 ..      57     159 ..      44     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                                       HHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHH...HTT-TTEEEEE--GGG-.---S CS
                              TehB  22 vveavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeike...kenlknistalydinea.klde 94 
                                       v+   +i + ++vld+g g g  ++ l+ +  +vta++  +   + ++e +     en++ ++ +  +++ a +ld 
  gi|330508464|ref|YP_004384892.1|  57 VIWETDITEKSRVLDIGAGPGTLAIPLAQKATHVTAVEPADGMCSVMREKMAeygVENITIVQKRWEEVDVArDLDP 133
                                       55556788999***************************998877777665441236888888888888876536999 PP

                                       -EEEEEEESSGGGS-.GGGHHHHHHH CS
                              TehB  95 rydfilstvvlmfle.aeripsiien 119
                                        yd ++++  l +++ +++i ++i+ 
  gi|330508464|ref|YP_004384892.1| 134 PYDVVVASFSLGMMDiRDAIEKMIQA 159
                                       99999988877444426777777765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.6e-05     0.018      48     132 ..      51     139 ..      42     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-05
                                       HHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG- CS
                              CMAS  48 laKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedl 124
                                       ++++++++   ++ + +++LdiG+G G+l++  +++   +v ++   +    +++++++e ++e+  ++  + +e++
  gi|330508464|ref|YP_004384892.1|  51 QNRIERVIWETDITEKSRVLDIGAGPGTLAIPLAQK-ATHVTAVEPADGMCSVMREKMAEYGVENI-TIVQKRWEEV 125
                                       56677777788899999*******************.99******999999999999999997665.5556678776 PP

                                       --......--SEEE CS
                              CMAS 125 de......kvdrvv 132
                                       d       ++d vv
  gi|330508464|ref|YP_004384892.1| 126 DVardldpPYDVVV 139
                                       64444445888887 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.3e-05     0.029       3      57 ..      67     119 ..      65     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-05
                                       EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEE CS
                    Methyltransf_4   3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilr 57 
                                       + vl+iG G G++ + lA+k  ++   ++E    +   + +k+++++++N+ i++
  gi|330508464|ref|YP_004384892.1|  67 SRVLDIGAGPGTLAIPLAQKATHV--TAVEPADGMCSVMREKMAEYGVENITIVQ 119
                                       6799****************9776..589***********************997 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     4e-05     0.027      71     130 ..      63     119 ..      55     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4e-05
                                       --TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEE CS
                              PCMT  71 lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvv 130
                                       +++++rvL++G+G G l+  la+   +   v ++e    +++  ++++ + ++en+++v 
  gi|330508464|ref|YP_004384892.1|  63 ITEKSRVLDIGAGPGTLAIPLAQKATH---VTAVEPADGMCSVMREKMAEYGVENITIVQ 119
                                       7899**************999976555...559*********************999875 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.6e-05     0.032      11      88 ..      63     147 ..      53     216 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                              MetW  11 ikpgsrvldlGcGdGellellke.ekqvdg....rGl.eldeegvaecvakGlsviqgdldk.dlenfedksfdyvv 80 
                                       i ++srvld+G+G G+l   l++   +v++     G+  + +e +ae     ++++q+  ++ d++   d  +d+vv
  gi|330508464|ref|YP_004384892.1|  63 ITEKSRVLDIGAGPGTLAIPLAQkATHVTAvepaDGMcSVMREKMAEYGVENITIVQKRWEEvDVARDLDPPYDVVV 139
                                       899**************876654044444311112331223344444444556666666543277777778888888 PP

                              MetW  81 lsqtlqat 88 
                                        s +l  +
  gi|330508464|ref|YP_004384892.1| 140 ASFSLGMM 147
                                       77777654 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.4e-05     0.051       3      82 ..      68     145 ..      66     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.4e-05
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSp 79 
                                        +lD+ +G G  +i +a++ ++v a+e     + ++ +    Ygv+ +it+v+  ++e+     l+   +d+v++S 
  gi|330508464|ref|YP_004384892.1|  68 RVLDIGAGPGTLAIPLAQKATHVTAVEPADGMCSVMREKMAEYGVE-NITIVQKRWEEVDVARDLDP-PYDVVVASF 142
                                       69******************************************96.699**999998655544444.499999998 PP

                   Methyltransf_15  80 PwG 82 
                                         G
  gi|330508464|ref|YP_004384892.1| 143 SLG 145
                                       777 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.074      13      78 ..      54     112 ..      45     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                   Methyltransf_32  13 vakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78 
                                       +++++ e ++ +++ +v+D+GaG g L+  la+    + ++v++++  + +++  ++  +++g  +
  gi|330508464|ref|YP_004384892.1|  54 IERVIWE-TDITEKSRVLDIGAGPGTLAIPLAQ----KATHVTAVEPADGMCSVMREKMAEYG--V 112
                                       5555555.4678899*****************9....589******99999999999988888..4 PP

>> DUF5541  Family of unknown function (DUF5541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00011     0.075      26      82 ..      25      84 ..      13     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                           DUF5541 26 dlgqashfihaavcsavr.wrvckgernfaerhilpaeleeqsnh..agmgpippatpvv 82
                                      ++g+  + i ++  sa+r w +ck e+n  er i+ +++ e+s     g gp   a+p+ 
  gi|330508464|ref|YP_004384892.1| 25 SPGRDCARIWSSKESALRfWDMCKKEQNRIERVIWETDITEKSRVldIGAGPGTLAIPLA 84
                                      577777888888999998699*********************986114555655666654 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00035      0.24       7      69 ..      64     123 ..      60     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                                       -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CT CS
                   Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDar 69 
                                        e+ ++lD+ a+PG    +   l +++ +v+Av+  +   + + e +   gv+n+++++    
  gi|330508464|ref|YP_004384892.1|  64 TEKSRVLDIGAGPGT---LAIPLAQKATHVTAVEPADGMCSVMREKMAEYGVENITIVQKRWE 123
                                       67889*********5...556777889*****************************9987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2251.41
//
Query:       gi|330508465|ref|YP_004384893.1|  [L=312]
Description: nucleoside recognition domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-05   23.9  20.9      0.012   15.9   9.5    3.2  2  Gate      Nucleoside recognition
  ------ inclusion threshold ------
       0.27   11.5   5.5       0.15   12.2   1.1    2.7  2  DPM3      Dolichol-phosphate mannosyltransferase subunit 3 (D


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 !   15.9   9.5   1.3e-06     0.012       6      94 ..      17      96 ..      13     202 .. 0.82
   2 !    7.4   7.4   0.00058       5.2       2     108 ..     181     280 ..     180     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-06
                              Gate  6 piillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtpks 84
                                      ++++l++++ +++++ +l++r++ l +p+++     l+  a+ ++++g+++  ++ ++ ++l+       + g+ + ++
  gi|330508465|ref|YP_004384893.1| 17 GTVFLMLFITGIMNEMGLFQRFSYLASPLVSLSR--LPAAAASTFVVGLGSALAANAMTARLR-------HDGQLSDRQ 86
                                      67899***************************66..**************5555555555777.......677777777 PP

                              Gate 85 alafllfvll 94
                                      a+   l+++ 
  gi|330508465|ref|YP_004384893.1| 87 AFLSALMNSV 96
                                      6644444443 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00058
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                       l++  + +++++l+ +ls+ +ll+ +    +p+ + +    + +++++l+  +a+  +++ +lg l        ++g
  gi|330508465|ref|YP_004384893.1| 181 LRIASLYFIMTFLVLYLSDAGLLQSLNV--APLASIFR--IPAETVIPLTIYVASPKAGIVLLGPLI-------QNG 246
                                       7888999****************99975..59999988..**************************6.......999 PP

                              Gate  79 fdtpksalafllf.vllytpcvat...lavivre 108
                                         ++ +al +l++ ++++ p +++   l+ + ++
  gi|330508465|ref|YP_004384893.1| 247 GISELKALMVLMLgSMFMLPVFTIrstLPNYTSI 280
                                       9999998755555055555666543336656555 PP

>> DPM3  Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.1   1.7e-05      0.15      17      63 ..      87     134 ..      85     136 .. 0.91
   2 ?   -0.5   0.2      0.16   1.5e+03      16      29 ..     185     198 ..     172     240 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                              DPM3  17 lwlalllrlvslpl.skvqdevvpvlPlwalvlfGayslatlgygvlt 63 
                                       ++l++l++ v++ + +    ++++v+P++ l + Gay++++l +g+++
  gi|330508465|ref|YP_004384893.1|  87 AFLSALMNSVPVYFrELFTYQLAFVVPVLGLYVGGAYAVVSLSTGLIK 134
                                       57899999999997799999************************9986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.16
                              DPM3  16 alwlalllrlvslp 29 
                                       +l++++++ ++ l+
  gi|330508465|ref|YP_004384893.1| 185 SLYFIMTFLVLYLS 198
                                       44444443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2200.06
//
Query:       gi|330508466|ref|YP_004384894.1|  [L=193]
Description: hypothetical protein MCON_2667 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.072   13.6   0.9        1.1    9.8   0.1    2.4  2  Sperm_Ag_HE2  Sperm antigen HE2


Domain annotation for each model (and alignments):
>> Sperm_Ag_HE2  Sperm antigen HE2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   6.1e-05       1.1       4      23 ..       5      24 ..       3      37 .. 0.85
   2 ?    1.7   0.0     0.019   3.5e+02      29      48 ..     162     181 ..     152     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 6.1e-05
                      Sperm_Ag_HE2  4 sfvsLLLvaLLfpGsSrass 23
                                      +f  LL v LL+pG+++as+
  gi|330508466|ref|YP_004384894.1|  5 FFLLLLAVFLLLPGQANASY 24
                                      466677788*********98 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.019
                      Sperm_Ag_HE2  29 tegprelreespgqgtngsq 48 
                                       +++p e++ esp+ g   + 
  gi|330508466|ref|YP_004384894.1| 162 PDKPAESQKESPAPGALAAS 181
                                       56799*******99876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1450.03
//
Query:       gi|330508467|ref|YP_004384895.1|  [L=447]
Description: adenylosuccinate lyase [Methanosaeta concilii GP6]
Scores for complete 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-49  169.0   0.1    2.3e-49  168.5   0.1    1.2  1  Lyase_1        Lyase
    7.8e-21   74.4   2.4    1.1e-20   74.0   0.1    2.3  2  ADSL_C         Adenylosuccinate lyase C-terminus
  ------ inclusion threshold ------
      0.034   14.5   0.0        6.4    7.2   0.0    2.6  2  Ribosomal_S13  Ribosomal protein S13/S18


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 !  168.5   0.1   3.8e-53   2.3e-49      20     310 ..      14     293 ..       6     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: 168.5 bits;  conditional E-value: 3.8e-53
                                       HHGGGHHHHHC......HHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHH CS
                           Lyase_1  20 enfrlseedik......alaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnev 90 
                                       e + ++eed +      ++aal++a +++++++  +a++i +a++  +        ++ k i+ ++g+++ +    v
  gi|330508467|ref|YP_004384895.1|  14 EMKAIWEEDFRlrclfrVEAALAQAEEELGMIPPGAAEEIARAAEVTRP-------QRAKEIEDEIGHDMMA---TV 80 
                                       4556666666677777799**************9999999999988877.......3346799999999877...88 PP

                                       HHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEE CS
                           Lyase_1  91 igellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvt 167
                                       ++ l +e     +++h g++snD+ +Ta  l++k++l e L+++l+++   l + a ++++ v +GrTh+q A+P+t
  gi|330508467|ref|YP_004384895.1|  81 LA-LAEESPRFGEWIHLGATSNDILDTATGLQIKASL-EILEEKLKKMLALLLDLAMQNRNLVCAGRTHGQIAVPTT 155
                                       88.666999****************************.88************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCC.THHHHHHHHHHHHHCSTEESSSHHHHHHC-H CS
                           Lyase_1 168 lgqelsayaealerdrerlkellkrllvellgggtavgtglnadp.efaelvakelakvtglpvkapnsfeavsdrD 243
                                        g  ++ +a ++ r+++rl+el++r  v++++g++++ ++++    e +e+v+++l+ ++       +  ++v +rD
  gi|330508467|ref|YP_004384895.1| 156 YGLRFAIWASEVGRHIQRLEELRPRAAVGKMSGAVGTQAAYGRFGmEIQERVMSHLELFEV------DVSNQVVQRD 226
                                       *********************************8888888865434999********5555......778889**** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHH CS
                           Lyase_1 244 avvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagrv 310
                                       +++e++ +++l+a  L k+  ++r l+ +e+ +ve+ + +++ GSS+MP+K+NP+++E + g a+ v
  gi|330508467|ref|YP_004384895.1| 227 RHAEMVCWMALVASTLDKIFIEMRTLQRTEIAEVEEGFGKKQVGSSTMPHKRNPIKSEQICGLARVV 293
                                       ************************************************************9999887 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.39   2.3e+03      25      54 ..      31      69 ..      18      72 .. 0.74
   2 !   74.0   0.1   1.8e-24   1.1e-20       1      72 [.     359     436 ..     359     437 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.39
                                      HHHHHHHHHHC.......HHHHHHT-HHHH.C.HHCHHH CS
                            ADSL_C 25 Vqeaamkawee.......llelLaadpevk.k.seeeld 54
                                      V++a ++a ee        +e +a  +ev+   +++e++
  gi|330508467|ref|YP_004384895.1| 31 VEAALAQAEEElgmippgAAEEIARAAEVTrPqRAKEIE 69
                                      555666666667877777778888888888447666776 PP

  == domain 2  score: 74.0 bits;  conditional E-value: 1.8e-24
                                       TGGGHHHHHHHHH.HTH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHHC..HHCHHHHHT-GGGCCTTHHHHHH CS
                            ADSL_C   1 GlifservllaLv.kglgReeAyelVqeaamkawee...llelLaadpevkk..seeeldalfdpayylgsadeivd 71 
                                       Gl ++e+v+++L+ kg+gR++A+e+ ++ +m a ee   l+++L+++++v+   ++ee+ al+dp++y+g a  +v+
  gi|330508467|ref|YP_004384895.1| 359 GLNMAENVMVELAkKGVGRQQAHEIMRQSSMTAFEEkkdLKDVLLENETVRSflKPEEISALLDPHQYIGTAVLQVE 435
                                       899**********66************************************66*999*******************9 PP

                                       H CS
                            ADSL_C  72 r 72 
                                       r
  gi|330508467|ref|YP_004384895.1| 436 R 436
                                       9 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0071        42      25      89 ..      47     116 ..      29     128 .. 0.67
   2 ?    7.2   0.0    0.0011       6.4      12      51 ..     365     403 ..     357     424 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0071
                     Ribosomal_S13  25 rrkakiilkkadvdedkrigelteeeiekieeivenkaq..ykipnwi...nrqkdikdGkdshvvendl 89 
                                         +a++i+++a+v + +r++e+++e  + ++ +v   a+   +  +wi      +di d ++  +++  l
  gi|330508467|ref|YP_004384895.1|  47 PGAAEEIARAAEVTRPQRAKEIEDEIGHDMMATVLALAEesPRFGEWIhlgATSNDILDTATGLQIKASL 116
                                       56899*****************998766666666553330033345553444566666666666666555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0011
                     Ribosomal_S13  12 kveialtaikGiGrrkakiilkkadvdedkrigelteeei 51 
                                       +v++ l++ kG+Gr++a++i+++  +      ++l++  +
  gi|330508467|ref|YP_004384895.1| 365 NVMVELAK-KGVGRQQAHEIMRQSSMTAFEEKKDLKDVLL 403
                                       55555554.9**************9998888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 3266.71
//
Query:       gi|330508468|ref|YP_004384896.1|  [L=214]
Description: metallo-beta-lactamase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-17   63.6   1.2    4.9e-16   59.3   0.5    2.5  2  Lactamase_B     Metallo-beta-lactamase superfamily
    0.00089   19.0   0.0     0.0017   18.0   0.0    1.5  1  ACT             ACT domain
     0.0014   18.2   0.1     0.0019   17.8   0.1    1.3  1  Lactamase_B_2   Beta-lactamase superfamily domain
     0.0019   18.1   0.0     0.0027   17.6   0.0    1.3  1  Lactamase_B_3   Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.11   12.4   0.1        0.4   10.7   0.0    2.0  2  Tachykinin      Tachykinin family
       0.22   11.2   0.0       0.27   10.8   0.0    1.1  1  Carbam_trans_N  Carbamoyltransferase N-terminus


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.5   1.7e-19   4.9e-16       6      79 ..      33     106 ..      30     141 .. 0.86
   2 ?    2.4   0.1     0.044   1.3e+02     145     175 ..     145     170 ..      99     191 .. 0.65

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 1.7e-19
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                       ++++li ++ g+i++DtG  ++++ ++++la+lgl+  d+d +++TH+H+DH+++++ + +a  + +   +++a
  gi|330508468|ref|YP_004384896.1|  33 SSVTLIKTERGWIIVDTGQVGDEEEILKALADLGLEKSDIDIIVNTHSHPDHCANNRLFSRAKTIYPKDGELIA 106
                                       789********************************************************999877666555555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.044
                                       EEEECTTTSSHHCCCCCC.TTCEEE-SHCHH CS
                       Lactamase_B 145 vlftGDallagetgridltlrgaevrdpsda 175
                                       v+++GDal++  +          ++  ++d 
  gi|330508468|ref|YP_004384896.1| 145 VVIAGDALPTLGNFQKKV-----PPAVHYDR 170
                                       677888888777777777.....33333333 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   5.8e-07    0.0017      18      66 ..      18      66 ..      13      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.8e-07
                                      HHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT 18 fgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66
                                      +++l d g Ni  + ++ +  k  +  ++v+++   d ee+l+al +l+
  gi|330508468|ref|YP_004384896.1| 18 GSILRDQGGNILDARSSVTLIKTERGWIIVDTGQVGDEEEILKALADLG 66
                                      789******************************************9985 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   6.3e-07    0.0019       2      62 ..      44     106 ..      43     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.3e-07
                                       EEEES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EEEEEEE CS
                     Lactamase_B_2   2 riLiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkklplya 62 
                                       +i++D+g    +   l+al    l ++  +id ++ th+H DH+a+   + +   ++pk+ +l+a
  gi|330508468|ref|YP_004384896.1|  44 WIIVDTGQVGDEEeILKALADLGLEKS--DIDIIVNTHSHPDHCANNRLFSRaktIYPKDGELIA 106
                                       777777766333333444423334455..9**************654444443666666555554 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 !   17.6   0.0   9.2e-07    0.0027      12      68 ..      38     100 ..      31     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.2e-07
                     Lactamase_B_3  12 letagarilvDPf.........kanlgyeppaeeaDlvlisqaledHahletlkqlaenvkvleeg 68 
                                       ++t+   i+vD +         ka ++++ ++ ++D+++ +++++dH++ ++l +   ++k++ ++
  gi|330508468|ref|YP_004384896.1|  38 IKTERGWIIVDTGqvgdeeeilKALADLGLEKSDIDIIVNTHSHPDHCANNRLFS---RAKTIYPK 100
                                       55555567777665555555543345667777*******************9988...66666553 PP

>> Tachykinin  Tachykinin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       2.2   6.5e+03       2       6 ..     117     121 ..     117     121 .. 0.85
   2 ?   10.7   0.0   0.00014       0.4       3      11 .]     201     209 ..     199     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.2
                                       -TCHH CS
                        Tachykinin   2 PkPdq 6  
                                       ++Pd+
  gi|330508468|ref|YP_004384896.1| 117 HSPDS 121
                                       89*97 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                                       TCHHHCCC- CS
                        Tachykinin   3 kPdqFvGLM 11 
                                       +P +FvGLM
  gi|330508468|ref|YP_004384896.1| 201 SPERFVGLM 209
                                       699****** PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.1e-05      0.27       9      70 ..      19      80 ..      11      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.1e-05
                    Carbam_trans_N  9 lflHDgavalvddgklvaaveeErltrikrdqklpklkaidyaleeagvelsdiDqivfdei 70
                                        l D +  ++d ++ v  +++Er   i   +++   ++i  al+  g+e+sdiD iv  + 
  gi|330508468|ref|YP_004384896.1| 19 SILRDQGGNILDARSSVTLIKTERGWIIVDTGQVGDEEEILKALADLGLEKSDIDIIVNTHS 80
                                      5677888899999*********************999********************98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1557.79
//
Query:       gi|330508469|ref|YP_004384897.1|  [L=1362]
Description: hypothetical protein MCON_2672 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00019   20.8   0.1        1.1    8.5   0.0    4.6  4  N6_Mtase  N-6 DNA Methylase
    0.00054   20.4   0.0      0.005   17.3   0.0    2.4  2  Eco57I    Eco57I restriction-modification methylase


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 ?    2.1   0.0     0.011        97      22      40 ..     563     581 ..     557     591 .. 0.86
   2 !    8.5   0.0   0.00012       1.1      45      70 ..     620     645 ..     611     727 .. 0.82
   3 ?    0.9   0.0     0.024   2.2e+02     122     138 ..     845     861 ..     829     886 .. 0.81
   4 ?    1.9   0.0     0.013   1.1e+02     165     203 ..     935     972 ..     903    1016 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.011
                          N6_Mtase  22 gksgGeffTPrevsklive 40 
                                        k +G ++TP  +++++++
  gi|330508469|ref|YP_004384897.1| 563 RKGTGSYYTPDGIVRFLAK 581
                                       5889***********9986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00012
                          N6_Mtase  45 ksgesvyDpacGsggllvqaekvlke 70 
                                         g  v+Dpa+Gsg +lv a++ +++
  gi|330508469|ref|YP_004384897.1| 620 LLGLEVVDPAMGSGHFLVAAANEITS 645
                                       556679**************998875 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.024
                          N6_Mtase 122 kdkkfdvvvaNppfnqk 138
                                       ++  fd vv Npp+   
  gi|330508469|ref|YP_004384897.1| 845 TEWGFDLVVMNPPWDVV 861
                                       45679*********875 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.013
                          N6_Mtase 165 fllhiieslkpkGraavvlangvLfrggkegkIrkalve 203
                                       f+   +  l+++G+ +vv+++g++  +g  + +r++l e
  gi|330508469|ref|YP_004384897.1| 935 FMERGMRLLAKGGTLSVVVPSGIITDEGG-KPLREKLFE 972
                                       777788999***************99775.457777765 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.2   1.8e+03       3      16 ..     849     862 ..     848     870 .. 0.85
   2 !   17.3   0.0   5.5e-07     0.005      24     105 ..     924    1005 ..     909    1006 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.2
                            Eco57I   3 fdviiGNPPYqese 16 
                                       fd ++ NPP+   +
  gi|330508469|ref|YP_004384897.1| 849 FDLVVMNPPWDVVK 862
                                       9********97665 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.5e-07
                            Eco57I   24 leekakdiyqkFvekalkle..dkylaliiparflasgkglkefrekllkdkklkklvefedskevFkdveikgg 96  
                                         ++ ++++++ F+e++++l    ++l++++p+  + +++g+k +rekl +  k++ ++efe+++ +F+dv+ +  
  gi|330508469|ref|YP_004384897.1|  924 RGSGDTNLWKLFMERGMRLLakGGTLSVVVPSGII-TDEGGKPLREKLFEG-KIRGIFEFENKRGIFPDVHRSYK 996 
                                        4566899************96567899******99.999********9986.6*****************99998 PP

                            Eco57I   97 ilvflkdkk 105 
                                         +++++dk+
  gi|330508469|ref|YP_004384897.1|  997 FALLFWDKD 1005
                                        888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.88u 0.31s 00:00:01.19 Elapsed: 00:00:00.47
# Mc/sec: 8758.61
//
Query:       gi|330508470|ref|YP_004384898.1|  [L=375]
Description: filamentation induced by cAMP protein Fic [Methanosaeta concilii GP6]
Scores for complete 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   91.4   0.0    7.6e-26   90.0   0.0    1.7  2  Fic_N     Fic/DOC family N-terminal
    2.6e-17   63.5   0.0    6.2e-17   62.3   0.0    1.7  1  Fic       Fic/DOC family
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.056   13.3   0.0    1.7  1  TrmB      Sugar-specific transcriptional regulator TrmB
      0.028   14.0   0.0      0.062   12.9   0.0    1.6  1  HTH_24    Winged helix-turn-helix DNA-binding
      0.052   13.6   0.1       0.12   12.4   0.1    1.6  1  HTH_29    Winged helix-turn helix
        0.1   12.6   0.0       0.19   11.7   0.0    1.5  1  MarR      MarR family


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 !   90.0   0.0   2.6e-29   7.6e-26       2      82 .]      22     112 ..      21     112 .. 0.94
   2 ?   -2.5   0.0       1.8   5.3e+03      48      74 ..     126     152 ..     122     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 2.6e-29
                             Fic_N   2 kllseAnralgeLdgllrllpnpelLirplvrkEAvlSSeIEgtqttlddlleaeadeeeeks..........kdvk 68 
                                       +l+++An+al+++dg+l  + np++L++pl+++EAvlSS+IEgtq++l+++l++ead  e ++          +d++
  gi|330508470|ref|YP_004384898.1|  22 TLIGKANAALARYDGILLGMVNPQVLLSPLTTREAVLSSRIEGTQASLEEVLQYEADVGEPRPdqeipdtpqiRDIH 98 
                                       6789****************************************************8888877778999999***** PP

                             Fic_N  69 EVlnYvkAleyGle 82 
                                       E++nY++A+ +++e
  gi|330508470|ref|YP_004384898.1|  99 EIINYRRAMGAAVE 112
                                       *********99986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                             Fic_N  48 tlddlleaeadeeeekskdvkEVlnYv 74 
                                       +l  +l    +  ++++ +++ ++nY+
  gi|330508470|ref|YP_004384898.1| 126 NLHRILLTGVRGGHKDPGEIRHIQNYI 152
                                       566667777777788888999999996 PP

>> Fic  Fic/DOC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   2.1e-20   6.2e-17       1      96 [.     118     222 ..     118     223 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.1e-20
                                       --SHHHHHHHHCHS-S----...--TS--SS-S.......T..EEEE---SCCCHHHHHHHHHHHHCHHT-S-HHHH CS
                               Fic   1 pltledllelhrlllqdige...eagefrdeev.......segklesalappeevpaeleelleylnelekeeplek 67 
                                       p++ +++++lhr+ll +++    ++ge+r  ++        ++++ + +++p  +  +l++++eyl  +++ +pl +
  gi|330508470|ref|YP_004384898.1| 118 PFSINTIRNLHRILLTGVRGghkDPGEIRHIQNyiappgtPIERATFIPPAPSILMDALSNWEEYLY-SNERDPLVQ 193
                                       68899*********99999999999***99888*******99*************************.********* PP

                                       HHHHHHHHHHH--SSS-HHHHHHHHHHHH CS
                               Fic  68 aaalhyefekiHPFaDGNgRtarlllnll 96 
                                       +++l ++fe iHPF DGNgR++r+++  +
  gi|330508470|ref|YP_004384898.1| 194 LSILKAQFELIHPFLDGNGRIGRMIVPII 222
                                       ************************98766 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   1.9e-05     0.056      16      53 ..     311     348 ..     302     361 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                                       HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB  16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53 
                                       +L ++   + ++ a ++g+p  ++++++++Le+kG+ +
  gi|330508470|ref|YP_004384898.1| 311 VLFSSPVISSRDFAIKSGIPNRTAQRIVERLEQKGILR 348
                                       5556666677888999*******************865 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 ?   12.9   0.0   2.1e-05     0.062      16      48 .]     316     348 ..     306     348 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                            HTH_24  16 prisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       p is r+ A ++g++  t  r ++rLe++G+++
  gi|330508470|ref|YP_004384898.1| 316 PVISSRDFAIKSGIPNRTAQRIVERLEQKGILR 348
                                       6688889999********************985 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.1e-05      0.12      27      53 ..     332     359 ..     327     365 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.1e-05
                            HTH_29  27 rtvyrwlkrfeegGlaalld.rrrsgrp 53 
                                       rt +r+++r e++G+  ll+ +++s+ p
  gi|330508470|ref|YP_004384898.1| 332 RTAQRIVERLEQKGILRLLReGKGSRSP 359
                                       89******************9**99987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.2e-05      0.19      10      48 ..     310     348 ..     299     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.2e-05
                                       HHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  10 rilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                                         l +++ +s  + a k+g+ + t+ r++ rLe+kG ++
  gi|330508470|ref|YP_004384898.1| 310 DVLFSSPVISSRDFAIKSGIPNRTAQRIVERLEQKGILR 348
                                       557778889999************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2553.27
//
Query:       gi|330508471|ref|YP_004384899.1|  [L=1063]
Description: helicase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-24   83.8   0.0      3e-23   82.3   0.0    1.9  1  Helicase_C  Helicase conserved C-terminal domain
    1.9e-20   73.1   0.0    1.3e-16   60.7   0.0    2.6  2  PLDc_2      PLD-like domain
    2.6e-09   36.3   0.1    1.2e-06   27.6   0.0    2.3  2  SNF2_N      SNF2 family N-terminal domain
    7.9e-06   26.0   0.0      0.007   16.4   0.0    2.7  2  ResIII      Type III restriction enzyme, res subunit
    0.00013   21.8   0.2       0.32   10.8   0.0    3.3  3  DEAD        DEAD/DEAH box helicase
    0.00092   19.2   0.1      0.058   13.4   0.1    2.4  1  Flavi_DEAD  Flavivirus DEAD domain
      0.002   18.0   0.4     0.0059   16.5   0.0    1.9  2  Bac_DnaA    Bacterial dnaA  protein
  ------ inclusion threshold ------
      0.017   15.4   0.2         11    6.2   0.0    3.9  3  AAA_22      AAA domain
      0.025   14.8   0.0      0.059   13.6   0.0    1.6  1  PLDc        Phospholipase D Active site motif
      0.027   14.2   0.2       0.78    9.4   0.1    2.8  2  IstB_IS21   IstB-like ATP binding protein
       0.11   12.1   0.1       0.27   10.8   0.1    1.6  1  DUF533      Protein of unknown function (DUF533)
       0.11   12.5   1.0       0.31   11.1   1.0    1.8  1  VHL_C       VHL box domain
       0.13   12.7   0.4       0.94   10.0   0.3    2.6  2  AHSP        Alpha-haemoglobin stabilising protein


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 !   82.3   0.0   2.2e-26     3e-23       2     111 .]     618     746 ..     617     746 .. 0.85

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 2.2e-26
                                       HHHHHHHHH....HHTTTTSEEEEEESSHHHHHH.HHHH...HHHTTSTEEEESTTSTHHHHHHHHHHHH..TTS.. CS
                        Helicase_C   2 kleallell....kleeeggkilifvntidrlek.vkll...lekkgikvavlhgelpqnereeileqfn..kge.. 66 
                                       kl+al ell     +e++g+k+l+f+++ d++e   k l   l+k+g k+ +l+g++ +nere+i+ +f   + +  
  gi|330508471|ref|YP_004384899.1| 618 KLLALGELLaedrVFESDGKKCLLFTQYMDTAEYiYKNLkghLQKQGKKINILTGKTAANEREKIIMAFApkA-Nkl 693
                                       66677777777777899*************9965633335557888***********************8542.157 PP

                                       ........SSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  67 ........sdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                               +d+Li+tdv+++G +++++n+Vin+dlp+n+ +++qr+GR+ R+g
  gi|330508471|ref|YP_004384899.1| 694 dsgtipeeTDILISTDVLSEGQNLQDANYVINYDLPWNPMRIVQRVGRVDRIG 746
                                       7777888799****************************************986 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.0   9.1e-20   1.3e-16       3     133 .]      22     176 ..      20     176 .. 0.86
   2 !    9.6   0.0   0.00058       0.8      10      49 ..     637     680 ..     630     723 .. 0.80

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 9.1e-20
                            PLDc_2   3 qliksAkksidiatyyfvsdrei..ldallk.aakrgvkvrilldskkd........................daga 52 
                                       +++k    ++ iat+yf+++ +      l + a+k++ ++r+l+++++                         + ++
  gi|330508471|ref|YP_004384899.1|  22 NALKDNDGRVSIATGYFNVEGYAelRSPLQEaAKKNDFHLRLLIGNEAVvkkdatpqceaeaegslpeeleglTIND 98 
                                       5666667799*******66655442667766588888********9655************************5555 PP

                            PLDc_2  53 vdeaslkelkellleagvevrvfetllgslHaKlylidgktvivGSsNltkrgldlnlElnvviedkelakeleeeF 129
                                       +  a  + l e+l++++ve+r     +++ HaK+y++d + ++vGSsN+t+ gl++n Eln  ++++ +++ +e++F
  gi|330508471|ref|YP_004384899.1|  99 NYAALVSDLVEFLRQEKVELRQNP--ERFSHAKCYIFD-DLAVVGSSNFTRPGLKKNIELNAALYQPSAQNLVEQWF 172
                                       556899*************99743..4678*******7.6************************************* PP

                            PLDc_2 130 erlw 133
                                       er w
  gi|330508471|ref|YP_004384899.1| 173 ERRW 176
                                       **99 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00058
                            PLDc_2  10 ksidiatyyfvsdreildallk.aakrgvkvrilldskkd...d 49 
                                       k++ + t+y+ + ++i+++l+  ++k+g+k++il++++++   +
  gi|330508471|ref|YP_004384899.1| 637 KKCLLFTQYMDTAEYIYKNLKGhLQKQGKKINILTGKTAAnerE 680
                                       789999****9*********888*************95543330 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 !    6.1   0.0    0.0028       3.9      54     109 ..     247     290 ..     232     309 .. 0.76
   2 !   27.6   0.0   8.4e-10   1.2e-06     177     299 ..     324     455 ..     307     474 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0028
                                       TT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  54 svrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslld 109
                                       + +G ++aD +GLGKT  +l l+    +  + ++ k         +++++P+++l+
  gi|330508471|ref|YP_004384899.1| 247 KYNGVLIADSTGLGKTHIALELLR---EYVAVRRLK---------AMVIAPSQVLK 290
                                       5678999*********99999998...323333333.........57777776654 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 8.4e-10
                                       S-SEEEES-GGGT--T.TSHHHHHHHH--..-S-E.EEE-S--SSS-HHHHHHHHHHH-TT...TT--HH..HHHHH CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxx..xxxx.xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx..xxxxx RF
                            SNF2_N 177 ewkrvvlDEghtlkns.tskaaeavskLs..tsnr.wiltGTPiqnsledlygLlkfLree...pfgekq..tfdkl 244
                                       + + +v+DE ++ +n  t++ a+ ++ ++   +++ +++t+TP+ nsl dly  l ++  +    f e      ++ 
  gi|330508471|ref|YP_004384899.1| 324 DYDLLVIDESQNYRNAsTNRYANLLKLIAggKRKMvVLMTATPVNNSLLDLYHQLTLITAGddsYFAELGipDLRSH 400
                                       56789**********978888888887774334443456*************8877776541114455334466666 PP

                                       THHHHHHHHHHHHHHHHTT-STTEE---GGGT--S---EEEEEEEEE--HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 245 lqrpieaqaekgrsrLlqllqrlmlrrakkdveknlPpkteeiiflklskverks 299
                                       +    +++ ++g+++++ ll ++m+rr+ + +  n P+ t +   +++ k +++ 
  gi|330508471|ref|YP_004384899.1| 401 FLSAERKELTEGIEQIVRLLDEIMIRRTRQFIIDNYPQTTINGKPVRFPKRQLRK 455
                                       666666899***********************99999999998888888888765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.1e-06     0.007       8      80 ..     234     303 ..     227     323 .. 0.76
   2 !    6.9   0.0    0.0042       5.8     132     169 ..     324     366 ..     300     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.1e-06
                                       HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG CS
                            ResIII   8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflse 80 
                                       Q++a  + +  l   + + +li+  TG GKT +a++l +++   ++  k+++++p++ l   ++ ++++ + +
  gi|330508471|ref|YP_004384899.1| 234 QQDAFSSAKRIL--AKYNGVLIADSTGLGKTHIALELLREYVAVRRL-KAMVIAPSQVLKAVWEPKLMEESIK 303
                                       666666665555..5777899*********************98665.********99998888666655555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0042
                                       T-SEEEEETGGGTTS...TTTHHHHHT-...--SEEEEEESS- CS
                            ResIII 132 rfdviiiDEaHrlgak..kswreilekf...keavllglTATp 169
                                        +d+++iDE+ +++ +  + + ++l+ +   k+++++ +TATp
  gi|330508471|ref|YP_004384899.1| 324 DYDLLVIDESQNYRNAstNRYANLLKLIaggKRKMVVLMTATP 366
                                       4679******99998744599999999888888*********9 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00023      0.32      11      59 ..     244     289 ..     234     294 .. 0.83
   2 !    6.2   0.0    0.0059       8.1     119     170 ..     322     367 ..     292     373 .. 0.70
   3 ?    0.1   0.0      0.43   5.9e+02      44      94 ..     633     682 ..     618     724 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                                       HH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHH CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  11 il.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreL 59 
                                       il + + vl+a  TG GKT ++l  + + v      ++ ka++++P++ L
  gi|330508471|ref|YP_004384899.1| 244 ILaKYNGVLIADSTGLGKTHIALELLREYV----AVRRLKAMVIAPSQVL 289
                                       45344689*************999888888....6899********9987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0059
                                       CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 119 lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       + +  +lV+DE +++ +    + + ++l+ +    + gk  + v++++AT+ 
  gi|330508471|ref|YP_004384899.1| 322 YIDYDLLVIDESQNYRNA-STNRYANLLKLI----AGGK-RKMVVLMTATPV 367
                                       566789*********998.555555657777....3444.334*******85 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.43
                                       TSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  44 gktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskl 94 
                                       +++g+k+l+ +     ae +++nlk  +++ + +++ i++g++a ++++k+
  gi|330508471|ref|YP_004384899.1| 633 ESDGKKCLLFTQYMDTAEYIYKNLKGHLQKQGKKIN-ILTGKTAANEREKI 682
                                       57788999999999999999****999999886665.66666666666666 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   4.2e-05     0.058      13     136 ..     257     366 ..     246     371 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.2e-05
                                       TTS-TTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTS-EEE-------------SEEEEEHHHHHHHHHH CS
                        Flavi_DEAD  13 PGaGktrkvlpelvkeaierrlrtlvLaPtrvvlaemeealkglevryktsavkeektgrelvdvmchatftkrlls 89 
                                        G Gkt+  l  l +  + rrl+++v+aP +v  a  e  l + +++ ++ ++  e+tg             +  ++
  gi|330508471|ref|YP_004384899.1| 257 TGLGKTHIALELLREYVAVRRLKAMVIAPSQVLKAVWEPKLMEESIKTMNVTI--ERTG-------------TASFQ 318
                                       699****9998887888899************998888888888887666555..2222.............23467 PP

                                       T------SEEEEETTT--SHHHHHHHHHHHHH.HHTTS-EEEEEESS- CS
                        Flavi_DEAD  90 pvrkknyeliimDeahflDPasiaarGyletk.aeegeaalilltatP 136
                                       p +  +y+l+++De+     as      l ++ a  ++  ++l+tatP
  gi|330508471|ref|YP_004384899.1| 319 PEKYIDYDLLVIDESQNYRNASTNRYANLLKLiAGGKRKMVVLMTATP 366
                                       888888888888888777777766655544440444555667788887 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.3e-06    0.0059      27     136 ..     241     361 ..     230     378 .. 0.66
   2 ?   -3.2   0.1       4.4   6.1e+03     205     214 ..     523     532 ..     493     577 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.3e-06
                                       HHSTTT.S--EEEE-SSSSSHHHH.HHHHHHHHHHH.......SSSS-EEEEEHHHHHHHHHHHHHT....T-HHHH CS
                          Bac_DnaA  27 aeapgkkynPlfiygevGlGktHL.lkaignevlen.......apelrvvYltaeeFlnelvkalrd....kkaeef 91 
                                       a+   +kyn ++i  ++GlGktH+ l+ +  +v  +       ap++ ++ +   + ++e +k+++     + +++f
  gi|330508471|ref|YP_004384899.1| 241 AKRILAKYNGVLIADSTGLGKTHIaLELLREYVAVRrlkamviAPSQVLKAVWEPKLMEESIKTMNVtierTGTASF 317
                                       5555679****************744555544433300001114444445566667777777765432322778899 PP

                                       H.HHHTT-SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEEEE CS
                          Bac_DnaA  92 k.eklrkvDvLliDDiqflagkektqeelfhtfnalleegkqvvls 136
                                       + ek+ + D+L+iD+ q   + +   + +  ++  + + ++++v+ 
  gi|330508471|ref|YP_004384899.1| 318 QpEKYIDYDLLVIDESQNYRNAS--TNRYANLLKLIAGGKRKMVVL 361
                                       8689***********99766544..566777777777666666654 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.4
                                       HHHHHHHHHH CS
                          Bac_DnaA 205 legalnrlka 214
                                       ++++++rl+ 
  gi|330508471|ref|YP_004384899.1| 523 IRTSIIRLVK 532
                                       4444443322 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0083        11      14     112 ..     257     347 ..     246     364 .. 0.54
   2 ?    4.8   0.0     0.024        33      24      99 ..     343     435 ..     337     437 .. 0.79
   3 ?   -2.7   0.0       4.8   6.7e+03      49      79 ..     950     979 ..     929    1011 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0083
                            AAA_22  14 sGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalrara 90 
                                       +G GKT+ + +ll++++++      r+  + v +ps         ++l+a+ +++   + s + +  ++e+   a +
  gi|330508471|ref|YP_004384899.1| 257 TGLGKTHIALELLREYVAV------RRLKAMVIAPS---------QVLKAVWEPKLM-EESIKTMNVTIERTGTASF 317
                                       5777777777777777643......22222222222.........233333333333.3444455555555555555 PP

                            AAA_22  91 v......ielliiDEaqhlr..seealeeL 112
                                                ll+iDE q+ r  s + + +L
  gi|330508471|ref|YP_004384899.1| 318 QpekyidYDLLVIDESQNYRnaSTNRYANL 347
                                       566666667888888888765544444444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.024
                            AAA_22  24 rlleqldeeakaee.erpevvfvtlpsst.sskdllrellralglelka................erlsseelleal 82 
                                       r+++ l   + ++  +r+ vv++t++  + s+ dl+++l  ++  + ++                er+++ e +e++
  gi|330508471|ref|YP_004384899.1| 343 RYANLL---KLIAGgKRKMVVLMTATPVNnSLLDLYHQLTLITAGDDSYfaelgipdlrshflsaERKELTEGIEQI 416
                                       555555...233336888899999999999**************99999*999999999999888777777888888 PP

                            AAA_22  83 eqalrarav..ielliiDE 99 
                                        + l++ +   ++ +iiD+
  gi|330508471|ref|YP_004384899.1| 417 VRLLDEIMIrrTRQFIIDN 435
                                       8888877778878888886 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.8
                            AAA_22  49 sstsskdllrellralglelkaerlsseell 79 
                                       +s+ +++l+ ++l al  ++ + r + +e++
  gi|330508471|ref|YP_004384899.1| 950 GSKHQRELRGMILAALSAGRIS-REDASEIY 979
                                       3335555666666665555555.44444444 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.3e-05     0.059       6      26 ..     127     146 ..     125     147 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                                       ---EEEETTTEEEEE---SSH CS
                              PLDc   6 HqKivivDdrvafvGgaNLcd 26 
                                       H+K +i+Dd  a+vG++N+++
  gi|330508471|ref|YP_004384899.1| 127 HAKCYIFDDL-AVVGSSNFTR 146
                                       **********.********97 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 ?   -2.4   0.0       2.5   3.4e+03      83     122 ..     104     141 ..     100     155 .. 0.77
   2 ?    9.4   0.1   0.00057      0.78      45     147 ..     246     364 ..     233     383 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.5
                         IstB_IS21  83 vedLveelkrarrdgklaralkrllkvdllilDdlgllpl 122
                                       v+dLve l++++ +  l ++ +r+ +++  i Ddl+++  
  gi|330508471|ref|YP_004384899.1| 104 VSDLVEFLRQEKVE--LRQNPERFSHAKCYIFDDLAVVGS 141
                                       57888888877665..557778999999999999988755 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00057
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavr.aglsvlfvrv.........edLve.elkra....rrdgklaralkrl 106
                                       +k +++++   +G GK+h+a  l +e v+ + l+ + +           ++L+e ++k+     +r g ++ + +++
  gi|330508471|ref|YP_004384899.1| 246 AKYNGVLIADSTGLGKTHIALELLREYVAvRRLKAMVIAPsqvlkavwePKLMEeSIKTMnvtiERTGTASFQPEKY 322
                                       56677888899999****99999876544333333322220001111112222212322211114555566666788 PP

                         IstB_IS21 107 lkvdllilDdl.gllpldqaeaellfeviekryerrsiiits 147
                                       +  dll++D+   + + + +  ++l+++i+    +  +++t+
  gi|330508471|ref|YP_004384899.1| 323 IDYDLLVIDESqNYRNASTNRYANLLKLIAGGKRKMVVLMTA 364
                                       999999999963699999999999999999887777777776 PP

>> DUF533  Protein of unknown function (DUF533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00019      0.27      65     112 ..     947     994 ..     915    1000 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                            DUF533  65 eeeeekaelllrAmiaAAkADGhideeErqrIlqeleelgldaeekal 112
                                       +++ +k+++ lr mi AA + G+i++e    I++ l++++l a e ++
  gi|330508471|ref|YP_004384899.1| 947 QKTGSKHQRELRGMILAALSAGRISREDASEIYAILNRQNLVAWEDEF 994
                                       36667788889***********************99999987766666 PP

>> VHL_C  VHL box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.0   0.00023      0.31      25      53 ..     583     611 ..     577     614 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             VHL_C  25 edyrrLeIarcLkeeLedsPnvlkDlqri 53 
                                        +y++L++ r Lke+Le+   +++Dl ri
  gi|330508471|ref|YP_004384899.1| 583 AEYDKLQMKRDLKEDLERLLVLKRDLDRI 611
                                       58**************************9 PP

>> AHSP  Alpha-haemoglobin stabilising protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00068      0.94      40      85 ..     205     252 ..     202     254 .. 0.88
   2 ?   -3.4   0.0       9.9   1.4e+04      42      70 ..     532     563 ..     519     572 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00068
                              AHSP  40 WvnlYinyykkkltGeqqeqdralq..elrqeLktlaspfLakyrafl 85 
                                       ++++  +yy+++l+  +q++ + l+   ++q+  ++a+  Laky+ +l
  gi|330508471|ref|YP_004384899.1| 205 YMKFLYEYYRPRLEELEQDKGKILElaGFQQDAFSSAKRILAKYNGVL 252
                                       689999****************8763379***************9877 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.9
                              AHSP  42 nlYinyykkkltGe....qqeqdralqelrqeL 70 
                                       ++Y +y+ k l        q   +al+++ + L
  gi|330508471|ref|YP_004384899.1| 532 KFY-EYFDKILASGkilsSQAFRKALNQIGNSL 563
                                       555.45555443320111233444555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1063 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:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.81u 0.27s 00:00:01.08 Elapsed: 00:00:00.43
# Mc/sec: 7351.78
//
Query:       gi|330508472|ref|YP_004384900.1|  [L=308]
Description: rRNA pseudouridine synthase [Methanosaeta concilii GP6]
Scores for complete sequence (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   87.2   0.9    1.5e-15   57.8   0.1    3.2  2  TruB_N    TruB family pseudouridylate synthase (N terminal do
    1.2e-22   79.8   0.2    2.1e-22   79.0   0.2    1.4  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    3.6e-17   62.1   0.1    6.5e-17   61.3   0.1    1.4  1  PUA       PUA domain
    1.8e-07   31.1   0.0    3.4e-07   30.2   0.0    1.5  1  DKCLD     DKCLD (NUC011) 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 !   57.8   0.1   3.4e-19   1.5e-15       1      51 [.      26      76 ..      26      80 .. 0.96
   2 !   23.1   0.1   1.7e-08   7.5e-05      72     149 .]      79     139 ..      75     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 3.4e-19
                                      HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEET CS
                            TruB_N  1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlg 51
                                      kr+l+++k+Gh+GtLDp++tG+L+v++g+aT++++ ll a KeY++ ++++
  gi|330508472|ref|YP_004384900.1| 26 KRILEVEKAGHSGTLDPKVTGILPVLLGDATRVMDTLLLAGKEYICLMHVH 76
                                      89********************************************99876 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 1.7e-08
                                       --HHHHHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTT CS
                            TruB_N  72 lteekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtY 148
                                       + ++++++v+ +f G i q pp  S+v                   + r+ tiy le+le+e ++v ++v c++GtY
  gi|330508472|ref|YP_004384900.1|  79 VPKKQITDVCGQFVGPILQKPPLKSSVV-----------------KELRTRTIYYLEVLEIEGQHVLMRVGCEAGTY 138
                                       67899*******************9998.................688***************************** PP

                                       H CS
                            TruB_N 149 i 149
                                       i
  gi|330508472|ref|YP_004384900.1| 139 I 139
                                       9 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.2   4.8e-26   2.1e-22       1      63 [.     140     206 ..     140     207 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 4.8e-26
                                       HHHHHHHHHHTTS-EEEEEEEEEEETTE.GG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
                          TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpf.deedmvtledLedavllyke..dee.LdrlllPlesal 63 
                                       R+Lc DiG+aLg+gA +eeLRRtr+gpf ++e +vtl++L da  +y e  +e+ L+r++lP+e+al
  gi|330508472|ref|YP_004384900.1| 140 RKLCYDIGLALGTGANMEELRRTRAGPFrEDETLVTLHQLIDAHVKYMEtgNENlLRRVILPVEAAL 206
                                       9***************************999999**********9999988777***********98 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.1   1.4e-20   6.5e-17       1      74 []     210     283 ..     210     283 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.4e-20
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveiervl 74 
                                       +r+v+ d++v+a+++ga L apG+++ + ++ +gd V++++ +ge+vav+ a++ssee+   k g+++ +erv+
  gi|330508472|ref|YP_004384900.1| 210 PRLVIADNSVDAICHGAPLAAPGLLSLQTEINRGDGVVLFTLKGEAVAVAQAELSSEEMLASKSGIVAATERVI 283
                                       699*****************************************************************999985 PP

>> DKCLD  DKCLD (NUC011) 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   3.4e-07      38      58 .]       2      22 ..       1      22 [. 0.96

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 7.6e-11
                                      HHHTEEEEEEE-SSS-HHHHH CS
                             DKCLD 38 yikyGvinLDKPsnPsSHEVV 58
                                      +++ G inLDK+s+P+SHEVV
  gi|330508472|ref|YP_004384900.1|  2 HLRLGAINLDKTSGPTSHEVV 22
                                      89******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2108.29
//
Query:       gi|330508473|ref|YP_004384901.1|  [L=174]
Description: cytidylate kinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-23   84.0   0.4    1.8e-12   47.7   0.8    2.0  2  Cytidylate_kin2  Cytidylate kinase-like family
    1.2e-10   42.0   0.1      2e-10   41.3   0.1    1.4  1  AAA_18           AAA domain
    2.8e-10   40.3   1.2    0.00041   20.2   0.5    2.1  2  Cytidylate_kin   Cytidylate kinase
      9e-08   32.6   0.2    1.6e-07   31.8   0.2    1.5  1  AAA_17           AAA domain
      3e-07   30.8   0.1    1.4e-06   28.7   0.0    1.9  2  AAA_28           AAA domain
    0.00019   21.8   0.0    0.00026   21.4   0.0    1.4  1  AAA              ATPase family associated with various cellul
    0.00084   19.5   0.1        1.4    9.0   0.1    2.2  2  SKI              Shikimate kinase
     0.0011   19.1   0.1     0.0018   18.4   0.1    1.6  1  ADK              Adenylate kinase
     0.0015   18.7   0.5      0.028   14.6   0.5    2.2  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.017   14.9   0.1      0.035   13.9   0.0    1.5  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.031   14.1   0.1       0.21   11.4   0.0    1.9  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.066   12.6   0.0        0.1   12.0   0.0    1.3  1  6PGD             6-phosphogluconate dehydrogenase, C-terminal
       0.87    9.3   4.4        1.2    8.9   1.9    2.0  2  Mitoc_L55        Mitochondrial ribosomal protein L55


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 !   34.5   0.0   1.5e-11   2.1e-08       1      54 [.       2      56 ..       2      67 .. 0.91
   2 !   47.7   0.8   1.3e-15   1.8e-12      87     178 ..      65     153 ..      58     154 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.5e-11
                   Cytidylate_kin2  1 iITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevders 54
                                      iIT+s++ G+g +t+++aL+ +Lglp ++  e+++++a+e+++s +e+ ++ e+ 
  gi|330508473|ref|YP_004384901.1|  2 IITVSGSPGTGTTTLARALSVQLGLPWVNSgELFRKIASEKNISVKEMNRMAEKG 56
                                      8***********************************************9999843 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 1.3e-15
                   Cytidylate_kin2  87 rvirelaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrrakyykkytgq 163
                                       ++ r+la+e+++V+ GR + ++L      l+v+l ++l  r++r+++re+   e+a ++ + +++ +a +ykky++ 
  gi|330508473|ref|YP_004384901.1|  65 DAQRSLAKERQGVFEGRLSGHLLDA---DLKVLLKSDLRTRAERISKRESKLLEDACQETRLREESEARRYKKYYNI 138
                                       567999*999*************99...8********************87789999999***************** PP

                   Cytidylate_kin2 164 dwgdaenYdlvlnts 178
                                       d++d + Ydlv++t 
  gi|330508473|ref|YP_004384901.1| 139 DINDLNVYDLVVDTG 153
                                       *************95 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.1   1.5e-13     2e-10       1     119 [.       3     115 ..       3     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.5e-13
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       I ++G pG+G ttla++Ls  lg+     g+  r++a+e++++  + + + ++  ++d    d +++ l +      
  gi|330508473|ref|YP_004384901.1|   3 ITVSGSPGTGTTTLARALSVQLGLpwvnsGELFRKIASEKNISVKEMNRMAEKGPEIDYLI-DDAQRSLAK------ 72 
                                       899******************999*888888888888888888888888444444444444.334444444...... PP

                            AAA_18  73 egknlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeak 119
                                        +   v++g+l+ ++ +a+ +   v L+ +  +++eR++kR+ +  +
  gi|330508473|ref|YP_004384901.1|  73 -ERQGVFEGRLSGHLLDADLK---VLLKSDLRTRAERISKRESKLLE 115
                                       .34459*********998876...*****************976544 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   4.3e-07   0.00059       1      38 [.       3      40 ..       3      54 .. 0.90
   2 !   20.2   0.5     3e-07   0.00041      94     173 ..      55     127 ..      40     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.3e-07
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRalal 38
                                      i++ G  g+G  ++aral+ +lgl ++++g+l+R +a 
  gi|330508473|ref|YP_004384901.1|  3 ITVSGSPGTGTTTLARALSVQLGLPWVNSGELFRKIAS 40
                                      8999******************************9985 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3e-07
                                       TSHHHHHHHHHHHHTT-BSSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHH CS
                    Cytidylate_kin  94 aipavRailvkklrelvkkarvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeikeR 170
                                       + p++   + + +r+l+k+ + v+eGR  g   + da+lK+ l+   ++Ra+R  k  ++      le+  +e + R
  gi|330508473|ref|YP_004384901.1|  55 KGPEIDYLIDDAQRSLAKERQGVFEGRLSGH--LLDADLKVLLKSDLRTRAERISKRESKL-----LEDACQETRLR 124
                                       567888889999***************7665..57*****************988774333.....44444444444 PP

                                       HHH CS
                    Cytidylate_kin 171 Dkl 173
                                        + 
  gi|330508473|ref|YP_004384901.1| 125 EES 127
                                       444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.2   1.2e-10   1.6e-07       2      82 ..       7      88 ..       6     139 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.2e-10
                                      E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHH.HSSEEEEEE CS
                            AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeea.kkkgvlvdg 78
                                      G PG G +t+++ l  ++g++ ++ G+l+r+ a++++  +k+ ++m++   e++  l + a++++a+e+ +  +  + g
  gi|330508473|ref|YP_004384901.1|  7 GSPGTGTTTLARALSVQLGLPWVNSGELFRKIASEKNIsVKEMNRMAEKGPEIDY-LIDDAQRSLAKERqGVFEGRLSG 84
                                      89**********************************9768888888877777765.77888888888742222335555 PP

                                      -SEE CS
                            AAA_17 79 hpri 82
                                      h   
  gi|330508473|ref|YP_004384901.1| 85 HLLD 88
                                      5543 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0     1e-09   1.4e-06       2      68 ..       3      72 ..       2      81 .. 0.82
   2 ?   -0.1   0.0       0.7   9.6e+02      57     107 ..     116     130 ..      93     154 .. 0.56

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1e-09
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwvedllafaervleeqleeea 68
                                      i ++G ++tG+Ttl++aL+ + g p+v   E +r+i +ek  + +++ +++e+  ++ +++ ++q++ ++
  gi|330508473|ref|YP_004384901.1|  3 ITVSGSPGTGTTTLARALSVQlGLPWVnsGELFRKIASEKNISVKEMNRMAEKGPEIDYLIDDAQRSLAK 72
                                      789****************666******************988777777667778888877777665444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.7
                            AAA_28  57 ervleeqleeeaaaaankvlfcDrglldtlaYarayggeaeaeleaaarek 107
                                       +++ e +l+ee +a                                    +
  gi|330508473|ref|YP_004384901.1| 116 DACQETRLREESEA------------------------------------R 130
                                       33333333333333....................................2 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.9e-07   0.00026       2      88 ..       4      85 ..       3     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.9e-07
                                      EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                               AAA  2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80
                                       ++G pGtG T+la+a+  +lg +   ++  el+ k+ +e++ +++e+ + a++       +iD++ +   ++  ++  
  gi|330508473|ref|YP_004384901.1|  4 TVSGSPGTGTTTLARALSVQLGLPW--VNSGELFRKIASEKNISVKEMNRMAEKGP-EIDYLIDDAQRSLAKE--RQGV 77
                                      589*****************99987..57899999*************99998764.3557788877655555..3555 PP

                                      HHHHHHHH CS
                               AAA 81 eeervvnq 88
                                      +e r+  +
  gi|330508473|ref|YP_004384901.1| 78 FEGRLSGH 85
                                      55555555 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0013       1.9       1      32 [.       9      40 ..       9      55 .. 0.85
   2 !    9.0   0.1     0.001       1.4      82     135 ..      86     139 ..      75     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0013
                                      TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHT CS
                               SKI  1 mGaGKstvGkllAkklglefiDlDeliekrtg 32
                                      +G+G +t++++l+ +lgl+++ + el+ k + 
  gi|330508473|ref|YP_004384901.1|  9 PGTGTTTLARALSVQLGLPWVNSGELFRKIAS 40
                                      69********************9999877655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.001
                                       HHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCSS CS
                               SKI  82 lkekgiviyLdvsleellerlkadkeRPllqekskeeelleela.ereplyeeaa 135
                                       l +  + ++L+ +l + +er++++++  ll++  +e++l+ee + +r + y +++
  gi|330508473|ref|YP_004384901.1|  86 LLDADLKVLLKSDLRTRAERISKRES-KLLEDACQETRLREESEaRRYKKYYNID 139
                                       44477889***************999.5888888888888888878988888775 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.3e-06    0.0018       1      53 [.       5      57 ..       5     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                                      EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkge 53
                                      + G+Pg+G  t a+ l  ++gl+ + +G+l+R+  +++    ke++++ +kg 
  gi|330508473|ref|YP_004384901.1|  5 VSGSPGTGTTTLARALSVQLGLPWVNSGELFRKIASEKNISVKEMNRMAEKGP 57
                                      579******************************99999999999999999985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.5     2e-05     0.028       2      86 ..       3      75 ..       2     136 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnl 80
                                      + + G pG+G +tla+ l  +lg   ++s +l+r+++ +++ s ++            n++a+k    ++++++d   +
  gi|330508473|ref|YP_004384901.1|  3 ITVSGSPGTGTTTLARALSVQLGLPWVNSGELFRKIASEKNISVKEM-----------NRMAEK--GPEIDYLIDDAQR 68
                                      5678*******************************998766655443...........344443..2334444444444 PP

                            AAA_33 81 sr.rera 86
                                      s  +er+
  gi|330508473|ref|YP_004384901.1| 69 SLaKERQ 75
                                      4224444 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.5e-05     0.035       1      38 [.       2      37 ..       2      69 .. 0.69
   2 ?   -2.2   0.0       2.1   2.9e+03      47      72 ..     122     147 ..      97     160 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsf 38
                                      +I v+gs G G+tt+ar+l   +g  +v++ e      
  gi|330508473|ref|YP_004384901.1|  2 IITVSGSPGTGTTTLARALSVQLGLPWVNSGEL--FRK 37
                                      8***********************999995444..222 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                               PRK  47 dleleerkrakekevsflspeandfd 72 
                                       +l+ e ++r+ +k ++ +  + n +d
  gi|330508473|ref|YP_004384901.1| 122 RLREESEARRYKKYYNIDINDLNVYD 147
                                       33334444444444444444444444 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.21       3      75 ..       2      69 ..       1      83 [. 0.74
   2 ?    0.9   0.0      0.25   3.5e+02     147     159 ..     142     154 ..      87     168 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                      EEEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS-GGGGTSTTSEEEETTSEEE-HHHHHHHHHHHHH CS
                               CPT  3 iilLnGgsssGKsslaralqevldepwlhlgvDafvealppkrqdeadglefeteleeigpeldlllaalyea 75
                                      ii   G++ +G ++laral  +l  pw++ g  +++ ++  ++  + ++++  +e+   gpe+d l++  +++
  gi|330508473|ref|YP_004384901.1|  2 IITVSGSPGTGTTTLARALSVQLGLPWVNSG--ELFRKIASEKNISVKEMNRMAEK---GPEIDYLIDDAQRS 69
                                      8999***********************9866..45566777777777777555433...45555555544444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.25
                                       TT---SEEEETTS CS
                               CPT 147 agaeyDlevDtsa 159
                                          +yDl vDt  
  gi|330508473|ref|YP_004384901.1| 142 DLNVYDLVVDTGR 154
                                       5678999999975 PP

>> 6PGD  6-phosphogluconate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.3e-05       0.1      76     129 ..       2      55 ..       1      85 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.3e-05
                              6PGD  76 ilDkagqkGTgkwtvqealelgvpvptiaeavfaRllSslkeervkaskllkee 129
                                       i  ++g+ GTg+ t   al+++  +p ++++  +R ++s+k+  vk  + ++e+
  gi|330508473|ref|YP_004384901.1|   2 IITVSGSPGTGTTTLARALSVQLGLPWVNSGELFRKIASEKNISVKEMNRMAEK 55 
                                       66778999******************************9999888877777432 PP

>> Mitoc_L55  Mitochondrial ribosomal protein L55
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.29   4.1e+02      55      88 ..      42      75 ..      34      83 .. 0.83
   2 ?    8.9   1.9   0.00087       1.2      79     115 ..     101     137 ..      85     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.29
                         Mitoc_L55 55 ikiryrEPrrilampvdldtLseeerrarlrkre 88
                                       +i+++E  r+ +   ++d L ++ +r   + r+
  gi|330508473|ref|YP_004384901.1| 42 KNISVKEMNRMAEKGPEIDYLIDDAQRSLAKERQ 75
                                      58999999999999999***99999998888775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00087
                         Mitoc_L55  79 errarlrkreaklkekkeeeeeleDdfdvekYkkfwk 115
                                        r  r+ kre+kl e   +e  l+++ ++ +Ykk+++
  gi|330508473|ref|YP_004384901.1| 101 TRAERISKRESKLLEDACQETRLREESEARRYKKYYN 137
                                       46679*****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1254.52
//
Query:       gi|330508474|ref|YP_004384902.1|  [L=202]
Description: integral membrane protein [Methanosaeta concilii GP6]
Scores for complete 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  140.9   8.2    4.1e-41  140.5   8.2    1.1  1  EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
  ------ inclusion threshold ------
      0.057   13.6   0.2        0.1   12.7   0.1    1.5  1  DUF3180     Protein of unknown function (DUF3180)
      0.064   13.7  13.9        6.5    7.1  13.9    2.8  1  DUF4199     Protein of unknown function (DUF4199)


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 !  140.5   8.2   6.9e-45   4.1e-41      14     169 ..      49     199 ..      36     200 .. 0.94

  Alignments for each domain:
  == domain 1  score: 140.5 bits;  conditional E-value: 6.9e-45
                        EMC3_TMCO1  14 lPivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqeelmedqsemmmd 90 
                                       l + +++++++++tgl+++l+qk+++d++ m++ q+++++lq  ++++q  gd+ k ++l+++q+++  +q +mm++
  gi|330508474|ref|YP_004384902.1|  49 LSFPVILFILAAITGLYASLVQKYTMDWDFMRRQQEKMRALQANMKAAQLAGDQSKVQSLQTEQMKMVSEQGKMMQM 125
                                       45567************************************************************************ PP

                        EMC3_TMCO1  91 qmkpmivtmipqiliffwlnsffsgfvvaklpfpltgrfksllqrglesldvrfvssiswYflcsfglsqiirklLg 167
                                       q+kpm++++i++i++f+w+++++++    ++ fp++g+ + ++    e + +++ ++++wYf+cs+ +sqiirk+L+
  gi|330508474|ref|YP_004384902.1| 126 QFKPMLYIGIISIPLFMWIYFYIHNSGGINMTFPFWGTHS-IT----EMVLGPILYWFYWYFVCSLPVSQIIRKALD 197
                                       *************************************988.99....99***************************9 PP

                        EMC3_TMCO1 168 ea 169
                                       ++
  gi|330508474|ref|YP_004384902.1| 198 IG 199
                                       75 PP

>> DUF3180  Protein of unknown function (DUF3180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.7e-05       0.1      19      69 ..      40      91 ..      19     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                           DUF3180 19 sygslpplpwlaavvllvlavvelvlAlqvrrrirgr.pgarqlepltaarl 69
                                        g+lp+  ++++v+l++la+++ ++A  v++++ +    +rq e ++a ++
  gi|330508474|ref|YP_004384902.1| 40 LLGWLPQTGLSFPVILFILAAITGLYASLVQKYTMDWdFMRRQQEKMRALQA 91
                                      7899****************************99554323366666666554 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  13.9    0.0011       6.5      46     162 ..      20     140 ..       3     194 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0011
                           DUF4199  46 flvylalkkyrkkn...lgGfisf..gqafgfgflislvagllsavfqyiyfnfi.dpdfienyiaeilekleeake 116
                                       f++ + + +yr+     +++ + +  + +++f +++++  + +++++  +  ++  d df+ ++ +++ +  +++k+
  gi|330508474|ref|YP_004384902.1|  20 FFLGVMIEDYRNLLgqvMDHLLGWlpQTGLSFPVILFI-LAAITGLYASLVQKYTmDWDFMRRQQEKMRALQANMKA 95 
                                       55556666666654322233344411234444444444.44455555555555666*********999776555544 PP

                           DUF4199 117 esae...eenaemseeeikealeslspiivalqsflgnliiGlilslii 162
                                       ++ +    ++ ++++e    +++++s+   ++q+ +  +++  i+s+++
  gi|330508474|ref|YP_004384902.1|  96 AQLAgdqSKVQSLQTE----QMKMVSEQGKMMQMQFKPMLYIGIISIPL 140
                                       4433202333334444....44444432334444444444444444442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1644  (0.091695); expected 358.6 (0.02)
Passed bias filter:                      820  (0.045736); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
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 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1403.38
//
Query:       gi|330508475|ref|YP_004384903.1|  [L=537]
Description: preprotein translocase subunit SecY [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-64  218.1  24.1    2.1e-64  217.7  24.1    1.1  1  SecY             SecY translocase
    3.1e-11   42.9   4.3    8.9e-11   41.5   4.3    1.9  1  Plug_translocon  Plug domain of Sec61p
  ------ inclusion threshold ------
        8.1    7.1   9.1        3.7    8.2   6.5    1.8  2  Flocculin_t3     Flocculin type 3 repeat


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 !  217.7  24.1   3.5e-68   2.1e-64       1     306 []      75     514 ..      75     514 .. 0.86

  Alignments for each domain:
  == domain 1  score: 217.7 bits;  conditional E-value: 3.5e-68
                                       BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS.-S.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC......... CS
                              SecY   1 sifaLGImPyitasIilqLl.tvvipkleelk.ke.geegrkkinqitryltvvlalvqalgialslg......... 65 
                                       +++ LGI+P++tasI+lqLl ++     e++k +  ++++++ ++++++ l++++ +v++l  +l+ g         
  gi|330508475|ref|YP_004384903.1|  75 TMMLLGIGPIVTASIVLQLLvGA-----EIIKlNLsDPRDQAIYQGTQKALVFLMVAVEGLPQVLG-Gyllpdegva 145
                                       7899****************999.....666665569***********************996654.3688999999 PP

                                       ........HH.HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHCCHSS..................- CS
                              SecY  66 ........lalllivlqltagtvllmwLgEqitekGiGnGisllifagivarlpkals..................g 116
                                               ++ lli++q+++g+ l+++++E+++++G+G+G+ l+i+agi+++l++ l+                  +
  gi|330508475|ref|YP_004384903.1| 146 nalgvslgIISLLIFIQVFIGGSLIVYMDEVVSKWGVGSGVGLFIVAGISQQLVTGLInpatgeaglsvgiipkwiD 222
                                       99999999889*******************************************77775877777777755554441 PP

                                       HHHH...........SS.........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBS.TT....S.S-EEEEETT CS
                              SecY 117 liel...........ale.......gilallllllvtllvillvvyveeaerripvqya.krgrkggqssylPlkln 174
                                          +           + +        i   +l+l+ t+l+illvv+ve+++++ip+ ++  r    g+++++P+kl+
  gi|330508475|ref|YP_004384903.1| 223 ---IirlqlisfdtlF-TsegirfiMITGGILALISTILIILLVVLVESTRIEIPLAHSrVR----GARGRFPVKLV 291
                                       ...0444444445441.1455656666689*****************************666....9********** PP

                                       CCCSCHHHHHHHHHH.............................................................. CS
                              SecY 175 yagviPiIfasslla.............................................................. 189
                                       ya+v+P+I++++++a                                                              
  gi|330508475|ref|YP_004384903.1| 292 YASVLPMILVRAIQAniemlgallasrlgtvstatvtgegvttvytgyssllgnfisqsqfdaatgaaisgqspqpv 368
                                       ******************************************99999999999999999999999999999988888 PP

                                       ................HHHCCCCS.........TCCCS....THHHHHHHHHHHHHH....HHHHHHTCT.THHHHH CS
                              SecY 190 ................lpstiaqfl........lalls....psvlyvvlyvlliif....Fayfyteit.fnpkev 233
                                                       +ps++++ +        +        + +l+v++  +++i+    Fa+f++e+t + pk+v
  gi|330508475|ref|YP_004384903.1| 369 sglmyflspiggpedwIPSMVTTSTagmaelgfS---PiagwQILLHVLTDSAFLIIggilFAIFWIETTgMGPKSV 442
                                       8888877777777776677775555665555542...044457778999988888888999**************** PP

                                       HHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
                              SecY 234 aenlkksggfipgir.pgketakyLekvlsritliGalflaliavlpdllgasligafggtslLivVgvaletv 306
                                       a ++++sg ++pg+r +  +++k +e++++++t+iG++++++++++++l+g+  +g  ggt+lL++V+++++++
  gi|330508475|ref|YP_004384903.1| 443 AAKIHNSGLQVPGYRrNPASIEKLMERYIPKVTVIGGVIIGVLTLIASLMGT--LGGAGGTGLLLAVSIVYRLY 514
                                       ****************9***********************************..999*************9875 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   4.3   1.5e-14   8.9e-11       1      35 []      41      74 ..      41      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.5e-14
                                      HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                   Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                      llY++l++iPL+G+s ++s+D+f  +Ra fA+++G
  gi|330508475|ref|YP_004384903.1| 41 LLYFILGNIPLFGLS-AASIDLFSSYRAFFAGSFG 74
                                      79************9.99***************98 PP

>> Flocculin_t3  Flocculin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.5   0.00061       3.7      22      40 ..     321     339 ..     316     340 .. 0.91
   2 ?   -2.4   0.0       1.3   7.5e+03      23      32 ..     386     395 ..     384     397 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00061
                      Flocculin_t3  22 gvstvTttvngvvTvYTTy 40 
                                       +vst+T+t +gv+TvYT y
  gi|330508475|ref|YP_004384903.1| 321 TVSTATVTGEGVTTVYTGY 339
                                       89***************77 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                      Flocculin_t3  23 vstvTttvng 32 
                                       +s vTt++ g
  gi|330508475|ref|YP_004384903.1| 386 PSMVTTSTAG 395
                                       5778888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3735.57
//
Query:       gi|330508476|ref|YP_004384904.1|  [L=125]
Description: 50S ribosomal protein L15 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-17   63.9   2.1      5e-17   62.8   2.1    1.6  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
     0.0041   16.5   0.1     0.0055   16.1   0.1    1.3  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   2.1   5.6e-21     5e-17       2     127 ..      26     123 ..      25     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 5.6e-21
                                       GGGTSSTTTTTTTTT-S--.......S--.........---GGG..---EEEEHHHHHHTTTTGTTS------EEEG CS
                    Ribosomal_L27A   2 GktgGrGhkGqkkrsgvkk.kpgfeGGqmplyrrlpkrGfknskfkkeykvvnlkdLdelideerleladeaeeidl 77 
                                       G +gGrG  G+ k++ +     g e G++         Gf + + ++e  vvn+++Ld+l+ ++         ++++
  gi|330508476|ref|YP_004384904.1|  26 GTRGGRGDSGKCKHHFMRSiLLGTEMGKH---------GFVRLPLAEEVDVVNVDELDQLAGQD--------GKVEI 85 
                                       89*************97776888999999.........***99999************666554........4799* PP

                                       GGTTTTSSS....SEEEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A  78 eelaeaglikkkdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                       +el            Kvlg+g++t+kl+vka  f+++Ak+kIeaaGG+++
  gi|330508476|ref|YP_004384904.1|  86 NEL------------KVLGRGRVTRKLEVKALGFTAAAKSKIEAAGGQAV 123
                                       ***............********************************987 PP

>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   6.2e-07    0.0055      95     120 ..      98     123 ..      73     125 .] 0.91

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.2e-07
                     Ribosomal_L18  95 PklsvaALrftetararilkaGGeil 120
                                        kl+v AL ft++a+++i++aGG+ +
  gi|330508476|ref|YP_004384904.1|  98 RKLEVKALGFTAAAKSKIEAAGGQAV 123
                                       599********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 922.35
//
Query:       gi|330508477|ref|YP_004384905.1|  [L=151]
Description: 50S ribosomal protein L30P [Methanosaeta concilii GP6]
Scores for complete sequence (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   57.1   0.1    2.4e-15   56.2   0.1    1.5  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 !   56.2   0.1   1.3e-19   2.4e-15       2      51 .]       3      52 ..       2      52 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.3e-19
                                      EEEE-S-STTS-HHHHHHHHHTT-SSTT.EEEE--SSHHHHHHHHHCCCGE CS
                     Ribosomal_L30  2 fVtrirsiigvppkvrktLqlLgLrkin.gtvvklntpsirGmLkkVkhlV 51
                                      +++r r+ +++ p++++tL +L  +++n ++vvk++ p +rGm++kVk++V
  gi|330508477|ref|YP_004384905.1|  3 AIVRLRGEVNLRPDIKDTLAMLHIHRVNhCVVVKED-PHYRGMIQKVKDYV 52
                                      79**************************99999999.*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.55
# Mc/sec: 827.89
//
Query:       gi|330508478|ref|YP_004384906.1|  [L=207]
Description: 30S ribosomal protein S5 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-23   82.9   1.4    1.2e-23   82.9   1.4    2.0  2  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
    2.6e-22   78.0   0.4    4.4e-22   77.3   0.4    1.4  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   1.4   1.3e-27   1.2e-23       1      65 []      55     119 ..      55     119 .. 0.98
   2 ?   -2.1   0.0      0.44   3.9e+03      51      65 .]     192     206 ..     186     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 1.3e-27
                                       XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                      Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                       l+++vl+i++vq++t++Grr +f+ +v+vG+++G++GlG+gk  +v +Ai+k+i++Ak+n+++v+
  gi|330508478|ref|YP_004384906.1|  55 LEDEVLDINMVQRMTDSGRRVKFRTTVIVGNRDGYIGLGEGKDVQVGKAIKKGIDNAKRNIMKVN 119
                                       799************************************************************96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.44
                                       HHHHHHHHHTEEE-- CS
                      Ribosomal_S5  51 rkAiekAkknlvpvp 65 
                                        kA+ +A  n + v+
  gi|330508478|ref|YP_004384906.1| 192 AKATYNALINTITVR 206
                                       599999999988885 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.4   4.9e-26   4.4e-22       2      65 ..     141     205 ..     140     207 .] 0.96

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 4.9e-26
                                       EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT CS
                    Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrsp 65 
                                       g+ g+v+v l+paprG Gi ag++ ++v+ +aGikDv++++ g +r++in++kAt++AL ++ ++
  gi|330508478|ref|YP_004384906.1| 141 GESGSVRVVLIPAPRGLGIAAGDTSKKVMDMAGIKDVWTRTAGsTRTTINFAKATYNALINTITV 205
                                       789********************************************************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1568.35
//
Query:       gi|330508479|ref|YP_004384907.1|  [L=169]
Description: 50S ribosomal protein L18 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-30  103.8   0.3      1e-19   71.1   0.0    2.3  2  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 
  ------ inclusion threshold ------
      0.044   14.1   0.0      0.064   13.6   0.0    1.2  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a
       0.14   11.9   0.0       0.28   10.9   0.0    1.4  2  ATPgrasp_Ter    ATP-grasp in the biosynthetic pathway with Te


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 !   71.1   0.0   1.7e-23     1e-19       2      98 ..       6      95 ..       5      99 .. 0.96
   2 !   30.7   0.1   4.6e-11   2.8e-07     134     163 .]     104     133 ..     100     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 1.7e-23
                     Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvglt 80
                                      r++v +rrr+egkt+Y+ r +l+         ++ R+vVr +n +++ q++ a++egdk+l +++s+el+ +g++  + 
  gi|330508479|ref|YP_004384907.1|  6 RYKVPLRRRKEGKTNYHVRYKLLLS-------KRPRVVVRKSNASTTLQLVVAELEGDKTLLTVNSRELKGFGFSSAVG 77
                                      9*********************984.......678******************************************** PP

                     Ribosomal_L5e 81 nyaaaYatglllarrllk 98
                                      n  aaY+tgll+++++l+
  gi|330508479|ref|YP_004384907.1| 78 NLPAAYLTGLLFGKKMLA 95
                                      ***************985 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 4.6e-11
                     Ribosomal_L5e 134 dvGLartttgakvfgalkgavdgglsiphs 163
                                       d+GL+ +t+g+++++a+kg+vd+g+++phs
  gi|330508479|ref|YP_004384907.1| 104 DIGLHASTKGNRIYAAIKGVVDAGVDVPHS 133
                                       9****************************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 ?   13.6   0.0   1.1e-05     0.064      11      93 ..      20     105 ..      11     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                                       HHHHTTT--TTSSS-EEEEEE-SS-EEEEEE.-T.TT--EEEEECS-SCCCT..S-SSSCHHHHHHHHHHHHHHHCH CS
                    Ribosomal_L18p  11 hkRirkklsgtaerprlvvfrsnrhiyaQvi.dd.vkgktlasastlekelk..lkstknkeaakkvgeliAerake 83 
                                       +  +r kl   ++rpr+vv +sn     Q++ ++   +ktl ++++ e +     +  +n  aa   g l+ ++ ++
  gi|330508479|ref|YP_004384907.1|  20 NYHVRYKLLL-SKRPRVVVRKSNASTTLQLVvAElEGDKTLLTVNSRELKGFgfSSAVGNLPAAYLTGLLFGKKMLA 95 
                                       4455666654.56*************999652441567899999988865434667788999999999999999999 PP

                                       HCHTC-EE-- CS
                    Ribosomal_L18p  84 kgiekvvfDr 93 
                                        g+e  v D 
  gi|330508479|ref|YP_004384907.1|  96 IGVEGGVADI 105
                                       9998777665 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.8e-05      0.28      32     109 ..      12      88 ..       4      99 .. 0.87
   2 ?   -3.2   0.0       1.1   6.6e+03      85     102 ..     115     132 ..     113     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.8e-05
                      ATPgrasp_Ter  32 pRrKekgglq.elekdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgysalaGvnlpylalkl 107
                                        RrKe g+ + +++++  l +  + ++++ ++++   + v e e+   LL +N+R   G+g s + G nlp ++l+ 
  gi|330508479|ref|YP_004384907.1|  12 RRRKE-GKTNyHVRYKLLLSKRPRVVVRKSNASTTLQLVVAELEGDKTLLTVNSRELKGFGFSSAVG-NLPAAYLTG 86 
                                       56777.66666999999999999999*******9999999999999******************999.999999887 PP

                      ATPgrasp_Ter 108 ll 109
                                       ll
  gi|330508479|ref|YP_004384907.1|  87 LL 88 
                                       76 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.1
                      ATPgrasp_Ter  85 RasGGlgysalaGvnlpy 102
                                       R+ ++++  + aGv++p+
  gi|330508479|ref|YP_004384907.1| 115 RIYAAIKGVVDAGVDVPH 132
                                       666677777788888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.20s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1446.92
//
Query:       gi|330508480|ref|YP_004384908.1|  [L=153]
Description: 50S ribosomal protein L19e [Methanosaeta concilii GP6]
Scores for complete 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  179.3   4.5    4.6e-53  179.2   4.5    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 !  179.2   4.5   2.6e-57   4.6e-53       3     143 ..       5     147 ..       3     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 179.2 bits;  conditional E-value: 2.6e-57
                                       HHHHHHHHHHTTS-GGGEEE..-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGG CS
                    Ribosomal_L19e   3 klqkrlaasvlkvGknrvwl..dpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsG 77 
                                       ++q+rlaas l++G++rvw+  dpe +  + +Aitredir+ i+dg I++kpkkgnsr+r+r++++k+++g+ +g+G
  gi|330508480|ref|YP_004384908.1|   5 TTQRRLAASELNIGESRVWInpDPELAGALGDAITREDIRSQISDGNIKAKPKKGNSRGRIRAKNAKRAYGHCKGPG 81 
                                       79******************77779999************************************************* PP

                                       G--S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT-X CS
                    Ribosomal_L19e  78 krkGtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiekk 143
                                       +r+G+k+aR p+kelW+++iRalR+ L+elr++++id++ Yr lYrk+kGge++++a+++++i++k
  gi|330508480|ref|YP_004384908.1|  82 HRRGAKGARSPRKELWMTKIRALRKRLRELRDTGQIDRHAYRLLYRKSKGGEYRSTAHMNSFIKAK 147
                                       ***************************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1192.07
//
Query:       gi|330508481|ref|YP_004384909.1|  [L=124]
Description: 50S ribosomal protein L32 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-33  114.0   0.2    5.2e-33  113.7   0.2    1.1  1  Ribosomal_L32e  Ribosomal protein L32


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.2   2.9e-37   5.2e-33       1     108 []      16     119 ..      16     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 2.9e-37
                                       ------TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE CS
                    Ribosomal_L32e   1 tkkFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenk 77 
                                       +++F+ h+s++++kl++swrkprG++n++r+++ ++ ++++ G+gspk++rg++psG+ ++ V+nv+eL + + +  
  gi|330508481|ref|YP_004384909.1|  16 KPEFNFHDSHKKKKLGTSWRKPRGLHNKLRQHIAAKGRVVQPGFGSPKAVRGYHPSGMAEIRVNNVAELAAAQGC-- 90 
                                       689******************************************************************988666.. PP

                                       ..EEEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                    Ribosomal_L32e  78 syaaeiahsVsskkrkeiverAaelgikVtN 108
                                         a++ia++V++kkr +i+++Aae+g+k++N
  gi|330508481|ref|YP_004384909.1|  91 --AVRIASAVGMKKRLDIQAKAAEMGLKILN 119
                                       ..89*************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 889.34
//
Query:       gi|330508482|ref|YP_004384910.1|  [L=176]
Description: 50S ribosomal protein L6 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-31  108.6   4.6    5.4e-20   71.9   1.2    2.1  2  Ribosomal_L6  Ribosomal protein L6


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   1.2     3e-24   5.4e-20       1      76 []      11      83 ..      11      83 .. 0.95
   2 !   38.3   0.1   8.8e-14   1.6e-09       1      76 []      95     169 ..      95     169 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 3e-24
                                      CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                      Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                      iP+gv+vs++  ++v+v+Gpkgel+r++++  ++e+ +e+ +v v ++ + +++++ ++gt  s+innm++GVt+g
  gi|330508482|ref|YP_004384910.1| 11 IPEGVTVSVD-RNVVTVKGPKGELSRTLSYP-DLEIRKEDLQVIVNSRVDRKRHRA-MVGTLASHINNMVTGVTKG 83
                                      8*********.5*******************.888889999999999999999999.*****************98 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 8.8e-14
                                       CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHH CS
                      Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGV 73 
                                       +P+  ++  ++  ++++lG+++++++++ +g++ve+      ++++v++g dke+v    A+i++++++   +++ +
  gi|330508482|ref|YP_004384910.1|  95 FPIQLKAASDELIINNFLGERKSRSARVLPGTKVEIG-----KDEVVITGMDKENVgqtmANIEQATRVHGFDVRIF 166
                                       7889999999999**********************99.....9********************************** PP

                                       HTC CS
                      Ribosomal_L6  74 teg 76 
                                       ++g
  gi|330508482|ref|YP_004384910.1| 167 QDG 169
                                       *98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1315.40
//
Query:       gi|330508483|ref|YP_004384911.1|  [L=129]
Description: 30S ribosomal protein S8 [Methanosaeta concilii GP6]
Scores for complete 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-27   93.7   0.0    1.1e-26   93.3   0.0    1.1  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3   0.0     6e-31   1.1e-26       1     127 []       4     129 .]       4     129 .] 0.82

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 6e-31
                                       -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCC..EEEEE-BSSS-SBSSS... CS
                      Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkk..ikielkynkkkksvik... 70 
                                       Dp+ad+++ i+Nae+++k e+ + pask++ + lkv+ ++Gyi +fe+  + k+ +  +k+ +++n+  ++vik   
  gi|330508483|ref|YP_004384911.1|   4 DPLADAMSVIKNAESVGKPECIIhPASKVIGRALKVMADRGYIGEFEFIdDGKSGMfrVKLLGRINR--CGVIKprf 78 
                                       9***********************************************8555555555666667766..****9433 PP

                                       ..EEEE-SBTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                      Ribosomal_S8  71 ..klkrvskpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                         k ++++k  +r            +++G++i+sT+kGvm++++Ar++++GG++layv+
  gi|330508483|ref|YP_004384911.1|  79 stKATEMEKWEKR--------FLPAKNFGVLILSTNKGVMAHSDARAQSLGGQLLAYVY 129
                                       3333333333333........334578*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 831.54
//
Query:       gi|330508484|ref|YP_004384912.1|  [L=50]
Description: 30S ribosomal protein S14p/S29e [Methanosaeta concilii GP6]
Scores for complete 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   48.5   3.9    5.6e-13   48.4   3.9    1.0  1  Ribosomal_S14   Ribosomal protein S14p/S29e
     0.0045   16.6   0.9     0.0055   16.3   0.9    1.1  1  zf-P11          P-11 zinc finger
  ------ inclusion threshold ------
       0.01   15.7   1.0       0.56   10.2   1.0    2.1  2  DUF4428         Domain of unknown function (DUF4428)
      0.013   15.3   3.1      0.018   14.8   3.1    1.4  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.033   14.4   0.5      0.033   14.4   0.5    1.1  1  FYVE_2          FYVE-type zinc finger
      0.073   13.1   0.3      0.074   13.1   0.3    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 !   48.4   3.9   1.9e-16   5.6e-13       8      54 .]       7      50 .]       1      50 [] 0.92

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.9e-16
                                      SS..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE-- CS
                     Ribosomal_S14  8 nssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKaS 54
                                       +  +r+ n C+ ++r  G++rk+g+  +R+cfRe A +   +G++K+S
  gi|330508484|ref|YP_004384912.1|  7 VY--GRGANVCKRCSRKNGLVRKYGIylCRQCFREIAPE---MGFEKYS 50
                                      44..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 !   16.3   0.9   1.8e-06    0.0055       1      28 [.      11      37 ..      11      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-06
                                      -SSSBTTTSS--SSEEE-SSSEEEHHHH CS
                            zf-P11  1 GplsCksCWfkdksLveCsdHYLClrCl 28
                                      G   Ck C  k ++Lv+    YLC++C+
  gi|330508484|ref|YP_004384912.1| 11 GANVCKRCSRK-NGLVRKYGIYLCRQCF 37
                                      6778****765.69*************7 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.4    0.0019       5.6      21      29 ..      13      21 ..       2      30 .. 0.79
   2 ?   10.2   1.0   0.00019      0.56       5      30 ..      18      40 ..      15      50 .] 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0019
                           DUF4428 21 yvCkdClkK 29
                                      +vCk C  K
  gi|330508484|ref|YP_004384912.1| 13 NVCKRCSRK 21
                                      8******99 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00019
                           DUF4428  5 CgkKigllkrlkleDgyvCkdClkKl 30
                                      C  K gl         y+C  C+ ++
  gi|330508484|ref|YP_004384912.1| 18 CSRKNGLVR---KYGIYLCRQCFREI 40
                                      888888888...7788********99 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   3.1     6e-06     0.018      23      50 ..      13      36 ..       4      40 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6e-06
                    zinc_ribbon_10 23 lICskChshnGlapkeeleevkyrCpkC 50
                                       +C+ C  +nGl+     ++  y C +C
  gi|330508484|ref|YP_004384912.1| 13 NVCKRCSRKNGLV----RKYGIYLCRQC 36
                                      59***********....77889***999 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.5   1.1e-05     0.033      79     101 ..      12      37 ..       2      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                            FYVE_2  79 lnvCkkCsve...nkkekvwlCkiCs 101
                                        nvCk+Cs++    +k  ++lC++C 
  gi|330508484|ref|YP_004384912.1|  12 ANVCKRCSRKnglVRKYGIYLCRQCF 37 
                                       69********776688999******6 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   2.5e-05     0.074     109     138 ..       7      36 ..       1      40 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                           DUF1451 109 vvglGtlvCekCgkelalkkteeippCpkC 138
                                       v g G  vC++C ++  l +   i  C +C
  gi|330508484|ref|YP_004384912.1|   7 VYGRGANVCKRCSRKNGLVRKYGIYLCRQC 36 
                                       7899************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 346.15
//
Query:       gi|330508485|ref|YP_004384913.1|  [L=168]
Description: 50S ribosomal protein L5 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-23   82.2   0.0    3.3e-23   81.7   0.0    1.3  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
    9.1e-17   61.1   0.5    1.6e-16   60.4   0.5    1.4  1  Ribosomal_L5    Ribosomal protein L5
  ------ inclusion threshold ------
      0.025   15.4   0.0      0.034   15.0   0.0    1.3  1  FctA            Spy0128-like isopeptide containing domain


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 !   81.7   0.0   5.5e-27   3.3e-23       1      84 [.      56     133 ..      56     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 5.5e-27
                    Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivtta 77 
                                       piG+k tLrg+ +++fl  +l+++ + lr       s+fd++Gn+sfGi+e+++fp+++yd+++gifGmd+++ +++
  gi|330508485|ref|YP_004384913.1|  56 PIGAKLTLRGKAAEDFLAIALKAAGNSLR------MSQFDQQGNFSFGIEEHTDFPGMRYDPEIGIFGMDVSVALKR 126
                                       8****************************......****************************************99 PP

                    Ribosomal_L5_C  78 ktdeear 84 
                                          + ar
  gi|330508485|ref|YP_004384913.1| 127 AGYRIAR 133
                                       8444333 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.5   2.7e-20   1.6e-16       3      57 .]       1      52 [.       1      52 [. 0.98

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 2.7e-20
                                      TTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                      Ribosomal_L5  3 MqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                      M +Pr++K+v+++gvGe+g++   l +a+ ++++It Q+Pv++ akk+ ++F+i+
  gi|330508485|ref|YP_004384913.1|  1 MLEPRIDKVVVHVGVGESGQR---LVNAETIMKTITKQQPVRSMAKKTLPTFNIK 52
                                      889******************...****************************996 PP

>> FctA  Spy0128-like isopeptide containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   5.6e-06     0.034       5      98 ..      30     128 ..      23     156 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.6e-06
                                       EEE.......----SEEEEEEEEE-TTS--SSSEEE----SS-EEEEEE-GTSEGTTS--SSSE.EEEEEEEEE-SS CS
                              FctA   5 KtLtg.....eslkddeFtFeltaeddaaeaakeekakkkeeaeeketaeegktFgeitfdkagktYtYtvsEekpe 76 
                                       Kt+t+       +k++  tF++++++    a+ +   k++e+  + + +++g+++   +fd++g ++ + ++E +  
  gi|330508485|ref|YP_004384913.1|  30 KTITKqqpvrSMAKKTLPTFNIKKKE-PIGAKLTLRGKAAEDFLAIALKAAGNSLRMSQFDQQG-NFSFGIEEHT-- 102
                                       55544555532223333467776643.222222222222222222222222448988999****.6*******44.. PP

                                       -..TEE--.-.-EEEEEEEEE.TTSS CS
                              FctA  77 k..GvtyD.t.atytvtvtvtdngdG 98 
                                       +  G+ yD +   + ++v v  +  G
  gi|330508485|ref|YP_004384913.1| 103 DfpGMRYDpEiGIFGMDVSVALKRAG 128
                                       257*****443333555555544445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1218.29
//
Query:       gi|330508486|ref|YP_004384914.1|  [L=234]
Description: 30S ribosomal protein S4E [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-16   59.7   0.0    4.2e-16   58.6   0.0    1.6  1  Ribosomal_S4e  Ribosomal family S4e
    3.5e-11   43.0   2.5    5.5e-11   42.4   2.5    1.3  1  RS4NT          RS4NT (NUC023) domain
      3e-07   30.2   0.7    6.5e-07   29.1   0.7    1.6  1  KOW            KOW motif
    0.00044   19.9   0.1    0.00076   19.2   0.1    1.4  1  S4             S4 domain
  ------ inclusion threshold ------
       0.05   13.4   0.0       0.12   12.2   0.0    1.6  1  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 !   58.6   0.0   1.2e-19   4.2e-16       2      75 .]      92     163 ..      91     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 1.2e-19
                                       TEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEETTTTEE CS
                     Ribosomal_S4e   2 genyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtirypdpdikvnDtvkidleenkI 75 
                                       +++yr+l d+kg f l   ++  a+ KL +i++kt+ ++++ ql+++dG++ + + + +kv+D+++++++e+ I
  gi|330508486|ref|YP_004384914.1|  92 DQQYRMLKDEKGMFYLSLLEPGSAR-KLARIENKTVLRGNKQQLNLSDGSNKLAEGD-YKVGDSLVLSIPEKDI 163
                                       689*********************9.******************************8.*************988 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   2.5   1.5e-14   5.5e-11       4      35 ..       2      33 ..       1      35 [. 0.96

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.5e-14
                                      ---EETTTS-TTS---SSSSSEE----SSSS- CS
                             RS4NT  4 kkHLKrlaAPkhWpldkkegvfavkPspGPHk 35
                                      ++H Krl+ P +Wp+++k++v+++k spGPH+
  gi|330508486|ref|YP_004384914.1|  2 SRHQKRLTIPVSWPVARKTSVWVPKSSPGPHS 33
                                      79*****************************8 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.7   1.8e-10   6.5e-07       1      31 [.     171     205 ..     171     206 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.8e-10
                                       TTSEEEESSSTTTTCEEEEEEEETTT....TEEEE CS
                               KOW   1 pGdhVkVvsGphkGktGkVvkvdqhk....vrVfv 31 
                                       +G+  +Vv+G+h G+tGk++++++ k    +rV++
  gi|330508486|ref|YP_004384914.1| 171 VGNLAMVVGGKHSGQTGKIKDIIKVKssqpNRVII 205
                                       7*****************************99997 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   2.1e-07   0.00076       1      48 []      38      86 ..      38      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.1e-07
                                      EEHHHHH.HHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                                S4  1 rRLdkvl.arlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                      ++L  v+   l+l+   reA++   +G+VlV+Gk  kd + +++  Dvi
  gi|330508486|ref|YP_004384914.1| 38 MPLLMVIrDMLKLVDNAREAKRVLYEGKVLVDGKSQKDHKLPIGIFDVI 86
                                      567777777899999***********************99999888886 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.4e-05      0.12      18      42 ..      49      73 ..      43      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.4e-05
                              S4_2 18 glvesGgeaKafiaegeVkvNGeve 42
                                      +lv++  eaK ++ eg+V+v+G+ +
  gi|330508486|ref|YP_004384914.1| 49 KLVDNAREAKRVLYEGKVLVDGKSQ 73
                                      46777789**************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 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:                        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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1796.68
//
Query:       gi|330508487|ref|YP_004384915.1|  [L=95]
Description: 50S ribosomal protein L24 domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-16   59.8   0.1    3.7e-16   59.3   0.1    1.2  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    4.4e-06   26.5   6.6    7.9e-06   25.7   6.6    1.6  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 !   59.3   0.1   4.1e-20   3.7e-16      23      82 .]       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 4.1e-20
                                      xxxxxxxxxxxxxxxxxxxxx................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Ribosomal_L26 23 msapLskeLrekygvrslpir................................gvtrekangttvpvgihpSkvvItkl 69
                                      m+apLs+ Lre+ + r+ ++r                                gv++ +a+gt+vp+ ihpS+vvI+kl
  gi|330508487|ref|YP_004384915.1|  1 MHAPLSRALREELKKRNAQLRkgdtvkvvrgdhagtegavedvdikrctikvaGVSNYRADGTEVPRTIHPSNVVIVKL 79
                                      99***************************************************************************** PP

                                      xx.xxxxxxxxxxx RF
                     Ribosomal_L26 70 kl.DkdrkkiLerk 82
                                      +l D +r+ki er+
  gi|330508487|ref|YP_004384915.1| 80 ELeDAEREKIFERR 93
                                      ************98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   6.6   8.8e-10   7.9e-06       1      28 [.      22      49 ..      22      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 8.8e-10
                                      TTSEEEESSSTTTTCEEEEEEEETTTTE CS
                               KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvr 28
                                      +Gd+VkVv+G h+G +G V++vd ++ +
  gi|330508487|ref|YP_004384915.1| 22 KGDTVKVVRGDHAGTEGAVEDVDIKRCT 49
                                      7**********************99844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 694.23
//
Query:       gi|330508488|ref|YP_004384916.1|  [L=132]
Description: 50S ribosomal protein L14b/L23e [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-38  130.2   1.5    4.6e-38  130.0   1.5    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 !  130.0   1.5   2.6e-42   4.6e-38       2     121 ..      12     131 ..      11     132 .] 0.95

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 2.6e-42
                                       .CSS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS CS
                     Ribosomal_L14   2 iqlktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdG 74 
                                       i+++++l+++DN+ga+++++i+v +++    +++ a +Gdi++vsvkk++p   +++++++kav++r++ke+rr+dG
  gi|330508488|ref|YP_004384916.1|  12 INTGAYLDCVDNTGARTLHVISVKNYRgvknRQPCAGIGDIVIVSVKKGTP---EMRKQIFKAVIIRQRKEFRRPDG 85 
                                       78899******************98776666679*****************...99********************* PP

                                       -EEEESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE CS
                     Ribosomal_L14  75 svirfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApev 121
                                         ++f+dnaaV+++++g p+G++++gpvare++e+ f ki+s A+ +
  gi|330508488|ref|YP_004384916.1|  86 LRVKFEDNAAVIVDDEGVPKGSEVKGPVAREVAER-FGKIASAASII 131
                                       **********************************9.********977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 945.45
//
Query:       gi|330508489|ref|YP_004384917.1|  [L=109]
Description: 30S ribosomal protein S17 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-26   90.0   3.3    9.5e-26   89.7   3.3    1.1  1  Ribosomal_S17    Ribosomal protein S17
     0.0032   17.8   0.2      0.014   15.7   0.0    2.0  2  Ribosomal_S17_N  Ribosomal_S17 N-terminal
  ------ inclusion threshold ------
      0.085   13.1   0.0       0.11   12.8   0.0    1.1  1  Ricin_B_lectin   Ricin-type beta-trefoil lectin domain
       0.31   10.8   2.1       0.63    9.8   2.1    1.4  1  zf-C3H1          Putative zinc-finger domain


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   3.3   2.1e-29   9.5e-26       2      68 .]      39     106 ..      38     106 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 2.1e-29
                                       EEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
                     Ribosomal_S17   2 vVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                                       +Vvsdkmd TvvV ++  +k  ky++++kr++k++ah++++  +k GD+V+i+ecrPlSktk++vvve
  gi|330508489|ref|YP_004384917.1|  39 TVVSDKMDNTVVVMRKFEKKATKYERFEKRQSKIHAHNPPCLeAKAGDRVKIAECRPLSKTKSYVVVE 106
                                       7*****************************************************************97 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.2e-06     0.014      33      69 .]       4      36 ..       1      36 [. 0.81
   2 ?   -0.3   0.0      0.32   1.4e+03      30      33 ..      63      66 ..      46      87 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.2e-06
                                      -----TT----GGGGS-----TTSSSSSS----S-EE CS
                   Ribosomal_S17_N 33 vknvglgfktPkeAiegtYiDkKCPFtGnvsirGriL 69
                                      ++++gl    P++  +    D KCPF G+  +rG+++
  gi|330508489|ref|YP_004384917.1|  4 MRDIGLDVAPPEKECN----DPKCPFHGTLPVRGQVF 36
                                      6777887777766555....99************996 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.32
                                      ---- CS
                   Ribosomal_S17_N 30 kryv 33
                                      +r+ 
  gi|330508489|ref|YP_004384917.1| 63 ERFE 66
                                      2222 PP

>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.4e-05      0.11      54     121 ..      35      96 ..      25     102 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                                       TTEEEEESSSSTTSBEEEEETTTTSG.GGCEEEETTTTEEEETTTSEEEEESTTSSTTTBEEEEEE.TS CS
                    Ricin_B_lectin  54 selCldvsstaegakvvlakChkgkg.nqrWefdkdgtqirhkksgkCLdvkgasksneklilkkcdsg 121
                                          C  vs++ +++ vv++k +k+ +  +r  f+k ++  +h+++  CL++k ++    ++ +++c++ 
  gi|330508489|ref|YP_004384917.1|  35 VFSCTVVSDKMDNTVVVMRKFEKKATkYER--FEKRQS-KIHAHNPPCLEAKAGD----RVKIAECRPL 96 
                                       557888889999999999999843333444..444455.68888999**999886....6777778765 PP

>> zf-C3H1  Putative zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.1   0.00014      0.63      10      18 ..      17      25 ..      16      25 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00014
                           zf-C3H1 10 vCnDpsCef 18
                                       CnDp+C+f
  gi|330508489|ref|YP_004384917.1| 17 ECNDPKCPF 25
                                      6******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 813.73
//
Query:       gi|330508490|ref|YP_004384918.1|  [L=97]
Description: ribonuclease P protein component 1 [Methanosaeta concilii GP6]
Scores for complete sequence (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    1.2e-21   76.4   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 !   76.4   0.0   6.8e-26   1.2e-21       2      84 .]       7      88 ..       6      88 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 6.8e-26
                                      HHCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHH CS
                           UPF0086  2 kLlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpad 80
                                      +L++++l+G++v+V + ++p +vg++G++v+Et+nt+ ++t +++v ++pK+++ ++f++ d  +++v Gs l+++p++
  gi|330508490|ref|YP_004384918.1|  7 NLARHELIGLDVQVESNSEPGIVGLRGRIVDETRNTFLLET-ERKVLRIPKKNASLTFTLPDGQRARVAGSVLISQPEN 84
                                      89***************************************.89****************9999*************** PP

                                      HHCH CS
                           UPF0086 81 Raer 84
                                      R+++
  gi|330508490|ref|YP_004384918.1| 85 RISK 88
                                      *986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 733.93
//
Query:       gi|330508491|ref|YP_004384919.1|  [L=66]
Description: 50S ribosomal protein L29 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-18   65.4   0.5    3.8e-18   65.2   0.5    1.0  1  Ribosomal_L29  Ribosomal L29 protein
     0.0089   16.1   0.2      0.032   14.4   0.2    1.9  1  MRP-L47        Mitochondrial 39-S ribosomal protein L47 (MRP-
  ------ inclusion threshold ------
      0.063   13.4   0.0      0.069   13.3   0.0    1.0  1  Fer4_14        4Fe-4S single cluster domain
       0.49   11.9   3.3       0.88   11.1   0.5    2.2  2  Toxin_36       Conantokin-G mollusc-toxin


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 !   65.2   0.5   8.5e-22   3.8e-18       2      57 .]       8      64 ..       7      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 8.5e-22
                                      HHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHHH CS
                     Ribosomal_L29  2 elrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlrer 57
                                      e+r+++ ee+ e+l +l+ eL + r    +g ++e+p+ri+ +R++IARikTv++er
  gi|330508491|ref|YP_004384919.1|  8 EIRNMNAEEISEELHKLESELIRERGVVTAGgAPEKPGRIKDIRRTIARIKTVQTER 64
                                      9************************9999998************************8 PP

>> MRP-L47  Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   7.1e-06     0.032      64      87 .]      41      64 ..       4      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.1e-06
                           MRP-L47 64 mpsperlkkvkesMeniktVlkeR 87
                                       ++p+r+k +++++++iktV +eR
  gi|330508491|ref|YP_004384919.1| 41 PEKPGRIKDIRRTIARIKTVQTER 64
                                      5789*****************999 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.069      30      76 ..      13      59 ..       3      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                           Fer4_14 30 teelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlke 76
                                      + e+++++l++l+ + i+ +g+v  GG P  + + k++ + + r+k+
  gi|330508491|ref|YP_004384919.1| 13 NAEEISEELHKLESELIRERGVVTAGGAPEKPGRIKDIRRTIARIKT 59
                                      5677889999**********************999999999999986 PP

>> Toxin_36  Conantokin-G mollusc-toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.28   1.3e+03       4      11 ..       8      15 ..       7      17 .. 0.83
   2 ?   11.1   0.5    0.0002      0.88       3      15 .]      19      31 ..      18      31 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.28
                          Toxin_36  4 ElqkMaee 11
                                      E+  M++e
  gi|330508491|ref|YP_004384919.1|  8 EIRNMNAE 15
                                      78899998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0002
                          Toxin_36  3 EElqkMaeeLiRE 15
                                      EEl k   eLiRE
  gi|330508491|ref|YP_004384919.1| 19 EELHKLESELIRE 31
                                      9***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 500.29
//
Query:       gi|330508492|ref|YP_004384920.1|  [L=278]
Description: 30S ribosomal protein S3P [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-21   77.0   0.2      2e-21   76.3   0.2    1.4  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    1.7e-14   53.3   0.0      3e-14   52.6   0.0    1.4  1  KH_2            KH domain
  ------ inclusion threshold ------
      0.059   13.2   1.4        0.1   12.4   0.2    2.0  3  KH_1            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.2   3.3e-25     2e-21       1      83 []      99     182 ..      99     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 3.3e-25
                                       HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTE CS
                    Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyG 75 
                                       +a++le+++ fR+a ++++rr+m+aga G++i++sG+L+ + ++r+ek+ +G++++  +++ + +d++++ a  k G
  gi|330508492|ref|YP_004384920.1|  99 LASSLERGWYFRKAGQSMMRRVMDAGALGCEIVISGKLT-GPRSRTEKFIAGYIKHsgKPAIDLVDRGYSVAVKKLG 174
                                       5899***********************************.9***************99******************* PP

                                       EEEEEEEE CS
                    Ribosomal_S3_C  76 iiGvkVwI 83 
                                       +iG++V+I
  gi|330508492|ref|YP_004384920.1| 175 VIGCQVRI 182
                                       ******98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   5.1e-18     3e-14       2      69 ..      17      83 ..      16      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 5.1e-18
                                      HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEE CS
                              KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVkln 69
                                      ++e+la e++ ag++++  +rt+ ++ i++++++pg+vIGkgG+ i+ki+ +l +++  l + ++ ++
  gi|330508492|ref|YP_004384920.1| 17 VNEYLADELERAGYGGMQMNRTPMGTQITVYAEKPGMVIGKGGKLIRKITRDLDRRFH-LDNPQIDVQ 83
                                      679******************************************************5.999999864 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.7e-05       0.1       4      27 ..      44      67 ..      41      72 .. 0.82
   2 ?   -3.3   0.0       1.4   8.3e+03      31      52 ..     128     134 ..     118     142 .. 0.70
   3 ?   -2.8   0.0      0.97   5.8e+03      30      40 ..     177     186 ..     177     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                                      EEEGGGHHHHHHTGGGHHHHHHHH CS
                              KH_1  4 ilvPsslvgriIGkgGsnIkeIre 27
                                      i+v +++ g +IGkgG+ I++I +
  gi|330508492|ref|YP_004384920.1| 44 ITVYAEKPGMVIGKGGKLIRKITR 67
                                      5566666799************87 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                                       -EEEEESSTT...T.-EEEEEE CS
                              KH_1  31 akIkvpksedegsderevtisG 52 
                                       +                ++isG
  gi|330508492|ref|YP_004384920.1| 128 CE---------------IVISG 134
                                       44...............55554 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.97
                                       T-EEEEESSTT CS
                              KH_1  30 gakIkvpksed 40 
                                       g++++++ ++d
  gi|330508492|ref|YP_004384920.1| 177 GCQVRII-PPD 186
                                       8999988.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2262.50
//
Query:       gi|330508493|ref|YP_004384921.1|  [L=153]
Description: 50S ribosomal protein L22 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-26   92.6   0.0    1.9e-26   92.3   0.0    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.0     1e-30   1.9e-26       1     103 []      17     149 ..      17     149 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 1e-30
                                       EEEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST............................THHHHHHHH CS
                     Ribosomal_L22   1 akgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk............................aakfvlklL 47 
                                       a+g +l++s+k++re++r++rgm +++A +yL++  + k+                            aa++vlk+L
  gi|330508493|ref|YP_004384921.1|  17 AMGMELHISPKHAREICRTLRGMRANRARDYLEDviALKRpvpfkrynrnvahrhglmgwdagrypekAAREVLKVL 93 
                                       57889******************************988999************************************ PP

                                       HHHHHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEEE CS
                     Ribosomal_L22  48 knaeanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvlk 103
                                        na+an e+kg++ ++l I ++    g++++++++rA+Gr++p + +++ ie+vl+
  gi|330508493|ref|YP_004384921.1|  94 DNAIANGEYKGMESEKLRIYHAGTLTGRTIQGWMPRAMGRATPKNTQTVTIEMVLT 149
                                       ******************************************************96 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:                      330  (0.0184059); 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: 00:00:00.38
# Mc/sec: 1205.23
//
Query:       gi|330508494|ref|YP_004384922.1|  [L=139]
Description: 30S ribosomal protein S19 [Methanosaeta concilii GP6]
Scores for complete 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-26   89.8   0.2    1.2e-25   89.2   0.2    1.2  1  Ribosomal_S19   Ribosomal protein S19
  ------ inclusion threshold ------
      0.085   11.9   0.0      0.091   11.8   0.0    1.1  1  Citrate_synt    Citrate synthase, C-terminal domain
       0.14   12.1   0.0       0.22   11.4   0.0    1.3  1  Myb_DNA-bind_7  Myb DNA-binding like


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   0.2     2e-29   1.2e-25       1      81 []      47     122 ..      44     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 2e-29
                                       .HHHSS.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS CS
                     Ribosomal_S19   1 rslkkg.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTr 76 
                                       rs+k+g  +++++ll++++      +k+ ++th R++ IlP+mvg  +++ynGk+f +ve+ +em+Gh +gEF++Tr
  gi|330508494|ref|YP_004384922.1|  47 RSIKRGlAKENKKLLANLK------NKDSVRTHIRNMLILPDMVGKSIEIYNGKSFEKVEVMPEMIGHFFGEFAMTR 117
                                       6778886677777777553......45679*********************************************** PP

                                       ----S CS
                     Ribosomal_S19  77 kpvkh 81 
                                        +v+h
  gi|330508494|ref|YP_004384922.1| 118 GRVQH 122
                                       ***99 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 ?   11.8   0.0   1.5e-05     0.091      13      82 ..      10      71 ..       2     104 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
                                      EEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHC.TTS--HHHHHHHHCSS CS
                      Citrate_synt 13 sevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelae.arklpekvlealealp 82
                                      s++ ++k+e +YRG+++ +La  k s+ee a l+     P + + +++k+ la+ ++kl  ++ ++ ++++
  gi|330508494|ref|YP_004384922.1| 10 SKLPKRKEEFLYRGRKMADLA--KLSIEELAGLF-----P-ARQRRSIKRGLAKeNKKLLANL-KNKDSVR 71
                                      666566677************..799***99999.....7.5666777777776233443333.2222333 PP

>> Myb_DNA-bind_7  Myb DNA-binding like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.7e-05      0.22      34      63 ..      38      67 ..      33      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.7e-05
                    Myb_DNA-bind_7 34 aklfpkrtrrqlKlKFkkEerknpelieka 63
                                      a lfp r+rr +K+   kE++k  +++++ 
  gi|330508494|ref|YP_004384922.1| 38 AGLFPARQRRSIKRGLAKENKKLLANLKNK 67
                                      679******************988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 940.96
//
Query:       gi|330508495|ref|YP_004384923.1|  [L=237]
Description: 50S ribosomal protein L2P [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-45  154.2   0.4      1e-44  151.7   0.3    1.9  2  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    1.1e-14   54.1   0.0    3.1e-14   52.7   0.0    1.8  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 ?    0.1   0.0     0.096   8.6e+02      49      68 ..      58      77 ..      35      82 .. 0.77
   2 !  151.7   0.3   1.2e-48     1e-44       2     123 ..      91     217 ..      90     224 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.096
                                      EEEETTS-EEEEETTSBEBE CS
                    Ribosomal_L2_C 49 tvklpSgevrkvssecrAti 68
                                       v l Sge+r++       i
  gi|330508495|ref|YP_004384923.1| 58 LVTLTSGEMRYILVPEGVCI 77
                                      68999*****9976655555 PP

  == domain 2  score: 151.7 bits;  conditional E-value: 1.2e-48
                                       SSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT CS
                    Ribosomal_L2_C   2 vGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehke 78 
                                       +Gn+lpl++ipeG  ++n+e++pg+gg++ars+G  a +va++  +++v+lpSge+++++ +c+AtiGvv++g++ +
  gi|330508495|ref|YP_004384923.1|  91 PGNTLPLSEIPEGIPICNVESQPGHGGQFARSSGVCAILVAHDVGQTVVQLPSGEMKWLNPKCMATIGVVAGGGRLD 167
                                       8*****************************************99********************************* PP

                                       ----STTHHHHT.....TBS----SSSS-TTTSSS--SSSS--SSSSTEE CS
                    Ribosomal_L2_C  79 kklgkAgrkrwl.....grrpkvrGvamnpvdHphGGGeGktksrkapvs 123
                                       k+l+kAg++  +     +++p vrGvamn+vdHp+GGG  ++++r + vs
  gi|330508495|ref|YP_004384923.1| 168 KPLVKAGKSFFKyrskpKNWPVVRGVAMNAVDHPFGGGGRQHPGRPKTVS 217
                                       *********9999999*********************9844555544433 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 !   52.7   0.0   3.4e-18   3.1e-14       6      76 ..      17      82 ..       4      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 3.4e-18
                                      --BSSTT--------EE-B--S-..--SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                      Ribosomal_L2  6 gritvrhrggGhkkkyrlidfkr..nkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                      +r+++++++         i++ +  ++e+vkg V++i++Dp+R+Ap++lv + +ge ryi+ peg+ +G+++ 
  gi|330508495|ref|YP_004384923.1| 17 YRAPSHRYRA-------DIKHLKrdQNETVKGIVQDIMRDPARTAPVGLVTLTSGEMRYILVPEGVCIGQEIA 82
                                      5555555555.......244433233455*****************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.67
# Mc/sec: 1071.53
//
Query:       gi|330508496|ref|YP_004384924.1|  [L=82]
Description: 50S ribosomal protein L23 [Methanosaeta concilii GP6]
Scores for complete 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-17   61.7   1.5    2.2e-16   60.0   1.5    1.7  1  Ribosomal_L23  Ribosomal protein L23
     0.0065   16.5   1.2       0.13   12.3   0.2    2.3  2  SapB_1         Saposin-like type B, region 1
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.011   15.5   0.0    1.1  1  DUF3804        Protein of unknown function (DUF3804)
      0.069   13.8   0.0      0.076   13.6   0.0    1.1  1  HNF-1_N        Hepatocyte nuclear factor 1 (HNF-1), N terminu


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 !   60.0   1.5   4.8e-20   2.2e-16       2      61 ..       2      62 ..       1      74 [. 0.88

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 4.8e-20
                                      SEEEE--SHHHHHHHTTE..EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESS CS
                     Ribosomal_L23  2 vilkPvitEkstklaekn.kyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrv 61
                                      +i++P++tEk t++ ++n ++ F V+ +a+K++ikka+e l++V+V +V+t++  + +k+ 
  gi|330508496|ref|YP_004384924.1|  2 IIKSPYVTEKVTSMIDSNdTLEFLVNTNATKPQIKKALEDLYDVDVLAVRTMITSQGQKKA 62
                                      899************99658*********************************98877653 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 !    5.2   0.2    0.0048        21       8      25 ..       7      24 ..       7      28 .. 0.85
   2 !   12.3   0.2   2.9e-05      0.13      13      32 ..      22      41 ..      20      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0048
                                      HHHHHHHHHH-SS--HHH CS
                            SapB_1  8 fvVkeveklLkdNkTeee 25
                                      +v  +v +++ +N+T e 
  gi|330508496|ref|YP_004384924.1|  7 YVTEKVTSMIDSNDTLEF 24
                                      68899**********875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.9e-05
                                      HHHHH-SS--HHHHHHHHHH CS
                            SapB_1 13 veklLkdNkTeeeIieaLek 32
                                      +e l++ N+T+ +I++aLe 
  gi|330508496|ref|YP_004384924.1| 22 LEFLVNTNATKPQIKKALED 41
                                      788999************97 PP

>> DUF3804  Protein of unknown function (DUF3804)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   2.4e-06     0.011       9      58 ..       2      51 ..       1      72 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-06
                                      HHHHHSSTTTTTTHHHHHB-TT--EE-TTS-EE-HHHHHHHHTSSSEEEE CS
                           DUF3804  9 lleafadrernksflldnatadflairpsgnpliakglenmydsddlvle 58
                                      ++++   +e+  s++ +n t +fl+   ++ p i k le++yd d l + 
  gi|330508496|ref|YP_004384924.1|  2 IIKSPYVTEKVTSMIDSNDTLEFLVNTNATKPQIKKALEDLYDVDVLAVR 51
                                      66777789999*********************************998775 PP

>> HNF-1_N  Hepatocyte nuclear factor 1 (HNF-1), N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.7e-05     0.076       4      36 ..      20      52 ..      17      79 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                           HNF-1_N  4 elLqrllesGltkeelihALedldrldrehgek 36
                                      ++L+ l+++ +tk+++ +ALedl ++d   +  
  gi|330508496|ref|YP_004384924.1| 20 DTLEFLVNTNATKPQIKKALEDLYDVDVLAVRT 52
                                      78999********************98444222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 549.75
//
Query:       gi|330508497|ref|YP_004384925.1|  [L=257]
Description: 50S ribosomal protein L4/L1 family [Methanosaeta concilii GP6]
Scores for complete 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-46  155.9   0.5    1.1e-45  155.7   0.5    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 !  155.7   0.5   6.2e-50   1.1e-45       1     191 [.      16     249 ..      16     250 .. 0.94

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 6.2e-50
                                       EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.......STTSTT CS
                      Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.......spiarg 69 
                                       +eL p+vF++++r+d+i+rav+a +anr q ++ +  a++ +s+   ++++  G+G +Rv +++       +p+a+g
  gi|330508497|ref|YP_004384925.1|  16 IEL-PAVFEEEYRPDIIKRAVLAAQANRLQAYGPHFyAGMNTSA--VSWGT--GHGTSRVLRLKngrraagVPMAVG 87 
                                       789.********************************9*******..5****..************************ PP

                                       ---SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES.---..-S.........S--HHHHHHHHHHTT-. CS
                      Ribosomal_L4  70 GgvahgpkperdystklnkKvrrlAlrsaLsakakqglllvvd.nle.ple.........esktkelvellkklgl. 134
                                       G++ h+p+p+  ys+k+nkK+rr+A+rsa++a+a++gl+++++ +++ +l+          skt++++++l + gl 
  gi|330508497|ref|YP_004384925.1|  88 GRRSHAPQPNAVYSEKVNKKERRKAIRSAIAATASSGLVEARGhKFSrELPvvakndleaLSKTSDIIKFLMAAGLw 164
                                       *******************************************87776777889999999*************8887 PP

                                       .........................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEE CS
                      Ribosomal_L4 135 .........................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvit 182
                                                                 +ks+Liv+++ d +l +aarnlpgv+ ++v+ ln++ l+++++    +v+t
  gi|330508497|ref|YP_004384925.1| 165 ddvlrakagrhiragkgklrgrkykGRKSLLIVAGN-DAGLGKAARNLPGVDFVTVDMLNAELLAPGTRagrlTVWT 240
                                       888888888888888888888888777899999986.**************************************** PP

                                       HHHHHHHHH CS
                      Ribosomal_L4 183 ksaveklee 191
                                       +s +ekl+ 
  gi|330508497|ref|YP_004384925.1| 241 ESSLEKLAG 249
                                       ******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 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:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1775.89
//
Query:       gi|330508498|ref|YP_004384926.1|  [L=334]
Description: 50S ribosomal protein L3 [Methanosaeta concilii GP6]
Scores for complete 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-91  304.6   0.0    6.9e-90  301.7   0.0    1.9  1  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.7   0.0   3.8e-94   6.9e-90       7     368 ..       5     332 ..       1     333 [. 0.94

  Alignments for each domain:
  == domain 1  score: 301.7 bits;  conditional E-value: 3.8e-94
                                       XXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC-- CS
                      Ribosomal_L3   7 eaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtvvetpp 83 
                                       ++pr+gsl ++prkRa++e+++++s+ ++d+     + +f+GyKaGmth+   +d+p s ++++e+  +vtv+e pp
  gi|330508498|ref|YP_004384926.1|   5 HRPRRGSLAYSPRKRAKSEVPRIRSWLEEDKA---RIAGFAGYKAGMTHVMMIDDRPRSLTEGMEISTPVTVLEVPP 78 
                                       78*************************99998...899*************************************** PP

                                       EEEEEEEEEEEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHHHSCSCE CS
                      Ribosomal_L3  84 mvivgvvgyvetprGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadleeikkeasvv 160
                                       m +v+v++y+  + Glr+  + wae+ls e+ r +               +++    +++ +   dl ++ +  + v
  gi|330508498|ref|YP_004384926.1|  79 MNVVAVRAYESYNGGLRPAGELWAENLSPELSRAM---------------TVPK---KTRGTAPGDLVALGDDIADV 137
                                       *********************************99...............2222...3334445589999999999* PP

                                       EEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT CS
                      Ribosomal_L3 161 rviahtvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGkGfeGvvkRWg 237
                                       rv++ht    + ++ +K ++++E+ +ngG++ ++l fa+  l ++v++++vF+ g+l+D  +vtkGkG++G+v+RWg
  gi|330508498|ref|YP_004384926.1| 138 RVLVHTNPTLVSGIPKKVPEIMEMPINGGSMNDRLSFAQTLLGQQVPISSVFELGDLMDTSAVTKGKGTQGPVRRWG 214
                                       ***************************************************************************** PP

                                       ----STTTSSS..SSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS..SS.TT CS
                      Ribosomal_L3 238 vkklprkthrg..lRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdltekeitPmG 312
                                       +   +rk++r+   R+v+++g+w+pa++s+ v++ Gq+Gyh+Rte+nk+++ ig+              + +itP+G
  gi|330508498|ref|YP_004384926.1| 215 IAMAKRKHARTgkVRHVGNLGPWHPAHISWRVPQLGQMGYHQRTEYNKRLMFIGT-------------DGSKITPDG 278
                                       ***********999*****************************************.............4679***** PP

                                       TCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TTCTS CS
                      Ribosomal_L3 313 GfvhyGevkndfilvkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidtaskf 368
                                       Gf+ yG++kn++il+kGsvpGp krlv++r+++++ ++  + +e+   ++++ sk+
  gi|330508498|ref|YP_004384926.1| 279 GFPGYGVIKNQYILIKGSVPGPIKRLVRMRHAMRPGKNFVKAPEL--LHVSQESKQ 332
                                       ***********************************9987777777..456666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2377.54
//
Query:       gi|330508499|ref|YP_004384927.1|  [L=279]
Description: hypothetical protein MCON_2704 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-55  189.0   0.0    1.5e-55  188.8   0.0    1.0  1  Methyltrn_RNA_3  Putative RNA methyltransferase
    0.00066   19.9   0.0        1.4    9.0   0.0    2.2  2  SpoU_methylase   SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_3  Putative RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.8   0.0   1.6e-59   1.5e-55       3     286 .]       8     272 ..       6     272 .. 0.89

  Alignments for each domain:
  == domain 1  score: 188.8 bits;  conditional E-value: 1.6e-59
                   Methyltrn_RNA_3   3 siaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelFpl 79 
                                        i+iPss++ + ++ +  t ++gqIARaaa+F+V++iv+++d+e ++      s f++ +L+Y+etP+YLrk l p 
  gi|330508499|ref|YP_004384927.1|   8 AILIPSSLTMESRDTRVNTLKVGQIARAAAVFRVSRIVIYRDQEYND------SRFISMILRYMETPQYLRKLLIPR 78 
                                       699*****************************************875......78********************** PP

                   Methyltrn_RNA_3  80 hkelkyaglLppldaphhl....rsse.egeyreGvvvekskekkskkklVniGlkkevklelkqevpegtRVtVkl 151
                                       ++el+++g+Lppl++ hh     ++s   ge+r G vve+  ++     +V+iG+++++ l ++++ p+g R  V++
  gi|330508499|ref|YP_004384927.1|  79 KEELRHVGMLPPLRTSHHPinskSESLkIGEFRVGAVVESVGSDGG--VWVEIGINRPIPLRTGEKYPVGQRLNVRI 153
                                       *******************997533334789****99998765544..5**************************** PP

                   Methyltrn_RNA_3 152 sseesveakvVspsepreeaglywGYsVrlakslsavftespfeggydlsigtserge.kveeklaelekkkefkhl 227
                                        s+e+  a+ V++++      +ywGY+ ++++sl+++++      + + ++++s++g+  + ++l el ++ ++++l
  gi|330508499|ref|YP_004384927.1| 154 FSQEPLAAEPVDQKDI----PHYWGYETEVVDSLESYLESM----RDTRIVLASRSGRaITPQALLELVQSGNKRDL 222
                                       *************999....5*****************997....45555559*99996677888888777789*** PP

                   Methyltrn_RNA_3 228 livfGg.vrgleaaleadeelklegekaeelFdlwlntvpnqgsrtirtEEavliaLalL 286
                                        ++fG+  rgl+a+l ++           + +  ++nt+p+qg++t+r+EEav+++LalL
  gi|330508499|ref|YP_004384927.1| 223 AVAFGSpARGLDAFLSKE---------SMKRY-EMINTIPHQGTETVRVEEAVFATLALL 272
                                       ******99****999555.........22233.479*********************987 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00016       1.4      15      46 ..      29      58 ..      25      74 .. 0.79
   2 !    8.6   0.0   0.00022         2      58     125 ..     177     254 ..     170     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHTT-SEEEEESGSSCTCGSHHHH CS
                    SpoU_methylase 15 lGaiaRtakafgaselvlvkprsadllnpeak 46
                                      +G iaR+a++f +s++v+ ++++   ++++++
  gi|330508499|ref|YP_004384927.1| 29 VGQIARAAAVFRVSRIVIYRDQEY--NDSRFI 58
                                      7*****************875543..555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00022
                                       EEEESSHHHHHHHHCCCTEEEEEESTT-SEGC.CSHHH........TTEEEEEEBTTTBS....-HHHHCTSSEEEE CS
                    SpoU_methylase  58 lkvvdsleealkelkeegfalvatslkgksls.eidlk........ekvalvfGnEdkGl....snelleladrlvk 121
                                        +vvdsle++l+ ++++  ++v +s++g+ ++ ++ l         +  a+ fG+  +Gl    s+e +++++ + +
  gi|330508499|ref|YP_004384927.1| 177 TEVVDSLESYLESMRDT--RIVLASRSGRAITpQA-LLelvqsgnkRDLAVAFGSPARGLdaflSKESMKRYEMINT 250
                                       5899***********99..8888888888888433.222445566799***********722225666777777777 PP

                                       ---- CS
                    SpoU_methylase 122 Ipms 125
                                       Ip +
  gi|330508499|ref|YP_004384927.1| 251 IPHQ 254
                                       7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 1467.87
//
Query:       gi|330508500|ref|YP_004384928.1|  [L=307]
Description: hypothetical protein MCON_2706 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


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:                      338  (0.0188521); 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: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.57
# Mc/sec: 1631.13
//
Query:       gi|330508501|ref|YP_004384929.1|  [L=155]
Description: hypothetical protein MCON_2707 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.6   0.0      0.037   13.2   0.0    1.1  1  PIF1      PIF1-like helicase


Domain annotation for each model (and alignments):
>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.1e-06     0.037     187     240 ..      95     148 ..      91     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-06
                                       -STTTT...........HHHHHHHHHHHCT---CCCCHH............... CS
                              PIF1 187 nmRllsesldetekkelkeFskwllkigdGkineedeeealieiPedlllkkse 240
                                         R +++ l++  +ke + + +w+l+ig+  +++++e+ ++++ Pe++ll++ +
  gi|330508501|ref|YP_004384929.1|  95 ACRSAAAALTKVSSKEAAAYKEWVLAIGQKVAEAAKEQGVAVSEPEEVLLNEVS 148
                                       578888899999*****************9999999999**********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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 0.33s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 907.12
//
Query:       gi|330508502|ref|YP_004384930.1|  [L=73]
Description: hypothetical protein MCON_2710 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 516.54
//
Query:       gi|330508503|ref|YP_004384931.1|  [L=376]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-22   78.2   0.1    8.4e-22   76.9   0.1    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.8e-21   76.6   0.0    3.9e-21   75.5   0.0    1.5  1  OrfB_IS605      Probable transposase
    3.9e-18   64.7   2.9    9.6e-18   63.4   2.9    1.7  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0016   18.4   0.3     0.0027   17.7   0.3    1.3  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.061   12.8   0.5       0.47   10.0   0.1    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.12   12.1   0.8        0.2   11.3   0.8    1.4  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.18   11.7   0.3       0.18   11.7   0.3    2.0  2  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.23   10.9   0.9        1.2    8.6   0.9    2.0  1  zf-ribbon_3     zinc-ribbon domain
       0.45   10.1   4.9        5.9    6.6   0.1    2.8  3  RecR            RecR protein


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 !   76.9   0.1   4.2e-25   8.4e-22       1      68 [.     293     360 ..     293     361 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 4.2e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++ l +  +yka  +G  v++v+p++TSk Cs+Cg   +++ls+r+++C++Cg+++drD+nAaiNil+
  gi|330508503|ref|YP_004384931.1| 293 WNMLVTLTSYKAASAGSVVVLVDPRNTSKMCSRCGTLIEKSLSDRVHNCTQCGLSMDRDWNAAINILR 360
                                       667777889*********************************************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0     2e-24   3.9e-21       4     117 ..     168     279 ..     165     281 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 2e-24
                        OrfB_IS605   4 veveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       ve e+  lp+ k + ++giD+G++ +at ++++   ++ ++r++++++ +la+++++l++  k++  +kka + + r
  gi|330508503|ref|YP_004384931.1| 168 VETEDVpLPPWKDGAVVGIDVGLESFATFSNGE---TIANPRFFREEEHELARAQRKLSKAPKGTPDRKKALKVVER 241
                                       5544334999999********************...***************************************** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       +h++++++r +++h+++++l+++   ++ e+Ln+++m+
  gi|330508503|ref|YP_004384931.1| 242 VHERIANKRYEFAHQVSHNLVDRFGLIAFEDLNIKGMV 279
                                       *************************************7 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   2.9   4.8e-21   9.6e-18       1      47 []       1      46 [.       1      46 [. 0.99

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 4.8e-21
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkayk+rlyPT  Q +k++rt++ +R+ YN+ La+rk+a+e+egk
  gi|330508503|ref|YP_004384931.1|  1 M-LKAYKFRLYPTRSQITKMERTLDLCRWTYNQTLAYRKNAWENEGK 46
                                      8.******************************************998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   1.3e-06    0.0027      10      44 ..     318     354 ..     314     357 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + +++Cs+Cgt +++  +   ++C +Cg ++d +++ 
  gi|330508503|ref|YP_004384931.1| 318 NTSKMCSRCGTLIEKSLSdrVHNCTQCGLSMDRDWNA 354
                                       6789*********9777799************99986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00024      0.47      11      31 ..     312     332 ..     308     337 .. 0.84
   2 ?    0.4   0.1      0.23   4.6e+02      22      28 ..     341     347 ..     339     351 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00024
                                       CHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon  11 lveDpergelvCtdCGlVled 31 
                                       +++Dp ++   C++CG+++e 
  gi|330508503|ref|YP_004384931.1| 312 VLVDPRNTSKMCSRCGTLIEK 332
                                       68999*9999*********96 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.23
                                       ESSSSBE CS
                      TF_Zn_Ribbon  22 CtdCGlV 28 
                                       Ct CGl 
  gi|330508503|ref|YP_004384931.1| 341 CTQCGLS 347
                                       *****85 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.8    0.0001       0.2       6      29 ..     323     346 ..     318     348 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                     zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCgl 29 
                                       C+rCG+  e++  ++   C +Cgl
  gi|330508503|ref|YP_004384931.1| 323 CSRCGTLIEKSLSDRVHNCTQCGL 346
                                       ***********************8 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.84   1.7e+03      37      45 ..     278     286 ..     276     289 .. 0.82
   2 ?   11.7   0.3   8.9e-05      0.18      10      38 ..     319     348 ..     315     351 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.84
                                       EE-CCCCTT CS
                              C1_1  37 lvHkkChek 45 
                                        vH++C+ k
  gi|330508503|ref|YP_004384931.1| 278 MVHNHCLAK 286
                                       59****876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 8.9e-05
                                       S--B-TTT-SB--S.SSS-EEEETTT--EE CS
                              C1_1  10 qptfCkhCgeflwg.kekqglkCswCkllv 38 
                                        ++ C+ Cg ++++ ++ +   C++C+l++
  gi|330508503|ref|YP_004384931.1| 319 TSKMCSRCGTLIEKsLSDRVHNCTQCGLSM 348
                                       5789********999***********9976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.9   0.00062       1.2       5      24 ..     323     346 ..     320     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00062
                       zf-ribbon_3   5 CPnCGa.p...lssddnvCpyCGt 24 
                                       C++CG+ +   ls+++ +C+ CG 
  gi|330508503|ref|YP_004384931.1| 323 CSRCGTlIeksLSDRVHNCTQCGL 346
                                       999997555557899*******96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.6   5.2e+03       6      16 ..      72      82 ..      72      83 .. 0.87
   2 ?    6.6   0.1     0.003       5.9      13      28 ..     317     332 ..     312     334 .. 0.77
   3 ?    5.4   0.3    0.0069        14      12      26 ..     334     348 ..     332     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.6
                                      HHHHHHHHHH- CS
                              RecR  6 aeaLqeakekv 16
                                      a++Lq++ e+v
  gi|330508503|ref|YP_004384931.1| 72 AQTLQNVQERV 82
                                      7899**99987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.003
                                       HHH-EE-TTT--EESS CS
                              RecR  13 kekvrhCsrCgnltee 28 
                                       +++ + CsrCg+l e+
  gi|330508503|ref|YP_004384931.1| 317 RNTSKMCSRCGTLIEK 332
                                       667799******9776 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0069
                                       HHHH-EE-TTT--EE CS
                              RecR  12 akekvrhCsrCgnlt 26 
                                       + ++v+ C +Cg   
  gi|330508503|ref|YP_004384931.1| 334 LSDRVHNCTQCGLSM 348
                                       679********9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); 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:                         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 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2790.36
//
Query:       gi|330508504|ref|YP_004384932.1|  [L=464]
Description: MATE efflux family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-54  183.7  44.6    2.1e-32  112.0  13.8    2.7  3  MatE             MatE
    1.7e-12   47.6  10.3    1.7e-12   47.6  10.3    5.7  6  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
        2.2    8.6   6.8        1.2    9.4   0.2    3.1  3  COX7C            Cytochrome c oxidase subunit VIIc


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 !  112.0  13.8   3.6e-36   2.1e-32       1     161 []      33     192 ..      33     192 .. 0.99
   2 ?   -3.0   0.1      0.82   4.9e+03      79      95 ..     207     218 ..     200     235 .. 0.52
   3 !   81.4  18.1     9e-27   5.4e-23       1     155 [.     254     413 ..     254     425 .. 0.93

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 3.6e-36
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+++++l+   ++l+  ++v++lgs+alAav+++++i+++++ ++ gl++++++ +++++Ga ++++a ++++++l+
  gi|330508504|ref|YP_004384932.1|  33 PMIVAMLILAAYNLVNAVWVAGLGSDALAAVGFVTPIFMVVVGLSNGLGAGVSSSISRRIGAQDKRGADNTTMHALL 109
                                       9**************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       l+ll+s i+++++ll  e++ls +++    l la++y +i++ g +++++++++++ilrg g+tk+++y++ +++l+
  gi|330508504|ref|YP_004384932.1| 110 LVLLVSMILTAVLLLTLEPLLSAMGAGS-SLGLAMEYGNIVFSGSIFMVFTNIAYAILRGEGDTKRTMYAMGAGSLI 185
                                       ************************9888.5*********************************************** PP

                              MatE 155 niplnyl 161
                                       n++l+++
  gi|330508504|ref|YP_004384932.1| 186 NAVLDPI 192
                                       ****986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.82
                              MatE  79 llllsliiallvllfse 95 
                                       ++++sl+i+++      
  gi|330508504|ref|YP_004384932.1| 207 GTVISLLIVAM-----V 218
                                       33333333333.....2 PP

  == domain 3  score: 81.4 bits;  conditional E-value: 9e-27
                              MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl 76 
                                       P+ +e+ll+s+  +i+++++ r+ g++a+A+++++++++++ +++l++++ta  +++g a+Ga+++ ++ +++++++
  gi|330508504|ref|YP_004384932.1| 254 PASVEFLLYSIDAIIINSMLVRVsGTDAVAVYTAGWRVIMMATIPLIAIATAEISVAGAAIGARRYGNLPVIHNYST 330
                                       999************************************************************************** PP

                              MatE  77 illlllsliiallvllfseqilslftqdee...vlelakrylrililgipalalqlvlsgilrgagktkvplyisli 150
                                       +l+++++ ++al++ +f++qi  +ft+++e   ++     ++++++l++p++++ ++++  ++gagk  ++l ++++
  gi|330508504|ref|YP_004384932.1| 331 KLGFAIGTVTALITGIFAPQITMFFTYTPEsahLAGTMVAFMHVMCLFYPFMSPGIMSACLFQGAGKGLTSLLLNVL 407
                                       ******************************4444444467899********************************99 PP

                              MatE 151 sl.lln 155
                                       +  +l 
  gi|330508504|ref|YP_004384932.1| 408 RDvVLI 413
                                       875554 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 ?   -0.7   3.0      0.22   1.3e+03      93     137 ..      32      73 ..      14      80 .. 0.43
   2 ?    2.4   3.2     0.025   1.5e+02      30      65 ..     107     142 ..     102     151 .. 0.82
   3 !   47.6  10.3   2.9e-16   1.7e-12       8      85 ..     152     233 ..     147     287 .. 0.80
   4 ?   -1.1   2.0       0.3   1.8e+03      20      61 ..     271     315 ..     255     318 .. 0.57
   5 ?   -2.5  12.4      0.81   4.9e+03      45     133 ..     320     424 ..     305     427 .. 0.64
   6 ?    2.8   7.5     0.019   1.2e+02       3      81 ..     373     454 ..     371     463 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.22
                   Polysacc_synt_C  93 kpllaalvmgiv.vylllllllgllllaalalllavlvgalvYlll 137
                                        p+++a+++ ++  +  + ++ gl +      l+av++   +++++
  gi|330508504|ref|YP_004384932.1|  32 GPMIVAMLILAAyNLVNAVWVAGLGS----DALAAVGFVTPIFMVV 73 
                                       33444444333312222223333332....3333333333333332 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.025
                   Polysacc_synt_C  30 ialkalvigalvklilnllliplfgivGaaiatvla 65 
                                       ++l++l++++++  +l l l pl++++Ga  +  la
  gi|330508504|ref|YP_004384932.1| 107 ALLLVLLVSMILTAVLLLTLEPLLSAMGAGSSLGLA 142
                                       567889999999999999999999999998776666 PP

  == domain 3  score: 47.6 bits;  conditional E-value: 2.9e-16
                   Polysacc_synt_C   8 siiflslstvlssiLqglgrqkialkalvigalvklilnllliplf..givGaaiatvlallvvavlnlya..lrrl 80 
                                       + if++++++  +iL g g +k++++a+ +g l++ +l  +li++   gi Gaa++tv++ll+va++++y+  +++ 
  gi|330508504|ref|YP_004384932.1| 152 GSIFMVFTNIAYAILRGEGDTKRTMYAMGAGSLINAVLDPILIYWAgmGIAGAAWGTVISLLIVAMVQIYWliVKKD 228
                                       689****************************************8773368******************665114556 PP

                   Polysacc_synt_C  81 lgikl 85 
                                       + ++l
  gi|330508504|ref|YP_004384932.1| 229 TYVSL 233
                                       66655 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.3
                   Polysacc_synt_C  20 siLqglgrqkialkalv...igalvklilnllliplfgivGaaia 61 
                                       s+L  +  +++++++++   + +++ + l  + + ++++ Gaai+
  gi|330508504|ref|YP_004384932.1| 271 SMLVRVSGTDAVAVYTAgwrVIMMATIPLIAIATAEISVAGAAIG 315
                                       444444444443333331114455666666777788888888876 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 0.81
                   Polysacc_synt_C  45 lnllliplfgi.vGaaiatvlallvvavln...lyalrrllgikl.......ellrrllkpllaalvmgiv.....v 105
                                        nl+ i+ +++ +G ai+tv al+++++     +++ +     +l       + +  l+ p+++  +m+++      
  gi|330508504|ref|YP_004384932.1| 320 GNLPVIHNYSTkLGFAIGTVTALITGIFAPqitMFFTYTPESAHLagtmvafMHVMCLFYPFMSPGIMSAClfqgaG 396
                                       6999999998879***********99987643333333333333366776665556666888888888888444444 PP

                   Polysacc_synt_C 106 ylllllllgllllaalalllavlvgalv 133
                                        +l++lll++l++  l++++a ++g+++
  gi|330508504|ref|YP_004384932.1| 397 KGLTSLLLNVLRDVVLITMVAFILGMVL 424
                                       5555555555555544666666566554 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.019
                   Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigal...vklilnllliplfgivGaaiatvlallvvavlnlya 76 
                                        +++l  +f+s  ++++ ++qg g+  + l+ +v+  +     +++ l ++  +g  G+ +++v++ +++++l + +
  gi|330508504|ref|YP_004384932.1| 373 HVMCLFYPFMSPGIMSACLFQGAGKGLTSLLLNVLRDVvliTMVAFILGMVLGLGQEGIWWGIVFGNIAGSLLSYLW 449
                                       6899999******************9999988886544111444444445566677999999999999999999888 PP

                   Polysacc_synt_C  77 lrrll 81 
                                       +r ++
  gi|330508504|ref|YP_004384932.1| 450 ARLYI 454
                                       77665 PP

>> COX7C  Cytochrome c oxidase subunit VIIc
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.073   4.4e+02      47      60 ..      61      74 ..      56      78 .. 0.85
   2 ?    9.4   0.2    0.0002       1.2      26      57 ..     319     352 ..     308     358 .. 0.89
   3 ?   -1.3   0.7      0.45   2.7e+03      37      56 ..     362     382 ..     354     384 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.073
                                      HHHHHHHHHHHHHH CS
                             COX7C 47 lgvgFalPFlavrw 60
                                       +vgF +P ++v++
  gi|330508504|ref|YP_004384932.1| 61 AAVGFVTPIFMVVV 74
                                      689*****999987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0002
                                       TTSSSS..--SSHHHHHHHHHHHHHHHHHHHHHH CS
                             COX7C  26 ysnLPF..sknnKipfavkywgflgvgFalPFla 57 
                                       y nLP   + + K +fa+  ++ l++g+++P ++
  gi|330508504|ref|YP_004384932.1| 319 YGNLPVihNYSTKLGFAIGTVTALITGIFAPQIT 352
                                       78****9999999******************776 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHH.HHHHHHH CS
                             COX7C  37 ipfavkywgflgv.gFalPFl 56 
                                       + +a  +++f+ v +++ PF+
  gi|330508504|ref|YP_004384932.1| 362 AHLAGTMVAFMHVmCLFYPFM 382
                                       677888999996526888997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.38
# Mc/sec: 3668.07
//
Query:       gi|330508505|ref|YP_004384933.1|  [L=658]
Description: excinuclease ABC subunit B [Methanosaeta concilii GP6]
Scores for complete 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-29   99.4   0.4    2.2e-28   98.2   0.4    1.7  1  UvrB_inter      UvrB interaction domain
    3.8e-22   77.9   1.6    9.1e-22   76.6   1.6    1.7  1  UvrB            Ultra-violet resistance protein B
    1.6e-15   57.4   0.2    5.4e-15   55.7   0.0    1.9  2  Helicase_C      Helicase conserved C-terminal domain
    1.7e-13   50.9   0.0    3.8e-12   46.5   0.0    2.4  2  ResIII          Type III restriction enzyme, res subunit
    1.3e-06   27.9   7.0    4.8e-06   26.1   7.0    2.0  1  UVR             UvrB/uvrC motif
    1.7e-05   24.7   0.0    0.00069   19.4   0.0    2.9  3  DEAD            DEAD/DEAH box helicase
     0.0095   16.2   0.5      0.073   13.3   0.0    2.8  4  AAA_22          AAA domain
  ------ inclusion threshold ------
      0.015   15.6   0.4        3.3    8.0   0.1    3.1  3  AAA_19          AAA domain
      0.021   14.5   0.1        0.2   11.3   0.0    2.5  3  SWI2_SNF2       SWI2/SNF2 ATPase
      0.025   14.7   0.1       0.22   11.7   0.0    2.4  2  AAA_33          AAA domain
      0.047   14.0   0.1        0.2   12.0   0.1    2.2  2  NIBRIN_BRCT_II  Second BRCT domain on Nijmegen syndrome break
      0.068   12.9   0.0       0.36   10.5   0.0    2.2  2  AAA_30          AAA domain
      0.073   12.0   0.0       0.13   11.2   0.0    1.3  1  Kinesin         Kinesin motor domain
       0.11   12.5   0.0        1.6    8.8   0.0    2.6  2  DUF3969         Protein of unknown function (DUF3969)


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 !   98.2   0.4   1.8e-31   2.2e-28       1      91 []     172     261 ..     172     261 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 1.8e-31
                        UvrB_inter   1 lelkvgqkidreellrkLvelqYerndvelkrGtFrvrGdtveifpasaeevairieffgdeiesireidpltgksl 77 
                                       +elkv+++i+r+++l++Lv++ Yer+d++l++G Frv+G+t++i+p +  +++irie+fg+++e+i+e+d +tgk +
  gi|330508505|ref|YP_004384933.1| 172 FELKVNERISRKDILERLVDILYERSDLDLSPGRFRVNGETIDIIPGY-FNNIIRIELFGNKVERISEVDRITGKRV 247
                                       589*********************************************.6*************************** PP

                        UvrB_inter  78 ekleeitifPakhf 91 
                                       e+++ + ++Pa+h+
  gi|330508505|ref|YP_004384933.1| 248 EDMSYFFVYPARHY 261
                                       *************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 !   76.6   1.6   7.1e-25   9.1e-22       1      43 []     559     601 ..     559     601 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 7.1e-25
                                       EE-SS--HHHHHHHHHHHHHHHHHHHHHHHHT------XXXXX CS
                              UvrB   1 lYADkiTdSMkkAideTerRReiQeaYNeehgItPktikKkir 43 
                                       lYAD++T+S+kkA++ TerRR++Q+aYN+ehgI+P+tikK+ir
  gi|330508505|ref|YP_004384933.1| 559 LYADRMTGSIKKAMETTERRRSLQMAYNQEHGIIPQTIKKPIR 601
                                       8****************************************96 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         7     9e+03      13      29 ..      67      83 ..      42     104 .. 0.59
   2 !   55.7   0.0   4.2e-18   5.4e-15      14     109 ..     451     551 ..     441     553 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7
                                      TTTTSEEEEEESSHHHH CS
                        Helicase_C 13 eeeggkilifvntidrl 29
                                      +++++ +l++v++++ +
  gi|330508505|ref|YP_004384933.1| 67 SQVQKPTLVIVHNKTLA 83
                                      33444444444444433 PP

  == domain 2  score: 55.7 bits;  conditional E-value: 4.2e-18
                                       TTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEE CS
                        Helicase_C  14 eeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVi 89 
                                       ++g+++l+ + t++ +e+ +++l ++++i++ +lh+e++  er ei+++ + g++dvL+  + + +G+dip+v ++ 
  gi|330508505|ref|YP_004384933.1| 451 SRGDRALVTTLTKRLAEElTDYL-SQNDIRARYLHSEIQPLERTEIIRELRLGKFDVLVGINLLREGLDIPEVGFIG 526
                                       67899999999999888767777.7788************************************************* PP

                                       ESSSS.....SSHHHHHHHHTTSSS CS
                        Helicase_C  90 nfdlp.....rnvtsyiqriGRtgR 109
                                       ++d++     r+ +s+iq iGR+ R
  gi|330508505|ref|YP_004384933.1| 527 ILDADkegflRDEKSLIQTIGRASR 551
                                       *****77777778**********99 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0     3e-15   3.8e-12       7      85 ..      29     105 ..      23     152 .. 0.75
   2 ?    1.8   0.0      0.16   2.1e+02     134     144 ..     338     351 ..     265     403 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3e-15
                                       HHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG... CS
                            ResIII   7 yQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayk 83 
                                        Q eai++l+  l+ ++++   +   TG+GKT++ a++i +++k      +l++v++k+l eq+++efk+f+++++ 
  gi|330508505|ref|YP_004384933.1|  29 SQPEAIDQLVLGLQ-RNERFQTLIGVTGSGKTYTVANVISQVQK-----PTLVIVHNKTLAEQLYNEFKEFFPDNRV 99 
                                       699**********8.55555559999*****************9.....8***********************9986 PP

                                       .....G CS
                            ResIII  84 e....i 85 
                                       e     
  gi|330508505|ref|YP_004384933.1| 100 EyfisY 105
                                       555442 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.16
                                       S...EEEEETGGGT CS
                            ResIII 134 d...viiiDEaHrl 144
                                       +   ++iiDE+H +
  gi|330508505|ref|YP_004384933.1| 338 PddfLLIIDESHQT 351
                                       2666999*****87 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   7.0   3.7e-09   4.8e-06       3      35 ..     621     653 ..     620     654 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.7e-09
                               UVR   3 likeLeeemeeAaenedFEkAAklRDqinalkk 35 
                                        i eLe+em  Aae+++FE+A +lRD +++l++
  gi|330508505|ref|YP_004384933.1| 621 AIIELEAEMMAAAERLEFERAIQLRDTVRRLER 653
                                       589****************************97 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.4e-07   0.00069      17      73 ..      48      96 ..      28     129 .. 0.75
   2 ?    1.3   0.0       0.2   2.5e+02     124     169 ..     342     404 ..     340     410 .. 0.59
   3 ?   -2.1   0.0       2.2   2.8e+03      47     103 ..     453     509 ..     443     511 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.4e-07
                                      EEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 17 vlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky 73
                                        + + TGsGKT   +  v+++v       ++ +l+++  + Laeq +n++k+f+  
  gi|330508505|ref|YP_004384933.1| 48 QTLIGVTGSGKTYT-VANVISQV-------QKPTLVIVHNKTLAEQLYNEFKEFFPD 96
                                      457789******98.66777666.......345699******************984 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.2
                                       EEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTT..........................SEEEEEESSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........................xxxxxxxxxx RF
                              DEAD 124 flVlDEadrlldqgfsdfinrilnqlpqitcdgklq..........................rqvivlSATl 169
                                       +l++DE ++ l q   + +nr  ++ ++       +                          r+vi++SAT+
  gi|330508505|ref|YP_004384933.1| 342 LLIIDESHQTLPQ--LRAMNRGDRSRKK-------NlvdygfrlpssydnrpldfeeferfmRNVIFVSATP 404
                                       5899999999888..2222322222211.......1222344455566677777888877777788888887 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.2
                                       S-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEETTSSHHHHHHHHHTT.CSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxx RF
                              DEAD  47 gpkalivePtreLaeqtlnnlkkfkkyidlrvl.liiggvaardqlskldng.vdivvg 103
                                       g +al+ + t+ Lae+  + l++       r+l + i+  ++++ +++l+ g  d++vg
  gi|330508505|ref|YP_004384933.1| 453 GDRALVTTLTKRLAEELTDYLSQNDIR--ARYLhSEIQPLERTEIIRELRLGkFDVLVG 509
                                       557777777888888777777665553..334335566666667777776444677665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   5.7e-05     0.073       4      45 ..      44      77 ..      42     152 .. 0.78
   2 ?   -3.5   0.1         9   1.2e+04      99     110 ..     290     306 ..     264     311 .. 0.66
   3 ?   -1.6   0.0       2.3     3e+03      94     103 ..     342     352 ..     339     365 .. 0.78
   4 ?   -3.3   0.0       7.7   9.9e+03      19      43 ..     459     483 ..     459     503 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.7e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfv 45
                                      ++++ +++G +G+GKT++++++ +q +        +p++v v
  gi|330508505|ref|YP_004384933.1| 44 NERFQTLIGVTGSGKTYTVANVISQVQ--------KPTLVIV 77
                                      678889*******************85........4544433 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9
                            AAA_22  99 Eaqhlr..s...eeale 110
                                       Ea++lr  +   +e++e
  gi|330508505|ref|YP_004384933.1| 290 EAHRLRqrTmhdMEMIE 306
                                       77777653134466655 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.3
                            AAA_22  94 lliiDEaqh.l 103
                                       lliiDE +  l
  gi|330508505|ref|YP_004384933.1| 342 LLIIDESHQtL 352
                                       79*****9856 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 7.7
                            AAA_22  19 Ttllrrlleqldeeakaeeerpevv 43 
                                       Ttl +rl+e+l+ + ++++ r++++
  gi|330508505|ref|YP_004384933.1| 459 TTLTKRLAEELTDYLSQNDIRARYL 483
                                       6777888887766655555444444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0026       3.3       9      36 ..      44      71 ..      36      83 .. 0.85
   2 ?   -0.6   0.0       1.2   1.5e+03      57     112 ..     278     349 ..     269     366 .. 0.53
   3 ?    3.6   0.0     0.059        76      43      75 ..     454     486 ..     437     613 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0026
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallve 36
                                      +e+   +++  G+GKT+++  +++ +++
  gi|330508505|ref|YP_004384933.1| 44 NERFQTLIGVTGSGKTYTVANVISQVQK 71
                                      6778899**************9998776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                            AAA_19  57 elrerlaalgae......atTiHrlalldfddlltealelle...........eaeeekklqeeellivDEfq 112
                                       el+erl++lg+        +T+H + +++ ++  +   ++ +           +    + + + +lli+DE+ 
  gi|330508505|ref|YP_004384933.1| 278 ELNERLQELGMIeahrlrQRTMHDMEMIEETGSCKGIENYSRhfdrrqpgeppYC-LIDYFPDDFLLIIDESH 349
                                       5556655555445566667777777664433333222222113333333333211.11223355577777765 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.059
                            AAA_19  43 eeillvaftgrAakelrerlaalgaeatTiHrl 75 
                                       ++ l+ ++t+r a+el++ l++ + +a+ +H+ 
  gi|330508505|ref|YP_004384933.1| 454 DRALVTTLTKRLAEELTDYLSQNDIRARYLHSE 486
                                       68899***************9999889988854 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016       0.2       6      73 ..      34      94 ..      29     104 .. 0.69
   2 ?   -1.8   0.0       1.5     2e+03     121     132 ..     340     351 ..     337     372 .. 0.82
   3 ?   -1.3   0.0       1.1   1.4e+03      74     106 ..     569     600 ..     546     623 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                         SWI2_SNF2  6 vekavervkegdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfakag 73
                                      + ++v  +++++r + +i   +GSGK++t + + ++++     +p++v+v   k L +Ql+++f+++ 
  gi|330508505|ref|YP_004384933.1| 34 IDQLVLGLQRNERFQTLI-GVTGSGKTYTVANVISQVQ-----KPTLVIVHN-KTLAEQLYNEFKEFF 94
                                      555555555544444444.468*****99776665555.....599988876.67*********9874 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                         SWI2_SNF2 121 niivlvDEaHRs 132
                                       ++++++DE+H +
  gi|330508505|ref|YP_004384933.1| 340 DFLLIIDESHQT 351
                                       6899******87 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.1
                         SWI2_SNF2  74 eekpkqaesrkeLkellekesekiifttiqKfe 106
                                       +++++++e+r++L+    +++++ii  ti+K  
  gi|330508505|ref|YP_004384933.1| 569 KKAMETTERRRSLQMAY-NQEHGIIPQTIKKPI 600
                                       44556677777777777.568889999998864 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 ..      50      89 ..      49     156 .. 0.76
   2 ?   -0.1   0.1      0.73   9.3e+02      13      43 ..     459     488 ..     459     644 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                            AAA_33  4 lvGlpGsGKstlaerl...lkklgavllssdtlrrrlfgt 40
                                      l+G+ GsGK++ + ++   ++k + v++   tl ++l+++
  gi|330508505|ref|YP_004384933.1| 50 LIGVTGSGKTYTVANVisqVQKPTLVIVHNKTLAEQLYNE 89
                                      69*************9555555559999999999999984 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.73
                            AAA_33  13 stlaerllkklgavllssdtlrrrlfgtdqq 43 
                                       +tl +rl+++l+ + ls++++r r+  ++ q
  gi|330508505|ref|YP_004384933.1| 459 TTLTKRLAEELTDY-LSQNDIRARYLHSEIQ 488
                                       67777777666643.5555555544433333 PP

>> NIBRIN_BRCT_II  Second BRCT domain on Nijmegen syndrome breakage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       9.4   1.2e+04      96     108 ..     260     272 ..     256     279 .. 0.80
   2 ?   12.0   0.1   0.00016       0.2      42     116 ..     553     630 ..     540     633 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.4
                    NIBRIN_BRCT_II  96 qrvIeesEildAi 108
                                       + vI+e+E+  A+
  gi|330508505|ref|YP_004384933.1| 260 HYVIPENELKAAV 272
                                       6799****99998 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00016
                    NIBRIN_BRCT_II  42 taedlvryvkkvage.edgselleskgvvvvrvrpkks.steewiaevenelakk.gqrvIeesEildAilacsask 115
                                           +v y++++ g  ++  e++e+++++ + ++++ +   ++  + + +++ +  + r I++s+i  Ai++ +a++
  gi|330508505|ref|YP_004384933.1| 553 ANSRVVLYADRMTGSiKKAMETTERRRSLQMAYNQEHGiIPQTIKKPIREKVVEItDTRHIPKSDIPNAIIELEAEM 629
                                       44567899999999997788889999999999999987667777778888998888******************998 PP

                    NIBRIN_BRCT_II 116 l 116
                                       +
  gi|330508505|ref|YP_004384933.1| 630 M 630
                                       7 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   0.00028      0.36       6      43 ..      30      70 ..      28     112 .. 0.76
   2 ?   -2.2   0.0       2.2   2.9e+03      45      81 ..     452     491 ..     442     518 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00028
                            AAA_30  6 Qaaaveal...ltsgdrvavltGpAGtGKttalkalreawe 43
                                      Q +a+++l   l+ ++r+++l G+ G+GKt++++ +   ++
  gi|330508505|ref|YP_004384933.1| 30 QPEAIDQLvlgLQRNERFQTLIGVTGSGKTYTVANVISQVQ 70
                                      55555555222466788***************998876665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.2
                            AAA_30  45 aggrviglAptgkaAkvLaeelg...ieastiakllkrlk 81 
                                       +g r ++ + t++ A++L++ l    i+a+ +++ ++ l+
  gi|330508505|ref|YP_004384933.1| 452 RGDRALVTTLTKRLAEELTDYLSqndIRARYLHSEIQPLE 491
                                       4567788889999999999744433378888888776666 PP

>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0001      0.13      82     136 ..      52     110 ..       4     115 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                                       ESTTSSHHHHHTBC..TTTSBSHHH....HHHHHHHHHHHHCTTTHEEEEEEEEEEEEEET CS
                           Kinesin  82 GqtgsGKTyTmegk..eeeeeGiip....raleelFesikkekeekekefsvkvsylEiYn 136
                                       G+tgsGKTyT+     + +++ ++        e+l+++ k+     +++++  +sy++ Y+
  gi|330508505|ref|YP_004384933.1|  52 GVTGSGKTYTVANVisQVQKPTLVIvhnkTLAEQLYNEFKEFFP--DNRVEYFISYYDYYQ 110
                                       9**********987774444444330111345666666665443..477788888887776 PP

>> DUF3969  Protein of unknown function (DUF3969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.58   7.4e+02      29      61 ..     165     197 ..     158     225 .. 0.87
   2 ?    8.8   0.0    0.0013       1.6      60      94 ..     244     288 ..     237     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.58
                           DUF3969  29 eeaesllFslemlelieelelsdelveiihkgm 61 
                                       e+++s+ F+l++ e+i+  ++ + lv+i  + +
  gi|330508505|ref|YP_004384933.1| 165 ENFQSMGFELKVNERISRKDILERLVDILYERS 197
                                       6789999*******************9987655 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0013
                           DUF3969  60 gmeLEDv.........esliPe.eLedsIdeielkclevLeelsk 94 
                                       g   ED+           +iPe eL+ ++d+i+ ++ e+L+el +
  gi|330508505|ref|YP_004384933.1| 244 GKRVEDMsyffvyparHYVIPEnELKAAVDSIKAELNERLQELGM 288
                                       5667777777778877789***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (658 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.43
# Mc/sec: 4580.38
//
Query:       gi|330508506|ref|YP_004384934.1|  [L=228]
Description: hypothetical protein MCON_2714 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1718.86
//
Query:       gi|330508507|ref|YP_004384935.1|  [L=227]
Description: hypothetical protein MCON_2715 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.19   12.1   0.2        8.8    6.7   0.0    2.2  2  FRD2      Bacteriophage FRD2 protein
        1.8    8.5   6.5         18    5.3   6.6    2.2  1  PIG-P     PIG-P
        2.8    7.6   7.9       0.66    9.7   0.8    2.1  2  DUF1673   Protein of unknown function (DUF1673)


Domain annotation for each model (and alignments):
>> FRD2  Bacteriophage FRD2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.018   1.1e+02      49      77 ..      54      82 ..      40      91 .. 0.87
   2 ?    6.7   0.0    0.0015       8.8      23      51 ..     175     203 ..     162     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.018
                              FRD2 49 elseeefycfreykeptseedevkdkvsg 77
                                      +ls+  +yc r   e ts  +e k ++ g
  gi|330508507|ref|YP_004384935.1| 54 NLSDSFLYCDRANYELTSAVNEAKINIRG 82
                                      6899999**************99988877 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0015
                              FRD2  23 gfdyvteiicangeiynddgmgddyfels 51 
                                        f y++ +i + g i  +dg+gd  f + 
  gi|330508507|ref|YP_004384935.1| 175 VFGYMAYLISSSGLIALNDGIGDGVFSIM 203
                                       4899********************99864 PP

>> PIG-P  PIG-P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   6.6     0.003        18      12      62 ..     100     183 ..      90     193 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.003
                             PIG-P  12 lstlafllyllwallP.................................eevlhalgityypnryWalavpayllml 55 
                                       l  ++f++  +  +                                   +e l++ g+   ++r W +a+p +++++
  gi|330508507|ref|YP_004384935.1| 100 LYAIVFAVLAILFFSMliyqhpqaeildvplwssffaglgasaqiltgvAEDLRRYGLATRYKRLWYMAIPLISMVF 176
                                       333333332222222233455688888888888888888888888888888899*****************988877 PP

                             PIG-P  56 vlyiyva 62 
                                         ++y++
  gi|330508507|ref|YP_004384935.1| 177 GYMAYLI 183
                                       7777765 PP

>> DUF1673  Protein of unknown function (DUF1673)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.8   0.00011      0.66     147     196 ..      93     142 ..      74     146 .. 0.83
   2 ?    1.8   1.2     0.028   1.7e+02     154     203 ..     164     209 ..     152     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                           DUF1673 147 lrwllrllllviflliavllillsyvesiagelqlgevvssfisglllll 196
                                       + + l  l++++f+++a+l+  + +++   +e+      ssf++gl+++ 
  gi|330508507|ref|YP_004384935.1|  93 YFFQLYGLYAIVFAVLAILFFSMLIYQHPQAEILDVPLWSSFFAGLGASA 142
                                       4578999*******************999999976569*******98865 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.028
                           DUF1673 154 lllviflliavllillsyvesiagelqlgevvssfisgllllllwliylq 203
                                       l  ++++li++++ ++ y+ s +g ++l+      i+  ++++++  +l+
  gi|330508507|ref|YP_004384935.1| 164 LWYMAIPLISMVFGYMAYLISSSGLIALN----DGIGDGVFSIMFICFLT 209
                                       667999*************9999999755....55555455555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); 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:                         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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1379.68
//
Query:       gi|330508508|ref|YP_004384936.1|  [L=187]
Description: hypothetical protein MCON_2718 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00051   19.9   3.6    0.00066   19.5   2.2    1.9  1  Nudix_N_2        Nudix N-terminal
     0.0016   18.3   0.1     0.0039   17.0   0.1    1.6  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
     0.0019   17.6   1.7      0.071   12.5   0.2    2.4  2  zf-ribbon_3      zinc-ribbon domain
     0.0034   17.4   0.3     0.0052   16.8   0.3    1.3  1  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.019   14.9   2.2       0.79    9.7   0.1    2.3  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.019   14.5   1.7      0.038   13.5   1.7    1.5  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.026   14.2   1.0       0.22   11.3   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.03   14.7   0.1      0.063   13.7   0.1    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.06   13.3   0.1       0.11   12.4   0.1    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.066   13.1   0.5       0.27   11.1   0.5    1.9  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
      0.077   13.2   1.5        1.9    8.7   0.1    2.8  2  zf-RING_7        C4-type zinc ribbon domain
       0.08   13.1   1.4       0.21   11.7   1.4    1.7  1  Zn-ribbon_8      Zinc ribbon domain
       0.12   12.5   0.8        7.6    6.7   0.1    2.3  2  UPF0547          Uncharacterised protein family UPF0547
       0.16   12.4   2.4         16    6.0   0.1    3.1  3  zf-IS66          zinc-finger binding domain of transposase IS
       0.21   11.5   5.8        5.2    7.1   5.8    2.2  1  Prok-RING_1      Prokaryotic RING finger family 1
       0.27   10.9   3.4        1.8    8.3   0.1    2.3  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.34   11.0   1.8        6.5    6.8   0.1    2.8  2  CpXC             CpXC protein
       0.56   10.2   2.4        9.2    6.3   2.4    2.3  2  zinc_ribbon_4    zinc-ribbon domain
       0.61    9.9   4.1        3.9    7.3   4.0    2.2  2  zinc_ribbon_5    zinc-ribbon domain
        1.1    9.1   3.0         13    5.6   3.1    2.3  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit


Domain annotation for each model (and alignments):
>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   2.2   7.4e-07   0.00066       2      32 ..       7      37 ..       7      37 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.4e-07
                                      B-TTT--B-EEE--TT-SS-EEEETTTTEEE CS
                         Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCgtih 32
                                      FC++CGt + + + + +++   +C++Cgt+h
  gi|330508508|ref|YP_004384936.1|  7 FCPACGTDTDHTLIKSGQENLVRCDDCGTVH 37
                                      9*********9999998888999*******9 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   4.4e-06    0.0039       2      34 ..       6      40 ..       6      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.4e-06
                                      EBESTTT...SBEEEEECSCCCEEEESSSS-EEESS CS
                    RNA_POL_M_15KD  2 kFCpkCg...NlLlpkedkegknfeCrqCgYeepad 34
                                      +FCp Cg   ++ l+k+++e+  + C+ Cg + p +
  gi|330508508|ref|YP_004384936.1|  6 IFCPACGtdtDHTLIKSGQEN-LVRCDDCGTVHPVE 40
                                      7*****99999**********.58******999975 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.2   7.9e-05     0.071      14      25 ..       3      14 ..       3      15 .. 0.88
   2 ?    4.0   0.1      0.04        36       3      10 ..      28      35 ..      26      40 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.9e-05
                       zf-ribbon_3 14 sddnvCpyCGtk 25
                                      +d+++Cp CGt+
  gi|330508508|ref|YP_004384936.1|  3 EDQIFCPACGTD 14
                                      699*******97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.04
                       zf-ribbon_3  3 vrCPnCGa 10
                                      vrC  CG+
  gi|330508508|ref|YP_004384936.1| 28 VRCDDCGT 35
                                      68888887 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   5.9e-06    0.0052      11      39 ..       4      38 ..       1      42 [. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.9e-06
                               DZR 11 darfCseCgtklkavaa........edrCpsCgekvd 39
                                      d++fC++Cgt+ +   +          rC+ Cg+  +
  gi|330508508|ref|YP_004384936.1|  4 DQIFCPACGTDTDH--TliksgqenLVRCDDCGTVHP 38
                                      789********653..134666689********9755 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.029        26      27      35 ..       7      15 ..       4      17 .. 0.76
   2 ?    9.7   0.1   0.00088      0.79      13      23 ..      29      38 ..      27      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.029
                           DUF35_N 27 vCphCgsdd 35
                                      +Cp Cg d+
  gi|330508508|ref|YP_004384936.1|  7 FCPACGTDT 15
                                      799998774 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00088
                           DUF35_N 13 rCpdCGtvqfP 23
                                      rC+dCGtv+ P
  gi|330508508|ref|YP_004384936.1| 29 RCDDCGTVH-P 38
                                      9*******4.5 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.7   4.2e-05     0.038       2      28 ..       7      36 ..       6      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.2e-05
                                      EETTTTC.EE.CHEETSTTCE.EESSSSBE CS
                      TF_Zn_Ribbon  2 kCPnCgs.tn.lveDpergel.vCtdCGlV 28
                                       CP Cg+ t+ ++    + +l +C dCG+V
  gi|330508508|ref|YP_004384936.1|  7 FCPACGTdTDhTLIKSGQENLvRCDDCGTV 36
                                      6******777789999999999******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 ?   11.3   0.1   0.00025      0.22      12      22 ..       4      14 ..       2      15 .. 0.84
   2 ?    1.3   0.1      0.34     3e+02       2       9 ..      30      37 ..      29      42 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                     zinc_ribbon_2 12 nakFCpyCGtp 22
                                      ++ FCp CGt 
  gi|330508508|ref|YP_004384936.1|  4 DQIFCPACGTD 14
                                      778******95 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.34
                     zinc_ribbon_2  2 CpnCGael 9 
                                      C  CG+ +
  gi|330508508|ref|YP_004384936.1| 30 CDDCGTVH 37
                                      77888755 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   7.1e-05     0.063       6      61 ..       8      58 ..       4      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-05
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCgastpwfkiaedeaeaekeaieaWNrR 61
                                      CP Cg +  +   ++++++    v C+dCg    +  + +++   + ++i +W +R
  gi|330508508|ref|YP_004384936.1|  8 CPACGTDTDHTLIKSGQEN---LVRCDDCGT--VHPVEVKRVRLVNLKVIVNWDDR 58
                                      *****98777777667666...9*******9..56667777777777777777777 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00013      0.11      20      45 ..       7      35 ..       2      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                     Zn_Tnp_IS1595 20 vCPhCgsr.kayrikt..rglfqCkeCrk 45
                                       CP+Cg +  ++ ik+    l +C +C++
  gi|330508508|ref|YP_004384936.1|  7 FCPACGTDtDHTLIKSgqENLVRCDDCGT 35
                                      5********999999999*********85 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 ?   11.1   0.5    0.0003      0.27      88     116 ..       6      35 ..       2      36 .. 0.85
   2 ?   -1.4   0.0       2.3   2.1e+03      11      39 ..     137     164 ..     131     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                                       TSTSSSTS.TCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  88 VlCkeCks.petelekeerllvlkCkaCga 116
                                       + C+ C+   + +l+k+++  +++C+ Cg 
  gi|330508508|ref|YP_004384936.1|   6 IFCPACGTdTDHTLIKSGQENLVRCDDCGT 35 
                                       89****96589999999888889*****96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.3
                                       -SSTT--EEEETT.EEEETTHHHHHHHHT CS
                      eIF-5_eIF-2B  11 ykmpklqvkvegkkktvivNfeeiakaLn 39 
                                       +++p  ++   g+ k  ++Nf+ i  +++
  gi|330508508|ref|YP_004384936.1| 137 ITVPGDELLEVGE-KRRVENFQFIIVKIK 164
                                       5566667777788.888999998876665 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 ?    2.5   0.1      0.19   1.7e+02      24      30 ..       6      12 ..       2      13 .. 0.83
   2 ?    8.7   0.1    0.0022       1.9      18      30 ..      21      34 ..      17      35 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.19
                                      EE-TTT- CS
                         zf-RING_7 24 vtCpeCG 30
                                      ++Cp CG
  gi|330508508|ref|YP_004384936.1|  6 IFCPACG 12
                                      89****9 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0022
                                      CCS.TB-EE-TTT- CS
                         zf-RING_7 18 rag.devvtCpeCG 30
                                      + g +++v+C+ CG
  gi|330508508|ref|YP_004384936.1| 21 KSGqENLVRCDDCG 34
                                      555577*******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 ?   11.7   1.4   0.00024      0.21       8      34 ..       8      35 ..       5      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                       Zn-ribbon_8  8 CeeCghefe.vlqsisdapltaCPeCgs 34
                                      C +Cg++ +  l ++ +++l+ C +Cg 
  gi|330508508|ref|YP_004384936.1|  8 CPACGTDTDhTLIKSGQENLVRCDDCGT 35
                                      *********8777777999999****97 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0085       7.6      15      22 ..       6      13 ..       3      14 .. 0.83
   2 ?    4.2   0.0     0.053        48      13      23 ..      26      36 ..      25      38 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0085
                           UPF0547 15 qfCphCGy 22
                                       fCp CG+
  gi|330508508|ref|YP_004384936.1|  6 IFCPACGT 13
                                      69*****8 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.053
                           UPF0547 13 aaqfCphCGyv 23
                                      + ++C +CG+v
  gi|330508508|ref|YP_004384936.1| 26 NLVRCDDCGTV 36
                                      5678*****98 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 ?    4.2   0.1     0.064        57       4      13 ..       8      18 ..       6      25 .. 0.78
   2 ?    6.0   0.1     0.017        16       4      20 ..      30      45 ..      29      53 .. 0.82
   3 ?   -0.1   0.0       1.4   1.3e+03      10      30 ..     143     163 ..     141     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.064
                           zf-IS66  4 CpcCGg.llkp 13
                                      Cp CG+ + + 
  gi|330508508|ref|YP_004384936.1|  8 CPACGTdTDHT 18
                                      *****955665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.017
                           zf-IS66  4 CpcCGgllkpigedrvr 20
                                      C++CG+ ++p++ +rvr
  gi|330508508|ref|YP_004384936.1| 30 CDDCGT-VHPVEVKRVR 45
                                      *****7.5999998887 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.4
                           zf-IS66  10 llkpigedrvreeldipPakf 30 
                                       +l ++ge+r+ e + ++ +k+
  gi|330508508|ref|YP_004384936.1| 143 ELLEVGEKRRVENFQFIIVKI 163
                                       57799**97779888887776 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   5.8    0.0058       5.2       6      30 ..       7      37 ..       3      39 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0058
                       Prok-RING_1  6 kCpvCgkelkee......dDiVvCpeCgtpy 30
                                       Cp+Cg   ++       + +V C++Cgt++
  gi|330508508|ref|YP_004384936.1|  7 FCPACGTDTDHTliksgqENLVRCDDCGTVH 37
                                      59999988776666667899*********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 ?    8.3   0.1     0.002       1.8       5      13 ..       7      15 ..       4      18 .. 0.86
   2 ?    3.1   0.5     0.085        76      23      31 ..      29      37 ..      28      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                     zf-NADH-PPase  5 FCgrCGapt 13
                                      FC+ CG+ t
  gi|330508508|ref|YP_004384936.1|  7 FCPACGTDT 15
                                      9*****977 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.085
                     zf-NADH-PPase 23 vCpaCgleh 31
                                      +C++Cg+ h
  gi|330508508|ref|YP_004384936.1| 29 RCDDCGTVH 37
                                      8*****998 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.074        66       2      15 ..       7      20 ..       6      22 .. 0.72
   2 ?    6.8   0.1    0.0073       6.5      30      52 ..      20      42 ..      17     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.074
                              CpXC  2 tCpaCgkefeaeiw 15
                                       CpaCg+ ++ ++ 
  gi|330508508|ref|YP_004384936.1|  7 FCPACGTDTDHTLI 20
                                      58899888887765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0073
                              CpXC 30 lldgslfeatCpkCgatakleap 52
                                      + +g+ + ++C++Cg+ + +e +
  gi|330508508|ref|YP_004384936.1| 20 IKSGQENLVRCDDCGTVHPVEVK 42
                                      7789999999*****99988766 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.4      0.01       9.2       3      34 ..       6      36 ..       5      38 .. 0.72
   2 ?    6.0   0.2     0.013        11       3      13 ..      28      38 ..      27      46 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.01
                     zinc_ribbon_4  3 itCpsCkakyeiddeklp.akgvkvrCskCghv 34
                                      i Cp+C++    d   ++ ++   vrC  Cg+v
  gi|330508508|ref|YP_004384936.1|  6 IFCPACGTD--TDHTLIKsGQENLVRCDDCGTV 36
                                      668888885..46666764555599*****997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.013
                     zinc_ribbon_4  3 itCpsCkakye 13
                                      ++C  C++++ 
  gi|330508508|ref|YP_004384936.1| 28 VRCDDCGTVHP 38
                                      55666666655 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.0    0.0043       3.9       3      34 ..       6      36 ..       5      39 .. 0.68
   2 ?    5.3   0.4     0.018        16       3      11 ..      28      36 ..      27      45 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0043
                     zinc_ribbon_5  3 irCpdCdtkFklvdsklKksg.kkVrCakCaev 34
                                      i Cp+C+t    +   +K  +   VrC  C+ v
  gi|330508508|ref|YP_004384936.1|  6 IFCPACGTD--TDHTLIKSGQeNLVRCDDCGTV 36
                                      67****986..3334455444246******998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.018
                     zinc_ribbon_5  3 irCpdCdtk 11
                                      +rC+dC+t 
  gi|330508508|ref|YP_004384936.1| 28 VRCDDCGTV 36
                                      689999885 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 ?    2.2   0.2      0.16   1.5e+02      15      24 ..       3      12 ..       2      15 .. 0.87
   2 ?    5.6   3.1     0.014        13       3      24 ..       8      34 ..       7      35 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.16
                                      SS----SSS- CS
                    DNA_RNApol_7kD 15 gdpiRCkeCG 24
                                      +d+i C  CG
  gi|330508508|ref|YP_004384936.1|  3 EDQIFCPACG 12
                                      58999****9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.014
                                      -SSS--B--...--..SSS----SSS- CS
                    DNA_RNApol_7kD  3 CgeCgaevs...lk..kgdpiRCkeCG 24
                                      C  Cg+++    +k  ++  +RC +CG
  gi|330508508|ref|YP_004384936.1|  8 CPACGTDTDhtlIKsgQENLVRCDDCG 34
                                      55566554333354224678******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1321.50
//
Query:       gi|330508509|ref|YP_004384937.1|  [L=269]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-18   64.9   0.5    1.2e-17   63.6   0.5    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.5e-11   43.9   0.1    4.1e-11   43.2   0.1    1.3  1  OrfB_IS605      Probable transposase
    1.9e-05   24.9   0.3    4.3e-05   23.7   0.3    1.6  1  C1_2            C1 domain
     0.0071   16.4   2.4       0.18   11.9   2.4    2.3  1  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
  ------ inclusion threshold ------
      0.059   13.4   1.0      0.059   13.4   1.0    1.8  2  DZR             Double zinc ribbon
      0.092   12.8   0.0       0.18   11.8   0.0    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.11   12.5   0.8       0.29   11.1   0.8    1.8  1  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
        0.3   11.3   2.0        0.6   10.3   2.0    1.5  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
        0.3   10.7   1.5        3.8    7.2   0.1    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.5     6e-21   1.2e-17       8      69 .]     193     251 ..     188     251 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 6e-21
                    OrfB_Zn_ribbon   8 leykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                        +yk + +Gi v +v+p++TSk+Cs+Cg  +++  ++  f+Cp+Cgf++++D+nAa+Ni +r
  gi|330508509|ref|YP_004384937.1| 193 TSYKIQGKGI-VAKVDPRNTSKNCSRCGLPGTR--KRHSFNCPKCGFSIHADLNAAYNIRNR 251
                                       5789998888.899*******************..************************986 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.1     2e-14   4.1e-11      12     114 ..      59     168 ..      49     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 2e-14
                        OrfB_IS605  12 kpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn....ykkasrklarlhrkr 84 
                                        ++g + +giDl+  n ++ v+ dg+  +++g   k ++k+++k i++lq+kl++ k      + + r l+rl +kr
  gi|330508509|ref|YP_004384937.1|  59 DVEGIHPVGIDLNETNAIVAVDADGNELFISGLDRKIKNKRTSKTIKRLQRKLAQRKAegknTRSVVRDLKRLRAKR 135
                                       56677789************************99999999999999999999888766555599999********** PP

                        OrfB_IS605  85 srrrkhllhklathliktlkev...gvetLnvg 114
                                       srr k++ + ++++li++  ++   + e+Ln g
  gi|330508509|ref|YP_004384937.1| 136 SRRTKDFCNCASKELIEWAPDNcvlVFEDLNFG 168
                                       ******************999865556777765 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.3   2.1e-08   4.3e-05      13      44 ..     207     240 ..     194     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.1e-08
                              C1_2  13 edssesfnCsaCgrkidgff..YsCseCdfslhv 44 
                                       ++++ s+nCs Cg +++ ++  ++C++C fs+h 
  gi|330508509|ref|YP_004384937.1| 207 DPRNTSKNCSRCGLPGTRKRhsFNCPKCGFSIHA 240
                                       578999*********8777789***********7 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   2.4   9.2e-05      0.18      11      28 ..     223     240 ..     171     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.2e-05
                          zf-Mss51  11 apkhvdfeCpdCGiptyc 28 
                                       ++k+ +f+Cp+CG++++ 
  gi|330508509|ref|YP_004384937.1| 223 TRKRHSFNCPKCGFSIHA 240
                                       68999***********97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       3.1   6.2e+03      13      17 ..     141     145 ..     134     159 .. 0.55
   2 ?   13.4   1.0   2.9e-05     0.059      10      41 ..     210     241 ..     204     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.1
                               DZR  13 rfCse 17 
                                        fC+ 
  gi|330508509|ref|YP_004384937.1| 141 DFCNC 145
                                       45543 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.9e-05
                               DZR  10 pdarfCseCgtklkavaaedrCpsCgekvdpe 41 
                                       + ++ Cs+Cg +  +  ++ +Cp+Cg +++++
  gi|330508509|ref|YP_004384937.1| 210 NTSKNCSRCGLPGTRKRHSFNCPKCGFSIHAD 241
                                       56788999999988888899999999887665 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 ?   11.8   0.0   8.9e-05      0.18      58      94 ..     200     236 ..     187     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.9e-05
                                       TT-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSS CS
                              HypA  58 egaeLeieevpvkvrCreCgkefeleekalrCpkCgs 94 
                                       +g + +++  + +  C++Cg  ++ ++++++CpkCg 
  gi|330508509|ref|YP_004384937.1| 200 KGIVAKVDPRNTSKNCSRCGLPGTRKRHSFNCPKCGF 236
                                       455566777888999*****9999887789*****95 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 ?   11.1   0.8   0.00014      0.29      13      37 ..     212     235 ..     199     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                       -TTTTTTSEETTE......E-TTTT CS
                         Anti-TRAP  13 CdaCngsGkiepeeprasleCPkCs 37 
                                        ++C + G  +++ +r s++CPkC+
  gi|330508509|ref|YP_004384937.1| 212 SKNCSRCGL-PGTRKRHSFNCPKCG 235
                                       568888885.6666999*******6 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.0    0.0003       0.6      15      40 .]     212     235 ..     211     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0003
                     Auto_anti-p27  15 aetCpvCgvPLmrdrkggkvyCvaCd 40 
                                       +++C++Cg P  r+r+     C+ C+
  gi|330508509|ref|YP_004384937.1| 212 SKNCSRCGLPGTRKRH--SFNCPKCG 235
                                       799**********775..888****6 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2     0.063   1.2e+02       3       9 ..     213     219 ..     211     221 .. 0.81
   2 ?    7.2   0.1    0.0019       3.8       2      14 ..     228     240 ..     227     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.063
                            zf_UBZ   3 ylCerCg 9  
                                         C+rCg
  gi|330508509|ref|YP_004384937.1| 213 KNCSRCG 219
                                       67****9 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0019
                            zf_UBZ   2 tylCerCgkeipe 14 
                                       ++ C++Cg +i  
  gi|330508509|ref|YP_004384937.1| 228 SFNCPKCGFSIHA 240
                                       699******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1910.45
//
Query:       gi|330508510|ref|YP_004384938.1|  [L=211]
Description: protein-L-isoaspartate O-methyltransferase [Methanosaeta concilii GP6]
Scores for complete 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-67  225.7   0.0    6.1e-67  225.4   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    5.6e-08   32.7   0.0    7.7e-08   32.3   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
      1e-05   26.1   0.0      2e-05   25.2   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
      2e-05   24.4   0.0    2.9e-05   23.9   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    0.00064   19.1   0.0    0.00077   18.9   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0041   17.7   0.0     0.0088   16.7   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
     0.0098   15.0   0.0      0.015   14.4   0.0    1.2  1  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
      0.019   14.3   0.0      0.026   13.8   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
       0.02   14.0   0.0      0.027   13.7   0.0    1.2  1  Methyltransf_3   O-methyltransferase
      0.031   13.4   0.0      0.041   12.9   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.034   13.7   0.0      0.055   13.0   0.0    1.3  1  MTS              Methyltransferase small domain
      0.063   12.9   0.0      0.086   12.5   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.074   12.3   0.1       0.11   11.7   0.1    1.3  1  Methyltransf_2   O-methyltransferase domain
      0.099   12.4   0.0       0.14   11.9   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)
       0.25   10.8   0.0       0.39   10.2   0.0    1.2  1  Methyltransf_4   Putative methyltransferase


Domain annotation for each model (and alignments):
>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.4   0.0   5.1e-70   6.1e-67      18     209 ..      16     204 ..       6     205 .. 0.97

  Alignments for each domain:
  == domain 1  score: 225.4 bits;  conditional E-value: 5.1e-70
                                       -HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHH CS
                              PCMT  18 sdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevGsGsGyltavlarl 94 
                                       ++ v++a++ v+R++fvp+++++ aYed pl+ig+++tiSaphmva++++ll++++g+++LevG+GsGy++avla l
  gi|330508510|ref|YP_004384938.1|  16 NESVLKAMARVPRDRFVPAQLRDRAYEDLPLPIGFGQTISAPHMVAIMCDLLDVRPGMKILEVGGGSGYHAAVLAAL 92 
                                       689************************************************************************** PP

                                       HCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS--HHHHHTEEEEEEEEE CS
                              PCMT  95 vgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiPealidQLkeGGrlvv 171
                                        g++g+v s+er+++l+ +a++nl++ +++ v+vv+gDG  G +e+aPYd+i v+a+ap +Pe+l +QL  GG+l++
  gi|330508510|ref|YP_004384938.1|  93 AGPEGQVFSVERMPDLALAARKNLQAAGIAGVTVVEGDGSLGLPEHAPYDRISVAASAPRVPEPLKEQLRVGGKLIL 169
                                       ***************************************************************************** PP

                                       EESBSSSEEEEEEEEETTTEEEEEEEEEE---B-BCCC CS
                              PCMT 172 PvgeeeeQvlklvdkkadgkvvikkleevrfvpltdke 209
                                       Pvg e++Q+l lv +k+   + +++++ v+fvpl +ke
  gi|330508510|ref|YP_004384938.1| 170 PVG-ETSQELVLVTRKN--GFAVEEKMGVIFVPLIGKE 204
                                       ***.9*********999..789999*********9987 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   6.4e-11   7.7e-08       4      78 ..      72     144 ..      70     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 6.4e-11
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDli 78 
                                       g+++l++G G+G+ + +la ++gp+++v+++++ ++    Ar+n+q  g+  v++ +gd    l+++   +++D i
  gi|330508510|ref|YP_004384938.1|  72 GMKILEVGGGSGYHAAVLAALAGPEGQVFSVERMPDLALAARKNLQAAGIAGVTVVEGDGSLgLPEH---APYDRI 144
                                       89*********************************************************99999976...778865 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.7e-08     2e-05       1      72 [.      75     148 ..      75     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.7e-08
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBC.CGBSSSTTTEEEEEEES CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgda.edlpfedgsfDlvvssg 72 
                                       +L++G G+G +++ la+  g +++v  v+  +++  aar++++++g+  v++v+gd    lp e++ +D + ++ 
  gi|330508510|ref|YP_004384938.1|  75 ILEVGGGSGYHAAVLAALAGpEGQVFSVERMPDLALAARKNLQAAGIaGVTVVEGDGsLGLP-EHAPYDRISVAA 148
                                       8***************99966*************************9*********944466.556999988754 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.4e-08   2.9e-05      29      97 ..      60     128 ..      51     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.4e-08
                             GCD14  29 isliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvt 97 
                                       ++++   L+++pG +++e G Gsg  +  +a   +P G++f++e   + a  ar++++  ++++++ v+
  gi|330508510|ref|YP_004384938.1|  60 VAIMCDLLDVRPGMKILEVGGGSGYHAAVLAALAGPEGQVFSVERMPDLALAARKNLQAAGIAGVTVVE 128
                                       56777889******************************************************9877664 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   6.5e-07   0.00077      41     125 ..      65     149 ..      58     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.5e-07
                                       HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-E CS
                   Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsf 117
                                       +l  v++g k+l+v gG+g  a+ l+  +g +g+v  ++  +++   ++k l+  g   +  + +++     e   +
  gi|330508510|ref|YP_004384938.1|  65 DLLDVRPGMKILEVGGGSGYHAAVLAALAGPEGQVFSVERMPDLALAARKNLQAAGIAGVTVVEGDGSLGLPEHAPY 141
                                       6677899**********************************************************986433344667 PP

                                       EEEEEES- CS
                   Ubie_methyltran 118 DvvtvsfG 125
                                       D + v+  
  gi|330508510|ref|YP_004384938.1| 142 DRISVAAS 149
                                       77777654 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   7.3e-06    0.0088       1      59 [.      76     137 ..      76     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.3e-06
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-T CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfed 59 
                                       L+vG G+G++a+ la  +   ++v+ v+  + +  +a+++ + +g+  v++v++d + l +++
  gi|330508510|ref|YP_004384938.1|  76 LEVGGGSGYHAAVLAALAgpeGQVFSVERMPDLALAARKNLQAAGIaGVTVVEGDGS-LGLPE 137
                                       89*************666699************************998999999988.67666 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.3e-05     0.015      65     105 ..      66     106 ..      57     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                                       --S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSH CS
                       Fibrillarin  65 elpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsp 105
                                        l +++g k+L +G +sG  ++ ++ + g+eg v++ve  p
  gi|330508510|ref|YP_004384938.1|  66 LLDVRPGMKILEVGGGSGYHAAVLAALAGPEGQVFSVERMP 106
                                       45789*********************************876 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.2e-05     0.026      52     131 ..      61     144 ..      56     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-05
                                       HHHHTTTT--TT-EEEEES-TTSHHHH..HHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG--- CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvr..raverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde 126
                                        ++++ l+++pGm++L++G G G+ +    a +  + +v+++    + a  a+k++++++++  + v+  +   l+e
  gi|330508510|ref|YP_004384938.1|  61 AIMCDLLDVRPGMKILEVGGGSGYHAAvlAALAGPEGQVFSVERMPDLALAARKNLQAAGIAGVTVVEGDGSLGLPE 137
                                       6789***************9999765400455555667777777777777777777777776666666666666665 PP

                                       ..--SEE CS
                              CMAS 127 ..kvdrv 131
                                         ++dr+
  gi|330508510|ref|YP_004384938.1| 138 haPYDRI 144
                                       5556665 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.2e-05     0.027      42     106 ..      66     129 ..      23     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                                       HHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES CS
                    Methyltransf_3  42 LvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekielieg 106
                                       L+++    ++le+G   Gy +  +a    ++G++ +++  ++ +  a+k +q ag+a  + + eg
  gi|330508510|ref|YP_004384938.1|  66 LLDVRPGMKILEVGGGSGYHAAVLAALAGPEGQVFSVERMPDLALAARKNLQAAGIAG-VTVVEG 129
                                       667777789**********998887777778************************974.455555 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.4e-05     0.041      23      84 ..      64     130 ..      50     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                                       HHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S- CS
                            RrnaAD  23 ldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdeklkvvhqD 84 
                                        d l++++ +++le+g G G   + La  a    qv ++E  ++La   +k+l+      ++vv+ D
  gi|330508510|ref|YP_004384938.1|  64 CDLLDVRPGMKILEVGGGSGYHAAVLAALAgpeGQVFSVERMPDLALAARKNLQaaGIAGVTVVEGD 130
                                       5678999************************999************999999986566677888777 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.6e-05     0.055      22      94 ..      62     136 ..      59     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-05
                                       HHHHHCHCCTCSEEEEET-TTSHHHHHHHHH.TTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST CS
                               MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalake.speaevtlvdvdarAlesakenleankle.vevvasdvleeve 94 
                                       ++ + l+ +   k+l +G G G+ +a+la+   pe +v  v+       +a++nl+a +++ v+vv+ d+   ++
  gi|330508510|ref|YP_004384938.1|  62 IMCDLLDVRPGMKILEVGGGSGYHAAVLAALaGPEGQVFSVERMPDLALAARKNLQAAGIAgVTVVEGDGSLGLP 136
                                       677889999999************999987516888899999998888899**********99999999877766 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 ?   12.5   0.0   7.2e-05     0.086       3      83 ..      66     144 ..      64     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.2e-05
                                       HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC.. CS
                   Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggel 79 
                                       lL+ +++ +il++  + G   + +a+l  ++g+v+ v++    + +  +nl+  g+  ++v+e+D++       ++ 
  gi|330508510|ref|YP_004384938.1|  66 LLDVRPGMKILEVGGGSGYHAAVLAALAGPEGQVFSVERMPDLALAARKNLQAAGIAGVTVVEGDGSLGL--PEHAP 140
                                       688889999********************************************************98652..22234 PP

                                       EEEE CS
                   Methyltr_RsmB-F  80 fDri 83 
                                       +Dri
  gi|330508510|ref|YP_004384938.1| 141 YDRI 144
                                       6666 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   9.5e-05      0.11      62     119 ..      71     130 ..      54     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.5e-05
                                       G-SEEEEET-TTSHHHHHHHH.H-TT-EEE.EEE-HHHHHHHHHHS-----TTEEEEES- CS
                    Methyltransf_2  62 glkslvDvGGGtGalakaivs.ayPtikvi.vfDlpeVveaAkehlsageeervefvgGd 119
                                       +  ++++vGGG+G  a+  ++ a P+ +v  v  +p+ + aA++ l+a+   +v++v+Gd
  gi|330508510|ref|YP_004384938.1|  71 PGMKILEVGGGSGYHAAVLAAlAGPEGQVFsVERMPDLALAARKNLQAAGIAGVTVVEGD 130
                                       556899*******9887655413466555413358************************9 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.14      27      46 ..      73      92 ..      57     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                            DUF938 27 ervLEiasGtGqHAvffApa 46
                                       ++LE++ G+G HA+ +A++
  gi|330508510|ref|YP_004384938.1| 73 MKILEVGGGSGYHAAVLAAL 92
                                      38**************9986 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00033      0.39       5      62 ..      75     133 ..      72     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00033
                                       EEEET-TTSHHHHHHH.HHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCC CS
                    Methyltransf_4   5 vleiGcGkGeflvalA.kknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalk 62 
                                       +le+G G+G +   lA  + P+ +++ +E   ++  ++ k+ +a ++  + +++gd   
  gi|330508510|ref|YP_004384938.1|  75 ILEVGGGSGYHAAVLAaLAGPEGQVFSVERMPDLALAARKNLQAAGIAGVTVVEGDGSL 133
                                       79*******99877751689*********************************999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.20s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1545.70
//
Query:       gi|330508511|ref|YP_004384939.1|  [L=509]
Description: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [Methanosaeta concilii GP6]
Scores for complete 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-84  281.6   0.0    4.6e-84  281.2   0.0    1.1  1  iPGM_N         BPG-independent PGAM N-terminus (iPGM_N)
    5.5e-83  278.1   0.0    6.3e-83  277.9   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
    0.00016   21.4   0.0    0.00039   20.1   0.0    1.6  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.032   14.3   0.0    1.7  1  PglZ           PglZ domain


Domain annotation for each model (and alignments):
>> iPGM_N  BPG-independent PGAM N-terminus (iPGM_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.2   0.0     1e-87   4.6e-84       1     215 []      80     290 ..      80     290 .. 0.97

  Alignments for each domain:
  == domain 1  score: 281.2 bits;  conditional E-value: 1e-87
                                       HHHHHHCTGGGG-HHHHHHHHHHHHCTSEEEEEEE-SS--SS--CHHHHHHHHHHHHTT-SEEEEEEEE-SSSSTTT CS
                            iPGM_N   1 inkaiedgslfenealkeaiekakkngkalHllGLlSdGgVHShidhllallelakeegvkkvvvhaflDGRDtapk 77 
                                       i+ a+e+g++++n++l+ea++ a+k g++lHl+GLlSdGgVHShi+hl+alle+a++ ++++v+vha+lDGRD++p+
  gi|330508511|ref|YP_004384939.1|  80 ISLAVEKGTFASNPVLHEAMNLARKGGSKLHLIGLLSDGGVHSHITHLYALLEMARSMDLSRVFVHAILDGRDVPPR 156
                                       6789************************************************************************* PP

                                       -HHHHHHHHHHHHHHCT--EEEEEEEHHHHT--SS-HHHHHHHHHHHCCSSSEEECTTHHHHHHHHHHTT--GGG-- CS
                            iPGM_N  78 saleyleeleeklkelgvgkiasvsGRyyaMDRdkrwervekaydalvkgegeskaesaveaieesyakgetDefve 154
                                       sal+y ++leek++++g+g+ a+vsGRyy+MDRd+rwervekay++lv geg + a+sa+ea+++ y++ge+Def+ 
  gi|330508511|ref|YP_004384939.1| 157 SALGYFRDLEEKFSQTGTGSTATVSGRYYTMDRDRRWERVEKAYRCLVYGEGLR-ADSAEEAVRKGYDRGENDEFIM 232
                                       **************************************************9977.789******************* PP

                                       -EEE...TCCGGS--TT-EEEE----CCCCHHHHHHHHSTTHHCC..--TT-EEEESS-S-T CS
                            iPGM_N 155 ptviaeegkkegtikdgDaviffNFRaDRareltraltdkefkefe.kakklklvtmteYde 215
                                       ptv+    +++g+++dgD++iffNFR+DRare+tra++dk+f+ef+ k+ ++++++mt+Yd+
  gi|330508511|ref|YP_004384939.1| 233 PTVV----DDKGMVDDGDSIIFFNFRPDRAREITRAFVDKDFQEFAtKPIRVHYTCMTQYDA 290
                                       ****....7889*********************************86777889*******95 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.9   0.0   1.4e-86   6.3e-83       2     246 ..       3     491 ..       2     493 .. 0.98

  Alignments for each domain:
  == domain 1  score: 277.9 bits;  conditional E-value: 1.4e-86
                                       EEEEEEETTBB----GGGTTHHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                     Metalloenzyme   2 kvvlvvlDGlGeapadelnaihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel........... 67 
                                       +++++++DG+G++p++e nai +A++P+l++L+ke+P + ++ka+g+avglp ++mgnsevgHl+l           
  gi|330508511|ref|YP_004384939.1|   3 PIAIIIMDGFGISPTQEGNAIAHARKPNLERLWKEYPTT-TLKASGLAVGLPRGQMGNSEVGHLNLgggrivyqdlt 78 
                                       689************************************.8************************************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|330508511|ref|YP_004384939.1|  79 rislavekgtfasnpvlheamnlarkggsklhligllsdggvhshithlyallemarsmdlsrvfvhaildgrdvpp 155
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|330508511|ref|YP_004384939.1| 156 rsalgyfrdleekfsqtgtgstatvsgryytmdrdrrwervekayrclvygeglradsaeeavrkgydrgendefim 232
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|330508511|ref|YP_004384939.1| 233 ptvvddkgmvddgdsiiffnfrpdrareitrafvdkdfqefatkpirvhytcmtqydatlnapvaypaenlidtlge 309
                                       ***************************************************************************** PP

                                       .........HHHHTT-----EEEEEEEE-S---SSHHHHHT--EEEE--SHHSTT--HHHHHHHHHHHH.CC.-SEE CS
                                       .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  68 .........lrisetvkfahvtffwnggrsgyfnpleereeipsdtvitfdlqpemkavevaekaldailsgkfdlv 135
                                                lri+et+k+ahvt+f+ngg+++  ++ e+r+ ips++v+t+dlqp+m+a+ev +++l  + sg++dlv
  gi|330508511|ref|YP_004384939.1| 310 vvsraglkqLRIAETEKYAHVTYFFNGGKEEVNPG-EDRVLIPSPKVATYDLQPQMSAYEVRDELLARLDSGRYDLV 385
                                       ****************************9876666.***************************************** PP

                                       EEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS.........-----EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                     Metalloenzyme 136 vvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdk.qplTsHtlepVPili 211
                                       v+n++n+DmvGHtg +ea+++a+e +D +v+ei+++i + +g +++tADHgnae+m+++d+ qp+T+Ht++pVPi +
  gi|330508511|ref|YP_004384939.1| 386 VLNFANPDMVGHTGIFEAAVKAVEVVDGCVGEIVNRILSLGGAVLLTADHGNAEKMQDSDTgQPHTAHTTNPVPISL 462
                                       **********************************************************9999*************99 PP

                                       ESTT----S--SSHHHHTT-TTEEEEGGGHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 212 vgkglapdkvkegakfrekggLanvaatllnllgl 246
                                       +  + +      + ++re+g La+va+t l+l+ +
  gi|330508511|ref|YP_004384939.1| 463 ITSDRK------SYRLREDGILADVAPTALELMHI 491
                                       999855......6899***************9976 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.79   3.6e+03       3      30 ..       6      37 ..       5      45 .. 0.73
   2 !   20.1   0.0   8.8e-08   0.00039     165     236 ..     372     439 ..     318     479 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.79
                                      EEEETT-B......TTHHHHHGSTSHHHHHHHHH CS
                      Phosphodiest  3 vislDGlr......adlldrlaellpnlaaLake 30
                                      +i++DG+        + + +   + pnl++L+ke
  gi|330508511|ref|YP_004384939.1|  6 IIIMDGFGisptqeGNAIAH--ARKPNLERLWKE 37
                                      68888888666555555555..699999999997 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 8.8e-08
                                       HHHHCT..SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EE CS
                      Phosphodiest 165 vlekel..ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGmad 236
                                       +l ++l  +++dl+++++ ++D vgH  G+ + +  +a++ vD ++g++++ +         +++l++DHG a+
  gi|330508511|ref|YP_004384939.1| 372 ELLARLdsGRYDLVVLNFANPDMVGH-TGIFE-AAVKAVEVVDGCVGEIVNRILSL----GGAVLLTADHGNAE 439
                                       233333569*****************.66665.55789***************999....779********665 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.1e-06     0.032     109     169 ..     379     437 ..     354     443 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.1e-06
                              PglZ 109 lkdkevvyivhnkvDalgdkasteqksfeaveeslk....elkelvkslleengykvlltaDHGf 169
                                        + +++v++   + D++g+  +     fea+ ++++     + e+v+++l   g  vlltaDHG+
  gi|330508511|ref|YP_004384939.1| 379 SGRYDLVVLNFANPDMVGHTGI-----FEAAVKAVEvvdgCVGEIVNRILSL-GGAVLLTADHGN 437
                                       4566777777777799999554.....5555555553344788888888888.***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3733.28
//
Query:       gi|330508512|ref|YP_004384940.1|  [L=415]
Description: peptidase, ArgE/DapE family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-37  127.9   0.0      5e-37  127.6   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.7e-17   63.3   0.0    5.2e-17   61.7   0.0    1.8  2  M20_dimer      Peptidase dimerisation domain
    9.4e-06   25.4   0.0    2.5e-05   24.0   0.0    1.6  2  Peptidase_M28  Peptidase family M28
    0.00087   18.4   0.0      0.035   13.1   0.0    2.3  2  Peptidase_M42  M42 glutamyl aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.6   0.0   1.1e-40     5e-37       2     205 ..      96     414 ..      95     415 .] 0.92

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 1.1e-40
                                       EEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.T CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                     Peptidase_M20   2 lgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.g 76 
                                       +++HlDvVp+e +  w+t pf + +++G++yGrG++d+kg+v+a+++al+al  ++ kpk+++ +l+++dEE+g+ +
  gi|330508512|ref|YP_004384940.1|  96 IYAHLDVVPAEGE--WDTdPFCAVQKNGRVYGRGVSDCKGSVAALVAALKALLSKK-KPKYNLSILLTTDEEVGGyS 169
                                       89*******8877..***************************************97.99*************98889 PP

                                       HHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................... RF
                     Peptidase_M20  77 Gakallegleerekvdavfelhieepgileagklaigvv...................................... 115
                                       G  +l++      +v++ + ++++++   +     +g++                                      
  gi|330508512|ref|YP_004384940.1| 170 GLCYLTD----LGQVKGDL-MLCMDGFSDD-----VGIGsngiitwdvmvkgrsahsgssflgvnaversilvmerl 236
                                       9999999....67888877.5567777777.....4444556779999999************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|330508512|ref|YP_004384940.1| 237 idlkkvvqarrsrlpasspvksvgienlmpilnitminggvkenivpdrcvlrgdrrvipeermeeameeieralep 313
                                       ***************************************************************************** PP

                                       ......EEEEEEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH...TTTEEE.EEEESS.GG CS
                                       ......xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx.xxxxxx.xx RF
                     Peptidase_M20 116 ......kvevelleggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff...agiptv.mifgpg.sg 180
                                             ++e++++ g++p+ ++ ++++v+ ++ea+e+ +g  ++l++ + g+ d ++     gipt+ +++g+  ++
  gi|330508512|ref|YP_004384940.1| 314 lrsegiDFELKFYPGYPPMSVDpEHAWVNEVREAVERRMGFMPQLSAAQ-GSLDQAYAtekTGIPTCvYGVGRQlES 389
                                       ****988999999************************999778887777.9*****99988888966255886646* PP

                                       CTTSTTTEEEHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 181 laHspnEyvdledlekgikvlarll 205
                                       ++H+pnE+v+++dle ++k+l +ll
  gi|330508512|ref|YP_004384940.1| 390 NIHAPNENVRIADLEGYTKFLIELL 414
                                       *********************9997 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.5   6.7e+03      91     108 ..     136     153 ..     134     154 .. 0.78
   2 !   61.7   0.0   1.2e-20   5.2e-17       1     103 [.     197     313 ..     197     318 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHTSCCSTT CS
                         M20_dimer  91 eevleeieeilekeaped 108
                                       +++ ++++++l+k++p++
  gi|330508512|ref|YP_004384940.1| 136 AALVAALKALLSKKKPKY 153
                                       677888999999999887 PP

  == domain 2  score: 61.7 bits;  conditional E-value: 1.2e-20
                                       SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC...................TCCTCCCCCEEC CS
                         M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia..............eerslprttlnvtgi 63 
                                       ig  G++++ + vkg+++Hsg    g+NA+e  + ++++l d+++ ++               +     + ln+t+i
  gi|330508512|ref|YP_004384940.1| 197 IGSNGIITWDVMVKGRSAHSGSSFLGVNAVERSILVMERLIDLKKVVQarrsrlpasspvksVGIENLMPILNITMI 273
                                       5789***************************************88888**************88888889******* PP

                                       CE-CCCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTS CS
                         M20_dimer  64 egGsaknvipdeaeakidiRllpgedpeevleeieeilek 103
                                       +gG + n++pd++ +  d+R+ p+e  ee++eeie +le 
  gi|330508512|ref|YP_004384940.1| 274 NGGVKENIVPDRCVLRGDRRVIPEERMEEAMEEIERALEP 313
                                       ************************************9986 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   5.6e-09   2.5e-05       1      76 [.      81     168 ..      81     193 .. 0.85
   2 ?   -2.0   0.0      0.55   2.5e+03     148     185 ..     366     404 ..     338     409 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.6e-09
                                       EEEEEESTTCESEEEEEEEE--B-TTT.............TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEE CS
                     Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvg.............rgp.ifvGAdDnAsgvaalLelarvlaasgsrpkrgv 63 
                                       N+ a+l+ +a +++l++ AH+D v+ +             +g     G+ D+  +vaal+  +++l + +++pk+++
  gi|330508512|ref|YP_004384940.1|  81 NLQADLSVGA-EKTLVIYAHLDVVPAEgewdtdpfcavqkNGRvYGRGVSDCKGSVAALVAALKALLS-KKKPKYNL 155
                                       6677888888.89************999**99999988663335668********************7.55****** PP

                                       EEEEESSCSGSSH CS
                     Peptidase_M28  64 rflffdaEEagll 76 
                                        +l+++ EE g +
  gi|330508512|ref|YP_004384940.1| 156 SILLTTDEEVGGY 168
                                       *********9755 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.55
                                       STTHHHHTTT--EEEE.CTSSS-TTTTSTTSSGGGB-HH CS
                     Peptidase_M28 148 sDhspflkagvpvldl.aetgfpevyHtprDtldnidkd 185
                                       + +++ +k g+p+  +    + ++++H p+ +++  d +
  gi|330508512|ref|YP_004384940.1| 366 DQAYATEKTGIPTCVYgVGRQLESNIHAPNENVRIADLE 404
                                       445566688888877667888889999999988877765 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   7.7e-06     0.035     122     170 ..     117     167 ..     110     194 .. 0.81
   2 ?    2.7   0.0     0.011        51     253     289 ..     367     406 ..     347     409 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.7e-06
                                       EETTECEEETTH.HHHHHHHHHHHHHHHHCTSS-S.SEEEEEEESTCTTTS CS
                     Peptidase_M42 122 elangkivskal.Ddragvavllellkelkeeele.atvylvatvqEEvGl 170
                                       + +ng++ ++ + D + +va+l+++lk+l +++ + +++ ++ t+ EEvG 
  gi|330508512|ref|YP_004384940.1| 117 VQKNGRVYGRGVsDCKGSVAALVAALKALLSKKKPkYNLSILLTTDEEVGG 167
                                       56788888887636699***********98888778*************94 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.011
                                       HHHHTSTTTSEEEEEEEEEB...STTSTTEEEEHHHHHHH CS
                     Peptidase_M42 253 gaihltgegvptalisiptr...yiHspvevahlddleat 289
                                       +a+ ++++g+pt + +++ +   +iH+p+e + + dle  
  gi|330508512|ref|YP_004384940.1| 367 QAYATEKTGIPTCVYGVGRQlesNIHAPNENVRIADLEGY 406
                                       67788899*********9753348************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3062.61
//
Query:       gi|330508513|ref|YP_004384941.1|  [L=144]
Description: molybdopterin-guanine dinucleotide biosynthesis protein B [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-17   61.9   0.2    6.7e-17   61.6   0.2    1.1  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
     0.0041   17.7   0.2     0.0054   17.3   0.2    1.4  1  AAA_18        AAA domain
     0.0043   16.4   0.6     0.0082   15.5   0.6    1.4  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
     0.0062   16.8   0.4     0.0089   16.3   0.4    1.4  1  AAA_28        AAA domain
     0.0092   16.1   0.4      0.011   15.8   0.4    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.017   15.2   0.0    1.4  1  AAA_14        AAA domain
      0.013   15.9   0.1      0.017   15.5   0.1    1.3  1  AAA_16        AAA ATPase domain
      0.018   15.4   0.0      0.062   13.7   0.0    1.8  2  RNA_helicase  RNA helicase
      0.027   14.7   0.2      0.036   14.4   0.2    1.4  1  AAA_22        AAA domain
      0.032   14.3   0.1      0.046   13.8   0.1    1.2  1  Dynamin_N     Dynamin family
       0.04   13.6   0.0      0.061   13.1   0.0    1.3  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.048   14.2   0.0      0.059   13.9   0.0    1.4  1  ABC_tran      ABC transporter
      0.055   13.0   0.3       0.08   12.5   0.3    1.3  1  GTP_EFTU      Elongation factor Tu GTP binding domain
      0.099   13.1   0.8        0.2   12.1   0.8    1.8  1  AAA           ATPase family associated with various cellular 
       0.11   12.7   0.1       0.17   12.1   0.1    1.3  1  Roc           Ras of Complex, Roc, domain of DAPkinase
       0.13   12.1   0.2       0.19   11.5   0.2    1.7  1  AAA_26        AAA domain
       0.13   11.8   0.1       0.21   11.2   0.1    1.4  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.14   12.3   0.4       0.17   12.0   0.4    1.5  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
       0.14   11.0   0.1       0.21   10.5   0.1    1.2  1  DUF463        YcjX-like family, DUF463


Domain annotation for each model (and alignments):
>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.2   7.1e-20   6.7e-17       1     114 [.       3     110 ..       3     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 7.1e-20
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikeleea 77 
                                       v+++vg++++GKTtL+e l++ l+++g +vgt+K  ++ + vd    D+ rh +AGA+ v+  ++ rl + +++   
  gi|330508513|ref|YP_004384941.1|   3 VIAVVGTKKTGKTTLVEALVRSLAKHG-KVGTVKNMVD-HPVD--RGDTRRHFDAGADVVIGLGEARLLVRRDRG-- 73 
                                       689*********************999.9*****8754.4455..56***********99988888887777754.. PP

                              MobB  78 elsleellarlse..vDlvlvEGfkkealpkievlrael 114
                                         +le  la l++  +D  +vEGfk+++l ki++   e+
  gi|330508513|ref|YP_004384941.1|  74 --DLESALAELERegMDYAVVEGFKNSSLFKIVMADIEV 110
                                       ..5777777775456*****************9876554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   5.8e-06    0.0054       1      40 [.       4      40 ..       4     119 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.8e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakengllle 40
                                      I++ Gt  +GKttl ++L ++l    ++++v + +++++ 
  gi|330508513|ref|YP_004384941.1|  4 IAVVGTKKTGKTTLVEALVRSL---AKHGKVGTVKNMVDH 40
                                      89****************9996...555555555555444 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.6   8.7e-06    0.0082      42      66 ..       4      28 ..       2      38 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.7e-06
                                      EEEE--TTSSHHHHHHHHHHHHHTT CS
                      FtsK_SpoIIIE 42 llvaGatgsGKStalntLilSlatt 66
                                      + v+G++++GK+t + +L+ Sla  
  gi|330508513|ref|YP_004384941.1|  4 IAVVGTKKTGKTTLVEALVRSLAKH 28
                                      579*******************975 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   9.5e-06    0.0089       2      31 ..       4      38 ..       3      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.5e-06
                            AAA_28  2 ivitGgestGKTtlleaLa....ar.gypvvpEaa 31
                                      i+++G+  tGKTtl+eaL     ++ ++ +v+ ++
  gi|330508513|ref|YP_004384941.1|  4 IAVVGTKKTGKTTLVEALVrslaKHgKVGTVKNMV 38
                                      89*************99873332444455666555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   1.2e-05     0.011       2      28 ..       4      30 ..       3     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                                      EEEEESTTSSHHHHHHHHHTSTEEESS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltgekaivsd 28
                                      +a+vG   +GK+tL+ al+++ a+ ++
  gi|330508513|ref|YP_004384941.1|  4 IAVVGTKKTGKTTLVEALVRSLAKHGK 30
                                      89******************9776554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.8e-05     0.017       3      27 ..       2      26 ..       1      57 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                            AAA_14  3 kilvitGaRrvGKTtllkqlikell 27
                                      k+++++G +++GKTtl++ l+++l 
  gi|330508513|ref|YP_004384941.1|  2 KVIAVVGTKKTGKTTLVEALVRSLA 26
                                      799*****************99887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   1.8e-05     0.017      27      60 ..       4      38 ..       2     139 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekdg.giflrgkc 60
                                      + ++G + +GK++lv++l r+l k+g + +++   
  gi|330508513|ref|YP_004384941.1|  4 IAVVGTKKTGKTTLVEALVRSLAKHGkVGTVKNMV 38
                                      7899********************95444433222 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.5e-05     0.062       1      34 [.       4      37 ..       4      52 .. 0.85
   2 ?   -1.0   0.0       2.4   2.2e+03      74      93 ..      93     112 ..      80     116 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsv 34
                                      i ++G + +GK+tl++ L+++l+k+ k  + +++
  gi|330508513|ref|YP_004384941.1|  4 IAVVGTKKTGKTTLVEALVRSLAKHGKVGTVKNM 37
                                      5689*******************99977766655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.4
                      RNA_helicase  74 irlvsstpyplnmasleekg 93 
                                        +  +s  +++ ma++e  +
  gi|330508513|ref|YP_004384941.1|  93 EGFKNSSLFKIVMADIEVSN 112
                                       55678888999999998665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   3.8e-05     0.036       7      39 ..       3      30 ..       1      92 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeer 39
                                      +++v+G + tGKTtl++ l+++l ++      +
  gi|330508513|ref|YP_004384941.1|  3 VIAVVGTKKTGKTTLVEALVRSLAKHG-----K 30
                                      799*******************96554.....3 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.9e-05     0.046       1      21 [.       4      24 ..       4      35 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-05
                                      EEEEEBTTTTHHHHHHHHHTS CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlge 21
                                      iavvG+ + GK+++++aL+++
  gi|330508513|ref|YP_004384941.1|  4 IAVVGTKKTGKTTLVEALVRS 24
                                      89****************975 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.5e-05     0.061       1      44 [.       1      41 [.       1      58 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                         PduV-EutP  1 mkkilliGkvgsGKttLtqalkgeelkYkktqaiefsdeviDtP 44
                                      mk i ++G+ ++GKttL +al     k  k  +    ++++D P
  gi|330508513|ref|YP_004384941.1|  1 MKVIAVVGTKKTGKTTLVEALVRSLAKHGKVGT---VKNMVDHP 41
                                      89999***************9887666655444...34555555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.2e-05     0.059      12      56 ..       2      50 ..       1     138 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.2e-05
                                      SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.....B-HHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.....qeles 56
                                      +++a+vG   +GK+tL+++l + l  + G++   ++ +++     +++++
  gi|330508513|ref|YP_004384941.1|  2 KVIAVVGTKKTGKTTLVEALVRSLA-KHGKVGTVKNMVDHpvdrgDTRRH 50
                                      5799******************997.566664334444443333444444 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 ?   12.5   0.3   8.5e-05      0.08       6      38 ..       4      36 ..       1      52 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.5e-05
                                      EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHH CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlyktgaiskkgekae 38
                                      i+++g   +GKtTL+++L+ ++ +  k g++++
  gi|330508513|ref|YP_004384941.1|  4 IAVVGTKKTGKTTLVEALVRSLAKHGKVGTVKN 36
                                      7899999************99999998888774 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   0.00021       0.2       3      24 ..       6      27 ..       4     142 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                                      EESSTTSSHHHHHHHHHHHHTH CS
                               AAA  3 lyGppGtGKTllakavakelgv 24
                                      ++G++ tGKT+l++a++++l  
  gi|330508513|ref|YP_004384941.1|  6 VVGTKKTGKTTLVEALVRSLAK 27
                                      799**************99843 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 ?   12.1   0.1   0.00018      0.17       2      30 ..       4      32 ..       2      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEET CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekeks 30
                                      + +vG +++GKt+l++ +v++  ++ +  
  gi|330508513|ref|YP_004384941.1|  4 IAVVGTKKTGKTTLVEALVRSLAKHGKVG 32
                                      579***************98877666555 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00021      0.19       3      49 ..       4      48 ..       2     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgieededse 49
                                      i v+gt  + GKT++  +Lvr+l +k  kvg +K +    ++ +d++
  gi|330508513|ref|YP_004384941.1|  4 IAVVGTK-KTGKTTLVEALVRSL-AKHGKVGTVKNMVDHPVDRGDTR 48
                                      5677774.68*************.9999*******999999877765 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 ?   11.2   0.1   0.00022      0.21       2      89 ..       3      93 ..       2     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                      EEEEEESTTCCHHHHHHHHH.CT--SS-EEEEESS-SSCHCCCCCCHCC.CT.....EEEETTTTECCH.CTT-HHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhll.enraglklavivNefgevsiDaellret.gve....ivelenGciCct.lredllkel 73
                                      v+ ++G   +GKTtL+++l+ + +++ k+  + N +    +D+   r++ +      ++ l +  +     r dl  +l
  gi|330508513|ref|YP_004384941.1|  3 VIAVVGTKKTGKTTLVEALVrSLAKHGKVGTVKNMVD-HPVDRGDTRRHfD-AgadvVIGLGEARLLVRrDRGDLESAL 79
                                      5677888889**********87788999999999776.8888777766632.234457888777776666788888888 PP

                                      HHHHHHHTT-SEEEEE CS
                              cobW 74 ealeereerldviliE 89
                                      ++le++   +d+ ++E
  gi|330508513|ref|YP_004384941.1| 80 AELEREG--MDYAVVE 93
                                      8888887..7777777 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 ?   12.0   0.4   0.00018      0.17       2      28 ..       5      30 ..       4     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                      EEEESSTTSSHHHHHHHHHHHHHHTT- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  2 aiastkGGvGKTtlaanLaralarrgl 28
                                      a+++tk  +GKTtl+ +L r+la++g+
  gi|330508513|ref|YP_004384941.1|  5 AVVGTK-KTGKTTLVEALVRSLAKHGK 30
                                      566666.79***************764 PP

>> DUF463  YcjX-like family, DUF463
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00022      0.21       3      29 ..       4      30 ..       3      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                            DUF463  3 lavTGLsraGKtvfitsLvnqLlaaek 29
                                      +av G  + GKt+++ +Lv+ L ++ k
  gi|330508513|ref|YP_004384941.1|  4 IAVVGTKKTGKTTLVEALVRSLAKHGK 30
                                      89********************95544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 960.62
//
Query:       gi|330508514|ref|YP_004384942.1|  [L=489]
Description: hypothetical protein MCON_2726 [Methanosaeta concilii GP6]
Scores for complete 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   69.4   0.1    4.3e-19   68.8   0.1    1.2  1  SBP_bac_3  Bacterial extracellular solute-binding proteins, f
    6.4e-06   26.1   0.0    1.4e-05   25.0   0.0    1.8  1  dCache_1   Cache domain


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 !   68.8   0.1   4.8e-23   4.3e-19       5     212 ..      29     235 ..      25     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 4.8e-23
                                       E-S-BTTTBEE-TTS-EESHHHHHHHHHHHHCT-EEEEEE..-.SGGGHHHHHHTTSSSEEESSEB--HHHHTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3   5 vdadypPfsykdengeltGfdvdlakaiakrlgvkvefvp..v.swdelipalksgkvDiaiaaititpeReekvdF 78 
                                       + ++ypP+++++ +g+l+G++vdl++ i +++gv++   +    +w+e  +   s +  ++  +++  peRe+ +  
  gi|330508514|ref|YP_004384942.1|  29 T-EQYPPYTFQE-DGKLQGISVDLLERIWQKMGVDLNRSIilLlPWTEGYQRTLSENNTVLF-TTARLPEREQLFKW 102
                                       4.79********.*********************9776666756******988888766666.7999********** PP

                                       ESESEEEEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHCTSEEEEESSHHHHHHHHHTTSSSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  79 sqpyfsagqvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkkgaeivefdtleealqaLkngrvda 155
                                         p  s   vll++++++    +i++++dLk  k+g+ ++ +  e l ++  +  +++  +  +  +++L++g++da
  gi|330508514|ref|YP_004384942.1| 103 VGPAASGRDVLLAKRDKN---VTIADPQDLKKYKIGAIKDDVVVERLLNSGLMREDLILENASAPIIEKLEDGSIDA 176
                                       *************96543...7999*******9*******88777766656667788888899999*********** PP

                                       EEEEHHHHHHHHHHCCGCCEEEE.ECGGCECEEEEEEETTTHH.HHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                         SBP_bac_3 156 vvadspvlaylvkknpdkkvvlv.eeplsseeyaiavrkgdse.Lrkainkalaelkad 212
                                       +++++ +   l+++ +++      + +l+++++++a++k+ ++  +  +++al++++++
  gi|330508514|ref|YP_004384942.1| 177 WAYNDLAGIVLIQEAGANVSNYEiAYVLAQNDAYFAFNKETPDsVVRSFQEALDSIREE 235
                                       ************999998887777999999999999999887527899********987 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.6e-09   1.4e-05      18     166 ..     247     380 ..     187     469 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.6e-09
                          dCache_1  18 lanniedvldslenlaetlasnpslqdlleepnra.neasreslqallksilksnpdisgvylvdadGqviassdps 93 
                                       + ++++  l+ l++     a+n                +  +++++ l ++  +n++is+   + +dG++i++  ++
  gi|330508514|ref|YP_004384942.1| 247 IQADLQGSLNDLDSDIANAAQNL-----------StAGLEGDAARRVLGELIGTNSNISNAVTIGKDGKIIVAEGRG 312
                                       44444444444444333333332...........1345567899999***********8887789*******98888 PP

                          dCache_1  94 sppnlegtddpadrdwykealaggggkpvisdpyvdqtggkpvitiavpiyddsgkfiGvlaadldldnlqdl 166
                                       s++    ++d+++++ + + l+++  +pv+s+     ++g + ++ia p+++++g+f+G + a + +d l d 
  gi|330508514|ref|YP_004384942.1| 313 SERAE--GADISNQEHIARLLQTK--IPVFSKQLP-LVEGYNGTSIAYPVFSPHGEFLGGISAIIEPDKLLDA 380
                                       87666..8****************..9*9997662.336999*****************99999988888774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3508.99
//
Query:       gi|330508515|ref|YP_004384943.1|  [L=398]
Description: extracellular ligand-binding receptor [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-49  169.2   0.0    2.2e-49  169.0   0.0    1.0  1  Peripla_BP_6  Periplasmic binding protein
    2.4e-26   92.7   0.0    3.3e-26   92.2   0.0    1.1  1  ANF_receptor  Receptor family ligand binding region
    2.5e-17   62.9   0.0    2.4e-10   40.0   0.1    2.8  2  Peripla_BP_5  Periplasmic binding protein domain
     0.0015   17.4   0.0     0.0023   16.8   0.0    1.2  1  LppC          LppC putative lipoprotein


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.0   0.0   4.9e-53   2.2e-49       1     341 [.      45     380 ..      45     381 .. 0.94

  Alignments for each domain:
  == domain 1  score: 169.0 bits;  conditional E-value: 4.9e-53
                                       EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETTEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-B CS
                      Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNaaGGinGrkielverDdaydpdraaeaarrlvdqdgvdalvgpl 77 
                                       ++kiG+++   G  +++  ++++ga +a++eiN+ GGi+G++iel+ +D ++d++   e+a+ l+  ++v a++g  
  gi|330508515|ref|YP_004384943.1|  45 TVKIGAIYNQVGSQSPLDLPSARGAGLAVDEINRLGGIDGKEIELILCDGKSDTANVGECAKALIA-ENVSAIIGLS 120
                                       79****************************************************************.********** PP

                                       SHHHHHHHHHHHHHHT-EEEESS-HHC..CTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEE.ESSHHHHHH CS
                      Peripla_BP_6  78 ssavaaavaevlakdgvpvigpagltg..ekcspyvfslgpsysaqasalveylakelggkkvalvy.adyafgreg 151
                                        ++ ++a+ +++ ++g+p+++ +++++   + ++  f +++ ++ qa+a++ey+ +e g+k+  l+   d  f r +
  gi|330508515|ref|YP_004384943.1| 121 DTDMVLAAGPITSAAGIPFVTSGATSPrlAEENEGLFLACFGDNVQARAGAEYAFNEMGIKTCSLLVdGDMEFARLL 197
                                       *********************88888634699999**************************999765277******* PP

                                       HHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC-C CS
                      Peripla_BP_6 152 iaalkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakrillvswsgs 228
                                       +  +k+  + +Gge++ e ++   ++d++ + +++ +a+ + ++la++++ + a++ a+++a++d +     +++g+
  gi|330508515|ref|YP_004384943.1| 198 AYYFKERYADLGGEIIMEAFIN--DSDQAILSQEVSDAHSEMIYLAAGPEEAKAVIEALRKADIDSP-----IFGGD 267
                                       **************99898877..99***************************************85.....45566 PP

                                       HHHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCTHCCHHHHH CS
                      Peripla_BP_6 229 eedlkalggeaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaagsltreavr 305
                                         d   l  +++  ++++t    d ++ ++ +fv+ay++ yg  pp ++f+a gy+a+ ll+ea+ +ags ++ea+ 
  gi|330508515|ref|YP_004384943.1| 268 SLDSLDLRRDGMGRIIFSTHALLDENSSRTGEFVRAYKSEYGY-PPENAFSALGYDAVKLLAEAIDRAGSSDPEAIF 343
                                       666688999999******************************9.578****************************** PP

                                       HHHHHS-.BECCCTCCBEECTTSBEE--EEEEEE-TS CS
                      Peripla_BP_6 306 aaleslg.fdgllgplkftaedhqasrpvyvvqvdgg 341
                                       +al + + f g++g++++ ++ + ++++v++v + +g
  gi|330508515|ref|YP_004384943.1| 344 QALGNTSgFSGVTGDISYQDDCRIPNKDVTIVSLIDG 380
                                       ***99999*******9999888889999999986655 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.0   7.4e-30   3.3e-26       7     351 ..      70     378 ..      65     381 .. 0.85

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 7.4e-30
                                       HHHHHHHHT-TTSSTTEEEEEEEEE-TT-HHHHHHHHHHHCCCCEEEEEE-SSHHHHHHHHHHHCCTT-EEEESS-- CS
                      ANF_receptor   7 klAveeinsdpnllpgiklgyeiidtccdfslaleaaldflkgkvvaviGpssssvsdavaslanlfkiPvisygst 83 
                                        lAv+ein+ +++ ++ +++++  d ++d++++ e a  +++ +v a+iG s  +++ a+  +++++ iP+++ g+t
  gi|330508515|ref|YP_004384943.1|  70 GLAVDEINRLGGIDGK-EIELILCDGKSDTANVGECAKALIAENVSAIIGLSDTDMVLAAGPITSAAGIPFVTSGAT 145
                                       59******99777765.*************************99********************************* PP

                                       -GGGG-TTTTTTEEESS--CHHHHHHHHH.HHHHTT--EEEEEEESS.HHHHHHHHHHHHHHHHTT-EEEEEEEEST CS
                      ANF_receptor  84 spelsdknryptflrtvpsdtsqaqAivd.ilkhfgWkkvaliysdd.dygesglqaleeeleergicvalkekipe 158
                                       sp l + n+   ++     d+ qa+A ++  ++++g k+ +l+++ d +  + ++++++e+ ++ g ++ +++ i+ 
  gi|330508515|ref|YP_004384943.1| 146 SPRLAEENE--GLFLACFGDNVQARAGAEyAFNEMGIKTCSLLVDGDmEFARLLAYYFKERYADLGGEIIMEAFIN- 219
                                       *********..7777888889*****9993567**************9***************************9. PP

                                       CHHHCHHHHHHHHHHTT.T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC..HHHHHTT- CS
                      ANF_receptor 159 ssnddevvrkllkeiks.karvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpeltgleaaegv 234
                                           d++ + l +e+++ ++  i+l + +e+a+ +++a r++ ++++    ++     +sl++++     ++ ++ +
  gi|330508515|ref|YP_004384943.1| 220 ----DSDQAILSQEVSDaHSEMIYLAAGPEEAKAVIEALRKADIDSP---IFGG----DSLDSLDL---RRDGMGRI 282
                                       ....66777778888888889*************************6...5532....23333322...22223333 PP

                                       E..EEEE--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSSHCCB-HHHH CS
                      ANF_receptor 235 l..gfrlkdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpgralscntlk 309
                                       +  + +l d ns ++ ef+         ++ ++++g  + ++++al YdaV llaeA++++++              
  gi|330508515|ref|YP_004384943.1| 283 IfsTHALLDENSSRTGEFV---------RAYKSEYGYPPENAFSALGYDAVKLLAEAIDRAGS-------------- 336
                                       31134448***********.........77888888888999********************3.............. PP

                                       CCHHHHHHHHHHHT-E.EEETTSCEEB-TTSBBE.-EEEEEEEE CS
                      ANF_receptor 310 pweggqkllrylrnvn.feGltGdvkfdengdrv.ptydilnlq 351
                                          + +++ ++l n++ f G+tGd+++ ++ + + +++ i+ l 
  gi|330508515|ref|YP_004384943.1| 337 --SDPEAIFQALGNTSgFSGVTGDISYQDDCRIPnKDVTIVSLI 378
                                       ..344555556665544**********99999999999999876 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.1   5.3e-14   2.4e-10       1      74 [.      46     118 ..      46     122 .. 0.97
   2 !   19.1   0.0   1.2e-07   0.00053     118     330 ..     164     370 ..     150     395 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 5.3e-14
                      Peripla_BP_5   1 ikvGvLhSlsGtmaisekslkdaallaieeinaagGvlgrkieavvvdpasdwelfaekaeklieedkvevvfG 74 
                                       +k+G ++ + G+ +  +    ++a la++ein+ gG++g++ie ++ d++sd++   e a++li+ ++v++++G
  gi|330508515|ref|YP_004384943.1|  46 VKIGAIYNQVGSQSPLDLPSARGAGLAVDEINRLGGIDGKEIELILCDGKSDTANVGECAKALIA-ENVSAIIG 118
                                       69**************************************************************9.89****99 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.2e-07
                      Peripla_BP_5 118 nqqaipavdyllselg.akrvflvGsdyvypretnrilkallkakggevvgeeYlplgssdvqkivakikkakpdvv 193
                                       n qa   ++y+++e+g ++  +lv  d  ++r  +  +k+  ++ gge+++e ++  ++sd + + +++ +a+++++
  gi|330508515|ref|YP_004384943.1| 164 NVQARAGAEYAFNEMGiKTCSLLVDGDMEFARLLAYYFKERYADLGGEIIMEAFI--NDSDQAILSQEVSDAHSEMI 238
                                       77888889999****94455678999**************************986..68898899999********* PP

                      Peripla_BP_5 194 lstinGdsnvafykelkeagikaekipvvs.lsvaeeelaaidaealvGhlaawnYfqsvdtpenkafvakfkarvg 269
                                       +     +++ a  ++l++a+i++   p++   s+   +l++ +   ++     +  +   ++ +  +fv+++k+++g
  gi|330508515|ref|YP_004384943.1| 239 YLAAGPEEAKAVIEALRKADIDS---PIFGgDSLDSLDLRRDGMGRIIFS---THALLDENSSRTGEFVRAYKSEYG 309
                                       *9999999999********9986...555313344444444333333222...22223345667789*********9 PP

                      Peripla_BP_5 270 edrvtndpmeaayiqvklwaqAvekagstdvekvreallgqe.lkapeGevkidpenhhlsk 330
                                            n+     y +vkl+a+A+ +ags+d+e++ +al +++ ++  +G ++ + + +   k
  gi|330508515|ref|YP_004384943.1| 310 Y-PPENAFSALGYDAVKLLAEAIDRAGSSDPEAIFQALGNTSgFSGVTGDISYQDDCRIPNK 370
                                       8.567899999*************************99876437777777776665555555 PP

>> LppC  LppC putative lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.2e-07    0.0023     331     523 ..     166     367 ..     145     373 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.2e-07
                                       HHHHHHHHHHHT.T-SSEEEEEESS.HHHHHHHHHHHHHHHHHHSS--EEEEESSGGG..HHHHHHHH-.TTTEEEE CS
                              LppC 331 eaesaAsklwad.gvRnplvlvpqn.dlGrRvveAFnerwqqlagtdaaielvdqpad..laqqlkdasrqdidavy 403
                                       +a++ A++++++ g+++   lv  + ++ r  +  F+er+  l+g+ +   ++++  +  l+q+++da++   + +y
  gi|330508515|ref|YP_004384943.1| 166 QARAGAEYAFNEmGIKTCSLLVDGDmEFARLLAYYFKERYADLGGEIIMEAFINDSDQaiLSQEVSDAHS---EMIY 239
                                       57788999998768999988888772555556678************99999998766548899999775...9*** PP

                                       E---HHHHHHHHHHHHT.T-TTEEEEE-GGG--HHT-HHHHHHTTT-EEEE-GGGG-SSSHHHHHHH.HHTTT-H.H CS
                              LppC 404 ivanskelaeikptlanasakdlklyasSrsvsgntkpeqdedlngiqfsdiPflvdpassikkkvaaklpeaeg.s 479
                                       ++a ++e++ +   l      d ++++   +    +    +  +  i fs+  +l +++s + + v a   e  +  
  gi|330508515|ref|YP_004384943.1| 240 LAAGPEEAKAVIEALRK-ADIDSPIFGGDSL---DSLDLRRDGMGRIIFSTHALLDENSSRTGEFVRAYKSEYGYpP 312
                                       ********999999999.555689***9999...677788999************9999999999987666666625 PP

                                       HHHHHHHHHHHHHHHTT.HHH.........HHHS.TT--EEETTEEEEE-TT-BE CS
                              LppC 480 llrLyAlGvDAyrLive.lne.........lkav.pgytidGlTGtLsldencnv 523
                                       +    AlG+DA +L  e +++         ++a  +  + +G+TG +s +++c++
  gi|330508515|ref|YP_004384943.1| 313 ENAFSALGYDAVKLLAEaIDRagssdpeaiFQALgNTSGFSGVTGDISYQDDCRI 367
                                       67788******98876524442222222334444466778999999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2924.67
//
Query:       gi|330508516|ref|YP_004384944.1|  [L=828]
Description: sulfatase family protein [Methanosaeta concilii GP6]
Scores for complete 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-91  305.4   0.1    6.3e-91  305.0   0.1    1.2  1  Sulfatase     Sulfatase
    1.2e-05   25.0   1.1    0.00038   20.2   1.1    2.3  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
     0.0009   19.4   0.0     0.0021   18.2   0.0    1.6  1  Laminin_G_3   Concanavalin A-like lectin/glucanases superfami
     0.0045   16.9   0.0      0.011   15.6   0.0    1.6  1  DUF4994       Domain of unknown function
     0.0094   16.2   0.2      0.022   15.0   0.2    1.7  1  DUF4976       Domain of unknown function (DUF4976)
  ------ inclusion threshold ------
      0.071   11.7   0.0       0.11   11.1   0.0    1.2  1  DUF229        Protein of unknown function (DUF229)


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.0   0.1   2.1e-94   6.3e-91       1     307 [.     107     535 ..     107     537 .. 0.98

  Alignments for each domain:
  == domain 1  score: 305.0 bits;  conditional E-value: 2.1e-94
                                       EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT.. CS
                         Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg.. 75 
                                       pnvv++++dd g+g+lg++gg+++ tpn+drla+ gl++tnf++++  csp+ra++ltgr+ h++gv+s  e++   
  gi|330508516|ref|YP_004384944.1| 107 PNVVFLVLDDIGYGGLGCFGGPVE-TPNIDRLAQGGLKYTNFHTTG-ICSPTRACMLTGRNLHSVGVGSLMEFASgy 181
                                       9**********************9.9*****************997.**************************99** PP

                                       ....HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC.......CTTTSEEEETSSSCHHTCCCCCCCCCE CS
                         Sulfatase  76 ....gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk.......nrgfdrflgfptgsaalkdpekseyng 141
                                             l ++ at+pe+l ++GY+t+++gkwhl +s+  +++        +rgf+rf+gf +  + +++p+ +++ +
  gi|330508516|ref|YP_004384944.1| 182 pgytTYLSKEAATMPEMLVGQGYDTYCVGKWHLAPSDSINAAGpydqwpmSRGFERFYGFLESHTSQWYPDLVSGST 258
                                       ************************************9988777999******************************9 PP

                                       CTCCC..TTTTCSHHHHHHHHHHHHH....HCCCTSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH.... CS
                         Sulfatase 142 evlrv..ppeggysddrlldealefl....larndkpfflylatlapHappeapdeyakkyatffddgseaar.... 208
                                       ++ ++  p+eg++++++l+++ ++++      ++dkpfflyla+ a H+p+++p+ y +ky+++fd+g++a+r    
  gi|330508516|ref|YP_004384944.1| 259 RIKPPatPEEGYHLSKDLVNQSIQYIsdgkSLQPDKPFFLYLAFGAGHWPHHVPKAYIDKYKGRFDMGWDAMRnqtl 335
                                       99888***********************954455*************************************999999 PP

                                       .....................................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEES CS
                         Sulfatase 209 .....................................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSD 248
                                                                            + +e+ ++ + y+D++igr+l++Le++g+l+nt++v++SD
  gi|330508516|ref|YP_004384944.1| 336 akekelgvvpentdlaprdqwvkawdnltedekkvyaRFAEVHAAYIDYTDEQIGRFLDYLEDSGQLNNTMIVVISD 412
                                       9999************************************************************************* PP

                                       SSSCCCG...............................................................HHTTSSS CS
                         Sulfatase 249 hgaslee...............................................................sngplrg 262
                                       +gas e+                                                               +n+p+++
  gi|330508516|ref|YP_004384944.1| 413 NGASPEGdangftntvmwansvseggdstgfqndflpirnitnistmlskideiggplsyptyplgwamaDNTPHKL 489
                                       ***************************************************************************** PP

                                       CTTCSSSHHHHBEEEEEEETTTSHC..EEECSEEEGGGHHHHHHHHT CS
                         Sulfatase 263 gkganayeggtrvPllvwwpgekap..rvseelvshiDlfptildla 307
                                       +k+ +++eggt++P++++wp+++++  ++++++ ++iD++pt+ld++
  gi|330508516|ref|YP_004384944.1| 490 YKW-TSHEGGTHDPMIIYWPDGIKEegGIRSQFCHAIDVVPTVLDVL 535
                                       ***.****************************************986 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   1.1   1.3e-07   0.00038      20     238 ..     130     419 ..     124     437 .. 0.55

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-07
                                       TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEEEEETTTTGG.GGGCTT... CS
                      Phosphodiest  20 llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgeyvvfvtededa.prwwqg... 92 
                                       ++pn+++La+ g++++n +++   +  p  a+++TG++  + G+ +   + +++  y+++  +++++ p+ ++g   
  gi|330508516|ref|YP_004384944.1| 130 ETPNIDRLAQGGLKYTNFHTTG--ICSPTRACMLTGRNLHSVGVGSLMEFASGYPGYTTYLSKEAATmPEMLVGqgy 204
                                       6899999999999999955544..45688999999999999999995555666666555555555448666666566 PP

                                       ....S-HHHHHHHTHTTCEEEES..ETTTTSEBTTCT.SC.TBHHSBTCT.CSTTS..................... CS
                      Phosphodiest  93 ....epiwdtaakarglkaaalf..wpgsevdystyyylvsetppryleddfnakv..................... 142
                                              w  a  +  ++aa  +  wp s    + y+ l+s+t++ y+ d ++ +                      
  gi|330508516|ref|YP_004384944.1| 205 dtycVGKWHLAPSD-SINAAGPYdqWPMSRGFERFYGFLESHTSQWYP-DLVSGSTrikppatpeegyhlskdlvnq 279
                                       65442235555555.444442221133333333334444443333333.2222222333332111111000033333 PP

                                       ..................................CHHHHHHHHHHHHHHHCHTHSHHHHHCTSSESEEEEEECCCHH CS
                      Phosphodiest 143 ..................................pledkvdkavlqtwldaafakvvlekelekpdlllvyleetDt 185
                                                                          + dk++ ++   w ++                          
  gi|330508516|ref|YP_004384944.1| 280 siqyisdgkslqpdkpfflylafgaghwphhvpkAYIDKYKGRFDMGWDAM-------------------------- 330
                                       334444444444444444444444443333333322223332222233333.......................... PP

                                       HHHHH-TTSHH..............................................HHHHHHHHHHHHHHHHHHHH CS
                      Phosphodiest 186 vgHkfGpdspe..............................................vedalrrvDkaigdLleald 216
                                                                                                +++++ + D+ ig++l++l+
  gi|330508516|ref|YP_004384944.1| 331 ----------RnqtlakekelgvvpentdlaprdqwvkawdnltedekkvyarfaevHAAYIDYTDEQIGRFLDYLE 397
                                       ..........1344444444444444444444444444555555566667777777799****************** PP

                                       HTTGTTTEEEEEEES---EEEH CS
                      Phosphodiest 217 erglsaetniilvSDHGmadvs 238
                                       + g  ++t i++ SD G+++  
  gi|330508516|ref|YP_004384944.1| 398 DSGQLNNTMIVVISDNGASPEG 419
                                       **999**************985 PP

>> 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 !   18.2   0.0     7e-07    0.0021      14     114 ..     684     786 ..     674     822 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7e-07
                       Laminin_G_3  14 lptssfTvsaWvkpdslpsaaqiiissssdg.rgfelgldgsgrlrfsvnagngaeesvtsgasvpageWtHvavty 89 
                                         +ss+T++a+v+++ ++s+ ++++s  ++   g++l++  +++l f +n  n + ++v+s ++vp+ge   + + +
  gi|330508516|ref|YP_004384944.1| 684 TRNSSYTLTAYVNTSGNDSE-GVLFS-IGGRfAGLSLYV-KDKHLIFDYNLFNMKHYRVSSINEVPEGE-ATLGFEF 756
                                       4599**************95.56661.344467888888.558*****9999999**************.5566666 PP

                       Laminin_G_3  90 d.....ggtlrlYvNGvevgsatltgglls 114
                                       +      g+ rl++NG+e gs + + ++++
  gi|330508516|ref|YP_004384944.1| 757 EktgrwKGEGRLFINGNEEGSVDMSFTVPA 786
                                       687766677************998877443 PP

>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.8e-06     0.011      68      95 ..     606     633 ..     587     635 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.8e-06
                           DUF4994  68 pqLydlkkdegekenvaekhpekvkelk 95 
                                         Ly+l++d++e +n+a+++p k++e+k
  gi|330508516|ref|YP_004384944.1| 606 WELYNLTDDVSEVHNLADQYPAKLEEMK 633
                                       57************************98 PP

>> DUF4976  Domain of unknown function (DUF4976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   7.4e-06     0.022      58     101 ..     602     643 ..     549     645 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.4e-06
                           DUF4976  58 didewelyDlkkDpkelknlyddpeyeevvkelkkkleelrkky 101
                                       ++d+wely+l +D +e++nl d+  y +  +e+k++  +  +ky
  gi|330508516|ref|YP_004384944.1| 602 QNDTWELYNLTDDVSEVHNLADQ--YPAKLEEMKDRWWAEASKY 643
                                       679*****************886..5555666776666655555 PP

>> DUF229  Protein of unknown function (DUF229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.6e-05      0.11     308     343 ..     379     414 ..     356     516 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.6e-05
                            DUF229 308 fnllealDedllkylkklekkgllentlvlllsDHG 343
                                        +++  +De++ ++l  le++g+l+nt+++++sD G
  gi|330508516|ref|YP_004384944.1| 379 AAYIDYTDEQIGRFLDYLEDSGQLNNTMIVVISDNG 414
                                       5677888***************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (828 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 5638.29
//
Query:       gi|330508517|ref|YP_004384945.1|  [L=428]
Description: anaerobic sulfatase-maturating protein [Methanosaeta concilii GP6]
Scores for complete 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   0.0    2.5e-14   54.0   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    5.2e-11   42.2   7.0    1.4e-10   40.9   7.0    1.8  1  SEC-C        SEC-C motif
    6.2e-08   33.1   0.2    1.5e-07   31.8   0.2    1.7  1  SPASM        Iron-sulfur cluster-binding domain
    0.00019   21.7   0.0    0.00036   20.8   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
    0.00097   19.3   0.0     0.0018   18.4   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0     7e-18   2.5e-14       4     167 .]      18     187 ..      16     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 7e-18
                                       ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTT..SEEEEEESSTGGGS.TTHHHHHHHHHHTC.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxx.. RF
                       Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekg..vkevilgggeplly.pdfvellerlakla.. 74 
                                       + +Cnl+C++C + ++++ ++ + ++  +e+le   + + + ++    ++ + ggep+l   df +   ++ ++   
  gi|330508517|ref|YP_004384945.1|  18 GAACNLGCKYCFFLSKKSLYPGSSFRMSDELLETYIRQYlEAQRipQATIAWQGGEPTLMgLDFFRRSVQIEHKYsr 94 
                                       679*************8888888888888887777666655555235556666****99544444444444444499 PP

                                       .CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH....HHHHHHT.CTSHHHHHHHHHHHHHHTTSETE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 .vpgiritvetngtlpdeeklerllelgvdrvslgleaadde....kvlklmn.rghtfeevlealeklreagikrv 145
                                        +  i +t+ tngtl+d+e+ e ++e +   + l+l+ + ++    +     + +++tf++v++a ++lr + ++  
  gi|330508517|ref|YP_004384945.1|  95 pDMIIQNTMQTNGTLLDDEWCEFFRENN-FLIGLSLDGPREFhdayR---VDKtGKPTFDRVMKAARLLRHHKVD-- 165
                                       99************************77.************985533...333488****************999.. PP

                                       EEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 146 vdrivglpGendeeleellell 167
                                       +++++ ++  n ++  e++++l
  gi|330508517|ref|YP_004384945.1| 166 YNILTTVHAANGDHPLEVYRFL 187
                                       7888888888888888888875 PP

>> SEC-C  SEC-C motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   7.0   3.8e-14   1.4e-10       1      19 []     408     426 ..     408     426 .. 0.98

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3.8e-14
                             SEC-C   1 RNdpCPCGSGkKYKkCCgp 19 
                                       RNd+CPCGSG+KYKkC+g+
  gi|330508517|ref|YP_004384945.1| 408 RNDACPCGSGLKYKKCHGR 426
                                       9****************97 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.2   4.1e-11   1.5e-07       4      68 .]     271     332 ..     265     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 4.1e-11
                             SPASM   4 psrslfInsdGdVvpCcvdkktyvee.lklGnireesleeIwnseeyqefrkskkfplielCrnCp 68 
                                         ++++++++Gd++ C    +++ve+ + lGni + +++ + +s + q+f + k ++l+e+Cr+C+
  gi|330508517|ref|YP_004384945.1| 271 CGTAMALEHNGDMYSC----DHFVEPkYLLGNIWKRDMAGLARSTKQQKFGRDKLDALPEYCRRCE 332
                                       46899***********....4555556************************78899999******6 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     1e-07   0.00036      14     115 ..      20     125 ..      17     143 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1e-07
                           Fer4_12  14 gCnlsCkgCfnketwsfk..sgkeftkelleeiie.dlkkesi..egltllGGEPllpenaeallelvkevkeekp. 84 
                                        Cnl Ck+Cf  + +s    s+  +++elle  i+  l+ ++i    +   GGEP l     ++ +   +++ +++ 
  gi|330508517|ref|YP_004384945.1|  20 ACNLGCKYCFFLSKKSLYpgSSFRMSDELLETYIRqYLEAQRIpqATIAWQGGEPTL--MGLDFFRRSVQIEHKYSr 94 
                                       6*********76666655115555567777776651566677765677789******..444444444445555553 PP

                           Fer4_12  85 ekdiwlytgytleelskkekeellkeidvlv 115
                                          i+  t  t+ +l+++e+ e+ +e ++l+
  gi|330508517|ref|YP_004384945.1|  95 PDMIIQNTMQTNGTLLDDEWCEFFRENNFLI 125
                                       2456667777888888778888888877765 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     5e-07    0.0018       6      90 ..      19     108 ..      17     130 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5e-07
                           Fer4_14   6 sgCnlsCkgCd..nketwks..elgkpqteelleqilk.dlkkseikiqglvltGGePLhyenkkellklvkrlkee 77 
                                       + Cnl Ck C+     +++    +    ++elle+ ++  l++++i ++ +   GGeP +    + + + v ++ ++
  gi|330508517|ref|YP_004384945.1|  19 AACNLGCKYCFflS--KKSLypGSSFRMSDELLETYIRqYLEAQRIPQATIAWQGGEPTLM-GLDFFRRSV-QIEHK 91 
                                       57*********553..444411344444566666766659******************743.333333333.34444 PP

                           Fer4_14  78 y..pekki..wletngt 90 
                                       y  p++ i  +++tngt
  gi|330508517|ref|YP_004384945.1|  92 YsrPDMIIqnTMQTNGT 108
                                       42444333225666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2773.58
//
Query:       gi|330508518|ref|YP_004384946.1|  [L=141]
Description: glyoxalase family protein [Methanosaeta concilii GP6]
Scores for complete 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   40.9   0.0    5.8e-10   39.4   0.0    1.7  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    5.7e-07   30.3   0.0    1.4e-06   29.0   0.0    1.6  1  Glyoxalase_6  Glyoxalase-like domain
    0.00052   19.9   0.0    0.00091   19.2   0.0    1.4  1  Glyoxalase_2  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   9.8e-14   5.8e-10       2     128 .]       5     124 ..       4     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 9.8e-14
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEE..EESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdn..teeteglriaffhaggghielvlneapsgaakhvkkieetvhh 76 
                                       ++ v+l v+dl+k+++FY++ LG+ ++ ++     + + + + a     +  ++l  n  ++g+         ++  
  gi|330508518|ref|YP_004384946.1|   5 LNIVTLGVRDLDKAIRFYRDGLGWPMSSVSAGdfAIFKLSTGTALALFPRELLALDANVRDPGGF--------GGIT 73 
                                       67899*************************92222222333333333333333333333333333........5669 PP

                                       EEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  77 vafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       +a+ + + e+v+  l ++ + g+++ ++ +   +g+  + yf DpdG+ +ei
  gi|330508518|ref|YP_004384946.1|  74 LAHNVATREEVDLVLSQAIQSGGSILKPAQAPEWGGYSG-YFADPDGHPWEI 124
                                       ***************************998888887776.7*********97 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   2.4e-10   1.4e-06       2     106 ..       8     124 ..       7     125 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.4e-10
                      Glyoxalase_6   2 vvldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe................paknrvHl 62 
                                       v+l ++d +++++F+++ lgw+ ++ +  + d + +++ +++a  l  ++                   +    +  
  gi|330508518|ref|YP_004384946.1|   8 VTLGVRDLDKAIRFYRDGLGWPMSSVS--AGDFAIFKLSTGTALALFPRE--LlaldanvrdpggfggiT----LAH 76 
                                       678899*******************99..444444444333333332222..233655455655542221....333 PP

                      Glyoxalase_6  63 dlav.edldaevarlvalGArvlreprdgthgr...vlaDPeGneFcv 106
                                       ++a+ e++d    ++++ G++ l++ +++++g+    +aDP+G+++ +
  gi|330508518|ref|YP_004384946.1|  77 NVATrEEVDLVLSQAIQSGGSILKPAQAPEWGGysgYFADPDGHPWEI 124
                                       343358999999********************9************987 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.5e-07   0.00091       3     114 ..       7     125 ..       5     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.5e-07
                                       ----EES-HHHHHHHHHHTT---EE.EE-SSEEEE..TTS-EEEEHHHHHH-------S..--SS-EEEEEE...S- CS
                      Glyoxalase_2   3 lillvvkdieeskkFYedvlelkik.ldfGenvsf..etgfalkedlkelinldesiae..qsnnfeLyFev...ed 71 
                                       ++ l v+d++++ +FY+d l  ++     G++  f  +tg+al    +el+ ld+++        + L  +v   e+
  gi|330508518|ref|YP_004384946.1|   7 IVTLGVRDLDKAIRFYRDGLGWPMSsVSAGDFAIFklSTGTALALFPRELLALDANVRDpgGFGGITLAHNVatrEE 83 
                                       56688*****************9963689999988445999999989999999998887656778888887622268 PP

                                       HHHHHHHH..GGGS-EEEEEEE-TTS-EEEEEE-TT--EEEEE CS
                      Glyoxalase_2  72 vdaflqklkeaeniellhelkekpWgqrvirfyDpDkhiiEig 114
                                       vd +l++  + +   +l++ +  +Wg    +f+DpD+h  Ei+
  gi|330508518|ref|YP_004384946.1|  84 VDLVLSQAIQSG-GSILKPAQAPEWGGYSGYFADPDGHPWEIA 125
                                       888887754444.58899999999**************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1029.93
//
Query:       gi|330508519|ref|YP_004384947.1|  [L=230]
Description: hypothetical protein MCON_2734 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1792.53
//
Query:       gi|330508520|ref|YP_004384948.1|  [L=233]
Description: alanyl-tRNA synthetase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-14   52.5   1.2    6.8e-14   51.7   1.2    1.4  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
    1.5e-10   40.2   0.0      2e-10   39.8   0.0    1.1  1  tRNA-synt_2c  tRNA synthetases class II (A)


Domain annotation for each model (and alignments):
>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   1.2   7.6e-18   6.8e-14       1      44 []     185     228 ..     185     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 7.6e-18
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +rvv+i+ ++ ++CgGtHv +TgeI+ +k+++ e+++k +rR+y
  gi|330508520|ref|YP_004384948.1| 185 IRVVEIEGVDRQACGGTHVGRTGEIKGIKLVKAENKGKANRRVY 228
                                       7*****779**********************************9 PP

>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   2.2e-14     2e-10     474     552 .]      15      89 ..       5      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 2.2e-14
                                       EEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXH CS
                      tRNA-synt_2c 474 efveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevde 550
                                       +f + v+ ++ +gv+L++T+fY++sGGq +D G ++ ++ ef v  v+  + +  h+++     l  gd+v++++d+
  gi|330508520|ref|YP_004384948.1|  15 SFDTTVADVKGDGVILEETAFYPQSGGQPSDLGSLFRDEDEFCVLRVEPSGPI--HIMDR--TGLAPGDRVSGRIDW 87 
                                       577889999***********************************988887765..67766..4799**********9 PP

                                       HH CS
                      tRNA-synt_2c 551 er 552
                                       +r
  gi|330508520|ref|YP_004384948.1|  88 DR 89 
                                       86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1617.44
//
Query:       gi|330508521|ref|YP_004384949.1|  [L=87]
Description: hypothetical protein MCON_2736 [Methanosaeta concilii GP6]
Scores for 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-07   28.6   0.1    9.2e-07   28.4   0.1    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 !   28.4   0.1   5.1e-11   9.2e-07       4      54 ..      32      80 ..      29      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.1e-11
                              UbiA  4 palvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmert 54
                                      ++++g ++a+g++p +++ +l +l+++++++ a++ NdyfD e D+   ++
  gi|330508521|ref|YP_004384949.1| 32 CVVAGEVIASGSVPEASIGILGFLAGFFISGTAMITNDYFDLEVDRV--NH 80
                                      7889999***************************************9..55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 680.06
//
Query:       gi|330508522|ref|YP_004384950.1|  [L=473]
Description: glutamate synthase [Methanosaeta concilii GP6]
Scores for complete 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-42  142.2   0.3      8e-42  141.6   0.3    1.3  1  Fer4_20         Dihydroprymidine dehydrogenase domain II, 4Fe
    6.9e-38  130.5   1.5      1e-37  130.0   1.5    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.6e-11   43.9   2.6    4.9e-05   23.8   0.1    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    7.7e-10   38.5   2.0    4.2e-05   23.0   0.1    3.3  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-07   31.7   2.3    2.2e-07   31.0   0.2    2.2  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    6.2e-07   28.9   2.3    0.00068   19.0   0.3    2.3  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    1.1e-06   29.0   0.2     0.0032   17.9   0.1    2.5  2  NAD_binding_7   Putative NAD(P)-binding
    2.9e-05   23.6   4.0    0.00076   18.9   0.3    2.3  2  FAD_oxidored    FAD dependent oxidoreductase
    0.00011   21.5   1.8    0.00011   21.5   1.8    2.4  3  FAD_binding_2   FAD binding domain
    0.00013   21.4   0.2       0.04   13.3   0.0    2.7  3  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0003   19.6   0.7     0.0003   19.6   0.7    2.4  3  HI0933_like     HI0933-like protein
    0.00036   19.9   0.3    0.00036   19.9   0.3    1.8  2  Thi4            Thi4 family
    0.00045   19.4   4.6     0.0014   17.8   0.2    2.8  3  GIDA            Glucose inhibited division protein A
    0.00075   18.9   0.2     0.0048   16.2   0.2    2.3  3  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0015   17.8   0.3      0.012   14.8   0.1    2.0  2  FAD_binding_3   FAD binding domain
     0.0027   17.2   0.7       0.43   10.0   0.0    2.6  3  PALP            Pyridoxal-phosphate dependent enzyme
     0.0039   16.8   4.5     0.0071   16.0   0.8    2.6  3  DAO             FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.013   16.1   0.6      0.013   16.1   0.6    2.5  2  Fer4_7          4Fe-4S dicluster domain
      0.018   14.2   0.0       0.43    9.7   0.0    2.6  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
       0.02   15.5   2.6       0.34   11.5   0.0    3.5  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.032   13.0   0.0      0.056   12.2   0.0    1.3  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
      0.033   13.9   0.0       0.72    9.5   0.0    2.3  2  ELFV_dehydrog   Glutamate/Leucine/Phenylalanine/Valine dehydr
      0.033   14.1   1.1        2.1    8.2   0.1    2.3  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.049   13.2   0.1       0.96    9.0   0.0    2.4  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.073   13.1   2.0       0.87    9.6   0.0    2.7  3  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
       0.11   12.6   0.8        2.2    8.4   0.1    3.0  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
       0.14   11.2   0.3       0.24   10.4   0.3    1.3  1  Lycopene_cycl   Lycopene cyclase protein
       0.16   12.2   0.1       0.16   12.2   0.1    1.8  2  Fer4_18         4Fe-4S dicluster domain
        0.4   10.7   6.0       0.27   11.2   0.4    2.7  2  NAD_binding_9   FAD-NAD(P)-binding
       0.54   10.5   7.8       0.14   12.3   2.3    2.5  2  Fer4_2          4Fe-4S binding domain
        1.9    9.1   8.1       0.34   11.5   0.5    2.6  2  Fer4_17         4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6   0.3   1.4e-44     8e-42       1     111 [.      23     132 ..      23     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 1.4e-44
                                       HTTS-S-SB----HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-HHHHHHHS-G CS
                           Fer4_20   1 raknfkevalglteeealeeAsRClqCkkapcvkgCPveidipefikkiaegnleeaakiiketnslpavcgrvCpq 77 
                                       r++nf+evalg+t e+a+ eA+RC+qCkk++cv+gCPv ++ipefi ++++g++ +aa  +k +nslp +cgrvCpq
  gi|330508522|ref|YP_004384950.1|  23 RRSNFEEVALGYTPEQAALEANRCIQCKKPKCVEGCPVGVNIPEFILALRDGDMPGAALSLKGKNSLPGICGRVCPQ 99 
                                       5789************************************************************************* PP

                                       GGTGCCS-GGGTTB.----HHHHHHHHHHHHHHT CS
                           Fer4_20  78 eelCegaCvlekkgkepvaigklerfvadaaree 111
                                       e +Ce++Cvl+kkg +p+aig+lerfvad++r +
  gi|330508522|ref|YP_004384950.1| 100 EVQCESRCVLGKKG-APIAIGRLERFVADWERVT 132
                                       **********9888.***************9865 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 !  130.0   1.5   1.7e-40     1e-37       2     294 .]     147     453 ..     146     453 .. 0.80

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 1.7e-40
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...HHHHCHHHHCCCCHCCTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias...evvkklnqgielllgeev 75 
                                       + +v+G+GpAGl++a +la+ g+kvt++   ++++ gg +l + + +++ ++ i++   e vk+l++++        
  gi|330508522|ref|YP_004384950.1| 147 SAAVVGSGPAGLTCAADLARMGHKVTIF---EALHEGGGVLVYGIPEFRLPKGIVRseiEYVKSLGAEL-------E 213
                                       568*************************...88999999999**********99996433333332222.......2 PP

                                       EEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCTTC.........TTBEECCSECHHHHHHCCSS-T. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx........xxxxxxxxxxxxxxxxxxxxxxx. RF
                       Pyr_redox_2  76 vkidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gipGv........aenvgklvrtldsaealklkllp. 142
                                       ++   gk +v++     ++  k  yd+++l +G+ + ++ ++pG+        +e+ ++   +l++a ++ +  +p 
  gi|330508522|ref|YP_004384950.1| 214 LDSVVGK-QVQI-----DELLKGGYDAVFLGIGAGAPRFlNVPGEnlsgiysaNEYLTR--VNLMKAYKFPDYDTPi 282
                                       2233455.6777.....5566778*********8655555*****76666643333333..356666666666666* PP

                                       ...SEEEEES-SHHHHHHHHHHHHHT-E.EEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE. CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       Pyr_redox_2 143 ...krivvvGgGyiGvElAaalaklgke.vtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge. 214
                                          k+++vvGgG+++++ A  + +lg++ v+++++r+r    ++ +l++  e+a+e+ Gv + + t+++++ g+++ 
  gi|330508522|ref|YP_004384950.1| 283 kkgKKVAVVGGGNVAMDAARSALRLGADeVHIIYRRSREE--MPARLEEV-ENAMEE-GVIFDFLTNPTRFLGDHRg 355
                                       *************************8866*********86..99999887.555555.******************9 PP

                                       ......EEEEEETTSCE...............EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTT CS
                                       ......xxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 215 ......klevvledgee...............idadlvvvavGvrpstelleeklglelderggivvdeflrtnvpg 270
                                              +e++l++ +                +++d+vv+avG  p++ +   +  l+ +++g +vvde++rt+++g
  gi|330508522|ref|YP_004384950.1| 356 mvnameVVEMELGEPDAsgrrsprvkkgsehiVNVDTVVIAVGTVPNPLITSSTPELKATKWGTLVVDERGRTTMEG 432
                                       99977644466666655788888888888888***************977558999999****************** PP

                                       EEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 271 iyaiGDvaggkggpelaqaAvqqG 294
                                       ++a GD++   +g +++  A+ +G
  gi|330508522|ref|YP_004384950.1| 433 VWAGGDIT---TGGATVISAMGAG 453
                                       ********...7777777777665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   1.6e-06    0.0009       2      31 ..     148     177 ..     147     182 .. 0.92
   2 !   23.8   0.1   8.4e-08   4.9e-05       1      74 [.     287     358 ..     287     364 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.6e-06
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvvers 31 
                                       ++vvG+G  gl +A+ la++g+kVt++e+ 
  gi|330508522|ref|YP_004384950.1| 148 AAVVGSGPAGLTCAADLARMGHKVTIFEAL 177
                                       79*************************976 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 8.4e-08
                                       EEEEECSSHHHHHHHHHHHHTT.SEEEEEESSSSSSTTSSHHHHHHH..HHHHHHTTEEEECSEEEEEEEEETTS.E CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelg.kkVtvversdkllrllDeeaskil..qeklekngievllntkveeiegsedg.v 73 
                                       kv+vvGgG++++++A  + +lg ++V+++ r+++        + ++l   e+  ++g+ + + t+++++ g+ +g v
  gi|330508522|ref|YP_004384950.1| 287 KVAVVGGGNVAMDAARSALRLGaDEVHIIYRRSREE------MPARLeeVENAMEEGVIFDFLTNPTRFLGDHRGmV 357
                                       79********************67********9877......33333225666667777777777777777777666 PP

                                       E CS
                         Pyr_redox  74 e 74 
                                       +
  gi|330508522|ref|YP_004384950.1| 358 N 358
                                       5 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 !   13.1   0.3   7.2e-05     0.042       2      29 ..     150     176 ..     149     186 .. 0.90
   2 !   23.0   0.1   7.2e-08   4.2e-05     161     203 ..     282     324 ..     228     437 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.2e-05
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEk 29 
                                       ++G GPaGl++a  l ++g  +++i E 
  gi|330508522|ref|YP_004384950.1| 150 VVGSGPAGLTCAADLARMGH-KVTIFEA 176
                                       8******************9.7999885 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 7.2e-08
                       Pyr_redox_3 161 kyagqkvvViGgknSavDaAlelvrkga.eVtvvtrgseiekee 203
                                         +g+kv+V+Gg+n a+DaA    r ga eV++++r+s  e++ 
  gi|330508522|ref|YP_004384950.1| 282 IKKGKKVAVVGGGNVAMDAARSALRLGAdEVHIIYRRSR-EEMP 324
                                       24699*********************9846******983.4433 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.2   3.8e-10   2.2e-07       1      33 [.     150     182 ..     150     196 .. 0.93
   2 ?   -0.3   0.1       2.3   1.3e+03       1      25 [.     290     315 ..     290     320 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3.8e-10
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33 
                                       +vG+G +Gl++A+ La+ g++v+++e+ +  GG
  gi|330508522|ref|YP_004384950.1| 150 VVGSGPAGLTCAADLARMGHKVTIFEALHEGGG 182
                                       8**************************988887 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.3
                                       EE--SHHHHHHHHHHHCCTE.EEEEE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagf.dvlll 25 
                                       +vG+G  ++ aA+ + + g+ +v+++
  gi|330508522|ref|YP_004384950.1| 290 VVGGGNVAMDAARSALRLGAdEVHII 315
                                       8*******999999888888557776 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1    0.0009      0.52      32      59 ..     149     176 ..     143     180 .. 0.91
   2 !   19.0   0.3   1.2e-06   0.00068      28     126 ..     285     423 ..     257     460 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0009
                                       EEESTSHHHHHHHHHHHHTT-EEEEEES CS
                       AlaDh_PNT_C  32 lviGgGvaGlqAiatakglgakVtvlDv 59 
                                        v+G G aGl  +a  +++g kVt+++ 
  gi|330508522|ref|YP_004384950.1| 149 AVVGSGPAGLTCAADLARMGHKVTIFEA 176
                                       79***********************985 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.2e-06
                                       --EEEEESTSHHHHHHHHHHHHTT-E.EEEEESS.....HHHHHHHHHTTTCECEE..................... CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgak.VtvlDvr.....parleqleslgakfvev..................... 77 
                                         kv v+GgG + + A++ a +lga+ V ++  r     parle++e+  ++ v                       
  gi|330508522|ref|YP_004384950.1| 285 GKKVAVVGGGNVAMDAARSALRLGADeVHIIYRRsreemPARLEEVENAMEEGVIFdfltnptrflgdhrgmvname 361
                                       458**********************6477764442222256677777733332333678888888888888888888 PP

                                       ..............HCHHHHHHHHHHHH-SEEEE---BTTSS---SC-HH..HHHTS-TTEEEEE CS
                       AlaDh_PNT_C  78 ..............lksqeellaeavkeadvvigtvlipGkkaPkLvtee..mvksMkpgsVivD 126
                                                     ++   ++ +e++ ++d v+ +v   G     L+t++   +k+ k g+ +vD
  gi|330508522|ref|YP_004384950.1| 362 vvemelgepdasgrRSPRVKKGSEHIVNVDTVVIAV---GTVPNPLITSStpELKATKWGTLVVD 423
                                       888888888887765556666677777777777664...33333455443124666666666666 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0042       2.4       5      36 ..     143     174 ..     140     195 .. 0.93
   2 !   17.9   0.1   5.6e-06    0.0032       6      54 ..     284     333 ..     283     401 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0042
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvv 36 
                                        +gk+  vvG G+ +++ +  l++ g kvt+ 
  gi|330508522|ref|YP_004384950.1| 143 PSGKSAAVVGSGPAGLTCAADLARMGHKVTIF 174
                                       57999*************************96 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 5.6e-06
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagak.vtvvapevkeeleelvklaeee 54 
                                       kgkkv vvGgG+vA+  +r+ l+ ga+ v+++  ++ ee++ +++  e+ 
  gi|330508522|ref|YP_004384950.1| 284 KGKKVAVVGGGNVAMDAARSALRLGADeVHIIYRRSREEMPARLEEVENA 333
                                       69***********************7549999999766666444433333 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   1.3e-06   0.00076       4      41 ..     150     187 ..     148     195 .. 0.93
   2 ?    5.8   0.4     0.013       7.6       2      24 ..     288     310 ..     287     320 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                      FAD_oxidored   4 VvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsg 41 
                                       VvG+gpaG+++A   ar+G kv + e     GG l  g
  gi|330508522|ref|YP_004384950.1| 150 VVGSGPAGLTCAADLARMGHKVTIFEALHEGGGVLVYG 187
                                       9********************************98876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGak 24 
                                       v VvGGg   + AA +A r Ga 
  gi|330508522|ref|YP_004384950.1| 288 VAVVGGGNVAMDAARSALRLGAD 310
                                       89*******************94 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   1.8   1.8e-07   0.00011       3      36 ..     149     182 ..     147     187 .. 0.89
   2 ?   -0.8   0.1         1   6.1e+02       2      28 ..     288     315 ..     287     324 .. 0.87
   3 ?   -1.2   0.0       1.4   8.2e+02     376     408 ..     420     446 ..     356     454 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.8e-07
                                       EEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2   3 iViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                        V+GsG AGL++A+ +a+ G+kv++ e  +e gg
  gi|330508522|ref|YP_004384950.1| 149 AVVGSGPAGLTCAADLARMGHKVTIFEALHEGGG 182
                                       7**************************9998666 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1
                                       EEEE--SHHHHHHHHHHHHTTT.-EEEE CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGl.kvavv 28 
                                       v V+G+G   + AA +a + G+ +v ++
  gi|330508522|ref|YP_004384950.1| 288 VAVVGGGNVAMDAARSALRLGAdEVHII 315
                                       89************99999998788776 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.4
                                       EEBETTSBESTTEEESSBTEEE-STCEESSSST CS
                     FAD_binding_2 376 vetdengrvldadgqpipGLYAaGevaaggvhg 408
                                       +++de+gr+      + +G +A G  + gg   
  gi|330508522|ref|YP_004384950.1| 420 LVVDERGRT------TMEGVWAGGDITTGGATV 446
                                       678888888......999999988888777655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.025        15      35      66 ..     144     175 ..     125     184 .. 0.88
   2 !   13.3   0.0     7e-05      0.04      35     117 ..     284     365 ..     260     369 .. 0.78
   3 ?   -1.9   0.1       3.2   1.8e+03      53     152 ..     445     461 ..     411     466 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.025
                                       TTSEEEEES-SHHHHHHHHHHHHTT-EEEEES CS
                      2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgmkviayd 66 
                                       sgk  +++G G  G + a  l+ +g kv++++
  gi|330508522|ref|YP_004384950.1| 144 SGKSAAVVGSGPAGLTCAADLARMGHKVTIFE 175
                                       799*************************9876 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7e-05
                                       TTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHHCHHHHTCEECSHHHHHHH...-SEEEE-S--STTTTT CS
                      2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkeeeeeelgvelvsleellae...sDivslhlpltpetrh 107
                                       +gk+v+++G G+++  +a+ +  +g+ +v ++ r+ +     ee+ ++l+++e++++e    D++++ +    + r+
  gi|330508522|ref|YP_004384950.1| 284 KGKKVAVVGGGNVAMDAARSALRLGAdEVHIIYRRSR-----EEMPARLEEVENAMEEgviFDFLTNPTRFLGDHRG 355
                                       79************************76666555544.....24566777788887773335888998999999999 PP

                                       SBSHHHHHCS CS
                      2-Hacid_dh_C 108 linaeelakm 117
                                       ++na e  +m
  gi|330508522|ref|YP_004384950.1| 356 MVNAMEVVEM 365
                                       9999887777 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.2
                                       HHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-G CS
                      2-Hacid_dh_C  53 krlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRG 129
                                                                                                                    
  gi|330508522|ref|YP_004384950.1| 445 T---------------------------------------------------------------------------- 445
                                       3............................................................................ PP

                                       GGB-HHHHHHHHHTTSCCEEEES CS
                      2-Hacid_dh_C 130 glvdeeaLleaLksgkiagaalD 152
                                              ++ a+ +gkia+a +D
  gi|330508522|ref|YP_004384950.1| 446 -------VISAMGAGKIAAADID 461
                                       .......4555556666666655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.7   5.1e-07    0.0003       3      33 ..     148     178 ..     146     185 .. 0.90
   2 ?   -0.7   0.1      0.74   4.3e+02       2      24 ..     287     309 ..     286     319 .. 0.79
   3 ?   -1.7   0.0       1.5   8.9e+02     144     173 ..     379     408 ..     364     425 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.1e-07
                                       EEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekak 33 
                                        +v+G G+AGl +A+ +a+ g++V+++e+ +
  gi|330508522|ref|YP_004384950.1| 148 AAVVGSGPAGLTCAADLARMGHKVTIFEALH 178
                                       68*************************9865 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.74
                                       SEEEE--SHHHHHHHHHHHHTT- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgk 24 
                                       +v+v+GgG   + aA sa + g+
  gi|330508522|ref|YP_004384950.1| 287 KVAVVGGGNVAMDAARSALRLGA 309
                                       79**********99999966654 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.5
                                       EEEE.TTEEEEESEEEE----SS-GGGT-- CS
                       HI0933_like 144 rvktkseeeleadklvlAtGGlSiPklGst 173
                                       rvk  se+ ++ d++v+A+G    P + s+
  gi|330508522|ref|YP_004384950.1| 379 RVKKGSEHIVNVDTVVIAVGTVPNPLITSS 408
                                       566667888999********9887776655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.3   6.2e-07   0.00036      21      59 ..     149     185 ..     144     211 .. 0.86
   2 ?   -2.6   0.1       4.6   2.6e+03      19      35 ..     287     303 ..     283     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.2e-07
                                       EEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTT CS
                              Thi4  21 vivGaGssGLtaayylakkpdlkvailersvspGGGawl 59 
                                       ++vG+G++GLt+a  la+  + kv+i+e+ +  GGG+  
  gi|330508522|ref|YP_004384950.1| 149 AVVGSGPAGLTCAADLARM-GHKVTIFEA-LHEGGGVLV 185
                                       69*****************.*******97.777888755 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.6
                                       EEEEE--SHHHHHHHHH CS
                              Thi4  19 DvvivGaGssGLtaayy 35 
                                        v++vG+G   + aa+ 
  gi|330508522|ref|YP_004384950.1| 287 KVAVVGGGNVAMDAARS 303
                                       58999999999999985 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   2.3e-06    0.0014       3      59 ..     149     205 ..     147     222 .. 0.73
   2 ?    2.1   0.1      0.14        79       1      24 [.     287     310 ..     287     327 .. 0.88
   3 ?   -0.5   0.1      0.87     5e+02     131     157 ..     380     406 ..     357     447 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                                       EEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SS.SSEEE-TTHHHHHHHHHHH CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLithkldtiaelsC.npsiggiakgllvrEidal 59 
                                        V+G G AG+ +A+ +ar+G+kv+++    +  + l++  p ++ + kg++  Ei+ +
  gi|330508522|ref|YP_004384950.1| 149 AVVGSGPAGLTCAADLARMGHKVTIFEALHEGGGVLVYgIPEFRLP-KGIVRSEIEYV 205
                                       69***********************954444444443324555544.66666666655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.14
                                       CEEEE-SSHHHHHHHHHHHHTT-- CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGak 24 
                                       +v V+GgG   + AA  a rlGa+
  gi|330508522|ref|YP_004384950.1| 287 KVAVVGGGNVAMDAARSALRLGAD 310
                                       699******************985 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.87
                                       EEETTS-EEEECEEEE--TT-BT-EEE CS
                              GIDA 131 vvtedgetikakavviatGtflkgkih 157
                                       v++ ++++++ ++vvia Gt  +  i 
  gi|330508522|ref|YP_004384950.1| 380 VKKGSEHIVNVDTVVIAVGTVPNPLIT 406
                                       677788899999********5555554 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   8.3e-06    0.0048       2      28 ..     156     182 ..     155     185 .. 0.92
   2 ?   -1.5   0.0         2   1.2e+03     383     430 ..     217     265 ..     195     270 .. 0.80
   3 ?   -1.7   0.0       2.4   1.4e+03     418     451 ..     429     460 ..     387     460 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.3e-06
                                       HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGG 28 
                                       aGL++A  L++ G++Vt++Ea    GG
  gi|330508522|ref|YP_004384950.1| 156 AGLTCAADLARMGHKVTIFEALHEGGG 182
                                       9********************888777 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                                       EEEEECCTETTTSSSEEE.BTTHHHHHHHHHHCH.HCSTTEEE.SGGGC CS
                     Amino_oxidase 383 tlvtrWhtdplargsysyvsvgpghedydplakp.egdprlffAGehts 430
                                       ++ ++ + d+l +g y +v  g g  + + l+ p e++++++ A e+ +
  gi|330508522|ref|YP_004384950.1| 217 VVGKQVQIDELLKGGYDAVFLGIGAGAPRFLNVPgENLSGIYSANEYLT 265
                                       55556667999999*********9999999999999999*999999976 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.4
                                       CSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                     Amino_oxidase 418 gdprlffAGehtsreypgtvegAilSGlraAari 451
                                        + ++   G+ t+    +tv  A+ +G+ aAa+i
  gi|330508522|ref|YP_004384950.1| 429 TMEGVWAGGDITT--GGATVISAMGAGKIAAADI 460
                                       5566666677777..667799*********9987 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   0.1   2.1e-05     0.012       5      33 ..     149     177 ..     146     180 .. 0.90
   2 ?    0.8   0.0      0.41   2.3e+02       3      36 ..     287     321 ..     286     329 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                                       EEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                       ++VG+GpaGl+ a  L++ G +v++ e  
  gi|330508522|ref|YP_004384950.1| 149 AVVGSGPAGLTCAADLARMGHKVTIFEAL 177
                                       79**********************99875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.41
                                       EEEEE--SHHHHHHHHHHHHTTHH.EEEEESSSSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvr.vvlvekrstt 36 
                                       +V++VG+G + + +a+   + G + v+++ +rs++
  gi|330508522|ref|YP_004384950.1| 287 KVAVVGGGNVAMDAARSALRLGADeVHIIYRRSRE 321
                                       69**************9999999878888888765 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00074      0.43      55     106 ..     145     214 ..     117     243 .. 0.90
   2 ?    4.6   0.1      0.03        18      53      89 ..     283     320 ..     268     339 .. 0.82
   3 ?   -1.0   0.0       1.6   9.1e+02     156     169 ..     388     401 ..     307     468 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00074
                                       TSEEEEEBSSHHHHHHHHHHHHHT-EEEEE..................EETTS-HHHHHHHHHTT-EEEE CS
                              PALP  55 aktvveassGNhgralAaaaallGlkvtiv..................vpadaspekvallrllGaevve 106
                                       +k  ++ +sG +g+ +Aa  a++G kvti+                  +p++   + ++  ++lGae+++
  gi|330508522|ref|YP_004384950.1| 145 GKSAAVVGSGPAGLTCAADLARMGHKVTIFealhegggvlvygipefrLPKGIVRSEIEYVKSLGAELEL 214
                                       67778899***********************************99999999999************9865 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.03
                                       TTTSEEEEEBSSHHHHHHHHHHHHHT-.EEEEEEETTS CS
                              PALP  53 tgaktvveassGNhgralAaaaallGl.kvtivvpada 89 
                                       +++k v++ ++GN ++ +A  a +lG  +v+i   ++ 
  gi|330508522|ref|YP_004384950.1| 283 KKGKKVAVVGGGNVAMDAARSALRLGAdEVHIIYRRSR 320
                                       5899**********************999999865554 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.6
                                       TTEEEEEEE-SSSH CS
                              PALP 156 gkpdavvvpvGgGg 169
                                        ++d+vv +vG+  
  gi|330508522|ref|YP_004384950.1| 388 VNVDTVVIAVGTVP 401
                                       45666777777654 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.8   1.2e-05    0.0071       3      29 ..     149     177 ..     147     183 .. 0.88
   2 ?    1.3   0.0      0.36   2.1e+02       1      29 [.     287     318 ..     287     334 .. 0.89
   3 ?   -2.0   0.1       3.5     2e+03     191     205 ..     388     402 ..     352     456 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                                       EEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO   3 viiGGGiiGlstAyeLarrg..Vtllekg 29 
                                       +++G+G +Gl++A +Lar g  Vt++e+ 
  gi|330508522|ref|YP_004384950.1| 149 AVVGSGPAGLTCAADLARMGhkVTIFEAL 177
                                       8***************99999******85 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.36
                                       EEEEECTSHHHHHHHHHHHHTT...EEEEESS CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg...Vtllekg 29 
                                       +v+++GGG + + +A+ + r g   V ++ ++
  gi|330508522|ref|YP_004384950.1| 287 KVAVVGGGNVAMDAARSALRLGadeVHIIYRR 318
                                       59**************9988888999999877 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.5
                                       EEEEEEEE--GGGHH CS
                               DAO 191 daadavVnaaGawsd 205
                                       + +d+vV+a G   +
  gi|330508522|ref|YP_004384950.1| 388 VNVDTVVIAVGTVPN 402
                                       356778888885544 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   0.6   2.2e-05     0.013      28      52 .]      34      62 ..       9      62 .. 0.68
   2 ?   -1.3   3.0       5.8   3.4e+03       7      16 ..      92     101 ..      90     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-05
                            Fer4_7 28 t..ekveidpekClgCga..CvavCPtga 52
                                         e++++++++C++C++  Cv+ CP+g+
  gi|330508522|ref|YP_004384950.1| 34 YtpEQAALEANRCIQCKKpkCVEGCPVGV 62
                                      1336779999*******999*******96 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.8
                            Fer4_7   7 aCvaaCpvka 16 
                                        C ++Cp+++
  gi|330508522|ref|YP_004384950.1|  92 ICGRVCPQEV 101
                                       6777777654 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.36   2.1e+02     192     218 ..     146     172 ..     139     179 .. 0.72
   2 ?    9.7   0.0   0.00075      0.43     187     227 ..     277     320 ..     233     335 .. 0.77
   3 ?   -1.3   0.0       1.6   9.2e+02     140     160 ..     381     401 ..     359     412 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.36
                       K_oxygenase 192 kriaVvGsGqSaaeifedllrrqkkve 218
                                       k+ aVvGsG  +   + dl+r  +kv+
  gi|330508522|ref|YP_004384950.1| 146 KSAAVVGSGPAGLTCAADLARMGHKVT 172
                                       666777777777777777777766554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00075
                       K_oxygenase 187 e....llakkriaVvGsGqSaaeifedllrrqkkvelklvtrsea 227
                                       +     +++k++aVvG+G  a + ++ +lr  +  e++++ r+++
  gi|330508522|ref|YP_004384950.1| 277 DydtpIKKGKKVAVVGGGNVAMDAARSALRLGA-DEVHIIYRRSR 320
                                       044447899******************999866.78999998876 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.6
                       K_oxygenase 140 aegeeeelearnlvlgvGtep 160
                                       ++g+e+ ++  ++v++vGt p
  gi|330508522|ref|YP_004384950.1| 381 KKGSEHIVNVDTVVIAVGTVP 401
                                       457777788888888888777 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.71   4.1e+02       3      30 ..     149     173 ..     147     180 .. 0.90
   2 ?   11.5   0.0   0.00059      0.34       1      46 [.     287     330 ..     287     363 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.71
                                       EEETTSHHHHHHHHHHHHTTS-GGCEEE CS
                     F420_oxidored   3 giiGaGnmgealasgllaagaqpheivv 30 
                                       +++G+G  g + a  l++ g   h++++
  gi|330508522|ref|YP_004384950.1| 149 AVVGSGPAGLTCAADLARMG---HKVTI 173
                                       899*****************...*9997 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00059
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHH CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeel 46 
                                       k++++G+Gn++   a+ +l+ g  + e+ ++ +r+ e++ +  ee+
  gi|330508522|ref|YP_004384950.1| 287 KVAVVGGGNVAMDAARSALRLG--ADEVHIIYRRSREEMPARLEEV 330
                                       79********************..7777777788877765555554 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 ?   12.2   0.0   9.7e-05     0.056     271     320 ..     284     336 ..     268     361 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.7e-05
                                       TT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHH...HHHHHHS.T CS
                    Oxidored_nitro 271 agkrvaiygdpdrvvalarllkelGmevvaagtetahrdde...erlkaelee 320
                                       +gk+va++g++  ++  ar    lG++ v+++++ ++++     e+++  +ee
  gi|330508522|ref|YP_004384950.1| 284 KGKKVAVVGGGNVAMDAARSALRLGADEVHIIYRRSREEMParlEEVENAMEE 336
                                       69*******************************99977766333333333333 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 ?    1.9   0.0      0.27   1.6e+02      31      68 ..     144     184 ..     133     225 .. 0.80
   2 ?    9.5   0.0    0.0012      0.72      30      60 ..     283     313 ..     263     317 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.27
                                       TTEEEEEE--SHHHHHHHHHHHHCT-EEE...EEEESSEEE CS
                     ELFV_dehydrog  31 egkrvaisGsGnvgsyaallltelgakvv...avsDssGvi 68 
                                       +gk+ a+ GsG  g  +a  l+++g+kv+   a+ ++ Gv+
  gi|330508522|ref|YP_004384950.1| 144 SGKSAAVVGSGPAGLTCAADLARMGHKVTifeALHEGGGVL 184
                                       689999***********99999***9997444555555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                                       STTEEEEEE--SHHHHHHHHHHHHCT-EEEE CS
                     ELFV_dehydrog  30 legkrvaisGsGnvgsyaallltelgakvva 60 
                                        +gk+va+ G Gnv+  aa+ + +lga  v 
  gi|330508522|ref|YP_004384950.1| 283 KKGKKVAVVGGGNVAMDAARSALRLGADEVH 313
                                       489**********************998765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0036       2.1       2      30 ..     148     176 ..     147     180 .. 0.92
   2 ?    4.4   0.1     0.052        30       1      48 [.     287     336 ..     287     364 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0036
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdi 30 
                                        av+G+G  G   aa +a+ g++V++++ 
  gi|330508522|ref|YP_004384950.1| 148 AAVVGSGPAGLTCAADLARMGHKVTIFEA 176
                                       69***********************9875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.052
                                       EEEEE--SCCHHHHHHHHHHTT-.EEEEE-S.-HHHHHHHHHHHHHHHHC CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagl.eVvlvdi.seealekalekiekslek 48 
                                       kvav+G G +    a  +++ g  eV+++ + s+e + + le++e+ +e+
  gi|330508522|ref|YP_004384950.1| 287 KVAVVGGGNVAMDAARSALRLGAdEVHIIYRrSREEMPARLEEVENAMEE 336
                                       79******************998458877653566666666666666654 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 ?    9.0   0.0    0.0017      0.96       4      28 ..     149     173 ..     146     177 .. 0.92
   2 ?    1.4   0.0      0.36   2.1e+02      64      89 ..     377     402 ..     356     418 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                                       EEE--STTHHHHHHHHHHCTSEEEE CS
                    UDPG_MGDP_dh_N   4 sviGlGYvGlvtaavlaeighevig 28 
                                       +v+G+G  Gl++aa la++gh+v++
  gi|330508522|ref|YP_004384950.1| 149 AVVGSGPAGLTCAADLARMGHKVTI 173
                                       89*********************96 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.36
                                       EEEES-HHHHHHC-SEEEE-----B- CS
                    UDPG_MGDP_dh_N  64 lsfttdvekaveeadvifiaVgTPsk 89 
                                       +    + ++++ + d ++iaVgT  +
  gi|330508522|ref|YP_004384950.1| 377 SPRVKKGSEHIVNVDTVVIAVGTVPN 402
                                       4555677899999*********9443 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 ?    9.6   0.0    0.0015      0.87      22      53 ..     144     175 ..     140     177 .. 0.95
   2 ?    2.1   0.0      0.31   1.8e+02      22      47 ..     284     309 ..     261     316 .. 0.82
   3 ?   -2.5   0.3       8.1   4.7e+03      32      50 ..     437     456 ..     429     462 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                                       TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE- CS
                     AdoHcyase_NAD  22 aGkvavvaGyGdvGkGcaaslkglGarvivte 53 
                                       +Gk a v+G G  G  caa l  +G +v++ e
  gi|330508522|ref|YP_004384950.1| 144 SGKSAAVVGSGPAGLTCAADLARMGHKVTIFE 175
                                       79**************************9977 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.31
                                       TTSEEEEE--SHHHHHHHHHHHHCT- CS
                     AdoHcyase_NAD  22 aGkvavvaGyGdvGkGcaaslkglGa 47 
                                        Gk++ v+G G+v   +a+s   lGa
  gi|330508522|ref|YP_004384950.1| 284 KGKKVAVVGGGNVAMDAARSALRLGA 309
                                       6999*************999888887 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8.1
                                       SHHHHHHHHHHHHCT-.EEE CS
                     AdoHcyase_NAD  32 GdvGkGcaaslkglGa.rvi 50 
                                       Gd+  G a+ + ++Ga ++ 
  gi|330508522|ref|YP_004384950.1| 437 GDITTGGATVISAMGAgKIA 456
                                       88888999999888873344 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       1.5   8.4e+02      12      42 ..     145     174 ..     141     177 .. 0.88
   2 ?    8.4   0.1    0.0038       2.2      11      46 ..     284     319 ..     279     340 .. 0.83
   3 ?   -1.1   0.0       3.1   1.8e+03      70      96 ..     384     411 ..     376     423 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.5
                                       T-EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                      Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvva 42 
                                       +k + ++G G  +   a  L++ g k v+++
  gi|330508522|ref|YP_004384950.1| 145 GKSAAVVGSGPAGLTCAADLARMGHK-VTIF 174
                                       67899***************999988.8875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0038
                                       TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSH CS
                      Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtl 46 
                                       k+kkv ++G G++a  +a+  l+ g+++v ++ R  
  gi|330508522|ref|YP_004384950.1| 284 KGKKVAVVGGGNVAMDAARSALRLGADEVHIIYRRS 319
                                       689**************************9987643 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.1
                                       HHHHHT-SEEEE-SSS.SS-SB-HHHHH CS
                      Shikimate_DH  70 kellaeadvvisatas.eepilekeeve 96 
                                       +e++ ++d v++a+++ ++p+++++  e
  gi|330508522|ref|YP_004384950.1| 384 SEHIVNVDTVVIAVGTvPNPLITSSTPE 411
                                       6889999999999875478888877655 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   0.00042      0.24       3      32 ..     149     176 ..     148     180 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00042
                     Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvliea 32 
                                       +v+G+GpAgl  Aa l  a++g kv++ ea
  gi|330508522|ref|YP_004384950.1| 149 AVVGSGPAGLTCAADL--ARMGHKVTIFEA 176
                                       69**************..9******99987 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00028      0.16      51      77 ..      36      64 ..       9      69 .. 0.76
   2 ?   -2.3   0.2       8.9   5.1e+03      66      76 ..      92     102 ..      88     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00028
                           Fer4_18 51 eerkekgagdcidce..scvkvcPtgidi 77
                                       e+++ +a+ ci+c+  +cv+ cP+g++i
  gi|330508522|ref|YP_004384950.1| 36 PEQAALEANRCIQCKkpKCVEGCPVGVNI 64
                                      4556778899****9445*********99 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.9
                           Fer4_18  66 scvkvcPtgid 76 
                                        c +vcP ++ 
  gi|330508522|ref|YP_004384950.1|  92 ICGRVCPQEVQ 102
                                       69999998875 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00047      0.27       1      40 [.     149     182 ..     149     189 .. 0.84
   2 ?    1.7   0.0       0.4   2.3e+02     135     155 ..     379     399 ..     356     400 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00047
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagr 40 
                                       a+vG Gp+Gl++++ L++       +++t+f+  + g g+
  gi|330508522|ref|YP_004384950.1| 149 AVVGSGPAGLTCAADLARM-----GHKVTIFEALHEG-GG 182
                                       89***************99.....59999***96665.43 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.4
                     NAD_binding_9 135 avlladgaslaadaVvLAlGh 155
                                       +v + +++ + +d Vv+A+G 
  gi|330508522|ref|YP_004384950.1| 379 RVKKGSEHIVNVDTVVIAVGT 399
                                       555666677888999999885 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.3   0.00024      0.14       5      21 ..      41      59 ..      37      60 .. 0.88
   2 ?    0.1   0.3       1.8     1e+03      14      22 .]      91      99 ..      91      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00024
                            Fer4_2  5 vdtdrCigCg..aCvsaCP 21
                                       +++rCi+C+  +Cv  CP
  gi|330508522|ref|YP_004384950.1| 41 LEANRCIQCKkpKCVEGCP 59
                                      6789*****999******* PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.8
                            Fer4_2 14 gaCvsaCPa 22
                                      g+C  +CP+
  gi|330508522|ref|YP_004384950.1| 91 GICGRVCPQ 99
                                      78999***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 ?   11.5   0.5    0.0006      0.34      38      60 ..      38      62 ..       7      63 .. 0.67
   2 ?    0.4   1.8       1.7   9.7e+02      51      60 ..      92     101 ..      89     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0006
                           Fer4_17 38 ekeekaslCieCg..eCerkCPqgl 60
                                      ++  +a++Ci+C+  +C++ CP g+
  gi|330508522|ref|YP_004384950.1| 38 QAALEANRCIQCKkpKCVEGCPVGV 62
                                      334599******9445******887 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.7
                           Fer4_17  51 eCerkCPqgl 60 
                                        C r+CPq++
  gi|330508522|ref|YP_004384950.1|  92 ICGRVCPQEV 101
                                       6999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3131.95
//
Query:       gi|330508523|ref|YP_004384951.1|  [L=308]
Description: hypothetical protein MCON_2739 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-12   47.0   3.4    4.2e-12   45.7   3.4    1.8  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
     0.0042   17.4   0.0     0.0069   16.7   0.0    1.3  1  FAD_binding_6    Oxidoreductase FAD-binding domain
  ------ inclusion threshold ------
       0.12   12.4   0.3       0.23   11.5   0.3    1.4  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain
       0.19   11.6   0.0       0.35   10.7   0.0    1.3  1  ATPase_2         ATPase domain predominantly from Archaea


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 !   45.7   3.4   9.4e-16   4.2e-12       3      41 ..     211     245 ..     209     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 9.4e-16
                                       --SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   3 rMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       +M++G+G+C++C+v++ g+    +k++C+dGP+F+++++
  gi|330508523|ref|YP_004384951.1| 211 IMVDGTGMCGACRVEVGGE----TKFACVDGPEFEGHDI 245
                                       8***************764....8*************98 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.5e-06    0.0069       3      96 ..       3      91 ..       1      93 [. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-06
                                      EEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHC CS
                     FAD_binding_6  3 kltekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLde 81
                                      ++++ke+v +++  ++fk p+ ++     +Gq+v++r++ kge++  +  ++  ++++G+++++   y  G  +  L+ 
  gi|330508523|ref|YP_004384951.1|  3 EIVTKETVAPNIIHMKFKAPKIAS--SAKPGQFVIIRVDEKGERI--PMGLAGWDEKEGTVDIV--FYVLGTSTAKLST 75
                                      57899************9997777..7889*********888754..667779999*****988..6888*******88 PP

                                      S-TT-EE.EEEEEE-S CS
                     FAD_binding_6 82 lkigdtl.eikGPlGk 96
                                      +  gd+l +i GPlGk
  gi|330508523|ref|YP_004384951.1| 76 MCEGDSLaNIAGPLGK 91
                                      666655428*****97 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   5.1e-05      0.23      54      73 ..     216     235 ..     201     241 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.1e-05
                            Fer2_3  54 egiCGscavainGkptlaCt 73 
                                        g+CG+c v++ G+++ aC 
  gi|330508523|ref|YP_004384951.1| 216 TGMCGACRVEVGGETKFACV 235
                                       79*****************6 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   7.8e-05      0.35      29      52 ..     156     181 ..     145     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.8e-05
                          ATPase_2  29 egsGKtaLlkeiienledkdk..yvi 52 
                                        g+GKta+ + +ie+ ++++k  ++i
  gi|330508523|ref|YP_004384951.1| 156 TGCGKTAWANDFIEQELQSGKkiNRI 181
                                       47*************98887733445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2366.40
//
Query:       gi|330508524|ref|YP_004384952.1|  [L=282]
Description: formate/nitrite family transporter [Methanosaeta concilii GP6]
Scores for complete 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-81  272.9  30.2    2.2e-81  272.7  30.2    1.0  1  Form_Nir_trans  Formate/nitrite transporter


Domain annotation for each model (and alignments):
>> Form_Nir_trans  Formate/nitrite transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.7  30.2   1.2e-85   2.2e-81      16     236 .]       1     264 [.       1     264 [. 0.96

  Alignments for each domain:
  == domain 1  score: 272.7 bits;  conditional E-value: 1.2e-85
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCT..............TCHHHHHHHHHCCCHHHHHHHHHT---CC CS
                    Form_Nir_trans  16 lsldklfllgilAGafigfgvllalvvaaalaes..............npglakllgglvFpvGlilvvllgaeLfT 78 
                                       ++++kl++lg+lAGa+i+fg+ll+ +va++l++               + gl+k+++g+vFpvGl+lvv++g+eLfT
  gi|330508524|ref|YP_004384952.1|   1 MTWQKLLVLGFLAGAYIAFGALLSEIVAGGLSNGtitgpdgeiwkiamPGGLVKFAAGAVFPVGLMLVVIAGSELFT 77 
                                       5899***************************8889*************99*************************** PP

                                       CCCCHHHHHHCTTSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTGG.....HHHHHHHHHCCCSS-HHHHHHHH CS
                    Form_Nir_trans  79 gntllltlavlkkkvslkkllknwlvvllgNliGsllvalllvvlsgll.....aekllsiaeaklslsfleaflrG 150
                                       gn+++++++vl++++sl+ l+knw +v++gNl+Gs++va++l++  gl+     a +++++a++k++l+f +aflrG
  gi|330508524|ref|YP_004384952.1|  78 GNCMFAPISVLNGEASLGGLVKNWSLVYVGNLVGSVFVAYFLAYQCGLFdnlpwAGWAATVANTKCGLDFSTAFLRG 154
                                       ************************************************777777*********************** PP

                                       HHHHHHHHHHHHHHCC-SSHHHHHHHHHHHHHHHHHCT---HHHHHHHHHHHHHH...................... CS
                    Form_Nir_trans 151 ilCNwlVclavwlalaakdvigkilaiflpifafvasgfeHsvanmfliplglll...................... 205
                                       i+CNwlVclavwla++++dvi+ki+ +++pi+afv++gfeHsvanmf+iplg+++                      
  gi|330508524|ref|YP_004384952.1| 155 IGCNWLVCLAVWLAISSEDVISKIFSCWFPIMAFVTIGFEHSVANMFFIPLGIFAandpaiaanlatagvattnlag 231
                                       *****************************************************777777777778888888877778 PP

                                       ..SHHHHHHHCHHHHHHHHHHHHHCCHHHHHHH CS
                    Form_Nir_trans 206 ..tvadfilknlipvtlGNivGGallvgllyly 236
                                          +++f++ nlipvtlGNivG+al+v+ ly+y
  gi|330508524|ref|YP_004384952.1| 232 gmGWYNFFITNLIPVTLGNIVGAALFVAALYWY 264
                                       7789****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1912.54
//
Query:       gi|330508525|ref|YP_004384953.1|  [L=416]
Description: major facilitator family transporter [Methanosaeta concilii GP6]
Scores for 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-42  143.2  49.0    9.5e-29  100.4  21.5    2.3  2  MFS_1       Major Facilitator Superfamily
    1.2e-06   27.4  26.9    0.00039   19.1  13.7    3.3  2  MFS_2       MFS/sugar transport protein
    4.3e-06   25.8  22.0     0.0029   16.5  11.2    2.7  2  MFS_1_like  MFS_1 like family
    0.00076   18.4   2.5    0.00076   18.4   2.5    2.0  2  LacY_symp   LacY proton/sugar symporter
  ------ inclusion threshold ------
      0.044   13.3   0.8      0.085   12.3   0.4    1.6  1  DUF3959     Protein of unknown function (DUF3959)
      0.086   12.8   4.1       0.43   10.5   0.0    3.3  4  SLATT_1     SMODS and SLOG-associating 2TM effector domain 1


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 !  100.4  21.5   3.2e-32   9.5e-29      13     247 ..      30     270 ..      12     274 .. 0.77
   2 !   48.2  21.4   2.3e-16   6.9e-13      36     166 ..     272     405 ..     262     416 .] 0.89

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 3.2e-32
                             MFS_1  13 silgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlll 89 
                                       ++ g++++ + +e +++   + g  + +   + +++++++Gr+ +r+G rr+++lg+ll+++g++l++fa+s+++++
  gi|330508525|ref|YP_004384953.1|  30 GFPGVMAS-LWQEMFHVGSGATGSTIFFMLSAVGIFMFLAGRWQERYGIRRMIILGILLTSIGCILAAFANSITMVY 105
                                       23333333.446668877777777555555578******************************77777977777*** PP

                             MFS_1  90 vlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafv 166
                                       +  +l G+++++++  +++l+ +w+p+ ++g++ g +s+ f+l+a++  ++ gl++ ++g+r + ++la+++l a++
  gi|330508525|ref|YP_004384953.1| 106 AWAFLNGAASCFVYIPALTLVQQWYPQ-RKGLVSGTVSMVFGLAAAIMSPVFGLMLNAFGYRNMSLVLAVLTLTAGL 181
                                       ***************************.********************999999999******************** PP

                             MFS_1 167 lfllllpeepperkrkspkeee..............kgtgpaplvpawkallkdpvlwillialllfffgfsglltl 229
                                       l++ + +e + ++  k++ e +              k  +++pl+   ++ l+ + +w+l+++++l++++  ++++l
  gi|330508525|ref|YP_004384953.1| 182 LGAYFARE-RDDETIKRQNEMRdalkrqiregneidKDEQRRPLT--VSETLHTRSFWFLWTTWILAGAAGVSMTVL 255
                                       85555532.222222223333346888888888884444444444..589999999***********9999999999 PP

                             MFS_1 230 lplylqevlglsglllag 247
                                       ++ y    lgl+  l+++
  gi|330508525|ref|YP_004384953.1| 256 STGY-GLSLGLP--LEGA 270
                                       9999.9999999..4444 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 2.3e-16
                             MFS_1  36 llltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlgagalfpagaalia 111
                                       l+lt++ l+ + + l  G++sdr+Grrrv+ l++l+ +l+ ++l+ +a  l++ ++l ++ Gl  g+lf+++a l+a
  gi|330508525|ref|YP_004384953.1| 272 LILTAFNLTNGTGRLASGYFSDRLGRRRVMSLAFLAAGLA-YFLFpLAGDLPTSAILAAVVGLSFGTLFSVSAPLVA 347
                                       799*************************************.55554545555************************* PP

                             MFS_1 112 dwfpkeergraigllsagfslGa.ilgpllggllasslg..Wravfyilaivsllafv 166
                                       d f  ++ g  +gl  a++++ a  lgp l+g+l+++ g  +  +f+ l+++slla++
  gi|330508525|ref|YP_004384953.1| 348 DCFGLDHFGAIFGLTFAAYGFLAgPLGPTLSGYLLDLNGgnFIPIFLYLGAFSLLAAL 405
                                       *****************99988879**********8877798899**********987 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1  13.7   1.3e-07   0.00039     259     387 ..      47     166 ..      40     169 .. 0.85
   2 !   13.2  15.3     8e-06     0.024     100     343 ..     104     350 ..     103     386 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-07
                             MFS_2 259 saasvfllvvtisal.lgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaall 334
                                       s a+ +++++++sa+ ++++l+ + + r+g +++++lg+llt ++ +l+ ++  ++++++++ +++ g +  +++++
  gi|330508525|ref|YP_004384953.1|  47 SGATGSTIFFMLSAVgIFMFLAGRWQERYGIRRMIILGILLTSIGCILAAFA--NSITMVYAWAFLNGAA--SCFVY 119
                                       5567788999*****************************************9..************9999..44444 PP

                             MFS_2 335 pwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgllLsafgyr 387
                                       +++++     y        r+g++ +++s++  la++i + v+gl+L+afgyr
  gi|330508525|ref|YP_004384953.1| 120 IPALTLVQQWYP------QRKGLVSGTVSMVFGLAAAIMSPVFGLMLNAFGYR 166
                                       444332212223......478*******************************6 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8e-06
                             MFS_2 100 llvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailafllvlilgglkserkgylifal 176
                                       ++++++l   +  +++ip  +lv +    y +R  l     ++s+++g++aai+ +++ l+l++      gy+ + l
  gi|330508525|ref|YP_004384953.1| 104 VYAWAFLNGAASCFVYIPALTLVQQW---YPQRKGLV--SGTVSMVFGLAAAIMSPVFGLMLNA-----FGYRNMSL 170
                                       678899999999999********999...99999885..5899*****9999999999888887.....******** PP

                             MFS_2 177 iialLmllgviivvlgtkervem..rkkekteqkeklslleq.............lkevfrnraflillllfllaal 238
                                       + a+L+l + ++ +++ +er+ +  +++++ +++ k +++e+             + e++  r f+ l ++ +la +
  gi|330508525|ref|YP_004384953.1| 171 VLAVLTLTAGLLGAYFARERDDEtiKRQNEMRDALKRQIREGneidkdeqrrpltVSETLHTRSFWFLWTTWILAGA 247
                                       *********************99965555555555555554322333333333336788999999999999988888 PP

                             MFS_2 239 algvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnl 314
                                       a++ +  l+  y    lg   + a ++l+++ + +  g +   ++  rlg+++++ l++l++ + ++l+ l+  ++l
  gi|330508525|ref|YP_004384953.1| 248 AGVSMTVLSTGYGL-SLGlPLEGAVLILTAFNLTNGTGRLASGYFSDRLGRRRVMSLAFLAAGLAYFLFPLA--GDL 321
                                       87777777776654.45534455555555667777799999******************9999999998888..*** PP

                             MFS_2 315 llflvllviagfgvgvaallpwsmladvv 343
                                        +  +l++++g+++g+++++ + ++ad++
  gi|330508525|ref|YP_004384953.1| 322 PTSAILAAVVGLSFGTLFSVSAPLVADCF 350
                                       ***************************97 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5  11.2   9.7e-07    0.0029     258     379 ..      46     165 ..      12     171 .. 0.85
   2 !   14.0   4.4   5.5e-06     0.016     160     379 ..     151     387 ..     150     394 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.7e-07
                        MFS_1_like 258 sntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaa 334
                                        +   Gs++++   a  ++ f+a ++ e++G+++++i+++l++ +  +l a+ ++  +v    +L+g++   ++  a
  gi|330508525|ref|YP_004384953.1|  46 GSGATGSTIFFMLSAVGIFMFLAGRWQERYGIRRMIILGILLTSIGCILAAFANSITMVYAWAFLNGAASCFVYIPA 122
                                       5567899999988888888899******************************************************* PP

                        MFS_1_like 335 veyvskiapksleatgqgllsglyfglGralGsliGGllwdlksa 379
                                        + v++  p++ ++ + g +s++ fgl  a+ s + Gl+ + ++ 
  gi|330508525|ref|YP_004384953.1| 123 LTLVQQWYPQR-KGLVSGTVSMV-FGLAAAIMSPVFGLMLNAFGY 165
                                       *********98.57788888776.999999988888888776665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.5e-06
                        MFS_1_like 160 ifafitGilidhysvnllpysallyvlaallvisllvvlilnetekesklkvtksl..................... 215
                                       i+++++G++++ +    +      +vla+l +++ l+ + +   +  + +k  +                       
  gi|330508525|ref|YP_004384953.1| 151 IMSPVFGLMLNAFGYRNMS-----LVLAVLTLTAGLLGAYFARERDDETIKRQNEMrdalkrqiregneidkdeqrr 222
                                       5566666666665553333.....23333333333332222222222222222222344566777777777777655 PP

                        MFS_1_like 216 .qvllnilknpeviifllvalilgmswgiienFlflYL.kelgasntllGslvalgvv..aeiplfffaeklleklG 288
                                           +    + + ++fl +++il  + g+  + l+  +  +lg +  l G++++l+++   + +  + + +  ++lG
  gi|330508525|ref|YP_004384953.1| 223 pL-TVSETLHTRSFWFLWTTWILAGAAGVSMTVLSTGYgLSLGLP--LEGAVLILTAFnlTNGTGRLASGYFSDRLG 296
                                       31.233344556677777777777777777777777663444444..555555555541033445567788899*** PP

                        MFS_1_like 289 hvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGral 365
                                        ++++ +a+la  l ++l  +  ++    ++ +  g+sfg+l+++ +  v++ ++  + + + gl  ++y  l + l
  gi|330508525|ref|YP_004384953.1| 297 RRRVMSLAFLAAGLAYFLFPLAGDLPTSAILAAVVGLSFGTLFSVSAPLVADCFGLDHFGAIFGLTFAAYGFLAGPL 373
                                       **********************99999999*********************************************** PP

                        MFS_1_like 366 GsliGGllwdlksa 379
                                       G  ++G+l dl++ 
  gi|330508525|ref|YP_004384953.1| 374 GPTLSGYLLDLNGG 387
                                       ********998775 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   2.5   2.5e-07   0.00076     273     411 ..      62     198 ..      29     200 .. 0.84
   2 ?   -2.5   2.0      0.55   1.6e+03      63     126 ..     288     347 ..     268     402 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.5e-07
                         LacY_symp 273 alimfiaplivnriGaknalliagvimsvrilgsafattalevvilkllhalevplllvgvfkyitsafdkr...ls 346
                                        + mf+a    +r G +  ++++ ++ s+  + +afa + + v     l      ++ + ++  +   + +r   +s
  gi|330508525|ref|YP_004384953.1|  62 GIFMFLAGRWQERYGIRRMIILGILLTSIGCILAAFANSITMVYAWAFLNGAASCFVYIPALTLVQQWYPQRkglVS 138
                                       368999************************9999***************************9999998887733245 PP

                         LacY_symp 347 atifligfqlskqlaivllstlaGklydkvGfqtaylvlgiivlsltlisvftlskskeqivlea 411
                                        t+ +     +  la+ ++s + G + +  G++++ lvl++++l+  l+++++ +++ + ++ ++
  gi|330508525|ref|YP_004384953.1| 139 GTVSM-----VFGLAAAIMSPVFGLMLNAFGYRNMSLVLAVLTLTAGLLGAYFARERDDETIKRQ 198
                                       55543.....44689999***********************************999988887765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.55
                         LacY_symp  63 fGlisdklGlkkellwvislllvlfapfliyvfepllqlnilvGalvGgvflGlvysagagaie 126
                                        G  sd+lG ++    ++++l   +a ++++  +  l +  ++ a+vG + +G  +s  a+++ 
  gi|330508525|ref|YP_004384953.1| 288 SGYFSDRLGRRRV--MSLAFLAAGLA-YFLFPLAGDLPTSAILAAVVG-LSFGTLFSVSAPLVA 347
                                       5778888887763..45666555555.444555555555555556665.677888888888774 PP

>> DUF3959  Protein of unknown function (DUF3959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   2.8e-05     0.085      77     171 ..     113     207 ..      77     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.8e-05
                           DUF3959  77 iaaciavipli.lrfrtyaitlgllalwgallwdikevqslavlgrlmnlltteklyllllvagfllggllantlkr 152
                                        a+c   ip++ l  + y    gl++   ++++ +       v+g ++n +   ++ l+l v   l  gll++ + r
  gi|330508525|ref|YP_004384953.1| 113 AASCFVYIPALtLVQQWYPQRKGLVSGTVSMVFGLAAAIMSPVFGLMLNAFGYRNMSLVLAVL-TLTAGLLGAYFAR 188
                                       4789999997625667799999****9999999999999999************999887766.57899******** PP

                           DUF3959 153 endnekqekpkvlkqkkkr 171
                                       e d+e  ++ + +++  kr
  gi|330508525|ref|YP_004384953.1| 189 ERDDETIKRQNEMRDALKR 207
                                       ***9999999888877666 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 ?    1.5   0.3     0.089   2.7e+02      25      56 ..      78     108 ..      70     121 .. 0.65
   2 ?   10.5   0.0   0.00014      0.43      10     110 ..     127     228 ..     123     232 .. 0.84
   3 ?   -1.0   0.1      0.55   1.6e+03      19      45 ..     229     255 ..     225     277 .. 0.69
   4 ?   -1.9   0.1      0.99     3e+03      32      61 ..     301     330 ..     292     337 .. 0.47

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.089
                           SLATT_1  25 krwrlllillellalllaalrafgelsv.dlvg 56 
                                       +r+ +l ill+ ++ +laa+   +++++  + +
  gi|330508525|ref|YP_004384953.1|  78 RRMIILGILLTSIGCILAAFA--NSITMvYAWA 108
                                       5666788999999*9999999..3333312223 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00014
                           SLATT_1  10 ldwYrkkaeeneraakrwr..lllillellalllaalrafgelsvdlvgvlaavaaallaWlelkqyeelaaaYsla 84 
                                       ++wY ++    + + ++++  ++ i+  +++l+l a++ + ++s+ +++vl+  a+ l a+++ ++ +e++++ + +
  gi|330508525|ref|YP_004384953.1| 127 QQWYPQRKGLVSGTVSMVFglAAAIMSPVFGLMLNAFG-YRNMSL-VLAVLTLTAGLLGAYFARERDDETIKRQNEM 201
                                       68999999999888888882235677889*********.999999.9****************************** PP

                           SLATT_1  85 aeeLeiiraalea.eateeewaklVad 110
                                          L+ + ++ ++ +++e++    V++
  gi|330508525|ref|YP_004384953.1| 202 RDALKRQIREGNEiDKDEQRRPLTVSE 228
                                       ****99999999856666666666665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.55
                           SLATT_1  19 eneraakrwrlllillellalllaalr 45 
                                       + + ++ ++ +++ +l ++a + +++ 
  gi|330508525|ref|YP_004384953.1| 229 TLHTRSFWFLWTTWILAGAAGVSMTVL 255
                                       567788888888877776666655544 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.99
                           SLATT_1  32 illellalllaalr..afgelsvdlvgvlaav 61 
                                       + l +la+ la++    +g+l+    ++laav
  gi|330508525|ref|YP_004384953.1| 301 MSLAFLAAGLAYFLfpLAGDLPT--SAILAAV 330
                                       33344444444443113444443..4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1040  (0.0580066); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 2829.80
//
Query:       gi|330508526|ref|YP_004384954.1|  [L=212]
Description: HAD-superfamily hydrolase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-13   50.9   0.0    4.7e-13   49.6   0.0    1.6  1  HAD_2            Haloacid dehalogenase-like hydrolase
    1.3e-09   38.6   0.0    3.6e-08   33.9   0.0    2.0  1  Hydrolase        haloacid dehalogenase-like hydrolase
     0.0002   21.9   0.1    0.00037   21.0   0.1    1.5  1  HAD              haloacid dehalogenase-like hydrolase
     0.0066   16.2   0.0      0.038   13.7   0.0    1.9  1  NIF              NLI interacting factor-like phosphatase
     0.0079   16.2   0.0      0.016   15.2   0.0    1.5  1  Hydrolase_like   HAD-hyrolase-like
  ------ inclusion threshold ------
      0.039   13.3   0.0      0.091   12.1   0.0    1.5  2  Put_Phosphatase  Putative Phosphatase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   1.6e-16   4.7e-13       4     176 ..       8     184 ..       5     186 .. 0.75

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.6e-16
                             HAD_2   4 DlDgTlldte...eliiqafnelleey.gls.elseee.lrkliglslrellrklgeseeeeekieellrkyneekk 74 
                                       D+DgTl++++   +++++ + +l++e  gl+    +e+ + +++ + ++ l ++   + + ++   + l++ +ee+ 
  gi|330508526|ref|YP_004384954.1|   8 DMDGTLVNSRfvdKVWMEGMPRLYAEStGLDlPAAREYvIGEYMKIGSDHLEWYDL-KFWIDK---FGLSIGKEELL 80 
                                       99******964447888888888766644444444444145666666644444433.355443...33444455444 PP

                             HAD_2  75 k...kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtse.dvekkKPdpeviekalek 147
                                       +   +e+++y++v+e+Le L +++y+l + ++  re ++ +l+ l+   yF  + +++ d+ + K +p ++ +++ +
  gi|330508526|ref|YP_004384954.1|  81 ElyeDEIEVYPEVEEVLELL-SENYELVVTSNAAREFIDIELDGLQ--GYFREVFSATsDFREVKKSPLLYGAICAH 154
                                       454589**************.99***************99998666..8**999987615555599*********** PP

                             HAD_2 148 lklkkeeviyvGDsp.tDieaakkagikvi 176
                                       l++ + ev+ +GD+  +D e+a  ag++++
  gi|330508526|ref|YP_004384954.1| 155 LDARPFEVLHIGDHYsYDYESALDAGLDAL 184
                                       ***************9**********9986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   1.2e-11   3.6e-08       1     210 []       2     180 ..       2     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.2e-11
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHH.HHHHHHHHHHH.HHHHHETTTE.HHHHTHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxx.xxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkal.vaaakarsgal.tgfatfigrg.ayaigkp 74 
                                       i+ + +D+dGTL++++  v +v+ +                    +   +a+  + +l +  + +ig+  ++     
  gi|330508526|ref|YP_004384954.1|   2 IRIISLDMDGTLVNSR-FVDKVWMEG-------------------MpRLYAESTGLDLpAAREYVIGEYmKIGSDHL 58 
                                       5778899999999888.666666666...................22334444433332222223344345555556 PP

                                       HHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHH.H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                         Hydrolase  75 ewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetae.r 150
                                       ew +              + ++   ++ +  ++l++++ + +  v+pe++e+++ L ++ +e+v+ ++  +e+ + +
  gi|330508526|ref|YP_004384954.1|  59 EWYDLK-----------FWIDKFGLSIGK-EELLELYEDEIE--VYPEVEEVLELLSEN-YELVVTSNAAREFIDiE 120
                                       666655...........444444444444.366666666655..************965.***************66 PP

                                       HHHHTTGGGE.SEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 151 aanqlGddyf.daviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                       +    G  yf ++  a+++    k sp  + a++  L ++p ev+++GD    D + +  Ag
  gi|330508526|ref|YP_004384954.1| 121 LDGLQG--YFrEVFSATSDFREVKKSPLLYGAICAHLDARPFEVLHIGDHYSyDYESALDAG 180
                                       666677..997777777777789999************************999998887776 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   1.2e-07   0.00037       3     150 ..       7     148 ..       5     176 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.2e-07
                               HAD   3 fDfDgTLldgdsle.lllrfllrrgaprlwralreklllal...frellrldraglaelleallaglseelaaeler 75 
                                       +D+DgTL+++   + ++++  + r   +   + ++++++++   + +++++  ++++  ++    gls   ++el +
  gi|330508526|ref|YP_004384954.1|   7 LDMDGTLVNSRFVDkVWME-GMPRLYAESTGLDLPAAREYVigeYMKIGSDHLEWYDLKFWIDKFGLS-IGKEELLE 81 
                                       6*********555545555.333333333333333344444444344444444445555554555555.34778888 PP

                               HAD  76 fvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelg..adevlatelevddrltgelglegkpvr 150
                                       +++++i+    +p++ e+l+  +++++++vv S++ r+++ + l+ l+  + ev +   +++  +        ++ +
  gi|330508526|ref|YP_004384954.1|  82 LYEDEIE---VYPEVEEVLE-LLSENYELVVTSNAAREFIDIELDGLQgyFREVFSATSDFR-EV-----KKSPLLY 148
                                       8887776...55********.77*********************988878777766622221.22.....3333333 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.3e-05     0.038       5      68 ..       7     122 ..       3     140 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                               NIF   5 LDLDetLvhskleks.k.............................................klkve.....gek.. 28 
                                       LD+D+tLv s++ ++                                               k         + +  
  gi|330508526|ref|YP_004384954.1|   7 LDMDGTLVNSRFVDKvWmegmprlyaestgldlpaareyvigeymkigsdhlewydlkfwidK---FglsigK-Eel 79 
                                       888888888887333225666667777777777777777777777777776666655444442...0232431.135 PP

                               NIF  29 ...vevsvlkRpgldefLkelsklyevvifTasseeyaeavid 68 
                                          +e  + + p ++e L+ ls++ye+v+ +++ +e+++  +d
  gi|330508526|ref|YP_004384954.1|  80 lelYEDEIEVYPEVEEVLELLSENYELVVTSNAAREFIDIELD 122
                                       55588889999*********************99998876555 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.4e-06     0.016       4      47 ..     142     185 ..     141     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.4e-06
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEE CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvL 47 
                                       K +p +y ++ ++l++ p evl iGD +  D ++A +aG++ ++
  gi|330508526|ref|YP_004384954.1| 142 KKSPLLYGAICAHLDARPFEVLHIGDHYSYDYESALDAGLDALF 185
                                       568999*********************************99865 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.77   2.3e+03       2      15 ..       4      17 ..       3      32 .. 0.73
   2 ?   12.1   0.0     3e-05     0.091      69     126 ..      86     138 ..      73     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.77
                   Put_Phosphatase  2 lvvfDFDktiided 15
                                      ++ +D D t++++ 
  gi|330508526|ref|YP_004384954.1|  4 IISLDMDGTLVNSR 17
                                      67899999999875 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3e-05
                   Put_Phosphatase  69 siplspglvelikslakkkleldliiiSDaNsffieeileaagledlFseiftNPaav 126
                                       +i + p++ e+++ l   +++++l++ S+a + fi+  l+  gl+ +F+e+f+  + +
  gi|330508526|ref|YP_004384954.1|  86 EIEVYPEVEEVLELL---SENYELVVTSNAAREFIDIELD--GLQGYFREVFSATSDF 138
                                       688899999999999...669***************8876..899*******988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.22s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1573.22
//
Query:       gi|330508527|ref|YP_004384955.1|  [L=255]
Description: hypothetical protein MCON_2745 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1885.77
//
Query:       gi|330508528|ref|YP_004384956.1|  [L=204]
Description: hypothetical protein MCON_2748 [Methanosaeta concilii GP6]
Scores for complete 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-58  196.7   0.0    3.6e-58  196.6   0.0    1.0  1  Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
  ------ inclusion threshold ------
      0.052   12.9   0.0       0.08   12.3   0.0    1.2  1  Methyltrans_RNA  RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.6   0.0     4e-62   3.6e-58       1     196 [.       1     197 [.       1     199 [. 0.96

  Alignments for each domain:
  == domain 1  score: 196.6 bits;  conditional E-value: 4e-62
                                       -EEEEEEESSEESSSHHHCCCTTTTTTSHHHHHHHHHHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S-- CS
                   Methyltrn_RNA_2   1 mrefvvlankapTdsdiplddlpGaagrldvlarcvsaalfvshgiRedvvvylvLegtpdpprtikieasevkkvs 77 
                                       mr fvv+++ka+T++ ++l+d+pG++grld+l+r+v aa+ +shgiR+dv vylvL+g+ + p+ti++ ++ +++ +
  gi|330508528|ref|YP_004384956.1|   1 MRIFVVVGHKATTQPSFSLEDIPGTSGRLDILCRSVTAAFVLSHGIRKDVLVYLVLLGG-ETPKTIRLVGETLRHLN 76 
                                       9********************************************************76.5789************* PP

                                       SSHHHHHHHHHHHHCHCCTGCCSEEEEETTEEEE---HHHHHHHHHCT.SEEEEESTTSEEGGGS---S...SEEEE CS
                   Methyltrn_RNA_2  78 pderniailikkalkaveeikkqekkvrpgltVrkegfealleelsek.ksiillkekGedisnakiel...nPvFi 150
                                       pder  a l+kkal av e   +++ +++g+ Vr+ g+e+lle l+++   +++l e+G d +  k+e+   +  F+
  gi|330508528|ref|YP_004384956.1|  77 PDERTTAALLKKAL-AV-EATPEWAMSTSGIFVRTGGLEKLLEDLKQRsVRLVYLREDGRDFRCLKDEPlerEMAFV 151
                                       **************.77.7999*********************998876899***************9999999*** PP

                                       EE-TT-SHHHHHHHHHCTTSEEEES-SS---HHHHHHHHHHHHHHH CS
                   Methyltrn_RNA_2 151 lgdHidlpeeeekllerlkakrvslgPlsLhadhcvtlihneldkk 196
                                       lgdH ++++eee+ll+ ++a+ v lgP+sLhadhc+++   +ld++
  gi|330508528|ref|YP_004384956.1| 152 LGDHTGMTAEEESLLASAGAEVVALGPTSLHADHCIVVTNWLLDTN 197
                                       **************************************99999986 PP

>> Methyltrans_RNA  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.9e-06      0.08     139     213 ..     112     183 ..     109     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.9e-06
                                       HHHHHHHCSCCEEEEEEETTSSEBGGGSSHCCHTHHCSEEEEEE--TT---HHHHHHHHHTTCEEEB-SSS---H CS
                   Methyltrans_RNA 139 lkelleelkeadlklildeeekksleelsekkkelkevkvlliiGPEGGfsekEiellkeagfkpvsLgpriLRt 213
                                       l++lle+lk+ +++l+  +e+  +   l+++  e   ++++++ G   G++++E +ll +ag++ v Lgp+ L +
  gi|330508528|ref|YP_004384956.1| 112 LEKLLEDLKQRSVRLVYLREDGRDFRCLKDEPLE---REMAFVLGDHTGMTAEEESLLASAGAEVVALGPTSLHA 183
                                       6789999999998777777755565555555554...399******************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1563.50
//
Query:       gi|330508529|ref|YP_004384957.1|  [L=81]
Description: hypothetical protein MCON_2749 [Methanosaeta concilii GP6]
Scores for complete 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-05   22.9   6.8    0.00011   22.5   6.8    1.2  1  TM2            TM2 domain
  ------ inclusion threshold ------
      0.013   15.0   4.5      0.015   14.7   4.5    1.0  1  ABC2_membrane  ABC-2 type transporter


Domain annotation for each model (and alignments):
>> TM2  TM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   6.8   1.2e-08   0.00011       2      49 ..       4      53 ..       3      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.2e-08
                               TM2  2 kksklvaylLwffLGglGvHRFYlGktgsGvlqlltfv....Gglgiwwlid 49
                                      +ks++ a++L ++  + G+ ++YlG++  G++ +l+++      +g++w++ 
  gi|330508529|ref|YP_004384957.1|  4 SKSAIFAVILNLL--IAGLGHIYLGYPRRGIILFLLSFligaMSAGLGWIVA 53
                                      79********998..88999****************9988775567777775 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   4.5   1.7e-06     0.015     106     162 ..       8      63 ..       2      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-06
                     ABC2_membrane 106 pvsllqalifllivyflvgldlsrfflflllllltalaasslgllisalapsfedas 162
                                       ++++++ l++  + ++ +g+++ r+++++ll +l++ ++ +lg+++++++ s++ ++
  gi|330508529|ref|YP_004384957.1|   8 IFAVILNLLIAGLGHIYLGYPR-RGIILFLLSFLIGAMSAGLGWIVAVIFCSYDAWQ 63 
                                       4455555555555555669999.6************************998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); 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):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.57
# Mc/sec: 429.99
//
Query:       gi|330508530|ref|YP_004384958.1|  [L=451]
Description: hypothetical protein MCON_2750 [Methanosaeta concilii GP6]
Scores for 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   28.9   0.0    2.6e-06   27.6   0.0    1.8  1  THUMP          THUMP domain
     0.0049   17.2   3.8      0.018   15.4   0.6    3.0  3  DnaJ_CXXCXGXG  DnaJ central domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   2.9e-10   2.6e-06      97     143 ..     134     195 ..      34     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.9e-10
                                       S...............SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                             THUMP  97 f...............eftsreinrevGkaivektglkVdlenPdivvrveiikdkayisid 143
                                       +               e  + e+nrevGk++   tg++ dl++Pd vv++ +   +a++++ 
  gi|330508530|ref|YP_004384958.1| 134 AeneellladggsrhaEPFKSELNREVGKRLSAITGKEFDLKDPDMVVHLNLETGEAELQVA 195
                                       455555556666666688899**************************************996 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.37   3.3e+03      17      23 ..      27      33 ..      18      43 .. 0.69
   2 ?    0.5   0.0     0.088   7.9e+02      11      23 ..      86      98 ..      81     105 .. 0.65
   3 !   15.4   0.6     2e-06     0.018       1      50 [.     217     261 ..     217     266 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.37
                     DnaJ_CXXCXGXG 17 CktCkGs 23
                                      C++C G+
  gi|330508530|ref|YP_004384958.1| 27 CDSCLGR 33
                                      4444443 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.088
                     DnaJ_CXXCXGXG 11 kgkkktCktCkGs 23
                                      ++k  +C+ C G+
  gi|330508530|ref|YP_004384958.1| 86 SEKDVRCTVCLGE 98
                                      3445557777664 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 2e-06
                     DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsGvvreeqk.t.lgp.fvqqsqstCpeCeGt 50 
                                       C++C+G+g        C++C+G+G++ +e++ + + p ++++ + + +  +G 
  gi|330508530|ref|YP_004384958.1| 217 CRECRGRG--------CPRCNGTGRMYQESVdElIRPaVIRAAEADDTVFHGA 261
                                       9*******........********65444442566665665555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 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:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3139.04
//
Query:       gi|330508531|ref|YP_004384959.1|  [L=96]
Description: 50S ribosomal protein L21e [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-33  113.2   1.7    4.7e-33  113.1   1.7    1.0  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1   1.7   2.6e-37   4.7e-33       1     100 [.       1      96 []       1      96 [] 0.99

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 2.6e-37
                                       X--S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEE CS
                    Ribosomal_L21e   1 mknskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivn 77 
                                       m++++g+r+++r+++sk++r  g++p+ ++++e++ G kV++ idps++kgmph+r+hGkt +v  v+kr+++++++
  gi|330508531|ref|YP_004384959.1|   1 MAHHHGMRKKSRDKLSKTVRSSGISPVVRAIQEFDTGSKVHVLIDPSIHKGMPHPRFHGKTAEV--VGKRGRAFVLK 75 
                                       89**************************************************************..*********** PP

                                       EEETTE..EEEEEE-GGGEEE-- CS
                    Ribosomal_L21e  78 kkvggkileKriivriehlkksk 100
                                       +++g+   +K++i+ +ehlk +k
  gi|330508531|ref|YP_004384959.1|  76 VTDGDA--TKTLITLPEHLKAQK 96 
                                       ******..************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 726.07
//
Query:       gi|330508532|ref|YP_004384960.1|  [L=114]
Description: DNA-directed RNA polymerase subunit F [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.6e-09   36.0   4.2    1.3e-08   35.2   4.2    1.3  1  RNA_pol_Rpb4  RNA polymerase Rpb4
  ------ inclusion threshold ------
      0.086   13.1   0.1       0.23   11.8   0.0    1.7  2  HHH_3         Helix-hairpin-helix motif


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 !   35.2   4.2   1.4e-12   1.3e-08       1     118 [.      11     110 ..       7     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.4e-12
                                       EE-HHHHHHHHHHHHHHHHCHHHHHTCCCCCHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTSTS CS
                      RNA_pol_Rpb4   1 lLsnsEvllvlkeeleerknkdkkeseddkisekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfeL 77 
                                       +L++ Ev+++l  ++ e+                +  +++l ++l++++ + +  fs+   ee+ + + el+k  ++
  gi|330508532|ref|YP_004384960.1|  11 FLTLAEVKEMLD-QIREK----------------RADEEELGYELRRAIRHAEL-FSKGSAEENTAMVAELMKMEKM 69 
                                       566777777776.44444................444579*************8.********************** PP

                                       THHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHH CS
                      RNA_pol_Rpb4  78 tkaEklqlvnlkPesavelktlieeleerfedeqleeiLde 118
                                       t+  ++++ +++P + +el+++ ++++  +++e+l +iL++
  gi|330508532|ref|YP_004384960.1|  70 TRTIAVKIADIRPVTKDELRAIYAKERFNLSEEELSNILEI 110
                                       ***************************************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 ?   -2.8   0.0       0.9   8.1e+03      46      58 ..      14      26 ..      13      31 .. 0.56
   2 ?   11.8   0.0   2.5e-05      0.23       9      34 ..      56      81 ..      54      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.9
                             HHH_3 46 Llkvkglgpktfe 58
                                      L +vk++ ++  e
  gi|330508532|ref|YP_004384960.1| 14 LAEVKEMLDQIRE 26
                                      5566666555444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.5e-05
                             HHH_3  9 NtAsaeeLqklpGlgpklAknIvayR 34
                                      NtA ++eL+k ++++ ++A +I + R
  gi|330508532|ref|YP_004384960.1| 56 NTAMVAELMKMEKMTRTIAVKIADIR 81
                                      9**********************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 895.97
//
Query:       gi|330508533|ref|YP_004384961.1|  [L=193]
Description: hypothetical protein MCON_2753 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-64  217.7   0.0    1.2e-64  217.6   0.0    1.0  1  DUF655    Protein of unknown function (DUF655)
    2.6e-05   24.4   0.0      4e-05   23.8   0.0    1.3  1  HHH_6     Helix-hairpin-helix motif
     0.0015   18.7   0.0      0.003   17.8   0.0    1.5  1  HHH_3     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.6   0.0   2.1e-68   1.2e-64       2     180 ..      10     187 ..       9     188 .. 0.99

  Alignments for each domain:
  == domain 1  score: 217.6 bits;  conditional E-value: 2.1e-68
                                       --EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GGGS CS
                            DUF655   2 eeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisyedL 78 
                                       ee a vLDylp+G++ d  r+++++p+vqa+ge+++ L+e++p++ v      +v+ig+g++d i++++r+i y +L
  gi|330508533|ref|YP_004384961.1|  10 EEIARVLDYLPYGRTPDS-RTYQKQPLVQAVGETNFVLMEMTPKEGVVPVAGARVYIGSGSRDVIDHVNRRIDYSEL 85 
                                       7899***********998.7********************************************************* PP

                                       -HHHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT-- CS
                            DUF655  79 tdvaraeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglk 155
                                       +++a+ eLp v++ iv e+E rf+++fn+a pit+R+HaLelLpg+gkkl++++l+eR++ +F+sF+d+ +rvkgl+
  gi|330508533|ref|YP_004384961.1|  86 SNSAKLELPFVIQTIVLEDEPRFIRYFNDAGPITTRMHALELLPGIGKKLMWSVLNERKKGPFKSFADLVERVKGLH 162
                                       ***************************************************************************** PP

                                       -HHHHHHHHHHHHHH-TTSS--SS- CS
                            DUF655 156 dpaeilverileEiedktekYylFv 180
                                       +p++++++ri +E+ d++ kY++F+
  gi|330508533|ref|YP_004384961.1| 163 NPEKLIAKRIEDELMDDRIKYRVFT 187
                                       ************************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 !   23.8   0.0   6.7e-09     4e-05      28      70 ..     124     163 ..     113     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.7e-09
                             HHH_6  28 GLaaikglgeaaaerivaeRekegpfksledlarrvdslnkrq 70 
                                       +L+ + g+g++ + ++++eR+ +gpfks++dl++rv+    ++
  gi|330508533|ref|YP_004384961.1| 124 ALELLPGIGKKLMWSVLNERK-KGPFKSFADLVERVKG--LHN 163
                                       688889**************9.8*************95..333 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     5e-07     0.003      14      52 ..     123     161 ..     119     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5e-07
                             HHH_3  14 eeLqklpGlgpklAknIvayReknGpfksreeLl.kvkgl 52 
                                         L+ lpG+g+kl   +++ R k+Gpfks+ +L+ +vkgl
  gi|330508533|ref|YP_004384961.1| 123 HALELLPGIGKKLMWSVLNER-KKGPFKSFADLVeRVKGL 161
                                       67999****************.99*********9779988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1340.63
//
Query:       gi|330508534|ref|YP_004384962.1|  [L=247]
Description: dimethyladenosine transferase [Methanosaeta concilii GP6]
Scores for complete 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-53  179.5   0.0    7.8e-53  179.2   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    1.3e-05   25.8   0.0    2.3e-05   25.0   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    0.00046   20.8   0.0    0.00088   19.9   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.026   14.1   0.0      0.042   13.4   0.0    1.3  1  MTS              Methyltransferase small domain
      0.064   13.1   0.0      0.091   12.6   0.0    1.3  1  Methyltransf_23  Methyltransferase domain


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.2   0.0   2.2e-56   7.8e-53       7     260 ..       2     237 ..       1     242 [. 0.92

  Alignments for each domain:
  == domain 1  score: 179.2 bits;  conditional E-value: 2.2e-56
                                       GCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S CS
                            RrnaAD   7 sygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhq 83 
                                       ++gq+fl++++++++I+++++l  ++ vleigpG+GilT+eLa ra  v ++E+d++La++l +    +++++v+h+
  gi|330508534|ref|YP_004384962.1|   2 RLGQHFLIDRSIVDSIVSHADLGLEDWVLEIGPGEGILTRELAARAGRVYAVEIDPDLAASLCN---TAPNVMVIHA 75 
                                       68************************************************************99...699******* PP

                                       -CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHH CS
                            RrnaAD  84 DflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvl 160
                                       D+l+  +p+            ++v+nlPy+is+++  +ll+  r+ +  ++l++qkefa+rl a+p sk ++rl+ +
  gi|330508534|ref|YP_004384962.1|  76 DALTVRLPQ----------YNKIVSNLPYNISSKITYRLLS--RP-FDLAVLMFQKEFAQRLKAEPASKIYGRLGMV 139
                                       *********..........349******************6..44.5799*************************** PP

                                       HHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTCHHHHHC CS
                            RrnaAD 161 reaftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllpggelqal 237
                                       + +f  ++++ +v +++f+P p vdsa+v+l++++e+ pq+d + + ++  +l+  +rk++++ l   +  + + a 
  gi|330508534|ref|YP_004384962.1| 140 AGFFSHIEILQNVSRKAFRPVPDVDSAIVRLRPRTER-PQVDPRAFMRLADILFRNRRKKVKKGLAAYGVDKMTLAE 215
                                       *************************************.8**************************988877776666 PP

                                       TT.T--TTTCCCCSGHHHHHHHH CS
                            RrnaAD 238 sstgindnalvkklsaeqtldif 260
                                        + +  +n++ ++l+++q++ ++
  gi|330508534|ref|YP_004384962.1| 216 LD-QSLINMRPEELTPDQVAGLI 237
                                       66.56777777777777776655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   6.3e-09   2.3e-05       1      71 [.      29      91 ..      29     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 6.3e-09
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvss 71
                                      vL++G G+G lt++la+r   ++v++v+i++++ +   + a    +nv ++++da ++ +++  ++ +vs+
  gi|330508534|ref|YP_004384962.1| 29 VLEIGPGEGILTRELAARA--GRVYAVEIDPDLAASLCNTA----PNVMVIHADALTVRLPQ--YNKIVSN 91
                                      9*****************6..9***********99999999....9*********9988775..7777774 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.4e-07   0.00088       1      58 [.      30      83 ..      30      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.4e-07
                                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS- CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfe 58
                                      L++G G G+l+++la r++rv++v++++ +   a+ ++  ++  v +++ada ++ ++
  gi|330508534|ref|YP_004384962.1| 30 LEIGPGEGILTRELAARAGRVYAVEIDPDLA--ASLCNTAPN--VMVIHADALTVRLP 83
                                      89*************9999**********99..444444444..77899999876665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.2e-05     0.042      31     120 ..      25     107 ..      13     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPf 107
                                       l++ vl +G G G+l+ +la++  +  v +v++d    + +  n + n   v v++ d+l      +++ ivsN P+
  gi|330508534|ref|YP_004384962.1|  25 LEDWVLEIGPGEGILTRELAARAGR--VYAVEIDPDLAA-SLCNTAPN---VMVIHADALTVRL-PQYNKIVSNLPY 94 
                                       56679*****************999..677777765333.33344444...4567777776555.6*********** PP

                                       TTTCHCHHHHHHH CS
                               MTS 108 hagkatelavaee 120
                                         ++++++++  +
  gi|330508534|ref|YP_004384962.1|  95 NISSKITYRLLSR 107
                                       9999998887766 PP

>> Methyltransf_23  Methyltransferase 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     0.091      26      57 ..      29      60 ..      19     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
                   Methyltransf_23 26 vLdiGcGtGillevlrengfsvtgvDlspeav 57
                                      vL+iG+G+Gil+++l+++   v++v+++p + 
  gi|330508534|ref|YP_004384962.1| 29 VLEIGPGEGILTRELAARAGRVYAVEIDPDLA 60
                                      9**************99999999999998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1948.66
//
Query:       gi|330508535|ref|YP_004384963.1|  [L=477]
Description: succinate-semialdehyde dehydrogenase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-165  551.6   0.0   1.3e-165  551.4   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
       0.14   11.6   0.0          1    8.8   0.0    2.1  2  DUF1487   Protein of unknown function (DUF1487)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  551.4   0.0  1.5e-169  1.3e-165      10     462 .]      22     473 ..      15     473 .. 0.98

  Alignments for each domain:
  == domain 1  score: 551.4 bits;  conditional E-value: 1.5e-169
                                       EEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHH CS
                            Aldedh  10 evinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaea 86 
                                         +nPa++e++a v+ +t++d++ a++aAk+af+ w+++  e+Rae+L+ aadl++er++ +a+l+t+e+Gkpl++a
  gi|330508535|ref|YP_004384963.1|  22 TICNPANQEPVALVSVGTRQDARMALEAAKKAFPLWSETACEKRAELLHSAADLVRERAKSIARLLTQEQGKPLKNA 98 
                                       579************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-T CS
                            Aldedh  87 raeveeaidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPae 163
                                       rae+ +++ +l+yyae+ ++  ge l++s + +++v r+P+Gv ++ItPWN+P+ l++wk+ p+laaG+t+v KP +
  gi|330508535|ref|YP_004384963.1|  99 RAEILSSAGILDYYAEEGRRNVGEWLATS-RGRSVVLRQPVGVAALITPWNYPVDLLSWKVGPCLAAGCTFVAKPPS 174
                                       ************************99995.899******************************************** PP

                                       TSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---E CS
                            Aldedh 164 etplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGkn 240
                                       ++p+ a+ +++++ +aglP+gv+nvv+g+gsevg++lve+p  +k++ftG+te+gr i+++aa ++krv+lElGG++
  gi|330508535|ref|YP_004384963.1| 175 RAPVAATEFVRAIYDAGLPAGVVNVVHGPGSEVGAELVENPISRKIAFTGETETGRWIMAQAALHIKRVSLELGGQS 251
                                       ***************************************************************************** PP

                                       EEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHH CS
                            Aldedh 241 plivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaql 317
                                       p+iv+ daD++ka++a+++ af+n+GQ+Ci+++r++v +++++ef+++lv ++++l++g++l+e++d+GP+ s++q+
  gi|330508535|ref|YP_004384963.1| 252 PFIVCGDADIEKAAAACAQRAFSNMGQICISVNRVYVADEVAEEFTDRLVHQTERLRIGNGLKENVDLGPMFSNEQR 328
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSS CS
                            Aldedh 318 ekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdt 393
                                       ek ++++++a ++ga+ll+Gg+  e +  ekgyf+ Ptvl+  +++m+i++eE+FGPV+++++f++++eai++aNd+
  gi|330508535|ref|YP_004384963.1| 329 EKTKEHMKDALDRGAELLCGGRePEGEAFEKGYFFLPTVLDRADHKMKIMREETFGPVAPIMRFETVDEAIKLANDS 405
                                       *********************998999************************************************** PP

                                       SEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                            Aldedh 394 eyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                       +yGLaa+++t+d+++  ++aerleaG v++N  ++ + ++ pfgG+k+Sg+Gre g++gle ++e+k++
  gi|330508535|ref|YP_004384963.1| 406 NYGLAAYIYTSDIATGIQAAERLEAGGVGVNINNVMDYQM-PFGGWKESGIGRELGHYGLESFLEIKHI 473
                                       **************************************99.**************************86 PP

>> DUF1487  Protein of unknown function (DUF1487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00011         1       8      60 ..     253     307 ..     250     312 .. 0.86
   2 ?   -0.4   0.0     0.071   6.4e+02     120     170 ..     390     439 ..     380     445 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00011
                           DUF1487   8 mvifedgDlnsalealveslkePfa..egavatvlveesirdefvervrsklkpl 60 
                                       ++++ d+D+++a+ a ++     ++  + +v  v v +++++ef +r+ ++ ++l
  gi|330508535|ref|YP_004384963.1| 253 FIVCGDADIEKAAAACAQRAFSNMGqiCISVNRVYVADEVAEEFTDRLVHQTERL 307
                                       59************9999988887722467889**************99998887 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.071
                           DUF1487 120 htFrnakEvvkllakeslkfasvsvwneklaavyelvarlnvdvftiNCak 170
                                         F +  E++kl++  +  +a  +++ + +a+  ++++rl+   + +N  +
  gi|330508535|ref|YP_004384963.1| 390 MRFETVDEAIKLANDSNYGLA-AYIYTSDIATGIQAAERLEAGGVGVNINN 439
                                       5699999***99987777665.599********999999998887777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3601.51
//
Query:       gi|330508536|ref|YP_004384964.1|  [L=108]
Description: hypothetical protein MCON_2757 [Methanosaeta concilii GP6]
Scores for complete 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   29.9   0.0    6.1e-07   29.4   0.0    1.2  1  HTH_3           Helix-turn-helix
    3.8e-05   23.2   0.0    7.3e-05   22.2   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    6.2e-05   22.7   0.0     0.0002   21.0   0.0    1.7  2  HTH_23          Homeodomain-like domain
    0.00062   19.6   0.0      0.001   18.9   0.0    1.4  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
    0.00082   18.7   0.0     0.0019   17.5   0.0    1.6  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
     0.0018   18.2   0.0     0.0028   17.6   0.0    1.2  1  HTH_37          Helix-turn-helix domain
      0.002   17.9   0.0     0.0032   17.3   0.0    1.3  1  P22_Cro         DNA-binding transcriptional regulator Cro
     0.0032   17.4   0.0     0.0044   17.0   0.0    1.3  1  HTH_19          Helix-turn-helix domain
     0.0048   17.3   0.0     0.0094   16.4   0.0    1.5  1  HTH_26          Cro/C1-type HTH DNA-binding domain
     0.0075   16.4   0.0      0.012   15.8   0.0    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
      0.019   14.7   0.0      0.039   13.8   0.0    1.5  1  HTH_10          HTH DNA binding domain
      0.021   14.7   0.0      0.039   13.8   0.0    1.4  1  MarR_2          MarR family
      0.023   14.8   0.0      0.039   14.1   0.0    1.4  1  HTH_28          Helix-turn-helix domain
      0.028   14.5   0.0      0.032   14.3   0.0    1.2  1  RepB            RepB plasmid partitioning protein
      0.043   13.8   0.0       0.07   13.1   0.0    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.048   13.5   0.4       0.87    9.5   0.0    2.3  2  HTH_5           Bacterial regulatory protein, arsR family
      0.049   13.3   0.0       0.34   10.6   0.0    2.1  2  Sigma70_r4_2    Sigma-70, region 4
       0.06   13.4   0.0      0.076   13.0   0.0    1.3  1  DUF483          Protein of unknown function (DUF483)
       0.11   12.8   0.0       0.16   12.3   0.0    1.4  1  KORA            TrfB plasmid transcriptional repressor


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   6.5e-10   6.1e-07       1      34 [.      20      53 ..      20      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 6.5e-10
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSS CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGer 34
                                      ++e + ++g+sq++++++lG+++ ++s++ + +r
  gi|330508536|ref|YP_004384964.1| 20 IAEELIKRGISQKDVSKMLGITPPAVSQYVSKKR 53
                                      678899***********************99876 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 !   22.2   0.0   7.8e-08   7.3e-05      16      40 ..      27      51 ..      18      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7.8e-08
                            HTH_24 16 prisqreLAerlglSpstvnrrlkr 40
                                       +isq++++++lg++p++v++++ +
  gi|330508536|ref|YP_004384964.1| 27 RGISQKDVSKMLGITPPAVSQYVSK 51
                                      58********************986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.1e-07    0.0002       6      40 ..      16      51 ..      14      58 .. 0.90
   2 ?   -1.6   0.0       2.8   2.6e+03      20      27 ..      83      90 ..      78      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.1e-07
                            HTH_23  6 eRlrillllae.GlsvreIAreLgvsrrTvyrwlkr 40
                                      +R+ i+  l + G+s+++++++Lg+++  v++++++
  gi|330508536|ref|YP_004384964.1| 16 IRAAIAEELIKrGISQKDVSKMLGITPPAVSQYVSK 51
                                      699999999989*********************887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.8
                            HTH_23 20 vreIAreL 27
                                      vr+I++++
  gi|330508536|ref|YP_004384964.1| 83 VRRICDIC 90
                                      78999887 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 !   18.9   0.0   1.1e-06     0.001       4      49 ..      24      69 ..      20      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                    YdaS_antitoxin  4 aieivGgqkaLAealgvsqqaVsqWlkgkkqvpaervpeIekatnG 49
                                      +i+   +qk + + lg++++aVsq ++ k++ ++e   +I +a++G
  gi|330508536|ref|YP_004384964.1| 24 LIKRGISQKDVSKMLGITPPAVSQYVSKKRGYNIEFREDIREAIGG 69
                                      6777889********************9999***999999999887 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 !   17.5   0.0   2.1e-06    0.0019      17      45 ..      17      46 ..      15      50 .. 0.91
   2 ?   -3.2   0.0       6.1   5.8e+03      42      48 ..      81      87 ..      80      88 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.1e-06
                      HTH_Tnp_ISL3 17 eayilellles.rsvkavArqlgvSwtTVw 45
                                      +a+i+e+l+++ +s k+v+++lg+++  V 
  gi|330508536|ref|YP_004384964.1| 17 RAAIAEELIKRgISQKDVSKMLGITPPAVS 46
                                      799**********************99986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.1
                      HTH_Tnp_ISL3 42 tTVwril 48
                                      + V+ri 
  gi|330508536|ref|YP_004384964.1| 81 DLVRRIC 87
                                      6789986 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.9e-06    0.0028      21      50 ..      18      47 ..      14      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.9e-06
                                      HHHHHHHHHCT--HHHHHHHHT--HHHHHH CS
                            HTH_37 21 laiaeliekrelsqseaaqllgiaqPkvsr 50
                                      +aiae + kr++sq+++ ++lgi+ P vs+
  gi|330508536|ref|YP_004384964.1| 18 AAIAEELIKRGISQKDVSKMLGITPPAVSQ 47
                                      579*************************97 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 !   17.3   0.0   3.4e-06    0.0032      11      42 ..      30      58 ..      21      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.4e-06
                                      SHHHHHHHHTS-HHHHHHHHTC--HHHHHHHH CS
                           P22_Cro 11 gvekvAkalgvtksAVsqWgeeiPelrayqie 42
                                      +++ v k lg+t+ AVsq    + ++r y+ie
  gi|330508536|ref|YP_004384964.1| 30 SQKDVSKMLGITPPAVSQY---VSKKRGYNIE 58
                                      578899*************...9999999999 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.6e-06    0.0044       8      62 ..      24      77 ..      18      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.6e-06
                            HTH_19  8 ReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqg 62
                                       +++g++q++++++lgi++   s++ + k+   ++e   +i ea g  +e l++g
  gi|330508536|ref|YP_004384964.1| 24 LIKRGISQKDVSKMLGITPPAVSQYVSKKR-GYNIEFREDIREAIGGLAEDLIDG 77
                                      679**********************99999.888888899999999998888887 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 !   16.4   0.0   9.9e-06    0.0094       4      34 ..      22      52 ..      19      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.9e-06
                            HTH_26  4 elmadrgitkseLargtgisaatlsrlvkgk 34
                                      e +++rgi+++++++++gi+ + +s +v++k
  gi|330508536|ref|YP_004384964.1| 22 EELIKRGISQKDVSKMLGITPPAVSQYVSKK 52
                                      6689***********************9987 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 !   15.8   0.0   1.3e-05     0.012      21      45 ..      27      51 ..      19      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                                      SSB-HHHHHHHHTS-HHHHHHHHHH CS
                    Fe_dep_repress 21 kvvktkdlaerLnvspssVsemlkk 45
                                        +++kd+++ L++ p+ Vs+ ++k
  gi|330508536|ref|YP_004384964.1| 27 RGISQKDVSKMLGITPPAVSQYVSK 51
                                      56899******************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 ?   13.8   0.0   4.1e-05     0.039      21      46 ..      26      51 ..      25      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.1e-05
                            HTH_10 21 PRrvtlkeLAkelGIskstlsehLrk 46
                                       R ++ k+++k lGI+++++s++++k
  gi|330508536|ref|YP_004384964.1| 26 KRGISQKDVSKMLGITPPAVSQYVSK 51
                                      59999*****************9976 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   4.2e-05     0.039      12      43 ..      22      50 ..      12      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                                      HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHH CS
                            MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilk 43
                                       +L  r+   ++++++ + lg++++avs+ + 
  gi|330508536|ref|YP_004384964.1| 22 EELIKRG---ISQKDVSKMLGITPPAVSQYVS 50
                                      4577777...9******************886 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.1e-05     0.039       2      35 ..      17      51 ..      16      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-05
                            HTH_28  2 RleiikllaaGh.svreaArelgisrrtvyrWikr 35
                                      R+ i ++l++ + s++++++ lgi++  v++ +++
  gi|330508536|ref|YP_004384964.1| 17 RAAIAEELIKRGiSQKDVSKMLGITPPAVSQYVSK 51
                                      8999999996555****************998876 PP

>> RepB  RepB plasmid partitioning protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.4e-05     0.032      10      44 ..      17      52 ..      11      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-05
                              RepB 10 rarfaarleerGvdreeiasalgldkqtvskmva.r 44
                                      ra+ a  l++rG +++++++ lg+++++vs++v+ +
  gi|330508536|ref|YP_004384964.1| 17 RAAIAEELIKRGISQKDVSKMLGITPPAVSQYVSkK 52
                                      788999***************************952 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.4e-05      0.07      17      44 ..      24      51 ..      10      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.4e-05
                                      EEEEEHHHHHHHHHTTSSHHHHHHHHHH CS
                         HTH_Crp_2 17 eielpltqeelAsmlGltretvsrilse 44
                                       i+  ++q++ + mlG+t+  vs+  s+
  gi|330508536|ref|YP_004384964.1| 24 LIKRGISQKDVSKMLGITPPAVSQYVSK 51
                                      566789*****************97765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00092      0.87      20      35 ..      33      48 ..      16      51 .. 0.87
   2 ?    1.9   0.2      0.22   2.1e+02      17      26 ..      85      94 ..      82     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00092
                                      HHHHHHTS-HHHHHHH CS
                             HTH_5 20 elaeelglsqstvShH 35
                                      + +++lg+++++vS++
  gi|330508536|ref|YP_004384964.1| 33 DVSKMLGITPPAVSQY 48
                                      7899**********97 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.22
                                      EHHHHHHHHT CS
                             HTH_5 17 cvcelaeelg 26
                                       +c+++++l+
  gi|330508536|ref|YP_004384964.1| 85 RICDICCMLQ 94
                                      6899999987 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00036      0.34      26      49 ..      28      51 ..      27      53 .. 0.92
   2 ?   -0.1   0.0      0.79   7.4e+02       1      14 [.      60      73 ..      60      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00036
                                      ---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 26 glsykEIAellgisegtVksrlsR 49
                                      g s+k+++++lgi++ +V +++s+
  gi|330508536|ref|YP_004384964.1| 28 GISQKDVSKMLGITPPAVSQYVSK 51
                                      679*****************9986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.79
                                      HHHHHHHHTTS-HH CS
                      Sigma70_r4_2  1 rqalrealaeLper 14
                                      r+ +rea+  L e+
  gi|330508536|ref|YP_004384964.1| 60 REDIREAIGGLAED 73
                                      6789****999886 PP

>> DUF483  Protein of unknown function (DUF483)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     8e-05     0.076      14      69 ..      11      64 ..       5      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8e-05
                            DUF483 14 kvrpaidplvseelgiyrrlddleiGkllgyPkCCvksfieekr.faidsehlkeie 69
                                      +v p+i   ++eel i+r++ + ++ k+lg     v+ ++ +kr + i+    ++i 
  gi|330508536|ref|YP_004384964.1| 11 NVLPSIRAAIAEEL-IKRGISQKDVSKMLGITPPAVSQYVSKKRgYNIEF--REDIR 64
                                      56788888888887.9**************************99888873..34444 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017      0.16      21      54 ..      18      51 ..       6      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                              KORA 21 veiargvLVegkkqadvatelgltkqavsqavkr 54
                                        ia +++  g +q+dv + lg+t  avsq v +
  gi|330508536|ref|YP_004384964.1| 18 AAIAEELIKRGISQKDVSKMLGITPPAVSQYVSK 51
                                      568888888999*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 790.01
//
Query:       gi|330508537|ref|YP_004384965.1|  [L=265]
Description: hypothetical protein MCON_2758 [Methanosaeta concilii GP6]
Scores for complete 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-09   34.7   0.0      8e-08   31.7   0.0    2.0  2  NAD_synthase   NAD synthase
    0.00037   20.3   0.0    0.00098   18.9   0.0    1.6  2  ATP_bind_3     PP-loop family
     0.0054   16.4   0.0     0.0079   15.9   0.0    1.2  1  Asn_synthase   Asparagine synthase
  ------ inclusion threshold ------
      0.011   14.5   0.0        2.9    6.6   0.0    2.4  2  tRNA_Me_trans  tRNA methyl transferase
       0.12   12.3   0.2         17    5.4   0.0    2.3  2  PUB            PUB domain
       0.13   11.8   0.0       0.27   10.8   0.0    1.5  1  ThiI           Thiamine biosynthesis protein (ThiI)
        0.2   11.7   0.0       0.26   11.3   0.0    1.3  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami


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 !   31.7   0.0   3.1e-11     8e-08      19      77 ..      18      75 ..       7     108 .. 0.83
   2 ?    0.5   0.0      0.11   2.7e+02     154     182 ..     151     177 ..     148     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3.1e-11
                                      SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEE CS
                      NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievk 77
                                      + +++  SGGvDSsl a+la ++lg e ++a++l s+  +++++e+a+alae+lg+e  
  gi|330508537|ref|YP_004384965.1| 18 ERLLISYSGGVDSSLLAKLAHDVLG-EGAVAVILDSEIYPRSELEEAVALAESLGLELR 75
                                      5677889*****************5.67889***********************98754 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.11
                                       S-HHHHHHHHHHTT--HHHHCS--B--SS CS
                      NAD_synthase 154 llKtevkeLakelnvPervlkkpPsAdLk 182
                                       ++K+++++La+ ++ P  v +kp sA L 
  gi|330508537|ref|YP_004384965.1| 151 ITKKDIRTLAQDMGLP--VWDKPSSACLA 177
                                       79*************9..89999999885 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.8e-07   0.00098       2     108 ..      20     126 ..      19     130 .. 0.78
   2 ?   -2.2   0.0       1.1   2.9e+03     137     162 ..     139     166 ..     133     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.8e-07
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H..HHCTTSTC CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv..akkkgknl 76 
                                       +l+ +SgG+DS +L +l+++        +va+ +d ++ ++s+ e+++  +l+++l+++l++e++++  ++  ++n 
  gi|330508537|ref|YP_004384965.1|  20 LLISYSGGVDSSLLAKLAHDVLG---EGAVAVILDSEIYPRSELEEAV--ALAESLGLELRVERFSIldDQAFSQNP 91 
                                       799***************99955...5899*********999988765..7999************98744333433 PP

                                       CCH..HHHHHH.HHHHHCHHCCT.CEEE---BHHH CS
                        ATP_bind_3  77 eea..ARelRY.evlkealkkegievlllAhhadD 108
                                        ++    ++R  ++lk++++keg+++++ + +adD
  gi|330508537|ref|YP_004384965.1|  92 STRcyICKKRSsAILKRVAQKEGMSCIADGVNADD 126
                                       33311335554167899999999999999999998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                                       TCCEE-CCC..T--HHHHHHHHHHTT-- CS
                        ATP_bind_3 137 sirlvRPlL..kvskeeleeylkekkik 162
                                       ++ ++ P++   ++k+++++++++ +++
  gi|330508537|ref|YP_004384965.1| 139 EEGIWHPFVdsGITKKDIRTLAQDMGLP 166
                                       5668888885558999999999988775 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.1e-06    0.0079      11      76 ..      11      76 ..       8      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.1e-06
                      Asn_synthase 11 krrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehte 76
                                      k+r r   ++ +  SGG+DSSl+a la   + + + ++ ++ e    +e++ a ++ae lg+e + 
  gi|330508537|ref|YP_004384965.1| 11 KDRIREKERLLISYSGGVDSSLLAKLAHDVLGEGAVAVILDSEIYPRSELEEAVALAESLGLELRV 76
                                      56777778888888*****************9888888888855999**************99544 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0011       2.9       2      22 ..      19      39 ..      18      80 .. 0.77
   2 ?    5.6   0.0    0.0022       5.7     170     194 ..     150     174 ..     143     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0011
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallke 22
                                      ++++  SgGVDSs+ a l ++
  gi|330508537|ref|YP_004384965.1| 19 RLLISYSGGVDSSLLAKLAHD 39
                                      567889********9998876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0022
                     tRNA_Me_trans 170 eltKeevrkiAkeaglavaekkdSq 194
                                        +tK+++r +A+++gl+v +k+ S 
  gi|330508537|ref|YP_004384965.1| 150 GITKKDIRTLAQDMGLPVWDKPSSA 174
                                       589*******************995 PP

>> PUB  PUB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0066        17      38      60 ..     188     210 ..     178     218 .. 0.78
   2 ?    4.8   0.0     0.011        27      26      61 ..     216     251 ..     212     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0066
                               PUB  38 kekvlplegavelLealGFeekn 60 
                                       +e +  +e+++e+L++lGF +++
  gi|330508537|ref|YP_004384965.1| 188 REGLRMVEEGEEYLKSLGFGQLR 210
                                       5667779************8765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                               PUB  26 kyrrIrleNkafkekvlplegavelLealGFeekne 61 
                                       k  rI le + +++ + + +++v  L+ +GFe  + 
  gi|330508537|ref|YP_004384965.1| 216 KTARIELEEQELERALACRQEIVMRLKCIGFEYVTL 251
                                       6779999**************9999******98765 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.27       8     160 ..      22     164 ..      15     175 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                              ThiI   8 aLlSgGiDSpVaaylllk.RGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekv 83 
                                          SgG+DS   a l+    G  +v+v l++e +   e +e        +a  ++ l ++l+v  f  + ++  +  
  gi|330508537|ref|YP_004384965.1|  22 ISYSGGVDSSLLAKLAHDvLGEGAVAVILDSEIYPRSELEE-------AVALAES-LGLELRVERFSILDDQAFS-Q 89 
                                       44578888877666654424666777777766655544444.......3333343.5577777777655555544.5 PP

                              ThiI  84 kekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlr.visavvnllilrPLi..gldKeeiiklAk 157
                                       ++ +++ ++k+    i ++va++eg++++ +G     V +  l+  r  i a+++  i  P +  g+ K++i  lA+
  gi|330508537|ref|YP_004384965.1|  90 NPSTRCYICKKRSSAILKRVAQKEGMSCIADG-----VNADDLDDYRpGIAACSEEGIWHPFVdsGITKKDIRTLAQ 161
                                       6678999999999******************9.....5666777776347778888888888766677888888887 PP

                              ThiI 158 eig 160
                                       ++g
  gi|330508537|ref|YP_004384965.1| 162 DMG 164
                                       766 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0001      0.26       2      68 ..      20      87 ..      19     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                                      EEEE--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHH CS
                       PAPS_reduct  2 lvvsvsgGkdslVllhLalkafkpv.pvvfvdtghefpetiefvdeleeryglrlkvyepeeevaeki 68
                                      l +s+sgG ds+ l +La  ++ ++   v +d +   +  +e   +l+e +gl+l v +  +  ++++
  gi|330508537|ref|YP_004384965.1| 20 LLISYSGGVDSSLLAKLAHDVLGEGaVAVILDSEIYPRSELEEAVALAESLGLELRVERFSILDDQAF 87
                                      679*********************62589999999999999999999999999998877666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); 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:                         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: 1914.27
//
Query:       gi|330508538|ref|YP_004384966.1|  [L=429]
Description: class V aminotransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.1e-114  383.3   0.0    1.1e-73  248.4   0.0    2.0  2  Aminotran_5      Aminotransferase class-V
    2.8e-07   30.2   0.0    3.7e-07   29.8   0.0    1.1  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    3.6e-05   23.2   0.0    4.5e-05   22.9   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0011   17.6   0.0     0.0016   17.1   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


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 !  248.4   0.0   2.4e-77   1.1e-73       1     215 [.      17     227 ..      17     252 .. 0.98
   2 !  133.2   0.0   2.4e-42   1.1e-38     219     371 .]     262     418 ..     255     418 .. 0.96

  Alignments for each domain:
  == domain 1  score: 248.4 bits;  conditional E-value: 2.4e-77
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlv 77 
                                       iyldsaAt+ +p+ Vl+a+  yy++y anv r+v++ ++ a + +++a+ kva +++ e+  + +ft++tte+inlv
  gi|330508538|ref|YP_004384966.1|  17 IYLDSAATSLTPEPVLEAVLSYYRSYRANVGRGVYRQAQIADQRYRDAHLKVAGFVGGED-GTAVFTRNTTESINLV 92 
                                       8**********************************************************7.**************** PP

                                       HHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE CS
                       Aminotran_5  78 alslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt 154
                                       a++l   +k+gd+iv+t +ehh+nl+pw +l+ + g++++vi  d+ g++dl +le ++n+kt+lva++h sn++Gt
  gi|330508538|ref|YP_004384966.1|  93 ARGL--DWKRGDRIVTTLLEHHSNLLPWMRLK-EVGIDLEVIAPDKMGRIDLADLERAINKKTRLVAMSHLSNALGT 166
                                       ****..59***********************8.88****************************************** PP

                                       B--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEH CS
                       Aminotran_5 155 iqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrk 215
                                       i p  e+g++++++g+l+l+Daaq+++h+ ++vk++++Dfl fsghK+lgPtG Gvl++r+
  gi|330508538|ref|YP_004384966.1| 167 ILPAREVGRICRERGVLFLLDAAQSLPHMAVNVKDIDCDFLCFSGHKMLGPTGSGVLWIRE 227
                                       ************************************************************8 PP

  == domain 2  score: 133.2 bits;  conditional E-value: 2.4e-42
                                       HTS..SS.STTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTST CS
                       Aminotran_5 219 ekleplllggemveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslp 295
                                        +l pll gg+mve+v  ++ tf+     +eaGTp + + iglgaa++yl++ig+++++ he +l+ +ll++l+ ++
  gi|330508538|ref|YP_004384966.1| 262 TELAPLLAGGGMVEDVFDDGFTFKRGYEGYEAGTPDISAGIGLGAAVDYLARIGIDEVHDHEMSLTRRLLKGLDGIG 338
                                       6789************************************************************************* PP

                                       TEEEES...-B-CTCBSEEEEEETTCSHHHHHHHHHHT.TEEEEEE-TTTHHHHHHTT.S.-EEEEE--TTS-HHHH CS
                       Aminotran_5 296 gvrlyg..pdkaerrasivsfnfkgvhaedvatlLdee.gIavrsGhhcaqplmkrlale.gtvRaSlyiynteeev 368
                                       g+++yg  +d+  +r ++vsf ++g+ ++++a +Ld++ +I++rsGhhc  plm++l+l+ gt RaSly+ynt ee+
  gi|330508538|ref|YP_004384966.1| 339 GLEVYGpgADSPVERGGVVSFGIEGLLPHEIALMLDQAsNICIRSGHHCCIPLMRHLGLKhGTARASLYLYNTDEEI 415
                                       *****955678899*********************************************989*************** PP

                                       HHH CS
                       Aminotran_5 369 drl 371
                                       ++l
  gi|330508538|ref|YP_004384966.1| 416 EKL 418
                                       987 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 !   29.8   0.0   8.3e-11   3.7e-07      32     151 ..      68     194 ..      50     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 8.3e-11
                                       HHHHHT..-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-T..TTSSB-GGGC CS
                   DegT_DnrJ_EryC1  32 faaylg..vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdp..dtynidpaai 104
                                       +a ++g  +  a+ + + t+++ l+ r l+ ++gd ++++ l   +   + ++l  + + ++v +  +   id a++
  gi|330508538|ref|YP_004384966.1|  68 VAGFVGgeDGTAVFTRNTTESINLVARGLDWKRGDRIVTTLLEHHSNLLPWMRLKEVGIDLEVIApdKMGRIDLADL 144
                                       5666664466799999*************************999988777776666666666543115679****** PP

                                       GGG--TTEEEEEEB-G...GGB---HHHHHHHHHHCT-EEEEE-TT-TT- CS
                   DegT_DnrJ_EryC1 105 eaaitertkaIlpVhl...yGqvadmdalkaiaakhglkvieDaAhAlGa 151
                                       e+ai+++t+ + + hl   +G +    ++ +i+++ g+ ++ DaA++l  
  gi|330508538|ref|YP_004384966.1| 145 ERAINKKTRLVAMSHLsnaLGTILPAREVGRICRERGVLFLLDAAQSLPH 194
                                       *************9984446888999********************9975 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     1e-08   4.5e-05      95     236 ..     125     248 ..      39     325 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1e-08
                                       --EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTH CS
                   Beta_elim_lyase  95 gvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARf 171
                                       g+ l  +  ++ G +dl++le+ai++      k++l+ +    n a G++++    rev  i++++g+ ++lD+A  
  gi|330508538|ref|YP_004384966.1| 125 GIDLEVIAPDKMGRIDLADLERAINK------KTRLVAMSHLSN-ALGTILPA---REVGRICRERGVLFLLDAAQS 191
                                       455566667777*************9......588999998888.47999997...78999*************965 PP

                                       HHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-.EEEEE-HH....HHHHHHHHHHHHT---SST CS
                   Beta_elim_lyase 172 anaakslgeivkemfsyvDsvtmslkKdllanvG.gvlafrddeledylaerveqrkylggglrqa 236
                                            ++++ vk++   +D +++s+ K l  + G gvl +r+   ed  ++  eqr++ g++++++
  gi|330508538|ref|YP_004384966.1| 192 ---LPHMAVNVKDI--DCDFLCFSGHKML-GPTGsGVLWIREL--EDG-KRNGEQRRAKGQRMSSH 248
                                       ...56779999998..8**********75.5788688888887..666.77778888888888765 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.5e-07    0.0016     112     203 ..     121     218 ..      76     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.5e-07
                                       HHHTTCEEEEEST.....TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.TTS CS
                   Cys_Met_Meta_PP 112 lkklgievkfvdt.....sdleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp.llq 182
                                       lk++gi+ +++ +      dl++le+ai+++t+lv +  ++n l  ++  +++ ++++++gvl ++D++ + p + +
  gi|330508538|ref|YP_004384966.1| 121 LKEVGIDLEVIAPdkmgrIDLADLERAINKKTRLVAMSHLSNALGTILPAREVGRICRERGVLFLLDAAQSLPhMAV 197
                                       555666666665522222467899*************************************************8888 PP

                                       -GGGGT-SEEEEETTTTTTCS CS
                   Cys_Met_Meta_PP 183 rplklgaDivvhSaTKylgGh 203
                                       +  + ++D  + S+ K lg  
  gi|330508538|ref|YP_004384966.1| 198 NVKDIDCDFLCFSGHKMLGPT 218
                                       888999**9999999988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2999.10
//
Query:       gi|330508539|ref|YP_004384967.1|  [L=251]
Description: formate dehydrogenase family accessory protein FdhD [Methanosaeta concilii GP6]
Scores for complete 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-60  204.3   0.0    2.5e-60  204.1   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 !  204.1   0.0   1.4e-64   2.5e-60       1     236 [.      23     249 ..      23     250 .. 0.89

  Alignments for each domain:
  == domain 1  score: 204.1 bits;  conditional E-value: 1.4e-64
                                       E--EEEEEEETTEEEEEEEE-SSSHHHHHHHHHHHCTS--SGGGEEEEEEETTTEEEE-S.........-------- CS
                         FdhD-NarQ   1 veEepltivvngrelatlmatpadleelalGfllsegliesaediesievdedeasvavatrakaedkeerrtakrv 77 
                                       +eE+pl+i++ngr++at+m++p++ +e+++G+l+se++++++e+iesiev+ d a++ va+  +a         +r 
  gi|330508539|ref|YP_004384967.1|  23 AEEVPLSIFINGRHFATAMISPQMRKEFVAGHLYSERIVSAVEEIESIEVEGDVARAIVANPIRAI------VPRRP 93 
                                       58***************************************************9999999554333......22345 PP

                                       -------.---...--H------..-----EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE.TTEEEEEEEESSH CS
                         FdhD-NarQ  78 vtsgCglcgkesleelletlelp..esdlklsaeallrlmdalrekqelfketggvHaaalfdadgellavreDvGR 152
                                       + sgCg    ++l    ++++lp  +sdl++++++ +++m+a++  +e++ +tggvH+++lfd ++  + + eD+GR
  gi|330508539|ref|YP_004384967.1|  94 IVSGCGG-IASFL----DESKLPriKSDLTINKKQAQEAMKAISL-SETHIATGGVHSVGLFD-QSGPVSIIEDIGR 163
                                       7899988.33334....4444444489****************97.677889**********9.777999******* PP

                                       HHHHHHHHHHHHT.TSS..-SSSEEEESS-B-HHHHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEEEEETTEE CS
                         FdhD-NarQ 153 HnAlDkviGaallegld..lsdkilvvsgRlssemvqKaaragipvlvsvsaptslavelAeeagltlvgfvrgkrf 227
                                       HnAlDk+iG ++++g    l + +  ++gR+ss+m  K+  agip++vs+ a+t la+++A+++gl ++gf+rgkr+
  gi|330508539|ref|YP_004384967.1| 164 HNALDKAIGSLIIKGERfdLGRAFAACTGRVSSDMALKCSVAGIPIVVSRGATTGLAITIAQRTGLGIIGFLRGKRL 240
                                       *************8875449999****************************************************** PP

                                       EEEE-GGGE CS
                         FdhD-NarQ 228 nvYtgaeRi 236
                                        vY+++eR 
  gi|330508539|ref|YP_004384967.1| 241 SVYANPERF 249
                                       *******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1853.77
//
Query:       gi|330508540|ref|YP_004384968.1|  [L=308]
Description: hypothetical protein MCON_2761 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-15   57.6   0.0    2.8e-15   56.6   0.0    1.6  1  ATP_bind_3       PP-loop family
    2.4e-07   29.9   0.1    3.1e-07   29.5   0.1    1.1  1  tRNA_Me_trans    tRNA methyl transferase
    0.00047   19.6   3.6    0.00047   19.6   3.6    2.1  2  zn-ribbon_14     Zinc-ribbon
      0.002   18.2   0.0      0.003   17.6   0.0    1.3  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
     0.0021   17.8   0.0      0.003   17.3   0.0    1.2  1  Asn_synthase     Asparagine synthase
  ------ inclusion threshold ------
      0.011   15.3   0.1      0.019   14.5   0.1    1.5  1  Diphthami_syn_2  Diphthamide synthase
      0.014   14.9   0.2      0.014   14.9   0.2    1.9  2  QueC             Queuosine biosynthesis protein QueC


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 !   56.6   0.0   1.1e-18   2.8e-15       2     179 ..      50     236 ..      49     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.1e-18
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H.......HHC CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv.......akk 71 
                                       ++vAvSgG DS+aLl +l +   ++++++va++vd g+    ++   + k+++++++++ +i +++        +  
  gi|330508540|ref|YP_004384968.1|  50 IAVAVSGGKDSTALLFALSRVLAEKEVEMVALTVDEGIAGYRDDTIVAAKRIARQMGVEQVIISFQEeygwsldE-- 124
                                       78*************************************************************999988877642.. PP

                                       TTSTCC....CHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETT.CCEE-C CS
                        ATP_bind_3  72 kgknle....eaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseias.irlvRP 143
                                          + e    +    +R ++l+ a+k+ g++ l+++h++dD a  ++++  +g     l+ +++++e  + i  + P
  gi|330508540|ref|YP_004384968.1| 125 MVVGAEvapcTYCGVFRKNALNCAAKSLGVTKLATGHNQDDEAQSVMMNYLKGDME-RLMRFRPRREQPGlIPRIKP 200
                                       2333330011445679************************************9986.67777777777666999*** PP

                                       CCT--HHHHHHHHHHTT---B--CGGGCTTSHHHHH CS
                        ATP_bind_3 144 lLkvskeeleeylkekkikwveDesNadekyeRnri 179
                                       l ++  +e+  y+  ++i +   e  + +   R  +
  gi|330508540|ref|YP_004384968.1| 201 LRDIPEKEIALYAMVNGIYFESRECPYARLSLRADV 236
                                       *************99999887766665555555555 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   1.2e-10   3.1e-07       2     125 ..      49     162 ..      48     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.2e-10
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekv 78 
                                       +++va+SgG DS+  ++ l +   e +  +++l+ +e+    +   ++ +  a+r+a+++g++  +++f++ey    
  gi|330508540|ref|YP_004384968.1|  49 RIAVAVSGGKDSTALLFALSRVLAEKEVEMVALTVDEGI---AGYRDDTIVAAKRIARQMGVEQVIISFQEEYGW-- 120
                                       89**********999888887766544433344444333...457788999**********************75.. PP

                     tRNA_Me_trans  79 feefleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHY 125
                                           l+e   G    P+  C    K +  l+ a ++lg+ +latGH 
  gi|330508540|ref|YP_004384968.1| 121 ---SLDEMVVGAEVAPCTYCGVFRKNA--LNCAAKSLGVTKLATGHN 162
                                       ...57888899*********9887754..5555556**********6 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.63   1.6e+03       3       8 ..     134     139 ..     133     145 .. 0.84
   2 !   19.6   3.6   1.8e-07   0.00047       2      29 ..     276     303 ..     275     305 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.63
                      zn-ribbon_14   3 CerCGy 8  
                                       C+ CG 
  gi|330508540|ref|YP_004384968.1| 134 CTYCGV 139
                                       9***97 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.8e-07
                      zn-ribbon_14   2 kCerCGylSSqkiCkACvLLegLnkgrp 29 
                                        C+ CG  +  k CkAC LL +L+ ++p
  gi|330508540|ref|YP_004384968.1| 276 ECRECGEPCVGKRCKACELLGRLRPNLP 303
                                       6***********************9999 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.2e-06     0.003       2     153 ..      50     218 ..      49     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-06
                                       EEEE--SSCTCHHHHHHHHHHCTTH....EEEEEE-STB..-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv....pvvfvdtghe..fpetiefvdeleeryglrlkvyepeeevaekinaek 72 
                                       ++v+vsgGkds++ll  +++++ ++      + vd g     ++ti   +++++++g++  + + +ee  +++ +  
  gi|330508540|ref|YP_004384968.1|  50 IAVAVSGGKDSTALLFALSRVLAEKevemVALTVDEGIAgyRDDTIVAAKRIARQMGVEQVIISFQEEYGWSLDEMV 126
                                       789************99999988854555789999998633689***************555556666667777777 PP

                                       -S-THHHCHHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S...........CEEE-CCCT CS
                       PAPS_reduct  73 hgsslyeeaaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek...........slrvfPlln 138
                                        g ++    ++ + + ++l+ a + l+ + l tG  +d++++   +++++ d +                r+ Pl +
  gi|330508540|ref|YP_004384968.1| 127 VGAEVAPCTYCGVFRKNALNCAAKSLGVTKLATGHNQDDEAQSVMMNYLKGDMERLMrfrprreqpglIPRIKPLRD 203
                                       677776669*****************************999988888877776643367777777887778888888 PP

                                       --HHHHHHHHHHCT- CS
                       PAPS_reduct 139 Wteedvwqyilreni 153
                                         e+++  y+  ++i
  gi|330508540|ref|YP_004384968.1| 204 IPEKEIALYAMVNGI 218
                                       888888888877766 PP

>> Asn_synthase  Asparagine synthase
   #    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      11      84 ..      40     119 ..      33     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.2e-06
                      Asn_synthase  11 krrl.radvpvGalLSGGlDSSliaalaarqsk.splktFsigfee....kgsdeakyakevaehlgtehtelvlte 81 
                                        +r+ +   ++++  SGG DS+++ + ++r ++ +++  ++++ +e     ++d + +ak++a+++g+e++ + ++e
  gi|330508540|ref|YP_004384968.1|  40 VNRMiEKGERIAVAVSGGKDSTALLFALSRVLAeKEVEMVALTVDEgiagYRDDTIVAAKRIARQMGVEQVIISFQE 116
                                       45554888899*******************9998889999999966776566777899***********99999988 PP

                      Asn_synthase  82 eel 84 
                                       e +
  gi|330508540|ref|YP_004384968.1| 117 EYG 119
                                       755 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   7.3e-06     0.019       2      45 ..      49      95 ..      48     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.3e-06
                   Diphthami_syn_2  2 kvavlysGGkDsi...laLykalkesevesLvsvisenkesymfhvv 45
                                      + av +sGGkDs+   +aL ++l e eve++   ++e+ + y+  ++
  gi|330508540|ref|YP_004384968.1| 49 RIAVAVSGGKDSTallFALSRVLAEKEVEMVALTVDEGIAGYRDDTI 95
                                      67999*******844468889********999999999998876654 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   5.5e-06     0.014       4      61 ..      52     114 ..      49     168 .. 0.81
   2 ?   -3.1   0.7       1.8   4.6e+03     196     196 ..     280     280 ..     242     294 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.5e-06
                                       EE--SSHHHHHHHHHHHHH-....SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE- CS
                              QueC   4 vllSGGlDSttvlalakkeg....kevealtfdYgqr..hkkeleaakkiakelgveehkildl 61 
                                       v +SGG DSt++l+  ++       e+ alt+d g    ++ ++ aak+ia+++gv e+ i++ 
  gi|330508540|ref|YP_004384968.1|  52 VAVSGGKDSTALLFALSRVLaekeVEMVALTVDEGIAgyRDDTIVAAKRIARQMGV-EQVIISF 114
                                       789*********9987664433114556678888876667788999**********.7766655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.8
                                       S CS
                              QueC 196 C 196
                                       C
  gi|330508540|ref|YP_004384968.1| 280 C 280
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2218.01
//
Query:       gi|330508541|ref|YP_004384969.1|  [L=524]
Description: hypothetical protein MCON_2762 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-15   56.6   0.3    7.3e-14   51.9   0.1    2.7  2  DDE_Tnp_1     Transposase DDE domain
  ------ inclusion threshold ------
      0.043   13.5   0.2       0.28   10.8   0.0    2.1  2  hGDE_central  Central domain of human glycogen debranching en


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 ?   -1.0   0.0      0.13   1.1e+03       3      30 ..      35      62 ..      33      75 .. 0.75
   2 !   51.9   0.1   8.1e-18   7.3e-14      24     213 ..     191     464 ..     167     465 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.13
                         DDE_Tnp_1  3 krevlivDattvrvpgtkedarwgykgg 30
                                      k+ ++ vD+++vr+++ +++ +++ k++
  gi|330508541|ref|YP_004384969.1| 35 KYLGRNVDGQPVRMRSAPSEIKEKTKKK 62
                                      6777889*********996666655544 PP

  == domain 2  score: 51.9 bits;  conditional E-value: 8.1e-18
                         DDE_Tnp_1  24 rwgyk.ggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYasaelldtlee 97 
                                        +gy+  g+  + +++ +++d   g+++ ++i+pg+ +d+ +l  +l+ ++++  ++ + ++D+G++s ++l +l +
  gi|330508541|ref|YP_004384969.1| 191 EYGYNrDGADLPQINMSLIMDKDKGIPVMYDIFPGSISDVSTLSGTLKKIKAHgvQNYVAVMDRGFFSLGNLCELLD 267
                                       45899899999****************************************************************** PP

                         DDE_Tnp_1  98 kgvdyiirlkkntklyrk....gaeskrrgrlrkhdrnkiltksqkrrnk........................... 143
                                       +++++++++k + + +++      ++  + ++  +++n+++  + ++ n                            
  gi|330508541|ref|YP_004384969.1| 268 NKISFVMAAKLQLNDLKQlmteAQKDIDDVKYLHKFNNEPIFAKPITYNIdnmevrgyvyydpkleqnekqtllsrl 344
                                       ***************9999999778888888888888888888888888899999999999999999999******* PP

                         DDE_Tnp_1 144 .....................................................skkekgdvyyvtntnsellsaeev 167
                                                                                            +++  g ++++++ +    +    
  gi|330508541|ref|YP_004384969.1| 345 ydireellkvrlkknsspqvafkekargfgnffewnvvdnrfdvsikqnavtqRMNKMGKYILFYSGDF---DWLNC 418
                                       ***************************************************764444444444444444...44455 PP

                         DDE_Tnp_1 168 aelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllaln 213
                                         lyr R +iE +Fk lk+   ++ l++++   ++ +++  +l+l 
  gi|330508541|ref|YP_004384969.1| 419 LSLYRERDEIEKSFKALKNEIDILPLNTHSEKTTRGFIFVAFLSLI 464
                                       69*************************************9999885 PP

>> hGDE_central  Central domain of human glycogen debranching enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.1e-05      0.28      93     166 ..      22      97 ..       4     120 .. 0.73
   2 ?    0.1   0.0     0.059   5.3e+02       3      34 ..     274     308 ..     273     406 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.1e-05
                                       .----SSEE----EEEE.E----EEEE.......ETT.TEEEEE--.S---SSEEEEEEEEETT--ST..HHHHHCS CS
                      hGDE_central  93 eykkdekfinGlpsklkeelkleevkvlkieevedee.eesvievefenfppGsvvvfetelsevdek..ldefaks 166
                                        y k++k i+  ++ l ++++ + v + +  ++ +e+ ++++ ev+ ++f  Gs++v+++ ++e++ +  l++   s
  gi|330508541|ref|YP_004384969.1|  22 YYDKEKKQIRHRSKYLGRNVDGQPVRMRSAPSEIKEKtKKKTAEVK-SSFDYGSILVLQSIMEELNLDryLENLLPS 97 
                                       567777788888888888999999999877777666669999****.************999976532234444333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.059
                                       HHHHHHHHHHHHHHHTT--S...EEEEEE.ETTEE CS
                      hGDE_central   3 ikakklLnklhkelakegfd...evhvdqleedii 34 
                                       ++ak  Ln+l++ + + + d     + ++ +++ i
  gi|330508541|ref|YP_004384969.1| 274 MAAKLQLNDLKQLMTEAQKDiddVKYLHKFNNEPI 308
                                       78999999999999877666444445565555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3535.33
//
Query:       gi|330508542|ref|YP_004384970.1|  [L=115]
Description: hypothetical protein MCON_2763 [Methanosaeta concilii GP6]
Scores for complete 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   92.3   0.1    2.1e-26   92.1   0.1    1.0  1  DUF86     Protein of unknown function DUF86


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.1   1.2e-30   2.1e-26       1     118 [.      13     108 ..      13     109 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 1.2e-30
                                       HHHHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHTTSS-HHHHH CS
                             DUF86   1 ikealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdyifeilaekgviaeepee 77 
                                       i+e+++ ++ef ++++++ef+sd+++  +v ++++v+gEa+++i+++                      +++++pe+
  gi|330508542|ref|YP_004384970.1|  13 IIEHMNYAEEFIRDMTFDEFKSDKKTVLSVTKCIEVVGEATKHIPDQ----------------------IRERYPEI 67 
                                       6889999****************************************......................******** PP

                                       HHHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHHHH CS
                             DUF86  78 pwrkmiglRNrLvHgYlgidpeivwsiikenlpdleefles 118
                                       pwr m+g R+rLvHgY+++d++ivw +++ + p+l+ +le 
  gi|330508542|ref|YP_004384970.1|  68 PWRDMAGIRDRLVHGYFKVDLSIVWTTVTIEFPELRSMLEN 108
                                       ************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 855.04
//
Query:       gi|330508543|ref|YP_004384971.1|  [L=97]
Description: nucleotidyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-14   52.2   0.7    6.4e-14   52.0   0.7    1.1  1  NTP_transf_2  Nucleotidyltransferase domain
    1.1e-12   47.8   0.2    1.4e-12   47.5   0.2    1.1  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
       0.11   12.6   0.0        0.3   11.2   0.0    1.7  1  FANCI_S1-cap  FANCI solenoid 1 cap


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.7   1.1e-17   6.4e-14       2      94 ..      12      96 ..      11      97 .] 0.94

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1.1e-17
                                      HHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECC CS
                      NTP_transf_2  2 kklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekle 80
                                      k  + +lk++++v+++ +fGS++rG+ + +SD+Dll+ ++e+        gl  ++  +  l+   g +vdlvt++ l+
  gi|330508543|ref|YP_004384971.1| 12 KDQKPILKKKFKVKEIGIFGSFVRGEQKDTSDLDLLIDFEEP-------IGLVQYVGLQNYLSDKIGEKVDLVTKSGLK 83
                                      567789************************************.......899*************************** PP

                                      CCTEEEEEECEEEH CS
                      NTP_transf_2 81 dpllvksileerpl 94
                                       p+++  il+e ++
  gi|330508543|ref|YP_004384971.1| 84 -PRVSGHILKEVIY 96
                                      .****999999887 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.2   2.3e-16   1.4e-12       4      87 ..      15      95 ..      12      97 .] 0.94

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 2.3e-16
                                      TTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHH CS
                           Polbeta  4 keilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeilk 82
                                      k il+k+ +++ + +FGS+++g++++ SD+Dl + ++e   l +++ l++ l+d  +g+kvDlv+ +  +p +  +ilk
  gi|330508543|ref|YP_004384971.1| 15 KPILKKKFKVKEIGIFGSFVRGEQKDTSDLDLLIDFEEPIGLVQYVGLQNYLSDK-IGEKVDLVTKSGLKPRVSGHILK 92
                                      6799***************************************************.9********99999999999999 PP

                                      S-EEE CS
                           Polbeta 83 egkll 87
                                        +++
  gi|330508543|ref|YP_004384971.1| 93 --EVI 95
                                      ..444 PP

>> FANCI_S1-cap  FANCI solenoid 1 cap
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     5e-05       0.3      16      49 ..      61      93 ..      58      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5e-05
                      FANCI_S1-cap 16 eLqkfLqtLkedeLtelitnsAlKGkevGallra 49
                                       Lq++L+  k +e ++l+t+s lK +  G +l+ 
  gi|330508543|ref|YP_004384971.1| 61 GLQNYLSD-KIGEKVDLVTKSGLKPRVSGHILKE 93
                                      69999987.567779*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 794.39
//
Query:       gi|330508544|ref|YP_004384972.1|  [L=211]
Description: hypothetical protein MCON_2766 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.4   0.0      0.032   14.0   0.0    1.2  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro


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 ?   14.0   0.0   1.8e-06     0.032      22     113 ..     104     206 ..     100     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-06
                                       HHHTTTS-STTEEEEEE--..SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHH. CS
                     ELFV_dehydrog  22 lkklkldslegkrvaisGs..GnvgsyaallltelgakvvavsDssGviydpeGldieellelkeerksvkeykks. 95 
                                       ++k ++++++g++  i Gs  Gnv  +  +   +lg + v +  s+G+iy+p+G   ++   + ++r   ++++ + 
  gi|330508544|ref|YP_004384972.1| 104 FDK-RGQTMHGSQTNIAGSfsGNVLFNQFNGPVSLGREAVDMRGSTGAIYKPSGPVNQQYRYYSKARDVSSKSEGQr 179
                                       556.7889**********999*********************************96666666655555555555445 PP

                                       .........STSTSEEESHHSHHHHSS CS
                     ELFV_dehydrog  96 .........sekkaeyieneeellelk 113
                                                + k+++ +e ++e++e++
  gi|330508544|ref|YP_004384972.1| 180 rikciflaaNPKGTQLLERDKEIWEIT 206
                                       566666667555677888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1718.08
//
Query:       gi|330508545|ref|YP_004384973.1|  [L=80]
Description: hypothetical protein MCON_2768 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00053   20.1   0.0    0.00058   20.0   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.3e-08   0.00058       7      54 ..      18      65 ..      12      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.3e-08
                   HicB_lk_antitox  7 kdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgee 54
                                       d+++ y+  vP+l+G++ +g+t +e  +n + aie ++   +  +  
  gi|330508545|ref|YP_004384973.1| 18 IDDQEPYSGEVPELKGIWATGKTQQEYQDNLRMAIEDWIAFSLRFDLP 65
                                      3999**********************************9876655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 617.39
//
Query:       gi|330508546|ref|YP_004384974.1|  [L=298]
Description: quinolinate synthetase complex subunit A [Methanosaeta concilii GP6]
Scores for 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-118  394.3   0.6   3.4e-118  394.2   0.6    1.0  1  NadA      Quinolinate synthetase A protein
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.26   11.3   0.0    1.7  2  DUF1246   Protein of unknown function (DUF1246)
       0.15   11.9   0.0       0.23   11.3   0.0    1.3  1  DarT      ssDNA thymidine ADP-ribosyltransferase, DarT


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 !  394.2   0.6  5.7e-122  3.4e-118       1     298 [.       3     294 ..       3     295 .. 0.98

  Alignments for each domain:
  == domain 1  score: 394.2 bits;  conditional E-value: 5.7e-122
                                       HHHHHHHHHHTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHSTTSEEE-SSTT- CS
                              NadA   1 eeikelkkeknavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLspekkvllpdlea 77 
                                       eei++lkke++a+ilaHnYq +++q+iad+ GDSleL+r+aa+ ++evivfcGV+FMaeta+iLsp+k+v+lp + a
  gi|330508546|ref|YP_004384974.1|   3 EEIQALKKERRATILAHNYQIPAVQDIADLAGDSLELSRAAAALDSEVIVFCGVDFMAETAAILSPQKRVVLPVKGA 79 
                                       68*************************************************************************** PP

                                       --HHHCT--HHHHHHHHHHSTTS-EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS-SEEEEES-HHHHHHHHHHH. CS
                              NadA  78 gCsladmitaeeveelkeelpdaavvtYvNssaevKalsdivcTSsnavkvvealkekkilflPDqnLgryvakklg 154
                                        C++a+mit ++++elk+ +p+aavv+YvNs+ae+Ka sdi+cTS+n v+vve+l+e++++f+PD+nL++yva++++
  gi|330508546|ref|YP_004384974.1|  80 WCPMAHMITPQQLDELKALYPQAAVVCYVNSTAEIKAKSDICCTSANGVQVVESLSEDEVIFVPDRNLAAYVARHTK 156
                                       ***************************************************************************95 PP

                                       SEEEEESSSS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-THH CS
                              NadA 155 ekkiilwkgaCsvHeefkaeeveelkeehpdakvlvHPEckeevveaadvvgSTsqiikavkeseakefiigTelgl 231
                                        kkii w+g+C+vH++f++e+v+++++ hp+a+vlvHPEc++ev+++ad+v ST++++k+ + ++a+e+iigTe+g+
  gi|330508546|ref|YP_004384974.1| 157 -KKIIPWDGYCYVHDQFTPEMVKAARKLHPQAEVLVHPECRPEVIDLADFVYSTAGMCKHPDINRAREYIIGTEVGM 232
                                       .58************************************************************************** PP

                                       HHHHHHH-TTSEEE.....ECSSSSSTTGGG--HHHHHHHHHHT-S.B----HHHHHHHHHHHHHHH CS
                              NadA 232 verlkkeapekefialsaeaaeeavCetMkkitleklleaLeeleeeeikvdeevaekAkkalerml 298
                                       ++rlkk++p++ef+ ls+    ea+C++Mkk+tl+++l+aL++le+ ++ v+ee+a +A+ a+erml
  gi|330508546|ref|YP_004384974.1| 233 IYRLKKAHPDREFYPLSD----EAICQNMKKTTLPDVLRALQTLEP-RVVVPEEIAVRARGAIERML 294
                                       **************5533....689*********************.*******************9 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.3e-05      0.26      57      83 ..     129     155 ..      95     165 .. 0.83
   2 ?   -3.6   0.0       1.7     1e+04      39      54 ..     247     262 ..     233     282 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.3e-05
                                       --HHHHHHTTCEE--BTTHHHHC-HHH CS
                           DUF1246  57 evqeklreenailvPhgsfveYvgiek 83 
                                       +v e+l e+++i+vP++ +++Yv+ ++
  gi|330508546|ref|YP_004384974.1| 129 QVVESLSEDEVIFVPDRNLAAYVARHT 155
                                       67899******************8765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.7
                                       TT-SEEEE.S.S..TT CS
                           DUF1246  39 kvidevivldkfkdil 54 
                                       ++ de i+ +  k  l
  gi|330508546|ref|YP_004384974.1| 247 PLSDEAICQNMKKTTL 262
                                       6666666655444433 PP

>> DarT  ssDNA thymidine ADP-ribosyltransferase, DarT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.9e-05      0.23     117     165 ..     153     200 ..      98     212 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.9e-05
                              DarT 117 frngledleeidwdlvyakswkntee..dsdrkerkqAEvLvkdsipleli 165
                                        +++ +    i wd ++    + t+e  ++ rk ++qAEvLv+ ++ +e i
  gi|330508546|ref|YP_004384974.1| 153 RHTKKK---IIPWDGYCYVHDQFTPEmvKAARKLHPQAEVLVHPECRPEVI 200
                                       444443...36666664433333434579***************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.22s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2178.79
//
Query:       gi|330508547|ref|YP_004384975.1|  [L=92]
Description: MoaD family protein [Methanosaeta concilii GP6]
Scores for complete 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   42.8   0.0      7e-11   42.6   0.0    1.0  1  ThiS      ThiS family


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   3.9e-15     7e-11       4      77 .]       8      92 .]       5      92 .] 0.94

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 3.9e-15
                                      TTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG........TTTTEEEEETTEEEGC.CTTTSB--TTCEEEEE CS
                              ThiS  4 faelrelag..eeelelaegstvaelleaLgerypela........lerrvavavNgeivpr.lwldtelkdgDevail 71
                                      fa  r + g  +  ++++eg+ +++ll+ L  ++  l+        l++ v++ + g+++++ + l+t+l+dgDe+a++
  gi|330508547|ref|YP_004384975.1|  8 FAGFRNILGkeKDIDLPGEGAMIRDLLNLLCHDHASLEpllfkegrLREDVNIFLSGKNIESlQSLETPLADGDELALF 86
                                      888999999977778889****************9999********99**************99*************** PP

                                      ESTTC- CS
                              ThiS 72 ppVaGG 77
                                      ++V GG
  gi|330508547|ref|YP_004384975.1| 87 TAVIGG 92
                                      *****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); 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 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 721.84
//
Query:       gi|330508548|ref|YP_004384976.1|  [L=217]
Description: TfuA-like protein [Methanosaeta concilii GP6]
Scores for complete 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   0.0    3.5e-43  146.1   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 !  146.1   0.0   1.9e-47   3.5e-43       1     120 []      49     166 ..      49     166 .. 0.99

  Alignments for each domain:
  == domain 1  score: 146.1 bits;  conditional E-value: 1.9e-47
                              TfuA   1 DGvfeqepavahkEilaalkegvavvGaasmGALRAaElaafGmigvGeiyeayrsgeledDdeVavlhapaelgye 77 
                                       DGvf+q+++vahkE+++al++g +v+Ga+smGALRA+El+ +Gm+gvG iy+ay++g l +DdeVa++++p   ++e
  gi|330508548|ref|YP_004384976.1|  49 DGVFFQDSSVAHKEVIYALDAGARVLGASSMGALRASELDVYGMEGVGLIYQAYKKGMLVSDDEVALTFDPF--TFE 123
                                       9**********************************************************************9..9** PP

                              TfuA  78 alsealvnlratlkaaveegiiseeeaaallelakelyykert 120
                                       + se+lvn+r +l++a+++g+i +  +++ll++a++ly++er+
  gi|330508548|ref|YP_004384976.1| 124 PHSEPLVNIRFNLEQAWQKGAIGTVGKDRLLRCAQALYFPERS 166
                                       *****************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1619.77
//
Query:       gi|330508549|ref|YP_004384977.1|  [L=406]
Description: putative methanogenesis marker protein 1 [Methanosaeta concilii GP6]
Scores for complete sequence (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  300.9   1.8    1.9e-89  300.2   1.6    1.4  2  YcaO      YcaO cyclodehydratase, ATP-ad Mg2+-binding


Domain annotation for each model (and alignments):
>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.16   2.9e+03     278     317 ..      16      55 ..       8      58 .. 0.65
   2 !  300.2   1.6     1e-93   1.9e-89       1     323 []      69     377 ..      69     377 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.16
                              YcaO 278 ssgdleedletllerlkaagld.vlvvdltrp.dlglpvvkv 317
                                       ++ ++ee  +++ ++l aag+  v  +d+t+   +g+pv   
  gi|330508549|ref|YP_004384977.1|  16 RAASPEETEKRIEAKLPAAGITrV--ADITNLdRIGIPVFSS 55 
                                       445777777788888888888744..5666545788888765 PP

  == domain 2  score: 300.2 bits;  conditional E-value: 1e-93
                              YcaO   1 nGkGateeaArasalgEalErysaegffrgdekrvr.asyrelegegaldpeelglyseeekdaadfvlepfdpdrp 76 
                                       nGkGat+ +Ar+sa++E+lErys e     +++ ++ a+y+ l +++al+p +l l++e          +  d+d +
  gi|330508549|ref|YP_004384977.1|  69 NGKGATPVEARVSAMMEGLERYSGE----VRDRELTiARYSSL-KAEALNPVDLILPTE----------AVADADAE 130
                                       8*********************977....44555555******.*************77..........8899**** PP

                              YcaO  77 idwvpgwsltdgeevlvPanlvylyeppegea.rlfletsnGlAaGntleeAilhGllEliERdafalawyerlplp 152
                                       i+wv gw+++++ee+ vPan+v++  p +++  rlf+++++GlA+Gn +eeAi+hGl E+iERda a++  +r   p
  gi|330508549|ref|YP_004384977.1| 131 IPWVLGWDIMNDEEIQVPANAVFH--PLSSDYkRLFRTNTSGLASGNMMEEAIFHGLAEVIERDAWAIVEATRHMGP 205
                                       ************************..7777778****************************************9999 PP

                              YcaO 153 rid..lasdpeirellerlreagievrlldatldlgipvvaavlvd....pklllvagaGahldpevAlerAltEla 223
                                        i   +  d++++ ller+++a ++v+l d+t+d++ip+ aa ++d    +++ll+ g+G+h +++vA++rAltE+a
  gi|330508549|ref|YP_004384977.1| 206 LISdvV--DEQAQGLLERFAAAEVDVYLRDITSDIDIPTCAAAADDiklrDPTLLTTGMGTHTSARVAVLRALTEVA 280
                                       888433..5*************************************87754499999******************** PP

                              YcaO 224 qsrltlisgaredpdfdeeladvatleradreallwlpeaaakrldfllfaewassgdleedletllerlkaagld. 299
                                       qsrlt+i+gared+   ++++++ ++er++r +++w++ +++k+++    ++  +s+d+  d++ ++ +l++agl+ 
  gi|330508549|ref|YP_004384977.1| 281 QSRLTQIHGAREDTVT-ADFRRQIGYERTKRLNRYWFDIGEKKSFAD-I-QSF-ESNDFLLDIKFMISKLEEAGLEr 353
                                       ****************.89*****************75555533333.3.244.347******************** PP

                              YcaO 300 vlvvdltrpdlglpvvkvivPgle 323
                                       ++vvdltr+++g+pvv+vivPgle
  gi|330508549|ref|YP_004384977.1| 354 AVVVDLTREEIGVPVVRVIVPGLE 377
                                       **********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2901.90
//
Query:       gi|330508550|ref|YP_004384978.1|  [L=146]
Description: phenylacetic acid degradation protein PaaD [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-12   47.1   0.1    2.8e-12   46.8   0.1    1.2  1  4HBT             Thioesterase superfamily
    6.2e-11   42.5   0.0    8.2e-11   42.2   0.0    1.1  1  DUF4442          Domain of unknown function (DUF4442)
    0.00054   19.3   0.0     0.0007   18.9   0.0    1.1  1  PS-DH            Polyketide synthase dehydratase
    0.00077   19.8   0.0    0.00093   19.5   0.0    1.1  1  4HBT_3           Thioesterase-like superfamily
     0.0046   16.6   0.0     0.0061   16.2   0.0    1.2  1  AAA_27           AAA domain
     0.0095   15.5   0.0      0.013   15.1   0.0    1.3  1  MaoC_dehydratas  MaoC like domain


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.1   9.5e-16   2.8e-12       3      79 .]      49     122 ..      47     122 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 9.5e-16
                                       SB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCEEE CS
                              4HBT   3 vvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrlva 79 
                                       + hg+++++llD a  + ++s+g    ++v++  ++ +l+p+r+g++l++e++ ++ +r++ ++e++v+ edgrlva
  gi|330508550|ref|YP_004384978.1|  49 TTHGAAIYSLLDAAFELTVNSHGT---VAVALGVNVSYLSPARPGETLRAEGKETNRSRKISSCEIRVTGEDGRLVA 122
                                       68*********************6...9**********************************************986 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   2.7e-14   8.2e-11      12     128 ..      14     126 ..       8     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 2.7e-14
                                       HSGGGGGG--EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S-- CS
                           DUF4442  12 kaPYfgtvgprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevdYlaka 88 
                                       + PY +  g+ i+ele+g+a +++k +  ++N ++t H+ Ai++l+++a+ l ++    ++ + +  g++v+Yl++a
  gi|330508550|ref|YP_004384978.1|  14 REPYARMFGIEIQELEAGHAILKMKTNEMMNNLFRTTHGAAIYSLLDAAFELTVNS---HGTVAVALGVNVSYLSPA 87 
                                       67***********************************************9775553...47888999********** PP

                                       -S-EEEEEE-TTS-TT--EEEEEEEEEEETTE.EEEEEEE CS
                           DUF4442  89 tgdltavaelepedvgekeelvvevevrdekgeevvraei 128
                                       + + t +ae ++ ++  ++    e++v+ e+g+ v+++++
  gi|330508550|ref|YP_004384978.1|  88 RPGETLRAEGKETNRS-RKISSCEIRVTGEDGRLVATCQA 126
                                       ***9999999998887.45566788888899999999875 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.3e-07    0.0007     208     290 ..      58     131 ..      43     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.3e-07
                                       HHHHHHH.HG..GG----------EEEEEEEEEEE-S...-BTS--EEEEEE----SS-EEEEEEEE-SS-BEEEEE CS
                             PS-DH 208 llDaalQ.llaaalsaeaekadaaylPvaierlrvyrpssaageelwvharleeegarsivadltlvdedGrvvaei 283
                                       llDaa+  ++        ++++++++ ++++  ++++  +++ge+l+++ + ++++ +  +++++++ edGr+va+ 
  gi|330508550|ref|YP_004384978.1|  58 LLDAAFElTV--------NSHGTVAVALGVNVSYLSP--ARPGETLRAEGKETNRSRKISSCEIRVTGEDGRLVATC 124
                                       8999999444........7899999999999888885..689**************9*******************9 PP

                                       ESEEEEE CS
                             PS-DH 284 eglrlrr 290
                                       + l  r+
  gi|330508550|ref|YP_004384978.1| 125 QALAYRM 131
                                       9998876 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.1e-07   0.00093      11     102 ..      50     142 ..      40     146 .] 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.1e-07
                                       .-HHHHHHHHHHHHHHT....-S.SS.EEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEEEET.TEEEEEEEE CS
                            4HBT_3  11 gyGGyvlAlalraaqrtv...pdprl.hslhvyFlrpgdag.pviyhvervrdGrsfstrtvelsqg.grpiftata 81 
                                        +G ++ +l+ +a + tv    ++ +   + v++l p+ +g  ++ + +++ + r++s ++++++ + gr ++t++a
  gi|330508550|ref|YP_004384978.1|  50 THGAAIYSLLDAAFELTVnshGTVAVaLGVNVSYLSPARPGeTLRAEGKETNRSRKISSCEIRVTGEdGRLVATCQA 126
                                       49***************9665222236699**********************************98659******** PP

                                       EEE---T.....---EE----- CS
                            4HBT_3  82 sfgraestgwe.lepaaapppv 102
                                          r+++     l p    p+ 
  gi|330508550|ref|YP_004384978.1| 127 LAYRMRD-RLPfL-P----PEA 142
                                       9999998.33322.2....222 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     2e-06    0.0061     105     156 ..       3      54 ..       1      72 [. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2e-06
                            AAA_27 105 evlaallggldretFealFgLdherLreGGealleaegelgqlLfeasaGla 156
                                       +++++l ++  re + ++Fg++ ++L++G   l  +++e+ + Lf    G a
  gi|330508550|ref|YP_004384978.1|   3 QCIKSLKEEFAREPYARMFGIEIQELEAGHAILKMKTNEMMNNLFRTTHGAA 54 
                                       66778888999****************9988888899********9998865 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.3e-06     0.013      53     104 ..      50     105 ..      38     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.3e-06
                                       --HHHHHHHHHHHHHHHHSTT.EGGGEEEEEEEE-S--BTTCEEEEEEEEEE...E CS
                   MaoC_dehydratas  53 ahGmltlaivaklveeelgdn.vvarvgeikvrFtkpVlpgdtlkvelevvg...k 104
                                       +hG   ++++ +++e  + +   va   + +v++ +p +pg+tl++e ++++   k
  gi|330508550|ref|YP_004384978.1|  50 THGAAIYSLLDAAFELTVNSHgTVAVALGVNVSYLSPARPGETLRAEGKETNrsrK 105
                                       799999999999999888888889999********************999984222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1115.70
//
Query:       gi|330508551|ref|YP_004384979.1|  [L=167]
Description: hypothetical protein MCON_2774 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.3   0.0      0.084   13.7   0.0    1.3  1  PriA_C    Primosomal protein N C-terminal domain


Domain annotation for each model (and alignments):
>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.7e-06     0.084      39      88 ..      74     122 ..      48     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.7e-06
                            PriA_C  39 eilgpapapiakikgryryqillksksrkalqkllkellekleklkkvrv 88 
                                       e  g +    a+ k+ryr+ +++  ++++al+++++ +  ++ek+  v++
  gi|330508551|ref|YP_004384979.1|  74 ESNGYILTSYARKKDRYRAIFVVPFSNKRALERFMESVSTETEKED-VKI 122
                                       45667777889******************************98874.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1125.19
//
Query:       gi|330508552|ref|YP_004384980.1|  [L=367]
Description: aspartate aminotransferase [Methanosaeta concilii GP6]
Scores for complete 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-65  220.1   0.0    5.2e-65  220.0   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    7.7e-11   41.9   0.0    1.2e-10   41.3   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    8.4e-09   34.8   0.0    1.3e-08   34.3   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    1.5e-07   31.0   0.2    3.4e-07   29.8   0.0    1.6  2  Beta_elim_lyase  Beta-eliminating lyase
    9.3e-06   24.4   0.0    1.5e-05   23.8   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0015   17.5   0.0      0.037   12.9   0.0    2.0  2  Alliinase_C      Allinase
  ------ inclusion threshold ------
      0.057   13.3   0.0       0.16   11.8   0.0    1.7  1  NIR_SIR_ferr     Nitrite/Sulfite reductase ferredoxin-like ha


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.0   0.0     2e-68   5.2e-65       4     362 ..      27     362 ..      24     363 .. 0.92

  Alignments for each domain:
  == domain 1  score: 220.0 bits;  conditional E-value: 2e-68
                                       EESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHH CS
                     Aminotran_1_2   4 inLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagal 80 
                                       +nLg +++++d    t+ ++++a+++ a ++g++  y+p+ g p+l+eala+ l r+++++ +++  + v+sGa+++
  gi|330508552|ref|YP_004384980.1|  27 VNLGLGQPDFD----TPSHIKRAAIR-AIEMGQCG-YTPNCGVPALREALAEKLMRENQIDCTAD-DIMVTSGASEA 96 
                                       8**********....***********.88888875.666666***********************.*********** PP

                                       HHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS CS
                     Aminotran_1_2  81 iealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesp 157
                                       + ++i +l +++g+e+lv dp++ sy +  rl g+  v++pl+  ed +++ ea+ e +++      kt++i+++sp
  gi|330508552|ref|YP_004384980.1|  97 LFLAIVAL-VDRGEEVLVGDPSFLSYAELTRLVGARPVSVPLD--EDLRITPEAIGERITK------KTRMIIINSP 164
                                       ********.9*******************************99..****************......********** PP

                                       -TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEE CS
                     Aminotran_1_2 158 hNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyil 234
                                       +NPtG+v t+e+ ++++++a+   + l++De+Y++f +  +     ++ +   +n+++v+ +sK ++++G+R+Gy++
  gi|330508552|ref|YP_004384980.1| 165 SNPTGSVQTEEQMRAIAEIADDEDIALLSDEVYEHFIYRGEH----ISPARFSDNVITVNAVSKTYAMTGWRLGYLA 237
                                       **************************************9653....666666779********************** PP

                                       E.EHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEE CS
                     Aminotran_1_2 235 g.naavvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmfll 309
                                       + n+a+ ++l++ +      ss+ qaa+++a+  +++    + +mr+++ +rr+ l+++++e g++ ++++++++l+
  gi|330508552|ref|YP_004384980.1| 238 ArNEAIEQHLKIHQYVQACaSSISQAAALEAICGPQD---CVRQMRDEFMSRRDLLVAGFREMGVDLTEPDGAFYLF 311
                                       *6666666666666544447****************7...9************************************ PP

                                       EEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 310 tdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                        ++     + ++ kL+   gv+ +pg+ f+   ++++Ri++ + ++++lee++++
  gi|330508552|ref|YP_004384980.1| 312 PRVGDG--DLVASKLARA-GVITVPGSAFGEggREHIRISY-AASRANLEEALRR 362
                                       *99977..5666668888.**************99******.99********987 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 !   41.3   0.0   4.7e-14   1.2e-10      42     144 ..      88     194 ..      72     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 4.7e-14
                                       EEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE.. CS
                   DegT_DnrJ_EryC1  42 iavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIl.. 116
                                         +s +++Al la+ al v++g+eV+v   +F++ a+  + +ga+pv v  d +++ i+p+ai + it++t+ I+  
  gi|330508552|ref|YP_004384980.1|  88 MVTSGASEALFLAIVAL-VDRGEEVLVGDPSFLSYAELTRLVGARPVSVPLD-EDLRITPEAIGERITKKTRMIIin 162
                                       44566789******998.888*******************************.89*******************944 PP

                                       .EB-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 117 .pVhlyGqva...dmdalkaiaakhglkvieD 144
                                        p +  G v    +m a+ +ia++ ++ +++D
  gi|330508552|ref|YP_004384980.1| 163 sPSNPTGSVQteeQMRAIAEIADDEDIALLSD 194
                                       44677888766679***************999 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0     5e-12   1.3e-08      61     165 ..      84     181 ..      72     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 5e-12
                                       GGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-- CS
                       Aminotran_5  61 eeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldeleklln 137
                                       +++i++tsG++ea+ l++ +l   +++g+e++v++      l   +el +  ga+ + +plde+ +++++++ + ++
  gi|330508552|ref|YP_004384980.1|  84 ADDIMVTSGASEALFLAIVAL---VDRGEEVLVGDPSF---L-SYAELTRLVGARPVSVPLDEDLRITPEAIGERIT 153
                                       489******************...********987544...4.6679****************************** PP

                                       TTEEEEEEESBETTTTEB--HHHHHHHH CS
                       Aminotran_5 138 ektklvaithvsnvtGtiqpveeigkla 165
                                       +kt++++i+  sn tG +q  e++ ++a
  gi|330508552|ref|YP_004384980.1| 154 KKTRMIIINSPSNPTGSVQTEEQMRAIA 181
                                       *****************99877765544 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   1.3e-10   3.4e-07      11     167 ..      40     194 ..      36     196 .. 0.82
   2 ?   -1.8   0.1      0.56   1.4e+03     238     238 ..     299     299 ..     206     363 .. 0.56

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.3e-10
                                       -HHHHHHHHCS----CCCT--HHHHHHHHHHHHHTT-SEEEE.......ES-HHHHHHHHH..HHH--TTEEEEEET CS
                   Beta_elim_lyase  11 teamsdaqaaamlGdesYgedktvnrLedavaelfgkeaalf.......vpqGtaAnsill..killqrgeevivte 78 
                                       +   ++a+ a+++G+  Y  + +v +L +a+ae +  e ++        v++G a++++ l   +l+ rgeev+v++
  gi|330508552|ref|YP_004384980.1|  40 SHIKRAAIRAIEMGQCGYTPNCGVPALREALAEKLMRENQIDctaddimVTSG-ASEALFLaiVALVDRGEEVLVGD 115
                                       555567779999*********************66666665445555535666.6677665226677********** PP

                                       T-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHH CS
                   Beta_elim_lyase  79 pahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaa 155
                                       p+     e      l g++++ ++ +e+  +++e++ + i++      k+++i++    n   G v + e++r++a+
  gi|330508552|ref|YP_004384980.1| 116 PSFLSYAEL---TRLVGARPVSVPLDEDLRITPEAIGERITK------KTRMIIINSPSNP-TGSVQTEEQMRAIAE 182
                                       **8887775...5568999********99***********99......689****999995.9************** PP

                                       HHHHCT-EEEEE CS
                   Beta_elim_lyase 156 iakkygiplhlD 167
                                       ia++++i l+ D
  gi|330508552|ref|YP_004384980.1| 183 IADDEDIALLSD 194
                                       *********988 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.56
                                       H CS
                   Beta_elim_lyase 238 v 238
                                       v
  gi|330508552|ref|YP_004384980.1| 299 V 299
                                       1 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 !   23.8   0.0   5.7e-09   1.5e-05      65     174 ..      81     195 ..      45     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.7e-09
                                       HT-SEEEEESSHHH.HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTEE CS
                   Cys_Met_Meta_PP  65 eggeaalavssGma.AiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdtsdleelekaikentk 139
                                       + ++  ++v+sG + A+++ai+al+  G+e++v d  + +  +l + v  + +++  +      +e++ + i+++t+
  gi|330508552|ref|YP_004384980.1|  81 DCTADDIMVTSGASeALFLAIVALVDRGEEVLVGDPSFLSYAELTRLVGARpVSVPLDEDLRITPEAIGERITKKTR 157
                                       55556677788876599*********************999999998888756777777667899************ PP

                                       EEEEESS-TTTT---...-HHHHHHHHHHTT-EEEEEG CS
                   Cys_Met_Meta_PP 140 lvylEtptnpllkvv...DiekiaklakkagvlvvvDn 174
                                       ++ + +p+np+ +v     +++ia++a ++++ ++ D 
  gi|330508552|ref|YP_004384980.1| 158 MIIINSPSNPTGSVQteeQMRAIAEIADDEDIALLSDE 195
                                       **********9888633368888999988888887776 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   1.4e-05     0.037     141     238 ..     159     270 ..     146     298 .. 0.71
   2 ?    2.5   0.0      0.02        52     317     362 ..     320     366 ..     299     367 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                                       EEEESS-TTT------.....--...-TT-EEEEEE-TT....-STTTS---S-B--SEEEEEHHHHHS-GGG-EEE CS
                       Alliinase_C 141 elvtsPnnPdgllrea.....vv...kgseakviyDlay....YWPhytpitskadedimLftlskltGhaGsrlGW 205
                                        ++ sP nP g ++ +     +    ++++  ++ D +y    Y  ++    + +d+ i + ++sk+   +G rlG+
  gi|330508552|ref|YP_004384980.1| 159 IIINSPSNPTGSVQTEeqmraIAeiaDDEDIALLSDEVYehfiYRGEHISPARFSDNVITVNAVSKTYAMTGWRLGY 235
                                       47889999999887421222122444666666777777732224444444456789999****************** PP

                                       EEES-HHHHH..HHHHHHHHHHSS--HHHHHHHHH CS
                       Alliinase_C 206 alvkdkevak..klveyieknsiGvskesqlrvlk 238
                                          +++++ +  k+ +y++  +  +s+ + l ++ 
  gi|330508552|ref|YP_004384980.1| 236 LAARNEAIEQhlKIHQYVQACASSISQAAALEAIC 270
                                       ******9987447899****999999998887765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.02
                                       HHHHHHTTTEEEEEGGGGTS-.TTEEEEESSS-HHHHHHHHHHHHTS CS
                       Alliinase_C 317 caevlrekkiltrsGevfeae.sryvrlsllkrdddfdvllerlkkl 362
                                       +a+ l +++++t  G+ f+ + ++++r+s   + ++ +  l+r+k++
  gi|330508552|ref|YP_004384980.1| 320 VASKLARAGVITVPGSAFGEGgREHIRISYAASRANLEEALRRMKDI 366
                                       45679999**********8751669****************999976 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 ?   11.8   0.0   6.4e-05      0.16      11      35 ..     158     186 ..     151     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.4e-05
                      NIR_SIR_ferr  11 mvrlrvpn...Gri.taeqlraladiaek 35 
                                       m+ ++ p+   G + t eq+ra+a+ia++
  gi|330508552|ref|YP_004384980.1| 158 MIIINSPSnptGSVqTEEQMRAIAEIADD 186
                                       666666655669998999*********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:01.37
# Mc/sec: 811.24
//
Query:       gi|330508553|ref|YP_004384981.1|  [L=127]
Description: translation initiation factor eIF-5A [Methanosaeta concilii GP6]
Scores for complete 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-07   30.0   0.2    8.9e-07   28.9   0.2    1.5  1  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi
    6.8e-06   26.0   0.0    1.2e-05   25.2   0.0    1.4  1  EFP_N     Elongation factor P (EF-P) KOW-like domain


Domain annotation for each model (and alignments):
>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.2   9.9e-11   8.9e-07       2      64 ..      69     123 ..      68     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 9.9e-11
                                       -EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG..GB-HHHHTT--TT-E..EEEEEETTEEE CS
                            eIF-5a   2 VkrkeyqLidIqdDgflsLmd.ddgetkeDlklpegelgkqikekfeegkdvlVtVlsamGeek 64 
                                       V+rk+ q+++I +D  ++Lmd  ++ t +   +p   + ++ k+k eegk+  V +l +mG+ k
  gi|330508553|ref|YP_004384981.1|  69 VERKTGQVLSI-GDTSVQLMDlGSYATID---VP---ITEDQKSKIEEGKE--VAYLAVMGRTK 123
                                       9**********.899******99999966...78...78999*********..********976 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 !   25.2   0.0   1.4e-09   1.2e-05       3      33 ..       8      38 ..       6      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.4e-09
                                      GG--TT-EEEETTEEEEEEEEEEEEETTS-- CS
                             EFP_N  3 selkkGlvieidgklyvVlefehvkpGkGqa 33
                                       elk G  + id ++++++++ h+kpGk ++
  gi|330508553|ref|YP_004384981.1|  8 RELKEGRYVIIDEEPCIIKSISHSKPGKHGS 38
                                      69*************************8653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 924.07
//
Query:       gi|330508554|ref|YP_004384982.1|  [L=261]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-14   54.1   0.0    3.2e-14   53.3   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    2.5e-14   53.5   0.0    4.3e-14   52.7   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    4.7e-12   46.5   0.0    8.6e-12   45.6   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    2.5e-09   37.8   0.0    4.2e-09   37.1   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    2.7e-09   37.0   0.0      4e-09   36.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.029   13.9   0.0      0.045   13.3   0.0    1.2  1  MTS              Methyltransferase small domain
       0.11   12.5   0.0       0.16   12.0   0.0    1.3  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   1.2e-17   3.2e-14       2      96 .]      52     148 ..      51     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1.2e-17
                                       EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC..T..SS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaek..l..pfednsfDlvvssevlhhv 74 
                                       dv cG G+ + +la + ++vvg+D s+em+++a +  +e++  ++f + ++e+  l   ++++s+ + vs+e+l+h+
  gi|330508554|ref|YP_004384982.1|  52 DVSCGLGYGSIELATASEEVVGIDGSPEMIERAMAGCQEPN--IRFNCLNLEEddLcrHIREGSCGAAVSFETLEHL 126
                                       99************888****************77777776..8888888885555457****************** PP

                                       CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                       +dp +a++++ R+L p+G++++
  gi|330508554|ref|YP_004384982.1| 127 NDPGRAVDQFSRILMPEGFFIC 148
                                       *******************986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.0   1.7e-17   4.3e-14      28     163 ..      52     190 ..      27     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.7e-17
                   Methyltransf_23  28 diGcGtGillevlrengfsvtgvDlspeaveiae......kakkaqkdqfdeqeaae.....pqgkfdlIvlrevle 93 
                                       d+ cG G+ + +l++   +v+g+D spe++e+a       +    ++ + + +e+ +      +g++  +v++e+le
  gi|330508554|ref|YP_004384982.1|  52 DVSCGLGYGSIELATASEEVVGIDGSPEMIERAMagcqepN---IRFNCLNLEED-DlcrhiREGSCGAAVSFETLE 124
                                       99******************************988884442...44444422222.134555889************ PP

                   Methyltransf_23  94 hvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGlevv 163
                                       h+ dp ++++q+ ++l p+G +++s+p++     ++ +d +++ ++  h ++f+  sl++++e+ G +v+
  gi|330508554|ref|YP_004384982.1| 125 HLNDPGRAVDQFSRILMPEGFFICSVPNV---ISESGDDAGLPKNR-SHKQWFNFPSLCRMVERRGMRVI 190
                                       ***************************97...56788999999999.*******************9986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   3.4e-15   8.6e-12       3      97 .]      52     144 ..      50     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 3.4e-15
                                       EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG..BS..SSTTTEEEEEEESTGG CS
                   Methyltransf_25   3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaed..lp..fedgsfDlvvssgalh 75 
                                       d+ cG G  +++la++   ++v+g+D s+em+e+a + +  +++n++f + ++e+  l     +gs+ + vs+ +l+
  gi|330508554|ref|YP_004384982.1|  52 DVSCGLGYGSIELATAS--EEVVGIDGSPEMIERAMAGC--QEPNIRFNCLNLEEddLCrhIREGSCGAAVSFETLE 124
                                       9*************994..********************..56899999999977333233699********888** PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       hl+d+   +a+++++r+L p+G
  gi|330508554|ref|YP_004384982.1| 125 HLNDPG--RAVDQFSRILMPEG 144
                                       **9665..99**********98 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   1.6e-12   4.2e-09       2      98 ..      52     145 ..      51     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.6e-12
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       ++ cG G  + +l+ +    e++g+D sp++i  ++    ++ n ++n+++le++dl  +  ++s  + v++++l+h
  gi|330508554|ref|YP_004384982.1|  52 DVSCGLGYGSIELATA--SEEVVGIDGSPEMI-ERAMAGCQEPNIRFNCLNLEEDDLCRHIREGSCGAAVSFETLEH 125
                                       899*************..**************.666677777888999999999999999999************** PP

                   Methyltransf_12  79 lkdirevldnirklLkpgGr 98 
                                       l+d+ +++d++ + L p+G 
  gi|330508554|ref|YP_004384982.1| 126 LNDPGRAVDQFSRILMPEGF 145
                                       ******************97 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   1.6e-12     4e-09       9     117 ..      52     156 ..      49     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.6e-12
                   Methyltransf_31   9 DlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.lekl.ledekfDlilsnev 83 
                                       D+ CG G+ ++ela       evvGiD s+e+ie+A + +q+    n++F   + ee   +  + + +    +s+e+
  gi|330508554|ref|YP_004384982.1|  52 DVSCGLGYGSIELAT---ASEEVVGIDGSPEMIERAMAGCQEP---NIRFNCLNLEEdDLCRhIREGSCGAAVSFET 122
                                       99************3...3468****************88833...788998888886444456779********** PP

                   Methyltransf_31  84 lnaladpdkileeiervlkpggilliedprllae 117
                                       l +l+dp  +  + +r l p+g ++++ p++ +e
  gi|330508554|ref|YP_004384982.1| 123 LEHLNDPGRAVDQFSRILMPEGFFICSVPNVISE 156
                                       **************************99995554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.7e-05     0.045      32      98 ..      47     114 ..      33     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC...EEEEE-STTTTSTTS-E CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle...vevvasdvleeveekkf 98 
                                        + ++D+ cG G+ +++la +s+e  v+ +d + + +e a + +++ +++   +++ + d+  ++ e+++
  gi|330508554|ref|YP_004384982.1|  47 IRLAADVSCGLGYGSIELATASEE--VVGIDGSPEMIERAMAGCQEPNIRfncLNLEEDDLCRHIREGSC 114
                                       45589***************9988..9******************9999966667777777777777666 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.1e-05      0.16      29      75 ..      50      92 ..      36     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.1e-05
                   Methyltransf_32 29 vvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75
                                       +Dv++G gY s  la      + +vvgid + e++e+a++  ++ +
  gi|330508554|ref|YP_004384982.1| 50 AADVSCGLGYGSIELAT----ASEEVVGIDGSPEMIERAMAGCQEPN 92
                                      57***************....4779*************998777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1885.38
//
Query:       gi|330508555|ref|YP_004384983.1|  [L=223]
Description: Ser/Thr protein phosphatase family protein [Methanosaeta concilii GP6]
Scores for complete 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   0.0    2.3e-15   56.6   0.0    2.2  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
    1.3e-15   58.0   0.0    2.7e-15   56.9   0.0    1.5  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    8.6e-15   55.8   0.0    1.2e-14   55.3   0.0    1.2  1  Metallophos    Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.032   14.2   0.0    1.3  1  Pik1           Yeast phosphatidylinositol-4-OH kinase Pik1


Domain annotation for each model (and alignments):
>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.022        97       7      47 ..       6      42 ..       2      50 .. 0.75
   2 !   56.6   0.0   5.2e-19   2.3e-15      85     249 ..      53     216 ..      47     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.022
                                      EEEEEE--TT-GGGHHHHHHHHHHH--SEEEEES-----HH CS
                     Metallophos_3  7 kvlaisdlkgevellerlveviedkdpDllvlvGdlvkaea 47
                                      ++l ++dl++ +e + +l    +d + Dl+ + Gdl +a +
  gi|330508555|ref|YP_004384983.1|  6 RILGLADLHDCTEGIRNL----KDLKYDLIAFCGDLHNASS 42
                                      677777777777776655....68899********966554 PP

  == domain 2  score: 56.6 bits;  conditional E-value: 5.2e-19
                                       HHTT-SEEEEE--TTS--HHHHHHHHHHTTTT-TTEEE-SSEEEEETTTEEEEEE-SEEESS--BS.SSS-EEEHH. CS
                     Metallophos_3  85 lgeldvpafvvPGkrDaPlevflreayeaevvfpnlkvvhesfaekeGevliaGmGGeivdgekee.efrLkYPaw. 159
                                       l +l+ p+++vPG++D      + +++e +    ++ v+h s + ++ e+ + GmGG i    +   +    Y +  
  gi|330508555|ref|YP_004384983.1|  53 LARLGPPVLIVPGNMDH--RDVVPDLWE-KA--GFI-VLHRSSFRHK-EYGFLGMGGMIARDPRRLgDPNRYYHRDd 122
                                       66778899999999996..456778888.43..444.4555544444.4899*******987766533333444431 PP

                                       HHHHHG.GGGGGS-.--EEEEEESS--S-SSTBTTBS---S-HHHHHHHHHH--SEEEE-SS--EE..EEETTEEEE CS
                     Metallophos_3 160 eveyrL.kvlkelk.drrkvlllatpPigelvadkglkekgsevvaelvktlnPevvvvghavkeh..eelgktlvv 232
                                       ev   L k  +e+   r k++++++pP g  ++  + +  gs ++  ++ +++P++v++gh + ++   ++g+tlvv
  gi|330508555|ref|YP_004384983.1| 123 EVYSVLeKAYQEVAgTRAKIVIVHQPPRGACDILYNGERSGSSELRRFIENYQPDLVLCGHIHEDRgeCHIGSTLVV 199
                                       4433445777887625679*************5555599************************9998568******* PP

                                       E--BGGGTEEEEEETTT CS
                     Metallophos_3 233 nPGaleeGdfavvdlee 249
                                       n G+l+ G  av+dl++
  gi|330508555|ref|YP_004384983.1| 200 NVGELRRGYGAVIDLND 216
                                       **************986 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 !   56.9   0.0   6.1e-19   2.7e-15       2     149 ..       6     207 ..       5     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 6.1e-19
                     Metallophos_2   2 klaiiSDlHsnldaleavlealkevgvdaiihaGDl......eeeepevleellela.pvlaVrGNnD......... 62 
                                       +++ ++DlH+  + +    + lk+ ++d+i ++GDl      e+++p + ++l +l  pvl+V+GN+D         
  gi|330508555|ref|YP_004384983.1|   6 RILGLADLHDCTEGI----RNLKDLKYDLIAFCGDLhnasstEGAKP-AAMALARLGpPVLIVPGNMDhrdvvpdlw 77 
                                       677899999655555....55566688********874444333344.778888877******************99 PP

                     Metallophos_2  63 ...............................eevveedvlreaaelgtdl.........p.eeaelelagekvlliH 98 
                                                                               r   + + ++         + +++e+   + k+ ++H
  gi|330508555|ref|YP_004384983.1|  78 ekagfivlhrssfrhkeygflgmggmiardpR--------RLGDPNRYYHrddevysvlEkAYQEVAGTRAKIVIVH 146
                                       99999999999998888888776554444321........22222222223333333322244444435555***** PP

                     Metallophos_2  99 gdpl...........gvkdalaellkeaeegsdvvvcGHtHvpeveke.ggvlvvnPGsvgep 149
                                       + p            +++ +l++ ++   ++ d+v+cGH+H+ + e + g++lvvn G+++++
  gi|330508555|ref|YP_004384983.1| 147 QPPRgacdilyngerSGSSELRRFIEN--YQPDLVLCGHIHEDRGECHiGSTLVVNVGELRRG 207
                                       *988*******8877777777777777..8888*********96665549*********9987 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0   2.7e-18   1.2e-14       1     204 []       5     187 ..       5     187 .. 0.70

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 2.7e-18
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCH CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegf 77 
                                       lril ++DlH      + + +++l  dl    k dl+ ++GDl + ++ e        al +++ pv +++GN +  
  gi|330508555|ref|YP_004384983.1|   5 LRILGLADLH-----DCTEGIRNLK-DL----KYDLIAFCGDLHNASSTEG-AKPAAMALARLGPPVLIVPGNMD-- 68 
                                       69********.....9999999966.66....99*************7777.5555555555567**********.. PP

                                       HH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE..EEEEEEESE...CEEETHHHHHHHHHHHSCHHHHCC. CS
                       Metallophos  78 ee.ellnkygylgifsepwrsdaevfnnlplaslgsgs..lkvlllhGg...spellvsldklgslnleleapepg. 147
                                        + ++ +          +w++ +  + +  ++     +  + +l + G    +p++   l + +++ ++      + 
  gi|330508555|ref|YP_004384983.1|  69 -HrDVVPD---------LWEKAGFIVLHRSSFR----HkeYGFLGMGGMiarDPRR---LGDPNRYYHR------Dd 122
                                       .2244444.........4555533333333333....2323555555552222222...2222222222......22 PP

                                       ..HHHHHH.HHHHTTCSEEEEEESSESS.....CSSSCSCCHHHHHHHHHHTTESEEEEESSSSE CS
                       Metallophos 148 ..dewlkd.lekrekadwvivlgHsply.....rgsgylfgdealedllkkygvdlvisGHtHvy 204
                                         +  l++ +++ ++++ +iv+ H p+       ++g   g+ +l+++ ++y++dlv++GH+H++
  gi|330508555|ref|YP_004384983.1| 123 evYSVLEKaYQEVAGTRAKIVIVHQPPRgacdiLYNGERSGSSELRRFIENYQPDLVLCGHIHED 187
                                       447777778888*********************9999999999999*****************85 PP

>> Pik1  Yeast phosphatidylinositol-4-OH kinase Pik1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.2e-06     0.032      17      46 ..     155     184 ..     153     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.2e-06
                                       -SS-SS.----TT--SS-SHHHHHHHHHHH CS
                              Pik1  17 ilFnlsaseqkkkkkfrENvsPalvLssav 46 
                                       il+n + s +++ ++f EN +P lvL++ +
  gi|330508555|ref|YP_004384983.1| 155 ILYNGERSGSSELRRFIENYQPDLVLCGHI 184
                                       7888888999999**************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        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 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1586.89
//
Query:       gi|330508556|ref|YP_004384984.1|  [L=240]
Description: hypothetical protein MCON_2779 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 1702.47
//
Query:       gi|330508557|ref|YP_004384985.1|  [L=194]
Description: iron-sulfur protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-11   42.7  23.5    2.9e-09   36.7   5.6    3.2  3  Fer4_5    4Fe-4S binding domain
    7.3e-10   38.2  19.9    2.4e-06   27.1   3.5    3.7  4  Fer4      4Fe-4S binding domain
      3e-09   36.9  14.0    8.9e-06   25.8  14.3    2.9  3  Fer4_9    4Fe-4S dicluster domain
      4e-08   33.0  17.9     0.0004   20.3   3.2    2.8  2  Fer4_6    4Fe-4S binding domain
    1.4e-07   32.0  15.3    0.00059   20.4   1.9    3.2  3  Fer4_7    4Fe-4S dicluster domain
    2.8e-07   30.6  12.2    7.4e-05   22.8   1.1    2.6  3  Fer4_21   4Fe-4S dicluster domain
    2.2e-06   27.8  10.1    2.2e-06   27.8  10.1    1.8  2  Fer4_18   4Fe-4S dicluster domain
    6.4e-06   26.2  15.4    6.4e-06   26.2  15.4    3.0  2  Fer4_10   4Fe-4S dicluster domain
    1.1e-05   25.2  10.5    0.00073   19.5   0.8    3.1  3  Fer4_2    4Fe-4S binding domain
    9.5e-05   23.3  17.1     0.0019   19.1   2.2    2.9  3  Fer4_16   4Fe-4S double cluster binding domain
    0.00013   22.8   6.3       0.15   13.0   0.6    2.3  2  Fer4_22   4Fe-4S dicluster domain
    0.00022   21.6  14.5      0.017   15.6   0.9    2.6  2  Fer4_8    4Fe-4S dicluster domain
    0.00023   21.6  17.1      0.047   14.2   1.9    2.9  3  Fer4_17   4Fe-4S dicluster domain
    0.00067   20.0  14.7     0.0054   17.1   3.3    3.3  3  Fer4_4    4Fe-4S binding domain
     0.0018   19.1   4.2     0.0018   19.1   4.2    3.8  4  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.052   14.1  18.4      0.069   13.7   2.2    2.7  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.29   11.3   0.2       0.29   11.3   0.2    1.6  2  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
        4.4    8.1  13.9         11    6.9   3.3    2.4  2  Fer4_15   4Fe-4S single cluster domain
        8.9    6.8   9.4       0.89   10.1   4.0    2.0  2  DUF202    Domain of unknown function (DUF202)


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 !   36.7   5.6   3.1e-12   2.9e-09       2      47 ..      17      62 ..      16      63 .. 0.89
   2 ?   -2.6   0.6       5.9   5.5e+03       8      14 ..      75      81 ..      64      88 .. 0.56
   3 !   17.3   3.0   3.6e-06    0.0034       9      39 ..     110     139 ..      99     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 3.1e-12
                            Fer4_5  2 allllilflaivlvtllfGRafCgWiCPfGalqellakllrrklgk 47
                                      ++ ll+ f+++++++ + GR+fCg++CP+G++ +++   l+r+l +
  gi|330508557|ref|YP_004384985.1| 17 GYILLLVFATLLIIAPFRGRWFCGNLCPRGSFVDFWLAPLSRRLAI 62
                                      678999****************************998877777765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.9
                            Fer4_5  8 lflaivl 14
                                      +f+a+++
  gi|330508557|ref|YP_004384985.1| 75 IFIALMG 81
                                      3333333 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 3.6e-06
                            Fer4_5   9 flaivlvtllfGRafCgWiCPfGalqellak 39 
                                        +ai++  ++  R +C  +CP G+lq +++ 
  gi|330508557|ref|YP_004384985.1| 110 SIAILFGVIIAPRTWCT-FCPMGTLQRIMGG 139
                                       5788888888*******.*********9985 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.2   1.2e+03      14      21 ..      39      46 ..      38      48 .. 0.80
   2 ?   -1.2   0.1       2.2   2.1e+03       8      11 ..     125     128 ..     123     133 .. 0.66
   3 !   20.4   1.7   3.4e-07   0.00032       3      20 ..     146     163 ..     144     164 .. 0.89
   4 !   27.1   3.5   2.5e-09   2.4e-06       7      23 ..     175     191 ..     172     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                                      HHHHSTTT CS
                              Fer4 14 CvevCPvg 21
                                      C + CP g
  gi|330508557|ref|YP_004384985.1| 39 CGNLCPRG 46
                                      88889987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.2
                                       SSS- CS
                              Fer4   8 CigC 11 
                                       C++C
  gi|330508557|ref|YP_004384985.1| 125 CTFC 128
                                       6655 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 3.4e-07
                                       EETTTSSS-THHHHHSTT CS
                              Fer4   3 ideekCigCGaCvevCPv 20 
                                        d ++Ci C++C +vCP 
  gi|330508557|ref|YP_004384985.1| 146 LDGDLCIDCKRCQKVCPM 163
                                       5789*************5 PP

  == domain 4  score: 27.1 bits;  conditional E-value: 2.5e-09
                                       TSSS-THHHHHSTTTEE CS
                              Fer4   7 kCigCGaCvevCPvgAI 23 
                                       +Ci+CG+Cv++CP +A+
  gi|330508557|ref|YP_004384985.1| 175 DCIKCGRCVDACPKDAL 191
                                       6***************7 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.8   1.7e+03       8      17 ..      39      48 ..      37      58 .. 0.67
   2 !   22.0   2.8   1.4e-07   0.00013       8      49 ..     125     164 ..     122     166 .. 0.91
   3 !   25.8  14.3   9.4e-09   8.9e-06       2      50 ..     151     190 ..     150     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.8
                            Fer4_9  8 CveaCpagvv 17
                                      C + Cp g +
  gi|330508557|ref|YP_004384985.1| 39 CGNLCPRGSF 48
                                      5566666655 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.4e-07
                            Fer4_9   8 CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       C+  Cp+g+ ++  ++ k +l+ +++  Ci+C++C ++Cp +
  gi|330508557|ref|YP_004384985.1| 125 CTF-CPMGTLQRIMGGSKYQLKLDGD-LCIDCKRCQKVCPMQ 164
                                       554.*****************99998.9************87 PP

  == domain 3  score: 25.8 bits;  conditional E-value: 9.4e-09
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       C++C++C+++Cp+++ v + +            +Ci+Cg+Cv+aCpk+a
  gi|330508557|ref|YP_004384985.1| 151 CIDCKRCQKVCPMQLRVFELQDLP---------DCIKCGRCVDACPKDA 190
                                       **************9887766554.........5*************97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   3.2   4.3e-07    0.0004       7      22 ..     149     164 ..     147     165 .. 0.92
   2 !   20.1   4.2   5.1e-07   0.00049       9      24 .]     176     191 ..     172     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.3e-07
                            Fer4_6   7 dkCigCgdCvrvCPeg 22 
                                       d+Ci+C +C +vCP++
  gi|330508557|ref|YP_004384985.1| 149 DLCIDCKRCQKVCPMQ 164
                                       89************98 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 5.1e-07
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       Ci Cg+Cv++CP +a+
  gi|330508557|ref|YP_004384985.1| 176 CIKCGRCVDACPKDAL 191
                                       ************9986 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.2   1.1e+03       7      15 ..      38      46 ..      36      54 .. 0.76
   2 !   16.0   4.3   1.5e-05     0.014      30      50 ..     143     163 ..     123     165 .. 0.71
   3 !   20.4   1.9   6.2e-07   0.00059       2      17 ..     176     191 ..     175     194 .] 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.2
                            Fer4_7  7 aCvaaCpvk 15
                                      +C + Cp +
  gi|330508557|ref|YP_004384985.1| 38 FCGNLCPRG 46
                                      577777765 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.5e-05
                            Fer4_7  30 kveidpekClgCgaCvavCPt 50 
                                       ++++d + C++C++C++vCP 
  gi|330508557|ref|YP_004384985.1| 143 QLKLDGDLCIDCKRCQKVCPM 163
                                       356778899999999999996 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 6.2e-07
                            Fer4_7   2 CigCgaCvaaCpvkai 17 
                                       Ci+Cg+Cv+aCp +a+
  gi|330508557|ref|YP_004384985.1| 176 CIKCGRCVDACPKDAL 191
                                       ************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 ?   -2.9   0.1       8.6   8.1e+03      47      52 ..      39      44 ..      37      47 .. 0.76
   2 !   22.8   1.1   7.8e-08   7.4e-05      16      53 ..     126     163 ..     122     167 .. 0.92
   3 !   14.6   1.3   2.8e-05     0.026       7      21 ..     175     189 ..     171     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8.6
                           Fer4_21 47 CssvCP 52
                                      C + CP
  gi|330508557|ref|YP_004384985.1| 39 CGNLCP 44
                                      778888 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 7.8e-08
                           Fer4_21  16 iaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                       + C+ ++ q i + +k +lk+  d C+ C+ C +vCP+
  gi|330508557|ref|YP_004384985.1| 126 TFCPMGTLQRIMGGSKYQLKLDGDLCIDCKRCQKVCPM 163
                                       579999*******************************8 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 2.8e-05
                           Fer4_21   7 kCigCgkCliaCedt 21 
                                       +Ci+Cg+C+ aC++ 
  gi|330508557|ref|YP_004384985.1| 175 DCIKCGRCVDACPKD 189
                                       699999999999965 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.3   2.1e+03       8      20 ..     126     138 ..     122     147 .. 0.78
   2 !   27.8  10.1   2.3e-09   2.2e-06      58      96 ..     147     187 ..     131     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.3
                           Fer4_18   8 yvcPyarvqsvly 20 
                                         cP + +q ++ 
  gi|330508557|ref|YP_004384985.1| 126 TFCPMGTLQRIMG 138
                                       4699999999885 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 2.3e-09
                           Fer4_18  58 agd.cidcescvkvcPtgidirkGlql.eciscllcidacd 96 
                                       +gd cidc+ c kvcP+++ + + + l +ci+c++c+dac 
  gi|330508557|ref|YP_004384985.1| 147 DGDlCIDCKRCQKVCPMQLRVFELQDLpDCIKCGRCVDACP 187
                                       4444******************9998878***********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 ?   -1.3   0.0       2.6   2.5e+03      17      21 ..     126     130 ..     122     141 .. 0.69
   2 !   26.2  15.4   6.7e-09   6.4e-06       3      56 .]     145     187 ..     143     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.6
                           Fer4_10  17 kaCPa 21 
                                       ++CP+
  gi|330508557|ref|YP_004384985.1| 126 TFCPM 130
                                       45887 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 6.7e-09
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       ++d d Ci C++C+k+CP+        + +  e +   ++ +C++cg Cv+aCP
  gi|330508557|ref|YP_004384985.1| 145 KLDGDLCIDCKRCQKVCPM--------QLRVFELQ---DLPDCIKCGRCVDACP 187
                                       67899**************........44444444...4569***********9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.9       6.5   6.1e+03      16      21 ..     125     129 ..     125     130 .. 0.83
   2 !   19.5   0.8   7.7e-07   0.00073       5      21 ..     146     162 ..     142     163 .. 0.89
   3 !   17.1   3.0   4.5e-06    0.0043       8      21 ..     174     187 ..     170     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.5
                            Fer4_2  16 CvsaCP 21 
                                       C + CP
  gi|330508557|ref|YP_004384985.1| 125 C-TFCP 129
                                       7.8999 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 7.7e-07
                            Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                        d d Ci C+ C+++CP
  gi|330508557|ref|YP_004384985.1| 146 LDGDLCIDCKRCQKVCP 162
                                       67799************ PP

  == domain 3  score: 17.1 bits;  conditional E-value: 4.5e-06
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                         Ci Cg Cv+aCP
  gi|330508557|ref|YP_004384985.1| 174 PDCIKCGRCVDACP 187
                                       44***********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 ?   -2.3   0.1       9.8   9.3e+03       8      14 ..      39      45 ..      38      49 .. 0.62
   2 !   15.0   0.7   3.9e-05     0.037       2      15 ..     151     164 ..     142     168 .. 0.83
   3 !   19.1   2.2     2e-06    0.0019       2      17 ..     176     191 ..     175     194 .] 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 9.8
                           Fer4_16  8 CaevCPt 14
                                      C + CP 
  gi|330508557|ref|YP_004384985.1| 39 CGNLCPR 45
                                      5556665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.9e-05
                           Fer4_16   2 CgtCgkCaevCPtn 15 
                                       C++C++C +vCP +
  gi|330508557|ref|YP_004384985.1| 151 CIDCKRCQKVCPMQ 164
                                       88888888888865 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 2e-06
                           Fer4_16   2 CgtCgkCaevCPtnai 17 
                                       C++Cg+C+++CP +a+
  gi|330508557|ref|YP_004384985.1| 176 CIKCGRCVDACPKDAL 191
                                       *************997 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.6   0.00019      0.17      72      95 ..     141     164 ..     132     165 .. 0.81
   2 !   13.0   0.6   0.00016      0.15      79      94 ..     173     188 ..     166     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                           Fer4_22  72 efkekfgesgCvGCgRCieacpvk 95 
                                       +++ k +   C+ C RC+++cp++
  gi|330508557|ref|YP_004384985.1| 141 KYQLKLDGDLCIDCKRCQKVCPMQ 164
                                       5566778899***********987 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00016
                           Fer4_22  79 esgCvGCgRCieacpv 94 
                                          C+ CgRC++acp+
  gi|330508557|ref|YP_004384985.1| 173 LPDCIKCGRCVDACPK 188
                                       568***********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 !   13.9   3.0   5.8e-05     0.054      49      64 ..     149     164 ..     124     167 .. 0.80
   2 !   15.6   0.9   1.8e-05     0.017       4      16 ..     175     187 ..     170     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-05
                            Fer4_8  49 wsCttcgaCtevCpvg 64 
                                       + C  c++C++vCp++
  gi|330508557|ref|YP_004384985.1| 149 DLCIDCKRCQKVCPMQ 164
                                       6788888888888875 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.8e-05
                            Fer4_8   4 kCieCgaCqsaCp 16 
                                       +Ci+Cg+C +aCp
  gi|330508557|ref|YP_004384985.1| 175 DCIKCGRCVDACP 187
                                       6888888888887 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.2   4.9e+03       8      15 ..      39      46 ..      38      61 .. 0.71
   2 !   13.1   6.0   0.00011      0.11      43      60 ..     148     165 ..     123     166 .. 0.79
   3 !   14.2   1.9     5e-05     0.047      45      59 ..     175     189 ..     170     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.2
                           Fer4_17  8 ClpeCpsy 15
                                      C + Cp++
  gi|330508557|ref|YP_004384985.1| 39 CGNLCPRG 46
                                      55566654 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00011
                           Fer4_17  43 aslCieCgeCerkCPqgl 60 
                                        +lCi C++C+++CP++l
  gi|330508557|ref|YP_004384985.1| 148 GDLCIDCKRCQKVCPMQL 165
                                       579*************98 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 5e-05
                           Fer4_17  45 lCieCgeCerkCPqg 59 
                                       +Ci+Cg+C+ +CP++
  gi|330508557|ref|YP_004384985.1| 175 DCIKCGRCVDACPKD 189
                                       799999999999986 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       3.5   3.3e+03      13      16 ..     127     130 ..     124     131 .. 0.69
   2 !   15.3   3.7   2.2e-05     0.021       2      17 .]     149     164 ..     148     164 .. 0.92
   3 !   17.1   3.3   5.7e-06    0.0054       4      16 ..     176     188 ..     171     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.5
                            Fer4_4  13 aCPq 16 
                                       +CP+
  gi|330508557|ref|YP_004384985.1| 127 FCPM 130
                                       6886 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.2e-05
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       + Ci+C++C  +CP++
  gi|330508557|ref|YP_004384985.1| 149 DLCIDCKRCQKVCPMQ 164
                                       67************86 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 5.7e-06
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       Ci Cg+Cv+aCP 
  gi|330508557|ref|YP_004384985.1| 176 CIKCGRCVDACPK 188
                                       ************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 ?    1.1   0.1         1   9.7e+02       7      14 ..      39      46 ..      37      47 .. 0.80
   2 ?   -1.8   0.8       8.7   8.2e+03       1       4 [.     125     128 ..     125     131 .. 0.68
   3 !    7.5   5.0    0.0093       8.8       1      12 [.     151     162 ..     151     164 .. 0.95
   4 !   19.1   4.2   1.9e-06    0.0018       1      15 []     176     190 ..     176     190 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1
                            Fer4_3  7 CvevCPvg 14
                                      C + CP g
  gi|330508557|ref|YP_004384985.1| 39 CGNLCPRG 46
                                      77889987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 8.7
                            Fer4_3   1 CtgC 4  
                                       Ct C
  gi|330508557|ref|YP_004384985.1| 125 CTFC 128
                                       7777 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0093
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+ C +C +vCP
  gi|330508557|ref|YP_004384985.1| 151 CIDCKRCQKVCP 162
                                       99********** PP

  == domain 4  score: 19.1 bits;  conditional E-value: 1.9e-06
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ Cg+Cv++CP++A
  gi|330508557|ref|YP_004384985.1| 176 CIKCGRCVDACPKDA 190
                                       *************98 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       6.9   6.5e+03      12      17 ..      39      44 ..      38      45 .. 0.87
   2 ?   13.7   2.2   7.3e-05     0.069       2      18 ..     147     163 ..     146     174 .. 0.83
   3 ?    9.5   4.3    0.0015       1.4       4      18 ..     174     188 ..     172     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.9
                           Fer4_13 12 CvelaP 17
                                      C++l+P
  gi|330508557|ref|YP_004384985.1| 39 CGNLCP 44
                                      99***9 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.3e-05
                           Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                       D d Ci+c+ C +++P 
  gi|330508557|ref|YP_004384985.1| 147 DGDLCIDCKRCQKVCPM 163
                                       8899************5 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0015
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                         Ci cg Cv+++P+
  gi|330508557|ref|YP_004384985.1| 174 PDCIKCGRCVDACPK 188
                                       57************6 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 ?   11.3   0.2   0.00031      0.29      48      88 ..     126     164 ..     120     172 .. 0.86
   2 ?   -2.3   0.3       5.3     5e+03      74      82 ..     175     183 ..     164     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                       HH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT- CS
                            ETF_QO  48 ryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsq 88 
                                        +CP g  + +     ++ +l+++   C+ Ck C+   p q
  gi|330508557|ref|YP_004384985.1| 126 TFCPMGTLQRIMGG--SKYQLKLDGDLCIDCKRCQKVCPMQ 164
                                       59999999988777..6999**************9877766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.3
                                       C--S--HHH CS
                            ETF_QO  74 nCvhCktCd 82 
                                       +C+ C  C 
  gi|330508557|ref|YP_004384985.1| 175 DCIKCGRCV 183
                                       699999884 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.0     0.012        11       2      19 ..     145     162 ..     144     172 .. 0.80
   2 ?    6.9   3.3     0.012        11       4      20 ..     172     188 ..     170     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                           Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                       ++D d+Ci c +C +++p
  gi|330508557|ref|YP_004384985.1| 145 KLDGDLCIDCKRCQKVCP 162
                                       68***************7 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
                           Fer4_15   4 DrdaCigcglCvaeape 20 
                                       D   Ci cg+Cv+++p+
  gi|330508557|ref|YP_004384985.1| 172 DLPDCIKCGRCVDACPK 188
                                       5678***********96 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       2.5   2.4e+03      46      55 ..      19      29 ..       7      39 .. 0.57
   2 ?   10.1   4.0   0.00094      0.89      13      59 ..      70     117 ..      68     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.5
                            DUF202 46 i.livlgiltl 55
                                      i l+v+++l++
  gi|330508557|ref|YP_004384985.1| 19 IlLLVFATLLI 29
                                      42333333333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00094
                            DUF202  13 WlRtslalialglallrffltgepsa.lgkilglilivlgiltllvgl 59 
                                       W+R+ + ++ +g+ ++r+  t+++ + +g+++ +++i+++ +++l+g+
  gi|330508557|ref|YP_004384985.1|  70 WIRIPIFIALMGFMIYRLLGTQGVVDrIGMVFVTLCIITTSIAILFGV 117
                                       *****************9665444442567777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1405.02
//
Query:       gi|330508558|ref|YP_004384986.1|  [L=352]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete 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   75.4   0.0    4.8e-21   74.6   0.0    1.4  1  DUF772       Transposase domain (DUF772)
    1.5e-15   57.4   4.6      5e-15   55.7   4.6    1.9  1  DDE_Tnp_1    Transposase DDE domain
      3e-05   23.8   0.3    0.00012   21.8   0.3    1.9  1  DDE_Tnp_4    DDE superfamily endonuclease
    3.1e-05   24.2   0.4    5.3e-05   23.4   0.4    1.4  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
      0.052   13.9   0.1       0.12   12.8   0.1    1.6  1  EnY2         Transcription factor e(y)2


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 !   74.6   0.0   1.3e-24   4.8e-21       1      72 [.      51     122 ..      51     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.3e-24
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp+++ ++m+k+l+lq ++glSd ele+++ +++sfr flg     + +pd+st + fR+rl+e    e+l++e
  gi|330508558|ref|YP_004384986.1|  51 GRPNIDIVIMVKALVLQSWFGLSDPELERQVTDRISFRIFLGT---TEVIPDFSTVWLFRERLIEcgrYEDLWKE 122
                                       9*****************************************5...389****************9999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   4.6   1.4e-18     5e-15      20     214 .]     177     340 ..     133     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.4e-18
                         DDE_Tnp_1  20 k............................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkql 68 
                                       +                             ++ w +kg k+++gyk hi++dt+ +li ++++t+++ hds++    
  gi|330508558|ref|YP_004384986.1| 177 PdfdkdllnisnnivssnakpkrlddgpiNEGTWAKKGSKSFFGYKGHILIDTEYHLIRKIETTTASLHDSQVDLG- 252
                                       0555555555555555555556666666677889999**********************************99777. PP

                         DDE_Tnp_1  69 ldelrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnksk 145
                                       +++l++      +aD+GY++a++  + +                            ++k+ r++ l  ++++rnk  
  gi|330508558|ref|YP_004384986.1| 253 INGLPR------YADKGYSGAKTQGYDA---------------------------AMKKAARGHKLGIKDILRNK-- 294
                                       777887......*******888877777...........................89******************.. PP

                         DDE_Tnp_1 146 kekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                              +++r+R+qiEr F+ +kr  + +++++ + +r+ +++++  +++n+
  gi|330508558|ref|YP_004384986.1| 295 -----------------------RISRKRSQIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNI 340
                                       .......................******************999************************7 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   3.4e-08   0.00012      77     130 ..     257     313 ..     195     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.4e-08
                         DDE_Tnp_4  77 vilaDkgFklse..kl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgr 130
                                          aDkg+ +++   +   ++k  ++++l  ++  +n++i++ r  +Er+++ +k+ 
  gi|330508558|ref|YP_004384986.1| 257 PRYADKGYSGAKtqGYdAAMKKAARGHKLGIKDILRNKRISRKRSQIERCFAVMKRA 313
                                       3469*****99954333455555********************************65 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 !   23.4   0.4   1.5e-08   5.3e-05      74     124 ..     294     343 ..     265     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.5e-08
                       DDE_Tnp_1_6  74 kaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                       k+  +kR+ ++E+ fa +kr++++  + ++ ++++ ++f++  +++N+++l
  gi|330508558|ref|YP_004384986.1| 294 KRISRKRS-QIERCFAVMKRAHNAGHVSVTTIARAGIKFMMNSIVYNIEQL 343
                                       45556665.***************************************997 PP

>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.3e-05      0.12       5      31 ..     107     133 ..     106     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       HHHHHHTTHHHHHHHHHHHHHHHTTHH CS
                              EnY2   5 qqkLvesGererlkelLrerLeesGWr 31 
                                       +++L+e G +e+l + L+++L+e G+ 
  gi|330508558|ref|YP_004384986.1| 107 RERLIECGRYEDLWKELQNQLDEKGFA 133
                                       589**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2355.43
//
Query:       gi|330508559|ref|YP_004384987.1|  [L=118]
Description: hypothetical protein MCON_2782 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.16   11.9   0.0    1.3  1  Mad3_BUB1_I  Mad3/BUB1 homology region 1


Domain annotation for each model (and alignments):
>> Mad3_BUB1_I  Mad3/BUB1 homology region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.2e-06      0.16      13      39 ..      15      41 ..       7      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.2e-06
                                      G....-THHHHHHHHHHHHHH-TT-T. CS
                       Mad3_BUB1_I 13 aeegdDpLelwlryikwieesypqssk 39
                                      aee++D L+++ + ++wi+++ p + +
  gi|330508559|ref|YP_004384987.1| 15 AEEMEDTLKAFADACNWINQNTPAKLR 41
                                      2899*******************9443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 925.27
//
Query:       gi|330508560|ref|YP_004384988.1|  [L=141]
Description: hypothetical protein MCON_2784 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.047   13.9   0.2      0.067   13.4   0.2    1.2  1  Bep_C_terminal  BID domain of Bartonella effector protein (Be


Domain annotation for each model (and alignments):
>> Bep_C_terminal  BID domain of Bartonella effector protein (Bep)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   3.8e-06     0.067      30      83 ..      18      70 ..      13      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-06
                    Bep_C_terminal 30 fkaidavlkdpalakellqkiaaepesigaLaGkkgllakraekqeRkaAeanv 83
                                      f+a +a lkd ++a+++l+ + ++pe + +L G+++l a++a ++eR+ Ae  +
  gi|330508560|ref|YP_004384988.1| 18 FRATKAQLKDMKTAAAILNMLSEKPEVLKKL-GDEYLEASNAPEEERDFAEYEL 70
                                      678899************************9.******************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1110.28
//
Query:       gi|330508561|ref|YP_004384989.1|  [L=161]
Description: hypothetical protein MCON_2785 [Methanosaeta concilii GP6]
Scores for complete sequence (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   28.6   0.0    2.3e-06   27.8   0.0    1.4  1  PqqD      Coenzyme PQQ synthesis protein D (PqqD)


Domain annotation for each model (and alignments):
>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.3e-10   2.3e-06      12      67 .]      93     149 ..      83     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.3e-10
                                       EEE--CHHHHHHHH-SSSS-HHHHHHHHHHHC.T--HHHHHHHHHHHHHHHHCTT-- CS
                              PqqD  12 yisLnetgafiWklldgersveeivaalaeey.dvdeeeaeadvlafldqLrekgli 67 
                                        +  n++g+ i +l+ g++s+ ei ++l+e++  v+ +++ +d l+fl+ L+e +li
  gi|330508561|ref|YP_004384989.1|  93 PFFINSSGSIICRLCTGKNSIKEIQKELKEIWfSVADDVLLRDGLSFLMLLEEMNLI 149
                                       5668***********************************************998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1177.51
//
Query:       gi|330508562|ref|YP_004384990.1|  [L=411]
Description: Radical SAM domain/B12 binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-20   73.2   0.9    5.1e-20   72.5   0.5    1.6  2  Radical_SAM  Radical SAM superfamily
    4.6e-19   68.6   0.1      8e-19   67.9   0.1    1.4  1  B12-binding  B12 binding domain
     0.0028   17.8   0.2     0.0091   16.1   0.2    1.9  1  Fer4_14      4Fe-4S single cluster domain
     0.0067   16.7   0.1       0.02   15.2   0.1    1.7  2  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.3   5.9e+03      63      75 ..      46      65 ..      19      95 .. 0.56
   2 !   72.5   0.5   1.1e-23   5.1e-20       1     167 []     164     327 ..     164     327 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
                                      HHHHHHHHHHTC.......C CS
                                      xxxxxxxxxxxx.......x RF
                       Radical_SAM 63 fvellerlakla.......v 75
                                       +++++++ak +        
  gi|330508562|ref|YP_004384990.1| 46 NAVDIAKAAKSHnpnikivF 65
                                      33333333333322222222 PP

  == domain 2  score: 72.5 bits;  conditional E-value: 1.1e-23
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavp 76 
                                       +++trgC+++C+fC++      ++++r++s  ++l+e++ + ++k  ++++ +  ++ ++ ++ v +l r +k+++ 
  gi|330508562|ref|YP_004384990.1| 164 IITTRGCPFNCIFCSTAAL--HGRKYRTRSANNVLDEMEFV-QDKYkINVISFADDNFTMKRNRVIELCRGIKERHL 237
                                       679**************96..9*******************.89999*****************9999999999777 PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglp 153
                                       +++  +++   l++++ le +   g+  + +g+e+a+ + vl+ +++g ++e+ +e +++  + gik  +++i+glp
  gi|330508562|ref|YP_004384990.1| 238 DFEWGCSARVDLLSKDLLEVMNSSGCKNIFFGIESASQR-VLDTVKKGFSIEKAKEMVKLTEKMGIKTHCSFILGLP 313
                                       88888888888888*************************.************************************* PP

                                       TTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                       Radical_SAM 154 Gendeeleellell 167
                                       +e+ e ++e+++++
  gi|330508562|ref|YP_004384990.1| 314 NETVESIDEMIRFV 327
                                       ***********996 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.1   1.8e-22     8e-19      27     120 ..       4      99 ..       1     100 [. 0.91

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 1.8e-22
                       B12-binding  27 agfeVqllganven...edivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetle 100
                                       +g+  ++++++      e++v+ i +++pd++g+++ +ts+++++ ++++++k+ +p++k+v+GG+h+++ ++++l 
  gi|330508562|ref|YP_004384990.1|   4 EGITAKIVDMDWGGfskEELVDMISKFDPDIIGITS-FTSNYANAVDIAKAAKSHNPNIKIVFGGVHATFIHRDVL- 78 
                                       56777777777766777*******************.***************************************. PP

                       B12-binding 101 ak.lgiddvvvgegedaleal 120
                                       +  +++d+vv+ ege a+ ++
  gi|330508562|ref|YP_004384990.1|  79 HTiPEVDIVVRYEGERAICEI 99 
                                       577*************99876 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     2e-06    0.0091       4      79 ..     166     237 ..     164     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-06
                           Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeyp 79 
                                        + gC+++C +C + +    ++ + +++++l+++   + ++++ki+ +++   + +  ++ + +++l++ +ke+  
  gi|330508562|ref|YP_004384990.1| 166 TTRGCPFNCIFCSTAALHGRKYRTRSANNVLDEME--FVQDKYKINVISFAD-DNF-TMKRNRVIELCRGIKERHL 237
                                       578****************************6554..99999999*777764.555.4678888999999988874 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 ?   -2.6   0.0       1.3     6e+03      67      91 ..      42      65 ..      22      89 .. 0.68
   2 !   15.2   0.1   4.4e-06      0.02       9     102 ..     164     252 ..     155     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
                           Fer4_12 67 enaeallelvkevkeekpekdiwly 91
                                      +n+   ++++k  k+++p+ +i ++
  gi|330508562|ref|YP_004384990.1| 42 SNYANAVDIAKAAKSHNPNIKI-VF 65
                                      5667777788888888886443.33 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.4e-06
                           Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpe 85 
                                       ++ + gC+++C +C   +++  k+ +   +++l+e+ e +++++++ ++ +  + +  ++++ ++el++ +ke+ ++
  gi|330508562|ref|YP_004384990.1| 164 IITTRGCPFNCIFCSTAALHGRKYRTRSANNVLDEM-EFVQDKYKINVISFADDNFT-MKRNRVIELCRGIKERHLD 238
                                       66789******************************6.68888888777777778777.79999**********9985 PP

                           Fer4_12  86 kdiwlytgytleelskk 102
                                          +++  +  ++l++k
  gi|330508562|ref|YP_004384990.1| 239 ---FEWGCSARVDLLSK 252
                                       ...66666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2852.80
//
Query:       gi|330508563|ref|YP_004384991.1|  [L=116]
Description: hypothetical protein MCON_2787 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-12   48.2   0.0    1.4e-12   48.0   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 !   48.0   0.0   7.6e-17   1.4e-12       2     110 ..       3     107 ..       2     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 7.6e-17
                                       TTEEEEEEE-S.--TTS--SEEEEEE-S-HHHHCHSEEEEEEEESSSTSSGCSTTEEEE-HH.HCSS.SSSSSSEEE CS
                        PemK_toxin   2 rGeIvlvdldp.srgseqgkrRpvvVvsndafnekntvivvpltskdkdkkklpfhvelese.ildl.ngldkdswv 75 
                                       +G+Ivlv + p +      k Rp++V+ +     +  v+++p+t++++d  +lp +  ++++  + + +gl+++sw 
  gi|330508563|ref|YP_004384991.1|   3 KGSIVLVHF-PfT-DLSSTKLRPALVLHEG----HLDVTIAPMTTQRPDP-PLPSDLLIRKGtLSFKaTGLKEESWL 72 
                                       699******.954.44447********765....458**********977.67*******995555578888***** PP

                                       ECCCEEEEEGGGEEEEEEE--HHHHHHHHHHHHHH CS
                        PemK_toxin  76 kldqirtvdkarlrkkigklsredlaevqralakl 110
                                       ++d+i+t++k  + + +gk ++++ ++v+++la+ 
  gi|330508563|ref|YP_004384991.1|  73 LIDKIATLEKMFIEGILGKADDDLKRDVNAKLAEC 107
                                       ********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 879.07
//
Query:       gi|330508564|ref|YP_004384992.1|  [L=190]
Description: hypothetical protein MCON_2789 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1291.60
//
Query:       gi|330508565|ref|YP_004384993.1|  [L=718]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-57  190.8  29.5    2.8e-15   56.4   0.5    5.1  7  TPR_12    Tetratricopeptide repeat
      1e-31  107.4  12.2    1.4e-05   24.7   0.2    6.3  6  TPR_1     Tetratricopeptide repeat
    1.2e-28   98.1   9.3    0.00012   21.8   0.2    6.7  6  TPR_10    Tetratricopeptide repeat
      7e-28   94.6  11.1    2.7e-05   23.9   0.0    7.3  6  TPR_7     Tetratricopeptide repeat
      4e-25   85.9  13.3    0.00056   19.8   0.1    7.2  6  TPR_2     Tetratricopeptide repeat
    2.7e-23   80.2   6.5    8.6e-05   22.5   0.1    7.0  6  TPR_8     Tetratricopeptide repeat
    1.4e-13   51.0   1.0    2.6e-09   36.9   0.1    3.0  3  TPR_MalT  MalT-like TPR region
    6.8e-12   45.4   0.1    1.8e-05   24.3   0.3    2.2  2  SNAP      Soluble NSF attachment protein, SNAP
      1e-11   44.7   6.9        6.1    7.7   0.0    8.6  7  TPR_6     Tetratricopeptide repeat
    1.3e-10   41.2  17.0        1.2   10.1   0.0    8.2  6  TPR_14    Tetratricopeptide repeat
    4.6e-10   39.1   0.0    8.5e-10   38.2   0.0    1.4  1  NB-ARC    NB-ARC domain
    7.5e-08   32.4   0.6       0.19   11.8   0.0    4.0  4  Rapsyn_N  Rapsyn N-terminal myristoylation and linker region
    1.1e-06   28.3  15.0      0.045   13.4   0.3    5.6  5  TPR_11    TPR repeat
    6.4e-06   26.7   0.1    2.4e-05   24.8   0.1    2.0  1  AAA_16    AAA ATPase domain
    1.2e-05   25.4   1.9      0.034   14.2   0.1    2.9  2  DUF3856   Domain of Unknown Function (DUF3856)
    1.7e-05   25.2   9.7       0.14   12.6   0.1    5.8  5  TPR_19    Tetratricopeptide repeat
    4.8e-05   23.5   0.2        2.5    8.2   0.0    4.5  5  DUF2753   Protein of unknown function (DUF2753)
     0.0004   20.9   0.9        3.9    8.1   0.0    4.4  4  DUF4810   Domain of unknown function (DUF4810)
    0.00072   19.8   2.3        6.8    7.3   0.0    5.3  5  TPR_17    Tetratricopeptide repeat
     0.0034   17.7   0.0     0.0093   16.2   0.0    1.7  1  AAA_22    AAA domain
  ------ inclusion threshold ------
      0.028   14.3   0.0      0.057   13.3   0.0    1.5  1  NACHT     NACHT domain
      0.062   13.5   2.5        6.9    7.0   0.1    4.2  4  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
       0.12   12.3   0.0          8    6.3   0.0    2.8  2  Wzy_C_2   Virulence factor membrane-bound polymerase, C-termi
       0.17   12.0   1.6        1.2    9.4   0.1    3.0  3  DUF4167   Domain of unknown function (DUF4167)
        0.2   11.2   0.0        1.4    8.4   0.0    2.2  2  ComR_TPR  ComR tetratricopeptide
       0.24   11.6   8.5        8.4    6.6   0.1    5.4  6  TPR_9     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2       2.2   1.5e+03      10      27 ..     354     371 ..     342     374 .. 0.64
   2 !   17.1   0.3   7.3e-06     0.005      23      76 ..     448     499 ..     445     500 .. 0.89
   3 !   44.9   0.5   1.6e-14   1.1e-11       7      77 .]     472     540 ..     466     540 .. 0.95
   4 !   56.4   0.5   4.1e-18   2.8e-15       4      77 .]     509     580 ..     506     580 .. 0.96
   5 !   45.5   1.9     1e-14   6.9e-12       3      77 .]     548     620 ..     546     620 .. 0.95
   6 !   43.6   0.4     4e-14   2.8e-11       8      77 .]     593     660 ..     587     660 .. 0.94
   7 !   42.4   0.0   9.5e-14   6.6e-11       4      77 .]     629     700 ..     626     700 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.2
                            TPR_12  10 aavlrrlgrydeAlelle 27 
                                       aa ++++g++ eA+e + 
  gi|330508565|ref|YP_004384993.1| 354 AASCLQAGEMGEAEERHA 371
                                       555555566666655554 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 7.3e-06
                            TPR_12  23 lellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +++le+a ++a++    d+ ++ +   n+g +y  +g++ +A+ ++++al i +
  gi|330508565|ref|YP_004384993.1| 448 IRWLETAADAAKQM--QDRGAEGAHFGNIGLAYADRGETGKAIVYYQQALTITR 499
                                       57899999999655..88899*****************************9976 PP

  == domain 3  score: 44.9 bits;  conditional E-value: 1.6e-14
                            TPR_12   7 nnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                        n++++++ +g+  +A+ ++++al i r++  +++ ++ ++l nLgr+y  lg++++A+e++ +al i+++
  gi|330508565|ref|YP_004384993.1| 472 GNIGLAYADRGETGKAIVYYQQALTITREI--GNRQDEGAILGNLGRAYANLGEPRKAIEHHDQALTIFKE 540
                                       599***************************..88999*******************************985 PP

  == domain 4  score: 56.4 bits;  conditional E-value: 4.1e-18
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       ++l nl+ +++ lg+  +A+e++++al i++++  +d+ ++ ttl+n+g++y alg+   A+e++e+a aia++
  gi|330508565|ref|YP_004384993.1| 509 AILGNLGRAYANLGEPRKAIEHHDQALTIFKEI--GDRRDEGTTLCNIGIAYAALGKIHNAIEYFEQAFAIARE 580
                                       7899*****************************..8999********************************986 PP

  == domain 5  score: 45.5 bits;  conditional E-value: 1e-14
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                        t+l n++ ++++lg+ + A+e++e+a +iar++  +++ ++ ++l  Lg++   lg+ ++A++++++alaia++
  gi|330508565|ref|YP_004384993.1| 548 GTTLCNIGIAYAALGKIHNAIEYFEQAFAIAREI--EERRNEGICLGCLGQANINLGEIRKAIDHYQQALAIARE 620
                                       57899*****************************..88889*******************************986 PP

  == domain 6  score: 43.6 bits;  conditional E-value: 4e-14
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                        l+++   lg+  +A++++++al+iar++  +d+  + ++l  Lg++y  lg++ +A+e++ +a  i+++
  gi|330508565|ref|YP_004384993.1| 593 CLGQANINLGEIRKAIDHYQQALAIAREI--GDRRSEGNSLGSLGTAYKNLGEPHKAIEHYDQARTIFRE 660
                                       68999999*********************..8999*******************************9985 PP

  == domain 7  score: 42.4 bits;  conditional E-value: 9.5e-14
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       ++l  l++++  lg+ ++A+e++++a+ i+r++  +d+ ++ ++  n++ ++  lg+ +eA++l  ealai+e+
  gi|330508565|ref|YP_004384993.1| 629 NSLGSLGTAYKNLGEPHKAIEHYDQARTIFREI--GDWRGEGNSIWNMSLVLNGLGNRAEAVKLAGEALAIYEQ 700
                                       56778****************************..9************************************96 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.3e-07   0.00016       5      30 ..     472     497 ..     470     498 .. 0.95
   2 !   22.4   0.0   1.1e-07   7.4e-05       3      30 ..     510     537 ..     509     540 .. 0.93
   3 !   24.7   0.2     2e-08   1.4e-05       3      30 ..     550     577 ..     549     580 .. 0.92
   4 !   20.1   0.3   5.6e-07   0.00038       4      31 ..     591     618 ..     589     620 .. 0.91
   5 !   21.1   0.0   2.7e-07   0.00019       4      30 ..     631     657 ..     629     660 .. 0.89
   6 ?   -0.8   0.0       2.4   1.6e+03      12      31 ..     679     698 ..     676     700 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   5 ynlGnayfklgkydeAleyyekALel 30 
                                        n+G+ay   g+  +A+ yy++AL++
  gi|330508565|ref|YP_004384993.1| 472 GNIGLAYADRGETGKAIVYYQQALTI 497
                                       69**********************86 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                       +l nlG ay +lg++ +A+e+ ++AL++
  gi|330508565|ref|YP_004384993.1| 510 ILGNLGRAYANLGEPRKAIEHHDQALTI 537
                                       588***********************98 PP

  == domain 3  score: 24.7 bits;  conditional E-value: 2e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                       +l+n+G ay  lgk   A+ey+e+A  +
  gi|330508565|ref|YP_004384993.1| 550 TLCNIGIAYAALGKIHNAIEYFEQAFAI 577
                                       69***********************877 PP

  == domain 4  score: 20.1 bits;  conditional E-value: 5.6e-07
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALeln 31 
                                       l  lG+a  +lg+  +A+++y++AL + 
  gi|330508565|ref|YP_004384993.1| 591 LGCLGQANINLGEIRKAIDHYQQALAIA 618
                                       6679*********************996 PP

  == domain 5  score: 21.1 bits;  conditional E-value: 2.7e-07
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALel 30 
                                       l  lG ay +lg++ +A+e+y++A ++
  gi|330508565|ref|YP_004384993.1| 631 LGSLGTAYKNLGEPHKAIEHYDQARTI 657
                                       678********************9665 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 2.4
                                       HHTT-HHHHHHHHHHHHHHS CS
                             TPR_1  12 fklgkydeAleyyekALeln 31 
                                         lg+  eA++   +AL ++
  gi|330508565|ref|YP_004384993.1| 679 NGLGNRAEAVKLAGEALAIY 698
                                       56899999999999999887 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   4.2e-06    0.0029       7      35 ..     473     501 ..     469     505 .. 0.93
   2 !   17.6   0.0   3.8e-06    0.0026       4      34 ..     510     540 ..     509     543 .. 0.92
   3 !   21.8   0.2   1.7e-07   0.00012       3      35 ..     549     581 ..     548     586 .. 0.93
   4 !   10.4   0.2   0.00067      0.46       4      35 ..     590     621 ..     589     624 .. 0.92
   5 !   12.3   0.0   0.00018      0.12       4      34 ..     630     660 ..     628     662 .. 0.91
   6 !   17.9   0.0     3e-06    0.0021       7      35 ..     673     701 ..     672     704 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.2e-06
                            TPR_10   7 NLanalrqrgrydeAealleealairrrl 35 
                                       N++ a+ +rg+  +A  ++++al i r++
  gi|330508565|ref|YP_004384993.1| 473 NIGLAYADRGETGKAIVYYQQALTITREI 501
                                       9*************************996 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.8e-06
                            TPR_10   4 slnNLanalrqrgrydeAealleealairrr 34 
                                       +l NL++a+ ++g+  +A +++++al i ++
  gi|330508565|ref|YP_004384993.1| 510 ILGNLGRAYANLGEPRKAIEHHDQALTIFKE 540
                                       689***********************99776 PP

  == domain 3  score: 21.8 bits;  conditional E-value: 1.7e-07
                            TPR_10   3 sslnNLanalrqrgrydeAealleealairrrl 35 
                                       ++l N+++a+ ++g+ + A +++e+a ai r++
  gi|330508565|ref|YP_004384993.1| 549 TTLCNIGIAYAALGKIHNAIEYFEQAFAIAREI 581
                                       6899**************************997 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00067
                            TPR_10   4 slnNLanalrqrgrydeAealleealairrrl 35 
                                       +l  L+ a  ++g+  +A +++++alai r++
  gi|330508565|ref|YP_004384993.1| 590 CLGCLGQANINLGEIRKAIDHYQQALAIAREI 621
                                       677899999*******************9986 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 0.00018
                            TPR_10   4 slnNLanalrqrgrydeAealleealairrr 34 
                                       sl  L+ a+ ++g+ ++A +++++a  i r+
  gi|330508565|ref|YP_004384993.1| 630 SLGSLGTAYKNLGEPHKAIEHYDQARTIFRE 660
                                       8899*********************998776 PP

  == domain 6  score: 17.9 bits;  conditional E-value: 3e-06
                            TPR_10   7 NLanalrqrgrydeAealleealairrrl 35 
                                       N++ +l  +g+++eA++l+ ealai++++
  gi|330508565|ref|YP_004384993.1| 673 NMSLVLNGLGNRAEAVKLAGEALAIYEQI 701
                                       88999**********************97 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     3e-06     0.002       3      34 ..     472     503 ..     470     505 .. 0.92
   2 !   23.9   0.0   3.9e-08   2.7e-05       2      35 ..     511     544 ..     510     545 .. 0.89
   3 !   21.8   0.1   1.8e-07   0.00012       1      34 [.     550     583 ..     550     585 .. 0.86
   4 !   15.2   0.0   2.4e-05     0.016       6      35 ..     595     624 ..     590     625 .. 0.86
   5 !   15.1   0.0   2.4e-05     0.017       1      27 [.     630     654 ..     630     665 .. 0.93
   6 ?    0.9   0.0      0.84   5.8e+02      12      29 ..     681     698 ..     671     704 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3e-06
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                        n++ +y ++G++ +Ai +y+q+L +t++ ++
  gi|330508565|ref|YP_004384993.1| 472 GNIGLAYADRGETGKAIVYYQQALTITREIGN 503
                                       69**********************99999876 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 3.9e-08
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       L nL+r+y +lG+ ++Aie++ q+L + k+ +d+
  gi|330508565|ref|YP_004384993.1| 511 LGNLGRAYANLGEPRKAIEHHDQALTIFKEIGDR 544
                                       89*********************88887887776 PP

  == domain 3  score: 21.8 bits;  conditional E-value: 1.8e-07
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       +L+n++ +y +lG+  +Aie++eq+ a++++ e+
  gi|330508565|ref|YP_004384993.1| 550 TLCNIGIAYAALGKIHNAIEYFEQAFAIAREIEE 583
                                       79**********************6677677665 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 2.4e-05
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +++  +lG+ ++Ai++y+q+La++++ +d+
  gi|330508565|ref|YP_004384993.1| 595 GQANINLGEIRKAIDHYQQALAIAREIGDR 624
                                       5555689******************99987 PP

  == domain 5  score: 15.1 bits;  conditional E-value: 2.4e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLa 27 
                                       +L  L+ +y +lG+  +Aie+y q  a
  gi|330508565|ref|YP_004384993.1| 630 SLGSLGTAYKNLGEPHKAIEHYDQ--A 654
                                       6899******************99..4 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.84
                             TPR_7  12 lGdyeeAielyeqsLalt 29 
                                       lG+++eA++l  ++La+ 
  gi|330508565|ref|YP_004384993.1| 681 LGNRAEAVKLAGEALAIY 698
                                       899999999999988775 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.7e-05     0.026       6      30 ..     473     497 ..     471     500 .. 0.92
   2 !   14.8   0.0   3.4e-05     0.023       3      31 ..     510     538 ..     508     541 .. 0.89
   3 !   19.3   0.1   1.2e-06   0.00081       4      31 ..     551     578 ..     549     581 .. 0.92
   4 !   19.8   0.1   8.1e-07   0.00056       4      32 ..     591     619 ..     588     621 .. 0.91
   5 !   15.0   0.0   2.8e-05      0.02       6      30 ..     633     657 ..     629     660 .. 0.88
   6 ?    5.5   0.0     0.031        22      14      32 ..     681     699 ..     672     701 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-05
                             TPR_2   6 nlGlayyklgdyeeAleafekAlel 30 
                                       n+Glay+ +g+  +A+ ++++Al +
  gi|330508565|ref|YP_004384993.1| 473 NIGLAYADRGETGKAIVYYQQALTI 497
                                       79*********************87 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.4e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                       +l nlG+ay++lg++ +A+e+ ++Al + 
  gi|330508565|ref|YP_004384993.1| 510 ILGNLGRAYANLGEPRKAIEHHDQALTIF 538
                                       5779*****************99999876 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 1.2e-06
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleld 31 
                                       l+n+G ay++lg+   A+e+fe+A +++
  gi|330508565|ref|YP_004384993.1| 551 LCNIGIAYAALGKIHNAIEYFEQAFAIA 578
                                       899*********************9987 PP

  == domain 4  score: 19.8 bits;  conditional E-value: 8.1e-07
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldP 32 
                                       l +lG+a ++lg+  +A++++++Al+++ 
  gi|330508565|ref|YP_004384993.1| 591 LGCLGQANINLGEIRKAIDHYQQALAIAR 619
                                       678**********************9975 PP

  == domain 5  score: 15.0 bits;  conditional E-value: 2.8e-05
                             TPR_2   6 nlGlayyklgdyeeAleafekAlel 30 
                                        lG ay +lg++ +A+e++++A  +
  gi|330508565|ref|YP_004384993.1| 633 SLGTAYKNLGEPHKAIEHYDQARTI 657
                                       59*******************9765 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.031
                             TPR_2  14 lgdyeeAleafekAleldP 32 
                                       lg+ +eA+++  +Al++++
  gi|330508565|ref|YP_004384993.1| 681 LGNRAEAVKLAGEALAIYE 699
                                       8***************986 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.4e-05     0.016       6      32 ..     473     499 ..     471     501 .. 0.93
   2 !   11.0   0.0   0.00057       0.4       4      30 ..     511     537 ..     509     540 .. 0.89
   3 !   22.5   0.1   1.2e-07   8.6e-05       3      32 ..     550     579 ..     548     581 .. 0.92
   4 !   11.5   0.1   0.00039      0.27       7      32 ..     594     619 ..     594     621 .. 0.94
   5 !   13.0   0.0   0.00013      0.09       4      27 ..     631     654 ..     628     658 .. 0.91
   6 ?    3.4   0.0      0.16   1.1e+02       5      32 ..     672     699 ..     669     701 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldp 32 
                                       n+g++y + g+  +A+ yy++al++ +
  gi|330508565|ref|YP_004384993.1| 473 NIGLAYADRGETGKAIVYYQQALTITR 499
                                       9**********************9976 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00057
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekalel 30 
                                       + nlg++y +lg+  +A+e   +al++
  gi|330508565|ref|YP_004384993.1| 511 LGNLGRAYANLGEPRKAIEHHDQALTI 537
                                       789****************99999887 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 1.2e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                        ++n+g +y  lg++++A+ey+e+a  +++
  gi|330508565|ref|YP_004384993.1| 550 TLCNIGIAYAALGKIHNAIEYFEQAFAIAR 579
                                       589**********************99987 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00039
                                       HHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekaleldp 32 
                                       lg++ ++lg++ +A+  y++al +++
  gi|330508565|ref|YP_004384993.1| 594 LGQANINLGEIRKAIDHYQQALAIAR 619
                                       79********************9987 PP

  == domain 5  score: 13.0 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyeka 27 
                                       +  lg +y++lg+ ++A+e y +a
  gi|330508565|ref|YP_004384993.1| 631 LGSLGTAYKNLGEPHKAIEHYDQA 654
                                       6789*****************998 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.16
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +n+++++  lg+  eA++   +al + +
  gi|330508565|ref|YP_004384993.1| 672 WNMSLVLNGLGNRAEAVKLAGEALAIYE 699
                                       6889999***********9999998865 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.22   1.5e+02      63     117 ..     451     505 ..     443     521 .. 0.66
   2 !   36.9   0.1   3.8e-12   2.6e-09      11     116 ..     518     624 ..     508     629 .. 0.93
   3 !   18.4   0.0   1.6e-06    0.0011       9     116 ..     596     704 ..     593     715 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.22
                          TPR_MalT  63 lqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqq 117
                                       l++a ++a+q +   +   ++  ++  +  +G+  +A+  y+qal+  +e g +q
  gi|330508565|ref|YP_004384993.1| 451 LETAADAAKQMQDRGAEGAHFGNIGLAYADRGETGKAIVYYQQALTITREIGNRQ 505
                                       4555555555555555666777777777778888888888888888777766655 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 3.8e-12
                          TPR_MalT  11 aiasgdaeralelArqALallpe.ddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqq 86 
                                       + + g++++a+e+  qAL++++e  d    ++++ ++G a+   G+ ++A + +++a ++ar+++  ++    l ++
  gi|330508565|ref|YP_004384993.1| 518 YANLGEPRKAIEHHDQALTIFKEiGDRRDEGTTLCNIGIAYAALGKIHNAIEYFEQAFAIAREIEERRNEGICLGCL 594
                                       67899****************9856777889********************************************** PP

                          TPR_MalT  87 aeilvaqGrLheAletyeqalqlateqglq 116
                                       ++  +  G+ ++A+++y+qal+ a+e g +
  gi|330508565|ref|YP_004384993.1| 595 GQANINLGEIRKAIDHYQQALAIAREIGDR 624
                                       ************************998765 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.6e-06
                          TPR_MalT   9 llaiasgdaeralelArqALallpe.ddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallall 84 
                                       +  i+ g++++a+++ +qALa+ +e  d  + +  + +lG+a+   G+ ++A +++ +a+++ r+++ ++    ++ 
  gi|330508565|ref|YP_004384993.1| 596 QANINLGEIRKAIDHYQQALAIAREiGDRRSEGNSLGSLGTAYKNLGEPHKAIEHYDQARTIFREIGDWRGEGNSIW 672
                                       566899999999999999999998856888889999999********999***********9999999999999999 PP

                          TPR_MalT  85 qqaeilvaqGrLheAletyeqalqlateqglq 116
                                         + +l   G   eA+++  +al+ +++ + +
  gi|330508565|ref|YP_004384993.1| 673 NMSLVLNGLGNRAEAVKLAGEALAIYEQIKSP 704
                                       99999999999999999999999999887665 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.3   2.6e-08   1.8e-05      58     181 ..     451     574 ..     417     583 .. 0.90
   2 !   18.6   0.0   1.5e-06     0.001      51     150 ..     604     703 ..     601     717 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.6e-08
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHH CS
                              SNAP  58 flkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrfrraAklkkeiaelyekelgdlek 133
                                        + aA++ ++++++   + ++ + + +y    ++ +A+  +++A +i  e g+ +  + +  +++  y +  g+ +k
  gi|330508565|ref|YP_004384993.1| 451 LETAADAAKQMQDRGAEGAHFGNIGLAYADRgETGKAIVYYQQALTITREIGNRQDEGAILGNLGRAYANL-GEPRK 526
                                       5789999999999999999999999999877588899*************999999999999*****9988.999** PP

                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              SNAP 134 AieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiyekv 181
                                       Aie+ ++A  ++++ +   +  + l+++   +a l+k ++Aie +e+ 
  gi|330508565|ref|YP_004384993.1| 527 AIEHHDQALTIFKEIGDRRDEGTTLCNIGIAYAALGKIHNAIEYFEQA 574
                                       ************999999999999999999999999999999999985 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.5e-06
                                       THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              SNAP  51 weeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrfrraAklkkeiaelyek 126
                                       +++A + +++a ++ ++++++ + +n++   +++yk+  +p++A+e++++A +i+ e g +r  ++   ++  +++ 
  gi|330508565|ref|YP_004384993.1| 604 IRKAIDHYQQALAIAREIGDRRSEGNSLGSLGTAYKNLgEPHKAIEHYDQARTIFREIGDWRGEGNSIWNMSLVLNG 680
                                       6789999999999999999999********999999988999******************99999999999877765 PP

                                       TT--HHHHHHHHHHHHHHHHHTT- CS
                              SNAP 127 elgdlekAieaYekAaelyeqeea 150
                                        lg+  +A++   +A  +yeq ++
  gi|330508565|ref|YP_004384993.1| 681 -LGNRAEAVKLAGEALAIYEQIKS 703
                                       .59999999999999999998665 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0089       6.1      14      32 ..      76      94 ..      63      95 .. 0.90
   2 ?    7.2   0.1     0.013         9       5      27 ..     473     495 ..     473     497 .. 0.91
   3 ?    5.1   0.0     0.059        41       5      21 ..     513     529 ..     513     545 .. 0.80
   4 ?    6.7   0.0     0.018        13       5      25 ..     553     573 ..     552     576 .. 0.93
   5 ?    4.8   0.1     0.076        52       6      27 ..     594     615 ..     594     618 .. 0.90
   6 ?    6.9   0.0     0.016        11       6      29 ..     634     657 ..     633     660 .. 0.88
   7 ?   -0.9   0.0         5   3.5e+03      10      30 ..     678     698 ..     670     701 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0089
                                      HHHHHHHHHHHHHHHH-TT CS
                             TPR_6 14 gdtdkAlealerlikeYPd 32
                                      g+t+ A e+ e+l ++YPd
  gi|330508565|ref|YP_004384993.1| 76 GKTALAYELAEKLARRYPD 94
                                      7999**************8 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerli 27 
                                       +++l+y   g+t kA+ ++++ +
  gi|330508565|ref|YP_004384993.1| 473 NIGLAYADRGETGKAIVYYQQAL 495
                                       58******99**********987 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.059
                                       HHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAle 21 
                                       +l+++y +lg+++kA+e
  gi|330508565|ref|YP_004384993.1| 513 NLGRAYANLGEPRKAIE 529
                                       59******988888886 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealer 25 
                                       +++ +y +lg+  +A+e++e+
  gi|330508565|ref|YP_004384993.1| 553 NIGIAYAALGKIHNAIEYFEQ 573
                                       5899****99**********8 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.076
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerli 27 
                                       l+++ ++lg+ +kA++ +++ +
  gi|330508565|ref|YP_004384993.1| 594 LGQANINLGEIRKAIDHYQQAL 615
                                       799999*99**********987 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlike 29 
                                       l+ +y++lg++ kA+e +++ ++ 
  gi|330508565|ref|YP_004384993.1| 634 LGTAYKNLGEPHKAIEHYDQARTI 657
                                       799****99*********998765 PP

  == domain 7  score: -0.9 bits;  conditional E-value: 5
                                       HHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6  10 yrklgdtdkAlealerlikeY 30 
                                       +  lg+ ++A+++  + +  Y
  gi|330508565|ref|YP_004384993.1| 678 LNGLGNRAEAVKLAGEALAIY 698
                                       445678888888877766655 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.088        61       8      29 ..     475     496 ..     474     501 .. 0.90
   2 !   10.1   0.0    0.0018       1.2       7      31 ..     514     538 ..     509     543 .. 0.90
   3 ?    7.0   0.1     0.018        12       8      31 ..     555     578 ..     553     584 .. 0.86
   4 !    9.9   0.0     0.002       1.4       6      31 ..     593     618 ..     590     622 .. 0.91
   5 !    8.3   0.0    0.0066       4.5       7      28 ..     634     655 ..     630     663 .. 0.90
   6 ?    5.0   0.1      0.08        55      10      43 ..     677     715 ..     673     716 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.088
                            TPR_14   8 aeallalGdpdeAiallrrala 29 
                                       + a++ +G++ +Ai ++++al 
  gi|330508565|ref|YP_004384993.1| 475 GLAYADRGETGKAIVYYQQALT 496
                                       6799****************96 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0018
                            TPR_14   7 laeallalGdpdeAiallrralala 31 
                                       l++a+++lG+p++Ai++ ++al  +
  gi|330508565|ref|YP_004384993.1| 514 LGRAYANLGEPRKAIEHHDQALTIF 538
                                       89******************99766 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.018
                            TPR_14   8 aeallalGdpdeAiallrralala 31 
                                       + a++alG+   Ai+++++a a a
  gi|330508565|ref|YP_004384993.1| 555 GIAYAALGKIHNAIEYFEQAFAIA 578
                                       789****************98765 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.002
                            TPR_14   6 alaeallalGdpdeAiallrralala 31 
                                       +l++a  +lG+ ++Ai+++++ala a
  gi|330508565|ref|YP_004384993.1| 593 CLGQANINLGEIRKAIDHYQQALAIA 618
                                       799********************975 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0066
                            TPR_14   7 laeallalGdpdeAiallrral 28 
                                       l+ a+ +lG+p +Ai+++++a 
  gi|330508565|ref|YP_004384993.1| 634 LGTAYKNLGEPHKAIEHYDQAR 655
                                       789****************995 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.08
                            TPR_14  10 allalGdpdeAiallrrala.....laPddaeawlllaq 43 
                                       +l  lG+ +eA++l+ +ala     + P  ++++l+la+
  gi|330508565|ref|YP_004384993.1| 677 VLNGLGNRAEAVKLAGEALAiyeqiKSPIAERVRLQLAE 715
                                       66779***************5555555666788888886 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   1.2e-12   8.5e-10       8     211 ..      53     246 ..      48     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.2e-12
                                       HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBT.EEEEEEEESXXHH.HHHHHXXHHHHHCCCTT CS
                            NB-ARC   8 viekLlekdelqslvvalvGmgGvGKttlakqilnksdevegrFd.svawvvvsktdks.eeiletilkeLslsedd 82 
                                       +++ L    + +  + +l GmgG+GKt la +  +k   + +r++ + + v +  t  +  +  e+++k++     +
  gi|330508565|ref|YP_004384993.1|  53 LKDLLA-DFDRGATITGLRGMGGIGKTALAYELAEK---LARRYPdGQILVELRGTGPEpMTPAEAMAKVVRIYYPE 125
                                       444444.7888999*******************999...88999758888876554433133344555555444333 PP

                                       SSSS-STTSHHHHHHHHCCCTTEEEEEEEE-SHHHH.....HHHHCHTTSEEEEEESBCCCCCCS-S-EEEEEESS- CS
                            NB-ARC  83 leekeeveslkrklvrlLltkrfllvlDDVweeedwdkigvvlparenrlrvllTTRdeevanavsatsekievelL 159
                                        +   ++ +l+r  + lL + r+l++lD  ++    +++   lp    ++ v++T+R +      +    ++ + +L
  gi|330508565|ref|YP_004384993.1| 126 AKLPGSEAELARIYHSLLHDLRVLMLLDNAFND---RQVRPLLP--PAGCGVIVTSRRKFT--LPG--LVPMDLDVL 193
                                       444433333777778888888************...56677788..89*********9865..233..699****** PP

                                       -HHHHHHHHHHCCTS-GGCHH..CHHH.HHHHHHHCTT-HHHHHHHHHHHC-T CS
                            NB-ARC 160 ekdeawellenkvfekkleekesleev.akeivekckGlPlalkvlggllstk 211
                                        +d+a ell    +++ + + e+l++  + +i+  c+ lPlal + g+ll+  
  gi|330508565|ref|YP_004384993.1| 194 PEDKAVELLLRLWNPEASPSTEQLKDKdLSRIACLCGYLPLALRAAGSLLANS 246
                                       *************999999999877653789999***************9965 PP

>> Rapsyn_N  Rapsyn N-terminal myristoylation and linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00053      0.37      13      78 ..     475     543 ..     473     545 .. 0.84
   2 ?    6.3   0.1     0.015        10      34      78 ..     539     583 ..     534     586 .. 0.85
   3 !   11.8   0.0   0.00028      0.19      45      78 ..     590     623 ..     584     625 .. 0.93
   4 ?   -1.1   0.0         3   2.1e+03      45      76 ..     630     661 ..     623     663 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00053
                          Rapsyn_N  13 GLklyesndtekalrvWrkvLkkt...sdregkfrvLGcLitahsemGkykealefalaqldiareled 78 
                                       GL   +  +t ka+  ++++L  t    +r++   +LG L +a++++G  ++a+e   + l i +e+ d
  gi|330508565|ref|YP_004384993.1| 475 GLAYADRGETGKAIVYYQQALTITreiGNRQDEGAILGNLGRAYANLGEPRKAIEHHDQALTIFKEIGD 543
                                       56666777899999999999977722256889999***************************9999876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.015
                          Rapsyn_N  34 kktsdregkfrvLGcLitahsemGkykealefalaqldiareled 78 
                                       k+  dr +    L  +  a++ +Gk ++a+e+  +   iare+e+
  gi|330508565|ref|YP_004384993.1| 539 KEIGDRRDEGTTLCNIGIAYAALGKIHNAIEYFEQAFAIAREIEE 583
                                       566677777777888888999**********************96 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00028
                          Rapsyn_N  45 vLGcLitahsemGkykealefalaqldiareled 78 
                                        LGcL +a  ++G  ++a++   + l iare+ d
  gi|330508565|ref|YP_004384993.1| 590 CLGCLGQANINLGEIRKAIDHYQQALAIAREIGD 623
                                       59*****************************976 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3
                          Rapsyn_N  45 vLGcLitahsemGkykealefalaqldiarel 76 
                                        LG L ta+ ++G  ++a+e   +   i re+
  gi|330508565|ref|YP_004384993.1| 630 SLGSLGTAYKNLGEPHKAIEHYDQARTIFREI 661
                                       599**********9999999877766666665 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.3   6.6e-05     0.045       1      24 [.     475     498 ..     475     500 .. 0.94
   2 ?    2.2   0.0      0.22   1.5e+02       1      23 [.     515     537 ..     514     537 .. 0.91
   3 ?    3.6   0.6     0.076        53       3      23 ..     557     577 ..     555     579 .. 0.89
   4 !   10.8   0.5   0.00045      0.31       2      23 ..     596     617 ..     595     620 .. 0.85
   5 ?    4.1   0.0     0.053        37       1      20 [.     635     654 ..     635     657 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.6e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkld 24 
                                       G ay ++G+  +Ai  Y++Al ++
  gi|330508565|ref|YP_004384993.1| 475 GLAYADRGETGKAIVYYQQALTIT 498
                                       89*******************986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.22
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                       G+ay  +G+  +Aie+  +Al +
  gi|330508565|ref|YP_004384993.1| 515 GRAYANLGEPRKAIEHHDQALTI 537
                                       899999***********999975 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.076
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkl 23 
                                       ay ++Gk+ +Aie +++A ++
  gi|330508565|ref|YP_004384993.1| 557 AYAALGKIHNAIEYFEQAFAI 577
                                       89**************99765 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00045
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkl 23 
                                       +a   +G++ +Ai +Y++Al++
  gi|330508565|ref|YP_004384993.1| 596 QANINLGEIRKAIDHYQQALAI 617
                                       555668**************98 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.053
                            TPR_11   1 GdayyeqGkyeeAieaYkkA 20 
                                       G ay  +G+  +Aie+Y +A
  gi|330508565|ref|YP_004384993.1| 635 GTAYKNLGEPHKAIEHYDQA 654
                                       66888899999********9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   3.4e-08   2.4e-05       2      52 ..      46      95 ..      45     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.4e-08
                            AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd...g 52
                                      + GR+eel+ Ll+ ++r +     ++ l+G+ G+GK++l+ el++ l ++   g
  gi|330508565|ref|YP_004384993.1| 46 FTGRDEELKDLLADFDRGA----TITGLRGMGGIGKTALAYELAEKLARRypdG 95
                                      89******99999999665....7999********************9996653 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1     5e-05     0.034      58     133 ..     511     584 ..     479     590 .. 0.80
   2 !    9.5   0.1    0.0014         1      17     126 ..     596     694 ..     591     711 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH...HH CS
                           DUF3856  58 haglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem...ia 131
                                          l  a+a+lg+  +a+e  d+al  f   G+ ++deG     ++++ + a++ lG+ ++a+++f++a  +   i+
  gi|330508565|ref|YP_004384993.1| 511 LGNLGRAYANLGEPRKAIEHHDQALTIFKEIGD-RRDEGT----TLCNIGIAYAALGKIHNAIEYFEQAFAIareIE 582
                                       567999**************************9.568886....68999*****************99865522255 PP

                                       H- CS
                           DUF3856 132 er 133
                                       er
  gi|330508565|ref|YP_004384993.1| 583 ER 584
                                       55 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0014
                                       HHHHHHT-HHHHHHHHHHHHHHHTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTS CS
                           DUF3856  17 ekqleegayeeaaasyrkalevsrtipaeeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleq 93 
                                       + +++ g+ ++a ++y++al ++r i    +   eG       +l  a+ +lg+ ++a+e  d+a   f   G+ + 
  gi|330508565|ref|YP_004384993.1| 596 QANINLGEIRKAIDHYQQALAIAREIGDRRS---EG---NSLGSLGTAYKNLGEPHKAIEHYDQARTIFREIGDWRG 666
                                       5566677778888888888888888876654...33...3567899*****************************99 PP

                                       THHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  94 deGklWiaavfsravaleelGrkdealkafrma 126
                                       ++ ++W          l++lG+++ea+k    a
  gi|330508565|ref|YP_004384993.1| 667 EGNSIWNMS-----LVLNGLGNRAEAVKLAGEA 694
                                       999988554.....4456666666665543333 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       5.4   3.7e+03      31      46 ..     353     368 ..     348     369 .. 0.83
   2 !   12.6   0.1   0.00021      0.14       3      47 ..     480     530 ..     478     545 .. 0.84
   3 !    8.5   0.3    0.0043       2.9       4      53 ..     561     616 ..     558     625 .. 0.84
   4 ?    5.1   0.0     0.046        32      10      51 ..     607     654 ..     602     667 .. 0.62
   5 ?    2.9   0.1      0.22   1.6e+02       8      33 ..     692     715 ..     680     717 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.4
                            TPR_19  31 LAeallalgqldeAea 46 
                                       +A  +l++g+  eAe+
  gi|330508565|ref|YP_004384993.1| 353 YAASCLQAGEMGEAEE 368
                                       78889*********97 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00021
                            TPR_19   3 aegdyaeAlalleqalqe.....dpknaearl.lLAeallalgqldeAeal 47 
                                       ++g    A+ +++qal+      + +++ a l +L +a+ +lg++ +A++ 
  gi|330508565|ref|YP_004384993.1| 480 DRGETGKAIVYYQQALTItreigNRQDEGAILgNLGRAYANLGEPRKAIEH 530
                                       789999**********998888866666666669**************986 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0043
                            TPR_19   4 egdyaeAlalleqalqedpk.....naearllL.AeallalgqldeAealLdalpe 53 
                                        g+  +A++++eqa++ + +     n+ + l+   +a ++lg++ +A++  +++++
  gi|330508565|ref|YP_004384993.1| 561 LGKIHNAIEYFEQAFAIAREieerrNEGICLGClGQANINLGEIRKAIDHYQQALA 616
                                       588999*********9955555566******877*************998887765 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.046
                            TPR_19  10 Alalleqalqedpk......naearllLAeallalgqldeAealLdal 51 
                                       A+++++qal+ + +       ++ +  L  a+ +lg++ +A++  d++
  gi|330508565|ref|YP_004384993.1| 607 AIDHYQQALAIAREigdrrsEGNSLGSLGTAYKNLGEPHKAIEHYDQA 654
                                       666666666553332223223333334599999999999998877766 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.22
                            TPR_19   8 aeAlalleqalqedpknaearllLAe 33 
                                        eAla++eq+  ++p  +++rl+LAe
  gi|330508565|ref|YP_004384993.1| 692 GEALAIYEQI--KSPIAERVRLQLAE 715
                                       4677777776..78889999999997 PP

>> DUF2753  Protein of unknown function (DUF2753)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0036       2.5      15      39 ..     482     506 ..     476     511 .. 0.83
   2 ?    0.6   0.0      0.81   5.6e+02      15      39 ..     522     546 ..     514     557 .. 0.82
   3 ?   -0.6   0.0       1.9   1.3e+03      16      39 ..     563     586 ..     549     589 .. 0.81
   4 !    7.1   0.0    0.0083       5.7      13      37 ..     600     624 ..     593     634 .. 0.77
   5 ?   -0.6   0.0         2   1.3e+03      14      35 ..     641     662 ..     633     676 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0036
                           DUF2753  15 edllrsilhyqqalalseelseaee 39 
                                        ++ ++i++yqqal++++e+ ++++
  gi|330508565|ref|YP_004384993.1| 482 GETGKAIVYYQQALTITREIGNRQD 506
                                       56789***************87765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.81
                           DUF2753  15 edllrsilhyqqalalseelseaee 39 
                                        ++ ++i h+ qal++ +e+ ++++
  gi|330508565|ref|YP_004384993.1| 522 GEPRKAIEHHDQALTIFKEIGDRRD 546
                                       578899*************976654 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.9
                           DUF2753  16 dllrsilhyqqalalseelseaee 39 
                                       +  ++i +++qa+a+++e++e+++
  gi|330508565|ref|YP_004384993.1| 563 KIHNAIEYFEQAFAIAREIEERRN 586
                                       456789999*********987654 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0083
                           DUF2753  13 keedllrsilhyqqalalseelsea 37 
                                       +  +  ++i hyqqala+++e+ ++
  gi|330508565|ref|YP_004384993.1| 600 NLGEIRKAIDHYQQALAIAREIGDR 624
                                       55667789*************9554 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 2
                           DUF2753  14 eedllrsilhyqqalalseels 35 
                                         ++ ++i hy qa ++ +e+ 
  gi|330508565|ref|YP_004384993.1| 641 LGEPHKAIEHYDQARTIFREIG 662
                                       467899********99988884 PP

>> DUF4810  Domain of unknown function (DUF4810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0057       3.9      21      70 ..     443     493 ..     435     497 .. 0.92
   2 ?    0.3   0.0       1.5     1e+03      49      77 ..     512     540 ..     509     543 .. 0.86
   3 ?    3.4   0.1      0.16   1.1e+02      48      70 ..     551     573 ..     518     577 .. 0.83
   4 ?    3.4   0.0      0.16   1.1e+02      49      77 ..     632     660 ..     598     664 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0057
                           DUF4810  21 skekqieklekiiekaeakgkkvpPGly.AelGllylkegkkeeaieafek 70 
                                       ++++qi  le + + a++ + + + G +  ++Gl y+++g++ +ai ++++
  gi|330508565|ref|YP_004384993.1| 443 HPQEQIRWLETAADAAKQMQDRGAEGAHfGNIGLAYADRGETGKAIVYYQQ 493
                                       6899**********************98589****************9997 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.5
                           DUF4810  49 AelGllylkegkkeeaieafekEkelfPE 77 
                                        +lG  y++ g+  +aie+ ++  + f E
  gi|330508565|ref|YP_004384993.1| 512 GNLGRAYANLGEPRKAIEHHDQALTIFKE 540
                                       689999***********999988887776 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.16
                           DUF4810  48 yAelGllylkegkkeeaieafek 70 
                                        +++G+ y+  gk ++aie+fe+
  gi|330508565|ref|YP_004384993.1| 551 LCNIGIAYAALGKIHNAIEYFEQ 573
                                       5899*****************97 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.16
                           DUF4810  49 AelGllylkegkkeeaieafekEkelfPE 77 
                                         lG+ y + g+ ++aie++++ ++ f E
  gi|330508565|ref|YP_004384993.1| 632 GSLGTAYKNLGEPHKAIEHYDQARTIFRE 660
                                       679*******************9999988 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.8   1.3e+03      18      33 ..     473     488 ..     470     489 .. 0.89
   2 !    7.3   0.0    0.0099       6.8      16      34 .]     511     529 ..     503     529 .. 0.90
   3 ?    0.0   0.0       2.1   1.5e+03      16      33 ..     551     568 ..     548     569 .. 0.83
   4 ?   -0.2   0.1       2.4   1.7e+03      16      33 ..     598     615 ..     594     616 .. 0.84
   5 ?    5.0   0.0     0.054        37      14      34 .]     629     649 ..     626     649 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.8
                            TPR_17  18 nLAelllknGdlmtAr 33 
                                       n + +++ +G++++A+
  gi|330508565|ref|YP_004384993.1| 473 NIGLAYADRGETGKAI 488
                                       8899********9996 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0099
                            TPR_17  16 ynnLAelllknGdlmtArq 34 
                                       + nL+++++++G++++A++
  gi|330508565|ref|YP_004384993.1| 511 LGNLGRAYANLGEPRKAIE 529
                                       669**************86 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 2.1
                            TPR_17  16 ynnLAelllknGdlmtAr 33 
                                       ++n + +++ +G+   A+
  gi|330508565|ref|YP_004384993.1| 551 LCNIGIAYAALGKIHNAI 568
                                       799999**9999988776 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.4
                            TPR_17  16 ynnLAelllknGdlmtAr 33 
                                         nL+e+ + +  +++A+
  gi|330508565|ref|YP_004384993.1| 598 NINLGEIRKAIDHYQQAL 615
                                       569999999999999997 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.054
                            TPR_17  14 daynnLAelllknGdlmtArq 34 
                                       +++  L+++++++G++ +A++
  gi|330508565|ref|YP_004384993.1| 629 NSLGSLGTAYKNLGEPHKAIE 649
                                       57778*************986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.4e-05    0.0093       4     100 ..      63     155 ..      61     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst....sskdllrellralglelkaerlsse 76 
                                       +a+i+ + G  G+GKT l+ +l+e+l ++      ++++++v+l + +    ++++ + +++r++  e+k  ++s+ 
  gi|330508565|ref|YP_004384993.1|  63 GATITGLRGMGGIGKTALAYELAEKLARR-----YPDGQILVELRGTGpepmTPAEAMAKVVRIYYPEAKL-PGSEA 133
                                       56677777889**************9555.....599999887777777777**************77777.66666 PP

                            AAA_22  77 ellealeqalraravielliiDEa 100
                                       el +  +  l++ +v  l+++D+a
  gi|330508565|ref|YP_004384993.1| 134 ELARIYHSLLHDLRV--LMLLDNA 155
                                       666666666666666..*****98 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.2e-05     0.057       5      32 ..      69      96 ..      66     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.2e-05
                                      EEC-TTTCHHHHHHHHHHHHCTS-SCCC CS
                             NACHT  5 lqGeaGsGKTtLlqklalawaegklpqg 32
                                      l+G  G+GKT+L+ +la+++a+++++++
  gi|330508565|ref|YP_004384993.1| 69 LRGMGGIGKTALAYELAEKLARRYPDGQ 96
                                      7899*******************99885 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       0.6   4.2e+02      61      76 ..     352     367 ..     343     369 .. 0.88
   2 ?   -0.7   0.0       2.4   1.7e+03      29      44 ..     514     529 ..     475     541 .. 0.55
   3 ?    7.0   0.1      0.01       6.9      39      81 ..     571     613 ..     556     614 .. 0.80
   4 ?    2.2   0.0      0.31   2.1e+02       5      49 ..     611     654 ..     610     661 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.6
                                       HHHHHHHHTT-HHHHH CS
                            ANAPC3  61 lfAqcllkLkkyeeAi 76 
                                       ++A ++l+ +++ eA+
  gi|330508565|ref|YP_004384993.1| 352 IYAASCLQAGEMGEAE 367
                                       89************97 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.4
                                       HHHHHHHTT-HHHHHH CS
                            ANAPC3  29 lAlclylngqykrAye 44 
                                       l+ ++ ++g+  +A+e
  gi|330508565|ref|YP_004384993.1| 514 LGRAYANLGEPRKAIE 529
                                       2333333333333333 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.01
                                       HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  39 ykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +++A+ ++r+ +++ +   c+ +++q+ + L+++ +Ai++++ 
  gi|330508565|ref|YP_004384993.1| 571 FEQAFAIAREIEERRNEGICLGCLGQANINLGEIRKAIDHYQQ 613
                                       78999999999555555569999***************99875 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                            ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka 49 
                                       y+ A+ +a  +    +   +++  l+ ++ ++g+ ++A+e +++a
  gi|330508565|ref|YP_004384993.1| 611 YQQALAIAREIG-DRRSEGNSLGSLGTAYKNLGEPHKAIEHYDQA 654
                                       666666666666.66666667777888888888888888887776 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.18   1.2e+02     127     175 ..     492     540 ..     470     547 .. 0.84
   2 ?    6.3   0.0     0.012         8     116     175 ..     601     660 ..     595     665 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.18
                           Wzy_C_2 127 aaklalarklihlsPepavierlilslallGdedeAeqilararalfpe 175
                                       ++ l  +r++  ++ e a++ +l  ++a lG + +A  + ++a  +f e
  gi|330508565|ref|YP_004384993.1| 492 QQALTITREIGNRQDEGAILGNLGRAYANLGEPRKAIEHHDQALTIFKE 540
                                       5566666666666667788889999******************999976 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                           Wzy_C_2 116 lgllplspenlaaklalarklihlsPepavierlilslallGdedeAeqilararalfpe 175
                                       lg + +  +++++ la ar++  +  e   +  l  ++  lG + +A  ++++ar +f e
  gi|330508565|ref|YP_004384993.1| 601 LGEIRKAIDHYQQALAIAREIGDRRSEGNSLGSLGTAYKNLGEPHKAIEHYDQARTIFRE 660
                                       55555666788999999999999999999999999***********************76 PP

>> DUF4167  Domain of unknown function (DUF4167)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.7   1.8e+03      24      45 ..     124     145 ..     111     148 .. 0.87
   2 ?    9.4   0.1    0.0017       1.2      59      75 .]     368     384 ..     360     384 .. 0.84
   3 ?   -2.1   0.0       6.5   4.5e+03      14      41 ..     626     653 ..     618     655 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.7
                           DUF4167  24 pdvkvrGtAqqliekYkqLard 45 
                                       p+ k++G+ ++l+  Y++L +d
  gi|330508565|ref|YP_004384993.1| 124 PEAKLPGSEAELARIYHSLLHD 145
                                       899**************99887 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0017
                           DUF4167  59 lQhAeHYfrilaeaqeq 75 
                                         hAeHY r+l++ +eq
  gi|330508565|ref|YP_004384993.1| 368 ERHAEHYWRVLSASNEQ 384
                                       57**********99875 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 6.5
                           DUF4167  14 srnrvfdsngpdvkvrGtAqqliekYkq 41 
                                       s+ ++  s g + k  G +++ ie Y q
  gi|330508565|ref|YP_004384993.1| 626 SEGNSLGSLGTAYKNLGEPHKAIEHYDQ 653
                                       4556777888889999999999999987 PP

>> ComR_TPR  ComR tetratricopeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.1   7.5e+02     194     214 ..     484     504 ..     478     507 .. 0.86
   2 ?    8.4   0.0     0.002       1.4     139     214 ..     550     624 ..     526     627 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHTT-H CS
                          ComR_TPR 194 iekAkelYqkAilfakllgde 214
                                         kA  +Yq+A+++++ +g++
  gi|330508565|ref|YP_004384993.1| 484 TGKAIVYYQQALTITREIGNR 504
                                       679999*********999986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHT--TTHHHHHHHHHHHHHHTS--HHHHHHHHHHHHHHHHHTT-H CS
                          ComR_TPR 139 vllsaltvllklkeyeklekllkvlnkimektqdfqkkpivlmlewKyylkvkkdiekAkelYqkAilfakllgde 214
                                       +l ++   ++ l++ ++  ++++++  i +++++  +  i+l    +  +    +i+kA  +Yq+A+++a+ +gd+
  gi|330508565|ref|YP_004384993.1| 550 TLCNIGIAYAALGKIHNAIEYFEQAFAIAREIEERRNEGICLGCLGQANI-NLGEIRKAIDHYQQALAIAREIGDR 624
                                       55666666777777777777777777788888888888888888888888.7799******************996 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.92   6.4e+02      36      58 ..     475     497 ..     449     511 .. 0.78
   2 ?    0.8   0.0      0.78   5.4e+02      35      50 ..     514     529 ..     510     550 .. 0.85
   3 ?    6.6   0.1     0.012       8.4      35      61 ..     554     580 ..     540     587 .. 0.87
   4 ?    3.4   0.1      0.13        88      36      65 ..     595     624 ..     593     626 .. 0.87
   5 ?   -2.3   0.0       7.6   5.3e+03      36      53 ..     635     652 ..     634     654 .. 0.80
   6 ?   -2.3   0.0       7.3     5e+03      56      72 ..     695     713 ..     676     714 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.92
                             TPR_9  36 GlllaqlGclsaAladLeaylal 58 
                                       Gl++a +G + +A+   +++l +
  gi|330508565|ref|YP_004384993.1| 475 GLAYADRGETGKAIVYYQQALTI 497
                                       88888888888888888887754 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.78
                             TPR_9  35 RGlllaqlGclsaAla 50 
                                        G+++a lG +++A++
  gi|330508565|ref|YP_004384993.1| 514 LGRAYANLGEPRKAIE 529
                                       699**********997 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                             TPR_9  35 RGlllaqlGclsaAladLeaylalapd 61 
                                        G+++a lG ++ A++ +e++ a+a +
  gi|330508565|ref|YP_004384993.1| 554 IGIAYAALGKIHNAIEYFEQAFAIARE 580
                                       599****************99988765 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.13
                             TPR_9  36 GlllaqlGclsaAladLeaylalapdapda 65 
                                       G+++  lG +++A++  +++la+a +  d+
  gi|330508565|ref|YP_004384993.1| 595 GQANINLGEIRKAIDHYQQALAIAREIGDR 624
                                       8999*****************999876665 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 7.6
                             TPR_9  36 GlllaqlGclsaAladLe 53 
                                       G ++  lG +++A++  +
  gi|330508565|ref|YP_004384993.1| 635 GTAYKNLGEPHKAIEHYD 652
                                       7789999****9998665 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 7.3
                             TPR_9  56 lalap..dapdaeairaqL 72 
                                       la+ +  + p ae++r qL
  gi|330508565|ref|YP_004384993.1| 695 LAIYEqiKSPIAERVRLQL 713
                                       4444444567777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (718 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.71u 0.24s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 4830.08
//
Query:       gi|330508566|ref|YP_004384994.1|  [L=61]
Description: hypothetical protein MCON_2792 [Methanosaeta concilii GP6]
Scores for complete 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-10   38.9   0.0    8.4e-10   38.8   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
     0.0077   16.2   0.0     0.0078   16.2   0.0    1.1  1  DUF1902          Domain of unknown function (DUF1902)


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   9.3e-14   8.4e-10       1      49 [.       3      51 ..       3      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 9.3e-14
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegli 49
                                      + i+iekd++  y    Pdl+Gc s g+ le+a++n++eai   l++ +
  gi|330508566|ref|YP_004384994.1|  3 FNIIIEKDDEGIYVAECPDLKGCLSEGEGLEDALENINEAIIGCLKSRL 51
                                      689**************************************98887655 PP

>> DUF1902  Domain of unknown function (DUF1902)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.7e-07    0.0078       9      48 ..      10      48 ..       2      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.7e-07
                                      ETTTTEEEEE-SSSTT---EESSHHHHHHHHHHHHHHHHH CS
                           DUF1902  9 DeeAgVWvaesddipGlvteaetleeLlkkleamipdlLe 48
                                      D+  g++vae+ d++G   e e le  l+ ++ +i   L+
  gi|330508566|ref|YP_004384994.1| 10 DD-EGIYVAECPDLKGCLSEGEGLEDALENINEAIIGCLK 48
                                      54.49************************99999977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 445.87
//
Query:       gi|330508567|ref|YP_004384995.1|  [L=381]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.3e-16   58.8   0.0    1.7e-15   57.8   0.0    1.5  2  Radical_SAM  Radical SAM superfamily
      8e-08   32.7   0.2    1.6e-07   31.7   0.2    1.5  1  SPASM        Iron-sulfur cluster-binding domain
    0.00053   20.3   0.0     0.0009   19.5   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
     0.0043   17.2   0.0     0.0073   16.4   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 !   57.8   0.0   3.8e-19   1.7e-15       3     165 ..      96     246 ..      94     248 .. 0.89
   2 ?   -3.6   0.0       2.8   1.2e+04      27      44 ..     341     358 ..     336     362 .. 0.72

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 3.8e-19
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                       v+++C+++C +C+ p+     + g++ls + i+  + ++  ++g   v++ ggep+l++d+ +l+    ++    + 
  gi|330508567|ref|YP_004384995.1|  96 VVKACPNDCLHCSAPS-----RQGQILSSDVIKGAISQA-LDMGSYLVTFDGGEPMLRKDLPDLVSSVDQR---AVA 163
                                       6899***********6.....9*****************.8*****************************8...788 PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGe 155
                                       +++++ ++l   e ++ l+e+g+  v ++++++ +e  +++++ r++ f++ l +++++ eag+  v  ++v  p  
  gi|330508567|ref|YP_004384995.1| 164 TSFTSGYHLT-LELARQLKEAGLYAVRISIDSPIEE-QHDRFRgRKGAFQDALSGVRNALEAGLL-VDLFMVTSP-H 236
                                       8888888886.*************************.5555555********************9.666666666.8 PP

                                       SHHHHHHHHH CS
                                       xxxxxxxxxx RF
                       Radical_SAM 156 ndeeleelle 165
                                       n + le+ ++
  gi|330508567|ref|YP_004384995.1| 237 NIDYLEDAFS 246
                                       8888887765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  27 rslsveeileevkelkae 44 
                                       +++s+eei +e+ ++ + 
  gi|330508567|ref|YP_004384995.1| 341 KEKSLEEIWREMTRYPWF 358
                                       678899999998887655 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.2   3.6e-11   1.6e-07       1      53 [.     312     359 ..     312     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3.6e-11
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse.eyqefr 53 
                                       Cfa++r + ++ dG   pC ++      +l +Gni+e+sleeIw+   +y +f+
  gi|330508567|ref|YP_004384995.1| 312 CFAGRRWIHVDGDGVALPCAYM------PLGFGNIKEKSLEEIWREMtRYPWFK 359
                                       9******************333......7***************9887888887 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 !   19.5   0.0     2e-07    0.0009      12     123 ..      97     200 ..      89     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2e-07
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdi 88 
                                       v+ C+  C  C +++    ++g+  ++++++ +i ++ +     +t+ GGEP+l   +++l +lv +v ++++    
  gi|330508567|ref|YP_004384995.1|  97 VKACPNDCLHCSAPS----RQGQILSSDVIKGAISQALDMGSYLVTFDGGEPML---RKDLPDLVSSVDQRAV--AT 164
                                       788999999988554....6788888899999999998999*************...99*************9..35 PP

                           Fer4_12  89 wlytgytle.elskkekeellkeidvlvdGkfeesl 123
                                         ++gy l  el ++ ke  l  + + +d + ee+ 
  gi|330508567|ref|YP_004384995.1| 165 SFTSGYHLTlELARQLKEAGLYAVRISIDSPIEEQH 200
                                       666777766245455667778888888888887654 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 !   16.4   0.0   1.6e-06    0.0073       6      97 ..      98     178 ..      95     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-06
                           Fer4_14   6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekk 82 
                                         C+  C  C   +    + g++ ++++++  +   ++ ++    +++ GGeP++    k+l +lv+ + ++   + 
  gi|330508567|ref|YP_004384995.1|  98 KACPNDCLHCSAPS----RQGQILSSDVIKGAI--SQALDMGSYLVTFDGGEPMLR---KDLPDLVSSVDQRA--VA 163
                                       57999999998776....889999999999999..6666666688*********55...9999*********9..99 PP

                           Fer4_14  83 iwletngtleielek 97 
                                         + +++ l +el +
  gi|330508567|ref|YP_004384995.1| 164 TSFTSGYHLTLELAR 178
                                       9999***99999883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.19s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3075.25
//
Query:       gi|330508568|ref|YP_004384996.1|  [L=311]
Description: polyprenyl synthetase [Methanosaeta concilii GP6]
Scores for 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-45  155.8   0.0    1.3e-45  155.5   0.0    1.3  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.5   0.0     7e-50   1.3e-45       4     226 ..      27     230 ..      24     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 155.5 bits;  conditional E-value: 7e-50
                                       HHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCH CS
                   polyprenyl_synt   4 leealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGn 80 
                                       l e+l+y+++a+GKr+Rpl+++l+aeal+ ++    ++ ++a ++el+haasLvhDDi D+ + RRG p+a +++G 
  gi|330508568|ref|YP_004384996.1|  27 LGEILSYVLSAPGKRVRPLILILSAEALGTPP---AQSISAALAIELVHAASLVHDDILDHGIERRGSPSALERFGP 100
                                       67899************************665...789*************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHH CS
                   polyprenyl_synt  81 klAindgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfal 157
                                       ++++++gd l +r+  l++ +  ++  +++ fs++++++ eG+l+dl ++        s e+y + +++KTa+lf++
  gi|330508568|ref|YP_004384996.1| 101 EASLLAGDWLISRSIDLISGY--SQ-PVIRAFSRACMDMSEGELMDL-SC---AG---SPEDYYQCITRKTASLFSA 167
                                       *********************..55.9********************.34...23...4889*************** PP

                                       HHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHC CS
                   polyprenyl_synt 158 pvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalel 226
                                       +++++ l++ga +e++++l+++gl+lGl +Q+ DD+  + g   + gK      q+  +tlp ++a + 
  gi|330508568|ref|YP_004384996.1| 168 SAKIGGLISGAGEEDVARLESYGLHLGLGYQVLDDLEEFLGL--DQGKS----SQKTSVTLPKIYASRS 230
                                       ***********9************************999976..44666....7777888888887773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2351.97
//
Query:       gi|330508569|ref|YP_004384997.1|  [L=196]
Description: hypothetical protein MCON_2795 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1422.30
//
Query:       gi|330508570|ref|YP_004384998.1|  [L=138]
Description: CoA-binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-33  115.9   0.0    1.5e-33  115.7   0.0    1.0  1  CoA_binding_2  CoA binding domain
      5e-06   27.1   0.0    6.8e-06   26.7   0.0    1.2  1  CoA_binding    CoA binding domain


Domain annotation for each model (and alignments):
>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   0.0   1.7e-37   1.5e-33       1     114 [.      18     133 ..      18     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 1.7e-37
                                       --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-..SEETTEES----T....T--EEEE-S-HHHHGGGHHHH CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpke..eeilgekvyaslaedpepvdlvdvftppeatpeivkea 75 
                                       rti VvG s++p k++y v + l++hg++ + Vnp+   ++ilgekv as+++ pe++d+vdvf++p+a+p++++ea
  gi|330508570|ref|YP_004384998.1|  18 RTICVVGISPDPYKPSYFVSEVLKRHGFKLYLVNPNCagQTILGEKVLASIQDVPEDIDIVDVFRRPSAVPALAEEA 94 
                                       79**********************************999*************758********************** PP

                                       HHH--SEEEE-TT---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  76 lalgakavwlqpgsedeeaaelaeeagirvvgdrCilve 114
                                       +++g  ++w+qpg+e++ea+++++++g rvv  rC ++e
  gi|330508570|ref|YP_004384998.1|  95 KKKGFGVFWMQPGTESPEAIKRLDREGFRVVAGRCAKIE 133
                                       *************************************98 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   7.6e-10   6.8e-06       5      91 ..      19     103 ..      15     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 7.6e-10
                                       EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHH CS
                       CoA_binding   5 kviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavde 81 
                                        ++v+G++    +  y ++e lk++  +++ vnp+ +g+++lg +v  s+++++e+  +d+  ++  + ++ + ++e
  gi|330508570|ref|YP_004384998.1|  19 TICVVGISPDPYKPSYFVSEVLKRHGFKLYLVNPNCAGQTILGEKVLASIQDVPED--IDIVDVFRRPSAVPALAEE 93 
                                       699************99***************************************..8888889999999999999 PP

                                       HHHTT-SEEE CS
                       CoA_binding  82 lveagikgiv 91 
                                       + ++g  + +
  gi|330508570|ref|YP_004384998.1|  94 AKKKGFGVFW 103
                                       9888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 983.69
//
Query:       gi|330508571|ref|YP_004384999.1|  [L=537]
Description: hypothetical protein MCON_2797 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-41  140.3   0.0    6.9e-41  139.0   0.0    1.7  1  DUF4277    Domain of unknown function (DUF4277)
      9e-11   41.8   0.0    2.4e-10   40.4   0.0    1.7  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.043   13.7   0.3       0.11   12.5   0.3    1.6  1  AT_hook    AT hook motif


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.0   0.0   1.2e-44   6.9e-41       3     109 .]       7     113 ..       5     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.0 bits;  conditional E-value: 1.2e-44
                           DUF4277   3 vksldhlglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfpeffedkplerLlgegve 79 
                                       +  ++hlg+vag +d+l+la++id+++pk+ ++++ ++ ++ka+ilngLg++ ++Lylfp+ff+++p+e+Llg+g+ 
  gi|330508571|ref|YP_004384999.1|   7 SYLIGHLGIVAGSFDALNLADVIDRVLPKRGSRNLPHSVIIKAMILNGLGYTGQRLYLFPNFFKTIPTEKLLGKGIC 83 
                                       5669************************************************************************* PP

                           DUF4277  80 aehlnddrlgrtLDklyeagvtklfteial 109
                                       +++lndd++grtLD++y++g+t+lf+ei+l
  gi|330508571|ref|YP_004384999.1|  84 PTDLNDDVVGRTLDAIYKYGATELFNEISL 113
                                       ***************************985 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0     4e-14   2.4e-10      41     213 ..     171     454 ..     128     455 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 4e-14
                         DDE_Tnp_1  41 avdtrsglilsvvitpgnvhdskglkqlldelrpr....kgklvlaDaGYasaelldtleekgvdyiirlkkntkly 113
                                       +v  + gl+l  +  +gn++d k l ++++  ++     ++   +aD++  ++e+++ +     ++i  ++  +++ 
  gi|330508571|ref|YP_004384999.1| 171 MVTNQFGLPLFTEAYSGNKSDKKSLMEMIQKTQQAidldDDNFWVADSALYTEENIKLMG-TETKWITHMPATVAEA 246
                                       566777999999999999999999999999999989999999999999977799999998.5555555554444444 PP

                         DDE_Tnp_1 114 rk..................................gaeskrrgrlrkhdrnkiltksqkrrnk............. 143
                                       +                                     + + ++r +k +++ki +++ ++                
  gi|330508571|ref|YP_004384999.1| 247 QEllssnlnmipgsdpryafyatdinyggvpqravvVWSKEMNERNEKTFERKIEKETIEAGKDlkklmrkkfacip 323
                                       445555666656577777777666666555555554244446777777777777777777666699999999***** PP

                         DDE_Tnp_1 144 ............................................................skkekgdvyyvtntnse 160
                                                                                                    + +k+ + +v+  n  
  gi|330508571|ref|YP_004384999.1| 324 dadndlrlwqsshphhlldnvrvvpvmekaekkrgrpkkdelltasymiqgeiklneealIEARKNLGRFVLASNQV 400
                                       ***************************************************************************** PP

                         DDE_Tnp_1 161 llsaeevaelyrlRwqiErvFkwlkrk.fgldrlryrglnrveaqllllllaln 213
                                       +l++e + ++y+ +  +Er F++lk+k f+   +++++ +r+ea  +++ l+l+
  gi|330508571|ref|YP_004384999.1| 401 DLDPEVMLNYYKGQQAVERGFRFLKDKsFHVSEVYLKKEERIEALCMIMVLSLL 454
                                       ************************************************999986 PP

>> AT_hook  AT hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   1.8e-05      0.11       2      10 ..     355     363 ..     354     365 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                           AT_hook   2 RkRGRPrKa 10 
                                       +kRGRP+K+
  gi|330508571|ref|YP_004384999.1| 355 KKRGRPKKD 363
                                       9*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 3521.30
//
Query:       gi|330508572|ref|YP_004385000.1|  [L=285]
Description: hypothetical protein MCON_2798 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2123.19
//
Query:       gi|330508573|ref|YP_004385001.1|  [L=51]
Description: hypothetical protein MCON_2802 [Methanosaeta concilii GP6]
Scores for complete 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   36.5   0.0    4.5e-09   36.5   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   2.5e-13   4.5e-09      16      53 ..       2      38 ..       1      50 [. 0.83

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.5e-13
                   HicB_lk_antitox 16 vvPdlpGcfsagdtleeaianakeaielhlegliedge 53
                                      ++P lpGc+s g t eea++n++eaiel+le  +ed+ 
  gi|330508573|ref|YP_004385001.1|  2 LFPALPGCISEGSTREEALKNIQEAIELYLEP-VEDDL 38
                                      69*****************************9.45554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 420.77
//
Query:       gi|330508574|ref|YP_004385002.1|  [L=109]
Description: IS3/IS66 family element, Orf1 protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-10   39.8   0.1    6.4e-10   39.2   0.1    1.5  1  HTH_Tnp_1  Transposase
     0.0043   16.8   0.0     0.0089   15.8   0.0    1.7  1  HTH_23     Homeodomain-like domain
      0.005   16.9   0.0      0.011   15.8   0.0    1.6  1  HTH_28     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.033   14.0   0.3      0.074   12.9   0.3    1.6  1  PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein k
      0.058   13.9   0.1       0.12   12.8   0.0    1.5  2  DUF4733    Domain of unknown function (DUF4733)


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.1   1.8e-13   6.4e-10       2      74 ..       3      75 ..       2     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.8e-13
                         HTH_Tnp_1  2 rrrrrwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyr.egeeaspaefeltaleeenrelkrel 74
                                      ++rrr+++ fK+++++e  e+gk+ +++Ar++g++p+   +W+ +     e+a   +    + +++++el+r+l
  gi|330508574|ref|YP_004385002.1|  3 KTRRRYDRDFKISVLAEL-EAGKPLAQIAREYGIHPSLPCRWKVELAeNPEKAFMGNGNKYKDQAKIAELERLL 75
                                      79***************9.***********************99886433333333333344466777777765 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   2.5e-06    0.0089       8      33 ..      14      39 ..       2      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-06
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrT 33
                                      +++l  l  G++ ++IAre+g++++ 
  gi|330508574|ref|YP_004385002.1| 14 ISVLAELEAGKPLAQIAREYGIHPSL 39
                                      567888888**************985 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.1e-06     0.011       1      27 [.      12      38 ..      12      39 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.1e-06
                            HTH_28  1 qRleiikllaaGhsvreaArelgisrr 27
                                      +++ ++ +l aG++ +++Are+gi+++
  gi|330508574|ref|YP_004385002.1| 12 FKISVLAELEAGKPLAQIAREYGIHPS 38
                                      7999********************996 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.1e-05     0.074       9      28 ..      67      86 ..      61      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                         PKcGMP_CC  9 RIRELEkrlaekdeEIqELr 28
                                      +I+ELE+ l + ++EI  L+
  gi|330508574|ref|YP_004385002.1| 67 KIAELERLLGQAHAEIDLLK 86
                                      9***************9888 PP

>> DUF4733  Domain of unknown function (DUF4733)
   #    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      29      67 ..       4      42 ..       1      52 [. 0.88
   2 ?   -2.0   0.0       1.4     5e+03      32      32 ..      91      91 ..      64     106 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.4e-05
                           DUF4733 29 qplrpqravleelsaplelsqplsgllddyGilPkhPrp 67
                                        +r+ r +   + a le  +pl+++  +yGi+P  P +
  gi|330508574|ref|YP_004385002.1|  4 TRRRYDRDFKISVLAELEAGKPLAQIAREYGIHPSLPCR 42
                                      56899999999***********************99976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                           DUF4733 32 r 32
                                       
  gi|330508574|ref|YP_004385002.1| 91 M 91
                                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 796.56
//
Query:       gi|330508575|ref|YP_004385003.1|  [L=292]
Description: transposase IS3 family protein integrase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-25   89.8   0.0    2.2e-25   89.1   0.0    1.3  1  rve            Integrase core domain
    2.7e-19   69.1   0.3    1.9e-18   66.3   0.3    2.1  2  HTH_21         HTH-like domain
    3.8e-16   58.6   0.1    9.1e-16   57.4   0.1    1.7  1  rve_3          Integrase core domain
    4.7e-08   33.1   3.6    9.4e-08   32.1   2.4    2.1  2  rve_2          Integrase core domain
    0.00016   21.9   0.3    0.00028   21.1   0.3    1.4  1  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.027   14.6   0.1         12    6.1   0.0    2.4  2  GP3_package    DNA-packaging protein gp3
      0.041   14.1   0.0       0.11   12.7   0.0    1.7  1  HTH_Tnp_Tc3_2  Transposase
      0.049   13.8   0.1       0.17   12.0   0.0    1.9  2  HTH_Tnp_1_2    Helix-turn-helix of insertion element transpos


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.0   9.9e-29   2.2e-25       5     117 ..     127     239 ..     124     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 9.9e-29
                               rve   5 gelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve..pervlsDngseyt 79 
                                       ++ w +D+t+v++      ++l+v++d +sr ++++ ls+++ ++++  +l +a++++ ++    ++++sD+g +y+
  gi|330508575|ref|YP_004385003.1| 127 NQAWASDITYVQLQHE--HIFLAVILDLYSRKCIGWELSRSIRSDLAMSALAKALKNRSKESleGLIHHSDQGVQYA 201
                                       899*********6655..5*****************************************8899************* PP

                               rve  80 skafrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                       sk++ + l+ ++i++s++r+g+p+dn+ +E+f++tlk 
  gi|330508575|ref|YP_004385003.1| 202 SKDYVDCLKAHDIQISMSRKGNPYDNAFAESFIKTLKV 239
                                       ************************************95 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.3   8.5e-22   1.9e-18       6      58 ..      49      99 ..      45     101 .. 0.90
   2 ?   -0.0   0.0      0.45     1e+03      13      33 ..     257     277 ..     248     292 .] 0.66

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 8.5e-22
                            HTH_21  6 llalireifeeskgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgvqrr 58
                                      l ++i+ei  e  + YGyrri+aeL+++g+ +vnhkrV RlMr+++L+++ ++
  gi|330508575|ref|YP_004385003.1| 49 LVNQIQEIALEF-PYYGYRRITAELQNRGY-AVNHKRVLRLMRQEKLLCYKKK 99
                                      7899********.9**************87.5*****************9544 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.45
                            HTH_21  13 ifeeskgrYGyrriwaeLrre 33 
                                       i++    +Y ++r++ +L+ +
  gi|330508575|ref|YP_004385003.1| 257 ICNFIENVYNHKRLHSALNYR 277
                                       555445577788888888854 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1   4.1e-19   9.1e-16       1      67 []     212     279 ..     212     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 4.1e-19
                             rve_3   1 lgielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawred.YNteRPHssLgykTP 67 
                                       ++i++s+++ g P++N+++Esf++tl+ e ++ + ++++++a +++ +++e  YN++R Hs+L+y++P
  gi|330508575|ref|YP_004385003.1| 212 HDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHSALNYRSP 279
                                       689***************************************99999999866*************99 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.4     3e+03      21      33 ..     196     208 ..     184     209 .. 0.74
   2 !   32.1   2.4   4.2e-11   9.4e-08       1      48 [.     231     283 ..     231     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                             rve_2  21 eeleaaiedYIew 33 
                                       + ++ a +dY+++
  gi|330508575|ref|YP_004385003.1| 196 QGVQYASKDYVDC 208
                                       556788999*986 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 4.2e-11
                             rve_2   1 EsfFgsLKtElvygetfktleeleaaiedYIew.YNnkRlk....glsPvqYr 48 
                                       Esf ++LK+E vy  +++t+e +   i ++Ie  YN+kRl+    + sPvq++
  gi|330508575|ref|YP_004385003.1| 231 ESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHsalnYRSPVQFE 283
                                       9******************************988*****988888*******8 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   1.3e-07   0.00028       2     139 ..     128     271 ..     127     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                     DDE_Tnp_IS240   2 kswrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkek.lepeeivtDkasayasalke 76 
                                       ++w+ D Tyv+ + +  +l  ++D  +r  +++ +s     + a  +l kalk+ + ++ e ++    +  + a k 
  gi|330508575|ref|YP_004385003.1| 128 QAWASDITYVQLQHEHIFLAVILDLYSRkCIGWELSRSIRSDLAMSALAKALKNRSkESLEGLIHHSDQGVQYASKD 204
                                       68************************************999************998455555665555555555555 PP

                     DDE_Tnp_IS240  77 lkr...egelfdevshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktl.agfeavknlrkgh 139
                                         +     + + ++s+   +y n   Es  +tlK++  + +  ++++ a + + + +e v+n+++ h
  gi|330508575|ref|YP_004385003.1| 205 YVDclkAHDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNIcNFIENVYNHKRLH 271
                                       44411123556788899999***************************99877625679999999977 PP

>> GP3_package  DNA-packaging protein gp3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0053        12      49      78 ..      19      55 ..      15      63 .. 0.82
   2 ?    6.1   0.0    0.0052        12      51      90 ..     236     275 ..     199     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0053
                                      HHHHT--HHHHHHHGG..SHHH.......HHHHHHHH CS
                       GP3_package 49 alyLgisrstlkeyekrkrefs.......etierikq 78
                                      +l+L++srs  +e+ kr+++f        +++++i++
  gi|330508575|ref|YP_004385003.1| 19 CLALDVSRSGYYEWLKRSEKFTaensessDLVNQIQE 55
                                      899***************9998666666666666555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0052
                                       HHT--HHHHHHHGG..SHHHHHHHHHHHHHHHHHHHHHHT CS
                       GP3_package  51 yLgisrstlkeyekrkrefsetierikqivenqqiegala 90 
                                        L + + +l+eye+ +  f ++ + i+++ +++++  al 
  gi|330508575|ref|YP_004385003.1| 236 TLKVEEVYLNEYETFEDAFRNICNFIENVYNHKRLHSALN 275
                                       6889999*******999****************9999876 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.9e-05      0.11       3      56 ..      52     105 ..      50     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                     HTH_Tnp_Tc3_2   3 rIvrlvrkdPritlreLanelkeeGksvsreTirrrLrkaglkkrkprkkplLs 56 
                                       +I +++ + P+  +r++++el+++G  v ++ + r +r+++l  +k + kp+ +
  gi|330508575|ref|YP_004385003.1|  52 QIQEIALEFPYYGYRRITAELQNRGYAVNHKRVLRLMRQEKLLCYKKKFKPVTT 105
                                       68888889999**********************************999999755 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.7e-05      0.17      33      61 ..      19      48 ..      13      58 .. 0.83
   2 ?   -2.7   0.1       2.7   6.1e+03      55      72 ..     225     243 ..     224     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.7e-05
                                      HHHHTS-HHHHHHHH.H-HHHHHHHHHHHH CS
                       HTH_Tnp_1_2 33 aeevgvsrsTlykWk.kkkeFieyvnelae 61
                                      +  + vsrs +y+W+ + ++F+++ +e ++
  gi|330508575|ref|YP_004385003.1| 19 CLALDVSRSGYYEWLkRSEKFTAENSESSD 48
                                      56789*********9889999999888765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHT.THHHHH CS
                       HTH_Tnp_1_2  55 yvnelaeeflee.eraevy 72 
                                       y n  ae+f+++ +++evy
  gi|330508575|ref|YP_004385003.1| 225 YDNAFAESFIKTlKVEEVY 243
                                       7899999999873557777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.21s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2120.56
//
Query:       gi|330508576|ref|YP_004385004.1|  [L=337]
Description: hypothetical protein MCON_2808 [Methanosaeta concilii GP6]
Scores for complete 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  146.2  33.5    1.7e-42  146.0  33.5    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 !  146.0  33.5   9.6e-47   1.7e-42       2     301 .]      14     315 ..      13     315 .. 0.88

  Alignments for each domain:
  == domain 1  score: 146.0 bits;  conditional E-value: 9.6e-47
                   LPG_synthase_TM   2 llglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayligl 78 
                                       l+  ++s +++ ++l+ ++   + ++l s+++ ++llal l+lls+l+++lr++ll   +g++is+  +++ +l+++
  gi|330508576|ref|YP_004385004.1|  14 LIPSLISFFVIIIILKLTNTVITYDVLTSIGVKFVLLALSLHLLSWLFGSLRIQLLAFIIGHKISFYLAFKTTLASN 90 
                                       677888988888889999*********************************************************** PP

                   LPG_synthase_TM  79 fvnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalalll 155
                                       f+ ++tP+++gGe++r+ +l+  +g+s+++a+a+v++erlld + l+ ++++ ++l    ++     l ++a++l++
  gi|330508576|ref|YP_004385004.1|  91 FLASLTPSSVGGEPMRIKMLAD-NGLSYGSAMAIVLAERLLDSILLLSALVVCFFLKELVPGL---GLKVGAAFLGI 163
                                       **********************.*******************999988888777777776665...88999999988 PP

                   LPG_synthase_TM 156 lavlalllllllrrrlarlarvlkrlarllarfarklasakr.........klvlasprrlllafllslliwlleal 223
                                       l +l ++l +l++ ++  +++++  ++++ +  ++ +a + +          ++++ + r++  f  +++ w++e+l
  gi|330508576|ref|YP_004385004.1| 164 LILLMIFLWMLIHNPE-SIKQLINWVRGKTKGGKTLTAVE-KqiwlfreavITLAGERIRMPTLFVVTIILWACEFL 238
                                       8888876666666554.44444444444443334334433.35888*****7777777779**************** PP

                   LPG_synthase_TM 224 tlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllll 300
                                       +  +ll +lg ++sl ++++++++++l++++p++PgG+G++E+++  l++++ v+++++++++ l+rlit+++ l +
  gi|330508576|ref|YP_004385004.1| 239 IPSVLLVGLGRNPSLISSITAQIIVSLISLAPLTPGGSGIAEVSMSYLYSMF-VPSYLLGVLVGLWRLITYFTNLTA 314
                                       ****************************************************.******************998877 PP

                   LPG_synthase_TM 301 G 301
                                       G
  gi|330508576|ref|YP_004385004.1| 315 G 315
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2526.11
//
Query:       gi|330508577|ref|YP_004385005.1|  [L=402]
Description: hypothetical protein MCON_2809 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-17   61.7   0.0      1e-16   60.9   0.0    1.4  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    4.7e-10   39.3   0.0    1.8e-08   34.1   0.0    2.0  2  Amino_oxidase  Flavin containing amine oxidoreductase
    1.3e-08   34.4   0.3    1.6e-07   30.8   0.3    2.0  2  FAD_binding_2  FAD binding domain
    1.4e-06   27.3   0.0    2.2e-05   23.4   0.1    2.0  2  HI0933_like    HI0933-like protein
    1.4e-06   28.0   0.0      3e-06   26.9   0.0    1.5  2  FAD_oxidored   FAD dependent oxidoreductase
    1.6e-06   28.0   0.1    7.8e-06   25.7   0.3    1.9  2  DAO            FAD dependent oxidoreductase
    0.00022   20.6   0.1      0.054   12.7   0.0    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    0.00074   18.8   0.2     0.0012   18.1   0.2    1.3  1  Thi4           Thi4 family
     0.0011   17.6   0.0     0.0015   17.2   0.0    1.2  1  GDI            GDP dissociation inhibitor
     0.0043   16.3   0.0      0.037   13.2   0.0    2.0  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.011   16.2   1.3       0.14   12.8   0.3    2.3  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.022   13.2   0.1      0.034   12.6   0.1    1.2  1  FMO-like       Flavin-binding monooxygenase-like
      0.026   13.6   0.0      0.038   13.1   0.0    1.2  1  GIDA           Glucose inhibited division protein A
      0.037   13.3   0.2      0.053   12.8   0.2    1.2  1  FAD_binding_3  FAD binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   7.9e-20     1e-16       1      68 []       8      74 ..       8      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 7.9e-20
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHHCCC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrllrel 68
                                      ++GaG+sGl+ A ++++++++vl+lek +++GG ++syev+g+rvd+g+h+++  +    +r+l++++
  gi|330508577|ref|YP_004385005.1|  8 VIGAGISGLLSALAISEENKSVLVLEKEEYIGGVCRSYEVDGYRVDTGPHTITRLE-RGPLRELMDRY 74
                                      8****************************************************985.79999999875 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.4e-11   1.8e-08       1      60 [.      13      73 ..      13      98 .. 0.94
   2 ?    3.3   0.0     0.033        42     201     350 ..     190     336 ..     161     357 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.4e-11
                                      HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET.TTHHHHHHHHH CS
                     Amino_oxidase  1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg.agnpllellke 60
                                      ++GL  A   ++ + +V+vlE ++ +GG +r+++ dGy +++G++++t+    pl el+++
  gi|330508577|ref|YP_004385005.1| 13 ISGLLSALAISEENKSVLVLEKEEYIGGVCRSYEVDGYRVDTGPHTITRlERGPLRELMDR 73
                                      8************************************************999999999987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.033
                                       CCCEETTHTHHHHHHHHH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEESCCS CS
                     Amino_oxidase 201 slllprgGlsqlpealae..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsPplp 275
                                       ++ +p+gGl+ +++++ +   + +++i + + V +i   ++ +   +++ +++ +  V+    ++ l   +++ +l 
  gi|330508577|ref|YP_004385005.1| 190 DQGYPKGGLQYIVNSILSsfPKNRVKIITIANVLKIGS-DERIEQVCTNDNNYGCETVIYSGFVSDLP--NLVNGLL 263
                                       455789************55555555556666666665.66677778999999999999999999999..6666664 PP

                                       HHHHHHHHHSEEEEEEEEEEEESSGGSGCSTSECE.CECCCEEETTTEEEEECC..ECCCSTTTEEEEEEEEEC.HH CS
                     Amino_oxidase 276 dekaeairnlgfgsvnkvilefdrkfwednalgqg.vlvseltttlgeafissd..fpsrappgkglvllvyvg.gd 348
                                       +e  + + +++ + +  + +  +++ + + ++  + +  se + +   +    +   +s ap+gk+lv ++++   +
  gi|330508577|ref|YP_004385005.1| 264 KEYIKNLTSIKRAKSLTIWVGLKGEIFTKYGS--EmWIDSEPYAWFVPT----SnyDSSLAPNGKQLVSFAFTRpSE 334
                                       46666666667777777777777777776432..222223333332222....133556799999998888887555 PP

                                       HH CS
                     Amino_oxidase 349 aa 350
                                       ++
  gi|330508577|ref|YP_004385005.1| 335 YN 336
                                       55 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.3   1.3e-10   1.6e-07       1      36 [.       5      40 ..       5      44 .. 0.96
   2 ?    1.2   0.0      0.12   1.5e+02     391     402 ..     384     395 ..     382     401 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.3e-10
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      Dv+ViG+G++GL +Al+++e++++v+v+eke++ gg
  gi|330508577|ref|YP_004385005.1|  5 DVVVIGAGISGLLSALAISEENKSVLVLEKEEYIGG 40
                                      9*******************************9987 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                                       SSBTEEE-STCE CS
                     FAD_binding_2 391 pipGLYAaGeva 402
                                       pi++LY++G ++
  gi|330508577|ref|YP_004385005.1| 384 PIKNLYCVGTDT 395
                                       8********997 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   1.7e-08   2.2e-05       1      36 [.       4      39 ..       4      41 .. 0.95
   2 ?    1.6   0.0     0.069        89     107     161 ..     197     249 ..     181     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.7e-08
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      +dv+viG+G +Gl+ A+++++++k+Vl+lek++ +g
  gi|330508577|ref|YP_004385005.1|  4 YDVVVIGAGISGLLSALAISEENKSVLVLEKEEYIG 39
                                      59*****************************98876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.069
                                       -CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE- CS
                       HI0933_like 107 kaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlA 161
                                         + iv+ +l+   +++vk+ +  +v ++ + ++++ +v t +++++ +++++ +
  gi|330508577|ref|YP_004385005.1| 197 GLQYIVNSILSSFPKNRVKIITIANVLKIGS-DERIEQVCT-NDNNYGCETVIYS 249
                                       55789999*********************65.555577777.9999999999865 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   2.4e-09     3e-06       1      66 [.       5      73 ..       5      80 .. 0.81
   2 ?   -3.3   0.0       3.4   4.4e+03      99     132 ..     211     245 ..     197     252 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.4e-09
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglv...atdignkaeeqvvtgiarefler 66
                                      DvvV+G+g++G+  A+a  ++ ++vl++e+++++GG   s  v     d+g+++ +++ +g  re+++r
  gi|330508577|ref|YP_004385005.1|  5 DVVVIGAGISGLLSALAISEENKSVLVLEKEEYIGGVCRSYEVdgyRVDTGPHTITRLERGPLRELMDR 73
                                      9***********************************987754422255666665567777777777776 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.4
                      FAD_oxidored  99 eagvtvllntrlvevekegkriesvtveske.g.rk 132
                                       +++v++++ + + ++  ++ rie+v++++++ g ++
  gi|330508577|ref|YP_004385005.1| 211 KNRVKIITIANVLKIGSDE-RIEQVCTNDNNyGcET 245
                                       4477777777788888775.9999999888776544 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.3   6.1e-09   7.8e-06       1      33 [.       5      39 ..       5      45 .. 0.91
   2 ?   -0.7   0.0      0.64   8.2e+02     150     199 ..     203     249 ..     200     368 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.1e-09
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      dvv+iG+Gi Gl  A++ ++++  V++lek++ +g
  gi|330508577|ref|YP_004385005.1|  5 DVVVIGAGISGLLSALAISEENksVLVLEKEEYIG 39
                                      9******************88669*******8887 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.64
                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEEEEEEEEEE- CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgve.rttp.gendaadavVna 199
                                       +++++ + ++ v+i++ ++v ++   d+++ +v  ++++ g    +++v+ +
  gi|330508577|ref|YP_004385005.1| 203 NSILSSFPKNRVKIITIANVLKI-GSDERIEQVCtNDNNyG----CETVIYS 249
                                       66777888899999999999999.33567888844333333....4666654 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 !   12.7   0.0   4.2e-05     0.054       1      42 [.       7      48 ..       7      63 .. 0.86
   2 !    5.8   0.0    0.0053       6.8      93     141 ..     211     259 ..     201     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.2e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nignsiyrypke 42
                                      ++iGaG  Gl +a+++ + +  ++l+lEk+  ig   + y  +
  gi|330508577|ref|YP_004385005.1|  7 VVIGAGISGLLSALAISEENK-SVLVLEKEeYIGGVCRSYEVD 48
                                      79******************8.8******97788888888665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0053
                       Pyr_redox_3  93 sfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnkl 141
                                       +++++i +  +V ++ ++++  +v t+ ++y +++vi +    d Pn+ 
  gi|330508577|ref|YP_004385005.1| 211 KNRVKIITIANVLKIGSDERIEQVCTNDNNYGCETVIYSGFVSDLPNLV 259
                                       5778999999***************************987666777764 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   9.7e-07    0.0012      18      55 ..       4      40 ..       1      44 [. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 9.7e-07
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                       Dvv++GaG sGL +a  ++++ +  v++le++  +GG
  gi|330508577|ref|YP_004385005.1|  4 YDVVVIGAGISGLLSALAISEE-NKSVLVLEKEEYIGG 40
                                      7*********************.99*******999998 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.2e-06    0.0015       3      47 ..       2      46 ..       1      82 [. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.2e-06
                                      XEECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG-EE- CS
                               GDI  3 eeydvivlGtGlkecilsGllsvdgkkvlhldrndyyGgesaslt 47
                                      ++ydv+v+G+G+   + +  +s ++k vl+l++++y Gg + s +
  gi|330508577|ref|YP_004385005.1|  2 NKYDVVVIGAGISGLLSALAISEENKSVLVLEKEEYIGGVCRSYE 46
                                      57**********9765555699*****************888765 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 !   13.2   0.0   2.9e-05     0.037       1      34 [.       4      37 ..       4      68 .. 0.86
   2 ?    0.9   0.0      0.17   2.2e+02     193     234 ..     209     249 ..     184     280 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegt 34
                                      +dvvviG+G+ Gl  al +++ +  v+++e+e++
  gi|330508577|ref|YP_004385005.1|  4 YDVVVIGAGISGLLSALAISEENKSVLVLEKEEY 37
                                      69*************************9965543 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.17
                                       HHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 193 lekeGvevklgtsvkeidgngeklevvledgeeidadlvvva 234
                                       + k+ v++ + ++v +i ++++ +e v ++ + + +++v+++
  gi|330508577|ref|YP_004385005.1| 209 FPKNRVKIITIANVLKIGSDER-IEQVCTNDNNYGCETVIYS 249
                                       4567788888888888877776.7766666666777777764 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   0.00011      0.14       2      35 ..       6      39 ..       5      45 .. 0.92
   2 ?    1.9   0.0      0.27   3.4e+02      46      76 ..     205     234 ..     199     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      vvv+G+G +gl  A a++e +k+V v+e ++ + 
  gi|330508577|ref|YP_004385005.1|  6 VVVIGAGISGLLSALAISEENKSVLVLEKEEYIG 39
                                      8***************************998775 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.27
                                       HHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                         Pyr_redox  46 lqeklekngievllntkveeiegsedgvesv 76 
                                       +  ++ kn +++++ ++v +i  +e+ +e+v
  gi|330508577|ref|YP_004385005.1| 205 ILSSFPKNRVKIITIANVLKIGSDER-IEQV 234
                                       55667799999999999999998877.6666 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.7e-05     0.034       4      42 ..       6      44 ..       3      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                          FMO-like  4 vaviGaGvsGlasikccleegleptcfersddiGGlwrf 42
                                      v viGaG+sGl s  +  ee+     +e+ + iGG+ r 
  gi|330508577|ref|YP_004385005.1|  6 VVVIGAGISGLLSALAISEENKSVLVLEKEEYIGGVCRS 44
                                      89*********************************9885 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     3e-05     0.038       1      37 [.       5      40 ..       5      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiae 37
                                      dv+ViG+G +G+  Ala+++ + +vl + +k + i+ 
  gi|330508577|ref|YP_004385005.1|  5 DVVVIGAGISGLLSALAISEENKSVLVL-EKEEYIGG 40
                                      79*******************9998877.66666665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   4.2e-05     0.053       2      33 ..       4      35 ..       3      42 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      +dV+++GaG +Gl++al  se   +v+++ek 
  gi|330508577|ref|YP_004385005.1|  4 YDVVVIGAGISGLLSALAISEENKSVLVLEKE 35
                                      79****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2926.42
//
Query:       gi|330508578|ref|YP_004385006.1|  [L=267]
Description: glycosyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-26   91.3   0.0    7.7e-26   90.9   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
      4e-15   56.3   0.0    1.5e-14   54.4   0.0    1.7  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.6e-08   34.3   0.0    3.4e-08   33.2   0.0    1.4  1  Glyco_transf_21  Glycosyl transferase family 21
    7.2e-06   26.0   0.0    1.6e-05   24.9   0.0    1.6  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    1.7e-05   24.4   0.0    3.9e-05   23.3   0.0    1.6  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
    0.00086   19.0   0.1      0.006   16.3   0.0    2.3  2  Glyco_tranf_2_5  Glycosyltransferase like family
  ------ inclusion threshold ------
       0.01   16.3   0.0      0.031   14.8   0.0    1.8  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.0     3e-29   7.7e-26       1     119 [.       4     114 ..       4     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 3e-29
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglr 76 
                                       sv++p+ Nee+++ ++les+ +q  p+  +eiiv D gS+D+tv+i+ ++a+     +vi  e++ G   ++n+g++
  gi|330508578|ref|YP_004385006.1|   4 SVIVPALNEESYIGACLESISEQtFPRNGYEIIVSDGGSNDNTVKIAGKYAD-----KVIVSEKR-GIWWGRNQGAE 74 
                                       8**********************999************************98.....99999988.*********** PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEE CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvvlgqrpri 119
                                        a+g+y++f+DaD+ +++d+le + ++le  g+  v  ++ + 
  gi|330508578|ref|YP_004385006.1|  75 FAKGKYLVFIDADTRIKEDYLETVHRYLES-GV--VGLTTAFE 114
                                       ***************************999.55..55444444 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 !   54.4   0.0   5.9e-18   1.5e-14       4     209 ..       3     191 ..       2     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 5.9e-18
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksra 78 
                                       ++v+Vp++nee+++g++les++ q+ pr  +e++v + +s + t++ a     ++ d   +v+v ++    +g  ++
  gi|330508578|ref|YP_004385006.1|   3 FSVIVPALNEESYIGACLESISEQTFPRngYEIIVSDGGSNDNTVKIA----GKYAD---KVIVSEK----RGIWWG 68 
                                       89***********************98889*************99966....47999...3666666....6889** PP

                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarral 155
                                        n++ + +k+++++++D+Dt++  d+l+ + +++  +  g+vg    ++ + + +     ++f+e   ++ +  +++
  gi|330508578|ref|YP_004385006.1|  69 RNQGAEFAKGKYLVFIDADTRIKEDYLETVHRYL-ES--GVVGLTTAFELDGADIK----TKFYEYISNCYLGLNSK 138
                                       *****************************99999.66..66665555555554444....34555555444444433 PP

                   Glyco_tranf_2_3 156 .gvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaav 209
                                        + + l G  ++++r+v+   +g+    +  +D++ +++lr++g       +++v
  gi|330508578|ref|YP_004385006.1| 139 iDNVSLIGINLCVPRDVFYKVGGFKN--YALEDAFFSRELRKEGRTYFLIQRKVV 191
                                       2345589**************77766..999*********999865555555544 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 !   33.2   0.0   1.3e-11   3.4e-08      25     151 ..      72     191 ..      67     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.3e-11
                   Glyco_transf_21  25 aleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpv.gsdakg.laaaleaaflntlagvlqaklsglg 99 
                                       + e ak ++lv+ D+d+r+k+dyLe++ ++le+  vgl t++ + g+d k+ ++  + +++l+ ++++         
  gi|330508578|ref|YP_004385006.1|  72 GAEFAKGKYLVFIDADTRIKEDYLETVHRYLESGVVGLTTAFELdGADIKTkFYEYISNCYLGLNSKIDNV------ 142
                                       5566999**********************************998666666436666666666555554433...... PP

                   Glyco_transf_21 100 favGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapia 151
                                         +G  + + r+++ ++GGf+    +  eD+++++ lr++G +  l ++ ++
  gi|330508578|ref|YP_004385006.1| 143 SLIGINLCVPRDVFYKVGGFKN---YALEDAFFSRELRKEGRTYFLIQRKVV 191
                                       56899999************99...999**************9998888766 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 !   24.9   0.0   6.4e-09   1.6e-05       1     119 [.      80     188 ..      80     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 6.4e-09
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvm.nvanwleelaalffaedhgkdilvrealgrvvpsvGsg 76 
                                       + +++DaDt++ +d+l+ + + l+s   ++v + + ++  +a++ ++++ + +++ ++    +     + v++ G +
  gi|330508578|ref|YP_004385006.1|  80 YLVFIDADTRIKEDYLETVHRYLES---GVVGLTTAFElDGADIKTKFYEY-ISNCYLG-LNSK---IDNVSLIGIN 148
                                       5799*******************98...45545555555566666666654.2333333.2332...35699***** PP

                   Glyco_trans_2_3  77 aflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpe 119
                                        +++r+++ +vgg++       ED +++  l+++G + +++  
  gi|330508578|ref|YP_004385006.1| 149 LCVPRDVFYKVGGFK---NYALEDAFFSRELRKEGRTYFLIQR 188
                                       ***************...6778************988777654 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.5e-08   3.9e-05       2     103 ..       5      99 ..       4     107 .. 0.71
   2 ?   -3.7   0.0       2.5   6.4e+03     168     182 ..     149     163 ..     143     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.5e-08
                   Glyco_tranf_2_2   2 vviplraseerhyieervlqkakyy..deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrG 76 
                                       v++p  ++ e  yi   +  +  +    +  e+iv d+gS +++++   +    +  v+  ++     +    rN+G
  gi|330508578|ref|YP_004385006.1|   5 VIVPALNE-E-SYIGACLESISEQTfpRNGYEIIVSDGGSNDNTVKIAGKYA-DKVIVS--EK----RGIWWGRNQG 72 
                                       56665443.3.37877775544443247789999999999999655444433.333444..44....377889**** PP

                   Glyco_tranf_2_2  77 askaesdlvlFlDaDcfissDkfekil 103
                                       a+ a++ +++F+DaD  i  D +e + 
  gi|330508578|ref|YP_004385006.1|  73 AEFAKGKYLVFIDADTRIKEDYLETVH 99 
                                       **********************99875 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.5
                   Glyco_tranf_2_2 168 ilinrraflevGGyD 182
                                       + + r  f +vGG+ 
  gi|330508578|ref|YP_004385006.1| 149 LCVPRDVFYKVGGFK 163
                                       567789999999995 PP

>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.98   2.5e+03       5      26 ..       9      30 ..       5      39 .. 0.65
   2 !   16.3   0.0   2.4e-06     0.006      30      91 ..      54     110 ..      43     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.98
                   Glyco_tranf_2_5  5 cvnneelyeeclsylenlevpe 26
                                        n+e+++ +cl+ +++ + p 
  gi|330508578|ref|YP_004385006.1|  9 ALNEESYIGACLESISEQTFPR 30
                                      5677788888888887777665 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.4e-06
                   Glyco_tranf_2_5  30 veiiairnaksiaeaynkalsasdakykvYlhqDvliinkdfikdlleiFkkdkkiGmiGvv 91 
                                       ++ + ++++  i  + n++++ ++ ky+v+++ D+ i  +d ++++ + +    + G++G++
  gi|330508578|ref|YP_004385006.1|  54 ADKVIVSEKRGIWWGRNQGAEFAKGKYLVFIDADTRIK-EDYLETVHRYL----ESGVVGLT 110
                                       6778899999*************************985.56777777776....67777775 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 ?   14.8   0.0   1.2e-05     0.031       2      81 ..      11      87 ..      10      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgfdr....ilvydndstDgtrailkelpe.vkllhvdksyederrqvellkallaryaeadwv 75
                                      ne+ +++++l+ + +  f r    i+v d +s D+t +i  ++++ v + + ++ + +++          a+ a+++++
  gi|330508578|ref|YP_004385006.1| 11 NEESYIGACLESISEQTFPRngyeIIVSDGGSNDNTVKIAGKYADkVIVSEKRGIWWGRN--------QGAEFAKGKYL 81
                                      99*********9999988444455****************99966488888888884322........22233445566 PP

                   Glyco_tranf_2_4 76 lvvDaD 81
                                      +++DaD
  gi|330508578|ref|YP_004385006.1| 82 VFIDAD 87
                                      666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1952.70
//
Query:       gi|330508579|ref|YP_004385007.1|  [L=493]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-15   56.2   0.0      1e-12   48.7   0.0    2.8  3  Radical_SAM  Radical SAM superfamily
    4.8e-06   26.9   1.0      7e-05   23.1   0.0    2.4  2  Fer4_12      4Fe-4S single cluster domain
    1.4e-05   25.2   0.8    9.4e-05   22.5   0.0    2.3  2  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.011        64       3      19 ..      76      92 ..      74      97 .. 0.86
   2 !   48.7   0.0   1.7e-16     1e-12       3     166 ..     101     261 ..      99     262 .. 0.88
   3 ?   -1.1   0.0      0.36   2.1e+03      13      41 ..     352     377 ..     351     386 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.011
                                      EESEESS--TTTSCCTT CS
                                      xxxxxxxxxxxxxxxxx RF
                       Radical_SAM  3 vtrgCnlrCsfCarpet 19
                                      +++gC+l+C  C ++++
  gi|330508579|ref|YP_004385007.1| 76 TSHGCPLDCGLCENHKS 92
                                      689***********974 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 1.7e-16
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH..HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelk..aekgvkevilgggepllypdfvellerlaklavpg 77 
                                       vt  Cnl C+ C        + +  + ++ +i+  ++ l+      +  + ++ggep+++ d+ +++  ++      
  gi|330508579|ref|YP_004385007.1| 101 VTSRCNLSCPICFADA----GNDKNEPTIGQIASMMQVLRdqIPVPCPAIQFSGGEPTMRVDLPDIVYLAKTM--GF 171
                                       799************6....66666666666666666666525555**************************9..8* PP

                                       EEEEEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                       xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                         i + tng+++   ++   +l + g+ +v+l  + +++e   + +++ + + + l+a+e+lr+ag  ++v + +++
  gi|330508579|ref|YP_004385007.1| 172 AQILLATNGLVLAsrPDLCHELIQSGLSTVYLQFDGVTPE-PYEAIRGVNLLPQKLRAIENLRQAGNLSTVLVPTLV 247
                                       ****************************************.56666599999************************* PP

                                       TTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                       Radical_SAM 153 pGendeeleellel 166
                                       +G nd +  +++++
  gi|330508579|ref|YP_004385007.1| 248 KGTNDGQAGDIVRF 261
                                       *****988888776 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.36
                                       TTSCCTTHHHHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  13 fCarpetvrregrgrslsveeileevkel 41 
                                       +C+ ++   + +  r+l+ve ++e v++ 
  gi|330508579|ref|YP_004385007.1| 352 YCQGGH---MIPITRFLDVEGLMENVRQR 377
                                       9****9...799********999999986 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.9     0.068   4.1e+02      13      26 ..      78      91 ..      66      95 .. 0.85
   2 !   23.1   0.0   1.2e-08     7e-05      12      79 ..     102     169 ..      92     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.068
                           Fer4_12 13 sgCnlsCkgCfnke 26
                                      +gC+l C  C n +
  gi|330508579|ref|YP_004385007.1| 78 HGCPLDCGLCENHK 91
                                      8*********9987 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 1.2e-08
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkev 79 
                                       +s+CnlsC+ Cf+ +  + ++ +  + + + ++++d      + + ++GGEP ++   ++++ l+k +
  gi|330508579|ref|YP_004385007.1| 102 TSRCNLSCPICFADAGNDKNEPTIGQIASMMQVLRDQIPVPCPAIQFSGGEPTMRVDLPDIVYLAKTM 169
                                       689*********999999999999997777777777778889************77777776666654 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 ?   -0.2   0.8      0.18   1.1e+03       7      19 ..      79      91 ..      76      94 .. 0.87
   2 !   22.5   0.0   1.6e-08   9.4e-05       5      91 ..     102     182 ..      99     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.18
                           Fer4_14  7 gCnlsCkgCdnke 19
                                      gC+l C  C n++
  gi|330508579|ref|YP_004385007.1| 79 GCPLDCGLCENHK 91
                                      9********9987 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.6e-08
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                       +s+CnlsC+ C+  +  +++  ++ +   + q+l+  ++  +    + ++GGeP +  + ++++ l k +       
  gi|330508579|ref|YP_004385007.1| 102 TSRCNLSCPICFADAGNDKNEPTIGQIASMMQVLR--DQIPVPCPAIQFSGGEPTMRVDLPDIVYLAKTMGF----A 172
                                       79**********99988888888888888889994..445555566*********99999999888876643....4 PP

                           Fer4_14  82 kiwletngtl 91 
                                       +i l tng++
  gi|330508579|ref|YP_004385007.1| 173 QILLATNGLV 182
                                       4777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 3597.19
//
Query:       gi|330508580|ref|YP_004385008.1|  [L=413]
Description: glycosyl transferase, group 1 family protein [Methanosaeta concilii GP6]
Scores for complete 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  106.0   0.0    3.6e-30  104.8   0.0    1.6  2  Glycos_transf_1  Glycosyl transferases group 1
    3.4e-26   92.3   0.1    6.7e-26   91.3   0.1    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.2e-23   84.0   0.0    2.2e-23   83.2   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
      6e-16   59.3   0.0    1.2e-15   58.4   0.0    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    2.5e-13   50.3   0.1    1.8e-10   40.9   0.1    2.3  1  Glyco_transf_5   Starch synthase catalytic domain
    1.9e-07   31.2   0.0    3.7e-07   30.3   0.0    1.4  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    7.8e-07   29.4   0.0    1.5e-06   28.5   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.074   13.1   0.0        1.4    8.9   0.0    2.6  3  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.68   1.5e+03      74     101 ..     166     195 ..     163     222 .. 0.67
   2 !  104.8   0.0   1.6e-33   3.6e-30      13     172 .]     218     372 ..     206     372 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.68
                                       GGGEEECCHSSSHHHHHHC..ESEEEEEES CS
                   Glycos_transf_1  74 nviflgevsredleellkn..adifvlpsi 101
                                       + i++ + ++++l++++++  ++i+++p  
  gi|330508580|ref|YP_004385008.1| 166 QMIVTTRRMQDELMQIYSIpeSKITIIPNG 195
                                       677888888999999999999999988854 PP

  == domain 2  score: 104.8 bits;  conditional E-value: 1.6e-33
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleel 89 
                                          +++++ gr++ +Kg+dll+++++l+ k+ + +vk++++G+g+++ e +++a el++++ ++flg+vs   +ee+
  gi|330508580|ref|YP_004385008.1| 218 PITPMVFFCGRMSIQKGPDLLVESIPLILKN-RGDVKFIFIGEGSMRTECERRAWELGIGEACRFLGYVSGPTKEEV 293
                                       557899************************9.**************************************999**** PP

                                       HHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHH CS
                   Glycos_transf_1  90 lknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlg 166
                                       l+++d++++ps++E+fGiv+lEA  a +pv+a+ a     ++++ e+Gll     +e++a  i++ll+++++ ++l 
  gi|330508580|ref|YP_004385008.1| 294 LNACDLVCIPSRNEPFGIVVLEAWDACKPVVATEA---VSIINNFEDGLLAYVQ-PESIAWCINRLLDSPDEMKKLA 366
                                       *********************************85...67999*****999887.*********************9 PP

                                       HHHHHH CS
                   Glycos_transf_1 167 enarkr 172
                                       +++++r
  gi|330508580|ref|YP_004385008.1| 367 YEGYNR 372
                                       999875 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.1     3e-29   6.7e-26       1     166 [.      27     196 ..      27     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 3e-29
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev.......elvvrvprvplpllkrllrslaflrrlrrllkr 70 
                                       +GG++ hv eL++aL +rGheV+++t+++d + ++         + + +++ + +  +k +   + ++ r+++++  
  gi|330508580|ref|YP_004385008.1|  27 IGGIAPHVSELSEALVKRGHEVHIFTRRGDFDVYDIIngvhyhrVAIENLGNIVFQMDKMCDALFESFERAQKIFG- 102
                                       7********************************9997774433333333333333444444444444444444444. PP

                    Glyco_transf_4  71 ekpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrl.lrradrviavSeatad 146
                                        k+D++H h+++++  al +++  +g++++lt+H+++ +++ +++ +     +    ++l    +++ i++++ ++d
  gi|330508580|ref|YP_004385008.1| 103 -KFDIIHGHDWHPV-KALNRIKSDYGLRYILTLHSSE-WGRNGNYFGDDISKEISHREWLgGYESQQMIVTTRRMQD 176
                                       .************7.788888889*************.6666666655555544445555689************** PP

                    Glyco_transf_4 147 elrerygvppekitVipnGv 166
                                       el++ y +p++kit+ipnG+
  gi|330508580|ref|YP_004385008.1| 177 ELMQIYSIPESKITIIPNGI 196
                                       *******************9 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 !   83.2   0.0   9.7e-27   2.2e-23       2     133 ..     221     357 ..     220     358 .. 0.87

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 9.7e-27
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHH.T.T-T.TEEEE---..THHHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleela.a.gleerveftGfv..edlaella 71 
                                       p + f+Gr+   +kg dll+e +pl++k+  dv+++++G+g+ r  e+e++a + g+ e ++f+G+v  + ++e+l+
  gi|330508580|ref|YP_004385008.1| 221 PMVFFCGRM-SIQKGPDLLVESIPLILKNrgDVKFIFIGEGSmR-TECERRAwElGIGEACRFLGYVsgPTKEEVLN 295
                                       7899*****.555**************77444*********965.69999885599999********9888****** PP

                                       H-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLle 133
                                       a+d++++Ps  e fg+++lEa  a +pvVat++     ++   e+gll+   +pe++a  i rLl+
  gi|330508580|ref|YP_004385008.1| 296 ACDLVCIPSrnEPFGIVVLEAWDACKPVVATEAVS---IInnFEDGLLAYV-QPESIAWCINRLLD 357
                                       *********999*******************8844...4442599999964.7**********997 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 !   58.4   0.0   5.1e-19   1.2e-15       1     160 []      28     195 ..      28     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 5.1e-19
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrps.pladlaalral....rrllrqrre 72 
                                       gGi+ +v el++aL++rGheV+++t++++ + ++   +gv++hr+ +   +   + + +++ al    +r+ +    
  gi|330508580|ref|YP_004385008.1|  28 GGIAPHVSELSEALVKRGHEVHIFTRRGDFDVYD-IINGVHYHRVAIENLGNiVFQMDKMCDALfesfERA-QKIFG 102
                                       8*************************88888774.367********9988754444544554442222444.34579 PP

                   Glyco_trans_4_4  73 rpdvvhahsptaglaarlarrrrgiplvvtlhg.lllrrgsgavrrlyral...errllrradavlvvseaeaeelr 145
                                       ++d++h h+++   a  +++   g+++++tlh+  ++r g+ +   + +++   e +      + +v+++ + +el 
  gi|330508580|ref|YP_004385008.1| 103 KFDIIHGHDWHPVKALNRIKSDYGLRYILTLHSsEWGRNGNYFGDDISKEIshrEWLGGYESQQMIVTTRRMQDELM 179
                                       **********8776666666599*********7466777766666666666522445555699************** PP

                   Glyco_trans_4_4 146 a.lgvpadrvvvvpng 160
                                       + + +p ++++++png
  gi|330508580|ref|YP_004385008.1| 180 QiYSIPESKITIIPNG 195
                                       *999***********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 !   40.9   0.1   8.1e-14   1.8e-10       2     183 ..      14     149 ..      13     181 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 8.1e-14
                    Glyco_transf_5   2 ilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleevaelskaaedevevevekvkvak 78 
                                       + ++++E    +k GG+a +v++L++aL k+gh+v++++ r ++         +v++                    
  gi|330508580|ref|YP_004385008.1|  14 VGIFSWESLYSVKIGGIAPHVSELSEALVKRGHEVHIFTRRGDF---------DVYD-------------------- 61 
                                       6689***********************************88822.........1222.................... PP

                    Glyco_transf_5  79 lkkdgvdvyfldnpeffdreg.lYgdkgedyednaerfalfsraalellekl...gwkpdvihahDWhtalvpallk 151
                                       +  +gv+++ +  +++    + ++            ++  ++ a  e  e+      k+d+ih hDWh + +   +k
  gi|330508580|ref|YP_004385008.1|  62 II-NGVHYHRVAIENLG---NiVF------------QMDKMCDALFESFERAqkiFGKFDIIHGHDWHPVKALNRIK 122
                                       22.499***99999965...2266............3444555555555553221336**************88888 PP

                    Glyco_transf_5 152 elykerglfkkiktvftiHNlayqgrfp..kdel 183
                                       + y         ++++t+H+ ++ ++ +   d++
  gi|330508580|ref|YP_004385008.1| 123 SDY-------GLRYILTLHSSEWGRNGNyfGDDI 149
                                       887.......49*********9999888663433 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 !   30.3   0.0   1.6e-10   3.7e-07      11     108 ..      32     135 ..      23     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.6e-10
                   Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvd....rkgpleyl..ka...f.klkklikkikPDv 77 
                                       +h+++l ++L krg+eVh++t++++ + +++ +g+h hr+ ++    + +++  +  ++   f +  k++   k+D+
  gi|330508580|ref|YP_004385008.1|  32 PHVSELSEALVKRGHEVHIFTRRGDFDVYDIINGVHYHRVAIEnlgnIVFQMDKMcdALfesFeRAQKIFG--KFDI 106
                                       79********************9999**************8776656444444443223122334444444..79** PP

                   Glyco_trans_4_2  78 vhahyakpygllgslaarlsgvipvvlsvwG 108
                                       +h h   p+  l ++     g  +++l+ + 
  gi|330508580|ref|YP_004385008.1| 107 IHGHDWHPVKALNRIK-SDYG-LRYILTLHS 135
                                       *****99987666663.3333.677777765 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 !   28.5   0.0   6.7e-10   1.5e-06       5      89 ..     303     385 ..     293     388 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 6.7e-10
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaeh 81 
                                       psr+e +  +++Ea  +  ++++++a ++ + f++g  ++ +  +e++a  i++ll++p+e +++a ++++r+ ae+
  gi|330508580|ref|YP_004385008.1| 303 PSRNEPFGIVVLEAWDACKPVVATEAVSIINNFEDG--LLAYVQPESIAWCINRLLDSPDEMKKLAYEGYNRIDAEF 377
                                       9999***********999999999888888888888..88888********************************** PP

                   Glyco_trans_1_2  82 tydhraeq 89 
                                       ++d  a +
  gi|330508580|ref|YP_004385008.1| 378 RWDSIASK 385
                                       ***98865 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 ?    8.9   0.0   0.00065       1.4      18      87 ..      37     104 ..      28     108 .. 0.84
   2 ?   -1.1   0.0      0.77   1.7e+03      31      89 ..     167     221 ..     158     246 .. 0.62
   3 ?    0.1   0.0      0.34   7.5e+02     100     122 ..     309     331 ..     289     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00065
                                       HHHHHHCTT-EEEEEEETCCCHHHHHHCCT-EEEE---GHCTT..CHHHHCCHHHHHHHHHHHHHHHHHH CS
                   Glyco_transf_28  18 lakeLkkegheVrylgtkrgleerlveeaglefepiageklrrklspknlkeilkvlkavvkakkilkea 87 
                                       l ++L k+gheV+ + t rg  +      g++++++a+e l + + +++ k    +++++++a+ki+ ++
  gi|330508580|ref|YP_004385008.1|  37 LSEALVKRGHEVH-IFTRRGDFDVYDIINGVHYHRVAIENLGN-IVFQMDKMCDALFESFERAQKIFGKF 104
                                       7899*********.99999988888889***********9888.88888888888888899999998876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.77
                                       EEEETCCCHHHHHHCCT-EEEE---GHCTT..CHHHHCCHHHHHHHHHHHHHHHHHHHH CS
                   Glyco_transf_28  31 ylgtkrgleerlveeaglefepiageklrrklspknlkeilkvlkavvkakkilkeakp 89 
                                        ++t+r+++++l + + ++  +i++   ++ ++ ++  +il    ++vk ++ + +++p
  gi|330508580|ref|YP_004385008.1| 167 MIVTTRRMQDELMQIYSIPESKITII--PNGIIRRKTPQILDA--GRVKERYGISPITP 221
                                       58889999999988787777777665..333455555555555..55555555555555 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.34
                                       CHCCCCCHCCCTTHCCCCCHCTS CS
                   Glyco_transf_28 100 slpaviaaplaripviihEqnai 122
                                        + +v++a+ a  pv+ +E+ +i
  gi|330508580|ref|YP_004385008.1| 309 FGIVVLEAWDACKPVVATEAVSI 331
                                       5789***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3014.79
//
Query:       gi|330508581|ref|YP_004385009.1|  [L=166]
Description: hypothetical protein MCON_2814 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-05   24.2   0.0    3.9e-05   23.4   0.0    1.3  1  MarR_2           MarR family
    0.00017   21.3   0.0    0.00035   20.3   0.0    1.5  1  HTH_IclR         IclR helix-turn-helix domain
    0.00027   20.8   0.0     0.0007   19.4   0.0    1.7  1  HTH_5            Bacterial regulatory protein, arsR family
    0.00043   20.1   0.0    0.00071   19.4   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0026   17.8   0.0     0.0055   16.7   0.0    1.6  1  HTH_20           Helix-turn-helix domain
     0.0053   16.3   0.1      0.016   14.7   0.0    1.9  2  HTH_24           Winged helix-turn-helix DNA-binding
     0.0077   16.0   0.0      0.016   14.9   0.0    1.5  1  HTH_DeoR         DeoR-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.023   14.6   0.0    1.4  1  MarR             MarR family
      0.028   14.9   0.0      0.054   14.0   0.0    1.5  1  HTH_27           Winged helix DNA-binding domain
      0.035   14.2   0.0      0.066   13.3   0.0    1.4  1  DprA_WH          DprA winged helix domain
       0.05   13.6   0.0       0.15   12.0   0.0    1.8  1  HTH_11           HTH domain
      0.065   13.6   0.0      0.092   13.1   0.0    1.4  1  Penicillinase_R  Penicillinase repressor
       0.09   12.9   0.0       0.14   12.2   0.0    1.3  1  DUF5343          Family of unknown function (DUF5343)
      0.091   12.9   0.1        1.6    8.9   0.0    2.2  2  B-block_TFIIIC   B-block binding subunit of TFIIIC
        0.1   12.9   0.0       0.23   11.9   0.0    1.5  1  Rrf2             Transcriptional regulator


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 !   23.4   0.0   3.3e-08   3.9e-05      13      61 ..      38      84 ..      37      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.3e-08
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      a+ + ++  +t  el++ +g+sks+vs   + L   GLv r+  p+DkR
  gi|330508581|ref|YP_004385009.1| 38 AISAKDP--VTLDELVQDTGYSKSTVSLNMNQLKNLGLVKRVVIPGDKR 84
                                      6888999..*********************************5555*99 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.9e-07   0.00035      15      50 ..      41      76 ..      37      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.9e-07
                                      TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      a  ++tl el + tg +kStv+  ++ L +lG+v++
  gi|330508581|ref|YP_004385009.1| 41 AKDPVTLDELVQDTGYSKSTVSLNMNQLKNLGLVKR 76
                                      45679*****************************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 !   19.4   0.0   5.9e-07    0.0007      13      46 ..      42      75 ..      38      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.9e-07
                                      TSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 13 egelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      + + +  el+ ++g s+stvS   ++L+++GLV+
  gi|330508581|ref|YP_004385009.1| 42 KDPVTLDELVQDTGYSKSTVSLNMNQLKNLGLVK 75
                                      5677888**************************7 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     6e-07   0.00071      19      65 ..      41      90 ..      33      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6e-07
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST...TTEEEE- CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr...pklYrav 65
                                      +++p t de+ +++g ++s+v   +++L++ GlV+r+      ++lY ++
  gi|330508581|ref|YP_004385009.1| 41 AKDPVTLDELVQDTGYSKSTVSLNMNQLKNLGLVKRVVIPgdkRHLYAPI 90
                                      67899*******************************98777778899987 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   4.6e-06    0.0055      19      57 ..      37      77 ..       7      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.6e-06
                                      H..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 19 L..araegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      L  + ++++t+ el +  + sk+t+s ++++L   gLv++v
  gi|330508581|ref|YP_004385009.1| 37 LaiSAKDPVTLDELVQDTGYSKSTVSLNMNQLKNLGLVKRV 77
                                      255789********************************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 ?   -2.6   0.0       3.6   4.3e+03       3       8 ..       9      14 ..       3      19 .. 0.58
   2 !   14.7   0.0   1.4e-05     0.016      12      48 .]      39      75 ..      37      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.6
                            HTH_24  3 etdrkI 8 
                                      +++r I
  gi|330508581|ref|YP_004385009.1|  9 DIRRHI 14
                                      344555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.4e-05
                            HTH_24 12 LqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + ++   +  eL + +g S+stv+  +++L++ Gl+k
  gi|330508581|ref|YP_004385009.1| 39 ISAKDPVTLDELVQDTGYSKSTVSLNMNQLKNLGLVK 75
                                      5667778999*************************97 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.4e-05     0.016      12      47 ..      42      77 ..      38      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                          HTH_DeoR 12 qgklsveelvellgvSeaTiRRDLneLeeqglltRt 47
                                      ++ ++++elv+  g+S+ T+   +n+L++ gl++R+
  gi|330508581|ref|YP_004385009.1| 42 KDPVTLDELVQDTGYSKSTVSLNMNQLKNLGLVKRV 77
                                      67799*****************************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.9e-05     0.023      12      58 ..      39      85 ..      37      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                      ++ ++p ++ eL    g skstv+    +L   Gl++R   p+D+R+
  gi|330508581|ref|YP_004385009.1| 39 ISAKDPVTLDELVQDTGYSKSTVSLNMNQLKNLGLVKRVVIPGDKRH 85
                                      567789999*************************************7 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.5e-05     0.054      14      59 ..      40      85 ..      29      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
                            HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre 59
                                         ++++l +l++ + +++s++s ++++L + GLv+r   + d+r 
  gi|330508581|ref|YP_004385009.1| 40 SAKDPVTLDELVQDTGYSKSTVSLNMNQLKNLGLVKRVVIPGDKRH 85
                                      56799******************************99988877775 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.5e-05     0.066      23      44 ..      42      63 ..      36      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.5e-05
                           DprA_WH 23 pePvhvDqLvrrtglpaaevsa 44
                                       +Pv++D+Lv++tg + ++vs 
  gi|330508581|ref|YP_004385009.1| 42 KDPVTLDELVQDTGYSKSTVSL 63
                                      59**************999985 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.15      11      44 ..      40      74 ..      36      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                            HTH_11 11 eargpisgeeLAeeLnvSrrtvrrdIkaLeelg.v 44
                                      +a++p++ +eL + ++ S++tv   + +L+ lg v
  gi|330508581|ref|YP_004385009.1| 40 SAKDPVTLDELVQDTGYSKSTVSLNMNQLKNLGlV 74
                                      78999**************************9961 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.7e-05     0.092      25      83 ..      48     108 ..      38     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.7e-05
                                       HT--GGG---HHHHHHHHHHHHHTTS-EEEEE..TTEEEEE----XXXXXXXXXXXXXXXX CS
                   Penicillinase_R  25 eeleeekelaysTVktllrrLvkKgllsreke..grafiYsplvseeeavasavkqlldkl 83 
                                       +el +++  ++sTV   +++L + gl++r      ++++Y+p ++ e ++ ++++ +++++
  gi|330508581|ref|YP_004385009.1|  48 DELVQDTGYSKSTVSLNMNQLKNLGLVKRVVIpgDKRHLYAPITDPETIKTNMLDAITKEV 108
                                       5677777899*******************9877689***************9999887765 PP

>> DUF5343  Family of unknown function (DUF5343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.14      28      80 ..      49     104 ..      38     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                           DUF5343  28 dflktlglkssnasliiplLkflGfldedGkptel...ykelrnedtskkalaeai 80 
                                       + +++ g+++s+ sl ++ Lk+lG++ +  +p ++   y  + +++t k+ + +ai
  gi|330508581|ref|YP_004385009.1|  49 ELVQDTGYSKSTVSLNMNQLKNLGLVKRVVIPGDKrhlYAPITDPETIKTNMLDAI 104
                                       345558*********************98666655111556666899998888877 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 ?    8.9   0.0    0.0013       1.6      20      55 ..      46      89 ..      34     112 .. 0.82
   2 ?    1.9   0.0      0.21   2.5e+02       3      17 ..     128     142 ..     126     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0013
                    B-block_TFIIIC 20 tqsdLakeskqdprslfyrlksLekkgLIvkqsii........d 55
                                      t  +L++ ++ +++ +   ++ L++ gL++++ i+         
  gi|330508581|ref|YP_004385009.1| 46 TLDELVQDTGYSKSTVSLNMNQLKNLGLVKRVVIPgdkrhlyaP 89
                                      66789999***********************9997665554442 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.21
                    B-block_TFIIIC   3 dqfklLelIassRys 17 
                                       d+  lLe+Ias R+s
  gi|330508581|ref|YP_004385009.1| 128 DAKYLLERIASLRQS 142
                                       56679******9986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.23      18      56 ..      38      75 ..      30      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                      HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      a  +++ pv+++e+ + ++ s+s ++  +++L++ glvk
  gi|330508581|ref|YP_004385009.1| 38 AISAKD-PVTLDELVQDTGYSKSTVSLNMNQLKNLGLVK 75
                                      555555.6******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1185.89
//
Query:       gi|330508582|ref|YP_004385010.1|  [L=134]
Description: RDD domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-14   53.4   5.3    4.7e-14   52.8   5.3    1.3  1  RDD       RDD family


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   5.3   2.6e-18   4.7e-14       2     141 .]       8     124 ..       7     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 2.6e-18
                               RDD   2 aslgrRllAfliDlvllliislllallivallnakasaneavagslllllllvlllvllvyqllllskkgqTlGkll 78 
                                        s+g+R++A+liD++l+++i + +++++ +             g   + ++l+l  +l++y++ l+ ++gq++Gk+ 
  gi|330508582|ref|YP_004385010.1|   8 SSWGDRFWAWLIDVLLICLIWYKIIIVLEV-------------GVFTISGILLLSSLLFIYWTSLEGYRGQSVGKMF 71 
                                       69****************************.............9999999*************************** PP

                               RDD  79 lglkvvdedgrklglaqaliRalllllllvlglslvlllllligflfvlf..srkrqalhDklag 141
                                       l++ v+   g+ + +  a   ++              ++ll++++l+ l+  +r+rq+l  k+++
  gi|330508582|ref|YP_004385010.1|  72 LKIAVTGPYGEQIRFRDAAAESF------------GKAFLLPVDVLMSLIlfQRSRQRLFNKISN 124
                                       ********************997............55566666666555555********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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 0.20s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 1096.01
//
Query:       gi|330508583|ref|YP_004385011.1|  [L=350]
Description: hypothetical protein MCON_2816 [Methanosaeta concilii GP6]
Scores for complete 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       0.21   11.9   0.0    3.5  4  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
  ------ inclusion threshold ------
       0.11   12.8   0.9         13    6.2   0.0    3.1  4  DUF11        Domain of unknown function DUF11


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 ?    0.2   0.0      0.11   9.4e+02       2      17 ..      55      70 ..      54      72 .. 0.90
   2 !   11.3   0.0   3.5e-05      0.31      44      78 ..     126     162 ..     117     163 .. 0.79
   3 ?   -2.9   0.0      0.94   8.4e+03      49      60 ..     196     207 ..     179     212 .. 0.64
   4 !   11.9   0.0   2.3e-05      0.21       4      79 .]     225     299 ..     222     299 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.11
                       NPCBM_assoc  2 epGetvtltltvtndg 17
                                      ++G+tvtl l +tn g
  gi|330508583|ref|YP_004385011.1| 55 KRGDTVTLYLDLTNYG 70
                                      79************98 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.5e-05
                       NPCBM_assoc  44 aaslapGetvea..tvkVtppagaaaGdyevtakarl 78 
                                       ++sl+ G+++++  ++++++++ a aG+y++ ++ ++
  gi|330508583|ref|YP_004385011.1| 126 VESLKSGDKTQFplKFTIKIGEHAPAGEYPLHLNMTY 162
                                       3488888887754499***************999876 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.94
                       NPCBM_assoc  49 pGetveatvkVt 60 
                                       +++tv +t++V+
  gi|330508583|ref|YP_004385011.1| 196 ANQTVPVTIRVK 207
                                       455555555554 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 2.3e-05
                       NPCBM_assoc   4 GetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakarlt 79 
                                       G+++++ +t  n g++++++   +ls  +  + ++ + a +  l+pG ++++ +++ + ++a + dy +  ++++t
  gi|330508583|ref|YP_004385011.1| 225 GKKQEIHATYRNIGEDPVRDAVARLSIFKPFS-STDDQAFIGNLEPGNETTVLFRMDVDSDATTKDYGISSEIKYT 299
                                       8999****************999999977777.668888888***************************9999986 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0    0.0097        87       9      26 ..      53      70 ..      45      72 .. 0.86
   2 ?   -2.6   0.0      0.79   7.1e+03       7      18 ..     124     137 ..     108     142 .. 0.56
   3 ?   -2.8   0.1      0.89     8e+03      68      81 ..     196     209 ..     175     219 .. 0.60
   4 ?    6.2   0.0    0.0014        13      56      84 ..     259     287 ..     232     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0097
                             DUF11  9 evrpGdtvtytltvtNtg 26
                                      e++ Gdtvt  l +tN+g
  gi|330508583|ref|YP_004385011.1| 53 EFKRGDTVTLYLDLTNYG 70
                                      6788************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.79
                             DUF11   7 ks..evrpGdtvty 18 
                                       ++   +++Gd++++
  gi|330508583|ref|YP_004385011.1| 124 QVveSLKSGDKTQF 137
                                       33334455555555 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.89
                             DUF11  68 esatlsftvrvtrt 81 
                                       +  t+ +t+rv+++
  gi|330508583|ref|YP_004385011.1| 196 ANQTVPVTIRVKKQ 209
                                       44455555555554 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0014
                             DUF11  56 saltsv.gsLeagesatlsftvrvtrtaas 84 
                                       + +  + g+Le+g+++t+ f++ v   a++
  gi|330508583|ref|YP_004385011.1| 259 DDQA-FiGNLEPGNETTVLFRMDVDSDATT 287
                                       2333.359***************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2426.05
//
Query:       gi|330508584|ref|YP_004385012.1|  [L=775]
Description: hydrophobe/amphiphile efflux-3 (HAE3) family efflux transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-48  165.6  19.7    7.2e-25   87.6   8.6    2.3  2  MMPL            MMPL family
    1.5e-08   34.6   9.1      3e-05   23.9   0.7    2.9  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
    4.6e-08   32.7   6.1    4.6e-08   32.7   6.1    2.6  2  SecD_SecF       Protein export membrane protein
    3.8e-07   28.2  24.4    4.6e-06   24.6   5.5    2.3  2  ACR_tran        AcrB/AcrD/AcrF family
  ------ inclusion threshold ------
        9.5    4.1  17.6      0.081   11.0   2.7    2.5  2  Patched         Patched family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   3.2   3.6e-27   1.3e-23      70     317 ..     107     384 ..      54     405 .. 0.76
   2 !   87.6   8.6     2e-28   7.2e-25      87     295 ..     530     736 ..     471     757 .. 0.86

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 3.6e-27
                              MMPL  70 f..........................lsdpdvaaafvSkDgkaaralvtlegdp..gsteadesvaairaaveear 118
                                                                  l+d     + + +D + +r++v +   +   +++  e +a+i +av+ a+
  gi|330508584|ref|YP_004385012.1| 107 IadivadaeyqssgirripsqerideiLADAGSSVQGLMPDSRHTRMIVGMPTTAtlTESQRGELLAEISSAVDFAE 183
                                       4333444444444444444444444444444455556668999999999876544114556667799********** PP

                              MMPL 119 pleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalll 195
                                        ++g    vtG +   a ++++ +++ + + ++  ++ +v Ll+v+r +  +llpl  v+++++ ++g +  + ++ 
  gi|330508584|ref|YP_004385012.1| 184 FPAGYSTTVTGDPSFQAAIQEVMNNSNGSVLLLCGLLMIVALLLVFRHVRWPLLPLPIVLLGIIWTVGAMG-FFHI- 258
                                       *********************************************************************32.3233. PP

                              MMPL 196 glelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpv 272
                                        +++ tf+   ++ ++i+ G+DYa+ +  R+ eel +g+++ ea+i +v+ ++  v++a  +  + +++L+ +++p+
  gi|330508584|ref|YP_004385012.1| 259 PMGMVTFA---AFPIMIGLGIDYAIQFHNRIDEELIKGKSSVEAAISTVNHVAIPVAIAVTVTEAGFIALLSSTVPS 332
                                       34444443...799*************************************************************** PP

                              MMPL 273 laqvGvaialGvlvdvlivlTllPAllvllGraalakprrkrkk..........r 317
                                       ++ +G ++ +G+++  l +l +   +l l  r+   +pr+k ++          +
  gi|330508584|ref|YP_004385012.1| 333 INDFGKVCMIGLVMCYLSALFVNTTVLYLSERK---SPRKKKAEghsedgsaigA 384
                                       *****************9998878888776666...4444433323555555550 PP

  == domain 2  score: 87.6 bits;  conditional E-value: 2e-28
                              MMPL  87 aaralvtlegdpgsteadesvaairaaveear....pleglkvevtGpaatladlrdasdrdlklievvtlvvilvi 159
                                        a++ v++  d++++++ e +a++ +  e+      p+ g+ v++tG+a+++a ++da  + +  + +++lv+i+++
  gi|330508584|ref|YP_004385012.1| 530 LAIVDVNIG-DAQTNLGTEGMARLIKSYEDDLawmtPPPGVSVRITGQAVLMATVMDALISGRVEMSLLGLVLIFIL 605
                                       457788887.89999999888888777777667888***************************************** PP

                              MMPL 160 LlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedr 236
                                       Ll +yr l+ allp+l  +v     +g + ++ +  gl+ +  +++l  +l+++vG+ Ya+l++ R+ eel++  d 
  gi|330508584|ref|YP_004385012.1| 606 LLAIYRDLIKALLPVLPMLV----VIGWMGLVMYYGGLKYTPLTATL-GALILGVGSEYAILMMERFYEELHNVGDP 677
                                       **************987655....44554556777788877777666.57889************************ PP

                              MMPL 237 eeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll 295
                                        ea+  + +++g++ +a+G+ v++ +++L+ + +++++++G++  l++++++  ++T+ 
  gi|330508584|ref|YP_004385012.1| 678 YEALKITANRIGSALVASGAAVIFGFAALMSSPFNIISNFGLVTVLSIVFALITTFTVF 736
                                       ****************************************************9999986 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 !   23.9   0.7   8.4e-09     3e-05      15     144 ..     241     371 ..     236     376 .. 0.84
   2 !   13.6   2.2   1.2e-05     0.044      24     140 ..     630     748 ..     616     760 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 8.4e-09
                                       HHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHH..HHTTTCHHHHHHHHHHHHCCCCHHCC CS
                    Sterol-sensing  15 ivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqr..tsrsldeseriaealgevgpsillts 89 
                                       ivll ++ ++g + ++ +++ ++++  +P + +  g+d    + + +++  ++ +++++  i  +   ++p +++ +
  gi|330508584|ref|YP_004385012.1| 241 IVLLGIIWTVGAMGFFHIPMGMVTFAAFP-IMIGLGIDYAIQFHNRIDEelIKGKSSVEAAISTVNHVAIPVAIAVT 316
                                       7999*********************9999.67899***998888888662245566667777777777778888899 PP

                                       CHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHH.HCTX CS
                    Sterol-sensing  90 ltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldirre.eser 144
                                       +te+  ++l  +++vp ++ F   +++++++ +l  +++ ++vL l +r+  ++++
  gi|330508584|ref|YP_004385012.1| 317 VTEAGFIALL-SSTVPSINDFGKVCMIGLVMCYLSALFVNTTVLYLSERKSpRKKK 371
                                       9999988854.699***********************************9866655 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.2e-05
                                       CCHH.HHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHH.HHHHTTTCHHHHHHHHHHHHCCCCHHCCCHHHHHHHH CS
                    Sterol-sensing  24 lgll.aylgltltliilevlPflvlavgvdnifvlvkav.qrtsrsldeseriaealgevgpsilltsltellalll 98 
                                       +gl+ +y gl++t++++  l  l+l vg +   ++++ + +++++  d  e ++ + +++g +++++ +  ++ ++ 
  gi|330508584|ref|YP_004385012.1| 630 MGLVmYYGGLKYTPLTA-TLGALILGVGSEYAILMMERFyEELHNVGDPYEALKITANRIGSALVASGAAVIFGFAA 705
                                       56551556899999999.9999********87776666505555555557888888888888888887777777775 PP

                                       HHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHH.HHHHHHH CS
                    Sterol-sensing  99 galtdvpavqeFclfaavavlvdFllqitfFvavL.sldirre 140
                                        +++ +  +++F l +++++++  +   t+Fv ++  ++i re
  gi|330508584|ref|YP_004385012.1| 706 LMSSPFNIISNFGLVTVLSIVFALITTFTVFVVLMiRMEIHRE 748
                                       56788999***********************988724566666 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   6.1   1.3e-11   4.6e-08      37     185 ..     214     361 ..     199     365 .. 0.81
   2 ?    1.7   1.3     0.041   1.5e+02      24      83 ..     687     744 ..     668     751 .. 0.65

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.3e-11
                                       HHHHHHHHHHHHHHHT-.HHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSSHHHHHHHHHHHHHH CS
                         SecD_SecF  37 llialvliliyvalrFe.wrvalaaiialvhDviitvgvlsllgievdlatvaalLtiiGYSvndtvvvfdrvrenl 112
                                       ll+  +l+++ + l F+  r++l  +  ++  +i tvg++  ++i++ + t aa   +iG  ++  +   +r+ e+l
  gi|330508584|ref|YP_004385012.1| 214 LLLCGLLMIVALLLVFRhVRWPLLPLPIVLLGIIWTVGAMGFFHIPMGMVTFAAFPIMIGLGIDYAIQFHNRIDEEL 290
                                       3333344555556666526899***9999***********************************************9 PP

                                       HH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTTTHHHHHHHHHHH CS
                         SecD_SecF 113 rkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgtyssifiaspllll 185
                                        k  + +++ +i +  +  +  +i+ ++t     +all  +  s++df  + ++Gl++  +s++f+++++l+l
  gi|330508584|ref|YP_004385012.1| 291 IK-GKSSVEAAISTVNHVAIPVAIAVTVT-EAGFIALLSSTVPSINDFGKVCMIGLVMCYLSALFVNTTVLYL 361
                                       98.55667777766666667766666666.556778889999**************************99876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHTT---- CS
                         SecD_SecF  24 svskelaekavlallialvliliyvalrFewrvalaaiialvhDviitvgvlsllgievd 83 
                                       ++++ l+ +++  ++++ +l+     ++   +++l  ++++v+ +i+t +v+++l i ++
  gi|330508584|ref|YP_004385012.1| 687 RIGSALVASGAAVIFGFAALMSSPFNII--SNFGLVTVLSIVFALITTFTVFVVLMIRME 744
                                       5566666666655555555554433333..567777888888888888888887765543 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   5.5   1.3e-09   4.6e-06     309     449 ..     183     325 ..     154     369 .. 0.86
   2 !    9.1  11.0   6.3e-05      0.23     325     482 ..     583     736 ..     549     759 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.3e-09
                                       GSSTTEEEEEEEESHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                          ACR_tran 309 slPegveivvvydrtefvrasieeVvkt.....LleaivLvvlvvflFLqnlratlipaiavPlsllgtfavlkalg 380
                                       ++P+g++++v+ d +   +a+i+eV ++     Ll+  +L ++ ++l  + +r  l p+ +v l ++ t+ ++ ++ 
  gi|330508584|ref|YP_004385012.1| 183 EFPAGYSTTVTGDPS--FQAAIQEVMNNsngsvLLLCGLLMIVALLLVFRHVRWPLLPLPIVLLGIIWTVGAMGFFH 257
                                       599***999999987..58889999876444456667778889999999**************************** PP

                                       --BCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGG CS
                          ACR_tran 381 fslNlltLfgLvlAiGlvvDdAiVvvEnierkleeegekpleaalksmkeiqgalvaialvllavflPi 449
                                       + + + t  +  + iGl +D Ai     i ++l + g++ +eaa+ +++ ++ ++   + v  a f+ +
  gi|330508584|ref|YP_004385012.1| 258 IPMGMVTFAAFPIMIGLGIDYAIQFHNRIDEELIK-GKSSVEAAISTVNHVAIPVAIAVTVTEAGFIAL 325
                                       **********************************9.******************977777777777654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 6.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHH..TT--BCHHHHHHHHHHHHHHH CS
                          ACR_tran 325 fvrasieeVvktLleaivLvvlvvflFLqnlratlipaiavPlsllgtfavlka..lgfslNlltLfgLvlAiGlvv 399
                                       + +a i+  v+  l+++vL+++ ++   ++l  +l p++ + +++     v++   l+++  + tL++L l++G   
  gi|330508584|ref|YP_004385012.1| 583 VMDALISGRVEMSLLGLVLIFILLLAIYRDLIKALLPVLPMLVVIGWMGLVMYYggLKYTPLTATLGALILGVGS-- 657
                                       556666666777789**********************8755444433334444411445566779******9997.. PP

                                       HHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHHHHHHHHHHHHHHH CS
                          ACR_tran 400 DdAiVvvEnierkleeegekpleaalksmkeiqgalvaialvllavflPilflgGveGklfrqfaltivlaillsvl 476
                                         Ai ++E  +++l++   +p ea + +++ i++alva+ +    v   +++l  +  ++  +f+l  vl+i+ +++
  gi|330508584|ref|YP_004385012.1| 658 EYAILMMERFYEELHN-VGDPYEALKITANRIGSALVASGAA---VIFGFAALMSSPFNIISNFGLVTVLSIVFALI 730
                                       89*************9.8899****************99864...55566788889999999999999999999998 PP

                                       HHHCCH CS
                          ACR_tran 477 valtlt 482
                                          t+ 
  gi|330508584|ref|YP_004385012.1| 731 TTFTVF 736
                                       888765 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   7.1      0.18   6.4e+02     651     801 ..     201     354 ..     169     370 .. 0.77
   2 ?   11.0   2.7   2.2e-05     0.081     262     388 ..     620     745 ..     607     772 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.18
                           Patched 651 qlltilpstiqnivlallcmfvvallfipelitvlvitlsivsidi.gviGflslWgvdLDpismitiimsiGfsvd 726
                                        +++++ +   +++l   ++++vall++   +   +  l iv + i  ++G + +  + +  ++ ++  + iG  +d
  gi|330508584|ref|YP_004385012.1| 201 AIQEVMNNSNGSVLLLCGLLMIVALLLVFRHVRWPLLPLPIVLLGIiWTVGAMGFFHIPMGMVTFAAFPIMIGLGID 277
                                       55666666666666666678999999998888877777777776541588999999999999999999999999999 PP

                           Patched 727 lsaHiayafvrsekd..dakeRvvealealgwPvvqgalSTilgvlvLlfvdsymvqvFfktvvLvvvigllHgLli 801
                                       ++     ++ ++  +  ++ e +++++++++ Pv  + + T +g + Ll      ++ F k  ++ +v+  l +L++
  gi|330508584|ref|YP_004385012.1| 278 YAIQFHNRIDEELIKgkSSVEAAISTVNHVAIPVAIAVTVTEAGFIALLSSTVPSINDFGKVCMIGLVMCYLSALFV 354
                                       98555444444433344777788888888999999999999999999987777778888888888888888877776 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.2e-05
                           Patched 262 lspvlAivsslGlllwl.GfrfnsivtvtPFLvLaiGvDdmflmvaawkrteakls........vkkrigealseag 329
                                       + p+l ++  +Gl+++  G+++   +     L+L++G   + lm++++ +   +          + +rig al+ +g
  gi|330508584|ref|YP_004385012.1| 620 VLPMLVVIGWMGLVMYYgGLKYTPLTATLGALILGVGSEYAILMMERFYEELHNVGdpyealkiTANRIGSALVASG 696
                                       458888888889866552799**********************9998765444443456677777777777777777 PP

                           Patched 330 vaitiTslTdvlsFgiGaittlpaiqlFciytavailfdfiYqitffaavlaiaakaea 388
                                        a+       ++ F++ + ++   i+ F ++t ++i+f+ i ++t+f  ++  ++   +
  gi|330508584|ref|YP_004385012.1| 697 AAV-------IFGFAALMSSPFNIISNFGLVTVLSIVFALITTFTVFVVLMIRME---I 745
                                       776.......799**************************9998888877765443...3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (775 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1100  (0.0613531); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.45
# Mc/sec: 5190.31
//
Query:       gi|330508585|ref|YP_004385013.1|  [L=174]
Description: hypothetical protein MCON_2818 [Methanosaeta concilii GP6]
Scores for complete sequence (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   25.1   0.1    3.3e-05   23.6   0.0    1.8  2  HTH_DeoR  DeoR-like helix-turn-helix domain
    0.00017   21.5   0.2    0.00055   19.8   0.0    1.9  3  HTH_11    HTH domain
     0.0012   18.3   0.0     0.0035   16.9   0.0    1.8  1  HTH_24    Winged helix-turn-helix DNA-binding
     0.0017   18.1   0.0     0.0056   16.4   0.0    1.9  1  HTH_IclR  IclR helix-turn-helix domain
     0.0023   17.9   0.1     0.0065   16.5   0.1    1.7  1  HTH_Mga   M protein trans-acting positive regulator (MGA) HTH
     0.0027   17.6   0.0     0.0063   16.4   0.0    1.7  1  HTH_36    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.033   14.1   0.0    1.6  1  TrmB      Sugar-specific transcriptional regulator TrmB
      0.021   14.7   0.1      0.034   14.0   0.1    1.4  1  SH3_13    ATP-dependent RecD-like DNA helicase SH3 domain
      0.086   12.8   0.0       0.15   12.0   0.0    1.5  1  HTH_43    Winged helix-turn helix
      0.089   12.5   0.0       0.25   11.0   0.0    1.7  1  GntR      Bacterial regulatory proteins, gntR family
       0.11   12.6   0.0        1.1    9.4   0.0    2.3  2  HTH_29    Winged helix-turn helix


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 !   23.6   0.0     2e-08   3.3e-05      11      47 ..      40      76 ..      36      80 .. 0.93
   2 ?   -2.4   0.0       2.5     4e+03      14      24 ..     159     169 ..     152     171 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2e-08
                          HTH_DeoR 11 qqgklsveelvellgvSeaTiRRDLneLeeqglltRt 47
                                      ++ ++s++ l+e  g+S++T+R  +n+Le+ g+ +R+
  gi|330508585|ref|YP_004385013.1| 40 ESESMSLDTLAEKTGYSKTTVRSNMNFLENLGMAHRV 76
                                      6789*****************************9997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.5
                          HTH_DeoR  14 klsveelvell 24 
                                       + +++el+e l
  gi|330508585|ref|YP_004385013.1| 159 HYTLKELIEVL 169
                                       44566666655 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.4e-07   0.00055      10      44 ..      39      77 ..      36      85 .. 0.80
   2 ?   -3.0   0.0       4.4   7.2e+03      32      45 ..     108     121 ..     106     125 .. 0.51
   3 ?   -3.3   0.0       5.7   9.3e+03       3       8 ..     163     168 ..     157     173 .. 0.48

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.4e-07
                            HTH_11 10 leargpisgeeLAeeLnvSrrtvrrdIkaLeelg.....v 44
                                      le+++ +s ++LAe+++ S++tvr  +  Le lg     v
  gi|330508585|ref|YP_004385013.1| 39 LESES-MSLDTLAEKTGYSKTTVRSNMNFLENLGmahrvV 77
                                      46666.9***************************774444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.4
                            HTH_11  32 vrrdIkaLeelgvp 45 
                                       vr  I ++  ++ +
  gi|330508585|ref|YP_004385013.1| 108 VREEIHSILRALNQ 121
                                       55555555444444 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.7
                            HTH_11   3 lqilel 8  
                                       + ++e 
  gi|330508585|ref|YP_004385013.1| 163 KELIEV 168
                                       222333 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   0.0   2.1e-06    0.0035      17      45 ..      43      71 ..      37      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.1e-06
                            HTH_24 17 risqreLAerlglSpstvnrrlkrLeeeG 45
                                      ++s   LAe++g S++tv+  ++ Le+ G
  gi|330508585|ref|YP_004385013.1| 43 SMSLDTLAEKTGYSKTTVRSNMNFLENLG 71
                                      577788********************998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.4e-06    0.0056      17      49 ..      42      74 ..      35      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.4e-06
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      + ++l  lA++tg +k+tv+  ++ L++lG+  
  gi|330508585|ref|YP_004385013.1| 42 ESMSLDTLAEKTGYSKTTVRSNMNFLENLGMAH 74
                                      569***************************976 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1     4e-06    0.0065      12      44 ..      36      67 ..      36      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4e-06
                           HTH_Mga 12 elLteneksltldelakeLglseltlqsdiseL 44
                                      +l++e ++s++ld+la+++g s  t++s  ++L
  gi|330508585|ref|YP_004385013.1| 36 TLFLE-SESMSLDTLAEKTGYSKTTVRSNMNFL 67
                                      68899.*********************977666 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.9e-06    0.0063      27      53 ..      45      71 ..      18      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.9e-06
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlG 53
                                      s +tla+++g sk Tv++  + Le lG
  gi|330508585|ref|YP_004385013.1| 45 SLDTLAEKTGYSKTTVRSNMNFLENLG 71
                                      689*********************999 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     2e-05     0.033      18      55 ..      39      76 ..      36      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      l++++++ d++ae++g ++++v + ++ Le+ G+ +r+
  gi|330508585|ref|YP_004385013.1| 39 LESESMSLDTLAEKTGYSKTTVRSNMNFLENLGMAHRV 76
                                      7999******************************9986 PP

>> SH3_13  ATP-dependent RecD-like DNA helicase SH3 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     0.034      13      41 ..     133     162 ..     119     168 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                            SH3_13  13 skkkkevkvggrv.frvgDkVmqlkNnydk 41 
                                       ++k+  + ++ r+ + + D+Vm l+N+y++
  gi|330508585|ref|YP_004385013.1| 133 AEKTSAIMRKTRQfYEEMDRVMELMNHYTL 162
                                       223334444444449999*********985 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.2e-05      0.15      15      66 ..      38      90 ..      32     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.2e-05
                                      HHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE-.-TTS-S--EEE CS
                            HTH_43 15 lideeeanvpklieltgmPRRtlqDtlkalaeldielefvq.egernnaGyyr 66
                                       +++e+ ++ +l e+tg+ + t+   ++ l++l++  + v+  g+r ++ ++r
  gi|330508585|ref|YP_004385013.1| 38 FLESESMSLDTLAEKTGYSKTTVRSNMNFLENLGMAHRVVDlAGKRRHDKQHR 90
                                      5788889********************************99989888765544 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00015      0.25      22      57 ..      42      76 ..      32      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                                      SB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 22 dkLPsereLaaefgVsrttvReALrrLeaeglverr 57
                                      + + s   La++ g s+ttvR  ++ Le  g+++r 
  gi|330508585|ref|YP_004385013.1| 42 ESM-SLDTLAEKTGYSKTTVRSNMNFLENLGMAHRV 76
                                      667.8889***********************99885 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.38   6.1e+02      20      45 ..       5      30 ..       5      36 .. 0.83
   2 ?    9.4   0.0   0.00066       1.1       9      46 ..      41      81 ..      37      99 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.38
                            HTH_29 20 kllglsrrtvyrwlkrfeegGlaall 45
                                      ++l l r+ ++ ++k  ++ G++ ++
  gi|330508585|ref|YP_004385013.1|  5 EMLALKRPIIDACIKSAQKNGWSDAM 30
                                      589999999*******9999987666 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00066
                            HTH_29  9 aeGvstvsqiAkllglsrrtvyrwlkrfeegGlaa....lld 46
                                      +e +s    +A+ +g+s++tv+   +  e+ G a     l  
  gi|330508585|ref|YP_004385013.1| 41 SESMS-LDTLAEKTGYSKTTVRSNMNFLENLGMAHrvvdLAG 81
                                      56676.999***************999999997655444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1391  (0.0775838); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1346.08
//
Query:       gi|330508586|ref|YP_004385014.1|  [L=165]
Description: sulfopyruvate decarboxylase subunit alpha [Methanosaeta concilii GP6]
Scores for complete 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-08   33.1   0.0    5.5e-08   32.6   0.0    1.4  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 !   32.6   0.0   3.1e-12   5.5e-08       6     106 ..       6     105 ..       1     165 [] 0.71

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 3.1e-12
                                       HHHHHHHHCT--EEEE---CCCHHHHCCHHCT..TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                      TPP_enzyme_N   6 alvraLkalgvehvfgvpGsrilplldalseeq.girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                       a+ r Lk++g++ +  vp+ ++ +ll  l e +  i++  +r E+g++  A ++  + g++ ++l+++  G+ n+++
  gi|330508586|ref|YP_004385014.1|   6 AIYRGLKRAGIDFAASVPCVNLQELLTLLGEDPdIIHLPATREEEGVGLCAGAW--MGGRRPALLMQN-SGLGNCIN 79 
                                       78999***************************9888888899999999999998..776666666666.48999999 PP

                                       HHHHH.HHHT--EEEEEEE--CCCHH CS
                      TPP_enzyme_N  82 alaeA.kvdriPllvlsgdrptslrg 106
                                       ala+  ++ +iPll++  +r+ + ++
  gi|330508586|ref|YP_004385014.1|  80 ALASLdMLYGIPLLIIISHRGGKGEP 105
                                       999864789*******9999877777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1283.78
//
Query:       gi|330508587|ref|YP_004385015.1|  [L=186]
Description: sulfopyruvate decarboxylase subunit beta [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-19   70.8   0.1    2.2e-19   69.8   0.1    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 !   69.8   0.1   1.2e-23   2.2e-19      24     147 ..      42     149 ..      15     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 1.2e-23
                                       ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-.SEEEEEEE-SBCCCHHHHHHHHTCCT CS
                      TPP_enzyme_C  24 sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnl.pitvvvlnNegygmtggqqepfggkr 99 
                                        ++lg+mG + ++++G++lakp+r+v+++ GDG+ lm+l  lat++ ++  ++++v+l+N +yg tg q++ +    
  gi|330508587|ref|YP_004385015.1|  42 FYMLGSMGMASSIGLGLALAKPKRRVMVLDGDGSVLMNLGTLATIALHGPkNFLLVILDNCCYGSTGSQPTCTCY-- 116
                                       3579*********************************************99*****************9876653.. PP

                                       TTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSS CS
                      TPP_enzyme_C 100 ksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkg 147
                                                  +d+a++a+++G++ + +v+++      eal +al+ +g
  gi|330508587|ref|YP_004385015.1| 117 ----------CTDLAAVARGAGIReVEKVDDP------EALTRALQGQG 149
                                       ..........469***********88899999......55555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1493.79
//
Query:       gi|330508588|ref|YP_004385016.1|  [L=434]
Description: putative methanogenesis marker 16 metalloprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.4e-110  369.5   0.0   1.5e-110  369.3   0.0    1.0  1  HcyBio    Homocysteine biosynthesis enzyme, sulfur-incorporat
    3.6e-08   33.1  10.4    0.00011   22.1   2.4    2.7  2  Fer4_6    4Fe-4S binding domain
    1.3e-07   31.7   9.1    2.6e-07   30.7   9.1    1.5  1  Fer4_9    4Fe-4S dicluster domain
    6.9e-07   29.8  10.5    2.1e-06   28.2  10.7    1.8  1  Fer4_7    4Fe-4S dicluster domain
    8.1e-07   28.6  11.2    2.1e-05   24.2   1.0    3.4  2  Fer4      4Fe-4S binding domain
    1.3e-05   25.0  13.0     0.0015   18.5   1.6    2.9  2  Fer4_2    4Fe-4S binding domain
    2.2e-05   24.4  11.5    0.00034   20.7  11.2    2.4  2  Fer4_10   4Fe-4S dicluster domain
    0.00026   21.1   8.3    0.00052   20.1   8.3    1.6  1  Fer4_21   4Fe-4S dicluster domain
    0.00062   20.3   8.7          1   10.0   0.7    2.4  2  Fer4_17   4Fe-4S dicluster domain
     0.0033   18.3   9.3       0.54   11.2   1.2    2.5  2  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.057   14.4   5.4      0.057   14.4   5.4    3.3  2  Fer4_3    4Fe-4S binding domain
      0.074   13.2   3.5       0.16   12.1   3.5    1.5  1  Fer4_11   4Fe-4S dicluster domain
       0.22    9.5   0.2       0.29    9.1   0.2    1.1  1  Bunya_G1  Bunyavirus glycoprotein G1
       0.96    9.9  11.9       0.54   10.7   2.0    2.4  3  Fer4_8    4Fe-4S dicluster domain
        1.4    9.7  10.3         10    6.9   1.2    2.8  2  Fer4_15   4Fe-4S single cluster domain
        4.7    8.0  23.9       0.16   12.5   3.6    3.1  2  Fer4_4    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> HcyBio  Homocysteine biosynthesis enzyme, sulfur-incorporation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.3   0.0  1.4e-113  1.5e-110       1     347 []      22     426 ..      22     426 .. 0.98

  Alignments for each domain:
  == domain 1  score: 369.3 bits;  conditional E-value: 1.4e-113
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx......xx RF
                            HcyBio   1 avVltaeelkklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaepkiki..ekvwLngvpayag......la 69 
                                       avVltaee+++lv++ ++++++eevDVVtt+T++vms+++a+l+++vaep++++  ++vwLng++a++g      l+
  gi|330508588|ref|YP_004385016.1|  22 AVVLTAEEVSRLVED-EDRSSLEEVDVVTTATRAVMSGTYAILSFPVAEPGSFQraRNVWLNGISAQVGpcpnenLG 97 
                                       8**************.999**********************************9999******************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio  70 avdlylgataeseddkeeeeyGGghviedLvagkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnY 146
                                        +dl++++ta s+d   + +yGGgh+++dLv+gk++++e++++e+       +++e  l+d+++a+++++R+a++nY
  gi|330508588|ref|YP_004385016.1|  98 LLDLIVFGTACSRD---RPDYGGGHLFRDLVEGKTIQVEVQTDEG-----GLLQAEAGLEDMPQARMFGSRHAFKNY 166
                                       *************3...449*************************.....9************************** PP

                                       xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 147 naavNssee...tiytymgelkpnlgnatysgaGelsPllnDpelktigiGtrilLgGaeGyvigeGTqsspekkre 220
                                       +a+vN++++   ti++ ++ ++p++++at+sg+G+++Pl+ Dp l+tigiGtrilL+GaeGyv+g+GT+ss++k+  
  gi|330508588|ref|YP_004385016.1| 167 SAFVNPGSRsvrTIFH-ARGFEPHCQGATFSGCGQINPLKCDPLLETIGIGTRILLNGAEGYVLGTGTRSSRDKP-- 240
                                       ********9999****.**********************************************************.. PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 221 ngvplgpagtLavigdlkeMspeylrgafltsyGpelivgvgipiPvldeevleelavkdedielpvvDvserrrer 297
                                                +L+ ++d+++M++ey+ g+f+t+ Gpe+i+++++piPv++ ++lee+a +d++i+lpv D+++r    
  gi|330508588|ref|YP_004385016.1| 241 ---------NLSGFADMHHMTAEYM-GGFVTGLGPECICSLAVPIPVTSPTILEEIARRDREIALPVNDINTR---- 303
                                       .........****************.***********************************************.... PP

                                       xxxxxxxxxxx.................................................................. RF
                            HcyBio 298 ktlgevsYael.................................................................. 308
                                       +++g+++Y+++                                                                  
  gi|330508588|ref|YP_004385016.1| 304 TVIGQANYGDVwedvdlevefdpqrcrgckkclveracpmravrydqearvairdgslcfhcglcvtecpngafrcr 380
                                       8**************************************************************************** PP

                                       .xxxxxxxx.....xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 309 .Gkieiegk.....ev.ktarlsslkrareiaeeLkewiekgeflL 347
                                        G+++++++     +v +++r+s++ ra +++ eLk++i++g+f++
  gi|330508588|ref|YP_004385016.1| 381 lGALRMKTSsgsvrSVpVVLRQSDRLRAVKLSGELKRRILEGSFRM 426
                                       *999998877777789999*************************86 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   2.4   9.7e-08   0.00011       2      23 ..     322     345 ..     321     346 .. 0.92
   2 !   15.1   1.2   1.6e-05     0.018       6      23 ..     359     376 ..     354     377 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.7e-08
                            Fer4_6   2 veidpdkCigCgdC..vrvCPega 23 
                                       ve+dp++C gC +C  +r+CP+ a
  gi|330508588|ref|YP_004385016.1| 322 VEFDPQRCRGCKKClvERACPMRA 345
                                       89************99999**876 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.6e-05
                            Fer4_6   6 pdkCigCgdCvrvCPega 23 
                                        ++C +Cg Cv+ CP ga
  gi|330508588|ref|YP_004385016.1| 359 GSLCFHCGLCVTECPNGA 376
                                       57899**********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 !   30.7   9.1   2.3e-10   2.6e-07       1      50 [.     328     376 ..     328     377 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.3e-10
                            Fer4_9   1 kCtgCgaC..veaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       +C gC++C  ++aCp+ +v++d+ +r a  +    + C++Cg Cv  Cp+ga
  gi|330508588|ref|YP_004385016.1| 328 RCRGCKKClvERACPMRAVRYDQEARVAIRDG---SLCFHCGLCVTECPNGA 376
                                       5*******99999***********99999765...48************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 !   28.2  10.7   1.9e-09   2.1e-06       1      52 []     328     376 ..     328     376 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.9e-09
                            Fer4_7   1 rCigCgaCv..aaCpvkaieldeeenekgtekvei.dpekClgCgaCvavCPtga 52 
                                       rC gC++C   +aCp++a+++d+e      ++v+i d + C +Cg Cv++CP ga
  gi|330508588|ref|YP_004385016.1| 328 RCRGCKKCLveRACPMRAVRYDQE------ARVAIrDGSLCFHCGLCVTECPNGA 376
                                       8*******7558*********997......3455526789************997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   3.4     0.004       4.5       1      15 [.     322     336 ..     322     347 .. 0.75
   2 !   24.2   1.0   1.8e-08   2.1e-05       4      23 ..     358     377 ..     355     378 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.004
                                       EEEETTTSSS-THHH CS
                              Fer4   1 vvideekCigCGaCv 15 
                                       v++d+ +C gC++C 
  gi|330508588|ref|YP_004385016.1| 322 VEFDPQRCRGCKKCL 336
                                       579***********4 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1.8e-08
                                       ETTTSSS-THHHHHSTTTEE CS
                              Fer4   4 deekCigCGaCvevCPvgAI 23 
                                       d ++C +CG+Cv  CP+gA 
  gi|330508588|ref|YP_004385016.1| 358 DGSLCFHCGLCVTECPNGAF 377
                                       6689**************97 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.6   1.4e-06    0.0015       3      21 ..     322     342 ..     320     343 .. 0.88
   2 !   12.8   2.1   8.5e-05     0.095       8      22 .]     360     374 ..     352     374 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                            Fer4_2   3 vvvdtdrCigCgaCv..saCP 21 
                                       v++d++rC gC++C+   aCP
  gi|330508588|ref|YP_004385016.1| 322 VEFDPQRCRGCKKCLveRACP 342
                                       789***********66699*9 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.5e-05
                            Fer4_2   8 drCigCgaCvsaCPa 22 
                                         C +Cg Cv+ CP+
  gi|330508588|ref|YP_004385016.1| 360 SLCFHCGLCVTECPN 374
                                       57************5 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7  11.2     3e-07   0.00034       2      56 .]     322     373 ..     321     373 .. 0.72
   2 !   14.3   1.8   2.9e-05     0.033       3      23 ..     356     376 ..     354     404 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3e-07
                           Fer4_10   2 vvidddtCirCgkCvk..aCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                       v++d+++C +C+kC    aCP+          +++e++v + + + C +cg Cv +CP
  gi|330508588|ref|YP_004385016.1| 322 VEFDPQRCRGCKKCLVerACPM------RAVRYDQEARVAIrDGSLCFHCGLCVTECP 373
                                       6789**********87568***......333333333333324578999********9 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.9e-05
                           Fer4_10   3 vidddtCirCgkCvkaCPadl 23 
                                       ++d + C +Cg Cv+ CP  +
  gi|330508588|ref|YP_004385016.1| 356 IRDGSLCFHCGLCVTECPNGA 376
                                       678899************954 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   8.3   4.6e-07   0.00052       3      52 ..     324     373 ..     322     379 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.6e-07
                           Fer4_21   3 idedkCigCgkCli..aCedtshqaieidaktvlkvv.edeCvGCnlCssvCP 52 
                                       +d+++C gC+kCl+  aC+   + a+++d++++++++  + C  C lC++ CP
  gi|330508588|ref|YP_004385016.1| 324 FDPQRCRGCKKCLVerACP---MRAVRYDQEARVAIRdGSLCFHCGLCVTECP 373
                                       6899********9755899...8********9999973689************ PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.7   0.00089         1      21      58 ..     301     343 ..     290     346 .. 0.68
   2 !    8.5  12.4    0.0026       2.9       2      59 ..     329     375 ..     328     376 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00089
                           Fer4_17  21 epkkllraaklglleeaeke...ekaslCieCgeCe..rkCPq 58 
                                       + ++++ +a++g++ e  +       ++C +C++C   r+CP+
  gi|330508588|ref|YP_004385016.1| 301 NTRTVIGQANYGDVWEDVDLeveFDPQRCRGCKKCLveRACPM 343
                                       566677777775444422221325789********87799**8 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0026
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       C++C+ Cl           e++ ++ra+++   e+  + +  slC +Cg+C+++CP+g
  gi|330508588|ref|YP_004385016.1| 329 CRGCKKCLV----------ERACPMRAVRYD-QEARVAIRDGSLCFHCGLCVTECPNG 375
                                       555555544..........233334444332.22222234569*************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 !   11.2   1.2   0.00048      0.54       1      28 [.     328     357 ..     328     360 .. 0.85
   2 !   11.2   1.6   0.00051      0.57       2      18 ..     362     378 ..     361     393 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00048
                           Fer4_16   1 rCgtCgkCa..evCPtnaikekkekeiear 28 
                                       rC +C+kC+   +CP +a++ ++e+++++r
  gi|330508588|ref|YP_004385016.1| 328 RCRGCKKCLveRACPMRAVRYDQEARVAIR 357
                                       6*******84479********998888776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00051
                           Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                       C  Cg C+  CP +a++
  gi|330508588|ref|YP_004385016.1| 362 CFHCGLCVTECPNGAFR 378
                                       99************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 ?    0.1   1.8       1.8     2e+03       1       8 [.     329     336 ..     329     345 .. 0.61
   2 ?   14.4   5.4   5.1e-05     0.057       1      15 []     362     376 ..     362     376 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.8
                            Fer4_3   1 CtgCgaCv 8  
                                       C gC  C+
  gi|330508588|ref|YP_004385016.1| 329 CRGCKKCL 336
                                       77887775 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 5.1e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C +Cg+Cv  CP+gA
  gi|330508588|ref|YP_004385016.1| 362 CFHCGLCVTECPNGA 376
                                       9*************9 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.5   0.00014      0.16       2      60 ..     321     378 ..     320     389 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                           Fer4_11   2 ewlflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivr 60 
                                       e++f p+ Cr C +    +++p++a+  d+e  + + d + +  ++  +v+ cP  ++r
  gi|330508588|ref|YP_004385016.1| 321 EVEFDPQRCRGCKKCLVERACPMRAVRYDQEARVAIRDGSLCF-HCGLCVTECPNGAFR 378
                                       57899*********9999************8888888888886.9999*****977665 PP

>> Bunya_G1  Bunyavirus glycoprotein G1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00026      0.29     732     800 ..     298     370 ..     292     394 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00026
                          Bunya_G1 732 gelkiklilgdvkyklfaesldltie...akcvgcidcfesiscelt.lvstieaicslksscdvfhdrilvk 800
                                        +++ + ++g+ +y    e +dl++e    +c gc +c+ +  c ++ +  + ea  +++     fh  + v+
  gi|330508588|ref|YP_004385016.1| 298 NDINTRTVIGQANYGDVWEDVDLEVEfdpQRCRGCKKCLVERACPMRaVRYDQEARVAIRDGSLCFHCGLCVT 370
                                       5788899*****************9855568*************99724568899999999999999888776 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   2.9      0.13   1.5e+02      48      62 ..     326     342 ..     286     345 .. 0.68
   2 ?    2.0  13.7      0.26   2.9e+02       4      64 ..     328     375 ..     325     376 .. 0.64
   3 ?   10.7   2.0   0.00048      0.54       5      17 ..     362     376 ..     358     414 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.13
                            Fer4_8  48 lwsCttcgaC..tevCp 62 
                                        ++C +c++C  +++Cp
  gi|330508588|ref|YP_004385016.1| 326 PQRCRGCKKClvERACP 342
                                       56677777773333455 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.26
                            Fer4_8   4 kCieCgaCq..saCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       +C +C  C    aCp+   +    +d++ ++a     +++         C +cg C+++Cp+g
  gi|330508588|ref|YP_004385016.1| 328 RCRGCKKCLveRACPMRAVR----YDQEARVAI----RDG-------SLCFHCGLCVTECPNG 375
                                       78888888866668833222....223333222....445.......79************86 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00048
                            Fer4_8   5 CieCgaCqsaCp..v 17 
                                       C +Cg+C ++Cp  +
  gi|330508588|ref|YP_004385016.1| 362 CFHCGLCVTECPngA 376
                                       788888888887441 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.2    0.0091        10       1      17 [.     322     338 ..     322     350 .. 0.90
   2 ?    6.3   2.3     0.014        16       4      20 ..     358     374 ..     356     380 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0091
                           Fer4_15   1 VvvDrdaCigcglCvae 17 
                                       V++D ++C gc  C+ e
  gi|330508588|ref|YP_004385016.1| 322 VEFDPQRCRGCKKCLVE 338
                                       899***********976 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                           Fer4_15   4 DrdaCigcglCvaeape 20 
                                       D ++C  cglCv+e+p+
  gi|330508588|ref|YP_004385016.1| 358 DGSLCFHCGLCVTECPN 374
                                       7789***********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 ?    5.6   6.5     0.025        27       1      16 [.     326     343 ..     326     344 .. 0.77
   2 ?   12.5   3.6   0.00014      0.16       4      16 ..     362     374 ..     358     383 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.025
                            Fer4_4   1 qerCigCgsC..vaaCPq 16 
                                       ++rC gC++C  ++aCP+
  gi|330508588|ref|YP_004385016.1| 326 PQRCRGCKKClvERACPM 343
                                       68********55555876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C++Cg Cv  CP 
  gi|330508588|ref|YP_004385016.1| 362 CFHCGLCVTECPN 374
                                       ************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3266.14
//
Query:       gi|330508589|ref|YP_004385017.1|  [L=330]
Description: aliphatic sulfonate ABC transporter substrate-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-32  113.2   0.1    2.8e-32  112.4   0.1    1.3  1  NMT1_2          NMT1-like family
    1.4e-15   57.8   0.0    1.9e-15   57.4   0.0    1.2  1  NMT1            NMT1/THI5 like
    0.00018   21.0   0.1      0.013   15.0   0.0    2.5  2  NMT1_3          NMT1-like family
  ------ inclusion threshold ------
      0.051   13.2   0.0      0.074   12.6   0.0    1.3  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub


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 !  112.4   0.1   6.2e-36   2.8e-32       6     247 ..      35     263 ..      31     267 .. 0.93

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 6.2e-36
                            NMT1_2   6 eqlklGfialtdaaplvvakekglfake....Glt.velekqaswaelrdkllagelDaahv.ltpapllidlGigg 76 
                                       ++l++G+++ t+    +va+e+g+ a+     G+t ++  ++  +   +++++agelD+a+v  +p +++i  G+  
  gi|330508589|ref|YP_004385017.1|  35 TTLRIGYQPSTHQIAEMVASEMGWWAEDlspfGITeIKEFEFPTGVPEMQAMVAGELDIAYVgTAPPISAIAAGL-- 109
                                       789************************99******9*999***********************************.. PP

                            NMT1_2  77 akadmkvlaslnlnGqaitlsnklkdkkvsdakalkdlvakkkas.kplkiavtfpgsthdlllrywLaaaGldpea 152
                                          + k++a++n +G +++++ +         ++         +s ++l i++  pgs +d+ ++ wL  +G+++ +
  gi|330508589|ref|YP_004385017.1| 110 ---PAKIVAAVNIKGSDLVVRPD------LAYSGP--------ESlEGLSIGTFPPGSIQDTVMKKWLTDNGVEV-S 168
                                       ...*****************965......333333........334899**************************.9 PP

                            NMT1_2 153 dvklvvvpppqmvanlkagtidgfcvgePwnaqavaegiGvtaltsqelwkdhPekvlgvredfveknpntaralvk 229
                                       +v++ ++ p  ++++l+ag+idg + + P ++  + +g G  ++ s+e w+dh ++ l+v+ ++++++p+++++++k
  gi|330508589|ref|YP_004385017.1| 169 EVDIKAMDPGPAMSALSAGRIDGVFLPHPAPSIVELNGKGKVVVASGEMWPDHACCSLVVTDKLIQEQPELVEQIIK 245
                                       99999999989999*************************************************************** PP

                            NMT1_2 230 alleAtkwldakkenrae 247
                                       ++++At++++  ++ +ae
  gi|330508589|ref|YP_004385017.1| 246 THIKATEYINTHPKEAAE 263
                                       **********85444444 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   4.2e-19   1.9e-15      28     216 .]      77     261 ..      44     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 4.2e-19
                                       -SSTTHHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--EEEEEECCC--SSGGGGTTSEEEE-S.-TT CS
                              NMT1  28 padpsdatelvasgkadfgvsyqesllaarakglpvvsvaallqeplsglivlkdsgikspkDLkGkrigyvg.spf 103
                                       p++    ++++ +g+ d++   +   + a a+glp + vaa++  + s l+v+ d   + p++L+G  ig+++ +++
  gi|330508589|ref|YP_004385017.1|  77 PTG-VPEMQAMVAGELDIAYVGTAPPISAIAAGLPAKIVAAVN-IKGSDLVVRPDLAYSGPESLEGLSIGTFPpGSI 151
                                       333.334566778999999999999999*************99.8899**********************9887999 PP

                                       HHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHHHHHTT--EEEE-GGGTT-----SEE CS
                              NMT1 104 ekallkallakdggdpsdvtlvnvggtslakalltgkvDaaiggyenwegvelesegkelrifaladlgvpdyyslv 180
                                       +++++k+ l  +g++ s+v +  ++   +++al +g++D ++    +   vel+ +    +++ ++   +pd     
  gi|330508589|ref|YP_004385017.1| 152 QDTVMKKWLTDNGVEVSEVDIKAMDPGPAMSALSAGRIDGVFLPHPAPSIVELNGK---GKVVVASGEMWPDHACCS 225
                                       ********************99999999999********99988888777776555...556666666677888889 PP

                                       EEEEHHHHHH-HHHHHHHHHHHHHHHHHHHHSHHHH CS
                              NMT1 181 litnekllkenpelvkkFlrAlkkGyeyalahPeea 216
                                       l++++kl++e+pelv+++++   k++ey+  hP+ea
  gi|330508589|ref|YP_004385017.1| 226 LVVTDKLIQEQPELVEQIIKTHIKATEYINTHPKEA 261
                                       999*******************************98 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.1    0.0056        25     150     177 ..      80     107 ..      36     125 .. 0.77
   2 !   15.0   0.0   2.8e-06     0.013      94     180 ..     123     206 ..     111     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0056
                            NMT1_3 150 gesadalkdgqldgaalvaGvPvsavtq 177
                                        + ++a+  g+ld a + +++P+sa++ 
  gi|330508589|ref|YP_004385017.1|  80 VPEMQAMVAGELDIAYVGTAPPISAIAA 107
                                       46789********************986 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.8e-06
                            NMT1_3  94 qlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealglsekdlklleelgygesadalkdgqldgaalvaGv 170
                                        lvv+ d   +  + l+g +++  p+gs +++ + + l   g++ +++++ + +++g++++al  g++dg++l+  +
  gi|330508589|ref|YP_004385017.1| 123 DLVVRPDLAYSGPESLEGLSIGTFPPGSIQDTVMKKWLTDNGVEVSEVDI-KAMDPGPAMSALSAGRIDGVFLP--H 196
                                       5677777777777888998888889***********************96.999********************..8 PP

                            NMT1_3 171 Pvsavtqlaa 180
                                       P+ ++ +l  
  gi|330508589|ref|YP_004385017.1| 197 PAPSIVELNG 206
                                       8888887765 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 ?   12.6   0.0   1.7e-05     0.074      43     162 ..      83     193 ..      72     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                                       HHHHHTTS-SEEE--HHHHHHHHHHS.-EEEEEEEEETT--SEEEEEEEEETTSS--SHHHHGG-EEEE--TT-TTT CS
                    Phosphonate-bd  43 vealragqvDiaflgplayvqardqa.gveplatrvrsdGsasyrsviivradsdiqsledLkgktiafvspsStsG 118
                                       ++a+ ag++Dia++g+ + + a +    ++ +a+           s ++vr+d ++   e L+g +i+   p S   
  gi|330508589|ref|YP_004385017.1|  83 MQAMVAGELDIAYVGTAPPISAIAAGlPAKIVAAVNI------KGSDLVVRPDLAYSGPESLEGLSIGTFPPGSIQ- 152
                                       69************99988887755334544444443......36779**************************99. PP

                                       THHHHHHTCCCCT--HHH.HSSEEEE--HHHHHHHHHTTSSSEEE CS
                    Phosphonate-bd 119 ylvpaalLvkeagldped.dfsevfsgshdaavlavlsgdadaaa 162
                                         v + +L  ++g+++++ d+++    +   a+ a+ +g++d  +
  gi|330508589|ref|YP_004385017.1| 153 DTVMKKWL-TDNGVEVSEvDIKA---MDPGPAMSALSAGRIDGVF 193
                                       66677789.69999887523333...2344566666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2247.05
//
Query:       gi|330508590|ref|YP_004385018.1|  [L=240]
Description: ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-22   79.3  11.1    2.9e-22   79.3  11.1    1.4  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.056   12.9   6.0      0.015   14.8   2.1    2.0  2  YibE_F        YibE/F-like protein


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.84   7.5e+03     108     122 ..      19      33 ..      17      40 .. 0.62
   2 !   79.3  11.1   3.2e-26   2.9e-22       2     168 ..      60     219 ..      59     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.84
                      BPD_transp_1 108 ppiitglilafggll 122
                                        p ++++++af+ ++
  gi|330508590|ref|YP_004385018.1|  19 LPSFSQVVFAFMENW 33 
                                       555666666666666 PP

  == domain 2  score: 79.3 bits;  conditional E-value: 3.2e-26
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrs 78 
                                       +++G++++    k+ld +++p++++l+ +P+++++++ +       ++g +++++ ++++++a+++++ +++++++s
  gi|330508590|ref|YP_004385018.1|  60 LPIGMIMG--WFKFLDSIFDPIVEILRPIPPLAWIPFAI------IWFGITNTAAGFIIFIGAVFPILTNTYMGFKS 128
                                       89******..99***************************......9******************************* PP

                      BPD_transp_1  79 lpkdlveaaralGasr.wqifrkvvlPnalppiitglilafggllggavlleflg.swpGlgtllleailgydysei 153
                                       lp+ +ve a++lGa++   ++r+v+lP +lp+i++g+++a+g+++   v++e++g s++Glg  +++++  y ++e 
  gi|330508590|ref|YP_004385018.1| 129 LPRVYVESAKVLGATKdLDLIRYVALPYSLPSIAAGIRIAMGIAWMCLVAAEMFGvSKNGLGFKIWDSYGHYRMDEV 205
                                       **************86489***********************************956778***************88 PP

                      BPD_transp_1 154 snggvlalviavlll 168
                                          ++++l+++ l++
  gi|330508590|ref|YP_004385018.1| 206 F-MYMIVLGLLGLAI 219
                                       8.6666666555544 PP

>> YibE_F  YibE/F-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.14   1.3e+03      76      97 ..      47      68 ..      24      84 .. 0.67
   2 ?   14.8   2.1   1.6e-06     0.015      80     143 ..     160     223 ..     101     228 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.14
                            YibE_F 76 aallgtllgvllalllallvik 97
                                         +g+ +g+l+al +++++++
  gi|330508590|ref|YP_004385018.1| 47 HFAIGMAGGLLIALPIGMIMGW 68
                                      4445666666666666666655 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.6e-06
                            YibE_F  80 gtllgvllalllallviklakltGlnseeaeellylplqgldlsglllagiligalGAvmDvai 143
                                       ++ +g+ +a+++a++++ +a++ G++++ + + +  ++ +  + ++++ +i++g+lG  +D + 
  gi|330508590|ref|YP_004385018.1| 160 SIAAGIRIAMGIAWMCLVAAEMFGVSKNGLGFKIWDSYGHYRMDEVFMYMIVLGLLGLAIDRTF 223
                                       6788999***********************999888877********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1734.26
//
Query:       gi|330508591|ref|YP_004385019.1|  [L=396]
Description: S-adenosylmethionine synthetase [Methanosaeta concilii GP6]
Scores for complete 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-175  583.4   1.2   2.2e-175  583.2   1.2    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 !  583.2   1.2  1.2e-179  2.2e-175       1     396 []       3     392 ..       3     392 .. 0.99

  Alignments for each domain:
  == domain 1  score: 583.2 bits;  conditional E-value: 1.2e-179
                                       --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEE CS
                   AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGG 77 
                                       rni+ve+l+++p+e+qe+E+vErKGiGHPDs+aDg+ae++sral++eyl++fga+lhhn+Dk+++vaG+s+p+fgGG
  gi|330508591|ref|YP_004385019.1|   3 RNIKVERLNQRPLEQQEIELVERKGIGHPDSVADGLAESISRALCQEYLDRFGAVLHHNTDKTQIVAGRSKPAFGGG 79 
                                       79*************************************************************************** PP

                                       EEEE-EEEEEEEEEEEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BE CS
                   AdoMet_Synthase  78 eviepieillsgratkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevpla 154
                                       evi p++ill+grat+ +++e+ipv++ia++aa++ l e+l++ld++++vi+d k+g gs+dL+dvf r   +vp+a
  gi|330508591|ref|YP_004385019.1|  80 EVICPLYILLTGRATRVFKEEEIPVDTIAIKAARKLLVESLSNLDVNNHVILDAKIGMGSSDLRDVFGR---KVPSA 153
                                       *********************************************************************...69*** PP

                                       SSSEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHH CS
                   AdoMet_Synthase 155 NDtSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevke 231
                                       NDtSfgvgyapls++e++v++ter l +  lkk++p++GeDiKvmg+R++++i+lT+a+alvdr+v++++eY+++k+
  gi|330508591|ref|YP_004385019.1| 154 NDTSFGVGYAPLSQTENIVYNTERELMN--LKKSIPAIGEDIKVMGMRQGDEINLTIACALVDRYVANMKEYADTKR 228
                                       **************************95..9********************************************** PP

                                       HHHHHHHHHHHHHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-T CS
                   AdoMet_Synthase 232 eikeeveelakkltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNP 308
                                       ei e+v ++ak++t+ r+v  ++N aD++ee+svy+tvtGtsaE+gDdG+vGRGNR+nGlitpnrpmslEA++GKNP
  gi|330508591|ref|YP_004385019.1| 229 EIVEHVIDFAKQFTS-RRVFAQMNVADNIEEGSVYITVTGTSAEMGDDGAVGRGNRANGLITPNRPMSLEATCGKNP 304
                                       ***********9999.************************************************************* PP

                                       TT-HHHHHHHHHHHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT-H CS
                   AdoMet_Synthase 309 vsHvGKiYnvlaneiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideeleki 385
                                       ++HvGKiYn+l+ e ak+i++ev+g++evy+++lsqiGkpideP++asvq+++++gv+++++++ ++ei+de+l +i
  gi|330508591|ref|YP_004385019.1| 305 INHVGKIYNLLSIEAAKQIAAEVQGIEEVYIKILSQIGKPIDEPHIASVQIVPKEGVDIKSLQDGATEILDEWLGSI 381
                                       ***************************************************************************** PP

                                       HHHHHHHTTT- CS
                   AdoMet_Synthase 386 eeiteeliegk 396
                                        +++++l +g+
  gi|330508591|ref|YP_004385019.1| 382 PKLQQMLFRGE 392
                                       *******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 3098.16
//
Query:       gi|330508592|ref|YP_004385020.1|  [L=283]
Description: AbpC/Nbp35 iron-sulfur cluster carrier protein [Methanosaeta concilii GP6]
Scores for 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-97  324.9   0.1    3.5e-97  324.7   0.1    1.0  1  ParA         NUBPL iron-transfer P-loop NTPase
    9.9e-15   54.7   0.0    3.6e-14   52.9   0.0    1.8  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    5.1e-09   35.8   0.0    7.4e-09   35.3   0.0    1.3  1  MipZ         ATPase MipZ
    1.9e-08   34.4   0.5    7.1e-07   29.3   0.1    2.2  2  AAA_31       AAA domain
    7.2e-06   25.4   2.2    0.00071   18.9   0.2    2.9  3  ArsA_ATPase  Anion-transporting ATPase
     0.0001   22.2   0.2     0.0014   18.5   0.2    2.1  1  AAA_26       AAA domain
    0.00059   19.4   0.1     0.0084   15.6   0.1    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
     0.0083   16.0   0.0      0.012   15.5   0.0    1.2  1  APS_kinase   Adenylylsulphate kinase
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.018   14.9   0.0    1.4  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
      0.038   13.6   0.0      0.072   12.7   0.0    1.4  1  AAA_25       AAA domain
       0.05   12.9   0.0      0.089   12.1   0.0    1.3  1  VirC1        VirC1 protein
      0.077   13.5   0.1       0.13   12.8   0.1    1.3  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 !  324.7   0.1  2.3e-100   3.5e-97       1     245 [.      35     278 ..      35     279 .. 0.98

  Alignments for each domain:
  == domain 1  score: 324.7 bits;  conditional E-value: 2.3e-100
                              ParA   1 kvkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmS 77 
                                       k+k+ i+++SgKGGVGKStv+vnlA aL   g+kvg+lDaDi+Gp+ip+llg+e+++    e+++ P +a gik+ S
  gi|330508592|ref|YP_004385020.1|  35 KIKHNIIIASGKGGVGKSTVSVNLARALLLDGFKVGILDADITGPNIPKLLGIEDRSLVLGEEGIRPADAGGIKAAS 111
                                       599*****************************************************9999999************** PP

                              ParA  78 igfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladv 153
                                       ++++l+s d++vvwrGpmk++aikq+++dv+wgelD+LiiDlPPGt+De l+v+q + +laga+iVttpqev+l d 
  gi|330508592|ref|YP_004385020.1| 112 MALVLSSPDSPVVWRGPMKMAAIKQFIQDVDWGELDFLIIDLPPGTSDEPLSVVQLIpDLAGAIIVTTPQEVSLLDS 188
                                       *********************************************************889***************** PP

                              ParA 154 kkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkep 230
                                       +ka++m+k++k++v+G++eNm+g++cp+c+++++if++ggge++aee++v++lg+ip+dp++++ +d+g+++v+   
  gi|330508592|ref|YP_004385020.1| 189 RKAVNMVKTMKLPVIGIIENMAGLMCPHCHQRIDIFQSGGGERMAEEMNVRFLGSIPIDPQVCSLGDAGQTFVEG-- 263
                                       **********************************************************************98865.. PP

                              ParA 231 eseaakaleeiaekv 245
                                       +++aa++++ i+e++
  gi|330508592|ref|YP_004385020.1| 264 DTPAADIFRLIVERL 278
                                       699999999998875 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 !   52.9   0.0   2.4e-17   3.6e-14       1     120 [.      40     252 ..      40     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 2.4e-17
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i+ias+kGGvGK+t+++nLaral  +g++V  +DaD  ++n   l g e    +                       
  gi|330508592|ref|YP_004385020.1|  40 IIIASGKGGVGKSTVSVNLARALLLDGFKVGILDADITGPNIPKLLGIED---Rslvlgeegirpadaggikaasma 113
                                       89***************************************993333333...335799999999************ PP

                                       .........................................................................CCHC CS
                                       .........................................................................xxxx RF
                              CbiA  55 .........................................................................dlkr 58 
                                                                                                                d  +
  gi|330508592|ref|YP_004385020.1| 114 lvlsspdspvvwrgpmkmaaikqfiqdvdwgeldfliidlppgtsdeplsvvqlipdlagaiivttpqevsllDSRK 190
                                       ********************************************************999999999999988887777 PP

                                       CCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC.........TS-EEEEEE--CCHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxx RF
                              CbiA  59 llellealgkkkalllkiagvvlnrvdgeneetllkealeelkqry.........gvpvlgviprdeavae 120
                                        ++++++++      l ++g++ n+ +    + +++ ++ +              +v++lg+ip d +v  
  gi|330508592|ref|YP_004385020.1| 191 AVNMVKTMK------LPVIGIIENMAGLMCPHCHQRIDIFQS---GggermaeemNVRFLGSIPIDPQVCS 252
                                       777777777......569999999877542222222222111...12223334447777777777766665 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0     5e-12   7.4e-09       1     134 [.      38     186 ..      38     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 5e-12
                                       EEEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHH..HHHHHHHHHHHT--......----EE.E CS
                              MipZ   1 hvivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlary..lenraataerkgls......Lplpea.l 68 
                                       h i+++  kGG Gkst++v +a aLl  G++v+ +d d+    + +   +e+r+ +  ++g++      ++ +++ l
  gi|330508592|ref|YP_004385020.1|  38 HNIIIASGKGGVGKSTVSVNLARALLLDGFKVGILDADITGPNIPKLlgIEDRSLVLGEEGIRpadaggIKAASMaL 114
                                       789***************************************9999844589**99999999832222223333303 PP

                                       -SSS-HHHHTTS-HHHHHHHHHHHHHHHH.HH-SEEEEE--.SS.--HHH..HHHHHT-SEEE..EEEESSHH CS
                              MipZ  69 alseaeeaeveeeeeaevaeleelvadle.aeldfividtP.Gs.dsals..rlahsladtlv..tPlndsfv 134
                                       +ls+   + v     +++a++++ ++d+   eldf++id P G+ d++ls  +l  +la +++  tP   s++
  gi|330508592|ref|YP_004385020.1| 115 VLSS-PDSPVVWRGPMKMAAIKQFIQDVDwGELDFLIIDLPpGTsDEPLSvvQLIPDLAGAIIvtTPQEVSLL 186
                                       4444.4444555556677999999999973589******8635414444311444444444322256555555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   4.7e-10   7.1e-07       4      40 ..      40      76 ..      37      94 .. 0.89
   2 ?    3.5   0.0     0.041        62     107     129 ..     134     157 ..     108     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 4.7e-10
                            AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40
                                      I ia  KGGvGK+T svnla al   g kv + D+D 
  gi|330508592|ref|YP_004385020.1| 40 IIIASGKGGVGKSTVSVNLARALLLDGFKVGILDADI 76
                                      789999*****************************96 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.041
                            AAA_31 107 lkellekvk.deYDyiiiDcpPsL 129
                                       +k+++++v+  e D+ iiD pP  
  gi|330508592|ref|YP_004385020.1| 134 IKQFIQDVDwGELDFLIIDLPPGT 157
                                       5777777763579*********65 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   4.7e-07   0.00071       2      32 ..      39      69 ..      38      77 .. 0.81
   2 ?    0.5   0.0      0.18   2.7e+02     110     134 ..     131     155 ..     127     170 .. 0.85
   3 ?    4.1   0.1     0.014        21     206     244 ..     171     209 ..     160     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.7e-07
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkv 32
                                      ++i+ +GKGGVGK+tvs  +a  l   g kv
  gi|330508592|ref|YP_004385020.1| 39 NIIIASGKGGVGKSTVSVNLARALLLDGFKV 69
                                      6899***************998876666666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHCSSSSEEEEESBS CS
                       ArsA_ATPase 110 ilsfeellkyvkeeeydvvvlDtaP 134
                                       +++ +++++ v+  e d +++D +P
  gi|330508592|ref|YP_004385020.1| 131 MAAIKQFIQDVDWGELDFLIIDLPP 155
                                       567889999999***********99 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.014
                                       TEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                       ArsA_ATPase 206 rtsfrlVvipEklslkEteRaikeLkkygikvdavivNk 244
                                        +  ++V++p ++sl ++++a++ +k +++ v  +i N 
  gi|330508592|ref|YP_004385020.1| 171 LAGAIIVTTPQEVSLLDSRKAVNMVKTMKLPVIGIIENM 209
                                       556789**************************9999885 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   9.2e-07    0.0014       2     194 ..      39     250 ..      38     252 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.2e-07
                            AAA_26   2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie.......ededselike....llgldqtyelpepl 67 
                                       +i++++   gvGK++vs  L+ral   g+kvg +   +tg +       e ++s ++ e     +++     +  +l
  gi|330508592|ref|YP_004385020.1|  39 NIIIASGKGGVGKSTVSVNLARALLLDGFKVGILDADITGPNipkllgiE-DRSLVLGEegirPADAGGIKAASMAL 114
                                       799******************************99988888878887532.33333333353322222224456689 PP

                            AAA_26  68 alsaplspelaarqegedidlekiv.kelekdadivvVEGagglg.vpiteellnadiaknlgapvilVargglgti 142
                                       +ls+p sp +  r  ++  ++++++ +  + + d+++++   g++ +p++  +l+ d+a +     i+V+++++ ++
  gi|330508592|ref|YP_004385020.1| 115 VLSSPDSPVV-WRGPMKMAAIKQFIqDVDWGELDFLIIDLPPGTSdEPLSVVQLIPDLAGA-----IIVTTPQEVSL 185
                                       9999977755.5566778888999944467799******9988885777777999999986.....89999999999 PP

                            AAA_26 143 nqllltiealrqknvrvlGvilNk....vrnp..e..........nvetlekksgipvlGvvPylpdl 194
                                        +   +++++++ +++v+G+i N     +  p               +++e+  +++ lG++P +p++
  gi|330508592|ref|YP_004385020.1| 186 LDSRKAVNMVKTMKLPVIGIIENMaglmC--PhcHqridifqsggGERMAEE-MNVRFLGSIPIDPQV 250
                                       99999****************99844432..134233444445533333333.369*******99875 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   5.6e-06    0.0084       4      35 ..      42      73 ..      39      83 .. 0.86
   2 ?    1.6   0.0       0.1   1.6e+02     193     239 ..     229     273 ..     169     281 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.6e-06
                         Fer4_NifH  4 aiyGkGGiGksttsqnlsaalaemgkkvlivG 35
                                         GkGG+Gkst s nl+ al  +g kv i+ 
  gi|330508592|ref|YP_004385020.1| 42 IASGKGGVGKSTVSVNLARALLLDGFKVGILD 73
                                      557*******************9999997665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.1
                         Fer4_NifH 193 iekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyre 239
                                        e++aee++++ l  +P d +v     + +t +e ++ +  a+ +r 
  gi|330508592|ref|YP_004385020.1| 229 GERMAEEMNVRFLGSIPIDPQVCSLGDAGQTFVEGDTPA--ADIFRL 273
                                       467999*************99998888888888766554..356655 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.3e-06     0.012       4      52 ..      40      88 ..      37     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.3e-06
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SS CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfs 52
                                      ++  +G  g GKst++++l+++L  +g +v +Ld d    ++ k Lg +
  gi|330508592|ref|YP_004385020.1| 40 IIIASGKGGVGKSTVSVNLARALLLDGFKVGILDADITGPNIPKLLGIE 88
                                      67889******************************98877777777765 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.2e-05     0.018       1      36 [.      45      80 ..      45      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqse 36
                                      G+  +GKST++ +L+  +l  g k+ ++D+D+  ++
  gi|330508592|ref|YP_004385020.1| 45 GKGGVGKSTVSVNLARALLLDGFKVGILDADITGPN 80
                                      66789**************************97665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.8e-05     0.072      32      58 ..      37      63 ..      30      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                            AAA_25 32 agelallaGapgtGKttlaldlalava 58
                                      ++ +++  G +g+GK+t+ ++la a++
  gi|330508592|ref|YP_004385020.1| 37 KHNIIIASGKGGVGKSTVSVNLARALL 63
                                      678999*****************9987 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     6e-05     0.089       4      40 ..      40      76 ..      38      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6e-05
                             VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfeade 40
                                      i ++s kGG Gk+t  + l  al  dg +v++++ad 
  gi|330508592|ref|YP_004385020.1| 40 IIIASGKGGVGKSTVSVNLARALLLDGFKVGILDADI 76
                                      67899******************************96 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   8.6e-05      0.13       1      22 [.      41      62 ..      41      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.6e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrl 22
                                      I+ +G+ GvGK+t++ +L++ l
  gi|330508592|ref|YP_004385020.1| 41 IIASGKGGVGKSTVSVNLARAL 62
                                      6668999***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2031.62
//
Query:       gi|330508593|ref|YP_004385021.1|  [L=302]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   50.8   0.0    3.7e-13   50.2   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
     0.0048   16.7   0.1       0.01   15.7   0.1    1.6  1  HTH_5        Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.017   15.0   0.0       0.21   11.5   0.0    2.5  2  MarR_2       MarR family
      0.032   14.3   0.1       0.13   12.3   0.0    2.1  2  HTH_20       Helix-turn-helix domain
      0.036   13.9   0.0       0.17   11.7   0.0    2.1  2  HTH_IclR     IclR helix-turn-helix domain
      0.061   13.6   0.0       0.13   12.6   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
       0.18   12.3   0.1        1.2    9.7   0.0    2.3  2  HTH_27       Winged helix DNA-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 !   50.2   0.0   1.4e-16   3.7e-13       5     163 ..      25     183 ..      22     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.4e-16
                                       SEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   5 rgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgir 79 
                                       + Cnl+C++C  ++t   + grgr+++++++l e++e + +       + g+gep+l  d+ + ++ +++     + 
  gi|330508593|ref|YP_004385021.1|  25 KTCNLDCIYCELGRTdCLTCGRGRFVPPQKVLGEIREKR-NEPfDYLTFAGSGEPTLSQDLGRVVAFAKET--VSRP 98 
                                       57*************9999*******************7.555255556679*********9999999999..9*** PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn..rghtfeevlealeklreagikrvvdrivglpG 154
                                       ++v+tn tl++   +++ + +  d v  +l+aa++  ++ +++  +g  +ee++++l+ +r+    +++  ++++ G
  gi|330508593|ref|YP_004385021.1|  99 VAVITNSTLLTSPAVRKEVAAA-DIVLPSLDAASPAAFQAINRpdPGLKIEEIIQGLKEFRREYSGEIWLEVMLVAG 174
                                       ***********77777777777.9************88888887788899*************9999********** PP

                                       TSHHHHHHH CS
                                       xxxxxxxxx RF
                       Radical_SAM 155 endeeleel 163
                                        nd+e + +
  gi|330508593|ref|YP_004385021.1| 175 INDHEADLI 183
                                       ****96555 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 !   15.7   0.1   3.9e-06      0.01       4      46 ..     241     283 ..     239     284 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.9e-06
                                       HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       R +IL +L++++ +  e+++  +l+ s    + k+L+  GL++
  gi|330508593|ref|YP_004385021.1| 241 RNRILDSLCRSPSTLEEICRLHDLTDSDAIKYCKILEHDGLIT 283
                                       99**************************************996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.24   6.2e+02      22      44 ..      79     101 ..      56     114 .. 0.80
   2 ?   11.5   0.0   8.1e-05      0.21       9      54 ..     243     285 ..     240     290 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.24
                                       EEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2  22 ltvgelarrlglsksavsrilkr 44 
                                          ++l r     k +vsr ++ 
  gi|330508593|ref|YP_004385021.1|  79 TLSQDLGRVVAFAKETVSRPVAV 101
                                       566899999999999***99986 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.1e-05
                                       HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       r+L  L r+p    t  e++r  +l+ s + + +k L+  GL++rr
  gi|330508593|ref|YP_004385021.1| 243 RILDSLCRSPS---TLEEICRLHDLTDSDAIKYCKILEHDGLITRR 285
                                       8999*****96...******************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.6   4.1e+03      29      44 ..       8      24 ..       7      24 .. 0.78
   2 ?   12.3   0.0   5.2e-05      0.13      12      57 ..     241     285 ..     239     288 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
                                      HHHHHHTS-HHH.HHHH CS
                            HTH_20 29 elaerldlsknt.lsyH 44
                                       l +rl+ls+   l +H
  gi|330508593|ref|YP_004385021.1|  8 VLSRRLGLSMGVdLLRH 24
                                      58899999998777766 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.2e-05
                                       HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57 
                                       R ril+ L  + + t++e++++ dl+++ + +  ++Le  gL++++
  gi|330508593|ref|YP_004385021.1| 241 RNRILDSL-CRSPSTLEEICRLHDLTDSDAIKYCKILEHDGLITRR 285
                                       669*****.**********************************998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.8   4.5e+03      10      26 ..     136     152 ..     135     154 .. 0.82
   2 ?   11.7   0.0   6.5e-05      0.17       7      50 ..     243     284 ..     239     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.8
                                       CT-CTTBSS-BHHHHHH CS
                          HTH_IclR  10 dalaeapqeltlselAr 26 
                                       +a+++ +++l++ e+ +
  gi|330508593|ref|YP_004385021.1| 136 QAINRPDPGLKIEEIIQ 152
                                       578899999***99976 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.5e-05
                                       HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       +iLd l + p   tl e++r  +l+ S +  +++ L++ G++++
  gi|330508593|ref|YP_004385021.1| 243 RILDSLCRSPS--TLEEICRLHDLTDSDAIKYCKILEHDGLITR 284
                                       57888877777..6***************************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 ?   12.6   0.0   4.9e-05      0.13      10      92 ..      22     106 ..      13     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.9e-05
                           Fer4_12  10 lfvsgCnlsCkgCfnketwsfk..sgkeft.kelleeiiedlkkesiegltllG.GEPllpenaeallelvkevkee 82 
                                       l+ + Cnl C +C    t + +  +g+ ++ +++l ei e+  +e  + lt+ G GEP l +    ++ ++ke  ++
  gi|330508593|ref|YP_004385021.1|  22 LRHKTCNLDCIYCELGRTDCLTcgRGRFVPpQKVLGEIREKR-NEPFDYLTFAGsGEPTLSQDLGRVVAFAKETVSR 97 
                                       67789********98888866622556665599999999887.667789999999*****77777777777766555 PP

                           Fer4_12  83 kpekdiwlyt 92 
                                        +  +i+ +t
  gi|330508593|ref|YP_004385021.1|  98 PV-AVITNST 106
                                       54.2444444 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 ?   -1.6   0.0       1.5     4e+03       2      28 ..     190     220 ..     190     222 .. 0.75
   2 ?    9.7   0.0   0.00047       1.2      17      50 ..     251     284 ..     244     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                            HTH_27   2 trqqalvLhlir....hrrrrkkladlcgrl 28 
                                       t+++++ L+++     +++r+ ++++ +++l
  gi|330508593|ref|YP_004385021.1| 190 TEPDRIQLNTVVrtpaEPVRPLSEEEMVRML 220
                                       5677778888888888888998887777776 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00047
                            HTH_27  17 rrkkladlcgrlnvedshisyslkkLtekGLver 50 
                                        +++l+++c+ ++++ds +++  k L+  GL++r
  gi|330508593|ref|YP_004385021.1| 251 SPSTLEEICRLHDLTDSDAIKYCKILEHDGLITR 284
                                       68999***************999********955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2311.48
//
Query:       gi|330508594|ref|YP_004385022.1|  [L=314]
Description: PBS lyase HEAT domain repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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  31.4    3.1e-19   69.2   0.2    4.5  5  HEAT_2           HEAT repeats
      4e-35  116.9  32.2    5.2e-07   29.7   0.1    9.6  9  HEAT_PBS         PBS lyase HEAT-like repeat
    1.9e-28   96.1   5.1      0.013   15.7   0.0    8.7  9  HEAT             HEAT repeat
    1.1e-13   51.4  15.7        0.2   12.2   0.0    8.8  8  HEAT_EZ          HEAT-like repeat
    6.2e-11   41.9   0.6        2.1    8.5   0.0    7.3  8  Arm              Armadillo/beta-catenin-like repeat
    1.2e-06   28.6   0.1        1.1    9.3   0.0    5.0  5  Cnd1             non-SMC mitotic condensation complex subunit
    8.3e-06   24.6   0.0       0.29    9.6   0.0    4.3  3  Adaptin_N        Adaptin N terminal region
  ------ inclusion threshold ------
      0.049   14.2   0.0         20    5.9   0.0    4.1  6  Vac14_Fab1_bd    Vacuolar 14 Fab1-binding region
        0.2   11.9   9.8       0.49   10.6   0.5    3.3  5  TetR_C_6         BetI-type transcriptional repressor, C-termi
       0.21   11.6   2.3       0.55   10.2   0.3    2.7  4  DUF615           Protein of unknown function (DUF615)
       0.81    9.6   3.0        3.8    7.4   0.1    3.0  3  Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal do
        1.8    8.2   6.4        7.9    6.1   0.1    3.3  3  DNA_alkylation   DNA alkylation repair enzyme


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 !   44.8   0.2   8.4e-15   1.3e-11       4      87 ..       7      90 ..       4      91 .. 0.94
   2 !   23.6   1.8   3.3e-08   4.9e-05      10      61 ..      76     128 ..      75     133 .. 0.74
   3 !   47.1   2.8   1.6e-15   2.3e-12       2      84 ..     100     179 ..      99     180 .. 0.93
   4 !   42.1   2.2   5.9e-14   8.8e-11       7      66 ..     164     223 ..     162     228 .. 0.91
   5 !   69.2   0.2   2.1e-22   3.1e-19       2      82 ..     222     302 ..     221     307 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 8.4e-15
                            HEAT_2  4 LlqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddddvvRe 81
                                      L++ l ++ d+  r++a++aL ++g+ ea++a+ e+l + e ++ R+  a+ Lg+ g+ +al+ L+ +l++d+d vvRe
  gi|330508594|ref|YP_004385022.1|  7 LIKKLGQSDDYFERQKAAWALVNLGD-EAVDAVAEALeKGEFSDLRYKSAWILGKTGSARALKPLCYALLSDPDHVVRE 84
                                      8999988999999*************.5*********66799************************************* PP

                            HEAT_2 82 aAaeaL 87
                                      ++a a+
  gi|330508594|ref|YP_004385022.1| 85 WSAAAM 90
                                      *99987 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 3.3e-08
                            HEAT_2  10 ndpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdp 61 
                                       +dpd+ vr   + a+  +gn+ea++ Lv ++ +d +++vR  aa+aL a+   
  gi|330508594|ref|YP_004385022.1|  76 SDPDHVVREWSAAAMEALGNQEAVQPLVLAMkRDGSRDVRLRAAMALRALEAA 128
                                       67888888888888888888888888888887777888888888888777655 PP

  == domain 3  score: 47.1 bits;  conditional E-value: 1.6e-15
                            HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddv 78 
                                       ++L+ a+++d + +vr +a++aL      ea +a+++ll+ +dp+vR +a + L++ig  ++lp  ++l++d++ +v
  gi|330508594|ref|YP_004385022.1| 100 QPLVLAMKRDGSRDVRLRAAMALR---ALEAAEAFRDLLSYDDPEVRGMATTGLAKIGYAQSLPDVARLMTDESAEV 173
                                       678889999**************7...567899****************************************9999 PP

                            HEAT_2  79 vReaAa 84 
                                       +R+aAa
  gi|330508594|ref|YP_004385022.1| 174 RRRAAA 179
                                       999987 PP

  == domain 4  score: 42.1 bits;  conditional E-value: 5.9e-14
                            HEAT_2   7 alendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpa 66 
                                       +l +d++ evrr+a+  +g+i+ +e ++ L+++l+d++ +vR +a ++Lg+i+ ++a+++
  gi|330508594|ref|YP_004385022.1| 164 RLMTDESAEVRRRAAAYMGEIAREEGIEPLTRALQDDEVDVRCEALKSLGKIKGERAADL 223
                                       6779*************************************************9998775 PP

  == domain 5  score: 69.2 bits;  conditional E-value: 2.1e-22
                            HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkelldddddd 77 
                                       d+ l+al  d++++vr++a+ aLg+ig+++al+aL+e++ + +d+++R+ aa++Lg+igd++a++ Lk+++++ + +
  gi|330508594|ref|YP_004385022.1| 222 DLALAAL-PDKEWKVRYTAVTALGEIGHDKALDALIEVMfSQDDEEIRAWAAWSLGEIGDERAIEPLKKAYKTCPTE 297
                                       5678999.9******************************999******************************99999 PP

                            HEAT_2  78 vvRea 82 
                                       v ++a
  gi|330508594|ref|YP_004385022.1| 298 VMKRA 302
                                       98874 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 !   15.7   0.5   1.1e-05     0.017       2      26 ..      20      43 ..      19      44 .. 0.92
   2 !    9.9   0.1   0.00089       1.3       1      22 [.      50      71 ..      50      76 .. 0.90
   3 !   13.1   0.2   8.2e-05      0.12       1      25 [.      82     106 ..      82     108 .. 0.93
   4 ?    5.9   1.5     0.017        25       1      21 [.     114     134 ..     114     137 .. 0.87
   5 ?    6.2   0.0     0.013        20       1      20 [.     142     161 ..     142     168 .. 0.87
   6 !   19.0   0.2   9.9e-07    0.0015       1      27 []     173     199 ..     173     199 .. 0.98
   7 !   12.1   0.1   0.00017      0.25       1      19 [.     204     222 ..     204     230 .. 0.92
   8 !   21.9   0.0   1.2e-07   0.00018       1      24 [.     235     258 ..     235     260 .. 0.96
   9 !   29.7   0.1   3.5e-10   5.2e-07       1      26 [.     267     292 ..     267     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS  2 RraAakaLgqlgdeeaipaLleaLq 26
                                      R  Aa+aL +lgd ea++a  eaL+
  gi|330508594|ref|YP_004385022.1| 20 RQKAAWALVNLGD-EAVDAVAEALE 43
                                      678**********.********997 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00089
                                      HHHHHHHHHHHCTSGGGHHHHH CS
                          HEAT_PBS  1 vRraAakaLgqlgdeeaipaLl 22
                                      +R+  a+ Lg+ g+ +a+ +L+
  gi|330508594|ref|YP_004385022.1| 50 LRYKSAWILGKTGSARALKPLC 71
                                      59****************9997 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 8.2e-05
                                       HHHHHHHHHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                       vR + a a+ +lg +ea+++L+ a 
  gi|330508594|ref|YP_004385022.1|  82 VREWSAAAMEALGNQEAVQPLVLAM 106
                                       9********************9886 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHCTSGGGHHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaL 21 
                                       vR +Aa aL +l + ea   L
  gi|330508594|ref|YP_004385022.1| 114 VRLRAAMALRALEAAEAFRDL 134
                                       8*************9997666 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHCTSGGGHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipa 20 
                                       vR  A+ +L+++g  +++p 
  gi|330508594|ref|YP_004385022.1| 142 VRGMATTGLAKIGYAQSLPD 161
                                       899***********999986 PP

  == domain 6  score: 19.0 bits;  conditional E-value: 9.9e-07
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vRr+Aa  +g++  ee i++L +aLqd
  gi|330508594|ref|YP_004385022.1| 173 VRRRAAAYMGEIAREEGIEPLTRALQD 199
                                       9*************************8 PP

  == domain 7  score: 12.1 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHCTSGGGHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaip 19 
                                       vR++A+k+Lg+++ e+a++
  gi|330508594|ref|YP_004385022.1| 204 VRCEALKSLGKIKGERAAD 222
                                       9*************99988 PP

  == domain 8  score: 21.9 bits;  conditional E-value: 1.2e-07
                                       HHHHHHHHHHHCTSGGGHHHHHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLlea 24 
                                       vR+ A+ aLg++g++ a++aL+e+
  gi|330508594|ref|YP_004385022.1| 235 VRYTAVTALGEIGHDKALDALIEV 258
                                       9*********************97 PP

  == domain 9  score: 29.7 bits;  conditional E-value: 3.5e-10
                                       HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                       +R++Aa++Lg++gde+ai++L++a +
  gi|330508594|ref|YP_004385022.1| 267 IRAWAAWSLGEIGDERAIEPLKKAYK 292
                                       69********************9976 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0       0.1   1.5e+02      17      28 ..      20      31 ..       6      33 .. 0.71
   2 ?   -2.4   0.0       5.7   8.6e+03      14      25 ..      48      59 ..      36      60 .. 0.66
   3 !   13.1   0.0   5.9e-05     0.088       3      27 ..      69      93 ..      67      96 .. 0.90
   4 !   10.9   0.2   0.00031      0.46       2      27 ..     100     125 ..      99     126 .. 0.93
   5 !    6.6   0.0    0.0072        11       5      27 ..     131     153 ..     129     156 .. 0.87
   6 !   15.3   0.0   1.2e-05     0.018       2      28 ..     159     185 ..     159     187 .. 0.90
   7 !   13.4   0.0   4.7e-05     0.071       4      27 ..     192     215 ..     190     216 .. 0.91
   8 !   15.7   0.0     9e-06     0.013      11      27 ..     230     246 ..     223     248 .. 0.92
   9 !   10.7   0.0   0.00034      0.51       5      28 ..     255     279 ..     251     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.1
                                      HHHHHHHHHHHH CS
                              HEAT 17 ReaAakaLgala 28
                                      R+ Aa+aL++l 
  gi|330508594|ref|YP_004385022.1| 20 RQKAAWALVNLG 31
                                      9*******9985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.7
                                      HHHHHHHHHHHH CS
                              HEAT 14 peVReaAakaLg 25
                                      ++ R+ +a+ Lg
  gi|330508594|ref|YP_004385022.1| 48 SDLRYKSAWILG 59
                                      556788888777 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 5.9e-05
                                      HHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT  3 PlllkllsDpspeVReaAakaLgal 27
                                      Pl+  llsDp+  VRe +a a+ al
  gi|330508594|ref|YP_004385022.1| 69 PLCYALLSDPDHVVREWSAAAMEAL 93
                                      89999***************99887 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00031
                                       HHHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsDpspeVReaAakaLgal 27 
                                        Pl+l + +D s +VR  Aa aL al
  gi|330508594|ref|YP_004385022.1| 100 QPLVLAMKRDGSRDVRLRAAMALRAL 125
                                       699********************987 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0072
                                       HHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgal 27 
                                       +  lls ++peVR +A   L+++
  gi|330508594|ref|YP_004385022.1| 131 FRDLLSYDDPEVRGMATTGLAKI 153
                                       6678999**********999988 PP

  == domain 6  score: 15.3 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsDpspeVReaAakaLgala 28 
                                       lP + +l++D+s+eVR+ Aa  +g++a
  gi|330508594|ref|YP_004385022.1| 159 LPDVARLMTDESAEVRRRAAAYMGEIA 185
                                       5778899******************98 PP

  == domain 7  score: 13.4 bits;  conditional E-value: 4.7e-05
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +l ++l+D++ +VR+ A+k+Lg++
  gi|330508594|ref|YP_004385022.1| 192 PLTRALQDDEVDVRCEALKSLGKI 215
                                       68999*****************97 PP

  == domain 8  score: 15.7 bits;  conditional E-value: 9e-06
                                       -SSHHHHHHHHHHHHHH CS
                              HEAT  11 DpspeVReaAakaLgal 27 
                                       D++++VR++A+ aLg++
  gi|330508594|ref|YP_004385022.1| 230 DKEWKVRYTAVTALGEI 246
                                       99*************99 PP

  == domain 9  score: 10.7 bits;  conditional E-value: 0.00034
                                       HHHHH.T-SSHHHHHHHHHHHHHHH CS
                              HEAT   5 llkll.sDpspeVReaAakaLgala 28 
                                       l++ + s ++ e+R+ Aa++Lg++ 
  gi|330508594|ref|YP_004385022.1| 255 LIEVMfSQDDEEIRAWAAWSLGEIG 279
                                       444442678999**********995 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.028        41      33      54 ..       7      29 ..       5      30 .. 0.75
   2 !    6.6   0.5    0.0077        11       4      54 ..      20      60 ..      17      95 .. 0.52
   3 ?    3.4   1.4     0.077   1.1e+02      28      55 .]      97     125 ..      87     125 .. 0.75
   4 !    6.7   0.4    0.0069        10      28      54 ..     126     152 ..     113     153 .. 0.74
   5 ?    5.5   0.1     0.017        26      34      49 ..     163     179 ..     157     181 .. 0.73
   6 !    9.0   0.0    0.0013         2      29      55 .]     189     215 ..     183     215 .. 0.90
   7 ?    5.6   0.1     0.015        23      41      55 .]     230     246 ..     220     246 .. 0.77
   8 !   12.2   0.0   0.00014       0.2      28      55 .]     250     278 ..     247     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.028
                           HEAT_EZ 33 LlalLnddsd.eVRaaAagaLgn 54
                                      L++ L  ++d   R++Aa+aL n
  gi|330508594|ref|YP_004385022.1|  7 LIKKLGQSDDyFERQKAAWALVN 29
                                      77778778885559******966 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0077
                           HEAT_EZ  4 RraAawaLGrlaggepellqplvpeilpaLlalLnddsd..eVRaaAagaLgn 54
                                      R  AawaL    +    l   +v+++  aL      +    + R+++a+ Lg+
  gi|330508594|ref|YP_004385022.1| 20 RQKAAWALV---N----LGDEAVDAVAEALE-----KGEfsDLRYKSAWILGK 60
                                      666666663...2....22222334444555.....44444445555555543 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.077
                           HEAT_EZ  28 eilpaLlalL.nddsdeVRaaAagaLgnl 55 
                                       e++ +L+ ++ +d s +VR  Aa aL++l
  gi|330508594|ref|YP_004385022.1|  97 EAVQPLVLAMkRDGSRDVRLRAAMALRAL 125
                                       56677777773555559999999999876 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0069
                           HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaLgn 54 
                                       e+  a+  lL+ d++eVR+ A   L++
  gi|330508594|ref|YP_004385022.1| 126 EAAEAFRDLLSYDDPEVRGMATTGLAK 152
                                       566788899999999999999877766 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.017
                           HEAT_EZ  34 lalLnddsdeV.RaaAa 49 
                                       ++l++d+s+eV R aAa
  gi|330508594|ref|YP_004385022.1| 163 ARLMTDESAEVrRRAAA 179
                                       456777888**766666 PP

  == domain 6  score: 9.0 bits;  conditional E-value: 0.0013
                           HEAT_EZ  29 ilpaLlalLnddsdeVRaaAagaLgnl 55 
                                        + +L ++L+dd+ +VR+ A+  Lg++
  gi|330508594|ref|YP_004385022.1| 189 GIEPLTRALQDDEVDVRCEALKSLGKI 215
                                       57899********************97 PP

  == domain 7  score: 5.6 bits;  conditional E-value: 0.015
                           HEAT_EZ  41 sd..eVRaaAagaLgnl 55 
                                       ++  +VR++A+ aLg +
  gi|330508594|ref|YP_004385022.1| 230 DKewKVRYTAVTALGEI 246
                                       33379*********986 PP

  == domain 8  score: 12.2 bits;  conditional E-value: 0.00014
                           HEAT_EZ  28 eilpaLlalL.nddsdeVRaaAagaLgnl 55 
                                       ++l+aL+  + + d+ e+Ra Aa+ Lg +
  gi|330508594|ref|YP_004385022.1| 250 KALDALIEVMfSQDDEEIRAWAAWSLGEI 278
                                       6788999666377888***********86 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.032        47      31      39 ..      22      30 ..      20      32 .. 0.86
   2 ?    0.4   0.0      0.52   7.7e+02      11      31 ..      64      84 ..      62      84 .. 0.83
   3 ?    2.8   0.0     0.086   1.3e+02       7      36 ..      92     122 ..      91     125 .. 0.80
   4 ?    5.4   0.0     0.013        20      15      37 ..     129     151 ..     119     153 .. 0.86
   5 ?    4.6   0.0     0.024        36      19      41 .]     164     186 ..     162     186 .. 0.92
   6 !    8.5   0.0    0.0014       2.1       8      37 ..     184     213 ..     183     215 .. 0.87
   7 ?   -2.2   0.0       3.2   4.8e+03      28      39 ..     235     246 ..     234     247 .. 0.82
   8 !    7.2   0.0    0.0036       5.4       9      39 ..     247     278 ..     244     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.032
                                      HHHHHHHHH CS
                               Arm 31 eAawALsNL 39
                                       AawAL NL
  gi|330508594|ref|YP_004385022.1| 22 KAAWALVNL 30
                                      59******9 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.52
                                      TTHHHHHHHHTTTSSHHHHHH CS
                               Arm 11 aGavppLvrLLssedeevqee 31
                                      a a++pL+  L s+ + v++e
  gi|330508594|ref|YP_004385022.1| 64 ARALKPLCYALLSDPDHVVRE 84
                                      568999*99999999888875 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.086
                                       HHHHTTHHHHHHHHTT.TSSHHHHHHHHHHH CS
                               Arm   7 avieaGavppLvrLLs.sedeevqeeAawAL 36 
                                       a+ ++ av+pLv  ++ +++ +v+  Aa AL
  gi|330508594|ref|YP_004385022.1|  92 ALGNQEAVQPLVLAMKrDGSRDVRLRAAMAL 122
                                       677889*********9988888877777666 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.013
                                       HHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  15 ppLvrLLssedeevqeeAawALs 37 
                                       +++ +LLs +d+ev+  A++ L+
  gi|330508594|ref|YP_004385022.1| 129 EAFRDLLSYDDPEVRGMATTGLA 151
                                       7899***************9986 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.024
                                       HHTTTSSHHHHHHHHHHHHHHTT CS
                               Arm  19 rLLssedeevqeeAawALsNLaa 41 
                                       rL+++e+ ev++ Aa+ ++ +a+
  gi|330508594|ref|YP_004385022.1| 164 RLMTDESAEVRRRAAAYMGEIAR 186
                                       7999************9999986 PP

  == domain 6  score: 8.5 bits;  conditional E-value: 0.0014
                                       HHHTTHHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm   8 vieaGavppLvrLLssedeevqeeAawALs 37 
                                       + +  +++pL r L+++ ++v++eA+  L+
  gi|330508594|ref|YP_004385022.1| 184 IAREEGIEPLTRALQDDEVDVRCEALKSLG 213
                                       556779*******************97776 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHH CS
                               Arm  28 vqeeAawALsNL 39 
                                       v+  A++AL+ +
  gi|330508594|ref|YP_004385022.1| 235 VRYTAVTALGEI 246
                                       67789****976 PP

  == domain 8  score: 7.2 bits;  conditional E-value: 0.0036
                                       HHTTHHHHHHHHTT.TSSHHHHHHHHHHHHHH CS
                               Arm   9 ieaGavppLvrLLs.sedeevqeeAawALsNL 39 
                                        +  a+++L++ +   +dee++  Aaw L+ +
  gi|330508594|ref|YP_004385022.1| 247 GHDKALDALIEVMFsQDDEEIRAWAAWSLGEI 278
                                       56789**********************99976 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 ?    3.7   0.0     0.039        59      27      54 ..      72      99 ..      65     123 .. 0.78
   2 ?    0.7   0.0      0.32   4.8e+02      32      50 ..     109     127 ..      96     153 .. 0.58
   3 !    7.2   0.0    0.0031       4.7      29      87 ..     134     186 ..     126     189 .. 0.69
   4 !    9.3   0.0    0.0007       1.1      21      89 ..     188     250 ..     186     272 .. 0.74
   5 ?    3.7   0.0     0.039        58      30      88 ..     228     281 ..     225     304 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.039
                              Cnd1 27 rkrLkDedpyVRktaaivvakLilndmv 54
                                      ++ L+D+d  VR+  a ++  L +++ v
  gi|330508594|ref|YP_004385022.1| 72 YALLSDPDHVVREWSAAAMEALGNQEAV 99
                                      5678888888888887777777666655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.32
                              Cnd1  32 DedpyVRktaaivvakLil 50 
                                       D +  VR  aa+++  L  
  gi|330508594|ref|YP_004385022.1| 109 DGSRDVRLRAAMALRALEA 127
                                       6666666666666655532 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0031
                              Cnd1  29 rLkDedpyVRktaaivvakL.ilndmvkekgflselaklleDenprVvanalaalteise 87 
                                        L+ +dp VR  a  ++ak+ +        + l ++a+l++De+++V+  a a + ei++
  gi|330508594|ref|YP_004385022.1| 134 LLSYDDPEVRGMATTGLAKIgYA-------QSLPDVARLMTDESAEVRRRAAAYMGEIAR 186
                                       56666777777777777776333.......346677788888888888888888888876 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0007
                              Cnd1  21 ylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteiseks 89 
                                       + +epL+++L+D++  VR  a+  + k+      k +   +  + +l D++ +V+  a++al ei + +
  gi|330508594|ref|YP_004385022.1| 188 EGIEPLTRALQDDEVDVRCEALKSLGKI------KGERAADLALAALPDKEWKVRYTAVTALGEIGHDK 250
                                       5689*****************9988874......44455555566778888888888888888887664 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.039
                              Cnd1  30 LkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisek 88 
                                       L D++  VR ta+ ++ ++       +k + + ++ + + ++++++a a  +l ei ++
  gi|330508594|ref|YP_004385022.1| 228 LPDKEWKVRYTAVTALGEIG-----HDKALDALIEVMFSQDDEEIRAWAAWSLGEIGDE 281
                                       66777777777777766542.....2333334445566777788888888888777665 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.018        27     413     445 ..      32      64 ..      27     129 .. 0.80
   2 !    9.6   0.0    0.0002      0.29      83     184 ..     130     219 ..     122     246 .. 0.77
   3 !    6.0   0.0    0.0025       3.8     412     446 ..     248     282 ..     240     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.018
                                       TTCHHHHCCTCCGXXSHHHHHHHHHHHHHTTTT CS
                         Adaptin_N 413 eeiiekLaellekieseearaaaiWllGeygel 445
                                       +e++  +ae+lek e+  +r++ +W+lG+ g+ 
  gi|330508594|ref|YP_004385022.1|  32 DEAVDAVAEALEKGEFSDLRYKSAWILGKTGSA 64 
                                       678889999999999999999999999987765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0002
                                       HHHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHH CS
                         Adaptin_N  83 slqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeike 159
                                       +++  l+  ++ +rg+A ++L++i+ ++ +    p++ +l++d+s+ vr+ Aa  +  + +       +  +e ++ 
  gi|330508594|ref|YP_004385022.1| 130 AFRDLLSYDDPEVRGMATTGLAKIGYAQSL----PDVARLMTDESAEVRRRAAAYMGEIARE------EG-IEPLTR 195
                                       566667888999999*******99987665....5667899************999888763......23.677888 PP

                                       CTT-SSHHHHHHHHHHHHHHHCCCC CS
                         Adaptin_N 160 llsdkdpgvvlaAvalleeikkndr 184
                                       +l+d+++ v   A++ l +i k +r
  gi|330508594|ref|YP_004385022.1| 196 ALQDDEVDVRCEALKSLGKI-KGER 219
                                       88999988888888888888.3333 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0025
                                       STTCHHHHCCTCCGXXSHHHHHHHHHHHHHTTTTX CS
                         Adaptin_N 412 heeiiekLaellekieseearaaaiWllGeygelv 446
                                       h++++  L+e++ +++ ee+ra a+W lGe+g++ 
  gi|330508594|ref|YP_004385022.1| 248 HDKALDALIEVMFSQDDEEIRAWAAWSLGEIGDER 282
                                       7899999************************9875 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 ?   -2.4   0.0       5.2   7.7e+03      35      47 ..      74      86 ..      67     108 .. 0.66
   2 ?   -2.0   0.0       3.7   5.5e+03      28      50 ..      99     121 ..      86     125 .. 0.71
   3 ?    0.7   0.0      0.54     8e+02      30      54 ..     160     184 ..     147     191 .. 0.69
   4 ?    1.2   0.0      0.37   5.6e+02      27      51 ..     188     212 ..     183     222 .. 0.78
   5 ?    5.9   0.0     0.013        20      32      54 ..     224     246 ..     217     261 .. 0.81
   6 ?   -1.9   0.0       3.4   5.1e+03      31      51 ..     258     275 ..     245     280 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.2
                     Vac14_Fab1_bd 35 cfsDkdsrvRyya 47
                                       +sD d+ vR ++
  gi|330508594|ref|YP_004385022.1| 74 LLSDPDHVVREWS 86
                                      3455555555443 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.7
                     Vac14_Fab1_bd  28 ivkpvlkcfsDkdsrvRyyacEs 50 
                                       + + vl++ +D ++ vR  a+ +
  gi|330508594|ref|YP_004385022.1|  99 VQPLVLAMKRDGSRDVRLRAAMA 121
                                       44567777788888888877655 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.54
                     Vac14_Fab1_bd  30 kpvlkcfsDkdsrvRyyacEslyni 54 
                                       + v + ++D++++vR  a+ ++  i
  gi|330508594|ref|YP_004385022.1| 160 PDVARLMTDESAEVRRRAAAYMGEI 184
                                       5566667777777776666655555 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.37
                     Vac14_Fab1_bd  27 eivkpvlkcfsDkdsrvRyyacEsl 51 
                                       e ++p+ ++++D++  vR  a  sl
  gi|330508594|ref|YP_004385022.1| 188 EGIEPLTRALQDDEVDVRCEALKSL 212
                                       56899999*********97666666 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.013
                     Vac14_Fab1_bd  32 vlkcfsDkdsrvRyyacEslyni 54 
                                        l+++ Dk+ +vRy+a+ +l  i
  gi|330508594|ref|YP_004385022.1| 224 ALAALPDKEWKVRYTAVTALGEI 246
                                       688999**********9998666 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 3.4
                     Vac14_Fab1_bd  31 pvlkcfsDkdsrvRyyacEsl 51 
                                       +   +fs +d+++R +a+ sl
  gi|330508594|ref|YP_004385022.1| 258 V---MFSQDDEEIRAWAAWSL 275
                                       2...46677888888887666 PP

>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       8.3   1.2e+04      56      62 ..      36      42 ..      23      51 .. 0.54
   2 ?   -0.7   0.1       1.1   1.6e+03      40      63 ..     104     127 ..      70     148 .. 0.57
   3 ?   10.6   0.5   0.00032      0.49       5      65 ..     128     189 ..     124     209 .. 0.83
   4 ?    1.7   0.1      0.19   2.8e+02      28      76 ..     179     227 ..     177     228 .. 0.80
   5 ?    6.5   0.2    0.0064       9.5       4      26 ..     251     273 ..     248     275 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.3
                                      HHHHHHH CS
                          TetR_C_6 56 allaela 62
                                      +++ae++
  gi|330508594|ref|YP_004385022.1| 36 DAVAEAL 42
                                      2233333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                          TetR_C_6  40 aelqrenyarlrsnlrallaelae 63 
                                        ++ r+  + +r + + +l++l +
  gi|330508594|ref|YP_004385022.1| 104 LAMKRDGSRDVRLRAAMALRALEA 127
                                       444444444444444444444444 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00032
                                       HHHHHHCCSTHSHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH.TT CS
                          TetR_C_6   5 lraileallpldqerraelavwlafwaeaardpelaelqrenyarlrsnlrallaelae.gg 65 
                                       ++a+ + l  +d+e r  +++ la +++a++ p++a+l+ +  a++r++ +a + e+a+ +g
  gi|330508594|ref|YP_004385022.1| 128 AEAFRDLLSYDDPEVRGMATTGLAKIGYAQSLPDVARLMTDESAEVRRRAAAYMGEIAReEG 189
                                       455555555599999999************************************99999433 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.19
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH.TTSCTTSTHHHHH CS
                          TetR_C_6  28 afwaeaardpelaelqrenyarlrsnlrallaelae.gglradadaeaaA 76 
                                       a+++e ar++ +  l r++++   +  +++l+ l + +   ++ad+++aA
  gi|330508594|ref|YP_004385022.1| 179 AYMGEIAREEGIEPLTRALQDDEVDVRCEALKSLGKiK-GERAADLALAA 227
                                       6788999999***********************99953.34444565555 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.0064
                                       HHHHHHHCCSTHSHHHHHHHHHH CS
                          TetR_C_6   4 rlraileallpldqerraelavw 26 
                                       +l+a++e +++ d+e+ +++a+w
  gi|330508594|ref|YP_004385022.1| 251 ALDALIEVMFSQDDEEIRAWAAW 273
                                       699******************** PP

>> DUF615  Protein of unknown function (DUF615)
   #    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      30      46 ..      25      41 ..       6      54 .. 0.64
   2 ?   -1.2   0.0       1.2   1.8e+03     102     140 ..      73     113 ..      61     138 .. 0.57
   3 ?   -1.5   0.0       1.5   2.2e+03      86     108 ..     118     140 ..      84     153 .. 0.62
   4 ?   10.2   0.3   0.00037      0.55      42      84 ..     162     202 ..     141     293 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.4
                            DUF615 30 lkklpldeelldallea 46
                                      ++ ++l +e +da++ea
  gi|330508594|ref|YP_004385022.1| 25 WALVNLGDEAVDAVAEA 41
                                      34445555555555554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                            DUF615 102 rLiaeddaaleelleeypev..DrqeLRqlirnarkekekn 140
                                       +L+++ d++++e+ +++ e+  +++ +  l+ +++++ +++
  gi|330508594|ref|YP_004385022.1|  73 ALLSDPDHVVREWSAAAMEAlgNQEAVQPLVLAMKRDGSRD 113
                                       56777777777777666665555555666666666554433 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.5
                            DUF615  86 seeetaalhelerwrdrLiaedd 108
                                        + + +al+ +e +rd L  +d 
  gi|330508594|ref|YP_004385022.1| 118 AAMALRALEAAEAFRDLLSYDDP 140
                                       33344777777888877666654 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00037
                            DUF615  42 alleakrikshrearrRqlqyigkllReadveairaalealkn 84 
                                         +++   +   e rrR   y g + Re+ +e++  al++ + 
  gi|330508594|ref|YP_004385022.1| 162 VARLMTDES--AEVRRRAAAYMGEIAREEGIEPLTRALQDDEV 202
                                       444444433..689***********************997665 PP

>> Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0025       3.8      88     124 ..      24      54 ..       8      55 .. 0.83
   2 ?    0.3   0.1      0.39   5.8e+02      71     119 ..      82     131 ..      77     137 .. 0.59
   3 ?   -0.3   0.0       0.6   8.9e+02      19      51 ..     200     232 ..     184     272 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0025
                   Peptidase_M17_N  88 ttiavalplegknsdekaeaaaegallglYrfdryks 124
                                       + ++v l       de++ a+ae+++ g +++ ryks
  gi|330508594|ref|YP_004385022.1|  24 AWALVNLG------DEAVDAVAEALEKGEFSDLRYKS 54 
                                       44555555......799*******************9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.39
                   Peptidase_M17_N  71 lrkaagaaaralkgakvttiavalp.legknsdekaeaaaegallglYrf 119
                                       +r+  +aa++al ++++ + +v+ +  +g+++    +a+a  al+++  f
  gi|330508594|ref|YP_004385022.1|  82 VREWSAAAMEALGNQEAVQPLVLAMkRDGSRDVRLRAAMALRALEAAEAF 131
                                       78888899999999555555555552333333355555666555555555 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.6
                   Peptidase_M17_N  19 ealagllsellkegdftGkagevlvlralsgek 51 
                                       ++ + + ++l + g+++G++   l l al+ ++
  gi|330508594|ref|YP_004385022.1| 200 DEVDVRCEALKSLGKIKGERAADLALAALPDKE 232
                                       555666677777777777777766666666554 PP

>> DNA_alkylation  DNA alkylation repair enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0053       7.9     156     197 ..       4      45 ..       1      68 [. 0.85
   2 ?    2.3   0.6      0.08   1.2e+02      43      87 ..      90     134 ..      78     247 .. 0.71
   3 ?    1.9   0.3      0.11   1.6e+02      36     118 ..     174     250 ..     154     276 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0053
                    DNA_alkylation 156 lleiaeelladkedfiqkAiGwaLrelsktdpdlveeFlekh 197
                                         e++++l ++ + f ++  +waL +l+ +  d+v e+lek 
  gi|330508594|ref|YP_004385022.1|   4 AHELIKKLGQSDDYFERQKAAWALVNLGDEAVDAVAEALEKG 45 
                                       56899999999999999999*******************984 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.08
                    DNA_alkylation  43 fkelkleeelqelaeeLwksperEerllAldlltqakkklaeadl 87 
                                        ++l ++e +q l+ ++ +++ r+ rl A++ l+  ++ +a+ dl
  gi|330508594|ref|YP_004385022.1|  90 MEALGNQEAVQPLVLAMKRDGSRDVRLRAAMALRALEAAEAFRDL 134
                                       455555577777888888888888888888888665555554433 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.11
                    DNA_alkylation  36 rklakeffkelkleeelqelaeeLwksperEerllAldlltqakkklaeadlelyeklvetinnWdlvDslaskivg 112
                                       r+ a  +  e+ +ee + e + + ++++e + r  Al+ l +   k ++a  +l ++ ++++++   v  +a + +g
  gi|330508594|ref|YP_004385022.1| 174 RRRAAAYMGEIAREEGI-EPLTRALQDDEVDVRCEALKSLGK--IKGERA-ADLALAALPDKEWK--VRYTAVTALG 244
                                       55555555555555333.555556666777777777777744..333333.55666666666654..4444455555 PP

                    DNA_alkylation 113 alladk 118
                                       ++ +dk
  gi|330508594|ref|YP_004385022.1| 245 EIGHDK 250
                                       555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); 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:                        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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 2329.12
//
Query:       gi|330508595|ref|YP_004385023.1|  [L=194]
Description: hypothetical protein MCON_2828 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-13   51.4   0.3    2.3e-13   50.6   0.3    1.4  1  CxxCxxCC  Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
      0.075   12.8   0.2       0.23   11.3   0.0    1.9  2  YycC      YycC-like protein


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 !   50.6   0.3   2.6e-17   2.3e-13       2      84 ..      51     149 ..      50     150 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2.6e-17
                          CxxCxxCC   2 CkeCgaCCk.elkvklteedlerlkaaevaeeeeeskkiak............adgrCvfldeetklCkiYeeRpki 65 
                                       C++Cg+CC+    ++l++ed ++l+++ ++  ++  kk++             +  +C+f+d+  + CkiY+ Rp  
  gi|330508595|ref|YP_004385023.1|  51 CQRCGTCCTtGDPIRLRPEDAAQLAKHLKIPLNRALKKYTIpdpkkpgvldfkHILPCKFYDRLAGGCKIYAARPWS 127
                                       *********77889*************************999**********999********************** PP

                          CxxCxxCC  66 crlfpas...ekeellaraetC 84 
                                       cr+fp+      ++  +++++C
  gi|330508595|ref|YP_004385023.1| 128 CRIFPFLgvyGSSDQVVVNPSC 149
                                       ******8777666666666666 PP

>> YycC  YycC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.6e-05      0.23       3      24 ..      63      84 ..      62      87 .. 0.90
   2 ?   -3.4   0.0         1   9.1e+03      32      45 ..     158     171 ..     157     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.6e-05
                              YycC  3 PlQiSpeTAvkLskkLnvPLEh 24
                                      P  + pe A +L+k+L++PL +
  gi|330508595|ref|YP_004385023.1| 63 PIRLRPEDAAQLAKHLKIPLNR 84
                                      78899***************86 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1
                              YycC  32 ILlqKlaelekeee 45 
                                       IL   + e++ e+e
  gi|330508595|ref|YP_004385023.1| 158 ILTRAMEEVQREQE 171
                                       67777888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1435.27
//
Query:       gi|330508596|ref|YP_004385024.1|  [L=189]
Description: GTP-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-15   55.0   0.0    9.2e-15   54.7   0.0    1.2  1  MMR_HSR1     50S ribosome-binding GTPase
    6.2e-11   42.1   0.0    5.5e-10   39.0   0.0    2.0  1  FeoB_N       Ferrous iron transport protein B
      0.001   18.7   0.0     0.0027   17.3   0.0    1.6  1  Ras          Ras family
     0.0011   18.5   0.0      0.069   12.7   0.0    2.3  2  GTP_EFTU     Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
       0.01   16.0   0.1      0.028   14.7   0.1    1.8  1  Roc          Ras of Complex, Roc, domain of DAPkinase
      0.011   15.6   0.0       0.11   12.3   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
      0.015   15.4   0.1       0.16   12.0   0.0    2.1  2  Dynamin_N    Dynamin family
       0.12   12.0   0.1       0.24   11.1   0.1    1.5  1  AAA_24       AAA domain
       0.15   11.8   0.0       0.24   11.2   0.0    1.3  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.21   11.0   0.0       0.32   10.4   0.0    1.4  1  SRPRB        Signal recognition particle receptor beta subuni


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 !   54.7   0.0   5.1e-18   9.2e-15       1      87 [.       4     101 ..       4     132 .. 0.68

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 5.1e-18
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCS.......SHHHHHH...HHH CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGli.......egaseek...glg 67 
                                       ev+++Gr+NvGKStL+  ltg+k+ ++++pg T+ + + +v     +i  vD+pG +       + a++ek    + 
  gi|330508596|ref|YP_004385024.1|   4 EVVLIGRSNVGKSTLFWELTGKKVPIGKRPGITQYPFKTKVG----NIFYVDMPG-YgfmfrttK-ADQEKtkdLIV 74 
                                       699**********************************99996....7********.634444331.22222233455 PP

                                       HHHHHHHC.TSEEEEEEETT......T CS
                          MMR_HSR1  68 kaflalee.adlillvvdas......e 87 
                                       + f+++ +   l++ v+da+      +
  gi|330508596|ref|YP_004385024.1|  75 HYFEEHAReILLAVQVIDAAsfldiaD 101
                                       555555554677778888665555440 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   3.1e-13   5.5e-10       2     128 ..       4     146 ..       3     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.1e-13
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----.SSSSSSSHHHHHHHHHHH.. CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGi.Yslsayseeekvardfll.. 75 
                                       +v+l+G  nvGk+tlf +ltg+k  +g  pG+t    ++k      ++  vD+PG  + + ++  +++ ++d+++  
  gi|330508596|ref|YP_004385024.1|   4 EVVLIGRSNVGKSTLFWELTGKKVPIGKRPGITQYPFKTK----VGNIFYVDMPGYgFMFRTTKADQEKTKDLIVhy 76 
                                       699*****************************96555544....5599*******8677788888999999998866 PP

                                       ....CTSSSEEEEEEEGGGH.........HHHHHHHHHHHH....TTSSEEEEEETHHHHHHTTEEE-HH CS
                            FeoB_N  76 ....eeepdvvvnvvdatnl.........ernLyLtlqlle....lgvpvvlalnmideaekkgieidlk 128
                                            +e+ + v+v+da+++         + ++ + ++l e    lg++ vla n++d + k+  +  l+
  gi|330508596|ref|YP_004385024.1|  77 feehAREILLAVQVIDAASFldiadrwegRGEVPMEIELWEflddLGLDSVLAANKMDRIAKQDRDGALD 146
                                       6432334456689999986423232222123455555554422226778888888888888776655555 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.5e-06    0.0027       2     115 ..       5     134 ..       4     142 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-06
                                       EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEE.EEEE..E.EEETTEEEEEEEEEE.TTSGGGHHHHHHHHTT.E CS
                               Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyesTigvd.fytk..e.ievdgkevkleiwDT.AGqeefkslrelyyrd.a 72 
                                       +vl+G s+vGK++l  + + +k +  + + i    f+tk  + + vd   + +    T A qe+ k l   y+++ a
  gi|330508596|ref|YP_004385024.1|   5 VVLIGRSNVGKSTLFWELTGKKVPIGKRPGITQYpFKTKvgNiFYVDMPGYGFMFRTTkADQEKTKDLIVHYFEEhA 81 
                                       89*************************9999433333331121334455555655555699******9999997538 PP

                                       SEEEEEEETTBHHHHHTHH.HHHH..HHHHHST.......TTSEEEEEEETTT CS
                               Ras  73 egillvyditsresfenvk.kwve..eikrvae.......envpivLvGnKvD 115
                                       + ill  ++ +++sf +++ +w    e+ +  e         +  vL +nK+D
  gi|330508596|ref|YP_004385024.1|  82 REILLAVQVIDAASFLDIAdRWEGrgEVPMEIElweflddLGLDSVLAANKMD 134
                                       89**************9997775312555555566666554567777777777 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.016        29       6      32 ..       5      31 ..       2      68 .. 0.86
   2 !   12.7   0.0   3.8e-05     0.069      96     143 ..      86     145 ..      36     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.016
                                      EEEEESTTSSHHHHHHHHHHHTTSSCH CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlyktgaisk 32
                                      +++ig  + GK+TL  +L+ k+  i k
  gi|330508596|ref|YP_004385024.1|  5 VVLIGRSNVGKSTLFWELTGKKVPIGK 31
                                      78999*********9999877766665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.8e-05
                                       EEEEEEETT...........TBSTHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHHHH CS
                          GTP_EFTU  96 gavlvvdav...........eGvepqteevlrlalkegvpiivfiNKmDrl.kaelkeiv 143
                                       +av v+da+           +G  p   e+++ + ++g+  +++ NKmDr+ k++ +   
  gi|330508596|ref|YP_004385024.1|  86 LAVQVIDAAsfldiadrwegRGEVPMEIELWEFLDDLGLDSVLAANKMDRIaKQDRDGAL 145
                                       56667777766666677766678888899*********************9755544444 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.5e-05     0.028       2      47 ..       5      50 ..       4     106 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEET.TTTEEEEEEECGGSGGC CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekeks.tigvdfltkevtkikgv 47
                                      vvl+G s+vGK++l+ +++ +k+   +++ ++++ f+tk v +i  v
  gi|330508596|ref|YP_004385024.1|  5 VVLIGRSNVGKSTLFWELTGKKVPIGKRPgITQYPFKTK-VGNIFYV 50
                                      89*****************99997555441445555554.4455554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.4e-05      0.11     100     122 ..       3      25 ..       1      47 [. 0.87
   2 ?    0.9   0.0      0.22   3.9e+02      46      98 ..     123     183 ..     117     188 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.4e-05
                                       SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpe 122
                                       k +vl+G S vGKStL  +l+++
  gi|330508596|ref|YP_004385024.1|   3 KEVVLIGRSNVGKSTLFWELTGK 25 
                                       5689************9999887 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.22
                                       T-EEEEEEE-GGG--HHH.........HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCT CS
                       RsgA_GTPase  46 giepvivlnKiDlleeee.........eleelkeelealgyevllvsaktkegleelkellk 98 
                                       g++ v++ nK+D + +++         e   +    ++++ +v  +sak + ++e l+++++
  gi|330508596|ref|YP_004385024.1| 123 GLDSVLAANKMDRIAKQDrdgaldlicERLGMLPPWTQWQDRVAPISAK-RGQIEPLRAVIS 183
                                       6677899999999999985555544443344444455555556666555.345555555555 PP

>> Dynamin_N  Dynamin family
   #    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       1      47 [.       5      51 ..       5      84 .. 0.70
   2 ?    5.0   0.0     0.013        23      91     134 ..      35      86 ..      34     102 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.1e-05
                                      EEEEEBTTTTHHHHHHHHHTS--S---SS.S---S-EEEEECCT---C CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpn.ptTrrplelqlgeeeeas 47
                                      ++++G  + GKS++   L+g+++ p+g+   +T+ p++ + g+  ++ 
  gi|330508596|ref|YP_004385024.1|  5 VVLIGRSNVGKSTLFWELTGKKV-PIGKRpGITQYPFKTKVGNIFYVD 51
                                      799*******************6.666652689999998886655544 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.013
                                       EEEEEEETTS-SEEEEE---B...-SSSGTTS....HHHHHHH.STTEEEEE CS
                         Dynamin_N  91 illkilsllvkgltlvDlPGl...dsvnkrdq....elvkeyi.kkadiila 134
                                       i+ ++++ +v ++  vD+PG+    ++ k dq    +l+ +y  ++a+ il+
  gi|330508596|ref|YP_004385024.1|  35 ITQYPFKTKVGNIFYVDMPGYgfmFRTTKADQektkDLIVHYFeEHAREILL 86 
                                       5678999999**********72224566666667777777777755544443 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00014      0.24       2      26 ..       2      26 ..       1      42 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                            AAA_24  2 klkiliyGpsgiGKTtlakelgpkp 26
                                      ++ ++++G s +GK+tl +el+ k 
  gi|330508596|ref|YP_004385024.1|  2 SKEVVLIGRSNVGKSTLFWELTGKK 26
                                      7899****************94443 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.24       2      26 ..       3      27 ..       2      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                         PduV-EutP  2 kkilliGkvgsGKttLtqalkgeel 26
                                      k+++liG++++GK tL  +l+g+++
  gi|330508596|ref|YP_004385024.1|  3 KEVVLIGRSNVGKSTLFWELTGKKV 27
                                      89******************99887 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 ?   10.4   0.0   0.00018      0.32       4      29 ..       3      28 ..       1      77 [. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                                      -EEEEE-STTSSHHHHHHHHHHSS-- CS
                             SRPRB  4 pavllvGlsdsGKTslftrLttdsvk 29
                                      + v+l+G s+ GK +lf  Lt ++v 
  gi|330508596|ref|YP_004385024.1|  3 KEVVLIGRSNVGKSTLFWELTGKKVP 28
                                      689*****************988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1415.49
//
Query:       gi|330508597|ref|YP_004385025.1|  [L=295]
Description: small conductance mechanosensitive ion channel (MscS) family transporter [Methanosaeta concilii GP6]
Scores for complete 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-38  130.4   0.2    6.1e-38  130.4   0.2    1.5  2  MS_channel       Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.045   14.4   2.6       0.09   13.4   2.6    1.5  1  Sm_multidrug_ex  Putative small multi-drug export 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 ?   -6.4   3.8         2   1.8e+04       5      14 ..      48      57 ..      42      66 .. 0.46
   2 !  130.4   0.2   6.8e-42   6.1e-38       7     204 ..     100     295 .]      94     295 .] 0.86

  Alignments for each domain:
  == domain 1  score: -6.4 bits;  conditional E-value: 2
                                      HHHHHHHHHH CS
                        MS_channel  5 kiliivvgil 14
                                      ++++i+++i 
  gi|330508597|ref|YP_004385025.1| 48 NLIVIIFIIF 57
                                      2222222222 PP

  == domain 2  score: 130.4 bits;  conditional E-value: 6.8e-42
                                       HHHHHHHHHHHHTTT--...SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE- CS
                        MS_channel   7 liivvgilivlsllgvn...vsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedig 80 
                                       +i++ g+++v+ ++ +     +a+la++G+lgla+g+a+kd++sn+ +Gi++ + +pf++GDlv++ +  G+Ved++
  gi|330508597|ref|YP_004385025.1| 100 TIYLAGLMLVILQIPQLhkvATAMLAGAGILGLAVGYAAKDSLSNFTSGIFIAIFQPFRVGDLVDFRGDYGQVEDLT 176
                                       455555555555555544449******************************************************** PP

                                       SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EE CS
                        MS_channel  81 lrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkell 157
                                       lr t irt d+r +++Pns ++t+ ++N++ ++++    v++ ++ ++d   +++++e+++e ++ +++v kd +l 
  gi|330508597|ref|YP_004385025.1| 177 LRHTVIRTADNRRIIVPNSIISTEPVINWTIREKEITWSVDFDLEKAAD---IDRAREIILEKARGHSQVPKDRPLS 250
                                       *******************************555555555555555566...*******************999998 PP

                                       EEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT- CS
                        MS_channel 158 vvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegi 204
                                       v l   +   l +++ v v+    +   +v +ei++ ++k+le++gi
  gi|330508597|ref|YP_004385025.1| 251 VQLISSKSAELVLRLEVTVPG--RNVASAVGNEIREAVIKELEAQGI 295
                                       888888888888889888888..789999***************998 PP

>> 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 ?   13.4   2.6     1e-05      0.09      21     118 ..      42     152 ..      29     154 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                   Sm_multidrug_ex  21 lvsvlgnllpvplillflrkllellkkkkllkklfekleekaekkseki..........ekygflGLllFva.iPLp 86 
                                        +s+++nl+++++i++++r + e+++++  l++ + ++ ++ae + ++             + ++GL+l +  iP  
  gi|330508597|ref|YP_004385025.1|  42 TISIIVNLIVIIFIIFIVRAVAEIVDQM--LRTHIPRVINRAEVRMDETmqlmirriasATIYLAGLMLVILqIPQL 116
                                       589********************88874..55555555555555444443334554443358899999876426632 PP

                   Sm_multidrug_ex  87 ...gTGawtGs.liasllglkkkkallaillGvlia 118
                                           T +  G+ +++   g   k++l   + G++ia
  gi|330508597|ref|YP_004385025.1| 117 hkvATAMLAGAgILGLAVGYAAKDSLSNFTSGIFIA 152
                                       222566666663456777777777777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2173.89
//
Query:       gi|330508598|ref|YP_004385026.1|  [L=338]
Description: magnesium and cobalt transport protein CorA [Methanosaeta concilii GP6]
Scores for complete 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-76  254.9   1.0    1.3e-75  254.4   1.0    1.1  1  CorA      CorA-like Mg2+ transporter protein
     0.0056   14.4   0.1     0.0072   14.0   0.1    1.1  1  ACR_tran  AcrB/AcrD/AcrF family
  ------ inclusion threshold ------
      0.064   13.7   0.7        0.1   13.0   0.7    1.3  1  CopD      Copper resistance protein D


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 !  254.4   1.0   2.2e-79   1.3e-75       4     292 .]      40     334 ..      38     336 .. 0.95

  Alignments for each domain:
  == domain 1  score: 254.4 bits;  conditional E-value: 2.2e-79
                              CorA   4 fvWldlssptee.eleeLaeelgldelaledlldseerprvedyddylllvlpsveldkseeeeeev.......pls 72 
                                       ++W++++ p +   le+L + +gl++l+led+l++ +rp+vedy+dy+++vl+ + +++ e+++e         ++s
  gi|330508598|ref|YP_004385026.1|  40 MIWINVDCPRQVySLEKLGACYGLHPLVLEDILTD-QRPKVEDYEDYIFIVLKMLYYEEAEDDDEIGdfnidmdQVS 115
                                       78*******9999********************87.***************************9999********** PP

                              CorA  73 illgdnflitvrreplealdevikrlk..deggkpkspgellyrlldeivdrlfellekleeeldeledeledstkk 147
                                       i++g+nf+i++ ++++++++ +++rl+  + + +++ +  l y  +d+ivd++f ++ekl ++ +eled + ++ + 
  gi|330508598|ref|YP_004385026.1| 116 IIFGKNFIISFKEKDVDIFRPLRERLRtsKGRIRKQGADYLAYSMIDSIVDHYFVIMEKLGDRFEELEDSVVSNPEP 192
                                       ***************************999999******************************************** PP

                              CorA 148 eilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtyss 224
                                       +il  +++l+r++  lr++++p+re++ +++++ d +l++++ + ylrd++d++ +++e +e+ r++  sl +ty s
  gi|330508598|ref|YP_004385026.1| 193 GILPAIYNLKRDMLFLRKSVWPLREAI-SRMQRMDSHLISETTRIYLRDVYDHTIQVIENIETFRDMSASLLETYLS 268
                                       ***************************.88888******************************************** PP

                              CorA 225 llserlNrvmkvLTvltaiflPlTlitGiyGmNfkglPelewsygypfvlllglmallailllfwfkr 292
                                        ls++lN+v+k+LT++++if+PlT+++G+yGmNf ++Pele++ygyp+v  l+lm+l+++++l++f+r
  gi|330508598|ref|YP_004385026.1| 269 SLSNKLNEVIKLLTIISTIFIPLTFLSGLYGMNFTHMPELEHPYGYPAV--LVLMLLVVAVMLAYFYR 334
                                       *************************************************..55555555555555543 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.2e-06    0.0072     399     463 ..     242     305 ..     240     330 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHH CS
                          ACR_tran 399 vDdAiVvvEnierkleeegekpleaalksmkeiqgalvaialvllavflPilflgGveGklfrqf 463
                                        D  i v+Enie    +  ++ le+ l s ++    ++ +  +++ +f+P+ fl+G+ G  f  +
  gi|330508598|ref|YP_004385026.1| 242 YDHTIQVIENIETFRDM-SASLLETYLSSLSNKLNEVIKLLTIISTIFIPLTFLSGLYGMNFTHM 305
                                       59999******999888.88999************************************999877 PP

>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.7   1.7e-05       0.1      10      63 ..     284     337 ..     276     338 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                              CopD  10 lalaavavvlvtGvvnallrvglagllttayG..rlllaKlalllvllalaalnrf 63 
                                       + ++ + +++++G++  +  + +++l + +yG   +l+++l++++v+la++ + ++
  gi|330508598|ref|YP_004385026.1| 284 ISTIFIPLTFLSGLYG-MNFTHMPELEH-PYGypAVLVLMLLVVAVMLAYFYRKKW 337
                                       5677788899999998.44444566655.67766****************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
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 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2195.00
//
Query:       gi|330508599|ref|YP_004385027.1|  [L=424]
Description: natural resistance-associated macrophage protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-96  323.8  24.1    1.3e-96  323.8  24.1    1.4  2  Nramp     Natural resistance-associated macrophage protein


Domain annotation for each model (and alignments):
>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.8  24.1    7e-101   1.3e-96       1     358 []      42     393 ..      42     393 .. 0.98
   2 ?   -5.8   2.7         1   1.8e+04      87     107 ..     395     415 ..     394     419 .. 0.62

  Alignments for each domain:
  == domain 1  score: 323.8 bits;  conditional E-value: 7e-101
                             Nramp   1 iatdlqaGaqfGykLlwvlllstllaillqelsarLGlvTgkglaelirerlpkkvsillwilaelaiiatdlaevi 77 
                                       i+t++ aGa+fGy+Llw+l+ +t++++++qe++ar+G+vTgkgla+lirer++ k +++l++  ++a+++t  ae++
  gi|330508599|ref|YP_004385027.1|  42 ITTYSIAGAHFGYSLLWLLIPITFALFVVQEMCARMGVVTGKGLADLIRERFGVKPTVVLLLGFIIANLCTTTAEFA 118
                                       79*************************************************************************** PP

                             Nramp  78 GaAialnllfgipllvgvlitavlvllllflekggyrklEaliialvlvialsFiaelflvkpdwgevlkglvvPsl 154
                                       G+A++++++ g++++v+v+++avlv+ +++   g+ r lE+++++  +v+ +++i++ +++kpdw+ +++++v+Psl
  gi|330508599|ref|YP_004385027.1| 119 GVAASMEIF-GVSKYVSVPAAAVLVWSIVV--MGNRRSLEKVFLIASSVY-ITYIISGLMLKPDWKFLFTQTVTPSL 191
                                       ******987.5*******************..9*****************.************************** PP

                             Nramp 155 pg.keslllavgilGatvmphnlflhsslvqerkitidrsekeealkyeriDtiialivaflinlailivaAavlys 230
                                       +  +++l++++gi+G+t++p+++f+ +s+++e++i+i    +e  +ky+++D++++++++ +++++i+ ++Aa++++
  gi|330508599|ref|YP_004385027.1| 192 SLeSGYLYMVIGIVGTTITPWMQFYLQSTIVEKGIKI----SE--YKYTKWDVYVGCLITDVVSYFIIFTCAATIFA 262
                                       **********************************888....77..******************************** PP

                             Nramp 231 ggkdvesledaaeaLepllGskaasvlFaigLlaaGlsStitgtlagqyvmegflglrislwlrrlitralafvpal 307
                                       gg  +e+++daa aL pl+G +++++lFa+gLl+a+l ++++++l+++y +++ +g+++ l++r+   +a +f+ ++
  gi|330508599|ref|YP_004385027.1| 263 GGIRIETAKDAALALFPLAG-EYSAWLFAFGLLNASLFAASILPLSTAYFLCEGMGWDSGLNKRF--GDAPQFYLLF 336
                                       ********************.7***************************************9999..99******** PP

                             Nramp 308 ivilligaele......lvkllvlsqvllslllPfaliplllltsskklMGefknsk 358
                                       ++++++ga +       l+ ++vls+v+++ llP++l+++l+l++++k+MG+++n+k
  gi|330508599|ref|YP_004385027.1| 337 TLLIAFGAIFIlipnapLLAIMVLSEVINGSLLPMVLLFILILINDRKIMGKYTNGK 393
                                       ******************************************************985 PP

  == domain 2  score: -5.8 bits;  conditional E-value: 1
                             Nramp  87 fgipllvgvlitavlvllllf 107
                                       f++  + +++i+ +l++ll++
  gi|330508599|ref|YP_004385027.1| 395 FNLIAWSTTIIMSILTVLLVV 415
                                       555666667777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3123.34
//
Query:       gi|330508600|ref|YP_004385028.1|  [L=453]
Description: Mg/Co/Ni transporter MgtE domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-28   98.6  10.8      3e-28   98.4   8.9    1.9  2  MgtE_N       MgtE intracellular N domain
    1.3e-19   70.4   5.5    3.9e-09   36.8   0.3    4.9  5  CBS          CBS domain
    1.4e-05   25.2   1.3      0.028   14.6   0.0    3.5  4  FliG_M       FliG middle domain
    0.00034   20.6   3.6      0.012   15.6   0.1    3.7  4  PRC          PRC-barrel domain
     0.0045   17.5   6.1       0.53   10.9   0.3    3.3  3  FliG_N       FliG N-terminal domain
  ------ inclusion threshold ------
      0.016   15.1   0.5      0.086   12.8   0.3    2.4  2  hnRNP_Q_AcD  Heterogeneous nuclear ribonucleoprotein Q acidic


Domain annotation for each model (and alignments):
>> MgtE_N  MgtE intracellular N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   8.9     1e-31     3e-28       1     100 [.     209     308 ..     209     310 .. 0.99
   2 ?   -0.9   0.0      0.87   2.6e+03      44      61 ..     383     400 ..     372     404 .. 0.47

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 1e-31
                                       S-HHHHHHCHCCS-HHHHHHHHHHS-HHHHHHHHCTS-CCCCCHHHHCS-HHHHHHHHCCS-HHHHHHHHCCCHHHH CS
                            MgtE_N   1 lhpadiaelleelpeeeraallrllpkeeaaevleeldedlqeeliealsdeelaelleeldsDdaadlleelpeek 77 
                                       lhpadia++leel++++r+++l  l +e+aae++ee+d+++q++++++++++++a++le++++Ddaadll  +pe+k
  gi|330508600|ref|YP_004385028.1| 209 LHPADIADILEELNNRDRLLILDSLGEETAAETMEEVDPEVQATMVNQMESDDVADILENMNPDDAADLLGIMPENK 285
                                       7**************************************************************************** PP

                                       HHHHHHCS-HHHHHHHHHHCTS- CS
                            MgtE_N  78 veellsaldeeereeieellsYp 100
                                       ++e+l++++e e+ee++el++Y+
  gi|330508600|ref|YP_004385028.1| 286 ASEVLELMNEVEAEEVRELMAYS 308
                                       **********************7 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.87
                                       HHHHCS-HHHHHHHHCCS CS
                            MgtE_N  44 eliealsdeelaelleel 61 
                                       e+++ l+ ++++e+++ l
  gi|330508600|ref|YP_004385028.1| 383 EVLSVLPTSTIEEVTNLL 400
                                       333333333333333322 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.6   1.1e+04      12      25 ..      58      71 ..      53      77 .. 0.76
   2 ?    1.0   0.0      0.19   5.8e+02      16      38 ..     212     232 ..     208     237 .. 0.79
   3 ?    0.2   0.0      0.35     1e+03       8      26 ..     276     294 ..     258     305 .. 0.70
   4 !   30.0   0.0   1.8e-10   5.3e-07       1      54 [.     312     370 ..     312     373 .. 0.88
   5 !   36.8   0.3   1.3e-12   3.9e-09       2      55 ..     377     430 ..     375     432 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.6
                                      EETTSBHHHHHHHH CS
                               CBS 12 vppdttleealelm 25
                                      + p +tl e+ +++
  gi|330508600|ref|YP_004385028.1| 58 LQPGDTLLEISRII 71
                                      67889999998886 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.19
                                       SBHHHHHHHHHHHTSSEEEEEET CS
                               CBS  16 ttleealelmrekgvsrlPVVde 38 
                                       ++++++le++  ++ +rl+++d+
  gi|330508600|ref|YP_004385028.1| 212 ADIADILEEL--NNRDRLLILDS 232
                                       6799999999..55589988865 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.35
                                       SCEEEETTSBHHHHHHHHH CS
                               CBS   8 dvvtvppdttleealelmr 26 
                                       d++ + p+   +e+lelm 
  gi|330508600|ref|YP_004385028.1| 276 DLLGIMPENKASEVLELMN 294
                                       4455667778889999993 PP

  == domain 4  score: 30.0 bits;  conditional E-value: 1.8e-10
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHT..SSEE.EE.E.ETTTBEEEEEEHHHHHHH CS
                               CBS   1 Vgdimtrdvvtvppdttleealelmrekg..vsrl.PV.V.dedgklvGivtlrDllra 54 
                                       +g++mt+d+v vp  +t++ ++ ++r++g  v+ + ++ V  ++g+l+G+ +lrDll a
  gi|330508600|ref|YP_004385028.1| 312 AGSLMTTDYVAVPSGCTVSNIFSILRRSGkeVDMIyYIyVqSDSGQLLGVMSLRDLLLA 370
                                       589**********************99888888775586687899***********987 PP

  == domain 5  score: 36.8 bits;  conditional E-value: 1.3e-12
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       + +m ++v++v p++t+ee+ +l+ ++++ ++PV de+g+++Givt  D l+ +
  gi|330508600|ref|YP_004385028.1| 377 STVMKKEVLSVLPTSTIEEVTNLLSKYDFLCVPVADEEGRILGIVTFDDALDEI 430
                                       569*********************88665588888**************99876 PP

>> FliG_M  FliG middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.019        56       7      45 ..     205     243 ..     203     245 .. 0.88
   2 !    6.8   0.0    0.0026       7.6      18      47 ..     228     257 ..     227     264 .. 0.93
   3 !   14.6   0.0   9.5e-06     0.028      17      48 ..     263     294 ..     260     307 .. 0.83
   4 ?   -2.6   0.0       2.2   6.6e+03      31      63 ..     384     398 ..     376     403 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.019
                                       HHTTS-HHHHHHHHHTS-HHHHHHHHHTS-HHHHHHHHH CS
                            FliG_M   7 llknEhPqtiAliLsyLdpeqAAevLseLpeelraevir 45 
                                        +++ hP  iA iL  L+      +L +L ee +ae++ 
  gi|330508600|ref|YP_004385028.1| 205 TINDLHPADIADILEELNNRDRLLILDSLGEETAAETME 243
                                       5788899999999*9999999999999999999999986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0026
                                       HHHHTS-HHHHHHHHHTS-HHHHHHHHHHH CS
                            FliG_M  18 liLsyLdpeqAAevLseLpeelraevirri 47 
                                       liL  L  e AAe ++e ++e++a  ++++
  gi|330508600|ref|YP_004385028.1| 228 LILDSLGEETAAETMEEVDPEVQATMVNQM 257
                                       799*********************999988 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 9.5e-06
                                       HHHHHTS-HHHHHHHHHTS-HHHHHHHHHHHH CS
                            FliG_M  17 AliLsyLdpeqAAevLseLpeelraevirria 48 
                                       A iL  ++p+ AA++L  +pe++++ev+  + 
  gi|330508600|ref|YP_004385028.1| 263 ADILENMNPDDAADLLGIMPENKASEVLELMN 294
                                       77999999999999999999999999987654 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 2.2
                                       HHHTS-HHHHHHHHHHHHTCCTCSHHHHHHHHH CS
                            FliG_M  31 vLseLpeelraevirriatlekvspevlkevee 63 
                                       vLs Lp    +ev                   +
  gi|330508600|ref|YP_004385028.1| 384 VLSVLPTSTIEEV------------------TN 398
                                       5555555444444..................44 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.1e-06     0.012       4      77 ..      32     102 ..      29     104 .. 0.78
   2 ?    3.4   0.2     0.027        80       9      34 ..     120     145 ..     117     188 .. 0.77
   3 ?   -2.8   0.0       2.3     7e+03      17      40 ..     338     361 ..     334     362 .. 0.78
   4 ?   -1.1   0.0      0.69   2.1e+03      13      26 ..     409     422 ..     403     428 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.1e-06
                                       CCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEE..EEEETTT.....-EEEEEGG.CEECCCTEEEETTS-G CS
                               PRC   4 frasdliGkeVytedGeklGkVkDvvidekegrvral..vvsvggflgigekevliPfdlavkigkdriivdapke 77 
                                        ++s+l G+++ +++G  +Gk++D+ + +++  ++++  ++ +++ l   +++v++P+   v ++++ i +d++++
  gi|330508600|ref|YP_004385028.1|  32 SFFSQLQGMKISDREGNAVGKLSDLALQPGDT-LLEIsrIIYTSNIL---REKVILPIS-SVGSINGDIRLDVSRD 102
                                       6799***********************99555.44441233333444...699999999.9999999999998877 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.027
                                       -TT-EEEETTSSEEEEEEEEEEETTT CS
                               PRC   9 liGkeVytedGeklGkVkDvvideke 34 
                                       + +++++++dG k+ +V+D+++    
  gi|330508600|ref|YP_004385028.1| 120 ILDRQIVDIDGLKVVRVNDILLGQVK 145
                                       67788888888888888888776544 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.3
                                       TTSSEEEEEEEEEEETTTTEEEEE CS
                               PRC  17 edGeklGkVkDvvidekegrvral 40 
                                       ++G+++  ++ +++  ++g+++++
  gi|330508600|ref|YP_004385028.1| 338 RSGKEVDMIYYIYVQSDSGQLLGV 361
                                       568888888889999988888776 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.69
                                       EEEETTSSEEEEEE CS
                               PRC  13 eVytedGeklGkVk 26 
                                       +V +e+G++lG V+
  gi|330508600|ref|YP_004385028.1| 409 PVADEEGRILGIVT 422
                                       78889999999884 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.3    0.0013         4      11      40 ..     229     258 ..     220     270 .. 0.89
   2 !   10.9   0.3   0.00018      0.53       6      41 ..     272     307 ..     269     313 .. 0.90
   3 ?   -2.2   0.0         2   6.1e+03      21      40 ..     382     401 ..     379     404 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0013
                                       HHHHCXHHHHHHHHTTSXHHHHHHHHHHHH CS
                            FliG_N  11 lllaLgeeeaaevlkhLdeeeiekltkeia 40 
                                       +l +Lgee+aae +++ d+e ++ +++++ 
  gi|330508600|ref|YP_004385028.1| 229 ILDSLGEETAAETMEEVDPEVQATMVNQME 258
                                       5668******************99999996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHCXHHHHHHHHTTSXHHHHHHHHHHHHC CS
                            FliG_N   6 qkaAilllaLgeeeaaevlkhLdeeeiekltkeias 41 
                                       + aA ll  + e++a+evl+ ++e e e++ + +a 
  gi|330508600|ref|YP_004385028.1| 272 DDAADLLGIMPENKASEVLELMNEVEAEEVRELMAY 307
                                       67999*************************999985 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2
                                       HHHHTTSXHHHHHHHHHHHH CS
                            FliG_N  21 aevlkhLdeeeiekltkeia 40 
                                       +evl+ L+ + ie++t+ ++
  gi|330508600|ref|YP_004385028.1| 382 KEVLSVLPTSTIEEVTNLLS 401
                                       68999999999999997655 PP

>> hnRNP_Q_AcD  Heterogeneous nuclear ribonucleoprotein Q acidic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.1   3.2e+03      31      40 ..     229     238 ..     207     255 .. 0.63
   2 ?   12.8   0.3   2.9e-05     0.086      27      61 ..     273     307 ..     244     311 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.1
                       hnRNP_Q_AcD  31 aLkslpeegA 40 
                                       +L sl ee A
  gi|330508600|ref|YP_004385028.1| 229 ILDSLGEETA 238
                                       3444444444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.9e-05
                       hnRNP_Q_AcD  27 raleaLkslpeegAlaVlkqfkesdlskvsNksay 61 
                                        a + L  +pe++A++Vl+ ++e+++++v+   ay
  gi|330508600|ref|YP_004385028.1| 273 DAADLLGIMPENKASEVLELMNEVEAEEVRELMAY 307
                                       57789999*********************998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3175.34
//
Query:       gi|330508601|ref|YP_004385029.1|  [L=159]
Description: Lrp/AsnC family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-16   57.9   0.1    2.2e-15   56.4   0.1    1.8  2  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    2.1e-12   46.4   0.3    3.5e-12   45.7   0.3    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    1.7e-11   43.7   1.6    2.9e-11   43.0   1.6    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    1.6e-05   24.7   0.1    2.6e-05   24.0   0.1    1.3  1  MarR_2           MarR family
     0.0003   20.8   0.0    0.00053   20.0   0.0    1.3  1  HTH_20           Helix-turn-helix domain
    0.00045   20.1   0.1    0.00081   19.3   0.1    1.3  1  MarR             MarR family
    0.00059   19.7   0.0      0.001   18.9   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.001   18.7   0.1     0.0023   17.6   0.1    1.6  1  Sigma70_r4_2     Sigma-70, region 4
     0.0015   18.3   0.0     0.0029   17.4   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
      0.003   18.0   0.1     0.0057   17.1   0.1    1.5  1  HTH_27           Winged helix DNA-binding domain
     0.0031   17.4   0.1     0.0057   16.6   0.1    1.4  1  HTH_11           HTH domain
     0.0043   16.9   0.0     0.0087   15.9   0.0    1.4  1  HxlR             HxlR-like helix-turn-helix
     0.0052   17.0   0.0     0.0094   16.1   0.0    1.3  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
     0.0079   16.2   0.1      0.015   15.3   0.1    1.4  1  HemN_C           HemN C-terminal domain
     0.0085   16.0   0.4      0.016   15.2   0.4    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.023   14.5   0.0    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
      0.051   13.3   0.4      0.096   12.4   0.4    1.4  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.053   13.3   0.0        0.1   12.4   0.0    1.4  1  HTH_10           HTH DNA binding domain
      0.059   13.2   0.1       0.11   12.3   0.1    1.4  1  LexA_DNA_bind    LexA DNA binding domain
       0.06   13.5   0.1       0.37   11.0   0.0    1.9  2  AsnC_trans_reg2  AsnC-like ligand binding domain
       0.11   12.5   0.0       0.21   11.6   0.0    1.4  1  HTH_Tnp_IS630    Transposase
       0.15   11.8   0.1       0.48   10.1   0.0    1.8  2  HTH_41           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.9   1.6e+03      28      48 ..      35      55 ..      14      80 .. 0.68
   2 !   56.4   0.1   2.7e-18   2.2e-15       2      73 ..      81     149 ..      78     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.9
                                      EEEEESSSSSEEEEEEESSHH CS
                    AsnC_trans_reg 28 ecyrvtGdydyllkvvvrdle 48
                                      e+ r +G +d  ++ + + ++
  gi|330508601|ref|YP_004385029.1| 35 EISRRSGIADATVQFRLKRMK 55
                                      444555555555555555554 PP

  == domain 2  score: 56.4 bits;  conditional E-value: 2.7e-18
                                       EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73 
                                       lv++++++   ++++ +al  +pe++e+y + G+yd++lkv++r le+l ++++++++s++gv++    +v+
  gi|330508601|ref|YP_004385029.1|  81 LVQTDSES---HDRAVRALVLIPEITEVYGILGEYDLFLKVWSRGLEELKTIINDRIRSVEGVKNLLEIVVM 149
                                       56777555...*****************************************************98777777 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.3   4.3e-15   3.5e-12       1      48 []      14      61 ..      14      61 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 4.3e-15
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      lde dr IL  L++++r+s +e+++r+g+  +tv  rlkr++++G+I+
  gi|330508601|ref|YP_004385029.1| 14 LDEVDRTILTNLREDSRMSLQEISRRSGIADATVQFRLKRMKSQGVIE 61
                                      79*********************************************7 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   1.6   3.6e-14   2.9e-11       1      42 []      14      55 ..      14      55 .. 0.98

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 3.6e-14
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LDe+Dr IL  L+ed+R+s +e+++r G++ +tv+ R++r++
  gi|330508601|ref|YP_004385029.1| 14 LDEVDRTILTNLREDSRMSLQEISRRSGIADATVQFRLKRMK 55
                                      8***************************************95 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   3.2e-08   2.6e-05       8      53 ..      19      62 ..      13      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.2e-08
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      + +L +L+   +  ++ +e+ rr g+  ++v+ +lkr+ ++G +er
  gi|330508601|ref|YP_004385029.1| 19 RTILTNLREDSR--MSLQEISRRSGIADATVQFRLKRMKSQGVIER 62
                                      567888877776..******************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   6.5e-07   0.00053       9      56 ..      15      62 ..      13      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.5e-07
                                      -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      ++v r il  L+++  +++ e+ +r +++++t+ ++L+ + + g +e+
  gi|330508601|ref|YP_004385029.1| 15 DEVDRTILTNLREDSRMSLQEISRRSGIADATVQFRLKRMKSQGVIER 62
                                      67889*****************************************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   9.9e-07   0.00081       8      50 ..      21      63 ..      15      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.9e-07
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      iL++l+e   +s++e+ +++g+  +tv   l+r+  +G ieR 
  gi|330508601|ref|YP_004385029.1| 21 ILTNLREDSRMSLQEISRRSGIADATVQFRLKRMKSQGVIERF 63
                                      9*****************************************6 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.3e-06     0.001       4      56 ..      12      64 ..      10      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                                      CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      l L e +  + + L +  +++ +ei++++g+  ++v+  L+++++ G++er  
  gi|330508601|ref|YP_004385029.1| 12 LELDEVDRTILTNLREDSRMSLQEISRRSGIADATVQFRLKRMKSQGVIERFT 64
                                      678888888999999999********************************965 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.8e-06    0.0023      10      49 ..      13      53 ..      12      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.8e-06
                                      TS-HHHHHHHH.HHHTS---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 10 eLperqreifl.lryleglsykEIAellgisegtVksrlsR 49
                                      eL e +r+i++ lr+   +s +EI+++ gi ++tV+ rl+R
  gi|330508601|ref|YP_004385029.1| 13 ELDEVDRTILTnLREDSRMSLQEISRRSGIADATVQFRLKR 53
                                      678888888875888889*********************99 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.5e-06    0.0029      14      50 ..      26      62 ..      20      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.5e-06
                                      TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +++ +++l+e++rr+g++ +tv   L+ +  +G +e+
  gi|330508601|ref|YP_004385029.1| 26 REDSRMSLQEISRRSGIADATVQFRLKRMKSQGVIER 62
                                      45566*****************999999999998875 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 !   17.1   0.1     7e-06    0.0057       3      64 ..      16      76 ..      14      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7e-06
                            HTH_27  3 rqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrl 64
                                      ++++ +L ++r ++ r++l ++++r  + d+++   lk++  +G++er +  a+  ++ +++
  gi|330508601|ref|YP_004385029.1| 16 EVDRTILTNLR-EDSRMSLQEISRRSGIADATVQFRLKRMKSQGVIERFTISASPAATGYTV 76
                                      57899******.**********************************9987666555555555 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1     7e-06    0.0057       3      54 ..      19      74 ..      18      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7e-06
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpIesepgr.GY 54
                                      ++il+ L ++++ +s +e++++ ++  +tv+ ++k+++++g    + I ++p   GY
  gi|330508601|ref|YP_004385029.1| 19 RTILTNL-REDSRMSLQEISRRSGIADATVQFRLKRMKSQGvierFTISASPAAtGY 74
                                      689999*.77778*****************************999999999998888 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-05    0.0087      10      67 ..      21      78 ..      18      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                                      HHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-T CS
                              HxlR 10 ilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYslte 67
                                      il++l +  ++  +e++r+  +i+  +   rL++++++g+ier +++  P    Y++t+
  gi|330508601|ref|YP_004385029.1| 21 ILTNLREdSRMSLQEISRRS-GIADATVQFRLKRMKSQGVIERFTISASPAATGYTVTA 78
                                      77778774566788999998.9*********************************9996 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.1e-05    0.0094      11      52 ..      19      60 ..      13      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 11 etIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                      +tI+t+  e +  + +++++r +++ ++V+  lk+++++G +
  gi|330508601|ref|YP_004385029.1| 19 RTILTNLREDSRMSLQEISRRSGIADATVQFRLKRMKSQGVI 60
                                      89*************************************965 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.9e-05     0.015       5      52 ..      15      61 ..      13      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                            HemN_C  5 drleEeiilgLRlreGldlaafeqrfgldleellaaaleklqeqGLLe 52
                                      d + ++i+  LR +  ++l+++  r+g++  +++++ l+++  qG +e
  gi|330508601|ref|YP_004385029.1| 15 DEVDRTILTNLREDSRMSLQEISRRSGIA-DATVQFRLKRMKSQGVIE 61
                                      77889***********************7.9999***********997 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   1.9e-05     0.016      19      53 ..      28      62 ..      12      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
                                      EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglisr 53
                                      + +++ +e++++ G+   tv   l+++k +g+i+r
  gi|330508601|ref|YP_004385029.1| 28 DSRMSLQEISRRSGIADATVQFRLKRMKSQGVIER 62
                                      4689*****************************95 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.9e-05     0.023       6      46 ..      20      61 ..      15      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-05
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       IL  L+e + ++  e+++  g+  +tv   Lk+++ +G++e
  gi|330508601|ref|YP_004385029.1| 20 TILTNLREdSRMSLQEISRRSGIADATVQFRLKRMKSQGVIE 61
                                      59999***566****************************997 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   0.00012     0.096       4      46 ..      20      62 ..      18      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                       il  l+++  +s++e++ + g+++aT+   L+ ++ qg+++R
  gi|330508601|ref|YP_004385029.1| 20 TILTNLREDSRMSLQEISRRSGIADATVQFRLKRMKSQGVIER 62
                                      69999***********************999999999999998 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012       0.1      23      49 ..      30      56 ..      27      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                            HTH_10 23 rvtlkeLAkelGIskstlsehLrkaes 49
                                      r++l+e++ + GI+++t++ +L++ +s
  gi|330508601|ref|YP_004385029.1| 30 RMSLQEISRRSGIADATVQFRLKRMKS 56
                                      789********************9876 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00013      0.11      27      58 ..      32      62 ..      21      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                      -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyier 58
                                      s  ei+r+ g++  ++v+ +Lk+++  G+ier
  gi|330508601|ref|YP_004385029.1| 32 SLQEISRRSGIA-DATVQFRLKRMKSQGVIER 62
                                      789********9.99***************98 PP

>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.94   7.7e+02      49      80 ..      22      53 ..      19      55 .. 0.78
   2 ?   11.0   0.0   0.00045      0.37       2      68 ..      72     139 ..      71     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.94
                   AsnC_trans_reg2 49 harseeeveevlaeiaaatgledyevLpstre 80
                                       ++ +e+ +  l+ei+++ g+ d  v + ++ 
  gi|330508601|ref|YP_004385029.1| 22 LTNLREDSRMSLQEISRRSGIADATVQFRLKR 53
                                      5566788899999*******999888777765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00045
                   AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevla.eiaaatg 68 
                                        G++ +a + ++++ e  +++ +++  +pe+t +Y    +y l+  v  r  ee++++++ +i++  g
  gi|330508601|ref|YP_004385029.1|  72 TGYTVTAIMLVQTDSESHDRAVRALVLIPEITEVYGILGEYDLFLKVWSRGLEELKTIINdRIRSVEG 139
                                       69************************************************999999998624555555 PP

>> HTH_Tnp_IS630  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00026      0.21      64      95 ..      24      55 ..      10      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                     HTH_Tnp_IS630 64 dvkknpdallkerakkfgvtpasllyalkklk 95
                                      ++++ + + l+e+ ++ g+  a++ + lk++k
  gi|330508601|ref|YP_004385029.1| 24 NLREDSRMSLQEISRRSGIADATVQFRLKRMK 55
                                      6789999************************9 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00059      0.48       9      37 ..      33      61 ..      30      62 .. 0.90
   2 ?   -2.6   0.0       5.5   4.5e+03       4      17 ..     132     145 ..     131     148 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00059
                            HTH_41  9 IeelakeleLSvGlvQkALklLeddkais 37
                                       +e++  +++   +vQ+ Lk ++++++i+
  gi|330508601|ref|YP_004385029.1| 33 LQEISRRSGIADATVQFRLKRMKSQGVIE 61
                                      5788999999999**************95 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.5
                            HTH_41   4 dRlktIeelakele 17 
                                       dR++++e   + le
  gi|330508601|ref|YP_004385029.1| 132 DRIRSVEGVKNLLE 145
                                       79999987766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1099.44
//
Query:       gi|330508602|ref|YP_004385030.1|  [L=177]
Description: hypothetical protein MCON_2836 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); 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:                         0  (0); expected 0.2 (1e-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: 1308.64
//
Query:       gi|330508603|ref|YP_004385031.1|  [L=156]
Description: bacterioferritin comigratory protein Bcp [Methanosaeta concilii GP6]
Scores for complete 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  133.1   0.0    5.9e-39  132.8   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    1.7e-18   66.7   0.0    2.1e-18   66.5   0.0    1.0  1  Redoxin     Redoxin
      4e-05   23.7   0.0      0.021   14.9   0.0    2.1  2  AhpC-TSA_2  AhpC/TSA antioxidant enzyme
  ------ inclusion threshold ------
       0.17   11.4   0.0        0.2   11.1   0.0    1.1  1  DUF899      Bacterial protein of unknown function (DUF899)
       0.17   11.8   0.0       0.31   10.9   0.0    1.5  1  SCO1-SenC   SCO1/SenC


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.8   0.0   1.6e-42   5.9e-39       1     123 [.       4     132 ..       4     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 1.6e-42
                                       TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfi 77 
                                       +gd apdf+l+ a g+++ l++ +gk++vl+fypkd++ +Ct+e+ ++ +++++f+++g+ev+g+s dsp+sh+kf+
  gi|330508603|ref|YP_004385031.1|   4 IGDVAPDFCLPGAGGQEICLNAHSGKWLVLYFYPKDNTSGCTREAMDFTAHLPDFRKLGAEVVGISRDSPASHEKFA 80 
                                       89*************************************************************************** PP

                                       HH-H.SSEEEE-TTSHHHHHTT-EETT......TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  78 ekeslnfpllsDeegkvakaygvlkee......kglalratfvidkegkiry 123
                                       +k+sl+++llsD+++ v ++yg++  +      + +++r+tf+id+egki+y
  gi|330508603|ref|YP_004385031.1|  81 AKHSLKVTLLSDPDHRVTESYGAWALKkmygkeSYGTVRSTFLIDPEGKIAY 132
                                       ************************8779***99999**************99 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.0   5.8e-22   2.1e-18       3     133 ..       5     136 ..       3     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 5.8e-22
                                       TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHHHHH CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndafvke 78 
                                       gd aPdf lp+   +g+++ l +  gk +v++f+p   +  C++e+  + ++l ++ ++ g +vv+++ d+ a   +
  gi|330508603|ref|YP_004385031.1|   5 GDVAPDFCLPG--AGGQEICLNAHSGKWLVLYFYPKDNTSGCTREAMdFTAHLPDF-RKLGAEVVGISRDSPASHEK 78 
                                       8999*****99..**********************************899999888.******************** PP

                                       HHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG....EEE-EEEEEEETTEEEEEEES CS
                           Redoxin  79 fwgkeglkfpvlsDgsaaftkalGlrleedaseg....lrtpryavidedgkvvyleve 133
                                       f++k++lk+++lsD+++ +t+++G +++ ++  g       +++++id +gk+ y+ + 
  gi|330508603|ref|YP_004385031.1|  79 FAAKHSLKVTLLSDPDHRVTESYG-AWALKKMYGkesyGTVRSTFLIDPEGKIAYIWRR 136
                                       ************************.666665555889888999***********98665 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   5.9e-06     0.021       4      53 ..      53     103 ..      50     109 .. 0.88
   2 !    8.8   0.0   0.00047       1.7      72     110 ..      99     135 ..      95     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.9e-06
                        AhpC-TSA_2   4 rdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalgl 53 
                                       + +p++++ g ++v+i+ ++p s +kF++    ++ l+ Dp+  + ++ g 
  gi|330508603|ref|YP_004385031.1|  53 AHLPDFRKLGAEVVGISRDSPaSHEKFAAKHSLKVTLLSDPDHRVTESYGA 103
                                       567999***************99*******************988777665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00047
                        AhpC-TSA_2  72 nllkrlkeigipgdlageltqrGGtflfdkqgelvyehr 110
                                       +++  ++ ++++g +++++t r  tfl+d++g+++y +r
  gi|330508603|ref|YP_004385031.1|  99 ESYGAWALKKMYG-KESYGTVR-STFLIDPEGKIAYIWR 135
                                       5667777777777.78999999.9**************9 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 ?   11.1   0.0   5.7e-05       0.2      85     175 ..      41     134 ..      30     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.7e-05
                            DUF899  85 CpgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsleeeqaseelpgl 161
                                        +gC+  a ++ ++l ++++ +  ++ +sr   ++ e++ ++   ++ + s+ + ++ + +++   ++ + +e  g+
  gi|330508603|ref|YP_004385031.1|  41 TSGCTREAMDFTAHLPDFRKLGAEVVGISRDSPASHEKFAAKHSLKVTLLSDPDHRVTESYGAWALKKMYGKESYGT 117
                                       579************************************************************99999999999887 PP

                            DUF899 162 ..svflrdd.grvfhtY 175
                                         s+fl d  g++   +
  gi|330508603|ref|YP_004385031.1| 118 vrSTFLIDPeGKIAYIW 134
                                       67888888767776666 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   8.7e-05      0.31       4     133 ..      11     129 ..       8     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.7e-05
                         SCO1-SenC   4 FelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyle 80 
                                       F l    g+++  +  +gk+ +++f     ++ C+ +  + ++ l ++ + +++v  +       rD+p+  +++++
  gi|330508603|ref|YP_004385031.1|  11 FCLPGAGGQEICLNAHSGKWLVLYFYPKDNTSGCTREAMDFTAHLPDFRKLGAEVVGI------SRDSPASHEKFAA 81 
                                       6666677888888899999999999999999999999999999999998887777555......5************ PP

                         SCO1-SenC  81 afdpriigltGskeeiakaakefrvyvekvedeesdytvdHsssvyLvdpdgr 133
                                       +++ +++ l+++   +++ + ++ ++    +++ +        s++L+dp+g+
  gi|330508603|ref|YP_004385031.1|  82 KHSLKVTLLSDPDHRVTESYGAWALKKMYGKESYG-----TVRSTFLIDPEGK 129
                                       ****************9999999988666555555.....5678899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1249.95
//
Query:       gi|330508604|ref|YP_004385032.1|  [L=348]
Description: hypothetical protein MCON_2838 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   14.2   0.0        2.5    8.4   0.0    3.1  3  DUF4352   Domain of unknown function (DUF4352)


Domain annotation for each model (and alignments):
>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.025   4.6e+02      66     114 ..      62     106 ..      45     115 .. 0.62
   2 ?    0.0   0.0     0.054   9.6e+02      25      42 ..     115     132 ..     104     134 .. 0.78
   3 ?    8.4   0.0   0.00014       2.5      35      74 ..     144     183 ..     137     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.025
                                       TTEEE-BEEESCCCCTTB--EEEE-TT-EEEEEEEEEESTT-CGEEEEE CS
                           DUF4352  66 gdgkeydadlsasskaddlflgtlnpGkkvtGklvFdvpkgkkkleLey 114
                                       + +++y+ + + +   d ++ + ln G +    ++F+vpk++  ++L+ 
  gi|330508604|ref|YP_004385032.1|  62 ASNATYQMMDQYDAVYDPAMYKPLNEGRQL---VYFVVPKDSL-FKLIT 106
                                       555555544444444444566666666554...8999999988.88776 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.054
                                       ETTS-CEETT-.SEEEEE CS
                           DUF4352  25 vgkneylqpdaggefliv 42 
                                          n + +p+ag+efl++
  gi|330508604|ref|YP_004385032.1| 115 ININWWATPKAGNEFLLI 132
                                       556778999*******98 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00014
                                       -.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEE CS
                           DUF4352  35 aggeflivdvtvkNkgkealtvnssqfkLkdgdgkeydad 74 
                                       ++++  +v+v+ +N+g +++ +++ +f L d+ g  y+a+
  gi|330508604|ref|YP_004385032.1| 144 PDEQGIVVQVRGQNNGTQDVVFSPENFVLLDQWGWPYSAT 183
                                       5678899**********************99887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2511.18
//
Query:       gi|330508605|ref|YP_004385033.1|  [L=668]
Description: methionyl-tRNA synthetase [Methanosaeta concilii GP6]
Scores for complete 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-147  490.6   0.0   3.5e-147  490.2   0.0    1.1  1  tRNA-synt_1g   tRNA synthetases class I (M)
    6.3e-25   87.1   1.0    1.4e-24   86.1   0.6    1.8  2  tRNA_bind      Putative tRNA binding domain
    6.6e-18   64.3   0.2    1.1e-07   30.5   0.0    4.0  3  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    2.9e-15   56.5   0.0    6.2e-15   55.5   0.0    1.6  1  Anticodon_1    Anticodon-binding domain of tRNA
    1.3e-13   51.0   0.0    2.3e-07   30.5   0.0    2.3  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    0.00039   19.4   0.0       0.77    8.6   0.0    2.2  2  tRNA-synt_1f   tRNA synthetases class I (K)
  ------ inclusion threshold ------
       0.33   11.0   7.4        1.1    9.4   7.4    1.9  1  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 !  490.2   0.0  1.4e-150  3.5e-147       1     390 [.       3     388 ..       3     389 .. 0.97

  Alignments for each domain:
  == domain 1  score: 490.2 bits;  conditional E-value: 1.4e-150
                                       EEEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHH CS
                      tRNA-synt_1g   1 vlvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikel 77 
                                       +lvt++lpYang+ HlGhl+++++aDif+R  r+ g+evlfvcg+D+hGtpi ++Ae++g+tp++l  k+h++++e+
  gi|330508605|ref|YP_004385033.1|   3 ILVTCGLPYANGPCHLGHLRTYVPADIFVRGLRKMGKEVLFVCGSDSHGTPIVVNAEAQGMTPKALSIKYHQHFDEI 79 
                                       69*************************************************************************** PP

                                       HHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE.- CS
                      tRNA-synt_1g  78 fkklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqc.e 153
                                       f+ ++i fd +g t++ + ++ ++e++++l e+g++y +ei  +ycpk+erflpdryveg+CP+c+ + argd+c  
  gi|330508605|ref|YP_004385033.1|  80 FQGMEIDFDFFGDTDDPACHNRTKEMVEALMENGYVYPREIDLAYCPKCERFLPDRYVEGECPYCG-KPARGDECdM 155
                                       ******************************************************************.78******77 PP

                                       TTSSB-E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS CS
                      tRNA-synt_1g 154 ecgkkleptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrd 230
                                        cg++lep e++n+ ++++g ++e+++++h+ff+ls f+++l e++  ++   + ++++++ ew++++Lkd++i+r+
  gi|330508605|ref|YP_004385033.1| 156 GCGRHLEPGEIKNAICKVCGGRAEYRKQTHYFFRLSGFRDFLLEHL--QTLGGTASARNYATEWVRSELKDWCITRN 230
                                       9*********************************************..4446999********************** PP

                                       -SSS-EETTECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHHT CS
                      tRNA-synt_1g 231 ldwGipvPgaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillga 307
                                       + wG+++Pg+++ v+YVW+dA+igYi++t+e++ ++   ++w+ yW  +k ++++hfig di+++H+ifwPa+l+ga
  gi|330508605|ref|YP_004385033.1| 231 MAWGVRFPGSDDLVVYVWVDAPIGYIAFTEEWCARS--GRDWEDYW--KKPSQIIHFIGGDIVYHHCIFWPAMLKGA 303
                                       *********************************555..79******..579************************** PP

                                       T----S-EEEE--EEE--------------H.HHHHHH.H-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCH CS
                      tRNA-synt_1g 308 elklpkkvvaheyltvegkKlSkSrgvvvka.kealer.ldadllRYylaaeapekkDldfswedfvervNseLadk 382
                                       +++lp++vva+++l++++kK+SkSrg+v+++ +++++r l++dllRYyla+ + ++k+++f w+ f ++vNseL+++
  gi|330508605|ref|YP_004385033.1| 304 GYTLPSAVVASGMLKIDDKKFSKSRGNVIWVkDDYMDRgLHPDLLRYYLASYTAHNKEVNFAWNIFADKVNSELVGA 380
                                       ******************************95579999*************************************** PP

                                       HHHHHHHH CS
                      tRNA-synt_1g 383 lgnlvnRv 390
                                       +gn++nR+
  gi|330508605|ref|YP_004385033.1| 381 FGNFINRA 388
                                       *******8 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.9   7.5e+03      28      41 ..     415     428 ..     413     437 .. 0.77
   2 !   86.1   0.6   5.3e-28   1.4e-24       1      96 []     574     666 ..     574     666 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.9
                                       SSEEEEEESCTTTS CS
                         tRNA_bind  28 eeprqivsgaknvy 41 
                                       e++ ++vsg++++ 
  gi|330508605|ref|YP_004385033.1| 415 ETMAEVVSGLEEYE 428
                                       56789****99986 PP

  == domain 2  score: 86.1 bits;  conditional E-value: 5.3e-28
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECC CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeel 77 
                                       +r+G++ +ae +++++kLl+l+vd+G+e+ rq+v+g+++ y++e+lv++kvvv++nlkp+kl G+eS++M+l+a+  
  gi|330508605|ref|YP_004385033.1| 574 IRIGEIKNAEAIKGSNKLLKLNVDIGGEI-RQVVAGIAQSYAKEDLVGTKVVVLVNLKPAKLFGIESQAMLLAAD-- 647
                                       79***************************.*********************************************.. PP

                                       ESSCEEEEEESST--TTCE CS
                         tRNA_bind  78 dekevgilelpadveaGek 96 
                                        e+   +l++ ++ve G+k
  gi|330508605|ref|YP_004385033.1| 648 VEGRAVLLRPREAVETGTK 666
                                       79999**********9985 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 !   30.5   0.0   4.3e-11   1.1e-07      28     174 ..       6     133 ..       2     140 .. 0.79
   2 !   18.6   0.0   1.7e-07   0.00045     359     432 ..     165     238 ..     155     265 .. 0.83
   3 !    8.2   0.0   0.00025      0.65     557     601 ..     317     364 ..     304     365 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 4.3e-11
                       tRNA-synt_1  28 vdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefrekv 104
                                       + g Py++G  H+Gh  + +  di +r  r  Gkevl+v G D +G +i  + e++ g + k               
  gi|330508605|ref|YP_004385033.1|   6 TCGLPYANGPCHLGHLRTYVPADIFVRGLRKMGKEVLFVCGSDSHGTPIVVNAEAQ-GMTPK--------------- 66 
                                       5678*********************************************8887777.33332............... PP

                       tRNA-synt_1 105 rewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktals 174
                                        +   +y+++  + ++  G+ +Dfd    T d+  ++ +ke+   l+++g +y ++  + +++k++  l 
  gi|330508605|ref|YP_004385033.1|  67 -ALSIKYHQHFDEIFQ--GMEIDFDFFGDTDDPACHNRTKEMVEALMENGYVYPREIDLAYCPKCERFLP 133
                                       .333456666666666..6677777777788888888888888888888888888888888888877665 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.7e-07
                       tRNA-synt_1 359 ehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswle.niqdWciSRqrwWGhrip 432
                                       e +  +c+  +   +yr ++ +f r++ ++d +l++++    +  s+++  ++w++ + +dWci R+  WG+r p
  gi|330508605|ref|YP_004385033.1| 165 EIKNAICKVCGGRAEYRKQTHYFFRLSGFRDFLLEHLQTLGGTA-SARNYATEWVRsELKDWCITRNMAWGVRFP 238
                                       5666678888888899******************9999776655.45566678887378*************998 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00025
                       tRNA-synt_1 557 rdeeGrKmSKslgNvidpld..vikkygadalRltli.lsdvgrdinl 601
                                       +  + +K SKs gNvi  +d  + + +  d lR++l+ ++   +++n+
  gi|330508605|ref|YP_004385033.1| 317 LKIDDKKFSKSRGNVIWVKDdyMDRGLHPDLLRYYLAsYTAHNKEVNF 364
                                       445669*********96554115556678********99999999886 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 !   55.5   0.0   2.4e-18   6.2e-15       1      92 [.     406     516 ..     406     595 .. 0.67

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 2.4e-18
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       d  +l++++++ +ev   +eey+f+ka ++++++   d+ ++y+++++p+   +s++d+   + + +l ++++l++l
  gi|330508605|ref|YP_004385033.1| 406 DADVLARIEETMAEVVSGLEEYEFKKATDSVMTL--ADYGNTYFQSHEPWKLVKSDKDAAGsVLRSCLQIAKALVIL 480
                                       5679*****************************8..99**************99987773335577778889***** PP

                       Anticodon_1  77 laPfmPfitEelwqr....................e 92 
                                       ++P+mP  ++ +w++                    +
  gi|330508605|ref|YP_004385033.1| 481 MEPVMPAKMQNAWKQlgmpgevskialedalvpldS 516
                                       *************44444443333333333333331 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 !   30.5   0.0   8.9e-11   2.3e-07      14     126 ..       6     120 ..       3     130 .. 0.85
   2 !   18.1   0.0   5.2e-07    0.0013     240     292 ..     310     365 ..     277     374 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 8.9e-11
                                       EEE.EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1e  14 vCG.ptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdlea 89 
                                       +CG p +   +hlGh R++v  Di+ r l+++g +v fv         i+ +a++++ + k+l+ k+ ++f + ++ 
  gi|330508605|ref|YP_004385033.1|   6 TCGlPYANGPCHLGHLRTYVPADIFVRGLRKMGKEVLFVCGSDSHGTPIVVNAEAQGMTPKALSIKYHQHFDEIFQG 82 
                                       57733456689******************************999999****************************** PP

                                       TT----SB-.-BGGGGHHHHHHHHHHHHHTTSEEE-TT CS
                      tRNA-synt_1e  90 Lnvlkptle.prvsekvdeiielvekliekgyaYavsd 126
                                       +++    +  +      +   e+ve l+e+gy Y+ + 
  gi|330508605|ref|YP_004385033.1|  83 MEIDFDFFGdTDDPACHNRTKEMVEALMENGYVYPREI 120
                                       ***9765541333444567889************9874 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 5.2e-07
                                       EEEEE--EEETTBE--TTTT---BHHH..HHTTS-HHHHHHHHHSS.-TTS-EEE- CS
                      tRNA-synt_1e 240 yflhnghlkiegekmsksLknfitikd..vlkkfdprqlRllllsa.hyrsqldfk 292
                                         + +g+lki+++k sks +n+i +kd  + +  +p  lR++l+s   ++++++f 
  gi|330508605|ref|YP_004385033.1| 310 AVVASGMLKIDDKKFSKSRGNVIWVKDdyMDRGLHPDLLRYYLASYtAHNKEVNFA 365
                                       56779********************9843335689********9851577888886 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00034      0.86      33      70 ..      12      49 ..       2      52 .. 0.87
   2 !    8.6   0.0    0.0003      0.77     275     322 ..     317     365 ..     301     375 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00034
                      tRNA-synt_1f 33 pSGliHiGnlrevltadlvaralrkrgeevrlilisDd 70
                                      + G+ H+G lr  + ad+ +r lrk+g+ev +++ sD 
  gi|330508605|ref|YP_004385033.1| 12 ANGPCHLGHLRTYVPADIFVRGLRKMGKEVLFVCGSDS 49
                                      469******************************99985 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0003
                      tRNA-synt_1f 275 llkggekmssSkGnvltled..wlevaepevlrflilrrkPkkakkldld 322
                                       l   ++k s+S+Gnv+ ++d  + + ++p++lr+++++    ++k++++ 
  gi|330508605|ref|YP_004385033.1| 317 LKIDDKKFSKSRGNVIWVKDdyMDRGLHPDLLRYYLAS-YTAHNKEVNFA 365
                                       4444569***********984445789********998.55566666655 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   7.4   0.00041       1.1       1      49 []     125     175 ..     117     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00041
                               DZR   1 CpqCgeelppdar..fCseCgtklkavaaedrC.psCgekvdpea...rfCpeCG 49 
                                       Cp+C++ lp++     C++Cg++ +     d C + Cg+ ++p++   ++C+ CG
  gi|330508605|ref|YP_004385033.1| 125 CPKCERFLPDRYVegECPYCGKPAR----GDECdMGCGRHLEPGEiknAICKVCG 175
                                       9999999999988779999999999....79995589999888652216699998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 4194.43
//
Query:       gi|330508606|ref|YP_004385034.1|  [L=577]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-51  173.2   0.0    4.8e-26   91.9   0.0    2.3  2  ABC_tran      ABC transporter
    2.9e-11   43.8   0.6      0.012   15.5   0.0    4.1  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.4e-08   34.9   0.3      0.006   16.5   0.0    2.7  2  RsgA_GTPase   RsgA GTPase
    1.3e-06   28.1   1.1      0.014   15.2   0.0    2.6  2  AAA_29        P-loop containing region of AAA domain
    5.9e-05   22.6   2.7      0.081   12.3   0.0    3.6  4  TniB          Bacterial TniB protein
      6e-05   23.3   3.3       0.41   10.9   0.1    4.1  3  AAA_22        AAA domain
    0.00038   19.9   5.0      0.037   13.5   0.1    3.6  3  SMC_N         RecF/RecN/SMC N terminal domain
     0.0013   19.3   3.6       0.55   10.7   1.0    2.4  2  AAA_23        AAA domain
     0.0015   18.8   0.0        1.7    8.9   0.0    2.5  2  AAA_28        AAA domain
     0.0031   17.5   0.0      0.084   12.8   0.0    2.5  2  Rad17         Rad17 P-loop domain
     0.0033   17.2   0.1        1.9    8.2   0.0    3.0  3  IstB_IS21     IstB-like ATP binding protein
     0.0038   16.8   1.4         22    4.5   0.0    4.5  5  AAA_25        AAA domain
     0.0044   16.8   1.9       0.35   10.6   0.3    3.1  2  AAA_30        AAA domain
     0.0094   16.3   0.0        4.8    7.5   0.1    2.6  2  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.028   14.7   0.2        5.5    7.3   0.5    2.9  2  DUF4358       Domain of unknown function (DUF4358)
      0.028   15.0   0.1        1.5    9.3   0.0    3.2  3  AAA_18        AAA domain
      0.028   13.6   0.2        1.2    8.3   0.0    2.4  2  NB-ARC        NB-ARC domain
      0.033   13.9   0.2          3    7.6   0.0    2.4  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.037   14.4   0.0        6.6    7.2   0.0    2.5  2  RNA_helicase  RNA helicase
      0.039   14.2   0.3        8.6    6.6   0.0    2.4  2  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.056   13.3   1.6        9.7    6.1   0.1    2.5  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.079   13.1   3.2       0.64   10.1   0.0    3.1  2  MMR_HSR1      50S ribosome-binding GTPase
      0.084   13.1   6.2       0.44   10.8   0.1    4.0  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.12   12.1   1.2          8    6.1   1.1    2.4  2  AAA_15        AAA ATPase domain
       0.12   12.5   0.5         10    6.3   0.0    2.8  3  AAA_33        AAA domain
       0.13   12.1   1.5        7.2    6.4   0.0    3.0  3  dNK           Deoxynucleoside kinase
       0.13   11.7   0.1        6.6    6.1   0.0    2.4  2  PhoH          PhoH-like protein
       0.15   11.7   0.4        3.6    7.3   0.4    2.6  2  PRK           Phosphoribulokinase / Uridine kinase family
       0.22   10.6   0.0         12    4.9   0.0    2.2  2  G-alpha       G-protein alpha subunit
        1.2    9.0   3.7         28    4.6   0.1    2.6  2  NACHT         NACHT domain
        1.2    7.8   3.1         32    3.1   0.1    3.6  4  ABC_ATPase    Predicted ATPase of the ABC class


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.0   8.3e-29   4.8e-26       1     136 [.      21     180 ..      21     181 .. 0.83
   2 !   79.3   0.0   6.7e-25   3.8e-22       2     136 ..     288     493 ..     287     494 .. 0.93

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 8.3e-29
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk +s++ ++ge+++ivG++G GKStL+k+l g+ + ++G+i++dg  ++  + +  + + ++     +l+++  + 
  gi|330508606|ref|YP_004385034.1|  21 LKAISFTAQPGEILGIVGKSGGGKSTLMKILRGMDRFDSGKITMDGITITP-DSSDEEIRARMAATAIHLQRDFALW 96 
                                       789**********************************************99.4444444444555555555555544 PP

                                       HH..........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSS CS
                                       xx..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpk 128
                                       ++                          ++de  ++ l  lgl++l+++  ++ ++ LSgG+kqr+++ar l+kkpk
  gi|330508606|ref|YP_004385034.1|  97 TEsalnnvvrrihsrktgyevlpipenaDYDEMYKEGLFYLGLVGLEKKA-SHLATILSGGEKQRLVIARQLAKKPK 172
                                       44456668999999999999999999877777799999999999966655.5788********************** PP

                                       EEEEESTT CS
                                       xxxxxxxx RF
                          ABC_tran 129 llllDEpt 136
                                       +lllDEp 
  gi|330508606|ref|YP_004385034.1| 173 VLLLDEPA 180
                                       *******6 PP

  == domain 2  score: 79.3 bits;  conditional E-value: 6.7e-25
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG.....B-HHHCCHCEEEE-SS--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke.....qeleslrkeigvlpqepqlfp 72 
                                       +n+++++++ge++ ++G++G GK+tLlk++ g   p++G + ++ g+++ +       +  +r+ +gv+ qe  l  
  gi|330508606|ref|YP_004385034.1| 288 ENLNFDINKGEITSFIGNSGGGKTTLLKIMQGVRMPDAGAVYYRyGDEWVDmltysPHRMNVRRTLGVMYQEFALYA 364
                                       79***************************************99999999989999999999**************** PP

                                       TSBHHHH......................................HHHTCHHHHHHHSTTGG............... CS
                                       xxxxxxx......................................xxxxxxxxxxxxxxxxx............... RF
                          ABC_tran  73 eltvren......................................esdeeiekalsklglke............... 96 
                                       + t+ ++                                       s+e+++ al++lgl+                
  gi|330508606|ref|YP_004385034.1| 365 GETIIDQiayqmgikstdvigyarsvaeemgisekvldiiyamadMSEEDAKSALESLGLTRdifkdlfprfpntea 441
                                       ***99999*************************99999999999877777999999999998999999999999999 PP

                                       ............TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  97 ............lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                   l+ +v+ + p++LSgG+ +r +la +l+ +p++++lDEp+
  gi|330508606|ref|YP_004385034.1| 442 qkfaepifdlldLDRSVMWKLPRQLSGGELVRASLAILLAAQPEVMILDEPF 493
                                       9999999999977777777888*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     2e-05     0.012       2      44 ..      34      77 ..      33      94 .. 0.70
   2 ?    1.4   0.0      0.38   2.2e+02     250     297 ..     163     211 ..     149     215 .. 0.64
   3 !    9.9   0.0     0.001       0.6       1      23 [.     299     321 ..     299     338 .. 0.87
   4 !   12.1   0.1   0.00022      0.13     235     298 ..     464     525 ..     424     530 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl.drdvegltdelsggggirk 44
                                       +++G+ g GKS+L+++l+++ r+  + +++++++ ++ ++  +
  gi|330508606|ref|YP_004385034.1| 34 LGIVGKSGGGKSTLMKILRGMDRFdSGKITMDGITITPDSSDEE 77
                                      579*****************977654444444444444444444 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.38
                            AAA_21 250 allralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTH 297
                                       +  +++kk+++ll+DEp +   P+   ++l+ +k+ ++  g  +++++H
  gi|330508606|ref|YP_004385034.1| 163 IARQLAKKPKVLLLDEPATMACPATKQEVLDAIKNVRDkLGLTIVVVSH 211
                                       4556677789*******76555555555555555555555555555555 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.001
                            AAA_21   1 lnvliGpNgsGKSnLLdaldlla 23 
                                       ++ +iG  g GK++LL+++++++
  gi|330508606|ref|YP_004385034.1| 299 ITSFIGNSGGGKTTLLKIMQGVR 321
                                       6889***************8874 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00022
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                       r+lS G +  + l  a+l a+++  + ++DEp   ++P  lr++   + k++s+ g+ +il++H 
  gi|330508606|ref|YP_004385034.1| 464 RQLSGGELVRASL--AILLAAQP-EVMILDEPFGDIDPITLREVSNAIkKINSEFGTTIILVSHH 525
                                       5666666655444..44444444.9***********************999999**********6 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.3e-05     0.013      81     130 ..      12      62 ..       3      66 .. 0.81
   2 !   16.5   0.0     1e-05     0.006      75     121 ..     272     319 ..     264     332 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-05
                                       E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                        ++ ++ e+l++++   +  ++  +vG+SG GKStL++ l++ ++   g++
  gi|330508606|ref|YP_004385034.1|  12 RLNDRDIEALKAISFTAQPgEILGIVGKSGGGKSTLMKILRGMDRFDSGKI 62 
                                       556667788888888888779999****************99887777766 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1e-05
                                       TTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  75 lgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                         ++v++ ++ +   +e+l+  +++ +++ ++G+SG GK+tL++ +++
  gi|330508606|ref|YP_004385034.1| 272 RSCQVCKGEVLDVLRIENLNFDINKgEITSFIGNSGGGKTTLLKIMQG 319
                                       55677777788888999999999988*****************99886 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.3   0.00055      0.32      21      39 ..      30      48 ..      19      51 .. 0.80
   2 !   15.2   0.0   2.4e-05     0.014      16      50 ..     291     325 ..     283     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00055
                            AAA_29 21 lkgatlltGpsGsGKSTll 39
                                      + ++  ++G+sG GKSTl+
  gi|330508606|ref|YP_004385034.1| 30 PGEILGIVGKSGGGKSTLM 48
                                      4456779**********97 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.4e-05
                            AAA_29  16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                        ++i+  ++t ++G+sG GK+Tll  +q + +p+ 
  gi|330508606|ref|YP_004385034.1| 291 NFDINKGEITSFIGNSGGGKTTLLKIMQGVRMPDA 325
                                       56777555****************88888877765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       0.7   4.1e+02      38      53 ..      34      49 ..      17      62 .. 0.84
   2 !   12.3   0.0   0.00014     0.081      78     160 ..     121     209 ..     110     219 .. 0.71
   3 ?   -2.3   0.1       4.3   2.5e+03      40      53 ..     302     315 ..     297     323 .. 0.87
   4 !    7.1   0.0    0.0055       3.2     106     160 ..     470     522 ..     448     529 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.7
                              TniB 38 lllvGdsnnGKtmive 53
                                      l +vG+s  GK+++++
  gi|330508606|ref|YP_004385034.1| 34 LGIVGKSGGGKSTLMK 49
                                      569**********987 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00014
                              TniB  78 ppkpdekrlyaaiLealgaplkara........rvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnal 146
                                       p+++d +++y++ L  lg    +++        +  ++++ v++   + k++vL++DE   +  + a +++e+l a+
  gi|330508606|ref|YP_004385034.1| 121 PENADYDEMYKEGLFYLGLVGLEKKashlatilSGGEKQRLVIARQLAKKPKVLLLDEPATMA-CPA-TKQEVLDAI 195
                                       66666666666666666544222222334333344466667776667779********99887.555.55689**** PP

                              TniB 147 ksLgnelkipivlv 160
                                       k+  ++l ++iv+v
  gi|330508606|ref|YP_004385034.1| 196 KNVRDKLGLTIVVV 209
                                       ************98 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.3
                              TniB  40 lvGdsnnGKtmive 53 
                                       ++G+s  GKt++++
  gi|330508606|ref|YP_004385034.1| 302 FIGNSGGGKTTLLK 315
                                       689********987 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0055
                              TniB 106 kleqqvlrllrelkvrvLiiDE.ihnllagsarkqreflnalksLgnelkipivlv 160
                                       +l ++ l++l + +++v+i+DE + ++      + re+ na+k+++ e+  +i+lv
  gi|330508606|ref|YP_004385034.1| 470 ELVRASLAILLAAQPEVMILDEpFGDI---DPITLREVSNAIKKINSEFGTTIILV 522
                                       56677889999***********44444...588899*****************998 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00071      0.41       7      91 ..      33     113 ..      28     219 .. 0.65
   2 ?    6.5   0.3     0.017       9.6       6      23 ..     298     315 ..     294     321 .. 0.85
   3 ?    2.3   0.0      0.33   1.9e+02      52     128 ..     440     522 ..     426     530 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00071
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsstsskdl.lrellralglelkaerlsseell 79 
                                       il ++G sG GK+tl++ l+  +         +++ +    +t++ ++s +++ +r+ + a++l+++   l +e  l
  gi|330508606|ref|YP_004385034.1|  33 ILGIVGKSGGGKSTLMKILRGMDR-------FDSGKItmdGITITPDSSDEEIrARMAATAIHLQRDF-ALWTESAL 101
                                       7779*************9998873.......2333333477777777777777677777777777777.33344444 PP

                            AAA_22  80 ealeqalrarav 91 
                                       + + + +++r++
  gi|330508606|ref|YP_004385034.1| 102 NNVVRRIHSRKT 113
                                       444444444433 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.017
                            AAA_22   6 gilvvtGesGtGKTtllr 23 
                                        i+  +G sG GKTtll+
  gi|330508606|ref|YP_004385034.1| 298 EITSFIGNSGGGKTTLLK 315
                                       67889***********98 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.33
                            AAA_22  52 sskdllrellralglelka.....erlsseellealeqalraravielliiDEaqh.lr..s.eealeeLrsllnls 119
                                       + +++++ ++  l+l+++      + ls  el++a    l a++  e++i+DE    ++  +  e+ + ++++    
  gi|330508606|ref|YP_004385034.1| 440 EAQKFAEPIFDLLDLDRSVmwklpRQLSGGELVRASLAILLAAQP-EVMILDEPFGdIDpiTlREVSNAIKKINS-- 513
                                       577888888888888777789888888999999999999999999.9*****94332332234555555555555.. PP

                            AAA_22 120 rkgvqliLv 128
                                       ++g+++iLv
  gi|330508606|ref|YP_004385034.1| 514 EFGTTIILV 522
                                       777777776 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 ?    5.1   0.1     0.024        14      70     197 ..      76     211 ..      18     230 .. 0.49
   2 ?   -0.4   0.2       1.1   6.4e+02      25      42 ..     298     315 ..     285     321 .. 0.83
   3 !   13.5   0.1   6.4e-05     0.037     117     206 ..     409     533 ..     358     543 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.024
                                       TCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                             SMC_N  70 ekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske........... 135
                                       e+ ++  a  +i+                                                    +           
  gi|330508606|ref|YP_004385034.1|  76 EEIRARMAATAIH---------------------------------------------------LQrdfalwtesal 101
                                       2222222222222...................................................2233333333333 PP

                                       ..................................................CS-HHHHHHHHHHHHHHHHCCS--SEE CS
                                       ..................................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ..................................................lLSgGektLvalaLlfAiqkvkpaply 162
                                                                                          LSgGek+     L++A q +k+  + 
  gi|330508606|ref|YP_004385034.1| 102 nnvvrrihsrktgyevlpipenadydemykeglfylglvglekkashlatILSGGEKQ----RLVIARQLAKKPKVL 174
                                       3333333333333333333333333333333333333444445566666678888887....566666666666677 PP

                                       EECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                             SMC_N 163 llDeidaaLDeknvkkvaellkekskn..aQfivisl 197
                                       llDe +     +  ++v + +k+ +++    ++v+s+
  gi|330508606|ref|YP_004385034.1| 175 LLDEPATMACPATKQEVLDAIKNVRDKlgLTIVVVSH 211
                                       7777777777777777777777766663344555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                                       SEEEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlld 42 
                                       ++t+ +G+ G GK+ ll 
  gi|330508606|ref|YP_004385034.1| 298 EITSFIGNSGGGKTTLLK 315
                                       58999*********9986 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 6.4e-05
                                       EE-HHHHHHHHHCTT-STT.....................................CS-HHHHHHHHHHHHHHHHCC CS
                                       xxxxxxxxxxxxxxxxxxx.....................................xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 117 evtkkevsellesagiske.....................................lLSgGektLvalaLlfAiqkv 156
                                       ++++++ ++ les g++++                                     +LSgGe   ++la+l+A q  
  gi|330508606|ref|YP_004385034.1| 409 DMSEEDAKSALESLGLTRDifkdlfprfpnteaqkfaepifdlldldrsvmwklprQLSGGELVRASLAILLAAQ-- 483
                                       56777888888888888889999999999999999999999999999999999999***************9976.. PP

                                       S--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                             SMC_N 157 kpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekad 206
                                        p+ +++lDe    +D    ++v++ +k+ +++  + +i +s++ +++++++
  gi|330508606|ref|YP_004385034.1| 484 -PE-VMILDEPFGDIDPITLREVSNAIKKINSEfgTTIILVSHHVDFVKEVS 533
                                       .44.679*********************887775578899999988888764 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1     0.004       2.3      20      39 ..      32      51 ..       2      54 .. 0.72
   2 !   10.7   1.0   0.00095      0.55      11      37 ..     288     315 ..     284     320 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.004
                            AAA_23 20 gltlItGpNGaGKTTildAi 39
                                       +  I+G+ G GK+T++  +
  gi|330508606|ref|YP_004385034.1| 32 EILGIVGKSGGGKSTLMKIL 51
                                      4778************9876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00095
                            AAA_23  11 rdqeidFsk.gltlItGpNGaGKTTild 37 
                                       ++ ++d +k  +t ++G+ G GKTT+l 
  gi|330508606|ref|YP_004385034.1| 288 ENLNFDINKgEITSFIGNSGGGKTTLLK 315
                                       56667777736***************97 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0029       1.7       4      70 ..      36     111 ..      34     118 .. 0.78
   2 !    7.2   0.0    0.0096       5.5       4      39 ..     302     341 ..     300     359 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0029
                            AAA_28   4 itGgestGKTtlleaLa..ar.........gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaa 69 
                                       i+G +++GK+tl++ L   +r         g+++ p++  e ++ ++a +  +l+   d+    e  l++ +++ ++
  gi|330508606|ref|YP_004385034.1|  36 IVGKSGGGKSTLMKILRgmDRfdsgkitmdGITITPDSSDEEIRARMAATAIHLQR--DFALWTESALNNVVRRIHS 110
                                       78999************772245555667799999*********999999999985..6766777777777777666 PP

                            AAA_28  70 a 70 
                                       +
  gi|330508606|ref|YP_004385034.1| 111 R 111
                                       5 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0096
                            AAA_28   4 itGgestGKTtlleaLaargyp....vvpEaareileekl 39 
                                       ++G +++GKTtll+ ++   +p    v+ +++ e ++ ++
  gi|330508606|ref|YP_004385034.1| 302 FIGNSGGGKTTLLKIMQGVRMPdagaVYYRYGDEWVDMLT 341
                                       79************99854333222244666666666555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00015     0.084      33      66 ..      19      52 ..      12     102 .. 0.90
   2 ?    1.7   0.0      0.36   2.1e+02      46      66 ..     298     318 ..     279     325 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                      e+lka +   ++ +iL i G sG gkst +k+L 
  gi|330508606|ref|YP_004385034.1| 19 EALKAISFTAQPGEILGIVGKSGGGKSTLMKILR 52
                                      689*****************************95 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.36
                             Rad17  46 riLLisGPsGCgkstvvkvLs 66 
                                       +i    G sG gk+t +k++ 
  gi|330508606|ref|YP_004385034.1| 298 EITSFIGNSGGGKTTLLKIMQ 318
                                       4667789***********985 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 !    8.2   0.0    0.0033       1.9      27      64 ..      10      48 ..       4      60 .. 0.83
   2 ?   -1.1   0.0       2.3   1.4e+03     102     137 ..     164     198 ..     147     223 .. 0.62
   3 ?    5.0   0.0      0.03        18      44     107 ..     294     357 ..     279     379 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0033
                         IstB_IS21 27 arsldkrkvkeLatlsfiekk.enivllGpsGvGKshla 64
                                      +  l+ r +++L + sf+++  e + ++G sG GKs l 
  gi|330508606|ref|YP_004385034.1| 10 TYRLNDRDIEALKAISFTAQPgEILGIVGKSGGGKSTLM 48
                                      5568899***********98615566**********885 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                         IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfeviekr 137
                                       a +   k+++l+lD+ ++      ++e+l + i++ 
  gi|330508606|ref|YP_004385034.1| 164 ARQLAKKPKVLLLDEPATMACPATKQEVL-DAIKNV 198
                                       3444567899****999887765555444.444444 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.03
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrll 107
                                       i+k e   ++G sG GK+ l   +    + +  +v++   ++ v  l    +  ++ r+l  + 
  gi|330508606|ref|YP_004385034.1| 294 INKGEITSFIGNSGGGKTTLLKIMQGVRMPDAGAVYYRYGDEWVDMLTYSPHRMNVRRTLGVMY 357
                                       778888999*********9988776666667778888888888888888888888777776554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.21   1.2e+02      35     103 ..      33      95 ..      27     117 .. 0.67
   2 ?    4.5   0.0     0.039        22     166     189 ..     189     212 ..     177     215 .. 0.90
   3 ?    3.7   0.0     0.068        39      30      50 ..     294     314 ..     289     318 .. 0.92
   4 ?   -3.3   0.0       9.5   5.5e+03     147     163 ..     400     416 ..     373     437 .. 0.55
   5 ?    0.3   0.0      0.74   4.3e+02     166     188 ..     502     524 ..     497     526 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.21
                            AAA_25  35 lallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarl 103
                                       +  ++G +g GK+tl      ++++G   ++      +  + +  + s +e+r R++a+  +l++d  l
  gi|330508606|ref|YP_004385034.1|  33 ILGIVGKSGGGKSTLM-----KILRGMDRFD-SGKITMDGITITPDSSDEEIRARMAATAIHLQRDFAL 95 
                                       5557888888998874.....5666666666.2235666677777777777777777777777555544 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.039
                            AAA_25 166 galvealeriarrtgaavllvhHv 189
                                       +++++a++++++++g ++++v H+
  gi|330508606|ref|YP_004385034.1| 189 QEVLDAIKNVRDKLGLTIVVVSHL 212
                                       7899*******************7 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.068
                            AAA_25  30 lpagelallaGapgtGKttla 50 
                                       + +ge++ ++G +g GKttl+
  gi|330508606|ref|YP_004385034.1| 294 INKGEITSFIGNSGGGKTTLL 314
                                       5799***************96 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 9.5
                            AAA_25 147 viDplsralggdensns 163
                                       v+D ++++ + +e++++
  gi|330508606|ref|YP_004385034.1| 400 VLDIIYAMADMSEEDAK 416
                                       44444444444444443 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 0.74
                            AAA_25 166 galvealeriarrtgaavllvhH 188
                                       +++ +a+++i  ++g +++lv H
  gi|330508606|ref|YP_004385034.1| 502 REVSNAIKKINSEFGTTIILVSH 524
                                       5677999**********999988 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.3   0.00061      0.35      13      46 ..      26      60 ..      13     209 .. 0.69
   2 ?    3.7   0.1     0.078        45      20      39 ..     299     318 ..     293     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00061
                            AAA_30 13 lltsgdrvavltGpAGtGKttalkalreaweaa.g 46
                                      +++++  +  ++G  G GK+t++k lr + + + g
  gi|330508606|ref|YP_004385034.1| 26 FTAQPGEILGIVGKSGGGKSTLMKILRGMDRFDsG 60
                                      5666677999****************999887733 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.078
                            AAA_30  20 vavltGpAGtGKttalkalr 39 
                                       ++   G  G GKtt+lk ++
  gi|330508606|ref|YP_004385034.1| 299 ITSFIGNSGGGKTTLLKIMQ 318
                                       67788***********9876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0083       4.8       8      45 ..      17      52 ..      14     178 .. 0.73
   2 ?    6.4   0.0     0.018        11      24      43 ..     297     316 ..     282     456 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0083
                            AAA_16  8 eleqLlsalervrsgrp.elvllsGesGvGKsslvrell 45
                                      ++e+L+++  ++ +  p e++ ++G sG GKs+l++ l+
  gi|330508606|ref|YP_004385034.1| 17 DIEALKAISFTA-Q--PgEILGIVGKSGGGKSTLMKILR 52
                                      555554433333.3..33899*************97665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.018
                            AAA_16  24 pelvllsGesGvGKsslvre 43 
                                       +e++ ++G+sG GK++l++ 
  gi|330508606|ref|YP_004385034.1| 297 GEITSFIGNSGGGKTTLLKI 316
                                       378999***********964 PP

>> DUF4358  Domain of unknown function (DUF4358)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.13        74      13      63 ..       3      51 ..       1      59 [. 0.83
   2 ?    7.3   0.5    0.0095       5.5      15      65 ..     370     421 ..     362     430 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                           DUF4358 13 deddlkklygldkddvedyvayvsassasadevlivkakdeedaeevkkal 63
                                      + ++l+k y l++ d+e  +a +    a+  e+l +  k+++ +++++k l
  gi|330508606|ref|YP_004385034.1|  3 QIENLSKTYRLNDRDIEALKAIS--FTAQPGEILGIVGKSGGGKSTLMKIL 51
                                      5689*************887764..58999999999999988877777765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0095
                           DUF4358  15 ddlkklygldkddvedyvayvsa.ssasadevlivkakdeedaeevkkalee 65 
                                       d++++++g++++dv +y+  v++ +++s   + i+ a     +e+ k+ale+
  gi|330508606|ref|YP_004385034.1| 370 DQIAYQMGIKSTDVIGYARSVAEeMGISEKVLDIIYAMADMSEEDAKSALES 421
                                       899*******************856666666667777777788999999986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0027       1.5       3      34 ..      36      65 ..      34     104 .. 0.74
   2 ?    1.6   0.0      0.67   3.9e+02       5      18 ..     304     317 ..     302     397 .. 0.86
   3 ?   -1.6   0.0       6.5   3.8e+03      57      88 ..     501     530 ..     484     537 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0027
                            AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvake 34
                                      + G++G GK+tl k L+ +    + ++++  +
  gi|330508606|ref|YP_004385034.1| 36 IVGKSGGGKSTLMKILRGMD--RFDSGKITMD 65
                                      89**************7775..4444444444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.67
                            AAA_18   5 GtpGvGKttlakeL 18 
                                       G +G GKttl k  
  gi|330508606|ref|YP_004385034.1| 304 GNSGGGKTTLLKIM 317
                                       889*******9876 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 6.5
                            AAA_18  57 ldklldaleenssaleegknlvidghlaeles 88 
                                       l ++++a+++++s  e g ++++ +h++++++
  gi|330508606|ref|YP_004385034.1| 501 LREVSNAIKKINS--EFGTTIILVSHHVDFVK 530
                                       4567888888875..88999999999998876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0     0.002       1.2      18      38 ..      30      49 ..      15     106 .. 0.85
   2 ?    2.7   0.1       0.1        59      22      38 ..     299     315 ..     285     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                                      SCSEEEEEEESTTSSHHHHHH CS
                            NB-ARC 18 lqslvvalvGmgGvGKttlak 38
                                      ++  ++++vG+ G GK+tl+k
  gi|330508606|ref|YP_004385034.1| 30 PG-EILGIVGKSGGGKSTLMK 49
                                      55.69**************96 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.1
                                       EEEEEESTTSSHHHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttlak 38 
                                       + ++ G  G GKttl+k
  gi|330508606|ref|YP_004385034.1| 299 ITSFIGNSGGGKTTLLK 315
                                       77999**********86 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.083        48       6      23 ..      36      53 ..      32      64 .. 0.89
   2 ?    7.6   0.0    0.0051         3       6      26 ..     302     322 ..     298     339 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.083
                         PduV-EutP  6 liGkvgsGKttLtqalkg 23
                                      ++Gk+g GK tL++ l+g
  gi|330508606|ref|YP_004385034.1| 36 IVGKSGGGKSTLMKILRG 53
                                      69************9998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0051
                         PduV-EutP   6 liGkvgsGKttLtqalkgeel 26 
                                       +iG++g GKttL + ++g ++
  gi|330508606|ref|YP_004385034.1| 302 FIGNSGGGKTTLLKIMQGVRM 322
                                       8*************9998765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.011       6.6       3      18 ..      36      51 ..      34     111 .. 0.80
   2 ?    4.8   0.0     0.064        37       3      41 ..     302     334 ..     300     349 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                      RNA_helicase  3 lyGpsgeGKStlakeL 18
                                      ++G+sg GKStl+k L
  gi|330508606|ref|YP_004385034.1| 36 IVGKSGGGKSTLMKIL 51
                                      78***********986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.064
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkkdsvysrnped 41 
                                       + G+sg GK+tl k      ++ + ++ ++ vy+r   d
  gi|330508606|ref|YP_004385034.1| 302 FIGNSGGGKTTLLKI-----MQGVRMPDAGAVYYR-YGD 334
                                       68***********99.....555557888888874.344 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.015       8.6       4      39 ..      36      72 ..      34      96 .. 0.77
   2 ?    5.1   0.1     0.044        25       4      18 ..     302     316 ..     300     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.015
                                      EESSTTSSHHHHHHCHCT.-CCC-EEETTTTEEEEEE CS
                               Roc  4 lvGdsgvGKtsllkrfve.dkfsekekstigvdfltk 39
                                      +vG+sg GK++l+k +   d+f++ + ++ g++++  
  gi|330508606|ref|YP_004385034.1| 36 IVGKSGGGKSTLMKILRGmDRFDSGKITMDGITITPD 72
                                      8************999765888888888888877654 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.044
                                       EESSTTSSHHHHHHC CS
                               Roc   4 lvGdsgvGKtsllkr 18 
                                       ++G+sg GKt+llk 
  gi|330508606|ref|YP_004385034.1| 302 FIGNSGGGKTTLLKI 316
                                       79**********985 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.017       9.7       1      18 [.      33      50 ..      33      59 .. 0.90
   2 ?    5.9   0.2      0.02        11       3      17 ..     301     315 ..     299     321 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
                              MobB  1 vlgivgksgsGKTtLlek 18
                                      +lgivgksg GK tL++ 
  gi|330508606|ref|YP_004385034.1| 33 ILGIVGKSGGGKSTLMKI 50
                                      79*************985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                              MobB   3 givgksgsGKTtLle 17 
                                       +++g+sg GKTtLl+
  gi|330508606|ref|YP_004385034.1| 301 SFIGNSGGGKTTLLK 315
                                       799**********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 ?   10.1   0.0    0.0011      0.64       3      29 ..      35      62 ..      33      89 .. 0.76
   2 ?    1.7   0.7      0.45   2.6e+02       4      20 ..     302     318 ..     300     426 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                                      EEEESTTSSHHHHHHHHHTS.TEEESSS CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge.kaivsdk 29
                                      +ivG++  GKStL++ l g  +   +++
  gi|330508606|ref|YP_004385034.1| 35 GIVGKSGGGKSTLMKILRGMdRFDSGKI 62
                                      8**************9988545444444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.45
                                       EEESTTSSHHHHHHHHH CS
                          MMR_HSR1   4 ivGrpNvGKStLinalt 20 
                                       ++G++  GK+tL++ + 
  gi|330508606|ref|YP_004385034.1| 302 FIGNSGGGKTTLLKIMQ 318
                                       79999999999998765 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.29   1.7e+02      27      42 ..     147     162 ..     128     196 .. 0.84
   2 ?   10.8   0.1   0.00076      0.44      33      89 ..     466     509 ..     459     510 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.29
                           SbcCD_C  27 srssgtlSGGekqfla 42 
                                       s+ ++ lSGGekq l+
  gi|330508606|ref|YP_004385034.1| 147 SHLATILSGGEKQRLV 162
                                       5556679999999886 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00076
                           SbcCD_C  33 lSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       lSGGe        + a+la l+        ++++++LDE F+ +D+ +++++ ++++
  gi|330508606|ref|YP_004385034.1| 466 LSGGEL-------VRASLAILLAA------QPEVMILDEPFGDIDPITLREVSNAIK 509
                                       666666.......34444444555......4899****************9999876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.087        50      25      45 ..      33      53 ..      18     130 .. 0.84
   2 ?    6.1   1.1     0.014         8      19      43 ..     292     317 ..     286     320 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.087
                            AAA_15 25 ltvliGkNnsGKSsilealdl 45
                                      +  ++Gk + GKS+++++l  
  gi|330508606|ref|YP_004385034.1| 33 ILGIVGKSGGGKSTLMKILRG 53
                                      5669*************9965 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.014
                            AAA_15  19 idlsee.ltvliGkNnsGKSsileal 43 
                                        d+++  +t +iG  + GK+++l+++
  gi|330508606|ref|YP_004385034.1| 292 FDINKGeITSFIGNSGGGKTTLLKIM 317
                                       3333335*****************98 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.018        10       4      65 ..      36     110 ..      33     118 .. 0.66
   2 ?   -2.6   0.0       9.5   5.5e+03      16      33 ..     164     181 ..     158     210 .. 0.65
   3 ?    3.3   0.1      0.15        85       4      17 ..     302     315 ..     299     325 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.018
                            AAA_33   4 lvGlpGsGKstlaerl.....lkklg.......avllssdt....lrrrlfgtdqqsktdytrvldrlyqilnelar 64 
                                       +vG +G GKstl + l         +       +++++ d+    +r r+++t  + ++d + +++++ + + ++++
  gi|330508606|ref|YP_004385034.1|  36 IVGKSGGGKSTLMKILrgmdrF---DsgkitmdGITITPDSsdeeIRARMAATAIHLQRDFALWTESALNNVVRRIH 109
                                       69**********9988553331...2445557777776666666566677777666666666677666665556554 PP

                            AAA_33  65 k 65 
                                       +
  gi|330508606|ref|YP_004385034.1| 110 S 110
                                       4 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9.5
                            AAA_33  16 aerllkklgavllssdtl 33 
                                       a++l+kk ++ ll++++ 
  gi|330508606|ref|YP_004385034.1| 164 ARQLAKKPKVLLLDEPAT 181
                                       677777777777777763 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.15
                            AAA_33   4 lvGlpGsGKstlae 17 
                                       ++G +G GK+tl++
  gi|330508606|ref|YP_004385034.1| 302 FIGNSGGGKTTLLK 315
                                       89*********986 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.19   1.1e+02       3      19 ..      36      52 ..      34      59 .. 0.86
   2 ?   -0.2   0.0       1.3   7.7e+02     119     152 ..      88     121 ..      74     132 .. 0.78
   3 ?    6.4   0.0     0.013       7.2       5      53 ..     304     364 ..     301     382 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.19
                                      EEESTTSSHHHHHHHHH CS
                               dNK  3 veGnIgaGKstlvklLs 19
                                      + G+ g GKstl+k+L+
  gi|330508606|ref|YP_004385034.1| 36 IVGKSGGGKSTLMKILR 52
                                      668899*********97 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.3
                                       HCCH-SEEEEEE--HHHHHHHHHHCTTCCCT.TS- CS
                               dNK 119 elakpdlliYLkasletclerikkRgreeek.kie 152
                                       +l+  d+  + +  l+++++ri+ R+  +e  +i+
  gi|330508606|ref|YP_004385034.1|  88 HLQ-RDFALWTESALNNVVRRIHSRKTGYEVlPIP 121
                                       455.8899999999***********9999876554 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.013
                                       ESTTSSHHHHHHHHHCCST...CEEEE-HHHHCCSSSS.........HHHHHHHHSHHHHH CS
                               dNK   5 GnIgaGKstlvklLskklg...vkvfeEpvdkwtnvqk.........nlLekfYkdpsrws 53 
                                       Gn g GK+tl+k+++         v++   d+w+ + +           L  +Y++++ ++
  gi|330508606|ref|YP_004385034.1| 304 GNSGGGKTTLLKIMQGVRMpdaGAVYYRYGDEWVDMLTysphrmnvrRTLGVMYQEFALYA 364
                                       899***********97543345677788888887777688888888889999999988876 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.12        68      19      49 ..      31      62 ..      13     116 .. 0.71
   2 ?    6.1   0.0     0.011       6.6      16      43 ..     294     322 ..     286     330 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                                      -SEEEEE--TTSST.THHHHHHHHHHHHTTS- CS
                              PhoH 19 ndivfaiGpaGtGK.tylavalavealkkkkv 49
                                       +i+ ++G++G GK t++ +  +++ + ++k+
  gi|330508606|ref|YP_004385034.1| 31 GEILGIVGKSGGGKsTLMKILRGMDRFDSGKI 62
                                      46999*********556677788888777665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
                                       HHH-SEEEEE--TTSSTT.HHHHHHHHHH CS
                              PhoH  16 lkkndivfaiGpaGtGKt.ylavalavea 43 
                                       ++k +i+  iG++G GKt +l ++ +v++
  gi|330508606|ref|YP_004385034.1| 294 INKGEITSFIGNSGGGKTtLLKIMQGVRM 322
                                       67889************825667777776 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4    0.0063       3.6       1      22 [.      33      54 ..      33     132 .. 0.76
   2 ?    1.8   0.0       0.3   1.7e+02       4      20 ..     302     318 ..     299     352 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0063
                               PRK  1 vIgvagsSGaGkttvarkleki 22
                                      ++g+ g+SG Gk+t+++ l+ +
  gi|330508606|ref|YP_004385034.1| 33 ILGIVGKSGGGKSTLMKILRGM 54
                                      689*************988643 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.3
                               PRK   4 vagsSGaGkttvarkle 20 
                                         g+SG Gktt+ + ++
  gi|330508606|ref|YP_004385034.1| 302 FIGNSGGGKTTLLKIMQ 318
                                       679********987665 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.049        28      28      46 ..      36      54 ..      13     159 .. 0.85
   2 ?    4.9   0.0     0.022        12      28      49 ..     302     323 ..     292     441 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.049
                                      EEESTTSSHHHHHHHHHHH CS
                           G-alpha 28 llGqseSGKsTilkqlkll 46
                                      ++G+s++GKsT++k l+ +
  gi|330508606|ref|YP_004385034.1| 36 IVGKSGGGKSTLMKILRGM 54
                                      79**********9988844 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.022
                                       EEESTTSSHHHHHHHHHHHCS- CS
                           G-alpha  28 llGqseSGKsTilkqlkllykk 49 
                                       ++G+s++GK+T+lk ++ + ++
  gi|330508606|ref|YP_004385034.1| 302 FIGNSGGGKTTLLKIMQGVRMP 323
                                       68*************9966555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.6     0.055        32       5      18 ..      36      49 ..      32      55 .. 0.86
   2 ?    4.6   0.1     0.049        28       6      18 ..     303     315 ..     299     329 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.055
                                      EEC-TTTCHHHHHH CS
                             NACHT  5 lqGeaGsGKTtLlq 18
                                      + G++G GK+tL++
  gi|330508606|ref|YP_004385034.1| 36 IVGKSGGGKSTLMK 49
                                      89**********97 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.049
                                       EC-TTTCHHHHHH CS
                             NACHT   6 qGeaGsGKTtLlq 18 
                                        G +G GKTtLl+
  gi|330508606|ref|YP_004385034.1| 303 IGNSGGGKTTLLK 315
                                       79*********96 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 ?    1.7   0.1      0.15        87     244     264 ..      31      51 ..      18      59 .. 0.83
   2 ?   -0.6   0.0      0.75   4.3e+02     376     413 ..     191     228 ..     153     247 .. 0.69
   3 ?    3.1   0.1     0.056        32     242     265 ..     294     318 ..     292     324 .. 0.87
   4 ?   -0.9   0.0      0.91   5.3e+02     375     413 ..     503     541 ..     495     544 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.15
                                       SSEEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 244 kGvtlIvGggfhGKsTLLeAl 264
                                         +  IvG    GKsTL++ l
  gi|330508606|ref|YP_004385034.1|  31 GEILGIVGKSGGGKSTLMKIL 51 
                                       44889************9966 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.75
                                       HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEET CS
                        ABC_ATPase 376 lvdrvrelykklgvstilvvggsgdyldvAdtvilmee 413
                                       ++d ++++++klg+++++v+   +    +Ad+ i +e+
  gi|330508606|ref|YP_004385034.1| 191 VLDAIKNVRDKLGLTIVVVSHLPEVHNYLADRLIWLEK 228
                                       45677777888888777776555555666777777776 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.056
                                       E-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAle 265
                                       i kG +t  +G    GK+TLL+ ++
  gi|330508606|ref|YP_004385034.1| 294 INKGeITSFIGNSGGGKTTLLKIMQ 318
                                       78899****************9665 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.91
                                       -HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEET CS
                        ABC_ATPase 375 plvdrvrelykklgvstilvvggsgdyldvAdtvilmee 413
                                        +++ ++++ +++g ++ilv+  ++   +v+++ ilme+
  gi|330508606|ref|YP_004385034.1| 503 EVSNAIKKINSEFGTTIILVSHHVDFVKEVSHRAILMEN 541
                                       56788999999********9999999999********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.46
# Mc/sec: 3768.14
//
Query:       gi|330508607|ref|YP_004385035.1|  [L=371]
Description: OB-fold nucleic acid binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   77.8   5.4    4.6e-09   36.1   0.1    3.5  3  tRNA_anti-codon  OB-fold nucleic acid binding domain
    3.5e-13   49.8   0.0    2.7e-06   27.3   0.0    3.1  3  CDC24_OB3        Cell division control protein 24, OB domain 
    2.7e-12   46.5   0.0     0.0032   17.3   0.0    3.2  3  REPA_OB_2        Replication protein A OB domain
  ------ inclusion threshold ------
      0.061   13.5   0.0         41    4.5   0.0    3.2  3  tRNA_anti_2      OB-fold nucleic acid binding domain
      0.078   13.3   0.2         46    4.4   0.0    3.3  3  MlaD             MlaD protein
      0.097   12.8   1.5        3.7    7.7   0.1    3.0  3  PRC              PRC-barrel domain
        0.1   12.4   0.0         23    4.7   0.0    2.8  3  Rep_fac-A_C      Replication factor-A C terminal domain
       0.16   12.2   0.0         14    6.0   0.0    3.1  3  UvrB_inter       UvrB interaction domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   2.1e-12   4.6e-09       1      62 [.      68     138 ..      68     147 .. 0.81
   2 !   22.5   0.1   3.7e-08   8.3e-05      11      69 ..     195     250 ..     187     252 .. 0.82
   3 !   20.0   0.1   2.2e-07   0.00049       5      69 ..     292     358 ..     278     360 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.1e-12
                                       EEEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTT..S-TTSEEEEEEEEEECT CS
                   tRNA_anti-codon   1 VtvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaen..lkeGdvvrvtGrvkrrp 62 
                                       Vt+ Grv+++s        d+s g+v++i+l D+tg+++v l++ e  +l ++  l ++++++v+G  k+  
  gi|330508607|ref|YP_004385035.1|  68 VTFTGRVIAVSpvrefqrsDGSLGRVANITLADETGSVRVALWD-ETAELIKSgdLAVDQCLKVRGLAKEGF 138
                                       89******************************************.444444433466888888888777764 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 3.7e-08
                                       EEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEE CS
                   tRNA_anti-codon  11 sdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelk 69 
                                       +d+++g v  ++l D+tg+++++l++   ++ +  l +G  +++  G v++r+g  le++
  gi|330508607|ref|YP_004385035.1| 195 RDGGKGQVRGVTLGDETGKVRLTLWD---EQAQMPLLKGETLEIVgGSVRERYGL-LEIQ 250
                                       3788999999****************...66666677777777777*******98.8886 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 2.2e-07
                                       EEEEEEE..EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEEC.TTSSEEEE CS
                   tRNA_anti-codon   5 Grvtsis..drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrr.pggelelk 69 
                                       G+v+  +  d+ +g+v++i + D++gri++ l+  e  + + +++ G   ++   +vk+  ++g lel+
  gi|330508607|ref|YP_004385035.1| 292 GEVREFQrdDGRMGRVANIYISDDSGRIRAALWG-EHVDRLVEVDLGYRAEIIdAQVKSGwNEG-LELS 358
                                       4455555999************************.88888888999999999888888887777.7776 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 !   27.3   0.0   1.2e-09   2.7e-06       2      71 ..      61     134 ..      60     143 .. 0.84
   2 !   13.4   0.0   2.1e-05     0.047       2      52 ..     170     223 ..     169     233 .. 0.83
   3 !    5.5   0.0    0.0055        12      10      54 ..     283     330 ..     275     340 .. 0.66

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.2e-09
                         CDC24_OB3   2 LrekmlnvtLlGrvvai.....freknsek.kkmdryslrieDttGaidatlweeagklhfk.rlrvGhlvllsgLa 71 
                                       +r++m nvt  Grv+a+     f ++++++  ++   +++++D+tG+++++lw+e+++l+++ +l v +++ + gLa
  gi|330508607|ref|YP_004385035.1|  61 IRPEMGNVTFTGRVIAVspvreF-QRSDGSlGRVA--NITLADETGSVRVALWDETAELIKSgDLAVDQCLKVRGLA 134
                                       6899*************996444.55555545555..9**********************99999999998888886 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.1e-05
                         CDC24_OB3   2 LrekmlnvtLlGrvvai.....freknsekkkmdryslrieDttGaidatlweeag 52 
                                       L+  m++v Ll+ vv+      f+ ++++k +++   +++ D+tG++++tlw+e +
  gi|330508607|ref|YP_004385035.1| 170 LKRDMSDVNLLAAVVDPgemreFERRDGGKGQVR--GVTLGDETGKVRLTLWDEQA 223
                                       8899***********9988776655555555555..9****************965 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0055
                         CDC24_OB3  10 tLlGrvvai.....freknsekkkmdryslrieDttGaidatlweeagkl 54 
                                       ++ G v ++     f +++++    ++ ++ i D++G i+a+lw e +  
  gi|330508607|ref|YP_004385035.1| 283 SVSGFVSGLgevreF-QRDDGR-MGRVANIYISDDSGRIRAALWGEHVDR 330
                                       455666666553222.445544.444559***************986654 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 !   16.8   0.0   2.1e-06    0.0046      18      90 ..      73     146 ..      64     152 .. 0.83
   2 !   17.3   0.0   1.4e-06    0.0032      12      63 ..     176     225 ..     167     260 .. 0.80
   3 !    8.6   0.0   0.00076       1.7       5      64 ..     274     331 ..     270     345 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.1e-06
                         REPA_OB_2  18 vvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfe...sseepvvalkgvkvsdFggrslsll 90 
                                        v  v++v+e+++ +++   +  ++tl De+g sv+v+lW+++ae ++      ++ + ++g+  + F g ++sl 
  gi|330508607|ref|YP_004385035.1|  73 RVIAVSPVREFQRSDGS-LGRVANITLADETG-SVRVALWDETAELIKsgdLAVDQCLKVRGLAKEGFAGTEVSLG 146
                                       56778888888888777.667789*******9.7***********9996555778899************999975 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.4e-06
                         REPA_OB_2  12 ivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaek 63 
                                        v +++ v + +e++e+ +++++ + + r +tl De+g +v++tlW+++a+ 
  gi|330508607|ref|YP_004385035.1| 176 DVNLLAAVVDPGEMREFERRDGG-KGQVRGVTLGDETG-KVRLTLWDEQAQM 225
                                       57789999999************.89***********9.59*******9986 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00076
                         REPA_OB_2   5 envekdsivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekf 64 
                                        +++++++  v g v+ ++ev+e+++ +++   +  ++ + D+sg+ ++ +lWg++ +++
  gi|330508607|ref|YP_004385035.1| 274 AELKEGMLSSVSGFVSGLGEVREFQRDDGR-MGRVANIYISDDSGR-IRAALWGEHVDRL 331
                                       566677777889999999999999988776.88889********96.9*******87765 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 ?    4.5   0.0     0.018        41      38      63 ..      93     118 ..      58     137 .. 0.72
   2 ?    3.0   0.0     0.052   1.2e+02      26      61 ..     187     225 ..     166     249 .. 0.70
   3 ?    2.0   0.0      0.11   2.4e+02      25      63 ..     291     332 ..     272     360 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.018
                       tRNA_anti_2  38 hvYftLkDekakisavifrsraaklk 63 
                                        + +tL De+ +++++++ ++a+ +k
  gi|330508607|ref|YP_004385035.1|  93 VANITLADETGSVRVALWDETAELIK 118
                                       55689**************9998877 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.052
                       tRNA_anti_2  26 Geisnlkr.ka.sg.hvYftLkDekakisavifrsraak 61 
                                       Ge  +++r    +g    +tL De+ k++ +++ ++a+ 
  gi|330508607|ref|YP_004385035.1| 187 GEMREFERrDGgKGqVRGVTLGDETGKVRLTLWDEQAQM 225
                                       666666532334553446789999999999999877753 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.11
                       tRNA_anti_2  25 rGeisnlkr.ka.sg.hvYftLkDekakisavifrsraaklk 63 
                                        Ge+ +++r     g  + + ++D++ +i+a+++ +++++l 
  gi|330508607|ref|YP_004385035.1| 291 LGEVREFQRdDGrMGrVANIYISDDSGRIRAALWGEHVDRLV 332
                                       588888874222233366778899999*******98887764 PP

>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.021        46      28      47 ..      90     109 ..      86     133 .. 0.83
   2 ?    1.7   0.0      0.14   3.2e+02      29      47 ..     200     218 ..     198     282 .. 0.87
   3 ?    3.1   0.0     0.053   1.2e+02      27      47 ..     303     323 ..     300     350 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.021
                              MlaD  28 vGrVtsitldpdtrrvtvtv 47 
                                        GrV++itl ++t +v+v +
  gi|330508607|ref|YP_004385035.1|  90 LGRVANITLADETGSVRVAL 109
                                       5********99999888755 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                              MlaD  29 GrVtsitldpdtrrvtvtv 47 
                                       G+V+ +tl ++t +v++t+
  gi|330508607|ref|YP_004385035.1| 200 GQVRGVTLGDETGKVRLTL 218
                                       99******99999998876 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.053
                              MlaD  27 tvGrVtsitldpdtrrvtvtv 47 
                                       ++GrV++i++++d+ r+++ +
  gi|330508607|ref|YP_004385035.1| 303 RMGRVANIYISDDSGRIRAAL 323
                                       68**********999997654 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.056   1.3e+02      21      43 ..      89     111 ..      83     125 .. 0.82
   2 ?   -1.4   0.0       1.1   2.6e+03      34      43 ..     199     208 ..     183     219 .. 0.59
   3 ?    7.7   0.1    0.0016       3.7      18      60 ..     300     337 ..     297     350 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.056
                                       EEEEEEEEEEETTTTEEEEEEEE CS
                               PRC  21 klGkVkDvvidekegrvralvvs 43 
                                        lG+V ++ + +++g vr ++ +
  gi|330508607|ref|YP_004385035.1|  89 SLGRVANITLADETGSVRVALWD 111
                                       69***************988765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                                       TTEEEEEEEE CS
                               PRC  34 egrvralvvs 43 
                                        g+vr++ ++
  gi|330508607|ref|YP_004385035.1| 199 KGQVRGVTLG 208
                                       3444444433 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0016
                                       TSSEEEEEEEEEEETTTTEEEEEEEEETTT.....-EEEEEGG CS
                               PRC  18 dGeklGkVkDvvidekegrvralvvsvggflgigekevliPfd 60 
                                       d+ + G+V +++i +++gr+ra++ ++       ++ v+++ +
  gi|330508607|ref|YP_004385035.1| 300 DDGRMGRVANIYISDDSGRIRAALWGEHV-----DRLVEVDLG 337
                                       56688*****************9887763.....366666555 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 ?    4.7   0.0      0.01        23      57      79 ..      95     117 ..      89     126 .. 0.90
   2 ?    4.0   0.0     0.017        37      59      78 ..     206     225 ..     203     236 .. 0.86
   3 ?   -1.6   0.0      0.89     2e+03      57      81 ..     309     333 ..     306     348 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.01
                                       EEEEE-SS-EEEEEEEHHHHHHH CS
                       Rep_fac-A_C  57 sikvsDstgqlwvtlFneaaekl 79 
                                       +i ++D+tg+++v l++e+ae +
  gi|330508607|ref|YP_004385035.1|  95 NITLADETGSVRVALWDETAELI 117
                                       7899****************976 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.017
                                       EEE-SS-EEEEEEEHHHHHH CS
                       Rep_fac-A_C  59 kvsDstgqlwvtlFneaaek 78 
                                        + D+tg++++tl++e+a+ 
  gi|330508607|ref|YP_004385035.1| 206 TLGDETGKVRLTLWDEQAQM 225
                                       678**************985 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.89
                                       EEEEE-SS-EEEEEEEHHHHHHHHS CS
                       Rep_fac-A_C  57 sikvsDstgqlwvtlFneaaekllg 81 
                                       +i +sD +g++++ l+ e+  +l+ 
  gi|330508607|ref|YP_004385035.1| 309 NIYISDDSGRIRAALWGEHVDRLVE 333
                                       6889**********99999888865 PP

>> UvrB_inter  UvrB interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.6   3.5e+03      63      91 .]      55      83 ..      52      83 .. 0.77
   2 ?    2.0   0.0      0.11   2.4e+02      39      71 ..      91     122 ..      87     132 .. 0.85
   3 ?    6.0   0.0     0.006        14      39      72 ..     305     337 ..     296     347 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.6
                        UvrB_inter 63 iesireidpltgkslekleeitifPakhf 91
                                      + +i +i+p+ g+++ +   i + P ++f
  gi|330508607|ref|YP_004385035.1| 55 LTKIGSIRPEMGNVTFTGRVIAVSPVREF 83
                                      56888888888888888888888888776 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                        UvrB_inter  39 Gdtveifpasaeevairieffgdeiesireidp 71 
                                       G + +i  a+ e   +r+ +++++ e i++ d 
  gi|330508607|ref|YP_004385035.1|  91 GRVANITLAD-ETGSVRVALWDETAELIKSGDL 122
                                       77889999**.89**********9999988765 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.006
                        UvrB_inter  39 Gdtveifpasaeevairieffgdeiesireidpl 72 
                                       G + +i+ ++ ++  ir  ++g+ ++++ e+d  
  gi|330508607|ref|YP_004385035.1| 305 GRVANIYISD-DSGRIRAALWGEHVDRLVEVDLG 337
                                       88899*****.89****************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2628.00
//
Query:       gi|330508608|ref|YP_004385036.1|  [L=325]
Description: DNA repair and recombination protein RadA [Methanosaeta concilii GP6]
Scores for 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-82  274.3   0.0    9.7e-82  274.1   0.0    1.0  1  Rad51            Rad51
    2.9e-13   50.2   1.3    6.8e-13   49.0   1.3    1.7  1  HHH_5            Helix-hairpin-helix domain
    7.4e-11   42.0   0.1    8.3e-05   22.2   0.0    2.2  2  RecA             recA bacterial DNA recombination protein
    2.2e-08   33.9   0.0    3.3e-08   33.3   0.0    1.3  1  AAA_25           AAA domain
    1.8e-06   27.5   4.7     0.0017   18.2   0.1    2.6  2  HHH              Helix-hairpin-helix motif
      4e-06   26.4   0.1    7.5e-06   25.5   0.1    1.4  1  ATPase           KaiC
    5.1e-06   26.5   0.3    1.3e-05   25.2   0.3    1.6  1  HHH_2            Helix-hairpin-helix motif
    8.5e-06   25.9   0.0    1.5e-05   25.1   0.0    1.5  1  Cdd1             Pathogenicity locus
    9.8e-05   22.8   0.0    0.00028   21.3   0.0    1.7  1  AAA              ATPase family associated with various cellul
    0.00035   20.3   0.0     0.0029   17.4   0.0    2.4  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
      0.001   18.9   0.0     0.0018   18.0   0.0    1.4  1  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.057   13.8   0.0    2.1  1  IMS_HHH          IMS family HHH motif
      0.027   14.7   0.3        6.7    7.0   0.1    3.3  3  HHH_3            Helix-hairpin-helix motif
      0.034   14.3   0.1       0.15   12.2   0.1    1.9  2  Ntox34           Bacterial toxin 34
      0.037   13.7   0.0       0.12   12.0   0.0    1.8  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.044   13.3   0.0       0.16   11.6   0.0    1.8  2  CobU             Cobinamide kinase / cobinamide phosphate gua
       0.06   12.5   0.1        2.3    7.3   0.0    2.1  2  NB-ARC           NB-ARC domain
      0.075   13.4   0.3       0.91    9.9   0.0    2.4  2  HHH_8            Helix-hairpin-helix domain
       0.08   13.4   0.0       0.17   12.3   0.0    1.6  1  BAF              Barrier to autointegration factor
      0.098   12.7   0.2       0.23   11.5   0.1    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.14   12.1   0.0       0.22   11.4   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
       0.15   12.7   0.1        1.2    9.7   0.0    2.3  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 !  274.1   0.0   1.2e-84   9.7e-82       2     254 ..      65     325 .]      64     325 .] 0.94

  Alignments for each domain:
  == domain 1  score: 274.1 bits;  conditional E-value: 1.2e-84
                                       S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEE CS
                             Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyid 78 
                                       gf ++  +le+r+++ ++tt +k++DelLgGG+et++i e++Gef++Gktq++h+l+v +qlp+e+gG +g ++ id
  gi|330508608|ref|YP_004385036.1|  65 GFETGDRILERRKQVGKVTTSCKSFDELLGGGMETQAIVELYGEFGCGKTQVAHQLAVNIQLPVEMGGLNGSVIIID 141
                                       799999*********************************************************************** PP

                                       SSS---GGGGHHHH.......HHTT--HHHHGGGEEEEE--STTHHHHHHH...HTHHHH..HHS-EEEEEEETTTG CS
                             Rad51  79 tegtfrperlveia.......erykldkeevlenvayaRaytiehqeellq...qaaall..aedkfallivDsvta 143
                                       te tfrper+ ++        +    ++e+ l+n+ +aRa++++hq  l +    +a+++  +e  ++llivDsvta
  gi|330508608|ref|YP_004385036.1| 142 TENTFRPERIDQMVkglppapDGRIWETEDFLKNINVARAFNSNHQILLAEsamDLAEKVkdSERPVRLLIVDSVTA 218
                                       *************988888876667899******************988773223455552245579********** PP

                                       GGCH-------THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEE CS
                             Rad51 144 lyRtdfsgrgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlal 220
                                       ++R+++ grg la+Rqqkl+k+l+ L ++ d  ++ +++tnqv++++d+    f +dp+kP+gG+vl+h+st Rl+l
  gi|330508608|ref|YP_004385036.1| 219 HFRAEYVGRGTLADRQQKLNKHLHDLMRFGDLNNALILVTNQVMSKPDT----FFGDPTKPVGGHVLGHTSTFRLYL 291
                                       ************************************************9....99********************** PP

                                       EE-STTEEEEEEES-SSS-S-EEEEEEETTEEE- CS
                             Rad51 221 rkgkgeeRivkvvdsPnlpeleavfaigeeGied 254
                                       rk kge+Ri+++vdsPnlp+ eavf+++++G++d
  gi|330508608|ref|YP_004385036.1| 292 RKSKGEKRIARLVDSPNLPDGEAVFSVTTDGLKD 325
                                       *******************************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 !   49.0   1.3   8.4e-16   6.8e-13       2      57 .]       4      59 ..       3      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 8.4e-16
                                      HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                             HHH_5  2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                      ++L +++G+Gp+tA +l +aG++s+e++a a++ eL ++  +G+ tA +ii  +++
  gi|330508608|ref|YP_004385036.1|  4 KLLEDLPGVGPATAEKLREAGFNSIEAIAVASPGELVSAAEVGEATAAKIIAGARE 59
                                      6899***********************************************99986 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.6e-06    0.0021      28      95 ..      76     148 ..      67     155 .. 0.80
   2 !   22.2   0.0     1e-07   8.3e-05     116     225 ..     191     297 ..     176     306 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                                       -----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH......HTT--EEEEESS----H CS
                              RecA  28 klkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq......kkggvaafidaehaldp 95 
                                       +++v  +++   ++d  lG GG+    i+e+yG    Gkt +a ++ +++q        +g +  id+e ++ p
  gi|330508608|ref|YP_004385036.1|  76 RKQVGKVTTSCKSFDELLG-GGMETQAIVELYGEFGCGKTQVAHQLAVNIQlpvemgGLNGSVIIIDTENTFRP 148
                                       57899999***********.***********************9998888833311123566778888887766 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1e-07
                                       HHHHHHHHHHHHTTT.--SEEEEE-TTT---STT--..---------HHHHHHHHHHHHHHHHHTTT--EEEEEEE- CS
                              RecA 116 Geqaleiadalvrsg.aidlivvdsvaalvpkaeie..Gemgdskvglqarlmsqalrkltgaisksntvvifinqi 189
                                        e+a+++a+++ +s   + l++vdsv+a   +ae    G ++d +       + + l  l    + +n++++  nq+
  gi|330508608|ref|YP_004385036.1| 191 AESAMDLAEKVKDSErPVRLLIVDSVTAHF-RAEYVgrGTLADRQQ-----KLNKHLHDLMRFGDLNNALILVTNQV 261
                                       699*********99736**********976.666540144555443.....446778888888888999999***** PP

                                       ----------------HHHHHHH-SEEEEEEEES-- CS
                              RecA 190 rekiGvmfgnpetttGGralkfyasvrldvrrieei 225
                                         k    fg+p    GG+ l   ++ rl +r+++  
  gi|330508608|ref|YP_004385036.1| 262 MSKPDTFFGDPTKPVGGHVLGHTSTFRLYLRKSKGE 297
                                       *******************************98765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   4.1e-11   3.3e-08      14     156 ..      81     221 ..      70     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 4.1e-11
                            AAA_25  14 dlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRl 90 
                                       ++ ++ ++ + l++g +  ++++ l+G  g+GKt +a +la+ + +  +  g     +g V+++++E++    ++R+
  gi|330508608|ref|YP_004385036.1|  81 KVTTSCKSFDELLGGGMETQAIVELYGEFGCGKTQVAHQLAVNIQLPVEMGG----LNGSVIIIDTENTF--RPERI 151
                                       5555556667788888899999***********************8775544....79***********8..79*** PP

                            AAA_25  91 ravgealrddarllvldlagv.eslpLfak.drggtl.ltadvdaleaaieeveg.vrlvviDplsralg 156
                                        ++ + l++  + +++  +++ ++++++ +  +++++ l++   +l++++++ e+ vrl+++D++++ ++
  gi|330508608|ref|YP_004385036.1| 152 DQMVKGLPPAPDGRIWETEDFlKNINVARAfNSNHQIlLAESAMDLAEKVKDSERpVRLLIVDSVTAHFR 221
                                       *******7777777888889999999987744555557899999********9889********998766 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1     2e-06    0.0017      11      29 ..       4      22 ..       2      23 .. 0.87
   2 !   10.4   1.0   0.00058      0.48       1      28 [.      27      54 ..      27      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-06
                                      HHHHTSTT-SHHHHHHHHH CS
                               HHH 11 eeLlalPGVGpktAeaIls 29
                                      + L++lPGVGp+tAe+ ++
  gi|330508608|ref|YP_004385036.1|  4 KLLEDLPGVGPATAEKLRE 22
                                      6799***********9875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00058
                                      SHHHHHTSSHHHHHTSTT-SHHHHHHHH CS
                               HHH  1 sleglipasreeLlalPGVGpktAeaIl 28
                                      s+e++  as+ eL++   VG++tA +I+
  gi|330508608|ref|YP_004385036.1| 27 SIEAIAVASPGELVSAAEVGEATAAKII 54
                                      689999********************98 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.1   9.2e-09   7.5e-06       1     131 [.      82     219 ..      82     243 .. 0.63

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 9.2e-09
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlik...gaekygepgvfvtveepa....edlrenaksl 70 
                                       v t  + +De+l gG+  +++v ++Ge G+GKt +a q +++    +e  g +g  + ++ ++    e + + +k l
  gi|330508608|ref|YP_004385036.1|  82 VTTSCKSFDELLGGGMETQAIVELYGEFGCGKTQVAHQLAVNiqlPVEMGGLNGSVIIIDTENtfrpERIDQMVKGL 158
                                       5688999*********************************9933223444555555555444433667777777766 PP

                            ATPase  71 ..GwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl 131
                                           d + +e e+ l  i++++  + +++    e+++ l+e++++   e  ++ +++Ds+t++
  gi|330508608|ref|YP_004385036.1| 159 ppAPDGRIWETEDFLKNINVARAFNSNHQILLAESAMDLAEKVKDS--ERPVRLLIVDSVTAH 219
                                       3323555555555555555555554422223344444444444442..334588888999887 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.3   1.6e-08   1.3e-05       9      52 ..      10      54 ..       8      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.6e-08
                             HHH_2  9 rhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsiv 52
                                      + VG +tA++L ++ F+s++a++ as  eL++  ++Ge +A++i+
  gi|330508608|ref|YP_004385036.1| 10 PGVGPATAEKLREAgFNSIEAIAVASPGELVSAAEVGEATAAKII 54
                                      78*********9866***************************997 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.9e-08   1.5e-05       5      46 ..       3      44 ..       1      53 [. 0.90

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.9e-08
                              Cdd1  5 lkelqdiPniGkalaedlvelGirsveelkgedpeelyekle 46
                                      +k l+d+P++G+a+ae+l+e G++s+e ++  +p el+++ e
  gi|330508608|ref|YP_004385036.1|  3 IKLLEDLPGVGPATAEKLREAGFNSIEAIAVASPGELVSAAE 44
                                      6789*********************************98876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   3.4e-07   0.00028       3     116 ..     105     266 ..     103     270 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.4e-07
                                       EESSTTSSHHHHHHHHHHHHTHE.............................................EEEEETTTC CS
                               AAA   3 lyGppGtGKTllakavakelgve.............................................fleisgsel 34 
                                       lyG  G+GKT +a+++a +++ +                                             + +i++++ 
  gi|330508608|ref|YP_004385036.1| 105 LYGEFGCGKTQVAHQLAVNIQLPvemgglngsviiidtentfrperidqmvkglppapdgriwetedfLKNINVARA 181
                                       9******************8755556666666666666666666666666666667777777777775566777776 PP

                                       SSS....STTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHH..TTCCCHHHHHHHHHHHHHHHHTTTSSSTEE CS
                               AAA  35 lsk....yvgesekkirelfkeakekakp.silfiDEidalaksr..sgseseeeervvnqLlteldgvkkkeskvi 104
                                       +++    ++ es+++++e +k+ ++   p   l++D + a ++++   +++  ++++ +n+ l+ l ++ + ++   
  gi|330508608|ref|YP_004385036.1| 182 FNSnhqiLLAESAMDLAEKVKDSER---PvRLLIVDSVTAHFRAEyvGRGTLADRQQKLNKHLHDLMRFGDLNN--A 253
                                       6448888888999999888888654...449**************88444555555555555555555555555..7 PP

                                       EEEEESS.GGGST CS
                               AAA 105 vigatnr.pdkld 116
                                       +i++tn+ ++k+d
  gi|330508608|ref|YP_004385036.1| 254 LILVTNQvMSKPD 266
                                       8999998555554 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.6e-06    0.0029       3      29 ..       6      32 ..       4      46 .. 0.82
   2 ?   -0.3   0.0       1.2     1e+03       8      19 ..      44      55 ..      38      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.6e-06
                   DNA_pol_lambd_f  3 FtkvyGVGpktAkkwyakGirtledlr 29
                                      +    GVGp+tA+k+ ++G+ ++e + 
  gi|330508608|ref|YP_004385036.1|  6 LEDLPGVGPATAEKLREAGFNSIEAIA 32
                                      56667*******************886 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                   DNA_pol_lambd_f  8 GVGpktAkkwya 19
                                       VG +tA k +a
  gi|330508608|ref|YP_004385036.1| 44 EVGEATAAKIIA 55
                                      59*****99875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.2e-06    0.0018       6      79 ..     104     221 ..      99     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                            AAA_24   6 liyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie............swedfldevv 57 
                                        +yG+ g GKT +a +l               ++++idte+ +    + +++++               edfl+ ++
  gi|330508608|ref|YP_004385036.1| 104 ELYGEFGCGKTQVAHQLavniqlpvemgglNGSVIIIDTENTF---RPERIDQMVkglppapdgriwETEDFLKNIN 177
                                       59***************************99**********55...6666666667889999***998889999998 PP

                            AAA_24  58 el......................aaeladyktlviDtidelee 79 
                                                               ++ +++ + l++D+++   +
  gi|330508608|ref|YP_004385036.1| 178 VArafnsnhqillaesamdlaekvKDSERPVRLLIVDSVTAHFR 221
                                       888889999999999999999999999999********997654 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     7e-05     0.057      13      31 ..       6      24 ..       6      25 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7e-05
                           IMS_HHH 13 itkipGiGgklgekLeklG 31
                                      + ++pG+G+ ++ekL+  G
  gi|330508608|ref|YP_004385036.1|  6 LEDLPGVGPATAEKLREAG 24
                                      679***********99877 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0082       6.7      14      32 ..       4      22 ..       2      53 .. 0.74
   2 ?    3.1   0.1      0.14   1.1e+02      11      32 ..      34      55 ..      30      68 .. 0.85
   3 ?    1.1   0.0      0.58   4.7e+02      27      42 ..      69      84 ..      63      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0082
                             HHH_3 14 eeLqklpGlgpklAknIva 32
                                      ++L+ lpG+gp++A+++ +
  gi|330508608|ref|YP_004385036.1|  4 KLLEDLPGVGPATAEKLRE 22
                                      68999*********99755 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.14
                             HHH_3 11 AsaeeLqklpGlgpklAknIva 32
                                      As  eL   + +g+++A +I+a
  gi|330508608|ref|YP_004385036.1| 34 ASPGELVSAAEVGEATAAKIIA 55
                                      89999999999******99997 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.58
                             HHH_3 27 AknIvayReknGpfks 42
                                       ++I++ R++ G++++
  gi|330508608|ref|YP_004385036.1| 69 GDRILERRKQVGKVTT 84
                                      689*********9875 PP

>> Ntox34  Bacterial toxin 34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00019      0.15       4      51 ..      48      94 ..      45     102 .. 0.89
   2 ?   -1.1   0.0       2.7   2.2e+03      21      60 ..     212     251 ..     211     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                            Ntox34  4 aliivliarrGnvadtGiteevedlindrfwsdGkkadiCdvldelie 51
                                      a    +ia     ad G  e  + ++ +r  + Gk ++ C+ +del+ 
  gi|330508608|ref|YP_004385036.1| 48 ATAAKIIAGAREAADVGGFETGDRIL-ERRKQVGKVTTSCKSFDELLG 94
                                      566678999999**************.999***************986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.7
                            Ntox34  21 iteevedlindrfwsdGkkadiCdvldelieaarraGdis 60 
                                       i++ v + +   +   G  ad+ + l++ +    r Gd+ 
  gi|330508608|ref|YP_004385036.1| 212 IVDSVTAHFRAEYVGRGTLADRQQKLNKHLHDLMRFGDLN 251
                                       6777888888888888999999999998888888899875 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00015      0.12      19     120 ..     105     222 ..      96     225 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                                       EEESTTSSHHHHHHHHHHHSSTS........S.EEEEEEESEEHHHHHHHHHHCHH.........SSGGGGEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx........x.xxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxx RF
                       ATP-synt_ab  19 ipgafgvGktvisqslskqsnsd........d.aiiyvgiGergnevaevleefpe.........gtimkrtvlvan 77 
                                       + g+fg+Gkt+++++l+ + +          + +ii      r + + ++++ +p          ++ + + + va 
  gi|330508608|ref|YP_004385036.1| 105 LYGEFGCGKTQVAHQLAVNIQLPvemgglngSvIIIDTENTFRPERIDQMVKGLPPapdgriwetEDFL-KNINVAR 180
                                       689**************9986558899997544555566666777788888877777765555422233.4444454 PP

                                       ETTS-HHHHHHHHHHHHHHHHHHHHTTSEE.EEEEETHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                       ATP-synt_ab  78 tsnepvaareasiytgitlAEyfrdqgknv.lliadslsrwaeA 120
                                         n+    +++ +  ++ lAE  +d ++ v lli+ds++ + +A
  gi|330508608|ref|YP_004385036.1| 181 AFNS--NHQILLAESAMDLAEKVKDSERPVrLLIVDSVTAHFRA 222
                                       4444..4578889999*********9998857899**9998877 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.2   1.8e+03       5      23 ..     107     125 ..     105     129 .. 0.79
   2 ?   11.6   0.0   0.00019      0.16      56     127 ..     190     262 ..     171     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.2
                              CobU   5 GgarSGKSefAeklaeesk 23 
                                       G   +GK ++A +la + +
  gi|330508608|ref|YP_004385036.1| 107 GEFGCGKTQVAHQLAVNIQ 125
                                       56678*********98765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00019
                              CobU  56 tveepldlaealkeeek.kevvLvDcltlwltnllleeeaek.veekleeeveellealkelkatvvlVsnEvg 127
                                       + e+  dlae++k++e+  + ++vD++t       + + + +  ++kl++++++l++ + +l++ ++lV+n v 
  gi|330508608|ref|YP_004385036.1| 190 LAESAMDLAEKVKDSERpVRLLIVDSVTAHFRAEYVGRGTLAdRQQKLNKHLHDLMR-FGDLNNALILVTNQVM 262
                                       568889******99888899********98887777655333378899999998886.5678999******995 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0028       2.3      17      41 ..      98     121 ..      84     131 .. 0.80
   2 ?    3.0   0.0     0.059        48     112     156 ..     166     210 ..     165     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0028
                                       TSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC  17 elqslvvalvGmgGvGKttlakqil 41 
                                       e q  +v l+G  G+GKt +a+q  
  gi|330508608|ref|YP_004385036.1|  98 ETQ-AIVELYGEFGCGKTQVAHQLA 121
                                       445.89**************99865 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.059
                                       E-SHHH.H.....HHHHCHTTSEEEEEESBCCCCCCS-S-EEEEEE CS
                            NB-ARC 112 Vweeed.wdkigvvlparenrlrvllTTRdeevanavsatsekiev 156
                                       +we+ed +++i+v++  +++  ++ll    +++a++v++ + ++++
  gi|330508608|ref|YP_004385036.1| 166 IWETEDfLKNINVARA-FNSNHQILLAESAMDLAEKVKDSERPVRL 210
                                       8*****8888888887.99*******************97666654 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0011      0.91      49      65 ..       6      22 ..       2      23 .. 0.89
   2 ?    0.6   0.1      0.94   7.7e+02      49      63 ..      39      53 ..      27      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                                      CTTSTT--HHHHHHHHH CS
                             HHH_8 49 ltklpgiGkkiaakiee 65
                                      l++lpg+G+++a+k++e
  gi|330508608|ref|YP_004385036.1|  6 LEDLPGVGPATAEKLRE 22
                                      688************99 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.94
                                      CTTSTT--HHHHHHH CS
                             HHH_8 49 ltklpgiGkkiaaki 63
                                      l +   +G+++aaki
  gi|330508608|ref|YP_004385036.1| 39 LVSAAEVGEATAAKI 53
                                      6666789*******9 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00021      0.17      15      42 ..       1      28 [.       1      33 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                               BAF 15 mgdKevtalaGigevlgkkLeekGfdkA 42
                                      m  K  ++l+G+g+  ++kL+e+Gf+  
  gi|330508608|ref|YP_004385036.1|  1 MAIKLLEDLPGVGPATAEKLREAGFNSI 28
                                      5668899******************975 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00028      0.23      18      44 ..      97     125 ..      76     130 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                                       H..TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  18 l..gdvilLeGdLGaGKTtlvrglakalg 44 
                                       +  ++++ L+G+ G+GKT+ +++la +++
  gi|330508608|ref|YP_004385036.1|  97 MetQAIVELYGEFGCGKTQVAHQLAVNIQ 125
                                       24356799**************9997765 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   0.00027      0.22      17      45 ..      97     125 ..      92     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                          ATPase_2  17 repneiyfiYGpegsGKtaLlkeiienle 45 
                                       +e++ i+ +YG  g+GKt++  +++ n +
  gi|330508608|ref|YP_004385036.1|  97 METQAIVELYGEFGCGKTQVAHQLAVNIQ 125
                                       588999*****************998864 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0015       1.2       1      90 [.     103     224 ..     103     230 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf...............gvnlrdvakenglllevdpe............aldesk 50 
                                       + l G  G+GKt++a+ L+   ++                        en  + e+ ++                  
  gi|330508608|ref|YP_004385036.1| 103 VELYGEFGCGKTQVAHQLAVNIQLpvemgglngsviiidT--------ENTFRPERIDQmvkglppapdgrI----- 166
                                       5689999***********6553335555544443333330........333333333333333332222211..... PP

                            AAA_18  51 rldedkldklldaleenss.........................aleegknlvidghlaelesea 90 
                                               +  d l++++                          +++    l++d++ a+++ e+
  gi|330508608|ref|YP_004385036.1| 167 -------WETEDFLKNINVarafnsnhqillaesamdlaekvkdSERPVRLLIVDSVTAHFRAEY 224
                                       .......1111111111111222223334444455566666664455555668888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2308.86
//
Query:       gi|330508609|ref|YP_004385037.1|  [L=339]
Description: cell surface protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.3e-21   75.0  32.0    6.3e-12   45.3  15.6    2.3  2  NosD        Periplasmic copper-binding protein (NosD)
    2.7e-20   72.8  41.4    1.1e-10   41.6  20.0    3.1  2  Beta_helix  Right handed beta helix region


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3  15.6   7.1e-16   6.3e-12      83     169 ..     117     207 ..      52     209 .. 0.88
   2 !   40.6  14.9   1.9e-14   1.7e-10      38     167 ..     188     330 ..     186     336 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 7.1e-16
                              NosD  83 sGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesn......qkiGi 153
                                        Gi ++s++ n+++ N+++++++ Gi l++ss+n+i +N + n ++Gifl+ns +nti++N+i+s+       ++Gi
  gi|330508609|ref|YP_004385037.1| 117 GGIRITSNN-NVIHRNEVKDSRT-GIVLQESSGNKIFYNDARNGGTGIFLRNSCDNTIERNEISSHgkdslgVSYGI 191
                                       566666555.9***********9.******************************************99999999*** PP

                              NosD 154 lllsssegntiynNyF 169
                                       +ll+ss++n i +N+ 
  gi|330508609|ref|YP_004385037.1| 192 YLLNSSNHNIIRKNII 207
                                       **************85 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 1.9e-14
                              NosD  38 rdgi.lldnssnntitgntienl...ryGihlensesntiedntlssne....sGialmsssnntlenNtisnnen. 105
                                       ++gi ll++s++n i++n i  +   + Gi++  se n ++dn++++++    +G+al +s+n+ +enNt+ +n + 
  gi|330508609|ref|YP_004385037.1| 188 SYGIyLLNSSNHNIIRKNIIDIGgliNGGIMIYCSEFNSVNDNEITGSGlfsgMGVALLESNNCLIENNTVASNGIl 264
                                       5688567778888889997766688999*******************9999999********99**********999 PP

                              NosD 106 .yGillsdssnntisnNti..s.nnnkGiflensssntitgNriesnqkiG..illlsssegntiynN 167
                                        +Gi l +s+nnti +N        +++i + +s++n+i+ N+ +s   +G  i  +++++gn++ +N
  gi|330508609|ref|YP_004385037.1| 265 gQGIRLMFSHNNTIDDNSLccYgPIGQAIAILQSENNRISANQAKSW-HWGrdIE-FEGASGNKLSGN 330
                                       99***************99553467899**************99987.4441155.666667777766 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 !   41.6  20.0   1.2e-14   1.1e-10      32     134 ..      99     207 ..      64     210 .. 0.73
   2 !   38.7  20.0   9.7e-14   8.7e-10      23     136 ..     188     310 ..     183     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.2e-14
                                       S-.EEES-EEES...-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EE CS
                        Beta_helix  32 snvvienneian...nsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylnyssnnti 105
                                       ++++ie+ +  n   + + Gi+i++ +nn+i++n++ d+  +gi l+++s+n i +n+ ++ g+ Gi+l +s +nti
  gi|330508609|ref|YP_004385037.1|  99 DGCLIEGIDAGNssgWHQGGIRITS-NNNVIHRNEVKDSR-TGIVLQESSGNKIFYNDARNGGT-GIFLRNSCDNTI 172
                                       2256666444445556788888886.88888888888888.88888888888888888888887.888888888888 PP

                                       ES-EEESTT......--SEE---TT---EEES-EE CS
                        Beta_helix 106 enNiidnna......gsGividdsssnvtvtnNti 134
                                       e+N i++ +       +Gi++ +ss+ + +++N+i
  gi|330508609|ref|YP_004385037.1| 173 ERNEISSHGkdslgvSYGIYLLNSSNHNIIRKNII 207
                                       88888888888888888888888885555777776 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 9.7e-14
                                       S-SEEE-SSS-.EEES-EEES...-SS-SEEE-TT-S-EEES-EEE---...SEEE-TT--S--EEES-EEES-..S CS
                        Beta_helix  23 gyGiylrgssnvvienneian...nsgsGiyilgssnntisnntisdnn...gggialfgasnnlienneitdn..g 91 
                                       +yGiyl +ssn+ i + +i +       Gi i++s+ n + +n+i++++   g g+al +++n lienn++  n   
  gi|330508609|ref|YP_004385037.1| 188 SYGIYLLNSSNHNIIRKNIIDiggLINGGIMIYCSEFNSVNDNEITGSGlfsGMGVALLESNNCLIENNTVASNgiL 264
                                       79*********55555555555888899**********************************************773 PP

                                       S-SEE-TT-S--EEES-EEESTT...--SEE---TT---EEES-EEES CS
                        Beta_helix  92 gsGiylnyssnntienNiidnna...gsGividdsssnvtvtnNtitn 136
                                       g Gi+l+ s+nnti +N +  ++   g++i i +s+ n++++ N +++
  gi|330508609|ref|YP_004385037.1| 265 GQGIRLMFSHNNTIDDNSL-CCYgpiGQAIAILQSE-NNRISANQAKS 310
                                       449*99999********99.66679***********.99999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); 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:                         2  (0.000111551); expected 0.2 (1e-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: 2470.78
//
Query:       gi|330508610|ref|YP_004385038.1|  [L=508]
Description: putative methanogenesis marker protein 14 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.4e-223  742.4   1.9   1.6e-223  742.2   1.9    1.0  1  DUF2114   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
      0.023   14.7   0.1      0.045   13.7   0.1    1.4  1  Borealin  Cell division cycle-associated protein 8


Domain annotation for each model (and alignments):
>> DUF2114  Uncharacterized protein conserved in archaea (DUF2114)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  742.2   1.9  1.7e-227  1.6e-223       1     448 [.      30     478 ..      30     479 .. 0.99

  Alignments for each domain:
  == domain 1  score: 742.2 bits;  conditional E-value: 1.7e-227
                           DUF2114   1 eyyivasvelGntttkciltatnletgktyllnktvkmtrdvrkpkegeevfgktlagveltresvaelvrdtlles 77 
                                       ++yivasve+Gntttk+iltat+l+tgkty++nktvkmtrdvr+pk+gee+f++t++g++lt+esvaelv++tl+es
  gi|330508610|ref|YP_004385038.1|  30 PFYIVASVEVGNTTTKSILTATDLNTGKTYIVNKTVKMTRDVRPPKPGEEIFAHTINGTPLTKESVAELVKNTLIES 106
                                       79*************************************************************************** PP

                           DUF2114  78 lkkakldieedldfvvrstGvvagfdspeevgelikaladGCleagvppkkmtpamskenlpeklrkyslldkvvfd 154
                                       +++a+ldi++dl+fvvrstGvva++dspe+vg +i+ala+GCl+agvpp+ mtpams++n+ ek+++y++++kv+f+
  gi|330508610|ref|YP_004385038.1| 107 HDRARLDIKTDLNFVVRSTGVVAELDSPEQVGIFIQALAQGCLDAGVPPRLMTPAMSIHNILEKFKRYTMIEKVIFM 183
                                       ***************************************************************************** PP

                           DUF2114 155 GavasvvpPkgktgvevvanemegeLvtaGikegakwtdvdfrnPcisidfGttLdGrivndeePyaktvgnfcGla 231
                                       Gavas++pP+g+tgvevvanemegeL+taGikeg++wtdvdfrnPc+s+dfGttLdGr++++e Pya+t+gn++Gla
  gi|330508610|ref|YP_004385038.1| 184 GAVASCFPPQGSTGVEVVANEMEGELATAGIKEGSRWTDVDFRNPCLSMDFGTTLDGRVTSEELPYAHTIGNLLGLA 260
                                       ***************************************************************************** PP

                           DUF2114 232 GaipdaivrGtglvdkklgaaldlfkekkkkkkkkkkikeyaekihelidiekvPkdrerfGtvPvdakaaeeagvv 308
                                       Gaipda+v+Gtglvd+k+ga+ld+f+    k    k++++ya++i+el+ iekvP +r+++G vPv+++aa++++vv
  gi|330508610|ref|YP_004385038.1| 261 GAIPDAVVQGTGLVDRKIGATLDIFDAGL-KPDYGKEAQAYADRIDELVIIEKVPLNRKKYGLVPVNPDAAAKNNVV 336
                                       **************************766.7889999**************************************** PP

                           DUF2114 309 liGcdvgengsdlekleeigaei..lekeglkvllavldevsakivkrlievaveeglveektaiGitGragitGkk 383
                                       liGcdvg ngsdlekl+ iga+i  +++++lkvl+ +ld  +a++++rl++v veeg+v+ ktaiG+tGragitG+k
  gi|330508610|ref|YP_004385038.1| 337 LIGCDVGVNGSDLEKLSGIGADInsTKSRDLKVLFGALDLAMARVARRLVQVGVEEGIVTGKTAIGVTGRAGITGNK 413
                                       **********************95567889*********************************************** PP

                           DUF2114 384 pelilekieelglyddkeenvvfvddgLarGaavmarCmnslGtpknPlGGvrggkCilkkrikl 448
                                       p+lile+i++lglyd++++nvvfvddgLarGaavmarCmns+GtpknPlGG r+g Cilkkr+ +
  gi|330508610|ref|YP_004385038.1| 414 PRLILEEIDKLGLYDHTDRNVVFVDDGLARGAAVMARCMNSMGTPKNPLGGLRKGGCILKKRMSY 478
                                       **************************************************************986 PP

>> Borealin  Cell division cycle-associated protein 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     5e-06     0.045      32      76 ..      58     105 ..      36     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5e-06
                          Borealin  32 tpkvdprlpkt.llRtpkagErvlsls..GSPlaegvvteevanvniP 76 
                                       t  v++ + +t  +R pk+gE ++  +  G+Pl +++v+e v n  i 
  gi|330508610|ref|YP_004385038.1|  58 TYIVNKTVKMTrDVRPPKPGEEIFAHTinGTPLTKESVAELVKNTLIE 105
                                       5557788899999***********98888*******998877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 4056.76
//
Query:       gi|330508611|ref|YP_004385039.1|  [L=240]
Description: hypothetical protein MCON_2847 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-06   27.6   0.1    4.3e-06   26.3   0.1    1.7  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
  ------ inclusion threshold ------
      0.011   15.8   0.0       0.02   15.0   0.0    1.3  1  zf-UDP           Zinc-binding RING-finger


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 !   26.3   0.1   4.8e-10   4.3e-06     100     195 ..      35     115 ..      10     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.8e-10
                                       GSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHCCCHCHST..HHHHHHHTHCHCHHHCC- CS
                   DNA_primase_lrg 100 idklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeilelwkeaftrteekFdkeyrynirhnyGk 176
                                       +++++++ fPpC++++++g   +++  h     l++Fl ++g+++ e+ +lw+ a+++         ++  r+  G 
  gi|330508611|ref|YP_004385039.1|  35 LNAISASEFPPCIKNIIRGP-GGEKGMHRRGAILASFLGQCGWNEKEAGSLWRGAIST--------EERIYRKWFG- 101
                                       4789999***********98.899999999999*********************9554........2233455688. PP

                                       STT--------HHHHHHS. CS
                   DNA_primase_lrg 177 egkrtnyspysCekiltkp 195
                                            n+ +++Ce++  ++
  gi|330508611|ref|YP_004385039.1| 102 -----NMNCPKCETMQRQS 115
                                       .....89999999995444 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.2e-06      0.02      44      72 ..      96     124 ..      89     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-06
                            zf-UDP  44 yerkdgnqsCPqCktrykrlkgsprvegd 72 
                                       y++  gn +CP+C+t+ ++ kg p +  +
  gi|330508611|ref|YP_004385039.1|  96 YRKWFGNMNCPKCETMQRQSKGYPDLGIE 124
                                       566679****************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1956.97
//
Query:       gi|330508612|ref|YP_004385040.1|  [L=214]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   0.0        0.1   12.5   0.0    1.8  1  Y_Y_Y     Y_Y_Y domain
      0.047   13.6   2.9        1.8    8.5   0.3    2.6  2  ChpA-C    ChpA-C


Domain annotation for each model (and alignments):
>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.2e-05       0.1      35      65 ..     183     212 ..     174     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                                       S--SEEEEEEEEEEETTS-B-SS-EEEEEEE CS
                             Y_Y_Y  35 nlppGdYtlkVkakdndgqwnyditslsfti 65 
                                       n ppG+Y + V+a +  g++ ++   l++++
  gi|330508612|ref|YP_004385040.1| 183 NVPPGKYSVNVSAASLQGSETFN-GVLQINV 212
                                       99********************9.6666655 PP

>> ChpA-C  ChpA-C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.003        27      33      50 ..     112     130 ..      99     136 .. 0.85
   2 ?    8.5   0.3    0.0002       1.8       9      26 ..     150     167 ..     141     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.003
                            ChpA-C  33 PVnv.cGntvnvvGllnpa 50 
                                       P+nv  G tvn+ +ll  a
  gi|330508612|ref|YP_004385040.1| 112 PINVtAGSTVNITALLAAA 130
                                       999945********99877 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0002
                            ChpA-C   9 aAeGaaagSpGvlSGNtv 26 
                                       +A+++ ++S G+ SGN v
  gi|330508612|ref|YP_004385040.1| 150 TASATIINSTGINSGNAV 167
                                       689999**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.57
# Mc/sec: 1136.98
//
Query:       gi|330508613|ref|YP_004385041.1|  [L=213]
Description: hypothetical protein MCON_2850 [Methanosaeta concilii GP6]
Scores for 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-18   64.5   0.5    3.6e-17   62.5   0.0    2.2  3  Acylphosphatase  Acylphosphatase
    1.4e-05   25.1   0.6    4.5e-05   23.4   0.5    1.7  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
    0.00062   19.8   7.9       0.01   15.9   4.5    2.7  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    0.00076   19.3   5.1      0.086   12.7   1.5    3.2  3  CdvA             CdvA-like coiled-coil domain
     0.0066   16.6   6.7      0.036   14.2   0.8    3.1  3  DUF5446          Family of unknown function (DUF5446)
     0.0081   16.3   2.8      0.014   15.5   2.8    1.4  1  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
  ------ inclusion threshold ------
      0.014   15.7   4.0       0.19   12.0   2.2    3.0  1  DUF4164          Domain of unknown function (DUF4164)
      0.017   15.4   5.4      0.025   14.8   4.7    1.6  1  DUF1359          Protein of unknown function (DUF1359)
      0.018   14.9  13.3          9    6.2   9.5    3.5  2  HSBP1            Heat shock factor binding protein 1
       0.02   15.4   3.7       0.61   10.7   3.7    2.7  1  YtxH             YtxH-like protein
      0.021   14.4   2.5        0.3   10.6   0.4    2.2  2  Fzo_mitofusin    fzo-like conserved region
      0.021   14.9   7.1      0.034   14.2   7.1    1.3  1  DUF1640          Protein of unknown function (DUF1640)
      0.033   12.9   3.5      0.091   11.4   0.2    1.9  2  DUF4455          Domain of unknown function (DUF4455)
      0.036   13.7   0.9      0.045   13.3   0.9    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
      0.038   14.2   0.6        1.3    9.3   0.1    2.7  3  DUF2703          Domain of unknown function (DUF2703)
      0.048   13.0   5.7      0.074   12.3   5.7    1.2  1  DUF3450          Protein of unknown function (DUF3450)
      0.053   13.6   9.2       0.49   10.4   7.8    2.8  2  DUF1664          Protein of unknown function (DUF1664)
      0.055   13.8   5.7       0.71   10.2   2.4    2.6  2  TBCA             Tubulin binding cofactor A
      0.059   13.5   5.7       0.16   12.0   5.7    1.7  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
      0.059   13.4   2.8        2.8    7.9   0.1    2.5  2  Phasin           Poly(hydroxyalcanoate) granule associated pr
        0.1   12.8   5.9       0.17   12.0   5.9    1.4  1  Fib_alpha        Fibrinogen alpha/beta chain family
       0.12   10.3   3.7       0.15   10.0   3.7    1.1  1  Prominin         Prominin
       0.13   12.5   7.9        5.5    7.4   2.9    3.1  2  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.25   12.2   2.8       0.77   10.6   2.0    2.1  2  FliT             Flagellar protein FliT
        0.3   11.2   3.7        7.6    6.7   0.3    2.8  3  YojJ             Bacterial membrane-spanning protein N-termin
       0.33   11.6   4.7       0.41   11.3   2.4    2.2  2  T3SS_basalb_I    Type III secretion basal body protein I, Ysc
       0.43    9.3   6.3       0.53    9.0   6.3    1.1  1  Tht1             Tht1-like nuclear fusion protein
       0.54   10.7   7.7        1.5    9.3   7.7    1.8  1  Syntaxin_2       Syntaxin-like protein
        1.3    9.5  13.4         14    6.2   0.4    4.9  5  FlaC_arch        Flagella accessory protein C (FlaC)
        2.2    8.6   4.9        3.9    7.7   0.3    2.6  2  DUF1283          Protein of unknown function (DUF1283)
        3.2    7.0   5.4        4.2    6.6   5.4    1.2  1  FAM76            FAM76 protein
        3.3    7.9   6.7         12    6.1   2.0    2.6  2  Herpes_UL14      Herpesvirus UL14-like protein


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 !   62.5   0.0   6.5e-20   3.6e-17       2      83 ..       5      86 ..       4      88 .. 0.95
   2 ?   -1.3   0.1       5.4     3e+03      54      54 ..     150     150 ..     109     185 .. 0.59
   3 ?   -0.9   0.1         4   2.3e+03      39      62 ..     159     183 ..     141     206 .. 0.60

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 6.5e-20
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      +++v+G+V++ g+R+ v ++A+ lglkG+v+Nl+dg+V+i aeg+e+k++ f e++  +++ + v+++e e ++ +++ 
  gi|330508613|ref|YP_004385041.1|  5 TAYVSGNVHQRGYRARVTDIARVLGLKGTVENLDDGRVKIIAEGDEDKLKWFEEAICIKNTLIDVSSIEKEYSTPRDDV 83
                                      689*******************************************************************999998888 PP

                   Acylphosphatase 81 kdF 83
                                      ++F
  gi|330508613|ref|YP_004385041.1| 84 NRF 86
                                      877 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.4
                   Acylphosphatase  54 l 54 
                                        
  gi|330508613|ref|YP_004385041.1| 150 N 150
                                       0 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 4
                   Acylphosphatase  39 Veivaeg.eeekvekfleelksgpp 62 
                                       V+i ++  + +  e ++ee++++ +
  gi|330508613|ref|YP_004385041.1| 159 VMIDLQKdTLSGQETLIEEVRQSRK 183
                                       5555555222334455555555433 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.5     8e-08   4.5e-05      56     150 ..     112     209 ..     101     210 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8e-08
                                       CHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHH...HHHHHHHHHHHHHHHHCHHHHHHHHH CS
                    Apolipoprotein  56 yrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavyaee...lrerlerhvealkarlapyveelrqk 129
                                        ++++++++g ++++++  l+  ++++++ l+ +++++ + l+ +++    l++ + ++ e+l + +   + e++ +
  gi|330508613|ref|YP_004385041.1| 112 AVNNMNQNIGGKIDQMNDNLSDKIDQMNDNLSDKIDQMNDNLSGKMDVmidLQKDTLSGQETLIEEVRQSRKEIKGR 188
                                       567899*************************************999977779************************* PP

                                       HHHHHHHHHH-----..---- CS
                    Apolipoprotein 130 laerleelkeslaphaeevee 150
                                       +++r + l++++a+ + ++++
  gi|330508613|ref|YP_004385041.1| 189 MDQRFDKLESEVAEMKVALKS 209
                                       ************999888775 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 ?   -2.6   0.0       9.1   5.1e+03     107     124 ..      27      43 ..      19      52 .. 0.64
   2 !   15.9   4.5   1.8e-05      0.01      39      95 ..      98     154 ..      89     158 .. 0.80
   3 ?    4.3   0.0     0.069        39      43      81 ..     168     205 ..     157     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 9.1
                      Baculo_PEP_C 107 tLnnllqalnnldlgals 124
                                        L +l  +++nld g ++
  gi|330508613|ref|YP_004385041.1|  27 VL-GLKGTVENLDDGRVK 43 
                                       44.566677777777665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.8e-05
                      Baculo_PEP_C  39 lldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsilt 95 
                                        ld+ +  L++l  +++++ +++  ++d++ +nL+d++ +++d+l+ +++ +n +l+
  gi|330508613|ref|YP_004385041.1|  98 RLDTAADHLKNLIVAVNNMNQNIGGKIDQMNDNLSDKIDQMNDNLSDKIDQMNDNLS 154
                                       4556666666666667776667777*************************9999985 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.069
                      Baculo_PEP_C  43 ietqLnalsedlksllaeldtrldtlltnLtdalnalqd 81 
                                       + +q ++l e+++++ +e++ r+d+ +++L++ +++++ 
  gi|330508613|ref|YP_004385041.1| 168 LSGQ-ETLIEEVRQSRKEIKGRMDQRFDKLESEVAEMKV 205
                                       4443.5677888888888888999999999888887764 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.9   1.6e+03      70      87 ..       7      24 ..       5      29 .. 0.82
   2 ?    6.7   0.4     0.011       6.2      23      68 ..     120     165 ..     111     172 .. 0.70
   3 !   12.7   1.5   0.00015     0.086      22      63 ..     166     207 ..     151     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.9
                              CdvA 70 yasGEidEeaYksaieai 87
                                      y+sG +  + Y++  + i
  gi|330508613|ref|YP_004385041.1|  7 YVSGNVHQRGYRARVTDI 24
                                      99*********9887766 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                              CdvA  23 ikekleealkklkekakelkeklkkrlkeledqikslekalanlki 68 
                                       i  k+++ ++ l +k ++ +++l+ ++++ +d+++    ++++l+ 
  gi|330508613|ref|YP_004385041.1| 120 IGGKIDQMNDNLSDKIDQMNDNLSDKIDQMNDNLSGKMDVMIDLQK 165
                                       4456777777777888888888888888888877777666776665 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00015
                              CdvA  22 eikekleealkklkekakelkeklkkrlkeledqikslekal 63 
                                       +     e+ ++++++ +ke+k ++++r ++le+++++++ al
  gi|330508613|ref|YP_004385041.1| 166 DTLSGQETLIEEVRQSRKEIKGRMDQRFDKLESEVAEMKVAL 207
                                       55555688899***************************9987 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.75   4.2e+02      21      66 ..      69     118 ..      62     121 .. 0.67
   2 ?    3.6   0.6      0.14        77      16      45 ..     119     148 ..      94     165 .. 0.60
   3 !   14.2   0.8   6.5e-05     0.036      26      59 ..     172     205 ..     156     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.75
                           DUF5446  21 ltevEkelse...avnet.eaekeekeeerldllekElkdLvlCigklek 66 
                                       ++++Eke s     vn+  +   + + + rld   + lk+L + ++++ +
  gi|330508613|ref|YP_004385041.1|  69 VSSIEKEYSTprdDVNRFyKLVDRGETDSRLDTAADHLKNLIVAVNNMNQ 118
                                       66777766542224555413455677888999999999999888887765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.14
                           DUF5446  16 eiEeeltevEkelseavneteaekeekeee 45 
                                       +i  +++++  +ls ++ + +     k+++
  gi|330508613|ref|YP_004385041.1| 119 NIGGKIDQMNDNLSDKIDQMNDNLSDKIDQ 148
                                       444445555555554444444433333333 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 6.5e-05
                           DUF5446  26 kelseavneteaekeekeeerldllekElkdLvl 59 
                                       + l e v++ ++e +   ++r d+le+E++++++
  gi|330508613|ref|YP_004385041.1| 172 ETLIEEVRQSRKEIKGRMDQRFDKLESEVAEMKV 205
                                       678899*************************876 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 !   15.5   2.8   2.5e-05     0.014      31     123 ..     106     198 ..      94     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-05
                         ApoLp-III  31 senlvdqlkqvikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqkla 107
                                        +nl+  ++++ +++  ++ + +d+l   +++++++++   d+++ + ++    + +lq+   sg ++l++e+ +  
  gi|330508613|ref|YP_004385041.1| 106 LKNLIVAVNNMNQNIGGKIDQMNDNLSDKIDQMNDNLSDKIDQMNDNLSGKMDVMIDLQKDTLSGQETLIEEVRQSR 182
                                       57888999**************************************9999999999********************* PP

                         ApoLp-III 108 eslkensqeakeklak 123
                                       +++k  + +  +kl+ 
  gi|330508613|ref|YP_004385041.1| 183 KEIKGRMDQRFDKLES 198
                                       ****999988888775 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.2   0.00034      0.19       3      66 ..     132     204 ..     117     210 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00034
                           DUF4164   3 tkeleaaltrLeaaldsLEkavdrrleaerkr..........deleaeiealgedrs....RLaeeLdqaearaarl 65 
                                       +++++++ ++L+ ++d++ + +  ++                +  e+ ie++++ r+    R+++++d+ e + a++
  gi|330508613|ref|YP_004385041.1| 132 SDKIDQMNDNLSDKIDQMNDNLSGKM-----DvmidlqkdtlSGQETLIEEVRQSRKeikgRMDQRFDKLESEVAEM 203
                                       45566666666666665554444433.....0333334444766666667777776622226666666666666665 PP

                           DUF4164  66 e 66 
                                       +
  gi|330508613|ref|YP_004385041.1| 204 K 204
                                       5 PP

>> DUF1359  Protein of unknown function (DUF1359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   4.7   4.4e-05     0.025      15      94 ..     100     179 ..      92     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.4e-05
                           DUF1359  15 eqkiarlkdvihdvkdqtelvklleddlksneikkddkleleltdrfsvlkssvkinvGtlisllkdniedntalis 91 
                                       ++    lk++i +v +  + +    d++++n   k d+++ +l+d++  ++ ++  ++  +i l kd + +  +li+
  gi|330508613|ref|YP_004385041.1| 100 DTAADHLKNLIVAVNNMNQNIGGKIDQMNDNLSDKIDQMNDNLSDKIDQMNDNLSGKMDVMIDLQKDTLSGQETLIE 176
                                       566678**********999999999***************************************************9 PP

                           DUF1359  92 elv 94 
                                       e+ 
  gi|330508613|ref|YP_004385041.1| 177 EVR 179
                                       975 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 ?    6.2   9.5     0.016         9       3      44 ..     109     154 ..     106     162 .. 0.65
   2 ?    3.8   0.1     0.095        53      32      46 ..     189     203 ..     183     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.016
                             HSBP1   3 LtavVenlLqqlqdkFqtmsdqilsriDdM....ssriDdLEksia 44 
                                       L  +V n+ q++  k ++m d++ ++iD+M    s +iD++  +++
  gi|330508613|ref|YP_004385041.1| 109 LIVAVNNMNQNIGGKIDQMNDNLSDKIDQMndnlSDKIDQMNDNLS 154
                                       5666777777777777778777777777773333445555555555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.095
                             HSBP1  32 MssriDdLEksiadl 46 
                                       M +r D LE  +a++
  gi|330508613|ref|YP_004385041.1| 189 MDQRFDKLESEVAEM 203
                                       778999999999876 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.7    0.0011      0.61      44      74 ..     123     153 ..      71     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0011
                              YtxH  44 lleeakekakekaedlkekvkekadelkekv 74 
                                        +++++++ ++k++++ +++++k+d++ +++
  gi|330508613|ref|YP_004385041.1| 123 KIDQMNDNLSDKIDQMNDNLSDKIDQMNDNL 153
                                       4444444444444444444444444444432 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   0.00054       0.3      76     132 ..     102     158 ..      99     177 .. 0.79
   2 ?    4.0   0.4      0.06        33      91     114 ..     181     204 ..     156     212 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00054
                     Fzo_mitofusin  76 atekLrlivsltsancshqvqqelsstfarlcqqvdetekeleeeikelekeie.kle 132
                                       a+++L+  + +  +n+++ +  +++++ ++l+ ++d+++++l+++i++++ +++ k++
  gi|330508613|ref|YP_004385041.1| 102 AADHLKNLI-VAVNNMNQNIGGKIDQMNDNLSDKIDQMNDNLSDKIDQMNDNLSgKMD 158
                                       556666555.467899999******************************998753455 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.06
                     Fzo_mitofusin  91 cshqvqqelsstfarlcqqvdete 114
                                        ++ ++ ++++ f++l+++v e++
  gi|330508613|ref|YP_004385041.1| 181 SRKEIKGRMDQRFDKLESEVAEMK 204
                                       222233333333333333333333 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   7.1   6.1e-05     0.034      42     151 ..      89     205 ..      81     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.1e-05
                           DUF1640  42 lvskselekseylqkaalselrkevqisersefaalrseteklqreleklkqkLreeidklkadirldlnleKgrir 118
                                       lv + e ++ + +   +l++l   v +++++   ++ + +++l  ++++++ +L ++id+++++   +++      +
  gi|330508613|ref|YP_004385041.1|  89 LVDRGETDSRLDTAADHLKNLIVAVNNMNQNIGGKIDQMNDNLSDKIDQMNDNLSDKIDQMNDNLSGKMDVMIDLQK 165
                                       6778888888888888999999999999999999******************************9988888888888 PP

                           DUF1640 119 eelakleaki.......qelnnkidrevsalrteiEsvKl 151
                                       + l+ +e  i       +e++ ++d+   +l +e+ ++K+
  gi|330508613|ref|YP_004385041.1| 166 DTLSGQETLIeevrqsrKEIKGRMDQRFDKLESEVAEMKV 205
                                       8888888888666666677777777777777777777775 PP

>> DUF4455  Domain of unknown function (DUF4455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00016     0.091     335     399 ..      96     160 ..      69     168 .. 0.81
   2 ?    8.3   3.0    0.0014      0.81      20     103 ..     121     202 ..     112     209 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                           DUF4455 335 aketeaqsesLfkffqeaaqlwevheaklekqeeelekkleqlrqkhdeenqakeaeLdklldkl 399
                                       + ++    ++L + +  + ++++    k+ +++++l++k++q  ++ ++++++++++L  ++d +
  gi|330508613|ref|YP_004385041.1|  96 DSRLDTAADHLKNLIVAVNNMNQNIGGKIDQMNDNLSDKIDQMNDNLSDKIDQMNDNLSGKMDVM 160
                                       55666677888888899999999999999*****************************9999977 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0014
                           DUF4455  20 asiseeveplileageellkklsesdeeiek.lfkkleddedlekltiqelqelwdkVaeeslkrkswIkeldetLe 95 
                                           +++ +++ +++ ++ + ls++ +++++ l +k+   + + +l++++l    + ++e ++ rk+   ++d++++
  gi|330508613|ref|YP_004385041.1| 121 GGKIDQMNDNLSDKIDQMNDNLSDKIDQMNDnLSGKM---DVMIDLQKDTLSGQETLIEEVRQSRKEIKGRMDQRFD 194
                                       3333344444444444444444444333333022233...4556666777777666777666666666667777777 PP

                           DUF4455  96 klEkeRae 103
                                       klE+e ae
  gi|330508613|ref|YP_004385041.1| 195 KLESEVAE 202
                                       77777665 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.9     8e-05     0.045     144     247 ..      94     198 ..      65     211 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8e-05
                      Exonuc_VII_L 144 eleeqleelerrlek...aikrlleekkqrleklasrlk.speellerkrqrldeleerleralkkqlkkkrerlee 216
                                       e  ++l++++++l++   a++++ ++   ++++++ +l+ + +++ ++ ++++d+++++l+ +++  ++ ++ +l+ 
  gi|330508613|ref|YP_004385041.1|  94 ETDSRLDTAADHLKNlivAVNNMNQNIGGKIDQMNDNLSdKIDQMNDNLSDKIDQMNDNLSGKMDVMIDLQKDTLSG 170
                                       55566666666555533255666677778888888888745555555569999999999999999888888888888 PP

                      Exonuc_VII_L 217 lkerlkekleekkerl.kklkerlelleekke 247
                                        ++ ++ ++++ ++++  ++ +r+++le   +
  gi|330508613|ref|YP_004385041.1| 171 QETLIE-EVRQSRKEIkGRMDQRFDKLE---S 198
                                       883333.344444444222222222222...2 PP

>> DUF2703  Domain of unknown function (DUF2703)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.92   5.1e+02       7      51 ..      88     132 ..      85     135 .. 0.77
   2 ?    9.3   0.1    0.0022       1.3      12      60 ..     129     178 ..     123     188 .. 0.82
   3 ?    2.1   0.0      0.38   2.1e+02      16      41 ..     187     212 ..     178     213 .] 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.92
                           DUF2703   7 hldlegetCercgeTgktleeavkelkeaLealgievelekvels 51 
                                        l++ get +r +++ + l++++  +++  +++g ++   + +ls
  gi|330508613|ref|YP_004385041.1|  88 KLVDRGETDSRLDTAADHLKNLIVAVNNMNQNIGGKIDQMNDNLS 132
                                       566678899999999999999999999988888888776666665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0022
                           DUF2703  12 getCercgeTgktleeavkelkeaLe.algievelekvelseeelarefl 60 
                                       ++  +++++++++l + ++++++ L+ ++++ + l+k +ls +e   e +
  gi|330508613|ref|YP_004385041.1| 129 DNLSDKIDQMNDNLSDKIDQMNDNLSgKMDVMIDLQKDTLSGQETLIEEV 178
                                       5678899******************8579************999886633 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.38
                           DUF2703  16 ercgeTgktleeavkelkeaLealgi 41 
                                        r+++  ++le+ v+e+k aL++ gi
  gi|330508613|ref|YP_004385041.1| 187 GRMDQRFDKLESEVAEMKVALKSKGI 212
                                       5788888999***********99987 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.7   0.00013     0.074      15     115 ..     100     202 ..      95     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyr.alkeeleslevyn.eqlerlvasqeqeiasleeqie 89 
                                       ++++d +++   + ++  + +  kid+++d+ ++  ++++ +l++++++++     +++ +++ q+ +++  e+ ie
  gi|330508613|ref|YP_004385041.1| 100 DTAADHLKNLIVAVNNMNQNIGGKIDQMNDNLSDKIDQMNdNLSDKIDQMNDNLsGKMDVMIDLQKDTLSGQETLIE 176
                                       677889999999999999999999999999999999988625888888887655158999***************** PP

                           DUF3450  90 eieeierelvpllekmidrLeqfvel 115
                                       e+++ ++e++  +++  d+Le  v++
  gi|330508613|ref|YP_004385041.1| 177 EVRQSRKEIKGRMDQRFDKLESEVAE 202
                                       *********************99875 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0         1   5.9e+02      80     111 ..      60      91 ..      29     102 .. 0.81
   2 ?   10.4   7.8   0.00087      0.49      44     120 ..     122     203 ..      95     209 .. 0.62

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1
                           DUF1664  80 eiskeikeevtevredlseigedvesvkeave 111
                                        ++k++  +v++++++ s+ ++dv+   ++v 
  gi|330508613|ref|YP_004385041.1|  60 ICIKNTLIDVSSIEKEYSTPRDDVNRFYKLVD 91 
                                       45678888999999999999999999988886 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00087
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqke....iskeikeevtevredlseigedve.svkeavegles 115
                                        ++ +  +++s+++ +  ++Ls++id+++++l   ++    ++k++ +  +++ e++++ +++++  +++ + +les
  gi|330508613|ref|YP_004385041.1| 122 GKIDQMNDNLSDKIDQMNDNLSDKIDQMNDNLSGKMDvmidLQKDTLSGQETLIEEVRQSRKEIKgRMDQRFDKLES 198
                                       23444446778999999999999999988876555540000455554444455555555555554356677777777 PP

                           DUF1664 116 kleri 120
                                       +++++
  gi|330508613|ref|YP_004385041.1| 199 EVAEM 203
                                       77766 PP

>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.068        38      16      78 ..      70     138 ..      61     155 .. 0.62
   2 ?   10.2   2.4    0.0013      0.71      40      79 ..     165     204 ..     140     211 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.068
                              TBCA  16 asYekEleeqearleklka.......dgded.eydlkkqeevleetkamipdlkkrlekavekLeelleee 78 
                                       +s ekE ++ +  ++++ +       d+    +    + ++++   ++m +++  ++++  ++L++ +++ 
  gi|330508613|ref|YP_004385041.1|  70 SSIEKEYSTPRDDVNRFYKlvdrgetDS--RlDTAADHLKNLIVAVNNMNQNIGGKIDQMNDNLSDKIDQM 138
                                       4555555555555555555444331133..23555566677777778888888888888888887777766 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0013
                              TBCA  40 eydlkkqeevleetkamipdlkkrlekavekLeelleeee 79 
                                       + +l  qe+++ee ++  +++k r+++ ++kLe+ ++e +
  gi|330508613|ref|YP_004385041.1| 165 KDTLSGQETLIEEVRQSRKEIKGRMDQRFDKLESEVAEMK 204
                                       2345567***************************998874 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   5.7   0.00029      0.16      79     184 ..      94     205 ..      48     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00029
                           UPF0242  79 eldeglktkeealeelqeeeeeLkee....ldakeee.lerlkeenqqLqekleaiae....dfeelkleleeqLae 146
                                       e+d  l+t +++l++l    ++++++    +d+++ + + +  + n +L+ k  ++       ++ +    +++L  
  gi|330508613|ref|YP_004385041.1|  94 ETDSRLDTAADHLKNLIVAVNNMNQNiggkIDQMNDNlSDKIDQMNDNLSDKIDQMNDnlsgKMDVMIDLQKDTLSG 170
                                       44556666667777665555555555555588887651568899999999999997665555455555566889999 PP

                           UPF0242 147 kqellqeyqetieeqrsvlekrqdqieqLeskVrDlny 184
                                       +++l++e +++ +e +  +++r d   +Les V  ++ 
  gi|330508613|ref|YP_004385041.1| 171 QETLIEEVRQSRKEIKGRMDQRFD---KLESEVAEMKV 205
                                       999999999999999999988866...57888777765 PP

>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0051       2.8      37      92 ..      86     146 ..      76     160 .. 0.48
   2 ?    5.2   0.6     0.036        20      37      69 ..     171     203 ..     154     212 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0051
                            Phasin  37 feaLvkeGeklekktkkvaeekleevr.......esvkskveevkekaeeqwdklekafderv 92 
                                       f +Lv++Ge+  +   ++a+++l+++        +++  k+++++++++++ d+++  + +++
  gi|330508613|ref|YP_004385041.1|  86 FYKLVDRGETDSRL--DTAADHLKNLIvavnnmnQNIGGKIDQMNDNLSDKIDQMNDNLSDKI 146
                                       55677777654442..22222222222000022244444444444444444444444444444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.036
                            Phasin  37 feaLvkeGeklekktkkvaeekleevresvksk 69 
                                        e+L++e ++ +k+ k  ++++ ++++++v ++
  gi|330508613|ref|YP_004385041.1| 171 QETLIEEVRQSRKEIKGRMDQRFDKLESEVAEM 203
                                       345555555555555555555555555544444 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 ?   12.0   5.9   0.00031      0.17      30     119 ..      96     190 ..      89     209 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00031
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHCCCHHHHHHHCCH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.....dnvikksskeleeeilrlketidaqe 101
                                       ++ +++  ++l+n +  ++n+++++   + +++d l +k  + +dn     d++  ++s +++  i   k+t++ qe
  gi|330508613|ref|YP_004385041.1|  96 DSRLDTAADHLKNLIVAVNNMNQNIGGKIDQMNDNLSDKIDQMNDNlsdkiDQMNDNLSGKMDVMIDLQKDTLSGQE 172
                                       56677788899999999999999999999999999999999999988444445555555555555555567777777 PP

                                       HHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 102 snirvLqnvlesneqkiq 119
                                       + i++ ++  ++ + ++ 
  gi|330508613|ref|YP_004385041.1| 173 TLIEEVRQSRKEIKGRMD 190
                                       777777777776665553 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.7   0.00027      0.15     245     335 ..     100     185 ..      80     209 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
                          Prominin 245 lenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcl..dqlpn 319
                                        ++  + k+++ +vn++ +++  + +q++d+l++  +++n+ ls+++      +++++l+  k+d+  +l  d+l+ 
  gi|330508613|ref|YP_004385041.1| 100 DTAADHLKNLIVAVNNMNQNIGGKIDQMNDNLSDKIDQMNDNLSDKID-----QMNDNLSG-KMDVMIDLqkDTLSG 170
                                       334444455555555555555555555555555555555555555444.....22222222.222222222233444 PP

                          Prominin 320 vdevlealeevletnl 335
                                        ++++e++++  ++ +
  gi|330508613|ref|YP_004385041.1| 171 QETLIEEVRQSRKE-I 185
                                       44444444433221.1 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 ?    7.3   0.5      0.01       5.8      24      50 ..     112     138 ..      95     140 .. 0.77
   2 ?    7.4   2.9    0.0098       5.5      25      93 ..     135     198 ..     133     209 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.01
                           BLOC1_2  24 lLeklNeaasekykklkdvaaslekkl 50 
                                        ++++N++   k+++++d++++  +++
  gi|330508613|ref|YP_004385041.1| 112 AVNNMNQNIGGKIDQMNDNLSDKIDQM 138
                                       578999999999999999887755555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0098
                           BLOC1_2  25 LeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                       + ++N + s k+++++d++++  + + +l++  ++l+ + + i+++ ++ +e++    ++D+   +LE+
  gi|330508613|ref|YP_004385041.1| 135 IDQMNDNLSDKIDQMNDNLSGKMDVMIDLQK--DTLSGQETLIEEVRQSRKEIK---GRMDQRFDKLES 198
                                       5689999999999999998888888888877..455555555555554444333...234444444443 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       3.3   1.8e+03      42      75 ..     105     138 ..      88     154 .. 0.56
   2 ?   10.6   2.0    0.0014      0.77      35      76 ..     163     204 ..     129     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHT CS
                              FliT  42 ekrellrrilandaeirallqprldelqkllgal 75 
                                       ++ +l+  +   ++ i   +++  d l+++++++
  gi|330508613|ref|YP_004385041.1| 105 HLKNLIVAVNNMNQNIGGKIDQMNDNLSDKIDQM 138
                                       4444555444444444444444444444444444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0014
                                       --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTH CS
                              FliT  35 lspaereekrellrrilandaeirallqprldelqkllgalr 76 
                                       l  +    ++ l++++++  +ei+ ++++r d+l++++ +++
  gi|330508613|ref|YP_004385041.1| 163 LQKDTLSGQETLIEEVRQSRKEIKGRMDQRFDKLESEVAEMK 204
                                       56666778899*************************998876 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.076        43      13      52 ..      94     133 ..      92     138 .. 0.87
   2 ?    0.5   0.1       1.2   6.5e+02      13      34 ..     130     151 ..     126     161 .. 0.71
   3 ?    6.7   0.3     0.014       7.6       3      35 ..     178     210 ..     176     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.076
                              YojJ  13 klkeeLeqiekeleevlkaldeedeClLcelesirekfae 52 
                                       ++   L  +  +l++ + a ++ ++ + ++++++ +++++
  gi|330508613|ref|YP_004385041.1|  94 ETDSRLDTAADHLKNLIVAVNNMNQNIGGKIDQMNDNLSD 133
                                       566778899999*********************9999876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                              YojJ  13 klkeeLeqiekeleevlkalde 34 
                                       +l  ++ q   +l++ +++++ 
  gi|330508613|ref|YP_004385041.1| 130 NLSDKIDQMNDNLSDKIDQMND 151
                                       5666777777777777777764 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.014
                              YojJ   3 ekcleeelkeklkeeLeqiekeleevlkaldee 35 
                                         ++ +e+k  + + + + e e+ e+  al+++
  gi|330508613|ref|YP_004385041.1| 178 VRQSRKEIKGRMDQRFDKLESEVAEMKVALKSK 210
                                       578999************************987 PP

>> T3SS_basalb_I  Type III secretion basal body protein I, YscI, HrpB, PscI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.4   0.00073      0.41       2      74 ..      82     169 ..      51     175 .. 0.66
   2 ?    0.8   0.1       1.4   7.8e+02      21      49 ..     172     200 ..     163     209 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00073
                     T3SS_basalb_I   2 dverFsqamsgs.................avlpespntlgdallqglsslkegldqameqvqrtlekakdgndpadl 61 
                                       dv+rF ++                     ++ +++++++g ++ q   +l++++dq  +++++++++    ++ +  
  gi|330508613|ref|YP_004385041.1|  82 DVNRFYKLVDRGetdsrldtaadhlknliVAVNNMNQNIGGKIDQMNDNLSDKIDQMNDNLSDKIDQM--NDNLSGK 156
                                       56666666666566666666555554444333445555555555555555555555555555555555..4588888 PP

                     T3SS_basalb_I  62 lkaqmsLsqatlq 74 
                                       ++++ +L + tl+
  gi|330508613|ref|YP_004385041.1| 157 MDVMIDLQKDTLS 169
                                       8888888887776 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.4
                     T3SS_basalb_I  21 ntlgdallqglsslkegldqameqvqrtl 49 
                                       +tl +++ q  +++k ++dq  ++++ ++
  gi|330508613|ref|YP_004385041.1| 172 ETLIEEVRQSRKEIKGRMDQRFDKLESEV 200
                                       34444444444444444555444444444 PP

>> Tht1  Tht1-like nuclear fusion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   6.3   0.00094      0.53     169     274 ..      96     210 ..      63     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00094
                              Tht1 169 dsfletkllhlrdsesvlddlarri....dkfdgklrs...vlendlkdirfkvndeimglvelets.eqegmvlek 237
                                       ds l+t   hl++    ++++++ i    d+ +++l +    ++++l+d   ++nd++ g + +  + +++ +  + 
  gi|330508613|ref|YP_004385041.1|  96 DSRLDTAADHLKNLIVAVNNMNQNIggkiDQMNDNLSDkidQMNDNLSDKIDQMNDNLSGKMDVMIDlQKDTLSGQE 172
                                       566899999997776666666665411113333333335445677899999999****9988766541556788899 PP

                              Tht1 238 eilekikqlksevd.dvnsiladlieelagykndlkek 274
                                        ++e+++q ++e+   +++ + +l  e+a  k  lk+k
  gi|330508613|ref|YP_004385041.1| 173 TLIEEVRQSRKEIKgRMDQRFDKLESEVAEMKVALKSK 210
                                       9************8458999999999***999999987 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   7.7    0.0026       1.5       7      76 ..     105     175 ..      99     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0026
                        Syntaxin_2   7 kinsnvstleklvkqLgtkkd..teelreklhelieeinelikktnellk.klsqldnsssds...qqklqkekLk 76 
                                       ++ +++   +++ + +g k d  +++l +k++++ +++++ i ++n++l+ k++ +++ ++d    q     e L 
  gi|330508613|ref|YP_004385041.1| 105 HLKNLIVAVNNMNQNIGGKIDqmNDNLSDKIDQMNDNLSDKIDQMNDNLSgKMDVMIDLQKDTlsgQ-----ETLI 175
                                       5789999************87779**********************999834455555443334441.....3333 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 ?   -0.8   0.0       3.8   2.2e+03      15      32 ..      68      85 ..      56      92 .. 0.71
   2 ?    6.2   0.4     0.025        14      13      37 ..      96     120 ..      90     136 .. 0.63
   3 ?    5.4   1.4     0.042        24      19      37 ..     135     153 ..     122     164 .. 0.60
   4 ?    1.5   1.1       0.7   3.9e+02       1      36 [.     145     181 ..     145     191 .. 0.65
   5 ?    1.8   0.1      0.56   3.2e+02       1      16 [.     192     207 ..     187     210 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.8
                         FlaC_arch 15 eletvkkeneelsksvee 32
                                       +++++ke +  +++v++
  gi|330508613|ref|YP_004385041.1| 68 DVSSIEKEYSTPRDDVNR 85
                                      677788887777777765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.025
                         FlaC_arch  13 steletvkkeneelsksveelkenV 37 
                                       +++l+t+ + +++l   v+++++n+
  gi|330508613|ref|YP_004385041.1|  96 DSRLDTAADHLKNLIVAVNNMNQNI 120
                                       5566666666666666666666666 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.042
                         FlaC_arch  19 vkkeneelsksveelkenV 37 
                                       + + n++ls++++++++n 
  gi|330508613|ref|YP_004385041.1| 135 IDQMNDNLSDKIDQMNDNL 153
                                       3344566666666666665 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.7
                         FlaC_arch   1 ridelEnkls.klsteletvkkeneelsksveelken 36 
                                       +id++   ls k++++++  k++++  ++ +ee+ ++
  gi|330508613|ref|YP_004385041.1| 145 KIDQMNDNLSgKMDVMIDLQKDTLSGQETLIEEVRQS 181
                                       5666666664367777777777777777777776665 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.56
                         FlaC_arch   1 ridelEnklsklstel 16 
                                       r d+lE+++ ++++ l
  gi|330508613|ref|YP_004385041.1| 192 RFDKLESEVAEMKVAL 207
                                       4566777776666655 PP

>> DUF1283  Protein of unknown function (DUF1283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.7      0.32   1.8e+02      31      50 ..     132     151 ..     104     174 .. 0.62
   2 ?    7.7   0.3     0.007       3.9      25      59 ..     176     210 ..     163     213 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.32
                           DUF1283  31 Rnkvnkrvekefdkadkaid 50 
                                        +k+++ ++   dk+d+  d
  gi|330508613|ref|YP_004385041.1| 132 SDKIDQMNDNLSDKIDQMND 151
                                       33444444444444443333 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.007
                           DUF1283  25 netrsLRnkvnkrvekefdkadkaidkrdkCeksa 59 
                                       +e r+ R+ +  r++++fdk + ++ +     ks+
  gi|330508613|ref|YP_004385041.1| 176 EEVRQSRKEIKGRMDQRFDKLESEVAEMKVALKSK 210
                                       678999*****************999887777776 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   5.4    0.0076       4.2     198     288 ..     115     203 ..      63     211 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0076
                             FAM76 198 eekesnetskksldsnssdhlvavt.qLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkeleke 273
                                       +++++ + + ++++ n sd++ +++ +L ++i +++ +l+ k  ++++ +k   + +  l+   +e+r+  ke++  
  gi|330508613|ref|YP_004385041.1| 115 NMNQNIGGKIDQMNDNLSDKIDQMNdNLSDKIDQMNDNLSGKMDVMIDLQKDTLSGQETLI---EEVRQSRKEIKGR 188
                                       2222222233355555555555554235555555555555554444444443222111111...1222222333333 PP

                             FAM76 274 akekieklekkirel 288
                                       ++++ +kle++++e+
  gi|330508613|ref|YP_004385041.1| 189 MDQRFDKLESEVAEM 203
                                       333344444443333 PP

>> Herpes_UL14  Herpesvirus UL14-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.0     0.021        12      91     117 ..     126     152 ..      84     175 .. 0.73
   2 ?    4.1   0.3     0.093        52      73     114 ..     166     207 ..     155     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.021
                       Herpes_UL14  91 ylspkllerldatedkllekedsLeea 117
                                        ++ +l++++d+ +d+l +k+d++++ 
  gi|330508613|ref|YP_004385041.1| 126 QMNDNLSDKIDQMNDNLSDKIDQMNDN 152
                                       466677777777777777777777664 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.093
                       Herpes_UL14  73 akveeqaelrsiLkanRrylspkllerldatedkllekedsL 114
                                         + +q  l +++   R+ ++  + +r+d+ e +++e +  L
  gi|330508613|ref|YP_004385041.1| 166 DTLSGQETLIEEVRQSRKEIKGRMDQRFDKLESEVAEMKVAL 207
                                       567899999999********************9999987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1276  (0.0711696); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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: 0.77u 0.39s 00:00:01.16 Elapsed: 00:00:00.56
# Mc/sec: 1142.31
//
Query:       gi|330508614|ref|YP_004385042.1|  [L=436]
Description: IS66 family element, transposase [Methanosaeta concilii GP6]
Scores for complete 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-48  163.1   0.0    1.5e-47  162.4   0.0    1.3  1  DDE_Tnp_IS66   Transposase IS66 family
    1.1e-05   25.7   4.6    1.1e-05   25.7   4.6    2.1  1  zf-IS66        zinc-finger binding domain of transposase IS66
    0.00029   20.0   0.0    0.00038   19.6   0.0    1.1  1  Med1           Mediator of RNA polymerase II transcription su
     0.0018   18.2   0.5     0.0044   17.0   0.5    1.6  1  DZR            Double zinc ribbon
      0.002   18.4   0.0     0.0045   17.2   0.0    1.7  1  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
       0.15   12.5   4.1        0.2   12.1   2.7    1.9  2  ZapB           Cell division protein ZapB
       0.26   11.1   2.6       0.72    9.7   2.6    1.7  1  DivIC          Septum formation initiator
       0.64   10.1   4.5       0.31   11.1   2.1    1.8  2  MCC-bdg_PDZ    PDZ domain of MCC-2 bdg protein for Usher synd
        2.2    8.1   6.5        2.4    8.0   0.1    2.4  2  zinc_ribbon_2  zinc-ribbon domain
        2.4    8.5   6.6        3.2    8.0   3.3    2.4  2  HALZ           Homeobox associated leucine zipper
        3.2    7.3   6.9        6.4    6.3   0.1    2.4  2  zf-ribbon_3    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 !  162.4   0.0   9.3e-51   1.5e-47       2     280 ..     147     406 ..     146     408 .. 0.88

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 9.3e-51
                      DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtl 77 
                                       + +g++++A++++ +y+d lP +++++ l+r  G++ls++t+ ++++ra+e+++p ++a+ ++++ ++++ +DET++
  gi|330508614|ref|YP_004385042.1| 147 GKFGNNVIAQATLMRYEDRLPHRKIQDTLKRIhGLALSPATIFDLTRRAGEAVRPEYDAILERIRGAPILYVDETGI 223
                                       57999************************************************************************ PP

                      DDE_Tnp_IS66  78 rvlkpgrgkgkksylWvyvtdkrkpavlfeyspsRggevaealLag.fkGvlvsDgyagYnklaeeqvthalCwaHl 153
                                               +g+k+++W++ t      ++f + +sRg++v  ++L+  fkG++v+Dg+++Y +++    +++ CwaHl
  gi|330508614|ref|YP_004385042.1| 224 H------VQGEKHWIWTFTTPS---ETFFVIRKSRGTNVLIEVLTRrFKGIIVCDGWKPYARFT---KNLQRCWAHL 288
                                       *......89***********88...9*****************9999****************5...899******* PP

                      DDE_Tnp_IS66 154 rRkfvdaeeakkksqaaaealarigklya.ierear.eaeaeerlalrqeesrpllaeleawleeqlkkvlpksklg 228
                                       +R+ +d++e  +   +a    + ++ ly+ ++++++ e ++e r+++ q+ ++     l++w++        + k++
  gi|330508614|ref|YP_004385042.1| 289 LRESKDLSETFG---EAVPLHEALKGLYEsLTKSLEcEPPPEVRMNIWQSAREV----LQHWIDR----EYLEVKVR 354
                                       ********9755...444444446666663344443332678888888885444....4455553....457789** PP

                      DDE_Tnp_IS66 229 kairyllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                       k+i ++ +  +  ++f+ +++v+ +NN+aERa+Rp v+ RK+ +++++ +G 
  gi|330508614|ref|YP_004385042.1| 355 KFIGKISNGFDYWFTFILNPGVETTNNRAERALRPHVVLRKILGTLRNRKGT 406
                                       ***********************************************99985 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 !   25.7   4.6   6.6e-09   1.1e-05       3      45 ..      89     132 ..      87     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.6e-09
                           zf-IS66   3 tCpcCGg.llkpigedrvreeldip.PakfrViehirpkyaCpcC 45 
                                        Cp+CG+ l  p   +    + +ip P+ ++V+e+ +  y CpcC
  gi|330508614|ref|YP_004385042.1|  89 RCPDCGAkLNLPFRFE-SKVIEEIPePQPVIVTEYKIAHYICPCC 132
                                       7******663366666.569999**999****************9 PP

>> Med1  Mediator of RNA polymerase II transcription subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.3e-07   0.00038      84     170 ..     246     347 ..     194     389 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.3e-07
                              Med1  84 ereeAseiLlrdLr..........ltkkldeFaanLer.....LarlDklsgd..pklncfealegleesLqklsql 143
                                       ++++ +++L+++L+           +k  ++F++nL+r     L +   ls      + ++eal+gl+esL+k  + 
  gi|330508614|ref|YP_004385042.1| 246 RKSRGTNVLIEVLTrrfkgiivcdGWKPYARFTKNLQRcwahlLRESKDLSETfgEAVPLHEALKGLYESLTKSLEC 322
                                       378899*******************************9544434444555555999*****************9777 PP

                              Med1 144 esks....h.welekk......deeleelglcssvGkp 170
                                       e       + w++ ++      d             ++
  gi|330508614|ref|YP_004385042.1| 323 EPPPevrmNiWQSAREvlqhwiD-------------RE 347
                                       76555666677744444433331.............33 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.5   2.7e-06    0.0044       9      47 ..      84     145 ..      80     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.7e-06
                               DZR   9 ppdarfCseCgtklkavaa.......................edrCpsCgekvdpearfCpe 47 
                                       +  a  C++Cg+kl+ + +                       ++ Cp C ++v ++++ Cp+
  gi|330508614|ref|YP_004385042.1|  84 EVTADRCPDCGAKLNLPFRfeskvieeipepqpvivteykiaHYICPCCRKEVVARDANCPH 145
                                       567889********97666999**************************************95 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.8e-06    0.0045       6      81 ..     218     285 ..     215     354 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.8e-06
                     DDE_Tnp_IS240   6 vDETyvkikGkwaYlyravDkegrildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkelkreg 81 
                                       vDET + ++G++++++           f+++k R+t+  + +l++ +k        iv D+ + ya+  k+l+r  
  gi|330508614|ref|YP_004385042.1| 218 VDETGIHVQGEKHWIWTFTTPSET--FFVIRKSRGTNVLIEVLTRRFKGI------IVCDGWKPYARFTKNLQRCW 285
                                       9***************98765544..48899*****************99......************99999844 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.7   0.00012       0.2      20      54 ..       7      41 ..       5      56 .. 0.89
   2 ?   -2.8   0.0       5.5   8.9e+03       8      20 ..     348     360 ..     338     362 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                              ZapB 20 itlLqmeieeLkeeneelkeenreleeeneqlkee 54
                                      i++L++++e L+ ene lk ++rele+ + + ++ 
  gi|330508614|ref|YP_004385042.1|  7 IRQLREQNELLRLENEMLKARIRELEARLAKYENA 41
                                      899***********************888887655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.5
                              ZapB   8 qLEskiqkaidti 20 
                                        LE k+ k i +i
  gi|330508614|ref|YP_004385042.1| 348 YLEVKVRKFIGKI 360
                                       4777777777666 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.6   0.00044      0.72      19      51 ..       7      39 ..       4      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00044
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkdLk 51
                                      ++ql+++ + l  e++ lka+++eLea++++++
  gi|330508614|ref|YP_004385042.1|  7 IRQLREQNELLRLENEMLKARIRELEARLAKYE 39
                                      679999999999999999999999999998874 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 ?   11.1   2.1   0.00019      0.31       6      41 ..       7      41 ..       4      43 .. 0.93
   2 ?   -4.0   0.0       9.7   1.6e+04       8      21 ..     308     321 ..     307     321 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                       MCC-bdg_PDZ  6 IeeLkaqnelLsltleerkqqseeLsldlgkaEsna 41
                                      I +L+ qnelL+l  e  k++  eL  +l k+E na
  gi|330508614|ref|YP_004385042.1|  7 IRQLREQNELLRLENEMLKARIRELEARLAKYE-NA 41
                                      89*******************************.54 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 9.7
                       MCC-bdg_PDZ   8 eLkaqnelLsltle 21 
                                        Lk   e L+++le
  gi|330508614|ref|YP_004385042.1| 308 ALKGLYESLTKSLE 321
                                       57777778888776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0015       2.4       1       9 [.      89      97 ..      87     100 .. 0.86
   2 ?    1.2   2.8       0.2   3.2e+02       2      18 ..     129     145 ..     128     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0015
                     zinc_ribbon_2  1 fCpnCGael 9 
                                      +Cp CGa+l
  gi|330508614|ref|YP_004385042.1| 89 RCPDCGAKL 97
                                      699999997 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.2
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpy 18 
                                       Cp C +e+  ++  Cp+
  gi|330508614|ref|YP_004385042.1| 129 CPCCRKEVVARDANCPH 145
                                       ********999988886 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.3     0.002       3.2      17      42 ..      10      35 ..       8      36 .. 0.93
   2 ?    0.6   0.1      0.43     7e+02       8      19 ..     307     318 ..     306     322 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.002
                              HALZ 17 LksdydsLkkenekLkaelqeLkekl 42
                                      L+ +++ L+ ene Lka ++eL ++l
  gi|330508614|ref|YP_004385042.1| 10 LREQNELLRLENEMLKARIRELEARL 35
                                      8899*******************997 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.43
                              HALZ   8 dvLKasYdaLks 19 
                                       ++LK  Y++L+ 
  gi|330508614|ref|YP_004385042.1| 307 EALKGLYESLTK 318
                                       577888888874 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0039       6.4       4      25 ..      89      96 ..      86      98 .. 0.64
   2 ?    2.4   2.8      0.07   1.1e+02       2      21 ..     126     145 ..     125     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0039
                       zf-ribbon_3  4 rCPnCGaplssddnvCpyCGtk 25
                                      rCP CGa              k
  gi|330508614|ref|YP_004385042.1| 89 RCPDCGA--------------K 96
                                      5666666..............3 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.07
                       zf-ribbon_3   2 tvrCPnCGa.plssddnvCpy 21 
                                       ++ CP C + +  ++d +Cp+
  gi|330508614|ref|YP_004385042.1| 126 HYICPCCRKeV-VARDANCPH 145
                                       688****9977.888999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2828.30
//
Query:       gi|330508615|ref|YP_004385043.1|  [L=813]
Description: putative ATP-dependent helicase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-21   76.8   0.0    3.5e-21   75.7   0.0    1.5  1  DEAD        DEAD/DEAH box helicase
    2.3e-13   50.4   0.0    8.3e-13   48.6   0.0    2.0  2  Helicase_C  Helicase conserved C-terminal domain
    1.2e-07   31.9   0.0    2.1e-07   31.1   0.0    1.4  1  ResIII      Type III restriction enzyme, res subunit
     0.0083   15.8   0.0      0.037   13.7   0.0    2.2  2  DSHCT       DSHCT (NUC185) domain
  ------ inclusion threshold ------
      0.059   13.6   0.1       0.23   11.6   0.1    2.0  1  K-box       K-box region
      0.079   12.2   0.0       0.22   10.8   0.0    1.7  1  CcmH        Cytochrome C biogenesis protein
        0.1   11.5   0.0       0.17   10.7   0.0    1.3  1  AAA_34      P-loop containing NTP hydrolase pore-1


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 !   75.7   0.0   1.4e-24   3.5e-21       2     169 ..     216     377 ..     215     382 .. 0.84

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 1.4e-24
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT...TS CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk...yi 74 
                                       ++Q++ai + l +g++ lv  +T++GK+l+  ++ +++++    + + k l+++P+ +La+q +++l+ + +   ++
  gi|330508615|ref|YP_004385043.1| 216 PVQSRAISAGLlEGKSQLVVSATATGKSLIGEMAGIKNLL----QGKGKLLFLVPLVALANQKYDQLSAYNElgfQT 288
                                       799****99888***************************5....67789********************99933223 PP

                                       TSEEE.EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  75 dlrvl.liiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                       ++rv  + i   ++r+ ++ l  ++di+ gt + +d++++t+k +l +v ++V+DE+++l d +++  +  ++++l+
  gi|330508615|ref|YP_004385043.1| 289 SIRVGtSRIRLGKKRKIVQSL--NADIISGTYEGIDQVIRTKK-SLGRVGTVVIDEVHMLEDAERGHRLAGMIARLR 362
                                       355543344444555566666..7***************9888.9*******************************6 PP

                                       HHCTTSTTTSEEEEEESSB CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              DEAD 151 qitcdgklqrqvivlSATl 169
                                       ++  +     q+i+lSAT+
  gi|330508615|ref|YP_004385043.1| 363 NAAPE----AQFIFLSATV 377
                                       55443....45*******8 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   3.3e-16   8.3e-13       8     111 .]     426     529 ..     417     529 .. 0.87
   2 ?   -4.0   0.0         7   1.8e+04      38      62 ..     736     760 ..     708     763 .. 0.76

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 3.3e-16
                                       HHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTT CS
                        Helicase_C   8 ellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipk 84 
                                       +l++++  +g+++if+n++++++  +l   +    +a++h+ l+  er++i e f +g++  +++t +++ G+d+p 
  gi|330508615|ref|YP_004385043.1| 426 KLISSTGYRGQTIIFTNSRKNCY--NLA--QAIPGAAAYHAGLQYPERKRIEELFGQGKISTVVTTAALAAGVDFPA 498
                                       566788999*************8..666..555788999*************************************9 PP

                                       ESEEEESSSS....SSHHHHHHHHTTSSSTT CS
                        Helicase_C  85 vnlVinfdlp....rnvtsyiqriGRtgRag 111
                                        ++V+   +      nv++++q+ GR+gR g
  gi|330508615|ref|YP_004385043.1| 499 SQVVFESLAMginwLNVHEFNQMLGRAGRPG 529
                                       9999866666777778*************75 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 7
                                       HTTSTEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  38 kkgikvavlhgelpqnereeileqf 62 
                                       +k+i+  +l+ + + ++ eei++ f
  gi|330508615|ref|YP_004385043.1| 736 QKSISLSILDLRAEGKSPEEIIDYF 760
                                       5578888888888999999999888 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 !   31.1   0.0   8.3e-11   2.1e-07       8     169 ..     218     377 ..     211     379 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 8.3e-11
                                       HHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG... CS
                            ResIII   8 QeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayk 83 
                                       Q +ai + l      + k  l++ aT tGK+l+  ++ i++ll+ ++  k lflvp  +l +q +++++ + +  ++
  gi|330508615|ref|YP_004385043.1| 218 QSRAISAGL-----LEGKSQLVVSATATGKSLIGeMAGIKNLLQGKG--KLLFLVPLVALANQKYDQLSAYNELGFQ 287
                                       555555555.....234678999********************9766..*******************999999987 PP

                                       ......GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T....... CS
                            ResIII  84 e.....igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk....... 148
                                             ++ +  g+k+k+   +s n++i+  t++ +d+ +      +++++ +r   ++iDE+H l +++       
  gi|330508615|ref|YP_004385043.1| 288 TsirvgTSRIRLGKKRKI--VQSLNADIISGTYEGIDQVI------RTKKSLGRVGTVVIDEVHMLEDAErghrlag 356
                                       667755444444554444..68999999999999999999......88999999**************855555565 PP

                                       TTHHHHHT---SEEEEEESS- CS
                            ResIII 149 swreilekfkeavllglTATp 169
                                        + ++ ++ +ea  + l+AT 
  gi|330508615|ref|YP_004385043.1| 357 MIARLRNAAPEAQFIFLSATV 377
                                       666677788889999999996 PP

>> DSHCT  DSHCT (NUC185) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.84   2.1e+03      73     111 ..      64     102 ..      24     105 .. 0.65
   2 !   13.7   0.0   1.5e-05     0.037     114     157 ..     767     810 ..     617     812 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.84
                             DSHCT  73 lkeiaeriakvsvesrldlglvevvyaWakgasfaelle 111
                                       l  +a  i  v  +s l+ +++e+ +++  ++ f +++ 
  gi|330508615|ref|YP_004385043.1|  64 LLRKAGAIYLVRGDSALEKRFMELLESYQLQYRFVQVCG 102
                                       334444444444555567788888888888888888875 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.5e-05
                             DSHCT 114 dldeGdiVRllrrleellrqlakaakvigneeLkkkaeeaieli 157
                                        ++ Gd++  l ++   l+ + ++a+v+g++eL+k+aee  ++i
  gi|330508615|ref|YP_004385043.1| 767 YAYQGDLINYLDQMVRYLEAIGSVARVLGKPELAKEAEEWKKKI 810
                                       5789***********************************99998 PP

>> K-box  K-box region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   9.1e-05      0.23      24      53 ..     682     711 ..     674     719 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.1e-05
                             K-box  24 klqrsqRkllGedleslslkeLqqLEqqLe 53 
                                       ++q sqR l G  l+ ls  +L+qLE++++
  gi|330508615|ref|YP_004385043.1| 682 HMQVSQRALHGSFLDLLSSSDLNQLERKIQ 711
                                       5899***********************997 PP

>> CcmH  Cytochrome C biogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   8.6e-05      0.22      61      85 ..     743     767 ..     734     770 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.6e-05
                                       HHHHHHHT--HHHHHHHHHHHHTTT CS
                              CcmH  61 vremlkaGksdeeivdylvarYGdf 85 
                                       + ++ ++Gks eei+dy+ +rYG +
  gi|330508615|ref|YP_004385043.1| 743 ILDLRAEGKSPEEIIDYFSDRYGMY 767
                                       6667789****************77 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   6.7e-05      0.17     173     221 ..     334     377 ..     247     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.7e-05
                            AAA_34 173 dGvivfDEchkaknlakseekkatktgkavlelqkklpkArvvYvsaTg 221
                                        G +v DE h +++++        + + ++ +l+++ p+A+++++saT 
  gi|330508615|ref|YP_004385043.1| 334 VGTVVIDEVHMLEDAER-----GHRLAGMIARLRNAAPEAQFIFLSATV 377
                                       489*********99985.....468999********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (813 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 5339.23
//
Query:       gi|330508616|ref|YP_004385044.1|  [L=262]
Description: hypothetical protein MCON_2853 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-08   34.3   0.0    4.4e-08   32.9   0.0    1.7  1  MarR_2          MarR family
    4.2e-08   32.6   0.1    9.5e-08   31.5   0.0    1.7  2  HTH_24          Winged helix-turn-helix DNA-binding
      1e-05   25.4   0.1    3.3e-05   23.7   0.0    1.9  2  MarR            MarR family
    5.4e-05   23.1   0.5    0.00032   20.6   0.0    2.4  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00015   22.2   0.0    0.00039   20.9   0.0    1.8  1  HTH_27          Winged helix DNA-binding domain
    0.00063   19.8   0.0     0.0014   18.6   0.0    1.6  1  HTH_3           Helix-turn-helix
     0.0012   18.8   0.0     0.0035   17.2   0.0    1.8  1  HTH_11          HTH domain
     0.0017   18.3   0.0      0.003   17.5   0.0    1.4  1  HTH_45          Winged helix-turn-helix
     0.0019   17.9   0.0     0.0046   16.7   0.0    1.6  1  HTH_IclR        IclR helix-turn-helix domain
     0.0054   17.0   0.0      0.018   15.4   0.0    1.8  1  Rrf2            Transcriptional regulator
     0.0074   16.6   0.0      0.024   14.9   0.0    1.8  1  Mnd1            Mnd1 HTH domain
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.028   14.2   0.0    1.6  1  HTH_23          Homeodomain-like domain
      0.016   15.4   0.1      0.054   13.7   0.0    1.9  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.016   14.8   0.2      0.053   13.2   0.0    2.0  2  GntR            Bacterial regulatory proteins, gntR family
      0.019   15.1   0.0      0.038   14.1   0.0    1.5  1  MerR_1          MerR HTH family regulatory protein
      0.021   14.5   0.0      0.034   13.9   0.0    1.2  1  DUF4364         Domain of unknown function (DUF4364)
      0.029   14.3   0.1      0.091   12.7   0.1    1.9  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.051   13.7   0.1       0.14   12.3   0.1    1.7  1  Mrr_N           Mrr N-terminal domain
      0.053   13.7   0.1       0.28   11.3   0.0    2.2  2  HTH_28          Helix-turn-helix domain
      0.069   13.0   0.0       0.16   11.9   0.0    1.7  1  HTH_5           Bacterial regulatory protein, arsR family
      0.082   12.8   0.0       0.21   11.5   0.0    1.6  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.086   12.7   0.0       0.22   11.4   0.0    1.6  1  P22_Cro         DNA-binding transcriptional regulator Cro
      0.099   12.7   0.0       0.23   11.6   0.0    1.6  1  HTH_13          HTH DNA binding domain
       0.12   12.4   0.0       0.22   11.6   0.0    1.4  1  HTH_Mga         M protein trans-acting positive regulator (MG


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   5.8e-11   4.4e-08       6      53 ..      12      58 ..       9      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 5.8e-11
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      + +++L +++++ ++ l+++e+a +lg++++a+s  +k+Lv  GLv++
  gi|330508616|ref|YP_004385044.1| 12 SRFQILVEIAAHQPN-LRQKEVANKLGVTPQAISEYIKELVVDGLVTT 58
                                      679**********96.******************************86 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   1.3e-10   9.5e-08       4      48 .]      12      57 ..       9      57 .. 0.92
   2 ?   -3.2   0.0       8.7   6.5e+03      39      46 ..     245     252 ..     244     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.3e-10
                            HTH_24  4 tdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       +++IL ++ + +p++ q+e+A +lg++p+++++++k+L+ +Gl++
  gi|330508616|ref|YP_004385044.1| 12 SRFQILVEIAAhQPNLRQKEVANKLGVTPQAISEYIKELVVDGLVT 57
                                      6799**77777799*****************************996 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.7
                            HTH_24  39 krLeeeGl 46 
                                        rLe+eGl
  gi|330508616|ref|YP_004385044.1| 245 TRLESEGL 252
                                       59***996 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   4.4e-08   3.3e-05       4      48 ..      12      57 ..      10      58 .. 0.89
   2 ?   -2.0   0.1       4.9   3.7e+03      37      46 ..     243     252 ..     242     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.4e-08
                                      HHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  4 tqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlie 48
                                      ++f iL+ ++ ++p l+++e a+klgv++ ++++ +++L+ +Gl++
  gi|330508616|ref|YP_004385044.1| 12 SRFQILVEIAAHQPnLRQKEVANKLGVTPQAISEYIKELVVDGLVT 57
                                      578889888777666*****************************96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.9
                                       HHHHHHHTTS CS
                              MarR  37 vldrLekkGl 46 
                                       +l+rLe +Gl
  gi|330508616|ref|YP_004385044.1| 243 LLTRLESEGL 252
                                       5789998886 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 !   20.6   0.0   4.3e-07   0.00032      20      57 ..      25      62 ..       1      70 [. 0.78
   2 ?   -0.6   0.0       1.8   1.4e+03      48      63 ..     152     168 ..     150     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.3e-07
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglis.rgrri 57
                                       +l q+e A+ lG+t++ +s  ++eL  +gl++  gr +
  gi|330508616|ref|YP_004385044.1| 25 PNLRQKEVANKLGVTPQAISEYIKELVVDGLVTtDGR-M 62
                                      489******************************5454.2 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.8
                                       TTSEE.E.TEEEEES-HH CS
                         HTH_Crp_2  48 eglis.r.grririldle 63 
                                       +glis   gr i++  + 
  gi|330508616|ref|YP_004385044.1| 152 RGLISlEeGR-ITLCKVP 168
                                       799**64245.9998776 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 !   20.9   0.0   5.2e-07   0.00039       7      68 .]      15      70 ..      11      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.2e-07
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      ++L  i+  +   ++++++ +l v+ ++is+ +k+L+  GLv      + ++++r+++T +G
  gi|330508616|ref|YP_004385044.1| 15 QILVEIAAHQPNLRQKEVANKLGVTPQAISEYIKELVVDGLV------TTDGRMRYSITKEG 70
                                      5666677677778899**************************......77789******998 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.9e-06    0.0014       9      31 ..      26      48 ..      20      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                                      THHHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3  9 glsqeeLAeklGvsrstisriEn 31
                                      +l q+e+A klGv++++is +++
  gi|330508616|ref|YP_004385044.1| 26 NLRQKEVANKLGVTPQAISEYIK 48
                                      899*****************986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.7e-06    0.0035       2      39 ..      13      50 ..      12      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.7e-06
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaL 39
                                      ++qil  + ++++++  +e A +L+v+ +++  +Ik+L
  gi|330508616|ref|YP_004385044.1| 13 RFQILVEIAAHQPNLRQKEVANKLGVTPQAISEYIKEL 50
                                      68999999788888**********************99 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.1e-06     0.003      21      73 ..      28      82 ..      10      86 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.1e-06
                            HTH_45 21 kkTkimykanLsykllnkYLdmLvekglikk.skekYvlTekGle.lleklkele 73
                                      ++ ++  k   + + +++Y++ Lv  gl+++     Y++T++G e lle+  el+
  gi|330508616|ref|YP_004385044.1| 28 RQKEVANKLGVTPQAISEYIKELVVDGLVTTdGRMRYSITKEGVEwLLESAAELK 82
                                      55556666666777899************6627778*******993456666665 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 !   16.7   0.0   6.1e-06    0.0046       6      52 .]      14      60 ..      14      60 .. 0.97

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.1e-06
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                      ++iL  +a++++ l+ +e+A+++g+++ + + +++ Lv  G+v++dg
  gi|330508616|ref|YP_004385044.1| 14 FQILVEIAAHQPNLRQKEVANKLGVTPQAISEYIKELVVDGLVTTDG 60
                                      799999**************************************996 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.4e-05     0.018      11      57 ..      14      58 ..       6      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.4e-05
                                      HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      +++l+++a+++ +  ++ +e+a++ ++ p+ ++  +++L   glv++
  gi|330508616|ref|YP_004385044.1| 14 FQILVEIAAHQPN--LRQKEVANKLGVTPQAISEYIKELVVDGLVTT 58
                                      789********96..8*****************************87 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.1e-05     0.024      20      48 ..      31      59 ..      28      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                              Mnd1 20 lapkekgivsqsVkdvlqsLvdDglveve 48
                                      +++ + g+++q + +++++Lv Dglv ++
  gi|330508616|ref|YP_004385044.1| 31 EVANKLGVTPQAISEYIKELVVDGLVTTD 59
                                      444559********************987 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.8e-05     0.028       2      45 ..       8      54 ..       7      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-05
                            HTH_23  2 asereRlrillllae...GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      ++e  R++il   a     l+++e+A +Lgv+++ ++ ++k  + +G
  gi|330508616|ref|YP_004385044.1|  8 KRESSRFQILVEIAAhqpNLRQKEVANKLGVTPQAISEYIKELVVDG 54
                                      567779********888**********************99876555 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 ?   13.7   0.0   7.2e-05     0.054      24      55 ..      28      59 ..      21      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.2e-05
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress 24 ktkdlaerLnvspssVsemlkkLekdGyveye 55
                                      ++k++a  L+v p  +se +k+L  dG+v + 
  gi|330508616|ref|YP_004385044.1| 28 RQKEVANKLGVTPQAISEYIKELVVDGLVTTD 59
                                      689**************************876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.1e-05     0.053      23      58 ..      26      60 ..      13      64 .. 0.87
   2 ?   -2.5   0.1       5.6   4.2e+03      45      53 ..     244     252 ..     244     252 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.1e-05
                                      B---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              GntR 23 kLPsereLaaefgVsrttvReALrrLeaeglverrq 58
                                       L +++e+a ++gV+ + + e +++L+ +glv+   
  gi|330508616|ref|YP_004385044.1| 26 NL-RQKEVANKLGVTPQAISEYIKELVVDGLVTTDG 60
                                      58.99***************************9765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.6
                                       HHHHHHTTS CS
                              GntR  45 LrrLeaegl 53 
                                       L rLe+egl
  gi|330508616|ref|YP_004385044.1| 244 LTRLESEGL 252
                                       789****97 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 ?   14.1   0.0     5e-05     0.038       4      39 ..      30      65 ..      27      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-05
                                      HHHHHHHTS-HHHHHHHHHHTT-S-EE-TTS-EEEE CS
                            MerR_1  4 gevakilgvtthtlrywekegllkpkrteggrryYt 39
                                      +eva++lgvt+  +  + ke ++    t+ gr +Y+
  gi|330508616|ref|YP_004385044.1| 30 KEVANKLGVTPQAISEYIKELVVDGLVTTDGRMRYS 65
                                      8*************************9999998886 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.6e-05     0.034      36      87 ..      43      91 ..      38     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                           DUF4364 36 lqqalseLvesglieeeekenktlykiTekGketlelfenripksirekide 87
                                      ++++++eLv +gl+++   +++ +y+iT++G e l +   ++    r  ++e
  gi|330508616|ref|YP_004385044.1| 43 ISEYIKELVVDGLVTT---DGRMRYSITKEGVEWLLESAAELKRYARVVMEE 91
                                      789************7...9*************9988888887777665555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00012     0.091       8      55 ..       8      59 ..       7      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                      HHCCCHCHHHH....HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB  8 eyEakvYlaLl....klgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      + E++ ++ L+     + +++ +e+a++lgv  + + e++++L+  GlV++ 
  gi|330508616|ref|YP_004385044.1|  8 KRESSRFQILVeiaaHQPNLRQKEVANKLGVTPQAISEYIKELVVDGLVTTD 59
                                      567777777776666678899****************************976 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00018      0.14      12      85 ..       5      74 ..       3      76 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                             Mrr_N 12 ladgsehrlkeirervaerf.glseeeraellpsgkqtrfknrvgWartyLkkagllespkrgvwkiTekGrevl 85
                                      l++++e+++ +i  ++a +  +l ++e+a  l    q      ++ ++++L+  gl++++ r  ++iT++G e+l
  gi|330508616|ref|YP_004385044.1|  5 LQSKRESSRFQILVEIAAHQpNLRQKEVANKLGVTPQ-----AISEYIKELVVDGLVTTDGRMRYSITKEGVEWL 74
                                      5665555556666666666667777777777744433.....566678999*********************998 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00038      0.28       2      34 ..      13      48 ..      12      61 .. 0.84
   2 ?   -1.3   0.0       3.3   2.5e+03      40      52 .]     197     209 ..     196     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00038
                            HTH_28  2 RleiikllaaGh...svreaArelgisrrtvyrWik 34
                                      R++i+ ++aa+    +++e+A++lg++++ ++  ik
  gi|330508616|ref|YP_004385044.1| 13 RFQILVEIAAHQpnlRQKEVANKLGVTPQAISEYIK 48
                                      8899999998866689999************98877 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.3
                            HTH_28  40 GiagLvprrrrpr 52 
                                       Gi++Lv  ++++r
  gi|330508616|ref|YP_004385044.1| 197 GIEALVALKKAGR 209
                                       99****9887665 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.16       4      46 ..      13      57 ..      10      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                                      HHHHHHHHTT.SS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  4 RlkILklLae.ge.lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      R +IL   a  ++ l   e a++lg+++ ++S++ k L   GLV+
  gi|330508616|ref|YP_004385044.1| 13 RFQILVEIAAhQPnLRQKEVANKLGVTPQAISEYIKELVVDGLVT 57
                                      67777777777777888999************************7 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 ?   11.5   0.0   0.00028      0.21      11      29 ..      29      47 ..      26      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                    YdaS_antitoxin 11 qkaLAealgvsqqaVsqWl 29
                                      qk++A +lgv++qa+s  +
  gi|330508616|ref|YP_004385044.1| 29 QKEVANKLGVTPQAISEYI 47
                                      89**************877 PP

>> P22_Cro  DNA-binding transcriptional regulator Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.22      12      29 ..      29      46 ..      28      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                                      HHHHHHHHTS-HHHHHHH CS
                           P22_Cro 12 vekvAkalgvtksAVsqW 29
                                      ++ vA+ lgvt++A+s+ 
  gi|330508616|ref|YP_004385044.1| 29 QKEVANKLGVTPQAISEY 46
                                      678*************97 PP

>> HTH_13  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0003      0.23       4      48 ..      17      64 ..      15      66 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                            HTH_13  4 LvelvlsrPlVsagmvakeLkvtpraalklvkelgl.RElT..GRgrf 48
                                      Lve+   +P    + va++L vtp+a  + +kel +   +T  GR r+
  gi|330508616|ref|YP_004385044.1| 17 LVEIAAHQPNLRQKEVANKLGVTPQAISEYIKELVVdGLVTtdGRMRY 64
                                      6777777888888889******************77422332266665 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0003      0.22       9      45 ..      15      51 ..       7      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                           HTH_Mga  9 kLlelLteneksltldelakeLglseltlqsdiseLn 45
                                      ++l  +  +++ l  +e+a++Lg +  ++ ++i eL 
  gi|330508616|ref|YP_004385044.1| 15 QILVEIAAHQPNLRQKEVANKLGVTPQAISEYIKELV 51
                                      555556667999999********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1966.43
//
Query:       gi|330508617|ref|YP_004385045.1|  [L=172]
Description: hypothetical protein MCON_2854 [Methanosaeta concilii GP6]
Scores for complete 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-66  220.8   0.0    7.3e-66  220.7   0.0    1.0  1  ArsR      ArsR transcriptional regulator
     0.0018   18.3   0.0     0.0055   16.7   0.0    1.7  2  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.042   13.7   0.0        2.4    8.1   0.0    2.4  2  MarR_2    MarR family
       0.12   12.6   0.0       0.22   11.8   0.0    1.4  1  DUF1598   Protein of unknown function (DUF1598)


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 !  220.7   0.0   1.6e-69   7.3e-66       1     157 [.       9     167 ..       9     169 .. 0.99

  Alignments for each domain:
  == domain 1  score: 220.7 bits;  conditional E-value: 1.6e-69
                              ArsR   1 indpveLvpllqvfdsetkkkvyeelskeWlteeeleeklgee..veealklLkkikliEsqWrmpepgekpekeYh 75 
                                       indp++Lvpllq+f+s+++kk+++els+eW te+el+  +g++  v+++++lL+k++liE++Wr+pepge+pekeYh
  gi|330508617|ref|YP_004385045.1|   9 INDPSDLVPLLQAFGSAVHKKIFDELSREWRTERELAGLFGDDagVHRSVALLRKSGLIETKWRVPEPGESPEKEYH 85 
                                       8******************************************999******************************* PP

                              ArsR  76 tsYskvqanfqcsledlsdiievafmsdeeleelvekiekeveegntsisdlsrklglsplfiralakrsekldvkG 152
                                       ++Ys++qanfq+++edls++i+++fmsdeel+e++ek++k+v+ gn+s+s+lsr+lgls++fir++akr+e l+v+G
  gi|330508617|ref|YP_004385045.1|  86 STYSRIQANFQATMEDLSELISLTFMSDEELREVTEKLQKMVNGGNNSLSNLSRELGLSQVFIRGVAKRAEGLAVRG 162
                                       ***************************************************************************** PP

                              ArsR 153 qrlel 157
                                       qr+e 
  gi|330508617|ref|YP_004385045.1| 163 QRIEP 167
                                       ***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   1.2e-06    0.0055       4      56 ..      19      69 ..      18      72 .. 0.95
   2 ?   -2.7   0.0       1.5   6.6e+03      26      38 ..     133     145 ..     131     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-06
                                      HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  4 aeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      + A+++ v  +i+++L ++e +t  ela ++ ++++ +++ ++ L++ gL+e+
  gi|330508617|ref|YP_004385045.1| 19 LQAFGSAVHKKIFDEL-SREWRTERELAGLF-GDDAGVHRSVALLRKSGLIET 69
                                      679999999*******.**************.********************8 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                                       -HHHHHHHHTS-H CS
                            HTH_20  26 taselaerldlsk 38 
                                       ++s l ++l+ls+
  gi|330508617|ref|YP_004385045.1| 133 SLSNLSRELGLSQ 145
                                       6788888888875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00054       2.4      34      54 ..      50      70 ..      45      77 .. 0.86
   2 ?    3.2   0.0     0.019        85      23      46 ..     133     156 ..     116     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00054
                                      SHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 34 sksavsrilkrLvaaGLverr 54
                                      + + v+r ++ L + GL+e++
  gi|330508617|ref|YP_004385045.1| 50 DDAGVHRSVALLRKSGLIETK 70
                                      5789***************97 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.019
                                       EHHHHHHHHTSSHHHHHHHHHHHH CS
                            MarR_2  23 tvgelarrlglsksavsrilkrLv 46 
                                       + + l r+lgls+  +  + kr++
  gi|330508617|ref|YP_004385045.1| 133 SLSNLSRELGLSQVFIRGVAKRAE 156
                                       7799********988888888876 PP

>> DUF1598  Protein of unknown function (DUF1598)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.9e-05      0.22      12      53 ..     115     154 ..     109     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.9e-05
                           DUF1598  12 klqqllksvkqrlspgeveklveglkkaLGrQdvtvtGipad 53 
                                       +l+++ +++++ +++g  ++ +++l ++LG+ +v ++G++ +
  gi|330508617|ref|YP_004385045.1| 115 ELREVTEKLQKMVNGG--NNSLSNLSRELGLSQVFIRGVAKR 154
                                       6777888887667777..7789*****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1200.48
//
Query:       gi|330508618|ref|YP_004385046.1|  [L=635]
Description: RNA-metabolising metallo-beta-lactamase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-28   96.0   6.7    5.3e-27   93.6   0.6    3.2  3  KH_7           KH domain
    2.1e-24   85.9   0.0    6.2e-24   84.4   0.0    1.8  2  Beta-Casp      Beta-Casp domain
    8.4e-15   55.3   0.5    4.1e-14   53.0   0.5    2.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.1e-14   54.1   0.0    2.2e-14   53.1   0.0    1.6  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    4.5e-12   45.8   0.0    8.4e-12   44.9   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    1.4e-09   37.7   0.1    3.8e-09   36.4   0.1    1.7  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0002   21.1   0.3     0.0077   16.0   0.0    3.0  2  KH_2           KH domain
    0.00028   20.8   0.0    0.00074   19.4   0.0    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0018   18.1   0.1     0.0051   16.7   0.1    1.7  1  KH_4           KH domain
  ------ inclusion threshold ------
      0.058   13.2   0.1       0.18   11.7   0.1    1.8  1  KH_1           KH domain


Domain annotation for each model (and alignments):
>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.6     3e-30   5.3e-27       1      68 []       4      71 ..       4      71 .. 0.97
   2 ?    4.8   0.1     0.016        28      10      28 ..      80      98 ..      75     124 .. 0.92
   3 ?   -3.9   0.1         8   1.4e+04      43      59 ..     158     174 ..     155     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 3e-30
                              KH_7  1 eevleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                                      eevl elk+k+++klP+++++t +eFEGPelViYt++pk++a++g++ir+lAkelrkR+v+RpD +vl
  gi|330508618|ref|YP_004385046.1|  4 EEVLFELKRKVQSKLPPDINVTGLEFEGPELVIYTDDPKKVADDGEIIRNLAKELRKRVVVRPDLKVL 71
                                      57889***********************************************************9987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.016
                              KH_7 10 kieeklPkevkitdveFEG 28
                                      ki+e +Pke+ +t+++F G
  gi|330508618|ref|YP_004385046.1| 80 KIQEVVPKEAVLTNYHFDG 98
                                      89***************99 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 8
                              KH_7  43 engdlirklAkelrkRi 59 
                                       e+++++r++ +++ + i
  gi|330508618|ref|YP_004385046.1| 158 ERKNILRTVGRKIHRDI 174
                                       67888888888888766 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.3   1.1e+04      76      87 ..     294     305 ..     293     307 .. 0.81
   2 !   84.4   0.0   3.5e-27   6.2e-24       2     110 .]     422     545 ..     421     545 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.3
                                       SSSHHHHHHHHH CS
                         Beta-Casp  76 egGrsrellkkl 87 
                                       ++G++re+lk+ 
  gi|330508618|ref|YP_004385046.1| 294 DSGMIREALKHT 305
                                       689999999986 PP

  == domain 2  score: 84.4 bits;  conditional E-value: 3.5e-27
                                       HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.......................E-SHH....HHH CS
                         Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae.......................veakslewmesk 55 
                                       qe++++Lee++++k   + ++p++ld+ ++++at+++++y+e                       v+ +s      k
  gi|330508618|ref|YP_004385046.1| 422 QEVMVVLEEAIRKKV--IDEVPVCLDG-MIYEATAIHTTYPEylnndlrdlifhkginpflaecfVQVES-----PK 490
                                       9**********9944..3459******.******************************999888744333.....44 PP

                                       H...HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  56 ke.elnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                       ++ e+ +   p+vila+sgml+gG++ e+lk+l +d++nt+++vgyqaegTlgr++
  gi|330508618|ref|YP_004385046.1| 491 QRtEIVE-GPPCVILATSGMLNGGPVIEYLKRLGPDEKNTLVIVGYQAEGTLGRRI 545
                                       3336655.579*******************************************97 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.5   2.3e-17   4.1e-14       4     162 ..     192     364 ..     190     405 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 2.3e-17
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHH..HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal..elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78 
                                       ++ +++l+ ++++ i+iD+G+    ++ a   ++  + ++++++dav+lTH+HlDH+G ++ l +     ++++   
  gi|330508618|ref|YP_004385046.1| 192 VGRSCMLLSTPESRIIIDCGINVGSDDSATpyLYVPEVYPLNQIDAVVLTHAHLDHAGLVPMLYKYGYEGPIYCTPP 268
                                       5679********************99999999********************************************* PP

                                       HHCCHCHHHHHHHHHCCHH..............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEET CS
                       Lactamase_B  79 apalfmeeaddaasrkgll..............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveyg 141
                                       ++ lf     d+ +  g +              l+     + + ++++ +++ + ++     ++ g++  h+++++g
  gi|330508618|ref|YP_004385046.1| 269 TRDLFVLLQLDYIEIAGREgnrlpydsgmireaLKHTITLNYGDVTDIAPDTKLTMHNA--GHILGSSIAHFHIGDG 343
                                       *********9999998888999****976555544444444444444444444444443..356778889******* PP

                                       TCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B 142 ggkvlftGDallagetgridl 162
                                         +v+ftGD  +++ ++ ++ 
  gi|330508618|ref|YP_004385046.1| 344 LYNVAFTGDYKFERTRLFDPA 364
                                       **********99988887776 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 !   53.1   0.0   1.2e-17   2.2e-14       1      62 []     562     626 ..     562     626 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.2e-17
                             RMMBL   1 tipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvfiP 62 
                                       t+++++++ ++d fSgH+d+++l+e++r++ p++  v  +HGee  +++la+ + + + i + +P
  gi|330508618|ref|YP_004385046.1| 562 TVKINLEVTTVDgFSGHSDRQQLMEYLRRIYPKPgrVLTNHGEEGNCLDLASSIYKRYRIPTMAP 626
                                       699***************************************************88887877665 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 !   44.9   0.0   4.7e-15   8.4e-12       1     169 [.     198     360 ..     198     377 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 4.7e-15
                     Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelekv..iptvdliLLshatlehlGayallyakfksklllnipvyatlpv 75 
                                       lL+  + +i++D+G +  ++++ +   ++ +v  ++++d+++L+ha l+h G  ++ly+     ++ + p+y+t p+
  gi|330508618|ref|YP_004385046.1| 198 LLSTPESRIIIDCGINVGSDDSATPYLYVPEVypLNQIDAVVLTHAHLDHAGLVPMLYK-----YGYEGPIYCTPPT 269
                                       56677899********77777666677777764578****************6666664.....67899******** PP

                     Lactamase_B_6  76 vkLGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGti..Wkis 150
                                         L  ++ ld+++ +g +g+      +   i+ea ++ +tl Y   +++     +  +t +naGh lG +i  ++i 
  gi|330508618|ref|YP_004385046.1| 270 RDLFVLLQLDYIEIAGREGNRL--PYDSGMIREALKHTITLNYGDVTDIAP---DTKLTMHNAGHILGSSIahFHIG 341
                                       *******999999888776443..3466679***************99995...4557789********98667788 PP

                     Lactamase_B_6 151 kesekivYavdwnhakesh 169
                                       +++ ++ +  d+  ++ ++
  gi|330508618|ref|YP_004385046.1| 342 DGLYNVAFTGDYKFERTRL 360
                                       8888888777777666655 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 !   36.4   0.1   2.1e-12   3.8e-09       2     144 ..     205     354 ..     204     379 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2.1e-12
                                       EEEES--TTHHHH..HTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH....... CS
                     Lactamase_B_2   2 riLiDagpdlrqq..alral.qPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla....... 68 
                                       ri+iD+g ++     a+++l  P   +  l++idaV+lthaH DH   +++l + ++ + p+y+++ +++       
  gi|330508618|ref|YP_004385046.1| 205 RIIIDCGINVGSDdsATPYLyVPE--VYPLNQIDAVVLTHAHLDHAGLVPMLYK-YGYEGPIYCTPPTRDlfvllql 278
                                       9********877788999996664..666778**************55666666.45558*******9997766655 PP

                                       ..........HCCTTCGHHHCHTT..........TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTS CS
                     Lactamase_B_2  69 ..........vleanfvylaleee..........pavnvheldwgesfelgdggleitatparhksgrrldrnagdt 125
                                                 +                       +  ++ +l+ g+ ++++ ++ ++t++ a h  g         +
  gi|330508618|ref|YP_004385046.1| 279 dyieiagregN------------RlpydsgmireALKHTITLNYGDVTDIA-PDTKLTMHNAGHILGS-------SI 335
                                       55544433220............1333333444445566777788888887.4678888888887777.......78 PP

                                       EEEEEECTTEEEEEESS-S CS
                     Lactamase_B_2 126 lGlriegggkrvyyigDtg 144
                                       + + i++g  +v+++gD +
  gi|330508618|ref|YP_004385046.1| 336 AHFHIGDGLYNVAFTGDYK 354
                                       8888888888888888865 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.15   2.7e+02      44      73 ..      48      84 ..      44      89 .. 0.65
   2 !   16.0   0.0   4.3e-06    0.0077      29      62 ..     103     136 ..      93     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.15
                                      GHHHHHHHHHHHHHHHHHHTTC.........EEEEEEEE CS
                              KH_2 44 Gsnikkigkelrkdieklegkk.........VklnivkV 73
                                      G+ i+++ kelrk++ +    +         + ++i +V
  gi|330508618|ref|YP_004385046.1| 48 GEIIRNLAKELRKRVVVRP--DlkvladpesAIIKIQEV 84
                                      8889**********94222..234555555555555555 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 4.3e-06
                                       EEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHH CS
                              KH_2  29 iviresqpgivIGkgGsnikkigkelrkdiekle 62 
                                       + i +++pg+vIG+ G+++++i+k ++   ++++
  gi|330508618|ref|YP_004385046.1| 103 VQIEAEKPGLVIGRHGATLREITKLIGWTPKVVR 136
                                       668899******************9986555555 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   4.1e-07   0.00074       6      51 ..     193     249 ..     191     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.1e-07
                     Lactamase_B_3   6 ghnsflletagarilvDPfkanlgyeppa............eeaDlvlisqaledHah 51 
                                       g +++ll+t++ ri++D +  n+g + +a             ++D+v++++a+ dHa 
  gi|330508618|ref|YP_004385046.1| 193 GRSCMLLSTPESRIIIDCGI-NVGSDDSAtpylyvpevyplNQIDAVVLTHAHLDHAG 249
                                       89***************883.44444444445666677777***************85 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   2.8e-06    0.0051      28      52 ..      98     122 ..      81     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.8e-06
                              KH_4  28 eveielnvegedlGrvIGkrGrtld 52 
                                       +++ e+++e e+ G+vIG++G tl+
  gi|330508618|ref|YP_004385046.1|  98 GETGEVQIEAEKPGLVIGRHGATLR 122
                                       5667899****************97 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0001      0.18       3      27 ..     102     126 ..     100     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                                       EEEEGGGHHHHHHTGGGHHHHHHHH CS
                              KH_1   3 rilvPsslvgriIGkgGsnIkeIre 27 
                                       ++++ +++ g++IG+ G++++eI +
  gi|330508618|ref|YP_004385046.1| 102 EVQIEAEKPGLVIGRHGATLREITK 126
                                       678888889**************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (635 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 4305.38
//
Query:       gi|330508619|ref|YP_004385047.1|  [L=206]
Description: proteasome subunit beta [Methanosaeta concilii GP6]
Scores for complete 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-53  180.8   1.0    2.2e-53  180.6   1.0    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 !  180.6   1.0   1.2e-57   2.2e-53       1     188 [.       4     185 ..       4     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 180.6 bits;  conditional E-value: 1.2e-57
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       v kGtt+vG+ +++gvvla+++rat+gs ++s++ ++Ki++idd +g+++aG ++Da+ lvr++++ea+ly+++ g+
  gi|330508619|ref|YP_004385047.1|   4 VFKGTTTVGVLCDGGVVLASESRATMGSFIASSQ-AKKIYQIDDLVGMTTAGGVGDAQSLVRMVQVEARLYKMQRGE 79 
                                       579***************************5555.8***************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                        ++v+    +v+++l++ + +++  pf+v+l+++gvd+ g p++y++d  G  iee+++va+Gsgs +a+++le+ y
  gi|330508619|ref|YP_004385047.1|  80 GLTVK----AVTTMLANILSSRRYYPFMVQLIMGGVDRYG-PRIYSLDALGGQIEERRIVATGSGSPVAYGVLEAMY 151
                                       *****....6666666666677779************777.************************************ PP

                                       STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEE CS
                        Proteasome 155 kedltleeavelavkalkealerdklsgknieva 188
                                       k+ +++e++  la +a+++al+rd++sg++ie++
  gi|330508619|ref|YP_004385047.1| 152 KPGISVEDGTVLAARAIHNALKRDSASGDKIELV 185
                                       ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1544.50
//
Query:       gi|330508620|ref|YP_004385048.1|  [L=271]
Description: hypothetical protein MCON_2857 [Methanosaeta concilii GP6]
Scores for complete sequence (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  330.7   8.6    1.3e-98  330.5   8.6    1.0  1  DUF63      Membrane protein of unknown function DUF63


Domain annotation for each model (and alignments):
>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.5   8.6  7.3e-103   1.3e-98       2     272 .]       5     271 .]       4     271 .] 0.99

  Alignments for each domain:
  == domain 1  score: 330.5 bits;  conditional E-value: 7.3e-103
                             DUF63   2 seFiykyYidpivykegYnivntltyaiiLivavyliykllkklkikidekfvlatipyvilgsslRvveDagllkp 78 
                                       +++iy+yYi+pi+y+++Yn+v+t+t+a++L++a++ ++kl+++++++ide++vl+t+py+++gsslRv+eDa++++p
  gi|330508620|ref|YP_004385048.1|   5 ADWIYRYYIHPIIYDTSYNPVDTITWAVVLGLAILGLVKLFRHYRLAIDERLVLSTLPYILAGSSLRVIEDAEIVQP 81 
                                       69*************************************************************************** PP

                             DUF63  79 plsyllitPliyflvflitlavlliskklekklkkdykklyaavGvvlvlvvlllLllteevvnlevlllvlllaav 155
                                       p+syllitPli+flvfl+t  +l++++++   l +++++ yaa+G++++l++l+lL+     +n +v+ +v++l ++
  gi|330508620|ref|YP_004385048.1|  82 PWSYLLITPLIFFLVFLVTAGSLTLTRRI---LGDQFHHGYAAIGLAWTLFNLMLLF-GVGLENGWVIGAVFALGSA 154
                                       *****************************...************************9.999**************** PP

                             DUF63 156 ltalvllllrklk.lellsdklnlllllahllDasatfvgidllgYvEqHvvpsfLidltGtalvmyplkllvlipv 231
                                       lt  +ll  r +  l++l d++nl++++ah+lDas+t++g+d++gY+E+Hvvp+fLidl+Gta+vmyplkl+vl+p+
  gi|330508620|ref|YP_004385048.1| 155 LTGGLLLSRRAIPsLSFLDDRFNLMIVYAHMLDASSTYLGVDWFGYYEKHVVPTFLIDLAGTAAVMYPLKLIVLLPA 231
                                       ***********9999************************************************************** PP

                             DUF63 232 lyildkevkeeeelrnlvklailvlGlaPgiRnllrmvlgv 272
                                       l+++dk++++++ lrnl+kla+++lGlaP++Rn+lr+ lgv
  gi|330508620|ref|YP_004385048.1| 232 LFMIDKAIDDRS-LRNLTKLALITLGLAPAVRNTLRLALGV 271
                                       ***********9.**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2081.80
//
Query:       gi|330508621|ref|YP_004385049.1|  [L=108]
Description: hypothetical protein MCON_2859 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); 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: 00:00:00.40
# Mc/sec: 817.11
//
Query:       gi|330508622|ref|YP_004385050.1|  [L=404]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete 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-141  469.4   0.0   4.6e-141  469.2   0.0    1.0  1  DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
    2.8e-06   27.5   0.0    8.9e-06   25.9   0.0    1.9  1  HTH_Tnp_Tc3_2    Transposase
    0.00039   20.5   0.0    0.00091   19.3   0.0    1.6  1  HTH_21           HTH-like domain
     0.0024   18.0   0.0     0.0038   17.3   0.0    1.3  1  GSH-S_N          Prokaryotic glutathione synthetase, N-termin
     0.0042   17.7   0.1      0.011   16.3   0.1    1.8  1  HTH_32           Homeodomain-like domain
  ------ inclusion threshold ------
      0.012   14.3   0.0       0.02   13.6   0.0    1.3  1  UPF0236          Uncharacterised protein family (UPF0236)
       0.02   14.5   0.3      0.073   12.7   0.1    2.0  3  HTH_33           Winged helix-turn helix
      0.031   14.2   0.4       0.11   12.4   0.1    2.1  2  HTH_12           Ribonuclease R winged-helix domain
      0.058   13.4   0.1       0.62   10.1   0.0    2.4  2  HTH_29           Winged helix-turn helix


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.2   0.0  2.3e-144  4.6e-141       1     308 []      91     398 ..      91     398 .. 1.00

  Alignments for each domain:
  == domain 1  score: 469.2 bits;  conditional E-value: 2.3e-144
                   DDE_Tnp_ISAZ013   1 dleelvepetrgdpesplrwttkslrklaeeLkeqghkvsaetvaelLkelgyslqsnrKtkegkkhpdrdaqFeki 77 
                                       dle+++e++t+gdp+s l+wt ks++++aeeL+++ghkvs++tv++lLke+gyslq+nrK+ egk+ p+rd+qF+++
  gi|330508622|ref|YP_004385050.1|  91 DLEKIMEESTAGDPMSLLKWTYKSTYAIAEELQSRGHKVSHDTVRRLLKESGYSLQANRKNLEGKSGPERDTQFRYV 167
                                       79*************************************************************************** PP

                   DDE_Tnp_ISAZ013  78 nekvkeaqeagqpvisvdtkkkeliGefkrsGkewrpkgepaevkdhdfvskeegkaipyGiydlaenegwvsvgtd 154
                                       +++++++ +ag+pvisvd+kkkel+G++k+sG++wr+kg+p+ v+++df+sk+ g+aipyG+yd+++neg+v++g++
  gi|330508622|ref|YP_004385050.1| 168 SSQAAKFIDAGDPVISVDAKKKELVGNYKNSGRTWRQKGQPELVNVYDFPSKAIGAAIPYGVYDPKRNEGVVNIGKS 244
                                       ***************************************************************************** PP

                   DDE_Tnp_ISAZ013 155 kdtaefavesirrwWqevgkarypkakrllitaDaggsnssrsrlwkkelqkladelgleiqvahfPpgtskwnkiE 231
                                       ++taefavesir+wW+ vgk+ry+ +k+lli+aD+ggsn+sr+r wk  lq+lade+g++i+v+hfPpgtskwnkiE
  gi|330508622|ref|YP_004385050.1| 245 HNTAEFAVESIRQWWNLVGKYRYAGCKNLLICADGGGSNGSRNRGWKFFLQQLADEIGITITVSHFPPGTSKWNKIE 321
                                       ***************************************************************************** PP

                   DDE_Tnp_ISAZ013 232 hRlfshitqnwrgrpltsvevvvnliaatttkkglkveaeldeksyetGikvskeemealeierdelhgewnytiap 308
                                       h++fs+i++nwrg+pl+s+e++++li++t+tkkgl++ea+ld+++yetGik+ +e+m++l+i+ +el++ wny+i+p
  gi|330508622|ref|YP_004385050.1| 322 HCMFSFISMNWRGKPLSSYETIIKLIGSTKTKKGLRIEARLDDRDYETGIKILDEDMARLKISVHELYPMWNYSIEP 398
                                       ***************************************************************************98 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.5e-09   8.9e-06      14      51 ..     113     150 ..      96     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.5e-09
                     HTH_Tnp_Tc3_2  14 itlreLanelkeeGksvsreTirrrLrkaglkkrkprk 51 
                                       ++  ++a+el+++G++vs+ T+rr L+++g++ +  rk
  gi|330508622|ref|YP_004385050.1| 113 KSTYAIAEELQSRGHKVSHDTVRRLLKESGYSLQANRK 150
                                       57779*****999******************9888777 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.5e-07   0.00091      26      59 ..     118     150 ..     116     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.5e-07
                            HTH_21  26 iwaeLrreggvrvnhkrVrRlMrelGLrgvqrrk 59 
                                       i+ eL+ +g+ +v+h +VrRl +e G+  + +rk
  gi|330508622|ref|YP_004385050.1| 118 IAEELQSRGH-KVSHDTVRRLLKESGYSLQANRK 150
                                       6789****99.5**************99888887 PP

>> GSH-S_N  Prokaryotic glutathione synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.9e-06    0.0038       8      60 ..     103     156 ..      96     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.9e-06
                           GSH-S_N   8 dplesikikkDttfalmleaqarghevfvleaadLslreg.katararkvevke 60 
                                       dp++ +k +  +t+a+++e q+rgh+v + ++++L  ++g +++a+ +++e k+
  gi|330508622|ref|YP_004385050.1| 103 DPMSLLKWTYKSTYAIAEELQSRGHKVSHDTVRRLLKESGySLQANRKNLEGKS 156
                                       9999***999*************************9987723455555555533 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   5.5e-06     0.011      20      73 .]      73     138 ..      51     138 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.5e-06
                            HTH_32  20 rprrgrpr..klsdevrariiallreep.........rWsprq...laarlaeregvkvShstvyriL 73 
                                       +p +gr+r     + +   + ++  ee+         +W+++    +a++l + +g kvSh tv+r+L
  gi|330508622|ref|YP_004385050.1|  73 KPGGGRKRvaDREPNLLNDLEKIM-EEStagdpmsllKWTYKStyaIAEEL-QSRGHKVSHDTVRRLL 138
                                       344557764435555666666666.433467779999997777777*****.888899********98 PP

>> UPF0236  Uncharacterised protein family (UPF0236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.9e-06      0.02     139     230 ..     119     216 ..     110     222 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.9e-06
                           UPF0236 139 aeklerivcqekvskeairqlvleigvalaaaekevkveikekrkvRvLyieaDg.lfvsrq......dgkkeeerl 208
                                       ae+l+++    kvs++++r+l  e g +l+a +k+ + + + +r+  + y+      f+         d kk+e   
  gi|330508622|ref|YP_004385050.1| 119 AEELQSR--GHKVSHDTVRRLLKESGYSLQANRKNLEGKSGPERDTQFRYVSSQAaKFIDAGdpvisvDAKKKELVG 193
                                       4555333..479***********************************999976531344433233322334444444 PP

                           UPF0236 209 lviheGrk.ekgsrleLvnrrdy 230
                                        +   Gr+ ++ ++ eLvn+ d+
  gi|330508622|ref|YP_004385050.1| 194 NYKNSGRTwRQKGQPELVNVYDF 216
                                       45666755356677778887665 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.4   2.9e+03      23      40 ..      97     114 ..      94     122 .. 0.83
   2 ?   12.7   0.1   3.7e-05     0.073      10      39 ..     118     146 ..     111     159 .. 0.85
   3 ?   -3.7   0.0       4.8   9.5e+03      13      26 ..     296     309 ..     295     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
                            HTH_33  23 svsgvyrlLkrlGfsyqk 40 
                                       ++s+ ++ +  l+++y++
  gi|330508622|ref|YP_004385050.1|  97 EESTAGDPMSLLKWTYKS 114
                                       6788888999999**997 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.7e-05
                            HTH_33  10 laqlieerfgvsysvsgvyrlLkrlGfsyq 39 
                                       +a+ ++ r g ++s+ +v+rlLk+ G+s q
  gi|330508622|ref|YP_004385050.1| 118 IAEELQSR-GHKVSHDTVRRLLKESGYSLQ 146
                                       66666666.999****************99 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.8
                            HTH_33  13 lieerfgvsysvsg 26 
                                        ++++ g++++vs+
  gi|330508622|ref|YP_004385050.1| 296 QLADEIGITITVSH 309
                                       5789999*999985 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.7e-05      0.11      17      40 ..     116     139 ..     107     149 .. 0.92
   2 ?   -2.9   0.0       3.5     7e+03      18      31 ..     357     370 ..     346     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.7e-05
                            HTH_12  17 keiaeeLkkrgydigeravRyrLr 40 
                                        +iaeeL+ rg +++  +vR+ L+
  gi|330508622|ref|YP_004385050.1| 116 YAIAEELQSRGHKVSHDTVRRLLK 139
                                       68*******************998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.5
                            HTH_12  18 eiaeeLkkrgydig 31 
                                       +i+  L +r+y+ g
  gi|330508622|ref|YP_004385050.1| 357 RIEARLDDRDYETG 370
                                       68888999998765 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00031      0.62       4      58 ..      27      82 ..      24      86 .. 0.78
   2 ?    0.2   0.0      0.39   7.8e+02      24      34 ..     129     139 ..     125     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00031
                            HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegG.laalld.rrrsgrprnrls 58
                                      a  +l+ G++ vs + +++g sr+t+++ +   e  + l+   + r+ +g +r+r+ 
  gi|330508622|ref|YP_004385050.1| 27 AAKALELGWGGVSKVSAITGFSRTTINKGIQELESNEdLKPPERlRK-PGGGRKRVA 82
                                      6678899999*****************98888776666888888554.676777654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.39
                            HTH_29  24 lsrrtvyrwlk 34 
                                       +s +tv+r lk
  gi|330508622|ref|YP_004385050.1| 129 VSHDTVRRLLK 139
                                       899*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.54u 0.21s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3103.81
//
Query:       gi|330508623|ref|YP_004385051.1|  [L=298]
Description: hypothetical protein MCON_2861 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-13   50.0   2.0    2.6e-13   50.0   2.0    2.1  1  TPR_12    Tetratricopeptide repeat
    2.9e-10   39.4   1.1    3.1e-07   30.0   0.3    3.0  2  TPR_2     Tetratricopeptide repeat
    5.8e-10   38.7   0.7    7.4e-05   22.5   0.1    2.9  2  TPR_10    Tetratricopeptide repeat
    1.6e-08   34.0   1.3    7.3e-08   31.9   0.2    2.6  2  TPR_1     Tetratricopeptide repeat
    1.7e-07   30.8   8.9    8.5e-06   25.4   0.2    4.4  3  TPR_7     Tetratricopeptide repeat
      2e-06   27.6   1.5    1.5e-05   24.8   0.1    3.0  2  TPR_8     Tetratricopeptide repeat
     0.0026   18.3   3.3      0.099   13.3   0.1    3.9  3  TPR_6     Tetratricopeptide repeat
     0.0045   17.7  10.1     0.0068   17.1   0.2    4.2  4  TPR_14    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.015   15.0   0.7      0.015   15.0   0.7    3.1  3  TPR_11    TPR repeat
      0.018   15.7   0.8      0.018   15.7   0.8    3.3  4  TPR_16    Tetratricopeptide repeat
      0.031   14.3   0.4       0.26   11.4   0.3    2.4  1  ANAPC5    Anaphase-promoting complex subunit 5
      0.052   13.8   0.0      0.096   13.0   0.0    1.4  1  APOC4     Apolipoprotein C4
        1.3    9.9   0.0        1.3    9.9   0.0    4.5  4  TPR_4     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   2.0   1.9e-16   2.6e-13       3      77 .]     208     280 ..     206     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.9e-16
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       a+ ln l+++++rlg+  +A+e++e+al i r++  +++ ++a+t  n++ +++ lg+  +A+ l +ealai+e+
  gi|330508623|ref|YP_004385051.1| 208 ASFLNLLGLAYARLGEPRKAIEHYEQALKISREI--GYRRGEANTHWNMSLAQDSLGKRSDAVGLAKEALAIYEQ 280
                                       677888****************************..9999*********************************96 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.3   2.3e-10   3.1e-07       2      31 ..     209     238 ..     208     241 .. 0.91
   2 !    7.1   0.0    0.0048       6.6       2      32 ..     249     279 ..     248     281 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.3e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                         l+ lGlay++lg++ +A+e++e+Al++ 
  gi|330508623|ref|YP_004385051.1| 209 SFLNLLGLAYARLGEPRKAIEHYEQALKIS 238
                                       5799************************97 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0048
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                         ++n+ la   lg+  +A+ + ++Al++++
  gi|330508623|ref|YP_004385051.1| 249 NTHWNMSLAQDSLGKRSDAVGLAKEALAIYE 279
                                       67999***********************987 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   5.4e-08   7.4e-05       2      35 ..     208     241 ..     208     242 .. 0.95
   2 !   13.6   0.1   3.5e-05     0.048       7      35 ..     253     281 ..     253     282 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.4e-08
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrl 35 
                                       As ln L+ a+ ++g+  +A +++e+al i r++
  gi|330508623|ref|YP_004385051.1| 208 ASFLNLLGLAYARLGEPRKAIEHYEQALKISREI 241
                                       6789**************************9985 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.5e-05
                            TPR_10   7 NLanalrqrgrydeAealleealairrrl 35 
                                       N++ a  ++g++ +A+ l++ealai++++
  gi|330508623|ref|YP_004385051.1| 253 NMSLAQDSLGKRSDAVGLAKEALAIYEQI 281
                                       77888889*******************85 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.2   5.3e-11   7.3e-08       3      31 ..     210     238 ..     208     240 .. 0.91
   2 ?   -0.6   0.1         1   1.4e+03      11      32 ..     258     279 ..     256     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 5.3e-11
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                                        l+ lG+ay +lg++ +A+e+ye+AL++ 
  gi|330508623|ref|YP_004385051.1| 210 FLNLLGLAYARLGEPRKAIEHYEQALKIS 238
                                       6899***********************96 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                                       HHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1  11 yfklgkydeAleyyekALelnP 32 
                                         +lgk  +A+   ++AL +++
  gi|330508623|ref|YP_004385051.1| 258 QDSLGKRSDAVGLAKEALAIYE 279
                                       5678888889888899998865 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       1.6   2.3e+03       4      11 ..     102     109 ..     100     128 .. 0.48
   2 !   25.4   0.2   6.2e-09   8.5e-06       2      31 ..     211     240 ..     211     245 .. 0.89
   3 !    7.5   0.2    0.0033       4.5       3      31 ..     252     280 ..     250     295 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.6
                             TPR_7   4 nLarlysr 11 
                                       +La++y r
  gi|330508623|ref|YP_004385051.1| 102 ALAHTYAR 109
                                       56666655 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 6.2e-09
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       L+ L+ +y rlG+ ++Aie+yeq+L + ++
  gi|330508623|ref|YP_004385051.1| 211 LNLLGLAYARLGEPRKAIEHYEQALKISRE 240
                                       799********************8877665 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0033
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkd 31 
                                        n+  ++ +lG++++A++l +++La+ ++
  gi|330508623|ref|YP_004385051.1| 252 WNMSLAQDSLGKRSDAVGLAKEALAIYEQ 280
                                       578889999*************9988655 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   1.1e-08   1.5e-05       2      33 ..     209     240 ..     208     241 .. 0.93
   2 ?   -0.1   0.1       1.1   1.5e+03       4      31 ..     251     278 ..     248     281 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.1e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       + +++lg++y  lg+  +A+e ye+al+++++
  gi|330508623|ref|YP_004385051.1| 209 SFLNLLGLAYARLGEPRKAIEHYEQALKISRE 240
                                       6789*************************975 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleld 31 
                                       ++n++++ ++lg+   A+   ++al + 
  gi|330508623|ref|YP_004385051.1| 251 HWNMSLAQDSLGKRSDAVGLAKEALAIY 278
                                       5677777777777777766666666554 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.8   3.8e+03      21      28 ..     124     131 ..     108     133 .. 0.74
   2 !   13.3   0.1   7.1e-05     0.099       6      28 ..     214     236 ..     213     238 .. 0.93
   3 ?    2.8   0.1      0.17   2.3e+02       5      25 ..     253     280 ..     250     287 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.8
                                       HHHHHHHH CS
                             TPR_6  21 ealerlik 28 
                                       e++e++i+
  gi|330508623|ref|YP_004385051.1| 124 EYYEDFIR 131
                                       57777776 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.1e-05
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                       l+l+y +lg+++kA+e +e+ +k
  gi|330508623|ref|YP_004385051.1| 214 LGLAYARLGEPRKAIEHYEQALK 236
                                       8******99***********987 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.17
                                       HHHHHHHHH.......HHHHHHHHHHHH CS
                             TPR_6   5 klalsyrkl.......gdtdkAlealer 25 
                                       ++ l++ +l       g + +Al+++e+
  gi|330508623|ref|YP_004385051.1| 253 NMSLAQDSLgkrsdavGLAKEALAIYEQ 280
                                       6777777762333333444555555555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1         1   1.4e+03      23      39 ..     107     122 ..      99     144 .. 0.54
   2 ?   -1.5   0.0       4.8   6.7e+03      10      23 ..     157     170 ..     152     193 .. 0.77
   3 !   17.1   0.2     5e-06    0.0068       6      30 ..     213     237 ..     208     245 .. 0.90
   4 ?    3.7   0.1       0.1   1.4e+02      13      36 ..     260     283 ..     248     295 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1
                            TPR_14  23 llrralalaPddaeawl 39 
                                       ++r++l   Pd+a ++l
  gi|330508623|ref|YP_004385051.1| 107 YARAWLT-SPDSALTRL 122
                                       3333333.444443332 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.8
                            TPR_14  10 allalGdpdeAial 23 
                                       a+ ++G +++A+++
  gi|330508623|ref|YP_004385051.1| 157 ACNRAGLWEAARTI 170
                                       66778888877764 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 5e-06
                            TPR_14   6 alaeallalGdpdeAiallrralal 30 
                                       +l+ a+++lG+p++Ai+++++al+ 
  gi|330508623|ref|YP_004385051.1| 213 LLGLAYARLGEPRKAIEHYEQALKI 237
                                       6999******************986 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.1
                            TPR_14  13 alGdpdeAiallrralalaPddae 36 
                                        lG+  +A+ l+++ala + + + 
  gi|330508623|ref|YP_004385051.1| 260 SLGKRSDAVGLAKEALAIYEQIES 283
                                       578888888888888888776544 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       3.7   5.1e+03      20      29 ..      69      78 ..      69      78 .. 0.91
   2 ?    5.4   0.1     0.011        15      27      42 .]     207     222 ..     204     222 .. 0.89
   3 ?   15.0   0.7   1.1e-05     0.015       1      24 [.     215     238 ..     215     240 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.7
                            TPR_11 20 AlkldPdnae 29
                                      Al+++ d+a+
  gi|330508623|ref|YP_004385051.1| 69 ALEISADDAN 78
                                      99*****996 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
                            TPR_11  27 naeayynLGlayykqG 42 
                                        a++++ LGlay+++G
  gi|330508623|ref|YP_004385051.1| 207 EASFLNLLGLAYARLG 222
                                       68899*********98 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 1.1e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkld 24 
                                       G ay  +G+  +Aie+Y++Alk++
  gi|330508623|ref|YP_004385051.1| 215 GLAYARLGEPRKAIEHYEQALKIS 238
                                       889*******************97 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2       2.1   2.9e+03      18      41 ..     102     123 ..      96     129 .. 0.68
   2 ?   -1.5   0.1       3.2   4.3e+03      22      50 ..     142     170 ..     131     184 .. 0.55
   3 ?   15.7   0.8   1.3e-05     0.018      31      63 ..     205     237 ..     191     240 .. 0.83
   4 ?   -1.4   0.1       2.8   3.9e+03      11      25 ..     262     276 ..     256     282 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.1
                            TPR_16  18 aaleaalkrdpssPdaaeAllllg 41 
                                       a+++++ +++  sPd   Al  l+
  gi|330508623|ref|YP_004385051.1| 102 ALAHTYARAWLTSPD--SALTRLA 123
                                       567888888888888..5555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.2
                            TPR_16  22 aalkrdpssPdaaeAllllgdaalrqgrl 50 
                                       a+l++++++ +a++++ +++ ++ ++   
  gi|330508623|ref|YP_004385051.1| 142 ALLDSQRDHILAVRSACNRAGLWEAARTI 170
                                       55555555544555555555555544444 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.3e-05
                            TPR_16  31 PdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                        d a +l+llg+a++r+g+  +A++ y+ al+ 
  gi|330508623|ref|YP_004385051.1| 205 YDEASFLNLLGLAYARLGEPRKAIEHYEQALKI 237
                                       568999999999999999999999999999875 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.8
                            TPR_16  11 gdyddAaaaleaalk 25 
                                       g+  dA+ ++++al+
  gi|330508623|ref|YP_004385051.1| 262 GKRSDAVGLAKEALA 276
                                       566666666666665 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00019      0.26      15      74 ..     116     241 ..     104     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                            ANAPC5  15 qqaldsLhryF.Dyvlsqnessq...................................................... 36 
                                       ++al  L +y+ D++ +q+++ q                                                      
  gi|330508623|ref|YP_004385051.1| 116 DSALTRLAEYYeDFIREQMQRGQtryalldsqrdhilavrsacnraglweaartitwaieeyldlqghgtervavvk 192
                                       68999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                            ANAPC5  37 .........kksyqya.lLnlaslh.adfghneeAvkaleeairlAren 74 
                                                + +y+ a  Lnl  l  a++g++ +A++  e a +++re 
  gi|330508623|ref|YP_004385051.1| 193 agleasrsdEARYDEAsFLNLLGLAyARLGEPRKAIEHYEQALKISREI 241
                                       99999999988898776899988752689******************95 PP

>> APOC4  Apolipoprotein C4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     7e-05     0.096      40      86 ..     110     158 ..      90     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7e-05
                             APOC4  40 qwfwgPeafqgfvqtyyddhlkdlgprtk...awlrsskdsllnkakslc 86 
                                        w+ +P++    +  yy+d +++  +r +   a l s +d++l   +s c
  gi|330508623|ref|YP_004385051.1| 110 AWLTSPDSALTRLAEYYEDFIREQMQRGQtryALLDSQRDHILA-VRSAC 158
                                       6**********************999977445778899999885.45556 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.4       3.2   4.5e+03       5      13 ..     101     109 ..      98     112 .. 0.62
   2 ?   -0.1   0.1       1.5   2.1e+03      10      22 ..     157     169 ..     157     170 .. 0.83
   3 ?    9.9   0.0   0.00091       1.3       3      26 .]     210     233 ..     208     233 .. 0.88
   4 ?   -1.0   0.0       3.1   4.3e+03      15      26 .]     269     280 ..     261     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.2
                             TPR_4   5 laLAralla 13 
                                       +aLA ++++
  gi|330508623|ref|YP_004385051.1| 101 HALAHTYAR 109
                                       566666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
                             TPR_4  10 allalGdldeAra 22 
                                       a+ ++G +++Ar+
  gi|330508623|ref|YP_004385051.1| 157 ACNRAGLWEAART 169
                                       5779999****97 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00091
                             TPR_4   3 allaLArallalGdldeAraller 26 
                                       +l +L+ a+++lG++  A ++ e+
  gi|330508623|ref|YP_004385051.1| 210 FLNLLGLAYARLGEPRKAIEHYEQ 233
                                       5668**************999987 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 3.1
                             TPR_4  15 GdldeAraller 26 
                                       G + eA+a+ e+
  gi|330508623|ref|YP_004385051.1| 269 GLAKEALAIYEQ 280
                                       667899999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); 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:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2081.70
//
Query:       gi|330508624|ref|YP_004385052.1|  [L=113]
Description: hypothetical protein MCON_2862 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-10   39.0   0.0    9.3e-10   38.7   0.0    1.2  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
      0.091   12.5   0.0       0.11   12.2   0.0    1.2  1  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0     1e-13   9.3e-10       2      47 ..      42      87 ..      41     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1e-13
                   HicB_lk_antitox  2 piaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhleg 47
                                      pi++e de+  y v+ P ++Gc+s+g+t++ea++n++e++++ le+
  gi|330508624|ref|YP_004385052.1| 42 PILVEIDENGLYIVSCPLFKGCHSWGETIDEAMKNISEVVDMCLEE 87
                                      89******************************************98 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 ?   12.2   0.0   1.2e-05      0.11      14      72 ..      16      75 ..       5      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.2e-05
                                      EEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEE..ESGGGSCHHHH CS
                      TPP_enzyme_M 14 pvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylg..mlglhgskaan 72
                                      p+ l+G+  +  +a+e  r++ ekl++P++      g++  ++pl+ g  ++g + ++a +
  gi|330508624|ref|YP_004385052.1| 16 PLSLLGNIFK-LEAQENKRSFMEKLHLPILVEIDENGLYIVSCPLFKGchSWGETIDEAMK 75
                                      5556666555.689999*****************************883355544333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 886.61
//
Query:       gi|330508625|ref|YP_004385053.1|  [L=81]
Description: YcfA-like protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-17   63.9   0.1    1.3e-17   63.6   0.1    1.1  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
  ------ inclusion threshold ------
      0.059   13.4   0.0      0.074   13.1   0.0    1.2  1  DUF1667     Protein of unknown function (DUF1667)


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.1   1.4e-21   1.3e-17       2      54 ..      10      61 ..       9      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.4e-21
                                      HCHHHHHHHTT-EEEEEETTEEEEE-TTSS-EEEEE.S-SSS--CCCHHHHHH CS
                        HicA_toxin  2 reviklLeklGfevvrqkGSHvrfkhpdkrgivtvppHpgkelkpgtlksIlk 54
                                      +++++ L++lGf v+r+kGSHvr++ +d+r  +tvp H+++e+++g+l++I++
  gi|330508625|ref|YP_004385053.1| 10 QDLLRFLKALGFIVIRTKGSHVRLRSEDGR-LTTVPIHSNREIPKGLLRKIIR 61
                                      79************************9999.89******************97 PP

>> DUF1667  Protein of unknown function (DUF1667)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.3e-06     0.074      23      51 ..      34      62 ..      22      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.3e-06
                           DUF1667 23 kveggelplvpVktsepipkekifevmke 51
                                      + e+g+l +vp+ ++++ipk ++ ++++e
  gi|330508625|ref|YP_004385053.1| 34 RSEDGRLTTVPIHSNREIPKGLLRKIIRE 62
                                      456899******************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 587.25
//
Query:       gi|330508626|ref|YP_004385054.1|  [L=49]
Description: hypothetical protein MCON_2864 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       215  (0.0119917); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 377.64
//
Query:       gi|330508627|ref|YP_004385055.1|  [L=616]
Description: carbon-monoxide dehydrogenase, catalytic subunit [Methanosaeta concilii GP6]
Scores for complete 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-168  561.6   0.3   1.8e-168  561.4   0.3    1.0  1  Prismane     Prismane/CO dehydrogenase family
  ------ inclusion threshold ------
      0.045   13.1   0.2      0.088   12.2   0.2    1.4  1  GMC_oxred_N  GMC oxidoreductase


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 !  561.4   0.3    2e-172  1.8e-168       1     510 [.      47     595 ..      47     596 .. 0.98

  Alignments for each domain:
  == domain 1  score: 561.4 bits;  conditional E-value: 2e-172
                                       -EE-SSTCT-ECSC....S.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCHTSTTTB-SHHH CS
                                       xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane   1 mfCrqCengpCrit....knkrGvCGkdadtavardlliavlkgaaahaahareladtliakalfktltnvnfddek 73 
                                       ++Cr+C++gpCri+    +++rGvCG++ad++var+ll+ +++gaaah++h+r++a+++ +  ++k+  ++ ++d +
  gi|330508627|ref|YP_004385055.1|  47 ICCRNCNMGPCRIDpfgeGASRGVCGATADIIVARNLLRSIAAGAAAHSDHGRDVAHAFQLIVEGKA-PSYCIKDPE 122
                                       6*****************************************************************9.********* PP

                                       HHHHHHHHHCHHHCCSSHHHHHHHHCCHHHCGGGS-SSHHHHHHHCCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane  74 klkrlaealgieeelkdieelaakvaevaledlskeenedirslkellpkglkglyaehaivlgyadeevveflakt 150
                                       kl+rl +++g++++          +a + +++++k++      ++ ++p+++ +l+++++i ++++d+e+ve++++t
  gi|330508627|ref|YP_004385055.1| 123 KLDRLMKEYGLDSPA--------LLAAAIMNEFGKQD--GPIQFTRRVPPQRLELWKKLGIDPRGVDREIVECMHRT 189
                                       ************999........67777899***995..555677889999************************** PP

                                       CCCTTSTHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHH-----EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 151 laglesdpldllskalrlGlld.lkgmelldeantslfGtPeppltevnlgvldkdkvnIlvsGHdladleelleqt 226
                                       ++g+++d+++l+ + lr++++d ++g+++++e+++++fGtP+p  +e+n+gv+++d+vn++v+GH++ ++e+++ ++
  gi|330508627|ref|YP_004385055.1| 190 HIGVDNDYVNLILHGLRTSISDgWGGSMIATELQDVIFGTPKPLFSEANMGVIKPDQVNLIVHGHEPLLSEMIVAAA 266
                                       ***************************************************************************** PP

                                       CTTCCCCCCC.....GCCCCCCHHHHHHHHHCCEEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCE CS
                                       xxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 227 egkglnvyth.....gemLpghcctalklkyrhlvgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktr 298
                                       +++++ + ++     g++L+g+ccta++l +r++v+++Gn+++qe+ ++tgav+a+vvd++Ci+p l  +a++++t+
  gi|330508627|ref|YP_004385055.1| 267 SDPDMIELARnegakGINLAGICCTANELLMRQGVPMAGNFLSQELIMATGAVEAMVVDVQCIMPALGPLASCFHTK 343
                                       *********999***************************************************************** PP

                                       EEEECTTB-.TTSEEE-.-CTTCHHHHHHHHHHHHCCHCCTTCGG.-............................HH CS
                                       xxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................xx RF
                          Prismane 299 littsevak.pgakhie.eeekadkdaseiiekAielakareekkve............................id 345
                                       +i+ts++ak pga+h+e +e++a ++a+ei+++Ai+++++r++++v+                            i+
  gi|330508627|ref|YP_004385055.1| 344 FISTSPKAKfPGATHMEfHEDTAGETAKEIVRTAIKNFRNRDPSRVQipdiktrcmagfsveaivsalggsldplIE 420
                                       *****************999999********************9999****************************** PP

                                       HHHTTSS-EEEEE-B---TTCGCC.HHHHHHHHCHHTTEEEEEECHHHHHCCCTTTTECGHHHHSTHC......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                          Prismane 346 aiksGtIkgvvlvvGCdnakkgrd.yytelakelikrdvlvltaGCakyalnklglgtieaaelageg......... 412
                                       aiksG I+g+ +vvGC+n+k ++d  ++ +++elik++vlvlt+GC++ a++k+gl+++eaae ag+g         
  gi|330508627|ref|YP_004385055.1| 421 AIKSGSIRGIGAVVGCNNPKITQDfGHIGMVRELIKNNVLVLTTGCNAQACAKAGLLQPEAAEKAGDGlkgvcqalg 497
                                       ***************************************************************************** PP

                                       EESEEEEESCCCHHHHHHHHHHHHHHTTSSGGGSSEEEEECC--SHHHHHHHHHHHHTT-CEEECSS-TTTT-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 413 iPrvLdvGsCvdnyrivvialklaealgvdindLplaalalewyeqKAvailltllalGinihlgptlpafgspnvl 489
                                       +P+vL++GsCvd++ri+v+a++la+algvdi+dLp a +a+ew+++KAv+i+++++++G+ ++lg+++p++gs+ v+
  gi|330508627|ref|YP_004385055.1| 498 VPPVLHMGSCVDISRILVAAAALANALGVDISDLPAAGAAPEWMSEKAVSIGAYVVSSGVFTVLGTVPPVMGSKAVA 574
                                       ***************************************************************************** PP

                                       HHHHCHHHHHHCEEEECHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 490 kvlvedfedriggivtveedp 510
                                       ++l++ ++d +g+ + ve+dp
  gi|330508627|ref|YP_004385055.1| 575 ELLTSGAKDVVGACFAVEPDP 595
                                       ********************9 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   9.8e-06     0.088     147     188 ..       8      51 ..       4      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.8e-06
                       GMC_oxred_N 147 keesplnkallkaaeelGlp.vprdlngk.hqcGvcllgvtcrt 188
                                       k   p+++ +l+a+e+ Gl+   ++l+++  qcG++ lg  cr+
  gi|330508627|ref|YP_004385055.1|   8 KSMDPACQEMLRACEKSGLEtAWDRLEKQqPQCGFGELGICCRN 51 
                                       56689***************644555555689*******88875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 4159.64
//
Query:       gi|330508628|ref|YP_004385056.1|  [L=172]
Description: 4Fe-4S binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-16   59.0  12.7    3.9e-16   59.0  12.7    1.8  2  Fer4_11        4Fe-4S dicluster domain
    7.7e-11   42.0  25.7    7.8e-06   26.0  10.8    2.9  3  Fer4_9         4Fe-4S dicluster domain
    1.3e-10   41.6  31.4    7.9e-05   23.2  10.8    3.0  3  Fer4_7         4Fe-4S dicluster domain
      3e-09   36.3  35.6    0.00011   21.9   3.9    5.1  5  Fer4           4Fe-4S binding domain
    1.2e-06   28.6  32.9      0.022   15.2   4.0    4.4  4  Fer4_4         4Fe-4S binding domain
    1.4e-06   28.3  29.1     0.0063   16.6  12.4    2.9  4  Fer4_10        4Fe-4S dicluster domain
    2.8e-06   27.1  37.3      0.012   15.6   2.8    4.6  4  Fer4_6         4Fe-4S binding domain
    6.1e-06   26.0  32.8     0.0064   16.5   1.8    4.2  4  Fer4_2         4Fe-4S binding domain
    8.6e-06   26.6  27.5       0.31   12.0   2.3    4.6  5  Fer4_16        4Fe-4S double cluster binding domain
    6.6e-05   23.0  27.3     0.0039   17.3   9.3    3.4  3  Fer4_21        4Fe-4S dicluster domain
     0.0023   18.4  28.9       0.25   11.9   2.4    4.2  4  Fer4_17        4Fe-4S dicluster domain
     0.0076   16.7  26.9       0.27   11.7   8.3    3.4  3  Fer4_8         4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.024   14.7   0.1      0.073   13.2   0.1    1.9  1  Fe_dep_repr_C  Iron dependent repressor, metal binding and di
      0.092   12.5  26.6      0.087   12.6   1.3    3.7  3  Fer4_20        Dihydroprymidine dehydrogenase domain II, 4Fe-
       0.11   13.5   4.5       0.11   13.5   4.5    4.3  4  Fer4_3         4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.4       1.6   1.9e+03      10      20 ..      14      22 ..       4      36 .. 0.56
   2 !   59.0  12.7   3.2e-19   3.9e-16       6      96 ..      58     143 ..      54     147 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.6
                           Fer4_11 10 CrhCleppCva 20
                                      C+ C   +C +
  gi|330508628|ref|YP_004385056.1| 14 CMGCR--SCEM 22
                                      33332..2222 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 3.2e-19
                           Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGl 82 
                                       +p +CrhC+++pCva++ ++a+v+d   G+V   e+++  ++ ++++ cPy +v +++e  ++ kCd c +      
  gi|330508628|ref|YP_004385056.1|  58 VPMICRHCQDAPCVAVCRTGALVQDSLSGVVERIEENCM-GCWMCAMICPYGVVGRKKEVRMAVKCDRCKSLE---- 129
                                       799***********************************7.**************************9997765.... PP

                           Fer4_11  83 lpacvescptgaln 96 
                                       +pacv +cptgal 
  gi|330508628|ref|YP_004385056.1| 130 VPACVAACPTGALI 143
                                       6**********986 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   7.6   4.6e-07   0.00055       1      50 [.      13      78 ..      13      79 .. 0.71
   2 !   18.6  11.8   1.3e-06    0.0016       2      50 ..      62     109 ..      61     110 .. 0.88
   3 !   26.0  10.8   6.6e-09   7.8e-06       1      50 [.      94     141 ..      94     142 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.6e-07
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase..............eaCigCga..CveaCpkga 50
                                      +C+gC++C+ aC  ++ + ++    ++ +                    C +C++  Cv++C +ga
  gi|330508628|ref|YP_004385056.1| 13 RCMGCRSCEMACAIEHSISKNLISSISEKPVPVrllyvekaegrnvpMICRHCQDapCVAVCRTGA 78
                                      6***********5555555555555554443335555556667777767**************997 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.3e-06
                            Fer4_9   2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       C  C+   Cv++C +g+ v+d+  + ++  +   e+C+gC  C+ +Cp g+
  gi|330508628|ref|YP_004385056.1|  62 CRHCQDapCVAVCRTGALVQDSLSGVVERIE---ENCMGCWMCAMICPYGV 109
                                       99**9777***************99999644...47************985 PP

  == domain 3  score: 26.0 bits;  conditional E-value: 6.6e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.....CveaCpkga 50 
                                       +C+gC  C   Cp+gvv +++  r+a        +C  C++     Cv+aCp+ga
  gi|330508628|ref|YP_004385056.1|  94 NCMGCWMCAMICPYGVVGRKKEVRMAV-------KCDRCKSlevpaCVAACPTGA 141
                                       6********************999999.......5******************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 !   23.2  10.8   6.6e-08   7.9e-05       1      52 []      13      78 ..      13      78 .. 0.68
   2 !   22.2  13.4   1.3e-07   0.00016       2      52 .]      95     141 ..      94     141 .. 0.88
   3 !   11.7   3.0   0.00025       0.3       1      20 [.     121     145 ..     121     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.6e-08
                            Fer4_7  1 rCigCgaCvaaCp.vkaield......eeenek.........gtekveidpekClgCga..CvavCPtga 52
                                      rC+gC+ C+ aC   + i+ +      e    k         ++++ + +p+ C +C+   CvavC tga
  gi|330508628|ref|YP_004385056.1| 13 RCMGCRSCEMACAiEHSISKNlissisE----KpvpvrllyvEKAEGRNVPMICRHCQDapCVAVCRTGA 78
                                      8***********6555555553322111....122334444444667889********999*******97 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.3e-07
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga..CvavCPtga 52 
                                       C+gC  C+  Cp++++  ++e       +++++ ++C + ++  Cva+CPtga
  gi|330508628|ref|YP_004385056.1|  95 CMGCWMCAMICPYGVVGRKKE------VRMAVKCDRCKSLEVpaCVAACPTGA 141
                                       *****************9886......56899999998876566*******98 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00025
                            Fer4_7   1 rCigCg.....aCvaaCpvkaield 20 
                                       +C  C+     aCvaaCp++a+ + 
  gi|330508628|ref|YP_004385056.1| 121 KCDRCKslevpACVAACPTGALIYS 145
                                       6999988888899999999887554 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.8     1e-05     0.012       3      18 ..       9      24 ..       7      24 .. 0.89
   2 !    6.1   0.7    0.0088        10      14      23 ..      70      79 ..      69      80 .. 0.93
   3 !   21.9   3.9     9e-08   0.00011       3      22 ..      90     109 ..      88     110 .. 0.89
   4 ?   -0.2   0.2      0.84     1e+03       7      12 ..     121     126 ..     119     127 .. 0.68
   5 !   12.5   1.5     8e-05     0.095      13      23 ..     132     142 ..     132     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                                      EETTTSSS-THHHHHS CS
                              Fer4  3 ideekCigCGaCvevC 18
                                      +  e+C+gC  C+++C
  gi|330508628|ref|YP_004385056.1|  9 VRLERCMGCRSCEMAC 24
                                      6679************ PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0088
                                      HHHHSTTTEE CS
                              Fer4 14 CvevCPvgAI 23
                                      Cv vC +gA+
  gi|330508628|ref|YP_004385056.1| 70 CVAVCRTGAL 79
                                      *********8 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 9e-08
                                       EETTTSSS-THHHHHSTTTE CS
                              Fer4   3 ideekCigCGaCvevCPvgA 22 
                                        +ee C+gC  C+++CP+g+
  gi|330508628|ref|YP_004385056.1|  90 RIEENCMGCWMCAMICPYGV 109
                                       579***************97 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.84
                                       TSSS-T CS
                              Fer4   7 kCigCG 12 
                                       kC +C+
  gi|330508628|ref|YP_004385056.1| 121 KCDRCK 126
                                       677774 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 8e-05
                                       HHHHHSTTTEE CS
                              Fer4  13 aCvevCPvgAI 23 
                                       aCv +CP+gA+
  gi|330508628|ref|YP_004385056.1| 132 ACVAACPTGAL 142
                                       7*********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 !   15.2   4.0   1.8e-05     0.022       2      14 ..      12      24 ..      11      25 .. 0.94
   2 ?    5.2   2.6     0.029        35       4      16 ..      62      76 ..      55      77 .. 0.88
   3 !   11.3   2.1   0.00035      0.41       2      17 .]      93     108 ..      92     108 .. 0.93
   4 !   13.8   1.5   5.4e-05     0.064       3      17 .]     121     140 ..     119     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                            Fer4_4  2 erCigCgsCvaaC 14
                                      erC gC+sC+ aC
  gi|330508628|ref|YP_004385056.1| 12 ERCMGCRSCEMAC 24
                                      9************ PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.029
                            Fer4_4  4 CigCgs..CvaaCPq 16
                                      C +C    Cva+C +
  gi|330508628|ref|YP_004385056.1| 62 CRHCQDapCVAVCRT 76
                                      99***779*****76 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00035
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       e+C gC  C  +CP+g
  gi|330508628|ref|YP_004385056.1|  93 ENCMGCWMCAMICPYG 108
                                       89************86 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 5.4e-05
                            Fer4_4   3 rCigCgs.....CvaaCPqg 17 
                                       +C +C+s     CvaaCP+g
  gi|330508628|ref|YP_004385056.1| 121 KCDRCKSlevpaCVAACPTG 140
                                       699***777777******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 !   14.4  10.3   2.5e-05      0.03       5      55 ..      10      74 ..       6      75 .. 0.92
   2 !   13.9  11.6   3.6e-05     0.043       7      56 .]      60     106 ..      54     106 .. 0.94
   3 !   16.6  12.4   5.3e-06    0.0063       5      56 .]      91     138 ..      87     138 .. 0.74
   4 !   10.9   2.4   0.00032      0.38       7      23 ..     120     141 ..     114     166 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                           Fer4_10  5 dddtCirCgkCvkaCPadl..............tsvgakgeaseeeavrkkvekCtgcg..aCveaC 55
                                        ++C++C+ C  aC   +              + v ++  + e+++ r ++  C +c    Cv++C
  gi|330508628|ref|YP_004385056.1| 10 RLERCMGCRSCEMAC--AIehsisknlissiseKPVPVRLLYVEKAEGRNVPMICRHCQdaPCVAVC 74
                                      5689***********..4668*************************************777****** PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.6e-05
                           Fer4_10   7 dtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                         C +C+   Cv++C     + ga  ++s +++v+   e+C+gc +C+ +CP
  gi|330508628|ref|YP_004385056.1|  60 MICRHCQdaPCVAVC-----RTGALVQDSLSGVVERIEENCMGCWMCAMICP 106
                                       57****9999*****.....78*****************************9 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 5.3e-06
                           Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg..aCveaCP 56 
                                        ++ C++C  C   CP+      +   +++e +  +k+++C   +  aCv+aCP
  gi|330508628|ref|YP_004385056.1|  91 IEENCMGCWMCAMICPY------GVVGRKKEVRMAVKCDRCKSLEvpACVAACP 138
                                       5789*************......444445555555567777776577******9 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00032
                           Fer4_10   7 dtCirCg.....kCvkaCPadl 23 
                                        +C rC+     +Cv+aCP+ +
  gi|330508628|ref|YP_004385056.1| 120 VKCDRCKslevpACVAACPTGA 141
                                       5677777666667777777754 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.4   6.9e-05     0.082       5      20 ..      10      25 ..       6      30 .. 0.84
   2 !    7.0   4.0    0.0055       6.6       9      24 .]      62      79 ..      60      79 .. 0.83
   3 !   15.6   2.8     1e-05     0.012       1      23 [.      87     109 ..      87     110 .. 0.93
   4 !    8.8   6.1    0.0015       1.8       8      24 .]     121     142 ..     118     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-05
                            Fer4_6  5 dpdkCigCgdCvrvCP 20
                                        ++C gC+ C+++C 
  gi|330508628|ref|YP_004385056.1| 10 RLERCMGCRSCEMACA 25
                                      5689***********5 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0055
                            Fer4_6  9 CigC.gd.CvrvCPegai 24
                                      C +C ++ Cv+vC +ga+
  gi|330508628|ref|YP_004385056.1| 62 CRHCqDApCVAVCRTGAL 79
                                      99995448*******997 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1e-05
                            Fer4_6   1 vveidpdkCigCgdCvrvCPega 23 
                                       vve  +++C gC  C+++CP+g+
  gi|330508628|ref|YP_004385056.1|  87 VVERIEENCMGCWMCAMICPYGV 109
                                       68999****************97 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0015
                            Fer4_6   8 kCigCgd.....CvrvCPegai 24 
                                       kC+ C       Cv++CP+ga+
  gi|330508628|ref|YP_004385056.1| 121 KCDRCKSlevpaCVAACPTGAL 142
                                       788887778888********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 !   16.5   1.8   5.3e-06    0.0064       4      20 ..       8      24 ..       5      25 .. 0.86
   2 !    6.6   3.6    0.0078       9.3       9      20 ..      61      74 ..      55      76 .. 0.86
   3 !   10.1   1.4   0.00058      0.69       5      22 .]      90     107 ..      86     107 .. 0.84
   4 !   10.3   3.5   0.00051       0.6       9      22 .]     121     139 ..     116     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.3e-06
                            Fer4_2  4 vvdtdrCigCgaCvsaC 20
                                      +v  +rC+gC++C  aC
  gi|330508628|ref|YP_004385056.1|  8 FVRLERCMGCRSCEMAC 24
                                      55679************ PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0078
                            Fer4_2  9 rCigCg..aCvsaC 20
                                      +C +C   +Cv +C
  gi|330508628|ref|YP_004385056.1| 61 ICRHCQdaPCVAVC 74
                                      7****888****** PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00058
                            Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                         +++C+gC  C   CP+
  gi|330508628|ref|YP_004385056.1|  90 RIEENCMGCWMCAMICPY 107
                                       56899****88******5 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00051
                            Fer4_2   9 rCigCg.....aCvsaCPa 22 
                                       +C +C+     aCv aCP+
  gi|330508628|ref|YP_004385056.1| 121 KCDRCKslevpACVAACPT 139
                                       7****8899*********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 !   10.6   0.6   0.00072      0.86      49      65 ..       9      25 ..       1      34 [. 0.72
   2 !    7.7   1.6    0.0058         7       2      20 ..      62      82 ..      61      94 .. 0.84
   3 !   12.0   2.3   0.00026      0.31      50      66 ..      91     107 ..      84     108 .. 0.84
   4 !    8.0   7.4    0.0048       5.7       1      25 [.      94     118 ..      94     131 .. 0.73
   5 !   11.3   1.8   0.00044      0.53       7      31 ..     132     156 ..     120     171 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00072
                           Fer4_16 49 kkqeaitgCdiCqdvCP 65
                                       + e+++gC+ C+++C 
  gi|330508628|ref|YP_004385056.1|  9 VRLERCMGCRSCEMACA 25
                                      45577888888888885 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0058
                           Fer4_16  2 CgtCgk..CaevCPtnaikek 20
                                      C  C+   C+ vC t+a+ ++
  gi|330508628|ref|YP_004385056.1| 62 CRHCQDapCVAVCRTGALVQD 82
                                      999*9999**********988 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00026
                           Fer4_16  50 kqeaitgCdiCqdvCPa 66 
                                       ++e+++gC +C+++CP+
  gi|330508628|ref|YP_004385056.1|  91 IEENCMGCWMCAMICPY 107
                                       46889***********8 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0048
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekei 25 
                                       +C +C  Ca++CP +++  kke ++
  gi|330508628|ref|YP_004385056.1|  94 NCMGCWMCAMICPYGVVGRKKEVRM 118
                                       5999999999999999998854443 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.00044
                           Fer4_16   7 kCaevCPtnaikekkekeieareci 31 
                                       +C+ +CPt+a+   +++e++  + +
  gi|330508628|ref|YP_004385056.1| 132 ACVAACPTGALIYSTQREFAEMMRK 156
                                       6*********998866766544443 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.7   2.3e-05     0.027      31      57 ..       4      30 ..       1      32 [. 0.79
   2 !   17.3   9.3   3.3e-06    0.0039       8      53 ..      62     107 ..      59     112 .. 0.76
   3 ?    1.8   2.6      0.22   2.6e+02      34      53 ..     118     139 ..     108     144 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                           Fer4_21 31 ktvlkvvedeCvGCnlCssvCPvedci 57
                                      ++ + v+ ++C+GC  C   C +e  i
  gi|330508628|ref|YP_004385056.1|  4 NKEIFVRLERCMGCRSCEMACAIEHSI 30
                                      556677889999999999999998877 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.3e-06
                           Fer4_21   8 CigCgk..CliaCedtshqai.eidaktvlkvvedeCvGCnlCssvCPv 53 
                                       C +C+   C+ +C++    a+ + + + v++ +e++C+GC +C+ +CP 
  gi|330508628|ref|YP_004385056.1|  62 CRHCQDapCVAVCRT---GALvQDSLSGVVERIEENCMGCWMCAMICPY 107
                                       777864449999*95...455144456688999***************4 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.22
                           Fer4_21  34 lkvvedeCvGCnl..CssvCPv 53 
                                       ++v  d+C   ++  C++ CP+
  gi|330508628|ref|YP_004385056.1| 118 MAVKCDRCKSLEVpaCVAACPT 139
                                       4555566666553338888886 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   2.4   0.00021      0.25      42      56 ..      10      24 ..       1      28 [. 0.80
   2 ?    5.2  10.6     0.026        31       2      60 ..      62     109 ..      61     110 .. 0.66
   3 !   10.8   2.3   0.00046      0.55      46      60 ..      95     109 ..      94     121 .. 0.63
   4 !    6.6   1.2    0.0096        11       2      31 ..     122     159 ..     121     171 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                           Fer4_17 42 kaslCieCgeCerkC 56
                                      + ++C++C+ Ce++C
  gi|330508628|ref|YP_004385056.1| 10 RLERCMGCRSCEMAC 24
                                      6799*********** PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.026
                           Fer4_17   2 CiqCgy..ClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60 
                                       C++C+   C+++C +++  ++    +++++              ++C++C +C++ CP+g+
  gi|330508628|ref|YP_004385056.1|  62 CRHCQDapCVAVCRTGALVQDSLSGVVERI-------------EENCMGCWMCAMICPYGV 109
                                       666665556666666666665555555441.............257************986 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00046
                           Fer4_17  46 CieCgeCerkCPqgl 60 
                                       C++C +C++ CP+g+
  gi|330508628|ref|YP_004385056.1|  95 CMGCWMCAMICPYGV 109
                                       666666666666554 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0096
                           Fer4_17   2 CiqCgy.....ClpeCpsyea...ydnepkkllraakl 31 
                                       C +C+      C+++Cp+++    ++ e ++++r+ ++
  gi|330508628|ref|YP_004385056.1| 122 CDRCKSlevpaCVAACPTGALiysTQREFAEMMRKEAA 159
                                       88888444455******988753333333466666444 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   8.3   0.00022      0.27       2      64 ..      11      77 ..      10      78 .. 0.69
   2 !    7.8   2.8    0.0038       4.5      49      64 ..      93     108 ..      79     109 .. 0.71
   3 ?    1.6  11.2      0.32   3.8e+02       4      31 ..      94     123 ..      92     171 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae.....dvqeeqvleeeealwsCttcga..CtevCpvg 64
                                      le+C++C  C+ aC + ++  k l ++  e+       +v++ ++   ++    C +c+   C+ vC +g
  gi|330508628|ref|YP_004385056.1| 11 LERCMGCRSCEMACAIEHSISKNLISSISEKPVpvrllYVEKAEG---RNVPMICRHCQDapCVAVCRTG 77
                                      689***********7555555444444444333233454444444...78899******999*****876 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0038
                            Fer4_8  49 wsCttcgaCtevCpvg 64 
                                       ++C++c +C+  Cp g
  gi|330508628|ref|YP_004385056.1|  93 ENCMGCWMCAMICPYG 108
                                       6788888888888766 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.32
                            Fer4_8   4 kCieCgaCqsaCp..vlrrtkkhlldarge 31 
                                       +C++C +C   Cp  v+ r+k+ ++  + +
  gi|330508628|ref|YP_004385056.1|  94 NCMGCWMCAMICPygVVGRKKEVRMAVKCD 123
                                       788888888888866333333333333333 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 ?   13.2   0.1   6.1e-05     0.073      32      54 ..      18      40 ..       5      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
                                      CHHHHCCCCGGGS-HHHHHHHHH CS
                     Fe_dep_repr_C 32 eaheeAerlEhalseelierlde 54
                                      + +e A+++Eh +s++li  + e
  gi|330508628|ref|YP_004385056.1| 18 RSCEMACAIEHSISKNLISSISE 40
                                      5699**************99865 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 ?    9.4   1.6   0.00069      0.83      19      52 ..       9      41 ..       2      54 .. 0.80
   2 ?    1.1   8.4      0.26   3.2e+02      24      52 ..      62      90 ..      47     113 .. 0.74
   3 ?   12.6   1.3   7.3e-05     0.087      17      63 ..     118     164 ..     107     171 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00069
                                      HHHTT----TT-HHHHCSTT---HH.HHHHHHHTT CS
                           Fer4_20 19 eeAsRClqCkkapcvkgCPveidip.efikkiaeg 52
                                         +RC+ C  + c+ +C +e +i  + i++i+e+
  gi|330508628|ref|YP_004385056.1|  9 VRLERCMGC--RSCEMACAIEHSISkNLISSISEK 41
                                      5668*****..89*********9962578888876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.26
                                      ----TT-HHHHCSTT---HHHHHHHHHTT CS
                           Fer4_20 24 ClqCkkapcvkgCPveidipefikkiaeg 52
                                      C +C++apcv+ C +   +++ ++ + e+
  gi|330508628|ref|YP_004385056.1| 62 CRHCQDAPCVAVCRTGALVQDSLSGVVER 90
                                      99***********9998777666655544 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 7.3e-05
                                       HHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHH CS
                           Fer4_20  17 aleeAsRClqCkkapcvkgCPveidipefikkiaegnleeaakiike 63 
                                        + + +RC + + + cv++CP+   i +  ++ ae   +eaa  i +
  gi|330508628|ref|YP_004385056.1| 118 MAVKCDRCKSLEVPACVAACPTGALIYSTQREFAEMMRKEAAARIAR 164
                                       334455666666899***********999999998888777766654 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   5.2      0.16   1.9e+02       1      11 [.      14      24 ..      14      27 .. 0.94
   2 ?   11.4   6.0   0.00044      0.52       1      15 []      62      78 ..      62      78 .. 0.92
   3 ?    2.2   5.9      0.37   4.4e+02       1      14 [.      95     108 ..      95     109 .. 0.89
   4 ?   13.5   4.5   9.1e-05      0.11       1      15 []     122     141 ..     122     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.16
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+gC+ C+ +C
  gi|330508628|ref|YP_004385056.1| 14 CMGCRSCEMAC 24
                                      ********999 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00044
                            Fer4_3  1 CtgCg..aCvevCPvgA 15
                                      C +C+  +Cv vC++gA
  gi|330508628|ref|YP_004385056.1| 62 CRHCQdaPCVAVCRTGA 78
                                      99**8778********9 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.37
                            Fer4_3   1 CtgC.gaCvevCPvg 14 
                                       C+gC + C   CP+g
  gi|330508628|ref|YP_004385056.1|  95 CMGCwM-CAMICPYG 108
                                       999977.******98 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 9.1e-05
                            Fer4_3   1 CtgCg.....aCvevCPvgA 15 
                                       C+ C      aCv +CP+gA
  gi|330508628|ref|YP_004385056.1| 122 CDRCKslevpACVAACPTGA 141
                                       999*6688999********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1197.77
//
Query:       gi|330508629|ref|YP_004385057.1|  [L=661]
Description: acetyl-coenzyme A synthetase [Methanosaeta concilii GP6]
Scores for complete 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-91  305.6   0.0    5.3e-91  305.3   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    2.2e-28   99.0   5.7    1.6e-27   96.2   3.8    2.6  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
    4.2e-18   65.0   3.7    4.2e-18   65.0   3.7    2.1  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.3   0.0   8.8e-95   5.3e-91       4     422 ..     101     540 ..      98     541 .. 0.89

  Alignments for each domain:
  == domain 1  score: 305.3 bits;  conditional E-value: 8.8e-95
                                       HHHHST.TSEEEEE....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEE CS
                       AMP-binding   4 qaaktp.dkvalvd....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvv 75 
                                       +a   + +kva+++     g+ + +TY +l+++vnrlA++L+s Gv+kgdrV+ +lp+ pe  +++la++k+Ga++ 
  gi|330508629|ref|YP_004385057.1| 101 HAHSEKrNKVAYYFvgepVGDAKAITYYQLYREVNRLANALKSVGVEKGDRVVTYLPMIPEQPITMLACAKIGAIHT 177
                                       55444449****8899*9889******************************************************** PP

                                       EEETTS-HHHHHHHHHHHTESEEE.......ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCS CS
                       AMP-binding  76 plnptltaeelayiledseakvli.......atvdsel.leklleaaakleavklvivldadellkeeelkeeeese 144
                                        + +++++  la  ++d+eakv++       +  +     ++++ea ++ ++vk+viv+++ +++   ++  +   +
  gi|330508629|ref|YP_004385057.1| 178 LVFSGFSSGGLASRVNDAEAKVVVtadgfyrR-GKPLPlKPNVDEALKNSPSVKKVIVVKRTGVSVPMTEGRDV-YY 252
                                       ************************99887642.34556689999*******************99996665555.44 PP

                                       CTT.S...-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHH.HHHHHHHHHHHC.SCCTTT-EEEESS-TTSCH CS
                       AMP-binding 145 eka.e...kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnl.vanvaslkletr.fklkeddvvlsilplahif 215
                                       ++      +++e+++l+p+d ++i+YTSGTTGkPKG+ + h+ + v ++++ +      ++++ddv++++++  +i+
  gi|330508629|ref|YP_004385057.1| 253 DDFvAgqsTKCETVPLDPEDRLFILYTSGTTGKPKGIEHAHGGYaVGAAQTTS---WvLDVHDDDVYWCTADAGWIT 326
                                       33341567889999***************************666144444432...2355788************** PP

                                       HHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEE CS
                       AMP-binding 216 glilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllg 291
                                       g+++ ++++l+ Ga+ +l++++++ +d ++++  ie+++v+v++++P++++++++sg++  ++k++dlss+r++ ++
  gi|330508629|ref|YP_004385057.1| 327 GHSYVIYGPLILGASSILYEGSPDfPDLGRWWSIIEEYGVSVFYSAPTAVRMFMKSGEE--FVKKYDLSSIRILASV 401
                                       ************************88899**************************8654..47788*********** PP

                                       SS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEE CS
                       AMP-binding 292 geplspellrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeG 365
                                       gepl+pe+  +fr+  g    ++++++++TEt+++v+ +pl    +k+gsv +plpg+   i De+  + vp g  G
  gi|330508629|ref|YP_004385057.1| 402 GEPLNPEAYMWFRKNIGSdqaPIMDTWWQTETGCHVV-APLAMTPEKPGSVCFPLPGMNTDIYDED-ANSVPLGYGG 476
                                       ***************999******************9.666666688******************9.9********* PP

                                       EEEEEET..TS-SEBTT-HHHHHHHEEE.....TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 366 ellvrgp..gvmkgYlkkpeataeafds.....egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                        ++   p  ++ + +++++ + ++ +++     +++ +  GD +++d+dGy +i gR++d++k+
  gi|330508629|ref|YP_004385057.1| 477 NIVQTAPwpSMLRAFFRDEIRYKKEYWDmywqvKPGTYLAGDKATRDKDGYWWIQGRIDDVLKV 540
                                       ***9988668*****************999977457**************************98 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.084     5e+02       2      19 ..     219     239 ..     218     249 .. 0.79
   2 !   96.2   3.8   2.8e-31   1.6e-27       1      76 []     549     627 ..     549     627 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.084
                                       HHHHHHSSTTEEEEEEE...- CS
                     AMP-binding_C   2 vEsalvshpaVaeaaVv...G 19 
                                       v +al ++p V+ + Vv   G
  gi|330508629|ref|YP_004385057.1| 219 VDEALKNSPSVKKVIVVkrtG 239
                                       789*************94444 PP

  == domain 2  score: 96.2 bits;  conditional E-value: 2.8e-31
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.---..HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.sea..leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evEsa vshp+VaeaaV+G pdevkGe +vaf++lk+g +e+  l++++  hvrk lgp+a p+kv+fv+++pktrs
  gi|330508629|ref|YP_004385057.1| 549 EVESAAVSHPKVAEAAVIGEPDEVKGEKIVAFIILKEGvVEEesLKKDISTHVRKVLGPVAYPDKVYFVKDVPKTRS 625
                                       8***********************************99633347********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|330508629|ref|YP_004385057.1| 626 GK 627
                                       *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 !   65.0   3.7     7e-22   4.2e-18       3      55 .]      44      97 ..      42      97 .. 0.97
   2 ?   -3.1   0.3       1.3   7.6e+03       7      15 ..     519     527 ..     491     532 .. 0.58

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 7e-22
                                      HHHHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  3 elykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                      e+ k+  +++ +FW+e+a+  +dW+kp++++ld+s++p++kWF+GGk+N++yN+
  gi|330508629|ref|YP_004385057.1| 44 EMRKWCSDNYIEFWDEMARTfVDWFKPYTQILDDSEKPHYKWFTGGKVNVAYNA 97
                                      899****************99********************************7 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
                                       HHHH-HHHH CS
                            ACAS_N   7 eSiedpeaF 15 
                                       ++ +d +++
  gi|330508629|ref|YP_004385057.1| 519 KATRDKDGY 527
                                       233444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (661 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 4477.56
//
Query:       gi|330508630|ref|YP_004385058.1|  [L=456]
Description: GvpD gas vesicle [Methanosaeta concilii GP6]
Scores for complete 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  126.7   0.0    1.9e-33  115.8   0.0    2.4  2  GvpD             GvpD gas vesicle protein
    5.3e-10   39.0   1.0    2.1e-08   33.8   0.1    2.9  2  ATPase           KaiC
    2.1e-05   25.0   0.0      4e-05   24.0   0.0    1.5  1  AAA_16           AAA ATPase domain
    0.00013   21.4   0.0       0.26   10.6   0.0    2.4  2  DnaB_C           DnaB-like helicase C terminal domain
     0.0013   19.2   0.0     0.0036   17.7   0.0    1.8  1  AAA              ATPase family associated with various cellul
     0.0013   19.3   0.0     0.0026   18.3   0.0    1.5  1  AAA_18           AAA domain
     0.0017   18.0   0.0      0.017   14.7   0.0    2.4  3  AAA_25           AAA domain
     0.0026   17.5   0.0      0.029   14.1   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
     0.0048   16.9   0.1       0.02   14.9   0.1    2.0  1  AAA_14           AAA domain
     0.0054   16.5   0.3      0.019   14.7   0.1    2.0  2  AAA_24           AAA domain
     0.0061   15.8   0.0      0.012   14.9   0.0    1.6  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.008   15.4   0.0      0.013   14.7   0.0    1.2  1  NB-ARC           NB-ARC domain
     0.0085   15.3   0.0      0.013   14.7   0.0    1.3  1  PIF1             PIF1-like helicase
  ------ inclusion threshold ------
      0.013   15.8   0.0      0.026   14.8   0.0    1.6  1  AAA_22           AAA domain
      0.016   14.4   0.0      0.025   13.8   0.0    1.2  1  TIP49            TIP49 P-loop domain
      0.021   14.6   0.0      0.032   14.0   0.0    1.2  1  AAA_11           AAA domain
      0.022   15.1   0.3      0.086   13.2   0.3    2.0  1  AAA_19           AAA domain
      0.023   14.6   0.1      0.052   13.5   0.1    1.6  1  NACHT            NACHT domain
      0.038   14.0   0.0      0.089   12.8   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
      0.039   14.5   0.0      0.075   13.5   0.0    1.5  1  ABC_tran         ABC transporter
      0.045   13.5   0.0      0.076   12.7   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.045   13.8   0.0      0.089   12.8   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
      0.047   13.9   0.0       0.17   12.1   0.0    1.9  2  AAA_33           AAA domain
      0.064   12.9   0.0      0.066   12.9   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.094   12.6   0.1       0.24   11.3   0.1    1.7  1  NTPase_1         NTPase
       0.13   11.7   0.0       0.31   10.6   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
       0.13   11.9   0.0       0.22   11.2   0.0    1.3  1  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   0.0   2.9e-36   1.9e-33       2     296 ..      14     312 ..      13     317 .. 0.81
   2 !    8.1   0.0    0.0013      0.86     381     475 ..     351     450 ..     341     455 .. 0.86

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 2.9e-36
                              GvpD   2 eqffdgeaGktllikGaPGtGktlftlrgldvlrresdvlyvstrvddetvseayfsgeaeldktalldllkdplel 78 
                                       ++ff+ + G+tllikG PGtGkt+++l+ + +l +e + +y+strvd   ++      e  l   ++++  +  l  
  gi|330508630|ref|YP_004385058.1|  14 KEFFHVDKGQTLLIKGMPGTGKTTLALEIMSSLCEERNGIYISTRVDPARLYATNPWIEKVLMPRNVVNATQTKLLG 90 
                                       78************************************************999885555555555555555555544 PP

                              GvpD  79 dldv...dvPiekld.lesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlv 151
                                        l++   d+       ++ +  f +  ++  ++++i +dsw+ v++y +  + +  + +  + ++  +ar+ + +lv
  gi|330508630|ref|YP_004385058.1|  91 SLNKtskDLSN-YYAvMDFFRLFFE-ETEEMDNPMIIIDSWDAVLNYTS--HLIGTSQHSFEQNICEFARDLDTHLV 163
                                       33330003332.2230333333444.4566788999***********75..7788888899999999********** PP

                              GvpD 152 lvletaansrleyivdGvvtl.......nvkeddrgrlrrdlrleklrGvrignrlqPftladGkfksitrvelvti 221
                                        v+e a   +l+yivdGvvt+       +   + r r +r+++leklrGv+i+++ +  tl +G+f+   +      
  gi|330508630|ref|YP_004385058.1| 164 FVSEFADVMPLDYIVDGVVTMeqfnlpgHAGGNMRNRYVRQIKLEKLRGVKINQKTYTVTLHNGRFRFFEPYREHND 240
                                       ********************987766666778999************************************988887 PP

                              GvpD 222 dtvtdeakyePlandkakfsvglrdldkllseGtdrGsvvildlgkdlsrdawsvlvlaairdflsqemgvavvp 296
                                           +++   P   ++ + s+g+ dld ++++G + Gs  +l++ +  ++  + +l+  a  + + +  gv ++p
  gi|330508630|ref|YP_004385058.1| 241 ARIVSDGVRVPDP-SEDRISTGIPDLD-IVTGGLKYGSCNVLEINHGVGKRYYQMLTALA-SNAIKNGRGVFILP 312
                                       7777788777765.4569********9.7789************9999998888887544.45666677777766 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0013
                              GvpD 381 ervreesegPllyvismdtayeafetrlg.dfanyva....lrndavilivkdgtelrtradrvadmhirlelsgda 452
                                       +  re++  P+l +i  d +   f+ +   ++ n ++      nd  +l+vk g e    a   ad+++ ++    +
  gi|330508630|ref|YP_004385058.1| 351 DALRERTGRPILNIIGLDSIEFSFGYKESlNLTNLMIrnwkETNDINVLVVKSGQESMNMAIHTADTYFLVNELNGG 427
                                       678999999***************9865525666666676666899***************************999* PP

                              GvpD 453 ivlygenkltsllgigvsdskri 475
                                       + lyg  + t    ++++d +ri
  gi|330508630|ref|YP_004385058.1| 428 LCLYGVIPRTEPYNMILEDRNRI 450
                                       ******99999889999998876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   3.1e-11   2.1e-08      18     221 ..      21     226 ..      18     235 .. 0.77
   2 ?    1.9   0.1      0.17   1.2e+02       1      32 [.     258     288 ..     258     310 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 3.1e-11
                            ATPase  18 egrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdl..ekleeegklaiidasesa 92 
                                       +g++ li G pGtGKt++al+ + + +e+  ++g+++++  ++  l+     +   l  +++ +  +  ++   +++
  gi|330508630|ref|YP_004385058.1|  21 KGQTLLIKGMPGTGKTTLALEIMSSLCEE--RNGIYISTRVDPARLYATNPWIEKVLmpRNVVNATQTKLLGSLNKT 95 
                                       6899*****************88877777..************9999876544433311344444455555555555 PP

                            ATPase  93 eesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeeke.avaReilrqlvrvl.kklgvTailvsekss 166
                                       +++   ++ ++++ + + + e  +e+    ++iDs +++ +y+++   +  + + q + ++ ++l++  ++vse   
  gi|330508630|ref|YP_004385058.1|  96 SKDL--SNYYAVMDFFRLFFEETEEMDNPMIIIDSWDAVlNYTSHLiGTSQHSFEQNICEFaRDLDTHLVFVSE--- 167
                                       5433..5788888999999999999999********9995444433144555666555455599**********... PP

                            ATPase 167 seeaaggygveefivdgvivLdlkeiee........elvRtleivkmRgtkhskkehpfeIte 221
                                           +       +ivdgv+ +++    +        + vR ++  k+Rg k+++k+++ +  +
  gi|330508630|ref|YP_004385058.1| 168 ----FADVMPLDYIVDGVVTMEQFNLPGhaggnmrnRYVRQIKLEKLRGVKINQKTYTVTLHN 226
                                       ....444555679*********99998899*****9*********************988776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.17
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGK 32 
                                       ++tgI+ lD ++ gG+  g+   +  + G GK
  gi|330508630|ref|YP_004385058.1| 258 ISTGIPDLDIVT-GGLKYGSCNVLEINHGVGK 288
                                       58*******775.***9999888888888888 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   6.1e-08     4e-05      22     106 ..      22      93 ..      12     170 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6.1e-08
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesaeleaw 97 
                                       g  + +l+ G++G+GK++l+ e++ +l++++ gi+++++ d            ++ a++  ++++l +   + ++a 
  gi|330508630|ref|YP_004385058.1|  22 G--QTLLIKGMPGTGKTTLALEIMSSLCEERnGIYISTRVDPA----------RLYATNPWIEKVLMP--RNVVNAT 84 
                                       3..679************************8799999999998..........333344445554444..3344444 PP

                            AAA_16  98 rekleeala 106
                                       ++kl+++l+
  gi|330508630|ref|YP_004385058.1|  85 QTKLLGSLN 93 
                                       444444444 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 !   10.6   0.0   0.00039      0.26      17      51 ..      20      53 ..      15     166 .. 0.80
   2 !    8.7   0.0    0.0015      0.98       2      53 ..     258     310 ..     257     351 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                                      XTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 17 qkgdliiiAarpsmGktalalniaenaavkeklpv 51
                                       kg+ ++i + p++Gkt+lal+i+++ +++++ ++
  gi|330508630|ref|YP_004385058.1| 20 DKGQTLLIKGMPGTGKTTLALEIMSSLCEERN-GI 53
                                      5788999*****************99886444.33 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0015
                                       BXSSTHHHHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHH..HHHHHCSTSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                            DnaB_C   2 lstgfkdLDkltsGlqkgdliiiAarpsmGktalalnia..enaavkeklpvav 53 
                                       +stg  dLD +t+Gl+ g   ++    ++Gk    +  a  +na  k+  +v +
  gi|330508630|ref|YP_004385058.1| 258 ISTGIPDLDIVTGGLKYGSCNVLEINHGVGKRYYQMLTAlaSNAI-KNGRGVFI 310
                                       799****************************98665555214444.44444443 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.5e-06    0.0036       1      72 [.      25     134 ..      25     164 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.5e-06
                                       EEEESSTTSSHHHHHHHHHHHH.....THE.........................EEEEETTTCSSS.........S CS
                               AAA   1 vllyGppGtGKTllakavakel.....gve.........................fleisgsellsk.........y 38 
                                       +l+ G pGtGKT+la  ++++l     g++                         +++   ++ll +          
  gi|330508630|ref|YP_004385058.1|  25 LLIKGMPGTGKTTLALEIMSSLceernGIYistrvdparlyatnpwiekvlmprnVVNATQTKLLGSlnktskdlsN 101
                                       5889*****************75544412133334444444444554444444444444444444335556666664 PP

                                       TTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHH CS
                               AAA  39 vgesekkirelfkeakekakpsilfiDEidalak 72 
                                         + ++ +r +f+e +e+     ++iD  da+ +
  gi|330508630|ref|YP_004385058.1| 102 YYAVMDFFRLFFEETEEMD-NPMIIIDSWDAVLN 134
                                       4556667777777777776.67777888777765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     4e-06    0.0026       2      93 ..      26     120 ..      25     134 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4e-06
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssalee 73 
                                       l+ G+pG+GKttla e+ ++l +    g+ ++  +   +l+ ++ +  ++   + ++   + kll  l++ s++l +
  gi|330508630|ref|YP_004385058.1|  26 LIKGMPGTGKTTLALEIMSSL-CeernGIYISTRVDPARLYATNPWIeKVLMPRNVVNATQTKLLGSLNKTSKDLSN 101
                                       688**************7776.4556788888888888888888777533333444444445556666655543333 PP

                            AAA_18  74 gknlvidghlaeleseaakd 93 
                                           v+d ++  +e+++  d
  gi|330508630|ref|YP_004385058.1| 102 YY-AVMDFFRLFFEETEEMD 120
                                       22.28888877777666555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.5e-05     0.017      29      61 ..      18      50 ..       3      67 .. 0.85
   2 ?   -2.0   0.0       3.5   2.3e+03     136     156 ..     115     134 ..      93     165 .. 0.79
   3 ?   -0.7   0.0       1.4     9e+02     160     181 ..     337     359 ..     330     364 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-05
                            AAA_25 29 llpagelallaGapgtGKttlaldlalavatGk 61
                                      ++ +g + l+ G pgtGKttlal+++ ++++ +
  gi|330508630|ref|YP_004385058.1| 18 HVDKGQTLLIKGMPGTGKTTLALEIMSSLCEER 50
                                      6789999*******************9998654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                            AAA_25 136 aieevegvrlvviDplsralg 156
                                       + ee  +  +++iD+ +++l+
  gi|330508630|ref|YP_004385058.1| 115 ETEE-MDNPMIIIDSWDAVLN 134
                                       4556.4678999999888776 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.4
                            AAA_25 160 nsnsdv.galvealeriarrtga 181
                                       ++++++ + l+e+++ +++rtg 
  gi|330508630|ref|YP_004385058.1| 337 DDARAWgKDLLEKWDALRERTGR 359
                                       567777899************95 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 !   14.1   0.0   4.4e-05     0.029      39      78 ..      14      53 ..       2      64 .. 0.81
   2 ?    0.5   0.0      0.64   4.2e+02      55      79 ..     283     309 ..     273     313 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.4e-05
                         IstB_IS21 39 atlsfiekkenivllGpsGvGKshlaialgveavraglsv 78
                                       +  +++k + +++ G +G+GK+ la  +  + +++   +
  gi|330508630|ref|YP_004385058.1| 14 KEFFHVDKGQTLLIKGMPGTGKTTLALEIMSSLCEERNGI 53
                                      5556799**********************99999865554 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.64
                         IstB_IS21  55 psGvGKsh..laialgveavraglsvl 79 
                                         GvGK +  + +al+ +a+++g  v+
  gi|330508630|ref|YP_004385058.1| 283 NHGVGKRYyqMLTALASNAIKNGRGVF 309
                                       5799999844568*********98875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1     3e-05      0.02       3      47 ..      23      66 ..      21     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3e-05
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla 47
                                      + l+i+G+  +GKTtl+ +++++l  ++++ +yi+   ++ + +a
  gi|330508630|ref|YP_004385058.1| 23 QTLLIKGMPGTGKTTLALEIMSSLC-EERNGIYISTRVDPARLYA 66
                                      6799*****************9998.999999*998776665444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   2.9e-05     0.019       2      94 ..      22     149 ..      21     156 .. 0.66
   2 ?   -2.3   0.0       4.7   3.1e+03      99     128 ..     371     401 ..     362     414 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                            AAA_24   2 klkiliyGpsgiGKTtlakel......gpkplfidtekGlksldadkfpdie..................swedfld 54 
                                       ++ +li G +g+GKTtla+e+      + + ++i t    ++l+a++ p ie                  s      
  gi|330508630|ref|YP_004385058.1|  22 GQTLLIKGMPGTGKTTLALEImsslceERNGIYISTRVDPARLYATN-PWIEkvlmprnvvnatqtkllgS------ 91 
                                       578999***************77777766667775555445555555.44554444455555544444441...... PP

                            AAA_24  55 evvel......................aaeladyktlviDtideleelclaevirqnekaes 94 
                                           l                      ++e+ d   ++iD+ d + +++++ + + ++ +e+
  gi|330508630|ref|YP_004385058.1|  92 ----LnktskdlsnyyavmdffrlffeETEEMDNPMIIIDSWDAVLNYTSHLIGTSQHSFEQ 149
                                       ....0444444455555556666669999999999999999999999999888776666555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.7
                            AAA_24  99 gdgkGygelaeefrrllkklqelrk.nvifi 128
                                        + +Gy+e  +  + ++++ +e+++ nv ++
  gi|330508630|ref|YP_004385058.1| 371 EFSFGYKESLNLTNLMIRNWKETNDiNVLVV 401
                                       5667777777777778888888877777666 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.8e-05     0.012       3      26 ..      24      50 ..      22     127 .. 0.75
   2 ?   -2.3   0.0         3     2e+03     232     285 ..      84     154 ..      60     155 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                           DUF2075  3 vvlVtGvaGtGKtvvllnllael...e 26
                                       +l++G +GtGKt ++l+++  l   +
  gi|330508630|ref|YP_004385058.1| 24 TLLIKGMPGTGKTTLALEIMSSLceeR 50
                                      689*****************9994320 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3
                           DUF2075 232 dakrl.aekkkkkskekdvkieegdfkl................pWnleekelkkpwaessdtleevgsey 285
                                       ++++l ++ +k++++  +++  ++ f+l                +W+   + +++    s++++e+  +e+
  gi|330508630|ref|YP_004385058.1|  84 TQTKLlGSLNKTSKDLSNYYAVMDFFRLffeeteemdnpmiiidSWDAVLNYTSHLIGTSQHSFEQNICEF 154
                                       33344377777788888888877446667888888888888888888888766666677778888888887 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     2e-05     0.013      19      44 ..      23      46 ..       9      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                                      CSEEEEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC 19 qslvvalvGmgGvGKttlakqilnks 44
                                      q   + + Gm+G GKttla +i++++
  gi|330508630|ref|YP_004385058.1| 23 Q--TLLIKGMPGTGKTTLALEIMSSL 46
                                      4..7889***************9974 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     2e-05     0.013       3      51 ..       3      51 ..       1      58 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                                      -HHHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCC CS
                              PIF1  3 neeQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegk 51
                                      ++eQ ++ +++ e  + +kg+++ ++G+ GtgKt l  +++++l +e++
  gi|330508630|ref|YP_004385058.1|  3 SNEQPSIPKEVKEFFHVDKGQTLLIKGMPGTGKTTLALEIMSSLCEERN 51
                                      689********9*9**********************9999998877655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.9e-05     0.026       5      38 ..      22      60 ..      19     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.9e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee.....e 38
                                       + l++ G +GtGKTtl+ +++++l+ee +  +      
  gi|330508630|ref|YP_004385058.1| 22 GQTLLIKGMPGTGKTTLALEIMSSLCEERNGIYistrvD 60
                                      56799********************98765555554431 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.8e-05     0.025      50      78 ..      22      50 ..      14      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 50 GravLlaGpsgtGktalaiaiskelgedv 78
                                      G+++L++G +gtGkt la+ i  +l e+ 
  gi|330508630|ref|YP_004385058.1| 22 GQTLLIKGMPGTGKTTLALEIMSSLCEER 50
                                      899******************99998765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.8e-05     0.032      17      44 ..      22      49 ..      11      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-05
                            AAA_11 17 seitliqGPPGtgKTktivellsqllsr 44
                                       +  li+G PGtgKT+  +e++s+l ++
  gi|330508630|ref|YP_004385058.1| 22 GQTLLIKGMPGTGKTTLALEIMSSLCEE 49
                                      45689******************99744 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   0.00013     0.086      10      39 ..      22      51 ..      15     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelgg 39
                                       ++ll+ + pGtGKT++  +i++ l e+++
  gi|330508630|ref|YP_004385058.1| 22 GQTLLIKGMPGTGKTTLALEIMSSLCEERN 51
                                      678999****************99998873 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   7.9e-05     0.052       2      26 ..      24      48 ..      23      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.9e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                      +++++G +G GKTtL+ ++++ + e
  gi|330508630|ref|YP_004385058.1| 24 TLLIKGMPGTGKTTLALEIMSSLCE 48
                                      799*****************98866 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013     0.089       8      52 ..       6      50 ..       3      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                      HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.. CS
                            ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkg 52
                                      Q ++ ++++e ++ ++ + +lik   GtGKT +a++++ +l +++
  gi|330508630|ref|YP_004385058.1|  6 QPSIPKEVKEFFHVDKGQTLLIKGMPGTGKTTLALEIMSSLCEER 50
                                      555566777777768888999******************998875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00011     0.075       6      41 ..      17      53 ..      15     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                                      EEEETTSEEEEEESTTSSHHHH.HHHHTTSS--SEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                          ABC_tran  6 lklkegekvaivGenGaGKStL.lkllagllkpteGe 41
                                      +++ +g+++ i G  G+GK+tL l++++ l +  +G 
  gi|330508630|ref|YP_004385058.1| 17 FHVDKGQTLLIKGMPGTGKTTLaLEIMSSLCEERNGI 53
                                      7899******************345555555555554 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.076       2      58 ..      26      79 ..      25      89 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalv 58
                                      +++G+pG GK+tl  +++++   l + r+ + + t+  p     ++ +++++lm++ 
  gi|330508630|ref|YP_004385058.1| 26 LIKGMPGTGKTTLALEIMSS---LCEERNGIYISTRVDPARLYATNPWIEKVLMPRN 79
                                      79****************99...4444443444444447777777788888888765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013     0.089       2      32 ..      25      55 ..      24      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvql 32
                                      +l++G pGtgK++la ++ + l+ e + + +
  gi|330508630|ref|YP_004385058.1| 25 LLIKGMPGTGKTTLALEIMSSLCEERNGIYI 55
                                      799**************99999665555444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00025      0.17       3      27 ..      26      54 ..      25     126 .. 0.78
   2 ?   -2.4   0.0       7.3   4.9e+03      51      73 ..     286     308 ..     280     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                            AAA_33  3 llvGlpGsGKstlaerllkklg....avl 27
                                      l+ G+pG+GK+tla +++  l     ++ 
  gi|330508630|ref|YP_004385058.1| 26 LIKGMPGTGKTTLALEIMSSLCeernGIY 54
                                      567***********998776654444444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.3
                            AAA_33  51 vldrlyqilnelarkalsagrnv 73 
                                       v +r yq+l +la  a + gr+v
  gi|330508630|ref|YP_004385058.1| 286 VGKRYYQMLTALASNAIKNGRGV 308
                                       55788999999999999999986 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   9.9e-05     0.066       8      49 ..      16     112 ..      11     411 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.9e-05
                                       HS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE.................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................... RF
                       ATP-synt_ab   8 lfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvg.................................... 48 
                                       +f + +Gq++li g  g+Gkt+++ +++    +++  iy+                                     
  gi|330508630|ref|YP_004385058.1|  16 FFHVDKGQTLLIKGMPGTGKTTLALEIMSSLCEERNGIYIStrvdparlyatnpwiekvlmprnvvnatqtkllgsl 92 
                                       677889******************66665544443666665445555555555555555555555555555555555 PP

                                       ...................E CS
                                       ...................x RF
                       ATP-synt_ab  49 ...................i 49 
                                                           
  gi|330508630|ref|YP_004385058.1|  93 nktskdlsnyyavmdffrlF 112
                                       55555555555555555550 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00036      0.24       2      26 ..      25      49 ..      24      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
                                      EEEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss 26
                                      ++i G+pG+GKtTl   +++ l ++
  gi|330508630|ref|YP_004385058.1| 25 LLIKGMPGTGKTTLALEIMSSLCEE 49
                                      6799**************9988554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00046      0.31      29      61 ..      18      50 ..      16      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00046
                             AAA_7 29 llknkkpvllvGptGtGKtviikdllkkldkek 61
                                      ++++++ +l+ G  GtGKt+++ +++++l +e+
  gi|330508630|ref|YP_004385058.1| 18 HVDKGQTLLIKGMPGTGKTTLALEIMSSLCEER 50
                                      6789999*****************999998554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00033      0.22      16      44 ..      20      49 ..      11      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                            AAA_30 16 sgdrvavltGpAGtGKttalkal.reawea 44
                                      ++ ++ +++G +GtGKtt+  ++   + e+
  gi|330508630|ref|YP_004385058.1| 20 DKGQTLLIKGMPGTGKTTLALEImSSLCEE 49
                                      5567899***********865552555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 3037.94
//
Query:       gi|330508631|ref|YP_004385059.1|  [L=124]
Description: hypothetical protein MCON_2870 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-05   23.6   0.0    8.5e-05   22.9   0.0    1.4  1  FaeA            FaeA-like protein
     0.0017   17.9   0.0     0.0027   17.2   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0019   18.0   0.0     0.0027   17.5   0.0    1.2  1  HTH_IclR        IclR helix-turn-helix domain
     0.0041   17.0   0.1     0.0063   16.4   0.1    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0077   16.0   0.1      0.075   12.9   0.0    2.2  3  HTH_23          Homeodomain-like domain
     0.0078   16.6   0.0      0.011   16.2   0.0    1.4  1  HTH_40          Helix-turn-helix domain
     0.0098   15.7   1.5      0.025   14.4   0.6    2.0  2  LacI            Bacterial regulatory proteins, lacI family
  ------ inclusion threshold ------
      0.037   14.0   0.0      0.063   13.2   0.0    1.4  1  TBPIP           TBPIP/Hop2 winged helix domain
      0.086   12.8   0.3       0.18   11.8   0.0    1.6  2  HTH_11          HTH domain
      0.087   13.0   0.2        1.3    9.2   0.0    2.2  2  HTH_17          Helix-turn-helix domain
       0.13   12.1   0.1       0.71    9.7   0.0    2.0  2  TetR_N          Bacterial regulatory proteins, tetR family
       0.14   12.4   0.8       0.24   11.6   0.8    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind


Domain annotation for each model (and alignments):
>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.7e-08   8.5e-05       2      59 ..       5      60 ..       4      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.7e-08
                                      HHHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSSSS-EEE CS
                              FaeA  2 keeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspvrrGvstlWe 59
                                      ke Ile + + + + +T ++A+ + +s   +  YL +L  eg ++ + v  G s lW+
  gi|330508631|ref|YP_004385059.1|  5 KERILEVIGESEVGLTTVDVAKKARVSKTTVIKYLSMLSSEGEVEFVEV--GPSKLWR 60
                                      89********9**********************************9887..5677776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.8e-06    0.0027       5      45 ..       5      46 ..       1      48 [. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.8e-06
                            HTH_24  5 drkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeG 45
                                      + +ILe++ + + +++  ++A++  +S++tv ++l  L +eG
  gi|330508631|ref|YP_004385059.1|  5 KERILEVIGEsEVGLTTVDVAKKARVSKTTVIKYLSMLSSEG 46
                                      679*******9999************************9988 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   1.8e-06    0.0027       7      49 ..       7      49 ..       7      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +iL+ ++e   +lt  ++A+++ ++k+tv  +L+ L  +G ve
  gi|330508631|ref|YP_004385059.1|  7 RILEVIGESEVGLTTVDVAKKARVSKTTVIKYLSMLSSEGEVE 49
                                      69*************************************9887 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   4.2e-06    0.0063      22      60 ..      18      56 ..      11      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.2e-06
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                       +t+ ++a+++ v++++v ++L+ L++ G Ve ++  p 
  gi|330508631|ref|YP_004385059.1| 18 GLTTVDVAKKARVSKTTVIKYLSMLSSEGEVEFVEVGPS 56
                                      68999***************************9987764 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0     5e-05     0.075       2      45 ..       2      46 ..       1      51 [. 0.84
   2 ?   -3.4   0.0       6.5   9.7e+03      34      40 ..      58      64 ..      53      69 .. 0.49
   3 ?    0.6   0.0      0.35   5.3e+02      19      32 ..     103     116 ..      97     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5e-05
                            HTH_23  2 asereRlr.illllaeGlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      as +eR++ ++    +Gl++ ++A++  vs+ Tv ++l+    eG
  gi|330508631|ref|YP_004385059.1|  2 ASYKERILeVIGESEVGLTTVDVAKKARVSKTTVIKYLSMLSSEG 46
                                      6667777779999999******************99998765555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.5
                            HTH_23 34 vyrwlkr 40
                                      ++r +++
  gi|330508631|ref|YP_004385059.1| 58 LWRTRNT 64
                                      4444433 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.35
                            HTH_23  19 svreIAreLgvsrr 32 
                                        +++I+++L + +r
  gi|330508631|ref|YP_004385059.1| 103 KTEQICKLLKRAKR 116
                                       57899999988765 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.1e-06     0.011      12      50 ..      18      55 ..      15     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.1e-06
                            HTH_40 12 glsieeIAkerglkesTIegHLaelieegeeidlerlvs 50
                                      gl+  ++Ak+ +++++T++++L  l  ege +++ ++ +
  gi|330508631|ref|YP_004385059.1| 18 GLTTVDVAKKARVSKTTVIKYLSMLSSEGE-VEFVEVGP 55
                                      89999************************8.88766544 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.98   1.5e+03      30      40 ..       4      14 ..       2      16 .. 0.81
   2 !   14.4   0.6   1.7e-05     0.025       4      20 ..      23      39 ..      20      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.98
                                      HHHHHHHHHHH CS
                              LacI 30 trerVeaamee 40
                                       +er+++++ e
  gi|330508631|ref|YP_004385059.1|  4 YKERILEVIGE 14
                                      589****9987 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.7e-05
                                      HHHHHCTS-HHHHHHHC CS
                              LacI  4 DVArlAGVSkaTVSrvL 20
                                      DVA++A VSk+TV ++L
  gi|330508631|ref|YP_004385059.1| 23 DVAKKARVSKTTVIKYL 39
                                      9************7766 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.2e-05     0.063      27      58 ..      26      58 ..      17      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                             TBPIP 27 qk.klgKtavqkaLdeLvdegkiieKeyGKqki 58
                                      +k +++Kt+v k L  L++eg + + e G +k+
  gi|330508631|ref|YP_004385059.1| 26 KKaRVSKTTVIKYLSMLSSEGEVEFVEVGPSKL 58
                                      4559******************99999887776 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   0.00012      0.18       4      43 ..       7      46 ..       5      55 .. 0.82
   2 ?   -1.9   0.1       2.2   3.3e+03       2      13 ..     104     115 ..     103     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                       ile + e++  ++  + A++  vS++tv +++  L++ g
  gi|330508631|ref|YP_004385059.1|  7 RILEVIGESEVGLTTVDVAKKARVSKTTVIKYLSMLSSEG 46
                                      6778886666668888999*****************9999 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                            HTH_11   2 llqilelLlear 13 
                                       ++qi +lL++a+
  gi|330508631|ref|YP_004385059.1| 104 TEQICKLLKRAK 115
                                       689999998876 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00089       1.3       2      23 ..      19      40 ..      19      62 .. 0.79
   2 ?    1.6   0.0      0.21   3.2e+02       3      13 ..     103     113 ..     102     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00089
                            HTH_17  2 ltveEaAelLgvsrstvyrlir 23
                                      lt+ ++A+  +vs++tv ++++
  gi|330508631|ref|YP_004385059.1| 19 LTTVDVAKKARVSKTTVIKYLS 40
                                      8999*************99974 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.21
                            HTH_17   3 tveEaAelLgv 13 
                                       ++e++++lL+ 
  gi|330508631|ref|YP_004385059.1| 103 KTEQICKLLKR 113
                                       69*******85 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00048      0.71      17      36 ..      19      38 ..       9      39 .. 0.90
   2 ?   -0.5   0.0      0.72   1.1e+03      32      41 ..      95     104 ..      93     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00048
                                      --HHHHHHHHTSSHHHHHHH CS
                            TetR_N 17 ttvreIAkrAGvskgalYry 36
                                      +t+ ++Ak+A vsk ++ +y
  gi|330508631|ref|YP_004385059.1| 19 LTTVDVAKKARVSKTTVIKY 38
                                      7899************9877 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.72
                                       HHHHHTSSHH CS
                            TetR_N  32 alYryFpsKe 41 
                                       ++Y  F+ K 
  gi|330508631|ref|YP_004385059.1|  95 TIYFSFRVKT 104
                                       89****9776 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8   0.00016      0.24       9      54 ..       4      50 ..       1      54 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress  9 YLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyvey 54
                                      Y e I+++ + +++  +t d+a+   vs+ +V + l+ L+++G ve 
  gi|330508631|ref|YP_004385059.1|  4 YKERILEVIGeSEVGLTTVDVAKKARVSKTTVIKYLSMLSSEGEVEF 50
                                      5566777777577778999************************8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); 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: 0.59u 0.37s 00:00:00.96 Elapsed: 00:00:00.58
# Mc/sec: 645.20
//
Query:       gi|330508632|ref|YP_004385060.1|  [L=206]
Description: tetrahydromethanopterin S-methyltransferase subunit A [Methanosaeta concilii GP6]
Scores for complete 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  194.0   0.0    1.8e-57  193.7   0.0    1.1  1  MtrA      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrA  Tetrahydromethanopterin S-methyltransferase, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.7   0.0     1e-61   1.8e-57       6     148 ..      19     156 ..      15     179 .. 0.94

  Alignments for each domain:
  == domain 1  score: 193.7 bits;  conditional E-value: 1e-61
                                       TTSS-S--S-EE--TT-SEEEE-TT-SS-HHHHHHCT-SEEE----TTHHHHHHHHHHHT-TT--EEEEEE---TTT CS
                              MtrA   6 egWPvvkGdyevGdaespvavvtlgshleeeavleaGaaiaGplktenlGiekvvanvisnpnirflivtGaevkGh 82 
                                       + WP v+G+y+ Gd+++ vavvtl+s ++ +     G+ai+Gp+ktenlG+ek+vanvisn+nirfliv+G e kGh
  gi|330508632|ref|YP_004385060.1|  19 DPWPPVRGEYRLGDPRAGVAVVTLASVFNPR-----GTAISGPCKTENLGLEKIVANVISNSNIRFLIVCGVESKGH 90 
                                       67************************99865.....88*************************************** PP

                                       -HHHHHHHHHHH-B-TTSBBTT--SSS-B-SSS-HHHHHHHHHH-EEEEEET---HHHHHHHHHHH CS
                              MtrA  83 itGqalkalhenGvdkekkivgakGaiPfienlteeaverfqeqvelvdlidtedvgaikakikel 148
                                       + G++l alh+nG+d++++i+g+kGaiPfi+nl+ +averfq+qvel+d i+ ed+++i++ ++++
  gi|330508632|ref|YP_004385060.1|  91 LPGNTLLALHKNGIDEKGRIIGSKGAIPFIQNLSVQAVERFQRQVELIDRIGLEDMKEIEKLVSQY 156
                                       ***********************************************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.55
# Mc/sec: 1118.69
//
Query:       gi|330508633|ref|YP_004385061.1|  [L=307]
Description: methyltetrahydromethanopterin S-methyltransferase subunit H [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-100  336.5   0.0   1.4e-100  336.3   0.0    1.0  1  MtrH      Tetrahydromethanopterin S-methyltransferase MtrH su


Domain annotation for each model (and alignments):
>> MtrH  Tetrahydromethanopterin S-methyltransferase MtrH subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.3   0.0  7.9e-105  1.4e-100       1     296 [.       6     295 ..       6     298 .. 0.98

  Alignments for each domain:
  == domain 1  score: 336.3 bits;  conditional E-value: 7.9e-105
                              MtrH   1 keqkvleiaGvkiGGqpGeyPtvlvgtifyakhkivedekkGifdkeaaealikkqeelsdktGnPalvqvvGetee 77 
                                       +eq+++++aGv++GGqpGe Ptvl gtify +h+ived+++Gifd++aae l+ +q els +tG P ++++  +t  
  gi|330508633|ref|YP_004385061.1|   6 NEQTIVNVAGVRFGGQPGELPTVLCGTIFYQGHRIVEDDERGIFDRAAAERLVLRQSELSSETGCPFVLHIYARTVS 82 
                                       69*************************************************************************** PP

                              MtrH  78 aivkyidfvadvtdaPllidstsaevklaaakyatevGladrviynsinasiedaeiealkesdveaaivlafnpmd 154
                                       a+ ky+df  +v+ +P+++ds++   +  a    +e+G+ad++iynsi+++++dae  al e +v++ai+la+np +
  gi|330508633|ref|YP_004385061.1|  83 ALQKYLDFAEEVWSGPFIVDSAERSTRSLALSLLSELGYADKAIYNSISIATDDAEARALLENEVDSAIILAYNPGE 159
                                       ***************************************************************************** PP

                              MtrH 155 ptvegklkileegegtaekgllelaeeaGiekplidvavtplgsgagaavkaslavkaklGlPvGsgihnvpsaWdw 231
                                       p veg + ile+g+ + + gl+ l+++ Gi++ lid  v+p+gsgag++++ s+  k++lGlPvGsgihn++s+W+w
  gi|330508633|ref|YP_004385061.1| 160 PGVEGAMRILENGGLVRDEGLIPLSKRLGISNILIDPGVVPMGSGAGSSLRFSVVAKSRLGLPVGSGIHNAVSSWQW 236
                                       ***************************************************************************** PP

                              MtrH 232 lrefkkkekekaaeyevadvganlvqvilgsdfvlyGPienakkvfPavamvdilikeaakelgv 296
                                       l++ +k+++      + +d +a  +q  +g+df+lyGPie  + +fPa am+dil++ea ++l v
  gi|330508633|ref|YP_004385061.1| 237 LKDRMKSNR------SCCDAAAACMQLAMGGDFLLYGPIESGEVIFPAAAMADILVAEAVRDLEV 295
                                       ***998765......4799******************************************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1676.47
//
Query:       gi|330508634|ref|YP_004385062.1|  [L=394]
Description: hypothetical protein MCON_2874 [Methanosaeta concilii GP6]
Scores for complete 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-155  516.0   0.0   6.3e-155  515.8   0.0    1.0  1  DUF521    Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  515.8   0.0  3.5e-159  6.3e-155       1     401 []       1     386 [.       1     386 [. 0.97

  Alignments for each domain:
  == domain 1  score: 515.8 bits;  conditional E-value: 3.5e-159
                            DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvptt 77 
                                       m+L+++eea+++G++Ge+l+ +meilvalG+i+gAerLvpv s++++gvsyk+igdagle++++l+   ++v vp++
  gi|330508634|ref|YP_004385062.1|   1 MYLSRDEEAIYRGDRGETLRRMMEILVALGDIYGAERLVPVRSVQIAGVSYKNIGDAGLEWISDLE---GQVVVPSI 74 
                                       9*****************************************************************...******** PP

                            DUF521  78 lnpigvdlerweelgvdeefaekqeriieayeklGveltftCtpyll.gnapkkGehlawsESsavvyaNSvlGarT 153
                                       lnp+g+dl r++e+g++eefa+kq+++ieay++lGv + +tCtpy++ ++  ++G+hlawsESsav+yaNSv+GarT
  gi|330508634|ref|YP_004385062.1|  75 LNPAGMDLFRYKEMGISEEFASKQRETIEAYRRLGVIIDCTCTPYQIyDSLAERGDHLAWSESSAVCYANSVIGART 151
                                       **********************************************779**************************** PP

                            DUF521 154 nreggpsalaaAitGrtpeyGlhldenRkptvlveveaesedeadygalGylvGkkvgeriPvlkglekpsedelKa 230
                                       nreggpsalaaA++G+t+ yG+hld nR+p++++e +ae  + +dygalG+lvGk+vg+++P+++  ++p++delKa
  gi|330508634|ref|YP_004385062.1| 152 NREGGPSALAAALIGKTALYGYHLDHNRQPSHVIEAKAE-LEGSDYGALGFLVGKEVGDGVPLFRLRSSPTKDELKA 227
                                       ***********************************9888.9************************99999******* PP

                            DUF521 231 lgAalaasgavalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlvalGcPhlsleElr 307
                                       lgAa+aasg+val++++gvTP+ ++ +++    +  e+i+i+ e++e+v++e      ++ d+valGcPh+s eEl+
  gi|330508634|ref|YP_004385062.1| 228 LGAAMAASGSVALYYVDGVTPKPPEPTANY---DGCERISIEWEEIEAVYDEH---GGDDADIVALGCPHCSGEELE 298
                                       **********************66655544...67****************77...9999***************** PP

                            DUF521 308 elaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYlp 384
                                       ++a+ll   ++kvk+e+wv+t+r++k+++ +l  v+++e++G++v++dtCmvvsp+++  +++k+++nSgKa+ Ylp
  gi|330508634|ref|YP_004385062.1| 299 RIADLL--AGQKVKKEMWVCTARKIKDACPDL--VARIESSGARVFCDTCMVVSPATE--GFEKMMVNSGKALVYLP 369
                                       ******..77888*****************99..**********************99..59*************** PP

                            DUF521 385 gltgvkvalgsleecve 401
                                       gl+gv++ +gsleec++
  gi|330508634|ref|YP_004385062.1| 370 GLGGVDATFGSLEECID 386
                                       ***************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.55
# Mc/sec: 2151.64
//
Query:       gi|330508635|ref|YP_004385063.1|  [L=133]
Description: hypothetical protein MCON_2875 [Methanosaeta concilii GP6]
Scores for complete 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  117.3   0.2    2.4e-34  117.0   0.2    1.1  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 !  117.0   0.2   1.3e-38   2.4e-34       1      80 []      25     104 ..      25     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 1.3e-38
                                       --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT- CS
                            DUF126   1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadi 77 
                                       +Sflg++dp+tG v+d+gh+l+g+si+gk+L++p+gkGStvgsyv+++l+k++ aPaA+i+ + +pi+a+Gai+++i
  gi|330508635|ref|YP_004385063.1|  25 ISFLGNIDPRTGMVVDPGHELYGESISGKVLIFPGGKGSTVGSYVIYQLKKRDLAPAAMINLRSEPIVAVGAIISGI 101
                                       8**************************************************************************** PP

                                       -EE CS
                            DUF126  78 Plv 80 
                                       Plv
  gi|330508635|ref|YP_004385063.1| 102 PLV 104
                                       *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.55
# Mc/sec: 733.79
//
Query:       gi|330508636|ref|YP_004385064.1|  [L=735]
Description: alpha glucan phosphorylase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-35  120.3   0.4    1.4e-34  118.8   0.1    2.0  2  DUF3417        Protein of unknown function (DUF3417)
      2e-26   92.5   0.0    2.3e-20   72.5   0.0    2.7  2  Phosphorylase  Carbohydrate phosphorylase


Domain annotation for each model (and alignments):
>> DUF3417  Protein of unknown function (DUF3417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   0.1   1.6e-38   1.4e-34       1     109 []      17     126 ..      17     126 .. 0.99
   2 ?   -3.5   0.0       1.6   1.5e+04      48      74 ..     693     719 ..     676     723 .. 0.66

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 1.6e-38
                           DUF3417   1 lpeeLekLeeLaknlwwswneeareLFksldpelweevghnPvklLeevsqerleelaedeeflarleavveefeey 77 
                                       lpe+++ L++L++nlwwsw++e reLFk l+++ w+ +ghnPvk+L++++++ l+ +++d++fl+++++v+++fe y
  gi|330508636|ref|YP_004385064.1|  17 LPERIAGLRKLTYNLWWSWHPEGRELFKLLHRQGWHLSGHNPVKMLNQMDAHMLKVASNDTHFLRHYDSVMARFEGY 93 
                                       8**************************************************************************** PP

                           DUF3417  78 leek.twfqkkaeeekkeaiAYFsaEfGlhesL 109
                                       +e + +wf   ++e+++ aiAYFsaE+Glh++L
  gi|330508636|ref|YP_004385064.1|  94 MEPEtSWFCAGSREPERCAIAYFSAEYGLHHAL 126
                                       **9989************************997 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.6
                           DUF3417  48 evsqerleelaedeeflarleavveef 74 
                                       + s++r+++  +d+ + + ++a++ e 
  gi|330508636|ref|YP_004385064.1| 693 NFSATRMAKEYTDKFYRQAIDAAMMER 719
                                       466777777778888887777776654 PP

>> Phosphorylase  Carbohydrate phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   2.4e-07    0.0021      23      69 ..     131     178 ..     127     190 .. 0.90
   2 !   72.5   0.0   2.6e-24   2.3e-20     215     581 ..     272     628 ..     228     632 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.4e-07
                                       SHHHHHHHHHHHHHHHTT-EEEEEEE--SCESEEEEE.ETTEEEEEEE CS
                     Phosphorylase  23 GGLGRLAacfldslatlelpavGygirYeyGlFkQki.edgaqveepd 69 
                                       GGLG LA  +l  ++ l++p vG g  Y  G  +Q +  dg+q+ + +
  gi|330508636|ref|YP_004385064.1| 131 GGLGFLAGDYLKECSDLGIPLVGLGFMYPQGYLRQMVsADGWQIGACE 178
                                       9************************************889***87655 PP

  == domain 2  score: 72.5 bits;  conditional E-value: 2.6e-24
                                       HHHEEEEEESSTTTTHHHHHHHHHHHCC---HHHHHHHHCCCEEEEE--SSGGGS-EEEHHHHHHHSHHHHHHHHHH CS
                     Phosphorylase 215 pekvaiqlnDtHPalaipelmriLvdeeglewdeaweitkktfaytnhtvlpealekwpvellekllprhleiieei 291
                                       +++ +++ln+ HPa+a+ e +r  v e+g++++ea e++++t+ +t ht +p   + +   llek l   l  +   
  gi|330508636|ref|YP_004385064.1| 272 EDYSVLHLNEGHPAFAVLERIREKV-EQGMNYSEASELVRNTTVFTTHTPVPAGHDAFAYPLLEKYLSSYLPTLD-- 345
                                       467899****************996.56***************************************99887655.. PP

                                       HHHHHHHHHHHSTT-HHHHHHHSSEETSCEEEHHHHHHHCCSEEEESSHHHHHHHHHTTTHHHHHHS..GGGEEE-- CS
                     Phosphorylase 292 nerfleevekklpedeeklerlsiieeekkvrmanlaivgshsvngvaalhsellkkevlkdfyely..pekfnnkt 366
                                         ++ e +++ l+ d           +  + +m  +a+  s   n+v++ h e+ ++     + +l      +  +t
  gi|330508636|ref|YP_004385064.1| 346 -LSMEEFLRQGLNPD-----------RPGEFNMTAFALRNSAYRNAVSKKHGEVSRSMWQPLWPHLPvdEVPIDYVT 410
                                       .44444444444334...........356789*********************9988776666666511456899** PP

                                       --B-CHHHCCCTSHHH.HHHHHHHCSSGGCCSG..GGGGGGGGGCCSHHHHHHHHHHHH........HHHHHHHHHH CS
                     Phosphorylase 367 nGitprrwlllanpel.aelitekigeewvkdl..eeLkkLekladdkefleelaeikq........enKerlaeli 432
                                       nGi    w+     +l  ++ ++ +g++w+++   +++ +L     d+ + ++ +++k+        + +++  e  
  gi|330508636|ref|YP_004385064.1| 411 NGIHVPTWIDR---RLgYDIFSRYMGRTWLEEHdeSRIWELVCEIPDEIIWNHHNAMKNmlitkikeRARNKWLEGG 484
                                       ********964...442689999******986611568888888888877777776665222211003333333322 PP

                                       HH.....HHSS---TTSEEEEEES-SCCCCTHHHHHHHHHHHHHHHHHSTTS----EEEEEE----TT-HHHHHHHH CS
                     Phosphorylase 433 ke.....kegvevdpeslfdvqvkRlheYkRqlLnvLhiitlYneikenpekkvvprtvifggkaapgYalAkkiik 504
                                       +e      +gv +dp++l     +R+  YkR +L +L+ +++ ++i ++p   + p  +if+gka    ++ k++++
  gi|330508636|ref|YP_004385064.1| 485 AEpgqimASGVLLDPAALTLGFARRFASYKRPTL-LLQDMDRLRRILNDP---WRPVQIIFAGKAHGDDQQSKMLLQ 557
                                       2222122346779999999999***********9.789999******998...********************9988 PP

                                       HHHHHHHHHCC-TTTCCCEEEEEETT-SHHHHHHHGGG-SEEEE---TTTSSS-SHHHHHHHTT-EEEEESSTCHHH CS
                     Phosphorylase 505 linsvaevvnndpevkdklkvvflenynvslaekiipaadlseqistagkeASGTgnmkfmlnGaltigtlDGanvE 581
                                        + + a+    d+  ++  +++f+e+y+  la+ ++ + d+  +  +  +eASGT+ mk  +nG   ++ lDG  +E
  gi|330508636|ref|YP_004385064.1| 558 QVFNAAK----DRVSGG--RIAFVEDYDELLAQYLVHGVDVWVNNPIPPMEASGTSGMKASVNGVPQLSVLDGWWIE 628
                                       7776653....444444..799***************************************************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (735 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.82u 0.33s 00:00:01.14 Elapsed: 00:00:00.56
# Mc/sec: 3980.46
//
Query:       gi|330508637|ref|YP_004385065.1|  [L=150]
Description: hypothetical protein MCON_2877 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 826.53
//
Query:       gi|330508638|ref|YP_004385066.1|  [L=48]
Description: hypothetical protein MCON_2878 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-11   42.1   1.0    6.6e-11   42.0   1.0    1.0  1  DUF2116   Uncharacterized protein containing a Zn-ribbon (DUF
  ------ inclusion threshold ------
        0.1   12.5   0.2        0.1   12.5   0.2    1.0  1  Tmemb_9   TMEM9


Domain annotation for each model (and alignments):
>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   1.0   7.3e-15   6.6e-11      15      58 ..       3      42 ..       1      43 [. 0.94

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 7.3e-15
                           DUF2116 15 ldesfCsekCqeeyekkrkkvarsqqilfgililllavvlvlkf 58
                                       de fC+e C+++y+++++k    qqi+f i+i+++ ++l+l++
  gi|330508638|ref|YP_004385066.1|  3 ADENFCDELCESKYKSAQRK----QQIMFIIFIIIMGLILILPS 42
                                      69******************....****************9987 PP

>> Tmemb_9  TMEM9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.2e-05       0.1      31      64 ..       4      40 ..       1      45 [. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                           Tmemb_9 31 elefcp.rCeCkyes..RntttikvvviivivvislL 64
                                      +++fc   Ce ky+s  R  +++ ++ ii++ +i +L
  gi|330508638|ref|YP_004385066.1|  4 DENFCDeLCESKYKSaqRKQQIMFIIFIIIMGLILIL 40
                                      55688626*****853378888888877777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1350  (0.075297); expected 358.6 (0.02)
Passed bias filter:                      783  (0.0436723); 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: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 270.42
//
Query:       gi|330508639|ref|YP_004385067.1|  [L=656]
Description: hypothetical protein MCON_2880 [Methanosaeta concilii GP6]
Scores for complete 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-60  204.0  74.2    1.1e-28  100.1  30.4    4.2  4  NosD            Periplasmic copper-binding protein (NosD)
    1.5e-45  154.8  89.8    4.7e-19   68.8  13.7    4.9  5  Beta_helix      Right handed beta helix region
    0.00046   19.0   1.7    0.00093   18.0   0.0    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 !   68.3  11.2     1e-22     6e-19      23     161 ..      89     225 ..      72     236 .. 0.91
   2 !   48.2  16.1   1.3e-16     8e-13      18     174 ..     195     354 ..     195     361 .. 0.89
   3 !   22.4   0.6     1e-08     6e-05      70     152 ..     341     422 ..     339     441 .. 0.56
   4 !  100.1  30.4   1.9e-32   1.1e-28      19     237 ..     445     647 ..     430     651 .. 0.90

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1e-22
                              NosD  23 nsegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnn.tlenN 98 
                                       +s+g+ +++ + + ++ +  +  s +n+i++n++e+ + +i  ++se+n i++n + +++ G+al + s+n  +++N
  gi|330508639|ref|YP_004385067.1|  89 SSDGCNLEGLTFQGYSGAAVHLLSRKNRIENNVFEDASPAILASGSEGNSINGNLIMNCQGGVALRDASENnSIDGN 165
                                       5799999******9999999**********************************************999777***** PP

                              NosD  99 tisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGilllssseg 161
                                       +i+++++ +i+l ++++n+i +N+is+ + Gi+l+nss+ +i+gN i+s  ++Gilll++s g
  gi|330508639|ref|YP_004385067.1| 166 EITSCNI-SIFLGEADGNSIIENNISDAYWGIWLDNSSQVQIEGNDIQSR-SHGILLLNGS-G 225
                                       *****99.******************************************.*****66655.4 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 1.3e-16
                              NosD  18 giqlensegseisnneisnsrdgilldnssnntitgn.....tienl....ryGihlensesntiedntlssnesGi 85 
                                       gi l+ns++ +i++n+i++ + gill n s+  +++n              + +  l n ++++ + n++++ e G+
  gi|330508639|ref|YP_004385067.1| 195 GIWLDNSSQVQIEGNDIQSRSHGILLLNGSGLYVSDNlvmidD---AgnstSRASLLANVSDVVFQRNKIDGGEIGL 268
                                       7999*********************************764441...2445588888999999*************** PP

                              NosD  86 almsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegn 162
                                       a  + +n+ l  N+i++++n  i+++d+ + +i+nN   + ++Gi+++nss+n i gN   +   i +  + ++e+n
  gi|330508639|ref|YP_004385067.1| 269 AALDCQNTELLYNNITQSNN-AIYIQDAYGLNINNNSLIEGDYGIRVDNSSQNSIIGNLARDF-VIALD-IGAAEDN 342
                                       ******99777777777777.8**************************************999.99999.******* PP

                              NosD 163 tiynNyFinnse 174
                                       +i +N+F++ + 
  gi|330508639|ref|YP_004385067.1| 343 RILKNQFVGITD 354
                                       *******87665 PP

  == domain 3  score: 22.4 bits;  conditional E-value: 1e-08
                              NosD  70 sntiedntlssne.sGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNri 145
                                       +n+i +n++ + + +++ ++ss n+ +  N++++  + Gi+l +s  n +++N+++n    +++e+ ++++  +N+i
  gi|330508639|ref|YP_004385067.1| 341 DNRILKNQFVGITdAAMQITSSGNCKILENEFTDGFR-GIMLIESPANLLQDNRFQNVTWSLYVES-QTKEGFNNSI 415
                                       4555555555555555555555555555566666655.6666666666666666665555555555.4455555555 PP

                              NosD 146 esnqkiG 152
                                       ++++ ++
  gi|330508639|ref|YP_004385067.1| 416 DESNVVD 422
                                       5554444 PP

  == domain 4  score: 100.1 bits;  conditional E-value: 1.9e-32
                              NosD  19 iqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsssnnt 94 
                                       +++ + +++ +   +i+ +rd+++l +s nn+i ++ i+++  G++l ns++n i +n +++n+ sG++l+ss +n 
  gi|330508639|ref|YP_004385067.1| 445 LTMAYCRNMAV--DNITITRDAVFLFDSMNNSIINSNISEC-FGMRLINSSGNDILGNLFNGNGySGLFLYSSDGNR 518
                                       55566677777..455557999*9*****************.*********************************** PP

                              NosD  95 lenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFi 170
                                       +e+N++s+ne++G +l  +++n i++N ++ n  +Gi+l+ s++n+i +N+i++n + G   ls s+gntiy N+Fi
  gi|330508639|ref|YP_004385067.1| 519 IEKNVASENEQNGLSLLSCNQNIIRDNSVQkNLVTGIWLNLSNDNQIYENNITAN-SLGSQ-LSFSTGNTIYHNNFI 593
                                       ******************************9999*********************.*****.*************** PP

                              NosD 171 nnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydgeDadgDGigDtpYeindgv.iDylpl 237
                                       +n e+  ++++ +n+W+  +           +gGNyWsd + +   g+  +D p +i++g+ iD++p 
  gi|330508639|ref|YP_004385067.1| 594 DNIEHSIDTEG-GNSWDAGN----------NTGGNYWSDHSAR---GNPSSDWPRSIKGGIaIDNYPF 647
                                       **999888775.****8877..........89*******8865...9999999999999999999996 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 ?   -2.5   0.0      0.67     4e+03      34      54 ..      31      51 ..      20      58 .. 0.64
   2 !   68.8  13.7   7.8e-23   4.7e-19       8     156 ..      90     231 ..      85     233 .. 0.94
   3 !   47.9  13.1   2.1e-16   1.2e-12       6     157 ..     249     393 ..     247     394 .. 0.95
   4 !   36.6  12.0   6.3e-13   3.8e-09      15     144 ..     391     534 ..     387     536 .. 0.74
   5 !   45.0  27.0   1.7e-15     1e-11       5     138 ..     489     623 ..     488     647 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.67
                                      .EEES-EEES-SS-SEEE-TT CS
                        Beta_helix 34 vvienneiannsgsGiyilgs 54
                                       +i++ +ia + g+ iy++ +
  gi|330508639|ref|YP_004385067.1| 31 KTIQDAVIAASDGDTIYVKPG 51
                                      466666666666666666543 PP

  == domain 2  score: 68.8 bits;  conditional E-value: 7.8e-23
                                       S-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT.--S--EEE CS
                        Beta_helix   8 ssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialf.gasnnlie 83 
                                       s+++++++ t+++ +g++++l + +n +ienn++++     i  +gs++n i +n i ++  gg+al+ ++ nn i+
  gi|330508639|ref|YP_004385067.1|  90 SDGCNLEGLTFQGYSGAAVHLLSRKN-RIENNVFED-ASPAILASGSEGNSINGNLIMNCQ-GGVALRdASENNSID 163
                                       455899********************.*********.************************.******9999***** PP

                                       S-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES- CS
                        Beta_helix  84 nneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnN 156
                                       +neit ++   i+l  ++ n+i +N+i++ + +Gi +d+ss +v +++N i + + +Gi + ++s+ ++v+ N
  gi|330508639|ref|YP_004385067.1| 164 GNEITSCNI-SIFLGEADGNSIIENNISDAY-WGIWLDNSS-QVQIEGNDIQSRS-HGILLLNGSG-LYVSDN 231
                                       *******65.9********************.*********.**********987.***9999999.999998 PP

  == domain 3  score: 47.9 bits;  conditional E-value: 2.1e-16
                                       -SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EE CS
                        Beta_helix   6 ngssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnli 82 
                                        ++s+v ++ n+i++ g  G+ + +++n+ +  n+i++ s + iyi+ + + +i nn+  ++  +gi ++++s+n i
  gi|330508639|ref|YP_004385067.1| 249 ANVSDVVFQRNKIDG-GEIGLAALDCQNTELLYNNITQ-SNNAIYIQDAYGLNINNNSLIEGD-YGIRVDNSSQNSI 322
                                       688999*********.9*********************.*******************99999.9************ PP

                                       ES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E CS
                        Beta_helix  83 enneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNt 157
                                        +n  +d     + +  +++n+i +N++ + + ++++i++s+ n+++  N +t+    Gi +++s + + +  N 
  gi|330508639|ref|YP_004385067.1| 323 IGNLARDFVI-ALDIGAAEDNRILKNQFVGITDAAMQITSSG-NCKILENEFTDGF-RGIMLIESPA-NLLQDNR 393
                                       ********76.899999*************************.************9.*******999.8887776 PP

  == domain 4  score: 36.6 bits;  conditional E-value: 6.3e-13
                                       SEEEES-SS-SEEE-SSS-.....EEES-EEES.................-SS-SEEE-TT-S-EEES-EEE---SE CS
                        Beta_helix  15 nntisnsggyGiylrgssn....vvienneian.................nsgsGiyilgssnntisnntisdnngg 70 
                                       +n ++n  +  +y++++++    + i+++++ +                  +   + + ++ n  ++n ti+    +
  gi|330508639|ref|YP_004385067.1| 391 DNRFQN-VTWSLYVESQTKegfnNSIDESNVVDfvpiaylfdqsetqirdRQLAHLTMAYCRNMAVDNITIT---RD 463
                                       666777.47777777777766664444333333333333444222222225555555666699999999999...36 PP

                                       EE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE- CS
                        Beta_helix  71 gialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiav 144
                                       ++ lf++ nn i n++i+++   G++l +ss n+i +N +++n+ sG+++++s+ ++++++N+++ n ++G+ +
  gi|330508639|ref|YP_004385067.1| 464 AVFLFDSMNNSIINSNISECF--GMRLINSSGNDILGNLFNGNGYSGLFLYSSD-GNRIEKNVASENEQNGLSL 534
                                       7*******************6..8******************************.****************875 PP

  == domain 5  score: 45.0 bits;  conditional E-value: 1.7e-15
                                       E-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--E CS
                        Beta_helix   5 ingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnl 81 
                                       in+s+n  i +n ++++g++G++l++s++++ie+n+ + n ++G+++l+++ n+i++n++  n  +gi+l+ ++ n 
  gi|330508639|ref|YP_004385067.1| 489 INSSGN-DILGNLFNGNGYSGLFLYSSDGNRIEKNVASENEQNGLSLLSCNQNIIRDNSVQKNLVTGIWLNLSNDNQ 564
                                       677788.9********************************************************************* PP

                                       EES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT...---EEES-EEES-S CS
                        Beta_helix  82 ienneitdnggsGiylnyssnntienNiidnnagsGividdss...snvtvtnNtitnnk 138
                                       i+ n+it n+  G +l+ s+ nti +N++ +n ++ i  + ++   ++++  +N  ++++
  gi|330508639|ref|YP_004385067.1| 565 IYENNITANSL-GSQLSFSTGNTIYHNNFIDNIEHSIDTEGGNswdAGNNTGGNYWSDHS 623
                                       *********88.99**999**************9******99999966666777777777 PP

>> Pectinesterase  Pectinesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.6e-07   0.00093       3      57 ..      21      71 ..      19     124 .. 0.79
   2 ?   -3.8   0.0      0.69   4.1e+03      89     125 ..     227     262 ..     221     264 .. 0.74
   3 ?   -1.3   0.2      0.11   6.8e+02     232     266 ..     595     629 ..     536     638 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-07
                                      EE-TTS-SSBSSHHHHHHHS-SS-SS-EEEEE-SEEEE--EEE-TTS-SEEEEES CS
                    Pectinesterase  3 vvakdgsgkfktiseavaavpeksekrfviyvkaGvYeenvevekkktnvvlvGd 57
                                      +v +dg +++kti++av a+++       iyvk G Y+e+v ++k+ + + l+G+
  gi|330508639|ref|YP_004385067.1| 21 IVDDDGFSNYKTIQDAVIAASDGD----TIYVKPGNYSEEVILNKSLSLMPLIGE 71
                                      7889**************998765....59**************99888778876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.69
                                       -EEES-EEEE---GGG----SEEE--TTEEEES-EEE CS
                    Pectinesterase  89 fiarditfentaGpekhqavalrvdsDlsvfyrcsle 125
                                       ++  ++ + + aG ++ +a  l   sD  vf r +++
  gi|330508639|ref|YP_004385067.1| 227 YVSDNLVMIDDAGNSTSRASLLANVSDV-VFQRNKID 262
                                       5667788889999999999888888885.67777666 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.11
                                       EE-TTB-TT-S--SSTTTTTTT-EEEEES-BSTT- CS
                    Pectinesterase 232 kiedvidpeGwleWngdfalktlyYgeyknsGpga 266
                                       +ie+ id+eG  +W++  +    y+++++ +G+ +
  gi|330508639|ref|YP_004385067.1| 595 NIEHSIDTEGGNSWDAGNNTGGNYWSDHSARGNPS 629
                                       46678999999999999999999999988888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.80u 0.31s 00:00:01.11 Elapsed: 00:00:00.55
# Mc/sec: 3621.51
//
Query:       gi|330508640|ref|YP_004385068.1|  [L=63]
Description: hypothetical protein MCON_2881 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.7e-15   54.6   0.1    9.1e-15   54.4   0.1    1.1  1  Sec61_beta  Sec61beta family
  ------ inclusion threshold ------
      0.025   15.1   0.0      0.027   15.0   0.0    1.1  1  DoxX        DoxX


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.1     1e-18   9.1e-15       1      40 [.      19      58 ..      19      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1e-18
                                      XXXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS CS
                        Sec61_beta  1 SsaGLlryyeedapgikidPkvVlvlsvafiasVilLhil 40
                                      SsaGL+ry+e d+ +ik +Pk+Vl+++++ +a+V+ L+i 
  gi|330508640|ref|YP_004385068.1| 19 SSAGLMRYFEADDDSIKFSPKMVLGVCIGAGAVVMGLNIA 58
                                      9*********5557************************96 PP

>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.1e-06     0.027      26      65 ..      20      63 .]       8      63 .] 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-06
                              DoxX 26 legtaasla....alglpppellaylaalvElvgglllllGllt 65
                                      ++g   +++    ++ + p ++l ++++++ +v+gl +++Gl++
  gi|330508640|ref|YP_004385068.1| 20 SAGLMRYFEadddSIKFSPKMVLGVCIGAGAVVMGLNIAFGLWP 63
                                      3334444447777999999***********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); 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: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 358.12
//
Query:       gi|330508641|ref|YP_004385069.1|  [L=400]
Description: hypothetical protein MCON_2882 [Methanosaeta concilii GP6]
Scores for complete 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  107.2   0.0    4.7e-30  104.5   0.0    1.9  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
      3e-09   36.3   0.0    5.8e-09   35.4   0.0    1.4  2  Aminotran_5      Aminotransferase class-V
    5.5e-07   29.1   0.0    4.4e-06   26.1   0.0    2.0  1  Aminotran_1_2    Aminotransferase class I and II
      0.006   15.9   0.0      0.012   15.0   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.019   14.3   0.0       0.03   13.6   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.0   1.3e-33   4.7e-30      75     355 ..      81     327 ..      72     345 .. 0.88

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 1.3e-33
                                       HHHHHHHHHHHHHHHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHHHCCEEEEEE CS
                     Pyridoxal_deC  75 PaltelevvvldwlaellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkeaeildklvlyts 151
                                       P ++ le  v+ +l+ellg p   l   + g +++g++es++ a+ Aa+++       +gk        +  +++  
  gi|330508641|ref|YP_004385069.1|  81 PGVAGLEEEVVRMLGELLGCP---L---ARGYISTGGTESNIQAIRAAKNE-------SGKC------GG--NIVVP 136
                                       77889****************...3...67**************9999964.......4433......23..45555 PP

                                       TTS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT CS
                     Pyridoxal_deC 152 dqahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekyd 228
                                       + ah s +k++ +l +++r  +ld + ++  ++ e +i e  ++       v ++Gtt  g+ d ++el d+  +++
  gi|330508641|ref|YP_004385069.1| 137 ASAHFSFDKIGDLLSLEVRKAELDSQLRVDLSSVESLIDEHTAA------LVGIAGTTEFGQVDPIEELSDLALEWG 207
                                       557***********************************999999......4569*********************** PP

                                       -EEEEE-TTGGGGGGSGGGGG...GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TTTT CS
                     Pyridoxal_deC 229 lwlHvDAAyaGsaficpeirh...llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLehedsd 302
                                       + lHvDAA++G  f+ p+      +++ ++ ++Sit+ phK++l+++ ++ l+++++e + +al+ e +YL      
  gi|330508641|ref|YP_004385069.1| 208 VHLHVDAAFGG--FVLPFLDRsfaWDFSLPGVKSITIDPHKMGLATIPAGGLLFRNQECM-NALETETHYLT----- 276
                                       ***********..*****988899********************************9986.67889*****9..... PP

                                       TSEECCCGSSSSSG.HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                     Pyridoxal_deC 303 vaadlgtkaiplsr.rvrilklwfvlralGveglqnqirksvelakyleklirk 355
                                            ++  +   r    ++  + v+  lG+eg+++ +  +++l   l    ++
  gi|330508641|ref|YP_004385069.1| 277 ---KARQASLTGTRsGAAAAATYAVMMHLGREGFREMVGYCMDLTDHLVRGAKE 327
                                       ...4677888888877888899999999***************99988776655 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   1.6e-12   5.8e-09      68     177 ..     109     215 ..      88     232 .. 0.90
   2 ?   -3.6   0.0       1.1   3.9e+03     250     288 ..     284     322 ..     264     333 .. 0.63

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.6e-12
                                       SSHHHHHHHHHHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEE CS
                       Aminotran_5  68 sGtteainlvalslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklv 143
                                        G+te++  ++++++++  k g +ivv ++ h +      ++ +   ++v++++ld++ ++dl+ +e+l++e t+++
  gi|330508641|ref|YP_004385069.1| 109 TGGTESNIQAIRAAKNEsGKCGGNIVVPASAHFSFD----KIGDLLSLEVRKAELDSQLRVDLSSVESLIDEHTAAL 181
                                       4788876666666666669**********9999977....9999999****************************** PP

                                       EEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 144 aithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                          +  ++ G ++p+ee+ +la + g+ ++vDaa
  gi|330508641|ref|YP_004385069.1| 182 VGIAGTTEFGQVDPIEELSDLALEWGVHLHVDAA 215
                                       *********************************8 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.1
                                       .SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHH CS
                       Aminotran_5 250 aGTpnvagiiglgaaleyleeigleaiekhekelaeyll 288
                                        GT   a++ +  a++ +l + g++++  +   l+++l+
  gi|330508641|ref|YP_004385069.1| 284 TGTRSGAAAAATYAVMMHLGREGFREMVGYCMDLTDHLV 322
                                       366666666666666666666777666666666666665 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 !   26.1   0.0   1.2e-09   4.4e-06      72     361 ..     107     390 ..      80     392 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.2e-09
                                       EEESHHHHHHHHHHHHHHHTTT-..EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTT CS
                     Aminotran_1_2  72 vvgsGagaliealifllklnpgd..eilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegn 146
                                       + ++G+ ++i+a+ ++ +   ++  +i+vp+  + s+++i  l  +ev++ +l+   + ++dl ++e +++e+++  
  gi|330508641|ref|YP_004385069.1| 107 ISTGGTESNIQAIRAAKNESGKCggNIVVPASAHFSFDKIGDLLSLEVRKAELD--SQLRVDLSSVESLIDEHTAAL 181
                                       56788888888888888544444336**************************99..999*************64443 PP

                                       ETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTT CS
                     Aminotran_1_2 147 kktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKaf 223
                                       +   +i+ ++     G+v + eel +l   a + +++l vD a++gfv+  ld   ++ +  ++++ ++       +
  gi|330508641|ref|YP_004385069.1| 182 V---GIAGTT---EFGQVDPIEELSDL---ALEWGVHLHVDAAFGGFVLPFLDRSFAWDFSLPGVKSITIDP--HKM 247
                                       3...444444...56************...9999***************94432222444444444344432..355 PP

                                       SSGGG-EEEEEE.EH..........HHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Aminotran_1_2 224 GlaGeRvGyilg.na..........avvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkel 288
                                       Gla +  G +l  n+          +++  +r++s      + +++aa+a+ +   +l ++ + em+    +++++l
  gi|330508641|ref|YP_004385069.1| 248 GLATIPAGGLLFrNQecmnaletetHYLTKARQASL---TgTRSGAAAAATYAVMMHLGREGFREMVGYCMDLTDHL 321
                                       555555555555444999999854444444444444...45555555555555555566779*************** PP

                                       HHHHHHSTEEEECCS.CSSEEEEEETHHCHHHHHHHHHHT.CTEEEEEGGGGTSTTEEEEEC.TTS-HHHHHHHHH CS
                     Aminotran_1_2 289 rdeLaelglkvlasq.sgmflltdlsaetakelskkLlee.vgvyvtpgtsftvpgrlRitv.Aglteeeleelve 361
                                       + + +e+g++ l+++  +++ l++ +++   ++ + L ++ ++v +t+  ++     lR+ +  ++++e+++ +++
  gi|330508641|ref|YP_004385069.1| 322 VRGAKEIGVEPLIEPvMNVVALRVPEPS---KVRERLMDRdWHVSITR--EP--NRALRLILmGHMSHENVDLFLK 390
                                       ********99999998999999999999...78888999999999999..33..4689999999999999997765 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.2e-06     0.012      70     169 ..     129     215 ..      62     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.2e-06
                                       TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB--- CS
                   Beta_elim_lyase  70 rgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvs 146
                                        g +++v   ah+ fd  g +  l+   +r+++ +++  +dl ++e++i+e+       +l+ ++ T++   Gqv +
  gi|330508641|ref|YP_004385069.1| 129 CGGNIVVPASAHFSFDKIGDLLSLE---VRKAELDSQLRVDLSSVESLIDEHT-----AALVGIAGTTEF--GQVDP 195
                                       3567788888999999999885554...44555555559************44.....59*********9..99866 PP

                                       HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 147 leelrevaaiakkygiplhlDgA 169
                                          ++e++++a + g++lh+D+A
  gi|330508641|ref|YP_004385069.1| 196 ---IEELSDLALEWGVHLHVDAA 215
                                       ...5677899************9 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.4e-06      0.03      47     146 ..     111     215 ..      92     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-06
                                       HHHHHHHHHHHTTTT...TT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEE...EEE CS
                   DegT_DnrJ_EryC1  47 GtaAlhlaLralgvg...pgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertka...Ilp 117
                                       Gt+++  a+ra + +    g  ++vp+   ++  +    l +++  ++ d  ++ +d +++e++i e t+a   I  
  gi|330508641|ref|YP_004385069.1| 111 GTESNIQAIRAAKNEsgkCGGNIVVPASAHFSFDKIGDLLSLEVRKAELD-SQLRVDLSSVESLIDEHTAAlvgIAG 186
                                       66666666666444433456677777777777777777777777777877.7799**************77222555 PP

                                       B-GGGB---HHHHHHHHHHCT-EEEEE-T CS
                   DegT_DnrJ_EryC1 118 VhlyGqvadmdalkaiaakhglkvieDaA 146
                                          +Gqv  +++l ++a ++g+ +  DaA
  gi|330508641|ref|YP_004385069.1| 187 TTEFGQVDPIEELSDLALEWGVHLHVDAA 215
                                       6789************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 2474.11
//
Query:       gi|330508642|ref|YP_004385070.1|  [L=760]
Description: phosphoenolpyruvate synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.3e-113  379.6   0.4   1.9e-113  379.0   0.4    1.2  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    6.5e-86  288.1   0.1    1.3e-85  287.1   0.0    1.5  2  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    2.8e-25   87.8   2.4    8.3e-25   86.3   2.4    1.9  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
    0.00027   20.2   0.1    0.00066   18.9   0.1    1.6  1  HpcH_HpaI        HpcH/HpaI aldolase/citrate lyase family
  ------ inclusion threshold ------
       0.12   12.8   0.0        9.4    6.6   0.0    2.9  2  Radical_SAM      Radical SAM superfamily


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 !  379.0   0.4  5.4e-117  1.9e-113       3     318 ..      17     324 ..      15     331 .. 0.98

  Alignments for each domain:
  == domain 1  score: 379.0 bits;  conditional E-value: 5.4e-117
                            PPDK_N   3 lvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelPe 79 
                                       +vGGKga+L+e++  +g+pvP gfa+ta+afr+f++++g+++k+ e+l+ +dv++ +el++a++++++li++a++P+
  gi|330508642|ref|YP_004385070.1|  17 IVGGKGASLGEMIG-IGVPVPGGFAVTAQAFRDFINRAGIADKLFEALN-VDVNQETELHRAEQTAKKLIMDAKVPK 91 
                                       8***********55.**********************************.7************************** PP

                            PPDK_N  80 eleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYrk 156
                                       ++eeaik  yeel+k+ g++ + vaVRSSataEDlp+asfaGqq+tyLn++g+e+v++a+++++aSl+ +rAi+Yr 
  gi|330508642|ref|YP_004385070.1|  92 DIEEAIKTRYEELCKREGKQ-VFVAVRSSATAEDLPDASFAGQQETYLNMRGAEDVFNAVRKCWASLYGARAIFYRV 167
                                       ***************99997.******************************************************** PP

                            PPDK_N 157 ekgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilekk 233
                                       e+g++h++v+l+++vq mv+s+  ++GV+fs  p+tG +  v+i+a++GlGe+VV+G v+pd++vv+++t+ki+++ 
  gi|330508642|ref|YP_004385070.1| 168 EQGFEHNKVNLSAIVQLMVDSE--KAGVMFSSQPSTG-EPLVVIEAAWGLGESVVSGSVSPDNYVVDRKTKKIVNRY 241
                                       **********************..*************.*************************************** PP

                            PPDK_N 234 igekeikivydekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaideeegklyllQaRpet 310
                                       i++kei+i++d k+++t++ +vp +++e+ +L+d+e+ eLa++++ +e+hyg p+diE+ ++  ++k+y+lQ+Rp+t
  gi|330508642|ref|YP_004385070.1| 242 IATKEIMITRDAKTHKTTTAKVPAKKKEAVVLTDKEIIELARYGEILEEHYGLPQDIEWGVE--KNKIYILQSRPIT 316
                                       **************************************************************..************* PP

                            PPDK_N 311 rtsekkek 318
                                       + s++k++
  gi|330508642|ref|YP_004385070.1| 317 TISSEKKA 324
                                       *9988775 PP

>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.5   5.3e+03      15      41 ..      76     102 ..      68     137 .. 0.73
   2 !  287.1   0.0   3.6e-89   1.3e-85      15     292 ..     462     747 ..     456     749 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.5
                                       CCCXBCEEEEEESSCHHHHHHHHCTXS CS
                   PEP-utilizers_C  15 kdgkkikvlaNidtpedaekalengae 41 
                                       ++ ++ k+++ ++ p+d+e+a +++ e
  gi|330508642|ref|YP_004385070.1|  76 AEQTAKKLIMDAKVPKDIEEAIKTRYE 102
                                       456667778888888888888777665 PP

  == domain 2  score: 287.1 bits;  conditional E-value: 3.6e-89
                                       CCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHH...........HHHHHHHHHHHTTTSEE CS
                   PEP-utilizers_C  15 kdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteee...........qaeaykkvleamngrpv 80 
                                       k+++++++ +N+++p+ ae+a+++ a+G+GLlR+E++++ + ++p               + + +k v++a+++rpv
  gi|330508642|ref|YP_004385070.1| 462 KPVTATEIKVNVSEPDRAEAAAATQADGVGLLRIEHMILGMGKTPNWYIrsgkteeyiseLISGIKVVADAFYPRPV 538
                                       5688999999*******************************9866544447899999999***************** PP

                                       EEEXXXSSCC..GGSGGCHHHH.XSXGGGSSXTHHHHCCSHHHHHHHHHHHHHHCC..CCEEEEEESSXXSHHHHHH CS
                   PEP-utilizers_C  81 vvRtlDiggd..kelpelkeepeevNPmlGfRgirlglsepelfetqlrAllrasa..agkleimlPmvasveelee 153
                                       +vRtlD+++d  + ++ ++ ep+e NPmlG+Rgir+ ++e + f+ +++A++r  +   +++ imlPmv++v+e+++
  gi|330508642|ref|YP_004385070.1| 539 WVRTLDAPTDefRAMEGGEGEPHEHNPMLGWRGIRRDMTETDHFRLEVKAFKRLHEmgLTNVGIMLPMVQHVSEFQK 615
                                       **********888899****************************************5555***************** PP

                                       HHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTT.SSEEEEXHHHHHHHHHTXXCCCHCHHHHSXTT CS
                   PEP-utilizers_C 154 akkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklake.vdFfSiGtNDLtQytlavdRdneevaklydpl 229
                                       ak+i++ +  +l+        k+ vG+MiE+p aal+++++++  +dF+S+GtNDLtQytlavdR+ne+va ly +l
  gi|330508642|ref|YP_004385070.1| 616 AKSIMRDEGLDLD--------KIDVGVMIETPGAALTIEDFIEDgIDFISFGTNDLTQYTLAVDRNNENVAGLYSEL 684
                                       *******966655........68********************99******************************** PP

                                       TCHHCCCHHHHHHHHHHCCXEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCT CS
                   PEP-utilizers_C 230 epavlrlikevikaaeekglkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqv 292
                                       +pavl+li++v+++++e+g+k++iCG+++++p++++ lv++G+ ++S++ ++v+++r ++a+ 
  gi|330508642|ref|YP_004385070.1| 685 HPAVLKLIEYVVEQCREAGVKTSICGQAGSYPEMAKKLVEMGITSISANIDAVATVRDTVARS 747
                                       **********************************************************99986 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   2.4   2.3e-28   8.3e-25       1      73 []     362     434 ..     362     434 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 2.3e-28
                                       G--S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers   1 kleegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                       k+++g+I+v+++t p++++g+++a +ivt++GGm +HaAiv+relg PaVvg+++at+ lk+g +itvDg +G
  gi|330508642|ref|YP_004385070.1| 362 KIKQGDIMVTKMTMPDMVPGMKRAGAIVTDEGGMACHAAIVSRELGCPAVVGTKKATSILKDGMEITVDGGKG 434
                                       5789*****************************************************99***********998 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 !   18.9   0.1   1.8e-07   0.00066      87     191 ..     601     705 ..     584     733 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.8e-07
                                       EEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEEEE-HHHHHH.HTT-TT CS
                         HpcH_HpaI  87 vvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgvflGaeDlsa.dlgtkr 162
                                       ++++P+v+   e ++++s++r          +++ + + iE+  + + +e+ ++ +g+d + +G++Dl+  +l   r
  gi|330508642|ref|YP_004385070.1| 601 GIMLPMVQHVSEFQKAKSIMRDEG----LDLDKIDVGVMIETPGAALTIEDFIE-DGIDFISFGTNDLTQyTLAVDR 672
                                       79*****************99766....77899*****************9986.9************853566666 PP

                                       STTSHHHH.........HHHHHHHHTTHCEEEEEEE.E CS
                         HpcH_HpaI 163 spegtevl.........dareriltaaraagiaaldtv 191
                                       ++e    l         + +e ++  +r ag+      
  gi|330508642|ref|YP_004385070.1| 673 NNENVAGLyselhpavlKLIEYVVEQCREAGV-----K 705
                                       55543333455555555999999999999999.....3 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.05   1.8e+02     117     155 ..     572     610 ..     490     619 .. 0.72
   2 ?    6.6   0.0    0.0026       9.4      46     112 ..     652     737 ..     641     747 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.05
                                       HHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 117 vlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                                       +++ m  ++ f   ++a+++l+e g+ +v ++++++  +
  gi|330508642|ref|YP_004385070.1| 572 IRRDMTETDHFRLEVKAFKRLHEMGLTNVGIMLPMVQHV 610
                                       444444444445556999999999999888888887765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0026
                                       TSEEEEEESSTGGGS......................TTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxx......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  46 gvkevilgggeplly......................pdfvellerlaklavpgiritvetngtlpdeeklerllel 100
                                       g++++ +g  + + y                       +++e++ + +++  +g+++++   ++   +e++++l+e+
  gi|330508642|ref|YP_004385070.1| 652 GIDFISFGTNDLTQYtlavdrnnenvaglyselhpavLKLIEYVVEQCRE--AGVKTSICGQAGSY-PEMAKKLVEM 725
                                       55566666555555566666666666666666644445566666666666..57777777777776.********** PP

                                       T-SEEEEEEBSS CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 101 gvdrvslgleaa 112
                                       g++ +s +++a+
  gi|330508642|ref|YP_004385070.1| 726 GITSISANIDAV 737
                                       ********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (760 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 4711.27
//
Query:       gi|330508643|ref|YP_004385071.1|  [L=384]
Description: molybdenum cofactor synthesis domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-32  112.4   0.1    3.4e-32  111.4   0.1    1.5  1  MoeA_N         MoeA N-terminal region (domain I and II)
    2.4e-24   85.6   0.0    8.1e-24   83.9   0.0    1.9  2  MoCF_biosynth  Probable molybdopterin binding domain
    4.6e-14   52.3   2.3    9.7e-14   51.3   0.1    2.7  4  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 !  111.4   0.1   5.7e-36   3.4e-32       6     157 .]      11     153 ..       8     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 5.7e-36
                                       HHHHHHHH-.HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--...........-S---T CS
                            MoeA_N   6 alaiilaal.eleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeepsaageeperllp 80 
                                       a++++l+++ +l++ e ++  + al rv+ ed++++ d+P+fd+SamDGYAvr+++++ga         +++++   
  gi|330508643|ref|YP_004385071.1|  11 ARRMLLERClPLKDIEeLNT-SCALDRVASEDIRSSADLPAFDRSAMDGYAVRSTDTKGA---------RPSGPRFI 77 
                                       55666677766655555898.889***********************************9.........55777888 PP

                                       T-EEEE-TTSB--TT--EEEEGGGE..E....EETTE..S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHHHHH CS
                            MoeA_N  81 ggavrimTGaplPegadaVvpvEdte.eeeaketvev..kavkpgenvrraGedikaGevllragtrltpaeiglla 154
                                       ++ +   TG ++Peg+da+v++Ed++ + e      +  +++++ +nv raGed+ +G++++++g+rl+p +++l+ 
  gi|330508643|ref|YP_004385071.1|  78 PDFIPQRTGMVVPEGYDAIVMLEDARvRGE--VL--EvtAEAHAYKNVARAGEDVMEGDTIFTEGHRLRPPDLALIS 150
                                       889999******************964322..22..1347889999******************************9 PP

                                       HCT CS
                            MoeA_N 155 svG 157
                                       ++G
  gi|330508643|ref|YP_004385071.1| 151 ALG 153
                                       998 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.42   2.5e+03      73     102 ..     116     145 ..     111     170 .. 0.66
   2 !   83.9   0.0   1.4e-27   8.1e-24       5     143 ..     170     302 ..     166     303 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.42
                                       -HHHHHHHHHSEE-HHHHHHHHHHHHHHCC CS
                     MoCF_biosynth  73 vtpealaklfekelegfeeafrrvslkpgk 102
                                       + ++ +a+++e+ +eg+ +  ++ +l+p  
  gi|330508643|ref|YP_004385071.1| 116 HAYKNVARAGEDVMEGDTIFTEGHRLRPPD 145
                                       556778999999999999999998888865 PP

  == domain 2  score: 83.9 bits;  conditional E-value: 1.4e-27
                                       E-HHHH........TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT-- CS
                     MoCF_biosynth   5 vGdell........sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDv 73 
                                       +G +l+        +g+++  ng +   ++++ g++v+k+++vpDd e+i+ea+ ++l++ d+i+++GGt+++++D+
  gi|330508643|ref|YP_004385071.1| 170 TGGKLVdigarrlePGEAYEINGLMARLYIEKWGANVRKTKIVPDDSERIREAISSNLDA-DMIVIIGGTSVGEKDY 245
                                       555555555555589999************************************999777.**************** PP

                                       HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  74 tpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                        p++l++++e         +++v+l+pgkp+ ++ +a  +r    ++i+LPG+p+a+   l ++++pa++
  gi|330508643|ref|YP_004385071.1| 246 APRILSEMGE-------LYVHGVRLQPGKPTAFGDVA--GR----PVICLPGYPVAALSNLYLFIRPAIK 302
                                       **********.......8***************9994..44....7*********************997 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 ?   -2.7   0.0       1.2   7.2e+03       4      33 ..      38      63 ..      37      68 .. 0.71
   2 ?   -1.9   0.1      0.68     4e+03      46      66 ..     113     133 ..     108     134 .. 0.78
   3 ?   -3.1   0.0       1.5     9e+03      15      35 ..     243     262 ..     241     264 .. 0.75
   4 !   51.3   0.1   1.6e-17   9.7e-14       1      71 [.     315     382 ..     315     383 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                                      ESS-EE--SSS-EEEEEEEES-S-EEEEEE CS
                            MoeA_C  4 laedlksdpgrreflRvilteedgeyvaep 33
                                      ++ed++s ++ + f R  ++    +y +++
  gi|330508643|ref|YP_004385071.1| 38 ASEDIRSSADLPAFDRSAMD----GYAVRS 63
                                      57888998888888888777....455555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.68
                                       TT--EEEEE-TT--EE-TT-E CS
                            MoeA_C  46 aeAnglivipegtegleaGee 66 
                                       aeA ++ ++ + +e++ +G++
  gi|330508643|ref|YP_004385071.1| 113 AEAHAYKNVARAGEDVMEGDT 133
                                       788888888888888888886 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.5
                                       -EEEEEEEES-S-EEEEEE-S CS
                            MoeA_C  15 reflRvilteedgeyvaeptg 35 
                                       +++ + il+ e ge++++ ++
  gi|330508643|ref|YP_004385071.1| 243 KDYAPRILS-EMGELYVHGVR 262
                                       578888888.77999999765 PP

  == domain 4  score: 51.3 bits;  conditional E-value: 1.6e-17
                                       EEEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE CS
                            MoeA_C   1 karlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevil 71 
                                       +ar  ++++s+pg  +++Rv  + edg+  +ep+  +g g+Lss a+A+g++v+pe+ eg+e+G+ Vev l
  gi|330508643|ref|YP_004385071.1| 315 QARVVRKMTSKPGYLSLVRVAFR-EDGQ--VEPIMVSGAGILSSVARADGFVVVPEELEGFEEGDMVEVVL 382
                                       588899*****************.5565..***************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2676.21
//
Query:       gi|330508644|ref|YP_004385072.1|  [L=210]
Description: hypothetical protein MCON_2890 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-15   56.9   0.6    1.6e-10   40.8   0.0    2.6  2  HTH_20          Helix-turn-helix domain
    1.2e-13   50.7   0.1    2.1e-08   33.9   0.0    2.5  2  HTH_5           Bacterial regulatory protein, arsR family
    1.9e-08   34.1   0.3     0.0038   17.1   0.0    2.7  3  TrmB            Sugar-specific transcriptional regulator TrmB
    1.7e-06   27.5   0.4       0.05   13.2   0.0    3.6  4  HTH_24          Winged helix-turn-helix DNA-binding
    6.3e-05   22.8   0.2       0.07   13.0   0.0    2.4  2  MarR_2          MarR family
    0.00014   22.0   0.0        0.4   10.9   0.0    2.6  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00024   21.4   0.0       0.35   11.2   0.0    2.5  2  Rrf2            Transcriptional regulator
    0.00024   20.7   0.3       0.82    9.4   0.1    2.7  2  GntR            Bacterial regulatory proteins, gntR family
    0.00034   20.7   0.0     0.0012   18.9   0.0    1.9  1  DprA_WH         DprA winged helix domain
     0.0033   16.3   0.6      0.005   15.7   0.6    1.2  1  Nup188_C        Nuclear pore protein NUP188 C-terminal domain
     0.0053   16.7   0.1        0.9    9.5   0.0    3.1  3  HTH_11          HTH domain
     0.0083   15.9   0.1        3.4    7.6   0.0    2.5  2  IF2_N           Translation initiation factor IF-2, N-termina
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.048   13.5   0.0    1.9  1  LexA_DNA_bind   LexA DNA binding domain
      0.034   14.1   0.0       0.23   11.5   0.0    2.4  1  PadR            Transcriptional regulator PadR-like family
      0.078   12.9   0.0        1.6    8.7   0.0    2.3  2  MarR            MarR family
      0.087   12.9   0.0       0.38   10.9   0.0    2.0  2  DUF2250         Uncharacterized protein conserved in archaea 
       0.12   12.7   0.1        1.1    9.6   0.0    2.1  2  DUF2513         Hypothetical protein (DUF2513)
       0.12   12.8   0.1        4.3    7.9   0.0    2.4  2  HTH_27          Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   1.7e-13   1.6e-10       3      56 ..       7      59 ..       6      63 .. 0.95
   2 !   13.8   0.1   4.6e-05     0.046      18      61 .]     166     208 ..     158     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.7e-13
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      ++++L+++ Rrril++L + +++ ++e a+rld+ ++ + +HL+ Le+agLve 
  gi|330508644|ref|YP_004385072.1|  7 LLDILGNENRRRILQLL-SFRPFYFNEMAKRLDVGPKAVIDHLEMLERAGLVEC 59
                                      7899*************.**********************************97 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.6e-05
                                       HHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  18 aLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       aL   +g+  sela rl+++ + + + L++L e  +v+++++ +
  gi|330508644|ref|YP_004385072.1| 166 AL-LCGGANSSELATRLEVPEAVVLDSLNKLKERSAVHLRGQQW 208
                                       55.5678889****************************998765 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 !   33.9   0.0   2.1e-11   2.1e-08       1      46 [.      13      58 ..      13      58 .. 0.97
   2 !   14.1   0.1   3.1e-05     0.031       5      41 ..     161     197 ..     158     198 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.1e-11
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +++R++IL+lL+ ++ ++ e a+ l++ + +v  HL +L+ aGLVe
  gi|330508644|ref|YP_004385072.1| 13 NENRRRILQLLSFRPFYFNEMAKRLDVGPKAVIDHLEMLERAGLVE 58
                                      589******************************************6 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_5   5 lkILklLaegelcvcelaeelglsqstvShHLkkLre 41 
                                       ++I+ +L  g + ++ela  l+++++ v   L+kL+e
  gi|330508644|ref|YP_004385072.1| 161 SEIMTALLCGGANSSELATRLEVPEAVVLDSLNKLKE 197
                                       58*********************************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 !   14.1   0.0   3.2e-05     0.032      16      63 ..      21      70 ..      19      74 .. 0.84
   2 ?   -2.9   0.0       6.5   6.5e+03       5      19 ..     102     116 ..     100     119 .. 0.74
   3 !   17.1   0.0   3.8e-06    0.0038       8      53 ..     158     202 ..     157     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr..pklYr 63
                                       Ll+  p   +e a++l+v    v + L+ Le++GlVe  +++  +k++r
  gi|330508644|ref|YP_004385072.1| 21 QLLSFRPFYFNEMAKRLDVGPKAVIDHLEMLERAGLVECYQEQgrRKYFR 70
                                      6899999999***************************9877665255554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.5
                                       HHHHHCCCHCHHHHH CS
                              TrmB   5 GLseyEakvYlaLlk 19 
                                       G+ e Ea+  l++lk
  gi|330508644|ref|YP_004385072.1| 102 GFEEAEASLDLKMLK 116
                                       899999987666665 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 3.8e-06
                                       HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB   8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53 
                                       + E+++ +aLl  g a+ +e+a +l+vp++ v ++L++L+++  V+
  gi|330508644|ref|YP_004385072.1| 158 QLESEIMTALL-CGGANSSELATRLEVPEAVVLDSLNKLKERSAVH 202
                                       68999999999.58899************************98886 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      0.16   1.6e+02       2      12 ..      13      23 ..      12      24 .. 0.90
   2 !   13.2   0.0     5e-05      0.05      21      48 .]      31      58 ..      30      58 .. 0.95
   3 ?   -3.0   0.0       5.8   5.7e+03      13      27 ..      61      75 ..      59      75 .. 0.81
   4 !    8.2   0.1    0.0018       1.8      16      43 ..     170     197 ..     157     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.16
                            HTH_24  2 detdrkILelL 12
                                      +e++r+IL+lL
  gi|330508644|ref|YP_004385072.1| 13 NENRRRILQLL 23
                                      799******98 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5e-05
                            HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +e A+rl++ p +v  +l+ Le++Gl++
  gi|330508644|ref|YP_004385072.1| 31 NEMAKRLDVGPKAVIDHLEMLERAGLVE 58
                                      699***********************96 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.8
                            HTH_24 13 qknprisqreLAerl 27
                                      q+++r  +  +A+r+
  gi|330508644|ref|YP_004385072.1| 61 QEQGRRKYFRIARRT 75
                                      889999999999985 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0018
                            HTH_24  16 prisqreLAerlglSpstvnrrlkrLee 43 
                                       ++ + +eLA rl ++ + v+  l++L+e
  gi|330508644|ref|YP_004385072.1| 170 GGANSSELATRLEVPEAVVLDSLNKLKE 197
                                       78999*********************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   7.1e-05      0.07       8      52 ..      17      58 ..       7      67 .. 0.85
   2 !    7.5   0.1    0.0036       3.6      10      49 ..     163     199 ..     157     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.1e-05
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +r+L  L  rp   +  +e a+rl++ + av  +l+ L++aGLve
  gi|330508644|ref|YP_004385072.1| 17 RRILQLLSFRP---FYFNEMAKRLDVGPKAVIDHLEMLERAGLVE 58
                                      67788888888...9*****************************8 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0036
                                       HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTT CS
                            MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaG 49 
                                       ++ aL +++    + +ela rl ++ + v   l++L ++ 
  gi|330508644|ref|YP_004385072.1| 163 IMTALLCGG---ANSSELATRLEVPEAVVLDSLNKLKERS 199
                                       677899998...699*********************9975 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0    0.0004       0.4      27      56 ..      32      61 ..      24      64 .. 0.90
   2 !    8.2   0.0    0.0028       2.7      24      51 ..     173     200 ..     169     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0004
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress 27 dlaerLnvspssVsemlkkLekdGyveyek 56
                                      ++a+rL+v p  V   l+ Le++G+ve  +
  gi|330508644|ref|YP_004385072.1| 32 EMAKRLDVGPKAVIDHLEMLERAGLVECYQ 61
                                      78************************9655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0028
                                       -HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress  24 ktkdlaerLnvspssVsemlkkLekdGy 51 
                                         ++la rL+v  + V  +l+kL++   
  gi|330508644|ref|YP_004385072.1| 173 NSSELATRLEVPEAVVLDSLNKLKERSA 200
                                       6799*******************99755 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00035      0.35      27      57 ..      29      59 ..      20      83 .. 0.88
   2 !    7.7   0.0    0.0044       4.4      26      56 ..     172     202 ..     162     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00035
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 27 sseeiaerqnispsylekilakLrkaglvks 57
                                        +e+a+r ++ p+ +   l++L++aglv+ 
  gi|330508644|ref|YP_004385072.1| 29 YFNEMAKRLDVGPKAVIDHLEMLERAGLVEC 59
                                      5689*************************85 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0044
                                       B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2  26 vsseeiaerqnispsylekilakLrkaglvk 56 
                                       ++s+e+a+r ++++ ++   l+kL++   v+
  gi|330508644|ref|YP_004385072.1| 172 ANSSELATRLEVPEAVVLDSLNKLKERSAVH 202
                                       5799*********************988776 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0014       1.3      28      61 ..      31      64 ..      30      66 .. 0.92
   2 !    9.4   0.1   0.00082      0.82      28      59 ..     175     206 ..     153     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0014
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglverrqgrG 61
                                      +e a++++V+   v   L +Le++glve  q +G
  gi|330508644|ref|YP_004385072.1| 31 NEMAKRLDVGPKAVIDHLEMLERAGLVECYQEQG 64
                                      6899************************988877 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00082
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR  28 reLaaefgVsrttvReALrrLeaeglverrqg 59 
                                       +eLa++++V   +v  +L++L+++  v+ r +
  gi|330508644|ref|YP_004385072.1| 175 SELATRLEVPEAVVLDSLNKLKERSAVHLRGQ 206
                                       79*************************99876 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.2e-06    0.0012      12      57 ..      14      59 ..       6      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                           DprA_WH 12 dlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlver 57
                                      + +rr+L++L++ P  + + ++r+ + + +v  +L +LE aGlve 
  gi|330508644|ref|YP_004385072.1| 14 ENRRRILQLLSFRPFYFNEMAKRLDVGPKAVIDHLEMLERAGLVEC 59
                                      679*****************************************85 PP

>> Nup188_C  Nuclear pore protein NUP188 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.6     5e-06     0.005     305     363 ..     109     167 ..      98     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5e-06
                                       ---HHHHHHHHHHHHT-HHHHHHHB---SHHHHHHHHS---.SS-S-SSHHHHHHHHHH CS
                          Nup188_C 305 ewdaasvkedvefwlssrklLrerlvplgerelelarkkaedesskaenrLeekvvael 363
                                       + d + +k+++  + ++r  Lre l  +++re+e++++ ++ ++ +aen+Le+++++ l
  gi|330508644|ref|YP_004385072.1| 109 SLDLKMLKDELLGLEKKRYELRELLAQIESREMEIKQRASSVAGFRAENQLESEIMTAL 167
                                       56788889999999999**************************************9876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0009       0.9       2      51 ..      16      64 ..      15      70 .. 0.82
   2 ?   -0.8   0.0       1.5   1.5e+03      39      49 ..     129     139 ..     128     140 .. 0.86
   3 ?    3.1   0.0     0.095        95      18      41 ..     174     197 ..     170     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0009
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIesepg 51
                                      ++ il+lL + r+ +  +e+A++L+v  ++v  +++ Le +g v+ + e+g
  gi|330508644|ref|YP_004385072.1| 16 RRRILQLL-SFRP-FYFNEMAKRLDVGPKAVIDHLEMLERAGlVECYQEQG 64
                                      57888888.6665.8999**********************99666555555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                            HTH_11  39 LeelgvpIese 49 
                                       L+el+++Ies+
  gi|330508644|ref|YP_004385072.1| 129 LRELLAQIESR 139
                                       9999****996 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.095
                            HTH_11  18 geeLAeeLnvSrrtvrrdIkaLee 41 
                                       ++eLA +L+v +++v   + +L+e
  gi|330508644|ref|YP_004385072.1| 174 SSELATRLEVPEAVVLDSLNKLKE 197
                                       78********99999998888887 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0034       3.4       7      26 ..      31      50 ..      31      55 .. 0.89
   2 ?    5.9   0.0     0.011        11       7      26 ..     175     194 ..     175     202 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0034
                             IF2_N  7 yeLAkeLgvkskevikkLfk 26
                                      +e Ak+L v +k vi++L++
  gi|330508644|ref|YP_004385072.1| 31 NEMAKRLDVGPKAVIDHLEM 50
                                      588***************54 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
                             IF2_N   7 yeLAkeLgvkskevikkLfk 26 
                                       +eLA +L v+ + v++ L+k
  gi|330508644|ref|YP_004385072.1| 175 SELATRLEVPEAVVLDSLNK 194
                                       69****************87 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.8e-05     0.048      29      64 ..      31      65 ..      26      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.8e-05
                                      HHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG-CC CS
                     LexA_DNA_bind 29 reiaralglkSpsaveehLkaLerKGyierdpgkpR 64
                                       e+a++l +  p+av  hL+ Ler G++e  +++ R
  gi|330508644|ref|YP_004385072.1| 31 NEMAKRLDVG-PKAVIDHLEMLERAGLVECYQEQGR 65
                                      599*****99.******************9887766 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00023      0.23      36      67 ..      46      73 ..      19      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                      HHHHHHHHTTSEEEEEE-STSSS-EEEEEESH CS
                              PadR 36 paLkrLekeglveseweesgegpprkyYrlTd 67
                                      + L+ Le+ glve ++e+    ++rky+r+++
  gi|330508644|ref|YP_004385072.1| 46 DHLEMLERAGLVECYQEQ----GRRKYFRIAR 73
                                      67999**********987....7******986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0016       1.6      17      51 ..      27      61 ..      13      67 .. 0.86
   2 ?    1.8   0.0      0.24   2.4e+02      16      42 ..     170     196 ..     169     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 17 plsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      p +  e+ak+l v + +v   l  Le++Gl+e ++
  gi|330508644|ref|YP_004385072.1| 27 PFYFNEMAKRLDVGPKAVIDHLEMLERAGLVECYQ 61
                                      566779*************************9766 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.24
                                       TTEEHHHHHHHHTS-HHHHHHHHHHHH CS
                              MarR  16 gplsvseLakklgvskstvtrvldrLe 42 
                                       g+++ seLa +l+v  + v   l +L 
  gi|330508644|ref|YP_004385072.1| 170 GGANSSELATRLEVPEAVVLDSLNKLK 196
                                       678999******998887777777665 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00038      0.38      21      57 ..      26      62 ..      10      78 .. 0.84
   2 ?   -1.1   0.0       2.1   2.1e+03      27      48 ..     176     197 ..     156     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                           DUF2250 21 nvdYaksiakeleipleevrellkkLeelGLlerveg 57
                                       + Y   +ak+l++  + v + l+ Le++GL+e +++
  gi|330508644|ref|YP_004385072.1| 26 RPFYFNEMAKRLDVGPKAVIDHLEMLERAGLVECYQE 62
                                      5668889**************************9875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.1
                           DUF2250  27 siakeleipleevrellkkLee 48 
                                        +a +le+p   v + l+kL+e
  gi|330508644|ref|YP_004385072.1| 176 ELATRLEVPEAVVLDSLNKLKE 197
                                       5678888999999999999886 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0011       1.1      40      66 ..      42      68 ..      17      80 .. 0.84
   2 ?    0.6   0.1      0.68   6.7e+02       8      23 ..     130     145 ..     110     167 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                           DUF2513 40 eeiiyhlkllaeagLieaekkkakssi 66
                                      + +i hl++l+ agL+e+++++ + ++
  gi|330508644|ref|YP_004385072.1| 42 KAVIDHLEMLERAGLVECYQEQGRRKY 68
                                      46899***************9988873 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.68
                           DUF2513   8 RdiLltleeletkees 23 
                                       R++L ++e+ e + ++
  gi|330508644|ref|YP_004385072.1| 130 RELLAQIESREMEIKQ 145
                                       5555555554444333 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0043       4.3      25      63 ..      34      70 ..      31      72 .. 0.79
   2 ?    2.5   0.0      0.21     2e+02      18      45 ..     171     198 ..     157     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0043
                            HTH_27 25 cgrlnvedshisyslkkLtekGLvertgdeadrrekrvr 63
                                      ++rl+v+  +++  l+ L+++GLve  +  + +r+k +r
  gi|330508644|ref|YP_004385072.1| 34 AKRLDVGPKAVIDHLEMLERAGLVECYQ--EQGRRKYFR 70
                                      689999999***************4443..346767776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.21
                            HTH_27  18 rkkladlcgrlnvedshisyslkkLtek 45 
                                       ++  ++l+ rl v  + +  sl+kL e+
  gi|330508644|ref|YP_004385072.1| 171 GANSSELATRLEVPEAVVLDSLNKLKER 198
                                       6678999******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1573.30
//
Query:       gi|330508645|ref|YP_004385073.1|  [L=725]
Description: AAA family ATPase [Methanosaeta concilii GP6]
Scores for complete 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-94  312.3   0.0    1.8e-47  161.1   0.0    2.3  2  AAA              ATPase family associated with various cellul
    2.3e-26   91.3   0.3    3.2e-12   46.1   0.0    2.8  2  AAA_lid_3        AAA+ lid domain
    8.8e-25   86.7   0.0    7.4e-24   83.7   0.1    2.5  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    2.8e-15   57.1   0.2    3.6e-07   30.7   0.0    3.0  2  AAA_16           AAA ATPase domain
    3.7e-13   49.5   0.1      4e-07   29.9   0.0    3.1  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.4e-11   42.8   0.5    1.6e-10   40.6   0.1    2.3  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.4e-10   41.6   0.0    0.00034   20.8   0.0    3.0  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.2e-09   37.8   0.2     0.0017   17.6   0.0    3.7  4  TIP49            TIP49 P-loop domain
    1.3e-09   38.4   0.0    0.00034   20.8   0.0    2.6  2  AAA_33           AAA domain
      5e-09   36.5   4.0      0.041   14.2   0.1    4.4  3  AAA_22           AAA domain
    6.8e-09   35.8   1.0     0.0036   17.3   0.1    3.8  2  AAA_5            AAA domain (dynein-related subfamily)
    2.6e-08   33.9   0.0     0.0073   16.3   0.0    2.4  2  AAA_14           AAA domain
    1.2e-06   28.4   0.0      0.016   15.0   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    1.6e-06   28.7   0.0      0.065   13.8   0.0    2.7  2  AAA_18           AAA domain
    1.1e-05   25.7   0.0       0.22   11.7   0.0    2.6  2  AAA_28           AAA domain
    2.8e-05   23.8   3.7        5.1    6.6   0.1    4.4  4  AAA_25           AAA domain
    4.8e-05   22.8   1.1       0.13   11.7   0.1    2.9  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    4.9e-05   23.3   0.0       0.28   11.2   0.0    2.8  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    5.2e-05   23.0   1.0       0.19   11.4   0.0    4.2  4  Sigma54_activat  Sigma-54 interaction domain
    6.5e-05   22.7   0.0       0.18   11.5   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    0.00014   22.4   0.0       0.45   11.0   0.0    2.6  2  ABC_tran         ABC transporter
    0.00016   21.3   0.0       0.24   10.9   0.0    2.9  2  AAA_7            P-loop containing dynein motor region
    0.00016   21.1   0.2        1.1    8.6   0.0    3.1  3  ATPase           KaiC
    0.00025   20.3   0.0      0.052   12.7   0.0    2.6  2  DUF815           Protein of unknown function (DUF815)
    0.00051   20.0   0.2        2.8    7.8   0.0    3.7  4  NACHT            NACHT domain
    0.00058   20.2   0.0        1.7    9.0   0.0    2.5  2  RNA_helicase     RNA helicase
    0.00063   19.1   0.0       0.46    9.7   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0009   19.0   0.0        1.9    8.2   0.0    2.5  2  AAA_24           AAA domain
    0.00094   18.5   0.0        0.6    9.4   0.0    2.4  2  Zeta_toxin       Zeta toxin
     0.0012   18.6   0.0       0.12   12.0   0.0    2.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0013   18.5   0.0          1    9.1   0.0    2.6  2  AAA_30           AAA domain
     0.0024   17.7   0.0       0.48   10.2   0.0    2.2  2  AAA_11           AAA domain
     0.0055   17.1   0.0        3.2    8.2   0.0    3.0  2  AAA_17           AAA domain
  ------ inclusion threshold ------
      0.018   14.9   0.0        3.3    7.5   0.0    2.9  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.023   15.0   2.9          5    7.4   0.3    3.3  2  AAA_19           AAA domain
      0.027   13.9   0.1        1.4    8.3   0.0    2.4  2  PhoH             PhoH-like protein
      0.031   13.7   0.0        3.8    6.9   0.0    2.4  2  SRPRB            Signal recognition particle receptor beta su
      0.035   13.2   0.3        3.8    6.5   0.0    2.5  3  Parvo_NS1        Parvovirus non-structural protein NS1
      0.057   13.2   0.0       0.12   12.2   0.0    1.5  1  Ribosomal_L7Ae   Ribosomal protein L7Ae/L30e/S12e/Gadd45 fami
      0.086   12.0   0.0        4.2    6.5   0.0    2.4  2  NB-ARC           NB-ARC domain
      0.089   12.7   0.6         19    5.1   0.0    3.9  4  NTPase_1         NTPase
      0.097   12.5   0.0         22    4.8   0.0    2.9  2  Bac_DnaA         Bacterial dnaA  protein
        0.1   12.2   0.0        2.5    7.7   0.0    2.6  2  Zot              Zonular occludens toxin (Zot)
       0.11   12.5   0.3       0.79    9.8   0.1    2.4  2  Vps4_C           Vps4 C terminal oligomerisation domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.1   0.0   4.4e-50   1.8e-47       1     131 [.     218     347 ..     218     348 .. 0.98
   2 !  149.1   0.0   2.2e-46   8.8e-44       1     131 [.     490     620 ..     490     621 .. 0.97

  Alignments for each domain:
  == domain 1  score: 161.1 bits;  conditional E-value: 4.4e-50
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+GppGtGKTl+a+ava e++++f++isg+e++sk+ gese+++r++f+ea++ a psi+fiDEid++a++r++ 
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAGETDANFISISGPEIVSKFYGESEQRLRQIFDEASKAA-PSIIFIDEIDSIAPKREEV 293
                                       79****************************************************999.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + + e+rvv+q+l+ +dg++++ ++vivi+atnrp+ ldpa++r gRfdr+iei+
  gi|330508645|ref|YP_004385073.1| 294 SGDLERRVVAQILSLMDGLSSR-GEVIVIAATNRPNALDPAIRRgGRFDREIEIG 347
                                       *********************7.66***************************986 PP

  == domain 2  score: 149.1 bits;  conditional E-value: 2.2e-46
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       +llyG pGtGKTll++a+a+e++v+f++++g+ellsk+vgese+ +re+f++a++ a p  +f+DEid+++++r sg
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATESNVNFISVKGPELLSKWVGESERAVREIFRKARQAA-PALVFFDEIDSIVPARgSG 565
                                       69******************************************************9.****************999 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       s+s ++ervv+q+lte+dg+ + + +v++++atnrpd ld+ llr gRfdr ++i+
  gi|330508645|ref|YP_004385073.1| 566 SDSHVTERVVSQFLTEMDGLMELK-DVVIVAATNRPDLLDSSLLRpGRFDRLVYIP 620
                                       **********************75.5**************************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 !   42.7   0.1   8.9e-14   3.6e-11       2      36 ..     371     405 ..     370     430 .. 0.78
   2 !   46.1   0.0   7.8e-15   3.2e-12       2      36 ..     643     677 ..     642     699 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 8.9e-14
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgik 36 
                                       +dl e+A  T+G++GADl alc+eAa+++l+r ++
  gi|330508645|ref|YP_004385073.1| 371 LDLMEIADSTHGFVGADLYALCKEAAMRTLERALP 405
                                       799****************************9554 PP

  == domain 2  score: 46.1 bits;  conditional E-value: 7.8e-15
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgik 36 
                                       v+ ++LA  Te++SGADl+ lcreA++lAlr+ i 
  gi|330508645|ref|YP_004385073.1| 643 VSAQWLADITENFSGADLEMLCREAGMLALREHIR 677
                                       77889***************************654 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 !   83.7   0.1   1.8e-26   7.4e-24       2      84 ..      11      92 ..      10      93 .. 0.98
   2 ?   -1.3   0.0       6.3   2.6e+03      20      63 ..     203     247 ..     203     249 .. 0.61

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 1.8e-26
                                      EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEE CS
                           CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtV 80
                                      LrVaea+++d+g+g++ri+p  +++lg+e+g vvei  + k +ai+wp+ ped+ ++iIr+dg+tR+n+g +i+ +V V
  gi|330508645|ref|YP_004385073.1| 11 LRVAEAYHKDAGKGVARINPIILAQLGVENGGVVEINARDKVYAIAWPGTPEDP-QDIIRIDGNTRSNLGTGIDNRVNV 88
                                      8***************************************************99.************************ PP

                                      EEE- CS
                           CDC48_N 81 rkae 84
                                      r+a+
  gi|330508645|ref|YP_004385073.1| 89 RRAT 92
                                      *986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.3
                                       -HHHHHHHTS-TTSEEEEEC.CCCEEEEEEEBSTTSTTTTEEEE- CS
                           CDC48_N  20 dpedmeelglepgdvveieg.krkTvaivwpaepedegkgiIrmd 63 
                                       +pe +++lg++p   v ++g   +   ++ +a   +++ + I ++
  gi|330508645|ref|YP_004385073.1| 203 HPELFSRLGINPPRGVLLHGpPGTGKTLIARAVAGETDANFISIS 247
                                       589999*****9999999985443223333333333346666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   8.8e-10   3.6e-07      16     139 ..     207     320 ..     185     322 .. 0.71
   2 !   22.9   0.1   2.2e-07   8.9e-05      24     126 ..     487     581 ..     477     595 .. 0.59

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 8.8e-10
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.aes 91 
                                       ++r+  + p+ vll+G++G+GK+ ++r+++ +  ++   f++    +       s +      e+ lrq+ de +++
  gi|330508645|ref|YP_004385073.1| 207 FSRLGINPPRGVLLHGPPGTGKTLIARAVAGETDAN---FISISGPEI-----VSKFYGE--SEQRLRQIFDEaSKA 273
                                       445555556*********************755555...766666666.....2233333..458888888883444 PP

                            AAA_16  92 aeleawrekleealaavpelagaeasrllellkrllallsrderplvl 139
                                       a    + +++++ +    e++g++++r+ +++ +l++ ls++++ +++
  gi|330508645|ref|YP_004385073.1| 274 APSIIFIDEIDSIAPKREEVSGDLERRVVAQILSLMDGLSSRGE-VIV 320
                                       5555566666666669999*****************77777666.333 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 2.2e-07
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.aesaeleawre 99 
                                       p+ +ll+G +G+GK+ lvr+l+++ +   + f++ k  +l     +s ++    + + +r++ ++  ++a +  + +
  gi|330508645|ref|YP_004385073.1| 487 PRGILLYGLPGTGKTLLVRALATESN---VNFISVKGPEL-----LSKWVGES-E-RAVREIFRKaRQAAPALVFFD 553
                                       499*******************8444...66999999999.....44466666.3.444555444134444444555 PP

                            AAA_16 100 kleealaavpelagaea.....srllellkrl 126
                                       ++++ + a ++     +     +r+  ++   
  gi|330508645|ref|YP_004385073.1| 554 EIDSIVPARGSG----SdshvtERVVSQFLTE 581
                                       555544433333....2223365555444444 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 !   29.9   0.0   9.9e-10     4e-07      35     103 ..     217     293 ..     208     337 .. 0.85
   2 !   15.8   0.0   2.1e-05    0.0087      36      95 ..     490     557 ..     484     616 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 9.9e-10
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveev 103
                                        vll+GpPG Gkt +a+ +a e ++++ + sgP +      e ++ l  ++ + ++    ++fidei  ++++ eev
  gi|330508645|ref|YP_004385073.1| 217 GVLLHGPPGTGKTLIARAVAGETDANFISISGPEIvskfygESEQRLRQIFDEASKAapSIIFIDEIDSIAPKREEV 293
                                       59*******************************984444444467788888877654338************99997 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.1e-05
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihr 95 
                                       +llyG PG Gkt l + +a+e +v++ +  gP l      e ++ +  ++ + ++    ++f dei  
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATESNVNFISVKGPELlskwvgESERAVREIFRKARQAapALVFFDEIDS 557
                                       8*******************************873222223334444555444433114566666655 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.6   2.3e+03      42      59 ..      63      80 ..      63      82 .. 0.87
   2 !   40.6   0.1   3.9e-13   1.6e-10       8      58 ..     114     164 ..      94     167 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.6
                                      CCCCSCEEECTSCCEEES CS
                           CDC48_2 42 ePkgpvgitetTeielgt 59
                                      +P ++ +i+ +T ++lgt
  gi|330508645|ref|YP_004385073.1| 63 DPQDIIRIDGNTRSNLGT 80
                                      689999******999987 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 3.9e-13
                                       HHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEE CS
                           CDC48_2   8 aylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielg 58 
                                       +yl r ++gr+v+kG+ +++e  +  + l+Vvst P+gpv +t +T+i + 
  gi|330508645|ref|YP_004385073.1| 114 QYLLRMLQGRAVVKGEMLRVEMINSSLNLAVVSTVPNGPVLVTQETIISIT 164
                                       49**********************************************885 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   8.3e-07   0.00034       6     105 ..     218     311 ..     214     314 .. 0.76
   2 !   17.1   0.0   1.1e-05    0.0044       6     100 ..     490     579 ..     485     586 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.3e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++a+a+a   ++    ++i +   e+      + + ++++  ++   +a +    i+++DEid i
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAGETDA----NFISISGPEIVS----KFYGESEQRLRQIFDEASKAApsIIFIDEIDSI 286
                                       57899**************99995....999999999888....55555555555555555555577********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk e+ + d  r  V + +L +++g
  gi|330508645|ref|YP_004385073.1| 287 APKrEEVSGDLERRVVAQ-ILSLMDG 311
                                       **8777777777765555.5666665 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.1e-05
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ill g  g+Gkt+l +ala   +v    ++i +   ell     + + +++   ++   +a +     v++DEid i
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATESNV----NFISVKGPELLS----KWVGESERAVREIFRKARQAApaLVFFDEIDSI 558
                                       7899999****************8....************....55555555566666666666699********** PP

                                       ---.---------HHHHHHHH CS
                             AAA_2  81 hpk.essgadvSregVqrdLL 100
                                        p  +s +     e V+  +L
  gi|330508645|ref|YP_004385073.1| 559 VPArGSGSDSHVTERVVSQFL 579
                                       **9533333334455555555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.3   1.3e+03     207     240 ..     146     179 ..     128     198 .. 0.77
   2 !   17.6   0.0   4.1e-06    0.0017      51      97 ..     216     260 ..     211     283 .. 0.87
   3 ?   -0.1   0.0         1   4.1e+02     221     258 ..     410     447 ..     406     466 .. 0.85
   4 !   14.6   0.0   3.4e-05     0.014      51     106 ..     488     542 ..     484     545 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.3
                                       ----S---S----XXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 207 velPkGevekkkevvqevtLhdlDvanarpqdll 240
                                         +P+G v   +e++ ++t   lD  + + +d+ 
  gi|330508645|ref|YP_004385073.1| 146 STVPNGPVLVTQETIISITRETLDELALHVRDIS 179
                                       4689**************9999998887776664 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 4.1e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       r+vLl Gp+gtGkt +a a++ e   d  f+++sg e+ s     +e
  gi|330508645|ref|YP_004385073.1| 216 RGVLLHGPPGTGKTLIARAVAGET--DANFISISGPEIVSKFYGESE 260
                                       89*******************985..689*********997665555 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1
                                       XXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXX CS
                             TIP49 221 vqevtLhdlDvanarpqdllslllqllkskkteitekl 258
                                        +++ L  lD  n+ ++d+ls l+++  s ++e+  ++
  gi|330508645|ref|YP_004385073.1| 410 KEDIPLDVLDNLNVTREDFLSALKKIEPSAMREVFVEV 447
                                       56889999***************999988888886655 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 3.4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                       r++Ll G +gtGkt l  a++ e   +v f++++g e+ s  v  +e ++ + +rk+
  gi|330508645|ref|YP_004385073.1| 488 RGILLYGLPGTGKTLLVRALATES--NVNFISVKGPELLSKWVGESErAVREIFRKA 542
                                       89*******************985..5****************99985678889997 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   8.3e-07   0.00034       2      47 ..     218     289 ..     218     348 .. 0.70
   2 !   15.0   0.0   5.2e-05     0.021       2      42 ..     490     532 ..     490     630 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.3e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt........................d 47 
                                       vll+G+pG+GK+  a+ ++ +++  ++ +s +++ ++ +g+ +q+++                        +
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAGETDanFISISGPEIVSKFYGESEQRLRqifdeaskaapsiifideidsiapK 289
                                       799******************9999999***********998888886666666666666666666666652 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.2e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdq 42 
                                       +ll GlpG+GK+ l++ l+ +    ++ +  ++l+++ +g+ +
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATESNvnFISVKGPELLSKWVGESE 532
                                       6789***************999988888888887777766433 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00019     0.079       8      29 ..     218     239 ..     214     250 .. 0.84
   2 ?    6.6   0.0     0.022       8.8      72     112 ..     257     305 ..     245     326 .. 0.67
   3 !   14.2   0.1    0.0001     0.041       8      48 ..     490     521 ..     485     592 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00019
                            AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                       ++++G++GtGKT+ +r ++ + 
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAGET 239
                                       689*************998776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.022
                            AAA_22  72 rlsseellealeqalraravielliiDEaqhlr..s........eealeeL 112
                                       + s+++l++ + +a++a+    ++ iDE++ +   +         +++ ++
  gi|330508645|ref|YP_004385073.1| 257 GESEQRLRQIFDEASKAAPS--IIFIDEIDSIApkReevsgdleRRVVAQI 305
                                       46777777777777777777..*********98752233334444444444 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 0.0001
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlp 48 
                                       ++++G +GtGKT+l+r l+ +          ++ +++v+ p
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATES---------NVNFISVKGP 521
                                       89****************9997.........5555555444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   8.7e-06    0.0036       1     133 [.     217     333 ..     217     337 .. 0.63
   2 !   13.9   0.1    0.0001     0.041       2      80 ..     490     561 ..     489     611 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.7e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEver 76 
                                       +vlL GppGtgK+ +a+ +a  + +++  + +++    +++ g+ e      ++  +++ +a +  ++i+++DE++ 
  gi|330508645|ref|YP_004385073.1| 217 GVLLHGPPGTGKTLIARAVAGETDANFISISGPEIV--SKFYGESE------QRLRQIFDEASKaAPSIIFIDEIDS 285
                                       59*********************9999999988844..34444444......2333444444445678888888888 PP

                                       --...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHH CS
                             AAA_5  77 ae...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspa 133
                                       +     ev + L +    + l+l++g    ++        + via++n+++     l+pa
  gi|330508645|ref|YP_004385073.1| 286 IApkrEEVSGDLERRVVAQILSLMDGLSSRGE--------VIVIAATNRPN----ALDPA 333
                                       76222345555555555555555544444433........66666666666....55555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.0001
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       +lL G pGtgK+ l++ la   n ++  v +++      l+ ++    g+ ++   ++ r+ar   ++++++DE++ 
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATESNVNFISVKGPE------LLSKWV---GESERAVREIFRKARqaAPALVFFDEIDS 557
                                       89*****************99999988888876......666666...45555556666666657777888888887 PP

                                       --HH CS
                             AAA_5  77 aese 80 
                                       + ++
  gi|330508645|ref|YP_004385073.1| 558 IVPA 561
                                       6655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.3e-05     0.017       5      77 ..     218     287 ..     215     325 .. 0.74
   2 !   16.3   0.0   1.8e-05    0.0073       5      77 ..     490     576 ..     487     625 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.3e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqevp 77 
                                       +++ G+  +GKT +++ ++ e      +++ i+  +   k + ++e +l +++ e  ++   +++f+DEi  + 
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAGETD---ANFISISGPEIVSKFYGESEqRLRQIFDEA-SKAAPSIIFIDEIDSIA 287
                                       7899***************9988...999999998877766665552455555554.455899*******9883 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.8e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd..kkladpekllelileklkeekktylflDEiqev... 76 
                                       +++ G+  +GKT l++ l+ e+      + +i+++ +++  k   ++e+  ++i++k+++    ++f+DEi  +   
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATESN-----VNFISVKGPELlsKWVGESERAVREIFRKARQAAPALVFFDEIDSIvpa 561
                                       6789999***********97766.....677777776662244445555555555554556899*******998666 PP

                            AAA_14  77 ..............p 77 
                                                     +
  gi|330508645|ref|YP_004385073.1| 562 rgsgsdshvtervvS 576
                                       666655555544444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00081      0.33       2      30 ..     218     246 ..     217     327 .. 0.81
   2 !   15.0   0.0     4e-05     0.016       2     112 ..     490     600 ..     489     616 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00081
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll+g PG++ktl+++a+a   d++f  i
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAGETDANFISI 246
                                       89********************9999766 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4e-05
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk. 77 
                                       +ll g+PG++ktllv+ala+  +++f  ++  p+ll    +G +   ++ +e+  k+      l++ dei+   p  
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATESNVNFISVK-GPELLSK-WVGESE--RAVREIFRKARQAAPALVFFDEIDSIVPAr 562
                                       799*********************999887.6788755.445542..223333333334445677778887766551 PP

                             AAA_3  78 ...tqsalleameerqvtvegethklpepflvlatqnP 112
                                          ++s + e +  + +t  +  ++l++  +v at+ P
  gi|330508645|ref|YP_004385073.1| 563 gsgSDSHVTERVVSQFLTEMDGLMELKDVVIVAATNRP 600
                                       11134445555555555666667777777777777766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00049       0.2       1      40 [.     218     278 ..     218     336 .. 0.61
   2 !   13.8   0.0   0.00016     0.065       1      30 [.     490     517 ..     490     594 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00049
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakengllle 40 
                                       +ll G+pG+GKt +a++++ ++ ++                     +++ d a++  +++ 
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAGETdANfisisgpeivskfygeseqrLRQIFDEASKAAPSII 278
                                       7899**************8887544577777766666666665554444444444444444 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00016
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrd 30 
                                       Ill G pG+GKt l ++L+ +    vn ++
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATES--NVNFIS 517
                                       99****************8875..222222 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00076      0.31       2      47 ..     218     268 ..     217     289 .. 0.73
   2 !   11.7   0.0   0.00055      0.22       2      31 ..     490     524 ..     489     554 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00076
                            AAA_28   2 ivitGgestGKTtlleaLa.ar...gypvv.pEaareileeklakgedalp 47 
                                       + + G+++tGKT +++a a ++    +++  pE++ +++ e  ++ +++ +
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAgETdanFISISgPEIVSKFYGESEQRLRQIFD 268
                                       6799***************73334245555777777777666666555544 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00055
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvv....pEaa 31 
                                       i + G ++tGKT l++aLa + +++ +    pE  
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATEsNVNFIsvkgPELL 524
                                       7899***************6653333311244443 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.019       7.6      36      53 ..     218     235 ..     210     239 .. 0.87
   2 ?    2.8   0.0      0.18        74     130     176 ..     263     309 ..     250     324 .. 0.80
   3 ?    6.6   0.1     0.012       5.1      36      54 ..     490     508 ..     482     511 .. 0.88
   4 ?    5.6   0.0     0.025        10     127     172 ..     532     578 ..     512     596 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll G+pgtGKt +a  +
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAV 235
                                       689*********998665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.18
                            AAA_25 130 vdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                       ++++ +++ + + +  + iD ++++ +  e+ + d  +++v+++ ++ 
  gi|330508645|ref|YP_004385073.1| 263 LRQIFDEASK-AAPSIIFIDEIDSIAPKREEVSGDLeRRVVAQILSLM 309
                                       5566666666.459**************88888886699999987765 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G pgtGKt l+  la
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALA 508
                                       69************98887 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.025
                            AAA_25 127 tadvdaleaaieevegvrlvviDplsralgg.densnsdv.galveal 172
                                       +++v+++ +++++ + ++lv +D +++++++ ++ s+s v +++v+++
  gi|330508645|ref|YP_004385073.1| 532 ERAVREIFRKARQ-AAPALVFFDEIDSIVPArGSGSDSHVtERVVSQF 578
                                       578999*******.66*************9997777777667777665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00031      0.13      25      43 ..     218     236 ..     214     239 .. 0.90
   2 ?   -1.6   0.0       3.6   1.5e+03     101     123 ..     269     291 ..     265     327 .. 0.72
   3 !    8.4   0.0    0.0031       1.3      25      43 ..     490     508 ..     480     512 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00031
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll GppG+GKt++a++++
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVA 236
                                       79*************9875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.6
                      Mg_chelatase 101 eislahnGvLfLDElpefkrkvl 123
                                       e s+a   ++f+DE+  +  k  
  gi|330508645|ref|YP_004385073.1| 269 EASKAAPSIIFIDEIDSIAPKRE 291
                                       67899999******998877654 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0031
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+G pG+GKt+l ++l+
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALA 508
                                       89*************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 !    8.7   0.0    0.0039       1.6      20      49 ..     216     247 ..     188     263 .. 0.78
   2 !   11.2   0.0    0.0007      0.28      21      51 ..     489     521 ..     473     524 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0039
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..--- CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evk 49 
                                       + +lL+G+ G+GKT ++r++a + + +  +++
  gi|330508645|ref|YP_004385073.1| 216 RGVLLHGPPGTGKTLIARAVAGETDANfiSIS 247
                                       349*****************988877655555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0007
                                       EEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        ilL+G  G+GKT lvr+la + +v+  +vk P
  gi|330508645|ref|YP_004385073.1| 489 GILLYGLPGTGKTLLVRALATESNVNfiSVKGP 521
                                       499*******************99987778776 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       8.4   3.4e+03     109     123 ..     112     126 ..     109     133 .. 0.85
   2 !   11.4   0.0   0.00048      0.19      24      58 ..     217     248 ..     208     337 .. 0.68
   3 ?    5.5   0.0      0.03        12      24      47 ..     489     512 ..     478     532 .. 0.84
   4 ?   -1.7   0.0       4.9     2e+03      92     108 ..     545     561 ..     534     619 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.4
                                       HHHHHHHHHHHSEEE CS
                   Sigma54_activat 109 lQekLlrvlqegeve 123
                                       +Q+ Llr+lq + v 
  gi|330508645|ref|YP_004385073.1| 112 GQQYLLRMLQGRAVV 126
                                       79********98875 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00048
                                       -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEET CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavnc 58 
                                        vl++G  GtGK+l+ara+  ++   +++f+++  
  gi|330508645|ref|YP_004385073.1| 217 GVLLHGPPGTGKTLIARAVAGET---DANFISISG 248
                                       69***************997544...466776654 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.03
                                       -EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheask 47 
                                        +l+ G  GtGK+ll ra+ ++s+
  gi|330508645|ref|YP_004385073.1| 489 GILLYGLPGTGKTLLVRALATESN 512
                                       69****************988776 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.9
                                       TTTSEEEEETGGGS-HH CS
                   Sigma54_activat  92 adgGtlfLDeigelple 108
                                       a    +f+Dei ++ ++
  gi|330508645|ref|YP_004385073.1| 545 AAPALVFFDEIDSIVPA 561
                                       55566666666665443 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00044      0.18      48      71 ..     216     239 ..     203     292 .. 0.82
   2 !    8.7   0.0    0.0033       1.4      49      71 ..     489     511 ..     482     555 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00044
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                        +++l Gp+G+GK+ +a a++ e+
  gi|330508645|ref|YP_004385073.1| 216 RGVLLHGPPGTGKTLIARAVAGET 239
                                       5799***************98764 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0033
                         IstB_IS21  49 nivllGpsGvGKshlaialgvea 71 
                                       +i+l G +G+GK+ l  al++e 
  gi|330508645|ref|YP_004385073.1| 489 GILLYGLPGTGKTLLVRALATES 511
                                       799****************9876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0    0.0011      0.45       6      60 ..     210     262 ..     208     315 .. 0.76
   2 !    8.7   0.0    0.0056       2.3       6      65 ..     482     539 ..     480     659 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0011
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrke 60 
                                       l +++ + v + G+ G+GK+ +++++ag+++     i + g ++ ++   +++++
  gi|330508645|ref|YP_004385073.1| 210 LGINPPRGVLLHGPPGTGKTLIARAVAGETDA--NFISISGPEIVSKFYGESEQR 262
                                       5677778899*******************974..555556666655444444444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0056
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlp 65 
                                       + +++ + + + G  G+GK+ L+++la +++     i ++g +l ++   ++++ ++ ++
  gi|330508645|ref|YP_004385073.1| 482 VGVRPPRGILLYGLPGTGKTLLVRALATESNV--NFISVKGPELLSKWVGESERAVREIF 539
                                       566677778999***************99874..55555666666655555555554444 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 !   10.9   0.0   0.00059      0.24      33      63 ..     215     244 ..     204     289 .. 0.85
   2 !    6.9   0.0    0.0098         4      34      58 ..     488     512 ..     474     519 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00059
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldkekyl 63 
                                        + vll Gp GtGKt+i++ +  + d  +++
  gi|330508645|ref|YP_004385073.1| 215 PRGVLLHGPPGTGKTLIARAVAGETD-ANFI 244
                                       5789**************99988888.4444 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0098
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                       + +ll+G  GtGKt++++ l ++ +
  gi|330508645|ref|YP_004385073.1| 488 RGILLYGLPGTGKTLLVRALATESN 512
                                       679**************99876655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0027       1.1      15      37 ..     211     233 ..     203     250 .. 0.86
   2 ?   -0.3   0.0       1.4   5.6e+02     117     153 ..     272     311 ..     244     324 .. 0.66
   3 !    8.1   0.0    0.0036       1.5      15      42 ..     483     510 ..     455     522 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0027
                            ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                       Gi   r vl+ G pGtGKt++a 
  gi|330508645|ref|YP_004385073.1| 211 GINPPRGVLLHGPPGTGKTLIAR 233
                                       7888899*************986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                            ATPase 117 eikakrvviDsitgl...ayeekeavaReilrqlvrvlkk 153
                                       +   + + iD i+++    +e + ++ R+ + q+++ + +
  gi|330508645|ref|YP_004385073.1| 272 KAAPSIIFIDEIDSIapkREEVSGDLERRVVAQILSLMDG 311
                                       3334667777777773214444555678888888887765 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0036
                            ATPase  15 GipegrvvlitGepGtGKtifalqFlik 42 
                                       G+   r +l++G pGtGKt+++   + +
  gi|330508645|ref|YP_004385073.1| 483 GVRPPRGILLYGLPGTGKTLLVRALATE 510
                                       66667889************98766555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0      0.03        12      52      83 ..     214     245 ..     162     328 .. 0.80
   2 !   12.7   0.0   0.00013     0.052      21      79 ..     446     513 ..     430     544 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.03
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLr 83 
                                       p + vLL G  GtGK  + +a+  e+ ++ + 
  gi|330508645|ref|YP_004385073.1| 214 PPRGVLLHGPPGTGKTLIARAVAGETDANFIS 245
                                       55679*****************9998877654 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00013
                            DUF815  21 evdevklddLvgidkqkealvente.......qfle..glpannvLLwGarGtGKSslvkallneyae 79 
                                       ev +v++d++ g+d+ k++lve +e       +f++   +p + +LL+G  GtGK  lv+al +e + 
  gi|330508645|ref|YP_004385073.1| 446 EVAQVHWDEVGGLDEAKRSLVEAVEwplmypeAFASvgVRPPRGILLYGLPGTGKTLLVRALATESNV 513
                                       56788889999999999999888753332222454421467899******************988664 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.013       5.1       3      21 ..     218     236 ..     216     242 .. 0.87
   2 ?   -1.9   0.0       6.6   2.7e+03      70     127 ..     264     323 ..     250     345 .. 0.61
   3 !    7.8   0.0    0.0068       2.8       3      23 ..     490     510 ..     488     514 .. 0.89
   4 ?   -0.2   0.0       2.1   8.4e+02      57     102 ..     523     568 ..     520     626 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.013
                                       EEEEC-TTTCHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqkla 21 
                                       v+l+G++G GKT  ++ +a
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVA 236
                                       89************99887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.6
                                       -CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEEEE CS
                             NACHT  70 sevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasllltv 127
                                       ++++ +  + + ++ + +D +D ++ + ++   + +++v   + +l+ + + ++  +++++
  gi|330508645|ref|YP_004385073.1| 264 RQIFDEASKAAPSIIF-IDEIDSIAPKREEvsgDLERRVVAQILSLMDGLSSRGEVIVIAA 323
                                       5545554455555544.68888888877778775555555566677777555555444433 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0068
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++l G +G GKT L++ la++
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATE 510
                                       7999**************986 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.1
                                       HHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.... CS
                             NACHT  57 llfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq.kek 102
                                       ll +   e++++v+e +   ++++  +L  +D +D +v   g  ++ 
  gi|330508645|ref|YP_004385073.1| 523 LLSKWVGESERAVRE-IFRKARQAAPALVFFDEIDSIVPARGSgSDS 568
                                       556666677777888.444567888899999***9999887775333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0052       2.1       1      22 [.     218     239 ..     218     287 .. 0.81
   2 !    9.0   0.0    0.0042       1.7       1      23 [.     490     512 ..     490     583 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0052
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakal 22 
                                       ++l+Gp+g+GK+++a+ +a + 
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAGET 239
                                       689************9976555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0042
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                       i+lyG +g+GK++l++ La++  
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATESN 512
                                       689**************998765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0011      0.46       4      35 ..     218     242 ..     215     294 .. 0.72
   2 !    7.3   0.0    0.0058       2.3       4      25 ..     490     511 ..     487     544 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertav 35 
                                       vl +G +GtGKt+++ +++ e         a+
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAGET-------DAN 242
                                       6889***********9999987.......333 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0058
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       +l  G +GtGKt++  +l++e 
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATES 511
                                       6789***********9999987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0047       1.9       5      26 ..     218     241 ..     215     296 .. 0.59
   2 !    8.1   0.0    0.0048         2       5      28 ..     490     515 ..     487     525 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0047
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkp 26 
                                       +l+ Gp+g+GKT +a+    + ++
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVagETDA 241
                                       799**********99988443333 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0048
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplf 28 
                                       il+yG +g+GKT l++ l  + ++ f
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALatESNVNF 515
                                       89************999866555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0015       0.6      16      51 ..     215     248 ..     209     264 .. 0.90
   2 ?    6.5   0.0     0.011       4.6      16      50 ..     487     519 ..     478     524 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       P  +ll G pG GK+ +a++++ e+  + n++ +++
  gi|330508645|ref|YP_004385073.1| 215 PRGVLLHGPPGTGKTLIARAVAGET--DANFISISG 248
                                       7779********************9..899998875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       P  ill G pG GK+ l ++l++e   + n++ ++
  gi|330508645|ref|YP_004385073.1| 487 PRGILLYGLPGTGKTLLVRALATES--NVNFISVK 519
                                       7889*******************98..88888776 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 ?    4.2   0.0     0.078        32       2      71 ..     219     283 ..     218     288 .. 0.75
   2 !   12.0   0.0   0.00031      0.12       3      71 ..     492     555 ..     490     558 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.078
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       + hG pG GK+ + r ++ +   ++ +++   e++++   +++++    +d++ +a+       i+++DE+
  gi|330508645|ref|YP_004385073.1| 219 LLHGPPGTGKTLIARAVAGETdANFISISG-PEIVSKFYGESEQRLRQIFDEASKAAP-----SIIFIDEI 283
                                       67**********999999998866666666.677777777777777777777777653.....48888886 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00031
                   Viral_helicase1   3 vhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                         G pG GK+ l+r l+ +s +++ +++   ell++++ ++++   + ++++ +a+       ++++DE+
  gi|330508645|ref|YP_004385073.1| 492 LYGLPGTGKTLLVRALATESnVNFISVKG-PELLSKWVGESERAVREIFRKARQAAP-----ALVFFDEI 555
                                       5699*************999988777777.9*******8888877777777777664.....47899986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0025         1      21      39 ..     218     236 ..     206     247 .. 0.85
   2 ?    6.6   0.0     0.014       5.6      22      39 ..     491     508 ..     477     517 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0025
                            AAA_30  21 avltGpAGtGKttalkalr 39 
                                       ++l+Gp+GtGKt + +a++
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVA 236
                                       689***********99986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.014
                            AAA_30  22 vltGpAGtGKttalkalr 39 
                                       +l G +GtGKt +++al+
  gi|330508645|ref|YP_004385073.1| 491 LLYGLPGTGKTLLVRALA 508
                                       788************996 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0012      0.48      20      37 ..     218     235 ..     202     272 .. 0.84
   2 ?    5.1   0.0     0.041        17      21      56 ..     491     522 ..     480     550 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                            AAA_11  20 tliqGPPGtgKTktivel 37 
                                       +l++GPPGtgKT    ++
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAV 235
                                       79**********665544 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.041
                            AAA_11  21 liqGPPGtgKTktivellsqllsrrkseeeksakpr 56 
                                       l+ G PGtgKT  + +l  + +     +    ++p+
  gi|330508645|ref|YP_004385073.1| 491 LLYGLPGTGKTLLVRALATESNV----NFISVKGPE 522
                                       78999**********99999842....223333333 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.047        19       2      26 ..     222     246 ..     221     285 .. 0.85
   2 !    8.2   0.0    0.0079       3.2       1      26 [.     493     518 ..     493     596 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.047
                                       E-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsa 26 
                                       G+PG GK+ +++ ++ + +  ++s 
  gi|330508645|ref|YP_004385073.1| 222 GPPGTGKTLIARAVAGETDANFISI 246
                                       9************999887777665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0079
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                       +G+PG GK+ +++ l+ + ++ ++s 
  gi|330508645|ref|YP_004385073.1| 493 YGLPGTGKTLLVRALATESNVNFISV 518
                                       7***************9999888875 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.008       3.3       4      33 ..     218     247 ..     216     324 .. 0.88
   2 ?    4.0   0.0       0.1        41       4      32 ..     490     518 ..     488     544 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.008
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                       +lL+G + +GK+ +ara+   +d+ ++ + 
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAGETDANFISIS 247
                                       89******************9999999876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.1
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhl 32 
                                       ilL G + +GK+ l+ral + ++  ++ +
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATESNVNFISV 518
                                       99****************99998888776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.3     0.012         5      12      30 ..     217     235 ..     212     274 .. 0.87
   2 ?    6.0   0.0     0.033        14      11      31 ..     488     508 ..     480     545 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.012
                            AAA_19  12 vllvtaGpGtGKTrvlkhi 30 
                                        +l+ ++pGtGKT + +++
  gi|330508645|ref|YP_004385073.1| 217 GVLLHGPPGTGKTLIARAV 235
                                       5899*********987765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.033
                            AAA_19  11 kvllvtaGpGtGKTrvlkhiv 31 
                                       + +l+ + pGtGKT ++++  
  gi|330508645|ref|YP_004385073.1| 488 RGILLYGLPGTGKTLLVRALA 508
                                       568999********9998765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0035       1.4      22      40 ..     218     236 ..     212     242 .. 0.87
   2 ?    2.9   0.0      0.15        63      24      42 ..     492     510 ..     488     517 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0035
                                       EEEE--TTSSTTHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavala 40 
                                       v   Gp GtGKt++a a+a
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVA 236
                                       5678***********9988 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.15
                                       EE--TTSSTTHHHHHHHHH CS
                              PhoH  24 aiGpaGtGKtylavalave 42 
                                         G  GtGKt+l  ala e
  gi|330508645|ref|YP_004385073.1| 492 LYGLPGTGKTLLVRALATE 510
                                       57889*******9999876 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 ?    4.2   0.0     0.063        26       5      49 ..     217     261 ..     214     280 .. 0.81
   2 ?    6.9   0.0    0.0092       3.8       5      29 ..     489     513 ..     486     534 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.063
                                       EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGT CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgs 49 
                                        vll G+  +GKT++  r   +++    +S+  ++++ k+ +e ++
  gi|330508645|ref|YP_004385073.1| 217 GVLLHGPPGTGKTLI-ARAVAGETDANFISIsGPEIVSKFYGESEQ 261
                                       599*********976.667788888999999888888888655554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0092
                                       EEEEE-STTSSHHHHHHHHHHSS-- CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvk 29 
                                        +ll Gl  +GKT+l   L t+s  
  gi|330508645|ref|YP_004385073.1| 489 GILLYGLPGTGKTLLVRALATESNV 513
                                       589****************999755 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       7.7   3.1e+03     178     217 ..     123     167 ..     121     179 .. 0.71
   2 ?    6.5   0.0    0.0094       3.8     117     135 ..     218     236 ..     211     241 .. 0.88
   3 ?    3.9   0.0     0.059        24     117     137 ..     490     510 ..     483     515 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.7
                         Parvo_NS1 178 kailggtavrvd.....qkekksveieqtpviitsnvditlvvsg 217
                                       +a+ +g+ +rv+      +    ++++  pv++t ++ i  +++ 
  gi|330508645|ref|YP_004385073.1| 123 RAVVKGEMLRVEminssLNLAVVSTVPNGPVLVTQETIISITRET 167
                                       788889999999655555555677888888999988888777765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0094
                         Parvo_NS1 117 vwfyGpantGktnlaeaIa 135
                                       v+++Gp+ tGkt +a+a a
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVA 236
                                       899*************987 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.059
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       +++yG + tGkt l +a+a+ 
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATE 510
                                       899***************975 PP

>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00029      0.12      47      84 ..     501     539 ..     496     550 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00029
                                       HHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSE.CSEEE CS
                    Ribosomal_L7Ae  47 kkllealckekevpyvkvkskkeLGelvgkkrp.vsala 84 
                                       + l+ al+ e +v++++vk+ + L ++vg++ + v  ++
  gi|330508645|ref|YP_004385073.1| 501 TLLVRALATESNVNFISVKGPELLSKWVGESERaVREIF 539
                                       45899*************************988444444 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.01       4.2      23      43 ..     218     238 ..     207     247 .. 0.86
   2 ?    2.6   0.0      0.15        63      23      43 ..     490     510 ..     487     516 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.01
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       v l+G +G GKt +a+ +  +
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAGE 238
                                       679************998765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.15
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       + l+G +G GKt l++    +
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATE 510
                                       579***********9887666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.047        19       2      32 ..     218     248 ..     217     267 .. 0.83
   2 ?   -0.5   0.0       2.4   9.8e+02      82     107 ..     260     286 ..     252     310 .. 0.70
   3 ?   -2.3   0.0       8.7   3.5e+03      99     119 ..     450     470 ..     428     477 .. 0.73
   4 ?    2.7   0.0      0.26   1.1e+02       2      32 ..     490     520 ..     489     555 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.047
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt + + v+ + + + ++++G
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAGETDANFISISG 248
                                       6789**********99999888777666666 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHH.HHH-EEEE---STT CS
                          NTPase_1  82 eelalealrkal.seadviviDEiGkm 107
                                       e+   +++++a    + +i iDEi ++
  gi|330508645|ref|YP_004385073.1| 260 EQRLRQIFDEASkAAPSIIFIDEIDSI 286
                                       56666666776634556******9665 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8.7
                                       EEE---STTGGG-HHHHHHHH CS
                          NTPase_1  99 iviDEiGkmElkskkfkeave 119
                                       +  DE+G +    +++ eave
  gi|330508645|ref|YP_004385073.1| 450 VHWDEVGGLDEAKRSLVEAVE 470
                                       4569****9999999999987 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.26
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       +++ G pG+GKt lv+ ++ + + + ++v+G
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATESNVNFISVKG 520
                                       678899*********9998887666666666 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.079        32      37     145 ..     218     331 ..     209     386 .. 0.69
   2 ?    4.8   0.0     0.053        22      37      63 ..     490     516 ..     484     658 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.079
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagk 112
                                       ++++g+ G Gkt + +a++ e+ +n      + +++ e ++++    +++  + f e  + +  ++ iD+i  +a k
  gi|330508645|ref|YP_004385073.1| 218 VLLHGPPGTGKTLIARAVAGETDAN-----FISISGPEIVSKFYGESEQRLRQIFDEASKaAPSIIFIDEIDSIAPK 289
                                       799*********9999998776555.....45678888888888877777777777777624467778888888877 PP

                                       HH.........HHHHHHHHHHHHHTTT-EEEEEESS-TTT-S CS
                          Bac_DnaA 113 ek.........tqeelfhtfnalleegkqvvlssDrsPkele 145
                                        +         +  +++ +++ l   g+ +v+++   P++l+
  gi|330508645|ref|YP_004385073.1| 290 REevsgdlerrVVAQILSLMDGLSSRGEVIVIAATNRPNALD 331
                                       431111111112334555566666677777777777777665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.053
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenap 63 
                                       +++yg  G Gkt L++a++ e   n+ 
  gi|330508645|ref|YP_004385073.1| 490 ILLYGLPGTGKTLLVRALATESNVNFI 516
                                       789*************99876554443 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0062       2.5       4      62 ..     219     283 ..     218     305 .. 0.77
   2 ?    1.3   0.0      0.55   2.2e+02      64      97 ..     530     563 ..     490     584 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0062
                               Zot   4 lvtGapGsgKts..gavkkdllp..alkegRkiitnidGlrlerieqvlgekvs.tarlirid.n 62 
                                       l +G+pG+gKt+  +av  +      + +g +i+ +  G   +r++q++ e+ + ++ +i+id +
  gi|330508645|ref|YP_004385073.1| 219 LLHGPPGTGKTLiaRAVAGETDAnfISISGPEIVSKFYGESEQRLRQIFDEASKaAPSIIFIDeI 283
                                       789********722456554443324448**********************9998999***9941 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.55
                               Zot  64 egaetlkefakwatidkgallviDEcqeifpvra 97 
                                       e++  + e++  a+ +  al+++DE   i p+r 
  gi|330508645|ref|YP_004385073.1| 530 ESERAVREIFRKARQAAPALVFFDEIDSIVPARG 563
                                       4455555666666667789999999988888764 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0019      0.79      17      44 ..     411     438 ..     408     442 .. 0.90
   2 ?   -1.0   0.0       4.3   1.8e+03      29      60 ..     692     723 ..     683     723 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0019
                            Vps4_C  17 mdipsdkllePpvtlkDflkalkkarpt 44 
                                       +dip d l + +vt++Dfl+alkk  p+
  gi|330508645|ref|YP_004385073.1| 411 EDIPLDVLDNLNVTREDFLSALKKIEPS 438
                                       58998999999**************998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.3
                            Vps4_C  29 vtlkDflkalkkarptVskeDLekheeFTkef 60 
                                       vt k f++a +  rp  sk+ L+ +++  +ef
  gi|330508645|ref|YP_004385073.1| 692 VTEKRFQEASEYIRPHLSKDMLQGYTKMIREF 723
                                       777889999999********999999877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (725 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.50
# Mc/sec: 4368.40
//
Query:       gi|330508646|ref|YP_004385074.1|  [L=670]
Description: ATP-dependent protease [Methanosaeta concilii GP6]
Scores for complete 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-34  117.4   4.3      1e-33  116.7   4.3    1.3  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    8.4e-27   94.1   0.0    1.3e-20   73.7   0.0    2.3  2  AAA_32           AAA domain
      5e-16   58.7   0.0    7.4e-09   35.3   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.8e-14   53.8   0.0    2.4e-08   33.9   0.0    2.7  2  Sigma54_activat  Sigma-54 interaction domain
    4.9e-13   49.3   0.0    4.7e-05   23.4   0.0    3.6  3  AAA_5            AAA domain (dynein-related subfamily)
    3.4e-09   36.6   0.9    6.7e-09   35.6   0.9    1.5  1  ChlI             Subunit ChlI of Mg-chelatase
    3.2e-07   29.7   0.3     0.0077   15.4   0.0    3.2  3  MCM              MCM P-loop domain
    4.3e-06   27.2   0.0       0.19   12.2   0.0    2.8  2  AAA              ATPase family associated with various cellul
    6.2e-05   23.3   0.0      0.005   17.1   0.0    2.8  2  AAA_22           AAA domain
    0.00014   22.0   0.0       0.12   12.5   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00017   21.4   0.0      0.095   12.4   0.0    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0003   20.6   0.0       0.25   11.2   0.0    3.0  3  AAA_3            ATPase family associated with various cellul
     0.0006   20.2   0.1      0.013   15.9   0.1    2.5  1  AAA_19           AAA domain
    0.00086   18.9   0.0     0.0057   16.2   0.0    2.2  2  AAA_7            P-loop containing dynein motor region
      0.001   19.4   0.0       0.15   12.5   0.0    2.7  2  AAA_16           AAA ATPase domain
      0.004   16.9   0.0      0.013   15.3   0.0    1.8  1  AAA_30           AAA domain
      0.004   17.5   0.8      0.014   15.8   0.1    2.2  2  MCM_lid          MCM AAA-lid domain
  ------ inclusion threshold ------
      0.019   13.9   0.0      0.051   12.5   0.0    1.7  1  AAA_10           AAA-like domain
      0.022   14.9   0.1        2.9    8.0   0.0    3.0  2  AAA_2            AAA domain (Cdc48 subfamily)
      0.023   14.7   0.2       0.18   11.8   0.2    2.3  2  DUF1676          Protein of unknown function (DUF1676)
      0.064   13.0   0.1       0.11   12.2   0.1    1.3  1  DUF2101          Predicted membrane protein (DUF2101)
      0.066   13.8   0.0       0.21   12.2   0.0    1.9  1  AAA_18           AAA domain
      0.083   13.0   0.0        9.5    6.3   0.0    2.6  2  MMR_HSR1         50S ribosome-binding GTPase
        0.1   13.1   0.0       0.54   10.8   0.0    2.2  2  ABC_tran         ABC transporter


Domain annotation for each model (and alignments):
>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   4.3   1.3e-36     1e-33      20     203 ..     455     635 ..     436     637 .. 0.86

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 1.3e-36
                                       SSSS--BSSEEEEEEEETTEEEEEEEEEEEES....S-S-EEEEES--HHHHHHHHHHHHHHTSS-GGGSS-SS-TT CS
                             Lon_C  20 eaekedqvGvvtGlawtevGGdlltieavllp....gkgklkltGklgdvmkesaqaalsyvrsraeelgidkevfe 92 
                                         ++ d++G v Gla     G +l i a ++p     +gk++ tGkl ++ ke+++    ++++    lg d    +
  gi|330508646|ref|YP_004385074.1| 455 FHSSGDEIGRVNGLAVMGDSGIVLPIMAEITPaqskEEGKIIATGKLQEIAKEAVTNVSVLIKKF---LGED---IT 525
                                       455789********************99988733224689*************988766666543...3333...56 PP

                                       T-EEEEEE-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEE CS
                             Lon_C  93 kkdihihvPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvilP 169
                                       kkd+hi +       +G sa +++ata++s+l g++v++ vamtG +++rG v+p+GG+ +k+ aa +agik+v++P
  gi|330508646|ref|YP_004385074.1| 526 KKDVHIQFIGTYEGVEGDSASISIATAVISALEGVPVKQTVAMTGSLSVRGDVMPVGGVTQKIEAAAQAGIKTVLIP 602
                                       89******9999999************************************************************** PP

                                       GGGGGGTTTS-HHHHTS-B--EESBHHHHHHHHB CS
                             Lon_C 170 kenekdlediPeevreeleiilveevdevlkaal 203
                                       k+n  d+  i +++++++eii+v++++ev++ a+
  gi|330508646|ref|YP_004385074.1| 603 KSNMGDVL-IDDSMKNSIEIIPVSNISEVFEFAM 635
                                       ******95.99*******************9987 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.4e-06     0.001       7      90 ..      65     143 ..      61     157 .. 0.82
   2 !   73.7   0.0   1.8e-23   1.3e-20     281     509 ..     205     432 ..     200     436 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
                            AAA_32   7 leeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePkalsLpa 83 
                                       ++++igq+ Ave ++ + + ++   ++ ++G++gtG+++l k + +e    e+ + D++   n +++++P++  +pa
  gi|330508646|ref|YP_004385074.1|  65 IDQVIGQDEAVEVIKKAASQRR---HVMLIGSPGTGKSMLGKAM-SELLPVEDLQ-DVLVYANPEDNNTPRVRVVPA 136
                                       5899***********9877655...9***********9876665.5666666655.5555569************** PP

                            AAA_32  84 GkGkelk 90 
                                       G+Gk+  
  gi|330508646|ref|YP_004385074.1| 137 GRGKQIV 143
                                       ****975 PP

  == domain 2  score: 73.7 bits;  conditional E-value: 1.8e-23
                            AAA_32 281 nvlvdnsetegaPVvvednptyanLfGkieyesemg..alvtdftlIkaGaLhkAnGGyLildaedlLeeplaWeaL 355
                                       ++lvdn+ +++aP v  +  +   L+G + ++  +     +  +++++ G++hkA+ G+L +d  + L+ p + ++L
  gi|330508646|ref|YP_004385074.1| 205 KLLVDNNGKKKAPYVDATGAHAGALLGDVRHDPFQSggLETPSHERVECGSIHKAHKGVLFIDEVNTLR-PESQQSL 280
                                       79****************************99754333555689********************99996.8899*** PP

                            AAA_32 356 kraLrskeikiesleeqlglistvsLkPepipldvKViLiGsrelYylLseyDpdfkklFkvkadFddemerteene 432
                                         aL+++  +i       + +s    + ep+p++   i  G+ +  + ++ +     k +  ++ + d+me t en 
  gi|330508646|ref|YP_004385074.1| 281 LTALQEGVYQITGQ---SERSSGALVRTEPVPCSFIMIAAGNLDAVQGMHPALRSRIKGYGYEVYMRDTMEDTLENR 354
                                       ************53...446788899*********99999999999999988888889999**************** PP

                            AAA_32 433 kkyarfias.ivkkekllpfdrsavarlieyssrlaedqeklstrfseiadllrEAdywakkegaevveaehVekAl 508
                                       +k++rf+a+ iv++ k+++f+++ava++++++ r ++++ +l++ ++++  l+r +  +a+ e++++ e +hV +A 
  gi|330508646|ref|YP_004385074.1| 355 NKLIRFVAQeIVRDGKIPHFTQDAVAEIMREAKRRSGRKGHLTLMLRDLGGLIRVSGDVARAESSHLTEVNHVMQAK 431
                                       ******985489999************************************************************96 PP

                            AAA_32 509 e 509
                                       +
  gi|330508646|ref|YP_004385074.1| 432 K 432
                                       5 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   9.9e-12   7.4e-09       3      55 ..      66     118 ..      64     126 .. 0.92
   2 !   20.7   0.0   2.8e-07   0.00021      96     157 ..     250     319 ..     241     354 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 9.9e-12
                      Mg_chelatase   3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55 
                                        +v+Gq+ea ++++ aa+ + +++l+G+pG+GK+ml k++++llp  + +++l
  gi|330508646|ref|YP_004385074.1|  66 DQVIGQDEAVEVIKKAASQRRHVMLIGSPGTGKSMLGKAMSELLPVEDLQDVL 118
                                       689******************************************98887776 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.8e-07
                      Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakak....v....efparfqlvaamN 157
                                       +++ G i +ah+GvLf+DE+  ++ +  ++L + l++g  +i+ ++++    +      p++f ++aa N
  gi|330508646|ref|YP_004385074.1| 250 RVECGSIHKAHKGVLFIDEVNTLRPESQQSLLTALQEGVYQITGQSERssgaLvrtePVPCSFIMIAAGN 319
                                       6788**************************9999999998886444320111211113567777777766 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.5e-06    0.0041      10      46 ..      73     109 ..      65     128 .. 0.86
   2 !   33.9   0.0   3.2e-11   2.4e-08      85     130 ..     252     297 ..     237     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.5e-06
                                       HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat  10 elleqikkvaktdlsvlitGesGtGKellaraiheas 46 
                                       e++e ikk+a+++ +v++ G  GtGK++l +a+ e  
  gi|330508646|ref|YP_004385074.1|  73 EAVEVIKKAASQRRHVMLIGSPGTGKSMLGKAMSELL 109
                                       68999***************************98755 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 3.2e-11
                                       BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSE CS
                   Sigma54_activat  85 kkGlfekadgGtlfLDeigelplelQekLlrvlqegevervGsske 130
                                       + G ++ka++G+lf+De+++l +e Q+ Ll++lqeg ++  G+s+ 
  gi|330508646|ref|YP_004385074.1| 252 ECGSIHKAHKGVLFIDEVNTLRPESQQSLLTALQEGVYQITGQSER 297
                                       34*************************************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 !   17.6   0.0     4e-06     0.003       1      30 [.      87     120 ..      87     132 .. 0.79
   2 !   23.4   0.0   6.4e-08   4.7e-05      65     137 ..     260     333 ..     222     334 .. 0.85
   3 ?    3.9   0.0     0.066        49      64     109 ..     384     446 ..     339     492 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4e-06
                                       EEEEE--SSSSHHHHHHHGGGGB....S--EEEE CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal....nreveyv 30 
                                       +v+L+G pGtgKs+l + ++++l     + v+++
  gi|330508646|ref|YP_004385074.1|  87 HVMLIGSPGTGKSMLGKAMSELLpvedLQDVLVY 120
                                       79********************976654444444 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 6.4e-08
                                       G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---..........-EEEEEESS--.-TT-TTHHHHTT CS
                             AAA_5  65 egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddller....frviatanpldrslnelspalrsR 137
                                       ++ +l++DEv+++++e ++sLl+ l e  +++    e+ + +   ++e+    f  ia++n     ++ + palrsR
  gi|330508646|ref|YP_004385074.1| 260 HKGVLFIDEVNTLRPESQQSLLTALQEGVYQITGQSERSSGALV-RTEPvpcsFIMIAAGNLDA--VQGMHPALRSR 333
                                       688****************************8777777777663.4444899999999999888..88888*****9 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.066
                                       -...................G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---.. CS
                             AAA_5  64 r...................egeilvlDEveraesevlnsLlslleerrllleeggelvkakndd 109
                                       r                    g i v ++v raes+ l +++ ++  +++    + e++ a+++ 
  gi|330508646|ref|YP_004385074.1| 384 ReakrrsgrkghltlmlrdlGGLIRVSGDVARAESSHLTEVNHVMQAKKMA--RSVEQQLADRYM 446
                                       144455555555556666888999999**********************99..666666666664 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.9   8.9e-12   6.7e-09      12     121 .]     495     605 ..     483     605 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 8.9e-12
                              ChlI  12 ftivGlpdtavkeskervrsalkn.sgfefpakkitvnLaPadlkkeGsafDLpiAigilaaleqieaeeetlflGe 87 
                                       +  +G +++  ke+   v   +k+  g ++ +k + +         eG + +++iA ++++ale +++++++ + G 
  gi|330508646|ref|YP_004385074.1| 495 IIATGKLQEIAKEAVTNVSVLIKKfLGEDITKKDVHIQFIGTYEGVEGDSASISIATAVISALEGVPVKQTVAMTGS 571
                                       55678899999***********99889************************************************** PP

                              ChlI  88 LsldGslrpvkgvlpialaakkegikkvivpken 121
                                       Ls  G++ pv gv++ + aa+++gik+v++pk+n
  gi|330508646|ref|YP_004385074.1| 572 LSVRGDVMPVGGVTQKIEAAAQAGIKTVLIPKSN 605
                                       *******************************998 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00045      0.33      53      83 ..      81     111 ..      57     117 .. 0.78
   2 !   15.4   0.0     1e-05    0.0077      85     152 ..     217     291 ..     207     295 .. 0.75
   3 ?   -0.6   0.1      0.77   5.7e+02      19      53 ..     512     546 ..     498     558 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00045
                                       BBCSS-EEEEEESSTSTHHHHHHHHHHHSSS CS
                               MCM  53 klrgdinvllvgdpgtaKsqlLkyveklapr 83 
                                           + +v+l+g pgt+Ks l k++++l+p 
  gi|330508646|ref|YP_004385074.1|  81 AASQRRHVMLIGSPGTGKSMLGKAMSELLPV 111
                                       455678***************9999998875 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1e-05
                                       EEEESSSSSSSHSSSEEEEESSSSS.......EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEE CS
                               MCM  85 vytsgkgssaagLtaavvrdeetge.......fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisi 152
                                        y+ ++g+ a  L   v++d+ ++          +e+G +  a+kGv+ iDe++  + e +++l+ a+ +   +i
  gi|330508646|ref|YP_004385074.1| 217 PYVDATGAHAGALLGDVRHDPFQSGgletpshERVECGSIHKAHKGVLFIDEVNTLRPESQQSLLTALQEGVYQI 291
                                       56666666666666666666655443333333569******************************9998776555 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.77
                                       HHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSB CS
                               MCM  19 vksiapsiyghedvkkaillqlfggvkkkledktk 53 
                                       v+ ++++ +g++  kk + +q +g+++  + d+++
  gi|330508646|ref|YP_004385074.1| 512 VSVLIKKFLGEDITKKDVHIQFIGTYEGVEGDSAS 546
                                       567889999999***********999987777554 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 !   11.7   0.0   0.00034      0.25       1      21 [.      88     108 ..      88     143 .. 0.89
   2 !   12.2   0.0   0.00025      0.19      58     125 ..     260     335 ..     247     338 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00034
                                       EEEESSTTSSHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavake 21 
                                       v+l+G pGtGK++l ka+ + 
  gi|330508646|ref|YP_004385074.1|  88 VMLIGSPGTGKSMLGKAMSEL 108
                                       68**************98765 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00025
                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS...................SSTEEEEEEESS..GG CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk...................eskvivigatnr..pd 113
                                       ++ +lfiDE+  l +++           ++ Llt+l++   +                      +i+i+a+n   ++
  gi|330508646|ref|YP_004385074.1| 260 HKGVLFIDEVNTLRPES-----------QQSLLTALQEGVYQitgqserssgalvrtepvpC-SFIMIAAGNLdaVQ 324
                                       359**********9999...........4444444443333333445555777******955.5********99999 PP

                                       GSTHHHHSTTSS CS
                               AAA 114 kldpallrgRfd 125
                                        + pal+ +R++
  gi|330508646|ref|YP_004385074.1| 325 GMHPALR-SRIK 335
                                       9*****9.8975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.6e-06     0.005       3      38 ..      83     126 ..      79     158 .. 0.75
   2 ?    2.8   0.0      0.18   1.3e+02      86     110 ..     256     282 ..     242     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.6e-06
                            AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeakaee........e 38 
                                       +++++++++G +GtGK++l + + e l+ e  ++         +
  gi|330508646|ref|YP_004385074.1|  83 SQRRHVMLIGSPGTGKSMLGKAMSELLPVEDLQDVlvyanpedN 126
                                       4899**********************987765544555555443 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.18
                            AAA_22  86 lraravielliiDEaqhlr..s.eeale 110
                                       ++++++ ++l iDE+  lr  s + +l+
  gi|330508646|ref|YP_004385074.1| 256 IHKAHK-GVLFIDEVNTLRpeSqQSLLT 282
                                       566677.9**********7653233333 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0087       6.5      13      43 ..      77     107 ..      72     122 .. 0.88
   2 !   12.5   0.0   0.00016      0.12      64      96 ..     255     295 ..     200     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0087
                                       HHHHHHT-SS-EEEEEETT--HHHHHHCC-- CS
                   Sigma54_activ_2  13 rLeqaaqsklpvfltGekGsgkelvArlLhk 43 
                                        +++aa++   v l+G +G+gk++  +++++
  gi|330508646|ref|YP_004385074.1|  77 VIKKAASQRRHVMLIGSPGTGKSMLGKAMSE 107
                                       58999*******************9998875 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00016
                                       HHHHTTTSEEEEEE-TT--HHHHHHHHHHHHH........H CS
                   Sigma54_activ_2  64 lleqakggtLylkdiadlskaeqkeLlellak........a 96 
                                       ++ +a+ g+L++ +++ l ++ q+ Ll +l++        +
  gi|330508646|ref|YP_004385074.1| 255 SIHKAHKGVLFIDEVNTLRPESQQSLLTALQEgvyqitgqS 295
                                       56789**************************9666666652 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00013     0.095       6      56 ..      65     108 ..      60     115 .. 0.76
   2 !    6.3   0.0    0.0098       7.3      84     116 ..     260     292 ..     255     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                            RuvB_N   6 leeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiake 56 
                                       +++ igq++    ++++ +aa +r+    hv+l+G+PG Gk+ l k +++ 
  gi|330508646|ref|YP_004385074.1|  65 IDQVIGQDEA---VEVIKKAASQRR----HVMLIGSPGTGKSMLGKAMSEL 108
                                       5667777754...556668888775....9*************99988765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0098
                            RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldiv 116
                                       +k vlfide+  l+++ ++ l +a+++   +i+
  gi|330508646|ref|YP_004385074.1| 260 HKGVLFIDEVNTLRPESQQSLLTALQEGVYQIT 292
                                       578*********************998766664 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.014        11       1      24 [.      87     110 ..      87     117 .. 0.91
   2 !   11.2   0.0   0.00034      0.25      63      98 ..     261     296 ..     246     335 .. 0.69
   3 ?   -2.5   0.0       5.7   4.2e+03      67      90 ..     361     387 ..     338     395 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                             AAA_3   1 hvllegvPGlaktllvkalakald 24 
                                       hv+l g PG++k +l ka+++ l 
  gi|330508646|ref|YP_004385074.1|  87 HVMLIGSPGTGKSMLGKAMSELLP 110
                                       9******************99875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00034
                             AAA_3  63 anllladeinrappktqsalleameerqvtvegeth 98 
                                       + +l+ de+n   p +q +ll a++e    ++g++ 
  gi|330508646|ref|YP_004385074.1| 261 KGVLFIDEVNTLRPESQQSLLTALQEGVYQITGQSE 296
                                       46899*********************7555544432 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.7
                             AAA_3  67 ladeinr...appktqsalleameerq 90 
                                       +a ei r    p  tq a+ e+m+e +
  gi|330508646|ref|YP_004385074.1| 361 VAQEIVRdgkIPHFTQDAVAEIMREAK 387
                                       466666522135568999999999876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.7e-05     0.013       6     126 ..      80     285 ..      71     292 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-05
                            AAA_19   6 e.alkekvllvtaGpGtGKTrvlkhivallvelggvkp..........eeillvaftgrAakelrerlaalgaeatT 71 
                                       + a++++++++++ pGtGK+ + k++ +ll  +  +++           + + v ++gr  + +  +  ++ ++ +T
  gi|330508646|ref|YP_004385074.1|  80 KaASQRRHVMLIGSPGTGKSMLGKAMSELLPVEDLQDVlvyanpednnTPRVRVVPAGRGKQIVDAQKLEARKKVQT 156
                                       347899*************9888877777766665544778888887777777888888877777666566666666 PP

                            AAA_19  72 iHrlal....................................................................... 77 
                                          + +                                                                       
  gi|330508646|ref|YP_004385074.1| 157 RNMFLMiivmalivyayymgqllfgiiaaallfislrymlpkedamvpkllvdnngkkkapyvdatgahagallgdv 233
                                       66654477777777888888888888888888888888888888888888888888888777666666666666664 PP

                            AAA_19  78 ....ldfddlltealelle.....eaeeekklqeee.llivDEfqdvd.elqyrLlkall 126
                                            +         + le     + e  +  ++++ +l++DE+  +  e q++Ll al 
  gi|330508646|ref|YP_004385074.1| 234 rhdpFQ--------SGGLEtpsheRVECGSIHKAHKgVLFIDEVNTLRpESQQSLLTALQ 285
                                       444422........22222444432222333344556999*******9999999999987 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.6e-06    0.0057      25      63 ..      77     115 ..      71     124 .. 0.86
   2 ?   -1.0   0.0       1.4   1.1e+03     100     115 ..     260     275 ..     256     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.6e-06
                             AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkldkekyl 63 
                                       ++++  +++++v+l+G+ GtGK+++ k + + l+ e+++
  gi|330508646|ref|YP_004385074.1|  77 VIKKAASQRRHVMLIGSPGTGKSMLGKAMSELLPVEDLQ 115
                                       5788999******************99998888876665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                             AAA_7 100 kklvvFvDDlnmpake 115
                                       +k v+F+D++n  ++e
  gi|330508646|ref|YP_004385074.1| 260 HKGVLFIDEVNTLRPE 275
                                       6789*******98776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0    0.0002      0.15      16      75 ..      78     136 ..      67     159 .. 0.64
   2 ?    4.0   0.0      0.08        59     134     159 ..     259     285 ..     249     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysalaqa 75 
                                       +++++s+r + v+l+G +G+GKs l ++  + l  +    ++++++ +++  ++p++ ++ a
  gi|330508646|ref|YP_004385074.1|  78 IKKAASQR-RHVMLIGSPGTGKSMLGKAMSELLPVEdlQDVLVYANPEDN--NTPRVRVVPA 136
                                       45555555.9***************9888876665533234466666666..6776554444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.08
                            AAA_16 134 erplvlvlDdlqwadeaslql.laaLl 159
                                       +++ vl++D++  ++++s+q  l aL 
  gi|330508646|ref|YP_004385074.1| 259 AHKGVLFIDEVNTLRPESQQSlLTALQ 285
                                       6778***************99565554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.7e-05     0.013       6      53 ..      71     121 ..      69     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                            AAA_30   6 Qaaaveal..ltsgdrvavltGpAGtGKttalkalreaweaa.ggrviglA 53 
                                       Q +ave +  ++s++r ++l G +GtGK+++ ka+ e++  +  ++v+++A
  gi|330508646|ref|YP_004385074.1|  71 QDEAVEVIkkAASQRRHVMLIGSPGTGKSMLGKAMSELLPVEdLQDVLVYA 121
                                       55555433224566679********************99888457888877 PP

>> MCM_lid  MCM AAA-lid 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     0.014      33      84 ..     383     435 ..     367     438 .. 0.85
   2 ?    0.2   0.1       1.4     1e+03      18      37 ..     433     452 ..     431     461 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                                       HHHHHTSS.TSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHHHHH CS
                           MCM_lid  33 lRkeeeds.krksipitvRqLesliRLseAlAklrlsevvteedveeairllk 84 
                                       +R+ +++s ++ +++   R L  liR+s  +A+ + s+  + ++v++a ++ +
  gi|330508646|ref|YP_004385074.1| 383 MREAKRRSgRKGHLTLMLRDLGGLIRVSGDVARAESSHLTEVNHVMQAKKMAR 435
                                       56666444467899999*******************************88765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.4
                                       ETCHHHHHHHHHHHHHHHHH CS
                           MCM_lid  18 lseeakeklseaYvelRkee 37 
                                       +  +++++l++ Y+e Rk+ 
  gi|330508646|ref|YP_004385074.1| 433 MARSVEQQLADRYMERRKDY 452
                                       6778899**********976 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.8e-05     0.051      13      70 ..      77     136 ..      71     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.8e-05
                            AAA_10  13 evkgsktnasasliiGdlGnGKSvlakllvlyisllg..gkaliiDpkkerekfketlpe 70 
                                        +k + ++  ++++iG++G GKS+l k +   + + +  + +++  p  ++   ++ +p+
  gi|330508646|ref|YP_004385074.1|  77 VIKKAASQRRHVMLIGSPGTGKSMLGKAMSELLPVEDlqDVLVYANPEDNNTPRVRVVPA 136
                                       57778888899******************9887765533777788888776666666655 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.093        69       6      32 ..      88     114 ..      84     160 .. 0.82
   2 ?    8.0   0.0    0.0038       2.9      63     131 ..     255     322 ..     248     375 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.093
                                       EEEE--TTSSHHHHHHHHHHHTT-... CS
                             AAA_2   6 illlgptgvGktelakalaellfvkke 32 
                                       ++l+g+ g+Gk++l ka++ell v++ 
  gi|330508646|ref|YP_004385074.1|  88 VMLIGSPGTGKSMLGKAMSELLPVEDL 114
                                       7899*****************998443 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0038
                                       -HHHHTTSEEEEETGGG-------------HHHHHHHHHHHH--EE-......------EE-T....T-EEEEEE-- CS
                             AAA_2  63 yvgaeegGivllDEidKihpkessgadvSregVqrdLLqileggtlt......dkqgrkvdtk....nilfImtgaf 129
                                        + ++ +G++++DE+    p           + q+ LL  l +g+ +       ++g  v+t+      ++I++g++
  gi|330508646|ref|YP_004385074.1| 255 SIHKAHKGVLFIDEVNTLRP-----------ESQQSLLTALQEGVYQitgqseRSSGALVRTEpvpcSFIMIAAGNL 320
                                       6778999*************...........6666666666666655556665666666666522223466666666 PP

                                       TT CS
                             AAA_2 130 gs 131
                                       ++
  gi|330508646|ref|YP_004385074.1| 321 DA 322
                                       65 PP

>> DUF1676  Protein of unknown function (DUF1676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00025      0.18     109     150 ..     142     186 ..     103     195 .. 0.71
   2 ?   -0.7   0.0       1.7   1.3e+03      67      90 ..     639     662 ..     626     666 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                           DUF1676 109 e......egRkkkkkkkklkkmllplllalk.lklklLlplalgllall 150
                                              e+R kk    + ++m+l++++++  + +  ++ l++g++a +
  gi|330508646|ref|YP_004385074.1| 142 IvdaqklEAR-KK---VQTRNMFLMIIVMALiVYAYYMGQLLFGIIAAA 186
                                       0223335888.33...45567888877777779999*******999865 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                           DUF1676  67 ekllleklerflkshslevklpee 90 
                                       ++ l+ekl++f ++ ++ +++pe+
  gi|330508646|ref|YP_004385074.1| 639 RTRLIEKLKKFATEKKIGINIPET 662
                                       57899****************987 PP

>> DUF2101  Predicted membrane protein (DUF2101)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.11      39      78 ..     159     200 ..     121     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                           DUF2101  39 ifllyli.islvlvf.lksllvlllaalleflllryilirni 78 
                                       +fl+ ++   +v+++ + +ll  ++aa+l+f+ lry+l ++ 
  gi|330508646|ref|YP_004385074.1| 159 MFLMIIVmALIVYAYyMGQLLFGIIAAALLFISLRYMLPKED 200
                                       56666662445667669999999**************98865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00028      0.21       1      44 [.      88     130 ..      88     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00028
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44 
                                       ++l G pG+GK+ l+k+ s++l  ++ l+dv+   ++++ ++p 
  gi|330508646|ref|YP_004385074.1|  88 VMLIGSPGTGKSMLGKAMSELL-PVEDLQDVLVYANPEDNNTPR 130
                                       789*****************95.256666666655555555555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.013       9.5       2      21 ..      88     107 ..      87     172 .. 0.79
   2 ?    3.9   0.0     0.073        55      16      88 ..     358     432 ..     354     457 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                                       EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                       v+++G p +GKS L +a+++
  gi|330508646|ref|YP_004385074.1|  88 VMLIGSPGTGKSMLGKAMSE 107
                                       89************999976 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.073
                                       HHHHHTSTEEESSSTTSSSSEEEEEEE...ETTEE........EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEE CS
                          MMR_HSR1  16 inaltgekaivsdkpgtTrdinegrvk...lkgke........ielvDtpGliegaseekglgkaflaleeadlill 81 
                                       i+   +e ++ +++p  T+d + + ++       +        + l D+ Gli     + ++++a  ++     + +
  gi|330508646|ref|YP_004385074.1| 358 IRFVAQEIVRDGKIPHFTQDAVAEIMReakR---RsgrkghltLMLRDLGGLIR---VSGDVARAESSHLT--EVNH 426
                                       44445567788999*******9999984430...2345555559*******986...12234444444332..4555 PP

                                       EEETTTT CS
                          MMR_HSR1  82 vvdasee 88 
                                       v++a+ +
  gi|330508646|ref|YP_004385074.1| 427 VMQAK-K 432
                                       55544.2 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00073      0.54       9      36 ..      83     110 ..      76     147 .. 0.88
   2 ?   -2.4   0.0       8.7   6.5e+03      35      73 ..     488     523 ..     469     573 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00073
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllk 36 
                                       ++ + v ++G+ G+GKS L k++++ll 
  gi|330508646|ref|YP_004385074.1|  83 SQRRHVMLIGSPGTGKSMLGKAMSELLP 110
                                       5667899****************99865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.7
                                       S--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  35 lkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpe 73 
                                        +++eG+i +   +l+e   +++  +++vl ++ +l ++
  gi|330508646|ref|YP_004385074.1| 488 QSKEEGKI-IATGKLQE-IAKEAVTNVSVLIKK-FLGED 523
                                       44477777.44445555.333344444444444.34444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (670 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1242  (0.0692732); expected 358.6 (0.02)
Passed bias filter:                      899  (0.0501422); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); 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: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.46
# Mc/sec: 4404.87
//
Query:       gi|330508647|ref|YP_004385075.1|  [L=439]
Description: TldD/PmbA family protein [Methanosaeta concilii GP6]
Scores for complete sequence (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  205.7   0.1    1.7e-60  205.3   0.1    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 !  205.3   0.1   9.5e-65   1.7e-60       2     279 .]       6     294 ..       5     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 205.3 bits;  conditional E-value: 9.5e-65
                                       EEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-... CS
                         PmbA_TldD   2 aevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea... 75 
                                       ++ r+ ++++t + ++ng++e++ +   +g++vr++ gg++gf++t+  +  +l + ++ a +ia++ + +++    
  gi|330508647|ref|YP_004385075.1|   6 YDTRILQGSRTRIVLDNGKLEEIAQVPFQGASVRALFGGAWGFVTTDRVD--GLGQEIDLAKRIARKIGRKEDLsla 80 
                                       577888999*************************999********77777..****************999999*** PP

                                       ................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEE CS
                         PmbA_TldD  76 ................eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqt 136
                                                       +++s eek++ll+e+e+a+  +      ++  +is+++a +s++    ++ +SeGld+e++
  gi|330508647|ref|YP_004385075.1|  81 eappgrsvlvpvkrdpKDLSLEEKVALLREIEDAA--K------VE--GISSTQAVYSEMDLVAHYSSSEGLDLESR 147
                                       ********************************882..2......22..89**********99999************ PP

                                       EEEEEEEEEEEE..S..TCS...ETEEEEEEEESSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHH CS
                         PmbA_TldD 137 rtrvslslsvia.dd..ggs...gdgmgggsgyedleeedleeiaeeaaekalasleakplppgkypVvlspeavgs 207
                                        tr+++ +s++a ++   ++   g  + g +g e +++ed+ ++a+++ e+a+a+l+ak++  g+ pVvl+ e +g+
  gi|330508647|ref|YP_004385075.1| 148 MTRMGFVISAVAhRNglYQTdgeG--RAGVGGLELFDREDPIALARQVGETAVALLDAKAARGGTHPVVLDQELAGV 222
                                       ************776363333223..33334446667788999********************************** PP

                                       HHHGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-.....-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 208 llheavghaleadavlegrSflkdklGekvaselltivddptsgglgsypfDdEGvptqrtvlIenGvLkny 279
                                       ++heavgha+e+d +leg S l++klG++++sel+t+ ddp     g+ypfDdEG  +q+tvl+enGvL++y
  gi|330508647|ref|YP_004385075.1| 223 FVHEAVGHATEGDIILEGDSCLEGKLGQRIGSELVTVKDDPSLMLNGYYPFDDEGSRAQETVLVENGVLRSY 294
                                       **********************88*****************647889***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3233.84
//
Query:       gi|330508648|ref|YP_004385076.1|  [L=265]
Description: extracellular nuclease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-05   24.4   0.0    6.8e-05   23.3   0.0    1.6  1  SNase          Staphylococcal nuclease homologue
  ------ inclusion threshold ------
       0.12   11.7   0.2       0.37   10.2   0.1    1.7  1  VPS13_mid_rpt  Repeating coiled region of VPS13


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 !   23.3   0.0   7.6e-09   6.8e-05       1      86 [.      74     163 ..      74     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 7.6e-09
                                       EEEETTEE-STSSBTTTTTSTTHHHHHHHHHHHHHHCSSEEEEE-S..SBSTTSEEEEEEEET........TEEHHH CS
                             SNase   1 kvrLvgidaPetakpkktvqpfgkeAkeflkklvlqkkvvvleldk..kkDkygrllayvyln........kknine 67 
                                       ++ L+++++P  +      +  g  A++f+  +++ k v ++++d    +D +grl+a  yl           n+n+
  gi|330508648|ref|YP_004385076.1|  74 RITLADVRSPDMK------AIQGPAARDFTYAVLMDKRVYLDVDDFnrGQDDEGRLIAVAYLAgaygqpipYPNFNL 144
                                       5788999999988......55699***********999998888878889************99*****9999**** PP

                                       HHHHTTSSEE---BTTSTT CS
                             SNase  68 eLvkeGlArvyevyeknee 86 
                                        Lv +G A ++++ +++++
  gi|330508648|ref|YP_004385076.1| 145 LLVDAGHAILANQTDNEFD 163
                                       *********9887765443 PP

>> VPS13_mid_rpt  Repeating coiled region of VPS13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   4.2e-05      0.37     100     150 ..     141     192 ..     136     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.2e-05
                     VPS13_mid_rpt 100 essllvlDlGhlsveselvdksaikeikskskqqyseed.leeleelmYDkf 150
                                       + +ll++D+Gh  +  +  ++ + k+ +++++++ s++d l+++ee++ +++
  gi|330508648|ref|YP_004385076.1| 141 NFNLLLVDAGHAILANQTDNEFDPKDWREEHNSEKSNSDtLQRVEENLRERL 192
                                       6799*****************9******999999888887888888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1325  (0.0739026); expected 358.6 (0.02)
Passed bias filter:                      813  (0.0453455); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2047.84
//
Query:       gi|330508649|ref|YP_004385077.1|  [L=122]
Description: hypothetical protein MCON_2895 [Methanosaeta concilii GP6]
Scores for complete 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   15.7   0.1      0.012   15.2   0.1    1.2  1  TRIC      TRIC channel


Domain annotation for each model (and alignments):
>> TRIC  TRIC channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   6.8e-07     0.012       8      45 ..      14      55 ..       9      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.8e-07
                                      HHH-HH..HHHHHHHHHHTHHHHHHHHHHTS-..TTGGGC-H CS
                              TRIC  8 srkhPl..acWlssmllcfagsiLsnlLlgep..lleplknt 45
                                       +k Pl  + W+ ++l + ag+iL+  +lg+p  ++e+++ +
  gi|330508649|ref|YP_004385077.1| 14 FWKTPLgiVIWFGALLAILAGGILALNFLGSPypVIEFFDAE 55
                                      5677753378********************863378888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 983.98
//
Query:       gi|330508650|ref|YP_004385078.1|  [L=299]
Description: cobalt chelatase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-54  184.8   0.0      1e-52  179.1   0.0    2.0  1  CbiK      Cobalt chelatase (CbiK)
    3.4e-08   33.8   0.0    0.00015   22.1   0.0    2.8  2  CbiX      CbiX


Domain annotation for each model (and alignments):
>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.1   0.0   1.1e-56     1e-52       2     260 ..      11     287 ..      10     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: 179.1 bits;  conditional E-value: 1.1e-56
                                       EEEEEE---S-HHHHHHHHHHHHHHHHHC-TTSEEEEEES-HHHHHHHHHHH------HHHHHHHHHHCT--EEEEE CS
                              CbiK   2 aillvsFGtsykdarektiekiekkvaaefpdyevfraftSsiiikklkerdeievdtpeealeklkeegykevivq 78 
                                       ++llv +G++ + a++ t+e+i    ++++p++ v+ aftS+ +ik+l+er++i +   eeal kl  +g k+v+vq
  gi|330508650|ref|YP_004385078.1|  11 GMLLVPYGSASPRAMA-TYENILALYRKDYPGMPVLLAFTSRLMIKRLQEREGIAIPNIEEALGKLSGQGCKQVVVQ 86 
                                       689************9.************************************************************ PP

                                       E--SCSSHHHHHHHHHHHHHGGGSS......EEEEE--SCS..........SHHHH.........HHHHHHHHT.TS CS
                              CbiK  79 plhiipGeeyeklkreVkkfkkkfe......kiklgrPlldy....kGvedsteDy.........kevvealkd.ei 135
                                       +l i+pG e+ +l++   +++kk        ki++g Pll+     + v +   D+         ke  e++++ ++
  gi|330508650|ref|YP_004385078.1|  87 SLQIVPGGEFHRLVSLSREYEKKDAdperrlKITIGLPLLSCledcRRVSEALPDLwrpsrdaesKEGDETVRKsQF 163
                                       *****************99987643222333789*****98521112233332332111111111444555554145 PP

                                       ----TTEEEEEEE---SCHHHHHHHHHHHHHHHCT-S.EEEEETTSSS-HHHHHHHHHHHT--EEEEEE-SSS--HH CS
                              CbiK 136 erarkdealvfvgHGtehesnavyaeldkvlkekdfkqvvvgtvegyPeveevieelkkkgikevkliPlmlvAGdH 212
                                           k+ea+++ gHGt h++ a+y+++ +vlk+  + qv +gt+eg+P++ e+i+elk  g+++v+l+P++lvAG H
  gi|330508650|ref|YP_004385078.1| 164 AVESKKEAVLLAGHGTGHPADAIYSQMAQVLKKD-YGQVLLGTIEGFPSLLEMIDELKVIGAQKVRLRPFLLVAGGH 239
                                       54559**************************986.899*************************************** PP

                                       HHCCCCSSSTTSHHHHHHHTT--EEE----GGGSHHHHHHHHHHHHHH CS
                              CbiK 213 aknDmasdeedswkealeaaGikveiilkgLGeieeirsifikhikea 260
                                       a+nD+ +   dswk+ le+aGi+v+ +l++LGeie i +i  +h  +a
  gi|330508650|ref|YP_004385078.1| 240 AENDISGPAPDSWKSSLERAGIEVDFHLSALGEIEGIVQILKEHSLKA 287
                                       **************************************9998886665 PP

>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0   0.00024       2.1      37      87 ..      65     117 ..      18     139 .. 0.79
   2 !   22.1   0.0   1.6e-08   0.00015      13     106 ..     187     281 ..     177     282 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00024
                                       ECCSCCSSHHHHC-SBSEEEEEEESSSSS..HHHHTHHHHHCT--SSSS-TTE CS
                              CbiX  37 epsleealrelaeqgvkrivvvPlflfaG..vhvkeDIpeeleeaeeahpkdv 87 
                                        p++eeal +l+ qg+k++vv  l + +G  +h    +++e+e+ ++++++  
  gi|330508650|ref|YP_004385078.1|  65 IPNIEEALGKLSGQGCKQVVVQSLQIVPGgeFHRLVSLSREYEKKDADPERRL 117
                                       59*******************99988888333444444555555555555444 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.6e-08
                                       HHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHH....HHHCT--SSSS-T CS
                              CbiX  13 eklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDI....peeleeaeeahpk 85 
                                       +  ++++ +k+   +v lg +e   psl e ++el   g++++ + P++l aG+h+++DI    p+  +   e+ + 
  gi|330508650|ref|YP_004385078.1| 187 YSQMAQVLKKDY-GQVLLGTIE-GFPSLLEMIDELKVIGAQKVRLRPFLLVAGGHAENDIsgpaPDSWKSSLERAGI 261
                                       444444444333.688888888.78***********************************55443233322222222 PP

                                       TEEEEE---CCCSCCHHHHHH CS
                              CbiX  86 dveieytepLGthplvaevlk 106
                                       +v++++ ++LG+ + ++++lk
  gi|330508650|ref|YP_004385078.1| 262 EVDFHL-SALGEIEGIVQILK 281
                                       455554.57888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2132.95
//
Query:       gi|330508651|ref|YP_004385079.1|  [L=145]
Description: alkylhydroperoxidase-like protein [Methanosaeta concilii GP6]
Scores for complete 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   57.0   0.1    2.1e-15   56.6   0.1    1.2  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.1   1.1e-19   2.1e-15      11      81 ..      64     133 ..      54     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.1e-19
                                       HHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHH CS
                               CMD  11 reallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAla 81 
                                       ++++l r+++L+pk+ eL+a+a++aa g + C+++H++aAl+aG++ +ei ++l +aa  +++ ++ + l+
  gi|330508651|ref|YP_004385079.1|  64 DFYVL-RPNSLEPKTAELLAVAAAAASGADKCLKVHMNAALRAGASLDEILDTLFIAALIGQTKVLASSLR 133
                                       45555.6999**************************************************99887777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1198.97
//
Query:       gi|330508652|ref|YP_004385080.1|  [L=192]
Description: tungsten formylmethanofuran dehydrogenase subunit E [Methanosaeta concilii GP6]
Scores for complete 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-41  138.9   0.0    1.2e-40  138.6   0.0    1.1  1  FmdE          FmdE, Molybdenum formylmethanofuran dehydrogena
    1.4e-06   28.1   2.0    2.9e-06   27.1   2.0    1.5  1  zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
  ------ inclusion threshold ------
      0.044   13.9   0.7       0.11   12.7   0.7    1.7  1  Zn-ribbon_8   Zinc ribbon domain
       0.06   13.6   1.0       0.12   12.6   0.2    1.9  2  LIM           LIM domain


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.6   0.0   2.7e-44   1.2e-40       1     131 [.      11     141 ..      11     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 138.6 bits;  conditional E-value: 2.7e-44
                                       HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEETT CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltfkkrk 77 
                                       fHGH+Cpgl++Gyr+ak+++++++    ++deelv+i+e++sC  DAiq+++gct Gkgnl ++dygk+a+tf++r+
  gi|330508652|ref|YP_004385080.1|  11 FHGHTCPGLAIGYRIAKYVKEHYPR---SQDEELVCIAENKSCSIDAIQFMLGCTAGKGNLLFKDYGKQAFTFYSRD 84 
                                       9**********************84...348********************************************** PP

                                       T-EEEEEEE-....CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHHHHHS.HHHHE CS
                              FmdE  78 tgkavrlklk....eelpelreklakgkakeekeeeeleeeleeaikkilnapeeelf 131
                                       ++ka+r++++    + ++elr+k+++g+  +e ++e++   +++a +k+l+a +e+++
  gi|330508652|ref|YP_004385080.1|  85 KNKALRIYFRggilKGMDELRQKMVQGELGPE-DRERMAAFRSQATEKVLSARDEDIL 141
                                       *****************************888.78899****************9986 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   2.0   6.5e-10   2.9e-06       5      33 ..     159     189 ..     155     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 6.5e-10
                      zf-dskA_traR   5 s..CeeCGEpIpeaRlralPgarlCveCqek 33 
                                       s  CeeCGE+ +e   r  +g++lC++C+e+
  gi|330508652|ref|YP_004385080.1| 159 SlkCEECGEEFMEILGRTAGGKVLCKSCFER 189
                                       566**************************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 ?   12.7   0.7   2.3e-05      0.11       7      32 ..     161     186 ..     159     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeC 32 
                                       +CeeCg+ef ++   +   ++ C++C
  gi|330508652|ref|YP_004385080.1| 161 KCEECGEEFMEILGRTAGGKVLCKSC 186
                                       8********9888666555555**** PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         1   4.5e+03      38      50 ..      31      43 ..      27      48 .. 0.73
   2 ?   12.6   0.2   2.7e-05      0.12      27      56 ..     160     189 ..     152     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1
                                      TT.CEEETTEEEE CS
                               LIM 38 egsfyekdgklyC 50
                                      e+++ ++d++l+C
  gi|330508652|ref|YP_004385080.1| 31 EHYPRSQDEELVC 43
                                      5556778889999 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.7e-05
                                       SB-TTT-SB-CTT.CEEETTEEEEHHHHHH CS
                               LIM  27 FtCsdCqkeLkegsfyekdgklyCkkdylk 56 
                                       ++C++C++e+ e       gk++Ck+++ +
  gi|330508652|ref|YP_004385080.1| 160 LKCEECGEEFMEILGRTAGGKVLCKSCFER 189
                                       89**********96666666********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1416.62
//
Query:       gi|330508653|ref|YP_004385081.1|  [L=285]
Description: hypothetical protein MCON_2899 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2103.65
//
Query:       gi|330508654|ref|YP_004385082.1|  [L=349]
Description: hypothetical protein MCON_2901 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-05   24.8   0.1    3.4e-05   23.6   0.1    1.6  1  MarR_2          MarR family
    0.00025   20.8   0.0    0.00047   19.9   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
    0.00065   19.5   0.2     0.0014   18.4   0.2    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.003   17.4   0.5     0.0063   16.4   0.5    1.6  1  MarR            MarR family
      0.005   15.7   0.0     0.0066   15.3   0.0    1.1  1  Amnionless      Amnionless
     0.0055   17.2   0.4      0.011   16.2   0.4    1.5  1  HTH_27          Winged helix DNA-binding domain
     0.0082   16.3   0.1       0.04   14.1   0.1    2.0  2  B-block_TFIIIC  B-block binding subunit of TFIIIC
  ------ inclusion threshold ------
      0.015   14.8   0.9       0.12   11.9   0.4    2.5  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.025   14.6   0.1      0.037   14.1   0.1    1.2  1  DUF2561         Protein of unknown function (DUF2561)
      0.053   13.2   0.1      0.086   12.5   0.1    1.2  1  Phage_TTP_12    Lambda phage tail tube protein, TTP
       0.07   12.8   0.5        7.7    6.1   0.0    2.3  2  SMC_ScpB        Segregation and condensation complex subunit 
      0.089   12.8   0.6       0.16   11.9   0.6    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.11   12.6   0.0       0.26   11.4   0.0    1.6  1  Trans_reg_C     Transcriptional regulatory protein, C termina


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 !   23.6   0.1   2.5e-08   3.4e-05       3      55 ..     278     329 ..     276     333 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.5e-08
                                       --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       lt  +  vL  L  r+gr + ++++  ++++sks++s il  ++++ L+++r+
  gi|330508654|ref|YP_004385082.1| 278 LTDKEQSVLKLLLQRGGR-MVQRDISYETDISKSSLSGILTSMEKRKLITKRE 329
                                       56677889999*****97.9*****************************9984 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.4e-07   0.00047       7      50 ..     284     327 ..     280     329 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.4e-07
                                       HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       ++L++l ++++++  ++++ +t+++kS+ +++L ++++++++++
  gi|330508654|ref|YP_004385082.1| 284 SVLKLLLQRGGRMVQRDISYETDISKSSLSGILTSMEKRKLITK 327
                                       599**************************************987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2     1e-06    0.0014       6      58 ..     278     331 ..     276     340 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1e-06
                                       HHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB   6 LseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       L++ E +v + Ll + g++  ++i+ e+++++s+   +L s+e++ l++++++ 
  gi|330508654|ref|YP_004385082.1| 278 LTDKEQSVLKLLLqRGGRMVQRDISYETDISKSSLSGILTSMEKRKLITKREKG 331
                                       8999*********555677889**************************998854 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5   4.6e-06    0.0063       1      51 [.     278     329 ..     278     342 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.6e-06
                                       --HHHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR   1 ltltqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                       lt  + ++L +l ++g+ + + ++     +sks+++ +l+ +ek+ li+++ 
  gi|330508654|ref|YP_004385082.1| 278 LTDKEQSVLKLLLQRGGrMVQRDISYETDISKSSLSGILTSMEKRKLITKRE 329
                                       67788899*******9988888**************************9986 PP

>> Amnionless  Amnionless
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.7e-06    0.0066     286     421 ..     127     257 ..     105     284 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.7e-06
                        Amnionless 286 deeiqivildpekgsyaerlaqelladiaehgealgilsaeletsgasssdssaagapgesaglvlgivfglvllll 362
                                       ++ ++ ++  +++  +ae   +++l+ + e g al+i++a++  +   +s +s ag +  ++++ ++  +++ l+ +
  gi|330508654|ref|YP_004385082.1| 127 SDGLDYLVYAANRSVVAEVYGHDILDPAVEIGYALQIDEATAALADTVTSAGSNAGIS--NLKMEILQYVAI-LITI 200
                                       55666667777889999999**************************999999988844..345555555666.4444 PP

                        Amnionless 363 lllillllllrrkgvlrlpqllkspsrreeveelkakldkgfdnprFdnv.esnekpeee 421
                                       llli+ +++l r++  r ++l          e++ ++++ g++n+  +   +s +k++  
  gi|330508654|ref|YP_004385082.1| 201 LLLIG-AVFLIRSSRRRSKPLGPEK-CPAAHEHMIKTQSSGHRNAEHEDQvQSAQKND-G 257
                                       55555.5555555554666643222.45666677778999*****9998853333322.2 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   0.4   7.9e-06     0.011       5      65 ..     282     339 ..     278     341 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.9e-06
                            HTH_27   5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlT 65 
                                       +  vL l+  r++r+ ++d++  +++++s+ s +l  ++++ L+++ ++   +r+  ++l+
  gi|330508654|ref|YP_004385082.1| 282 EQSVLKLLLQRGGRMVQRDISYETDISKSSLSGILTSMEKRKLITKREK---GRTNIIELS 339
                                       55678888889*********************************55544...577666665 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 ?   -1.5   0.0       2.2     3e+03      30      45 ..      76      91 ..      71      92 .. 0.84
   2 !   14.1   0.1   2.9e-05      0.04      20      52 ..     297     329 ..     296     340 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.2
                    B-block_TFIIIC 30 qdprslfyrlksLekk 45
                                       ++r l+ ++++L++k
  gi|330508654|ref|YP_004385082.1| 76 DESRQLYAITNALTSK 91
                                      5789*********986 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.9e-05
                    B-block_TFIIIC  20 tqsdLakeskqdprslfyrlksLekkgLIvkqs 52 
                                        q+d++ e++++++sl ++l s+ek +LI+k++
  gi|330508654|ref|YP_004385082.1| 297 VQRDISYETDISKSSLSGILTSMEKRKLITKRE 329
                                       699****************************86 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   8.8e-05      0.12       5      48 .]     282     326 ..     278     326 .. 0.83
   2 ?    0.1   0.0      0.43   5.9e+02      14      26 ..     329     341 ..     328     343 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.8e-05
                            HTH_24   5 drkIL.elLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       +  +L  lLq+ +r+ qr+++ ++++S+s ++  l  +e+  lI+
  gi|330508654|ref|YP_004385082.1| 282 EQSVLkLLLQRGGRMVQRDISYETDISKSSLSGILTSMEKRKLIT 326
                                       55667345666888*************************999985 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.43
                            HTH_24  14 knprisqreLAer 26 
                                       +++r+++ eL+er
  gi|330508654|ref|YP_004385082.1| 329 EKGRTNIIELSER 341
                                       799*********8 PP

>> DUF2561  Protein of unknown function (DUF2561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.7e-05     0.037      42     136 ..     166     267 ..     157     281 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                           DUF2561  42 atvaLvdL..grGfaksaedshttwvLyavivvsalvivgavPlLLrarrvaeae.....Paarargaperaaaapa 111
                                       at aL+d   + G +   ++ +   + y+ i +++l+++gav l+  +rr ++       Paa+++  +++++ +++
  gi|330508654|ref|YP_004385082.1| 166 ATAALADTvtSAGSNAGISNLKMEILQYVAILITILLLIGAVFLIRSSRRRSKPLgpekcPAAHEHMIKTQSSGHRN 242
                                       677788752255666666777788899***************99999999887653333333333222222222222 PP

                           DUF2561 112 rgadapaeraeaeeasaekaealre 136
                                       +  +   + a+ +++s+e ++++++
  gi|330508654|ref|YP_004385082.1| 243 AEHEDQVQSAQKNDGSEEFRAGMAD 267
                                       2222333334555555555555444 PP

>> Phage_TTP_12  Lambda phage tail tube protein, TTP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   6.3e-05     0.086      26     112 ..     234     322 ..     227     339 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.3e-05
                      Phage_TTP_12  26 keltpgeltadsidatylddpn.dwketiqGlksaGetsvtlaWvpGedtdkllvelf.asGevrqyrikfpnGtvd 100
                                       k    g  +a+++d+    ++n   +e+++G+ ++ e+s  +a    +  ++ l  l  + G++ q  i +   +++
  gi|330508654|ref|YP_004385082.1| 234 KTQSSGHRNAEHEDQVQSAQKNdGSEEFRAGMADTSEISAVMATLTDK-EQSVLKLLLqRGGRMVQRDISYETDISK 309
                                       555678999999999999888868999****************88755.5556655550566778999***998875 PP

                      Phage_TTP_12 101 .vfegwisslgka 112
                                        + +g ++s++k 
  gi|330508654|ref|YP_004385082.1| 310 sSLSGILTSMEKR 322
                                       2688999999885 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 ?    6.1   0.0    0.0056       7.7      53      94 ..     155     196 ..     153     201 .. 0.93
   2 ?    4.7   0.1     0.015        21     106     147 ..     307     344 ..     271     347 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0056
                          SMC_ScpB  53 vaggyrlvtkpelaevvkklvkekkktrLsqaaletLaiIay 94 
                                       v+ gy l++ ++ a ++ ++++  +++ +s+ ++e+L ++a+
  gi|330508654|ref|YP_004385082.1| 155 VEIGYALQIDEATAALADTVTSAGSNAGISNLKMEILQYVAI 196
                                       6679************************************97 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.015
                          SMC_ScpB 106 iRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFle 147
                                       i  ++ ++++ ++ +r+li++++    +gr+ + +++e+F +
  gi|330508654|ref|YP_004385082.1| 307 ISKSSLSGILTSMEKRKLITKRE----KGRTNIIELSERFKN 344
                                       56677899************999....999999999999975 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 ?   11.9   0.6   0.00012      0.16      21      57 ..     295     335 ..     274     341 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E..TEE.E CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis.r..grr.i 57 
                                       ++ q++++    ++ +++s il+ +++++li+ r  gr+ i
  gi|330508654|ref|YP_004385082.1| 295 RMVQRDISYETDISKSSLSGILTSMEKRKLITkRekGRTnI 335
                                       5779999*************************643233343 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.26       5      28 ..     277     300 ..     274     303 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                       E-SHHHHHHHHHHHHTTTSEEEHH CS
                       Trans_reg_C   5 eltpkefklLelLlenpgrvvsre 28 
                                       +lt ke ++L+lLl++ gr+v+r+
  gi|330508654|ref|YP_004385082.1| 277 TLTDKEQSVLKLLLQRGGRMVQRD 300
                                       79*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 2691.01
//
Query:       gi|330508655|ref|YP_004385083.1|  [L=107]
Description: hypothetical protein MCON_2904 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.5e-06   25.6   0.8    1.8e-05   24.7   0.8    1.5  1  HTH_20       Helix-turn-helix domain
  ------ inclusion threshold ------
      0.079   13.5   0.1       0.15   12.6   0.1    1.4  1  AAA_assoc_C  C-terminal AAA-associated domain
      0.081   13.0   0.3       0.12   12.4   0.3    1.4  1  HemN_C       HemN C-terminal domain
       0.09   12.7   0.5       0.52   10.2   0.5    2.1  1  HTH_5        Bacterial regulatory protein, arsR family
       0.12   12.4   0.1       0.28   11.2   0.1    1.6  1  HTH_29       Winged helix-turn helix


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.8     5e-09   1.8e-05       2      57 ..      21      73 ..      20      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5e-09
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      ++++AL +P Rrr+l +   ++ lt+ ++a++++  +  l+y+L+ Le agL+ev 
  gi|330508655|ref|YP_004385083.1| 21 MVHHALENPIRRRMLILM-NEGHLTVDAIAKEVG--DRMLDYQLHRLELAGLLEVH 73
                                      799************999.*************75..555********99*****97 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 ?   12.6   0.1   4.1e-05      0.15      20      43 ..      63      86 ..      54     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                       AAA_assoc_C 20 aaelLglveveegdielTelGrkf 43
                                       +el gl+ev++g+i+lT++G ++
  gi|330508655|ref|YP_004385083.1| 63 RLELAGLLEVHDGQITLTDAGLAY 86
                                      67899****************876 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   3.4e-05      0.12      41      65 ..      60      84 ..      34      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                            HemN_C 41 aleklqeqGLLeldggrlrltprGr 65
                                      +l +l+ +GLLe ++g + lt++G+
  gi|330508655|ref|YP_004385083.1| 60 QLHRLELAGLLEVHDGQITLTDAGL 84
                                      799********************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 ?   10.2   0.5   0.00015      0.52       1      44 [.      28      69 ..      28      72 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGL 44
                                      +p R+++L l++eg l+v  +a+e+g     ++++L +L+ aGL
  gi|330508655|ref|YP_004385083.1| 28 NPIRRRMLILMNEGHLTVDAIAKEVG--DRMLDYQLHRLELAGL 69
                                      699********************987..4456666666666666 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   7.9e-05      0.28       1      23 [.      31      53 ..      31      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.9e-05
                            HTH_29  1 RaqallllaeGvstvsqiAkllg 23
                                      R ++l+l++eG+ tv  iAk +g
  gi|330508655|ref|YP_004385083.1| 31 RRRMLILMNEGHLTVDAIAKEVG 53
                                      77899***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 792.69
//
Query:       gi|330508656|ref|YP_004385084.1|  [L=350]
Description: tRNA-splicing endonuclease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-49  165.7   0.2    1.3e-23   82.8   0.0    2.4  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    2.6e-39  132.7   0.4    2.1e-20   72.1   0.0    2.5  2  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
     0.0013   18.9   0.4       0.56   10.4   0.1    2.4  2  tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-t


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.0   2.2e-27   1.3e-23       1      85 []      79     162 ..      79     162 .. 0.98
   2 !   80.6   0.2   1.1e-26   6.6e-23       1      79 [.     257     338 ..     257     342 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 2.2e-27
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE..TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY..qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklila 75 
                                       f+ +y+vy+dLre+Gy+v++G     dFrvY  +++p+++ +e+ V+v+se+ +l+++d+++ vrla +++Kkl+la
  gi|330508656|ref|YP_004385084.1|  79 FEFRYVVYKDLRERGYYVQPG---RPDFRVYprGGHPGKGPAEFYVLVISERNPLPLKDIMEPVRLAGQMRKKLMLA 152
                                       899******************...67*************************************************** PP

                                       EETTTSCEEE CS
                     tRNA_int_endo  76 ivdaegdvty 85 
                                       ivd+e d+t+
  gi|330508656|ref|YP_004385084.1| 153 IVDEESDITF 162
                                       ********96 PP

  == domain 2  score: 80.6 bits;  conditional E-value: 1.1e-26
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE...TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY...qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklil 74 
                                       f+lk+ +yrdLrek +vv++G+kFG++FrvY   ++  +  hseylV+ ++ d+ + +p ls+avrlahsv+K +++
  gi|330508656|ref|YP_004385084.1| 257 FELKLGAYRDLREKSLVVKTGFKFGTHFRVYkqvHGTLKVPHSEYLVHAIPLDHVFMPPVLSRAVRLAHSVRKLMVF 333
                                       899****************************9888888999************************************ PP

                                       EEETT CS
                     tRNA_int_endo  75 aivda 79 
                                       a+ d+
  gi|330508656|ref|YP_004385084.1| 334 AYPDD 338
                                       **965 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 !   58.4   0.1     7e-20   4.2e-16       2      67 .]       6      69 ..       5      69 .. 0.95
   2 !   72.1   0.0   3.5e-24   2.1e-20       3      65 ..     183     245 ..     182     247 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 7e-20
                                      EEEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHHH CS
                   tRNA_int_endo_N  2 egeLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevvkggeplsfeell 67
                                      ++++++dr+ +   ea  +l+e+g++G+  +++ L+LslvEA+YLl++ ++++++++++l+f+ ++
  gi|330508656|ref|YP_004385084.1|  6 RAQFEDDRIRLGP-EALPELFEQGYFGR-PKGKGLELSLVEAAYLLDRSRIKIMRNEKELDFRSFF 69
                                      7899********7.99************.8********************************9985 PP

  == domain 2  score: 72.1 bits;  conditional E-value: 3.5e-24
                                       EEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEE.TTSEEE-HHH CS
                   tRNA_int_endo_N   3 geLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevv.kggeplsfee 65 
                                       ++L++drv+++d+ea++ l+e+gf+Gk   +e+LqLslvE++YLlekGkl+++ ++g+p+++  
  gi|330508656|ref|YP_004385084.1| 183 ATLLEDRVVLWDTEASRLLHESGFFGK-PVGERLQLSLVESAYLLEKGKLQLTdRQGRPVDLPA 245
                                       68*************************.8******************************99765 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 !    6.4   0.0    0.0017       9.9      43      70 ..      31      56 ..      20      58 .. 0.84
   2 !   10.4   0.1   9.4e-05      0.56      23      70 ..     187     233 ..     133     235 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0017
                   tRNA_int_end_N2 43 Gvsra.rrgrlwLlpeEaLYLvErGsldi 70
                                      G   + + + l+L   Ea YL++r +++i
  gi|330508656|ref|YP_004385084.1| 31 G---RpKGKGLELSLVEAAYLLDRSRIKI 56
                                      3...448899**************99887 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9.4e-05
                   tRNA_int_end_N2  23 rdrvvvvespkarGkhfktmGvsra.rrgrlwLlpeEaLYLvErGsldi 70 
                                       +drvv  + +     +++  G   +    rl L   E  YL+E G+l++
  gi|330508656|ref|YP_004385084.1| 187 EDRVVLWDTE--ASRLLHESGFFGKpVGERLQLSLVESAYLLEKGKLQL 233
                                       5666666644..66777777766677899******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); 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):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2629.59
//
Query:       gi|330508657|ref|YP_004385085.1|  [L=384]
Description: hypothetical protein MCON_2908 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2724.92
//
Query:       gi|330508658|ref|YP_004385086.1|  [L=161]
Description: hypothetical protein MCON_2909 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-19   69.0   0.3    5.3e-19   68.7   0.3    1.2  1  APS_kinase       Adenylylsulphate kinase
    3.8e-06   27.1   0.3    4.9e-06   26.7   0.3    1.2  1  AAA_33           AAA domain
    0.00013   21.8   0.0     0.0002   21.2   0.0    1.2  1  CPT              Chloramphenicol phosphotransferase-like prot
  ------ inclusion threshold ------
      0.016   15.7   0.3      0.023   15.3   0.3    1.2  1  AAA_18           AAA domain
      0.033   13.6   0.1      0.036   13.5   0.1    1.1  1  KTI12            Chromatin associated protein KTI12
      0.053   13.7   0.1        0.1   12.7   0.1    1.6  1  Cytidylate_kin2  Cytidylate kinase-like family


Domain annotation for each model (and alignments):
>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.3   1.8e-22   5.3e-19      21     154 ..       2     139 ..       1     143 [. 0.92

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1.8e-22
                                       HHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEEEE----SHHHHHHHHHHHH CS
                        APS_kinase  21 alekkLvekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivlvafisPyreeReaarelle 97 
                                       +++k+L+e+gi+v++L+ d++R+ ++ +  ++ee+R+     +a + k la+++  v++ + +  r+ R+ ar+l+ 
  gi|330508658|ref|YP_004385086.1|   2 EVKKRLQERGIEVKILQLDEIRRVITPEPKYTEEERDIVYASLAYMGKILAEENKNVIIDATANRRRYRDLARQLIP 78 
                                       7899************************************************************************* PP

                                       CHTEEEEEEEE--HHHHHHHT........TTSHHHHHHTTSSSSHTTTSS-----SS-SEEEETT CS
                        APS_kinase  98 ealkfievfvdtplevceerD........pkglYkkareGeikeftGidspYeaPenpelvvdtd 154
                                          +f evf+++plevc++r+        pk +Ykka + +   ++G++ +Ye+P +pe++vd++
  gi|330508658|ref|YP_004385086.1|  79 ---NFAEVFIRAPLEVCMDREerrnaafsPKDIYKKAGR-KNALVPGVNVAYEEPISPEIEVDAA 139
                                       ...4*************98864444555589******88.66789*****************975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.3   1.7e-09   4.9e-06      20     121 ..       7     102 ..       2     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.7e-09
                            AAA_33  20 lkklg..avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnlsrrerarflklarr 94 
                                       l+++g  + +l  d++rr ++++    +++  + +d +y+ l+ + ++ +++++nvi+dat  +rr r+  ++l + 
  gi|330508658|ref|YP_004385086.1|   7 LQERGieVKILQLDEIRRVITPE----PKYTEEERDIVYASLAYMGKILAEENKNVIIDATANRRRYRDLARQLIP- 78 
                                       55666445557777777777754....3344456677888887777777889999*******99999999999999. PP

                            AAA_33  95 lgvpvrivvvetdeetlkeRlakRaan 121
                                          +++ v+++++ e++ +R ++R+a+
  gi|330508658|ref|YP_004385086.1|  79 ---NFAEVFIRAPLEVCMDREERRNAA 102
                                       ...5778*****************996 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   6.8e-08    0.0002      61     172 ..      33     153 ..       4     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.8e-08
                                       E-HHHHHHHHHHHHHHHHHHHTT-EEEEEE--TTTHHHHHHHHHHHTTS-EEEEEEE--HHHHHHHHHHHTS..... CS
                               CPT  61 igpeldlllaalyeavaamaraGnnvivDdvilekewlvdllrrllsgldvllVGvrcplevlerRelergd..... 132
                                       ++ e+d ++a+l+   +  a++ +nvi+D +  +++   dl+r+l+ ++    V +r+plev   Re +r       
  gi|330508658|ref|YP_004385086.1|  33 TEEERDIVYASLAYMGKILAEENKNVIID-ATANRRRYRDLARQLIPNF--AEVFIRAPLEVCMDREERRNAafspk 106
                                       378889999999999999999********.66666668********665..55668***********9998878888 PP

                                       .......SSTTHHHHHTTGGGTT---SEEEETTSS-HHHHHHHHHTT CS
                               CPT 133 .......RepGlaalqaeavHagaeyDlevDtsaktpeecArairer 172
                                              R+  l      a  ++++  +evD++ + p e+   i++r
  gi|330508658|ref|YP_004385086.1| 107 diykkagRKNALVPGVNVAYEEPISPEIEVDAAVSSPLESSSYIADR 153
                                       88844444433444444445567788889999988888888888776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   7.5e-06     0.023      14     114 ..       3     100 ..       1     113 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.5e-06
                            AAA_18  14 lakeLskrlgfgvnlrdvakenglllevdpe..aldeskrldedkldklldaleenssaleegknlvidghlaeles 88 
                                       + k+L++r+    +  ++++ ++++   +pe   ++e++ ++   l++  ++l e      e+kn++id   +  ++
  gi|330508658|ref|YP_004385086.1|   3 VKKRLQERG----IEVKILQLDEIRRVITPEpkYTEEERDIVYASLAYMGKILAE------ENKNVIIDATANRRRY 69 
                                       667777773....556788888888888888656666666666666666666666......56899***99998887 PP

                            AAA_18  89 eaakdikk......vvLtaspeelleRlekRg 114
                                        ++ +         v+++a+ e++++R e+R+
  gi|330508658|ref|YP_004385086.1|  70 RDLARQ-LipnfaeVFIRAPLEVCMDREERRN 100
                                       766643.3589****************99997 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.2e-05     0.036      20     126 ..       2     104 ..       1     144 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHTT--EEEE-THHHH...TTSSS--GGGHHHHHHHHHHHHHHHH.TT.SEEEE-S---SHHHHHHHHHHH CS
                             KTI12  20 eLakaleeekrsvvviddeslg..iekdsykdsakekalRsslrsavkrdL.skekvVIvDslnyikgfRYeLycia 93 
                                       e++k l+e++++v +++ + ++  i+ ++ k +++e+++  +  + + + L +++k VI+D+++  + +R     +a
  gi|330508658|ref|YP_004385086.1|   2 EVKKRLQERGIEVKILQLDEIRrvITPEP-KYTEEERDIVYASLAYMGKILaEENKNVIIDATANRRRYR----DLA 73 
                                       67899************888887644444.556667776666666666655267899******9888887....58* PP

                                       HHTT-EEEEEEEE--HHHHHHHHHHTT-S..S- CS
                             KTI12  94 kaakttlcvvyvvapldvlvkwneereekeeye 126
                                       ++   +++ v++ apl+v++ ++e r+ +  ++
  gi|330508658|ref|YP_004385086.1|  74 RQLIPNFAEVFIRAPLEVCMDREERRNAA--FS 104
                                       ***********************999977..43 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.5e-05       0.1     112     149 ..      77     115 ..      29     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                   Cytidylate_kin2 112 rpnvlrvfltapledrvkrvaere.glseeearekiket 149
                                       +pn   vf+ aple++++r ++r+   s++++++k  ++
  gi|330508658|ref|YP_004385086.1|  77 IPNFAEVFIRAPLEVCMDREERRNaAFSPKDIYKKAGRK 115
                                       789999*************99999566999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1218.68
//
Query:       gi|330508659|ref|YP_004385087.1|  [L=106]
Description: hypothetical protein MCON_2911 [Methanosaeta concilii GP6]
Scores for complete sequence (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  131.4   0.5    1.5e-38  131.0   0.5    1.2  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 !  131.0   0.5   8.2e-43   1.5e-38       1      96 []      19     104 ..      19     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 131.0 bits;  conditional E-value: 8.2e-43
                               MC1   1 dkrnfalrdedGeeisvfsGkqPrqaaLkaarrletadseeeakeeeirLrekGtkkvhiyegkaeeeeaPddkpdW 77 
                                       +krnfalrd++G+ei+vfsGkqPrqaaLkaa+r+ t+          irLre+Gtkkvhi++g++ ++ +P+++p+W
  gi|330508659|ref|YP_004385087.1|  19 EKRNFALRDKEGNEIGVFSGKQPRQAALKAANRGFTD----------IRLRERGTKKVHIFQGERIQVPKPSNAPKW 85 
                                       79**********************************9..........****************************** PP

                               MC1  78 ledkitkanvskqgiekle 96 
                                       ++++i+k+nv+k g+ekle
  gi|330508659|ref|YP_004385087.1|  86 MPANIWKPNVKKLGVEKLE 104
                                       *****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 799.89
//
Query:       gi|330508660|ref|YP_004385088.1|  [L=104]
Description: 50S ribosomal protein L12 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-16   59.4  17.7    4.8e-16   59.1  17.7    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
  ------ inclusion threshold ------
       0.01   16.0   3.7      0.015   15.5   3.7    1.3  1  TetR_C_31      Tetracyclin repressor-like, C-terminal domain
       0.22   11.9   0.0       0.33   11.3   0.0    1.3  1  EF-hand_14     EF-hand domain
        1.5    7.4   7.2        1.9    7.1   7.2    1.0  1  Adeno_PV       Adenovirus minor core protein PV


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 !   59.1  17.7   1.1e-19   4.8e-16       2      88 .]      17     103 ..      16     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 1.1e-19
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX CS
                     Ribosomal_60s   2 ptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEe 78 
                                       +t+e ik+v+ a+gv ++++r+k+lv+aleg+di ++l+++aa  +aaaaa+ aaaaaa a+aa+eek++ +e++ e
  gi|330508660|ref|YP_004385088.1|  17 VTEEGIKNVVAASGVAADDVRIKALVAALEGVDISKVLSQAAAVPVAAAAAPVAAAAAATAPAAKEEKEESKEAA-E 92 
                                       89***************************************9996677777777777777777777777777765.4 PP

                                       --SS--.STTT CS
                     Ribosomal_60s  79 edddmG.fgLF 88 
                                       e   +G ++LF
  gi|330508660|ref|YP_004385088.1|  93 ESGVEGlGALF 103
                                       55577777998 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 ?   15.5   3.7   3.3e-06     0.015      51     102 ..      18      71 ..       8      81 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.3e-06
                                       HHHHHHHHHHHHCSS-HHHHHHHHHHHHHHHHHHHHHSG.TS-H.HHHHHHHHH CS
                         TetR_C_31  51 lrealaallaalGlpdpeeaarllvaaldGllldrLagp.aadp.raevrellr 102
                                        +e +  ++aa+G+++++ ++ +lvaal+G+ ++ +  + aa p +a+++ + +
  gi|330508660|ref|YP_004385088.1|  18 TEEGIKNVVAASGVAADDVRIKALVAALEGVDISKVLSQaAAVPvAAAAAPVAA 71 
                                       566778899*****77777************99999887533333222222222 PP

>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.3e-05      0.33      16      52 ..      16      52 ..       3      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.3e-05
                        EF-hand_14 16 klsvakllkaLaetGirkdDpRLkellkklkkvekek 52
                                      ++  + + +++a++G+  dD R+k l+ +l+ v+ +k
  gi|330508660|ref|YP_004385088.1| 16 DVTEEGIKNVVAASGVAADDVRIKALVAALEGVDISK 52
                                      55666778899*******************9887665 PP

>> Adeno_PV  Adenovirus minor core protein PV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   7.2   0.00042       1.9     200     265 ..      17      82 ..      10      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00042
                          Adeno_PV 200 vrvrpikqvapglgvqtvdvqipttsstsiatategmetqtspvasavadaavqaaaaaasktste 265
                                       v    ik+v    gv + dv+i +  ++        + +q++ v  a a a v aaaaa++ ++ e
  gi|330508660|ref|YP_004385088.1|  17 VTEEGIKNVVAASGVAADDVRIKALVAALEGVDISKVLSQAAAVPVAAAAAPVAAAAAATAPAAKE 82 
                                       566789****************99888877777777778888777777777777777776655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1218  (0.0679346); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 769.48
//
Query:       gi|330508661|ref|YP_004385089.1|  [L=324]
Description: 50S ribosomal protein L10 [Methanosaeta concilii GP6]
Scores for complete 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-22   77.3   0.0    1.6e-21   76.3   0.0    1.5  1  Ribosomal_L10  Ribosomal protein L10
    4.2e-20   71.5   1.2    1.7e-19   69.6   0.4    2.3  3  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    3.4e-07   30.7  10.6    7.8e-07   29.6   9.5    2.3  2  Ribosomal_60s  60s Acidic ribosomal protein


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.0   2.7e-25   1.6e-21       2      97 ..      11     106 ..      10     108 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 2.7e-25
                                       SCCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.S.SCGCCSS CS
                     Ribosomal_L10   2 tkekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeek.lkellkg 77 
                                        +e+K + v+el ++++k+++v vv ++++++ +lq++R +lr+n +e+++v+nt++rrAle ++ + k l+++++ 
  gi|330508661|ref|YP_004385089.1|  11 IPEWKVKEVDELVDKISKSRVVGVVGLREIPADNLQKMRGDLRGN-VEIRMVRNTIARRALEASPVQIKpLADFIED 86 
                                       589******************************************.*******************96447******* PP

                                       SEEEEEESS-TCHHHHCCCC CS
                     Ribosomal_L10  78 pvalvftnedpvalakvlee 97 
                                       ++al+f++ +p++l ++le+
  gi|330508661|ref|YP_004385089.1|  87 QTALIFSDLNPFKLNSMLEK 106
                                       ****************9997 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 ?   -1.8   0.0      0.55   3.3e+03      23      42 ..      89     108 ..      64     108 .. 0.73
   2 !   69.6   0.4   2.8e-23   1.7e-19       2      71 .]     114     183 ..     114     183 .. 0.99
   3 ?   -2.2   0.0      0.71   4.2e+03      21      33 ..     236     248 ..     212     252 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.55
                      RL10P_insert  23 gsiepeLrklglptklkkGk 42 
                                       + i + L+  +l+  l+kGk
  gi|330508661|ref|YP_004385089.1|  89 ALIFSDLNPFKLNSMLEKGK 108
                                       45667788888888888886 PP

  == domain 2  score: 69.6 bits;  conditional E-value: 2.8e-23
                      RL10P_insert   2 raGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                       +aGt A++d++i+ag+++  Pg+++ +L+++g+p+ +k Gk+v++++ +++k+Ge++ ++ a++Lk ++i
  gi|330508661|ref|YP_004385089.1| 114 KAGTRAPKDIVIEAGETSFSPGPMVGKLQAAGIPAAIKGGKVVINQKITLAKEGEVVPAKTAEILKTMEI 183
                                       89*****************************************************************998 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.71
                      RL10P_insert  21 aPgsiepeLrklg 33 
                                       +P++i p L+k++
  gi|330508661|ref|YP_004385089.1| 236 TPATIGPMLQKAQ 248
                                       3899999999875 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.6   1.6e+04      32      45 ..      16      29 ..      10      34 .. 0.76
   2 !   29.6   9.5   1.3e-10   7.8e-07       1      88 []     234     323 ..     234     323 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.6
                                      XXXXXXXXXXXXXX CS
                     Ribosomal_60s 32 gkdieellangaak 45
                                       k+++el+ +++++
  gi|330508661|ref|YP_004385089.1| 16 VKEVDELVDKISKS 29
                                      58899998888765 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1.3e-10
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaakla....aaaaaaaaaaaaaaaaaaaeekkkee 73 
                                       +pt ++i  +l++a +++ a  +++   ++    +e +la++aa+++     a +  a aa+aa aa+aaeek++e+
  gi|330508661|ref|YP_004385089.1| 234 YPTPATIGPMLQKAQTKARALVLDA--GMIIPSMMEFILAKAAANASaiagLASGQKAQAAPAATAAPAAEEKQEEK 308
                                       5999999*******99655555555..55555555666666666666665544455555666666666666666666 PP

                                       XX.XX--SS--.STTT CS
                     Ribosomal_60s  74 eeeEeedddmG.fgLF 88 
                                       +e Ee d ++G ++LF
  gi|330508661|ref|YP_004385089.1| 309 KE-EEGDTAAGlGALF 323
                                       66.78999***99**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2525.39
//
Query:       gi|330508662|ref|YP_004385090.1|  [L=210]
Description: 50S ribosomal protein L1P [Methanosaeta concilii GP6]
Scores for complete sequence (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  165.7   0.0    1.3e-48  165.4   0.0    1.0  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4   0.0   7.3e-53   1.3e-48       6     204 .]      16     205 ..       7     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 7.3e-53
                                       -SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT CS
                      Ribosomal_L1   6 kkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyk 82 
                                        +kf+esv++a+nl +++   + +r+  ++ Lph+lgk++ki++++++++a     ak+ag  ++vi+++++k+   
  gi|330508662|ref|YP_004385090.1|  16 ARKFAESVDLAINLHNIDLSLPGNRVDAEVILPHGLGKPTKIAVFAAGETAL---RAKSAG-ADRVISGDEIKEFAG 88 
                                       689*************************************************...9*****.*************** PP

                                       -HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEE CS
                      Ribosomal_L1  83 sfeakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsv 159
                                       +++a rkl++e+++f+a+ + mp ++k LG+++gkr+kmP+p       ++dv+ +v+++++  + +r+++  ++++
  gi|330508662|ref|YP_004385090.1|  89 DKRAARKLADEYKFFIAETQFMPVIGKSLGSILGKRGKMPTPL--P--PTQDVTPQVQRLKN-MTRIRSRDRPTFHL 160
                                       *******************************************..4..368***********.6699********** PP

                                       EEEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS- CS
                      Ribosomal_L1 160 kvGklsftaeelaeNieavvkalvekvpkkwkniksiylkttmsp 204
                                        +G+ +++++ela+Nieavv +l++ ++ +  n+ks+y+kttm+p
  gi|330508662|ref|YP_004385090.1| 161 TIGNRNMNTKELADNIEAVVVKLEQTLKDGRHNLKSVYVKTTMGP 205
                                       ********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1652.35
//
Query:       gi|330508663|ref|YP_004385091.1|  [L=158]
Description: 50S ribosomal protein L11 [Methanosaeta concilii GP6]
Scores for complete 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   75.9   0.6    2.5e-21   75.3   0.6    1.4  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    2.4e-18   66.4   1.5    8.8e-18   64.6   1.0    1.9  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 !   75.3   0.6   2.8e-25   2.5e-21       5      61 ..       2      58 ..       1      62 [. 0.93

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 2.8e-25
                   Ribosomal_L11_N  5 vkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyq 61
                                      ++vv+  vp+GkA+++PplGpaLGplG+n+++++ ++n++T+d +g+++pVk+ v++
  gi|330508663|ref|YP_004385091.1|  2 ANVVEALVPGGKASAGPPLGPALGPLGVNVAQVVAKINEETSDLNGMQVPVKVIVKS 58
                                      679999*************************************************54 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 ?   -0.1   0.0      0.15   1.3e+03      38      58 ..      35      58 ..      23      58 .. 0.66
   2 !   64.6   1.0   9.8e-22   8.8e-18       2      70 .]      68     133 ..      67     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.15
                                      HHHHHGG..GHT.XS.SHHHHHHH CS
                     Ribosomal_L11 38 IAkiKks..dln.aalsleaavks 58
                                      +Aki  +  dln ++++++ +vks
  gi|330508663|ref|YP_004385091.1| 35 VAKINEEtsDLNgMQVPVKVIVKS 58
                                      344444322788888888888876 PP

  == domain 2  score: 64.6 bits;  conditional E-value: 9.8e-22
                                       --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                     Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                       tPpts+l++k++g ekg+g   k+t+G+++++qv +IA iK++ l ++ sl++a+++++gtA s+G +V
  gi|330508663|ref|YP_004385091.1|  68 TPPTSALIIKEVGGEKGTGD--KTTIGDLTMEQVLKIANIKRKGLLSK-SLKNAAREVIGTAGSVGATV 133
                                       9****************999..589*****************999988.*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.19s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1362.29
//
Query:       gi|330508664|ref|YP_004385092.1|  [L=151]
Description: 50S ribosomal protein L24 [Methanosaeta concilii GP6]
Scores for complete 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   82.2   0.1    2.6e-23   81.7   0.1    1.2  1  Spt5-NGN         Early transcription elongation factor of RNA
      9e-09   35.0   0.4    1.9e-06   27.6   0.1    2.4  2  KOW              KOW motif
  ------ inclusion threshold ------
      0.061   13.2   0.3      0.098   12.6   0.3    1.3  1  Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal dom


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.1   4.4e-27   2.6e-23       1      84 []       5      84 ..       5      84 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 4.4e-27
                          Spt5-NGN  1 siwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikE 79
                                      si+ vk+ta+qEr+va ++++     a+ke+++I++ ++pd lkGy++vE++ ++ v++a++gip++r+v +g ++i E
  gi|330508664|ref|YP_004385092.1|  5 SIYVVKTTANQERSVANMIAQI----ARKEKYDIRALLVPDVLKGYVLVESPAPEIVDQAIQGIPHARSVIKGASNIGE 79
                                      69*****************998....89999************************************************ PP

                          Spt5-NGN 80 vedll 84
                                      ve++l
  gi|330508664|ref|YP_004385092.1| 80 VEHFL 84
                                      ***98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   3.2e-10   1.9e-06       2      32 .]      96     126 ..      95     126 .. 0.95
   2 !    5.4   0.0    0.0031        19       1       9 [.     139     147 ..     139     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.2e-10
                                       TSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW   2 GdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32 
                                       G +V+ +sGp+kG++++V++vd  k+ ++v+
  gi|330508664|ref|YP_004385092.1|  96 GAIVELISGPFKGEKARVKRVDLAKEEITVE 126
                                       999**********************999997 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0031
                                       TTSEEEESS CS
                               KOW   1 pGdhVkVvs 9  
                                       +GdhV+V+s
  gi|330508664|ref|YP_004385092.1| 139 RGDHVRVLS 147
                                       6******97 PP

>> Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   1.6e-05     0.098      22      51 .]     115     145 ..     112     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                                       EEEEESSEEEEEEES.SSTEEEEETTEEEEE CS
                   Glyco_hydro_65C  22 rVrvtpeevtvtles.gepltievyGeevtL 51 
                                       rV++++ee+tv+l +   p++i+v+G  v++
  gi|330508664|ref|YP_004385092.1| 115 RVDLAKEEITVELFEaMVPIPITVRGDHVRV 145
                                       799***********8455*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1126.72
//
Query:       gi|330508665|ref|YP_004385093.1|  [L=198]
Description: hypothetical protein MCON_2917 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-05   23.6   0.0       0.23   11.3   0.0    2.9  2  HTH_23        Homeodomain-like domain
    0.00019   20.9   0.0       0.26   10.9   0.0    3.2  3  GerE          Bacterial regulatory proteins, luxR family
    0.00022   20.9   0.0      0.044   13.5   0.0    2.5  2  HTH_38        Helix-turn-helix domain
    0.00052   19.6   0.0      0.056   13.1   0.0    2.6  2  Sigma70_r4_2  Sigma-70, region 4
     0.0021   18.1   0.2      0.039   14.0   0.0    2.6  3  HTH_3         Helix-turn-helix
     0.0045   16.6   0.0       0.15   11.7   0.0    2.3  2  CENP-B_N      CENP-B N-terminal DNA-binding domain
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.027   14.3   0.0    1.7  1  HTH_5         Bacterial regulatory protein, arsR family
      0.028   13.9   0.0      0.051   13.1   0.0    1.4  1  MazG_C        MazG C-terminal domain
      0.035   14.4   0.0       0.26   11.6   0.0    2.2  2  HTH_Tnp_1     Transposase
      0.041   14.3   0.0      0.057   13.8   0.0    1.4  1  GcrA          GcrA cell cycle regulator
      0.046   13.8   0.0         12    6.0   0.0    2.4  2  HTH_7         Helix-turn-helix domain of resolvase
      0.058   12.8   0.0       0.42   10.0   0.0    2.4  3  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
      0.063   13.4   0.0       0.71   10.1   0.0    2.4  3  HTH_28        Helix-turn-helix domain
      0.074   12.6   0.4       0.55    9.8   0.1    2.7  3  Sigma70_r4    Sigma-70, region 4


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 !    9.3   0.0   0.00079         1      10      28 ..      67      85 ..      63     106 .. 0.95
   2 !   11.3   0.0   0.00018      0.23      10      41 ..     117     148 ..     113     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00079
                            HTH_23 10 illllaeGlsvreIAreLg 28
                                      +++l+ +Gls +eIA++Lg
  gi|330508665|ref|YP_004385093.1| 67 VVRLFYKGLSDTEIAEQLG 85
                                      8999**************8 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00018
                            HTH_23  10 illllaeGlsvreIAreLgvsrrTvyrwlkry 41 
                                        ++l+    sv++ A++L v ++T++ +++ +
  gi|330508665|ref|YP_004385093.1| 117 FIRLAEANRSVKDMAEALRVAPSTISEYRNIF 148
                                       689999999*****************999988 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    0.0002      0.26       9      28 ..      66      85 ..      57      99 .. 0.83
   2 !    6.0   0.0    0.0065       8.3      17      38 ..     124     145 ..     116     148 .. 0.84
   3 ?   -1.0   0.0      0.99   1.3e+03      27      38 ..     170     181 ..     164     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                      HHHHHHCTTS-HHHHHHHHT CS
                              GerE  9 evLrllaeGksnkeIAeeln 28
                                      +v rl+++G+s +eIAe+l+
  gi|330508665|ref|YP_004385093.1| 66 SVVRLFYKGLSDTEIAEQLG 85
                                      799***************97 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0065
                                       TS-HHHHHHHHTS-HHHHHHHH CS
                              GerE  17 GksnkeIAeelniSekTVkvhk 38 
                                         s+k+ Ae+l +++ T++ ++
  gi|330508665|ref|YP_004385093.1| 124 NRSVKDMAEALRVAPSTISEYR 145
                                       5689**************9887 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.99
                                       HTS-HHHHHHHH CS
                              GerE  27 lniSekTVkvhk 38 
                                        ++Se+ V+vh 
  gi|330508665|ref|YP_004385093.1| 170 QDVSERMVTVHT 181
                                       589999999996 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.019        24       4      31 ..      58      85 ..      56      88 .. 0.85
   2 !   13.5   0.0   3.4e-05     0.044      15      38 ..     119     142 ..     117     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.019
                            HTH_38  4 hLsleeReeIerllaeGlslreIArrLg 31
                                      +L++e+     rl  +Gls  eIA +Lg
  gi|330508665|ref|YP_004385093.1| 58 KLTPEQLSSVVRLFYKGLSDTEIAEQLG 85
                                      677777777779999***********98 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.4e-05
                            HTH_38  15 rllaeGlslreIArrLgrspsTIs 38 
                                       rl +++ s++++A  L ++psTIs
  gi|330508665|ref|YP_004385093.1| 119 RLAEANRSVKDMAEALRVAPSTIS 142
                                       577899*****************8 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   4.4e-05     0.056      12      54 .]      61     100 ..      58     102 .. 0.88
   2 ?    3.7   0.0     0.039        49      20      43 ..     118     141 ..     110     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                                       -HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  12 perqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                       pe+ + ++ l +++gls  EIAe+lg  +++ ++ +sRAr kL
  gi|330508665|ref|YP_004385093.1|  61 PEQLSSVVRL-FYKGLSDTEIAEQLG--DRALNKTVSRARIKL 100
                                       6777888888.89************6..999999999999887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.039
                                       HHHHTS---HHHHHHHHT--HHHH CS
                      Sigma70_r4_2  20 llryleglsykEIAellgisegtV 43 
                                       +  ++ + s k+ Ae l + ++t+
  gi|330508665|ref|YP_004385093.1| 118 IRLAEANRSVKDMAEALRVAPSTI 141
                                       55567788*************997 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.6   3.3e+03       1      17 [.      50      66 ..      50      70 .. 0.77
   2 ?    0.6   0.0      0.49   6.2e+02       8      20 ..      73      85 ..      73      98 .. 0.77
   3 !   14.0   0.0   3.1e-05     0.039       5      29 ..     119     144 ..     117     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.6
                                      HHHHHHHTTHHHHHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAe 17
                                      +k++  q +l+ e+L+ 
  gi|330508665|ref|YP_004385093.1| 50 IKQYNIQTKLTPEQLSS 66
                                      78888888999999875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.49
                                      TTHHHHHHHHHHT CS
                             HTH_3  8 lglsqeeLAeklG 20
                                      +gls +e+Ae lG
  gi|330508665|ref|YP_004385093.1| 73 KGLSDTEIAEQLG 85
                                      699999***9999 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3.1e-05
                                       HH.HTTHHHHHHHHHHTSSHHHHHHH CS
                             HTH_3   5 Rk.qlglsqeeLAeklGvsrstisri 29 
                                       R+ +++ s +++Ae+l v +stis +
  gi|330508665|ref|YP_004385093.1| 119 RLaEANRSVKDMAEALRVAPSTISEY 144
                                       66699*******************99 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.092   1.2e+02       5      33 ..      57      85 ..      49      95 .. 0.90
   2 !   11.7   0.0   0.00011      0.15      11      41 ..     113     143 ..     111     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.092
                                      SS--HHHHHHHHHHHHCTT-HHHHHHHHT CS
                          CENP-B_N  5 rsLTlreKievIqrleegeSkaelarrfn 33
                                      + LT+++ + v+++   g S  e+a +++
  gi|330508665|ref|YP_004385093.1| 57 TKLTPEQLSSVVRLFYKGLSDTEIAEQLG 85
                                      78*************99999999997765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHCTT-HHHHHHHHT--CCHHHH CS
                          CENP-B_N  11 eKievIqrleegeSkaelarrfnvpestlsd 41 
                                       +K e I++ e + S+++ a  + v +st+s+
  gi|330508665|ref|YP_004385093.1| 113 DKDEFIRLAEANRSVKDMAEALRVAPSTISE 143
                                       78899************************96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.1e-05     0.027      11      34 ..     120     143 ..     119     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                                       HTTSSEEHHHHHHHHTS-HHHHHH CS
                             HTH_5  11 LaegelcvcelaeelglsqstvSh 34 
                                       Lae +++v + ae+l++ +st+S+
  gi|330508665|ref|YP_004385093.1| 120 LAEANRSVKDMAEALRVAPSTISE 143
                                       899********************8 PP

>> MazG_C  MazG C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     4e-05     0.051     109     149 ..      19      59 ..       2      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                            MazG_C 109 salvfseakelelfeeseeldlellktikelvaglEvekrk 149
                                       +++v ++a+++  +++s e++  ll  ++e+++++ ++++ 
  gi|330508665|ref|YP_004385093.1|  19 TKVVEKQATRHGSLRGSGEIEQALLGVVREMIKQYNIQTKL 59 
                                       5678899*****************************99865 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.74   9.5e+02       8      33 ..      60      84 ..      46      96 .. 0.65
   2 ?   11.6   0.0    0.0002      0.26      12      48 ..     114     149 ..     110     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.74
                         HTH_Tnp_1  8 sdefKariVreslepgksvsevArrh 33
                                      ++e+  ++Vr+    g s  e+A+++
  gi|330508665|ref|YP_004385093.1| 60 TPEQLSSVVRLF-YKGLSDTEIAEQL 84
                                      444444455554.4455555555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0002
                         HTH_Tnp_1  12 KariVreslepgksvsevArrhgvspnqLykWrrqyr 48 
                                       K +++r++ e+ +sv++ A+ + v p++ +  r  + 
  gi|330508665|ref|YP_004385093.1| 114 KDEFIRLA-EANRSVKDMAEALRVAPSTISEYRNIFD 149
                                       77899***.*********************9998774 PP

>> GcrA  GcrA cell cycle regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.4e-05     0.057       4      40 ..      60      96 ..      57     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-05
                              GcrA  4 tdErvelLkklwleGlSasqiaaqlggvsRnAViGkv 40
                                      t E+ +   +l+ +GlS ++ia+qlg  + n  + ++
  gi|330508665|ref|YP_004385093.1| 60 TPEQLSSVVRLFYKGLSDTEIAEQLGDRALNKTVSRA 96
                                      6788889999****************66666555554 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 ?    6.0   0.0    0.0097        12       5      32 ..      58      85 ..      56      85 .. 0.93
   2 ?    5.3   0.0     0.017        21      12      38 ..     115     141 ..     106     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0097
                                      SS-HHHHGGGGSSTTTT--STTTSSSS- CS
                             HTH_7  5 klskndinrvvkLleeGisiskIAkevn 32
                                      kl+++++ +vv+L  +G s ++IA++++
  gi|330508665|ref|YP_004385093.1| 58 KLTPEQLSSVVRLFYKGLSDTEIAEQLG 85
                                      789999*******************975 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.017
                                       GGGGSSTTTT--STTTSSSS---SSSS CS
                             HTH_7  12 nrvvkLleeGisiskIAkevnisRsTv 38 
                                       ++ ++L e+  s+++ A+++ +++sT+
  gi|330508665|ref|YP_004385093.1| 115 DEFIRLAEANRSVKDMAEALRVAPSTI 141
                                       7778999999****************8 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.2   4.1e+03      31      38 ..      78      85 ..      76      88 .. 0.76
   2 ?   10.0   0.0   0.00033      0.42      22      44 ..     119     141 ..     115     144 .. 0.84
   3 ?   -1.2   0.0       1.1   1.4e+03       8      16 ..     155     163 ..     153     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.2
                      HTH_Tnp_ISL3 31 kavArqlg 38
                                      +++A+qlg
  gi|330508665|ref|YP_004385093.1| 78 TEIAEQLG 85
                                      57788776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00033
                      HTH_Tnp_ISL3  22 elllesrsvkavArqlgvSwtTV 44 
                                       +l+  +rsvk+ A+ l+v ++T+
  gi|330508665|ref|YP_004385093.1| 119 RLAEANRSVKDMAEALRVAPSTI 141
                                       4555669***************9 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.1
                      HTH_Tnp_ISL3   8 rrsriTlrl 16 
                                       +r ++T+r+
  gi|330508665|ref|YP_004385093.1| 155 ERDGYTKRF 163
                                       6889****9 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.87   1.1e+03      24      38 ..      59      73 ..      46      80 .. 0.78
   2 ?   -1.9   0.0         3   3.9e+03      12      23 ..      74      85 ..      66      85 .. 0.76
   3 ?   10.1   0.0   0.00055      0.71       5      38 ..     117     150 ..     116     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.87
                            HTH_28 24 isrrtvyrWikryee 38
                                      ++++++++ ++ + +
  gi|330508665|ref|YP_004385093.1| 59 LTPEQLSSVVRLFYK 73
                                      589999999999876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3
                            HTH_28 12 GhsvreaArelg 23
                                      G s +e+A++lg
  gi|330508665|ref|YP_004385093.1| 74 GLSDTEIAEQLG 85
                                      557789999998 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00055
                            HTH_28   5 iikllaaGhsvreaArelgisrrtvyrWikryee 38 
                                        i+l+ a +sv++ A++l + ++t++  ++ +++
  gi|330508665|ref|YP_004385093.1| 117 FIRLAEANRSVKDMAEALRVAPSTISEYRNIFDS 150
                                       58899999*****************988777765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.7   2.2e+03      30      39 ..      43      52 ..      41      55 .. 0.86
   2 ?    9.8   0.1   0.00043      0.55       4      31 ..      58      85 ..      57     104 .. 0.87
   3 ?   -2.6   0.0       3.3   4.2e+03      20      38 ..     124     142 ..     119     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                                      HTS-HHHHHH CS
                        Sigma70_r4 30 lgiSrerVrq 39
                                      lg+ re ++q
  gi|330508665|ref|YP_004385093.1| 43 LGVVREMIKQ 52
                                      8999****99 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00043
                                      HS-HHHHHHHHHHHTTT--HHHHHHHHT CS
                        Sigma70_r4  4 sLpererevlelrfgeglTleEIgerlg 31
                                      +L++++   ++  f++gl+  EI+e+lg
  gi|330508665|ref|YP_004385093.1| 58 KLTPEQLSSVVRLFYKGLSDTEIAEQLG 85
                                      79*************************8 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.3
                                       T--HHHHHHHHTS-HHHHH CS
                        Sigma70_r4  20 glTleEIgerlgiSrerVr 38 
                                       +++ ++ +e l +  ++++
  gi|330508665|ref|YP_004385093.1| 124 NRSVKDMAEALRVAPSTIS 142
                                       6777888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); 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: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1099.70
//
Query:       gi|330508666|ref|YP_004385094.1|  [L=80]
Description: DNA-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-23   81.6   0.8    3.3e-23   81.5   0.8    1.0  1  HTH_45    Winged helix-turn-helix
     0.0022   17.7   0.0     0.0025   17.6   0.0    1.2  1  DUF4364   Domain of unknown function (DUF4364)
     0.0039   17.0   0.0     0.0053   16.6   0.0    1.1  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.096   12.2   0.0       0.12   11.9   0.0    1.2  1  GerE      Bacterial regulatory proteins, luxR family
      0.098   12.5   0.1       0.12   12.3   0.1    1.3  1  HxlR      HxlR-like 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 !   81.5   0.8   9.1e-27   3.3e-23       1      75 [.       2      78 ..       2      80 .] 0.94

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 9.1e-27
                            HTH_45  1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli...kkskekYvlTekGlelleklkeleel 75
                                      +Rsk  Ii++IL ++  ++a+kTki+y+anL++++++ YL+ L+e+gli   ++ +  Y++TekG+ell +lk +++ 
  gi|330508666|ref|YP_004385094.1|  2 KRSKDLIISQILLVC-AKGANKTKIVYQANLNFRTVDPYLKLLMERGLInakREPNLIYQTTEKGEELLGSLKAIQRE 78
                                      8**************.*********************************776667789***************99985 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   0.0   6.9e-07    0.0025      28      74 ..      28      73 ..      15      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.9e-07
                           DUF4364 28 neytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfe 74
                                      +  +n+ ++  +l+ L+e gli+++ +e + +y+ TekG+e l  ++
  gi|330508666|ref|YP_004385094.1| 28 QANLNFRTVDPYLKLLMERGLINAK-REPNLIYQTTEKGEELLGSLK 73
                                      55689******************95.5999***********997765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.5e-06    0.0053      16      65 ..      13      62 ..      11      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-06
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE- CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYrav 65
                                       L++ + a+ ++i  ++++   +v  +L+ L+++Gl++ +++   +Y+++
  gi|330508666|ref|YP_004385094.1| 13 LLVCAKGANKTKIVYQANLNFRTVDPYLKLLMERGLINAKREPNLIYQTT 62
                                      588*************************************9999999865 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.4e-05      0.12       9      44 ..      11      46 ..      10      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                                      HHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHH CS
                              GerE  9 evLrllaeGksnkeIAeelniSekTVkvhksnimkK 44
                                      ++L  +a+G   ++I ++ n+  +TV  +++ +m++
  gi|330508666|ref|YP_004385094.1| 11 QILLVCAKGANKTKIVYQANLNFRTVDPYLKLLMER 46
                                      89*****************************99986 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   3.2e-05      0.12      34      80 ..      34      76 ..       6      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.2e-05
                                      HHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHH CS
                              HxlR 34 kmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelk 80
                                      ++    L+ L + gli+++  p       Y+ tekG++l   l++++
  gi|330508666|ref|YP_004385094.1| 34 RTVDPYLKLLMERGLINAKREP----NLIYQTTEKGEELLGSLKAIQ 76
                                      5566678999999999987653....489**********99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 590.19
//
Query:       gi|330508667|ref|YP_004385095.1|  [L=339]
Description: RNA methylase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.5e-19   68.2   0.0    4.1e-18   65.8   0.0    1.9  1  UPF0020        Putative RNA methylase family UPF0020
    1.3e-08   35.1   0.1    2.3e-08   34.2   0.1    1.4  1  THUMP          THUMP domain
  ------ inclusion threshold ------
      0.031   13.9   0.0      0.054   13.1   0.0    1.4  1  Cons_hypoth95  Conserved hypothetical protein 95
      0.035   13.8   0.0      0.099   12.3   0.0    1.7  2  N6_N4_Mtase    DNA methylase


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   9.2e-22   4.1e-18       2     192 ..     161     322 ..     160     327 .. 0.82

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 9.2e-22
                                       SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH-- CS
                           UPF0020   2 gyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelk 78 
                                       + ++f++p+ L +++A++lv+l+++++ge+llDP+ G+ +il+Ea+l+g ++                         
  gi|330508667|ref|YP_004385095.1| 161 HLKPFFHPGVLMPRMARSLVNLTQIRAGERLLDPFAGTCGILVEACLMGIECL------------------------ 213
                                       6789*************************************************........................ PP

                                       EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHH.HHHHHHHHHHHHH CS
                           UPF0020  79 lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkal.ekLYseflrelkr 154
                                         g++ + r+v+ga  N+e+++ +    ++  da+ L lk++++   v + PYG++     +  e+L +e l+el r
  gi|330508667|ref|YP_004385095.1| 214 --GIEAQGRLVKGAICNLENMNCA----LVLGDAKRLALKDASIYGAVLDIPYGRSARILASSkEDLLKESLSELFR 284
                                       ..******************9875....556788888877889999999*******99765555************* PP

                                       H-TT..-EEEEEESSHHHHHCC---..ESEEEEEEETTEE CS
                           UPF0020 155 vlrgggrlvlltsenkalekaleer..alrkvkeknvklg 192
                                       v+r g r+v+++ +   + + ++++  ++ + ++ +v+ +
  gi|330508667|ref|YP_004385095.1| 285 VIRPGRRMVIVADGP--IDSQISNAgfRVIQSHLDRVHRS 322
                                       ****55555555444..34444444225556666666666 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.1   5.2e-12   2.3e-08      18     143 ..      35     146 ..      22     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 5.2e-12
                                       EEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESS CS
                             THUMP  18 eagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrg 94 
                                        + +++++ve  g     d ++l ++l      +r+i v+++ceadled+ +++  +  +       ++++r++r +
  gi|330508667|ref|YP_004385095.1|  35 SYLDQCLIVEAEGL----DVRALGDRLAM---THRIIEVMAICEADLEDLARSVALLSLPDE-----SYRIRARRIK 99 
                                       45555666666555....56666555555...67********************99988665.....********** PP

                                       STSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                             THUMP  95 khfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisid 143
                                       +  +  +  ++ e+G+ +  k+  + dl++P i +r+ i   k+ ++++
  gi|330508667|ref|YP_004385095.1| 100 NA-SPRADAVEHEIGRVLLGKGI-RADLKSPNIELRAVITSGKIILGVE 146
                                       *9.********************.**********************985 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05     0.054      41     108 ..     187     249 ..     172     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS- CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallkla 108
                                        g+r+LD faG++++ +EA   g  +++ +e + + vk    nle++++      +  da++ +lk a
  gi|330508667|ref|YP_004385095.1| 187 AGERLLDPFAGTCGILVEACLMG-IECLGIEAQGRLVKGAICNLENMNCA----LVLGDAKRLALKDA 249
                                       57889**************9999.57999*********999999999955....56667666666653 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.2e-05     0.099     170     223 ..     165     219 ..      89     226 .. 0.87
   2 ?   -1.4   0.0      0.36   1.6e+03      33      57 ..     273     297 ..     255     328 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.2e-05
                                       ---SS---HHHHHHHHHHHS-T.T-EEEETT-TTTHHHHHHHHTT-EEEEEESSH CS
                       N6_N4_Mtase 170 kkHpaqkPvallerlIklstkk.gdivlDpFaGSGtTavaakelgrkfiGieiee 223
                                         Hp +    +++ l++l+    g+  lDpFaG+  ++v+a  +g +++Gie + 
  gi|330508667|ref|YP_004385095.1| 165 FFHPGVLMPRMARSLVNLTQIRaGERLLDPFAGTCGILVEACLMGIECLGIEAQG 219
                                       4578888889999999988777699***************************875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHEEEEEEEEEEE- CS
                       N6_N4_Mtase  33 eflekvlkevrrvLkddgsifinid 57 
                                       ++l++ l+e+ rv  ++  ++i  d
  gi|330508667|ref|YP_004385095.1| 273 DLLKESLSELFRVIRPGRRMVIVAD 297
                                       5788999999999999999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2500.25
//
Query:       gi|330508668|ref|YP_004385096.1|  [L=361]
Description: hypothetical protein MCON_2921 [Methanosaeta concilii GP6]
Scores for complete 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-09   35.8   0.0    1.4e-08   35.0   0.0    1.3  1  APH       Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.033   13.8   0.0    1.6  2  RIO1      RIO1 family


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   1.5e-12   1.4e-08      66     209 ..     116     268 ..      88     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.5e-12
                                       ETTEEEEEEE----EE-SS.......HHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHC.....HTCCHHHHHH CS
                               APH  66 eigllfalieyvpgrsllr.......klsaaqlpellealgeflaalhqvdpaalpladfla.....qdlellrqle 130
                                       ++  +f+l+e ++g+ +         +   + + + + al ++la++h++ ++++p+ + ++      d e+   + 
  gi|330508668|ref|YP_004385096.1| 116 DACEYFLLMEKIEGKEYFFdlervkeEGATDLDHDRVIALSSYLAQIHAT-KEDCPPLYQRKiretvGDGECIFGIL 191
                                       4444678888888877666566677544445677889999**********.999****8887555556777999999 PP

                                       CHHHCCCGCCTCCHHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHC CS
                               APH 131 satarllaselldlleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlav 207
                                       +  +++   + +d+l+e+e+   +++++l+ +  + + +HgD+hp+N++++++ +    v+D  +  +g ++ D+  
  gi|330508668|ref|YP_004385096.1| 192 DDYPDSSTFLDPDELQEIEKVCVEWRWKLRSKVHRLSMVHGDFHPWNIMFREGTDF--SVLDRSRGEWGEAADDITA 266
                                       999988888888899*****98888888888889*****************55554..4999777777777777766 PP

                                       CH CS
                               APH 208 ll 209
                                       l+
  gi|330508668|ref|YP_004385096.1| 267 LA 268
                                       66 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.67     6e+03      83     100 ..     122     138 ..     115     161 .. 0.59
   2 ?   13.8   0.0   3.6e-06     0.033     106     149 ..     208     252 ..     194     255 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.67
                                       EEEE--EETTEEGGBHHH CS
                              RIO1  83 lvmefigedgvaapklkd 100
                                       l+me i+ +++   +l+ 
  gi|330508668|ref|YP_004385096.1| 122 LLMEKIEGKEY-FFDLER 138
                                       66777763332.233333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.6e-06
                                       HHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--G CS
                              RIO1 106 eaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDv 149
                                       e+e++  e   ++r  +++  +vH+D+  +N+++ e+ ++ ++D 
  gi|330508668|ref|YP_004385096.1| 208 EIEKVCVEWRWKLRSKVHRLSMVHGDFHPWNIMFREGtDFSVLDR 252
                                       444445555558999999******************989988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2877.62
//
Query:       gi|330508669|ref|YP_004385097.1|  [L=414]
Description: adenosylhomocysteinase [Methanosaeta concilii GP6]
Scores for complete 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  223.9   0.0    3.8e-39  134.6   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    5.6e-52  176.1   0.1    1.1e-51  175.1   0.0    1.5  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    3.4e-09   36.3   0.1    6.8e-09   35.3   0.1    1.5  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    5.7e-06   26.0   0.0    1.1e-05   25.1   0.0    1.4  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
     0.0013   19.0   0.1     0.0057   16.9   0.0    2.1  2  TrkA_N         TrkA-N domain
  ------ inclusion threshold ------
      0.016   14.5   0.1      0.029   13.6   0.1    1.4  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      0.059   12.7   0.1       0.11   11.7   0.1    1.5  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.6   0.0   1.5e-42   3.8e-39       4     138 ..       2     131 ..       1     135 [. 0.97
   2 !   89.3   0.0   9.4e-29   2.4e-25     171     286 ..     131     408 ..     128     414 .] 0.98

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 1.5e-42
                                       -S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase   4 vkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstq 80 
                                       vkd++lae+G k+ie a + mp l  ++ee+++ekplkgari+ +lh+t++ta Li tLva Gaev  +  n  stq
  gi|330508669|ref|YP_004385097.1|   2 VKDLALAEAGEKRIEWARRHMPVLDRIKEEFEREKPLKGARIVACLHVTVETANLITTLVAGGAEVAVTGSNPLSTQ 78 
                                       9**************************************************************************** PP

                                       HHHHHHHCCTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  81 deaaaaiaeagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhk 138
                                       de+aaa+a++g+ v+a++ge++ ey +ci++al+      +pn+ lDdG D  +++hk
  gi|330508669|ref|YP_004385097.1|  79 DEVAAALAARGLFVYAFRGENETEYYDCIKKALEL-----KPNVSLDDGADTIAIIHK 131
                                       *********************************66.....7***************98 PP

  == domain 2  score: 89.3 bits;  conditional E-value: 9.4e-29
                                       THHCCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                         AdoHcyase 171 kkytellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD........................... 220
                                       k+++el++++ G  eetttGv rL  +a+++ Ll p i vnd+ tk  fD                           
  gi|330508669|ref|YP_004385097.1| 131 KEHPELAAQMLGGCEETTTGVVRLRAMAEDKALLYPVIAVNDAETKMMFDnrygtgqstlhgimqatnflfagktvv 207
                                       678999*********************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|330508669|ref|YP_004385097.1| 208 vcgygwcgrgfamrakglganvivieieprkaleaamdgyrvmplgqaaplgdlfvtltgninvlrkehfalmkdqa 284
                                       ***************************************************************************** PP

                                       ..........................................................S-HHHHHHHHHHHHHHHHH CS
                                       ..........................................................xxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 221 ..........................................................hpsfvmsasftnqvlaqie 239
                                                                                                 hp  vm++sf+nq+l+   
  gi|330508669|ref|YP_004385097.1| 285 ivansghfnveidipalekmagekneiqnnvteyklpdgrrlyllaegrlinlaaaygHPPEVMDMSFANQALSVRY 361
                                       ***************************************************************************** PP

                                       HHHTTSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 240 lfkkekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyig 286
                                       + ++ ++ +k+vy +p ++D +va+l+l+++g + ++lt eq +y++
  gi|330508669|ref|YP_004385097.1| 362 IVEQGRSLKKSVYSVPVEIDRRVAELKLASMGLETEKLTAEQEKYLH 408
                                       ****999**************************************97 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.9   7.3e+03      41      57 ..      59      75 ..      42      82 .. 0.71
   2 !  175.1   0.0   4.3e-55   1.1e-51       1     161 [.     181     341 ..     181     342 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.9
                                      HHHHCT-EEEEE-S-HH CS
                     AdoHcyase_NAD 41 slkglGarvivtevdPi 57
                                      +l + Ga v vt  +P+
  gi|330508669|ref|YP_004385097.1| 59 TLVAGGAEVAVTGSNPL 75
                                      45566777777777666 PP

  == domain 2  score: 175.1 bits;  conditional E-value: 4.3e-55
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTT CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvk 77 
                                       n yg+ +s + gi++at++l+aGk++vv+GyG  G+G a   kglGa viv e++P  al aam+G++v+ l +++ 
  gi|330508669|ref|YP_004385097.1| 181 NRYGTGQSTLHGIMQATNFLFAGKTVVVCGYGWCGRGFAMRAKGLGANVIVIEIEPRKALEAAMDGYRVMPLGQAAP 257
                                       78*************************************************************************** PP

                                       T-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSB CS
                     AdoHcyase_NAD  78 kadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrl 154
                                        +d++vt tGn +++++eh++ mkd+aiv+n Ghf+ eid+ ale++a +k+e++ +v +++l+dg+++ llaeGrl
  gi|330508669|ref|YP_004385097.1| 258 LGDLFVTLTGNINVLRKEHFALMKDQAIVANSGHFNVEIDIPALEKMAGEKNEIQNNVTEYKLPDGRRLYLLAEGRL 334
                                       ***************************************************************************** PP

                                       CHHHTS- CS
                     AdoHcyase_NAD 155 lnlgcat 161
                                       +nl++a 
  gi|330508669|ref|YP_004385097.1| 335 INLAAAY 341
                                       ***9986 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1   2.7e-12   6.8e-09      33     128 ..     200     291 ..     174     310 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.7e-12
                                       -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSB CS
                      2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhli 109
                                         +gktv + G+G  G+ +a r+k++g++vi+++  ++k  e++  g++++ l ++    D  +  +     + +++
  gi|330508669|ref|YP_004385097.1| 200 LFAGKTVVVCGYGWCGRGFAMRAKGLGANVIVIEIEPRKALEAAMDGYRVMPLGQAAPLGDLFVTLTG----NINVL 272
                                       5689**********************************99999999***************8877654....899** PP

                                       SHHHHHCSTTTEEEEESS- CS
                      2-Hacid_dh_C 110 naeelakmkkgailiNtaR 128
                                        +e++a+mk++ai+ N + 
  gi|330508669|ref|YP_004385097.1| 273 RKEHFALMKDQAIVANSGH 291
                                       ***************9886 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 !   25.1   0.0   4.1e-09   1.1e-05       3     101 ..     202     296 ..     200     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.1e-09
                                       HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHH CS
                              IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyee 79 
                                        gk+++v GyG  G+  a+  +  g +v+v   e +k + +A  +g++v+ + +a+   d+ ++l+    + +v+++
  gi|330508669|ref|YP_004385097.1| 202 AGKTVVVCGYGWCGRGFAMRAKGLGANVIVIEIEPRK-ALEAAMDGYRVMPLGQAAPLGDLFVTLTG---NINVLRK 274
                                       79**************************998888875.5567789******************9986...4689999 PP

                                       HTGGG--TT-EEEESSSHHHHT CS
                              IlvN  80 eiepnlkegkalafahGfnihf 101
                                       e    +k+++++a +  fn+  
  gi|330508669|ref|YP_004385097.1| 275 EHFALMKDQAIVANSGHFNVEI 296
                                       9999999999999999999976 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2     3e+03      59      83 ..      37      62 ..       9      91 .. 0.66
   2 !   16.9   0.0   2.2e-06    0.0057       1      45 [.     206     250 ..     206     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                      TGGGESEEEE-.SSSHHHHHHHHHHH CS
                            TrkA_N 59 giekadaviaa.tgddeanilavlla 83
                                       ++ a++v ++ +   +an++++l+a
  gi|330508669|ref|YP_004385097.1| 37 PLKGARIVACLhVTVETANLITTLVA 62
                                      45555555555233446677776666 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.2e-06
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEE CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevv 45 
                                       ++++G+G  Gr  a + +  g  +v+vi+ +++++ e++ +g++v+
  gi|330508669|ref|YP_004385097.1| 206 VVVCGYGWCGRGFAMRAKGlGA-NVIVIEIEPRKALEAAMDGYRVM 250
                                       79*****************777.6***************9999986 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.1e-05     0.029     138     177 ..     201     238 ..     162     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                                       CSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 138 lkllpkrivvvGgGyiGvElAaalaklgkevtlveardrl 177
                                        +   k +vv+G G +G  +A+ ++ lg++v ++e  +r 
  gi|330508669|ref|YP_004385097.1| 201 FAG--KTVVVCGYGWCGRGFAMRAKGLGANVIVIEIEPRK 238
                                       333..67****************************99985 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   0.1   4.5e-05      0.11      28      65 ..     203     240 ..     177     288 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.5e-05
                                       --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHH CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparle 65 
                                         +v+v G G  G   +  akglga+V v++++p+++ 
  gi|330508669|ref|YP_004385097.1| 203 GKTVVVCGYGWCGRGFAMRAKGLGANVIVIEIEPRKAL 240
                                       3468999*************************998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.38
# Mc/sec: 3277.31
//
Query:       gi|330508670|ref|YP_004385098.1|  [L=414]
Description: amidohydrolase family protein [Methanosaeta concilii GP6]
Scores for complete 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-61  207.5   0.0    3.9e-61  207.3   0.0    1.0  1  Amidohydro_1  Amidohydrolase family
    9.3e-12   45.2   0.0    5.2e-08   32.8   0.0    2.3  2  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.016   14.6   0.0      0.025   13.9   0.0    1.2  1  A_deaminase   Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.3   0.0   6.6e-65   3.9e-61       2     343 ..      50     386 ..      49     387 .. 0.93

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 6.6e-65
                                       EEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHH CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgie 64 
                                        +PGl++ H+Hl +sllrg      l+ wl          +++e+++++++ g+ ++++ G+t  +dm++      +
  gi|330508670|ref|YP_004385098.1|  50 AIPGLVNCHTHLAMSLLRGYaddmELMPWLeekiwplearLTEEDVYWGVKLGCLELIRFGITCYNDMYY----FPD 122
                                       69********************99999999****************************************....999 PP

                                       HHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHH CS
                      Amidohydro_1  65 alleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkea 141
                                         ++a++e+  glr ++++v++d  ++e  + ++e +++++      k d+++ +a++ph+a+++s+e+l  a + a
  gi|330508670|ref|YP_004385098.1| 123 VTAQATKEM--GLRGFISGVVFD-MKPE-LLSQVEPFIKRW------KDDELIRPAVGPHAAYTCSEETLLRAGEIA 189
                                       99******8..************.6656.677888898888......5788999*********************** PP

                                       HHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHH CS
                      Amidohydro_1 142 kkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahc 218
                                       ++++++v++H++et +ev   +   g     ++++e+++slgll++ +l++ h+v+l+ ++  ll +r  +a+v++c
  gi|330508670|ref|YP_004385098.1| 190 DRHQAMVHMHISETWKEVDGFLLSRG-----KSPVEYLDSLGLLNS-RLTAIHCVWLSEEDCYLLEKR--KANVVSC 258
                                       *****************977777777.....56*************.*********************..******* PP

                                       HHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHH CS
                      Amidohydro_1 219 pfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAk 295
                                        +sn++l+sg+++l+ ++++Gv+v lgtD+a s+n+l+l+e++++ + +q+  +++   + ++++++ ++aT n+ +
  gi|330508670|ref|YP_004385098.1| 259 TASNLKLASGIAPLNTLMKAGVNVCLGTDSACSNNNLSLFEDMKVTAIVQKNAYHT--PAAFTAEQIWQFATENAYR 333
                                       ***********************************************999977776..455**************** PP

                                       HTT-TTTSSSS-TTSB--EEEECC.CT........CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 296 alglddkvGsievGkdADlvvvdl.di........laafvglkkdgnvkkvivkGkl 343
                                       a+gl  + G   vG  ADl+++dl ++         +++v++   g v+++iv+G++
  gi|330508670|ref|YP_004385098.1| 334 AFGL--NNG-MSVGANADLALIDLkKPwfypqsniVSHLVYSMA-GGVDTTIVNGRV 386
                                       ****..9**.9*************84466667788999999988.66********97 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   5.2e-05      0.31       6      24 ..      46      64 ..      41      77 .. 0.80
   2 !   32.8   0.0   8.8e-12   5.2e-08     354     472 ..     266     387 ..     155     388 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.2e-05
                      Amidohydro_3  6 kGrlvlPGFvDsHtHlagg 24
                                      kG+l +PG+v  HtHla  
  gi|330508670|ref|YP_004385098.1| 46 KGKLAIPGLVNCHTHLAMS 64
                                      8**************7654 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 8.8e-12
                      Amidohydro_3 354 argstpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledr 430
                                       a+g++p+++l++agv+v+lg+D   ++ ++++ ++++     + + + +     ++ e++ +  T+++ +a+gl   
  gi|330508670|ref|YP_004385098.1| 266 ASGIAPLNTLMKAGVNVCLGTD-SACSNNNLSLFEDMKVTAIVQK-NAYHTPAAFTAEQIWQFATENAYRAFGLNN- 339
                                       7889******************.8888889998888887777777.6788888***********************. PP

                      Amidohydro_3 431 kGtLevGadADlvvld.adpldvdppelaear.......vrltvvdGrvv 472
                                         +  vGa ADl+++d ++p   +++++++ +       v  t+v+Grv+
  gi|330508670|ref|YP_004385098.1| 340 --GMSVGANADLALIDlKKPWFYPQSNIVSHLvysmaggVDTTIVNGRVL 387
                                       ..59*************9************99****************96 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.3e-06     0.025     232     296 ..     246     307 ..     241     333 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-06
                                       HHHHHCT-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCCT-S.HHHHHHHHHHH CS
                       A_deaminase 232 yllalaqiplevcPlSNvalgafleyaenPlkeflerglnvslntDDPlqfgtt.LieeYaiaaqv 296
                                       yll +++  +  c +SN +l    +    Pl++++++g+nv l+tD     +   L e+++++a v
  gi|330508670|ref|YP_004385098.1| 246 YLLEKRKANVVSCTASNLKL----ASGIAPLNTLMKAGVNVCLGTDSACSNNNLsLFEDMKVTAIV 307
                                       678888899999********....77789*****************98765543499999998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2630.79
//
Query:       gi|330508671|ref|YP_004385099.1|  [L=570]
Description: divergent AAA domain family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-18   65.6   0.0    8.8e-18   64.2   0.0    1.8  1  HATPase_c_4      Putative ATP-dependent DNA helicase recG C-t
    1.1e-14   54.9   0.0    1.8e-14   54.1   0.0    1.3  1  AlbA_2           Putative DNA-binding domain
      2e-07   30.4   0.7    6.5e-05   22.4   0.0    2.9  2  HTH_24           Winged helix-turn-helix DNA-binding
    3.8e-06   26.7   1.1      0.002   18.0   0.0    3.0  3  MarR_2           MarR family
    1.1e-05   25.4   1.9      0.019   15.1   0.2    2.9  2  HTH_20           Helix-turn-helix domain
    1.5e-05   24.6   0.9     0.0035   17.1   0.0    3.5  3  HTH_23           Homeodomain-like domain
    1.6e-05   24.6   0.7     0.0027   17.5   0.0    3.0  2  HTH_IclR         IclR helix-turn-helix domain
    3.4e-05   23.7   0.2       0.17   11.8   0.0    2.5  2  TrmB             Sugar-specific transcriptional regulator Trm
    0.00053   20.1   0.6     0.0028   17.7   0.0    2.6  2  HTH_28           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.3   0.0       0.45   10.2   0.0    2.4  2  DUF4423          Domain of unknown function (DUF4423)
      0.012   15.5   0.1       0.17   11.9   0.0    2.8  3  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.013   15.7   0.1      0.054   13.7   0.0    2.1  2  PaaX             PaaX-like protein
      0.017   15.2   4.4       0.22   11.7   0.1    3.6  3  AbiEi_4          Transcriptional regulator, AbiEi antitoxin
      0.041   14.1   0.7       0.17   12.1   0.1    2.2  2  HTH_17           Helix-turn-helix domain
      0.061   13.1   0.0       0.17   11.7   0.0    1.8  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.089   13.3   0.4        3.2    8.3   0.1    2.6  2  HTH_27           Winged helix DNA-binding domain
       0.12   12.6   0.0        0.8    9.9   0.0    2.2  2  SgrR_N           Sugar transport-related sRNA regulator N-ter
       0.14   12.5   0.0       0.47   10.8   0.0    2.0  1  Penicillinase_R  Penicillinase repressor
       0.16   12.1   0.1        4.5    7.5   0.0    2.5  2  DUF2250          Uncharacterized protein conserved in archaea


Domain annotation for each model (and alignments):
>> HATPase_c_4  Putative ATP-dependent DNA helicase recG C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   9.4e-21   8.8e-18       3      87 ..     314     398 ..     313     399 .. 0.92

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 9.4e-21
                       HATPase_c_4   3 kvqieifdDRleItspGglpggvtveskllegrssaRNelLasllerlrlmeergsGiqrilealeeaglpepefr. 78 
                                        v+++  +DR+eI++pGg+p+gv +++ ll  +++ RN+ La++++r +++e+ ++Gi++i+ +  ++g p+p+++ 
  gi|330508671|ref|YP_004385099.1| 314 AVHVQWHEDRIEISNPGGFPEGVRLDN-LLVTPPRPRNPSLADAFKRAGIVERTARGIDTIFFEQLRNGRPAPSYEr 389
                                       599***********************9.8**********************************************94 PP

                       HATPase_c_4  79 edgssftvt 87 
                                       ++++++ ++
  gi|330508671|ref|YP_004385099.1| 390 SSETDVILV 398
                                       555666665 PP

>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.0   1.9e-17   1.8e-14       1     112 [.      14     125 ..      14     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 1.9e-17
                            AlbA_2   1 EdellEfKeslgnklkkrersiakticAfaNseg...GtlliGVeDdgkvvGv..ecsdqeedqlrlelksiikrfk 72 
                                       E+ ++EfK + + +l+++   +++ ++++aN +g   G+ll+GVeDdg+++G   + s ++ d   + +  i++r++
  gi|330508671|ref|YP_004385099.1|  14 ESLNVEFKGEEKASLSDSA--LVEAVICLANRSGvepGWLLVGVEDDGRITGSrpRHSGEKTD-TYRVSALIANRTR 87 
                                       8899****99999999743..**********854445****************6333333344.4444555999*** PP

                            AlbA_2  73 pkvlpdiervelkgkkvlvvkvekskkkplyeneegvvyi 112
                                       p++ +++e +e++g++vlvv+v+ s+ ++  ++ eg++  
  gi|330508671|ref|YP_004385099.1|  88 PSLACRVEIIEIDGRYVLVVEVPTSRTPV--STPEGKYQR 125
                                       *************************9998..555555544 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 ?    5.3   0.2     0.015        15       5      47 ..     426     468 ..     426     469 .. 0.94
   2 !   22.4   0.0   6.9e-08   6.5e-05       8      45 ..     510     547 ..     508     548 .. 0.97

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.015
                            HTH_24   5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       d+ +L+ ++ + r++ +e A+ +  + +  ++ l+rL+e Gl+
  gi|330508671|ref|YP_004385099.1| 426 DLLLLNHVYLERRTTAKEAAKIIQKPENEARAALERLVEGGLL 468
                                       6778999999******************************997 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 6.9e-08
                            HTH_24   8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeG 45 
                                       +L++++k++ is +e+Ae +++S +   r lk+Le+eG
  gi|330508671|ref|YP_004385099.1| 510 VLQYVEKHGEISRAEVAELCHISGPQAYRLLKKLEREG 547
                                       79**********************************99 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         5   4.7e+03      43      54 ..     355     366 ..     353     369 .. 0.80
   2 !    6.3   0.2     0.009       8.5       9      54 ..     428     471 ..     421     478 .. 0.81
   3 !   18.0   0.0   2.1e-06     0.002       2      52 ..     500     550 ..     499     570 .] 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5
                                       HHHHHTTSEEEE CS
                            MarR_2  43 krLvaaGLverr 54 
                                       + + +aG ver+
  gi|330508671|ref|YP_004385099.1| 355 DAFKRAGIVERT 366
                                       67899*****98 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.009
                                       HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                        +L++++ + +   t++e a+  + +   +  +l+rLv+ GL+e +
  gi|330508671|ref|YP_004385099.1| 428 LLLNHVYLERR--TTAKEAAKIIQKPENEARAALERLVEGGLLEAS 471
                                       56777777765..899***************************977 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 2.1e-06
                                       T--HHHH..HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2   2 gltpaqa..rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52 
                                       g++p q+  +vL ++  +++  ++ +e+a+ +++s + + r+lk+L++ G+++
  gi|330508671|ref|YP_004385099.1| 500 GFEPLQWgqMVLQYVEKHGE--ISRAEVAELCHISGPQAYRLLKKLEREGHLT 550
                                       56655554469999*****9..****************************984 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2     2e-05     0.019      20      60 ..     434     474 ..     419     475 .. 0.86
   2 !    8.8   0.0    0.0017       1.6      14      52 ..     509     547 ..     508     554 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                                       STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  20 araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                         ++  ta+e a+ ++ + n+++  L+ L+e gL+e  +eg
  gi|330508671|ref|YP_004385099.1| 434 YLERRTTAKEAAKIIQKPENEARAALERLVEGGLLEASGEG 474
                                       678999******************************99998 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0017
                                       HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCT CS
                            HTH_20  14 rilraLaraegltaselaerldlskntlsyHLrvLeeag 52 
                                       ++l++    ++ + +e+ae++ +s  ++++ L++Le+ g
  gi|330508671|ref|YP_004385099.1| 509 MVLQYVEKHGEISRAEVAELCHISGPQAYRLLKKLEREG 547
                                       578888889999************************977 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.53     5e+02      17      28 ..     194     205 ..     180     207 .. 0.86
   2 ?    2.7   0.1      0.12   1.2e+02      24      49 ..     476     504 ..     476     505 .. 0.90
   3 !   17.1   0.0   3.7e-06    0.0035      10      45 ..     509     547 ..     507     552 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.53
                            HTH_23  17 GlsvreIAreLg 28 
                                        l+ +eIA++Lg
  gi|330508671|ref|YP_004385099.1| 194 ELPDQEIAKALG 205
                                       4799*******9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                            HTH_23  24 AreLgvsrrTvyrw..lkry.reeGlegl 49 
                                       Ar+++   +T++r   + +y r +G+e+l
  gi|330508671|ref|YP_004385099.1| 476 ARAYHLCASTYRRLgeRAAYiRTHGFEPL 504
                                       899***********999999777999998 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 3.7e-06
                            HTH_23  10 illllae...GlsvreIAreLgvsrrTvyrwlkryreeG 45 
                                       ++l + e    +s++e+A+++++s  + yr lk+ ++eG
  gi|330508671|ref|YP_004385099.1| 509 MVLQYVEkhgEISRAEVAELCHISGPQAYRLLKKLEREG 547
                                       555566567779**********************98899 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2      0.04        37      17      50 ..     438     470 ..     427     472 .. 0.85
   2 !   17.5   0.0   2.9e-06    0.0027       7      48 ..     509     549 ..     507     552 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.04
                                       SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       +  t +e A+ +  p   ++  L  Lve G++e 
  gi|330508671|ref|YP_004385099.1| 438 R-TTAKEAAKIIQKPENEARAALERLVEGGLLEA 470
                                       3.478999999*********************96 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.9e-06
                                       HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48 
                                       ++L++++++++  + +e+A+ ++++ + ++RlL+ L+++G +
  gi|330508671|ref|YP_004385099.1| 509 MVLQYVEKHGE-ISRAEVAELCHISGPQAYRLLKKLEREGHL 549
                                       68888888888.899************************976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0012       1.1      21      58 ..     437     474 ..     429     484 .. 0.85
   2 !   11.8   0.0   0.00018      0.17      19      52 ..     516     549 ..     509     562 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                                       CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                        + ta+e a+++  p++ +  +L++L++ Gl e + + 
  gi|330508671|ref|YP_004385099.1| 437 RRTTAKEAAKIIQKPENEARAALERLVEGGLLEASGEG 474
                                       5689****************************998754 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00018
                                       HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSE CS
                              TrmB  19 klgpatadeiaeelgvprskvYevLrsLedkGlV 52 
                                       k+g+ +  e+ae   ++ +++Y+ L++Le+ G  
  gi|330508671|ref|YP_004385099.1| 516 KHGEISRAEVAELCHISGPQAYRLLKKLEREGHL 549
                                       78999999**********************9965 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       6.8   6.5e+03      19      32 ..     476     489 ..     476     493 .. 0.85
   2 !   17.7   0.0     3e-06    0.0028       6      40 ..     510     547 ..     508     557 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.8
                            HTH_28  19 ArelgisrrtvyrW 32 
                                       Ar+++++ +t +r+
  gi|330508671|ref|YP_004385099.1| 476 ARAYHLCASTYRRL 489
                                       8999**99999986 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3e-06
                            HTH_28   6 iklla..aGh.svreaArelgisrrtvyrWikryeegG 40 
                                       ++++   +G+ s++e+A++ +is  + yr++k++e +G
  gi|330508671|ref|YP_004385099.1| 510 VLQYVekHGEiSRAEVAELCHISGPQAYRLLKKLEREG 547
                                       4455523467**************************98 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00048      0.45      38      77 ..     440     477 ..     428     491 .. 0.87
   2 ?    2.4   0.0      0.12   1.1e+02      34      73 ..     518     554 ..     505     566 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00048
                           DUF4423  38 dpeelakrlrpkisaeevekalefLlklgllkkdedgkyr 77 
                                       + +e ak+++   ++ e+++ale+L++ gll+ +++gk r
  gi|330508671|ref|YP_004385099.1| 440 TAKEAAKIIQ--KPENEARAALERLVEGGLLEASGEGKAR 477
                                       5667788888..99**********************9977 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                           DUF4423  34 dfkadpeelakrlrpkisaeevekalefLlklgllkkded 73 
                                        +  + +e+a+ ++  is  ++ + l+ L++ g l+  + 
  gi|330508671|ref|YP_004385099.1| 518 GE-ISRAEVAELCH--ISGPQAYRLLKKLEREGHLTPIGT 554
                                       33.7889*******..***************999887665 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 ?   -2.8   0.0       6.8   6.4e+03      21      33 ..     194     206 ..     180     208 .. 0.76
   2 ?   -0.6   0.0       1.4   1.3e+03      44      65 ..     356     378 ..     353     380 .. 0.68
   3 ?   11.9   0.0   0.00018      0.17      21      54 ..     519     553 ..     505     562 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.8
                                       EHHHHHHHHHTTS CS
                         HTH_Crp_2  21 pltqeelAsmlGl 33 
                                        l  +e+A  lG+
  gi|330508671|ref|YP_004385099.1| 194 ELPDQEIAKALGA 206
                                       4677999999996 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                                       HHHHTTSEEET.EEEEES-HHHH CS
                         HTH_Crp_2  44 eLkreglisrg.rririldleaL 65 
                                       ++kr+g+++r  r+i     e+L
  gi|330508671|ref|YP_004385099.1| 356 AFKRAGIVERTaRGIDTIFFEQL 378
                                       69*******64244765555555 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00018
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis.rg 54 
                                        ++++e A+++ ++  +  r+l++L+reg ++  g
  gi|330508671|ref|YP_004385099.1| 519 EISRAEVAELCHISGPQAYRLLKKLEREGHLTpIG 553
                                       589**************************988644 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.7e-05     0.054      37      67 ..     452     482 ..     446     485 .. 0.90
   2 ?   -2.3   0.0       5.9   5.6e+03      44      64 ..     540     561 ..     514     562 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-05
                              PaaX  37 eslvRaalsRlakaGwlvrekegrrsfYrLs 67 
                                       e+  Raal Rl++ G+l ++ eg++  Y+L 
  gi|330508671|ref|YP_004385099.1| 452 ENEARAALERLVEGGLLEASGEGKARAYHLC 482
                                       6779********************9999996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.9
                              PaaX  44 lsRlakaGwlvrek.egrrsfY 64 
                                       l  l+++G l++   +gr + Y
  gi|330508671|ref|YP_004385099.1| 540 LKKLEREGHLTPIGtKGRSVKY 561
                                       5678888888887414555555 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.4   1.4e+03      19      32 ..     178     195 ..     164     195 .. 0.67
   2 ?    2.6   0.0      0.17   1.6e+02      30      45 ..     355     370 ..     347     370 .. 0.81
   3 ?   11.7   0.1   0.00023      0.22      14      44 ..     520     556 ..     510     557 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.4
                           AbiEi_4  19 l...ea.aGispsalrrL 32 
                                           ++ +G+s+ al++L
  gi|330508671|ref|YP_004385099.1| 178 RrmiREsRGRSDAALAEL 195
                                       0555666*****999987 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.17
                           AbiEi_4  30 rrLvrkGwLvrlrrGv 45 
                                       + + r+G ++r +rG+
  gi|330508671|ref|YP_004385099.1| 355 DAFKRAGIVERTARGI 370
                                       56789**********7 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00023
                           AbiEi_4  14 fttrelea.aGisp.sa...lrrLvrkGwLvrlr.rG 44 
                                       ++++e+++ ++is  +a   l +L r+G L+ ++ +G
  gi|330508671|ref|YP_004385099.1| 520 ISRAEVAElCHISGpQAyrlLKKLEREGHLTPIGtKG 556
                                       799***********555***************99888 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.6   2.5e+03       3      33 ..     440     474 ..     440     480 .. 0.56
   2 ?   12.1   0.1   0.00018      0.17       5      40 ..     523     563 ..     520     564 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.6
                            HTH_17   3 tveEaAelLgv....srstvyrlirrgelpaakiG 33 
                                       t +EaA++        r+ + rl+  g l a + G
  gi|330508671|ref|YP_004385099.1| 440 TAKEAAKIIQKpeneARAALERLVEGGLLEASGEG 474
                                       56777777666333344555555666666555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00018
                            HTH_17   5 eEaAelLgvsrstvyrli....rrgelpaak.iGrrwripr 40 
                                       +E+Ael ++s   +yrl+    r+g l + + +Gr++++ r
  gi|330508671|ref|YP_004385099.1| 523 AEVAELCHISGPQAYRLLkkleREGHLTPIGtKGRSVKYER 563
                                       7*****************77777*******99***999876 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00018      0.17       4      44 ..     509     549 ..     507     552 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                          HTH_DeoR   4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44 
                                         l++++++g +s  e++el+ +S   + R L++Le +g l
  gi|330508671|ref|YP_004385099.1| 509 MVLQYVEKHGEISRAEVAELCHISGPQAYRLLKKLEREGHL 549
                                       579*********************99999999999888876 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 ?    8.3   0.1    0.0034       3.2       5      53 ..     426     473 ..     423     484 .. 0.78
   2 ?    2.2   0.0      0.27   2.5e+02      16      49 ..     517     550 ..     508     562 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0034
                            HTH_27   5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgd 53 
                                       + l+L++++  +rr ++++ ++  +     +  +l++L+e GL+e +g 
  gi|330508671|ref|YP_004385099.1| 426 DLLLLNHVY-LERRTTAKEAAKIIQKPENEARAALERLVEGGLLEASGE 473
                                       4567*****.777777788888888888888899**********77655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.27
                            HTH_27  16 rrrkkladlcgrlnvedshisyslkkLtekGLve 49 
                                       +++ + a++++   ++  ++   lkkL++ G ++
  gi|330508671|ref|YP_004385099.1| 517 HGEISRAEVAELCHISGPQAYRLLKKLEREGHLT 550
                                       444555899999999999999*********9883 PP

>> SgrR_N  Sugar transport-related sRNA regulator N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.7   1.6e+03      17      50 ..     436     469 ..     428     478 .. 0.84
   2 ?    9.9   0.0   0.00084       0.8       5      58 ..     505     558 ..     503     562 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.7
                            SgrR_N  17 evevtLqelAdvlfCsrRhartlLkkmqeegwle 50 
                                       e ++t +e A+++   +  ar  L+++ e g+le
  gi|330508671|ref|YP_004385099.1| 436 ERRTTAKEAAKIIQKPENEARAALERLVEGGLLE 469
                                       5678899999999999999999999999999886 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00084
                            SgrR_N   5 qyerLlqhfegkevevtLqelAdvlfCsrRhartlLkkmqeegwleWqpevGRg 58 
                                       q+ +++ ++ +k+ e++ +e+A++++ s   a  lLkk+++eg l+    +GR 
  gi|330508671|ref|YP_004385099.1| 505 QWGQMVLQYVEKHGEISRAEVAELCHISGPQAYRLLKKLEREGHLTPIGTKGRS 558
                                       56677888999999******************************9988888885 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0005      0.47       9     110 ..     430     529 ..     426     568 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0005
                                       HHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----X.XXXXXXXXXXXXXXXX CS
                   Penicillinase_R   9 meilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvse.eeavasavkqlldklf 84 
                                       +++++ + ++t+ke  + ++++    ++  +  l+rLv+ gll++  eg+a +Y+  +s  +++ ++a+   ++ + 
  gi|330508671|ref|YP_004385099.1| 430 LNHVYLERRTTAKEAAKIIQKP----ENEARAALERLVEGGLLEASGEGKARAYHLCASTyRRLGERAAYIRTHGFE 502
                                       5677777778888888888888....6666789********************986666515666777777777777 PP

                                       XXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                   Penicillinase_R  85 egsvkelvaafveee.klseddleeLr 110
                                         +  ++v++ ve++ ++s  +++eL 
  gi|330508671|ref|YP_004385099.1| 503 PLQWGQMVLQYVEKHgEISRAEVAELC 529
                                       779***********99******99985 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0047       4.5      11      54 ..     427     470 ..     422     479 .. 0.84
   2 ?    1.5   0.0      0.34   3.2e+02      12      64 ..     509     563 ..     501     566 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0047
                           DUF2250  11 lkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLler 54 
                                       l +l+h+       ak  ak +++p +e+r +l++L e GLle 
  gi|330508671|ref|YP_004385099.1| 427 LLLLNHVYLERRTTAKEAAKIIQKPENEARAALERLVEGGLLEA 470
                                       5566666666667799**************************96 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.34
                           DUF2250  12 kvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerv..egktikrte 64 
                                       +vl++++k +      +a+  +i+  ++ +llkkLe+ G l+    +g+++k+++
  gi|330508671|ref|YP_004385099.1| 509 MVLQYVEKHGEISRAEVAELCHISGPQAYRLLKKLEREGHLTPIgtKGRSVKYER 563
                                       5777777766666667899999999**************9986411577777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3753.83
//
Query:       gi|330508672|ref|YP_004385100.1|  [L=276]
Description: CAAX amino terminal protease family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-06   26.4  21.4    7.5e-05   23.0  21.4    2.7  1  CPBP      CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
      0.041   12.7   0.2      0.073   11.9   0.2    1.3  1  DUF3537   Protein of unknown function (DUF3537)


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 !   23.0  21.4   8.4e-09   7.5e-05       6      91 ..     124     221 ..       9     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8.4e-09
                                       HHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGGHHHH...........HHHHHHHHHHHH CS
                              CPBP   6 lvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpngpsv...........llaalaGlvlgy 71 
                                        +++ ++++a+ lEE+++ g++   +q+ +s ++a+li + + +++H+p  +s+           +l++ + ++  +
  gi|330508672|ref|YP_004385100.1| 124 PFIFGLFFFAAALEEIGYTGYVTDPMQALYSALAACLIIGSIHAIWHWPSMISMgmapglfiwgsILTVSFRILTVW 200
                                       45666999*********************998******************5554556666666779999999***** PP

                                       HHHHT.T-HHHHHHHHHHHHH CS
                              CPBP  72 lylkt.gsllaaillHallnl 91 
                                       ly +t +s++aail+Ha++n+
  gi|330508672|ref|YP_004385100.1| 201 LYNNTgNSVFAAILFHAVTNT 221
                                       ****945799*********97 PP

>> DUF3537  Protein of unknown function (DUF3537)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   8.1e-06     0.073     105     182 ..     140     219 ..     135     222 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.1e-06
                           DUF3537 105 eYtaelersfrlLallvlpcflvelaykiiwfssvaseipllgnsvllsvvvl.vlelasWvYr.tavfllvcvLFr 179
                                       +Yt  +++ ++ L   ++ c+++  ++ i+   s+ s   + g  ++ s++ + +  l+ W+Y+ t+  +++++LF+
  gi|330508672|ref|YP_004385100.1| 140 GYTGYVTDPMQALYSALAACLIIGSIHAIWHWPSMISMGMAPGLFIWGSILTVsFRILTVWLYNnTGNSVFAAILFH 216
                                       799999999********************9765555443444446666665550556678***7377999******* PP

                           DUF3537 180 liC 182
                                        + 
  gi|330508672|ref|YP_004385100.1| 217 AVT 219
                                       986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); 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: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.59
# Mc/sec: 1420.73
//
Query:       gi|330508673|ref|YP_004385101.1|  [L=175]
Description: hypothetical protein MCON_2929 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-12   47.3   0.0    2.9e-12   47.1   0.0    1.1  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    1.3e-05   25.4   0.0    1.8e-05   24.9   0.0    1.3  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
    8.6e-05   22.8   0.0    9.9e-05   22.6   0.0    1.2  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro
  ------ inclusion threshold ------
      0.099   12.8   0.3       0.19   11.9   0.2    1.6  2  DUF3333          Domain of unknown function (DUF3333)


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   6.4e-16   2.9e-12       2     143 .]      34     172 ..      33     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 6.4e-16
                                       EEEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCS.SEEEEEEEEEETTTTEEEE CS
                   Polyketide_cyc2   2 vkvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggr.gtvreelvevdpegrllsy 77 
                                       ++++++v+i+a++ kVw +++dfe++p+W p++++  ++ ++g   +   ++   gr  t   +++  +p +r l++
  gi|330508673|ref|YP_004385101.1|  34 RTIQTEVTINATASKVWQVLTDFEAYPQWNPFIRQIDGAIQPGQ--QLIIELNLSGRtMTFNPTVLFMQP-ERELRW 107
                                       67899*****************************9988743444..44467776676677999*******.999999 PP

                                       EEE..SSS-TSEEEEEEEEECCET.EEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Polyketide_cyc2  78 riv.kpvpvanyvatwtvtpdggg.trvtwtgefdagplggpfekpaaakavkgdleagLerLkarle 143
                                        ++ +  ++++++ ++ ++p g++  r+  + +f++  +  pf+++ + +  +  +++  ++L++++e
  gi|330508673|ref|YP_004385101.1| 108 LGRfSIPGIFDGEHSLNIEPLGANrVRFIQSETFRG--ILVPFSGA-ILNDTEQSFQEMNQALREHAE 172
                                       998899****************87688999999994..66666544.445777778888888777765 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0     4e-09   1.8e-05       1      26 [.      42      67 ..      42     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4e-09
                                      ESS-HHHHHHHHTTTGGCCSCCCCEE CS
                    Polyketide_cyc  1 vpapadqvyalvadvesypeflphcs 26
                                      ++a a++v+++++d+e yp+++p+++
  gi|330508673|ref|YP_004385101.1| 42 INATASKVWQVLTDFEAYPQWNPFIR 67
                                      799********************987 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.2e-08   9.9e-05       1      85 [.      43     127 ..      43     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.2e-08
                                       SS-HHHHHHHHH-HHHHHHH.EEEEEEEE--STTEEEEEEETTTSEEEEEEEEEEEEETTTEEEEEEEEETSETEEE CS
                             AHSA1   1 dapperVfraltdpellkrW.ftlteaemdlrpGgkfrlrdspdgkefgnegeylevvpperlvytwrledepeeee 76 
                                       +a++++V+++ltd e+  +W   + +++  ++pG +  ++ +  g+ ++++ ++l ++p+++l +  r+  ++   +
  gi|330508673|ref|YP_004385101.1|  43 NATASKVWQVLTDFEAYPQWnPFIRQIDGAIQPGQQLIIELNLSGRTMTFNPTVLFMQPERELRWLGRFSIPG-IFD 118
                                       5899****************87788888888*****9997779**********************97766333.334 PP

                                       EEEEEEEEE CS
                             AHSA1  77 stvtielee 85 
                                        + ++++e+
  gi|330508673|ref|YP_004385101.1| 119 GEHSLNIEP 127
                                       555555555 PP

>> DUF3333  Domain of unknown function (DUF3333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   4.3e-05      0.19      26      58 ..      13      45 ..       3      67 .. 0.87
   2 ?   -3.0   0.0       1.7   7.5e+03      11      22 ..     102     113 ..     100     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.3e-05
                           DUF3333 26 llfLviLlvsIvskGltAFtqteitleveldae 58
                                      l+ LviL + ++  + t+ tq +i+ ev+++a+
  gi|330508673|ref|YP_004385101.1| 13 LILLVILYIAMLVAANTSITQRTIQTEVTINAT 45
                                      78899*************************987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                           DUF3333  11 ErrFrlyGiaAi 22 
                                       Er +r++G ++i
  gi|330508673|ref|YP_004385101.1| 102 ERELRWLGRFSI 113
                                       999*****9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 940.05
//
Query:       gi|330508674|ref|YP_004385102.1|  [L=111]
Description: carboxymuconolactone decarboxylase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-11   42.9   0.0    4.3e-11   42.7   0.0    1.1  1  CMD       Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
       0.07   12.4   0.0      0.071   12.4   0.0    1.1  1  GAPES1    Gammaproteobacterial periplasmic sensor domain


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 !   42.7   0.0   4.8e-15   4.3e-11       1      83 [.      23     105 ..      23     107 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 4.8e-15
                                       HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHH.HHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHH CS
                               CMD   1 pellraltalreallareggLdpkereLialavsaangceyCv.daHtraAleaGvteeeiaevlaqaaayagwpaa 76 
                                       p+l++a++al+ea++  +  Ld +++ Lia+++ aa   e    +  + a +e Gvt++ei +vl++   ++g+p +
  gi|330508674|ref|YP_004385102.1|  23 PDLYEAIVALNEAAYT-GKVLDYRTQKLIAMGINAAASDERATkKQMISAIKEFGVTKDEIVDVLRVVLLTSGMPPF 98 
                                       99*************9.999*********************88888888889***********************99 PP

                                       HHHHHHH CS
                               CMD  77 raAlaaa 83 
                                       ++ ++++
  gi|330508674|ref|YP_004385102.1|  99 TKGMKIL 105
                                       9988876 PP

>> GAPES1  Gammaproteobacterial periplasmic sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.9e-06     0.071     109     199 ..       7      92 ..       1     105 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-06
                            GAPES1 109 skddyskglGtleekfryyldlkkryvyfyelidsrkfilsnwsflkkgtigidrkdidklftGrtvlssiyqdddt 185
                                       ++  +++g+ +++   r y dl +  v ++e   + k    ++  +k  ++gi+  + d+  t + ++s i + + t
  gi|330508674|ref|YP_004385102.1|   7 EQVFFGEGMAMVK---RDYPDLYEAIVALNEAAYTGKV--LDYRTQKLIAMGINAAASDERATKKQMISAIKEFGVT 78 
                                       5555555555554...4567777777777776655553..3566677789*************************** PP

                            GAPES1 186 qenvlslltPvyla 199
                                       +++++ +l  v l+
  gi|330508674|ref|YP_004385102.1|  79 KDEIVDVLRVVLLT 92 
                                       *******9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.89
# Mc/sec: 377.19
//
Query:       gi|330508675|ref|YP_004385103.1|  [L=577]
Description: chloride channel (ClC) family chloride transporter [Methanosaeta concilii GP6]
Scores for complete 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-82  277.2  28.3    2.1e-82  277.2  28.3    2.0  2  Voltage_CLC  Voltage gated chloride channel
    2.5e-23   82.3   1.9    7.3e-12   45.6   0.2    2.6  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 !    7.1   1.0   0.00031       2.8     165     215 ..      18      72 ..       5      73 .. 0.77
   2 !  277.2  28.3   2.3e-86   2.1e-82       1     353 [.      65     414 ..      65     415 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00031
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH..CHHHH.HHH.HHHHHHHHHHH CS
                       Voltage_CLC 165 ilfvllGilgGllgalfvrlllkverlfrkle..klkik.krl.epalvgllvgl 215
                                       +l +++Gi gGl +++f +l+  ++ +f  +    l+ +  ++ +p+l+gl+vg 
  gi|330508675|ref|YP_004385103.1|  18 LLSIVVGISGGLGAVAFRKLVELSHDFFFGFLlpLLPNSyFVVlLPVLGGLIVGP 72 
                                       3589*********************976665434555557555599999999986 PP

  == domain 2  score: 277.2 bits;  conditional E-value: 2.3e-86
                                       HHHHHHHHCCCCC-GGGSC-SHHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHH CS
                       Voltage_CLC   1 lggllagllvklvapeaagsGipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsr 77 
                                       lggl++g l++++apea+g Gi++++ al+++ g ++ r  lv +++s++t+gsG+s+GreGp+  iGA++gs++++
  gi|330508675|ref|YP_004385103.1|  65 LGGLIVGPLIYKLAPEAKGDGISHIMIALQRFTGDIRKRAGLVLIFTSAITLGSGGSAGREGPIALIGASAGSAIGK 141
                                       589************************************************************************** PP

                                       HTT.--SHHHHHHHHHHHHHHHHHHHT-HHHHHHHHCTTTSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S-.T-- CS
                       Voltage_CLC  78 llklsrndrdrrlvaaGaAAGiAAaFnaPlgGvlfalEevsrefslrallpvfvasvvaalvlrlllgeepafgeve 154
                                        ++ls +d  + l  +G+A+GiAA+FnaP+gG++f++E++s++f++  ++p+++a+vv+  v+  l+   p+f   +
  gi|330508675|ref|YP_004385103.1| 142 AIRLSARD-LKVLTCCGVASGIAATFNAPMGGAIFSMEVISKKFTSLDAVPILLAAVVGKAVATELIDPVPEFV--N 215
                                       *****999.999******************************************************99999996..4 PP

                                       -...--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC..CSSSSCC CS
                       Voltage_CLC 155 slfalsllelilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgllvgllglllpa.svlgggye 230
                                         f +++++++l +++G l+G+l+ l+v+ ++++e +f++l   +++ +l+pa++gl  g++g+++ +  ++g gye
  gi|330508675|ref|YP_004385103.1| 216 PNFYFTTFDMVLCFFIGPLFGFLSFLWVKGYYFFEDRFQDL---PLPDILKPAVGGLTAGVCGIFFFEfGIMGVGYE 289
                                       458899**********************************9...9999*******************99******** PP

                                       HHHHHC...TT-S-HHHHHH...HHHHHHHHHHHHHCTT-CSBSHHHHHHHHHHHHHHHHHHHHHH-CTSSC...HH CS
                       Voltage_CLC 231 liasll...egstlllsllllllllllkllataltlgsgvpgGifaPsLviGAalGrlvglvlalllpgaassdpga 304
                                        i++++   ++ + +  lllll l llk+lat+ t+gsg +gG+faP+L+iG+++G + g+++++l+p++ + +p  
  gi|330508675|ref|YP_004385103.1| 290 GINNIFmlaARAPATDLLLLLLALGLLKMLATSSTVGSGGSGGVFAPTLYIGTMFGLAAGMLAEILAPDQIA-NPLD 365
                                       *****98853333366778889999*****************************************998777.5799 PP

                                       HHHHCCTHHHHHCCS-HHHHHHHHHHCC--GCCHHHHHHHHHHHHHHHC CS
                       Voltage_CLC 305 falvGmaaflagvtrapltaiviviEltgdlelllplmlavliAkavad 353
                                       + l+Gm+a++ag+++aplt+i++++E+tg+++ l+ l++++++++ va+
  gi|330508675|ref|YP_004385103.1| 366 YGLLGMGALFAGTAGAPLTCIFMITEMTGNYSGLPSLIICCITSYTVAR 414
                                       ***********************************************97 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.1   9.4e-13   8.5e-09       1      53 [.     446     497 ..     446     501 .. 0.93
   2 !   45.6   0.2   8.1e-16   7.3e-12       1      55 [.     508     564 ..     508     566 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 9.4e-13
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHT..SSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 Vgdimtrdvvtvppdttleealelmrekg..vsrlPVVdedgklvGivtlrDllr 53 
                                       Vg+ m+++v+tv+p + ++e+ + +  ++  ++++PVV ++g+lvG++t  D+ r
  gi|330508675|ref|YP_004385103.1| 446 VGEAMHKEVITVSPLCRISEVRDGI--YRcnYTGFPVV-DEGRLVGMITFDDIRR 497
                                       8999********************9..777799*****.6*************98 PP

  == domain 2  score: 45.6 bits;  conditional E-value: 8.1e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT..BEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedg..klvGivtlrDllral 55 
                                       V+++  r ++t++p ++ + a+++m e++v+rl VV++d+  kl+Gi+t++D++ra 
  gi|330508675|ref|YP_004385103.1| 508 VKEVAVRAPITINPHQSAKMAMDIMYENDVGRLAVVEKDDpqKLIGIITRSDVIRAY 564
                                       788888999****************9999*******5555569***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3780.63
//
Query:       gi|330508676|ref|YP_004385104.1|  [L=596]
Description: extracellular nuclease [Methanosaeta concilii GP6]
Scores for 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-06   26.9   0.1    6.5e-06   25.8   0.1    1.5  1  Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family


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 !   25.8   0.1   3.6e-10   6.5e-06      17     233 .]     320     586 ..     296     586 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.6e-10
                                       HHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHH.............TTCEEEEECCH................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxx................ RF
                     Exo_endo_phos  17 rrsdrladlltaydaDvlgLQEvdddelsriplllal.............ggflgasstsp................ 64 
                                        + + + + +t  +aDv+gL E+ +d + ++ +  +l              ++ + + +sp                
  gi|330508676|ref|YP_004385104.1| 320 LQRAKIIQAITDMKADVIGLIEIENDGYGNLSAIHDLcdglnaredgiglENYSFVDPGSPklgddlisvgliynrt 396
                                       5677899999999**************99998777778888888888776333333333336667777777777777 PP

                                       ........................................................ECSSSTTSSEEEEEECSTEEE CS
                                       ........................................................xxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos  65 ........................................................tgggggggnggavlsrfplts 85 
                                                                                                                    
  gi|330508676|ref|YP_004385104.1| 397 tirpigkaattsmgafssgnrqplaqtfeeistlerltvvvvhlksknppggdevaN-------------------- 453
                                       776666677444444444443333333333333333333333333333333333331.................... PP

                                       EEEEEEEETSSSSGCEEEEEEEEEEEEEEE.......CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos  86 lfrrtfiefndlvaalrreplaakleqlni.......ashrdhdlvrdlqllalllqvealnadrgapvivaGDfNa 155
                                                                             +++++ ++ ++   + +    + +  ++  ++++GD+N+
  gi|330508676|ref|YP_004385104.1| 454 -----------------------------GdnrdcgdGQGYWNGDRTRAANELIDWLSSDPTGSHDPDYLILGDMNS 501
                                       .............................355555665667777788888888888888888889999********* PP

                                       STSGGGBSCGHHHHHHCTTTHHSSCESCETTTTTTTTTTTEB-BEEEEEECHHHCCEEEEEEECCHHEEC....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                     Exo_endo_phos 156 rpsdddsrvlrtrglalapapvglyllgggptptyvtraggsrlDrilaspalalfrsgvlppplalvrr....... 225
                                         ++d+   l  +g  +        +l  ++ ++yv ++ ++ lD+ilasp+l+ +++g  ++  ++  +       
  gi|330508676|ref|YP_004385104.1| 502 YRNEDPIMALKRAGYVNQ-----ISSLLASNSYSYVFQGRWGELDHILASPSLTGQVTGASIWHINSDESpdfgysg 573
                                       888888888888888886.....8***************************99999999999988877779999999 PP

                                       .....TSSCSSSB CS
                                       .....xxxxxxxx RF
                     Exo_endo_phos 226 .....ealtlSDH 233
                                            +++ +SDH
  gi|330508676|ref|YP_004385104.1| 574 iwsspDKYRCSDH 586
                                       9999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3993.16
//
Query:       gi|330508677|ref|YP_004385105.1|  [L=318]
Description: hypothetical protein MCON_2934 [Methanosaeta concilii GP6]
Scores for complete 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-06   26.6   0.1    3.1e-05   24.0   0.1    2.2  2  Polbeta       Polymerase beta, Nucleotidyltransferase
    7.3e-05   23.0   0.1    0.00015   22.0   0.1    1.5  1  NTP_transf_2  Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.018   14.9   0.1      0.048   13.5   0.0    1.7  2  DUF294        Putative nucleotidyltransferase DUF294


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   5.2e-09   3.1e-05      10      55 ..      33      79 ..      29     115 .. 0.76
   2 ?   -0.5   0.0      0.22   1.3e+03      71      91 ..     149     169 ..     144     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.2e-09
                                      HHHHHSTTEEEEEE-S---.---EEEEEEEESS---HHHHHHHHHHH CS
                           Polbeta 10 ekeielaylFGSrakgkar.eeSDiDlavllkekldleeelelaael 55
                                      e++i++++lFGS a+g++   +SD+Dl + +k++  + +  ++a+ l
  gi|330508677|ref|YP_004385105.1| 33 EDDIDFILLFGSAARGEFIlGKSDVDLIIQTKSDAAVRRVERFAESL 79
                                      569**************99569**********996665555555444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.22
                                       TS-HHHHHHHHHS-EEEES-S CS
                           Polbeta  71 eapplllyeilkegkllyskd 91 
                                       +++++lly++  egk+l+ +d
  gi|330508677|ref|YP_004385105.1| 149 ASQLTLLYKMKYEGKILFGRD 169
                                       566899999999*****9998 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   2.5e-08   0.00015      16      48 ..      38      78 ..      23     134 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.5e-08
                                      EEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH.......H CS
                      NTP_transf_2 16 kvvlfGSyarGtalkg.SDiDllvvlpeevsre.......k 48
                                       + lfGS+arG++  g SD+Dl++ +++++           
  gi|330508677|ref|YP_004385105.1| 38 FILLFGSAARGEFILGkSDVDLIIQTKSDAAVRrverfaeS 78
                                      5889*********************9999654466666662 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     8e-06     0.048      53      99 ..      40      84 ..       5      88 .. 0.84
   2 ?   -2.2   0.0      0.55   3.3e+03      45      56 ..     287     301 ..     243     302 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8e-06
                            DUF294 53 lvmGSeGReEqtlktDqDnalvledeeeeaareyfaelaervneaLa 99
                                      l +GS++R+E +l    D  l+++  +++aa ++++++ae +  +L+
  gi|330508677|ref|YP_004385105.1| 40 LLFGSAARGEFILGK-SDVDLIIQT-KSDAAVRRVERFAESLFWRLN 84
                                      679********9975.566688888.7899999*******9988886 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.55
                            DUF294  45 k...ppvpfallvmG 56 
                                           +  +f+l+++G
  gi|330508677|ref|YP_004385105.1| 287 GsrwEALRFCLVAFG 301
                                       233345566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2282.67
//
Query:       gi|330508678|ref|YP_004385106.1|  [L=2314]
Description: hypothetical protein MCON_2937 [Methanosaeta concilii GP6]
Scores for complete 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-187  607.0  28.2    4.8e-09   36.7   0.1   22.3 22  Ig_3           Immunoglobulin domain
   1.7e-160  521.6  26.7    6.9e-07   29.3   0.0   25.1 22  I-set          Immunoglobulin I-set domain
   4.6e-103  337.7  47.6    5.6e-05   23.4   0.0   22.1 22  Ig_2           Immunoglobulin domain
    1.3e-31  108.2  43.4      0.088   12.7   0.1   20.1 20  PKD            PKD domain
    9.3e-19   67.4  32.9        2.5    8.3   0.0   18.2 18  ig             Immunoglobulin domain
      3e-18   65.9  10.5         16    5.8   0.0   17.8 21  Ig_4           T-cell surface glycoprotein CD3 delta chain
    6.4e-12   45.6  59.2         12    6.1   0.0   26.9 31  V-set          Immunoglobulin V-set domain
    1.7e-11   43.7  13.6        5.6    6.8   0.0   15.0 19  PKD_3          PKD-like domain
    5.1e-06   26.3   6.9         45    4.1   0.0   10.1 10  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
      7e-06   26.2   3.2         42    4.4   0.0    8.9 11  Ribosomal_S15  Ribosomal protein S15
     0.0001   22.5  22.5        2.2    8.5   0.0   12.6 16  Receptor_2B4   Natural killer cell receptor 2B4
  ------ inclusion threshold ------
        2.2    8.7   7.7        2.7    8.3   2.3    3.4  2  DUF5122        Domain of unknown function (DUF5122) beta-prop


Domain annotation for each model (and alignments):
>> Ig_3  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   5.7e-09   8.5e-06       2      79 .]     423     490 ..     422     490 .. 0.92
   2 !   31.7   0.1   1.2e-10   1.8e-07       1      79 []     507     575 ..     507     575 .. 0.93
   3 !   33.1   0.1   4.3e-11   6.4e-08       1      75 [.     592     656 ..     592     658 .. 0.92
   4 !   29.0   0.0   7.9e-10   1.2e-06       7      79 .]     687     748 ..     679     748 .. 0.81
   5 !   27.7   0.0   2.1e-09   3.1e-06       1      79 []     765     833 ..     765     833 .. 0.88
   6 !   22.1   0.0   1.1e-07   0.00017       2      79 .]     851     918 ..     850     918 .. 0.90
   7 !   19.2   0.0   9.1e-07    0.0014       1      79 []     935    1003 ..     935    1003 .. 0.88
   8 !   28.8   0.2   9.1e-10   1.4e-06       2      79 .]    1021    1088 ..    1020    1088 .. 0.90
   9 !   27.6   0.1   2.3e-09   3.4e-06       2      79 .]    1106    1173 ..    1105    1173 .. 0.89
  10 !   30.5   0.1   2.7e-10     4e-07       2      79 .]    1191    1258 ..    1190    1258 .. 0.90
  11 !   26.8   0.0     4e-09     6e-06       2      79 .]    1276    1343 ..    1275    1343 .. 0.89
  12 !   27.3   0.0   2.7e-09   4.1e-06       1      79 []    1360    1428 ..    1360    1428 .. 0.90
  13 !   21.0   0.0   2.5e-07   0.00038       1      79 []    1445    1513 ..    1445    1513 .. 0.89
  14 !   27.4   0.0   2.5e-09   3.8e-06       2      79 .]    1531    1598 ..    1530    1598 .. 0.90
  15 !   27.5   0.0   2.4e-09   3.6e-06       2      79 .]    1616    1683 ..    1615    1683 .. 0.89
  16 !   33.7   0.1   2.7e-11   4.1e-08       2      79 .]    1701    1768 ..    1700    1768 .. 0.93
  17 !   36.7   0.1   3.2e-12   4.8e-09       1      79 []    1785    1853 ..    1785    1853 .. 0.90
  18 !   22.2   0.0     1e-07   0.00016       2      79 .]    1871    1938 ..    1871    1938 .. 0.90
  19 !   26.4   0.0   5.4e-09     8e-06       2      76 ..    1956    2020 ..    1955    2022 .. 0.85
  20 !   27.0   0.0   3.5e-09   5.2e-06       2      79 .]    2041    2108 ..    2041    2108 .. 0.89
  21 !   33.6   0.0   2.9e-11   4.3e-08       2      79 .]    2126    2193 ..    2126    2193 .. 0.90
  22 !   16.1   0.0   8.3e-06     0.012      11      79 .]    2221    2279 ..    2213    2279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 5.7e-09
                                       EEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEEEE CS
                              Ig_3   2 PvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCvAs 78 
                                       P I ++p + ++ e ++++++  a gn p +++W kng+   +         + ++ s++i+ ++  d+G+Y+ ++s
  gi|330508678|ref|YP_004385106.1| 423 PMIEIQPADYSACEDQEARFNVVAAGNGPISYQWSKNGS---Q---I----AGATTDSYIIPAAKLADAGSYRVRVS 489
                                       999*********************888888*********...3...2....3678889******************* PP

                                       E CS
                              Ig_3  79 N 79 
                                       N
  gi|330508678|ref|YP_004385106.1| 490 N 490
                                       9 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 1.2e-10
                                       EEEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEEE CS
                              Ig_3   1 kPvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCvA 77 
                                       kPv+ ++p ++++ eg++v L+ +a+g+ p +++W+knge   +        ++ +++++ is++ ++d+G Y+  +
  gi|330508678|ref|YP_004385106.1| 507 KPVVEIEPLDEIACEGSEVLLNAQASGTEPLNYQWKKNGE---N---I----TGANTNRYLISSILPTDEGDYSLAV 573
                                       9************************888888*********...5...3....478999****************999 PP

                                       EE CS
                              Ig_3  78 sN 79 
                                       sN
  gi|330508678|ref|YP_004385106.1| 574 SN 575
                                       98 PP

  == domain 3  score: 33.1 bits;  conditional E-value: 4.3e-11
                                       EEEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEE CS
                              Ig_3   1 kPvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtC 75 
                                       +P+I v+p s++v  g++v+++ ++ gn + t++W+k+g    +        ++ + + L+is ++ +d+G+Y+ 
  gi|330508678|ref|YP_004385106.1| 592 RPKILVQPISQTVCTGSPVSFEVQVAGNESYTYQWQKDGL---N---I----TAANAAVLSISAANSTDQGNYSV 656
                                       5************************999999*********...5...3....478999***************86 PP

  == domain 4  score: 29.0 bits;  conditional E-value: 7.9e-10
                                       CCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEEEEE CS
                              Ig_3   7 ppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCvAsN 79 
                                       p s+  + eg+++ L   ++g++p ti+W+k+g ++     +     + +  s++i+n+t++dsG+Y+ ++sN
  gi|330508678|ref|YP_004385106.1| 687 PASKK-ICEGSDIALVADVTGSDPITIQWMKDGLQI-----P-----GANLDSFVIKNATRNDSGSYSLIVSN 748
                                       33333.79***********999999*********32.....2.....567789******************99 PP

  == domain 5  score: 27.7 bits;  conditional E-value: 2.1e-09
                                       EEEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEEE CS
                              Ig_3   1 kPvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCvA 77 
                                       +P+I v+p +  v +g  +t++ +a+++ p +++W+k+g k           ++ +s  +ti++ + sd G+Y+ ++
  gi|330508678|ref|YP_004385106.1| 765 RPEILVQPANLRVCQGAAATFSVQAKSSEPLSYQWFKDGIK------I----DGATSEYYTIPQTNLSDMGSYSVQV 831
                                       5************************555555*********4......2....3567778****************99 PP

                                       EE CS
                              Ig_3  78 sN 79 
                                        N
  gi|330508678|ref|YP_004385106.1| 832 AN 833
                                       98 PP

  == domain 6  score: 22.1 bits;  conditional E-value: 1.1e-07
                                       EEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEEEE CS
                              Ig_3   2 PvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCvAs 78 
                                       P+I ++p + ++ +g  ++++ +ae++ p +++W+k+g    +   +     + +s ++ i+  + +d+G+Y+ + +
  gi|330508678|ref|YP_004385106.1| 851 PKILLQPANLKICQGAAAKFEVQAESSEPLSYQWLKDGV---N--IP-----AATSDTYAIPASNLNDTGSYSVQIT 917
                                       9***********************666666*********...5..23.....678899****************999 PP

                                       E CS
                              Ig_3  79 N 79 
                                       N
  gi|330508678|ref|YP_004385106.1| 918 N 918
                                       9 PP

  == domain 7  score: 19.2 bits;  conditional E-value: 9.1e-07
                                        EEEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEE CS
                              Ig_3    1 kPvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtC 75  
                                        +P+I ++p + ++ +g +++++ ++e++ p +++W+k+g ++     +     + +  ++ti+ ++  d G+Y+ 
  gi|330508678|ref|YP_004385106.1|  935 RPKILLHPANLKICQGAKAKFEVQIESTEPLKYQWLKDGIEI-----P-----GATDDRYTIDLADIADMGSYSV 999 
                                        5************************777766*********42.....2.....5667799**************9 PP

                                        EEEE CS
                              Ig_3   76 vAsN 79  
                                         + N
  gi|330508678|ref|YP_004385106.1| 1000 LVAN 1003
                                        9988 PP

  == domain 8  score: 28.8 bits;  conditional E-value: 9.1e-10
                                        EEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEE CS
                              Ig_3    2 PvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCv 76  
                                        P I ++p+s+ v +g ++ ++ +ae++ p +++W+k+g k           ++ +s s+ti++ + sd+G+Y+ +
  gi|330508678|ref|YP_004385106.1| 1021 PDILAQPTSQNVCQGTRAAFSVQAESSEPLSYQWLKEGIK------I----EGATSESYTIPQTSLSDTGSYSVQ 1085
                                        99**********************666666*********4......2....3677889***************** PP

                                        EEE CS
                              Ig_3   77 AsN 79  
                                        +sN
  gi|330508678|ref|YP_004385106.1| 1086 VSN 1088
                                        **9 PP

  == domain 9  score: 27.6 bits;  conditional E-value: 2.3e-09
                                        EEEECCCSCEEEETTS-EEEEEEEEEES--.EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEE CS
                              Ig_3    2 PvItvppsstvvtegesvtLtCeaegnppp.titWykngeklssnstsssissegssssLtisnvtksdsGtYtC 75  
                                        P I ++p+s++v +g  +t++ +a  +++p +++W+k+g    +        ++  s ++ti+  + +d+G+Y+ 
  gi|330508678|ref|YP_004385106.1| 1106 PDILAQPTSQKVCQGTAATFSVQA-RSSEPlSYQWLKDGV---N---I----QGAASDTYTIPASNLNDTGSYSV 1169
                                        99**********************.555566*********...5...3....3678899***************9 PP

                                        EEEE CS
                              Ig_3   76 vAsN 79  
                                        + +N
  gi|330508678|ref|YP_004385106.1| 1170 QLRN 1173
                                        9988 PP

  == domain 10  score: 30.5 bits;  conditional E-value: 2.7e-10
                                        EEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEE CS
                              Ig_3    2 PvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCv 76  
                                        P+I ++p+s+ v +g ++ ++ +a+++ p +++W+k+g k           ++ +s s+ i+ ++ sd+G+Y+ +
  gi|330508678|ref|YP_004385106.1| 1191 PQILSQPTSQNVCQGTRAAFSVQAKSSEPLSYQWFKDGIK------I----DGATSESYAIPAASLSDTGSYSVQ 1255
                                        9***********************555555*********4......2....3567889***************** PP

                                        EEE CS
                              Ig_3   77 AsN 79  
                                        +sN
  gi|330508678|ref|YP_004385106.1| 1256 VSN 1258
                                        **9 PP

  == domain 11  score: 26.8 bits;  conditional E-value: 4e-09
                                        EEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEE CS
                              Ig_3    2 PvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCv 76  
                                        P+I ++p  +   eg + t++ +ae++ p +++W+k+g k           ++ +s  +ti++ + sd G+Y+ +
  gi|330508678|ref|YP_004385106.1| 1276 PEILIQPVGQRGCEGATTTFSVQAESSEPLSYQWFKDGIK------I----DGATSEYYTIPQTNLSDMGSYSVQ 1340
                                        9***********************666666*********4......2....3567778***************** PP

                                        EEE CS
                              Ig_3   77 AsN 79  
                                        +sN
  gi|330508678|ref|YP_004385106.1| 1341 VSN 1343
                                        **9 PP

  == domain 12  score: 27.3 bits;  conditional E-value: 2.7e-09
                                        EEEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEE CS
                              Ig_3    1 kPvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtC 75  
                                        +P+I ++p + ++ +g  ++++ +ae++ p +++W+k+g    +   +     + +s ++ti+ ++ +d+G+Y+ 
  gi|330508678|ref|YP_004385106.1| 1360 RPKILLQPANLKICQGAAAKFEVQAESSEPLSYQWLKDGA---N--IP-----GATSDTYTIPAAKLNDTGSYSV 1424
                                        5************************666666*********...5..23.....67889***************** PP

                                        EEEE CS
                              Ig_3   76 vAsN 79  
                                        ++ N
  gi|330508678|ref|YP_004385106.1| 1425 QVAN 1428
                                        9998 PP

  == domain 13  score: 21.0 bits;  conditional E-value: 2.5e-07
                                        EEEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEE CS
                              Ig_3    1 kPvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtC 75  
                                        +P+I ++p + ++ +g  +t++ ea+++ p +++W+k+g ++     +     + +  ++ti+ ++  d G+Y+ 
  gi|330508678|ref|YP_004385106.1| 1445 RPKILLQPANLMICQGAAATFHVEASSYEPIEYQWLKDGIEI-----P-----GATDDRYTIDLADIADVGSYSV 1509
                                        5************************888888*********42.....2.....5667799*************99 PP

                                        EEEE CS
                              Ig_3   76 vAsN 79  
                                         + N
  gi|330508678|ref|YP_004385106.1| 1510 LVAN 1513
                                        9988 PP

  == domain 14  score: 27.4 bits;  conditional E-value: 2.5e-09
                                        EEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEE CS
                              Ig_3    2 PvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCv 76  
                                        P I ++p+ + + +g  vt+  +a+++ p +++W+k+g    +   +     +  s ++ti+ ++ sd G+Y+ +
  gi|330508678|ref|YP_004385106.1| 1531 PDILAQPTRQRICQGTMVTFAVQAKSSEPLRYQWLKDGV---N--IP-----GAASDTYTIPAANLSDMGSYSVQ 1595
                                        99**********************555555*********...5..23.....67889****************** PP

                                        EEE CS
                              Ig_3   77 AsN 79  
                                        +sN
  gi|330508678|ref|YP_004385106.1| 1596 VSN 1598
                                        **9 PP

  == domain 15  score: 27.5 bits;  conditional E-value: 2.4e-09
                                        EEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEE CS
                              Ig_3    2 PvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCv 76  
                                        P I ++p+ ++v +g  +t++ +a+++ p +++W+++g    +   +     + +s s+ti  ++ sd+G+Y+  
  gi|330508678|ref|YP_004385106.1| 1616 PDILAQPTGQKVCQGTAATFSVQAKSSEPLSYQWLRDGA---N--IP-----DATSESYTILAANLSDTGSYSVL 1680
                                        99**********************555555*********...5..23.....678899***************99 PP

                                        EEE CS
                              Ig_3   77 AsN 79  
                                        + N
  gi|330508678|ref|YP_004385106.1| 1681 VAN 1683
                                        988 PP

  == domain 16  score: 33.7 bits;  conditional E-value: 2.7e-11
                                        EEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEE CS
                              Ig_3    2 PvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCv 76  
                                        P I v+p+s +  eg  +t+  +a+g+ p +++Wyk+g+   +        ++ +s+s++i+ +++sd+G+Y+ +
  gi|330508678|ref|YP_004385106.1| 1701 PDILVQPKSLETCEGAAATFGVKASGGEPLEYQWYKDGT---E---I----EGATSNSYSIPVASPSDRGSYWVQ 1765
                                        99**********************999999*********...5...3....467899****************** PP

                                        EEE CS
                              Ig_3   77 AsN 79  
                                        ++N
  gi|330508678|ref|YP_004385106.1| 1766 VRN 1768
                                        *99 PP

  == domain 17  score: 36.7 bits;  conditional E-value: 3.2e-12
                                        EEEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEE CS
                              Ig_3    1 kPvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtC 75  
                                        kP+I vpp+s+++ +g+ vt+t ++e++ p +++W+k+g k      +     + ++  +ti ++  +d+G+Y+ 
  gi|330508678|ref|YP_004385106.1| 1785 KPEILVPPTSQKICQGSAVTFTVQVESSKPLSYQWFKDGIK-I----P-----GATQDVYTIARAVLNDTGSYWV 1849
                                        9************************666666*********4.2....2.....567789**************** PP

                                        EEEE CS
                              Ig_3   76 vAsN 79  
                                        +A N
  gi|330508678|ref|YP_004385106.1| 1850 QAAN 1853
                                        **99 PP

  == domain 18  score: 22.2 bits;  conditional E-value: 1e-07
                                        EEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEE CS
                              Ig_3    2 PvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCv 76  
                                        P+I +pp s++v eg  +t+  +ae++ + +++W+k+g ++           e +   +ti++  k d G+Y  +
  gi|330508678|ref|YP_004385106.1| 1871 PEIHLPPASQKVCEGAAATFFVQAESSEALSYQWFKDGIEIY----------EATADAYTIPRTGKFDMGNYMVQ 1935
                                        9***********************888888*********433..........4556689**************** PP

                                        EEE CS
                              Ig_3   77 AsN 79  
                                        ++N
  gi|330508678|ref|YP_004385106.1| 1936 VRN 1938
                                        999 PP

  == domain 19  score: 26.4 bits;  conditional E-value: 5.4e-09
                                        EEEECCCSCEEEETTS-EEEEEEEEEES--.EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEE CS
                              Ig_3    2 PvItvppsstvvtegesvtLtCeaegnppp.titWykngeklssnstsssissegssssLtisnvtksdsGtYtC 75  
                                        P+I vpp+ + v +g+ +t++ +a+++ +p +++W+k+g+ ++          + +  ++ti+ +t  d+ +Y+ 
  gi|330508678|ref|YP_004385106.1| 1956 PKILVPPKGQRVCQGDAATFSVQASSS-EPlSYQWFKDGKMIQ----------GATADTYTIPAATFGDTASYSV 2019
                                        9***********************555.555*********433..........4566799999999999999987 PP

                                        E CS
                              Ig_3   76 v 76  
                                        +
  gi|330508678|ref|YP_004385106.1| 2020 Q 2020
                                        6 PP

  == domain 20  score: 27.0 bits;  conditional E-value: 3.5e-09
                                        EEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEE CS
                              Ig_3    2 PvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCv 76  
                                        P I+++p s++v +g +vt++ +a +++p +++W+k+g ++           +     +ti+++   d+G+Y+ +
  gi|330508678|ref|YP_004385106.1| 2041 PAISLQPASQIVCQGTPVTFNVRAISDDPLSYQWFKDGVEIP----------GAIAEVYTIQKAITGDKGSYYVQ 2105
                                        89**********************666666*********422..........455678***************** PP

                                        EEE CS
                              Ig_3   77 AsN 79  
                                        A+N
  gi|330508678|ref|YP_004385106.1| 2106 ARN 2108
                                        **9 PP

  == domain 21  score: 33.6 bits;  conditional E-value: 2.9e-11
                                        EEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEE CS
                              Ig_3    2 PvItvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCv 76  
                                        P+I v+p+s++v eg+++t+t  a++ +p t++W k+g+ + +         + +s +Lti +++ +d G+Y+  
  gi|330508678|ref|YP_004385106.1| 2126 PEILVQPTSQKVCEGSTATFTVLAKSAQPLTYQWIKGGR-IIP---------GANSEELTIFDANMEDMGEYRVA 2190
                                        9***********************666666*********.333.........678899***************99 PP

                                        EEE CS
                              Ig_3   77 AsN 79  
                                         sN
  gi|330508678|ref|YP_004385106.1| 2191 ISN 2193
                                        998 PP

  == domain 22  score: 16.1 bits;  conditional E-value: 8.3e-06
                                        EEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEEEEE CS
                              Ig_3   11 tvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCvAsN 79  
                                         ++  ge+v +  + ++  +++++W knge + +         ++ s sL+i n ++sdsG Y+ ++sN
  gi|330508678|ref|YP_004385106.1| 2221 LIADAGETVAFIMKGTAVGANSYQWEKNGE-IIP---------GEVSPSLIILNPRPSDSGGYRLTVSN 2279
                                        557789999999999999999*********.344.........466779******************99 PP

>> I-set  Immunoglobulin I-set domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   8.4e-10   1.3e-06       1      85 [.     423     498 ..     423     504 .. 0.89
   2 !   20.3   0.0     3e-07   0.00044       1      84 [.     508     582 ..     508     587 .. 0.86
   3 !   22.5   0.1   5.7e-08   8.5e-05       1      76 [.     593     659 ..     593     675 .. 0.86
   4 !   29.3   0.0   4.6e-10   6.9e-07       8      86 ..     688     757 ..     684     760 .. 0.89
   5 !   27.4   0.0   1.8e-09   2.6e-06       1      86 [.     766     842 ..     766     846 .. 0.90
   6 !   22.1   0.0   7.9e-08   0.00012       1      86 [.     851     927 ..     851     932 .. 0.87
   7 !   25.8   0.0   5.6e-09   8.3e-06       1      86 [.     936    1012 ..     936    1017 .. 0.85
   8 !   22.4   0.1   6.3e-08   9.4e-05       1      87 [.    1021    1098 ..    1021    1101 .. 0.89
   9 !   20.6   0.0   2.3e-07   0.00034       1      86 [.    1106    1182 ..    1106    1187 .. 0.88
  10 !   25.0   0.1   9.5e-09   1.4e-05       1      88 [.    1191    1270 ..    1191    1272 .. 0.85
  11 !   23.0   0.0   4.1e-08   6.1e-05       2      86 ..    1277    1352 ..    1276    1357 .. 0.82
  12 !   26.0   0.0   4.8e-09   7.2e-06       1      86 [.    1361    1437 ..    1361    1441 .. 0.90
  13 !   18.3   0.0   1.2e-06    0.0018       1      86 [.    1446    1522 ..    1446    1527 .. 0.87
  14 !   23.9   0.0   2.1e-08   3.2e-05       1      87 [.    1531    1608 ..    1531    1611 .. 0.90
  15 !   21.0   0.0   1.8e-07   0.00026       1      86 [.    1616    1692 ..    1616    1697 .. 0.87
  16 !   23.6   0.0   2.7e-08     4e-05       1      82 [.    1701    1773 ..    1701    1781 .. 0.87
  17 !   23.9   0.1   2.2e-08   3.2e-05       1      86 [.    1786    1862 ..    1786    1867 .. 0.87
  18 !   25.5   0.0     7e-09     1e-05       1      86 [.    1871    1947 ..    1871    1950 .. 0.91
  19 !   18.8   0.0   8.4e-07    0.0013       1      78 [.    1956    2024 ..    1956    2036 .. 0.83
  20 !   23.9   0.0   2.1e-08   3.2e-05       1      85 [.    2041    2116 ..    2041    2122 .. 0.87
  21 !   24.3   0.0   1.6e-08   2.4e-05       1      80 [.    2126    2196 ..    2126    2207 .. 0.88
  22 !   14.7   0.0   1.6e-05     0.024       6      88 ..    2217    2290 ..    2213    2291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 8.4e-10
                                       EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEEEE CS
                             I-set   1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtckatn 77 
                                       p +++++ d  + e++++++++ + G++++s +W k+gs+++            + + +I  ++ +D+G+Y+++++n
  gi|330508678|ref|YP_004385106.1| 423 PMIEIQPADYSACEDQEARFNVVAAGNGPISYQWSKNGSQIAG------AT---TDSYIIPAAKLADAGSYRVRVSN 490
                                       78999*************************************6......22...34689****************** PP

                                       TSEEEEEE CS
                             I-set  78 sagkaeak 85 
                                         g+ e++
  gi|330508678|ref|YP_004385106.1| 491 ACGSIESN 498
                                       *9987764 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 3e-07
                                       EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEEEE CS
                             I-set   1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtckatn 77 
                                       p++++++ d  + eG++v l+++++G+++++ +W+k+g++++           ++ +  Is++ + DeG+Y++ ++n
  gi|330508678|ref|YP_004385106.1| 508 PVVEIEPLDEIACEGSEVLLNAQASGTEPLNYQWKKNGENITG---------ANTNRYLISSILPTDEGDYSLAVSN 575
                                       5677777788889****************************96.........23346789***************** PP

                                       TSEEEEE CS
                             I-set  78 sagkaea 84 
                                         g ae+
  gi|330508678|ref|YP_004385106.1| 576 ICGMAES 582
                                       9998886 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 5.7e-08
                                       EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEEE CS
                             I-set   1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtckat 76 
                                       pk+  ++ +++v +G+ v++e++v G++  + +W+kdg +++           + + L Is +++ D+G+Y++ + 
  gi|330508678|ref|YP_004385106.1| 593 PKILVQPISQTVCTGSPVSFEVQVAGNESYTYQWQKDGLNITA---------ANAAVLSISAANSTDQGNYSVIIG 659
                                       788999999*****************************99995.........345799*************99875 PP

  == domain 4  score: 29.3 bits;  conditional E-value: 4.6e-10
                                       CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEEEETSEEEEE CS
                             I-set   8 kdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtckatnsagkaea 84 
                                        + ++ eG+++ l ++v+G+ +++++W+kdg ++            +  +++I+n++++D+G+Y++ ++n  g+ e+
  gi|330508678|ref|YP_004385106.1| 688 ASKKICEGSDIALVADVTGSDPITIQWMKDGLQIPG---------ANLDSFVIKNATRNDSGSYSLIVSNDCGQIES 755
                                       5678899***************************96.........34469***********************9987 PP

                                       EE CS
                             I-set  85 ka 86 
                                        a
  gi|330508678|ref|YP_004385106.1| 756 IA 757
                                       65 PP

  == domain 5  score: 27.4 bits;  conditional E-value: 1.8e-09
                                       EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEEEE CS
                             I-set   1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtckatn 77 
                                       p++  ++ ++ v +G +++++++++ ++++s +W+kdg ++          +      tI + + sD+G+Y++++ n
  gi|330508678|ref|YP_004385106.1| 766 PEILVQPANLRVCQGAAATFSVQAKSSEPLSYQWFKDGIKIDG------ATS---EYYTIPQTNLSDMGSYSVQVAN 833
                                       788999***********************************95......222...3568****************** PP

                                       TSEEEEEEE CS
                             I-set  78 sagkaeaka 86 
                                       +  ++e++a
  gi|330508678|ref|YP_004385106.1| 834 NCSQVESEA 842
                                       *99999876 PP

  == domain 6  score: 22.1 bits;  conditional E-value: 7.9e-08
                                       EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEEEE CS
                             I-set   1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtckatn 77 
                                       pk+  ++ ++++ +G ++++e+++e ++++s +W+kdg ++          +    t  I   + +D+G+Y++++tn
  gi|330508678|ref|YP_004385106.1| 851 PKILLQPANLKICQGAAAKFEVQAESSEPLSYQWLKDGVNIPA------ATS---DTYAIPASNLNDTGSYSVQITN 918
                                       7888999*********************************996......233...477899999************* PP

                                       TSEEEEEEE CS
                             I-set  78 sagkaeaka 86 
                                       +  + e++a
  gi|330508678|ref|YP_004385106.1| 919 NCSQIESEA 927
                                       *87777654 PP

  == domain 7  score: 25.8 bits;  conditional E-value: 5.6e-09
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        pk+  ++ ++++ +G ++++e+++e +++++ +W+kdg e+         +++   + tI+ ++++D+G+Y++ +
  gi|330508678|ref|YP_004385106.1|  936 PKILLHPANLKICQGAKAKFEVQIESTEPLKYQWLKDGIEIPG-------ATD--DRYTIDLADIADMGSYSVLV 1001
                                        67888999*********************************96.......344..3567999999********** PP

                                        EETSEEEEEEE CS
                             I-set   76 tnsagkaeaka 86  
                                         ns  + e++a
  gi|330508678|ref|YP_004385106.1| 1002 ANSCSQIESEA 1012
                                        ***77766554 PP

  == domain 8  score: 22.4 bits;  conditional E-value: 6.3e-08
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        p +  ++++++v +G+++ +++++e ++++s +W+k+g +++         +    + tI + + sD+G+Y++++
  gi|330508678|ref|YP_004385106.1| 1021 PDILAQPTSQNVCQGTRAAFSVQAESSEPLSYQWLKEGIKIEG------ATS---ESYTIPQTSLSDTGSYSVQV 1086
                                        67889999*********************************96......222...3679**************** PP

                                        EETSEEEEEEEE CS
                             I-set   76 tnsagkaeakae 87  
                                        +n+  + e++a 
  gi|330508678|ref|YP_004385106.1| 1087 SNNCSRIESEAA 1098
                                        ***988887775 PP

  == domain 9  score: 20.6 bits;  conditional E-value: 2.3e-07
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        p +  ++++++v +G++++++++++ ++++s +W+kdg +++           a+ t tI   + +D+G+Y+++ 
  gi|330508678|ref|YP_004385106.1| 1106 PDILAQPTSQKVCQGTAATFSVQARSSEPLSYQWLKDGVNIQG------A---ASDTYTIPASNLNDTGSYSVQL 1171
                                        6788999*********************************996......3...345889**************** PP

                                        EETSEEEEEEE CS
                             I-set   76 tnsagkaeaka 86  
                                        +n+  + e++a
  gi|330508678|ref|YP_004385106.1| 1172 RNNCSQIESEA 1182
                                        ***87776654 PP

  == domain 10  score: 25.0 bits;  conditional E-value: 9.5e-09
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        p++  ++++++v +G+++ ++++++ ++++s +W+kdg ++          +    +  I  ++ sD+G+Y++++
  gi|330508678|ref|YP_004385106.1| 1191 PQILSQPTSQNVCQGTRAAFSVQAKSSEPLSYQWFKDGIKIDG------ATS---ESYAIPAASLSDTGSYSVQV 1256
                                        78999************************************96......222...3678**************** PP

                                        EET.SEEEEEEEEE CS
                             I-set   76 tns.agkaeakaeL 88  
                                        +n+ ++ +++ a+L
  gi|330508678|ref|YP_004385106.1| 1257 SNNcSQIKSEAASL 1270
                                        ***44445555566 PP

  == domain 11  score: 23.0 bits;  conditional E-value: 4.1e-08
                                        EEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEEE CS
                             I-set    2 kftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtckat 76  
                                        ++ +++  +   eG + ++++++e ++++s +W+kdg ++          +      tI + + sD+G+Y+++++
  gi|330508678|ref|YP_004385106.1| 1277 EILIQPVGQRGCEGATTTFSVQAESSEPLSYQWFKDGIKIDG------ATS---EYYTIPQTNLSDMGSYSVQVS 1342
                                        6666777777789***************************95......222...3568***************** PP

                                        ETSEEEEEEE CS
                             I-set   77 nsagkaeaka 86  
                                        n+  + e++a
  gi|330508678|ref|YP_004385106.1| 1343 NNCSQIESEA 1352
                                        **77766554 PP

  == domain 12  score: 26.0 bits;  conditional E-value: 4.8e-09
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        pk+  ++ ++++ +G ++++e+++e ++++s +W+kdg ++             + t tI  ++ +D+G+Y++++
  gi|330508678|ref|YP_004385106.1| 1361 PKILLQPANLKICQGAAAKFEVQAESSEPLSYQWLKDGANIPG------AT---SDTYTIPAAKLNDTGSYSVQV 1426
                                        7888999***********************************6......22...34789**************** PP

                                        EETSEEEEEEE CS
                             I-set   76 tnsagkaeaka 86  
                                         n+  + e+++
  gi|330508678|ref|YP_004385106.1| 1427 ANNCSQIESEV 1437
                                        ***99988876 PP

  == domain 13  score: 18.3 bits;  conditional E-value: 1.2e-06
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        pk+  ++ ++ + +G ++++ ++++  ++++ +W+kdg e+         +++   + tI+ ++++D G+Y++ +
  gi|330508678|ref|YP_004385106.1| 1446 PKILLQPANLMICQGAAATFHVEASSYEPIEYQWLKDGIEIPG-------ATD--DRYTIDLADIADVGSYSVLV 1511
                                        6888899999*******************************96.......344..3567899999********** PP

                                        EETSEEEEEEE CS
                             I-set   76 tnsagkaeaka 86  
                                         n+  ++e++a
  gi|330508678|ref|YP_004385106.1| 1512 ANNCSQVESEA 1522
                                        ***88888765 PP

  == domain 14  score: 23.9 bits;  conditional E-value: 2.1e-08
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        p +  +++++ + +G+ v++ ++++ +++++ +W+kdg ++            a+ t tI  ++ sD+G+Y++++
  gi|330508678|ref|YP_004385106.1| 1531 PDILAQPTRQRICQGTMVTFAVQAKSSEPLRYQWLKDGVNIPG------A---ASDTYTIPAANLSDMGSYSVQV 1596
                                        6788899999*******************************96......2...345889**************** PP

                                        EETSEEEEEEEE CS
                             I-set   76 tnsagkaeakae 87  
                                        +n+  + e++a 
  gi|330508678|ref|YP_004385106.1| 1597 SNNCSQIESEAA 1608
                                        ***999998876 PP

  == domain 15  score: 21.0 bits;  conditional E-value: 1.8e-07
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        p +  +++ ++v +G++++++++++ ++++s +W++dg ++         ++  + + tI  ++ sD+G+Y++ +
  gi|330508678|ref|YP_004385106.1| 1616 PDILAQPTGQKVCQGTAATFSVQAKSSEPLSYQWLRDGANIPD-------AT--SESYTILAANLSDTGSYSVLV 1681
                                        6688899999********************************6.......22..246799*************** PP

                                        EETSEEEEEEE CS
                             I-set   76 tnsagkaeaka 86  
                                         n+  + e++a
  gi|330508678|ref|YP_004385106.1| 1682 ANKCNQIESEA 1692
                                        ***88877664 PP

  == domain 16  score: 23.6 bits;  conditional E-value: 2.7e-08
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        p +  ++k++e+ eG ++++ ++++G ++++ +W+kdg+e++        +++   +  I  +++sD G+Y +++
  gi|330508678|ref|YP_004385106.1| 1701 PDILVQPKSLETCEGAAATFGVKASGGEPLEYQWYKDGTEIEG-------ATS--NSYSIPVASPSDRGSYWVQV 1766
                                        678899************************************6.......222..34579999************ PP

                                        EETSEEE CS
                             I-set   76 tnsagka 82  
                                        +ns  + 
  gi|330508678|ref|YP_004385106.1| 1767 RNSCSQI 1773
                                        **97765 PP

  == domain 17  score: 23.9 bits;  conditional E-value: 2.2e-08
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        p++  +++++++ +G++v+++++ve ++++s +W+kdg ++         +++     tI ++  +D+G+Y ++a
  gi|330508678|ref|YP_004385106.1| 1786 PEILVPPTSQKICQGSAVTFTVQVESSKPLSYQWFKDGIKIPG-------ATQ--DVYTIARAVLNDTGSYWVQA 1851
                                        7888999***********************************6.......233..34689*************** PP

                                        EETSEEEEEEE CS
                             I-set   76 tnsagkaeaka 86  
                                         n+  + ++ a
  gi|330508678|ref|YP_004385106.1| 1852 ANNCSQIKSGA 1862
                                        **987766654 PP

  == domain 18  score: 25.5 bits;  conditional E-value: 7e-09
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        p++  ++ +++v eG ++++ +++e ++ +s +W+kdg e+ +      t++      tI +  + D+G+Y +++
  gi|330508678|ref|YP_004385106.1| 1871 PEIHLPPASQKVCEGAAATFFVQAESSEALSYQWFKDGIEIYE-----ATADA----YTIPRTGKFDMGNYMVQV 1936
                                        67888999********************************985.....45555....68**************** PP

                                        EETSEEEEEEE CS
                             I-set   76 tnsagkaeaka 86  
                                        +ns g++e+ka
  gi|330508678|ref|YP_004385106.1| 1937 RNSCGSVESKA 1947
                                        ********997 PP

  == domain 19  score: 18.8 bits;  conditional E-value: 8.4e-07
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        pk+  ++k + v +G++++++++++ ++++s +W+kdg+ ++        ++    t tI  ++  D+ +Y++++
  gi|330508678|ref|YP_004385106.1| 1956 PKILVPPKGQRVCQGDAATFSVQASSSEPLSYQWFKDGKMIQG-------ATA--DTYTIPAATFGDTASYSVQI 2021
                                        789999***********************************96.......222..35678888888888888887 PP

                                        EET CS
                             I-set   76 tns 78  
                                        + +
  gi|330508678|ref|YP_004385106.1| 2022 RDR 2024
                                        655 PP

  == domain 20  score: 23.9 bits;  conditional E-value: 2.1e-08
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        p ++ ++ ++ v +G+ v++++++  + ++s +W+kdg e+       + +       tI+++ + D+G+Y ++a
  gi|330508678|ref|YP_004385106.1| 2041 PAISLQPASQIVCQGTPVTFNVRAISDDPLSYQWFKDGVEIPG----AIAEVY-----TIQKAITGDKGSYYVQA 2106
                                        6788899999999*****************************5....566655.....9**************** PP

                                        EETSEEEEEE CS
                             I-set   76 tnsagkaeak 85  
                                        +ns g+ e++
  gi|330508678|ref|YP_004385106.1| 2107 RNSCGQIESE 2116
                                        ***9987654 PP

  == domain 21  score: 24.3 bits;  conditional E-value: 1.6e-08
                                        EEEEES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEE CS
                             I-set    1 pkftqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtcka 75  
                                        p++  ++++++v eG+++++++ ++  ++++ +W k+g+ +            ++ +LtI +++++D+G+Y++ +
  gi|330508678|ref|YP_004385106.1| 2126 PEILVQPTSQKVCEGSTATFTVLAKSAQPLTYQWIKGGRIIPG------A---NSEELTIFDANMEDMGEYRVAI 2191
                                        788999*********************************9995......3...3458****************** PP

                                        EETSE CS
                             I-set   76 tnsag 80  
                                        +n  g
  gi|330508678|ref|YP_004385106.1| 2192 SNGCG 2196
                                        **977 PP

  == domain 22  score: 14.7 bits;  conditional E-value: 1.6e-05
                                        S-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEEEETSE CS
                             I-set    6 klkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtckatnsag 80  
                                        +++ + +  Ge+v + ++ + ++  s +W k+g+ +        +v+    +L+I n ++sD+G Y+++++n  g
  gi|330508678|ref|YP_004385106.1| 2217 EPDCLIADAGETVAFIMKGTAVGANSYQWEKNGEIIPG------EVS---PSLIILNPRPSDSGGYRLTVSNGCG 2282
                                        55666788899999999999999999999999999885......344...59*********************** PP

                                        EEEEEEEE CS
                             I-set   81 kaeakaeL 88  
                                        ++++k+++
  gi|330508678|ref|YP_004385106.1| 2283 SNKSKMSV 2290
                                        ***99886 PP

>> Ig_2  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   7.4e-08   0.00011      25      79 .]     448     504 ..     426     504 .. 0.87
   2 !   23.4   0.0   3.8e-08   5.6e-05       8      65 ..     516     575 ..     507     589 .. 0.82
   3 !   17.8   0.1     2e-06     0.003       5      60 ..     598     655 ..     592     675 .. 0.80
   4 !   18.0   0.0   1.8e-06    0.0027       9      68 ..     690     751 ..     679     762 .. 0.83
   5 !   13.6   0.1   4.3e-05     0.064       9      65 ..     775     833 ..     765     843 .. 0.77
   6 !    8.1   0.0    0.0023       3.4      23      65 ..     874     918 ..     855     930 .. 0.79
   7 ?    5.1   0.0      0.02        30      24      60 ..     960     998 ..     941    1013 .. 0.77
   8 !   15.1   0.3   1.5e-05     0.022       5      65 ..    1026    1088 ..    1022    1099 .. 0.86
   9 !   13.5   0.1   4.5e-05     0.067       5      65 ..    1111    1173 ..    1107    1186 .. 0.85
  10 !   19.7   0.3   5.3e-07   0.00079       5      72 ..    1196    1265 ..    1191    1272 .. 0.81
  11 !   13.3   0.1   5.4e-05      0.08       9      67 ..    1285    1345 ..    1277    1357 .. 0.76
  12 !   12.8   0.1   7.8e-05      0.12      23      65 ..    1384    1428 ..    1365    1440 .. 0.78
  13 !    7.8   0.0    0.0028       4.2      13      60 ..    1459    1508 ..    1446    1522 .. 0.76
  14 !   19.7   0.0   5.5e-07   0.00082       5      65 ..    1536    1598 ..    1532    1609 .. 0.85
  15 !   14.8   0.0   1.8e-05     0.027       6      65 ..    1622    1683 ..    1616    1697 .. 0.80
  16 !   21.3   0.1   1.6e-07   0.00025      23      66 ..    1724    1769 ..    1705    1780 .. 0.82
  17 !   16.8   0.1   4.4e-06    0.0066       4      65 ..    1788    1853 ..    1785    1862 .. 0.82
  18 !   10.1   0.0   0.00052      0.78       4      73 ..    1873    1946 ..    1870    1951 .. 0.80
  19 !   17.4   0.0   2.8e-06    0.0042       4      60 ..    1959    2018 ..    1956    2027 .. 0.84
  20 !   21.2   0.0   1.8e-07   0.00027       3      77 ..    2044    2120 ..    2042    2122 .. 0.87
  21 !   18.0   0.0   1.9e-06    0.0028       5      79 .]    2131    2207 ..    2126    2207 .. 0.89
  22 !   19.4   0.0   6.7e-07     0.001      30      74 ..    2242    2288 ..    2233    2293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.4e-08
                              Ig_2  25 gnpppkvqwykggevin.sspn.ffinavsaedsgtYtCrarntkggevsrpveltv 79 
                                       gn p+++qw+k+g+ i   +++ ++i+a+ + d+g+Y+ r++n  g+  s+p+ ltv
  gi|330508678|ref|YP_004385106.1| 448 GNGPISYQWSKNGSQIAgATTDsYIIPAAKLADAGSYRVRVSNACGSIESNPAVLTV 504
                                       67789************745555888*****************9999***9998886 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 3.8e-08
                              Ig_2   8 ptvvtegepvtLtCsapgnpppkvqwykggevin.sspn.ffinavsaedsgtYtCrarn 65 
                                       +    eg++v L+ +a+g +p ++qw k+ge i   ++n ++i+++ ++d g Y   ++n
  gi|330508678|ref|YP_004385106.1| 516 DEIACEGSEVLLNAQASGTEPLNYQWKKNGENITgANTNrYLISSILPTDEGDYSLAVSN 575
                                       36679*************************99998555569*************999988 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 2e-06
                              Ig_2   5 rpsptvvtegepvtLtCsapgnpppkvqwykggevinsspn..ffinavsaedsgtYt 60 
                                       +p +++v +g+pv++  ++ gn+ +++qw+k+g  i       + i+a++ +d+g+Y 
  gi|330508678|ref|YP_004385106.1| 598 QPISQTVCTGSPVSFEVQVAGNESYTYQWQKDGLNITAANAavLSISAANSTDQGNYS 655
                                       566699****************99*********7777554446677***********7 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 1.8e-06
                              Ig_2   9 tvvtegepvtLtCsapgnpppkvqwykggevin.sspn.ffinavsaedsgtYtCrarntkg 68 
                                         + eg+++ L  ++ g+ p+++qw k+g  i+  + + f+i++++ +dsg+Y  +++n+ g
  gi|330508678|ref|YP_004385106.1| 690 KKICEGSDIALVADVTGSDPITIQWMKDGLQIPgANLDsFVIKNATRNDSGSYSLIVSNDCG 751
                                       5688999999999999999**************644444777****************9765 PP

  == domain 5  score: 13.6 bits;  conditional E-value: 4.3e-05
                              Ig_2   9 tvvtegepvtLtCsapgnpppkvqwykggevin.sspn.ffinavsaedsgtYtCrarn 65 
                                        +v +g   t++ +a++++p ++qw+k+g  i   + + ++i++ +++d g+Y  ++ n
  gi|330508678|ref|YP_004385106.1| 775 LRVCQGAAATFSVQAKSSEPLSYQWFKDGIKIDgATSEyYTIPQTNLSDMGSYSVQVAN 833
                                       5688888888888999*************9999544445677***********999988 PP

  == domain 6  score: 8.1 bits;  conditional E-value: 0.0023
                              Ig_2  23 apgnpppkvqwykggevin.sspn.ffinavsaedsgtYtCrarn 65 
                                       a +++p ++qw k+g  i+  + + + i+a +++d g+Y  + +n
  gi|330508678|ref|YP_004385106.1| 874 AESSEPLSYQWLKDGVNIPaATSDtYAIPASNLNDTGSYSVQITN 918
                                       4488999************633445889***********877766 PP

  == domain 7  score: 5.1 bits;  conditional E-value: 0.02
                              Ig_2  24 pgnpppkvqwykggevinsspn..ffinavsaedsgtYt 60 
                                        + +p k+qw k+g +i+  ++  ++i  +   d g+Y 
  gi|330508678|ref|YP_004385106.1| 960 ESTEPLKYQWLKDGIEIPGATDdrYTIDLADIADMGSYS 998
                                       378899************444446889999999999996 PP

  == domain 8  score: 15.1 bits;  conditional E-value: 1.5e-05
                              Ig_2    5 rpsptvvtegepvtLtCsapgnpppkvqwykggevin..sspnffinavsaedsgtYtCrarn 65  
                                        +p++++v +g    ++ +a +++p ++qw k+g  i+  +s +++i++ s++d g+Y  +++n
  gi|330508678|ref|YP_004385106.1| 1026 QPTSQNVCQGTRAAFSVQAESSEPLSYQWLKEGIKIEgaTSESYTIPQTSLSDTGSYSVQVSN 1088
                                        678899******99999****************9999644444778************99998 PP

  == domain 9  score: 13.5 bits;  conditional E-value: 4.5e-05
                              Ig_2    5 rpsptvvtegepvtLtCsapgnpppkvqwykggevin..sspn.ffinavsaedsgtYtCrarn 65  
                                        +p+++ v +g   t++ +a +++p ++qw k+g  i+     + ++i+a +++d g+Y  + rn
  gi|330508678|ref|YP_004385106.1| 1111 QPTSQKVCQGTAATFSVQARSSEPLSYQWLKDGVNIQgaA-SDtYTIPASNLNDTGSYSVQLRN 1173
                                        577899***************************9999643.335889***********999988 PP

  == domain 10  score: 19.7 bits;  conditional E-value: 5.3e-07
                              Ig_2    5 rpsptvvtegepvtLtCsapgnpppkvqwykggevin..sspnffinavsaedsgtYtCrarntkggevs 72  
                                        +p++++v +g    ++ +a++++p ++qw+k+g  i   +s ++ i+a+s++d g+Y  +++n   + +s
  gi|330508678|ref|YP_004385106.1| 1196 QPTSQNVCQGTRAAFSVQAKSSEPLSYQWFKDGIKIDgaTSESYAIPAASLSDTGSYSVQVSNNCSQIKS 1265
                                        5777*****************************9999644444788***************995555555 PP

  == domain 11  score: 13.3 bits;  conditional E-value: 5.4e-05
                              Ig_2    9 tvvtegepvtLtCsapgnpppkvqwykggevin.sspn.ffinavsaedsgtYtCrarntk 67  
                                        ++  eg + t++ +a +++p ++qw+k+g  i   + + ++i++ +++d g+Y  +++n  
  gi|330508678|ref|YP_004385106.1| 1285 QRGCEGATTTFSVQAESSEPLSYQWFKDGIKIDgATSEyYTIPQTNLSDMGSYSVQVSNNC 1345
                                        5556677777777888999**********9999544445677***************9954 PP

  == domain 12  score: 12.8 bits;  conditional E-value: 7.8e-05
                              Ig_2   23 apgnpppkvqwykggevin..sspn.ffinavsaedsgtYtCrarn 65  
                                        a +++p ++qw k+g  i+  +  + ++i+a+ ++d g+Y  ++ n
  gi|330508678|ref|YP_004385106.1| 1384 AESSEPLSYQWLKDGANIPgaT-SDtYTIPAAKLNDTGSYSVQVAN 1428
                                        4488999************743.335889***********999987 PP

  == domain 13  score: 7.8 bits;  conditional E-value: 0.0028
                              Ig_2   13 egepvtLtCsapgnpppkvqwykggevinsspn..ffinavsaedsgtYt 60  
                                        +g   t++ +a++++p+++qw k+g +i+  ++  ++i  +   d g+Y 
  gi|330508678|ref|YP_004385106.1| 1459 QGAAATFHVEASSYEPIEYQWLKDGIEIPGATDdrYTIDLADIADVGSYS 1508
                                        4555555556789****************444446899999999999996 PP

  == domain 14  score: 19.7 bits;  conditional E-value: 5.5e-07
                              Ig_2    5 rpsptvvtegepvtLtCsapgnpppkvqwykggevin..sspn.ffinavsaedsgtYtCrarn 65  
                                        +p+ +++ +g +vt+  +a++++p  +qw k+g  i+   s + ++i+a++++d g+Y  +++n
  gi|330508678|ref|YP_004385106.1| 1536 QPTRQRICQGTMVTFAVQAKSSEPLRYQWLKDGVNIPgaAS-DtYTIPAANLSDMGSYSVQVSN 1598
                                        56779********************************6433.35899*************9999 PP

  == domain 15  score: 14.8 bits;  conditional E-value: 1.8e-05
                              Ig_2    6 psptvvtegepvtLtCsapgnpppkvqwykggevinsspn..ffinavsaedsgtYtCrarn 65  
                                        p+ + v +g   t++ +a++++p ++qw ++g  i++ ++  ++i+a++++d g+Y   + n
  gi|330508678|ref|YP_004385106.1| 1622 PTGQKVCQGTAATFSVQAKSSEPLSYQWLRDGANIPDATSesYTILAANLSDTGSYSVLVAN 1683
                                        3348899999999999********************655555778***********865555 PP

  == domain 16  score: 21.3 bits;  conditional E-value: 1.6e-07
                              Ig_2   23 apgnpppkvqwykggevin.sspn.ffinavsaedsgtYtCrarnt 66  
                                        a+g +p ++qwyk+g++i+  + n + i+ +s++d+g+Y  ++rn+
  gi|330508678|ref|YP_004385106.1| 1724 ASGGEPLEYQWYKDGTEIEgATSNsYSIPVASPSDRGSYWVQVRNS 1769
                                        5688999************745555888***********9999985 PP

  == domain 17  score: 16.8 bits;  conditional E-value: 4.4e-06
                              Ig_2    4 lrpsp..tvvtegepvtLtCsapgnpppkvqwykggevin.sspn.ffinavsaedsgtYtCrarn 65  
                                        + ++p  + + +g+ vt+t ++ +++p ++qw+k+g  i+  +++ ++i ++ ++d g+Y  +a n
  gi|330508678|ref|YP_004385106.1| 1788 ILVPPtsQKICQGSAVTFTVQVESSKPLSYQWFKDGIKIPgATQDvYTIARAVLNDTGSYWVQAAN 1853
                                        444443588***************99**********99997788877789999*****99766655 PP

  == domain 18  score: 10.1 bits;  conditional E-value: 0.00052
                              Ig_2    4 lrpsp..tvvtegepvtLtCsapgnpppkvqwykggevin.sspn.ffinavsaedsgtYtCrarntkggevsr 73  
                                        +  +p  + v eg   t+  +a ++++ ++qw+k+g +i   + + ++i++    d g+Y  ++rn+ g+  s+
  gi|330508678|ref|YP_004385106.1| 1873 IHLPPasQKVCEGAAATFFVQAESSEALSYQWFKDGIEIYeATADaYTIPRTGKFDMGNYMVQVRNSCGSVESK 1946
                                        55444458899999999999999*99**********5555266667888****************977766554 PP

  == domain 19  score: 17.4 bits;  conditional E-value: 2.8e-06
                              Ig_2    4 lrpsp.tvvtegepvtLtCsapgnpppkvqwykggevin.sspn.ffinavsaedsgtYt 60  
                                        l p++ ++v +g+  t++ +a++++p ++qw+k+g+ i+  + + ++i+a++ +d  +Y 
  gi|330508678|ref|YP_004385106.1| 1959 LVPPKgQRVCQGDAATFSVQASSSEPLSYQWFKDGKMIQgATADtYTIPAATFGDTASYS 2018
                                        556669*********************************644456888999988888775 PP

  == domain 20  score: 21.2 bits;  conditional E-value: 1.8e-07
                              Ig_2    3 vlrpsptvvtegepvtLtCsapgnpppkvqwykggevinsspn..ffinavsaedsgtYtCrarntkggevsrpv 75  
                                         l+p ++ v +g pvt++ +a ++ p ++qw+k+g +i+      ++i+++  +d+g+Y  +arn+ g+  s ++
  gi|330508678|ref|YP_004385106.1| 2044 SLQPASQIVCQGTPVTFNVRAISDDPLSYQWFKDGVEIPGAIAevYTIQKAITGDKGSYYVQARNSCGQIESETA 2118
                                        689999**************99999**************6544467889999*************9888888777 PP

                              Ig_2   76 el 77  
                                        +l
  gi|330508678|ref|YP_004385106.1| 2119 NL 2120
                                        76 PP

  == domain 21  score: 18.0 bits;  conditional E-value: 1.9e-06
                              Ig_2    5 rpsptvvtegepvtLtCsapgnpppkvqwykggevin..sspnffinavsaedsgtYtCrarntkggevsrpvel 77  
                                        +p+++ v eg++ t+t  a++ +p ++qw kgg++i+  +s +++i  ++ ed g Y+   +n+ g  +s+ v l
  gi|330508678|ref|YP_004385106.1| 2131 QPTSQKVCEGSTATFTVLAKSAQPLTYQWIKGGRIIPgaNSEELTIFDANMEDMGEYRVAISNGCGFIDSNAVSL 2205
                                        677799*******************************866666788************99999888899999998 PP

                              Ig_2   78 tv 79  
                                        +v
  gi|330508678|ref|YP_004385106.1| 2206 IV 2207
                                        87 PP

  == domain 22  score: 19.4 bits;  conditional E-value: 6.7e-07
                              Ig_2   30 kvqwykggevin..sspnffinavsaedsgtYtCrarntkggevsrp 74  
                                        ++qw k+ge+i+   sp+++i++  ++dsg Y+ +++n+ g+ +s++
  gi|330508678|ref|YP_004385106.1| 2242 SYQWEKNGEIIPgeVSPSLIILNPRPSDSGGYRLTVSNGCGSNKSKM 2288
                                        7***********887898777*****************888877764 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.094   1.4e+02      11      60 ..     437     488 ..     430     496 .. 0.72
   2 ?    0.9   0.0      0.27   4.1e+02       9      59 ..     520     572 ..     516     574 .. 0.77
   3 !   10.0   0.2   0.00039      0.58       3      31 ..     599     627 ..     597     657 .. 0.81
   4 !    6.6   0.1    0.0047         7       6      60 ..     775     831 ..     770     834 .. 0.80
   5 ?    3.8   0.0     0.034        51       6      34 ..     860     887 ..     855     918 .. 0.67
   6 ?    1.5   0.0      0.19   2.8e+02       7      30 ..     946     969 ..     942     978 .. 0.93
   7 !    7.7   0.1     0.002         3       5      60 ..    1029    1086 ..    1025    1092 .. 0.74
   8 !    9.4   0.2    0.0006       0.9       3      61 ..    1112    1172 ..    1110    1174 .. 0.74
   9 !   12.7   0.1   5.9e-05     0.088       5      60 ..    1199    1256 ..    1195    1260 .. 0.94
  10 ?    5.4   0.1     0.011        17       4      60 ..    1283    1341 ..    1280    1345 .. 0.80
  11 !    6.3   0.0    0.0059       8.8       6      60 ..    1370    1426 ..    1365    1429 .. 0.78
  12 ?    1.4   0.0      0.19   2.9e+02       5      30 ..    1454    1479 ..    1450    1486 .. 0.91
  13 ?    4.2   0.0     0.026        39       3      34 ..    1537    1567 ..    1535    1599 .. 0.66
  14 !    5.9   0.1    0.0076        11       3      30 ..    1622    1649 ..    1620    1681 .. 0.82
  15 ?    3.5   0.1     0.042        63      11      61 ..    1715    1767 ..    1706    1771 .. 0.73
  16 !    9.9   0.1   0.00043      0.64       3      35 ..    1792    1823 ..    1790    1851 .. 0.80
  17 ?   -0.5   0.0      0.74   1.1e+03       6      34 ..    1880    1907 ..    1876    1936 .. 0.83
  18 !    6.2   0.1    0.0062       9.2       5      46 ..    1964    2007 ..    1960    2022 .. 0.67
  19 !   10.1   0.0   0.00037      0.55       4      35 ..    2048    2078 ..    2045    2117 .. 0.78
  20 !    8.9   0.0   0.00087       1.3       1      30 [.    2130    2159 ..    2130    2170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.094
                                       SEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-S.....SEEEEEEE CS
                               PKD  11 gatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYls.....pGeYeVtv 60 
                                        ++++f+ + +   +++y+W  +     q+    t +++ ++     +G+Y V+v
  gi|330508678|ref|YP_004385106.1| 437 DQEARFNVVAAGNGPISYQWSKNG---SQIAGATTDSYIIPAakladAGSYRVRV 488
                                       68899999999999******9999...5555555555544444566699998876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.27
                                       BSSEEEEEEEES.-SS-SEEEEE--SS..--EEEEETTEEEEEE-SSEEEEEE CS
                               PKD   9 vpgatvaftaavpdganvtysWdfgdg..svvqvlseptvthtYlspGeYeVt 59 
                                       + g +v ++a+    ++++y+W  + +  + + + +    ++ ++ +G+Y + 
  gi|330508678|ref|YP_004385106.1| 520 CEGSEVLLNAQASGTEPLNYQWKKNGEniTGANTNRYLISSILPTDEGDYSLA 572
                                       6689999*****99999*****9998877666666666667777777777665 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00039
                                       ---S--BSSEEEEEEEES.-SS-SEEEEE CS
                               PKD   3 asptvlvpgatvaftaavpdganvtysWd 31 
                                       + ++ +++g +v f+ +v+  +++ty+W+
  gi|330508678|ref|YP_004385106.1| 599 PISQTVCTGSPVSFEVQVAGNESYTYQWQ 627
                                       557899**********************8 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0047
                                       S--BSSEEEEEEEES.-SS-SEEEEE--SS...--EEEEETTEEEEEE-SSEEEEEEE CS
                               PKD   6 tvlvpgatvaftaavpdganvtysWdfgdg...svvqvlseptvthtYlspGeYeVtv 60 
                                         +++ga ++f+ +  + ++++y+W f dg   + ++++    +    +  G+Y V+v
  gi|330508678|ref|YP_004385106.1| 775 LRVCQGAAATFSVQAKSSEPLSYQW-FKDGikiDGATSEYYTIPQTNLSDMGSYSVQV 831
                                       6699*********************.99988887777776666666777777777776 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.034
                                       S--BSSEEEEEEEES.-SS-SEEEEE--S CS
                               PKD   6 tvlvpgatvaftaavpdganvtysWdfgd 34 
                                         +++ga + f+ + ++ ++++y+W + d
  gi|330508678|ref|YP_004385106.1| 860 LKICQGAAAKFEVQAESSEPLSYQW-LKD 887
                                       5689*********************.455 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.19
                                       --BSSEEEEEEEES.-SS-SEEEE CS
                               PKD   7 vlvpgatvaftaavpdganvtysW 30 
                                        +++ga + f+ + ++ +++ y+W
  gi|330508678|ref|YP_004385106.1| 946 KICQGAKAKFEVQIESTEPLKYQW 969
                                       589********************* PP

  == domain 7  score: 7.7 bits;  conditional E-value: 0.002
                                        -S--BSSEEEEEEEES.-SS-SEEEEE--SS...--EEEEETTEEEEEE-SSEEEEEEE CS
                               PKD    5 ptvlvpgatvaftaavpdganvtysWdfgdg...svvqvlseptvthtYlspGeYeVtv 60  
                                        ++ +++g+ +af+ + ++ ++++y+W    g     ++++s   +  + + +G+Y V+v
  gi|330508678|ref|YP_004385106.1| 1029 SQNVCQGTRAAFSVQAESSEPLSYQWL-KEGikiEGATSESYTIPQTSLSDTGSYSVQV 1086
                                        5679**********************5.4444555555555555555555588888887 PP

  == domain 8  score: 9.4 bits;  conditional E-value: 0.0006
                                        ---S--BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-S....SEEEEEEEE CS
                               PKD    3 asptvlvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYls....pGeYeVtvt 61  
                                        ++++ +++g+ ++f+ + ++ ++++y+W + dg + q   + t t+   s    +G+Y V+++
  gi|330508678|ref|YP_004385106.1| 1112 PTSQKVCQGTAATFSVQARSSEPLSYQW-LKDGVNIQGAASDTYTIPA-SnlndTGSYSVQLR 1172
                                        567899**********************.5664444444444444444.34888999999985 PP

  == domain 9  score: 12.7 bits;  conditional E-value: 5.9e-05
                                        -S--BSSEEEEEEEES.-SS-SEEEEE--SS...--EEEEETTEEEEEE-SSEEEEEEE CS
                               PKD    5 ptvlvpgatvaftaavpdganvtysWdfgdg...svvqvlseptvthtYlspGeYeVtv 60  
                                        ++ +++g+ +af+ +  + ++++y+W f dg   + ++++s   +  + + +G+Y V+v
  gi|330508678|ref|YP_004385106.1| 1199 SQNVCQGTRAAFSVQAKSSEPLSYQW-FKDGikiDGATSESYAIPAASLSDTGSYSVQV 1256
                                        56699*********************.******************************98 PP

  == domain 10  score: 5.4 bits;  conditional E-value: 0.011
                                        --S--BSSEEEEEEEES.-SS-SEEEEE--SS...--EEEEETTEEEEEE-SSEEEEEEE CS
                               PKD    4 sptvlvpgatvaftaavpdganvtysWdfgdg...svvqvlseptvthtYlspGeYeVtv 60  
                                        +++  + gat +f+ + ++ ++++y+W f dg   + ++++    +    +  G+Y V+v
  gi|330508678|ref|YP_004385106.1| 1283 VGQRGCEGATTTFSVQAESSEPLSYQW-FKDGikiDGATSEYYTIPQTNLSDMGSYSVQV 1341
                                        56667889*******************.99988887777777677777777777777776 PP

  == domain 11  score: 6.3 bits;  conditional E-value: 0.0059
                                        S--BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-S...SEEEEEEE CS
                               PKD    6 tvlvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYls...pGeYeVtv 60  
                                          +++ga + f+ + ++ ++++y+W + dg +    ++ t t+  ++   +G+Y V+v
  gi|330508678|ref|YP_004385106.1| 1370 LKICQGAAAKFEVQAESSEPLSYQW-LKDGANIPGATSDTYTIPAAKlndTGSYSVQV 1426
                                        5689*********************.66666666666666666555566699999998 PP

  == domain 12  score: 1.4 bits;  conditional E-value: 0.19
                                        -S--BSSEEEEEEEES.-SS-SEEEE CS
                               PKD    5 ptvlvpgatvaftaavpdganvtysW 30  
                                          ++++ga ++f+    + +++ y+W
  gi|330508678|ref|YP_004385106.1| 1454 NLMICQGAAATFHVEASSYEPIEYQW 1479
                                        5799********************** PP

  == domain 13  score: 4.2 bits;  conditional E-value: 0.026
                                        ---S--BSSEEEEEEEES.-SS-SEEEEE--S CS
                               PKD    3 asptvlvpgatvaftaavpdganvtysWdfgd 34  
                                        ++++ +++g+ v+f  +  + ++++y+W   d
  gi|330508678|ref|YP_004385106.1| 1537 PTRQRICQGTMVTFAVQAKSSEPLRYQWL-KD 1567
                                        5677899*********************4.44 PP

  == domain 14  score: 5.9 bits;  conditional E-value: 0.0076
                                        ---S--BSSEEEEEEEES.-SS-SEEEE CS
                               PKD    3 asptvlvpgatvaftaavpdganvtysW 30  
                                        ++++ +++g+ ++f+ +  + ++++y+W
  gi|330508678|ref|YP_004385106.1| 1622 PTGQKVCQGTAATFSVQAKSSEPLSYQW 1649
                                        66899*********************** PP

  == domain 15  score: 3.5 bits;  conditional E-value: 0.042
                                        SEEEEEEEES.-SS-SEEEEE--SS..--EEEEETTEEEEEE-SSEEEEEEEE CS
                               PKD   11 gatvaftaavpdganvtysWdfgdg..svvqvlseptvthtYlspGeYeVtvt 61  
                                        ga ++f      g+++ y+W+ +      +++ s + +  +++ +G+Y V+v+
  gi|330508678|ref|YP_004385106.1| 1715 GAAATFGVKASGGEPLEYQWYKDGTeiEGATSNSYSIPVASPSDRGSYWVQVR 1767
                                        5556666666789*******9666256566666666666666669****9996 PP

  == domain 16  score: 9.9 bits;  conditional E-value: 0.00043
                                        ---S--BSSEEEEEEEES.-SS-SEEEEE--SS CS
                               PKD    3 asptvlvpgatvaftaavpdganvtysWdfgdg 35  
                                        ++++ +++g  v+ft +v++ ++++y+W f dg
  gi|330508678|ref|YP_004385106.1| 1792 PTSQKICQGSAVTFTVQVESSKPLSYQW-FKDG 1823
                                        556889**********************.6776 PP

  == domain 17  score: -0.5 bits;  conditional E-value: 0.74
                                        S--BSSEEEEEEEES.-SS-SEEEEE--S CS
                               PKD    6 tvlvpgatvaftaavpdganvtysWdfgd 34  
                                        + ++ ga ++f  + ++ + ++y+W f d
  gi|330508678|ref|YP_004385106.1| 1880 QKVCEGAAATFFVQAESSEALSYQW-FKD 1907
                                        678999999****************.555 PP

  == domain 18  score: 6.2 bits;  conditional E-value: 0.0062
                                        -S--BSSEEEEEEEES.-SS-SEEEEE--SS...--EEEEETTEE CS
                               PKD    5 ptvlvpgatvaftaavpdganvtysWdfgdg...svvqvlseptv 46  
                                        ++ +++g  ++f+ +  + ++++y+W f dg     ++  +   +
  gi|330508678|ref|YP_004385106.1| 1964 GQRVCQGDAATFSVQASSSEPLSYQW-FKDGkmiQGATADTYTIP 2007
                                        67899*********************.999955533333333333 PP

  == domain 19  score: 10.1 bits;  conditional E-value: 0.00037
                                        --S--BSSEEEEEEEES.-SS-SEEEEE--SS CS
                               PKD    4 sptvlvpgatvaftaavpdganvtysWdfgdg 35  
                                         ++ +++g++v+f+ +  ++++++y+W f dg
  gi|330508678|ref|YP_004385106.1| 2048 ASQIVCQGTPVTFNVRAISDDPLSYQW-FKDG 2078
                                        45889**********************.6665 PP

  == domain 20  score: 8.9 bits;  conditional E-value: 0.00087
                                        EE---S--BSSEEEEEEEES.-SS-SEEEE CS
                               PKD    1 vsasptvlvpgatvaftaavpdganvtysW 30  
                                        v+++++ ++ g t++ft    +++++ty+W
  gi|330508678|ref|YP_004385106.1| 2130 VQPTSQKVCEGSTATFTVLAKSAQPLTYQW 2159
                                        56788999********************** PP

>> ig  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.016        24      24      80 ..     449     494 ..     436     500 .. 0.81
   2 !    7.8   0.0    0.0025       3.7      10      71 ..     521     570 ..     519     583 .. 0.80
   3 ?    5.8   0.0     0.011        16      10      71 ..     694     743 ..     689     754 .. 0.84
   4 ?    1.8   0.0      0.18   2.7e+02       4      84 ..     773     841 ..     770     843 .. 0.76
   5 ?    5.8   0.2      0.01        15      15      79 ..    1039    1091 ..    1026    1099 .. 0.74
   6 ?    1.4   0.1      0.25   3.7e+02       4      80 ..    1113    1177 ..    1111    1183 .. 0.75
   7 ?    4.7   0.1     0.024        35       8      83 ..    1202    1265 ..    1195    1269 .. 0.76
   8 ?    0.6   0.1      0.44   6.5e+02      19      83 ..    1298    1350 ..    1282    1354 .. 0.70
   9 ?    4.5   0.0     0.026        38      25      86 ..    1388    1438 ..    1374    1439 .. 0.77
  10 ?    0.4   0.0       0.5   7.5e+02      21      84 ..    1555    1606 ..    1538    1609 .. 0.68
  11 ?    2.1   0.1      0.15   2.2e+02       7      71 ..    1626    1678 ..    1621    1690 .. 0.81
  12 !    7.0   0.0    0.0044       6.6       3      79 ..    1707    1771 ..    1705    1778 .. 0.83
  13 !    6.6   0.1    0.0059       8.9       3      79 ..    1792    1856 ..    1790    1864 .. 0.81
  14 ?   -0.5   0.0      0.94   1.4e+03      55      84 ..    1917    1946 ..    1877    1948 .. 0.77
  15 ?    2.9   0.0     0.085   1.3e+02       2      39 ..    1961    1997 ..    1960    2019 .. 0.83
  16 ?   -0.6   0.0      0.99   1.5e+03      10      76 ..    2054    2108 ..    2048    2119 .. 0.68
  17 !    8.3   0.0    0.0017       2.5       3      71 ..    2132    2188 ..    2130    2197 .. 0.87
  18 ?    3.4   0.0     0.058        87      54      86 ..    2257    2289 ..    2228    2290 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.016
                                       SCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEEEEEEETTEE CS
                                ig  24 tkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYtCevnnsgss 80 
                                       + p+++ W+k+g++    +           + s +i+ +++ daG+Y+ +v+n+ +s
  gi|330508678|ref|YP_004385106.1| 449 NGPISYQWSKNGSQIAGAT-----------TDSYIIPAAKLADAGSYRVRVSNACGS 494
                                       5567788888888877775...........59***************9999997665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0025
                                       TTS-EEEEEEEESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEE CS
                                ig  10 eGesatLtCsvstqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYt 71 
                                       eG+ + L+  +s +t+p+++ Wkk+g+  +   +           ++ lis+  + d+G+Y 
  gi|330508678|ref|YP_004385106.1| 521 EGSEVLLNAQAS-GTEPLNYQWKKNGENITGANT-----------NRYLISSILPTDEGDYS 570
                                       79999*******.************999888877...........66777777777777775 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.011
                                       TTS-EEEEEEEESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEE CS
                                ig  10 eGesatLtCsvstqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYt 71 
                                       eG+ + L   v+ +++p+++ W k+g + +                s+ i ++t++d+G+Y 
  gi|330508678|ref|YP_004385106.1| 694 EGSDIALVADVT-GSDPITIQWMKDGLQIPGANL-----------DSFVIKNATRNDSGSYS 743
                                       567777777777.999999999999999999999...........89999999999999996 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.18
                                       SEEEEETTS-EEEEEEEESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEEEEEEETTEE CS
                                ig   4 plvlvleGesatLtCsvstqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYtCevnnsgss 80 
                                        +++v +G  at++  ++ +++p+++ W+k+ + ki +++          s+  +i+++ + d G+Y  +v n+ s+
  gi|330508678|ref|YP_004385106.1| 773 ANLRVCQGAAATFSVQAK-SSEPLSYQWFKD-GIKIDGAT----------SEYYTIPQTNLSDMGSYSVQVANNCSQ 837
                                       566777888888888888.999999999765.56666666..........788888888888888888888888777 PP

                                       EEEE CS
                                ig  81 vtls 84 
                                       v+++
  gi|330508678|ref|YP_004385106.1| 838 VESE 841
                                       7765 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.01
                                        EEEEEEESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEEEEEEETTE CS
                                ig   15 tLtCsvstqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYtCevnnsgs 79  
                                         ++  ++ +++p+++ W keg  kie+++          s+s +i+++++ d+G+Y  +v+n+ s
  gi|330508678|ref|YP_004385106.1| 1039 AFSVQAE-SSEPLSYQWLKEG-IKIEGAT----------SESYTIPQTSLSDTGSYSVQVSNNCS 1091
                                        5555555.7788888888776.4566655..........9*****************99999866 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.25
                                        SEEEEETTS-EEEEEEEESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEEEEEEETT CS
                                ig    4 plvlvleGesatLtCsvstqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYtCevnnsg 78  
                                        ++  v +G+ at++  ++ +++p+++ W k+g ++i+++           s + +i+   ++d+G+Y  ++ n+ 
  gi|330508678|ref|YP_004385106.1| 1113 TSQKVCQGTAATFSVQAR-SSEPLSYQWLKDG-VNIQGAA----------SDTYTIPASNLNDTGSYSVQLRNNC 1175
                                        566677899999999999.9999999998755.5666655..........7888888888888888887777766 PP

                                        EE CS
                                ig   79 ss 80  
                                        s+
  gi|330508678|ref|YP_004385106.1| 1176 SQ 1177
                                        65 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.024
                                        EETTS-EEEEEEEESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEEEEEEETTEEEE CS
                                ig    8 vleGesatLtCsvstqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYtCevnnsgssvt 82  
                                        v +G++a ++  ++ +++p+++ W+k ++ ki +++          s+s  i+ +++ d+G+Y  +v+n+ s+ +
  gi|330508678|ref|YP_004385106.1| 1202 VCQGTRAAFSVQAK-SSEPLSYQWFK-DGIKIDGAT----------SESYAIPAASLSDTGSYSVQVSNNCSQIK 1264
                                        55677777777777.88888888865.556777766..........9******************9999888766 PP

                                        E CS
                                ig   83 l 83  
                                        +
  gi|330508678|ref|YP_004385106.1| 1265 S 1265
                                        5 PP

  == domain 8  score: 0.6 bits;  conditional E-value: 0.44
                                        EEESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEEEEEEETTEEEEE CS
                                ig   19 svstqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYtCevnnsgssvtl 83  
                                         ++ +++p+++ W+k ++ ki +++          s+  +i+++ + d G+Y  +v+n+ s+ ++
  gi|330508678|ref|YP_004385106.1| 1298 QAE-SSEPLSYQWFK-DGIKIDGAT----------SEYYTIPQTNLSDMGSYSVQVSNNCSQIES 1350
                                        444.66777777755.445555555..........788899999999999999999998777666 PP

  == domain 9  score: 4.5 bits;  conditional E-value: 0.026
                                        CTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEEEEEEETTEEEEEEEE CS
                                ig   25 kptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYtCevnnsgssvtlsvs 86  
                                        +p+++ W k+g   +             +s + +i+ ++++d+G+Y  +v n+ s+ +++vs
  gi|330508678|ref|YP_004385106.1| 1388 EPLSYQWLKDGANIPGA-----------TSDTYTIPAAKLNDTGSYSVQVANNCSQIESEVS 1438
                                        55566666555555544...........5799***************999999988888775 PP

  == domain 10  score: 0.4 bits;  conditional E-value: 0.5
                                        ESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEEEEEEETTEEEEEE CS
                                ig   21 stqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYtCevnnsgssvtls 84  
                                        + +++p+ + W k+g   +              s + +i+ + + d G+Y  +v+n+ s+ +++
  gi|330508678|ref|YP_004385106.1| 1555 K-SSEPLRYQWLKDGVNIPGA-----------ASDTYTIPAANLSDMGSYSVQVSNNCSQIESE 1606
                                        5.5555555555544444333...........368999999*********99999998877766 PP

  == domain 11  score: 2.1 bits;  conditional E-value: 0.15
                                        EEETTS-EEEEEEEESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEE CS
                                ig    7 lvleGesatLtCsvstqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYt 71  
                                         v +G+ at++  ++ +++p+++ W ++g   +             +s+s +i  + + d+G+Y 
  gi|330508678|ref|YP_004385106.1| 1626 KVCQGTAATFSVQAK-SSEPLSYQWLRDGANIPDA-----------TSESYTILAANLSDTGSYS 1678
                                        566788888888888.9999999999998888877...........5699999999999999996 PP

  == domain 12  score: 7.0 bits;  conditional E-value: 0.0044
                                        ESEEEEETTS-EEEEEEEESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEEEEEEET CS
                                ig    3 kplvlvleGesatLtCsvstqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYtCevnns 77  
                                        ++++++ eG  at+  ++s + +p+++ W k+g++ ie+++          s+s  i+ +++ d G+Y+ +v ns
  gi|330508678|ref|YP_004385106.1| 1707 PKSLETCEGAAATFGVKAS-GGEPLEYQWYKDGTE-IEGAT----------SNSYSIPVASPSDRGSYWVQVRNS 1769
                                        5667777899999999999.99*******987765.55555..........8*****************999998 PP

                                        TE CS
                                ig   78 gs 79  
                                         s
  gi|330508678|ref|YP_004385106.1| 1770 CS 1771
                                        66 PP

  == domain 13  score: 6.6 bits;  conditional E-value: 0.0059
                                        ESEEEEETTS-EEEEEEEESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEEEEEEET CS
                                ig    3 kplvlvleGesatLtCsvstqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYtCevnns 77  
                                        +++  + +G+ +t+t  v+ ++kp+++ W+k+g   +  +           +   +i ++ ++d+G+Y+ ++ n+
  gi|330508678|ref|YP_004385106.1| 1792 PTSQKICQGSAVTFTVQVE-SSKPLSYQWFKDGIKIPGAT-----------QDVYTIARAVLNDTGSYWVQAANN 1854
                                        667777799**********.*********98877666664...........599999999999999999777776 PP

                                        TE CS
                                ig   78 gs 79  
                                         s
  gi|330508678|ref|YP_004385106.1| 1855 CS 1856
                                        55 PP

  == domain 14  score: -0.5 bits;  conditional E-value: 0.94
                                        EEEEECSSTGGGTEEEEEEEEETTEEEEEE CS
                                ig   55 sslliskvteedaGtYtCevnnsgssvtls 84  
                                           +i+++ + d G+Y+ +v ns +sv+++
  gi|330508678|ref|YP_004385106.1| 1917 DAYTIPRTGKFDMGNYMVQVRNSCGSVESK 1946
                                        567889999999999999999999888775 PP

  == domain 15  score: 2.9 bits;  conditional E-value: 0.085
                                        EESEEEEETTS-EEEEEEEESSSCTSEEEEEESSSSCS CS
                                ig    2 akplvlvleGesatLtCsvstqtkptdvtWkkegqtki 39  
                                        ++++ +v +G+ at++  +s +++p+++ W+k+g+  +
  gi|330508678|ref|YP_004385106.1| 1961 PPKGQRVCQGDAATFSVQAS-SSEPLSYQWFKDGKMIQ 1997
                                        577788899***********.**********9987554 PP

  == domain 16  score: -0.6 bits;  conditional E-value: 0.99
                                        TTS-EEEEEEEESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEEEEEEE CS
                                ig   10 eGesatLtCsvstqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYtCevnn 76  
                                        +G+ +t++ ++  +++p+++ W+k+g + +               +  +i+k+   d G+Y  ++ n
  gi|330508678|ref|YP_004385106.1| 2054 QGTPVTFNVRAI-SDDPLSYQWFKDGVEIPGAIA-----------EVYTIQKAITGDKGSYYVQARN 2108
                                        577778888888.899999999999887776644...........5566666666666666555555 PP

  == domain 17  score: 8.3 bits;  conditional E-value: 0.0017
                                        ESEEEEETTS-EEEEEEEESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEE CS
                                ig    3 kplvlvleGesatLtCsvstqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYt 71  
                                        +++  v eG++at+t  ++ +  p+++ W+k g   +              s++l+i  + +ed G+Y+
  gi|330508678|ref|YP_004385106.1| 2132 PTSQKVCEGSTATFTVLAK-SAQPLTYQWIKGGRIIPGAN-----------SEELTIFDANMEDMGEYR 2188
                                        6778899************.**********9887776664...........6***************96 PP

  == domain 18  score: 3.4 bits;  conditional E-value: 0.058
                                        EEEEEECSSTGGGTEEEEEEEEETTEEEEEEEE CS
                                ig   54 ssslliskvteedaGtYtCevnnsgssvtlsvs 86  
                                        s sl+i + ++ d+G Y+ +v+n  +s+++++s
  gi|330508678|ref|YP_004385106.1| 2257 SPSLIILNPRPSDSGGYRLTVSNGCGSNKSKMS 2289
                                        349***************999999988888876 PP

>> Ig_4  T-cell surface glycoprotein CD3 delta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       6.5   9.7e+03      14      38 ..     453     477 ..     451     486 .. 0.74
   2 ?    5.8   0.0     0.011        16       3      45 ..     524     569 ..     522     578 .. 0.79
   3 ?    0.3   0.0      0.59   8.9e+02       9      45 ..     619     654 ..     613     656 .. 0.82
   4 ?    4.0   0.0      0.04        60      14      46 ..     711     743 ..     702     764 .. 0.91
   5 ?    0.2   0.0      0.63   9.4e+02      13      48 ..     795     830 ..     786     841 .. 0.79
   6 ?    4.0   0.0     0.041        61      12      48 ..     878     915 ..     869     934 .. 0.83
   7 ?   -2.3   0.0       3.8   5.7e+03      14      34 ..     966     988 ..     957     994 .. 0.76
   8 ?    1.6   0.0      0.22   3.3e+02      13      48 ..    1050    1085 ..    1041    1097 .. 0.83
   9 ?    4.5   0.0     0.028        42      13      48 ..    1135    1170 ..    1126    1183 .. 0.85
  10 ?    1.6   0.0      0.23   3.5e+02      13      49 ..    1220    1256 ..    1211    1271 .. 0.81
  11 ?    0.5   0.0      0.51   7.7e+02      12      48 ..    1303    1340 ..    1294    1359 .. 0.80
  12 ?    4.3   0.0     0.032        48      12      49 ..    1388    1426 ..    1379    1445 .. 0.78
  13 ?   -2.8   0.0       5.3     8e+03      14      34 ..    1476    1498 ..    1471    1503 .. 0.78
  14 ?    1.3   0.0      0.28   4.2e+02      13      48 ..    1560    1595 ..    1546    1608 .. 0.80
  15 ?   -0.7   0.0       1.2   1.8e+03      13      45 ..    1645    1677 ..    1636    1692 .. 0.80
  16 ?    4.2   0.0     0.034        50      14      48 ..    1731    1765 ..    1725    1775 .. 0.89
  17 ?    5.7   0.0     0.012        18      10      52 ..    1811    1853 ..    1802    1861 .. 0.82
  18 ?   -1.2   0.0       1.7   2.5e+03       9      45 ..    1895    1932 ..    1889    1950 .. 0.74
  19 ?   -0.3   0.0      0.88   1.3e+03      13      36 ..    1985    2008 ..    1976    2020 .. 0.78
  20 ?    3.5   0.0     0.059        89      14      48 ..    2071    2105 ..    2065    2119 .. 0.85
  21 ?   -0.5   0.0         1   1.5e+03      14      45 ..    2156    2187 ..    2147    2190 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.5
                                       -EEEEETTEE---SS----EEEETT CS
                              Ig_4  14 eitwlkdkkeikesnkktldLgkri 38 
                                       +++w k++++i  ++++++ + +  
  gi|330508678|ref|YP_004385106.1| 453 SYQWSKNGSQIAGATTDSYIIPAAK 477
                                       589********99998876665555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.011
                                       EEEEE-SSS-S-...EEEEETTEE---SS----EEEETTS--EEEE CS
                              Ig_4   3 kVlLtCnsskke...itwlkdkkeikesnkktldLgkriedprglY 45 
                                       +VlL+ + s +e   ++w+k++++i+ +n++++ + +++  ++g Y
  gi|330508678|ref|YP_004385106.1| 524 EVLLNAQASGTEplnYQWKKNGENITGANTNRYLISSILPTDEGDY 569
                                       677777666533344**************99998888887777766 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.59
                                       SSS-S-EEEEETTEE---SS----EEEETTS--EEEE CS
                              Ig_4   9 nsskkeitwlkdkkeikesnkktldLgkriedprglY 45 
                                       n+s  +++w+kd+ +i+ +n   l++ +  + ++g Y
  gi|330508678|ref|YP_004385106.1| 619 NES-YTYQWQKDGLNITAANAAVLSISAANSTDQGNY 654
                                       444.589*************99999999988888888 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.04
                                       -EEEEETTEE---SS----EEEETTS--EEEEE CS
                              Ig_4  14 eitwlkdkkeikesnkktldLgkriedprglYq 46 
                                       +i+w+kd+ +i  +n ++  +++ + +++g Y+
  gi|330508678|ref|YP_004385106.1| 711 TIQWMKDGLQIPGANLDSFVIKNATRNDSGSYS 743
                                       69*****************************96 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.63
                                       S-EEEEETTEE---SS----EEEETTS--EEEEEEE CS
                              Ig_4  13 keitwlkdkkeikesnkktldLgkriedprglYqCq 48 
                                        +++w+kd+ +i+ ++++ +++ ++   + g Y+ q
  gi|330508678|ref|YP_004385106.1| 795 LSYQWFKDGIKIDGATSEYYTIPQTNLSDMGSYSVQ 830
                                       579************999999999999888988765 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.041
                                       -.S-EEEEETTEE---SS----EEEETTS--EEEEEEE CS
                              Ig_4  12 k.keitwlkdkkeikesnkktldLgkriedprglYqCq 48 
                                       +  +++wlkd+ +i  ++++t+ + ++  ++ g Y+ q
  gi|330508678|ref|YP_004385106.1| 878 EpLSYQWLKDGVNIPAATSDTYAIPASNLNDTGSYSVQ 915
                                       44579******************************866 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 3.8
                                       -EEEEETTEE---SS--..--EE CS
                              Ig_4  14 eitwlkdkkeikesnkk..tldL 34 
                                       +++wlkd+ ei  ++++  t+dL
  gi|330508678|ref|YP_004385106.1| 966 KYQWLKDGIEIPGATDDryTIDL 988
                                       699********999888555555 PP

  == domain 8  score: 1.6 bits;  conditional E-value: 0.22
                                        S-EEEEETTEE---SS----EEEETTS--EEEEEEE CS
                              Ig_4   13 keitwlkdkkeikesnkktldLgkriedprglYqCq 48  
                                         +++wlk++ +i+ ++++++++ +++  + g Y+ q
  gi|330508678|ref|YP_004385106.1| 1050 LSYQWLKEGIKIEGATSESYTIPQTSLSDTGSYSVQ 1085
                                        579************************999*99866 PP

  == domain 9  score: 4.5 bits;  conditional E-value: 0.028
                                        S-EEEEETTEE---SS----EEEETTS--EEEEEEE CS
                              Ig_4   13 keitwlkdkkeikesnkktldLgkriedprglYqCq 48  
                                         +++wlkd+ +i+ + ++t+++ ++  ++ g Y+ q
  gi|330508678|ref|YP_004385106.1| 1135 LSYQWLKDGVNIQGAASDTYTIPASNLNDTGSYSVQ 1170
                                        579******************************865 PP

  == domain 10  score: 1.6 bits;  conditional E-value: 0.23
                                        S-EEEEETTEE---SS----EEEETTS--EEEEEEEE CS
                              Ig_4   13 keitwlkdkkeikesnkktldLgkriedprglYqCqg 49  
                                         +++w+kd+ +i+ ++++++ + + +  + g Y+ q 
  gi|330508678|ref|YP_004385106.1| 1220 LSYQWFKDGIKIDGATSESYAIPAASLSDTGSYSVQV 1256
                                        579************************9999998764 PP

  == domain 11  score: 0.5 bits;  conditional E-value: 0.51
                                        -.S-EEEEETTEE---SS----EEEETTS--EEEEEEE CS
                              Ig_4   12 k.keitwlkdkkeikesnkktldLgkriedprglYqCq 48  
                                        +  +++w+kd+ +i+ ++++ +++ ++   + g Y+ q
  gi|330508678|ref|YP_004385106.1| 1303 EpLSYQWFKDGIKIDGATSEYYTIPQTNLSDMGSYSVQ 1340
                                        44579*************99999999999999999766 PP

  == domain 12  score: 4.3 bits;  conditional E-value: 0.032
                                        -.S-EEEEETTEE---SS----EEEETTS--EEEEEEEE CS
                              Ig_4   12 k.keitwlkdkkeikesnkktldLgkriedprglYqCqg 49  
                                        +  +++wlkd+ +i  ++++t+++ +   ++ g Y+ q 
  gi|330508678|ref|YP_004385106.1| 1388 EpLSYQWLKDGANIPGATSDTYTIPAAKLNDTGSYSVQV 1426
                                        44579******************************8663 PP

  == domain 13  score: -2.8 bits;  conditional E-value: 5.3
                                        -EEEEETTEE---SS--..--EE CS
                              Ig_4   14 eitwlkdkkeikesnkk..tldL 34  
                                        e++wlkd+ ei  ++++  t+dL
  gi|330508678|ref|YP_004385106.1| 1476 EYQWLKDGIEIPGATDDryTIDL 1498
                                        689********999887555555 PP

  == domain 14  score: 1.3 bits;  conditional E-value: 0.28
                                        S-EEEEETTEE---SS----EEEETTS--EEEEEEE CS
                              Ig_4   13 keitwlkdkkeikesnkktldLgkriedprglYqCq 48  
                                          ++wlkd+ +i  + ++t+++ +    + g Y+ q
  gi|330508678|ref|YP_004385106.1| 1560 LRYQWLKDGVNIPGAASDTYTIPAANLSDMGSYSVQ 1595
                                        469*************99*99999999999999766 PP

  == domain 15  score: -0.7 bits;  conditional E-value: 1.2
                                        S-EEEEETTEE---SS----EEEETTS--EEEE CS
                              Ig_4   13 keitwlkdkkeikesnkktldLgkriedprglY 45  
                                         +++wl+d+ +i +++++++++ +    + g Y
  gi|330508678|ref|YP_004385106.1| 1645 LSYQWLRDGANIPDATSESYTILAANLSDTGSY 1677
                                        579***********9999988888887777777 PP

  == domain 16  score: 4.2 bits;  conditional E-value: 0.034
                                        -EEEEETTEE---SS----EEEETTS--EEEEEEE CS
                              Ig_4   14 eitwlkdkkeikesnkktldLgkriedprglYqCq 48  
                                        e++w+kd++ei+ ++++++++   +  +rg Y+ q
  gi|330508678|ref|YP_004385106.1| 1731 EYQWYKDGTEIEGATSNSYSIPVASPSDRGSYWVQ 1765
                                        689*****************************976 PP

  == domain 17  score: 5.7 bits;  conditional E-value: 0.012
                                        SS-.S-EEEEETTEE---SS----EEEETTS--EEEEEEEE.SS CS
                              Ig_4   10 ssk.keitwlkdkkeikesnkktldLgkriedprglYqCqgeek 52  
                                        ssk  +++w+kd+ +i  ++++ +++ + + ++ g Y+ q+ ++
  gi|330508678|ref|YP_004385106.1| 1811 SSKpLSYQWFKDGIKIPGATQDVYTIARAVLNDTGSYWVQA-AN 1853
                                        4444679*******************************886.33 PP

  == domain 18  score: -1.2 bits;  conditional E-value: 1.7
                                        SSS-.S-EEEEETTEE---SS----EEEETTS--EEEE CS
                              Ig_4    9 nssk.keitwlkdkkeikesnkktldLgkriedprglY 45  
                                        +ss+  +++w+kd+ ei e++ + +++ ++ + + g Y
  gi|330508678|ref|YP_004385106.1| 1895 ESSEaLSYQWFKDGIEIYEATADAYTIPRTGKFDMGNY 1932
                                        55555789*********999988777766666555555 PP

  == domain 19  score: -0.3 bits;  conditional E-value: 0.88
                                        S-EEEEETTEE---SS----EEEE CS
                              Ig_4   13 keitwlkdkkeikesnkktldLgk 36  
                                         +++w+kd+k i+ ++ +t+++ +
  gi|330508678|ref|YP_004385106.1| 1985 LSYQWFKDGKMIQGATADTYTIPA 2008
                                        579**********99988877655 PP

  == domain 20  score: 3.5 bits;  conditional E-value: 0.059
                                        -EEEEETTEE---SS----EEEETTS--EEEEEEE CS
                              Ig_4   14 eitwlkdkkeikesnkktldLgkriedprglYqCq 48  
                                        +++w+kd+ ei  +  + ++++k i+ ++g Y  q
  gi|330508678|ref|YP_004385106.1| 2071 SYQWFKDGVEIPGAIAEVYTIQKAITGDKGSYYVQ 2105
                                        689***********************888888755 PP

  == domain 21  score: -0.5 bits;  conditional E-value: 1
                                        -EEEEETTEE---SS----EEEETTS--EEEE CS
                              Ig_4   14 eitwlkdkkeikesnkktldLgkriedprglY 45  
                                        +++w+k++  i  +n+++l++ +   ++ g Y
  gi|330508678|ref|YP_004385106.1| 2156 TYQWIKGGRIIPGANSEELTIFDANMEDMGEY 2187
                                        589************99999988888888877 PP

>> V-set  Immunoglobulin V-set domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.58   8.7e+02      79     108 ..     475     504 ..     467     505 .. 0.72
   2 ?   -0.4   0.0      0.86   1.3e+03      77     108 ..     558     589 ..     522     590 .. 0.76
   3 ?   -1.6   0.1       1.9   2.9e+03      70      92 ..     636     658 ..     607     674 .. 0.76
   4 ?    2.7   0.0     0.094   1.4e+02      76      97 ..     730     750 ..     718     757 .. 0.82
   5 ?    4.0   0.2     0.036        54       3      37 ..     772     803 ..     770     838 .. 0.70
   6 ?    1.8   0.0      0.17   2.6e+02      76     100 ..     815     839 ..     809     847 .. 0.75
   7 ?   -0.2   0.1      0.71   1.1e+03      80      96 ..     904     919 ..     856     924 .. 0.73
   8 ?    0.9   0.1      0.33   4.9e+02      80     101 ..     904     925 ..     898     932 .. 0.72
   9 ?   -0.6   0.1      0.96   1.4e+03       2      36 ..    1026    1057 ..    1025    1066 .. 0.91
  10 ?    4.1   0.1     0.035        52      75      99 ..    1069    1092 ..    1059    1100 .. 0.79
  11 ?    2.1   0.1      0.15   2.2e+02       2      36 ..    1111    1142 ..    1110    1156 .. 0.91
  12 ?    0.3   0.0       0.5   7.5e+02      77     102 ..    1156    1181 ..    1153    1187 .. 0.71
  13 ?    3.9   0.4     0.041        61       5      92 ..    1199    1256 ..    1195    1272 .. 0.42
  14 ?    2.5   0.1      0.11   1.6e+02      76     105 ..    1325    1354 ..    1319    1357 .. 0.74
  15 ?   -2.5   0.0       3.9   5.9e+03       4      37 ..    1368    1398 ..    1366    1406 .. 0.82
  16 ?    3.0   0.1     0.074   1.1e+02      76     102 ..    1410    1436 ..    1392    1442 .. 0.77
  17 ?   -3.7   0.0       9.3   1.4e+04       9      35 ..    1458    1481 ..    1452    1483 .. 0.83
  18 ?    1.5   0.0      0.23   3.4e+02      76      99 ..    1580    1602 ..    1566    1611 .. 0.79
  19 ?    1.8   0.0      0.18   2.7e+02       3      37 ..    1622    1653 ..    1620    1660 .. 0.87
  20 !    5.9   0.0    0.0095        14      72     108 ..    1661    1697 ..    1653    1698 .. 0.80
  21 ?    0.0   0.0      0.63   9.4e+02       2      38 ..    1706    1739 ..    1705    1749 .. 0.90
  22 ?    1.0   0.0      0.32   4.7e+02      77      95 ..    1751    1769 ..    1736    1780 .. 0.77
  23 ?    0.2   0.1      0.56   8.3e+02       3      36 ..    1792    1822 ..    1791    1834 .. 0.87
  24 ?    0.4   0.0      0.47     7e+02      76     100 ..    1835    1858 ..    1827    1866 .. 0.79
  25 ?   -0.9   0.0       1.2   1.8e+03       3      36 ..    1877    1907 ..    1876    1926 .. 0.90
  26 ?    2.1   0.0      0.15   2.2e+02       3      38 ..    1962    1994 ..    1960    2027 .. 0.85
  27 ?   -2.0   0.0       2.6   3.9e+03       3      36 ..    2047    2077 ..    2046    2083 .. 0.85
  28 ?    0.6   0.1      0.42   6.3e+02      76     106 ..    2090    2120 ..    2087    2122 .. 0.75
  29 ?   -0.8   0.0       1.2   1.7e+03       2      36 ..    2131    2162 ..    2130    2165 .. 0.88
  30 ?    4.9   0.0     0.019        28      74     107 ..    2173    2206 ..    2160    2208 .. 0.80
  31 !    6.1   0.0    0.0082        12      72     105 ..    2257    2289 ..    2233    2293 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.58
                                       SESGGG-EEEEEEEECSSEEE.EEEEEEEEE CS
                             V-set  79 nltlsDsGtYtCavvpsgegv.fgkgtrLtV 108
                                        ++l+D+G+Y+++ v++ +g+ +++   LtV
  gi|330508678|ref|YP_004385106.1| 475 AAKLADAGSYRVR-VSNACGSiESNPAVLTV 504
                                       5789*********.55555554665555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.86
                                       ESSESGGG-EEEEEEEECSSEEE.EEEEEEEEE CS
                             V-set  77 iqnltlsDsGtYtCavvpsgegv.fgkgtrLtV 108
                                       i+++ ++D+G Y++av ++ +g  +++ ++++V
  gi|330508678|ref|YP_004385106.1| 558 ISSILPTDEGDYSLAV-SNICGMaESGAVHISV 589
                                       7778889999999995.4444443666666666 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.9
                                       TTEEEEEESSESGGG-EEEEEEE CS
                             V-set  70 kgdfsltiqnltlsDsGtYtCav 92 
                                        + + l i+ ++ +D+G Y++ +
  gi|330508678|ref|YP_004385106.1| 636 ANAAVLSISAANSTDQGNYSVII 658
                                       66788999999999999998765 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.094
                                       EESSESGGG-EEEEEEEECSSE CS
                             V-set  76 tiqnltlsDsGtYtCavvpsge 97 
                                        i+n+t++DsG+Y++  v++++
  gi|330508678|ref|YP_004385106.1| 730 VIKNATRNDSGSYSLI-VSNDC 750
                                       599**********998.55555 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.036
                                       ESEEEEETTSEEEEEEEEESSSCTTTSEEEEEEEE CS
                             V-set   3 prevtvaeGesvtLpCtlssseseeslsvyWyrqp 37 
                                       p  + v +G+ +t++++ +ss   e ls++W+++ 
  gi|330508678|ref|YP_004385106.1| 772 PANLRVCQGAAATFSVQAKSS---EPLSYQWFKDG 803
                                       778889999999999999999...99999999965 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.17
                                       EESSESGGG-EEEEEEEECSSEEEE CS
                             V-set  76 tiqnltlsDsGtYtCavvpsgegvf 100
                                       ti + +lsD G+Y+++v ++  +v+
  gi|330508678|ref|YP_004385106.1| 815 TIPQTNLSDMGSYSVQVANNCSQVE 839
                                       677899**********644444334 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 0.71
                                       ESGGG-EEEEEEEECSS CS
                             V-set  80 ltlsDsGtYtCavvpsg 96 
                                        +l+D+G+Y+++ ++++
  gi|330508678|ref|YP_004385106.1| 904 SNLNDTGSYSVQ-ITNN 919
                                       567788888888.4444 PP

  == domain 8  score: 0.9 bits;  conditional E-value: 0.33
                                       ESGGG-EEEEEEEECSSEEE.EE CS
                             V-set  80 ltlsDsGtYtCavvpsgegv.fg 101
                                        +l+D+G+Y+++ +++++++ ++
  gi|330508678|ref|YP_004385106.1| 904 SNLNDTGSYSVQ-ITNNCSQiES 925
                                       6799********.6666655254 PP

  == domain 9  score: -0.6 bits;  conditional E-value: 0.96
                                        EESEEEEETTSEEEEEEEEESSSCTTTSEEEEEEE CS
                             V-set    2 tprevtvaeGesvtLpCtlssseseeslsvyWyrq 36  
                                        +p++ +v +G+++ ++++  ss   e ls++W+++
  gi|330508678|ref|YP_004385106.1| 1026 QPTSQNVCQGTRAAFSVQAESS---EPLSYQWLKE 1057
                                        689999***********99999...*******985 PP

  == domain 10  score: 4.1 bits;  conditional E-value: 0.035
                                        EEESSESGGG-EEEEEEEECSSEEE CS
                             V-set   75 ltiqnltlsDsGtYtCavvpsgegv 99  
                                         ti + +lsD+G+Y+++ v++++++
  gi|330508678|ref|YP_004385106.1| 1069 YTIPQTSLSDTGSYSVQ-VSNNCSR 1092
                                        578899***********.5666555 PP

  == domain 11  score: 2.1 bits;  conditional E-value: 0.15
                                        EESEEEEETTSEEEEEEEEESSSCTTTSEEEEEEE CS
                             V-set    2 tprevtvaeGesvtLpCtlssseseeslsvyWyrq 36  
                                        +p++ +v +G+ +t++++  ss   e ls++W+++
  gi|330508678|ref|YP_004385106.1| 1111 QPTSQKVCQGTAATFSVQARSS---EPLSYQWLKD 1142
                                        689999**************99...*******997 PP

  == domain 12  score: 0.3 bits;  conditional E-value: 0.5
                                        ESSESGGG-EEEEEEEECSSEEEEEE CS
                             V-set   77 iqnltlsDsGtYtCavvpsgegvfgk 102 
                                        i   +l+D+G+Y+++++++  + +++
  gi|330508678|ref|YP_004385106.1| 1156 IPASNLNDTGSYSVQLRNNCSQIESE 1181
                                        666789*********76555444555 PP

  == domain 13  score: 3.9 bits;  conditional E-value: 0.041
                                        EEEEETTSEEEEEEEEESSSCTTTSEEEEEEEETTS...SEEEEEEEECTTEEEEESTTTEEEEEEGTTTEEEEE CS
                             V-set    5 evtvaeGesvtLpCtlssseseeslsvyWyrqppgk...epeeliayysnkskeekkkgrfslrkdpskgdfslt 76  
                                        + +v +G+++ ++++ +ss   e ls++W+++  +    + e                              s  
  gi|330508678|ref|YP_004385106.1| 1199 SQNVCQGTRAAFSVQAKSS---EPLSYQWFKDGIKIdgaTSE------------------------------SYA 1240
                                        5555555555556655555...55666665543221211111..............................112 PP

                                        ESSESGGG-EEEEEEE CS
                             V-set   77 iqnltlsDsGtYtCav 92  
                                        i  ++lsD+G+Y+++v
  gi|330508678|ref|YP_004385106.1| 1241 IPAASLSDTGSYSVQV 1256
                                        2233444444444443 PP

  == domain 14  score: 2.5 bits;  conditional E-value: 0.11
                                        EESSESGGG-EEEEEEEECSSEEEEEEEEE CS
                             V-set   76 tiqnltlsDsGtYtCavvpsgegvfgkgtr 105 
                                        ti + +lsD G+Y+++v ++  + +++  +
  gi|330508678|ref|YP_004385106.1| 1325 TIPQTNLSDMGSYSVQVSNNCSQIESEAAN 1354
                                        677899**********65444444666555 PP

  == domain 15  score: -2.5 bits;  conditional E-value: 3.9
                                        SEEEEETTSEEEEEEEEESSSCTTTSEEEEEEEE CS
                             V-set    4 revtvaeGesvtLpCtlssseseeslsvyWyrqp 37  
                                          ++  +G+ +++ ++  ss   e ls++W+++ 
  gi|330508678|ref|YP_004385106.1| 1368 ANLKICQGAAAKFEVQAESS---EPLSYQWLKDG 1398
                                        55666789999999999988...*******9975 PP

  == domain 16  score: 3.0 bits;  conditional E-value: 0.074
                                        EESSESGGG-EEEEEEEECSSEEE.EEE CS
                             V-set   76 tiqnltlsDsGtYtCavvpsgegv.fgk 102 
                                        ti  ++l+D+G+Y+++v ++++++ +++
  gi|330508678|ref|YP_004385106.1| 1410 TIPAAKLNDTGSYSVQV-ANNCSQiESE 1436
                                        6778899*********5.5555552444 PP

  == domain 17  score: -3.7 bits;  conditional E-value: 9.3
                                        ETTSEEEEEEEEESSSCTTTSEEEEEE CS
                             V-set    9 aeGesvtLpCtlssseseeslsvyWyr 35  
                                         +G+ +t++++ ss+   e  +++W++
  gi|330508678|ref|YP_004385106.1| 1458 CQGAAATFHVEASSY---EPIEYQWLK 1481
                                        589999****99999...999999998 PP

  == domain 18  score: 1.5 bits;  conditional E-value: 0.23
                                        EESSESGGG-EEEEEEEECSSEEE CS
                             V-set   76 tiqnltlsDsGtYtCavvpsgegv 99  
                                        ti  ++lsD G+Y+++v ++++++
  gi|330508678|ref|YP_004385106.1| 1580 TIPAANLSDMGSYSVQV-SNNCSQ 1602
                                        6777899*********5.555544 PP

  == domain 19  score: 1.8 bits;  conditional E-value: 0.18
                                        ESEEEEETTSEEEEEEEEESSSCTTTSEEEEEEEE CS
                             V-set    3 prevtvaeGesvtLpCtlssseseeslsvyWyrqp 37  
                                        p+  +v +G+ +t++++ +ss   e ls++W+r+ 
  gi|330508678|ref|YP_004385106.1| 1622 PTGQKVCQGTAATFSVQAKSS---EPLSYQWLRDG 1653
                                        66678999***********99...********975 PP

  == domain 20  score: 5.9 bits;  conditional E-value: 0.0095
                                        EEEEEESSESGGG-EEEEEEEECSSEEE.EEEEEEEEE CS
                             V-set   72 dfsltiqnltlsDsGtYtCavvpsgegv.fgkgtrLtV 108 
                                        + s ti  ++lsD+G+Y++ v ++++++ +++ +rL V
  gi|330508678|ref|YP_004385106.1| 1661 SESYTILAANLSDTGSYSVLV-ANKCNQiESEAVRLDV 1697
                                        557789999***********5.5555555999999988 PP

  == domain 21  score: 0.0 bits;  conditional E-value: 0.63
                                        EESEEEEETTSEEEEEEEEESSSCTTTSEEEEEEEET CS
                             V-set    2 tprevtvaeGesvtLpCtlssseseeslsvyWyrqpp 38  
                                        +p+++++ eG+ +t+ ++ s     e l+++Wy++ +
  gi|330508678|ref|YP_004385106.1| 1706 QPKSLETCEGAAATFGVKASGG---EPLEYQWYKDGT 1739
                                        6999*************99998...********9765 PP

  == domain 22  score: 1.0 bits;  conditional E-value: 0.32
                                        ESSESGGG-EEEEEEEECS CS
                             V-set   77 iqnltlsDsGtYtCavvps 95  
                                        i  +++sD G+Y+++v++s
  gi|330508678|ref|YP_004385106.1| 1751 IPVASPSDRGSYWVQVRNS 1769
                                        556799*********7443 PP

  == domain 23  score: 0.2 bits;  conditional E-value: 0.56
                                        ESEEEEETTSEEEEEEEEESSSCTTTSEEEEEEE CS
                             V-set    3 prevtvaeGesvtLpCtlssseseeslsvyWyrq 36  
                                        p++ +  +G  vt+++++ ss   + ls++W+++
  gi|330508678|ref|YP_004385106.1| 1792 PTSQKICQGSAVTFTVQVESS---KPLSYQWFKD 1822
                                        5566677899*********99...********96 PP

  == domain 24  score: 0.4 bits;  conditional E-value: 0.47
                                        EESSESGGG-EEEEEEEECSSEEEE CS
                             V-set   76 tiqnltlsDsGtYtCavvpsgegvf 100 
                                        ti  + l+D+G+Y+++  ++++++ 
  gi|330508678|ref|YP_004385106.1| 1835 TIARAVLNDTGSYWVQ-AANNCSQI 1858
                                        5777889*********.66666654 PP

  == domain 25  score: -0.9 bits;  conditional E-value: 1.2
                                        ESEEEEETTSEEEEEEEEESSSCTTTSEEEEEEE CS
                             V-set    3 prevtvaeGesvtLpCtlssseseeslsvyWyrq 36  
                                        p + +v eG+ +t+ ++  ss   e ls++W+++
  gi|330508678|ref|YP_004385106.1| 1877 PASQKVCEGAAATFFVQAESS---EALSYQWFKD 1907
                                        6788999*********99999...********96 PP

  == domain 26  score: 2.1 bits;  conditional E-value: 0.15
                                        ESEEEEETTSEEEEEEEEESSSCTTTSEEEEEEEET CS
                             V-set    3 prevtvaeGesvtLpCtlssseseeslsvyWyrqpp 38  
                                        p+   v +G  +t++++ sss   e ls++W+++ +
  gi|330508678|ref|YP_004385106.1| 1962 PKGQRVCQGDAATFSVQASSS---EPLSYQWFKDGK 1994
                                        55577889********99999...********9765 PP

  == domain 27  score: -2.0 bits;  conditional E-value: 2.6
                                        ESEEEEETTSEEEEEEEEESSSCTTTSEEEEEEE CS
                             V-set    3 prevtvaeGesvtLpCtlssseseeslsvyWyrq 36  
                                        p +  v +G+ vt+++   s    + ls++W+++
  gi|330508678|ref|YP_004385106.1| 2047 PASQIVCQGTPVTFNVRAISD---DPLSYQWFKD 2077
                                        677788899999*99988887...9*******96 PP

  == domain 28  score: 0.6 bits;  conditional E-value: 0.42
                                        EESSESGGG-EEEEEEEECSSEEE.EEEEEEE CS
                             V-set   76 tiqnltlsDsGtYtCavvpsgegv.fgkgtrL 106 
                                        tiq++   D G+Y+++   +++g+ ++++ +L
  gi|330508678|ref|YP_004385106.1| 2090 TIQKAITGDKGSYYVQA-RNSCGQiESETANL 2120
                                        79999999********5.55555537766666 PP

  == domain 29  score: -0.8 bits;  conditional E-value: 1.2
                                        EESEEEEETTSEEEEEEEEESSSCTTTSEEEEEEE CS
                             V-set    2 tprevtvaeGesvtLpCtlssseseeslsvyWyrq 36  
                                        +p++ +v eG ++t+++  +s    + l ++W ++
  gi|330508678|ref|YP_004385106.1| 2131 QPTSQKVCEGSTATFTVLAKSA---QPLTYQWIKG 2162
                                        689999***********88877...9999999987 PP

  == domain 30  score: 4.9 bits;  conditional E-value: 0.019
                                        EEEESSESGGG-EEEEEEEECSSEEE.EEEEEEEE CS
                             V-set   74 sltiqnltlsDsGtYtCavvpsgegv.fgkgtrLt 107 
                                        +lti +++++D G Y++a +++g+g   ++ ++L 
  gi|330508678|ref|YP_004385106.1| 2173 ELTIFDANMEDMGEYRVA-ISNGCGFiDSNAVSLI 2206
                                        79****************.7777776566666665 PP

  == domain 31  score: 6.1 bits;  conditional E-value: 0.0082
                                        EEEEEESSESGGG-EEEEEEEECSSEEEEEEEEE CS
                             V-set   72 dfsltiqnltlsDsGtYtCavvpsgegvfgkgtr 105 
                                        + sl i n ++sDsG Y++  v++g+g+ +++++
  gi|330508678|ref|YP_004385106.1| 2257 SPSLIILNPRPSDSGGYRLT-VSNGCGSNKSKMS 2289
                                        569*****************.8999988777776 PP

>> PKD_3  PKD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.5   3.7e+03      32      44 ..     536     548 ..     522     556 .. 0.74
   2 ?    0.7   0.0       0.3   4.5e+02      15      46 ..     604     635 ..     599     661 .. 0.58
   3 ?   -0.3   0.0      0.62   9.2e+02       9      51 ..     771     815 ..     767     832 .. 0.70
   4 ?    4.9   0.0     0.014        21       2      64 ..     851     916 ..     850     919 .. 0.76
   5 !    6.8   0.0    0.0038       5.6       2      52 ..     936     986 ..     935    1002 .. 0.78
   6 ?   -0.8   0.0      0.89   1.3e+03      16      56 ..    1033    1075 ..    1024    1087 .. 0.68
   7 ?   -0.0   0.0       0.5   7.4e+02      14      65 ..    1116    1172 ..    1108    1174 .. 0.70
   8 ?   -3.0   0.0       4.3   6.4e+03      24      51 ..    1296    1325 ..    1290    1341 .. 0.58
   9 !    6.2   0.0    0.0057       8.5       2      62 ..    1361    1424 ..    1360    1428 .. 0.75
  10 ?    0.7   0.0      0.31   4.6e+02       2      51 ..    1446    1495 ..    1445    1511 .. 0.79
  11 ?   -0.7   0.0      0.83   1.2e+03      15      44 ..    1542    1571 ..    1534    1597 .. 0.70
  12 ?    2.6   0.0     0.079   1.2e+02      12      51 ..    1624    1665 ..    1618    1682 .. 0.73
  13 ?   -3.0   0.0       4.2   6.2e+03      34      44 ..    1731    1741 ..    1709    1756 .. 0.78
  14 ?    2.6   0.0     0.078   1.2e+02      14      53 ..    1796    1837 ..    1787    1850 .. 0.80
  15 ?   -1.6   0.0       1.5   2.3e+03      11      44 ..    1878    1911 ..    1871    1937 .. 0.71
  16 ?    1.4   0.0      0.18   2.7e+02      11      54 ..    1963    2008 ..    1956    2022 .. 0.72
  17 ?   -1.8   0.0       1.8   2.7e+03       2      44 ..    2041    2081 ..    2041    2107 .. 0.59
  18 ?    2.6   0.0     0.075   1.1e+02      14      64 ..    2136    2191 ..    2126    2193 .. 0.78
  19 ?   -1.1   0.0       1.1   1.6e+03      32      44 ..    2240    2252 ..    2213    2257 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.5
                             PKD_3  32 naafaWtieGkiv 44 
                                         +++W+ +G+ +
  gi|330508678|ref|YP_004385106.1| 536 PLNYQWKKNGENI 548
                                       457*******965 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.3
                             PKD_3  15 vkvgreltiaPtvenaenaafaWtieGkivst 46 
                                       v +g+++ ++ +v   e  +++W  +G  +  
  gi|330508678|ref|YP_004385106.1| 604 VCTGSPVSFEVQVAGNESYTYQWQKDGLNITA 635
                                       5667777776555555555599*999985443 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.62
                             PKD_3   9 etegykvkvgreltiaPtvenaenaafaWtieGkiv..steptyt 51 
                                       + ++++v  g   t++ + +++e   ++W  +G ++   t + yt
  gi|330508678|ref|YP_004385106.1| 771 QPANLRVCQGAAATFSVQAKSSEPLSYQWFKDGIKIdgATSEYYT 815
                                       55789999999999999999999999*****99864223444444 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.014
                             PKD_3   2 PvIsLdletegykvkvgreltiaPtvenaenaafaWtieGki..vsteptytf...teeelgsyevtl 64 
                                       P+I L  + +++k+  g   +++ + e++e   ++W  +G      t  ty     + +  gsy v++
  gi|330508678|ref|YP_004385106.1| 851 PKILL--QPANLKICQGAAAKFEVQAESSEPLSYQWLKDGVNipAATSDTYAIpasNLNDTGSYSVQI 916
                                       66766..8899*****************************9535667777765222345567777766 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.0038
                             PKD_3   2 PvIsLdletegykvkvgreltiaPtvenaenaafaWtieGkiv..steptytf 52 
                                       P+I L    +++k+  g + +++ ++e+ e  +++W  +G ++   t+  yt 
  gi|330508678|ref|YP_004385106.1| 936 PKILL--HPANLKICQGAKAKFEVQIESTEPLKYQWLKDGIEIpgATDDRYTI 986
                                       55555..6689*****************************9763357777765 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 0.89
                             PKD_3   16 kvgreltiaPtvenaenaafaWtieGkiv..steptytfteee 56  
                                          g+   ++ + e++e   ++W  eG ++   t ++yt  +++
  gi|330508678|ref|YP_004385106.1| 1033 CQGTRAAFSVQAESSEPLSYQWLKEGIKIegATSESYTIPQTS 1075
                                        5666666777778888888******986432677778766554 PP

  == domain 7  score: -0.0 bits;  conditional E-value: 0.5
                             PKD_3   14 kvkvgreltiaPtvenaenaafaWtieGki....vsteptytf.teeelgsyevtle 65  
                                        kv  g+  t++ +  ++e   ++W  +G       s+  t+   + +  gsy v+l+
  gi|330508678|ref|YP_004385106.1| 1116 KVCQGTAATFSVQARSSEPLSYQWLKDGVNiqgaASDTYTIPAsNLNDTGSYSVQLR 1172
                                        788888889988888999999******985244344444443323477888888887 PP

  == domain 8  score: -3.0 bits;  conditional E-value: 4.3
                             PKD_3   24 aPtvenaenaafaWtieGkiv..steptyt 51  
                                        + + e++e   ++W  +G ++   t + yt
  gi|330508678|ref|YP_004385106.1| 1296 SVQAESSEPLSYQWFKDGIKIdgATSEYYT 1325
                                        555567777779999999764213334444 PP

  == domain 9  score: 6.2 bits;  conditional E-value: 0.0057
                             PKD_3    2 PvIsLdletegykvkvgreltiaPtvenaenaafaWtieGkiv..steptytf...teeelgsyev 62  
                                        P+I L  + +++k+  g   +++ + e++e   ++W  +G+ +   t  tyt    + +  gsy v
  gi|330508678|ref|YP_004385106.1| 1361 PKILL--QPANLKICQGAAAKFEVQAESSEPLSYQWLKDGANIpgATSDTYTIpaaKLNDTGSYSV 1424
                                        67777..8899*****************************97522466666641113445566655 PP

  == domain 10  score: 0.7 bits;  conditional E-value: 0.31
                             PKD_3    2 PvIsLdletegykvkvgreltiaPtvenaenaafaWtieGkiv..steptyt 51  
                                        P+I L  + +++ +  g   t+  + ++ e  +++W  +G ++   t+  yt
  gi|330508678|ref|YP_004385106.1| 1446 PKILL--QPANLMICQGAAATFHVEASSYEPIEYQWLKDGIEIpgATDDRYT 1495
                                        66666..788999999*******9999*************876335666666 PP

  == domain 11  score: -0.7 bits;  conditional E-value: 0.83
                             PKD_3   15 vkvgreltiaPtvenaenaafaWtieGkiv 44  
                                        +  g+ +t+a + +++e   ++W  +G  +
  gi|330508678|ref|YP_004385106.1| 1542 ICQGTMVTFAVQAKSSEPLRYQWLKDGVNI 1571
                                        77899999999999999999*****99854 PP

  == domain 12  score: 2.6 bits;  conditional E-value: 0.079
                             PKD_3   12 gykvkvgreltiaPtvenaenaafaWtieGkiv..steptyt 51  
                                        g kv  g+  t++ + +++e   ++W  +G+ +   t ++yt
  gi|330508678|ref|YP_004385106.1| 1624 GQKVCQGTAATFSVQAKSSEPLSYQWLRDGANIpdATSESYT 1665
                                        5689999999999999999999*********86223455555 PP

  == domain 13  score: -3.0 bits;  conditional E-value: 4.2
                             PKD_3   34 afaWtieGkiv 44  
                                        +++W+ +G+++
  gi|330508678|ref|YP_004385106.1| 1731 EYQWYKDGTEI 1741
                                        599****9986 PP

  == domain 14  score: 2.6 bits;  conditional E-value: 0.078
                             PKD_3   14 kvkvgreltiaPtvenaenaafaWtieGkiv..steptytft 53  
                                        k+  g+ +t++ +ve++    ++W  +G ++   t+ +yt  
  gi|330508678|ref|YP_004385106.1| 1796 KICQGSAVTFTVQVESSKPLSYQWFKDGIKIpgATQDVYTIA 1837
                                        7899***********************987533567777765 PP

  == domain 15  score: -1.6 bits;  conditional E-value: 1.5
                             PKD_3   11 egykvkvgreltiaPtvenaenaafaWtieGkiv 44  
                                        +  kv  g   t+  + e++e   ++W  +G ++
  gi|330508678|ref|YP_004385106.1| 1878 ASQKVCEGAAATFFVQAESSEALSYQWFKDGIEI 1911
                                        555777778888888888999999***9999876 PP

  == domain 16  score: 1.4 bits;  conditional E-value: 0.18
                             PKD_3   11 egykvkvgreltiaPtvenaenaafaWtieGkiv..steptytfte 54  
                                        +g +v  g   t++ + +++e   ++W  +Gk++   t  tyt   
  gi|330508678|ref|YP_004385106.1| 1963 KGQRVCQGDAATFSVQASSSEPLSYQWFKDGKMIqgATADTYTIPA 2008
                                        666788888899998888999999********76324666776554 PP

  == domain 17  score: -1.8 bits;  conditional E-value: 1.8
                             PKD_3    2 PvIsLdletegykvkvgreltiaPtvenaenaa..faWtieGkiv 44  
                                        P IsL+       v  g+++t++  v  + ++   ++W  +G ++
  gi|330508678|ref|YP_004385106.1| 2041 PAISLQPA--SQIVCQGTPVTFN--VRAISDDPlsYQWFKDGVEI 2081
                                        67777433..3458889999996..55444443359999998865 PP

  == domain 18  score: 2.6 bits;  conditional E-value: 0.075
                             PKD_3   14 kvkvgreltiaPtvenaenaafaWtieGki....vstept.ytfteeelgsyevtl 64  
                                        kv  g+  t++   ++a+  +++W+  G+i     s+e t +  + e +g+y v +
  gi|330508678|ref|YP_004385106.1| 2136 KVCEGSTATFTVLAKSAQPLTYQWIKGGRIipgaNSEELTiFDANMEDMGEYRVAI 2191
                                        677788888888888999999********945544777763467889999999977 PP

  == domain 19  score: -1.1 bits;  conditional E-value: 1.1
                             PKD_3   32 naafaWtieGkiv 44  
                                         + ++W  +G+i+
  gi|330508678|ref|YP_004385106.1| 2240 ANSYQWEKNGEII 2252
                                        3448888888876 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 ?   -2.0   0.0       2.4   3.6e+03      38      47 ..     708     718 ..     700     719 .. 0.75
   2 ?    1.7   0.0      0.16   2.4e+02      34      47 ..     789     803 ..     780     804 .. 0.81
   3 ?    1.8   0.0      0.15   2.3e+02      34      47 ..    1214    1228 ..    1199    1229 .. 0.83
   4 ?    1.8   0.0      0.15   2.2e+02      34      47 ..    1299    1313 ..    1291    1314 .. 0.74
   5 ?   -1.9   0.0       2.2   3.3e+03      38      48 ..    1728    1739 ..    1721    1739 .. 0.77
   6 ?    2.0   0.0      0.13     2e+02      33      47 ..    1809    1823 ..    1801    1824 .. 0.72
   7 ?    0.3   0.0      0.44   6.6e+02      35      47 ..    1896    1908 ..    1836    1909 .. 0.72
   8 ?    4.1   0.0      0.03        45      35      49 ..    1980    1995 ..    1971    1995 .. 0.79
   9 ?    3.0   0.0     0.066        99      32      47 ..    2062    2078 ..    2052    2079 .. 0.84
  10 ?   -0.3   0.0      0.68     1e+03      31      49 ..    2146    2165 ..    2138    2165 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.4
                                       TC.T-EESTT- CS
                            ACAS_N  38 gp.fikWFeGG 47 
                                       +p  i+W+++G
  gi|330508678|ref|YP_004385106.1| 708 DPiTIQWMKDG 718
                                       3459******9 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.16
                                       CSTTTC.T-EESTT- CS
                            ACAS_N  34 dgskgp.fikWFeGG 47 
                                        +s +p +++WF++G
  gi|330508678|ref|YP_004385106.1| 789 AKSSEPlSYQWFKDG 803
                                       5667788*******9 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.15
                                        CSTTTC.T-EESTT- CS
                            ACAS_N   34 dgskgp.fikWFeGG 47  
                                         +s +p +++WF++G
  gi|330508678|ref|YP_004385106.1| 1214 AKSSEPlSYQWFKDG 1228
                                        5667788*******9 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.15
                                        CSTTTC.T-EESTT- CS
                            ACAS_N   34 dgskgp.fikWFeGG 47  
                                         +s +p +++WF++G
  gi|330508678|ref|YP_004385106.1| 1299 AESSEPlSYQWFKDG 1313
                                        4556677*******9 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 2.2
                                        TC.T-EESTT-E CS
                            ACAS_N   38 gp.fikWFeGGk 48  
                                        +p +++W+++G+
  gi|330508678|ref|YP_004385106.1| 1728 EPlEYQWYKDGT 1739
                                        56799*****96 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.13
                                        ECSTTTC.T-EESTT- CS
                            ACAS_N   33 ldgskgp.fikWFeGG 47  
                                        +++s +p +++WF++G
  gi|330508678|ref|YP_004385106.1| 1809 VESS-KPlSYQWFKDG 1823
                                        4454.555*******9 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 0.44
                                        STTTCT-EESTT- CS
                            ACAS_N   35 gskgpfikWFeGG 47  
                                        +s++ +++WF++G
  gi|330508678|ref|YP_004385106.1| 1896 SSEALSYQWFKDG 1908
                                        3444589999998 PP

  == domain 8  score: 4.1 bits;  conditional E-value: 0.03
                                        STTTC.T-EESTT-EE CS
                            ACAS_N   35 gskgp.fikWFeGGkl 49  
                                        +s +p +++WF++Gk+
  gi|330508678|ref|YP_004385106.1| 1980 SSSEPlSYQWFKDGKM 1995
                                        566778********95 PP

  == domain 9  score: 3.0 bits;  conditional E-value: 0.066
                                        SECSTTTC.T-EESTT- CS
                            ACAS_N   32 vldgskgp.fikWFeGG 47  
                                        v   s++p +++WF++G
  gi|330508678|ref|YP_004385106.1| 2062 VRAISDDPlSYQWFKDG 2078
                                        667889999*******9 PP

  == domain 10  score: -0.3 bits;  conditional E-value: 0.68
                                        -SECSTTTC.T-EESTT-EE CS
                            ACAS_N   31 kvldgskgp.fikWFeGGkl 49  
                                        +vl +s +p  ++W +GG++
  gi|330508678|ref|YP_004385106.1| 2146 TVLAKSAQPlTYQWIKGGRI 2165
                                        68999999*9********85 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.91   1.4e+03      10      25 ..     819     834 ..     817     840 .. 0.80
   2 ?    2.2   0.0      0.14     2e+02      12      30 ..     906     924 ..     903     929 .. 0.84
   3 ?    3.1   0.0     0.075   1.1e+02      11      31 ..    1075    1095 ..    1072    1101 .. 0.84
   4 ?    0.3   0.0      0.56   8.4e+02      12      29 ..    1161    1178 ..    1158    1182 .. 0.81
   5 ?    1.1   0.0      0.32   4.8e+02      13      30 ..    1247    1264 ..    1243    1271 .. 0.84
   6 ?   -1.9   0.0       2.8   4.1e+03      11      30 ..    1330    1349 ..    1328    1353 .. 0.81
   7 ?    4.4   0.0     0.028        42      12      30 ..    1416    1434 ..    1413    1439 .. 0.86
   8 ?   -2.7   0.0       4.7   6.9e+03      13      30 ..    1587    1604 ..    1584    1609 .. 0.83
   9 ?   -1.6   0.0       2.1   3.2e+03      12      30 ..    1671    1689 ..    1667    1691 .. 0.83
  10 ?   -3.5   0.0       8.4   1.3e+04      11      27 ..    1755    1771 ..    1754    1774 .. 0.80
  11 ?    1.5   0.0      0.24   3.6e+02      13      32 ..    1842    1861 ..    1836    1867 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.91
                                       SSTT-TSSHHHHHHHH CS
                     Ribosomal_S15  10 rhekDtGspevqiall 25 
                                       ++  D Gs  vq+a+ 
  gi|330508678|ref|YP_004385106.1| 819 TNLSDMGSYSVQVANN 834
                                       5668**********85 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                                       TT-TSSHHHHHHHHHHHHH CS
                     Ribosomal_S15  12 ekDtGspevqiallterIn 30 
                                        +DtGs  vqi +   +I+
  gi|330508678|ref|YP_004385106.1| 906 LNDTGSYSVQITNNCSQIE 924
                                       58*********98877775 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.075
                                        STT-TSSHHHHHHHHHHHHHH CS
                     Ribosomal_S15   11 hekDtGspevqiallterInn 31  
                                        +  DtGs  vq+ +   rI++
  gi|330508678|ref|YP_004385106.1| 1075 SLSDTGSYSVQVSNNCSRIES 1095
                                        567***********9999976 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.56
                                        TT-TSSHHHHHHHHHHHH CS
                     Ribosomal_S15   12 ekDtGspevqiallterI 29  
                                         +DtGs  vq+ +   +I
  gi|330508678|ref|YP_004385106.1| 1161 LNDTGSYSVQLRNNCSQI 1178
                                        58********98877776 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.32
                                        T-TSSHHHHHHHHHHHHH CS
                     Ribosomal_S15   13 kDtGspevqiallterIn 30  
                                         DtGs  vq+ +   +I+
  gi|330508678|ref|YP_004385106.1| 1247 SDTGSYSVQVSNNCSQIK 1264
                                        6*********99888887 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 2.8
                                        STT-TSSHHHHHHHHHHHHH CS
                     Ribosomal_S15   11 hekDtGspevqiallterIn 30  
                                        +  D Gs  vq+ +   +I+
  gi|330508678|ref|YP_004385106.1| 1330 NLSDMGSYSVQVSNNCSQIE 1349
                                        667*********98777775 PP

  == domain 7  score: 4.4 bits;  conditional E-value: 0.028
                                        TT-TSSHHHHHHHHHHHHH CS
                     Ribosomal_S15   12 ekDtGspevqiallterIn 30  
                                         +DtGs  vq+a+   +I+
  gi|330508678|ref|YP_004385106.1| 1416 LNDTGSYSVQVANNCSQIE 1434
                                        58**********9888886 PP

  == domain 8  score: -2.7 bits;  conditional E-value: 4.7
                                        T-TSSHHHHHHHHHHHHH CS
                     Ribosomal_S15   13 kDtGspevqiallterIn 30  
                                         D Gs  vq+ +   +I+
  gi|330508678|ref|YP_004385106.1| 1587 SDMGSYSVQVSNNCSQIE 1604
                                        69********98777775 PP

  == domain 9  score: -1.6 bits;  conditional E-value: 2.1
                                        TT-TSSHHHHHHHHHHHHH CS
                     Ribosomal_S15   12 ekDtGspevqiallterIn 30  
                                          DtGs  v +a+  ++I+
  gi|330508678|ref|YP_004385106.1| 1671 LSDTGSYSVLVANKCNQIE 1689
                                        57**********9888885 PP

  == domain 10  score: -3.5 bits;  conditional E-value: 8.4
                                        STT-TSSHHHHHHHHHH CS
                     Ribosomal_S15   11 hekDtGspevqiallte 27  
                                        ++ D Gs  vq+ +   
  gi|330508678|ref|YP_004385106.1| 1755 SPSDRGSYWVQVRNSCS 1771
                                        689********987655 PP

  == domain 11  score: 1.5 bits;  conditional E-value: 0.24
                                        T-TSSHHHHHHHHHHHHHHH CS
                     Ribosomal_S15   13 kDtGspevqiallterInnl 32  
                                        +DtGs  vq+a+   +I++ 
  gi|330508678|ref|YP_004385106.1| 1842 NDTGSYWVQAANNCSQIKSG 1861
                                        7***********99999875 PP

>> Receptor_2B4  Natural killer cell receptor 2B4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.045        67      73      99 ..     471     497 ..     456     505 .. 0.87
   2 ?   -2.6   0.0       4.2   6.2e+03      75      97 ..     558     580 ..     552     587 .. 0.81
   3 ?   -0.5   0.0      0.94   1.4e+03      71      91 ..     639     659 ..     616     673 .. 0.79
   4 !    8.5   0.0    0.0014       2.2      72      98 ..     728     754 ..     707     762 .. 0.89
   5 ?   -3.4   0.0       7.4   1.1e+04      76      98 ..     817     839 ..     813     843 .. 0.81
   6 ?    3.3   0.0     0.062        93      74      99 ..     900     925 ..     889     933 .. 0.84
   7 ?   -3.6   0.0       8.8   1.3e+04      75      97 ..    1071    1093 ..    1068    1097 .. 0.78
   8 ?   -2.0   0.0       2.7     4e+03      74      98 ..    1155    1179 ..    1150    1188 .. 0.80
   9 ?    1.3   0.0      0.25   3.8e+02      72     100 ..    1238    1266 ..    1227    1273 .. 0.84
  10 ?    3.9   0.0     0.039        59      74      97 ..    1410    1433 ..    1403    1443 .. 0.85
  11 ?   -0.4   0.0      0.89   1.3e+03      74      98 ..    1580    1604 ..    1575    1612 .. 0.84
  12 ?   -0.1   0.0      0.69     1e+03      72     100 ..    1663    1691 ..    1658    1698 .. 0.82
  13 ?   -0.9   0.0       1.2   1.8e+03      78     101 ..    1924    1947 ..    1905    1953 .. 0.81
  14 ?   -3.7   0.0         9   1.3e+04      75     102 ..    2091    2118 ..    2089    2123 .. 0.81
  15 ?   -0.3   0.0      0.79   1.2e+03      73     105 ..    2174    2206 ..    2169    2208 .. 0.84
  16 ?   -1.3   0.0       1.7   2.5e+03      72      99 ..    2259    2286 ..    2256    2294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.045
                                       EEESS-SGGG-EEEEEEEEETTSCEEE CS
                      Receptor_2B4  73 lsiksaklqdsGlylleitnisGkvct 99 
                                         i +akl d+G y + ++n  G + +
  gi|330508678|ref|YP_004385106.1| 471 YIIPAAKLADAGSYRVRVSNACGSIES 497
                                       6799*****************998865 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.2
                                       ESS-SGGG-EEEEEEEEETTSCE CS
                      Receptor_2B4  75 iksaklqdsGlylleitnisGkv 97 
                                       i s    d G y l ++ni G  
  gi|330508678|ref|YP_004385106.1| 558 ISSILPTDEGDYSLAVSNICGMA 580
                                       566667899*********99975 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.94
                                       TEEEESS-SGGG-EEEEEEEE CS
                      Receptor_2B4  71 lalsiksaklqdsGlylleit 91 
                                         lsi +a+  d G y + i 
  gi|330508678|ref|YP_004385106.1| 639 AVLSISAANSTDQGNYSVIIG 659
                                       3589************88775 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0014
                                       EEEESS-SGGG-EEEEEEEEETTSCEE CS
                      Receptor_2B4  72 alsiksaklqdsGlylleitnisGkvc 98 
                                       +++ik a  +dsG y l ++n  G++ 
  gi|330508678|ref|YP_004385106.1| 728 SFVIKNATRNDSGSYSLIVSNDCGQIE 754
                                       678*******************99986 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 7.4
                                       SS-SGGG-EEEEEEEEETTSCEE CS
                      Receptor_2B4  76 ksaklqdsGlylleitnisGkvc 98 
                                         ++l d G y ++++n   +v 
  gi|330508678|ref|YP_004385106.1| 817 PQTNLSDMGSYSVQVANNCSQVE 839
                                       5678999********99988876 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.062
                                       EESS-SGGG-EEEEEEEEETTSCEEE CS
                      Receptor_2B4  74 siksaklqdsGlylleitnisGkvct 99 
                                       +i +++l+d+G y ++itn   ++ +
  gi|330508678|ref|YP_004385106.1| 900 AIPASNLNDTGSYSVQITNNCSQIES 925
                                       688999*************9887765 PP

  == domain 7  score: -3.6 bits;  conditional E-value: 8.8
                                        ESS-SGGG-EEEEEEEEETTSCE CS
                      Receptor_2B4   75 iksaklqdsGlylleitnisGkv 97  
                                        i  + l d+G y ++++n   ++
  gi|330508678|ref|YP_004385106.1| 1071 IPQTSLSDTGSYSVQVSNNCSRI 1093
                                        5667899*******999987665 PP

  == domain 8  score: -2.0 bits;  conditional E-value: 2.7
                                        EESS-SGGG-EEEEEEEEETTSCEE CS
                      Receptor_2B4   74 siksaklqdsGlylleitnisGkvc 98  
                                        +i +++l+d+G y +++ n   ++ 
  gi|330508678|ref|YP_004385106.1| 1155 TIPASNLNDTGSYSVQLRNNCSQIE 1179
                                        678999*******999998877665 PP

  == domain 9  score: 1.3 bits;  conditional E-value: 0.25
                                        EEEESS-SGGG-EEEEEEEEETTSCEEEE CS
                      Receptor_2B4   72 alsiksaklqdsGlylleitnisGkvctk 100 
                                        + +i +a l d+G y ++++n   +++++
  gi|330508678|ref|YP_004385106.1| 1238 SYAIPAASLSDTGSYSVQVSNNCSQIKSE 1266
                                        567999**************998887765 PP

  == domain 10  score: 3.9 bits;  conditional E-value: 0.039
                                        EESS-SGGG-EEEEEEEEETTSCE CS
                      Receptor_2B4   74 siksaklqdsGlylleitnisGkv 97  
                                        +i +akl+d+G y ++++n   ++
  gi|330508678|ref|YP_004385106.1| 1410 TIPAAKLNDTGSYSVQVANNCSQI 1433
                                        689**************9987766 PP

  == domain 11  score: -0.4 bits;  conditional E-value: 0.89
                                        EESS-SGGG-EEEEEEEEETTSCEE CS
                      Receptor_2B4   74 siksaklqdsGlylleitnisGkvc 98  
                                        +i +a+l d G y ++++n   ++ 
  gi|330508678|ref|YP_004385106.1| 1580 TIPAANLSDMGSYSVQVSNNCSQIE 1604
                                        6889*************99877665 PP

  == domain 12  score: -0.1 bits;  conditional E-value: 0.69
                                        EEEESS-SGGG-EEEEEEEEETTSCEEEE CS
                      Receptor_2B4   72 alsiksaklqdsGlylleitnisGkvctk 100 
                                        + +i +a+l d+G y + ++n+  ++ ++
  gi|330508678|ref|YP_004385106.1| 1663 SYTILAANLSDTGSYSVLVANKCNQIESE 1691
                                        56799************999998877665 PP

  == domain 13  score: -0.9 bits;  conditional E-value: 1.2
                                        -SGGG-EEEEEEEEETTSCEEEEE CS
                      Receptor_2B4   78 aklqdsGlylleitnisGkvctkn 101 
                                        + + d G y++++ n  G v +k+
  gi|330508678|ref|YP_004385106.1| 1924 TGKFDMGNYMVQVRNSCGSVESKA 1947
                                        556799**************9875 PP

  == domain 14  score: -3.7 bits;  conditional E-value: 9
                                        ESS-SGGG-EEEEEEEEETTSCEEEEEE CS
                      Receptor_2B4   75 iksaklqdsGlylleitnisGkvctknf 102 
                                        i+ a   d G y ++  n  G++ +++ 
  gi|330508678|ref|YP_004385106.1| 2091 IQKAITGDKGSYYVQARNSCGQIESETA 2118
                                        77788899***********999987665 PP

  == domain 15  score: -0.3 bits;  conditional E-value: 0.79
                                        EEESS-SGGG-EEEEEEEEETTSCEEEEEEEEE CS
                      Receptor_2B4   73 lsiksaklqdsGlylleitnisGkvctknfqll 105 
                                        l+i  a+++d G y + i+n  G + +++  l+
  gi|330508678|ref|YP_004385106.1| 2174 LTIFDANMEDMGEYRVAISNGCGFIDSNAVSLI 2206
                                        78899***************9999887776655 PP

  == domain 16  score: -1.3 bits;  conditional E-value: 1.7
                                        EEEESS-SGGG-EEEEEEEEETTSCEEE CS
                      Receptor_2B4   72 alsiksaklqdsGlylleitnisGkvct 99  
                                        +l i   +  dsG y l ++n  G  ++
  gi|330508678|ref|YP_004385106.1| 2259 SLIILNPRPSDSGGYRLTVSNGCGSNKS 2286
                                        5777788889**********99887655 PP

>> DUF5122  Domain of unknown function (DUF5122) beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.25   3.8e+02       2      28 ..     109     136 ..     108     140 .. 0.74
   2 ?    8.3   2.3    0.0018       2.7       3      31 ..     214     243 ..     212     243 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.25
                           DUF5122   2 pDGKIlVaGsftsy.ngssdfalvRLna 28 
                                       +DG  +VaG + sy +g +d  l++ ++
  gi|330508678|ref|YP_004385106.1| 109 ADGGYIVAGRTRSYgSGMYDVWLMKVDP 136
                                       79**********8867766665555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0018
                           DUF5122   3 DGKIlVaGsft.syngssdfalvRLnaDGs 31 
                                       DG  +VaG+++ + ng sd  l++++++G+
  gi|330508678|ref|YP_004385106.1| 214 DGGFVVAGTTGsWGNGDSDALLIKIDSNGN 243
                                       9999*******888***************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                        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: 1.05u 0.28s 00:00:01.33 Elapsed: 00:00:00.52
# Mc/sec: 13509.76
//
Query:       gi|330508679|ref|YP_004385107.1|  [L=192]
Description: hypothetical protein MCON_2938 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-10   38.9   0.0    1.4e-09   38.1   0.0    1.4  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 !   38.1   0.0   8.1e-14   1.4e-09       5     116 ..      21     159 ..      18     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 8.1e-14
                                       HHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TS..SEEEEEES................HHHHHHHHH.HCTTEEH CS
                              PK_C   5 kaaveaaeelgakaIvvltesGetArliskyrpk..vpiiavtp................neltarqla.lyrGvyp 62 
                                       + + e+++ l++++ v ++++G+tA ++  ++++  +++i+v +                +el  r  + ++ G   
  gi|330508679|ref|YP_004385107.1|  21 RLVQERSSSLNIRKLVLASTTGSTAVKAKDFFSRdgIKLIVVPHqwdfhreqnafpepltREL-RREGHeVHFGTML 96 
                                       56778999***********************99999********8877766666665553222.4444436666655 PP

                                       HH.HHHHH.........TTSHHHHH...HHHHHH.......TTSS-STSEEEEEE-SSSS..SS--EEEE CS
                              PK_C  63 vlvekakt......aestdellrea...vkvake.......aglvkkgdevvvtaGtpkgesgttNtlrV 116
                                       ++ +          a+++ +llr +   vkv+ e       agl+ +g++v+++aGt +g    ++t+ V
  gi|330508679|ref|YP_004385107.1|  97 FHTD---GlygsnsATTMANLLRCFcqgVKVCFEivlmatdAGLLVSGEKVIAIAGTASG----SDTALV 159
                                       5544...1334333445555677668889999999999999*******************....999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1384.78
//
Query:       gi|330508680|ref|YP_004385108.1|  [L=170]
Description: NADH dehydrogenase/NAD(P)H nitroreductase [Methanosaeta concilii GP6]
Scores for complete 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   77.0   0.1      7e-11   42.5   0.1    2.0  2  Nitroreductase  Nitroreductase family
    4.1e-11   42.8   0.0    1.9e-10   40.7   0.0    2.3  1  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
      0.021   14.7   0.0      0.036   13.9   0.0    1.4  1  DUF5547         Family of unknown function (DUF5547)


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.1   1.2e-14     7e-11       1      52 [.       5      56 ..       5      64 .. 0.90
   2 !   33.3   0.0   7.4e-12   4.4e-08      82     170 .]      63     149 ..      54     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.2e-14
                                      HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHH CS
                    Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryk 52
                                      +r RrSiRk++d +++++ ++++ eaa r+Ps+ +++pwr++ ++dk+ ++ 
  gi|330508680|ref|YP_004385108.1|  5 LRDRRSIRKYKDVKIDEQIIDQLKEAALRSPSSRGINPWRLLFITDKDMLEV 56
                                      589*****************************************98887654 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 7.4e-12
                                       HHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGG.........GGHHH CS
                    Nitroreductase  82 kaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfd.........eaaee 149
                                       +   +l+ga + +v+          a +++ ++ + d+++a   l+L+ ++lGlgsc+i   +         e+   
  gi|330508680|ref|YP_004385108.1|  63 SGSGFLKGASLGVVV---------IARDEESDVWIEDCSIASIILQLTGQSLGLGSCWIQIRNrmhndgqtsED--Y 128
                                       566778888888888.........677777777789***************************77777764444..6 PP

                                       HHHHHT-S..SEEEEEEEEE- CS
                    Nitroreductase 150 vrkllglpdeeeivvliavGy 170
                                       +rk l+lp++ ++ ++ia+Gy
  gi|330508680|ref|YP_004385108.1| 129 IRKALDLPEGSKVECMIAFGY 149
                                       ********************9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   3.2e-14   1.9e-10       4     143 ..       3     160 ..       1     169 [. 0.73

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 3.2e-14
                                       HHHHH--B---B--S---HHHHHHHHH-----S...S--.---EE..E.................-SSSSEEEE--- CS
                    TM1586_NiRdase   4 eaiekRhsvRkYkdealeeelleelkeaieeinkesgle.lqlvid.enka....fkskvaklgkfkgvpnyialvg 74 
                                       ++++ R+s+RkYkd +++e+++++lkea+ +  +  g++  +l +  +++     +++k ++ g+ kg++  +++++
  gi|330508680|ref|YP_004385108.1|   3 DILRDRRSIRKYKDVKIDEQIIDQLKEAALRSPSSRGINpWRLLFItDKDMlevlSRAKQSGSGFLKGASLGVVVIA 79 
                                       67889***********************9999888887643433330333211113455566778888888778777 PP

                                       -SS..HHHHHHHHHHHHHHHHHHHHTT-EEEEES--SST.....................T-S-EEEEE-BS----. CS
                    TM1586_NiRdase  75 ekk..edleekaGYygeqlvLkltalGlgtcWvggtykk..........kkakvelkkgeklvivIalGyaktklve 139
                                       +++  + + e +      l L  ++lGlg+cW+ +               +++++l++g k+ ++Ia+Gy+++ + +
  gi|330508680|ref|YP_004385108.1|  80 RDEesDVWIEDCSIASIILQLTGQSLGLGSCWIQIRNRMhndgqtsedyIRKALDLPEGSKVECMIAFGYPDEIKEP 156
                                       7764467788998888888888899*******98654333344554455567799****************998876 PP

                                       ---- CS
                    TM1586_NiRdase 140 akrk 143
                                       + + 
  gi|330508680|ref|YP_004385108.1| 157 HPKS 160
                                       6554 PP

>> DUF5547  Family of unknown function (DUF5547)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.1e-06     0.036      49     113 ..      15      81 ..      10      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.1e-06
                           DUF5547  49 mdskvddrliqgtekskle.pvtqlfqntkkirledtdq.enftrsegtGtGylsekalGsvvyvke 113
                                        d k+d+++i + + + l  p ++ ++  + + + d d  e ++r++++G+G+l + +lG vv+ ++
  gi|330508680|ref|YP_004385108.1|  15 KDVKIDEQIIDQLKEAALRsPSSRGINPWRLLFITDKDMlEVLSRAKQSGSGFLKGASLGVVVIARD 81 
                                       6889999999887777775277777777777778888763779*******************99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1183.24
//
Query:       gi|330508681|ref|YP_004385109.1|  [L=192]
Description: hypothetical protein MCON_2942 [Methanosaeta concilii GP6]
Scores for complete 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-20   73.3  11.8    4.3e-20   72.7  10.4    1.8  2  DUF937    Bacterial protein of unknown function (DUF937)


Domain annotation for each model (and alignments):
>> DUF937  Bacterial protein of unknown function (DUF937)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7  10.4   2.4e-24   4.3e-20       5     136 ..      11     135 ..       7     136 .. 0.94
   2 ?   -0.6   0.0      0.11   1.9e+03      91     104 ..     145     158 ..     138     189 .. 0.60

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 2.4e-24
                            DUF937   5 gqlggapiqqlaqqlGedeaqaesalsaalpallgalaqnaaspgGlgdLlgallggglggggLgdllsllqngglg 81 
                                       + + g++++ l++++G+de++++sal++ lp+llga+ ++a+s++G+  +l++l   +  g+ ++d+ + ++ ++ +
  gi|330508681|ref|YP_004385109.1|  11 QLMAGDNLSILSSKVGADEQSTKSALEMGLPLLLGAMSSKASSNDGANAILSGLA-DSAKGNSMQDMAKYFGSSSSS 86 
                                       4567899999********************************************7.57788***********88887 PP

                            DUF937  82 eqaqswdgpaiLasllGakqqqvisalsqqtGlsrgevlqlLallaPevmsqLtk 136
                                              gp++L+s+lG+    ++++++++tGl ++ v+qlL +++P+++++Ltk
  gi|330508681|ref|YP_004385109.1|  87 F------GPGMLNSILGSSMIPIQQSIAKKTGLPQEVVGQLLTMALPLILGYLTK 135
                                       7......***********************************************8 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.11
                            DUF937  91 aiLasllGakqqqv 104
                                       ++L++ll+++ + +
  gi|330508681|ref|YP_004385109.1| 145 DDLSKLLDEQSKMA 158
                                       55666666665222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1395.74
//
Query:       gi|330508682|ref|YP_004385110.1|  [L=107]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 829.03
//
Query:       gi|330508683|ref|YP_004385111.1|  [L=146]
Description: hypothetical protein MCON_2944 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-15   55.2   1.4    1.1e-14   54.9   1.4    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    3.2e-06   27.4   0.3    3.6e-06   27.2   0.3    1.1  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro
     0.0027   17.9   0.2     0.0033   17.6   0.2    1.3  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   1.4   1.8e-18   1.1e-14       5     143 .]      12     142 ..       9     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1.8e-18
                                       EEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCSSEEEEEEEEEETTTTEEEEEEE. CS
                   Polyketide_cyc2   5 tvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggrgtvreelvevdpegrllsyrivk 81 
                                       +++v+++a+pe++w+++   ++wp W + v+ + +e  g+ a+g+++ +++g   t+r ++++ +  +++l ++++ 
  gi|330508683|ref|YP_004385111.1|  12 SREVEVEASPETIWDIIVAVDSWPDWNSDVKAAFIE--GDLAVGTRFSWKAGQ-LTIRSTVLQMER-PHHLVWTGT- 83 
                                       789****************************88455..444456667888888.79********97.9*******5. PP

                                       SSS-TSEEEEEEEEECCET....EEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Polyketide_cyc2  82 pvpvanyvatwtvtpdggg....trvtwtgefdagplggpfekpaaakavkgdleagLerLkarle 143
                                       + +++  v  w+++ +g+     ++ +w+g      l+  +  +++++++ + ++++L  Lk+++e
  gi|330508683|ref|YP_004385111.1|  84 TTGIK-AVHLWQIEKRGEKalvrSEESWEG-----LLPSIL-RGTMKRMLSRSIQQTLLYLKREAE 142
                                       66766.9999*******9867667777888.....344665.5678*****************998 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.3   6.1e-10   3.6e-06       2      96 ..      19     108 ..      18     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6.1e-10
                                       S-HHHHHHHHH-HHHHHHH...EEEEEEEE--STTEEEEEEETTTSEEEEEEEEEEEEETTTEEEEEEEEETSETEE CS
                             AHSA1   2 apperVfraltdpellkrW...ftlteaemdlrpGgkfrlrdspdgkefgnegeylevvpperlvytwrledepeee 75 
                                       a+pe++++ +   +    W    + + +e dl +G +f++    + ++ +++ ++l++++p++lv+t  +     + 
  gi|330508683|ref|YP_004385111.1|  19 ASPETIWDIIVAVDSWPDWnsdVKAAFIEGDLAVGTRFSW----KAGQLTIRSTVLQMERPHHLVWTGTTT----GI 87 
                                       89**************************************....6789*******************5544....56 PP

                                       EEEEEEEEEEETTEEEEEEEE CS
                             AHSA1  76 estvtieleeegggTrltlth 96 
                                       +++  +++e+ g++  ++ ++
  gi|330508683|ref|YP_004385111.1|  88 KAVHLWQIEKRGEKALVRSEE 108
                                       677777777777776666665 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   5.5e-07    0.0033       1      35 [.      17      74 ..      17     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.5e-07
                                      ESS-HHHHHHHHTTTGGCCSCCCCEE.......................EEEE.SSSE CS
                    Polyketide_cyc  1 vpapadqvyalvadvesypeflphcs.......................svevleeae 35
                                      v+a+++++++++  v+s+p++++ ++                       +++vl+ ++
  gi|330508683|ref|YP_004385111.1| 17 VEASPETIWDIIVAVDSWPDWNSDVKaafiegdlavgtrfswkagqltiRSTVLQMER 74
                                      79************************44444444444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1084.34
//
Query:       gi|330508684|ref|YP_004385112.1|  [L=184]
Description: hypothetical protein MCON_2946 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.058   12.7   0.0      0.078   12.2   0.0    1.2  1  Hydrolase_4  Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.4e-06     0.078       7      42 ..     108     143 ..     104     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.4e-06
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGh 42 
                                       +vl++G + + +r + la++La+ G+a+++lD+r  
  gi|330508684|ref|YP_004385112.1| 108 IVLLPGATVTKEREQGLAKRLADLGYATITLDQRNL 143
                                       8999*****************************955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1446.18
//
Query:       gi|330508685|ref|YP_004385113.1|  [L=436]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete 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   27.8   0.6    2.7e-05   23.8   0.6    2.1  1  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
      0.088   13.3   4.0       0.13   12.8   1.7    2.4  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.15   12.2   0.6        7.5    6.8   0.1    2.4  2  Zn-ribbon_8      Zinc ribbon domain
       0.21   11.2   0.6         12    5.6   0.1    2.4  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.27   11.3   2.8        1.3    9.1   3.1    1.9  2  DZR              Double zinc ribbon
       0.66   10.0   2.5        7.3    6.7   0.3    2.6  2  YhfH             YhfH-like protein
        6.2    6.4   5.5         77    2.9   5.5    2.4  1  TF_Zn_Ribbon     TFIIB zinc-binding


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 !   23.8   0.6     1e-08   2.7e-05     111     259 ..     188     381 ..     146     393 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1e-08
                      DDE_Tnp_IS66 111 sRggevaealLag.....fkGvlvsDgyagYnklae....eqvthalCwaHlrRkfvdaeeakkksqaaaealar.. 176
                                       s  ++++e +L        + ++v+D y gY+++ +    ++v h++C+ Hl   +v+   +k   ++ +e l++  
  gi|330508685|ref|YP_004385113.1| 188 SKDADTIEGFLRRnldtqKQIFIVTDLYRGYSNVFKrvfgNKVIHQFCLLHLNKLIVNDFPRKT--SIEQELLKYkm 262
                                       55566666666655554445699**********9999***************999887776643..44444444442 PP

                      DDE_Tnp_IS66 177 igklya.............ierearea...........eae.........erlalrqeesrpllaelea.wleeql. 218
                                       ++ +++              e+ +r +           e           + + +r++es+ l+++ ++  l++ + 
  gi|330508685|ref|YP_004385113.1| 263 LNIFFNreleieflstlieEEKMMR-QrsnkeykswiaE-AkhlfydfvrRLELRRRRESKNLEQRTYHeALNNFKf 337
                                       4444445555555555543233332.1233344334331.0333333442555666777788877655504444448 PP

                      DDE_Tnp_IS66 219 ...kkvlpksklgkairyllkrweallrfledgrvpidNNaaER 259
                                          ++ +    ++k ++++ + w++l+ f    + p +NN +E+
  gi|330508685|ref|YP_004385113.1| 338 lkmQSDSFMISVRKRLDKIEELWPNLTAFYFTDNAPATNNPIEN 381
                                       777666677789*******************************9 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.7     5e-05      0.13       8      51 ..      44     118 ..      43     123 .. 0.62
   2 ?   -1.0   0.0      0.99   2.5e+03      14      29 ..     284     299 ..     282     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                   Zn_ribbon_recom   8 CgeCGspmtr......rkrkgkr.......hyYrCstyrrkgk..................k.Csnh...sireekl 49 
                                       C eCG+pm++      +    kr         Y C+++ ++ +                  + C+     ++++e++
  gi|330508685|ref|YP_004385113.1|  44 CPECGHPMSHngfntcQ----KRhlgganvGKYLCGACGKSTEedrdfwiklkadffgivtEiCTRLrlnHVSYEVI 116
                                       **********5543322....22355558889999988766655556666666666665531466544556666666 PP

                   Zn_ribbon_recom  50 ee 51 
                                       e+
  gi|330508685|ref|YP_004385113.1| 117 ES 118
                                       65 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.99
                   Zn_ribbon_recom  14 pmtrrkrkgkrhyYrC 29 
                                       +m r+++++++  ++ 
  gi|330508685|ref|YP_004385113.1| 284 KMMRQRSNKEYKSWIA 299
                                       7999999999988875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0029       7.5      26      35 ..      40      50 ..      25      53 .. 0.60
   2 ?    3.3   0.1     0.036        93       6      17 ..      72      83 ..      71      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                       Zn-ribbon_8 26 lta.CPeCgse 35
                                       ++ CPeCg++
  gi|330508685|ref|YP_004385113.1| 40 VPPlCPECGHP 50
                                      3444****986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.036
                       Zn-ribbon_8  6 YrCeeCghefev 17
                                      Y C +Cg+  e+
  gi|330508685|ref|YP_004385113.1| 72 YLCGACGKSTEE 83
                                      89*****99885 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0046        12       4      14 ..      43      53 ..      43      57 .. 0.86
   2 ?    3.5   0.1     0.021        54       2      15 ..      71      84 ..      70      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0046
                            zf_UBZ  4 lCerCgkeipe 14
                                      lC++Cg+++++
  gi|330508685|ref|YP_004385113.1| 43 LCPECGHPMSH 53
                                      6*******987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.021
                            zf_UBZ  2 tylCerCgkeipes 15
                                       ylC  Cgk+ +e+
  gi|330508685|ref|YP_004385113.1| 71 KYLCGACGKSTEED 84
                                      69*******97765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.9     0.002         5      30      46 ..      43      60 ..      26      63 .. 0.76
   2 ?    9.1   3.1    0.0005       1.3      15      43 ..      44      86 ..      41     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.002
                               DZR 30 rCpsCgek.vdpearfCp 46
                                       Cp+Cg++  ++++++C+
  gi|330508685|ref|YP_004385113.1| 43 LCPECGHPmSHNGFNTCQ 60
                                      688888886666777775 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0005
                               DZR 15 CseCgtklkavaa................edrCpsCgekvdpear 43
                                      C+eCg++++   +                ++ C +Cg++++++  
  gi|330508685|ref|YP_004385113.1| 44 CPECGHPMSH--NgfntcqkrhlgganvgKYLCGACGKSTEEDRD 86
                                      5566655552..123555555555556669999999998877665 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0028       7.3       7      24 ..      35      52 ..      31      61 .. 0.85
   2 ?    2.6   0.1     0.055   1.4e+02      15      26 ..      73      84 ..      67      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0028
                              YhfH  7 FfrnLPkKkCteCGkeie 24
                                      +fr++ +  C+eCG  + 
  gi|330508685|ref|YP_004385113.1| 35 IFRKIVPPLCPECGHPMS 52
                                      799999999*****9986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.055
                              YhfH 15 kCteCGkeieEq 26
                                       C  CGk  eE 
  gi|330508685|ref|YP_004385113.1| 73 LCGACGKSTEED 84
                                      6******99995 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   5.5      0.03        77       3      32 ..      44      84 ..      43      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.03
                                      ETTTTCEEC...........HEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon  3 CPnCgstnl...........veDpergelvCtdCGlVledn 32
                                      CP+Cg+++            +  ++ g ++C++CG   e++
  gi|330508685|ref|YP_004385113.1| 44 CPECGHPMShngfntcqkrhLGGANVGKYLCGACGKSTEED 84
                                      99999987458888888777777999999999999877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3379.06
//
Query:       gi|330508686|ref|YP_004385114.1|  [L=135]
Description: hypothetical protein MCON_2948 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00032   19.5   0.0    0.00039   19.2   0.0    1.1  1  AXE1      Acetyl xylan esterase (AXE1)


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 !   19.2   0.0   2.2e-08   0.00039     168     205 ..       1      38 [.       1      72 [. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.2e-08
                                       STTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEEES CS
                              AXE1 168 lpevDeeRvavlGasqGGalalavaalekrikavvady 205
                                       +pe+D+eR+  +G+s G   a+ + al++r k v+a  
  gi|330508686|ref|YP_004385114.1|   1 MPEIDPERIIYAGESNGARTAIIACALDERSKGVLALS 38 
                                       799*******************************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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: 0.38u 0.19s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1132.02
//
Query:       gi|330508687|ref|YP_004385115.1|  [L=267]
Description: iron-sulfur cluster-binding protein [Methanosaeta concilii GP6]
Scores for complete 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   34.9  11.6    4.1e-06   26.4   1.8    2.3  2  Fer4      4Fe-4S binding domain
    6.9e-07   30.1   9.9    2.3e-06   28.5   9.9    1.8  1  Fer4_16   4Fe-4S double cluster binding domain
    3.4e-06   27.1   8.7    0.00037   20.5  11.3    2.1  2  Fer4_10   4Fe-4S dicluster domain
    9.4e-06   25.5  10.2     0.0025   17.8   2.6    2.3  2  Fer4_6    4Fe-4S binding domain
    5.5e-05   23.7   8.8    0.00011   22.7   8.8    1.5  1  Fer4_7    4Fe-4S dicluster domain
    0.00028   21.0  20.5     0.0014   18.7  10.1    1.9  2  Fer4_9    4Fe-4S dicluster domain
     0.0012   19.4   7.8     0.0049   17.4   8.1    1.8  2  Fer4_17   4Fe-4S dicluster domain
     0.0012   18.8   9.2       0.13   12.4   2.2    2.4  2  Fer4_2    4Fe-4S binding domain
     0.0057   16.8   8.5       0.12   12.6   0.8    2.2  2  Fer4_18   4Fe-4S dicluster domain
     0.0061   17.4  14.9       0.18   12.8   6.1    2.4  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.021   15.3   9.9       0.31   11.5  10.7    2.1  2  Fer4_8    4Fe-4S dicluster domain
      0.027   15.3   3.2        1.7    9.6   0.2    2.2  2  Fer4_22   4Fe-4S dicluster domain
      0.029   14.9   3.5       0.77   10.3   1.6    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.042   14.4   9.4        0.2   12.2   2.0    2.6  2  Fer4_4    4Fe-4S binding domain
      0.093   12.9  13.0       0.54   10.4  13.0    2.0  1  Fer4_21   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 !   26.4   1.8   3.4e-09   4.1e-06       2      23 ..     170     191 ..     169     192 .. 0.92
   2 !   13.6   2.5   3.6e-05     0.043      11      21 ..     221     231 ..     221     232 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.4e-09
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       + de +C  C++Cv++CPv+A+
  gi|330508687|ref|YP_004385115.1| 170 IRDEKLCSECMRCVKMCPVNAL 191
                                       679******************8 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.6e-05
                                       -THHHHHSTTT CS
                              Fer4  11 CGaCvevCPvg 21 
                                       CG+C++vCPvg
  gi|330508687|ref|YP_004385115.1| 221 CGICIKVCPVG 231
                                       *********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 !   28.5   9.9   1.9e-09   2.3e-06       2      66 ..     176     230 ..     175     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.9e-09
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       C +C +C+++CP+na++e+     ++++       +kk++ae++++ + q+ i  C+iC +vCP+
  gi|330508687|ref|YP_004385115.1| 176 CSECMRCVKMCPVNALDER-----DYPQGLT----NKKSCAEHSNELN-QKGISPCGICIKVCPV 230
                                       *******************.....6666643....4666777666655.7789***********8 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5  11.3   3.1e-07   0.00037       3      56 .]     170     229 ..     168     229 .. 0.70
   2 !    9.9   0.2   0.00067       0.8      11      23 ..     220     232 ..     219     250 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.1e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.....tsvgakgeaseeeavrkkvekCtg............cgaCveaCP 56 
                                       ++d++ C +C +Cvk+CP+++       +g +           + ++C +            cg C+++CP
  gi|330508687|ref|YP_004385115.1| 170 IRDEKLCSECMRCVKMCPVNAlderdYPQGLT-----------NKKSCAEhsnelnqkgispCGICIKVCP 229
                                       68999**************4444444333333...........3355666666666666669********9 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00067
                           Fer4_10  11 rCgkCvkaCPadl 23 
                                        Cg C k+CP+ l
  gi|330508687|ref|YP_004385115.1| 220 PCGICIKVCPVGL 232
                                       5*********943 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   2.6   2.1e-06    0.0025       5      24 .]     172     191 ..     169     191 .. 0.92
   2 !   12.1   0.9   0.00013      0.16      12      22 ..     221     231 ..     204     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.1e-06
                            Fer4_6   5 dpdkCigCgdCvrvCPegai 24 
                                       d+ +C  C++Cv+ CP +a+
  gi|330508687|ref|YP_004385115.1| 172 DEKLCSECMRCVKMCPVNAL 191
                                       899**************997 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00013
                            Fer4_6  12 CgdCvrvCPeg 22 
                                       Cg C++vCP g
  gi|330508687|ref|YP_004385115.1| 221 CGICIKVCPVG 231
                                       *********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 !   22.7   8.8     9e-08   0.00011       2      51 ..     176     231 ..     175     232 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 9e-08
                            Fer4_7   2 CigCgaCvaaCpvkaielde....eenekgt..ekveidpekClgCgaCvavCPtg 51 
                                       C +C +Cv++Cpv+a++ ++     +n+k +  ++ e+++   + Cg C++vCP+g
  gi|330508687|ref|YP_004385115.1| 176 CSECMRCVKMCPVNALDERDypqgLTNKKSCaeHSNELNQKGISPCGICIKVCPVG 231
                                       9***************97761111222222222333455555556*********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 !   15.2   2.7   1.5e-05     0.018      33      50 ..     173     190 ..     162     191 .. 0.78
   2 !   18.7  10.1   1.2e-06    0.0014       2      49 ..     176     231 ..     175     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                            Fer4_9  33 eeaCigCgaCveaCpkga 50 
                                       e+ C +C++Cv+ Cp +a
  gi|330508687|ref|YP_004385115.1| 173 EKLCSECMRCVKMCPVNA 190
                                       357999999999999886 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.2e-06
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase.......eaCig.CgaCveaCpkg 49 
                                       C +C +Cv++Cp ++  e++ ++   +++  +       ++ i+ Cg C+++Cp g
  gi|330508687|ref|YP_004385115.1| 176 CSECMRCVKMCPVNALDERDYPQGLTNKKSCAehsnelnQKGISpCGICIKVCPVG 231
                                       ***********9999998888888887665557888998555444*********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 !   17.4   8.1   4.1e-06    0.0049       2      61 .]     176     233 ..     175     233 .. 0.85
   2 !    7.5   0.1    0.0049       5.9       5      18 ..     221     234 ..     219     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.1e-06
                           Fer4_17   2 CiqCgyClpeCpsyea.ydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgld 61 
                                       C++C  C+++Cp ++   +++p+ l ++ +++++ ++ +++ +s    Cg C ++CP gld
  gi|330508687|ref|YP_004385115.1| 176 CSECMRCVKMCPVNALdERDYPQGLTNKKSCAEHSNELNQKGIS---PCGICIKVCPVGLD 233
                                       *************99846679*******8888777777777776...57999*****9997 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0049
                           Fer4_17   5 CgyClpeCpsyeay 18 
                                       Cg C+++Cp + ++
  gi|330508687|ref|YP_004385115.1| 221 CGICIKVCPVGLDR 234
                                       99999999987664 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   2.2   0.00011      0.13       5      21 ..     171     187 ..     167     188 .. 0.88
   2 !   10.3   0.7    0.0005       0.6      13      21 ..     221     229 ..     213     230 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                            Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                        d+  C +C  Cv+ CP
  gi|330508687|ref|YP_004385115.1| 171 RDEKLCSECMRCVKMCP 187
                                       68999************ PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0005
                            Fer4_2  13 CgaCvsaCP 21 
                                       Cg+C+++CP
  gi|330508687|ref|YP_004385115.1| 221 CGICIKVCP 229
                                       ********* PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   2.8     0.004       4.8      60      79 ..     175     195 ..     167     215 .. 0.77
   2 !   12.6   0.8    0.0001      0.12      52      78 ..     209     235 ..     197     243 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.004
                           Fer4_18  60 dcidcescvkvcPtg.idirk 79 
                                        c +c  cvk+cP++ +d r+
  gi|330508687|ref|YP_004385115.1| 175 LCSECMRCVKMCPVNaLDERD 195
                                       599**********86367666 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0001
                           Fer4_18  52 erkekgagdcidcescvkvcPtgidir 78 
                                       + +e ++     c+ c+kvcP+g+d r
  gi|330508687|ref|YP_004385115.1| 209 HSNELNQKGISPCGICIKVCPVGLDRR 235
                                       333444455567*************77 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   6.1   0.00015      0.18       1      15 []     176     190 ..     176     190 .. 0.97
   2 !    9.5   1.5    0.0018       2.1       4      14 ..     221     231 ..     218     231 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C  C++Cv+ CPv+A
  gi|330508687|ref|YP_004385115.1| 176 CSECMRCVKMCPVNA 190
                                       999**********99 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0018
                            Fer4_3   4 CgaCvevCPvg 14 
                                       Cg C +vCPvg
  gi|330508687|ref|YP_004385115.1| 221 CGICIKVCPVG 231
                                       999******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 ?   11.5  10.7   0.00026      0.31       5      64 ..     176     231 ..     172     232 .. 0.59
   2 ?    7.0   0.1    0.0069       8.2       8      22 ..     221     235 ..     219     258 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                            Fer4_8   5 CieCgaCqsaCpvlrrtk..khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       C eC++C ++Cpv            ++++  + +++++   +++++   + cg C +vCpvg
  gi|330508687|ref|YP_004385115.1| 176 CSECMRCVKMCPVNALDErdYPQGLTNKKSCA-EHSNEL--NQKGI---SPCGICIKVCPVG 231
                                       ************54443311333333333333.222222..24444...5678899999997 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0069
                            Fer4_8   8 CgaCqsaCpvlrrtk 22 
                                       Cg C + Cpv  +++
  gi|330508687|ref|YP_004385115.1| 221 CGICIKVCPVGLDRR 235
                                       888888888776655 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2    0.0014       1.7      78      95 ..     172     189 ..     149     190 .. 0.82
   2 ?    6.3   0.3     0.014        17      71      95 ..     207     231 ..     193     232 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                           Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                       +e+ C  C RC+++cpv+
  gi|330508687|ref|YP_004385115.1| 172 DEKLCSECMRCVKMCPVN 189
                                       7899***********986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                           Fer4_22  71 sefkekfgesgCvGCgRCieacpvk 95 
                                       +e+ ++ +++g   Cg Ci++cpv+
  gi|330508687|ref|YP_004385115.1| 207 AEHSNELNQKGISPCGICIKVCPVG 231
                                       35667778999999********986 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.6   0.00064      0.77       2      17 ..     172     187 ..     171     195 .. 0.92
   2 ?    3.7   0.0     0.075        89       8      17 ..     220     229 ..     214     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00064
                           Fer4_13   2 DrdtCiacgaCvelaP 17 
                                       D++ C++c+ Cv+++P
  gi|330508687|ref|YP_004385115.1| 172 DEKLCSECMRCVKMCP 187
                                       6788***********9 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.075
                           Fer4_13   8 acgaCvelaP 17 
                                        cg+C +++P
  gi|330508687|ref|YP_004385115.1| 220 PCGICIKVCP 229
                                       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 ?   12.2   2.0   0.00017       0.2       3      17 .]     175     189 ..     173     194 .. 0.90
   2 ?    5.8   1.0      0.02        24       7      17 .]     221     231 ..     220     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                        C +C++Cv  CP++
  gi|330508687|ref|YP_004385115.1| 175 LCSECMRCVKMCPVN 189
                                       6************75 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.02
                            Fer4_4   7 CgsCvaaCPqg 17 
                                       Cg C+ +CP+g
  gi|330508687|ref|YP_004385115.1| 221 CGICIKVCPVG 231
                                       9********75 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  13.0   0.00045      0.54       4      53 ..     172     230 ..     169     233 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00045
                           Fer4_21   4 dedkCigCgkCliaCedtshqai........eidaktvl.kvvedeCvGCnlCssvCPv 53 
                                       de+ C +C +C+++C+ ++ +          +++ +++  ++ ++    C +C++vCPv
  gi|330508687|ref|YP_004385115.1| 172 DEKLCSECMRCVKMCPVNALDERdypqgltnKKSCAEHSnELNQKGISPCGICIKVCPV 230
                                       7889************877776677765443222223332444566678*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1975.45
//
Query:       gi|330508688|ref|YP_004385116.1|  [L=640]
Description: acetyl-CoA hydrolase/N-GNAT family acetyltransferase fusion protein [Methanosaeta concilii GP6]
Scores for 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-63  211.0   0.0    1.3e-62  210.3   0.0    1.3  1  AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal 
    1.5e-46  158.9   0.0    2.9e-46  158.0   0.0    1.4  1  AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal 
    2.6e-11   43.8   0.0    5.3e-11   42.8   0.0    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.2e-09   38.1   0.0      4e-09   37.3   0.0    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    3.1e-06   27.5   0.1      8e-06   26.2   0.1    1.7  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    9.3e-05   22.4   0.1    0.00022   21.2   0.1    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    0.00017   21.8   0.1    0.00032   20.9   0.1    1.4  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00044   19.7   0.1        1.1    8.6   0.0    3.0  3  CoA_trans        Coenzyme A transferase
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.041   13.8   0.0    1.9  2  DeoRC            DeoR C terminal sensor domain
      0.014   13.8   0.1        2.3    6.4   0.0    2.2  2  Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, trans
      0.029   14.3   0.0      0.064   13.2   0.0    1.5  1  FR47             FR47-like protein
      0.029   14.5   0.1      0.085   13.0   0.1    1.7  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.3   0.0   8.5e-66   1.3e-62       1     154 []     283     436 ..     283     436 .. 0.99

  Alignments for each domain:
  == domain 1  score: 210.3 bits;  conditional E-value: 8.5e-66
                                       S-HHHHHHHTT-TTEEE-BHHHHT-HHHHTTSTTEEEEEE-SEEETTS-EESSECTTCCTCGGTTHHHHHHHHHHST CS
                   AcetylCoA_hyd_C   1 GskklydfldenpkielrpveyvndpeviaqnkkvvsinsalevdltGqvnseslggrvvsGvGgqldFvrgaalsk 77 
                                       Gs++ ydfldenp+ie+++++y+n+p +i++n+ +++insa+evdltGq+++eslgg+++sG+Ggq dF+rga ls+
  gi|330508688|ref|YP_004385116.1| 283 GSRDTYDFLDENPSIEFKRIDYTNNPLIISRNRMMTAINSAMEVDLTGQATAESLGGTFYSGTGGQADFMRGAVLSP 359
                                       899************************************************************************** PP

                                       T-EEEEE--SEETTTTEESEESS-STTSSECE-TTT-SEEEETTEEEE-TT--HHHHHHHHHTTS-HHHHHHHHHHH CS
                   AcetylCoA_hyd_C  78 ggksiialpStakkgeiSrIvpslkegahvtttrhdvdyvvTEyGiadLrgkslreraealikiAhpdfreeLleea 154
                                       ggk+i+a+pSta ++++SrIvp+l+ega++t tr dv+y+vTEyGia+L+gk++rera+ li+iAhp+fr++L+e+a
  gi|330508688|ref|YP_004385116.1| 360 GGKTILAFPSTALNDSVSRIVPVLQEGAGITLTRGDVHYMVTEYGIAYLHGKNIRERAMDLIAIAHPKFRPWLIEAA 436
                                       *************************************************************************9976 PP

>> AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.0   0.0   1.9e-49   2.9e-46      11     191 ..      14     192 ..       5     196 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.0 bits;  conditional E-value: 1.9e-49
                   AcetylCoA_hydro  11 epeeaaelvkngshielsgftavgtakaipkylakrkvekenvkkkllidlavgavlsagPeeevleekdavlyrpa 87 
                                        pe++ +   ++shi+ ++++++gt +++p++l+ + v+++n ++k ++d++   ++++g  +++++ek+  ++r  
  gi|330508688|ref|YP_004385116.1|  14 YPEKFLPPEVIFSHIHAGDRIFIGTGCGEPQFLVAELVNYVNNNPKAFFDAELIHIWTLG-VAPYTDEKFQDNFRLD 89 
                                       48899999999*************************************************.**************** PP

                   AcetylCoA_hydro  88 pkqvgellrkainqglvsfvdkhlsevpqklekgfvpiDvalieataldedGylnlGvgvrakKviiEvaelvvivv 164
                                       +++vg+ +r  +n g++++++++ls vp+++  + vp+D+al++++ +d++Gyl lG++v+++K++ E ae+vv++v
  gi|330508688|ref|YP_004385116.1|  90 SFFVGDSTRNPVNRGAADYTPIFLSSVPDLFRSEMVPVDIALVQTSLPDKHGYLSLGISVDVVKAALEKAEVVVAQV 166
                                       ***************************************************************************** PP

                   AcetylCoA_hydro 165 kknpPrvngydelialdkvdyivvdpe 191
                                       ++n+Pr +g d++i++  +d+i  ++e
  gi|330508688|ref|YP_004385116.1| 167 NENMPRTHG-DGFIHIKDIDFILPHDE 192
                                       *********.*************9997 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0   3.5e-14   5.3e-11      24     117 .]     513     611 ..     487     611 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 3.5e-14
                                       HHHH....HHSTTCEEEEEEET....TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT CS
                    Acetyltransf_1  24 fees....fsleaegllvaeed....geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree 92 
                                        +++    +s+  e l v++e     +++i+  ++  +pd   ++ +   ++V+ ey+g+G+G++Ll +l  +ar++
  gi|330508688|ref|YP_004385116.1| 513 LQDFvvvdWSRKMEILAVIKEKererETIIALGQYELNPD---KYLAEVAIVVKDEYHGMGVGKELLSYLTYIARRH 586
                                       3333333334444455555555466677************...888888**************************** PP

                                       TESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  93 gikkivlaveedndaairlYeklGF 117
                                       g+    +++ + n+a++ l+ek+GF
  gi|330508688|ref|YP_004385116.1| 587 GLLGFTADTLVENKAMVSLFEKMGF 611
                                       **66688*****************9 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   2.7e-12     4e-09       2     137 ..     472     611 ..     471     612 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.7e-12
                    Acetyltransf_3   2 LlLrplteeD...leal.felrsdpevmrylpepltleeaeewlera....waeeseeegygwaivl.kdtgviGsv 69 
                                       + Lrp++ +D   l+++ + l +d   mr+++     ++ +++l+++    w +    +   +a+++ k+ +   ++
  gi|330508688|ref|YP_004385116.1| 472 IFLRPVKITDetmLKDFfYDLSEDSMYMRFFSA--RKDMPHKRLQDFvvvdWSR----KMEILAVIKeKERERETII 542
                                       579999999966666663467788889998654..5588899999986656654....4445666553333224444 PP

                    Acetyltransf_3  70 glrdleeedee..aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                        l ++e ++++  ae+ ++++++++g G+++e ++ l+ +a +++gl  + a +  eN+a++ ++ek+Gf
  gi|330508688|ref|YP_004385116.1| 543 ALGQYELNPDKylAEVAIVVKDEYHGMGVGKELLSYLTYIA-RRHGLLGFTADTLVENKAMVSLFEKMGF 611
                                       4444444444444*******************999877666.9999***********************9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   5.4e-09     8e-06       6      74 ..     541     611 ..     524     613 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.4e-09
                                       EEEEETTEEEEEEEEEEESTCTEE..EEE-GGGTTSSHHHHHHHH....TT.SEEEEE..EEEE.THHHHHHHHHHT CS
                    Acetyltransf_7   6 fVaeddgkivGfialslldaeitr..laVdpeyrgkGiGraLlea....ae.kgiile..qlel.naekaikfYekl 72 
                                       ++a      +G++ l +++ ++ +  ++V+ ey+g G+G++Ll +    a+ +g+       +l ++++ ++++ek+
  gi|330508688|ref|YP_004385116.1| 541 IIA------LGQYELNPDK-YLAEvaIVVKDEYHGMGVGKELLSYltyiARrHGLL-GftADTLvENKAMVSLFEKM 609
                                       345......5777666665.44445699****************756541155533.223334434435577***** PP

                                       TE CS
                    Acetyltransf_7  73 GF 74 
                                       GF
  gi|330508688|ref|YP_004385116.1| 610 GF 611
                                       ** PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   1.5e-07   0.00022      57     113 ..     560     618 ..     526     628 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.5e-07
                   Acetyltransf_10  57 lfVdpeyrgqGigkaLleaveeeaekdgikl..eltvnaspyavpfYeklGFkavgeeq 113
                                       ++V++ey+g G+gk+Ll ++   a+++g+    + t+ ++++ v+++ek+GF + ++ +
  gi|330508688|ref|YP_004385116.1| 560 IVVKDEYHGMGVGKELLSYLTYIARRHGLLGftADTLVENKAMVSLFEKMGFYTEKRRE 618
                                       489*********************99998878777888888***********8875543 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   2.2e-07   0.00032      56     141 ..     537     618 ..     510     625 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.2e-07
                    Acetyltransf_4  56 esdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkal 132
                                       e ++i++  +++ +++   +  ae+ + +++     +g+g+el+ +l  ++++ +++ ++a + ++n++ + +++++
  gi|330508688|ref|YP_004385116.1| 537 ERETIIALGQYE-LNP--DKYLAEVAIVVKD-EYHGMGVGKELLSYLTYIARRHGLLGFTADTLVENKAMVSLFEKM 609
                                       467888888888.666..66899******85.79******************************************* PP

                    Acetyltransf_4 133 GFelvgifk 141
                                       GF  +++ +
  gi|330508688|ref|YP_004385116.1| 610 GFYTEKRRE 618
                                       **8877655 PP

>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0019       2.9       9      43 ..      26      57 ..      21      81 .. 0.82
   2 ?   -0.5   0.0      0.46   6.8e+02     149     192 ..     127     168 ..     123     176 .. 0.82
   3 !    8.6   0.0   0.00076       1.1       2      63 ..     207     262 ..     206     369 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0019
                                      CTT--TTEEEEE-SBTTBTHHHHHHHHHHHHTTTS CS
                         CoA_trans  9 akeikdGmtvavGGFgligiPealiaalarsgvkd 43
                                      + +i+ G+ +++G  +++g+P+ l+a+l++  +++
  gi|330508688|ref|YP_004385116.1| 26 S-HIHAGDRIFIG--TGCGEPQFLVAELVNYVNNN 57
                                      4.89*********..*************9876444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.46
                                       EEEEEEECCEEETTCSEESSGGGHTTHSHHHHHHEEEEEEEEEE CS
                         CoA_trans 149 advalikaskadeegnlvfeksagnfnkpaiaeaakvtilevee 192
                                       +d+al++ s  d++g+l+   s+   +  a+  +a+v++++v e
  gi|330508688|ref|YP_004385116.1| 127 VDIALVQTSLPDKHGYLSLGISVDVVK-AALE-KAEVVVAQVNE 168
                                       69***************9999998888.4444.79999999987 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00076
                                       CHHHHHHCTT--TTEEEEE-SBTTBT.HHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTT CS
                         CoA_trans   2 etaaeavakeikdGmtvavGGFglig.iPealiaalarsgvkdltviiseagvlglgplllng 63 
                                       +++ + va+ i+dG+t+ vG     g iP + +++l ++   ++  ++ e    g+  l+++g
  gi|330508688|ref|YP_004385116.1| 207 QRIGKYVARIIEDGSTIQVG----YGlIPDEVVHSLENK---KDLGVHTELLSDGIVELMKKG 262
                                       5677899*************....888**9999998776...444444444444444444444 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.2   7.7e+03      15      28 ..      26      39 ..      23      43 .. 0.86
   2 ?   13.8   0.0   2.8e-05     0.041       7      50 ..     207     250 ..     205     265 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.2
                             DeoRC 15 eliedgdtifldaG 28
                                      ++i+ gd if+++G
  gi|330508688|ref|YP_004385116.1| 26 SHIHAGDRIFIGTG 39
                                      78999******988 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.8e-05
                             DeoRC   7 rrIAkaAaeliedgdtifldaGtTtlelaraLaekknltvvTns 50 
                                       +rI+k++a++iedg+ti ++ G    e+++ L++kk+l v T  
  gi|330508688|ref|YP_004385116.1| 207 QRIGKYVARIIEDGSTIQVGYGLIPDEVVHSLENKKDLGVHTEL 250
                                       79**************************************9975 PP

>> Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0016       2.3     137     206 ..     125     192 ..     117     205 .. 0.75
   2 ?    5.0   0.0    0.0042       6.3     448     482 ..     391     424 ..     380     444 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0016
                   Mal_decarbox_Al 137 iP.nvalvaaekadreGnlytGantedtPaiveatafkdgiviaqvneivdklpr.vdiPadwvdfvveadk 206
                                       +P ++alv ++  d++G l  G + +    +v a+  k  +v+aqvne + +      i  + +df++  d+
  gi|330508688|ref|YP_004385116.1| 125 VPvDIALVQTSLPDKHGYLSLGISVD----VVKAALEKAEVVVAQVNENMPRTHGdGFIHIKDIDFILPHDE 192
                                       55369******************986....899999999********9654332202245555666665555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0042
                   Mal_decarbox_Al 448 iygddvthvvteeGiayllkaesleereqairava 482
                                       +   dv ++vte Giayl+  +++ er   + a+a
  gi|330508688|ref|YP_004385116.1| 391 LTRGDVHYMVTEYGIAYLHG-KNIRERAMDLIAIA 424
                                       55679************985.56666666665665 PP

>> FR47  FR47-like protein
   #    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      26      80 ..     559     614 ..     537     619 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                                       EEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  26 alqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfeki 80 
                                       a+ v++e  ++G g+ l + l++  ++ g    ++ +  +N++  +l+ek+Gf   
  gi|330508688|ref|YP_004385116.1| 559 AIVVKDEYHGMGVGKELLSYLTYIARRHGLlGFTADTLVENKAMVSLFEKMGFYTE 614
                                       789*******************98888886256788999**************765 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.7e-05     0.085      11      58 ..     541     588 ..     532     589 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-05
                   Acetyltransf_CG  11 evafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                        +a  +Ye ++++ l+   ++V++e+ G G++k+L  +    ar++gl
  gi|330508688|ref|YP_004385116.1| 541 IIALGQYELNPDKYLAEVAIVVKDEYHGMGVGKELLSYLTYIARRHGL 588
                                       567779999999999999********************9999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.24s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 4521.40
//
Query:       gi|330508689|ref|YP_004385117.1|  [L=190]
Description: hypothetical protein MCON_2954 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-14   54.6   0.1    1.5e-14   54.3   0.1    1.1  1  NT5C      5' nucleotidase, deoxy (Pyrimidine), cytosolic type
  ------ inclusion threshold ------
      0.093   12.4   0.0       0.16   11.7   0.0    1.4  1  Apo-CIII  Apolipoprotein CIII (Apo-CIII)


Domain annotation for each model (and alignments):
>> NT5C  5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.1   1.7e-18   1.5e-14       4     155 ..       5     156 ..       2     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1.7e-18
                              NT5C   4 vlvDlDgvladlygkmlevankrfeatllpeevsswdleefvkPeqreslyrfltepglFadlepipgarevLeela 80 
                                       + vD+Dgvlad + ++l+ ++++++   ++ +v    + +f   e  e++ r l  p++  ++  i g+++ +++l+
  gi|330508689|ref|YP_004385117.1|   5 IAVDIDGVLADQVAAVLREIEREYGLIYSKSDVDRAHW-TFEGREVWEEISRLLSDPEYVMQVPIIHGSQKAIKKLS 80 
                                       78*******************************96555.56678********************************* PP

                              NT5C  81 degrlvvitaallqfydavkekveWldehlplipyrnlvlvkekdlvrgDvlidDapknleklrgrs.....ilfds 152
                                        +  + v+ta+      + + +  Wl  h+p ++      ++ k+ v +DvlidD   n+ ++         ilf++
  gi|330508689|ref|YP_004385117.1|  81 HH-DVFVVTARRPH---TEEATRRWLSAHFPSLKGYYWARTGTKHNVPSDVLIDDLDINIVEFVKSDpdrhgILFQH 153
                                       *9.77888877655...6778899**********999999*******************998865444555788888 PP

                              NT5C 153 ptn 155
                                       p  
  gi|330508689|ref|YP_004385117.1| 154 PWS 156
                                       765 PP

>> Apo-CIII  Apolipoprotein CIII (Apo-CIII)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.7e-05      0.16      37      54 ..      96     114 ..      62     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.7e-05
                          Apo-CIII  37 qA.rgWvtdslssLkdYws 54 
                                       +A r W++ ++ sLk+Y+ 
  gi|330508689|ref|YP_004385117.1|  96 EAtRRWLSAHFPSLKGYYW 114
                                       4459************853 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1493.72
//
Query:       gi|330508690|ref|YP_004385118.1|  [L=142]
Description: hypothetical protein MCON_2955 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-07   31.7   0.0    2.3e-07   31.1   0.0    1.2  1  OrfB_IS605  Probable transposase


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 !   31.1   0.0   1.3e-11   2.3e-07      10      97 ..      42     129 ..      33     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.3e-11
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       ++ ++ ++  g+D+Gin La+ +t+d + +++ g ++k++    +ke+++lq+   +    +   r l+++    +r
  gi|330508690|ref|YP_004385118.1|  42 KNIVDASTFMGVDVGINCLAVASTTDKQCKFFAGGEIKNHRNIRSKERQRLQKAGGRYLGTRSSMRTLRKIAGLETR 118
                                       5667788999*******************************************988887778888888888888888 PP

                        OrfB_IS605  87 rrkhllhklat 97 
                                       +++ + hk+++
  gi|330508690|ref|YP_004385118.1| 119 FMTAVNHKVSH 129
                                       88888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1141.16
//
Query:       gi|330508691|ref|YP_004385119.1|  [L=450]
Description: transposase, IS4 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-25   89.8   0.0    3.3e-25   89.0   0.0    1.4  1  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
      0.014   14.7   0.3      0.021   14.1   0.3    1.3  1  DDE_Tnp_2    Archaeal putative transposase ISC1217
      0.019   13.3   0.0       0.03   12.6   0.0    1.2  1  DDE_Tnp_1_4  Transposase DDE domain group 1
      0.075   13.0   1.0        1.4    8.9   0.1    2.8  3  Tudor_FRX1   Fragile X mental retardation Tudor 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 !   89.0   0.0   7.3e-29   3.3e-25       2     212 ..     133     371 ..     132     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 7.3e-29
                         DDE_Tnp_1   2 skrevlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkq..lldelrprk 76 
                                       s+r+v i D+t +r +++ +d+++     k  +g+k+  ++++    + s+ i p n++d+k+lk   ++      k
  gi|330508691|ref|YP_004385119.1| 133 SFRDVMIQDSTIIRLHKSLADKWPATRSRKVAAGVKVAFLTSAIANSPKSISILPENTNDVKTLKIgpWV------K 203
                                       6899***************9999988899999********************************995555......7 PP

                         DDE_Tnp_1  77 gklvlaDaGYasaelldtleekgvdyiirlkkntklyrk.............gaeskrrgrlrkhdrnkiltksqkr 140
                                       + ++l D G+ +++l+ ++ e+g+++++rlk+n++ ++              + +++++ +l+k d    ++ + ++
  gi|330508691|ref|YP_004385119.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVgtnqvrntrgvdlNGKHLKDIKLEKSDDIFDVNVEVSF 280
                                       789************************************99777666666663444444444444444444444444 PP

                         DDE_Tnp_1 141 rnk...................skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrgl 198
                                       +++                    +++++++ y+tn++s+ l a+eva+ y+ Rw++E +Fk+lk+++ ld   ++++
  gi|330508691|ref|YP_004385119.1| 281 DRRsyrgeskkdnkifrlvaiyNTEAEEHHFYLTNISSDILNASEVAAVYSGRWEVELIFKELKSRYALDQITTKSP 357
                                       4447777777777799999999999**************************************************** PP

                         DDE_Tnp_1 199 nrveaqllllllal 212
                                        ++ea ++  +l+l
  gi|330508691|ref|YP_004385119.1| 358 YAIEALIWVSILTL 371
                                       *******9998876 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   4.6e-06     0.021     219     288 ..     274     346 ..     202     384 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                         DDE_Tnp_2 219 rhvpvaelPeGeylveyl.dtvikllvlddykkdgrrylfstdln...dtdediittWenrWdievlirelkal 288
                                        +v+v+ + + +y  e   d+ i  lv +   + +  +++ t++    + + ++ + +  rW++e +++elk+ 
  gi|330508691|ref|YP_004385119.1| 274 VNVEVS-FDRRSYRGESKkDNKIFRLVAIYNTEAEEHHFYLTNISsdiLNASEVAAVYSGRWEVELIFKELKSR 346
                                       445543.7777888887767777767777777888999**999973335799********************73 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.6e-06      0.03     217     368 ..     204     372 ..     197     399 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.6e-06
                       DDE_Tnp_1_4 217 kilvRgDSafarpellkwceergvdYviglaknsrlealiaelvekakteaaekkek................erey 277
                                       +i++  D +f + +l++ + e+g ++v +l++n++     ++ v +++  + + k+                 e+++
  gi|330508691|ref|YP_004385119.1| 204 DIILLIDLGFYKYQLFSRIVENGGSFVSRLKSNANPLIVGTNQVRNTRGVDLNGKHLkdikleksddifdvnvEVSF 280
                                       578889999**********************999877766666666666666654436799999999**99999999 PP

                       DDE_Tnp_1_4 278 refayqaesWskerrVvakaerpaeglnlrfvvTsla..klspeelyeqlYcaRGemEnrIKeakldlaadrtsshs 352
                                        +  y+ es + ++   + a +++e  +++f +T+++   l+++e+   +Y  R e+E  +Ke k+  a+d++ ++s
  gi|330508691|ref|YP_004385119.1| 281 DRRSYRGESKKDNKIFRLVAIYNTEAEEHHFYLTNISsdILNASEVA-AVYSGRWEVELIFKELKSRYALDQITTKS 356
                                       99999999855444333334455556667999****99888999999.9*************************999 PP

                       DDE_Tnp_1_4 353 faaNqlrlllsalAyn 368
                                         a ++ +++s l   
  gi|330508691|ref|YP_004385119.1| 357 PYAIEALIWVSILTLL 372
                                       9999988888887654 PP

>> Tudor_FRX1  Fragile X mental retardation Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00031       1.4      17      36 ..      22      41 ..      18      44 .. 0.88
   2 ?    1.1   0.0     0.085   3.8e+02      18      31 ..     269     282 ..     257     291 .. 0.89
   3 ?   -2.6   0.0       1.2   5.4e+03      13      36 ..     313     337 ..     311     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00031
                        Tudor_FRX1 17 vkdvhedsltvaFennWqpe 36
                                       kd+ e++lt +Fe +W  +
  gi|330508691|ref|YP_004385119.1| 22 EKDIVEQELTRMFESKWIRD 41
                                      59***************765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.085
                        Tudor_FRX1  18 kdvhedsltvaFen 31 
                                        d+++ ++ v+F+ 
  gi|330508691|ref|YP_004385119.1| 269 DDIFDVNVEVSFDR 282
                                       59**********96 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.2
                        Tudor_FRX1  13 ykafvkdvhed.sltvaFennWqpe 36 
                                       +  +  d+++  ++ +++   W  e
  gi|330508691|ref|YP_004385119.1| 313 LTNISSDILNAsEVAAVYSGRWEVE 337
                                       5566778888526888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3368.64
//
Query:       gi|330508692|ref|YP_004385120.1|  [L=390]
Description: Xaa-Pro dipeptidase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-32  110.6   0.0    1.1e-31  110.2   0.0    1.2  1  Peptidase_M24  Metallopeptidase family M24
    5.2e-14   53.0   0.0      1e-13   52.1   0.0    1.5  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   0.0   1.2e-35   1.1e-31       3     208 ..     142     373 ..     140     374 .. 0.80

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 1.2e-35
                                       HHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTT.........TCEESS....SSEEEEGGGGGS..... CS
                     Peptidase_M24   3 irkaariasaaleavleaikpgvterelaaeieattlkrhg.........arglaf....ppivasgenaav..... 61 
                                        ++aa++  + +  v ++ik+g+te el   +e +++  +g         +          + + sg  aa+     
  gi|330508692|ref|YP_004385120.1| 142 AKEAAQMLVEGFSTVPDHIKEGMTEVELMCRMESEMR-LMGhqgslrfrrF----NsivpIGHIMSGSSAAIpsfla 213
                                       589******************************8854.3443456555442....0334356677777777733333 PP

                                       ............TTTBCSSSB--TTEEEEEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STT CS
                     Peptidase_M24  62 ............lhytpndrvlkegdlvlidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpG 126
                                                   +h+ p+ r++k++++v +d  +  +gy++D tr +++Gk +pe  e+yea  ++ ea+ +++kpG
  gi|330508692|ref|YP_004385120.1| 214 sptggkgtsvvfPHG-PGYRKIKRNEPVFVDTVGICNGYIADATRIFSLGKIEPELVEAYEASCQIEEAIAREMKPG 289
                                       333333333333444.34566******************************************************** PP

                                       SBHHHHHHHHHHHHHHTTB....CCGBSS.......CSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEE CS
                     Peptidase_M24 127 vtlseidaaarevlesagl....akffph.......glGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyf 192
                                       +t++e+ +  +   ++ g+    +            ++GHgvGle+ +  p ++     ++k++eGm++++Ep+i  
  gi|330508692|ref|YP_004385120.1| 290 RTARELFELSESEGARLGYgdflG----GpvgskcgFVGHGVGLELDEY-PVLA---PLDHKIQEGMTIAVEPKII- 357
                                       ***************999966662....233335669**********98.*998...4599*************99. PP

                                       ETTTEEEEEBEEEEEE CS
                     Peptidase_M24 193 apgeggvriedtvlvt 208
                                        pg+g+  +edt+l t
  gi|330508692|ref|YP_004385120.1| 358 YPGKGVLGVEDTFLTT 373
                                       89***********987 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   1.1e-17     1e-13       1     132 []      14     133 ..      14     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.1e-17
                                       HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.TTSEEEEEST CS
                      Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadga.lllvdalryteaaeesatveevveydd 76 
                                       R+++l+++m++  +d++l+++  +++Y++G+     + gl++ +++dg+ ++++      +a+ees  + ev++ + 
  gi|330508692|ref|YP_004385120.1|  14 RIKKLKDRMDD--IDGALLFQAVDMCYFSGT----AQDGLVY-IPRDGEpIIMMK-RSLVRAKEES--PLEVRPLK- 79 
                                       89999999985..******************....7888888.9*****666666.9999999999..89999887. PP

                                       HSSHHHHHHHHHHHHT.-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHSC CS
                      Creatinase_N  77 pvealadllkellese.krvgveldaltvafyealkealpdaelvdaselieelRvv 132
                                          ++ +l ++l+ +   ++g+e+d+l+++fy ++ +al+da++vd+ e i+++R v
  gi|330508692|ref|YP_004385120.1|  80 ---NMRNLKEDLGIKTsATIGLEMDVLPCSFYFRVNKALEDASFVDVAERIKHIRSV 133
                                       ...57777777777677**************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2909.56
//
Query:       gi|330508693|ref|YP_004385121.1|  [L=327]
Description: hypothetical protein MCON_2959 [Methanosaeta concilii GP6]
Scores for complete 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   82.5   7.0    3.2e-23   81.9   7.0    1.2  1  YdjM         LexA-binding, inner membrane-associated putative
     0.0023   18.0   0.1     0.0038   17.2   0.1    1.4  1  Zn_dep_PLPC  Zinc dependent phospholipase C
     0.0035   17.1   5.7     0.0076   16.0   5.8    1.5  1  DUF4184      Domain of unknown function (DUF4184)


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 !   81.9   7.0   5.3e-27   3.2e-23       1     165 [.       1     179 [.       1     186 [. 0.75

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 5.3e-27
                              YdjM   1 MdgltHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllfla 77 
                                       Md ++Hall  +lg  l  +        +la++vlg+++PD+D+  +++++  ++ s+    l+ HRgftH++lf +
  gi|330508693|ref|YP_004385121.1|   1 MDFFSHALLPYLLGRFLRIRRD------YLAALVLGGIAPDLDVLVVWINQI-HPTSY----LIVHRGFTHTFLFGF 66 
                                       999***********99988875......79*************776666655.56677....689************ PP

                              YdjM  78 llalvlllllrlfgrsa.............lrlgll.lllgvlsHlllDlltkyGvpllwPfskkkvrlsllfiiid 140
                                       ++a++ll+l+ + + ++             + ++l+   +g++sHl+lD lt+ Gvpl++P++ ++++ +++   i+
  gi|330508693|ref|YP_004385121.1|  67 FVAAILLFLVSRGWIKTrsrgivtedlqfsA-TTLAySYAGIISHLFLDFLTSGGVPLFYPLTAARYSAEIFSR-IE 141
                                       *****9999999999889********99743.333347788**********************98888777666.33 PP

                              YdjM 141 plltll...............srrglvalelvllvlylvi 165
                                        +++ +               +  +   + +++l+++lvi
  gi|330508693|ref|YP_004385121.1| 142 IVIMIAtllfmaklfrdrpemKIDKK--VSAAFLIFLLVI 179
                                       32222246777778877665322222..233333333444 PP

>> Zn_dep_PLPC  Zinc dependent phospholipase C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   6.4e-07    0.0038      11     107 ..       9     117 ..       2     172 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.4e-07
                                       HHH....HHH-..HHHTHHHHHHHHHGGGG..-TT....-GGG...--BTTT.TB-HHHHS-HHHHHHHHHHHHHHH CS
                       Zn_dep_PLPC  11 avlpalkkkrk..lklnkaalllGsvaPDleylfn....assh...syktht.kagllgedhhweetgkfllllikk 77 
                                          p l+++     ++++aal+lG +aPDl +l         h   + + h+ +++ +         g f+++    
  gi|330508693|ref|YP_004385121.1|   9 L--PYLLGRFLriRRDYLAALVLGGIAPDLDVLVVwinqI--HptsYLIVHRgFTHTF-------LFGFFVAAILLF 74 
                                       3..444444445567***************7665544331..1222444455333333.......445555555555 PP

                                       HHC..................T-HHHHHHHHHHHHHHHHHHTS CS
                       Zn_dep_PLPC  78 lre........ly.....ksegslklaafllGvlsHyvaDvft 107
                                       l +        +       ++ ++ la  + G++sH++ D+ t
  gi|330508693|ref|YP_004385121.1|  75 LVSrgwiktrsRGivtedLQFSATTLAYSYAGIISHLFLDFLT 117
                                       54544444433114444533448899**************987 PP

>> DUF4184  Domain of unknown function (DUF4184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   5.8   1.3e-06    0.0076       5     166 ..       4     156 ..       3     212 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-06
                           DUF4184   5 lsHpaavlpl.kllkrkrlslsaLviGslaPDveyflrlkakstltHtllglllvdlplalllalvfhlvikkplla 80 
                                       +sH+ + + l + l+ +r  l+aLv+G +aPD+ +++ +    +  H    l++       +l+ +f   + + ll 
  gi|330508693|ref|YP_004385121.1|   4 FSHALLPYLLgRFLRIRRDYLAALVLGGIAPDLDVLVVWI---NQIHPTSYLIVHRGFTHTFLFGFF---VAAILLF 74 
                                       5665555555666777777899**************7555...445554444444433333333333...3333333 PP

                           DUF4184  81 llP.aalarrlkksaerkslkallvvvvsaliGaatHvlwDsfTHedgwfvrlipvlqssvagdvplykllqhgstl 156
                                       l++  +++ r ++   +++l+     +     G+++H+++D +T      v l+  l+++  ++ +++  +++++ +
  gi|330508693|ref|YP_004385121.1|  75 LVSrGWIKTR-SRGIVTEDLQFSATTLAYSYAGIISHLFLDFLTSG---GVPLFYPLTAAR-YSAEIFSRIEIVIMI 146
                                       3331344444.444444455444333333578***********943...455566666666.666777777766666 PP

                           DUF4184 157 lGlvviivvl 166
                                       ++l++++ ++
  gi|330508693|ref|YP_004385121.1| 147 ATLLFMAKLF 156
                                       6555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2455.58
//
Query:       gi|330508694|ref|YP_004385122.1|  [L=261]
Description: hypothetical protein MCON_2960 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2036.28
//
Query:       gi|330508695|ref|YP_004385123.1|  [L=525]
Description: hypothetical protein MCON_2964 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00092   19.5   0.0      0.003   17.8   0.0    1.8  1  DUF11          Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.038   13.8   0.0      0.074   12.9   0.0    1.4  1  Vac_ImportDeg  Vacuolar import and degradation 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 !   17.8   0.0   3.3e-07     0.003       8      80 ..     229     301 ..     224     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-07
                             DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas.qgtasaltsvgsLeagesatlsftvrvtr 80 
                                       + +++G+++tyt+t  N+  ++  ++vv+    + + +++++ +  +  + +++++ +++g+  ++++ ++  +
  gi|330508695|ref|YP_004385123.1| 229 KSAAAGGKITYTITYGNNDFQPV-DIVVRENYDPKTVFIESQPApDPGSNNRWTIPAVAPGKHGQIKIVMKTVK 301
                                       46899******************.******9999999999988878888899999********99999887554 PP

>> Vac_ImportDeg  Vacuolar import and degradation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.2e-06     0.074      18      79 ..     290     352 ..     277     355 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.2e-06
                     Vac_ImportDeg  18 kyevkvelktvdle.eslltGfleikglteekpeittffegeiidekysfltkkkkwkaseet 79 
                                       + ++k+ +ktv+ + +  + G+++  gl+++   ++t fe +ii++++++l+ +++++as +t
  gi|330508695|ref|YP_004385123.1| 290 HGQIKIVMKTVKPAaKADIEGTVSGIGLSSTRGMLSTEFERYIITNSVQILAGNRSYSASLDT 352
                                       5689*******9874778***************************************998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3879.03
//
Query:       gi|330508696|ref|YP_004385124.1|  [L=212]
Description: hypothetical protein MCON_2966 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-66  222.3   0.0    3.4e-66  222.1   0.0    1.0  1  DUF99     Protein of unknown function DUF99


Domain annotation for each model (and alignments):
>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.1   0.0   1.9e-70   3.4e-66       2     182 ..       9     200 ..       8     201 .. 0.97

  Alignments for each domain:
  == domain 1  score: 222.1 bits;  conditional E-value: 1.9e-70
                                       GSEEEEEEEEE....................-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TT CS
                             DUF99   2 eirvlGiddsfferkk...............kdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrler 63 
                                       ++rvlGi++sf  ++                ++++s+l+Gvvmradr+vdg+a++r++v+G+Dat+a++e+++rl+r
  gi|330508696|ref|YP_004385124.1|   9 ALRVLGIAESF--ERPcalssdpvsttlsppMSSWSMLAGVVMRADRRVDGLAYARASVGGDDATRAVLEICRRLDR 83 
                                       68*********..3446788899999*************************************************** PP

                                       TTEEEEEESSSEETTTEE--HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT.. CS
                             DUF99  64 edirvvlldGitiagFNvvDlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevektg 140
                                       +di++++l+G +i++FN++Dl +++ee+++P+i++t+ee++ g lek+Lr++fp++ee++e++++lg+r++++ ktg
  gi|330508696|ref|YP_004385124.1|  84 RDINALFLSGAAISWFNIIDLVAVFEEVSRPLICLTYEESE-G-LEKYLREYFPEPEEKIERYRSLGMREKIRLKTG 158
                                       *****************************************.8.********************************* PP

                                       ..EEEEEESS-HHHHHHHHHHC-SSSSS-HHHHHHHHHHHHH CS
                             DUF99 141 eelyvravGieleeaaklvrkltlegriPEPlRvAhliAsal 182
                                       +el+vr++G+++eea+ l++k+tl+gr+PEP+R+A+++A+a+
  gi|330508696|ref|YP_004385124.1| 159 YELFVRVHGATVEEARILLNKFTLDGRVPEPVRLARMAARAA 200
                                       ****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1563.46
//
Query:       gi|330508697|ref|YP_004385125.1|  [L=194]
Description: acylphosphatase [Methanosaeta concilii GP6]
Scores for complete sequence (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   70.4   0.7    3.8e-19   68.9   0.1    2.0  3  Acylphosphatase  Acylphosphatase
    0.00018   21.4   1.5    0.00077   19.4   0.6    2.1  2  Apolipoprotein   Apolipoprotein A1/A4/E domain
     0.0019   17.9   0.1     0.0023   17.7   0.1    1.2  1  DUF4559          Domain of unknown function (DUF4559)
     0.0056   17.1   0.4      0.015   15.7   0.1    1.9  2  Snapin_Pallidin  Snapin/Pallidin
     0.0075   16.3   0.9      0.028   14.5   0.7    2.0  2  DUF1664          Protein of unknown function (DUF1664)
     0.0081   16.2   0.0        1.2    9.2   0.0    2.3  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
  ------ inclusion threshold ------
      0.011   15.8   0.5       0.03   14.4   0.3    1.8  2  COG2             COG (conserved oligomeric Golgi) complex com
      0.014   15.9   0.1      0.063   13.8   0.0    2.1  2  Spectrin         Spectrin repeat
      0.036   14.1   0.0      0.051   13.7   0.0    1.2  1  DUF1115          Protein of unknown function (DUF1115)
      0.048   14.1   1.3        0.2   12.1   0.4    2.5  3  ZapA             Cell division protein ZapA
       0.14   12.1   0.0       0.25   11.4   0.0    1.5  1  Cbl_N            CBL proto-oncogene N-terminal domain 1
       0.16   11.3   0.0       0.24   10.8   0.0    1.2  1  Glyco_hydro_85   Glycosyl hydrolase family 85
       0.22   11.7   4.2       0.26   11.5   1.1    2.5  2  DUF5446          Family of unknown function (DUF5446)
        1.1    9.4   2.8        7.2    6.8   0.3    2.7  3  YojJ             Bacterial membrane-spanning protein N-termin


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 !   68.9   0.1     3e-22   3.8e-19       2      83 ..       5      86 ..       4      88 .. 0.96
   2 ?   -1.4   0.0       2.6   3.3e+03      48      70 ..     132     153 ..     123     163 .. 0.61
   3 ?   -3.2   0.0       9.4   1.2e+04      62      62 ..     175     175 ..     153     191 .. 0.51

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 3e-22
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      +++v+G+VQ  g+R  v  +A+ +glkGyv+Nlsd +V+ivaeg e+++e+fle+++ +++ + v+e+e+e + +++ +
  gi|330508697|ref|YP_004385125.1|  5 TAYVSGKVQMAGYRSKVVTIARVFGLKGYVMNLSDSRVKIVAEGHEADLERFLEAIRIKNTLIDVEEIEAEFSGANGSY 83
                                      689********************************************************************99999999 PP

                   Acylphosphatase 81 kdF 83
                                      ++F
  gi|330508697|ref|YP_004385125.1| 84 EEF 86
                                      888 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.6
                   Acylphosphatase  48 ekvekfleelksgppkarvdeve 70 
                                       + +++fl+e++ ++    +d+++
  gi|330508697|ref|YP_004385125.1| 132 DGMSSFLKEISGKQD-QIIDRID 153
                                       456777777775554.4444443 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 9.4
                   Acylphosphatase  62 p 62 
                                       +
  gi|330508697|ref|YP_004385125.1| 175 E 175
                                       2 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.029        37     104     127 ..      95     118 ..      40     142 .. 0.61
   2 !   19.4   0.6   6.1e-07   0.00077       5      98 ..      98     193 ..      94     194 .] 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHHHHCHHHHHHH CS
                    Apolipoprotein 104 lrerlerhvealkarlapyveelr 127
                                          rl+++++ lk+ +++ +e +r
  gi|330508697|ref|YP_004385125.1|  95 TDARLDQAADYLKELISAVREGFR 118
                                       233333333333333333333333 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 6.1e-07
                                       CCCCHHHHHCCHHHCHHCHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHH CS
                    Apolipoprotein   5 sldelkayaeeleeqlaplaq...elrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapy 78 
                                       +ld+++ y++el + + +  +   +  d +  +l++++  l +e++   +++ +++d+++e++ +++ ++r++l++ 
  gi|330508697|ref|YP_004385125.1|  98 RLDQAADYLKELISAVREGFRdngSKLDSMGSKLDGMSSFL-KEISGKQDQIIDRIDDAREEIVSEVCGMRSDLKSR 173
                                       56667777777777777775545457778888888888888.9999999**************************** PP

                                       HHHHHHHHHHCHHCCHHCHC CS
                    Apolipoprotein  79 teelrerlaadaeelqeqla 98 
                                       tee+ +r++ d+ e++ +++
  gi|330508697|ref|YP_004385125.1| 174 TEERLQRIESDVTEIKAKMR 193
                                       ****************9987 PP

>> DUF4559  Domain of unknown function (DUF4559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.8e-06    0.0023     166     309 ..      46     193 ..      17     194 .] 0.73

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.8e-06
                           DUF4559 166 mkeymkkilrLledlk...tvpeleeaeeaieellkilkqefeislke..ddevrvltdvllslqklkeleeellke 237
                                       ++ +  +++r+le+++   t+ ++ee+e +    +   ++ f++  ++  d+ ++  +d    l++l    +e +++
  gi|330508697|ref|YP_004385125.1|  46 AEGHEADLERFLEAIRiknTLIDVEEIEAEFSGANGSYEEFFKVAGERetDARLDQAAD---YLKELISAVREGFRD 119
                                       56799999999998754356777777777777776666666666655534444444455...47889999999**** PP

                           DUF4559 238 datkldelvlraeeqkiskeellkelqvlkeflnknkd..Lkenlkedvkklqeieekldkldedvtelkkkvd 309
                                       ++ kld++ ++ +      +e++ +   + + ++  ++    e+ +       + ee+l+++++dvte+k+k+ 
  gi|330508697|ref|YP_004385125.1| 120 NGSKLDSMGSKLDGMSSFLKEISGKQDQIIDRIDDAREeiVSEVCGMRSDLKSRTEERLQRIESDVTEIKAKMR 193
                                       **************9999999955555555555555544444444444345567899**************995 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       7.9     1e+04      15      25 ..      99     109 ..      94     114 .. 0.50
   2 !   15.7   0.1   1.2e-05     0.015      12      80 ..     128     193 ..     123     194 .] 0.92

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.9
                   Snapin_Pallidin  15 ldeldeklkel 25 
                                       ld+  + lkel
  gi|330508697|ref|YP_004385125.1|  99 LDQAADYLKEL 109
                                       33333334333 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.2e-05
                   Snapin_Pallidin  12 epkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeya.kKLvnikkrmsslnerlq 80 
                                        +kld + + lke+  +Q++  +++d  +e++  ++e+    + +dlk+   ++L++i+ ++++++ +++
  gi|330508697|ref|YP_004385125.1| 128 GSKLDGMSSFLKEISGKQDQIIDRIDDAREEI--VSEVCG--MRSDLKSRTeERLQRIESDVTEIKAKMR 193
                                       6789999999**********************..899999..99****99879*************9986 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.028        36      85     124 .]     106     145 ..      93     145 .. 0.55
   2 !   14.5   0.7   2.2e-05     0.028      38      96 ..     133     192 ..     110     194 .] 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.028
                           DUF1664  85 ikeevtevredlseigedvesvkeaveglesklerieekQ 124
                                       +ke +++vre+ ++ g++++s+ +   g+ s l++i++kQ
  gi|330508697|ref|YP_004385125.1| 106 LKELISAVREGFRDNGSKLDSMGSKLDGMSSFLKEISGKQ 145
                                       3444555566666666666666666666666666666665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.2e-05
                           DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkkldeqk.eiskeikeevtevredl 96 
                                       ++s++++++s + +q+ + + ++++++ s++  + + l++ + e  + i+++vte++ ++
  gi|330508697|ref|YP_004385125.1| 133 GMSSFLKEISGKQDQIIDRIDDAREEIVSEVCGMRSDLKSRTeERLQRIESDVTEIKAKM 192
                                       677777888888888888888888888888888877776654145677777777777765 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   0.0   0.00095       1.2      13      94 ..      48     131 ..      41     142 .. 0.65
   2 !    5.9   0.0    0.0098        13      19      80 ..     135     189 ..     126     194 .] 0.40

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00095
                      Baculo_PEP_C  13 nqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksl.laeldtrldtlltnLtdalnalqdtlr...n 85 
                                       ++  dL   L+air +n+ i  +++++ ++  +  ++ +e +k +   e d+rld++++ L++ + a+ + +r   +
  gi|330508697|ref|YP_004385125.1|  48 GHEADLERFLEAIRIKNTLI--DVEEIEAEFSGANGSYEEFFKVAgERETDARLDQAADYLKELISAVREGFRdngS 122
                                       56799************999..555555555554444333333221246667***************9966661113 PP

                      Baculo_PEP_C  86 eLtnlnsil 94 
                                       +L+++ s+l
  gi|330508697|ref|YP_004385125.1| 123 KLDSMGSKL 131
                                       455544444 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0098
                      Baculo_PEP_C  19 tnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq 80 
                                       +  L+ i  ++ qi+  +  + ++i +++  + +dlk       +r ++ l+++++ + +++
  gi|330508697|ref|YP_004385125.1| 135 SSFLKEISGKQDQIIDRIDDAREEIVSEVCGMRSDLK-------SRTEERLQRIESDVTEIK 189
                                       3334444444444444444444444444444444444.......333333333333333333 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.1   1.4e+03      53      79 ..      82     111 ..      69     127 .. 0.52
   2 ?   14.4   0.3   2.3e-05      0.03      58     113 ..     125     180 ..      96     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                              COG2  53 dyadFvslSghLvg...lqeeleevespla 79 
                                        y++F+++ g+      l+++ ++++  ++
  gi|330508697|ref|YP_004385125.1|  82 SYEEFFKVAGERETdarLDQAADYLKELIS 111
                                       566666666542111112333333333333 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.3e-05
                              COG2  58 vslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                        s++++L g+ + l+e++ +  ++ ++++++re++      ++s l+ ++e + +r
  gi|330508697|ref|YP_004385125.1| 125 DSMGSKLDGMSSFLKEISGKQDQIIDRIDDAREEIVSEVCGMRSDLKSRTEERLQR 180
                                       47899********************************************9999887 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.11   1.5e+02      37      89 ..      63     117 ..      45     121 .. 0.79
   2 ?   13.8   0.0   4.9e-05     0.063       6      87 ..      99     183 ..      97     194 .] 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTT.HTTHHHHHHHHHHHHHHH CS
                          Spectrin  37 qallkkhkaleaelaaqqervkalnelaekl.ldeg.hsaseeieerleelnerW 89 
                                       ++ l + +++eae++ + +  ++  ++a +  +d+  ++a+++++e +++++e +
  gi|330508697|ref|YP_004385125.1|  63 KNTLIDVEEIEAEFSGANGSYEEFFKVAGEReTDARlDQAADYLKELISAVREGF 117
                                       3444488999999999999999999999999777778889999999999998876 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.9e-05
                                       HHHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTT....HTTHHH CS
                          Spectrin   6 faqdadeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqer.vkalnelaeklldeg....hsasee 77 
                                       + q ad l+e i+  +e    +d g++l+++ ++l+ +  + +e++ +q++ ++++++  e++++e      + + +
  gi|330508697|ref|YP_004385125.1|  99 LDQAADYLKELISAVREGF--RDNGSKLDSMGSKLDGMSSFLKEISGKQDQiIDRIDDAREEIVSEVcgmrSDLKSR 173
                                       67899999999**999999..999***********************666626999999999988884444555566 PP

                                       HHHHHHHHHH CS
                          Spectrin  78 ieerleelne 87 
                                       +eerl+ +++
  gi|330508697|ref|YP_004385125.1| 174 TEERLQRIES 183
                                       6666666665 PP

>> DUF1115  Protein of unknown function (DUF1115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     4e-05     0.051      11      65 ..      15      68 ..       6     122 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-05
                           DUF1115 11 pkhrfkvdknAkqlsltGvvllg.pkfnlvvveGgekaikkYkklmlrrikWteee 65
                                         r kv + A   +l+G v+   ++   +v+eG e +++++ + +  rik t ++
  gi|330508697|ref|YP_004385125.1| 15 AGYRSKVVTIARVFGLKGYVMNLsDSRVKIVAEGHEADLERFLEAI--RIKNTLID 68
                                      56799*************77766666689*************9999..88866444 PP

>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.1   2.6e+03      24      61 ..       3      42 ..       1      63 [. 0.57
   2 ?   12.1   0.4   0.00016       0.2      10      42 ..      87     119 ..      83     185 .. 0.84
   3 ?   -1.1   0.0         2   2.6e+03      19      29 ..     175     185 ..     158     193 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.1
                              ZapA 24 eaaklvdekikeireaggnlseerllvm..aaLnladell 61
                                      ++ ++v  k+++   ++++++  r+  +    +nl+d   
  gi|330508697|ref|YP_004385125.1|  3 KLTAYVSGKVQMAGYRSKVVTIARVFGLkgYVMNLSDSRV 42
                                      6667777777776666666665555544444445555444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00016
                              ZapA  10 ytlaceegeeeylreaaklvdekikeireaggn 42 
                                       +++a+e++  ++l +aa+++ e i+++re ++ 
  gi|330508697|ref|YP_004385125.1|  87 FKVAGERETDARLDQAADYLKELISAVREGFRD 119
                                       789**************************9994 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2
                              ZapA  19 eeylreaaklv 29 
                                       ee+l++++  v
  gi|330508697|ref|YP_004385125.1| 175 EERLQRIESDV 185
                                       55555555444 PP

>> Cbl_N  CBL proto-oncogene N-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.25      27     102 ..      99     171 ..      80     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                       --SSSS-HHHHHHHHHHHHHHHHHHS..-HHHHTT-HHHHHHHHHHHHHHHHHHHHHHTTHHHHT-TTSHHHHHHH CS
                             Cbl_N  27 LknspPylldllpdtaqlLrevaekrrekeealseaeylriflanllkkskqvakLfkeakeklfeeeselRrqLt 102
                                       L ++  yl++l++ +++ +r+  +k    ++ +s+ + ++ fl+++  k +q++  + +a+e++ +e   +R +L 
  gi|330508697|ref|YP_004385125.1|  99 LDQAADYLKELISAVREGFRDNGSKL---DSMGSKLDGMSSFLKEISGKQDQIIDRIDDAREEIVSEVCGMRSDLK 171
                                       55555566666666666555544432...444899999*********************************99986 PP

>> Glyco_hydro_85  Glycosyl hydrolase family 85
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00019      0.24      83     128 ..      17      63 ..       4      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHHT--EEEEEEEE-...STTGGGHHHHHHHHHHHHHH CS
                    Glyco_hydro_85  83 vadkLielAkyygFdGwliNiEta.lkalskekaeklkefleylree 128
                                       +  k + +A+ +g  G+ +N   + +k + + + ++l++fle +r +
  gi|330508697|ref|YP_004385125.1|  17 YRSKVVTIARVFGLKGYVMNLSDSrVKIVAEGHEADLERFLEAIRIK 63 
                                       66799****************99989889999999******998855 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       0.7     9e+02      40      58 ..      92     110 ..      62     117 .. 0.64
   2 ?   11.5   1.1    0.0002      0.26      17      57 ..     148     188 ..     134     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.7
                           DUF5446  40 eekeeerldllekElkdLv 58 
                                       e + ++rld+  + lk+L 
  gi|330508697|ref|YP_004385125.1|  92 ERETDARLDQAADYLKELI 110
                                       4456777777777777775 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0002
                           DUF5446  17 iEeeltevEkelseavneteaekeekeeerldllekElkdL 57 
                                       i + ++ + +e+ + v   +   ++  eerl+++e+ + ++
  gi|330508697|ref|YP_004385125.1| 148 IIDRIDDAREEIVSEVCGMRSDLKSRTEERLQRIESDVTEI 188
                                       5578999*******************************996 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.8   7.5e+03      41      49 ..      67      75 ..      57      81 .. 0.54
   2 ?    2.3   0.1      0.14   1.8e+02      15      41 ..     135     161 ..     129     163 .. 0.81
   3 ?    6.8   0.3    0.0057       7.2       4      33 ..     164     193 ..     161     194 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.8
                              YojJ 41 celesirek 49
                                       + e+i  +
  gi|330508697|ref|YP_004385125.1| 67 IDVEEIEAE 75
                                      233333333 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                              YojJ  15 keeLeqiekeleevlkaldeedeClLc 41 
                                          L++i+++ +++++ +d   e + +
  gi|330508697|ref|YP_004385125.1| 135 SSFLKEISGKQDQIIDRIDDAREEIVS 161
                                       566999**********99988776655 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0057
                              YojJ   4 kcleeelkeklkeeLeqiekeleevlkald 33 
                                       +   + lk+ + e L+ ie ++ e+ +++ 
  gi|330508697|ref|YP_004385125.1| 164 CGMRSDLKSRTEERLQRIESDVTEIKAKMR 193
                                       666789*******************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.51
# Mc/sec: 1142.70
//
Query:       gi|330508698|ref|YP_004385126.1|  [L=278]
Description: hypothetical protein MCON_2969 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-12   46.8   0.3    7.5e-12   45.6   0.3    1.7  1  LTD       Lamin Tail Domain
  ------ inclusion threshold ------
       0.24   11.5   2.0       0.37   10.9   2.0    1.2  1  CBP_BcsO  Cellulose biosynthesis protein BcsO


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.3   8.4e-16   7.5e-12       3     110 ..     157     257 ..     155     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 8.4e-16
                               LTD   3 aaagdvvIsevmedgagnnanefvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsgttsasn 78 
                                       a++ +v I++v++ +++    ++v+++N    ++d++gw+le a    ++fp+   +l+ g ++ v++g g+ +a++
  gi|330508698|ref|YP_004385126.1| 157 APSVKVTIARVVDTPGD----KYVQVANEAVGEWDMTGWTLESAGVAtFVFPQL--VLEDGTSIKVHEGMGAGTATD 227
                                       67889********9944....************************99*******..6************88887777 PP

                               LTD  79 gskasssavwnnggdavaLydasgevvdsvgy 110
                                        +++s+++ w +    v+L+da+g++ +s+++
  gi|330508698|ref|YP_004385126.1| 228 IYTNSTEPLWVD--NIVTLKDAAGNILTSYDV 257
                                       777777777765..4888********999876 PP

>> CBP_BcsO  Cellulose biosynthesis protein BcsO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.0   4.1e-05      0.37      94     172 ..      42     117 ..      26     132 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.1e-05
                          CBP_BcsO  94 raaqislfnallaslasaesvsiiaPvtiasrePvsapqpaaltiet.vppatvrphplasaaavseasaaseasrf 169
                                        ++  ++ n  + + a+a    i    +     Pv++  p    +et v  + v   p+ +++a   a a+  asrf
  gi|330508698|ref|YP_004385126.1|  42 LTNATNVTNMTAVTNATAAIETINVTEAPVEEVPVVE-TPV---VETpVVDTPVNETPMNETPAEEVAVATETASRF 114
                                       4455666666666666666655543333333356666.333...444133334455699999999999999****** PP

                          CBP_BcsO 170 kkl 172
                                       k+l
  gi|330508698|ref|YP_004385126.1| 115 KQL 117
                                       **8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2014.00
//
Query:       gi|330508699|ref|YP_004385127.1|  [L=75]
Description: hypothetical protein MCON_2970 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.5   0.2      0.035   13.5   0.2    1.1  1  DUF2391   Putative integral membrane protein (DUF2391)
      0.036   14.1   0.6       0.04   13.9   0.6    1.1  1  TAP35_44  Tapetum specific protein TAP35/TAP44


Domain annotation for each model (and alignments):
>> DUF2391  Putative integral membrane protein (DUF2391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   3.9e-06     0.035     107     145 ..      14      51 ..       3      72 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-06
                           DUF2391 107 avplaiGvalaralLggdeeeeeeeekeeeeeaatladl 145
                                        ++l+iG+al++++L++d +++e+e+++ ++  + ++++
  gi|330508699|ref|YP_004385127.1|  14 LMALSIGAALSEEVLDEDLNASENESTNMTNV-TNMTNV 51 
                                       4789*************977776666552222.233332 PP

>> TAP35_44  Tapetum specific protein TAP35/TAP44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   4.5e-06      0.04       1      56 [.       1      53 [.       1      68 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-06
                          TAP35_44  1 mskiskvsslclllilltflssqlvlslrspklqseaaaseqtkvddsssmakide 56
                                      ms   k+ss  +l+ ll+ ls   +ls  ++    +a++ e+t++ + + m+++ +
  gi|330508699|ref|YP_004385127.1|  1 MS---KISSGLVLFSLLMALSIGAALSEEVLDEDLNASENESTNMTNVTNMTNVTN 53
                                      55...5555559999*************************************9943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1402  (0.0781973); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 526.64
//
Query:       gi|330508700|ref|YP_004385128.1|  [L=443]
Description: cobyrinic Acid a,c-diamide synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-40  138.7   0.0    2.5e-40  138.2   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    1.2e-17   64.4   0.1    6.3e-11   42.5   0.0    2.2  2  AAA_26         AAA domain
    2.7e-16   59.8   0.0    4.4e-16   59.1   0.0    1.4  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
      0.003   17.2   0.0     0.0045   16.7   0.0    1.2  1  Peptidase_S51  Peptidase family S51
  ------ inclusion threshold ------
      0.046   13.6   0.0      0.078   12.8   0.0    1.3  1  SNO            SNO glutamine amidotransferase family
       0.12   11.6   0.0       0.21   10.8   0.0    1.3  1  DUF1611        Domain of unknown function (DUF1611_C) P-loop 


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2   0.0   8.5e-44   2.5e-40       1     192 [.     240     426 ..     240     429 .. 0.92

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 8.5e-44
                          GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeag 75 
                                       +i+v+r++a+ +y+  +l  Le++++  v+f+p  +++l +d+d ++++Gg++++ + +l+r+   +++ik+a+e+g
  gi|330508700|ref|YP_004385128.1| 240 RIGVARDRAFCFYYheNLLELERHGADLVYFSP-LEDKL-PDVDGLYIGGGYPELYASQLERA-PARKQIKKASEDG 313
                                       69*******************************.88899.56********************9.899********** PP

                          GATase_3  76 gpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel........aaegeevkGyEi 144
                                       +p++g+CGGl++LG  +e + g      + ++ g L+++t +ek +l+    g+v++        a  g  ++G+E+
  gi|330508700|ref|YP_004385128.1| 314 MPIYGECGGLMYLGAALESEAG------SFKMAGALPCTTFMEK-RLM--ALGYVKAevsernplADVGRSLRGHEF 381
                                       *****************99876......7**************9.888..5666555668899887778******** PP

                          GATase_3 145 HsGrtilkekakpllkvkvggnng.ekdGavkksedgnvlGtYlHglfd 192
                                       H++r i +++a+  lk+++g+++  ++dG+v++    n+++ YlH +f 
  gi|330508700|ref|YP_004385128.1| 382 HYSRCICDRDARYCLKLSRGKGIAdGRDGLVEN----NTMAGYLHTHFY 426
                                       *****************88666667******77....**********96 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2     2e-07    0.0006       4      30 ..       2      28 ..       1      37 [. 0.88
   2 !   42.5   0.0   2.1e-14   6.3e-11      97     194 ..      75     175 ..      59     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2e-07
                            AAA_26  4 fvtgtdtgvGKTvvslgLvralkrkgv 30
                                      +++gt  gvGKT+++lgL++al+++g 
  gi|330508700|ref|YP_004385128.1|  2 LIAGTHSGVGKTTITLGLMAALRARGL 28
                                      79********************88876 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 2.1e-14
                            AAA_26  97 kdadivvVEGagglgvp..iteellnadiaknlgapvilVargglgtinqllltiealr.qknvrvlGvilNkvrnp 170
                                       + ad+ vVEG+ gl ++   te  ++a++ak l++pv+lV++++  +  ++++ + ++  + +vr++G ilN+v ++
  gi|330508700|ref|YP_004385128.1|  75 EGADVAVVEGVMGLFDGmdGTEVGSTAQVAKILDIPVLLVINVHGMSRSAAAMELGFASyDPGVRLAGTILNRVGSK 151
                                       56899**********9944567799********************99999999999998467*************** PP

                            AAA_26 171 envetlekksgipvlGvvPylpdl 194
                                       + +++l++    pv+G++P ++++
  gi|330508700|ref|YP_004385128.1| 152 RHLDMLKSCLAKPVFGALPRDKEM 175
                                       *******************99986 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 !   59.1   0.0   1.5e-19   4.4e-16       2     126 ..       2     182 ..       1     185 [. 0.87

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 1.5e-19
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH........HTTEB-HHHH................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxx................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai........leglendiep................ 54 
                                       +ia+t +GvGKTt++++L++al  rgl V++++++p+    ++                                  
  gi|330508700|ref|YP_004385128.1|   2 LIAGTHSGVGKTTITLGLMAALRARGLVVQPYKVGPDFIDPSHhtaicgrpS--------Lnldpfmmseegvrrsf 70 
                                       79***********************************777776554433330........1446677777777779* PP

                                       .............................................CCHCCCHHHHHHCHCHHHH.....EEEEEEEE CS
                                       .............................................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxx RF
                              CbiA  55 .............................................dlkrllellealgkkkall...lkiagvvlnr 83 
                                                                                    ++  ++++++a+  ++a     +++ag +lnr
  gi|330508700|ref|YP_004385128.1|  71 fsalegadvavvegvmglfdgmdgtevgstaqvakildipvllviNVHGMSRSAAAMELGFASYdpgVRLAGTILNR 147
                                       ************************************************************9999************* PP

                                       ESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  84 vdgeneetllkealeelkqrygvpvlgviprdeavaeaparge 126
                                       v+++++  +lk+ l       + pv+g +prd++  e  +r++
  gi|330508700|ref|YP_004385128.1| 148 VGSKRHLDMLKSCL-------AKPVFGALPRDKEM-EMKSRHL 182
                                       **997777666666.......66**********97.7777765 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.5e-06    0.0045      76     136 ..     273     333 ..     257     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GGG CS
                     Peptidase_S51  76 ieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesiett 136
                                       +e+kl + d++y+gGG     +++l++  + k +++a ++g+++ G   G +  g  +e++
  gi|330508700|ref|YP_004385128.1| 273 LEDKLPDVDGLYIGGGYPELYASQLERAPARKQIKKASEDGMPIYGECGGLMYLGAALESE 333
                                       789999*****************************************99999888777665 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.6e-05     0.078      29      88 ..     275     333 ..     252     344 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                                       GGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB CS
                               SNO  29 edlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelene 88 
                                       ++l +vd+l i GG     +  +er    +++++  +++  +++G C Gl++l + le+e
  gi|330508700|ref|YP_004385128.1| 275 DKLPDVDGLYIGGGYPELYASQLERAPARKQIKKASEDG-MPIYGECGGLMYLGAALESE 333
                                       6799**********9999999999999777776666655.**************999987 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 ?   10.8   0.0     7e-05      0.21      16      45 ..       2      31 ..       1      41 [. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7e-05
                           DUF1611 16 lvvGTdcavGKrttaleleealeerGlkaa 45
                                      l+ GT + vGK t +l l +al++rGl ++
  gi|330508700|ref|YP_004385128.1|  2 LIAGTHSGVGKTTITLGLMAALRARGLVVQ 31
                                      899***********************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3192.93
//
Query:       gi|330508701|ref|YP_004385129.1|  [L=246]
Description: hypothetical protein MCON_2972 [Methanosaeta concilii GP6]
Scores for complete 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  218.3   0.0      1e-64  218.1   0.0    1.0  1  DUF166         Domain of unknown function
     0.0014   19.1   0.0     0.0024   18.3   0.0    1.4  1  CoA_binding_2  CoA binding domain
     0.0096   16.0   0.0      0.026   14.7   0.0    1.7  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 !  218.1   0.0   1.7e-68     1e-64       2     219 ..       5     219 ..       4     220 .. 0.99

  Alignments for each domain:
  == domain 1  score: 218.1 bits;  conditional E-value: 1.7e-68
                            DUF166   2 vltsgeyGervvenilnepdferslivavvevpeeldefiedpeelLpe......lkeaDiviaytlhpDlllelae 72 
                                       v+++g+yGer+ e+i++++dfe    v+ v+vpe l+ fiedpee+++e      +++aD++i yt hpDl+ e+++
  gi|330508701|ref|YP_004385129.1|   5 VIKRGKYGERLLETIKDHTDFE----VVSVDVPEILPGFIEDPEEFVRElnldpqIFQADLLILYTFHPDLTPEIVR 77 
                                       899*******************....*************************************************** PP

                            DUF166  73 kakekkvkalivpaeapkaglrkelkekleelgievavpkpfCsleeegkpkideFleefGkPelevevkdgkikkV 149
                                        a +++vka+i+p   ++ag + el++ +e  +i+++v++++C+lee g p id+F++++GkPelev+ kdgki+ V
  gi|330508701|ref|YP_004385129.1|  78 LAGKEGVKAVIIPGGIGRAGSITELEKIAEVHNIHIEVDEICCTLEECGVPAIDQFAKKLGKPELEVQTKDGKISGV 154
                                       ***************************************************************************** PP

                            DUF166 150 eVlrsapCGstwyvakklkGkeveeaeekageahqsYpClAsmerdfelketklhkAgyihkeavekAlk 219
                                       +Vlr++pCG+tw++a +++Gk v ea++  g+ +q+YpC+A+++     + +++h++g++hk+a+e+Al+
  gi|330508701|ref|YP_004385129.1| 155 RVLRGSPCGATWHAATDIVGKTVAEAPSLTGLFCQQYPCRAVRG-----GPGGIHTSGDLHKDAMERALG 219
                                       ********************************************.....*******************97 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.1e-07    0.0024      11     106 ..       7     114 ..       1     124 [. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.1e-07
                                       -TTSHHHHHHHHHHHHT.--EEEESSS-...SEETT.EES----T......T--EEEE-S.-HHHHGGGHHHHHHH- CS
                     CoA_binding_2  11 npgkfgykvlryllehg.lpvvpVnpke...eeilg.ekvyaslae.d.pepvdlvdvft.ppeatpeivkealalg 79 
                                       ++gk+g ++l+ +++h  ++vv V   e   + i+  e+ +++l+  +   + dl+ ++t +p+ tpeiv+ a+++g
  gi|330508701|ref|YP_004385129.1|   7 KRGKYGERLLETIKDHTdFEVVSVDVPEilpGFIEDpEEFVRELNLdPqIFQADLLILYTfHPDLTPEIVRLAGKEG 83 
                                       679************776999999888888877777566788888534678888777776599************** PP

                                       -SEEEE-TT....---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  80 akavwlqpg....sedeeaaelaeeagirvv 106
                                       +kav++  g        e+ ++ae ++i ++
  gi|330508701|ref|YP_004385129.1|  84 VKAVIIPGGigraGSITELEKIAEVHNIHIE 114
                                       ******9997776555666666666766655 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.3e-06     0.026       9     114 ..       8     107 ..       1     115 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.3e-06
                                       TSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S.-HHHHHHHH CS
                            DapB_N   9 sGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFT.tpeavlenl 84 
                                       +G+ G+++++++++++d+e+v++   +  +            ++ ++  + +l+  + +ad li +T +p+ + e +
  gi|330508701|ref|YP_004385129.1|   8 RGKYGERLLETIKDHTDFEVVSVDVPEILPGF--------IEDPEEFVRELNLDPQIFQADLLILYTfHPDLTPEIV 76 
                                       6*******************998444332222........2235666667899999999********99******** PP

                                       HHHHHTT-EEEE--SS-.-HHHHHHHHHHTT CS
                            DapB_N  85 klalekgvklViGTTGl.seeelaeleelak 114
                                       +la ++gvk+Vi   G+  +  + ele++a+
  gi|330508701|ref|YP_004385129.1|  77 RLAGKEGVKAVIIPGGIgRAGSITELEKIAE 107
                                       ************8888764555566655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 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:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1724.82
//
Query:       gi|330508702|ref|YP_004385130.1|  [L=299]
Description: fumarase subunit alpha [Methanosaeta concilii GP6]
Scores for complete 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-92  308.8   0.0    3.7e-92  308.6   0.0    1.0  1  Fumerase  Fumarate hydratase (Fumerase)


Domain annotation for each model (and alignments):
>> Fumerase  Fumarate hydratase (Fumerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.6   0.0   2.1e-96   3.7e-92       2     268 ..      14     295 ..      13     297 .. 0.95

  Alignments for each domain:
  == domain 1  score: 308.6 bits;  conditional E-value: 2.1e-96
                          Fumerase   2 eaveealkeastelpedvlealkkalekEesenakevleqlleNaeiAaeeklplCqDTGiavvfvkigeevevetg 78 
                                       +a+ +al +a+t+lp++vle++k+ le+E++++a+++l+ +l+N+++A ++ lp+CqDTG+a+++v +g+++ + + 
  gi|330508702|ref|YP_004385130.1|  14 DATVRALYRAETSLPPWVLERIKEGLERETNPLARSQLQFMLDNVSLAGSRGLPICQDTGLAIFHVLMGQDL-ILDF 89 
                                       678899*****************************************************************9.6999 PP

                          Fumerase  79 dleeaineGvreaykegplRksvvadplerkntgd....nlPavihielvpgdeleitvlakGgGsenksklkmlnp 151
                                       dl+eai++Gvr+a+++ plR+++v dpl+r+n++d    ++P  i +++ +g++l+it+++kG+Gsen+s ++mlnp
  gi|330508702|ref|YP_004385130.1|  90 DLQEAIAQGVRRATSQIPLRPNAV-DPLTRENSKDntgpGMP-DIILDQARGQSLSITAFPKGAGSENMSLVMMLNP 164
                                       ************************.**********8888889.9999999*************************** PP

                          Fumerase 152 sdglegvkkfvletvkeagtnaCpPlvlgvgiGgtseeaallakkallrelgeenpdee.................l 211
                                       +d   + ++f++++v+e  +naCpPl+lg+giGg+++ aa+lak+all+ ++ +  ++e                 +
  gi|330508702|ref|YP_004385130.1| 165 AD---DPMEFIVDAVRERAANACPPLFLGIGIGGSFDLAARLAKHALLNMHRIQPYSQEssqradrsitlttspeeI 238
                                       76...******************************************888877775555567788888888888777 PP

                          Fumerase 212 aeleeellekinklgiGpqGlGGkttvldvkierlprhiAslpvavnvsCsadRrak 268
                                       ++lee+l++++n+lgiGp+GlGG+ttvl+ +ie++ +h+Aslpva+n++C+a+R+a+
  gi|330508702|ref|YP_004385130.1| 239 KKLEESLMKRLNNLGIGPMGLGGDTTVLGLRIEKALCHTASLPVAINFQCWANRSAT 295
                                       ******************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2201.89
//
Query:       gi|330508703|ref|YP_004385131.1|  [L=178]
Description: fumarase subunit beta [Methanosaeta concilii GP6]
Scores for complete 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-32  111.4   0.0      5e-32  110.9   0.0    1.1  1  Fumerase_C  Fumarase C-terminus


Domain annotation for each model (and alignments):
>> Fumerase_C  Fumarase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.0   2.8e-36     5e-32      32     205 ..       6     166 ..       2     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 2.8e-36
                        Fumerase_C  32 LnqketeeelskykvgtrlllsGkllvaRDaaHkrlkerlekgeelpeyvklkdrviYyaGPvktpedeavgsaGPT 108
                                       L+++  +e+++k+++g+ + l+Gk+++aRD aH+ ++   ++g+++p    l++ ++Y++GP+ +  d  v saGPT
  gi|330508703|ref|YP_004385131.1|   6 LHTPLCQEDVKKLNAGDIVFLKGKVFTARDKAHALIR---RQGSPVP----LEGAALYHCGPIIQ--DDSVISAGPT 73 
                                       7778899*****************************9...6899999....67*********965..556789**** PP

                        Fumerase_C 109 TatRmdkyvekllkktgllimlaKgnrskkvleaikkhggvYLgaiGG.aAilakkaikkvevvefeelGm.EAiye 183
                                       T++Rm +y++++l+  g+ ++++Kg+   +       +++vYL   GG +A  a++   +++ v+f+elGm E i+e
  gi|330508703|ref|YP_004385131.1|  74 TSGRMARYTDEILA-LGVKAIIGKGGLPGEPF----LNRAVYLAYPGGcGAAAASQ--LRIRAVHFPELGMaESIWE 143
                                       *************8.79********9866654....3689********75555544..357899************* PP

                        Fumerase_C 184 ievedf.pafvvvddkGndlfke 205
                                       +e ed+ p +v+vd+ G dl+++
  gi|330508703|ref|YP_004385131.1| 144 LEAEDLgPMVVAVDSYGRDLYQD 166
                                       *****988999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1420.15
//
Query:       gi|330508704|ref|YP_004385132.1|  [L=199]
Description: hypothetical protein MCON_2975 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-45  154.9   0.0    2.1e-45  154.5   0.0    1.2  1  DUF5616   Domain of unknown function (DUF5616)
    1.3e-11   44.0   0.1    2.1e-11   43.3   0.1    1.4  1  DUF434    Protein of unknown function (DUF434)
     0.0065   16.9   0.2      0.028   14.9   0.1    2.1  2  DUF2664   Protein of unknown function (DUF2664)


Domain annotation for each model (and alignments):
>> DUF5616  Domain of unknown function (DUF5616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.5   0.0   3.6e-49   2.1e-45       2     139 ..      49     186 ..      48     187 .. 0.99

  Alignments for each domain:
  == domain 1  score: 154.5 bits;  conditional E-value: 3.6e-49
                           DUF5616   2 eelkgkelliDGfNvlitlesalsgevlllcdDgviRDlagvrgkyklveeteealelilellkelkvkkvifllDk 78 
                                       e+lk+++++iDG+Nvlit+es+l g++++ cdDg++RD +g++++yk+++ t  al++il+ll++++++++++llD+
  gi|330508704|ref|YP_004385132.1|  49 EDLKDQTIFIDGYNVLITTESLLGGHPVYSCDDGFLRDSRGIFRSYKISSLTALALNQILDLLAQAGPARTEVLLDQ 125
                                       799************************************************************************** PP

                           DUF5616  79 pvSnSgelaklireileeaglegevelvknvDkeLkeseeivatsDsvildkvksvldlaa 139
                                       ++S+Sge+a+li+ ++++++l g+++++++vD+ Lk++++iv tsD+ ++d+ ++v+dl++
  gi|330508704|ref|YP_004385132.1| 126 QMSRSGEMAELIKGMMADRHLCGTARTARDVDRLLKATRGIVLTSDGNVIDSLDHVMDLPR 186
                                       ***********************************************************98 PP

>> DUF434  Protein of unknown function (DUF434)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.1   3.5e-15   2.1e-11      13      56 .]       1      44 [.       1      44 [. 0.96

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 3.5e-15
                            DUF434 13 LnRGYpkksalelVgnhYqLskrqRlaLaRcvssdeeiearksK 56
                                      ++RGYpk+sa+++++nh++L  ++R ++ R+++ ++ ++ r+s+
  gi|330508704|ref|YP_004385132.1|  1 MDRGYPKDSAVRFISNHHRLAIEERFIMMRVIVRSDVAQIRRSR 44
                                      69***************************************985 PP

>> DUF2664  Protein of unknown function (DUF2664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   4.7e-06     0.028      14      45 ..      11      42 ..       5      59 .. 0.81
   2 ?   -1.6   0.0      0.63   3.8e+03      48      84 ..      78     112 ..      74     114 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.7e-06
                           DUF2664 14 kirlGerhrLsvqqalivarviikedtaesqr 45
                                       + + ++hrL+++  +i++rvi+++d a+ +r
  gi|330508704|ref|YP_004385132.1| 11 VRFISNHHRLAIEERFIMMRVIVRSDVAQIRR 42
                                      5667789*******************998666 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.63
                           DUF2664  48 sslaafLdkqkaalrvelkalkqLekldvDeilDsla 84 
                                       s+  +fL + + + r    ++  L  l  ++ilD la
  gi|330508704|ref|YP_004385132.1|  78 SCDDGFLRDSRGIFRSY--KISSLTALALNQILDLLA 112
                                       66777777777777653..455667777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1602.10
//
Query:       gi|330508705|ref|YP_004385133.1|  [L=149]
Description: hypothetical protein MCON_2976 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.041   14.0   0.2      0.041   14.0   0.2    2.2  2  Imm72     Immunity protein 72


Domain annotation for each model (and alignments):
>> Imm72  Immunity protein 72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   2.3e-06     0.041      40      67 ..      43      70 ..      34      75 .. 0.85
   2 ?   -0.3   0.9     0.069   1.2e+03      56      67 ..      73      84 ..      71      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-06
                             Imm72 40 GskaydvllestddlrdvrWrlvWedtr 67
                                      G+  y   + +tdd++ v W l+W+d++
  gi|330508705|ref|YP_004385133.1| 43 GMPLYRTNIFTTDDEQAVSWLLIWRDSK 70
                                      55567777888***************97 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.069
                             Imm72 56 dvrWrlvWedtr 67
                                       v Wr  W + r
  gi|330508705|ref|YP_004385133.1| 73 TVEWRWYWPEGR 84
                                      599*****9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1190.15
//
Query:       gi|330508706|ref|YP_004385134.1|  [L=239]
Description: glucose-6-phosphate isomerase [Methanosaeta concilii GP6]
Scores for 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  150.0   0.0    4.9e-44  149.8   0.0    1.1  1  GPI       Glucose-6-phosphate isomerase (GPI)
     0.0021   17.7   0.0     0.0055   16.4   0.0    1.7  1  Cupin_2   Cupin domain


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 !  149.8   0.0   5.4e-48   4.9e-44      22     174 ..      32     182 ..      14     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 5.4e-48
                               GPI  22 etldddvaYevsdslktaeegerlaadqliydvtvilPgkiGeEriktrGHyHkevd.rrstrPEvYevlkGealml 97 
                                          +++ +Y+++d + +  +g++l++++l+yd+t+i+Pg +G E+ikt GHyH+       t+PE+Yevl+Geal+l
  gi|330508706|ref|YP_004385134.1|  32 GRENFELYYMFRDLFLSRADGDKLRDQNLRYDITIIPPGMMGSEYIKTAGHYHPLAPgSAVTYPELYEVLEGEALYL 108
                                       45689*************************************************9888999**************** PP

                               GPI  98 LekPeglkvddvivvevkartvvivPPnygHvsinigeedLvmanlvpkdagqdYdviakarGmaayiieegevlrk 174
                                       L+k +     dv+ ++  a++ v+vPPnygH++in +++ L m+n+v +d+++ Yd+i+ ++G a+ +  +g  + +
  gi|330508706|ref|YP_004385134.1| 109 LQKEDL---SDVVAINAAAGDKVLVPPNYGHITINRSNKTLKMSNFVARDFSSLYDPIKEKGGGAYFFTRDGWIKNP 182
                                       ***998...9*******************************************************999988866555 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.1e-07    0.0055      21      67 ..      96     148 ..      82     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.1e-07
                                       EEEEEEESEEEEEECTE......EEEEETTEEEEE-TT-EEEEEE-SSS-EEE CS
                           Cupin_2  21 effyVleGegeltvdge......eveleaGdsvyfpagtpHrfrNtgdeparl 67 
                                       e++ VleGe+ + +  e       +   aGd v++p++  H  +N++++ +++
  gi|330508706|ref|YP_004385134.1|  96 ELYEVLEGEALYLLQKEdlsdvvAINAAAGDKVLVPPNYGHITINRSNKTLKM 148
                                       777899999999988777888889999**********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        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 0.18s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 2005.23
//
Query:       gi|330508707|ref|YP_004385135.1|  [L=312]
Description: UbiA family prenyltransferase [Methanosaeta concilii GP6]
Scores for complete 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  144.9  18.4    3.1e-42  144.6  18.4    1.1  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.6  18.4   1.8e-46   3.1e-42       4     246 ..      31     278 ..      26     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 1.8e-46
                              UbiA   4 palvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilg 80 
                                       +al+++ + +g  p+l  +++++lg ++a+++++++Nd  D+e D+     p RPl+s ++++++a  ++i+l++++
  gi|330508707|ref|YP_004385135.1|  31 SALLAVYAVEGTLPPLIPFVIAVLGSYCAITSSYVYNDCCDIEVDKV--GMPCRPLPSAKLNKRQAQSWSIFLFLVA 105
                                       455555555566677789*****************************..**************************** PP

                              UbiA  81 llllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgsl........sllallla 149
                                       l+ + l+lnp +++ +++a +l+ +Y+  + Kr t++  +++g+++gl+pl+ w a+            +++ l+la
  gi|330508707|ref|YP_004385135.1| 106 LSAA-LYLNPESFVALVAATILASIYS-AWAKRNTPFSWIFVGLSYGLVPLGVWLAMEPAGilkagagiHPASLILA 180
                                       ****.**********************.6***************************7776677888888******** PP

                              UbiA 150 lavflltwaialandlrdregDrkagiktlpvvlGrkaarillalllavllla.llllllalllllylllalllaal 225
                                       +++ +  w++  + + rd+egDr+ gi+t+p+++G ++++ ++al++++ +++ ++l l+ +l+++y+++a++++++
  gi|330508707|ref|YP_004385135.1| 181 AMICITDWGFTNCDASRDVEGDRREGIPTTPATFGIAVTAKMVALFWLAGIALsIALGLASGLGWFYFIAAIVSGGW 257
                                       *****************************************844444444444355666666666666666666666 PP

                              UbiA 226 allraarlvrrrdakkaakff 246
                                       +l     +vr  +ak++++ff
  gi|330508707|ref|YP_004385135.1| 258 LLSQNQDFVRHPTAKRGEQFF 278
                                       666666677777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2302.54
//
Query:       gi|330508708|ref|YP_004385136.1|  [L=181]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   4.4        1.9    8.3   0.2    3.8  5  YL1_C     YL1 nuclear protein C-terminal domain
      0.077   13.0   1.8         32    4.6   0.0    3.3  4  PepSY_2   Peptidase propeptide and YPEB domain
      0.088   13.7   0.2       0.31   12.0   0.2    2.0  1  EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
       0.13   12.3   5.0        1.8    8.7   5.0    2.4  1  OCRE      OCRE domain


Domain annotation for each model (and alignments):
>> YL1_C  YL1 nuclear protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.2   5.4e+03      19      26 ..     103     110 ..     103     111 .. 0.86
   2 ?    5.2   0.1    0.0041        18      11      17 ..     112     118 ..     108     120 .. 0.92
   3 ?    8.3   0.2   0.00042       1.9      11      22 ..     124     135 ..     123     137 .. 0.93
   4 ?   -1.6   0.0      0.54   2.4e+03      11      17 ..     136     142 ..     135     144 .. 0.86
   5 ?   -0.3   0.0      0.21   9.2e+02      11      17 ..     148     154 ..     147     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                             YL1_C  19 pYanveay 26 
                                       pY +  ay
  gi|330508708|ref|YP_004385136.1| 103 PYGDTPAY 110
                                       89999999 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0041
                             YL1_C  11 YrDPkTg 17 
                                       Y+DP+Tg
  gi|330508708|ref|YP_004385136.1| 112 YFDPVTG 118
                                       ******9 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00042
                             YL1_C  11 YrDPkTgLpYan 22 
                                       Y DP Tg  Y++
  gi|330508708|ref|YP_004385136.1| 124 YVDPITGQHYYT 135
                                       9*********97 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.54
                             YL1_C  11 YrDPkTg 17 
                                       Y+D  +g
  gi|330508708|ref|YP_004385136.1| 136 YTDSNSG 142
                                       9**9987 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 0.21
                             YL1_C  11 YrDPkTg 17 
                                       Y+ P Tg
  gi|330508708|ref|YP_004385136.1| 148 YFNPETG 154
                                       9*****9 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.022        98       2      20 ..       8      26 ..       4      35 .. 0.77
   2 ?    1.3   0.0     0.078   3.5e+02      72      83 ..     112     123 ..     111     124 .. 0.90
   3 ?    2.4   0.0     0.036   1.6e+02      66      79 ..     118     131 ..     115     135 .. 0.91
   4 ?    4.6   0.0    0.0071        32      60      81 ..     136     157 ..     128     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.022
                           PepSY_2  2 aalalalallaaaAlAgrr 20
                                      a+++l+++ll + AlA+++
  gi|330508708|ref|YP_004385136.1|  8 AMALLIACLLVGNALAQEN 26
                                      56778888888*****554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.078
                           PepSY_2  72 kldpatgevvke 83 
                                       ++dp+tge vk+
  gi|330508708|ref|YP_004385136.1| 112 YFDPVTGERVKT 123
                                       89******9985 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.036
                           PepSY_2  66 Gkkveikldpatge 79 
                                       G++v+ ++dp tg+
  gi|330508708|ref|YP_004385136.1| 118 GERVKTYVDPITGQ 131
                                       99**********97 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.0071
                           PepSY_2  60 egldkdGkkveikldpatgevv 81 
                                       ++   +Gk v ++++p+tge +
  gi|330508708|ref|YP_004385136.1| 136 YTDSNSGKLVYVYFNPETGEPI 157
                                       5556789************976 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   6.9e-05      0.31      37      66 ..      87     140 ..       2     148 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.9e-05
                          EphA2_TM  37 k....................skeekkeeensgkkglktYvDP......htYEDPn 66 
                                       k                    ++++  +  +++  ++ktYvDP       tY D n
  gi|330508708|ref|YP_004385136.1|  87 KnlsvmrdwlgdsfvdpygdtPAYSYFDPVTGE--RVKTYVDPitgqhyYTYTDSN 140
                                       044455555555555444432222222333333..6*******7777666777766 PP

>> OCRE  OCRE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   5.0    0.0004       1.8      12      47 ..     122     155 ..     103     175 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0004
                              OCRE  12 GyYyDpetGyYYDpntglyydsrtgr..yysydettkt 47 
                                       + Y Dp+tG +Y+    +y+ds++g+  y++++++t++
  gi|330508708|ref|YP_004385136.1| 122 KTYVDPITGQHYY----TYTDSNSGKlvYVYFNPETGE 155
                                       2445555554444....444444443335555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 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:                        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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1426.74
//
Query:       gi|330508709|ref|YP_004385137.1|  [L=161]
Description: hypothetical protein MCON_2981 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0074   17.1   1.0       0.01   16.7   1.0    1.2  1  SGP       Sulphur globule protein


Domain annotation for each model (and alignments):
>> SGP  Sulphur globule protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.0   5.7e-07      0.01      26      80 ..      86     142 ..      63     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.7e-07
                               SGP  26 dgsgdfnmnmsgrgr.grgygrGygrygygapygYgypygygaPyg..pYgagapYga 80 
                                       +++ dfn++ sg ++ g   ++Gy  y y+ p    ++y y  Py   p++    Y+ 
  gi|330508709|ref|YP_004385137.1|  86 NSWKDFNLTESGIAQvGVDPFKGYPIYAYKIPRTGETKYFYLDPYTnePFYV-DGYAG 142
                                       5689***********9****************96666999*99*98776554.45543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1176.48
//
Query:       gi|330508710|ref|YP_004385138.1|  [L=150]
Description: hypothetical protein MCON_2982 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1093.03
//
Query:       gi|330508711|ref|YP_004385139.1|  [L=76]
Description: hypothetical protein MCON_2983 [Methanosaeta concilii GP6]
Scores for complete 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-12   45.4   2.6    6.9e-12   45.2   2.6    1.0  1  MtN3_slv    Sugar efflux transporter for intercellular exchan
    1.2e-07   31.4   1.0    1.2e-07   31.4   1.0    1.7  2  PQ-loop     PQ loop repeat
  ------ inclusion threshold ------
       0.11   11.8   1.6       0.13   11.6   1.6    1.0  1  OST3_OST6   OST3 / OST6 family, transporter family
        3.3    7.5   4.8        1.4    8.7   2.4    1.5  2  Gemini_mov  Geminivirus putative movement protein


Domain annotation for each model (and alignments):
>> MtN3_slv  Sugar efflux transporter for intercellular exchange
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   2.6   1.5e-15   6.9e-12      19      85 ..       5      71 ..       2      73 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.5e-15
                          MtN3_slv 19 lsilrkiikkksveelsfllflagllsallWllYGllkkdaliiivNlvgvlleliylllflvyakk 85
                                      ++++ ki+++ sv+++s+++ l   l+ +lWllYGl ++d ++i+ N++ +l+ ++ + +++ y k+
  gi|330508711|ref|YP_004385139.1|  5 VPQILKIYRTESVSDVSLIMLLQFSLGMFLWLLYGLYIQDRILIVSNTISFLTLMVATGMYMKYRKS 71
                                      67899***********************************************************875 PP

>> PQ-loop  PQ loop repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   1.0   2.6e-11   1.2e-07      15      54 ..       2      41 ..       1      48 [. 0.92
   2 ?   -0.8   0.0       0.3   1.3e+03      44      52 ..      50      58 ..      46      63 .. 0.52

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.6e-11
                           PQ-loop 15 vsyiPQiikNykrkSteGlSilflllwllGdilsllylil 54
                                      + ++PQi+k+y++ S++ +S+ +ll   lG +l+lly + 
  gi|330508711|ref|YP_004385139.1|  2 FGFVPQILKIYRTESVSDVSLIMLLQFSLGMFLWLLYGLY 41
                                      679*********************************9875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.3
                           PQ-loop 44 Gdilsllyl 52
                                      ++++s+l+l
  gi|330508711|ref|YP_004385139.1| 50 SNTISFLTL 58
                                      444444443 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.6   2.9e-05      0.13     141     205 ..       9      70 ..       4      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                         OST3_OST6 141 irikrppnyskiiitallvlllvlllklrrklllkilksktlwavlslliillftsGymfnqIrg 205
                                       ++i+r   +s + +++ll ++l+++l l + l+   ++++ l+   ++ +  l+++  m+ + r+
  gi|330508711|ref|YP_004385139.1|   9 LKIYRTESVSDVSLIMLLQFSLGMFLWLLYGLY---IQDRILIVSNTISFLTLMVATGMYMKYRK 70 
                                       68999999*********************9999...7*************************998 PP

>> Gemini_mov  Geminivirus putative movement protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.4   0.00031       1.4      37      66 ..      20      49 ..      12      54 .. 0.76
   2 ?   -1.8   0.0       0.6   2.7e+03      40      55 ..      53      68 ..      51      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00031
                        Gemini_mov 37 vgeiailtlvavlvlYLlytlvlkDlilvl 66
                                      v  i++l +   + l+Lly l+ +D il++
  gi|330508711|ref|YP_004385139.1| 20 VSLIMLLQFSLGMFLWLLYGLYIQDRILIV 49
                                      555555555555679*************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.6
                        Gemini_mov 40 iailtlvavlvlYLly 55
                                      i++ltl+    +Y+ y
  gi|330508711|ref|YP_004385139.1| 53 ISFLTLMVATGMYMKY 68
                                      7788888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 588.89
//
Query:       gi|330508712|ref|YP_004385140.1|  [L=93]
Description: hypothetical protein MCON_2984 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 767.55
//
Query:       gi|330508713|ref|YP_004385141.1|  [L=114]
Description: ArsR family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete 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   59.9   2.1    1.7e-14   53.4   0.0    2.9  3  HTH_5            Bacterial regulatory protein, arsR family
    2.8e-11   43.3   0.1    1.2e-10   41.2   0.0    1.9  2  HTH_20           Helix-turn-helix domain
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.13   11.8   0.0    1.1  1  DNA_pol_viral_N  DNA polymerase (viral) N-terminal domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.2    0.0026        15       2      13 ..       8      19 ..       7      19 .. 0.87
   2 !   53.4   0.0   2.9e-18   1.7e-14       1      45 [.      19      63 ..      19      65 .. 0.97
   3 ?    0.2   0.0      0.12   7.1e+02       1      24 [.      78     102 ..      78     105 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0026
                                      HHHHHHHHHHTT CS
                             HTH_5  2 ptRlkILklLae 13
                                      + RlkIL++L++
  gi|330508713|ref|YP_004385141.1|  8 ELRLKILSALSD 19
                                      67********96 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 2.9e-18
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      dptRl++L +L+ ge+cvce+  ++  sqst+S HL++L ea+++
  gi|330508713|ref|YP_004385141.1| 19 DPTRLELLEYLSGGERCVCEILPAFSRSQSTISKHLNILFEADIL 63
                                      8*****************************************997 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.12
                                       SHHHHHHHHHHTT.SSEEHHHHHHH CS
                             HTH_5   1 dptRlkILklLae.gelcvcelaee 24 
                                       dp+  ++++l+ +   + +++lae+
  gi|330508713|ref|YP_004385141.1|  78 DPQVFELVRLVDQmALKQISQLAEA 102
                                       5666777777777777888888875 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   2.1e-14   1.2e-10       2      57 ..      12      66 ..      11      70 .. 0.95
   2 ?   -0.2   0.0      0.18   1.1e+03      41      52 ..      92     103 ..      80     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 2.1e-14
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +i++AL++P+R+++l +L +++++++ e+  +++ s++t+s+HL++L ea++++++
  gi|330508713|ref|YP_004385141.1| 12 KILSALSDPTRLELLEYL-SGGERCVCEILPAFSRSQSTISKHLNILFEADILDRR 66
                                      699***************.**********************************987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHCT CS
                            HTH_20  41 lsyHLrvLeeag 52 
                                       + +++ +L+eag
  gi|330508713|ref|YP_004385141.1|  92 ALKQISQLAEAG 103
                                       667788888877 PP

>> DNA_pol_viral_N  DNA polymerase (viral) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.1e-05      0.13     148     194 ..      48      95 ..      32     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                   DNA_pol_viral_N 148 akvrkylnrlykaGilykriskrlvsfk.GkPyswelqylvkqtsvrd 194
                                         + k+ln l++a il +ri  + + +    P  +el  lv q   ++
  gi|330508713|ref|YP_004385141.1|  48 STISKHLNILFEADILDRRIDGKKTLYSiKDPQVFELVRLVDQMALKQ 95 
                                       567899*************9877666651579999********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 872.92
//
Query:       gi|330508714|ref|YP_004385142.1|  [L=361]
Description: permease [Methanosaeta concilii GP6]
Scores for complete 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-74  248.2  21.9    1.9e-73  247.2  21.9    1.5  1  ArsP_1           Predicted permease
  ------ inclusion threshold ------
      0.035   13.8   0.1      0.035   13.8   0.1    4.4  4  Phage_holin_2_3  Bacteriophage holin family HP1
       0.17   11.6   0.1       0.17   11.6   0.1    2.7  3  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l
        1.8    8.2   8.5       0.18   11.4   0.7    3.0  2  CLLAC            CLLAC-motif containing domain
        4.1    7.9   0.0        4.1    7.9   0.0    3.6  4  FeoB_associated  FeoB-associated Cys-rich membrane protein


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 !  247.2  21.9   5.4e-77   1.9e-73       5     293 ..      14     357 ..      11     358 .. 0.94

  Alignments for each domain:
  == domain 1  score: 247.2 bits;  conditional E-value: 5.4e-77
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1   5 altlfasilleallaLvlgflisgaiqvfvkeekiielLg.prnrlisllvaallGfllpvCscsavPlarrllkkG 80 
                                       + tl++++  ++l++Lv++f+i+gai++ ++++++ +++g ++++ + + va+ +G +l+vCsc+++P+++++ k+G
  gi|330508714|ref|YP_004385142.1|  14 LATLLEYLSAHVLTCLVPAFFIAGAIAALLNKDTVLKYFGaDAPKWLCYSVASTSGTILAVCSCTILPMFAGIEKRG 90 
                                       6799************************************************************************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                            ArsP_1  81 aplgaavaFlvaaPainiiaiiltlillgwqllvarivlalivaiviglvleylfkeeelekaarevaeaglek... 154
                                       a++g+a+aFl+++Pain +aiilt+ +lg++l+var+v+a+ +a+vigl++  +f++++ + ++ + +     +   
  gi|330508714|ref|YP_004385142.1|  91 AGIGPATAFLFSGPAINLMAIILTARVLGLDLGVARAVAAVFMAVVIGLIMAAIFQRHDPSCKNDAAPSSF--Dvdp 165
                                       **********************************************************9888887666644..2459 PP

                                       ..................................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 155 ..................................................ltlkpklealkafaknevkewlelgky 181
                                                                                         + +  + e++ af ++++   ++++++
  gi|330508714|ref|YP_004385142.1| 166 dpdqmsrpkyitgtfmavlvaillvatssaiellpkaiivgaliavaaflMNRYYQPEEKSAFLEETWWLTRKIFPL 242
                                       99*****************************************9999988777777778888******999****** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx.xxxxxxxxxxxxx RF
                            ArsP_1 182 LiiGvaiagviqaflpesvllsllggnsvsssllamligvvlyvcslgevpfiaalfe..sgl.alGsalAfLlagp 255
                                       L++G+++ gvi  flp +++ +++g+ s+ + +la++ig +ly+ +l evp++ +lf+   g+ a+G+alA+Llagp
  gi|330508714|ref|YP_004385142.1| 243 LVVGTFVTGVIGYFLPVEWVRTIFGTSSFLACFLASVIGSLLYMPTLLEVPVVGTLFGysTGVtAAGPALALLLAGP 319
                                       ********************************************************9722455257*********** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 256 llslpellillkvlkkklvavllglvvvsvvlaglvin 293
                                       +lslp+++++  + ++k+++v++ lvv++++l+g++++
  gi|330508714|ref|YP_004385142.1| 320 SLSLPNMIVIWRIVGAKKASVYISLVVILSTLVGMLYG 357
                                       ***********************************996 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 ?   -2.0   0.5       0.9   3.2e+03      27      41 ..      65      79 ..      63      80 .. 0.82
   2 ?   -0.1   1.6      0.22     8e+02      27      36 ..     134     143 ..     133     145 .. 0.89
   3 ?   13.8   0.1   9.9e-06     0.035      27      49 ..     202     224 ..     175     229 .. 0.87
   4 ?   -1.3   2.0      0.54   1.9e+03       6      38 ..     268     303 ..     263     308 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.9
                   Phage_holin_2_3 27 AiviGIicgvvTfli 41
                                      A+  G i++v++++i
  gi|330508714|ref|YP_004385142.1| 65 ASTSGTILAVCSCTI 79
                                      667799999999987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.22
                   Phage_holin_2_3  27 AiviGIicgv 36 
                                       A+viG+i+++
  gi|330508714|ref|YP_004385142.1| 134 AVVIGLIMAA 143
                                       99******97 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 9.9e-06
                   Phage_holin_2_3  27 AiviGIicgvvTfliNwyykrke 49 
                                       Ai++G +++v+ fl+N yy+ +e
  gi|330508714|ref|YP_004385142.1| 202 AIIVGALIAVAAFLMNRYYQPEE 224
                                       9******************9876 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.54
                   Phage_holin_2_3   6 laAYisSavavvlGll....sLseWAiviGIicgvvT 38 
                                       ++++++   a+v+G l    +L e+  v+G ++g  T
  gi|330508714|ref|YP_004385142.1| 268 TSSFLACFLASVIGSLlympTLLEVP-VVGTLFGYST 303
                                       56888889999999666788999964.5677777666 PP

>> Phage_holin_2_4  Bacteriophage holin family, superfamily II-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   2.5       4.4   1.6e+04      24      24 ..     123     123 ..      84     144 .. 0.57
   2 ?   11.6   0.1   4.7e-05      0.17      37      57 ..     204     224 ..     182     238 .. 0.87
   3 ?   -3.0   0.2       1.7   6.2e+03      27      48 ..     334     355 ..     331     356 .. 0.74

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 4.4
                   Phage_holin_2_4  24 s 24 
                                       +
  gi|330508714|ref|YP_004385142.1| 123 G 123
                                       2 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.7e-05
                   Phage_holin_2_4  37 lvGlavAliGlLvnWyYkrea 57 
                                       +vG+++A++ +L+n yY+ e 
  gi|330508714|ref|YP_004385142.1| 204 IVGALIAVAAFLMNRYYQPEE 224
                                       89***************9875 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.7
                   Phage_holin_2_4  27 GflasselialvGlavAliGlL 48 
                                       G   +s  i+lv ++  l+G+L
  gi|330508714|ref|YP_004385142.1| 334 GAKKASVYISLVVILSTLVGML 355
                                       5566777888888888888887 PP

>> CLLAC  CLLAC-motif containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.8      0.37   1.3e+03       9      25 ..      26      43 ..      25      44 .. 0.81
   2 ?   11.4   0.7   5.1e-05      0.18       8      17 ..     271     280 ..     268     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.37
                             CLLAC  9 LvCLL.ACiitTaigVLi 25
                                      L+CL  A +i+ ai+ L+
  gi|330508714|ref|YP_004385142.1| 26 LTCLVpAFFIAGAIAALL 43
                                      6788767799****9996 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.1e-05
                             CLLAC   8 FLvCLLACii 17 
                                       FL+C+LA++i
  gi|330508714|ref|YP_004385142.1| 271 FLACFLASVI 280
                                       9*******99 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       0.3   1.1e+03      11      20 ..     135     144 ..     127     154 .. 0.45
   2 ?   -3.0   0.5       2.9     1e+04       4      10 ..     184     190 ..     181     195 .. 0.46
   3 ?    7.9   0.0    0.0011       4.1       3      16 ..     203     216 ..     201     226 .. 0.84
   4 ?   -2.6   0.1       2.2     8e+03      16      26 ..     328     338 ..     326     339 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.3
                   FeoB_associated  11 aavafvirrl 20 
                                       +++++++  +
  gi|330508714|ref|YP_004385142.1| 135 VVIGLIMAAI 144
                                       2333333333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.9
                   FeoB_associated   4 IVgliia 10 
                                       +V+++++
  gi|330508714|ref|YP_004385142.1| 184 LVAILLV 190
                                       2333333 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0011
                   FeoB_associated   3 iIVgliiaaavafv 16 
                                       iIVg++ia+a++++
  gi|330508714|ref|YP_004385142.1| 203 IIVGALIAVAAFLM 216
                                       9********99987 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 2.2
                   FeoB_associated  16 virrlikkkkk 26 
                                       vi+r++ +kk+
  gi|330508714|ref|YP_004385142.1| 328 VIWRIVGAKKA 338
                                       68999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       950  (0.0529868); 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:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2361.79
//
Query:       gi|330508715|ref|YP_004385143.1|  [L=189]
Description: adenine phosphoribosyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-19   68.9   0.7    4.2e-19   68.6   0.7    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.024   14.1   0.0      0.035   13.5   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase
      0.089   12.3   0.0       0.12   11.9   0.0    1.2  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.7   7.1e-23   4.2e-19      13     141 ..      37     168 ..      32     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 7.1e-23
                                       EEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...........EE----T CS
                      Pribosyltran  13 davarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes...rlledpa 86 
                                       d +++  a+i++ +n   d +v+++  G+p++  l+   ++pl+++rk+ky  ++  e++++   ++    l ++ +
  gi|330508715|ref|YP_004385143.1|  37 DLIREVTANIVRIANLDVDKIVTVEAMGIPIGIVLSILCDIPLVIIRKRKYGLPNEVEISQVTGYSRsqlYLNGINR 113
                                       589999*************************99888888*******************998776655999999**** PP

                                       TSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS. CS
                      Pribosyltran  87 gkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvf 141
                                       g +V++VDD+++tGgTl+a+l+ ++ +g+e++ ++ +v+++ ++e  + + ++++
  gi|330508715|ref|YP_004385143.1| 114 GDRVIVVDDVISTGGTLQATLDSMELAGAEVMDTVIVVERGNGAELLRSKGYNLK 168
                                       ****************************************999998887777666 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.8e-06     0.035     120     155 ..     113     148 ..      87     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.8e-06
                           UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIl 155
                                       + ++v+++D vi+TGg+++a ++ +  +g+++ + +
  gi|330508715|ref|YP_004385143.1| 113 RGDRVIVVDDVISTGGTLQATLDSMELAGAEVMDTV 148
                                       4578*******************9999777654433 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.12     119     148 ..     112     141 ..     101     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                          PRTase_2 119 aaakelvLvDDEistGktalnliralqekl 148
                                       ++ +++++vDD istG t+ +++++++ + 
  gi|330508715|ref|YP_004385143.1| 112 NRGDRVIVVDDVISTGGTLQATLDSMELAG 141
                                       566889*************99999887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1296.65
//
Query:       gi|330508716|ref|YP_004385144.1|  [L=263]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-17   63.0   0.0    6.3e-17   62.1   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    9.8e-15   55.0   0.0    1.8e-14   54.2   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
      1e-13   51.3   0.0    1.5e-13   50.8   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    3.8e-11   43.1   0.0    1.4e-10   41.3   0.0    1.8  1  Methyltransf_23  Methyltransferase domain
    4.5e-09   36.9   0.0      9e-09   36.0   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    9.3e-08   31.8   0.0    1.9e-07   30.8   0.0    1.4  1  MTS              Methyltransferase small domain
      1e-06   28.3   0.0    1.6e-06   27.7   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.6e-06   27.2   0.0    3.6e-06   26.7   0.0    1.2  1  NodS             Nodulation protein S (NodS)
    5.6e-06   25.9   0.0    8.1e-06   25.4   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    7.5e-06   25.4   0.0    1.1e-05   24.9   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00011   21.4   0.0    0.00015   20.9   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0012   18.1   0.0     0.0018   17.6   0.0    1.1  1  N2227            N2227-like protein
     0.0015   18.2   0.0      0.002   17.8   0.0    1.2  1  TPMT             Thiopurine S-methyltransferase (TPMT)
      0.005   16.4   0.0     0.0065   16.1   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0081   15.6   0.0      0.013   15.0   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.022   14.5   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.056   13.0   0.0      0.084   12.5   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
      0.059   13.3   0.0       0.11   12.5   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
      0.085   12.8   0.0       0.13   12.3   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.19   11.1   0.0       0.24   10.7   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


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 !   62.1   0.0     7e-20   6.3e-17       1      72 [.      46     114 ..      46     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 7e-20
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEES CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssg 72 
                                       +Ld+GcGtGr++++la+r+  + vtg+D+s+eml++a+  a+++++nv++++ da ++++++ s+D  ++  
  gi|330508716|ref|YP_004385144.1|  46 ILDVGCGTGRHSIELARRG--YAVTGLDLSAEMLARAADAARSKKVNVQWIRSDAARFQLPN-SYDGAICLC 114
                                       8*****************5..**************************************996.999999843 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0     2e-17   1.8e-14       1      96 []      47     150 ..      47     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 2e-17
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EE.EEEEES.-CCC-. CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfD.lvvsse.vlhhv. 74 
                                       LdvGcGtGr++ +la+rg+ v+g+Dls+eml++a ++a+ ++++v+++++da ++++++ s+D ++++ e ++  + 
  gi|330508716|ref|YP_004385144.1|  47 LDVGCGTGRHSIELARRGYAVTGLDLSAEMLARAADAARSKKVNVQWIRSDAARFQLPN-SYDgAICLCEgAFGLLg 122
                                       8********************************************************99.66614444443555558 PP

                                       ..C....CHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 ..e....dpekalkeiaRvLkpgGllvi 96 
                                         +    +p ++l +i R Lkp  + v+
  gi|330508716|ref|YP_004385144.1| 123 kgDdpigQPLSILCNISRSLKPQAKAVF 150
                                       551566699*************988765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   1.7e-16   1.5e-13       4     126 ..      43     167 ..      41     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.7e-16
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g ++lD+GCGtG+ ++ela++   +  v+G+D s+e++ +A   a+++++ nv+  ++d+  ++  l  +++D  ++
  gi|330508716|ref|YP_004385144.1|  43 GGSILDVGCGTGRHSIELARR---GYAVTGLDLSAEMLARAADAARSKKV-NVQWIRSDAARFQ--LP-NSYDGAIC 112
                                       6789***************66...456*******************9999.8**********99..66.9***9777 PP

                   Methyltransf_31  81 n..evl.......naladpdkileeiervlkpggilliedprllaelpakveees 126
                                          +++       + +  p +il +i+r lkp+   + +  ++la  ++++ ++ 
  gi|330508716|ref|YP_004385144.1| 113 LceGAFgllgkgdDPIGQPLSILCNISRSLKPQAKAVFTVLNALASIRRNANKDV 167
                                       533333777************************9999999996666665555444 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   1.6e-13   1.4e-10      12     125 ..      34     158 ..      18     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.6e-13
                   Methyltransf_23  12 klerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqg......k 82 
                                       ++e+l+   r gg++Ld+GcGtG+ + +l+++g+ vtg Dls e+ ++a+  + a++++++ q ++ +++      +
  gi|330508716|ref|YP_004385144.1|  34 LTEELA--VRDGGSILDVGCGTGRHSIELARRGYAVTGLDLSAEMLARAA--DAARSKKVNVQWIRSDAArfqlpnS 106
                                       344444..59999***********************************95..5555555544544444444555556 PP

                   Methyltransf_23  83 fdlIvl.....revlehvpdpp....ellrqiatllkpgGylllseplaslk 125
                                       +d +++     + +l+  +dp     + l +i + lkp++ +++++ +a ++
  gi|330508716|ref|YP_004385144.1| 107 YDGAIClcegaFGLLGKGDDPIgqplSILCNISRSLKPQAKAVFTVLNALAS 158
                                       66554322222788999998555555999999999***99999999987543 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0     1e-11     9e-09       1      97 [.      47     146 ..      47     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1e-11
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas..nv 75 
                                       L++GcGtG+ + +l+++  +  +tg+D+s++++++a+   ++++     nv++   d++  + ++s+D  +++  ++
  gi|330508716|ref|YP_004385144.1|  47 LDVGCGTGRHSIELARR--GYAVTGLDLSAEMLARAADAARSKK----VNVQWIRSDAARFQLPNSYDGAICLceGA 117
                                       8****************..**************44444444433....46666666666666668***999775688 PP

                   Methyltransf_12  76 lhhl.......kdirevldnirklLkpgG 97 
                                       +  l        ++ ++l ni + Lkp +
  gi|330508716|ref|YP_004385144.1| 118 FGLLgkgddpiGQPLSILCNISRSLKPQA 146
                                       88888888888888888888888888875 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.1e-10   1.9e-07       8     102 ..      20     111 ..      17     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.1e-10
                                       TTSTTTTS--HHHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEE CS
                               MTS   8 pgvFskdklDkGsklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevev 84 
                                        +vF k+ +    ++L e l  +  g++lD+GcG+G  +++la++     vt +d +a+ l+ a   ++++k++v+ 
  gi|330508716|ref|YP_004385144.1|  20 ENVFTKNTIQE-VNFLTEELAVRDGGSILDVGCGTGRHSIELARRGYA--VTGLDLSAEMLARAADAARSKKVNVQW 93 
                                       68888888865.689*****************************8877..9************************** PP

                                       EE-STTTTSTTS-EEEEE CS
                               MTS  85 vasdvleeveekkfdliv 102
                                       + sd+     ++++d  +
  gi|330508716|ref|YP_004385144.1|  94 IRSDAARFQLPNSYDGAI 111
                                       ****99887778888655 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.7e-09   1.6e-06      38     127 ..      33     121 ..      23     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.7e-09
                                       HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS- CS
                   Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed 114
                                       f+++  av+ g ++lDv +Gtg  +++l++   + + v++lD++++mL  + + ++ + k+n++++ ++a +++  +
  gi|330508716|ref|YP_004385144.1|  33 FLTEELAVRDGGSILDVGCGTGRHSIELAR---RGYAVTGLDLSAEMLARAADAAR-SKKVNVQWIRSDAARFQLPN 105
                                       66777899*****************99975...5679************9988766.5688*******998755443 PP

                                       ...T-EEEEEEES-GG CS
                   Ubie_methyltran 115 ...dsfDvvtvsfGlr 127
                                          ++  +   +fGl 
  gi|330508716|ref|YP_004385144.1| 106 sydGAICLCEGAFGLL 121
                                       1114444444556665 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0     4e-09   3.6e-06      38     112 ..      37     112 ..      12     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4e-09
                              NodS  38 slaqgsiadalevGcaaGalterlapyckrltvvdvveeaiararervk.esshiswivsdvqqfstdekfdlivv 112
                                        la ++ +++l+vGc +G  + +la     +t +d+  e +ara    + ++ +++wi sd  +f++ + +d  ++
  gi|330508716|ref|YP_004385144.1|  37 ELAVRDGGSILDVGCGTGRHSIELARRGYAVTGLDLSAEMLARAADAARsKKVNVQWIRSDAARFQLPNSYDGAIC 112
                                       466777899**********************************98654414489******************8776 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0     9e-09   8.1e-06      25      97 ..      37     108 ..      17     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 9e-09
                                       HCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EE CS
                              TehB  25 avkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderyd 97 
                                          + + g +ld+gcg gr s+ l+  gy vt +d  ++ +a   + +  ++++ ++    d    +l + yd
  gi|330508716|ref|YP_004385144.1|  37 ELAVRDGGSILDVGCGTGRHSIELARRGYAVTGLDLSAEMLARAADAARSKKVN-VQWIRSDAARFQLPNSYD 108
                                       5556677899**************************999999988888777776.666666666666767776 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.2e-08   1.1e-05      47     107 ..      27      86 ..      11     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.2e-08
                                       HHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHT CS
                              CMAS  47 qlaKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvde 107
                                        ++ ++ + e l +++G  +Ld+GcG G   ++ ++r +  v gl lS+e  ++a ++  +
  gi|330508716|ref|YP_004385144.1|  27 TIQEVNFLTEELAVRDGGSILDVGCGTGRHSIELARR-GYAVTGLDLSAEMLARAADAARS 86 
                                       456788999****************************.************99888766544 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.7e-07   0.00015      24     110 ..      36     138 ..      20     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.7e-07
                                       HHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-CCGHHHHHHHCT... CS
                            RrnaAD  24 dklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.kdeklkvvhqDflkfetpeevte... 96 
                                       ++l +++   +l++g G+G  + eLa r   v+ l l  +++++  ++ + k+ +++++  D+  f++p+ + +   
  gi|330508716|ref|YP_004385144.1|  36 EELAVRDGGSILDVGCGTGRHSIELARRGYAVTGLDLSAEMLARAADAARsKKVNVQWIRSDAARFQLPNSY-Dgai 111
                                       4566668889****************************9999999998887999****************55.5588 PP

                                       .............TTCCCCEEEEEEE- CS
                            RrnaAD  97 .............kdsihqeflvvanl 110
                                                     d i+q++ +  n+
  gi|330508716|ref|YP_004385144.1| 112 clcegafgllgkgDDPIGQPLSILCNI 138
                                       888888888888888888888888887 PP

>> N2227  N2227-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     2e-06    0.0018      36      92 ..      22      77 ..      13      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                                      HHHHHHHHHHHHHS-T......T-EEEEET-TT-HHHHHHHHTT-EEEEEE--HHHH CS
                             N2227 36 alykpiieelkelvpseskerekvkilvPGaGlGrlavelatkgyqvegnEfsyfml 92
                                      +  k  i+e++ l++ e   r+  +il  G+G+Gr ++ela+ gy+v g ++s+ ml
  gi|330508716|ref|YP_004385144.1| 22 VFTKNTIQEVNFLTE-ELAVRDGGSILDVGCGTGRHSIELARRGYAVTGLDLSAEML 77
                                      555666667666655.5777888899999************************9998 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.3e-06     0.002      29      81 ..      33      86 ..       2     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                                      HHHT..T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTT CS
                              TPMT 29 flda.lkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanl 81
                                      fl + l++  g+++l  +CG +   + lA +g+ v G++ls   ++++++ a +
  gi|330508716|ref|YP_004385144.1| 33 FLTEeLAVRDGGSILDVGCGTGRHSIELARRGYAVTGLDLSAEMLARAADAARS 86
                                      44444899999999999**************************99997665554 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.2e-06    0.0065       3      59 ..      45      99 ..      43     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.2e-06
                   Methyltransf_15  3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvf 59
                                       ilD+ +G+G  +i++a+ +  v +++ + e la a+  a++   + +++++  d  
  gi|330508716|ref|YP_004385144.1| 45 SILDVGCGTGRHSIELARRGYAVTGLDLSAEMLARAADAARSK--KVNVQWIRSDAA 99
                                      58*****************99********************99..667899988875 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.4e-05     0.013       5      63 ..      46     101 ..      42     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                                       EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCH CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkv 63 
                                       +l++GcG G++ ++lA +     + G++++ +++a++ ++++ +++ N++ +r+da ++
  gi|330508716|ref|YP_004385144.1|  46 ILDVGCGTGRHSIELARRG--YAVTGLDLSAEMLARAADAARSKKV-NVQWIRSDAARF 101
                                       79**************986..6778************999888776.9*******9654 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.4e-05     0.022      58     130 ..      27      95 ..       5     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                                       -HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEE CS
                              PCMT  58 aphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvv 130
                                        ++ v +++e l +++g ++L+vG+G+G ++  lar   +   v +++ ++e+ ++a    + ++  nv+ + 
  gi|330508716|ref|YP_004385144.1|  27 TIQEVNFLTEELAVRDGGSILDVGCGTGRHSIELAR---RGYAVTGLDLSAEMLARAADAARSKK-VNVQWIR 95 
                                       455677899999*****************9987665...55667788888888888876655443.3555555 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.4e-05     0.084      10      71 ..      39     101 ..      31     113 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.4e-05
                              MetW  10 likpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecv..akGlsviqgdldkdlenf 71 
                                        +++g  +ld+GcG G     l+ +++    Gl+l++e +a++   a+  +v  + + +d + f
  gi|330508716|ref|YP_004385144.1|  39 AVRDGGSILDVGCGTGRHSIELA-RRGYAVTGLDLSAEMLARAAdaARSKKVNVQWIRSDAARF 101
                                       58999***********9877774.4899999999999999877422566666666666666655 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.11      12      66 ..      40      92 ..      36     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                   Methyltransf_18 12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledk 66
                                      v++g +++D+G+  g  +i+l+++g a  v+  D++++ l++a + +++++++ +
  gi|330508716|ref|YP_004385144.1| 40 VRDGGSILDVGCGTGRHSIELARRGYA--VTGLDLSAEMLARAADAARSKKVNVQ 92
                                      788999*****************9998..99***************999988644 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014      0.13      23      78 ..      40      89 ..      23     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                   Methyltransf_32 23 esgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78
                                       ++  +++DvG+G g  s  la      ++ v+g+d+++e+ ++a + a+  +  +
  gi|330508716|ref|YP_004385144.1| 40 VRDGGSILDVGCGTGRHSIELAR----RGYAVTGLDLSAEMLARAADAARSKK--V 89
                                      4456689***************9....599***********999988776655..4 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00027      0.24     158     212 ..      39      92 ..      24     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                              PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveak 212
                                        v+ g ++lDvG+G+G  +i  a+ g   v+++D+    +  a++ a+  kv+ +
  gi|330508716|ref|YP_004385144.1|  39 AVRDGGSILDVGCGTGRHSIELARRGY-AVTGLDLSAEMLARAADAARSKKVNVQ 92 
                                       488999**************9999986.589999998888888777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1789.40
//
Query:       gi|330508717|ref|YP_004385145.1|  [L=114]
Description: ArsR family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete 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   56.2   2.0    2.5e-13   49.6   0.0    2.9  3  HTH_5     Bacterial regulatory protein, arsR family
    7.4e-10   38.7   0.2    2.2e-09   37.2   0.0    1.8  2  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
       0.16   11.6   0.1       0.83    9.2   0.1    1.9  1  CARMIL_C  CARMIL C-terminus


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 !    5.5   0.2    0.0026        15       2      13 ..       8      19 ..       7      19 .. 0.87
   2 !   49.6   0.0   4.2e-17   2.5e-13       1      45 [.      19      63 ..      19      65 .. 0.97
   3 ?   -0.0   0.0      0.14   8.2e+02       1      24 [.      78     102 ..      78     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0026
                                      HHHHHHHHHHTT CS
                             HTH_5  2 ptRlkILklLae 13
                                      + RlkIL++L++
  gi|330508717|ref|YP_004385145.1|  8 ELRLKILSALSD 19
                                      67********96 PP

  == domain 2  score: 49.6 bits;  conditional E-value: 4.2e-17
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      dp Rl++L +L+ ge+cvce+  ++  sqst+S HL++L ea+++
  gi|330508717|ref|YP_004385145.1| 19 DPIRLELLEFLSGGERCVCEILPAFSRSQSTISKHLNILFEADIL 63
                                      8*****************************************997 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.14
                                       SHHHHHHHHHHTT.SSEEHHHHHHH CS
                             HTH_5   1 dptRlkILklLae.gelcvcelaee 24 
                                       dp+  ++++l+ +   + +++lae+
  gi|330508717|ref|YP_004385145.1|  78 DPQVFELVRLVDRmALKQISQLAEA 102
                                       5666677777777777888888875 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   3.6e-13   2.2e-09       2      57 ..      12      66 ..      11      70 .. 0.95
   2 ?   -1.0   0.1      0.32   1.9e+03      43      52 ..      94     103 ..      83     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 3.6e-13
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +i++AL++P R+++l  L +++++++ e+  +++ s++t+s+HL++L ea++++++
  gi|330508717|ref|YP_004385145.1| 12 KILSALSDPIRLELLEFL-SGGERCVCEILPAFSRSQSTISKHLNILFEADILDRR 66
                                      699***************.**********************************987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.32
                                       HHHHHHHHCT CS
                            HTH_20  43 yHLrvLeeag 52 
                                       +++ +L+eag
  gi|330508717|ref|YP_004385145.1|  94 KQISQLAEAG 103
                                       5667777776 PP

>> CARMIL_C  CARMIL C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00014      0.83      49      83 ..       6      40 ..       2      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00014
                          CARMIL_C 49 lnEvkLsvaaalsDrivDevLesLsrsqkkLaehl 83
                                      ++E++L + +alsD i  e+Le Ls   +   e+l
  gi|330508717|ref|YP_004385145.1|  6 VSELRLKILSALSDPIRLELLEFLSGGERCVCEIL 40
                                      89**************9999999997655555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 864.40
//
Query:       gi|330508718|ref|YP_004385146.1|  [L=364]
Description: permease [Methanosaeta concilii GP6]
Scores for complete 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-73  247.3  25.1    3.9e-73  246.2  25.1    1.6  1  ArsP_1           Predicted permease
  ------ inclusion threshold ------
      0.058   13.2   0.1      0.058   13.2   0.1    4.5  4  Phage_holin_2_3  Bacteriophage holin family HP1
       0.37   10.6   3.3       0.35   10.6   0.1    2.7  2  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l
        1.5    8.5   8.5       0.18   11.4   0.7    3.2  2  CLLAC            CLLAC-motif containing domain


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 !  246.2  25.1   8.7e-77   3.9e-73       5     293 ..      17     360 ..      14     361 .. 0.93

  Alignments for each domain:
  == domain 1  score: 246.2 bits;  conditional E-value: 8.7e-77
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1   5 altlfasilleallaLvlgflisgaiqvfvkeekiielLg.prnrlisllvaallGfllpvCscsavPlarrllkkG 80 
                                       + tl++++  ++l++Lv++f+i+gai++ ++++++ +++g ++++ + + va+ +G +l+vCsc+++P+++++ k+G
  gi|330508718|ref|YP_004385146.1|  17 LATLLEYLSAHVLTCLVPAFFIAGAIAALLNKDTVLKYFGaDAPKWLCYSVASTSGTILAVCSCTILPMFAGIEKRG 93 
                                       6799************************************************************************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                            ArsP_1  81 aplgaavaFlvaaPainiiaiiltlillgwqllvarivlalivaiviglvleylfkeeelekaarevaeaglek... 154
                                       a++g+a+aFl+++Pain +aiilt+ +lg++l++ar+v+a+i+a+vigl++  +f++++ + ++   +   +     
  gi|330508718|ref|YP_004385146.1|  94 AGIGPATAFLFSGPAINLMAIILTARVLGLDLGIARAVAAVIMAVVIGLIMAAMFQKHDPSCKTDVAPSMIQ-Adpk 169
                                       *********************************************************998877765544333.2589 PP

                                       .................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 155 .................................................ltlkpklealkafaknevkewlelgkyL 182
                                                                                        +    + e++ af ++++    +++++L
  gi|330508718|ref|YP_004385146.1| 170 pdqmsrpnyitgtfmavlvaillvatssaiellpkaiivgaliavaaflMNKYYEPEEKSAFLEETWWLTKKIFPLL 246
                                       9****************************************998887653333344466679999998889999*** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx RF
                            ArsP_1 183 iiGvaiagviqaflpesvllsllggnsvsssllamligvvlyvcslgevpfiaalfesg...lalGsalAfLlagpl 256
                                       ++G+++ gvi  flp +++ +++g+ s+ + +la++ig +ly+ +l evp++ +lf+     +a+G+alA+Llagp+
  gi|330508718|ref|YP_004385146.1| 247 VVGTFVTGVIGYFLPVEWVRTIFGTSSFLACFLASVIGSLLYMPTLLEVPIVGTLFGYStgvMAAGPALALLLAGPS 323
                                       ********************************************************7432349************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 257 lslpellillkvlkkklvavllglvvvsvvlaglvin 293
                                       lslp+++++  + ++k+++v++ lvv++++l+g++++
  gi|330508718|ref|YP_004385146.1| 324 LSLPSMIVIWRIIGAKKASVYISLVVILSTLVGMLYG 360
                                       **********************************996 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 ?   -2.1   0.5      0.73   3.3e+03      27      41 ..      68      82 ..      66      83 .. 0.82
   2 ?    0.2   1.4      0.14   6.4e+02      27      36 ..     137     146 ..     135     148 .. 0.89
   3 ?   13.2   0.1   1.3e-05     0.058      27      49 ..     205     227 ..     178     231 .. 0.86
   4 ?   -0.7   2.4      0.28   1.3e+03       6      41 ..     271     309 ..     266     311 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.73
                   Phage_holin_2_3 27 AiviGIicgvvTfli 41
                                      A+  G i++v++++i
  gi|330508718|ref|YP_004385146.1| 68 ASTSGTILAVCSCTI 82
                                      667799999999987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.14
                   Phage_holin_2_3  27 AiviGIicgv 36 
                                       A+viG+i+++
  gi|330508718|ref|YP_004385146.1| 137 AVVIGLIMAA 146
                                       99******97 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 1.3e-05
                   Phage_holin_2_3  27 AiviGIicgvvTfliNwyykrke 49 
                                       Ai++G +++v+ fl+N yy  +e
  gi|330508718|ref|YP_004385146.1| 205 AIIVGALIAVAAFLMNKYYEPEE 227
                                       9******************8665 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.28
                   Phage_holin_2_3   6 laAYisSavavvlGll....sLseWAiviGIicgvvTfli 41 
                                       ++++++   a+v+G l    +L e+ i +G ++g  T ++
  gi|330508718|ref|YP_004385146.1| 271 TSSFLACFLASVIGSLlympTLLEVPI-VGTLFGYSTGVM 309
                                       578899999999997668899999765.588888877655 PP

>> Phage_holin_2_4  Bacteriophage holin family, superfamily II-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   7.9e-05      0.35      37      57 ..     207     227 ..     184     238 .. 0.88
   2 ?   -2.9   0.4       1.3     6e+03      26      48 ..     336     358 ..     330     359 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.9e-05
                   Phage_holin_2_4  37 lvGlavAliGlLvnWyYkrea 57 
                                       +vG+++A++ +L+n yY  e 
  gi|330508718|ref|YP_004385146.1| 207 IVGALIAVAAFLMNKYYEPEE 227
                                       89***************8765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                   Phage_holin_2_4  26 aGflasselialvGlavAliGlL 48 
                                       +G   +s  i+lv ++  l+G+L
  gi|330508718|ref|YP_004385146.1| 336 IGAKKASVYISLVVILSTLVGML 358
                                       56667777888888888888887 PP

>> CLLAC  CLLAC-motif containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.8       0.3   1.3e+03       9      25 ..      29      46 ..      28      47 .. 0.81
   2 ?   11.4   0.7   4.1e-05      0.18       8      17 ..     274     283 ..     271     287 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.3
                             CLLAC  9 LvCLL.ACiitTaigVLi 25
                                      L+CL  A +i+ ai+ L+
  gi|330508718|ref|YP_004385146.1| 29 LTCLVpAFFIAGAIAALL 46
                                      6788767799****9996 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 4.1e-05
                             CLLAC   8 FLvCLLACii 17 
                                       FL+C+LA++i
  gi|330508718|ref|YP_004385146.1| 274 FLACFLASVI 283
                                       9*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.22s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2739.26
//
Query:       gi|330508719|ref|YP_004385147.1|  [L=187]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.018   15.5   0.0    1.3  1  But2      Ubiquitin 3 binding protein But2 C-terminal domain


Domain annotation for each model (and alignments):
>> But2  Ubiquitin 3 binding protein But2 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   9.8e-07     0.018      59     137 ..      80     170 ..      72     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.8e-07
                              But2  59 qletssytlsG...sgkfkfsklaapatesttynnkPavkeelgk.ttlspGnaytiasf........pCpagqavs 123
                                       +  + +  ++G   +gk++++ ++ +a ++ t++ +P+  ++    ++++ +   t + +        +C +g ++s
  gi|330508719|ref|YP_004385147.1|  80 SSANLKIYVKGverPGKVTLYLYDNAAMNTVTWADQPEYDSQALGsIEIQETGWQTWDATdfvkkaavECSEGCSFS 156
                                       444444555555559***********************9876544499998888887777779999999****9999 PP

                              But2 124 yevssagdtsLeff 137
                                       +++ + +d s++f 
  gi|330508719|ref|YP_004385147.1| 157 VVLVADEDASISFA 170
                                       99999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1318.51
//
Query:       gi|330508720|ref|YP_004385148.1|  [L=364]
Description: cytochrome c biogenesis transmembrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-17   63.1  14.6    4.8e-17   62.6  14.6    1.3  1  DsbD           Cytochrome C biogenesis protein transmembrane 
    2.1e-08   34.3  36.5    2.2e-07   31.0  19.9    2.3  3  DsbD_2         Cytochrome C biogenesis protein transmembrane 
    8.5e-05   22.5   0.0     0.0002   21.4   0.0    1.6  1  Thioredoxin_3  Thioredoxin domain
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.022   15.0   0.0    1.5  1  Glutaredoxin   Glutaredoxin
      0.031   14.4   2.1      0.031   14.4   2.1    2.4  2  YtpI           YtpI-like protein
       0.17   12.1   0.1         20    5.3   0.0    2.2  2  Thioredoxin_4  Thioredoxin
       0.57    9.0  18.4     0.0069   15.3   4.3    3.0  3  LptF_LptG      Lipopolysaccharide export system permease LptF


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 !   62.6  14.6   1.9e-20   4.8e-17       1     208 [.     147     356 ..     147     361 .. 0.76

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1.9e-20
                              DsbD   1 aflaGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkev 77 
                                       +f aGll+ + PC+l+++    s +   s + ++        l+   lF lG+ +v+  +g++   + q      ++
  gi|330508720|ref|YP_004385148.1| 147 VFAAGLLAGFNPCLLAILAFLASTVL-ASSGRRR------DLLTMIALFSLGIFVVYYIFGVGLFNVLQEK-STATM 215
                                       599*************9865554443.2222222......24788899***************98888876.78899 PP

                              DsbD  78 irrvaglivillGlhflgvfk.....ievleklklllkikkka.elsvl.galllGltFalgwsPCigPvlasvlal 147
                                        + v + + ++lGl++++  +      + l ++   +k  + a   ++l   +llG +F+l+ +PC+g v  +++ +
  gi|330508720|ref|YP_004385148.1| 216 FKLVLAAVLLILGLTQMEDGRrlnagRDSLFRTDWAMKYVHGAlASKRLsSYFLLGALFSLVKAPCVGAVYIAIIGV 292
                                       99***************8444666664444444444444433313334414589*********************** PP

                              DsbD 148 aaskeslakgallllvyvlGlaipfllvglllel..lkkklkslkkysk.aveiaggvllvllG 208
                                        +s++  ++g+++l++y lG+++p+ll+g++++l    +++  ++++ k a+++++g+ l++l 
  gi|330508720|ref|YP_004385148.1| 293 ISSHGYSSSGLIYLMLYNLGIVLPVLLLGVIMTLgmSPEQVDDFRNNHKvAIRVITGLTLIILA 356
                                       *****************************99876114467888876655268888888777664 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         4     1e+04      77      84 ..      14      21 ..       5      43 .. 0.51
   2 !   16.9   8.6   1.8e-06    0.0045     107     198 ..     135     229 ..     107     230 .. 0.73
   3 !   31.0  19.9   8.5e-11   2.2e-07       2     178 ..     147     333 ..     146     357 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4
                            DsbD_2 77 lgllllll 84
                                      ++l+++ll
  gi|330508720|ref|YP_004385148.1| 14 VALFMVLL 21
                                      22222222 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.8e-06
                            DsbD_2 107 llkklakklkslasalllGllnGllpCgl.vysalllal.asgsaleGalvm.laFgLGTlpalllfgl.llgllsk 179
                                       +l++l     s  + +++Gll G+ pC l ++++l+  + as+   +  l+m ++F+LG +++  +fg+ l++ l++
  gi|330508720|ref|YP_004385148.1| 135 ALQNLNL--SSAVTVFAAGLLAGFNPCLLaILAFLASTVlASSGRRRDLLTMiALFSLGIFVVYYIFGVgLFNVLQE 209
                                       4444443..78999*************88544444444314444445566652679***988888888636899999 PP

                            DsbD_2 180 klrkkllr.lagvllillgl 198
                                       k ++++++ +++++l++lgl
  gi|330508720|ref|YP_004385148.1| 210 KSTATMFKlVLAAVLLILGL 229
                                       ********777888888886 PP

  == domain 3  score: 31.0 bits;  conditional E-value: 8.5e-11
                            DsbD_2   2 afllgLlgsl.hClgmCggivlalslskpkra...l.alllynlGRilsYallGalvgllgsvlqlageleglrall 73 
                                       +f++gLl+++ +Cl+   +++++  l+++ r+   l  ++l++lG  + Y ++G+    l +vlq  +++     ++
  gi|330508720|ref|YP_004385148.1| 147 VFAAGLLAGFnPCLLAILAFLASTVLASSGRRrdlLtMIALFSLGIFVVYYIFGVG---LFNVLQEKSTA----TMF 216
                                       799*******9*****9999999988887543233335****************74...55566555544....456 PP

                            DsbD_2  74 gvllgllllllglklllkkkllkler....lgkllsrllkklakklkslasalllGllnGll..pC.glvysallla 143
                                       +++l+++ll+lgl  +  ++ l+ +r       +  +++   +++ k+l+s +llG+l++l+  pC g vy a++ +
  gi|330508720|ref|YP_004385148.1| 217 KLVLAAVLLILGLTQMEDGRRLNAGRdslfRTDWAMKYVHGALAS-KRLSSYFLLGALFSLVkaPCvGAVYIAIIGV 292
                                       666666666666666644433333331111335555555555554.9**************877**99********* PP

                            DsbD_2 144 lasgsa.leGalvmlaFgLGTlpalllfglllgll.....s 178
                                       ++s+ + ++G ++++++ LG ++++ll+g++++l       
  gi|330508720|ref|YP_004385148.1| 293 ISSHGYsSSGLIYLMLYNLGIVLPVLLLGVIMTLGmspeqV 333
                                       *997761568888999***********99999885333330 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   7.7e-08    0.0002       2      56 ..      30      89 ..      29     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.7e-08
                                      EEEE.ESSSSTTCHHHHHHHHHHCHCCTCEC..EEECC.TTHHHH.HHCT-SSSSEEECT CS
                     Thioredoxin_3  2 eikv.lgpgCakCpklekavkeaaaekgika..evekv.tdfeei.ekygVmsvPalvid 56
                                      ei v  +pgC kC ++e+a++e++ + + +   ev+   ++   i ++++V  vP+++i 
  gi|330508720|ref|YP_004385148.1| 30 EITViTSPGCSKCAAAERALTEVLSNYQESTfeEVIFSsEEGHRIvKEHKVKDVPSIIIG 89
                                      688956999*****************97444476665558888899************96 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   8.4e-06     0.022       1      58 [.      31      91 ..      31      93 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.4e-06
                                      EEEEESTSSHHHHHHHHHH.....HHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTE CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlL.....kelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgk 58
                                      +++ t+p+C  C++a r+L     +++   fee+  + + e    +ke  +v+ vP + i+  
  gi|330508720|ref|YP_004385148.1| 31 ITVITSPGCSKCAAAERALtevlsNYQESTFEEVIFSSE-EGHRIVKEH-KVKDVPSIIIGSS 91
                                      7899***************44444344455766666665.444444444.7888888888765 PP

>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.3         7   1.8e+04      63      73 ..       9      19 ..       7      22 .. 0.55
   2 ?   14.4   2.1   1.2e-05     0.031      12      77 ..     164     236 ..     158     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 7
                              YtpI 63 avflvlGlanl 73
                                      av+l ++l+ +
  gi|330508720|ref|YP_004385148.1|  9 AVLLTVALFMV 19
                                      55666655544 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.2e-05
                              YtpI  12 vyykvkafrtkdplekkllsakasialGlfli..lfginqlll.....lestvalvvgavflvlGlanlfaGi 77 
                                       + + + ++ + + ++++ll+  a  +lG+f++  +fg+ ++       + ++++lv +av+l+lGl ++  G 
  gi|330508720|ref|YP_004385148.1| 164 LAFLASTVLASSGRRRDLLTMIALFSLGIFVVyyIFGVGLFNVlqeksTATMFKLVLAAVLLILGLTQMEDGR 236
                                       5556667777888999999999*********844688886554455556677899***********9987775 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.011        27      17      42 ..      31      56 ..      25      71 .. 0.85
   2 ?    5.3   0.0    0.0079        20     131     157 ..      73      98 ..      57     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.011
                                      EEEEE-TT-HHHHHHHHHHHHHHHHH CS
                     Thioredoxin_4 17 vieyedlrCphCakfeeeveklleey 42
                                      +++ ++  C+ Ca+ e+ + ++l+ y
  gi|330508720|ref|YP_004385148.1| 31 ITVITSPGCSKCAAAERALTEVLSNY 56
                                      56668999***************999 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0079
                                       HHHHHHT--SS-EEEETTEEE-TT--H CS
                     Thioredoxin_4 131 keakkagiestPtfiingekveepqty 157
                                       + +k+++++ +P++ii+  ++  +++y
  gi|330508720|ref|YP_004385148.1|  73 RIVKEHKVKDVPSIIIGSSVIG-YKDY 98 
                                       45699************99985.5555 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 ?   -0.5   0.1      0.17   4.4e+02      77      90 ..      27      40 ..       6      49 .. 0.61
   2 ?   15.3   4.3   2.7e-06    0.0069     265     349 ..     145     229 ..      49     233 .. 0.74
   3 ?    1.3   2.7     0.046   1.2e+02      31      73 ..     290     327 ..     262     328 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.17
                         LptF_LptG 77 edsEltalrsaGis 90
                                      ++sE+t++ s G s
  gi|330508720|ref|YP_004385148.1| 27 ANSEITVITSPGCS 40
                                      35666666666665 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.7e-06
                         LptF_LptG 265 vrryraelhkrlalplaclvfaliaaplglvkrrggrglr.lliaillfvlyyvllslgkalaengvlppilaawlp 340
                                       v+ ++a l   +   l++++++l +  l+ + rr+ + +  +l+++++fv+yy++   +++  ++ ++++ +  ++ 
  gi|330508720|ref|YP_004385148.1| 145 VTVFAAGLLAGFNPCLLAILAFLASTVLASSGRRRDLLTMiALFSLGIFVVYYIFGVGLFNVLQE-KSTATMFKLVL 220
                                       556666666667777889999999999999997777777779************99988888777.55566666666 PP

                         LptF_LptG 341 nilflllgl 349
                                        +++l+lgl
  gi|330508720|ref|YP_004385148.1| 221 AAVLLILGL 229
                                       666666666 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.046
                         LptF_LptG  31 ldllvgkglpvgdllelilynlpyilelalPlavLlavlltfg 73 
                                       ++ + ++g++ + l+    y ++y l ++lP+ +Ll+v++t+g
  gi|330508720|ref|YP_004385148.1| 290 IGVISSHGYSSSGLI----YLMLYNLGIVLPV-LLLGVIMTLG 327
                                       555555555555555....5555566777776.8899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2611.93
//
Query:       gi|330508721|ref|YP_004385149.1|  [L=78]
Description: redox-active disulfide protein 2 [Methanosaeta concilii GP6]
Scores for complete 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   88.3   1.0    2.8e-25   88.2   1.0    1.0  1  Thioredoxin_3  Thioredoxin domain
    0.00083   19.5   0.0     0.0013   18.9   0.0    1.3  1  Glutaredoxin   Glutaredoxin
     0.0039   17.1   0.0     0.0039   17.1   0.0    1.1  1  Thioredoxin    Thioredoxin
     0.0054   16.9   0.2      0.015   15.5   0.0    1.6  2  Thioredoxin_4  Thioredoxin
  ------ inclusion threshold ------
      0.056   13.8   0.0      0.061   13.7   0.0    1.2  1  ArsD           Arsenical resistance operon trans-acting repre


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 !   88.2   1.0   7.8e-29   2.8e-25       1      75 [.       2      76 ..       2      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 7.8e-29
                                      EEEEEESSSSTTCHHHHHHHHHHCHCCTCECEEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
                     Thioredoxin_3  1 meikvlgpgCakCpklekavkeaaaekgikaevekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirkll 75
                                      ++i+vlg+gCakC+ l k+v++a+ae+g++aev+kv  ++ei+++gVm++Pal+idgk  ++G++ ++eei+++l
  gi|330508721|ref|YP_004385149.1|  2 VKIEVLGTGCAKCKSLLKNVEKAVAELGVSAEVVKVDSIQEIMDRGVMMTPALYIDGKSMMAGRTATVEEIKRML 76
                                      68**********************************************************************998 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.6e-07    0.0013      12      59 ..      11      60 ..       9      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.6e-07
                                      HHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHH..TSSSSSEEEETTEE CS
                      Glutaredoxin 12 CkkakrlLkelgvkfeeidvdkdeeireelkels..gvrtvPqvfidgkh 59
                                      C+k k lLk+   +++e  v+++    + ++e++  gv+  P ++idgk 
  gi|330508721|ref|YP_004385149.1| 11 CAKCKSLLKNVEKAVAELGVSAEVVKVDSIQEIMdrGVMMTPALYIDGKS 60
                                      889999998888888888888888888888888888************95 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.1e-06    0.0039      24      83 ..       5      61 ..       1      78 [] 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                                      EEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTE CS
                       Thioredoxin 24 eFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngk 83
                                      e   + C++Ck+l   +ek+  el     ++kvd  ++     + +v + P+l++  ++ 
  gi|330508721|ref|YP_004385149.1|  5 EVLGTGCAKCKSLLKNVEKAVAELGVSAEVVKVDSIQE---IMDRGVMMTPALYIDGKSM 61
                                      566678*******************9999999998876...6677999999997755444 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.038   1.4e+02      24      48 ..      10      35 ..       3      41 .. 0.73
   2 !   15.5   0.0   4.2e-06     0.015     112     165 ..      20      77 ..      15      78 .] 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.038
                                      T-HHHHHHHHHHH.HHHHHHHHTTSE CS
                     Thioredoxin_4 24 rCphCakfeeeve.klleeyidtGkv 48
                                       C  C+ + ++ve ++ e  ++++ v
  gi|330508721|ref|YP_004385149.1| 10 GCAKCKSLLKNVEkAVAELGVSAEVV 35
                                      699****9999994455555666555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.2e-06
                                       HHTS-------HHHHHHHHHHH..HHHT--SS-EEEETTEEE..-TT--HHHHHHHHT CS
                     Thioredoxin_4 112 kfeacleeekldalveaeskea..kkagiestPtfiingekv..eepqtyeelkalid 165
                                       ++e++++e  ++a+v++ +  +    +g+ +tP ++i+g+ +   +  t+ee+k++++
  gi|330508721|ref|YP_004385149.1|  20 NVEKAVAELGVSAEVVKVDSIQeiMDRGVMMTPALYIDGKSMmaGRTATVEEIKRMLQ 77 
                                       577888888888999887766633667*************953477889999999987 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 ?   13.7   0.0   1.7e-05     0.061      55      98 ..      34      76 ..      11      78 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                              ArsD 55 FvenkavkellekkgaeaLPlvlvdgeivktgrYptreelaewl 98
                                       v+ ++++e+++ +g+ + P +++dg+ +++gr  t ee++++l
  gi|330508721|ref|YP_004385149.1| 34 VVKVDSIQEIMD-RGVMMTPALYIDGKSMMAGRTATVEEIKRML 76
                                      466778888887.8**************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 618.88
//
Query:       gi|330508722|ref|YP_004385150.1|  [L=363]
Description: rhodanese domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.9e-18   65.1   0.0    3.3e-08   34.0   0.0    2.3  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   1.9e-12   3.3e-08      11     106 ..     131     227 ..     124     228 .. 0.76
   2 !   28.8   0.0   7.9e-11   1.4e-06      11      97 ..     261     343 ..     256     350 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.9e-12
                         Rhodanese  11 kgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvy.....cdgggr 78 
                                       +++ +llDv++++   k hI g++ +     +++++ ++++l+ + el+e     gi+ ++++v+y     c gg +
  gi|330508722|ref|YP_004385150.1| 131 NEN-VLLDVSESA---KEHISGSIAI-----PYQEFLQGDSLKSVPELAEIlgnaGISSDDPLVIYgeclpCGGGPS 198
                                       444.399999866...58********.....77777777777777777777788************44444445555 PP

                         Rhodanese  79 aaaa..aallkklGyknvsvldGGfkawke 106
                                        a+a  +++lk+lG+++v++l+G +++wk 
  gi|330508722|ref|YP_004385150.1| 199 -ASAyvYWMLKSLGHEDVRILNGYVQDWKD 227
                                       .5555699******666***********96 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 7.9e-11
                         Rhodanese  11 kgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel..gidnkktvvvycdgggraaaaaal 85 
                                       +g+++++D+R+  eYe g Ip A+++     ++++  +++ l ++ el e+   +d++++vv + ++g + + ++ +
  gi|330508722|ref|YP_004385150.1| 261 SGQAQVVDARTVLEYESGTIPSAISI-----PYESVLDGDKLRNVNELDERffILDKEQQVVAFTNTGFKGSVLWLA 332
                                       455679********************.....555555555555555555555555***************7777989 PP

                         Rhodanese  86 lkklGyknvsvl 97 
                                       l+ +Gy + +++
  gi|330508722|ref|YP_004385150.1| 333 LEIMGY-DARLY 343
                                       988996.44433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 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:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2567.56
//
Query:       gi|330508723|ref|YP_004385151.1|  [L=517]
Description: rhodanese domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-19   69.8   0.0    8.9e-10   39.0   0.0    2.4  2  Rhodanese  Rhodanese-like domain
     0.0029   17.8   0.2     0.0081   16.4   0.0    1.8  2  Imm75      Putative Immunity protein 75


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 !   28.2   0.0   2.3e-10   2.1e-06      15     106 ..     130     225 ..     116     226 .. 0.73
   2 !   39.0   0.0     1e-13   8.9e-10      13      95 ..     261     339 ..     255     346 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.3e-10
                         Rhodanese  15 a.llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvy.....cdgggr.aaaaaa 84 
                                       + +lD++p++      I+gAvn++ ++++ +  + ++  e+ e l + gi++++ +v+      c gg + a ++++
  gi|330508723|ref|YP_004385151.1| 130 DiVLDISPSAT---RYIEGAVNINYERFYAEGGRFRSVGEIAELLGQAGISRNDSLVIAgeclpCGGGPSpAVFSYW 203
                                       24899998765...67*******6666666666666666666666666*********98444445566665555599 PP

                         Rhodanese  85 llkklGykn.vsvldGGfkawke 106
                                       +lk+lG ++ v+vldG++++w++
  gi|330508723|ref|YP_004385151.1| 204 ILKYLG-QEkVRVLDGSIEDWAA 225
                                       ******.666***********97 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 1e-13
                         Rhodanese  13 kvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel..gidnkktvvvycdgggraaaaaallk 87 
                                       +++++D+Rpp +++ g+IpgA+n+     + ++ +e++     e+l++   g+d+ +++vvy + g  a+ ++ +l+
  gi|330508723|ref|YP_004385151.1| 261 GAQIVDARPPGDFSIGSIPGAINI-----PFESVVEDETVRAQEDLEKVfvGLDKARPIVVYTNVGVEASLVWFALT 332
                                       346*********************.....334444444444444444448899***************888899999 PP

                         Rhodanese  88 klGyknvs 95 
                                         Gy + +
  gi|330508723|ref|YP_004385151.1| 333 LSGY-DAR 339
                                       9995.544 PP

>> Imm75  Putative Immunity protein 75
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.3   1.1e+04      51      71 ..      38      57 ..      33      63 .. 0.67
   2 !   16.4   0.0   9.1e-07    0.0081      29      72 ..     309     349 ..     300     359 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.3
                             Imm75 51 pdfagtptfgrrlyrlrdwtd 71
                                      p +agt t g       dwtd
  gi|330508723|ref|YP_004385151.1| 38 PALAGTET-GEFCPTCPDWTD 57
                                      67777776.555666778886 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 9.1e-07
                             Imm75  29 dkadrlmvttsvgeearlvyfnpdfagtptfgrrlyrlrdwtdd 72 
                                       dka  ++v t vg ea lv+f   ++g   +  rly  rdw ++
  gi|330508723|ref|YP_004385151.1| 309 DKARPIVVYTNVGVEASLVWFALTLSG---YDARLYTWRDWLEN 349
                                       89999*****************99988...678********876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 3831.23
//
Query:       gi|330508724|ref|YP_004385152.1|  [L=289]
Description: hypothetical protein MCON_2999 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-43  148.7  40.7      2e-43  148.7  40.7    1.4  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 !  148.7  40.7   1.1e-47     2e-43       2     235 ..      38     278 ..      36     279 .. 0.90

  Alignments for each domain:
  == domain 1  score: 148.7 bits;  conditional E-value: 1.1e-47
                              TauE   2 llagllaGfvagllGiGggliavPlLll.l.lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliG 76 
                                       +++g++aG+++gl+G Gg  i++P+  + + +++++a++t+++av++t++sg + h+ r+n+d +++l+++ ++++G
  gi|330508724|ref|YP_004385152.1|  38 VVVGFIAGVLGGLIGTGGCSIMLPAIHFwMgYSAPLAIGTTIFAVIFTAISGGYGHLVRRNLDRKAVLWIGGAGILG 114
                                       799*********************99998888*************************999***************** PP

                              TauE  77 allGallllllpse..llkllfgvlllllallmll.rkkr..srak....grerrptaillvligglvGllsGllGi 144
                                       ++lG++l++ l ++  ll+l++g++ ll a++m++  ++r     +    + + r++ +  +++g+l+G+l+G++G 
  gi|330508724|ref|YP_004385152.1| 115 VILGSWLFTMLVDHidLLQLILGLAFLLPAIRMIWeGAGRakP--RqegnEIPGRKSHW--AVFGFLIGILTGIVGL 187
                                       *********99999778*****************973333332..23333444444455..667788********** PP

                              TauE 145 GgGfllvpllllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlsertl 221
                                       GgG  lvp l++l+g p+  + ++sl+++++ ++++  + +++g v ++++l+l++g+++Ga+lGa + +r+++ tl
  gi|330508724|ref|YP_004385152.1| 188 GGGYALVPGLIYLFGAPVYITMGSSLAVMIPLAAVAGSIKLYQGFVALTTALILGAGTIVGAQLGAAVIKRFKPNTL 264
                                       ***************************999999999999899*********************************** PP

                              TauE 222 rrlfallllvlgvk 235
                                       +++f+l  l++++k
  gi|330508724|ref|YP_004385152.1| 265 KLIFGLYFLYVSAK 278
                                       *********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2246.81
//
Query:       gi|330508725|ref|YP_004385153.1|  [L=132]
Description: hypothetical protein MCON_3001 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.08   11.6   1.3       0.72    8.5   0.5    1.9  2  Ecm29      Proteasome stabiliser
       0.17   12.0   0.8        5.5    7.1   0.2    2.2  2  TetR_C_34  Tetracyclin repressor-like, C-terminal domain
       0.47   10.0   7.4        2.2    7.8   5.7    2.0  2  BID        BH3 interacting domain (BID)
        4.6    7.5   6.3    1.2e+02    3.0   0.1    3.7  4  BET        Bromodomain extra-terminal - transcription regulat


Domain annotation for each model (and alignments):
>> Ecm29  Proteasome stabiliser
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.5   0.00016      0.72      93     170 ..       2      79 ..       1      81 [. 0.82
   2 ?    1.8   0.0     0.016        73      89     109 ..      84     104 ..      81     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00016
                             Ecm29  93 dRlsaeerkellpkllkgis.....kkpsqhqarlfnlllklLgklklpprgskedealkellglsdkpedakflle 164
                                       +R+s++e++ l+  +++++      ++++q++a+++ +++++++++   ++g++  + ++ +l+l +  +d+  + +
  gi|330508725|ref|YP_004385153.1|   2 ERMSTDEKQRLMDGMMEKFFadltpEEKQQMMASMMPMMMEMMPQM---MEGKDPGNMMEMMLELMR--KDMPAMQQ 73 
                                       8****************88777777888888889999999999955...357787778888899885..99999999 PP

                             Ecm29 165 ffldfl 170
                                       ++++++
  gi|330508725|ref|YP_004385153.1|  74 MMTKMM 79 
                                       998886 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.016
                             Ecm29  89 ekgidRlsaeerkellpkllk 109
                                       ++ ++R+ +eer+e++p+++ 
  gi|330508725|ref|YP_004385153.1|  84 SMMLPRIGKEERVEFIPRMVA 104
                                       678999999999999999876 PP

>> TetR_C_34  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2    0.0012       5.5      51      85 ..      14      48 ..       8      70 .. 0.86
   2 ?    3.3   0.0     0.019        85      48      78 ..      77     107 ..      70     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0012
                         TetR_C_34 51 aalleralPelseeqaaallaaalalvaglwplah 85
                                        ++e+++ +l++e+ ++++a ++ +++ ++p   
  gi|330508725|ref|YP_004385153.1| 14 DGMMEKFFADLTPEEKQQMMASMMPMMMEMMPQMM 48
                                      56899999*******************99999765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.019
                         TetR_C_34  48 erlaalleralPelseeqaaallaaalalva 78 
                                       +++ ++l+  lP++++e+ ++++ +++a++ 
  gi|330508725|ref|YP_004385153.1|  77 KMMPQCLSMMLPRIGKEERVEFIPRMVAVLL 107
                                       5677899999*************99999875 PP

>> BID  BH3 interacting domain (BID)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   5.7   0.00049       2.2      95     155 ..       3      62 ..       2      81 .. 0.83
   2 ?    2.0   0.0     0.029   1.3e+02      86     127 ..      84     124 ..      73     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00049
                                       HHHCCSSTTSHHHHHHHHHCHCCCCCCCCHHHHHHHHHHHCTS--SSHCHHHHHHHHHHHH CS
                               BID  95 eldksiqpklvneLaaqfvneslseedrrkkLaaaleqvmqtipkDlekekamLvltmlLa 155
                                       ++ ++ + +l++ + ++f   +l+ e++++++a+ +  +m+ +p+ +e      ++ m+L 
  gi|330508725|ref|YP_004385153.1|   3 RMSTDEKQRLMDGMMEKFFA-DLTPEEKQQMMASMMPMMMEMMPQMMEGKDPGNMMEMMLE 62 
                                       56677788999999999998.99*************************9988888888874 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHCCSSTTSHHHHHHHHHCHCCCCCCCCHHHH CS
                               BID  86 arqLaqiGDeldksiqpklvneLaaqfvneslseedrrkkLa 127
                                          L +iG e   +  p++v  L +q  +  ++ee+r++ + 
  gi|330508725|ref|YP_004385153.1|  84 SMMLPRIGKEERVEFIPRMVAVLLEQGSD-GMTEEERTDLMK 124
                                       55677888888888889999999888777.677787776554 PP

>> BET  Bromodomain extra-terminal - transcription regulation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.026   1.2e+02       2      13 ..       4      15 ..       3      18 .. 0.87
   2 ?   -0.4   0.3      0.29   1.3e+03       2      12 ..      24      34 ..      23      49 .. 0.77
   3 ?    2.6   0.0     0.034   1.5e+02      18      37 ..      53      72 ..      50      77 .. 0.85
   4 ?    2.6   0.0     0.035   1.6e+02       2      17 ..     114     129 ..     113     132 .] 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.026
                               BET  2 mtyeeKkeLsee 13
                                      m+++eK+ L+++
  gi|330508725|ref|YP_004385153.1|  4 MSTDEKQRLMDG 15
                                      9*******9875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.29
                               BET  2 mtyeeKkeLse 12
                                      +t eeK++ + 
  gi|330508725|ref|YP_004385153.1| 24 LTPEEKQQMMA 34
                                      68899999765 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.034
                               BET 18 pgeklgrvveIIqerepelq 37
                                      pg++++ ++e++++++p  q
  gi|330508725|ref|YP_004385153.1| 53 PGNMMEMMLELMRKDMPAMQ 72
                                      899*************7654 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.035
                               BET   2 mtyeeKkeLseeInkL 17 
                                       mt ee++ L++++ k 
  gi|330508725|ref|YP_004385153.1| 114 MTEEERTDLMKRVAKI 129
                                       9*********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1303  (0.0726756); expected 358.6 (0.02)
Passed bias filter:                      747  (0.0416643); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.51
# Mc/sec: 784.94
//
Query:       gi|330508726|ref|YP_004385154.1|  [L=415]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete 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-24   85.3   0.1    4.8e-24   84.5   0.1    1.4  1  Transposase_20  Transposase IS116/IS110/IS902 family
    5.7e-23   81.5   0.3    4.4e-22   78.6   0.0    2.5  3  DEDD_Tnp_IS110  Transposase
  ------ inclusion threshold ------
      0.053   11.5   0.1      0.069   11.1   0.1    1.1  1  Prominin        Prominin


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.1   8.1e-28   4.8e-24       2      86 ..     249     334 ..     248     335 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 8.1e-28
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaaira 78 
                                       ++ +s+pGiG++ aa++laeig+ r f+++++la+++G++p ++qS++k   g+i+k+G++++R++L++ A+aa+++
  gi|330508726|ref|YP_004385154.1| 249 QIAMSVPGIGFTAAATILAEIGNYRDFSTSDKLASWCGIVPNVYQSADKLITGSITKQGSKHIRWMLVQVAQAALKK 325
                                       6789*********************************************99***********************966 PP

                    Transposase_20  79 n.pelrayy 86 
                                       + +++r+++
  gi|330508726|ref|YP_004385154.1| 326 ReSRFRRFF 334
                                       659999885 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   7.4e-26   4.4e-22       1     151 [.       9     150 ..       9     153 .. 0.90
   2 ?   -1.0   0.0      0.24   1.5e+03      20      40 ..     186     206 ..     179     218 .. 0.78
   3 ?   -2.4   0.0      0.65   3.9e+03      26      69 ..     322     365 ..     316     369 .. 0.71

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 7.4e-26
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G+D++k+   a++++++g+++ ++  ++d ++l  + ++   +  +  v++e+tg y++ +v+++le++i++++ n
  gi|330508726|ref|YP_004385154.1|   9 CGVDIHKRFLIATILSRDGTKIQKR-YSTDIDDLFGFRDW-VLENNCDCVAIESTGVYWY-PVNAVLENKIELILAN 82 
                                       7********************8775.67777767777777.3335667799********9.588999********** PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLd 151
                                       ++++k++      ++KtD++D+++IA++++  + + p++  +++ ++Lr+ltr re+lvk+r++ kn++++ L+
  gi|330508726|ref|YP_004385154.1|  83 ARQIKHT-----PGRKTDSIDSEWIAEVAL-NNLIYPSRIFPKEERDLRRLTRTRESLVKMRSQIKNQVHQGLE 150
                                       ******9.....59****************.**************************************99886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.24
                    DEDD_Tnp_IS110  20 kvllservpndeegleallek 40 
                                       +++ s+rv+n+e++++a +  
  gi|330508726|ref|YP_004385154.1| 186 EEIPSKRVKNNEDKIRAAIRT 206
                                       678899********9998876 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.65
                    DEDD_Tnp_IS110  26 rvpndeeglealleklaakagevlvvveatghygallvafllea 69 
                                        +++ e+++++++ +++a++g+   vv    ++   l+++l ++
  gi|330508726|ref|YP_004385154.1| 322 ALKKRESRFRRFFLRIKARKGHNVAVVALARKILCILYHLLMNQ 365
                                       56778888888888888888877777777777777777766655 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   1.2e-05     0.069     174     304 ..     133     270 ..     125     321 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.2e-05
                          Prominin 174 sketvkrgled.lrtflkdvpqhidhvlvqnyeelekhvsddLddag..khlgldl.adtlesnvlpaLaelerlle 246
                                       s  ++++++++ + + l++ + ++ +vl  n+ +   h++d L + +  + +++++ ++++++n  +  a++++ l+
  gi|330508726|ref|YP_004385154.1| 133 SLVKMRSQIKNqVHQGLESCSIKLSSVLSDNFGKSGRHILDGLIKGEniDRIIEEIpSKRVKNNEDKIRAAIRTGLD 209
                                       4555555555414566899999999*************999996655456788888345677776667778888888 PP

                          Prominin 247 nlk..eakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsn.lCqseeCskilssle 304
                                       +++   ++ +L+++++l+k+L +  s+++d ++g k+dl+ a+s   ++ +   +il +  
  gi|330508726|ref|YP_004385154.1| 210 ETQifLIQSHLNTIDSLTKKLDEIDSEIKDKISGRKKDLQIAMSVpGIGFTAAATILAEIG 270
                                       877335789*******************************999986666555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); 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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3072.51
//
Query:       gi|330508727|ref|YP_004385155.1|  [L=260]
Description: 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-64  217.7   0.0    2.1e-64  217.3   0.0    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    8.7e-55  185.2   0.0    1.1e-54  184.9   0.0    1.1  1  adh_short     short chain dehydrogenase
    5.4e-16   59.0   0.0    7.3e-16   58.6   0.0    1.1  1  KR            KR domain
     0.0039   16.7   0.1     0.0064   16.0   0.1    1.4  1  Epimerase     NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
       0.17   11.4   0.0       0.61    9.6   0.0    1.8  2  MTS           Methyltransferase small domain


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.3   0.0   5.8e-68   2.1e-64       3     234 .]      15     258 ..      13     258 .. 0.95

  Alignments for each domain:
  == domain 1  score: 217.3 bits;  conditional E-value: 5.8e-68
                                       TTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvnna 77 
                                         gIG+aiA+ la+eGa  ++t +++e+ +k ve++ +++g++ ++++DVtde+ +e++ ++v ek+g++Dilvnna
  gi|330508727|ref|YP_004385155.1|  15 TYGIGEAIARVLAKEGALSIITGRSREEgRKVVEAINSAGGRSeYYPLDVTDEKRIEEVSKAVYEKYGRIDILVNNA 91 
                                       57**************************99999999999996659******************************** PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealt 152
                                       g+a + ++p++e  r+e++ ++dvn++++fl++k+++p+m+++  g+iv +ss+ + ++ p+  ay+a+Kaa   ++
  gi|330508727|ref|YP_004385155.1|  92 GVAGP-NKPTHEYARAEWEWVFDVNVTGAFLCTKYVVPYMQRQksGNIVYISSIYGIIGAPDLPAYHATKAANRVMA 167
                                       *****.**********************************99989******************************** PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT.........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGT CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgikg.........fdelleelearaplgrlgtpeevaeaalfLasdeas 220
                                       +  A  +++++iRvN+v+pg+i T++++++ +          +el+++l+a++p+g++g+p+++a  +l+L+sdea+
  gi|330508727|ref|YP_004385155.1| 168 KIDALLYAKDNIRVNSVHPGFIWTPLVDNFLQeqcnksglsCEELKKQLDAKHPIGHIGEPDDIAYGVLYLVSDEAK 244
                                       **************************888765455445555678********************************* PP

                                       T--SEEEEESTTGG CS
                      adh_short_C2 221 yitGqtlvvDgGlt 234
                                       ++tG++l++DgG+t
  gi|330508727|ref|YP_004385155.1| 245 FVTGSELIIDGGYT 258
                                       *************8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.9   0.0   3.1e-58   1.1e-54       2     190 ..       8     197 ..       7     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 184.9 bits;  conditional E-value: 3.1e-58
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                       v+++tG + GIG aia+ lakeGa  ++++rs e+ ++v++ ++++g +  ++++Dvtd++++e++ +++ +k+g++
  gi|330508727|ref|YP_004385155.1|   8 VAIITGSTYGIGEAIARVLAKEGALSIITGRSREEGRKVVEAINSAGGRSEYYPLDVTDEKRIEEVSKAVYEKYGRI 84 
                                       89*************************************************************************** PP

                                       SEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  79 dvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       d+LvnNAG+   ++p++e+  +ewe v++vN+tg+fl+t+ v+p+m +q+sG+Iv +sS+ g  + + ++aY A+Ka
  gi|330508727|ref|YP_004385155.1|  85 DILVNNAGVaGPNKPTHEYARAEWEWVFDVNVTGAFLCTKYVVPYMQRQKSGNIVYISSIYGIIGAPDLPAYHATKA 161
                                       *********8899**************************************************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakel 190
                                       a + +++  a  +a+++irvn+v+PG++ T+++ + 
  gi|330508727|ref|YP_004385155.1| 162 ANRVMAKIDALLYAKDNIRVNSVHPGFIWTPLVDNF 197
                                       *******************************98876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0     2e-19   7.3e-16       4     155 ..      10     162 ..       8     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2e-19
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       +itG + g+G ++ar la++ga +++ ++Rs   +e+ ++ ++++++ g + e++++Dv+d++ +e++ +++ ++ +
  gi|330508727|ref|YP_004385155.1|  10 IITGSTYGIGEAIARVLAKEGALSII-TGRS---REEGRKVVEAINSAGGRSEYYPLDVTDEKRIEEVSKAVYEKYG 82 
                                       8*********************9985.8999...5677779************************************ PP

                                       ---EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  81 pikGvihaAgvlr.dklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaa 152
                                       +i   ++ Agv+  +k+  e   +++e v+   v+Ga    +++ +    ++   +v++SSi g++g++   +Y a+
  gi|330508727|ref|YP_004385155.1|  83 RIDILVNNAGVAGpNKPTHEYARAEWEWVFDVNVTGAFLCTKYVVPymqrQKSGNIVYISSIYGIIGAPDLPAYHAT 159
                                       ***********996789999****************988877665445559999********************875 PP

                                       HHH CS
                                KR 153 Naf 155
                                        a 
  gi|330508727|ref|YP_004385155.1| 160 KAA 162
                                       443 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.8e-06    0.0064       2     120 ..      10     146 ..       9     166 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-06
                                       EEETTTSHHHHHHHHHHHHCT.SE.EEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHH...HH..T CS
                         Epimerase   2 lVtGatGfiGsalvkallekg.ye.vigldrlssasntarledl.......elveldltdrsalerlfk...ee..q 64 
                                       ++tG t  iG a+++ l+++g    ++g++r++ ++  ++   +       e + ld+td++++e++ k   e+  +
  gi|330508727|ref|YP_004385155.1|  10 IITGSTYGIGEAIARVLAKEGaLSiITGRSREEGRKVVEA---InsaggrsEYYPLDVTDEKRIEEVSKavyEKygR 83 
                                       79*******************6444556666644444444...2456***************776654411133479 PP

                                       -SEEEE--S---HHH.HHHSHHH....HHHHHTHH....HHHHHHHHHHHTCTEEEEEEEGGGGT CS
                         Epimerase  65 pdavihlAavggvaa.ssedpad....fieknlqg....tlnlleaarkagvkrllflsSsevYG 120
                                       +d+ ++ A+v+g++  ++e++ +    +++ n+ g    t  ++ ++++++  +++++sS  +YG
  gi|330508727|ref|YP_004385155.1|  84 IDILVNNAGVAGPNKpTHEYARAewewVFDVNVTGaflcTKYVVPYMQRQKSGNIVYISS--IYG 146
                                       999999999776654144444431222445665552222455666666777778888887..666 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.48   1.7e+03     126     143 ..      23      40 ..      16      52 .. 0.78
   2 ?    9.6   0.0   0.00017      0.61      20      98 ..     123     202 ..     120     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.48
                                       HHHEEEEEEEEEEEETTS CS
                               MTS 126 keaLkegGeLliVanrkl 143
                                       +++L+++G L i++ r  
  gi|330508727|ref|YP_004385155.1|  23 ARVLAKEGALSIITGRSR 40 
                                       689999****99987765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00017
                                       HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTT CS
                               MTS  20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleanklevevvasdvleevee 95 
                                       +k  + +++ ++sg+++ + + +G++ga  + ++  ++  + v ++  Al  ak n++ n ++  ++++ +++++ +
  gi|330508727|ref|YP_004385155.1| 123 TKYVVPYMQRQKSGNIVYISSIYGIIGAPDLPAYHATKaANRVMAKIDALLYAKDNIRVNSVHPGFIWTPLVDNFLQ 199
                                       7788999*********************9777777666599999*******************99**9999999887 PP

                                       S-E CS
                               MTS  96 kkf 98 
                                       +++
  gi|330508727|ref|YP_004385155.1| 200 EQC 202
                                       776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2005.92
//
Query:       gi|330508728|ref|YP_004385156.1|  [L=278]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0051   17.1   0.0      0.021   15.2   0.0    1.9  2  DUF4376   Domain of unknown function (DUF4376)


Domain annotation for each model (and alignments):
>> DUF4376  Domain of unknown function (DUF4376)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-06     0.021      30      87 ..      42     102 ..      37     104 .. 0.87
   2 ?   -2.5   0.0      0.38   6.8e+03      60      71 ..     223     234 ..     202     243 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-06
                           DUF4376  30 rarlsgvllsaklageqgee...aWtladntvvtLtadqlialgqavaqhkqaifdrerel 87 
                                        + +++ ++++k+ ++++e      +  d  +v Lta+ + a++  ++ ++++i+ +++e+
  gi|330508728|ref|YP_004385156.1|  42 YRFVTETAMEFKSIEDSTEIsmlILRSRDSGAVNLTAQNMSAIISEISSYGDEIYNTQQEV 102
                                       56778888889998888777888889999****************************9986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.38
                           DUF4376  60 tLtadqlialgq 71 
                                        Lt+d +++l +
  gi|330508728|ref|YP_004385156.1| 223 SLTPDIMEQLSD 234
                                       466666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1973.42
//
Query:       gi|330508729|ref|YP_004385157.1|  [L=118]
Description: 4Fe-4S ferredoxin, iron-sulfur binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   24.0  13.3      0.023   15.3   0.4    2.5  2  Fer4_7    4Fe-4S dicluster domain
    8.2e-05   22.3  12.8    0.00062   19.5   3.9    2.9  2  Fer4      4Fe-4S binding domain
     0.0019   18.2   3.7     0.0019   18.2   3.7    2.7  3  Fer4_6    4Fe-4S binding domain
     0.0035   17.4   2.4     0.0035   17.4   2.4    2.9  3  Fer4_2    4Fe-4S binding domain
     0.0077   16.4  12.4     0.0077   16.4  12.4    2.0  2  Fer4_9    4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.02   15.0  12.1       0.02   15.0  12.1    2.2  3  Fer4_21   4Fe-4S dicluster domain
      0.036   14.6   1.4      0.036   14.6   1.4    2.8  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.046   13.8  16.9      0.071   13.2   1.5    2.4  2  Fer4_10   4Fe-4S dicluster domain
       0.19   11.8   0.0        3.8    7.7   0.0    2.3  2  DUF3885   Domain of unknown function (DUF3885)


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 !   15.3   0.4   1.2e-05     0.023      30      46 ..      15      31 ..       3      42 .. 0.84
   2 !   12.6   7.1   7.7e-05      0.15       2      28 ..      52      79 ..      51     118 .] 0.66

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                            Fer4_7 30 kveidpekClgCgaCva 46
                                      +++idpekC+ Cg+C++
  gi|330508729|ref|YP_004385157.1| 15 HPTIDPEKCVKCGMCMN 31
                                      6799***********86 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.7e-05
                            Fer4_7  2 Ci.gCgaCvaaCpvkaieldeeenekgt 28
                                      Ci gC+ C++ C+ +ai+++e+e  +++
  gi|330508729|ref|YP_004385157.1| 52 CIvGCNTCANLCMGNAISFPEKETIREI 79
                                      766*****************98777643 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   3.9   3.1e-07   0.00062       1      15 [.      16      30 ..      16      33 .. 0.93
   2 !    7.1   1.6    0.0024       4.9       9      23 ..      54      68 ..      54      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.1e-07
                                      EEEETTTSSS-THHH CS
                              Fer4  1 vvideekCigCGaCv 15
                                      ++id+ekC++CG C+
  gi|330508729|ref|YP_004385157.1| 16 PTIDPEKCVKCGMCM 30
                                      68************8 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0024
                                      SS-THHHHHSTTTEE CS
                              Fer4  9 igCGaCvevCPvgAI 23
                                      +gC++C++ C  +AI
  gi|330508729|ref|YP_004385157.1| 54 VGCNTCANLCMGNAI 68
                                      79********66666 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   3.7   9.4e-07    0.0019       2      17 ..      16      31 ..      15      32 .. 0.92
   2 !    9.0   3.2   0.00078       1.6       2      20 ..      45      64 ..      44      68 .. 0.81
   3 ?   -7.7   4.7         9   1.8e+04       9      12 ..     112     116 ..     111     116 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.4e-07
                            Fer4_6  2 veidpdkCigCgdCvr 17
                                      ++idp+kC+ Cg C++
  gi|330508729|ref|YP_004385157.1| 16 PTIDPEKCVKCGMCMN 31
                                      89************85 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00078
                            Fer4_6  2 veidpdkCi.gCgdCvrvCP 20
                                      v+  p+ Ci gC+ C++ C 
  gi|330508729|ref|YP_004385157.1| 45 VVARPNQCIvGCNTCANLCM 64
                                      67789***88******9996 PP

  == domain 3  score: -7.7 bits;  conditional E-value: 9
                            Fer4_6   9 Ci.gC 12 
                                       C+ gC
  gi|330508729|ref|YP_004385157.1| 112 CDgGC 116
                                       77446 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   2.4   1.7e-06    0.0035       1      20 [.      14      32 ..      14      34 .. 0.93
   2 !    7.9   3.1    0.0018       3.7       3      20 ..      45      63 ..      43      64 .. 0.81
   3 ?   -7.7   5.9         9   1.8e+04      10      15 ..     112     116 ..     109     118 .] 0.47

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.7e-06
                            Fer4_2  1 apvvvdtdrCigCgaCvsaC 20
                                      +++ +d+++C+ Cg C  +C
  gi|330508729|ref|YP_004385157.1| 14 WHPTIDPEKCVKCGMC-MNC 32
                                      79**************.777 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0018
                            Fer4_2  3 vvvdtdrCi.gCgaCvsaC 20
                                      vv+ ++ Ci gC++C + C
  gi|330508729|ref|YP_004385157.1| 45 VVARPNQCIvGCNTCANLC 63
                                      6666889*66*****9999 PP

  == domain 3  score: -7.7 bits;  conditional E-value: 9
                            Fer4_2  10 CigCga 15 
                                       C g g 
  gi|330508729|ref|YP_004385157.1| 112 CDG-GC 116
                                       432.33 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4  12.4   3.9e-06    0.0077       1      51 []      22      68 ..      22      68 .. 0.89
   2 ?    0.9  12.7      0.27   5.3e+02       3      34 ..      54     109 ..      51     118 .] 0.67

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.9e-06
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaC.igCgaCveaCpkgai 51
                                      kC++Cg C++ C  +v+   + +  ++  +    +C +gC++C++ C  +ai
  gi|330508729|ref|YP_004385157.1| 22 KCVKCGMCMN-CGRNVYDWTEEGPVVARPN----QCiVGCNTCANLCMGNAI 68
                                      7*********.******9999999988654....6*999********98876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.27
                            Fer4_9   3 tgCgaCveaCpagvvvedaaerkarlraase........................e 34 
                                       +gC++C + C  ++++  ++e+++++ ++++                        +
  gi|330508729|ref|YP_004385157.1|  54 VGCNTCANLCMGNAISFPEKETIREIYKREKiwskvkkqleeegkiktkqkseeeS 109
                                       47999999999999999998888888777666666655555555555555555553 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0  12.1   9.8e-06      0.02       2      52 ..      17      64 ..      16      70 .. 0.75
   2 ?    8.5   3.1    0.0011       2.1       6      27 ..      50      69 ..      45      83 .. 0.63
   3 ?   -3.1   1.1       4.4   8.8e+03      40      41 ..     110     111 ..      93     118 .] 0.52

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.8e-06
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeC.vGCnlCssvCP 52
                                      +id++kC++Cg C+  C  + ++    +++  +  + ++C vGCn C++ C 
  gi|330508729|ref|YP_004385157.1| 17 TIDPEKCVKCGMCM-NCGRNVYD---WTEEGPVVARPNQCiVGCNTCANLCM 64
                                      69***********7.57755554...5555566667888857*********5 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0011
                           Fer4_21  6 dkCi.gCgkCliaCedtshqaie 27
                                      ++Ci gC+ C+  C     +ai+
  gi|330508729|ref|YP_004385157.1| 50 NQCIvGCNTCANLCMG---NAIS 69
                                      5665467777777764...4444 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4.4
                           Fer4_21  40 eC 41 
                                        C
  gi|330508729|ref|YP_004385157.1| 110 GC 111
                                       22 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.4   1.8e-05     0.036       1      27 [.      18      44 ..      18      51 .. 0.87
   2 ?    0.8   4.0      0.38   7.5e+02       5      16 ..      51      63 ..      48      66 .. 0.85
   3 ?   -1.5   1.0       1.9   3.8e+03      33      40 ..     101     108 ..      73     117 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddegg 27
                                      +D ++C+ cg C +   +v++  +eg 
  gi|330508729|ref|YP_004385157.1| 18 IDPEKCVKCGMCMNCGRNVYDWTEEGP 44
                                      899******************999864 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.38
                           Fer4_13  5 tCi.acgaCvela 16
                                      +Ci +c++C++l+
  gi|330508729|ref|YP_004385157.1| 51 QCIvGCNTCANLC 63
                                      77659******99 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.9
                           Fer4_13  33 eqptseee 40 
                                        +++seee
  gi|330508729|ref|YP_004385157.1| 101 TKQKSEEE 108
                                       22333444 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.5   3.6e-05     0.071       1      17 [.      15      31 ..      15      41 .. 0.89
   2 ?    5.9   8.0     0.007        14       3      41 ..      46     104 ..      44     118 .] 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                           Fer4_10  1 kvvidddtCirCgkCvk 17
                                      ++ id+++C++Cg C++
  gi|330508729|ref|YP_004385157.1| 15 HPTIDPEKCVKCGMCMN 31
                                      5689***********98 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.007
                           Fer4_10   3 vidddtCi.rCgkCvkaCPadl....................tsvgakgeaseeeavrkk 41 
                                       v  +++Ci +C++C + C + +                    ++v+++ e++++ + + k
  gi|330508729|ref|YP_004385157.1|  46 VARPNQCIvGCNTCANLC-MGNaisfpeketireiykrekiwSKVKKQLEEEGKIKTKQK 104
                                       678999*77*********.65589999888888888888877333333333333333333 PP

>> DUF3885  Domain of unknown function (DUF3885)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.13   2.6e+02      28      38 .]       2      12 ..       1      12 [. 0.91
   2 ?    7.7   0.0    0.0019       3.8      10      29 ..      67      86 ..      65      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.13
                           DUF3885 28 dWIlDYdreei 38
                                       W++ Y re+i
  gi|330508729|ref|YP_004385157.1|  2 AWLVGYPREKI 12
                                      5********98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0019
                           DUF3885 10 dvisnnketlkelYekyndW 29
                                       + + +ket++e+Y++ + W
  gi|330508729|ref|YP_004385157.1| 67 AISFPEKETIREIYKREKIW 86
                                      67899*********987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1508  (0.0841095); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         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: 897.36
//
Query:       gi|330508730|ref|YP_004385158.1|  [L=269]
Description: hypothetical protein MCON_3008 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-47  161.0   0.0    4.3e-47  160.7   0.0    1.1  1  DUF169    Uncharacterised ArCR, COG2043
  ------ inclusion threshold ------
       0.24    9.5   0.0       0.34    9.0   0.0    1.1  1  Pox_F12L  Poxvirus F12L protein


Domain annotation for each model (and alignments):
>> DUF169  Uncharacterised ArCR, COG2043
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.7   0.0   4.7e-51   4.3e-47       2     205 ..      27     232 ..      26     233 .. 0.96

  Alignments for each domain:
  == domain 1  score: 160.7 bits;  conditional E-value: 4.7e-51
                            DUF169   2 LaealrlktePVavkfsdekpelpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfkelpeklks 78 
                                       ++  l+l+ +PV+v f++ ++ ++ +  ki +++r+Cq+ + ar +g+ vv++ae ++Cp +a a+Gf++lpe l++
  gi|330508730|ref|YP_004385158.1|  27 MKAILGLSASPVGVRFLNAEEAVE-GA-KILDRHRYCQALMRAR-HGQNVVLDAEGISCPAAAQAFGFRPLPEPLRT 100
                                       7889***************99743.33.455667**********.******************************** PP

                            DUF169  79 g.....egylkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrlnvs 150
                                       g      g+++ +++a++++e++p le+g++  + + pLekae+ Pd+vv+  + e+lm++v ++++++gg+r++++
  gi|330508730|ref|YP_004385158.1| 101 GkglvgFGIVSEEKVAQEMFEQMPHLEKGAIGQIHLFPLEKAEQLPDLVVVEDEVEKLMWIVLSYMHAQGGERVQSN 177
                                       ***************************************************************************** PP

                            DUF169 151 fpgngaaCadivaypykegepniglgdpgarkfaklkddelafgiPyelleemve 205
                                       ++  +a+C d++++py e++ n+++g++g+r ++++  +e ++g+P++ l+++++
  gi|330508730|ref|YP_004385158.1| 178 TAVLQATCVDSTVIPYLEKRLNFSFGCYGCRDATDMASGEAVLGFPASYLPDIIQ 232
                                       **************************************************99986 PP

>> Pox_F12L  Poxvirus F12L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   3.8e-05      0.34       8      45 ..      44      81 ..      41      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 3.8e-05
                          Pox_F12L  8 nekdtlevvtalkevklsivlartreGkgvivsaenle 45
                                      n++++ e  + l++++++ +l+r+r+G+ v+++ae+++
  gi|330508730|ref|YP_004385158.1| 44 NAEEAVEGAKILDRHRYCQALMRARHGQNVVLDAEGIS 81
                                      56788899999************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2022.64
//
Query:       gi|330508731|ref|YP_004385159.1|  [L=100]
Description: hypothetical protein MCON_3009 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 739.79
//
Query:       gi|330508732|ref|YP_004385160.1|  [L=61]
Description: hypothetical protein MCON_3010 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 467.25
//
Query:       gi|330508733|ref|YP_004385161.1|  [L=73]
Description: ferredoxin [Methanosaeta concilii GP6]
Scores for complete 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   68.7   2.0    5.4e-19   68.5   2.0    1.1  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    7.4e-16   58.7   3.5    8.4e-16   58.5   3.5    1.0  1  Fer4_15   4Fe-4S single cluster domain
    4.7e-05   23.0   9.3    0.00033   20.3   5.4    2.4  2  Fer4      4Fe-4S binding domain
      7e-05   22.9   3.5    0.00035   20.6   3.6    1.9  1  Fer4_10   4Fe-4S dicluster domain
     0.0011   19.1   0.3     0.0011   19.1   0.3    1.8  2  Fer4_21   4Fe-4S dicluster domain
     0.0017   18.9   0.3     0.0026   18.3   0.3    1.3  1  Fer4_17   4Fe-4S dicluster domain
     0.0049   16.9   2.8     0.0049   16.9   2.8    2.3  2  Fer4_2    4Fe-4S binding domain
     0.0052   17.4   4.0      0.013   16.1   1.4    2.1  2  Fer4_7    4Fe-4S dicluster domain
     0.0083   16.2   2.5     0.0083   16.2   2.5    2.3  2  Fer4_6    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.034   14.6   2.7      0.049   14.1   2.7    1.5  1  Fer4_8    4Fe-4S dicluster domain
      0.057   13.6   3.3      0.057   13.6   3.3    2.1  2  Fer4_9    4Fe-4S dicluster domain
       0.15   11.7   0.0       0.23   11.0   0.0    1.3  1  GCIP      Grap2 and cyclin-D-interacting


Domain annotation for each model (and alignments):
>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   2.0   3.6e-22   5.4e-19       1      58 []       6      72 ..       6      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 3.6e-22
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqpts.........eeekadaeeAadaCPvesIgv 58
                                      +Dr+ Ci+cg+C+e +Pd+Fee+++++ s+v+e+ ++         +++ +++ +A daCP e I+v
  gi|330508733|ref|YP_004385161.1|  6 IDREGCISCGTCWEDCPDFFEENPDDNLSQVVEKYRTgglgegeapDDLLSCVVDASDACPAEVIHV 72
                                      8*******************************95443355555555********************7 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   3.5   5.6e-19   8.4e-16       1      66 []       4      72 ..       4      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 5.6e-19
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfelde.dglasvl..lddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                      Vv+Dr+ Ci+cg C++ +p++fe++  d l++v+    +g ++ege pdd+  ++ +A +aCP+++I+v
  gi|330508733|ref|YP_004385161.1|  4 VVIDREGCISCGTCWEDCPDFFEENPdDNLSQVVekYRTGGLGEGEAPDDLLSCVVDASDACPAEVIHV 72
                                      89***********************95578888877556778899**********************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   5.4   2.2e-07   0.00033       1      19 [.       4      22 ..       4      23 .. 0.95
   2 ?    4.3   0.1     0.027        40      16      23 ..      63      70 ..      62      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.2e-07
                                      EEEETTTSSS-THHHHHST CS
                              Fer4  1 vvideekCigCGaCvevCP 19
                                      vvid e Ci CG+C e CP
  gi|330508733|ref|YP_004385161.1|  4 VVIDREGCISCGTCWEDCP 22
                                      69***************** PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.027
                                      HHSTTTEE CS
                              Fer4 16 evCPvgAI 23
                                      ++CP ++I
  gi|330508733|ref|YP_004385161.1| 63 DACPAEVI 70
                                      79***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 !   20.6   3.6   2.3e-07   0.00035       1      24 [.       3      36 ..       3      68 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.3e-07
                           Fer4_10  1 kvvidddtCirCgkCvkaCPadl..........t 24
                                      kvvid++ Ci Cg+C + CP  +           
  gi|330508733|ref|YP_004385161.1|  3 KVVIDREGCISCGTCWEDCPDFFeenpddnlsqV 36
                                      689*****************97777777775431 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.3   7.2e-07    0.0011       2      20 ..       5      23 ..       4      43 .. 0.89
   2 ?   -0.5   0.1      0.94   1.4e+03      48      57 ..      62      70 ..      50      72 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.2e-07
                           Fer4_21  2 ridedkCigCgkCliaCed 20
                                      +id++ Ci+Cg C   C+d
  gi|330508733|ref|YP_004385161.1|  5 VIDREGCISCGTCWEDCPD 23
                                      69***************98 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.94
                           Fer4_21 48 ssvCPvedci 57
                                      s+ CP  ++i
  gi|330508733|ref|YP_004385161.1| 62 SDACPA-EVI 70
                                      456774.555 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   1.7e-06    0.0026       2      49 ..      11      60 ..      10      69 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                           Fer4_17  2 CiqCgyClpeCps.yeaydn.epkkllraaklglleeaekeekaslCieC 49
                                      Ci+Cg C + Cp  +e++++ +  +++++++ g l+e e+ +   +C+  
  gi|330508733|ref|YP_004385161.1| 11 CISCGTCWEDCPDfFEENPDdNLSQVVEKYRTGGLGEGEAPDDLLSCVVD 60
                                      ************62444554156689999888766666777777777755 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.8   3.3e-06    0.0049       2      21 ..       3      22 ..       2      23 .. 0.89
   2 ?    2.3   0.4      0.14   2.1e+02      18      22 .]      63      67 ..      55      67 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.3e-06
                            Fer4_2  2 pvvvdtdrCigCgaCvsa.CP 21
                                      +vv+d++ Ci+Cg+C +  CP
  gi|330508733|ref|YP_004385161.1|  3 KVVIDREGCISCGTC-WEdCP 22
                                      689************.77798 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                            Fer4_2 18 saCPa 22
                                      +aCPa
  gi|330508733|ref|YP_004385161.1| 63 DACPA 67
                                      89997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.4   8.4e-06     0.013      29      49 ..       2      22 ..       1      24 [. 0.92
   2 ?    1.8   0.0      0.25   3.7e+02      10      17 ..      63      70 ..      48      72 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.4e-06
                            Fer4_7 29 ekveidpekClgCgaCvavCP 49
                                       kv+id e C++Cg C + CP
  gi|330508733|ref|YP_004385161.1|  2 TKVVIDREGCISCGTCWEDCP 22
                                      57899***************9 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.25
                            Fer4_7 10 aaCpvkai 17
                                      +aCp+++i
  gi|330508733|ref|YP_004385161.1| 63 DACPAEVI 70
                                      67887776 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.5   5.5e-06    0.0083       1      20 [.       3      22 ..       3      28 .. 0.92
   2 ?    2.6   0.4       0.1   1.6e+02      17      24 .]      63      70 ..      57      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.5e-06
                            Fer4_6  1 vveidpdkCigCgdCvrvCP 20
                                      +v+id++ Ci+Cg C   CP
  gi|330508733|ref|YP_004385161.1|  3 KVVIDREGCISCGTCWEDCP 22
                                      79*************99999 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.1
                            Fer4_6 17 rvCPegai 24
                                      ++CP+ +i
  gi|330508733|ref|YP_004385161.1| 63 DACPAEVI 70
                                      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 ?   14.1   2.7   3.3e-05     0.049       4      27 ..      10      34 ..       7      69 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                            Fer4_8  4 kCieCgaCqsaCpvlrrtk.khlld 27
                                       Ci Cg C + Cp + +++ +++l+
  gi|330508733|ref|YP_004385161.1| 10 GCISCGTCWEDCPDFFEENpDDNLS 34
                                      6***********9555544333333 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   3.3   3.8e-05     0.057      34      48 ..       9      23 ..       1      26 [. 0.77
   2 ?    1.3   0.1      0.26   3.8e+02      10      17 ..      63      70 ..      55      72 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                            Fer4_9 34 eaCigCgaCveaCpk 48
                                      e Ci+Cg+C e Cp 
  gi|330508733|ref|YP_004385161.1|  9 EGCISCGTCWEDCPD 23
                                      369999999999995 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.26
                            Fer4_9 10 eaCpagvv 17
                                      +aCpa+v+
  gi|330508733|ref|YP_004385161.1| 63 DACPAEVI 70
                                      57888876 PP

>> GCIP  Grap2 and cyclin-D-interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00015      0.23      93     123 ..       8      39 ..       5      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                                       --------HHHHHHHTT.TTS-SSHHHHHHHH CS
                              GCIP  93 eetlistGvVWeaCdal.kklpkdNktAilra 123
                                       +e  is+G++We C  + ++ p dN++ ++ +
  gi|330508733|ref|YP_004385161.1|   8 REGCISCGTCWEDCPDFfEENPDDNLSQVVEK 39 
                                       67789*********8887********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 585.80
//
Query:       gi|330508734|ref|YP_004385162.1|  [L=93]
Description: hypothetical protein MCON_3013 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   13.1   0.0      0.072   12.9   0.0    1.1  1  Fam20C    Golgi casein kinase, C-terminal, Fam20


Domain annotation for each model (and alignments):
>> Fam20C  Golgi casein kinase, C-terminal, Fam20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     4e-06     0.072     132     164 ..       6      38 ..       2      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-06
                            Fam20C 132 GrpshdelsilaPlyqCClirkstlerlkllas 164
                                       G  +   +sil P +qCC++r + + r  ++a+
  gi|330508734|ref|YP_004385162.1|   6 GLVQDGRFSILMPRHQCCTVRLTRIARPASIAE 38 
                                       66677789*************988777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.20s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 786.20
//
Query:       gi|330508735|ref|YP_004385163.1|  [L=197]
Description: ABC transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-21   75.4  16.1    4.1e-21   75.4  16.1    1.8  2  ABC2_membrane    ABC-2 type transporter
    4.7e-16   58.8  22.7    5.4e-16   58.6  22.7    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
    2.3e-05   23.8  21.5    5.9e-05   22.5  21.5    1.5  1  ABC2_membrane_2  ABC-2 family transporter protein
     0.0025   17.5   8.7     0.0035   17.0   8.7    1.2  1  DUF368           Domain of unknown function (DUF368)


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 !   75.4  16.1   9.3e-25   4.1e-21      63     208 ..      13     157 ..      10     159 .. 0.91
   2 ?    0.3   0.5      0.09     4e+02     105     125 ..     166     185 ..     158     196 .. 0.52

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 9.3e-25
                     ABC2_membrane  63 lafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrfflfllllll 139
                                       ++ +a+  +++ +e + ++ler+ +sp+  ++a +l+ v+++++++ll++li l+i++++ g+++ + + f+l ++l
  gi|330508735|ref|YP_004385163.1|  13 TS-TAVGPAILPWEARSKTLERLISSPV-EVWALLLGGVFASFVFGLLISLIPLAIAVLM-GVEVVHLLVFCLGMIL 86 
                                       44.677777788999*************.*******************************.****766********* PP

                     ABC2_membrane 140 talaasslgllisalaps..fedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                        ++++ sl++l+s++ p+  + ++++l+slv +pl++ sG+f+p++ mp w q ia ++Plty++++ r++
  gi|330508735|ref|YP_004385163.1|  87 ATICFASLSILLSVYPPTdvLATVMMLSSLVRFPLVFISGVFVPVEEMPAWGQTIASASPLTYFIDLARYS 157
                                       ***************887335666777799*******************9*****************9985 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.09
                     ABC2_membrane 105 lpvsllqalifllivyflvgl 125
                                       lp+ l++ ++f+l+++++ ++
  gi|330508735|ref|YP_004385163.1| 166 LPIDLAVLVVFTLLFLVV-SI 185
                                       344444444444444443.44 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 !   58.6  22.7   1.2e-19   5.4e-16     186     344 ..      25     185 ..      11     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 1.2e-19
                   ABC2_membrane_3 186 Ekesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afglgipfgnlglllllfllfglayialgylls 260
                                       E +s+++e++++s+v +++++l+ ++++f+ +ll++l+ l++  + g  +++ +l++++l ++l  +++++l+ lls
  gi|330508735|ref|YP_004385163.1|  25 EARSKTLERLISSPVEVWALLLGGVFASFVFGLLISLIPLAIavLMG--VEVVHLLVFCLGMILATICFASLSILLS 99 
                                       66899*********************************999766888..9999************************ PP

                   ABC2_membrane_3 261 slfknsetaqilifivil...llsgffgglfpledlpsalkwifsiiPffapglgllrlitgdplweillsliilal 334
                                       +   + + a + +++ +l   +l +++g+++p+e +p + ++i+s  P+++++++     tg++++++ ++l++l++
  gi|330508735|ref|YP_004385163.1| 100 VYPPTDVLATV-MMLSSLvrfPLVFISGVFVPVEEMPAWGQTIASASPLTYFIDLARYSTTGVSYYSLPIDLAVLVV 175
                                       **988877765.44444446488888888899************************8888999999999******** PP

                   ABC2_membrane_3 335 favvylllal 344
                                       f++++l++++
  gi|330508735|ref|YP_004385163.1| 176 FTLLFLVVSI 185
                                       *******987 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5  21.5   1.3e-08   5.9e-05     100     280 ..      25     185 ..      14     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.3e-08
                   ABC2_membrane_2 100 EkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivlaledllllvvasvlllllv 175
                                       E  ++Tl++l s+Pv  +++llg + ++++ gl+  ++ l ++             vl + +++ l+v+ + ++l++
  gi|330508735|ref|YP_004385163.1|  25 EARSKTLERLISSPVEVWALLLGGVFASFVFGLLiSLIPLAIA-------------VLMGVEVVHLLVFCLGMILAT 88 
                                       8889***************************777555555555.............344667777777777777777 PP

                   ABC2_membrane_2 176 .vflalglllSsvarssreaaalalglfv.vlailvpivlygvaellagpavpqeindflsllsptsayntllneil 250
                                        +f++l++llS+   + + a+ ++l+ +v + ++++++v  +v e++a       + +++   sp  ++  l +  +
  gi|330508735|ref|YP_004385163.1|  89 iCFASLSILLSVYPPTDVLATVMMLSSLVrFPLVFISGVFVPVEEMPA-------WGQTIASASPLTYFIDLARYST 158
                                       7************************98772556777777778888888.......7777999999999988888888 PP

                   ABC2_membrane_2 251 agsdlnalgstatnllilllllavllvlgy 280
                                       +g +   ++s +  l++l++ ++ +lv+++
  gi|330508735|ref|YP_004385163.1| 159 TGVS---YYSLPIDLAVLVVFTLLFLVVSI 185
                                       8885...88999999999999999999886 PP

>> DUF368  Domain of unknown function (DUF368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   8.7   7.9e-07    0.0035     131     225 ..      23     116 ..       8     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.9e-07
                            DUF368 131 pveteeslvfvflaGaiaicAmilPGiSGSfiL.lllGlYelllealkeldvkvllvfllGavvGllsfsrvlsall 206
                                       p e  ++++  +++  + + A++l G+  Sf+  ll+ l +l +++l  ++v  llvf+lG+++  ++f+  ls+ll
  gi|330508735|ref|YP_004385163.1|  23 PWEARSKTLERLISSPVEVWALLLGGVFASFVFgLLISLIPLAIAVLMGVEVVHLLVFCLGMILATICFAS-LSILL 98 
                                       4556667777899999***************98788999999***************************96.79999 PP

                            DUF368 207 kkyrsltlavliGlmlGsl 225
                                       + y+ + + + + +ml sl
  gi|330508735|ref|YP_004385163.1|  99 SVYPPTDVLA-TVMMLSSL 116
                                       9998654432.33555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1435.55
//
Query:       gi|330508736|ref|YP_004385164.1|  [L=471]
Description: hypothetical protein MCON_3016 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-42  142.5 133.2    1.4e-08   34.7   9.9    7.8 10  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.37   10.9   0.0    1.9  1  Mrr_N           Mrr N-terminal domain


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   3.9e-05      0.35      21      46 ..      89     115 ..      85     116 .. 0.85
   2 !   18.0  13.4   2.7e-07    0.0024       1      44 [.     102     157 ..     102     160 .. 0.71
   3 !   25.6   8.8   1.1e-09   9.8e-06       1      45 [.     146     191 ..     146     193 .. 0.92
   4 !   31.9   5.5   1.2e-11   1.1e-07       1      47 [.     190     237 ..     190     238 .. 0.96
   5 !   32.2   1.6     1e-11     9e-08       1      47 [.     234     281 ..     234     282 .. 0.94
   6 !   29.4   8.1   7.2e-11   6.5e-07       1      48 []     267     315 ..     267     315 .. 0.98
   7 !   28.8   6.5   1.1e-10   9.8e-07       1      47 [.     278     325 ..     278     326 .. 0.95
   8 !   23.8   8.5   4.2e-09   3.8e-05       1      48 []     300     348 ..     300     348 .. 0.88
   9 !   34.7   9.9   1.6e-12   1.4e-08       1      47 [.     311     358 ..     311     359 .. 0.98
  10 !   28.3   3.8   1.6e-10   1.5e-06       1      45 [.     344     388 ..     344     390 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.9e-05
                    Pentapeptide_3  21 asFsnadF.gsadFsgarFtgdvdFsg 46 
                                       +  +n+ + g++dF +++F++ v+F +
  gi|330508736|ref|YP_004385164.1|  89 VVIKNSIIcGRVDFNNTQFHKQVRFVN 115
                                       556899999***********99**987 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.7e-07
                    Pentapeptide_3   1 FsganFsgaadFr...........gatFsgaasFsnadF.gsadFsgarFtgdvdF 44 
                                       F++++F++ ++F            ++tF+++a F+++ F  + +F+g+rF+g ++F
  gi|330508736|ref|YP_004385164.1| 102 FNNTQFHKQVRFVnvffveyalfvNSTFNDDAAFDHSIFlKEGSFEGSRFDGKANF 157
                                       89999999999996666666666677777777777777777777777777766666 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 1.1e-09
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFs 45 
                                       F+g++F+g a+F  ++F+++asF++a F g adFs a+F+   +F 
  gi|330508736|ref|YP_004385164.1| 146 FEGSRFDGKANFFQTRFNRPASFDGAKFgGVADFSLAQFHSVGNFA 191
                                       99**************************88*********9777775 PP

  == domain 4  score: 31.9 bits;  conditional E-value: 1.2e-11
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       F  ++Fs +a F+++ F+g a F  ++F +++ F g+rF+++++F+ga
  gi|330508736|ref|YP_004385164.1| 190 FASSQFSSDALFDKTDFKGEAKFIASQFnQDVEFNGTRFEKETSFEGA 237
                                       789*************************77****************98 PP

  == domain 5  score: 32.2 bits;  conditional E-value: 1e-11
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFg.sadFsgarFtgdvdFsga 47 
                                       F+ga Fsg+a+F++++F+ +++ ++ +++ +++F++++F+g + F  a
  gi|330508736|ref|YP_004385164.1| 234 FEGAKFSGSAQFSESVFNESVDLNSVQLEkEVRFDRTQFEGPAFFAKA 281
                                       99**************************66**********99999766 PP

  == domain 6  score: 29.4 bits;  conditional E-value: 7.2e-11
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsgat 48 
                                       F++++F+g+a+F +a F++ + F +++F  +a+F ++ F  d+ F+++t
  gi|330508736|ref|YP_004385164.1| 267 FDRTQFEGPAFFAKAKFDDLVEFGDCNFlKNATFKESDFQVDAIFNNTT 315
                                       9*********************************************997 PP

  == domain 7  score: 28.8 bits;  conditional E-value: 1.1e-10
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFg.sadFsgarFtgdvdFsga 47 
                                       F  a F++ + F +++F + a+F+++dF+ +a F +++F   ++Fsg+
  gi|330508736|ref|YP_004385164.1| 278 FAKAKFDDLVEFGDCNFLKNATFKESDFQvDAIFNNTTFLEPAEFSGS 325
                                       8899************************88**********88****98 PP

  == domain 8  score: 23.8 bits;  conditional E-value: 4.2e-09
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsgat 48 
                                       F+++ F+ +a F ++tF  +a Fs+++F g adF g+ F  d+dFs+++
  gi|330508736|ref|YP_004385164.1| 300 FKESDFQVDAIFNNTTFLEPAEFSGSNFlGFADFGGSKFLYDADFSDSI 348
                                       7788888889999999999999999999999999999999999999985 PP

  == domain 9  score: 34.7 bits;  conditional E-value: 1.6e-12
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       F++++F  +a F+g++F g a+F ++ F  +adFs+++F+g +dFs++
  gi|330508736|ref|YP_004385164.1| 311 FNNTTFLEPAEFSGSNFLGFADFGGSKFlYDADFSDSIFSGPADFSRT 358
                                       9********************************************997 PP

  == domain 10  score: 28.3 bits;  conditional E-value: 1.6e-10
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFs 45 
                                       Fs+++Fsg+adF+++ Fs+ ++F n++F  +++F+ ++++ + +++
  gi|330508736|ref|YP_004385164.1| 344 FSDSIFSGPADFSRTAFSDRVNFYNTQFkKNVHFESSQIN-TINLT 388
                                       999*************************88****999987.66665 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.1e-05      0.37      48      85 ..     358     395 ..     340     396 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.1e-05
                             Mrr_N  48 trfknrvgWartyLkkagllespkrgvwkiTekGrevl 85 
                                       t f++rv++++t+ kk    es++  ++ +T +G ++l
  gi|330508736|ref|YP_004385164.1| 358 TAFSDRVNFYNTQFKKNVHFESSQINTINLTRAGYDWL 395
                                       789*******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 3203.51
//
Query:       gi|330508737|ref|YP_004385165.1|  [L=250]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-36  124.6   0.0      4e-36  124.1   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    5.6e-24   84.7   0.0    1.2e-23   83.6   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    5.7e-24   84.6   0.0    1.9e-23   82.9   0.0    1.8  2  Methyltransf_11  Methyltransferase domain
    4.3e-22   78.6   0.0    6.6e-22   78.0   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      1e-13   51.8   0.0    1.8e-13   51.1   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    9.6e-13   48.3   0.0    1.3e-12   47.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    7.9e-10   38.8   0.0    1.6e-09   37.9   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.6e-09   36.9   0.0    3.7e-09   36.4   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.4e-06   27.9   0.0    2.9e-06   26.9   0.0    1.5  1  MTS              Methyltransferase small domain
    1.6e-06   28.2   0.0    3.8e-06   26.9   0.0    1.5  2  Methyltransf_8   Hypothetical methyltransferase
    0.00024   20.5   0.0    0.00035   20.0   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00047   19.9   0.0    0.00077   19.2   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
     0.0011   19.0   0.0     0.0017   18.4   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
     0.0035   17.5   0.0     0.0073   16.4   0.0    1.5  1  FtsJ             FtsJ-like methyltransferase
  ------ inclusion threshold ------
      0.016   14.6   0.0      0.029   13.7   0.0    1.4  1  GidB             rRNA small subunit methyltransferase G
      0.033   14.2   0.0      0.079   12.9   0.0    1.8  1  ADH_zinc_N       Zinc-binding dehydrogenase
      0.043   13.3   0.0       0.13   11.7   0.0    1.8  3  Methyltransf_4   Putative methyltransferase
      0.048   12.8   0.0      0.087   11.9   0.0    1.4  1  Fibrillarin      Fibrillarin
      0.068   12.9   0.0      0.096   12.4   0.0    1.2  1  Met_10           Met-10+ like-protein


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 !  124.1   0.0   4.3e-39     4e-36       2     145 ..      74     213 ..      73     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 4.3e-39
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       ++g +vlDlG+G+G+++f +a ++gp ++v+G+D+++e+i++Arena+  g++nv+F  g+ e+l+  +ed+++D++
  gi|330508737|ref|YP_004385165.1|  74 KEGETVLDLGSGAGFDSFLAANRVGPTGKVIGVDMTPEMINRARENAAIGGYSNVQFLPGELEDLP--VEDNSVDIV 148
                                       68899*************************************************************..********* PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedprllaelpakveeeskay.evvegakigtqkdely 145
                                       +sn+v+n+++d++k+++e++rvlkpgg+l+++d  l +elp  ++++ + y ++++ga    +kd + 
  gi|330508737|ref|YP_004385165.1| 149 ISNCVINLVPDKKKAFMEAFRVLKPGGRLMVSDLVLRQELPLRIKNSIEGYiGCISGAV---MKDAYL 213
                                       *****************************************999988887777776666...555555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.0   1.2e-26   1.2e-23       1      97 []      79     175 ..      79     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 1.2e-26
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEEST.G CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssga.l 74 
                                       vLdlG G G +++ +a+r+g  +kv+gvD+++em+++are+a+  g+ nv+f+ g++edlp ed+s+D+v+s+ + +
  gi|330508737|ref|YP_004385165.1|  79 VLDLGSGAGFDSFLAANRVGpTGKVIGVDMTPEMINRARENAAIGGYsNVQFLPGELEDLPVEDNSVDIVISN-CvI 154
                                       9******************669********************988889************************5.659 PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                       ++++  d +ka+ e++rvLkpgG
  gi|330508737|ref|YP_004385165.1| 155 NLVP--DKKKAFMEAFRVLKPGG 175
                                       9887..677*************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.0     2e-26   1.9e-23       1      96 []      80     179 ..      80     179 .. 0.96
   2 ?   -2.0   0.0       6.2   5.9e+03       3      25 ..     200     222 ..     199     239 .. 0.69

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 2e-26
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhh 73 
                                       Ld+G+G+G  +   a+r+   ++v+gvD+++em+++a+e+a   g  +v+f+ +++e+lp+edns+D+v+s+ v++ 
  gi|330508737|ref|YP_004385165.1|  80 LDLGSGAGFDSFLAANRVgptGKVIGVDMTPEMINRARENAAIGGYsNVQFLPGELEDLPVEDNSVDIVISNCVINL 156
                                       8**************6666***********************99999****************************** PP

                                       -CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllvi 96 
                                       v+d +ka+ e+ RvLkpgG+l++
  gi|330508737|ref|YP_004385165.1| 157 VPDKKKAFMEAFRVLKPGGRLMV 179
                                       ********************986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.2
                                       ET-TTSHHHHHHHHTTSEEEEEE CS
                   Methyltransf_11   3 vGcGtGrlaealakrgarvvgvD 25 
                                       +Gc +G+++++    + r  g+D
  gi|330508737|ref|YP_004385165.1| 200 IGCISGAVMKDAYLDAIRSAGFD 222
                                       67888888777775555555555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0     7e-25   6.6e-22      43     153 ..      71     181 ..      66     199 .. 0.94

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 7e-25
                                       --S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEE CS
                   Ubie_methyltran  43 vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDv 119
                                        + k+g++vlD+ +G+g  +f  ++ vg +gkv+++D+ ++m++ +++ +   g++n++fl ++ e+Lp ed+s D+
  gi|330508737|ref|YP_004385165.1|  71 ASIKEGETVLDLGSGAGFDSFLAANRVGPTGKVIGVDMTPEMINRARENAAIGGYSNVQFLPGELEDLPVEDNSVDI 147
                                       56799************************************************************************ PP

                                       EEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran 120 vtvsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                       v     +  v+Dk+ka+ ea+rvlkpGGrl+v +
  gi|330508737|ref|YP_004385165.1| 148 VISNCVINLVPDKKKAFMEAFRVLKPGGRLMVSD 181
                                       9888888889********************9855 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   1.9e-16   1.8e-13       1      99 []      80     177 ..      80     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.9e-16
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       L++G+G G  ++  +++  p+ +++gvD  p++i++a+e  a  +  n++++  e +dl  +d  +s+D+v++++v+
  gi|330508737|ref|YP_004385165.1|  80 LDLGSGAGFDSFLAANRVgPTGKVIGVDMTPEMINRARENAAIGGYSNVQFLPGELEDLPVED--NSVDIVISNCVI 154
                                       89*********9999999****************66666655555544444444444444443..6*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGrl 99 
                                       + ++d+++++ ++ ++LkpgGrl
  gi|330508737|ref|YP_004385165.1| 155 NLVPDKKKAFMEAFRVLKPGGRL 177
                                       *********************97 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   1.4e-15   1.3e-12      20     123 ..      73     185 ..      62     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.4e-15
                   Methyltransf_23  20 lraggrvLdiGcGtG.illevlrengf..svtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfdlIv 87 
                                        ++g  vLd+G G G      + + g   +v+gvD+ pe++++a+      + ++ q+ +   ++ ++++++ d+++
  gi|330508737|ref|YP_004385165.1|  73 IKEGETVLDLGSGAGfDSFLAANRVGPtgKVIGVDMTPEMINRARenaaigGYSNVQFLPGELEDLPVEDNSVDIVI 149
                                       678999*********54444445556689*******************9997777777777778************* PP

                   Methyltransf_23  88 lrevlehvpdppellrqiatllkpgGylllseplas 123
                                       ++ v++ vpd  +++  +++ lkpgG+l++s+   +
  gi|330508737|ref|YP_004385165.1| 150 SNCVINLVPDKKKAFMEAFRVLKPGGRLMVSDLVLR 185
                                       *******************************97544 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 !   37.9   0.0   1.6e-12   1.6e-09      68     171 ..      70     179 ..      64     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.6e-12
                                       HTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEE CS
                              PCMT  68 llelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYd 144
                                       l ++k+g+ vL++GsG+G+ + + a+ vg++g+v++++ ++e++++a++n    +++nv++  g+ +    e    d
  gi|330508737|ref|YP_004385165.1|  70 LASIKEGETVLDLGSGAGFDSFLAANRVGPTGKVIGVDMTPEMINRARENAAIGGYSNVQFLPGELEDLPVEDNSVD 146
                                       45699********************************************************9999776666666677 PP

                                       EEEESSBBSS--H...HH...HHTEEEEEEEEE CS
                              PCMT 145 aihvgaaapeiPe...al...idQLkeGGrlvv 171
                                        ++     + +P+   a+   ++ Lk+GGrl+v
  gi|330508737|ref|YP_004385165.1| 147 IVISNCVINLVPDkkkAFmeaFRVLKPGGRLMV 179
                                       776666667777422233111556888888887 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0     4e-12   3.7e-09     159     266 ..      73     187 ..      68     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 4e-12
                              PrmA 159 vkegeevlDvGtGSGiLa.iaaakLga.kkvvavDiDevAvkvakeNaelNkvea.klevalseell.keekadviv 231
                                       +kege+vlD+G G+G  + +aa ++g   kv++vD+ +  ++ a+eNa++ + ++ ++     e+l+ +++++d+++
  gi|330508737|ref|YP_004385165.1|  73 IKEGETVLDLGSGAGFDSfLAANRVGPtGKVIGVDMTPEMINRARENAAIGGYSNvQFLPGELEDLPvEDNSVDIVI 149
                                       789*************9967999**96269**********************99977732344555544899***** PP

                              PrmA 232 aNILaevl...ielaedikklvkeggllilSGilkeka 266
                                       +N + + +    +   ++ +++k+gg+l++S ++ +++
  gi|330508737|ref|YP_004385165.1| 150 SNCVINLVpdkKKAFMEAFRVLKPGGRLMVSDLVLRQE 187
                                       **9999993333455678899**********9887775 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   3.1e-09   2.9e-06      31     137 ..      75     179 ..      62     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.1e-09
                                       TCSEEEEET-TTSHHHHHHHHH.TTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT.TSTTS-EEEEEE- CS
                               MTS  31 lsgkvlDlGcGaGvlgaalake.speaevtlvdvdarAlesakenleankle.vevvasdvle.eveekkfdlivsN 104
                                       + ++vlDlG+GaG+ +  +a++  p+ +v  vd   + ++ a+en++  + + v+++  ++ +  ve++++d+++sN
  gi|330508737|ref|YP_004385165.1|  75 EGETVLDLGSGAGFDSFLAANRvGPTGKVIGVDMTPEMINRARENAAIGGYSnVQFLPGELEDlPVEDNSVDIVISN 151
                                       3678***********9888766167888**********************999******998746889********* PP

                                       --STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                               MTS 105 PPfhagkatelavaeeliaeAkeaLkegGeLli 137
                                         +    +      ++ + eA ++Lk+gG+L++
  gi|330508737|ref|YP_004385165.1| 152 CVINLVPD-----KKKAFMEAFRVLKPGGRLMV 179
                                       99988877.....556677899********986 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.6   4.3e+03      71      82 ..      74      85 ..      61     111 .. 0.55
   2 !   26.9   0.0     4e-09   3.8e-06     110     162 ..     132     185 ..     124     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.6
                                      -TTS-EEEES-T CS
                    Methyltransf_8 71 kdnlvvadlGcG 82
                                      k+  +v dlG G
  gi|330508737|ref|YP_004385165.1| 74 KEGETVLDLGSG 85
                                      334455566655 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 4e-09
                                       ES-TTS-S--TT-EEEEEE.ES---SS-HHHHHHHHHHHEEEEEEEEEEEEGGG CS
                    Methyltransf_8 110 acdlakvPledesvdvavf.clslmgtnladflkeanrvlkvGGllkvaevksr 162
                                       + +l  +P+ed+svd+++  c+  ++ + ++   ea rvlk+GG l+v+++  r
  gi|330508737|ref|YP_004385165.1| 132 PGELEDLPVEDNSVDIVISnCVINLVPDKKKAFMEAFRVLKPGGRLMVSDLVLR 185
                                       567899***********95499999999999999**************987655 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.7e-07   0.00035      59     170 ..      72     185 ..      67     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.7e-07
                                       T--TT-EEEEES-TTSHHHHHHHHHH-..-EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SE CS
                              CMAS  59 elkpGmtlLdiGcGWGslvrraveryd..vkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdr 130
                                       ++k+G+t+Ld+G G G     a++r +   kv+g+ +  e  ++a+++ + ++   +v+ +  + edl+     vd 
  gi|330508737|ref|YP_004385165.1|  72 SIKEGETVLDLGSGAGFDSFLAANRVGptGKVIGVDMTPEMINRARENAA-IGGYSNVQFLPGELEDLPVednSVDI 147
                                       689**********************974359***************9865.56688999999999999754569*** PP

                                       EEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE- CS
                              CMAS 131 vvsvgafehvgkenydtffkklkkllkedGllllhtitsl 170
                                       v+s  +++ v  ++ ++ f +++++lk++G+l++  ++ +
  gi|330508737|ref|YP_004385165.1| 148 VISNCVINLVPDKK-KA-FMEAFRVLKPGGRLMVSDLVLR 185
                                       ***99999997665.44.667789********99776655 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.1e-07   0.00077      75     128 ..      99     151 ..      88     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.1e-07
                                       HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE- CS
                           UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtn 128
                                       ++ k++g+D+ ++++++areNa   g    ++f   +  +L+ ++++vd++++n
  gi|330508737|ref|YP_004385165.1|  99 PTGKVIGVDMTPEMINRARENAAIGGY-SNVQFLPGELEDLPVEDNSVDIVISN 151
                                       56689*****************86665.57999999******8888*******9 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.8e-06    0.0017      24      89 ..      74     135 ..      66     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                   Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsi 89 
                                       ++ +tv+D+G+G g+ sf  a  ++    kv+g+d+  e++++a++ a+  g  + ++++f  ++ 
  gi|330508737|ref|YP_004385165.1|  74 KEGETVLDLGSGAGFDSFLAAN-RVGPTGKVIGVDMTPEMINRARENAAIGG--Y-SNVQFLPGEL 135
                                       56789**********9999998.77799****************99988766..6.6677766655 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.8e-06    0.0073      19      93 ..      73     150 ..      68     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.8e-06
                                       S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS........HHH...TTEEEECS-CCCSSHHHHHCHCHH CS
                              FtsJ  19 fkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm........apl...pgvttiqgditdpetiekikeals 84 
                                       +k+g+tv+Dlg++ G  s  +++r+g++gkv++vD+ p         a +   ++v+++ g   d  ++++      
  gi|330508737|ref|YP_004385165.1|  73 IKEGETVLDLGSGAGFDSFLAANRVGPTGKVIGVDMTPEminrarenAAIggySNVQFLPGELEDLPVEDN------ 143
                                       6799********************************66557766554333555677777666666555553...... PP

                                       HSSEEEEEE CS
                              FtsJ  85 erkvdlvvs 93 
                                          vd+v+s
  gi|330508737|ref|YP_004385165.1| 144 --SVDIVIS 150
                                       ..3444444 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.1e-05     0.029      44     128 ..      72     157 ..      67     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.1e-05
                                       CS-CCC-.EEEETSTTTTTHHHHH.HH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC.TTTTT-EEE CS
                              GidB  44 llkekrdkviDvGsGaGlPGipLa.iarpelkltLleslekkiaFLeevkeelklenveivearaee.kqeeekydv 118
                                        +ke + +v+D+GsGaG+ +   a  + p+ k++ ++ +   i+  +e  +  + +nv+++  ++e+   e +++d+
  gi|330508737|ref|YP_004385165.1|  72 SIKEGE-TVLDLGSGAGFDSFLAAnRVGPTGKVIGVDMTPEMINRARENAAIGGYSNVQFLPGELEDlPVEDNSVDI 147
                                       456666.7**********99766525889999999*********999*99999*************97778889999 PP

                                       EEEC-SSSHH CS
                              GidB 119 vtsRAlasln 128
                                       v+s  + +l 
  gi|330508737|ref|YP_004385165.1| 148 VISNCVINLV 157
                                       9999988874 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.3e-05     0.079      13     102 ..      97     195 ..      56     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.3e-05
                                       TT-..EEEEEESSHHHHHHHHHTT.ESEEEETTTCHHHHHHHHHTT.TSSEEEEEESSC......SHHHHHHHHHCE CS
                        ADH_zinc_N  13 lGa..eviavdsseeklelakklG.adevinykeadlverikeltg.gegvdvvfecvG......sgatleaalkll 79 
                                        G   +vi+vd ++e +  a+++     + n  +  l  ++++l   ++ vd+v+           ++++ +a+++l
  gi|330508737|ref|YP_004385165.1|  97 VGPtgKVIGVDMTPEMINRARENAaIGGYSNV-Q-FLPGELEDLPVeDNSVDIVISNCVinlvpdKKKAFMEAFRVL 171
                                       555569****************8735555555.4.6999*****96699***9664333244447799********* PP

                                       EEEEEEEECSC.TSSEEEEEHHHH CS
                        ADH_zinc_N  80 kpgGrlvvvGg.gkgeeefdlrnl 102
                                       kpgGrl+v  + + +e +++++n 
  gi|330508737|ref|YP_004385165.1| 172 KPGGRLMVSDLvLRQELPLRIKNS 195
                                       ******998777777777666665 PP

>> Methyltransf_4  Putative methyltransferase
   #    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       4      59 ..      78     134 ..      75     149 .. 0.87
   2 ?   -3.3   0.0       5.5   5.2e+03     102     114 ..     166     178 ..     161     182 .. 0.73
   3 ?   -3.4   0.0       6.1   5.7e+03      42      70 ..     213     241 ..     208     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                                       EEEEET-TTS.HHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES- CS
                    Methyltransf_4   4 vvleiGcGkG.eflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgd 59 
                                       +vl++G+G G ++ +a     P+ +++G+++  ++++++ ++++  +++N++ l g+
  gi|330508737|ref|YP_004385165.1|  78 TVLDLGSGAGfDSFLAANRVGPTGKVIGVDMTPEMINRARENAAIGGYSNVQFLPGE 134
                                       799*******66777778889*******************************99988 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.5
                                       HHHHHEEEEEEEE CS
                    Methyltransf_4 102 elarvLkkgGvle 114
                                       e+ rvLk+gG l 
  gi|330508737|ref|YP_004385165.1| 166 EAFRVLKPGGRLM 178
                                       456899***9986 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6.1
                                       HHHHHHCTTSSEEEEES-CCCHHHHCS-T CS
                    Methyltransf_4  42 lkkiealelkNlrilrgdalkvllelled 70 
                                       l++i+  ++  +++++  a++ + ++++ 
  gi|330508737|ref|YP_004385165.1| 213 LDAIRSAGFDEVAVIEESAFNRFADSVSS 241
                                       67788888888999999998888877765 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.3e-05     0.087      60     108 ..      65     113 ..      42     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.3e-05
                                       HTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHH CS
                       Fibrillarin  60 lkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvl 108
                                        + ++   ik+g+ vL lG+++G      ++ vg++g+v +v+++p ++
  gi|330508737|ref|YP_004385165.1|  65 GNPIALASIKEGETVLDLGSGAGFDSFLAANRVGPTGKVIGVDMTPEMI 113
                                       56677789*****************999****************99876 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0001     0.096      97     146 ..      72     122 ..      67     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                                       T--TT-EEEETT-TTTCCH.HHCCHHTTSSEEEEEES-HHHHHHHHHHHHH CS
                            Met_10  97 lveegevVvdvfAGiGpfa.ipiakyskakrvlaidlnPesvkylkenikl 146
                                        ++ege+V+d+  G G+ + +++ + +   +v+++d+ Pe ++  +en + 
  gi|330508737|ref|YP_004385165.1|  72 SIKEGETVLDLGSGAGFDSfLAANRVGPTGKVIGVDMTPEMINRARENAAI 122
                                       589*************98834666788999**********99999998776 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:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1711.85
//
Query:       gi|330508738|ref|YP_004385166.1|  [L=91]
Description: AbrB family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-06   26.9   0.0    4.7e-06   26.4   0.0    1.3  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


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 !   26.4   0.0   2.6e-10   4.7e-06       3      33 ..      27      57 ..      25      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.6e-10
                                      ETTEEEEEE-CCCHHHCCEECTCEEEEEECT CS
                    MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdg 33
                                      v++ g++++Pk++r+ + ir+Gd++ ++ ++
  gi|330508738|ref|YP_004385166.1| 27 VDERGQMVLPKDIRERAKIRPGDKLAVVSME 57
                                      8899********************9887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 667.82
//
Query:       gi|330508739|ref|YP_004385167.1|  [L=100]
Description: hypothetical protein MCON_3019 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 779.86
//
Query:       gi|330508740|ref|YP_004385168.1|  [L=135]
Description: ArsR family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete 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   74.5   0.5    4.5e-21   74.5   0.5    1.8  3  HTH_5            Bacterial regulatory protein, arsR family
    3.2e-15   55.9   0.1      5e-15   55.3   0.1    1.3  1  HTH_20           Helix-turn-helix domain
    6.3e-05   22.8   0.0    0.00016   21.5   0.0    1.6  2  TrmB             Sugar-specific transcriptional regulator Trm
     0.0025   17.6   0.0     0.0031   17.3   0.0    1.2  1  DUF742           Protein of unknown function (DUF742)
     0.0028   17.8   0.0      0.027   14.7   0.0    2.1  2  PaaX             PaaX-like protein
      0.008   15.9   0.0      0.016   15.0   0.0    1.6  1  HTH_23           Homeodomain-like domain
  ------ inclusion threshold ------
      0.013   15.3   0.5      0.023   14.5   0.1    1.7  2  HTH_IclR         IclR helix-turn-helix domain
      0.021   14.4   0.2       0.12   12.0   0.0    2.1  2  HTH_24           Winged helix-turn-helix DNA-binding
      0.058   13.3   0.0       0.14   12.1   0.0    1.6  1  MarR_2           MarR family
      0.098   13.0   0.1       0.19   12.1   0.1    1.5  1  Penicillinase_R  Penicillinase repressor


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.8   8.5e+03      17      24 ..      14      21 ..      10      23 .. 0.69
   2 ?   -2.9   0.1       3.7   6.6e+03       4      13 ..      31      40 ..      30      41 .. 0.76
   3 !   74.5   0.5   2.5e-24   4.5e-21       1      46 [.      59     104 ..      59     105 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.8
                                      EHHHHHHH CS
                             HTH_5 17 cvcelaee 24
                                       +c la+ 
  gi|330508740|ref|YP_004385168.1| 14 AICSLARL 21
                                      57888875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.7
                                      HHHHHHHHTT CS
                             HTH_5  4 RlkILklLae 13
                                      R ++L++L++
  gi|330508740|ref|YP_004385168.1| 31 RTRMLMSLMK 40
                                      7788999876 PP

  == domain 3  score: 74.5 bits;  conditional E-value: 2.5e-24
                                       SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       dp Rl+I+klL egelcvce++ +l+++qst+ShHL++LreaGLV+
  gi|330508740|ref|YP_004385168.1|  59 DPCRLRIVKLLKEGELCVCEIMTALDKPQSTTSHHLSILREAGLVR 104
                                       899******************************************6 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.1   2.8e-18     5e-15       2      60 ..      52     109 ..      51     110 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 2.8e-18
                                       HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20   2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                       ++++A+a+P R+ri ++L  +++l++ e++ +ld +++t s+HL +L+eagLv+ ++ g
  gi|330508740|ref|YP_004385168.1|  52 EVFKAVADPCRLRIVKLL-KEGELCVCEIMTALDKPQSTTSHHLSILREAGLVRERKDG 109
                                       79****************.*************************************988 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.6   4.7e+03      56      62 ..      48      54 ..      32      58 .. 0.46
   2 !   21.5   0.0   9.1e-08   0.00016      16      65 ..      67     117 ..      66     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.6
                                      SSTTTEE CS
                              TrmB 56 kgrpklY 62
                                      +g+  ++
  gi|330508740|ref|YP_004385168.1| 48 EGEVEVF 54
                                      3333333 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 9.1e-08
                                       HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE- CS
                              TrmB  16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYrav 65 
                                       +Llk+g++ + ei  +l+ p+s+    L+ L ++GlV+ +k     +Yr +
  gi|330508740|ref|YP_004385168.1|  67 KLLKEGELCVCEIMTALDKPQSTTSHHLSILREAGLVRERKDGkWSYYRLA 117
                                       7************************************99995525577665 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.7e-06    0.0031      22      92 ..      35     110 ..      21     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
                            DUF742  22 dldletlvvaeagapea.....arlqpehrailrLcre.plsVaelaAelklPvgvvrvLlsdLldaglltvrapvt 92 
                                        ++l+  +     +  +     a + p + +i++L +e  l V e+  +l+ P +++   ls L +agl++ r+   
  gi|330508740|ref|YP_004385168.1|  35 LMSLMKAIDIDGPEG-EvevfkAVADPCRLRIVKLLKEgELCVCEIMTALDKPQSTTSHHLSILREAGLVRERKDGK 110
                                       444444444333222.12333377889999********9*******************************9887655 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.28   4.9e+02      18      36 ..      27      45 ..      15      51 .. 0.81
   2 !   14.7   0.0   1.5e-05     0.027      29      69 ..      79     119 ..      66     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.28
                              PaaX 18 ggaiwlgsLirllaelGis 36
                                      ++  + + L  l+++++i+
  gi|330508740|ref|YP_004385168.1| 27 RARSRTRMLMSLMKAIDID 45
                                      45557789999*****997 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.5e-05
                              PaaX  29 llaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsdk 69 
                                       ++ +l+  +s+    ls l +aG++++ k+g+ s+YrL+d 
  gi|330508740|ref|YP_004385168.1|  79 IMTALDKPQSTTSHHLSILREAGLVRERKDGKWSYYRLADS 119
                                       56666666666666788899*******************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     9e-06     0.016       7      46 ..      62     102 ..      60     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9e-06
                            HTH_23   7 Rlrillllae.GlsvreIAreLgvsrrTvyrwlkryreeGl 46 
                                       Rlri++ll+e  l+v eI ++L+ +++T ++ l+  re Gl
  gi|330508740|ref|YP_004385168.1|  62 RLRIVKLLKEgELCVCEIMTALDKPQSTTSHHLSILREAGL 102
                                       9*****************************99999998887 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.8     5e+03       1       8 [.      37      44 ..      33      44 .. 0.78
   2 ?   14.5   0.1   1.3e-05     0.023      19      50 ..      74     105 ..      63     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.8
                                      HHHHHHHH CS
                          HTH_IclR  1 sldRalai 8 
                                      sl++a++i
  gi|330508740|ref|YP_004385168.1| 37 SLMKAIDI 44
                                      68888876 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.3e-05
                                       -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  19 ltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       l + e+  +++ p St++++L+ L e G+v+ 
  gi|330508740|ref|YP_004385168.1|  74 LCVCEIMTALDKPQSTTSHHLSILREAGLVRE 105
                                       44779*************************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 ?   12.0   0.0   6.6e-05      0.12      11      48 .]      68     104 ..      60     104 .. 0.86
   2 ?   -0.3   0.0      0.44   7.9e+02      30      44 ..     117     131 ..     115     135 .] 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.6e-05
                            HTH_24  11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       lL++ + ++  e+  +l+ ++st++ +l  L e+Gl++
  gi|330508740|ref|YP_004385168.1|  68 LLKE-GELCVCEIMTALDKPQSTTSHHLSILREAGLVR 104
                                       5555.888889*************************96 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.44
                            HTH_24  30 SpstvnrrlkrLeee 44 
                                         s+vn+ +k+  e 
  gi|330508740|ref|YP_004385168.1| 117 ADSAVNEMIKQAREL 131
                                       568999999987765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.7e-05      0.14      26      56 ..      78     108 ..      64     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-05
                                       HHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  26 elarrlglsksavsrilkrLvaaGLverrpg 56 
                                       e+  +l+ ++s++s +l  L +aGLv++r++
  gi|330508740|ref|YP_004385168.1|  78 EIMTALDKPQSTTSHHLSILREAGLVRERKD 108
                                       788899999*******************986 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0001      0.19      14      65 ..      70     117 ..      63     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                       HHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE-- CS
                   Penicillinase_R  14 ekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYspl 65 
                                       ++ge+ v e++++l+++    +sT+   l+ L + gl++++k+g+   Y+ +
  gi|330508740|ref|YP_004385168.1|  70 KEGELCVCEIMTALDKP----QSTTSHHLSILREAGLVRERKDGKWSYYRLA 117
                                       66788999999999999....9***********************9999754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1092.07
//
Query:       gi|330508741|ref|YP_004385169.1|  [L=299]
Description: permease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-63  215.0  24.7    1.4e-63  214.9  24.7    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 !  214.9  24.7   7.5e-68   1.4e-63       2     293 ..       6     295 ..       5     296 .. 0.94

  Alignments for each domain:
  == domain 1  score: 214.9 bits;  conditional E-value: 7.5e-68
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1   2 laealtlfasilleallaLvlgflisgaiqvfvkeekiielLgprnrlisllvaallGfllpvCscsavPlarrllk 78 
                                       la a+++f+ i++e +++ + + +++g+iq +v+ e+i++ Lg r+r+++++++a +G+l+p+Cscs +Pl  ++l 
  gi|330508741|ref|YP_004385169.1|   6 LATAMSFFIEIAVELIVLFIGITFLVGLIQEYVPDETIKKALGGRHRILGSFLGAGFGALTPFCSCSTIPLLLGMLN 82 
                                       67899************************************************************************ PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1  79 kGaplgaavaFlvaaPainiiaiiltlillgwqllvarivlalivaiviglvleylfkeeelekaarevaeaglekl 155
                                       +G+p++ a+aFl+a+P +n+++i l +illgw+++++++++++++aivigl+l  l  +++++  a     +g  + 
  gi|330508741|ref|YP_004385169.1|  83 AGVPFASAMAFLFASPLLNPVIISLFIILLGWKITALYFSVTFLAAIVIGLMLDSLGFAAQVKSVAAV---RGCCDC 156
                                       ******************************************************99999999888853...456665 PP

                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 156 tlkpklealka.faknevkewlelgkyLiiGvaiagviqaflpesvllsllggnsvsssllamligvvlyvcslgev 231
                                       + ++ ++++ +  a+ +   +++l++yL++G+ i+++i++f+p++ + s++g+++ +++++a++igv++y+ +++ +
  gi|330508741|ref|YP_004385169.1| 157 EQAEDAKSRVQrSARFAFSLFRQLVPYLLLGAGIGAFIHGFVPTELISSIAGSGNPFAVPVAAIIGVPIYIRAETMI 233
                                       555555544443777788889******************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 232 pfiaalfesglalGsalAfLlagpllslpellillkvlkkklvavllglvvvsvvlaglvin 293
                                       p+  al+e+g+++G +lA+ + g+  s+pel +l++++k+k++a+++++++ ++v++g+++n
  gi|330508741|ref|YP_004385169.1| 234 PIGLALIEKGMGTGAVLALVIGGAGASIPELTLLSAIFKRKMLAAFVLTIITIAVAVGYLAN 295
                                       ***********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2189.20
//
Query:       gi|330508742|ref|YP_004385170.1|  [L=171]
Description: arsenate reductase ArsC [Methanosaeta concilii GP6]
Scores for complete 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-17   62.5   0.1    6.8e-17   62.2   0.1    1.2  1  LMWPc     Low molecular weight phosphotyrosine protein phosph


Domain annotation for each model (and alignments):
>> LMWPc  Low molecular weight phosphotyrosine protein phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.1   3.8e-21   6.8e-17       1     139 [.      22     158 ..      22     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 3.8e-21
                                       EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTSTTT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHHH CS
                             LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgalvgkradpravevlkekgislsghvarqlskeelae 77 
                                       vlf C+ N++RS+mAe l+r+      ++++ e++SaG+       +dprav ++ e gi++sg++++  ++     
  gi|330508742|ref|YP_004385170.1|  22 VLFLCTHNSARSQMAEGLLRAM-----YGDRYEAYSAGVD---PTAVDPRAVRAMSEIGIDISGQRSKSTQEFLDTV 90 
                                       89*******************9.....7889*********...789******************************* PP

                                       SSEEEESSHHHHHH..HHHHCCTTGGGGEEEGGGGSSTSS---HT......TSSHHHHHHHHHHHHHHHH CS
                             LMWPc  78 lDlilamdeenkre..leslapekekakvkllgeyteqldieDPy......ygeieafeevldeieeavk 139
                                       +D  +++++++ +   ++s+++e   a++ + +e   +    DP+       +e++af++v+de+++ + 
  gi|330508742|ref|YP_004385170.1|  91 FDQAVTVCDRARQAcpICSTEIE-LPARTPRARE-VIHRSFLDPAatrgskEEEMQAFRKVRDEMKDWIS 158
                                       ********998854225666666.6678888888.5788999999886654555999****999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1213.44
//
Query:       gi|330508743|ref|YP_004385171.1|  [L=83]
Description: ferredoxin [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-16   58.1   3.6    1.2e-15   57.8   3.6    1.1  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    5.3e-13   49.5   4.9    6.4e-13   49.2   4.9    1.1  1  Fer4_15   4Fe-4S single cluster domain
    0.00032   20.8   3.5    0.00074   19.6   3.5    1.6  1  Fer4_10   4Fe-4S dicluster domain
     0.0014   18.4   3.2     0.0014   18.4   3.2    2.5  3  Fer4      4Fe-4S binding domain
     0.0049   16.9   4.2      0.068   13.3   4.2    2.0  1  Fer4_19   Divergent 4Fe-4S mono-cluster
  ------ inclusion threshold ------
      0.011   15.9   4.7      0.025   14.7   4.7    1.8  1  Fer4_21   4Fe-4S dicluster domain
      0.013   16.0   2.9      0.029   14.9   2.9    1.6  1  Fer4_17   4Fe-4S dicluster domain
      0.098   12.8   2.8      0.098   12.8   2.8    2.2  3  Fer4_9    4Fe-4S dicluster domain
       0.15   12.7   1.5       0.15   12.7   1.5    2.2  2  Fer4_7    4Fe-4S dicluster domain
       0.69   10.1   6.9        0.5   10.5   2.1    2.4  2  Fer4_6    4Fe-4S binding domain
          7    7.0   8.9       0.25   11.5   2.8    1.8  2  Fer4_2    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   3.6   7.1e-19   1.2e-15       1      58 []       6      73 ..       6      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 7.1e-19
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqpts..........eeekadaeeAadaCPvesIgv 58
                                      +Dr+ Ci+cg+C+  +Pd+F+e +++g+s++ae+ +           e+++++a++ a++CP + Igv
  gi|330508743|ref|YP_004385171.1|  6 IDREGCISCGQCWGDCPDLFDESEQDGKSQIAEKFRIagkldegvafEDQEECAKKVAEECPSQVIGV 73
                                      8*******************************953323345556778*******************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 !   49.2   4.9   3.9e-16   6.4e-13       1      65 [.       4      72 ..       4      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 3.9e-16
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfelde.dglasvl....lddgeiaegevpddeeeaaqeAaraCPvdAIr 65
                                      V +Dr+ Ci+cg+C+  +p++f + e dg++++     ++ g+++eg   +d+ee+a++ a++CP ++I 
  gi|330508743|ref|YP_004385171.1|  4 VSIDREGCISCGQCWGDCPDLFDESEqDGKSQIAekfrIA-GKLDEGVAFEDQEECAKKVAEECPSQVIG 72
                                      89**********************9989***999888754.6778899999****************996 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   3.5   4.5e-07   0.00074       2      46 ..       4      67 ..       3      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.5e-07
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl...................tsvgakgeaseeeavrkkvekCt 46
                                      v id++ Ci Cg+C   CP  +                   + +++ +++++ee  +k+ e+C+
  gi|330508743|ref|YP_004385171.1|  4 VSIDREGCISCGQCWGDCPDLFdeseqdgksqiaekfriagKLDEGVAFEDQEECAKKVAEECP 67
                                      789****************966998888877777666666666666666666666666666665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   3.2   8.3e-07    0.0014       2      19 ..       5      22 ..       4      24 .. 0.93
   2 ?   -2.7   0.1         4   6.5e+03       4       8 ..      54      58 ..      53      59 .. 0.76
   3 ?    1.8   0.0      0.15   2.4e+02      15      23 ..      63      71 ..      63      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.3e-07
                                      EEETTTSSS-THHHHHST CS
                              Fer4  2 videekCigCGaCvevCP 19
                                       id e Ci CG+C   CP
  gi|330508743|ref|YP_004385171.1|  5 SIDREGCISCGQCWGDCP 22
                                      79***************9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4
                                      ETTTS CS
                              Fer4  4 deekC 8 
                                      d+e C
  gi|330508743|ref|YP_004385171.1| 54 DQEEC 58
                                      67888 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.15
                                      HHHSTTTEE CS
                              Fer4 15 vevCPvgAI 23
                                      +e CP  +I
  gi|330508743|ref|YP_004385171.1| 63 AEECPSQVI 71
                                      689**9887 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 !   13.3   4.2   4.2e-05     0.068       6      56 ..       2      68 ..       1      73 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.2e-05
                           Fer4_19  6 itiednrelCihsgnCvkglpevFdpkrk...pwi.............kpdeast.....eeiievverCPS 56
                                      i+++ +re Ci+ g+C+   p++Fd +++     i                   +     e +++v+e+CPS
  gi|330508743|ref|YP_004385171.1|  2 INVSIDREGCISCGQCWGDCPDLFDESEQdgkSQIaekfriagkldegV-----AfedqeECAKKVAEECPS 68
                                      88999********************988632223357777777433322.....244444778888889998 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   4.7   1.6e-05     0.025       2      20 ..       5      23 ..       4      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                           Fer4_21  2 ridedkCigCgkCliaCed 20
                                       id++ Ci+Cg+C   C+d
  gi|330508743|ref|YP_004385171.1|  5 SIDREGCISCGQCWGDCPD 23
                                      59***************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 ?   14.9   2.9   1.8e-05     0.029       2      46 ..      11      66 ..      10      71 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                           Fer4_17  2 CiqCgyClpeCpsyeaydne..pkkllraakl.glleeaeke........ekaslC 46
                                      Ci+Cg C   Cp + + +++  + ++++++++ g+l+e  +         ++a++C
  gi|330508743|ref|YP_004385171.1| 11 CISCGQCWGDCPDLFDESEQdgKSQIAEKFRIaGKLDEGVAFedqeecakKVAEEC 66
                                      99999999999976554433226679999988634444222201111222455555 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.8     6e-05     0.098      34      48 ..       9      23 ..       1      26 [. 0.77
   2 ?    7.5   8.4    0.0029       4.7       2      34 ..      11      56 ..      10      71 .. 0.56
   3 ?    1.5   0.2       0.2   3.3e+02      10      18 ..      64      72 ..      55      79 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-05
                            Fer4_9 34 eaCigCgaCveaCpk 48
                                      e Ci+Cg+C   Cp 
  gi|330508743|ref|YP_004385171.1|  9 EGCISCGQCWGDCPD 23
                                      37***********95 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0029
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase.............e 34
                                      C++Cg+C   Cp    + ++ ++    ++++              e
  gi|330508743|ref|YP_004385171.1| 11 CISCGQCWGDCPDLFDESEQDGKSQIAEKFRIagkldegvafedqE 56
                                      8888888888877666555555554444444355556666665554 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.2
                            Fer4_9 10 eaCpagvvv 18
                                      e Cp++v+ 
  gi|330508743|ref|YP_004385171.1| 64 EECPSQVIG 72
                                      446666665 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   1.5     9e-05      0.15      31      49 ..       4      22 ..       1      25 [. 0.89
   2 ?    6.7   6.9    0.0069        11       2      50 ..      11      68 ..      10      70 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9e-05
                            Fer4_7 31 veidpekClgCgaCvavCP 49
                                      v id e C++Cg+C   CP
  gi|330508743|ref|YP_004385171.1|  4 VSIDREGCISCGQCWGDCP 22
                                      6789999***********9 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0069
                            Fer4_7  2 CigCgaCvaaCp..vkaieldeeenekgtekveidpekClg......Cga.CvavCPt 50
                                      Ci Cg+C   Cp   +  e d +++ +++ +++++ ++ +       C +  +++CP+
  gi|330508743|ref|YP_004385171.1| 11 CISCGQCWGDCPdlFDESEQDGKSQIAEKFRIAGKLDEGVAfedqeeCAKkVAEECPS 68
                                      9999999999995555555555555555555544444433211111132223446666 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.1   0.00031       0.5       2      20 ..       4      22 ..       3      28 .. 0.85
   2 ?    2.0   0.2      0.16   2.5e+02      17      24 .]      64      71 ..      56      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                            Fer4_6  2 veidpdkCigCgdCvrvCP 20
                                      v id++ Ci+Cg C   CP
  gi|330508743|ref|YP_004385171.1|  4 VSIDREGCISCGQCWGDCP 22
                                      689***********65555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.16
                            Fer4_6 17 rvCPegai 24
                                        CP ++i
  gi|330508743|ref|YP_004385171.1| 64 EECPSQVI 71
                                      46**9997 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   2.8   0.00015      0.25       4      21 ..       5      22 ..       3      23 .. 0.87
   2 ?   -2.9   0.1       5.9   9.6e+03      20      21 ..      66      67 ..      63      68 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                            Fer4_2  4 vvdtdrCigCgaCvsa.CP 21
                                       +d++ Ci+Cg C +  CP
  gi|330508743|ref|YP_004385171.1|  5 SIDREGCISCGQC-WGdCP 22
                                      689**********.87788 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.9
                            Fer4_2 20 CP 21
                                      CP
  gi|330508743|ref|YP_004385171.1| 66 CP 67
                                      88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 622.08
//
Query:       gi|330508744|ref|YP_004385172.1|  [L=110]
Description: hypothetical protein MCON_3025 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 868.35
//
Query:       gi|330508745|ref|YP_004385173.1|  [L=1320]
Description: hypothetical protein MCON_3027 [Methanosaeta concilii GP6]
Scores for complete 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   0.0    8.2e-06   26.1   0.0    1.5  1  DUF4297   Domain of unknown function (DUF4297)
  ------ inclusion threshold ------
       0.12   12.6   0.0        0.4   11.0   0.0    1.9  1  IF3_N     Translation initiation factor IF-3, N-terminal doma
       0.16   11.9   0.1       0.39   10.7   0.1    1.6  1  PSDC      Phophatidylserine decarboxylase


Domain annotation for each model (and alignments):
>> DUF4297  Domain of unknown function (DUF4297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.4e-09   8.2e-06       6     159 ..      32     171 ..      30     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.4e-09
                           DUF4297   6 setkkrfryQyawAlvkvlkl.ddekddyavfcEfheDivilddksspakfefyQVKtkesgkwtdeeLtkakkgkk 81 
                                       ++  ++ +yQ ++++++ ++l  d++ + ++++E +eD ++l       + e++QVKt+++  w+ ++L + k+   
  gi|330508745|ref|YP_004385173.1|  32 AANIRGIKYQILYSVLRAFDLyADDNAYGSIRLEGIEDLDLLGL---RLEDEYIQVKTSQE-PWKWSQLKSYKNS-- 102
                                       55567889*************77888888************766...78889*****7666.8888888777333.. PP

                           DUF4297  82 kkksSilgKllksekdfprriaklafVsnaplsltlkekkislslrsevalselskedikklekslkdelgvekad. 157
                                          +  ++ +l+   +  + + ++++V n +l+ +l++  +  s      l +++k++i+++  +l+ + g + ++ 
  gi|330508745|ref|YP_004385173.1| 103 ---KGPIENFLEI--YRLNPNCHFVLVVNFQLKGDLEKLAQIES------LPPRDKKIIEEMFRKLCHQIGASTTEa 168
                                       ...468*****66..99999999999999999666666655533......999******999999999999886664 PP

                           DUF4297 158 .ai 159
                                        a+
  gi|330508745|ref|YP_004385173.1| 169 dAL 171
                                       333 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 ?   11.0   0.0   6.7e-05       0.4      30      62 ..    1237    1269 ..    1215    1274 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.7e-05
                                        HHHHHHTSEEEEEESSSSS-EEEEE-HHHHHHH CS
                             IF3_N   30 rlaeekgldLVevspnaepPVcrimdygkfrYe 62  
                                        +l ++ + +L+e++ +     c+imdy k  Y 
  gi|330508745|ref|YP_004385173.1| 1237 KLYDRHKSRLIEIQADFGIAACKIMDYLKAEYS 1269
                                        566778899*********************997 PP

>> PSDC  Phophatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   6.6e-05      0.39       4      64 ..     996    1054 ..     994    1070 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.6e-05
                              PSDC    4 vqelkdliesdprlrmlfssmfeevpskkpykkdptgk.kqirdyeellellnhilttapef 64  
                                        v+++  +++  p+++ +f++ fe+vp    y + ++ + +++++ye l +ll+  + ++p+ 
  gi|330508745|ref|YP_004385173.1|  996 VHNFLCAVKYLPEMHSIFNQLFENVP---DYFDVSELDiSEVKNYEILADLLDVWIIEPPKT 1054
                                        78889999999***************...6665555556*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); 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: 0.80u 0.25s 00:00:01.05 Elapsed: 00:00:00.44
# Mc/sec: 9066.57
//
Query:       gi|330508746|ref|YP_004385174.1|  [L=433]
Description: cytochrome c biogenesis transmembrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-20   73.9  13.8    3.5e-20   72.8  13.8    1.6  1  DsbD      Cytochrome C biogenesis protein transmembrane regio
    1.9e-10   41.0  19.4    7.1e-07   29.3   3.0    2.6  2  DsbD_2    Cytochrome C biogenesis protein transmembrane regio
    1.4e-06   28.2   0.0    5.9e-06   26.2   0.0    1.8  1  AhpC-TSA  AhpC/TSA family
    0.00024   20.8   0.0    0.00053   19.7   0.0    1.5  1  Redoxin   Redoxin


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8  13.8   7.8e-24   3.5e-20       2     212 ..     183     424 ..     182     425 .. 0.76

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 7.8e-24
                              DsbD   2 flaGllsflsPCilpliPaylsyisgvsved...vktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvk 75 
                                       f  G++++lsPC ++l+ a++sy+ +   +d   +kt  +  + ++  + F lG++ vf  +g+  + +g  +++  
  gi|330508746|ref|YP_004385174.1| 183 FALGIVTSLSPCSIALLLAMFSYVMTARRKDeylRKTASASKEGFMIGIAFTLGMAAVFFIVGFFLSDIGVFIRQ-A 258
                                       677*********************99998883323343444489**************************99955.6 PP

                              DsbD  76 evirrvaglivillGlhflgvfk...........ievleklkll........................lkikkkael 117
                                       +    +agl++i+lG++++  +            +                                 ++++     
  gi|330508746|ref|YP_004385174.1| 259 RFFDLAAGLLMIILGINIIKPIGeiiepvrsrlsF--------GrgnsdaideetiaekkgimerlvsVSMNLFRYS 327
                                       7899**************97554444455555550........0555555555555566666666555333333444 PP

                              DsbD 118 svlgalllGltFalgwsPCigPvlasvlala.askeslakgallllvyvlGlaipfllvglllellkkkl.kslkky 192
                                        ++ga+ lG+ Falgw+PC+  +++ vl++  +++ + + gal+l+v+ +G ++p++ ++ ++  +  ++ ++    
  gi|330508746|ref|YP_004385174.1| 328 AFIGAFTLGVFFALGWAPCAVSLVFPVLIWLiSQDVTPLGGALMLFVFGVGHGVPVIPIATFSRAVGGQIgEKYIAA 404
                                       489****************99888888877515666778899********************998875542334444 PP

                              DsbD 193 skaveiaggvllvllGvlll 212
                                        k ++++ g+ ++++G++++
  gi|330508746|ref|YP_004385174.1| 405 GKHITKIFGLAVIVIGLIYA 424
                                       56777888888899999875 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   8.7   1.4e-06    0.0065     107     198 ..     167     274 ..     146     275 .. 0.74
   2 !   29.3   3.0   1.6e-10   7.1e-07     114     198 ..     322     421 ..     294     422 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-06
                            DsbD_2 107 llkklakkl.kslasalllGllnGllpC..glvysalllalas..........gsal.eGalvmlaFgLGTlpalll 169
                                        ++ +a++   ++ ++++lG++++l pC  +l+++++ +++++          +sa+ eG ++ +aF LG   ++++
  gi|330508746|ref|YP_004385174.1| 167 GFEGIASRQgINYLGMFALGIVTSLSPCsiALLLAMFSYVMTArrkdeylrktASASkEGFMIGIAFTLGMAAVFFI 243
                                       555555554468899*************5445777777777654444444333455447****************** PP

                            DsbD_2 170 fglllgllskklr.kkllr.lagvllillgl 198
                                       +g++l+ ++  +r ++++  +ag+l+i+lg+
  gi|330508746|ref|YP_004385174.1| 244 VGFFLSDIGVFIRqARFFDlAAGLLMIILGI 274
                                       **********998457788677888888886 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 1.6e-10
                            DsbD_2 114 kl...kslasalllGlln..GllpCgl..vysalllalas.gsaleGalvmlaFgLGTlpalllfglllgllskklr 182
                                       +l     + +a++lG+++  G++pC++  v+++l++ +++   +l+Gal++++Fg+G  ++++ ++++++ ++ ++ 
  gi|330508746|ref|YP_004385174.1| 322 NLfrySAFIGAFTLGVFFalGWAPCAVslVFPVLIWLISQdVTPLGGALMLFVFGVGHGVPVIPIATFSRAVGGQIG 398
                                       33354788899****7653399***7655999999999773589**************9999999999999977555 PP

                            DsbD_2 183 .......kkllrlagvllillgl 198
                                              k+++++ g+++i++gl
  gi|330508746|ref|YP_004385174.1| 399 ekyiaagKHITKIFGLAVIVIGL 421
                                       44445669999999***999997 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.3e-09   5.9e-06       5      96 ..       2     132 ..       1     142 [. 0.59

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.3e-09
                                       ----EEESTTCEEEECHHHTTSEEEEEEEST..ST-CCHHHHHHHHHHCHHHCCCT..TEEEEEEESSSCH.HHHHH CS
                          AhpC-TSA   5 apdfelknadgetvslsdykgkpvvlffypk..dwcpvCttelpalaklyeefker..gvevigvsvdspe.shkkf 76 
                                       apdf++ + dg++vsls y+g+ v+l +++     c  C++ l a  +++ +++e   gv++i ++v +   s+   
  gi|330508746|ref|YP_004385174.1|   2 APDFQAVDLDGKNVSLSGYRGEAVLLHITNIenPLCRECENALDAQTNQLSQLAEMdpGVNIITLNVRKNSySLDGR 78 
                                       9********************88888775540034555556666656666666643458899998886665333333 PP

                                       HHH-H...................................SSEEEE-TTSHHHH CS
                          AhpC-TSA  77 iekes..................................lnfpllsDeegkvak 96 
                                         +e+                                   +  +l D+eg+va 
  gi|330508746|ref|YP_004385174.1|  79 ELAEGwwnanitgpwiedfdpypltgkyidystleggfaNPTLILIDKEGNVAG 132
                                       333336666644444444445555555555555555544444445555555555 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.2e-07   0.00053       6     130 ..       2     133 ..       1     147 [. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.2e-07
                                       B---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHH....HHHTHHHHH.HCSTTTEEEEEESSSHH.. CS
                           Redoxin   6 aPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehp....yleklaell.kekgvdvvavvadndaf.. 75 
                                       aPdf+   ++ dg++vsls ++g  v++ +      P C++  +    + ++l++l+ ++ gv+++ +++ ++++  
  gi|330508746|ref|YP_004385174.1|   2 APDFQA--VDLDGKNVSLSGYRGEAVLLHITNI-ENPLCRECENaldaQTNQLSQLAeMDPGVNIITLNVRKNSYsl 75 
                                       7****6..66***************88877777.9999776444446888888776424779**********99999 PP

                                       .....HHHHHHH..TT-TSEEEE-TTSHHHHHTT-TTEEE.GGG.EEE-EEEEEEETTEEEEE CS
                           Redoxin  76 .....vkefwgk..eglkfpvlsDgsaaftkalGlrleedaseg.lrtpryavidedgkvvyl 130
                                            +  +w++  +g +++   D+     k ++        eg ++ p++++id++g+v  l
  gi|330508746|ref|YP_004385174.1|  76 dgrelAEGWWNAniTG-PWIEDFDPYPLTGKYIDYS----TLEGgFANPTLILIDKEGNVAGL 133
                                       9999677777765433.4555555777777777744....234458************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2819.66
//
Query:       gi|330508747|ref|YP_004385175.1|  [L=181]
Description: hypothetical protein MCON_3029 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1289.15
//
Query:       gi|330508748|ref|YP_004385176.1|  [L=139]
Description: ArsR family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-17   60.8   0.5    1.7e-16   59.8   0.5    1.6  1  HTH_5     Bacterial regulatory protein, arsR family
    2.4e-13   49.9   0.0    3.6e-13   49.4   0.0    1.3  1  HTH_20    Helix-turn-helix domain
     0.0029   17.5   0.0     0.0057   16.5   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0091   16.2   0.0      0.017   15.3   0.0    1.6  1  PaaX      PaaX-like protein
  ------ inclusion threshold ------
      0.052   14.0   0.0       0.12   12.9   0.0    1.7  2  HTH_27    Winged helix DNA-binding domain
      0.082   12.9   0.0       0.15   12.0   0.0    1.4  1  HTH_45    Winged helix-turn-helix
      0.097   12.4   0.0       0.56    9.9   0.0    1.9  2  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 !   59.8   0.5   6.8e-20   1.7e-16       1      46 [.      53      98 ..      53      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 6.8e-20
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      dp RlkIL+lL+egelc+ce++  ++ +qs +ShHL++L++aGL++
  gi|330508748|ref|YP_004385176.1| 53 DPCRLKILSLLREGELCACEIMIGVDRPQSSTSHHLSILKNAGLIK 98
                                      899*****************************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.0   1.4e-16   3.6e-13       2      61 .]      46     104 ..      45     104 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.4e-16
                                       HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20   2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       +i+ A+a+P R++il++L r+++l+a e++  +d ++++ s+HL +L  agL++ ++ gr
  gi|330508748|ref|YP_004385176.1|  46 EIFQAMADPCRLKILSLL-REGELCACEIMIGVDRPQSSTSHHLSILKNAGLIKERKDGR 104
                                       79****************.**************************************997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.2e-06    0.0057      16      63 ..      61     109 ..      59     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.2e-06
                                       HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEE CS
                              TrmB  16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYr 63 
                                        Ll++g++ a ei   +++p+s+    L+ L+++Gl++ +k gr  +Yr
  gi|330508748|ref|YP_004385176.1|  61 SLLREGELCACEIMIGVDRPQSSTSHHLSILKNAGLIKERKdGRWSRYR 109
                                       79***********************************999944455666 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.7e-06     0.017      44      68 ..      88     112 ..      64     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.7e-06
                              PaaX  44 lsRlakaGwlvrekegrrsfYrLsd 68 
                                       ls l++aG++++ k+gr s YrLs+
  gi|330508748|ref|YP_004385176.1|  88 LSILKNAGLIKERKDGRWSRYRLSE 112
                                       7889********************8 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         7   1.8e+04      36      44 ..       5      14 ..       4      15 .. 0.73
   2 ?   12.9   0.0   4.6e-05      0.12      28      66 ..      77     112 ..      59     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7
                            HTH_27 36 s.yslkkLte 44
                                      s ++++++t+
  gi|330508748|ref|YP_004385176.1|  5 SkEAVDRMTR 14
                                      6688888887 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.6e-05
                            HTH_27  28 lnvedshisyslkkLtekGLvertgdeadrrekrvrlTd 66 
                                       +++ +s++s  l+ L ++GL+   + ++d+r +r+rl++
  gi|330508748|ref|YP_004385176.1|  77 VDRPQSSTSHHLSILKNAGLI---KERKDGRWSRYRLSE 112
                                       68899999*************...444899*******98 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.9e-05      0.15      10      54 ..      58     102 ..      55     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.9e-05
                            HTH_45  10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkske 54 
                                        IL+ ++ege    +im  ++   + ++  L++L + glik++k+
  gi|330508748|ref|YP_004385176.1|  58 KILSLLREGELCACEIMIGVDRPQSSTSHHLSILKNAGLIKERKD 102
                                       79**************************************88653 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.23   5.9e+02     119     152 ..      29      66 ..      20      75 .. 0.66
   2 ?    9.9   0.0   0.00022      0.56      52      78 ..      81     107 ..      74     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.23
                           DUF4423 119 issltlaiskedyek....ikkeirefrkkilaiaees 152
                                       + slt+ +++e+++     ++ + + +r kil++++e 
  gi|330508748|ref|YP_004385176.1|  29 LRSLTIDLDEEELKTeseiFQAMADPCRLKILSLLREG 66 
                                       56778888888776522214445556777777777765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00022
                           DUF4423  52 aeevekalefLlklgllkkdedgkyrq 78 
                                       ++ +++ l++L+++gl+k+ +dg++ +
  gi|330508748|ref|YP_004385176.1|  81 QSSTSHHLSILKNAGLIKERKDGRWSR 107
                                       6677889*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1059.66
//
Query:       gi|330508749|ref|YP_004385177.1|  [L=288]
Description: rhodanese domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.8e-22   78.2   0.0    1.1e-13   51.6   0.0    2.2  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   6.1e-18   1.1e-13      12     107 .]      96     192 ..      87     192 .. 0.71
   2 !   24.6   0.0   1.6e-09   2.8e-05      11      74 ..     225     285 ..     220     288 .] 0.70

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 6.1e-18
                         Rhodanese  12 gkva.llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvycdgggr.aaaa 82 
                                          + ++D+++ + Y+++hI++A+++     s+   + +  l+  eel++l    g+++++ vvvy++   +  a++
  gi|330508749|ref|YP_004385177.1|  96 S--DvIIDASNGDGYAASHIKNAIHI----PSKDFLDSNGNLKGDEELSRLlgeaGLSKEDSVVVYGSAERSgEAQL 166
                                       3..24*********************....3333333333333333333334559************9988866666 PP

                         Rhodanese  83 aa.llkklGykn.vsvldGGfkawkea 107
                                       a   l+ lG ++ v++l+G++++wk+a
  gi|330508749|ref|YP_004385177.1| 167 AFlVLRHLG-QDdVRLLEGSLDDWKAA 192
                                       5535556**.788***********985 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.6e-09
                         Rhodanese  11 kgkvallDvRppeeYekghIpgAvnv.skdtlsrakkseapllelpeellelgidnkktvvvycd 74 
                                       +g+++++DvRp++++ kg+Ipg+  + +++ +++ k  ++ +l ++    +  +d++ ++vvy d
  gi|330508749|ref|YP_004385177.1| 225 SGQARIVDVRPFVDFGKGRIPGSTALdPANVIKGDKIKNGGDLGTV---FS-RLDKDMPIVVYSD 285
                                       45556*********************54444444444444443333...33.2577*******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2271.28
//
Query:       gi|330508750|ref|YP_004385178.1|  [L=370]
Description: arsenical-resistance protein [Methanosaeta concilii GP6]
Scores for complete 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-63  212.4  13.6    4.8e-63  212.4  13.6    1.8  3  SBF       Sodium Bile acid symporter family


Domain annotation for each model (and alignments):
>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       0.5     9e+03     135     141 ..      27      33 ..      13      43 .. 0.50
   2 !  212.4  13.6   2.7e-67   4.8e-63       1     194 [.      60     257 ..      60     258 .. 0.99
   3 ?   -2.3   0.1      0.17     3e+03     123     123 ..     287     287 ..     264     344 .. 0.59

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 0.5
                               SBF 135 livviiP 141
                                       +++ i+ 
  gi|330508750|ref|YP_004385178.1|  27 FVAMILG 33 
                                       2222222 PP

  == domain 2  score: 212.4 bits;  conditional E-value: 2.7e-67
                               SBF   1 ailLilmmfpmglkveveklkellkrpkalllglvlqwvikPllmfilakillrdlklepelavGlilvglapggam 77 
                                       ai+Lilmm+p+++kv++e+l+++++++k l l+lv++w+++P+lmf+la+i+lrd    p l+ G+il+gla+++am
  gi|330508750|ref|YP_004385178.1|  60 AIGLILMMYPPLAKVKYEELGQVFTDRKVLGLSLVQNWIVGPILMFALAVIFLRDS---PHLMYGIILIGLARCIAM 133
                                       69*****************************************************9...****************** PP

                               SBF  78 snvwtylakGdlelsvvlvalstllailltPlllyllaksl.......eqttlkvpieeivksvlivviiPliaGil 147
                                       ++vw++la+G +e+++ lv l+++++++++++++y++++ l        +t+++v+i++i++sv+i+++iP++aGi+
  gi|330508750|ref|YP_004385178.1| 134 VIVWNELACGCTEYCAALVGLNSIFQVFFYSIYAYIFITVLpaalgiaAGTAVDVTISQIAESVFIYLGIPFLAGIV 210
                                       ***********************************************99**************************** PP

                               SBF 148 lryillkhkGrewfeskllpavspisligllltivvifalkgelive 194
                                       +r  l++ +G++w+e  +lp +sp++l++ll+tivv+f+lkg++iv+
  gi|330508750|ref|YP_004385178.1| 211 TRFSLIQARGKSWYERDFLPRISPLTLVALLFTIVVMFSLKGDYIVQ 257
                                       *********************************************97 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.17
                               SBF 123 l 123
                                       l
  gi|330508750|ref|YP_004385178.1| 287 L 287
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3056.59
//
Query:       gi|330508751|ref|YP_004385179.1|  [L=265]
Description: Fe-S cluster domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   45.9   0.4      7e-12   44.8   0.4    1.6  1  FeS       Putative Fe-S cluster
    8.3e-08   32.2   0.1    3.6e-07   30.1   0.1    2.1  2  HTH_20    Helix-turn-helix domain
    0.00078   19.4   0.0     0.0013   18.6   0.0    1.4  1  TBP       Transcription factor TFIID (or TATA-binding protein
    0.00098   18.9   0.2     0.0037   17.1   0.2    2.0  1  HTH_5     Bacterial regulatory protein, arsR family
     0.0022   17.6   0.2       0.11   12.1   0.0    2.1  2  ArsR      ArsR transcriptional regulator


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 !   44.8   0.4   1.9e-15     7e-12       1      33 []     213     245 ..     213     245 .. 0.99

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.9e-15
                               FeS   1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33 
                                       LP t+C  CG+++C afA +lv  e+++++C+p
  gi|330508751|ref|YP_004385179.1| 213 LPRTDCQICGEQSCYAFAIKLVGRETEIDKCTP 245
                                       9******************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1     1e-10   3.6e-07       4      59 ..      12      64 ..       9      65 .. 0.93
   2 ?   -2.5   0.0       1.5   5.5e+03      14      29 ..     208     223 ..     207     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1e-10
                                      HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  4 aeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                        A+a+ +Rr+i+++L  ++++t +e+ +++++++  l+yHL+ L +agL ++++ 
  gi|330508751|ref|YP_004385179.1| 12 SNAMANATRRKIMAML-VEKERTKEEIEQAVGGTM--LDYHLQMLKQAGLADTRGD 64
                                      679*************.**************8888..*************999875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                                       HHHHHHSTCTTB-HHH CS
                            HTH_20  14 rilraLaraegltase 29 
                                       +i+++L+r +++ ++e
  gi|330508751|ref|YP_004385179.1| 208 EIYQYLPRTDCQICGE 223
                                       799***9999988876 PP

>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   3.7e-07    0.0013      40      83 ..     146     187 ..     116     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.7e-07
                                       SEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHH CS
                               TBP  40 glvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilk 83 
                                       +l+++  + ++ ++i+s+G+v++t  kse e+re+++ + + ++
  gi|330508751|ref|YP_004385179.1| 146 ALIIQ--RGNILITIYSTGSVTMTMIKSEAEAREVLEDLKKTIN 187
                                       44443..34799*************************9988886 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 !   17.1   0.2     1e-06    0.0037       3      46 ..      19      60 ..      17      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-06
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      tR+kI+ +L e+e++  e+  ++g +   +++HL +L++aGL +
  gi|330508751|ref|YP_004385179.1| 19 TRRKIMAMLVEKERTKEEIEQAVGGT--MLDYHLQMLKQAGLAD 60
                                      9*********************9976..7*************86 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   3.1e-05      0.11      12      60 ..      13      62 ..       5      65 .. 0.89
   2 ?    3.4   0.0     0.014        51      83     120 ..     152     189 ..     149     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                              ArsR 12 qvfdsetkkkvyeelskeWlteeeleeklgee.veealklLkkikliEsq 60
                                      +++ ++t +k++  l ++  t+ee+e+ +g    +  l++Lk+++l +++
  gi|330508751|ref|YP_004385179.1| 13 NAMANATRRKIMAMLVEKERTKEEIEQAVGGTmLDYHLQMLKQAGLADTR 62
                                      56788999*********************99978999********98876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.014
                              ArsR  83 anfqcsledlsdiievafmsdeeleelvekiekeveeg 120
                                        n+ +++   + + + +++s+ e +e+ e+++k+++e 
  gi|330508751|ref|YP_004385179.1| 152 GNILITIYSTGSVTMTMIKSEAEAREVLEDLKKTINEA 189
                                       5889999999999999999********99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1101  (0.0614089); expected 358.6 (0.02)
Passed bias filter:                      905  (0.0504769); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 1974.29
//
Query:       gi|330508752|ref|YP_004385180.1|  [L=120]
Description: DsrE/DsrF family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-20   71.9   0.0    6.3e-20   71.7   0.0    1.0  1  DrsE      DsrE/DsrF-like family


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   3.5e-24   6.3e-20       1     116 [.       2     119 ..       2     120 .] 0.88

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 3.5e-24
                                       -EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEE CS
                              DrsE   1 kkvfilvtggpygseaarealelalaaaalghevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvC 77 
                                       k ++i+ t gpy s++a+ a+++a  a++   +v++f+y d+v+++++gq  np+++k   +l+++l++ g+ + +C
  gi|330508752|ref|YP_004385180.1|   2 KTLTIILTDGPYISQYADMAFKIASRALNV-FQVNIFLYLDAVHIPKSGQ--NPSNFKITGKLFQELADRGAVVRAC 75 
                                       6789***********888888887655444.69***************66..999********************** PP

                                       HHHHHHTT--GGGE-...T-..-EEEE-HHHHHHHHHH-SEEEE CS
                              DrsE  78 gqaakargldededl...gv..gvevsglgelaelqnegdrvit 116
                                       + +a+arg+ ++ed    +   g+++ +l +lae++ ++drvi 
  gi|330508752|ref|YP_004385180.1|  76 ARCAAARGYRAEEDGtcpDYlqGIKITSLYDLAEMLEKSDRVIA 119
                                       **********888555442257********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 00:00:00.39
# Mc/sec: 925.26
//
Query:       gi|330508753|ref|YP_004385181.1|  [L=113]
Description: DsrE/DsrF family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-08   34.9   0.0    1.8e-08   34.8   0.0    1.0  1  DrsE      DsrE/DsrF-like family
     0.0046   17.1   0.1       0.01   16.0   0.1    1.5  1  DsrH      DsrH like protein
  ------ inclusion threshold ------
      0.086   12.6   0.2       0.24   11.2   0.2    1.8  2  TOM6p     Mitochondrial import receptor subunit TOM6 homolog


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   2.9e-12   1.8e-08       2     115 ..       3     111 ..       2     113 .] 0.89

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.9e-12
                                       EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEH CS
                              DrsE   2 kvfilvtggpygseaarealelalaaaalghevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCg 78 
                                       ++f+l  ++pygse+a+  l++a + ++++  v++ +y dGv+l+l+gq++   d +nl++ l a+ e   ++++ +
  gi|330508753|ref|YP_004385181.1|   3 SIFYLLDSAPYGSEKAYGVLNAAAVSIKMD--VNLGLYADGVYLALAGQDTSLLDVPNLSDILYAYPEL--RVMAHE 75 
                                       6899999*******8888777777777766..9*********************************998..6***** PP

                                       HHHHHTT--GGGE-T--EEEE-HHHHHHHHHH-SEEE CS
                              DrsE  79 qaakargldededlgvgvevsglgelaelqnegdrvi 115
                                        ++ +rgl +  ++   ve+++  ++ + ++ +d +i
  gi|330508753|ref|YP_004385181.1|  76 PSLTERGLLSRGLV-ERVELVDEEDFMKQALAADGLI 111
                                       *********76566.69*********99999999887 PP

>> DsrH  DsrH like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.7e-06      0.01      24      83 ..      37     106 ..      22     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-06
                                       E-GGGGGGGBTTBTTH....HHHHTS.....SSEEEEEHHHHHHTT-T.TSB-TTSEEE-HHHHHHHHHH CS
                              DsrH  24 LieDgVyaalkgsrll....kalkea.....svklyaLkeDleARGlt.eqlsegvkvidydgfVeltvk 83 
                                       L  DgVy+al+g++++     +l+++     +++++a ++ l  RGl  + l e+v+++d ++f ++++ 
  gi|330508753|ref|YP_004385181.1|  37 LYADGVYLALAGQDTSlldvPNLSDIlyaypELRVMAHEPSLTERGLLsRGLVERVELVDEEDFMKQALA 106
                                       889******9997654222234444488899*****************666*************998875 PP

>> TOM6p  Mitochondrial import receptor subunit TOM6 homolog
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2     4e-05      0.24      47      67 ..      33      53 ..      28      63 .. 0.84
   2 ?   -2.7   0.0       0.9   5.4e+03      37      52 ..      96     111 ..      93     112 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4e-05
                             TOM6p 47 lnlGlfaaGvwlarnlsdidl 67
                                      +nlGl+a Gv+la    d  l
  gi|330508753|ref|YP_004385181.1| 33 VNLGLYADGVYLALAGQDTSL 53
                                      8***********987777665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.9
                             TOM6p  37 drndfrrnlllnlGlf 52 
                                       d +df +  l   Gl 
  gi|330508753|ref|YP_004385181.1|  96 DEEDFMKQALAADGLI 111
                                       7788888887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       175  (0.00976072); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 855.25
//
Query:       gi|330508754|ref|YP_004385182.1|  [L=98]
Description: sulfur relay protein TusB/DsrH family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-09   37.8   0.0    1.9e-09   37.5   0.0    1.1  1  DsrH      DsrH like protein
  ------ inclusion threshold ------
      0.028   14.8   0.0       0.45   10.9   0.0    2.1  1  DrsE      DsrE/DsrF-like family


Domain annotation for each model (and alignments):
>> DsrH  DsrH like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   2.1e-13   1.9e-09       4      71 ..      13      76 ..      10      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2.1e-13
                                      GGS.-HHHHHHT--TT-..EEEE-GGGGGGGBTTBTTHHHHHTSSSEEEEEHHHHHHTT-TTSB-TTSEE CS
                              DsrH  4 fesnalksclrllqegD..avlLieDgVyaalkgsrllkalkeasvklyaLkeDleARGlteqlsegvkv 71
                                       +s++ + clrl+++gD   ++L +DgVy +l++    + +++ ++k++a keDl+ARG++    egv+v
  gi|330508754|ref|YP_004385182.1| 13 PQSERAELCLRLMEHGDdpVLYLAGDGVYNLLDE----ALMEKWPGKVMACKEDLDARGVQ--AGEGVRV 76
                                      5677999**********77799*********993....445555999*************9..3455554 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.1e-05      0.45      27      90 ..      24      72 ..       5      93 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.1e-05
                                      HHTTT-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT.-EEEEEHHHHHHTT--GGG CS
                              DrsE 27 aaalghevsvffygdGvllllkgqtanpadeknlaellkalkeyg.vklyvCgqaakargldede 90
                                      + + g + ++ + gdGv++ll                 +al+e+   k+++C++ ++arg+ + e
  gi|330508754|ref|YP_004385182.1| 24 LMEHGDDPVLYLAGDGVYNLLD----------------EALMEKWpGKVMACKEDLDARGVQAGE 72
                                      4555567777777777777777................356665568899999999999999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 758.96
//
Query:       gi|330508755|ref|YP_004385183.1|  [L=99]
Description: hypothetical protein MCON_3041 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); 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:                         0  (0); expected 0.2 (1e-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 0.31s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 529.08
//
Query:       gi|330508756|ref|YP_004385184.1|  [L=258]
Description: GNAT family acetyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-06   26.9   0.0    6.9e-06   26.3   0.0    1.3  1  Acetyltransf_1  Acetyltransferase (GNAT) family
      0.001   19.8   0.0     0.0013   19.4   0.0    1.3  1  Acetyltransf_3  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.019   14.9   0.0       0.04   13.9   0.0    1.5  1  FR47            FR47-like protein
      0.033   14.6   0.1      0.078   13.4   0.0    1.7  2  Acetyltransf_7  Acetyltransferase (GNAT) domain
      0.099   12.7   0.0       0.28   11.3   0.0    1.7  2  Acetyltransf_9  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.9e-09   6.9e-06      21     117 .]      63     171 ..      41     171 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.9e-09
                                       HHHHHHHHHSTTCEEEE.EEETTEEEEEEEEEEEET..............TSTTEEEEEEEEESGGGTTSSHHHHHH CS
                    Acetyltransf_1  21 eeefeesfsleaegllv.aeedgeliGfisllkipd..............ekggvayieslaVspeyrgkGlGsaLl 82 
                                       e+  +++   ++e  ++ ++ +++l+++  ++                    ++ a++  +aV+p +rg Gl ++L 
  gi|330508756|ref|YP_004385184.1|  63 EYLSRIF---QTELSVLgVLAEEKLAAYSIIRYPGMekdnlgrdlnlaeeDLKKLAHLQAIAVHPHFRGCGLQRELA 136
                                       2224455...555333347888888888844444445555577777777755999********************** PP

                                       HHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  83 ealeerareegikkivlaveedndaairlYeklGF 117
                                        a ++ +++ g++ i ++v++ n  + + +  +GF
  gi|330508756|ref|YP_004385184.1| 137 AAHLQVLESSGYEHICCTVSPKNPVSLNNLLSCGF 171
                                       *****99999****99999999*999877767887 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.7e-07    0.0013      85     138 .]     120     172 ..      34     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.7e-07
                    Acetyltransf_3  85 ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       + ++p+f+g G+ +e ++a l+++ e  g+e+++++++++N+ S + l ++Gf+
  gi|330508756|ref|YP_004385184.1| 120 IAVHPHFRGCGLQRELAAAHLQVL-ESSGYEHICCTVSPKNPVSLNNLLSCGFR 172
                                       778999******************.8888************************6 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.1e-05      0.04      22      80 ..     115     174 ..     105     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                                       SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfeki 80 
                                         l a+ v+p +r+ Gl + l++a  + +   g+ ++   v ++N  s + + + Gf+++
  gi|330508756|ref|YP_004385184.1| 115 AHLQAIAVHPHFRGCGLQRELAAAHLQVLESSGYeHICCTVSPKNPVSLNNLLSCGFRVR 174
                                       6899*************************9988626777888999999888888888765 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.2e-05     0.078      24      52 ..     110     147 ..      78     173 .. 0.69
   2 ?   -2.6   0.0       2.2   7.8e+03      63      71 ..     236     244 ..     216     245 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                                       S....TCTEEEEE-GGGTTSSHHHHHHHH....TT.SE CS
                    Acetyltransf_7  24 d....aeitrlaVdpeyrgkGiGraLlea....ae.kg 52 
                                       d    a++  +aV+p++rg G+ r+L +a     e +g
  gi|330508756|ref|YP_004385184.1| 110 DlkklAHLQAIAVHPHFRGCGLQRELAAAhlqvLEsSG 147
                                       1344446667***************9886333311444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.2
                                       HHHHHHHHH CS
                    Acetyltransf_7  63 ekaikfYek 71 
                                       ek++ fY+k
  gi|330508756|ref|YP_004385184.1| 236 EKSEIFYRK 244
                                       256779988 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   4.7e+03      32      55 ..      62      86 ..      49      92 .. 0.72
   2 ?   11.3   0.0   7.9e-05      0.28      72     110 ..     113     151 ..      99     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                                      HHHHHHHHTTS.EEEEEEETTEEEE CS
                    Acetyltransf_9 32 reyfrkllees.rvlgaedngelvg 55
                                      +ey++++++ +  vlg+  +++l++
  gi|330508756|ref|YP_004385184.1| 62 EEYLSRIFQTElSVLGVLAEEKLAA 86
                                      4667777776557888888888876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.9e-05
                                       EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EE CS
                    Acetyltransf_9  72 kaagvtgVavapehrgrgvlskLlaraleemreegqpls 110
                                       k a + ++av+p+ rg g+ ++L a++l+ +++ g++ +
  gi|330508756|ref|YP_004385184.1| 113 KLAHLQAIAVHPHFRGCGLQRELAAAHLQVLESSGYEHI 151
                                       5689999************************99998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1421.73
//
Query:       gi|330508757|ref|YP_004385185.1|  [L=354]
Description: CoB--CoM heterodisulfide reductase iron-sulfur subunit D [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-31  106.8   5.8    3.6e-16   59.1   0.1    2.8  3  CCG       Cysteine-rich domain
    9.5e-12   45.2   4.2    9.5e-12   45.2   4.2    2.1  2  Fer4_8    4Fe-4S dicluster domain
    2.3e-10   40.8   3.9    2.3e-10   40.8   3.9    3.3  3  Fer4_17   4Fe-4S dicluster domain
    2.7e-08   33.8  20.2    8.8e-07   29.0  10.8    3.3  4  Fer4_10   4Fe-4S dicluster domain
    2.3e-07   31.3   4.9    2.3e-07   31.3   4.9    2.2  2  Fer4_7    4Fe-4S dicluster domain
    1.4e-05   25.2   9.2    1.4e-05   25.2   9.2    3.1  3  Fer4_9    4Fe-4S dicluster domain
    0.00017   21.5  15.4    0.00064   19.7   4.0    3.4  3  Fer4_2    4Fe-4S binding domain
    0.00044   20.0  20.5     0.0062   16.3   3.3    3.0  2  Fer4      4Fe-4S binding domain
    0.00073   19.7   4.2       0.72   10.1   0.1    2.9  3  Fer4_18   4Fe-4S dicluster domain
     0.0029   18.5  14.9      0.026   15.4  13.0    3.1  3  Fer4_16   4Fe-4S double cluster binding domain
     0.0062   16.9  20.1      0.011   16.1   0.8    3.9  4  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.016   15.3   1.6      0.016   15.3   1.6    3.4  3  Fer4_6    4Fe-4S binding domain
      0.025   14.7  13.9       0.18   12.0   0.6    3.5  4  Fer4_21   4Fe-4S dicluster domain
       0.29   11.7  13.4       0.61   10.7   0.6    3.1  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.86   10.4   0.1       0.86   10.4   0.1    3.4  3  Fer4_15   4Fe-4S single cluster 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 ?   -2.4   0.2       4.8   5.7e+03      65      81 ..       4      21 ..       1      23 [. 0.63
   2 !   50.3   0.1   1.8e-16   2.1e-13       1      85 []     138     217 ..     138     217 .. 0.96
   3 !   59.1   0.1     3e-19   3.6e-16       1      84 [.     249     333 ..     249     334 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.8
                               CCG 65 aeet.gadaivtacpgCl 81
                                      +++   a  +++ c++C 
  gi|330508757|ref|YP_004385185.1|  4 MKQDkRAFNLCVRCGTCR 21
                                      555324556889999997 PP

  == domain 2  score: 50.3 bits;  conditional E-value: 1.8e-16
                               CCG   1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtac 77 
                                       ++yf+gC +  ++y e+ k++  ll++ g++l +   e+CCG++  r+g++  a +l ++n ++++e ga  ++t c
  gi|330508757|ref|YP_004385185.1| 138 YVYFVGC-MNSYRYHETAKNTFSLLSRFGATLLPG--EQCCGSPLLRMGFD--ASELIEENSRQIREIGASTVITGC 209
                                       68*****.*************************76..*************9..799********************* PP

                               CCG  78 pgCllqlk 85 
                                       +gC+++lk
  gi|330508757|ref|YP_004385185.1| 210 AGCYTTLK 217
                                       *****986 PP

  == domain 3  score: 59.1 bits;  conditional E-value: 3e-19
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGaggg.rsgkeelaealakrnvetaeetgadai 73 
                                       v+y+d+Chl+r++  y+++r++++++    +ve++   + + CCG ggg r+g+++l++++a+r++e + + ++d+i
  gi|330508757|ref|YP_004385185.1| 249 VTYHDPCHLGRHNriYEQPRQVIRAI--CRLVEMKASrNAARCCGGGGGvRAGYKDLSLQMARRRLEDVPD-DVDYI 322
                                       89************************..56777777778999**987761566777***************.7**** PP

                               CCG  74 vtacpgCllql 84 
                                       vt cp C  +l
  gi|330508757|ref|YP_004385185.1| 323 VTSCPLCIRNL 333
                                       *******7766 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   4.2   7.9e-15   9.5e-12       3      65 .]      12      79 ..      10      79 .. 0.83
   2 ?   -3.0   0.0       8.7     1e+04      45      54 ..     320     329 ..     297     331 .. 0.60

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 7.9e-15
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaae.dvqeeqvlee....eealwsCttcgaCtevCpvgi 65
                                      + C++Cg C++ Cp++ +++ ++ ++rg+ +  ++ ++ +l++     ++l++Cttcg Cte+Cp gi
  gi|330508757|ref|YP_004385185.1| 12 NLCVRCGTCRTVCPAFLESGWESANTRGRMMIiKELTSGRLQAdgdvLRSLNTCTTCGLCTENCPAGI 79
                                      67******************999999999999633333333336667899***************997 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.7
                            Fer4_8  45 eealwsCttc 54 
                                       ++++ sC  c
  gi|330508757|ref|YP_004385185.1| 320 DYIVTSCPLC 329
                                       4556666555 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   3.9     2e-13   2.3e-10       2      60 ..      14      79 ..      13      80 .. 0.82
   2 ?   -0.6   0.0       1.7     2e+03      33      49 ..     196     212 ..     177     214 .. 0.69
   3 ?    1.8   0.1      0.31   3.7e+02      12      48 ..     255     291 ..     252     296 .. 0.65

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2e-13
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraakl......glleeaeke....ekaslCieCgeCerkCPqgl 60
                                      C +Cg C+ +Cp + + ++e ++++ ++++      g+l++   +    +  ++C++Cg+C++ CP+g+
  gi|330508757|ref|YP_004385185.1| 14 CVRCGTCRTVCPAFLESGWESANTRGRMMIikeltsGRLQA---DgdvlRSLNTCTTCGLCTENCPAGI 79
                                      ********************999999988887443333333...245678****************997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                           Fer4_17  33 lleeaekeekaslCieC 49 
                                       +++e+ +++++  C++C
  gi|330508757|ref|YP_004385185.1| 196 QIREIGASTVITGCAGC 212
                                       44455555788888888 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.31
                           Fer4_17  12 Cpsyeaydn..epkkllraaklglleeaekeekaslCie 48 
                                       C  ++ ++   +p++++ra  + +l e++++++a +C++
  gi|330508757|ref|YP_004385185.1| 255 CHLGRHNRIyeQPRQVIRA--ICRLVEMKASRNAARCCG 291
                                       7766665541146677777..334556678899999987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0  10.8   7.3e-10   8.8e-07       7      56 .]      12      76 ..       7      76 .. 0.90
   2 !   18.0   1.9     2e-06    0.0023       5      24 ..      61      86 ..      57     106 .. 0.69
   3 ?   -2.1   0.1       3.7   4.5e+03      11      15 ..     208     212 ..     193     215 .. 0.65
   4 ?   -1.2   0.0       1.9   2.2e+03      42      48 ..     323     329 ..     307     344 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 7.3e-10
                           Fer4_10  7 dtCirCgkCvkaCPadl...............tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      + C+rCg+C+++CPa l                +  ++g    ++ v   +  Ct+cg C+e CP
  gi|330508757|ref|YP_004385185.1| 12 NLCVRCGTCRTVCPAFLesgwesantrgrmmiIKELTSGRLQADGDVLRSLNTCTTCGLCTENCP 76
                                      68*************88************9987777777777788888899*************9 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2e-06
                           Fer4_10  5 dddtCirCgkCvkaCPadl......t 24
                                        +tC+ Cg C++ CPa +      +
  gi|330508757|ref|YP_004385185.1| 61 SLNTCTTCGLCTENCPAGIsppeiiE 86
                                      6789*************774444331 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.7
                           Fer4_10  11 rCgkC 15 
                                       +C+ C
  gi|330508757|ref|YP_004385185.1| 208 GCAGC 212
                                       34444 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 1.9
                           Fer4_10  42 vekCtgc 48 
                                       v +C+ c
  gi|330508757|ref|YP_004385185.1| 323 VTSCPLC 329
                                       5555555 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   4.9   1.9e-10   2.3e-07       2      52 .]      14      79 ..      13      79 .. 0.75
   2 ?   -2.0   0.0       4.8   5.8e+03      36      42 ..     207     213 ..     185     215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.9e-10
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgt...............ekveidpekClgCgaCvavCPtga 52
                                      C+ Cg C  +Cp+   + +e++n +g+                +v  + ++C++Cg C + CP+g+
  gi|330508757|ref|YP_004385185.1| 14 CVRCGTCRTVCPAFLESGWESANTRGRmmiikeltsgrlqadGDVLRSLNTCTTCGLCTENCPAGI 79
                                      ********************9999976444443333333333333556789************996 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.8
                            Fer4_7  36 ekClgCg 42 
                                       + C gC+
  gi|330508757|ref|YP_004385185.1| 207 TGCAGCY 213
                                       4566664 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   2.6   7.3e-05     0.087      32      47 ..      10      25 ..       1      28 [. 0.69
   2 !   25.2   9.2   1.1e-08   1.4e-05       2      49 ..      14      78 ..      13      80 .. 0.78
   3 ?   -1.4   0.0       2.2   2.7e+03      35      39 ..     208     212 ..     185     215 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.3e-05
                            Fer4_9 32 seeaCigCgaCveaCp 47
                                        + C+ Cg+C  +Cp
  gi|330508757|ref|YP_004385185.1| 10 AFNLCVRCGTCRTVCP 25
                                      2267999999999999 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.1e-08
                            Fer4_9  2 CtgCgaCveaCpagvv.vedaaerkarlraase................eaCigCgaCveaCpkg 49
                                      C++Cg+C ++Cpa +    ++a++  r+ + +e                + C++Cg C+e Cp g
  gi|330508757|ref|YP_004385185.1| 14 CVRCGTCRTVCPAFLEsGWESANTRGRMMIIKEltsgrlqadgdvlrslNTCTTCGLCTENCPAG 78
                                      ***********887763444444444555555577889999999*****99************98 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.2
                            Fer4_9  35 aCigC 39 
                                        C gC
  gi|330508757|ref|YP_004385185.1| 208 GCAGC 212
                                       34444 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   4.0   5.4e-07   0.00064       9      22 .]      13      26 ..       7      26 .. 0.92
   2 !   15.2   3.7   1.4e-05     0.017       8      22 .]      63      77 ..      57      77 .. 0.91
   3 ?   -2.8   0.6       7.3   8.8e+03      10      14 ..     209     213 ..     207     214 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.4e-07
                            Fer4_2  9 rCigCgaCvsaCPa 22
                                       C++Cg+C+++CPa
  gi|330508757|ref|YP_004385185.1| 13 LCVRCGTCRTVCPA 26
                                      7************8 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.4e-05
                            Fer4_2  8 drCigCgaCvsaCPa 22
                                      ++C+ Cg C+ +CPa
  gi|330508757|ref|YP_004385185.1| 63 NTCTTCGLCTENCPA 77
                                      69************8 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.3
                            Fer4_2  10 CigCg 14 
                                       C gC 
  gi|330508757|ref|YP_004385185.1| 209 CAGCY 213
                                       66664 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   3.3   5.2e-06    0.0062       6      19 ..      12      25 ..      11      26 .. 0.92
   2 !   15.2   2.0   1.2e-05     0.014       7      21 ..      64      78 ..      60      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.2e-06
                                      TTSSS-THHHHHST CS
                              Fer4  6 ekCigCGaCvevCP 19
                                      ++C++CG+C  vCP
  gi|330508757|ref|YP_004385185.1| 12 NLCVRCGTCRTVCP 25
                                      68************ PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.2e-05
                                      TSSS-THHHHHSTTT CS
                              Fer4  7 kCigCGaCvevCPvg 21
                                       C+ CG+C e CP g
  gi|330508757|ref|YP_004385185.1| 64 TCTTCGLCTENCPAG 78
                                      7************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 !    9.9   0.4   0.00069      0.82      52      74 ..       5      27 ..       1      31 [. 0.79
   2 !   10.1   0.1    0.0006      0.72      54      75 ..      58      79 ..      34      85 .. 0.75
   3 ?   -1.8   0.0       2.9   3.5e+03      63      79 ..     318     335 ..     297     338 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00069
                           Fer4_18 52 erkekgagdcidcescvkvcPtg 74
                                      ++ +++ + c+ c++c +vcP  
  gi|330508757|ref|YP_004385185.1|  5 KQDKRAFNLCVRCGTCRTVCPAF 27
                                      445667889************75 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0006
                           Fer4_18 54 kekgagdcidcescvkvcPtgi 75
                                        ++ + c++c+ c + cP gi
  gi|330508757|ref|YP_004385185.1| 58 VLRSLNTCTTCGLCTENCPAGI 79
                                      4567789*************99 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.9
                           Fer4_18  63 dcescvkvcPtgi.dirk 79 
                                       d ++ v+ cP  i ++r+
  gi|330508757|ref|YP_004385185.1| 318 DVDYIVTSCPLCIrNLRD 335
                                       456777888877634555 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 !   15.4  13.0   2.2e-05     0.026       2      66 ..      14      77 ..      13      78 .. 0.75
   2 !   12.9   3.0   0.00014      0.17       1      16 [.      64      79 ..      64     111 .. 0.75
   3 ?   -0.5   0.0       2.1   2.5e+03      52      60 ..     204     212 ..     184     215 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeieare.cisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66
                                      C++Cg C  vCP+   ++ ++++ + r+  i++ t ++ ++  d  +    + +t C+ C++ CPa
  gi|330508757|ref|YP_004385185.1| 14 CVRCGTCRTVCPAFLESGWESANTRGRMmIIKELTSGRLQADGDVLRSL--NTCTTCGLCTENCPA 77
                                      ************8766666444444444255557777777777777777..99************8 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00014
                           Fer4_16  1 rCgtCgkCaevCPtna 16
                                      +C+tCg C+e CP++ 
  gi|330508757|ref|YP_004385185.1| 64 TCTTCGLCTENCPAGI 79
                                      5************985 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.1
                           Fer4_16  52 eaitgCdiC 60 
                                       + itgC+ C
  gi|330508757|ref|YP_004385185.1| 204 TVITGCAGC 212
                                       456999988 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.8   9.4e-06     0.011       2      15 ..      12      25 ..       6      37 .. 0.89
   2 !   12.4   1.9   0.00015      0.18       2      16 ..      63      77 ..      62      81 .. 0.91
   3 ?   -1.0   0.3       2.9   3.4e+03       6      11 ..     208     213 ..     207     215 .. 0.68
   4 ?   -1.3   0.2       3.6   4.3e+03       6      11 ..     325     330 ..     324     331 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.4e-06
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      + C++Cg C+ +CP
  gi|330508757|ref|YP_004385185.1| 12 NLCVRCGTCRTVCP 25
                                      56************ PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00015
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++C+ Cg C+  CP 
  gi|330508757|ref|YP_004385185.1| 63 NTCTTCGLCTENCPA 77
                                      79************7 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.9
                            Fer4_4   6 gCgsCv 11 
                                       gC  C+
  gi|330508757|ref|YP_004385185.1| 208 GCAGCY 213
                                       777776 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.6
                            Fer4_4   6 gCgsCv 11 
                                        C+ C+
  gi|330508757|ref|YP_004385185.1| 325 SCPLCI 330
                                       588886 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.0   0.00011      0.13       7      21 ..      12      26 ..      12      31 .. 0.93
   2 ?   15.3   1.6   1.3e-05     0.016       7      23 ..      63      79 ..      60      80 .. 0.92
   3 ?   -1.6   0.4       2.8   3.3e+03      11      17 ..     208     214 ..     207     215 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                            Fer4_6  7 dkCigCgdCvrvCPe 21
                                      ++C+ Cg C +vCP+
  gi|330508757|ref|YP_004385185.1| 12 NLCVRCGTCRTVCPA 26
                                      79************7 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.3e-05
                            Fer4_6  7 dkCigCgdCvrvCPega 23
                                      + C+ Cg C+ +CP+g+
  gi|330508757|ref|YP_004385185.1| 63 NTCTTCGLCTENCPAGI 79
                                      78************985 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.8
                            Fer4_6  11 gCgdCvr 17 
                                       gC  C++
  gi|330508757|ref|YP_004385185.1| 208 GCAGCYT 214
                                       6777765 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7   0.00047      0.56      39      52 ..      12      25 ..       2      30 .. 0.78
   2 ?   12.0   0.6   0.00015      0.18      39      53 ..      63      77 ..      47      80 .. 0.86
   3 ?   -0.8   0.0       1.5   1.8e+03      42      48 ..     207     213 ..     185     217 .. 0.62
   4 ?   -2.8   0.1       5.9   7.1e+03      43      48 ..     325     330 ..     320     332 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
                           Fer4_21 39 deCvGCnlCssvCP 52
                                      + Cv C  C +vCP
  gi|330508757|ref|YP_004385185.1| 12 NLCVRCGTCRTVCP 25
                                      46888888888888 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00015
                           Fer4_21 39 deCvGCnlCssvCPv 53
                                      ++C+ C lC++ CP 
  gi|330508757|ref|YP_004385185.1| 63 NTCTTCGLCTENCPA 77
                                      68***********94 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.5
                           Fer4_21  42 vGCnlCs 48 
                                       +GC+ C+
  gi|330508757|ref|YP_004385185.1| 207 TGCAGCY 213
                                       5555554 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 5.9
                           Fer4_21  43 GCnlCs 48 
                                        C lC+
  gi|330508757|ref|YP_004385185.1| 325 SCPLCI 330
                                       455554 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   0.00051      0.61       6      21 ..      14      29 ..      12      38 .. 0.88
   2 ?    6.8   3.2    0.0081       9.7       4      17 ..      63      76 ..      62      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00051
                           Fer4_13  6 CiacgaCvelaPdvFe 21
                                      C+ cg+C+ ++P + e
  gi|330508757|ref|YP_004385185.1| 14 CVRCGTCRTVCPAFLE 29
                                      ************9876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0081
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      +tC+ cg+C e +P
  gi|330508757|ref|YP_004385185.1| 63 NTCTTCGLCTENCP 76
                                      69************ PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.053        63       7      23 ..      13      29 ..      11      53 .. 0.87
   2 ?   10.4   0.1   0.00072      0.86       6      30 ..      63      93 ..      62     111 .. 0.78
   3 ?   -1.9   0.1       4.9   5.8e+03      49      59 ..     280     290 ..     278     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.053
                           Fer4_15  7 aCigcglCvaeapevfe 23
                                      +C  cg C +++p + e
  gi|330508757|ref|YP_004385185.1| 13 LCVRCGTCRTVCPAFLE 29
                                      7************8766 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00072
                           Fer4_15  6 daCigcglCvaea......pevfeldedgla 30
                                      ++C+ cglC +++      pe++e + + la
  gi|330508757|ref|YP_004385185.1| 63 NTCTTCGLCTENCpagispPEIIERARRMLA 93
                                      58***********777777777777766666 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.9
                           Fer4_15  49 eeaaqeAaraC 59 
                                       ++a + Aar+C
  gi|330508757|ref|YP_004385185.1| 280 MKASRNAARCC 290
                                       56778899999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2498.05
//
Query:       gi|330508758|ref|YP_004385186.1|  [L=164]
Description: hypothetical protein MCON_3045 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-17   63.2   0.0    4.1e-17   62.7   0.0    1.3  1  HIT       HIT domain
    9.9e-09   35.7   0.0    1.5e-08   35.1   0.0    1.3  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    1.7e-05   24.7   0.0    2.3e-05   24.2   0.0    1.3  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 !   62.7   0.0   6.9e-21   4.1e-17       5      97 ..      22     109 ..      18     110 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 6.9e-21
                                       -CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGG CS
                               HIT   5 pstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngaha 81 
                                       p+  +yed+l+la+ld++p ++gh+Lvipk+h++ +h+l+++e a l++++k va+++   ++ ++++++       
  gi|330508758|ref|YP_004385186.1|  22 PCYRIYEDELSLAILDVNPFSKGHCLVIPKRHVPWWHELSDDENASLFKVAKVVAEKMMIALEPDFVCMYA-----R 93 
                                       7788********************************************************99988888887.....8 PP

                                       T-SSSS-EEEEEEC-T CS
                               HIT  82 gqsvahlHiHviprre 97 
                                       g  ++h Hi ++p+++
  gi|330508758|ref|YP_004385186.1|  94 GRRIPHTHIFLVPTYQ 109
                                       99*******9999886 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   2.5e-12   1.5e-08       2      85 ..      11      91 ..      10     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.5e-12
                                      -HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEE CS
                            DcpS_C  2 wvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdae 80
                                      ++f++++ g  p   +yede  +++ D++p +k h+lvipkr+++  ++L++++     +++++ak v+e+++++++++
  gi|330508758|ref|YP_004385186.1| 11 CIFCQIVAGDLPCYRIYEDELSLAILDVNPFSKGHCLVIPKRHVPWWHELSDDENA---SLFKVAKVVAEKMMIALEPD 86
                                      9*************************************************877665...44666666666666666666 PP

                                      EE--S CS
                            DcpS_C 81 elrvg 85
                                      ++ ++
  gi|330508758|ref|YP_004385186.1| 87 FVCMY 91
                                      55555 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 !   24.2   0.0   3.8e-09   2.3e-05      39     109 ..      35     107 ..       5     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.8e-09
                                       ---.S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHH.HHHHHTT--EEEEEE-SSS-----EEEEE- CS
                          CwfJ_C_1  39 lpk.gpLssgHvliipieHisallsldeevldeirkfrkalv.kmykkqdkdavvfEissersvHlaiqvipv 109
                                       +   +p s+gH+l+ip  H++   +l++++  ++ k  k ++ km  + + d v      +r +H++i ++p 
  gi|330508758|ref|YP_004385186.1|  35 ILDvNPFSKGHCLVIPKRHVPWWHELSDDENASLFKVAKVVAeKMMIALEPDFVCMYARGRRIPHTHIFLVPT 107
                                       4444788*****************************999997369********9999999********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1247.22
//
Query:       gi|330508759|ref|YP_004385187.1|  [L=454]
Description: FAD linked oxidase [Methanosaeta concilii GP6]
Scores for complete 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-58  196.6   0.0    6.7e-58  196.3   0.0    1.1  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    5.4e-44  149.3   0.0      1e-43  148.4   0.0    1.5  1  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.3   0.0   7.4e-62   6.7e-58       1     249 [.     209     451 ..     209     452 .. 0.92

  Alignments for each domain:
  == domain 1  score: 196.3 bits;  conditional E-value: 7.4e-62
                                       --SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHH CS
                     FAD-oxidase_C   1 lpearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeae 77 
                                       lp++r++++++f+s eaa +av ++ ++gi p+a+e++d+++l++ + ++++     ++ + ++l+e++g++ +   
  gi|330508759|ref|YP_004385187.1| 209 LPKERRLVFASFESAEAAGQAVIAVFSQGITPSACEILDRTTLKVLRLVDPK--LALPDDGDVILFEVDGSR-DSTA 282
                                       599*************************************************..566666667889******.6666 PP

                                       HHHHHHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHH CS
                     FAD-oxidase_C  78 eelealveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalld 154
                                       e++e ++e+ ++  +++      + +e+e++w+aR+ + + ++++  k+  +++ eD+ vP++++++l+++++++ +
  gi|330508759|ref|YP_004385187.1| 283 EAAE-QIEKVCRPMAITI--RQASGREMEPIWAARRLVGAAISRLDPKKTRIYMGEDVGVPIKQIPALIKRVQQITA 356
                                       6666.6777777666664..345778889***********999999999999************************* PP

                                       HHHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THHHH CS
                     FAD-oxidase_C 155 kyglevvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglal 231
                                       + g+ ++ +gH+gdgnlh+ + +d++d+++++r+++++d++ ++a++lgG++s EHG+Gl++++y+ +++g+e l++
  gi|330508759|ref|YP_004385187.1| 357 SVGIPAMKYGHIGDGNLHVALFIDVNDPDQWDRLRTAADRIHRAALSLGGTVSSEHGIGLARAEYMAEQVGKESLNV 433
                                       ***************************************************************************** PP

                                       HHHHHHHH-TT--BSTT- CS
                     FAD-oxidase_C 232 mrriKaalDPkgiLNPgk 249
                                       mr+iK+ lDP+giLNPgk
  gi|330508759|ref|YP_004385187.1| 434 MRAIKKSLDPRGILNPGK 451
                                       *****************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 !  148.4   0.0   1.1e-47     1e-43       1     139 []      34     173 ..      34     173 .. 0.98

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 1.1e-47
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgd 76 
                                       p+ vvrp+++ ev++++ l+ne+++pv++rG+Gs+l+g+a   +ggvvld+s ++rile+d e+ ++ ve+Gv+ ++
  gi|330508759|ref|YP_004385187.1|  34 PDFVVRPANTGEVSRIMMLCNERDVPVVARGAGSGLAGGASpVSGGVVLDMSGMDRILEMDLENLQVIVEPGVVAEK 110
                                       899**********************************777669********99************************ PP

                                       HHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEEE CS
                     FAD_binding_4  77 lvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrls 139
                                       l++al+++g++++++pgs + +t+GG+i+ n++G++s kyG++r++vl levvladG+v++++
  gi|330508759|ref|YP_004385187.1| 111 LNWALEPHGFFFPPDPGSSSFCTIGGMISYNSSGMRSVKYGTTRSYVLDLEVVLADGRVIHTG 173
                                       ************************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2950.42
//
Query:       gi|330508760|ref|YP_004385188.1|  [L=519]
Description: cytochrome c biogenesis transmembrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-19   70.5  16.6    1.1e-18   67.9  16.6    2.2  1  DsbD          Cytochrome C biogenesis protein transmembrane r
    8.9e-09   35.6  21.6    0.00017   21.6   4.7    2.8  2  DsbD_2        Cytochrome C biogenesis protein transmembrane r
    1.8e-05   24.6   0.0    3.7e-05   23.6   0.0    1.5  1  AhpC-TSA      AhpC/TSA family
     0.0046   16.7   0.0     0.0079   15.9   0.0    1.3  1  Redoxin       Redoxin
  ------ inclusion threshold ------
        2.4    7.8   5.9       0.33   10.6   0.5    2.2  2  CPP1-like     Protein CHAPERONE-LIKE PROTEIN OF POR1-like
        9.1    5.8   9.0       0.73    9.3   0.6    2.7  3  E1-E2_ATPase  E1-E2 ATPase


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 !   67.9  16.6   3.7e-22   1.1e-18       2     211 ..     258     509 ..     257     511 .. 0.77

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 3.7e-22
                              DsbD   2 flaGllsflsPCilpliPaylsyisgvsved..vktekkkv.kvllkallFvlGlslvfvslglsaaflgqllkdvk 75 
                                       fl G+ ++l+PC ++l+ a +sy+ +v  +d   +++++   + ++  + F lG+++vf  lgl ++++g  ++d+ 
  gi|330508760|ref|YP_004385188.1| 258 FLLGIFTSLAPCSIALMIAVFSYVMTVRRKDeyLRASASTSrEGFMIGVAFTLGMAVVFFVLGLFISQIGVFFRDS- 333
                                       999************************99983334444444689*****************************886. PP

                              DsbD  76 evirrvaglivillGlhflgvfk...........ievleklkll................................. 108
                                       ++   +ag i+++lG+     +            +                                          
  gi|330508760|ref|YP_004385188.1| 334 KIFDLLAGSIMVMLGIGSFKPLGeiiepvtsrmrF--------Hqagvdgtdepsdgpgsaslaepmeeeksllqka 402
                                       688999*********97665444554455333330........1445677777777777777777777777778777 PP

                              DsbD 109 ....lkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaaske.slakgallllvyvlGlaipfllvgllle 180
                                           l  +      ++ga+ lG+ Falgw+PC+  ++  vl++ as++   + g ++l+++ +G ++p++ ++ ++ 
  gi|330508760|ref|YP_004385188.1| 403 vefsL--NLFRYSAFIGAFTLGIFFALGWAPCALSMVMPVLIWLASQDvAPLVGGTMLFFFGIGHGVPIIPITTFSR 477
                                       66432..333334479****************98888888877666661568999****************999999 PP

                              DsbD 181 llkkkl.kslkkyskaveiaggvllvllGvll 211
                                       ++  ++ ++  +  ++ +++ g+l++l+G+++
  gi|330508760|ref|YP_004385188.1| 478 MVGGRIgEKYISVGEWTSKIFGLLVILVGLVY 509
                                       88754424455566788888999999999987 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   8.9   5.5e-07    0.0016     103     198 ..     238     349 ..     223     350 .. 0.71
   2 !   21.6   4.7   5.6e-08   0.00017     101     197 ..     396     506 ..     385     508 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.5e-07
                            DsbD_2 103 llsrllkklakkl.kslasalllGllnGllpCglvysalllalas.............gsaleGalvmlaFgLGTlp 165
                                        l++++++  ++   + ++++llG++++l+pC + +++++++ ++             +   eG ++ +aF LG  +
  gi|330508760|ref|YP_004385188.1| 238 ALWTRMENEVSRKdVTAFGMFLLGIFTSLAPCSIALMIAVFSYVMtvrrkdeylrasaSTSREGFMIGVAFTLGMAV 314
                                       344455444433358999**************7744443333222122333333211144458************** PP

                            DsbD_2 166 alllfglllgllskklr.kkllr.lagvllillgl 198
                                       +++++gl++++++  +r  k++  lag ++++lg+
  gi|330508760|ref|YP_004385188.1| 315 VFFVLGLFISQIGVFFRdSKIFDlLAGSIMVMLGI 349
                                       **************999778888789999999997 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 5.6e-08
                            DsbD_2 101 gkllsrllkklakkl..kslasalllGlln..GllpCgl..vysalllalasg.saleGalvmlaFgLGTlpalllf 170
                                       ++ll+++++  ++ +    + +a++lG+++  G++pC+l  v+++l++ ++++  +l G+ ++++Fg+G  ++++ +
  gi|330508760|ref|YP_004385188.1| 396 KSLLQKAVEFSLNLFrySAFIGAFTLGIFFalGWAPCALsmVMPVLIWLASQDvAPLVGGTMLFFFGIGHGVPIIPI 472
                                       4555555555555445578899*****8753399***776588888888876526899************9999999 PP

                            DsbD_2 171 glllgllskklr......kkllr.lagvllillg 197
                                       ++++++++ ++        +++  + g+l+il+g
  gi|330508760|ref|YP_004385188.1| 473 TTFSRMVGGRIGekyisvGEWTSkIFGLLVILVG 506
                                       9999999887773333443333326666666666 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.2e-08   3.7e-05       3     121 ..      48     178 ..      47     180 .. 0.64

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.2e-08
                                       SB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCT...TEEEEEEESSSCH..... CS
                          AhpC-TSA   3 dkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefker...gvevigvsvdspe..... 71 
                                        +apdf ++ +d+++++lsd+ g+pvvl +++  + p C +  ++l+ ++ee++++   + +v +v+ +  +     
  gi|330508760|ref|YP_004385188.1|  48 AQAPDFFATSWDQRSFNLSDFMGSPVVLHITNI-ENPLCIECEKSLSGQVEELAALkalDTNVQIVTLNLRKnpysi 123
                                       59****************************988.8788888888888877777654222445555544444433455 PP

                                       ...HHHHHHHH-H.SSEEEE-.TTSHHHHHTT-EETT.TTECSCEEEEE-TTSBE CS
                          AhpC-TSA  72 ...shkkfiekeslnfpllsD.eegkvakaygvlkee.kglalratfvidkegki 121
                                          +++++  + ++++p + D     +  +y  +++   g   ++ ++id+eg i
  gi|330508760|ref|YP_004385188.1| 124 dgrELAQTWWEVNITWPWIEDlDPYPIGSKYLDYWTVrGGSSNPTIVLIDREGRI 178
                                       5554444444444788887775223343343333232266677777777777766 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.7e-06    0.0079       4     127 ..      48     178 ..      45     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-06
                                       SBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HH...HHHTHH.HHHTHHHHHH.CSTTTEEEEEESSSHH CS
                           Redoxin   4 dkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPt...Csaehp.yleklaellk.ekgvdvvavvadndaf 75 
                                       ++aPdf    +  d+ s++ls+f g +vv+ +      P    C +++  ++e+la+l++ + +v++v ++  ++++
  gi|330508760|ref|YP_004385188.1|  48 AQAPDFFA--TSWDQRSFNLSDFMGSPVVLHITNI-ENPLcieCEKSLSgQVEELAALKAlDTNVQIVTLNLRKNPY 121
                                       56899986..569**************99977766.7777555788888******7764326789999999999999 PP

                                       ......HHHHHHHTT-TSEEEE-.TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEE CS
                           Redoxin  76 ......vkefwgkeglkfpvlsD.gsaaftkalGlrleedaseglrtpryavidedgkv 127
                                               + w + ++++p + D     + +++  ++++  ++    p+ ++id++g++
  gi|330508760|ref|YP_004385188.1| 122 sidgreLAQTWWEVNITWPWIEDlDPYPIGSKYLDYWTVRGGS--SNPTIVLIDREGRI 178
                                       9999886666667777999999864567777777788877666..79999999999998 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 ?   10.6   0.5   0.00011      0.33      92     166 ..     243     316 ..     214     351 .. 0.79
   2 ?   -1.2   0.6      0.45   1.3e+03     141     194 ..     399     446 ..     392     447 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                         CPP1-like  92 ssedlliraavflvlavltlvapaesvpalllalglgasiyflnrKekklgravlltlvgLvvGlllGsllasll 166
                                        ++++ ++ ++  ++ +l ++++ +   +++l++++++ ++ ++rK + l  ++ ++  g+++G+++  ++a+++
  gi|330508760|ref|YP_004385188.1| 243 MENEVSRKDVTAFGMFLLGIFTSLAP-CSIALMIAVFSYVMTVRRKDEYLRASASTSREGFMIGVAFTLGMAVVF 316
                                       56778888888999999999999999.9********************999999999999999987766555554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.45
                         CPP1-like 141 lgravlltlvgLvvGlllGsllasllqvdvalsglsseellvslvtlvllwlvs 194
                                       l +av ++l ++  ++++G++  +++     +++ +++   +s+v+ vl+wl+s
  gi|330508760|ref|YP_004385188.1| 399 LQKAVEFSLNLFRYSAFIGAFTLGIF-----FALGWAPC-ALSMVMPVLIWLAS 446
                                       56788888888888888888888876.....44458888.88999999999987 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.3      0.16   4.7e+02     149     170 ..     257     278 ..     232     289 .. 0.63
   2 ?   -2.2   0.1      0.86   2.6e+03     127     141 ..     310     324 ..     291     348 .. 0.51
   3 ?    9.3   0.6   0.00024      0.73     135     178 ..     406     449 ..     398     451 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHS-TTHHHHHHHH CS
                      E1-E2_ATPase 149 lralallvaaiPcaLplavpla 170
                                       ++ l+++++  Pc ++l++ + 
  gi|330508760|ref|YP_004385188.1| 257 MFLLGIFTSLAPCSIALMIAVF 278
                                       4567777777777777776654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.86
                                       HHHHHHHHHS-STTT CS
                      E1-E2_ATPase 127 lliallvflialllg 141
                                       l +a+++f++ l++ 
  gi|330508760|ref|YP_004385188.1| 310 LGMAVVFFVLGLFIS 324
                                       233333333333322 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00024
                                       HS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 135 lialllgkslaeallralallvaaiPcaLplavplalalgarrl 178
                                        ++l++    + a++ ++ ++++  PcaL +++p+ + l+ +  
  gi|330508760|ref|YP_004385188.1| 406 SLNLFRYSAFIGAFTLGIFFALGWAPCALSMVMPVLIWLASQDV 449
                                       5666777777799999**********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3533.79
//
Query:       gi|330508761|ref|YP_004385189.1|  [L=190]
Description: hypothetical protein MCON_3048 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   12.1   0.0       0.87    9.8   0.0    1.9  2  Thioredoxin_7  Thioredoxin-like


Domain annotation for each model (and alignments):
>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   4.9e-05      0.87      16      34 ..      73      91 ..      69      94 .. 0.90
   2 ?   -0.6   0.0     0.084   1.5e+03      72      81 ..     135     144 ..     114     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 4.9e-05
                                      HT--EEEEE--TT-HHHHH CS
                     Thioredoxin_7 16 rgkpvlvffgaswcftCqa 34
                                      + +p+l+ ++ ++c +C++
  gi|330508761|ref|YP_004385189.1| 73 EDRPLLILIHQNNCLPCVT 91
                                      789**************86 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.084
                                       ---SSEEEEE CS
                     Thioredoxin_7  72 eqgvPvvafl 81 
                                       +q+vP+ +fl
  gi|330508761|ref|YP_004385189.1| 135 KQYVPTTIFL 144
                                       499**99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1277.41
//
Query:       gi|330508762|ref|YP_004385190.1|  [L=107]
Description: hypothetical protein MCON_3050 [Methanosaeta concilii GP6]
Scores for complete 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   50.0   0.1    3.1e-13   49.7   0.1    1.2  1  DUF2582   Winged helix-turn-helix domain (DUF2582)


Domain annotation for each model (and alignments):
>> DUF2582  Winged helix-turn-helix domain (DUF2582)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.1   1.7e-17   3.1e-13       6      61 ..      46     101 ..      37     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.7e-17
                                       HHHHHHHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEETTEE CS
                           DUF2582   6 iGenAGkvwhlLnengeislkelkrktglsdkelalAiGWLaREdKivierkekel 61 
                                        G nAG +w lL+ +g + + el+++  l  +++  A+GWL RE+Ki +++k +  
  gi|330508762|ref|YP_004385190.1|  46 FGINAGIIWDLLSLKGPMPARELAKSAALRIDDVHGALGWLGREGKINVNKKGRSR 101
                                       69************************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 823.06
//
Query:       gi|330508763|ref|YP_004385191.1|  [L=197]
Description: hypothetical protein MCON_3052 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-14   54.0  14.8    1.5e-14   53.7  14.8    1.1  1  AA_permease_2  Amino acid permease
    3.2e-09   35.9  12.5    4.1e-09   35.5  12.5    1.2  1  AA_permease    Amino acid permease
  ------ inclusion threshold ------
       0.15   12.2   0.4       0.15   12.2   0.4    3.1  4  AA_permease_C  C-terminus of AA_permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7  14.8   2.5e-18   1.5e-14     270     401 ..      28     162 ..      18     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2.5e-18
                     AA_permease_2 270 kvvaiivvilialsllgaintavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassa 345
                                       + +++i++i++ ++    ++  +++ssr+++ +a  g lP  +a+v+ ++++p+ a+il++i+++ ++  fl    +
  gi|330508763|ref|YP_004385191.1|  28 PNASAIISIMALFATTNTVLLMLLASSRIIYGMASSGSLPPILASVHpRTHAPWIATILSMIIAMSFV--FL----E 98 
                                       55788999999999999**********************************************96654..53....6 PP

                     AA_permease_2 346 aynfllsvsslgliisyllliigalilrkkrphlkr.......pgk.ilvaiigalfllfllva 401
                                       ++ f+++v ++ +++ ++++ + ++ lr+k+p+  r       +gk +++  +g+lf+l++l+ 
  gi|330508763|ref|YP_004385191.1|  99 DIAFVANVNNFTVFVTFIVINAVLISLRYKKPQIARpfrvpisWGKlAVLPVLGILFNLLMLIQ 162
                                       89********************************995556665555446777788888888865 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5  12.5   6.9e-13   4.1e-09     275     428 ..      17     160 ..       9     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 6.9e-13
                       AA_permease 275 pfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisll 350
                                       pf  + +++  + ++ +i ++ l a++++++ +l ++sR++y +a +g +P   ++++ + + P+ a +lsmii++ 
  gi|330508763|ref|YP_004385191.1|  17 PFSDIARYALGPNASAIISIMALFATTNTVLLMLLASSRIIYGMASSGSLPpILASVHPRTHAPWIATILSMIIAMS 93 
                                       6777777888888999***********************************8999999******************* PP

                       AA_permease 351 alllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiill 427
                                       +++l+ +        +f+ +++ +  ++++++i++ ++ +R +   +   ++ +++ +  + l v  vl +l  +l+
  gi|330508763|ref|YP_004385191.1|  94 FVFLEDI--------AFVANVNNFTVFVTFIVINAVLISLRYK---KPQIARPFRVPISWGKLAVLPVLGILFNLLM 159
                                       **55554........55699999************99988877...3444455666666666655555555554444 PP

                       AA_permease 428 i 428
                                       +
  gi|330508763|ref|YP_004385191.1| 160 L 160
                                       4 PP

>> AA_permease_C  C-terminus of AA_permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3      0.74   4.4e+03      16      26 ..      43      53 ..      34      60 .. 0.71
   2 ?   -0.8   0.5      0.28   1.7e+03      29      41 ..      81      93 ..      77     100 .. 0.75
   3 ?   -1.5   0.2      0.45   2.7e+03      28      38 ..     111     121 ..      93     127 .. 0.62
   4 ?   12.2   0.4   2.4e-05      0.15       8      26 ..     147     165 ..     136     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.74
                     AA_permease_C 16 vNiyLmlqLds 26
                                      +N+ L++ L s
  gi|330508763|ref|YP_004385191.1| 43 TNTVLLMLLAS 53
                                      57778777765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.28
                     AA_permease_C 29 wirfgvwmligll 41
                                      wi  +  m+i + 
  gi|330508763|ref|YP_004385191.1| 81 WIATILSMIIAMS 93
                                      9999999999654 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.45
                     AA_permease_C  28 twirfgvwmli 38 
                                        ++ f+v  ++
  gi|330508763|ref|YP_004385191.1| 111 VFVTFIVINAV 121
                                       34555555444 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 2.4e-05
                     AA_permease_C   8 flPalsIlvNiyLmlqLds 26 
                                       +lP+l+Il+N+ +++qL++
  gi|330508763|ref|YP_004385191.1| 147 VLPVLGILFNLLMLIQLET 165
                                       79***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1499.62
//
Query:       gi|330508764|ref|YP_004385192.1|  [L=165]
Description: hypothetical protein MCON_3053 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0045   16.3   1.1     0.0045   16.3   1.1    1.7  2  Trypan_glycop  Trypanosome variant surface glycoprotein (A-ty


Domain annotation for each model (and alignments):
>> Trypan_glycop  Trypanosome variant surface glycoprotein (A-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2     0.039   6.9e+02     265     284 ..      19      38 ..       7      55 .. 0.53
   2 !   16.3   1.1   2.5e-07    0.0045     236     290 ..      76     130 ..      48     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.039
                     Trypan_glycop 265 alkavqeklqekvlndtaal 284
                                       a+ka+q++++ek++ + ++l
  gi|330508764|ref|YP_004385192.1|  19 AIKAAQKSESEKKALNIEKL 38 
                                       34444444444444333333 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.5e-07
                     Trypan_glycop 236 qelnltlaakeianstaegahalwkdafkalkavqeklqekvlndtaallkesel 290
                                       q ++ltl  + +++ ta+++ a+ kd +ka+ka+qe ++ + + +++ +lk++ +
  gi|330508764|ref|YP_004385192.1|  76 QTIQLTLVPARSTTRTATRTEAFEKDLVKAIKAIQEGIKNASEGEPKFTLKDASV 130
                                       555599***********************************99999999998544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1119  (0.0624129); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1286.24
//
Query:       gi|330508765|ref|YP_004385193.1|  [L=376]
Description: hypothetical protein MCON_3054 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-17   63.8   0.0    2.9e-17   63.0   0.0    1.5  1  CHAT           CHAT domain
  ------ inclusion threshold ------
      0.039   13.2   0.0      0.061   12.5   0.0    1.3  1  Peptidase_C25  Peptidase family C25


Domain annotation for each model (and alignments):
>> CHAT  CHAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.0   3.2e-21   2.9e-17     131     288 ..     220     366 ..     100     368 .. 0.79

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 3.2e-21
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx RF
                              CHAT 131 tesalksals.rryrvvHfatHgvfnanpplqsglvlsaenseedglLtaeeilelnldg...aelVvLsACqtglg 203
                                       +     + l+ +++++ Hfa+Hg f+++ p++s ++l      ++++L+ ++i   ++ +     l++++AC+tg+ 
  gi|330508765|ref|YP_004385193.1| 220 EVL---EWLEhQNFSIMHFACHGEFDEKMPSRSPIIL------SGQPLRPDDINT-KFGEgrqRPLIFINACHTGRT 286
                                       433...444559*************************......589********9.999889999**********87 PP

                                       xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CHAT 204 evi...dgegvlgLaralllaGarsviaslwpVddeatalLmkrfyqnlla.glskaeALreaqlkllsgkrdqkps 276
                                         +    g   +++++ ++   + + i+  w+Vdd+ ++l++k fy++ll+ + ++a+A r+a+ ++++ k +    
  gi|330508765|ref|YP_004385193.1| 287 GSSltwLGGWPVCFVNIAH---VGAFIGAMWEVDDQLAVLFAKSFYTALLRdKFPIAQAFRHAREEIRRAKPY---- 356
                                       7766777888888887655...789**************************999****************986.... PP

                                       xxxxxxxxxxxx RF
                              CHAT 277 hapyyWaaFili 288
                                          + W a++l+
  gi|330508765|ref|YP_004385193.1| 357 --NSSWLAYVLY 366
                                       ..4678888876 PP

>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.8e-06     0.061     271     377 ..     272     372 ..     231     373 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.8e-06
                                       --EEEEEESSSTT-TTSSS-..-HHHHHHHSTTSSEEEEEEESS---SS--SHHHHHHHHHHHHHHH...T-S-SS- CS
                     Peptidase_C25 271 klpiaitaaCltgafdeetkr.sfgeklvlnangGavayigatrlgysgvndrlsraffealfadaartlGeallla 346
                                       + p+++ +aC+tg+  ++  +   g  +   + +   a+iga +++ ++    + ++f+ al++d+  ++++a+++a
  gi|330508765|ref|YP_004385193.1| 272 QRPLIFINACHTGRTGSS-LTwLGGWPVCFVNIAHVGAFIGAMWEVDDQLAVLFAKSFYTALLRDKF-PIAQAFRHA 346
                                       56999999******9554.4453333333455555779*************************9999.6******** PP

                                       HHHHHHH..............EEEEE-TT-- CS
                     Peptidase_C25 347 knelletglaqsiskgmnkrtfnllGDPalr 377
                                       + e   + + ++     +   ++l+ DP+ +
  gi|330508765|ref|YP_004385193.1| 347 REEIRRA-KPYN----SSWLAYVLYADPEAM 372
                                       *988853.3333....24466*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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 0.29s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2825.48
//
Query:       gi|330508766|ref|YP_004385194.1|  [L=801]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-252  816.0  77.6    9.8e-26   89.9   0.4   13.7 15  TPR_12           Tetratricopeptide repeat
   6.6e-216  693.4  36.7    4.1e-16   58.3   0.1   16.1 16  TPR_10           Tetratricopeptide repeat
   3.9e-107  346.1  21.8      4e-07   29.6   0.1   15.5 15  TPR_1            Tetratricopeptide repeat
    2.6e-96  308.8  34.7    6.9e-06   25.7   0.0   16.0 16  TPR_7            Tetratricopeptide repeat
    2.7e-82  264.2  30.5    5.3e-05   23.1   0.1   15.6 15  TPR_8            Tetratricopeptide repeat
    2.4e-79  255.2  32.8    0.00012   21.9   0.1   16.0 16  TPR_2            Tetratricopeptide repeat
      8e-59  191.9  53.5     0.0022   18.2   0.0   15.8 15  TPR_17           Tetratricopeptide repeat
    2.1e-52  175.5  28.4    0.00064   20.2   0.0   14.6 15  TPR_19           Tetratricopeptide repeat
    2.5e-52  175.2  42.8    2.6e-07   31.2   0.9   12.4 14  TPR_16           Tetratricopeptide repeat
    2.1e-34  119.4   0.0      4e-10   39.6   0.0    5.8  5  TPR_MalT         MalT-like TPR region
      2e-33  113.9   0.0       0.18   11.8   0.0   15.5 16  TPR_3            Tetratricopeptide repeat
    1.9e-29   99.8  34.8        1.7    9.6   0.1   15.5 15  TPR_14           Tetratricopeptide repeat
    7.1e-23   80.5   6.8       0.18   12.0   0.0   12.8 13  DUF630           Protein of unknown function (DUF630)
    8.2e-21   72.4   0.0         24    5.9   0.0   13.7 14  TPR_4            Tetratricopeptide repeat
    1.9e-20   73.5   0.0    9.6e-05   21.9   0.0    4.9  5  SNAP             Soluble NSF attachment protein, SNAP
    4.5e-17   61.5  31.3         11    6.9   0.0   15.7 15  TPR_6            Tetratricopeptide repeat
    1.3e-15   57.3  12.3       0.36   10.9   0.0   10.6  9  ANAPC5           Anaphase-promoting complex subunit 5
    3.1e-14   53.2   7.6      0.058   13.6   0.2   10.1 10  TPR_5            Tetratrico peptide repeat
    1.5e-12   47.5  21.0      0.078   13.2   0.0   10.2 11  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    1.7e-11   44.6   0.0         96    3.7   0.0   12.3 14  DUF4404          Domain of unknown function (DUF4404)
    1.2e-10   41.5   0.0         23    5.0   0.0   10.1 12  TetR_C_32        Tetracyclin repressor-like, C-terminal domai
    1.9e-09   37.0  50.2       0.11   12.2   0.4   16.1 19  TPR_11           TPR repeat
    4.2e-07   29.9  11.1         14    5.8   0.0   10.2 12  MIT              MIT (microtubule interacting and transport) 
    8.8e-07   29.3   0.4         14    6.1   0.0    7.5 11  RPN6_N           26S proteasome regulatory subunit RPN6 N-ter
    1.3e-06   28.4   1.9       0.28   11.0   0.1    5.3  6  Clathrin         Region in Clathrin and VPS
    6.9e-06   26.2  13.5         17    5.8   0.0   10.5 12  Ribosomal_L6e_N  Ribosomal protein L6, N-terminal domain
      5e-05   22.5   1.4         58    2.6   0.0    8.0 11  Asparaginase_II  L-asparaginase II
    5.1e-05   22.7  43.3        2.8    7.5   0.0   14.0 15  DUF1897          Domain of unknown function (DUF1897)
     0.0012   18.9   0.0         58    3.8   0.0    6.7  8  DUF5532          Family of unknown function (DUF5532)
     0.0033   17.9  28.4        2.9    8.3   0.7   10.9  9  BTAD             Bacterial transcriptional activator domain
  ------ inclusion threshold ------
      0.011   15.5   5.1         33    4.1   0.0    7.3  8  RPN7             26S proteasome subunit RPN7
      0.027   14.7  26.0         36    4.7   0.1   10.6  9  FCH              Fes/CIP4, and EFC/F-BAR homology domain
      0.063   13.4   2.8    3.2e+02    1.5   0.0    5.6  5  Vault_4          Major Vault Protein repeat domain
      0.083   12.2   0.0        7.6    5.7   0.0    3.7  4  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.21   11.6   2.0         62    3.6   0.0    5.0  6  DUF2199          Uncharacterized protein conserved in bacteri
       0.67   10.2   5.1         61    4.0   0.0    6.0  7  Arg_decarb_HB    Arginine decarboxylase helical bundle domain
       0.77    9.2   4.2         36    3.8   0.1    4.9  6  14-3-3           14-3-3 protein
        6.2    6.3  21.1         31    4.0   0.0    8.0 10  Foie-gras_1      Foie gras liver health family 1


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.3   3.3e-17   1.6e-14      11      77 .]      19      85 ..      11      85 .. 0.92
   2 !   74.6   0.1   1.2e-23   5.7e-21       8      74 ..      58     124 ..      58     127 .. 0.98
   3 !   42.8   0.1     1e-13   4.9e-11      30      77 .]     122     169 ..     120     169 .. 0.95
   4 !   76.2   1.7   3.9e-24   1.8e-21       3      74 ..     137     208 ..     136     208 .. 0.97
   5 !   89.9   0.4   2.1e-28   9.8e-26       3      77 .]     179     253 ..     178     253 .. 0.97
   6 !   43.4   0.2   6.4e-14     3e-11      25      73 ..     243     291 ..     243     293 .. 0.96
   7 !   76.5   1.5     3e-24   1.4e-21       3      77 .]     263     337 ..     261     337 .. 0.97
   8 !   44.0   0.1   4.2e-14     2e-11      28      77 .]     330     379 ..     330     379 .. 0.96
   9 !   44.0   0.1   4.2e-14     2e-11      26      74 ..     370     418 ..     370     419 .. 0.97
  10 !   81.9   0.4   6.4e-26     3e-23       2      77 .]     388     463 ..     387     463 .. 0.97
  11 !   58.3   0.0   1.5e-18   7.1e-16      16      77 .]     444     505 ..     444     505 .. 0.98
  12 !   71.9   0.9   8.3e-23   3.9e-20       4      77 .]     474     547 ..     473     547 .. 0.97
  13 !   80.4   0.5   1.9e-25   9.1e-23       3      77 .]     515     589 ..     515     589 .. 0.97
  14 !   61.5   0.2   1.5e-19   7.1e-17      16      77 .]     570     631 ..     570     631 .. 0.98
  15 !   82.1   0.5   5.3e-26   2.5e-23       2      77 .]     598     673 ..     597     673 .. 0.97

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 3.3e-17
                            TPR_12 11 avlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77
                                         r  g+y +A+++ e+ ++++ +++ G dhp++a++l+nL++lyr +gry +A+ l+++a +i++k
  gi|330508766|ref|YP_004385194.1| 19 IDFRNDGNYIQAIAFAEELRDLIwQKV-GYDHPDYAASLNNLAELYRSMGRYNDAEPLFRQAAEICRK 85
                                      556789*****************8998.9************************************996 PP

  == domain 2  score: 74.6 bits;  conditional E-value: 1.2e-23
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       nla+++r +gry +A+ l+++a ei+r++lG+dhp++at+l+nL+ +y+ +gry++A+ l+ ++++i
  gi|330508766|ref|YP_004385194.1|  58 NLAELYRSMGRYNDAEPLFRQAAEICRKSLGEDHPDYATSLNNLALVYYSMGRYDDAEPLFCQVTEI 124
                                       8***************************************************************998 PP

  == domain 3  score: 42.8 bits;  conditional E-value: 1e-13
                            TPR_12  30 leiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                        ei+ ++lG+dhp+ at l+nL++lyr  gry eA++l+++a++i++k
  gi|330508766|ref|YP_004385194.1| 122 TEIWGKSLGEDHPNCATGLNNLAELYRSIGRYSEAERLFRQATEIRRK 169
                                       589*99***************************************996 PP

  == domain 4  score: 76.2 bits;  conditional E-value: 3.9e-24
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       at lnnla+++r  gry eA++l+++a ei+r++lG+dhp++a++l+nL++lyr +gry eA+ l+++a++i
  gi|330508766|ref|YP_004385194.1| 137 ATGLNNLAELYRSIGRYSEAERLFRQATEIRRKSLGEDHPNYAASLNNLAILYRSMGRYNEAEPLFRKAIEI 208
                                       67799****************************************************************997 PP

  == domain 5  score: 89.9 bits;  conditional E-value: 2.1e-28
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       a++lnnla ++r +gry eA+ l++ka+ei+rr+lG+dhp++at+l+nL+ +y+ +gry eA+ l+++a++i++k
  gi|330508766|ref|YP_004385194.1| 179 AASLNNLAILYRSMGRYNEAEPLFRKAIEIWRRSLGEDHPNYATSLNNLALVYDSMGRYSEAEPLFRQATEIRRK 253
                                       67899*******************************************************************996 PP

  == domain 6  score: 43.4 bits;  conditional E-value: 6.4e-14
                            TPR_12  25 llekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       l+++a ei+r++lG+dhp+++++l+nL+ ly+ +gry +A+ l+++a++
  gi|330508766|ref|YP_004385194.1| 243 LFRQATEIRRKSLGEDHPDYSQSLNNLAGLYYSMGRYSDAEPLYRKAIE 291
                                       689********************************************98 PP

  == domain 7  score: 76.5 bits;  conditional E-value: 3e-24
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       +++lnnla +++ +gry +A+ l++ka+e + ++lG+dhp++a++l+nL++lyr +gry +A+ l+++a++i++k
  gi|330508766|ref|YP_004385194.1| 263 SQSLNNLAGLYYSMGRYSDAEPLYRKAIENWGKSLGEDHPAYAQSLNNLAELYRSMGRYSDAEPLYRKATEIRRK 337
                                       67899*******************************************************************996 PP

  == domain 8  score: 44.0 bits;  conditional E-value: 4.2e-14
                            TPR_12  28 kaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       ka ei+r++lG+dhp+++++l+nL+ +y+  gry +A+ l+++a++i +k
  gi|330508766|ref|YP_004385194.1| 330 KATEIRRKSLGEDHPDYSQSLNNLALMYYSIGRYSDAEPLFRQATEIQRK 379
                                       6889*******************************************986 PP

  == domain 9  score: 44.0 bits;  conditional E-value: 4.2e-14
                            TPR_12  26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +++a ei+r++lG+ hp++a++l+nL++lyr +gry +A+ l+++a++i
  gi|330508766|ref|YP_004385194.1| 370 FRQATEIQRKSLGEAHPDYAQSLNNLAELYRSMGRYSDAEPLFRQATEI 418
                                       68999******************************************98 PP

  == domain 10  score: 81.9 bits;  conditional E-value: 6.4e-26
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                        a++lnnla+++r +gry +A+ l+++a ei+r++lG+dhp++a++l+nL+ lyr +gry +A+ l+++a++i +k
  gi|330508766|ref|YP_004385194.1| 388 YAQSLNNLAELYRSMGRYSDAEPLFRQATEIWRKSLGEDHPEYAASLNNLAVLYRSMGRYSDAEPLFRQATEIWRK 463
                                       6899********************************************************************9885 PP

  == domain 11  score: 58.3 bits;  conditional E-value: 1.5e-18
                            TPR_12  16 lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       +gry +A+ l+++a ei+r++lG+dhp+ at l+nL++lyr  gry +A+ l+++a++i +k
  gi|330508766|ref|YP_004385194.1| 444 MGRYSDAEPLFRQATEIWRKSLGEDHPNCATGLNNLAELYRSVGRYSDAEPLFRQATEIWRK 505
                                       79********************************************************9885 PP

  == domain 12  score: 71.9 bits;  conditional E-value: 8.3e-23
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       t lnnla+++r  gry +A+ l+++a ei+r++lG+dhp++a++l+n ++lyr + ry +A++l+++a++i +k
  gi|330508766|ref|YP_004385194.1| 474 TGLNNLAELYRSVGRYSDAEPLFRQATEIWRKSLGEDHPDYAASLNNRAELYRSMSRYNDAESLFRQATEIWRK 547
                                       6799******************************************************************9885 PP

  == domain 13  score: 80.4 bits;  conditional E-value: 1.9e-25
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       a++lnn+a+++r + ry +A++l+++a ei+r++lG+dhp++at+l+nL+ +y+ +gry eA+ l+++a++i++k
  gi|330508766|ref|YP_004385194.1| 515 AASLNNRAELYRSMSRYNDAESLFRQATEIWRKSLGGDHPNYATSLNNLALVYDSMGRYSEAEPLFRQATEIRRK 589
                                       57899*******************************************************************996 PP

  == domain 14  score: 61.5 bits;  conditional E-value: 1.5e-19
                            TPR_12  16 lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       +gry eA+ l+++a ei+r++lG dhp++a++l+nL+ ly+ +gry +A+ l+++a++i +k
  gi|330508766|ref|YP_004385194.1| 570 MGRYSEAEPLFRQATEIRRKSLGRDHPDYAQSLNNLAGLYYSMGRYSDAEPLFRQATEIWRK 631
                                       79********************************************************9885 PP

  == domain 15  score: 82.1 bits;  conditional E-value: 5.3e-26
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                        a++lnnla +++ +gry +A+ l+++a ei+r++lG+dhp++a++l+nL+ lyr +gry +A+ l+++a++i++k
  gi|330508766|ref|YP_004385194.1| 598 YAQSLNNLAGLYYSMGRYSDAEPLFRQATEIWRKSLGEDHPDYAQSLNNLAVLYRSMGRYSDAEPLFRQATEIRRK 673
                                       6899*********************************************************************996 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.022        10      11      42 .]      20      51 ..      12      51 .. 0.83
   2 !   52.8   0.2   4.4e-17   2.1e-14       2      42 .]      53      93 ..      53      93 .. 0.99
   3 !   39.3   0.0     8e-13   3.8e-10       2      42 .]      95     135 ..      95     135 .. 0.98
   4 !   44.5   0.1   1.9e-14   8.8e-12       2      42 .]     137     177 ..     136     177 .. 0.95
   5 !   58.3   0.1   8.6e-19   4.1e-16       2      42 .]     179     219 ..     179     219 .. 0.98
   6 !   50.6   0.0   2.2e-16   1.1e-13       2      42 .]     221     261 ..     221     261 .. 0.99
   7 !   37.7   0.0   2.6e-12   1.2e-09       4      41 ..     265     302 ..     264     303 .. 0.97
   8 !   49.9   0.1   3.8e-16   1.8e-13       2      42 .]     305     345 ..     305     345 .. 0.98
   9 !   41.8   0.0   1.4e-13   6.4e-11       4      42 .]     349     387 ..     348     387 .. 0.98
  10 !   48.4   0.0   1.1e-15   5.3e-13       2      42 .]     389     429 ..     389     429 .. 0.98
  11 !   50.1   0.0   3.2e-16   1.5e-13       2      42 .]     431     471 ..     431     471 .. 0.98
  12 !   45.7   0.0   7.8e-15   3.7e-12       2      42 .]     473     513 ..     472     513 .. 0.96
  13 !   37.0   0.1   4.3e-12   2.1e-09       2      42 .]     515     555 ..     515     555 .. 0.98
  14 !   50.6   0.0   2.3e-16   1.1e-13       2      42 .]     557     597 ..     557     597 .. 0.99
  15 !   49.7   0.0   4.5e-16   2.1e-13       2      42 .]     599     639 ..     599     639 .. 0.98
  16 !   43.7   0.0   3.3e-14   1.5e-11       2      41 ..     641     680 ..     641     681 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.022
                            TPR_10 11 alrqrgrydeAealleealai.rrrllGpdHPd 42
                                        r+ g+y +A a++ee  ++ ++++ G dHPd
  gi|330508766|ref|YP_004385194.1| 20 DFRNDGNYIQAIAFAEELRDLiWQKV-GYDHPD 51
                                      56899****************66666.9****8 PP

  == domain 2  score: 52.8 bits;  conditional E-value: 4.4e-17
                            TPR_10  2 AsslnNLanalrqrgrydeAealleealairrrllGpdHPd 42
                                      A+slnNLa ++r++gry++Ae l+++a +i+r+ lG+dHPd
  gi|330508766|ref|YP_004385194.1| 53 AASLNNLAELYRSMGRYNDAEPLFRQAAEICRKSLGEDHPD 93
                                      89**************************************9 PP

  == domain 3  score: 39.3 bits;  conditional E-value: 8e-13
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllGpdHPd 42 
                                       A+slnNLa +++++gryd+Ae l+ ++ +i+ + lG+dHP+
  gi|330508766|ref|YP_004385194.1|  95 ATSLNNLALVYYSMGRYDDAEPLFCQVTEIWGKSLGEDHPN 135
                                       89**************************************5 PP

  == domain 4  score: 44.5 bits;  conditional E-value: 1.9e-14
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllGpdHPd 42 
                                       A+ lnNLa ++r+ gry eAe+l+++a +irr+ lG+dHP+
  gi|330508766|ref|YP_004385194.1| 137 ATGLNNLAELYRSIGRYSEAERLFRQATEIRRKSLGEDHPN 177
                                       5669************************************5 PP

  == domain 5  score: 58.3 bits;  conditional E-value: 8.6e-19
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllGpdHPd 42 
                                       A+slnNLa+++r++gry+eAe l+++a++i+rr lG+dHP+
  gi|330508766|ref|YP_004385194.1| 179 AASLNNLAILYRSMGRYNEAEPLFRKAIEIWRRSLGEDHPN 219
                                       89**************************************5 PP

  == domain 6  score: 50.6 bits;  conditional E-value: 2.2e-16
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllGpdHPd 42 
                                       A+slnNLa ++ ++gry eAe l+++a +irr+ lG+dHPd
  gi|330508766|ref|YP_004385194.1| 221 ATSLNNLALVYDSMGRYSEAEPLFRQATEIRRKSLGEDHPD 261
                                       89**************************************9 PP

  == domain 7  score: 37.7 bits;  conditional E-value: 2.6e-12
                            TPR_10   4 slnNLanalrqrgrydeAealleealairrrllGpdHP 41 
                                       slnNLa +++++gry +Ae l+++a++ + + lG+dHP
  gi|330508766|ref|YP_004385194.1| 265 SLNNLAGLYYSMGRYSDAEPLYRKAIENWGKSLGEDHP 302
                                       8************************************9 PP

  == domain 8  score: 49.9 bits;  conditional E-value: 3.8e-16
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllGpdHPd 42 
                                       A slnNLa ++r++gry +Ae l+++a +irr+ lG+dHPd
  gi|330508766|ref|YP_004385194.1| 305 AQSLNNLAELYRSMGRYSDAEPLYRKATEIRRKSLGEDHPD 345
                                       789*************************************9 PP

  == domain 9  score: 41.8 bits;  conditional E-value: 1.4e-13
                            TPR_10   4 slnNLanalrqrgrydeAealleealairrrllGpdHPd 42 
                                       slnNLa ++++ gry +Ae l+++a +i+r+ lG+ HPd
  gi|330508766|ref|YP_004385194.1| 349 SLNNLALMYYSIGRYSDAEPLFRQATEIQRKSLGEAHPD 387
                                       8*************************************9 PP

  == domain 10  score: 48.4 bits;  conditional E-value: 1.1e-15
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllGpdHPd 42 
                                       A slnNLa ++r++gry +Ae l+++a +i+r+ lG+dHP+
  gi|330508766|ref|YP_004385194.1| 389 AQSLNNLAELYRSMGRYSDAEPLFRQATEIWRKSLGEDHPE 429
                                       789*************************************7 PP

  == domain 11  score: 50.1 bits;  conditional E-value: 3.2e-16
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllGpdHPd 42 
                                       A+slnNLa+++r++gry +Ae l+++a +i+r+ lG+dHP+
  gi|330508766|ref|YP_004385194.1| 431 AASLNNLAVLYRSMGRYSDAEPLFRQATEIWRKSLGEDHPN 471
                                       89**************************************5 PP

  == domain 12  score: 45.7 bits;  conditional E-value: 7.8e-15
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllGpdHPd 42 
                                       A+ lnNLa ++r++gry +Ae l+++a +i+r+ lG+dHPd
  gi|330508766|ref|YP_004385194.1| 473 ATGLNNLAELYRSVGRYSDAEPLFRQATEIWRKSLGEDHPD 513
                                       5669************************************9 PP

  == domain 13  score: 37.0 bits;  conditional E-value: 4.3e-12
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllGpdHPd 42 
                                       A+slnN a ++r++ ry++Ae l+++a +i+r+ lG dHP+
  gi|330508766|ref|YP_004385194.1| 515 AASLNNRAELYRSMSRYNDAESLFRQATEIWRKSLGGDHPN 555
                                       89**************************************5 PP

  == domain 14  score: 50.6 bits;  conditional E-value: 2.3e-16
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllGpdHPd 42 
                                       A+slnNLa ++ ++gry eAe l+++a +irr+ lG+dHPd
  gi|330508766|ref|YP_004385194.1| 557 ATSLNNLALVYDSMGRYSEAEPLFRQATEIRRKSLGRDHPD 597
                                       89**************************************9 PP

  == domain 15  score: 49.7 bits;  conditional E-value: 4.5e-16
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllGpdHPd 42 
                                       A slnNLa +++++gry +Ae l+++a +i+r+ lG+dHPd
  gi|330508766|ref|YP_004385194.1| 599 AQSLNNLAGLYYSMGRYSDAEPLFRQATEIWRKSLGEDHPD 639
                                       789*************************************9 PP

  == domain 16  score: 43.7 bits;  conditional E-value: 3.3e-14
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllGpdHP 41 
                                       A slnNLa+++r++gry +Ae l+++a +irr++lG d+ 
  gi|330508766|ref|YP_004385194.1| 641 AQSLNNLAVLYRSMGRYSDAEPLFRQATEIRRKVLGKDPL 680
                                       789*********************************9985 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.2   4.5e-08   2.1e-05       1      32 [.      53      84 ..      53      86 .. 0.93
   2 !   19.0   0.0   1.8e-06   0.00085       2      23 ..      96     117 ..      95     118 .. 0.89
   3 !   21.2   0.0   3.8e-07   0.00018       2      32 ..     138     168 ..     137     170 .. 0.92
   4 !   29.6   0.1   8.4e-10     4e-07       1      30 [.     179     208 ..     179     211 .. 0.94
   5 !   24.5   0.0   3.3e-08   1.6e-05       2      32 ..     222     252 ..     221     254 .. 0.92
   6 !   24.0   0.1   4.9e-08   2.3e-05       2      29 ..     264     291 ..     263     293 .. 0.95
   7 !   26.5   0.0     8e-09   3.8e-06       1      32 [.     305     336 ..     305     338 .. 0.93
   8 !   21.9   0.0   2.2e-07   0.00011       2      32 ..     348     378 ..     347     380 .. 0.92
   9 !   23.0   0.0     1e-07   4.8e-05       1      30 [.     389     418 ..     389     422 .. 0.93
  10 !   23.7   0.0   6.1e-08   2.9e-05       1      30 [.     431     460 ..     431     464 .. 0.92
  11 !   18.4   0.0   2.9e-06    0.0014       2      30 ..     474     502 ..     473     506 .. 0.91
  12 !   18.7   0.0   2.3e-06    0.0011       1      30 [.     515     544 ..     515     548 .. 0.92
  13 !   24.5   0.0   3.3e-08   1.6e-05       2      32 ..     558     588 ..     557     590 .. 0.92
  14 !   21.5   0.0   2.9e-07   0.00014       1      30 [.     599     628 ..     599     632 .. 0.93
  15 !   24.9   0.0   2.6e-08   1.2e-05       1      31 [.     641     671 ..     641     673 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.5e-08
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnP 32
                                      a +l+nl+ +y+++g+y++A+  +++A e++ 
  gi|330508766|ref|YP_004385194.1| 53 AASLNNLAELYRSMGRYNDAEPLFRQAAEICR 84
                                      6789************************9976 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHHHHTT-HHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAley 23 
                                        +l+nl+++y+++g+yd+A+  
  gi|330508766|ref|YP_004385194.1|  96 TSLNNLALVYYSMGRYDDAEPL 117
                                       679****************875 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 3.8e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                         l+nl+ +y++ g+y eA+  +++A e++ 
  gi|330508766|ref|YP_004385194.1| 138 TGLNNLAELYRSIGRYSEAERLFRQATEIRR 168
                                       579************************9986 PP

  == domain 4  score: 29.6 bits;  conditional E-value: 8.4e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a +l+nl+ +y+++g+y+eA+  ++kA+e+
  gi|330508766|ref|YP_004385194.1| 179 AASLNNLAILYRSMGRYNEAEPLFRKAIEI 208
                                       6789*************************8 PP

  == domain 5  score: 24.5 bits;  conditional E-value: 3.3e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                        +l+nl+++y ++g+y eA+  +++A e++ 
  gi|330508766|ref|YP_004385194.1| 222 TSLNNLALVYDSMGRYSEAEPLFRQATEIRR 252
                                       679************************9986 PP

  == domain 6  score: 24.0 bits;  conditional E-value: 4.9e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALe 29 
                                       ++l+nl+ +y+++g+y +A+  y+kA+e
  gi|330508766|ref|YP_004385194.1| 264 QSLNNLAGLYYSMGRYSDAEPLYRKAIE 291
                                       579************************8 PP

  == domain 7  score: 26.5 bits;  conditional E-value: 8e-09
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a++l+nl+ +y+++g+y +A+  y+kA e++ 
  gi|330508766|ref|YP_004385194.1| 305 AQSLNNLAELYRSMGRYSDAEPLYRKATEIRR 336
                                       789**************************986 PP

  == domain 8  score: 21.9 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       ++l+nl+++y++ g+y +A+  +++A e++ 
  gi|330508766|ref|YP_004385194.1| 348 QSLNNLALMYYSIGRYSDAEPLFRQATEIQR 378
                                       579*************************986 PP

  == domain 9  score: 23.0 bits;  conditional E-value: 1e-07
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a++l+nl+ +y+++g+y +A+  +++A e+
  gi|330508766|ref|YP_004385194.1| 389 AQSLNNLAELYRSMGRYSDAEPLFRQATEI 418
                                       789************************998 PP

  == domain 10  score: 23.7 bits;  conditional E-value: 6.1e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a +l+nl+++y+++g+y +A+  +++A e+
  gi|330508766|ref|YP_004385194.1| 431 AASLNNLAVLYRSMGRYSDAEPLFRQATEI 460
                                       6789***********************998 PP

  == domain 11  score: 18.4 bits;  conditional E-value: 2.9e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                         l+nl+ +y++ g+y +A+  +++A e+
  gi|330508766|ref|YP_004385194.1| 474 TGLNNLAELYRSVGRYSDAEPLFRQATEI 502
                                       579***********************998 PP

  == domain 12  score: 18.7 bits;  conditional E-value: 2.3e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a +l+n++ +y+++ +y++A+  +++A e+
  gi|330508766|ref|YP_004385194.1| 515 AASLNNRAELYRSMSRYNDAESLFRQATEI 544
                                       6789***********************998 PP

  == domain 13  score: 24.5 bits;  conditional E-value: 3.3e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                        +l+nl+++y ++g+y eA+  +++A e++ 
  gi|330508766|ref|YP_004385194.1| 558 TSLNNLALVYDSMGRYSEAEPLFRQATEIRR 588
                                       679************************9986 PP

  == domain 14  score: 21.5 bits;  conditional E-value: 2.9e-07
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a++l+nl+ +y+++g+y +A+  +++A e+
  gi|330508766|ref|YP_004385194.1| 599 AQSLNNLAGLYYSMGRYSDAEPLFRQATEI 628
                                       789************************998 PP

  == domain 15  score: 24.9 bits;  conditional E-value: 2.6e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                       a++l+nl+++y+++g+y +A+  +++A e++
  gi|330508766|ref|YP_004385194.1| 641 AQSLNNLAVLYRSMGRYSDAEPLFRQATEIR 671
                                       789************************9997 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       3.8   1.8e+03       9      23 ..      21      35 ..      19      38 .. 0.85
   2 !   24.3   0.1   4.3e-08     2e-05       1      31 [.      55      85 ..      55      90 .. 0.89
   3 !   14.0   0.0   8.4e-05      0.04       1      22 [.      97     118 ..      97     128 .. 0.93
   4 !   22.2   0.2     2e-07   9.5e-05       2      29 ..     140     165 ..     140     174 .. 0.86
   5 !   23.7   0.0   6.5e-08   3.1e-05       1      31 [.     181     211 ..     181     216 .. 0.89
   6 !   21.0   0.0   4.9e-07   0.00023       1      29 [.     223     249 ..     223     258 .. 0.86
   7 !   20.2   0.0   8.6e-07    0.0004       1      30 [.     265     292 ..     265     299 .. 0.91
   8 !   24.7   0.1     3e-08   1.4e-05       1      29 [.     307     333 ..     307     342 .. 0.86
   9 !   16.6   0.1   1.2e-05    0.0057       1      29 [.     349     375 ..     349     384 .. 0.89
  10 !   24.1   0.0   4.8e-08   2.3e-05       1      29 [.     391     417 ..     391     426 .. 0.87
  11 !   24.5   0.0   3.6e-08   1.7e-05       1      29 [.     433     459 ..     433     468 .. 0.87
  12 !   21.9   0.0   2.4e-07   0.00011       2      29 ..     476     501 ..     476     510 .. 0.87
  13 !   16.0   0.1   1.9e-05     0.009       1      28 [.     517     542 ..     517     551 .. 0.88
  14 !   21.0   0.0   4.9e-07   0.00023       1      29 [.     559     585 ..     559     594 .. 0.86
  15 !   18.8   0.0   2.5e-06    0.0012       1      29 [.     601     627 ..     601     636 .. 0.87
  16 !   25.7   0.0   1.5e-08   6.9e-06       1      30 [.     643     677 ..     643     682 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.8
                             TPR_7  9 ysrlGdyeeAielye 23
                                      ++++G+y +Ai + e
  gi|330508766|ref|YP_004385194.1| 21 FRNDGNYIQAIAFAE 35
                                      6899*******9866 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 4.3e-08
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31
                                      +L+nLa+ly+++G+y +A+ l++q+ ++++ 
  gi|330508766|ref|YP_004385194.1| 55 SLNNLAELYRSMGRYNDAEPLFRQAAEICRK 85
                                      79**********************9888765 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 8.4e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAiely 22 
                                       +L+nLa +y ++G+y++A+ l+
  gi|330508766|ref|YP_004385194.1|  97 SLNNLALVYYSMGRYDDAEPLF 118
                                       79*****************998 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 2e-07
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLalt 29 
                                       L+nLa+ly++ G+y+eA++l++q  a++
  gi|330508766|ref|YP_004385194.1| 140 LNNLAELYRSIGRYSEAERLFRQ--ATE 165
                                       89*********************..544 PP

  == domain 5  score: 23.7 bits;  conditional E-value: 6.5e-08
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       +L+nLa ly+++G+y eA+ l++++++++++
  gi|330508766|ref|YP_004385194.1| 181 SLNNLAILYRSMGRYNEAEPLFRKAIEIWRR 211
                                       79**********************9988876 PP

  == domain 6  score: 21.0 bits;  conditional E-value: 4.9e-07
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       +L+nLa +y ++G+y+eA+ l++q  a++
  gi|330508766|ref|YP_004385194.1| 223 SLNNLALVYDSMGRYSEAEPLFRQ--ATE 249
                                       79**********************..544 PP

  == domain 7  score: 20.2 bits;  conditional E-value: 8.6e-07
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       +L+nLa ly ++G+y++A+ ly++  a+++
  gi|330508766|ref|YP_004385194.1| 265 SLNNLAGLYYSMGRYSDAEPLYRK--AIEN 292
                                       79**********************..7764 PP

  == domain 8  score: 24.7 bits;  conditional E-value: 3e-08
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       +L+nLa+ly+++G+y++A+ ly++  a++
  gi|330508766|ref|YP_004385194.1| 307 SLNNLAELYRSMGRYSDAEPLYRK--ATE 333
                                       79**********************..543 PP

  == domain 9  score: 16.6 bits;  conditional E-value: 1.2e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       +L+nLa +y + G+y++A+ l++q  a++
  gi|330508766|ref|YP_004385194.1| 349 SLNNLALMYYSIGRYSDAEPLFRQ--ATE 375
                                       79**********************..765 PP

  == domain 10  score: 24.1 bits;  conditional E-value: 4.8e-08
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       +L+nLa+ly+++G+y++A+ l++q  a++
  gi|330508766|ref|YP_004385194.1| 391 SLNNLAELYRSMGRYSDAEPLFRQ--ATE 417
                                       79**********************..554 PP

  == domain 11  score: 24.5 bits;  conditional E-value: 3.6e-08
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       +L+nLa+ly+++G+y++A+ l++q  a++
  gi|330508766|ref|YP_004385194.1| 433 SLNNLAVLYRSMGRYSDAEPLFRQ--ATE 459
                                       79**********************..554 PP

  == domain 12  score: 21.9 bits;  conditional E-value: 2.4e-07
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLalt 29 
                                       L+nLa+ly+++G+y++A+ l++q  a++
  gi|330508766|ref|YP_004385194.1| 476 LNNLAELYRSVGRYSDAEPLFRQ--ATE 501
                                       89*********************..554 PP

  == domain 13  score: 16.0 bits;  conditional E-value: 1.9e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       +L+n a+ly+++ +y +A++l++q  a+
  gi|330508766|ref|YP_004385194.1| 517 SLNNRAELYRSMSRYNDAESLFRQ--AT 542
                                       79**********************..65 PP

  == domain 14  score: 21.0 bits;  conditional E-value: 4.9e-07
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       +L+nLa +y ++G+y+eA+ l++q  a++
  gi|330508766|ref|YP_004385194.1| 559 SLNNLALVYDSMGRYSEAEPLFRQ--ATE 585
                                       79**********************..543 PP

  == domain 15  score: 18.8 bits;  conditional E-value: 2.5e-06
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       +L+nLa ly ++G+y++A+ l++q  a++
  gi|330508766|ref|YP_004385194.1| 601 SLNNLAGLYYSMGRYSDAEPLFRQ--ATE 627
                                       79**********************..554 PP

  == domain 16  score: 25.7 bits;  conditional E-value: 1.5e-08
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt.......k 30 
                                       +L+nLa+ly+++G+y++A+ l++q  a++       k
  gi|330508766|ref|YP_004385194.1| 643 SLNNLAVLYRSMGRYSDAEPLFRQ--ATEirrkvlgK 677
                                       79**********************..55433444444 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.7e-06    0.0008       2      33 ..      54      85 ..      53      86 .. 0.92
   2 !   14.8   0.0   5.4e-05     0.025       1      30 [.      95     124 ..      95     124 .. 0.93
   3 !   19.5   0.0   1.6e-06   0.00075       3      33 ..     139     169 ..     137     170 .. 0.92
   4 !   22.0   0.1   2.6e-07   0.00012       2      30 ..     180     208 ..     179     208 .. 0.94
   5 !   23.0   0.0   1.2e-07   5.7e-05       1      33 [.     221     253 ..     221     254 .. 0.94
   6 !   15.9   0.1   2.2e-05     0.011       2      29 ..     264     291 ..     263     292 .. 0.95
   7 !   23.1   0.1   1.1e-07   5.3e-05       1      33 [.     305     337 ..     305     338 .. 0.95
   8 !   16.0   0.1   2.2e-05      0.01       2      33 ..     348     379 ..     347     380 .. 0.94
   9 !   18.3   0.0   3.8e-06    0.0018       1      30 [.     389     418 ..     389     421 .. 0.96
  10 !   16.3   0.0   1.7e-05    0.0079       2      30 ..     432     460 ..     431     463 .. 0.94
  11 !   12.4   0.0   0.00031      0.15       3      30 ..     475     502 ..     473     505 .. 0.93
  12 !   12.6   0.1   0.00026      0.12       2      30 ..     516     544 ..     515     547 .. 0.94
  13 !   23.0   0.0   1.2e-07   5.7e-05       1      33 [.     557     589 ..     557     590 .. 0.94
  14 !   15.2   0.0   3.8e-05     0.018       1      30 [.     599     628 ..     599     631 .. 0.96
  15 !   20.4   0.0   8.1e-07   0.00038       1      33 [.     641     673 ..     641     674 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.7e-06
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                                       +++nl+ +y+++g+y+ A+  +++a e+ ++
  gi|330508766|ref|YP_004385194.1| 54 ASLNNLAELYRSMGRYNDAEPLFRQAAEICRK 85
                                      689*************************9875 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5.4e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a +++nl+++y ++g+y+ A+  + +++e+
  gi|330508766|ref|YP_004385194.1|  95 ATSLNNLALVYYSMGRYDDAEPLFCQVTEI 124
                                       5689*********************99986 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        ++nl+ +y++ g+y eA+  +++a+e++++
  gi|330508766|ref|YP_004385194.1| 139 GLNNLAELYRSIGRYSEAERLFRQATEIRRK 169
                                       689*************************986 PP

  == domain 4  score: 22.0 bits;  conditional E-value: 2.6e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                        +++nl+ +y+++g+y+eA+  ++ka+e+
  gi|330508766|ref|YP_004385194.1| 180 ASLNNLAILYRSMGRYNEAEPLFRKAIEI 208
                                       6899***********************97 PP

  == domain 5  score: 23.0 bits;  conditional E-value: 1.2e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a +++nl+++y+++g+y eA+  +++a+e++++
  gi|330508766|ref|YP_004385194.1| 221 ATSLNNLALVYDSMGRYSEAEPLFRQATEIRRK 253
                                       5689**************************986 PP

  == domain 6  score: 15.9 bits;  conditional E-value: 2.2e-05
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                       ++++nl+ +y ++g+y  A+  y+ka+e
  gi|330508766|ref|YP_004385194.1| 264 QSLNNLAGLYYSMGRYSDAEPLYRKAIE 291
                                       789***********************98 PP

  == domain 7  score: 23.1 bits;  conditional E-value: 1.1e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++++nl+ +y+++g+y  A+  y+ka+e++++
  gi|330508766|ref|YP_004385194.1| 305 AQSLNNLAELYRSMGRYSDAEPLYRKATEIRRK 337
                                       789***************************986 PP

  == domain 8  score: 16.0 bits;  conditional E-value: 2.2e-05
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++++nl++ y + g+y  A+  +++a+e++++
  gi|330508766|ref|YP_004385194.1| 348 QSLNNLALMYYSIGRYSDAEPLFRQATEIQRK 379
                                       789**************************986 PP

  == domain 9  score: 18.3 bits;  conditional E-value: 3.8e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a++++nl+ +y+++g+y  A+  +++a+e+
  gi|330508766|ref|YP_004385194.1| 389 AQSLNNLAELYRSMGRYSDAEPLFRQATEI 418
                                       789************************997 PP

  == domain 10  score: 16.3 bits;  conditional E-value: 1.7e-05
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                        +++nl+ +y+++g+y  A+  +++a+e+
  gi|330508766|ref|YP_004385194.1| 432 ASLNNLAVLYRSMGRYSDAEPLFRQATEI 460
                                       689***********************997 PP

  == domain 11  score: 12.4 bits;  conditional E-value: 0.00031
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekalel 30 
                                        ++nl+ +y++ g+y  A+  +++a+e+
  gi|330508766|ref|YP_004385194.1| 475 GLNNLAELYRSVGRYSDAEPLFRQATEI 502
                                       689**********************997 PP

  == domain 12  score: 12.6 bits;  conditional E-value: 0.00026
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                        +++n + +y+++ +y+ A++ +++a+e+
  gi|330508766|ref|YP_004385194.1| 516 ASLNNRAELYRSMSRYNDAESLFRQATEI 544
                                       6899**********************997 PP

  == domain 13  score: 23.0 bits;  conditional E-value: 1.2e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a +++nl+++y+++g+y eA+  +++a+e++++
  gi|330508766|ref|YP_004385194.1| 557 ATSLNNLALVYDSMGRYSEAEPLFRQATEIRRK 589
                                       5689**************************986 PP

  == domain 14  score: 15.2 bits;  conditional E-value: 3.8e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a++++nl+ +y ++g+y  A+  +++a+e+
  gi|330508766|ref|YP_004385194.1| 599 AQSLNNLAGLYYSMGRYSDAEPLFRQATEI 628
                                       789************************997 PP

  == domain 15  score: 20.4 bits;  conditional E-value: 8.1e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++++nl+ +y+++g+y  A+  +++a+e++++
  gi|330508766|ref|YP_004385194.1| 641 AQSLNNLAVLYRSMGRYSDAEPLFRQATEIRRK 673
                                       789***************************986 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       3.1   1.5e+03      13      27 ..      23      37 ..      20      40 .. 0.83
   2 !   20.2   0.2   9.3e-07   0.00044       1      32 [.      53      84 ..      53      86 .. 0.92
   3 !   14.2   0.0   7.4e-05     0.035       2      24 ..      96     118 ..      95     120 .. 0.89
   4 !   20.0   0.1   1.1e-06   0.00051       2      31 ..     138     167 ..     137     170 .. 0.91
   5 !   21.9   0.1   2.5e-07   0.00012       1      30 [.     179     208 ..     179     208 .. 0.94
   6 !   18.6   0.0   2.9e-06    0.0014       2      31 ..     222     251 ..     221     254 .. 0.91
   7 !   17.7   0.0   5.5e-06    0.0026       3      29 ..     265     291 ..     263     292 .. 0.94
   8 !   19.2   0.1   1.8e-06   0.00087       1      31 [.     305     335 ..     305     338 .. 0.91
   9 !   17.3   0.0   7.5e-06    0.0036       3      32 ..     349     378 ..     347     380 .. 0.91
  10 !   17.2   0.0   8.5e-06     0.004       1      30 [.     389     418 ..     389     418 .. 0.93
  11 !   17.0   0.0   9.2e-06    0.0043       1      30 [.     431     460 ..     431     460 .. 0.93
  12 !   14.7   0.0   5.1e-05     0.024       2      30 ..     474     502 ..     473     502 .. 0.93
  13 !   12.9   0.1   0.00019     0.092       1      30 [.     515     544 ..     515     544 .. 0.93
  14 !   18.6   0.0   2.9e-06    0.0014       2      31 ..     558     587 ..     557     590 .. 0.91
  15 !   16.5   0.0   1.4e-05    0.0067       1      30 [.     599     628 ..     599     628 .. 0.93
  16 !   18.0   0.0   4.5e-06    0.0021       1      30 [.     641     670 ..     641     673 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.1
                             TPR_2 13 klgdyeeAleafekA 27
                                      + g+y +A+++ e+ 
  gi|330508766|ref|YP_004385194.1| 23 NDGNYIQAIAFAEEL 37
                                      679*******99986 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 9.3e-07
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldP 32
                                      a  l+nl+++y+ +g+y++A+ +f++A e++ 
  gi|330508766|ref|YP_004385194.1| 53 AASLNNLAELYRSMGRYNDAEPLFRQAAEICR 84
                                      5679*************************986 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 7.4e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleaf 24 
                                         l+nl+l+yy +g+y++A+ +f
  gi|330508766|ref|YP_004385194.1|  96 TSLNNLALVYYSMGRYDDAEPLF 118
                                       579****************8765 PP

  == domain 4  score: 20.0 bits;  conditional E-value: 1.1e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                        +l+nl+++y+  g+y eA+++f++A e+ 
  gi|330508766|ref|YP_004385194.1| 138 TGLNNLAELYRSIGRYSEAERLFRQATEIR 167
                                       689***********************9986 PP

  == domain 5  score: 21.9 bits;  conditional E-value: 2.5e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a  l+nl+ +y+ +g+y+eA+ +f+kA+e+
  gi|330508766|ref|YP_004385194.1| 179 AASLNNLAILYRSMGRYNEAEPLFRKAIEI 208
                                       5679************************96 PP

  == domain 6  score: 18.6 bits;  conditional E-value: 2.9e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                         l+nl+l+y  +g+y eA+ +f++A e+ 
  gi|330508766|ref|YP_004385194.1| 222 TSLNNLALVYDSMGRYSEAEPLFRQATEIR 251
                                       579***********************9986 PP

  == domain 7  score: 17.7 bits;  conditional E-value: 5.5e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                                        l+nl+ +yy +g+y +A+ +++kA+e
  gi|330508766|ref|YP_004385194.1| 265 SLNNLAGLYYSMGRYSDAEPLYRKAIE 291
                                       689**********************97 PP

  == domain 8  score: 19.2 bits;  conditional E-value: 1.8e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       a+ l+nl+++y+ +g+y +A+ +++kA e+ 
  gi|330508766|ref|YP_004385194.1| 305 AQSLNNLAELYRSMGRYSDAEPLYRKATEIR 335
                                       5689***********************9986 PP

  == domain 9  score: 17.3 bits;  conditional E-value: 7.5e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                        l+nl+l yy  g+y +A+ +f++A e+  
  gi|330508766|ref|YP_004385194.1| 349 SLNNLALMYYSIGRYSDAEPLFRQATEIQR 378
                                       689**********************99875 PP

  == domain 10  score: 17.2 bits;  conditional E-value: 8.5e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a+ l+nl+++y+ +g+y +A+ +f++A e+
  gi|330508766|ref|YP_004385194.1| 389 AQSLNNLAELYRSMGRYSDAEPLFRQATEI 418
                                       5689***********************885 PP

  == domain 11  score: 17.0 bits;  conditional E-value: 9.2e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a  l+nl+ +y+ +g+y +A+ +f++A e+
  gi|330508766|ref|YP_004385194.1| 431 AASLNNLAVLYRSMGRYSDAEPLFRQATEI 460
                                       5679***********************885 PP

  == domain 12  score: 14.7 bits;  conditional E-value: 5.1e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAlel 30 
                                        +l+nl+++y+  g+y +A+ +f++A e+
  gi|330508766|ref|YP_004385194.1| 474 TGLNNLAELYRSVGRYSDAEPLFRQATEI 502
                                       689***********************885 PP

  == domain 13  score: 12.9 bits;  conditional E-value: 0.00019
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a  l+n++++y+ + +y++A+ +f++A e+
  gi|330508766|ref|YP_004385194.1| 515 AASLNNRAELYRSMSRYNDAESLFRQATEI 544
                                       5679***********************885 PP

  == domain 14  score: 18.6 bits;  conditional E-value: 2.9e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                         l+nl+l+y  +g+y eA+ +f++A e+ 
  gi|330508766|ref|YP_004385194.1| 558 TSLNNLALVYDSMGRYSEAEPLFRQATEIR 587
                                       579***********************9986 PP

  == domain 15  score: 16.5 bits;  conditional E-value: 1.4e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a+ l+nl+ +yy +g+y +A+ +f++A e+
  gi|330508766|ref|YP_004385194.1| 599 AQSLNNLAGLYYSMGRYSDAEPLFRQATEI 628
                                       5679***********************885 PP

  == domain 16  score: 18.0 bits;  conditional E-value: 4.5e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a+ l+nl+ +y+ +g+y +A+ +f++A e+
  gi|330508766|ref|YP_004385194.1| 641 AQSLNNLAVLYRSMGRYSDAEPLFRQATEI 670
                                       5689***********************998 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.6   2.7e-05     0.013       9      33 ..      49      73 ..      47      73 .. 0.95
   2 !   18.2   0.0   4.7e-06    0.0022       8      33 ..      90     115 ..      82     115 .. 0.91
   3 !   10.4   0.0    0.0015      0.69       9      33 ..     133     157 ..     131     158 .. 0.87
   4 !   17.2   0.3     1e-05    0.0049       8      33 ..     174     199 ..     173     199 .. 0.94
   5 !   16.6   0.0   1.5e-05    0.0071       8      33 ..     216     241 ..     201     241 .. 0.82
   6 !   12.0   0.1   0.00045      0.21       8      33 ..     258     283 ..     257     283 .. 0.92
   7 !   16.3   0.2     2e-05    0.0095       1      33 [.     285     325 ..     285     325 .. 0.77
   8 !   14.3   0.0   8.3e-05     0.039       8      33 ..     342     367 ..     327     367 .. 0.89
   9 !   17.9   0.2   5.8e-06    0.0028       7      33 ..     383     409 ..     383     409 .. 0.94
  10 !   14.6   0.1   6.6e-05     0.031       8      33 ..     426     451 ..     421     451 .. 0.93
  11 !    8.8   0.0    0.0049       2.3       9      33 ..     469     493 ..     462     493 .. 0.87
  12 !   12.2   0.1    0.0004      0.19       8      33 ..     510     535 ..     505     536 .. 0.91
  13 !   15.3   0.1     4e-05     0.019       9      33 ..     553     577 ..     545     577 .. 0.92
  14 !   12.4   0.1   0.00033      0.16       9      33 ..     595     619 ..     588     619 .. 0.90
  15 !   16.8   0.1   1.3e-05    0.0063       8      33 ..     636     661 ..     631     661 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-05
                            TPR_17  9 dPnnadaynnLAelllknGdlmtAr 33
                                      +P++a ++nnLAel+++ G++ +A+
  gi|330508766|ref|YP_004385194.1| 49 HPDYAASLNNLAELYRSMGRYNDAE 73
                                      7********************9996 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 4.7e-06
                            TPR_17   8 ldPnnadaynnLAelllknGdlmtAr 33 
                                        +P++a ++nnLA ++++ G++++A+
  gi|330508766|ref|YP_004385194.1|  90 DHPDYATSLNNLALVYYSMGRYDDAE 115
                                       47**********************96 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0015
                            TPR_17   9 dPnnadaynnLAelllknGdlmtAr 33 
                                       +Pn a  +nnLAel++++G++ +A+
  gi|330508766|ref|YP_004385194.1| 133 HPNCATGLNNLAELYRSIGRYSEAE 157
                                       56778889*************9997 PP

  == domain 4  score: 17.2 bits;  conditional E-value: 1e-05
                            TPR_17   8 ldPnnadaynnLAelllknGdlmtAr 33 
                                        +Pn+a ++nnLA l+++ G++ +A+
  gi|330508766|ref|YP_004385194.1| 174 DHPNYAASLNNLAILYRSMGRYNEAE 199
                                       58*********************996 PP

  == domain 5  score: 16.6 bits;  conditional E-value: 1.5e-05
                            TPR_17   8 ldPnnadaynnLAelllknGdlmtAr 33 
                                        +Pn+a ++nnLA ++ + G++ +A+
  gi|330508766|ref|YP_004385194.1| 216 DHPNYATSLNNLALVYDSMGRYSEAE 241
                                       37********************9996 PP

  == domain 6  score: 12.0 bits;  conditional E-value: 0.00045
                            TPR_17   8 ldPnnadaynnLAelllknGdlmtAr 33 
                                        +P+++ ++nnLA l+++ G++ +A+
  gi|330508766|ref|YP_004385194.1| 258 DHPDYSQSLNNLAGLYYSMGRYSDAE 283
                                       58********************9986 PP

  == domain 7  score: 16.3 bits;  conditional E-value: 2e-05
                            TPR_17   1 lylkalel........dPnnadaynnLAelllknGdlmtAr 33 
                                       ly+ka+e+        +P +a ++nnLAel+++ G++ +A+
  gi|330508766|ref|YP_004385194.1| 285 LYRKAIENwgkslgedHPAYAQSLNNLAELYRSMGRYSDAE 325
                                       57777777444333335889*****************9986 PP

  == domain 8  score: 14.3 bits;  conditional E-value: 8.3e-05
                            TPR_17   8 ldPnnadaynnLAelllknGdlmtAr 33 
                                        +P+++ ++nnLA  ++++G++ +A+
  gi|330508766|ref|YP_004385194.1| 342 DHPDYSQSLNNLALMYYSIGRYSDAE 367
                                       48********************9986 PP

  == domain 9  score: 17.9 bits;  conditional E-value: 5.8e-06
                            TPR_17   7 eldPnnadaynnLAelllknGdlmtAr 33 
                                       e +P++a ++nnLAel+++ G++ +A+
  gi|330508766|ref|YP_004385194.1| 383 EAHPDYAQSLNNLAELYRSMGRYSDAE 409
                                       679********************9986 PP

  == domain 10  score: 14.6 bits;  conditional E-value: 6.6e-05
                            TPR_17   8 ldPnnadaynnLAelllknGdlmtAr 33 
                                        +P +a ++nnLA+l+++ G++ +A+
  gi|330508766|ref|YP_004385194.1| 426 DHPEYAASLNNLAVLYRSMGRYSDAE 451
                                       58********************9986 PP

  == domain 11  score: 8.8 bits;  conditional E-value: 0.0049
                            TPR_17   9 dPnnadaynnLAelllknGdlmtAr 33 
                                       +Pn a  +nnLAel+++ G++ +A+
  gi|330508766|ref|YP_004385194.1| 469 HPNCATGLNNLAELYRSVGRYSDAE 493
                                       56668889*************9986 PP

  == domain 12  score: 12.2 bits;  conditional E-value: 0.0004
                            TPR_17   8 ldPnnadaynnLAelllknGdlmtAr 33 
                                        +P++a ++nn+Ael+++  ++ +A+
  gi|330508766|ref|YP_004385194.1| 510 DHPDYAASLNNRAELYRSMSRYNDAE 535
                                       58***************999999987 PP

  == domain 13  score: 15.3 bits;  conditional E-value: 4e-05
                            TPR_17   9 dPnnadaynnLAelllknGdlmtAr 33 
                                       +Pn+a ++nnLA ++ + G++ +A+
  gi|330508766|ref|YP_004385194.1| 553 HPNYATSLNNLALVYDSMGRYSEAE 577
                                       6********************9996 PP

  == domain 14  score: 12.4 bits;  conditional E-value: 0.00033
                            TPR_17   9 dPnnadaynnLAelllknGdlmtAr 33 
                                       +P++a ++nnLA l+++ G++ +A+
  gi|330508766|ref|YP_004385194.1| 595 HPDYAQSLNNLAGLYYSMGRYSDAE 619
                                       7********************9986 PP

  == domain 15  score: 16.8 bits;  conditional E-value: 1.3e-05
                            TPR_17   8 ldPnnadaynnLAelllknGdlmtAr 33 
                                        +P++a ++nnLA+l+++ G++ +A+
  gi|330508766|ref|YP_004385194.1| 636 DHPDYAQSLNNLAVLYRSMGRYSDAE 661
                                       58********************9986 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.1   2.8e-05     0.013       4      48 ..      24      76 ..      22      80 .. 0.85
   2 !   17.1   0.0   1.3e-05     0.006       7      45 ..      76     115 ..      75     123 .. 0.90
   3 !   12.0   0.0   0.00049      0.23      17      57 ..     129     169 ..     126     171 .. 0.88
   4 !   14.7   0.1   6.8e-05     0.032      16      49 ..     170     203 ..     168     208 .. 0.87
   5 !   12.1   0.0   0.00044      0.21       9      56 ..     204     252 ..     201     255 .. 0.84
   6 !   12.2   0.0   0.00041      0.19      16      47 ..     254     285 ..     244     292 .. 0.84
   7 !   13.0   0.1   0.00023      0.11      16      54 ..     296     334 ..     284     339 .. 0.82
   8 !    9.0   0.0     0.004       1.9      16      57 ..     338     379 ..     328     381 .. 0.87
   9 !   18.7   0.1     4e-06    0.0019       5      51 ..     361     415 ..     361     421 .. 0.84
  10 !   12.9   0.0   0.00025      0.12      16      51 ..     422     457 ..     412     463 .. 0.82
  11 !    8.3   0.0    0.0071       3.3      17      52 ..     465     500 ..     453     507 .. 0.81
  12 !   15.4   0.0   4.2e-05      0.02       5      53 ..     487     543 ..     487     558 .. 0.85
  13 !    9.5   0.0    0.0029       1.4      18      57 ..     550     589 ..     539     593 .. 0.85
  14 !   20.2   0.0   1.4e-06   0.00064       4      52 ..     570     626 ..     569     632 .. 0.87
  15 !   13.4   0.0   0.00018     0.085      16      54 ..     632     670 ..     622     674 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-05
                            TPR_19  4 egdyaeAlalleqalqe........dpknaearllLAeallalgqldeAealL 48
                                      +g+y +A+a+ e++ +          p++a+ + +LAe++ ++g++++Ae l 
  gi|330508766|ref|YP_004385194.1| 24 DGNYIQAIAFAEELRDLiwqkvgydHPDYAASLNNLAELYRSMGRYNDAEPLF 76
                                      5899999999999554466668888************************9766 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.3e-05
                            TPR_19   7 yaeAlalleqal.qedpknaearllLAeallalgqldeAe 45 
                                       + +A+++ ++ l ++ p++a  + +LA +++++g++d+Ae
  gi|330508766|ref|YP_004385194.1|  76 FRQAAEICRKSLgEDHPDYATSLNNLALVYYSMGRYDDAE 115
                                       5799******85488************************8 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00049
                            TPR_19  17 alqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       + ++ p+ a  + +LAe++ + g++ eAe+l  ++ e  ++
  gi|330508766|ref|YP_004385194.1| 129 LGEDHPNCATGLNNLAELYRSIGRYSEAERLFRQATEIRRK 169
                                       5688999999999*******************999887665 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 6.8e-05
                            TPR_19  16 qalqedpknaearllLAeallalgqldeAealLd 49 
                                       ++ ++ p++a+ + +LA+++ ++g+++eAe l  
  gi|330508766|ref|YP_004385194.1| 170 SLGEDHPNYAASLNNLAILYRSMGRYNEAEPLFR 203
                                       567899***********************97765 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 0.00044
                            TPR_19   9 eAlalleqal.qedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                        A+++ ++ l ++ p++a  + +LA ++ ++g++ eAe l  ++ e  +
  gi|330508766|ref|YP_004385194.1| 204 KAIEIWRRSLgEDHPNYATSLNNLALVYDSMGRYSEAEPLFRQATEIRR 252
                                       6777777764388*************************99998887665 PP

  == domain 6  score: 12.2 bits;  conditional E-value: 0.00041
                            TPR_19  16 qalqedpknaearllLAeallalgqldeAeal 47 
                                       ++ ++ p+++  + +LA +++++g++ +Ae l
  gi|330508766|ref|YP_004385194.1| 254 SLGEDHPDYSQSLNNLAGLYYSMGRYSDAEPL 285
                                       45689************************966 PP

  == domain 7  score: 13.0 bits;  conditional E-value: 0.00023
                            TPR_19  16 qalqedpknaearllLAeallalgqldeAealLdalpee 54 
                                       ++ ++ p +a  + +LAe++ ++g++ +Ae l  ++ e 
  gi|330508766|ref|YP_004385194.1| 296 SLGEDHPAYAQSLNNLAELYRSMGRYSDAEPLYRKATEI 334
                                       45689************************9887777665 PP

  == domain 8  score: 9.0 bits;  conditional E-value: 0.004
                            TPR_19  16 qalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       ++ ++ p+++  + +LA  +++ g++ +Ae l  ++ e +++
  gi|330508766|ref|YP_004385194.1| 338 SLGEDHPDYSQSLNNLALMYYSIGRYSDAEPLFRQATEIQRK 379
                                       45689*************************999999887776 PP

  == domain 9  score: 18.7 bits;  conditional E-value: 4e-06
                            TPR_19   5 gdyaeAlalleqalqe........dpknaearllLAeallalgqldeAealLdal 51 
                                       g+y +A +l++qa +          p++a  + +LAe++ ++g++ +Ae l  ++
  gi|330508766|ref|YP_004385194.1| 361 GRYSDAEPLFRQATEIqrkslgeaHPDYAQSLNNLAELYRSMGRYSDAEPLFRQA 415
                                       8999********874455555555************************9887776 PP

  == domain 10  score: 12.9 bits;  conditional E-value: 0.00025
                            TPR_19  16 qalqedpknaearllLAeallalgqldeAealLdal 51 
                                       ++ ++ p++a+ + +LA ++ ++g++ +Ae l  ++
  gi|330508766|ref|YP_004385194.1| 422 SLGEDHPEYAASLNNLAVLYRSMGRYSDAEPLFRQA 457
                                       34689************************9887776 PP

  == domain 11  score: 8.3 bits;  conditional E-value: 0.0071
                            TPR_19  17 alqedpknaearllLAeallalgqldeAealLdalp 52 
                                       + ++ p+ a  + +LAe++ + g++ +Ae l  ++ 
  gi|330508766|ref|YP_004385194.1| 465 LGEDHPNCATGLNNLAELYRSVGRYSDAEPLFRQAT 500
                                       45889999999*****************98877765 PP

  == domain 12  score: 15.4 bits;  conditional E-value: 4.2e-05
                            TPR_19   5 gdyaeAlalleqal........qedpknaearllLAeallalgqldeAealLdalpe 53 
                                       g+y +A +l++qa         ++ p++a+ + + Ae++ ++ ++++Ae l  ++ e
  gi|330508766|ref|YP_004385194.1| 487 GRYSDAEPLFRQATeiwrkslgEDHPDYAASLNNRAELYRSMSRYNDAESLFRQATE 543
                                       79999*******764444444466*************************99988765 PP

  == domain 13  score: 9.5 bits;  conditional E-value: 0.0029
                            TPR_19  18 lqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                         + p++a  + +LA ++ ++g++ eAe l  ++ e  ++
  gi|330508766|ref|YP_004385194.1| 550 GGDHPNYATSLNNLALVYDSMGRYSEAEPLFRQATEIRRK 589
                                       4679************************999998887665 PP

  == domain 14  score: 20.2 bits;  conditional E-value: 1.4e-06
                            TPR_19   4 egdyaeAlalleqalqe........dpknaearllLAeallalgqldeAealLdalp 52 
                                       +g+y eA +l++qa +          p++a  + +LA +++++g++ +Ae l  ++ 
  gi|330508766|ref|YP_004385194.1| 570 MGRYSEAEPLFRQATEIrrkslgrdHPDYAQSLNNLAGLYYSMGRYSDAEPLFRQAT 626
                                       89***********975566666666************************98877765 PP

  == domain 15  score: 13.4 bits;  conditional E-value: 0.00018
                            TPR_19  16 qalqedpknaearllLAeallalgqldeAealLdalpee 54 
                                       ++ ++ p++a  + +LA ++ ++g++ +Ae l  ++ e 
  gi|330508766|ref|YP_004385194.1| 632 SLGEDHPDYAQSLNNLAVLYRSMGRYSDAEPLFRQATEI 670
                                       34689*************************998888765 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.4   0.00027      0.13      26      62 ..      45      81 ..      43      86 .. 0.83
   2 !   24.5   0.2   6.9e-08   3.2e-05       2      56 ..      58     118 ..      57     128 .. 0.90
   3 !   22.8   0.1   2.2e-07    0.0001       2      61 ..     100     164 ..      99     170 .. 0.93
   4 !   21.2   0.3   7.2e-07   0.00034       2      64 ..     142     209 ..     141     212 .. 0.90
   5 !   22.9   0.1   2.1e-07    0.0001       2      61 ..     184     248 ..     183     254 .. 0.92
   6 !   31.2   0.9   5.5e-10   2.6e-07       2      61 ..     268     332 ..     267     338 .. 0.92
   7 !   25.0   0.3   4.6e-08   2.2e-05       2      61 ..     310     374 ..     310     380 .. 0.85
   8 !   21.7   0.3   4.9e-07   0.00023       7      62 ..     357     417 ..     357     422 .. 0.87
   9 !   26.5   0.5   1.6e-08   7.5e-06       2      62 ..     394     459 ..     393     464 .. 0.87
  10 !   25.9   0.1   2.5e-08   1.2e-05       2      62 ..     436     501 ..     435     506 .. 0.91
  11 !   21.5   0.9   5.8e-07   0.00027       2      62 ..     478     543 ..     477     548 .. 0.86
  12 !   20.7   0.2   1.1e-06    0.0005       2      61 ..     520     584 ..     519     590 .. 0.89
  13 !   24.7   0.3     6e-08   2.8e-05       2      62 ..     562     627 ..     561     632 .. 0.85
  14 !   29.2   0.4   2.2e-09     1e-06       2      61 ..     604     668 ..     603     673 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00027
                            TPR_16 26 rdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62
                                       ++++Pd a++l++l++++   gr+ +A+ l+r a++
  gi|330508766|ref|YP_004385194.1| 45 VGYDHPDYAASLNNLAELYRSMGRYNDAEPLFRQAAE 81
                                      5678899999999999999999999999999999876 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 6.9e-08
                            TPR_16   2 alaraalragdyddAaaaleaalk.....rdpssPdaaeAllllgdaalrqgrlaeAa.al 56 
                                       +la +++  g+y dA++++++a +     ++ ++Pd a +l++l+++++  gr+++A+  +
  gi|330508766|ref|YP_004385194.1|  58 NLAELYRSMGRYNDAEPLFRQAAEicrksLGEDHPDYATSLNNLALVYYSMGRYDDAEpLF 118
                                       6899*******************76666689999************************555 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 2.2e-07
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraal 61 
                                       +la+ ++  g+yddA++++ ++++ +++s       +a  l++l++++   gr+ eA+ l+r a 
  gi|330508766|ref|YP_004385194.1| 100 NLALVYYSMGRYDDAEPLFCQVTEIWGKSLGedhpnCATGLNNLAELYRSIGRYSEAERLFRQAT 164
                                       699***********************9888888888**************************985 PP

  == domain 4  score: 21.2 bits;  conditional E-value: 7.2e-07
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                       +la +++  g+y +A++++++a++ +++s        a++l++l+ ++   gr+ eA+ l+r+a++ +
  gi|330508766|ref|YP_004385194.1| 142 NLAELYRSIGRYSEAERLFRQATEIRRKSLGedhpnYAASLNNLAILYRSMGRYNEAEPLFRKAIEIW 209
                                       68999******************9887766677777***************************99765 PP

  == domain 5  score: 22.9 bits;  conditional E-value: 2.1e-07
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraal 61 
                                       +la +++  g+y +A+++++ a++ +++s        a +l++l++++   gr+ eA+ l+r a 
  gi|330508766|ref|YP_004385194.1| 184 NLAILYRSMGRYNEAEPLFRKAIEIWRRSLGedhpnYATSLNNLALVYDSMGRYSEAEPLFRQAT 248
                                       6899********************998877788888**************************985 PP

  == domain 6  score: 31.2 bits;  conditional E-value: 5.5e-10
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraal 61 
                                       +la +++  g+y dA+++++ a++++++s        a++l++l++++   gr+ +A+ lyr+a 
  gi|330508766|ref|YP_004385194.1| 268 NLAGLYYSMGRYSDAEPLYRKAIENWGKSLGedhpaYAQSLNNLAELYRSMGRYSDAEPLYRKAT 332
                                       699***********************9876677777**************************986 PP

  == domain 7  score: 25.0 bits;  conditional E-value: 4.6e-08
                            TPR_16   2 alaraalragdyddAaaaleaalk.....rdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       +la +++  g+y dA+++++ a++     ++ ++Pd  ++l++l+++++  gr+ +A+ l+r a 
  gi|330508766|ref|YP_004385194.1| 310 NLAELYRSMGRYSDAEPLYRKATEirrksLGEDHPDYSQSLNNLALMYYSIGRYSDAEPLFRQAT 374
                                       5899******************99322223446677**************************985 PP

  == domain 8  score: 21.7 bits;  conditional E-value: 4.9e-07
                            TPR_16   7 alragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       ++  g+y dA++++++a++ +++s        a++l++l++++   gr+ +A+ l+r a +
  gi|330508766|ref|YP_004385194.1| 357 YYSIGRYSDAEPLFRQATEIQRKSLGeahpdYAQSLNNLAELYRSMGRYSDAEPLFRQATE 417
                                       56779**************998865556666**************************9965 PP

  == domain 9  score: 26.5 bits;  conditional E-value: 1.6e-08
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       +la +++  g+y dA++++++a++ +++s        a++l++l++++   gr+ +A+ l+r a +
  gi|330508766|ref|YP_004385194.1| 394 NLAELYRSMGRYSDAEPLFRQATEIWRKSLGedhpeYAASLNNLAVLYRSMGRYSDAEPLFRQATE 459
                                       6899********************887654455555**************************9965 PP

  == domain 10  score: 25.9 bits;  conditional E-value: 2.5e-08
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       +la +++  g+y dA++++++a++ +++s       +a  l++l++++   gr+ +A+ l+r a +
  gi|330508766|ref|YP_004385194.1| 436 NLAVLYRSMGRYSDAEPLFRQATEIWRKSLGedhpnCATGLNNLAELYRSVGRYSDAEPLFRQATE 501
                                       588899******************998877788888**************************9965 PP

  == domain 11  score: 21.5 bits;  conditional E-value: 5.8e-07
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       +la +++  g+y dA++++++a++ +++s        a++l+++++++   +r+ +A+ l+r a +
  gi|330508766|ref|YP_004385194.1| 478 NLAELYRSVGRYSDAEPLFRQATEIWRKSLGedhpdYAASLNNRAELYRSMSRYNDAESLFRQATE 543
                                       6899*******************9886543344444**************************9965 PP

  == domain 12  score: 20.7 bits;  conditional E-value: 1.1e-06
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraal 61 
                                       ++a +++   +y dA+ ++++a++ +++s        a +l++l++++   gr+ eA+ l+r a 
  gi|330508766|ref|YP_004385194.1| 520 NRAELYRSMSRYNDAESLFRQATEIWRKSLGgdhpnYATSLNNLALVYDSMGRYSEAEPLFRQAT 584
                                       57999*******************887666677777**************************985 PP

  == domain 13  score: 24.7 bits;  conditional E-value: 6e-08
                            TPR_16   2 alaraalragdyddAaaaleaalk.....rdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       +la+ +   g+y +A++++++a++     +++++Pd a++l++l+ +++  gr+ +A+ l+r a +
  gi|330508766|ref|YP_004385194.1| 562 NLALVYDSMGRYSEAEPLFRQATEirrksLGRDHPDYAQSLNNLAGLYYSMGRYSDAEPLFRQATE 627
                                       68999999***************8333334556788**************************9965 PP

  == domain 14  score: 29.2 bits;  conditional E-value: 2.2e-09
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraal 61 
                                       +la +++  g+y dA++++++a++ +++s        a++l++l++++   gr+ +A+ l+r a 
  gi|330508766|ref|YP_004385194.1| 604 NLAGLYYSMGRYSDAEPLFRQATEIWRKSLGedhpdYAQSLNNLAVLYRSMGRYSDAEPLFRQAT 668
                                       699********************9886543344444**************************985 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00047      0.22      79     183 ..      52     117 ..      22     132 .. 0.59
   2 !   31.5   0.0   2.5e-10   1.2e-07      83     193 ..     140     253 ..     128     261 .. 0.89
   3 !   21.8   0.0   2.2e-07    0.0001      85     194 ..     268     380 ..     255     391 .. 0.89
   4 !   22.1   0.0   1.8e-07   8.6e-05      82     193 ..     391     505 ..     381     506 .. 0.84
   5 !   39.6   0.0   8.6e-13     4e-10      34     265 ..     425     666 ..     424     730 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00047
                          TPR_MalT  79 allallqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql 155
                                        + +l  +ae+++  Gr  +A+ +++qa +  +++ ++  p +   l  la ++y +++ + Ae             
  gi|330508766|ref|YP_004385194.1|  52 YAASLNNLAELYRSMGRYNDAEPLFRQAAEICRKSLGEDHPDYATSLNNLALVYYSMGRYDDAE------------- 115
                                       3445556666666666666666666666666666666666666666666666666666666665............. PP

                          TPR_MalT 156 epeaaldayvllarialaqGdleeAetl 183
                                                                  l
  gi|330508766|ref|YP_004385194.1| 116 --------------------------PL 117
                                       ..........................44 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 2.5e-10
                          TPR_MalT  83 llqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql..ep 157
                                       l  +ae+++  Gr  eA+++++qa++  +++ ++  p +   l  la l++ +++  eAe   +++ie+ ++   e 
  gi|330508766|ref|YP_004385194.1| 140 LNNLAELYRSIGRYSEAERLFRQATEIRRKSLGEDHPNYAASLNNLAILYRSMGRYNEAEPLFRKAIEIWRRSlgED 216
                                       56789***************************************************************999954455 PP

                          TPR_MalT 158 eaald.ayvllarialaqGdleeAetllekaeelare 193
                                       +  ++ ++  la ++ + G+ +eAe l+++a+e  r+
  gi|330508766|ref|YP_004385194.1| 217 HPNYAtSLNNLALVYDSMGRYSEAEPLFRQATEIRRK 253
                                       5555448899*********************998765 PP

  == domain 3  score: 21.8 bits;  conditional E-value: 2.2e-07
                          TPR_MalT  85 qqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql..epea 159
                                        +a ++   Gr  +A+ +y++a++   ++ ++  p++   l  la+l++ +++   Ae   +++ e+ ++   e + 
  gi|330508766|ref|YP_004385194.1| 268 NLAGLYYSMGRYSDAEPLYRKAIENWGKSLGEDHPAYAQSLNNLAELYRSMGRYSDAEPLYRKATEIRRKSlgEDHP 344
                                       567788888************************************************************95445555 PP

                          TPR_MalT 160 al.dayvllarialaqGdleeAetllekaeelares 194
                                        + +++  la  +++ G+ ++Ae l+++a+e  r+s
  gi|330508766|ref|YP_004385194.1| 345 DYsQSLNNLALMYYSIGRYSDAEPLFRQATEIQRKS 380
                                       5547999***********************998876 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 1.8e-07
                          TPR_MalT  82 allqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql..e 156
                                       +l  +ae+++  Gr  +A+ +++qa++  +++ ++  p +   l  la l++ +++   Ae   +++ e+ ++   e
  gi|330508766|ref|YP_004385194.1| 391 SLNNLAELYRSMGRYSDAEPLFRQATEIWRKSLGEDHPEYAASLNNLAVLYRSMGRYSDAEPLFRQATEIWRKSlgE 467
                                       667899999999**********************9999999999999**********************99995433 PP

                          TPR_MalT 157 peaal.dayvllarialaqGdleeAetllekaeelare 193
                                        +      +  la+++ + G+ ++Ae l+++a+e  r+
  gi|330508766|ref|YP_004385194.1| 468 DHPNCaTGLNNLAELYRSVGRYSDAEPLFRQATEIWRK 505
                                       3333315777899999999********99999988765 PP

  == domain 5  score: 39.6 bits;  conditional E-value: 8.6e-13
                          TPR_MalT  34 ddllariaatavlGeasllqGdleaAlqalqeaeklarqa...dslhvallallqqaeilvaqGrLheAletyeqal 107
                                       +d+++ +a + +l+  +   G+  +A+  +++a +++r+    d+++  ++ l  +ae+++  Gr  +A+ +++qa+
  gi|330508766|ref|YP_004385194.1| 425 EDHPEYAASLNNLAVLYRSMGRYSDAEPLFRQATEIWRKSlgeDHPN-CATGLNNLAELYRSVGRYSDAEPLFRQAT 500
                                       57777778888899999999***************985541114444.77888899********************* PP

                          TPR_MalT 108 qlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql..epeaald.ayvllarialaqGdleeAe 181
                                       +  +++ ++  p +   l  +a+l++ + +   Ae   +++ e+ ++   + +  ++ ++  la ++ + G+ +eAe
  gi|330508766|ref|YP_004385194.1| 501 EIWRKSLGEDHPDYAASLNNRAELYRSMSRYNDAESLFRQATEIWRKSlgGDHPNYAtSLNNLALVYDSMGRYSEAE 577
                                       **********************************************9446666666449999*************** PP

                          TPR_MalT 182 tllekaeelaresn..fhvdwlanaeevr.vrlwlaqgdlaaaerwleaae...lpsdddnhfle.lelrnlarvll 251
                                        l+++a+e  r+s    h d  + +     ++     g+ ++ae++ ++a+   ++s + +h  + + l nla ++ 
  gi|330508766|ref|YP_004385194.1| 578 PLFRQATEIRRKSLgrDHPDYAQSLNNLAgLY--YSMGRYSDAEPLFRQATeiwRKSLGEDHPDYaQSLNNLAVLYR 652
                                       *********99875436777766656655254..4799999999999999534344555444433045688999999 PP

                          TPR_MalT 252 algrydeAleller 265
                                         gry++A+ l ++
  gi|330508766|ref|YP_004385194.1| 653 SMGRYSDAEPLFRQ 666
                                       99***999987655 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       9.3   4.4e+03      14      23 ..      24      33 ..      23      33 .. 0.81
   2 ?    4.6   0.0     0.069        33      13      32 ..      65      82 ..      59      84 .. 0.87
   3 !   11.8   0.0   0.00039      0.18       7      24 ..     101     118 ..      97     121 .. 0.90
   4 ?    5.2   0.0     0.047        22      15      33 ..     151     167 ..     144     169 .. 0.89
   5 ?    1.3   0.0      0.76   3.6e+02      13      26 ..     191     202 ..     182     205 .. 0.80
   6 !    8.1   0.0    0.0056       2.6       7      33 ..     227     251 ..     223     253 .. 0.87
   7 !    7.5   0.0    0.0087       4.1       7      27 ..     269     287 ..     265     289 .. 0.87
   8 ?    2.9   0.0      0.24   1.2e+02      13      33 ..     317     335 ..     311     337 .. 0.83
   9 !    9.7   0.0    0.0018      0.85       7      33 ..     353     377 ..     349     379 .. 0.90
  10 ?    4.1   0.0       0.1        48      13      32 ..     401     418 ..     395     419 .. 0.87
  11 ?    4.7   0.0     0.067        32      13      32 ..     443     460 ..     434     461 .. 0.83
  12 ?    1.7   0.0      0.56   2.6e+02      15      32 ..     487     502 ..     480     503 .. 0.88
  13 ?    1.4   0.0       0.7   3.3e+02      16      32 ..     530     544 ..     525     545 .. 0.87
  14 !    8.1   0.0    0.0056       2.6       7      33 ..     563     587 ..     559     589 .. 0.87
  15 !   10.8   0.0   0.00083      0.39       7      32 ..     605     628 ..     601     629 .. 0.88
  16 ?    6.3   0.0      0.02       9.4      13      33 ..     653     671 ..     644     673 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.3
                                      TT-HHHHHHH CS
                             TPR_3 14 kkkyqeArel 23
                                       ++y +A+ +
  gi|330508766|ref|YP_004385194.1| 24 DGNYIQAIAF 33
                                      59*****965 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.069
                                      HTT-HHHHHHH..HHHHHHH CS
                             TPR_3 13 nkkkyqeArelfsYallail 32
                                      ++++y++A+ l  ++++a +
  gi|330508766|ref|YP_004385194.1| 65 SMGRYNDAEPL--FRQAAEI 82
                                      69*********..99*9976 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00039
                                       HHHHHHHTT-HHHHHHH. CS
                             TPR_3   7 yAaefynkkkyqeArelf 24 
                                       +A ++y++++y++A+ lf
  gi|330508766|ref|YP_004385194.1| 101 LALVYYSMGRYDDAEPLF 118
                                       7*************9884 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.047
                                       T-HHHHHHH..HHHHHHH- CS
                             TPR_3  15 kkyqeArelfsYallaild 33 
                                       ++y+eA+ l  +++++ ++
  gi|330508766|ref|YP_004385194.1| 151 GRYSEAERL--FRQATEIR 167
                                       89*******..99***997 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.76
                                       HTT-HHHHHHH..H CS
                             TPR_3  13 nkkkyqeArelfsY 26 
                                       ++++y+eA+ l  +
  gi|330508766|ref|YP_004385194.1| 191 SMGRYNEAEPL--F 202
                                       79******999..4 PP

  == domain 6  score: 8.1 bits;  conditional E-value: 0.0056
                                       HHHHHHHTT-HHHHHHH..HHHHHHH- CS
                             TPR_3   7 yAaefynkkkyqeArelfsYallaild 33 
                                       +A ++ ++++y+eA+ l  +++++ ++
  gi|330508766|ref|YP_004385194.1| 227 LALVYDSMGRYSEAEPL--FRQATEIR 251
                                       6777889**********..99***997 PP

  == domain 7  score: 7.5 bits;  conditional E-value: 0.0087
                                       HHHHHHHTT-HHHHHHH..HH CS
                             TPR_3   7 yAaefynkkkyqeArelfsYa 27 
                                       +A  +y++++y++A+ l  Y+
  gi|330508766|ref|YP_004385194.1| 269 LAGLYYSMGRYSDAEPL--YR 287
                                       5668***********99..75 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.24
                                       HTT-HHHHHHH..HHHHHHH- CS
                             TPR_3  13 nkkkyqeArelfsYallaild 33 
                                       ++++y++A+ l  Y+ ++ ++
  gi|330508766|ref|YP_004385194.1| 317 SMGRYSDAEPL--YRKATEIR 335
                                       69*********..98887776 PP

  == domain 9  score: 9.7 bits;  conditional E-value: 0.0018
                                       HHHHHHHTT-HHHHHHH..HHHHHHH- CS
                             TPR_3   7 yAaefynkkkyqeArelfsYallaild 33 
                                       +A  +y+ ++y++A+ l  +++++ ++
  gi|330508766|ref|YP_004385194.1| 353 LALMYYSIGRYSDAEPL--FRQATEIQ 377
                                       7999*************..99***998 PP

  == domain 10  score: 4.1 bits;  conditional E-value: 0.1
                                       HTT-HHHHHHH..HHHHHHH CS
                             TPR_3  13 nkkkyqeArelfsYallail 32 
                                       ++++y++A+ l  +++++ +
  gi|330508766|ref|YP_004385194.1| 401 SMGRYSDAEPL--FRQATEI 418
                                       69*********..9999975 PP

  == domain 11  score: 4.7 bits;  conditional E-value: 0.067
                                       HTT-HHHHHHH..HHHHHHH CS
                             TPR_3  13 nkkkyqeArelfsYallail 32 
                                       ++++y++A+ l  +++++ +
  gi|330508766|ref|YP_004385194.1| 443 SMGRYSDAEPL--FRQATEI 460
                                       79*********..9999975 PP

  == domain 12  score: 1.7 bits;  conditional E-value: 0.56
                                       T-HHHHHHH..HHHHHHH CS
                             TPR_3  15 kkyqeArelfsYallail 32 
                                       ++y++A+ l  +++++ +
  gi|330508766|ref|YP_004385194.1| 487 GRYSDAEPL--FRQATEI 502
                                       89*******..9999975 PP

  == domain 13  score: 1.4 bits;  conditional E-value: 0.7
                                       -HHHHHHH..HHHHHHH CS
                             TPR_3  16 kyqeArelfsYallail 32 
                                       +y++A+ l  +++++ +
  gi|330508766|ref|YP_004385194.1| 530 RYNDAESL--FRQATEI 544
                                       8*******..99*9975 PP

  == domain 14  score: 8.1 bits;  conditional E-value: 0.0056
                                       HHHHHHHTT-HHHHHHH..HHHHHHH- CS
                             TPR_3   7 yAaefynkkkyqeArelfsYallaild 33 
                                       +A ++ ++++y+eA+ l  +++++ ++
  gi|330508766|ref|YP_004385194.1| 563 LALVYDSMGRYSEAEPL--FRQATEIR 587
                                       6777889**********..99***997 PP

  == domain 15  score: 10.8 bits;  conditional E-value: 0.00083
                                       HHHHHHHTT-HHHHHHH..HHHHHHH CS
                             TPR_3   7 yAaefynkkkyqeArelfsYallail 32 
                                       +A  +y++++y++A+ l  +++++ +
  gi|330508766|ref|YP_004385194.1| 605 LAGLYYSMGRYSDAEPL--FRQATEI 628
                                       5668*************..9999975 PP

  == domain 16  score: 6.3 bits;  conditional E-value: 0.02
                                       HTT-HHHHHHH..HHHHHHH- CS
                             TPR_3  13 nkkkyqeArelfsYallaild 33 
                                       ++++y++A+ l  +++++ ++
  gi|330508766|ref|YP_004385194.1| 653 SMGRYSDAEPL--FRQATEIR 671
                                       79*********..99***997 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1     0.008       3.8       7      33 ..      59      85 ..      53      96 .. 0.86
   2 ?    4.6   0.0      0.15        72       7      31 ..     101     125 ..      98     130 .. 0.84
   3 !    9.5   0.2    0.0041       1.9       7      31 ..     143     167 ..     140     181 .. 0.86
   4 !    8.9   0.0    0.0065       3.1       7      31 ..     185     209 ..     179     222 .. 0.87
   5 ?    6.6   0.0     0.036        17       7      30 ..     227     250 ..     224     262 .. 0.87
   6 !    9.6   0.0    0.0039       1.9       7      35 ..     269     297 ..     265     308 .. 0.82
   7 !    9.1   0.1    0.0056       2.6       7      30 ..     311     334 ..     305     346 .. 0.87
   8 ?    6.1   0.0      0.05        24       7      43 ..     353     390 ..     349     392 .. 0.83
   9 !    9.6   0.1    0.0037       1.7       7      33 ..     395     421 ..     389     434 .. 0.84
  10 ?    6.8   0.0      0.03        14       7      31 ..     437     461 ..     431     469 .. 0.87
  11 ?    8.1   0.1     0.011       5.4       7      31 ..     479     503 ..     476     517 .. 0.85
  12 ?    2.8   0.1      0.57   2.7e+02       7      31 ..     521     545 ..     513     554 .. 0.76
  13 ?    6.8   0.0      0.03        14       7      31 ..     563     587 ..     560     601 .. 0.84
  14 ?    7.4   0.0     0.019         9       7      32 ..     605     630 ..     599     643 .. 0.84
  15 ?    6.3   0.0     0.044        21       7      30 ..     647     670 ..     641     682 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.008
                            TPR_14  7 laeallalGdpdeAiallrralalaPd 33
                                      lae+++  G++ +A+ l+r+a + + +
  gi|330508766|ref|YP_004385194.1| 59 LAELYRSMGRYNDAEPLFRQAAEICRK 85
                                      89*******************997654 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.15
                            TPR_14   7 laeallalGdpdeAiallrralala 31 
                                       la +++  G++d+A+ l+ ++ + +
  gi|330508766|ref|YP_004385194.1| 101 LALVYYSMGRYDDAEPLFCQVTEIW 125
                                       899*************997777665 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0041
                            TPR_14   7 laeallalGdpdeAiallrralala 31 
                                       lae+++  G++ eA++l+r+a +  
  gi|330508766|ref|YP_004385194.1| 143 LAELYRSIGRYSEAERLFRQATEIR 167
                                       89*******************9854 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0065
                            TPR_14   7 laeallalGdpdeAiallrralala 31 
                                       la +++  G++ eA+ l+r+a++ +
  gi|330508766|ref|YP_004385194.1| 185 LAILYRSMGRYNEAEPLFRKAIEIW 209
                                       899*******************965 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.036
                            TPR_14   7 laeallalGdpdeAiallrralal 30 
                                       la ++   G++ eA+ l+r+a + 
  gi|330508766|ref|YP_004385194.1| 227 LALVYDSMGRYSEAEPLFRQATEI 250
                                       79999****************985 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.0039
                            TPR_14   7 laeallalGdpdeAiallrralalaPdda 35 
                                       la +++  G++ +A+ l+r+a++ + +++
  gi|330508766|ref|YP_004385194.1| 269 LAGLYYSMGRYSDAEPLYRKAIENWGKSL 297
                                       7999*******************877665 PP

  == domain 7  score: 9.1 bits;  conditional E-value: 0.0056
                            TPR_14   7 laeallalGdpdeAiallrralal 30 
                                       lae+++  G++ +A+ l+r+a + 
  gi|330508766|ref|YP_004385194.1| 311 LAELYRSMGRYSDAEPLYRKATEI 334
                                       89*******************985 PP

  == domain 8  score: 6.1 bits;  conditional E-value: 0.05
                            TPR_14   7 laeallalGdpdeAiallrralalaPdda.eawlllaq 43 
                                       la  ++  G++ +A+ l+r+a + + +++ ea+  +aq
  gi|330508766|ref|YP_004385194.1| 353 LALMYYSIGRYSDAEPLFRQATEIQRKSLgEAHPDYAQ 390
                                       67788999***************877776577777776 PP

  == domain 9  score: 9.6 bits;  conditional E-value: 0.0037
                            TPR_14   7 laeallalGdpdeAiallrralalaPd 33 
                                       lae+++  G++ +A+ l+r+a + + +
  gi|330508766|ref|YP_004385194.1| 395 LAELYRSMGRYSDAEPLFRQATEIWRK 421
                                       89*******************996544 PP

  == domain 10  score: 6.8 bits;  conditional E-value: 0.03
                            TPR_14   7 laeallalGdpdeAiallrralala 31 
                                       la +++  G++ +A+ l+r+a + +
  gi|330508766|ref|YP_004385194.1| 437 LAVLYRSMGRYSDAEPLFRQATEIW 461
                                       788999***************9876 PP

  == domain 11  score: 8.1 bits;  conditional E-value: 0.011
                            TPR_14   7 laeallalGdpdeAiallrralala 31 
                                       lae+++  G++ +A+ l+r+a + +
  gi|330508766|ref|YP_004385194.1| 479 LAELYRSVGRYSDAEPLFRQATEIW 503
                                       89*******************9965 PP

  == domain 12  score: 2.8 bits;  conditional E-value: 0.57
                            TPR_14   7 laeallalGdpdeAiallrralala 31 
                                       +ae+++   ++ +A+ l+r+a + +
  gi|330508766|ref|YP_004385194.1| 521 RAELYRSMSRYNDAESLFRQATEIW 545
                                       6778888888888888888887755 PP

  == domain 13  score: 6.8 bits;  conditional E-value: 0.03
                            TPR_14   7 laeallalGdpdeAiallrralala 31 
                                       la ++   G++ eA+ l+r+a +  
  gi|330508766|ref|YP_004385194.1| 563 LALVYDSMGRYSEAEPLFRQATEIR 587
                                       79999****************9854 PP

  == domain 14  score: 7.4 bits;  conditional E-value: 0.019
                            TPR_14   7 laeallalGdpdeAiallrralalaP 32 
                                       la +++  G++ +A+ l+r+a + + 
  gi|330508766|ref|YP_004385194.1| 605 LAGLYYSMGRYSDAEPLFRQATEIWR 630
                                       8999*****************99654 PP

  == domain 15  score: 6.3 bits;  conditional E-value: 0.044
                            TPR_14   7 laeallalGdpdeAiallrralal 30 
                                       la +++  G++ +A+ l+r+a + 
  gi|330508766|ref|YP_004385194.1| 647 LAVLYRSMGRYSDAEPLFRQATEI 670
                                       788999***************884 PP

>> DUF630  Protein of unknown function (DUF630)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       4.3     2e+03      38      50 ..      49      61 ..      47      65 .. 0.87
   2 ?    4.7   0.0     0.074        35      25      49 ..      77     102 ..      73     104 .. 0.81
   3 ?    6.8   0.1     0.016       7.3      21      49 ..     157     186 ..     154     191 .. 0.85
   4 ?    4.2   0.0       0.1        48      25      49 ..     203     228 ..     197     241 .. 0.83
   5 ?    5.8   0.0     0.033        15      24      49 ..     244     270 ..     239     272 .. 0.82
   6 ?    5.5   0.0     0.041        19      30      50 ..     293     313 ..     284     318 .. 0.79
   7 ?    4.8   0.0     0.068        32      30      49 ..     335     354 ..     326     357 .. 0.82
   8 !   12.0   0.0   0.00038      0.18      25      50 ..     371     397 ..     367     402 .. 0.84
   9 ?    4.4   0.0      0.09        42      25      49 ..     413     438 ..     409     444 .. 0.82
  10 ?    3.1   0.0      0.24   1.1e+02      25      49 ..     497     522 ..     493     532 .. 0.82
  11 ?    2.3   0.0      0.41   1.9e+02      23      49 ..     537     564 ..     533     577 .. 0.82
  12 ?    6.6   0.0     0.018       8.4      23      49 ..     579     606 ..     574     608 .. 0.82
  13 ?    6.1   0.0     0.026        12      25      49 ..     623     648 ..     619     654 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.3
                            DUF630 38 HaaYlqSLrnvga 50
                                      H +Y++SL+n ++
  gi|330508766|ref|YP_004385194.1| 49 HPDYAASLNNLAE 61
                                      889******9875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.074
                            DUF630  25 kqAve.aRyaLAaaHaaYlqSLrnvg 49 
                                       +qA+e  R++L + H +Y+ SL+n +
  gi|330508766|ref|YP_004385194.1|  77 RQAAEiCRKSLGEDHPDYATSLNNLA 102
                                       55555379***************986 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.016
                            DUF630  21 krllkqAve.aRyaLAaaHaaYlqSLrnvg 49 
                                        rl +qA e +R++L + H +Y++SL+n +
  gi|330508766|ref|YP_004385194.1| 157 ERLFRQATEiRRKSLGEDHPNYAASLNNLA 186
                                       58899999845678*************987 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.1
                            DUF630  25 kqAve.aRyaLAaaHaaYlqSLrnvg 49 
                                       ++A+e  R++L + H +Y+ SL+n +
  gi|330508766|ref|YP_004385194.1| 203 RKAIEiWRRSLGEDHPNYATSLNNLA 228
                                       566663699**************987 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.033
                            DUF630  24 lkqAve.aRyaLAaaHaaYlqSLrnvg 49 
                                        +qA e +R++L + H +Y qSL+n +
  gi|330508766|ref|YP_004385194.1| 244 FRQATEiRRKSLGEDHPDYSQSLNNLA 270
                                       67777735789*************976 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.041
                            DUF630  30 aRyaLAaaHaaYlqSLrnvga 50 
                                         ++L + H aY+qSL+n ++
  gi|330508766|ref|YP_004385194.1| 293 WGKSLGEDHPAYAQSLNNLAE 313
                                       46789999*********9875 PP

  == domain 7  score: 4.8 bits;  conditional E-value: 0.068
                            DUF630  30 aRyaLAaaHaaYlqSLrnvg 49 
                                       +R++L + H +Y qSL+n +
  gi|330508766|ref|YP_004385194.1| 335 RRKSLGEDHPDYSQSLNNLA 354
                                       7899*************986 PP

  == domain 8  score: 12.0 bits;  conditional E-value: 0.00038
                            DUF630  25 kqAve.aRyaLAaaHaaYlqSLrnvga 50 
                                       +qA e +R++L +aH +Y+qSL+n ++
  gi|330508766|ref|YP_004385194.1| 371 RQATEiQRKSLGEAHPDYAQSLNNLAE 397
                                       66665489***************9885 PP

  == domain 9  score: 4.4 bits;  conditional E-value: 0.09
                            DUF630  25 kqAve.aRyaLAaaHaaYlqSLrnvg 49 
                                       +qA e  R++L + H +Y++SL+n +
  gi|330508766|ref|YP_004385194.1| 413 RQATEiWRKSLGEDHPEYAASLNNLA 438
                                       5555536999*************987 PP

  == domain 10  score: 3.1 bits;  conditional E-value: 0.24
                            DUF630  25 kqAve.aRyaLAaaHaaYlqSLrnvg 49 
                                       +qA e  R++L + H +Y++SL+n +
  gi|330508766|ref|YP_004385194.1| 497 RQATEiWRKSLGEDHPDYAASLNNRA 522
                                       5555536999************9865 PP

  == domain 11  score: 2.3 bits;  conditional E-value: 0.41
                            DUF630  23 llkqAve.aRyaLAaaHaaYlqSLrnvg 49 
                                       l +qA e  R++L   H +Y+ SL+n +
  gi|330508766|ref|YP_004385194.1| 537 LFRQATEiWRKSLGGDHPNYATSLNNLA 564
                                       566666646999999**********987 PP

  == domain 12  score: 6.6 bits;  conditional E-value: 0.018
                            DUF630  23 llkqAve.aRyaLAaaHaaYlqSLrnvg 49 
                                       l +qA e +R++L   H +Y+qSL+n +
  gi|330508766|ref|YP_004385194.1| 579 LFRQATEiRRKSLGRDHPDYAQSLNNLA 606
                                       567777735789*************976 PP

  == domain 13  score: 6.1 bits;  conditional E-value: 0.026
                            DUF630  25 kqAve.aRyaLAaaHaaYlqSLrnvg 49 
                                       +qA e  R++L + H +Y+qSL+n +
  gi|330508766|ref|YP_004385194.1| 623 RQATEiWRKSLGEDHPDYAQSLNNLA 648
                                       5555536999*************987 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.16        75       2      26 .]      54      78 ..      53      78 .. 0.90
   2 ?    5.9   0.0     0.051        24       4      23 ..      98     117 ..      95     118 .. 0.87
   3 ?    5.0   0.0       0.1        47       5      26 .]     141     162 ..     137     162 .. 0.89
   4 ?    3.5   0.0       0.3   1.4e+02       2      25 ..     180     203 ..     179     204 .. 0.89
   5 ?    4.0   0.0      0.22     1e+02       4      26 .]     224     246 ..     221     246 .. 0.90
   6 ?   -0.3   0.0       5.3   2.5e+03       5      25 ..     267     287 ..     264     288 .. 0.86
   7 ?    4.0   0.0      0.21        99       2      25 ..     306     329 ..     305     330 .. 0.88
   8 ?   -0.7   0.0       7.3   3.4e+03       6      26 .]     352     372 ..     348     372 .. 0.83
   9 ?    5.5   0.0     0.073        34       2      26 .]     390     414 ..     389     414 .. 0.91
  10 ?    4.1   0.0       0.2        93       2      26 .]     432     456 ..     431     456 .. 0.90
  11 ?    5.0   0.0       0.1        49       4      26 .]     476     498 ..     473     498 .. 0.91
  12 ?    4.0   0.0      0.22     1e+02       4      26 .]     560     582 ..     557     582 .. 0.90
  13 ?    1.8   0.0       1.1   5.1e+02       2      26 .]     600     624 ..     599     624 .. 0.89
  14 ?    4.1   0.0      0.19        91       2      26 .]     642     666 ..     641     666 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.16
                             TPR_4  2 rallaLArallalGdldeAraller 26
                                      + l +LA+++   G++ +A+ l+++
  gi|330508766|ref|YP_004385194.1| 54 ASLNNLAELYRSMGRYNDAEPLFRQ 78
                                      56789*****************997 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.051
                             TPR_4   4 llaLArallalGdldeAral 23 
                                       l +LA +++  G++d+A+ l
  gi|330508766|ref|YP_004385194.1|  98 LNNLALVYYSMGRYDDAEPL 117
                                       569**************976 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.1
                             TPR_4   5 laLArallalGdldeAraller 26 
                                        +LA+++   G++ eA++l+++
  gi|330508766|ref|YP_004385194.1| 141 NNLAELYRSIGRYSEAERLFRQ 162
                                       6899999999**********97 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.3
                             TPR_4   2 rallaLArallalGdldeAralle 25 
                                       + l +LA ++   G++ eA+ l++
  gi|330508766|ref|YP_004385194.1| 180 ASLNNLAILYRSMGRYNEAEPLFR 203
                                       56789***************9998 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.22
                             TPR_4   4 llaLArallalGdldeAraller 26 
                                       l +LA ++   G++ eA+ l+++
  gi|330508766|ref|YP_004385194.1| 224 LNNLALVYDSMGRYSEAEPLFRQ 246
                                       569*****************997 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 5.3
                             TPR_4   5 laLArallalGdldeAralle 25 
                                        +LA +++  G++ +A+ l +
  gi|330508766|ref|YP_004385194.1| 267 NNLAGLYYSMGRYSDAEPLYR 287
                                       5899999999*******9987 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.21
                             TPR_4   2 rallaLArallalGdldeAralle 25 
                                       + l +LA+++   G++ +A+ l +
  gi|330508766|ref|YP_004385194.1| 306 QSLNNLAELYRSMGRYSDAEPLYR 329
                                       56789***************9988 PP

  == domain 8  score: -0.7 bits;  conditional E-value: 7.3
                             TPR_4   6 aLArallalGdldeAraller 26 
                                       +LA  ++  G++ +A+ l+++
  gi|330508766|ref|YP_004385194.1| 352 NLALMYYSIGRYSDAEPLFRQ 372
                                       7888888889******99997 PP

  == domain 9  score: 5.5 bits;  conditional E-value: 0.073
                             TPR_4   2 rallaLArallalGdldeAraller 26 
                                       + l +LA+++   G++ +A+ l+++
  gi|330508766|ref|YP_004385194.1| 390 QSLNNLAELYRSMGRYSDAEPLFRQ 414
                                       56789*****************997 PP

  == domain 10  score: 4.1 bits;  conditional E-value: 0.2
                             TPR_4   2 rallaLArallalGdldeAraller 26 
                                       + l +LA ++   G++ +A+ l+++
  gi|330508766|ref|YP_004385194.1| 432 ASLNNLAVLYRSMGRYSDAEPLFRQ 456
                                       56789*****************997 PP

  == domain 11  score: 5.0 bits;  conditional E-value: 0.1
                             TPR_4   4 llaLArallalGdldeAraller 26 
                                       l +LA+++   G++ +A+ l+++
  gi|330508766|ref|YP_004385194.1| 476 LNNLAELYRSVGRYSDAEPLFRQ 498
                                       569*****************997 PP

  == domain 12  score: 4.0 bits;  conditional E-value: 0.22
                             TPR_4   4 llaLArallalGdldeAraller 26 
                                       l +LA ++   G++ eA+ l+++
  gi|330508766|ref|YP_004385194.1| 560 LNNLALVYDSMGRYSEAEPLFRQ 582
                                       569*****************997 PP

  == domain 13  score: 1.8 bits;  conditional E-value: 1.1
                             TPR_4   2 rallaLArallalGdldeAraller 26 
                                       + l +LA +++  G++ +A+ l+++
  gi|330508766|ref|YP_004385194.1| 600 QSLNNLAGLYYSMGRYSDAEPLFRQ 624
                                       56779999**************997 PP

  == domain 14  score: 4.1 bits;  conditional E-value: 0.19
                             TPR_4   2 rallaLArallalGdldeAraller 26 
                                       + l +LA ++   G++ +A+ l+++
  gi|330508766|ref|YP_004385194.1| 642 QSLNNLAVLYRSMGRYSDAEPLFRQ 666
                                       56789*****************997 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.01       4.9      59     124 ..      57     125 ..      46     148 .. 0.54
   2 !   19.7   0.0   9.7e-07   0.00046      40     184 ..     142     292 ..     128     299 .. 0.84
   3 !   21.3   0.0   3.2e-07   0.00015      39     181 ..     309     457 ..     295     468 .. 0.84
   4 !   21.9   0.0     2e-07   9.6e-05      38     181 ..     392     541 ..     381     551 .. 0.81
   5 !   16.8   0.0   7.4e-06    0.0035      41     180 ..     521     666 ..     488     675 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.01
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHHHT...-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                              SNAP  59 lkaAecqeklkekdeaanayveAakcykkv...speeAvealekAieiytekgrfrraAklkkeiaely 124
                                        ++Ae++++++  ++a   + +Aa++ +k+   +  + +++l++ + +y ++gr + a  l  ++ e+ 
  gi|330508766|ref|YP_004385194.1|  57 NNLAELYRSMGRYNDAEPLFRQAAEICRKSlgeDHPDYATSLNNLALVYYSMGRYDDAEPLFCQVTEIW 125
                                       445555555555555555555555555555444333344444444455555555555555555555555 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 9.7e-07
                                       HHHHHHHHTT-THHHHHHHHHHHHHHHH.TT-HH.HHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHT..T-HH CS
                              SNAP  40 qAAnayklakkweeAgeaflkaAecqek.lkekd.eaanayveAakcykkv.speeAvealekAieiytek..grfr 111
                                       + A++y+   +++eA + f +a e+++k l+e++ + a ++ + a  y++  + +eA   ++kAiei+ ++  +   
  gi|330508766|ref|YP_004385194.1| 142 NLAELYRSIGRYSEAERLFRQATEIRRKsLGEDHpNYAASLNNLAILYRSMgRYNEAEPLFRKAIEIWRRSlgEDHP 218
                                       56999***********************97766524566666655566655599*************9875334556 PP

                                       HHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT..-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHT CS
                              SNAP 112 raAklkkeiaelyekelgdlekAieaYekAaelyeqee..akalankcllkvAelsaelekyekAieiyekvakk 184
                                       + A+  +++a +y++  g++++A   +++A e+ ++     + + ++ l ++A l+ ++++y++A  +y k +++
  gi|330508766|ref|YP_004385194.1| 219 NYATSLNNLALVYDSM-GRYSEAEPLFRQATEIRRKSLgeDHPDYSQSLNNLAGLYYSMGRYSDAEPLYRKAIEN 292
                                       7788899*******99.****************988753378899************************999876 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 3.2e-07
                                       HHHHHHHHHTT-THHHHHHHHHHHHHHHH.TT-HH.HHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHT.T-HH CS
                              SNAP  39 eqAAnayklakkweeAgeaflkaAecqek.lkekd.eaanayveAakcykkv.speeAvealekAieiytek.grfr 111
                                       ++ A++y+   ++++A   + ka e+++k l+e++ + ++++ + a +y +  + ++A   +++A ei  ++ g  +
  gi|330508766|ref|YP_004385194.1| 309 NNLAELYRSMGRYSDAEPLYRKATEIRRKsLGEDHpDYSQSLNNLALMYYSIgRYSDAEPLFRQATEIQRKSlGEAH 385
                                       566999***********************96665538899999988888777699************9655435543 PP

                                       .HHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT..-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              SNAP 112 .raAklkkeiaelyekelgdlekAieaYekAaelyeqee..akalankcllkvAelsaelekyekAieiyekv 181
                                          A+  +++aely +  g++++A   +++A e++++     + +    l ++A l+ ++++y++A  ++ + 
  gi|330508766|ref|YP_004385194.1| 386 pDYAQSLNNLAELYRSM-GRYSDAEPLFRQATEIWRKSLgeDHPEYAASLNNLAVLYRSMGRYSDAEPLFRQA 457
                                       2679***********99.*****************98753366677888999**************9999875 PP

  == domain 4  score: 21.9 bits;  conditional E-value: 2e-07
                                       HHHHHHHHHHTT-THHHHHHHHHHHHHHHH.TT-HH.HHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHT..T- CS
                              SNAP  38 yeqAAnayklakkweeAgeaflkaAecqek.lkekd.eaanayveAakcykkv.speeAvealekAieiytek..gr 109
                                       +++ A++y+   ++++A   f +a e+ +k l+e++ e a ++ + a  y++  + ++A   +++A ei+ ++  + 
  gi|330508766|ref|YP_004385194.1| 392 LNNLAELYRSMGRYSDAEPLFRQATEIWRKsLGEDHpEYAASLNNLAVLYRSMgRYSDAEPLFRQATEIWRKSlgED 468
                                       55668999999999999999999999998886665536777777777777776699999999999999998754356 PP

                                       HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT..-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              SNAP 110 frraAklkkeiaelyekelgdlekAieaYekAaelyeqee..akalankcllkvAelsaelekyekAieiyekv 181
                                         + A+  +++aely +  g++++A   +++A e++++     + +    l + Ael+ ++ +y++A  ++ + 
  gi|330508766|ref|YP_004385194.1| 469 HPNCATGLNNLAELYRSV-GRYSDAEPLFRQATEIWRKSLgeDHPDYAASLNNRAELYRSMSRYNDAESLFRQA 541
                                       778999999999999998.9999999999999999998753356677788889999999999999999999875 PP

  == domain 5  score: 16.8 bits;  conditional E-value: 7.4e-06
                                       HHHHHHHTT-THHHHHHHHHHHHHHHH..TT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHH.TT-HH.H CS
                              SNAP  41 AAnayklakkweeAgeaflkaAecqek..lkekdeaanayveAakcykkv.speeAvealekAieiyte.kgrfr.r 112
                                        A++y+   ++++A + f +a e+ +k   +++ + a+++ + a +y +  + +eA   +++A ei  +  gr +  
  gi|330508766|ref|YP_004385194.1| 521 RAELYRSMSRYNDAESLFRQATEIWRKslGGDHPNYATSLNNLALVYDSMgRYSEAEPLFRQATEIRRKsLGRDHpD 597
                                       34445555555555555555555444442333334444444444444444344455555555555432212332213 PP

                                       HHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT..-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              SNAP 113 aAklkkeiaelyekelgdlekAieaYekAaelyeqee..akalankcllkvAelsaelekyekAieiyek 180
                                        A+  +++a ly +  g++++A   +++A e++++     + +  + l ++A l+ ++++y++A  ++ +
  gi|330508766|ref|YP_004385194.1| 598 YAQSLNNLAGLYYSM-GRYSDAEPLFRQATEIWRKSLgeDHPDYAQSLNNLAVLYRSMGRYSDAEPLFRQ 666
                                       344444445554444.667777777777777776654225556666777777777777777777666665 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.14        65       5      27 ..      58      80 ..      58      83 .. 0.89
   2 ?    3.8   0.0      0.23   1.1e+02       5      19 ..     100     114 ..     100     125 .. 0.88
   3 ?    6.9   0.1     0.024        11       5      28 ..     142     165 ..     142     170 .. 0.88
   4 ?    6.2   0.0     0.038        18       5      29 ..     184     208 ..     184     212 .. 0.90
   5 ?    4.0   0.0       0.2        96       5      28 ..     226     249 ..     226     254 .. 0.88
   6 ?    6.9   0.0     0.023        11       6      33 .]     269     296 ..     268     296 .. 0.89
   7 ?    5.8   0.1     0.051        24       5      28 ..     310     333 ..     307     338 .. 0.89
   8 ?    2.5   0.0      0.61   2.9e+02       5      28 ..     352     375 ..     349     380 .. 0.88
   9 ?    6.0   0.0     0.046        22       5      28 ..     394     417 ..     391     422 .. 0.88
  10 ?    5.0   0.0     0.096        45       5      28 ..     436     459 ..     436     464 .. 0.87
  11 ?    2.4   0.0      0.65   3.1e+02       5      28 ..     478     501 ..     478     506 .. 0.84
  12 ?    2.4   0.1      0.63     3e+02       6      28 ..     521     543 ..     520     548 .. 0.86
  13 ?    4.0   0.0       0.2        96       5      28 ..     562     585 ..     562     590 .. 0.88
  14 ?    2.5   0.0      0.59   2.8e+02       6      28 ..     605     627 ..     604     632 .. 0.84
  15 ?    4.5   0.0      0.14        66       5      27 ..     646     668 ..     643     671 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.14
                                      HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  5 klalsyrklgdtdkAlealerli 27
                                      +la++yr++g++ +A  ++++  
  gi|330508766|ref|YP_004385194.1| 58 NLAELYRSMGRYNDAEPLFRQAA 80
                                      69*************99999875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkA 19 
                                       +lal y+++g++d+A
  gi|330508766|ref|YP_004385194.1| 100 NLALVYYSMGRYDDA 114
                                       69***********99 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                       +la++yr+ g++++A +++++  +
  gi|330508766|ref|YP_004385194.1| 142 NLAELYRSIGRYSEAERLFRQATE 165
                                       69******88**********9876 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.038
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlike 29 
                                       +la +yr++g++ +A  ++++ i+ 
  gi|330508766|ref|YP_004385194.1| 184 NLAILYRSMGRYNEAEPLFRKAIEI 208
                                       5899*****************9985 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                       +lal y ++g++++A  ++++  +
  gi|330508766|ref|YP_004385194.1| 226 NLALVYDSMGRYSEAEPLFRQATE 249
                                       59**************99999876 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPdS 33 
                                       la +y+++g++++A  ++++ i+++ +S
  gi|330508766|ref|YP_004385194.1| 269 LAGLYYSMGRYSDAEPLYRKAIENWGKS 296
                                       6778*******************98766 PP

  == domain 7  score: 5.8 bits;  conditional E-value: 0.051
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                       +la++yr++g++++A  ++++  +
  gi|330508766|ref|YP_004385194.1| 310 NLAELYRSMGRYSDAEPLYRKATE 333
                                       69**************99999876 PP

  == domain 8  score: 2.5 bits;  conditional E-value: 0.61
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                       +lal y++ g++++A  ++++  +
  gi|330508766|ref|YP_004385194.1| 352 NLALMYYSIGRYSDAEPLFRQATE 375
                                       699*****88*****999999866 PP

  == domain 9  score: 6.0 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                       +la++yr++g++++A  ++++  +
  gi|330508766|ref|YP_004385194.1| 394 NLAELYRSMGRYSDAEPLFRQATE 417
                                       69***************9999876 PP

  == domain 10  score: 5.0 bits;  conditional E-value: 0.096
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                       +la +yr++g++++A  ++++  +
  gi|330508766|ref|YP_004385194.1| 436 NLAVLYRSMGRYSDAEPLFRQATE 459
                                       599**************9999876 PP

  == domain 11  score: 2.4 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                       +la++yr+ g++++A  ++++  +
  gi|330508766|ref|YP_004385194.1| 478 NLAELYRSVGRYSDAEPLFRQATE 501
                                       59******66******99999876 PP

  == domain 12  score: 2.4 bits;  conditional E-value: 0.63
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                       +a++yr++ ++ +A  ++++  +
  gi|330508766|ref|YP_004385194.1| 521 RAELYRSMSRYNDAESLFRQATE 543
                                       799****99**********9877 PP

  == domain 13  score: 4.0 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                       +lal y ++g++++A  ++++  +
  gi|330508766|ref|YP_004385194.1| 562 NLALVYDSMGRYSEAEPLFRQATE 585
                                       59**************99999876 PP

  == domain 14  score: 2.5 bits;  conditional E-value: 0.59
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                       la +y+++g++++A  ++++  +
  gi|330508766|ref|YP_004385194.1| 605 LAGLYYSMGRYSDAEPLFRQATE 627
                                       6778***********99999876 PP

  == domain 15  score: 4.5 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerli 27 
                                       +la +yr++g++++A  ++++  
  gi|330508766|ref|YP_004385194.1| 646 NLAVLYRSMGRYSDAEPLFRQAT 668
                                       699************99999876 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.19        90      39      73 ..      51      85 ..      22      91 .. 0.83
   2 !    9.8   0.4    0.0017      0.82      36      73 ..     158     211 ..      47     217 .. 0.73
   3 !    7.7   0.7    0.0079       3.7      13      68 ..     219     290 ..     216     385 .. 0.62
   4 ?    6.3   0.0     0.021        10      12      73 ..     344     421 ..     338     426 .. 0.74
   5 !    9.0   0.0    0.0031       1.4      12      74 ..     386     464 ..     382     484 .. 0.85
   6 ?   -2.0   0.0       7.9   3.7e+03      46      73 ..     478     505 ..     469     516 .. 0.87
   7 ?    6.0   0.1     0.026        12      36      73 ..     536     589 ..     488     595 .. 0.74
   8 !   10.9   0.0   0.00077      0.36      12      73 ..     554     631 ..     551     637 .. 0.92
   9 ?    6.8   0.0     0.015       6.8      13      72 ..     597     672 ..     595     681 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.19
                            ANAPC5 39 syqyalLnlaslhadfghneeAvkaleeairlAre 73
                                       y  +l nla l  ++g +++A   ++ a ++ r+
  gi|330508766|ref|YP_004385194.1| 51 DYAASLNNLAELYRSMGRYNDAEPLFRQAAEICRK 85
                                      68888999******************999999987 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0017
                            ANAPC5  36 q................kksyqyalLnlaslhadfghneeAvkaleeairlAre 73 
                                       +                + +y  +l nla+l  ++g ++eA   ++ ai++ r 
  gi|330508766|ref|YP_004385194.1| 158 RlfrqateirrkslgedHPNYAASLNNLAILYRSMGRYNEAEPLFRKAIEIWRR 211
                                       044444444444555556789999999***************999999999775 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0079
                            ANAPC5  13 dYqqaldsLhryFDyvlsqnessq................kksyqyalLnlaslhadfghneeAvkaleeai 68 
                                       +Y ++l++L   +D +   +e +                 +  y  +l nla l +++g + +A    + ai
  gi|330508766|ref|YP_004385194.1| 219 NYATSLNNLALVYDSMGRYSEAEPlfrqateirrkslgedHPDYSQSLNNLAGLYYSMGRYSDAEPLYRKAI 290
                                       667777777777777666666665666677777777776644555555555555555555555443333333 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.021
                            ANAPC5  12 kdYqqaldsLhryFDyvlsqnessq.................kksyqyalLnlaslhadfghneeAvkaleeairlA 71 
                                        dY+q+l++L  ++ y+++  ++ +                 +  y  +l nla l  ++g + +A   ++ a+++ 
  gi|330508766|ref|YP_004385194.1| 344 PDYSQSLNNLALMY-YSIGRYSDAEplfrqateiqrkslgeaHPDYAQSLNNLAELYRSMGRYSDAEPLFRQATEIW 419
                                       57888888887766.44444444444677777788888887777888889999999999999999999999998887 PP

                            ANAPC5  72 re 73 
                                       r+
  gi|330508766|ref|YP_004385194.1| 420 RK 421
                                       75 PP

  == domain 5  score: 9.0 bits;  conditional E-value: 0.0031
                            ANAPC5  12 kdYqqaldsLhryFDyvlsqnessq................kksyqyalLnlaslhadfghneeAvkaleeairlAr 72 
                                        dY q+l++L + +  +   ++ +                 + +y  +l nla+l  ++g + +A   ++ a+++ r
  gi|330508766|ref|YP_004385194.1| 386 PDYAQSLNNLAELYRSMGRYSDAEPlfrqateiwrkslgedHPEYAASLNNLAVLYRSMGRYSDAEPLFRQATEIWR 462
                                       589999999999997666666655588999999999999988999999************************99988 PP

                            ANAPC5  73 en 74 
                                       ++
  gi|330508766|ref|YP_004385194.1| 463 KS 464
                                       75 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 7.9
                            ANAPC5  46 nlaslhadfghneeAvkaleeairlAre 73 
                                       nla l  + g + +A   ++ a+++ r+
  gi|330508766|ref|YP_004385194.1| 478 NLAELYRSVGRYSDAEPLFRQATEIWRK 505
                                       8999************999999999886 PP

  == domain 7  score: 6.0 bits;  conditional E-value: 0.026
                            ANAPC5  36 q................kksyqyalLnlaslhadfghneeAvkaleeairlAre 73 
                                       +                + +y ++l nla +  ++g + eA   ++ a+++ r+
  gi|330508766|ref|YP_004385194.1| 536 SlfrqateiwrkslggdHPNYATSLNNLALVYDSMGRYSEAEPLFRQATEIRRK 589
                                       244455556666666667789999999999999999999999999999999876 PP

  == domain 8  score: 10.9 bits;  conditional E-value: 0.00077
                            ANAPC5  12 kdYqqaldsLhryFDyvlsqnessq................kksyqyalLnlaslhadfghneeAvkaleeairlAr 72 
                                        +Y ++l++L   +D +   +e +                 +  y  +l nla l +++g + +A   ++ a+++ r
  gi|330508766|ref|YP_004385194.1| 554 PNYATSLNNLALVYDSMGRYSEAEPlfrqateirrkslgrdHPDYAQSLNNLAGLYYSMGRYSDAEPLFRQATEIWR 630
                                       58**************999999888999***********988899999************************99988 PP

                            ANAPC5  73 e 73 
                                       +
  gi|330508766|ref|YP_004385194.1| 631 K 631
                                       6 PP

  == domain 9  score: 6.8 bits;  conditional E-value: 0.015
                            ANAPC5  13 dYqqaldsLhryFDyvlsqnessq.................kksyqyalLnlaslhadfghneeAvkaleeairlAr 72 
                                       dY q+l++L   + y+++  ++ +                 +  y  +l nla+l  ++g + +A   ++ a+++ r
  gi|330508766|ref|YP_004385194.1| 597 DYAQSLNNLAGLY-YSMGRYSDAEplfrqateiwrkslgedHPDYAQSLNNLAVLYRSMGRYSDAEPLFRQATEIRR 672
                                       7888888888877.444444444457888888888888877778888899999999999999999999999998877 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.89   4.2e+02      12      29 ..      64      81 ..      54     117 .. 0.77
   2 ?    5.0   0.0      0.06        28      43      93 ..     142     198 ..      95     228 .. 0.53
   3 ?    5.3   0.0     0.047        22       8      28 ..     228     248 ..     221     251 .. 0.88
   4 !   13.6   0.2   0.00012     0.058       6      90 ..     268     363 ..     263     398 .. 0.64
   5 ?    4.9   0.0     0.062        29      10      64 ..     356     415 ..     347     422 .. 0.71
   6 ?    2.9   0.0      0.25   1.2e+02      13      63 ..     401     456 ..     390     465 .. 0.61
   7 ?    4.3   0.0       0.1        47      11      65 ..     441     500 ..     431     518 .. 0.70
   8 ?    1.6   0.0      0.68   3.2e+02      11      28 ..     483     500 ..     472     543 .. 0.84
   9 ?    5.4   0.0     0.043        20       8      28 ..     564     584 ..     558     594 .. 0.88
  10 ?    6.6   0.0     0.019         9       7      66 ..     605     669 ..     599     681 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.89
                             TPR_5 12 DstGhedkavplYrraLa 29
                                       s+G+ + a+pl+r+a +
  gi|330508766|ref|YP_004385194.1| 64 RSMGRYNDAEPLFRQAAE 81
                                      577888888888888754 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.06
                             TPR_5  43 qLassLRnlGeaeealaLLraeleapsdeldd......alaaflaLvLsdlgrerea 93 
                                        La   R +G+  ea++L r+ +e + + l +      a    la+   ++gr +ea
  gi|330508766|ref|YP_004385194.1| 142 NLAELYRSIGRYSEAERLFRQATEIRRKSLGEdhpnyaASLNNLAILYRSMGRYNEA 198
                                       577777777777777777776655443333211111113333445555555555554 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.047
                             TPR_5   8 agarDstGhedkavplYrraL 28 
                                       a + Ds+G+  +a+pl+r+a 
  gi|330508766|ref|YP_004385194.1| 228 ALVYDSMGRYSEAEPLFRQAT 248
                                       6789***************96 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 0.00012
                             TPR_5   6 eragarDstGhedkavplYrraLae.....GLagarrrratiqLassLRnlGeaeealaLLraeleapsdel..... 72 
                                       + ag   s+G+   a+plYr+a+++     G +     +    La   R +G+  +a+ L r+ +e + + l     
  gi|330508766|ref|YP_004385194.1| 268 NLAGLYYSMGRYSDAEPLYRKAIENwgkslGEDHPAYAQSLNNLAELYRSMGRYSDAEPLYRKATEIRRKSLgedhp 344
                                       5689999****************98655444555667788889****************999876654433310000 PP

                             TPR_5  73 ..ddalaaflaLvLsdlgre 90 
                                         +++l+  laL+  + gr 
  gi|330508766|ref|YP_004385194.1| 345 dySQSLN-NLALMYYSIGRY 363
                                       0033333.356666666664 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.062
                             TPR_5  10 arDstGhedkavplYrraLa...eGLagar..rrratiqLassLRnlGeaeealaLLrae 64 
                                       +  s+G+   a+pl+r+a +   + L +a+    +    La   R +G+  +a+ L r+ 
  gi|330508766|ref|YP_004385194.1| 356 MYYSIGRYSDAEPLFRQATEiqrKSLGEAHpdYAQSLNNLAELYRSMGRYSDAEPLFRQA 415
                                       5668999999******99763334454444115666778888888888888888887765 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.25
                             TPR_5  13 stGhedkavplYrraLa...eGLagarrr..ratiqLassLRnlGeaeealaLLra 63 
                                       s+G+   a+pl+r+a +   + L + +         La   R +G+  +a+ L r+
  gi|330508766|ref|YP_004385194.1| 401 SMGRYSDAEPLFRQATEiwrKSLGEDHPEyaASLNNLAVLYRSMGRYSDAEPLFRQ 456
                                       77888888888888865333444433332003334577777777777777766665 PP

  == domain 7  score: 4.3 bits;  conditional E-value: 0.1
                             TPR_5  11 rDstGhedkavplYrraLa...eGLagarrrrat..iqLassLRnlGeaeealaLLrael 65 
                                         s+G+   a+pl+r+a +   + L + +   at    La   R +G+  +a+ L r+ +
  gi|330508766|ref|YP_004385194.1| 441 YRSMGRYSDAEPLFRQATEiwrKSLGEDHPNCATglNNLAELYRSVGRYSDAEPLFRQAT 500
                                       567888888888888887533355555554444422578888888888888888777654 PP

  == domain 8  score: 1.6 bits;  conditional E-value: 0.68
                             TPR_5  11 rDstGhedkavplYrraL 28 
                                         s+G+   a+pl+r+a 
  gi|330508766|ref|YP_004385194.1| 483 YRSVGRYSDAEPLFRQAT 500
                                       568999999999999986 PP

  == domain 9  score: 5.4 bits;  conditional E-value: 0.043
                             TPR_5   8 agarDstGhedkavplYrraL 28 
                                       a + Ds+G+  +a+pl+r+a 
  gi|330508766|ref|YP_004385194.1| 564 ALVYDSMGRYSEAEPLFRQAT 584
                                       6789***************96 PP

  == domain 10  score: 6.6 bits;  conditional E-value: 0.019
                             TPR_5   7 ragarDstGhedkavplYrraLa...e..GLagarrrratiqLassLRnlGeaeealaLLraele 66 
                                        ag   s+G+   a+pl+r+a +   +  G +     +    La   R +G+  +a+ L r+ +e
  gi|330508766|ref|YP_004385194.1| 605 LAGLYYSMGRYSDAEPLFRQATEiwrKslGEDHPDYAQSLNNLAVLYRSMGRYSDAEPLFRQATE 669
                                       6899999**************86333422445566778888999999999999999999987765 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 !   10.4   0.8    0.0013       0.6       4      78 ..      26     117 ..      23     121 .. 0.67
   2 !    8.7   0.2    0.0043       2.1       5      46 ..      69     118 ..      66     163 .. 0.60
   3 ?    4.5   0.1     0.089        42      29      79 ..     143     202 ..     131     205 .. 0.66
   4 !   13.2   0.0   0.00017     0.078       3      79 ..     193     286 ..     191     289 .. 0.82
   5 ?    3.1   0.1      0.24   1.1e+02      26      56 ..     266     297 ..     256     316 .. 0.73
   6 !   10.8   0.5   0.00091      0.43       4      79 ..     278     370 ..     275     400 .. 0.65
   7 ?    4.1   0.0      0.11        53       5      51 ..     363     418 ..     360     456 .. 0.72
   8 ?    2.9   0.0      0.27   1.3e+02       4      50 ..     404     459 ..     401     499 .. 0.72
   9 ?    2.3   0.0      0.41   1.9e+02       5      50 ..     489     543 ..     485     552 .. 0.61
  10 !    9.1   0.1    0.0032       1.5       4      78 ..     530     621 ..     527     625 .. 0.73
  11 ?    2.3   0.0      0.43     2e+02       4      50 ..     614     669 ..     611     676 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                                       -HHHHHHHHHHHH.........HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H........HHHHHHH CS
                            ANAPC3   4 nyknAiflaerll.....a...aetespedayllAlclylngqykrAyellrka.klnsksl........gcrylfA 63 
                                       ny  Ai +ae l      +    +++ + ++  lA+ + ++g+y+ A  l+r+a ++  ksl         ++  +A
  gi|330508766|ref|YP_004385194.1|  26 NYIQAIAFAEELRdliwqKvgyDHPDYAASLNNLAELYRSMGRYNDAEPLFRQAaEICRKSLgedhpdyaTSLNNLA 102
                                       66667777777776666422323333344455579999999998888877777777777777777667777788888 PP

                                       HHHHHTT-HHHHHHH CS
                            ANAPC3  64 qcllkLkkyeeAiaa 78 
                                        +++ +++y++A+ +
  gi|330508766|ref|YP_004385194.1| 103 LVYYSMGRYDDAEPL 117
                                       999999999998765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0043
                                       HHHHHHHHHHHH.........HHH--HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   5 yknAiflaerll........aaetespedayllAlclylngqykrAyell 46 
                                       y++A+ l+  +         + +++ + ++  lAl++y++g+y+ A  l+
  gi|330508766|ref|YP_004385194.1|  69 YNDAEPLFRQAAeicrkslgEDHPDYATSLNNLALVYYSMGRYDDAEPLF 118
                                       66666666666655443323344444445555799999999999886554 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.089
                                       HHHHHHHTT-HHHHHHHHHCT.SHHHC-H........HHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3  29 lAlclylngqykrAyellrka.klnsksl........gcrylfAqcllkLkkyeeAiaaL 79 
                                       lA+ + + g+y +A +l+r+a +++ ksl        +++  +A  +  +++y+eA+ ++
  gi|330508766|ref|YP_004385194.1| 143 LAELYRSIGRYSEAERLFRQAtEIRRKSLgedhpnyaASLNNLAILYRSMGRYNEAEPLF 202
                                       688888888888888888888888888886444433333333333333567777776555 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.00017
                                       T-HHHHHHHHHHHH.........HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H........HHHHHH CS
                            ANAPC3   3 nnyknAiflaerll........aaetespedayllAlclylngqykrAyellrka.klnsksl........gcrylf 62 
                                       ++y++A+ l+ ++         + +++ + ++  lAl++ ++g+y +A  l+r+a +++ ksl        +++  +
  gi|330508766|ref|YP_004385194.1| 193 GRYNEAEPLFRKAIeiwrrslgEDHPNYATSLNNLALVYDSMGRYSEAEPLFRQAtEIRRKSLgedhpdysQSLNNL 269
                                       68999999999999777765555666666666678********************9999999988888888889999 PP

                                       HHHHHHTT-HHHHHHHH CS
                            ANAPC3  63 AqcllkLkkyeeAiaaL 79 
                                       A  ++ +++y +A+ ++
  gi|330508766|ref|YP_004385194.1| 270 AGLYYSMGRYSDAEPLY 286
                                       99999999999988665 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H CS
                            ANAPC3  26 ayllAlclylngqykrAyellrka.klnsksl 56 
                                       +  lA  +y++g+y  A  l+rka +  +ksl
  gi|330508766|ref|YP_004385194.1| 266 LNNLAGLYYSMGRYSDAEPLYRKAiENWGKSL 297
                                       4558999********99999999966666666 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.00091
                                       -HHHHHHHHHHHH.........HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H........HHHHHHH CS
                            ANAPC3   4 nyknAiflaerll........aaetespedayllAlclylngqykrAyellrka.klnsksl........gcrylfA 63 
                                       +y +A+ l+ ++         + ++  ++++  lA+ + ++g+y  A  l+rka +++ ksl        +++  +A
  gi|330508766|ref|YP_004385194.1| 278 RYSDAEPLYRKAIenwgkslgEDHPAYAQSLNNLAELYRSMGRYSDAEPLYRKAtEIRRKSLgedhpdysQSLNNLA 354
                                       66666666666665555433334444444455567777777777777777777777777776666666666666666 PP

                                       HHHHHTT-HHHHHHHH CS
                            ANAPC3  64 qcllkLkkyeeAiaaL 79 
                                         ++ +++y +A+ ++
  gi|330508766|ref|YP_004385194.1| 355 LMYYSIGRYSDAEPLF 370
                                       6666666666665444 PP

  == domain 7  score: 4.1 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHH.........HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SH CS
                            ANAPC3   5 yknAiflaerll........aaetespedayllAlclylngqykrAyellrka.kl 51 
                                       y +A+ l+  +         +a+++ ++++  lA+ + ++g+y  A  l+r+a ++
  gi|330508766|ref|YP_004385194.1| 363 YSDAEPLFRQATeiqrkslgEAHPDYAQSLNNLAELYRSMGRYSDAEPLFRQAtEI 418
                                       66666666666666555445577777777777899999999999999888888555 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.27
                                       -HHHHHHHHHHHH.........HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.S CS
                            ANAPC3   4 nyknAiflaerll........aaetespedayllAlclylngqykrAyellrka.k 50 
                                       +y +A+ l+  +         + ++e + ++  lA  + ++g+y  A  l+r+a +
  gi|330508766|ref|YP_004385194.1| 404 RYSDAEPLFRQATeiwrkslgEDHPEYAASLNNLAVLYRSMGRYSDAEPLFRQAtE 459
                                       66777777777775555433335555555555589999999999999888888744 PP

  == domain 9  score: 2.3 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHH......HHH--HHHHHHH...HHHHHHTT-HHHHHHHHHCT.S CS
                            ANAPC3   5 yknAiflaerll.....aaetespedayll...AlclylngqykrAyellrka.k 50 
                                       y +A+ l+  +      +   ++p+ a  l   A+ + ++++y+ A  l+r+a +
  gi|330508766|ref|YP_004385194.1| 489 YSDAEPLFRQATeiwrkSLGEDHPDYAASLnnrAELYRSMSRYNDAESLFRQAtE 543
                                       5555555555554444212233333333333569999999999999999998844 PP

  == domain 10  score: 9.1 bits;  conditional E-value: 0.0032
                                       -HHHHHHHHHHHH.........HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H........HHHHHHH CS
                            ANAPC3   4 nyknAiflaerll.....a...aetespedayllAlclylngqykrAyellrka.klnsksl........gcrylfA 63 
                                       +y++A+ l+  +      +    +++ + ++  lAl++ ++g+y +A  l+r+a +++ ksl        +++  +A
  gi|330508766|ref|YP_004385194.1| 530 RYNDAESLFRQATeiwrkSlggDHPNYATSLNNLALVYDSMGRYSEAEPLFRQAtEIRRKSLgrdhpdyaQSLNNLA 606
                                       5666666666666555431222455555556668********************99999999888888888888888 PP

                                       HHHHHTT-HHHHHHH CS
                            ANAPC3  64 qcllkLkkyeeAiaa 78 
                                         ++ +++y +A+ +
  gi|330508766|ref|YP_004385194.1| 607 GLYYSMGRYSDAEPL 621
                                       888888888888755 PP

  == domain 11  score: 2.3 bits;  conditional E-value: 0.43
                                       -HHHHHHHHHHHH.........HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.S CS
                            ANAPC3   4 nyknAiflaerll........aaetespedayllAlclylngqykrAyellrka.k 50 
                                       +y +A+ l+  +         + +++ ++++  lA  + ++g+y  A  l+r+a +
  gi|330508766|ref|YP_004385194.1| 614 RYSDAEPLFRQATeiwrkslgEDHPDYAQSLNNLAVLYRSMGRYSDAEPLFRQAtE 669
                                       6777777777777666654444555555666668***********99999999844 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.92   4.3e+02      61      82 ..      46      67 ..      25      68 .. 0.85
   2 ?    1.0   0.0       1.4   6.7e+02      61      82 ..      88     109 ..      71     109 .. 0.88
   3 ?   -0.8   0.0       5.3   2.5e+03      62      82 ..     131     151 ..     126     152 .. 0.85
   4 ?    1.1   0.0       1.4   6.4e+02      61      82 ..     172     193 ..     153     193 .. 0.84
   5 ?    2.0   0.0      0.69   3.3e+02      61      82 ..     214     235 ..     196     235 .. 0.87
   6 ?    1.4   0.0       1.1   5.2e+02      61      82 ..     256     277 ..     239     277 .. 0.87
   7 ?    3.7   0.0       0.2        96      57      82 ..     294     319 ..     279     319 .. 0.81
   8 ?    0.9   0.0       1.5   7.2e+02      61      82 ..     340     361 ..     323     361 .. 0.84
   9 ?    2.7   0.0      0.43     2e+02      60      82 ..     381     403 ..     364     404 .. 0.85
  10 ?    1.7   0.0      0.86     4e+02      61      82 ..     424     445 ..     407     445 .. 0.89
  11 ?   -1.6   0.0       9.2   4.4e+03      62      77 ..     467     482 ..     455     487 .. 0.82
  12 ?    0.2   0.0       2.5   1.2e+03      63      82 ..     552     571 ..     546     571 .. 0.92
  13 ?    0.6   0.0       1.9   8.8e+02      62      82 ..     593     613 ..     575     613 .. 0.87
  14 ?    3.1   0.0      0.31   1.5e+02      61      82 ..     634     655 ..     617     655 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.92
                           DUF4404 61 eeeHPklagvlreildsLanmG 82
                                        +HP+ a  l+++++   +mG
  gi|330508766|ref|YP_004385194.1| 46 GYDHPDYAASLNNLAELYRSMG 67
                                      569*************999999 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.4
                           DUF4404  61 eeeHPklagvlreildsLanmG 82 
                                        e+HP+ a  l++++ +  +mG
  gi|330508766|ref|YP_004385194.1|  88 GEDHPDYATSLNNLALVYYSMG 109
                                       589***********99998888 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 5.3
                           DUF4404  62 eeHPklagvlreildsLanmG 82 
                                       e+HP+ a  l+++++   ++G
  gi|330508766|ref|YP_004385194.1| 131 EDHPNCATGLNNLAELYRSIG 151
                                       89*********9998877776 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 1.4
                           DUF4404  61 eeeHPklagvlreildsLanmG 82 
                                        e+HP+ a  l++++    +mG
  gi|330508766|ref|YP_004385194.1| 172 GEDHPNYAASLNNLAILYRSMG 193
                                       689**********998888887 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.69
                           DUF4404  61 eeeHPklagvlreildsLanmG 82 
                                        e+HP+ a  l++++ +  +mG
  gi|330508766|ref|YP_004385194.1| 214 GEDHPNYATSLNNLALVYDSMG 235
                                       589***********99999998 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 1.1
                           DUF4404  61 eeeHPklagvlreildsLanmG 82 
                                        e+HP+ ++ l++++    +mG
  gi|330508766|ref|YP_004385194.1| 256 GEDHPDYSQSLNNLAGLYYSMG 277
                                       589**********998888887 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.2
                           DUF4404  57 verFeeeHPklagvlreildsLanmG 82 
                                        +   e+HP  a+ l+++++   +mG
  gi|330508766|ref|YP_004385194.1| 294 GKSLGEDHPAYAQSLNNLAELYRSMG 319
                                       556679**************999999 PP

  == domain 8  score: 0.9 bits;  conditional E-value: 1.5
                           DUF4404  61 eeeHPklagvlreildsLanmG 82 
                                        e+HP+ ++ l++++ +  ++G
  gi|330508766|ref|YP_004385194.1| 340 GEDHPDYSQSLNNLALMYYSIG 361
                                       589**********998766666 PP

  == domain 9  score: 2.7 bits;  conditional E-value: 0.43
                           DUF4404  60 FeeeHPklagvlreildsLanmG 82 
                                         e HP+ a+ l+++++   +mG
  gi|330508766|ref|YP_004385194.1| 381 LGEAHPDYAQSLNNLAELYRSMG 403
                                       5689*************999999 PP

  == domain 10  score: 1.7 bits;  conditional E-value: 0.86
                           DUF4404  61 eeeHPklagvlreildsLanmG 82 
                                        e+HP+ a  l++++    +mG
  gi|330508766|ref|YP_004385194.1| 424 GEDHPEYAASLNNLAVLYRSMG 445
                                       589************9999998 PP

  == domain 11  score: -1.6 bits;  conditional E-value: 9.2
                           DUF4404  62 eeHPklagvlreilds 77 
                                       e+HP+ a  l+++++ 
  gi|330508766|ref|YP_004385194.1| 467 EDHPNCATGLNNLAEL 482
                                       89*****999999875 PP

  == domain 12  score: 0.2 bits;  conditional E-value: 2.5
                           DUF4404  63 eHPklagvlreildsLanmG 82 
                                       +HP+ a  l++++ +  +mG
  gi|330508766|ref|YP_004385194.1| 552 DHPNYATSLNNLALVYDSMG 571
                                       8***********99999998 PP

  == domain 13  score: 0.6 bits;  conditional E-value: 1.9
                           DUF4404  62 eeHPklagvlreildsLanmG 82 
                                       ++HP+ a+ l++++    +mG
  gi|330508766|ref|YP_004385194.1| 593 RDHPDYAQSLNNLAGLYYSMG 613
                                       79**********998888887 PP

  == domain 14  score: 3.1 bits;  conditional E-value: 0.31
                           DUF4404  61 eeeHPklagvlreildsLanmG 82 
                                        e+HP+ a+ l++++    +mG
  gi|330508766|ref|YP_004385194.1| 634 GEDHPDYAQSLNNLAVLYRSMG 655
                                       589************9999998 PP

>> TetR_C_32  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.15        73      46      80 ..      70     104 ..      65     104 .. 0.90
   2 ?   -0.2   0.0       1.9   9.1e+02      48      68 ..     114     134 ..     111     144 .. 0.82
   3 ?    5.0   0.0     0.049        23      46      80 ..     196     230 ..     194     233 .. 0.87
   4 ?   -0.7   0.0       2.8   1.3e+03      46      69 ..     238     261 ..     236     270 .. 0.83
   5 ?   -1.6   0.0       5.3   2.5e+03      47      77 ..     323     353 ..     321     356 .. 0.79
   6 ?   -2.3   0.0       8.8   4.2e+03      48      69 ..     366     387 ..     363     396 .. 0.77
   7 ?    4.1   0.0     0.089        42      47      75 ..     407     435 ..     396     440 .. 0.82
   8 ?    2.9   0.0      0.21     1e+02      47      68 ..     449     470 ..     446     480 .. 0.83
   9 ?    3.6   0.0      0.13        63      47      69 ..     491     513 ..     488     520 .. 0.85
  10 ?   -1.9   0.0       6.7   3.2e+03      47      69 ..     575     597 ..     573     605 .. 0.82
  11 ?    4.1   0.0     0.092        43      47      72 ..     617     642 ..     614     650 .. 0.80
  12 ?   -0.3   0.0       2.1     1e+03      47      70 ..     659     682 ..     657     690 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.15
                         TetR_C_32  46 eeirPlhealerivaellgedaedeevrlrtlsiv 80 
                                       ++ +Pl+++ ++i ++ lged  d ++ l  l++v
  gi|330508766|ref|YP_004385194.1|  70 NDAEPLFRQAAEICRKSLGEDHPDYATSLNNLALV 104
                                       5679********************99999888876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.9
                         TetR_C_32  48 irPlhealerivaellgedae 68 
                                        +Pl+ ++++i+++ lged  
  gi|330508766|ref|YP_004385194.1| 114 AEPLFCQVTEIWGKSLGEDHP 134
                                       68****************965 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.049
                         TetR_C_32  46 eeirPlhealerivaellgedaedeevrlrtlsiv 80 
                                       +e +Pl++   +i+++ lged    ++ l  l++v
  gi|330508766|ref|YP_004385194.1| 196 NEAEPLFRKAIEIWRRSLGEDHPNYATSLNNLALV 230
                                       6889*****************98888888777765 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.8
                         TetR_C_32  46 eeirPlhealerivaellgedaed 69 
                                       +e +Pl+++ ++i ++ lged  d
  gi|330508766|ref|YP_004385194.1| 238 SEAEPLFRQATEIRRKSLGEDHPD 261
                                       5789***************99766 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 5.3
                         TetR_C_32  47 eirPlhealerivaellgedaedeevrlrtl 77 
                                       + +Pl++  ++i ++ lged  d +  l  l
  gi|330508766|ref|YP_004385194.1| 323 DAEPLYRKATEIRRKSLGEDHPDYSQSLNNL 353
                                       578****************988776665555 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 8.8
                         TetR_C_32  48 irPlhealerivaellgedaed 69 
                                        +Pl+++ ++i ++ lge+  d
  gi|330508766|ref|YP_004385194.1| 366 AEPLFRQATEIQRKSLGEAHPD 387
                                       6899999999999999987554 PP

  == domain 7  score: 4.1 bits;  conditional E-value: 0.089
                         TetR_C_32  47 eirPlhealerivaellgedaedeevrlr 75 
                                       + +Pl+++ ++i+++ lged  + +  l 
  gi|330508766|ref|YP_004385194.1| 407 DAEPLFRQATEIWRKSLGEDHPEYAASLN 435
                                       679****************9777665555 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.21
                         TetR_C_32  47 eirPlhealerivaellgedae 68 
                                       + +Pl+++ ++i+++ lged  
  gi|330508766|ref|YP_004385194.1| 449 DAEPLFRQATEIWRKSLGEDHP 470
                                       679****************965 PP

  == domain 9  score: 3.6 bits;  conditional E-value: 0.13
                         TetR_C_32  47 eirPlhealerivaellgedaed 69 
                                       + +Pl+++ ++i+++ lged  d
  gi|330508766|ref|YP_004385194.1| 491 DAEPLFRQATEIWRKSLGEDHPD 513
                                       679****************9766 PP

  == domain 10  score: -1.9 bits;  conditional E-value: 6.7
                         TetR_C_32  47 eirPlhealerivaellgedaed 69 
                                       e +Pl+++ ++i ++ lg+d  d
  gi|330508766|ref|YP_004385194.1| 575 EAEPLFRQATEIRRKSLGRDHPD 597
                                       77999999999999999998655 PP

  == domain 11  score: 4.1 bits;  conditional E-value: 0.092
                         TetR_C_32  47 eirPlhealerivaellgedaedeev 72 
                                       + +Pl+++ ++i+++ lged  d + 
  gi|330508766|ref|YP_004385194.1| 617 DAEPLFRQATEIWRKSLGEDHPDYAQ 642
                                       679*****************877555 PP

  == domain 12  score: -0.3 bits;  conditional E-value: 2.1
                         TetR_C_32  47 eirPlhealerivaellgedaede 70 
                                       + +Pl+++ ++i ++ lg+d+ d+
  gi|330508766|ref|YP_004385194.1| 659 DAEPLFRQATEIRRKVLGKDPLDR 682
                                       579****************99775 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.34   1.6e+02      25      42 .]      50      67 ..      49      67 .. 0.90
   2 !   12.2   0.4   0.00023      0.11       3      42 .]      62     109 ..      60     109 .. 0.82
   3 ?    5.4   0.0     0.032        15       3      25 ..     146     168 ..     144     171 .. 0.90
   4 ?    1.1   0.0      0.71   3.3e+02      25      42 .]     176     193 ..     173     193 .. 0.88
   5 !    8.4   0.2    0.0036       1.7       4      42 .]     189     235 ..     186     235 .. 0.82
   6 ?   -0.9   0.0       2.8   1.3e+03       6      25 ..     233     252 ..     231     254 .. 0.84
   7 ?    5.6   0.1     0.026        12       3      22 ..     272     291 ..     270     292 .. 0.94
   8 ?    6.1   0.1     0.019       9.1       3      25 ..     314     336 ..     302     338 .. 0.92
   9 ?    4.8   0.5     0.047        22       3      41 ..     356     402 ..     354     403 .. 0.71
  10 ?    0.5   0.0       1.1   5.1e+02       3      23 ..     398     418 ..     396     418 .. 0.81
  11 ?    0.6   0.0      0.97   4.6e+02      25      42 .]     428     445 ..     425     445 .. 0.87
  12 ?   -0.2   0.0       1.8   8.3e+02       3      23 ..     440     460 ..     438     460 .. 0.82
  13 ?   -1.8   0.0       5.5   2.6e+03       3      20 ..     482     499 ..     470     502 .. 0.65
  14 ?   -0.1   0.0       1.6   7.6e+02      25      38 ..     512     525 ..     509     544 .. 0.70
  15 ?    3.9   0.2     0.089        42      25      42 .]     554     571 ..     552     571 .. 0.90
  16 ?   -1.1   0.0       3.4   1.6e+03       7      25 ..     570     588 ..     569     590 .. 0.84
  17 ?    4.8   0.1     0.049        23      25      42 .]     596     613 ..     593     628 .. 0.89
  18 ?    2.9   0.1      0.19        90      25      42 .]     638     655 ..     635     655 .. 0.88
  19 ?    1.2   0.0      0.65   3.1e+02       3      24 ..     650     671 ..     648     673 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.34
                            TPR_11 25 PdnaeayynLGlayykqG 42
                                      Pd+a  ++nL+++y  +G
  gi|330508766|ref|YP_004385194.1| 50 PDYAASLNNLAELYRSMG 67
                                      9************97776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00023
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkld........PdnaeayynLGlayykqG 42 
                                       +y++ G+y++A   +++A +++        Pd+a+ ++nL+l+yy +G
  gi|330508766|ref|YP_004385194.1|  62 LYRSMGRYNDAEPLFRQAAEICrkslgedhPDYATSLNNLALVYYSMG 109
                                       5888888888888888888887666666669**************998 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.032
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldP 25 
                                       +y++ G+y eA   +++A +++ 
  gi|330508766|ref|YP_004385194.1| 146 LYRSIGRYSEAERLFRQATEIRR 168
                                       79******************986 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.71
                            TPR_11  25 PdnaeayynLGlayykqG 42 
                                       P++a  ++nL+ +y  +G
  gi|330508766|ref|YP_004385194.1| 176 PNYAASLNNLAILYRSMG 193
                                       9**********9997766 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0036
                            TPR_11   4 yyeqGkyeeAieaYkkAlkl........dPdnaeayynLGlayykqG 42 
                                       y++ G+y+eA   ++kA+++         P++a+ ++nL+l+y  +G
  gi|330508766|ref|YP_004385194.1| 189 YRSMGRYNEAEPLFRKAIEIwrrslgedHPNYATSLNNLALVYDSMG 235
                                       99999999999999999998666666667999999999999996665 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 2.8
                            TPR_11   6 eqGkyeeAieaYkkAlkldP 25 
                                       + G+y eA   +++A +++ 
  gi|330508766|ref|YP_004385194.1| 233 SMGRYSEAEPLFRQATEIRR 252
                                       579*****999999999975 PP

  == domain 7  score: 5.6 bits;  conditional E-value: 0.026
                            TPR_11   3 ayyeqGkyeeAieaYkkAlk 22 
                                       +yy+ G+y +A   Y+kA++
  gi|330508766|ref|YP_004385194.1| 272 LYYSMGRYSDAEPLYRKAIE 291
                                       5*****************97 PP

  == domain 8  score: 6.1 bits;  conditional E-value: 0.019
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldP 25 
                                       +y++ G+y +A   Y+kA +++ 
  gi|330508766|ref|YP_004385194.1| 314 LYRSMGRYSDAEPLYRKATEIRR 336
                                       79*****************9975 PP

  == domain 9  score: 4.8 bits;  conditional E-value: 0.047
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkld........PdnaeayynLGlayykq 41 
                                       +yy+ G+y +A   +++A ++         Pd+a  ++nL+++y  +
  gi|330508766|ref|YP_004385194.1| 356 MYYSIGRYSDAEPLFRQATEIQrkslgeahPDYAQSLNNLAELYRSM 402
                                       68888888888888888888864444444488888888888888665 PP

  == domain 10  score: 0.5 bits;  conditional E-value: 1.1
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkl 23 
                                       +y++ G+y +A   +++A ++
  gi|330508766|ref|YP_004385194.1| 398 LYRSMGRYSDAEPLFRQATEI 418
                                       79********97777777765 PP

  == domain 11  score: 0.6 bits;  conditional E-value: 0.97
                            TPR_11  25 PdnaeayynLGlayykqG 42 
                                       P++a  ++nL+++y  +G
  gi|330508766|ref|YP_004385194.1| 428 PEYAASLNNLAVLYRSMG 445
                                       99*********9997766 PP

  == domain 12  score: -0.2 bits;  conditional E-value: 1.8
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkl 23 
                                       +y++ G+y +A   +++A ++
  gi|330508766|ref|YP_004385194.1| 440 LYRSMGRYSDAEPLFRQATEI 460
                                       59********97777777765 PP

  == domain 13  score: -1.8 bits;  conditional E-value: 5.5
                            TPR_11   3 ayyeqGkyeeAieaYkkA 20 
                                       +y++ G+y +A   +++A
  gi|330508766|ref|YP_004385194.1| 482 LYRSVGRYSDAEPLFRQA 499
                                       566777777775555555 PP

  == domain 14  score: -0.1 bits;  conditional E-value: 1.6
                            TPR_11  25 PdnaeayynLGlay 38 
                                       Pd+a  ++n++++y
  gi|330508766|ref|YP_004385194.1| 512 PDYAASLNNRAELY 525
                                       67777777777766 PP

  == domain 15  score: 3.9 bits;  conditional E-value: 0.089
                            TPR_11  25 PdnaeayynLGlayykqG 42 
                                       P++a+ ++nL+l+y  +G
  gi|330508766|ref|YP_004385194.1| 554 PNYATSLNNLALVYDSMG 571
                                       9*************7666 PP

  == domain 16  score: -1.1 bits;  conditional E-value: 3.4
                            TPR_11   7 qGkyeeAieaYkkAlkldP 25 
                                        G+y eA   +++A +++ 
  gi|330508766|ref|YP_004385194.1| 570 MGRYSEAEPLFRQATEIRR 588
                                       699****999999999975 PP

  == domain 17  score: 4.8 bits;  conditional E-value: 0.049
                            TPR_11  25 PdnaeayynLGlayykqG 42 
                                       Pd+a  ++nL+ +yy +G
  gi|330508766|ref|YP_004385194.1| 596 PDYAQSLNNLAGLYYSMG 613
                                       899999999999999887 PP

  == domain 18  score: 2.9 bits;  conditional E-value: 0.19
                            TPR_11  25 PdnaeayynLGlayykqG 42 
                                       Pd+a  ++nL+++y  +G
  gi|330508766|ref|YP_004385194.1| 638 PDYAQSLNNLAVLYRSMG 655
                                       9***********997766 PP

  == domain 19  score: 1.2 bits;  conditional E-value: 0.65
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkld 24 
                                       +y++ G+y +A   +++A +++
  gi|330508766|ref|YP_004385194.1| 650 LYRSMGRYSDAEPLFRQATEIR 671
                                       59*********99999999986 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2       1.5   6.9e+02       5      42 ..      54      91 ..      51     105 .. 0.78
   2 ?   -0.6   0.0       2.9   1.4e+03      17      32 ..     150     165 ..     137     177 .. 0.73
   3 ?    3.8   0.0      0.13        61       4      40 ..     179     215 ..     177     224 .. 0.82
   4 ?    5.8   0.0     0.031        14       4      38 ..     221     255 ..     219     275 .. 0.82
   5 ?    4.0   0.0      0.11        54      18      50 ..     277     309 ..     272     318 .. 0.78
   6 ?    0.1   0.1       1.8   8.4e+02      11      33 ..     312     334 ..     303     353 .. 0.74
   7 ?   -0.6   0.1         3   1.4e+03      11      43 ..     396     428 ..     387     441 .. 0.76
   8 ?    2.7   0.0      0.28   1.3e+02       4      50 ..     431     477 ..     428     485 .. 0.81
   9 ?    1.2   0.0      0.84   3.9e+02      11      56 ..     480     525 ..     472     539 .. 0.75
  10 ?    5.2   0.0     0.047        22       4      33 ..     557     586 ..     555     606 .. 0.88
  11 ?   -1.5   0.0       5.9   2.8e+03      18      45 ..     613     640 ..     611     656 .. 0.77
  12 ?   -1.1   0.0       4.4   2.1e+03       5      38 ..     642     675 ..     639     685 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.5
                               MIT  5 lelvkkAveeDnagnyeeAlelYkealelLlqalkekn 42
                                       +l + A  + + g y +A  l+++a e++ + l e++
  gi|330508766|ref|YP_004385194.1| 54 ASLNNLAELYRSMGRYNDAEPLFRQAAEICRKSLGEDH 91
                                      556666777777899*************9999887644 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.9
                               MIT  17 agnyeeAlelYkeale 32 
                                        g y+eA +l+++a e
  gi|330508766|ref|YP_004385194.1| 150 IGRYSEAERLFRQATE 165
                                       5778888888888876 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.13
                               MIT   4 AlelvkkAveeDnagnyeeAlelYkealelLlqalke 40 
                                       A +l + A+ + + g y eA  l+++a+e++   l e
  gi|330508766|ref|YP_004385194.1| 179 AASLNNLAILYRSMGRYNEAEPLFRKAIEIWRRSLGE 215
                                       66677888889999***************99888765 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.031
                               MIT   4 AlelvkkAveeDnagnyeeAlelYkealelLlqal 38 
                                       A +l + A  +D+ g y+eA  l+++a e+  + l
  gi|330508766|ref|YP_004385194.1| 221 ATSLNNLALVYDSMGRYSEAEPLFRQATEIRRKSL 255
                                       6778899********************98755555 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.11
                               MIT  18 gnyeeAlelYkealelLlqalkekneerrellr 50 
                                       g y++A  lY++a+e + + l e+++   + l 
  gi|330508766|ref|YP_004385194.1| 277 GRYSDAEPLYRKAIENWGKSLGEDHPAYAQSLN 309
                                       789************999988876665555555 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 1.8
                               MIT  11 AveeDnagnyeeAlelYkealel 33 
                                       A  + + g y++A  lY++a e+
  gi|330508766|ref|YP_004385194.1| 312 AELYRSMGRYSDAEPLYRKATEI 334
                                       5555567899*********9886 PP

  == domain 7  score: -0.6 bits;  conditional E-value: 3
                               MIT  11 AveeDnagnyeeAlelYkealelLlqalkekne 43 
                                       A  + + g y++A  l+++a e++ + l e+++
  gi|330508766|ref|YP_004385194.1| 396 AELYRSMGRYSDAEPLFRQATEIWRKSLGEDHP 428
                                       556666789999999999999999998886555 PP

  == domain 8  score: 2.7 bits;  conditional E-value: 0.28
                               MIT   4 AlelvkkAveeDnagnyeeAlelYkealelLlqalkekneerrellr 50 
                                       A +l + Av + + g y++A  l+++a e++ + l e++++    l 
  gi|330508766|ref|YP_004385194.1| 431 AASLNNLAVLYRSMGRYSDAEPLFRQATEIWRKSLGEDHPNCATGLN 477
                                       6778889999999******************9999876666655555 PP

  == domain 9  score: 1.2 bits;  conditional E-value: 0.84
                               MIT  11 AveeDnagnyeeAlelYkealelLlqalkekneerrellrekieeY 56 
                                       A  + + g y++A  l+++a e++ + l e+++     l +++e Y
  gi|330508766|ref|YP_004385194.1| 480 AELYRSVGRYSDAEPLFRQATEIWRKSLGEDHPDYAASLNNRAELY 525
                                       555666799*****************99986665555555555544 PP

  == domain 10  score: 5.2 bits;  conditional E-value: 0.047
                               MIT   4 AlelvkkAveeDnagnyeeAlelYkealel 33 
                                       A +l + A  +D+ g y+eA  l+++a e+
  gi|330508766|ref|YP_004385194.1| 557 ATSLNNLALVYDSMGRYSEAEPLFRQATEI 586
                                       6778899*******************9875 PP

  == domain 11  score: -1.5 bits;  conditional E-value: 5.9
                               MIT  18 gnyeeAlelYkealelLlqalkekneer 45 
                                       g y++A  l+++a e++ + l e+++  
  gi|330508766|ref|YP_004385194.1| 613 GRYSDAEPLFRQATEIWRKSLGEDHPDY 640
                                       7899999999999999999888755554 PP

  == domain 12  score: -1.1 bits;  conditional E-value: 4.4
                               MIT   5 lelvkkAveeDnagnyeeAlelYkealelLlqal 38 
                                        +l + Av + + g y++A  l+++a e+  ++l
  gi|330508766|ref|YP_004385194.1| 642 QSLNNLAVLYRSMGRYSDAEPLFRQATEIRRKVL 675
                                       5666788999999999999999999988755555 PP

>> RPN6_N  26S proteasome regulatory subunit RPN6 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       1.1   5.3e+02      33      63 ..      51      81 ..      32      86 .. 0.83
   2 ?    0.6   0.0       1.5   7.2e+02      32      63 ..     134     165 ..     106     169 .. 0.75
   3 ?    1.9   0.0       0.6   2.8e+02       8      61 ..     152     205 ..     144     212 .. 0.85
   4 ?   -1.1   0.0       5.1   2.4e+03       8      63 ..     194     249 ..     186     255 .. 0.83
   5 ?    6.1   0.0      0.03        14       8      60 ..     278     330 ..     270     337 .. 0.85
   6 ?    5.8   0.0     0.035        16       9      63 ..     363     417 ..     356     422 .. 0.85
   7 ?   -1.9   0.0       8.5     4e+03      33      63 ..     429     459 ..     420     465 .. 0.81
   8 ?   -0.3   0.0       2.8   1.3e+03      31      63 ..     469     501 ..     440     507 .. 0.73
   9 ?   -0.7   0.0       3.7   1.7e+03      11      64 ..     491     544 ..     480     548 .. 0.73
  10 ?    0.1   0.0       2.1   9.8e+02       8      63 ..     572     627 ..     564     632 .. 0.83
  11 ?    0.7   0.0       1.4   6.5e+02      10      63 ..     616     669 ..     606     674 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.1
                            RPN6_N 33 eqeqalleLgelyrdqkkaeeLaelikesrs 63
                                      ++ ++l +L+elyr+ ++ ++   l+++  +
  gi|330508766|ref|YP_004385194.1| 51 DYAASLNNLAELYRSMGRYNDAEPLFRQAAE 81
                                      5678999*********999998888887765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.5
                            RPN6_N  32 reqeqalleLgelyrdqkkaeeLaelikesrs 63 
                                        +  + l +L+elyr+ ++ +e  +l+++ ++
  gi|330508766|ref|YP_004385194.1| 134 PNCATGLNNLAELYRSIGRYSEAERLFRQATE 165
                                       55667899********9999999999988765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.6
                            RPN6_N   8 dpkeaeelykeilskkskedeealreqeqalleLgelyrdqkkaeeLaelikes 61 
                                       +++eae+l+++  + + k+  e   ++ ++l +L+ lyr+ ++ +e   l+++ 
  gi|330508766|ref|YP_004385194.1| 152 RYSEAERLFRQATEIRRKSLGEDHPNYAASLNNLAILYRSMGRYNEAEPLFRKA 205
                                       68899999999999999888899999**************99999988887765 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 5.1
                            RPN6_N   8 dpkeaeelykeilskkskedeealreqeqalleLgelyrdqkkaeeLaelikesrs 63 
                                       +++eae l+++ ++   ++  e   ++ ++l +L+ +y + ++ +e   l+++ ++
  gi|330508766|ref|YP_004385194.1| 194 RYNEAEPLFRKAIEIWRRSLGEDHPNYATSLNNLALVYDSMGRYSEAEPLFRQATE 249
                                       678899999999988888888888999999*******9999999988888877665 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.03
                            RPN6_N   8 dpkeaeelykeilskkskedeealreqeqalleLgelyrdqkkaeeLaelike 60 
                                       ++++ae ly++ +++  k+  e   ++ q+l +L+elyr+ ++ ++   l ++
  gi|330508766|ref|YP_004385194.1| 278 RYSDAEPLYRKAIENWGKSLGEDHPAYAQSLNNLAELYRSMGRYSDAEPLYRK 330
                                       6889**********999999999****************99988776666555 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.035
                            RPN6_N   9 pkeaeelykeilskkskedeealreqeqalleLgelyrdqkkaeeLaelikesrs 63 
                                       +++ae l+++  + + k+  ea  ++ q+l +L+elyr+ ++ ++   l+++ ++
  gi|330508766|ref|YP_004385194.1| 363 YSDAEPLFRQATEIQRKSLGEAHPDYAQSLNNLAELYRSMGRYSDAEPLFRQATE 417
                                       678888999988888888889999****************999999888888766 PP

  == domain 7  score: -1.9 bits;  conditional E-value: 8.5
                            RPN6_N  33 eqeqalleLgelyrdqkkaeeLaelikesrs 63 
                                       e+ ++l +L+ lyr+ ++ ++   l+++ ++
  gi|330508766|ref|YP_004385194.1| 429 EYAASLNNLAVLYRSMGRYSDAEPLFRQATE 459
                                       56788999*******9999998888888766 PP

  == domain 8  score: -0.3 bits;  conditional E-value: 2.8
                            RPN6_N  31 lreqeqalleLgelyrdqkkaeeLaelikesrs 63 
                                         +  + l +L+elyr+ ++ ++   l+++ ++
  gi|330508766|ref|YP_004385194.1| 469 HPNCATGLNNLAELYRSVGRYSDAEPLFRQATE 501
                                       555667899*******99999888888887766 PP

  == domain 9  score: -0.7 bits;  conditional E-value: 3.7
                            RPN6_N  11 eaeelykeilskkskedeealreqeqalleLgelyrdqkkaeeLaelikesrsf 64 
                                       +ae l+++  +   k+  e   ++ ++l + +elyr+ ++ ++  +l+++ +++
  gi|330508766|ref|YP_004385194.1| 491 DAEPLFRQATEIWRKSLGEDHPDYAASLNNRAELYRSMSRYNDAESLFRQATEI 544
                                       555555555555555555666788889999999***999999999999988765 PP

  == domain 10  score: 0.1 bits;  conditional E-value: 2.1
                            RPN6_N   8 dpkeaeelykeilskkskedeealreqeqalleLgelyrdqkkaeeLaelikesrs 63 
                                       +++eae l+++  + + k+  +   ++ q+l +L+ ly + ++ ++   l+++ ++
  gi|330508766|ref|YP_004385194.1| 572 RYSEAEPLFRQATEIRRKSLGRDHPDYAQSLNNLAGLYYSMGRYSDAEPLFRQATE 627
                                       577888888888888888888889999************99999988888887766 PP

  == domain 11  score: 0.7 bits;  conditional E-value: 1.4
                            RPN6_N  10 keaeelykeilskkskedeealreqeqalleLgelyrdqkkaeeLaelikesrs 63 
                                       ++ae l+++  +   k+  e   ++ q+l +L+ lyr+ ++ ++   l+++ ++
  gi|330508766|ref|YP_004385194.1| 616 SDAEPLFRQATEIWRKSLGEDHPDYAQSLNNLAVLYRSMGRYSDAEPLFRQATE 669
                                       55666666665555555567778999************9999988888887665 PP

>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.19        91       9      55 ..      55     105 ..      51     124 .. 0.83
   2 ?    4.6   0.0     0.056        27      48     135 ..     143     237 ..     129     243 .. 0.60
   3 ?    4.1   0.0      0.08        38      11      67 ..     183     246 ..     177     282 .. 0.73
   4 !   11.0   0.1    0.0006      0.28       8     139 ..     306     451 ..     303     453 .. 0.84
   5 ?    2.0   0.0      0.37   1.7e+02      88     137 ..     520     575 ..     476     579 .. 0.71
   6 ?    3.3   0.0      0.14        68      27      79 ..     542     594 ..     517     663 .. 0.50

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.19
                                       -CCCCHHHHHCTT-HHHHCHHHCCHHHCHTS....--HHHHHHHHHHHHHT CS
                          Clathrin   9 dlsrvvklfeeaglleelleyLekvlkedsk....enpalqtallelyaky 55 
                                       +l+ + +l+ + g+++ + ++ +++++ ++k    ++p++ t+l+ l++ y
  gi|330508766|ref|YP_004385194.1|  55 SLNNLAELYRSMGRYNDAEPLFRQAAEICRKslgeDHPDYATSLNNLALVY 105
                                       5778999999***************97777777889********9999988 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.056
                                       HHHHHHHTT-HHHHHHTTSS---S-TTHHHHHHHT-S.SHHHHHHHHHTTXTHSSHSSX.SSSSHCSCHHH.....H CS
                          Clathrin  48 llelyakyddpqeleeflkknnnydlekvaklcekad.lyeeavilykkinefkkaisl.lkklkdfddai.....e 117
                                       l+ely   ++++e+e+ +++ +++ ++++++   ++    + + ily+ ++++++a  l  k  + +++ +     +
  gi|330508766|ref|YP_004385194.1| 143 LAELYRSIGRYSEAERLFRQATEIRRKSLGEDHPNYAaSLNNLAILYRSMGRYNEAEPLfRKAIEIWRRSLgedhpN 219
                                       55555555556666666666666666555555422222444556677777777776666666666666666666666 PP

                                       TTTTTXXSHHHHHHHHHH CS
                          Clathrin 118 yaakvsnpelweklleal 135
                                       ya  ++n +l+++ ++ +
  gi|330508766|ref|YP_004385194.1| 220 YATSLNNLALVYDSMGRY 237
                                       777777766666655555 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.08
                                       CCCHHHHHCTT-HHHHCHHHCCHHHCHTS....--HHHHHHHHHHHHHT...T-HHHHHHTTSS CS
                          Clathrin  11 srvvklfeeaglleelleyLekvlkedsk....enpalqtallelyaky...ddpqeleeflkk 67 
                                       + +  l+ + g+++e+ ++ +k+++  ++    ++p++ t+l+ l++ y   ++++e+e+ +++
  gi|330508766|ref|YP_004385194.1| 183 NNLAILYRSMGRYNEAEPLFRKAIEIWRRslgeDHPNYATSLNNLALVYdsmGRYSEAEPLFRQ 246
                                       5556677788888888888888884444455558888888888888888555556666666555 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.0006
                                       S-CCCCHHHHHCTT-HHHHCHHHCCHHHCHTS....--HHHHHHHHHHHHHT...T-HHHHHHTTSS---S-TTHHH CS
                          Clathrin   8 idlsrvvklfeeaglleelleyLekvlkedsk....enpalqtallelyaky...ddpqeleeflkknnnydlekva 77 
                                       ++l+ + +l+ + g++  + ++ +k+ +  +k    ++p++  +l+ l++ y   ++++++e+ +++ +++++++++
  gi|330508766|ref|YP_004385194.1| 306 QSLNNLAELYRSMGRYSDAEPLYRKATEIRRKslgeDHPDYSQSLNNLALMYysiGRYSDAEPLFRQATEIQRKSLG 382
                                       667778888888888888888888888444445666999999999999999999988******************** PP

                                       HHH.HT-SSHHHHHHHHHTTXTHSSHSSX.SSSSHCSCHHH.....HTTTTTXXSHHHHHHHHHHHSSX CS
                          Clathrin  78 klc.ekadlyeeavilykkinefkkaisl.lkklkdfddai.....eyaakvsnpelwekllealldkk 139
                                       +     a+  + + +ly+ ++++++a  l  +  + +++ +     eyaa ++n +++++ ++ + d +
  gi|330508766|ref|YP_004385194.1| 383 EAHpDYAQSLNNLAELYRSMGRYSDAEPLfRQATEIWRKSLgedhpEYAASLNNLAVLYRSMGRYSDAE 451
                                       **955566899**************99898889999999999999***********9999888877765 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.37
                                       HHHHHHHTTXTHSSHSSX.SSSSHCSCHHH.....HTTTTTXXSHHHHHHHHHHHS CS
                          Clathrin  88 eavilykkinefkkaisl.lkklkdfddai.....eyaakvsnpelwekllealld 137
                                        + +ly+ ++++++a sl  +  + +++ +     +ya  ++n +l+++ ++ + +
  gi|330508766|ref|YP_004385194.1| 520 NRAELYRSMSRYNDAESLfRQATEIWRKSLggdhpNYATSLNNLALVYDSMGRYSE 575
                                       46678888888888888777777777777777778888888888888776666655 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.14
                                       CHHHCCHHHCHTS--HHHHHHHHHHHHHT...T-HHHHHHTTSS---S-TTHHHHH CS
                          Clathrin  27 leyLekvlkedskenpalqtallelyaky...ddpqeleeflkknnnydlekvakl 79 
                                       +e  +k l     ++p++ t+l+ l++ y   ++++e+e+ +++ +++ ++++++ 
  gi|330508766|ref|YP_004385194.1| 542 TEIWRKSL---GGDHPNYATSLNNLALVYdsmGRYSEAEPLFRQATEIRRKSLGRD 594
                                       22223333...227777777777777777666567777777777777666666654 PP

>> Ribosomal_L6e_N  Ribosomal protein L6, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.035        17      14      33 ..     145     164 ..     140     174 .. 0.85
   2 ?   -0.7   0.0       3.7   1.8e+03      14      33 ..     187     206 ..     182     213 .. 0.85
   3 ?    0.2   0.0       1.9   8.9e+02      12      33 ..     226     248 ..     221     257 .. 0.77
   4 ?   -0.9   0.0       4.4   2.1e+03      19      33 ..     276     290 ..     270     298 .. 0.84
   5 ?    1.5   0.0      0.78   3.7e+02      14      33 ..     313     332 ..     306     341 .. 0.84
   6 ?    1.8   0.0      0.62   2.9e+02      17      33 ..     358     374 ..     347     383 .. 0.78
   7 ?    1.0   0.0       1.1   5.2e+02      14      33 ..     397     416 ..     390     424 .. 0.84
   8 ?    2.4   0.0      0.41     2e+02      14      33 ..     439     458 ..     432     466 .. 0.85
   9 ?    3.9   0.0      0.14        65      14      33 ..     481     500 ..     476     510 .. 0.85
  10 ?    0.1   0.0       2.1   9.8e+02      12      33 ..     562     584 ..     558     592 .. 0.77
  11 ?   -2.0   0.1       9.4   4.4e+03      19      33 ..     612     626 ..     607     632 .. 0.81
  12 ?    2.6   0.0      0.33   1.6e+02      14      33 ..     649     668 ..     642     696 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.035
                   Ribosomal_L6e_N  14 vLvrGIgRYSrsamysrkal 33 
                                        L r IgRYS +   +r+a 
  gi|330508766|ref|YP_004385194.1| 145 ELYRSIGRYSEAERLFRQAT 164
                                       5899********99999986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.7
                   Ribosomal_L6e_N  14 vLvrGIgRYSrsamysrkal 33 
                                       +L r  gRY  +   +rka+
  gi|330508766|ref|YP_004385194.1| 187 ILYRSMGRYNEAEPLFRKAI 206
                                       588999************97 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.9
                   Ribosomal_L6e_N  12 NpvLv.rGIgRYSrsamysrkal 33 
                                       N++Lv +  gRYS +   +r+a 
  gi|330508766|ref|YP_004385194.1| 226 NLALVyDSMGRYSEAEPLFRQAT 248
                                       566643678*****999999886 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 4.4
                   Ribosomal_L6e_N  19 IgRYSrsamysrkal 33 
                                        gRYS +    rka+
  gi|330508766|ref|YP_004385194.1| 276 MGRYSDAEPLYRKAI 290
                                       69*****99999997 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.78
                   Ribosomal_L6e_N  14 vLvrGIgRYSrsamysrkal 33 
                                        L r  gRYS +    rka 
  gi|330508766|ref|YP_004385194.1| 313 ELYRSMGRYSDAEPLYRKAT 332
                                       588999******99999986 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.62
                   Ribosomal_L6e_N  17 rGIgRYSrsamysrkal 33 
                                         IgRYS +   +r+a 
  gi|330508766|ref|YP_004385194.1| 358 YSIGRYSDAEPLFRQAT 374
                                       57******999999886 PP

  == domain 7  score: 1.0 bits;  conditional E-value: 1.1
                   Ribosomal_L6e_N  14 vLvrGIgRYSrsamysrkal 33 
                                        L r  gRYS +   +r+a 
  gi|330508766|ref|YP_004385194.1| 397 ELYRSMGRYSDAEPLFRQAT 416
                                       588999*****999999885 PP

  == domain 8  score: 2.4 bits;  conditional E-value: 0.41
                   Ribosomal_L6e_N  14 vLvrGIgRYSrsamysrkal 33 
                                       vL r  gRYS +   +r+a 
  gi|330508766|ref|YP_004385194.1| 439 VLYRSMGRYSDAEPLFRQAT 458
                                       899********999999885 PP

  == domain 9  score: 3.9 bits;  conditional E-value: 0.14
                   Ribosomal_L6e_N  14 vLvrGIgRYSrsamysrkal 33 
                                        L r +gRYS +   +r+a 
  gi|330508766|ref|YP_004385194.1| 481 ELYRSVGRYSDAEPLFRQAT 500
                                       5899*******999999885 PP

  == domain 10  score: 0.1 bits;  conditional E-value: 2.1
                   Ribosomal_L6e_N  12 NpvLv.rGIgRYSrsamysrkal 33 
                                       N++Lv +  gRYS +   +r+a 
  gi|330508766|ref|YP_004385194.1| 562 NLALVyDSMGRYSEAEPLFRQAT 584
                                       555643678*****999999885 PP

  == domain 11  score: -2.0 bits;  conditional E-value: 9.4
                   Ribosomal_L6e_N  19 IgRYSrsamysrkal 33 
                                        gRYS +   +r+a 
  gi|330508766|ref|YP_004385194.1| 612 MGRYSDAEPLFRQAT 626
                                       69***9999998875 PP

  == domain 12  score: 2.6 bits;  conditional E-value: 0.33
                   Ribosomal_L6e_N  14 vLvrGIgRYSrsamysrkal 33 
                                       vL r  gRYS +   +r+a 
  gi|330508766|ref|YP_004385194.1| 649 VLYRSMGRYSDAEPLFRQAT 668
                                       899********999999986 PP

>> Asparaginase_II  L-asparaginase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.27   1.3e+02     184     217 ..      49      82 ..      32     100 .. 0.78
   2 ?   -2.9   0.0       5.8   2.7e+03     185     205 ..      92     112 ..      88     116 .. 0.83
   3 ?   -1.6   0.0       2.3   1.1e+03     185     213 ..     134     162 ..     132     180 .. 0.73
   4 ?    0.3   0.0      0.62   2.9e+02     185     209 ..     176     200 ..     172     213 .. 0.82
   5 ?    1.1   0.0      0.33   1.6e+02     185     213 ..     218     246 ..     214     267 .. 0.78
   6 ?    2.0   0.0      0.18        87     185     216 ..     302     333 ..     298     356 .. 0.80
   7 ?    0.1   0.0      0.71   3.3e+02     185     217 ..     386     418 ..     373     435 .. 0.76
   8 ?    0.7   0.0      0.44   2.1e+02     185     216 ..     428     459 ..     424     489 .. 0.76
   9 ?   -2.7   0.0       4.8   2.3e+03     185     213 ..     470     498 ..     466     517 .. 0.76
  10 ?    2.6   0.0      0.12        58     184     226 ..     553     597 ..     535     607 .. 0.77
  11 ?   -1.0   0.0       1.4   6.8e+02     185     213 ..     638     666 ..     634     675 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.27
                   Asparaginase_II 184 aPlfalpLkglArafarlaaaaegleraealerv 217
                                        P +a +L++lA +++++++ +++ +  ++++++
  gi|330508766|ref|YP_004385194.1|  49 HPDYAASLNNLAELYRSMGRYNDAEPLFRQAAEI 82 
                                       6999***************988887744444444 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.8
                   Asparaginase_II 185 PlfalpLkglArafarlaaaa 205
                                       P +a++L++lA ++ ++++ +
  gi|330508766|ref|YP_004385194.1|  92 PDYATSLNNLALVYYSMGRYD 112
                                       889***********9998754 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.3
                   Asparaginase_II 185 PlfalpLkglArafarlaaaaegle..raea 213
                                       P  a+ L++lA +++++++ +e+ +  r  +
  gi|330508766|ref|YP_004385194.1| 134 PNCATGLNNLAELYRSIGRYSEAERlfR--Q 162
                                       889999***********99877776432..3 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.62
                   Asparaginase_II 185 PlfalpLkglArafarlaaaaegle 209
                                       P +a +L++lA +++++++ +e+ +
  gi|330508766|ref|YP_004385194.1| 176 PNYAASLNNLAILYRSMGRYNEAEP 200
                                       99***************99766555 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.33
                   Asparaginase_II 185 PlfalpLkglArafarlaaaaegle..raea 213
                                       P +a++L++lA ++ ++++ +e+ +  r  +
  gi|330508766|ref|YP_004385194.1| 218 PNYATSLNNLALVYDSMGRYSEAEPlfR--Q 246
                                       99***************99877777432..3 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.18
                   Asparaginase_II 185 PlfalpLkglArafarlaaaaegleraealer 216
                                       P++a +L++lA +++++++ +++ +  +++++
  gi|330508766|ref|YP_004385194.1| 302 PAYAQSLNNLAELYRSMGRYSDAEPLYRKATE 333
                                       99****************98888774444433 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 0.71
                   Asparaginase_II 185 PlfalpLkglArafarlaaaaegleraealerv 217
                                       P +a +L++lA +++++++ +++ +  ++++++
  gi|330508766|ref|YP_004385194.1| 386 PDYAQSLNNLAELYRSMGRYSDAEPLFRQATEI 418
                                       88999*************988887744444444 PP

  == domain 8  score: 0.7 bits;  conditional E-value: 0.44
                   Asparaginase_II 185 PlfalpLkglArafarlaaaaegleraealer 216
                                       P +a +L++lA +++++++ +++ +  +++++
  gi|330508766|ref|YP_004385194.1| 428 PEYAASLNNLAVLYRSMGRYSDAEPLFRQATE 459
                                       899**************998888774444444 PP

  == domain 9  score: -2.7 bits;  conditional E-value: 4.8
                   Asparaginase_II 185 PlfalpLkglArafarlaaaaegleraea 213
                                       P  a+ L++lA +++++++ +++ +  ++
  gi|330508766|ref|YP_004385194.1| 470 PNCATGLNNLAELYRSVGRYSDAEPLFRQ 498
                                       889999*********99998777763333 PP

  == domain 10  score: 2.6 bits;  conditional E-value: 0.12
                   Asparaginase_II 184 aPlfalpLkglArafarlaaaaegle..raealervaaamrahPe 226
                                        P +a++L++lA ++ ++++ +e+ +  r++++ r  +  r+hP+
  gi|330508766|ref|YP_004385194.1| 553 HPNYATSLNNLALVYDSMGRYSEAEPlfRQATEIRRKSLGRDHPD 597
                                       69*****************98888775544444444444456665 PP

  == domain 11  score: -1.0 bits;  conditional E-value: 1.4
                   Asparaginase_II 185 PlfalpLkglArafarlaaaaegleraea 213
                                       P +a +L++lA +++++++ +++ +  ++
  gi|330508766|ref|YP_004385194.1| 638 PDYAQSLNNLAVLYRSMGRYSDAEPLFRQ 666
                                       88999************998887773333 PP

>> DUF1897  Domain of unknown function (DUF1897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0058       2.8      15      35 ..      60      80 ..      49      81 .. 0.82
   2 ?   -1.3   0.0       3.4   1.6e+03      18      28 ..     105     115 ..     105     121 .. 0.87
   3 !    7.1   0.2     0.008       3.8      15      33 ..     144     162 ..     144     165 .. 0.84
   4 ?    4.4   0.0     0.056        26      18      28 ..     189     199 ..     188     204 .. 0.94
   5 ?    0.4   0.0      0.98   4.6e+02      18      33 ..     231     246 ..     231     249 .. 0.83
   6 ?   -2.2   0.2       6.4     3e+03      18      28 ..     273     283 ..     270     287 .. 0.89
   7 ?    4.4   0.2     0.055        26      15      28 ..     312     325 ..     312     331 .. 0.88
   8 ?   -1.6   0.0         4   1.9e+03      18      30 ..     357     369 ..     355     374 .. 0.80
   9 ?    5.8   0.0      0.02       9.4      15      33 ..     396     414 ..     384     417 .. 0.84
  10 ?    3.5   0.0      0.11        51      18      33 ..     441     456 ..     440     459 .. 0.84
  11 ?    3.7   0.0     0.093        44      15      33 ..     480     498 ..     480     501 .. 0.82
  12 ?    0.1   0.0       1.3   5.9e+02      15      33 ..     522     540 ..     511     543 .. 0.77
  13 ?    0.4   0.0      0.98   4.6e+02      18      33 ..     567     582 ..     567     585 .. 0.83
  14 ?   -1.3   0.0       3.2   1.5e+03      18      30 ..     609     621 ..     608     626 .. 0.80
  15 ?    3.5   0.0      0.11        51      18      33 ..     651     666 ..     650     669 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0058
                           DUF1897 15 aeYYrsiGmheeAeaieqqik 35
                                      ae Yrs+G   +Ae   +q++
  gi|330508766|ref|YP_004385194.1| 60 AELYRSMGRYNDAEPLFRQAA 80
                                      789***********8888876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.4
                           DUF1897  18 YrsiGmheeAe 28 
                                       Y s+G  ++Ae
  gi|330508766|ref|YP_004385194.1| 105 YYSMGRYDDAE 115
                                       77********9 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.008
                           DUF1897  15 aeYYrsiGmheeAeaieqq 33 
                                       ae YrsiG   eAe   +q
  gi|330508766|ref|YP_004385194.1| 144 AELYRSIGRYSEAERLFRQ 162
                                       688***********87666 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.056
                           DUF1897  18 YrsiGmheeAe 28 
                                       Yrs+G   eAe
  gi|330508766|ref|YP_004385194.1| 189 YRSMGRYNEAE 199
                                       **********9 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.98
                           DUF1897  18 YrsiGmheeAeaieqq 33 
                                       Y s+G   eAe   +q
  gi|330508766|ref|YP_004385194.1| 231 YDSMGRYSEAEPLFRQ 246
                                       89********976665 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 6.4
                           DUF1897  18 YrsiGmheeAe 28 
                                       Y s+G   +Ae
  gi|330508766|ref|YP_004385194.1| 273 YYSMGRYSDAE 283
                                       779***99998 PP

  == domain 7  score: 4.4 bits;  conditional E-value: 0.055
                           DUF1897  15 aeYYrsiGmheeAe 28 
                                       ae Yrs+G   +Ae
  gi|330508766|ref|YP_004385194.1| 312 AELYRSMGRYSDAE 325
                                       688********999 PP

  == domain 8  score: -1.6 bits;  conditional E-value: 4
                           DUF1897  18 YrsiGmheeAeai 30 
                                       Y siG   +Ae  
  gi|330508766|ref|YP_004385194.1| 357 YYSIGRYSDAEPL 369
                                       779******9965 PP

  == domain 9  score: 5.8 bits;  conditional E-value: 0.02
                           DUF1897  15 aeYYrsiGmheeAeaieqq 33 
                                       ae Yrs+G   +Ae   +q
  gi|330508766|ref|YP_004385194.1| 396 AELYRSMGRYSDAEPLFRQ 414
                                       788**********976655 PP

  == domain 10  score: 3.5 bits;  conditional E-value: 0.11
                           DUF1897  18 YrsiGmheeAeaieqq 33 
                                       Yrs+G   +Ae   +q
  gi|330508766|ref|YP_004385194.1| 441 YRSMGRYSDAEPLFRQ 456
                                       **********976655 PP

  == domain 11  score: 3.7 bits;  conditional E-value: 0.093
                           DUF1897  15 aeYYrsiGmheeAeaieqq 33 
                                       ae Yrs+G   +Ae   +q
  gi|330508766|ref|YP_004385194.1| 480 AELYRSVGRYSDAEPLFRQ 498
                                       688**********976655 PP

  == domain 12  score: 0.1 bits;  conditional E-value: 1.3
                           DUF1897  15 aeYYrsiGmheeAeaieqq 33 
                                       ae Yrs+    +Ae   +q
  gi|330508766|ref|YP_004385194.1| 522 AELYRSMSRYNDAESLFRQ 540
                                       788****999999977666 PP

  == domain 13  score: 0.4 bits;  conditional E-value: 0.98
                           DUF1897  18 YrsiGmheeAeaieqq 33 
                                       Y s+G   eAe   +q
  gi|330508766|ref|YP_004385194.1| 567 YDSMGRYSEAEPLFRQ 582
                                       89********976665 PP

  == domain 14  score: -1.3 bits;  conditional E-value: 3.2
                           DUF1897  18 YrsiGmheeAeai 30 
                                       Y s+G   +Ae  
  gi|330508766|ref|YP_004385194.1| 609 YYSMGRYSDAEPL 621
                                       77********965 PP

  == domain 15  score: 3.5 bits;  conditional E-value: 0.11
                           DUF1897  18 YrsiGmheeAeaieqq 33 
                                       Yrs+G   +Ae   +q
  gi|330508766|ref|YP_004385194.1| 651 YRSMGRYSDAEPLFRQ 666
                                       **********976655 PP

>> DUF5532  Family of unknown function (DUF5532)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.2   5.6e+02      22      82 ..      58     119 ..      49     124 .. 0.78
   2 ?   -0.4   0.0       2.5   1.2e+03      22      82 ..     142     203 ..     130     212 .. 0.72
   3 ?   -1.3   0.0       4.9   2.3e+03      49      86 ..     212     249 ..     173     255 .. 0.75
   4 ?   -2.2   0.0       9.1   4.3e+03      49      82 ..     254     287 ..     245     292 .. 0.81
   5 ?    2.3   0.0      0.38   1.8e+02      22      85 ..     310     374 ..     294     381 .. 0.66
   6 ?    3.8   0.0      0.12        58      45      85 ..     376     416 ..     373     423 .. 0.88
   7 ?   -2.2   0.0       9.4   4.4e+03      22      31 ..     478     487 ..     431     493 .. 0.67
   8 ?    0.4   0.0       1.4   6.8e+02      49      86 ..     632     669 ..     623     674 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.2
                           DUF5532  22 sLpeLYalvenfnkeskK.snllkthgislkEAqkmLsqnLnalsltsetdvreedsqpvlt 82 
                                        L eLY ++  +n       +   +++ sl E     + +Ln l+l  +  +r +d++p++ 
  gi|330508766|ref|YP_004385194.1|  58 NLAELYRSMGRYNDAEPLfRQAAEICRKSLGEDHPDYATSLNNLALVYYSMGRYDDAEPLFC 119
                                       57888888888886554314456789999999999999999999999999999999999875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.5
                           DUF5532  22 sLpeLYalvenfnkeskKs.nllkthgislkEAqkmLsqnLnalsltsetdvreedsqpvlt 82 
                                        L eLY ++  ++   +   +   + + sl E     + +Ln l+   +  +r ++++p+++
  gi|330508766|ref|YP_004385194.1| 142 NLAELYRSIGRYSEAERLFrQATEIRRKSLGEDHPNYAASLNNLAILYRSMGRYNEAEPLFR 203
                                       58899998888875443321234556778888888888888888888888888888888775 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.9
                           DUF5532  49 slkEAqkmLsqnLnalsltsetdvreedsqpvltckvv 86 
                                       sl E     + +Ln l+l  +  +r  +++p++++++ 
  gi|330508766|ref|YP_004385194.1| 212 SLGEDHPNYATSLNNLALVYDSMGRYSEAEPLFRQATE 249
                                       66666666677888888888888898899998887654 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 9.1
                           DUF5532  49 slkEAqkmLsqnLnalsltsetdvreedsqpvlt 82 
                                       sl E     sq+Ln l+   +  +r  d++p+++
  gi|330508766|ref|YP_004385194.1| 254 SLGEDHPDYSQSLNNLAGLYYSMGRYSDAEPLYR 287
                                       6666666779999999999999999999999875 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.38
                           DUF5532  22 sLpeLYalvenfnk.eskKsnllkthgislkEAqkmLsqnLnalsltsetdvreedsqpvltckv 85 
                                        L eLY ++  ++  e    +   + + sl E     sq+Ln l+l  +  +r  d++p++++++
  gi|330508766|ref|YP_004385194.1| 310 NLAELYRSMGRYSDaEPLYRKATEIRRKSLGEDHPDYSQSLNNLALMYYSIGRYSDAEPLFRQAT 374
                                       45666666665554123334445566667777777888888888888888888888888887654 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.12
                           DUF5532  45 thgislkEAqkmLsqnLnalsltsetdvreedsqpvltckv 85 
                                       +++ sl EA    +q+Ln l+   +  +r  d++p++++++
  gi|330508766|ref|YP_004385194.1| 376 IQRKSLGEAHPDYAQSLNNLAELYRSMGRYSDAEPLFRQAT 416
                                       56779*******************************98764 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 9.4
                           DUF5532  22 sLpeLYalve 31 
                                        L eLY +v 
  gi|330508766|ref|YP_004385194.1| 478 NLAELYRSVG 487
                                       5778887775 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 1.4
                           DUF5532  49 slkEAqkmLsqnLnalsltsetdvreedsqpvltckvv 86 
                                       sl E     +q+Ln l++  +  +r  d++p++++++ 
  gi|330508766|ref|YP_004385194.1| 632 SLGEDHPDYAQSLNNLAVLYRSMGRYSDAEPLFRQATE 669
                                       6666666679**********************998764 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1         1   4.8e+02     101     133 ..      58      90 ..      43     103 .. 0.80
   2 ?    1.3   0.1      0.87   4.1e+02     100     133 ..     141     174 ..     126     184 .. 0.80
   3 ?    3.2   2.6      0.24   1.1e+02      86     131 ..     295     340 ..     179     352 .. 0.50
   4 ?    1.3   0.0       0.9   4.2e+02      92     131 ..     343     382 ..     337     394 .. 0.83
   5 ?    2.8   0.1       0.3   1.4e+02      17      49 ..     400     432 ..     387     444 .. 0.69
   6 ?    1.6   0.0      0.72   3.4e+02      19      45 ..     444     470 ..     433     486 .. 0.66
   7 !    8.3   0.7    0.0061       2.9      19     134 ..     486     595 ..     473     605 .. 0.81
   8 ?    2.9   0.0      0.28   1.3e+02      20      46 ..     613     639 ..     598     654 .. 0.62
   9 ?    0.0   0.0       2.2   1.1e+03     106     134 ..     651     679 ..     642     682 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS-- CS
                              BTAD 101 qlmrAlarsGrqaeALevYerlrrlLaeeLgve 133
                                        l + ++ +Gr ++A   ++++ ++ ++ Lg +
  gi|330508766|ref|YP_004385194.1|  58 NLAELYRSMGRYNDAEPLFRQAAEICRKSLGED 90 
                                       566668899***************999999975 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.87
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS-- CS
                              BTAD 100 rqlmrAlarsGrqaeALevYerlrrlLaeeLgve 133
                                         l + ++  Gr +eA + ++++ ++ ++ Lg +
  gi|330508766|ref|YP_004385194.1| 141 NNLAELYRSIGRYSEAERLFRQATEIRRKSLGED 174
                                       5566668889*************99999999965 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.24
                                       HHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS CS
                              BTAD  86 ealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLg 131
                                       ++l + hP   ++   l + ++ +Gr ++A   Y+++ ++ ++ Lg
  gi|330508766|ref|YP_004385194.1| 295 KSLGEDHPAYAQSLNNLAELYRSMGRYSDAEPLYRKATEIRRKSLG 340
                                       2333445555555566666666666666666666666666666666 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.9
                                       STT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS CS
                              BTAD  92 hPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLg 131
                                       hP   ++   l + ++  Gr ++A   ++++ ++ ++ Lg
  gi|330508766|ref|YP_004385194.1| 343 HPDYSQSLNNLALMYYSIGRYSDAEPLFRQATEIQRKSLG 382
                                       66666677788899******************99999998 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.3
                                       HHTT-HHHHHHHHHHHHTT--SSTTGGGTTSTT CS
                              BTAD  17 laagdpeeaaelleaAlalwrGpaladleagew 49 
                                        + g+   a  l+++A ++wr ++ +d +++  
  gi|330508766|ref|YP_004385194.1| 400 RSMGRYSDAEPLFRQATEIWRKSLGEDHPEYAA 432
                                       455677777788888888888888888766554 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 0.72
                                       TT-HHHHHHHHHHHHTT--SSTTGGGT CS
                              BTAD  19 agdpeeaaelleaAlalwrGpaladle 45 
                                        g+   a  l+++A ++wr ++ +d +
  gi|330508766|ref|YP_004385194.1| 444 MGRYSDAEPLFRQATEIWRKSLGEDHP 470
                                       355566666777777777777776644 PP

  == domain 7  score: 8.3 bits;  conditional E-value: 0.0061
                                       TT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT- CS
                              BTAD  19 agdpeeaaelleaAlalwrGpaladleagewleaererleelrlealealaeaelrlGraeealaelealvaehPlr 95 
                                        g+   a  l+++A ++wr ++ +d +++     +r++l +     + +  +ae+ + +a e+ ++  +l   hP  
  gi|330508766|ref|YP_004385194.1| 486 VGRYSDAEPLFRQATEIWRKSLGEDHPDYAASLNNRAELYR----SMSRYNDAESLFRQATEIWRK--SLGGDHPNY 556
                                       5777889999***************9998888888877754....456666677777788888875..567899999 PP

                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS--- CS
                              BTAD  96 ErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvep 134
                                        ++   l + +  +Gr +eA   ++++ ++ ++ Lg + 
  gi|330508766|ref|YP_004385194.1| 557 ATSLNNLALVYDSMGRYSEAEPLFRQATEIRRKSLGRDH 595
                                       999999999999999999999999999999999999864 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.28
                                       T-HHHHHHHHHHHHTT--SSTTGGGTT CS
                              BTAD  20 gdpeeaaelleaAlalwrGpaladlea 46 
                                       g+   a  l+++A ++wr ++ +d ++
  gi|330508766|ref|YP_004385194.1| 613 GRYSDAEPLFRQATEIWRKSLGEDHPD 639
                                       444455556666666666666666555 PP

  == domain 9  score: 0.0 bits;  conditional E-value: 2.2
                                       HHHTT-HHHHHHHHHHHHHHHHHHHS--- CS
                              BTAD 106 larsGrqaeALevYerlrrlLaeeLgvep 134
                                       ++ +Gr ++A   ++++ ++ ++ Lg +p
  gi|330508766|ref|YP_004385194.1| 651 YRSMGRYSDAEPLFRQATEIRRKVLGKDP 679
                                       5679*******************999998 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   0.0       1.7   8.3e+02      36      66 ..      53      83 ..      44      88 .. 0.86
   2 ?    4.1   0.0     0.071        33      36      64 ..     137     165 ..     132     208 .. 0.87
   3 ?    1.2   0.0      0.56   2.6e+02      34      64 ..     261     291 ..     236     296 .. 0.86
   4 ?    0.8   0.0      0.76   3.6e+02      36      64 ..     305     333 ..     302     343 .. 0.86
   5 ?   -0.2   0.0       1.5   7.1e+02      36      63 ..     347     374 ..     333     385 .. 0.82
   6 ?   -0.1   0.0       1.4   6.4e+02      34      63 ..     387     416 ..     373     422 .. 0.82
   7 ?   -1.5   0.0       3.7   1.7e+03      36      63 ..     473     500 ..     469     503 .. 0.85
   8 ?   -1.0   0.0       2.7   1.3e+03      34      63 ..     597     626 ..     572     629 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.7
                                      HHHHHHHHHHHHHCT-HHHHHHHHHTCCCC- CS
                              RPN7 36 rrakldlaehYlkigdleeAlkaysrireyc 66
                                      ++  ++lae Y ++g ++ A  +++++ e c
  gi|330508766|ref|YP_004385194.1| 53 AASLNNLAELYRSMGRYNDAEPLFRQAAEIC 83
                                      667889**************99999998877 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.071
                                       HHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  36 rrakldlaehYlkigdleeAlkaysrire 64 
                                       + + ++lae Y +ig ++eA ++++++ e
  gi|330508766|ref|YP_004385194.1| 137 ATGLNNLAELYRSIGRYSEAERLFRQATE 165
                                       567899*****************998543 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.56
                                       HHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  34 eirrakldlaehYlkigdleeAlkaysrire 64 
                                       +  +  ++la  Y+++g ++ A  +y++++e
  gi|330508766|ref|YP_004385194.1| 261 DYSQSLNNLAGLYYSMGRYSDAEPLYRKAIE 291
                                       56788999*******************9987 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.76
                                       HHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  36 rrakldlaehYlkigdleeAlkaysrire 64 
                                       ++  ++lae Y ++g ++ A  +y+++ e
  gi|330508766|ref|YP_004385194.1| 305 AQSLNNLAELYRSMGRYSDAEPLYRKATE 333
                                       678899******************99654 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  36 rrakldlaehYlkigdleeAlkaysrir 63 
                                        +  ++la  Y++ig ++ A  +++++ 
  gi|330508766|ref|YP_004385194.1| 347 SQSLNNLALMYYSIGRYSDAEPLFRQAT 374
                                       6778899999******999999998854 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  34 eirrakldlaehYlkigdleeAlkaysrir 63 
                                       + ++  ++lae Y ++g ++ A  +++++ 
  gi|330508766|ref|YP_004385194.1| 387 DYAQSLNNLAELYRSMGRYSDAEPLFRQAT 416
                                       6789999***************99998875 PP

  == domain 7  score: -1.5 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  36 rrakldlaehYlkigdleeAlkaysrir 63 
                                       + + ++lae Y ++g ++ A  +++++ 
  gi|330508766|ref|YP_004385194.1| 473 ATGLNNLAELYRSVGRYSDAEPLFRQAT 500
                                       567899************9999988865 PP

  == domain 8  score: -1.0 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  34 eirrakldlaehYlkigdleeAlkaysrir 63 
                                       + ++  ++la  Y+++g ++ A  +++++ 
  gi|330508766|ref|YP_004385194.1| 597 DYAQSLNNLAGLYYSMGRYSDAEPLFRQAT 626
                                       568889999999*****9999999888865 PP

>> FCH  Fes/CIP4, and EFC/F-BAR homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.077        36      12      48 ..      30      67 ..      26     150 .. 0.81
   2 ?    0.0   0.1       2.3   1.1e+03      33      47 ..     178     192 ..     176     242 .. 0.52
   3 ?    2.7   1.1      0.32   1.5e+02      32      44 ..     303     315 ..     259     338 .. 0.60
   4 ?    2.1   0.1      0.49   2.3e+02      32      47 ..     345     360 ..     343     384 .. 0.83
   5 ?    4.6   0.5     0.085        40      32      48 ..     387     403 ..     379     467 .. 0.75
   6 ?   -1.9   0.0       9.2   4.3e+03      32      47 ..     513     528 ..     512     550 .. 0.74
   7 ?   -1.4   0.0       6.2   2.9e+03      32      46 ..     555     569 ..     553     583 .. 0.84
   8 ?    2.4   0.0      0.42     2e+02      32      47 ..     597     612 ..     596     635 .. 0.80
   9 ?    1.6   0.0      0.71   3.3e+02      32      46 ..     639     653 ..     637     677 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.077
                                      HHHHHHHHHHHHHHHHHHHH.HHHHHHHHHCT----TT CS
                               FCH 12 gialledlqeflkeRaeiEk.eYakkLqkLakkylkrr 48
                                       ia+ e+l++++ ++   +  +Ya++L++La+ y + +
  gi|330508766|ref|YP_004385194.1| 30 AIAFAEELRDLIWQKVGYDHpDYAASLNNLAELYRSMG 67
                                      5777777777777777777559********99998854 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.3
                                       HHHHHHHHCT----T CS
                               FCH  33 YakkLqkLakkylkr 47 
                                       Ya++L++La  y + 
  gi|330508766|ref|YP_004385194.1| 178 YAASLNNLAILYRSM 192
                                       666666666555543 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.32
                                       HHHHHHHHHCT-- CS
                               FCH  32 eYakkLqkLakky 44 
                                        Ya++L++La+ y
  gi|330508766|ref|YP_004385194.1| 303 AYAQSLNNLAELY 315
                                       3555555555554 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.49
                                       HHHHHHHHHCT----T CS
                               FCH  32 eYakkLqkLakkylkr 47 
                                       +Y+++L++La  y++ 
  gi|330508766|ref|YP_004385194.1| 345 DYSQSLNNLALMYYSI 360
                                       7*********999884 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.085
                                       HHHHHHHHHCT----TT CS
                               FCH  32 eYakkLqkLakkylkrr 48 
                                       +Ya++L++La+ y + +
  gi|330508766|ref|YP_004385194.1| 387 DYAQSLNNLAELYRSMG 403
                                       89999999999998864 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 9.2
                                       HHHHHHHHHCT----T CS
                               FCH  32 eYakkLqkLakkylkr 47 
                                       +Ya++L++ a+ y + 
  gi|330508766|ref|YP_004385194.1| 513 DYAASLNNRAELYRSM 528
                                       79****9999988875 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 6.2
                                       HHHHHHHHHCT---- CS
                               FCH  32 eYakkLqkLakkylk 46 
                                       +Ya +L++La  y++
  gi|330508766|ref|YP_004385194.1| 555 NYATSLNNLALVYDS 569
                                       6********988877 PP

  == domain 8  score: 2.4 bits;  conditional E-value: 0.42
                                       HHHHHHHHHCT----T CS
                               FCH  32 eYakkLqkLakkylkr 47 
                                       +Ya++L++La  y++ 
  gi|330508766|ref|YP_004385194.1| 597 DYAQSLNNLAGLYYSM 612
                                       7*********999885 PP

  == domain 9  score: 1.6 bits;  conditional E-value: 0.71
                                       HHHHHHHHHCT---- CS
                               FCH  32 eYakkLqkLakkylk 46 
                                       +Ya++L++La  y +
  gi|330508766|ref|YP_004385194.1| 639 DYAQSLNNLAVLYRS 653
                                       7*********88776 PP

>> Vault_4  Major Vault Protein repeat domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.68   3.2e+02      30      44 ..     412     426 ..     409     432 .. 0.85
   2 ?    1.3   0.0      0.77   3.6e+02      30      44 ..     454     468 ..     451     471 .. 0.85
   3 ?    1.3   0.0      0.75   3.6e+02      30      44 ..     496     510 ..     493     514 .. 0.85
   4 ?    0.3   0.0       1.6   7.3e+02      30      42 ..     538     550 ..     535     554 .. 0.84
   5 ?    1.3   0.0      0.77   3.6e+02      30      44 ..     622     636 ..     619     639 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.68
                           Vault_4  30 lteeEelWeKeLped 44 
                                        ++  e+W+K+L ed
  gi|330508766|ref|YP_004385194.1| 412 FRQATEIWRKSLGED 426
                                       67889*******876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.77
                           Vault_4  30 lteeEelWeKeLped 44 
                                        ++  e+W+K+L ed
  gi|330508766|ref|YP_004385194.1| 454 FRQATEIWRKSLGED 468
                                       67889******9875 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.75
                           Vault_4  30 lteeEelWeKeLped 44 
                                        ++  e+W+K+L ed
  gi|330508766|ref|YP_004385194.1| 496 FRQATEIWRKSLGED 510
                                       67889******9875 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 1.6
                           Vault_4  30 lteeEelWeKeLp 42 
                                        ++  e+W+K+L 
  gi|330508766|ref|YP_004385194.1| 538 FRQATEIWRKSLG 550
                                       67889*****996 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.77
                           Vault_4  30 lteeEelWeKeLped 44 
                                        ++  e+W+K+L ed
  gi|330508766|ref|YP_004385194.1| 622 FRQATEIWRKSLGED 636
                                       67889******9875 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 ?    5.7   0.0     0.016       7.6     298     331 ..      30      63 ..      19      68 .. 0.88
   2 ?    0.4   0.0      0.65     3e+02     272     328 ..     300     354 ..     297     361 .. 0.85
   3 ?   -0.5   0.1       1.2   5.9e+02     297     331 ..     365     399 ..     341     405 .. 0.75
   4 ?   -1.6   0.0       2.8   1.3e+03     276     327 ..     598     647 ..     575     653 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.016
                              HemX 298 vkaflkeldeLaeqsvsvdvPdklkslslLekll 331
                                       + af +el +L  q+v  d Pd ++sl+ L++l 
  gi|330508766|ref|YP_004385194.1|  30 AIAFAEELRDLIWQKVGYDHPDYAASLNNLAELY 63 
                                       55899*************************9986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.65
                              HemX 272 qnelYkqsLeevstwvrsyFdtddeavkaflkeldeLaeqsvsvdvPdklkslslLe 328
                                       ++  Y+qsL++ ++  rs    + +++  ++ + +e+  +s   d Pd ++sl+ L+
  gi|330508766|ref|YP_004385194.1| 300 DHPAYAQSLNNLAELYRSM--GRYSDAEPLYRKATEIRRKSLGEDHPDYSQSLNNLA 354
                                       6678999999999999995..56666778999999******************9986 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.2
                              HemX 297 avkaflkeldeLaeqsvsvdvPdklkslslLekll 331
                                       ++  +  + +e++ +s   + Pd ++sl+ L++l 
  gi|330508766|ref|YP_004385194.1| 365 DAEPLFRQATEIQRKSLGEAHPDYAQSLNNLAELY 399
                                       55566777889999999999**********99986 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 2.8
                              HemX 276 YkqsLeevstwvrsyFdtddeavkaflkeldeLaeqsvsvdvPdklkslslL 327
                                       Y+qsL++ +     y + + +++  +  + +e+  +s   d Pd ++sl+ L
  gi|330508766|ref|YP_004385194.1| 598 YAQSLNNLAGLY--YSMGRYSDAEPLFRQATEIWRKSLGEDHPDYAQSLNNL 647
                                       444444444332..22333444455555555666666666666666666666 PP

>> DUF2199  Uncharacterized protein conserved in bacteria (DUF2199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.7   1.3e+03      76     110 ..     199     233 ..     196     240 .. 0.88
   2 ?   -1.9   0.0       6.5     3e+03      78     110 ..     285     317 ..     280     321 .. 0.85
   3 ?    1.4   0.0      0.63     3e+02      76     110 ..     409     443 ..     405     449 .. 0.88
   4 ?    3.6   0.0      0.13        62      76     111 ..     493     528 ..     489     539 .. 0.88
   5 ?   -1.8   0.0         6   2.8e+03      76     110 ..     535     569 ..     532     574 .. 0.88
   6 ?   -1.4   0.0       4.6   2.2e+03      76     110 ..     619     653 ..     615     658 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.7
                           DUF2199  76 eesFerylekfeqeereseetyfgwlanaipvYes 110
                                       e  F+++ e + ++  e++++y   l+n   vY+s
  gi|330508766|ref|YP_004385194.1| 199 EPLFRKAIEIWRRSLGEDHPNYATSLNNLALVYDS 233
                                       55699999********************9999976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.5
                           DUF2199  78 sFerylekfeqeereseetyfgwlanaipvYes 110
                                        ++++ e++ ++  e+++ y   l+n  + Y s
  gi|330508766|ref|YP_004385194.1| 285 LYRKAIENWGKSLGEDHPAYAQSLNNLAELYRS 317
                                       5889999*****99**********999999965 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.63
                           DUF2199  76 eesFerylekfeqeereseetyfgwlanaipvYes 110
                                       e  F++++e + ++  e++++y + l+n    Y s
  gi|330508766|ref|YP_004385194.1| 409 EPLFRQATEIWRKSLGEDHPEYAASLNNLAVLYRS 443
                                       56799***********************9999965 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.13
                           DUF2199  76 eesFerylekfeqeereseetyfgwlanaipvYest 111
                                       e  F++++e + ++  e+++ y + l+n+ + Y s 
  gi|330508766|ref|YP_004385194.1| 493 EPLFRQATEIWRKSLGEDHPDYAASLNNRAELYRSM 528
                                       56799***************************9664 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 6
                           DUF2199  76 eesFerylekfeqeereseetyfgwlanaipvYes 110
                                       e+ F++++e + ++   ++++y   l+n   vY+s
  gi|330508766|ref|YP_004385194.1| 535 ESLFRQATEIWRKSLGGDHPNYATSLNNLALVYDS 569
                                       6779999*******999***********9999976 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 4.6
                           DUF2199  76 eesFerylekfeqeereseetyfgwlanaipvYes 110
                                       e  F++++e + ++  e+++ y   l+n    Y s
  gi|330508766|ref|YP_004385194.1| 619 EPLFRQATEIWRKSLGEDHPDYAQSLNNLAVLYRS 653
                                       5669999*******99*******999999998865 PP

>> Arg_decarb_HB  Arginine decarboxylase helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       5.1   2.4e+03       6      20 ..      54      76 ..      50     105 .. 0.62
   2 ?   -1.9   0.0       9.1   4.3e+03      27      27 ..     160     160 ..     137     209 .. 0.60
   3 ?   -0.4   0.0       2.9   1.4e+03      11      41 ..     243     273 ..     222     312 .. 0.77
   4 ?    0.5   0.0       1.5   7.3e+02       6      38 ..     306     354 ..     301     359 .. 0.71
   5 ?    4.0   0.0      0.13        61      11      42 ..     369     400 ..     367     423 .. 0.87
   6 ?   -0.8   0.0         4   1.9e+03       8      36 ..     476     520 ..     466     527 .. 0.65
   7 ?   -1.6   0.0       7.2   3.4e+03      19      41 ..     620     651 ..     596     658 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5.1
                     Arg_decarb_HB  6 ellqnLwelleels........q 20
                                      + l+nL+el++++          
  gi|330508766|ref|YP_004385194.1| 54 ASLNNLAELYRSMGryndaeplF 76
                                      56788888888887444444440 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 9.1
                     Arg_decarb_HB  27 y 27 
                                       +
  gi|330508766|ref|YP_004385194.1| 160 F 160
                                       1 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.9
                     Arg_decarb_HB  11 LwelleelsqrnlqEiyhDavhyldearelF 41 
                                       L++ ++e+++++l E + D  + l+ +  l+
  gi|330508766|ref|YP_004385194.1| 243 LFRQATEIRRKSLGEDHPDYSQSLNNLAGLY 273
                                       5556666778888888888888888887776 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.5
                     Arg_decarb_HB   6 ellqnLwelleels................qrnlqEiyhDavhyldear 38 
                                       + l+nL+el++++                 +++l E + D  + l+ + 
  gi|330508766|ref|YP_004385194.1| 306 QSLNNLAELYRSMGrysdaeplyrkateirRKSLGEDHPDYSQSLNNLA 354
                                       6688888888888877777777666666667778888887777777665 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.13
                     Arg_decarb_HB  11 LwelleelsqrnlqEiyhDavhyldearelFr 42 
                                       L++ ++e+++++l E++ D  + l+ + el+r
  gi|330508766|ref|YP_004385194.1| 369 LFRQATEIQRKSLGEAHPDYAQSLNNLAELYR 400
                                       67778889999999999999999999999997 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 4
                     Arg_decarb_HB   8 lqnLwelleels................qrnlqEiyhDavhylde 36 
                                       l+nL+el++++                 +++l E + D    l+ 
  gi|330508766|ref|YP_004385194.1| 476 LNNLAELYRSVGrysdaeplfrqateiwRKSLGEDHPDYAASLNN 520
                                       678888888888777777774444455555555555555555555 PP

  == domain 7  score: -1.6 bits;  conditional E-value: 7.2
                     Arg_decarb_HB  19 s.........qrnlqEiyhDavhyldearelF 41 
                                                 +++l E + D  + l+ +  l+
  gi|330508766|ref|YP_004385194.1| 620 PlfrqateiwRKSLGEDHPDYAQSLNNLAVLY 651
                                       04333333446777777777777766666665 PP

>> 14-3-3  14-3-3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         4   1.9e+03     137     171 ..      71     105 ..      52     113 .. 0.64
   2 ?    0.9   0.0      0.56   2.6e+02     136     190 ..     154     207 ..     144     234 .. 0.74
   3 ?   -0.5   0.0       1.5   7.3e+02     137     195 ..     197     254 ..     190     269 .. 0.76
   4 ?    3.8   0.1     0.076        36     136     176 ..     322     362 ..     311     401 .. 0.79
   5 ?   -1.5   0.0         3   1.4e+03     137     171 ..     407     441 ..     384     470 .. 0.69
   6 ?    0.3   0.0      0.88   4.2e+02     135     190 ..     531     585 ..     482     605 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4
                                       HHHHHHHHHHHHHHTTTGCC-HHHHHHHHHHHHHH CS
                            14-3-3 137 kakeaYeeAleiakkelqpthpirLglaLNySVfl 171
                                       +a+  +++A ei++k+l + hp +   + N ++ +
  gi|330508766|ref|YP_004385194.1|  71 DAEPLFRQAAEICRKSLGEDHPDYATSLNNLALVY 105
                                       45555666777777777766666555555555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.56
                                       HHHHHHHHHHHHHHHTTTGCC-HHHHHHHHHHHHHHHCTT--HHHHHHHHHHHHH CS
                            14-3-3 136 ekakeaYeeAleiakkelqpthpirLglaLNySVflyeilnspekAcelakkafd 190
                                       ++a++ +++A+ei +k+l + hp + + + N ++ ly  +   ++A  l +ka++
  gi|330508766|ref|YP_004385194.1| 154 SEAERLFRQATEIRRKSLGEDHPNYAASLNNLAI-LYRSMGRYNEAEPLFRKAIE 207
                                       5688899999999999999999998765555555.56667777777777776665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHTTTGCC-HHHHHHHHHHHHHHHCTT--HHHHHHHHHHHHHCCHCC CS
                            14-3-3 137 kakeaYeeAleiakkelqpthpirLglaLNySVflyeilnspekAcelakkafdeaiae 195
                                       +a+  +++A+ei +++l + hp + +  LN   + y+ +   ++A  l ++a +   + 
  gi|330508766|ref|YP_004385194.1| 197 EAEPLFRKAIEIWRRSLGEDHPNY-ATSLNNLALVYDSMGRYSEAEPLFRQATEIRRKS 254
                                       677778899999999999999987.5678888888899999998888888887655555 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.076
                                       HHHHHHHHHHHHHHHTTTGCC-HHHHHHHHHHHHHHHCTT- CS
                            14-3-3 136 ekakeaYeeAleiakkelqpthpirLglaLNySVflyeiln 176
                                       ++a+  Y++A+ei +k+l + hp +   + N ++++y i +
  gi|330508766|ref|YP_004385194.1| 322 SDAEPLYRKATEIRRKSLGEDHPDYSQSLNNLALMYYSIGR 362
                                       568889*****************999999999999998854 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHHHTTTGCC-HHHHHHHHHHHHHH CS
                            14-3-3 137 kakeaYeeAleiakkelqpthpirLglaLNySVfl 171
                                       +a+  +++A+ei +k+l + hp + + + N +V++
  gi|330508766|ref|YP_004385194.1| 407 DAEPLFRQATEIWRKSLGEDHPEYAASLNNLAVLY 441
                                       55666777777777777777777666555666554 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 0.88
                                       HHHHHHHHHHHHHHHHTTTGCC-HHHHHHHHHHHHHHHCTT--HHHHHHHHHHHHH CS
                            14-3-3 135 aekakeaYeeAleiakkelqpthpirLglaLNySVflyeilnspekAcelakkafd 190
                                        ++a++ +++A+ei +k+l   hp + +  LN   + y+ +   ++A  l ++a +
  gi|330508766|ref|YP_004385194.1| 531 YNDAESLFRQATEIWRKSLGGDHPNY-ATSLNNLALVYDSMGRYSEAEPLFRQATE 585
                                       45677888888888888888888876.56777777778888888888777777765 PP

>> Foie-gras_1  Foie gras liver health family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.9   2.3e+03     195     222 ..      58      85 ..      53      86 .. 0.85
   2 ?   -1.6   0.0       3.5   1.7e+03     195     222 ..     142     169 ..     137     171 .. 0.84
   3 ?   -1.5   0.1       3.3   1.6e+03     195     223 ..     184     212 ..     177     213 .. 0.89
   4 ?   -0.6   0.1       1.7   8.1e+02     194     216 ..     309     331 ..     222     339 .. 0.69
   5 ?   -1.8   0.0       4.1   1.9e+03     195     222 ..     352     379 ..     346     381 .. 0.84
   6 ?    3.8   0.0     0.077        36     195     223 ..     394     422 ..     384     423 .. 0.91
   7 ?    1.7   0.1      0.35   1.7e+02     195     223 ..     436     464 ..     430     465 .. 0.91
   8 ?    2.7   0.0      0.16        77     195     223 ..     478     506 ..     472     507 .. 0.92
   9 ?    0.9   0.1      0.58   2.8e+02     197     223 ..     522     548 ..     515     549 .. 0.90
  10 ?    4.0   0.0     0.066        31     195     223 ..     604     632 ..     579     633 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.9
                       Foie-gras_1 195 eiAeeylrlgdwkkalellqpltlsyrk 222
                                       ++Ae y  +g++++a  l++ ++ + rk
  gi|330508766|ref|YP_004385194.1|  58 NLAELYRSMGRYNDAEPLFRQAAEICRK 85 
                                       78999************99999877776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.5
                       Foie-gras_1 195 eiAeeylrlgdwkkalellqpltlsyrk 222
                                       ++Ae y  +g++++a +l++ +t + rk
  gi|330508766|ref|YP_004385194.1| 142 NLAELYRSIGRYSEAERLFRQATEIRRK 169
                                       689999*************998766665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.3
                       Foie-gras_1 195 eiAeeylrlgdwkkalellqpltlsyrke 223
                                       ++A  y  +g++++a  l++ +  ++r++
  gi|330508766|ref|YP_004385194.1| 184 NLAILYRSMGRYNEAEPLFRKAIEIWRRS 212
                                       67888999***************9**997 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.7
                       Foie-gras_1 194 leiAeeylrlgdwkkalellqpl 216
                                        ++Ae y  +g++++a  l++ +
  gi|330508766|ref|YP_004385194.1| 309 NNLAELYRSMGRYSDAEPLYRKA 331
                                       25666666677777766666665 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 4.1
                       Foie-gras_1 195 eiAeeylrlgdwkkalellqpltlsyrk 222
                                       ++A  y+ +g++++a  l++ +t + rk
  gi|330508766|ref|YP_004385194.1| 352 NLALMYYSIGRYSDAEPLFRQATEIQRK 379
                                       68889*************9999877666 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.077
                       Foie-gras_1 195 eiAeeylrlgdwkkalellqpltlsyrke 223
                                       ++Ae y  +g++++a  l++ +t ++rk+
  gi|330508766|ref|YP_004385194.1| 394 NLAELYRSMGRYSDAEPLFRQATEIWRKS 422
                                       799************************97 PP

  == domain 7  score: 1.7 bits;  conditional E-value: 0.35
                       Foie-gras_1 195 eiAeeylrlgdwkkalellqpltlsyrke 223
                                       ++A  y  +g++++a  l++ +t ++rk+
  gi|330508766|ref|YP_004385194.1| 436 NLAVLYRSMGRYSDAEPLFRQATEIWRKS 464
                                       6889999********************97 PP

  == domain 8  score: 2.7 bits;  conditional E-value: 0.16
                       Foie-gras_1 195 eiAeeylrlgdwkkalellqpltlsyrke 223
                                       ++Ae y  +g++++a  l++ +t ++rk+
  gi|330508766|ref|YP_004385194.1| 478 NLAELYRSVGRYSDAEPLFRQATEIWRKS 506
                                       78999**********************97 PP

  == domain 9  score: 0.9 bits;  conditional E-value: 0.58
                       Foie-gras_1 197 Aeeylrlgdwkkalellqpltlsyrke 223
                                       Ae y  + ++++a  l++ +t ++rk+
  gi|330508766|ref|YP_004385194.1| 522 AELYRSMSRYNDAESLFRQATEIWRKS 548
                                       7889999******************97 PP

  == domain 10  score: 4.0 bits;  conditional E-value: 0.066
                       Foie-gras_1 195 eiAeeylrlgdwkkalellqpltlsyrke 223
                                       ++A  y+ +g++++a  l++ +t ++rk+
  gi|330508766|ref|YP_004385194.1| 604 NLAGLYYSMGRYSDAEPLFRQATEIWRKS 632
                                       78889**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (801 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 1.15u 0.27s 00:00:01.42 Elapsed: 00:00:00.62
# Mc/sec: 3867.21
//
Query:       gi|330508767|ref|YP_004385195.1|  [L=185]
Description: phenylacrylic acid decarboxylase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-26   91.9   0.0    4.7e-26   91.4   0.0    1.2  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.0   2.6e-30   4.7e-26       1     125 [.       1     163 [.       1     172 [. 0.87

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 2.6e-30
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS.....TCSSHHHHHHCT...........TE CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.redpilhielrr...........wa 65 
                                       ++i++gi+G++++ ++++lle+Lk +g+ +++++t++A+k+i+ e ++ a+  e+ + h+   +            +
  gi|330508767|ref|YP_004385195.1|   1 MEIVVGISGASGVQYGIRLLEALKAKGCTTHLIITDSARKIIEIETSSPARgVEELAAHVYAPKdfsapvasgshLF 77 
                                       68*****************************************99443333445555555553367777777777** PP

                                       SEEEEEEEEHHHHHHHHTT--SSHH............................HHHHHTHCCTTEEEEE.--HHCCT CS
                      Flavoprotein  66 dllviaPasantlakianGiadnll............................tlilratakkpiliaPamnpamye 114
                                       d+lv++P+s+ tl+ ia+G +d+l+                             +++ a+++++++i+P + pa+y+
  gi|330508767|ref|YP_004385195.1|  78 DALVVIPCSMGTLSGIACGSSDTLItrcadvclkekrrlilvpretplsliqlRNMV-AASEAGAVILP-ACPAFYS 152
                                       ***********************************************9998863333.5799*******.******* PP

                                       CSTCHHHHHHH CS
                      Flavoprotein 115 npqtlknlekl 125
                                       +p++l +l+++
  gi|330508767|ref|YP_004385195.1| 153 QPKSLAELVDV 163
                                       *****999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.38u 0.19s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1613.40
//
Query:       gi|330508768|ref|YP_004385196.1|  [L=247]
Description: hypothetical protein MCON_3058 [Methanosaeta concilii GP6]
Scores for complete 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   47.4   0.0    2.4e-12   47.0   0.0    1.1  1  RlaP          RNA repair pathway DNA polymerase beta family
  ------ inclusion threshold ------
      0.099   12.9   0.0       0.19   12.0   0.0    1.5  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> RlaP  RNA repair pathway DNA polymerase beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   2.7e-16   2.4e-12      14     226 ..      23     242 ..      11     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 2.7e-16
                              RlaP  14 eeeevkilyacesGSrawGfpspdsDyDvrfiyiepaewylglert....rdvielpiddelDlvgwelrKalrLll 86 
                                       + ++++i y + +GS+ w ++ + sD+D+  iy  p++ +l+ e+     r+ ++    +  D+ gwe+   + Ll 
  gi|330508768|ref|YP_004385196.1|  23 KGRGMRIQYISCVGSHMWKMENETSDIDLVMIYTVPTRRILRGEKFpatiRQEMVARRGGIYDTLGWEIGHLIDLLI 99 
                                       333569***********************************9844333479999999999***************** PP

                              RlaP  87 ksNptvlewlsspivyledtseleellrlaekvflsrrvahhYlgmakkqlrry.....lkgeevr........lKk 150
                                       k+N + +    sp+v     s+l+e l++  ++ l r+++h   gma++q+++      l     +         K 
  gi|330508768|ref|YP_004385196.1| 100 KGNINAIWYATSPLV--IMPSALQEELSAIVQANLCRESYHSIKGMAESQIESEtgqlkL-----SgaglvkrpGKG 169
                                       ***************..888888999999999999****************987444442.....344444455899 PP

                              RlaP 151 ylyvlRpllagrwllekgetpPmefesllaalvdasleaeieeLlaikkggeekeagkrvpeldafiere.Lesaee 226
                                       y  +lR +  g +ll++ +   + +e  ++  + ++l++ +++L ++ ++++  +  ++ +  ++f+ r+ L+++ e
  gi|330508768|ref|YP_004385196.1| 170 YRTALRSINFGIELLREAR---ISYEPVMHDPTHEELKEGMNQLDEAYRQSMLPDL-PDEDQFRDFLLRQrLKEMDE 242
                                       9999999999999999999...4788888888888888888888888877777777.45555555555554666665 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.2e-05      0.19      17      74 ..      32      98 ..      17     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.2e-05
                                      EEEEHHHHCTTSCTTSSEEEEEEESTTCHHH.........HHHEHHHHHHHHCCCEEECTTEEEEEE CS
                      NTP_transf_2 17 vvlfGSyarGtalkgSDiDllvvlpeevsre.........kkeegleklaeiikfleellglevdlv 74
                                      + ++GS      +++SDiDl+ ++  ++ r          +++e   ++  i + l +  g+ +dl+
  gi|330508768|ref|YP_004385196.1| 32 ISCVGSHMWKMENETSDIDLVMIYTVPTRRIlrgekfpatIRQEMVARRGGIYDTLGWEIGHLIDLL 98
                                      66888888888999*************9877888777777555555555666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1845.45
//
Query:       gi|330508769|ref|YP_004385197.1|  [L=303]
Description: deoxyhypusine synthase [Methanosaeta concilii GP6]
Scores for 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-99  333.4   0.0    1.2e-99  333.3   0.0    1.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.3   0.0  6.5e-104   1.2e-99       2     287 ..      18     296 ..      17     297 .. 0.97

  Alignments for each domain:
  == domain 1  score: 333.3 bits;  conditional E-value: 6.5e-104
                                DS   2 llesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikal 78 
                                       l++ ++++gf a++l++a+di+++m  + + t fl+l+++++++G+r++++dl++ ++vdv+vtT++++ +D+i+++
  gi|330508769|ref|YP_004385197.1|  18 LVRGWSQCGFGARRLAQAADIYERML-SGDFTKFLTLSGAMVPAGMRHVVSDLIRGGHVDVLVTTGANLVHDIIESY 93 
                                       8999*********************5.6799********************************************** PP

                                DS  79 gkktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelGkeindeeSilyw 155
                                       +  + lg  e +d++Lr  g+ Ri+++++++e++ +fe+ +++i+ +  e   ++s ++l++ lG++i+de+Sil++
  gi|330508769|ref|YP_004385197.1|  94 SC-HTLGCAESNDSSLRTIGVSRIYDVFIRDEDFVAFEELMQSIFPESAE---SISGRQLLNILGSRISDERSILRS 166
                                       *9.********************************************998...49********************** PP

                                DS 156 AykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnan.lmr 231
                                       Ay+ ++pvfcpal D+++G+q+++f+   ++kkl++d+++Dire+ di+++++++g++i+GGGvpK+++l+++ ++ 
  gi|330508769|ref|YP_004385197.1| 167 AYDMEVPVFCPALPDSMIGLQAWMFS---QTKKLSVDAFADIREIVDICYNSERAGVVIVGGGVPKNFTLQSMlVTP 240
                                       **************************...7888****************************************5557 PP

                                DS 232 ngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                                       n +d a+++tt+++++G+lsgatl+Ea+Swgki+++a+ v+vy+DaTi+lPL+v a
  gi|330508769|ref|YP_004385197.1| 241 NSFDLAIQLTTDTPENGGLSGATLSEAISWGKISESASYVTVYGDATITLPLMVGA 296
                                       9****************************************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2365.80
//
Query:       gi|330508770|ref|YP_004385198.1|  [L=134]
Description: F420H2 dehydrogenase subunit A [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-30  105.3   5.2    1.4e-30  105.3   5.2    2.0  2  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch
  ------ inclusion threshold ------
        4.5    7.1   7.9       0.23   11.2   1.1    2.1  2  MaAIMP_sms   Putative methionine and alanine importer, small 


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 ?    2.5   0.4     0.018   1.6e+02      36      52 ..       4      20 ..       1      27 [. 0.85
   2 !  105.3   5.2   1.6e-34   1.4e-30       3      99 .]      27     133 ..      24     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.018
                                      --HHCHHHHHHHHHHHH CS
                       Oxidored_q4 36 lrfsvkfylvallFliF 52
                                      +++ v +y+  ++Fli+
  gi|330508770|ref|YP_004385198.1|  4 EPMAVVYYIPLIIFLIM 20
                                      678999********996 PP

  == domain 2  score: 105.3 bits;  conditional E-value: 1.6e-34
                                       HHHHHHCHSS-----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST.......HHHH. CS
                       Oxidored_q4   3 lllllsallgpkkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkel.....glfg. 73 
                                       ++l++ ++++p+kp+++kls YE G++p+++a++++sv++yl+a++F+iFDvev+fl+pw+ ++ ++          
  gi|330508770|ref|YP_004385198.1|  27 AALAAIKIIAPNKPSRQKLSIYEGGLKPIRDAKIQYSVQYYLFAIVFVIFDVEVLFLYPWIYVYANEamqkfM--Vf 101
                                       5677788999****************************************************98877554441..13 PP

                                       ......HHHHHHHHHHHHHHHHHHHHH-S-XX CS
                       Oxidored_q4  74 ......liemllFllillvglvYewkkgaLeW 99 
                                             ++emllF+++llvgl+Y++kk+aL+W
  gi|330508770|ref|YP_004385198.1| 102 gsmniaVFEMLLFIIVLLVGLIYAIKKEALRW 133
                                       3555558************************* PP

>> MaAIMP_sms  Putative methionine and alanine importer, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.8      0.18   1.6e+03      11      28 ..      14      32 ..       6      40 .. 0.61
   2 ?   11.2   1.1   2.6e-05      0.23       5      24 ..     107     126 ..     104     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.18
                        MaAIMP_sms 11 LFiviiWGGLv.laliaLr 28
                                      L i +i G +v +a++a +
  gi|330508770|ref|YP_004385198.1| 14 LIIFLIMGAIVpIAALAAI 32
                                      4455666766645555554 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2.6e-05
                        MaAIMP_sms   5 AiimmvLFiviiWGGLvlal 24 
                                       A+  m+LFi+++  GL++a+
  gi|330508770|ref|YP_004385198.1| 107 AVFEMLLFIIVLLVGLIYAI 126
                                       7889**************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 921.42
//
Query:       gi|330508771|ref|YP_004385199.1|  [L=190]
Description: F420H2 dehydrogenase subunit B [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.4e-20   71.3   0.0    9.4e-20   70.8   0.0    1.3  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.0   5.2e-24   9.4e-20      43     131 .]      94     177 ..      68     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 5.2e-24
                                       TTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS- CS
                       Oxidored_q6  43 ekeadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvgeevgellevvpvdinipGCPp 119
                                        ++ dv++++G +trk  +  ++l+e ++++k++ia+G+CA++GG +  +++++    +++  ++ p+d++ipGCPp
  gi|330508771|ref|YP_004385199.1|  94 PRQTDVMIISGYLTRKYLPVFKNLWENMPEPKWCIAIGECAISGGPF--YDSYNI---IQNTGDYFPIDVYIPGCPP 165
                                       4599*******************************************..664444...4578899************ PP

                                       -HHHHHHHHHHH CS
                       Oxidored_q6 120 hpeailetllal 131
                                       +pe++le+l++l
  gi|330508771|ref|YP_004385199.1| 166 RPEQFLEGLMNL 177
                                       ********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1369.54
//
Query:       gi|330508772|ref|YP_004385200.1|  [L=570]
Description: F420H2 dehydrogenase subunit D [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-79  266.9   0.3    2.8e-76  256.2   0.1    2.8  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
      5e-31  107.9   0.0    9.9e-31  106.9   0.0    1.5  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
    2.5e-07   30.0   0.0    6.4e-07   28.6   0.0    1.7  2  NiFeSe_Hases    Nickel-dependent hydrogenase
  ------ inclusion threshold ------
       0.19   10.4   0.0       0.27    9.9   0.0    1.1  1  efThoc1         THO complex subunit 1 transcription elongatio


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 ?   -1.0   0.0      0.17   7.7e+02     108     152 ..      34      81 ..      32      98 .. 0.79
   2 !  256.2   0.1   6.3e-80   2.8e-76       6     271 .]     330     570 .]     327     570 .] 0.97

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.17
                                       TTHHHHSS-SSG..GGS-------SSB.SHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa 108 yDlRkaepYeaY..deldfdvpvgeeg.DvydRylvrveEmrqSlkIi 152
                                       +D  k ++ + Y  d+l fd   g++g D  +R  + v E+  S  I 
  gi|330508772|ref|YP_004385200.1|  34 VDSKKIRDVCKYmtDKLGFDHYAGSAGvDWIARNEMEVVEIMASYGIH 81 
                                       6666777777776689999999999865999*********99998874 PP

  == domain 2  score: 256.2 bits;  conditional E-value: 6.3e-80
                                       HHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSS CS
                    Complex1_49kDa   6 tvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkg 82 
                                       ++  y++ +Reki++l+e+vtGaRlt+s++r+GGv++Dlpeg+ e++++++ +++++++e+ +l+ +++i+++R+++
  gi|330508772|ref|YP_004385200.1| 330 APWQYMIMDREKIISLIESVTGARLTHSFVRFGGVRNDLPEGFDEQCRKVFPYMKSRIEEFIELFAQDPIYHARMEN 406
                                       57789************************************************************************ PP

                                       SS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                    Complex1_49kDa  83 vgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqalekl 159
                                       +g +s e+a ++g++G vlRa+Gv+yD+R ++p  +Y eldf+v++g++gD+ dR+ + ++Em +S++Iieq+l+k+
  gi|330508772|ref|YP_004385200.1| 407 IGSISPETAKRIGCAGRVLRAAGVPYDMRIEDPILVYPELDFKVVTGTRGDSADRIDCTLREMLESIHIIEQCLDKI 483
                                       ***************************************************************************** PP

                                       -.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HH CS
                    Complex1_49kDa 160 pegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlkiraps 236
                                       p+gp+++e+   ++pk                      k+p+ge+y +vE p+Ge+g+y++sdg++kpyr+k+r p 
  gi|330508772|ref|YP_004385200.1| 484 PSGPIKTEA---KIPK----------------------KIPAGEAYYRVEDPRGEMGMYVISDGGDKPYRVKVRGPF 535
                                       ****88843...2233......................46************************************* PP

                                       HHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 237 fvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       ++++q+l+ ll+g ++aD+vai gs+d + +e DR
  gi|330508772|ref|YP_004385200.1| 536 YATFQTLTPLLEGVYIADAVAIAGSMDGCPSESDR 570
                                       **********************************9 PP

>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   0.0   2.2e-34   9.9e-31       1     117 [.      32     149 ..      32     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 2.2e-34
                                       EE--HHHHHHHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--.S-.-EEEEEE....-S-BEE--TTT-S CS
                    Complex1_30kDa   1 lvvepedllevakflkdeeelgfdvlsdltavDek.eerfevvyhllsl.eknerirvkvevdeeepevpSvtdlfp 75 
                                       ++v+++++++v+k++ d  +lgfd+ +   +vD+  ++++evv +++s+  +n+  ++kv++++++p+vpS++d++ 
  gi|330508772|ref|YP_004385200.1|  32 VTVDSKKIRDVCKYMTD--KLGFDHYAGSAGVDWIaRNEMEVVEIMASYgIHNVVAMLKVKTPRDNPSVPSLVDMYW 106
                                       5899*************..5*************9999************8788888999999*************** PP

                                       THHHHHHHHHHHSHHBCTTSSTSS-SSSSTTSSS-.TTSTTS- CS
                    Complex1_30kDa  76 gadwyEREayDmfGivfeghpdlrrillpedfegh.PLRkdfp 117
                                       +a+wyERE+++mfGi+feghp+l  +ll +  +g  P+Rkdf+
  gi|330508772|ref|YP_004385200.1| 107 NANWYERETWEMFGINFEGHPELYPLLLSDPLVGVwPWRKDFK 149
                                       ****************************99965544******7 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.4e-10   6.4e-07       1      68 [.     248     315 ..     248     325 .. 0.97
   2 ?   -3.3   0.0      0.69   3.1e+03     393     439 ..     476     518 ..     446     527 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.4e-10
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhiv 68 
                                       +G+E+i+++r   +  ++++R+C V + +   +   ave+ lg+++p  a++ir +++    +++h++
  gi|330508772|ref|YP_004385200.1| 248 KGIEKIMENRSWLQGITYTDRMCYVAALSNNECYCGAVERLLGLEVPLRAQYIRVILEELSRIQSHLI 315
                                       59****************************************************************97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.69
                                       HHHHHHHHHTTB---B--TT-SGGGS-SEEEEEEEEEETTEEEEEEE CS
                      NiFeSe_Hases 393 ldelvenikkgdtetaneekldkkevpkeakGvglveapRGaLsHwi 439
                                       +++  ++i +g    +++e   +k++p+  + +  ve pRG ++ ++
  gi|330508772|ref|YP_004385200.1| 476 IEQCLDKIPSG---PIKTEAKIPKKIPA-GEAYYRVEDPRGEMGMYV 518
                                       33444444444...33344444677787.889999999999998765 PP

>> efThoc1  THO complex subunit 1 transcription elongation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   6.1e-05      0.27      36      57 ..     374     394 ..     370     414 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 6.1e-05
                           efThoc1  36 dgcrkffdYlesriewfkekgf 57 
                                       ++crk+f+Y+ srie+f e  f
  gi|330508772|ref|YP_004385200.1| 374 EQCRKVFPYMKSRIEEFIE-LF 394
                                       68***************98.56 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3637.11
//
Query:       gi|330508773|ref|YP_004385201.1|  [L=350]
Description: F420H2 dehydrogenase subunit H [Methanosaeta concilii GP6]
Scores for complete 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-102  342.2  17.6   3.1e-102  341.9  17.6    1.0  1  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.9  17.6  1.7e-106  3.1e-102       4     297 ..      29     341 ..      26     343 .. 0.96

  Alignments for each domain:
  == domain 1  score: 341.9 bits;  conditional E-value: 1.7e-106
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTS--S-SST.TTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHH CS
                            NADHdh   4 llllvvlllvvalltlleRkvlAriqdRlGPnrvG.plGllqplaDalKlllKediipkkadkllfllapvlalila 79 
                                       ++l +v+ + ++l+++++Rkv++ + +R GPnrvG  +G+lq+ aDa+Kl++Ked+ip+++dk ++++ap++a + +
  gi|330508773|ref|YP_004385201.1|  29 AVLSAVVNVGAMLVIWADRKVMSDFCNRFGPNRVGgRWGILQLGADAIKLFTKEDVIPAGVDKGVYVWAPIIASAGT 105
                                       455566777888**********************8699*************************************** PP

                                       HCTTTTS-SSS..........SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHH CS
                            NADHdh  80 llafaviPfge..........vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalgls 146
                                       +l+ a+iPfg+          v+a+++++ +++ a +s++ +++++aG++sn+kY++lGa+R +a mi+yEv++g++
  gi|330508773|ref|YP_004385201.1| 106 MLVAAAIPFGAlhiggknyplVVANMDISAFYVEAALSIMSIAVFMAGYSSNNKYSILGAFRGIARMIAYEVPMGVC 182
                                       **********5556678899********************************************************* PP

                                       HHHHHHHH-SS-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHH CS
                            NADHdh 147 llavvllagslslseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalffla 223
                                       +++v+++a+sl+l eive+q+ +w++++q+l+f+if+ial+  ++r+PFD  eae+E++ G+ tEYsg++++l++++
  gi|330508773|ref|YP_004385201.1| 183 VISVAVMAHSLNLVEIVESQT-VWYAFAQPLGFVIFMIALVTDLGRVPFDQSEAEEEIICGYSTEYSGIRWGLLYFQ 258
                                       ********************6.9****************************************************** PP

                                       HHHHHHHHHHHHHHHCT.SS-HCCS.........HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHH CS
                            NADHdh 224 eyanmvlvsalavllFlgGwllpfs.........gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllpla 291
                                       ey n +l s+l++llFlgGw++p++         +++w+l+Kv+++++++i+ira+l RlR+dq+++lgwk++lpl+
  gi|330508773|ref|YP_004385201.1| 259 EYNNFLLGSILVSLLFLGGWHGPIIpiplldmvsPMIWLLMKVIIVIWFIILIRAALFRLRIDQVTDLGWKWMLPLS 335
                                       ***********************999*************************************************** PP

                                       HHHHHH CS
                            NADHdh 292 lanlll 297
                                       ++nl +
  gi|330508773|ref|YP_004385201.1| 336 ILNLGW 341
                                       ***976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2477.33
//
Query:       gi|330508774|ref|YP_004385202.1|  [L=193]
Description: 4Fe-4S ferredoxin, iron-sulfur binding domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-13   49.4  19.4    3.7e-07   29.7   5.3    2.2  2  Fer4      4Fe-4S binding domain
    1.9e-10   41.2  13.7    3.5e-10   40.3  13.7    1.5  1  Fer4_7    4Fe-4S dicluster domain
      2e-09   37.4  20.8    1.7e-07   31.3  11.4    2.0  2  Fer4_10   4Fe-4S dicluster domain
    8.1e-08   32.3  14.1    2.3e-07   30.8  14.2    1.7  1  Fer4_21   4Fe-4S dicluster domain
    8.5e-08   32.3  10.6    1.9e-07   31.1  10.7    1.6  1  Fer4_9    4Fe-4S dicluster domain
    2.6e-07   30.3  11.8     0.0003   20.7   2.6    2.4  2  Fer4_2    4Fe-4S binding domain
    5.3e-07   30.1   5.4     0.0028   18.2   0.5    2.6  2  Fer4_17   4Fe-4S dicluster domain
      5e-06   27.3  15.5     0.0014   19.5   1.8    3.0  2  Fer4_16   4Fe-4S double cluster binding domain
    5.6e-05   23.0  18.7     0.0054   16.8   6.2    2.3  2  Fer4_6    4Fe-4S binding domain
    0.00032   21.0  14.6     0.0032   17.8   2.4    2.4  2  Fer4_4    4Fe-4S binding domain
    0.00041   20.7  14.7     0.0013   19.1  13.9    2.1  2  Fer4_8    4Fe-4S dicluster domain
    0.00071   20.3  18.6       0.19   12.5   3.0    3.0  2  Fer4_15   4Fe-4S single cluster domain
     0.0009   20.0  10.0     0.0093   16.8   0.8    2.5  3  Fer4_22   4Fe-4S dicluster domain
  ------ inclusion threshold ------
        0.4   11.7  26.1        1.1   10.4   9.0    2.4  2  Fer4_3    4Fe-4S binding domain
       0.43   10.8  12.2    1.9e+02    2.2  12.2    2.5  1  Fer4_18   4Fe-4S dicluster domain
          6    7.5  20.7        2.4    8.8   0.9    3.2  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   6.2   5.6e-09   6.3e-06       3      24 .]      44      65 ..      42      65 .. 0.90
   2 !   29.7   5.3   3.3e-10   3.7e-07       1      24 []      83     106 ..      83     106 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.6e-09
                                      EETTTSSS-THHHHHSTTTEEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                       d   CigCG C+ vCP+ +I+
  gi|330508774|ref|YP_004385202.1| 44 LDATICIGCGSCARVCPNSCIE 65
                                      68899*************9996 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 3.3e-10
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       ++id+ +C++CG+Cv+ CPv++++
  gi|330508774|ref|YP_004385202.1|  83 PQIDYGRCMFCGLCVDECPVECLK 106
                                       68*******************985 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3  13.7   3.2e-13   3.5e-10       2      51 ..      49     103 ..      48     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 3.2e-13
                            Fer4_7   2 CigCgaCvaaCpvkaield.....eeenekgtekveidpekClgCgaCvavCPtg 51 
                                       CigCg C+++Cp+++ie+      +  ++k+++ ++id+ +C++Cg Cv++CP++
  gi|330508774|ref|YP_004385202.1|  49 CIGCGSCARVCPNSCIEMVhfkfgNPLKNKKMQFPQIDYGRCMFCGLCVDECPVE 103
                                       *****************885544434456677889******************96 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3  11.4   1.5e-10   1.7e-07       4      56 .]      44     101 ..      41     101 .. 0.93
   2 !   18.4   1.9   1.5e-06    0.0017       3      24 ..      84     114 ..      82     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.5e-10
                           Fer4_10   4 idddtCirCgkCvkaCPadl.....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +d+  Ci+Cg C ++CP +       + g+  ++++ +  ++++++C++cg Cv++CP
  gi|330508774|ref|YP_004385202.1|  44 LDATICIGCGSCARVCPNSCiemvhFKFGNPLKNKKMQFPQIDYGRCMFCGLCVDECP 101
                                       68999*************88999988899999999999999****************9 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.5e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.........t 24 
                                       +id  +C+ Cg Cv+ CP+            
  gi|330508774|ref|YP_004385202.1|  84 QIDYGRCMFCGLCVDECPVEClkmgkkvimA 114
                                       6889999999999999999666644444440 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8  14.2   2.1e-10   2.3e-07       3      59 .]      44     107 ..      42     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.1e-10
                           Fer4_21   3 idedkCigCgkCliaCedtshqai.......eidaktvl.kvvedeCvGCnlCssvCPvedciem 59 
                                       +d   CigCg+C+ +C++++++ +        +++k ++ ++   +C+ C lC++ CPv +c++m
  gi|330508774|ref|YP_004385202.1|  44 LDATICIGCGSCARVCPNSCIEMVhfkfgnpLKNKKMQFpQIDYGRCMFCGLCVDECPV-ECLKM 107
                                       57789*******************555554312222333345578*************9.**998 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1  10.7   1.7e-10   1.9e-07       2      49 ..      49     103 ..      48     105 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.7e-10
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase.......eaCigCgaCveaCpkg 49 
                                       C+gCg+C ++Cp+  +++ +++  + l+++++        +C++Cg Cv+ Cp +
  gi|330508774|ref|YP_004385202.1|  49 CIGCGSCARVCPNSCIEMVHFKFGNPLKNKKMqfpqidyGRCMFCGLCVDECPVE 103
                                       **************************9999889******99************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 !   20.7   2.6   2.7e-07    0.0003       5      22 .]      44      61 ..      41      61 .. 0.89
   2 !   14.5   1.9   2.5e-05     0.028       3      21 ..      83     101 ..      82     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.7e-07
                            Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                       d+ +CigCg+C  +CP+
  gi|330508774|ref|YP_004385202.1| 44 LDATICIGCGSCARVCPN 61
                                      57889************5 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.5e-05
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       +++d  rC+ Cg Cv+ CP
  gi|330508774|ref|YP_004385202.1|  83 PQIDYGRCMFCGLCVDECP 101
                                       789**************** PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.5   2.5e-06    0.0028      38      59 ..      41      62 ..       6      63 .. 0.75
   2 !   13.9   0.5   5.2e-05     0.058      42      58 ..      86     102 ..      66     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.5e-06
                           Fer4_17 38 ekeekaslCieCgeCerkCPqg 59
                                      + e  a  Ci+Cg C+r+CP++
  gi|330508774|ref|YP_004385202.1| 41 IHELDATICIGCGSCARVCPNS 62
                                      33457899************85 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.2e-05
                           Fer4_17  42 kaslCieCgeCerkCPq 58 
                                         ++C+ Cg+C+ +CP 
  gi|330508774|ref|YP_004385202.1|  86 DYGRCMFCGLCVDECPV 102
                                       55677777777777774 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   1.8   1.3e-06    0.0014       2      20 ..      49      67 ..      48      86 .. 0.80
   2 !   11.8   6.2   0.00031      0.35       1      29 [.      89     116 ..      89     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-06
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++Cg Ca vCP ++i++ 
  gi|330508774|ref|YP_004385202.1| 49 CIGCGSCARVCPNSCIEMV 67
                                      ****************987 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00031
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeieare 29 
                                       rC  Cg C++ CP++++k+  +k+i a  
  gi|330508774|ref|YP_004385202.1|  89 RCMFCGLCVDECPVECLKMG-KKVIMAGW 116
                                       6999**************99.45554443 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   6.2   4.8e-06    0.0054       5      21 ..      45      61 ..      44      66 .. 0.87
   2 !   11.8   4.6   0.00018       0.2       1      22 [.      82     103 ..      82     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.8e-06
                            Fer4_6  5 dpdkCigCgdCvrvCPe 21
                                      d+  CigCg C+rvCP 
  gi|330508774|ref|YP_004385202.1| 45 DATICIGCGSCARVCPN 61
                                      6779************5 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00018
                            Fer4_6   1 vveidpdkCigCgdCvrvCPeg 22 
                                       +++id+ +C  Cg Cv+ CP  
  gi|330508774|ref|YP_004385202.1|  82 FPQIDYGRCMFCGLCVDECPVE 103
                                       689*****************75 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   2.4   2.9e-06    0.0032       4      15 ..      49      60 ..      38      72 .. 0.90
   2 !    8.3   4.6    0.0032       3.6       3      16 ..      89     102 ..      87     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-06
                            Fer4_4  4 CigCgsCvaaCP 15
                                      CigCgsC ++CP
  gi|330508774|ref|YP_004385202.1| 49 CIGCGSCARVCP 60
                                      ************ PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0032
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       rC  Cg Cv+ CP+
  gi|330508774|ref|YP_004385202.1|  89 RCMFCGLCVDECPV 102
                                       8999*********7 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1  13.9   1.1e-06    0.0013       3      64 ..      47     103 ..      45     104 .. 0.85
   2 !   11.5   4.3   0.00029      0.32       4      17 ..      89     111 ..      86     184 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                            Fer4_8   3 ekCieCgaCqsaCp.vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                         Ci+Cg C   Cp ++ ++ ++++ ++ ++++ +q  q        ++C+ cg C+++Cpv+
  gi|330508774|ref|YP_004385202.1|  47 TICIGCGSCARVCPnSCIEMVHFKFGNPLKNKK-MQFPQI-----DYGRCMFCGLCVDECPVE 103
                                       67***********96667777888888888888.888888.....58**************96 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00029
                            Fer4_8   4 kCieCgaCqsaCp.........v 17 
                                       +C+ Cg+C ++Cp         v
  gi|330508774|ref|YP_004385202.1|  89 RCMFCGLCVDECPveclkmgkkV 111
                                       79999999999995444333330 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   3.0   0.00017      0.19       3      20 ..      44      61 ..      43      66 .. 0.91
   2 !   12.3   7.8    0.0002      0.22       3      44 ..      85     148 ..      84     166 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                           Fer4_15  3 vDrdaCigcglCvaeape 20
                                      +D + Cigcg C++++p+
  gi|330508774|ref|YP_004385202.1| 44 LDATICIGCGSCARVCPN 61
                                      899*************97 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0002
                           Fer4_15   3 vDrdaCigcglCvaeapevfeldedglasvl........................lddgeiaegev 44 
                                       +D  +C+ cglCv+e+p  +e  + g++++                         ++d e + +++
  gi|330508774|ref|YP_004385202.1|  85 IDYGRCMFCGLCVDECP--VECLKMGKKVIMagwerkdivkgpdflatkrfsakeVADLEAEAKRI 148
                                       8999************9..88888999987788888888888888766666555433222222222 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.8   8.3e-06    0.0093      74      94 ..      41      61 ..       5      63 .. 0.66
   2 !    7.0   2.3    0.0092        10      74      95 ..      82     103 ..      65     104 .. 0.75
   3 ?    5.7   3.1     0.023        26       1      25 [.      89     113 ..      89     184 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.3e-06
                           Fer4_22 74 kekfgesgCvGCgRCieacpv 94
                                       ++ +++ C+GCg C ++cp+
  gi|330508774|ref|YP_004385202.1| 41 IHELDATICIGCGSCARVCPN 61
                                      3456999************97 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0092
                           Fer4_22  74 kekfgesgCvGCgRCieacpvk 95 
                                         +++   C+ Cg C++ cpv+
  gi|330508774|ref|YP_004385202.1|  82 FPQIDYGRCMFCGLCVDECPVE 103
                                       4566888999*********986 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.023
                           Fer4_22   1 rClsCgaCtlvCptCsCfdvedet.k 25 
                                       rC+ Cg C   Cp   C ++ +++  
  gi|330508774|ref|YP_004385202.1|  89 RCMFCGLCVDECPV-ECLKMGKKViM 113
                                       69999999999985.67777666543 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   9.0   0.00098       1.1       1      13 [.      49      61 ..      49      63 .. 0.94
   2 ?    7.1   9.2     0.011        12       1      13 [.      90     102 ..      90     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00098
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+gCg C +vCP+
  gi|330508774|ref|YP_004385202.1| 49 CIGCGSCARVCPN 61
                                      ************6 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.011
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+ Cg+Cv+ CPv
  gi|330508774|ref|YP_004385202.1|  90 CMFCGLCVDECPV 102
                                       99**********8 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2  12.2      0.17   1.9e+02      57     102 ..      45     107 ..      32     117 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.17
                           Fer4_18  57 gagdcidcescvkvcPtg.idi..........rkGlql......eciscllcidacdkvmekl 102
                                       +a+ ci c+sc +vcP   i++           k +q+       c+ c+lc+d c     k+
  gi|330508774|ref|YP_004385202.1|  45 DATICIGCGSCARVCPNScIEMvhfkfgnplkNKKMQFpqidygRCMFCGLCVDECPVECLKM 107
                                       556799999999999964233211111111112334433333334888999999987555455 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   5.6    0.0026       2.9       4      18 ..      47      61 ..      44      63 .. 0.87
   2 ?    8.8   0.9    0.0022       2.4       1      17 [.      85     101 ..      85     123 .. 0.89
   3 ?   -0.4   0.7       1.6   1.8e+03      31      49 ..     148     165 ..     125     166 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0026
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                        Ci+cg+C+ ++P+
  gi|330508774|ref|YP_004385202.1| 47 TICIGCGSCARVCPN 61
                                      66************7 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0022
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       +D  +C+ cg+Cv+ +P
  gi|330508774|ref|YP_004385202.1|  85 IDYGRCMFCGLCVDECP 101
                                       67889***********9 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.6
                           Fer4_13  31 vaeqptseeekadaeeAad 49 
                                       +a+++   ++ka a++Aa+
  gi|330508774|ref|YP_004385202.1| 148 IAAEKA-AAKKAAAKDAAA 165
                                       333333.445666777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1225  (0.0683251); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1362.85
//
Query:       gi|330508775|ref|YP_004385203.1|  [L=100]
Description: F420H2 dehydrogenase subunit K [Methanosaeta concilii GP6]
Scores for complete 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-23   81.3   6.2    3.6e-23   81.2   6.2    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   6.2     2e-27   3.6e-23       2     103 ..       7      95 ..       6     100 .] 0.96

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 2e-27
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHH CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaiviga 78 
                                       + ll+ ++f+iGlyg+++++n +k ++++el++n++n++lv++++++              ++ +q+++L+ i+++a
  gi|330508775|ref|YP_004385203.1|   7 YILLASIMFTIGLYGLITQKNGVKLMMCIELLLNSANINLVAFSAYQ-------------PNMNGQVFALFSIALAA 70 
                                       678999*****************************************.............9**************** PP

                                       HHHHHHHHHHHHHHHHSSS-BCCG- CS
                       Oxidored_q2  79 aetavgLallvrlyreygtddvqel 103
                                       ae+ vg a+l++lyr ygt+d++++
  gi|330508775|ref|YP_004385203.1|  71 AEAGVGFAILIALYRLYGTIDLDNI 95 
                                       ***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 734.43
//
Query:       gi|330508776|ref|YP_004385204.1|  [L=679]
Description: F420H2 dehydrogenase subunit L [Methanosaeta concilii GP6]
Scores for complete 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-75  252.1  26.6    9.2e-75  251.6  25.5    2.0  1  Proton_antipo_M  Proton-conducting membrane transporter
    2.5e-15   56.3   0.2    2.5e-15   56.3   0.2    3.9  5  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
     0.0096   15.6   0.3        0.3   10.7   0.0    2.9  3  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 !  251.6  25.5   1.5e-78   9.2e-75       1     281 [.     127     418 ..     127     438 .. 0.90

  Alignments for each domain:
  == domain 1  score: 251.6 bits;  conditional E-value: 1.5e-78
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefe.elskal.... 72 
                                       a++Ll+l++++Elv+l++ylLig+w++kp++++A+ k+fl+t++g++++L +i++lyn+  +l+++ +  ++l    
  gi|330508776|ref|YP_004385204.1| 127 ADNLLQLFIFWELVGLCSYLLIGFWYRKPSAAAAAKKAFLTTRVGDVMFLAAIIVLYNNLVNLNITlNPGEYLlqfp 203
                                       79********************************************************9997777632223334557 PP

                   Proton_antipo_M  73 .....elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavss 143
                                             + +   +l+l++l ll g++ Ks+q+plh+Wlpda +e+Pt vsa++ Aat+v+agv+l++r+++l+  ++
  gi|330508776|ref|YP_004385204.1| 204 viyahIAEIPPDQLTLIALGLLGGAVGKSGQFPLHVWLPDA-MEGPTTVSAMIhAATMVTAGVFLVARMFPLFY-AA 278
                                       887644445556789999***********************.********************************.9* PP

                   Proton_antipo_M 144 neisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialav...atqygveaaiihllthalfkallFl 217
                                       +     ++++++ ++l++++++l+ +diKr+lA+S++s+lG+m+ +l+v    ++ +v  +++hl+ h++fkallFl
  gi|330508776|ref|YP_004385204.1| 279 PHGLTAVAAVGAFTALFAATMGLTAFDIKRVLAFSTVSQLGFMMAGLGVgaaVGAFAVGVSMFHLIGHSFFKALLFL 355
                                       ***********************************************99544466778889**************** PP

                   Proton_antipo_M 218 lagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavsli 281
                                       +agsvi++  +t+d+r++gg  k+m  +  ++l++ lslaG P+++gF+sk++i++ a++++  
  gi|330508776|ref|YP_004385204.1| 356 CAGSVIHAV-NTNDMREMGGVGKYMKWTMYTMLIGSLSLAGFPLFTGFFSKDEIIMIAYEYGIA 418
                                       *****9987.9***********************************************998754 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 !   56.3   0.2   4.1e-19   2.5e-15      11      55 ..      68     112 ..      62     114 .. 0.95
   2 ?   -2.0   0.0      0.65   3.9e+03      30      37 ..     249     256 ..     248     257 .. 0.91
   3 ?   -2.6   0.1         1   6.2e+03      24      42 ..     319     337 ..     304     337 .. 0.76
   4 ?   -3.4   0.1       1.7     1e+04      32      54 ..     468     486 ..     465     489 .. 0.67
   5 ?    0.7   0.6     0.096   5.7e+02      11      34 ..     643     666 ..     630     670 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 4.1e-19
                   Proton_antipo_N  11 sieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfa 55 
                                       ++++g+l+D+ls++mll+v++v +l+h+Y  gYM +d+g +R+fa
  gi|330508776|ref|YP_004385204.1|  68 DFNVGILIDPLSLIMLLMVSLVVTLIHIYGNGYMNGDPGAARYFA 112
                                       699*****************************************8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.65
                   Proton_antipo_N  30 tfvsllvh 37 
                                       t+vs+++h
  gi|330508776|ref|YP_004385204.1| 249 TTVSAMIH 256
                                       89*****9 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1
                   Proton_antipo_N  24 lmllvvtfvsllvhlYSig 42 
                                        +++   +v++ v  +++g
  gi|330508776|ref|YP_004385204.1| 319 GFMMAGLGVGAAVGAFAVG 337
                                       4677778899998888876 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 1.7
                   Proton_antipo_N  32 vsllvhlYSigYMa.ddegyqRFf 54 
                                       v l +  +++g+ a +d     F+
  gi|330508776|ref|YP_004385204.1| 468 VILAIFAFAFGFAAqHD-----FY 486
                                       67788888888877344.....44 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.096
                   Proton_antipo_N  11 sieigfllDklsalmllvvtfvsl 34 
                                       +++ g+  + ++alml +v +v +
  gi|330508776|ref|YP_004385204.1| 643 KVQTGVVQNYVTALMLGIVVLVIA 666
                                       57778888899*****99999866 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 ?   -2.3   0.1      0.47   2.8e+03      98     116 ..     384     402 ..     374     406 .. 0.80
   2 !   10.7   0.0   5.1e-05       0.3      85     116 ..     447     479 ..     431     494 .. 0.79
   3 ?    1.3   0.0     0.038   2.3e+02     165     190 ..     554     579 ..     551     602 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.47
                   Proton_antipo_C  98 ntmlfpllvLvlftlfvGl 116
                                       +tml+  l L+ f lf G+
  gi|330508776|ref|YP_004385204.1| 384 YTMLIGSLSLAGFPLFTGF 402
                                       6888888888888888887 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.1e-05
                   Proton_antipo_C  85 enkktlsy.PhEsdntmlfpllvLvlftlfvGl 116
                                       + k+ ++y  hEs++ ml pl++L++f +  G+
  gi|330508776|ref|YP_004385204.1| 447 TGKERSNYgKHESPWVMLGPLVILAIFAFAFGF 479
                                       44454444159*****************99998 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.038
                   Proton_antipo_C 165 ialfGifiAsllYkpvysslqnldli 190
                                       +al Gi+iA l+Y    +++++ +++
  gi|330508776|ref|YP_004385204.1| 554 VALGGILIAALFYWDRVKKFDPSQVT 579
                                       8999*********9999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (679 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1085  (0.0605165); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 4109.25
//
Query:       gi|330508777|ref|YP_004385205.1|  [L=500]
Description: F420H2 dehydrogenase subunit M [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-73  246.0  28.2    9.2e-73  245.0  28.2    1.5  1  Proton_antipo_M  Proton-conducting membrane transporter
    0.00068   19.7   3.9    0.00068   19.7   3.9    5.0  4  Oxidored_q5_N    NADH-ubiquinone oxidoreductase chain 4, amin
  ------ inclusion threshold ------
      0.024   14.7   0.2      0.024   14.7   0.2    4.2  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 !  245.0  28.2   1.5e-76   9.2e-73       1     293 []     125     425 ..     125     425 .. 0.91

  Alignments for each domain:
  == domain 1  score: 245.0 bits;  conditional E-value: 1.5e-76
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg....tlefeelskal. 72 
                                       a d +l+y+++E+vl+p+++Lig w+   ++ +A++k+f++t ++sl++Ll+i++ly        +  f+ l +   
  gi|330508777|ref|YP_004385205.1| 125 ALDFFLFYIFWEIVLIPMFFLIGSWGGP-RKDYAAIKFFIYTHVASLVMLLAIFALYFTYQlpdgSRTFDMLTLLKa 200
                                       57899********************765.99***********************99876544445666666655544 PP

                   Proton_antipo_M  73 ...elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssne 145
                                             +    l++++  ll+g+lvK++++p+h+Wlpda+veaPt++s+ lAa+l+k+g+++l+r+++++   ++++
  gi|330508777|ref|YP_004385205.1| 201 tqnPEIFPPALLNIIFAGLLLGFLVKMPAFPFHTWLPDAHVEAPTAGSVVLAALLLKMGGYGLFRIIVPMLpSVDKI 277
                                       466666677788999999*****************************************************899999 PP

                   Proton_antipo_M 146 isqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsv 222
                                          +++i+a++s+++g+++alaq diK+l+AySs+sh+G++++++++    ++++a+++ ++h++++  lF+ ag +
  gi|330508777|ref|YP_004385205.1| 278 FVTIIAIIAVLSIVYGAFLALAQKDIKKLVAYSSVSHMGFVTLGAVALVPLSIQGAMFQQFSHGIITCVLFMSAGTI 354
                                       99*********************************************9999***********************766 PP

                   Proton_antipo_M 223 iyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvlt 293
                                        ++ + tr i+++ggLa +mP +a++++ ++++  GlP+++gF+++f++L++a+a  ++ ++++ ++++v+t
  gi|330508777|ref|YP_004385205.1| 355 -QHVVGTRIIADLGGLADRMPKFAVIMMAGFMASLGLPGMSGFVAEFMTLTGAYATLPVYVMIVvFLSIVIT 425
                                       .6677*************************************************998777666636666665 PP

>> Oxidored_q5_N  NADH-ubiquinone oxidoreductase chain 4, amino terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   3.9   1.1e-07   0.00068       3      93 ..       9     109 ..       7     123 .. 0.59
   2 ?    0.0   1.3      0.15     9e+02       5      43 ..     139     178 ..     129     197 .. 0.54
   3 ?   -1.7   0.7      0.51   3.1e+03      34      40 ..     285     291 ..     263     349 .. 0.56
   4 ?   -1.3   5.5      0.37   2.2e+03      22      75 ..     412     465 ..     380     477 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-07
                     Oxidored_q5_N   3 killptlmliplvllskkkllwststlvslllallsll.l............lnlsssfslsnlsyllglDslSapL 66 
                                       +illp+l  i++ ++ +k +++   ++ sl  ++lsl  +            + +++      ++y+lg+D + +pL
  gi|330508777|ref|YP_004385205.1|   9 MILLPLLGAIVSFFVGTKAKFV--ALIASLAPLVLSLQmYmefdksstmmqfVESYNWVPSIGVKYTLGVDGIGFPL 83 
                                       5666666666666665554442..222222222222221111111111100033333333346899*********** PP

                     Oxidored_q5_N  67 ilLSlWllpLmilASqkhlkkepknrq 93 
                                       +lLS+ +++L+i+ S+  +kk p+++ 
  gi|330508777|ref|YP_004385205.1|  84 VLLSTIVTVLVIIYSWGETKK-PNQYF 109
                                       ****************99999.66554 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.15
                     Oxidored_q5_N   5 llptlmliplvllskkkllwststlvslllallsll.lln 43 
                                       l+p+++li ++   +k +  + +++++ + +l++ll ++ 
  gi|330508777|ref|YP_004385205.1| 139 LIPMFFLIGSWGGPRKDYAAIKFFIYTHVASLVMLLaIFA 178
                                       4455555444444344455555555555555555553333 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.51
                     Oxidored_q5_N  34 lallsll 40 
                                       +a+ls++
  gi|330508777|ref|YP_004385205.1| 285 IAVLSIV 291
                                       2222222 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.37
                     Oxidored_q5_N  22 llwststlvslllallsllllnlsssfslsnlsyllglDslSapLilLSlWllp 75 
                                       + +++++++s+++++   l+ +++ +f     +y+   D   + L  +S+ +l 
  gi|330508777|ref|YP_004385205.1| 412 VYVMIVVFLSIVITAAYHLWAMQKAMFGPILRKYMDVHDPHAYELFSMSMIILL 465
                                       344566667777777777777777777777777777778888888888887664 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.3      0.65   3.9e+03      11      27 ..      42      58 ..      40      59 .. 0.73
   2 ?   14.7   0.2     4e-06     0.024       2      42 ..      62     100 ..      61     113 .. 0.82
   3 ?   -1.9   0.4      0.61   3.7e+03      26      40 ..     161     175 ..     155     179 .. 0.63
   4 ?   -2.2   0.7      0.79   4.7e+03      19      37 ..     275     290 ..     270     293 .. 0.55
   5 ?   -4.6   1.1         3   1.8e+04      27      36 ..     415     424 ..     412     431 .. 0.58
   6 ?   -2.3   0.1      0.82   4.9e+03      42      51 ..     444     454 ..     443     465 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.65
                   Proton_antipo_N 11 sieigfllDklsalmll 27
                                      s+++ + +Dk s +m +
  gi|330508777|ref|YP_004385205.1| 42 SLQMYMEFDKSSTMMQF 58
                                      56677888998888865 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4e-06
                   Proton_antipo_N   2 ftWlsvgglsieigfllDklsalmllvvtfvsllvhlYSig 42 
                                       ++W+++  + ++ ++ +D++    +l+ t+v++lv++YS+g
  gi|330508777|ref|YP_004385205.1|  62 YNWVPS--IGVKYTLGVDGIGFPLVLLSTIVTVLVIIYSWG 100
                                       678883..34999999***********************98 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.61
                   Proton_antipo_N  26 llvvtfvsllvhlYS 40 
                                        ++ t v++lv+l +
  gi|330508777|ref|YP_004385205.1| 161 FFIYTHVASLVMLLA 175
                                       556666777776644 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 0.79
                   Proton_antipo_N  19 Dklsalmllvvtfvsllvh 37 
                                       Dk+ ++ ++++ ++s   +
  gi|330508777|ref|YP_004385205.1| 275 DKIFVTIIAIIAVLS---I 290
                                       555555555554444...3 PP

  == domain 5  score: -4.6 bits;  conditional E-value: 3
                   Proton_antipo_N  27 lvvtfvsllv 36 
                                       ++v f+s ++
  gi|330508777|ref|YP_004385205.1| 415 MIVVFLSIVI 424
                                       4455555444 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 0.82
                   Proton_antipo_N  42 gYMa.ddegyq 51 
                                       +YM+ +d++  
  gi|330508777|ref|YP_004385205.1| 444 KYMDvHDPHAY 454
                                       69998898644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3139.23
//
Query:       gi|330508778|ref|YP_004385206.1|  [L=498]
Description: F420H2 dehydrogenase subunit N [Methanosaeta concilii GP6]
Scores for 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  214.3  30.0      2e-63  214.3  30.0    3.2  2  Proton_antipo_M  Proton-conducting membrane transporter
  ------ inclusion threshold ------
       0.83    9.3   2.5        1.7    8.2   2.5    1.5  1  GET2             GET complex subunit GET2


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 ?   -5.2   5.6       1.7   1.6e+04      76      76 ..      69      69 ..      11     119 .. 0.48
   2 !  214.3  30.0   2.3e-67     2e-63       1     292 [.     120     435 ..     120     436 .. 0.87

  Alignments for each domain:
  == domain 1  score: -5.2 bits;  conditional E-value: 1.7
                   Proton_antipo_M 76 l 76
                                      +
  gi|330508778|ref|YP_004385206.1| 69 V 69
                                      1 PP

  == domain 2  score: 214.3 bits;  conditional E-value: 2.3e-67
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       + dL++l++g+El +l++y ++++ k+k k+leA++k+f++++++s ++L+g++lly++tg++ + +++ a +    
  gi|330508778|ref|YP_004385206.1| 120 SVDLVTLFVGFELASLSTYAMAAFDKTK-KNLEAAMKYFIYGSVSSAFMLFGFSLLYGMTGSTRLADVAAA-SVESF 194
                                       569*********************9887.9***************************************99.55555 PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllil 153
                                         ++l++ll++++g+++K+a+vp+h+W pd y++aP+ vsallAa   k+g  + +r+ll+    +  e++  ++il
  gi|330508778|ref|YP_004385206.1| 195 GAATLVALLFVIAGFAFKMALVPFHMWAPDTYEGAPALVSALLAAGSKKMGFAAAFRVLLIALvAMRVEWYLAFAIL 271
                                       5667778888999******************************999**********9999999899*********** PP

                   Proton_antipo_M 154 aiismllgslvalaqtdiKrllAySsishlGymlialav....at...............qygveaaiihllthalf 211
                                       a+++m lg+l+a  q++++r+lAySsi++ Gy+ ia++v     +               q g+++a++++l hal+
  gi|330508778|ref|YP_004385206.1| 272 AAVTMTLGNLAACWQNNVRRILAYSSIAQAGYIAIAFVVvgaaYGdapvnvlnlgmfpadQLGIAGALLLILGHALM 348
                                       *********************************9998774322002222222222222225689************* PP

                   Proton_antipo_M 212 kallFllagsviyere.....ktrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslill 283
                                       k + F+ + +v +  +     + +di +y+gLa + P++a ++l+++++laG+Pptag+++kf ++++a+  +l++l
  gi|330508778|ref|YP_004385206.1| 349 KTGAFIGSAQVASMVSksdaeDPDDISNYAGLASRAPVTAFCMLIFMFALAGIPPTAGYIGKFVLFSSAIYSGLVWL 425
                                       *****9876664332244455889*************************************************9999 PP

                   Proton_antipo_M 284 vla.vvasvl 292
                                       +++ ++ s+l
  gi|330508778|ref|YP_004385206.1| 426 AVLaILNSAL 435
                                       9986777766 PP

>> GET2  GET complex subunit GET2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.5   0.00019       1.7     181     250 ..      74     150 ..      68     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00019
                              GET2 181 kklkarfllvrllllllnfvYhvfrssks.......alvralteasvrnFftvFltfEvvllsiyylllkkiekenk 250
                                       + +ka+fl+v ll++++ +  +  ++s++       a v ++  +s+   +t+F+ fE+++ls+y ++    +k+n 
  gi|330508778|ref|YP_004385206.1|  74 QFFKAVFLIVSLLVVIASLSKYTGKGSDEffallllATVGMMIVSSSVDLVTLFVGFELASLSTYAMAAFDKTKKNL 150
                                       7799*******99999665555546666689999886666666666699****************998755555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 3515.29
//
Query:       gi|330508779|ref|YP_004385207.1|  [L=66]
Description: hypothetical protein MCON_3072 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 482.82
//
Query:       gi|330508780|ref|YP_004385208.1|  [L=281]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-32  112.0   0.0    5.2e-32  111.2   0.0    1.4  1  ABC_tran     ABC transporter
      4e-16   59.7   3.0    2.1e-10   40.9   0.1    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    5.3e-09   36.2   0.3    0.00033   20.5   0.1    2.1  2  AAA_15       AAA ATPase domain
    9.4e-09   35.0   0.2    2.9e-08   33.4   0.2    1.7  1  SMC_N        RecF/RecN/SMC N terminal domain
    1.1e-05   25.0   0.1    2.4e-05   24.0   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0014   19.2   0.1     0.0019   18.7   0.1    1.3  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.026   14.7   0.0      0.042   14.1   0.0    1.4  1  AAA_28       AAA domain
      0.032   14.2   0.2      0.066   13.1   0.0    1.5  2  RsgA_GTPase  RsgA GTPase
      0.089   12.7   0.5       0.55   10.1   0.1    2.0  2  NACHT        NACHT domain
       0.15   12.4   0.1        0.2   12.0   0.1    1.5  1  AAA_16       AAA ATPase domain
       0.16   11.7   0.2        1.6    8.4   0.0    2.1  2  AAA_24       AAA domain
       0.17   12.1   0.0        2.5    8.4   0.0    2.3  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 !  111.2   0.0   3.5e-35   5.2e-32       1     137 []      25     180 ..      25     180 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 3.5e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.........B-HHHCCHCEEEE-SS. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxx. RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.........qeleslrkeigvlpqe. 67 
                                       lk++++k+++ge v i+G+nG+GKStLl++l gl+ pt+G+    g++++e         + ++ +r ++g+++q+ 
  gi|330508780|ref|YP_004385208.1|  25 LKDITIKINRGEQVTIIGSNGSGKSTLLAVLNGLVYPTAGDFFAFGHPVTEevfdsikenKFRTYFRTKVGFVFQNs 101
                                       799***************************************888***99999999999888999***********8 PP

                                       .--S-TTSBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEE CS
                                       .xxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  68 .pqlfpeltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkll 130
                                         qlf+ + v e+             e ++++e++++ +++ +l+d+      ++LSgG+k++v++a +l+++p++l
  gi|330508780|ref|YP_004385208.1| 102 dIQLFSST-VFEEiafgplqlnipleEVKARVEDIIEMMQIAKLRDRAP----HTLSGGEKKKVCIATVLVNNPDVL 173
                                       78888888.88888************99***************999998....************************ PP

                                       EEESTTT CS
                                       xxxxxxx RF
                          ABC_tran 131 llDEpta 137
                                       llDEp+a
  gi|330508780|ref|YP_004385208.1| 174 LLDEPSA 180
                                       *****75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.6   6.8e-07     0.001       4      26 ..      40      67 ..      38      95 .. 0.66
   2 !   40.9   0.1   1.4e-13   2.1e-10     211     303 .]     144     215 ..     117     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.8e-07
                            AAA_21  4 liGpNgsGKSnLLdaldllarl.....d 26
                                      +iG NgsGKS+LL  l +l        +
  gi|330508780|ref|YP_004385208.1| 40 IIGSNGSGKSTLLAVLNGLVYPtagdfF 67
                                      9***************999322444444 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 1.4e-13
                            AAA_21 211 svderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                       ++                  ++ ++ lS G k+  +++t l   +   ++ll+DEp +gL+P+ +  l+ell+els 
  gi|330508780|ref|YP_004385208.1| 144 LR------------------DRAPHTLSGGEKKKVCIATVLVNNP---DVLLLDEPSAGLDPRTQLWLIELLRELSH 199
                                       43..................445788****************999...9**************************** PP

                            AAA_21 288 ngaQviltTHSpllld 303
                                        g  +i +TH+ +++d
  gi|330508780|ref|YP_004385208.1| 200 AGKTIITATHDLEIMD 215
                                       9************997 PP

>> AAA_15  AAA ATPase 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   0.00033      13      50 ..      24      62 ..      23     137 .. 0.75
   2 !   14.2   0.0   1.8e-05     0.027     322     368 ..     168     213 ..     162     214 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.2e-07
                            AAA_15 13 slkdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      +lkd++i+++     ++iG N+sGKS++l +l+ +   +
  gi|330508780|ref|YP_004385208.1| 24 ALKDITIKINRGeQVTIIGSNGSGKSTLLAVLNGLVYPT 62
                                      5899999999988899****************8776655 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.8e-05
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                       +++++ll++EP a L p  q  li+ll+el+  +k  +i  TH   i
  gi|330508780|ref|YP_004385208.1| 168 NNPDVLLLDEPSAGLDPRTQLWLIELLRELSHAGK-TIITATHDLEI 213
                                       57899*****************************8.78888**8765 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 !   33.4   0.2   1.9e-11   2.9e-08      23     205 ..      35     216 ..      20     231 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.9e-11
                                       TSSEEEEEESTTSSHHHHHHHHH...HHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAil...FvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiek 94 
                                        +    i+G+NGSGKs ll  +    +     +  ++ +  ++++  +  +++ +   + +v  +f+n+d +     
  gi|330508780|ref|YP_004385208.1|  35 GE-QVTIIGSNGSGKSTLLAVLNglvYPTAG-DFFAFGHPVTEEVFDSikENKFRTYFRTKVGFVFQNSDIQ---LF 106
                                       33.45799********998766411133332.33356666666665554337777888999999*****999...33 PP

                                       SCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-S...TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  95 eevsisrrvkrkgeseykingkevtkkevsellesagis...kelLSgGektLvalaLlfAiqkvkpaplyllDeid 168
                                       ++++ +  ++   + ++ +++ +++ +++ e+++ a++    +++LSgGek+ v +a ++    v+   + llDe  
  gi|330508780|ref|YP_004385208.1| 107 SSTVFEEIAFGPLQLNIPLEEVKARVEDIIEMMQIAKLRdraPHTLSGGEKKKVCIATVL----VNNPDVLLLDEPS 179
                                       4455555566666789999****************9997222569*******99998874....55556779***** PP

                                       TTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 169 aaLDeknvkkvaellkeksknaQfivislreemleka 205
                                       a LD +    + ell+e s+    i+++ ++  + ++
  gi|330508780|ref|YP_004385208.1| 180 AGLDPRTQLWLIELLRELSHAGKTIITATHDLEIMDM 216
                                       *******************998888886655444443 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 !   24.0   0.1   1.6e-08   2.4e-05      15      50 ..      28      63 ..      22      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.6e-08
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                       ti+i++ + + ++G +GsGKSTll  ++ l +p+ 
  gi|330508780|ref|YP_004385208.1| 28 ITIKINRGEQVTIIGSNGSGKSTLLAVLNGLVYPTA 63
                                      5788987779***************77777777765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.3e-06    0.0019      12      74 ..      27      89 ..      17     153 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                            AAA_23 12 dqeidFskg.ltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdve.iesegkvkay 74
                                      d +i  ++g  + I+G NG+GK+T+l  +    y  ++++     ++ ++++v    +e+k ++y
  gi|330508780|ref|YP_004385208.1| 27 DITIKINRGeQVTIIGSNGSGKSTLLAVLNGLVYPTAGDFFAF--GHPVTEEVFdSIKENKFRTY 89
                                      555555554134599*************999999888777663..33333333212222333444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.8e-05     0.042       2      41 ..      38      88 ..      37     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                            AAA_28  2 ivitGgestGKTtlleaLa......ar.....gypvvpEaareileeklak 41
                                      + i+G  ++GK+tll+ L+      a      g+pv +E++  i e+k ++
  gi|330508780|ref|YP_004385208.1| 38 VTIIGSNGSGKSTLLAVLNglvyptAGdffafGHPVTEEVFDSIKENKFRT 88
                                      78*****************77777611455669999999999888777655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.4e-05     0.066      88     121 ..      23      57 ..       3      66 .. 0.82
   2 ?   -3.3   0.0       4.8   7.2e+03      22      48 ..     205     231 ..     202     259 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       e+l++++ +++  + ++++G+ G GKStL+ +l++
  gi|330508780|ref|YP_004385208.1|  23 EALKDITIKINRgEQVTIIGSNGSGKSTLLAVLNG 57 
                                       66777887777769999*************99976 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.8
                                       EEESTTTT--HHHHHHHHHHHHHTT-E CS
                       RsgA_GTPase  22 vvslkepelslnlldrfLvlaeekgie 48 
                                       ++++++ e+   + +r +v+ e+++i+
  gi|330508780|ref|YP_004385208.1| 205 ITATHDLEIMDMISKRSIVMGEDHRIK 231
                                       555555555555555666655555553 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00037      0.55       2      19 ..      37      54 ..      36      59 .. 0.88
   2 ?    0.6   0.0      0.32   4.8e+02      90     132 ..     175     211 ..     139     225 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00037
                                      CEEEEC-TTTCHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqk 19
                                      +v + G +GsGK+tLl+ 
  gi|330508780|ref|YP_004385208.1| 37 QVTIIGSNGSGKSTLLAV 54
                                      6889***********985 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.32
                                       STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCH CS
                             NACHT  90 lDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpral 132
                                       lDe ++ l++    +++ +L el+r+  l+ a   +++ +  l
  gi|330508780|ref|YP_004385208.1| 175 LDEPSAGLDP----RTQLWLIELLRE--LSHAGKTIITATHDL 211
                                       4777887777....889999999999..666666665555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00013       0.2      14      45 ..      27      56 ..      20     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                            AAA_16 14 salervrsgrpelvllsGesGvGKsslvrell 45
                                      ++   ++ +r+e v ++G  G+GKs+l+  l 
  gi|330508780|ref|YP_004385208.1| 27 DIT--IKINRGEQVTIIGSNGSGKSTLLAVLN 56
                                      443..444555889*************97665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0011       1.6       4      22 ..      37      55 ..      34      98 .. 0.85
   2 ?    1.1   0.0      0.18   2.7e+02     110     130 ..     189     209 ..     185     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                      ++ i+G++g+GK+tl++ l
  gi|330508780|ref|YP_004385208.1| 37 QVTIIGSNGSGKSTLLAVL 55
                                      689************9877 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.18
                            AAA_24 110 efrrllkklqelrknvifiah 130
                                       ++++ll+ l++++k++i   h
  gi|330508780|ref|YP_004385208.1| 189 WLIELLRELSHAGKTIITATH 209
                                       77899**********998777 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0017       2.5      30      89 ..     149     195 ..     128     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0017
                           SbcCD_C  30 sgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                         tlSGGek     +++a  l           +++++++LDE  ++lD++++  l+ell+
  gi|330508780|ref|YP_004385208.1| 149 PHTLSGGEK---KKVCIATVL----------VNNPDVLLLDEPSAGLDPRTQLWLIELLR 195
                                       567777777...445555222..........23589999*********999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); 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 0.30s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 1900.34
//
Query:       gi|330508781|ref|YP_004385209.1|  [L=312]
Description: cobalt ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete 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-34  118.4  12.0    4.9e-34  117.9  12.0    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 !  117.9  12.0   2.7e-38   4.9e-34       4     215 ..      53     275 ..      52     280 .. 0.80

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 2.7e-38
                                       CCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH.HHHTTS---.....HHHHHHHCCCHCHHHHHHHHHHE. CS
                              CbiQ   4 vlhrldprvkliwlfllllalvlapnlvtlliiialll.lllllvilp.....rvlaqalilpllflllgllillf. 73 
                                       vl  ldpr kli ++++++a++l+  l +l++i  l+l +++l++i+      rv++++++++++  l+      + 
  gi|330508781|ref|YP_004385209.1|  53 VLQSLDPRAKLISILAIVFATSLIGDLNVLIFIYLLTLlFAYLSKIDVlffikRVWLFIPVFAGIIALP------Mi 123
                                       57889**********************999666555431344444444654444444444433333333......24 PP

                                       ....................EECTTEEE....E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS-- CS
                              CbiQ  74 .............qlittegefvfaggg.qisitseGllrglllalRiltllslllllalTTppeeltsslerlgvP 136
                                                       ++  ++    +   i it++G++ ++ +++R+++++s+++ll++TT+ + l++sl+++gvP
  gi|330508781|ref|YP_004385209.1| 124 fnifipgdplihlAILGPGAHLGPFSLPeSIYITRQGTVAAVIFTMRVAACVSAVVLLFITTSKQVLFKSLRSVGVP 200
                                       445568998888533444444443333379*********************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS.. CS
                              CbiQ 137 lelalillLayRfiflLleevqrikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtgse 213
                                       +  +l+l  ayR+iflL+e v++++ A k+R++++  g+  + + +g  ++  ++r+l+++e+v  Am++RG++g  
  gi|330508781|ref|YP_004385209.1| 201 KLYVLTLEMAYRYIFLLMELVREMYIAKKARTIRA-GGLFDEQKWMGGRMGYTLIRSLDMSEKVHMAMTSRGFNG-- 274
                                       ***********************************.999999*********************************.. PP

                                       .. CS
                              CbiQ 214 er 215
                                        +
  gi|330508781|ref|YP_004385209.1| 275 -E 275
                                       .3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.16s 00:00:00.47 Elapsed: 00:00:00.47
# Mc/sec: 2016.14
//
Query:       gi|330508782|ref|YP_004385210.1|  [L=272]
Description: hypothetical protein MCON_3078 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.079   13.0   0.2       0.19   11.8   0.2    1.6  1  Pico_P1A  Picornavirus coat protein (VP4)


Domain annotation for each model (and alignments):
>> Pico_P1A  Picornavirus coat protein (VP4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   1.1e-05      0.19      19      39 ..     211     231 ..     201     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                                       SSSS--EEEEE--SSSGGGS- CS
                          Pico_P1A  19 snGsslnyttinyykdaassa 39 
                                       +n + + y+++nyy+d a +a
  gi|330508782|ref|YP_004385210.1| 211 YNTTKVSYIEVNYYRDNAREA 231
                                       89999************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1455.44
//
Query:       gi|330508783|ref|YP_004385211.1|  [L=228]
Description: beta-lactamase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-20   72.1   2.8    1.7e-19   70.6   2.8    1.8  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.5e-07   31.1   0.0      2e-07   30.8   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.047   13.1   0.0      0.083   12.3   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   2.8   2.8e-23   1.7e-19       7     193 ..      26     201 ..      23     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 2.8e-23
                                       EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH..C CS
                       Lactamase_B   7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap..a 81 
                                       ++yl++ +  ++LiD+G++  ++++ +++++lg +p +v ++i TH H+DHiGgl+ ++++++ +++a++++ +  +
  gi|330508783|ref|YP_004385211.1|  26 YVYLVDAKSCLVLIDAGVGYGNDKIEKNIRSLGSEPAQVWHIIATHCHIDHIGGLHLWRDKYGSKIIAHELDRAgiE 102
                                       79*******************************************************************98876225 PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE..TTCCEEEECTTTSSHH CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey..gggkvlftGDallage 156
                                       ++++e+  a++++ +   + +++ + +   e+  +++g  +++v ++pgh++g+++v++  ++g+vlf  D    + 
  gi|330508783|ref|YP_004385211.1| 103 GKNNELTAASMYGVD---YRPVMLDTILSGEHNQIRLGEMEFKVLHTPGHTPGSISVYIdtPEGRVLFGQDIHG-PF 175
                                       666666666666653...56667777777777777777777777777777777777776669*****9877777.44 PP

                                       CCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEE CS
                       Lactamase_B 157 tgridltlrgaevrdpsdaekyldsllklaglkaevl 193
                                        +++d            d  ++++s++kl +l+a+ l
  gi|330508783|ref|YP_004385211.1| 176 SPSWDS-----------DMVEWRRSMRKLLDLEADFL 201
                                       444444...........45555555555556666665 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   3.3e-11     2e-07       3     144 ..      37     172 ..      36     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3.3e-11
                                       EEES--TTHHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEE.......HHHHHHCC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyap.......kgvlavle 71 
                                       +LiDag +     +   ++ + l +e++++  ++ th+H+DH+ gl   r  +++  +++a+       +g   +l+
  gi|330508783|ref|YP_004385211.1|  37 VLIDAGVGYGND-K-IEKNIRsLGSEPAQVWHIIATHCHIDHIGGLHLWRDKYGS--KIIAHeldragiEGKNNELT 109
                                       79******6544.2.225667799*********************9999996554..56777443322244444555 PP

                                       TTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S CS
                     Lactamase_B_2  72 anfvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg 144
                                       a + y ++ ++  v++ ++  ge  ++  g++e+++   ++ ++          +++ i++++ rv+++ D  
  gi|330508783|ref|YP_004385211.1| 110 AASMYGVDYRP--VMLDTILSGEHNQIRLGEMEFKVLHTPGHTPG--------SISVYIDTPEGRVLFGQDIH 172
                                       55555555555..77777777777777667899999999999999........99***********9999975 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.4e-05     0.083       5      59 ..      33      87 ..      29      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                     Lactamase_B_6  5 dnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakf 59
                                       ++ +L+D G+   ++++e+ ++ l +   +v +i+ +h  ++h+G++ l   k+
  gi|330508783|ref|YP_004385211.1| 33 KSCLVLIDAGVGYGNDKIEKNIRSLGSEPAQVWHIIATHCHIDHIGGLHLWRDKY 87
                                      56789*******999********************************96554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1589.21
//
Query:       gi|330508784|ref|YP_004385212.1|  [L=347]
Description: RNA 3'-phosphate cyclase [Methanosaeta concilii GP6]
Scores for complete 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-81  271.6   0.1      4e-81  271.4   0.1    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
      4e-16   59.4   0.1      9e-16   58.3   0.1    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 !  271.4   0.1   4.5e-85     4e-81       2     222 .]       9     332 ..       8     332 .. 0.99

  Alignments for each domain:
  == domain 1  score: 271.4 bits;  conditional E-value: 4.5e-85
                                       TTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC   2 gegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikagey 78 
                                       gegGgqi+Rta+aL a+tgk+v+I++IR++R+kPGL+aqh++a+ +la i++a+++g + gs+e+ F+Pgei++g+y
  gi|330508784|ref|YP_004385212.1|   9 GEGGGQIVRTAVALCAVTGKSVHISKIRQGRPKPGLAAQHAHAIAALASICQAKTSGISPGSSEISFSPGEIQGGSY 85 
                                       8**************************************************************************** PP

                                       EEEEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC  79 evdigtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkGg 155
                                       e++igtAGs tlllq+llp+ll a++p++l+++GgT+v+++p+vdy+++v+lp+l+rfg ++++l+l+krG+yp+G+
  gi|330508784|ref|YP_004385212.1|  86 EISIGTAGSATLLLQCLLPALLRANTPTTLSVQGGTDVQWSPTVDYFQNVFLPALQRFG-AKASLKLEKRGYYPHGQ 161
                                       ***********************************************************.8**************** PP

                                       EEEEEEEE-.-S---EB............................................................ CS
                                       xxxxxxxxxxxxxxxxx............................................................ RF
                               RTC 156 Gevelevepskklkpie............................................................ 172
                                       G+v++++eps +l++ +                                                            
  gi|330508784|ref|YP_004385212.1| 162 GNVVCSIEPS-ELQAAHlestgvrnasgdrsemeisgishcsnlpenvakrqadaaagalleagfeanialevlrlp 237
                                       ********96.89999999********************************************************** PP

                                       ...............................................BSS-HHHHHHHHHHHHHHT.-EEEEESS-- CS
                                       ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC 173 ...............................................acvDehlqdqlilfmaLakgksrirvaelt 202
                                                                                      a vD hl+dqli+++aLa g  +++++e++
  gi|330508784|ref|YP_004385212.1| 238 stgsgitlwsdsprvhigasslgkrglpaervgksaaeelalelasgASVDVHLADQLIPYLALAGG--SYSTREIS 312
                                       *****************************************************************98..6******* PP

                                       HHHHHHHHHHHHHSS-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                               RTC 203 lhtetairvieqflgvkfkv 222
                                       lht t+i+++e+fl+ k+++
  gi|330508784|ref|YP_004385212.1| 313 LHTSTNIWTAEHFLERKISI 332
                                       ***************99976 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 !   58.3   0.1     1e-19     9e-16       8     102 ..     194     281 ..     193     282 .. 0.93

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1e-19
                                       EEEEEEEEESS-THHHHHHHHHHHHHHTTTSSEEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEEEEEEE-TT CS
                        RTC_insert   8 rirGvafaarvspsvanrmveaargvLnkllpdvyiytdvvkegkesgkspGfgisLvaetttegvllgaealgekg 84 
                                       +i+G++++++++ +va+r+++aa g L +++ + +i+++v      +  s G+gi+L+  +   +v +ga++lg++g
  gi|330508784|ref|YP_004385212.1| 194 EISGISHCSNLPENVAKRQADAAAGALLEAGFEANIALEV-L----RLPSTGSGITLWSDS--PRVHIGASSLGKRG 263
                                       699********************************99994.3....44568**********..57************ PP

                                       --HHHHHHHHHHHHHHHH CS
                        RTC_insert  85 vppedvGeeaaeeLleei 102
                                        p+e+vG+ aaeeL  e+
  gi|330508784|ref|YP_004385212.1| 264 LPAERVGKSAAEELALEL 281
                                       **************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2479.29
//
Query:       gi|330508785|ref|YP_004385213.1|  [L=407]
Description: Bcr/CflA subfamily drug resistance transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-44  152.1  44.2    1.9e-44  152.1  44.2    1.7  2  MFS_1     Major Facilitator Superfamily
    1.1e-10   40.7  31.2    2.2e-06   26.5   3.7    2.9  2  MFS_2     MFS/sugar transport protein
      5e-10   38.8  11.0      5e-10   38.8  11.0    3.0  3  Sugar_tr  Sugar (and other) transporter
    6.4e-05   21.6   5.5    6.4e-05   21.6   5.5    2.1  2  TRI12     Fungal trichothecene efflux pump (TRI12)
  ------ inclusion threshold ------
      0.062   11.6   0.1      0.062   11.6   0.1    3.4  4  OATP      Organic Anion Transporter Polypeptide (OATP) 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 !  152.1  44.2   5.3e-48   1.9e-44       2     352 ..      28     364 ..      27     365 .. 0.86
   2 ?   -0.6   2.0      0.14     5e+02     142     172 ..     366     395 ..     356     404 .. 0.39

  Alignments for each domain:
  == domain 1  score: 152.1 bits;  conditional E-value: 5.3e-48
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       +++ +++ l+ ++++palp  +++ +++s+ +++l l ++++++a+++l++G+lsd++Grr++l++gl++++l+++l
  gi|330508785|ref|YP_004385213.1|  28 AFLSAFVPLSTDLYLPALP-GMSKYFQVSAEQVNLTLIFFFIVFAAGMLFWGPLSDKYGRRPILIAGLAIYSLAGFL 103
                                       7889999************.******************************************************777 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       +++ s+    l+++r+lq++g++++ ++++a+i d++  ++r + ++++s+++ ++++ +p+lg+ll+   +Wr+vf
  gi|330508785|ref|YP_004385213.1| 104 CAI-SQDInQLIAFRILQAIGGSSASAVAMAMIKDVYDSRNREMILAWVSSMVLISPMAAPVLGALLLGFTSWRGVF 179
                                       776.55555******************************************************************** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfff.gfsglltll 230
                                       ++l++++++a  l + l ++e  + +   +  +       ++   +  +lk+p +++lli++ l +f  ++++ + +
  gi|330508785|ref|YP_004385213.1| 180 VVLGVIGFVA--LSGSLALVETLNTRYTGTLSQ-------SIGR-LAVVLKNPGFLSLLIVFSLLSFsSMAFIASSS 246
                                       **********..667777666666666666555.......5555.78889999998566666555440555577888 PP

                             MFS_1 231 plylqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllv 306
                                        +y  + +gls  l+++++++ +l+++g ++  l  rls+r+ r  +++ ++++++l+ l+++ l+    ++++ ++
  gi|330508785|ref|YP_004385213.1| 247 YIY-IDGFGLSeKLFSLYFAFNALGMIGGPM--LYLRLSKRFRRYSIIIAGFISTFLGGLLVYHLGSL--QPWIFAL 318
                                       888.*******98888887777777777777..********999888888888888888888888888..7777777 PP

                             MFS_1 307 lvl.iGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                       +++ +++ +++++++ ++l+ +   +e +g+as+l++ +g l+g++g
  gi|330508785|ref|YP_004385213.1| 319 CLFpATTMGSCIRTPGANLMLEQQ-EEDTGSASALMSCFGILMGSMG 364
                                       777355588888999999999997.6***********9999999887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.14
                             MFS_1 142 gllasslgWravfyilaivsllafv.lfllll 172
                                        +++    W+ +  il+++ +l++v +  l+l
  gi|330508785|ref|YP_004385213.1| 366 TVIS--QEWSNTIRILGLMNILVGVlCLCLWL 395
                                       2222..22555555555555555444222222 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   3.7   6.1e-10   2.2e-06     253     345 ..      50     141 ..      15     146 .. 0.83
   2 !   23.4  14.8   5.5e-09     2e-05     149     324 ..     152     323 ..     142     339 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.1e-10
                             MFS_2 253 yvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlll.qpsnlllflvllviagfg 327
                                       ++   +++++++ l++++i  ++g+++w pl  ++g++ + ++g++++ + ++l+ +  + ++l++f +l++i+g +
  gi|330508785|ref|YP_004385213.1|  50 KYFQvSAEQVNLTLIFFFIVFAAGMLFWGPLSDKYGRRPILIAGLAIYSLAGFLCAISqDINQLIAFRILQAIGGSS 126
                                       44444889999999999*********************9999998888766666666659999999999**999999 PP

                             MFS_2 328 vgvaallpwsmladvvDy 345
                                          a  ++++m+ dv+D 
  gi|330508785|ref|YP_004385213.1| 127 ---ASAVAMAMIKDVYDS 141
                                       ...99999*******996 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 5.5e-09
                             MFS_2 149 laailafllvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnra 225
                                         ++l++++++   g      g++ +  ++++L ++g++++ +g    ve  + ++    +  + ++ l  v++n+ 
  gi|330508785|ref|YP_004385213.1| 152 SSMVLISPMAAPVLG--ALLLGFTSWRGVFVVLGVIGFVAL-SGSLALVE--TLNTRYTGTLSQSIGRLAVVLKNPG 223
                                       444555555444444..444577777778888888887777.55555553..456666677777889999******* PP

                             MFS_2 226 flillllfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltiv 301
                                       fl ll++f+l +++ +   + + Y + +  g +++ +s+++++  ++++ g +l  +l kr+ ++ ++++g+++t++
  gi|330508785|ref|YP_004385213.1| 224 FLSLLIVFSLLSFSSMAFIASSSYIYIDGFGlSEKLFSLYFAFNALGMIGGPMLYLRLSKRFRRYSIIIAGFISTFL 300
                                       ************************999999*9********************************************* PP

                             MFS_2 302 llvlvlllqpsnlllflvllvia 324
                                       +++lv+ l+  + ++f ++l+ a
  gi|330508785|ref|YP_004385213.1| 301 GGLLVYHLGSLQPWIFALCLFPA 323
                                       ********888888888887654 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8  11.0   1.4e-13     5e-10      17     194 ..      28     199 ..      24     205 .. 0.90
   2 ?    0.7   0.8     0.052   1.9e+02      53      92 ..     265     304 ..     244     321 .. 0.66
   3 ?    1.6   1.4     0.027        96     140     191 ..     347     397 ..     344     402 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.4e-13
                                       HCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  17 gvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlq 93 
                                       ++++af+ l+  ++   l   ++  + s+ ++ l++ +f+++ ++G lf g+l+d++GR+++l+++ ++++ +++l+
  gi|330508785|ref|YP_004385213.1|  28 AFLSAFVPLSTDLYLPALPGMSKYFQVSAEQVNLTLIFFFIVFAAGMLFWGPLSDKYGRRPILIAGLAIYSLAGFLC 104
                                       566666666666666666666666666777889999999************************************** PP

                                       H-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHH CS
                          Sugar_tr  94 aaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgw 170
                                       a+++    + +li+ R+l  ig   as+++   i+ +   + R ++  +  +++ +  + a ++g+ l  +++   w
  gi|330508785|ref|YP_004385213.1| 105 AISQ---DINQLIAFRILQAIGGSSASAVAMAMIKDVYDSRNREMILAWVSSMVLISPMAAPVLGALLLGFTS---W 175
                                       ****...9************************************************************99999...* PP

                                       HHHHHCCHHHHHHHHHHGGGS--- CS
                          Sugar_tr 171 rillglqlvpallllilllflPES 194
                                       r  + +  v+  + l + l l E+
  gi|330508785|ref|YP_004385213.1| 176 RGVFVVLGVIGFVALSGSLALVET 199
                                       ****99999998888888887776 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.052
                                       HTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH.HHHHHH CS
                          Sugar_tr  53 siflvGaiiGslfagllgdrfGRkkslliaavlf.vigavl 92 
                                       + f++ ++iG+ +++l   +  R++s++ia++++ + g++l
  gi|330508785|ref|YP_004385213.1| 265 A-FNALGMIGGPMLYLRLSKRFRRYSIIIAGFIStFLGGLL 304
                                       4.455556666666655555558888888777651555555 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHGGGS CS
                          Sugar_tr 140 vslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllilllfl 191
                                       +s   l+  fGil++++ ++++ ++ sn  + ril  ++++  +l l l+l+l
  gi|330508785|ref|YP_004385213.1| 347 GSASALMSCFGILMGSMGMTVIsQEWSN--TIRILGLMNILVGVLCLCLWLLL 397
                                       667789999******9999888566666..89999999999998888877776 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   5.5   1.8e-08   6.4e-05      81     209 ..      60     189 ..      41     201 .. 0.81
   2 ?   -0.1   0.1     0.064   2.3e+02      72     123 ..     251     303 ..     217     330 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.8e-08
                             TRI12  81 slfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgvaagpagaspl.fvg 156
                                       +l   ++ +  a  +l  g l+d++grrp++i+   +  +   + + ++ +n l+a   l  +    a a  + ++ 
  gi|330508785|ref|YP_004385213.1|  60 NLTLIFFFIVFAAGMLFWGPLSDKYGRRPILIAGLAIYSLAGFLCAISQDINQLIAFRILQAIGGSSASAVAMaMIK 136
                                       444555667788999******************977766666677788999*9999888877777777765543789 PP

                             TRI12 157 elmsnktkflgllivsipvvvtsglspylgqrlaiqgswrwifyiyiitsaia 209
                                       ++   + + + l  vs  v++   ++p lg  l    swr +f +  ++  +a
  gi|330508785|ref|YP_004385213.1| 137 DVYDSRNREMILAWVSSMVLISPMAAPVLGALLLGFTSWRGVFVVLGVIGFVA 189
                                       9999999************************************9987766655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.064
                             TRI12  72 qdvgqsen.sslfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgai 123
                                       +  g se+  sl+ ++ ++g     ++  rl+ rf r  ++i+  i  ++g +
  gi|330508785|ref|YP_004385213.1| 251 DGFGLSEKlFSLYFAFNALGMIGGPMLYLRLSKRFRRYSIIIAGFISTFLGGL 303
                                       44566665236666666777777778888999999999999999998877765 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1     0.099   3.5e+02     324     370 ..      51      96 ..      26     111 .. 0.56
   2 ?   11.6   0.1   1.7e-05     0.062     139     193 ..     117     171 ..     107     176 .. 0.93
   3 ?   -2.3   1.1      0.28   9.9e+02     517     517 ..     278     278 ..     207     332 .. 0.58
   4 ?   -1.4   4.2      0.14   5.2e+02     336     382 ..     346     396 ..     339     400 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.099
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 324 qFslsaseAnlltGvvvipgaalGillgGllvkklklsakklaklvl 370
                                        F++sa + nl + +++ +++a+G+l+ G l  k+  ++  +a l++
  gi|330508785|ref|YP_004385213.1|  51 YFQVSAEQVNLTL-IFFFIVFAAGMLFWGPLSDKYGRRPILIAGLAI 96 
                                       4555555555543.333334445555555555555444444433333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.7e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 139 qlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllk 193
                                        +l++iG++   +++++ i D  +++n  + l++++++ ++ p+ + +lG+lll 
  gi|330508785|ref|YP_004385213.1| 117 RILQAIGGSSASAVAMAMIKDVYDSRNREMILAWVSSMVLISPMAAPVLGALLLG 171
                                       6899***********************************************9986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.28
                                       x RF
                              OATP 517 f 517
                                       +
  gi|330508785|ref|YP_004385213.1| 278 Y 278
                                       1 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.14
                                       xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 336 tGvvvipgaalGillgG....llvkklklsakklaklvlvvsllsllllll 382
                                       tG+++ +++++Gil+g     ++ + +  +++ l  ++++v++l+l+l ll
  gi|330508785|ref|YP_004385213.1| 346 TGSASALMSCFGILMGSmgmtVISQEWSNTIRILGLMNILVGVLCLCLWLL 396
                                       566666666666666651111567778888888888888888888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); 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:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 2890.30
//
Query:       gi|330508786|ref|YP_004385214.1|  [L=195]
Description: iron-sulfur flavoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (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  116.2   0.0    1.3e-33  116.0   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    3.5e-08   33.4   0.0    4.6e-08   33.0   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   0.0   1.4e-37   1.3e-33       1     147 [.       1     150 [.       1     157 [. 0.91

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 1.4e-37
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--...---HCHGHT....CGGSHHHHHHHHHHH CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc.alcdkdlese....gqtsddvaellekia 71 
                                       mki++isGS+rk +nt+ l+++a++ ++e g+++e +  ++l    c +  d+    +    ++++dd+ ++l++++
  gi|330508786|ref|YP_004385214.1|   1 MKIVGISGSPRKAGNTEFLLNEALAVAAEYGFQTERLLCSELnFDFCsDCGDC----SkgkpCPNKDDMHKVLRAMQ 73 
                                       9*************************************999955554433333....335669************** PP

                                       H-SCEEEEEEECTTCE-HHHHHHHHCHT-..SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEECS CS
                           FMN_red  72 aadaliivtPeYngsysgllKnalDrlsr.trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpra 146
                                       +a+++i+++P+Y+g+++++lK+++Dr+ + +r++  lr+K++ ++avgg+r+gg++ + +  ++++ + g+ivv++ 
  gi|330508786|ref|YP_004385214.1|  74 EAEGIIVASPVYFGNVTAQLKAIFDRTIPlRRQGFRLRNKIGCAIAVGGSRNGGQEKTLESIHAWMhIQGMIVVGD- 149
                                       ***************************999***********************************9889****998. PP

                                       E CS
                           FMN_red 147 a 147
                                       +
  gi|330508786|ref|YP_004385214.1| 150 D 150
                                       4 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   5.1e-12   4.6e-08       1     167 [.       1     144 [.       1     169 [. 0.70

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 5.1e-12
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTT..CHHHHHHH.HHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeek..padveseq.iek 74 
                                       mki+ i ++pr++  ++  l++++++ +++ g    t+r L  + +  ++ ++      ++ k  p + ++ + + +
  gi|330508786|ref|YP_004385214.1|   1 MKIVGISGSPRKA-GNTEFLLNEALAVAAEYG-F-QTERLLCSELNFDFCSDCGD---CSKGKpcPNKDDMHKvLRA 71 
                                       9***********6.777888888888888888.5.34555555433334443333...44444445555556668** PP

                                       HHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTT.TSEEEEEEEESS-GGGSSTTSSS-S- CS
                      Flavodoxin_2  75 llaadaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLk.gkkalvivttGgpeesyqerglegaa 150
                                       +++a+ i++++P+++ +v a+lK+ +Dr     +            +g++  +k+ +++++Gg+          g +
  gi|330508786|ref|YP_004385214.1|  72 MQEAEGIIVASPVYFGNVTAQLKAIFDRTIPLRR------------QGFRlRNKIGCAIAVGGSRN--------G-G 127
                                       ****************************744433............55666888999999999932........2.3 PP

                                       HHHHHHHHHHHHHHTT- CS
                      Flavodoxin_2 151 mdellpplrgilgfiGi 167
                                        + +l   +++++  G+
  gi|330508786|ref|YP_004385214.1| 128 QEKTLESIHAWMHIQGM 144
                                       34555566666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1405.53
//
Query:       gi|330508787|ref|YP_004385215.1|  [L=86]
Description: PRC-barrel domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-13   50.1   1.1    2.4e-13   49.9   1.1    1.0  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   1.1   1.4e-17   2.4e-13       5      73 ..       4      73 ..       1      77 [. 0.94

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.4e-17
                                      CS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.......-EEEEEGG.CEECCCTEEEET CS
                               PRC  5 rasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi..gekevliPfdlavkigkdriivd 73
                                      ++++l  ++Vyt +G ++G+V D v+d+++g v +l +++ +++ +  ++k ++iP++ +v +++d+ii++
  gi|330508787|ref|YP_004385215.1|  4 EITSLLEQDVYTQKGIYVGRVDDAVLDPDNGVVSGLALGDVNRDLFdsKGKGIVIPYR-WVTAVGDIIIIR 73
                                      5799************************************9996669***********.**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 623.07
//
Query:       gi|330508788|ref|YP_004385216.1|  [L=233]
Description: tRNAHis guanylyltransferase [Methanosaeta concilii GP6]
Scores for complete 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   60.3   0.0    2.9e-16   59.6   0.0    1.2  1  Thg1      tRNAHis guanylyltransferase
      8e-07   29.2   0.0    1.1e-06   28.9   0.0    1.1  1  Thg1C     Thg1 C terminal domain


Domain annotation for each model (and alignments):
>> Thg1  tRNAHis guanylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0   3.2e-20   2.9e-16      13     123 ..      17     120 ..       7     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 3.2e-20
                              Thg1  13 llpntlivvRiDGrgFhkfskkhkfekPnDeralklmneaakelvkefe.divlaYgqSDEislvlsketklynrra 88 
                                       l  + ++v R DGrgF+++ +  +f+kP+D  ++++m ++a+ l+++   +++la+ +SDEi+l++ ++   + +r+
  gi|330508788|ref|YP_004385216.1|  17 LRARPPLVARADGRGFKNILA--GFKKPYDAGFASAMASSASGLFEDSGlSPLLAFMFSDEINLIFLAAP--FGGRI 89 
                                       5667789**************..***********************99669*****************99..***** PP

                              Thg1  89 qklvslvaslftaafvkllskafeelpsFDarvvl 123
                                       +k+ slva+ ++aa   +l k +    s D+r ++
  gi|330508788|ref|YP_004385216.1|  90 EKIDSLVAGSLSAALSLQLAKPV----SMDCRTIP 120
                                       ****************9999996....58888876 PP

>> Thg1C  Thg1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.2e-10   1.1e-06       2      80 ..     125     201 ..     124     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.2e-10
                             Thg1C   2 nlrDYlsWRqvDchinnlYNttFWalvqkgglteqeaeeeLkgtlskdkneiLfsefginYnnepeifrkGsvlvre 78 
                                       ++r+Yl  Rq ++  n ++   F++l   +g +++ a e+L+g   ++ +e++f++ gin ++ p+  r+G +++r+
  gi|330508788|ref|YP_004385216.1| 125 EIREYLIERQNETWRNHVFSYGFYMLQ-DEGIDPAGAMERLRGMKEHEIHELVFQR-GINLAKTPSWERRGIMIYRD 199
                                       79*********************9885.9*************************76.*****************998 PP

                             Thg1C  79 ke 80 
                                       ++
  gi|330508788|ref|YP_004385216.1| 200 ER 201
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1590.22
//
Query:       gi|330508789|ref|YP_004385217.1|  [L=262]
Description: hypothetical protein MCON_3084 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00051   19.7   0.1        1.7    8.4   0.0    3.7  4  Sigma70_r4_2  Sigma-70, region 4
  ------ inclusion threshold ------
      0.034   13.1   2.4      0.029   13.3   0.9    1.5  2  MFS_1         Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00019       1.7      10      43 ..      80     113 ..      78     114 .. 0.93
   2 ?   -3.1   0.0      0.73   6.6e+03      10      23 ..     123     136 ..     122     137 .. 0.81
   3 ?    2.5   0.0     0.013   1.1e+02      24      41 ..     167     184 ..     165     185 .. 0.89
   4 !    3.8   0.0     0.005        45       7      19 ..     239     251 ..     237     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00019
                                       TS-HHHHHHHHHHHTS---HHHHHHHHT--HHHH CS
                      Sigma70_r4_2  10 eLperqreifllryleglsykEIAellgisegtV 43 
                                       eL+e+ +++f  ++l+ l+ +  Ae+l++s + +
  gi|330508789|ref|YP_004385217.1|  80 ELSEKAKTAFDNKDLDSLPMQSLAEELKLSLAGI 113
                                       8*****************************8766 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.73
                                       TS-HHHHHHHHHHH CS
                      Sigma70_r4_2  10 eLperqreifllry 23 
                                       +L+ r  +++ll++
  gi|330508789|ref|YP_004385217.1| 123 QLSGRVMTAILLSA 136
                                       78889999999987 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.013
                                       TS---HHHHHHHHT--HH CS
                      Sigma70_r4_2  24 leglsykEIAellgiseg 41 
                                        e++++ +I++ +++se+
  gi|330508789|ref|YP_004385217.1| 167 QEDKPQPDISQNMNLSEN 184
                                       5899************96 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.005
                                       HHTTS-HHHHHHH CS
                      Sigma70_r4_2   7 alaeLperqreif 19 
                                        +++Lp++ rei+
  gi|330508789|ref|YP_004385217.1| 239 YIESLPPENREII 251
                                       599********97 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.9   3.2e-06     0.029     212     273 ..      12      70 ..       2      79 .. 0.79
   2 ?   -2.8   0.0      0.26   2.3e+03     127     138 ..     129     140 ..     115     150 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-06
                             MFS_1 212 llialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgr 273
                                       + + ++++++++++l+++l l   + +++  +  + +l+al+a+v++i+++ ++ + +r ++
  gi|330508789|ref|YP_004385217.1|  12 WALNAIIIAIAIYALMQYLGL--TTLMKFY-YQDSFILSALPAIVSIISGVALATFFKRRKK 70 
                                       666677777899999999999..8888888.8899999999999999999999999988554 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.26
                             MFS_1 127 sagfslGailgp 138
                                       ++++ l+a+++ 
  gi|330508789|ref|YP_004385217.1| 129 MTAILLSAVVAL 140
                                       222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1970.96
//
Query:       gi|330508790|ref|YP_004385218.1|  [L=475]
Description: ribulose bisphosphate carboxylase, large chain (form II) [Methanosaeta concilii GP6]
Scores for complete 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-90  302.9   0.0    8.1e-66  222.2   0.0    2.1  2  RuBisCO_large    Ribulose bisphosphate carboxylase large chai
    1.7e-29  102.5   0.0    3.3e-29  101.5   0.0    1.5  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 !  222.2   0.0   9.1e-70   8.1e-66       4     220 ..     147     361 ..     144     364 .. 0.96
   2 !   78.9   0.0     4e-26   3.6e-22     200     299 .]     369     469 ..     363     469 .. 0.91

  Alignments for each domain:
  == domain 1  score: 222.2 bits;  conditional E-value: 9.1e-70
                                       HHHHHH...T--EEEEE-SSSS---HHHHHHHHHHHHTT-.SEEE--TT-SSBTTB-HHHHHHHHHHHHHHHHHHHS CS
                     RuBisCO_large   4 verevlnkegrpilGtiiKPklGLspknyarvvyelllgglDfiKdDEnlnsqpfarlkdrieavaeaikraqdetG 80 
                                       ++r +ln+++rpilGtiiKPk+GL++++ya+v+y+++ gg Df+K+DE++++q f+++ + +++v  a+++a +etG
  gi|330508790|ref|YP_004385218.1| 147 DMRTYLNVHDRPILGTIIKPKMGLTSSEYAEVCYDFWVGGGDFVKNDEPQADQDFCPYDKMVKYVKMAMDKAVKETG 223
                                       7899************************************************************************* PP

                                       S--EEEEE---SSHHHHHHHHHHHHHHHGG....EEEEEHHHH-HHHHHHHHHHSTTS..EEEEE-TTTHHHHS.T- CS
                     RuBisCO_large  81 ekklyalnitaddleemlrraefvketgge....ivlvdvlviGfaaitslrkafrknelllHlHraghgaltr.qs 152
                                       +kk++++n++ +d + m++r e++ e+g e    ++l+d++++G+ a+++lr++ ++  ++lH+Hraghg +tr ++
  gi|330508790|ref|YP_004385218.1| 224 KKKVHSFNVSSADFDTMIERCEMIREAGFEpgsyAFLIDGITAGWMAVQTLRRRYPD--VFLHFHRAGHGGFTRpEN 298
                                       ***************************9888899********************665..5**************999 PP

                                       -SEE-HHHHHHHHHHHT-SEEE---TTSSSBS--GG......GHHHHHHHHSSEEE-SS-EEE-TT-- CS
                     RuBisCO_large 153 khGisfrvlakllRLlGvdhlhtgtvgvgklegdesvvkgfkdtlrekmleedeaegiffeqdlaslk 220
                                         G+s+ vl+k++RL+G++++htgt+gvgk+ g ++     +d   ++ + + e +g ff+q+++ ++
  gi|330508790|ref|YP_004385218.1| 299 PIGFSVLVLSKFARLAGASGIHTGTAGVGKMAGSPE-----EDVTAARNILKVEGKGHFFTQNWGRIP 361
                                       9***********************************.....88889999***************9875 PP

  == domain 2  score: 78.9 bits;  conditional E-value: 4e-26
                                       HHHHSSEEE-SS-E.EE-TT----EEEEESS--TTTHHHHHHHHS---SEEE-HHHHHTSTT-HHHHHHHHHHHHHH CS
                     RuBisCO_large 200 kmleedeaegiffe.qdlaslkavlpvasgGihagqlpellenlgesdvilqaGGGilgHpdgaaaGakalrqalea 275
                                       km+e d a+  ++e  ++ +lk++ p++sgG++   l+ +++ +g  d i+++G G ++Hp g+ aGa al qa ea
  gi|330508790|ref|YP_004385218.1| 369 KMVEMDDAHHVVLEdDSWRGLKKCCPIISGGLNPTLLEPFIDVMGGIDFITTMGAGCHAHPRGTRAGAMALVQACEA 445
                                       5777777777766615699********************************************************** PP

                                       HHHT--HHHHHTT-HHHHHHHHHX CS
                     RuBisCO_large 276 aveGadleeyAkehkeLarAlesw 299
                                        ++ +d+ +yAk+h+eLa+A+e +
  gi|330508790|ref|YP_004385218.1| 446 YKNKIDIADYAKDHRELAEAIEFF 469
                                       *********************987 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 !  101.5   0.0   3.7e-33   3.3e-29      11     120 .]      28     134 ..      17     134 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 3.7e-33
                   RuBisCO_large_N  11 etdllaafrvePaegvsveeaaaavAaeSStgtwtevsttkdellkklkakvyeieeveeekelvkiAYplelFeeg 87 
                                       ++ lla+f++ P+  +++ +aaa+vAaeSStgt+ +v t+++ + + ++a+vy+++    ek+lv+iAYp +lF+++
  gi|330508790|ref|YP_004385218.1|  28 GEYLLAVFHLIPSGELNIMQAAAEVAAESSTGTNFAVKTETP-FSRVMNALVYKVDI---EKNLVWIAYPWRLFDRN 100
                                       6679**************************************.************76...79*************98 PP

                   RuBisCO_large_N  88 .sipqllssiaGnifgmkavkalrleDirlPkay 120
                                        ++ ++++ iaGn +gmk++kal+l Di++P+++
  gi|330508790|ref|YP_004385218.1| 101 gNVQNIMTYIAGNALGMKEIKALKLLDIWFPPSM 134
                                       8******************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3438.54
//
Query:       gi|330508791|ref|YP_004385219.1|  [L=293]
Description: cache domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-34  116.6   0.3    6.9e-21   74.7   0.3    2.1  2  sCache_2         Single Cache domain 2
    3.9e-28   98.5   0.0    1.3e-27   96.8   0.0    1.7  1  dCache_2         Cache domain
     0.0066   16.6   0.0        1.8    8.7   0.0    2.2  2  sCache_3_2       Single cache domain 3
     0.0096   15.2   0.0      0.016   14.5   0.0    1.4  1  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
  ------ inclusion threshold ------
       0.14   12.3   0.1        1.2    9.3   0.0    2.3  2  DUF4261          Domain of unknown function (DUF4261)
       0.16   12.2   0.7       0.28   11.5   0.7    1.4  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
        0.3   11.3   0.9         20    5.4   0.5    2.1  2  SMBP             Small metal-binding protein


Domain annotation for each model (and alignments):
>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   1.4e-13   3.6e-10      53     153 ..      64     166 ..      38     168 .. 0.79
   2 !   74.7   0.3   2.7e-24   6.9e-21      29     144 ..     177     293 .]     171     293 .] 0.93

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.4e-13
                          sCache_2  53 G.....kgYffvldedgtllvhPfnpqleGknasnlkDanGkyiirelvkeakkkgggfvtylwkkpge.geveekl 123
                                       G     + Y+f++d +gt+l+hP+np+l+G+      D n++ ++   ++ ak  ggg +++ +++p+  g++e k 
  gi|330508791|ref|YP_004385219.1|  64 GsfvrgDLYIFAYDFNGTCLAHPINPELVGQTSLL--DINDVDVVGREIALAK-RGGGTMYIVFPNPSHeGKEELKQ 137
                                       35555589**********************86543..6666668888888888.8**************66666666 PP

                          sCache_2 124 ayvkyfepWdwvigtgvylddinkavekil 153
                                        + + +     ++g+g yl+di++ +++  
  gi|330508791|ref|YP_004385219.1| 138 LHLESVN-DSMYLGSGRYLSDIQASFDQGE 166
                                       6666555.589*************999875 PP

  == domain 2  score: 74.7 bits;  conditional E-value: 2.7e-24
                          sCache_2  29 sgkiteeeaqeevkelvnglkfgdG..kgYffvldedgtllvhPfnpqleGknasnlkDanGkyiirelvkeakkkg 103
                                       + k+ +e+ +e++ ++ n++  +      Y+f++d++g++l+ + +p+l+G+n+++ +D+nG+y+i+++ ++ak +g
  gi|330508791|ref|YP_004385219.1| 177 ALKYAQENGKEKALQAFNDPEGNFArdGLYIFAYDYEGQNLALSHQPELVGTNRIDAQDPNGVYFIQQITDMAK-NG 252
                                       56788999999999999999887777466*********************************************.** PP

                          sCache_2 104 ggfvtylwkkpge.geveeklayvkyfepWdwvigtgvyldd 144
                                       +gf++y +++p+   ++e kl+yv+ + +  w++g+g+y +d
  gi|330508791|ref|YP_004385219.1| 253 DGFAYYVYPDPSNnMTQELKLSYVMDVDG-TWFLGSGIYSSD 293
                                       *************999***********99.7********998 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.0   5.1e-31   1.3e-27      90     293 ..      66     292 ..      53     293 .] 0.90

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 5.1e-31
                          dCache_2  90 ydggegyyfiidskgtlilhpdspsleG.knlldlkdkdGryiiremiklakkkgeGfveytwpkp.dekkprkkis 164
                                       +++g+ y+f++d +gt+++hp +p+l G ++lld+ d d   ++  +i la k+g G +   +p+p  e+k++ k +
  gi|330508791|ref|YP_004385219.1|  66 FVRGDLYIFAYDFNGTCLAHPINPELVGqTSLLDINDVD---VVGREIALA-KRGGGTMYIVFPNPsHEGKEELKQL 138
                                       7899************************88999999999...999999999.7888**********88888888888 PP

                          dCache_2 165 yvkyfepldwiIGtgaylddieeelk.......................qellktlksi..ryg.nngyifiydtdg 215
                                                +++G+g+yl+di++  +                       +++l+ +++   +++ ++ yif+yd++g
  gi|330508791|ref|YP_004385219.1| 139 HLESVND-SMYLGSGRYLSDIQASFDqgerdelvdfvnealkyaqengkEKALQAFNDPegNFArDGLYIFAYDYEG 214
                                       8887776.59**********************************************975227885668********* PP

                          dCache_2 216 niilhplkkelngknllevkdkkgkl.lqelleaakkkgegfveYkwpkpsgd.kerkKisyvryfppwdWiigtgv 290
                                       + ++  +++el+g+n+++ +d++g++ +q++ +   k+g+gf  Y++p+ps++ +++ K+syv  +    W++g+g+
  gi|330508791|ref|YP_004385219.1| 215 QNLALSHQPELVGTNRIDAQDPNGVYfIQQITD-MAKNGDGFAYYVYPDPSNNmTQELKLSYVMDVDG-TWFLGSGI 289
                                       9999999*******************6666666.555778**************************99.9******* PP

                          dCache_2 291 yld 293
                                       y +
  gi|330508791|ref|YP_004385219.1| 290 YSS 292
                                       *86 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0   0.00071       1.8      35      77 ..      51      95 ..      16     124 .. 0.70
   2 !    6.0   0.0    0.0049        13      54      75 ..     181     227 ..     143     247 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00071
                        sCache_3_2 35 apesglqalvddvrritgvd.yvvitDeegrvlahp.dpaevgrk 77
                                       +e++lq+  d + +   +d y++++D  g+ lahp +p+ vg++
  gi|330508791|ref|YP_004385219.1| 51 GMENALQEFNDPTGSFVRGDlYIFAYDFNGTCLAHPiNPELVGQT 95
                                      334444444444444444449**************7477788876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0049
                        sCache_3_2  54 d........................yvvitDeegrvlahpdpa.evg 75 
                                       +                        y++++D eg+ la +++   vg
  gi|330508791|ref|YP_004385219.1| 181 AqengkekalqafndpegnfardglYIFAYDYEGQNLALSHQPeLVG 227
                                       3455555555555666666667777**************99874455 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 !   14.5   0.0   6.3e-06     0.016     193     281 ..     200     293 .]     177     293 .] 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.3e-06
                   Cache_3-Cache_2 193 vGktG.ylyvldgkgdkkgkliihptlk..gknvldlkdadgesvvkkllkk...ksgsleyelk...kdekgrekl 260
                                       ++++G y++++d +g    +l ++ +++  g+n +d++d +g ++++++ +     +g+++y +    ++ +++ kl
  gi|330508791|ref|YP_004385219.1| 200 FARDGlYIFAYDYEG---QNLALSHQPElvGTNRIDAQDPNGVYFIQQITDMaknGDGFAYYVYPdpsNNMTQELKL 273
                                       566664666666664...345555555556*************77777666555599*****999885555555566 PP

                   Cache_3-Cache_2 261 avftyfepwdWvivasvyede 281
                                       +++  +++  W ++++ y+++
  gi|330508791|ref|YP_004385219.1| 274 SYVMDVDG-TWFLGSGIYSSD 293
                                       66666654.599999888876 PP

>> DUF4261  Domain of unknown function (DUF4261)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.45   1.1e+03      19      40 ..      30      51 ..      25      53 .. 0.82
   2 ?    9.3   0.0   0.00047       1.2      10      41 ..     155     186 ..     154     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.45
                           DUF4261 19 glepeevvellyniasYileng 40
                                        + +ev+++l  ++ Y+ +ng
  gi|330508791|ref|YP_004385219.1| 30 TASADEVIAFLDEAVAYVDNNG 51
                                      56789************97776 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00047
                           DUF4261  10 lpdlevhfsglepeevvellyniasYilengv 41 
                                       l d+++ f ++e +e+v++ + ++ Y  eng+
  gi|330508791|ref|YP_004385219.1| 155 LSDIQASFDQGERDELVDFVNEALKYAQENGK 186
                                       78************************999986 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.7   0.00011      0.28      41      86 ..      12      57 ..       8      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                           SbcCD_C 41 laylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatlle 86
                                      l++l ++aa+   + s+++ + +  + fLDEA + +D++ ++++l+
  gi|330508791|ref|YP_004385219.1| 12 LMSLSVLAAITLCIASDQTASADEVIAFLDEAVAYVDNNGMENALQ 57
                                      789999*****999998877888999*************9999987 PP

>> SMBP  Small metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.5     0.008        20       4      52 ..       9      58 ..       3      61 .. 0.79
   2 ?    4.1   0.0     0.021        54      42      66 ..     163     186 ..     155     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.008
                                      XXXXXXXXXXXXXXXXXXXX--.HHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                              SMBP  4 isallaalvlalfsssavaaee.hlaeAiehaeaAvahgkaghakalveH 52
                                      + al++++vla++    ++ ++ +++e i  + +Ava ++++ +++ +++
  gi|330508791|ref|YP_004385219.1|  9 MVALMSLSVLAAITLCIASDQTaSADEVIAFLDEAVAYVDNNGMENALQE 58
                                      456777777777666666666589****************9999888775 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.021
                                       HTT-HHHHHHHHHHHHHHHHHH... CS
                              SMBP  42 kaghakalveHaeealkhakaaaek 66 
                                       ++g+ ++lv+  +ealk+a++   k
  gi|330508791|ref|YP_004385219.1| 163 DQGERDELVDFVNEALKYAQEN-GK 186
                                       678899**************99.22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2163.83
//
Query:       gi|330508792|ref|YP_004385220.1|  [L=656]
Description: alkyl/aryl-sulfatase [Methanosaeta concilii GP6]
Scores for complete 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-51  172.4   0.5    1.6e-50  171.2   0.5    1.7  1  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    1.1e-35  123.5   0.3    1.6e-35  122.9   0.3    1.3  1  Lactamase_B      Metallo-beta-lactamase superfamily
    4.6e-32  111.0   0.1    1.1e-31  109.8   0.1    1.7  1  Alkyl_sulf_C     Alkyl sulfatase C-terminal
    6.9e-07   29.0   0.0    1.4e-06   27.9   0.0    1.5  1  Lactamase_B_2    Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.092   12.2   1.0       0.16   11.3   1.0    1.4  1  Glyco_hydro_9    Glycosyl hydrolase family 9
       0.17   12.1   0.0       0.35   11.0   0.0    1.6  1  HNH_2            HNH endonuclease


Domain annotation for each model (and alignments):
>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.2   0.5   5.4e-54   1.6e-50       1     138 [.     392     529 ..     392     530 .. 0.99

  Alignments for each domain:
  == domain 1  score: 171.2 bits;  conditional E-value: 5.4e-54
                                       -CCCHHHC----HHHHTSGGGSSSSS-HHHHHHHHHHHHH-S--S-GGGTS---HHHHHHHHHHHTTSHHHHHHHHH CS
                   Alkyl_sulf_dimr   1 tpdeiaekvklPeslanepylreyYGtvehnvraiyqrylGWfdgnPanLnplppeekakrlvelmGgaekvlekak 77 
                                       t+deia+++ lP+sl++ +y++++YG++   v+a yq+ylG++d+nP nL++lppee a+++ e+mGga++vle++ 
  gi|330508792|ref|YP_004385220.1| 392 TMDEIANMIVLPQSLQKYWYTHGFYGQIYMGVKATYQKYLGFYDANPINLKRLPPEEFARNITEYMGGADAVLERLA 468
                                       89*************************************************************************** PP

                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRniYlsgakelrn 138
                                       +++++g+y+++a+++n+lvfadp+n +a+e++a+aleqlgyqaes+++Rn+Yl ga+elr+
  gi|330508792|ref|YP_004385220.1| 469 RDYDAGNYQLVATIANYLVFADPDNIKAREMEAAALEQLGYQAESGPARNAYLVGAMELRS 529
                                       ***********************************************************96 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.9   0.3   5.4e-39   1.6e-35       2     197 .]     130     355 ..     129     355 .. 0.99

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 5.4e-39
                                       CCCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                       Lactamase_B   2 gpdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78 
                                       g d +++ li  d+g+i+iD+ ++ e+araa +l  + l+  +v+avi++H+H+DH+ g++g++ + +v++g+v+ +
  gi|330508792|ref|YP_004385220.1| 130 GYDLTSMSLIKSDTGWIIIDPMMTVETARAAMDLVNRTLGYYPVKAVIYSHPHVDHYQGVKGVITEKQVASGEVEVI 206
                                       5677899********************************************************************** PP

                                       HHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSH CS
                       Lactamase_B  79 apalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallag 155
                                       apa+fm++a                    + e++++g+a+ rr+ y++gg +++   g v++g gk    G a+l++
  gi|330508792|ref|YP_004385220.1| 207 APAGFMDHA--------------------ISENVYAGTAMQRRGMYMYGGLLPHDEKGLVDNGLGKRTPFGSASLIA 263
                                       *********....................************************************************ PP

                                       HCCCCCC...................................................TTCEEE-SHCHHHHHHHHH CS
                       Lactamase_B 156 etgridl..................................................tlrgaevrdpsdaekyldsl 182
                                       +t++i++                                                  tlrga+ rdp +++++ld++
  gi|330508792|ref|YP_004385220.1| 264 PTIDITEtgqnltidgvdmqfhyctnteapveidiwfpdhkalfmaencvatlhnilTLRGAQIRDPLSWAECLDEA 340
                                       ***************************************************************************** PP

                                       HHHHHHCHSEEEESS CS
                       Lactamase_B 183 lklaglkaevlvpgH 197
                                       ++l g+ aev++++H
  gi|330508792|ref|YP_004385220.1| 341 RRLYGDQAEVVFTAH 355
                                       **************9 PP

>> Alkyl_sulf_C  Alkyl sulfatase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   0.1   3.6e-35   1.1e-31       2     126 .]     538     656 .]     537     656 .] 0.95

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 3.6e-35
                                       X--HHCCCCS-HHHHHHHHHHHB-HHHHTT-EEEEEEEETTTTEEEEEEEETTEEEE.ECT---TTSSEEEEE-HHH CS
                      Alkyl_sulf_C   2 taspdvlaalsleqlfDylAirvdgpkaadkdltinlvvtDvdekyllrlsngvLthtrkaaqaddadltvtltreq 78 
                                        +s+dv+ a+s++ql+Dy+A+r++++ka ++d+++n+++ D++e  l++++n+vL++   ++++d+a+ltv+++r++
  gi|330508792|ref|YP_004385220.1| 538 MISADVISAMSINQLLDYIAVRLNSQKADGEDFRMNMIINDTGESALIQVNNSVLVY-WIDEHSDEAALTVHMPRKT 613
                                       579******************************************************.667778************* PP

                                       HHHHHTTSS-HHHHHHTTTEEEEE-TCHHHHHHCTB----TT--SSSS CS
                      Alkyl_sulf_C  79 LvalllgkatlgkevaagklkieGdaealakllslldefdpaFnIVtP 126
                                       L++l+l     +  v   +++ieGda++++ ++++ld fdp FnI+ P
  gi|330508792|ref|YP_004385220.1| 614 LEQLAL-----DPSVPPANVTIEGDASVFEGFVGVLDLFDPSFNIILP 656
                                       ****96.....5667779****************************98 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   4.8e-10   1.4e-06       2      80 ..     145     225 ..     144     240 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 4.8e-10
                                       EEEES--TT...HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EEEEEEEEHHHHHHCCT CS
                     Lactamase_B_2   2 riLiDagpd...lrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkklplyapkgvlavlea 72 
                                       +i+iD++      r+  + +   v++     p++aV+++h H+DH++g+  + +    +  +++++ap+g +++  +
  gi|330508792|ref|YP_004385220.1| 145 WIIIDPMMTvetARAA-MDL---VNRTLGYYPVKAVIYSHPHVDHYQGVKGVITekqVASGEVEVIAPAGFMDHAIS 217
                                       9********4443333.222...22333557*****************99998876555555***********9988 PP

                                       TCGHHHCH CS
                     Lactamase_B_2  73 nfvylale 80 
                                       + vy+ + 
  gi|330508792|ref|YP_004385220.1| 218 ENVYAGTA 225
                                       88887665 PP

>> Glyco_hydro_9  Glycosyl hydrolase family 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.0   5.5e-05      0.16     245     362 ..     415     535 ..     313     563 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.5e-05
                                       BTTB-HHHHHHHHHHHHHHSHHCC..........H.....HHHHHHHHHHB-TTS-BES-SSSHHHHHHHHHHHHHH CS
                     Glyco_hydro_9 245 sWdnkvagaqlllagllslalkee......kakasieaaadkykseaegyytpgglaylyewgslryvanaafllll 315
                                        +++ + g+++ + ++l ++ + +         +++++++++y   a+++   ++la +y+ g+ + va+ a +l+ 
  gi|330508792|ref|YP_004385220.1| 415 FYGQIYMGVKATYQKYLGFYDA-NpinlkrLPPEEFARNITEYMGGADAV--LERLARDYDAGNYQLVATIANYLVF 488
                                       3344444444444444333211.123333323345556666665555555..678888******************* PP

                                       HHHTS.S..HHHHHHHHHHHHHHTTTTTSSBSBTTSSSSB-S--B-H CS
                     Glyco_hydro_9 316 aadltgdakeyrdfaksqldyllGrNplgqsYvvGygekspknphhr 362
                                       a   + +a+e++++a +ql y   + p    Y+vG  e   k+p  +
  gi|330508792|ref|YP_004385220.1| 489 ADPDNIKAREMEAAALEQLGYQAESGPARNAYLVGAMELRSKEPVQA 535
                                       **77899999*************************988877777655 PP

>> HNH_2  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012      0.35      11      69 ..     350     415 ..     312     416 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                             HNH_2  11 lleaAHIiP.......wslssffndlilnrfeigrillekgstidspsNgllLspdiHklFdqflf 69 
                                       ++  AH+ P        +l++ ++d++ + +++ ++l +kg t+d  +N++ L  ++ k++  + f
  gi|330508792|ref|YP_004385220.1| 350 VVFTAHNWPrygndkvIELLENQRDMYKYINDQTLNLINKGYTMDEIANMIVLPQSLQKYWYTHGF 415
                                       6668999994444444333333333477777779**************************977766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.28s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 4498.95
//
Query:       gi|330508793|ref|YP_004385221.1|  [L=64]
Description: hypothetical protein MCON_3091 [Methanosaeta concilii GP6]
Scores for complete 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  113.4   2.7    3.7e-33  113.3   2.7    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 !  113.3   2.7   2.1e-37   3.7e-33       1      61 []       2      62 ..       2      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 2.1e-37
                           DUF2196  1 dgktrkdikpGleVeivlkkdqrtGklteGiVkdilTnssthphGIKVrLedGeVGRVqei 61
                                      dgk+rkdikpGl+VeivlkkdqrtGk+teG+V++ilTnss+hphGIKVrL dG+VGRV++i
  gi|330508793|ref|YP_004385221.1|  2 DGKNRKDIKPGLKVEIVLKKDQRTGKRTEGVVAQILTNSSFHPHGIKVRLADGQVGRVARI 62
                                      689*******************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 464.08
//
Query:       gi|330508794|ref|YP_004385222.1|  [L=121]
Description: hypothetical protein MCON_3092 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   14.4   0.2      0.053   13.9   0.2    1.2  1  FAM219A   Protein family FAM219A


Domain annotation for each model (and alignments):
>> FAM219A  Protein family FAM219A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   2.9e-06     0.053      88     119 ..      55      85 ..      40      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-06
                           FAM219A  88 yrldeiPddedldliPPkalassvcacclges 119
                                       +rld +Pd edl  +  +a+  s c  c++++
  gi|330508794|ref|YP_004385222.1|  55 FRLDKLPD-EDLKYLAERAMDGSECLLCIAPQ 85 
                                       8******5.9****************998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 860.97
//
Query:       gi|330508795|ref|YP_004385223.1|  [L=68]
Description: hypothetical protein MCON_3095 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0093   16.0   0.7       0.02   14.9   0.7    1.6  2  zinc_ribbon_6   Zinc-ribbon
  ------ inclusion threshold ------
      0.056   13.7   1.2      0.081   13.2   1.2    1.2  1  LIM             LIM domain
      0.057   13.5   3.1       0.13   12.3   3.1    1.6  1  DZR             Double zinc ribbon
      0.085   12.8   3.4       0.14   12.1   3.2    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.27   11.2   3.1       0.66   10.0   3.1    1.7  1  zinc_ribbon_4   zinc-ribbon domain
        0.4   10.3   3.1       0.66    9.6   0.2    2.0  2  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.7   6.8e-06      0.02      26      53 ..      25      55 ..      19      57 .. 0.81
   2 ?    0.9   0.1      0.16   4.6e+02      30      38 ..      50      58 ..      45      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.8e-06
                     zinc_ribbon_6 26 kkvkilCnDCekksevkfhvlglk...CkeC 53
                                      ++++++C  C+k+++v+f+  g +   C+eC
  gi|330508795|ref|YP_004385223.1| 25 EMTDVTCSECGKQTQVPFKPDGSRpvyCSEC 55
                                      6789***************999763336666 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.16
                     zinc_ribbon_6 30 ilCnDCekk 38
                                      ++C  C +k
  gi|330508795|ref|YP_004385223.1| 50 VYCSECYQK 58
                                      889999877 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.2   2.7e-05     0.081      28      57 ..      30      59 ..      27      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.7e-05
                                      B-TTT-SB-CTT.CEEETT.E.EEEHHHHHHH CS
                               LIM 28 tCsdCqkeLkegsfyekdg.k.lyCkkdylkk 57
                                      tCs+C+k+ +   ++  dg + +yC+++y+k 
  gi|330508795|ref|YP_004385223.1| 30 TCSECGKQTQV--PFKPDGsRpVYCSECYQKH 59
                                      8******8655..5999995369******985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.1   4.3e-05      0.13      12      39 ..      28      60 ..      21      65 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                               DZR 12 arfCseCgtklkavaa.....edrCpsCgekvd 39
                                      + +CseCg++ + + +     +  C++C +k  
  gi|330508795|ref|YP_004385223.1| 28 DVTCSECGKQTQVPFKpdgsrPVYCSECYQKHR 60
                                      568999999977555577888999999987754 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.2   4.8e-05      0.14      25      55 ..      25      58 ..      19      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.8e-05
                    OrfB_Zn_ribbon 25 ayTSktCseCgsknke...alsgrtfkCpnCgfe 55
                                      + T  tCseCg++ +    ++ +r ++C++C  +
  gi|330508795|ref|YP_004385223.1| 25 EMTDVTCSECGKQTQVpfkPDGSRPVYCSECYQK 58
                                      44889*******99999999999********766 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.1   0.00022      0.66       3      33 ..      29      57 ..      26      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
                     zinc_ribbon_4  3 itCpsCkakyeiddeklpakgvkvrCskCgh 33
                                      +tC +C+++ +++ +  p++ + v Cs C +
  gi|330508795|ref|YP_004385223.1| 29 VTCSECGKQTQVPFK--PDGSRPVYCSECYQ 57
                                      89***********98..99999*******87 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00022      0.66       2      12 ..      28      38 ..      27      44 .. 0.81
   2 ?    1.4   0.3     0.081   2.4e+02       4      10 ..      51      57 ..      49      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00022
                            zf_UBZ  2 tylCerCgkei 12
                                       ++C++Cgk+ 
  gi|330508795|ref|YP_004385223.1| 28 DVTCSECGKQT 38
                                      589******85 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.081
                            zf_UBZ  4 lCerCgk 10
                                       C++C +
  gi|330508795|ref|YP_004385223.1| 51 YCSECYQ 57
                                      6****65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 502.73
//
Query:       gi|330508796|ref|YP_004385224.1|  [L=157]
Description: hypothetical protein MCON_3096 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       470  (0.0262145); 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: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.57
# Mc/sec: 824.10
//
Query:       gi|330508797|ref|YP_004385225.1|  [L=60]
Description: hypothetical protein MCON_3097 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 332.38
//
Query:       gi|330508798|ref|YP_004385226.1|  [L=130]
Description: hypothetical protein MCON_3100 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-30  105.5   0.1    2.9e-30  105.4   0.1    1.0  1  DUF488    Protein of unknown function, DUF488
  ------ inclusion threshold ------
      0.091   12.3   0.0       0.15   11.7   0.0    1.3  1  DUF3884   Protein of unknown function (DUF3884)
       0.13   11.3   0.0       0.16   11.0   0.0    1.1  1  Dak1_2    Dihydroxyacetone kinase family


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 !  105.4   0.1   4.8e-34   2.9e-30       2     122 .]       7     113 ..       6     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 4.8e-34
                            DUF488   2 lervydllkkdgvrvlvDVRlwPrSrnpgfskealkedlkeagiaYvwlkelgpsrelrkwfkhdp.rweefferYa 77 
                                        ervy +  + g+r+lvD RlwPr    g+ k++ + dl        w+k+++ps+elrkwf+hdp +weef+er+ 
  gi|330508798|ref|YP_004385226.1|   7 TERVYSAPASGGFRILVD-RLWPR----GLAKDETRIDL--------WMKDIAPSNELRKWFGHDPgKWEEFKERFF 70 
                                       699***************.*****....***********........****************************** PP

                            DUF488  78 aeleskeaakealeelkelakkg.vaLlcaekdperchrvvlaeyl 122
                                       +el+ k   +e +++l++ a+++ +++l+a+kd e++++v l+eyl
  gi|330508798|ref|YP_004385226.1|  71 RELDLK---AELVDQLISKAEESdLIFLYAAKDAEHNNAVALKEYL 113
                                       ****94...49*********************************98 PP

>> DUF3884  Protein of unknown function (DUF3884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.4e-05      0.15      35      63 ..      52      80 ..      47      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                           DUF3884 35 deWiChSdlekeeFkkkFlelteltvdeV 63
                                      + W  h   ++eeFk++F+  ++l ++ V
  gi|330508798|ref|YP_004385226.1| 52 RKWFGHDPGKWEEFKERFFRELDLKAELV 80
                                      689999999**********9999988765 PP

>> Dak1_2  Dihydroxyacetone kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.6e-05      0.16     253     291 ..      77     117 ..      71     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.6e-05
                            Dak1_2 253 kkllkkl..ldedselvtilygedvseeeaealaekleeky 291
                                        +l+++l   +e+s+l+ +++++d++ ++a al+e+le++ 
  gi|330508798|ref|YP_004385226.1|  77 AELVDQLisKAEESDLIFLYAAKDAEHNNAVALKEYLEARM 117
                                       57888986678899***********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 918.28
//
Query:       gi|330508799|ref|YP_004385227.1|  [L=153]
Description: NADH dehydrogenase (ubiquinone), 24 kDa subunit [Methanosaeta concilii GP6]
Scores for complete 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-50  170.1   0.0    2.8e-50  170.0   0.0    1.0  1  2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
  ------ inclusion threshold ------
      0.061   13.1   0.0       0.33   10.8   0.0    2.0  2  HTH_23           Homeodomain-like domain


Domain annotation for each model (and alignments):
>> 2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.0   0.0   3.1e-54   2.8e-50       3     144 ..      11     152 ..       9     153 .] 0.99

  Alignments for each domain:
  == domain 1  score: 170.0 bits;  conditional E-value: 3.1e-54
                                       HHHTTS--GGGGHHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHHHHHTTSSSS-SS---SEEEEEE-SHHHHTT CS
                   2Fe-2S_thioredx   3 eiiakypekrsaliplLklvQeeegwlpeealeevaellgvppaevyevatFYsmfnlkpvgkyviqvCtttpCalr 79 
                                       e+i+ y+ k+++li+lL ++Q+e++w++++al+e++e+l++pp+++y +a+FY+ ++lkp+gk++i+vC++t+C++r
  gi|330508799|ref|YP_004385227.1|  11 EMIDGYKGKEGSLIQLLLDLQSEFNWISKDALQEISERLKIPPSRIYRIASFYEAISLKPIGKHKISVCMGTACQVR 87 
                                       78999************************************************************************ PP

                                       THHHHHHHHHHHHT--TT-B-TTSSEEEEEES--S-GGGSSEEEESSSSEEES-HHHHHHHHHHH CS
                   2Fe-2S_thioredx  80 gseeilealekklgikagettadgkftleeveClGaCanaPvvqindevyedltpekveeilekl 144
                                       gs  il+++e+kl+ik+g tt+d++ftl++v+ClG+Ca +Pv++++d+++++lt ++ve+i++k+
  gi|330508799|ref|YP_004385227.1|  88 GSGMILDRTESKLKIKQGGTTPDMRFTLKRVNCLGCCAIGPVMVVDDDYHGRLTSDRVERIIKKY 152
                                       **************************************************************997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.6e-05      0.33      20      37 ..      42      59 ..      23      65 .. 0.84
   2 ?   -0.6   0.0      0.14   1.2e+03      34      41 ..     145     152 ..     140     153 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.6e-05
                            HTH_23 20 vreIAreLgvsrrTvyrw 37
                                       +eI+++L ++++ +yr+
  gi|330508799|ref|YP_004385227.1| 42 LQEISERLKIPPSRIYRI 59
                                      68***************9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.14
                            HTH_23  34 vyrwlkry 41 
                                       v r++k+y
  gi|330508799|ref|YP_004385227.1| 145 VERIIKKY 152
                                       89999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 00:00:00.43
# Mc/sec: 1074.83
//
Query:       gi|330508800|ref|YP_004385228.1|  [L=628]
Description: NADH:ubiquinone oxidoreductase, nadh-binding subunit [Methanosaeta concilii GP6]
Scores for complete 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-44  150.0   0.0    7.7e-44  149.2   0.0    1.4  1  Complex1_51K     Respiratory-chain NADH dehydrogenase 51 Kd s
    4.8e-32  109.9   0.3    4.8e-32  109.9   0.3    2.6  3  NADH_4Fe-4S      NADH-ubiquinone oxidoreductase-F iron-sulfur
    6.9e-10   38.3  14.3    1.3e-06   27.9   3.9    3.8  4  Fer4             4Fe-4S binding domain
    4.8e-09   35.9   2.3      1e-08   34.9   2.3    1.6  1  SLBB             SLBB domain
    1.9e-07   31.1  21.7    2.1e-06   27.7  11.9    3.5  4  Fer4_10          4Fe-4S dicluster domain
    3.7e-07   30.2   9.5    3.7e-07   30.2   9.5    2.5  2  Fer4_9           4Fe-4S dicluster domain
    5.6e-07   29.3  22.7    0.00054   19.9   2.3    4.5  4  Fer4_2           4Fe-4S binding domain
    8.1e-07   29.1   8.8    8.1e-07   29.1   8.8    2.4  2  Fer4_21          4Fe-4S dicluster domain
    1.5e-06   28.0  25.8    0.00051   20.0   2.9    4.0  3  Fer4_6           4Fe-4S binding domain
    2.1e-06   28.2   8.7    2.1e-06   28.2   8.7    2.8  2  Fer4_7           4Fe-4S dicluster domain
    0.00023   21.6  11.9      0.038   14.5   2.8    2.9  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
     0.0011   19.0   3.0      0.003   17.6   3.0    1.7  1  Fer4_11          4Fe-4S dicluster domain
     0.0016   18.9  12.7      0.054   14.0   0.7    3.2  3  Fer4_8           4Fe-4S dicluster domain
     0.0016   18.3   0.0     0.0038   17.1   0.0    1.5  1  2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
  ------ inclusion threshold ------
      0.012   16.1  15.8       0.12   12.9   1.4    3.5  3  Fer4_17          4Fe-4S dicluster domain
       0.76   10.9  22.8       0.24   12.4   3.8    3.6  3  Fer4_3           4Fe-4S binding domain
        4.2    8.4  22.9       0.13   13.2   3.1    3.2  3  Fer4_16          4Fe-4S double cluster binding domain
        8.2    6.7   9.9         37    4.6   9.9    2.0  1  Fer4_18          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2   0.0   7.7e-47   7.7e-44       1     151 [.     179     350 ..     179     351 .. 0.96

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 7.7e-47
                      Complex1_51K   1 vkeagivGrGGagfPthvKlkakakkkk..kylivNaaEcEPgltkDrllmreepheileGlkiaaealgaekgvig 75 
                                       vk+++++GrGG+gfPt+ K+k+++++    ky+ivN++E++Pg ++Dr lm+ +ph++leGl+iaa+a+g +kg+i+
  gi|330508800|ref|YP_004385228.1| 179 VKRSNLRGRGGGGFPTGRKWKSTREAPGepKYVIVNCDEGDPGAFMDRALMEGNPHSVLEGLIIAAYAMGSHKGFIY 255
                                       799*********************955599*********************************************** PP

                      Complex1_51K  76 vrdekpeaiealekalaeakaagl...........ldievvklagkYpaGeekaLiesltgr.evprgkpp..advg 138
                                       vr e+p a+++ + al++a++ gl           +d++++++ag +++Ge++aL+++l+g  + pr k    +++g
  gi|330508800|ref|YP_004385228.1| 256 VRMEYPLAVQNATLALQQAREYGLlgenilgtgfdFDVSIHRGAGSFVSGESTALMNALEGWvGEPRPKYVhtSQKG 332
                                       *********************999**************************************98888875545999* PP

                      Complex1_51K 139 v.....vvnNveTlaavy 151
                                       +     ++nNveT+a+v+
  gi|330508800|ref|YP_004385228.1| 333 LwgrpsALNNVETFANVP 350
                                       ****************97 PP

>> NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.9   0.3   4.8e-35   4.8e-32       2      85 .]     462     545 ..     461     545 .. 0.98
   2 ?   -2.9   0.8       7.4   7.3e+03      13      28 ..     567     582 ..     563     585 .. 0.81
   3 ?   -1.7   0.8       3.2   3.2e+03      12      23 ..     596     607 ..     591     621 .. 0.72

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 4.8e-35
                                       HHHHHHHHHHHH--S--HHHHIIIIHHHHHHHHHTBT---HHHHHHHHHHHHHHSS--SSTHHHHHHHHHHHHHHHH CS
                       NADH_4Fe-4S   2 varrllefyaaesCGkCtpCreGtkrllelleriaagegteedldlleelaetikgtslCalgdsaanpvlsalrkF 78 
                                       +ar++++f+ +esCGkC pCreG+kr+ e+l+ i++g+gte d+++l+e+ae ++++slCalg++a+npvls++r+F
  gi|330508800|ref|YP_004385228.1| 462 LARYFVDFLCSESCGKCLPCREGLKRMREILDAIESGRGTETDIQTLQEIAELMRTASLCALGRTAVNPVLSTIRYF 538
                                       79*************************************************************************** PP

                                       HHHHHH. CS
                       NADH_4Fe-4S  79 reefeah 85 
                                       ree++ah
  gi|330508800|ref|YP_004385228.1| 539 REEYDAH 545
                                       *****98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.4
                                       H--S--HHHHIIIIHH CS
                       NADH_4Fe-4S  13 esCGkCtpCreGtkrl 28 
                                       e C  C  Cre  +++
  gi|330508800|ref|YP_004385228.1| 567 EICIGCDLCRENCPQG 582
                                       67999*****987775 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.2
                                       HH--S--HHHHI CS
                       NADH_4Fe-4S  12 aesCGkCtpCre 23 
                                       +  C +C+ C e
  gi|330508800|ref|YP_004385228.1| 596 QSKCMRCGICFE 607
                                       667888888876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       1.4   1.4e+03       1       8 [.     451     458 ..     451     459 .. 0.91
   2 ?   -3.0   1.9       7.9   7.8e+03      11      14 ..     475     478 ..     473     481 .. 0.77
   3 !   27.9   3.9   1.3e-09   1.3e-06       2      24 .]     563     585 ..     562     585 .. 0.94
   4 !   24.5   2.7   1.6e-08   1.6e-05       2      20 ..     593     611 ..     592     614 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.4
                                       EEEETTTS CS
                              Fer4   1 vvideekC 8  
                                       +vide+ C
  gi|330508800|ref|YP_004385228.1| 451 IVIDEDTC 458
                                       69****** PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.9
                                       -THH CS
                              Fer4  11 CGaC 14 
                                       CG+C
  gi|330508800|ref|YP_004385228.1| 475 CGKC 478
                                       9999 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 1.3e-09
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        id+e CigC +C e CP gAI+
  gi|330508800|ref|YP_004385228.1| 563 SIDPEICIGCDLCRENCPQGAIY 585
                                       69********************6 PP

  == domain 4  score: 24.5 bits;  conditional E-value: 1.6e-08
                                       EEETTTSSS-THHHHHSTT CS
                              Fer4   2 videekCigCGaCvevCPv 20 
                                       v+d++kC++CG+C e+CP 
  gi|330508800|ref|YP_004385228.1| 593 VVDQSKCMRCGICFEICPK 611
                                       89****************6 PP

>> SLBB  SLBB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   2.3     1e-11     1e-08       2      57 ..     374     423 ..     373     424 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1e-11
                                       EEEESSBSS-EEEEEETT-BHHHHHHTTT-SBSS.........-E.EEE-SSSSS-- CS
                              SLBB   2 VtVtGeVkrPgnyevpigttlsdlieqaGGltddadlksvnLarl.avipgGpmmgi 57 
                                       + ++G+V++ g +evp+g+tl+d+i++ GG+ +          +l  v  gGp+ gi
  gi|330508800|ref|YP_004385228.1| 374 FSLVGKVNNTGLVEVPMGMTLADIIYKIGGGIPGNK-------KLkGVQTGGPSGGI 423
                                       6789******************************99.......99999*****9987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       6.5   6.5e+03       2       9 ..     451     458 ..     450     460 .. 0.86
   2 ?   -0.9   2.4       1.9   1.9e+03       7      16 ..     473     482 ..     468     484 .. 0.76
   3 !   27.7  11.9   2.1e-09   2.1e-06       3      56 .]     563     610 ..     561     610 .. 0.91
   4 !   17.4   2.2   3.5e-06    0.0035       2      24 ..     592     614 ..     591     625 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.5
                           Fer4_10   2 vvidddtC 9  
                                       +vid+dtC
  gi|330508800|ref|YP_004385228.1| 451 IVIDEDTC 458
                                       79****** PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                           Fer4_10   7 dtCirCgkCv 16 
                                       ++C +C  C+
  gi|330508800|ref|YP_004385228.1| 473 ESCGKCLPCR 482
                                       6788888886 PP

  == domain 3  score: 27.7 bits;  conditional E-value: 2.1e-09
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        id++ Ci+C  C++ CP+     ga+++++++ av +  +kC++cg C e+CP
  gi|330508800|ref|YP_004385228.1| 563 SIDPEICIGCDLCRENCPQ-----GAIYKDDGGFAVVD-QSKCMRCGICFEICP 610
                                       69*****************.....88888888888777.99************9 PP

  == domain 4  score: 17.4 bits;  conditional E-value: 3.5e-06
                           Fer4_10   2 vvidddtCirCgkCvkaCPadlt 24 
                                       +v+d+++C+rCg C + CP +++
  gi|330508800|ref|YP_004385228.1| 592 AVVDQSKCMRCGICFEICPKKVR 614
                                       5889***************9543 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.6       0.4     4e+02       4      16 ..     473     485 ..     454     500 .. 0.73
   2 !   30.2   9.5   3.7e-10   3.7e-07       2      49 ..     569     612 ..     568     613 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.4
                            Fer4_9   4 g.CgaCveaCpagv 16 
                                       + Cg+C + C  g+
  gi|330508800|ref|YP_004385228.1| 473 EsCGKCLP-CREGL 485
                                       33666666.65555 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 3.7e-10
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       C+gC+ C e Cp+g++ +d+++  +  +     +C+ Cg C+e+Cpk+
  gi|330508800|ref|YP_004385228.1| 569 CIGCDLCRENCPQGAIYKDDGGFAVVDQS----KCMRCGICFEICPKK 612
                                       ****************9999998888754....7************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 ?    0.0   0.0       1.2   1.2e+03       3      10 ..     451     458 ..     449     460 .. 0.87
   2 ?    2.7   1.6      0.16   1.6e+02       3      17 ..     465     479 ..     463     483 .. 0.58
   3 !   19.9   2.3   5.4e-07   0.00054       4      22 .]     563     581 ..     560     581 .. 0.92
   4 !   17.7   1.3   2.8e-06    0.0028       3      21 ..     592     610 ..     590     611 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.2
                            Fer4_2   3 vvvdtdrC 10 
                                       +v+d+d+C
  gi|330508800|ref|YP_004385228.1| 451 IVIDEDTC 458
                                       89****** PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.16
                            Fer4_2   3 vvvdtdrCi.gCgaCv 17 
                                       ++vd   C  +Cg+C+
  gi|330508800|ref|YP_004385228.1| 465 YFVDFL-CSeSCGKCL 479
                                       555655.753577773 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 5.4e-07
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                        +d+++CigC  C+ +CP+
  gi|330508800|ref|YP_004385228.1| 563 SIDPEICIGCDLCRENCPQ 581
                                       69****************6 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 2.8e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       +vvd  +C++Cg+C   CP
  gi|330508800|ref|YP_004385228.1| 592 AVVDQSKCMRCGICFEICP 610
                                       589***************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 ?   -2.6   0.8       6.5   6.4e+03      11      15 ..     475     479 ..     468     489 .. 0.67
   2 !   29.1   8.8   8.1e-10   8.1e-07       3      52 ..     564     610 ..     562     617 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.5
                           Fer4_21  11 CgkCl 15 
                                       CgkCl
  gi|330508800|ref|YP_004385228.1| 475 CGKCL 479
                                       55553 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 8.1e-10
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                       id++ CigC +C   C++    ai +d+   + v +++C+ C +C ++CP
  gi|330508800|ref|YP_004385228.1| 564 IDPEICIGCDLCRENCPQ---GAIYKDDGGFAVVDQSKCMRCGICFEICP 610
                                       9****************5...89****99999999*************** 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   3.2      0.16   1.6e+02       1      15 [.     450     478 ..     450     481 .. 0.86
   2 !   16.0   4.2   9.1e-06     0.009       4      24 .]     564     584 ..     563     584 .. 0.96
   3 !   20.0   2.9   5.2e-07   0.00051       1      21 [.     591     611 ..     591     615 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.16
                            Fer4_6   1 vveidpdkCi..............gCgdC 15 
                                       +++id+d C               +Cg+C
  gi|330508800|ref|YP_004385228.1| 450 IIVIDEDTCAvdlaryfvdflcseSCGKC 478
                                       689******88999999988888889999 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 9.1e-06
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       idp+ CigC+ C  +CP gai
  gi|330508800|ref|YP_004385228.1| 564 IDPEICIGCDLCRENCPQGAI 584
                                       9****************9998 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 5.2e-07
                            Fer4_6   1 vveidpdkCigCgdCvrvCPe 21 
                                       ++++d++kC  Cg C+ +CP 
  gi|330508800|ref|YP_004385228.1| 591 FAVVDQSKCMRCGICFEICPK 611
                                       689*****************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 ?   -0.6   0.5       2.1   2.1e+03      40      44 ..     474     478 ..     436     483 .. 0.61
   2 !   28.2   8.7   2.1e-09   2.1e-06       2      51 ..     569     612 ..     568     613 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.1
                            Fer4_7  40 gCgaC 44 
                                       +Cg+C
  gi|330508800|ref|YP_004385228.1| 474 SCGKC 478
                                       46666 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 2.1e-09
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       CigC  C ++Cp++ai+ d+         +++d++kC+ Cg C + CP++
  gi|330508800|ref|YP_004385228.1| 569 CIGCDLCRENCPQGAIYKDDG------GFAVVDQSKCMRCGICFEICPKK 612
                                       *****************9885......467999***************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 !   14.5   2.8   3.8e-05     0.038       1      31 [.     564     594 ..     564     596 .. 0.86
   2 !   12.8   2.1   0.00013      0.13       1      18 [.     594     611 ..     594     612 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-05
                           Fer4_13   1 VDrdtCiacgaCvelaPdvFeeddeggasvv 31 
                                       +D + Ci+c++C+e +P+   ++d+gg +vv
  gi|330508800|ref|YP_004385228.1| 564 IDPEICIGCDLCRENCPQGAIYKDDGGFAVV 594
                                       79999************98888888887776 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00013
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VD+++C+ cg+C e++P+
  gi|330508800|ref|YP_004385228.1| 594 VDQSKCMRCGICFEICPK 611
                                       9****************6 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   3.0     3e-06     0.003       2      60 ..     561     615 ..     560     623 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3e-06
                           Fer4_11   2 ewlflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivr 60 
                                        + + pe+C  C    C + +p++ai+kd+  G  ++d++++  ++  + e cP k+  
  gi|330508800|ref|YP_004385228.1| 561 SYSIDPEICIGCD--LCRENCPQGAIYKDD-GGFAVVDQSKCM-RCGICFEICPKKVRA 615
                                       56789*******7..7*************9.9999*******7.9*********88765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.5       2.7   2.7e+03       4      12 ..     474     482 ..     470     523 .. 0.68
   2 !   12.2   0.5   0.00019      0.18       4      17 ..     568     581 ..     565     593 .. 0.76
   3 !   14.0   0.7   5.4e-05     0.054       2      19 ..     596     618 ..     595     628 .] 0.73

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.7
                            Fer4_8   4 kCieCgaCq 12 
                                       +C++C  C+
  gi|330508800|ref|YP_004385228.1| 474 SCGKCLPCR 482
                                       344444443 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00019
                            Fer4_8   4 kCieCgaCqsaCpv 17 
                                        Ci+C +C+++Cp 
  gi|330508800|ref|YP_004385228.1| 568 ICIGCDLCRENCPQ 581
                                       599*********93 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 5.4e-05
                            Fer4_8   2 lekCieCgaCqsaCp.....vlr 19 
                                        +kC++Cg C++ Cp     v+r
  gi|330508800|ref|YP_004385228.1| 596 QSKCMRCGICFEICPkkvraVVR 618
                                       589***********966554444 PP

>> 2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.8e-06    0.0038      63     143 ..      23     101 ..      17     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.8e-06
                                       --SEEEEEE-SHHHHTTTHHHHHHHHHHHHT--TT-B-TTSSEEEEEES--S-GGGSSEEEE..SSSSEEES-HHHH CS
                   2Fe-2S_thioredx  63 vgkyviqvCtttpCalrgseeilealekklgikagettadgkftleeveClGaCanaPvvqi..ndevyedltpekv 137
                                         k  + +C +t C   g++ +++a+++ l ik+g    +++++++e+ C G C+++  v++   + +y  + +++v
  gi|330508800|ref|YP_004385228.1|  23 STKPLVAICAGTGCLTLGARLVVRAFQEYL-IKKG---LEKEIEIKETGCPGFCEKGTLVVVypRGVYYIGVHQDDV 95 
                                       567789***********************9.7776...5789****************9999555679999999999 PP

                                       HHHHHH CS
                   2Fe-2S_thioredx 138 eeilek 143
                                        +i+e+
  gi|330508800|ref|YP_004385228.1|  96 PDIVEE 101
                                       999876 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.6      0.13   1.3e+02       4      31 ..     474     497 ..     470     525 .. 0.50
   2 ?   12.9   1.4   0.00012      0.12       2      18 ..     569     585 ..     554     591 .. 0.75
   3 ?    8.4   1.0    0.0032       3.1      45      59 ..     598     612 ..     592     620 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.13
                           Fer4_17   4 qCgyClpeCpsyeaydnepkkllraakl 31 
                                       +Cg Clp C  + ++     ++l a+++
  gi|330508800|ref|YP_004385228.1| 474 SCGKCLP-CREGLKRMR---EILDAIES 497
                                       6999999.887655332...34444444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00012
                           Fer4_17   2 CiqCgyClpeCpsyeay 18 
                                       Ci+C  C+++Cp++++y
  gi|330508800|ref|YP_004385228.1| 569 CIGCDLCRENCPQGAIY 585
                                       66666666666666555 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0032
                           Fer4_17  45 lCieCgeCerkCPqg 59 
                                       +C+ Cg C + CP++
  gi|330508800|ref|YP_004385228.1| 598 KCMRCGICFEICPKK 612
                                       566666666666655 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.9       3.6   3.6e+03       6      11 ..     470     475 ..     456     480 .. 0.68
   2 ?   12.4   3.8   0.00024      0.24       1      15 []     569     583 ..     569     583 .. 0.98
   3 ?    8.9   3.4    0.0031       3.1       1      14 [.     599     612 ..     599     613 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.6
                            Fer4_3   6 aCvevC 11 
                                       +C e+C
  gi|330508800|ref|YP_004385228.1| 470 LCSESC 475
                                       566666 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00024
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gC +C e CP gA
  gi|330508800|ref|YP_004385228.1| 569 CIGCDLCRENCPQGA 583
                                       *************98 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0031
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+ Cg C+e CP++
  gi|330508800|ref|YP_004385228.1| 599 CMRCGICFEICPKK 612
                                       999*********97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.1   0.00013      0.13       2      28 ..     569     597 ..     568     600 .. 0.76
   2 ?    8.4   2.8     0.004         4       1      14 [.     598     611 ..     590     612 .. 0.63
   3 ?    8.6   3.0    0.0037       3.7       1      15 [.     598     612 ..     598     620 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                           Fer4_16   2 CgtCgkCaevCPtnaikek..kekeiear 28 
                                       C++C  C e CP++ai ++    +++++ 
  gi|330508800|ref|YP_004385228.1| 569 CIGCDLCRENCPQGAIYKDdgGFAVVDQS 597
                                       ****************9884444555555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.004
                           Fer4_16   1 rCgtCgkCaevCPt 14 
                                       +C +Cg C e+CP 
  gi|330508800|ref|YP_004385228.1| 598 KCMRCGICFEICPK 611
                                       35666666666664 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0037
                           Fer4_16   1 rCgtCgkCaevCPtn 15 
                                       +C +Cg C e+CP +
  gi|330508800|ref|YP_004385228.1| 598 KCMRCGICFEICPKK 612
                                       599999999999987 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   9.9     0.037        37      61     101 ..     569     615 ..     545     623 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.037
                           Fer4_18  61 cidcescvkvcPtgidirk..Gl....qleciscllcidacdkvmek 101
                                       ci c+ c + cP g   ++  G+    q +c+ c+ c + c k + +
  gi|330508800|ref|YP_004385228.1| 569 CIGCDLCRENCPQGAIYKDdgGFavvdQSKCMRCGICFEICPKKVRA 615
                                       9***********997665533334455899***********765444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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):              18  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 4430.97
//
Query:       gi|330508801|ref|YP_004385229.1|  [L=474]
Description: iron-sulfur cluster/F420 dehydrogenase/hydrogenase fusion protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-33  115.5   0.0    4.6e-33  114.2   0.0    1.6  1  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    4.2e-17   62.0   0.0    9.7e-17   60.8   0.0    1.7  1  Fer2_4       2Fe-2S iron-sulfur cluster binding domain
    4.3e-13   49.2   0.1      9e-13   48.2   0.1    1.5  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
      3e-08   33.5   0.1      3e-08   33.5   0.1    2.8  2  Fer2         2Fe-2S iron-sulfur cluster binding domain
    3.1e-07   30.4   8.3    3.1e-07   30.4   8.3    2.2  1  Fer4_21      4Fe-4S dicluster domain
    3.4e-06   26.6   2.4    3.4e-06   26.6   2.4    3.2  3  Fer4         4Fe-4S binding domain
    6.8e-06   26.6   9.4    6.8e-06   26.6   9.4    2.6  2  Fer4_7       4Fe-4S dicluster domain
    6.1e-05   23.9   9.5    0.00071   20.5   0.3    3.4  3  Fer4_16      4Fe-4S double cluster binding domain
    9.6e-05   22.3  21.2     0.0056   16.7   4.0    3.4  3  Fer4_6       4Fe-4S binding domain
    0.00028   21.0  15.9    0.00079   19.5  11.5    3.3  3  Fer4_9       4Fe-4S dicluster domain
     0.0035   17.4  22.8     0.0091   16.1  13.5    3.0  4  Fer4_10      4Fe-4S dicluster domain
     0.0042   17.1   2.8     0.0042   17.1   2.8    3.6  3  Fer4_2       4Fe-4S binding domain
     0.0048   17.3  12.0     0.0066   16.9   9.8    2.5  2  Fer4_8       4Fe-4S dicluster domain
      0.009   16.8   7.2      0.059   14.2   0.5    2.7  2  Fer4_22      4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.24   11.6  11.6       0.56   10.4   2.0    2.7  2  Fer4_18      4Fe-4S dicluster domain
       0.38   11.5   7.9        2.9    8.7   1.3    3.3  3  Fer4_15      4Fe-4S single cluster domain
        0.6   10.7  14.2        3.3    8.3   4.1    3.1  3  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I


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 !  114.2   0.0   4.3e-36   4.6e-33       2     139 ..     293     429 ..     292     441 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 4.3e-36
                       FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqk.....kklkekilltiglfCggnfspealrk.lleelgvdpedvkklefrgkgkfrv 72 
                                       ++vavvGtPCqi+ +rkl++      ++ ++  +++glfC ++f+++ lr+  +  lg+d ed  k+++  kg++++
  gi|330508801|ref|YP_004385229.1| 293 RRVAVVGTPCQIRVIRKLEQldyfkDEFPDAEIFLVGLFCFESFDYRRLRDhAKGLLGIDIEDADKIQI-AKGRYIA 368
                                       79*****************999*999999**********************99999*************.9****** PP

                       FrhB_FdhB_C  73 elkd.ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeelle 139
                                       +l   e+++s+ ele+ ir++C++C d +++lADis+G+v      g ++eg+s v+vr+ekg++ll+
  gi|330508801|ref|YP_004385229.1| 369 TLDGmEHSCSVRELENDIREGCRFCGDLVSRLADISIGSV------G-SAEGYSSVIVRSEKGKKLLD 429
                                       8888999*********************************......8.******************97 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   9.2e-20   9.7e-17       5      81 ..       2      77 ..       1      78 [. 0.92

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 9.2e-20
                            Fer2_4  5 tltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVeve..gepn.vracstpvedGlkvetq 80
                                      ++ +D+++++++  +t+++A+l +g+++p++c++      l++ g+Cr C Ve+e  g+++ v ac  p+edGl+v+t 
  gi|330508801|ref|YP_004385229.1|  2 RFWIDDQQLEAQTSSTILEAALSAGIKIPTLCHH----PALESYGSCRLCTVEIEknGKKRfVTACNYPIEDGLVVRTA 76
                                      799*******************************....99**************966444438***************8 PP

                            Fer2_4 81 t 81
                                      t
  gi|330508801|ref|YP_004385229.1| 77 T 77
                                      7 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 !   48.2   0.1   8.6e-16     9e-13      14      74 ..     222     281 ..     215     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 8.6e-16
                       FrhB_FdhB_N  14 kaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYtlspnl 74 
                                       ++q+GG+vt+ll+++L++g id+++vv +  ++   +++ + + e +++a G+kY  ++ l
  gi|330508801|ref|YP_004385229.1| 222 QGQDGGVVTSLLARCLDKGVIDAAVVVYQR-ENNGGRAAAVDDIEGVIKAKGTKYVRVSAL 281
                                       69**************************99.4668********************955444 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1   2.8e-11     3e-08       8      75 ..       8      65 ..       5      68 .. 0.76
   2 ?   -2.3   0.9       4.1   4.3e+03      35      43 ..     125     132 ..      96     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.8e-11
                                      EEEEEETTTHBHHHHHHHTTTTTSTTSSSS......SSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGS CS
                              Fer2  8 vevevadgettlldaaeenggidipysCgg......ggCgtClvevlegevqsdetelegeeldegklrlaCqt 75
                                      +++e+++  +t+l+aa ++ gi ip++C++      g+C+ C+ve+++           g++   +  ++aC  
  gi|330508801|ref|YP_004385229.1|  8 QQLEAQT-SSTILEAALSA-GIKIPTLCHHpalesyGSCRLCTVEIEK----------NGKK---R-FVTACNY 65
                                      4666655.555*******9.***************999*******982..........2222...2.4588875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.1
                                       SSSSSSSTT CS
                              Fer2  35 CggggCgtC 43 
                                       Cg  +C++C
  gi|330508801|ref|YP_004385229.1| 125 CG-LCCRVC 132
                                       44.457766 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   8.3     3e-10   3.1e-07       3      57 ..     117     178 ..     116     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3e-10
                           Fer4_21   3 idedkCigCgkCliaCed.tshqaieidaktvl.......kvvedeCvGCnlCssvCPvedci 57 
                                       ++e+kCi Cg+C+ +C +  ++ ai+++++ +          ++++C++C  Cs vCP+  +i
  gi|330508801|ref|YP_004385229.1| 117 LEEEKCILCGLCCRVCGEmVGVFAINFQNRGTDrsvgapyGELSEDCIACGACSLVCPT-SAI 178
                                       579*************8725899**8776542222233223469**************7.666 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   6.9    0.0017       1.7       4      18 ..     118     132 ..     115     134 .. 0.87
   2 !   26.6   2.4   3.2e-09   3.4e-06       6      24 .]     161     179 ..     159     179 .. 0.94
   3 ?   -3.3   0.8         9   9.5e+03       7      12 ..     389     394 ..     387     394 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                                       ETTTSSS-THHHHHS CS
                              Fer4   4 deekCigCGaCvevC 18 
                                        eekCi CG+C  vC
  gi|330508801|ref|YP_004385229.1| 118 EEEKCILCGLCCRVC 132
                                       69*********8888 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 3.2e-09
                                       TTSSS-THHHHHSTTTEEE CS
                              Fer4   6 ekCigCGaCvevCPvgAIt 24 
                                       e+Ci+CGaC  vCP+ AI+
  gi|330508801|ref|YP_004385229.1| 161 EDCIACGACSLVCPTSAIS 179
                                       89***************95 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 9
                                       TSSS-T CS
                              Fer4   7 kCigCG 12 
                                        C +CG
  gi|330508801|ref|YP_004385229.1| 389 GCRFCG 394
                                       366666 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   9.4   6.4e-09   6.8e-06       1      52 []     121     177 ..     121     177 .. 0.70
   2 ?   -2.2   0.1       6.4   6.8e+03       4       9 ..     389     394 ..     385     396 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 6.4e-09
                            Fer4_7   1 rCigCgaCvaaCp..vkaield..eeenekgtekveid.pekClgCgaCvavCPtga 52 
                                       +Ci Cg C ++C   v+++ ++  ++  ++ +  ++++ +e+C+ CgaC  vCPt a
  gi|330508801|ref|YP_004385229.1| 121 KCILCGLCCRVCGemVGVFAINfqNRGTDRSVGAPYGElSEDCIACGACSLVCPTSA 177
                                       7***********75555554440044444444555665479*************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.4
                            Fer4_7   4 gCgaCv 9  
                                       gC++C 
  gi|330508801|ref|YP_004385229.1| 389 GCRFCG 394
                                       788885 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    0.0079       8.3      41      64 ..     110     132 ..      77     134 .. 0.67
   2 !   20.5   0.3   6.7e-07   0.00071       2      23 ..     163     182 ..     162     207 .. 0.82
   3 ?   -1.5   0.1       4.8   5.1e+03      34      60 ..     370     393 ..     353     395 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0079
                           Fer4_16  41 laedeekckkqeaitgCdiCqdvC 64 
                                       ++e ++k + +e+++ C+ C +vC
  gi|330508801|ref|YP_004385229.1| 110 VIEPRFKLE-EEKCILCGLCCRVC 132
                                       444444444.68899999999999 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 6.7e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekkek 23 
                                       C+ Cg+C  vCPt+ai+++  +
  gi|330508801|ref|YP_004385229.1| 163 CIACGACSLVCPTSAISAQ--R 182
                                       *****************98..3 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.8
                           Fer4_16  34 ntaekkdlaedeekckkqeaitgCdiC 60 
                                        + ++++++ +e +++++e   gC+ C
  gi|330508801|ref|YP_004385229.1| 370 LDGMEHSCSVRELENDIRE---GCRFC 393
                                       4555555555565555555...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 ?   -1.2   0.2       2.3   2.5e+03      11      16 ..      43      48 ..      29      50 .. 0.59
   2 !   13.9   4.5   4.2e-05     0.044       6      22 ..     119     135 ..     118     140 .. 0.89
   3 !   16.7   4.0   5.3e-06    0.0056       9      24 .]     163     178 ..     160     178 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.3
                            Fer4_6 11 gCgdCv 16
                                      +C+ C+
  gi|330508801|ref|YP_004385229.1| 43 SCRLCT 48
                                      599996 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.2e-05
                            Fer4_6   6 pdkCigCgdCvrvCPeg 22 
                                       ++kCi Cg C rvC e 
  gi|330508801|ref|YP_004385229.1| 119 EEKCILCGLCCRVCGEM 135
                                       79************985 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 5.3e-06
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       Ci Cg+C  vCP+ ai
  gi|330508801|ref|YP_004385229.1| 163 CIACGACSLVCPTSAI 178
                                       *************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 !    9.0   4.7    0.0015       1.6      11      47 ..      94     133 ..      92     136 .. 0.79
   2 !   19.5  11.5   7.5e-07   0.00079       1      51 []     121     178 ..     121     178 .. 0.68
   3 ?   -1.3   0.1       2.4   2.5e+03      23      40 ..     379     394 ..     365     395 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                            Fer4_9  11 aCpagvvvedaaerkarlraase...eaCigCgaCveaCp 47 
                                        Cp++  ++d a+++  ++ + +   e+Ci Cg C  +C 
  gi|330508801|ref|YP_004385229.1|  94 RCPKEKQIQDLAREYGVIEPRFKleeEKCILCGLCCRVCG 133
                                       588888888877777777666557889************5 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 7.5e-07
                            Fer4_9   1 kCtgCgaCveaC.........pagvvvedaaerkarlraase....eaCigCgaCveaCpkgai 51 
                                       kC+ Cg C ++C         +++    d++ +        +    e+Ci CgaC  +Cp+ ai
  gi|330508801|ref|YP_004385229.1| 121 KCILCGLCCRVCgemvgvfaiNFQNRGTDRSVGAP------YgelsEDCIACGACSLVCPTSAI 178
                                       7***********77655444333333333333333......2456678*************987 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.4
                            Fer4_9  23 erkarlraaseeaCigCg 40 
                                        r+ +++++  e C +Cg
  gi|330508801|ref|YP_004385229.1| 379 VRELENDIR--EGCRFCG 394
                                       444444444..4599998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   6.1     0.015        16      38      55 ..     114     132 ..      93     133 .. 0.53
   2 !   16.1  13.5   8.6e-06    0.0091       4      56 .]     117     174 ..     114     174 .. 0.81
   3 !   14.9   1.8   2.1e-05     0.022       7      24 ..     161     181 ..     154     207 .. 0.75
   4 ?   -2.8   0.3       6.7   7.1e+03      40      49 ..     385     394 ..     376     395 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
                           Fer4_10  38 vrk.kvekCtgcgaCveaC 55 
                                         k   ekC+ cg C ++C
  gi|330508801|ref|YP_004385229.1| 114 RFKlEEEKCILCGLCCRVC 132
                                       5444555666666666655 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 8.6e-06
                           Fer4_10   4 idddtCirCgkCvkaCPadl......tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                       +++++Ci Cg C ++C           + +++g +   +a  +  +e+C++cgaC  +CP
  gi|330508801|ref|YP_004385229.1| 117 LEEEKCILCGLCCRVC--GEmvgvfaINFQNRGTDRSVGAPYGeLSEDCIACGACSLVCP 174
                                       6889************..4457****66666666666666666599*************9 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 2.1e-05
                           Fer4_10   7 dtCirCgkCvkaCPadl...t 24 
                                       + Ci Cg+C  +CP+++   +
  gi|330508801|ref|YP_004385229.1| 161 EDCIACGACSLVCPTSAisaQ 181
                                       68************9664330 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 6.7
                           Fer4_10  40 kkvekCtgcg 49 
                                       +  e C +cg
  gi|330508801|ref|YP_004385229.1| 385 DIREGCRFCG 394
                                       4556677776 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   0.6       4.4   4.6e+03      12      17 ..      43      48 ..      42      49 .. 0.74
   2 !    8.0   4.7    0.0031       3.3       2      20 ..     114     132 ..     113     132 .. 0.83
   3 !   17.1   2.8     4e-06    0.0042       7      22 .]     160     175 ..     154     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.4
                            Fer4_2 12 gCgaCv 17
                                      +C+ C+
  gi|330508801|ref|YP_004385229.1| 43 SCRLCT 48
                                      599995 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0031
                            Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                       +++ ++++Ci Cg C  +C
  gi|330508801|ref|YP_004385229.1| 114 RFKLEEEKCILCGLCCRVC 132
                                       68899********775777 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 4e-06
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                       ++ Ci+CgaC  +CP+
  gi|330508801|ref|YP_004385229.1| 160 SEDCIACGACSLVCPT 175
                                       466************7 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       8.6     9e+03       8      12 ..      44      48 ..      39      90 .. 0.70
   2 !   16.9   9.8   6.3e-06    0.0066       3      64 ..     120     176 ..     118     178 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.6
                            Fer4_8  8 CgaCq 12
                                      C +C+
  gi|330508801|ref|YP_004385229.1| 44 CRLCT 48
                                      55554 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.3e-06
                            Fer4_8   3 ekCieCgaCqsaC.pvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       ekCi Cg+C   C  ++  ++ ++  ++rg     v    +    e  + C +cgaC+ vCp++
  gi|330508801|ref|YP_004385229.1| 120 EKCILCGLCCRVCgEMVGVFAiNF--QNRGTDRS-VGAPYG----ELSEDCIACGACSLVCPTS 176
                                       69***********43555554444..55555445.445555....5579*************86 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.3     0.043        45      78      93 ..     118     133 ..      86     137 .. 0.73
   2 !   14.2   0.5   5.6e-05     0.059       1      18 [.     162     179 ..     162     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.043
                           Fer4_22  78 gesgCvGCgRCieacp 93 
                                       +e++C+ Cg C ++c 
  gi|330508801|ref|YP_004385229.1| 118 EEEKCILCGLCCRVCG 133
                                       6677777777777775 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.6e-05
                           Fer4_22   1 rClsCgaCtlvCptCsCf 18 
                                       +C++CgaC+lvCpt    
  gi|330508801|ref|YP_004385229.1| 162 DCIACGACSLVCPTSAIS 179
                                       5*************8655 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   2.4     0.015        16      51      75 ..     112     136 ..      77     144 .. 0.76
   2 ?   10.4   2.0   0.00053      0.56      57      74 ..     159     176 ..     140     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
                           Fer4_18  51 eerkekgagdcidcescvkvcPtgi 75 
                                       e r + ++ +ci c+ c +vc   +
  gi|330508801|ref|YP_004385229.1| 112 EPRFKLEEEKCILCGLCCRVCGEMV 136
                                       5555667888999999999997655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00053
                           Fer4_18  57 gagdcidcescvkvcPtg 74 
                                        + dci+c++c  vcPt 
  gi|330508801|ref|YP_004385229.1| 159 LSEDCIACGACSLVCPTS 176
                                       568*************96 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.3    0.0028       2.9       2      21 ..     116     135 ..     115     152 .. 0.85
   2 ?    5.2   0.3     0.034        36       6      20 ..     161     175 ..     160     200 .. 0.89
   3 ?   -2.2   0.0         7   7.4e+03      26      51 ..     411     434 ..     385     441 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0028
                           Fer4_15   2 vvDrdaCigcglCvaeapev 21 
                                       ++++++Ci cglC +++ e+
  gi|330508801|ref|YP_004385229.1| 116 KLEEEKCILCGLCCRVCGEM 135
                                       5899************9765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.034
                           Fer4_15   6 daCigcglCvaeape 20 
                                       + Ci cg+C  ++p+
  gi|330508801|ref|YP_004385229.1| 161 EDCIACGACSLVCPT 175
                                       68**********985 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7
                           Fer4_15  26 edglasvllddgeiaeg.evpddeeea 51 
                                        +g++sv++  +e  +g  + d++  +
  gi|330508801|ref|YP_004385229.1| 411 AEGYSSVIVR-SE--KGkKLLDWLSFC 434
                                       3466666653.33..222555555555 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 ?    7.5   1.3    0.0057       6.1       2      18 ..     118     134 ..     117     143 .. 0.87
   2 ?    8.3   4.1    0.0031       3.3       4      18 ..     161     175 ..     160     176 .. 0.90
   3 ?   -2.7   0.0       8.9   9.4e+03      16      33 ..     245     262 ..     242     270 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0057
                           Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                       ++++Ci cg+C+ ++ +
  gi|330508801|ref|YP_004385229.1| 118 EEEKCILCGLCCRVCGE 134
                                       579***********976 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0031
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                       + CiacgaC  ++P 
  gi|330508801|ref|YP_004385229.1| 161 EDCIACGACSLVCPT 175
                                       68************5 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 8.9
                           Fer4_13  16 aPdvFeeddeggasvvae 33 
                                       a  v++++++gg+++ ++
  gi|330508801|ref|YP_004385229.1| 245 AVVVYQRENNGGRAAAVD 262
                                       445677777777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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):              17  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3208.13
//
Query:       gi|330508802|ref|YP_004385230.1|  [L=124]
Description: hypothetical protein MCON_3105, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 901.37
//
Query:       gi|330508803|ref|YP_004385231.1|  [L=187]
Description: hypothetical protein MCON_3107 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00025   21.1   2.4      0.011   15.7   0.3    2.2  2  CoA_binding_3  CoA-binding domain
  ------ inclusion threshold ------
      0.048   13.7   0.5        0.5   10.4   0.0    2.0  2  DUF3043        Protein of unknown function (DUF3043)
       0.23   11.9   5.0       0.15   12.5   2.7    1.8  2  DUF1211        Protein of unknown function (DUF1211)


Domain annotation for each model (and alignments):
>> CoA_binding_3  CoA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.1    0.0023        14      17      54 ..      23      61 ..      13      87 .. 0.74
   2 !   15.7   0.3   1.9e-06     0.011      20      71 ..     115     167 ..     100     184 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0023
                     CoA_binding_3 17 lllrvlsawllvllllallsfslkdafSR.lwlaywavv 54
                                       ++ +++  ++  +l+++ s+ +k +++R +wl+y++ +
  gi|330508803|ref|YP_004385231.1| 23 RAKLITMKLAFITVLFGVSSVDVKIEIARiFWLIYFVPL 61
                                      5555666666677777777778899****8888888733 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.9e-06
                     CoA_binding_3  20 rvlsawllvllllallsf..slkdafSRlwlaywavvglvllivsrllvravlr 71 
                                       +++++++++l+++a++    s+++++ +lw+a w v++l ++i+  ++ +++l 
  gi|330508803|ref|YP_004385231.1| 115 NMFFSVIVTLGAAAFIHSqqSWTEHLMKLWFAVWLVISLGVIIAL-WMRHQALI 167
                                       445555555555555444334458999************988865.66666554 PP

>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2     0.043   2.6e+02      72     124 ..      43      70 ..      16      81 .. 0.54
   2 ?   10.4   0.0   8.4e-05       0.5      65     145 ..     100     182 ..      90     186 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.043
                           DUF3043  72 VDsrrnlgelflplalvvlvlllvslvkvpevqavvsllllvllllvvidgil 124
                                       VD ++ ++ +f+ + +v                          l+++  d ++
  gi|330508803|ref|YP_004385231.1|  43 VDVKIEIARIFWLIYFV-------------------------PLVAISYDLYI 70 
                                       34444444444444333.........................44444444444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 8.4e-05
                           DUF3043  65 RryvRDlVDsrrnlgelflplalvvlvl.llv.slvkvpevqavvsllllvllllvvidgillgrkvkkkvrekFpe 139
                                        r++  + Ds    +++f+ +++ + ++ ++  +++ ++ + ++   ++lv+ l v+i  ++  + + k++ +  p+
  gi|330508803|ref|YP_004385231.1| 100 ERFCTSYRDSLAPSANMFFSVIVTLGAAaFIHsQQSWTEHLMKLWFAVWLVISLGVIIALWMRHQALIKNIGNYTPN 176
                                       56666777888899999999999999994444444455555555556777788888999999899999999999996 PP

                           DUF3043 140 tesekg 145
                                       ++++k+
  gi|330508803|ref|YP_004385231.1| 177 DNKNKK 182
                                       665554 PP

>> DUF1211  Protein of unknown function (DUF1211)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.68   4.1e+03      45      49 ..      32      36 ..      13      60 .. 0.60
   2 ?   12.5   2.7   2.5e-05      0.15      10      67 ..     118     174 ..     113     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.68
                                      HHHHH CS
                           DUF1211 45 sFlvv 49
                                      +F++v
  gi|330508803|ref|YP_004385231.1| 32 AFITV 36
                                      33333 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHS---HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                           DUF1211  10 fAIaiTLlvleikvpeeellaallellpsllayllsFlvvasfWlnhhrlfrrikkvd 67 
                                       f++++TL +  + +  ++++++ l +l   ++ ++s  v++ +W+ h+ l+++i +++
  gi|330508803|ref|YP_004385231.1| 118 FSVIVTLGAAAFIHS-QQSWTEHLMKLWFAVWLVISLGVIIALWMRHQALIKNIGNYT 174
                                       899999999977555.45555555555567899******************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1372.05
//
Query:       gi|330508804|ref|YP_004385232.1|  [L=277]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-36  123.2   0.0    1.3e-35  122.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.1e-23   83.7   0.0    3.4e-23   82.1   0.0    1.9  1  Methyltransf_11  Methyltransferase domain
    1.2e-23   83.6   0.0    2.7e-23   82.5   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    8.3e-19   67.8   0.1    1.5e-18   67.0   0.1    1.4  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.6e-12   46.9   0.0    3.4e-12   46.5   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.7e-11   44.8   0.0    3.1e-11   43.9   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    1.1e-10   41.7   0.0    1.7e-10   41.0   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    6.2e-07   29.1   0.0    8.9e-07   28.6   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.4e-06   27.6   0.1    4.7e-06   26.6   0.1    1.6  1  Methyltransf_8   Hypothetical methyltransferase
    2.4e-05   24.1   0.0    4.2e-05   23.3   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020
    2.5e-05   23.9   0.0    5.2e-05   22.9   0.0    1.6  1  MTS              Methyltransferase small domain
    0.00017   21.6   0.0    0.00039   20.5   0.0    1.6  2  Methyltransf_32  Methyltransferase domain
     0.0016   17.8   0.0     0.0021   17.4   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0062   16.0   0.0      0.015   14.8   0.0    1.6  2  Methyltransf_4   Putative methyltransferase
  ------ inclusion threshold ------
      0.019   15.1   0.0      0.051   13.7   0.0    1.7  1  UBA_2            Ubiquitin associated domain (UBA)
      0.025   13.7   0.0      0.041   13.1   0.0    1.2  1  Methyltransf_3   O-methyltransferase
       0.03   14.4   0.0       0.14   12.3   0.0    2.0  2  FtsJ             FtsJ-like methyltransferase
      0.031   13.4   0.0      0.054   12.6   0.0    1.4  1  Fibrillarin      Fibrillarin
      0.056   13.4   0.0      0.093   12.7   0.0    1.3  1  Methyltransf_18  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 !  122.4   0.0   1.4e-38   1.3e-35       3     148 ..      78     219 ..      76     224 .. 0.95

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 1.4e-38
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                       +g  vlD G+G+G+++f + +++gp ++v+G+Di+ e++e+Ar+n++k g+ n+ F+qgd e+++  ++d+ +D+++
  gi|330508804|ref|YP_004385232.1|  78 EGEIVLDMGSGAGFDCFLASDRVGPSGKVIGVDITSEMVEKARANSRKGGYANIDFRQGDLENMP--VADNYVDVVI 152
                                       56779************************************************************..9********* PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedprllaelpakveeeskay.evvegakigtqkdelyell 148
                                       sn+v+n+++++  +++e++rvlkpgg+l+++d+ ll+elp+ v+++ +ay +++ ga+   +kd++ +++
  gi|330508804|ref|YP_004385232.1| 153 SNCVINLIPNKRMAFREAFRVLKPGGRLAVSDVVLLKELPEFVKSSTEAYiGCLAGAI---MKDDYLDII 219
                                       ******************************************************9999...777776665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.0   3.6e-26   3.4e-23       1      96 []      83     182 ..      83     182 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 3.6e-26
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhh 73 
                                       Ld+G+G+G  +    +r+   ++v+gvD++ em++ a++++++ g  +++f+++d+e++p++dn++D+v+s+ v++ 
  gi|330508804|ref|YP_004385232.1|  83 LDMGSGAGFDCFLASDRVgpsGKVIGVDITSEMVEKARANSRKGGYaNIDFRQGDLENMPVADNYVDVVISNCVINL 159
                                       8***********9997777************************999******************************* PP

                                       -CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllvi 96 
                                       +++ + a++e+ RvLkpgG+l++
  gi|330508804|ref|YP_004385232.1| 160 IPNKRMAFREAFRVLKPGGRLAV 182
                                       ********************975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.0   2.8e-26   2.7e-23       1      97 []      82     178 ..      82     178 .. 0.94

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 2.8e-26
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEEST.G CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssga.l 74 
                                       vLd+G G G +++ +++r+g ++kv+gvDi++em+e+ar++ ++ g+ n++f+qgd+e++p +d+ +D+v+s+ + +
  gi|330508804|ref|YP_004385232.1|  82 VLDMGSGAGFDCFLASDRVGpSGKVIGVDITSEMVEKARANSRKGGYaNIDFRQGDLENMPVADNYVDVVISN-CvI 157
                                       9******************669********************998889************************5.659 PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                       ++++  + + a++e++rvLkpgG
  gi|330508804|ref|YP_004385232.1| 158 NLIP--NKRMAFREAFRVLKPGG 178
                                       9998..56799***********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 ?   -3.5   0.0       5.7   5.4e+03      53      70 ..      31      48 ..       9      53 .. 0.65
   2 !   67.0   0.1   1.6e-21   1.5e-18      46     153 ..      77     184 ..      71     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.7
                                      EES-TT-HHHHHHHHHHH CS
                   Ubie_methyltran 53 DvagGtgDlafklsdsvg 70
                                        ++G +D+  +ls+ +g
  gi|330508804|ref|YP_004385232.1| 31 RCCSGDADIPEELSKRMG 48
                                      457788888877777665 PP

  == domain 2  score: 67.0 bits;  conditional E-value: 1.6e-21
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEE CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtv 122
                                        +g+ vlD+ +G+g   f  sd vg +gkv+++Di ++m++ +++  ++ g+ ni+f q++ e++p  d+  Dvv  
  gi|330508804|ref|YP_004385232.1|  77 SEGEIVLDMGSGAGFDCFLASDRVGPSGKVIGVDITSEMVEKARANSRKGGYANIDFRQGDLENMPVADNYVDVVIS 153
                                       68999********************************************************************9977 PP

                                       ES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran 123 sfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                          +  +++k  a++ea+rvlkpGGrl v +
  gi|330508804|ref|YP_004385232.1| 154 NCVINLIPNKRMAFREAFRVLKPGGRLAVSD 184
                                       7778889*******************99865 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   3.6e-15   3.4e-12      20     120 ..      76     185 ..      43     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3.6e-15
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlren.gf..svtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfdlIv 87 
                                       l +g  vLd+G G G  + +++++ g   +v+gvD+ +e+ve+a+      +  +  + q d ++ ++ +++ d+++
  gi|330508804|ref|YP_004385232.1|  76 LSEGEIVLDMGSGAGFDCFLASDRvGPsgKVIGVDITSEMVEKARansrkgGYANIDFRQGDLENMPVADNYVDVVI 152
                                       667889*********88888866646689***************999999944444444555558888999****** PP

                   Methyltransf_23  88 lrevlehvpdppellrqiatllkpgGylllsep 120
                                       ++ v++ +p+  +++r +++ lkpgG+l +s++
  gi|330508804|ref|YP_004385232.1| 153 SNCVINLIPNKRMAFREAFRVLKPGGRLAVSDV 185
                                       ******************************996 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   3.3e-14   3.1e-11       1      99 []      83     180 ..      83     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 3.3e-14
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnv 75 
                                       L+ G+G G   +   ++  p  +++gvDi ++++e+a++  +k +    +n+++++ dl++ +   +++D+v++++v
  gi|330508804|ref|YP_004385232.1|  83 LDMGSGAGFDCFLASDRVgPSGKVIGVDITSEMVEKARANSRKGGY---ANIDFRQGDLENMPVAdNYVDVVISNCV 156
                                       899*****999999999999**************777666666665...455555555544443356********** PP

                   Methyltransf_12  76 lhhlkdirevldnirklLkpgGrl 99 
                                       ++ ++++r +++++ ++LkpgGrl
  gi|330508804|ref|YP_004385232.1| 157 INLIPNKRMAFREAFRVLKPGGRL 180
                                       **********************97 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   1.8e-13   1.7e-10      68     171 ..      73     182 ..      67     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.8e-13
                                       HTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SE. CS
                              PCMT  68 llelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPY. 143
                                       l +l++g+ vL++GsG+G+   + +  vg++g+v++++ + e+ve+a++n +k +++n+ ++ gD ++  + +  Y 
  gi|330508804|ref|YP_004385232.1|  73 LASLSEGEIVLDMGSGAGFDCFLASDRVGPSGKVIGVDITSEMVEKARANSRKGGYANIDFRQGDLENM-PVADNYv 148
                                       45699************************************************************7654.4444451 PP

                                       EEEEESSBBSS--HH......HHHTEEEEEEEEE CS
                              PCMT 144 daihvgaaapeiPea......lidQLkeGGrlvv 171
                                       d+++     + iP++       ++ Lk+GGrl v
  gi|330508804|ref|YP_004385232.1| 149 DVVISNCVINLIPNKrmafreAFRVLKPGGRLAV 182
                                       5555555567788651111114577899998865 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   9.4e-10   8.9e-07     160     262 ..      77     186 ..      72     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9.4e-10
                              PrmA 160 kegeevlDvGtGSGiLa.iaaakLgak.kvvavDiDevAvkvakeNaelNkvea.klevalseellk.eekadviva 232
                                        ege vlD+G G+G    +a+ ++g + kv++vDi +  v+ a++N ++ + ++  ++    e+++  ++ +dv+++
  gi|330508804|ref|YP_004385232.1|  77 SEGEIVLDMGSGAGFDCfLASDRVGPSgKVIGVDITSEMVEKARANSRKGGYANiDFRQGDLENMPVaDNYVDVVIS 153
                                       6789**********96538999***7549********************99999666544445555347899***** PP

                              PrmA 233 NILaevl..iel.aedikklvkeggllilSGil 262
                                       N + + +   ++   ++ +++k+gg+l++S ++
  gi|330508804|ref|YP_004385232.1| 154 NCVINLIpnKRMaFREAFRVLKPGGRLAVSDVV 186
                                       *****9944344257899***********9875 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1     5e-09   4.7e-06     108     159 ..     133     185 ..      77     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5e-09
                                       EEES-TTS-S--TT-EEEEEE.ES---SS-HHHHHHHHHHHEEEEEEEEEEEE CS
                    Methyltransf_8 108 vvacdlakvPledesvdvavf.clslmgtnladflkeanrvlkvGGllkvaev 159
                                           dl ++P++d+ vdv++  c+  +  n +   +ea rvlk+GG l v++v
  gi|330508804|ref|YP_004385232.1| 133 FRQGDLENMPVADNYVDVVISnCVINLIPNKRMAFREAFRVLKPGGRLAVSDV 185
                                       56789**************954999999999*******************998 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   4.4e-08   4.2e-05      77     128 ..     104     154 ..      94     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.4e-08
                                       --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE- CS
                           UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtn 128
                                        k++g+D+ +++v++ar N +k g +  i+f+q d  +++ +++ vdv+++n
  gi|330508804|ref|YP_004385232.1| 104 GKVIGVDITSEMVEKARANSRKGGYA-NIDFRQGDLENMPVADNYVDVVISN 154
                                       5799*****************99986.69***********88889******9 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.5e-08   5.2e-05      32     137 ..      79     182 ..      61     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.5e-08
                                       CSEEEEET-TTSHHHHHHH.HHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTT.STTS-EEEEEE-- CS
                               MTS  32 sgkvlDlGcGaGvlgaala.kespeaevtlvdvdarAlesakenleankle.vevvasdvlee.veekkfdlivsNP 105
                                        + vlD+G+GaG+    +  +  p+ +v  vd+  + +e a++n ++ + + +++++ d+ +  v+++ +d+++sN 
  gi|330508804|ref|YP_004385232.1|  79 GEIVLDMGSGAGFDCFLASdRVGPSGKVIGVDITSEMVEKARANSRKGGYAnIDFRQGDLENMpVADNYVDVVISNC 155
                                       4569********977655515679999*********************9999********8752669999******9 PP

                                       -STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                               MTS 106 PfhagkatelavaeeliaeAkeaLkegGeLli 137
                                        +    +      +  ++eA ++Lk+gG+L +
  gi|330508804|ref|YP_004385232.1| 156 VINLIPN-----KRMAFREAFRVLKPGGRLAV 182
                                       8877666.....34458999999999999975 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.4   4.1e+03      60      94 ..      10      44 ..       8      62 .. 0.65
   2 !   20.5   0.0   4.1e-07   0.00039      26      92 ..      79     141 ..      70     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.4
                   Methyltransf_32 60 keelvekaekraeklgkkfnkrlsfaelsieeats 94
                                      k+++ e   ++a++  +++++r+   +++i e+ s
  gi|330508804|ref|YP_004385232.1| 10 KRAVKEGYARIAKQATSDYASRCCSGDADIPEELS 44
                                      55566666777777777787777777777766654 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 4.1e-07
                   Methyltransf_32  26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieea 92 
                                        + v+D+G+G g+  f  ++ ++  + kv+g+d+ +e+veka++  +k g  + +++ f +++ e+ 
  gi|330508804|ref|YP_004385232.1|  79 GEIVLDMGSGAGFDCFLASD-RVGPSGKVIGVDITSEMVEKARANSRKGG--Y-ANIDFRQGDLENM 141
                                       56799********9999998.77799**********************99..8.9999999988766 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.3e-06    0.0021      58     172 ..      74     190 ..      70     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-06
                                       TT--TT-EEEEES-TTSHHHHHHHHHH-..-EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--S CS
                              CMAS  58 lelkpGmtlLdiGcGWGslvrraveryd..vkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvd 129
                                       ++l +G+ +Ld+G G G  +  a +r +   kv+g+ + +e  ++a+++  + + + + + +  d e+++     vd
  gi|330508804|ref|YP_004385232.1|  74 ASLSEGEIVLDMGSGAGFDCFLASDRVGpsGKVIGVDITSEMVEKARANSRKGGYA-NIDFRQGDLENMPVadnYVD 149
                                       5799********************99873358***************999998865.4566666666664333499* PP

                                       EEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--H CS
                              CMAS 130 rvvsvgafehvgkenydtffkklkkllkedGllllhtitslhk 172
                                        v+s  +++ + +++ +  f++++++lk++G+l++  ++ l++
  gi|330508804|ref|YP_004385232.1| 150 VVISNCVINLIPNKRMA--FREAFRVLKPGGRLAVSDVVLLKE 190
                                       ***********999876..999***********9988776655 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.6e-05     0.015       3      60 ..      80     138 ..      78     153 .. 0.86
   2 ?   -3.1   0.0         5   4.8e+03     102     117 ..     169     183 ..     164     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                                       EEEEEET-TTS.HHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                    Methyltransf_4   3 pvvleiGcGkG.eflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                                        +vl++G+G G +  +a     P+ +++G++i +++v+k+ ++ ++ ++ N+   +gd 
  gi|330508804|ref|YP_004385232.1|  80 EIVLDMGSGAGfDCFLASDRVGPSGKVIGVDITSEMVEKARANSRKGGYANIDFRQGDL 138
                                       6899******955667777778******************************9999984 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5
                                       HHHHHEEEEEEEEEEE CS
                    Methyltransf_4 102 elarvLkkgGvlelaT 117
                                       e+ rvLk+gG l + +
  gi|330508804|ref|YP_004385232.1| 169 EAFRVLKPGGRLAV-S 183
                                       56789999999864.4 PP

>> UBA_2  Ubiquitin associated domain (UBA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.4e-05     0.051       4      22 ..      38      56 ..      36      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-05
                             UBA_2  4 dvvsaLsktMGYdkdeIie 22
                                      d+ ++Lsk+MGY  +eI+ 
  gi|330508804|ref|YP_004385232.1| 38 DIPEELSKRMGYTEEEIQA 56
                                      66689************85 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.3e-05     0.041      42     108 ..      73     138 ..      69     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-05
                                       HHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-H CS
                    Methyltransf_3  42 LvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegda 108
                                       L +l++   vl++G   G+  +  +  + + Gk++ +di  e +e a+   +k g+a  i++++gd 
  gi|330508804|ref|YP_004385232.1|  73 LASLSEGEIVLDMGSGAGFDCFLASDRVGPSGKVIGVDITSEMVEKARANSRKGGYA-NIDFRQGDL 138
                                       5678888899*******************************************9998.5*****984 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.6   2.5e+03      79     114 ..       9      48 ..       4      60 .. 0.70
   2 ?   12.3   0.0   0.00014      0.14      20      93 ..      77     153 ..      69     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.6
                                       HCHCHHH...SSEEEEEE--S.-SS-CHHHHHHHHHCCCC CS
                              FtsJ  79 ikealse...rkvdlvvsDga.pdvsgvhdldeylqsqLl 114
                                       ik+a++e   r ++  +sD a  ++sg  d++e l+ ++ 
  gi|330508804|ref|YP_004385232.1|   9 IKRAVKEgyaRIAKQATSDYAsRCCSGDADIPEELSKRMG 48 
                                       5555555455667888999884577999999998887665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00014
                                       -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEES.SSS.......HHH....TTEEEECS-CCCSSHHHHHCHCHH CS
                              FtsJ  20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDl.qpm.......apl....pgvttiqgditdpetiekikeals 84 
                                       ++g+ v+D g++ G  +  ++ r+g++gkv++vD+  +m       + +     ++ + qgd  ++ ++++      
  gi|330508804|ref|YP_004385232.1|  77 SEGEIVLDMGSGAGFDCFLASDRVGPSGKVIGVDItSEMvekaranS-RkggyANIDFRQGDLENMPVADNY----- 147
                                       578889*******999999****************778888765431.233445777779998888777743..... PP

                                       HSSEEEEEE CS
                              FtsJ  85 erkvdlvvs 93 
                                          vd+v+s
  gi|330508804|ref|YP_004385232.1| 148 ---VDVVIS 153
                                       ...444444 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.8e-05     0.054      49     108 ..      57     116 ..      18     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.8e-05
                                       -TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHH CS
                       Fibrillarin  49 npfrsKlaaailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvl 108
                                        p  s l+ +  + ++   +++g+ vL +G+++G      sD vg++g+v +v+ ++ ++
  gi|330508804|ref|YP_004385232.1|  57 APPESNLGLGCGNPVALASLSEGEIVLDMGSGAGFDCFLASDRVGPSGKVIGVDITSEMV 116
                                       466789999999999999************************************987765 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.8e-05     0.093      12      87 ..      76     152 ..      71     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.8e-05
                   Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvke..gkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdt 85 
                                       +++g++v+D G+  g+ +++l++   g   kvi +Di ++ +eka++n +k g+  +i++r +d  +   +++ vd+
  gi|330508804|ref|YP_004385232.1|  76 LSEGEIVLDMGSGAGF-DCFLASDrvGPSGKVIGVDITSEMVEKARANSRKGGY-ANIDFRQGDLENMPVADNyVDV 150
                                       56799999***99886.66666541266889*******************9988.67****9994444335554665 PP

                   Methyltransf_18  86 vv 87 
                                       v+
  gi|330508804|ref|YP_004385232.1| 151 VI 152
                                       54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1958.21
//
Query:       gi|330508805|ref|YP_004385233.1|  [L=171]
Description: appr-1-p processing enzyme family [Methanosaeta concilii GP6]
Scores for complete 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-44  149.9   0.0    3.9e-44  149.5   0.0    1.2  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 !  149.5   0.0   2.2e-48   3.9e-44       1     118 []      23     135 ..      23     135 .. 0.99

  Alignments for each domain:
  == domain 1  score: 149.5 bits;  conditional E-value: 2.2e-48
                                       EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHH CS
                             Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvgplftsskskeeeel 77 
                                       VnAaNs+llggggv+gaih+aag++l+ ec+++    ggc++Gea +t++y+lpa++vihtvgp+++ ++s++e++l
  gi|330508805|ref|YP_004385233.1|  23 VNAANSSLLGGGGVDGAIHKAAGPELLGECRQI----GGCPVGEARITRGYRLPARFVIHTVGPVWR-GGSEGEDQL 94 
                                       9********************************....99***************************8.8******** PP

                                       HHHHHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHHH CS
                             Macro  78 lakayknalelaeekgiksvafPaistGifgvpweeaarva 118
                                       la++y+++ +lae+ +iks+afPaistG +g+p e+a r+a
  gi|330508805|ref|YP_004385233.1|  95 LARCYQSCFALAEKYEIKSIAFPAISTGAYGFPIERACRIA 135
                                       *************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1247.77
//
Query:       gi|330508806|ref|YP_004385234.1|  [L=1026]
Description: two-component hybrid sensor and regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-31  108.6   0.0    4.5e-31  107.6   0.0    1.5  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    1.3e-26   92.9   0.1    2.8e-26   91.9   0.1    1.6  1  Response_reg     Response regulator receiver domain
      2e-20   73.1   0.0    7.6e-10   39.0   0.0    3.4  3  PAS_4            PAS fold
    1.2e-19   70.1   1.6    1.2e-18   66.9   0.3    2.7  2  HisKA            His Kinase A (phospho-acceptor) domain
    2.3e-17   63.1   0.0    4.1e-07   30.2   0.0    3.7  3  PAS_9            PAS domain
    3.4e-10   39.9   0.0    4.3e-07   29.9   0.0    2.9  2  PAS              PAS fold
      1e-05   25.4   0.0    0.00033   20.6   0.0    2.6  2  PAS_8            PAS domain
    0.00026   21.2   0.0        1.1    9.6   0.0    3.6  3  PAS_3            PAS fold
     0.0004   20.9   0.0        1.1    9.9   0.0    3.7  4  PAS_10           PAS domain
      0.001   18.4   0.0     0.0023   17.2   0.0    1.5  1  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
     0.0024   17.7   0.2        1.1    9.0   0.1    2.4  2  dCache_1         Cache domain
     0.0046   16.8   0.0      0.012   15.4   0.0    1.6  1  HATPase_c_3      Histidine kinase-, DNA gyrase B-, and HSP90-
  ------ inclusion threshold ------
      0.072   11.7   0.7       0.11   11.1   0.7    1.2  1  Strabismus       Strabismus protein
       0.36   10.9   1.3          3    7.9   0.0    2.7  3  DUF3801          Protein of unknown function (DUF3801)
        1.3    8.3   3.7         13    5.0   0.2    2.2  2  FmiP_Thoc5       Fms-interacting protein/Thoc5


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 !  107.6   0.0   3.8e-34   4.5e-31       1     110 [.     759     873 ..     759     875 .. 0.94

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 3.8e-34
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE.....TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTS CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikase.....ddlvisveDnGiGipkedlkklfekfsq.ddstkrgg 71 
                                       gd++rL qi++nl+ Navkf t++gei v+++ ++      ++++ v+D+GiGip++++ +lf +fsq d+st+r++
  gi|330508806|ref|YP_004385234.1| 759 GDPTRLCQILINLLNNAVKF-TEQGEIAVSVSNTNlddggYEIHFAVKDTGIGIPEDKMSRLFRSFSQvDASTARKY 834
                                       799*****************.***********7325557899999******************************** PP

                                       TSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  72 ggtGlGlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       ggtGlGl+i+kkl+e+m+G++wves  g G+ f+ft++ 
  gi|330508806|ref|YP_004385234.1| 835 GGTGLGLAISKKLTEMMNGRMWVESAVGVGSVFHFTIRA 873
                                       ***********************************9875 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   0.1   2.3e-29   2.8e-26       1     111 [.     909    1020 ..     909    1021 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 2.3e-29
                                        EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTT..SE CS
                      Response_reg    1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpe..lp 73  
                                        +l+++D+ +++ +++++l + gy + ++a++g eal+ l+++++dli++D++mp+mdGle+++eir++ pe  ++
  gi|330508806|ref|YP_004385234.1|  909 ILLAEDNVVNQIVTKKMLSKLGY-NADVASSGIEALKALEKKRYDLIFMDVQMPEMDGLEAAREIRRRWPEggPK 982 
                                        89*********************.*****************************************999955559* PP

                                        EEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg   74 viiltahseeedavealkagaddflsKpfdpeeLlkal 111 
                                        +i++ta + + d + +l ag+d++++Kp ++e++++al
  gi|330508806|ref|YP_004385234.1|  983 IIAVTASAFKGDQEMCLAAGMDGYIMKPTKIEAIREAL 1020
                                        ***********************************997 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   6.3e-13   7.6e-10       7     109 ..     380     479 ..     378     480 .. 0.94
   2 !   20.9   0.0   2.7e-07   0.00033       4      49 ..     499     544 ..     496     558 .. 0.89
   3 !    9.1   0.0    0.0013       1.5      74     110 .]     589     626 ..     573     626 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 6.3e-13
                             PAS_4   7 alavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyel 83 
                                       a+ +ldp +r +++N + +e +g++++e+lG +++e +  ++ +   + ++r++  ++++e   ++ +   +r++  
  gi|330508806|ref|YP_004385234.1| 380 AVEYLDPFMRLIWINDNLQESIGLSADEMLGARCYEAVFGRSEPCSGCTVARAINMGASQEGDLITPD---GRTWIS 453
                                       56689*******************************99999****************99999996666...****** PP

                             PAS_4  84 rllPlrdesGevigvlvisrDiTerr 109
                                       r +Pl+d++G++igv+ +++Di++r+
  gi|330508806|ref|YP_004385234.1| 454 RSSPLKDADGKIIGVVHVLIDISARK 479
                                       ***********************997 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.7e-07
                             PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeeda 49 
                                       lpda++v+d++g+v+ +N+a++++ g+ +e +lGk ++e+  +  +
  gi|330508806|ref|YP_004385234.1| 499 LPDATFVVDKNGKVISWNRAIEKITGVKAELILGKGDYEYSLPFYG 544
                                       8*************************************98766544 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0013
                             PAS_4  74 l.pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       l ++++ +++ +++ l d++G+  g+++ +rDiT+r+r
  gi|330508806|ref|YP_004385234.1| 589 LqGKGDAYLLGSASALYDSNGDYWGAIESIRDITDRKR 626
                                       3577788888899***********************97 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.29   3.5e+02      20      56 ..     465     497 ..     464     501 .. 0.70
   2 !   66.9   0.3     1e-21   1.2e-18       1      66 [.     644     711 ..     644     712 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.29
                                       HHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHH CS
                             HisKA  20 ilgnaeaLkregklteelkeyletiesearrldhlve 56 
                                       i+g +++L +        k + + +++++rrl +++e
  gi|330508806|ref|YP_004385234.1| 465 IIGVVHVLIDI----SARKSAERALKESERRLADIIE 497
                                       78889999882....3444455566667779999997 PP

  == domain 2  score: 66.9 bits;  conditional E-value: 1e-21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       ++++fla+++HE+rtP++a++g +e+L++e  +klt  ++e +e i+ +++ l+++++++Ldl++iea
  gi|330508806|ref|YP_004385234.1| 644 AKSEFLANMSHEIRTPMNAVIGLTELLMDEkdEKLTSAQRECVEMIRISGDTLLSIINNILDLTKIEA 711
                                       589************************999999*********************************98 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0     2e-09   2.4e-06      11     103 ..     388     476 ..     378     477 .. 0.92
   2 !   30.2   0.0   3.5e-10   4.1e-07       1     104 []     500     623 ..     500     623 .. 0.69
   3 ?   -0.0   0.0      0.89   1.1e+03      19      89 ..     924     995 ..     909    1002 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2e-09
                             PAS_9  11 grilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspv 85 
                                        r++++N+ + + +G s++e+lg ++ + +   ++p + +++++a+++g     ++e +li+++g+t     + sp+
  gi|330508806|ref|YP_004385234.1| 388 MRLIWINDNLQESIGLSADEMLGARCYEAVfgRSEPCSGCTVARAINMGA----SQEGDLITPDGRTWI--SRSSPL 458
                                       5789**********************************************....999999****97777..8889** PP

                             PAS_9  86 kdddgelvgiivilrDit 103
                                       kd+dg+++g++ +l+Di+
  gi|330508806|ref|YP_004385234.1| 459 KDADGKIIGVVHVLIDIS 476
                                       *****************9 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 3.5e-10
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlf.................vtdpeanerlraaleqgrk. 59 
                                       pd++++++++g+++++N+a ++++G ++e +lgk   +                                    +  
  gi|330508806|ref|YP_004385234.1| 500 PDATFVVDKNGKVISWNRAIEKITGVKAELILGKGDYEYSlpfygerrptlidmakgI----------------DPk 560
                                       68999999**************************955555445655555555666653................333 PP

                             PAS_9  60 ..kerevevvlirkngetfw................vlltaspvkdddgelvgiivilrDite 104
                                         +e+e+ +++ ++++e  +                 l +as+++d++g ++g+i  +rDit+
  gi|330508806|ref|YP_004385234.1| 561 idPEFEKKYENLKRDEENNLlvgeaymplqgkgdayLLGSASALYDSNGDYWGAIESIRDITD 623
                                       44444444444444443333444444444444444377************************6 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.89
                             PAS_9  19 aalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkddd 89 
                                       ++l  lGy+ ++v    i+ l   +++ ++  +++ ++ +++  e ++e+  + ++g++  + +tas++k d+
  gi|330508806|ref|YP_004385234.1| 924 KMLSKLGYN-ADVASSGIEALKalEKKRYDLIFMDVQMPEMDGLEAAREIRRRWPEGGPKIIAVTASAFKGDQ 995
                                       566666666.334555555555556666777788888889988999999999999**9999999999997653 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0057       6.8      17     113 .]     384     475 ..     378     475 .. 0.84
   2 !   29.9   0.0   3.6e-10   4.3e-07       2      44 ..     491     533 ..     490     538 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0057
                                       EETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEE CS
                               PAS  17 vDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevra 93 
                                       +D   r +++N++ +e  Gls++e+lg   ++ ++  +    +    +++++ +++ ++e ++ ++dgr   +  r 
  gi|330508806|ref|YP_004385234.1| 384 LDPFMRLIWINDNLQESIGLSADEMLGARCYEAVFGRS---EPCSGCTVARAINMGASQEGDLITPDGR--TWISRS 455
                                       5666778899*************************986...7777778888888888888888886765..477899 PP

                                       EEEEETTEEEEEEEEEEEES CS
                               PAS  94 spvrdaggeilgflgvlrdi 113
                                       sp+ da+g+i+g++ vl di
  gi|330508806|ref|YP_004385234.1| 456 SPLKDADGKIIGVVHVLIDI 475
                                       **************999997 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 3.6e-10
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTS CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgk 44 
                                       +l  i+e lpd++fvvD++g+++ +N+a+e+++G ++e +lgk
  gi|330508806|ref|YP_004385234.1| 491 RLADIIEFLPDATFVVDKNGKVISWNRAIEKITGVKAELILGK 533
                                       56779999*****************************999987 PP

>> PAS_8  PAS domain
   #    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      20      48 ..     385     416 ..     376     432 .. 0.78
   2 !   20.6   0.0   2.7e-07   0.00033       2      46 ..     491     531 ..     490     556 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.25
                             PAS_8  20 gd..rivdvNqaalellGys.adlkgellgql 48 
                                       +   r++++N+  +e  G+s ++++g+ + + 
  gi|330508806|ref|YP_004385234.1| 385 DPfmRLIWINDNLQESIGLSaDEMLGARCYEA 416
                                       34569***************999999988654 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 2.7e-07
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGysadlkgellg 46 
                                       rl  ++e +pd+ +vvd +g+ ++ +N+a ++++G    +k+el+ 
  gi|330508806|ref|YP_004385234.1| 491 RLADIIEFLPDATFVVDkNGK-VISWNRAIEKITG----VKAELIL 531
                                       88999************7777.*************....6666653 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00094       1.1       2      87 ..     391     470 ..     390     472 .. 0.92
   2 ?    5.8   0.0     0.014        17       2      22 ..     513     533 ..     512     575 .. 0.88
   3 ?    1.2   0.0      0.39   4.7e+02      53      79 ..     969     995 ..     953    1001 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00094
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       i ++++ +e +G+s++e+lg   +++++v     +    ++++a++ g+  ++e  ++++dG + w+ +r ++++d 
  gi|330508806|ref|YP_004385234.1| 391 IWINDNLQESIGLSADEMLGA--RCYEAVFGRSEPCSGCTVARAINMGA--SQEGDLITPDGRT-WI-SRSSPLKDA 461
                                       6799*****************..**************************..9**********98.65.5669***** PP

                             PAS_3  79 ngkpvrvig 87 
                                       +gk++ v+ 
  gi|330508806|ref|YP_004385234.1| 462 DGKIIGVVH 470
                                       ***999875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.014
                             PAS_3   2 iyvserveeilGyspeellgk 22 
                                       i++++++e+i+G+ +e +lgk
  gi|330508806|ref|YP_004385234.1| 513 ISWNRAIEKITGVKAELILGK 533
                                       89***************9999 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.39
                             PAS_3  53 egeyRirrkdGeyrwveararvirden 79 
                                         e+R+r++ G+   +  +a++++ ++
  gi|330508806|ref|YP_004385234.1| 969 AREIRRRWPEGGPKIIAVTASAFKGDQ 995
                                       679******************996554 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00093       1.1      71     105 ..     442     475 ..     378     476 .. 0.83
   2 ?   -1.1   0.0       2.5     3e+03      11      32 ..     502     523 ..     495     529 .. 0.82
   3 ?    6.2   0.0     0.013        15      73     106 .]     586     622 ..     553     622 .. 0.70
   4 ?   -2.5   0.0       6.3   7.6e+03      38      68 ..     876     906 ..     870     924 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00093
                            PAS_10  71 evvvpkngkwvlvrylpyrdedgeiaGvvetfvDi 105
                                       +  ++ +g++ + r +p++d dg+i Gvv +++Di
  gi|330508806|ref|YP_004385234.1| 442 D-LITPDGRTWISRSSPLKDADGKIIGVVHVLIDI 475
                                       4.3467999999**********************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.5
                            PAS_10  11 eltflDdnlqirrFtpaakklf 32 
                                       ++  +D+n +++ +++a++k+ 
  gi|330508806|ref|YP_004385234.1| 502 ATFVVDKNGKVISWNRAIEKIT 523
                                       57789***********999886 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.013
                            PAS_10  73 vvp...kngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                       ++p   k + + l   ++++d +g++ G++e + Dit
  gi|330508806|ref|YP_004385234.1| 586 YMPlqgKGDAYLLGSASALYDSNGDYWGAIESIRDIT 622
                                       34344566677788999*******************7 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 6.3
                            PAS_10  38 dvGrpladihpkkavknveeviealrtgekd 68 
                                        +G+pl+  +p++ + + ++ i++l +++++
  gi|330508806|ref|YP_004385234.1| 876 IIGEPLDLSKPDNLYAHGKQKIKDLERSNSE 906
                                       6899999999999999999999999988776 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 !   17.2   0.0   1.9e-06    0.0023     131     190 ..     428     487 ..     409     490 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.9e-06
                   Cache_3-Cache_2 131 pvykavlagetYvGra.kvfgkwYvTaYePikdadgkViGilyVgvdqsealkslrkelkk 190
                                       +v+ a++ g +  G   +  g+  +++ +P+kdadgk+iG++ V +d+ +a ks +++lk+
  gi|330508806|ref|YP_004385234.1| 428 TVARAINMGASQEGDLiTPDGRTWISRSSPLKDADGKIIGVVHVLIDI-SARKSAERALKE 487
                                       67777777777777651457899*************************.999999988875 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0054       6.4     131     161 ..     447     476 ..     431     477 .. 0.86
   2 !    9.0   0.1   0.00093       1.1      57     153 ..     478     614 ..     476     616 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0054
                          dCache_1 131 tggkpvitiavpiyddsgkfiGvlaadldld 161
                                       + g++ i+ ++p+ d++gk+iGv+ + +d++
  gi|330508806|ref|YP_004385234.1| 447 D-GRTWISRSSPLKDADGKIIGVVHVLIDIS 476
                                       5.8899999***************9999987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00093
                          dCache_1  57 reslqallksilksnpdi.....sgvylvdadGqviassdpssppnleg............................ 100
                                       r+s++++lk+  ++ +di     ++ ++vd++G+vi+ ++++ ++ + +                            
  gi|330508806|ref|YP_004385234.1| 478 RKSAERALKESERRLADIieflpDATFVVDKNGKVIS-WNRAIEKITGVkaelilgkgdyeyslpfygerrptlidm 553
                                       67777888886666666655557899*********96.88888855555********99999999999999999999 PP

                          dCache_1 101 ......tddpadrdwykealaggggkpvisdpyvdqt..ggkpvitiavpiyddsgkfiGv 153
                                             + dp  +  y + + ++++  +++++y++    g+ + +  a+++yd +g ++G+
  gi|330508806|ref|YP_004385234.1| 554 akgidpKIDPEFEKKYENLKRDEENNLLVGEAYMPLQgkGDAYLLGSASALYDSNGDYWGA 614
                                       99766655554444588888888899999****766665567999********99*99997 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 !   15.4   0.0     1e-05     0.012       7      81 ..     768     843 ..     763     872 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                       HATPase_c_3   7 laelvdNsld.Adaenvkievnknrgkt....geivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGlk 78 
                                       l+ l++N++   +  ++ ++v++ + ++      + ++D G G++e+++ + +r  ++     ++++++G  G+G  
  gi|330508806|ref|YP_004385234.1| 768 LINLLNNAVKfTEQGEIAVSVSNTNLDDggyeIHFAVKDTGIGIPEDKMSRLFRSFSQVDA--STARKYGGTGLG-- 840
                                       6778889998777788999988766444333378899**************9985555555..389*********.. PP

                       HATPase_c_3  79 lAs 81 
                                       lA+
  gi|330508806|ref|YP_004385234.1| 841 LAI 843
                                       444 PP

>> Strabismus  Strabismus protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7   9.4e-05      0.11     171     222 ..     156     208 ..     132     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.4e-05
                        Strabismus 171 lvllltlsYWlFygvrvlekk.ekdyksivqyavslvdalLFihylavvLlel 222
                                       +++  +l++W+F++  v+ +  + + +  ++ a s++d++LF+  + +vL +l
  gi|330508806|ref|YP_004385234.1| 156 VIISAALVFWIFFFAPVVSSLnTITLELTISLAYSMMDIVLFVALVRLVLSKL 208
                                       33445789*******999886367888899****************9999765 PP

>> DUF3801  Protein of unknown function (DUF3801)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       6.3   7.5e+03     150     170 ..     622     642 ..     605     664 .. 0.67
   2 ?    7.9   0.0    0.0025         3      63      97 ..     790     831 ..     784     835 .. 0.87
   3 ?    0.2   0.0      0.58   6.9e+02      14      36 ..     887     909 ..     880     917 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.3
                           DUF3801 150 ekkpsvrkklekfkervkekk 170
                                       ++++ v ++l++ ke ++ ++
  gi|330508806|ref|YP_004385234.1| 622 TDRKRVEEELQRSKEMAESAT 642
                                       445555555555555554443 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0025
                           DUF3801  63 dkn.dkgqteiifraedad......ainrafqrmklvdkadv 97 
                                       + n d+g +ei+f+ +d+       ++ r f+ ++ vd  ++
  gi|330508806|ref|YP_004385234.1| 790 NTNlDDGGYEIHFAVKDTGigipedKMSRLFRSFSQVDASTA 831
                                       56789*************9999999***********887665 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.58
                           DUF3801  14 dkkktkGktslkkLlkkggdlkv 36 
                                       d+   +Gk+++k+L +++ +l+ 
  gi|330508806|ref|YP_004385234.1| 887 DNLYAHGKQKIKDLERSNSELNI 909
                                       556689************99975 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.011        13      88     126 ..     339     377 ..     330     391 .. 0.80
   2 ?    4.0   0.4     0.022        26     112     154 ..     629     671 ..     620     686 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.011
                        FmiP_Thoc5  88 dehelmlaRLewEleqRkelaeqlkeleekkkkleqeie 126
                                       de ++ l     E+e+Rk++++ l+e e++k +++   +
  gi|330508806|ref|YP_004385234.1| 339 DERNQLLTTTLTEIEERKRVEKSLRESEQEKAAILGGLK 377
                                       556666666678********************9987555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.022
                        FmiP_Thoc5 112 keleekkkkleqeieekkkfLssLppkLkslkkatkplqealg 154
                                       +el+++k+ +e++++ k +fL +++ ++++ ++a+  l e l 
  gi|330508806|ref|YP_004385234.1| 629 EELQRSKEMAESATRAKSEFLANMSHEIRTPMNAVIGLTELLM 671
                                       57899*************************9999999999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1026 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1145  (0.063863); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.84u 0.31s 00:00:01.14 Elapsed: 00:00:00.43
# Mc/sec: 7097.21
//
Query:       gi|330508807|ref|YP_004385235.1|  [L=430]
Description: aspartate aminotransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-46  156.9   0.0    9.7e-46  156.6   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.6   0.0   5.4e-50   9.7e-46       4     347 ..      39     383 ..      36     386 .. 0.88

  Alignments for each domain:
  == domain 1  score: 156.6 bits;  conditional E-value: 5.4e-50
                                       EESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHH CS
                     Aminotran_1_2   4 inLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagal 80 
                                        n+g ++ ++     ++  v++a +     +   + y+p +gl +l+ea+a f++++  ++ + +  v+vg+G+++l
  gi|330508807|ref|YP_004385235.1|  39 YNFGLGQSPFP----VPAPVVEALRL----HAHEKDYLPVKGLSALKEAVAGFHRQKDLVEANSD-CVLVGPGSKEL 106
                                       56677777776....66666666654....566789*******************8888888888.*********** PP

                                       HHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTE.TEEEEEEES CS
                     Aminotran_1_2  81 iealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnk.ktkvilves 156
                                         +l  ++      ei+vp+p + sy + +++ g ++   +++ e+++h+ ++ l + l+   e++  ++++++++ 
  gi|330508807|ref|YP_004385235.1| 107 MFLLQLVFY----GEIIVPTPCWVSYVPQAQILGKKISLLHTSFEDKWHISADRLRQHLEG--EQDLyRPRILVLNY 177
                                       ******995....48*********************************************8..455568******** PP

                                       S-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT..EEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 157 phNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn..llivgslsKafGlaGeRvG 231
                                       p NP+G  +t +el++++++a++y+++l++De+Y+ +  +       ++ v+++    ++i ++lsK  G+ G+R+G
  gi|330508807|ref|YP_004385235.1| 178 PGNPDGLTYTADELKEIARVAREYEIILLSDEIYGQLHHKGG-----HVSVARYYPegTIISSGLSKWCGAGGWRLG 249
                                       ***************************************954.....8899998888******************** PP

                                       EEEEEH...HHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS CS
                     Aminotran_1_2 232 yilgna...avvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq 303
                                        ++  +   ++ + ++ +++  +   s++ q+a ++a + +  ++++l ++r+ l  + ++++ +La++g+ v a++
  gi|330508807|ref|YP_004385235.1| 250 TFTFPQsldWLMESMAAVASETYTsvSAPIQYAGVQAFRGSMAIERYLWNARRILSVLGQRCYRNLADAGVRVHAPE 326
                                       ****776999999999999988888*******************99******************************* PP

                                       CSSEEEEEETHH..........CHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEE CS
                     Aminotran_1_2 304 sgmflltdlsae..........takelskkLleevgvyvtpgtsftv...pgrlRit 347
                                       ++++++ d+s+           + + l++ Ll+e+gv+++pg+ f+    +   Ri+
  gi|330508807|ref|YP_004385235.1| 327 GAFYMFPDFSPFsrrlakknvlNSTMLCERLLQEKGVAMLPGRAFERpheELTARIS 383
                                       ************555555555555555555**************9986644455665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2877.19
//
Query:       gi|330508808|ref|YP_004385236.1|  [L=582]
Description: KamA family protein [Methanosaeta concilii GP6]
Scores for 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   29.4   0.0    2.5e-06   28.0   0.0    1.8  1  Radical_SAM  Radical SAM superfamily
     0.0037   17.4   0.0     0.0085   16.2   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   2.8e-10   2.5e-06       2      95 ..     290     390 ..     289     440 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.8e-10
                                       EEESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTT..HHHHHHHHHHTC. CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx. RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypd..fvellerlakla. 74 
                                        +++ C++ C++C+r++  +++   ++  ++e+i++ +++++++     v+l+gg+pl+ +d  + ++l rl+++  
  gi|330508808|ref|YP_004385236.1| 290 KPYESCPQICVYCQRNWEiSSPLMASALAPMEKIEAAIDWFYEHEEMMDVLLTGGDPLVMDDslIDRILNRLSQIPh 366
                                       57789************************************84444*************976223344444444449 PP

                                       CCTEEEEEEECSSCHG...HHHHH CS
                                       xxxxxxxxxxxxxxxx...xxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpd...eekle 95 
                                        + ir++  t++t+p    ee  e
  gi|330508808|ref|YP_004385236.1| 367 LKSIRVASRTPATVPQrltEELCE 390
                                       999999999999999555444444 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.5e-07    0.0085       7      87 ..     294     374 ..     290     392 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.5e-07
                           Fer4_14   7 gCnlsCkgCdnketwks..elgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                       +C+  C+ C ++ + +s   +      e +e+ ++ ++++e  ++ + ltGG+PL  ++++ ++++++rl +  + k
  gi|330508808|ref|YP_004385236.1| 294 SCPQICVYCQRNWEISSplMASALAPMEKIEAAIDWFYEHEEMMD-VLLTGGDPL-VMDDSLIDRILNRLSQIPHLK 368
                                       79999****977777764445556666777788877777777666.*********.558999999999998877666 PP

                           Fer4_14  82 kiwlet 87 
                                       +i++ +
  gi|330508808|ref|YP_004385236.1| 369 SIRVAS 374
                                       666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.23s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 4509.29
//
Query:       gi|330508809|ref|YP_004385237.1|  [L=334]
Description: small conductance mechanosensitive ion channel (MscS) family transporter [Methanosaeta concilii GP6]
Scores for complete 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-24   85.9   8.1    2.7e-24   85.9   8.1    2.2  2  MS_channel  Mechanosensitive ion channel
    4.3e-05   22.9   0.5    0.00076   18.8   0.0    2.0  2  DUF2515     Protein of unknown function (DUF2515)
  ------ inclusion threshold ------
      0.048   13.0  16.9      0.072   12.4  16.9    1.2  1  AgrB        Accessory gene regulator B


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 ?   -3.6   2.3       1.1   6.6e+03      18      31 ..      28      41 ..      12      52 .. 0.54
   2 !   85.9   8.1   4.5e-28   2.7e-24       5     205 ..      72     295 ..      69     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.1
                                      HTTT--SCCHHHHH CS
                        MS_channel 18 sllgvnvsallavl 31
                                      s+++  + +++a+l
  gi|330508809|ref|YP_004385237.1| 28 SYINRTIITIIAIL 41
                                      55444444444443 PP

  == domain 2  score: 85.9 bits;  conditional E-value: 4.5e-28
                                       HHHHHHHHHHHHHHTTT--.SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE- CS
                        MS_channel   5 kiliivvgilivlsllgvn.vsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedig 80 
                                       ++ i++++  i+++ ++v+ + +ll ++G++++a ++  +d+ +nlv+G++++f+  +k+GD++e+++ +G V+di+
  gi|330508809|ref|YP_004385237.1|  72 LYSIYLLINFIIIWIIWVEdIRTLLLGFGLVAAAFTISIQDVAKNLVGGLVIMFNSIYKVGDRIEVAGKKGDVIDIN 148
                                       46778888888888888888********************************************************* PP

                                       SSEEEE.........EETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-T CS
                        MS_channel  81 lrttki.........rtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekp 148
                                       l+ t+i          +++gr+   Pn  ++++++ N+++    ++++++  + y+sd  ++e   + +++++ ++ 
  gi|330508809|ref|YP_004385237.1| 149 LLHTTImemsewvssDQHTGRLSSLPNFLVLSNAVNNYTKDFSFVWDEITLPISYDSDWRAAE---SLIMDIVIQET 222
                                       *****933333333335689**************************************55555...55555555555 PP

                                       TB-T..................TS-EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHH.HHHT-- CS
                        MS_channel 149 evlk..................dkellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkil.eeegie 205
                                       ++ k                  + + + ++ +++d+ ++++ r++++    +++  ++++i +ri +++ ++egi+
  gi|330508809|ref|YP_004385237.1| 223 HMMKeyaeeeishmqrkyyilkSSTDPGIFFKLTDNWIELTARYVAPA---RQRRILRTKISRRILEEIqRSEGIR 295
                                       554445556999999999999988888999999999999999999999...8888999999999765551445665 PP

>> DUF2515  Protein of unknown function (DUF2515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.014        81     168     210 ..      35      76 ..      18      90 .. 0.76
   2 !   18.8   0.0   1.3e-07   0.00076     182     306 ..     114     242 ..     102     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.014
                           DUF2515 168 lqlnavlfPtkekkkgklvGlsvkefesveeRielgkkLaalL 210
                                       +++ a+l+ +    ++ l  +++k+f+s+++R  + k L+++ 
  gi|330508809|ref|YP_004385237.1|  35 ITIIAILMIYIV-FRVLLEDRIIKNFTSTDKRYYFSKMLYSIY 76 
                                       555555555555.5566777899*****************985 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.3e-07
                           DUF2515 182 kgklvGlsvkefe...sveeRiel.gkk..LaalLfkpklkekilefakevehtgSRadyekhlfslkkeakklysp 252
                                        ++lvG  v  f+   +v +Rie+ gkk  + ++    ++  ++ e++++ +htg  +   ++l    ++a ++y++
  gi|330508809|ref|YP_004385237.1| 114 AKNLVGGLVIMFNsiyKVGDRIEVaGKKgdVIDINLLHTTIMEMSEWVSSDQHTGRLSSLPNFLVL--SNAVNNYTK 188
                                       56788888888872224678**97456533333333356677899**********98888888877..999****** PP

                           DUF2515 253 tlrevykdvkheeakkedWfkkkkevlkllkkeeekkeieltekyekkleklel 306
                                        ++ v+++++   +  +dW + +  +++++ +e++ ++   +e+  + ++k ++
  gi|330508809|ref|YP_004385237.1| 189 DFSFVWDEITLPISYDSDWRAAESLIMDIVIQETHMMKEYAEEEISHMQRKYYI 242
                                       ********************9999999999999998888888888888887665 PP

>> AgrB  Accessory gene regulator B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4  16.9   1.2e-05     0.072      82     180 ..      10     109 ..       7     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                              AgrB  82 slliflllillakllslslslllillliilliisliiilllaPvdtpnkpisskekkkklki..lsiivllilliia 156
                                       sl +f ++++l+ ++  s  +++ ++++i++i++++i++++   d   k  +s++k+ ++ +  +si++l+ ++ii 
  gi|330508809|ref|YP_004385237.1|  10 SLAVFAFVLWLTTFIYQSS-YINRTIITIIAILMIYIVFRVLLEDRIIKNFTSTDKRYYFSKmlYSIYLLINFIIIW 85 
                                       8999**********98887.9999***********************************998745555555555555 PP

                              AgrB 157 lllknekisnaillglllvavlql 180
                                       +++ +   + ++ +gl+++a+ ++
  gi|330508809|ref|YP_004385237.1|  86 IIWVEDIRTLLLGFGLVAAAFTIS 109
                                       555777777899999997777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1344  (0.0749624); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2234.17
//
Query:       gi|330508810|ref|YP_004385238.1|  [L=535]
Description: cation transport protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-43  147.8  26.8    1.2e-40  139.5  26.8    3.0  1  TrkH            Cation transport protein
  ------ inclusion threshold ------
        4.6    6.6   9.6         12    5.2   4.5    2.6  2  TMEM43          Transmembrane protein 43


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 !  139.5  26.8   1.3e-44   1.2e-40      13     491 ..      48     529 ..      38     535 .] 0.89

  Alignments for each domain:
  == domain 1  score: 139.5 bits;  conditional E-value: 1.3e-44
                              TrkH  13 ialgavllfldkeskyplalkddfqivkaaeialsvdgtlklllesaslafldalfeavsgltttglsvivveeslp 89 
                                       i++g  l++    +k  +  kd+f  v   ++    +g+l+ l     l+  da fe++sg+tttg++   +++s  
  gi|330508810|ref|YP_004385238.1|  48 IIVGLILKHFG--EKSDMGRKDAFAAVSFGWLMAGLIGALPYL--LLGLGLVDAFFESMSGFTTTGATILSEYDSQH 120
                                       45555444442..334577788999999999999999999977..678999*************************9 PP

                              TrkH  90 rsgltlraqlq......................................................qiGglgvvvlay 112
                                       ++ l  +a+ +                                                      ++Gg+g++ l  
  gi|330508810|ref|YP_004385238.1| 121 YWTLSKEAVHSslayalvertthqlihwspigiieldfgltlnfidlltiketyfgllfwrsfsqFLGGMGIILLFI 197
                                       99999999888999*************************************************************** PP

                              TrkH 113 lslptlgrgsaflylseaqkeelggkelrslselikilvvyyvgleilafvllvvliytakaysevvdstgvsplww 189
                                       ++lp lg  +  ly+ e  +    +  ++++++++k+ + +y+gl+ + ++ll           +++      p+++
  gi|330508810|ref|YP_004385238.1| 198 AILPNLGVAGRELYSVEGLGL-MKEALTPRVKSTAKAFWGIYLGLTGMEALLL---------VAAGL------PVYD 258
                                       *****************9765.556789*************************.........78898......**** PP

                              TrkH 190 affhsmSafnnlGfsltpnSlasfnknivillvaiifiilGnigFpillrviiaikkkilrdlkqikeslsflldlp 266
                                        +++s+S+++++Gfs  + S+a +n+ i++++++ if +lG+++F i  ++i++   k+l+         ++++d +
  gi|330508810|ref|YP_004385238.1| 259 SLCTSFSSISTAGFSPRAYSIAEYNS-ILVEAIICIFLLLGGTNFIIYHQIILK---KNLN---------YLIRDAE 322
                                       **************************.******************999988875...4555.........499**** PP

                              TrkH 267 rrcftLllasgfvwllllelavlnvtdnilfilldegslvvksipkg..srvlkalFqsvstrta.GF.svvdlsnl 339
                                       +r+ ++++ +++++l+                       ++++ip g  ++ + ++Fq+++t t+ GF + + ++++
  gi|330508810|ref|YP_004385238.1| 323 FRFYIIIVFISIIILM-----------------------IFGQIPGGffDALRSSVFQVITTMTTtGFvNNFNYDSW 376
                                       ****444433333333.......................45566655446899********99999**778****** PP

                              TrkH 340 hpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkavskksidgkhlerqllvdlwslflvlli 416
                                       + a k++l+l m igg+ gSt gg++  +v+++ + + +e+ +  +pkav ++++  k ++++ + ++  ++ +++ 
  gi|330508810|ref|YP_004385238.1| 377 SLAAKLVLMLLMIIGGCTGSTGGGMKVGRVLIVLKYVHAELIRSLHPKAVITIRMADKVVKENTVKSVILFIQLYVM 453
                                       ****************************************************************9999998888888 PP

                              TrkH 417 ilile..glklsdvqepdfsffdiLfevvSaygtvGLSlGaknaslsaqlttisklvlialmirGrlrglpvlldra 491
                                       i+il    + +++  +p+f  + ++ + + ++g vG+++G   a  +  +++++k++  + m +Grl++lpv+l + 
  gi|330508810|ref|YP_004385238.1| 454 IFILAavAFSITEASNPQFGSLSAISAAACCLGVVGPGFG-VVAMDFNAISESGKVLATFCMYIGRLEILPVVLMFL 529
                                       777761246899****************************.7777788899999********************997 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   4.5    0.0013        12     187     237 ..       5      54 ..       2      57 .. 0.81
   2 ?    3.1   0.2    0.0057        51     159     222 ..     416     479 ..     402     497 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0013
                            TMEM43 187 wllRllGfllmflglllllsplsvlvslipllgelvglgla.lvalllslsl 237
                                        +lR+lG+l m+lg+l+l+  +   ++  pl  ++v++g++ l+a++++l+l
  gi|330508810|ref|YP_004385238.1|   5 IILRILGMLAMLLGTLMLIPGIVSAIYKEPL--GVVAFGISsLLAIIVGLIL 54 
                                       689*************999999888888999..7777777757777777766 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0057
                            TMEM43 159 deielleegevsaeemfakeksenklltwllRllGfllmflglllllsplsvlvslipllgelv 222
                                       + i +l+++ v    m +k  +en+++  +l +  ++++f+  ++++s+ ++    +  l+ ++
  gi|330508810|ref|YP_004385238.1| 416 ELIRSLHPKAVITIRMADKVVKENTVKSVILFIQLYVMIFILAAVAFSITEASNPQFGSLSAIS 479
                                       567888999998999**************************99999999766555444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3262.06
//
Query:       gi|330508811|ref|YP_004385239.1|  [L=135]
Description: hypothetical protein MCON_3118 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
       0.01   16.2   1.9      0.012   16.0   0.8    1.7  2  DUF4969         Domain of unknown function (DUF4969)
  ------ inclusion threshold ------
      0.029   14.5   8.0      0.034   14.2   8.0    1.2  1  MCU             Mitochondrial calcium uniporter
      0.057   13.6   7.8       0.07   13.3   7.8    1.1  1  SesA            N-terminal domain on NACHT_NTPase and P-loop 
      0.063   12.6  11.1      0.084   12.2  11.1    1.2  1  DUF4407         Domain of unknown function (DUF4407)
      0.082   13.0   1.6         16    5.6   0.0    3.3  3  TRPM_tetra      Tetramerisation domain of TRPM
      0.087   12.8   4.4       0.12   12.3   4.4    1.3  1  FixH            FixH
       0.11   10.4   3.1       0.11   10.3   3.1    1.0  1  V_ATPase_I      V-type ATPase 116kDa subunit family
       0.27   11.3  19.0      0.058   13.4  11.4    2.0  2  YscO-like       YscO-like protein
       0.28   10.5   4.6       0.97    8.7   4.8    1.7  1  ThrE            Putative threonine/serine exporter
       0.29   10.9  21.6       0.38   10.5  21.6    1.1  1  ERM             Ezrin/radixin/moesin family
       0.32   11.4   9.9       0.39   11.1   9.9    1.1  1  CCDC53          Subunit CCDC53 of WASH complex
       0.32   11.1   4.9       0.42   10.7   4.9    1.1  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
       0.33    9.7   5.1       0.41    9.4   5.1    1.1  1  Presenilin      Presenilin
       0.43    9.4  11.9       0.59    9.0  11.9    1.2  1  Spc7            Spc7 kinetochore protein
       0.82    9.7  10.5        1.1    9.4  10.5    1.2  1  FAD-SLDH        Membrane bound FAD containing D-sorbitol dehy
       0.91   10.2   2.9        1.8    9.3   2.7    1.7  1  ParE_toxin      ParE toxin of type II toxin-antitoxin system,
          1    8.5   5.9        1.4    8.1   5.9    1.1  1  TMPIT           TMPIT-like protein
        1.1    7.8   9.5        1.2    7.6   9.5    1.0  1  AAA_13          AAA domain
        1.1    9.6  17.9        1.5    9.2  17.9    1.2  1  DUF3486         Protein of unknown function (DUF3486)
        1.2    8.3  15.6        1.6    7.9  15.6    1.1  1  VSG_B           Trypanosomal VSG domain
        1.3    7.5  15.6        1.6    7.2  15.6    1.0  1  Borrelia_P83    Borrelia P83/100 protein
        1.4    8.4   7.0        1.7    8.1   7.0    1.0  1  SMYLE_N         Short myomegalin-like EB1 binding proteins, N
          2    8.0   5.5        2.4    7.8   5.5    1.1  1  ATP-synt_ab     ATP synthase alpha/beta family, nucleotide-bi
          2    6.2   5.3        2.3    6.1   5.3    1.1  1  Prominin        Prominin
        2.1    8.4   7.1        2.6    8.2   7.1    1.0  1  TP53IP5         Cellular tumour antigen p53-inducible 5
        2.2    8.8   5.9          7    7.2   0.2    2.2  2  NPV_P10         Nucleopolyhedrovirus P10 protein
        2.7    8.1  23.5        3.7    7.6  23.5    1.1  1  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
        2.9    7.0  21.3          5    6.3  20.2    1.7  2  ISG65-75        Invariant surface glycoprotein
        3.1    8.3  14.2        1.5    9.4  11.1    1.8  2  MRFAP1          MORF4 family-associated protein1
        3.8    7.7   6.3        4.9    7.3   5.9    1.4  1  CHDCT2          CHDCT2 (NUC038) domain
        4.4    8.1  10.6         44    4.8  10.6    2.0  1  DUF2203         Uncharacterized conserved protein (DUF2203)
        7.3    6.9  12.1         11    6.3   1.6    2.9  2  XhlA            Haemolysin XhlA
        8.9    6.0  36.8    3.3e+03   -2.4  36.8    2.1  1  GARP            Glutamic acid/alanine-rich protein of Trypano
        9.5    5.1   7.1         10    4.9   7.1    1.0  1  XRN_M           Xrn1 helical domain
        9.6    6.7  11.9         10    6.6   7.2    2.5  2  DUF3357         Domain of unknown function (DUF3357)


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 !   16.0   0.8   2.3e-05     0.012       1      62 [.       1      61 [.       1      74 [. 0.77
   2 ?   -1.8   0.0       7.8     4e+03      29      40 ..      71      82 ..      65     108 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.3e-05
                           DUF4969  1 mkkRgllLvsvLvlFillavaCsdsedn....eesveiilkeielsvddpiklvdengeatvevdv 62
                                      mk   ++L  +L+l + +++a ++  d        ve + k++e++        +en  a ++  +
  gi|330508811|ref|YP_004385239.1|  1 MKNVVVILAAALMLLVAVTTASAEETDKvaeaAMQVEESAKQVEIA-----AQLTENATADLKSAA 61
                                      788899***************998665422113579999*****99.....788899888776665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.8
                           DUF4969 29 eesveiilkeie 40
                                       + +e i+k  e
  gi|330508811|ref|YP_004385239.1| 71 TTAAENITKAAE 82
                                      455555555443 PP

>> MCU  Mitochondrial calcium uniporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   8.0   6.7e-05     0.034       2     108 ..      27     134 ..       5     135 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-SSSSSSTSSSSSHHHHHHHHHHHHH-SHHHHHHH CS
                               MCU   2 degieaaavlsesgvvialstlleeeeakvllrvkqlvkalesalnveeeqlkkereleekleelreelepleekke 78 
                                       d+ +eaa  ++es  ++ +  +l+e+ +++l++  + v++l++ ++++e+ +k  +++e+k ee ++  e++ e+ +
  gi|330508811|ref|YP_004385239.1|  27 DKVAEAAMQVEESAKQVEIAAQLTENATADLKSAAEHVENLTANTTAAENITKAAEKVEQKAEEASQAAEKVDEAAQ 103
                                       55666777778888888777777777788888888888888888888888888888888888888889999999888 PP

                                       HTCCCGGGCHHHH.GGGHHHHHHHHTHHHHH CS
                               MCU  79 eidekAerrtrrl.lwagLallavqlgilar 108
                                       + +e+Ae+      + a+L++lav + +l r
  gi|330508811|ref|YP_004385239.1| 104 KAEEAAEKVPGFAaALAALGFLAVAFIALRR 134
                                       8888888877654156788999998888866 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 ?   13.3   7.8   0.00014      0.07       3      89 ..      18     104 ..      16     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00014
                              SesA   3 stiaiveaaiklydaikdikglpeaFrevgkrLplvqetLedaksqlesskldedtesaikpvlesckekatkleei 79 
                                        t+a  e + k+ +a+ ++++  +  + +++  +   + L++a +++e+ ++++++ ++i++++e++++ka++ ++ 
  gi|330508811|ref|YP_004385239.1|  18 VTTASAEETDKVAEAAMQVEESAKQVEIAAQLTENATADLKSAAEHVENLTANTTAAENITKAAEKVEQKAEEASQA 94 
                                       5788899999999******************99******************************************** PP

                              SesA  80 fekvapapad 89 
                                        ekv +a+++
  gi|330508811|ref|YP_004385239.1|  95 AEKVDEAAQK 104
                                       ****554444 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  11.1   0.00016     0.084     152     253 ..      21     125 ..       6     132 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                           DUF4407 152 aearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld.......atarlaalraelae 221
                                       a+a+ +++ aea+ +++       ++v+   + +++++a+l+ a + +++l+a+ +       a+++++++ +e+++
  gi|330508811|ref|YP_004385239.1|  21 ASAEETDKVAEAAMQVEE----SAKQVEIAAQLTENATADLKSAAEHVENLTANTTaaenitkAAEKVEQKAEEASQ 93 
                                       334444444444444433....22234445555666666666666666666666556677777899*********** PP

                           DUF4407 222 leaerakeraasqaaaaaddGllarlealdrl 253
                                       ++++ ++++++ ++aa++  G++a l al+ l
  gi|330508811|ref|YP_004385239.1|  94 AAEKVDEAAQKAEEAAEKVPGFAAALAALGFL 125
                                       **************************999866 PP

>> TRPM_tetra  Tetramerisation domain of TRPM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.6      0.11        56       8      27 ..      26      45 ..      24      74 .. 0.67
   2 ?    1.0   0.1      0.91   4.7e+02      49      49 ..      71      71 ..      55      93 .. 0.61
   3 ?    5.6   0.0     0.032        16       7      35 ..      94     122 ..      88     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.11
                        TRPM_tetra  8 tERvEnmsmkveevneKenl 27
                                      t++v +  m+vee  + + +
  gi|330508811|ref|YP_004385239.1| 26 TDKVAEAAMQVEESAKQVEI 45
                                      79999999999997666653 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.91
                        TRPM_tetra 49 t 49
                                      t
  gi|330508811|ref|YP_004385239.1| 71 T 71
                                      2 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.032
                        TRPM_tetra   7 ttERvEnmsmkveevneKenlikaSLqsl 35 
                                        +E+v++  +k ee  eK+    a L +l
  gi|330508811|ref|YP_004385239.1|  94 AAEKVDEAAQKAEEAAEKVPGFAAALAAL 122
                                       58****************98777777665 PP

>> FixH  FixH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.4   0.00024      0.12      18      87 ..       5      74 ..       3     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00024
                              FixH 18 vvvvvnltmlylAvstkdglvvddyYkkGkainqelarakaaqalglsadvaldegeltitlrdaagkpv 87
                                      vv+ +   ml +Av+t++  ++d+  ++  +  ++ ++ + a++l  +a+++l+ +++ ++  +a++  +
  gi|330508811|ref|YP_004385239.1|  5 VVILAAALMLLVAVTTASAEETDKVAEAAMQVEESAKQVEIAAQLTENATADLKSAAEHVENLTANTTAA 74
                                      89999**************************************************777777644444433 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 ?   10.3   3.1   0.00022      0.11      60     133 ..      32     104 ..       6     133 .. 0.40

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                        V_ATPase_I  60 eesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleeeeeeeeeeeseeeee 133
                                       ++++ ++++k+++   + +e+++++lk+  e+ e+l+++++ +++ ++  ek+++  ee+++ +e+  +e++++
  gi|330508811|ref|YP_004385239.1|  32 AAMQVEESAKQVEIAAQLTENATADLKSAAEHVENLTANTTAAENITKAAEKVEQKAEEASQAAEK-VDEAAQK 104
                                       122222222222222222333333344444444444444443333333333333333322111111.1111111 PP

>> YscO-like  YscO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4  11.4   0.00011     0.058      84     147 ..      27      93 ..      22      94 .. 0.88
   2 ?    1.4   8.1      0.57   2.9e+02      81     111 ..      79     109 ..      70     115 .. 0.45

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHH CS
                         YscO-like  84 eelkqeekkvekQkekVkvAerkvEqareelakkrkeveklekhk...eewlkevkkeeekreeleq 147
                                       +++++ + +ve+  ++V++A+++ E+a  +l+ ++  ve l+ +    e+ +k + k e+k+ee  q
  gi|330508811|ref|YP_004385239.1|  27 DKVAEAAMQVEESAKQVEIAAQLTENATADLKSAAEHVENLTANTtaaENITKAAEKVEQKAEEASQ 93 
                                       6788999********************************9987643338999999999999999766 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         YscO-like  81 vvkeelkqeekkvekQkekVkvAerkvEqar 111
                                         +e+++q++++  +  ekV +A++k E+a 
  gi|330508811|ref|YP_004385239.1|  79 KAAEKVEQKAEEASQAAEKVDEAAQKAEEAA 109
                                       2233444444444444444444444444443 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.8    0.0019      0.97       7     124 ..      10     126 ..       4     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0019
                              ThrE   7 GeiLlesGaetyrvedtmkriaralgleevevfvtptsiivsv.deeeesitt.vrrvrsrgvnleklsevnelsre 81 
                                       + ++l     t+  e+t k + +a+++   e ++    i  ++ ++    ++   ++v++ + n++  + + + +++
  gi|330508811|ref|YP_004385239.1|  10 AALMLLVAVTTASAEETDKVAEAAMQV---EESAKQVEIAAQLtENATADLKSaAEHVENLTANTTAAENITKAAEK 83 
                                       555555555555555554444444444...3333344444444222222333336669******************* PP

                              ThrE  82 iaageisleeaeerLdeIerskpryprwlvvlaaglaaaafal 124
                                       ++++  ++ +a e+ de  ++ ++    +  +aa+laa +f  
  gi|330508811|ref|YP_004385239.1|  84 VEQKAEEASQAAEKVDEAAQKAEEAAEKVPGFAAALAALGFLA 126
                                       **************************************99975 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  21.6   0.00074      0.38      32     126 ..      23     112 ..      16     121 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00074
                               ERM  32 eetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerL 108
                                        e+ ++ ae a ++ee a++ e  a+  e++++ lk +ae      e+l +++  a +++++ +e++e+k+eea++ 
  gi|330508811|ref|YP_004385239.1|  23 AEETDKVAEAAMQVEESAKQVEIAAQLTENATADLKSAAEH----VENLTANT-TAAENITKAAEKVEQKAEEASQA 94 
                                       33444444444444444444444444444444444443332....23344444.44556778888888888888888 PP

                               ERM 109 keeleeareaeeeakekl 126
                                        e++ ea ++ eea+ek+
  gi|330508811|ref|YP_004385239.1|  95 AEKVDEAAQKAEEAAEKV 112
                                       888888888888888886 PP

>> CCDC53  Subunit CCDC53 of WASH complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   9.9   0.00076      0.39      23     104 ..      33     110 ..      19     126 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00076
                            CCDC53  23 LvevekrlqrleitlalLEak...LsSip.gleeveaeaaeastsddnaarkgppppppsseaaaaaaqaeeasqae 95 
                                        ++ve++ +++ei  +l E+    L+S+   +e+++a++ +       aa++ +++ +++ ++a++a+qa+e+  ++
  gi|330508811|ref|YP_004385239.1|  33 AMQVEESAKQVEIAAQLTENAtadLKSAAeHVENLTANT-T-------AAENITKAAEKVEQKAEEASQAAEKVDEA 101
                                       589****************76444665542333333333.2.......33333333333333333333333333333 PP

                            CCDC53  96 esaeeeaee 104
                                       +++ eea+e
  gi|330508811|ref|YP_004385239.1| 102 AQKAEEAAE 110
                                       333333332 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 ?   10.7   4.9   0.00082      0.42      43     135 ..       7     107 ..       3     117 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00082
                           UPF0242  43 aaaGsLlllllllkwekalkekl........ekskleekeaklteld.eglktkeealeelqeeeeeLkeeldakee 110
                                       ++a+ L+ll+ +++ + +++ k+        e+ k  e  a+lte+   +lk  +e++e+l++++    e++ +  e
  gi|330508811|ref|YP_004385239.1|   7 ILAAALMLLVAVTTASAEETDKVaeaamqveESAKQVEIAAQLTENAtADLKSAAEHVENLTANTTAA-ENITKAAE 82 
                                       55667767777776666666666765554432222222233333333445555555555555544433.33333333 PP

                           UPF0242 111 elerlkeenqqLqekleaiaedfee 135
                                       ++e+  ee  q  ek  ++a+  ee
  gi|330508811|ref|YP_004385239.1|  83 KVEQKAEEASQAAEKVDEAAQKAEE 107
                                       3444444444444444444433332 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.1   0.00079      0.41     222     307 ..      20     106 ..       4     121 .. 0.36

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00079
                        Presenilin 222 vlaaeek.kaevaeseeeeeaekkkeeasesskeeeseeesseksaqsse...seeeseeesseaessaeesseeke 294
                                       +++aee+ k+++a+ + ee+a++ + +a+ +++++++ ++++e+ ++ ++     e+ +++++++e++aee s+ +e
  gi|330508811|ref|YP_004385239.1|  20 TASAEETdKVAEAAMQVEESAKQVEIAAQLTENATADLKSAAEHVENLTAnttAAENITKAAEKVEQKAEEASQAAE 96 
                                       22222222333333333444444443444333333333333333333332111222222222222222222222222 PP

                        Presenilin 295 seessesseeeee 307
                                          + ++++++ e
  gi|330508811|ref|YP_004385239.1|  97 ---KVDEAAQKAE 106
                                       ...2222111111 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  11.9    0.0011      0.59     152     250 ..      23     119 ..      12     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                              Spc7 152 eedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeq 228
                                        e+ +++++   +++e  +++e   +  e+  ++l++aae +e+++ +   ++ e+++++ +++e+k +e ++  e+
  gi|330508811|ref|YP_004385239.1|  23 AEETDKVAEAAMQVEESAKQVEIAAQLTENATADLKSAAEHVENLTAN--TTAAENITKAAEKVEQKAEEASQAAEK 97 
                                       566777778888888888888777777777888888888888887766..467788888888888888899999999 PP

                              Spc7 229 leeleekieelkeqkseleeei 250
                                       ++e ++k ee++e+   + +++
  gi|330508811|ref|YP_004385239.1|  98 VDEAAQKAEEAAEKVPGFAAAL 119
                                       9999888888888876666655 PP

>> FAD-SLDH  Membrane bound FAD containing D-sorbitol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  10.5    0.0021       1.1       8     106 ..       9     107 ..       5     121 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0021
                          FAD-SLDH   8 kgaalllaaaalasll.aaaaaaaaassaelaqFlqvSqlLtgrkkLdpalgarlyaalvaedaefkaqlaaLaall 83 
                                        +a++ll+a+++as+  + + a+aa + +e+a+ +++++ Lt++ + d + +a   ++l+a+    ++ +++ a+ +
  gi|330508811|ref|YP_004385239.1|   9 AAALMLLVAVTTASAEeTDKVAEAAMQVEESAKQVEIAAQLTENATADLKSAAEHVENLTANTTAAEN-ITKAAEKV 84 
                                       44444444444444446678899999999*******************************96655444.44444444 PP

                          FAD-SLDH  84 ekqkakdveallaa.aaadaalkd 106
                                       e qka+++++ +++ + a+++ ++
  gi|330508811|ref|YP_004385239.1|  85 E-QKAEEASQAAEKvDEAAQKAEE 107
                                       3.4555555555443444444444 PP

>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.7    0.0035       1.8       3      49 ..      49      98 ..      47     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0035
                                      EEHHHHHHHHHHHHHHHCC-H...HHHHHHHHHHHHHHHHHHHTTTSEEC CS
                        ParE_toxin  3 ltprAlkdlkkiadyiardgp...aakrfldaleealellaenpalgrpr 49
                                      lt+ A +dlk +a+++++  +   aa+ +++a e+  +  +e++++ ++ 
  gi|330508811|ref|YP_004385239.1| 49 LTENATADLKSAAEHVENLTAnttAAENITKAAEKVEQKAEEASQAAEKV 98
                                      7999************9444334889999999998888888888887774 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.9    0.0027       1.4       5      83 ..      34     110 ..      23     123 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0027
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkv 81 
                                        ++e+++k++e +a+  ++ +++l++  +++  +++ ++  +++++++ +k+++++ ee ++++e+++e  +++++ 
  gi|330508811|ref|YP_004385239.1|  34 MQVEESAKQVEIAAQLTENATADLKSAAEHVE-NLTANTTAAENITKAAEKVEQKA-EEASQAAEKVDEAAQKAEEA 108
                                       23444444444444333333334333333332.23333444455555555555543.45555666666666655555 PP

                             TMPIT  82 lk 83 
                                        +
  gi|330508811|ref|YP_004385239.1| 109 AE 110
                                       44 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   9.5    0.0024       1.2     363     445 ..      28     108 ..      11     124 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0024
                            AAA_13 363 kiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeael 439
                                       k+ ++  +v+e  ++++   + ++n +++ ++a++ +e   ++   +e  + +k+ +k+e+++e++ +++++  +++
  gi|330508811|ref|YP_004385239.1|  28 KVAEAAMQVEESAKQVEIAAQLTENATADLKSAAEHVENLTANTTAAE--NITKAAEKVEQKAEEASQAAEKVDEAA 102
                                       223344445555555555555555555555555555555444433222..444444444444444444444444444 PP

                            AAA_13 440 kkleee 445
                                       +k+ee 
  gi|330508811|ref|YP_004385239.1| 103 QKAEEA 108
                                       443332 PP

>> DUF3486  Protein of unknown function (DUF3486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  17.9    0.0029       1.5      78     170 ..      18     108 ..       3     125 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0029
                           DUF3486  78 veelgdeedddvtealiellqtllfellmaleeeeeeeidpkeakeLakalaklerasvaskkrraeirkeaaeaaa 154
                                       v  + +ee+d+v+ea++++ ++ + ++ +a++ +e++++d k+a+e   +l + ++a+ + +k +++++++a+ea +
  gi|330508811|ref|YP_004385239.1|  18 VTTASAEETDKVAEAAMQV-EESAKQVEIAAQLTENATADLKSAAEHVENLTANTTAAENITKAAEKVEQKAEEASQ 93 
                                       4455666666799988885.566666666666688889999999999888888888888888888888888776555 PP

                           DUF3486 155 aaaeevakaaGlsaet 170
                                       a ae+v++aa   +e+
  gi|330508811|ref|YP_004385239.1|  94 A-AEKVDEAAQKAEEA 108
                                       5.55553333112333 PP

>> VSG_B  Trypanosomal VSG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  15.6     0.003       1.6      59     158 ..      19     107 ..       8     120 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.003
                             VSG_B  59 sladedwlnkfaeeedda.katktkkaakkncgalkafWkeakkaakakkkk...eltrpantrararanekiqqia 131
                                       ++a ++  +k ae++ +  +  k+ + a++  + + a              +    ++++ n +a+++a+e+i ++a
  gi|330508811|ref|YP_004385239.1|  19 TTASAEETDKVAEAAMQVeESAKQVEIAAQLTENATA--------------DlksAAEHVENLTANTTAAENITKAA 81 
                                       4444444444444444433333333334444444444..............34445555555555555555555555 PP

                             VSG_B 132 ekaaeiyseikkekekakkar..aeklkk 158
                                       ek+++ ++e+ +++ek+++a+  a   ++
  gi|330508811|ref|YP_004385239.1|  82 EKVEQKAEEASQAAEKVDEAAqkA---EE 107
                                       555555555555555555443222...22 PP

>> Borrelia_P83  Borrelia P83/100 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  15.6    0.0031       1.6     267     345 ..      21     110 ..      16     120 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0031
                      Borrelia_P83 267 sskkedkkva......eekkreiekaqkeikkkdeeakkakdak....aedlkke..skaeekeaedkeleakkere 331
                                        s++e +kva      ee  +++e a + +++++ ++k a ++     a+  + e  +ka ek  e+k +ea +  e
  gi|330508811|ref|YP_004385239.1|  21 ASAEETDKVAeaamqvEESAKQVEIAAQLTENATADLKSAAEHVenltANTTAAEniTKAAEKV-EQKAEEASQAAE 96 
                                       4555555664444445666677777777777777777777777555555555555555666665.777777777777 PP

                      Borrelia_P83 332 evaeDlqkikeevk 345
                                       +v e  qk  e+ +
  gi|330508811|ref|YP_004385239.1|  97 KVDEAAQKAEEAAE 110
                                       77777777666554 PP

>> SMYLE_N  Short myomegalin-like EB1 binding proteins, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.0    0.0034       1.7     208     287 ..      29     108 ..      15     126 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0034
                           SMYLE_N 208 geeeeavselaaaelaeaksssegesleeespassvesLdtavdvvkpakkkeeesekeakedeksdslseekteae 284
                                        +e +++ e++a++ + a++ +e+ + + +s+a  ve L+++++++++ +k +e+ e++a+e++++ ++ +e  + +
  gi|330508811|ref|YP_004385239.1|  29 VAEAAMQVEESAKQVEIAAQLTENATADLKSAAEHVENLTANTTAAENITKAAEKVEQKAEEASQAAEKVDEAAQKA 105
                                       33334444555555555556666666678888999****99999888888777766666666665555555533333 PP

                           SMYLE_N 285 ssl 287
                                       ++ 
  gi|330508811|ref|YP_004385239.1| 106 EEA 108
                                       333 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 ?    7.8   5.5    0.0046       2.4      43     142 ..      16     120 ..       2     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0046
                                       EEEEEEESEEHHHHHHHHHHCHHSS....GGGGEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  43 aiiyvgiGergnevaevleefpegt....imkrtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadsls 115
                                       + +  +  e +++vae  ++++e+     i ++ +  a    +++a+ +    + +t+AE   +  ++v   a++ s
  gi|330508811|ref|YP_004385239.1|  16 VAVTTASAEETDKVAEAAMQVEESAkqveIAAQLTENATADLKSAAEHVENLTANTTAAENITKAAEKVEQKAEEAS 92 
                                       567778899999**********94444557777777766667788888888888899******************** PP

                                       HHHHHHHHHHHHTTTSBEGG.GSBTTHH CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                       ATP-synt_ab 116 rwaeAlreislrlgempadq.gypaylg 142
                                       + ae + e + +++e   +  g+ a l+
  gi|330508811|ref|YP_004385239.1|  93 QAAEKVDEAAQKAEEAAEKVpGFAAALA 120
                                       ***********99998776337877776 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.3    0.0045       2.3     628     704 ..      31     112 ..      11     121 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0045
                          Prominin 628 tlaekleelanelsngk...knlkqslkneaqdlraiqqelvlp..lessvkklkksvkkldeensdlqesikklla 699
                                       + a ++ee a++++ +    +n+   lk++a++++++ ++++    ++++++k++++ ++ ++ +++  e+ +k  +
  gi|330508811|ref|YP_004385239.1|  31 EAAMQVEESAKQVEIAAqltENATADLKSAAEHVENLTANTTAAenITKAAEKVEQKAEEASQAAEKVDEAAQKAEE 107
                                       34444444444443333555678899999999999988876543227777777777777766666666666666666 PP

                          Prominin 700 avera 704
                                       a+e+ 
  gi|330508811|ref|YP_004385239.1| 108 AAEKV 112
                                       65554 PP

>> TP53IP5  Cellular tumour antigen p53-inducible 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   7.1     0.005       2.6      56     147 ..      23     112 ..      10     122 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.005
                           TP53IP5  56 ssgenevlekvkqnneelqearalekkleskklestkepkelkskewkeeskvrnkakgspaavpkkeeqaeaevpk 132
                                       +   ++v e + q +e+ +++++ ++ +e+++++ + +++++++   + +++  ++  +  + v++k e+a + ++k
  gi|330508811|ref|YP_004385239.1|  23 AEETDKVAEAAMQVEESAKQVEIAAQLTENATADLKSAAEHVEN--LTANTTAAENITKAAEKVEQKAEEASQAAEK 97 
                                       23345577777788888888888888888888887777777754..5555555666667777888888888888888 PP

                           TP53IP5 133 tsrgeglntkaqkkq 147
                                       + + ++++++a +k 
  gi|330508811|ref|YP_004385239.1|  98 VDEAAQKAEEAAEKV 112
                                       888887777776654 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.7      0.14        72      18      62 ..      27      68 ..      12      77 .. 0.68
   2 ?    7.2   0.2     0.014         7       9      54 ..      77     122 ..      71     127 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.14
                           NPV_P10 18 dkVdalqqqvddvqenlpdvtelnekL.daqsaqLaeletkvenIq 62
                                      dk   + ++  +v+e  ++v+ + ++L ++ +a L++  ++ven +
  gi|330508811|ref|YP_004385239.1| 27 DK---VAEAAMQVEESAKQVE-IAAQLtENATADLKSAAEHVENLT 68
                                      34...4566667777888866.555553677888988888888876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.014
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLael 54 
                                       I ++ ++v++k +  +q+ ++v+e  ++ +e  ek+ + +a+La+l
  gi|330508811|ref|YP_004385239.1|  77 ITKAAEKVEQKAEEASQAAEKVDEAAQKAEEAAEKVPGFAAALAAL 122
                                       77889999***************************99999999987 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 ?    7.6  23.5    0.0073       3.7       9     103 ..      17     111 ..      12     112 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0073
                        TPR_MLP1_2   9 eikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesaka 85 
                                        ++++++e+++  a+++   e+  kq eia++  ++    l   ae v++l+a  + ++++++ +++++++ae+a++
  gi|330508811|ref|YP_004385239.1|  17 AVTTASAEETDKVAEAAMQVEESAKQVEIAAQLTENATADLKSAAEHVENLTANTTAAENITKAAEKVEQKAEEASQ 93 
                                       5677889999999999999*********************************************************9 PP

                        TPR_MLP1_2  86 eleeseesweeqkeelek 103
                                       + e+  e+ ++ +e+ ek
  gi|330508811|ref|YP_004385239.1|  94 AAEKVDEAAQKAEEAAEK 111
                                       999999999999988775 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.4      0.39     2e+02       3      26 ..      11      33 ..       9      43 .. 0.60
   2 ?    6.3  20.2    0.0097         5      53     131 ..      37     114 ..      20     123 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.39
                          ISG65-75  3 vllvalaaalaaeesaekdqekad 26
                                      +l++ +a+++a+ e+++k+  +a 
  gi|330508811|ref|YP_004385239.1| 11 ALMLLVAVTTASAEETDKVA-EAA 33
                                      56777777777777777733.333 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0097
                          ISG65-75  53 dyllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekaeka 129
                                       ++  k+++ +++  ena++ ++   e++e+l+++  + ++   ++aek+++ +eeA ++++k +e a+ka e+aek+
  gi|330508811|ref|YP_004385239.1|  37 EESAKQVEIAAQLTENATADLKSAAEHVENLTANT-TAAENITKAAEKVEQKAEEASQAAEKVDEAAQKAEEAAEKV 112
                                       34556677777777888888888888888888874.44444455557888888888888888888888888888776 PP

                          ISG65-75 130 sk 131
                                        +
  gi|330508811|ref|YP_004385239.1| 113 PG 114
                                       55 PP

>> MRFAP1  MORF4 family-associated protein1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4         2     1e+03      79      99 ..      23      43 ..      13      53 .. 0.59
   2 ?    9.4  11.1    0.0028       1.5      58     115 ..      48     107 ..      35     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2
                            MRFAP1 79 aeaeervaklcakaerkakea 99
                                      ae  ++va  + ++e+ ak++
  gi|330508811|ref|YP_004385239.1| 23 AEETDKVAEAAMQVEESAKQV 43
                                      344456666666666655543 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0028
                            MRFAP1  58 eikseveaseesaldparsPga..eaeervaklcakaerkakeaarmgkrlvelvrrier 115
                                       ++  +  a+ +sa +++++  a   a e ++k ++k+e+ka ea++ ++++ e  ++ e+
  gi|330508811|ref|YP_004385239.1|  48 QLTENATADLKSAAEHVENLTAntTAAENITKAAEKVEQKAEEASQAAEKVDEAAQKAEE 107
                                       445566789999***99986651168899************************9999876 PP

>> CHDCT2  CHDCT2 (NUC038) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   5.9    0.0096       4.9      68     125 ..      42      99 ..      26     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0096
                            CHDCT2  68 alvieeqlrraallnlqeekekvgslaqrfaelellaeshqkllkesaagnknanavl 125
                                        + i  ql   a+ +l++++e+v++l ++ + +e+++++ +k+ +++++ +++a++v 
  gi|330508811|ref|YP_004385239.1|  42 QVEIAAQLTENATADLKSAAEHVENLTANTTAAENITKAAEKVEQKAEEASQAAEKVD 99 
                                       46788999999999999**********************9999999999888888765 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  10.6     0.086        44       7      87 ..      52     130 ..       7     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.086
                           DUF2203   7 eAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleagl 83 
                                       +A+a L    e +e+l a ++ +e++ ++ e+ +++ae  ea++++++++e+++++ee+ e++  + + +  l  + 
  gi|330508811|ref|YP_004385239.1|  52 NATADLKSAAEHVENLTANTTAAENITKAAEKVEQKAE--EASQAAEKVDEAAQKAEEAAEKVPGFAAALAALGFLA 126
                                       55555555666666666666666666555555555543..3677777788888888888877777777777776666 PP

                           DUF2203  84 vDFp 87 
                                       v F 
  gi|330508811|ref|YP_004385239.1| 127 VAFI 130
                                       6665 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.6     0.022        11       5      50 ..      28      73 ..      22      78 .. 0.82
   2 ?    4.8   3.8     0.065        33       7      38 ..      82     109 ..      72     122 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.022
                              XhlA  5 rlerietkldnleervdkleekaaeaeekiknleedlkklesnqkW 50
                                      ++++   ++++  ++v+   +  ++a + +k++ e +++l++n++ 
  gi|330508811|ref|YP_004385239.1| 28 KVAEAAMQVEESAKQVEIAAQLTENATADLKSAAEHVENLTANTTA 73
                                      55566666667777777778888999*****************986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.065
                              XhlA   7 erietkldnleervdkleekaaeaeekiknle 38 
                                       e++e+k ++ ++      ek +ea +k++++ 
  gi|330508811|ref|YP_004385239.1|  82 EKVEQKAEEASQ----AAEKVDEAAQKAEEAA 109
                                       334444444444....4444444444444444 PP

>> GARP  Glutamic acid/alanine-rich protein of Trypanosoma
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4  36.8       6.5   3.3e+03      23      97 ..      48     122 ..      14     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.5
                              GARP  23 sleeeaaaaaskaskAkarseeaverAesaaendteakelvkrakeaaaeateAaeaAetaasevegeaanlkav 97 
                                       +l e+a+a+ ++a++  ++  +    Ae+  +  ++ ++ +++a +aa+++ eAa++Ae aa++v g+aa l+a+
  gi|330508811|ref|YP_004385239.1|  48 QLTENATADLKSAAEHVENLTANTTAAENITKAAEKVEQKAEEASQAAEKVDEAAQKAEEAAEKVPGFAAALAAL 122
                                       456667777777777777777777777766666666777778888888888888888888888888888888775 PP

>> XRN_M  Xrn1 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   7.1      0.02        10      85     156 ..      27     100 ..       2     116 .. 0.41

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.02
                             XRN_M  85 eredrkekklakeeeaskedaaneeaavaeeklseskvaksaeaeaeaeaeaeaeakaekekr..ekaekelee 156
                                       ++ ++++++ ++++++ + +a+ +e+a+a+ k++ ++v++  +++++ae+ ++a++k e++ +  ++a ++++e
  gi|330508811|ref|YP_004385239.1|  27 DKVAEAAMQVEESAKQVEIAAQLTENATADLKSAAEHVENLTANTTAAENITKAAEKVEQKAEeaSQAAEKVDE 100
                                       33334444444444444444444444444444444444442222222222222222211111100111111111 PP

>> DUF3357  Domain of unknown function (DUF3357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   7.2      0.02        10      24      72 ..       2      47 ..       1     104 [. 0.80
   2 ?    2.4   0.4      0.41   2.1e+02      12      39 ..     102     130 ..      89     135 .] 0.47

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.02
                           DUF3357 24 laavliasalvvlvvlvalagvrlagqaslvapgevavsetaesvsaav 72
                                      + +v+i++a+++l+v+v++a++++  +   va+  ++v+e a++v++a+
  gi|330508811|ref|YP_004385239.1|  2 KNVVVILAAALMLLVAVTTASAEETDK---VAEAAMQVEESAKQVEIAA 47
                                      568899999999999988885433333...5556677777766664433 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.41
                           DUF3357  12 aaaaaararr.pllaavliasalvvlvvl 39 
                                       a++a + a++ p  aa l+a + ++++++
  gi|330508811|ref|YP_004385239.1| 102 AQKAEEAAEKvPGFAAALAALGFLAVAFI 130
                                       23333344443444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3881  (0.216465); expected 358.6 (0.02)
Passed bias filter:                     1338  (0.0746277); expected 358.6 (0.02)
Passed Vit filter:                       244  (0.0136092); 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):              35  [number of targets reported over threshold]
# CPU time: 0.75u 0.37s 00:00:01.12 Elapsed: 00:00:00.50
# Mc/sec: 812.49
//
Query:       gi|330508812|ref|YP_004385240.1|  [L=103]
Description: hypothetical protein MCON_3121, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-14   52.1   3.9    7.9e-14   51.7   3.9    1.2  1  TM2             TM2 domain
    0.00063   19.7   1.0    0.00079   19.4   1.0    1.1  1  DZR             Double zinc ribbon
      0.001   18.4   5.4     0.0015   17.8   5.4    1.2  1  zf-ribbon_3     zinc-ribbon domain
     0.0077   16.3   6.4      0.011   15.8   6.4    1.2  1  UPF0547         Uncharacterised protein family UPF0547
  ------ inclusion threshold ------
        5.8    7.0   7.5        2.8    8.0   2.0    2.2  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon


Domain annotation for each model (and alignments):
>> TM2  TM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   3.9   2.2e-17   7.9e-14       2      44 ..      34      78 ..      33      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 2.2e-17
                               TM2  2 kksklvaylLwffLGglGvHRFYlGktgsGvlqlltfv..Gglgi 44
                                      ++s+++a+lL++fLG+ G+H+FYlG +++G++++l ++   g+ i
  gi|330508812|ref|YP_004385240.1| 34 GRSRITAALLALFLGIAGAHKFYLGSIKMGIIYILISLtaIGFAI 78
                                      689**********************************98744444 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.0   2.2e-07   0.00079       1      25 [.       3      27 ..       3      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.2e-07
                               DZR  1 CpqCgeelppdarfCseCgtklkav 25
                                      Cp+C++ +++ a+ C+ Cg ++k  
  gi|330508812|ref|YP_004385240.1|  3 CPECKSCIDNAAKICPICGLRIKHL 27
                                      9******************998855 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   5.4   4.2e-07    0.0015       5      26 .]       3      24 ..       2      24 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.2e-07
                       zf-ribbon_3  5 CPnCGa.plssddnvCpyCGtkl 26
                                      CP+C++ + +  +++Cp CG ++
  gi|330508812|ref|YP_004385240.1|  3 CPECKScI-DNAAKICPICGLRI 24
                                      ******55.***********986 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   6.4     3e-06     0.011       3      21 ..       3      21 ..       2      23 .. 0.98

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3e-06
                           UPF0547  3 CPeCeakvPvaaqfCphCG 21
                                      CPeC + +  aa++Cp CG
  gi|330508812|ref|YP_004385240.1|  3 CPECKSCIDNAAKICPICG 21
                                      ******************9 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.0   0.00078       2.8      20      27 ..       1       8 [.       1      11 [. 0.87
   2 ?    2.4   0.3     0.044   1.6e+02      16      26 ..      11      21 ..      10      24 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00078
                    PhnA_Zn_Ribbon 20 lvCpeCah 27
                                      ++CpeC++
  gi|330508812|ref|YP_004385240.1|  1 MICPECKS 8 
                                      9*****97 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.044
                    PhnA_Zn_Ribbon 16 dgallvCpeCa 26
                                      d+a  +Cp C+
  gi|330508812|ref|YP_004385240.1| 11 DNAAKICPICG 21
                                      667779**997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 767.85
//
Query:       gi|330508813|ref|YP_004385241.1|  [L=286]
Description: neutral zinc metallopeptidase family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.2e-112  376.1   0.4   1.4e-112  375.9   0.4    1.0  1  Zn_peptidase   Putative neutral zinc metallopeptidase
  ------ inclusion threshold ------
      0.022   14.8   0.0      0.034   14.2   0.0    1.3  1  YolD           YolD-like protein
       0.14   12.5   0.0        0.2   11.9   0.0    1.2  1  Peptidase_M91  Effector protein


Domain annotation for each model (and alignments):
>> Zn_peptidase  Putative neutral zinc metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.9   0.4  2.3e-116  1.4e-112       1     289 [.       1     279 [.       1     280 [. 0.92

  Alignments for each domain:
  == domain 1  score: 375.9 bits;  conditional E-value: 2.3e-116
                      Zn_peptidase   1 mrwrgrresdnvedrrassggegaGGggkgrslggktgllvlilvlvgllfGvdlsallglgqesstaeaaaqsseg 77 
                                       m+wr  r+s+n+edrr ssg++g       +++gg +gl++l+l+l+++++Gvd+ ++++ g + st  ++++s+  
  gi|330508813|ref|YP_004385241.1|   1 MKWRTGRKSENIEDRR-SSGISG-------KAAGGIGGLGILLLLLISMFLGVDPGQIIQ-GID-STGASSQGSQM- 66 
                                       9***************.555533.......234455789********************9.333.33323444443. PP

                      Zn_peptidase  78 taeeaedeqkefvsvvladtedtWtqifk.ekgktyqkpklvlfsrvvrsaCGtassatGPfyCPadrkvyldlsff 153
                                        ++e ++e++efvs vl+dte tW++if+ + g+ty +pklvlfs+ v+saCG+ass +GPfyCP+d+kvyldl+f 
  gi|330508813|ref|YP_004385241.1|  67 -STEEQNESAEFVSLVLGDTEATWSDIFAeDLGRTYIEPKLVLFSGGVQSACGQASSQVGPFYCPSDQKVYLDLEFL 142
                                       .3334699********************9679********************************************* PP

                      Zn_peptidase 154 delkqklgaaGdfaaayviahevGhhvqnllGilekveqarqgaseaeanqlsvrleLqadcfaGvWansvqqkg.l 229
                                       +el+++lga+Gdfa+ayvi+hevGhhvq l+G l+ v+++++  s++ean+lsv leLqadc+aGvWan+++q+  +
  gi|330508813|ref|YP_004385241.1| 143 KELQDRLGATGDFAQAYVISHEVGHHVQTLTGTLQYVDTMNKRVSQKEANELSVALELQADCYAGVWANRASQQDlI 219
                                       ***********************************************************************999978 PP

                      Zn_peptidase 230 lekgdieealnaakaiGddtLqkqsqgrvvPdsfthGtsqqrqrWfkrGfesGdlaqcdt 289
                                       le gdiee lnaa+a+Gdd+Lqkqsqg+vvPdsfthGts+qr+  f++G+esGdl  cd+
  gi|330508813|ref|YP_004385241.1| 220 LEPGDIEEGLNAASAVGDDRLQKQSQGYVVPDSFTHGTSAQRVASFRKGLESGDLFACDS 279
                                       **********************************************************97 PP

>> YolD  YolD-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.7e-06     0.034      21      80 ..     134     193 ..     131     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.7e-06
                              YolD  21 kpeLDeqqleeineklqealeeeqpvtityyedgeleevtgyiekidelnkelkledeed 80 
                                       k  LD + l+e++ +l     + q+  i++   ++++++tg+++++d++nk+++ +++++
  gi|330508813|ref|YP_004385241.1| 134 KVYLDLEFLKELQDRLGATGDFAQAYVISHEVGHHVQTLTGTLQYVDTMNKRVSQKEANE 193
                                       56789999999*****9999*********************************9999876 PP

>> Peptidase_M91  Effector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.4e-05       0.2      21     127 ..      54     191 ..      48     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                     Peptidase_M91  21 LdmlsssptGqqlLeelksskse......gerkltikelvdedngtakyee....................kekgeg 71 
                                       +d  ++s +G+q+ +e +++++e      g+ + t ++++ ed g++  e+                    +  +  
  gi|330508813|ref|YP_004385241.1|  54 IDSTGASSQGSQMSTEEQNESAEfvslvlGDTEATWSDIFAEDLGRTYIEPklvlfsggvqsacgqassqvGPFYCP 130
                                       67778888888888888888888777777666677777655555555555555666666666665555554666678 PP

                     Peptidase_M91  72 tdaeinynpafsseeegkegrPs.....avLyHElaHaydalngtlddgeydgkdeedssg 127
                                       +d+++ ++ +f  e +++ g        +v+ HE+ H  + l+gtl+   + +k+ +++++
  gi|330508813|ref|YP_004385241.1| 131 SDQKVYLDLEFLKELQDRLGATGdfaqaYVISHEVGHHVQTLTGTLQYVDTMNKRVSQKEA 191
                                       889999999988883333333334667688*****************99888877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2140.45
//
Query:       gi|330508814|ref|YP_004385242.1|  [L=376]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-22   78.3   0.1    8.4e-22   76.9   0.1    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.3e-21   75.4   0.0    8.9e-21   74.3   0.0    1.4  1  OrfB_IS605      Probable transposase
    1.4e-15   56.5   2.9    3.5e-15   55.2   2.9    1.7  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0015   18.6   0.3     0.0027   17.7   0.3    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
       0.06   12.9   0.5       0.47   10.0   0.1    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.12   12.1   0.8        0.2   11.3   0.8    1.4  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.18   11.7   0.3       0.18   11.7   0.3    2.0  2  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.22   11.0   0.9        1.2    8.6   0.9    2.1  1  zf-ribbon_3     zinc-ribbon domain
       0.47   10.1   4.9        5.9    6.6   0.1    2.8  3  RecR            RecR protein


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 !   76.9   0.1   4.2e-25   8.4e-22       1      68 [.     293     360 ..     293     361 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 4.2e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++ l +  +yka  +G  v++v+p++TSk Cs+Cg   +++ls+r+++C++Cg+++drD+nAaiNil+
  gi|330508814|ref|YP_004385242.1| 293 WNMLVTLTSYKAASAGSVVVLVDPRNTSKMCSRCGTLIEKSLSDRVHNCTQCGLSMDRDWNAAINILR 360
                                       667777889*********************************************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   4.5e-24   8.9e-21       4     117 ..     168     279 ..     165     281 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 4.5e-24
                        OrfB_IS605   4 veveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       ve e+  lp+ k + ++giD+G++ +at ++++   ++ ++r++++++ +la+++++l++  k++  +kka + + r
  gi|330508814|ref|YP_004385242.1| 168 VETEDVpLPPWKDGAVVGIDVGLESFATFSNGE---TIANPRFFREEEHELARAQRKLSKAPKGTPDRKKALKVVER 241
                                       5544334999999********************...***************************************** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       +h++++++r +++h+++++l+++   +  e+Ln+++m+
  gi|330508814|ref|YP_004385242.1| 242 VHERIANKRYEFAHQVSHNLVDRFGLISFEDLNIKGMV 279
                                       *************************************7 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   2.9   1.7e-18   3.5e-15       1      47 []       1      46 [.       1      46 [. 0.99

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.7e-18
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lka k+rlyPT+ Q +k++rt   +R+ YN+ La+rk+a+e+egk
  gi|330508814|ref|YP_004385242.1|  1 M-LKACKFRLYPTKSQITKMERTPNLCRWTYNQTLAYRKNAWENEGK 46
                                      8.9*****************************************998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   1.3e-06    0.0027      10      44 ..     318     354 ..     314     357 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + +++Cs+Cgt +++  +   ++C +Cg ++d +++ 
  gi|330508814|ref|YP_004385242.1| 318 NTSKMCSRCGTLIEKSLSdrVHNCTQCGLSMDRDWNA 354
                                       6789*********9777799************99986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00024      0.47      11      31 ..     312     332 ..     308     337 .. 0.84
   2 ?    0.4   0.1      0.23   4.6e+02      22      28 ..     341     347 ..     339     351 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00024
                                       CHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon  11 lveDpergelvCtdCGlVled 31 
                                       +++Dp ++   C++CG+++e 
  gi|330508814|ref|YP_004385242.1| 312 VLVDPRNTSKMCSRCGTLIEK 332
                                       68999*9999*********96 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.23
                                       ESSSSBE CS
                      TF_Zn_Ribbon  22 CtdCGlV 28 
                                       Ct CGl 
  gi|330508814|ref|YP_004385242.1| 341 CTQCGLS 347
                                       *****85 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.8    0.0001       0.2       6      29 ..     323     346 ..     318     348 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                     zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCgl 29 
                                       C+rCG+  e++  ++   C +Cgl
  gi|330508814|ref|YP_004385242.1| 323 CSRCGTLIEKSLSDRVHNCTQCGL 346
                                       ***********************8 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.84   1.7e+03      37      45 ..     278     286 ..     276     289 .. 0.82
   2 ?   11.7   0.3   8.9e-05      0.18      10      38 ..     319     348 ..     315     351 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.84
                                       EE-CCCCTT CS
                              C1_1  37 lvHkkChek 45 
                                        vH++C+ k
  gi|330508814|ref|YP_004385242.1| 278 MVHNHCLAK 286
                                       59****876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 8.9e-05
                                       S--B-TTT-SB--S.SSS-EEEETTT--EE CS
                              C1_1  10 qptfCkhCgeflwg.kekqglkCswCkllv 38 
                                        ++ C+ Cg ++++ ++ +   C++C+l++
  gi|330508814|ref|YP_004385242.1| 319 TSKMCSRCGTLIEKsLSDRVHNCTQCGLSM 348
                                       5789********999***********9976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.9   0.00062       1.2       5      24 ..     323     346 ..     320     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00062
                       zf-ribbon_3   5 CPnCGa.p...lssddnvCpyCGt 24 
                                       C++CG+ +   ls+++ +C+ CG 
  gi|330508814|ref|YP_004385242.1| 323 CSRCGTlIeksLSDRVHNCTQCGL 346
                                       999997555557899*******96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.6   5.2e+03       6      16 ..      72      82 ..      72      83 .. 0.87
   2 ?    6.6   0.1     0.003       5.9      13      28 ..     317     332 ..     312     334 .. 0.77
   3 ?    5.4   0.3    0.0069        14      12      26 ..     334     348 ..     332     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.6
                                      HHHHHHHHHH- CS
                              RecR  6 aeaLqeakekv 16
                                      a++Lq++ e+v
  gi|330508814|ref|YP_004385242.1| 72 AQTLQNVQERV 82
                                      7899**99987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.003
                                       HHH-EE-TTT--EESS CS
                              RecR  13 kekvrhCsrCgnltee 28 
                                       +++ + CsrCg+l e+
  gi|330508814|ref|YP_004385242.1| 317 RNTSKMCSRCGTLIEK 332
                                       667799******9776 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0069
                                       HHHH-EE-TTT--EE CS
                              RecR  12 akekvrhCsrCgnlt 26 
                                       + ++v+ C +Cg   
  gi|330508814|ref|YP_004385242.1| 334 LSDRVHNCTQCGLSM 348
                                       679********9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2533.75
//
Query:       gi|330508815|ref|YP_004385243.1|  [L=91]
Description: DNA-directed RNA polymerase subunit L [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-18   65.9   0.0    2.8e-18   65.5   0.0    1.2  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
    1.6e-05   24.3   0.0    2.3e-05   23.7   0.0    1.3  1  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   3.1e-22   2.8e-18       2      74 ..      13      84 ..      12      85 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 3.1e-22
                                      EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHHH CS
                       RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicdelee 74
                                      + +e+ gE hT++nlLr++llk+++V +a+Y+ ++P  ++  +r  t+ + +p+ aLk+a ++++d+cde+++
  gi|330508815|ref|YP_004385243.1| 13 AVIEFVGEGHTILNLLRTELLKDKRVLMATYDTKFPVMDNPVFRLVTN-GADPIIALKEATSRIIDQCDEFSS 84
                                      6799*******************************************7.69*******************986 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.6e-09   2.3e-05       3      69 .]      16      79 ..      14      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.6e-09
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  3 llrgvdhtlgNaLRrillsevpgvaiea.....pvvkvntdkdklilevetdgslkPeealkeAlkiLkekl 69
                                      ++ g++ht+ N LR  ll +   v +++     pv       d+ +++  t+g+ +P  alkeA   +++++
  gi|330508815|ref|YP_004385243.1| 16 EFVGEGHTILNLLRTELL-KDKRVLMATydtkfPV------MDNPVFRLVTNGA-DPIIALKEATSRIIDQC 79
                                      5689**************.7777777777999999......89999*******9.9*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 665.49
//
Query:       gi|330508816|ref|YP_004385244.1|  [L=186]
Description: hypothetical protein MCON_3128 [Methanosaeta concilii GP6]
Scores for complete 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   38.5   0.1    1.3e-09   37.7   0.1    1.4  1  ECR1_N         Exosome complex exonuclease RRP4 N-terminal re
    0.00097   19.2   1.5     0.0016   18.6   1.5    1.3  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
     0.0083   16.3   0.7      0.016   15.3   0.7    1.4  1  NOB1_Zn_bind   Nin one binding (NOB1) Zn-ribbon like
  ------ inclusion threshold ------
      0.032   14.8   0.1      0.061   13.9   0.1    1.5  1  EXOSC1         Exosome component EXOSC1/CSL4
      0.045   13.8   0.3      0.074   13.1   0.3    1.3  1  DZR            Double zinc ribbon
      0.064   13.3   0.1        0.1   12.7   0.1    1.3  1  Zn_Tnp_IS91    Transposase zinc-binding domain
      0.083   12.9   0.5       0.14   12.2   0.6    1.4  1  HypA           Hydrogenase/urease nickel incorporation, metal
      0.084   13.3   0.4        1.2    9.6   0.0    2.6  3  ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L
       0.25   11.1   1.0        2.9    7.6   0.0    2.2  2  zf-RRN7        Zinc-finger of RNA-polymerase I-specific TFIIB
        0.4   10.7   1.4       0.99    9.4   1.4    1.6  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
        4.9    7.2   6.4         12    5.9   5.5    2.2  2  DUF1610        Domain of unknown function (DUF1610)
        5.4    6.6   6.6       0.87    9.1   1.0    2.0  2  zf-ribbon_3    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1   8.5e-13   1.3e-09       1      37 [.       6      42 ..       6      43 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 8.5e-13
                                      EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEEE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGtvev 37
                                      +V+PG+++++ eef++G  TY r+g i+A+ aG v+v
  gi|330508816|ref|YP_004385244.1|  6 FVLPGDTVGSLEEFVPGDYTYAREGMIFATTAGLVKV 42
                                      7**********************************97 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.5   1.1e-06    0.0016      16      40 .]     148     170 ..     146     170 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                     Auto_anti-p27  16 etCpvCgvPLmrdrkggkvyCvaCd 40 
                                       ++C +C + Lmr  k+gk++C++C+
  gi|330508816|ref|YP_004385244.1| 148 AYCNRCLTGLMR--KEGKLICPNCG 170
                                       69**********..689*******6 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.7   1.1e-05     0.016      10      38 ..     149     178 ..     145     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                      NOB1_Zn_bind  10 rChaCfk.vtkdmtkkFCpkCGnktLkrva 38 
                                        C  C + ++++  k  Cp+CGn+  ++++
  gi|330508816|ref|YP_004385244.1| 149 YCNRCLTgLMRKEGKLICPNCGNNETRKMS 178
                                       588888856799************999987 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.1e-05     0.061       4      51 ..      63     115 ..      58     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                                       TT-EEEEEEEEEESSEEEEEEEEECTB.....SBCCCEEECCCTTSS--STST CS
                            EXOSC1   4 egdvVLarvtrlrkkqalveilsvege.....nnvlsdsgvgangegavkeie 51 
                                        gd+V + v++l+ + ++v++  ++g          +  +++++++++vk+++
  gi|330508816|ref|YP_004385244.1|  63 HGDIVVGEVIDLKDSLVIVSLAFKKGYedrpiSDEEATIHISNVKNSYVKDLR 115
                                       59**********************99864444334445789999999998863 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3     5e-05     0.074      13      37 ..     148     172 ..     142     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5e-05
                               DZR  13 rfCseCgtklkavaaedrCpsCgek 37 
                                        +C++C t l + + +  Cp+Cg  
  gi|330508816|ref|YP_004385244.1| 148 AYCNRCLTGLMRKEGKLICPNCGNN 172
                                       69********99999*******986 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 ?   12.7   0.1   6.8e-05       0.1      17      72 ..     125     178 ..     106     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.8e-05
                       Zn_Tnp_IS91  17 rpsqrkavekilrCrtaalGfaryeCeeCghekivyfsCksrhCpsCqkkateewl 72 
                                       + ++ ++ +  l+ ++++lG+ +  C+ C   + ++ + ++  Cp+C++++t+++ 
  gi|330508816|ref|YP_004385244.1| 125 KAKIVDERQMRLSTGDEDLGVIKAYCNRCL--TGLMRKEGKLICPNCGNNETRKMS 178
                                       5556666667788899*************7..45667777888********99876 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.6   9.3e-05      0.14      69      98 ..     146     175 ..      97     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.3e-05
                                       -EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA  69 vkvrCreCgkefeleekalrCpkCgsadve 98 
                                       +k++C++C +    +e +l Cp+Cg+++++
  gi|330508816|ref|YP_004385244.1| 146 IKAYCNRCLTGLMRKEGKLICPNCGNNETR 175
                                       5789*****88887754799*****99876 PP

>> ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.8   5.6e+03      34      46 ..      51      63 ..      49      65 .. 0.81
   2 ?    9.6   0.0   0.00079       1.2      19      32 ..      94     107 ..      86     113 .. 0.87
   3 ?    0.4   0.0      0.61   9.2e+02      33      43 ..     164     175 ..     163     178 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.8
                     ribosomal_L24 34 vdpkcgkptrvgf 46
                                      v pk++ p+++ +
  gi|330508816|ref|YP_004385244.1| 51 VIPKTNAPVKLNH 63
                                      6699999999876 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00079
                     ribosomal_L24  19 iiekEapIhvSnVm 32 
                                       i ++Ea Ih+SnV+
  gi|330508816|ref|YP_004385244.1|  94 ISDEEATIHISNVK 107
                                       7789*********6 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.61
                     ribosomal_L24  33 lvdpkcgkp.tr 43 
                                       l++p+cg   tr
  gi|330508816|ref|YP_004385244.1| 164 LICPNCGNNeTR 175
                                       99****754365 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.4      0.14   2.2e+02      23      28 ..     149     154 ..     148     155 .. 0.86
   2 ?    7.6   0.0     0.002       2.9      19      31 ..     161     173 ..     160     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.14
                           zf-RRN7  23 yCrrCh 28 
                                       yC+rC 
  gi|330508816|ref|YP_004385244.1| 149 YCNRCL 154
                                       9****6 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.002
                           zf-RRN7  19 dGfyyCrrChtqe 31 
                                       +G+ +C +C++ e
  gi|330508816|ref|YP_004385244.1| 161 EGKLICPNCGNNE 173
                                       6889999999865 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 ?    9.4   1.4   0.00066      0.99      16      33 ..     160     178 ..     148     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00066
                     Zn_Tnp_IS1595  16 png.fvCPhCgsrkayrik 33 
                                       ++g  +CP+Cg+ + ++++
  gi|330508816|ref|YP_004385244.1| 160 KEGkLICPNCGNNETRKMS 178
                                       445478******9888876 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.3   1.9e+03       7      18 ..      93     103 ..      92     103 .. 0.82
   2 ?    5.9   5.5    0.0084        12      18      24 .]     165     171 ..     150     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
                           DUF1610   7 elaprEravvFp 18 
                                       ++ ++E a++++
  gi|330508816|ref|YP_004385244.1|  93 PISDEE-ATIHI 103
                                       788999.**985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0084
                           DUF1610  18 pCPNCGE 24 
                                       +CPNCG+
  gi|330508816|ref|YP_004385244.1| 165 ICPNCGN 171
                                       7*****7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   7.0     0.026        39      13      24 ..     160     171 ..     146     172 .. 0.63
   2 ?    9.1   1.0   0.00058      0.87       4      11 ..     165     172 ..     162     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.026
                       zf-ribbon_3  13 ssddnvCpyCGt 24 
                                       +++  +Cp+CG 
  gi|330508816|ref|YP_004385244.1| 160 KEGKLICPNCGN 171
                                       667777888875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00058
                       zf-ribbon_3   4 rCPnCGap 11 
                                        CPnCG++
  gi|330508816|ref|YP_004385244.1| 165 ICPNCGNN 172
                                       58888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1431.95
//
Query:       gi|330508817|ref|YP_004385245.1|  [L=198]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete 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   60.2   0.0    2.4e-16   59.7   0.0    1.1  1  MTS              Methyltransferase small domain
    1.3e-13   51.0   0.1      2e-13   50.4   0.1    1.2  1  Methyltransf_31  Methyltransferase domain
    1.5e-12   48.0   0.1    2.4e-12   47.4   0.1    1.3  1  Methyltransf_25  Methyltransferase domain
    6.7e-11   42.2   1.9    4.7e-10   39.5   1.9    1.9  1  UPF0020          Putative RNA methylase family UPF0020
    1.8e-10   40.7   0.7    2.4e-10   40.3   0.7    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.7e-09   38.2   0.0    2.6e-09   37.6   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    2.8e-06   27.1   0.0    3.9e-06   26.6   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    7.5e-06   25.9   0.0    8.8e-06   25.6   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.3e-05   24.8   0.0    1.9e-05   24.3   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    2.4e-05   25.0   0.1    3.9e-05   24.3   0.1    1.4  1  Methyltransf_12  Methyltransferase domain
     0.0003   20.4   0.0    0.00046   19.9   0.0    1.2  1  NodS             Nodulation protein S (NodS)
    0.00033   20.0   0.1       0.04   13.2   0.0    2.1  2  CMAS             Mycolic acid cyclopropane synthetase
    0.00041   20.4   0.0    0.00051   20.1   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
    0.00047   19.8   0.0    0.00061   19.4   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
     0.0097   15.8   0.1      0.015   15.2   0.1    1.2  1  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.013   15.2   0.0    1.3  1  Met_10           Met-10+ like-protein
      0.015   15.0   0.0       0.17   11.6   0.0    2.0  2  N6_N4_Mtase      DNA methylase
      0.016   14.6   0.0      0.021   14.2   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.017   14.6   0.1       0.16   11.4   0.1    2.0  2  Methyltransf_4   Putative methyltransferase
      0.019   14.7   0.0      0.025   14.4   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.066   12.3   0.0       0.08   12.0   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.091   12.3   0.0       0.12   11.8   0.0    1.3  1  DOT1             Histone methylation protein DOT1
       0.12   11.6   0.0       0.54    9.5   0.0    1.8  1  N6_Mtase         N-6 DNA Methylase
       0.13   11.6   0.0       0.18   11.1   0.0    1.3  1  Methyltransf_10  RNA methyltransferase


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   3.2e-19   2.4e-16      22     126 ..      37     135 ..      31     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 3.2e-19
                                       HHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-E CS
                               MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkf 98 
                                       l+l +l ++l g+v DlGcG+Gvl++ +a +  +   + v++d+ Al+ a++n+e+ +++v+++  dv +    + +
  gi|330508817|ref|YP_004385245.1|  37 LFLAALRNDL-GTVCDLGCGTGVLAIGAALMGAR--AVGVEIDKDALATARKNAENLGVHVDFIRADVRKLEL-EGI 109
                                       6788899955.57***************999888..799****************************987666.9** PP

                                       EEEEE---STTTCHCHHHHHHHHHHHHH CS
                               MTS  99 dlivsNPPfhagkatelavaeeliaeAk 126
                                       d++++NPPf a+ka e    ++++ +A+
  gi|330508817|ref|YP_004385245.1| 110 DTVIMNPPFGAQKASE--GDRAFLSTAQ 135
                                       ************9944..4455666655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.1   2.6e-16     2e-13       6      84 ..      48     118 ..      44     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2.6e-16
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       +v+DlGCGtG l++ +a ++  +a+ vG++i+++a+  Ar+na++lg+  v F ++d+ +le  l  e +D ++ n 
  gi|330508817|ref|YP_004385245.1|  48 TVCDLGCGTGVLAIGAA-LM--GARAVGVEIDKDALATARKNAENLGVH-VDFIRADVRKLE--L--EGIDTVIMNP 116
                                       79***************.65..6899**********************6.***********9..4..57****9996 PP

                   Methyltransf_31  83 vl 84 
                                       ++
  gi|330508817|ref|YP_004385245.1| 117 PF 118
                                       66 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.1   3.2e-15   2.4e-12       1      92 [.      49     137 ..      49     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 3.2e-15
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhh 76 
                                       v dlGcGtG l++ +a   g a+ +gv+i++++l++ar++ae+ g++v+f+++d+++l++e   +D v+++   +  
  gi|330508817|ref|YP_004385245.1|  49 VCDLGCGTGVLAIGAALM-G-ARAVGVEIDKDALATARKNAENLGVHVDFIRADVRKLELEG--IDTVIMN-PpFGA 120
                                       79*************988.5.*************************************9886..9***995.44766 PP

                                       .SSHHHHHHHHHHHHHH CS
                   Methyltransf_25  77 .lsdedlekalkeiarv 92 
                                           e  +++l+ + r+
  gi|330508817|ref|YP_004385245.1| 121 qKASEGDRAFLSTAQRI 137
                                       33333345566666665 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   1.9   6.3e-13   4.7e-10      17     140 ..      33     127 ..      26     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 6.3e-13
                                       HHHHHHHTT--TT.S-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHH CS
                           UPF0020  17 Aaalvrlagwkpg.epllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqga 92 
                                       Aa ++ la ++++  +  D  CG+G ++I aal+ga+++                          g+++d+ ++++a
  gi|330508817|ref|YP_004385245.1|  33 AAEILFLAALRNDlGTVCDLGCGTGVLAIGAALMGARAV--------------------------GVEIDKDALATA 83 
                                       666666666665534667777*****************9..........................************ PP

                                       HHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHH CS
                           UPF0020  93 reNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskka 140
                                       r+Nae+ gv   ++f  ad++kL+  eg +d+++ npP+G    s+++
  gi|330508817|ref|YP_004385245.1|  84 RKNAENLGV--HVDFIRADVRKLE-LEG-IDTVIMNPPFGAQKASEGD 127
                                       *****9887..599**********.885.***********98776655 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.7   3.2e-13   2.4e-10     159     233 ..      43     115 ..      33     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 3.2e-13
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadvivaN 233
                                        +   +v D+G+G+G+Lai+aa++ga+ +v+v iD+ A+  a++Nae  +v+  + + +  + l+ e +d ++ N
  gi|330508817|ref|YP_004385245.1|  43 RNDLGTVCDLGCGTGVLAIGAALMGAR-AVGVEIDKDALATARKNAENLGVHVDF-IRADVRKLELEGIDTVIMN 115
                                       445569*******************96.68*****************99999877.4444444445667777766 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   3.5e-12   2.6e-09       2      68 ..      51     115 ..      50     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3.5e-12
                                       EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEE CS
                   Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvss 68 
                                       d+GcGtG la   a  gar vgv+++k +l++a+++a++ g++v+f++ad++kl +e   +D v+++
  gi|330508817|ref|YP_004385245.1|  51 DLGCGTGVLAIGAALMGARAVGVEIDKDALATARKNAENLGVHVDFIRADVRKLELEG--IDTVIMN 115
                                       9****************************************************88876..8888776 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   5.2e-09   3.9e-06      44     145 ..      48     140 ..      33     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5.2e-09
                                       EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE- CS
                     Cons_hypoth95  44 rvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflD 120
                                       +v Dl +G+G+l++ A+  g ++av ve dk a+++ ++n e+l+++     +++ ++++l+ +      +d v ++
  gi|330508817|ref|YP_004385245.1|  48 TVCDLGCGTGVLAIGAALMG-ARAVGVEIDKDALATARKNAENLGVH---VDFIRADVRKLELE-----GIDTVIMN 115
                                       678*****************.57899*******************65...56666666666555.....48****** PP

                                       -SSSTTCH.HHHHHHHHHTT-EEEE CS
                     Cons_hypoth95 121 PPyakellieevlelleekkllken 145
                                       PP+ ++++ e   + l + + +++n
  gi|330508817|ref|YP_004385245.1| 116 PPFGAQKASEGDRAFLSTAQRIARN 140
                                       ****999866666666666666655 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.2e-08   8.8e-06       8      62 ..      31      95 ..      22     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.2e-08
                   Methyltransf_23  8 elsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..........k 62
                                       +++++++l++ ++  g v+d+GcGtG l+  ++  g+  +gv+++  a + a+           
  gi|330508817|ref|YP_004385245.1| 31 SVAAEILFLAALRNDLGTVCDLGCGTGVLAIGAALMGARAVGVEIDKDALATARknaenlgvhvD 95
                                      567899*****9*********************************98887777644444444440 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 !   24.3   0.0   2.5e-08   1.9e-05       3      84 ..      48     121 ..      46     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.5e-08
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSp 79 
                                       ++ Dl +G+G  +i  al++ + +++ei+++ la a +Nae  gv  +++++ +dv    +kl+le i  d v++ p
  gi|330508817|ref|YP_004385245.1|  48 TVCDLGCGTGVLAIGAALMGARAVGVEIDKDALATARKNAENLGV--HVDFIRADV----RKLELEGI--DTVIMNP 116
                                       578**************************************9987..699999996....67788888..9****** PP

                   Methyltransf_15  80 PwGGp 84 
                                       P G  
  gi|330508817|ref|YP_004385245.1| 117 PFGAQ 121
                                       *9965 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   5.3e-08   3.9e-05       2      73 ..      51     115 ..      50     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.3e-08
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas 73 
                                       ++GcGtG l+   +    +++ +gv+i+++a+ ++++k a++ + ++++++ +++ l+ +      D+v+++
  gi|330508817|ref|YP_004385245.1|  51 DLGCGTGVLAIGAALM--GARAVGVEIDKDAL-ATARKNAENLGVHVDFIRADVRKLELE----GIDTVIMN 115
                                       89*****999998888..**************.999999999999999999999986543....89****97 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   6.1e-07   0.00046      32     111 ..      34     113 ..      24     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.1e-07
                              NodS  32 aqilrlslaqgsiadalevGcaaGalterlapyckrltvvdvveeaiararervkes.shiswivsdvqqfstdekf 107
                                       a+il l+   ++++ + ++Gc +G l+   a +  r   v++ ++a+a ar+  ++   h+ +i +dv++++++   
  gi|330508817|ref|YP_004385245.1|  34 AEILFLAALRNDLGTVCDLGCGTGVLAIGAALMGARAVGVEIDKDALATARKNAENLgVHVDFIRADVRKLELEG-I 109
                                       57889999999******************************************998636***********99864.4 PP

                              NodS 108 dliv 111
                                       d+++
  gi|330508817|ref|YP_004385245.1| 110 DTVI 113
                                       5555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   5.3e-05      0.04      65     111 ..      48      93 ..      32     115 .. 0.85
   2 ?    5.0   0.0     0.017        13     174     192 ..     143     160 ..     119     166 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                                       EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SS CS
                              CMAS  65 tlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldle 111
                                       t+ d+GcG G l++ a+   +++ vg+ + k+  ++a+k+ ++l+++
  gi|330508817|ref|YP_004385245.1|  48 TVCDLGCGTGVLAIGAALM-GARAVGVEIDKDALATARKNAENLGVH 93 
                                       789***********99988.*********************999965 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.017
                                       HHHCTTCCCHHHHHHTSTT CS
                              CMAS 174 elaerglklkfidkeiFPg 192
                                       +l++rg +  fi+k+iFP+
  gi|330508817|ref|YP_004385245.1| 143 TLHNRGSH-DFIKKYIFPN 160
                                       44545544.9********7 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.8e-07   0.00051      24      87 ..      44      99 ..      24     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.8e-07
                   Methyltransf_32 24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfael 87
                                      ++  tv+D+G+G g L+   al    ++ + vg+++ ++  ++a+k ae+lg     ++ f+ +
  gi|330508817|ref|YP_004385245.1| 44 NDLGTVCDLGCGTGVLAIGAAL----MGARAVGVEIDKDALATARKNAENLGV----HVDFIRA 99
                                      55679***************99....79************************4....4444444 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   8.2e-07   0.00061      10     104 ..      42     140 ..      34     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.2e-07
                              MetW  10 likpgsrvldlGcGdGellellkeekqvdgrGleldeegvaec..vakGlsviqgdldkdlenfedksfdyvvlsqt 84 
                                       l ++  +v dlGcG G l  + +   + ++ G+e+d++++a +   a  l v+ + +  d+ + e +  d v+++  
  gi|330508817|ref|YP_004385245.1|  42 LRNDLGTVCDLGCGTGVL-AIGAALMGARAVGVEIDKDALATArkNAENLGVHVDFIRADVRKLELEGIDTVIMNPP 117
                                       5567789*********86.566677999********99998772256789999999******************987 PP

                              MetW  85 lqatrn...pkevldellrigrr 104
                                       + a +     +  l+   ri+r+
  gi|330508817|ref|YP_004385245.1| 118 FGAQKAsegDRAFLSTAQRIARN 140
                                       65544311145677888888765 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     2e-05     0.015      14      87 ..      45     113 ..      36     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                   Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvv 87 
                                       +  +v+D G+  g+l+i ++  g   +++ ++i + +l++a++n+e+ g+  +++++ +d   kl+ e +dtv+
  gi|330508817|ref|YP_004385245.1|  45 DLGTVCDLGCGTGVLAIGAALMG--ARAVGVEIDKDALATARKNAENLGV--HVDFIRADV-RKLELEGIDTVI 113
                                       45589*************99766..57*******************9988..577777665.444433466666 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.8e-05     0.013      94     180 ..      39     120 ..      30     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                                       HHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EE CS
                            Met_10  94 laklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqlad 170
                                       la+l ++  +V+d+  G G +ai +a    + r ++++++ ++    ++n +   +   v  i +D+r++   + +d
  gi|330508817|ref|YP_004385245.1|  39 LAALRNDLGTVCDLGCGTGVLAIGAAL--MGARAVGVEIDKDALATARKNAEN--LGVHVDFIRADVRKLE-LEGID 110
                                       5666677789****************9..666679**************9874..6667889********8.6778* PP

                                       EEEE--TTTG CS
                            Met_10 171 rvvmnlpksa 180
                                        v+mn p  a
  gi|330508817|ref|YP_004385245.1| 111 TVIMNPPFGA 120
                                       *****98665 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00022      0.17     186     229 ..      40      83 ..       8      85 .. 0.80
   2 ?    1.6   0.0      0.25   1.9e+02       1      44 [.     109     143 ..     109     180 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                                       HHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHH CS
                       N6_N4_Mtase 186 klstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvela 229
                                        ++ ++ ++v D  +G+G  a+ a+ +g +++G+ei++ ++ +a
  gi|330508817|ref|YP_004385245.1|  40 AALRNDLGTVCDLGCGTGVLAIGAALMGARAVGVEIDKDALATA 83 
                                       445555689****************************9987766 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.25
                                       EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHH CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrr 44 
                                       +d+++  pP++++k          ++   ++l+  ++++++++ 
  gi|330508817|ref|YP_004385245.1| 109 IDTVIMNPPFGAQKA---------SEGDRAFLSTAQRIARNIYT 143
                                       799*********999.........33334555555555555554 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.8e-05     0.021      50     133 ..      48     127 ..      36     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.8e-05
                                       EEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-G CS
                   Ubie_methyltran  50 kvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGl 126
                                       +v D+ +Gtg la+  +  +g   + v+++i+++ L +++k +++ g+ +++f+ a+  +L+ e     ++   fG 
  gi|330508817|ref|YP_004385245.1|  48 TVCDLGCGTGVLAIGAA-LMG--ARAVGVEIDKDALATARKNAENLGV-HVDFIRADVRKLELEGIDTVIMNPPFGA 120
                                       789*********99854.334..457899****************997.7***********9987444455556666 PP

                                       GG-S-HH CS
                   Ubie_methyltran 127 rnvtDkl 133
                                       +  ++ +
  gi|330508817|ref|YP_004385245.1| 121 QKASEGD 127
                                       6666555 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00022      0.16       4      51 ..      48      93 ..      46     111 .. 0.87
   2 ?    0.8   0.0      0.39   2.9e+02      47      78 ..     135     167 ..     123     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTS CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelk 51
                                      +v+++GcG G + +  A + +    +G+Ei ++ +a++ k++e+l+++
  gi|330508817|ref|YP_004385245.1| 48 TVCDLGCGTGVLAIGAALMGA--RAVGVEIDKDALATARKNAENLGVH 93
                                      589*******99999999877..579***************9999775 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.39
                                       HCTTSSEEEEES-C.CCHHHHCS-TTSEEEEEE CS
                    Methyltransf_4  47 alelkNlrilrgda.lkvllelledgslekifi 78 
                                       ++ ++N++ l++    +++++++ ++ +++++ 
  gi|330508817|ref|YP_004385245.1| 135 QRIARNIYTLHNRGsHDFIKKYIFPNVVQEVYC 167
                                       55678999888777699************9984 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.3e-05     0.025      62     132 ..      32     100 ..      20     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHTT.--T.T-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT  62 valalelle.lkk.garvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                       va+ + +l  l++    v ++G+G+G l+ + a l+g+++  v++e  k+  ++a++n ++l+++ v ++ +D
  gi|330508817|ref|YP_004385245.1|  32 VAAEILFLAaLRNdLGTVCDLGCGTGVLA-IGAALMGARA--VGVEIDKDALATARKNAENLGVH-VDFIRAD 100
                                       4444444444544145799*******995.6777888766..9******************9986.4444444 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.08       9      94 ..      23     110 ..      16     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                       G--EE--HHHHHHHHHHH-GGTTS.EEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S CS
                            RrnaAD   9 gqnflknkkvineIldklnleekl.tvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.kdeklkvvhq 83 
                                         ++ +  +v++eIl  + l+++l tv ++g G+G+l    a +    v +E+d++ ++  +k+ + ++  +  + +
  gi|330508817|ref|YP_004385245.1|  23 REQYATPASVAAEILFLAALRNDLgTVCDLGCGTGVLAIGAALMGARAVGVEIDKDALATARKNAEnLGVHVDFIRA 99 
                                       5688888999***********77648***********999999999**********999999977778888888999 PP

                                       -CCGHHHHHHH CS
                            RrnaAD  84 Dflkfetpeev 94 
                                       D+ k e+    
  gi|330508817|ref|YP_004385245.1| 100 DVRKLELEGID 110
                                       99998876644 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.12      46     104 ..      49     105 ..      20     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                                       EEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTTB----EE CS
                              DOT1  46 FvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlklfGkklakie 104
                                         DLG G G + + aal  g + +vGvEi ++a + a+k++e l  ++++   ++ k+e
  gi|330508817|ref|YP_004385245.1|  49 VCDLGCGTGVLAIGAALM-GAR-AVGVEIDKDALATARKNAENLGVHVDFIRADVRKLE 105
                                       68*******988887775.444.7****************9999888777666666655 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00072      0.54      27     140 ..      25     123 ..      17     154 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00072
                          N6_Mtase  27 effTPrevsklivell..epksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhg 101
                                       ++ TP +v   i  l+   +  g +v D  cG+g l + a+ +              G+e+++ + + a+ N    g
  gi|330508817|ref|YP_004385245.1|  25 QYATPASVAAEILFLAalRNDLG-TVCDLGCGTGVLAIGAALM---------GARAVGVEIDKDALATARKNAENLG 91 
                                       67788888776665553244445.4888888888887777653.........4566788888888888888876555 PP

                          N6_Mtase 102 ieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqkew 140
                                       ++++      +d     k  + + +d+v+ Nppf++++ 
  gi|330508817|ref|YP_004385245.1|  92 VHVD---FIRADVR---KL-ELEGIDTVIMNPPFGAQKA 123
                                       5555...2333322...22.3678**********99843 PP

>> Methyltransf_10  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00024      0.18     107     193 ..      50     124 ..      38     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                                       EEES-TTTTHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHHT.T-TTTEEEEE--TT-SCCHHSSTTSS-EEEEEE CS
                   Methyltransf_10 107 ldiGvGanCiyPllGvteyGWrfvgsevddvslasakaivesnsklsdaiklrkqkekkaifdglieenerydvtlC 183
                                        d+G G+  +   +G+ + G r vg e+d+ +la+a+++ e   +l  ++   +   +k  ++g+       d ++ 
  gi|330508817|ref|YP_004385245.1|  50 CDLGCGTGVL--AIGAALMGARAVGVEIDKDALATARKNAE---NLGVHVDFIRADVRKLELEGI-------DTVIM 114
                                       5667766655..59***********************9865...488899999988888877776.......77888 PP

                                       -S---SS--- CS
                   Methyltransf_10 184 nPPfhaslae 193
                                       nPPf a++a 
  gi|330508817|ref|YP_004385245.1| 115 NPPFGAQKAS 124
                                       9999876543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1417.84
//
Query:       gi|330508818|ref|YP_004385246.1|  [L=786]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-30  105.4   7.5    1.9e-11   44.1   0.2    5.6  6  TPR_12    Tetratricopeptide repeat
    1.3e-21   75.4   4.5    0.00021   21.0   0.1    6.7  6  TPR_1     Tetratricopeptide repeat
    1.3e-20   71.8  15.0    6.5e-05   22.7   0.1    7.6  6  TPR_7     Tetratricopeptide repeat
    6.6e-20   69.6  10.0     0.0015   18.5   0.5    7.5  6  TPR_2     Tetratricopeptide repeat
    2.8e-16   58.3  11.3      0.084   13.1   0.0    7.3  7  TPR_8     Tetratricopeptide repeat
    5.6e-13   48.3  17.0     0.0054   16.6   0.1    7.7  8  TPR_10    Tetratricopeptide repeat
    6.3e-09   35.6   2.3    0.00048   19.6   0.1    2.9  3  TPR_MalT  MalT-like TPR region
    5.8e-07   29.1   1.1     0.0001   21.9   0.0    3.9  3  TPR_11    TPR repeat
    2.3e-06   27.9  18.8       0.21   12.5   0.0    8.0  7  TPR_14    Tetratricopeptide repeat
    1.4e-05   25.7  13.3      0.065   13.9   2.9    6.1  6  TPR_16    Tetratricopeptide repeat
    2.1e-05   24.3   1.4     0.0022   17.7   0.1    3.9  3  RPN7      26S proteasome subunit RPN7
    0.00012   21.6   8.4     0.0026   17.3   0.3    3.4  4  SNAP      Soluble NSF attachment protein, SNAP
    0.00048   20.6  11.9         13    6.6   0.0    7.0  7  TPR_6     Tetratricopeptide repeat
     0.0015   18.7   4.0       0.91   10.1   0.2    4.7  4  TPR_17    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.022   15.0   0.0        0.1   12.8   0.0    2.1  1  Coat_F    Coat F domain
      0.029   13.9   5.6        1.7    8.1   0.0    3.1  3  SPO22     Meiosis protein SPO22/ZIP4 like
      0.055   13.3   0.3         11    5.9   0.0    3.2  3  Clathrin  Region in Clathrin and VPS
      0.071   13.7   0.1         37    5.0   0.0    3.8  3  DUF4810   Domain of unknown function (DUF4810)
      0.089   12.9  10.0          2    8.7   0.1    5.5  5  TPR_9     Tetratricopeptide repeat
      0.096   12.3   0.0        7.1    6.3   0.0    3.1  3  TAP_C     TAP C-terminal domain
       0.19   11.9   0.7        2.3    8.4   0.0    3.1  2  DUF2508   Protein of unknown function (DUF2508)


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.4   2.2e-08   1.9e-05       8      71 ..      69     127 ..      63     133 .. 0.92
   2 !   44.1   0.2   2.2e-14   1.9e-11       3      73 ..     141     209 ..     139     213 .. 0.95
   3 !   37.1   0.0   3.4e-12   2.9e-09       2      77 .]     180     253 ..     179     253 .. 0.93
   4 !   26.5   0.0   7.1e-09     6e-06       5      72 ..     223     288 ..     219     293 .. 0.89
   5 ?   -1.8   0.1       4.8   4.1e+03      46      65 ..     301     322 ..     295     324 .. 0.59
   6 ?   -1.8   0.0       4.7     4e+03      62      72 ..     387     397 ..     377     402 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.2e-08
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                       +l++++r  g y  A++ +++al ++      d  l    ++nLg++y ++g+++ A  +++++
  gi|330508818|ref|YP_004385246.1|  69 RLGDICRSTGLYSLAISAYNRALSLC-----SDPVLRPVLQNNLGQAYARQGDLARAAFYYKKS 127
                                       79************************.....67789**************************98 PP

  == domain 2  score: 44.1 bits;  conditional E-value: 2.2e-14
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       a +l nl++++r+  ++d A+e++ ++l  +++   +d ++ a+    Lgr+y  +g+ + A +++e++l+
  gi|330508818|ref|YP_004385246.1| 141 AHVLGNLGSAYRQNRDWDRAIEYCYRSLKTFEEQ--GDDLGIAQMTGSLGRIYADMGERDLATRYFEKSLE 209
                                       78999**************************999..8999******************************8 PP

  == domain 3  score: 37.1 bits;  conditional E-value: 3.4e-12
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       +a++   l+ +++ +g+ d A +++ek+le ++rl  +d+  +a+++  +gr+ + + +++ A +++ ++l+++e+
  gi|330508818|ref|YP_004385246.1| 180 IAQMTGSLGRIYADMGERDLATRYFEKSLEDFQRL--GDKKSAAWIMDRMGRIASDRYDWDSAKSYFSQSLDLFEE 253
                                       5788888****************************..66667************9888***************985 PP

  == domain 4  score: 26.5 bits;  conditional E-value: 7.1e-09
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       ++ +++ +   + ++d A +++ ++l++++++  ++     ++l n+gr++++ g+   A+e le+a+
  gi|330508818|ref|YP_004385246.1| 223 IMDRMGRIASDRYDWDSAKSYFSQSLDLFEEY--GQTQSKGIVLSNMGRMQLEKGDASSARESLEKAI 288
                                       55468888888889****************99..78889***************************96 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 4.8
                            TPR_12  46 ttlrnLgrlyral..gryeeAl 65 
                                       ++l  L+ +y+ l  g +eeA+
  gi|330508818|ref|YP_004385246.1| 301 NALSSLAAAYSTLakGSLEEAE 322
                                       4666777777532236666665 PP

  == domain 6  score: -1.8 bits;  conditional E-value: 4.7
                            TPR_12  62 eeAlelleeal 72 
                                       +eA+e+ ++al
  gi|330508818|ref|YP_004385246.1| 387 QEAVEIAQKAL 397
                                       34444444444 PP

>> TPR_1  Tetratricopeptide 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    0.0099       5      33 ..      68      96 ..      65      97 .. 0.93
   2 !   16.9   0.5   4.6e-06     0.004       4      26 ..     104     126 ..     101     128 .. 0.92
   3 !   21.0   0.1   2.4e-07   0.00021       3      29 ..     143     169 ..     141     173 .. 0.92
   4 !   10.1   0.0   0.00067      0.57       7      29 ..     187     209 ..     185     209 .. 0.95
   5 ?   -0.5   0.0       1.5   1.3e+03      16      33 ..     236     253 ..     236     254 .. 0.84
   6 ?    6.0   0.0     0.013        11       3      30 ..     263     290 ..     262     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  5 ynlGnayfklgkydeAleyyekALelnPn 33
                                      ++lG ++++ g y  A+ +y++AL+l+ +
  gi|330508818|ref|YP_004385246.1| 68 KRLGDICRSTGLYSLAISAYNRALSLCSD 96
                                      69***********************9865 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.6e-06
                                       HHHHHHHHHHTT-HHHHHHHHHH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyek 26 
                                        +nlG+ay ++g++  A  yy+k
  gi|330508818|ref|YP_004385246.1| 104 QNNLGQAYARQGDLARAAFYYKK 126
                                       59********************9 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 2.4e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALe 29 
                                       +l nlG ay+++ ++d A+ey+ + L+
  gi|330508818|ref|YP_004385246.1| 143 VLGNLGSAYRQNRDWDRAIEYCYRSLK 169
                                       689*********************998 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00067
                                       HHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   7 lGnayfklgkydeAleyyekALe 29 
                                       lG +y  +g+ d A  y+ek Le
  gi|330508818|ref|YP_004385246.1| 187 LGRIYADMGERDLATRYFEKSLE 209
                                       9********************98 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 1.5
                                       -HHHHHHHHHHHHHHSTT CS
                             TPR_1  16 kydeAleyyekALelnPn 33 
                                       ++d A  y+++ L l ++
  gi|330508818|ref|YP_004385246.1| 236 DWDSAKSYFSQSLDLFEE 253
                                       678999*******99765 PP

  == domain 6  score: 6.0 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                       +l n+G + +++g+   A e  ekA+ l
  gi|330508818|ref|YP_004385246.1| 263 VLSNMGRMQLEKGDASSARESLEKAIHL 290
                                       689***********************88 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   9.7e-05     0.083       4      32 ..      69      97 ..      67      97 .. 0.94
   2 !   15.4   0.3   1.6e-05     0.014       3      31 ..     105     134 ..     102     137 .. 0.87
   3 !   22.7   0.1   7.7e-08   6.5e-05       2      32 ..     144     174 ..     143     178 .. 0.84
   4 !   14.3   0.0   3.7e-05     0.031       4      27 ..     186     209 ..     184     222 .. 0.92
   5 ?    4.2   0.0     0.061        52       4      28 ..     226     250 ..     223     255 .. 0.88
   6 ?    6.1   0.0     0.015        13       2      29 ..     264     289 ..     263     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.7e-05
                             TPR_7  4 nLarlysrlGdyeeAielyeqsLaltkdp 32
                                      +L++++++ G y+ Ai+ y ++L l++dp
  gi|330508818|ref|YP_004385246.1| 69 RLGDICRSTGLYSLAISAYNRALSLCSDP 97
                                      7**********************999997 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.6e-05
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsL.altkd 31 
                                       +nL+++y r+Gd ++A+ +y++s   ++k+
  gi|330508818|ref|YP_004385246.1| 105 NNLGQAYARQGDLARAAFYYKKSAcCFEKS 134
                                       8*********************87676666 PP

  == domain 3  score: 22.7 bits;  conditional E-value: 7.7e-08
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       L nL+++y++ +d+++Aie++ +sL + +++
  gi|330508818|ref|YP_004385246.1| 144 LGNLGSAYRQNRDWDRAIEYCYRSLKTFEEQ 174
                                       89*******************9999555544 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 3.7e-05
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLa 27 
                                        L+r+y ++G+++ A +++e+sL+
  gi|330508818|ref|YP_004385246.1| 186 SLGRIYADMGERDLATRYFEKSLE 209
                                       69*******************884 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.061
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLal 28 
                                       +++r+ s++ d++ A +++ qsL l
  gi|330508818|ref|YP_004385246.1| 226 RMGRIASDRYDWDSAKSYFSQSLDL 250
                                       799******************9966 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.015
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLalt 29 
                                       L+n++r++ + Gd + A e +e+  a++
  gi|330508818|ref|YP_004385246.1| 264 LSNMGRMQLEKGDASSARESLEK--AIH 289
                                       89*********************..665 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00019      0.17       6      32 ..      69      95 ..      65      97 .. 0.92
   2 !   18.5   0.5   1.7e-06    0.0015       4      27 ..     104     127 ..     101     128 .. 0.92
   3 !   12.4   0.1   0.00016      0.13       3      24 ..     143     164 ..     141     172 .. 0.87
   4 !   10.4   0.0   0.00066      0.57       7      29 ..     187     209 ..     186     212 .. 0.95
   5 ?    6.7   0.0      0.01       8.9       5      33 ..     225     253 ..     221     254 .. 0.88
   6 !    8.6   0.0    0.0026       2.3       3      30 ..     263     290 ..     261     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                             TPR_2  6 nlGlayyklgdyeeAleafekAleldP 32
                                      +lG++++  g y  A+ a+++Al+l+ 
  gi|330508818|ref|YP_004385246.1| 69 RLGDICRSTGLYSLAISAYNRALSLCS 95
                                      89**********************985 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.7e-06
                             TPR_2   4 lynlGlayyklgdyeeAleafekA 27 
                                        +nlG+ay+++gd+++A+ +++k+
  gi|330508818|ref|YP_004385246.1| 104 QNNLGQAYARQGDLARAAFYYKKS 127
                                       68********************96 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00016
                             TPR_2   3 alynlGlayyklgdyeeAleaf 24 
                                       +l nlG ay+++ d+++A+e++
  gi|330508818|ref|YP_004385246.1| 143 VLGNLGSAYRQNRDWDRAIEYC 164
                                       7889****************97 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00066
                             TPR_2   7 lGlayyklgdyeeAleafekAle 29 
                                       lG++y+ +g+ + A ++fek+le
  gi|330508818|ref|YP_004385246.1| 187 LGRIYADMGERDLATRYFEKSLE 209
                                       8********************97 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.01
                             TPR_2   5 ynlGlayyklgdyeeAleafekAleldPn 33 
                                        ++G+++  + d++ A+ +f ++l l ++
  gi|330508818|ref|YP_004385246.1| 225 DRMGRIASDRYDWDSAKSYFSQSLDLFEE 253
                                       68999999999**************9875 PP

  == domain 6  score: 8.6 bits;  conditional E-value: 0.0026
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                       +l n+G+  +++gd   A+e +ekA+ l
  gi|330508818|ref|YP_004385246.1| 263 VLSNMGRMQLEKGDASSARESLEKAIHL 290
                                       789**********************977 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   9.9e-05     0.084       6      32 ..      69      95 ..      69      97 .. 0.92
   2 !   12.5   0.8   0.00016      0.13       5      27 ..     105     127 ..     103     128 .. 0.93
   3 !   10.8   0.0   0.00056      0.48       1      29 [.     141     169 ..     141     173 .. 0.92
   4 !   12.2   0.0   0.00019      0.16       6      29 ..     186     209 ..     181     209 .. 0.93
   5 ?    0.1   0.0       1.5   1.3e+03      18      31 ..     238     251 ..     226     254 .. 0.81
   6 !    8.9   0.0    0.0022       1.9       5      28 ..     265     288 ..     263     293 .. 0.91
   7 ?   -1.7   0.1       5.5   4.7e+03      18      29 ..     387     398 ..     386     399 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.9e-05
                                      HHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8  6 nlgsiylklgdyeeAkeyyekaleldp 32
                                      +lg+i++++g y  A+++y++al+l  
  gi|330508818|ref|YP_004385246.1| 69 RLGDICRSTGLYSLAISAYNRALSLCS 95
                                      69**********************976 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyeka 27 
                                       +nlg++y  +gd+  A  yy+k 
  gi|330508818|ref|YP_004385246.1| 105 NNLGQAYARQGDLARAAFYYKKS 127
                                       89*******************95 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00056
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekale 29 
                                       a+++ nlgs+y++  d + A+ey+ + l+
  gi|330508818|ref|YP_004385246.1| 141 AHVLGNLGSAYRQNRDWDRAIEYCYRSLK 169
                                       67899******************998886 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00019
                                       HHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekale 29 
                                        lg+iy ++g+ + A  y+ek le
  gi|330508818|ref|YP_004385246.1| 186 SLGRIYADMGERDLATRYFEKSLE 209
                                       59*******************997 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHH CS
                             TPR_8  18 eeAkeyyekaleld 31 
                                       ++Ak+y+ + l+l 
  gi|330508818|ref|YP_004385246.1| 238 DSAKSYFSQSLDLF 251
                                       79*******99985 PP

  == domain 6  score: 8.9 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekal 28 
                                        n+g+  l++gd  +A e++eka+
  gi|330508818|ref|YP_004385246.1| 265 SNMGRMQLEKGDASSARESLEKAI 288
                                       589999*****************8 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 5.5
                                       HHHHHHHHHHHH CS
                             TPR_8  18 eeAkeyyekale 29 
                                       +eA+e  +kal+
  gi|330508818|ref|YP_004385246.1| 387 QEAVEIAQKALS 398
                                       589999999997 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   0.00014      0.12       5      28 ..     104     127 ..     102     134 .. 0.84
   2 !   16.6   0.1   6.4e-06    0.0054       2      32 ..     141     171 ..     140     173 .. 0.90
   3 !   13.5   0.0   5.7e-05     0.048       7      35 ..     186     214 ..     181     216 .. 0.91
   4 ?    4.6   0.0     0.037        32       2      31 ..     221     250 ..     220     254 .. 0.89
   5 ?    4.6   0.0     0.036        31       5      30 ..     264     289 ..     263     293 .. 0.93
   6 ?   -0.6   0.1       1.5   1.3e+03       4      15 ..     302     313 ..     301     322 .. 0.81
   7 ?    1.1   0.1      0.47     4e+02      19      30 ..     387     398 ..     386     400 .. 0.76
   8 ?   -2.4   0.2       5.7   4.9e+03      14      26 ..     517     529 ..     516     530 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                            TPR_10   5 lnNLanalrqrgrydeAealleea 28 
                                       +nNL+ a+ ++g++++A  +++++
  gi|330508818|ref|YP_004385246.1| 104 QNNLGQAYARQGDLARAAFYYKKS 127
                                       8***************98777666 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 6.4e-06
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealair 32 
                                       A  l NL+ a+rq +++d+A +++ ++l + 
  gi|330508818|ref|YP_004385246.1| 141 AHVLGNLGSAYRQNRDWDRAIEYCYRSLKTF 171
                                       78899*********************99875 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 5.7e-05
                            TPR_10   7 NLanalrqrgrydeAealleealairrrl 35 
                                        L++++ ++g++d A +++e++l+  +rl
  gi|330508818|ref|YP_004385246.1| 186 SLGRIYADMGERDLATRYFEKSLEDFQRL 214
                                       59*********************987765 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.037
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealai 31 
                                       A ++  ++++ ++r+++d A  ++ ++l++
  gi|330508818|ref|YP_004385246.1| 221 AWIMDRMGRIASDRYDWDSAKSYFSQSLDL 250
                                       778999****************99999876 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.036
                            TPR_10   5 lnNLanalrqrgrydeAealleeala 30 
                                       l+N++++  + g+   A++ le+a+ 
  gi|330508818|ref|YP_004385246.1| 264 LSNMGRMQLEKGDASSARESLEKAIH 289
                                       89**********************96 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 1.5
                            TPR_10   4 slnNLanalrqr 15 
                                       +l+ La+a++ +
  gi|330508818|ref|YP_004385246.1| 302 ALSSLAAAYSTL 313
                                       799999999876 PP

  == domain 7  score: 1.1 bits;  conditional E-value: 0.47
                            TPR_10  19 deAealleeala 30 
                                       +eA++++++al+
  gi|330508818|ref|YP_004385246.1| 387 QEAVEIAQKALS 398
                                       788888888875 PP

  == domain 8  score: -2.4 bits;  conditional E-value: 5.7
                            TPR_10  14 qrgrydeAealle 26 
                                       + +r+ eA a+le
  gi|330508818|ref|YP_004385246.1| 517 DARRLIEAAAILE 529
                                       5677888888876 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     6e-06    0.0051      35     190 ..      96     250 ..      71     255 .. 0.86
   2 !   19.6   0.1   5.6e-07   0.00048      11     101 ..     231     323 ..     227     329 .. 0.82
   3 ?   -1.1   0.2       1.1   9.7e+02       9      33 ..     379     402 ..     369     431 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6e-06
                          TPR_MalT  35 dllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlat 111
                                       d   r +   +lG a+  qGdl++A   +++      + + l   +  l  ++  +++  + + A+e ++++l+  +
  gi|330508818|ref|YP_004385246.1|  96 DPVLRPVLQNNLGQAYARQGDLARAAFYYKKSACCFEKSEDLLGLAHVLGNLGSAYRQNRDWDRAIEYCYRSLKTFE 172
                                       44567777889************999999999999999999999999999************************999 PP

                          TPR_MalT 112 eqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlepeaald.ayvllarialaqGdleeAetlleka 187
                                       eqg   l ++++   +l++++ ++++ + A ++ ++++e  ++l+ + +++ +   + ria  + d++ A++++ + 
  gi|330508818|ref|YP_004385246.1| 173 EQGDD-LGIAQMT-GSLGRIYADMGERDLATRYFEKSLEDFQRLGDKKSAAwIMDRMGRIASDRYDWDSAKSYFSQS 247
                                       88877.8999988.999**********************99999665555526778999999999999999999887 PP

                          TPR_MalT 188 eel 190
                                         l
  gi|330508818|ref|YP_004385246.1| 248 LDL 250
                                       655 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 5.6e-07
                          TPR_MalT  11 aiasgdaeralelArqALallpe.ddllariaatavlGeasllqGdleaAlqalqeaekla.rqadslhvallallq 85 
                                       a  + d ++a+ +  q L+l++e  +  +++++++++G+ +l +Gd  +A+++l++a++l+ r+a+   + +l+ l 
  gi|330508818|ref|YP_004385246.1| 231 ASDRYDWDSAKSYFSQSLDLFEEyGQTQSKGIVLSNMGRMQLEKGDASSARESLEKAIHLIsRNAQPGYQNALSSLA 307
                                       555666666777777777777763467788****************************9752777777888999999 PP

                          TPR_MalT  86 qaeilvaqGrLheAle 101
                                        a  + a+G+L+eA++
  gi|330508818|ref|YP_004385246.1| 308 AAYSTLAKGSLEEAED 323
                                       *************976 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.1
                          TPR_MalT   9 llaiasgdaeralelArqALallpe 33 
                                        +  ++ d  +a+e+A++AL+ l+ 
  gi|330508818|ref|YP_004385246.1| 379 RISGYTSDQ-EAVEIAQKALSSLDM 402
                                       344444454.499999999998865 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.2e-07    0.0001       1      42 []      71     115 ..      71     115 .. 0.93
   2 ?   -1.4   0.0       2.2   1.9e+03       1      15 [.     148     162 ..     148     163 .. 0.91
   3 ?    3.1   0.0     0.088        75       1      28 [.     268     295 ..     268     313 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-07
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPd...naeayynLGlayykqG 42 
                                       Gd++++ G y  Ai aY++Al l++d    + + +nLG+ay++qG
  gi|330508818|ref|YP_004385246.1|  71 GDICRSTGLYSLAISAYNRALSLCSDpvlRPVLQNNLGQAYARQG 115
                                       9*************************555578************9 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                            TPR_11   1 GdayyeqGkyeeAie 15 
                                       G ay++  +++ Aie
  gi|330508818|ref|YP_004385246.1| 148 GSAYRQNRDWDRAIE 162
                                       889****9***9997 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.088
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdna 28 
                                       G++  e+G+   A e+++kA+ l + na
  gi|330508818|ref|YP_004385246.1| 268 GRMQLEKGDASSARESLEKAIHLISRNA 295
                                       6667799**************9977777 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.046        39       6      34 ..      69      97 ..      66     104 .. 0.88
   2 ?    7.4   0.4      0.01       8.9       7      27 ..     107     127 ..     101     144 .. 0.85
   3 !   12.5   0.0   0.00024      0.21       7      34 ..     147     174 ..     141     186 .. 0.88
   4 ?    5.3   0.1      0.05        42       7      31 ..     187     211 ..     181     229 .. 0.85
   5 ?   -0.2   0.0         3   2.5e+03       5      33 ..     225     253 ..     219     258 .. 0.83
   6 ?    0.8   0.1       1.4   1.2e+03       8      28 ..     268     288 ..     264     303 .. 0.86
   7 ?    1.9   0.3      0.65   5.5e+02       8      40 ..     490     521 ..     489     526 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.046
                            TPR_14  6 alaeallalGdpdeAiallrralalaPdd 34
                                      +l+++++  G +  Ai +++ral+l+ d+
  gi|330508818|ref|YP_004385246.1| 69 RLGDICRSTGLYSLAISAYNRALSLCSDP 97
                                      79999*******************99774 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.01
                            TPR_14   7 laeallalGdpdeAiallrra 27 
                                       l++a++++Gd+++A+ ++++ 
  gi|330508818|ref|YP_004385246.1| 107 LGQAYARQGDLARAAFYYKKS 127
                                       89*************999985 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00024
                            TPR_14   7 laeallalGdpdeAiallrralalaPdd 34 
                                       l++a+++++d+d+Ai+++ r l+++ ++
  gi|330508818|ref|YP_004385246.1| 147 LGSAYRQNRDWDRAIEYCYRSLKTFEEQ 174
                                       899********************98754 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.05
                            TPR_14   7 laeallalGdpdeAiallrralala 31 
                                       l+++++  G+ d A +++++ l+++
  gi|330508818|ref|YP_004385246.1| 187 LGRIYADMGERDLATRYFEKSLEDF 211
                                       89*******************9965 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 3
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPd 33 
                                        +++++   + d+d A  ++ + l+l+ +
  gi|330508818|ref|YP_004385246.1| 225 DRMGRIASDRYDWDSAKSYFSQSLDLFEE 253
                                       577888999999*********99998865 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 1.4
                            TPR_14   8 aeallalGdpdeAiallrral 28 
                                       ++  l+ Gd   A++ l++a+
  gi|330508818|ref|YP_004385246.1| 268 GRMQLEKGDASSARESLEKAI 288
                                       6777899***********997 PP

  == domain 7  score: 1.9 bits;  conditional E-value: 0.65
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawll 40 
                                       a++++a+Gd++ + ++l  + +++P++++a++l
  gi|330508818|ref|YP_004385246.1| 490 AKLHAAAGDLRHSGKHLSSL-EKDPKERDARRL 521
                                       78999999999999999999.88**99999865 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.022        19      40      61 ..      70      91 ..      69      96 .. 0.88
   2 !   13.9   2.9   7.6e-05     0.065      13      56 ..      80     123 ..      78     129 .. 0.89
   3 !    8.0   0.0    0.0052       4.5      34      62 ..     141     169 ..     132     175 .. 0.85
   4 ?    2.0   0.1      0.38   3.3e+02       3      27 ..     187     211 ..     186     222 .. 0.88
   5 ?    1.2   0.0      0.71   6.1e+02       4      54 ..     228     288 ..     226     298 .. 0.56
   6 ?    0.6   0.2       1.1   9.2e+02       8      53 ..     272     321 ..     265     324 .. 0.49

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.022
                            TPR_16 40 lgdaalrqgrlaeAaalyraal 61
                                      lgd++   g + +A+ +y++al
  gi|330508818|ref|YP_004385246.1| 70 LGDICRSTGLYSLAISAYNRAL 91
                                      9**************9999998 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.6e-05
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaal 56 
                                       y  A+ a+++al + +++ +++  +++lg+a++rqg+la+Aa +
  gi|330508818|ref|YP_004385246.1|  80 YSLAISAYNRALSLCSDPVLRPVLQNNLGQAYARQGDLARAAFY 123
                                       788************88888*********************944 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0052
                            TPR_16  34 aeAllllgdaalrqgrlaeAaalyraalr 62 
                                       a+ l +lg a+ ++ ++++A++++ + l+
  gi|330508818|ref|YP_004385246.1| 141 AHVLGNLGSAYRQNRDWDRAIEYCYRSLK 169
                                       6778899**************99998775 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.38
                            TPR_16   3 laraalragdyddAaaaleaalkrd 27 
                                       l+r++++ g+ d A +++e  l+++
  gi|330508818|ref|YP_004385246.1| 187 LGRIYADMGERDLATRYFEKSLEDF 211
                                       89*****************999998 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.71
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPd.............aaeAllllgdaalrqgrlaeAa 54 
                                       +r+a ++ d+d A  ++ + l+++    +               +++l++gda  ++  l++A+
  gi|330508818|ref|YP_004385246.1| 228 GRIASDRYDWDSAKSYFSQSLDLF---EEygqtqskgivlsnMGRMQLEKGDASSARESLEKAI 288
                                       566666667777777777777777...3333455544444444455555555555555555554 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 1.1
                            TPR_16   8 lragdyddAaaaleaalkrdpssPd....aaeAllllgdaalrqgrlaeA 53 
                                       l+ gd   A++ le a+ + ++  +    +a ++l+ + + l++g l+eA
  gi|330508818|ref|YP_004385246.1| 272 LEKGDASSARESLEKAIHLISRNAQpgyqNALSSLAAAYSTLAKGSLEEA 321
                                       55566666666666655544333334333444444444444444555555 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.51   4.4e+02     115     135 ..      73      93 ..       5      98 .. 0.66
   2 ?    1.2   0.1       0.3   2.6e+02      39      61 ..     104     126 ..     102     132 .. 0.78
   3 !   17.7   0.1   2.6e-06    0.0022      11     145 ..     156     315 ..     151     331 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.51
                                       HHHHHHHHHHHTT-HHHHHHH CS
                              RPN7 115 lkvyeGlallairkfkeAael 135
                                       +  + Gl++lai  +++A +l
  gi|330508818|ref|YP_004385246.1|  73 ICRSTGLYSLAISAYNRALSL 93 
                                       444566777777777776655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHCT-HHHHHHHHHT CS
                              RPN7  39 kldlaehYlkigdleeAlkaysr 61 
                                       +++l++ Y++ gdl+ A  +y++
  gi|330508818|ref|YP_004385246.1| 104 QNNLGQAYARQGDLARAAFYYKK 126
                                       67788888888888888888876 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 2.6e-06
                                       HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHH...HHHHHHHHHH CS
                              RPN7  11 knekeleeLdaelkdakenlgkeeirrakldlaehYlkigdleeAlkaysrireyctslkhkid...mllnlirvai 84 
                                        ++  +e   + lk  +e++ +  i++    l++ Y+++g+++ A +++++ +e+   l+ k +   ++ ++ r+a 
  gi|330508818|ref|YP_004385246.1| 156 DWDRAIEYCYRSLKTFEEQGDDLGIAQMTGSLGRIYADMGERDLATRYFEKSLEDFQRLGDKKSaawIMDRMGRIAS 232
                                       5677777778899999**************************************99998876552225557779999 PP

                                       HTT-HHHHHHHHHHHHCSSS---.......................HHHHHHHHHHHHHHHHHTT-HHHHHHHHCTS CS
                              RPN7  85 ffndwdlvskylekakellekggd......................werknrlkvyeGlallairkfkeAaellldi 139
                                        + dwd++++y ++  +l e+ g+                        r+   k++  +   a+  ++ A + l ++
  gi|330508818|ref|YP_004385246.1| 233 DRYDWDSAKSYFSQSLDLFEEYGQtqskgivlsnmgrmqlekgdasSARESLEKAIHLISRNAQPGYQNALSSLAAA 309
                                       *******************9998878888887777777777775544444444555555666666677777777777 PP

                                       -GGGT. CS
                              RPN7 140 lstfts 145
                                        st+++
  gi|330508818|ref|YP_004385246.1| 310 YSTLAK 315
                                       666655 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.1   3.5e+03     118     143 ..      68      92 ..      63      95 .. 0.83
   2 !   17.3   0.3     3e-06    0.0026      43     176 ..     109     242 ..     103     245 .. 0.90
   3 !    7.2   0.4    0.0034       2.9      89     174 ..     236     321 ..     230     328 .. 0.84
   4 ?    0.5   0.5      0.39   3.4e+02      48     104 ..     340     400 ..     335     414 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.1
                                       HHHHHHHHHTT--HHHHHHHHHHHHH CS
                              SNAP 118 keiaelyekelgdlekAieaYekAae 143
                                       k +++++ +  g ++ Ai+aY++A  
  gi|330508818|ref|YP_004385246.1|  68 KRLGDICRST-GLYSLAISAYNRALS 92 
                                       6788888888.999999999999975 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3e-06
                                       HHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                              SNAP  43 nayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrfrraAklkk 118
                                       +ay  + ++ +A+  + k A c ek ++    a+ + + +++y+++ + ++A+e   ++ +++ e+g     A+++ 
  gi|330508818|ref|YP_004385246.1| 109 QAYARQGDLARAAFYYKKSACCFEKSEDLLGLAHVLGNLGSAYRQNrDWDRAIEYCYRSLKTFEEQGDDLGIAQMTG 185
                                       6788889999**********************************998999*************************** PP

                                       HHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHH CS
                              SNAP 119 eiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAie 176
                                       +++ +y +  g+ + A++++ek  e ++  + k +a  ++ ++  ++++  +++ A  
  gi|330508818|ref|YP_004385246.1| 186 SLGRIYADM-GERDLATRYFEKSLEDFQRLGDKKSAAWIMDRMGRIASDRYDWDSAKS 242
                                       *******77.******************999888888888888888777777777665 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0034
                                       -HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                              SNAP  89 speeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAels 165
                                       + ++A + ++++ +++ e g+ +  +    +++ +  ++ gd ++A e+ ekA +l + + +   +n +   +A +s
  gi|330508818|ref|YP_004385246.1| 236 DWDSAKSYFSQSLDLFEEYGQTQSKGIVLSNMGRMQLEK-GDASSARESLEKAIHLISRNAQPGYQNALSSLAAAYS 311
                                       556788999999999999999999999999999999988.9999999999999999999999999998888888887 PP

                                       HHTT.-HHHH CS
                              SNAP 166 aele.kyekA 174
                                       +  + ++e+A
  gi|330508818|ref|YP_004385246.1| 312 TLAKgSLEEA 321
                                       7655455555 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.39
                                       TT-THHHHHHHHHHH....HHHHHTT-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHH CS
                              SNAP  48 akkweeAgeaflkaA....ecqeklkekdeaanayveAakcykkvspeeAvealekAieiy 104
                                       +k++ +A++ fl++A    ++q ++k k+e a++    a +   +s +eAve  +kA + +
  gi|330508818|ref|YP_004385246.1| 340 SKNFGRASDRFLELAsslpKMQADIKTKSEIAKCRSYLARISGYTSDQEAVEIAQKALSSL 400
                                       7999999999999992222345555556666665555555555568889999998887765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       1.1   9.2e+02       5      27 ..      69      91 ..      69      94 .. 0.86
   2 ?    4.8   1.0     0.058        50       5      25 ..     106     126 ..     106     126 .. 0.90
   3 ?    6.6   0.0     0.016        13       5      24 ..     146     166 ..     146     171 .. 0.79
   4 ?    2.0   0.1      0.48   4.1e+02       6      29 ..     187     210 ..     186     212 .. 0.88
   5 ?   -0.8   0.0       3.7   3.2e+03       5      25 ..     226     246 ..     222     251 .. 0.74
   6 ?    5.9   0.0     0.028        24       5      27 ..     266     288 ..     263     290 .. 0.90
   7 ?   -1.8   0.0       7.7   6.6e+03      16      27 ..     386     397 ..     370     399 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.1
                                      HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  5 klalsyrklgdtdkAlealerli 27
                                      +l+   r++g ++ A+ a++r +
  gi|330508818|ref|YP_004385246.1| 69 RLGDICRSTGLYSLAISAYNRAL 91
                                      68888899889********9987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.058
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealer 25 
                                       +l+++y ++gd ++A  ++++
  gi|330508818|ref|YP_004385246.1| 106 NLGQAYARQGDLARAAFYYKK 126
                                       69*************999875 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHHHHH.HHH CS
                             TPR_6   5 klalsyrklgdtdkAle.ale 24 
                                       +l+ +yr+  d+d+A+e  ++
  gi|330508818|ref|YP_004385246.1| 146 NLGSAYRQNRDWDRAIEyCYR 166
                                       5899***977*******5555 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlike 29 
                                       l++ y  +g+ d A +++e+ +++
  gi|330508818|ref|YP_004385246.1| 187 LGRIYADMGERDLATRYFEKSLED 210
                                       799***************996665 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealer 25 
                                       ++++      d+d A+ ++ +
  gi|330508818|ref|YP_004385246.1| 226 RMGRIASDRYDWDSAKSYFSQ 246
                                       677777764499999999987 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerli 27 
                                       ++++ +++ gd++ A+e le+ i
  gi|330508818|ref|YP_004385246.1| 266 NMGRMQLEKGDASSARESLEKAI 288
                                       799*****89**********987 PP

  == domain 7  score: -1.8 bits;  conditional E-value: 7.7
                                       HHHHHHHHHHHH CS
                             TPR_6  16 tdkAlealerli 27 
                                        ++A+e+ ++ +
  gi|330508818|ref|YP_004385246.1| 386 DQEAVEIAQKAL 397
                                       579999999987 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.2    0.0011      0.91       2      32 ..      87     120 ..      86     122 .. 0.79
   2 ?    5.6   0.0     0.027        23      13      34 .]     141     162 ..     139     162 .. 0.90
   3 ?   -1.1   0.0         4   3.4e+03      15      34 .]     263     282 ..     258     282 .. 0.84
   4 ?   -0.6   0.1       2.6   2.2e+03       9      33 ..     296     322 ..     289     323 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                            TPR_17   2 ylkaleldPnn...adaynnLAelllknGdlmtA 32 
                                       y +al l+ +    +++ nnL+++++++Gdl++A
  gi|330508818|ref|YP_004385246.1|  87 YNRALSLCSDPvlrPVLQNNLGQAYARQGDLARA 120
                                       667777765555567888*************998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.027
                            TPR_17  13 adaynnLAelllknGdlmtArq 34 
                                       a ++ nL+ ++++n d+++A++
  gi|330508818|ref|YP_004385246.1| 141 AHVLGNLGSAYRQNRDWDRAIE 162
                                       56899***************86 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4
                            TPR_17  15 aynnLAelllknGdlmtArq 34 
                                       ++ n+++ +l++Gd   Ar+
  gi|330508818|ref|YP_004385246.1| 263 VLSNMGRMQLEKGDASSARE 282
                                       788999999****9988875 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.6
                            TPR_17   9 dPnnadaynnLAelll..knGdlmtAr 33 
                                        P + +a+  LA +++   +G l++A+
  gi|330508818|ref|YP_004385246.1| 296 QPGYQNALSSLAAAYStlAKGSLEEAE 322
                                       4888899999****9977777777776 PP

>> Coat_F  Coat F domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012       0.1      16      51 ..      83     118 ..      81     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                            Coat_F  16 aarnyataitEasnpelRqtlkqilneeiemqeelf 51 
                                       a+++y+ a+  +s+p lR +l++ l ++ + q +l 
  gi|330508818|ref|YP_004385246.1|  83 AISAYNRALSLCSDPVLRPVLQNNLGQAYARQGDLA 118
                                       6899************************99998875 PP

>> SPO22  Meiosis protein SPO22/ZIP4 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0019       1.7       3      71 ..     112     176 ..     110     185 .. 0.91
   2 ?    6.7   0.2    0.0051       4.4       4     114 ..     193     293 ..     190     327 .. 0.72
   3 ?    0.0   1.0      0.56   4.8e+02      57     114 ..     349     406 ..     277     506 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0019
                             SPO22   3 wkegdldlAehmlskakceenllrldpeeaeeLarllyniGksllskkkyeeavkWLqraldilekqes 71 
                                        ++gdl+ A ++++k+      ++ + e+++ La++l n G +  ++++++ a+ +  r+l+ +e+q +
  gi|330508818|ref|YP_004385246.1| 112 ARQGDLARAAFYYKKSA----CCFEKSEDLLGLAHVLGNLGSAYRQNRDWDRAIEYCYRSLKTFEEQGD 176
                                       58*************65....899999***********************************9998866 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0051
                             SPO22   4 kegdldlAehmlskakceenllrldpeeaeeLarllyniGksllskkkyeeavkWLqraldilekqesesksssdls 80 
                                       ++g +dlA  +++k+   e  +rl   + ++ a ++ ++G+ ++++ ++++a  +++++ld++e  e ++++s    
  gi|330508818|ref|YP_004385246.1| 193 DMGERDLATRYFEKS--LEDFQRL--GDKKSAAWIMDRMGRIASDRYDWDSAKSYFSQSLDLFE--EYGQTQS---- 259
                                       578999********4..4444444..555555555555666666666*****************..3333333.... PP

                             SPO22  81 elrlsvlrllarayle.ldqeesyekalkavell.q 114
                                         +  vl  + r  le  d ++  e+ +ka++l+ +
  gi|330508818|ref|YP_004385246.1| 260 --KGIVLSNMGRMQLEkGDASSARESLEKAIHLIsR 293
                                       ..6777888888888888888888888888888752 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.56
                             SPO22  57 kWLqraldilekqesesksssdlselrlsvlrllarayleldqeesyekalkavell.....q 114
                                       ++L+ a ++ + q++ +++s       +++  +lar    ++++e  e a+ka++ l     +
  gi|330508818|ref|YP_004385246.1| 349 RFLELASSLPKMQADIKTKS-----EIAKCRSYLARISGYTSDQEAVEIAQKALSSLdmaaeN 406
                                       67777777777444444444.....44566667777777777888888888888887665432 PP

>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.012        11      71      95 ..      65      89 ..      51     107 .. 0.89
   2 ?    3.7   0.0     0.062        53      92     115 ..     150     174 ..      94     183 .. 0.81
   3 ?   -2.5   0.0         5   4.3e+03      32      56 ..     286     311 ..     280     320 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                                      S-TTHHHHHHHT-SSHHHHHHHHHT CS
                          Clathrin 71 ydlekvaklcekadlyeeavilykk 95
                                      y +++++++c+ ++ly +a+  y++
  gi|330508818|ref|YP_004385246.1| 65 YEIKRLGDICRSTGLYSLAISAYNR 89
                                      99******************99986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.062
                                       HHHTTXTHSSHSS.XSSSSHCSCHH CS
                          Clathrin  92 lykkinefkkais.llkklkdfdda 115
                                        y+ ++++++ai+ +++ lk f+++
  gi|330508818|ref|YP_004385246.1| 150 AYRQNRDWDRAIEyCYRSLKTFEEQ 174
                                       699999******9669999999886 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5
                                       CHH.HCHTS--HHHHHHHHHHHHHTT CS
                          Clathrin  32 kvl.kedskenpalqtallelyakyd 56 
                                       k++ + ++ ++p +q+al  l+a y 
  gi|330508818|ref|YP_004385246.1| 286 KAIhLISRNAQPGYQNALSSLAAAYS 311
                                       55523334488999999999999885 PP

>> DUF4810  Domain of unknown function (DUF4810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0       0.2   1.7e+02      44      81 ..     100     137 ..      94     139 .. 0.86
   2 ?    5.0   0.0     0.043        37      49      75 ..     185     211 ..     179     213 .. 0.88
   3 ?   -0.1   0.0       1.6   1.4e+03      48      70 ..     264     286 ..     230     296 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.2
                           DUF4810  44 pPGlyAelGllylkegkkeeaieafekEkelfPESatf 81 
                                        P l+ +lG  y+++g+ + a  +++k    f  S+ +
  gi|330508818|ref|YP_004385246.1| 100 RPVLQNNLGQAYARQGDLARAAFYYKKSACCFEKSEDL 137
                                       5777889*******************999999888765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.043
                           DUF4810  49 AelGllylkegkkeeaieafekEkelf 75 
                                         lG +y+++g+++ a ++fek  e f
  gi|330508818|ref|YP_004385246.1| 185 GSLGRIYADMGERDLATRYFEKSLEDF 211
                                       679*****************9977666 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.6
                           DUF4810  48 yAelGllylkegkkeeaieafek 70 
                                         ++G ++l++g+ + a+e +ek
  gi|330508818|ref|YP_004385246.1| 264 LSNMGRMQLEKGDASSARESLEK 286
                                       56899999999999999998876 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.57   4.9e+02      28      65 ..      63     100 ..      62     108 .. 0.83
   2 ?    2.8   0.6      0.15   1.3e+02      14      51 ..      83     123 ..      73     127 .. 0.69
   3 ?    8.7   0.1    0.0023         2       2      26 ..     148     172 ..     147     227 .. 0.74
   4 ?    2.0   0.0      0.28   2.4e+02      36      58 ..     268     290 ..     264     302 .. 0.87
   5 ?   -1.0   0.1       2.4     2e+03      45      68 ..     492     521 ..     491     526 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.57
                             TPR_9  28 dpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       d++e+   G +    G +s A+ + +++l+l+ d+  +
  gi|330508818|ref|YP_004385246.1|  63 DIYEIKRLGDICRSTGLYSLAISAYNRALSLCSDPVLR 100
                                       78888888999999999***************887655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.15
                             TPR_9  14 alavverllllaPd...dpeerrdRGlllaqlGclsaAlad 51 
                                       a+ +++r l l +d   +p +    G+++a++G+l+ A++ 
  gi|330508818|ref|YP_004385246.1|  83 AISAYNRALSLCSDpvlRPVLQNNLGQAYARQGDLARAAFY 123
                                       566666666663331113556667899********999975 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0023
                             TPR_9   2 kaiaireedweralavverllllaP 26 
                                        +++ +++dw+ra++++ r l  + 
  gi|330508818|ref|YP_004385246.1| 148 GSAYRQNRDWDRAIEYCYRSLKTFE 172
                                       5789***************998744 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.28
                             TPR_9  36 GlllaqlGclsaAladLeaylal 58 
                                       G+++ + G+ s A++ Le +++l
  gi|330508818|ref|YP_004385246.1| 268 GRMQLEKGDASSARESLEKAIHL 290
                                       8999999***********99864 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 2.4
                             TPR_9  45 lsaAladLeayl......alapdapdaeai 68 
                                       l+aA+ dL +        +++p+ +da+++
  gi|330508818|ref|YP_004385246.1| 492 LHAAAGDLRHSGkhlsslEKDPKERDARRL 521
                                       578888888766555555888877777765 PP

>> TAP_C  TAP C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.24     2e+02      23      46 ..     338     359 ..     337     360 .. 0.88
   2 ?   -1.5   0.0       2.4   2.1e+03       9      32 ..     422     445 ..     420     447 .. 0.89
   3 ?    6.3   0.0    0.0084       7.1      15      40 ..     725     750 ..     723     754 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.24
                                       STTT-HHHHHHHHHHHG..GGS-G CS
                             TAP_C  23 qnnWdyerAlqvFeelkakgkIPp 46 
                                       ++  ++ rA+  F el   +++P+
  gi|330508818|ref|YP_004385246.1| 338 EASKNFGRASDRFLELA--SSLPK 359
                                       67789************..99996 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                                       HH-B-HHHHHHHHSSTTT-HHHHH CS
                             TAP_C   9 qtgMnlewsqkcLeqnnWdyerAl 32 
                                        +gM    s  +L +  W + +A+
  gi|330508818|ref|YP_004385246.1| 422 VSGMREARSIGLLGDEPWRLAKAV 445
                                       69****************999997 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0084
                                       HHHHHHHSSTTT-HHHHHHHHHHHG. CS
                             TAP_C  15 ewsqkcLeqnnWdyerAlqvFeelka 40 
                                       ew+++ Le+++ d++ A+  F+e+++
  gi|330508818|ref|YP_004385246.1| 725 EWPERGLEDSGPDFREAVPEFKESTS 750
                                       8**********************985 PP

>> DUF2508  Protein of unknown function (DUF2508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0027       2.3      22      46 ..     230     254 ..     227     260 .. 0.83
   2 ?   -0.9   0.0       2.2   1.9e+03      15      37 ..     465     487 ..     462     490 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0027
                           DUF2508  22 IektkeelesakslfensvDlsdel 46 
                                       I++ + +++saks+f +s+Dl +e+
  gi|330508818|ref|YP_004385246.1| 230 IASDRYDWDSAKSYFSQSLDLFEEY 254
                                       677789**************87766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.2
                           DUF2508  15 deeLleeIektkeelesakslfe 37 
                                       d  +++++e++k ++ +++++++
  gi|330508818|ref|YP_004385246.1| 465 DTSFVSALENLKASMTAERKTED 487
                                       5678999***********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (786 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 4893.78
//
Query:       gi|330508819|ref|YP_004385247.1|  [L=413]
Description: peptide chain release factor eRF/aRF subunit 1 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-43  146.6   0.0    7.6e-43  146.0   0.0    1.3  1  eRF1_2          eRF1 domain 2
    2.6e-30  105.2   0.1    5.1e-30  104.3   0.1    1.5  1  eRF1_3          eRF1 domain 3
    1.4e-13   51.2   0.0    2.5e-13   50.4   0.0    1.4  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
      3e-13   49.9   0.0    5.9e-13   48.9   0.0    1.5  1  eRF1_1          eRF1 domain 1
    2.4e-11   44.1   0.0    5.3e-11   42.9   0.0    1.5  1  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact


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 !  146.0   0.0   2.1e-46   7.6e-43       2     133 .]     140     271 ..     139     271 .. 0.99

  Alignments for each domain:
  == domain 1  score: 146.0 bits;  conditional E-value: 2.1e-46
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTES CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklk 78 
                                       +glivld++eA igllkg+ +e lk+++++vP+K+++Ggqs++rf+ lr  +++ f+k+++e+an+afl +d ++l+
  gi|330508819|ref|YP_004385247.1| 140 FGLIVLDRREAAIGLLKGKYIESLKTLTSTVPGKQRKGGQSSHRFQQLRLIAIHDFYKRIGESANDAFLPIDPKDLE 216
                                       89*************************************************************************** PP

                                       EEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHCC CS
                            eRF1_2  79 giilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlkd 133
                                       gi+++gp+++keef+++ +l++el+ kv+  +dvsy++esgl e++++a+e+l+d
  gi|330508819|ref|YP_004385247.1| 217 GILIGGPSPTKEEFVEGGFLHHELQRKVLAALDVSYTDESGLYELVDTAQEQLAD 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 !  104.3   0.1   1.4e-33   5.1e-30       2     112 ..     275     409 ..     274     410 .. 0.90

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 1.4e-33
                                       HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSH.HHHHS................... CS
                            eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdt.lkekv................... 58 
                                        q+k+++ +f++el  d+g+a+YG++ev++ le+gAv+ LL+se+l+++r + ++                      
  gi|330508819|ref|YP_004385247.1| 275 TQDKEIMRRFMKELVSDKGLAAYGEKEVRHNLELGAVDVLLLSEDLRKTRAKiVCT-Nrscdytdsqtrsgssepvg 350
                                       699***********************************************995544.3599***************9 PP

                                       ..-HHH-HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                            eRF1_3  59 ..ketgeelelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                          ++ + l++ e   ++ +l + +e sga+v+iis+e+eeG+ql +afgGiaaiLRyk
  gi|330508819|ref|YP_004385247.1| 351 tcLKCSSPLTIEEevdIVSDLSKLAELSGAEVKIISTEFEEGAQLFRAFGGIAAILRYK 409
                                       9955554444333444******************************************9 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   7.1e-17   2.5e-13       2     126 ..     126     254 ..     126     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 7.1e-17
                    baeRF_family10   2 ylapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAe 78 
                                       yl+pL e l + + +g++++dr++a++    +  +e  +++++ vpg++++gg+ s +rfq+ +   ++ ++k+++e
  gi|330508819|ref|YP_004385247.1| 126 YLEPLEEMLADKRTFGLIVLDRREAAIGLLKGKYIESLKTLTSTVPGKQRKGGQ-SSHRFQQLRLIAIHDFYKRIGE 201
                                       79****************************************************.********************** PP

                    baeRF_family10  79 llaklleerg...verlvlgGdeeetaalld..rlpkalrarvvgtlplpvda 126
                                        +++++ + +   +e +++gG+   ++++++   l+ +l+++v + l+++ ++
  gi|330508819|ref|YP_004385247.1| 202 SANDAFLPIDpkdLEGILIGGPSPTKEEFVEggFLHHELQRKVLAALDVSYTD 254
                                       *****97655555*********999999986448************9998855 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   1.7e-16   5.9e-13       6     128 ..      19     133 ..      12     134 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.7e-16
                                       ECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT...SS CS
                            eRF1_1   6 rdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd...ag 79 
                                       r+ +++g+++++L++++d+++++++  ++++++++++++++v+r          +v+  L++ + ++++ ++   +g
  gi|330508819|ref|YP_004385247.1|  19 RSKKGRGTELISLYIPPDKQISDVTSQLREEYGQASNIKSRVTR---------LSVQGSLESAMSRLKLIPKppeNG 86 
                                       37789*************************************99.........9*****************9999** PP

                                       EEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                            eRF1_1  80 vlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                       v+ + G v  + +    ++  +  le+++p+ +++++ ++sf+le+L+e+
  gi|330508819|ref|YP_004385247.1|  87 VVLFIGSVDIGAN---RTELFSAALEPPDPIVTYRYHcDSSFYLEPLEEM 133
                                       ********99999...7999***************999***********8 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   1.5e-14   5.3e-11       4     125 ..     142     266 ..     139     275 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.5e-14
                           acVLRF1   4 gvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae.... 76 
                                       +++l+rr + a+g+++g+ +++ k+ t+ v g+ ++GG+S  Rf++ r   + + ++++ e a++ + + +++    
  gi|330508819|ref|YP_004385247.1| 142 LIVLDRREA-AIGLLKGKYIESLKTLTSTVPGKQRKGGQSSHRFQQLRLIAIHDFYKRIGESANDAFLPIDPKdleg 217
                                       5899*****.*********************************************************8777777789 PP

                           acVLRF1  77 vvlgGdrslvaevledarlaplatlareelldvpdprravLedavrrar 125
                                       +++gG+  + +e+ e   l++  ++++ ++ldv   +++ L + v+ a+
  gi|330508819|ref|YP_004385247.1| 218 ILIGGPSPTKEEFVEGGFLHHELQRKVLAALDVSYTDESGLYELVDTAQ 266
                                       ***************9886665555555677777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); 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 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2776.85
//
Query:       gi|330508820|ref|YP_004385248.1|  [L=166]
Description: hypothetical protein MCON_3132 [Methanosaeta concilii GP6]
Scores for complete 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   0.0    2.2e-10   40.8   0.0    2.0  1  RNA_binding  RNA binding
     0.0091   16.1   0.0      0.011   15.7   0.0    1.2  1  T2SSM        Type II secretion system (T2SS), protein M


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 !   40.8   0.0   2.5e-14   2.2e-10       2     117 ..       6     109 ..       5     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.5e-14
                                       EEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCHHHHHH CS
                       RNA_binding   2 ievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeeikeLlk 78 
                                       ++v   v+ TE  ++V  a++n++p                  + i + +++  +  ++l++l++llr++ei    +
  gi|330508820|ref|YP_004385248.1|   6 VTVYSAVQLTERVDRVVLAIENIFPGL---------------IMDIRTDRIDAYDGPQSLRRLHRLLRSQEILDAAR 67 
                                       78888999*****************55...............467778888887789***************88888 PP

                                       CCHCCB-TTSEEEEEEEHHHHHTT---BESSSS...EEEEEE CS
                       RNA_binding  79 eleervdekgklylrldKQaaylgklslvegdd...vIkvki 117
                                       ++ er    + ++++l+KQaay+g +s++ +++   + +++i
  gi|330508820|ref|YP_004385248.1|  68 SVLERGRSCNIIHFQLSKQAAYMGMVSFPPQEEslgSLHIQI 109
                                       88888888899******************9999777666666 PP

>> T2SSM  Type II secretion system (T2SS), protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.3e-06     0.011      87     147 ..      83     142 ..      42     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHCT--EEEEEEETT.EEEEEE--B-HHHHHHHHHHHHHHS--EEEEEEEEE---- CS
                             T2SSM  87 vtrsarqagLalarlqpqgdgsvqvwleevpfeallrWLaeleeqqgvsveeadldradep 147
                                       ++++a+  g+  +  q +  gs+ ++++  + e++++WLa +  + gv vee+dl ++ ++
  gi|330508820|ref|YP_004385248.1|  83 LSKQAAYMGMVSFPPQEESLGSLHIQIQATDPERVIDWLAPVT-ENGVAVEEIDLFEGTSD 142
                                       667788888888888999999**********************.**********9877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1187.42
//
Query:       gi|330508821|ref|YP_004385249.1|  [L=258]
Description: AP endonuclease [Methanosaeta concilii GP6]
Scores for complete 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-29  102.6   0.5    2.7e-29  102.1   0.3    1.3  2  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 !  102.1   0.3   1.5e-33   2.7e-29       3     210 .]      19     216 ..      17     216 .. 0.95
   2 ?   -3.8   0.0      0.41   7.3e+03      65      76 ..     242     253 ..     225     256 .. 0.53

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 1.5e-33
                                       HHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHHH CS
                      AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraiel 78 
                                       +++++G+ g E+   + +  +e    +l e rk+++ +gl i+ + ++++ +   ++  +   +ee v+++k +++l
  gi|330508821|ref|YP_004385249.1|  19 QLEDLGYSGWEIVNEGRQRLTE---GNLPEARKIVETTGLVITIHLPYSDLNLASVN--Q-PiWEETVRQMKTCLDL 89 
                                       6789****************96...6***************9999999999998874..3.259999********** PP

                                       HHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTT CS
                      AP_endonuc_2  79 aaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavds 153
                                       a+++ a+l v+hpG+++ ++   +++aw + +++++e++d+a   ++++a+E++ + ++ lg+  ee++ +++ vd+
  gi|330508821|ref|YP_004385249.1|  90 ASDF-ARLAVVHPGHFSPLGMHMPDAAWLQNIKGIQEICDHASNLDMRVAVENMVNMPAILGRrpEEIEGIIETVDR 165
                                       ****.*****************************************************99999************** PP

                                       TTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 154 pnvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeGei 210
                                       +n+g+ +D+gH++ + ++v+d+lr l+d + h+H++D+ g     rd+h+p+g G++
  gi|330508821|ref|YP_004385249.1| 166 DNLGFIFDVGHANTN-GNVEDFLR-LKDMMIHIHAHDNHG----ERDEHLPVGNGTV 216
                                       **************9.******96.8**************....***********86 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHH CS
                      AP_endonuc_2  65 reesvdalkrai 76 
                                        ++sv++lkr +
  gi|330508821|ref|YP_004385249.1| 242 GQRSVKRLKRLL 253
                                       334455555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1987.08
//
Query:       gi|330508822|ref|YP_004385250.1|  [L=208]
Description: translin family protein [Methanosaeta concilii GP6]
Scores for 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   0.1    7.6e-10   39.1   0.1    1.9  1  Translin  Translin family
  ------ inclusion threshold ------
      0.042   13.5   0.7        1.8    8.3   0.3    2.4  2  DUF2576   Protein of unknown function (DUF2576)
       0.05   13.4   0.1       0.15   11.9   0.0    1.8  2  UBA_4     UBA-like domain


Domain annotation for each model (and alignments):
>> Translin  Translin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.1   1.3e-13   7.6e-10       3     193 ..      25     186 ..      23     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.3e-13
                                       HHHHHHHHHHHHHHHHHHHHHHHTTGSSTTTHHHHHHH.HHHHHHHHHHHTTSS..........GHHHHGGGTH.HH CS
                          Translin   3 reriikasrditaaskkiifllhrvrsekteaqdkkakikkeakeklkeiakllasvaeelqgsnayrYqrqisggl 79 
                                       re+   +sr + ++    i ++hr       + + ++++ +ea+e+l++i++ll        +++  rY+  + g+ 
  gi|330508822|ref|YP_004385250.1|  25 REEALSLSRRVIRLCSSSIRSMHRN------EFPAAKRLVDEAAEELEKIRELL-------GNHQDVRYAGFVDGAE 88 
                                       5666666666666666666666663......34455665699999999999999.......667999********** PP

                                       HHHHHHHHHHHHHHHSS---HHHHHHHTT.---SSSSSS---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHHH CS
                          Translin  80 qeliealsfahYletqtLitleevqkilealkeneedafhltpedYllGlfdLtgELmRfainsvalgdkeekplqi 156
                                       qe+ ea+s ++ +++++++t  ev+  l+                Yl Gl d++gEL R     + +g ++ +    
  gi|330508822|ref|YP_004385250.1|  89 QEYAEAISVYSIITRNEILTPAEVGVELA---------------NYLAGLGDVCGELRRHILDLIRSGRAK-DGEYF 149
                                       ***************99999999998887...............6**************999999999977.99*** PP

                                       HHHHHHHHHHHHTS----HH...HHHHHTTHHHHHHH CS
                          Translin 157 lkflrelragfellnlkndsakdlrkKldvlkqsvkK 193
                                       l+ ++e++  + l++ +  +++ lr+K d  ++ +++
  gi|330508822|ref|YP_004385250.1| 150 LEVMEEIYYLLMLFDYPDAITRGLRRKSDLARSMLER 186
                                       ****************966699*******99988876 PP

>> DUF2576  Protein of unknown function (DUF2576)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3   0.00029       1.8      12      43 ..      20      51 ..      16      54 .. 0.91
   2 ?    3.0   0.0     0.013        77      23      44 ..     130     150 ..     127     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00029
                           DUF2576 12 DrDqikreLnsLrrnvhDLCtrsGtsfDCnkf 43
                                      D+D+ + e  sL r v  LC  s  s+  n f
  gi|330508822|ref|YP_004385250.1| 20 DKDRAREEALSLSRRVIRLCSSSIRSMHRNEF 51
                                      8999999****************999998887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.013
                           DUF2576  23 LrrnvhDLCtrsGtsfDCnkfL 44 
                                       Lrr + DL  rsG + D   fL
  gi|330508822|ref|YP_004385250.1| 130 LRRHILDL-IRSGRAKDGEYFL 150
                                       9******9.59**999999888 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.74   4.4e+03      15      25 ..      64      75 ..      61      76 .. 0.74
   2 ?   11.9   0.0   2.5e-05      0.15       9      33 ..     168     195 ..     168     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.74
                             UBA_4 15 e.ekArqlLean 25
                                      e ek+r+lL  +
  gi|330508822|ref|YP_004385250.1| 64 ElEKIRELLGNH 75
                                      459999999777 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.5e-05
                             UBA_4   9 aiT.Ga..deekArqlLeannWdLerAi 33 
                                       aiT G     + Ar++Le++ +dL +A+
  gi|330508822|ref|YP_004385250.1| 168 AITrGLrrKSDLARSMLERTRGDLTNAL 195
                                       567666445599***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1639.22
//
Query:       gi|330508823|ref|YP_004385251.1|  [L=536]
Description: O-phosphoseryl-tRNA(Cys) synthetase [Methanosaeta concilii GP6]
Scores for complete 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-51  173.4   0.0    5.4e-48  163.6   0.0    2.1  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    9.5e-15   54.4   0.2    2.7e-14   53.0   0.2    1.8  1  SepRS_C          O-phosphoseryl-tRNA synthetase C-terminal do
    9.9e-12   44.7   0.0    3.9e-08   33.0   0.0    2.3  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
  ------ inclusion threshold ------
      0.046   12.8   0.0         14    4.7   0.0    2.7  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)
       0.12   12.3   0.1       0.24   11.3   0.1    1.6  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
       0.16   12.0   0.1       0.39   10.8   0.1    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 !    7.7   0.0   0.00074       2.2       5      43 ..      35      73 ..      31      88 .. 0.84
   2 !  163.6   0.0   1.8e-51   5.4e-48      18     240 ..     123     355 ..     104     359 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00074
                                      SSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSE CS
                      tRNA-synt_2d  5 tlpgkrieagklhpltkvleeikeiflelgfeevegpev 43
                                       +p ++++ g++hp+ +++++++e +++lgf+e+ +p +
  gi|330508823|ref|YP_004385251.1| 35 RYPRNSYSFGSVHPIFDTVQKLREAYIRLGFNEAMNPVM 73
                                      5677888899***********************998753 PP

  == domain 2  score: 163.6 bits;  conditional E-value: 1.8e-51
                                       HHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHH CS
                      tRNA-synt_2d  18 pltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirt 94 
                                         ++ +e +++i++++++ +veg+++     ++ aL   +      ++ +F+  k  ka++++++LR+h+t+ ++ +
  gi|330508823|ref|YP_004385251.1| 123 LSAEEVEALRQILHSYKKGKVEGDDL--VGEIAHALSAHDALIGTVLEKVFPEFKGLKAEATSRTLRSHMTSGWFLS 197
                                       55667899**************8887..577899******************************************* PP

                                       H....TTS-SSEEEEEEEEEEBSST.-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTST.EEEEEEECE CS
                      tRNA-synt_2d  95 l....ekkkppikiisigrvfRrda.vDathlaeFhqveglvvdenvsladlkgvleellkklfgae.vkvrfrpsy 165
                                       l     ++++pi+++s++r+fRr++ +Da +l+++++++++++de+vs++d k+v++ ll+++ g++ +++r + + 
  gi|330508823|ref|YP_004385251.1| 198 LsnlhYRQRLPIRLFSVDRCFRREQaEDAARLMSYYSASCVIMDEDVSIEDGKAVADGLLSQF-GFQkFQFRPDDKR 273
                                       *98888899****************99************************************.99979999999** PP

                                       ETTEEEEEEEEEEE.........CCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHH CS
                      tRNA-synt_2d 166 fpftePsaevdvyl.........vekkkkwlEllgaGmvrpevleavgideevsgfafGlGveRlamlkygieDiRe 233
                                       ++++ P+++++vy+         ++ +++w+E++++G+++p++l++++i   ++++++GlGveR+am+ ++ +D+R+
  gi|330508823|ref|YP_004385251.1| 274 SKYYVPGTQIEVYAyhpglvgsaTKYSSGWVEVATFGIYSPTALSQYDI--PYPVMNLGLGVERIAMILHNSQDVRA 348
                                       *************9*********99************************..************************** PP

                                       HHTT.HH CS
                      tRNA-synt_2d 234 lvendlr 240
                                       l +++++
  gi|330508823|ref|YP_004385251.1| 349 LSYPQFQ 355
                                       *998655 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 !   53.0   0.2   8.9e-18   2.7e-14       1      31 []     435     465 ..     435     465 .. 1.00

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 8.9e-18
                                       EEEEEETTEEEEEES-TTTCCHHHHSEEEEE CS
                           SepRS_C   1 NEvyVYdGnIlGvPdtekwkearenGvsTGI 31 
                                       NE++V++ n++G+P+t++w+ea+++GvsTGI
  gi|330508823|ref|YP_004385251.1| 435 NEIVVHKQNVMGIPRTSRWEEAFNEGVSTGI 465
                                       ******************************9 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00021      0.62       3      50 ..      34      81 ..      32      91 .. 0.86
   2 !   33.0   0.0   1.3e-11   3.9e-08      72     208 ..     184     327 ..     179     331 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00021
                   tRNA_synthFbeta  3 stlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldk 50
                                      ++ P+ +   g+ ++ +++ +klr++ + +G+nE+++  +v ++++ +
  gi|330508823|ref|YP_004385251.1| 34 ERYPRNSYSFGSVHPIFDTVQKLREAYIRLGFNEAMNPVMVEAQDVYR 81
                                      567888888899999*************************99988755 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 1.3e-11
                   tRNA_synthFbeta  72 svlRtsLlpglLevlarNlargnedvrlFEigkvflkdseeel..peeerhlaivltgkreeeswsekaravdfydl 146
                                        +lR+ +++g    l++   r+   +rlF + ++f+ +++e+          ++v++            ++v+ +d 
  gi|330508823|ref|YP_004385251.1| 184 RTLRSHMTSGWFLSLSNLHYRQRLPIRLFSVDRCFRREQAEDAarLMSYYSASCVIMD-----------EDVSIEDG 249
                                       5789999999888877765555555*************44444113444444445555...........55****** PP

                   tRNA_synthFbeta 147 kgivealleslgiekvefep..aehpalhpgrsAeikvdgk..............evGvlGelhpevleafdlkqrv 207
                                       k++++ ll+++g++k++f+p  +  +++ pg + e+++                 ev  +G  +p  l ++d++++v
  gi|330508823|ref|YP_004385251.1| 250 KAVADGLLSQFGFQKFQFRPddKRSKYYVPGTQIEVYAYHPglvgsatkyssgwvEVATFGIYSPTALSQYDIPYPV 326
                                       ********************666699**********6644444555566666667********************98 PP

                   tRNA_synthFbeta 208 y 208
                                       +
  gi|330508823|ref|YP_004385251.1| 327 M 327
                                       6 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 ?   -1.5   0.0      0.34     1e+03     162     183 ..      54      75 ..      36     101 .. 0.68
   2 ?    4.6   0.0    0.0049        15      72     116 ..     194     233 ..     175     244 .. 0.75
   3 ?    4.7   0.0    0.0045        14     287     308 ..     329     350 ..     318     359 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.34
                                       EE-SSS-EEEEHHHHHHHHHTS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 162 kdlkkpfkrltykeaieklnei 183
                                       ++l++ ++rl ++ea++ +  +
  gi|330508823|ref|YP_004385251.1|  54 QKLREAYIRLGFNEAMNPVMVE 75 
                                       4555556666666666654433 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0049
                                       EE-E-S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  72 ffaLtqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFt 116
                                       +f L  s   y+++l +      f++ r+FR E+ +    l  ++
  gi|330508823|ref|YP_004385251.1| 194 WF-LSLSNLHYRQRLPIR----LFSVDRCFRREQAEDAARLMSYY 233
                                       44.777877788877665....9***********98777665665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0045
                                       EEEEHHHHHHHHCT-SSGGGCS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 287 lglGldRlvmlllgsesIrdvi 308
                                       lglG++R+ m+l +s+++r ++
  gi|330508823|ref|YP_004385251.1| 329 LGLGVERIAMILHNSQDVRALS 350
                                       79****************9865 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 ?   11.3   0.1   8.2e-05      0.24      31      51 ..     204     223 ..     177     344 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.2e-05
                                       EBGGSSEEEEEEEEEEBTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  31 rskrLPlklyqiqtkyRdEks 51 
                                       r +rLP++l+ + +++R+E+ 
  gi|330508823|ref|YP_004385251.1| 204 R-QRLPIRLFSVDRCFRREQA 223
                                       3.56***************97 PP

>> Lambda_Bor  Bor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00013      0.39      55      71 ..     301     317 ..     292     320 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                        Lambda_Bor  55 ngLlgvvTlGIYtPrtt 71 
                                        g ++v T+GIY+P+  
  gi|330508823|ref|YP_004385251.1| 301 SGWVEVATFGIYSPTAL 317
                                       67799*********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); 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: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3743.03
//
Query:       gi|330508824|ref|YP_004385252.1|  [L=232]
Description: ribose 5-phosphate isomerase [Methanosaeta concilii GP6]
Scores for complete 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-60  203.2   0.0    2.7e-60  202.9   0.0    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    1.2e-07   31.8   0.4      1e-05   25.5   0.4    2.2  1  DeoRC           DeoR C terminal sensor domain
     0.0032   16.7   0.3      0.007   15.5   0.1    1.6  2  Sugar-bind      Putative sugar-binding domain


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.9   0.0   4.5e-64   2.7e-60       2     170 ..      56     220 ..      55     223 .. 0.96

  Alignments for each domain:
  == domain 1  score: 202.9 bits;  conditional E-value: 4.5e-64
                                       EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESS CS
                    Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlvek 78 
                                       gvptS+q+e+la e +i+l+sl++++ +dlaiDGaD+vd +l +iKGgG+a++rEK+v  +ak f+++ad+sK+ve+
  gi|330508824|ref|YP_004385252.1|  56 GVPTSFQAEQLAIESNIRLTSLNQHPVLDLAIDGADQVDINLMVIKGGGAAHTREKVVSCSAKWFVIVADQSKFVER 132
                                       7**************************************************************************** PP

                                       TTSS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEE CS
                    Rib_5-P_isom_A  79 lgkfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVve 155
                                       l   pvPveV+p a++ + r+le+l ggkp+lR++ +kdgpv+Tdngn+++Dv+f ++iedp++l+++++ ipGVve
  gi|330508824|ref|YP_004385252.1| 133 LT-WPVPVEVIPIAFRLTGRRLEEL-GGKPVLRQGLRKDGPVITDNGNFVMDVDF-GTIEDPRSLAAKISLIPGVVE 206
                                       *6.********************75.*********99******************.6788***************** PP

                                       ESEE-S--SEEEEEE CS
                    Rib_5-P_isom_A 156 tGlFlgladkvlvgk 170
                                       +G+F +l d++++++
  gi|330508824|ref|YP_004385252.1| 207 HGIFDNL-DELYLAR 220
                                       ****988.6777766 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.4   1.7e-09     1e-05       2      41 ..       7      46 ..       6     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.7e-09
                             DeoRC  2 naeeKrrIAkaAaeliedgdtifldaGtTtlelaraLaek 41
                                      n+++K++ ++aAael+++g+++ l++G+T+++ +++L e+
  gi|330508824|ref|YP_004385252.1|  7 NSAAKKAAGEAAAELVRNGMVVGLGTGSTVAWTIKRLGER 46
                                      7899********************************9876 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.2e-06     0.007      34      76 ..       6      49 ..       1      71 [. 0.81
   2 ?   -1.5   0.0      0.18   1.1e+03     127     160 ..      75     111 ..      62     116 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-06
                                      HHHHHHHHHHHHHHHH--TTEEEEE-SSHHHHHHHHHTHH.CCH CS
                        Sugar-bind 34 vlealgraaaqllesllkdgdvvgvgwGrtlsavaealtp.ksl 76
                                       ++a+ +aa++   +l+++g+vvg+g+G t++ ++++l +  + 
  gi|330508824|ref|YP_004385252.1|  6 SNSAAKKAAGEAAAELVRNGMVVGLGTGSTVAWTIKRLGErVRE 49
                                      4556667888899999*******************999874444 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.18
                                       HHHHTSHHHHHHHHHHHT-SEEEEE-...EEHCCCCH CS
                        Sugar-bind 127 eallaersikevlelakkadvalvGi...Gsaseeak 160
                                        +l + ++   +++ a+++d+ l+ i   G+a++++k
  gi|330508824|ref|YP_004385252.1|  75 TSLNQHPVLDLAIDGADQVDINLMVIkggGAAHTREK 111
                                       6788889999999999999998887755455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1609.04
//
Query:       gi|330508825|ref|YP_004385253.1|  [L=111]
Description: cupin domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   38.9   0.0    7.4e-10   38.4   0.0    1.3  1  Cupin_2          Cupin domain
    3.6e-07   30.2   0.0    4.4e-07   29.9   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
    1.1e-05   25.0   0.0    1.6e-05   24.5   0.0    1.3  1  Cupin_3          Protein of unknown function (DUF861)
     0.0013   18.5   0.0     0.0014   18.4   0.0    1.2  1  Cupin_6          Cupin
     0.0022   18.2   0.0     0.0032   17.7   0.0    1.2  1  CENP-C_C         Mif2/CENP-C like
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.026   14.3   0.0    1.5  1  EutQ             Ethanolamine utilisation protein EutQ
      0.019   15.2   0.0      0.029   14.5   0.0    1.3  1  Ectoine_synth    Ectoine synthase
      0.051   13.7   0.0      0.065   13.4   0.0    1.1  1  ARD              ARD/ARD' family
      0.052   13.2   0.0      0.059   13.1   0.0    1.1  1  AraC_binding_2   AraC-binding-like domain
      0.073   13.1   0.0      0.089   12.8   0.0    1.2  1  HemeBinding_Shp  Cell surface heme-binding protein Shp
      0.077   13.4   0.0       0.11   13.0   0.0    1.2  1  Ppnp             Pyrimidine/purine nucleoside phosphorylase


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 !   38.4   0.0   4.5e-13   7.4e-10       8      69 ..      48     108 ..      41     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 4.5e-13
                                       TEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEE CS
                           Cupin_2   8 GesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllv 69 
                                       G+   +h+ p   +++ +++Ge+e+t+ g+ ++l +Gd+++ pag+pH+++  +   + l++
  gi|330508825|ref|YP_004385253.1|  48 GQGLSEHTAPFD-ALVNIVDGEVEITISGKAYRLAKGDCIILPAGEPHALKAISRFKMLLVM 108
                                       556666777776.9999**********************************99955555554 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   2.7e-10   4.4e-07       9      65 ..      44     100 ..      37     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.7e-10
                                       TTSTT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-T CS
                      AraC_binding   9 agypdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesds 65 
                                       a + +++ ++h+ ++  ++ +++G++ +++ g+ y+l +Gd ++lp gepH + + s
  gi|330508825|ref|YP_004385253.1|  44 AFDIGQGLSEHTAPFDALVNIVDGEVEITISGKAYRLAKGDCIILPAGEPHALKAIS 100
                                       5566788899*******************************************9988 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 !   24.5   0.0   9.6e-09   1.6e-05       6      65 ..      39      97 ..      34     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 9.6e-09
                                      CCEEEEEEEECEEEEECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEEECCC CS
                           Cupin_3  6 vfswgiwectpGkfrltyeedEfcyileGevkvtpeggetvelraGDlvvlpkglsgtwd 65
                                      + + + +    G  + t + d ++ i+ Gev++t  +g++++l +GD + lp+g   +++
  gi|330508825|ref|YP_004385253.1| 39 TATIFAFDIGQGLSEHTAPFDALVNIVDGEVEITI-SGKAYRLAKGDCIILPAGEPHALK 97
                                      55666666777777788889999************.******************865555 PP

>> Cupin_6  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.5e-07    0.0014      35      74 ..      60      97 ..      30     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.5e-07
                           Cupin_6 35 alhvvlrGscwlidpasgepvrLsagdvvllpggephvla 74
                                      al+ ++ G++ ++  +  +  rL++gd+++lp geph+l 
  gi|330508825|ref|YP_004385253.1| 60 ALVNIVDGEVEITISG--KAYRLAKGDCIILPAGEPHALK 97
                                      6778999******767..67******************95 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.9e-06    0.0032      39      73 ..      64      98 ..      53     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
                                      EEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE CS
                          CENP-C_C 39 ViqGrvevtvsktsfvigkgsvFqvPagneysieN 73
                                      ++ G+ve+t+s++ ++++kg+  + Pag   +++ 
  gi|330508825|ref|YP_004385253.1| 64 IVDGEVEITISGKAYRLAKGDCIILPAGEPHALKA 98
                                      689*************************9988765 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.6e-05     0.026      90     139 ..      53     102 ..       3     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                              EutQ  90 dwtlnydeidyvieGrldvlidGrkvvaeaGdviliPkgskiefsvtdea 139
                                       + t  +d +  +++G++++ i G+      Gd i++P g    +   +  
  gi|330508825|ref|YP_004385253.1|  53 EHTAPFDALVNIVDGEVEITISGKAYRLAKGDCIILPAGEPHALKAISRF 102
                                       5677899999***************************9976665555555 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.8e-05     0.029      63     106 ..      66     107 ..      53     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                       E--EEEEETTT--EEEE-TTEEEEETTT-EEEEEESS-EEEEEE CS
                     Ectoine_synth  63 eGegeveeledgevyeikpgtlYlldkhdkHllrakkelrlvcv 106
                                       +  geve + +g+ y++ +g++ +l   + H l+a + ++++ v
  gi|330508825|ref|YP_004385253.1|  66 D--GEVEITISGKAYRLAKGDCIILPAGEPHALKAISRFKMLLV 107
                                       4..56666678**************************9998866 PP

>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     4e-05     0.065      44     133 ..       9      94 ..       2     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4e-05
                               ARD  44 deeeaeeeekilktkeeekkdi.dvevlkestpnfdeklekFfeEhlhedeeirliveGtgyFdvrskdeawirvlv 119
                                        +  ++ +e ++++++ +++   +++ ++ +   f   + + ++Eh+  ++ +  iv+G+    +   ++a+    +
  gi|330508825|ref|YP_004385253.1|   9 AAPRVKRLEDLVAYQDGSVVSReIIHKSTGTATIFAFDIGQGLSEHTAPFDALVNIVDGEV--EITISGKAYR---L 80 
                                       4555566666666666555544357778888888888899999***************997..6777888887...9 PP

                               ARD 120 ekGDLivlPagiyh 133
                                        kGD i+lPag  h
  gi|330508825|ref|YP_004385253.1|  81 AKGDCIILPAGEPH 94 
                                       9**********999 PP

>> AraC_binding_2  AraC-binding-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.6e-05     0.059      61     106 ..      64     109 ..      36     111 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.6e-05
                    AraC_binding_2  61 plsGraeveqggrevvlgpgdavvldpgrpyrlrwsadceqlvlri 106
                                       ++ G++e++  g+ ++l+ gd+++l +g+p  l    ++++l+++i
  gi|330508825|ref|YP_004385253.1|  64 IVDGEVEITISGKAYRLAKGDCIILPAGEPHALKAISRFKMLLVMI 109
                                       678******************************9999999999998 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 ?   12.8   0.0   5.5e-05     0.089      27      54 ..      40      67 ..      22      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.5e-05
                   HemeBinding_Shp 27 ggehsfdigqgmvegtvysdamlevsda 54
                                          +fdigqg+ e t   da++++ d 
  gi|330508825|ref|YP_004385253.1| 40 ATIFAFDIGQGLSEHTAPFDALVNIVDG 67
                                      34578*******************9985 PP

>> Ppnp  Pyrimidine/purine nucleoside phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.5e-05      0.11       5      76 ..      21      92 ..      18     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.5e-05
                                      EECCCTEEEEEEEETTSEEEEEEEE-SEC..EEEEESS-EEEEEEESEEEEEETT-SS-EEEETT-EEEE-TTE CS
                              Ppnp  5 vyfdgkvksravefadgskktvGvmlpge..yeFgtsakEvmevvsGelevklpgeeewktykagesFevpans 76
                                       y dg v+sr++  +++ ++t+     g+   e ++    ++++v+Ge+e++++g+    ++++g+   +pa +
  gi|330508825|ref|YP_004385253.1| 21 AYQDGSVVSREIIHKSTGTATIFAFDIGQglSEHTAPFDALVNIVDGEVEITISGKA--YRLAKGDCIILPAGE 92
                                      599*************99***999998765366777778899************987..344444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 795.59
//
Query:       gi|330508826|ref|YP_004385254.1|  [L=247]
Description: metallo-beta-lactamase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-19   69.6   0.1    3.1e-19   69.3   0.1    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.4e-08   35.0   2.0    4.9e-07   29.9   0.3    2.6  3  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0039   17.1   0.0     0.0066   16.4   0.0    1.4  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 !   69.3   0.1   5.1e-23   3.1e-19       3     200 ..      32     212 ..      31     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 5.1e-23
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EE....EEEEEEHHHHHHCCTTCG CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkk....lplyapkgvlavleanfv 75 
                                       +L+D+g +++   l +       + +++id V+l+h H DH+++ll l+ +r+ +    l +++p+g+++  e+   
  gi|330508826|ref|YP_004385254.1|  32 LLLDCGAGTLLR-LDQV-----GAGPEAIDTVVLSHLHLDHVHDLLALANGRYLSglqgLSIFGPAGTREWFESLQA 102
                                       689999996544.3333.....67788***********************55544455699*********9988755 PP

                                       HHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHH CS
                     Lactamase_B_2  76 ylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeige 152
                                       +    e  + +v+el++ +sf+++  g++i a +a h+            l++r+e +++ ++y+gDt+   +++++
  gi|330508826|ref|YP_004385254.1| 103 AYPNLERMESHVQELKAMDSFSIK--GFDIFAEEALHSVTA---------LAYRLEAEERVIVYSGDTEPS-ARVAA 167
                                       5544444699*************9..777999999998887.........*******************54.58899 PP

                                       HHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 153 rlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                       + +g dll++++ + e+        H tp +   ++   + kr+vl+H
  gi|330508826|ref|YP_004385254.1| 168 LADGSDLLIHECSFPEPFD---VTNHTTPLKLGNMLSNHDLKRVVLTH 212
                                       **************99988...789**********************9 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.3   8.3e-11   4.9e-07      14      65 ..      28      74 ..      16      80 .. 0.79
   2 ?    3.2   0.0     0.013        77     128     155 ..     136     163 ..     111     184 .. 0.85
   3 ?   -0.9   0.1      0.23   1.4e+03      44      53 ..     204     213 ..     198     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 8.3e-11
                                      TTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCT CS
                       Lactamase_B 14 dggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglv 65
                                      ++  +L D+G +t   +      ++g +p+ +d+v+l+HlHlDH+ +l  l+
  gi|330508826|ref|YP_004385254.1| 28 NDLPLLLDCGAGTLLRLD-----QVGAGPEAIDTVVLSHLHLDHVHDLLALA 74
                                      555667777777777776.....6**********************999887 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.013
                                       TTSTSCCEEEEEETTCCEEEECTTTSSH CS
                       Lactamase_B 128 gpghghghgvveygggkvlftGDallag 155
                                        +  +++ +++e++++ ++++GD+ +++
  gi|330508826|ref|YP_004385254.1| 136 LHSVTALAYRLEAEERVIVYSGDTEPSA 163
                                       6777889999**************9876 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.23
                                       GEEEEE-SBS CS
                       Lactamase_B  44 dvdavilTHl 53 
                                       d+++v+lTHl
  gi|330508826|ref|YP_004385254.1| 204 DLKRVVLTHL 213
                                       899******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 !   16.4   0.0   1.1e-06    0.0066      30     116 ..      47     161 ..      20     177 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-06
                     Lactamase_B_3  30 yeppaeeaDlvlisqaledHahletlkqlaenvkvlee................................gesle.v 73 
                                       +++ +e +D v++s+ + dH h     +   n ++l++                                 ++l+ +
  gi|330508826|ref|YP_004385254.1|  47 VGAGPEAIDTVVLSHLHLDHVHDLLALA---NGRYLSGlqglsifgpagtrewfeslqaaypnlermeshVQELKaM 120
                                       455679****************886666...5666666555666666665555555555555555554332333313 PP

                     Lactamase_B_3  74 ggleiravatshdavggsergenngflleqdgltiyhlGhlah 116
                                       ++++i+++   +++    +  +  +++le ++  i++ G++  
  gi|330508826|ref|YP_004385254.1| 121 DSFSIKGFDIFAEEA--LHSVTALAYRLEAEERVIVYSGDTEP 161
                                       455555555555433..34667799*****9******999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1819.12
//
Query:       gi|330508827|ref|YP_004385255.1|  [L=231]
Description: SPP-like hydrolase [Methanosaeta concilii GP6]
Scores for complete 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   90.2   0.0    1.4e-15   57.7   0.0    2.1  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    4.8e-07   30.3   0.2     0.0033   17.8   0.0    2.3  2  Hydrolase        haloacid dehalogenase-like hydrolase
    0.00025   20.3   0.0     0.0015   17.7   0.0    1.9  2  Trehalose_PPase  Trehalose-phosphatase
     0.0029   17.2   0.0      0.026   14.1   0.0    2.0  1  S6PP             Sucrose-6F-phosphate phosphohydrolase
     0.0055   17.1   0.1       0.18   12.2   0.0    2.3  2  HAD              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 !   30.7   0.0   6.9e-11   2.5e-07       1      89 [.       5      92 ..       5     118 .. 0.87
   2 !   57.7   0.0   3.9e-19   1.4e-15     178     250 ..     141     213 ..     134     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 6.9e-11
                                      EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE..ECTTTEEEEE- CS
                       Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali..ddekgkilyks 77
                                      ia+D+DGTL + +  + +++  aik+l    + v+++TG+ + + + v   lg   ++ia NG++    + + +il+++
  gi|330508827|ref|YP_004385255.1|  5 IAVDIDGTLTDMNRVLCPESLLAIKRLF---VPVILSTGNTHCFSRTVSVILGTPRIFIAENGGVLsySEDELEILADQ 80
                                      89*************************9...***********************************8666666777777 PP

                                      -B-HHHHHHHHH CS
                       Hydrolase_3 78 tiskedvkeiik 89
                                      ++ ++++ ++ +
  gi|330508827|ref|YP_004385255.1| 81 QVCEDAFLRLSE 92
                                      777777666655 PP

  == domain 2  score: 57.7 bits;  conditional E-value: 3.9e-19
                                       EEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTH CS
                       Hydrolase_3 178 yleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedG 250
                                        + i  + v+Kgt+l+++a++ln+++ + +a+GD++ D +M+e+ag+   +gn+++ +k+++dyv k+    G
  gi|330508827|ref|YP_004385255.1| 141 AVHIKDRRVNKGTGLTRIAQHLNLDPMDFAAIGDSMSDRPMFEVAGFRASVGNGRPGLKEISDYVAKKDFGAG 213
                                       56788899*********************************************************99875555 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00013      0.45       1      17 [.       2      18 ..       2      67 .. 0.85
   2 !   17.8   0.0   9.1e-07    0.0033     150     210 .]     124     186 ..     110     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                      SSEEEEESBTTTBCHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                         Hydrolase  1 iktvvfDkdGTLttgep 17
                                      ik+++ D+dGTLt+ ++
  gi|330508827|ref|YP_004385255.1|  2 IKAIAVDIDGTLTDMNR 18
                                      89***********9873 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 9.1e-07
                                       HHHHHTT..GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 150 raanqlG..ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       r a++lG   d++d  +a+ i+     +  g+ ++++ L+ +p + a++GD++ D ++++ Ag
  gi|330508827|ref|YP_004385255.1| 124 RRADELGlpVDIVDTAFAVHIKDRRVNKGTGLTRIAQHLNLDPMDFAAIGDSMSDRPMFEVAG 186
                                       778999998888899999999999999********************************9998 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.1   3.6e+02       2      12 ..       7      17 ..       6      26 .. 0.87
   2 !   17.7   0.0   4.1e-07    0.0015     145     204 ..     132     188 ..     118     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.1
                                      EETBTTTB--- CS
                   Trehalose_PPase  2 lDydGTlspiv 12
                                      +D+dGTl+++ 
  gi|330508827|ref|YP_004385255.1|  7 VDIDGTLTDMN 17
                                      7*******986 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 4.1e-07
                                       --EEEE-SSEEEEE-S---HHHHHHHHHHTS--------EEEEEE-SSTTHHHHTTS-TT CS
                   Trehalose_PPase 145 dlevtqgkkvvevrpqgvsKGkaverlleslgsadseddfvlciGDdrtDedmFsvlrkt 204
                                       ++++ +    v ++ ++v+KG  ++r+ ++l+ +  + df+ +iGD  +D  mF+v   +
  gi|330508827|ref|YP_004385255.1| 132 PVDIVDTAFAVHIKDRRVNKGTGLTRIAQHLNLD--PMDFA-AIGDSMSDRPMFEVAGFR 188
                                       566666777899*********************9..78888.9************98766 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   7.2e-06     0.026     134     211 ..     120     196 ..       2     212 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.2e-06
                                       HHHHHHHHTTTS-EEEEEETTTEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHH.TSSSEEEE-TT- CS
                              S6PP 134 keleqlLekreldvkviyssgkdlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeell.ignvlgVvVgna 209
                                        +l ++  + +l+v+++     ++ +  +r +kg  l+ +a++l+l++  +   Gds  D+ ++ ++++++  Vgn 
  gi|330508827|ref|YP_004385255.1| 120 GALVRRADELGLPVDIV-DTAFAVHIKDRRVNKGTGLTRIAQHLNLDPMDFAAIGDSMSDRPMFeVAGFRA-SVGNG 194
                                       44444446666666665.4455677888999*********************************6666654.56776 PP

                                       -H CS
                              S6PP 210 qe 211
                                       ++
  gi|330508827|ref|YP_004385255.1| 195 RP 196
                                       65 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.037   1.3e+02       2      13 ..       6      17 ..       5      47 .. 0.82
   2 !   12.2   0.0   5.1e-05      0.18     121     188 .]     128     183 ..     120     183 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.037
                               HAD  2 lfDfDgTLldgd 13
                                        D+DgTL+d +
  gi|330508827|ref|YP_004385255.1|  6 AVDIDGTLTDMN 17
                                      57******9965 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.1e-05
                               HAD 121 elg.adevlatelevddrltgelglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                       elg + ++++t ++v  +++ +      + +g    + l +   a++ ++d+ +  a+GDs+sD p+++
  gi|330508827|ref|YP_004385255.1| 128 ELGlPVDIVDTAFAV--HIKDR-----RVNKG----TGLTR--IAQHLNLDPMDFAAIGDSMSDRPMFE 183
                                       555555566663332..22222.....33333....55555..5557788888899***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1774.59
//
Query:       gi|330508828|ref|YP_004385256.1|  [L=224]
Description: hypothetical protein MCON_3140 [Methanosaeta concilii GP6]
Scores for 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   50.8   0.7      2e-13   50.8   0.7    1.9  2  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1     0.099   1.8e+03       2      25 ..      15      39 ..      14      62 .. 0.54
   2 !   50.8   0.7   1.1e-17     2e-13       2      84 ..      90     184 ..      89     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.099
                          CxxCxxCC  2 Cke.CgaCCkelkvklteedlerlk 25
                                      C + C   C e k + + ++l r +
  gi|330508828|ref|YP_004385256.1| 15 CHQlCRSSCIEDKRQERHKELLRNR 39
                                      8888866666444444444443333 PP

  == domain 2  score: 50.8 bits;  conditional E-value: 1.1e-17
                          CxxCxxCC   2 CkeCgaCCk..elkvklteedlerlkaaevaeeeeeskkiak......adgrCvfldeetklCkiYeeRpkicrlfp 70 
                                       C++Cg CC    ++  l++ed++r++a+   ++ e  +++ +       +++C+f+d+ ++ CkiYe Rp++cr +p
  gi|330508828|ref|YP_004385256.1|  90 CQQCGLCCFtpGAGLLLEKEDFDRIAAKIGKRKLERLSRFDRaldgwiLKQPCPFYDHAKRGCKIYEIRPLTCRKYP 166
                                       ********978889999********9998877777777777799***99**************************** PP

                          CxxCxxCC  71 as....ekeellaraetC 84 
                                        +    +  ++la++ +C
  gi|330508828|ref|YP_004385256.1| 167 LHpplaQLPYNLAVDAFC 184
                                       987776666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1785.65
//
Query:       gi|330508829|ref|YP_004385257.1|  [L=154]
Description: hypothetical protein MCON_3142 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00076   19.3   2.2    0.00076   19.3   2.2    1.9  2  OEP          Outer membrane efflux protein
  ------ inclusion threshold ------
        0.1   12.5   0.0       0.17   11.7   0.0    1.5  1  TFIIIC_sub6  TFIIIC subunit triple barrel domain


Domain annotation for each model (and alignments):
>> OEP  Outer membrane efflux protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1     0.071   6.4e+02      14      30 ..      13      30 ..       2      43 .. 0.55
   2 !   19.3   2.2   8.5e-08   0.00076     126     178 ..      56     108 ..      54     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.071
                               OEP 14 dlkaaeaeieaa.eanlk 30
                                       l+a++ +i++a e  +k
  gi|330508829|ref|YP_004385257.1| 13 GLAAYQDAIRSAnEDLIK 30
                                      344444444444333333 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 8.5e-08
                               OEP 126 laeealklaekalelaearykaGlislldvlqaqvrllqaraelaeaeqqlql 178
                                       l+++  ++a+++ + a ++++  l+++  vlq qv+++qa+++++ a+ ++ +
  gi|330508829|ref|YP_004385257.1|  56 LYNKIKDAAKRTEDEASDLLNSDLATANPVLQLQVNYYQAQSQRLYAKMEIMD 108
                                       678999*********************55******************998865 PP

>> TFIIIC_sub6  TFIIIC subunit triple barrel domain
   #    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      17      55 ..      63      99 ..      18     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
                                      ----T.....T-EEEEE-TTSSS-EEEETTEEEEEEEE- CS
                       TFIIIC_sub6 17 faeraeeeeakkdlqilgLdtenPlisigdkvfeGewee 55
                                       a+   +e++ +dl  ++L t nP+++ + + ++ + ++
  gi|330508829|ref|YP_004385257.1| 63 AAK--RTEDEASDLLNSDLATANPVLQLQVNYYQAQSQR 99
                                      333..35999999********************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1109.00
//
Query:       gi|330508830|ref|YP_004385258.1|  [L=90]
Description: hypothetical protein MCON_3144 [Methanosaeta concilii GP6]
Scores for complete 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   56.0   0.0    3.5e-15   55.7   0.0    1.0  1  HTH_45    Winged helix-turn-helix
     0.0017   18.1   0.0     0.0019   18.0   0.0    1.2  1  DUF4364   Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.058   13.3   0.0      0.083   12.8   0.0    1.5  1  HxlR      HxlR-like helix-turn-helix
       0.11   13.0   0.0       0.14   12.6   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 !   55.7   0.0   7.9e-19   3.5e-15       1      74 [.       5      81 ..       5      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 7.9e-19
                            HTH_45  1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkelee 74
                                      rR+   I ++IL+ +  ++a+kT+i+ kanL++  +++ ++ L+++gl     + sk  Y++T kG el + + ++++
  gi|330508830|ref|YP_004385258.1|  5 RRTNDIIASEILKLC-MNGASKTRIIHKANLNFLSAKSHIESLMNNGLMeavpTGSKVIYRTTPKGAELSRVFGQFHS 81
                                      899999*********.99******************************877677799************998888876 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.3e-07    0.0019      25      74 ..      28      77 ..      11      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-07
                           DUF4364 25 ileneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfe 74
                                      i+ +  +n+++ ++ ++ L+++gl e+  + +k +y+ T+kG+e  + f 
  gi|330508830|ref|YP_004385258.1| 28 IIHKANLNFLSAKSHIESLMNNGLMEAVPTGSKVIYRTTPKGAELSRVFG 77
                                      5678889**********************9**************999886 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05     0.083      43      81 ..      46      81 ..       1      88 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                                      HHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHH CS
                              HxlR 43 LeqdglierevypevPpkveYsltekGrslepvlqelkk 81
                                      L ++gl+e+++   ++ kv Y+ t+kG +l+ v+ +++ 
  gi|330508830|ref|YP_004385258.1| 46 LMNNGLMEAVP---TGSKVIYRTTPKGAELSRVFGQFHS 81
                                      44455544433...4679**************9988775 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.2e-05      0.14      17      68 .]      21      69 ..      11      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.2e-05
                            HTH_27 17 rrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +++++++++ + n++  ++ + ++ L ++GL+e  +       + +r T+kG
  gi|330508830|ref|YP_004385258.1| 21 NGASKTRIIHKANLNFLSAKSHIESLMNNGLMEAVPTG---SKVIYRTTPKG 69
                                      577899**************************666553...66********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 699.39
//
Query:       gi|330508831|ref|YP_004385259.1|  [L=280]
Description: hypothetical protein MCON_3145 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2029.47
//
Query:       gi|330508832|ref|YP_004385260.1|  [L=195]
Description: 50S ribosomal proteinL15 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-77  260.1  11.1    1.2e-77  260.0  11.1    1.0  1  Ribosomal_L15e  Ribosomal L15


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.0  11.1   6.7e-82   1.2e-77       1     190 [.       3     189 ..       3     190 .. 0.99

  Alignments for each domain:
  == domain 1  score: 260.0 bits;  conditional E-value: 6.7e-82
                                       -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..--- CS
                    Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskg 77 
                                       ++y+y+ ++w ++++ ++ +l + rl  +rqe++v+++erptrldrAr+LGYkakqGi+v+rv+vrrGgr+k  s++
  gi|330508832|ref|YP_004385260.1|   3 SFYSYIGDAWSSPREGYVGALRQDRLKAWRQESTVQKIERPTRLDRARALGYKAKQGIIVARVKVRRGGRRK--SRY 77 
                                       68**********************************************************************..*** PP

                                       SS---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGG CS
                    Ribosomal_L15e  78 ktgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkv 154
                                        ++rk++++gvn++++aks+q+iaeer+gr+++n++vLnSYwv+eDg++k+yEvilvDp++++i++dk++ w++++v
  gi|330508832|ref|YP_004385260.1|  78 ERNRKTSKMGVNTITMAKSIQRIAEERAGRRYRNMEVLNSYWVAEDGKQKFYEVILVDPHSTSIKSDKDLCWVADNV 154
                                       ***************************************************************************** PP

                                       GTTGGGGT-SHHHHHHTT-S-SS.TT-TTTSS-TGG CS
                    Ribosomal_L15e 155 hkhRelrGltsagkksRGlrkkglkgaekirgsrra 190
                                       h++R++rG+tsag+k+RG r+kg  g+ek+r+ +ra
  gi|330508832|ref|YP_004385260.1| 155 HRGRAVRGKTSAGRKGRGQRHKG-FGTEKTRPGIRA 189
                                       ***********************.999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1447.80
//
Query:       gi|330508833|ref|YP_004385261.1|  [L=138]
Description: hypothetical protein MCON_3147 [Methanosaeta concilii GP6]
Scores for complete 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-32  111.5   0.0    3.6e-32  111.1   0.0    1.1  1  RNA_binding  RNA binding
  ------ inclusion threshold ------
      0.071   13.4   0.1        0.1   12.8   0.1    1.3  1  DUF2267      Uncharacterized conserved protein (DUF2267)


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 !  111.1   0.0     4e-36   3.6e-32       1     115 [.       4     116 ..       4     120 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 4e-36
                                       EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCHHHHH CS
                       RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeeikeLl 77 
                                       ki++rafv  TEde +V+eals ++p +  +i++++a Gh+gn+i+ilea l++k+a+++++ l+e+l +e+  +L 
  gi|330508833|ref|YP_004385261.1|   4 KISIRAFVAVTEDEGRVREALSIFVPLD--HISSQTALGHFGNEIKILEASLRRKEAQAFFQILHEQLPSEDSFRLH 78 
                                       699***********************88..69********************************************* PP

                                       HCCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEE CS
                       RNA_binding  78 keleervdekgklylrldKQaaylgklslvegddvIkv 115
                                       +e++er++  ++++lrldKQaay+g ++l+e++d+  +
  gi|330508833|ref|YP_004385261.1|  79 HEIPERLEGASHFHLRLDKQAAYKGLFRLTESKDALDI 116
                                       **********************************8876 PP

>> DUF2267  Uncharacterized conserved protein (DUF2267)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.2e-05       0.1      63     120 ..      22      86 ..       6      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                                       S......-----SHHHHHHHHHHTS.....E.HHHHHHHHHHHHHHHS-HHHHHHHHHTS-HHHH CS
                           DUF2267  63 e......pgkrfdreeflervaeelgvdped.aeqaaraVfaalkealsegeiedvaaqLPkdlr 120
                                       e      p + +++++ l +  +e ++ +++ +++ a+a f+ l+e+l+ ++  ++ ++ P+ l+
  gi|330508833|ref|YP_004385261.1|  22 EalsifvPLDHISSQTALGHFGNEIKILEASlRRKEAQAFFQILHEQLPSEDSFRLHHEIPERLE 86 
                                       15555656678899999999999999888888999999999999999999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 968.25
//
Query:       gi|330508834|ref|YP_004385262.1|  [L=225]
Description: ribonuclease P protein component 3 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-31  109.4   0.0    2.1e-31  109.1   0.0    1.1  1  RNase_P_p30  RNase P subunit p30


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 !  109.1   0.0   1.2e-35   2.1e-31       8     213 ..      10     204 ..       6     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 1.2e-35
                                       H.........HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H..HHH CS
                       RNase_P_p30   8 psddskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpskl.qrl 83 
                                       ++++s++ sr+++++++lgy g++i++t    +  +p+a e           +++g+++  + +++++d ++l  r+
  gi|330508834|ref|YP_004385262.1|  10 YPEGSSSASRMALKAKSLGYGGIIICNTAP-GNLFRPEAAE-----------RIRGIEVAIGAEVMAKDVKSLrSRI 74 
                                       5666677779********************.6666666666...........999****************999*** PP

                                       HHHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEESHHHHHS-HHHHHHH CS
                       RNase_P_p30  84 skvrqkfdllavrPttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEinyspllrdsglaRrnf 160
                                       + +r +++ll +r  te+++r a e+++vD+++  ++sr p g+    +raA  ++va+ ++++p +r sg+ R+++
  gi|330508834|ref|YP_004385262.1|  75 TSLRPRYHLLLIRAATEELVRTASEDPNVDVLIPSYSSRRPLGIA--AARAAKLNQVAIGFDLGPFFRLSGRHRSRW 149
                                       *****************************************9886..6889999*********************** PP

                                       HHHHHHHHHHHHH..--EEEE--BSSGGG---HHHHHHHHHHHT--HHHHHHTTT CS
                       RNase_P_p30 161 isnarkllrltrg..kgvviSSgAesplelRnpydiinLlktlGLeedrakeavs 213
                                       ++ + ++l+l+r+   +++++ gA+s+l+lR+p+dii+L++++G+e ++a  a+s
  gi|330508834|ref|YP_004385262.1| 150 LESLGRNLQLARKfdLRLLLTVGARSHLDLRSPRDIIALAEVMGFEHQEACRALS 204
                                       *************9999********************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1605.95
//
Query:       gi|330508835|ref|YP_004385263.1|  [L=179]
Description: ribonuclease P protein component 2 [Methanosaeta concilii GP6]
Scores for 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   0.1    1.7e-15   57.1   0.0    1.4  2  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 !   57.1   0.0   9.7e-20   1.7e-15       1     102 [.      13     107 ..      13     108 .. 0.94
   2 ?   -3.7   0.0      0.81   1.4e+04      55      61 ..     129     135 ..     122     141 .. 0.60

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 9.7e-20
                                       EEEEEEEEESS......-HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT-- CS
                     RNase_P_Rpp14   1 RYllveilypdeeeelteksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtlit 77 
                                       RY+++++  +    e++ k+l+k+i +s ++lfGd+g++k +   ++++f+   + +i+R +++++++++a+L+ i+
  gi|330508835|ref|YP_004385263.1|  13 RYMIFQLEAEG---EIEGKDLIKEIIASQHTLFGDIGSAKNRL--HLISFDG--RQGILRFHHKHMDQARATLASIH 82 
                                       9*********9...5789*******************999888..6777776..89********************* PP

                                       EETTEEEEEEEEEEESSHHHHHHHT CS
                     RNase_P_Rpp14  78 kiegrpvvfrvvrvsGTikkaeeea 102
                                       +i+g+++ ++  +vsGTik+a e++
  gi|330508835|ref|YP_004385263.1|  83 SIQGTRAALQAKGVSGTIKSATEKY 107
                                       *********************9987 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.81
                                       TEEEEEE CS
                     RNase_P_Rpp14  55 staiiRc 61 
                                       s +iiR+
  gi|330508835|ref|YP_004385263.1| 129 SGCIIRT 135
                                       3345554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1374.51
//
Query:       gi|330508836|ref|YP_004385264.1|  [L=221]
Description: exosome complex RNA-binding protein RRP4 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-09   38.1   0.4    2.5e-09   37.4   0.4    1.3  1  KH_6          KH domain
    1.8e-06   27.7   0.1    3.3e-06   26.8   0.1    1.5  1  KH_1          KH domain
    4.2e-06   27.0   0.0    1.5e-05   25.2   0.0    1.9  2  S1            S1 RNA binding domain
    5.3e-06   26.1   0.0    1.3e-05   24.9   0.0    1.6  1  ECR1_N        Exosome complex exonuclease RRP4 N-terminal reg
    5.3e-05   23.0   0.3    9.9e-05   22.1   0.3    1.4  1  KH_2          KH domain
  ------ inclusion threshold ------
       0.04   13.8   0.0      0.084   12.7   0.0    1.5  1  Alpha-amyl_C  Alpha-amylase, C terminal


Domain annotation for each model (and alignments):
>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.4   8.3e-13   2.5e-09       1      42 [.     137     181 ..     137     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 8.3e-13
                              KH_6   1 GmlfeVslslvrRll...nhvLeeLgkagpfeiavGlNGriWvks 42 
                                       G+++e+s   v+Rl+     ++++L+k++ + i vG+NGriW+++
  gi|330508836|ref|YP_004385264.1| 137 GQVIEISHTRVPRLIgkgGSMISMLKKEVNCSIFVGQNGRIWING 181
                                       99*************9995555999999***************86 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   1.1e-09   3.3e-06       3      64 ..     139     193 ..     137     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.1e-09
                                       EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHH CS
                              KH_1   3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkeli 64 
                                       +i++ +  v+r+IGkgGs+I  +++e +++I v  +      +  + i G +++ + A++ i
  gi|330508836|ref|YP_004385264.1| 139 VIEISHTRVPRLIGKGGSMISMLKKEVNCSIFVG-Q------NGRIWINGCADDTDLALKTI 193
                                       7899*********************88*****75.3......34688888666688877766 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   0.0       1.4   4.1e+03      30      52 ..       5      26 ..       2      32 .. 0.59
   2 !   25.2   0.0     5e-09   1.5e-05       2      68 ..      55     121 ..      54     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                                      EEEEGGGSSSSCEESCHHHCEET CS
                                S1 30 gfvpaselsrdarvedpdevlkv 52
                                      + vp  +ls da +++++ ++ +
  gi|330508836|ref|YP_004385264.1|  5 VVVPGDLLSEDA-KRSGEGTYIK 26
                                      678888888884.4444444433 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 5e-09
                                       STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTT CS
                                S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrr 68 
                                       p+ g+ v G+V+++t  + +V++  + +g++++se + +   ++ ++ l++G  +  +v +vd + +
  gi|330508836|ref|YP_004385264.1|  55 PAPGDNVIGVVKDITFSNWIVDINSPYDGLLHISEFPKRIESDEMSKYLRIGSSIMTRVKDVDPTMK 121
                                       678999*********************************99999*******************8866 PP

>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   4.2e-09   1.3e-05       1      34 [.       5      37 ..       5      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.2e-09
                                      EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGt 34
                                      +V+PG+ l +++   +G+GTY+++g++y+ + G 
  gi|330508836|ref|YP_004385264.1|  5 VVVPGDLL-SEDAKRSGEGTYIKDGSVYSLLYGL 37
                                      69******.888899****************995 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.3   3.3e-08   9.9e-05      26      69 ..     137     180 ..     120     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.3e-08
                                       EEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEE CS
                              KH_2  26 rviiviresqpgivIGkgGsnikkigkelrkdieklegkkVkln 69 
                                       + +i i   +  ++IGkgGs+i +++ke++  i + +++++++n
  gi|330508836|ref|YP_004385264.1| 137 GQVIEISHTRVPRLIGKGGSMISMLKKEVNCSIFVGQNGRIWIN 180
                                       5678889999***********************99999999987 PP

>> Alpha-amyl_C  Alpha-amylase, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.8e-05     0.084      27      57 ..      70     100 ..      58     105 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.8e-05
                      Alpha-amyl_C  27 Fsdsv..ielkysGeLllssssFPkkikeskli 57 
                                       Fs+ +  i++ y G L +  s+FPk+i ++++ 
  gi|330508836|ref|YP_004385264.1|  70 FSNWIvdINSPYDGLLHI--SEFPKRIESDEMS 100
                                       665431277788886655..56*******9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1700.39
//
Query:       gi|330508837|ref|YP_004385265.1|  [L=253]
Description: exosome complex exonuclease 1 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-33  114.5   0.0      7e-33  113.9   0.0    1.3  1  RNase_PH    3' exoribonuclease family, domain 1
    2.9e-16   59.2   0.1    5.3e-16   58.4   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 !  113.9   0.0   7.9e-37     7e-33       1     132 []      25     154 ..      25     154 .. 0.93

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 7.9e-37
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CC.EEEECCCCECCCCEC-C...S...HHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddae.galdveveyapfasgerrregrpsdeei 76 
                                       elR+++ie g+l++a+GS+y+e+G +kv+a+v+gp+e++p+   ++++   +  ++++a+f+ +er+r   p++++ 
  gi|330508837|ref|YP_004385265.1|  25 ELRPVKIEVGILARADGSCYIEMGGNKVIAAVYGPREVHPRHL-QEVTrAIVRYRYNMASFSVEERKR-PGPDRRSY 99 
                                       79************************************77776.444424499999999*******77.56****** PP

                                       HHHHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  77 elsrlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                       els++  +al+p+il++ +p+s id++++vl++d  ++  a inaa +ALadagip
  gi|330508837|ref|YP_004385265.1| 100 ELSKVSREALEPVILTSFFPRSVIDVFVEVLQADA-GTRTAGINAAAVALADAGIP 154
                                       ***********************************.*******************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 !   58.4   0.1   5.9e-20   5.3e-16       2      67 .]     158     221 ..     157     221 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 5.9e-20
                                       --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHHH CS
                        RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkkg 67 
                                       ++++++ gkv+d++vlDp keE++ +++dl++a++ ++++ tlm+++g+ l+++++ +a+ +A kg
  gi|330508837|ref|YP_004385265.1| 158 MISSCAAGKVGDTIVLDPMKEEDNFGQADLPIAMTPNGDI-TLMQMDGN-LTPDEFGQAVTMAMKG 221
                                       7899************************************.********.*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1903.21
//
Query:       gi|330508838|ref|YP_004385266.1|  [L=258]
Description: exosome complex exonuclease 2 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.9e-26   91.8   0.0    7.2e-26   91.3   0.0    1.3  1  RNase_PH    3' exoribonuclease family, domain 1
    3.8e-08   33.3   0.2    6.7e-08   32.5   0.2    1.4  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.0     8e-30   7.2e-26       1     132 []      30     165 ..      30     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 8e-30
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeie 77 
                                       ++R++sie +v+++a+GSa+++lG+ +vl++v+++  e p+++ +++ g++ ++ e+ p+as++++  g p++  ie
  gi|330508838|ref|YP_004385266.1|  30 QYREISIERDVIRKAEGSALVKLGSSQVLVGVKMQPGE-PFQD-SPNRGVIITNAELVPLASPSFEP-GPPNEVGIE 103
                                       68**********************************99.7777.667799***************77.9******** PP

                                       HHHHHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  78 lsrlleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                       l+rl++r +r+s  +        ++k+ + + id+++l++ g ++lda++++a+ AL+ +++p
  gi|330508838|ref|YP_004385266.1| 104 LARLVDRGVRESKAVdlealciePGKKVWIVFIDVHILDDCG-NILDAASLGAISALLCTKVP 165
                                       **************8888889999999***************.******************98 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.2   7.4e-12   6.7e-08       1      66 [.     181     246 ..     181     247 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 7.4e-12
                                       S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHH CS
                        RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkk 66 
                                       +++ia t   + d ++ Dp  eEe++++ +lt+  +++++++ ++k+g + l++e++ + i++A +
  gi|330508838|ref|YP_004385266.1| 181 DIPIATTAIEFSDVLMFDPGVEEEAIANTKLTVITTTNGDICGMQKSGTGMLNPEQVYRIIDIACE 246
                                       589999999999***************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1869.21
//
Query:       gi|330508839|ref|YP_004385267.1|  [L=93]
Description: 50S ribosomal protein L37a [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-30  104.5   1.5    2.6e-30  104.3   1.5    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
    8.7e-05   22.4   1.4    0.00013   21.8   1.4    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0025   17.8   0.3     0.0046   17.0   0.3    1.5  1  Elf1             Transcription elongation factor Elf1 like
     0.0048   16.8   4.0     0.0075   16.2   4.0    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0054   16.8   1.2       0.23   11.6   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.018   14.9   3.1        1.1    9.2   2.8    2.2  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.022   15.3   0.1      0.031   14.8   0.1    1.3  1  RPA_interact_C   Replication protein A interacting C-terminal
      0.025   14.5   3.1      0.055   13.4   3.1    1.6  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
      0.025   14.9   0.4      0.039   14.3   0.4    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.026   14.2   0.4       0.04   13.6   0.4    1.3  1  A2L_zn_ribbon    A2L zinc ribbon domain
      0.076   12.9   0.8       0.13   12.2   0.8    1.4  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.077   12.6   1.0        3.6    7.2   0.3    2.5  2  Sgf11            Sgf11 (transcriptional regulation protein)
      0.079   13.0   1.5        1.3    9.0   0.1    2.1  2  CpXC             CpXC protein
      0.098   12.2   0.8       0.16   11.5   0.8    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.16   11.8   0.5         15    5.5   0.1    2.2  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
       0.16   11.7   3.2        2.7    7.8   0.2    2.2  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.18   11.9   2.7        5.5    7.1   0.2    2.2  2  Rubredoxin       Rubredoxin
       0.18   11.8   2.1        3.8    7.6   0.3    1.9  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.19   11.8   3.1       0.77    9.9   0.3    2.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.21   12.0   4.6        1.3    9.5   0.8    2.3  2  DUF4379          Probable Zinc-ribbon domain
       0.23   10.9   4.1        1.2    8.7   4.1    2.0  1  zf-ribbon_3      zinc-ribbon domain
       0.24   11.1   5.6        1.3    8.8   0.7    2.3  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.27   11.3   6.1        3.5    7.8   6.1    2.1  1  UPF0547          Uncharacterised protein family UPF0547
       0.28   11.2   1.6       0.55   10.2   0.1    2.0  1  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
        0.3   10.9   2.3         12    5.8   0.2    2.3  2  zf-C2H2_11       zinc-finger C2H2-type
       0.35   11.0   2.7        1.6    8.8   0.3    2.0  2  Mut7-C           Mut7-C RNAse domain
       0.37   10.6   4.3        3.2    7.6   0.4    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.48   10.9   4.1        5.1    7.7   0.3    2.3  2  zf-H2C2_2        Zinc-finger double domain
       0.51   10.4   5.9        3.4    7.7   4.1    2.7  2  Ogr_Delta        Ogr/Delta-like zinc finger
       0.88   10.2   3.7         18    6.0   0.3    2.4  2  zf-C2H2          Zinc finger, C2H2 type


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 !  104.3   1.5   4.4e-33   2.6e-30       2      82 ..       8      88 ..       7      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 4.4e-33
                                      XXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH-X CS
                   Ribosomal_L37ae  2 tkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsaktvksai 80
                                       kk ++a ++g+rYG++ rk v+++e++++a+y Cp+cg++kvkR+++ iw+C+kcg+t+aGg++ pet+ +++v +++
  gi|330508839|ref|YP_004385267.1|  8 GKKSRSAARFGARYGRKSRKLVADLEEKSKASYDCPQCGRNKVKRTSTAIWSCRKCGYTFAGGSFLPETSLGRSVLRSL 86
                                      799************************************************************************9998 PP

                                      XX CS
                   Ribosomal_L37ae 81 rr 82
                                      ++
  gi|330508839|ref|YP_004385267.1| 87 KK 88
                                      87 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.4   2.3e-07   0.00013      25      56 ..      36      67 ..      19      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.3e-07
                    OrfB_Zn_ribbon 25 ayTSktCseCgsknkealsgrtfkCpnCgfea 56
                                      +  S +C++Cg+++ ++ s+  + C++Cg+++
  gi|330508839|ref|YP_004385267.1| 36 SKASYDCPQCGRNKVKRTSTAIWSCRKCGYTF 67
                                      45899************************985 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.3   7.8e-06    0.0046       3      55 ..      23      67 ..      18      77 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.8e-06
                              Elf1  3 RkkkakkrkkkkkkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesf 55
                                      Rk+++        +k + ++dCp C+ +     k+ k++++a+ sC++Cg +f
  gi|330508839|ref|YP_004385267.1| 23 RKSRKL--VADLEEKSKASYDCPQCGRN-----KV-KRTSTAIWSCRKCGYTF 67
                                      454333..4445566899**********.....44.45689********9887 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 !   16.2   4.0   1.2e-05    0.0075      21      46 .]      42      66 ..      35      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                     Zn_Tnp_IS1595 21 CPhCgsrkayriktrglfqCkeCrkq 46
                                      CP Cg  k+ r++t   + C++C+++
  gi|330508839|ref|YP_004385267.1| 42 CPQCGRNKVKRTST-AIWSCRKCGYT 66
                                      *****99******9.********985 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   0.00038      0.23      26      38 ..      38      52 ..      23      53 .. 0.78
   2 ?    4.1   0.1     0.085        51       8      15 ..      60      67 ..      58      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00038
                       Zn-ribbon_8 26 lta.CPeCgs.evrr 38
                                          CP+Cg  +v+r
  gi|330508839|ref|YP_004385267.1| 38 ASYdCPQCGRnKVKR 52
                                      3445******99998 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.085
                       Zn-ribbon_8  8 CeeCghef 15
                                      C++Cg +f
  gi|330508839|ref|YP_004385267.1| 60 CRKCGYTF 67
                                      9****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 ?    5.5   0.3     0.026        15      17      28 ..      35      46 ..      28      49 .. 0.71
   2 ?    9.2   2.8    0.0018       1.1       4      31 ..      42      67 ..      42      72 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                                      SCCCE.EEESSSS CS
                    RNA_POL_M_15KD 17 kegkn.feCrqCg 28
                                      k++   ++C qCg
  gi|330508839|ref|YP_004385267.1| 35 KSK-AsYDCPQCG 46
                                      333.359*****7 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0018
                                      ESTTTSBEEEEECSCCCE.EEESSSS-EE CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegkn.feCrqCgYee 31
                                      Cp Cg    +k+++  +    Cr+CgY +
  gi|330508839|ref|YP_004385267.1| 42 CPQCG---RNKVKRTSTAiWSCRKCGYTF 67
                                      66666...3566666666788******87 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   5.2e-05     0.031       2      27 ..      42      69 ..      41      92 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.2e-05
                    RPA_interact_C  2 CPvCkkrklkets.evifCe.Cglrlet 27
                                      CP C ++k+k+ts  + +C+ Cg +++ 
  gi|330508839|ref|YP_004385267.1| 42 CPQCGRNKVKRTStAIWSCRkCGYTFAG 69
                                      ***********9966678*99**99987 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.1   9.2e-05     0.055       5      33 ..      40      66 ..      39      70 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.2e-05
                    Zn_ribbon_SprT  5 YrCtgCgreythhlsi.rrhnYrCrrCkgt 33
                                      Y C++Cgr+ ++ +++     + Cr+C+ t
  gi|330508839|ref|YP_004385267.1| 40 YDCPQCGRN-KVKRTStAI--WSCRKCGYT 66
                                      88*****65.555555455..99****855 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   6.5e-05     0.039       3      36 ..      39      65 ..      37      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.5e-05
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCga 36
                                       ++CP Cg  +v+ +s+  ++       C +Cg+
  gi|330508839|ref|YP_004385267.1| 39 SYDCPQCGRNKVKRTSTAIWS-------CRKCGY 65
                                      589**********99988875.......999999 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   6.7e-05      0.04       5      31 ..      41      67 ..      37      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.7e-05
                     A2L_zn_ribbon  5 vCsvCggngilnseqgylvCieCgasf 31
                                       C  Cg+n++  +  ++ +C +Cg++f
  gi|330508839|ref|YP_004385267.1| 41 DCPQCGRNKVKRTSTAIWSCRKCGYTF 67
                                      5999*******9999**********99 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.8   0.00022      0.13       9      38 ..      37      67 ..      29      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                                      SS--B-TTT-SB--S.SSS-EEEETTT--EE CS
                              C1_1  9 kqptfCkhCgeflwg.kekqglkCswCkllv 38
                                      k +  C +Cg    +  ++ +++C+ C++++
  gi|330508839|ref|YP_004385267.1| 37 KASYDCPQCGRNKVKrTSTAIWSCRKCGYTF 67
                                      56667****9988677************985 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.3    0.0061       3.6       3      13 ..      38      48 ..      36      49 .. 0.83
   2 ?    3.7   0.0     0.077        46       3      19 ..      56      72 ..      54      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0061
                                      -EEE-TTTSSE CS
                             Sgf11  3 eyvtCpnCgRq 13
                                      + ++Cp CgR+
  gi|330508839|ref|YP_004385267.1| 38 ASYDCPQCGRN 48
                                      5689******5 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.077
                                      -EEE-TTTSSEEEGGGH CS
                             Sgf11  3 eyvtCpnCgRqiaasRF 19
                                      +  +C  Cg + a++ F
  gi|330508839|ref|YP_004385267.1| 56 AIWSCRKCGYTFAGGSF 72
                                      6679*****88888877 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0023       1.3      23      47 ..      25      49 ..      22      58 .. 0.83
   2 ?    4.7   0.1     0.049        29      29      47 ..      49      67 ..      47      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0023
                              CpXC 23 dpelkeklldgslfeatCpkCgata 47
                                      + +l+++l ++s  ++ Cp+Cg++ 
  gi|330508839|ref|YP_004385267.1| 25 SRKLVADLEEKSKASYDCPQCGRNK 49
                                      56889999999999********865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.049
                              CpXC 29 klldgslfeatCpkCgata 47
                                      k+   s   + C kCg+t+
  gi|330508839|ref|YP_004385267.1| 49 KVKRTSTAIWSCRKCGYTF 67
                                      6777788889******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 ?   11.5   0.8   0.00026      0.16       2      27 ..      41      65 ..      40      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                                      EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                       CP Cg  + v  ++++   C +CG+
  gi|330508839|ref|YP_004385267.1| 41 DCPQCGRNK-VKRTSTAIWSCRKCGY 65
                                      6*****988.9**************6 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.025        15       5      20 ..      31      46 ..      28      46 .. 0.83
   2 ?    4.7   0.1     0.046        27      15      24 ..      55      68 ..      48      72 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.025
                         zf-C2H2_3  5 dlgqksfgasqCkeCg 20
                                      dl  ks+ +  C++Cg
  gi|330508839|ref|YP_004385267.1| 31 DLEEKSKASYDCPQCG 46
                                      77888877888****8 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.046
                         zf-C2H2_3 15 q....CkeCgMvYn 24
                                      +    C +Cg +++
  gi|330508839|ref|YP_004385267.1| 55 TaiwsCRKCGYTFA 68
                                      23555*****8876 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0044       2.7      38      51 ..      33      46 ..      27      49 .. 0.85
   2 ?    4.8   0.4     0.038        23      39      52 ..      52      65 ..      47      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0044
                    zinc_ribbon_10 38 eeleevkyrCpkCg 51
                                      ee+++ +y Cp+Cg
  gi|330508839|ref|YP_004385267.1| 33 EEKSKASYDCPQCG 46
                                      789999*******9 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.038
                    zinc_ribbon_10 39 eleevkyrCpkCga 52
                                      + ++  + C kCg 
  gi|330508839|ref|YP_004385267.1| 52 RTSTAIWSCRKCGY 65
                                      566779******97 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2    0.0092       5.5      34      45 ..      39      50 ..      37      52 .. 0.84
   2 ?    4.9   0.2     0.043        26       2      11 ..      58      67 ..      57      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0092
                                      T-BBTTTB-BGG CS
                        Rubredoxin 34 dWvCPdCgveke 45
                                       + CP+Cg +k 
  gi|330508839|ref|YP_004385267.1| 39 SYDCPQCGRNKV 50
                                      589*****9986 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.043
                                      EEETTT-BEE CS
                        Rubredoxin  2 yeCkvCgyvY 11
                                      + C+ Cgy +
  gi|330508839|ref|YP_004385267.1| 58 WSCRKCGYTF 67
                                      8999999986 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   0.3    0.0064       3.8      83      99 ..      35      52 ..      23      56 .. 0.72
   2 ?    3.7   0.1     0.097        58      68      81 ..      55      68 ..      50      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0064
                                      HHH.HHS-TTTSSS-EEE CS
                              HypA 83 eek.alrCpkCgsadvei 99
                                      ++k ++ Cp+Cg+++v+ 
  gi|330508839|ref|YP_004385267.1| 35 KSKaSYDCPQCGRNKVKR 52
                                      333467999999999875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.097
                                      --EEEETTTS-EEE CS
                              HypA 68 pvkvrCreCgkefe 81
                                       +   Cr+Cg++f 
  gi|330508839|ref|YP_004385267.1| 55 TAIWSCRKCGYTFA 68
                                      56788*****9986 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 ?    9.9   0.3    0.0013      0.77      10      23 ..      33      46 ..       3      51 .. 0.80
   2 ?    3.0   0.1      0.18   1.1e+02      16      25 ..      57      66 ..      47      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                          zf-Mss51 10 tapkhvdfeCpdCG 23
                                      +++++ +++Cp+CG
  gi|330508839|ref|YP_004385267.1| 33 EEKSKASYDCPQCG 46
                                      37999********9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.18
                          zf-Mss51 16 dfeCpdCGip 25
                                         C +CG+ 
  gi|330508839|ref|YP_004385267.1| 57 IWSCRKCGYT 66
                                      578*****96 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.081        48      25      36 ..      35      46 ..      21      54 .. 0.72
   2 ?    9.5   0.8    0.0021       1.3      25      39 ..      53      67 ..      47      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.081
                           DUF4379 25 kkkvwWkCakCg 36
                                      k k++  C++Cg
  gi|330508839|ref|YP_004385267.1| 35 KSKASYDCPQCG 46
                                      556666666666 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0021
                           DUF4379 25 kkkvwWkCakCgheW 39
                                      +  + W C+kCg+++
  gi|330508839|ref|YP_004385267.1| 53 TSTAIWSCRKCGYTF 67
                                      56899*******987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.1    0.0019       1.2       5      24 ..      42      65 ..      39      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0019
                       zf-ribbon_3  5 CPnCGa.plssddnv...CpyCGt 24
                                      CP+CG  +++   ++   C +CG+
  gi|330508839|ref|YP_004385267.1| 42 CPQCGRnKVKRTSTAiwsCRKCGY 65
                                      ******77**99996666999997 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4     0.045        27       2       7 ..      41      46 ..      40      51 .. 0.63
   2 ?    8.8   0.7    0.0022       1.3       1      11 [.      58      68 ..      58      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.045
                      Rubredoxin_2  2 vCsqCG 7 
                                       C qCG
  gi|330508839|ref|YP_004385267.1| 41 DCPQCG 46
                                      555555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0022
                      Rubredoxin_2  1 YvCsqCGfesa 11
                                      ++C++CG+++a
  gi|330508839|ref|YP_004385267.1| 58 WSCRKCGYTFA 68
                                      79******975 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.1    0.0058       3.5       3      24 ..      42      67 ..      41      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0058
                           UPF0547  3 CPeCea.kv...PvaaqfCphCGyvF 24
                                      CP+C + kv   ++a  +C+ CGy F
  gi|330508839|ref|YP_004385267.1| 42 CPQCGRnKVkrtSTAIWSCRKCGYTF 67
                                      99997645533379**********99 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00093      0.55      26      44 ..      35      53 ..      26      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00093
                                      ......E-TTTTTSSEEE- CS
                         Anti-TRAP 26 eprasleCPkCsGkglipT 44
                                      + +as +CP+C+ +++  T
  gi|330508839|ref|YP_004385267.1| 35 KSKASYDCPQCGRNKVKRT 53
                                      4789********9998777 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 ?    4.9   0.1     0.038        23       3      13 ..      38      48 ..      36      48 .. 0.86
   2 ?    5.8   0.2      0.02        12       7      15 ..      60      68 ..      54      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.038
                        zf-C2H2_11  3 stcqCleCGlc 13
                                      +++ C +CG++
  gi|330508839|ref|YP_004385267.1| 38 ASYDCPQCGRN 48
                                      7899*****96 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.02
                        zf-C2H2_11  7 CleCGlcft 15
                                      C++CG  f+
  gi|330508839|ref|YP_004385267.1| 60 CRKCGYTFA 68
                                      *****9997 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1       0.2   1.2e+02     111     131 ..      27      47 ..      19      48 .. 0.80
   2 ?    8.8   0.3    0.0027       1.6     114     138 ..      48      72 ..      47      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.2
                            Mut7-C 111 rvpekvyeeadeftrCekCrk 131
                                       ++ + + e++++ + C++C++
  gi|330508839|ref|YP_004385267.1|  27 KLVADLEEKSKASYDCPQCGR 47 
                                       56667788888899*****98 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0027
                            Mut7-C 114 ekvyeeadeftrCekCrkvfWkGsh 138
                                       +kv++++++++ C+kC+  f +Gs 
  gi|330508839|ref|YP_004385267.1|  48 NKVKRTSTAIWSCRKCGYTFAGGSF 72 
                                       578899999***********99985 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.4    0.0053       3.2      15      21 ..      40      47 ..      30      49 .. 0.68
   2 ?    5.9   4.7     0.018        11       2      21 ..      42      65 ..      42      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0053
                     zinc_ribbon_2 15 F.CpyCGt 21
                                      + Cp+CG 
  gi|330508839|ref|YP_004385267.1| 40 YdCPQCGR 47
                                      36888885 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.018
                     zinc_ribbon_2  2 CpnCGaelqdnakF....CpyCGt 21
                                      Cp+CG+   ++       C +CG+
  gi|330508839|ref|YP_004385267.1| 42 CPQCGRNKVKRTSTaiwsCRKCGY 65
                                      999999998865556999999997 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.4     0.072        43      14      22 ..      39      47 ..      33      55 .. 0.78
   2 ?    7.7   0.3    0.0085       5.1      14      25 ..      57      68 ..      48      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.072
                         zf-H2C2_2 14 pyeCplCdk 22
                                       y Cp C+ 
  gi|330508839|ref|YP_004385267.1| 39 SYDCPQCGR 47
                                      499****85 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0085
                         zf-H2C2_2 14 pyeCplCdkaFk 25
                                      ++ C +C+++F+
  gi|330508839|ref|YP_004385267.1| 57 IWSCRKCGYTFA 68
                                      578********6 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 ?   -1.9   0.0       5.8   3.5e+03      11      23 ..      22      34 ..      19      39 .. 0.79
   2 ?    7.7   4.1    0.0058       3.4       2      17 ..      42      57 ..      41      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.8
                         Ogr_Delta 11 artsrnlskdvre 23
                                       r+sr l +d+ e
  gi|330508839|ref|YP_004385267.1| 22 GRKSRKLVADLEE 34
                                      5899998887765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0058
                         Ogr_Delta  2 CPhCgapaaartsrnl 17
                                      CP+Cg + + rts+++
  gi|330508839|ref|YP_004385267.1| 42 CPQCGRNKVKRTSTAI 57
                                      *************975 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3      0.06        36       1       8 [.      40      47 ..      40      55 .. 0.85
   2 ?    6.0   0.3     0.031        18       2      10 ..      59      67 ..      58      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.06
                                      EEETTTTE CS
                           zf-C2H2  1 ykCpdCgk 8 
                                      y Cp Cg+
  gi|330508839|ref|YP_004385267.1| 40 YDCPQCGR 47
                                      88*****6 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.031
                                      EETTTTEEE CS
                           zf-C2H2  2 kCpdCgksF 10
                                       C +Cg++F
  gi|330508839|ref|YP_004385267.1| 59 SCRKCGYTF 67
                                      6*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 691.65
//
Query:       gi|330508840|ref|YP_004385268.1|  [L=45]
Description: DNA-directed RNA polymerase subunit P [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-09   36.5   8.8    3.8e-09   36.1   8.8    1.2  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
    7.3e-05   22.3   1.1       0.22   11.1   0.0    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
    0.00011   21.5   0.2     0.0091   15.4   0.1    2.1  2  zf-ribbon_3      zinc-ribbon domain
    0.00035   20.4   0.8    0.00045   20.1   0.8    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0034   17.4   0.5     0.0034   17.4   0.5    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0042   17.0   0.2     0.0046   16.9   0.2    1.1  1  zf-C2HC5         Putative zinc finger motif, C2HC5-type
     0.0053   16.4   2.4      0.011   15.4   2.4    1.5  1  zinc_ribbon_2    zinc-ribbon domain
     0.0067   16.5   3.6      0.011   15.8   3.6    1.5  1  Zn-ribbon_8      Zinc ribbon domain
      0.007   16.3   4.5      0.031   14.2   0.4    2.0  2  DUF951           Bacterial protein of unknown function (DUF95
  ------ inclusion threshold ------
      0.014   15.3   3.0       0.24   11.4   0.1    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.016   15.1   2.1      0.052   13.4   0.2    2.0  2  Cys_rich_CPXG    Cysteine-rich CPXCG
      0.026   14.8   0.5      0.026   14.8   0.5    1.1  1  DUF2072          Zn-ribbon containing protein
       0.03   14.3   0.8       0.14   12.2   1.0    1.5  1  DZR              Double zinc ribbon
      0.031   14.4   0.3      0.036   14.1   0.3    1.1  1  Spt4             Spt4/RpoE2 zinc finger
      0.033   14.0   2.4        4.5    7.2   0.1    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.052   13.4   1.2       0.09   12.7   1.3    1.4  2  C1_1             Phorbol esters/diacylglycerol binding domain
      0.052   13.5   4.3        1.3    9.0   4.3    2.2  1  zinc_ribbon_4    zinc-ribbon domain
      0.052   13.1   2.8      0.078   12.5   2.8    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.09   12.5   0.7        2.3    8.0   0.1    2.0  2  YacG             DNA gyrase inhibitor YacG
      0.095   12.7   1.3       0.44   10.6   0.1    1.9  2  CpXC             CpXC protein
       0.13   12.5   2.9        2.3    8.5   0.5    2.1  2  DUF2197          Uncharacterized protein conserved in bacteri
       0.14   12.4   2.0       0.72   10.2   0.1    2.0  2  DUF3268          zinc-finger-containing domain
       0.53    9.9   5.7       0.33   10.6   0.8    2.1  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        1.5    8.8   8.5         30    4.6   8.4    2.1  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
        3.4    7.8   7.2         18    5.6   7.2    1.9  1  UPF0547          Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   8.8   5.3e-12   3.8e-09       1      32 []       3      35 ..       3      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 5.3e-12
                                      -B-SSS--B----.SSS----SSS-----B--- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevslk.kgdpiRCkeCGhRilYKkR 32
                                      Y+C +C++ v+++ +   iRC +CGhRil+K+R
  gi|330508840|ref|YP_004385268.1|  3 YKCTRCKKIVEIDyEYSGIRCPYCGHRILMKER 35
                                      9**********7615578**************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 !   10.4   0.2   0.00051      0.37       3      15 ..       3      15 ..       2      18 .. 0.86
   2 !   11.1   0.0   0.00031      0.22       3      18 ..      21      36 ..      19      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00051
                            zf_UBZ  3 ylCerCgkeipes 15
                                      y C rC+k ++++
  gi|330508840|ref|YP_004385268.1|  3 YKCTRCKKIVEID 15
                                      99******99876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00031
                            zf_UBZ  3 ylCerCgkeipeselq 18
                                      + C+ Cg++i++ e++
  gi|330508840|ref|YP_004385268.1| 21 IRCPYCGHRILMKERP 36
                                      68**********9997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.028        20       3      14 ..       3      14 ..       1      16 [. 0.79
   2 !   15.4   0.1   1.3e-05    0.0091       3      11 ..      21      30 ..      19      35 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.028
                       zf-ribbon_3  3 vrCPnCGaplss 14
                                      ++C +C+++++ 
  gi|330508840|ref|YP_004385268.1|  3 YKCTRCKKIVEI 14
                                      7899***97776 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-05
                       zf-ribbon_3  3 vrCPnCGa.p 11
                                      +rCP+CG+ +
  gi|330508840|ref|YP_004385268.1| 21 IRCPYCGHrI 30
                                      7999999977 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.8   6.3e-07   0.00045       9      38 ..       2      30 ..       1      43 [. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.3e-07
                    OrfB_Zn_ribbon  9 eykakeyGikveevnpayTSktCseCgskn 38
                                      +yk++ + +k++e++ +y+  +C+ Cg++ 
  gi|330508840|ref|YP_004385268.1|  2 AYKCT-RCKKIVEIDYEYSGIRCPYCGHRI 30
                                      78998.66899*****************96 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.5   4.8e-06    0.0034      71      95 ..       3      29 ..       1      44 [. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.8e-06
                                      EEETTTS-EEECHHH..HHS-TTTSSS CS
                              HypA 71 vrCreCgkefeleek..alrCpkCgsa 95
                                      ++C++C+k +e++ +   +rCp Cg++
  gi|330508840|ref|YP_004385268.1|  3 YKCTRCKKIVEIDYEysGIRCPYCGHR 29
                                      79*********98743678******86 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   6.4e-06    0.0046      17      49 ..       2      35 ..       1      42 [. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.4e-06
                          zf-C2HC5 17 apnClnCGkiiCakegls.kpCsfCgspllssee 49
                                      a  C+ C ki+ +  ++s  +C++Cg+ +l +e 
  gi|330508840|ref|YP_004385268.1|  2 AYKCTRCKKIVEIDYEYSgIRCPYCGHRILMKER 35
                                      678********999988888*******9998775 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.4   1.6e-05     0.011       1      22 [.       4      29 ..       4      30 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                     zinc_ribbon_2  1 fCpnCGaelqdnakF....CpyCGtp 22
                                      +C++C + ++ +  +    CpyCG+ 
  gi|330508840|ref|YP_004385268.1|  4 KCTRCKKIVEIDYEYsgirCPYCGHR 29
                                      8*********888888********96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   3.6   1.6e-05     0.011       6      34 ..       3      28 ..       2      35 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs 34
                                      Y+C++C++  e+     + + + CP Cg+
  gi|330508840|ref|YP_004385268.1|  3 YKCTRCKKIVEIDY---EYSGIRCPYCGH 28
                                      *******9999555...555999*****8 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.043        31      32      42 ..       4      14 ..       1      19 [. 0.85
   2 !   14.2   0.4   4.4e-05     0.031      30      54 ..      20      45 .]      18      45 .] 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.043
                            DUF951 32 kClgcgrevml 42
                                      kC++c+++v +
  gi|330508840|ref|YP_004385268.1|  4 KCTRCKKIVEI 14
                                      9******9976 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.4e-05
                            DUF951 30 klkClgcgrevml.pRskfekkikkv 54
                                       ++C  cg+ +++ +R +  kk+k v
  gi|330508840|ref|YP_004385268.1| 20 GIRCPYCGHRILMkERPTTVKKMKAV 45
                                      59*******99963699999***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 ?    4.9   0.5     0.037        26      38      45 ..       3      10 ..       1      11 [. 0.88
   2 ?   11.4   0.1   0.00033      0.24      18      27 ..      20      29 ..      18      43 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.037
                     Zn_Tnp_IS1595 38 fqCkeCrk 45
                                      ++C +C+k
  gi|330508840|ref|YP_004385268.1|  3 YKCTRCKK 10
                                      9*****97 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00033
                     Zn_Tnp_IS1595 18 gfvCPhCgsr 27
                                      g +CP+Cg+r
  gi|330508840|ref|YP_004385268.1| 20 GIRCPYCGHR 29
                                      789*****98 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.36   2.6e+02       1      15 [.       3      17 ..       3      20 .. 0.73
   2 ?   13.4   0.2   7.3e-05     0.052       1      11 [.      21      31 ..      21      33 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.36
                     Cys_rich_CPXG  1 iqCPyCgeeievlvD 15
                                      ++C  C + +e++ +
  gi|330508840|ref|YP_004385268.1|  3 YKCTRCKKIVEIDYE 17
                                      679999988887655 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.3e-05
                     Cys_rich_CPXG  1 iqCPyCgeeie 11
                                      i CPyCg++i 
  gi|330508840|ref|YP_004385268.1| 21 IRCPYCGHRIL 31
                                      78******985 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.5   3.6e-05     0.026       2      30 ..       3      31 ..       2      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.6e-05
                           DUF2072  2 HkCtkCekvfedgskeilkGCpsCGgkkF 30
                                       kCt+C+k+ e   +     Cp CG +  
  gi|330508840|ref|YP_004385268.1|  3 YKCTRCKKIVEIDYEYSGIRCPYCGHRIL 31
                                      59*********999977788*****9865 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.0    0.0002      0.14      29      49 .]       3      27 ..       1      27 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                               DZR 29 drCpsCgekvdpearf....CpeCG 49
                                      ++C +C++ v+ + ++    Cp+CG
  gi|330508840|ref|YP_004385268.1|  3 YKCTRCKKIVEIDYEYsgirCPYCG 27
                                      6899999999999999999999998 PP

>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   5.1e-05     0.036       4      37 ..       5      40 ..       3      44 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.1e-05
                              Spt4  4 CllCklvkted.qFeeegCpnC.eilelkgdkekvs 37
                                      C++Ck +++ d ++    Cp+C + + +k+  ++v+
  gi|330508840|ref|YP_004385268.1|  5 CTRCKKIVEIDyEYSGIRCPYCgHRILMKERPTTVK 40
                                      ****98777653788889****98888998877766 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.5    0.0073       5.2      29      36 ..       3      10 ..       1      12 [. 0.85
   2 ?    7.2   0.1    0.0063       4.5       1       9 [.      21      29 ..      21      33 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0073
                           TFIIS_C 29 ykCtkCgh 36
                                      ykCt C++
  gi|330508840|ref|YP_004385268.1|  3 YKCTRCKK 10
                                      9*****97 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0063
                           TFIIS_C  1 akCpkCgsr 9 
                                      ++Cp Cg+r
  gi|330508840|ref|YP_004385268.1| 21 IRCPYCGHR 29
                                      579999998 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.3   0.00012      0.09      13      36 ..       4      28 ..       1      31 [. 0.88
   2 ?    4.7   0.0     0.038        27      13      23 ..      22      32 ..      14      40 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                      B-TTT-SB--S.SSS-EEEETTT-- CS
                              C1_1 13 fCkhCgeflwg.kekqglkCswCkl 36
                                      +C+ C+++++   e+ g++C  C+ 
  gi|330508840|ref|YP_004385268.1|  4 KCTRCKKIVEIdYEYSGIRCPYCGH 28
                                      8********888***********86 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.038
                                      B-TTT-SB--S CS
                              C1_1 13 fCkhCgeflwg 23
                                      +C +Cg  + +
  gi|330508840|ref|YP_004385268.1| 22 RCPYCGHRILM 32
                                      68888888844 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.3    0.0018       1.3       1      35 [.       1      30 [.       1      31 [. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0018
                     zinc_ribbon_4  1 MkitCpsCkakyeiddeklpakgvkvrCskCghvF 35
                                      M   C +Ck+  eid e      + +rC+ Cgh +
  gi|330508840|ref|YP_004385268.1|  1 MAYKCTRCKKIVEIDYE-----YSGIRCPYCGHRI 30
                                      66689999999999996.....7889*******76 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.8   0.00011     0.078       1      27 [.       3      28 ..       3      33 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                      EEETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGl 27
                                      ykC  C+   ++ D+e   ++C+ CG 
  gi|330508840|ref|YP_004385268.1|  3 YKCTRCKK-IVEIDYEYSGIRCPYCGH 28
                                      89*****6.3699************96 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.082        59       2      13 ..       4      15 ..       3      19 .. 0.74
   2 ?    8.0   0.1    0.0032       2.3       1      14 [.      21      34 ..      21      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.082
                              YacG  2 kCPtCkkevews 13
                                      kC  Ckk ve++
  gi|330508840|ref|YP_004385268.1|  4 KCTRCKKIVEID 15
                                      688888888765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0032
                              YacG  1 vkCPtCkkevewse 14
                                      ++CP C++++ ++e
  gi|330508840|ref|YP_004385268.1| 21 IRCPYCGHRILMKE 34
                                      68******998887 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.16   1.1e+02      38      52 ..       3      17 ..       1      20 [. 0.72
   2 ?   10.6   0.1   0.00061      0.44      34      51 ..      17      34 ..      14      44 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.16
                              CpXC 38 atCpkCgatakleap 52
                                      ++C +C + ++++++
  gi|330508840|ref|YP_004385268.1|  3 YKCTRCKKIVEIDYE 17
                                      678888887777765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00061
                              CpXC 34 slfeatCpkCgataklea 51
                                      ++  ++Cp+Cg+++ ++ 
  gi|330508840|ref|YP_004385268.1| 17 EYSGIRCPYCGHRILMKE 34
                                      566799******998864 PP

>> DUF2197  Uncharacterized protein conserved in bacteria (DUF2197)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.5    0.0032       2.3       1      16 [.       1      16 [.       1      20 [. 0.87
   2 ?    4.9   0.1     0.043        31       5      22 ..      23      40 ..      19      44 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0032
                           DUF2197  1 mrvkCvlCdkveeidd 16
                                      m  kC+ C k+ eid 
  gi|330508840|ref|YP_004385268.1|  1 MAYKCTRCKKIVEIDY 16
                                      778***********96 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.043
                           DUF2197  5 CvlCdkveeiddesllaK 22
                                      C  C +   + ++ ++ K
  gi|330508840|ref|YP_004385268.1| 23 CPYCGHRILMKERPTTVK 40
                                      555555555555555555 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.3      0.22   1.5e+02      29      42 ..       1      14 [.       1      19 [. 0.80
   2 ?   10.2   0.1     0.001      0.72       3      17 ..      21      35 ..      18      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.22
                           DUF3268 29 llylCpkCdayvgv 42
                                      ++y C++C   v +
  gi|330508840|ref|YP_004385268.1|  1 MAYKCTRCKKIVEI 14
                                      68999999988876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.001
                           DUF3268  3 trCpyCGekvilvsa 17
                                      +rCpyCG+++ +++ 
  gi|330508840|ref|YP_004385268.1| 21 IRCPYCGHRILMKER 35
                                      79******9988765 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.8   0.00046      0.33       7      18 ..       3      14 ..       1      20 [. 0.93
   2 ?    2.3   0.4      0.18   1.3e+02       8      14 ..      22      28 ..      18      32 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00046
                                      EE-TTT--EEEE CS
                   Desulfoferrod_N  7 YkCevCGniVeV 18
                                      YkC+ C  iVe+
  gi|330508840|ref|YP_004385268.1|  3 YKCTRCKKIVEI 14
                                      **********98 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.18
                                      E-TTT-- CS
                   Desulfoferrod_N  8 kCevCGn 14
                                      +C  CG 
  gi|330508840|ref|YP_004385268.1| 22 RCPYCGH 28
                                      8*****6 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   8.4     0.042        30       4      34 ..       2      30 ..       2      34 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.042
                    Zn_ribbon_SprT  4 vYrCtgCgreythhlsirrhn..YrCrrCkgtL 34
                                      +Y+Ct+C+     +  i+ +    rC++C+ ++
  gi|330508840|ref|YP_004385268.1|  2 AYKCTRCK----KIVEIDYEYsgIRCPYCGHRI 30
                                      599****9....566666666889999999776 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   7.2     0.024        18      15      23 ..      21      29 ..       4      29 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.024
                           UPF0547 15 qfCphCGyv 23
                                       +Cp+CG++
  gi|330508840|ref|YP_004385268.1| 21 IRCPYCGHR 29
                                      58*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 355.32
//
Query:       gi|330508841|ref|YP_004385269.1|  [L=136]
Description: hypothetical protein MCON_3157 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      150  (0.00836633); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 966.14
//
Query:       gi|330508842|ref|YP_004385270.1|  [L=75]
Description: hypothetical protein MCON_3158 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-05   25.0   0.0    1.9e-05   24.7   0.0    1.1  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0     1e-09   1.9e-05      11      72 ..      12      72 ..       5      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1e-09
                                      HHHHHHHHHHHHHHCHC-TTECEEEEEE.ETT.EEEEEEEESSHHHHHHHHHHHHHHHHHHHHH CS
                              Pcc1 11 erlAsialrtLqvDkelsplavkrslsl.egn.vLqveykAttnrmLRvavngfleslglvlet 72
                                      + + + ++++L+++     +  + +++l eg+ ++++++  ++  +LR+a+n++++++++++e+
  gi|330508842|ref|YP_004385270.1| 12 P-HSQEIYEALAPELNDEIH--RSNIELvEGPgFVRLKILGEDVVSLRAALNTWIRLVKIAIEM 72
                                      4.677899*****9666444..33444414535*****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 598.16
//
Query:       gi|330508843|ref|YP_004385271.1|  [L=120]
Description: prefoldin subunit beta [Methanosaeta concilii GP6]
Scores for complete 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-23   82.0  18.6    2.8e-23   81.9  18.6    1.0  1  Prefoldin_2   Prefoldin subunit
  ------ inclusion threshold ------
      0.018   14.5   3.2      0.027   13.9   3.2    1.2  1  FliD_C        Flagellar hook-associated protein 2 C-terminus
      0.022   14.4   7.6       0.03   13.9   7.6    1.2  1  DUF4795       Domain of unknown function (DUF4795)
      0.045   14.1   0.0      0.067   13.5   0.0    1.3  1  DUF5503       Family of unknown function (DUF5503)
      0.085   13.0   2.3       0.33   11.1   0.1    2.3  2  CinA_KH       Damage-inducible protein CinA KH domain
       0.22   11.6   0.1       0.22   11.6   0.1    2.6  2  DegQ          DegQ (SacQ) family
       0.38   10.2  10.8       0.47    9.9  10.8    1.0  1  LRRFIP        LRRFIP family
       0.47   10.6   8.4        4.7    7.4   8.5    1.9  1  Fib_alpha     Fibrinogen alpha/beta chain family
       0.84   10.4   5.6         10    6.9   0.8    2.0  2  Phage_Mu_F    Phage Mu protein F like protein
       0.91    7.0  12.4        1.5    6.2  12.4    1.3  1  DUF3584       Protein of unknown function (DUF3584)
       0.98    9.2  10.0        1.2    8.9  10.0    1.1  1  DUF724        Protein of unknown function (DUF724)
        1.7    8.7   9.6        6.4    6.8   4.8    2.1  2  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
          2    8.2  16.1        2.4    7.9   3.3    2.1  2  Phage_GP20    Phage minor structural protein GP20
        2.5    7.4  18.8       0.39   10.0   7.7    2.0  2  DUF3450       Protein of unknown function (DUF3450)
        2.6    8.1   8.7         19    5.2   8.7    1.9  1  Laminin_II    Laminin Domain II
        2.7    8.3  13.3        1.2    9.4   3.5    2.2  2  JIP_LZII      JNK-interacting protein  leucine zipper II
        3.8    5.9   7.7        7.2    5.0   7.7    1.5  1  Herpes_UL6    Herpesvirus UL6 like
        4.3    7.7   7.4        3.8    7.9   3.4    2.0  2  DUF2098       Uncharacterized protein conserved in archaea (D
        6.1    6.9   9.8        4.4    7.4   1.4    2.1  2  DUF1664       Protein of unknown function (DUF1664)
        7.2    6.9  14.7          3    8.1   4.6    2.1  2  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
        7.5    6.9  12.7         16    5.8   5.5    2.3  2  WXG100        Proteins of 100 residues with WXG


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 !   81.9  18.6   3.2e-26   2.8e-23       1     105 [.      10     114 ..      10     115 .. 0.99

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 3.2e-26
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketleke 77 
                                       q++++++qqlqqq q++++q++q+e  ++e e +l+ele+ ++d+ +yk+vG++l+  dk +++eeL+erk+ ++ +
  gi|330508843|ref|YP_004385271.1|  10 QNQLAQLQQLQQQAQAVMTQKTQIEGLIRETEAALKELEKSADDAVIYKSVGELLFRADKLKLTEELKERKDMMDIR 86 
                                       89*************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHCCTS- CS
                       Prefoldin_2  78 iktlekqleklekeleelkeelqkklqq 105
                                       +kt+ kq+e+++ ++++l+e+l++ l+q
  gi|330508843|ref|YP_004385271.1|  87 LKTMAKQEERIQGRFTQLQEQLKQSLGQ 114
                                       ************************9986 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   3.2   3.2e-05     0.027     145     227 ..       8     111 ..       3     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHHHHHHTTTSS.......SXSHHHHHHHHHHHHHSTT.SHHH.....................HHHHHXX CS
                            FliD_C 145 alkenpssveelFsgstsqektvtsdsglatrlenllksyvkssngtlq.....................tasknlt 200
                                       +++++++++++l  ++  +  + t+ +gl+ ++e +lk++ ks ++++                      +++++++
  gi|330508843|ref|YP_004385271.1|   8 QIQNQLAQLQQLQQQAQAVMTQKTQIEGLIRETEAALKELEKSADDAVIyksvgellfradklklteelkERKDMMD 84 
                                       78999999999999998888889999999999999999999888777777888888888777766666667777777 PP

                                       XXHHHHHHHHHHHHHCHHHHHHHHHHH CS
                            FliD_C 201 kqikdldkkiedldkrletleerlkkq 227
                                        ++k+++k+ e ++ r ++l+e+lk+ 
  gi|330508843|ref|YP_004385271.1|  85 IRLKTMAKQEERIQGRFTQLQEQLKQS 111
                                       777777777777777777777777665 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   7.6   3.5e-05      0.03      14     102 ..      14     113 ..       2     117 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-05
                           DUF4795  14 eaieklqeelekleekvkelekrledkekklealkkqieelekvk........adkeeveeelaekadkeaLatkvs 82 
                                       +++++lq++ + +  +++++e+ ++++e  l+ l+k++++    k        adk +++eel+e  d  +++ k+ 
  gi|330508843|ref|YP_004385271.1|  14 AQLQQLQQQAQAVMTQKTQIEGLIRETEAALKELEKSADDAVIYKsvgellfrADKLKLTEELKERKDMMDIRLKTM 90 
                                       44555555555566666666666666666666666666665555555566666666666666666666666666655 PP

                           DUF4795  83 rdq...fDeakkeLekmleelle 102
                                        +q   ++ ++++L+++l++ l 
  gi|330508843|ref|YP_004385271.1|  91 AKQeerIQGRFTQLQEQLKQSLG 113
                                       55555555555555555555444 PP

>> DUF5503  Family of unknown function (DUF5503)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.8e-05     0.067       8      56 ..      25      73 ..      18      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.8e-05
                           DUF5503  8 slktqpvqlnkvtsntestikqhelvsddaiinelsselvsclgngkft 56
                                      ++ tq  q++ +  +te+++k+ e  +dda+i +   el+    + k+t
  gi|330508843|ref|YP_004385271.1| 25 AVMTQKTQIEGLIRETEAALKELEKSADDAVIYKSVGELLFRADKLKLT 73
                                      5789*****************************9999998766666665 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3      0.35     3e+02      47      65 ..      28      46 ..      12      51 .. 0.80
   2 ?   11.1   0.1   0.00039      0.33      35      69 ..      80     114 ..      58     115 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.35
                                      EEHHHHHHHHH....HHHH CS
                           CinA_KH 47 aneeeaealiapveeeire 65
                                       ++++ e li ++e++++e
  gi|330508843|ref|YP_004385271.1| 28 TQKTQIEGLIRETEAALKE 46
                                      5788999999999999886 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00039
                                       TTEEEEEEE...EEHHHHHHHHH....HHHHHTTT CS
                           CinA_KH  35 egevtvRltakaaneeeaealiapveeeirerlgd 69 
                                       ++ +++Rl   a++ee  + +  +++e++++ lg+
  gi|330508843|ref|YP_004385271.1|  80 KDMMDIRLKTMAKQEERIQGRFTQLQEQLKQSLGQ 114
                                       56789****************************97 PP

>> DegQ  DegQ (SacQ) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00026      0.22      16      36 ..      33      53 ..      30      60 .. 0.86
   2 ?    0.0   0.3       1.1   9.3e+02      15      25 ..      71      81 ..      55      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                              DegQ 16 LEneirETtdSLrniNKSiDQ 36
                                      +E  irET + L+++ KS D 
  gi|330508843|ref|YP_004385271.1| 33 IEGLIRETEAALKELEKSADD 53
                                      5777**************996 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.1
                              DegQ 15 rLEneirETtd 25
                                      +L  e++E +d
  gi|330508843|ref|YP_004385271.1| 71 KLTEELKERKD 81
                                      56677888776 PP

>> LRRFIP  LRRFIP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  10.8   0.00055      0.47     147     249 ..       9     111 ..       4     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00055
                            LRRFIP 147 lerlkrqlealkleldelkeklkqrdeLiedhglvlveeeatdgekeeesssssksalvskeaaellesa..gegtl 221
                                       ++++  ql++l+++ + +  +  q + Li +    l+e e++ ++  ++  +s    l  +++++l e+    + + 
  gi|330508843|ref|YP_004385271.1|   9 IQNQLAQLQQLQQQAQAVMTQKTQIEGLIRETEAALKELEKSADD--AVIYKSVGELLFRADKLKLTEELkeRKDMM 83 
                                       577788999999999999999999999**9999888887777776..66777778888899999998888656899* PP

                            LRRFIP 222 dvrLkklaeekeeLleeveklkqqleee 249
                                       d+rLk +a++ e+++    +l++ql+++
  gi|330508843|ref|YP_004385271.1|  84 DIRLKTMAKQEERIQGRFTQLQEQLKQS 111
                                       *************************975 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   8.5    0.0054       4.7      29     119 ..       8      98 ..       1     112 [. 0.71

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0054
                                       CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHCCCHHHHHHHCCHHH CS
                         Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskel..eeeilrlketidaqesn 103
                                       + ++   +l++l+++ + +  +++++e l++e++  l+e +ks++  d vi ks  el  + + l+l e++++    
  gi|330508843|ref|YP_004385271.1|   8 QIQNQLAQLQQLQQQAQAVMTQKTQIEGLIRETEAALKELEKSAD--DAVIYKSVGELlfRADKLKLTEELKERKDM 82 
                                       556777899*******************************99999..566666666652455666666666666655 PP

                                       HHHHHHHHHHHHHHHH CS
                         Fib_alpha 104 irvLqnvlesneqkiq 119
                                       +    +++ ++e++iq
  gi|330508843|ref|YP_004385271.1|  83 MDIRLKTMAKQEERIQ 98 
                                       5554455555555555 PP

>> Phage_Mu_F  Phage Mu protein F like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3     0.014        12      12      74 ..       1      62 [.       1      72 [. 0.80
   2 ?    6.9   0.8     0.012        10      19      61 ..      71     109 ..      67     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.014
                        Phage_Mu_F 12 arGegeeelakelkkrgqlssrsrlrtiartetlraynaarlaqeaaskevkkekwryvavkd 74
                                      ++Ge   +++ +l++  ql +++++ ++ +t+   +   +++a ++ +k + +  + y+ v +
  gi|330508843|ref|YP_004385271.1|  1 MSGELPPQIQNQLAQLQQLQQQAQAVMTQKTQIEGLIRETEAALKELEKSADDA-VIYKSVGE 62
                                      5788888999*******9999999999999999999999988876666666555.67777665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
                        Phage_Mu_F  19 elakelkkrgqlssrsrlrtiartetlraynaarlaqeaaske 61 
                                       +l++elk+r ++++  rl+t+a++e +    ++r  q +++ +
  gi|330508843|ref|YP_004385271.1|  71 KLTEELKERKDMMDI-RLKTMAKQEERI---QGRFTQLQEQLK 109
                                       789999999999777.*********997...666666444433 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  12.4    0.0018       1.5     401     500 ..      11     110 ..       3     115 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0018
                           DUF3584 401 erleaireekdrlkaaieealealesqlrkqleaqkeel..neeekelesrlselklrldsatateEeleqieeade 475
                                       ++l+++++ ++ + +a   +  ++e   r + ea+ +el  + + + + ++++el +r+d+ + teE++e++   d 
  gi|330508843|ref|YP_004385271.1|  11 NQLAQLQQLQQ-QAQAVMTQKTQIEGLIR-ETEAALKELekSADDAVIYKSVGELLFRADKLKLTEELKERKDMMDI 85 
                                       44333333333.34444444455555555.33344444400445566788999999999999999999999999999 PP

                           DUF3584 476 alekaqeelekaeaevealqaeeeq 500
                                       +l+ + ++ e+ + +  +lq++++q
  gi|330508843|ref|YP_004385271.1|  86 RLKTMAKQEERIQGRFTQLQEQLKQ 110
                                       9999999999999999999998877 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  10.0    0.0014       1.2      90     183 ..       9     110 ..       7     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0014
                            DUF724  90 lqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeid..elekkilelerqlallk......ekkeaadk 158
                                       +q++l +L +l+++ + +++++ ++e  i+e e++ ++le++ d   + k + el  +++ lk      e+k+ +d 
  gi|330508843|ref|YP_004385271.1|   9 IQNQLAQLQQLQQQAQAVMTQKTQIEGLIRETEAALKELEKSADdaVIYKSVGELLFRADKLKlteelkERKDMMDI 85 
                                       788999999999999999999999999999999999999999886656777777777777777888887999999** PP

                            DUF724 159 eiarlkseaekleeeledveqeFea 183
                                       +++++ +++e+++ +  + +++ ++
  gi|330508843|ref|YP_004385271.1|  86 RLKTMAKQEERIQGRFTQLQEQLKQ 110
                                       ************9999999988876 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 ?    6.8   4.8    0.0075       6.4      25      74 ..       9      53 ..       5      62 .. 0.51
   2 ?    4.6   0.1     0.037        32      34      58 ..      88     112 ..      65     117 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0075
                      Baculo_PEP_C 25 irlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtd 74
                                      i++q++q+  ql+++ +a+ tq    +++++ l+ e +++l++l +  +d
  gi|330508843|ref|YP_004385271.1|  9 IQNQLAQL-QQLQQQAQAVMTQ----KTQIEGLIRETEAALKELEKSADD 53
                                      44444444.4444444444333....344455555555555555554444 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.037
                      Baculo_PEP_C  34 aqlatlldaietqLnalsedlksll 58 
                                         +a++ + i++++++l+e+lk++l
  gi|330508843|ref|YP_004385271.1|  88 KTMAKQEERIQGRFTQLQEQLKQSL 112
                                       3344455555555555555555544 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 ?    6.8   4.9    0.0065       5.6      33      78 ..       8      53 ..       3      68 .. 0.76
   2 ?    7.9   3.3    0.0029       2.4      26      67 ..      68     110 ..      54     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0065
                        Phage_GP20 33 qlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiad 78
                                      q++++  qL++L+++a+ + + ++qie l  + ++a +e e+   d
  gi|330508843|ref|YP_004385271.1|  8 QIQNQLAQLQQLQQQAQAVMTQKTQIEGLIRETEAALKELEKSADD 53
                                      7777778888888888888888888888888888888888776555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0029
                        Phage_GP20  26 erdtlkeqlkdrdkqLe.dLkkkakdneeLqkqieelqaknkk 67 
                                       ++ +l+e+lk+r   ++  Lk++ak  e +q  +++lq+++k+
  gi|330508843|ref|YP_004385271.1|  68 DKLKLTEELKERKDMMDiRLKTMAKQEERIQGRFTQLQEQLKQ 110
                                       66789999***99999977*********************998 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   7.7   0.00045      0.39      45      91 ..       8      54 ..       3      67 .. 0.89
   2 ?    3.8   3.3     0.035        30      53      90 ..      73     110 ..      63     115 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00045
                           DUF3450 45 ekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91
                                      + q+ la++++l++++++   ++ q e l+++ e+ +++le++ +++
  gi|330508843|ref|YP_004385271.1|  8 QIQNQLAQLQQLQQQAQAVMTQKTQIEGLIRETEAALKELEKSADDA 54
                                      678999************************************99987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.035
                           DUF3450  53 yralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                        ++lke+++ +++  + ++++ +  + ++++l+eq+++
  gi|330508843|ref|YP_004385271.1|  73 TEELKERKDMMDIRLKTMAKQEERIQGRFTQLQEQLKQ 110
                                       45667777777777777777777777777777777664 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   8.7     0.023        19      13      71 ..      10      70 ..       3     115 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.023
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXX--TTTTT CS
                        Laminin_II 13 kevleqlaplsqnlentkeklseinrsveetnekvkdankairdA..rrsvkkLeklapqL 71
                                      ++ l+ql++l+q+ + +  +  +i++ ++et++ +k++ k  +dA   +sv +L   a++L
  gi|330508843|ref|YP_004385271.1| 10 QNQLAQLQQLQQQAQAVMTQKTQIEGLIRETEAALKELEKSADDAviYKSVGELLFRADKL 70
                                      4445555666666666666666666666666666666666665552224555555555544 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 ?    4.6   2.2     0.044        38      43      71 .]      17      45 ..       8      50 .. 0.83
   2 ?    9.4   3.5    0.0014       1.2      32      71 .]      70     109 ..      63     109 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.044
                          JIP_LZII 43 eiLreEleslqkakerlesrikelEeelk 71
                                      + L++  ++++++k+++e  i+e+E+ lk
  gi|330508843|ref|YP_004385271.1| 17 QQLQQQAQAVMTQKTQIEGLIRETEAALK 45
                                      57889999999999999999999998886 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0014
                          JIP_LZII  32 IarvdeLtsereiLreEleslqkakerlesrikelEeelk 71 
                                       ++ ++eL+++++++   l+++ k+ er++ r ++l+e+lk
  gi|330508843|ref|YP_004385271.1|  70 LKLTEELKERKDMMDIRLKTMAKQEERIQGRFTQLQEQLK 109
                                       66689*********************************98 PP

>> Herpes_UL6  Herpesvirus UL6 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   7.7    0.0084       7.2     371     442 ..       6      80 ..       2     116 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0084
                        Herpes_UL6 371 eeqineqfdtiekLkkenelllkklkelekeLerlreeakkeakarevdlltsstda....slenlpessalsklk 442
                                         qi++q+ ++++L+++ + ++++  ++e  ++++++  k+  +++++d +  +         ++l   ++l++ k
  gi|330508843|ref|YP_004385271.1|   6 PPQIQNQLAQLQQLQQQAQAVMTQKTQIEGLIRETEAALKE-LEKSADDAVIYKSVGellfRADKLKLTEELKERK 80 
                                       569***************************99999666555.3333333333222220122334444445555444 PP

>> DUF2098  Uncharacterized protein conserved in archaea (DUF2098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.6       0.3   2.5e+02      47      84 ..      17      51 ..       9      61 .. 0.48
   2 ?    7.9   3.4    0.0044       3.8      37      84 ..      61     105 ..      40     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.3
                           DUF2098 47 evidekekkkekeekekedleelekkekeleeevdeek 84
                                      + ++   ++ +   ++k+++e l ++ ++  +e+++++
  gi|330508843|ref|YP_004385271.1| 17 QQLQ---QQAQAVMTQKTQIEGLIRETEAALKELEKSA 51
                                      3333...4444444444555544444444443444333 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0044
                           DUF2098  37 tdLyYrvdtLevidekekkkekeekekedleelekkekeleeevdeek 84 
                                        +L++r+d+L++++   + ke+++  +  l+++ k+e+ ++ ++ + +
  gi|330508843|ref|YP_004385271.1|  61 GELLFRADKLKLTE---ELKERKDMMDIRLKTMAKQEERIQGRFTQLQ 105
                                       579***********...8999999999999***999999995555444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.7     0.036        30      78     121 ..      12      48 ..       3      56 .. 0.45
   2 ?    7.4   1.4    0.0051       4.4      62      98 ..      74     110 ..      56     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.036
                           DUF1664  78 qkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       q +  ++++       ++ +++ ++ ++++ ++++ e+ l+++e
  gi|330508843|ref|YP_004385271.1|  12 QLAQLQQLQ-------QQAQAVMTQKTQIEGLIRETEAALKELE 48 
                                       333333333.......3333333333444444444444444433 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0051
                           DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlse 98 
                                       ++L++r d +d +l+ +++  + i+   t+++e+l++
  gi|330508843|ref|YP_004385271.1|  74 EELKERKDMMDIRLKTMAKQEERIQGRFTQLQEQLKQ 110
                                       6899999999999999999999999999999999987 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.6    0.0035         3      55     101 ..       9      55 ..       7      57 .. 0.90
   2 ?    4.9   2.2     0.034        29      10     103 ..      68     107 ..      55     116 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0035
                                       HHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  55 lskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                       ++++ +++ + +++a++++ +  ++   + ++ea+lkele+  ++++
  gi|330508843|ref|YP_004385271.1|   9 IQNQLAQLQQLQQQAQAVMTQKTQIEGLIRETEAALKELEKSADDAV 55 
                                       7788999999999***************************9988865 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.034
                                       -HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHH CS
                      Seryl_tRNA_N  10 npeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkal 86 
                                       +                                                        + +eel+++ + +  +lk++
  gi|330508843|ref|YP_004385271.1|  68 DKL------------------------------------------------------KLTEELKERKDMMDIRLKTM 90 
                                       333......................................................45566666666666666666 PP

                                       HHHHHHHHHHHHHHHCT CS
                      Seryl_tRNA_N  87 eaelkeleaelekllla 103
                                        ++++ ++ ++++l  +
  gi|330508843|ref|YP_004385271.1|  91 AKQEERIQGRFTQLQEQ 107
                                       66666666655555443 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   5.5     0.019        16       5      38 ..      15      48 ..       8      51 .. 0.88
   2 ?    5.5   0.7     0.023        20       9      36 ..      83     110 ..      79     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.019
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCG CS
                            WXG100  5 dpeelrqaaarfqkqaeeledelqrlkaevdalq 38
                                      + ++l+q a+++ +q++++e+++++ +a +++l+
  gi|330508843|ref|YP_004385271.1| 15 QLQQLQQQAQAVMTQKTQIEGLIRETEAALKELE 48
                                      57999******************99999999883 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   9 lrqaaarfqkqaeeledelqrlkaevda 36 
                                       ++   ++++kq+e+++++ ++l+ ++++
  gi|330508843|ref|YP_004385271.1|  83 MDIRLKTMAKQEERIQGRFTQLQEQLKQ 110
                                       5556688999999999999999988855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2461  (0.137264); expected 358.6 (0.02)
Passed bias filter:                      904  (0.0504211); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 888.69
//
Query:       gi|330508844|ref|YP_004385272.1|  [L=61]
Description: hypothetical protein MCON_3161 [Methanosaeta concilii GP6]
Scores for complete sequence (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   2.2    1.4e-19   70.1   2.2    1.0  1  CooT      CO dehydrogenase accessory protein CooT


Domain annotation for each model (and alignments):
>> CooT  CO dehydrogenase accessory protein CooT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   2.2     8e-24   1.4e-19       1      60 [.       1      59 [.       1      60 [. 0.95

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 8e-24
                              CooT  1 MCeanvyllkngkeeelvmedVdkiepeedgvvltdifGeekevegkIkeidLvehkiil 60
                                      MCe++vy lk+g   e+vme+V+++ +++++v+l++ifG+ +eveg+I e++++++   +
  gi|330508844|ref|YP_004385272.1|  1 MCELTVYTLKGGVR-EKVMESVVRLMVHDGKVILEGIFGDSMEVEGRISEVNIMSQSATI 59
                                      *********99977.9*************************************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 499.36
//
Query:       gi|330508845|ref|YP_004385273.1|  [L=189]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1476.83
//
Query:       gi|330508846|ref|YP_004385274.1|  [L=341]
Description: deoxyhypusine synthase [Methanosaeta concilii GP6]
Scores for complete 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-91  304.4   0.0    8.5e-91  304.2   0.0    1.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.2   0.0   4.7e-95   8.5e-91       1     287 [.      27     315 ..      27     316 .. 0.97

  Alignments for each domain:
  == domain 1  score: 304.2 bits;  conditional E-value: 4.7e-95
                                DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlika 77 
                                       el+  ++++gfq+ +lg +++++++m  de++tiflgl+++++++Gl e+ia+l +e+ vd++v+T++++ +Dl++ 
  gi|330508846|ref|YP_004385274.1|  27 ELVGDMGRMGFQGGQLGASLRVWERM-MDEDVTIFLGLAGAMVPAGLGEFIAYLLRERKVDCLVSTGANLFHDLCEG 102
                                       6999**********************.799*********************************************** PP

                                DS  78 lgkktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelGkeindeeSily 154
                                       lg  ++ g+  +dd+ L+e +i+Ri++++v++ +++k++++++++++ l+++ ++ s++el++ +Gk +  ++ il 
  gi|330508846|ref|YP_004385274.1| 103 LGIIHFRGSSCADDAYLNECKIDRIYDVFVSEIELHKADNYISDFVKGLDQD-RRYSSRELMEMVGKGLP-DTTILG 177
                                       *************************************************984.678*************5.789*** PP

                                DS 155 wAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanlm. 230
                                       +A+k+++p+f+pal D+s G++++++   +e  ++ +d +kD++e+++i+ ++ +tg+i++GGGvpK++i++++++ 
  gi|330508846|ref|YP_004385274.1| 178 AAHKAGVPIFVPALGDSSWGIGMVIAL--REGCRVLVDQIKDVDEITRIVERSAQTGVIYIGGGVPKNFIQQTEVIa 252
                                       *********************999999..79999****************************************999 PP

                                DS 231 ......rngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                                             + g+ ya+++t +++++G+lsg+t++EavSwgk+k+ea++v+v++DaTi++PL+v+a
  gi|330508846|ref|YP_004385274.1| 253 elignySGGHSYAIQYTADSPHWGGLSGCTFEEAVSWGKVKKEASKVQVFSDATITVPLVVQA 315
                                       999988679***************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2529.62
//
Query:       gi|330508847|ref|YP_004385275.1|  [L=347]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete 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-19   67.9   1.2    2.4e-18   65.8   0.1    2.3  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    7.9e-09   35.8   0.0    1.3e-08   35.1   0.0    1.3  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.028   13.9   0.7       0.14   11.7   0.2    1.9  2  DUF334          Domain of unknown function (DUF334)


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 ?    0.2   0.1      0.12     7e+02      54      64 ..     203     213 ..     184     214 .. 0.68
   2 !   65.8   0.1   4.1e-22   2.4e-18       1      69 []     255     324 ..     255     324 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.12
                    OrfB_Zn_ribbon  54 feadrDvnAai 64 
                                       ++++rDvn +i
  gi|330508847|ref|YP_004385275.1| 203 ARFHRDVNHCI 213
                                       569****9876 PP

  == domain 2  score: 65.8 bits;  conditional E-value: 4.1e-22
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l++++ yka  +G++++ ++payTS++C+ C  +++  ++++++f C  Cgf+  +D+ Aa+Ni+ r
  gi|330508847|ref|YP_004385275.1| 255 FYQLRQYIDYKAAIAGVPLICIDPAYTSQECPICHLISRSnRPTRDEFSCVCCGFSGPADTIAARNIAAR 324
                                       899***********************************9999*************************976 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   2.2e-12   1.3e-08       4     111 ..     130     233 ..     127     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.2e-12
                        OrfB_IS605   4 veveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       v v+v+ ++k  +++++g+DlGi+n+a+ + ++     ++g ++ +   +  + +a lqs+  +s     a+r l++
  gi|330508847|ref|YP_004385275.1| 130 VVVDVPePKKSVPQNVLGVDLGIKNIAVDSSGE----EFSGEKIEKVRSKIDNLKADLQSCGTDS-----AKRHLKK 197
                                       5555553888899******************99....899*********************7777.....6888888 PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathli....ktlkevgvetL 111
                                       l+ k +r+ +++ h ++++l+    +t  ++++e+L
  gi|330508847|ref|YP_004385275.1| 198 LSGKEARFHRDVNHCISKKLVakaiDTSSAIVLEDL 233
                                       888888888888887777776111144445566666 PP

>> DUF334  Domain of unknown function (DUF334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.073   4.3e+02     106     146 ..      18      59 ..       8      78 .. 0.75
   2 ?   11.7   0.2   2.3e-05      0.14      76     148 ..     187     261 ..     167     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.073
                            DUF334 106 lkrvdaeelkiilrkdvykvreeidrm.lrevkrshehyqkr 146
                                       l+  +  el++i+ +d+ ++     +m +r + +s e y++ 
  gi|330508847|ref|YP_004385275.1|  18 LHTANKIELQKIVYRDIREMFGISAQMaVRAISKSCEAYKRD 59 
                                       666777888999999998887766666479999999999753 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.3e-05
                            DUF334  76 ikselkkatkdfrdkskkvrndfvdllqkklkrvdaeelkiilrkdvykvreeidrmlrevkrshe..hyqkrqk 148
                                        + + k+  k + +k  + + d  + + kkl     +    i+  d+y++re i     + ++ h+   yq rq 
  gi|330508847|ref|YP_004385275.1| 187 GTDSAKRHLKKLSGKEARFHRDVNHCISKKLVAKAIDTSSAIVLEDLYGIRERITVPKAQRRKQHNwsFYQLRQY 261
                                       466788999999*******************9999999999************9876666666664227999996 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:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2564.00
//
Query:       gi|330508848|ref|YP_004385276.1|  [L=652]
Description: arginine decarboxylase [Methanosaeta concilii GP6]
Scores for complete 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  142.2   0.0    2.4e-41  141.8   0.0    1.2  1  Orn_Arg_deC_N   Pyridoxal-dependent decarboxylase, pyridoxal 
    2.6e-18   66.0   0.3    8.7e-18   64.4   0.1    2.0  2  Arg_decarb_HB   Arginine decarboxylase helical bundle domain
  ------ inclusion threshold ------
      0.014   16.0   0.5      0.052   14.1   0.1    2.2  2  Arg_decarbox_C  Arginine decarboxylase C-terminal helical ext


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 !  141.8   0.0     4e-45   2.4e-41      13     247 .]      84     339 ..      72     339 .. 0.91

  Alignments for each domain:
  == domain 1  score: 141.8 bits;  conditional E-value: 4e-45
                                       HHCT...CCEEEEEGGG---HHHHHHHHHTT....EEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHHHHHH. CS
                     Orn_Arg_deC_N  13 kalp...rikvfYavKansdlavlellaelG....lgldcaSkaElelvlaagvsperiifanpckqreelryale. 81 
                                       ++++    +++++++K+n+ ++v+e + + G    +g++++ kaEl ++l++g +     ++n++k++++lr al+ 
  gi|330508848|ref|YP_004385276.1|  84 EEFNysgTYQPIFPMKVNQRKEVIEYIIKYGakhkIGMEVGTKAELLAALSLGLPRYAPLICNGYKDEDYLRLALSi 160
                                       555555689**********************998889************************************9862 PP

                                       CTHT..EEEESSHHHHHHHHHHHCC....EEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHC...HHHHHHHHHHHH CS
                     Orn_Arg_deC_N  82 kgvk..vvtvdnveeleklaklape....akvllRiktdvsaatcelistggessKFGaale...eavealleaake 149
                                       ++ +  +++vd +ee++ + k a+     ++v +R+k+ +  ++ +++ +gges KFG +++   e ++ l+e    
  gi|330508848|ref|YP_004385276.1| 161 HNLNniIIVVDLFEEIYDILKYADAmgvvPRVGMRVKL-FARGSGRWVESGGESAKFGLSTSealELMRILEERGLT 236
                                       55556789***************9999***********.*******************9998666777788888889 PP

                                       TTEEEEEEE---BSSC-SCHHHHHHHHHHHHHHHHHHHHT---SEEE--S-BS-HCSTTSSSST......HHHHHHH CS
                     Orn_Arg_deC_N 150 enlqlvGvsfHvGSgvsdleafvkavekalklfdelaelGvklkiLdvGGGfgveyeeeeeplk......leeiaek 220
                                        +l++  ++fH+GS+++d+++ ++a+++a++++ +++++  +++ L+vGGG++v+y++ + +++      l+e+a++
  gi|330508848|ref|YP_004385276.1| 237 SSLKM--LHFHIGSQITDIRTVKNAMNEAARVYAKARKM-ADIEYLNVGGGLSVDYNGSNTATPssanysLQEYAND 310
                                       99999..*****************************998.59***************8777766788999******* PP

                                       HHHHHHHHHH..TSSS-EEEE--SHHHHG CS
                     Orn_Arg_deC_N 221 irealeeafp..gdkevtiiaEpGRalva 247
                                       i   +++++   + + +ti++E+GRa++a
  gi|330508848|ref|YP_004385276.1| 311 IVYTVQKICDdeEVPCPTIVSESGRAIAA 339
                                       *********9989999**********987 PP

>> Arg_decarb_HB  Arginine decarboxylase helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.3   1.4e+04      21      36 ..     302     317 ..     297     319 .. 0.81
   2 !   64.4   0.1   1.5e-21   8.7e-18       2      80 ..     364     442 ..     363     445 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.3
                     Arg_decarb_HB  21 rnlqEiyhDavhylde 36 
                                        +lqE+ +D v+ +++
  gi|330508848|ref|YP_004385276.1| 302 YSLQEYANDIVYTVQK 317
                                       5799999999998876 PP

  == domain 2  score: 64.4 bits;  conditional E-value: 1.5e-21
                     Arg_decarb_HB   2 edapellqnLwelleelsqrnlqEiyhDavhyldearelFrlGllsLeerAkaEqlylaicrkirkllkeeerapre 78 
                                       ++ap  + +L   ++e++  n+ E yhDa++y+de+ + F+lG + LeerAk+E+l++++c+k + l+ke+ ++ +e
  gi|330508848|ref|YP_004385276.1| 364 DEAPMQIDDLCSAFKEINIDNYKEHYHDALQYRDELYDSFNLGNIGLEERAKGETLFWMVCKKAAFLAKEAGDESDE 440
                                       799*****************************************************************999999888 PP

                     Arg_decarb_HB  79 il 80 
                                        l
  gi|330508848|ref|YP_004385276.1| 441 FL 442
                                       44 PP

>> Arg_decarbox_C  Arginine decarboxylase C-terminal helical extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.1   1.3e+04      33      48 ..     125     140 ..     121     140 .. 0.82
   2 ?   14.1   0.1   8.7e-06     0.052      17      51 .]     589     623 ..     574     623 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.1
                    Arg_decarbox_C  33 erqalleeleagLkgy 48 
                                       ++++ll++l  gL  y
  gi|330508848|ref|YP_004385276.1| 125 TKAELLAALSLGLPRY 140
                                       68899**999999766 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8.7e-06
                    Arg_decarbox_C  17 erlrrqveaagrLtpeerqalleeleagLkgyTYL 51 
                                       e + r v ++  ++ +e +++ +el++ LkgyTY+
  gi|330508848|ref|YP_004385276.1| 589 EIMDRCVTRKESIRKRELEQIEAELNRTLKGYTYF 623
                                       55666666667999********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); 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 0.28s 00:00:00.91 Elapsed: 00:00:00.41
# Mc/sec: 4779.22
//
Query:       gi|330508849|ref|YP_004385277.1|  [L=177]
Description: hypothetical protein MCON_3167 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 1308.93
//
Query:       gi|330508850|ref|YP_004385278.1|  [L=518]
Description: hypothetical protein MCON_3168 [Methanosaeta concilii GP6]
Scores for complete 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   37.0   0.2    9.9e-09   35.1   0.2    2.0  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
      0.043   13.5   0.0       0.16   11.7   0.0    1.9  2  Transket_pyr  Transketolase, pyrimidine binding domain
      0.051   13.3   0.0        4.6    6.9   0.0    2.2  2  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
       0.79    9.3   3.0       0.65    9.6   0.1    2.3  3  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.2   2.2e-12   9.9e-09       1      95 [.     359     441 ..     359     482 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.2e-12
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       d+Gc+ + a+rl     p++ ++  +   +G ++++A+G +      + +a+vGD +++++ lq l++a  ++ +++
  gi|330508850|ref|YP_004385278.1| 359 DAGCSIR-ASRL-----PYQSVD--VVYGLGSSIGVASGFST-----KGIALVGDYALAHSgLQGLINALWQKRDLL 422
                                       5677766.4444.....878777..8999************9.....58**************************** PP

                                       EEEEE-SBCCCHHHHHHHH CS
                      TPP_enzyme_C  77 vvvlnNegygmtggqqepf 95 
                                        vvl N + +mtggq+ p 
  gi|330508850|ref|YP_004385278.1| 423 AVVLKNDVAAMTGGQEVPD 441
                                       ***************8765 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.5e-05      0.16      50     175 ..      44     162 ..       9     165 .. 0.82
   2 ?   -1.6   0.0      0.41   1.8e+03     144     169 ..     458     481 ..     457     483 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.5e-05
                                       EEE--S-HHHHHHHHHHHHHHCTTEEEEE.EEEHHHHGGGHHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTS CS
                      Transket_pyr  50 vidsgisEqavlgfavGaalagpllvive.aqFgdFangAqiyadqairsgeakgklkvgvvtrlpigvgedGpehq 125
                                       + + +i E+ +l +a+Ga+++g  + +v+  q g  +n     ad+ ++  +a +++ +g+v+ ++  +g +G   q
  gi|330508850|ref|YP_004385278.1|  44 NAEISINEKVALEIALGASATGL-RSMVVvKQVG--MN---ALADPLVI--SATHNIGSGLVLIAGDDLGPRGS--Q 110
                                       67889*****************4.4433303444..34...35888888..9*******************997..7 PP

                                       BSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHS..SS.SEEEEEE-SSEE CS
                      Transket_pyr 126 saeleaflrlipglkvvrPsdpaetkhllrrairr..edrkPvvlrlpksll 175
                                         ++ +f+  +++l  + P dp+++++ + +a+      r Pv++r +  ll
  gi|330508850|ref|YP_004385278.1| 111 VEMDSRFYGPLAKLPLLDPRDPENLYASILEAYSLseGLRVPVIVRVTAPLL 162
                                       899***********************99999998865568899998876665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.41
                                       -SSHHHHHHHHHHHHHSSS.SEEEEE CS
                      Transket_pyr 144 PsdpaetkhllrrairredrkPvvlr 169
                                       P++ +e++++l++ ++r  ++P++++
  gi|330508850|ref|YP_004385278.1| 458 PATVQEAEQILQEELAR--NGPSAIV 481
                                       89999***********5..5699886 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 ?    4.1   0.1    0.0074        33      46      66 ..      51      71 ..      46     102 .. 0.85
   2 ?    6.9   0.0     0.001       4.6     122     160 ..     126     164 ..     107     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0074
                                      HHHHHHHHHHHHCTT-EEEEE CS
                             POR_N 46 EigaisaviGAaaaGaraaTa 66
                                      E  a + ++GA+a+G r+++ 
  gi|330508850|ref|YP_004385278.1| 51 EKVALEIALGASATGLRSMVV 71
                                      7779999***********986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.001
                                       EEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHHH.H CS
                             POR_N 122 vlasenvqeafdlalvAfnlAekvrvPvivlfDgfllsh 160
                                       +l +++ +  +  +l+A+ l+e +rvPviv + + ll +
  gi|330508850|ref|YP_004385278.1| 126 LLDPRDPENLYASILEAYSLSEGLRVPVIVRVTAPLLAE 164
                                       67789999*********************9876666655 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 ?    9.6   0.1   0.00014      0.65       3     169 ..      12     167 ..      10     170 .. 0.80
   2 ?   -1.6   0.1      0.39   1.7e+03      45      69 ..     196     221 ..     193     230 .. 0.77
   3 ?   -2.1   0.0      0.58   2.6e+03      79     140 ..     407     468 ..     394     481 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHC CS
                      TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatna 79 
                                       + +a+ +a  ++g+ +   vpG  i++l   l++e       + +E +a  +A g +    + +vv+ ++g +a+  
  gi|330508850|ref|YP_004385278.1|  12 GLKAVMQAADDAGAASRTYVPGYPITDLAAGLNAE------ISINEKVALEIALGASATGLRSMVVVKQVGMNALAD 82 
                                       66778888888899999999999999999999999......799***********9777777777777779988877 PP

                                       HHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSE.EEE-SSGGGHHHHHHHHHHHHHSSS--EE CS
                      TPP_enzyme_N  80 ltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtky.aervtspeelpealrrAirtalsgrpgPv 155
                                          +   +  ++ l++++gd    + +    q +   + ++ p++k     +++pe+l   + +A+  + +g + Pv
  gi|330508850|ref|YP_004385278.1|  83 PLVISATHNIGSGLVLIAGDDLGPRGS----Q-VEMDSRFYGPLAKLpLLDPRDPENLYASILEAYSLS-EGLRVPV 153
                                       6777777777*********97666666....5.444566778888774678999999999999999999.9999999 PP

                                       EEEEEHHHCC-EEE CS
                      TPP_enzyme_N 156 ylelpkdvlleevd 169
                                        + + + +l ee++
  gi|330508850|ref|YP_004385278.1| 154 IVRVTAPLLAEECP 167
                                       99999988888886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.39
                                       -SSHHHHHHHHHHHHHHH.TS-EEEE CS
                      TPP_enzyme_N  45 arhEqgaafaAdgyarat.gkpgvvl 69 
                                        +hE ++a aA + + ++ +++  ++
  gi|330508850|ref|YP_004385278.1| 196 RHHEKTMARAAGAAFSSSlNRMKKCA 221
                                       58*********998888767666655 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.58
                                       CHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCS..SEEEE-SSGGGHHHHH CS
                      TPP_enzyme_N  79 altalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvt..kyaervtspeelpeal 140
                                       +l +l++A   +  ll+++  ++++     + q++ d +al++ +   + ++ +++++e++++l
  gi|330508850|ref|YP_004385278.1| 407 GLQGLINALWQKRDLLAVVLKNDVAAMT--GGQEVPDLTALLEGLLptRGFDLPATVQEAEQIL 468
                                       4666666666666666666666666666..3443557777766443113333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.86
# Mc/sec: 1823.14
//
Query:       gi|330508851|ref|YP_004385279.1|  [L=299]
Description: putative methanogenesis marker protein 11 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-10   41.4   0.0    9.6e-08   32.1   0.0    3.3  2  DUF1743   Domain of unknown function (DUF1743)


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   5.4e-12   9.6e-08       1     113 [.     152     240 ..     152     243 .. 0.94
   2 !    2.3   0.0    0.0093   1.7e+02       1      15 [.     274     288 ..     274     295 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 5.4e-12
                                       TTHHHHHHHHHH-..-TT....S-EEEEEEEE-GGGTT---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTS CS
                           DUF1743   1 grgiiGAtaalganiale....dstyEllaYreperwgerevdeesvieadektypetfdnvDlshklvvlvPhtpd 73 
                                       +++++GAt++l +nia++    +++y                                     +sh+lv+l+P +p+
  gi|330508851|ref|YP_004385279.1| 152 DSKTVGATWSLIHNIAQKvdrpEARY-------------------------------------ISHSLVQLFP-VPT 190
                                       7899************9877766777.....................................**********.*** PP

                                       S........EEEEEEES-HHHHHHHHHCSEE..S-EEC..EEEEEESTTS CS
                           DUF1743  74 p........vlfGirgedpeallkaakeilskeeesee..mavfrtnqgt 113
                                       +        v+f++ + + e +l  ++++l+k+++se+  mavfr+++++
  gi|330508851|ref|YP_004385279.1| 191 KtqncvstvVEFACLPGRGEGMLGDFRALLQKYTVSEQtgMAVFRDFDPS 240
                                       **********************************************9987 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.0093
                                       TTHHHHHHHHHH-.. CS
                           DUF1743   1 grgiiGAtaalgani 15 
                                       g+g+iGA+aal +n 
  gi|330508851|ref|YP_004385279.1| 274 GQGLIGAIAALPFNA 288
                                       78********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1975.48
//
Query:       gi|330508852|ref|YP_004385280.1|  [L=62]
Description: hypothetical protein MCON_3172 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 456.87
//
Query:       gi|330508853|ref|YP_004385281.1|  [L=109]
Description: hypothetical protein MCON_3173 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-07   31.1   0.0    2.8e-07   30.9   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 !   30.9   0.0   1.5e-11   2.8e-07       2     109 ..       2     105 ..       1     107 [. 0.84

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.5e-11
                                       TTEEEEEEE-S--TTS--SEEEEEE-S-HHHHCHSEEEEEEEESSSTSSGCSTTEEEE-HH.HCSS..SSSSSSEEE CS
                        PemK_toxin   2 rGeIvlvdldpsrgseqgkrRpvvVvsndafnekntvivvpltskdkdkkklpfhvelese.ildl..ngldkdswv 75 
                                       +G+Iv v + p      +k+Rp++V+ +++      v+ + ++s+ +     +++v +  +       +gl++ds++
  gi|330508853|ref|YP_004385281.1|   2 KGDIVFVRF-PYTDMTNAKPRPALVLHEEKD----EVVLAYISSRVPIVPT-KTDVLVLRSdS-FFeaTGLKRDSVI 71 
                                       79*******.97766669********98843....59*********87755.88888776622.22468888***** PP

                                       ECCCEEEEEGGGEEEEEEE--HHHHHHHHHHHHH CS
                        PemK_toxin  76 kldqirtvdkarlrkkigklsredlaevqralak 109
                                       kl  ++t+ k  + +  g+ + ++  e++++la+
  gi|330508853|ref|YP_004385281.1|  72 KLSVLATLKKWFIEGLFGEADGTLRHEINTKLAL 105
                                       *************9******99999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 806.39
//
Query:       gi|330508854|ref|YP_004385282.1|  [L=425]
Description: tRNA pseudouridine synthase D [Methanosaeta concilii GP6]
Scores for complete 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-155  517.9   0.0     2e-155  517.7   0.0    1.0  1  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  517.7   0.0  1.1e-159    2e-155       2     416 .]      11     420 ..      10     420 .. 0.98

  Alignments for each domain:
  == domain 1  score: 517.7 bits;  conditional E-value: 1.1e-159
                              TruD   2 lgielyvtdtegigGrlrespeDFiVeEieefsgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaG 78 
                                       lg+++y+td++g+gG +r++peDF+V E+ e       + g+ylv++vek++wdt++l+re++r+l+is+kr+g+aG
  gi|330508854|ref|YP_004385282.1|  11 LGMDYYITDSPGCGGIIRRNPEDFLVVEVFED---LGYEGGRYLVIEVEKTDWDTHHLIREMSRHLRISQKRFGWAG 84 
                                       79***************************333...56799************************************* PP

                              TruD  79 tKDkrAvTtQlisirkvepeelealeikdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeileele 155
                                       tKDkrA+T+Q isi++++++el +++++d++++v+gr++r++ lGdL GN+F i++r++ + ++ a+++++++ee++
  gi|330508854|ref|YP_004385282.1|  85 TKDKRAITRQRISIMNLDESELDRIRLPDIKINVLGRTNRAVGLGDLLGNRFSITIREL-SCPDPARSLASVSEEIK 160
                                       **********************************************************6.678889*********** PP

                              TruD 156 ekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpkslr 232
                                       +++gv NyfGvQRFG +rp+thlvG+a+ +g+ eeA++++++ p+  e+e+treare ++e+gd+++a +++p  l+
  gi|330508854|ref|YP_004385282.1| 161 RHKGVANYFGVQRFGDIRPITHLVGEALARGKAEEAARIFLALPYAGEQERTREARERLWESGDIQAARNDFPGYLH 237
                                       ***************************************************************************** PP

                              TruD 233 yErallkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeerlpdtdrlq 309
                                       +E a+l++Lae+p+dy++++ +l+ nL+rlFvhAyqSylFNr+ls Rl++ +plde++ GDvv+f++  +pd+d++q
  gi|330508854|ref|YP_004385282.1| 238 HELAMLNYLAEHPGDYAHSFDVLSVNLKRLFVHAYQSYLFNRILSLRLAKSMPLDEALVGDVVCFSKGGMPDMDKTQ 314
                                       ***************************************************************************** PP

                              TruD 310 lvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaillrve 386
                                        vte+n e+++rl++rgrafvt+pl+G e++laeg++geier+vl+ee++ +e Fk+ + p+l+s+GtrR +l++v+
  gi|330508854|ref|YP_004385282.1| 315 EVTEDNLEAIARLVNRGRAFVTLPLIGFESRLAEGRQGEIERQVLQEEDILPEGFKVVENPDLGSRGTRRTALCPVD 391
                                       ********************************************************9999****************9 PP

                              TruD 387 dlelsaeedeltleFsLpkGsYATvvlrEi 416
                                         +++ e+d+++leF LpkGsYATvvlrE+
  gi|330508854|ref|YP_004385282.1| 392 P-KIRVEGDSAQLEFILPKGSYATVVLREY 420
                                       7.789999*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2776.60
//
Query:       gi|330508855|ref|YP_004385283.1|  [L=117]
Description: hypothetical protein MCON_3175 [Methanosaeta concilii GP6]
Scores for complete 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  129.3   0.1      9e-38  129.2   0.1    1.0  1  PTH2      Peptidyl-tRNA hydrolase PTH2


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.2   0.1     5e-42     9e-38       2     116 ..       4     116 ..       3     117 .] 0.98

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 5e-42
                                       EEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SE CS
                              PTH2   2 kmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglpa 78 
                                       k+++v+r+DLk+s+Gk+a+q+ahAav++v++++k+ ++ ++++eW+ egqkk+vl+v+  ++L +l++ a+++g+p+
  gi|330508855|ref|YP_004385283.1|   4 KQCIVIREDLKLSAGKLAVQVAHAAVMAVERAEKM-DR-SVVSEWKAEGQKKVVLRVSGVSDLFRLREDAERAGIPS 78 
                                       9*********************************9.77.8************************************* PP

                                       EEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB CS
                              PTH2  79 alirDagrtqiepgtkTvlaigPapksivdkvtgkLkl 116
                                       a+++Dag t+i+pgt T+l++gPa  +++dkvtgkL+l
  gi|330508855|ref|YP_004385283.1|  79 AIVADAGLTEIPPGTITALGLGPAHGKLMDKVTGKLRL 116
                                       ************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 852.85
//
Query:       gi|330508856|ref|YP_004385284.1|  [L=440]
Description: toprim domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   47.5   0.3    5.5e-12   46.0   0.3    1.9  1  Toprim_4       Toprim domain
    9.3e-07   29.2   0.0    2.3e-06   27.9   0.0    1.7  1  Toprim_2       Toprim-like
    1.9e-05   24.8   0.9    0.00023   21.4   0.2    2.9  2  Toprim         Toprim domain
  ------ inclusion threshold ------
       0.17   12.0   0.1       0.31   11.2   0.1    1.5  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


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 !   46.0   0.3   1.2e-15   5.5e-12       2      85 ..     172     267 ..     171     271 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.2e-15
                          Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklkt.enlve....aekkvkevilaldgDa.....eGe 68 
                                       +i +VEg+aDvl+l k+gikn+vav g+++ p+  + +  +k  +++++    +e +vke++++ d D+     +G+
  gi|330508856|ref|YP_004385284.1| 172 AILVVEGRADVLNLLKYGIKNAVAVGGTNV-PPTIADLCAKKVvTAFTDgdrgGELIVKELLQVADIDYvarapDGK 247
                                       799***************************.888888777777799999********************99999999 PP

                          Toprim_4  69 ataerlae...llleegvkv 85 
                                        + ++  +   + l++++ v
  gi|330508856|ref|YP_004385284.1| 248 SVEDMTQKeivRALRQKIPV 267
                                       88888777665444666655 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   5.1e-10   2.3e-06       2      84 ..     175     247 ..     174     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5.1e-10
                          Toprim_2   2 vfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellreagvrekir 78 
                                       v+Eg  D+l l+++gik   n+va+gGt+++++ ++l +++    v   +D D+ G+  +k+l +++      + ++
  gi|330508856|ref|YP_004385284.1| 175 VVEGRADVLNLLKYGIK---NAVAVGGTNVPPTIADLCAKK---VVTAFTDGDRGGELIVKELLQVADI----DYVA 241
                                       9***************9...********8888888888877...36666************99988842....2344 PP

                          Toprim_2  79 elpegk 84 
                                       + p+gk
  gi|330508856|ref|YP_004385284.1| 242 RAPDGK 247
                                       455555 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.24   1.1e+03       5      37 ..      21      72 ..      19     156 .. 0.50
   2 !   21.4   0.2     5e-08   0.00023       2      90 ..     173     239 ..     172     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.24
                                      ESSHHHHHHHHHTHT...................STEEEEEEESSSSEEEHS CS
                            Toprim  5 vEgpsdaktiakalg...................sgfqavtaslGhildlet 37
                                      vE p  +++i    +                   + ++++t+s G+     +
  gi|330508856|ref|YP_004385284.1| 21 VERPDVVGAIFGQTEgllgsdldlrdlqktgrlgRIDVQITSSGGKSSGTIS 72
                                      5555555555444334444445555555555555556666666666555444 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 5e-08
                                       EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEE.CSSSHHHH CS
                            Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiila.tDpDreGe 77 
                                       + +vEg +d+ ++ k+   g ++++a+ G+ +  +                        + a++++ a tD+Dr Ge
  gi|330508856|ref|YP_004385284.1| 173 ILVVEGRADVLNLLKY---GIKNAVAVGGTNVPPTI---------------------ADLCAKKVVTAfTDGDRGGE 225
                                       78**************...9**********997766.....................335588999988******** PP

                                       HHHHHHHHHHT.HH CS
                            Toprim  78 aiawellevlk.el 90 
                                        i +ell+v++ ++
  gi|330508856|ref|YP_004385284.1| 226 LIVKELLQVADiDY 239
                                       *******9998544 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 ?   11.2   0.1   6.9e-05      0.31      12      76 ..     133     196 ..     127     269 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.9e-05
                     Metallophos_2  12 nldaleavlealke.vgvdaiihaGDleeeepevleellelapvlaVrGNnDeev...veedvlreaae 76 
                                       n+ ++e++ e++k+ v+v+ iih+G     ++ +  ++l+   +l+V G+ D  v   ++  + ++ a 
  gi|330508856|ref|YP_004385284.1| 133 NILETEEITEEIKQsVRVEEIIHLGK---DNLPAGPNVLDSDAILVVEGRAD--VlnlLKYGIKNAVAV 196
                                       66778899988887699********9...6666999****99**********..223333334444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3419.27
//
Query:       gi|330508857|ref|YP_004385285.1|  [L=345]
Description: NMD3 family protein [Methanosaeta concilii GP6]
Scores for complete 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-46  156.5   0.0    9.6e-46  156.2   0.0    1.1  1  NMD3           NMD3 family
     0.0098   15.9   4.4      0.047   13.7   2.8    2.6  2  DZR            Double zinc ribbon
  ------ inclusion threshold ------
      0.061   13.6   1.2        5.9    7.2   0.2    2.6  2  FeoA           FeoA domain
       0.13   11.7   9.8        5.9    6.4   0.1    2.9  2  zf-ribbon_3    zinc-ribbon domain
          3    7.3   9.9        2.7    7.4   1.1    3.0  3  zf-TFIIB       Transcription factor zinc-finger
        3.2    7.4  10.3        0.3   10.7   1.1    3.2  3  RecR           RecR protein
        5.5    6.7   7.5        5.3    6.8   0.1    3.2  3  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain


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 !  156.2   0.0   3.8e-49   9.6e-46       1     242 [.       5     236 ..       5     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: 156.2 bits;  conditional E-value: 3.8e-49
                              NMD3   1 CcrCGkeieelinglCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvse 77 
                                       C++CG++ e   +glC++C ++++++++ ++ +ev +C+ Cg+ + kgkW   +   ++++++++  ++ +++ +++
  gi|330508857|ref|YP_004385285.1|   5 CPKCGQPAE---DGLCPQCRMNSIRLIQFPDVVEVVICSVCGSQQIKGKW---QFPDSRSIEDLAAGAAADSVWLHH 75 
                                       ********6...89************************************...67888899999999999******* PP

                              NMD3  78 eveevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqk 154
                                       e+ + ++e vd +   ++   +r+ + ++++g++ +   ++++++ ev+v++k   C+rCsr+ag+y++++vQ+R++
  gi|330508857|ref|YP_004385285.1|  76 EFIHPNIE-VDLR---KVG-ATRYIAGMRIRGSFME---QMVEETGEVPVRIKLVACERCSRMAGKYFQSTVQLRGN 144
                                       *******9.9999...555.78899*********44...6899********************************** PP

                              NMD3 155 ..relteeehkrtfelleqli....lkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvs 225
                                         r +++ e +++ ++++++     + +d+ +fi+++kevk GlD+ +gs++ +r++++++++++ggk+ e+ klv+
  gi|330508857|ref|YP_004385285.1| 145 gsRPISSREMEECRRMAQDMAdagyRGGDQLSFIQDMKEVKGGLDIILGSTQLGRRMARAVQERFGGKLLETCKLVG 221
                                       99999*****************9999999************************************************ PP

                              NMD3 226 edkksgkevyrltysvr 242
                                       + k+ +++vyr t++vr
  gi|330508857|ref|YP_004385285.1| 222 K-KE-NRDVYRSTLLVR 236
                                       *.66.9*********98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   2.8   1.8e-05     0.047       1      44 [.       5      53 ..       5      56 .. 0.77
   2 ?    0.2   0.0      0.31   7.8e+02      28      38 ..     121     131 ..     101     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                               DZR  1 CpqCgeelppdarfCseCgtk...lkavaa......edrCpsCgek.vdpearf 44
                                      Cp+Cg++  +++  C++C+ +   l    +         C+ Cg++ ++ +++f
  gi|330508857|ref|YP_004385285.1|  5 CPKCGQP--AEDGLCPQCRMNsirL---IQfpdvveVVICSVCGSQqIKGKWQF 53
                                      9****98..66679****9995553...33455888999*****9977777777 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.31
                               DZR  28 edrCpsCgekv 38 
                                         +C +C++++
  gi|330508857|ref|YP_004385285.1| 121 LVACERCSRMA 131
                                       56899998876 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0023       5.9      20      70 ..     156     205 ..     138     208 .. 0.89
   2 ?    4.6   0.0     0.015        38      24      46 ..     318     340 ..     280     345 .] 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0023
                                       T.SSHHHHHHHHT--TT-EEEEEE.E-TTS-SEEEEETTEEEEE-HHHHTTE CS
                              FeoA  20 edpellrrLremGlvpGarievva.rapfggplvvrvgdtrvaLgreeAqaI 70 
                                       e +++++ +++ G + G ++  ++  +  +g l + +g t   Lgr++A+a+
  gi|330508857|ref|YP_004385285.1| 156 ECRRMAQDMADAGYRGGDQLSFIQdMKEVKGGLDIILGST--QLGRRMARAV 205
                                       34889999***************988999********999..9*******98 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.015
                                       HHHHHHHHT--TT-EEEEEEE-T CS
                              FeoA  24 llrrLremGlvpGarievvarap 46 
                                       l+ r r + + pG+++evv+ a+
  gi|330508857|ref|YP_004385285.1| 318 LASRPRGLEVEPGEEVEVVRTAD 340
                                       55666778899999999998765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.1    0.0042        11       5      22 ..       5      20 ..       3      22 .. 0.86
   2 ?    6.4   0.1    0.0023       5.9       3      16 ..      37      51 ..      35      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0042
                       zf-ribbon_3  5 CPnCGaplssddnvCpyC 22
                                      CP+CG+p  ++d  Cp C
  gi|330508857|ref|YP_004385285.1|  5 CPKCGQP--AEDGLCPQC 20
                                      *******..777788888 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0023
                       zf-ribbon_3  3 vrCPnCGa.plssdd 16
                                      v C+ CG+ +++  +
  gi|330508857|ref|YP_004385285.1| 37 VICSVCGSqQIKGKW 51
                                      78******7788655 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.4     0.007        18       2      10 ..       5      13 ..       4      15 .. 0.84
   2 ?    7.4   1.1     0.001       2.7       2      26 ..      17      43 ..      16      43 .. 0.88
   3 ?   -2.2   0.1         1   2.6e+03      17      25 ..     122     127 ..     114     132 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.007
                          zf-TFIIB  2 CPkCqdele 10
                                      CPkC+++ e
  gi|330508857|ref|YP_004385285.1|  5 CPKCGQPAE 13
                                      *****9977 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.001
                          zf-TFIIB  2 CPkCqd.eleesergg.veidyCpqCr 26
                                      CP C+  + + +++ + ve+  C  C+
  gi|330508857|ref|YP_004385285.1| 17 CPQCRMnSIRLIQFPDvVEVVICSVCG 43
                                      *****769******776******9997 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1
                          zf-TFIIB  17 veidyCpqC 25 
                                       v    C++C
  gi|330508857|ref|YP_004385285.1| 122 V---ACERC 127
                                       4...45555 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   0.00012       0.3      18      35 ..       4      21 ..       3      24 .. 0.91
   2 ?    1.1   0.2      0.12     3e+02      16      23 ..      36      43 ..      34      46 .. 0.72
   3 ?   -0.9   0.2      0.49   1.3e+03      16      23 ..     121     128 ..     117     131 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                                      E-TTT--EESSSS-CCCC CS
                              RecR 18 hCsrCgnlteedlCaICs 35
                                       C++Cg  +e+ lC+ C+
  gi|330508857|ref|YP_004385285.1|  4 LCPKCGQPAEDGLCPQCR 21
                                      6****************8 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.12
                                      -EE-TTT- CS
                              RecR 16 vrhCsrCg 23
                                      v  Cs+Cg
  gi|330508857|ref|YP_004385285.1| 36 VVICSVCG 43
                                      55688887 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.49
                                       -EE-TTT- CS
                              RecR  16 vrhCsrCg 23 
                                       +  C+rC 
  gi|330508857|ref|YP_004385285.1| 121 LVACERCS 128
                                       56799995 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0021       5.3       6      13 ..       5      12 ..       2      14 .. 0.84
   2 ?   -0.7   0.6      0.45   1.2e+03      24      28 ..      17      21 ..      16      21 .. 0.77
   3 ?    2.3   0.1     0.052   1.3e+02       6      12 ..      39      45 ..      38      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0021
                     zf-NADH-PPase  6 CgrCGapt 13
                                      C++CG+p 
  gi|330508857|ref|YP_004385285.1|  5 CPKCGQPA 12
                                      ******96 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.45
                     zf-NADH-PPase 24 CpaCg 28
                                      Cp+C+
  gi|330508857|ref|YP_004385285.1| 17 CPQCR 21
                                      99996 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.052
                     zf-NADH-PPase  6 CgrCGap 12
                                      C+ CG+ 
  gi|330508857|ref|YP_004385285.1| 39 CSVCGSQ 45
                                      9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2332.57
//
Query:       gi|330508858|ref|YP_004385286.1|  [L=121]
Description: hypothetical protein MCON_3178 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-24   84.4   0.0    6.6e-24   84.0   0.0    1.2  1  DUF424       Protein of unknown function (DUF424)
  ------ inclusion threshold ------
      0.053   13.4   0.0      0.065   13.1   0.0    1.1  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


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 !   84.0   0.0   7.3e-28   6.6e-24       1      92 []      31     121 .]      31     121 .] 0.97

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 7.3e-28
                                       EEETTE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG CS
                            DUF424   1 yrtddllklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpds 77 
                                       yr++ + +l+avcd ++lg++f+eg+l+++v+  fyg e+as  e+ ++L+ at aN+vg ++v+ a+  G vd+d+
  gi|330508858|ref|YP_004385286.1|  31 YRHGAE-TLIAVCDCDILGREFREGNLHIEVCSDFYGDEKASLSEVEDALRGATMANLVGCKVVKHAILLGWVDEDN 106
                                       567777.9********************************************************************* PP

                                       -EEETTEEEEEEEE- CS
                            DUF424  78 Vlvidgvphaqigkl 92 
                                       Vl idgv +aq++++
  gi|330508858|ref|YP_004385286.1| 107 VLSIDGVLYAQMVRM 121
                                       *************98 PP

>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.2e-06     0.065      61     125 ..      23      98 ..       8     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.2e-06
                                       EHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-T.EE...........-HHHHHHHC.S-E.EEE-SSS--HHHHH CS
                       Oxidored_q6  61 ealellkelaekakaviavGtCAafGGipaaannp.sv...........geevgellevvpvdinipGCPphpeail 125
                                       +a   lk ++  a+++iav +C + G  ++ +n + +v           ++ev+++l+   +  n+ GC + ++ail
  gi|330508858|ref|YP_004385286.1|  23 TAQICLKTYRHGAETLIAVCDCDILGREFREGNLHiEVcsdfygdekasLSEVEDALRGATM-ANLVGCKVVKHAIL 98 
                                       55556788999******************988877633566665554433666777777999.******99988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 907.98
//
Query:       gi|330508859|ref|YP_004385287.1|  [L=694]
Description: minichromosome maintenance protein MCM [Methanosaeta concilii GP6]
Scores for complete 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-97  323.5   0.0    6.7e-97  323.0   0.0    1.2  1  MCM              MCM P-loop domain
    2.4e-33  114.7   0.0    4.1e-33  113.9   0.0    1.3  1  MCM_OB           MCM OB domain
    3.4e-27   94.7   0.1      1e-26   93.2   0.0    1.9  2  MCM_lid          MCM AAA-lid domain
    7.6e-09   35.2   0.1    1.3e-06   28.0   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.5e-07   32.0   0.1    2.2e-06   28.2   0.1    2.8  2  MCM_N            MCM N-terminal domain
    2.4e-06   27.6   0.0    6.4e-06   26.2   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00025   20.9   0.0    0.00078   19.3   0.0    1.8  1  AAA_3            ATPase family associated with various cellul
     0.0018   18.0   0.0      0.019   14.7   0.0    2.2  1  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.097   13.1   0.1       0.34   11.3   0.0    2.0  2  AAA              ATPase family associated with various cellul
       0.13   12.7   0.0       0.54   10.6   0.0    2.1  1  AAA_16           AAA ATPase domain
       0.15   11.8   0.3        1.5    8.5   0.3    2.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d


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 !  323.0   0.0  4.1e-100   6.7e-97       2     223 ..     262     484 ..     261     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 323.0 bits;  conditional E-value: 4.1e-100
                                       HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHH CS
                               MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyve 78 
                                       +e+i e++++++i+ek+ +siapsiyg++dvk+a+ lql++g +k+l+d++++rgdi++llvgdpg+aKsqlL+y+ 
  gi|330508859|ref|YP_004385287.1| 262 EEAIMEMSRDPEIYEKIKDSIAPSIYGYDDVKEALGLQLVSGFEKHLPDGARIRGDIHILLVGDPGIAKSQLLRYMV 338
                                       789************************************************************************** PP

                                       HHSSSEEEEESSSSSSSHSSSEEEEESSSSS.EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEES CS
                               MCM  79 klapravytsgkgssaagLtaavvrdeetge.fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaK 154
                                       kl+pr++ytsgk+s++agLta+ v+de  +  +++eaGalvladkG+++iDe+dkm++ed+salhEamEqqtis+aK
  gi|330508859|ref|YP_004385287.1| 339 KLSPRGIYTSGKSSTSAGLTATAVKDELGDGrWTIEAGALVLADKGIAAIDEMDKMNNEDKSALHEAMEQQTISVAK 415
                                       **************************986555********************************************* PP

                                       SSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHH CS
                               MCM 155 aGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivsl 223
                                       aG++atL++r+s+laAanpk gr+dk +++a +inl++al+srFDlifvl D++d+++D+++aehi+++
  gi|330508859|ref|YP_004385287.1| 416 AGVMATLKSRCSLLAAANPKLGRFDKYEPIAPQINLTPALMSRFDLIFVLTDDPDTKRDSAIAEHILKS 484
                                       ******************************************************************985 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   0.0   2.5e-36   4.1e-33       2     125 ..      94     223 ..      93     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 2.5e-36
                                       XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEES---......-SB-..TTT-HHH-EEE-GGGS CS
                            MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvevelee......PrkCeekeCeskdpfkleteks 72 
                                       +R+lrs+higkl  ++G+v +a+ev+pk+++a+f+c++cg t   e +         kC +++C++ +pfkl   +s
  gi|330508859|ref|YP_004385287.1|  94 TRELRSDHIGKLLAIDGLVRTATEVRPKIVSAAFQCQRCGFTFFKEQTGnkfedqNLKCMNQACDRGGPFKLLLAQS 170
                                       7***************************************966632222344444559*******999********* PP

                                       EEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEEE CS
                            MCM_OB  73 kfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyral 125
                                       kfvd qk+++QEspe++  G+ P++l+v leddl  ++ PGdrv v G+++++
  gi|330508859|ref|YP_004385287.1| 171 KFVDAQKIRVQESPEDLRGGQQPQTLDVELEDDLAGRIFPGDRVIVNGVLKSY 223
                                       *************************************************9876 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       6.8   1.1e+04      70      84 ..     499     513 ..     497     515 .. 0.84
   2 !   93.2   0.0   6.2e-30     1e-26       1      86 [.     519     603 ..     519     604 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.8
                                       SE-HHHHHHHHHHHH CS
                           MCM_lid  70 vvteedveeairllk 84 
                                       ++++ed+++a+ +++
  gi|330508859|ref|YP_004385287.1| 499 EISQEDIDNALTVIE 513
                                       78999*****99986 PP

  == domain 2  score: 93.2 bits;  conditional E-value: 6.2e-30
                                       HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHH CS
                           MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedve 77 
                                       e+lrkY+ayar++++P+l+eeake + ++Yv lR + +ds +k +p+t+RqLe+liRL eA+A+lrls++vt  d++
  gi|330508859|ref|YP_004385287.1| 519 EMLRKYVAYARKNVFPTLTEEAKEFFLNYYVGLRTQGQDS-NKPVPVTARQLEALIRLGEASARLRLSREVTGVDAQ 594
                                       689********************************99766.9*********************************** PP

                                       HHHHHHHHH CS
                           MCM_lid  78 eairllkes 86 
                                       +++++l+++
  gi|330508859|ref|YP_004385287.1| 595 RVVKILEAC 603
                                       *****9987 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     0.009        15      21      47 ..     316     342 ..     312     355 .. 0.88
   2 !   28.0   0.0   7.8e-10   1.3e-06      92     158 ..     367     434 ..     349     459 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.009
                      Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsllp 47 
                                       G  ++llvG pG  K+ l + + +l p
  gi|330508859|ref|YP_004385287.1| 316 GDIHILLVGDPGIAKSQLLRYMVKLSP 342
                                       7889**************999998877 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 7.8e-10
                      Mg_chelatase  92 Gggs.kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                       G g+ +++ G++ la +G+  +DE+ +++++   +L e +e++++++++a   ++  +r+ l+aa+Np
  gi|330508859|ref|YP_004385287.1| 367 GDGRwTIEAGALVLADKGIAAIDEMDKMNNEDKSALHEAMEQQTISVAKAGVMATLKSRCSLLAAANP 434
                                       55555999***********************************************************9 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   1.3e-09   2.2e-06       4      75 ..       9      70 ..       6      96 .. 0.88
   2 ?   -0.4   0.0       1.1   1.8e+03      61      86 ..     593     618 ..     591     648 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.3e-09
                             MCM_N  4 FedFLeefkddsededgekkYrdqlqemaer..ekttLevdlddLaafdeeLaeailenpkeylplleealkev 75
                                      +e+FL++             Y d + ++a+   ++++L ++++dL++fd+++ae+++enp e +++ + a+ e+
  gi|330508859|ref|YP_004385287.1|  9 WEEFLRSR------------YWDDILKLADSypDERSLKIQFSDLEKFDPDFAEELMENPDETIEAARTAILEL 70
                                      56666655............999999999988899********************************9999775 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                             MCM_N  61 pkeylplleealkevvkklepsykdd 86 
                                        ++++++le++l++v  + e  + d+
  gi|330508859|ref|YP_004385287.1| 593 AQRVVKILEACLRKVGVDPETGFLDA 618
                                       6899*********9987766655554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   3.9e-09   6.4e-06       1     124 [.     319     436 ..     319     459 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.9e-09
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEE...EE--TT--HHHHH--B--.........--------G-SEEEEESG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnrevey...vqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEv 74 
                                       ++lLvG+pG++Ks+l +++ ++  r + +      ++++t++ +k ++   +g+   + ++lv     + i+ +DE 
  gi|330508859|ref|YP_004385287.1| 319 HILLVGDPGIAKSQLLRYMVKLSPRGIYTsgkSSTSAGLTATAVKDELG--DGRWTIEAGALV--LADKGIAAIDEM 391
                                       79********************965555412146677788888888877..8999999*****..88999******* PP

                                       GG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                             AAA_5  75 eraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                       ++++ e  ++L+  +e++++++++ g     k+       +++a+anp  
  gi|330508859|ref|YP_004385287.1| 392 DKMNNEDKSALHEAMEQQTISVAKAGVMATLKSR-----CSLLAAANPKL 436
                                       *********************9988877777764.....99999999875 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 !   19.3   0.0   4.8e-07   0.00078       1     112 [.     319     434 ..     319     440 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.8e-07
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftp.dllPsdilGtevfeeke.kefefkkGpvf.an..llladein 72 
                                       h+ll g PG+ak +l + + k   l+ + i         + ++ t v +e    ++++++G+++ a+  +   de++
  gi|330508859|ref|YP_004385287.1| 319 HILLVGDPGIAKSQLLRYMVK---LSPRGIYTSGkSSTSAGLTATAVKDELGdGRWTIEAGALVlADkgIAAIDEMD 392
                                       99***********99888755...5555554443144667888888888754499******976343337778**** PP

                             AAA_3  73 rappktqsalleameerqvtveg..ethklpepflvlatqnP 112
                                       + +   +sal eame+++++v++     +l++   +la+ nP
  gi|330508859|ref|YP_004385287.1| 393 KMNNEDKSALHEAMEQQTISVAKagVMATLKSRCSLLAAANP 434
                                       *****************9998751156789999******999 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.019      23     145 ..     318     436 ..     310     443 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-E.EEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEE CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpf.vavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlf 98 
                                       +++l++G+ G  K+ l r + + s+r       +   a ++++ ++ eL    +G +    + ++G++  ad+G+  
  gi|330508859|ref|YP_004385287.1| 318 IHILLVGDPGIAKSQLLRYMVKLSPRGIYTSgKSSTSAGLTATAVKDEL---GDGRW----TIEAGALVLADKGIAA 387
                                       5666666666666666666666666543322022333344555555554...23333....3568************ PP

                                       EETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEESS-H CS
                   Sigma54_activat  99 LDeigelplelQekLlrvlqegev..ervGsskeikvdvriiaatnedl 145
                                       +De+ +++ e  + L ++++++++   + G  ++ k  + ++aa+n +l
  gi|330508859|ref|YP_004385287.1| 388 IDEMDKMNNEDKSALHEAMEQQTIsvAKAGVMATLKSRCSLLAAANPKL 436
                                       ********************997622699***************99887 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.34       1     126 [.     320     441 ..     320     446 .. 0.66
   2 ?   -3.8   0.0       9.7   1.6e+04     115     128 ..     451     463 ..     450     465 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.....STTHHHHHHHHHHHHHHHTS....TSEEEEEETGG CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk.....yvgesekkirelfkeakeka....kpsilfiDEid 68 
                                       +ll+G pG+ K+ l + ++k +  + + +sg++ +s       v++   + r ++++    a    ++ i  iDE+d
  gi|330508859|ref|YP_004385287.1| 320 ILLVGDPGIAKSQLLRYMVKLS-PRGIYTSGKSSTSAgltatAVKDELGDGRWTIEA---GAlvlaDKGIAAIDEMD 392
                                       699*************999984.5555666666663333222444444444444443...235555679******** PP

                                       GHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS.GGGSTHHHHS.TTSSE CS
                               AAA  69 alaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr.pdkldpallr.gRfdr 126
                                       ++++++            ++L +++++++ + +k  v+++ ++  + l  a  + gRfd+
  gi|330508859|ref|YP_004385287.1| 393 KMNNED-----------KSALHEAMEQQTISVAKAGVMATLKSrCSLLAAANPKlGRFDK 441
                                       ***999...........8888888888888866555555555535555555556666665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.7
                                       STHHHHSTTSSEEE CS
                               AAA 115 ldpallrgRfdrki 128
                                       l+pal+ +Rfd ++
  gi|330508859|ref|YP_004385287.1| 451 LTPALM-SRFDLIF 463
                                       789***.9**9876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00033      0.54      26      88 ..     319     368 ..     311     446 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                        +ll+G++G+ Ks l+r     l+ + gi+++gk   +            l++ + ++++l +
  gi|330508859|ref|YP_004385287.1| 319 HILLVGDPGIAKSQLLRYMV-KLSPR-GIYTSGKSSTS----------AGLTA-TAVKDELGD 368
                                       689***************99.68888.77777777777..........33333.444444444 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 ?    8.5   0.3   0.00095       1.5      35     115 ..     319     413 ..     288     429 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00095
                            RuvB_N  35 hvllyGpPGlGkttlakiiak....elgvklk......itsgPvlekagd....laalltnleekdvlfideihrls 97 
                                       h+ll+G PG+ k+ l + + k     + ++ k       t++ v ++ gd    + a    l +k +  ide+ +++
  gi|330508859|ref|YP_004385287.1| 319 HILLVGDPGIAKSQLLRYMVKlsprGIYTSGKsstsagLTATAVKDELGDgrwtIEAGALVLADKGIAAIDEMDKMN 395
                                       999999999999988765544111122222221000002333333444443333455556788999999******** PP

                            RuvB_N  98 raveevlysamedfrldi 115
                                       ++ +  l+ ame  ++ +
  gi|330508859|ref|YP_004385287.1| 396 NEDKSALHEAMEQQTISV 413
                                       ************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (694 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); 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: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 4754.78
//
Query:       gi|330508860|ref|YP_004385288.1|  [L=438]
Description: nodulation protein NfeD [Methanosaeta concilii GP6]
Scores for complete sequence (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   41.7   0.1    4.7e-10   39.7   0.1    2.1  1  NfeD      NfeD-like C-terminal, partner-binding
  ------ inclusion threshold ------
       0.03   13.3   0.8      0.046   12.7   0.8    1.3  1  SDH_sah   Serine dehydrogenase proteinase
        0.1   11.6   0.0       0.16   10.9   0.0    1.4  1  FMN_dh    FMN-dependent dehydrogenase


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 !   39.7   0.1   7.8e-14   4.7e-10       4      83 ..     358     434 ..     354     435 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 7.8e-14
                                       XXXXXXXXXXXXXS---SSS--S.S---GGTTSEEEEEE-BS.-EEEEETTEEEEEE-.SSB-TT-EEEEEEE-SSS CS
                              NfeD   4 vvsvlllvllrplllkklkkkekktnaealiGkegvvledig.tGrvkvdGeeWsarsegeiekgerVrVveveGlt 79 
                                       ++++ + ++++++++ ++         +   G+e+v++++++ +G v ++Ge+W a++eg++ekge+V +v++ G  
  gi|330508860|ref|YP_004385288.1| 358 ILGLFMAFAIYKVAQARFAP----MVIDVFEGEEAVAIDRLDpKGYVLFQGEYWLAEAEGTVEKGEKVIIVARGGGQ 430
                                       67777888888888888833....5677899**********668***************99**************** PP

                                       EEEE CS
                              NfeD  80 liVe 83 
                                       l+V+
  gi|330508860|ref|YP_004385288.1| 431 LKVR 434
                                       ***7 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.8   7.8e-06     0.046      77     186 ..      50     157 ..      22     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.8e-06
                           SDH_sah  77 dseevlrai.rltpkd.kpidliihtpGGlvlaatqiakalkehkaktrviv.ph..yamsGGtlialaadeiilde 148
                                         + vl a+ r+  +d + + l++ tpGG    +t+i + + e   ++   v p    a s Gt+i + +d   + +
  gi|330508860|ref|YP_004385288.1|  50 SDDIVLAALeRAEAEDaRALMLLLDTPGGGLAETTEILRLIDESDIPVIGYVhPEgaAAWSAGTIILIGSDIAAMAP 126
                                       45556777634444552678999******999999****999999988765536522578***************** PP

                           SDH_sah 149 navlGpvdpqlgqypaasilkvvekkeakdiddktlil 186
                                       ++++G  +p +   p+ s + v + k ++       i+
  gi|330508860|ref|YP_004385288.1| 127 HTIIGSAQP-VQFSPTGSTVPVNDSKTTNA------IV 157
                                       ******999.56679999999988888554......34 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.7e-05      0.16     119     185 ..      48     114 ..      32     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.7e-05
                                       CSSHHHHHHHHHHHHHCTESEEEEESSTSS---BHHHHHCT--BSTT-T.G.TTGGGSTSGSCCTTH CS
                            FMN_dh 119 pkdrelteellkraeaagykalvltvDtpvlgkRerdlrngfslppklklrnllqelakpewaaeal 185
                                       p +++++ + l+raea +++al+l +Dtp  g  e  +  ++  +  + +  +++  +  +w+a++ 
  gi|330508860|ref|YP_004385288.1|  48 PASDDIVLAALERAEAEDARALMLLLDTPGGGLAETTEILRLIDESDIPVIGYVHPEGAAAWSAGTI 114
                                       67789999************************99988888777777766666677777666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3183.86
//
Query:       gi|330508861|ref|YP_004385289.1|  [L=283]
Description: hypothetical protein MCON_3181 [Methanosaeta concilii GP6]
Scores for complete 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  127.3   2.0    9.4e-37  126.7   2.0    1.3  1  Band_7       SPFH domain / Band 7 family
    1.3e-06   28.3   0.6    2.1e-06   27.6   0.1    1.7  2  Band_7_1     SPFH domain-Band 7 family
  ------ inclusion threshold ------
      0.071   13.8   0.0       0.14   12.8   0.0    1.5  1  Ground-like  Ground-like domain
       0.43   10.5   2.9        3.5    7.6   0.3    2.5  2  DUF5402      Family of unknown function (DUF5402)


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 !  126.7   2.0   2.1e-40   9.4e-37       2     176 ..      23     191 ..      22     193 .. 0.98

  Alignments for each domain:
  == domain 1  score: 126.7 bits;  conditional E-value: 2.1e-40
                            Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapkl 78 
                                       i++e e+ v++r G+ s+v++pG+ fi+P++++v++ ++rv+t+dv + + v+t+D+++v +d++++yrv  d++k+
  gi|330508861|ref|YP_004385289.1|  23 IVREYERVVIFRLGRFSGVKGPGIFFIIPIIDRVILLDLRVFTIDVAK-QVVITRDNVSVEVDAVIYYRV-VDPAKA 97 
                                       799*********************************************.*********************.****** PP

                            Band_7  79 vaaveresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaq 155
                                       v +v    +n++   + + + +lr v+++ +l++lls+r+el+++l++ l +  + +G+ v+ v+++d+++p+  ++
  gi|330508861|ref|YP_004385289.1|  98 VIQV----ENYRVATSLLSQTTLRDVLGQIELDDLLSKRDELNKKLQEILDKHTDPWGIKVTAVTLRDVSLPESMRR 170
                                       ****....********************************************************************* PP

                            Band_7 156 alaakqaaeaeaqaeiaraea 176
                                       a+a+ +++e+e++ +i  a +
  gi|330508861|ref|YP_004385289.1| 171 AIAKQAESEREKRSRIILADG 191
                                       ************999988866 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.6     7e+03      18      42 ..      23      47 ..      19      51 .. 0.83
   2 !   27.6   0.1   4.7e-10   2.1e-06     144     208 ..     115     177 ..      69     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.6
                          Band_7_1 18 ivregqeavfvneGqiaDvfapGty 42
                                      ivre  + v  + G+ + v +pG +
  gi|330508861|ref|YP_004385289.1| 23 IVREYERVVIFRLGRFSGVKGPGIF 47
                                      8999999999999999999998876 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 4.7e-10
                          Band_7_1 144 rlsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkras 208
                                       +l dvl+  +i + dl +k +el +kl+e l+++ +  G+++++++++++slpe++++a+ k+a+
  gi|330508861|ref|YP_004385289.1| 115 TLRDVLG--QIELDDLLSKRDELNKKLQEILDKHTDPWGIKVTAVTLRDVSLPESMRRAIAKQAE 177
                                       4556665..57888************************************************987 PP

>> Ground-like  Ground-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.1e-05      0.14       6      55 ..     136     198 ..     135     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                       Ground-like   6 nseLkkiieenm.............kqssasdskkaiqkaleekfgssfevicsegdfsytif 55 
                                       n++L++i++++              + s ++++++ai k++e++ +++  +i ++g+f+ + +
  gi|330508861|ref|YP_004385289.1| 136 NKKLQEILDKHTdpwgikvtavtlrDVSLPESMRRAIAKQAESEREKRSRIILADGEFQASKT 198
                                       78999999986666777777777877888999**************************98654 PP

>> DUF5402  Family of unknown function (DUF5402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3   0.00079       3.5      47      94 ..      55     103 ..      38     113 .. 0.85
   2 ?    2.8   0.1     0.025   1.1e+02       3      23 ..     126     146 ..     124     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00079
                           DUF5402  47 Glevddveifkekileklkelakdleikad.vvyarvvPGtaevidlav 94 
                                        + + d+ +f  ++ +++     ++++++d v+y rvv  ++ vi+++ 
  gi|330508861|ref|YP_004385289.1|  55 RVILLDLRVFTIDVAKQVVITRDNVSVEVDaVIYYRVVDPAKAVIQVEN 103
                                       566789**********************99568******9999999865 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.025
                           DUF5402   3 dkllkdreklekklqnllgke 23 
                                       d ll++r++l+kklq++l k+
  gi|330508861|ref|YP_004385289.1| 126 DDLLSKRDELNKKLQEILDKH 146
                                       579999***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2094.06
//
Query:       gi|330508862|ref|YP_004385290.1|  [L=60]
Description: 30S ribosomal protein S27a [Methanosaeta concilii GP6]
Scores for complete sequence (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   67.2   3.0    1.4e-18   66.8   3.0    1.2  1  Ribosomal_S27   Ribosomal protein S27a
    0.00037   20.6   1.3    0.00053   20.1   1.3    1.3  1  Ribosomal_L37e  Ribosomal protein L37e
     0.0039   17.2   0.7     0.0042   17.1   0.7    1.2  1  DUF1451         Zinc-ribbon containing domain
  ------ inclusion threshold ------
      0.024   14.1   2.6       0.04   13.5   2.6    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.03   14.1   3.2       0.92    9.3   0.2    2.2  2  zinc_ribbon_2   zinc-ribbon domain
      0.034   14.3   1.6        0.8    9.9   0.4    2.2  2  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
      0.066   13.1   1.2       0.15   12.0   1.2    1.6  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.11   12.2   5.0       0.21   11.3   5.0    1.5  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.16   11.9   5.0        1.3    9.0   4.9    2.0  2  Nudix_N_2       Nudix N-terminal
       0.17   12.0   1.3       0.33   11.1   1.3    1.5  1  DUF2387         Probable metal-binding protein (DUF2387)
       0.23   10.9   6.7       0.54    9.7   0.4    2.1  2  zf-ribbon_3     zinc-ribbon domain
       0.55   10.2   5.2        5.9    7.0   5.4    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.63    9.6   2.1         11    5.7   0.1    2.1  2  zf_C2H2_10      C2H2 type 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 !   66.8   3.0     1e-21   1.4e-18       1      45 []      14      56 ..      14      56 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 1e-21
                                      SSSSCCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
                     Ribosomal_S27  1 vlkyYkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                                      v kyY++ + ++++  +  Cpr CG+Gvf+A+h dR++CGkCg+T
  gi|330508862|ref|YP_004385290.1| 14 VSKYYELGG-DTIKSRKSVCPR-CGNGVFLADHGDRQSCGKCGYT 56
                                      78*******.9***********.*********************9 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.3   3.8e-07   0.00053      17      43 ..      30      59 ..      20      60 .] 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.8e-07
                    Ribosomal_L37e 17 ilCrrCgkrsy...hvqkktCascGypsak 43
                                       +C rCg+  +   h  +++C++cGy + k
  gi|330508862|ref|YP_004385290.1| 30 SVCPRCGNGVFladHGDRQSCGKCGYTEFK 59
                                      68*********7778889********7654 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.7   3.1e-06    0.0042     107     144 ..      22      59 ..       5      60 .] 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.1e-06
                           DUF1451 107 GevvglGtlvCekCgkelalkkteeippCpkCgateFr 144
                                       G+ +   + vC +Cg+ + l   +  + C kCg teF+
  gi|330508862|ref|YP_004385290.1|  22 GDTIKSRKSVCPRCGNGVFLADHGDRQSCGKCGYTEFK 59 
                                       788888899****************************7 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.6   2.9e-05      0.04       2      27 ..      31      55 ..      30      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                                      EETTTTCEECHEETSTTCE.EESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergel.vCtdCGl 27
                                      +CP Cg+   v+ +++g+   C++CG+
  gi|330508862|ref|YP_004385290.1| 31 VCPRCGNG--VFLADHGDRqSCGKCGY 55
                                      7*****96..4555599*********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 ?    9.3   0.2   0.00066      0.92       2       7 ..      32      37 ..      22      39 .. 0.65
   2 ?    5.8   0.4    0.0084        12      16      21 ..      50      55 ..      43      56 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00066
                     zinc_ribbon_2  2 CpnCGa 7 
                                      Cp+CG+
  gi|330508862|ref|YP_004385290.1| 32 CPRCGN 37
                                      555555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0084
                     zinc_ribbon_2 16 CpyCGt 21
                                      C +CG+
  gi|330508862|ref|YP_004385290.1| 50 CGKCGY 55
                                      888886 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 ?    3.7   0.0     0.051        71       1       9 [.      31      39 ..      31      45 .. 0.78
   2 ?    9.9   0.4   0.00058       0.8      37      46 ..      49      58 ..      47      60 .] 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.051
                    zinc_ribbon_13  1 kCpKCgnte 9 
                                      +Cp+Cgn  
  gi|330508862|ref|YP_004385290.1| 31 VCPRCGNGV 39
                                      6*****975 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00058
                    zinc_ribbon_13 37 sCknCgYtel 46
                                      sC +CgYte+
  gi|330508862|ref|YP_004385290.1| 49 SCGKCGYTEF 58
                                      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 ?   12.0   1.2   0.00011      0.15       4      31 ..      32      57 ..      30      58 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      ESTTTS.BEEEEECSCCCEEEESSSS-EE CS
                    RNA_POL_M_15KD  4 CpkCgN.lLlpkedkegknfeCrqCgYee 31
                                      Cp CgN   l + ++  +   C +CgY e
  gi|330508862|ref|YP_004385290.1| 32 CPRCGNgVFLADHGDRQS---CGKCGYTE 57
                                      ******645555555555...******75 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   5.0   0.00015      0.21       6      32 .]      32      58 ..      27      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                     zf-NADH-PPase  6 CgrCGaptepaeggwarvCpaCglehY 32
                                      C+rCG  + +a++g    C  Cg+  +
  gi|330508862|ref|YP_004385290.1| 32 CPRCGNGVFLADHGDRQSCGKCGYTEF 58
                                      ***********************9766 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.5     0.012        17      24      29 ..      31      36 ..      26      40 .. 0.71
   2 ?    9.0   4.9   0.00096       1.3       3      32 ..      32      57 ..      31      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.012
                                      EETTTT CS
                         Nudix_N_2 24 vCpaCg 29
                                      vCp+Cg
  gi|330508862|ref|YP_004385290.1| 31 VCPRCG 36
                                      666665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00096
                                      -TTT--B-EEE--TT-SS-EEEETTTTEEE CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgtih 32
                                      C+ CG+ v l+    D+  R  C +Cg++ 
  gi|330508862|ref|YP_004385290.1| 32 CPRCGNGVFLA----DHGDRQSCGKCGYTE 57
                                      9*****97665....8999********975 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.3   0.00024      0.33      10      40 ..      31      57 ..      29      60 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                           DUF2387 10 vCPrCsemDkirmweedeveyrECvsCgftd 40
                                      vCPrC +     ++  d+ +   C +Cg+t+
  gi|330508862|ref|YP_004385290.1| 31 VCPRCGN----GVFLADHGDRQSCGKCGYTE 57
                                      9****98....59999*************98 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4   0.00039      0.54      13      24 ..      26      37 ..      22      39 .. 0.70
   2 ?    7.0   6.8    0.0028       3.9       4      24 ..      31      55 ..      28      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00039
                       zf-ribbon_3 13 ssddnvCpyCGt 24
                                      +s+ +vCp CG 
  gi|330508862|ref|YP_004385290.1| 26 KSRKSVCPRCGN 37
                                      667777777775 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0028
                       zf-ribbon_3  4 rCPnCGa.p.lss..ddnvCpyCGt 24
                                       CP+CG+ + l++  d + C +CG+
  gi|330508862|ref|YP_004385290.1| 31 VCPRCGNgVfLADhgDRQSCGKCGY 55
                                      5*******99765556789999997 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   5.4    0.0043       5.9      19      45 ..      30      55 ..      26      56 .. 0.72
   2 ?    4.1   0.3     0.034        48      16      28 ..      45      57 ..      42      60 .] 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0043
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrk 45
                                       vCP+Cg+  +    +  +  C +C++
  gi|330508862|ref|YP_004385290.1| 30 SVCPRCGNGVFLADHG-DRQSCGKCGY 55
                                      69*****775555555.6777999987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.034
                     Zn_Tnp_IS1595 16 pngfvCPhCgsrk 28
                                      ++++ C +Cg+++
  gi|330508862|ref|YP_004385290.1| 45 GDRQSCGKCGYTE 57
                                      5678899999875 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 ?    3.9   0.2     0.029        40       5       9 ..      32      36 ..      29      39 .. 0.82
   2 ?    5.7   0.1    0.0079        11       4      10 ..      49      55 ..      47      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.029
                        zf_C2H2_10  5 CPKCq 9 
                                      CP+C+
  gi|330508862|ref|YP_004385290.1| 32 CPRCG 36
                                      ****8 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0079
                        zf_C2H2_10  4 sCPKCqe 10
                                      sC KC++
  gi|330508862|ref|YP_004385290.1| 49 SCGKCGY 55
                                      9*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 442.59
//
Query:       gi|330508863|ref|YP_004385291.1|  [L=102]
Description: 30S ribosomal protein S24e [Methanosaeta concilii GP6]
Scores for complete 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-25   87.8   0.7    4.2e-25   87.5   0.7    1.1  1  Ribosomal_S24e  Ribosomal protein S24e
  ------ inclusion threshold ------
      0.019   15.0   0.1      0.024   14.7   0.1    1.1  1  DUF1198         Protein of unknown function (DUF1198)


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 !   87.5   0.7   4.7e-29   4.2e-25       1      78 [.      20      96 ..      20      97 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 4.7e-29
                                      EEEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS---S CS
                    Ribosomal_S24e  1 vvdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekkk 78
                                      v++v+H++ +tps++++ e+la+ ++++  lv+v++++t+fG+++t+G+akiY+++e+a+++E+ h+++Rn++++ ++
  gi|330508863|ref|YP_004385291.1| 20 VFKVIHDE-STPSRKSVVERLAATMNSKVGLVYVDSLKTEFGKRETQGYAKIYETAERAEQVERAHIIERNTFTKPEE 96
                                      79******.***************************************************************999876 PP

>> DUF1198  Protein of unknown function (DUF1198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.7e-06     0.024      22      72 ..      29      83 ..      18      88 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-06
                                      HHHHHH.HHHHHHHHT..--THHHHHHHHTS-HHHHHHHHHHHHH.S-HHHHHHH CS
                           DUF1198 22 sdtrra.ikrlserLk..iepvyveslldemGktageefvrylsr.gneehlqna 72
                                      + +r++ ++rl+  ++  +  vyv+sl +e+Gk++++ + +  ++ + +e++++a
  gi|330508863|ref|YP_004385291.1| 29 TPSRKSvVERLAATMNskVGLVYVDSLKTEFGKRETQGYAKIYETaERAEQVERA 83
                                      344554157777766522667******************9966551555666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 777.75
//
Query:       gi|330508864|ref|YP_004385292.1|  [L=164]
Description: hypothetical protein MCON_3184 [Methanosaeta concilii GP6]
Scores for complete 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-42  142.2   0.1    8.4e-42  141.8   0.1    1.2  1  DUF359     Protein of unknown function (DUF359)
     0.0016   18.4   0.0     0.0023   18.0   0.0    1.4  1  VRR_NUC    VRR-NUC domain
  ------ inclusion threshold ------
       0.02   15.1   0.1      0.067   13.4   0.1    1.9  2  CRS1_YhbY  CRS1 / YhbY (CRM) domain


Domain annotation for each model (and alignments):
>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.8   0.1   1.4e-45   8.4e-42       2     125 ..      39     160 ..      38     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 141.8 bits;  conditional E-value: 1.4e-45
                            DUF359   2 tknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdGE 78 
                                       + +llk++i+Pdla+vD+ktkR ++ ++  ++   ++++++++evkNp++t+teeli++ik++l+ +e+v+i+V+GE
  gi|330508864|ref|YP_004385292.1|  39 AFYLLKSSIVPDLAVVDNKTKRAQLPDHILQS--LEHNSYKRVEVKNPPATLTEELIDQIKDSLAGKERVKIVVEGE 113
                                       6789*******************777733333..3679*************************************** PP

                            DUF359  79 EDLavlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellekf 125
                                       EDLa+lpail+ap gsvv+YGqpdeG vlvk+t e+k ++ el++k+
  gi|330508864|ref|YP_004385292.1| 114 EDLATLPAILYAPPGSVVIYGQPDEGSVLVKATPEMKMYIDELMKKM 160
                                       *********************************************98 PP

>> VRR_NUC  VRR-NUC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.8e-07    0.0023      47      86 ..      54      91 ..      20     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.8e-07
                                      HCHHHHSSTS-SEEEEETTTTE..EEEEEEE-TT----HH CS
                           VRR_NUC 47 edyrglrsGvPDLilwieeqkryvflliEvKgpgdrlsdn 86
                                       d++++r+ +PD il   e+++  ++ +EvK p   l+++
  gi|330508864|ref|YP_004385292.1| 54 VDNKTKRAQLPDHILQSLEHNS--YKRVEVKNPPATLTEE 91
                                      69999***************98..**********998875 PP

>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       0.9   5.4e+03      60      70 ..      21      28 ..      10      41 .. 0.46
   2 ?   13.4   0.1   1.1e-05     0.067      25      58 ..      86     117 ..      65     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.9
                         CRS1_YhbY 60 maeiLeektgg 70
                                      m ++L+   g+
  gi|330508864|ref|YP_004385292.1| 21 MRDELQ---GA 28
                                      333332...23 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.1e-05
                         CRS1_YhbY  25 aGvtkevvdeiheklkteelvkvkcegppalnmk 58 
                                       a +t+e++d+i++ l  +e vk+ +eg ++l   
  gi|330508864|ref|YP_004385292.1|  86 ATLTEELIDQIKDSLAGKERVKIVVEGEEDL--A 117
                                       789**********************977665..4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1303.58
//
Query:       gi|330508865|ref|YP_004385293.1|  [L=61]
Description: DNA-directed RNA polymerase subunit E' [Methanosaeta concilii GP6]
Scores for complete 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   53.3   0.2    2.9e-14   52.9   0.2    1.1  1  Spt4         Spt4/RpoE2 zinc finger
     0.0027   17.2   2.9     0.0039   16.7   2.9    1.2  1  RecR         RecR protein
  ------ inclusion threshold ------
      0.061   13.2   1.6      0.091   12.6   1.6    1.2  1  Prok-RING_4  Prokaryotic RING finger family 4


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.2   4.8e-18   2.9e-14       2      77 .]       4      61 .]       3      61 .] 0.96

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 4.8e-18
                              Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                      +AC++C+++++ +      Cp+C            s ++s++++G+v+i+dp++S +A++  l+ k pg+YAlkv+
  gi|330508865|ref|YP_004385293.1|  4 QACRECRRIVEGQV-----CPIC-----------NSASLSKDWSGYVVIIDPKESIIAEK--LEIKLPGKYALKVR 61
                                      8**********999.....****...........899***********************..************96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   2.9   6.6e-07    0.0039      18      37 ..       5      24 ..       4      25 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.6e-07
                                      E-TTT--EESSSS-CCCCST CS
                              RecR 18 hCsrCgnlteedlCaICsdp 37
                                       C++C+ + e  +C+IC++ 
  gi|330508865|ref|YP_004385293.1|  5 ACRECRRIVEGQVCPICNSA 24
                                      5****************985 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 ?   12.6   1.6   1.5e-05     0.091      21      38 ..       6      23 ..       5      30 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                       Prok-RING_4 21 CkeCfdskdlssCPlCqr 38
                                      C+eC    + + CP+C++
  gi|330508865|ref|YP_004385293.1|  6 CRECRRIVEGQVCPICNS 23
                                      ****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 442.64
//
Query:       gi|330508866|ref|YP_004385294.1|  [L=194]
Description: DNA-directed RNA polymerase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-18   65.7   0.0    5.8e-18   65.0   0.0    1.4  1  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
    6.7e-13   48.8   0.1    1.4e-12   47.8   0.1    1.5  1  S1             S1 RNA binding domain
    0.00023   21.4   0.2    0.00056   20.2   0.2    1.6  1  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
  ------ inclusion threshold ------
       0.05   13.7   0.0       0.28   11.3   0.0    2.1  1  S1_2           S1 domain


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0   1.3e-21   5.8e-18       3      70 .]      10      77 ..       8      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 1.3e-21
                                      EEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                       SHS2_Rpb7-N  3 tvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                      + r+eP +lg++le+a++++l++kyeg v++slG ivavl   +++eg++l g+Gs+y++V f+ lvF
  gi|330508866|ref|YP_004385294.1| 10 VARIEPDHLGDPLEAAVERALRDKYEGVVDKSLGTIVAVLGADDIGEGHILAGDGSIYYEVNFDTLVF 77
                                      789****************************************************************9 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.1   3.1e-16   1.4e-12       1      69 [.      78     155 ..      78     160 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 3.1e-16
                                       HSTTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEEEETTT CS
                                S1   1 kpekgevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlkvdkdr 67 
                                       kpe  e++eGeV++++k+Gaf  lg + +g++++s++ ++             +++++ l +Gd+v+++v+ v  ++
  gi|330508866|ref|YP_004385294.1|  78 KPEMQEIIEGEVVEIVKFGAFLSLG-PFDGLLHVSQITNEyisydeknarLVSKESNKSLGEGDRVRARVIAVSLNE 153
                                       678889*******************.***********************9778999*****************9888 PP

                                       TE CS
                                S1  68 rr 69 
                                       ++
  gi|330508866|ref|YP_004385294.1| 154 KE 155
                                       76 PP

>> RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   1.2e-07   0.00056       1      93 [.      79     176 ..      79     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.2e-07
                                       -STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEEEEEEE- CS
                     RNA_pol_Rbc25   1 PfvgevltgkiksstregikvslgffddifvpkelLfepsefdeeeqawvweveeeeelyldvgeeirfrveeeifv 77 
                                       P ++e+++g + +  + g ++slg fd ++   +   e+ ++de++   v +   e++  l  g+++r rv  ++ +
  gi|330508866|ref|YP_004385294.1|  79 PEMQEIIEGEVVEIVKFGAFLSLGPFDGLLHVSQITNEYISYDEKNARLVSK---ESNKSLGEGDRVRARVIAVSLN 152
                                       7789************************999999**********99887755...5788899*************** PP

                                       ------HHHHHCHHH........C CS
                     RNA_pol_Rbc25  78 dvkpkspkeaeleee........e 93 
                                       +++p+++k   + ++         
  gi|330508866|ref|YP_004385294.1| 153 EKEPRESKIGLTMRQtglgklewL 176
                                       999999887666655555544331 PP

>> S1_2  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.2e-05      0.28       4      37 ..      84     116 ..      83     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.2e-05
                              S1_2   4 intlkvlretdfgyfLqkdesgevlLpkkevpee 37 
                                       i + +v+++ +fg+fL+ +   + lL+ +++++e
  gi|330508866|ref|YP_004385294.1|  84 IIEGEVVEIVKFGAFLSLGP-FDGLLHVSQITNE 116
                                       78899*************99.9*******99966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1484.12
//
Query:       gi|330508867|ref|YP_004385295.1|  [L=135]
Description: hypothetical protein MCON_3187 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-36  123.4   0.0    6.3e-36  123.2   0.0    1.0  1  PIN_9     PIN like domain
  ------ inclusion threshold ------
      0.061   13.1   0.0        0.1   12.4   0.0    1.4  1  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.2   0.0     7e-40   6.3e-36       1     115 [.      11     124 ..      11     125 .. 0.97

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 7e-40
                             PIN_9   1 vilDtnaLmipvqfgvdifeelerllgsvelvvpkavleELerlakag.kgkertaakvalsLaerceiveaeeeka 76 
                                       vi+DtnaLm+  qfgvdif el rl g+ve +vp +v  EL++la  + kg+++taa+val Laerc+iv +++  a
  gi|330508867|ref|YP_004385295.1|  11 VIIDTNALMTAEQFGVDIFGELLRL-GYVEWLVPAQVKGELRSLADGAdKGRDKTAARVALGLAERCTIVGIDNCPA 86 
                                       8************************.******************8765267**********************999* PP

                             PIN_9  77 DdailelakeldaavlvTnDreLkkrllekgipvilLRq 115
                                       D ai ela++ +aav+ TnD++Lkkrl +kgi+vi+LRq
  gi|330508867|ref|YP_004385295.1|  87 DRAIEELAEKEGAAVF-TNDKALKKRLFSKGITVIYLRQ 124
                                       ****************.*********************8 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.1e-05       0.1      36      76 ..      86     124 ..      74     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                           DUF5615  36 sDeeileyAkeedriivTkDkDFgellllggpppgvillrl 76 
                                        D++i e+A++e+++++T+Dk   ++l+++g    vi+lr+
  gi|330508867|ref|YP_004385295.1|  86 ADRAIEELAEKEGAAVFTNDKALKKRLFSKG--ITVIYLRQ 124
                                       69*******************9999888887..47888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 910.68
//
Query:       gi|330508868|ref|YP_004385296.1|  [L=431]
Description: protein synthesis factor, GTP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-32  111.8   0.2    3.9e-32  110.4   0.2    1.8  1  eIF2_C         Initiation factor eIF2 gamma, C terminal
    3.1e-30  105.2   0.8    2.6e-29  102.1   0.8    2.1  1  GTP_EFTU       Elongation factor Tu GTP binding domain
    5.4e-08   33.1   0.7    1.7e-07   31.5   0.7    2.0  1  GTP_EFTU_D2    Elongation factor Tu domain 2
    4.8e-06   26.6   0.9    0.00046   20.1   0.1    2.5  2  RsgA_GTPase    RsgA GTPase
    0.00041   20.4   0.0    0.00094   19.3   0.0    1.7  1  MMR_HSR1       50S ribosome-binding GTPase
     0.0018   18.3   0.1     0.0039   17.2   0.1    1.5  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
     0.0031   17.1   0.1      0.077   12.6   0.0    2.3  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.053   12.7   0.1      0.098   11.8   0.1    1.3  1  G-alpha        G-protein alpha subunit
      0.081   13.0   0.2       0.16   12.0   0.2    1.5  1  Nop10p         Nucleolar RNA-binding protein, Nop10p family
       0.11   12.3   0.3        2.4    7.9   0.0    2.5  2  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
        4.3    7.2   7.1        3.7    7.4   0.6    3.1  3  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 !  110.4   0.2   2.4e-35   3.9e-32       2      86 .]     344     429 ..     343     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 2.4e-35
                                       EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESS.EEEEEEEEEEE-STTEEEEEEEEETTS CS
                            eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkd.eakvkLkkPvcaekgekialsRrvekr 77 
                                       +++++++ller+vgv++e++ve+++++E+Lmln+G+a+t+gvvts+++  +++v+Lk+Pvcaekg+++a+sRr+++r
  gi|330508868|ref|YP_004385296.1| 344 AFTMNMQLLERVVGVTDESSVEPIHSSEPLMLNVGTATTVGVVTSAREGgVVQVQLKRPVCAEKGDRVAVSRRIGAR 420
                                       589*********************************************559************************** PP

                                       EEEEEEEEE CS
                            eIF2_C  78 WrLiGwGei 86 
                                       WrLiG+G+i
  gi|330508868|ref|YP_004385296.1| 421 WRLIGVGSI 429
                                       *******97 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 !  102.1   0.8   1.6e-32   2.6e-29       4     193 ..      28     219 ..      25     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 1.6e-32
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................ CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................ 64 
                                       +nig++ghvDhGKtTL+ +L    g            + +D+++eE +rgi+i    +                   
  gi|330508868|ref|YP_004385296.1|  28 VNIGMVGHVDHGKTTLVRALS---G------------SWTDQHSEEVKRGISIRLGYADATfrkcpscpdpdaftve 89 
                                       8*****************998...1............2489999999999999999988888899999999999999 PP

                                       ........TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEES CS
                          GTP_EFTU  65 ........ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNK 131
                                               +++  ++++++D+PGH+  + ++  g++++Dgavlv++a+e  ++pqt+e+l  +   g+  i+++ NK
  gi|330508868|ref|YP_004385296.1|  90 ekcphcgaDTEILRTVSFVDSPGHETLMATMLCGAAIMDGAVLVISANEPcPQPQTKEHLMALDITGIDrIVIVQNK 166
                                       *99998855777899*********************************9879*****************788888** PP

                                       CGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                          GTP_EFTU 132 mDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                       +D + ++e+ e  +++k ++      ++  +++   + p+v++Sa ++ +v+ +++a+ e++p
  gi|330508868|ref|YP_004385296.1| 167 IDLVsREEVMEHYQQIK-DF------IKGTVAE---KAPIVPISAQQNLNVDLVIKAIEEYIP 219
                                       ****9999999999999.66......5555544...57***********************98 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.7     1e-10   1.7e-07       1      72 [.     251     331 ..     251     333 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1e-10
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEE......EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS...GS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke......ivtrissletfhededeavaganaGvivaikgled...ai 67 
                                       G+v++g++ +G+l+ Gd+++i++   ++ ++      i+t++  l++  + ++e  +g+ +Gv+++++++ +   a 
  gi|330508868|ref|YP_004385296.1| 251 GGVIGGSLNQGVLHAGDKIEICPgRLVDYEGrkqwvpIQTKVVTLLAGSQSQEEITPGGLIGVGTLLDPIMTksdA- 326
                                       89*********************8777666699**********************************998766635. PP

                                       STTCE CS
                       GTP_EFTU_D2  68 ivGdt 72 
                                       +vG++
  gi|330508868|ref|YP_004385296.1| 327 LVGQV 331
                                       77776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.019        30     103     137 ..      31      62 ..       6      65 .. 0.72
   2 !   20.1   0.1   2.8e-07   0.00046      13      87 ..     124     204 ..     100     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.019
                                       EEECSTTSSHHHHHHHHCTT-----S--------- CS
                       RsgA_GTPase 103 vlvGqSGvGKStLinallpelelktgevseklgrG 137
                                        +vG+   GK+tL+ al ++    t + se+ +rG
  gi|330508868|ref|YP_004385296.1|  31 GMVGHVDHGKTTLVRALSGS---WTDQHSEEVKRG 62 
                                       47899999**********97...555555555555 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 2.8e-07
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE- CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllv 82 
                                       +a +d +++v+s++ep  ++++ +  L+++  +gi ++viv nKiDl+++ee      +++++ + + a   +++ +
  gi|330508868|ref|YP_004385296.1| 124 AAIMDGAVLVISANEPCPQPQT-KEHLMALDITGIdRIVIVQNKIDLVSREEvmehyqQIKDFIKGTVAEKAPIVPI 199
                                       7889**********88877766.667888899999789999***********6664444444444444445555555 PP

                                       -TTTH CS
                       RsgA_GTPase  83 saktk 87 
                                       sa+++
  gi|330508868|ref|YP_004385296.1| 200 SAQQN 204
                                       55555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.7e-07   0.00094       1      98 [.      29     149 ..      29     200 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.7e-07
                                       EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE..ETTEE........................... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk..lkgke........................... 47 
                                       +++ vG+   GK+tL++al+g+ + + s++    + i+ g  +  ++  +                           
  gi|330508868|ref|YP_004385296.1|  29 NIGMVGHVDHGKTTLVRALSGSwTDQHSEEVKRGISIRLGYADatFR--Kcpscpdpdaftveekcphcgadteilr 103
                                       5899*****************98667777777777777666552233..2335666667777777777777788888 PP

                                       .EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT...TTCSHHHHHHHH CS
                          MMR_HSR1  48 .ielvDtpGliegaseekglgkaflalee.adlillvvdas...eeklkpldeele 98 
                                        + +vD pG  e       l  ++l     +d ++lv++a+       +p+ +e  
  gi|330508868|ref|YP_004385296.1| 104 tVSFVDSPG-HE------TLMATMLCGAAiMDGAVLVISANepcP---QPQTKEHL 149
                                       8********.44......566666654444799999998773330...33333332 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   2.4e-06    0.0039      58     100 ..     160     214 ..     157     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.4e-06
                      MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                        ++v NKiDl+s ee+ e +++              +v+iSa+++ln+d + ++i
  gi|330508868|ref|YP_004385296.1| 160 IVIVQNKIDLVSREEVMEHYQQikdfikgtvaekAPIVPISAQQNLNVDLVIKAI 214
                                       57899**********999988778999999998668999**********999888 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.077   1.3e+02       4      21 ..      31      48 ..      28      62 .. 0.76
   2 !   12.6   0.0   4.8e-05     0.077     103     167 ..     118     184 ..     105     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.077
                                      EEEESTTCCHHHHHHHHH CS
                              cobW  4 vltGflGsGKTtLlnhll 21
                                      +++G +  GKTtL+++l 
  gi|330508868|ref|YP_004385296.1| 31 GMVGHVDHGKTTLVRALS 48
                                      57888899******9986 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.8e-05
                                       SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEE..E-HHHHCHC..HHHHHHHHH CS
                              cobW 103 eeelksdltldavvavvDaknleaeeekieekaedqlaaadllvl..nKtDlldeeallekleerlr 167
                                       ++ l+ ++ +d+ v v++a++   + +++e+++   ++  d +v+  nK+Dl++ e+ +e+ +++ +
  gi|330508868|ref|YP_004385296.1| 118 ATMLCGAAIMDGAVLVISANEPCPQPQTKEHLMALDITGIDRIVIvqNKIDLVSREEVMEHYQQIKD 184
                                       5567778889*********9999999999************887666*********88887777655 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1     6e-05     0.098       4      54 ..       9      58 ..       6      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6e-05
                                      XXXXXXXXXXXXXXXXE..EEEEEEEESTTSSHHHHHHHHHHHCS----HH CS
                           G-alpha  4 ssaidkslkaerkarkkkrevkllllGqseSGKsTilkqlkllykkgfsee 54
                                      ++++d++ +a+  a kk  ev++ ++G+ + GK+T+++ l    ++++see
  gi|330508868|ref|YP_004385296.1|  9 EDKSDQKTEAKTPASKK-PEVNIGMVGHVDHGKTTLVRALSGSWTDQHSEE 58
                                      56777777777777777.9********************998888888877 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2    0.0001      0.16       5      28 ..      74     100 ..      71     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                       -EE-TTT-...-EESSSB-TTT-SB-B CS
                            Nop10p   5 lrkcgkcr...vYTLkkvcpecggptk 28 
                                        rkc++c      T +++cp+cg++t+
  gi|330508868|ref|YP_004385296.1|  74 FRKCPSCPdpdAFTVEEKCPHCGADTE 100
                                       688999988889*************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 ?    7.9   0.0    0.0015       2.4       4      23 ..      30      49 ..      27      58 .. 0.88
   2 ?    1.6   0.2      0.13   2.1e+02      41     142 ..     108     215 ..      99     216 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0015
                         PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                      i ++G+v+ GKttL +al+g
  gi|330508868|ref|YP_004385296.1| 30 IGMVGHVDHGKTTLVRALSG 49
                                      5689**************98 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.13
                         PduV-EutP  41 iDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfasvfnkeviGi.....i.tkidlaedeenie.. 109
                                       +D+PG    +++l+ ++ + +a  d  +lv +a+e+ +  p++  ++++ ++ Gi     +  kidl++ ee +e  
  gi|330508868|ref|YP_004385296.1| 108 VDSPG----HETLMATMLCGAAIMDGAVLVISANEP-CPQPQTKEHLMALDITGIdriviVqNKIDLVSREEVMEhy 179
                                       66666....455666666667667776777776655.4556667777777776643332123588888555444311 PP

                         PduV-EutP 110 .aveelLksaGaek..ifevsavekegieellkyle 142
                                        + ++++k   aek  i  +sa ++ +++ ++k +e
  gi|330508868|ref|YP_004385296.1| 180 qQIKDFIKGTVAEKapIVPISAQQNLNVDLVIKAIE 215
                                       144555555445443368888888888888877776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3      0.31   5.1e+02       1       5 [.      76      80 ..      70      80 .. 0.61
   2 ?    7.4   0.6    0.0023       3.7       1       7 [.      91      97 ..      91      99 .. 0.80
   3 ?    0.6   0.0      0.31   5.1e+02       5      14 ..     122     131 ..     121     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.31
                     zinc_ribbon_2  1 fCpnC 5 
                                      +Cp+C
  gi|330508868|ref|YP_004385296.1| 76 KCPSC 80
                                      45555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0023
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +Cp+CGa
  gi|330508868|ref|YP_004385296.1| 91 KCPHCGA 97
                                      7999997 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.31
                     zinc_ribbon_2   5 CGaelqdnak 14 
                                       CGa + d+a+
  gi|330508868|ref|YP_004385296.1| 122 CGAAIMDGAV 131
                                       9****99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3088.40
//
Query:       gi|330508869|ref|YP_004385297.1|  [L=320]
Description: cell surface protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.0      2e-22   79.4   0.0    1.4  1  Inhibitor_I42  Chagasin family peptidase inhibitor I42
    4.7e-18   65.3   0.7    6.7e-18   64.8   0.6    1.3  1  NosD           Periplasmic copper-binding protein (NosD)


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 !   79.4   0.0   2.3e-26     2e-22       2      90 ..     232     317 ..     231     318 .. 0.93

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 2.3e-26
                                       EETT-EEEEEEEE-CCCT-EEEEEE--TTTEEE-TTTCECCECCESTTSSEEEEEEEEESSSEEEEEEEEEE-TTST CS
                     Inhibitor_I42   2 vkvgetieieLpenpttGYsWtvdasdseglkllseeyipdesdelvGaggthvwtfkalkpGettiefkyarpwek 78 
                                       ++vge++ i+L++npttGY W+vd    ++l+l s+++ +++s+ ++Ga+gt+++ f+ l pG+tti f+y+r+we+
  gi|330508869|ref|YP_004385297.1| 232 ARVGEEFIISLSANPTTGYGWNVDYD-HSLLNLKSSDFRASSSK-ALGASGTSIFVFEPLMPGKTTIYFVYKRSWEN 306
                                       689*******************8876.8****************.******************************** PP

                                       SS--SC.EEEEE CS
                     Inhibitor_I42  79 ateaeertftlt 90 
                                         ++++  f+++
  gi|330508869|ref|YP_004385297.1| 307 IVADAR-AFQVE 317
                                       *77666.88876 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.6   7.5e-22   6.7e-18     161     240 ..     131     209 ..      71     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 7.5e-22
                              NosD 161 gntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylg..GNyWsdydgeDadgDGigDtpYeindgviDyl 235
                                         tiy N+F   +++v  ++    +Wn++    +++++    +  GNyW+dy geD++gDGigD+p  +n+++iD++
  gi|330508869|ref|YP_004385297.1| 131 PATIYLNDF-PGKNSVCPED--VATWNSSRMISYQYNSRVQRSflGNYWADYAGEDKNGDGIGDEPVVLNQDNIDNY 204
                                       479******.8888999888..89******999999988877777******************************** PP

                              NosD 236 plvnp 240
                                       pl++p
  gi|330508869|ref|YP_004385297.1| 205 PLMQP 209
                                       ***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2382.07
//
Query:       gi|330508870|ref|YP_004385298.1|  [L=309]
Description: thiamine-monophosphate kinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-21   76.2   0.3    4.3e-21   75.4   0.3    1.4  1  AIRS      AIR synthase related protein, N-terminal domain
    4.7e-09   36.6   0.4    8.6e-09   35.7   0.4    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 !   75.4   0.3   4.8e-25   4.3e-21       1      94 []      24     134 ..      24     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 4.8e-25
                                       SSSEE........EEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HH CS
                              AIRS   1 dDaav........vvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp......wl 55 
                                       dD+av        v++td     +l ++++f        +G+ avavnlsD+aamGA+P ++l +  lp       +
  gi|330508870|ref|YP_004385298.1|  24 DDCAVidagerylVASTD-----MLHQKTDFpdimnpwqMGWMAVAVNLSDIAAMGAEPAGVLIAAGLPpeadqyFI 95 
                                       899955555555599***.....*****999********************************************** PP

                                       HHHHHHHHHHHHHTT-EEEEEEEEEESSEEEEEEEEEEE CS
                              AIRS  56 eevvrglaeaaeelgvplvgGdtsfsneptisvtavGlv 94 
                                       +e+++g++++a+ +g+ ++gGdt ++ e+ti+ t +G v
  gi|330508870|ref|YP_004385298.1|  96 DELFSGFGDCAALYGTRILGGDTDSHLELTITGTSLGFV 134
                                       *************************************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 !   35.7   0.4   9.6e-13   8.6e-09       1     148 [.     146     285 ..     146     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 9.6e-13
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgala 77 
                                       ++Gd+l  tgslG  g g + +++ +++++l      ++ +l  + +++++rala + g v+a+ D ++ GL+ +l+
  gi|330508870|ref|YP_004385298.1| 146 RAGDLLCTTGSLGAAGGG-LWAWQNGAKSEL------ITSLLEPEPRLKEARALAKS-GSVTAMMDNSD-GLALSLS 213
                                       68****************.555888888875......788888889**********8.***********.8****** PP

                                       HHHHTTTEEEEEECG....THHHHHHHH..HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEEEE CS
                            AIRS_C  78 emapasgvgaeidld....kvpifdele..splemllsensGrllvavppeea.davlaileeeglpeaavIGevta 147
                                        + + sgvg+ ++ d    ++ +++ ++  ++++m+ls+     lv+  + +  +a++++++       +vIGev++
  gi|330508870|ref|YP_004385298.1| 214 DLSEVSGVGFLVYQDklplAPGLVEMVGqeNAIDMALSAGGDYELVFTLRSSGlEAARRACD------LTVIGEVVE 284
                                       ***************66654444444448899999999888887777777777355555544......79*****99 PP

                                       S CS
                            AIRS_C 148 k 148
                                       +
  gi|330508870|ref|YP_004385298.1| 285 E 285
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2248.43
//
Query:       gi|330508871|ref|YP_004385299.1|  [L=110]
Description: transposase, IS605 OrfB family, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-22   79.6   0.1    2.4e-22   78.6   0.1    1.5  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0015   18.5   0.2     0.0026   17.8   0.2    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.014   14.9   0.3       0.48   10.0   0.0    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.019   13.9   0.1      0.021   13.7   0.1    1.0  1  Pestivirus_E2   Pestivirus envelope glycoprotein E2
      0.057   13.0   3.9        3.2    7.4   0.1    2.6  3  RecR            RecR protein
        1.6    8.3   5.2        3.2    7.3   2.3    2.6  2  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.8   8.3e+03       4      15 ..       9      20 ..       8      23 .. 0.67
   2 !   78.6   0.1     8e-26   2.4e-22       1      68 [.      27      94 ..      27      95 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.8
                    OrfB_Zn_ribbon  4 lkeqleykakey 15
                                      ++++l++ +  +
  gi|330508871|ref|YP_004385299.1|  9 IQNMLKNHCLAK 20
                                      678888877655 PP

  == domain 2  score: 78.6 bits;  conditional E-value: 8e-26
                    OrfB_Zn_ribbon  1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68
                                      ++ l +  +yka  +G  v++v+p++TSk Cs+Cg  ++++ls+r+++C++Cg+++drD+nAaiNil+
  gi|330508871|ref|YP_004385299.1| 27 WNMLVTLTSYKAASAGSMVVLVDPRNTSKMCSRCGILVEKTLSDRVHNCTQCGLSLDRDWNAAINILR 94
                                      677778889*********************************************************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   8.6e-07    0.0026      10      44 ..      52      88 ..      48      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.6e-07
                               DZR 10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44
                                      + +++Cs+Cg  ++++ +   ++C +Cg ++d +++ 
  gi|330508871|ref|YP_004385299.1| 52 NTSKMCSRCGILVEKTLSdrVHNCTQCGLSLDRDWNA 88
                                      6799*********9877799************99986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00016      0.48      11      31 ..      46      66 ..      41      71 .. 0.84
   2 ?    2.9   0.1     0.026        78      22      30 ..      75      83 ..      73      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00016
                                      CHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon 11 lveDpergelvCtdCGlVled 31
                                      +++Dp ++   C++CG ++e 
  gi|330508871|ref|YP_004385299.1| 46 VLVDPRNTSKMCSRCGILVEK 66
                                      689*************99996 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.026
                                      ESSSSBEEE CS
                      TF_Zn_Ribbon 22 CtdCGlVle 30
                                      Ct CGl l+
  gi|330508871|ref|YP_004385299.1| 75 CTQCGLSLD 83
                                      *****9765 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   0.1     7e-06     0.021     119     184 ..      13      79 ..       7      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7e-06
                                       EEETTEEEESS-CT--EEEEEEEE-SSS--EEEEEEE.EE-S-B---TT---EEEETTEEEEEEE-S CS
                     Pestivirus_E2 119 llngpafqmvcpigwtgtvsctsfnmdtlattvvrty.rrskpfphrqgcitqknlgedlhncilgg 184
                                       l n    + +  ++w   v+ ts++  +  + vv    r +  +  r g++ +k l + +hnc   g
  gi|330508871|ref|YP_004385299.1|  13 LKNHCLAKSISDVAWNMLVTLTSYKAASAGSMVVLVDpRNTSKMCSRCGILVEKTLSDRVHNCTQCG 79 
                                       5566666788999************99998888876526677899******************8765 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.3   6.8e+03       5      12 ..      18      25 ..      18      28 .. 0.79
   2 ?    7.4   0.1    0.0011       3.2      12      29 ..      50      67 ..      46      68 .. 0.76
   3 ?    6.7   0.6    0.0018       5.5      12      23 ..      68      79 ..      66      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.3
                                      HHHHHHHH CS
                              RecR  5 LaeaLqea 12
                                      La++++++
  gi|330508871|ref|YP_004385299.1| 18 LAKSISDV 25
                                      89999887 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0011
                                      HHHH-EE-TTT--EESSS CS
                              RecR 12 akekvrhCsrCgnlteed 29
                                       +++ + CsrCg l e++
  gi|330508871|ref|YP_004385299.1| 50 PRNTSKMCSRCGILVEKT 67
                                      5677799*****998765 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0018
                                      HHHH-EE-TTT- CS
                              RecR 12 akekvrhCsrCg 23
                                      + ++v+ C +Cg
  gi|330508871|ref|YP_004385299.1| 68 LSDRVHNCTQCG 79
                                      679********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 ?    7.3   2.3    0.0011       3.2       5      24 ..      57      80 ..      54      82 .. 0.76
   2 ?   -2.9   0.0       1.7   5.2e+03      18      20 ..     107     109 ..     105     110 .] 0.59

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                       zf-ribbon_3  5 CPnCG...ap.lssddnvCpyCGt 24
                                      C++CG   ++ ls+++ +C+ CG 
  gi|330508871|ref|YP_004385299.1| 57 CSRCGilvEKtLSDRVHNCTQCGL 80
                                      88888555323799*********7 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                       zf-ribbon_3  18 vCp 20 
                                       +Cp
  gi|330508871|ref|YP_004385299.1| 107 ACP 109
                                       465 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 769.72
//
Query:       gi|330508872|ref|YP_004385300.1|  [L=204]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-19   69.5   2.3    2.1e-19   68.8   2.3    1.4  1  HTH_OrfB_IS605  Helix-turn-helix domain
      1e-07   32.2   0.0    2.1e-07   31.2   0.0    1.5  1  OrfB_IS605      Probable transposase


Domain annotation for each model (and alignments):
>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   2.3   2.3e-23   2.1e-19       1      47 []       1      46 [.       1      46 [. 0.99

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 2.3e-23
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkayk+r+yPT+ Q++k++rt++ +R+ YN+ La+rk+a+e+egk
  gi|330508872|ref|YP_004385300.1|  1 M-LKAYKFRIYPTKSQRTKMERTLDLCRWTYNQTLAYRKDAWEKEGK 46
                                      8.*******************************************98 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   2.3e-11   2.1e-07      10      67 ..     114     168 ..      91     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.3e-11
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkks 67 
                                       ++++k ++ +g+D+G++ +at+++++   ++ ++r++++++ +la+ +++l++  k++
  gi|330508872|ref|YP_004385300.1| 114 TYPQKDGSLVGVDVGLESFATLSNGE---TIANPRFFREEETELARVQRKLSKVPKGT 168
                                       677899999*****************...***********************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1414.81
//
Query:       gi|330508873|ref|YP_004385301.1|  [L=245]
Description: Aquaporin [Methanosaeta concilii GP6]
Scores for complete 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-48  164.6  18.2    3.2e-48  164.4  18.2    1.0  1  MIP        Major intrinsic protein
  ------ inclusion threshold ------
        2.7    7.6   9.2        5.4    6.6   2.3    2.6  2  CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like


Domain annotation for each model (and alignments):
>> MIP  Major intrinsic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.4  18.2   3.5e-52   3.2e-48       7     227 .]       3     239 ..       1     239 [. 0.89

  Alignments for each domain:
  == domain 1  score: 164.4 bits;  conditional E-value: 3.5e-52
                                       HHHHHHHHHHHHHHHHHHHHH.HHHCCCSSCS.....SSSTTSS..........HHHHHHHHHHHHHHHHHHHHHHH CS
                               MIP   7 flravlAEflatlllvfigvg.salnvkkkvs.....slaslvs..........vtleavalafglalavlvylaag 67 
                                       + ++ +AE+++t++lv++g g +a+++  ++                       +++ a+ +af++a+a+ +y+++ 
  gi|330508873|ref|YP_004385301.1|   3 LAKRSIAEAVGTFILVYFGAGaAAITLMISQGssppnP-----FnigigtlgglGDWFAIGMAFAIAIAASIYALGR 74 
                                       57899****************66666665555344440.....2555566677799********************* PP

                                       CHT-S-SHHHHHHHHHTTSSSHHHHHHHHHHHHHHHHHHHHHHHH.HCHHHHHHTTTTSSSSSTTSSHHHHHHHHHH CS
                               MIP  68 iSGaHlNPavTlallvarkisllrailYivaQllGaivaaallkl.ltkglesraglfanslkpglsagqalvvEii 143
                                       iSGaHlNPavT+all +r++sl  ai Yi aQl+Ga va+ l  + + + ++++ gl+a+++ pg++ +qa++vE i
  gi|330508873|ref|YP_004385301.1|  75 ISGAHLNPAVTIALLATRRFSLGDAIPYILAQLVGASVASFLFAAsVGMDAVTVGGLGATAPFPGIGYWQAVMVEAI 151
                                       ************************************99997776515566689999********************* PP

                                       HHHHHHHHHHHHCSTTSSSSTCHGHHHHHHHHHHHHHHHHHHHHST-SSHHHHHHHHHHHTH......STTTTHHHH CS
                               MIP 144 ltfvLvlvvfaltddkrkvslgelaplaigllvaliilvgipltGaamNpArslgpavvlnk......fedhwvylv 214
                                        tf+L+l++++++ d+++   g +a+l+igl+v  ii   +++tG ++NpAr +gp +  +       ++++ +y++
  gi|330508873|ref|YP_004385301.1| 152 GTFLLMLTIMGVAVDRQAPP-G-FAGLVIGLVVGGIITTIGNITGSSLNPARTFGPYIGDYIlggnslWHFFPIYII 226
                                       ***************99988.5.6*********************************988888899*********** PP

                                       HHHHHHHHHHHHH CS
                               MIP 215 GPliGailgalvY 227
                                       GP+ Ga+++a++Y
  gi|330508873|ref|YP_004385301.1| 227 GPVAGALIAAFLY 239
                                       ***********99 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 ?    4.2   1.4    0.0033        30      92     166 ..      12     108 ..       1     132 [. 0.64
   2 ?    6.6   2.3    0.0006       5.4     100     167 ..     125     191 ..     118     203 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0033
                         CPP1-like  92 ssedlliraavflvlavltlvapaes..................vpalllalglgasiyflnrKek.klgravlltl 149
                                        ++ +l+  ++ ++ + l++ ++++                    ++++ a++++asiy l r ++ +l  av+++l
  gi|330508873|ref|YP_004385301.1|  12 VGTFILVYFGAGAAAITLMISQGSSPpnpfnigigtlgglgdwfAIGMAFAIAIAASIYALGRISGaHLNPAVTIAL 88 
                                       55556666666666666666666655777777777777777777778888899999999998865546777777777 PP

                         CPP1-like 150 vg...LvvGlllGsllasll 166
                                       ++   +++G ++  +la+l+
  gi|330508873|ref|YP_004385301.1|  89 LAtrrFSLGDAIPYILAQLV 108
                                       65333555555555555555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0006
                         CPP1-like 100 aavflvlavltlvapaesvpalllalglgasiyflnrKekklgravlltlvgLvvGlllGsllasllq 167
                                       a++ ++l++ + + +     + +++ ++g+ +++l+     + r +  +++gLv+Gl++G+++ ++ +
  gi|330508873|ref|YP_004385301.1| 125 AVTVGGLGATAPFPGIGY-WQAVMVEAIGTFLLMLTIMGVAVDRQAPPGFAGLVIGLVVGGIITTIGN 191
                                       566666666666666666.777778888888888888888888888899**************98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); 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):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1641.01
//
Query:       gi|330508874|ref|YP_004385302.1|  [L=69]
Description: hypothetical protein MCON_3194 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-36  124.7   4.3    1.1e-36  124.6   4.3    1.0  1  DUF2180          Uncharacterized protein conserved in archaea
  ------ inclusion threshold ------
      0.011   16.6   3.5       0.35   11.7   0.7    2.2  2  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
      0.029   14.1   0.8      0.051   13.3   0.8    1.3  1  zf-UBP_var       Variant UBP zinc finger
      0.045   13.9   0.7       0.06   13.5   0.7    1.3  1  FYVE             FYVE zinc finger
      0.086   13.2   1.6       0.15   12.4   1.6    1.5  1  Transp_Tc5_C     Tc5 transposase C-terminal domain
       0.45   10.5   4.7        5.5    7.0   2.2    2.3  2  Prok-RING_1      Prokaryotic RING finger family 1


Domain annotation for each model (and alignments):
>> DUF2180  Uncharacterized protein conserved in archaea (DUF2180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.6   4.3   3.7e-40   1.1e-36       1      67 [.       1      67 [.       1      68 [. 0.98

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 3.7e-40
                           DUF2180  1 mkCYeCakegkdtdavaiCivCGkGvCkdHlvreeievweGgypfpakklkktlprilCkeClealk 67
                                      mkCY Ca  +kdtdavaiCi+CG+GvC+dHlvree+e+weGgypfp+kk+k+tlprilCk+C++a++
  gi|330508874|ref|YP_004385302.1|  1 MKCYLCALAQKDTDAVAICILCGMGVCMDHLVREELEIWEGGYPFPSKKMKRTLPRILCKPCYAAYH 67
                                      9***************************************************************997 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 ?   11.7   0.7   0.00012      0.35       2      30 ..       2      30 ..       1      30 [. 0.92
   2 ?    5.8   0.1    0.0085        25       8      22 ..      47      62 ..      43      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                   Tnp_zf-ribbon_2  2 RCkvClkkkikkeTriiCqeCdvplCrnh 30
                                       C+ C      + +  iC  C+ + C+ h
  gi|330508874|ref|YP_004385302.1|  2 KCYLCALAQKDTDAVAICILCGMGVCMDH 30
                                      5******888888**************87 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0085
                   Tnp_zf-ribbon_2  8 kkkikke.TriiCqeC 22
                                      +kk+k+   ri C+ C
  gi|330508874|ref|YP_004385302.1| 47 SKKMKRTlPRILCKPC 62
                                      689999445999*999 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 ?   13.3   0.8   1.7e-05     0.051      15      44 ..       3      32 ..       2      36 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                        zf-UBP_var 15 CvycFdtpesedGlyvcLkcFlgfckkhae 44
                                      C +c   +++ d + +c+ c +g+c +h+ 
  gi|330508874|ref|YP_004385302.1|  3 CYLCALAQKDTDAVAICILCGMGVCMDHLV 32
                                      99*************************986 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.7     2e-05      0.06      11      67 ..       2      67 ..       1      68 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                                      B-TTT--B--SSS--EE-TTT--EE-STTS.-EEE.EE........GGGTEEEEEEE-HHHHHHHH CS
                              FYVE 11 kCeiCakkFsllrrrhhCrlCGkvvCekCs.sklvall........ekeaeeksvrvCkeClaels 67
                                      kC  Ca + + +     C lCG  vC ++  ++ ++ +        +k++ + +  +Ck C+a ++
  gi|330508874|ref|YP_004385302.1|  2 KCYLCALAQKDTDAVAICILCGMGVCMDHLvREELEIWeggypfpsKKMKRTLPRILCKPCYAAYH 67
                                      67788887777788888*********9987334444448999998666677777788****99875 PP

>> Transp_Tc5_C  Tc5 transposase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.6   5.2e-05      0.15      30      57 ..       6      33 ..       1      38 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-05
                      Transp_Tc5_C 30 CkiegCselafikCarCkellCFdHfvv 57
                                      C++   +  a+  C+ C + +C dH+v 
  gi|330508874|ref|YP_004385302.1|  6 CALAQKDTDAVAICILCGMGVCMDHLVR 33
                                      5555556668888*************95 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   2.2    0.0018       5.5       6      27 ..       2      23 ..       1      31 [. 0.92
   2 ?    4.2   0.0     0.014        42      21      31 ..      57      67 ..      45      69 .] 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0018
                       Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCg 27
                                      kC +C  + k+ d + +C  Cg
  gi|330508874|ref|YP_004385302.1|  2 KCYLCALAQKDTDAVAICILCG 23
                                      8*******99999999*****9 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.014
                       Prok-RING_1 21 VvCpeCgtpyH 31
                                      + C  C + yH
  gi|330508874|ref|YP_004385302.1| 57 ILCKPCYAAYH 67
                                      68********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 537.65
//
Query:       gi|330508875|ref|YP_004385303.1|  [L=499]
Description: hypothetical protein MCON_3195 [Methanosaeta concilii GP6]
Scores for complete 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-276  916.6   1.8   3.5e-276  916.4   1.8    1.0  1  DUF2193   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2193  Uncharacterized protein conserved in archaea (DUF2193)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  916.4   1.8  1.9e-280  3.5e-276       2     498 .]       3     499 .]       2     499 .] 1.00

  Alignments for each domain:
  == domain 1  score: 916.4 bits;  conditional E-value: 1.9e-280
                           DUF2193   2 elyekmidealaaqkadvevikkkrgkefkiedakayvdavkkmkaaegqskevidLhkesvkahyeilksltdtvr 78 
                                       ely+km++ea+aaq+adve++k+krg++f++edakay+d+v+kmka+egqsk+vi+Lh++sv++hye++kslt+t+r
  gi|330508875|ref|YP_004385303.1|   3 ELYRKMVEEAMAAQRADVETVKRKRGQSFEVEDAKAYLDVVNKMKAIEGQSKSVIALHVDSVNSHYEVMKSLTKTIR 79 
                                       89*************************************************************************** PP

                           DUF2193  79 PeddpfvehyqtPaileiLyeeDeefrksvekfieaieksealigkeavrrygGfyGptcvvDfalipGstsnvvnk 155
                                       PeddpfvehyqtPaileiL+e+De+f+ks+++fi+ +++sealig+ea+rry+GfyGptcvvDfalipGstsnvvn+
  gi|330508875|ref|YP_004385303.1|  80 PEDDPFVEHYQTPAILEILCEQDESFKKSLKAFIDGVGRSEALIGLEAARRYAGFYGPTCVVDFALIPGSTSNVVNR 156
                                       ***************************************************************************** PP

                           DUF2193 156 ilkkvdipeehkkaiLaaksWglntsygiGdefakaieegktlaeavekevealksiyeePveaqaklmdeaglksf 232
                                       ilk++dip+ hk+aiLaaksWg+ntsygiG++fa++ e+g++laeav+ke++++k+iye+P+eaq klmd+ag++sf
  gi|330508875|ref|YP_004385303.1| 157 ILKTIDIPDVHKQAILAAKSWGMNTSYGIGEVFAQEAEKGTSLAEAVRKEIDEIKYIYESPIEAQGKLMDAAGHQSF 233
                                       ***************************************************************************** PP

                           DUF2193 233 dvrkymeeykkkmepvvkaalddgvhyanivtvPaycvGDiahhisqstynmckddvvlaiieavtevlestlrkal 309
                                       dvrkym+eykk+m p+v+aa+++gvhy+ni+t+PaycvGDiahhisqst+nmckddv++a+ieavtev+ stl+++l
  gi|330508875|ref|YP_004385303.1| 234 DVRKYMTEYKKRMMPAVRAAMNEGVHYGNILTIPAYCVGDIAHHISQSTFNMCKDDVIMAVIEAVTEVMGSTLNNSL 310
                                       ***************************************************************************** PP

                           DUF2193 310 eklkseydvlslatgasaaavekileldgfnaemvvdlltkrfhnyvqlyptrgaaaeLhnvDflDliyrGeklldk 386
                                       +++k+e++ l+latga+a+ave+i eldgfna+ +vdlltkrfhnyvqlyptrgaaaeLhn+Df+D+iyrG+k+ldk
  gi|330508875|ref|YP_004385303.1| 311 DSFKNEHQPLNLATGAAASAVEYIAELDGFNAIGIVDLLTKRFHNYVQLYPTRGAAAELHNCDFMDMIYRGWKVLDK 387
                                       ***************************************************************************** PP

                           DUF2193 387 arrakagseeklvpkvkglevdlspieenevlmnpqryayPacaitvrfsalmrlaDyPClLtsepvtatlltniia 463
                                       arr k+g   klvp+++g++vdl+pi++nevlmnpqryayPacaitvrfsalmrl+DyPClLtsepvtat++tniia
  gi|330508875|ref|YP_004385303.1| 388 ARRLKNGLGGKLVPRISGFDVDLEPIHRNEVLMNPQRYAYPACAITVRFSALMRLSDYPCLLTSEPVTATMMTNIIA 464
                                       ***************************************************************************** PP

                           DUF2193 464 lekekaaaParvCknCasaslidarheyCqwkeav 498
                                       l+ke +a+ParvCknCasa+l+d+rh+yCq++eav
  gi|330508875|ref|YP_004385303.1| 465 LHKEIPASPARVCKNCASAALVDFRHSYCQYREAV 499
                                       *********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3508.58
//
Query:       gi|330508876|ref|YP_004385304.1|  [L=78]
Description: redox-active disulfide protein 2 [Methanosaeta concilii GP6]
Scores for complete 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   0.7    2.8e-25   88.2   0.7    1.0  1  Thioredoxin_3   Thioredoxin domain
      0.002   18.1   0.0      0.002   18.1   0.0    1.1  1  Thioredoxin     Thioredoxin
      0.002   18.3   0.2     0.0045   17.2   0.3    1.5  2  Thioredoxin_4   Thioredoxin
      0.008   16.4   0.1      0.015   15.5   0.1    1.5  1  Glutaredoxin    Glutaredoxin
  ------ inclusion threshold ------
      0.017   15.4   0.0      0.033   14.5   0.0    1.4  1  ArsD            Arsenical resistance operon trans-acting repr
       0.11   11.8   0.1       0.11   11.8   0.1    1.1  1  Methyltransf_2  O-methyltransferase 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 !   88.2   0.7   9.2e-29   2.8e-25       1      75 [.       2      76 ..       2      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 9.2e-29
                                      EEEEEESSSSTTCHHHHHHHHHHCHCCTCECEEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
                     Thioredoxin_3  1 meikvlgpgCakCpklekavkeaaaekgikaevekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirkll 75
                                      ++i+v+g+gCakC+ l k+v++a++e+g++ae++kv  ++ei+++gVm++Pal+idgk v +G++ ++ee++++l
  gi|330508876|ref|YP_004385304.1|  2 VKIEVMGTGCAKCKSLLKNVQKAVEESGTDAEIIKVDSIQEIMDRGVMMTPALYIDGKSVLTGRTATVEELKRML 76
                                      68**********************************************************************998 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.6e-07     0.002      23      82 ..       4      60 ..       1      78 [] 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.6e-07
                                      EEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETT CS
                       Thioredoxin 23 veFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkng 82
                                      +e + + C++Ck+l   ++k+ ee   +  ++kvd  ++     + +v + P+l++  ++
  gi|330508876|ref|YP_004385304.1|  4 IEVMGTGCAKCKSLLKNVQKAVEESGTDAEIIKVDSIQE---IMDRGVMMTPALYIDGKS 60
                                      6667788****************************9877...667799999999664443 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.039   1.2e+02      19      41 ..       5      27 ..       2      41 .. 0.73
   2 !   17.2   0.3   1.5e-06    0.0045     111     165 ..      19      77 ..      11      78 .] 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.039
                                      EEE-TT-HHHHHHHHHHHHHHHH CS
                     Thioredoxin_4 19 eyedlrCphCakfeeevekllee 41
                                      e +   C  C+ + ++v+k +ee
  gi|330508876|ref|YP_004385304.1|  5 EVMGTGCAKCKSLLKNVQKAVEE 27
                                      55667899999999999976665 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.5e-06
                                       HHHTS-------HHHHHHHHHHH..HHHT--SS-EEEETTEEE..-TT--HHHHHHHHT CS
                     Thioredoxin_4 111 ekfeacleeekldalveaeskea..kkagiestPtfiingekv..eepqtyeelkalid 165
                                       +++++++ee+  da++ + +  +    +g+ +tP ++i+g+ v   +  t+eelk++++
  gi|330508876|ref|YP_004385304.1|  19 KNVQKAVEESGTDAEIIKVDSIQeiMDRGVMMTPALYIDGKSVltGRTATVEELKRMLK 77 
                                       5678899999999999776665533677**************65577899999999987 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   5.1e-06     0.015      12      60 .]      11      61 ..       4      61 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.1e-06
                                      HHHHHHHH.......HHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEEE CS
                      Glutaredoxin 12 CkkakrlL.......kelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkhv 60
                                      C+k k lL       +e g + e+i vd      +e++++ gv+  P ++idgk v
  gi|330508876|ref|YP_004385304.1| 11 CAKCKSLLknvqkavEESGTDAEIIKVDSI----QEIMDR-GVMMTPALYIDGKSV 61
                                      566666661112222555555666666664....555555.************976 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 ?   14.5   0.0   1.1e-05     0.033      56      98 ..      35      76 ..      26      78 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                              ArsD 56 venkavkellekkgaeaLPlvlvdgeivktgrYptreelaewl 98
                                      ++ ++++e+++ +g+ + P +++dg+ v+tgr  t eel+++l
  gi|330508876|ref|YP_004385304.1| 35 IKVDSIQEIMD-RGVMMTPALYIDGKSVLTGRTATVEELKRML 76
                                      66778888887.8***************************997 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.6e-05      0.11     143     181 ..      12      53 ..       9      78 .] 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHHHHHH--TT-...EEEEEE----TTS---HHHHH CS
                    Methyltransf_2 143 ekcvklLkrvkkalpagG...kvivveavlgadpsgeletel 181
                                       +kc+ lLk+v+ka+ + G   ++i v+++ +   +g + t  
  gi|330508876|ref|YP_004385304.1|  12 AKCKSLLKNVQKAVEESGtdaEIIKVDSIQEIMDRGVMMTPA 53 
                                       58*************877333688888887766665555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 548.08
//
Query:       gi|330508877|ref|YP_004385305.1|  [L=126]
Description: hypothetical protein MCON_3197 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-32  109.4   6.2      1e-31  109.1   6.2    1.1  1  DGC       DGC domain


Domain annotation for each model (and alignments):
>> DGC  DGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.1   6.2   5.8e-36     1e-31       2     106 .]      16     120 ..      15     120 .. 0.99

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 5.8e-36
                               DGC   2 vvsCsGasnvGqlaneaavklakegeakmiclagvgagveelvelaksarkiiaidGCpleCakkilekagvkpdeh 78 
                                       vv+CsGa+nvGq+an+aav+l+ke+ a ++cla+v+a++e++v++a++a  +i idGCp++Ca k+l++ +++p+ +
  gi|330508877|ref|YP_004385305.1|  16 VVACSGACNVGQIANQAAVDLSKEDVAGFFCLAAVAAHIEAMVKSAREAGMMISIDGCPVQCAAKTLQHLEIEPAIQ 92 
                                       89**********************99*************************************************** PP

                               DGC  79 lvvtdlgikkeekldlseeeiekvveav 106
                                       ++vt+lgi+k+++l+++++ + kvve+v
  gi|330508877|ref|YP_004385305.1|  93 IIVTELGIEKTQDLSIDQDVCSKVVEQV 120
                                       *************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 931.49
//
Query:       gi|330508878|ref|YP_004385306.1|  [L=379]
Description: hypothetical protein MCON_3198 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-17   62.8   0.0    2.7e-09   37.5   0.0    2.3  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.1e-09   9.2e-05      12     106 ..     140     236 ..     127     237 .. 0.77
   2 !   37.5   0.0   1.5e-13   2.7e-09      10      97 ..     269     352 ..     265     359 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.1e-09
                         Rhodanese  12 gkva.llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel...gidnkktvvvy.....cdgggr. 78 
                                          + llDv++       hI+g++ +   ++ ++  +++ l+   e ++ l   gi++++ vv+y     c gg + 
  gi|330508878|ref|YP_004385306.1| 140 A--DiLLDVSENSS---LHIEGSIYI---PYMEFFLQPGILKPADEVASILgeaGISREDSVVIYgeclpCGGGPSv 208
                                       3..24999999776...5********...777777777777777777777799************555555666666 PP

                         Rhodanese  79 aaaaaallkklGyknvsvldGGfkawke 106
                                       a+ +++++k+lG+++ +vldG  ++w+ 
  gi|330508878|ref|YP_004385306.1| 209 ATYVYWMMKSLGHEKAKVLDGTAEDWAT 236
                                       6666999999**766********99975 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 1.5e-13
                         Rhodanese  10 ekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvycdgggraaaa 82 
                                       ++g+v+++D+R+p+e++ g Ipg++++       +++s   ++++  e++ +     ++++++vvv+ ++g++ + +
  gi|330508878|ref|YP_004385306.1| 269 KSGQVQIIDARTPPEFAMGTIPGSISM-------PYESVLADKKITGEDRLDmvfmVLNKNQPVVVFTNTGMKGSVV 338
                                       677889*********************.......5555555555555555555899999**************7777 PP

                         Rhodanese  83 aallkklGyknvsvl 97 
                                       + +l+ +Gy + +++
  gi|330508878|ref|YP_004385306.1| 339 WFALEMMGY-DARLY 352
                                       999999996.44443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2679.60
//
Query:       gi|330508879|ref|YP_004385307.1|  [L=559]
Description: hypothetical protein MCON_3199 [Methanosaeta concilii GP6]
Scores for complete 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-19   69.0   0.0    1.9e-11   44.5   0.0    2.6  2  Rhodanese        Rhodanese-like domain
  ------ inclusion threshold ------
        0.1   12.0   0.0        0.3   10.5   0.0    1.7  2  NMD3             NMD3 family
       0.14   11.9   0.0       0.35   10.6   0.0    1.6  1  Polysacc_syn_2C  Polysaccharide biosynthesis protein C-termin


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 !   21.7   0.0   3.6e-08   0.00022      15     106 ..     163     257 ..     146     258 .. 0.73
   2 !   44.5   0.0   3.1e-15   1.9e-11      13      95 ..     293     371 ..     286     377 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.6e-08
                         Rhodanese  15 allDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvy.....cdgggr.aaaa.aa 84 
                                       ++lD++p+++     I+gAvn++ d++  +  +  p  e+   l + gi+ ++ + +      c gg + a    ++
  gi|330508879|ref|YP_004385307.1| 163 VVLDISPSAA---AYIEGAVNLNYDRFFSEGGEIVPASEMARLLGDAGISSNDSLLIAgeclpCGGGPSpAF-FtYW 235
                                       2899998877...67*******66666666666666666655555559999999998744444667777444.3599 PP

                         Rhodanese  85 llkklGyknvsvldGGfkawke 106
                                       +lk+lG+++v+vl+G +++wk+
  gi|330508879|ref|YP_004385307.1| 236 ALKYLGHEKVRVLEGTIEDWKA 257
                                       ******766***********96 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 3.1e-15
                         Rhodanese  13 kvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel...gidnkktvvvycdgggraaaaaall 86 
                                       +++++D+Rp+++Ye g+IpgA+n+        + +  ++  +p+e+l++   ++d+++ vvvy + g  aa ++ +l
  gi|330508879|ref|YP_004385307.1| 293 GAQIVDARPANAYELGSIPGAINI------PYENVLVNDSMMPKEMLKErflDLDKNRSVVVYTNIGVEAALLWFAL 363
                                       456*********************......777788888888888888888888***************9999**** PP

                         Rhodanese  87 kklGyknvs 95 
                                        + Gy + +
  gi|330508879|ref|YP_004385307.1| 364 NESGY-DAR 371
                                       99995.544 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.1e-05       0.3      36      90 ..      57     107 ..      49     137 .. 0.69
   2 ?   -2.1   0.0      0.35   2.1e+03      27      45 ..     432     450 ..     427     462 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.1e-05
                              NMD3  36 evCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvseeveevkvelvdae 90 
                                       e+C++C  + + + W++++ + ee+++++ ++ ++++++     +e k++  +ae
  gi|330508879|ref|YP_004385307.1|  57 EFCPTCPDWTNLDGWLEKKAAYEEDMKNVQQNGLQNEMN----NNELKIKTAEAE 107
                                       79********9999*666666666666666666555555....344455544444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.35
                              NMD3  27 tegiekievevCkeCgryl 45 
                                       +++++k++v+ C++Cg  +
  gi|330508879|ref|YP_004385307.1| 432 ANQEPKLTVKGCATCGFGS 450
                                       56678899*******9655 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 ?   10.6   0.0   5.8e-05      0.35       4      17 ..     180     193 ..     179     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.8e-05
                   Polysacc_syn_2C   4 dLNYdkYfseGeek 17 
                                       +LNYd++fseG e 
  gi|330508879|ref|YP_004385307.1| 180 NLNYDRFFSEGGEI 193
                                       6**********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 3947.50
//
Query:       gi|330508880|ref|YP_004385308.1|  [L=486]
Description: membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       977  (0.0544927); 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:                         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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3275.80
//
Query:       gi|330508881|ref|YP_004385309.1|  [L=181]
Description: phosphoesterase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-25   88.3   0.0      8e-25   87.9   0.0    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    0.00079   20.0   0.2      0.026   15.0   0.0    2.1  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 !   87.9   0.0     9e-29     8e-25       2     158 ..       3     143 ..       2     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 9e-29
                     Metallophos_2   2 klaiiSDlH..snldaleavlealkevgvdaiihaGDleeeepevleellelapvlaVrGNnDeevveedvlreaae 76 
                                       +++++SD+H  +  +++eav++ ++++  d i+haGD+  ++ +++ +l++l +++aVrGN D           + +
  gi|330508881|ref|YP_004385309.1|   3 RIIALSDTHlmEDDRLPEAVVALASKA--DIILHAGDF--ISVQAHSALKDLGRLVAVRGNSD-----------SPQ 64 
                                       6899*****99999999******9999..*********..9999999999999**********...........999 PP

                     Metallophos_2  77 lgtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgd 153
                                       l++ lp+++++e++g+k++l+H   +g +   ae++ + e++ +v+v+GH+H+p +ek   +l++ PGs ++pr + 
  gi|330508881|ref|YP_004385309.1|  65 LKRLLPKREVIEVEGVKIGLVHMASHGSDLVGAEMMAR-EMNCEVLVFGHIHRPLIEKG-RRLLICPGSTSQPRMSA 139
                                       ***********************965555555666666.67777************987.99************999 PP

                     Metallophos_2 154 petya 158
                                       p  +a
  gi|330508881|ref|YP_004385309.1| 140 PS-VA 143
                                       84.33 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     3e-06     0.026       2      75 ..       3      61 ..       2      82 .. 0.67
   2 ?    3.0   0.1     0.014   1.3e+02     182     204 .]      98     117 ..      77     117 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-06
                                      EEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS CS
                       Metallophos  2 rilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe 75
                                      ri+ ++D+H   ++ +l++++ +l    ++ k+d++l+aGD++     +      l+ l++    +++++GN +
  gi|330508881|ref|YP_004385309.1|  3 RIIALSDTH-LMEDDRLPEAVVAL----AS-KADIILHAGDFISVQAHSA-----LKDLGR----LVAVRGNSD 61
                                      899******.33334444444444....34.89********999885555.....344444....466888888 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.014
                                       HHHHHHHHHTTESEEEEESSSSE CS
                       Metallophos 182 ealedllkkygvdlvisGHtHvy 204
                                       e +    ++ +  + ++GH+H++
  gi|330508881|ref|YP_004385309.1|  98 EMM---AREMNCEVLVFGHIHRP 117
                                       333...47788999*******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1314.10
//
Query:       gi|330508882|ref|YP_004385310.1|  [L=396]
Description: hypothetical protein MCON_3204 [Methanosaeta concilii GP6]
Scores for complete 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-06   27.0   0.0      0.029   14.2   0.0    2.9  2  SIS       SIS domain


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   6.6e-05       1.2      58      96 ..      97     135 ..      53     139 .. 0.94
   2 !   14.2   0.0   1.6e-06     0.029       5      92 ..     234     315 ..     230     319 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 6.6e-05
                                       EEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHH CS
                               SIS  58 ilisfsgetkdlvaaaelakergakiiaITdskgsplar 96 
                                       i+is sget ++++ +     rg+ i +IT +k+ ++++
  gi|330508882|ref|YP_004385310.1|  97 IAISGSGETQSVNKYISDFITRGGDIKLITANKEGTAYK 135
                                       9********************************998876 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.6e-06
                                       SSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTS CS
                               SIS   5 akriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakerga 81 
                                       + r ++ G G+s+ +a+ + + + ++++i +   d  +      +  + +d+ i i+ +g+t + ++   la ++ga
  gi|330508882|ref|YP_004385310.1| 234 SGRYIIGGVGRSGLVARAFEMRFTHLNKISYWERDFNT------PSFQIGDVYIPITGTGNTYEALEGTTLALKKGA 304
                                       6788999****************999999887666555......678899*************************** PP

                                       EEEEEESSTTS CS
                               SIS  82 kiiaITdskgs 92 
                                        +  IT +++s
  gi|330508882|ref|YP_004385310.1| 305 DVMPITANPSS 315
                                       *******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 2695.53
//
Query:       gi|330508883|ref|YP_004385311.1|  [L=354]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-06   27.1   0.4    3.9e-06   27.1   0.4    1.9  2  OrfB_IS605      Probable transposase
    7.2e-06   25.8   0.0      3e-05   23.8   0.0    2.1  1  OrfB_Zn_ribbon  Putative transposase DNA-binding 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 ?   -1.7   0.2      0.36   3.3e+03      43      69 ..      97     123 ..      71     141 .. 0.66
   2 !   27.1   0.4   4.3e-10   3.9e-06      11     106 ..     166     259 ..     153     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.36
                        OrfB_IS605  43 grrlksdykylakeiaelqsklkkskn 69 
                                       +  ++++ ++++++  e++ +l +s++
  gi|330508883|ref|YP_004385311.1|  97 SIDYDTRIFAFREKDEEISVTLLRSRQ 123
                                       455666677777777777777777765 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 4.3e-10
                        OrfB_IS605  11 pkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn..ykkasrklarlhrkrs 85 
                                       ++    +++g+DlGi ++a++++++     + g+ +k  +  +a  +a lq+k+ k ++  ++++++ ++rl+ k +
  gi|330508883|ref|YP_004385311.1| 166 EQIHVDTVLGVDLGITDIAVTSEGQ----KFGGKTIKLIKNHYASMRAVLQQKAVKGTRssRRRCRELQQRLSGKEA 238
                                       55566789****************9....78999999999***********99988888899*************** PP

                        OrfB_IS605  86 rrrkhllhklathliktlkev 106
                                       r  +   h++ ++++ + +e+
  gi|330508883|ref|YP_004385311.1| 239 RYQRQINHEIGKAIVTRAQEI 259
                                       **************9999887 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 !   23.8   0.0   3.4e-09     3e-05       1      29 [.     292     320 ..     292     325 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.4e-09
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSk 29 
                                       f++lke+l+yka  +G+++++v+payTS 
  gi|330508883|ref|YP_004385311.1| 292 FYQLKEFLSYKALVAGVPLVLVDPAYTSR 320
                                       899*************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2439.47
//
Query:       gi|330508884|ref|YP_004385312.1|  [L=356]
Description: hypothetical protein MCON_3207 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-56  190.5   0.1    2.7e-56  190.1   0.1    1.2  1  DUF1297      Domain of unknown function (DUF1297)
    2.3e-41  140.6   0.0    3.9e-41  139.8   0.0    1.4  1  DUF1246      Protein of unknown function (DUF1246)
    6.7e-06   26.2   0.0    1.8e-05   24.9   0.0    1.7  1  ATP-grasp_3  ATP-grasp domain
    0.00069   19.2   0.0     0.0018   17.8   0.0    1.6  2  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
     0.0066   16.1   0.0      0.011   15.3   0.0    1.3  1  RimK         RimK-like ATP-grasp domain
  ------ inclusion threshold ------
      0.049   13.2   0.5       0.25   10.9   0.0    2.0  2  ATP-grasp    ATP-grasp domain
       0.15   11.2   0.0       0.24   10.5   0.0    1.2  1  TTL          Tubulin-tyrosine ligase family


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 !  190.1   0.1   1.1e-59   2.7e-56      18     188 .]     179     356 .]     166     356 .] 0.93

  Alignments for each domain:
  == domain 1  score: 190.1 bits;  conditional E-value: 1.1e-59
                                       HHHCCEEEEE---SEEEEEEEEEETTT........TEEEEEEEEEEEEEECCCHCCS-HHHH.HCCT----EEEEEE CS
                           DUF1297  18 edlkkasieeyvvGanfnlnyfysplk........eevellgidrRyesnldglvrlpakeq.lelevepeyvvvGn 85 
                                       ++ +k +i+e+++G+++++++fysp+k        + +e+lgidrR+esn d++ r+ + ++  ++ + p++vv+Gn
  gi|330508884|ref|YP_004385312.1| 179 SSQEKYTIQEFILGTRYYIHFFYSPIKpdgyrlskGSLEMLGIDRRVESNADEIFRIGSMKElADAGIYPSFVVTGN 255
                                       467889****************************9**********************87655167888********* PP

                                       EEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--CCHHHTTSS CS
                           DUF1297  86 ipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegspyskllfge 162
                                        p+vlREsll+++felge++ve++ +l+  G+iG F+L+++vt++le+ vf++saRiv+gtn+y++gspys    + 
  gi|330508884|ref|YP_004385312.1| 256 LPLVLRESLLPRAFELGERVVETSLDLFG-GMIGAFSLETIVTDELEFKVFEISARIVAGTNLYINGSPYSDF-VEP 330
                                       **************************997.*****************************************86.588 PP

                                       ---HHHHHHHHHHHHHHCT-GGGCEE CS
                           DUF1297 163 plsmGrrialEikeaiekdrleeivt 188
                                        ls Grria Eik+a e d leeivt
  gi|330508884|ref|YP_004385312.1| 331 GLSNGRRIAQEIKRANELDLLEEIVT 356
                                       9************************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 !  139.8   0.0   1.5e-44   3.9e-41       1     122 []      21     142 ..      21     142 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 1.5e-44
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTTTT-..SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTH CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekfkvi..devivldkfkdilkeevqeklreenailvPhgsf 75 
                                       iat++SHs+lqi++gA++egf+tl +c  +  ++Y++f+++  d++i+++++k +l+    ++l+++ ai++Phgs+
  gi|330508884|ref|YP_004385312.1|  21 IATICSHSSLQIFHGARREGFKTLGICIGQPPRFYDAFPLAkpDKFICVESYKALLDYA--DDLVADSAIVIPHGSL 95 
                                       89************************************99999*************766..**************** PP

                                       HHHC-HHHHHC-SS-EES-TTHHHHHCSHHHHHHHHHHTT-BB--BE CS
                           DUF1246  76 veYvgiekieelkvpifGnrkllrwEerrekkrkyLekAgiriPkki 122
                                       veY+gie++e+l+vp+fGnr++l wE++re++r+++ kAg+++P+++
  gi|330508884|ref|YP_004385312.1|  96 VEYLGIERFESLAVPTFGNRRVLAWESDREMEREWMLKAGVNVPMRF 142
                                       ********************************************976 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0     7e-09   1.8e-05       9     109 ..     129     256 ..     122     314 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 7e-09
                                       HHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.........EEEE---SEEEEEEEEE.S CS
                       ATP-grasp_3   9 kkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve..lvqefieGkplSvsllsdg 83 
                                       +++ +agv+vP  ++ e+++  + +++vK   + gg + ++++ kee+++++ ++e   +qefi G+ + + +  + 
  gi|330508884|ref|YP_004385312.1| 129 EWMLKAGVNVP--MRFEKADDIDRPVIVKYHGAKGGRGFFIAKTKEELQSKMSSQEkyTIQEFILGTRYYIHFFYSP 203
                                       6788999****..***************************************999899**********999988776 PP

                                       SSEEEEEEEEEEEET...............................TEEEEEE CS
                       ATP-grasp_3  84 ekvlvlavnrqliekaeke...........................fvyaGnv 109
                                        k     +++  +e+ + +                           fv +Gn+
  gi|330508884|ref|YP_004385312.1| 204 IKPDGYRLSKGSLEMLGIDrrvesnadeifrigsmkeladagiypsFVVTGNL 256
                                       66665555555555433334455555555555555555555555555555555 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.9e-07    0.0018      31      74 ..     142     185 ..     131     198 .. 0.86
   2 ?   -2.9   0.0       1.5   3.9e+03     155     180 ..     287     311 ..     283     315 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.9e-07
                                       HHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  31 laiakeigyPviikaafglGGkGmrvarneeelaelvkkalaea 74 
                                        + a++i  Pvi+k   + GG+G  +a+++eel+  +++  + +
  gi|330508884|ref|YP_004385312.1| 142 FEKADDIDRPVIVKYHGAKGGRGFFIAKTKEELQSKMSSQEKYT 185
                                       56799****************************99888766655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.5
                                       EEEEEEEEEEETTTTEEEEEEEESS- CS
                       CPSase_L_D2 155 vgagtveflldpkskeyyviEvNtRl 180
                                       +ga  +e ++   + e+ v E+ +R+
  gi|330508884|ref|YP_004385312.1| 287 IGAFSLETIVTD-ELEFKVFEISARI 311
                                       566667777775.8999999999998 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.4e-06     0.011      39      82 ..     148     190 ..     133     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.4e-06
                                       .-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--EEEEE- CS
                              RimK  39 lrfPvvvKsvegsqGikvvlakkeqklkqvlealkeailvqeyi 82 
                                       +  Pv+vK   ++ G + ++ak++++l++ +++ +e+  +qe+i
  gi|330508884|ref|YP_004385312.1| 148 IDRPVIVKYHGAKGGRGFFIAKTKEELQSKMSS-QEKYTIQEFI 190
                                       678***************************987.5677889999 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   9.7e-05      0.25      23      71 ..     144     189 ..     134     193 .. 0.84
   2 ?   -0.3   0.1      0.26   6.7e+02     134     159 ..     285     310 ..     257     312 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.7e-05
                                       HHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE- CS
                         ATP-grasp  23 aaeelglpvvvKarrlgydGkGqsvvrseedleqalealkeekvivEef 71 
                                        a++++ pv+vK   ++  G+G ++ + +e+l++ ++    ek  + ef
  gi|330508884|ref|YP_004385312.1| 144 KADDIDRPVIVK-YHGAKGGRGFFIAKTKEELQSKMSSQ--EKYTIQEF 189
                                       4589********.999*****************988877..56666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.26
                                       TSSEEEEEEEEEETTCTEEEEEEESS CS
                         ATP-grasp 134 ggvGvfavElFvledgellvnElapR 159
                                       g++G f++E  v+++ e  v E++ R
  gi|330508884|ref|YP_004385312.1| 285 GMIGAFSLETIVTDELEFKVFEISAR 310
                                       45799********8888999999998 PP

>> TTL  Tubulin-tyrosine ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.3e-05      0.24      61     109 ..     145     190 ..     116     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.3e-05
                                       TS--S-..B----SS---XX------BSSTHHHHHHHH..SSS-EEEEB-- CS
                               TTL  61 aekees..ntwIvKpsasarGkgirvfnkledikkivsqsqkeplvvqkYi 109
                                       a+      + +IvK +  + G+g ++ ++ e+++   ++s++e++ +q++i
  gi|330508884|ref|YP_004385312.1| 145 AD---DidRPVIVKYHGAKGGRGFFIAKTKEELQ--SKMSSQEKYTIQEFI 190
                                       22...134689***********************..6999**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2650.09
//
Query:       gi|330508885|ref|YP_004385313.1|  [L=313]
Description: integral membrane protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-14   53.0  13.3    3.9e-14   53.0  13.3    2.5  3  EamA             EamA-like transporter family
  ------ inclusion threshold ------
        3.7    6.8  28.9      0.074   12.4  11.8    2.2  2  Glucos_trans_II  Glucosyl transferase GtrII


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 !   53.0  13.3   4.4e-18   3.9e-14       3     136 ..       3     134 ..       1     135 [. 0.95
   2 !    3.9  14.6    0.0065        58      12     111 ..     171     274 ..     166     280 .. 0.83
   3 ?   -2.8   0.1      0.72   6.5e+03     124     135 ..     301     312 ..     297     313 .] 0.68

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 4.4e-18
                              EamA   3 gillallaalfwaiyfvlskillrkv..spltltfvrfliagillliiallkegklaklslkdwllllllgllgtvl 77 
                                       +++la+l+++f++i++vl k ll+++  ++ ++ + + l+  i+ ++++l+ + k+   ++ + l+ lllg+l ++ 
  gi|330508885|ref|YP_004385313.1|   3 WLILAFLGTVFFSIAGVLDKLLLENYtyDSKAYIVCQALVQLIFIIPVMLFVGVKF---TYPESLFALLLGCLQIFP 76 
                                       689*********************99778889999*********************...99999999****999988 PP

                              EamA  78 afllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       + +++++al+  +as++s + +  Pvf+li s++l+ge l+ k ++g +l ++G+l+++
  gi|330508885|ref|YP_004385313.1|  77 T-FFYMKALQIEEASKVSAMEYAYPVFVLIGSIFLFGEILSPKCYAGGLLLIIGTLFLS 134
                                       8.59****************************************************987 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0065
                              EamA  12 lfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl...aklslkdwllllllgl.lgtvlafllffy 84 
                                       ++ a+y++  k+ll +++ ++l  +++l   i+ +++++++ ++      + + ++++ +l++     +l+ ++ + 
  gi|330508885|ref|YP_004385313.1| 171 ILTAAYYLSLKYLLFSIDEWSLYIWSSLGTLIVAMPLMAVRSIREevfGFFGRGSFAIGALISEeAFQFLGLIFSIF 247
                                       6779999999******************9999999999999999955555555555555444445667888889999 PP

                              EamA  85 alkktsasnaslitslePvftlilsvl 111
                                       a   +s++ +s + +l+P++t++l ++
  gi|330508885|ref|YP_004385313.1| 248 AYAIGSVTLVSSVGALQPILTVMLIMI 274
                                       9999******************99776 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.72
                              EamA 124 givlillGvlli 135
                                       +++++++Gv+++
  gi|330508885|ref|YP_004385313.1| 301 AFMMVIVGVYFV 312
                                       567777777776 PP

>> Glucos_trans_II  Glucosyl transferase GtrII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   9.1     0.034     3e+02     219     297 .]      21     111 ..       4     111 .. 0.72
   2 ?   12.4  11.8   8.2e-06     0.074      44     191 ..     160     312 ..     122     313 .] 0.76

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.034
                   Glucos_trans_II 219 s.....isnygvkpkklllililliliilllalllkkkkkkkksllllllllllllpfalnlil..........lks 280
                                       +     +++y +k + + ++l+ li+ii +++++ +k  + ++   l++lll  l  f +++++          +++
  gi|330508885|ref|YP_004385313.1|  21 DkllleNYTYDSKAYIVCQALVQLIFIIPVMLFVGVKFTYPES---LFALLLGCLQIFPTFFYMkalqieeaskVSA 94 
                                       1444456678888888888899999999999999999999988...6777777777777777777778887777777 PP

                   Glucos_trans_II 281 sllrprtlmpygvvllf 297
                                         +++ +++ +g+++lf
  gi|330508885|ref|YP_004385313.1|  95 MEYAYPVFVLIGSIFLF 111
                                       77777777777887775 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 8.2e-06
                   Glucos_trans_II  44 lyslsPflsgilailllalsailivklfdkkskf......lsilisalfisfPiflenlsFmfdslvmalalllavl 114
                                         s+ Pf+s ++  +   ls   + + +d +s        + i+++ l+++  i  e++ F     ++a++ l +  
  gi|330508885|ref|YP_004385313.1| 160 SPSIRPFMSFWILTAAYYLSLKYLLFSIDEWSLYiwsslgTLIVAMPLMAVRSIREEVFGFF-GRGSFAIGALISEE 235
                                       3355555555555555555555566666666655****9888888899999999999****9.555*********** PP

                   Glucos_trans_II 115 aayllvkknkllkllvsalllaislgiYQaylnvyialllilllrdlldekkklkeilkkllllllvliisfvlyll 191
                                       a+ +l    +++ ++++ + l+ s+g+ Q  l v+++++l  l  +l +e +   ++ +++ + ++++++ +++y++
  gi|330508885|ref|YP_004385313.1| 236 AFQFLGLIFSIFAYAIGSVTLVSSVGALQPILTVMLIMILGALAPRLAKELNERTDRSSLMQKGAAFMMVIVGVYFV 312
                                       *************************************8887777778555555555555555666778888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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: 2345.30
//
Query:       gi|330508886|ref|YP_004385314.1|  [L=157]
Description: hypothetical protein MCON_3212 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0014   18.5   0.1     0.0018   18.1   0.1    1.2  1  DUF2157          Predicted membrane protein (DUF2157)
  ------ inclusion threshold ------
      0.011   15.8   0.9      0.027   14.6   0.0    1.9  2  Phage_holin_3_3  LydA holin phage, holin superfamily III
       0.77    9.9   5.0       0.33   11.0   1.4    2.1  2  TssO             Type VI secretion system, TssO


Domain annotation for each model (and alignments):
>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   3.1e-07    0.0018      36     123 ..      21     134 ..       6     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.1e-07
                           DUF2157  36 eallvlGall.lglGlilfvAanWqglsrlvkfllllvllllslllgavlwrdr....................... 88 
                                        +l + G ll ++lG i f   n ++++r++k+ l ++ +ll l++ + +   +                       
  gi|330508886|ref|YP_004385314.1|  21 SILRISGLLLtVTLGAIYFSFDNSDTIPRFTKLFLFISSILLGLAIFVSIFTLKiksryileniefinamqettdne 97 
                                       56666676662679********************99999888877764444444579******************99 PP

                           DUF2157  89 ..rvpprlgeallllaalllgaaialvgqifqlsgda 123
                                           ++++  +l+ +++l++g   + + q ++   + 
  gi|330508886|ref|YP_004385314.1|  98 nkWTNRAVKVMLAAVSSLVIGMIAFAICQAYNDMLNN 134
                                       9766778888899999999999999999999855555 PP

>> Phage_holin_3_3  LydA holin phage, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.37   2.2e+03      38      49 ..      59      70 ..      50      78 .. 0.59
   2 ?   14.6   0.0   4.6e-06     0.027      14      53 ..      88     129 ..      86     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.37
                   Phage_holin_3_3 38 SgfvGllvfllc 49
                                      S++ Gl  f   
  gi|330508886|ref|YP_004385314.1| 59 SILLGLAIFVSI 70
                                      555554444333 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.6e-06
                   Phage_holin_3_3  14 sylmrakkgrrrfsike..llleivvSgfvGllvfllceelg 53 
                                       + ++++ +++ +++ +   ++l +v+S+++G+++f++c +++
  gi|330508886|ref|YP_004385314.1|  88 NAMQETTDNENKWTNRAvkVMLAAVSSLVIGMIAFAICQAYN 129
                                       56666667766666655779******************9986 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.15   9.1e+02      19      37 ..      29      46 ..      22      50 .. 0.79
   2 ?   11.0   1.4   5.6e-05      0.33      15      59 ..      53      96 ..      42     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.15
                              TssO 19 vtvlllflivffffksspl 37
                                      +++++l+ +++f+f +s++
  gi|330508886|ref|YP_004385314.1| 29 LLTVTLG-AIYFSFDNSDT 46
                                      5667777.99999998876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.6e-05
                              TssO 15 llFlvtvlllflivffffkssplqekeillkelerkkkfeekqke 59
                                      l ++++++ll+l++f + + +++++  il +++e +++++e  ++
  gi|330508886|ref|YP_004385314.1| 53 LFLFISSILLGLAIFVSIFTLKIKSRYIL-ENIEFINAMQETTDN 96
                                      45677899*********************.888888888776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1198  (0.0668191); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); 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):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1079.21
//
Query:       gi|330508887|ref|YP_004385315.1|  [L=313]
Description: hypothetical protein MCON_3213 [Methanosaeta concilii GP6]
Scores for complete 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   50.4   0.0    1.2e-10   40.8   0.0    2.2  2  SDH_sah       Serine dehydrogenase proteinase
    0.00012   22.0   0.0    0.00065   19.6   0.0    2.1  2  CLP_protease  Clp protease
     0.0008   19.5   0.0     0.0016   18.5   0.0    1.5  1  HTH_AraC      Bacterial regulatory helix-turn-helix proteins,
  ------ inclusion threshold ------
      0.051   14.4   0.4       0.11   13.4   0.4    1.5  1  DUF4482       Domain of unknown function (DUF4482)


Domain annotation for each model (and alignments):
>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   2.8e-14   1.2e-10      87     164 ..      63     142 ..      15     155 .. 0.89
   2 !    7.6   0.0   0.00038       1.7     191     245 ..     190     249 ..     184     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.8e-14
                           SDH_sah  87 ltpkdkpidliihtpGGlvlaatqiakalkeh.kaktrvivphyamsGGtlialaadeiildenavlGpvdpqlgqy 162
                                        t  d  +d+ii + GG + aa +ia  ++++ +++ +  +p +a s  tlia + + i++ +   lGp+dpq++q+
  gi|330508887|ref|YP_004385315.1|  63 YTNIDGKLDVIIDSAGGDINAAYNIASLFQKYgNSELTFFIPRWAKSAATLIACSGETILMTPVGELGPLDPQITQI 139
                                       5677889********************9998736899**************************************97 PP

                           SDH_sah 163 .pa 164
                                        pa
  gi|330508887|ref|YP_004385315.1| 140 nPA 142
                                       355 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00038
                           SDH_sah 191 kkaikqveefvyellkdkyde.....ekakeiakklteGrwthdypltveelkelGlevn 245
                                        kai+  e+++ ++lk+++++     +   +ia+ l+     h + + ++e++++Gl+ +
  gi|330508887|ref|YP_004385315.1| 190 AKAIEISEQYLTKVLKERMGKtgklvQEPSKIARCLSREYTDHGFCINLNEARSIGLNAD 249
                                       5999999************9833222345789999*999999***************876 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.4e-07   0.00065      16      98 ..      38     120 ..       9     128 .. 0.84
   2 ?   -0.8   0.0      0.27   1.2e+03     131     174 ..     192     246 ..     186     250 .. 0.54

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.4e-07
                                       TTEEEEES-BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHS.SS-EEEEEEEEEETHHHH CS
                      CLP_protease  16 eriiflgseiddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyi.kpdvsticlGlaaSmgsl 91 
                                        r  +l  +i++ + +k+  +L +   ++ d ++ ++i+s GG+++a++ I+ ++q   +++ + +   +a S+++l
  gi|330508887|ref|YP_004385315.1|  38 RRCFILWANITQPFVDKVYDELRTK-YTNIDGKLDVIIDSAGGDINAAYNIASLFQKYgNSELTFFIPRWAKSAATL 113
                                       4455567788888888999888877.7788889**********************99846666555669******** PP

                                       HHHTS-T CS
                      CLP_protease  92 llaagek 98 
                                       ++++ge+
  gi|330508887|ref|YP_004385315.1| 114 IACSGET 120
                                       ****986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHHHHHTS-HHHHHH...........HHCSTEEEEHHHHHHHTS CS
                      CLP_protease 131 ellkikerlneilakhtgqslekiek...........dldrdtflsaeeAveyGL 174
                                        ++  ++ l+++l+++ g++ + +++            +d  + ++ +eA + GL
  gi|330508887|ref|YP_004385315.1| 192 AIEISEQYLTKVLKERMGKTGKLVQEpskiarclsreYTDHGFCINLNEARSIGL 246
                                       4444555555555555554444444333333344444555556677777777776 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   3.6e-07    0.0016       3      36 ..     178     211 ..     176     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.6e-07
                                       CCCSCT--HHHHHHHTTSSHHHHHHHHHHHSSS- CS
                          HTH_AraC   3 enlstnltiediAdelgfSrsyFsrlFkketGmt 36 
                                         l+ +lt++++A +  +S++y+++++k+++G+t
  gi|330508887|ref|YP_004385315.1| 178 KRLQFPLTLGSFAKAIEISEQYLTKVLKERMGKT 211
                                       57899***************************98 PP

>> DUF4482  Domain of unknown function (DUF4482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   2.4e-05      0.11      28      55 ..      10      37 ..       5      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                           DUF4482 28 ERkewesqwkelqkkieeLqkevklrrk 55
                                      E ke+++q kel  ki eL ++++ +r+
  gi|330508887|ref|YP_004385315.1| 10 ESKEVDEQIKELDVKITELVQKIEAKRE 37
                                      88**********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      819  (0.0456802); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.24s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 2372.65
//
Query:       gi|330508888|ref|YP_004385316.1|  [L=61]
Description: hypothetical protein MCON_3214 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-17   60.9   0.1      9e-17   60.7   0.1    1.1  1  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5


Domain annotation for each model (and alignments):
>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.1     5e-21     9e-17       1      43 []       7      49 ..       7      49 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 5e-21
                             RHH_5  1 SkRvnvtLPeelleeLeewAdeegRsvSnlaafLvekalreaq 43
                                      SkRv+vtLP++ +e+Le++A+e+g+++Snl+++++ k++re++
  gi|330508888|ref|YP_004385316.1|  7 SKRVAVTLPDDAREFLEQEAKETGVPLSNLMSYIAVKYVREEK 49
                                      9***************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 426.84
//
Query:       gi|330508889|ref|YP_004385317.1|  [L=402]
Description: transposase, IS4 family protein/SWIM domain fusion [Methanosaeta concilii GP6]
Scores for complete sequence (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   74.2   0.2    3.2e-20   72.7   0.2    1.7  1  DDE_Tnp_1  Transposase DDE domain
    1.4e-05   24.7   0.5    2.8e-05   23.7   0.5    1.4  1  SWIM       SWIM zinc finger


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 !   72.7   0.2   3.5e-24   3.2e-20       6     214 .]     207     382 ..     203     382 .. 0.92

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 3.5e-24
                         DDE_Tnp_1   6 vlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr.kgklvl 81 
                                        + vD+t +r+++++++   +++++k ++++k+h+    ++ ++ +v+it++ ++ds+++ +l++      +   v+
  gi|330508889|ref|YP_004385317.1| 207 DFSVDSTGFRTTTFSAYNGVKHGQKKEHQWVKAHLCAGVKTNVVAAVAITDAYSNDSPQFGPLIKKTSNGfTINEVT 283
                                       678************88888*********************************************9874499999** PP

                         DDE_Tnp_1  82 aDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntn 158
                                       aD +Y+s+++l++++  g+   i+++kn+                  ++ +    + k +++               
  gi|330508889|ref|YP_004385317.1| 284 ADLAYSSRANLEEVKNVGGMAFIPYRKNA-----------------TGKSRGSALWSKMFHY--------------- 328
                                       ***************99999999995555.................7777777888888888............... PP

                         DDE_Tnp_1 159 sellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                        ++l   e++e y++R+ iE + + +krkfg + l+++++ + +++ll++++a+nl
  gi|330508889|ref|YP_004385317.1| 329 -FQLNRDEFMEHYHKRSNIEATNAAIKRKFG-ETLKSKNPVAQVNELLAKIIAYNL 382
                                       .88889999**********************.***********************8 PP

>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.5   3.1e-09   2.8e-05      16      34 ..      50      68 ..      49      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.1e-09
                              SWIM 16 tCsCpefqkngipCkHalA 34
                                      tC+Cp+f + g  CkH++A
  gi|330508889|ref|YP_004385317.1| 50 TCTCPDFVYRGGKCKHIAA 68
                                      8*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2821.62
//
Query:       gi|330508890|ref|YP_004385318.1|  [L=305]
Description: ribonuclease Z [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-23   82.4   0.1    1.2e-11   44.5   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    1.3e-12   48.1   0.8      4e-11   43.3   0.1    2.8  2  Lactamase_B    Metallo-beta-lactamase superfamily
    2.1e-07   30.5   0.0    4.1e-07   29.6   0.0    1.5  1  Lactamase_B_4  tRNase Z endonuclease


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   2.1e-15   1.2e-11       3     134 ..      32     151 ..      30     156 .. 0.86
   2 !   36.1   0.1   7.5e-13   4.5e-09     132     201 .]     198     267 ..     174     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 2.1e-15
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE..EEEEEEHHHHHHCCTTC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkk..lplyapkgvlavleanf 74 
                                       +L+D+g ++  q++ra+        + +++ ++lth H+DH+ g++ l e   ++++   +++ +p ++++ +e   
  gi|330508890|ref|YP_004385318.1|  32 LLFDCGEGTQRQMMRAR------TGMMRLNYIFLTHLHADHILGIPGLLEtmaFQGRVepITIAGPIHTARLVECFK 102
                                       79******888877775......6789***********************97744443679999*******999988 PP

                                       GHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTT CS
                     Lactamase_B_2  75 vylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrieggg 134
                                       + + + ++++v + el +++ ++++  g +++a++ rh+ +          lG+++e+++
  gi|330508890|ref|YP_004385318.1| 103 SVCYFSRNFEVIALELSPEDVVKMK--GYQVRAIETRHSVPS---------LGYVLEEDQ 151
                                       8888888877889999999999998..799***********9.........999999554 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 7.5e-13
                                       CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH...HHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 132 gggkrvyyigDtgyipeeigerlggadllllditayeddemir...hmgHltpeeaveaaadlgakrlvliHi 201
                                       ++g++v+y+gDt  +  ++++  +gadll++d  + +d  mi+   +  H+t +ea+e+a+++g++ l+l+Hi
  gi|330508890|ref|YP_004385318.1| 198 RPGRKVVYTGDTRPCR-SVEDAGRGADLLIHDSALASD--MIEwamETKHSTAKEAAELARRAGVRHLILTHI 267
                                       689**********999.556688*********999999..777789**************************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 !   43.3   0.1   6.7e-15     4e-11       3      87 ..      17      96 ..      15     241 .. 0.76
   2 ?   -0.2   0.1      0.14   8.3e+02      36      52 ..     250     266 ..     235     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 6.7e-15
                                      CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B  3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81
                                      +++ +++li  +g+ +L+D+G +t++++++     ++ +  ++ +++lTHlH+DHi g +gl e+  +  ++++++ + 
  gi|330508890|ref|YP_004385318.1| 17 ERNPSAILINREGEMLLFDCGEGTQRQMMR-----ARTGMMRLNYIFLTHLHADHILGIPGLLETMAFQGRVEPITIAG 90
                                      677899***********************8.....8****************************999999999988887 PP

                                      CHCHHH CS
                       Lactamase_B 82 lfmeea 87
                                      +++ ++
  gi|330508890|ref|YP_004385318.1| 91 PIHTAR 96
                                      777666 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.14
                                       HHHTSGGGGEEEEE-SB CS
                       Lactamase_B  36 aalglkpkdvdavilTH 52 
                                       aa+      v+++ilTH
  gi|330508890|ref|YP_004385318.1| 250 AAELARRAGVRHLILTH 266
                                       456777889******** PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   6.9e-11   4.1e-07       6      62 ..      14      68 ..      10      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 6.9e-11
                     Lactamase_B_4  6 ptsDtsgPlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkvswssig 62
                                      pt++ + + +l++ + +  lf ++gEgtQR ++  ++ + +l+ iFLt+ +  ++i 
  gi|330508890|ref|YP_004385318.1| 14 PTPERNPSAILINREGEMLLF-DCGEGTQRQMMRARTGMMRLNYIFLTHLH-ADHIL 68
                                      6777776777777777999**.***************************99.66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 2110.22
//
Query:       gi|330508891|ref|YP_004385319.1|  [L=209]
Description: hypothetical protein MCON_3218 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1601.81
//
Query:       gi|330508892|ref|YP_004385320.1|  [L=925]
Description: histidine-protein kinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-41  138.8   0.6    4.3e-29  100.9   0.2    2.6  2  Response_reg  Response regulator receiver domain
      6e-30  104.0   0.2    1.2e-29  103.1   0.2    1.5  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
      1e-17   63.9   0.0      1e-17   63.9   0.0    2.5  3  HisKA         His Kinase A (phospho-acceptor) domain
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.049   13.5   0.0    1.4  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
      0.095   13.0   0.5       0.21   11.9   0.5    1.5  1  DUF2098       Uncharacterized protein conserved in archaea (D
       0.23   10.7   1.7       0.34   10.2   1.7    1.2  1  FmiP_Thoc5    Fms-interacting protein/Thoc5


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 !   35.9   0.0   2.3e-12   6.9e-09       2     110 ..     668     772 ..     667     774 .. 0.89
   2 !  100.9   0.2   1.4e-32   4.3e-29       1     110 [.     805     913 ..     805     915 .. 0.98

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 2.3e-12
                                       EEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT.TTSEEEEE CS
                      Response_reg   2 livdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed.pelpviil 77 
                                       li+dD+  ++e l ++ ++ g+  +  a++ +e   +l++e++d++l+D +m + dG +l+++i+ +   e+  ++l
  gi|330508892|ref|YP_004385320.1| 668 LIIDDNGSALEMLIRATRSLGM-ITNGASSLQEGKTHLEREEYDVVLMDAMMTDEDGQDLAEKIKSKRyGEVWLVLL 743
                                       8*********************.999**************************************8877577888888 PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlka 110
                                       +  +    +    k+ ad+ l Kp++  +L++ 
  gi|330508892|ref|YP_004385320.1| 744 SPLG----RGSSSKVMADGWLNKPVKALQLRNL 772
                                       8655....4677788899999999988888775 PP

  == domain 2  score: 100.9 bits;  conditional E-value: 1.4e-32
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       +l ++D+p++r++  ++l++ gy + ++ae+g ++l+ l+e+ +d++l+D++mp+mdGle++++ir+  +++ +i++
  gi|330508892|ref|YP_004385320.1| 805 ILMAEDNPVNRKVALSMLKRLGY-QADVAENGLKVLQALQEKPYDIVLMDVQMPEMDGLEATRRIRDSGYNTCIIAM 880
                                       899********************.***************************************************** PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlka 110
                                       tahs  e + e+l+ag++ ++sKp+++eeL   
  gi|330508892|ref|YP_004385320.1| 881 TAHSMGESRDECLDAGMNAYISKPIEIEELARV 913
                                       *****************************9876 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 !  103.1   0.2     4e-33   1.2e-29       1     108 [.     523     637 ..     523     641 .. 0.91

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 4e-33
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE.......EETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCH CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveika.......seddlvisveDnGiGipkedlkklfekfsq.ddstkr 69 
                                       gd  rLrq++ nl++Navkf t+ g++ +++++       ++++l++ v+D+GiGi++e++ +lf++f+q d+s++r
  gi|330508892|ref|YP_004385320.1| 523 GDVNRLRQVLVNLLGNAVKF-TDRGDVVLKVSSrrlegsdDKVELHFAVRDTGIGISPENQSELFQSFTQvDSSKTR 598
                                       7999****************.9899998888876666543339********************************** PP

                                       TSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEE CS
                         HATPase_c  70 ggggtGlGlsivkklvelmgGeiwvesepgrGttftftl 108
                                       ++ggtGlGl+i++ +ve+mgG+iw ese g G++f+f +
  gi|330508892|ref|YP_004385320.1| 599 SYGGTGLGLAISRGIVERMGGRIWAESEIGTGSSFYFDF 637
                                       ***********************************9965 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 ?   -3.7   0.4       4.5   1.3e+04      33      46 ..     369     382 ..     359     394 .. 0.50
   2 !   63.9   0.0   3.4e-21     1e-17       1      66 [.     411     475 ..     411     476 .. 0.95
   3 ?   -3.6   0.1       4.1   1.2e+04      50      59 ..     768     777 ..     765     783 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.5
                                       -HSSCHHHHHHHHH CS
                             HisKA  33 lteelkeyleties 46 
                                       + ee+k++ e++e+
  gi|330508892|ref|YP_004385320.1| 369 AEEEVKRLNEDLEE 382
                                       33444443333333 PP

  == domain 2  score: 63.9 bits;  conditional E-value: 3.4e-21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC...T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre.gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       +++ fl +++HE+rtP++ai+g+a +L+ + +k  +e++++l+ti++++  l+++++d+Ld+s+i++
  gi|330508892|ref|YP_004385320.1| 411 AKSNFLDNMSHEIRTPMNAIIGMARLLQGTdIK--PEQRDFLDTIQKSGSALLAIIDDILDYSKIDG 475
                                       5899***********************887666..******************************97 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.1
                                       HHHHHHHHHH CS
                             HisKA  50 rldhlvedlL 59 
                                       +l++l+edl 
  gi|330508892|ref|YP_004385320.1| 768 QLRNLLEDLI 777
                                       7888888883 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.6e-05     0.049       4      80 ..     529     608 ..     526     616 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                       HATPase_c_3   4 ekAlaelvdNsld.Adaenvkievnknrgkt......geivieDdGkGmseeelknalrlatsskeakrkstslGkk 73 
                                       +++l+ l+ N++   d   v ++v+ +r +         + ++D G G+s+e+  + ++  t+  +  +k +s+G  
  gi|330508892|ref|YP_004385320.1| 529 RQVLVNLLGNAVKfTDRGDVVLKVSSRRLEGsddkveLHFAVRDTGIGISPENQSELFQSFTQVDS--SKTRSYGGT 603
                                       5788999999998888888888888666222335556899****************9986666666..489999999 PP

                       HATPase_c_3  74 GiGlklA 80 
                                       G+Gl  A
  gi|330508892|ref|YP_004385320.1| 604 GLGL--A 608
                                       9995..3 PP

>> DUF2098  Uncharacterized protein conserved in archaea (DUF2098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.5     7e-05      0.21      32      76 ..     347     391 ..     341     409 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7e-05
                           DUF2098  32 vkLdstdLyYrvdtLevidekekkkekeekekedleelek.kekel 76 
                                       + L+++ L+Yr  +Le+++++ k +e+ ++ +edlee  + +  el
  gi|330508892|ref|YP_004385320.1| 347 IILNENALLYREAQLEIAERR-KAEEEVKRLNEDLEERVRlRTAEL 391
                                       56899*************965.555555555555555433033333 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.7   0.00011      0.34      70     153 ..     356     437 ..     344     479 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                        FmiP_Thoc5  70 yeeapeeiskpedtkkeadehelmlaRLewEleqRkelae.....qlkeleekkkkleqeieekkkfLssLppkLks 141
                                       y+ea+ ei+       e+ + e+ ++RL+ +le+R +l +     + k+l   k k+e++ + k +fL++++ ++++
  gi|330508892|ref|YP_004385320.1| 356 YREAQLEIA-------ERRKAEEEVKRLNEDLEERVRLRTaeleaTNKDLLVAKAKAEAAARAKSNFLDNMSHEIRT 425
                                       556666662.......33677899***********8876511111556777789********************999 PP

                        FmiP_Thoc5 142 lkkatkplqeal 153
                                        ++a+  + + l
  gi|330508892|ref|YP_004385320.1| 426 PMNAIIGMARLL 437
                                       888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (925 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.80u 0.26s 00:00:01.06 Elapsed: 00:00:00.44
# Mc/sec: 6258.14
//
Query:       gi|330508893|ref|YP_004385321.1|  [L=261]
Description: histone deacetylase family protein [Methanosaeta concilii GP6]
Scores for 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  117.1   0.2      3e-26   92.6   0.2    3.0  3  Hist_deacetyl  Histone deacetylase domain
  ------ inclusion threshold ------
      0.072   13.1   0.0       0.18   11.8   0.0    1.7  1  B12-binding    B12 binding domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0032        29       3      53 ..      27      69 ..      16      71 .. 0.76
   2 !   92.6   0.2   3.3e-30     3e-26      85     181 ..      70     162 ..      66     172 .. 0.92
   3 !   17.9   0.0   1.9e-07    0.0017     230     294 ..     184     248 ..     167     259 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0032
                                      CGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  3 enpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelles 53
                                      enp+R+s   e l+   +       +i+p +a+ e++++vH +e++ ++++
  gi|330508893|ref|YP_004385321.1| 27 ENPDRVSLPAEMLEGL-E-------FIEPIPADLEDIARVHGPEHIGRVKT 69
                                      6666666433333332.3.......5899*****************99875 PP

  == domain 2  score: 92.6 bits;  conditional E-value: 3.3e-30
                                       TTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  85 pktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDvDv 161
                                       +++++aa la+g+++ a+++ + g  + af+l+rPpgHHa +++a G C++Nn+aia+++++   +++rv+i+D+D+
  gi|330508893|ref|YP_004385321.1|  70 SGLYDAAVLAAGGAICAAEQAVGG--DPAFALIRPPGHHASSNRAWGMCFFNNMAIAVQKIRP--KAERVLIIDIDL 142
                                       67899*****************99..9**********************************99..567********* PP

                                       S--HHHHHHCTT-TTEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 162 HhGnGteeafysdpdvltlS 181
                                       H+G+Gt ++f+ d +v ++ 
  gi|330508893|ref|YP_004385321.1| 143 HFGDGTVSIFRGDRNVKIVN 162
                                       **************998765 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 1.9e-07
                                       HHHHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-.G..EEEEE-S---HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxx RF
                     Hist_deacetyl 230 lrpvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkv.k.kvvllleGGYnle 294
                                       +++++  f+ d++ vsaGfD++ +d  g   l+ e+y e+ k ++e +++    +  +lleGGY+++
  gi|330508893|ref|YP_004385321.1| 184 VKEAFLGFDCDIVGVSAGFDTYLEDWGGL--LKREDYREIGKAIREGSEEEcMgRRFALLEGGYHPD 248
                                       3444556999***************9886..57889**********99998877**********985 PP

>> B12-binding  B12 binding domain
   #    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      29      80 ..     170     223 ..     155     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                       B12-binding  29 feVqllganven..edivaairaekpdvvglSalltsqleavkelvel..lkrirp 80 
                                       fe  +l+++++   +++ +a   ++ d+vg+Sa + ++le+   l+++   ++i++
  gi|330508893|ref|YP_004385321.1| 170 FE--YLNMDQSRylAQVKEAFLGFDCDIVGVSAGFDTYLEDWGGLLKRedYREIGK 223
                                       44..5666666666**************************9999999877555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1805.32
//
Query:       gi|330508894|ref|YP_004385322.1|  [L=208]
Description: hypothetical protein MCON_3221 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1515.33
//
Query:       gi|330508895|ref|YP_004385323.1|  [L=45]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       159  (0.00886831); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 329.94
//
Query:       gi|330508896|ref|YP_004385324.1|  [L=417]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete 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   88.4   0.1    5.4e-25   87.5   0.1    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family
    3.7e-21   75.6   0.0    6.6e-21   74.8   0.0    1.4  1  DEDD_Tnp_IS110  Transposase
  ------ inclusion threshold ------
      0.036   14.4   1.0      0.081   13.2   0.1    2.0  2  Init_tRNA_PT    Rit1 DUSP-like domain


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.1     9e-29   5.4e-25       2      83 ..     249     330 ..     248     336 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 9e-29
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaaira 78 
                                       +++ s+pG+G++ aa+++ae+gd r f+sa+++a+y+G++p+++qS++k r g+i+k G++++Rr+L+e A a++r+
  gi|330508896|ref|YP_004385324.1| 249 KIILSVPGVGFISAATIIAEMGDYRDFPSADKMAKYFGIVPSVYQSAGKLRTGKITKTGSKHMRRILVEVAKAISRT 325
                                       6899***********************************************************************99 PP

                    Transposase_20  79 npelr 83 
                                       ++ +r
  gi|330508896|ref|YP_004385324.1| 326 KKNSR 330
                                       75554 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0   1.1e-24   6.6e-21       1     153 [.       9     152 ..       9     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.1e-24
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G D++kd   a++i+++g +l +er++++++gl a+ ++   ++++ + +ve+tg ++++++++ le +++ ++ n
  gi|330508896|ref|YP_004385324.1|   9 CGADIHKDFLIATMISRSGLKL-QERFNMNQDGLLAFRSW-IINHRCQRLAVESTGGFWYPIFTI-LEGHVEFILAN 82 
                                       79*************9999885.668**************.889****************88876.7899******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdqv 153
                                       ++++++++     ++KtD++D++ IA + +  + ++p++  +++y++Lr++tr+re+lv+ r++ kn++++ L   
  gi|330508896|ref|YP_004385324.1|  83 AYQIRNIE-----HKKTDKLDSERIAIYCL-NNLITPSRIYPKDYRDLRSITRARETLVNARSKIKNQIHQSLSTC 152
                                       *****995.....89***************.****************************************99765 PP

>> Init_tRNA_PT  Rit1 DUSP-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.2   7.1e+03      26      43 ..     133     152 ..     119     162 .. 0.47
   2 ?   13.2   0.1   1.4e-05     0.081      10      80 ..     304     378 ..     296     389 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                      Init_tRNA_PT  26 dfvrkrlsedkk..kkilva 43 
                                       + v++r++ +++  +++  +
  gi|330508896|ref|YP_004385324.1| 133 TLVNARSKIKNQihQSLSTC 152
                                       33333333322222333333 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.4e-05
                      Init_tRNA_PT  10 gKkgsknLrtalpkivdfvrkrlsedkk....kkilvacetGkdlsvgvaLailcklfddakls...eeqsesnitK 79 
                                        K+gsk++r +l ++ ++++++ ++++     ++il+ c + +   v++a  +lc ++   +l    e+ +e+++tK
  gi|330508896|ref|YP_004385324.1| 304 TKTGSKHMRRILVEVAKAISRTKKNSRLmrffQRILARCGKKNIATVALARKVLCIIY---HLLmnhENYQEPEVTK 377
                                       49*****************99966655599**99******999999999888888888...2222235666777777 PP

                      Init_tRNA_PT  80 d 80 
                                       +
  gi|330508896|ref|YP_004385324.1| 378 T 378
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2963.98
//
Query:       gi|330508897|ref|YP_004385325.1|  [L=289]
Description: transposase IS605 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-21   77.3   0.0    2.3e-21   76.3   0.0    1.4  1  OrfB_IS605      Probable transposase
    3.2e-09   36.1   0.8    8.5e-09   34.8   0.8    1.7  1  HTH_OrfB_IS605  Helix-turn-helix 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 !   76.3   0.0   2.5e-25   2.3e-21       4     117 ..     157     268 ..     154     270 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 2.5e-25
                        OrfB_IS605   4 veveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       ve e+  lp+ k + ++giD+G++ +at ++++   ++ ++r++++++ +la+++++l++  k++  +kka + + r
  gi|330508897|ref|YP_004385325.1| 157 VETEDVpLPPWKDGAVVGIDVGLESFATFSNGE---TIANPRFFREEEHELARAQRKLSKAPKGTPDRKKALKVVER 230
                                       5544334999999********************...***************************************** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       +h++++++r +++h+++++l+++   ++ e+Ln+++m+
  gi|330508897|ref|YP_004385325.1| 231 VHERIANKRYEFAHQVSHNLVDRFGLIAFEDLNIKGMV 268
                                       *************************************7 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.8   9.5e-13   8.5e-09      15      47 .]       3      35 ..       2      35 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 9.5e-13
                    HTH_OrfB_IS605 15 eQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                       Q +k++rt++ +R+ YN+ La+rk+a+e+egk
  gi|330508897|ref|YP_004385325.1|  3 SQITKMERTLDLCRWTYNQTLAYRKNAWENEGK 35
                                      7*****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2088.40
//
Query:       gi|330508898|ref|YP_004385326.1|  [L=201]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (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  109.2   0.0    1.9e-31  108.8   0.0    1.1  1  DDE_3     DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.063   13.5   0.0       0.12   12.5   0.0    1.5  1  rve_2     Integrase core domain
       0.11   12.3   0.3        2.3    8.1   0.0    2.5  3  rve_3     Integrase core domain


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8   0.0   3.2e-35   1.9e-31      15     145 ..      10     171 ..       2     172 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 3.2e-35
                             DDE_3  15 vrrrawakkGkrer.leeygrrgrvnligaldekgglaf.vtfeetlnaedfaeflerlletalqakkivlilDnas 89 
                                         +  ++ +Gk er ++ey+r+g++++i+++ +++g++  + + +t+n++df+ ++++++e+ l+  +++++ Dn++
  gi|330508898|ref|YP_004385326.1|  10 KHPGLPMAPGKVERrEFEYIRHGTQSFIVSFAVANGKVDtISCGDTRNEDDFVSHIKEVVERSLSTSRWHFVADNLN 86 
                                       5666799********************************99************************************ PP

                             DDE_3  90 iHkseslrelveee.............................adrlellylPpySPelNpiEivwsklkrellkrr 137
                                       iHksesl+++v++                              +++++++y+P ++++ N++Ei++s+l+r+ll+r+
  gi|330508898|ref|YP_004385326.1|  87 IHKSESLVRYVADVsdldidlgikgrdgilksietresfladpSHSIVFHYTPIHASWMNQVEIWFSILVRKLLRRA 163
                                       ***************************************************************************** PP

                             DDE_3 138 sfksldeL 145
                                       sf s+ +L
  gi|330508898|ref|YP_004385326.1| 164 SFASINDL 171
                                       ****9998 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     2e-05      0.12       3      36 ..     151     184 ..     149     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
                             rve_2   3 fFgsLKtElvygetfktleeleaaiedYIewYNn 36 
                                        F +L ++l++ + f++++ l+a++  ++e++N+
  gi|330508898|ref|YP_004385326.1| 151 WFSILVRKLLRRASFASINDLNAKVLAFVEYFNK 184
                                       699999***************************7 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.04   2.4e+02       5      21 ..       7      23 ..       4      29 .. 0.88
   2 ?   -3.4   0.0       1.5   8.9e+03      19      33 ..      69      83 ..      67      93 .. 0.65
   3 ?    8.1   0.0   0.00038       2.3      24      55 ..     153     184 ..     131     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.04
                             rve_3  5 lsyiapgkPqqNglvEs 21
                                      l++ +pg P+  g+vE+
  gi|330508898|ref|YP_004385326.1|  7 LERKHPGLPMAPGKVER 23
                                      56789***********9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                             rve_3 19 vEsfngtlrdellne 33
                                      vE++  t r +++  
  gi|330508898|ref|YP_004385326.1| 69 VERSLSTSRWHFVAD 83
                                      677777766666554 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00038
                             rve_3  24 gtlrdellneelfrslaearekleawredYNt 55 
                                         l ++ll + +f s++++++k+ a++e++N+
  gi|330508898|ref|YP_004385326.1| 153 SILVRKLLRRASFASINDLNAKVLAFVEYFNK 184
                                       556678899999*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1473.64
//
Query:       gi|330508899|ref|YP_004385327.1|  [L=80]
Description: transposase IS605 family [Methanosaeta concilii GP6]
Scores for complete 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   77.7   0.1    5.1e-22   77.6   0.1    1.0  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0013   18.8   0.2     0.0016   18.4   0.2    1.1  1  DZR             Double zinc ribbon
     0.0019   17.7   0.6      0.044   13.3   0.1    2.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.011   15.9   0.3      0.014   15.5   0.3    1.1  1  FYVE            FYVE zinc finger
      0.012   15.2   2.1       0.87    9.2   3.2    2.1  2  RecR            RecR protein
      0.019   14.8   0.2      0.027   14.3   0.2    1.1  1  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.034   13.6   0.8       0.48    9.9   0.8    2.2  1  zf-ribbon_3     zinc-ribbon domain
      0.069   13.1   0.3        3.4    7.7   0.1    2.1  2  YhfH            YhfH-like protein


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 !   77.6   0.1   2.3e-25   5.1e-22       9      68 ..       5      64 ..       1      65 [. 0.97

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 2.3e-25
                    OrfB_Zn_ribbon  9 eykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68
                                      +yka  +G  v++v+p++TSk Cs+Cg   +++ls+r+++C+ Cg+++drD+nAaiNil+
  gi|330508899|ref|YP_004385327.1|  5 SYKAASAGSVVVLVDPRNTSKMCSRCGTLIEKSLSDRVHNCTLCGLSMDRDWNAAINILR 64
                                      7*********************************************************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   7.2e-07    0.0016      10      44 ..      22      58 ..      18      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.2e-07
                               DZR 10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44
                                      + +++Cs+Cgt +++  +   ++C  Cg ++d +++ 
  gi|330508899|ref|YP_004385327.1| 22 NTSKMCSRCGTLIEKSLSdrVHNCTLCGLSMDRDWNA 58
                                      6799********99777799*************9996 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1     2e-05     0.044      11      32 ..      16      37 ..      12      41 .. 0.84
   2 ?    2.9   0.1     0.035        79      22      29 ..      45      52 ..      43      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                                      CHEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon 11 lveDpergelvCtdCGlVledn 32
                                      +++Dp ++   C++CG+++e  
  gi|330508899|ref|YP_004385327.1| 16 VLVDPRNTSKMCSRCGTLIEKS 37
                                      689****************975 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.035
                                      ESSSSBEE CS
                      TF_Zn_Ribbon 22 CtdCGlVl 29
                                      Ct CGl +
  gi|330508899|ref|YP_004385327.1| 45 CTLCGLSM 52
                                      *****955 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.3   6.5e-06     0.014       5      33 ..      20      50 ..      17      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.5e-06
                                      ...--SB-TTT--B-..-SSS--EE-TTT-- CS
                              FYVE  5 ddsevkkCeiCakkF..sllrrrhhCrlCGk 33
                                      + +++k C+ C +    sl+ r h C lCG 
  gi|330508899|ref|YP_004385327.1| 20 PRNTSKMCSRCGTLIekSLSDRVHNCTLCGL 50
                                      567899*******9976789**********6 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.2   0.00039      0.87      11      34 ..      19      48 ..      16      48 .. 0.71
   2 ?    6.2   0.2    0.0035       7.8      12      27 ..      38      53 ..      36      56 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00039
                                      HHHHH-EE-TTT--EESSS......S-CCC CS
                              RecR 11 eakekvrhCsrCgnlteed......lCaIC 34
                                      + +++ + CsrCg+l e+        C+ C
  gi|330508899|ref|YP_004385327.1| 19 DPRNTSKMCSRCGTLIEKSlsdrvhNCTLC 48
                                      55677799*******887744444448888 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0035
                                      HHHH-EE-TTT--EES CS
                              RecR 12 akekvrhCsrCgnlte 27
                                      + ++v+ C  Cg   +
  gi|330508899|ref|YP_004385327.1| 38 LSDRVHNCTLCGLSMD 53
                                      7799*******97655 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 ?   14.3   0.2   1.2e-05     0.027      10      39 ..      23      53 ..      19      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                      S--B-TTT-SB--S.SSS-EEEETTT--EE- CS
                              C1_1 10 qptfCkhCgeflwg.kekqglkCswCkllvH 39
                                       ++ C+ Cg ++++ ++ +   C+ C+l+++
  gi|330508899|ref|YP_004385327.1| 23 TSKMCSRCGTLIEKsLSDRVHNCTLCGLSMD 53
                                      6789********999***********99865 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.8   0.00021      0.48       5      24 ..      27      50 ..      24      52 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00021
                       zf-ribbon_3  5 CPnCGa.p...lssddnvCpyCGt 24
                                      C++CG+ +   ls+++ +C+ CG 
  gi|330508899|ref|YP_004385327.1| 27 CSRCGTlIeksLSDRVHNCTLCGL 50
                                      99***8554456889999999995 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0015       3.4      13      24 ..      24      35 ..      21      38 .. 0.87
   2 ?    3.7   0.0     0.028        63      15      24 ..      44      53 ..      42      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
                              YhfH 13 kKkCteCGkeie 24
                                      +K C+ CG  ie
  gi|330508899|ref|YP_004385327.1| 24 SKMCSRCGTLIE 35
                                      69******9887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.028
                              YhfH 15 kCteCGkeie 24
                                       Ct CG  ++
  gi|330508899|ref|YP_004385327.1| 44 NCTLCGLSMD 53
                                      6*****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); 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:                         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 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 619.25
//
Query:       gi|330508900|ref|YP_004385328.1|  [L=161]
Description: hypothetical protein MCON_3228 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-26   91.3   0.0    3.9e-26   90.8   0.0    1.2  1  TFX_C            DNA_binding protein, TFX, C-term
    3.9e-07   29.5   0.6    1.3e-06   27.8   0.3    2.0  2  Sigma70_r4       Sigma-70, region 4
    3.2e-05   23.4   0.1    8.5e-05   22.0   0.1    1.8  1  GerE             Bacterial regulatory proteins, luxR family
    0.00012   21.7   1.6     0.0014   18.3   0.2    2.7  2  HTH_23           Homeodomain-like domain
    0.00037   20.4   0.5     0.0008   19.3   0.1    1.8  2  HTH_37           Helix-turn-helix domain
    0.00038   20.7   0.4     0.0009   19.5   0.4    1.7  1  HTH_31           Helix-turn-helix domain
    0.00057   19.8   0.1     0.0017   18.3   0.0    1.8  2  HTH_19           Helix-turn-helix domain
    0.00095   19.2   0.2     0.0026   17.8   0.1    1.9  1  HTH_3            Helix-turn-helix
     0.0022   17.9   0.1      0.081   12.8   0.1    2.3  2  MarR_2           MarR family
     0.0026   18.0   0.1     0.0045   17.2   0.1    1.4  1  KORA             TrfB plasmid transcriptional repressor
     0.0028   17.3   0.1       0.01   15.5   0.0    2.1  2  Sigma70_r4_2     Sigma-70, region 4
     0.0065   16.2   0.0      0.034   13.9   0.0    2.1  2  HTH_38           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   15.1   0.1      0.038   14.0   0.1    1.7  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.038   14.1   0.0       0.11   12.6   0.0    1.8  1  HTH_7            Helix-turn-helix domain of resolvase
      0.058   13.0   0.1       0.18   11.4   0.0    1.9  2  HTH_24           Winged helix-turn-helix DNA-binding
       0.08   12.6   0.0       0.14   11.8   0.0    1.4  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus


Domain annotation for each model (and alignments):
>> TFX_C  DNA_binding protein, TFX, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.0   3.5e-29   3.9e-26       1      83 []      75     157 ..      75     157 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 3.5e-29
                                       SS-HHHHHHHH---EEEEE--GGGHHHHHHHHHHHHHHHS-S----HHHHHHHHHHH-SSS-----SSS-EEEEESS CS
                             TFX_C   1 AreTlaflealdapvlvtieeGtdlfdipkiiyaeadkagikvkydtieLikllreeapeaikgrvvkedlevyite 77 
                                       A++T++++ +++ap+++ ++eGtd+fdip++i+a+ad++gik++ ++++++ +lr+++p+ +++rv+ +d+++y++e
  gi|330508900|ref|YP_004385328.1|  75 AQRTVQQWMMIRAPISLFVKEGTDVFDIPRMIFAAADEMGIKLHVTSMDILVQLRRNEPRLFHKRVLGRDVRIYMKE 151
                                       899************************************************************************** PP

                                       SSSEEE CS
                             TFX_C  78 dGeirv 83 
                                       +Ge +v
  gi|330508900|ref|YP_004385328.1| 152 NGETMV 157
                                       **9876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.3   1.1e-09   1.3e-06       5      47 ..      30      71 ..      29      74 .. 0.93
   2 ?   -2.4   0.0       3.1   3.4e+03      18      28 ..     151     161 .]     143     161 .] 0.76

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.1e-09
                                      S-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                        Sigma70_r4  5 LpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrk 47
                                      L+ r+  vl++r  +gl+++++++rlg +r+ ++ +ekrA ++
  gi|330508900|ref|YP_004385328.1| 30 LTKRQLAVLQMRH-QGLSQQDVADRLGTTRSNISILEKRAHKN 71
                                      899*********6.999***********************765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.1
                                       TTT--HHHHHH CS
                        Sigma70_r4  18 geglTleEIge 28 
                                       + g T+ E++e
  gi|330508900|ref|YP_004385328.1| 151 ENGETMVEVAE 161
                                       77889999997 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   7.6e-08   8.5e-05       3      38 ..      30      65 ..      28      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.6e-08
                                      S-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHH CS
                              GerE  3 LskRErevLrllaeGksnkeIAeelniSekTVkvhk 38
                                      L+kR++ vL++  +G+s +++A++l+    ++++  
  gi|330508900|ref|YP_004385328.1| 30 LTKRQLAVLQMRHQGLSQQDVADRLGTTRSNISILE 65
                                      9*************************9999988755 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   1.3e-06    0.0014       6      40 ..      33      67 ..      29      75 .. 0.81
   2 ?    2.3   0.2      0.14   1.6e+02      27      37 ..      72      82 ..      65      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                            HTH_23  6 eRlrillllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                      + l +l++  +Gls++++A++Lg +r+ ++   kr
  gi|330508900|ref|YP_004385328.1| 33 RQLAVLQMRHQGLSQQDVADRLGTTRSNISILEKR 67
                                      44568889999***************977766666 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                            HTH_23 27 LgvsrrTvyrw 37
                                        + +rTv++w
  gi|330508900|ref|YP_004385328.1| 72 IARAQRTVQQW 82
                                      56779****** PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   7.1e-07    0.0008      27      54 ..      40      67 ..      19      76 .. 0.89
   2 ?   -3.2   0.0       7.7   8.7e+03       9      17 ..     109     117 ..     105     127 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.1e-07
                                      HHHCT--HHHHHHHHT--HHHHHHHHTT CS
                            HTH_37 27 iekrelsqseaaqllgiaqPkvsrllrg 54
                                      +++++lsq+++a +lg++++++s l++ 
  gi|330508900|ref|YP_004385328.1| 40 MRHQGLSQQDVADRLGTTRSNISILEKR 67
                                      789*********************9985 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.7
                                       HHHHHHHHH CS
                            HTH_37   9 daeelkaKa 17 
                                        a+e+ +K 
  gi|330508900|ref|YP_004385328.1| 109 AADEMGIKL 117
                                       344444443 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.4     8e-07    0.0009      11      39 ..      40      69 ..      30      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8e-07
                            HTH_31 11 era.GLsqeevAerlgvsestlsrlEqGrr 39
                                       r+ GLsq++vA+rlg ++s +s lE  ++
  gi|330508900|ref|YP_004385328.1| 40 MRHqGLSQQDVADRLGTTRSNISILEKRAH 69
                                      4444*******************9998665 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.5e-06    0.0017      10      34 ..      42      66 ..      41      81 .. 0.88
   2 ?   -2.8   0.0       5.9   6.6e+03      28      39 ..     146     156 ..     143     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                            HTH_19 10 elgltqeelaerlgisrskisaiEn 34
                                      + gl+q+++a+rlg++rs is +E+
  gi|330508900|ref|YP_004385328.1| 42 HQGLSQQDVADRLGTTRSNISILEK 66
                                      569******************9996 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.9
                            HTH_19  28 kisaiEngkkdv 39 
                                       +i++ Eng++ +
  gi|330508900|ref|YP_004385328.1| 146 RIYMKENGET-M 156
                                       6788888877.5 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.3e-06    0.0026       7      31 ..      42      66 ..      38      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                                      HTTHHHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisriEn 31
                                       +glsq+++A++lG +rs is +E+
  gi|330508900|ref|YP_004385328.1| 42 HQGLSQQDVADRLGTTRSNISILEK 66
                                      69******************97776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   7.2e-05     0.081      16      41 ..      41      64 ..      31      71 .. 0.80
   2 ?    2.8   0.0     0.094   1.1e+02       5      21 ..     119     139 ..     114     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.2e-05
                                      CTTTSEEEHHHHHHHHTSSHHHHHHH CS
                            MarR_2 16 rrpgrdltvgelarrlglsksavsri 41
                                      r+ g  l+++++a+rlg ++s++s +
  gi|330508900|ref|YP_004385328.1| 41 RHQG--LSQQDVADRLGTTRSNISIL 64
                                      4555..*****************976 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.094
                                       HHHHHHHHHHHCTTTS....E CS
                            MarR_2   5 paqarvLaaLgrrpgr....d 21 
                                       ++  ++L  L+r+++r    +
  gi|330508900|ref|YP_004385328.1| 119 VTSMDILVQLRRNEPRlfhkR 139
                                       67899*********9855541 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1     4e-06    0.0045      31      73 ..      44      87 ..      33      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4e-06
                              KORA 31 gkkqadvatelgltkqavsqavkrvwaahaere.epaglerVsv 73
                                      g +q+dva++lg t+ ++s ++kr+ ++ a  + + +++  + +
  gi|330508900|ref|YP_004385328.1| 44 GLSQQDVADRLGTTRSNISILEKRAHKNIARAQrTVQQWMMIRA 87
                                      568**********************9998887767888887766 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.7   5.3e+03      28      40 ..       4      16 ..       3      18 .. 0.75
   2 !   15.5   0.0   9.1e-06      0.01      11      44 ..      30      62 ..      30      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.7
                                      -HHHHHHHHT--H CS
                      Sigma70_r4_2 28 sykEIAellgise 40
                                       ++E Ae+++ se
  gi|330508900|ref|YP_004385328.1|  4 EHEEGAEKMDDSE 16
                                      5899999997665 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 9.1e-06
                                      S-HHHHHHHHHHHTS---HHHHHHHHT--HHHHH CS
                      Sigma70_r4_2 11 LperqreifllryleglsykEIAellgisegtVk 44
                                      L++rq +++ +r+ +gls++++A +lg++ +++ 
  gi|330508900|ref|YP_004385328.1| 30 LTKRQLAVLQMRH-QGLSQQDVADRLGTTRSNIS 62
                                      7889999999965.***************99985 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0     3e-05     0.034      15      38 ..      39      62 ..      32      62 .. 0.90
   2 ?   -1.4   0.0       1.8   2.1e+03      16      27 ..     149     160 ..     148     161 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
                            HTH_38 15 rllaeGlslreIArrLgrspsTIs 38
                                      +++ +Gls+ ++A rLg  +s Is
  gi|330508900|ref|YP_004385328.1| 39 QMRHQGLSQQDVADRLGTTRSNIS 62
                                      7899****************9876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                            HTH_38  16 llaeGlslreIA 27 
                                       + + G+++ e+A
  gi|330508900|ref|YP_004385328.1| 149 MKENGETMVEVA 160
                                       67899*****99 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.4e-05     0.038      21      39 ..      44      62 ..      21      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-05
                                      EHHHHHHHHHTTSSHHHHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvs 39
                                       l+q++ A++lG+tr+ +s
  gi|330508900|ref|YP_004385328.1| 44 GLSQQDVADRLGTTRSNIS 62
                                      59*************9988 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 ?   12.6   0.0   9.6e-05      0.11      10      36 ..      33      59 ..      26      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.6e-05
                                      HHGGGGSSTTTT--STTTSSSS---SS CS
                             HTH_7 10 dinrvvkLleeGisiskIAkevnisRs 36
                                      ++  v++++ +G s +++A++++++Rs
  gi|330508900|ref|YP_004385328.1| 33 RQLAVLQMRHQGLSQQDVADRLGTTRS 59
                                      57789*********************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.18      14      34 ..      41      61 ..      35      63 .. 0.89
   2 ?   -3.4   0.0       6.5   7.3e+03       6      15 ..     122     131 ..     120     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                            HTH_24 14 knprisqreLAerlglSpstv 34
                                      ++ ++sq+++A+rlg ++s++
  gi|330508900|ref|YP_004385328.1| 41 RHQGLSQQDVADRLGTTRSNI 61
                                      5889*************9987 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.5
                            HTH_24   6 rkILelLqkn 15 
                                        +IL  L++n
  gi|330508900|ref|YP_004385328.1| 122 MDILVQLRRN 131
                                       6799888887 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 ?   11.8   0.0   0.00013      0.14      17      39 ..      41      63 ..      29      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                   Cation_ATPase_N 17 lenGLtqaeaaerlkkyGpNelk 39
                                      + +GL+q+++a+rl +  +N+  
  gi|330508900|ref|YP_004385328.1| 41 RHQGLSQQDVADRLGTTRSNISI 63
                                      679****************9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1190.93
//
Query:       gi|330508901|ref|YP_004385329.1|  [L=259]
Description: putative thiazole biosynthesis enzyme [Methanosaeta concilii GP6]
Scores for complete 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-76  254.1   4.4    1.1e-75  253.8   4.4    1.0  1  Thi4           Thi4 family
    2.7e-05   24.3   0.1    2.7e-05   24.3   0.1    2.4  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      6e-05   22.4   0.3    8.8e-05   21.9   0.3    1.4  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    6.1e-05   22.6   1.3      9e-05   22.0   1.3    1.1  1  FAD_oxidored   FAD dependent oxidoreductase
     0.0059   15.9   0.2       0.01   15.1   0.2    1.5  1  FAD_binding_3  FAD binding domain
  ------ inclusion threshold ------
      0.012   14.4   3.4      0.043   12.5   1.0    2.0  2  HI0933_like    HI0933-like protein
      0.033   13.3   0.0      0.054   12.6   0.0    1.2  1  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
      0.039   13.0   5.1      0.062   12.4   0.6    2.2  2  FAD_binding_2  FAD binding domain
       0.11   12.4   0.2       0.28   11.1   0.2    1.7  1  NAD_binding_9  FAD-NAD(P)-binding
       0.14   11.1   1.7       0.45    9.5   0.2    2.1  2  Lycopene_cycl  Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.8   4.4   6.4e-79   1.1e-75       1     235 []       9     239 ..       9     239 .. 0.98

  Alignments for each domain:
  == domain 1  score: 253.8 bits;  conditional E-value: 6.4e-79
                                       HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHH CS
                              Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelL 77 
                                       ++aive y+e +l+  e + ++vGaG++ L aa+ la++ ++k++++e+++s+GGG w+GG++f +ivv++ a  +L
  gi|330508901|ref|YP_004385329.1|   9 TKAIVEGYLESFLENTEVEAALVGAGPANLVAAKRLAEA-NIKTVLFEKRLSVGGGLWGGGMMFPRIVVQQAAIRIL 84 
                                       79*************************************.************************************* PP

                                       HHTT---EEESSEEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTC..TTTSS.- CS
                              Thi4  78 delgikyedegdyvvvkdaalftstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvela..hdtqscv 152
                                       +e gi+y+++ ++++v+++++ +++l++++++ a+++++n v+veD+++re+++v G+vinwt+ e+a  h     v
  gi|330508901|ref|YP_004385329.1|  85 EEYGIRYHEHCKGYYVANSIETVAKLTARAID-AGAQIVNLVTVEDVMIREQDRVVGLVINWTAAEMAqiH-----V 155
                                       ********************************.**********************************9666.....* PP

                                       B-EEEEEEEEEE--GSSSTTTTHHHHHH.HHCTTTS-----ECB-HHHHHHHHHHHECEEETTEEE-THHHHHHHT- CS
                              Thi4 153 DPlvirakvvvdatGhdgeivavvvkki.kleakiekvkgeksldaekaedaivkktrevvpnlyvaGmevaevdga 228
                                       DPl ira+ v+d tGh++++  vv++ki   +  i+ vkgek+++ae++e+++v+ t+ev+p+l+vaGm++a+v g+
  gi|330508901|ref|YP_004385329.1| 156 DPLCIRARYVIDGTGHEASVCRVVARKIpGAIIGIDGVKGEKPMWAEVGERTVVEMTQEVYPGLVVAGMAAAAVCGG 232
                                       ****************************5456679****************************************** PP

                                       EB--SB- CS
                              Thi4 229 nRmGpif 235
                                       +RmGpif
  gi|330508901|ref|YP_004385329.1| 233 PRMGPIF 239
                                       ******9 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   1.5e-08   2.7e-05       2      33 ..      31      62 ..      30      99 .. 0.90
   2 ?   -3.9   0.8       9.6   1.7e+04       7      13 ..     222     228 ..     221     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.5e-08
                                      E--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                     NAD_binding_8  2 vGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                      vGaG + lvaA +La+a+++ +l+ekr ++GG
  gi|330508901|ref|YP_004385329.1| 31 VGAGPANLVAAKRLAEANIKTVLFEKRLSVGG 62
                                      9******************************8 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 9.6
                                       HHHHHHH CS
                     NAD_binding_8   7 sGlvaAy 13 
                                       +G++aA+
  gi|330508901|ref|YP_004385329.1| 222 AGMAAAA 228
                                       7898887 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.3   4.9e-08   8.8e-05       4      89 ..      29     126 ..      27     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.9e-08
                                       EEE--SHHHHHHHHHHHHHTS-EEEEE.........TTHCHHHCSHHHHCHHHHHHHHHHHHH.HHHHCH..HHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx..xxxxx RF
                       Pyr_redox_2   4 vviGgGpAGlaaaltlaqagakvtlve.........legtclnggcllskallgvaedaeias.evvkkl..nqgie 68 
                                       + +G+GpA l aa++la+a++k++l+e          +g +++ ++++++a+ ++ e++ i+  e++k +   ++ie
  gi|330508901|ref|YP_004385329.1|  29 ALVGAGPANLVAAKRLAEANIKTVLFEkrlsvggglWGGGMMFPRIVVQQAAIRILEEYGIRYhEHCKGYyvANSIE 105
                                       579***********************999986566666666666666677777777777666695555541134488 PP

                                       CCHCCTCEEEEESCEEEEETE CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  69 lllgeevvkidpgkkkvklek 89 
                                       ++++ ++ +id g++ v l +
  gi|330508901|ref|YP_004385329.1| 106 TVAKLTARAIDAGAQIVNLVT 126
                                       888877888888887766643 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   1.3     5e-08     9e-05       5     144 ..      31     170 ..      28     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5e-08
                      FAD_oxidored   5 vGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrq..rgga..rlk. 76 
                                       vG+gpa ++AA   a+a  k++L e+r  +GG l +g+++ +      +q++ +i +e+  r ++  +g++  + + 
  gi|330508901|ref|YP_004385329.1|  31 VGAGPANLVAAKRLAEANIKTVLFEKRLSVGGGLWGGGMMFPRIVV--QQAAIRILEEYGIRYHEhcKGYYvaN-Si 104
                                       9******************************999998876655533..57888888888888877655555431.23 PP

                      FAD_oxidored  77 krskw.ntfepevakavleemlaeagvtvllntrlveveke..gkriesvtveskegrktirAkvfiDATg 144
                                       ++ ++ ++   ++ +++++ +  e +v +  + r+v+ + +    ++ ++ v        irA+++iD+Tg
  gi|330508901|ref|YP_004385329.1| 105 ETVAKlTARAIDAGAQIVNLVTVE-DVMIREQDRVVGLVINwtAAEMAQIHV----DPLCIRARYVIDGTG 170
                                       444433478888888888877777.999999999999998732233555555....49************8 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   5.8e-06      0.01       2     117 ..      26     148 ..      25     179 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.8e-06
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS........S--EEEHHHHHHHHHTT-HHHHHHHSEECC CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp........radglnqrtmellrqlGledrilaegapne 70 
                                       ++ + VGaGpa l++a+ L+ea +++vl ekr +             r  +++q  +++l++ G+    + +g+  +
  gi|330508901|ref|YP_004385329.1|  26 VEAALVGAGPANLVAAKRLAEANIKTVLFEKRLSVGGGLwgggmmfpR-IVVQQAAIRILEEYGIRYHEHCKGYYVA 101
                                       78899**************************86654433111111102.3456667777777777666666665444 PP

                                       CCEEEEEEECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHH CS
                     FAD_binding_3  71 lmgealynelsdtpkaradlelesspervtvypqteleriLvehaee 117
                                       ++ e++ +   +  +a a++  + + e+v +  q+++  +++++ ++
  gi|330508901|ref|YP_004385329.1| 102 NSIETVAKLTARAIDAGAQIVNLVTVEDVMIREQDRVVGLVINWTAA 148
                                       44444433323334555555555666666666666666655555555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.0   2.4e-05     0.043       3      37 ..      28      62 ..      26      70 .. 0.88
   2 ?    2.3   0.1     0.031        56      79     141 ..      77     136 ..      75     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                                      EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekakklgr 37
                                       + +G+G+A l aA ++a+++ +++l+ek  ++g 
  gi|330508901|ref|YP_004385329.1| 28 AALVGAGPANLVAAKRLAEANIKTVLFEKRLSVGG 62
                                      678**************************988885 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.031
                                       HHHHHHHHHHTT--EEE-STTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE CS
                       HI0933_like  79 nedlialveelgvelkeedsgrlFpvsdkaedivdallkelkeagvklrletevksvekeedg 141
                                       +++ i+++ee+g++++e+ +g  + v+ ++ + v  l++++ +ag ++    +v++v  +e+ 
  gi|330508901|ref|YP_004385329.1|  77 QQAAIRILEEYGIRYHEHCKG--YYVA-NSIETVAKLTARAIDAGAQIVNLVTVEDVMIREQD 136
                                       578899**********99888..5555.56888888999999999999999999998654443 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 ?   12.6   0.0     3e-05     0.054       6      54 ..      29      78 ..      25      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                       K_oxygenase  6 igiGiGpsnLsLailleevkkelkalflerqpefa...Whpgmllegaelqi 54
                                      + +G+Gp+nL  a +l+e++  +k++ +e++ +++   W  gm+++   +q 
  gi|330508901|ref|YP_004385329.1| 29 ALVGAGPANLVAAKRLAEAN--IKTVLFEKRLSVGgglWGGGMMFPRIVVQQ 78
                                      679**************999..*********9875555********998886 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   3.5e-05     0.062       4      43 ..      30      68 ..      27      78 .. 0.85
   2 ?    2.9   0.4     0.027        48     118     200 ..      88     170 ..      65     202 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
                                      EE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S CS
                     FAD_binding_2  4 ViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqG 43
                                       +G+G A L+AA ++aea+ k+++ ek  ++gg + w +G
  gi|330508901|ref|YP_004385329.1| 30 LVGAGPANLVAAKRLAEANIKTVLFEKRLSVGGGL-WGGG 68
                                      69*************************99987754.5544 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.027
                                       T-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEE.CTTEEEEEEEEET......TTTCE CS
                     FAD_binding_2 118 glsatartlhdaadarretlvtghallarlvesarkagvdfqerteadeLiv.edgrvtGavvenp......esgre 187
                                       g + + +++ + ++a      +  + +a l ++a +ag ++ +   ++++++ e++rv+G v++             
  gi|330508901|ref|YP_004385329.1|  88 GIRYH-EHCKGYYVA------NSIETVAKLTARAIDAGAQIVNLVTVEDVMIrEQDRVVGLVINWTaaemaqI---- 153
                                       45555.566666665......6667788888888888899999999999877345599999988554322221.... PP

                                       E....EEEESEEEE--- CS
                     FAD_binding_2 188 v....rirakavvlatg 200
                                       +     ira+ v++ tg
  gi|330508901|ref|YP_004385329.1| 154 HvdplCIRARYVIDGTG 170
                                       14444666666666555 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00016      0.28       1      42 [.      29      65 ..      29      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvw 42
                                      a+vGaGp+ l +++rL++      +++  lf+++ + g g+ w
  gi|330508901|ref|YP_004385329.1| 29 ALVGAGPANLVAAKRLAEA-----NIKTVLFEKRLSvG-GGLW 65
                                      79***************99.....59999999976636.8888 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00025      0.45       3      31 ..      29      55 ..      27      65 .. 0.86
   2 ?    0.6   0.1      0.13   2.3e+02     126     142 ..     156     171 ..      97     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00025
                     Lycopene_cycl  3 vviGaGpAglslAarlteakpglkvvlie 31
                                      +++GaGpA+l  A+rl  a++++k vl e
  gi|330508901|ref|YP_004385329.1| 29 ALVGAGPANLVAAKRL--AEANIKTVLFE 55
                                      68**************..88888888776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                     Lycopene_cycl 126 ggrkirarlvvdargla 142
                                       +   irar v+d++g  
  gi|330508901|ref|YP_004385329.1| 156 DPLCIRARYVIDGTG-H 171
                                       334799999999999.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1636.43
//
Query:       gi|330508902|ref|YP_004385330.1|  [L=318]
Description: NAD-dependent epimerase/dehydratase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-46  158.2   0.0    2.7e-46  158.0   0.0    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.7e-45  154.2   0.0    8.3e-45  153.6   0.0    1.2  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.6e-18   66.7   0.0      2e-18   66.4   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.7e-18   66.8   0.0    1.3e-17   63.9   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    3.6e-13   49.2   0.0    4.8e-13   48.8   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    3.9e-11   42.6   0.4    1.7e-05   24.1   0.0    2.7  2  NAD_binding_4    Male sterility protein
    1.2e-08   35.0   0.0      2e-08   34.4   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.045   13.3   0.0       0.26   10.8   0.0    2.1  2  NmrA             NmrA-like family
      0.064   13.2   0.3         13    5.7   0.1    2.3  2  KR               KR domain


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.0   0.0   1.3e-49   2.7e-46       1     241 []       8     242 ..       8     242 .. 0.95

  Alignments for each domain:
  == domain 1  score: 158.0 bits;  conditional E-value: 1.3e-49
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE-- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlA 72 
                                       ilVtG++GfiGs+lv++ll    ev++ld+ ss++ + +++       +l ++dl++++ l+++++  + d ++hlA
  gi|330508902|ref|YP_004385330.1|   8 ILVTGGAGFIGSHLVERLLLD-NEVTVLDNFSSGRIEFLEPYRdipdfHLLTGDLMNPKILDNAVS--GKDFIFHLA 81 
                                       8******************76.59*******88877777666699*99******************..99******* PP

                                       S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHH CS
                         Epimerase  73 avggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlag 149
                                       a  +v+  sed    +e+n+  t+nllea+rk++v+++ f s+s+vYG+ a++p+ e+   gpl p s Y+a+Kl  
  gi|330508902|ref|YP_004385330.1|  82 ANPDVKLGSEDTHVHLEQNVLATYNLLEAMRKNDVRQMAFTSTSTVYGEAAQVPTPEDY--GPLLPISLYGASKLSC 156
                                       ****************************************************9977777..8*************** PP

                                       HHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHH CS
                         Epimerase 150 eklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvl 226
                                       e l+ +y ++++++  i r  n++G+r      ++v+  +irk+ e+  ++ +lg+g+++  +l v+D+++a+++++
  gi|330508902|ref|YP_004385330.1| 157 EALISSYCHTFQMQSWIYRFANIVGER----GTHGVLVDFIRKLRENSGKLEILGSGKQRKSYLEVKDCIRAMIHAV 229
                                       ***************************....9999***********8889*************************** PP

                                       HHHTT-STTEEEEES CS
                         Epimerase 227 ehvdagdkgeiyniG 241
                                       eh  +  + +++niG
  gi|330508902|ref|YP_004385330.1| 230 EH--SSGEVNVFNIG 242
                                       **..334567****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 !  153.6   0.0   4.2e-48   8.3e-45       1     324 [.       9     302 ..       9     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: 153.6 bits;  conditional E-value: 4.2e-48
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+l+e+Ll    ev+++++ ss    grie l+        ++++l  gDl + + l+++++    d
  gi|330508902|ref|YP_004385330.1|   9 LVTGGAGFIGSHLVERLLLD-NEVTVLDNFSS----GRIEFLEP--YR-DIPDFHLLTGDLMNPKILDNAVSGK--D 75 
                                       9****************987.78888765544....56766653..22.34789******************99..8 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.S-----SHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.tpfyPrsPY 153
                                        +++LAA   V+   e+ +  +e nvl+t++LLea+r+  ++   ++ ++Sts+vYG++++vp  E+  p+ P s Y
  gi|330508902|ref|YP_004385330.1|  76 FIFHLAANPDVKLGSEDTHVHLEQNVLATYNLLEAMRKNDVR---QMAFTSTSTVYGEAAQVPTPEDyGPLLPISLY 149
                                       9*************************************8875...6888**************988768******** PP

                                       HHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                       +a+Kl+++ ++ +y ++++++  + ++ n  + r g + v   +++++ +  ++  +  +lG ++++++++ vkD +
  gi|330508902|ref|YP_004385330.1| 150 GASKLSCEALISSYCHTFQMQSWIYRFANIVGER-GTHGV---LVDFIRKLRENSGKLEILGSGKQRKSYLEVKDCI 222
                                       ********************************99.56655...677777777777777778**************** PP

                                       HHHHHHHHCSS---..EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkped..yviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdl 305
                                       +am  ++++ + e   ++i++ +++ v e++++ + ++g +          v     + + +  +d +  r g+v+l
  gi|330508902|ref|YP_004385330.1| 223 RAMIHAVEHSSGEVnvFNIGSEDSVDVTEIADIVVGQMGLD---------RV-----EYNYTGGIDGRGWR-GDVKL 284
                                       *******9976655005555555555666666666666553.........22.....22345568988887.79*** PP

                                       --B-THHHHHHH----SS- CS
                     GDP_Man_Dehyd 306 llgdaskakeeLgWkpkvs 324
                                       +l  ++k+k +LgW+p+ +
  gi|330508902|ref|YP_004385330.1| 285 MLLSIEKIK-RLGWSPELG 302
                                       ********9.8****9975 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 !   66.4   0.0     1e-21     2e-18       1     229 [.       9     229 ..       9     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 1e-21
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD..lrespelleelskvnvkkviegDvtdkdkleealegvdvvihlas 75 
                                       +vtGgaGF+G++lv++L+  +   ev vlD     + e le  + +   ++++gD+++ + l++a+ g d ++hla+
  gi|330508902|ref|YP_004385330.1|   9 LVTGGAGFIGSHLVERLLLDN---EVTVLDnfSSGRIEFLEPYRDIPDFHLLTGDLMNPKILDNAVSGKDFIFHLAA 82 
                                       69****************988...6*****43334456677777777777*************************** PP

                         3Beta_HSD  76 lvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKa 151
                                         dv+     +    + nv  T n+lea +k++vr + +tS+  v g+   + ++     e + + l+ + y  sK 
  gi|330508902|ref|YP_004385330.1|  83 NPDVKLgSEDTHVHLEQNVLATYNLLEAMRKNDVRQMAFTSTSTVYGE---AAQVP--TPEDYGPLLPISLYGASKL 154
                                       ***98536666778899*****************************99...56665..3456778899********* PP

                         3Beta_HSD 152 laEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgNvawahi 226
                                         E+l+ +          ++     R a i Ge+ +  +lv ++++l  +  +l  +g+ ++ +++  v     a i
  gi|330508902|ref|YP_004385330.1| 155 SCEALISSYCH-----TFQMQSWIYRFANIVGERGThgVLVDFIRKLRENSGKLEILGSGKQRKSYLEVKDCIRAMI 226
                                       *****988777.....3367777779999999976522688899999998888888999888888888887777777 PP

                         3Beta_HSD 227 lAa 229
                                        A+
  gi|330508902|ref|YP_004385330.1| 227 HAV 229
                                       776 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   6.4e-21   1.3e-17       1     251 [.       8     264 ..       8     285 .. 0.81

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 6.4e-21
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       +lvtG++G iGs+lv+++l  +  ++ +l++      e+ + + +++ +       + + gd+ + + l++a++  +
  gi|330508902|ref|YP_004385330.1|   8 ILVTGGAGFIGSHLVERLLLDN--EVTVLDNFSSGRIEFLEPY-RDIPDF------HLLTGDLMNPKILDNAVS--G 73 
                                       89***************99764..6777887777776666665.344442......3568**************..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGG....GSS...........--SHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDK....Avn...........PtnvmG 139
                                        d++fh AA   V l  e ++  +++Nvl+t n++ea  +++v+++ + St      A++           P++++G
  gi|330508902|ref|YP_004385330.1|  74 KDFIFHLAANPDVKLGSEDTHVHLEQNVLATYNLLEAMRKNDVRQMAFTSTSTvygeAAQvptpedygpllPISLYG 150
                                       **************************************************97522223323344444444489**** PP

                                       HHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGTTS..SHHHHHHHHHTT.SSEEES-TT-EE.EEE-HHHHHHH CS
                   Polysacc_synt_2 140 atKrlaekllqalakeseekktkfvvvRfGNVlgSrGS..viplFkkqikeg.gpvtvTdpemtR.yfmtieeavqL 212
                                       a+K+ +e l+ ++ ++    +++  + Rf N++g rG   v+  F ++++e+ g++ +  +   R  ++ +++ ++ 
  gi|330508902|ref|YP_004385330.1| 151 ASKLSCEALISSYCHTF---QMQSWIYRFANIVGERGThgVLVDFIRKLRENsGKLEILGSGKQRkSYLEVKDCIRA 224
                                       **********9999888...7899999*******99855577777777766559**9987765553789******** PP

                                       HHHHHHH--SS-EEEE--...-EEEHHHHHHHH........ CS
                   Polysacc_synt_2 213 vlqalalakggeifvldmG..epvkivdlakalielsglee 251
                                       +++a++++ +ge+ v ++G  ++v ++++a  ++  +gl+ 
  gi|330508902|ref|YP_004385330.1| 225 MIHAVEHS-SGEVNVFNIGseDSVDVTEIADIVVGQMGLDR 264
                                       ****9986.688889888844699*******9998888754 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 !   48.8   0.0   2.4e-16   4.8e-13       2     235 ..       7     264 ..       6     274 .. 0.84

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 2.4e-16
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE- CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvna 58 
                                        ilvtG+ G +Gs+L+++l  ++ ev+ l++                     + dl +++ ++++++   +d++ ++
  gi|330508902|ref|YP_004385330.1|   7 SILVTGGAGFIGSHLVERLLLDN-EVTVLDNFssgrieflepyrdipdfhllTGDLMNPKILDNAVSG--KDFIFHL 80 
                                       59**************9998766.67777544569*******************************99..899**** PP

                                       -----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TT.S----SSHHHHHHHHHH CS
                     RmlD_sub_bind  59 AAytavDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeed.detsPlnvYGrtKlaGE 133
                                       AA  +v    ++ +   + n+ a+ +l ea ++ ++ ++ + St  V+  +++ p  ed  +  P+++YG++Kl  E
  gi|330508902|ref|YP_004385330.1|  81 AANPDVKLGSEDTHVHLEQNVLATYNLLEAMRKNDVrQMAFTSTSTVYGEAAQVPTPEDyGPLLPISLYGASKLSCE 157
                                       ***********************************945899*******9999998666525789************* PP

                                       HHHHHH-S....SEEEEEE-SEESSSSS-..HHHHHHHHHHH-SEEEEES..S-EE--EEHHHHHHHHHHHHHHCHH CS
                     RmlD_sub_bind 134 qavlaagk....kalivRtswvygekgkn..fvktmlrlakereelkvva..DqlgsPTsardlAevllqllekaae 202
                                         + ++++    + +i R++ + ge+g    +v  + +l +++ +l++     q  s  +++d  +++++++e++  
  gi|330508902|ref|YP_004385330.1| 158 ALISSYCHtfqmQSWIYRFANIVGERGTHgvLVDFIRKLRENSGKLEILGsgKQRKSYLEVKDCIRAMIHAVEHSS- 233
                                       *****7653333789*********97754336777888889999***98622566666677777777777776666. PP

                                       .GGG-EEEE---BS-EEHHHHHHHHHHHHCHTT CS
                     RmlD_sub_bind 203 ekelagvyHlanegetswlefArailkeagads 235
                                             v+ +++e+++   e+A+ ++ ++g d+
  gi|330508902|ref|YP_004385330.1| 234 --GEVNVFNIGSEDSVDVTEIADIVVGQMGLDR 264
                                       ..4788999999999999999999998887765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   3.5e-06     0.007       1      21 [.      10      30 ..      10      36 .. 0.86
   2 !   24.1   0.0   8.6e-09   1.7e-05      84     212 ..      70     185 ..      59     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.5e-06
                                      EE-TTSHHHHHHHHHHHHHS- CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttp 21
                                      +TG+ GF+G++L+e+LL +++
  gi|330508902|ref|YP_004385330.1| 10 VTGGAGFIGSHLVERLLLDNE 30
                                      7****************8875 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 8.6e-09
                                       HHHH--EEEE--SS-S.S...TTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H.... CS
                     NAD_binding_4  84 laeevdviihsaAtvnfd...epykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegek 157
                                        ++  d i+h aA+ +++   e++++ l+ Nv++t ++le  +k     ++ + ST++v+ge  + v          
  gi|330508902|ref|YP_004385330.1|  70 AVSGKDFIFHLAANPDVKlgsEDTHVHLEQNVLATYNLLEAMRKNDVR-QMAFTSTSTVYGEAAQ-V---------- 134
                                       5566799******9776522259999**************99987777.**************94.3.......... PP

                                       ..HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSS CS
                     NAD_binding_4 158 eekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgeskt 212
                                            + e          Y  sK   E l+ ++ +  +++  i+R  +i+ge  t
  gi|330508902|ref|YP_004385330.1| 135 ----PTPEDYGPLLPISLYGASKLSCEALISSYCHTFQMQSWIYRFANIVGERGT 185
                                       ....44455555555669****************999999**********97655 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 !   34.4   0.0     1e-11     2e-08       1     107 [.      12     133 ..      12     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1e-11
                                       TTTSHHHHHHHHHHHHC-T-EEEEEET.THHHCHHHH...CTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvR.npeklaele...aeeglevvegdvtdvedlaealkgadaVvsalggggk 73 
                                       G+ G +G++lv++ll ++  evt+l   ++ +++ le   + +  ++++gd+++++ l +a++g d ++  +++ + 
  gi|330508902|ref|YP_004385330.1|  12 GGAGFIGSHLVERLLLDN--EVTVLDNfSSGRIEFLEpyrDIPDFHLLTGDLMNPKILDNAVSGKDFIFHLAANPDV 86 
                                       99***************6..88877431366777666554779*************************999966666 PP

                                       .....HHHH........HHHHHHHHHHCT--EEEEEEETTTTSGCGC CS
                    NAD_binding_10  74 .....deeg........aknivdaakeagvkRfvlvsaigvgdevpg 107
                                            d+++        + n+++a+++++v+++ + s+  v+ e+++
  gi|330508902|ref|YP_004385330.1|  87 klgseDTHVhleqnvlaTYNLLEAMRKNDVRQMAFTSTSTVYGEAAQ 133
                                       66654222266667799************************986544 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013      0.26       1      73 [.       8      82 ..       8     125 .. 0.79
   2 ?   -0.4   0.0      0.34   6.8e+02     158     226 ..     194     261 ..     185     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                      EEESSTTSHHHHHHHHHHHH.HT-EEEEEES-S-SHHHHHHHHSTTEEE.ES-TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA  1 IlviGaTGrqGksvvrallk.aghkvralvRdtkselakslkeaGvelv.kgdlddkeslvealkgvdvvfsvtg 73
                                      Ilv+G++G +G+++v+ ll  ++ +v       + e ++   + +   +  gdl + ++l++a++g d +f   +
  gi|330508902|ref|YP_004385330.1|  8 ILVTGGAGFIGSHLVERLLLdNEVTVLDNFSSGRIEFLEPYRDIPDFHLlTGDLMNPKILDNAVSGKDFIFHLAA 82
                                      89*************88775144444444445577888888999976555******************9998765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.34
                                       EEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHT CS
                              NmrA 158 gdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkig 226
                                        +++++  k+++lg g+    +l +++D  +++i+++++ +   ++    +++ + ++ei+++   ++g
  gi|330508902|ref|YP_004385330.1| 194 RKLRENSGKLEILGSGKQRKSYL-EVKDCIRAMIHAVEHSSGEVNVFNIGSEDSVDVTEIADIVVGQMG 261
                                       55566667999999999888888.999999999999999776655555577888888888888777766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0064        13       3      21 ..       8      26 ..       7      34 .. 0.85
   2 ?    5.2   0.0    0.0091        18     100     147 ..      88     134 ..      77     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0064
                                      EEEETTTSHHHHHHHHHHH CS
                                KR  3 ylitGGlGgLGlelarwla 21
                                       l+tGG+G +G +l++ l+
  gi|330508902|ref|YP_004385330.1|  8 ILVTGGAGFIGSHLVERLL 26
                                      69************99886 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0091
                                       --HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-H CS
                                KR 100 mtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqa 147
                                       + +ed +  l+  v ++ nL e+++++++  +  f+S ++++g+a q+
  gi|330508902|ref|YP_004385330.1|  88 LGSEDTHVHLEQNVLATYNLLEAMRKNDVRQM-AFTSTSTVYGEAAQV 134
                                       567788888999999***********999987.68899*****99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1983.34
//
Query:       gi|330508903|ref|YP_004385331.1|  [L=342]
Description: rhodanese domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.6e-21   75.1   0.0    6.3e-15   55.6   0.0    2.2  2  Rhodanese  Rhodanese-like domain
  ------ inclusion threshold ------
      0.093   12.7   0.0        1.5    8.9   0.0    2.8  4  Dicty_CAD  Cell-cell adhesion domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   7.1e-19   6.3e-15       8     103 ..     110     203 ..     106     207 .. 0.89
   2 !   17.3   0.0   5.6e-07     0.005       2     101 ..     235     330 ..     234     333 .. 0.74

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 7.1e-19
                         Rhodanese   8 llekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel.gidnkktvvvycdgggr.aaaa 82 
                                       l+e+++ ++lDvR++++Y++ghIpgA+n+   + ++ +k+   +  l +e+l + gi   +++ +y+d++++ a ++
  gi|330508903|ref|YP_004385331.1| 110 LIENDR-IVLDVRSAQKYQEGHIPGARNL---YWKDLQKDGVLDPILAQEALGQaGIIASDRLLIYGDSSDHgAPFV 182
                                       445666.5*********************...88888999999999999999999*****************99999 PP

                         Rhodanese  83 aallkklGyknvsvldGGfka 103
                                        ++l +lG++++s+ldGG++a
  gi|330508903|ref|YP_004385331.1| 183 FWALSYLGHEDISLLDGGIDA 203
                                       99******666********97 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.6e-07
                         Rhodanese   2 akelkellekgkvallDvRppeeYekghI.pgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdggg 77 
                                       ++ l  ll+  ++ +lD+R++ eY k +I ++A  +s d+++  k s  +++ ++e+l    +d+  t vvy+    
  gi|330508903|ref|YP_004385331.1| 235 PESLDGLLGLSDISILDARDFSEYGKNRItNEAMPLSLDRIY--KDSGIKDASILEDLFGSRLDESGTAVVYGTP-- 307
                                       67777888888888***************8889999333333..334445555556666668899*******943.. PP

                         Rhodanese  78 raaaaaallkklGyknvsvldGGf 101
                                        a ++   l+ +G +n  +l+G +
  gi|330508903|ref|YP_004385331.1| 308 EAYSLFFSLRLMG-YNATLLEGDW 330
                                       3468888888899.7999999977 PP

>> Dicty_CAD  Cell-cell adhesion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.24   2.1e+03      43      65 ..      82     104 ..      78     118 .. 0.69
   2 ?   -1.3   0.0      0.25   2.3e+03      17      28 ..     213     224 ..     207     228 .. 0.80
   3 ?   -3.0   0.0      0.86   7.7e+03       4      21 ..     257     274 ..     255     276 .. 0.75
   4 ?    8.9   0.0   0.00016       1.5      11      50 ..     298     340 ..     293     342 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.24
                         Dicty_CAD  43 neefeiksgkvefdGeeydipes 65 
                                       n + + +s  +e +  +y++++ 
  gi|330508903|ref|YP_004385331.1|  82 NSQAQAESNTIEDKSADYPVASI 104
                                       55667778888888888888764 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.25
                         Dicty_CAD  17 lPaPrifPppyf 28 
                                       + aP i+P+ y+
  gi|330508903|ref|YP_004385331.1| 213 ANAPSITPTNYT 224
                                       568******997 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.86
                         Dicty_CAD   4 edGestisGkaitlPaPr 21 
                                       e G+ +i+ +a++l   r
  gi|330508903|ref|YP_004385331.1| 257 EYGKNRITNEAMPLSLDR 274
                                       789999999999876555 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.00016
                         Dicty_CAD  11 sGkaitlPaPrifPppyfirfleYkt...eGklwdneefeiks 50 
                                       sG a+ + +P  +   + +r+++Y+    eG+ w++ ++++  
  gi|330508903|ref|YP_004385331.1| 298 SGTAVVYGTPEAYSLFFSLRLMGYNAtllEGDWWKETRWAVSN 340
                                       899*********************954559******9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2618.28
//
Query:       gi|330508904|ref|YP_004385332.1|  [L=260]
Description: fructose bisphosphate aldolase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-60  205.3   0.2    1.2e-60  205.1   0.2    1.0  1  DeoC       DeoC/LacD family aldolase
     0.0066   16.1   0.0      0.019   14.6   0.0    1.7  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil
  ------ inclusion threshold ------
      0.011   15.1   0.0       0.92    8.8   0.0    2.5  2  TMP-TENI   Thiamine monophosphate synthase
      0.077   12.4   7.2        1.2    8.4   0.2    2.5  2  NMO        Nitronate monooxygenase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.1   0.2   2.7e-64   1.2e-60       2     235 .]      13     228 ..      12     228 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.1 bits;  conditional E-value: 2.7e-64
                                       EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTE CS
                              DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqr 78 
                                       vi+++D++v  ++++++      + +k+++++++++ga+a ++++g +  ++++y++d +l+++l+++t l ++++ 
  gi|330508904|ref|YP_004385332.1|  13 VIIPMDHGVTVGPIKGI------KSVKNIADAVARGGADAAVVHKGAATFGHRGYGRDLGLIIHLSASTALGPDPNN 83 
                                       89***************......8***************************************************** PP

                                       EEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHH CS
                              DeoC  79 dvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvae 155
                                       +v+ va+veea++ GAdav+++v++   g+e+e ++l  +++++  c+e+g+pl++++y+r+ +ikde+ +++ +a+
  gi|330508904|ref|YP_004385332.1|  84 KVL-VATVEEALKIGADAVSIHVNV---GAEDESRMLSTLGEISRHCQEWGMPLLAMMYPRGRKIKDEY-SAESIAH 155
                                       ***.*********************...*****************************************.******* PP

                                       HHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEES CS
                              DeoC 156 AarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvlsG 229
                                       Aarv+aelGaDi+K+++         +d ++f  v++++pvp vv++GG+   +e d+l++ve A+ ++ga Gv++G
  gi|330508904|ref|YP_004385332.1| 156 AARVGAELGADIVKTNYS--------GDPDSFASVVDSCPVP-VVIAGGPkveTELDLLRMVEGAI-ASGARGVAIG 222
                                       ******************........****************.********99999**********.********** PP

                                       HHHHTT CS
                              DeoC 230 Raifqk 235
                                       R++fq+
  gi|330508904|ref|YP_004385332.1| 223 RNVFQH 228
                                       ****97 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.2e-06     0.019      81     224 ..      12     237 ..       5     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.2e-06
                                       HHHHTTESEEEEEGTGHHHHHHHHHHHHHHTT............................................. CS
                         OMPdecase  81 arikewadivtvhavaGkasvkalaeaaekwg............................................. 112
                                       a i+   + vtv +  G +svk +a+a ++ g                                             
  gi|330508904|ref|YP_004385332.1|  12 AVIIPMDHGVTVGPIKGIKSVKNIADAVARGGadaavvhkgaatfghrgygrdlgliihlsastalgpdpnnkvlva 88 
                                       55666668899999999999999999998888999999999999999999999999999999999999999999999 PP

                                       .......................................S.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHT CS
                         OMPdecase 113 .......................................nrgllilaqmsskgnlmlqekgytqacveaarehkaed 150
                                                                              + g+ +la+m   g     e  y  + + +a++  ae 
  gi|330508904|ref|YP_004385332.1|  89 tveealkigadavsihvnvgaedesrmlstlgeisrhcqEWGMPLLAMMYPRGRKIKDE--YSAESIAHAARVGAE- 162
                                       999999999999999999999999999999999999999999************99999..999999999999977. PP

                                       TESEEECCCHTHHHHHHTTCSCEEEHHHTT.......EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHH CS
                         OMPdecase 151 fvmGfvaqetlnateedaddfihltpgigl.......eqggdgkgqqyntpekligiagadiiivGRgIlkagdpve 220
                                          G+   +t    + d d f  ++  + +        + ++ +++ + ++e++i  +ga  + +GR +++ +dp+ 
  gi|330508904|ref|YP_004385332.1| 163 --LGADIVKTNY--SGDPDSFASVVDSCPVpvviaggPKVETELDLLR-MVEGAIA-SGARGVAIGRNVFQHQDPEL 233
                                       ..6776666633..455679********99888777666677777775.5777766.79****************97 PP

                                       HHHH CS
                         OMPdecase 221 eaer 224
                                        ++r
  gi|330508904|ref|YP_004385332.1| 234 ITRR 237
                                       7766 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00021      0.92      11      61 ..      82     134 ..      74     136 .. 0.88
   2 ?    3.7   0.1    0.0074        33     139     179 ..     176     223 ..     149     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00021
                          TMP-TENI  11 kneellevveealkggvtlvqlRek..eldarellelaeklaalcrkygvpli 61 
                                       +n+ l+++veealk g+++v +       d++++l    ++ + c++ g+pl+
  gi|330508904|ref|YP_004385332.1|  82 NNKVLVATVEEALKIGADAVSIHVNvgAEDESRMLSTLGEISRHCQEWGMPLL 134
                                       57789***********999999888767899****************999986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0074
                          TMP-TENI 139 leglkelaealeiPvvaiGGitlenvaevl.......eagadgvavvs 179
                                        + ++ +++++ +Pvv  GG + e+  ++l       ++ga+gva+ +
  gi|330508904|ref|YP_004385332.1| 176 PDSFASVVDSCPVPVVIAGGPKVETELDLLrmvegaiASGARGVAIGR 223
                                       567788999999********9988766666677777799999999866 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.1   0.00096       4.3     137     173 ..      23      64 ..       5     104 .. 0.72
   2 ?    8.4   0.2   0.00027       1.2     186     223 ..     180     223 ..     152     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00096
                               NMO 137 vvliptissvkearkvearG.aDaliv.qGpeaGGhqG...t 173
                                       v  i  i svk++  + arG aDa +v +G +  Gh+G   +
  gi|330508904|ref|YP_004385332.1|  23 VGPIKGIKSVKNIADAVARGgADAAVVhKGAATFGHRGygrD 64 
                                       44567899****8877777669*8766379999*****5440 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00027
                               NMO 186 pqvldavdiPviAaGG......iidrrgvaaaLalGAsgvqigt 223
                                       ++v+d   +Pv+ aGG      +   r v+ a+a GA gv+ig 
  gi|330508904|ref|YP_004385332.1| 180 ASVVDSCPVPVVIAGGpkveteLDLLRMVEGAIASGARGVAIGR 223
                                       56777777********443332223467899***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1984.81
//
Query:       gi|330508905|ref|YP_004385333.1|  [L=360]
Description: hypothetical protein MCON_3233 [Methanosaeta concilii GP6]
Scores for complete 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   0.0       0.58   10.4   0.0    3.1  2  CARDB            CARDB
     0.0049   17.1   0.0        1.7    9.0   0.0    2.9  2  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
  ------ inclusion threshold ------
       0.02   15.2   0.1        1.5    9.1   0.0    2.4  2  DUF11            Domain of unknown function DUF11
       0.28   11.6   1.0       0.49   10.8   0.1    1.7  2  FeoB_associated  FeoB-associated Cys-rich membrane protein


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 !    5.0   0.0    0.0066        29       2      74 ..      42     133 ..      41     144 .. 0.61
   2 !   10.4   0.0   0.00013      0.58      12      72 ..     191     262 ..     183     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0066
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE....................SEE- CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv....................psLa 58 
                                       pDL +  ++  + + ++  +t++v ++N+ ta++++ + +  ld + ++   +                     sL 
  gi|330508905|ref|YP_004385333.1|  42 PDLDI--SSVYGRLDTNGPSTLYVLLHNNATAQATERQESQELDLDPAKARGItaelvsddervrvlsgpqmaGSLG 116
                                       66666..5556666666666666666666666665555554444444433333334455555556666677779999 PP

                                       CTEEEEEEEEEE-S.-S CS
                             CARDB  59 agesttvsftwtte.at 74 
                                       +ge+ttv+f   +e a+
  gi|330508905|ref|YP_004385333.1| 117 PGENTTVEFMALAEgAE 133
                                       99999999988777554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00013
                                       -SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE..EEEEE.........SEE-CTEEEEEEEEEE-S CS
                             CARDB  12 pseafvgeentitvtvkNqGtaasgatkvalyldgelv..gtvtv.........psLaagesttvsftwtte 72 
                                       +++a +ge+ +++v v+N+G++a+ + +++  ++      g+  v         + L+ag++++ ++ + te
  gi|330508905|ref|YP_004385333.1| 191 EGAARPGEATELEVVVANEGDEAAIDLRLEARANSPFLraGDELVnesdekqnyKDLEAGSEASFELMVLTE 262
                                       678899*************************99999888766666888888888888888888888777776 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 !    4.8   0.0    0.0076        34      41      79 .]     109     146 ..     102     146 .. 0.83
   2 !    9.0   0.0   0.00037       1.7       2      67 ..     195     267 ..     194     279 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0076
                       NPCBM_assoc  41 pasaaslapGetveatvkVtppagaaaGdyevtakarlt 79 
                                       p+ a sl pGe ++++++    +ga+ G y+ +++++++
  gi|330508905|ref|YP_004385333.1| 109 PQMAGSLGPGENTTVEFM-ALAEGAEVGIYPARLRLSYS 146
                                       555669**********95.78899*********999985 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00037
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslsl..P...eGWt.vvevspasaa.slapGetveatvkVtppagaaa 67 
                                       +pGe ++l+++v+n+g++aa +++l++++  P   +G + v e++ ++   +l++G +++++++V    ++  
  gi|330508905|ref|YP_004385333.1| 195 RPGEATELEVVVANEGDEAAIDLRLEARAnsPflrAGDElVNESDEKQNYkDLEAGSEASFELMVLTEGNTTS 267
                                       79*********************99988744533344445555555444346666666666666655555555 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.02        89      36      79 ..      82     130 ..      52     136 .. 0.63
   2 ?    9.1   0.0   0.00034       1.5       9      81 ..     193     264 ..     181     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.02
                             DUF11  36 tDtlPaglayvsvsasqgtasaltsv.......gsLeagesatlsftvrvt 79 
                                        D+ Pa  +++++   +   +++  v       gsL +ge +t++f + + 
  gi|330508905|ref|YP_004385333.1|  82 LDLDPAKARGITAELVSDDERVR--VlsgpqmaGSLGPGENTTVEFMALAE 130
                                       45557777777666662222233..233667789***********998876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00034
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtl..P...aglayvsvsasqgtasaltsvgsLeagesatlsftvrvtr 80 
                                       ++rpG++++  ++v N g  +a +++++     P   ag ++v  s        +++ ++Leag++a +++ v    
  gi|330508905|ref|YP_004385333.1| 193 AARPGEATELEVVVANEGDEAAIDLRLEARAnsPflrAGDELVNESDE------KQNYKDLEAGSEASFELMVLTEG 263
                                       79********************99999987754466688888888888......33337999999988877766555 PP

                             DUF11  81 t 81 
                                        
  gi|330508905|ref|YP_004385333.1| 264 N 264
                                       4 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 ?   -2.4   0.1       1.5   6.6e+03       4      13 ..      17      26 ..      13      37 .. 0.52
   2 ?   10.8   0.1   0.00011      0.49       5      27 ..     322     344 ..     321     347 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.5
                   FeoB_associated  4 IVgliiaaav 13
                                      I  l ++aav
  gi|330508905|ref|YP_004385333.1| 17 ILFLFLLAAV 26
                                      2222233333 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                   FeoB_associated   5 VgliiaaavafvirrlikkkkkG 27 
                                       +++i+++a+a++ ++++k+  +G
  gi|330508905|ref|YP_004385333.1| 322 ILIILILAAAYIYFKNFKRNGSG 344
                                       7889999***********98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 2857.58
//
Query:       gi|330508906|ref|YP_004385334.1|  [L=436]
Description: amino acid permease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-46  158.0  47.6    4.1e-46  157.7  47.6    1.0  1  AA_permease_2   Amino acid permease
    5.5e-29  101.1  52.4    1.6e-28   99.5  52.3    1.6  1  AA_permease     Amino acid permease
    1.4e-11   43.8  18.0    1.4e-11   43.8  18.0    2.3  2  Spore_permease  Spore germination protein
  ------ inclusion threshold ------
       0.26   10.3   1.8       0.67    9.0   1.8    1.7  1  TMEM237         Transmembrane protein 237


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 !  157.7  47.6   9.3e-50   4.1e-46       1     400 [.      11     398 ..      11     409 .. 0.90

  Alignments for each domain:
  == domain 1  score: 157.7 bits;  conditional E-value: 9.3e-50
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       l+ll +++  +g+++g+gi++    +a+ +g a+++++ +++li  l  +l yaEl+s++p+   +y yt++afg +
  gi|330508906|ref|YP_004385334.1|  11 LGLLEVTISGVGIILGAGIYALIgeAAGLAGNAVWISFALSALIA-LLTGLSYAELASMFPKAAAEYEYTSQAFGGF 86 
                                       789999**************998888888***************9.89***************************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilki 152
                                       +afl++w+  f+ v+++a+++  +a+y++ ++g        +++  aia+l+++ l+ ++gi +s +++ +l+++  
  gi|330508906|ref|YP_004385334.1|  87 LAFLVGWMIIFSGVVGAATVSLGFAGYFQALTGT-------PILPSAIALLAVLSLVLLFGITHSTRLAIVLTTVEA 156
                                       ******************************9862.......466678999*************************** PP

                     AA_permease_2 153 llpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigl 227
                                       l  l+++i  g+ ++  g  +        + p g+ g+l + + ++++f+Gfe ++  see+k    ++p+++++++
  gi|330508906|ref|YP_004385334.1| 157 L-GLVLVIYMGIPYL--GSVD-----LLEMSPLGSAGILQASALIFFAFIGFEEIVKLSEEAKDpeINIPRGLVLAI 225
                                       5.7788998999998..3333.....446788899999999999*****************887646********** PP

                     AA_permease_2 228 livlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealar 304
                                       + +++ly+lv+i+++ v++++e++ +s    +++  ++ + g+ +++i++i++ ++    ++  +++ssr+++ +a 
  gi|330508906|ref|YP_004385334.1| 226 SASIILYILVAISAVSVLGWEELSCSSA---PFSDIARYALGPNASAIISIMALFATTNTVLLMLLASSRIIYGMAS 299
                                       ***********************98776...56666666667*********************************** PP

                     AA_permease_2 305 dgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlk 380
                                        g lP  +a+v+ ++++p+ a+il++i+++ ++  fl    +++ f+++v ++ +++ ++++ + ++ lr+k+p+  
  gi|330508906|ref|YP_004385334.1| 300 SGSLPPILASVHpRTHAPWIATILSMIIAMSFV--FL----EDIAFVANVNNFTVFVTFIVINAVLISLRYKKPQIA 370
                                       ****************************96654..53....689********************************9 PP

                     AA_permease_2 381 rpgk........ilvaiigalfllfllv 400
                                       rp +        +++  +g+lf+l++l+
  gi|330508906|ref|YP_004385334.1| 371 RPFRvpislgklAVLPVLGILFNLLMLI 398
                                       9776455555555666777888888776 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.5  52.3   3.6e-32   1.6e-28       4     429 ..      18     398 ..      15     410 .. 0.85

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 3.6e-32
                       AA_permease   4 vialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGl 80 
                                       +  +g + G+g++  +g +++ aG  +++++++l+ ++ +l++ls +e+a+++pk+++ y y s+  g  l+f +G+
  gi|330508906|ref|YP_004385334.1|  18 ISGVGIILGAGIYALIGEAAGLAGN-AVWISFALSALIALLTGLSYAELASMFPKAAAEYEYTSQAFGGFLAFLVGW 93 
                                       5567778888888888888888888.88************************************************* PP

                       AA_permease  81 nylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivg 157
                                       +  fs+++++a    + + ++q +   t  p +   ++ +l+vl+++ l+g+  + +  ++l+ +  + ++ +i +g
  gi|330508906|ref|YP_004385334.1|  94 MIIFSGVVGAATVSLGFAGYFQAL---TGTP-ILPSAIALLAVLSLVLLFGITHSTRLAIVLTTVEALGLVLVIYMG 166
                                       *99999999888866666666666...4444.3334667889999999*********9999**********999999 PP

                       AA_permease 158 iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPk 234
                                       i +l + ++ +                  p g         ++++ + + ++faf G+e ++ +++E+kdPe +iP+
  gi|330508906|ref|YP_004385334.1| 167 IPYLGSVDLLEM----------------SPLG--------SAGILQASALIFFAFIGFEEIVKLSEEAKDPEINIPR 219
                                       544444444444................2333........468********************************** PP

                       AA_permease 235 ailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysa 311
                                       +   ++   +i+Y+l+++++++++++  l+  +       pf  + +++  + ++ +i ++ l a++++++ +l ++
  gi|330508906|ref|YP_004385334.1| 220 GLVLAISASIILYILVAISAVSVLGWEELSCSS------APFSDIARYALGPNASAIISIMALFATTNTVLLMLLAS 290
                                       ****************************88887......49************************************ PP

                       AA_permease 312 sRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsy 387
                                       sR++y +a +g +P   ++++ + + P+ a +lsmii++ +++l+ +        +f+ +++ +  ++++++i++ +
  gi|330508906|ref|YP_004385334.1| 291 SRIIYGMASSGSLPpILASVHPRTHAPWIATILSMIIAMSFVFLEDI--------AFVANVNNFTVFVTFIVINAVL 359
                                       **************8999999*********************55554........5669****************** PP

                       AA_permease 388 lrfRkalkyqgrsieelgfkaallplgvilvlaaliiillil 429
                                       + +R +   +   ++ +++ + l+ l v  vl +l  +l++ 
  gi|330508906|ref|YP_004385334.1| 360 ISLRYK---KPQIARPFRVPISLGKLAVLPVLGILFNLLMLI 398
                                       *99888...445566778888887777777666666665554 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8  18.0   3.1e-15   1.4e-11      12     249 ..      21     258 ..      10     302 .. 0.82
   2 ?    1.8   4.7      0.02        87     110     165 ..     314     368 ..     306     383 .. 0.70

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 3.1e-15
                    Spore_permease  12 vsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpektl.iellkkilgkwLGsllsilfil 87 
                                       v ++lG+gi  l + +a  a+   Wis  l ++i+l+  l + +l + fp+    +e+ ++ +g +L++l + ++i 
  gi|330508906|ref|YP_004385334.1|  21 VGIILGAGIYALIGEAAGLAGNAVWISFALSALIALLTGLSYAELASMFPKAAAeYEYTSQAFGGFLAFLVGWMIIF 97 
                                       7899****************99****************************986549**************9988877 PP

                    Spore_permease  88 yFlllaafelRefseliqvflledtplwiiilllllvilYlvvkGieslareflfiivilliilllil...lfslkl 161
                                         ++ aa++   f+    + +l+ tp+    + ll+v  +++  Gi+  +r+ ++++++  + l+l++   +  l++
  gi|330508906|ref|YP_004385334.1|  98 SGVVGAATVSLGFAGY--FQALTGTPILPSAIALLAVLSLVLLFGITHSTRLAIVLTTVEALGLVLVIymgIPYLGS 172
                                       7777777777777765..55799******9*********************65555555444443333111456778 PP

                    Spore_permease 162 aeiknlrPvlgngikpvlkslkttslsflgveillllvpflkdkk.kvkkaallgvlistllyllttlivilvlsve 237
                                       +++  + P+   g   +l+++  + ++f+g+e ++ l +  kd++ ++ + ++l++  s++ly+l+ + +++vl+ e
  gi|330508906|ref|YP_004385334.1| 173 VDLLEMSPLGSAG---ILQASALIFFAFIGFEEIVKLSEEAKDPEiNIPRGLVLAISASIILYILVAISAVSVLGWE 246
                                       8888888887777...5899***********************985789**************************** PP

                    Spore_permease 238 qlkkatwptlsl 249
                                       +l+ +  p+ ++
  gi|330508906|ref|YP_004385334.1| 247 ELSCSSAPFSDI 258
                                       *99887776555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.02
                    Spore_permease 110 edtplwiiilllllvilYlvvkGieslareflfiivilliilllillfslklaeik 165
                                       ++ p ++ il +++ + ++  + i  +a  +  ++v++++i++  +l+sl++ +++
  gi|330508906|ref|YP_004385334.1| 314 THAPWIATILSMIIAMSFVFLEDIAFVAN-VNNFTVFVTFIVINAVLISLRYKKPQ 368
                                       46778888899999999999999999995.44444444444455555566665555 PP

>> TMEM237  Transmembrane protein 237
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.8   0.00015      0.67     133     175 ..     222     264 ..     221     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00015
                           TMEM237 133 vlayPaqslfYlllalstvsalDrldLakastalrklitldng 175
                                       vla  a++++Y+l+a+s vs+l+  +L+  s  +  ++++  g
  gi|330508906|ref|YP_004385334.1| 222 VLAISASIILYILVAISAVSVLGWEELSCSSAPFSDIARYALG 264
                                       68999******************99998888777666666533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2911.65
//
Query:       gi|330508907|ref|YP_004385335.1|  [L=347]
Description: YihY family protein [Methanosaeta concilii GP6]
Scores for complete 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  163.0  19.8    1.4e-46  159.2  19.8    2.0  1  Virul_fac_BrkB  Virulence factor BrkB
  ------ inclusion threshold ------
      0.013   16.1   0.4      0.013   16.1   0.4    2.9  4  Nucleos_tra2_N  Na+ dependent nucleoside transporter N-termin
        4.6    7.2   7.0         13    5.7   7.0    1.8  1  PetG            Cytochrome B6-F complex subunit 5


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 !  159.2  19.8   2.3e-50   1.4e-46       4     254 ..      47     323 ..      44     327 .. 0.81

  Alignments for each domain:
  == domain 1  score: 159.2 bits;  conditional E-value: 2.3e-50
                    Virul_fac_BrkB   4 dlsllAaalayytllSlfPlllvllavlgl.lglddelqeqlldllaev.........................lpe 54 
                                       + ++ Aaa+ayy+l+SlfP+l++l+ + +  l+ ++e  +ql++++ ++                         lp 
  gi|330508907|ref|YP_004385335.1|  47 ESWDAAAAIAYYSLFSLFPMLILLVILGTSfLQ-TKENYHQLMNFIGGIlppaeslareniqviqdlgdklnmhLP- 121
                                       56789***********************66365.89999******9999766666666666666666666665555. PP

                    Virul_fac_BrkB  55 gaaevvedilqrllnqa.slgllglavllwsasggvsalrralnkiygveesrsflrkrllsllllllllvllllsl 130
                                          ++++++++++l+ +  +g+ + a+llwsa+g++  l + +++++   e+r+ l  rl+ ++++  ll+ l++  
  gi|330508907|ref|YP_004385335.1| 122 -LKDLLQENVNQILHLRlPVGIAAGAGLLWSATGVFVILSKNIDRAWSNSEGRNPLEWRLVGIAMVGSLLIGLIILS 197
                                       .679999999989988899******************************9999999888888888854444444444 PP

                    Virul_fac_BrkB 131 vlsvflqslllasa..pllglglelsellllqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwll 205
                                       +++v l  ll +s+   l + g  + +l   +ll  l++ +++++af++lY+++p+v  r+++a+ Ga++a+l+w+l
  gi|330508907|ref|YP_004385335.1| 198 MVVVSLIGLLDFSLglLLGEGGVYHMPL-ESKLLYRLFPDVVIFIAFTILYWWAPKVDIRWSDAAFGAFVATLCWEL 273
                                       4444444445655566333334444444.367777778888************************************ PP

                    Virul_fac_BrkB 206 vkilfslylsnfa.synaiYGslgaliilllWlylsalilLlGaelnael 254
                                        k +f++yl++   +   +YGslg+++il+lW+yls+li L+Ga l a++
  gi|330508907|ref|YP_004385335.1| 274 SKMGFAWYLESGLsNHMLVYGSLGTVVILMLWIYLSGLICLFGAHLVAQM 323
                                       *********99774559*****************************9986 PP

>> Nucleos_tra2_N  Na+ dependent nucleoside transporter N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.4   1.4e+04      29      41 ..      67      79 ..      63      89 .. 0.60
   2 ?   16.1   0.4   2.2e-06     0.013      10      43 ..     166     199 ..     154     212 .. 0.91
   3 ?   -0.6   0.3      0.36   2.2e+03      33      60 ..     239     266 ..     237     270 .. 0.79
   4 ?   -4.3   0.8         3   1.8e+04       1      14 [.     296     309 ..     296     311 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.4
                                      HHHHHHHHHHHHT CS
                    Nucleos_tra2_N 29 lllQfvlAlfvlk 41
                                      l+l ++l+  +l+
  gi|330508907|ref|YP_004385335.1| 67 LILLVILGTSFLQ 79
                                      4444444444444 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.2e-06
                                       HHHT-S-GGG--HHHHHHHHHHHHHHHHHHHTSH CS
                    Nucleos_tra2_N  10 awllSenrkainwrtVigglllQfvlAlfvlktp 43 
                                       aw  Se r+   wr+V+++++  ++++l++l + 
  gi|330508907|ref|YP_004385335.1| 166 AWSNSEGRNPLEWRLVGIAMVGSLLIGLIILSMV 199
                                       89****************************9865 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.36
                                       HHHHHHHHTSHHHHHHHHHHHHHHHHHH CS
                    Nucleos_tra2_N  33 fvlAlfvlktpagrdvfkalsdlvqall 60 
                                       +++A+ +l++ a++  +++   ++ a++
  gi|330508907|ref|YP_004385335.1| 239 IFIAFTILYWWAPKVDIRWSDAAFGAFV 266
                                       6899999999998888888777777665 PP

  == domain 4  score: -4.3 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHT- CS
                    Nucleos_tra2_N   1 lGllvllliawllS 14 
                                       lG +v+l++ + lS
  gi|330508907|ref|YP_004385335.1| 296 LGTVVILMLWIYLS 309
                                       57777777766665 PP

>> PetG  Cytochrome B6-F complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   7.0    0.0022        13       1      22 [.     185     207 ..     185     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0022
                              PetG   1 MvEpLLlG.iVLGLvpVTlaGLF 22 
                                       Mv  LL+G i+L +v+V+l+GL+
  gi|330508907|ref|YP_004385335.1| 185 MVGSLLIGlIILSMVVVSLIGLL 207
                                       999*****668**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2443.70
//
Query:       gi|330508908|ref|YP_004385336.1|  [L=408]
Description: hypothetical protein MCON_3236 [Methanosaeta concilii GP6]
Scores for 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-49  166.5  35.4    1.3e-48  165.8  35.4    1.2  1  AI-2E_transport  AI-2E family transporter
  ------ inclusion threshold ------
        1.5    9.3   3.0        1.1    9.8   0.4    2.1  2  Sperm_Ag_HE2     Sperm antigen HE2


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 !  165.8  35.4   1.5e-52   1.3e-48       4     324 ..      13     357 ..       7     359 .. 0.85

  Alignments for each domain:
  == domain 1  score: 165.8 bits;  conditional E-value: 1.5e-52
                   AI-2E_transport   4 ilvllllllalypfis...elllplliAlvlayllnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvpllia 77 
                                         +l++++  +    +    ++ pll+++++a++l pv+ ++     ++ l++++ lll+++++++++ + ++ +++
  gi|330508908|ref|YP_004385336.1|  13 AVLLIVFISTV----YvtkAFIAPLLLSFFFAFVLLPVYSRIYCLTGRKNLSAFMSLLLVVLFFMIFLSSALNAIAT 85 
                                       23344444444....34456**********************88888888888888888888889999999999999 PP

                   AI-2E_transport  78 qltqlvkslp...............ayidslqnilnelpslleelen....................liqalkqsls 119
                                        ++ l++s +                ++d l                                    +   ++  ++
  gi|330508908|ref|YP_004385336.1|  86 ETSGLFSSQEdivqsidiyitqkteESFDTLHV-------------VlnnlvsestadetverlremVRPFIEAPRD 149
                                       999999999967777777666655533333333.............1333333344445467777875566666677 PP

                   AI-2E_transport 120 kilsnilssi....lnsllsllasllglilslvlvllllffllldgeklrqgilkllpervrervkailrelektls 192
                                       +ils++l++i    +n +++++++l+ l+ ++++ ++++++ll  g   ++g+l +lper  e ++ ++ el+k++ 
  gi|330508908|ref|YP_004385336.1| 150 RILSDLLPQIafeaTNLATGFISELPVLMSQFFVAIMITYYLLIGGSSAVKGFLLILPER--ELMNYFMGELNKIYN 224
                                       77777777777777*********************************************9..*************** PP

                   AI-2E_transport 193 gylrgqvlvaliigvlvfigllilgvpyalllailvglanliPyiGavivlipiaiialltgg.ikevlivlivvll 268
                                       ++++  +l++li+g+l++ig++++gv y++l+++++ +++l+P+iG+ i+++pi i++ll+g+    + ++++++++
  gi|330508908|ref|YP_004385336.1| 225 NLFNVYLLTSLITGLLAAIGFALFGVSYPFLWGLTTAIFALLPMIGPPIIFVPICIYFLLIGNyLSGIGLFIYSLIF 301
                                       ***************************************************************88889999999*** PP

                   AI-2E_transport 269 vqliegnilePklmgkrlglhplvillsllaggklfGlvGlilavpltavikaile 324
                                       +++i +n+++Pkl ++++++hp ++ll++ a + + G++G+i++++l++++ a+++
  gi|330508908|ref|YP_004385336.1| 302 INTIPENVIRPKLASQGAKIHPSITLLAFAAPIFVVGFLGFIIGPLLYGFLLAAFR 357
                                       ***************************************************99986 PP

>> Sperm_Ag_HE2  Sperm antigen HE2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4   0.00012       1.1       2      38 ..      59      96 ..      58     101 .. 0.82
   2 ?   -2.5   0.1      0.81   7.3e+03       8      15 ..     180     187 ..     174     200 .. 0.44

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00012
                      Sperm_Ag_HE2  2 lpsfvsLLLvaLLfp.GsSrassvnhqategprelree 38
                                      l++f+sLLLv+L+f   +S+a +    +t g+ +++e+
  gi|330508908|ref|YP_004385336.1| 59 LSAFMSLLLVVLFFMiFLSSALNAIATETSGLFSSQED 96
                                      899**********9877888888888888887777775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.81
                      Sperm_Ag_HE2   8 LLLvaLLf 15 
                                         +va+++
  gi|330508908|ref|YP_004385336.1| 180 QFFVAIMI 187
                                       44444432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1249  (0.0696637); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 2654.93
//
Query:       gi|330508909|ref|YP_004385337.1|  [L=356]
Description: hypothetical protein MCON_3237 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-31  109.8  27.1    1.7e-31  109.6  27.1    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 !  109.6  27.1   9.6e-36   1.7e-31       2     324 ..      14     329 ..      13     332 .. 0.91

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 9.6e-36
                   AI-2E_transport   2 llilvllllllalypfiselllplliAlvlayllnpvvkfL.kkrgvkrvlavllvlllllvllvllvlllvpllia 77 
                                       +l+ v+lll+l+ ++f+ +l   +++++v+ yl  pv + + k+r +    a++++++ l+++++  v+  +    +
  gi|330508909|ref|YP_004385337.1|  14 WLFAVTLLLILLSSYFLWPLQDGIVLGIVFTYLGRPVRDLFgKRRQIGSLAAIICIIAPLSIIFAAGVFEAA----S 86 
                                       6777777777777777777**********************8888888888888888888888888888777....* PP

                   AI-2E_transport  78 qltqlvkslpayidslqnilnelpslleelenliqalkqslskilsnilssilns.llsllasllglilslvlvlll 153
                                       ql+ l ++  ++++  q++++++  + ++     ++l + +++ +   ls +++  + +l  +l+ ++l+l++ + +
  gi|330508909|ref|YP_004385337.1|  87 QLRWLQSHRAQIVATGQEFISSIY-IPQFI---FDELSRGMDNLMGIGLSMLTSLpVFDLGTTLTLGLLNLLIAFCV 159
                                       ***********************9.45555...689*************999886477999999999********** PP

                   AI-2E_transport 154 lffllldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvgl 230
                                       +++ll+dg++l+  ++ +l ++  ++  + l +++ +lsg++ g++ +a++ ++++  +++++ +p +l +a ++ l
  gi|330508909|ref|YP_004385337.1| 160 CYYLLVDGDRLLGATIDFLRQKKGDFELRCLGRIDGILSGIYTGSISTAMVYAIASVPIFYLFDIPRPLAMASIILL 236
                                       **********************999999************************************************* PP

                   AI-2E_transport 231 anliPyiGavivlipiaiialltggikevlivlivvllvqliegnilePklmgkrlglhplvillsllaggklfGlv 307
                                       a ++P++  ++v++ +a+  ++  g++e+ ++++ + ++++ ++ +++P+++  r ++hp+++ll++l+gg ++G++
  gi|330508909|ref|YP_004385337.1| 237 AGVVPFLT-WLVFLLTAVSRYIEMGPMEAAVFFFAASVLVAAVELVVRPYIVYARSSIHPMLVLLAFLGGGLVGGVF 312
                                       *******6.66666668888888888999999999999999999********************************* PP

                   AI-2E_transport 308 Glilavpltavikaile 324
                                       G++la+ ++++i  i++
  gi|330508909|ref|YP_004385337.1| 313 GFFLAPAMLGTISGIYQ 329
                                       ********999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2581.57
//
Query:       gi|330508910|ref|YP_004385338.1|  [L=239]
Description: hypothetical protein MCON_3238 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); 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:                         0  (0); expected 0.2 (1e-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 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1833.37
//
Query:       gi|330508911|ref|YP_004385339.1|  [L=345]
Description: hypothetical protein MCON_3239 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-10   38.7   0.2    4.2e-09   36.5   0.2    1.9  1  NurA      NurA domain


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.2   2.3e-13   4.2e-09       2     241 ..      49     299 ..      48     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.3e-13
                                       EEEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEE........................ CS
                              NurA   2 rvaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdel........................ 54 
                                       +++AvDGSng +     + + l+++++v+ + ++ +++    +v++ +p++++                        
  gi|330508911|ref|YP_004385339.1|  49 NIYAVDGSNGIIFDLPSVSFNLIRAGYVSYIAKNWQKTILFDKVFKADPDNYRyqfeadlsksfninsnfvlaktel 125
                                       89**********555556666666677777777777776777777777777778*********************** PP

                                       HHHHHHHHHHHHHH.HHHHHCGGCCSCEEEEECSHHCCCHHHHHHHHHHHHHHHHHHHHHHTT-.TTCEEEEESS-S CS
                              NurA  55 errirllmetlElk.lgallleekgedllllDGsligslvefdelheeleyeeylyslsrllea.glnlvgvaKsfr 129
                                       +r    ++e+ E+  l++   ++k+ dl+l+DG + ++             +e+l+++    e   l+l++++Ks++
  gi|330508911|ref|YP_004385339.1| 126 DRLSTYYRELQEYIaLYEAISDAKKGDLVLYDGDFAYWMD---------PFGEVLKMIFDEAEDkDLDLLAISKSST 193
                                       *************989999999*****************9.........6777777776666669***********9 PP

                                       CTCCHCCC......S--HHHHCCHHCCHCH---STTS-HHHHTT.-HCCHHHHHH-EEEEEEESSTTTTEEEEEHHH CS
                              NurA 130 skellnllletlligesisDiallgallrkpgytspllkilrek.pllrealidkeiyfaYvrlegggsilrleipa 205
                                        +  +         ++ i  + ++g+ l + +  +++  ++ ++ p  r ++ + +iy+  ++   +++++rl+ p+
  gi|330508911|ref|YP_004385339.1| 194 FSWGKSFS------KPFILHTGYVGSQLIS-NNPWHIELSEKNIkPQPRGKNWNGKIYVVKLHP-NSEFVFRLDAPQ 262
                                       99999989......99************77.4447777766666999999999999**999997.9********999 PP

                                       HHHCCHHHHHHHHHH....TTB-SSSBCCHHHHHHHHC CS
                              NurA 206 evstakdedvlslla..sqrlsisGYprpLalAhelak 241
                                        vs  +++  l +l   s+  ++ GYp++L +Ah+   
  gi|330508911|ref|YP_004385339.1| 263 YVS-VRIDNALGHLSaySKSSECLGYPHALFRAHRDIA 299
                                       887.89999999998899****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2441.16
//
Query:       gi|330508912|ref|YP_004385340.1|  [L=540]
Description: hypothetical protein MCON_3240 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-23   84.3   2.5      7e-23   81.9   2.5    2.0  1  DUF87          Helicase HerA, central domain
  ------ inclusion threshold ------
      0.026   14.4   0.0      0.099   12.6   0.0    2.1  2  RHH_1          Ribbon-helix-helix protein, copG family
      0.028   13.0   0.1      0.058   12.0   0.0    1.5  2  DUF853         Bacterial protein of unknown function (DUF853)
      0.098   12.4   0.9       0.37   10.5   0.1    2.3  2  DUF4325        STAS-like domain of unknown function (DUF4325)
       0.92    8.3   3.2        2.5    6.9   0.1    2.7  3  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   2.5     2e-26     7e-23       2     227 .]     157     385 ..     156     385 .. 0.76

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 2e-26
                             DUF87   2 eiGrllsgse....vpvyldlnklvtrHlAilgsTGsGKSntvavLleelle.....kkgatililDpHGEYgkal. 68 
                                       e+G+l +gs+    + v+l+  ++  +H++++++TG+GKSn+++v  ++ ++     + ++ +l+ DpHGEY   + 
  gi|330508912|ref|YP_004385340.1| 157 EVGYLRNGSQvveeIGVKLNS-EIMDHHMGVFATTGMGKSNFMKVFAASCMKkasmgESKLGLLLADPHGEYLMGSa 232
                                       788888777777668899999.888**************************9999999999***********99998 PP

                             DUF87  69 .........ekllsekvkvitpspsa.....kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakak 131
                                                 +++++ ++ +++ ++      + ++lki +++++p ++l l++e     +++q++++e + ++    
  gi|330508912|ref|YP_004385340.1| 233 knntkgllhLSEYKNGLRCYSTNNKNakenaEVETLKIGIRDINPTDILPLFGE----WRPAQKEAIEIMDSEN--- 302
                                       899999999888888888888877779999999*********************....3333554444333322... PP

                             DUF87 132 eekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidl 208
                                            ++  e++++ +e      + ++ + +++i+ ++++l+ llr+ + +  ++++ i+++  k  kegk+  id+
  gi|330508912|ref|YP_004385340.1| 303 ----AADWLESFKENRE------LVIKDIHEKTIEVIKRRLNLLLRYSYID--EKNSSIDKI-IKQLKEGKVILIDM 366
                                       ....2222222222222......2235556677777777777666666666..333333333.2445999999**** PP

                             DUF87 209 sgvdelaqqlvvsvilrri 227
                                        g++e+    + s+++rri
  gi|330508912|ref|YP_004385340.1| 367 EGIKERSELFLLSLLSRRI 385
                                       *****************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 ?   -3.3   0.0       2.9     1e+04      18      29 ..     364     376 ..     363     381 .. 0.76
   2 ?   12.6   0.0   2.8e-05     0.099       2      25 ..     507     531 ..     506     533 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.9
                                       HHHHT.SSHHHHH CS
                             RHH_1  18 arrrg.rSrSelI 29 
                                       ++++g + rSel+
  gi|330508912|ref|YP_004385340.1| 364 IDMEGiKERSELF 376
                                       6777888899987 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.8e-05
                                       EEEEEEHHHHHHHHHHHHHHT.SSH CS
                             RHH_1   2 vsirldeellerLdelarrrg.rSr 25 
                                       v+i+l+e+++++L e  ++++ +Sr
  gi|330508912|ref|YP_004385340.1| 507 VTIHLYEDYIKQLKEQDKDLNrSSR 531
                                       8********************6666 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 ?   -3.1   0.0      0.62   2.2e+03      13      44 ..     173     204 ..     168     212 .. 0.81
   2 ?   12.0   0.0   1.6e-05     0.058     176     365 ..     324     500 ..     285     512 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.62
                            DUF853  13 lalalklanrhGliaGatGtGktvtLqvlaes 44 
                                       ++l+ ++++ h  +   tG Gk   ++v+a s
  gi|330508912|ref|YP_004385340.1| 173 VKLNSEIMDHHMGVFATTGMGKSNFMKVFAAS 204
                                       56777888889888899******999999876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.6e-05
                            DUF853 176 asvgaiqreLltLeqqGaekffGePaLdledllrtdadGrGvislLaadkllqsPklyatfLlWllse..LfeeLPe 250
                                       +++++i+r+L  L +    ++  e + +++ +++  ++  G + l++++ + ++ +l   fLl lls   L e   +
  gi|330508912|ref|YP_004385340.1| 324 KTIEVIKRRLNLLLR---YSYIDEKNSSIDKIIKQLKE--GKVILIDMEGIKERSEL---FLLSLLSRriLDEYQKD 392
                                       555555555544443...34555666666666665533..44556666666666666...46666664324455567 PP

                            DUF853 251 vGdldkPklvfffdeahLLfndapkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpk 327
                                         d dk    +  +ea  ++ +   + +   e + r  r  GvG+  +tq+P  + +  L+q+ + v  +l     +
  gi|330508912|ref|YP_004385340.1| 393 SLDNDKNTCLIAIEEAQRVLGGGDGS-ISGFEIIAREGRKFGVGLCAITQQPKLVDKLLLSQFNTLVIMGLG--DRN 466
                                       77888888888899998888776655.5678999999******************************99997..468 PP

                            DUF853 328 dqkavkaaadtfranpefdveeaiteLgvGealvsvLd 365
                                       d+k++  +a+   +  ++d    i+ L+ Gea++s+L+
  gi|330508912|ref|YP_004385340.1| 467 DRKCLEESAKQDLT--TLD--VEIQTLEKGEAIISTLK 500
                                       99999998875333..333..4599***********96 PP

>> DUF4325  STAS-like domain of unknown function (DUF4325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.48   1.7e+03       7      29 ..     118     140 ..     115     142 .. 0.80
   2 ?   10.5   0.1    0.0001      0.37       7      35 ..     350     377 ..     349     394 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.48
                           DUF4325   7 dkilkpllkegekvelDFdgves 29 
                                       +k+ k+ +k+ +++ l F++ve 
  gi|330508912|ref|YP_004385340.1| 118 KKMGKKEFKKSKTIPLKFSEVEK 140
                                       56667778999999999999986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0001
                           DUF4325   7 dkilkpllkegekvelDFdgvesigssFl 35 
                                       dki+k+l keg+ + +D++g+++ +  Fl
  gi|330508912|ref|YP_004385340.1| 350 DKIIKQL-KEGKVILIDMEGIKERSELFL 377
                                       7999999.*************98777776 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 ?   -1.4   0.0      0.24   8.5e+02     174     206 ..      32      68 ..      12      82 .. 0.66
   2 ?    6.9   0.1    0.0007       2.5       6      55 ..     172     227 ..     168     240 .. 0.75
   3 ?    0.6   0.3     0.059   2.1e+02     158     277 ..     316     438 ..     289     473 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.24
                     TrwB_AAD_bind 174 tlatnlevlelLa......ekgerFSireWleeedesgw 206
                                        +++ ++ ++++       e g++FSi+++  ++de  +
  gi|330508912|ref|YP_004385340.1|  32 IISKDVREFHFIIpydervELGQIFSIKDYSVKDDE--I 68 
                                       566677777777644433344559****99888864..3 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0007
                     TrwB_AAD_bind   6 gvplpkeretqhilivGttGsGKtqalekllrairarg......draivlDltGaf 55 
                                       gv l+ e  ++h+ ++ ttG+GK++ ++ + ++  +++         + +D++G++
  gi|330508912|ref|YP_004385340.1| 172 GVKLNSEIMDHHMGVFATTGMGKSNFMKVFAASCMKKAsmgeskLGLLLADPHGEY 227
                                       56777888899****************98877766665444444456666666666 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.059
                     TrwB_AAD_bind 158 alvaeeaertaasiratlatnlevlelLaekgerFSireWleeedesgwlfltskaeqrallrpllsawldlaikal 234
                                        ++++ +e+t + i+  l+  l+  ++++ek++  Si + +++ +e++++ +  +  ++     lls++      + 
  gi|330508912|ref|YP_004385340.1| 316 LVIKDIHEKTIEVIKRRLNLLLRY-SYIDEKNS--SIDKIIKQLKEGKVILIDMEGIKERSELFLLSLLSRRILDEY 389
                                       456677788888888888877764.78888888..999999999988888888877777766666666544444444 PP

                     TrwB_AAD_bind 235 ls.lpesrerrlWfflDElpaL.....grleelksllaegRkfGgavvl 277
                                        +   +++++ +   + E + +     g ++ ++ ++ egRkfG+ + +
  gi|330508912|ref|YP_004385340.1| 390 QKdSLDNDKNTCLIAIEEAQRVlgggdGSISGFEIIAREGRKFGVGLCA 438
                                       4323334444556666666655444445677777777777777765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); 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: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 3775.64
//
Query:       gi|330508913|ref|YP_004385341.1|  [L=382]
Description: Ser/Thr protein phosphatase family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-15   55.8   0.5    1.3e-14   55.2   0.5    1.4  1  Metallophos    Calcineurin-like phosphoesterase
      6e-10   39.5   0.1    9.6e-10   38.9   0.1    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.012   14.9   0.1       0.27   10.5   0.1    2.3  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 !   55.2   0.5   2.2e-18   1.3e-14       1     138 [.       1     171 [.       1     233 [. 0.75

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 2.2e-18
                                       EEEEEEESBTB..................TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHH CS
                       Metallophos   1 lrilvigDlHl..................algggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaa 59 
                                       ++i++++D Hl                  +     ++ ++ ++d+++++ kpd++++aGD++++  +  ++l+ ++ 
  gi|330508913|ref|YP_004385341.1|   1 MKIVHMSDSHLgfsaynkvdqygrniieeK----IYQGFEHAIDKIIKDIKPDAIVHAGDVFHHVRPRIRTLYVFKS 73 
                                       89***********************55554....5555555555555555***************777777777777 PP

                                       HHHH....TSEEEEEC-TTS...............CHHH.HHHHHHHHHHHH.....HHHHEHHHCEEETSEEEEEE CS
                       Metallophos  60 lvky....pipvylllGNHe...............gfee.ellnkygylgif.....sepwrsdaevfnnlplaslg 111
                                        ++     +ip +++ GNH+               g+e+  + ++++y+ i       + +  + +   +l  +s +
  gi|330508913|ref|YP_004385341.1|  74 AIEKldkkKIPTIIISGNHDapksssttspfslfeGLEHiHVVHRNEYESIPirdyvFHCIPFCLDNRAYLDEFSKI 150
                                       7777777789************************9999999999999999996555555555557777777777777 PP

                                       TTE.EEEEEEESECEEETHHHHHHHHHH CS
                       Metallophos 112 sgs.lkvlllhGgspellvsldklgsln 138
                                       + +  +vl++hG        +++l+   
  gi|330508913|ref|YP_004385341.1| 151 KPTgSDVLVMHGL-------IESLKDKR 171
                                       77788*******9.......22222222 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 !   38.9   0.1   1.6e-13   9.6e-10       1     135 [.       1     205 [.       1     235 [. 0.68

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.6e-13
                     Metallophos_2   1 MklaiiSDlHsnldaleav....................lealkevgvdaiihaGDl.eeeep.........evlee 47 
                                       Mk++++SD+H  ++a ++v                     +++k+ ++dai+haGD+   + p         +++e+
  gi|330508913|ref|YP_004385341.1|   1 MKIVHMSDSHLGFSAYNKVdqygrniieekiyqgfehaiDKIIKDIKPDAIVHAGDVfHHVRPrirtlyvfkSAIEK 77 
                                       **********555555555555777777777777777766788999**********988888877766666557777 PP

                     Metallophos_2  48 llela.pvlaVrGNnD.................eev.veedvlreaaelgtdl..............peeaelel.. 89 
                                       l + + p +++ GN+D                 e + v+++   e+ ++++++               e     +  
  gi|330508913|ref|YP_004385341.1|  78 LDKKKiPTIIISGNHDapksssttspfslfeglEHIhVVHRNEYESIPIRDYVfhcipfcldnraylDE-----Fsk 149
                                       77777********************99999988444577777777777777778888888755443222.....222 PP

                     Metallophos_2  90 ...agekvlliHgdpl.........gvkdalaellkeaeegsd..vvvcGHtHvpeveke 135
                                           g +vl++Hg                  ++ l+++  +s+  ++++GH H +   +e
  gi|330508913|ref|YP_004385341.1| 150 ikpTGSDVLVMHGLIEslkdkrlrtV----GEHELSDSFLKSYfsYIALGHYHNQAQIAE 205
                                       3447777******9558777754443....333333333334457********9844333 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   4.5e-05      0.27      76     125 ..      69     118 ..      32     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.5e-05
                                       HHHHHHHHHHHTT-SEEEEE--TTS--HHHHHHHHHHTTTT-TTEEE-SS CS
                     Metallophos_3  76 klldklfrelgeldvpafvvPGkrDaPlevflreayeaevvfpnlkvvhe 125
                                        ++  + ++l++ ++p++++ G++DaP        +       +++vvh 
  gi|330508913|ref|YP_004385341.1|  69 YVFKSAIEKLDKKKIPTIIISGNHDAPKSSSTTSPFSLFEGLEHIHVVHR 118
                                       567788999******************98877777776666777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.22s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2706.61
//
Query:       gi|330508914|ref|YP_004385342.1|  [L=1059]
Description: hypothetical protein MCON_3242 [Methanosaeta concilii GP6]
Scores for complete 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   79.9   0.3    2.9e-22   79.2   0.3    1.3  1  SMC_N         RecF/RecN/SMC N terminal domain
      2e-12   47.5   6.2      2e-12   47.5   6.2    3.6  3  AAA_15        AAA ATPase domain
    6.2e-09   36.6  87.2    8.1e+02    0.4  87.2    6.5  1  AAA_23        AAA domain
    1.9e-08   33.9   0.0    3.7e-08   33.0   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    1.2e-05   25.4   0.0    3.2e-05   24.1   0.0    1.7  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
    8.1e-05   22.3   0.0    8.1e-05   22.3   0.0    4.1  4  AAA_27        AAA domain
    0.00016   21.6   0.3    0.00016   21.6   0.3    3.1  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0002   21.9   4.3    0.00038   21.0   0.1    3.5  2  ABC_tran      ABC transporter
  ------ inclusion threshold ------
      0.013   15.3   0.4      0.043   13.6   0.0    2.1  2  MukB          MukB N-terminal
        2.3    7.4   7.5        0.6    9.3   0.6    2.9  3  OMS28_porin   OMS28 porin


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 !   79.2   0.3   1.6e-25   2.9e-22       2     212 ..       3    1047 ..       2    1054 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 1.6e-25
                                        EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N    2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkk 76  
                                        l++l+++nFk y  ++++++f++++t i+G+NGSGKs +++Ai + L  ++a    s   ++li++  + ++ + 
  gi|330508914|ref|YP_004385342.1|    3 LNKLVLRNFKKY--RRATIEFQEGLTGIIGSNGSGKSTIVEAIAWALYGNKA----SLIKRNLIKN-THANENEP 70  
                                        799*********..69*******************************87777....3445679998.66667777 PP

                                        EEEEEEEEETTEESSSSSSCEEEEEEEETTSE...EEEEETTEEE-H..HHHHHHHHCT.T-STT.......... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx..xxxxxxxxxx.xxxxx.......... RF
                             SMC_N   77 aeveitfdnedkklkiekeevsisrrvkrkge...seykingkevtk..kevsellesa.giske.......... 135 
                                         e+++++++++ +       ++i r++k k+     + +in+  +++  ++v ++le+  +is +          
  gi|330508914|ref|YP_004385342.1|   71 VEITLFISQDNID-------MKIIRNMKGKNLipdATLYINDDIISSgtRDVDKMLEEIlNISYQdfmktfyarq 138 
                                        8888866555555.......7788887777744559999**9998877799*99999852576669********* PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508914|ref|YP_004385342.1|  139 kdldnllkeggmgkreyllkllgledikesaleqiksdrssledqrsrlagalgeigevqarlmeasreisfvre 213 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508914|ref|YP_004385342.1|  214 glvegerceaqllgekelrlmeldvlnqkmnsygilaerasrlqeearslevliardegrlkeieaskrllekig 288 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508914|ref|YP_004385342.1|  289 paldrltgvlsrlelleprrnlyeeisrkiavaksrlegdraalekdekrlvqlegdrarldellpqeedykevq 363 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508914|ref|YP_004385342.1|  364 vllarleelreryakislsqkedairlqgarsnlvradrsiedlqrasaryeelwpaieeekrlkveqtklsgek 438 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508914|ref|YP_004385342.1|  439 erqreldllesqkkalagriaalreaaakirenllglgdlegregelrrqdrdldslgselnnaladlrgslkvq 513 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508914|ref|YP_004385342.1|  514 entyleneralkkvstlgreglcptcerpiegqrdlllgkyqfalaqakeereklkgmaasltekiegvassrsr 588 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508914|ref|YP_004385342.1|  589 lagafedlnakkslrsalqadmrnadlqikeateemegimamvgsfgpvsfdakrlqdveaaltklapmaeecqg 663 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508914|ref|YP_004385342.1|  664 lavrkeelprrvlereaikeeietlakrgehleeqirelgysesqyieakrlwesckfpheqfitllertkeipa 738 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508914|ref|YP_004385342.1|  739 leekialqrseiekasrslvelersvkdlgfdpeeyssllaerkrlaqaeeeankikirlalepevkeklaesqg 813 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|330508914|ref|YP_004385342.1|  814 alearqldiariraemeslaysqrthemaklalaeaernlvasqkelsdkrirlgvleaelarlkeeekrkkehq 888 
                                        *************************************************************************** PP

                                        .........................................................................CS CS
                                        .........................................................................xx RF
                             SMC_N  136 .........................................................................lL 137 
                                                                                                                   
  gi|330508914|ref|YP_004385342.1|  889 krleetsrrlevvemtrglvndfmdqvlirvkndiakaaseileevsgkysllkidddfniqvedggnyypisRY 963 
                                        *************************************************************************** PP

                                        -HHHHHHHHHHHHHHHHCC........S--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCC CS
                                        xxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                             SMC_N  138 SgGektLvalaLlfAiqkv........kpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemle 203 
                                        SgGe  ++a+++++Ai ++        +  ++ +lDe+    D ++++k+ ++l++ +++  Q+i is+ +++  
  gi|330508914|ref|YP_004385342.1|  964 SGGEIDMIAVSVRVAISEYlmrfgpdgESYSFLILDEVFGSQDIEHREKMIQMLRSLEERfPQIIAISHISDVQG 1038
                                        ***************7665333333334579*************************999967*******999888 PP

                                        C-SCEEEEE CS
                                        xxxxxxxxx RF
                             SMC_N  204 kadklvgvt 212 
                                        + d+++ v 
  gi|330508914|ref|YP_004385342.1| 1039 QFDNTLLVV 1047
                                        887766655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   6.2   1.1e-15     2e-12       1     165 [.       1     160 [.       1     328 [. 0.61
   2 ?    0.3   1.4      0.25   4.4e+02     155     261 ..     355     463 ..     309     519 .. 0.75
   3 ?    2.5   4.8     0.053        95     153     364 ..     806    1032 ..     682    1036 .. 0.69

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.1e-15
                            AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdi 77 
                                       M ++k+ ++NF++++ ++i+++e lt +iG N+sGKS+i+ea+ + l  +     k   + k +l ++ + +e+ ++
  gi|330508914|ref|YP_004385342.1|   1 MLLNKLVLRNFKKYRRATIEFQEGLTGIIGSNGSGKSTIVEAIAWALYGN-----K-ASLIKRNLIKNTHANENEPV 71 
                                       899****************************************9988866.....2.33344444444477777888 PP

                            AAA_15  78 kIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks........... 143
                                       +I++     +++++++k+ +       ++  k+++ d   +i+d ++   + +++++  ++ ++             
  gi|330508914|ref|YP_004385342.1|  72 EITLFI---SQDNIDMKIIR-------NMKGKNLIPDATLYINDDIISSGTRDVDKMLEEILNISYqdfmktfyarq 138
                                       888777...22222111111.......11222233333333333333322222222222221111111111222222 PP

                            AAA_15 144 kkelpkekeeklekekeelkid 165
                                       k  ++ +ke    k+++ lk+ 
  gi|330508914|ref|YP_004385342.1| 139 KDLDNLLKEGGMGKREYLLKLL 160
                                       3333444444444444444444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.25
                            AAA_15 155 lekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsd.....edsekkssllgklkekil 226
                                       +e++ +e+++    l++l +++ ++  +++  +  +  +   + l  a+R+++d      ++e+ ++++++ k+ ++
  gi|330508914|ref|YP_004385342.1| 355 QEEDYKEVQVLLARLEELRERYAKISLSQK--EDAIRLQGARSNLVRADRSIEDlqrasARYEELWPAIEEEKRLKV 429
                                       455555555555566666665555555555..6778888888999999****99999999999999****9999999 PP

                            AAA_15 227 eealqekl..eeelteklkeiqeklkeidkklaeelk 261
                                       e   q+kl  e+e +++l+ +++  k + + +a+  +
  gi|330508914|ref|YP_004385342.1| 430 E---QTKLsgEKERQRELDLLESQKKALAGRIAALRE 463
                                       9...467778888888888888888888887765554 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.053
                            AAA_15  153 eklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsd.....edsekkssllgklk 222 
                                        ekl +++  l+  + d+ ++  ++e+   ++         ++ kl l +a+Rn        +d+     +l++ +
  gi|330508914|ref|YP_004385342.1|  806 EKLAESQGALEARQLDIARIRAEMESLAYSQR------THEMAKLALAEAERNLVAsqkelSDKRIRLGVLEAEL 874 
                                        44444444444444444444444444443333......5556666666666665552232233333445788888 PP

                            AAA_15  223 ekileealqekleeelteklkeiqeklkeidkklaeelkkilkkkidkikkfnykgkkneeieik.......... 287 
                                         +++ee +++k +++  e+ ++ +e ++ + + +++   ++l+   ++i k    + +++ ++++          
  gi|330508914|ref|YP_004385342.1|  875 ARLKEEEKRKKEHQKRLEETSRRLEVVEMTRGLVNDFMDQVLIRVKNDIAKAASEILEEVSGKYSllkidddfni 949 
                                        888888888888666666666666666666666666666333333333333333333333333334445555566 PP

                            AAA_15  288 ....ddeelplnknGsGvqrllllillileaekk...dekeeknvilliEEPEahLHpqaqkvlikllkelandn 355 
                                             +++ p+++ + G   ++ +++  +  e       + e++ +l+++E   ++ +++ + +i+ l++l +  
  gi|330508914|ref|YP_004385342.1|  950 qvedGGNYYPISRYSGGEIDMIAVSVRVAISEYLmrfGPDGESYSFLILDEVFGSQDIEHREKMIQMLRSLEERF 1024
                                        666999******************9999999888888899999****************************9999 PP

                            AAA_15  356 ktQviitTH 364 
                                          Q+i  +H
  gi|330508914|ref|YP_004385342.1| 1025 P-QIIAISH 1032
                                        9.**99988 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4  87.2      0.45   8.1e+02       1     176 [.       5     188 ..       5     902 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.45
                            AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvel 77 
                                       kL ++nf+++r+ +i+F  glt I+G NG+GK+Ti++Ai +aLyg +        + ++++ ++ ++  + ++ ve+
  gi|330508914|ref|YP_004385342.1|   5 KLVLRNFKKYRRATIEFQEGLTGIIGSNGSGKSTIVEAIAWALYGNK-------ASLIKRNLIKNTHA-NENEPVEI 73 
                                       799******************************************43.......45666777775554.44455677 PP

                            AAA_23  78 t.fenkdgrytrsiererelskkkgkttkkaklellei.......deleqfisellgskkiilnlilflgqerfeef 146
                                       t f ++d+++ ++i     ++  kgk+   +++  +++       ++ +++++e+l+++++ +   ++  q++ +++
  gi|330508914|ref|YP_004385342.1|  74 TlFISQDNID-MKI----IRNM-KGKNLIPDATLYINDdiissgtRDVDKMLEEILNISYQDFMKTFYARQKDLDNL 144
                                       6666777743.333....2222.223332222222222244446799**************************7666 PP

                            AAA_23 147 el...kdkke.........rleel.ekeleeledekkllekl....e 176
                                       ++   +              le++ e +le+++ +++ le++     
  gi|330508914|ref|YP_004385342.1| 145 LKeggM---GkreyllkllGLEDIkESALEQIKSDRSSLEDQrsrlA 188
                                       653331...22223333343333312224444444444444422220 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 !   33.0   0.0     2e-11   3.7e-08       1      50 [.       3      51 ..       3      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2e-11
                            AAA_29  1 LkrlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      L++l l N   +++ tie++ +g t ++G +GsGKST++ Ai+  L+++k
  gi|330508914|ref|YP_004385342.1|  3 LNKLVLRNFKKYRRATIEFQ-EGLTGIIGSNGSGKSTIVEAIAWALYGNK 51
                                      678889999**********9.779************************98 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.8e-08   3.2e-05      27      89 ..     957    1018 ..     941    1019 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.8e-08
                           SbcCD_C   27 srssgtlSGGekqflaylalaaalaalyssaeg.repalrlvfLDEAFsklDeesiatllelle 89  
                                        +  +++ SGGe   ++++ +  a++ ++ +  g + +++++++LDE F++ D e +++++++l+
  gi|330508914|ref|YP_004385342.1|  957 YYPISRYSGGEI-DMIAVSVRVAISEYLMRF-GpDGESYSFLILDEVFGSQDIEHREKMIQMLR 1018
                                        6688999*****.999999999***999998.6689*************************997 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   4.5e-08   8.1e-05       1      91 [.       1      93 [.       1     151 [. 0.73
   2 ?   -2.8   2.3       2.3   4.1e+03     124     166 ..     382     408 ..     324     470 .. 0.47
   3 ?   -1.9   1.0       1.1   2.1e+03     147     203 ..     557     616 ..     543     620 .. 0.75
   4 ?   -1.7   0.6         1   1.9e+03     143     202 ..     803     865 ..     797     869 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4.5e-08
                            AAA_27  1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipe....rtkdnflhdakkLrigavle 75
                                      M l++L L+ + k+   +++f+   ++l+ i+G+N +GKst+++Ai   l+G ++    r   +  h++++  ++ +l 
  gi|330508914|ref|YP_004385342.1|  1 MLLNKLVLRNFKKYRRATIEFQ---EGLTGIIGSNGSGKSTIVEAIAWALYGNKAslikRNLIKNTHANENEPVEITLF 76
                                      8899*****************8...89*************************765111133334445554444443332 PP

                            AAA_27 76 .eadgeelefaRrkgrk 91
                                       ++d+  +++ R+ + k
  gi|330508914|ref|YP_004385342.1| 77 iSQDNIDMKIIRNMKGK 93
                                      24555556666655544 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
                            AAA_27 124 gLdherLreGGealleaegelgqlLfeasaGlaslrevleaLe 166
                                       + +++++                 L  a++ l +  + +e+L+
  gi|330508914|ref|YP_004385342.1| 382 SQKEDAI----------------RLQGARSNLVRADRSIEDLQ 408
                                       2222222................23333333333333333332 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.1
                            AAA_27 147 lLfeasaGlaslrevleaLeaeadelfkprkskk...rainealeeleeakkelreaqvr 203
                                       +L +a+   ++l+ + ++L+++ + + ++r++     + +n++++  +++++ +r+a+++
  gi|330508914|ref|YP_004385342.1| 557 ALAQAKEEREKLKGMAASLTEKIEGVASSRSRLAgafEDLNAKKSLRSALQADMRNADLQ 616
                                       688999999999999999999999999999998744445555555666777778877776 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1
                            AAA_27 143 elgqlLfeasaGlaslrevleaLeaeadelfkprkskk...rainealeeleeakkelreaqv 202
                                       e+ + L e++++l+  +  +++++ae+++l  ++++++    a++ea+++l + +kel ++ +
  gi|330508914|ref|YP_004385342.1| 803 EVKEKLAESQGALEARQLDIARIRAEMESLAYSQRTHEmakLALAEAERNLVASQKELSDKRI 865
                                       556667777777777777777888888877444444432224566677777777777766655 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 !   21.6   0.3     9e-08   0.00016       1      24 [.      25      48 ..      25     128 .. 0.76
   2 ?   -2.4   0.1       1.8   3.2e+03     208     208 ..     363     363 ..     267     464 .. 0.60
   3 ?   -0.0   3.5      0.34   6.1e+02     219     297 ..     884    1032 ..     729    1036 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 9e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                      l+++iG NgsGKS++ +a+ ++  
  gi|330508914|ref|YP_004385342.1| 25 LTGIIGSNGSGKSTIVEAIAWALY 48
                                      699****************99843 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                            AAA_21 208 l 208
                                       +
  gi|330508914|ref|YP_004385342.1| 363 Q 363
                                       2 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.34
                            AAA_21  219 r.............................................................gvvflengdgqel 232 
                                        +                                                             ++ + ++++g+  
  gi|330508914|ref|YP_004385342.1|  884 KkehqkrleetsrrlevvemtrglvndfmdqvlirvkndiakaaseileevsgkysllkiddDFNIQVEDGGNYY 958 
                                        033333333333445555555555555555555555555555556666666666677777778888888888888 PP

                            AAA_21  233 parelSdGtkrllalltallralkkg.........sllliDEpEngLHPkllrrllellkelsrngaQviltTH 297 
                                        p++  S G   ++a+ + ++               s+l++DE+  + + +  ++ +++l++l+++  Q+i+ +H
  gi|330508914|ref|YP_004385342.1|  959 PISRYSGGEIDMIAVSVRVAISEYLMrfgpdgesySFLILDEVFGSQDIEHREKMIQMLRSLEERFPQIIAISH 1032
                                        88888888888864444444333333556666888999999999999999999999***999999*******99 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   2.1e-07   0.00038      13      80 ..      25     114 ..      15     194 .. 0.57
   2 ?   -0.6   1.0      0.99   1.8e+03      53      67 ..     859     873 ..     725     984 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.1e-07
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren......... 79 
                                       +++i+G+nG+GKSt+++++a  l  ++ ++ ++ + +k+ +  e    ei  +  +++++ ++ +r+          
  gi|330508914|ref|YP_004385342.1|  25 LTGIIGSNGSGKSTIVEAIAWALYGNKASL-IKRNLIKNtHANENEPVEITLFISQDNIDMKI-IRNMkgknlipda 99 
                                       789****************98776655554.34333333323333333443333333333333.2222333444444 PP

                                       ..............H CS
                                       ..............x RF
                          ABC_tran  80 ..............e 80 
                                                     +
  gi|330508914|ref|YP_004385342.1| 100 tlyinddiissgtrD 114
                                       444445666555440 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.99
                                       -HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxx RF
                          ABC_tran  53 eleslrkeigvlpqe 67 
                                       el+  r ++gvl+ e
  gi|330508914|ref|YP_004385342.1| 859 ELSDKRIRLGVLEAE 873
                                       333333333444444 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.4e-05     0.043       8      62 ..       5      59 ..       2      68 .. 0.89
   2 ?   -3.7   0.1       4.7   8.5e+03     127     149 ..     357     379 ..     342     394 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                                      EEEEEEETTEEEEEE-HHHHHHHHHS--SHHHHHHHHHHHHHHS--TTT------ CS
                              MukB  8 sltlinWnGffartfdldelvttlsGgnGaGksttmaafvtaliPdlsllhfrnt 62
                                       l+l n++ +   t ++ e +t + G+nG+Gkst++ a+  al  + + l  rn+
  gi|330508914|ref|YP_004385342.1|  5 KLVLRNFKKYRRATIEFQEGLTGIIGSNGSGKSTIVEAIAWALYGNKASLIKRNL 59
                                      6899999999999******************************999999988886 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.7
                                       TT--HHHHHEE--SSS--EE--H CS
                              MukB 127 edvkltdvlleklddkkarvrel 149
                                       ed k  +vll +l++ ++r  ++
  gi|330508914|ref|YP_004385342.1| 357 EDYKEVQVLLARLEELRERYAKI 379
                                       44455555555555555555444 PP

>> OMS28_porin  OMS28 porin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.1   5.6e+03      72      90 ..     162     180 ..     161     212 .. 0.61
   2 ?    0.5   0.2      0.16   2.8e+02     175     237 ..     794     856 ..     778     867 .. 0.84
   3 ?    9.3   0.6   0.00033       0.6     178     246 ..     873     942 ..     860     945 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.1
                       OMS28_porin  72 legvresslelvesndagv 90 
                                       le ++es+le ++s+ + +
  gi|330508914|ref|YP_004385342.1| 162 LEDIKESALEQIKSDRSSL 180
                                       7889999999998876654 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.16
                       OMS28_porin 175 tkeefakveqvketlmaseraldetvqeaqkvlnmvnglnpsnkdqvlakkdvakaisnvvkv 237
                                        k  +a   +vke l  s+ al+    +  ++   ++ l  s++   +ak  +a a  n+v  
  gi|330508914|ref|YP_004385342.1| 794 IKIRLALEPEVKEKLAESQGALEARQLDIARIRAEMESLAYSQRTHEMAKLALAEAERNLVAS 856
                                       4555666678*************9999999**999********************99999865 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00033
                       OMS28_porin 178 efakveqvketlmaseraldetvqeaqkvlnmvnglnpsnkdqvl..akkdvakaisnvvkvaqgardltk 246
                                       e+a++++  +     ++ l+et +    v++m  gl     dqvl   k+d+aka s+++    g   l k
  gi|330508914|ref|YP_004385342.1| 873 ELARLKEEEKRKKEHQKRLEETSRR-LEVVEMTRGLVNDFMDQVLirVKNDIAKAASEILEEVSGKYSLLK 942
                                       5555555555555667788888776.5799**************944589*********998888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1059 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1709  (0.0953204); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 1.24u 0.37s 00:00:01.61 Elapsed: 00:00:00.50
# Mc/sec: 6362.49
//
Query:       gi|330508915|ref|YP_004385343.1|  [L=537]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-41  140.2   0.0      6e-41  139.2   0.0    1.6  1  DUF4277    Domain of unknown function (DUF4277)
    8.1e-12   45.2   0.2    5.7e-11   42.5   0.2    2.0  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.0   6.7e-45     6e-41       3     109 .]      10     116 ..       8     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 6.7e-45
                           DUF4277   3 vksldhlglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfpeffedkplerLlgegve 79 
                                       + sldhlglva+++d+lg++e+ide ipk++++k+s++ ++ka+++ngLgf +r+Ly+fp++fe+++lerL+++gv 
  gi|330508915|ref|YP_004385343.1|  10 TLSLDHLGLVAAIFDALGISEVIDESIPKTRNCKLSHSAIIKAMVINGLGFAERRLYIFPSYFENLALERLFNPGVV 86 
                                       679************************************************************************** PP

                           DUF4277  80 aehlnddrlgrtLDklyeagvtklfteial 109
                                       +e++n+d++grtLD++ ++g t+lf++ia+
  gi|330508915|ref|YP_004385343.1|  87 PEDFNEDVVGRTLDRINKFGSTALFNNIAM 116
                                       ****************************86 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.2   6.4e-15   5.7e-11       9     213 ..     131     455 ..     124     456 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 6.4e-15
                         DDE_Tnp_1   9 vDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                       vD t++ v+g                  +d+rw        + + + +++++  g++l v+ ++gn++d k+l++++
  gi|330508915|ref|YP_004385343.1| 131 VDTTSFGVHGDYegldcnpameitlghpKDGRW------DLKQFIVSMVTNQC-GIPLFVQAHSGNKSDKKTLIETI 200
                                       666666666666666666554444444444444......55667788888888.9********************** PP

                         DDE_Tnp_1  70 delrpr....kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrn 142
                                       ++++ +     + ++ aD++ +s e+++ l      +i r++  +++ ++      +++++ +dr+ i++++ +  +
  gi|330508915|ref|YP_004385343.1| 201 QMFKSNldfsGKNYFAADSALFSSENIRLLG-DSTLWITRVPTTVREVKDLQRLDLEMKTCSDDRYSIFETEINYGG 276
                                       **********************999999999.55559****888888888666669999999999999999999999 PP

                         DDE_Tnp_1 143 k............................................................................ 143
                                                                                                                    
  gi|330508915|ref|YP_004385343.1| 277 Idqkwvvvdsremhaskaktfdrrigkeftearkslkklgyivfaceadarkaadrwisenphftltglsiceiskr 353
                                       99*************************************************************************** PP

                         DDE_Tnp_1 144 ...............................skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrk.f 188
                                                                      + ++   + +v+  n+++l+ e + ++y+ +  +E  F++lk+k f
  gi|330508915|ref|YP_004385343.1| 354 idskrgrpkkdeqlekgyliegevqrneatiANERSRLGRFVLASNDKTLEGELMLQYYKGQNAVEKGFRFLKDKsF 430
                                       ******************************99999999*************************************** PP

                         DDE_Tnp_1 189 gldrlryrglnrveaqllllllaln 213
                                       +   +++++ +r+ea  +++ l+l+
  gi|330508915|ref|YP_004385343.1| 431 RVAEVYLKKEERIEALSMIMVLSLL 455
                                       *******************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3605.01
//
Query:       gi|330508916|ref|YP_004385344.1|  [L=446]
Description: hypothetical protein MCON_3246 [Methanosaeta concilii GP6]
Scores for complete 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-20   72.9   0.9    5.9e-20   71.9   0.9    1.5  1  Laminin_G_3  Concanavalin A-like lectin/glucanases superfamil


Domain annotation for each model (and alignments):
>> Laminin_G_3  Concanavalin A-like lectin/glucanases superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.9   3.3e-24   5.9e-20       1     147 [.     177     332 ..     177     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 3.3e-24
                       Laminin_G_3   1 dggsdyvtlpd.aslptssf...TvsaWvkpdslpsaaqiiis....sssdg...rgfelgl..dgsgrlrfsvnag 64 
                                       dg++dyv++ + ++ pt ++   ++++Wv+++s+p ++ +  s    +   g   +gf+lg   + s++l f+++ag
  gi|330508916|ref|YP_004385344.1| 177 DGSGDYVRVGNvHQNPTRDLkqgSIEMWVRLESAPKDFVLAASgreyG---GsydDGFYLGThsRYSKNLVFMIWAG 250
                                       6899*****99666555544444*************998888776542...13567999998434455*******99 PP

                       Laminin_G_3  65 ngaeesvtsgasvpa..geWtHvavtydggtlrlYvNGvevgsatltggllsatsgplviGrdpggddpfdGlidev 139
                                       +  ++ ++sg + ++  geW Hv +t+    + ++v+G ++g++++tggl++++ +++ iG d++  ++ +Gli  v
  gi|330508916|ref|YP_004385344.1| 251 G--WKVADSGIPPEDliGEWRHVMGTWGPRGVEIWVDGILKGTNPHTGGLPNPNYATVLIGTDSW-RSDTHGLIGSV 324
                                       6..**********************************************9999************.799******** PP

                       Laminin_G_3 140 riynrals 147
                                        i+++ +s
  gi|330508916|ref|YP_004385344.1| 325 VIWDDQRS 332
                                       ****9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 3142.33
//
Query:       gi|330508917|ref|YP_004385345.1|  [L=394]
Description: geranylgeranyl reductase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-12   44.6   0.3    1.4e-06   27.6   0.0    2.2  2  Lycopene_cycl   Lycopene cyclase protein
    4.5e-09   36.0   2.5    0.00023   20.5   0.0    3.1  3  FAD_binding_3   FAD binding domain
    4.5e-08   32.7   0.4    0.00013   21.3   0.3    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.3e-07   28.7   1.1      2e-06   26.8   0.6    1.9  2  HI0933_like     HI0933-like protein
    5.9e-07   29.4   1.8     0.0046   16.6   0.5    2.3  2  DAO             FAD dependent oxidoreductase
    6.3e-06   25.8   2.1    6.3e-06   25.8   2.1    1.7  2  FAD_oxidored    FAD dependent oxidoreductase
    6.7e-05   21.9   0.5       0.26   10.1   0.3    2.7  3  Trp_halogenase  Tryptophan halogenase
    0.00012   22.2   0.4    0.00046   20.4   0.4    2.0  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00021   20.5   0.3    0.00027   20.2   0.3    1.3  1  GIDA            Glucose inhibited division protein A
    0.00064   19.0   0.2     0.0013   18.0   0.2    1.4  1  Thi4            Thi4 family
     0.0013   17.9   2.7     0.0033   16.6   2.7    1.7  1  FAD_binding_2   FAD binding domain
      0.008   15.5   1.8      0.011   15.1   0.1    1.8  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0092   15.3   0.2      0.035   13.4   0.4    1.7  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.076   12.3   0.0       0.12   11.6   0.0    1.2  1  Amino_oxidase   Flavin containing amine oxidoreductase
       0.11   13.1   0.0       0.71   10.5   0.1    2.2  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.2e-09   1.4e-06       1     148 [.       9     160 ..       9     171 .. 0.81
   2 !   15.0   0.1   8.3e-06    0.0099     242     329 ..     248     340 ..     240     346 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.2e-09
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga....leecvehsWsgtivylddgk 73 
                                       Dv+viGaGpAg s+Aa+  +ak g + v++e  p + +p +        +l +      ++v  + +g+ +y ++g+
  gi|330508917|ref|YP_004385345.1|   9 DVAVIGAGPAG-SMAAKY-AAKSGANAVILEEHPAVGWPVECAGLLGLGALAEselpGSSFVLRRMKGAAIYSPGGN 83 
                                       9**********.566666.6****************999887554443333334655689999*************9 PP

                     Lycopene_cycl  74 killg...raYgrvsskrlkeellerlvengv.klleakvesveeeeageslvvleggrkirarlvvdarglaslkk 146
                                       + +      +   v ++ + +  + +  ++gv  +l + v +++ e + es+  + gg +ira++v+ a g  +++ 
  gi|330508917|ref|YP_004385345.1|  84 RLDFKaqdPRASVVDRRLFDRAAACEALHEGVeMRLCSPVRRIRREGE-ESVLSIGGGDEIRASIVISAEG-VRGRL 158
                                       98877554566788999999888877775666167899********99.**********************.66655 PP

                     Lycopene_cycl 147 ar 148
                                       ar
  gi|330508917|ref|YP_004385345.1| 159 AR 160
                                       54 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 8.3e-06
                     Lycopene_cycl 242 viPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres........slsarawatlwpr 310
                                        +P+  g+++  ++q  l +G aag v+P+ G  +   l +a+ +a  +aaa++ +        + ++r w++  +r
  gi|330508917|ref|YP_004385345.1| 248 GLPL--GPPPVTVAQGLLVVGDAAGQVKPTSGGGIYPGLVAAK-IAGGVAAAAAMEgdgsaqrlQEYDRIWRANLGR 321
                                       5788..8888888888*******************99999999.88888888887789999999999999**99999 PP

                     Lycopene_cycl 311 erkrqreffrllglalllk 329
                                       e        r+l+++  ++
  gi|330508917|ref|YP_004385345.1| 322 ELEIGMRANRMLNRMSAKE 340
                                       9999999999999886655 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.9e-07   0.00023       2      33 ..       8      39 ..       7      42 .. 0.94
   2 !    6.1   0.0    0.0047       5.6     148     175 ..     138     165 ..      84     239 .. 0.72
   3 !    7.9   0.4    0.0014       1.6     286     336 ..     262     313 ..     258     322 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.9e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                       dV+++GaGpaG m+a+  ++ G + v++e +
  gi|330508917|ref|YP_004385345.1|  8 FDVAVIGAGPAGSMAAKYAAKSGANAVILEEH 39
                                      69****************************98 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0047
                                       TEEEEEEEEEEEE--GTT-HHHHHHTGG CS
                     FAD_binding_3 148 geeetvrakYlvGaDGgrStvrktlgie 175
                                       g   ++ra  ++ a+G+r++ ++++gi 
  gi|330508917|ref|YP_004385345.1| 138 GGGDEIRASIVISAEGVRGRLARQAGIM 165
                                       33468*********************86 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0014
                                       EEE-GGGTEEE-STTSHHHHHHHHHHHHH.HHHHHHHHTTSS-GGGGHHHHH CS
                     FAD_binding_3 286 vflaGDAaHihpPtgGqGlNtaiqDavnL.awkLaavlkGeAkeelLdtYee 336
                                       ++++GDAa  + Pt G G+  ++  a    + + aa+++G+++ ++L+ Y++
  gi|330508917|ref|YP_004385345.1| 262 LLVVGDAAGQVKPTSGGGIYPGLVAAKIAgGVAAAAAMEGDGSAQRLQEYDR 313
                                       799*****************9988876551567788999********99986 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.3   1.1e-07   0.00013       1      34 [.       8      40 ..       8      76 .. 0.85
   2 !    9.3   0.0   0.00051       0.6     191     240 ..     108     157 ..      89     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.1e-07
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegt 34
                                      +dv+viG+GpAG  aa+++a++ga+ +++ +e  
  gi|330508917|ref|YP_004385345.1|  8 FDVAVIGAGPAGSMAAKYAAKSGANAVIL-EEHP 40
                                      69**********************99999.4443 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00051
                                       HHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 191 ealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrps 240
                                        +  +eGve++l + v +i+++ge+  +  + g+ei a+ v+ a Gvr +
  gi|330508917|ref|YP_004385345.1| 108 CEALHEGVEMRLCSPVRRIRREGEESVLSIGGGDEIRASIVISAEGVRGR 157
                                       334455******************6669*******************987 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.6   1.7e-09     2e-06       1      43 [.       8      50 ..       8      55 .. 0.93
   2 ?   -0.4   0.0       0.3   3.6e+02     119     163 ..     110     153 ..     104     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.7e-09
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                      +dv+viG+G+AG maA  aak g++ ++le+ +++g  +  +G
  gi|330508917|ref|YP_004385345.1|  8 FDVAVIGAGPAGSMAAKYAAKSGANAVILEEHPAVGWPVECAG 50
                                      59********************************998777777 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.3
                                       HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 119 lkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       + ++gv++rl + v+++++e ++   +++ +++e++a+ ++ A G
  gi|330508917|ref|YP_004385345.1| 110 ALHEGVEMRLCSPVRRIRREGEE-SVLSIGGGDEIRASIVISAEG 153
                                       55689************887777.788888999999999998877 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.5   3.8e-06    0.0046       1      33 [.       9      43 ..       9      65 .. 0.90
   2 !   11.7   0.0   0.00012      0.14     136     210 ..      90     162 ..      61     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.8e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      dv++iG+G +G+ +A ++a+ g   ++le ++ +g
  gi|330508917|ref|YP_004385345.1|  9 DVAVIGAGPAGSMAAKYAAKSGanAVILEEHPAVG 43
                                      8********************9*******997666 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00012
                                       EETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE..EECTEEEEEEEE..EEE--GGGHHHHH CS
                               DAO 136 fypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgve..rttpgendaada..vVnaaGawsdllg 208
                                        +p + +vd + + +a a +a   Gve+++ ++v+++++e+     v          d+++a  v+ a G+  +l++
  gi|330508917|ref|YP_004385345.1|  90 QDPRASVVDRRLFDRAAACEALHEGVEMRLCSPVRRIRREG-E-ESVLsiG----GGDEIRAsiVISAEGVRGRLAR 160
                                       67898999*****************************7764.3.3332231....2235677768888887765653 PP

                                       TT CS
                               DAO 209 ll 210
                                       ++
  gi|330508917|ref|YP_004385345.1| 161 QA 162
                                       33 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   2.1   5.3e-09   6.3e-06       1      35 [.       9      43 ..       9     165 .. 0.72
   2 ?   -3.2   0.1       3.3   3.9e+03     406     424 ..     290     308 ..     288     316 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.3e-09
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG 35
                                      Dv V+G+gpaG +AA  Aa++Ga+ +++ee++ +G
  gi|330508917|ref|YP_004385345.1|  9 DVAVIGAGPAGSMAAKYAAKSGANAVILEEHPAVG 43
                                      9*******************************998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.3
                      FAD_oxidored 406 AaGvaAalaleegvaprdv 424
                                       A GvaAa a+e + + + +
  gi|330508917|ref|YP_004385345.1| 290 AGGVAAAAAMEGDGSAQRL 308
                                       5677777777766666655 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.3   0.00021      0.26       1      30 [.       9      36 ..       9      45 .. 0.78
   2 !    8.2   0.0   0.00081      0.97     151     217 ..      97     162 ..      82     208 .. 0.87
   3 ?   -0.2   0.0      0.28   3.3e+02     316     338 ..     260     282 ..     250     322 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEE CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtl 30
                                      ++ ++G+G+aG++aA + ak + +  +v l
  gi|330508917|ref|YP_004385345.1|  9 DVAVIGAGPAGSMAAKYAAKSGAN--AVIL 36
                                      589**************9999844..4544 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00081
                                       E-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIII CS
                    Trp_halogenase 151 ldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqa 217
                                       +d++l+++     a ++Gv+++    v   ++ +g+ + l +  g e+ a ++i + G rg+l  qa
  gi|330508917|ref|YP_004385345.1|  97 VDRRLFDRAAACEALHEGVEMRLCSPVRR-IRREGEESVLSIGGGDEIRASIVISAEGVRGRLARQA 162
                                       899*****************998776543.33344444566677*******************9997 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.28
                                       TTEEE-CCCTEE--CCCS-HHHH CS
                    Trp_halogenase 316 knvvalGlasgfvePlestsihl 338
                                       ++++ +G+a+g v P  + +i+ 
  gi|330508917|ref|YP_004385345.1| 260 QGLLVVGDAAGQVKPTSGGGIYP 282
                                       67889************999984 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 !   20.4   0.4   3.9e-07   0.00046       1      32 [.      12      43 ..      12      60 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.9e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      ++GaG +G+ aA ++ak g++ ++le ++ +G
  gi|330508917|ref|YP_004385345.1| 12 VIGAGPAGSMAAKYAAKSGANAVILEEHPAVG 43
                                      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 !   20.2   0.3   2.2e-07   0.00027       1      31 [.       9      39 ..       9     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.2e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                                      dv ViG+G AG+ AA  aa++Ga+ +++ ++
  gi|330508917|ref|YP_004385345.1|  9 DVAVIGAGPAGSMAAKYAAKSGANAVILEEH 39
                                      79**********************9998655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   1.1e-06    0.0013      18      55 ..       8      44 ..       4      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                       Dv+++GaG++G  aa+y ak+ + + +ile++ ++G 
  gi|330508917|ref|YP_004385345.1|  8 FDVAVIGAGPAGSMAAKYAAKS-GANAVILEEHPAVGW 44
                                      59*******************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 !   16.6   2.7   2.7e-06    0.0033       1      35 [.       9      43 ..       9      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                      Dv ViG+G AG +AA  aa+ G++ +++e  +++g
  gi|330508917|ref|YP_004385345.1|  9 DVAVIGAGPAGSMAAKYAAKSGANAVILEEHPAVG 43
                                      9****************************998876 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 !   15.1   0.1   8.9e-06     0.011      30      63 ..       9      42 ..       4      54 .. 0.90
   2 ?   -1.1   0.1      0.78   9.3e+02      35      69 ..     277     313 ..     266     347 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.9e-06
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrpar 63
                                       v viG+G aG  A++ a++ ga+ ++l+  pa+
  gi|330508917|ref|YP_004385345.1|  9 DVAVIGAGPAGSMAAKYAAKSGANAVILEEHPAV 42
                                      699************************9998876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.78
                                       STSHH.HHHHHHHHHHTT-EEEE.EESSHHHHHHHHH CS
                       AlaDh_PNT_C  35 GgGva.GlqAiatakglgakVtv.lDvrparleqles 69 
                                       GgG+  Gl A+++a g+ a   +  D +++rl++ + 
  gi|330508917|ref|YP_004385345.1| 277 GGGIYpGLVAAKIAGGVAAAAAMeGDGSAQRLQEYDR 313
                                       6776338888888888776544314666666666666 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 !   13.4   0.4   2.9e-05     0.035       2      32 ..      12      41 ..      11      44 .. 0.88
   2 ?   -1.6   0.0       1.1   1.3e+03      95     133 ..     114     153 ..     104     159 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-05
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgni 32
                                      +iGaGPaG  aa  + k+g  + +ilE + +
  gi|330508917|ref|YP_004385345.1| 12 VIGAGPAGSMAAKYAAKSGA-NAVILEEHPA 41
                                      8******************9.689***9854 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                       Pyr_redox_3  95 elpiklfeeVesvkkedegfevetske.tyeAkkviiAtG 133
                                        ++ +l + V+++ +e+e+ +++   + +++A+ vi A G
  gi|330508917|ref|YP_004385345.1| 114 GVEMRLCSPVRRIRREGEESVLSIGGGdEIRASIVISAEG 153
                                       4445555666666666666666655544677777776666 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.12     214     259 ..     109     151 ..     105     155 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                       HHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE- CS
                     Amino_oxidase 214 ealaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvT 259
                                       eal+e   g++ rl ++V++i+reg++  + +  g++++a  V+++
  gi|330508917|ref|YP_004385345.1| 109 EALHE---GVEMRLCSPVRRIRREGEESVLSIGGGDEIRASIVISA 151
                                       78999...*********************************99997 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00059      0.71       2      34 ..      10      42 ..       9      47 .. 0.90
   2 ?   -0.9   0.0       2.2   2.6e+03      49      73 ..     109     134 ..      98     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00059
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkl 34
                                      v+v+G+G  g ++A+++a+ g++  ++e ++ +
  gi|330508917|ref|YP_004385345.1| 10 VAVIGAGPAGSMAAKYAAKSGANAVILEEHPAV 42
                                      89********************99999988876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.2
                                       HHHHTTEEEECSEEEEEEEEETTS.E CS
                         Pyr_redox  49 klekngievllntkveeiegsedg.v 73 
                                       +  ++g+e++l + v +i+ ++++ v
  gi|330508917|ref|YP_004385345.1| 109 EALHEGVEMRLCSPVRRIRREGEEsV 134
                                       55578999999999999998887644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 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:                        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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2870.37
//
Query:       gi|330508918|ref|YP_004385346.1|  [L=131]
Description: hypothetical protein MCON_3251 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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 0.30s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 902.22
//
Query:       gi|330508919|ref|YP_004385347.1|  [L=283]
Description: Ku protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-29  100.8   0.2    1.2e-28  100.3   0.2    1.2  1  Ku        Ku70/Ku80 beta-barrel domain


Domain annotation for each model (and alignments):
>> Ku  Ku70/Ku80 beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.2   6.5e-33   1.2e-28       3     199 ..      41     213 ..      39     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 6.5e-33
                                Ku   3 ggvsipVklykateeakkpkfkkldketnepvkvetkyvcsdtgevdeedivkgyeyGge.vvpltkeelekiksfd 78 
                                       g+v+ipVk  +++++ ++++f++l+k +++   +  k++c++ +ev   div gy +G+e +v+l+k+e++k k+  
  gi|330508919|ref|YP_004385347.1|  41 GLVNIPVKAVSMIRN-TRISFRMLHKACKT--PISFKRYCQEGEEVMLADIVYGYPLGNEkYVVLEKKEIDKAKPES 114
                                       78************8.9*************..78889****9666************7766**************55 PP

                                Ku  79 skglkllgFvplseilkeylsikssyfiyPddkdekgstkafsaLveamleskkvaivrfvlrskskprlvaLvPqe 155
                                       + ++ l  Fv+  e++++y+  +++y ++P       s++a+s+L+  m++++k+ai r++++s+++p +v  + q 
  gi|330508919|ref|YP_004385347.1| 115 RSTIALDRFVSFFEVDPHYF--EKTYLLLP-----DRSEEAYSLLRAVMEKTGKAAIGRITMHSRERPVIVHYYRQ- 183
                                       ********************..********.....345669**************************999988888. PP

                                Ku 156 eelsseeekeglvlvtLpfaddiRslkfpsl.deeeeekknkpte 199
                                                 ++   t++++d+iR ++  s+ +     + ++p+e
  gi|330508919|ref|YP_004385347.1| 184 ----------AIAATTMRYPDEIRDPSGYSVlK-----ELPEPSE 213
                                       ..........89************877777722.....3344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2106.14
//
Query:       gi|330508920|ref|YP_004385348.1|  [L=315]
Description: DNA polymerase LigD [Methanosaeta concilii GP6]
Scores for complete 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  104.7   0.0    6.8e-30  104.2   0.0    1.2  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
      1e-21   77.4   0.0    1.6e-21   76.7   0.0    1.3  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
    9.1e-05   22.8   0.0    0.00017   22.0   0.0    1.4  1  RNA_ligase       RNA ligase
     0.0024   17.9   0.0      0.027   14.5   0.0    2.6  2  DNA_ligase_OB_2  DNA ligase OB-like domain
     0.0056   16.5   0.0       0.15   11.9   0.0    2.2  2  mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.0   1.9e-33   6.8e-30      17     204 .]      15     195 ..       6     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 1.9e-33
                                       TTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEEEETTTTCBEHH CS
                    DNA_ligase_A_M  17 leekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElvavdketgeilpf 93 
                                       ++++ +i+E K+DG+R      +++v l  Rrl dit+++pel  al ++      +++lDGE+ ++   ++ i +f
  gi|330508920|ref|YP_004385348.1|  15 FSREGWIFEPKIDGTRCIAS-AQKRVLLSNRRLADITYRYPELASALGSLQ-G---ECVLDGEITVF---KKGIPNF 83 
                                       4567899*********7776.99********************99985544.4...5*********7...4568899 PP

                                       HHHCHHHHCHC..CTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEESSHHHHH CS
                    DNA_ligase_A_M  94 qklasrkkkkk..kveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslevkdveele 168
                                        +la+r  ++   ++  + + ++++++vFDiL ld+esl+++plkeR+++L + l+ + ++ e ++ ++ +  e+ e
  gi|330508920|ref|YP_004385348.1|  84 RSLAERDHQNDpiRIDYLSRAMPASYVVFDILSLDKESLIHLPLKERKRILFRELEADLKDSETVTLID-SFPEKGE 159
                                       99999974444456899999********************************99966555555555444.4458889 PP

                                       HHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 169 elleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                       + ++ a+++g+EG+v K  +s Y pg rs++w+K+K
  gi|330508920|ref|YP_004385348.1| 160 DYFQAALKMGIEGVVGKRLESLYLPGIRSQDWVKIK 195
                                       ***********************************9 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.0   4.5e-25   1.6e-21       2      99 .]     215     304 ..     214     304 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 4.5e-25
                                       GGSEEEEEEEEEETTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEESEEE CS
                    DNA_ligase_A_C   2 gglvgslllgvyddgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfaeit 78 
                                       +  +g lllg+y +g+l+y+ +vg+Gf+d+el++++ ++   +r+kppf +++p++ +  vW+eP++vv+V++ e t
  gi|330508920|ref|YP_004385348.1| 215 TPYFGGLLLGAYSQGELVYISRVGSGFTDEELQDITGRF--SPREKPPF-SNPPAT-AGVVWIEPKMVVQVTALERT 287
                                       6789***********************************..68999***.444444.3459**************** PP

                                       CTSSSTTEECT-EEEEE-TTS CS
                    DNA_ligase_A_C  79 asgkykaslRfPrfkrlReDk 99 
                                       ++g     lR P+f+r+R+Dk
  gi|330508920|ref|YP_004385348.1| 288 HDG----GLRAPVFLRMRDDK 304
                                       ***....*************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   4.7e-08   0.00017       3     161 .]      20     195 ..      18     195 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4.7e-08
                                       EEEEEE-SSEEEEEEEETTEEEEETTCEBCTTTHHHHHHTHHHHHHHHHHHHH....ECCEEEEEEEES........ CS
                        RNA_ligase   3 vvvtEKlDGtnfriylvkevgvasRsqilpfgeekfkefkrwaaalrkklkekla..neelilyGElig........ 69 
                                       ++ + K+DGt++  + +k+v + +R+             ++ +     +l++ l+    e +l GE+          
  gi|330508920|ref|YP_004385348.1|  20 WIFEPKIDGTRCIASAQKRVLLSNRRLAD---------ITYRYP----ELASALGslQGECVLDGEITVfkkgipnf 83 
                                       88999*****9999998756666666554.........122333....44444555545799999999988555433 PP

                                       .......SS..TTSS.................EEEEEEEEEEECTTBECE--HHHH.HHHHHCCT.......B..EE CS
                        RNA_ligase  70 ......hsikygglpk................efyvFdifdirdkeeqrylspdev.ealakglg.......tvpvl 116
                                             +        +                 ++vFdi+ ++ ke+   l+ +e+ ++l ++l+       tv ++
  gi|330508920|ref|YP_004385348.1|  84 rslaerD--------HqndpiridylsrampaSYVVFDILSLD-KESLIHLPLKERkRILFRELEadlkdseTVTLI 151
                                       3333220........2445566666666777799******886.667788888888777777665556677788888 PP

                                       EEE.SSHHHHHCCC.HHHHTC--EEEEEESSSSBE.TTE.BSEEEEE CS
                        RNA_ligase 117 yegkflaaeellelllskgnkrEGlVikpeselyk.nkg.raifKvk 161
                                        +++ ++++ +++     +   EG+V k  ++ly    + ++++K+k
  gi|330508920|ref|YP_004385348.1| 152 DSFPEKGEDYFQAA---LKMGIEGVVGKRLESLYLpGIRsQDWVKIK 195
                                       77766644444444...3559**************99999*****97 PP

>> DNA_ligase_OB_2  DNA ligase OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.78   2.8e+03      44      53 ..      49      58 ..      47      59 .. 0.85
   2 !   14.5   0.0   7.5e-06     0.027      23      66 .]     235     301 ..     209     301 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.78
                                      EEEEEE-TTS CS
                   DNA_ligase_OB_2 44 itykyqelts 53
                                      ity+y el s
  gi|330508920|ref|YP_004385348.1| 49 ITYRYPELAS 58
                                      9****99875 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 7.5e-06
                                       EEE-SS--HHHHHH.........................HHHTT-EEEEEEE-TTSSSS-EEEEEEEE- CS
                   DNA_ligase_OB_2  23 fkiGsGlsdaqRen.........................ppkiGkiitykyqeltskgvpRfPsflrvR 66 
                                        ++GsG++d++ ++                         +p    ++++ + e t++g +R P+flr+R
  gi|330508920|ref|YP_004385348.1| 235 SRVGSGFTDEELQDitgrfsprekppfsnppatagvvwiEP--KMVVQVTALERTHDGGLRAPVFLRMR 301
                                       589********999999999999998888655555433323..3478********************98 PP

>> mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.034   1.2e+02      23      81 ..      25      75 ..      15      86 .. 0.77
   2 !   11.9   0.0   4.2e-05      0.15      91     130 ..     107     146 ..      96     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.034
                                      EESSEEEEEEEEECTEEEEEEETTS-EEEESSST-BTTSSSSTCTSBGGSEEEEEEEEE CS
                   mRNA_cap_enzyme 23 KaDGiRylmllteeeegvylidRenevyrvenlrfprekdkeklekvldetllDgElvi 81
                                      K DG+R++   +++   v l +R      +   r+p+    + l  ++ e +lDgE+ +
  gi|330508920|ref|YP_004385348.1| 25 KIDGTRCIASAQKR---VLLSNRRL--ADIT-YRYPELA--SALGSLQGECVLDGEITV 75
                                      88999998665555...88888864..5666.7899888..4567999999****9977 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.2e-05
                                       EEEEEEEEEEETTEEGTTSBHHHHHHHHHHHTHHHHHHHH CS
                   mRNA_cap_enzyme  91 lryliyDivaingvtvaeeplskRleilkkelikprneek 130
                                         y+++Di+ ++  ++ + pl++R +il +el    ++++
  gi|330508920|ref|YP_004385348.1| 107 ASYVVFDILSLDKESLIHLPLKERKRILFRELEADLKDSE 146
                                       67*****************************986665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2474.48
//
Query:       gi|330508921|ref|YP_004385349.1|  [L=439]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-25   87.4   0.0    1.3e-24   86.3   0.0    1.6  1  Transposase_20  Transposase IS116/IS110/IS902 family
    9.3e-23   80.8   0.2    3.7e-22   78.9   0.0    2.0  2  DEDD_Tnp_IS110  Transposase
     0.0059   16.4   0.1      0.015   15.1   0.1    1.7  1  YfkB            YfkB-like domain
  ------ inclusion threshold ------
       0.12   11.3   0.1       0.79    8.6   0.0    2.1  2  UPF0261         Uncharacterised protein family (UPF0261)


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0     3e-28   1.3e-24       2      86 ..     249     334 ..     248     335 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 3e-28
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaai.r 77 
                                       ++++sipGi ++  +++l+eig+ r f++++qla+++Gl+p en+S++kkr+ +i+krG++++R +L+eaA++++  
  gi|330508921|ref|YP_004385349.1| 249 AIVMSIPGIAFISGSVILSEIGNYRDFQTPEQLAKWCGLNPGENESAGKKRKCGITKRGSKYIRVVLVEAAQTIAnM 325
                                       589********************************************************************999955 PP

                    Transposase_20  78 anpelrayy 86 
                                       +n  l ++y
  gi|330508921|ref|YP_004385349.1| 326 KNTGLSRFY 334
                                       569999888 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   8.3e-26   3.7e-22       1     151 [.       9     150 ..       9     152 .. 0.93
   2 ?   -1.5   0.0      0.46     2e+03      28      70 ..     323     366 ..     312     370 .. 0.63

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 8.3e-26
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G Dv+kd ++a+++  ++   ++e++ +++++l+++ ++ +a+ ++ +v++eatg y+ +++ + l++ i+++v n
  gi|330508921|ref|YP_004385349.1|   9 CGADVHKDLIVATITG-DEVPSIRENFGTTKSELDRFRNW-LADNKCEQVAFEATGVYWIPIYDV-LSRTIDTIVAN 82 
                                       799******9999984.66666778999999999999999.88999*************999998.6789******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLd 151
                                       pl++k +      ++K+D+kD+k IA l +  ++++ +++ +++ +eLr+ltr+r+ +vk+rt++knr+++ L 
  gi|330508921|ref|YP_004385349.1|  83 PLQIKSIP-----NDKSDSKDSKRIATLCL-NNQIKRSRVFSDEDRELRNLTRARSGYVKTRTQFKNRIHKYLS 150
                                       ******95.....8****************.****************************************996 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.46
                    DEDD_Tnp_IS110  28 pn.deeglealleklaakagevlvvveatghygallvaflleag 70 
                                       +n +  gl+++ ++l++k+++   +v    +   l++++l +++
  gi|330508921|ref|YP_004385349.1| 323 ANmKNTGLSRFYKRLSKKKEHNVAIVAVARKLICLIYHLLINQE 366
                                       44144678888888666666666666666666666666766665 PP

>> YfkB  YfkB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.4e-06     0.015      91     150 ..     317     377 ..     306     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-06
                              YfkB  91 gdeealgnikeekledvfekwke.sklakslnchcpavkclGpnvlvknayykevdfkkrk 150
                                         +++++n+k++ l+  +++ ++ ++ +  +     ++ cl   +l+++ +y+evd +krk
  gi|330508921|ref|YP_004385349.1| 317 EAAQTIANMKNTGLSRFYKRLSKkKEHNVAIVAVARKLICLIYHLLINQEFYQEVDCRKRK 377
                                       56789***************9873567788999999**********************998 PP

>> UPF0261  Uncharacterised protein family (UPF0261)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00018      0.79     195     224 ..      34      63 ..      30      64 .. 0.96
   2 ?   -0.4   0.1     0.096   4.3e+02     156     192 ..     311     347 ..     307     356 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00018
                           UPF0261 195 fGvttpavdairelLeeegyevlvFhAtGt 224
                                       fG+t+   d+ r+ L+++++e ++F AtG+
  gi|330508921|ref|YP_004385349.1|  34 FGTTKSELDRFRNWLADNKCEQVAFEATGV 63 
                                       9****************************6 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.096
                           UPF0261 156 lrkvLsnAaaaiaGmakaeekskeekeeeeekplvai 192
                                       +r vL +Aa+ ia m ++  ++  ++ ++++ + vai
  gi|330508921|ref|YP_004385349.1| 311 IRVVLVEAAQTIANMKNTGLSRFYKRLSKKKEHNVAI 347
                                       6889*************99999988877777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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 0.25s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3341.59
//
Query:       gi|330508922|ref|YP_004385350.1|  [L=439]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-25   87.4   0.0    1.3e-24   86.3   0.0    1.6  1  Transposase_20  Transposase IS116/IS110/IS902 family
    9.3e-23   80.8   0.2    3.7e-22   78.9   0.0    2.0  2  DEDD_Tnp_IS110  Transposase
     0.0059   16.4   0.1      0.015   15.1   0.1    1.7  1  YfkB            YfkB-like domain
  ------ inclusion threshold ------
       0.12   11.3   0.1       0.79    8.6   0.0    2.1  2  UPF0261         Uncharacterised protein family (UPF0261)


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0     3e-28   1.3e-24       2      86 ..     249     334 ..     248     335 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 3e-28
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaai.r 77 
                                       ++++sipGi ++  +++l+eig+ r f++++qla+++Gl+p en+S++kkr+ +i+krG++++R +L+eaA++++  
  gi|330508922|ref|YP_004385350.1| 249 AIVMSIPGIAFISGSVILSEIGNYRDFQTPEQLAKWCGLNPGENESAGKKRKCGITKRGSKYIRVVLVEAAQTIAnM 325
                                       589********************************************************************999955 PP

                    Transposase_20  78 anpelrayy 86 
                                       +n  l ++y
  gi|330508922|ref|YP_004385350.1| 326 KNTGLSRFY 334
                                       569999888 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   8.3e-26   3.7e-22       1     151 [.       9     150 ..       9     152 .. 0.93
   2 ?   -1.5   0.0      0.46     2e+03      28      70 ..     323     366 ..     312     370 .. 0.63

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 8.3e-26
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G Dv+kd ++a+++  ++   ++e++ +++++l+++ ++ +a+ ++ +v++eatg y+ +++ + l++ i+++v n
  gi|330508922|ref|YP_004385350.1|   9 CGADVHKDLIVATITG-DEVPSIRENFGTTKSELDRFRNW-LADNKCEQVAFEATGVYWIPIYDV-LSRTIDTIVAN 82 
                                       799******9999984.66666778999999999999999.88999*************999998.6789******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLd 151
                                       pl++k +      ++K+D+kD+k IA l +  ++++ +++ +++ +eLr+ltr+r+ +vk+rt++knr+++ L 
  gi|330508922|ref|YP_004385350.1|  83 PLQIKSIP-----NDKSDSKDSKRIATLCL-NNQIKRSRVFSDEDRELRNLTRARSGYVKTRTQFKNRIHKYLS 150
                                       ******95.....8****************.****************************************996 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.46
                    DEDD_Tnp_IS110  28 pn.deeglealleklaakagevlvvveatghygallvaflleag 70 
                                       +n +  gl+++ ++l++k+++   +v    +   l++++l +++
  gi|330508922|ref|YP_004385350.1| 323 ANmKNTGLSRFYKRLSKKKEHNVAIVAVARKLICLIYHLLINQE 366
                                       44144678888888666666666666666666666666766665 PP

>> YfkB  YfkB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.4e-06     0.015      91     150 ..     317     377 ..     306     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-06
                              YfkB  91 gdeealgnikeekledvfekwke.sklakslnchcpavkclGpnvlvknayykevdfkkrk 150
                                         +++++n+k++ l+  +++ ++ ++ +  +     ++ cl   +l+++ +y+evd +krk
  gi|330508922|ref|YP_004385350.1| 317 EAAQTIANMKNTGLSRFYKRLSKkKEHNVAIVAVARKLICLIYHLLINQEFYQEVDCRKRK 377
                                       56789***************9873567788999999**********************998 PP

>> UPF0261  Uncharacterised protein family (UPF0261)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00018      0.79     195     224 ..      34      63 ..      30      64 .. 0.96
   2 ?   -0.4   0.1     0.096   4.3e+02     156     192 ..     311     347 ..     307     356 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00018
                           UPF0261 195 fGvttpavdairelLeeegyevlvFhAtGt 224
                                       fG+t+   d+ r+ L+++++e ++F AtG+
  gi|330508922|ref|YP_004385350.1|  34 FGTTKSELDRFRNWLADNKCEQVAFEATGV 63 
                                       9****************************6 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.096
                           UPF0261 156 lrkvLsnAaaaiaGmakaeekskeekeeeeekplvai 192
                                       +r vL +Aa+ ia m ++  ++  ++ ++++ + vai
  gi|330508922|ref|YP_004385350.1| 311 IRVVLVEAAQTIANMKNTGLSRFYKRLSKKKEHNVAI 347
                                       6889*************99999988877777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3330.10
//
Query:       gi|330508923|ref|YP_004385351.1|  [L=98]
Description: hypothetical protein MCON_3260 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 687.35
//
Query:       gi|330508924|ref|YP_004385352.1|  [L=51]
Description: hypothetical protein MCON_3263 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      135  (0.0075297); 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: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 400.25
//
Query:       gi|330508925|ref|YP_004385353.1|  [L=218]
Description: hypothetical protein MCON_3264 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-40  138.1   0.0    1.8e-40  137.6   0.0    1.3  1  Cas6b_C   Cas6b C-terminal domain
    3.2e-35  120.3   0.0    7.1e-35  119.2   0.0    1.6  2  Cas6b_N   Cas6b N-terminal domain


Domain annotation for each model (and alignments):
>> Cas6b_C  Cas6b C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.6   0.0   2.1e-44   1.8e-40       1     113 [.     105     216 ..     105     217 .. 0.98

  Alignments for each domain:
  == domain 1  score: 137.6 bits;  conditional E-value: 2.1e-44
                           Cas6b_C   1 glseelieYkfltpwlaLnqenykkykklkseeekkellekiLvgnilsmakglgvtveekievkiteveekkvklk 77 
                                       g++ee+++Y+f++pwlaL qeny+ky ++ seee+++ll++iLvgnils++kglg+  +e+i++++ +++++ ++lk
  gi|330508925|ref|YP_004385353.1| 105 GCTEEILSYSFAMPWLALSQENYAKYVAA-SEEERRDLLRRILVGNILSASKGLGYVAKEHIRLDLGRMKDEICMLK 180
                                       5899*************************.*********************************************** PP

                           Cas6b_C  78 eqkmlafkgeFktnfliPdylGlGksvsrGfGtvkk 113
                                       ++k+++f+geF+t f iPd++GlGksvsrGfG+v++
  gi|330508925|ref|YP_004385353.1| 181 GTKVTGFRGEFTTCFAIPDHMGLGKSVSRGFGAVMR 216
                                       *********************************986 PP

>> Cas6b_N  Cas6b N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   0.0     8e-39   7.1e-35       1     102 [.       1     102 [.       1     103 [. 0.97
   2 ?   -2.7   0.0       0.7   6.3e+03      15      31 ..     179     195 ..     171     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 8e-39
                           Cas6b_N   1 mklktltlkfkeek.lkeseaeklRGafankfkeeellHnHkedkliYrYPliQYkvidgkplilgieegaellkei 76 
                                       m+lk+l+l++++   ++  +a+klRG+fa++f+e++llH+H +dkliYrYPliQYk++dg+pl++gi+egae+lk+i
  gi|330508925|ref|YP_004385353.1|   1 MNLKILRLTLHSAApMRG-DAAKLRGFFATSFNEHALLHQHVTDKLIYRYPLIQYKMLDGSPLVMGINEGAEVLKDI 76 
                                       89************7887.********************************************************** PP

                           Cas6b_N  77 fkkidelklgekklelkekelelkee 102
                                       ++k+de+klge++++++e+ +++k+e
  gi|330508925|ref|YP_004385353.1|  77 YDKFDEIKLGESNYTIMERGVTVKSE 102
                                       *********************99987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.7
                           Cas6b_N  15 lkeseaeklRGafankf 31 
                                       lk ++++ +RG f + f
  gi|330508925|ref|YP_004385353.1| 179 LKGTKVTGFRGEFTTCF 195
                                       66778889999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1624.54
//
Query:       gi|330508926|ref|YP_004385354.1|  [L=822]
Description: crispr-associated helicase Cas3 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-07   32.1   0.3    5.2e-07   29.8   0.1    2.2  2  ResIII          Type III restriction enzyme, res subunit
    2.3e-06   27.5   0.0    1.1e-05   25.3   0.0    2.1  2  DEAD            DEAD/DEAH box helicase
    1.5e-05   25.3   0.0    2.9e-05   24.3   0.0    1.4  1  HD_6            HD domain
    0.00022   21.5   0.0     0.0009   19.6   0.0    2.1  1  Helicase_C      Helicase conserved C-terminal domain
     0.0034   16.8   0.0       0.46    9.9   0.0    2.7  3  PhoH            PhoH-like protein
     0.0057   17.2   0.9      0.025   15.2   0.9    2.2  1  DUF5600         Domain of unknown function (DUF5600)
  ------ inclusion threshold ------
      0.046   13.8   0.0       0.11   12.5   0.0    1.7  1  Viral_cys_rich  Viral cysteine rich
      0.061   13.6   1.9       0.37   11.1   0.0    3.0  3  PqqD            Coenzyme PQQ synthesis protein D (PqqD)
       0.18   10.5   0.1       0.66    8.6   0.1    1.9  1  SNF2_N          SNF2 family N-terminal domain
        0.2   12.3   0.7         11    6.8   0.1    3.2  2  DUSP            DUSP domain
       0.25   11.4   4.2       0.64   10.1   0.1    3.5  4  AAA_14          AAA domain


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   3.2e-10   5.2e-07      21     168 ..     282     469 ..     265     472 .. 0.70
   2 ?   -1.5   0.0       1.3   2.2e+03      55     110 ..     527     597 ..     516     634 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.2e-10
                                       ...........TTSEEE.EEESTTSTHHHHHHHHHHHH-S..........-EEEEESSHHHHHHHHHHG........ CS
                            ResIII  21 s.........krdkrgl.ikmaTGtGKTlvaaklierllkkgkee.....kflflvprkslleqtleef........ 74 
                                       +         + d+r+l ++ +TGtGKTl++++++ +l+   k+e     +++   p +s+++q +  f        
  gi|330508926|ref|YP_004385354.1| 282 EdamvgisdwNLDNRILsLNVPTGTGKTLTSLSFALKLRDRLKKEknftpRIIYALPFLSIIDQNYAVFddvvtqgg 358
                                       355666666777788888*********************999988999******************99966677766 PP

                                       ...........GGGTGG.............GEEEESSS-B--.......-SEEEEEH.HHHHHTH........HHHT CS
                            ResIII  75 ...........kkflseayke.........igkkvsgdkkkakekdstnkkilvtti.qsldadseeeeeeseellr 130
                                                                      + +++ d+      +  n++i+vtt  q ++   +++++   ++ +
  gi|330508926|ref|YP_004385354.1| 359 rlkdsrlllkhH--------HladvsykteDNDEYKADESLL-LLEGWNAEIIVTTFwQYFYTLFSNKNKLLRKFNK 426
                                       666654333331........0222222112333444444444.6777788888888637777778777888888888 PP

                                       TT-SEEEEETGGGTTS.TTTHHH.......HHT---SEEEEEESS CS
                            ResIII 131 drfdviiiDEaHrlgakkswrei.......lekfkeavllglTAT 168
                                        ++ +ii DE+  +   + w+ i        ekf+ ++++ +TAT
  gi|330508926|ref|YP_004385354.1| 427 LANSIIILDEVQAVPH-QYWQLIhdatkmlCEKFN-SYVVFVTAT 469
                                       9999*******98888.777777333333355555.666666888 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                                       .-EEEEESSHHHHHHHHHHG..............GGGTGG....GEEEESSS-B--........-SEEEEE CS
                            ResIII  55 ekflflvprkslleqtleef..............kkflseaykeigkkvsgdkkka.kekdstnkkilvtt 110
                                       + fl++ +++s  +  ++ +              ++++++++ e   k++g ++k+  +++  ++k++v+t
  gi|330508926|ref|YP_004385354.1| 527 KDFLIVLNTISAANDVYNFVkglelvntenfylsTNVIPKERLERIRKIKGPSEKReANESLRKRKVIVST 597
                                       56666666666655555333444444444446667778888877666677666666344444555555554 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   6.8e-09   1.1e-05      17     169 ..     298     470 ..     287     476 .. 0.65
   2 ?   -2.4   0.0       2.2   3.6e+03      43      72 ..     522     551 ..     506     598 .. 0.59

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 6.8e-09
                                       EEEEESTTSSHHHH...HHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST..............S CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............x RF
                              DEAD  17 vlvaaeTGsGKTla...flipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid..............l 76 
                                       + ++ +TG+GKTl    f++ + +++ + +++ +p++++  P  +++ q +  +  +  + +               
  gi|330508926|ref|YP_004385354.1| 298 LSLNVPTGTGKTLTslsFALKLRDRLKK-EKNFTPRIIYALPFLSIIDQNYAVFDDVVTQGGrlkdsrlllkhhhlA 373
                                       56789*******9944455555566644.78889********************99999533444544543222221 PP

                                       EEEEEET.......TSSHHHHHHHH.HTT..CSEEEEEHHHHHHHH..HCTSSH..CTTE..EEEEEETHHHHHHTT CS
                                       xxxxxxx.......xxxxxxxxxxx.xxx..xxxxxxxxxxxxxxx..xxxxxx..xxxx..xxxxxxxxxxxxxxx RF
                              DEAD  77 rvlliig.......gvaardqlskl.dng..vdivvgtpgrlddll..stgkln..lsqv..rflVlDEadrlldqg 137
                                                     +++++ + s l  +g  ++i+v+t  + +  l  +++kl   ++++  ++++lDE++ +  q 
  gi|330508926|ref|YP_004385354.1| 374 ------DvsyktedNDEYKADESLLlLEGwnAEIIVTTFWQYFYTLfsNKNKLLrkFNKLanSIIILDEVQAVPHQ- 443
                                       ......1222222333333333333324467********8888855574444323566666689***********9. PP

                                       THHHHHHHHHHSHHHCTTSTTTSEEEEEESSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 138 fsdfinrilnqlpqitcdgklqrqvivlSATl 169
                                       + + i+   + l   +++ ++   v++++AT 
  gi|330508926|ref|YP_004385354.1| 444 YWQLIHDATKML---CEKFNS--YVVFVTATE 470
                                       555555544444...555554..49999**95 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.2
                                       TTSTS-EEEEEESSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkk 72 
                                       +g++++  liv  t + a++++n +k +  
  gi|330508926|ref|YP_004385354.1| 522 TGNPEKDFLIVLNTISAANDVYNFVKGLEL 551
                                       466667788888888888888887775544 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.8e-08   2.9e-05      45     150 ..      41     159 ..      16     192 .. 0.61

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.8e-08
                                       S-HHHHHHHHHHHHHCCCGGGSSHHHHTTS----TTS-.....-GGGT----HHHHHHHHHH............... CS
                              HD_6  45 leeealrrllaflaalHDlGKaspaFqakvpelaekleeaglelekelekarHdslgaalle............... 106
                                        +++ l + + ++ + HDlGKa++ Fq    e  e+ + ++l+ +   ++++H+ l+a +                 
  gi|330508926|ref|YP_004385354.1|  41 DDKDLLTDAAYLIGVTHDLGKATKFFQEYIIETDERKK-RSLKAK---DTTHHGLLSAFFAYavikeylhqseikgg 113
                                       4455566677777889*************966655443.444444...89**********44444444444444444 PP

                                       .HHHH....HHHHHHHTTTS---HHHHHTSS-HHHHTTHHHHHHHHHHH CS
                              HD_6 107 .evar....slaaavggHHGkppkeeeekaekkssaaedweeaqkelle 150
                                        +  +      +  v  HHG   ++ +e +e ++++++ + ++ +e +e
  gi|330508926|ref|YP_004385354.1| 114 lA--DylpiISFLTVKRHHGNLMNAMDEISEVDAEKDK-ILKVAREQIE 159
                                       31..1443355667889***777766666655555443.3333333333 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 !   19.6   0.0   5.5e-07    0.0009      12     109 ..     522     630 ..     509     632 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.5e-07
                                       HTTTTSEEEEEESSHHHHHH.HHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHH..TTS..........SSEEEES CS
                        Helicase_C  12 leeeggkilifvntidrlek.vklllekk..gikvavlhgelpqnereeileqfn..kge..........sdvLiat 73 
                                       + + +++ li++nti+ +++  ++++  +  + +  +l  +   +er+e +++ +  + e          ++v+++t
  gi|330508926|ref|YP_004385354.1| 522 TGNPEKDFLIVLNTISAANDvYNFVKGLElvNTENFYLSTNVIPKERLERIRKIKgpS-EkreaneslrkRKVIVST 597
                                       567788999999**99665553333222233667778888888888888888887541.1456677777688***** PP

                                       GGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  74 dvaerGidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       + +e G+di ++++V +  +p  ++s++q +GR+ R
  gi|330508926|ref|YP_004385354.1| 598 QLIEAGVDI-DADMVYRDFAP--MDSINQVAGRCNR 630
                                       *********.69998876666..7899999999998 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.6   5.9e+03      71      91 ..     212     232 ..     202     245 .. 0.78
   2 !    9.9   0.0   0.00028      0.46      18      57 ..     294     338 ..     277     349 .. 0.74
   3 ?    3.7   0.0     0.022        36     118     136 ..     427     445 ..     424     457 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.6
                                       -------TTTHHHHHHHTTTS CS
                              PhoH  71 dleekvdpylrplydaLkdll 91 
                                        l+ek d yl  +++ L++ l
  gi|330508926|ref|YP_004385354.1| 212 HLNEKSDLYLYFITQFLYSAL 232
                                       578999999999999998765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00028
                                       H-SEEEEE--TTSSTTHHHHHHHHHHHHT....TS-S.EEEEEE- CS
                              PhoH  18 kndivfaiGpaGtGKtylavalavealkk....kkvk.riiltrp 57 
                                       +n i+    p+GtGKt+ +++ a+++  +    k+++ rii++ p
  gi|330508926|ref|YP_004385354.1| 294 DNRILSLNVPTGTGKTLTSLSFALKLRDRlkkeKNFTpRIIYALP 338
                                       577888899***************975432112333337777666 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.022
                                       B-SEEEEE-SGGG--HHHH CS
                              PhoH 118 lndafvilDEAQnttkeqm 136
                                       l+++++ilDE Q + ++  
  gi|330508926|ref|YP_004385354.1| 427 LANSIIILDEVQAVPHQYW 445
                                       89**********9877655 PP

>> DUF5600  Domain of unknown function (DUF5600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.9   1.5e-05     0.025      30      88 ..     691     748 ..     667     766 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                           DUF5600  30 empsvfgkekkkkeLieelpeiyekvsrkhnlplgdFPdvekfkeklkaldftkfkklk 88 
                                        ++  +g+ek k++L+   +  ++++s+k +l  +d+P+v++f e l ++  + +kk +
  gi|330508926|ref|YP_004385354.1| 691 AVKMGMGDEKSKENLACLAQLSFRDLSKKFKLIEEDYPKVNVFVE-LDETAVEIWKKYQ 748
                                       34445899***********************************87.4444444444443 PP

>> Viral_cys_rich  Viral cysteine rich
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.8e-05      0.11      37      81 ..     649     693 ..     620     695 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.8e-05
                    Viral_cys_rich  37 cdrllgGicaPLsvinnatLyaeLskqlnetnlaeLsdlYikavs 81 
                                        +++++ i+ P  + + ++  +++ + + e ++ eL+++Y+kav+
  gi|330508926|ref|YP_004385354.1| 649 RKEFYKYIYDPFLMSKTLDTLKNINDTIKESDFLELNNKYFKAVK 693
                                       478999*************************************98 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3       1.3   2.1e+03      26      59 ..     161     192 ..     153     196 .. 0.72
   2 ?   -2.0   0.0       2.8   4.5e+03      50      61 ..     538     549 ..     532     550 .. 0.84
   3 ?   11.1   0.0   0.00023      0.37       9      45 ..     730     766 ..     722     772 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                                       -SSSS-.HHHHHHHHHHHCT--HHHHHHHHHHHHH CS
                              PqqD  26 ldgers.veeivaalaeeydvdeeeaeadvlafld 59 
                                       +d  ++ ++ei + l+ e    + +++ d+++ ld
  gi|330508926|ref|YP_004385354.1| 161 MDMDKTeLSEILELLLSEE---KINLKIDIDKILD 192
                                       5555566999999999554...5557777777765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHH CS
                              PqqD  50 aeadvlafldqL 61 
                                       a++dv +f++ L
  gi|330508926|ref|YP_004385354.1| 538 AANDVYNFVKGL 549
                                       89*******987 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00023
                                       -..EEE--CHHHHHHHH-SSSS-HHHHHHHHHHHCT- CS
                              PqqD   9 tgkyisLnetgafiWklldgersveeivaalaeeydv 45 
                                        + +++L+et+ +iWk  ++ r   ++ ++++++ ++
  gi|330508926|ref|YP_004385354.1| 730 VNVFVELDETAVEIWKKYQDMRMEKDLKERIRKKLEI 766
                                       45568*************9989899988888877665 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 ?    8.6   0.1   0.00041      0.66      65     214 ..     305     469 ..     302     473 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00041
                                       TS--HHHHHHHHH...HHTTTS---.......S-EEEE-.-H.HHHHHHHHHHHHH-TTS.-EEE--SSHHHH.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.... RF
                            SNF2_N  65 GLGKTvqvlalilaqrakeekdkekkrkdtlagptLivv.Pa.slldqWeneierhvsss.alrvlvyggqkk.... 134
                                       G GKT+++l++ l++r+  +       k++  +p +i + P  s++dq +  ++  v ++ +l+     ++ +    
  gi|330508926|ref|YP_004385354.1| 305 GTGKTLTSLSFALKLRDRLK-------KEKNFTPRIIYAlPFlSIIDQNYAVFDDVVTQGgRLK-----DS-Rlllk 368
                                       78888888888885544322.......3344566666543667888888888877776541231.....11.12333 PP

                                       ...............-----------------EEEE-HHHHHHHT.........TTS-S-S-SEEEES-GGGT--T. CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            SNF2_N 135 ...............mkkkntkvapklladydvvittYdvlsreaelq...kkrsvlkqvewkrvvlDEghtlkns. 192
                                                      + k  + ++    +++++++tt+  +     ++   k   +++++    ++lDE + +  + 
  gi|330508926|ref|YP_004385354.1| 369 hhhladvsyktedndEYKADESLLLLEGWNAEIIVTTFWQYFYTL-FSnknKLLRKFNKLANSIIILDEVQAVPHQy 444
                                       344567788777766555556666777899*******98776444.443447778888999**********999886 PP

                                       ...TSHHHHHHHH---S-EEEE-S- CS
                                       ...xxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 193 ...tskaaeavskLstsnrwiltGT 214
                                             a++++++  +s+ + +t+T
  gi|330508926|ref|YP_004385354.1| 445 wqlIHDATKMLCEKFNSYVVFVTAT 469
                                       5442444555544445555555555 PP

>> DUSP  DUSP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.19     3e+02      33      66 ..     180     220 ..     102     234 .. 0.75
   2 ?    6.8   0.1    0.0065        11      51      90 ..     383     424 ..     341     426 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.19
                                       S--.SB-CGGGB..............TTTEB-SS--BTTTEE CS
                              DUSP  33 kpg.pIdnsdllkappltk.......engrlkpnlqegrdye 66 
                                       k++ +Id +++l +++l++       +++rl ++l+e++d +
  gi|330508926|ref|YP_004385354.1| 180 KINlKIDIDKIL-DYILQDapreigrKEKRLVRHLNEKSDLY 220
                                       455589999999.56666667777899999999999998844 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0065
                                       TTTEB-SS--B..TTTEEEEEHHHHHHHHHHC-T----EEEE CS
                              DUSP  51 engrlkpnlqe..grdyeivpeevwkfLvqwYgggpeikrkv 90 
                                       ++++  ++l +  g++ ei+    w+++++ + +++++ rk 
  gi|330508926|ref|YP_004385354.1| 383 DEYKADESLLLleGWNAEIIVTTFWQYFYTLFSNKNKLLRKF 424
                                       4455555554456********************999998886 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      0.95   1.5e+03      29      49 ..     146     166 ..     120     217 .. 0.61
   2 ?   10.1   0.1   0.00039      0.64      46      99 ..     414     468 ..     390     481 .. 0.66
   3 ?   -0.4   0.1      0.68   1.1e+03      50      83 ..     475     508 ..     446     511 .. 0.70
   4 ?   -1.1   0.1       1.1   1.7e+03      53      86 ..     513     549 ..     480     560 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.95
                            AAA_14  29 kkesilyinldderdkkladp 49 
                                       +k++il ++ ++ +  +++++
  gi|330508926|ref|YP_004385354.1| 146 EKDKILKVAREQIESMDMDKT 166
                                       344444444444444333333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00039
                            AAA_14  46 ladpekllelileklkeekktylflDEiqev.....pewekalkslvdegknldvivtG 99 
                                       +++++kll+ + ++     +++++lDE+q v     + + +a k l+++ + + v+vt 
  gi|330508926|ref|YP_004385354.1| 414 FSNKNKLLRKFNKL----ANSIIILDEVQAVphqywQLIHDATKMLCEKFNSYVVFVTA 468
                                       34444455555554....5689*********4433333567777777777777777776 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.68
                            AAA_14  50 ekllelileklkeekktylflDEiqevpewekal 83 
                                       ++ + +i+e ++++++++  lD i  +p++e+al
  gi|330508926|ref|YP_004385354.1| 475 DEAIGEIKEIVQKKEEYFRGLDRIELIPRIETAL 508
                                       3345566666656688889999999999999987 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.1
                            AAA_14  53 lelilek.lke..ekktylflDEiqevpewekalksl 86 
                                        +++lek +++  ek+ +++l  i+ ++++++++k+l
  gi|330508926|ref|YP_004385354.1| 513 FKVLLEKdITGnpEKDFLIVLNTISAANDVYNFVKGL 549
                                       2344444333345666667777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (822 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.46
# Mc/sec: 5332.56
//
Query:       gi|330508927|ref|YP_004385355.1|  [L=237]
Description: CRISPR-associated protein Cas5 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.5e-07   29.7   0.0    6.9e-07   29.4   0.0    1.2  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 !   29.4   0.0   3.8e-11   6.9e-07       2      57 ..       6      62 ..       5     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.8e-11
                                      EEEEEECCEE-EB-TTCCSCCCBESS--HHHHHHHHHHHHT--TTS-.-CCCCTTEE CS
                         Cas_Cas5d  2 LllrlegplasfgrpsrkveretydvPtkSavlGllaaalGirrddd.leelkpalr 57
                                      +++ ++g++a f+  +      ty +P+++a+ Gl++a+ G++  +   +  k  ++
  gi|330508927|ref|YP_004385355.1|  6 IVFDVWGDYAHFRKNYSTSSPLTYSFPPRTALSGLIGAVVGLDKAEYfRHFCKVDAN 62
                                      89****************************************998875333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.58
# Mc/sec: 1227.72
//
Query:       gi|330508928|ref|YP_004385356.1|  [L=306]
Description: crispr-associated protein, Csh2 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-63  212.3   0.0      1e-62  212.0   0.0    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 !  212.0   0.0   5.6e-67     1e-62       1     251 [.       7     254 ..       7     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 212.0 bits;  conditional E-value: 5.6e-67
                          Cas_Cas7   1 nryefvllfdvkngNpNGDpdagnkPRidpetgeglvsDvclKrkiRnyvekakeekeiyvkekkv......lnekk 71 
                                       nr e+++l+d+++gNpNGDp+++nkPRid+etg +lv+Dv+lKr+iR+y+ + k  +ei+v+e         +++ k
  gi|330508928|ref|YP_004385356.1|   7 NRSEILFLYDIRDGNPNGDPMDENKPRIDEETGANLVTDVRLKRTIRDYLYNFKA-QEIFVREIIYdtqngyIQDGK 82 
                                       899*************************************************997.789997765544333344444 PP

                          Cas_Cas7  72 eeaykdeekkelreamcenffDvRtFGavmstgvngqvr.GpVqltfarslepvlpeeqsitrmaateekkekekkq 147
                                       ++a+ d e  + +e+++++++DvR+FG+v++ + ++++  GpVq++++rsl++v +  ++ t  +a++e  +   kq
  gi|330508928|ref|YP_004385356.1|  83 KRAK-DFE--DKAERILNECIDVRLFGGVIPLKDDSITYtGPVQFKMGRSLHRVSMMHIKGTGAFASKE-GS---KQ 152
                                       4444.333..35899****************876666667**************999999999999888.33...79 PP

                          Cas_Cas7 148 rtmgrkhivpyglYrahgfinanlaektgfseeDlellkeallnmfehdrsaargemevrkllvfehesklgnapaa 224
                                        t+ ++ ++ y+l+ ++g+in+n+a++t+++eeDl+ll e ++n++++  s+++ ++ +r ll +++    +n+   
  gi|330508928|ref|YP_004385356.1| 153 ATFREEDFLAYSLISFYGIINENAAKHTHLTEEDLKLLLEGIWNGTKSLISRSKAGQVPRLLLKVNY--SKENYHIG 227
                                       *******************************************************************..55566666 PP

                          Cas_Cas7 225 klfdlvkvekkdeveparsfedyeitv 251
                                        l +++k+e +  +e++r+ +dy+++v
  gi|330508928|ref|YP_004385356.1| 228 DLDKMLKLETEIPHENIRDTTDYQLDV 254
                                       66777***9998999*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.39s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1635.42
//
Query:       gi|330508929|ref|YP_004385357.1|  [L=627]
Description: crispr-associated protein [Methanosaeta concilii GP6]
Scores for complete 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-172  575.2  25.3   2.1e-172  575.1  25.3    1.0  1  Cas_TM1802      CRISPR-associated protein TM1802 (cas_TM1802)
  ------ inclusion threshold ------
      0.053   13.8   2.2      0.063   13.6   0.3    2.1  2  Retrotrans_gag  Retrotransposon gag protein
        1.2    9.2   5.4       0.62   10.2   0.1    2.7  3  Spore_III_AB    Stage III sporulation protein AB (spore_III_A
        1.5    8.8   4.1         17    5.5   0.2    3.2  4  DUF1870         Domain of unknown function (DUF1870)


Domain annotation for each model (and alignments):
>> Cas_TM1802  CRISPR-associated protein TM1802 (cas_TM1802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  575.1  25.3  4.7e-176  2.1e-172       1     607 [.       1     609 [.       1     610 [. 0.96

  Alignments for each domain:
  == domain 1  score: 575.1 bits;  conditional E-value: 4.7e-176
                        Cas_TM1802   1 MleaikeiGeillggegekdeleqltedpkae..kkhvliinfdtekekleykgveeidleefdekktakylYlkkg 75 
                                       M++a+ +iG++++   g++++l++++e+p+++  +k vli+ ++++++++ ++++     +ef++    +ylY kkg
  gi|330508929|ref|YP_004385357.1|   1 MIDAVSRIGNYIQMTYGGDNLLSTFIENPNSNgkYKFVLIVILKETEGNYLFSHIA---FDEFSD--YPRYLY-KKG 71 
                                       9**********888899***************************999999999777...9*****..88****.*** PP

                        Cas_TM1802  76 nangsnssqtykttkklekllskkipnlldleklgveknlseeekellkkiekelsknkekiakelekklkkiknek 152
                                        +ng+++++t+k++ +++k+++++++++  +++ ++ + +s+eeke lkk++ +l+++ke i+ el++k++++ +++
  gi|330508929|ref|YP_004385357.1|  72 PSNGTDATPTSKVAGDIWKTFQNRFLKW--FQNYETYD-ISKEEKESLKKMNMALRDQKETILAELNEKFSQK-RSD 144
                                       ****************************..77777766.*********************************9.557 PP

                        Cas_TM1802 153 evvlltlki....dgkylgdieeyrevllrklierlfekkkekkkkskegvCsvCgeekeevtgdvstklkfkfytt 225
                                       e +++tl+i    +++ylgd+++++++llrk +++++ kk+++++ +k++ CsvC+  k+ev+g++     ++f+t+
  gi|330508929|ref|YP_004385357.1| 145 EYAIITLGIerggNIRYLGDLQAFKNILLRKGKDKYYLKKSQGESLGKDSACSVCRGTKDEVYGFAIP---WTFHTF 218
                                       9*********99999*************************************************9978...****** PP

                        Cas_TM1802 226 DkpgFasg.fnkknawknfpiCeeCarkLeaGkkyleeklsfkfyglnyyvIPkfif..slekvleeiidilsslkk 299
                                       DkpgF++g f+ +++wkn+p+C +Ca++Le+Gkky+ee+l+f fyg++y+++Pk+ f  +++++l+e++ il + + 
  gi|330508929|ref|YP_004385357.1| 219 DKPGFIAGgFKVNESWKNTPVCFDCAKHLEVGKKYIEENLDFGFYGFRYLLVPKLAFgrDDNETLKEVLGILGNKD- 294
                                       *********************************************************99999************65. PP

                        Cas_TM1802 300 lkkleklekklkkrldldeeeileeledekdvlllnfLFyerksqsafrilllieDVppsrlskilkakekvdekf. 375
                                       +k++ k+++++k+r+++deee+le ++d+kd+++ +++Fy+ k+qs++rillli+ ++psrl+++++akekvde+f 
  gi|330508929|ref|YP_004385357.1| 295 QKRNLKINREVKNRITSDEEEVLEFVKDQKDFFSNSLIFYK-KEQSSYRILLLIDGILPSRLKALFDAKEKVDERFk 370
                                       67**************************************5.**********************************5 PP

                        Cas_TM1802 376 ..nkli..l..eekaslkftfgslykffpirkkkkkdddkykkfLeivnsifkgrpisyslLikqflelirksfkne 446
                                         n+ i  +  +ek++l+f+fg+l++ffp+++ k++++dk+  fLe+v++if g +isy lL++++++++r++f+++
  gi|330508929|ref|YP_004385357.1| 371 iyNDSIlsEdqREKNHLEFNFGVLRRFFPSES-KNRTFDKI--FLEVVDKIFVGDQISYYLLMGFIMSKVREAFIKG 444
                                       55444476156899**************7777.********..********************************** PP

                        Cas_TM1802 447 ekeekeiaykvlkanlllkFLeelnllkg...........gkkmdegelelkvedeekldeffkeyietlnyteqkk 512
                                             ++ ++l+ +lll+++eelnl+k            g+ + + e+ ++++ e+++++ff+ +++++n t++kk
  gi|330508929|ref|YP_004385357.1| 445 Y----PTNITTLNGFLLLHYIEELNLFKAnkvemkdmneqGNGVLRIEELESLPLEQRVERFFEANKSFFN-TDAKK 516
                                       *....9*********************99999988888888888888888889999***************.***** PP

                        Cas_TM1802 513 alFLlGvLlgellniQykkrkskPflkkLnglgmderdikrllnevinKlrqYkknlykkkelleaiakyllesesn 589
                                       a+FL G+L+++llniQ++++k++Pf++kL+gl+m+e  ikrll+e++nKl++Y kn+y  k l+ +ia++++ ++ n
  gi|330508929|ref|YP_004385357.1| 517 ATFLEGALTQMLLNIQWNDKKATPFRSKLHGLKMNEALIKRLLPEIQNKLEEYGKNYY--KDLESLIANHFVLAGVN 591
                                       *******************************************************998..***************99 PP

                        Cas_TM1802 590 wklskdElnFyflsGysl 607
                                       wk+ +dEl+Fyf++G+ +
  gi|330508929|ref|YP_004385357.1| 592 WKEVDDELSFYFVLGMDM 609
                                       ****************87 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   1.4e-05     0.063      26      65 ..      86     125 ..      56     150 .. 0.83
   2 ?   -2.6   0.1       1.6     7e+03      27      51 ..     384     408 ..     371     411 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                    Retrotrans_gag  26 sesWkdlkkaflktflpserkdqleeelsslrQgtesvre 65 
                                        ++Wk+++++flk f++ e++d ++ee  sl++ ++ +r+
  gi|330508929|ref|YP_004385357.1|  86 GDIWKTFQNRFLKWFQNYETYDISKEEKESLKKMNMALRD 125
                                       79**********************************9997 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                    Retrotrans_gag  27 esWkdlkkaflktflpserkdqlee 51 
                                       ++  +++  +l++f+pse k+++ +
  gi|330508929|ref|YP_004385357.1| 384 KNHLEFNFGVLRRFFPSESKNRTFD 408
                                       5777888888999999888887755 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 ?    0.4   0.2      0.14   6.1e+02      71     119 ..      90     140 ..      77     154 .. 0.59
   2 ?   10.2   0.1   0.00014      0.62      98     145 ..     271     318 ..     267     326 .. 0.90
   3 ?   -3.1   0.1       1.6   7.3e+03     130     154 ..     549     573 ..     543     576 .. 0.51

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.14
                                       HHHHHHHH..STSS-HHHHHHHHHHHHGGG.S---HHHHHHHHHHHHHHT- CS
                      Spore_III_AB  71 eevaerlee.kegesfeeaweeavekllkk.laLkkedkeilkelgeslgy 119
                                       +++ +r+ +  ++ + +++ +e+ e+l+k  +aL ++   il+el e++ +
  gi|330508929|ref|YP_004385357.1|  90 KTFQNRFLKwFQNYETYDISKEEKESLKKMnMALRDQKETILAELNEKFSQ 140
                                       444444444344555555555555555332277777777777777776665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00014
                                       GGS---HHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Spore_III_AB  98 kklaLkkedkeilkelgeslgysdregqlkalelaleeleeeieeare 145
                                       +kla+ ++d e lke+   lg+ d + +lk  + ++++++  +ee  e
  gi|330508929|ref|YP_004385357.1| 271 PKLAFGRDDNETLKEVLGILGNKDQKRNLKINREVKNRITSDEEEVLE 318
                                       578999**********************************99999876 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHHHHHHT-XXX CS
                      Spore_III_AB 130 elaleeleeeieeareeakkkekly 154
                                       ++ ++ +++ + e++++ ++++k y
  gi|330508929|ref|YP_004385357.1| 549 KMNEALIKRLLPEIQNKLEEYGKNY 573
                                       4444445555555555555555544 PP

>> DUF1870  Domain of unknown function (DUF1870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2    0.0038        17      40      90 ..     105     171 ..      87     178 .. 0.83
   2 ?   -2.0   0.1      0.81   3.6e+03      64      89 ..     303     328 ..     286     343 .. 0.49
   3 ?   -3.2   0.0       1.8   8.2e+03      78     104 ..     500     527 ..     463     530 .. 0.66
   4 ?    2.9   0.0     0.023   1.1e+02      56     100 ..     549     593 ..     541     609 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0038
                                       SS---HHHHHHHHHHHHHHHHHHHHHHHHHCCS-S--................EEE--SSHHHHHTT CS
                           DUF1870  40 alpipdeivaelkelkklrkkkieeiveklndrigns................tlryystlteflkv 90 
                                       +  i++e +++lk++    +++ e i+ +ln++  ++                 +ry ++l++f+++
  gi|330508929|ref|YP_004385357.1| 105 TYDISKEEKESLKKMNMALRDQKETILAELNEKFSQKrsdeyaiitlgierggNIRYLGDLQAFKNI 171
                                       56789999999****9999999999999999999776788899999999999999999999999875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.81
                                       HHHHHHCCS-S--EEE--SSHHHHHT CS
                           DUF1870  64 eiveklndrignstlryystlteflk 89 
                                         v++   + +++ l + +++++f +
  gi|330508929|ref|YP_004385357.1| 303 REVKNRITSDEEEVLEFVKDQKDFFS 328
                                       33322222222334444444444432 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.8
                                       EE--SSHHHH.HTTSTT--HHHHHHHHH CS
                           DUF1870  78 lryystltef.lkvypeadalqWklhqs 104
                                        r++   ++f +++ + a++l+  l q+
  gi|330508929|ref|YP_004385357.1| 500 ERFFEANKSFfNTDAKKATFLEGALTQM 527
                                       4777766654156667777777666665 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHCCS-S--EEE--SSHHHHHTTSTT--HHHHH CS
                           DUF1870  56 klrkkkieeiveklndrignstlryystlteflkvypeadalqWk 100
                                       k+ + +i+  + ++++++++    yy++l++    +     ++Wk
  gi|330508929|ref|YP_004385357.1| 549 KMNEALIKRLLPEIQNKLEEYGKNYYKDLESLIANHFVLAGVNWK 593
                                       5778999999*******************9988877777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1106  (0.0616878); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); 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: 0.73u 0.37s 00:00:01.10 Elapsed: 00:00:00.54
# Mc/sec: 3499.41
//
Query:       gi|330508930|ref|YP_004385358.1|  [L=211]
Description: crispr-associated protein Cas4 [Methanosaeta concilii GP6]
Scores for complete 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   63.0   3.5    4.3e-17   62.7   3.5    1.1  1  Cas_Cas4  Domain of unknown function DUF83
    3.2e-07   30.5   6.9    6.1e-07   29.6   4.3    1.9  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.096   12.8   0.1       0.65   10.3   0.0    2.3  2  TPR_2     Tetratricopeptide repeat


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 !   62.7   3.5   7.1e-21   4.3e-17       6     161 ..      29     211 .]      24     211 .] 0.79

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 7.1e-21
                          Cas_Cas4   6 qyyliCkrklwlish.ei.tleensetvelGkllhe......esyerek.........kevelse........siki 57 
                                         yl+C+r +++++  +i + ee+  +v+ G+ lhe      +               ke+++ +        ++++
  gi|330508930|ref|YP_004385358.1|  29 LEYLFCPRFIFFMHClGIaQREERRYKVQKGRELHEsrekvnRD----YvrkrlncvrKEISV-YltsqkyhfKGEV 100
                                       579***********9877245667789*********66555433....144347778877776.2346799999*** PP

                          Cas_Cas4  58 Dvve.kekeklvvvEvKkskkk...eeaaklQllyY.lllLekkgveikeGvleypkekkre.evelteelreelek 128
                                       D v   e++++ + ++K  + k    + +k+Q   Y ll++e+ gv++k+G++ y  +++ + e+ +++++ e++++
  gi|330508930|ref|YP_004385358.1| 101 DEVLfLEDGTAAPLDYKYAEFKntvYRTHKFQAALYgLLIMEHFGVDVKRGFVCYTRSNNYVaEIDFKQKDYEKAKE 177
                                       *9988899999999999876553335677***99993555669************998876527************* PP

                          Cas_Cas4 129 aikeieeiisse.kppkvkkkkiCkkCayaelCl 161
                                       +++ei  ii++  +p+ +k+k +C  C y+++C+
  gi|330508930|ref|YP_004385358.1| 178 IVREILMIIQRGyYPDGTKQKARCVDCTYRNICV 211
                                       ************4555567777***********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 !    4.5   0.5    0.0046        28       3      48 ..      24      70 ..      23      84 .. 0.75
   2 !   29.6   4.3     1e-10   6.1e-07      88     254 ..      54     210 ..      48     211 .] 0.67

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0046
                          PDDEXK_1  3 SvsrletfleCplrfflryllgl..reeeeleapdlGtlvHaaleefy 48
                                      +vs    +l Cp+  f+ + lg+  ree + +  + G+ +H+  e++ 
  gi|330508930|ref|YP_004385358.1| 24 TVSDALEYLFCPRFIFFMHCLGIaqREERRYKV-QKGRELHESREKVN 70
                                      5788889******99999*****6555444443.77*****9877665 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1e-10
                          PDDEXK_1  88 ylaeklkevleklverlaeeleakrgfrpvalelefg..gekvrLkGriDrvd.dkegelriiDyKtgsappkskel 161
                                       y  +k +e+ e+  ++ ++    ++ +  v+ e+++   ++k+ +kG +D v   ++g++  +DyK ++   + k+ 
  gi|330508930|ref|YP_004385358.1|  54 YKVQKGRELHESREKVNRD--YVRKRLNCVRKEISVYltSQKYHFKGEVDEVLfLEDGTAAPLDYK-YA---EFKNT 124
                                       4444444444444223444..333335566666555564699***********888889*******.55...22221 PP

                          PDDEXK_1 162 aelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkkmalteeeleallqeleelaeeilagefp 238
                                           + +Q +lY l+++e+   + + +++ + y r        ++ v++++ ++++ e++++ ++e++  i++g +p
  gi|330508930|ref|YP_004385358.1| 125 VYRTHKFQAALYGLLIMEH--FGVDVKRGFVCYTRS-------NNYVAEIDFKQKDYEKAKEIVREILMIIQRGYYP 192
                                       1235566************..443322555555555.......6777777888999999999999998888877666 PP

                          PDDEXK_1 239 arpskk..CeyCpyksvC 254
                                           +k  C  C y+ +C
  gi|330508930|ref|YP_004385358.1| 193 DGTKQKarCVDCTYRNIC 210
                                       55555588********** PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.54   3.2e+03       4      18 ..      41      55 ..      39      55 .. 0.85
   2 ?   10.3   0.0   0.00011      0.65       4      28 ..     159     183 ..     156     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.54
                             TPR_2  4 lynlGlayyklgdye 18
                                       ++lG a ++  +y+
  gi|330508930|ref|YP_004385358.1| 41 MHCLGIAQREERRYK 55
                                      6899***99999995 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00011
                             TPR_2   4 lynlGlayyklgdyeeAleafekAl 28 
                                       +++ +++ +k++dye+A+e  ++ l
  gi|330508930|ref|YP_004385358.1| 159 NNYVAEIDFKQKDYEKAKEIVREIL 183
                                       67889999**********9877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); 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: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1146.40
//
Query:       gi|330508931|ref|YP_004385359.1|  [L=95]
Description: crispr-associated protein Cas2 [Methanosaeta concilii GP6]
Scores for complete 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   78.4   0.3      4e-22   78.2   0.3    1.1  1  CRISPR_Cas2  CRISPR associated protein Cas2


Domain annotation for each model (and alignments):
>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.3   2.2e-26     4e-22       1      75 [.       1      73 [.       1      74 [. 0.98

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 2.2e-26
                                      EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCHHHT CS
                       CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekqfek 75
                                      mlv+v+YDi ++++ r++vaki+k+yG+ rvQ+S F+g+l++++ + l  +++ iid++ ds+++++++e++f k
  gi|330508931|ref|YP_004385359.1|  1 MLVWVIYDI-SENRYRSRVAKICKNYGLFRVQKSAFLGDLNRNESDSLTLECEAIIDES-DSVYVFPMCEDCFDK 73
                                      99*******.***********************************************99.*************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 542.42
//
Query:       gi|330508932|ref|YP_004385360.1|  [L=374]
Description: crispr-associated protein Cas1 [Methanosaeta concilii GP6]
Scores for complete 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-78  263.1   0.0      3e-78  262.9   0.0    1.1  1  Cas_Cas1  CRISPR associated protein Cas1
  ------ inclusion threshold ------
      0.017   14.9   0.4      0.041   13.6   0.2    1.6  2  DUF4194   Domain of unknown function (DUF4194)


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 !  262.9   0.0   3.3e-82     3e-78       1     282 [.       3     289 ..       3     290 .. 0.97

  Alignments for each domain:
  == domain 1  score: 262.9 bits;  conditional E-value: 3.3e-82
                                       EEEESTEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEESTEEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEE.S CS
                          Cas_Cas1   1 lyvteqgaylrkkgerlvvekegeekkeiplediesivifgevslstkalrllaekgipvvflsengkylgrlep.e 76 
                                       l+++++gaylrk+g+ + v++e++ + ei + +++si+i++ + ++t+a++l+++++i++vfl+++g ++gr+++ +
  gi|330508932|ref|YP_004385360.1|   3 LVINSYGAYLRKNGNCFLVKREDR-SFEIAVGKVNSILITTAAYITTDAIKLAVDNNIDIVFLDSHGDPYGRVWHpK 78 
                                       689*******************88.9*************************************************88 PP

                                       SSSTHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTT..HHHHCHCHHHHHHHHHHHH-.....H CS
                          Cas_Cas1  77 esgnvelrraQyraaddeekrlelakkivagklenqrkvlrrlkrdree..eeleeaieeleellekleka.....e 146
                                         +++++rr+Q++++d+ + +l+lak++   klenq  +l r+ + ree  + l+  i e+e+ +e+++++     +
  gi|330508932|ref|YP_004385360.1|  79 LGSTTLIRRRQLEVYDTLD-GLNLAKEWGLRKLENQIDLLGRMGKTREEkrDLLDGYILEIENSRERMKRLrgtieS 154
                                       8999999********9988.***************************7778999****************9999*99 PP

                                       SHHHHHHHHHHHHHHHHHHHHHHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--T CS
                          Cas_Cas1 147 sleeLrgiEGeaakaYfeafdkllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedr 223
                                        ++ ++g+EG+aa+aYfea++++++e+++f gRsr+p+kD++NalL++gY++lys v + +  +gLdPy+GfLH+d+
  gi|330508932|ref|YP_004385360.1| 155 RRQDMLGLEGKAARAYFEAISSIMPEKYRFAGRSRNPAKDEFNALLNYGYGVLYSLVEKGCIIAGLDPYLGFLHSDS 231
                                       99*************************************************************************** PP

                                       TSS-HHHHHHHHHHHHHHCHHHHHHHHHTTSS-GGGEEEETTEEEE-HHHHHHHHHHHH CS
                          Cas_Cas1 224 pgrpsLalDLmEefRpllvDrlvlslinkrqlkekdFekeengvlLteegrkkfleafe 282
                                       ++++sL++D++E+fR  +vD++v+ l+++r++k+  Fe  e+g+ L++eg+ +++e ++
  gi|330508932|ref|YP_004385360.1| 232 YNKKSLVFDIIEMFRI-YVDETVVFLFSRRMVKDGFFEPLEQGMGLSKEGKAALIESLN 289
                                       ***************7.9*************************************9876 PP

>> DUF4194  Domain of unknown function (DUF4194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   4.6e-06     0.041      31     133 ..      45     155 ..      41     160 .. 0.87
   2 ?   -2.6   0.0      0.46   4.1e+03     103     131 ..     172     201 ..     163     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.6e-06
                           DUF4194  31 yLadlglelvldedegvaflrqveaeeeee......lprllrrrsLsleetllLlvLRklyqeaeregs..lservv 99 
                                       y     ++l +d++  ++fl + ++  ++         +l+rrr+L  ++tl  l L k++  ++ e +  l +r+ 
  gi|330508932|ref|YP_004385360.1|  45 YITTDAIKLAVDNNIDIVFLDSHGDPYGRVwhpklgSTTLIRRRQLEVYDTLDGLNLAKEWGLRKLENQidLLGRMG 121
                                       666677899****************88888******99***********************999999999999**** PP

                           DUF4194 100 vsveeivekles.flpldrdeakfkkrldaalrkl 133
                                        ++ee ++ l    l  ++++++  krl++++++ 
  gi|330508932|ref|YP_004385360.1| 122 KTREEKRDLLDGyILEIENSRER-MKRLRGTIESR 155
                                       **********9966666666555.99999998765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.46
                           DUF4194 103 eeivekles.flpldrdeakfkkrldaalr 131
                                       e i + + + +  ++r++ + k++++a+l+
  gi|330508932|ref|YP_004385360.1| 172 EAISSIMPEkYRFAGRSRNPAKDEFNALLN 201
                                       566666666677778888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2083.58
//
Query:       gi|330508933|ref|YP_004385361.1|  [L=68]
Description: hypothetical protein MCON_3273 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-14   53.1   0.3      4e-14   52.8   0.3    1.1  1  DUF104          Protein of unknown function DUF104
  ------ inclusion threshold ------
       0.05   13.5   1.3      0.085   12.8   0.5    1.8  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.3   4.4e-18     4e-14       4      54 ..       3      51 ..       1      54 [. 0.94

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 4.4e-18
                            DUF104  4 vIeavYEnGvLKPLekvdLkEGeevkikIeeakeilkklkgilkeadeeel 54
                                       ++a+YEn+vLKPLek+dL EG  v+i+I +  + +++l g+lk++d++++
  gi|330508933|ref|YP_004385361.1|  3 MVKARYENNVLKPLEKLDLTEGDVVEIEIVK--SNADRLVGLLKDIDIDSV 51
                                      589****************************..***********9999976 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   9.5e-06     0.085      17      36 ..      17      35 ..      12      48 .. 0.79
   2 ?   -0.7   0.0      0.17   1.5e+03      35      41 ..      59      65 ..      49      68 .] 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.5e-06
                                      HHCCEECTCEEEEEECTTCC CS
                    MazE_antitoxin 17 felgireGdevelevdgdki 36
                                      ++l++ eGd ve+e+++   
  gi|330508933|ref|YP_004385361.1| 17 EKLDLTEGDVVEIEIVKS-N 35
                                      689************984.3 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.17
                                      CCCCCCC CS
                    MazE_antitoxin 35 kiilrpl 41
                                      +i++r++
  gi|330508933|ref|YP_004385361.1| 59 DIWVRKV 65
                                      7999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 482.10
//
Query:       gi|330508934|ref|YP_004385362.1|  [L=139]
Description: PIN domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-07   30.1   0.7    6.4e-07   29.9   0.7    1.1  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.016   16.0   0.1      0.022   15.5   0.1    1.3  1  PIN_3     PIN domain
      0.022   15.2   0.2       0.03   14.8   0.2    1.3  1  PIN_12    PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.7   1.1e-10   6.4e-07       1     119 [.       2     121 ..       2     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.1e-10
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEB CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpi 73 
                                       +++DT+++++++ +++ +  ++ ll  +     + +++  ++  +  +l r   + +++++++++  ++++l+i ++
  gi|330508934|ref|YP_004385362.1|   2 YLIDTNIFLEAMLERKYRNDCLTLLRMIdkgeINAFVTTYSIHSIETILDR-IGNLDALRTFLKSIGRMKGLNIYNT 77 
                                       68**********666666666666665556599999999999999999999.7777777777777777777777775 PP

                                       CHHHHHHHHHHHHHHH..SBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                               PIN  74 daeiaeeaaeialkyg..llpnDaliaAtAkehgikliatfDedfrrv 119
                                       d ++ + + + +      l+  Dal   + k+ ++++i +fD++f+ +
  gi|330508934|ref|YP_004385362.1|  78 DLRDELAVIDEM---AvdLDFDDALQSYVTKKLNLQII-SFDRHFDGI 121
                                       555555544444...335******************99.******876 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   3.6e-06     0.022       3      59 ..       3      59 ..       1     101 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                             PIN_3  3 vlDtnvlldallfdsp..aarkildaletgaitlvvsprlldElervlarelaypqfkl 59
                                      ++Dtn++l+a+l ++   +   +l+++ +g+i ++v+   +  +e +l+r    +  +l
  gi|330508934|ref|YP_004385362.1|  3 LIDTNIFLEAMLERKYrnDCLTLLRMIDKGEINAFVTTYSIHSIETILDRI--GNLDAL 59
                                      79**********776577777888888******************999887..444444 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2     5e-06      0.03       3     105 ..       4     108 ..       3     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5e-06
                            PIN_12   3 iDTnifldeffrlseeealkklleliesgkiklivpdivld..Eflknrekkieeskklekalkslsklksakkkln 77 
                                       iDTnifl+  ++ ++ +++  ll+ i++g+i+ +v+   ++  E++  r  ++++ +++ k++ +++ l+  + +l 
  gi|330508934|ref|YP_004385362.1|   4 IDTNIFLEAMLERKYRNDCLTLLRMIDKGEINAFVTTYSIHsiETILDRIGNLDALRTFLKSIGRMKGLNIYNTDLR 80 
                                       9*******99999999*************888776654444115555555556655777777777777777666666 PP

                            PIN_12  78 ekkkllslkeikkkieekveeslkklle 105
                                       ++ + +++ +++ +++++++++++k l+
  gi|330508934|ref|YP_004385362.1|  81 DELAVIDEMAVDLDFDDALQSYVTKKLN 108
                                       6666666666666666666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1075.45
//
Query:       gi|330508935|ref|YP_004385363.1|  [L=437]
Description: hypothetical protein MCON_3275 [Methanosaeta concilii GP6]
Scores for complete 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-12   44.4   0.0    1.4e-11   43.9   0.0    1.1  1  DUF1100        Alpha/beta hydrolase of unknown function (DUF1
    2.9e-09   36.7   0.0    5.6e-07   29.2   0.0    2.5  1  Peptidase_S9   Prolyl oligopeptidase family
    3.8e-07   30.9   0.0    7.8e-07   29.9   0.0    1.5  1  Abhydrolase_6  Alpha/beta hydrolase family
    7.4e-06   25.4   0.0    1.6e-05   24.3   0.0    1.5  1  Hydrolase_4    Serine aminopeptidase, S33
    8.3e-06   25.9   0.0    1.5e-05   25.0   0.0    1.4  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
    4.3e-05   22.4   0.0    8.6e-05   21.4   0.0    1.5  1  AXE1           Acetyl xylan esterase (AXE1)
    8.5e-05   22.3   0.0     0.0036   16.9   0.0    2.2  1  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
     0.0021   17.7   0.1     0.0069   16.1   0.1    1.8  2  Abhydrolase_1  alpha/beta hydrolase fold
     0.0091   15.9   0.0      0.016   15.1   0.0    1.3  1  Abhydrolase_3  alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.028   14.0   0.0      0.068   12.7   0.0    1.5  1  DLH            Dienelactone hydrolase family
       0.15   12.0   0.0       0.24   11.3   0.0    1.3  1  UPF0227        Uncharacterised protein family (UPF0227)


Domain annotation for each model (and alignments):
>> DUF1100  Alpha/beta hydrolase of unknown function (DUF1100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   8.4e-15   1.4e-11      81     320 ..      66     318 ..      53     344 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 8.4e-15
                           DUF1100  81 delldtvvGyrsGn...wiyewaklgmlhqkkaaee..kde..eaaeellaaallysiag.yphlkgdnlalqa.qv 148
                                       +e ldt    ++G+   w  +w + +      a e   +++  +a e++l a+++y  ag y  ++ d+  + +   
  gi|330508935|ref|YP_004385363.1|  66 NECLDTAFRIKDGDaesWYGQWNRTAARLESTAEEFlaSGHkiSAKEAFLRASNYYRNAGfYLDINPDDPRIVStWE 142
                                       678999999888854449999***999999999875222323588999********999956788888876655156 PP

                           DUF1100 149 lanrayeeaakklkyvlkqlelpvekkkitgflhlpktd.kplpvvlvsaGldslqtdmyrlfrdylakkdiamlti 224
                                        +   + +aa+ ++ +++ + +p++++++ g+l l  ++ +  p+++v +G+d    ++y    ++   ++  +l  
  gi|330508935|ref|YP_004385363.1| 143 KSHDCFIKAANLSSGLIRPVRIPFQNTTLPGYLCLVDGNgTSRPTLIVHTGFDGTGEELYFGVAKFAIDRGYNVLIF 219
                                       7999********************************9762578********************************** PP

                           DUF1100 225 dlpsvGassk...wkltedssllhqavlkeladvpyvdhtrvgliGfrfGanvavrlaflesekvkavvalGavvhd 298
                                       + p  G   +    ++  d       v++  +++  vd  r++l+G  fG+  a r a ++ +++ a++a G v +d
  gi|330508935|ref|YP_004385363.1| 220 EGPGQGEMIRvqgMPFRPDWEAAVTPVIDFAQNLSEVDPDRIALMGISFGGYLAPRAAAFD-HRIAACIANGGV-YD 294
                                       ******987633368999**************************************99876.79******9985.55 PP

                           DUF1100 299 llts..skklqkvpkmyldvlasr 320
                                       + +s  +k+l ++ ++  d  asr
  gi|330508935|ref|YP_004385363.1| 295 FNASvmQKALPNMEEILSDENASR 318
                                       444411233444444455655665 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   3.5e-10   5.6e-07      11     139 ..     210     332 ..     202     437 .] 0.71

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 3.5e-10
                                       HCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GG CS
                      Peptidase_S9  11 adrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpd 87 
                                        drGy v++ ++ G g++ +     ++ ++  +       +++++ + + vd++r+a++G S+GGyl+  a++  ++
  gi|330508935|ref|YP_004385363.1| 210 IDRGYNVLIFEGPGQGEMIRVQGMPFRPDWEAAV----TPVIDFAQNLSEVDPDRIALMGISFGGYLAPRAAA-FDH 281
                                       5667777777766666555555555555554432....335555555579***********************.888 PP

                                       G-SEEEEESE---CCCHHCSTTS.THHHCCCC--TTTCHHHHHHHHHH-CGGG CS
                      Peptidase_S9  88 lFkaavaevpvvdvlrydsdtdl.lteeymewgnpeeneegykelspyspldn 139
                                       + +a +a+ +v+d  ++  ++ l   ee     n+  ++e  +e+s+y +   
  gi|330508935|ref|YP_004385363.1| 282 RIAACIANGGVYDFNASVMQKALpNMEEILSDENA--SREFDQEMSEYMKQSI 332
                                       889*************9999877755567776666..5555578888877554 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   4.8e-10   7.8e-07      10     208 ..     198     414 ..     187     425 .. 0.52

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 4.8e-10
                                       ....GCHHHHHHHHCCT.CEEEEE--TTST..........S-GGCS--HHH....CHHHHHHHCCTT..TTSEEEEE CS
                     Abhydrolase_6  10 sassWlvapLaallaag.vhvlapDlpGhG..........rsdpppldled....ladlaalldelaagggpvvlvG 71 
                                       + + ++   +a+++ ++ + vl++  pG+G          r      d+e+    + d+a+ l e+  +++++ l+G
  gi|330508935|ref|YP_004385363.1| 198 GEELYF--GVAKFAIDRgYNVLIFEGPGQGemirvqgmpfR-----PDWEAavtpVIDFAQNLSEV--DPDRIALMG 265
                                       345555..5555666666777*********66666554431.....55555322367777777777..59******* PP

                                       ETCHHHHHHHHHHCC...EEEEES-..----TTT...S----TTHHHHHHTT-C.CCCHCCH..S-HSCCCCHHHCC CS
                     Abhydrolase_6  72 HSlGGalalaaapla.lvvgvlldppptalpagl...laaalelllallallrl.lawlsre..plprlfladedad 141
                                        S+GG+la +aa+   ++++++ ++   ++ + +   ++ al+ ++  l+ + +  ++++++  ++  + ++     
  gi|330508935|ref|YP_004385363.1| 266 ISFGGYLAPRAAAFDhRIAACIANG---GVYDFNasvMQKALPNMEEILSDENAsREFDQEMseYMK-QSIE----- 333
                                       **********666666555566666...444444366555555555555533332455543221222.3333..... PP

                                       CCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGC.............EEECTT-C......HHHHCHHCCCH.STTEEE CS
                     Abhydrolase_6 142 aawrarlarlaallaglgllpaaawadlpvpl.............lvlggeDp......lvprllerlla.qagarl 198
                                       + w++ +           + ++++++++ +p+             lv+ ++D         ++l+++l   ++   +
  gi|330508935|ref|YP_004385363.1| 334 TGWAVEHGMIVFG-----AQTPSEYFRMIAPYtlkdvaglircptLVV-DSDNdtllagQARPLYDALTGpKEYLLF 404
                                       3333333111111.....112334444444444444333333334454.3333346666555666666663333333 PP

                                       TCE...SS.S- CS
                     Abhydrolase_6 199 pvvlpgaG.Hl 208
                                        ++ +gaG H+
  gi|330508935|ref|YP_004385363.1| 405 -TTEEGAGlHC 414
                                       .6666776555 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   9.8e-09   1.6e-05      19     216 ..     201     394 ..     184     405 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 9.8e-09
                       Hydrolase_4  19 ryaelaeaLaaqGfavyalDhrGhGrsegkrg..hvpsfddyvdDlaafvekvkeehpelplfllGhSmGGlially 93 
                                        y  +a+   ++G++v+++   G+G+    +g    p+++  v+ +  f +++ e  p++ + l+G S GG++a ++
  gi|330508935|ref|YP_004385363.1| 201 LYFGVAKFAIDRGYNVLIFEGPGQGEMIRVQGmpFRPDWEAAVTPVIDFAQNLSEVDPDR-IALMGISFGGYLAPRA 276
                                       57888999999****************9555544689*****************999998.9*************** PP

                       Hydrolase_4  94 llrypdkvaglilsaPalkikaklkappllklllkllgkllpklqvsnnlkadslsrdpevvaayeadplvhgkitv 170
                                       ++  ++ +a+ i  + +++ +a++ ++++l  + ++l+    + ++ ++  ++++ +  e   a+e+  +v   + +
  gi|330508935|ref|YP_004385363.1| 277 AAFDHR-IAACIANGGVYDFNASV-MQKALPNMEEILSDENASREF-DQEMSEYMKQSIETGWAVEHGMIV---FGA 347
                                       *88888.9*************876.666666666666666666666.334444444444444444444444...333 PP

                       Hydrolase_4 171 rlllelldamk..rleeraakitlPllllhGeaDkvvdpeasrelyer 216
                                       ++  e +++++  +l++ a  i+ P+l++ +++D++   +++r ly++
  gi|330508935|ref|YP_004385363.1| 348 QTPSEYFRMIApyTLKDVAGLIRCPTLVVDSDNDTLLA-GQARPLYDA 394
                                       33333333333226888899999999999999999887.455566655 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 !   25.0   0.0   9.3e-09   1.5e-05      10      93 ..     247     327 ..     243     351 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 9.3e-09
                                       HHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEEETTE..EE----B-GGG-EE-T CS
                            BAAT_C  10 inyllrhpkvkkdkigllGiSkGgelalllasflkkisavvlingsavvvegklvykdeskvlpelklsmeklkvnk 86 
                                       i++ ++ ++v  d+i+l+GiS+Gg la   a+f + i a+++ ng+++ +++  + k     ++e+  +++  +++ 
  gi|330508935|ref|YP_004385363.1| 247 IDFAQNLSEVDPDRIALMGISFGGYLAPRAAAFDHRIAACIA-NGGVYDFNASVMQKAL-PNMEEILSDENA-SREF 320
                                       7999*********************************99886.7777777555555533.445554444333.3444 PP

                                       TS-EE-T CS
                            BAAT_C  87 nglldiv 93 
                                       ++++  +
  gi|330508935|ref|YP_004385363.1| 321 DQEMSEY 327
                                       4444444 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   5.3e-08   8.6e-05     161     204 ..     246     289 ..     235     310 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 5.3e-08
                                       HHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEEE CS
                              AXE1 161 lveivaslpevDeeRvavlGasqGGalalavaalekrikavvad 204
                                       +++ +++l+evD++R+a +G s GG la  +aa+++ri+a +a+
  gi|330508935|ref|YP_004385363.1| 246 VIDFAQNLSEVDPDRIALMGISFGGYLAPRAAAFDHRIAACIAN 289
                                       68999*********************************998875 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.2e-06    0.0036      52     261 ..     208     403 ..     181     414 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-06
                                       HHHHTT-EEEEEE-TTSTTS...-S---TTTTTHHHHHHHHHHHHHHC.TTEEEEEEEEEECHHHHHHHHHCTT--T CS
                     Peptidase_S15  52 vfvarGYavVvqdvrGtggS...eGeftvgdsdeaedgadvidWlakq.pwsnGkVgmtGiSYlGttqllaaatgvp 124
                                       + ++rGY v++ ++ G+g+    +G+     +d  +++  vid +++  +   ++++ +GiS++G+++  aaa +  
  gi|330508935|ref|YP_004385363.1| 208 FAIDRGYNVLIFEGPGQGEMirvQGMPF--RPDWEAAVTPVIDFAQNLsEVDPDRIALMGISFGGYLAPRAAAFD-H 281
                                       4689999999999999986411155444..5888899999*******999***********************55.5 PP

                                       TEEEEEEECE-S-TCCCCSECTTEEBCCHHHHHHHHHCCCCHHTSSS-STTHHHHHHHHHHCHCCCCCCTTHHHTHH CS
                     Peptidase_S15 125 alkaivpeaaisdlyddyyregGlvrapgglswedldllaealtsrradegdalkaaaryeaasdellaeldrqtpv 201
                                       +++a ++  ++ d+   +++++ l   +++ls     +  e  ++ ++  ++ +++ ++  +++    +        
  gi|330508935|ref|YP_004385363.1| 282 RIAACIANGGVYDFNA-SVMQKALPNMEEILSD--ENASREFDQEMSEYMKQSIETGWA-VEHGMIVFG-------- 346
                                       5666666667677666.5555555555555433..223333333333333333333332.222222222........ PP

                                       HHCCCC--SSSHHHHTT-HHH...HHCT--S-EEEEEECCSSTTCCHHHHHHHHHCCTT-EEE CS
                     Peptidase_S15 202 eselletgdydafWkdrnlse...dadkvkapvllvgGwnDwnvkngaiklyealkapgvkli 261
                                              +  +++ + +++++    a  +++p+l+v + nD+  + +a  ly+al+ p+++l+
  gi|330508935|ref|YP_004385363.1| 347 ------AQTPSEYFRMIAPYTlkdVAGLIRCPTLVVDSDNDTLLAGQARPLYDALTGPKEYLL 403
                                       ......233334444444442111447788888888888886666888888888888887665 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   4.2e-06    0.0069       3     107 ..     188     299 ..     186     345 .. 0.71
   2 ?   -1.6   0.0         1   1.6e+03     210     235 ..     369     394 ..     313     408 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.2e-06
                                       EEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB....CHHSHHHHHHHHHHH..HHHCTTSS CS
                     Abhydrolase_1   3 lvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacin...ddygtasvaddldri..ldalgddk 74 
                                       l+++ G+ g++  +  +g+a+   ++g+ v+++  +G g+  +     +   +d++ a v  ++d++  l   + d+
  gi|330508935|ref|YP_004385363.1| 188 LIVHTGFDGTG-EELYFGVAKFAIDRGYNVLIFEGPGQGEMIRVQG--MpfrPDWEAA-VTPVIDFAqnLSEVDPDR 260
                                       44455554444.3444447776666688888888666666654444..3447777765.7777774445999***** PP

                                       EEEEEETHHHHHHHHHHHHHGGGEEEEEEESE.......C CS
                     Abhydrolase_1  75 ltlvGhSmGGmialayaaeyperVkalvllga.......i 107
                                       ++l+G S+GG +a  +aa +++r++a+++ g+       +
  gi|330508935|ref|YP_004385363.1| 261 IALMGISFGGYLAPRAAA-FDHRIAACIANGGvydfnasV 299
                                       ******************.8***********965554442 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                                       HHSEEEEEEETTCSSSCHHHHHHHHH CS
                     Abhydrolase_1 210 vlaptlvisgtsDplvppkaledlaq 235
                                       + +ptlv+ +++D l   +a   +++
  gi|330508935|ref|YP_004385363.1| 369 IRCPTLVVDSDNDTLLAGQARPLYDA 394
                                       46799999999998877666666655 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.5e-06     0.016      63     112 ..     250     295 ..     236     395 .. 0.47

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.5e-06
                                       HH.HHTETTCEEEEEEETHHHHHHHHHH...HHHHHTT---EEEEEEESE-SST CS
                     Abhydrolase_3  63 aw.elgadpsrivlaGdSaGGnlaaava...lrardegepkvagqvliyPvtdl 112
                                       a+   ++dp+ri+l+G S GG la  +a   +        ++a+++    v d+
  gi|330508935|ref|YP_004385363.1| 250 AQnLSEVDPDRIALMGISFGGYLAPRAAafdH--------RIAACIANGGVYDF 295
                                       4424459*****************98882221........23333333333322 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.2e-05     0.068      86     128 ..     247     289 ..     237     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.2e-05
                               DLH  86 vaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavaf 128
                                       ++++++ +ev++++++++G  +GG la   aa + +++a++a 
  gi|330508935|ref|YP_004385363.1| 247 IDFAQNLSEVDPDRIALMGISFGGYLAPRAAAFDHRIAACIAN 289
                                       78999****************************9999999975 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.24      51      91 ..     251     292 ..     235     332 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                           UPF0227  51 klvaelgddnillvGssLGGyyatrl.gerfglrqvllnPal 91 
                                       + ++e+ +d+i+l+G s GGy+a r  ++ + +++ + n  +
  gi|330508935|ref|YP_004385363.1| 251 QNLSEVDPDRIALMGISFGGYLAPRAaAFDHRIAACIANGGV 292
                                       6677888999*************9862567888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2850.20
//
Query:       gi|330508936|ref|YP_004385364.1|  [L=90]
Description: hypothetical protein MCON_3276 [Methanosaeta concilii GP6]
Scores for complete 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   72.5   0.0    2.9e-20   72.3   0.0    1.1  1  Dodecin   Dodecin


Domain annotation for each model (and alignments):
>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.0   1.6e-24   2.9e-20       1      64 []       6      70 ..       6      70 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 1.6e-24
                                      EEEEEEEEEEESS-HHHHHHHHHHHHHHH-SSEEEEEEEEEEEEE.CTTCCEEEEEEEEEEEE-S CS
                           Dodecin  1 VyKvielvGsSpkSwedAiqnAiaeAsktlrnirwveVketrahv.edgkiaeYqvtlkvgFrle 64
                                      Vy+ ielvGsSp +wedA++nAi++A+k++ n+r++ V e++a++ e+g+i  Y+++l+++ ++e
  gi|330508936|ref|YP_004385364.1|  6 VYRAIELVGSSPIGWEDAAKNAIDTAHKSIWNLRIARVAELDAKLdEKGNIILYRIKLRISLKYE 70
                                      8********************************************888*************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 707.45
//
Query:       gi|330508937|ref|YP_004385365.1|  [L=917]
Description: formate dehydrogenase subunit alpha [Methanosaeta concilii GP6]
Scores for complete 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-89  299.6   0.0    4.6e-89  299.3   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    1.2e-29  102.5   0.0    2.5e-29  101.6   0.0    1.5  1  Molydop_binding  Molydopterin dinucleotide binding domain
    3.9e-17   62.1   0.0    1.4e-16   60.3   0.0    2.1  2  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
    6.1e-17   61.3   0.3    4.1e-16   58.7   0.3    2.5  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
    6.9e-07   28.7   9.6     0.0013   18.3   3.5    2.9  2  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
    1.4e-06   28.8  15.6    0.00039   20.9   9.6    4.5  4  Fer4_7           4Fe-4S dicluster domain
    2.3e-06   27.2   2.4    2.3e-06   27.2   2.4    4.3  4  Fer4             4Fe-4S binding domain
    0.00013   22.1   3.4    0.00013   22.1   3.4    2.9  2  Fer4_21          4Fe-4S dicluster domain
    0.00018   21.6  10.4    0.00018   21.6  10.4    4.1  5  Fer4_9           4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.033   15.1   6.1      0.033   15.1   6.1    5.0  3  Fer4_3           4Fe-4S binding domain
       0.21   11.7   3.2        1.1    9.4   3.2    2.3  1  Fer4_19          Divergent 4Fe-4S mono-cluster
       0.34   11.1   9.0       0.37   11.0   0.1    2.9  2  Fer4_18          4Fe-4S dicluster domain
        3.8    8.3   8.0         16    6.3   1.3    2.9  2  Fer4_15          4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.3   0.0   3.3e-92   4.6e-89       1     416 [.     299     706 ..     299     721 .. 0.95

  Alignments for each domain:
  == domain 1  score: 299.3 bits;  conditional E-value: 3.3e-92
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       R ++P+++   r +G+F+++sWdeAl+l+a++++++++ ygpd+   fss++ + +e+ ++ +kl++++++  ++++
  gi|330508937|ref|YP_004385365.1| 299 RFTTPLIK---R-NGQFEPASWDEALDLVARRFTEIQDRYGPDSLGAFSSSRCT-NEENYLVQKLARAVFK--TNNV 368
                                       889*****...9.*********************************99998888.999999**********..9*** PP

                                       ECCGGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSS CS
                     Molybdopterin  78 dwyadlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpr 150
                                       d++a++++a  +      +gs+ +     +n++ ++e++d+ +++GsN  e +p++  +i+kaa+++ ak+iv +pr
  gi|330508937|ref|YP_004385365.1| 369 DNCARVCHAPSVtglaACFGSGAA-----TNSFDQIEDADVLFIIGSNTTEAHPVVSLKIIKAARNG-AKIIVADPR 439
                                       *********999887666666533.....446669******************************96.********* PP

                                       B-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHH CS
                     Molybdopterin 151 yaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarel 227
                                       + el  +a+ wl  kpgt  al++am++vil+e+++d +f++++t g+e++++ ++++ +e+++++++v a+ ++e 
  gi|330508937|ref|YP_004385365.1| 440 KIELVDRASVWLNQKPGTSIALINAMMNVILKEGLEDRDFIDRRTMGFENLQKTVEEYPPERASQITGVAAEDIIEA 516
                                       ***************************************************************************** PP

                                       HHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCC CS
                     Molybdopterin 228 arnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvksl 304
                                       ar +a++++ +mii+G g+++++ g+ +++ + nLa+l+gnvg+  +g   l+Gq++++g a+++galp     ++ 
  gi|330508937|ref|YP_004385365.1| 517 ARLYASADK-AMIIYGLGITEHTTGTSNVMSLGNLAMLTGNVGRRSTGIMPLRGQNNVQG-ACDMGALPNVHVGYQP 591
                                       ********9.**************************************************.*******888877777 PP

                                       TT...HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSH CS
                     Molybdopterin 305 ke...ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrlts 378
                                       ++    + kf   ++  l+ +p+++++++++    ++++ ly+lg++p ++ +d+n+v  +le+ld++vv +++ t+
  gi|330508937|ref|YP_004385365.1| 592 VTdagIRSKFEEAWKVALPSVPGQTSTQMIERNPGKEIRGLYILGEDPAHTEPDTNRVRSTLESLDFLVVQEIFPTE 668
                                       7799988999999999***************9999****************************************** PP

                                       HHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-S CS
                     Molybdopterin 379 talyaDiiLPaatwyEkedlytndegrfqhlkqavspp 416
                                       t +yaD+iLPaa++ E ++++tn+e+r+q+ ++a+++ 
  gi|330508937|ref|YP_004385365.1| 669 TTRYADVILPAASFAECDGTFTNGERRIQRVRKAIPAL 706
                                       ***********************************985 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   0.0   1.8e-32   2.5e-29       1     111 []     803     909 ..     803     909 .. 0.99

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 1.8e-32
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfm 76 
                                       l+L+tgr++++++ + +tr++     + p e +ei+p+dA++l+i+dG++V+v+srrGsv+ +a+vt+   +G++fm
  gi|330508937|ref|YP_004385365.1| 803 LILTTGRRREHYNCGSMTRRSKGIMWVWPeEAIEISPADARELEIEDGETVVVSSRRGSVKTKARVTDKSSRGMAFM 879
                                       79*************************************************************************** PP

                                       ESSHCC.....S-GHCTS--SCSTTT--CSTT-EE CS
                   Molydop_binding  77 pfgwweagekggnaNaltddatdplsgtpefksva 111
                                        f++ +     + +N lt++a+dp+++tpe+k++a
  gi|330508937|ref|YP_004385365.1| 880 SFHYQD-----VLTNLLTNAALDPQAKTPEYKACA 909
                                       ****99.....*********************996 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0     1e-19   1.4e-16       3      81 ..       3      78 ..       1      79 [. 0.96
   2 ?   -3.3   0.0       7.1   9.8e+03       9      31 ..     841     863 ..     840     878 .. 0.68

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 1e-19
                            Fer2_4  3 pvtltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnv.racstpvedGlkvetq 80
                                      +++l +D++ev+vp+G+t+++A+  +g +vp +c++      l+++g+C+ C+V veg      +c tp+++G++v+t 
  gi|330508937|ref|YP_004385365.1|  3 EIKLLIDDREVSVPQGSTILDAARIAGSYVPSLCHH----PDLKPIGSCKLCIVSVEGLDYYpLSCNTPAAEGMVVHTR 77
                                      68999*******************************....89****************999889*************98 PP

                            Fer2_4 81 t 81
                                      t
  gi|330508937|ref|YP_004385365.1| 78 T 78
                                      7 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.1
                            Fer2_4   9 DGkevtvpeGdtvasAllangvd 31 
                                       D +e++ + G+tv     + +v+
  gi|330508937|ref|YP_004385365.1| 841 DARELEIEDGETVVVSSRRGSVK 863
                                       55788889999998766655555 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.3   2.9e-19   4.1e-16       2      52 ..     242     292 ..     241     295 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 2.9e-19
                                       EEEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHC CS
                    Molybdop_Fe4S4   2 kvvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtller 52 
                                       ++v t+CpyCgvgC+l+++   ++i +v + +d+ vn+g++CvKG ++le 
  gi|330508937|ref|YP_004385365.1| 242 RTVVTICPYCGVGCSLDLKISEDRILSVTPSRDGAVNRGQACVKGHFGLEE 292
                                       6899*******************************************9986 PP

>> NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.5   9.1e-07    0.0013       1      28 [.      85     115 ..      85     125 .. 0.81
   2 !   13.1   0.4   3.7e-05     0.051      16      39 ..     127     150 ..     124     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.1e-07
                   NADH-G_4Fe-4S_3   1 RktilellLa..nHpldCltCdknGnC.eLQ 28 
                                       R+ +le+lLa  nHp  Cl C++  +C eL 
  gi|330508937|ref|YP_004385365.1|  85 RRHTLEMLLAltNHPTSCLFCERKNECgELR 115
                                       899999997555***************5555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.7e-05
                   NADH-G_4Fe-4S_3  16 CltCdknGnCeLQdlayelgvees 39 
                                       C +C++ G CeLQ+ +   g +++
  gi|330508937|ref|YP_004385365.1| 127 CKYCPNDGQCELQEAVTFTGLDRI 150
                                       999***********9988888776 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   1.3         1   1.4e+03      32      44 ..      96     111 ..      63     124 .. 0.65
   2 ?    2.9   7.1      0.13   1.7e+02       3      48 ..     125     184 ..     124     186 .. 0.66
   3 !   20.9   9.6   2.8e-07   0.00039       2      52 .]     174     229 ..     173     229 .. 0.69
   4 !   20.4   0.3   4.1e-07   0.00056       2      43 ..     215     253 ..     214     379 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1
                            Fer4_7  32 eidpekClgCga...C 44 
                                       + +p++Cl+C++   C
  gi|330508937|ref|YP_004385365.1|  96 TNHPTSCLFCERkneC 111
                                       779999**99643334 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.13
                            Fer4_7   3 igCgaCvaa..Cp.vkaieldeeenek...........gtekveidpekClgCgaCvavC 48 
                                       +gC++C +   C  ++a++++  ++ +           + +  + +++ C+ C +C++ C
  gi|330508937|ref|YP_004385365.1| 125 VGCKYCPNDgqCElQEAVTFTGLDRIRyqtsfrdmpvlREPFFDRNYNLCIMCSRCIRMC 184
                                       689999864338788888888776666434333333332244477788999999999999 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 2.8e-07
                            Fer4_7   2 CigCgaCvaaCp.vkaieldeeenek..gtekv....eidpekClgCgaCvavCPtga 52 
                                       Ci C +C ++C  v+ + +    n++   + ++     +++ +C +CgaCv++CPtga
  gi|330508937|ref|YP_004385365.1| 174 CIMCSRCIRMCDeVRGLGILF--NNPdfHRNHWigpeSLQEADCKFCGACVDACPTGA 229
                                       ***********8533333332..2331222333455488999**************98 PP

  == domain 4  score: 20.4 bits;  conditional E-value: 4.1e-07
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga 43 
                                       C  CgaCv+aCp++a+ ++ e+  ++ ++v+   + C +Cg+
  gi|330508937|ref|YP_004385365.1| 215 CKFCGACVDACPTGALFIRSEKWIRPDRTVV---TICPYCGV 253
                                       999************9999886665544333...33444443 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       3.1   4.2e+03       9      14 ..     125     130 ..     125     133 .. 0.72
   2 !   10.4   1.9   0.00032      0.45       4      18 ..     170     184 ..     167     186 .. 0.92
   3 !   27.2   2.4   1.6e-09   2.3e-06       5      23 ..     212     230 ..     210     231 .. 0.91
   4 ?   -3.4   1.0       7.8   1.1e+04      13      18 ..     370     375 ..     370     375 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.1
                                       SS-THH CS
                              Fer4   9 igCGaC 14 
                                       +gC++C
  gi|330508937|ref|YP_004385365.1| 125 VGCKYC 130
                                       577777 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00032
                                       ETTTSSS-THHHHHS CS
                              Fer4   4 deekCigCGaCvevC 18 
                                       ++++Ci C +C+ +C
  gi|330508937|ref|YP_004385365.1| 170 NYNLCIMCSRCIRMC 184
                                       899************ PP

  == domain 3  score: 27.2 bits;  conditional E-value: 1.6e-09
                                       TTTSSS-THHHHHSTTTEE CS
                              Fer4   5 eekCigCGaCvevCPvgAI 23 
                                       e +C +CGaCv++CP+gA+
  gi|330508937|ref|YP_004385365.1| 212 EADCKFCGACVDACPTGAL 230
                                       568***************8 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 7.8
                                       HHHHHS CS
                              Fer4  13 aCvevC 18 
                                       +C+ vC
  gi|330508937|ref|YP_004385365.1| 370 NCARVC 375
                                       5***** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.4       8.5   1.2e+04      42      48 ..     125     131 ..     123     142 .. 0.76
   2 !   22.1   3.4   9.2e-08   0.00013       6      55 ..     172     228 ..     169     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8.5
                           Fer4_21  42 vGCnlCs 48 
                                       vGC+ C 
  gi|330508937|ref|YP_004385365.1| 125 VGCKYCP 131
                                       7888884 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 9.2e-08
                           Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvl........kvvedeCvGCnlCssvCPved 55 
                                       + Ci C +C+ +C++     i +++   +         ++e +C  C  C++ CP+ +
  gi|330508937|ref|YP_004385365.1| 172 NLCIMCSRCIRMCDEVRGLGILFNNPDFHrnhwigpeSLQEADCKFCGACVDACPT-G 228
                                       78************9888888665544333445787667799*************6.4 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.6       1.1   1.5e+03      33      42 ..      87     111 ..      62     121 .. 0.61
   2 !    9.3   4.2   0.00088       1.2       4      47 ..     126     185 ..     125     190 .. 0.70
   3 !   21.6  10.4   1.3e-07   0.00018       2      50 ..     174     229 ..     173     230 .. 0.69
   4 ?   -2.4   0.2       4.1   5.6e+03       5      18 ..     248     261 ..     246     284 .. 0.69
   5 ?   -3.2   0.1       7.1   9.9e+03       7      14 ..     370     377 ..     367     382 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.1
                            Fer4_9  33 e............eaCigCga...C 42 
                                                    ++C++C++   C
  gi|330508937|ref|YP_004385365.1|  87 HtlemllaltnhpTSCLFCERkneC 111
                                       1344566677777889999876664 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00088
                            Fer4_9   4 gCgaC..veaCpagvvvedaaerkarlraase................eaCigCgaCveaCp 47 
                                       gC++C    +C+ + +v   +   +r++                    + Ci+C +C+  C 
  gi|330508937|ref|YP_004385365.1| 126 GCKYCpnDGQCELQEAVTFTGLDRIRYQT--SfrdmpvlrepffdrnyNLCIMCSRCIRMCD 185
                                       89999443457555555554444444433..2346899999999999999***********7 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 1.3e-07
                            Fer4_9   2 CtgCgaCveaC.....pagvvvedaaerkarlraase.....eaCigCgaCveaCpkga 50 
                                       C+ C +C+++C          +  +++ + r+++ +       +C +CgaCv+aCp+ga
  gi|330508937|ref|YP_004385365.1| 174 CIMCSRCIRMCdevrgL---GILFNNPDFHRNHWIGPeslqeADCKFCGACVDACPTGA 229
                                       ***********886552...333344444443333334446778*************97 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 4.1
                            Fer4_9   5 CgaCveaCpagvvv 18 
                                       C +C   C  ++ +
  gi|330508937|ref|YP_004385365.1| 248 CPYCGVGCSLDLKI 261
                                       88888888666654 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 7.1
                            Fer4_9   7 aCveaCpa 14 
                                       +C ++C a
  gi|330508937|ref|YP_004385365.1| 370 NCARVCHA 377
                                       57777755 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   4.2     0.016        23       1      11 [.     174     184 ..     174     186 .. 0.96
   2 ?   15.1   6.1   2.4e-05     0.033       1      15 []     215     229 ..     215     229 .. 0.97
   3 ?   -2.0   0.2       7.3     1e+04       7      11 ..     371     375 ..     369     376 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.016
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C++C++C + C
  gi|330508937|ref|YP_004385365.1| 174 CIMCSRCIRMC 184
                                       **********9 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.4e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C  CgaCv++CP+gA
  gi|330508937|ref|YP_004385365.1| 215 CKFCGACVDACPTGA 229
                                       99************9 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 7.3
                            Fer4_3   7 CvevC 11 
                                       C +vC
  gi|330508937|ref|YP_004385365.1| 371 CARVC 375
                                       99999 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 ?    9.4   3.2   0.00078       1.1      11      61 ..     170     232 ..     168     235 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00078
                           Fer4_19  11 nrelCihsgnCvk......glpevF...dpkrkpwikpd...easteeiievverCPSGALsy 61 
                                       n +lCi    C++      gl+ +F   d +r+ wi p+   ea+ +   + v+ CP GAL +
  gi|330508937|ref|YP_004385365.1| 170 NYNLCIMCSRCIRmcdevrGLGILFnnpDFHRNHWIGPEslqEADCKFCGACVDACPTGALFI 232
                                       567888888888833333344444643345899***887222455577789**********76 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.0     0.027        37      85      98 ..     174     187 ..     168     193 .. 0.85
   2 ?   11.0   0.1   0.00026      0.37      57      74 ..     211     228 ..     201     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.027
                           Fer4_18  85 ciscllcidacdkv 98 
                                       ci c++ci  cd+v
  gi|330508937|ref|YP_004385365.1| 174 CIMCSRCIRMCDEV 187
                                       99999999999988 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00026
                           Fer4_18  57 gagdcidcescvkvcPtg 74 
                                       +++dc  c++cv+ cPtg
  gi|330508937|ref|YP_004385365.1| 211 QEADCKFCGACVDACPTG 228
                                       689*************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 ?    4.8   0.8     0.036        49       6      21 ..     172     187 ..     166     191 .. 0.86
   2 ?    6.3   1.3     0.012        16       6      20 ..     213     227 ..     209     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.036
                           Fer4_15   6 daCigcglCvaeapev 21 
                                       ++Ci+c +C++ ++ev
  gi|330508937|ref|YP_004385365.1| 172 NLCIMCSRCIRMCDEV 187
                                       68***********997 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                           Fer4_15   6 daCigcglCvaeape 20 
                                         C  cg+Cv+++p+
  gi|330508937|ref|YP_004385365.1| 213 ADCKFCGACVDACPT 227
                                       67***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (917 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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):              13  [number of targets reported over threshold]
# CPU time: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 6133.57
//
Query:       gi|330508938|ref|YP_004385366.1|  [L=201]
Description: hypothetical protein MCON_3278 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-08   35.8   0.0    1.7e-08   35.1   0.0    1.3  1  TIR_2          TIR domain
      0.002   18.6   0.2     0.0038   17.7   0.2    1.4  1  zf-C4pol       C4-type zinc-finger of DNA polymerase delta
  ------ inclusion threshold ------
      0.045   13.8   0.1       0.09   12.8   0.1    1.5  1  DZR            Double zinc ribbon
      0.046   13.1   0.6        2.8    7.5   0.1    2.3  2  zf-ribbon_3    zinc-ribbon domain
       0.27   11.0   1.2        2.8    7.8   0.1    2.2  2  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   4.7e-12   1.7e-08       1     114 [.       5     117 ..       5     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 4.7e-12
                             TIR_2   1 VFiSyssedkewaeklaeaLeaagirvwldrwdlkpgedweeeieeaiessdvvlvvlspaylesewcreeleaale 77 
                                       V+iSy   d++ a +l  aL + g++ ++  ++ +p  ++ +++  ai++s++++++ +++  +s+   +e+ +a  
  gi|330508938|ref|YP_004385366.1|   5 VYISYDPDDEDLALRLSLALGRVGLESYVALYNQSPAISLADRVSFAIRNSECLVALATRKGSRSPALCQEIGLARG 81 
                                       89*************************9999999*********************************99*******7 PP

                             TIR_2  78 aaeegkkrlipvlle.pekppl.aslqyidlskk.deeal 114
                                            ++ +ip+  e  + p l  +l+++ ++++ +++a+
  gi|330508938|ref|YP_004385366.1|  82 ----IDQLIIPLQEEgAQLPFLiDQLRALPFRREsFADAI 117
                                       ....3666****9995366654699999999866665655 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 !   17.7   0.2   1.1e-06    0.0038      10      51 ..     134     173 ..     121     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                          zf-C4pol  10 kalCkkCrsdkqesllkllsrlkelekklneletvCqsCaqg 51 
                                       + +C +C  ++ +++l+ ++++ ++++k   let+C  C q+
  gi|330508938|ref|YP_004385366.1| 134 RVVCPQCG-EEMTQYLTDQDEVDSAQEKGIFLETICSYC-QN 173
                                       679****6.88899*************************.44 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.5e-05      0.09      14      37 ..     136     174 ..     130     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                               DZR  14 fCseCgtklkavaa...............edrCpsCgek 37 
                                       +C++Cg+++ ++ +               e+ C+ C+  
  gi|330508938|ref|YP_004385366.1| 136 VCPQCGEEMTQYLTdqdevdsaqekgiflETICSYCQNT 174
                                       7*******9998889999******************986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1   0.00077       2.8       4      10 ..     136     142 ..     134     145 .. 0.72
   2 ?    3.6   0.0     0.013        47      17      23 ..     166     172 ..     164     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00077
                       zf-ribbon_3   4 rCPnCGa 10 
                                        CP+CG+
  gi|330508938|ref|YP_004385366.1| 136 VCPQCGE 142
                                       5888885 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.013
                       zf-ribbon_3  17 nvCpyCG 23 
                                       ++C yC+
  gi|330508938|ref|YP_004385366.1| 166 TICSYCQ 172
                                       6788886 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1   0.00077       2.8       2       8 ..     137     143 ..     135     145 .. 0.61
   2 ?    1.6   0.1     0.069   2.5e+02      15      19 ..     167     171 ..     165     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00077
                     zinc_ribbon_2   2 CpnCGae 8  
                                       Cp+CG+e
  gi|330508938|ref|YP_004385366.1| 137 CPQCGEE 143
                                       6666655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.069
                     zinc_ribbon_2  15 FCpyC 19 
                                        C+yC
  gi|330508938|ref|YP_004385366.1| 167 ICSYC 171
                                       57777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1468.00
//
Query:       gi|330508939|ref|YP_004385367.1|  [L=811]
Description: CoB--CoM heterodisulfide reductase subunit A [Methanosaeta concilii GP6]
Scores for complete 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-51  171.8   0.1    4.3e-48  162.4   0.1    3.0  2  FlpD           Methyl-viologen-reducing hydrogenase, delta su
    1.2e-21   75.6  48.6    2.4e-08   33.4   3.5    5.2  4  Fer4           4Fe-4S binding domain
    2.8e-17   62.9   0.0    6.3e-17   61.7   0.0    1.6  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    3.9e-16   59.7  23.8    0.00013   22.9   0.3    4.7  4  Fer4_16        4Fe-4S double cluster binding domain
    6.4e-15   55.5  33.7    1.7e-07   31.7  12.7    4.8  4  Fer4_7         4Fe-4S dicluster domain
    1.8e-14   53.1  56.6      8e-06   25.7   4.1    5.3  4  Fer4_6         4Fe-4S binding domain
      8e-13   48.3  36.2    5.8e-07   29.5  13.9    4.2  4  Fer4_10        4Fe-4S dicluster domain
    2.9e-12   46.5  34.8    3.4e-07   30.3  11.9    3.3  2  Fer4_9         4Fe-4S dicluster domain
    2.4e-11   43.6  42.3    7.4e-09   35.6  12.2    4.3  3  Fer4_21        4Fe-4S dicluster domain
      4e-11   42.3  46.7    0.00034   20.5   2.9    5.4  5  Fer4_2         4Fe-4S binding domain
      3e-10   40.4  13.1     0.0065   16.9   0.0    4.8  4  Fer4_8         4Fe-4S dicluster domain
    2.2e-09   37.2   0.9    4.3e-09   36.2   0.9    1.4  1  FAD_oxidored   FAD dependent oxidoreductase
    1.3e-08   34.8   1.3    1.2e-05   25.1   1.2    2.6  2  DAO            FAD dependent oxidoreductase
    6.9e-08   32.4  36.3     0.0073   16.7   4.6    5.2  4  Fer4_4         4Fe-4S binding domain
    1.3e-07   31.7   0.0    3.1e-07   30.5   0.0    1.6  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    3.8e-06   26.3   1.0    5.8e-06   25.6   1.0    1.2  1  FAD_binding_2  FAD binding domain
      1e-05   26.0  26.2      0.063   13.8   0.2    4.5  4  Fer4_17        4Fe-4S dicluster domain
    3.1e-05   23.3   1.0    4.4e-05   22.8   0.1    1.7  2  GIDA           Glucose inhibited division protein A
    6.6e-05   22.3   0.0    0.00014   21.2   0.0    1.5  1  Thi4           Thi4 family
    0.00012   22.7  27.1      0.044   14.5   0.7    4.9  4  Fer4_15        4Fe-4S single cluster domain
     0.0003   21.3   0.8     0.0012   19.3   0.5    2.1  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0006   19.1   0.3      0.001   18.4   0.3    1.3  1  FAD_binding_3  FAD binding domain
     0.0015   17.3   0.7     0.0015   17.3   0.7    1.5  2  HI0933_like    HI0933-like protein
     0.0032   16.8   0.2     0.0063   15.8   0.2    1.5  1  Amino_oxidase  Flavin containing amine oxidoreductase
     0.0032   16.8   0.0      0.021   14.1   0.2    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.016   15.4   4.8      0.016   15.4   4.8    3.7  3  Fer4_18        4Fe-4S dicluster domain
      0.017   14.2   0.5      0.038   13.0   0.5    1.6  1  Lycopene_cycl  Lycopene cyclase protein
      0.018   16.0   5.0      0.018   16.0   5.0    6.0  4  Fer4_3         4Fe-4S binding domain
       0.02   14.2   0.4      0.042   13.1   0.4    1.5  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.027   15.3   2.0      0.027   15.3   2.0    4.5  4  Fer4_22        4Fe-4S dicluster domain
       0.16   12.0   0.9        3.1    7.8   0.4    2.4  2  NAD_binding_9  FAD-NAD(P)-binding
       0.34   11.5  36.0       0.29   11.7   3.5    4.5  4  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I


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 ?    5.9   0.0     0.021        12      47      83 ..     522     562 ..     519     571 .. 0.76
   2 !  162.4   0.1   7.6e-51   4.3e-48       1     123 []     649     771 ..     649     771 .. 0.99

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                              FlpD  47 alekGadgVlvlgChpgd....ChyvkGnekaerrveklke 83 
                                         e+ +dgV+++gC  g         +G+  a++ +++l++
  gi|330508939|ref|YP_004385367.1| 522 PVEAHIDGVFIAGCASGPkeipISIAQGSAAAAKAIRLLQK 562
                                       667889********988766765666888888888777776 PP

  == domain 2  score: 162.4 bits;  conditional E-value: 7.6e-51
                              FlpD   1 ilaFlCnwcayaaadlagvsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGnekaerr 77 
                                       i+aFlCnwc+y aadlag+sr+qyp+n r irv+Cs+rvdp+f+l+al++GadgVl++gC+ g+Chy++Gn++a +r
  gi|330508939|ref|YP_004385367.1| 649 IIAFLCNWCSYGAADLAGTSRIQYPTNARNIRVMCSARVDPSFVLEALRRGADGVLIAGCRIGECHYHDGNYQALQR 725
                                       9**************************************************************************** PP

                              FlpD  78 veklkelleelgiepeRvrleevsaaegekfaevikefvekikeLG 123
                                       v+ lk +le++gi+p Rv++++++a+ege  a+ ++ef  ++k++G
  gi|330508939|ref|YP_004385367.1| 726 VNVLKGVLEKIGINPGRVKIVWCAASEGEIYAQDLREFIGELKAIG 771
                                       ******************************************9987 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   7.8      0.13        73       2      22 ..     237     258 ..     236     260 .. 0.88
   2 !   26.3   7.7   7.6e-09   4.2e-06       3      23 ..     286     306 ..     284     307 .. 0.92
   3 !   33.4   3.5   4.3e-11   2.4e-08       2      24 .]     573     595 ..     572     595 .. 0.95
   4 !   29.7   5.8   6.3e-10   3.5e-07       2      24 .]     601     623 ..     600     623 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
                                       EEETTTSSS-.THHHHHSTTTE CS
                              Fer4   2 videekCigC.GaCvevCPvgA 22 
                                       ++d+ +C gC ++C++vCPv++
  gi|330508939|ref|YP_004385367.1| 237 YVDPVLCKGCiNECADVCPVEV 258
                                       689999999999*******986 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 7.6e-09
                                       EETTTSSS-THHHHHSTTTEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                       +d+  CigCG+Cve CP+ A 
  gi|330508939|ref|YP_004385367.1| 286 VDPKACIGCGRCVESCPTQAV 306
                                       8******************97 PP

  == domain 3  score: 33.4 bits;  conditional E-value: 4.3e-11
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       ++d+++Ci+C++Cv+vCP  AI+
  gi|330508939|ref|YP_004385367.1| 573 YVDPDLCIKCKLCVDVCPQKAIS 595
                                       89*******************95 PP

  == domain 4  score: 29.7 bits;  conditional E-value: 6.3e-10
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       ++de  C gCG C+ +CPv+AI+
  gi|330508939|ref|YP_004385367.1| 601 YVDEAACKGCGSCAAACPVDAIK 623
                                       89********************6 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   1.1e-19   6.3e-17       1     294 []     141     549 ..     141     553 .. 0.79

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.1e-19
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...........TTHCHHHCSHHH...HCHHHHHHHHHHHHH...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxx...xxxxxxxxxxxxxxx...... RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...........legtclnggcll...skallgvaedaeias...... 57 
                                       kdv+v+GgG+AG+aaal+la ag+ v lve           l++ +++++c++    +++ +v  +++i +      
  gi|330508939|ref|YP_004385367.1| 141 KDVMVVGGGVAGIAAALDLADAGFHVFLVErrptiggymalLTDVFPTNDCSIcvlGPKMSEVFNHPNITLytysev 217
                                       69***************************99999999*************987666889999999999888****** PP

                                       .......................................HHHHCHHHHCCCCHC....................... CS
                                       .......................................xxxxxxxxxxxxxxx....................... RF
                       Pyr_redox_2  58 .......................................evvkklnqgielllg....................... 72 
                                                                              ev +++  gi ++++                       
  gi|330508939|ref|YP_004385367.1| 218 lgvegsvgnftvsgvhraryvdpvlckgcinecadvcpvEVPNEYDFGIGKRKAiyvpypqavplsacvdpkacigc 294
                                       *************************************9977777888888888888888888777777766666665 PP

                                       CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.......................TTBEECC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxxx RF
                       Pyr_redox_2  73 eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv......................aenvgklv 127
                                         +v+  p +  vkl +    ++++i  +++++AtG +p+d   + +                      +++ g++v
  gi|330508939|ref|YP_004385367.1| 295 GRCVESCPTQ-AVKLDQV--VEHFTINVGAIIVATGWQPFDAARKEEygfgrlrdvvttlqmermlnasGPTKGEVV 368
                                       5577777777.7777544..689*******************66655455667777777766666666666666666 PP

                                       SECHHHHHHCCSS-T...SEEEEES-SHHHHHHHHH........HHHH.T-EEEEEESSSSSSTTS-HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx........xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 128 rtldsaealklkllp...krivvvGgGyiGvElAaa........lakl.gkevtlveardrllraldkelsaaleea 192
                                       r+++   a + + l+    r + vG+ y++  +++a        + k+ g+++t+ +   r   a+++  ++++ +a
  gi|330508939|ref|YP_004385367.1| 369 RPSTGQVAQSIAFLQcvgSRDATVGNIYCSRICCMAslknaqliAEKYpGSDITIYYIDIR---ACGEGYEEFYVRA 442
                                       666666666666666888888***************7554443335555558886666444...5699999998876 PP

                                       HHHTTEEEEESCEEEEEEETTE....EEE.EEETTSCEEEESEEEE-S-EEES-HHCS..HCCT-EEEETTEEE--. CS
                                       xxxxxxxxxxxxxxxxxxxxxx....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx. RF
                       Pyr_redox_2 193 lekeGvevklgtsvkeidgnge....kle.vvledgeeidadlvvvavGvrpstelle..eklglelderggivvd. 261
                                           G++++ +++v  i++ +     + e +++++ +++  d  v++vG++p+++     + lgl   +++++++  
  gi|330508939|ref|YP_004385367.1| 443 Q-MLGINFV-RARVSSIEEVDGdiylRFEdTQTGEIKRVRHDIAVLSVGLEPDKSADVlgNLLGLSRRPDRFFEIAh 517
                                       4.45*****.9999999988885644444666666666***************8775488999*********96651 PP

                                       TTS...BESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 262 efl...rtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                       +++   +  ++g++ +G +a   +gp+ ++ +++qG
  gi|330508939|ref|YP_004385367.1| 518 PKMrpvEAHIDGVFIAG-CA---SGPKEIPISIAQG 549
                                       566544568*******9.56...5555555555554 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 ?    7.6   0.9     0.013       7.5       2      16 ..     243     258 ..     242     272 .. 0.80
   2 !   22.9   0.3   2.3e-07   0.00013       2      26 ..     291     313 ..     290     339 .. 0.82
   3 !   20.2   1.9   1.5e-06   0.00085       2      22 ..     579     599 ..     578     605 .. 0.85
   4 !   22.2   1.5   3.6e-07    0.0002       2      42 ..     607     647 ..     606     660 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.013
                           Fer4_16   2 CgtCgk.CaevCPtna 16 
                                       C++C + Ca+vCP+++
  gi|330508939|ref|YP_004385367.1| 243 CKGCINeCADVCPVEV 258
                                       9999655999999875 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 2.3e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeie 26 
                                       C++Cg+C+e+CPt+a+k +  +++e
  gi|330508939|ref|YP_004385367.1| 291 CIGCGRCVESCPTQAVKLD--QVVE 313
                                       *****************99..5554 PP

  == domain 3  score: 20.2 bits;  conditional E-value: 1.5e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                       C++C+ C++vCP++ai+ k+ 
  gi|330508939|ref|YP_004385367.1| 579 CIKCKLCVDVCPQKAISVKSP 599
                                       ****************98854 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 3.6e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdla 42 
                                       C++Cg Ca +CP++aik++     ++ ++i ++t+ kk+++
  gi|330508939|ref|YP_004385367.1| 607 CKGCGSCAAACPVDAIKMRLFSDEQILAQIRAATEVKKEFP 647
                                       *****************996666666666667777777765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   1.0   0.00053      0.29      29      51 ..     233     257 ..     190     258 .. 0.76
   2 !   24.6   0.3   5.2e-08   2.9e-05       1      24 [.     290     313 ..     273     348 .. 0.88
   3 !   31.7  12.7     3e-10   1.7e-07       2      52 .]     579     621 ..     578     621 .. 0.95
   4 !   18.0   3.9   5.8e-06    0.0033       1      25 [.     606     630 ..     606     658 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00053
                            Fer4_7  29 ekv.eidpekClgCga.CvavCPtg 51 
                                       +++ ++dp  C gC + C++vCP++
  gi|330508939|ref|YP_004385367.1| 233 HRArYVDPVLCKGCINeCADVCPVE 257
                                       444257899*****877******97 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 5.2e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeen 24 
                                       +CigCg+Cv+ Cp++a++ld++ +
  gi|330508939|ref|YP_004385367.1| 290 ACIGCGRCVESCPTQAVKLDQVVE 313
                                       599999999999999999998754 PP

  == domain 3  score: 31.7 bits;  conditional E-value: 3e-10
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       Ci+C+ Cv++Cp+kai+++          +++d+  C gCg+C+a+CP++a
  gi|330508939|ref|YP_004385367.1| 579 CIKCKLCVDVCPQKAISVKSP--------AYVDEAACKGCGSCAAACPVDA 621
                                       ******************886........799*****************97 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 5.8e-06
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeene 25 
                                       +C gCg C+aaCpv+ai+++ +++e
  gi|330508939|ref|YP_004385367.1| 606 ACKGCGSCAAACPVDAIKMRLFSDE 630
                                       5*****************9865554 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   5.0   0.00012     0.067       4      22 ..     238     257 ..     237     259 .. 0.91
   2 !   25.7   4.1   1.4e-08     8e-06       4      23 ..     286     305 ..     286     306 .. 0.95
   3 !   24.6   3.8   3.3e-08   1.8e-05       2      24 .]     572     594 ..     571     594 .. 0.92
   4 !   20.6   5.6   5.7e-07   0.00032       2      24 .]     600     622 ..     599     622 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                            Fer4_6   4 idpdkCigC.gdCvrvCPeg 22 
                                       +dp +C gC ++C++vCP  
  gi|330508939|ref|YP_004385367.1| 238 VDPVLCKGCiNECADVCPVE 257
                                       89****************86 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 1.4e-08
                            Fer4_6   4 idpdkCigCgdCvrvCPega 23 
                                       +dp +CigCg+Cv  CP++a
  gi|330508939|ref|YP_004385367.1| 286 VDPKACIGCGRCVESCPTQA 305
                                       79*****************9 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 3.3e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       + +dpd+Ci C  Cv+vCP +ai
  gi|330508939|ref|YP_004385367.1| 572 AYVDPDLCIKCKLCVDVCPQKAI 594
                                       679****************8887 PP

  == domain 4  score: 20.6 bits;  conditional E-value: 5.7e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       + +d+ +C gCg C+++CP +ai
  gi|330508939|ref|YP_004385367.1| 600 AYVDEAACKGCGSCAAACPVDAI 622
                                       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 !    8.3   3.0    0.0045       2.5       4      23 ..     238     258 ..     235     286 .. 0.73
   2 !   19.1   5.8   1.8e-06     0.001       4      24 ..     286     310 ..     283     402 .. 0.82
   3 !   29.5  13.9     1e-09   5.8e-07       3      56 .]     573     618 ..     571     618 .. 0.96
   4 !   16.8   3.1   9.5e-06    0.0053       3      24 ..     601     627 ..     599     645 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0045
                           Fer4_10   4 idddtCirCg.kCvkaCPadl 23 
                                       +d+  C +C  +C ++CP+ +
  gi|330508939|ref|YP_004385367.1| 238 VDPVLCKGCInECADVCPVEV 258
                                       68899****77********33 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.8e-06
                           Fer4_10   4 idddtCirCgkCvkaCPadl....t 24 
                                       +d++ Ci+Cg+Cv++CP+++    +
  gi|330508939|ref|YP_004385367.1| 286 VDPKACIGCGRCVESCPTQAvkldQ 310
                                       699***************5544430 PP

  == domain 3  score: 29.5 bits;  conditional E-value: 1e-09
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       ++d+d Ci+C+ Cv++CP+        +++s +++  ++  +C gcg+C++aCP
  gi|330508939|ref|YP_004385367.1| 573 YVDPDLCIKCKLCVDVCPQ--------KAISVKSPAYVDEAACKGCGSCAAACP 618
                                       789****************........99************************9 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 9.5e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.....t 24 
                                       ++d+  C +Cg C +aCP+d+      
  gi|330508939|ref|YP_004385367.1| 601 YVDEAACKGCGSCAAACPVDAikmrlF 627
                                       679999*************66444330 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   9.6   1.5e-08   8.3e-06       2      50 ..     243     305 ..     242     306 .. 0.90
   2 !   30.3  11.9   6.1e-10   3.4e-07       2      51 .]     579     622 ..     577     622 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.5e-08
                            Fer4_9   2 CtgC.gaCveaCpagvvvedaaerkarlraase.............eaCigCgaCveaCpkga 50 
                                       C gC ++C ++Cp +v +e +++   r  ++               +aCigCg+Cve Cp++a
  gi|330508939|ref|YP_004385367.1| 243 CKGCiNECADVCPVEVPNEYDFGIGKRKAIYVPypqavplsacvdpKACIGCGRCVESCPTQA 305
                                       99**556**************999988877666899*************************97 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 6.1e-10
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       C++C+ Cv++Cp+++++ ++ ++ ++       aC gCg+C++aCp +ai
  gi|330508939|ref|YP_004385367.1| 579 CIKCKLCVDVCPQKAISVKSPAYVDEA------ACKGCGSCAAACPVDAI 622
                                       ***********************9997......7*************987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   1.5    0.0025       1.4      38      54 ..     240     257 ..     221     259 .. 0.78
   2 !   19.7   2.4   1.2e-06    0.0007       1      30 [.     284     310 ..     284     320 .. 0.81
   3 !   35.6  12.2   1.3e-11   7.4e-09       1      59 []     572     624 ..     572     624 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0025
                           Fer4_21  38 edeCvGC.nlCssvCPve 54 
                                          C GC n C++vCPve
  gi|330508939|ref|YP_004385367.1| 240 PVLCKGCiNECADVCPVE 257
                                       457****899******95 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.2e-06
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieida 30 
                                       A +d++ CigCg+C+ +C+   +qa+++d+
  gi|330508939|ref|YP_004385367.1| 284 ACVDPKACIGCGRCVESCP---TQAVKLDQ 310
                                       7899***************...57777765 PP

  == domain 3  score: 35.6 bits;  conditional E-value: 1.3e-11
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                       A +d+d Ci+C++C+ +C+    +ai++++ ++  v e  C GC  C++ CPv d+i+m
  gi|330508939|ref|YP_004385367.1| 572 AYVDPDLCIKCKLCVDVCP---QKAISVKSPAY--VDEAACKGCGSCAAACPV-DAIKM 624
                                       789****************...599*9987766..99***************9.***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 ?   -2.0   0.2         9     5e+03      12      17 ..     190     195 ..     189     196 .. 0.79
   2 ?    6.6   3.7     0.016         9       4      21 ..     237     255 ..     234     256 .. 0.87
   3 !   17.6   6.9     5e-06    0.0028       4      22 .]     285     303 ..     282     303 .. 0.92
   4 !   20.5   2.9   6.1e-07   0.00034       3      22 .]     572     591 ..     570     591 .. 0.93
   5 !   19.5   4.3   1.3e-06   0.00071       2      21 ..     599     618 ..     598     619 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9
                            Fer4_2  12 gCgaCv 17 
                                        C++Cv
  gi|330508939|ref|YP_004385367.1| 190 DCSICV 195
                                       699997 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.016
                            Fer4_2   4 vvdtdrCigC.gaCvsaCP 21 
                                       +vd+  C gC + C ++CP
  gi|330508939|ref|YP_004385367.1| 237 YVDPVLCKGCiNECADVCP 255
                                       678889*****99****** PP

  == domain 3  score: 17.6 bits;  conditional E-value: 5e-06
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                        vd+ +CigCg Cv +CP+
  gi|330508939|ref|YP_004385367.1| 285 CVDPKACIGCGRCVESCPT 303
                                       69****************7 PP

  == domain 4  score: 20.5 bits;  conditional E-value: 6.1e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       ++vd+d Ci C+ Cv++CP+
  gi|330508939|ref|YP_004385367.1| 572 AYVDPDLCIKCKLCVDVCPQ 591
                                       689****************6 PP

  == domain 5  score: 19.5 bits;  conditional E-value: 1.3e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       p++vd+++C gCg+C  aCP
  gi|330508939|ref|YP_004385367.1| 599 PAYVDEAACKGCGSCAAACP 618
                                       679***************** PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3       0.1        58      50      65 .]     242     258 ..     217     258 .. 0.82
   2 !   16.9   0.0   1.2e-05    0.0065       3      18 ..     289     304 ..     287     379 .. 0.79
   3 !   12.4   0.1    0.0003      0.17      49      64 ..     577     592 ..     547     597 .. 0.81
   4 !   11.9   1.3   0.00043      0.24       4      17 ..     606     619 ..     603     659 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.1
                            Fer4_8  50 sCttcga.CtevCpvgi 65 
                                        C +c + C++vCpv++
  gi|330508939|ref|YP_004385367.1| 242 LCKGCINeCADVCPVEV 258
                                       57777444999999875 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.2e-05
                            Fer4_8   3 ekCieCgaCqsaCpvl 18 
                                       ++Ci+Cg+C ++Cp+ 
  gi|330508939|ref|YP_004385367.1| 289 KACIGCGRCVESCPTQ 304
                                       58***********943 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.0003
                            Fer4_8  49 wsCttcgaCtevCpvg 64 
                                       + C  c+ C++vCp++
  gi|330508939|ref|YP_004385367.1| 577 DLCIKCKLCVDVCPQK 592
                                       6788888888888875 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00043
                            Fer4_8   4 kCieCgaCqsaCpv 17 
                                       +C +Cg C +aCpv
  gi|330508939|ref|YP_004385367.1| 606 ACKGCGSCAAACPV 619
                                       57777777777763 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.9   7.7e-12   4.3e-09       1      38 [.     142     179 ..     142     188 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 7.7e-12
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38 
                                       Dv+VvGGg+aG+aAA+  a aG  v Lve+r+ +GG +
  gi|330508939|ref|YP_004385367.1| 142 DVMVVGGGVAGIAAALDLADAGFHVFLVERRPTIGGYM 179
                                       9***********************************88 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   1.2   2.1e-08   1.2e-05       1      33 [.     142     176 ..     142     179 .. 0.95
   2 !    7.0   0.0     0.007       3.9     152     210 ..     438     499 ..     313     530 .. 0.63

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.1e-08
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                       dv ++GGG++G+++A++La +g  V l+e+++ +g
  gi|330508939|ref|YP_004385367.1| 142 DVMVVGGGVAGIAAALDLADAGfhVFLVERRPTIG 176
                                       89*****************99**********9988 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.007
                                       HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE..EEE--GGGHHHH.HTT CS
                               DAO 152 laraaealGveilegtevtgleeedgkvwgverttp.gendaada..vVnaaGawsdll.gll 210
                                       ++ +a+ lG+++++  +v ++ee dg+++  +++t+ ge++++++   V++ G+  d++ + l
  gi|330508939|ref|YP_004385367.1| 438 FYVRAQMLGINFVRA-RVSSIEEVDGDIYLRFEDTQtGEIKRVRHdiAVLSVGLEPDKSaDVL 499
                                       6678999*******8.*****99888855544777778884345556******9988552333 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   2.6       1.2   6.7e+02       4      16 ..     243     256 ..     241     260 .. 0.70
   2 !   16.7   4.6   1.3e-05    0.0073       2      17 .]     289     304 ..     288     305 .. 0.91
   3 !   15.8   3.2   2.5e-05     0.014       1      17 []     576     592 ..     576     592 .. 0.91
   4 !   14.8   2.6   5.4e-05     0.031       3      16 ..     606     619 ..     604     625 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.2
                            Fer4_4   4 CigCg.sCvaaCPq 16 
                                       C gC   C ++CP+
  gi|330508939|ref|YP_004385367.1| 243 CKGCInECADVCPV 256
                                       44444459999996 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.3e-05
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       + CigCg+Cv +CP++
  gi|330508939|ref|YP_004385367.1| 289 KACIGCGRCVESCPTQ 304
                                       78************86 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 2.5e-05
                            Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                       ++ Ci C+ Cv++CPq+
  gi|330508939|ref|YP_004385367.1| 576 PDLCIKCKLCVDVCPQK 592
                                       588************85 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 5.4e-05
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        C gCgsC aaCP+
  gi|330508939|ref|YP_004385367.1| 606 ACKGCGSCAAACPV 619
                                       6************7 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   5.5e-10   3.1e-07       1      39 [.     145     183 ..     145     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 5.5e-10
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EEC CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasye 39 
                                       +vG+G++G +aA  La+agf+v l+e+r+ +GG +a  +
  gi|330508939|ref|YP_004385367.1| 145 VVGGGVAGIAAALDLADAGFHVFLVERRPTIGGYMALLT 183
                                       8********************************998554 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   1.0     1e-08   5.8e-06       1      36 [.     142     177 ..     142     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1e-08
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                       Dv V+G+G+AG aAAl +a+aG  v +ve  +  gg
  gi|330508939|ref|YP_004385367.1| 142 DVMVVGGGVAGIAAALDLADAGFHVFLVERRPTIGG 177
                                       9****************************9998887 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   1.9      0.75   4.2e+02      46      59 ..     243     257 ..     235     259 .. 0.65
   2 ?    6.6  12.3     0.021        12       2      58 ..     243     303 ..     242     306 .. 0.64
   3 !   13.8   0.2   0.00011     0.063      44      59 ..     577     592 ..     550     594 .. 0.83
   4 !   11.5   1.6   0.00058      0.33       1      49 [.     606     657 ..     606     659 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.75
                           Fer4_17  46 CieC.geCerkCPqg 59 
                                       C +C +eC+ +CP +
  gi|330508939|ref|YP_004385367.1| 243 CKGCiNECADVCPVE 257
                                       444435666666655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.021
                           Fer4_17   2 CiqCgy.ClpeCpsyeaydn....epkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       C +C   C+++Cp    ++      ++k ++  +++ +   ++    + Ci+Cg+C+++CP 
  gi|330508939|ref|YP_004385367.1| 243 CKGCINeCADVCPVEVPNEYdfgiGKRKAIYVPYPQAV-PLSACVDPKACIGCGRCVESCPT 303
                                       99998559999998666444112234445554444322.223334789*************7 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 0.00011
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                       +lCi+C++C+ +CPq+
  gi|330508939|ref|YP_004385367.1| 577 DLCIKCKLCVDVCPQK 592
                                       7899999999999985 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00058
                           Fer4_17   1 rCiqCgyClpeCpsyea..ydnepkkllraaklg.lleeaeke...ekaslCieC 49 
                                       +C +Cg C+++Cp  ++  + +  +++l++++++ ++++   e     a lC+ C
  gi|330508939|ref|YP_004385367.1| 606 ACKGCGSCAAACPVDAIkmRLFSDEQILAQIRAAtEVKK---EfplIIAFLCNWC 657
                                       5999********987665445567778888777413333...2223467777776 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   7.8e-08   4.4e-05       1      29 [.     142     172 ..     142     202 .. 0.83
   2 ?   -3.3   0.1       6.5   3.6e+03     355     389 ..     527     561 ..     525     562 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.8e-08
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE..E CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..t 29 
                                       dv+V+GgG AG++AAl +a +G++v L+   
  gi|330508939|ref|YP_004385367.1| 142 DVMVVGGGVAGIAAALDLADAGFHVFLVerR 172
                                       79*************************9441 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.5
                                       SBTEEE-CGGGTB-SHHHHHHHHHHHHHHHHHHHC CS
                              GIDA 355 vkgLflAGqinGteGYeEaaaqGllAGinaarkak 389
                                       ++g+f+AG  +G +    ++aqG  A+  a r ++
  gi|330508939|ref|YP_004385367.1| 527 IDGVFIAGCASGPKEIPISIAQGSAAAAKAIRLLQ 561
                                       678999999999988888999**999999988765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   2.5e-07   0.00014      16      60 ..     139     182 ..     125     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.5e-07
                                       TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTT CS
                              Thi4  16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlG 60 
                                       ++ Dv++vG+G +G++aa  la + +++v ++er+ ++GG + l 
  gi|330508939|ref|YP_004385367.1| 139 VNKDVMVVGGGVAGIAAALDLADA-GFHVFLVERRPTIGGYMALL 182
                                       678*********************.***************88765 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.7       1.1   6.3e+02       7      61 ..     242     256 ..     237     264 .. 0.57
   2 !   14.5   0.7   7.8e-05     0.044       3      24 ..     286     307 ..     285     338 .. 0.83
   3 !   10.7   1.5    0.0012      0.67       2      20 ..     573     591 ..     572     596 .. 0.93
   4 !    9.8   3.9    0.0023       1.3       2      19 ..     601     618 ..     600     646 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.1
                           Fer4_15   7 aCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPv 61 
                                       +C gc                                        + e a++CPv
  gi|330508939|ref|YP_004385367.1| 242 LCKGC----------------------------------------INECADVCPV 256
                                       55555........................................4444555555 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 7.8e-05
                           Fer4_15   3 vDrdaCigcglCvaeapevfel 24 
                                       vD +aCigcg+Cv+ +p+  ++
  gi|330508939|ref|YP_004385367.1| 286 VDPKACIGCGRCVESCPTQAVK 307
                                       899*************975544 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0012
                           Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                       +vD d+Ci c lCv+++p+
  gi|330508939|ref|YP_004385367.1| 573 YVDPDLCIKCKLCVDVCPQ 591
                                       69***************85 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0023
                           Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                       +vD+ aC gcg C+a++p
  gi|330508939|ref|YP_004385367.1| 601 YVDEAACKGCGSCAAACP 618
                                       69***************6 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.5   2.2e-06    0.0012       2      35 ..     143     176 ..     142     183 .. 0.93
   2 ?   -1.3   0.0       5.9   3.3e+03      50      72 ..     204     226 ..     197     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.2e-06
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       v+vvGgG+ g+ +A  la+ g +V +ver++++ 
  gi|330508939|ref|YP_004385367.1| 143 VMVVGGGVAGIAAALDLADAGFHVFLVERRPTIG 176
                                       89*****************************997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.9
                                       HHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  50 lekngievllntkveeiegsedg 72 
                                       + + +i++++ ++v  +egs  +
  gi|330508939|ref|YP_004385367.1| 204 FNHPNITLYTYSEVLGVEGSVGN 226
                                       55569*************98765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.3   1.8e-06     0.001       3      34 ..     142     173 ..     140     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                       dV++VG+G aG+ +al L+ aG  v lve+r 
  gi|330508939|ref|YP_004385367.1| 142 DVMVVGGGVAGIAAALDLADAGFHVFLVERRP 173
                                       8*****************************96 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.7   2.7e-06    0.0015       2      36 ..     142     176 ..     141     181 .. 0.94
   2 ?   -3.9   0.1       7.5   4.2e+03     378     394 ..     211     227 ..     209     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.7e-06
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       dv+v+GgG AG+ aA+ +a++g +V l+e+ +++g
  gi|330508939|ref|YP_004385367.1| 142 DVMVVGGGVAGIAAALDLADAGFHVFLVERRPTIG 176
                                       8*****************************99988 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7.5
                                       EEE-GGGBSEEE-TTTH CS
                       HI0933_like 378 LffaGEvlDvegvtGGy 394
                                       L+   Evl veg +G +
  gi|330508939|ref|YP_004385367.1| 211 LYTYSEVLGVEGSVGNF 227
                                       89999*********977 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   1.1e-05    0.0063       1      28 [.     150     177 ..     150     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBT CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGG 28 
                                       +aG+aaA  L++aGf V ++E r+ +GG
  gi|330508939|ref|YP_004385367.1| 150 VAGIAAALDLADAGFHVFLVERRPTIGG 177
                                       69*************************9 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.2   3.7e-05     0.021     165     199 ..     141     175 ..     130     246 .. 0.76
   2 ?   -0.9   0.0       1.4   7.9e+02     232     305 .]     451     534 ..     438     534 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.7e-05
                       Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgsei 199
                                       ++v+V+Gg+  ++ aAl+l+++g +V +v r+ +i
  gi|330508939|ref|YP_004385367.1| 141 KDVMVVGGGVAGIAAALDLADAGFHVFLVERRPTI 175
                                       56666666666666666666666666666666554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                       Pyr_redox_3 232 naevkeikekeeeykvktedgkkvev....kddvvlatGykpd..lsflkk.slfeldedgrpvlteete...etnv 298
                                       +a+v +i+e +  + +++ed+++ e+    +d  vl +G +pd  +++l +  +++++ d++ ++   ++   e  +
  gi|330508939|ref|YP_004385367.1| 451 RARVSSIEEVDGDIYLRFEDTQTGEIkrvrHDIAVLSVGLEPDksADVLGNlLGLSRRPDRFFEIAHPKMrpvEAHI 527
                                       56899999999999999888766555556556677779999994456788877777777776655554433337888 PP

                       Pyr_redox_3 299 pglflaG 305
                                       +g+f+aG
  gi|330508939|ref|YP_004385367.1| 528 DGVFIAG 534
                                       8888887 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.5      0.72   4.1e+02      61      75 ..     243     258 ..     191     263 .. 0.74
   2 ?    6.8   2.2     0.013       7.2      60      74 ..     290     304 ..     280     326 .. 0.79
   3 ?   15.4   4.8   2.9e-05     0.016      61      96 ..     579     618 ..     561     634 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.72
                           Fer4_18  61 cidc.escvkvcPtgi 75 
                                       c  c + c +vcP+++
  gi|330508939|ref|YP_004385367.1| 243 CKGCiNECADVCPVEV 258
                                       3333245667888765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.013
                           Fer4_18  60 dcidcescvkvcPtg 74 
                                        ci c+ cv+ cPt+
  gi|330508939|ref|YP_004385367.1| 290 ACIGCGRCVESCPTQ 304
                                       699999999999986 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 2.9e-05
                           Fer4_18  61 cidcescvkvcPtg.idirkGlqle...ciscllcidacd 96 
                                       ci+c+ cv+vcP + i ++    ++   c  c+ c  ac 
  gi|330508939|ref|YP_004385367.1| 579 CIKCKLCVDVCPQKaISVKSPAYVDeaaCKGCGSCAAACP 618
                                       ************7549999987653333999*******95 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   6.8e-05     0.038       1      35 [.     142     174 ..     142     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.8e-05
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieasps 35 
                                       Dv+v+G+G Ag++ A  l  a +g +v l+e  p 
  gi|330508939|ref|YP_004385367.1| 142 DVMVVGGGVAGIAAALDL--ADAGFHVFLVERRPT 174
                                       9*****************..99********98776 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.6     0.057        32       1      13 [.     243     256 ..     243     258 .. 0.91
   2 ?   16.0   5.0   3.2e-05     0.018       1      15 []     291     305 ..     291     305 .. 0.93
   3 ?   13.9   4.2   0.00014     0.081       1      15 []     579     593 ..     579     593 .. 0.97
   4 ?    9.8   7.3     0.003       1.7       1      15 []     607     621 ..     607     621 .. 0.97

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.057
                            Fer4_3   1 CtgC.gaCvevCPv 13 
                                       C gC + C +vCPv
  gi|330508939|ref|YP_004385367.1| 243 CKGCiNECADVCPV 256
                                       99**889******7 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.2e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCg+Cve+CP+ A
  gi|330508939|ref|YP_004385367.1| 291 CIGCGRCVESCPTQA 305
                                       ************866 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 0.00014
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C +Cv+vCP +A
  gi|330508939|ref|YP_004385367.1| 579 CIKCKLCVDVCPQKA 593
                                       ************998 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.003
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gCg C  +CPv+A
  gi|330508939|ref|YP_004385367.1| 607 CKGCGSCAAACPVDA 621
                                       9************98 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   7.5e-05     0.042      30      62 ..     142     174 ..     136     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.5e-05
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62 
                                        v+v+GgGvaG++A+   +  g +V +++ rp+
  gi|330508939|ref|YP_004385367.1| 142 DVMVVGGGVAGIAAALDLADAGFHVFLVERRPT 174
                                       69************************9999986 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   0.9       1.2   6.9e+02      78      95 ..     239     257 ..     228     258 .. 0.78
   2 ?   15.3   2.0   4.9e-05     0.027      78      95 ..     287     304 ..     276     305 .. 0.86
   3 ?    4.3   0.7      0.13        72      77      94 ..     574     591 ..     545     593 .. 0.66
   4 ?    9.0   2.7    0.0046       2.6      76      95 ..     601     620 ..     591     621 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.2
                           Fer4_22  78 gesgCvGC.gRCieacpvk 95 
                                       +   C GC + C ++cpv+
  gi|330508939|ref|YP_004385367.1| 239 DPVLCKGCiNECADVCPVE 257
                                       6678999966899999986 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.9e-05
                           Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                       + ++C+GCgRC+e+cp++
  gi|330508939|ref|YP_004385367.1| 287 DPKACIGCGRCVESCPTQ 304
                                       6789***********986 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.13
                           Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                       ++   C+ C  C+++cp+
  gi|330508939|ref|YP_004385367.1| 574 VDPDLCIKCKLCVDVCPQ 591
                                       566667777777777765 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0046
                           Fer4_22  76 kfgesgCvGCgRCieacpvk 95 
                                        ++e +C GCg C +acpv+
  gi|330508939|ref|YP_004385367.1| 601 YVDEAACKGCGSCAAACPVD 620
                                       468999***********985 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.4    0.0055       3.1       2      39 ..     145     177 ..     144     185 .. 0.86
   2 ?    1.9   0.0      0.34   1.9e+02     113     149 ..     443     479 ..     433     490 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0055
                     NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gag 39 
                                       +vG+G++G+a++  L++       +++ l++++++ g g
  gi|330508939|ref|YP_004385367.1| 145 VVGGGVAGIAAALDLADA-----GFHVFLVERRPTiG-G 177
                                       9**************999.....6********98845.3 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.34
                     NAD_binding_9 113 egvtvevhraevvdleeradgqavlladgaslaadaV 149
                                       + + ++++ra+v ++ee ++  +++ +d ++ ++++V
  gi|330508939|ref|YP_004385367.1| 443 QMLGINFVRARVSSIEEVDGDIYLRFEDTQTGEIKRV 479
                                       457899*************999998888776444433 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   1.7       6.3   3.6e+03      43      53 ..     246     256 ..     238     258 .. 0.62
   2 ?   10.8   3.3     0.001      0.57       1      18 [.     286     303 ..     286     304 .. 0.94
   3 ?   11.7   3.5   0.00052      0.29       1      18 [.     574     591 ..     574     592 .. 0.95
   4 ?    7.3   4.3     0.012       6.9       1      17 [.     602     618 ..     602     623 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.3
                           Fer4_13  43 daeeAadaCPv 53 
                                       +++e ad CPv
  gi|330508939|ref|YP_004385367.1| 246 CINECADVCPV 256
                                       55666666666 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.001
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VD + Ci+cg Cve +P 
  gi|330508939|ref|YP_004385367.1| 286 VDPKACIGCGRCVESCPT 303
                                       899**************5 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00052
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VD d Ci c++Cv+++P+
  gi|330508939|ref|YP_004385367.1| 574 VDPDLCIKCKLCVDVCPQ 591
                                       89***************6 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.012
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD+  C +cg+C++++P
  gi|330508939|ref|YP_004385367.1| 602 VDEAACKGCGSCAAACP 618
                                       899*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (811 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.50u 0.17s 00:00:00.67 Elapsed: 00:00:00.66
# Mc/sec: 3700.83
//
Query:       gi|330508940|ref|YP_004385368.1|  [L=176]
Description: CoB-CoM heterodisulfide reductase subunit C [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-10   40.0   9.0      8e-10   39.0   9.0    1.5  1  Fer4_8    4Fe-4S dicluster domain
    8.7e-08   32.2   8.9      2e-07   31.1   8.9    1.6  1  Fer4_9    4Fe-4S dicluster domain
    4.7e-07   30.3  19.7      4e-06   27.3   9.8    1.7  2  Fer4_17   4Fe-4S dicluster domain
    6.8e-06   26.6   7.6    1.5e-05   25.5   7.6    1.6  1  Fer4_7    4Fe-4S dicluster domain
      1e-05   25.5  11.7    3.2e-05   24.0  12.0    1.7  1  Fer4_10   4Fe-4S dicluster domain
    8.4e-05   22.2  12.0       0.01   15.6   3.4    2.3  2  Fer4      4Fe-4S binding domain
    0.00035   20.5  13.6      0.008   16.2   4.6    2.3  2  Fer4_2    4Fe-4S binding domain
     0.0011   19.9  11.8       0.06   14.3  12.2    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
     0.0086   16.1  12.1      0.009   16.1   2.5    2.3  2  Fer4_6    4Fe-4S binding domain
     0.0099   16.0  12.7      0.048   13.8  12.7    1.9  1  Fer4_21   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   15.8  10.2      0.017   15.6   2.8    2.3  2  Fer4_4    4Fe-4S binding domain
      0.031   14.8   0.5      0.031   14.8   0.5    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.055   14.4  15.9       0.58   11.2   5.0    2.4  2  Fer4_3    4Fe-4S binding domain
        0.2   11.8   7.8        1.9    8.7   2.2    2.3  2  Fer4_18   4Fe-4S dicluster domain
       0.44   11.3   4.6        8.8    7.1   0.2    2.4  2  Fer4_15   4Fe-4S single cluster domain
        5.5    7.9  14.6        1.3    9.9   4.9    2.3  3  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 !   39.0   9.0   7.1e-13     8e-10       2      65 .]      21      82 ..      20      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 7.1e-13
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                      ++ Ci+Cg C ++Cp+++ +k   +   +   ++   ++++   +e+lw Ct+c  Ct++Cp gi
  gi|330508940|ref|YP_004385368.1| 21 VRTCIQCGTCSASCPTAHLMKpSIRRLVKLCLEG---RREEALHNETLWLCTSCLLCTVRCPRGI 82
                                      789************9999975555555555555...2222235899***************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 !   31.1   8.9   1.8e-10     2e-07       2      49 ..      24      81 ..      23      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.8e-10
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase..........eaCigCgaCveaCpkg 49
                                      C++Cg+C ++Cp+ + ++ + +r ++l  ++           + C++C  C+ +Cp+g
  gi|330508940|ref|YP_004385368.1| 24 CIQCGTCSASCPTAHLMKPSIRRLVKLCLEGRreealhnetlWLCTSCLLCTVRCPRG 81
                                      ****************9999999999866555889*********************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 !   15.2   2.2     2e-05     0.023      41      58 ..      19      36 ..       6      39 .. 0.80
   2 !   27.3   9.8   3.6e-09     4e-06       2      60 ..      24      82 ..      23      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                           Fer4_17 41 ekaslCieCgeCerkCPq 58
                                      e++ +Ci+Cg C+++CP 
  gi|330508940|ref|YP_004385368.1| 19 EEVRTCIQCGTCSASCPT 36
                                      678899999999999995 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 3.6e-09
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60
                                      CiqCg C ++Cp+   ++   ++l++    g+ eea  +e+  lC++C +C+ +CP g+
  gi|330508940|ref|YP_004385368.1| 24 CIQCGTCSASCPTAHLMKPSIRRLVKLCLEGRREEALHNETLWLCTSCLLCTVRCPRGI 82
                                      **************9999866666666666999999999*****************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 !   25.5   7.6   1.3e-08   1.5e-05       1      52 []      23      82 ..      23      82 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.3e-08
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek.....gtekveidpek...ClgCgaCvavCPtga 52
                                      +Ci+Cg C a Cp+  ++ +   +       g+++ +++ e+   C++C  C  +CP g+
  gi|330508940|ref|YP_004385368.1| 23 TCIQCGTCSASCPTAHLMKPSIRRLVklcleGRREEALHNETlwlCTSCLLCTVRCPRGI 82
                                      6************88888764322113444444444444443333************986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0  12.0   2.8e-08   3.2e-05       5      56 .]      20      79 ..      16      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.8e-08
                           Fer4_10  5 dddtCirCgkCvkaCPadl.......tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                      +  tCi+Cg+C ++CP+ +       + v+   e  +eea +   ++ Ct c  C+  CP
  gi|330508940|ref|YP_004385368.1| 20 EVRTCIQCGTCSASCPTAHlmkpsirRLVKLCLEGRREEALHNeTLWLCTSCLLCTVRCP 79
                                      5689*************88*****997788877777777777669**************9 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   3.4   9.2e-06      0.01       8      20 ..      24      36 ..      22      37 .. 0.93
   2 !   11.6   1.4   0.00016      0.18       7      21 ..      67      81 ..      67      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.2e-06
                                      SSS-THHHHHSTT CS
                              Fer4  8 CigCGaCvevCPv 20
                                      Ci CG+C   CP+
  gi|330508940|ref|YP_004385368.1| 24 CIQCGTCSASCPT 36
                                      ************8 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00016
                                      TSSS-THHHHHSTTT CS
                              Fer4  7 kCigCGaCvevCPvg 21
                                      +C+ C +C   CP g
  gi|330508940|ref|YP_004385368.1| 67 LCTSCLLCTVRCPRG 81
                                      6************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 !   16.2   4.6   7.2e-06     0.008       7      22 .]      21      36 ..      17      36 .. 0.87
   2 !    9.4   1.7    0.0011       1.2       9      21 ..      67      79 ..      60      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.2e-06
                            Fer4_2  7 tdrCigCgaCvsaCPa 22
                                       ++Ci+Cg+C  +CP+
  gi|330508940|ref|YP_004385368.1| 21 VRTCIQCGTCSASCPT 36
                                      569*******888**7 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                            Fer4_2  9 rCigCgaCvsaCP 21
                                       C++C  C+  CP
  gi|330508940|ref|YP_004385368.1| 67 LCTSCLLCTVRCP 79
                                      5*******666*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 !   14.3  12.2   5.3e-05      0.06       1      65 [.      23      79 ..      23      81 .. 0.72
   2 !    8.3   1.5     0.004       4.5       2      16 ..      68      82 ..      67     119 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.3e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                      +C++Cg C  +CPt+++ +++     +r+ ++      ++ +e++ +++  + +t C  C+  CP
  gi|330508940|ref|YP_004385368.1| 23 TCIQCGTCSASCPTAHLMKPS-----IRRLVKL---CLEGRREEALHNETLWLCTSCLLCTVRCP 79
                                      5*******************4.....3444443...22333444444445689***********9 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.004
                           Fer4_16  2 CgtCgkCaevCPtna 16
                                      C++C  C+  CP + 
  gi|330508940|ref|YP_004385368.1| 68 CTSCLLCTVRCPRGI 82
                                      ************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 !   16.1   2.5     8e-06     0.009       9      22 ..      24      37 ..      22      39 .. 0.89
   2 ?    5.1   2.3     0.023        25       8      22 ..      67      81 ..      67      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8e-06
                            Fer4_6  9 CigCgdCvrvCPeg 22
                                      Ci+Cg C + CP++
  gi|330508940|ref|YP_004385368.1| 24 CIQCGTCSASCPTA 37
                                      ************96 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.023
                            Fer4_6  8 kCigCgdCvrvCPeg 22
                                      +C++C  C++ CP g
  gi|330508940|ref|YP_004385368.1| 67 LCTSCLLCTVRCPRG 81
                                      6***********965 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8  12.7   4.3e-05     0.048       6      52 ..      22      79 ..      17      83 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-05
                           Fer4_21  6 dkCigCgkCliaCedtshqai...........eidakt.vlkvvedeCvGCnlCssvCP 52
                                       +Ci+Cg C  +C++ +h              e+  ++  ++ +   C+ C lC+  CP
  gi|330508940|ref|YP_004385368.1| 22 RTCIQCGTCSASCPT-AHLMKpsirrlvklclEGRREEaLHNETLWLCTSCLLCTVRCP 79
                                      58************5.5432233366665544333333133334458************ PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   2.8   1.6e-05     0.017       3      16 ..      23      36 ..      21      40 .. 0.93
   2 ?    4.4   0.8     0.059        66       4      16 ..      68      80 ..      62      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      +Ci+Cg C a+CP+
  gi|330508940|ref|YP_004385368.1| 23 TCIQCGTCSASCPT 36
                                      5************7 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.059
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C+ C  C+  CP 
  gi|330508940|ref|YP_004385368.1| 68 CTSCLLCTVRCPR 80
                                      9*******99996 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.5   2.7e-05     0.031       4      24 ..      22      42 ..      20      60 .. 0.86
   2 ?    2.6   1.9      0.18     2e+02       6      17 ..      68      79 ..      66      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                           Fer4_13  4 dtCiacgaCvelaPdvFeedd 24
                                       tCi cg+C + +P    +++
  gi|330508940|ref|YP_004385368.1| 22 RTCIQCGTCSASCPTAHLMKP 42
                                      59************9776666 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.18
                           Fer4_13  6 CiacgaCvelaP 17
                                      C++c +C   +P
  gi|330508940|ref|YP_004385368.1| 68 CTSCLLCTVRCP 79
                                      ***********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 ?   11.2   5.0   0.00052      0.58       1      13 [.      24      36 ..      24      38 .. 0.95
   2 ?    8.7   3.1    0.0033       3.6       1      14 [.      68      81 ..      68      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00052
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C++Cg+C  +CP+
  gi|330508940|ref|YP_004385368.1| 24 CIQCGTCSASCPT 36
                                      ************6 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0033
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      Ct C +C + CP g
  gi|330508940|ref|YP_004385368.1| 68 CTSCLLCTVRCPRG 81
                                      9***********98 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.2    0.0017       1.9      55      74 ..      18      37 ..       3      53 .. 0.80
   2 ?    6.2   0.5      0.01        12      50      75 ..      57      82 ..      44      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
                           Fer4_18 55 ekgagdcidcescvkvcPtg 74
                                       +++  ci+c++c + cPt 
  gi|330508940|ref|YP_004385368.1| 18 GEEVRTCIQCGTCSASCPTA 37
                                      567789************95 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.01
                           Fer4_18 50 keerkekgagdcidcescvkvcPtgi 75
                                      +e  ++++   c++c  c   cP gi
  gi|330508940|ref|YP_004385368.1| 57 EEALHNETLWLCTSCLLCTVRCPRGI 82
                                      45556667778************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 ?    5.4   0.8     0.028        31       7      20 ..      23      36 ..      20      45 .. 0.88
   2 ?    7.1   0.2    0.0079       8.8       7      22 ..      67      82 ..      65     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.028
                           Fer4_15  7 aCigcglCvaeape 20
                                      +Ci cg C a +p+
  gi|330508940|ref|YP_004385368.1| 23 TCIQCGTCSASCPT 36
                                      8***********97 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0079
                           Fer4_15  7 aCigcglCvaeapevf 22
                                      +C++c lC  ++p+ +
  gi|330508940|ref|YP_004385368.1| 67 LCTSCLLCTVRCPRGI 82
                                      8***********9765 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.9    0.0012       1.3       1      17 [.      23      39 ..      23      61 .. 0.88
   2 ?    2.7   2.6       0.2   2.3e+02       2      13 ..      68      79 ..      39      82 .. 0.75
   3 ?    2.9   2.4      0.18     2e+02       2      14 ..      68      80 ..      67     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                           Fer4_22  1 rClsCgaCtlvCptCsC 17
                                      +C++Cg+C++ Cpt + 
  gi|330508940|ref|YP_004385368.1| 23 TCIQCGTCSASCPTAHL 39
                                      5*************875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.2
                           Fer4_22  2 ClsCgaCtlvCp 13
                                      C sC  Ct+ Cp
  gi|330508940|ref|YP_004385368.1| 68 CTSCLLCTVRCP 79
                                      566666666665 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.18
                           Fer4_22  2 ClsCgaCtlvCpt 14
                                      C sC  Ct+ Cp 
  gi|330508940|ref|YP_004385368.1| 68 CTSCLLCTVRCPR 80
                                      8999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 955.23
//
Query:       gi|330508941|ref|YP_004385369.1|  [L=281]
Description: CoB-CoM heterodisulfide reductase subunit B [Methanosaeta concilii GP6]
Scores for complete 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-28   96.4   0.6    1.2e-13   51.0   0.0    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 !   43.7   0.2   1.3e-15   2.3e-11       2      85 .]       4      80 ..       3      80 .. 0.91
   2 !   51.0   0.0     7e-18   1.2e-13       1      85 []     135     222 ..     135     222 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.3e-15
                               CCG  2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgC 80
                                      ay++gC +     +e++++++++++ l +eleele+ +CCGa ++  ++e +a  la+rn+++ e      ivt c+ C
  gi|330508941|ref|YP_004385369.1|  4 AYYPGC-VSLSTGKEMDRSTRAVFSSLEIELEELEDWNCCGATHV--SNEMVATGLAARNMSQTEL----DIVTSCSIC 75
                                      8*****.999999*****************************998..666689999*999999887....4******** PP

                               CCG 81 llqlk 85
                                      + +l+
  gi|330508941|ref|YP_004385369.1| 76 YSNLR 80
                                      *9885 PP

  == domain 2  score: 51.0 bits;  conditional E-value: 7e-18
                               CCG   1 vayfdgChllraa...ypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadai 73 
                                       va ++gC l r+    +pe++ +l+kl++ l ++ +++ +k  CCG +++   kee a++ a r ++ a+e+ga++i
  gi|330508941|ref|YP_004385369.1| 135 VAAYYGCLLSRPPgvySPEYPVVLEKLIRILQADAVDFrRKTFCCGGPIFMP-KEEAANETAYRILKDAKEAGAEVI 210
                                       789****7777779**9*******************999*********9955.5559******************** PP

                               CCG  74 vtacpgCllqlk 85 
                                       +t cp C+++l+
  gi|330508941|ref|YP_004385369.1| 211 ITVCPLCQFMLD 222
                                       **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.35s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1548.84
//
Query:       gi|330508942|ref|YP_004385370.1|  [L=169]
Description: hypothetical protein MCON_3285 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.71    8.6   7.5          1    8.0   7.3    1.3  1  DUF2207        Predicted membrane protein (DUF2207)
        1.7    8.3  11.9        5.5    6.6   8.2    2.1  2  DUF4131        Domain of unknown function (DUF4131)
        4.1    5.6  12.1        4.9    5.3  12.1    1.1  1  DUF2070        Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   7.3   0.00017         1     353     432 ..      40     141 ..      31     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00017
                           DUF2207 353 fkkalkkwksavkk...kergyfdkkgkkklkklsalglgliilglilillallllvll.................. 408
                                       f+++++k+++ ++    k+++ f+k+    ++++     +++ l++++i l+++++++                   
  gi|330508942|ref|YP_004385370.1|  40 FNDKINKINEYLELhllKRYNRFSKR---VKNYSKWNRSFIFTLLFVVISLSVYQFISNsatslldymtyyygfakl 113
                                       77778888888888555555555555...4444444444444455555544444444445578899999******** PP

                           DUF2207 409 ....lvfllilllillliaiivlllfsr 432
                                           l   l+ +l++l +++i+l+++++
  gi|330508942|ref|YP_004385370.1| 114 vlipLRRVLLASLAILAVMFILLFIARS 141
                                       *999888888888888888888888743 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1    0.0091        54      26      53 ..      54      97 ..      19     110 .. 0.63
   2 ?    6.6   8.2   0.00093       5.5       3      49 ..     116     162 ..     114     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0091
                           DUF4131 26 r................rprrrvllllllllllallgfalrapq 53
                                                       +++r ++++ll++ + ++++ +++   
  gi|330508942|ref|YP_004385370.1| 54 HllkrynrfskrvknysKWNRSFIFTLLFVVISLSVYQFISNSA 97
                                      05555555566666666777777777777777777777766554 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00093
                           DUF4131   3 lplalvllalllllllllllllrrrprrrvllllllllllallgfal 49 
                                       +pl  vlla+l++l++  +ll+  r +++ +++++++ll++++ ++l
  gi|330508942|ref|YP_004385370.1| 116 IPLRRVLLASLAILAVMFILLFIARSTPKKMIGAFAILLFMFGNILL 162
                                       577778899999999888888888*****************998876 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  12.1   0.00082       4.9       4     142 ..      62     157 ..      51     169 .] 0.41

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.00082
                           DUF2070   4 lskyifrlPswkvsllliillalligllaflssklfgillfglpalvaflltlpvlrilggrltykrslflalltel 80 
                                       +sk ++                                                         +++rs+++ ll+ +
  gi|330508942|ref|YP_004385370.1|  62 FSKRVKNY------------------------------------------------------SKWNRSFIFTLLFVV 84 
                                       23333334......................................................555555444444444 PP

                           DUF2070  81 ivviisllaillsallqalvllalvls............lalvfalrllvlvavsdesllkavlpaliqpllai 142
                                       i++ ++ + +  ++ l +++++++ ++             +l++  ++++l+++++++++k++  a++++l+++
  gi|330508942|ref|YP_004385370.1|  85 ISLSVYQFISNSATSLLDYMTYYYGFAklvliplrrvllASLAILAVMFILLFIARSTPKKMI-GAFAILLFMF 157
                                       443333333333333334444444444444555555554444444444444444444444444.2222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 921.18
//
Query:       gi|330508943|ref|YP_004385371.1|  [L=184]
Description: hypothetical protein MCON_3287 [Methanosaeta concilii GP6]
Scores for complete 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   1.8    2.9e-28   98.0   1.8    1.2  1  DUF1003   Protein of unknown function (DUF1003)
  ------ inclusion threshold ------
      0.076   12.3   0.1      0.098   11.9   0.1    1.1  1  SecY      SecY translocase


Domain annotation for each model (and alignments):
>> DUF1003  Protein of unknown function (DUF1003)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   1.8   3.2e-32   2.9e-28       2     100 ..      76     169 ..      75     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 3.2e-32
                           DUF1003   2 GsakFlvlftaivilWialnllvlpglkpfDpypFillnlvlslqaalaaplIllsqnRqadrdrvraeedrqvnlk 78 
                                       Gs++F++ ++++v++W++ln ++    +++DpypFi++nl++slq+a++a lIl+sqnRq   dr++a++d+ +n +
  gi|330508943|ref|YP_004385371.1|  76 GSWRFILAQSILVAVWVLLNATA--YMQAWDPYPFIFMNLIFSLQSAYTASLILMSQNRQ---DRLKAHNDYLMNIR 147
                                       9*******************997..8*********************************9...899*********** PP

                           DUF1003  79 aeaeiekLtrevaalrealgev 100
                                       ae+e ++++++ aa++ al+e 
  gi|330508943|ref|YP_004385371.1| 148 AEEESKAVLDNFAAQNRALEEI 169
                                       ****************999986 PP

>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.1e-05     0.098     181     263 ..      80     162 ..      73     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHHCCCCS...TCCCSTHHHHHHHHHHHHHHHHHHHHTCT.THHHHHHHCCHHTBSSSCTTTTCHHHH CS
                              SecY 181 iIfassllalpstiaqfl..lallspsvlyvvlyvlliifFayfyteit.fnpkevaenlkksggfipgirpgketa 254
                                        I+a+s+l+   ++++ +  +++ +p   y ++++ li+ +   yt+   + +++  + lk ++ ++ +ir ++e +
  gi|330508943|ref|YP_004385371.1|  80 FILAQSILVAVWVLLNATayMQAWDP---YPFIFMNLIFSLQSAYTASLiLMSQNRQDRLKAHNDYLMNIRAEEESK 153
                                       68899998887777665522222223...999999999999999998877999999********************* PP

                                       HHHHHHHHH CS
                              SecY 255 kyLekvlsr 263
                                        +L++   +
  gi|330508943|ref|YP_004385371.1| 154 AVLDNFAAQ 162
                                       *99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1020.94
//
Query:       gi|330508944|ref|YP_004385372.1|  [L=182]
Description: CopG family transcriptional regulator [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-08   33.2   0.0    6.6e-08   32.2   0.0    1.5  1  RHH_1           Ribbon-helix-helix protein, copG family
     0.0054   16.8   0.0     0.0097   16.0   0.0    1.5  1  B2-adapt-app_C  Beta2-adaptin appendage, C-terminal sub-domai
     0.0061   16.6   0.2      0.014   15.4   0.0    1.7  1  Mei5_like       Putative double-strand recombination repair-l


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 !   32.2   0.0   1.1e-11   6.6e-08       1      35 [.       6      40 ..       6      41 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.1e-11
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlre 35
                                      r++i ldee++ ++ ++++++++S+Sel+Re l++
  gi|330508944|ref|YP_004385372.1|  6 RITIALDEETAGLFKKMKEDSNMSQSELMRESLKF 40
                                      8******************************9975 PP

>> B2-adapt-app_C  Beta2-adaptin appendage, C-terminal sub-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-06    0.0097       7      59 ..      88     136 ..      85     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-06
                    B2-adapt-app_C   7 dreeFlekWkslpesneqsltlsnnvastspdaleekLqanniftiAkrgveg 59 
                                       ++e+F ++ k++  ++ +++  +      +++++ ++L+ +n+ft+ k g+++
  gi|330508944|ref|YP_004385372.1|  88 EKEKFWSLHKEVSRAHAEQFKHKL--F--NAETILRRLEICNLFTMNKTGKNE 136
                                       789********************9..4..******************776543 PP

>> Mei5_like  Putative double-strand recombination repair-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.4e-06     0.014      16      67 ..      70     130 ..      55     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.4e-06
                         Mei5_like  16 alevde.kafyklkekksekkkn........rRySDqFkdplfiekdiyrKLkliekfkkk 67 
                                       +l +d+  +f +  e + ek+k         r + +qFk +lf++ +i r+L + + f  +
  gi|330508944|ref|YP_004385372.1|  70 ILDIDHwIMFLSFIETHPEKEKFwslhkevsRAHAEQFKHKLFNAETILRRLEICNLFTMN 130
                                       5666666666666666555555466667777**********************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 989.49
//
Query:       gi|330508945|ref|YP_004385373.1|  [L=160]
Description: hypothetical protein MCON_3292 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       724  (0.0403815); 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:                         0  (0); expected 0.2 (1e-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 0.35s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 872.69
//
Query:       gi|330508946|ref|YP_004385374.1|  [L=221]
Description: triose-phosphate isomerase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-11   44.3   0.0    1.6e-11   44.1   0.0    1.2  1  TIM       Triosephosphate isomerase
    0.00044   19.6   0.1     0.0012   18.2   0.1    1.7  1  ThiG      Thiazole biosynthesis protein ThiG
    0.00077   18.9   0.4    0.00077   18.9   0.4    1.5  2  NMO       Nitronate monooxygenase
  ------ inclusion threshold ------
      0.039   13.0   0.2      0.074   12.1   0.2    1.4  1  FMN_dh    FMN-dependent dehydrogenase
       0.12   11.5   0.0        0.2   10.8   0.0    1.5  1  IGPS      Indole-3-glycerol phosphate synthase


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   4.4e-15   1.6e-11       2     132 ..       3     128 ..       2     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 4.4e-15
                                       EEEEE-TBTS-HH..HHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BH CS
                               TIM   2 liagNwKmnktle..eakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsa 76 
                                       +i+ N+K++ + +  ea  l++ ++   ++ +v++++ap++  ++++++ +   k+ ++aq v+    G fTG v+a
  gi|330508946|ref|YP_004385374.1|   3 IIVLNFKTYRESTgpEALRLAEICEDIARDYSVQMIVAPQTADIHAISREV---KIPVYAQHVDGVGYGGFTGHVTA 76 
                                       78899**999666115555555566666669**************988877...5********************** PP

                                       HHHHHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE---HHHHHT CS
                               TIM  77 emlkdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCvGEtleerea 132
                                       + +k +g++  +i HsErr  + +     ++ ++a+ + gl  i+C  +  ++r a
  gi|330508946|ref|YP_004385374.1|  77 ASIKAAGARGSLINHSERRIKLADM----EASLSACRDLGLASIICTNNVATTRAA 128
                                       *******************998876....556788999999999999888877765 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   3.3e-07    0.0012     169     213 ..     164     209 ..     140     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.3e-07
                                       HHHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSH CS
                              ThiG 169 iiieea.kvPvivDAGigspsdaaqamelGadavllntavaeakdp 213
                                        + + a +v v+  AGi + +d   a++lG ++vll++ + +akd 
  gi|330508946|ref|YP_004385374.1| 164 AVKKIApRVGVLCGAGITHGEDLRSALDLGSEGVLLASGIIKAKDQ 209
                                       4555556899**********************************96 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.65   2.3e+03     162     172 ..      62      72 ..      27      89 .. 0.47
   2 !   18.9   0.4   2.1e-07   0.00077     129     231 ..     105     209 ..      96     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.65
                               NMO 162 vqGpeaGGhqG 172
                                       v+G   GG +G
  gi|330508946|ref|YP_004385374.1|  62 VDGVGYGGFTG 72 
                                       33333333333 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.1e-07
                               NMO 129 varlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd.....iPviAaG 200
                                       + +  ++g++ i+ +  v   r+++a+ +D + v+ pe  G  G  +v  k   ++v   ++av+     + v+   
  gi|330508946|ref|YP_004385374.1| 105 LSACRDLGLASIICTNNVATTRAAAALEPDYVAVEPPELIGS-G-IPVS-KANPNVVSDSVSAVKkiaprVGVLCGA 178
                                       55667899999**************************98764.3.3443.45677777777777779899******* PP

                               NMO 201 GiidrrgvaaaLalGAsgvqigtrfLltkes 231
                                       Gi  ++++  aL lG +gv +++  + +k+ 
  gi|330508946|ref|YP_004385374.1| 179 GITHGEDLRSALDLGSEGVLLASGIIKAKDQ 209
                                       ***********************99999985 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   2.1e-05     0.074     264     303 ..     164     203 ..     151     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                                       HHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 264 iveavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                        v++++ r+ vl+  Gi++G+D   Al lG ++vll+  +
  gi|330508946|ref|YP_004385374.1| 164 AVKKIAPRVGVLCGAGITHGEDLRSALDLGSEGVLLASGI 203
                                       2444455999*************************98665 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.5e-05       0.2     202     254 .]     164     216 ..      94     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.5e-05
                                       HCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHHH CS
                              IGPS 202 LaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekairel 254
                                        +k++   v + +  Gi++ ed+++  + g +++L  + +++++d+++a+++l
  gi|330508946|ref|YP_004385374.1| 164 AVKKIAPRVGVLCGAGITHGEDLRSALDLGSEGVLLASGIIKAKDQRQALEDL 216
                                       33445567889999**********************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1219.42
//
Query:       gi|330508947|ref|YP_004385375.1|  [L=88]
Description: acylphosphatase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-24   84.2   0.0    6.9e-24   84.1   0.0    1.0  1  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.14   12.3   0.0    1.1  1  BLUF             Sensors of blue-light using FAD


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 !   84.1   0.0   7.7e-28   6.9e-24       1      85 []       3      86 ..       3      86 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 7.7e-28
                   Acylphosphatase  1 vrllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeee 79
                                      v+++v+GrVQgv++R+++r++Ak+lg++G+vrN + g Ve+v+ege+++v ++l+++ksgp  + v  +e +e+e+++ 
  gi|330508947|ref|YP_004385375.1|  3 VHVRVSGRVQGVYYRAYTRDRAKSLGINGWVRNIPGGGVEAVLEGERRQVGELLKAMKSGPSGSVVLGMELSEIEAKGY 81
                                      5899*************************************************************************99 PP

                   Acylphosphatase 80 fkdFei 85
                                       +dFei
  gi|330508947|ref|YP_004385375.1| 82 -NDFEI 86
                                      .***98 PP

>> BLUF  Sensors of blue-light using FAD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.6e-05      0.14      27      90 ..      21      85 ..      11      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHTEEEEEEEE.TTEEEEEEEEEHHHHHHHHHHHHT-TTEEEEEEEEEEEESS-SSTTCS CS
                              BLUF 27 renNkelgitGvLlyd.egvflQvLEGeeeaveelyerIkkDpRhkdvevleeeeieersFskws 90
                                      r++ k+lgi G +    +g +  vLEGe+++v el++ +k+ p  + v  +e +eie + +++++
  gi|330508947|ref|YP_004385375.1| 21 RDRAKSLGINGWVRNIpGGGVEAVLEGERRQVGELLKAMKSGPSGSVVLGMELSEIEAKGYNDFE 85
                                      566677778887754336777889*****************999999999999999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 504.83
//
Query:       gi|330508948|ref|YP_004385376.1|  [L=56]
Description: ferredoxin [Methanosaeta concilii GP6]
Scores for complete 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   40.3  21.1    3.2e-05   23.6   4.6    2.1  2  Fer4        4Fe-4S binding domain
    6.8e-07   30.1  17.1     0.0012   19.7   3.1    2.0  2  Fer4_16     4Fe-4S double cluster binding domain
    2.4e-06   27.3  15.7      0.001   19.1   1.6    2.3  2  Fer4_2      4Fe-4S binding domain
    4.2e-05   23.4  19.8     0.0017   18.3   3.8    2.3  2  Fer4_6      4Fe-4S binding domain
    6.9e-05   22.9  20.4    0.00033   20.8  20.8    1.7  2  Fer4_9      4Fe-4S dicluster domain
    8.7e-05   23.0  21.0     0.0063   17.1   2.6    2.1  3  Fer4_7      4Fe-4S dicluster domain
    0.00038   20.5  19.4     0.0017   18.5  19.4    1.8  1  Fer4_21     4Fe-4S dicluster domain
    0.00064   20.0  18.1     0.0081   16.6   1.5    2.3  2  Fer4_4      4Fe-4S binding domain
     0.0008   19.5  21.1      0.015   15.4   3.8    2.0  2  Fer4_10     4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.037   14.5   2.3      0.037   14.5   2.3    2.1  2  Fer4_8      4Fe-4S dicluster domain
       0.05   14.6  27.6       0.05   14.5   4.5    2.3  2  Fer4_3      4Fe-4S binding domain
      0.081   13.1  18.7      0.088   13.0   2.7    2.0  2  Fer4_18     4Fe-4S dicluster domain
        0.1   13.1  21.1       0.46   11.1   3.0    2.1  2  Fer4_17     4Fe-4S dicluster domain
       0.93   10.4  23.1        1.8    9.4  11.3    2.1  2  Fer4_22     4Fe-4S dicluster domain
        1.4    9.5  19.6        1.7    9.2   7.8    2.1  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 !   23.0   8.6     4e-08   4.8e-05       2      20 ..       3      21 ..       2      25 .. 0.91
   2 !   23.6   4.6   2.7e-08   3.2e-05       7      24 .]      36      53 ..      33      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4e-08
                                      EEETTTSSS-THHHHHSTT CS
                              Fer4  2 videekCigCGaCvevCPv 20
                                      +++  kC +CGaCv+vCP+
  gi|330508948|ref|YP_004385376.1|  3 TVNRYKCCYCGACVSVCPT 21
                                      68999*************8 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 2.7e-08
                                      TSSS-THHHHHSTTTEEE CS
                              Fer4  7 kCigCGaCvevCPvgAIt 24
                                      +C  CG+C ++CPvgA++
  gi|330508948|ref|YP_004385376.1| 36 DCKECGICTKICPVGALE 53
                                      7***************86 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   6.2   8.6e-06      0.01       1      20 [.       8      27 ..       8      35 .. 0.86
   2 !   19.7   3.1   9.9e-07    0.0012       2      19 ..      37      54 ..      36      56 .] 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.6e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C  Cg+C++vCPt a++  
  gi|330508948|ref|YP_004385376.1|  8 KCCYCGACVSVCPTCALELV 27
                                      5***************9977 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 9.9e-07
                           Fer4_16  2 CgtCgkCaevCPtnaike 19
                                      C++Cg C+++CP++a++ 
  gi|330508948|ref|YP_004385376.1| 37 CKECGICTKICPVGALEV 54
                                      ***************986 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   6.7   3.7e-05     0.044       5      22 .]       4      21 ..       1      21 [. 0.86
   2 !   19.1   1.6   8.3e-07     0.001       9      21 ..      36      48 ..      30      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.7e-05
                            Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                      v++ +C  CgaCvs+CP+
  gi|330508948|ref|YP_004385376.1|  4 VNRYKCCYCGACVSVCPT 21
                                      67788888*********7 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 8.3e-07
                            Fer4_2  9 rCigCgaCvsaCP 21
                                       C +Cg+C++ CP
  gi|330508948|ref|YP_004385376.1| 36 DCKECGICTKICP 48
                                      4************ PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   8.1    0.0003      0.35       3      21 ..       3      21 ..       1      24 [. 0.85
   2 !   18.3   3.8   1.4e-06    0.0017       9      24 .]      37      52 ..      34      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                            Fer4_6  3 eidpdkCigCgdCvrvCPe 21
                                      ++++ kC  Cg+Cv+vCP+
  gi|330508948|ref|YP_004385376.1|  3 TVNRYKCCYCGACVSVCPT 21
                                      677888888*********7 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.4e-06
                            Fer4_6  9 CigCgdCvrvCPegai 24
                                      C  Cg C+++CP ga+
  gi|330508948|ref|YP_004385376.1| 37 CKECGICTKICPVGAL 52
                                      99************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 !    9.4  10.7     0.001       1.2      35      49 ..       8      22 ..       2      24 .. 0.75
   2 !   20.8  20.8   2.8e-07   0.00033       1      50 [.       8      51 ..       8      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.001
                            Fer4_9 35 aCigCgaCveaCpkg 49
                                      +C  CgaCv +Cp+ 
  gi|330508948|ref|YP_004385376.1|  8 KCCYCGACVSVCPTC 22
                                      688899999999974 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.8e-07
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      kC+ CgaCv++Cp+++ +  +   +++       +C +Cg C+++Cp ga
  gi|330508948|ref|YP_004385376.1|  8 KCCYCGACVSVCPTCALELVETWLEISA------DCKECGICTKICPVGA 51
                                      7**************9988877777775......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 !   10.8  11.4   0.00049      0.59      33      50 ..       4      21 ..       2      23 .. 0.83
   2 !   10.7  11.0   0.00052      0.62       1      19 [.       8      26 ..       8      36 .. 0.70
   3 !   17.1   2.6   5.3e-06    0.0063       2      19 ..      37      54 ..      36      56 .] 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00049
                            Fer4_7 33 idpekClgCgaCvavCPt 50
                                      ++  kC +CgaCv+vCPt
  gi|330508948|ref|YP_004385376.1|  4 VNRYKCCYCGACVSVCPT 21
                                      56679************8 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00052
                            Fer4_7  1 rCigCgaCvaaCpvkaiel 19
                                      +C  CgaCv++Cp+ a+el
  gi|330508948|ref|YP_004385376.1|  8 KCCYCGACVSVCPTCALEL 26
                                      5666777777777666665 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 5.3e-06
                            Fer4_7  2 CigCgaCvaaCpvkaiel 19
                                      C +Cg C++ Cpv+a+e+
  gi|330508948|ref|YP_004385376.1| 37 CKECGICTKICPVGALEV 54
                                      999*********999986 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5  19.4   1.4e-06    0.0017       3      58 ..       4      53 ..       2      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      +++ kC  Cg C+ +C++ + + +e+     +  ++ +C  C +C+++CPv +++e
  gi|330508948|ref|YP_004385376.1|  4 VNRYKCCYCGACVSVCPTCALELVET-----WLEISADCKECGICTKICPV-GALE 53
                                      7889*************876666653.....5567899************9.7765 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   9.2    0.0018       2.2       3      16 ..       8      21 ..       6      27 .. 0.90
   2 !   16.6   1.5   6.8e-06    0.0081       4      17 .]      37      50 ..      28      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0018
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      +C  Cg+Cv++CP+
  gi|330508948|ref|YP_004385376.1|  8 KCCYCGACVSVCPT 21
                                      6888*********6 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 6.8e-06
                            Fer4_4  4 CigCgsCvaaCPqg 17
                                      C +Cg C+ +CP+g
  gi|330508948|ref|YP_004385376.1| 37 CKECGICTKICPVG 50
                                      9***********86 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8  22.1   8.1e-05     0.097       4      56 .]       4      48 ..       1      48 [. 0.91
   2 !   15.4   3.8   1.3e-05     0.015       6      21 ..      34      49 ..      29      56 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.1e-05
                           Fer4_10  4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +++ +C  Cg+Cv++CP+         + +  e+  + + +C +cg C+++CP
  gi|330508948|ref|YP_004385376.1|  4 VNRYKCCYCGACVSVCPT--------CALELVETWLEISADCKECGICTKICP 48
                                      67789*************........88889999999999************9 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-05
                           Fer4_10  6 ddtCirCgkCvkaCPa 21
                                      +  C +Cg C+k CP+
  gi|330508948|ref|YP_004385376.1| 34 SADCKECGICTKICPV 49
                                      567************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 ?    6.9  10.9    0.0069       8.3       4      18 ..       8      22 ..       5      31 .. 0.78
   2 ?   14.5   2.3   3.1e-05     0.037      47      64 ..      33      50 ..      23      51 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0069
                            Fer4_8  4 kCieCgaCqsaCpvl 18
                                      kC  CgaC s Cp++
  gi|330508948|ref|YP_004385376.1|  8 KCCYCGACVSVCPTC 22
                                      788888888888876 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.1e-05
                            Fer4_8 47 alwsCttcgaCtevCpvg 64
                                      +   C +cg Ct+ Cpvg
  gi|330508948|ref|YP_004385376.1| 33 ISADCKECGICTKICPVG 50
                                      556777777777777775 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  15.1     0.022        27       1      14 [.       9      22 ..       9      23 .. 0.86
   2 ?   14.5   4.5   4.2e-05      0.05       1      15 []      37      51 ..      37      51 .. 0.97

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.022
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C  CgaCv vCP+ 
  gi|330508948|ref|YP_004385376.1|  9 CCYCGACVSVCPTC 22
                                      679*********85 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.2e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C  Cg C + CPvgA
  gi|330508948|ref|YP_004385376.1| 37 CKECGICTKICPVGA 51
                                      99************9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   8.2    0.0076         9      59      73 ..       7      21 ..       3      27 .. 0.87
   2 ?   13.0   2.7   7.4e-05     0.088      57      74 ..      33      50 ..      24      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0076
                           Fer4_18 59 gdcidcescvkvcPt 73
                                       +c  c++cv+vcPt
  gi|330508948|ref|YP_004385376.1|  7 YKCCYCGACVSVCPT 21
                                      57************9 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.4e-05
                           Fer4_18 57 gagdcidcescvkvcPtg 74
                                       ++dc +c+ c k+cP+g
  gi|330508948|ref|YP_004385376.1| 33 ISADCKECGICTKICPVG 50
                                      579*************97 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  10.4     0.004       4.7       1      17 [.       8      24 ..       8      32 .. 0.85
   2 ?   11.1   3.0   0.00039      0.46       2      15 ..      37      50 ..      36      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.004
                           Fer4_17  1 rCiqCgyClpeCpsyea 17
                                      +C+ Cg+C+ +Cp+++ 
  gi|330508948|ref|YP_004385376.1|  8 KCCYCGACVSVCPTCAL 24
                                      69999999999999875 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00039
                           Fer4_17  2 CiqCgyClpeCpsy 15
                                      C +Cg C++ Cp +
  gi|330508948|ref|YP_004385376.1| 37 CKECGICTKICPVG 50
                                      88999999999875 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  11.3    0.0015       1.8       1      17 [.       8      24 ..       8      36 .. 0.86
   2 ?    7.4   3.9    0.0065       7.8       2      14 ..      37      49 ..      36      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                           Fer4_22  1 rClsCgaCtlvCptCsC 17
                                      +C  CgaC  vCptC  
  gi|330508948|ref|YP_004385376.1|  8 KCCYCGACVSVCPTCAL 24
                                      7**************75 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0065
                           Fer4_22  2 ClsCgaCtlvCpt 14
                                      C +Cg Ct +Cp 
  gi|330508948|ref|YP_004385376.1| 37 CKECGICTKICPV 49
                                      9999999999995 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 ?    9.2   7.8    0.0015       1.7       1      18 [.       4      21 ..       4      22 .. 0.94
   2 ?    6.5   3.9     0.011        13       5      17 ..      36      48 ..      33      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      V+r +C  cgaCv+++P 
  gi|330508948|ref|YP_004385376.1|  4 VNRYKCCYCGACVSVCPT 21
                                      8999*************6 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                           Fer4_13  5 tCiacgaCvelaP 17
                                       C +cg+C +++P
  gi|330508948|ref|YP_004385376.1| 36 DCKECGICTKICP 48
                                      6***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 312.32
//
Query:       gi|330508949|ref|YP_004385377.1|  [L=391]
Description: geranylgeranyl reductase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-14   53.4   4.2    3.1e-11   43.1   0.5    3.0  2  FAD_binding_3   FAD binding domain
    5.8e-09   35.8   4.8    3.1e-08   33.4   4.8    1.9  1  FAD_oxidored    FAD dependent oxidoreductase
    2.3e-08   33.5   0.6    6.4e-07   28.8   0.2    2.4  2  FAD_binding_2   FAD binding domain
    9.9e-08   31.1   0.4    1.5e-07   30.5   0.4    1.3  1  HI0933_like     HI0933-like protein
    3.5e-07   29.5   0.1     0.0012   17.8   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
    1.2e-06   27.9   0.5    0.00068   18.8   0.2    2.1  2  Lycopene_cycl   Lycopene cyclase protein
    9.4e-06   25.1   0.2    2.6e-05   23.6   0.1    1.9  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.1e-05   23.4   0.3    5.1e-05   23.4   0.3    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.5e-05   22.5   1.4    0.00039   19.7   1.4    2.2  1  Thi4            Thi4 family
     0.0002   21.0   2.3      0.023   14.3   0.3    2.6  3  DAO             FAD dependent oxidoreductase
    0.00052   19.2   2.5    0.00052   19.2   2.5    1.7  2  GIDA            Glucose inhibited division protein A
     0.0016   17.8   0.2     0.0027   17.1   0.2    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.021   14.1   0.5      0.021   14.1   0.5    1.5  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.043   12.9   0.1      0.075   12.1   0.1    1.3  1  SE              Squalene epoxidase
      0.052   14.1   0.3       0.39   11.2   0.1    2.5  3  XdhC_C          XdhC Rossmann domain
       0.13   12.2   2.5       0.11   12.3   0.6    1.9  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
        9.6    6.8   8.4       0.23   12.0   0.3    2.4  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 !   43.1   0.5   2.9e-14   3.1e-11       1     177 [.       2     169 ..       2     197 .. 0.82
   2 !    7.9   0.2    0.0015       1.5     285     337 ..     271     324 ..     263     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 2.9e-14
                                       EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS.--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEE CS
                     FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpr.adglnqrtmellrqlGledrilaegapnelmgeal 76 
                                       ++dV++VGaGp G m+a+  + aG +vv++ekr++  +  r a+g+ +r +   +++  e + +a      + g   
  gi|330508949|ref|YP_004385377.1|   2 KCDVIVVGAGPGGSMAAKTAAAAGLNVVMLEKRQEIGDPVRcAEGVGKRALC--KMVKPEPEWIASE----VKGAKI 72 
                                       69*******************************9998888658999999875..4454555555544....667777 PP

                                       EEECCCCCEEEEEHHCH.HCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEE CS
                     FAD_binding_3  77 ynelsdtpkaradlele.sspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeet 152
                                       y +      +++ ++++ s+ e  +v+  + ++r+L+ +a+++g++v  kt+  sl+ ++ gv   v   + g   +
  gi|330508949|ref|YP_004385377.1|  73 YSP----DGSSIVMSEDrSGSEVGYVLERKVFDRALAMQAARAGARVLVKTRAASLLMND-GVPYGVNAIQVGDPLK 144
                                       777....4455666655266667789999999**********************999865.666666666678888* PP

                                       EEEEEEEE--GTT-HHHHHHTGGEE CS
                     FAD_binding_3 153 vrakYlvGaDGgrStvrktlgiefe 177
                                       ++a  ++GaDG+ S+v + +gi+ +
  gi|330508949|ref|YP_004385377.1| 145 IEAPIIIGADGVESKVGRWAGIDTT 169
                                       *******************999855 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0015
                                       TEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHHH.TTSS-GGGGHHHHHH CS
                     FAD_binding_3 285 rvflaGDAaHihpPtgGqGlNtaiqDavnLawkLaavl.kGeAkeelLdtYeee 337
                                        v+l+GDAa  + P +G G+  a++  v  +   a+++  G+  +e L  Yee+
  gi|330508949|ref|YP_004385377.1| 271 GVMLVGDAARQTDPLTGGGILNAMEAGVIAGEVAAKAIaAGNVAREGLREYEER 324
                                       69*****************99999888888777776552578888888888875 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   4.8   2.9e-11   3.1e-08       1     159 [.       4     171 ..       4     185 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.9e-11
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll..tsglv.atdignkaeeqvvtgiarefl.erlrq.rgg 72 
                                       Dv+VvG+gp+G +AA +Aa aG +v+++e+r+ +G  +  + g++  +++++ ++e   + ia e+  +++   +g+
  gi|330508949|ref|YP_004385377.1|   4 DVIVVGAGPGGSMAAKTAAAAGLNVVMLEKRQEIGDPVrcAEGVGkRALCKMVKPE--PEWIASEVKgAKIYSpDGS 78 
                                       9**********************************744213333323344433333..3334444431223222233 PP

                      FAD_oxidored  73 a..rlkkrskwn...tfepevakavleemlaeagvtvllntrlvevekegkr...iesvtveskegrktirAkvfiD 141
                                       +    ++rs+ +   + e +v+ ++l    a+ag +vl +tr+ +  ++++    +++++v +     +i+A+++i 
  gi|330508949|ref|YP_004385377.1|  79 SivMSEDRSGSEvgyVLERKVFDRALAMQAARAGARVLVKTRAASLLMNDGVpygVNAIQVGD---PLKIEAPIIIG 152
                                       344222333321355999999999999999******************984434588888854...9*********9 PP

                      FAD_oxidored 142 ATg.dGdlaalaGvpyrvG 159
                                       A g + +++ +aG+ +++ 
  gi|330508949|ref|YP_004385377.1| 153 ADGvESKVGRWAGIDTTLN 171
                                       9776888999999888765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.2   6.1e-10   6.4e-07       1      43 [.       4      46 ..       4      62 .. 0.91
   2 ?    2.5   0.0     0.058        61     147     184 ..     104     139 ..      96     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 6.1e-10
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqG 43
                                      DviV+G+G +G +AA +aa aGl+v+++ek qe g    +++G
  gi|330508949|ref|YP_004385377.1|  4 DVIVVGAGPGGSMAAKTAAAAGLNVVMLEKRQEIGDPVRCAEG 46
                                      9********************************9888888877 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.058
                                       HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTT CS
                     FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenpes 184
                                       l+ +a +ag +++ +t+a++L+++dg  +G+ +   + 
  gi|330508949|ref|YP_004385377.1| 104 LAMQAARAGARVLVKTRAASLLMNDGVPYGVNAI--QV 139
                                       66778888999*************9955555444..33 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.4   1.4e-10   1.5e-07       1      51 [.       3      54 ..       3      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.4e-10
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHC.GGGT-EEEE CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilis.GgGrcNvTn 51
                                      +dviv+G+G+ G maA +aa++g +V++lek +++g  ++ + G G+  +  
  gi|330508949|ref|YP_004385377.1|  3 CDVIVVGAGPGGSMAAKTAAAAGLNVVMLEKRQEIGDPVRCAeGVGKRALCK 54
                                      59**********************************9999875777766555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.3    0.0003      0.32       1      35 [.       4      35 ..       4      57 .. 0.85
   2 !   17.8   0.0   1.2e-06    0.0012     140     368 ..      85     326 ..      64     349 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0003
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                      ++++vG+G+ G++aA + a a+   l+v ++e+ +
  gi|330508949|ref|YP_004385377.1|  4 DVIVVGAGPGGSMAAKTAAAAG---LNVVMLEKRQ 35
                                      699**************99999...8999999853 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.2e-06
                                       TS-B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-...EEEEEETTS-EEE-SEEEE-SGGG-II CS
                    Trp_halogenase 140 dglsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgr...veslrledgreveadlfiDcsGfrgll 213
                                       d  s+ + +y l+++ +++ L   a ++G +++  + +   l +dg    v+++++ d  ++ea ++i + G ++++
  gi|330508949|ref|YP_004385377.1|  85 D-RSGSEVGYVLERKVFDRALAMQAARAGARVLVKTRAASLLMNDGVpygVNAIQVGDPLKIEAPIIIGADGVESKV 160
                                       3.6778899**********************99888888777777744449***********************987 PP

                                       .....IIIIT-.--EEE-TTT----EEEEEEEE--H---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHH CS
                    Trp_halogenase 214 .....ieqaLk.tgfedwsdvLltdrAlavqveseelvepytrataekaGWtWkiPLqhrlgn.Gyvyssahaddde 283
                                            i+ +L+ + +e+ +++L+ d ++      ++  + y +     +G  W  P  ++l n G+ +  ++    e
  gi|330508949|ref|YP_004385377.1| 161 grwagIDTTLNlKDIESCAQFLVLDPGID-----DDYTKFYLGNSIAPSGYAWSFPKGEKLANvGLGVLGSRSRPGE 232
                                       33333677776345677777776666664.....667777887777789*****************99999999*** PP

                                       HHHHHHHHCT--TTTS-EEEE---EE......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT- CS
                    Trp_halogenase 284 AlaellaeldgkleaeprkirfttGr......rkqawvknvvalGlasgfvePlestsihliqa....alrrLlall 350
                                       A++ l++  + k   + + +++ +G        ++a  ++v+++G+a+   +Pl + +i  +++    a +  ++ +
  gi|330508949|ref|YP_004385377.1| 233 AIRLLREFTK-KHFPNGKIVEMVVGGdpcsgpIQSATAHGVMLVGDAARQTDPLTGGGILNAMEagviAGEVAAKAI 308
                                       **98877666.4444459999999988999999**************************999885554445556666 PP

                                       -BTT--HHHHHHHHHHHH CS
                    Trp_halogenase 351 pdksdepaaiaefnreva 368
                                       +++ ++   + e++++ +
  gi|330508949|ref|YP_004385377.1| 309 AAGNVAREGLREYEERWR 326
                                       666666666677776665 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   6.4e-07   0.00068       1     144 [.       4     159 ..       4     176 .. 0.71
   2 !    7.4   0.0    0.0019         2     228     314 ..     243     335 ..     233     355 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.4e-07
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlgaleecv..ehsW.....sgtivyld 70 
                                       Dv+v+GaGp g s+Aa+  +a++gl+vv++e  +++   ++ v + e+ +  al ++v  e  W     +g+ +y +
  gi|330508949|ref|YP_004385377.1|   4 DVIVVGAGPGG-SMAAKT-AAAAGLNVVMLEKRQEI---GDPVRCAEGVGKRALCKMVkpEPEWiasevKGAKIYSP 75 
                                       9********88.666666.69**********99999...77788888888888777772234563333366777889 PP

                     Lycopene_cycl  71 dgkkillg.......raYgrvsskrlkeellerlv.engvklleakvesveeeea...geslvvleggrkirarlvv 136
                                       dg++i ++         Y  +++k + + l+ + +  +++ l++ +++s   ++    g   + + +  ki+a++++
  gi|330508949|ref|YP_004385377.1|  76 DGSSIVMSedrsgseVGY-VLERKVFDRALAMQAArAGARVLVKTRAASLLMNDGvpyGVNAIQVGDPLKIEAPIII 151
                                       999988877766654445.4689999999999999444455678888887544432435556666666699999999 PP

                     Lycopene_cycl 137 darglasl 144
                                        a g+ s+
  gi|330508949|ref|YP_004385377.1| 152 GADGVESK 159
                                       99995444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0019
                     Lycopene_cycl 228 lglkvkevveeEqgviPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres....... 297
                                       ++    ++ve   g  P   g+  ++++  v+ +G aa  + P TG  + +++ +   +a  +aa +          
  gi|330508949|ref|YP_004385377.1| 243 KHFPNGKIVEMVVGGDPC-SGPIQSATAHGVMLVGDAARQTDPLTGGGILNAMEAGV-IAGEVAAKAIAAgnvareg 317
                                       556666666666666677.44445556666**********************97554.6655555554442333344 PP

                     Lycopene_cycl 298 .slsarawatlwprerkr 314
                                          +++ w++  +r+ +r
  gi|330508949|ref|YP_004385377.1| 318 lREYEERWREGIGRHLAR 335
                                       444444444444444444 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   2.4e-08   2.6e-05       2      33 ..       4      35 ..       3     101 .. 0.88
   2 ?   -2.7   0.0       2.6   2.8e+03      16      36 ..     105     125 ..     102     169 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.4e-08
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                      dv+v+G+Gp+G  aa+t+a+ag++v+++e+++
  gi|330508949|ref|YP_004385377.1|  4 DVIVVGAGPGGSMAAKTAAAAGLNVVMLEKRQ 35
                                      89**************************7443 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.6
                                       HHHHHHHTS-EEEEETTHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  16 altlaqagakvtlvelegtcl 36 
                                       a+++a+aga+v++  +   +l
  gi|330508949|ref|YP_004385377.1| 105 AMQAARAGARVLVKTRAASLL 125
                                       555555555555544333333 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.3   4.9e-08   5.1e-05       1      32 [.       7      38 ..       7      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.9e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      +vGaG +G+ aA ++a ag++v+ lekr+ +G
  gi|330508949|ref|YP_004385377.1|  7 VVGAGPGGSMAAKTAAAAGLNVVMLEKRQEIG 38
                                      8******************************9 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.4   3.7e-07   0.00039      17      55 ..       2      39 ..       1     174 [. 0.73

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.7e-07
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                      + Dv++vGaG+ G  aa++ a + +l+v++le++  +G 
  gi|330508949|ref|YP_004385377.1|  2 KCDVIVVGAGPGGSMAAKTAAAA-GLNVVMLEKRQEIGD 39
                                      68****************99999.*********999885 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.3   2.2e-05     0.023       1      33 [.       4      38 ..       4      44 .. 0.96
   2 !    6.0   0.0    0.0074       7.8     148     231 ..     100     188 ..      88     309 .. 0.61
   3 ?   -2.3   0.0       2.5   2.6e+03      41      77 ..     296     329 ..     288     338 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      dv+++G+G  G+ +A  +a++g  V+ lek+ ++g
  gi|330508949|ref|YP_004385377.1|  4 DVIVVGAGPGGSMAAKTAAAAGlnVVMLEKRQEIG 38
                                      9******************************8887 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0074
                                       HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE..EEE--GGGHH..HHHTT.CTTTSEEE CS
                               DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaada..vVnaaGawsd..llgll.keldlpis 218
                                       + +ala +a+++G+++l +t++ +l  +dg  +gv ++ + g   +++a  ++ a G+ s+   ++++  +l+l+  
  gi|330508949|ref|YP_004385377.1| 100 FDRALAMQAARAGARVLVKTRAASLLMNDGVPYGV-NAIQvGDPLKIEApiIIGADGVESKvgRWAGIdTTLNLKDI 175
                                       6689********************86678888888.43333433245666588888888775444444444444545 PP

                                       EEEEEEEEEEECC CS
                               DAO 219 pvrgqvlvlkpls 231
                                          +q lvl+p  
  gi|330508949|ref|YP_004385377.1| 176 ESCAQFLVLDPGI 188
                                       5667777775543 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.5
                                       EEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSS CS
                               DAO  41 sgllhsglrylpeaselarlslealeelreleeelgi 77 
                                       +g++++ ++ ++   +   +++e+l+e++e  +e gi
  gi|330508949|ref|YP_004385377.1| 296 AGVIAGEVAAKAI--AAGNVAREGLREYEERWRE-GI 329
                                       5777777764443..3448899999999887777.63 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   2.5   4.9e-07   0.00052       1      44 [.       4      47 ..       4      58 .. 0.78
   2 ?   -2.0   0.0       1.4   1.4e+03      15      30 ..     105     120 ..     102     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.9e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT-.-SSSSEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiae.lsCnpsi 44
                                      dviV+G+G  G+ AA +aa +G++v+++ +k ++i+  + C + +
  gi|330508949|ref|YP_004385377.1|  4 DVIVVGAGPGGSMAAKTAAAAGLNVVML-EKRQEIGDpVRCAEGV 47
                                      8**************************9.6666666513455555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                                       HHHHHHTT--EEEEES CS
                              GIDA  15 AlaaarlGakvlLith 30 
                                       A++aar+Ga+vl  t 
  gi|330508949|ref|YP_004385377.1| 105 AMQAARAGARVLVKTR 120
                                       89*********98765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   2.5e-06    0.0027      29      92 ..       3      70 ..       1      73 [. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.5e-06
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH...TTTC.ECEEHCHHHHHHHHHHHH- CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles...lgak.fvevlksqeellaeavkea 92
                                      + v+v+G+G  G  A++ta++ g +V++l++r++    ++    +g++  ++++k + e +a++vk a
  gi|330508949|ref|YP_004385377.1|  3 CDVIVVGAGPGGSMAAKTAAAAGLNVVMLEKRQEIGDPVRCaegVGKRaLCKMVKPEPEWIASEVKGA 70
                                      78******************************998777665455444413455666666666666655 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 ?   14.1   0.5     2e-05     0.021       1      33 [.       6      38 ..       6      43 .. 0.90
   2 ?   -4.0   0.0       6.6     7e+03     180     198 ..     105     123 ..     104     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nig 33
                                      i++GaGP G  aa ++  agl +++ lEk  +ig
  gi|330508949|ref|YP_004385377.1|  6 IVVGAGPGGSMAAKTAAAAGL-NVVMLEKRqEIG 38
                                      89*******************.7*****985666 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 6.6
                       Pyr_redox_3 180 AlelvrkgaeVtvvtrgse 198
                                       A++ +r+ga+V v tr ++
  gi|330508949|ref|YP_004385377.1| 105 AMQAARAGARVLVKTRAAS 123
                                       8899999***999998765 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.2e-05     0.075     125     156 ..     265     296 ..     260     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-05
                                SE 125 sknekkGlillGDalnmRHPltggGmtvalnD 156
                                       ++ + +G++l+GDa     PltggG+  a++ 
  gi|330508949|ref|YP_004385377.1| 265 QSATAHGVMLVGDAARQTDPLTGGGILNAMEA 296
                                       556789*******************9877765 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00037      0.39       1      40 [.       5      44 ..       5     128 .. 0.77
   2 ?   -1.8   0.0       3.9   4.1e+03      10      30 ..     101     121 ..      93     157 .. 0.77
   3 ?   -0.8   0.0       1.9     2e+03      72      89 ..     221     238 ..     213     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-T CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfp 40
                                      ++++Gag+ +   a+ aaa+g++v+++++r+e+ ++ r +
  gi|330508949|ref|YP_004385377.1|  5 VIVVGAGPGGSMAAKTAAAAGLNVVMLEKRQEIGDPVRCA 44
                                      689****************************988665555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.9
                                       HHHHHHHHHHHTEEEEEEES- CS
                            XdhC_C  10 aqalarlaaalgfrvtvvdpr 30 
                                        +ala  aa++g rv v    
  gi|330508949|ref|YP_004385377.1| 101 DRALAMQAARAGARVLVKTRA 121
                                       578888888888888775544 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.9
                                       EEESS-HHHHHHHCTTS. CS
                            XdhC_C  72 igllGSrkkaarrlerlr 89 
                                       +g+lGSr++  +  + lr
  gi|330508949|ref|YP_004385377.1| 221 LGVLGSRSRPGEAIRLLR 238
                                       799****99888777774 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 ?   12.3   0.6   0.00011      0.11       2      34 ..       5      37 ..       4      57 .. 0.91
   2 ?   -2.4   0.0       3.5   3.7e+03      13      32 ..     103     122 ..     101     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      v v+GaG  G+  a+ +a+agl+Vv+++ ++e+
  gi|330508949|ref|YP_004385377.1|  5 VIVVGAGPGGSMAAKTAAAAGLNVVMLEKRQEI 37
                                      78**************************99875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.5
                                       HHHHHHHHTT-EEEEE-S-H CS
                           3HCDH_N  13 giaavfasagleVvlvdise 32 
                                        +a+++a+ag +V +  +++
  gi|330508949|ref|YP_004385377.1| 103 ALAMQAARAGARVLVKTRAA 122
                                       579999******99987765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   0.00022      0.23       2      35 ..       5      38 ..       4      57 .. 0.91
   2 ?   -2.4   1.3       7.1   7.5e+03       6      19 ..     287     300 ..     286     310 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v+vvG+G  g ++A+++a+ g +V ++e + ++ 
  gi|330508949|ref|YP_004385377.1|  5 VIVVGAGPGGSMAAKTAAAAGLNVVMLEKRQEIG 38
                                      89****************************9998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.1
                                       CSSHHHHHHHHHHH CS
                         Pyr_redox   6 GgGyiglElAgala 19 
                                       GgG ++ ++Ag++a
  gi|330508949|ref|YP_004385377.1| 287 GGGILNAMEAGVIA 300
                                       88888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.74u 0.35s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 2119.63
//
Query:       gi|330508950|ref|YP_004385378.1|  [L=182]
Description: hypothetical protein MCON_3297 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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      0.024   14.7   0.0    1.6  1  DUF61     Protein of unknown function DUF61


Domain annotation for each model (and alignments):
>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.3e-06     0.024      23      86 ..      66     132 ..      60     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-06
                                       HHHHHT--EEEB.TTS-EEE--HHHHHHHH.TTS-GGGGGT-EESEEEEE-SSS..SE..EEEES-H CS
                             DUF61  23 kelLeeekptivtkdgsehrfdkeeleklk.eilpeelwdklkLPIllemdpel..gesvylvrgka 86 
                                        e+ + e +++v+ +++  ++++eel +l  e+ p   +++l+LP ll+ ++    ++  +++ +++
  gi|330508950|ref|YP_004385378.1|  66 DEVHADESQIVVKSSDEIVEIRREELAELMdERYPTTGHQRLNLPGLLFLQSGPalQSASAMILRRE 132
                                       56778899999*9*************8875267************7777665432255556665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1144.45
//
Query:       gi|330508951|ref|YP_004385379.1|  [L=125]
Description: hypothetical protein MCON_3298 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   14.5   0.0      0.049   13.8   0.0    1.3  1  HTH_34    Winged helix DNA-binding domain
      0.094   12.6   0.1       0.22   11.5   0.1    1.7  2  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 ?   13.8   0.0   5.5e-06     0.049       5      73 ..      32     101 ..      30     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-06
                            HTH_34   5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievd..kefkgkkprtllriTpeGreafkkyv 73 
                                       ++++La vdea+ +e+     + + + s+ +++L ++++ie +  k   +++p+ ++++ ++G e+  k++
  gi|330508951|ref|YP_004385379.1|  32 LITFLANVDEASSREIEMGSDLRQPEVSIAMRTLRDNNWIEEKeiKREGKGRPMKVYSL-KAGIEEVIKHF 101
                                       6899************************************8652233333458888887.66666666665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.28   2.5e+03      22      37 ..      13      28 ..       6      34 .. 0.67
   2 ?   11.5   0.1   2.4e-05      0.22      17      59 ..      36      84 ..      20      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.28
                                      CCHHCHHCCCTTSSCH CS
                              TrmB 22 patadeiaeelgvprs 37
                                       ++  e  + lgvpr+
  gi|330508951|ref|YP_004385379.1| 13 DMEFVETLRSLGVPRN 28
                                      5555566677788875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.4e-05
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......T CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......p 59
                                      L + ++a+ +ei   +++ ++ v  ++r L d  ++e ++ +      p
  gi|330508951|ref|YP_004385379.1| 36 LANVDEASSREIEMGSDLRQPEVSIAMRTLRDNNWIEEKEIKregkgrP 84
                                      346789999****************************999776666663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 875.47
//
Query:       gi|330508952|ref|YP_004385380.1|  [L=86]
Description: FeoA domain-containing protein [Methanosaeta concilii GP6]
Scores for 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-18   64.5   0.0      9e-18   64.3   0.0    1.0  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0     5e-22     9e-18       2      73 ..       5      75 ..       4      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 5e-22
                                      EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA  2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                       Ls ++ +++ ei +++ e    +rr+++mG++ G+r++ +   pfggp+v+++++++++Lgr++A++I Ve
  gi|330508952|ref|YP_004385380.1|  5 ELSRAPCNQTLEIHSVNGE-YGWERRFESMGIRRGSRVRKITCHPFGGPVVIELNGSKISLGRGIAAKIEVE 75
                                      59999***********988.99*************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       183  (0.0102069); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 630.82
//
Query:       gi|330508953|ref|YP_004385381.1|  [L=270]
Description: imidazoleglycerol phosphate synthase, cyclase subunit [Methanosaeta concilii GP6]
Scores for complete 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-76  256.1   0.0      3e-76  255.9   0.0    1.0  1  His_biosynth  Histidine biosynthesis protein
    0.00028   20.1   0.0       0.28   10.2   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
     0.0012   18.2   0.1          1    8.7   0.0    2.2  2  TMP-TENI      Thiamine monophosphate synthase
     0.0017   17.8   0.3      0.081   12.3   0.1    2.1  2  NMO           Nitronate monooxygenase
  ------ inclusion threshold ------
      0.026   13.9   0.1       0.37   10.1   0.0    2.1  2  ThiG          Thiazole biosynthesis protein ThiG
      0.037   13.4   0.3       0.83    9.0   0.1    2.1  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
       0.13   11.7   0.0       0.36   10.2   0.0    1.7  2  PcrB          PcrB family
       0.14   11.4   0.0        5.5    6.1   0.0    2.1  2  DHO_dh        Dihydroorotate dehydrogenase


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.9   0.0   1.3e-79     3e-76       1     227 [.       5     251 ..       5     253 .. 0.95

  Alignments for each domain:
  == domain 1  score: 255.9 bits;  conditional E-value: 1.3e-79
                                       EEEEEEEE....ETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-S CS
                      His_biosynth   1 riipalDl....kdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevf 73 
                                       riip+lD+      G+vV   kG +f++ ryag p+ela +y+++gade++++D++a+++ re+++++++++  +vf
  gi|330508953|ref|YP_004385381.1|   5 RIIPCLDCdlgvPGGRVV---KGIEFKQIRYAGVPWELADQYYQDGADEIVFLDITASSDRRETMTSVIKKTSLSVF 78 
                                       8******96665678999...******************************************************** PP

                                       SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE......C........... CS
                      His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr......g........... 133
                                       +p+ vGGGI+sl + +e+++agadkv ++t+a+k+p+li+e+a ++g+q++v+aiDa+r      g           
  gi|330508953|ref|YP_004385381.1|  79 VPLAVGGGISSLAQSREVFNAGADKVTVNTSALKRPDLISEIAGRYGNQAVVLAIDAKRrysqedGrnmvqteegpc 155
                                       ***********************************************************8877661667778889** PP

                                       .EEEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHH CS
                      His_biosynth 134 .ykvaikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkel 209
                                        +++  +g+re tg+da+++akk+ +lgageillt++drdGt+ G+d++lt ++a+ v++pviasGG++++e++ e+
  gi|330508953|ref|YP_004385381.1| 156 wFECSYYGGREFTGIDAIDWAKKAVSLGAGEILLTSMDRDGTKLGFDIPLTAAVARMVRVPVIASGGCANPEHMLEV 232
                                       9**************************************************************************** PP

                                       HHTTC.SEEEESHHHHTTS CS
                      His_biosynth 210 ksegv.davivgsalyege 227
                                       ++++  +a++++s+++++e
  gi|330508953|ref|YP_004385381.1| 233 FQKTDaSAALAASIFHFQE 251
                                       *88888**********997 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00013      0.28     177     225 ..      72     119 ..      57     150 .. 0.83
   2 !    8.1   0.0   0.00056       1.3     175     211 ..     206     242 ..     170     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                                       HHHHH-S..S-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH CS
                               Dus 177 evkqavs..ipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae 225
                                       +     s  +p+ + G+I ++ + +++ +  Gad v +   al++P l+ e
  gi|330508953|ref|YP_004385381.1|  72 KTSL--SvfVPLAVGGGISSLAQSREVFNA-GADKVTVNTSALKRPDLISE 119
                                       3333..355*******************99.****************9985 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00056
                                       HHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEE CS
                               Dus 175 IkevkqavsipviaNGdIkdaedaqaileetGadgvm 211
                                        ++v + v++pvia G++ ++e + ++ ++t a + +
  gi|330508953|ref|YP_004385381.1| 206 TAAVARMVRVPVIASGGCANPEHMLEVFQKTDASAAL 242
                                       5789999***********************9988765 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00099       2.2     139     177 ..      67     106 ..      38     110 .. 0.73
   2 !    8.7   0.0   0.00045         1     119     171 ..     181     236 ..     170     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00099
                          TMP-TENI 139 leglkelaealeiPvvaiGGit.lenvaevleagadgvav 177
                                        + +k+++ ++ +P+ + GGi+ l++  ev++agad v v
  gi|330508953|ref|YP_004385381.1|  67 TSVIKKTSLSVFVPLAVGGGISsLAQSREVFNAGADKVTV 106
                                       4556667777779********6379************988 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00045
                          TMP-TENI 119 YigvGpifpTdtKkdaeplgle..glkelaealeiPvvaiGGi.tlenvaevleag 171
                                        +g+G i  T+   d + lg +  + +++a+++++Pv+a GG  ++e++ ev+++ 
  gi|330508953|ref|YP_004385381.1| 181 SLGAGEILLTSMDRDGTKLGFDipLTAAVARMVRVPVIASGGCaNPEHMLEVFQKT 236
                                       689999999999999977776522679999999*********64789998888654 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.016        36     181     224 ..      66     109 ..      56     116 .. 0.75
   2 !   12.3   0.1   3.6e-05     0.081     144     237 ..     171     258 ..     166     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.016
                               NMO 181 lfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                        ++++++    v +P+   GGi    +   ++ +GA  v + t 
  gi|330508953|ref|YP_004385381.1|  66 MTSVIKKTSLSVFVPLAVGGGISSLAQSREVFNAGADKVTVNTS 109
                                       45566666666668888888888888888888888888888775 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.6e-05
                               NMO 144 ssvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvq 220
                                        +++ a+k+ ++Ga  + ++ ++  G +  +++       L + v+  v +PviA GG  + + +  ++    + ++
  gi|330508953|ref|YP_004385381.1| 171 DAIDWAKKAVSLGAGEILLTSMDRDGTKLGFDI------PLTAAVARMVRVPVIASGGCANPEHMLEVFQKTDASAA 241
                                       566777777777777777777776555432444......689999999****************9999999999999 PP

                               NMO 221 igtrfLltkesdakdah 237
                                       +++     +e+  +d+ 
  gi|330508953|ref|YP_004385381.1| 242 LAASIFHFQECSIRDVK 258
                                       99999999999888775 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   0.00016      0.37     167     214 ..      70     117 ..      27     146 .. 0.77
   2 ?    1.9   0.0     0.051   1.1e+02     169     195 ..     208     234 ..     171     250 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                                       HHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHH CS
                              ThiG 167 lkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpv 214
                                       +k    ++ vP+ v  Gi s  +  ++++ Gad v +nt+  +  d +
  gi|330508953|ref|YP_004385381.1|  70 IKKTSLSVFVPLAVGGGISSLAQSREVFNAGADKVTVNTSALKRPDLI 117
                                       4444445679****************************9876665554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.051
                                       HHHHH-SS-BEEES---SHHHHHHHHH CS
                              ThiG 169 iiieeakvPvivDAGigspsdaaqame 195
                                        + + ++vPvi   G  +p++  ++++
  gi|330508953|ref|YP_004385381.1| 208 AVARMVRVPVIASGGCANPEHMLEVFQ 234
                                       4455679*************9998876 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 ?    9.0   0.1   0.00037      0.83     126     171 ..      65     110 ..      64     111 .. 0.92
   2 ?    2.2   0.0     0.045     1e+02     132     160 ..     207     235 ..     203     245 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00037
                                       GGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE--HH CS
                      G3P_antiterm 126 lvpkvikeikkelkipiiaGGLietkedveealkaGaiavstsnke 171
                                       ++ +vik+++ ++ +p+  GG i++  + +e+++aGa+ v++ +++
  gi|330508953|ref|YP_004385381.1|  65 TMTSVIKKTSLSVFVPLAVGGGISSLAQSREVFNAGADKVTVNTSA 110
                                       57899***********************************987765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.045
                                       CTSTTS...EEEEESS--SHHHHHHHCTT CS
                      G3P_antiterm 132 keikkelkipiiaGGLietkedveealka 160
                                       +++ + +++p+ia+G   + e++ e++++
  gi|330508953|ref|YP_004385381.1| 207 AAVARMVRVPVIASGGCANPEHMLEVFQK 235
                                       5677889********99999999888765 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00016      0.36     156     209 ..      51     108 ..      47     122 .. 0.76
   2 ?   -2.1   0.0      0.98   2.2e+03     180     203 ..     214     237 ..     202     243 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00016
                                       EEEEE-TTSSS-HHHHHHHHHHHSSSE...EEEESS--SHHHHHHHHCC.SSEEEE-C CS
                              PcrB 156 liYlEasGaledveevialkkklekar...livGGGirsaEkAkevvea.ADvivvGn 209
                                       +++l+    ++  e +  + kk + +    l vGGGi s  + +ev +a AD + v +
  gi|330508953|ref|YP_004385381.1|  51 IVFLDITASSDRRETMTSVIKKTSLSVfvpLAVGGGISSLAQSREVFNAgADKVTVNT 108
                                       56777766777778888888887765422278********************998866 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.98
                                       SSEEEEESS--SHHHHHHHHCCSS CS
                              PcrB 180 karlivGGGirsaEkAkevveaAD 203
                                          +i  GG  ++E+  ev ++ D
  gi|330508953|ref|YP_004385381.1| 214 RVPVIASGGCANPEHMLEVFQKTD 237
                                       444455555555555555554444 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0025       5.5     245     278 ..      79     112 ..      63     123 .. 0.76
   2 ?    3.2   0.0     0.019        42     239     281 ..     211     252 ..     203     263 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0025
                                       S-EEEESS--SHHHHHHHHHHTECEEEESHHHHH CS
                            DHO_dh 245 ipiIgvGGiesgeDalekieaGAslvqvytalvf 278
                                       +p+   GGi+s     e ++aGA  v v t   +
  gi|330508953|ref|YP_004385381.1|  79 VPLAVGGGISSLAQSREVFNAGADKVTVNTSALK 112
                                       7888889*********************998743 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.019
                                       HHTTT.S-EEEESS--SHHHHHHHHH.HTECEEEESHHHHHHGT CS
                            DHO_dh 239 krlkkeipiIgvGGiesgeDalekie.aGAslvqvytalvfegp 281
                                       ++++  +p+I++GG    e  le ++   As+    + ++f++ 
  gi|330508953|ref|YP_004385381.1| 211 RMVR--VPVIASGGCANPEHMLEVFQkTDASAALAASIFHFQEC 252
                                       4444..9***********99999886356777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1812.41
//
Query:       gi|330508954|ref|YP_004385382.1|  [L=201]
Description: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit [Methanosaeta concilii GP6]
Scores for complete 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   76.5   0.0    2.4e-21   76.4   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
    9.7e-07   28.8   0.0      0.012   15.5   0.0    2.0  2  SNO            SNO glutamine amidotransferase family
    3.2e-05   23.8   0.6      0.042   13.6   0.1    2.2  2  Peptidase_C26  Peptidase C26
    0.00083   19.0   0.2     0.0013   18.3   0.0    1.4  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.0   5.3e-25   2.4e-21       4     187 ..       7     196 ..       4     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 5.3e-25
                                       ESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EE CS
                            GATase   4 DnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiL 75 
                                       D++ ++  ++ +al  +g + ++ +          +l +++gi+v +G+g+ g          + +  ++++++P+L
  gi|330508954|ref|YP_004385382.1|   7 DYGMGNLFSIYNALEYVGGNPKIARDP---G----ELAGAKGIVV-PGVGAFGscmnqLSRFSDSLLSCFQEGVPML 75 
                                       555555555555555555555555522...1....2467888877.68888888634433333334445558***** PP

                                       EETHHHHHHHHHTTT............EEE...EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCH CS
                            GATase  76 GICLGmQllaiefgr............kvv...kekekehhggtmrlgddetallyglknevierhrHryevnpkel 137
                                       GIC GmQ+l++e+ +            kvv        +++g+++   +++ +++ g ++    ++ H+y  +p   
  gi|330508954|ref|YP_004385382.1|  76 GICVGMQVLFQESEEspgapglgwiegKVVrlpDGVMIPQMGWNSLYIKHRVEIFDGISEGDMFYFVHSYYGQP--- 149
                                       ***************999999999999888777556679**********999*********************9... PP

                                       HHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 138 epaglevtakseddeelmeiiekknpfvgvQFHPEststpegpellfnfl 187
                                         ++ +++a+++++ el+++++k+n ++++QFHPE+ s+p+g ++l+nf+
  gi|330508954|ref|YP_004385382.1| 150 -RDKSVIAATTDHGVELAAAVHKDN-LFATQFHPEK-SGPKGLRILKNFV 196
                                       .66678889998999*********9.*********6.78999*****996 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.7e-06     0.012      12     100 ..      17     104 ..      10     131 .. 0.80
   2 !   11.8   0.0   3.6e-05      0.16     146     186 ..     155     199 ..     140     201 .] 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-06
                                       HHHHHHTTSEEEEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB CS
                               SNO  12 veaikkclaenktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelene 88 
                                        +a++ ++ + k  +++ +la+  ++++PG  +   s + +   + ++ll   +++  ++lG C G+ +l +e e++
  gi|330508954|ref|YP_004385382.1|  17 YNALEYVGGNPKIARDPGELAGAKGIVVPGVGAF-GSCMNQLSRFSDSLLSCFQEG-VPMLGICVGMQVLFQESEES 91 
                                       567777888889999**************96432.2334444678899*9999999.9**********999998877 PP

                                       .SS-SS--CCEEE CS
                               SNO  89 .lvktlellkvkv 100
                                          + l+ ++ kv
  gi|330508954|ref|YP_004385382.1|  92 pGAPGLGWIEGKV 104
                                       5666666665555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.6e-05
                                       EEEECT.T.EEEEEE.ETTEEEESS-GGGST.THCHHHHHHHHHH CS
                               SNO 146 vlyeld.g.eivvak.qkkilatsfhPelae.ddirvhdyfveev 186
                                       ++  +d g e+ +a  +++++at fhPe +  ++ r+ + fv++ 
  gi|330508954|ref|YP_004385382.1| 155 IAATTDhGvELAAAVhKDNLFATQFHPEKSGpKGLRILKNFVRST 199
                                       333333366888877455**********9863789******9975 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   9.5e-06     0.042     101     118 ..      67      84 ..      62      87 .. 0.90
   2 !    8.5   0.0   0.00034       1.5     186     216 .]     153     182 ..     143     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.5e-06
                     Peptidase_C26 101 alergvPilgiCrGlqll 118
                                       + ++gvP+lgiC G+q+l
  gi|330508954|ref|YP_004385382.1|  67 CFQEGVPMLGICVGMQVL 84 
                                       6789************98 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00034
                     Peptidase_C26 186 rveAvaeDgviEaieseeakafvlgvQwHPE 216
                                        v+A ++D  +E   + +++  +++ Q+HPE
  gi|330508954|ref|YP_004385382.1| 153 SVIAATTDHGVELAAAVHKD-NLFATQFHPE 182
                                       6899999*****88888755.99*******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 !   18.3   0.0     3e-07    0.0013      59     115 ..      55     104 ..      12     117 .. 0.83
   2 ?   -2.7   0.0      0.83   3.7e+03     171     188 ..     166     180 ..     143     181 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3e-07
                          GATase_3  59 lresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageveglglLdiet 115
                                        + s++ +++ +  ++g+p+lgiC G+q+L +e e++ g        +glg+++ ++
  gi|330508954|ref|YP_004385382.1|  55 NQLSRFSDSLLSCFQEGVPMLGICVGMQVLFQESEESPGA-------PGLGWIEGKV 104
                                       56678999************************99887765.......7777776665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.83
                          GATase_3 171 dGavkksedgnvlGtYlH 188
                                         av   +++n+++t +H
  gi|330508954|ref|YP_004385382.1| 166 AAAV---HKDNLFATQFH 180
                                       3333...34699999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1477.78
//
Query:       gi|330508955|ref|YP_004385383.1|  [L=415]
Description: glutamate dehydrogenase [Methanosaeta concilii GP6]
Scores for complete 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-70  235.8   1.9    7.5e-70  235.4   1.9    1.1  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    4.3e-54  181.9   0.0      8e-54  181.0   0.0    1.5  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
     0.0065   15.9   0.0      0.011   15.1   0.0    1.3  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 !  235.4   1.9   1.3e-73   7.5e-70       1     243 []     180     413 ..     180     413 .. 0.99

  Alignments for each domain:
  == domain 1  score: 235.4 bits;  conditional E-value: 1.3e-73
                                       T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHC.T-EEEEEEESSEEEEETTEE-H CS
                     ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltel.gakvvavsDssGviydpeGldi 76 
                                       GGs +r +aT++G +y+++e++++l++d l+ +++ai+G+Gn gsya  l++el g kvvavsDs+G  ++p G++ 
  gi|330508955|ref|YP_004385383.1| 180 GGSCGRSDATARGGMYALREAARELGID-LSRATIAIQGYGNAGSYAHSLAKELfGSKVVAVSDSKGGAFNPAGIEP 255
                                       9***************************.************************99********************** PP

                                       HHHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HH CS
                     ELFV_dehydrog  77 eellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqe 153
                                       +e  ++k+e+ +v++++     +a+ i+ne ellel+vdil+ +A++n+i++ena  +ik  +k+++E AN+ptt+e
  gi|330508955|ref|YP_004385383.1| 256 AEASSVKAETCTVASIP-----DAKRISNE-ELLELNVDILIVAALENVITKENAG-NIK--AKIILELANGPTTPE 323
                                       *****************.....5799***7.*************************.***..*************** PP

                                       HHHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHH CS
                     ELFV_dehydrog 154 AkeileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqelvkgania 230
                                       A+eil +++v v+pd++aNaGGVtvS++Em+qn++r+ w+ eev ++l+++m+ +++ v+++ ++y+ +++++a+++
  gi|330508955|ref|YP_004385383.1| 324 ADEILFNNKVHVIPDFLANAGGVTVSYFEMVQNIMRYCWSFEEVYQRLDERMTMAYQGVLAASRQYNINMRQAAYTV 400
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHCT CS
                     ELFV_dehydrog 231 gfekvaeamkaqG 243
                                       ++ +v++amk +G
  gi|330508955|ref|YP_004385383.1| 401 AVARVVDAMKTRG 413
                                       **********998 PP

>> ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   0.0   1.3e-57     8e-54       1     130 []      34     162 ..      34     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 1.3e-57
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       p+r ++v++pv++d+G++++++gyr+q+++algP+kGGiR+hp+ ++d+v+aLaa+mt+K++l++lp+GG+kggv++
  gi|330508955|ref|YP_004385383.1|  34 PRREFHVSIPVRMDDGSIKIFQGYRVQYNDALGPCKGGIRYHPDETIDTVRALAAWMTWKTSLLGLPLGGGKGGVIC 110
                                       67899************************************************************************ PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeykk 130
                                       +pk+ls+ e er++r +v+ +  + iGp++DvpApDv+t+++ maw++dey+k
  gi|330508955|ref|YP_004385383.1| 111 NPKELSTGEQERLCRGYVDMVW-QNIGPERDVPAPDVYTTPQMMAWMMDEYSK 162
                                       **********************.999*************************85 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.8e-06     0.011      18      70 ..     190     245 ..     182     285 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-06
                                       HHTTCC..HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHH CS
                      2-Hacid_dh_C  18 vregew..ksekallgkelsgktvGiiGlGrIGqavakrlk.afgmkviaydrskk 70 
                                        r g +  ++ ++ lg +ls+ t++i G+G+ G+ +  ++k  fg kv+a++ sk 
  gi|330508955|ref|YP_004385383.1| 190 ARGGMYalREAARELGIDLSRATIAIQGYGNAGSYAHSLAKeLFGSKVVAVSDSKG 245
                                       45555566677788999************************88********99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3046.96
//
Query:       gi|330508956|ref|YP_004385384.1|  [L=242]
Description: oxidoreductase FAD/NAD [Methanosaeta concilii GP6]
Scores for complete 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   59.5   0.0    6.1e-16   59.0   0.0    1.2  1  NAD_binding_1  Oxidoreductase NAD-binding domain
    7.9e-07   29.4   0.0    1.2e-06   28.8   0.0    1.3  1  FAD_binding_6  Oxidoreductase FAD-binding domain
    1.7e-05   25.0   0.0    2.3e-05   24.6   0.0    1.3  1  NAD_binding_6  Ferric reductase NAD binding domain
     0.0053   16.8   0.1      0.049   13.7   0.1    2.3  2  FAD_binding_8  FAD-binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   1.4e-19   6.1e-16       1     107 [.     106     209 ..     106     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.4e-19
                                       EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSH CS
                     NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrv 77 
                                       m++gG Gi+P+rs+++ ++++ k  t + l+y nr+e+++ + ++l  +++++p+ l v  + ++++  w+g  gr+
  gi|330508956|ref|YP_004385384.1| 106 MLSGGIGITPLRSMIKFCTDK-KTSTDISLLYSNRNEDEIPFYDDLMPMQRANPR-LVVNMTITNPSPAWRGLSGRL 180
                                       9*******************8.999************************999999.66666689************* PP

                                       HHHHHHHHHHHSSTTEEEEEECSHHHHHHH CS
                     NAD_binding_1  78 qdalleellslkkeethvyvCGppgMikav 107
                                       + ++++ +++ + +e  +yv Gp++M++ +
  gi|330508956|ref|YP_004385384.1| 181 NGEMIKSTVP-QWAERIYYVSGPQPMVESM 209
                                       **********.99*************9975 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 !   28.8   0.0   2.7e-10   1.2e-06      11      98 ..      14      96 ..       4      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.7e-10
                                      CTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHCS-TT-EEE CS
                     FAD_binding_6 11 sedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLdelkigdtle 89
                                      +++++ +rf+ p  ++ + +++Gq+ fl +    e+++++ ++ ss+ ++ +le+  k++ g ++s+++d l++gdtl+
  gi|330508956|ref|YP_004385384.1| 14 TKSVKSIRFEKP--EH-FSYLPGQWTFLIFGDGPERIMKPLSFSSSP-TEDHLEV-TKKLTGLRFSELIDDLEVGDTLS 87
                                      455555555555..55.889***********77788******55555.5678875.6999999**************** PP

                                      EEEEE-SEE CS
                     FAD_binding_6 90 ikGPlGkfe 98
                                      ++GP+G+f+
  gi|330508956|ref|YP_004385384.1| 88 LDGPYGSFS 96
                                      *******96 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 !   24.6   0.0   5.1e-09   2.3e-05       1      65 [.     101     159 ..     101     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.1e-09
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_6   1 yenvllvagGiGitpfisilkdllkkskkealktkkikliwvvressslewfkdvLneleeekse 65 
                                       ++ v +++gGiGitp+ s++k +  k        + i+l  ++r+++++  ++d++  +++ +++
  gi|330508956|ref|YP_004385384.1| 101 HDKVCMLSGGIGITPLRSMIKFCTDKKT-----STDISLLYSNRNEDEIPFYDDLMP-MQRANPR 159
                                       789*****************99988886.....999*****************9997.4444444 PP

>> FAD_binding_8  FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   1.1e-05     0.049       8     106 ..       9      93 ..       2      96 .. 0.71
   2 ?   -3.4   0.0       2.3     1e+04      12      33 ..     180     201 ..     179     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                     FAD_binding_8   8 kvalleedliklkvskpkkslkykaGqyvyini.pslsklfwqsHPFtiasapeddklslvikvksgltkklakkll 83 
                                       kv    + + +++++kp++ + y +Gq+ ++ +     ++   + P ++ s+p +d+l++  k ++        +++
  gi|330508956|ref|YP_004385384.1|   9 KVIKRTKSVKSIRFEKPEH-FSYLPGQWTFLIFgDGPERI---MKPLSFSSSPTEDHLEVTKKLTGL-------RFS 74 
                                       44445588889*******8.*************7666656...99***********99985433322.......223 PP

                     FAD_binding_8  84 ssskkelenkkaklkvlidGPYG 106
                                       +     +++ +   ++ +dGPYG
  gi|330508956|ref|YP_004385384.1|  75 EL----IDDLEVGDTLSLDGPYG 93 
                                       32....33444455677777777 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.3
                     FAD_binding_8  12 leedliklkvskpkkslkykaG 33 
                                       l++++ik +v++  ++ +y +G
  gi|330508956|ref|YP_004385384.1| 180 LNGEMIKSTVPQWAERIYYVSG 201
                                       5788999888888887887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1724.19
//
Query:       gi|330508957|ref|YP_004385385.1|  [L=296]
Description: prephenate dehydrogenase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-50  171.5   0.0    1.9e-50  171.3   0.0    1.0  1  PDH            Prephenate dehydrogenase
    6.6e-08   32.9   0.0    1.1e-07   32.2   0.0    1.4  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    3.4e-06   27.6   0.0    9.2e-06   26.2   0.0    1.8  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
    0.00027   20.4   0.0    0.00056   19.3   0.0    1.5  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
  ------ inclusion threshold ------
      0.058   13.4   0.2       0.44   10.6   0.0    2.4  3  B12-binding    B12 binding domain
      0.077   12.4   0.0       0.13   11.7   0.0    1.4  1  Epimerase      NAD dependent epimerase/dehydratase family


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 !  171.3   0.0   6.4e-54   1.9e-50       1     258 []      17     264 ..      17     264 .. 0.96

  Alignments for each domain:
  == domain 1  score: 171.3 bits;  conditional E-value: 6.4e-54
                                       HHHHHHHTT--SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE CS
                               PDH   1 laralrrkgfkvtvigydideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitD 77 
                                       +ar+ + kg +v + g +   +k e a++lg+ ++ +  +++v+e d+v+++v +e++ ev++++ap ++ + li+D
  gi|330508957|ref|YP_004385385.1|  17 FARYFKSKGWEVAIWGPS---GKVEVAERLGVRYAHDM-MAEVEESDVVLVSVLIEKTVEVIRQVAPRMHSGSLIMD 89 
                                       69999999*999999976...556667799******99.9************************************* PP

                                       --S--CHHHHHHHHHCC..GCEEEEEES---S-SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEE CS
                               PDH  78 vgsvKekvvreleellkegksfvgghPmaGteksGvdaareelfenavviLtPtektdkealekvkelleevgarvi 154
                                       v+svK  +vr+++   ++g++  g+hPm+G+           ++ ++  i tP e +  ++l  +++l+e  ga+++
  gi|330508957|ref|YP_004385385.1|  90 VTSVKSGPVRAMKTYAPKGVEALGTHPMFGP--------TMPSLFGQTIIFTPVEGKTGKWLGVIRSLFESDGAKIE 158
                                       *******************************........888899**********9999****************** PP

                                       E--HHHHHHHHHHHTHHHHHHHHHHHHHHHCHHCCCCHHHHCGTCCHHHHH....CGGGS-HHHHHHHHHHTHHHHH CS
                               PDH 155 lmspeeHDrvvavvshlphvvaialaatlkekkndekeirklasggfrdvt....RiaksnPelwadilleNkeavl 227
                                        +++eeHD+ +avv+ l+h+++i++ a+lk+   d + + ++ s+ ++ ++    Ri ++nPel+a+i+++ k   +
  gi|330508957|ref|YP_004385385.1| 159 ILEAEEHDETMAVVQALTHFAYISIGAALKALDFDVQRSHRFMSPVYEIMIdfvgRILDQNPELYASIQMNPKA--A 233
                                       *********************************************************************96666..8 PP

                                       HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                               PDH 228 ealdkfikelkklkelienedaeeLvellke 258
                                        a++ f  e+ +l e   ++d+e + ++++e
  gi|330508957|ref|YP_004385385.1| 234 AARQAFVSECMRLCEKTDDGDMEGFKQMMRE 264
                                       999*************************986 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 !   32.2   0.0   3.6e-11   1.1e-07       6     113 ..       9     113 ..       5     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 3.6e-11
                                       --SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--T CS
                     NAD_binding_2   6 GlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkk 82 
                                       G+G+ Gs +a+ ++++g++va++  +  kve +   g++ a+++ + v++ dvv++ v  +k v evi+++++++++
  gi|330508957|ref|YP_004385385.1|   9 GTGETGSWFARYFKSKGWEVAIWGPS-GKVEVAERLGVRYAHDMMAEVEESDVVLVSVLIEKTV-EVIRQVAPRMHS 83 
                                       99**********************87.999999999***********************98877.69********** PP

                                       T-EEEE-S---HHHHHHHHHHHHHTT-EEEE CS
                     NAD_binding_2  83 gdilidgstsspedtrelakelkekglkfld 113
                                       g++++d+++++    r ++++ + kg++ l+
  gi|330508957|ref|YP_004385385.1|  84 GSLIMDVTSVKSGPVRAMKTY-APKGVEALG 113
                                       *********998777666554.566776666 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   3.1e-09   9.2e-06       1      95 [.       3      91 ..       3      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.1e-09
                                      EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHH CS
                     F420_oxidored  1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevl 78
                                      +i i+ G+G+ g+ +a+ + ++g    e+ +     p+   e ae+lgv+  + d    +ee+dvv+++v  e++ ev+
  gi|330508957|ref|YP_004385385.1|  3 RILILgGTGETGSWFARYFKSKG---WEVAIW---GPSGKVEVAERLGVRYAH-DMMAEVEESDVVLVSVLIEKTVEVI 74
                                      578999*****************...999977...7888899***********.88888999***************** PP

                                      HHCGHHHHTTSEEEEES CS
                     F420_oxidored 79 selakdalkgklvisvl 95
                                      +++a++ ++g+l+ +v+
  gi|330508957|ref|YP_004385385.1| 75 RQVAPRMHSGSLIMDVT 91
                                      **************997 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 !   19.3   0.0   1.9e-07   0.00056      42     104 ..       8      69 ..       3      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.9e-07
                                       ES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S--STT CS
                      2-Hacid_dh_C  42 iGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlpltpe 104
                                        G+G+ G+ +a+++k+ g +v ++ +s k e  +e+lgv+++ ++ + ++esD+v + + ++ +
  gi|330508957|ref|YP_004385385.1|   8 GGTGETGSWFARYFKSKGWEVAIWGPSGKVEV-AERLGVRYAhDMMAEVEESDVVLVSVLIE-K 69 
                                       49***************************888.9999**8877************9988544.3 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015      0.44      19      74 ..      16      80 ..      15     101 .. 0.87
   2 ?   -1.5   0.0       0.8   2.4e+03      25      46 ..     151     174 ..     142     217 .. 0.60
   3 ?   -0.4   0.0      0.38   1.1e+03      20      56 ..     183     224 ..     169     278 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                       B12-binding 19 vlaaalrdagfeVqllganven...........edivaairaekpdvvglSalltsqleavkelvel 74
                                      + a++++ +g+eV + g   ++           +d++a++++   dvv++S+l+ +++e +++++ +
  gi|330508957|ref|YP_004385385.1| 16 WFARYFKSKGWEVAIWGPSGKVevaerlgvryaHDMMAEVEES--DVVLVSVLIEKTVEVIRQVAPR 80
                                      579999**********8888778899****9999999999888..*************999999877 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.8
                       B12-binding  25 rdagfeVqllganven..edivaa 46 
                                       + +g ++++l+a+ ++   ++v+a
  gi|330508957|ref|YP_004385385.1| 151 ESDGAKIEILEAEEHDetMAVVQA 174
                                       555555555555554322222222 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.38
                       B12-binding  20 laaalrdagfeVqllganven.....edivaairaekpdvvg 56 
                                       + aal++  f+Vq      ++      d+v +i + +p++ +
  gi|330508957|ref|YP_004385385.1| 183 IGAALKALDFDVQRSHRFMSPvyeimIDFVGRILDQNPELYA 224
                                       666666666666644333333455556666666666666544 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.2e-05      0.13       1      31 [.       4      34 ..       4      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.2e-05
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES- CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrl 31
                                      il++G+tG  Gs +++++++kg+ev  +   
  gi|330508957|ref|YP_004385385.1|  4 ILILGGTGETGSWFARYFKSKGWEVAIWGPS 34
                                      89**********************9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2214.25
//
Query:       gi|330508958|ref|YP_004385386.1|  [L=284]
Description: shikimate 5-dehydrogenase [Methanosaeta concilii GP6]
Scores for complete 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-24   83.9   0.0    1.4e-23   83.0   0.0    1.5  1  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
      6e-15   54.7   0.7    1.3e-14   53.6   0.7    1.6  1  SDH_C            Shikimate 5'-dehydrogenase C-terminal domain
    1.7e-13   50.8   0.0    2.9e-13   50.0   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    2.2e-06   28.1   0.1    4.8e-06   27.1   0.1    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    2.8e-05   23.5   0.0    4.5e-05   22.9   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    4.3e-05   22.9   0.1     0.0033   16.8   0.1    2.2  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
    0.00062   20.0   0.5     0.0043   17.3   0.4    2.2  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0019   17.5   0.4     0.0032   16.8   0.4    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0034   16.9   0.1     0.0052   16.3   0.1    1.3  1  adh_short        short chain dehydrogenase
     0.0041   16.7   0.1     0.0078   15.8   0.1    1.6  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
  ------ inclusion threshold ------
      0.034   14.6   0.1      0.055   13.9   0.1    1.3  1  NAD_binding_7    Putative NAD(P)-binding
      0.037   13.6   0.2       0.07   12.7   0.2    1.5  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      0.048   14.5   0.0      0.075   13.9   0.0    1.3  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
       0.13   12.3   0.2       0.29   11.2   0.1    1.5  2  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
       0.17   11.1   0.0       0.23   10.7   0.0    1.2  1  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas


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 !   83.0   0.0   1.1e-26   1.4e-23       1      83 []       6      89 ..       6      89 .. 0.95

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 1.1e-26
                                      EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGG.SSEE-HHHHHHT CS
                    Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeavipl.ldelseeAkaig 78
                                      ++G+pi+hSlSPa++naaf+alg++g y+af+v+ ++l++av ++ a g+ Gln TiP+Ke++++l   e+++ A+aig
  gi|330508958|ref|YP_004385386.1|  6 IFGDPIEHSLSPAMQNAAFRALGMDGCYHAFRVSRSRLKDAVIGADAMGFGGLNLTIPLKEEALSLdFLEADDLARAIG 84
                                      79*************************************************************975433699******* PP

                                      --SEE CS
                    Shikimate_dh_N 79 AvNti 83
                                      AvNti
  gi|330508958|ref|YP_004385386.1| 85 AVNTI 89
                                      ****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 !   53.6   0.7   1.1e-17   1.3e-14       4      31 .]     245     272 ..     242     272 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.1e-17
                                       HHHHHHHHHHHHHHS----HHHHHHHHH CS
                             SDH_C   4 MLveQgaeqFelWTGrepPvevMreall 31 
                                       MLv+Qga++Fe+WTGr++P++vM++a++
  gi|330508958|ref|YP_004385386.1| 245 MLVYQGARAFEIWTGRKAPADVMERAVR 272
                                       **************************97 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   2.5e-16   2.9e-13       9      84 ..     124     195 ..     116     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 2.5e-16
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SS CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisata 84 
                                       ++k+++vlliGaG  a+ +a +L ++g++ v +aNR+l+ra+ela +++g       l +l+ l+++adv+i at+
  gi|330508958|ref|YP_004385386.1| 124 KVKGSRVLLIGAGGAARAIAYALDREGAE-VSIANRNLKRAHELAASVGGI---SYCLCDLEPLVRQADVIINATS 195
                                       7899***********************99.******************999...77788999999*********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 !   27.1   0.1     4e-09   4.8e-06       2      69 ..     130     194 ..     129     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4e-09
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.-EEECECHHHHHHH-SEEEE-S CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.vkvtavdneeaaeeadvvvlav 69 
                                       + +iGaG  ++a+a  l ++g    e+ +a +rn ++a ela+++g ++ +  d e ++++adv++ a 
  gi|330508958|ref|YP_004385386.1| 130 VLLIGAGGAARAIAYALDREG---AEVSIA-NRNLKRAHELAASVGgISYCLCDLEPLVRQADVIINAT 194
                                       5689*****************...****88.***********99998999999************9876 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 !   22.9   0.0   3.7e-08   4.5e-05      23     100 ..     112     195 ..      99     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.7e-08
                                       C..HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH..CHHHHTCEEC..SHHHHHHH-S CS
                      2-Hacid_dh_C  23 w..ksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee..eeeelgvelv..sleellaesD 93 
                                       w   s  +  g +++g++v +iG+G  ++a+a  l   g++v + +r+ k+ +  +++  g++++  +le l++++D
  gi|330508958|ref|YP_004385386.1| 112 WgaLSALQDAGVKVKGSRVLLIGAGGAARAIAYALDREGAEVSIANRNLKRAHelAASVGGISYClcDLEPLVRQAD 188
                                       5544556778899***********************************9998865555666666556********** PP

                                       EEEE-S- CS
                      2-Hacid_dh_C  94 ivslhlp 100
                                       ++++++ 
  gi|330508958|ref|YP_004385386.1| 189 VIINATS 195
                                       **98765 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 !   16.8   0.1   2.8e-06    0.0033      22     113 ..     113     230 ..     107     248 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.8e-06
                                       HHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTS.................CCHHHHHCCSS CS
                     THF_DHG_CYH_C  22 gvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchskt.................kdlaeitread 81 
                                       g ++ l+++g++++g +v+ +G++    +++a  L +++a V++++++                   dl+ ++r+ad
  gi|330508958|ref|YP_004385386.1| 113 GALSALQDAGVKVKGSRVLLIGAGGA-ARAIAYALDREGAEVSIANRNLkrahelaasvggisyclCDLEPLVRQAD 188
                                       778889999*************9986.7999999999866666665443112222222223323336888899**** PP

                                       EEEE-S......S-TT-B-GGGS-TT-EEEE---EEC....- CS
                     THF_DHG_CYH_C  82 ivvvav......GkpelikaemvkegavviDvGinrv....e 113
                                       +++ a+      G  ++i++  +k+ +vv D+ +nr      
  gi|330508958|ref|YP_004385386.1| 189 VIINATsvgmreGDGRIIDSRLLKSHHVVFDIVYNREtellW 230
                                       ***9975555556789******************99844443 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.4   3.6e-06    0.0043       1      48 [.     130     174 ..     130     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.6e-06
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTC CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvr 48 
                                       vl+iGaG+ ++a+a  l r++    e+ +a r+++++++laa++ g++
  gi|330508958|ref|YP_004385386.1| 130 VLLIGAGGAARAIAYALDREGA---EVSIANRNLKRAHELAASVGGIS 174
                                       79******************97...6**************99874442 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 !   16.8   0.4   2.7e-06    0.0032      21     101 ..     121     196 ..     114     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.7e-06
                                       CEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE CS
                       AlaDh_PNT_C  21 GgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvig 97 
                                       +gv+ v+ ++vl iG+G a  + + +  + ga+V + + + +r+++l +  +     ++     l+  v++adv+i 
  gi|330508958|ref|YP_004385386.1| 121 AGVK-VKGSRVLLIGAGGAARAIAYALDREGAEVSIANRNLKRAHELAASVGG----ISYCLCDLEPLVRQADVIIN 192
                                       5788.99**********9987777777899*************9999984444....35555678888999999998 PP

                                       ---B CS
                       AlaDh_PNT_C  98 tvli 101
                                       +  +
  gi|330508958|ref|YP_004385386.1| 193 ATSV 196
                                       8766 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   4.3e-06    0.0052       3      59 ..     130     181 ..     128     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.3e-06
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTT CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvt 59 
                                       vl +Ga+ G  raia++l +eGa+v +++r+ ++++e+a++++     + ++ +D++
  gi|330508958|ref|YP_004385386.1| 130 VLLIGAG-GAARAIAYALDREGAEVSIANRNLKRAHELAASVGG----ISYCLCDLE 181
                                       6778877.9*******************************9997....778888876 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   6.6e-06    0.0078       2      67 ..     125     193 ..     104     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.6e-06
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT...-EEEEHHHHHHT-SEEEE- CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeeg...fevltvaeavkkadvvmil 67 
                                       +kg ++ +iG G  ++a a  l   g +v +++r+ ++  + A + g   +   +++ +v++adv+++ 
  gi|330508958|ref|YP_004385386.1| 125 VKGSRVLLIGAGGAARAIAYALDREGAEVSIANRNLKRAHELAASVGgisYCLCDLEPLVRQADVIINA 193
                                       68899********************************9999988876333456678889******9875 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.6e-05     0.055       3      69 ..     123     194 ..     122     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                     NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele.....elvklaeeelekdlegadlviaat 69 
                                       +++kg +vl++G+G  A   ++ l ++ga+v +   ++k+++e     + +++   +le  + +ad++i at
  gi|330508958|ref|YP_004385386.1| 123 VKVKGSRVLLIGAGGAARAIAYALDREGAEVSIANRNLKRAHElaasvGGISYCLCDLEPLVRQADVIINAT 194
                                       5899****************************9999876665544334222222333455566666666666 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   5.9e-05      0.07       4      50 ..     136     180 ..     134     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.9e-05
                                       TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.EEE--T CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae.vlecDV 50 
                                        g +raiA al +eGaev ++++n ++   ++ela+++g   ++ cD 
  gi|330508958|ref|YP_004385386.1| 136 GGAARAIAYALDREGAEVSIANRNLKR---AHELAASVGGIsYCLCDL 180
                                       5789*****************999998...889999888654677876 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.3e-05     0.075       2      86 ..     129     214 ..     128     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.3e-05
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE..EESSHHHHHTCTT..ESEEEE-S-GGG CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve..aysdleelladpe..idavivatpngt 74 
                                       rv++iGaG +++  +    ++ +++ev  + +++ +ra+++a+s g    +  dle l+++ +  i+a +v+++ g 
  gi|330508958|ref|YP_004385386.1| 129 RVLLIGAGGAARAIA-YALDR-EGAEVS-IANRNLKRAHELAASVGGIsyCLCDLEPLVRQADviINATSVGMREGD 202
                                       799****99999888.33333.566665.99**********9998766588999******88445999999999988 PP

                                       HHHHHHHHHHTT CS
                      GFO_IDH_MocA  75 heelakaaleag 86 
                                       ++ +  ++l+ +
  gi|330508958|ref|YP_004385386.1| 203 GRIIDSRLLKSH 214
                                       887777777765 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 ?   -0.9   0.0       1.3   1.5e+03      28      49 ..     104     125 ..     100     126 .. 0.88
   2 ?   11.2   0.1   0.00025      0.29      19      87 ..     123     195 ..     114     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                                       EE--SHHHHHHHHHHHHCT-EE CS
                     AdoHcyase_NAD  28 vaGyGdvGkGcaaslkglGarv 49 
                                       + Gy   G G+ ++l+ +G +v
  gi|330508958|ref|YP_004385386.1| 104 IQGYNTDGWGALSALQDAGVKV 125
                                       789****************988 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00025
                                       S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-..S-HHHHHHHHCTT..-EE--HHHCTTT-SEEEE-SS CS
                     AdoHcyase_NAD  19 vllaGkvavvaGyGdvGkGcaaslkglGarvivte..vdPicalqaameG..fevvtleevvkkadivvtttG 87 
                                       v + G  ++++G G   +  a +l   Ga v +++  +     l a++ G  + +  le +v++ad+++ +t 
  gi|330508958|ref|YP_004385386.1| 123 VKVKGSRVLLIGAGGAARAIAYALDREGAEVSIANrnLKRAHELAASVGGisYCLCDLEPLVRQADVIINATS 195
                                       6688999**************************972255667799999995567899************9985 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00019      0.23     160     200 ..     123     163 ..     101     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                       Pyr_redox_3 160 hkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseie 200
                                        k++g +v+ iG++  a  +A+ l r+gaeV+++ r+ ++ 
  gi|330508958|ref|YP_004385386.1| 123 VKVKGSRVLLIGAGGAARAIAYALDREGAEVSIANRNLKRA 163
                                       47899*****************************9986544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1822.13
//
Query:       gi|330508959|ref|YP_004385387.1|  [L=407]
Description: hypothetical protein MCON_3309 [Methanosaeta concilii GP6]
Scores for complete 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-55  186.4  18.1    5.3e-55  186.4  18.1    2.9  2  DUF92     Integral membrane protein DUF92


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.1   7.4         1   1.8e+04     146     185 ..      91     135 ..      12     138 .. 0.59
   2 !  186.4  18.1   2.9e-59   5.3e-55       2     235 ..     176     390 ..     175     391 .. 0.92

  Alignments for each domain:
  == domain 1  score: -6.1 bits;  conditional E-value: 1
                             DUF92 146 llGllasllGalliallavlllllel...............lillltlaGllGsl 185
                                       l+G +a ll  ++++          +               +++l++l Gl G++
  gi|330508959|ref|YP_004385387.1|  91 LTGSIAHLLITVALG----------YplaiwisagtipkesAMFLAVLGGLSGTF 135
                                       222222222222222..........011223333444455455666666666665 PP

  == domain 2  score: 186.4 bits;  conditional E-value: 2.9e-59
                             DUF92   2 ltlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKa..kleeekegaRdav 76 
                                       ++l+l++ a+  k+ + s++++ ++vg+l+++   gl +fllll+F+l+g  +t++++++K+  +++++++gaR+++
  gi|330508959|ref|YP_004385387.1| 176 FALILGVGAYWAKAADISAVISETIVGFLVIIF-AGLSWFLLLLIFYLMGGGFTRYGYAKKEklGIAQSHGGARGYK 251
                                       68999***********************99988.6778*********************99988999999******* PP

                             DUF92  77 qVlanslvalllally..lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnGgVsllGlla 151
                                       +V++nslv+l++a++y  +++dl+++++++s+A++++DTlaSE+G+++s+ kpr+ittlk+++pG++GgV+llG  a
  gi|330508959|ref|YP_004385387.1| 252 NVFSNSLVPLAMAVFYgiYGNDLFVYAFIGSVATANGDTLASEIGETSSS-KPRMITTLKETEPGVDGGVTLLGEGA 327
                                       ****************76559************************88887.************************** PP

                             DUF92 152 sllGalliallavlllllel.lillltlaGllGsllDSlLGatlqasvvdkrtgkvvegeggekvvsGldlLdNnaV 227
                                       sllGal+i++la+++ ++ l  i+++t+aG+lG+++DSlLGatlq++                        L+Nn+V
  gi|330508959|ref|YP_004385387.1| 328 SLLGALIISILAAISGMTGLlGIVIGTAAGFLGTNFDSLLGATLQSR----------------------GTLSNNGV 382
                                       *********9988887766679999*********************9......................56777777 PP

                             DUF92 228 Nllsallt 235
                                       Nl +++++
  gi|330508959|ref|YP_004385387.1| 383 NLAATAFG 390
                                       77777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 2778.93
//
Query:       gi|330508960|ref|YP_004385388.1|  [L=203]
Description: di-trans,poly-cis-decaprenylcistransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-28   99.3   0.0    8.4e-27   94.1   0.0    2.0  2  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.0    0.0025        45      21      47 ..      33      59 ..      27      64 .. 0.90
   2 !   94.1   0.0   4.7e-31   8.4e-27      98     224 .]      80     202 ..      60     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0025
                                      HHHHHHHHHHHHHHHHHTT-SEEEEEE CS
                      Prenyltransf 21 hkaGaealkeilelclelgvkvvtvYa 47
                                      + +G+++l++i+e++ ++g   + +Y 
  gi|330508960|ref|YP_004385388.1| 33 FDEGLDKLRDIIEWSRSMGLASLVLYI 59
                                      578******************999995 PP

  == domain 2  score: 94.1 bits;  conditional E-value: 4.7e-31
                                       HHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHHCTSTT..TSSS-SEEE CS
                      Prenyltransf  98 dvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeideetlekhlytakalpdpDlli 173
                                       ++  + ++a   t  +  ++ +++ + Yg+++e++ea+r+l++e++e +   e+ide+++e++l    + ++pDl+i
  gi|330508960|ref|YP_004385388.1|  80 QISLHTADADLLTG-SGGRMRVTVSLGYGGKREVTEAFRDLLSEVEEGRLIpEDIDEKAIESRLRF--S-QKPDLVI 152
                                       44455555666666.4455**********************988854433248899*********9..4.78***** PP

                                       EESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                      Prenyltransf 174 RtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                       R +G++ lS+F++wq+ayselyf+dv W  ++k d+l+a+++yq rerrfg
  gi|330508960|ref|YP_004385388.1| 153 RAGGKQ-LSDFMIWQSAYSELYFTDVNWLRLRKIDFLRAIRDYQGRERRFG 202
                                       **9976.******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1529.76
//
Query:       gi|330508961|ref|YP_004385389.1|  [L=214]
Description: RNA 2'-phosphotransferase, Tpt1/KptA family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-23   82.8   0.0    3.8e-23   82.5   0.0    1.1  1  PTS_2-RNA     RNA 2'-phosphotransferase, Tpt1 / KptA family
  ------ inclusion threshold ------
       0.14   11.0   0.0       0.14   11.0   0.0    1.1  1  Herpes_ORF11  Herpesvirus dUTPase protein


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 !   82.5   0.0   4.3e-27   3.8e-23       2     180 ..      30     194 ..      29     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 4.3e-27
                         PTS_2-RNA   2 revqlskaLsyiLRhgaekegLkiredGyvkvedlLelpklkslkvtleeikevVesndKqRFelveleelliranq 78 
                                       r++ql++ ++  LRh + + gL++++ G++++++l e  + +++ ++ e + ++ +s++KqR+e   +++  ira  
  gi|330508961|ref|YP_004385389.1|  30 RTEQLGRLVAGGLRHFPLDLGLEMDSRGWIDLSKLGEVVQKRHRWANKEMVIALAQSDPKQRYE---ISNQRIRARY 103
                                       678999****************************9998777776699*****************...54568***** PP

                         PTS_2-RNA  79 ghsikkvesselllepiesaeelpevvvHgTylkawesilasggLkrmsrnhihlatglpgekevisgmrksaevli 155
                                       ghs+ ++     +l++   + +lp+ +++g + ++ ++il + gLk +s++++hl+t+ p+++  + g r+ +  +i
  gi|330508961|ref|YP_004385389.1| 104 GHSM-DI-----ELDHP--ECHLPR-LYYGASEEEADRIL-EIGLKSASQRYVHLSTT-PNKAWDVAGYRTGNPKVI 169
                                       ***6.32.....24442..334788.**************.88**************7.7788899*********** PP

                         PTS_2-RNA 156 yidvekaladgikfyvsengviLte 180
                                        +d++ a ++g+k+++ +++++++e
  gi|330508961|ref|YP_004385389.1| 170 QVDAAPAREAGVKMMTVNDDIVISE 194
                                       ********************99986 PP

>> Herpes_ORF11  Herpesvirus dUTPase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.5e-05      0.14     182     236 ..     117     193 ..      29     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.5e-05
                      Herpes_ORF11 182 k.....................asagrkdvrlsqeralvcrvnairtGk.nylrvtvamsrdaasesvhlriqVdva 236
                                                             +sa + +v+ls+++++ + v ++rtG+ ++++v+ a+ r+a  +++ +   + ++
  gi|330508961|ref|YP_004385389.1| 117 HlprlyygaseeeadrileiglKSASQRYVHLSTTPNKAWDVAGYRTGNpKVIQVDAAPAREAGVKMMTVNDDIVIS 193
                                       055555555666666666677789************************85678999999999998888877776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1492.52
//
Query:       gi|330508962|ref|YP_004385390.1|  [L=316]
Description: hypothetical protein MCON_3313 [Methanosaeta concilii GP6]
Scores for complete 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-82  275.2   0.2    6.3e-82  275.0   0.2    1.0  1  GCHY-1    Type I GTP cyclohydrolase folE2
  ------ inclusion threshold ------
       0.01   16.3   0.2       0.36   11.4   0.0    2.8  2  FolB      Dihydroneopterin aldolase


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 !  275.0   0.2     7e-86   6.3e-82       1     259 []       6     298 ..       6     298 .. 0.93

  Alignments for each domain:
  == domain 1  score: 275.0 bits;  conditional E-value: 7e-86
                                       .XXXXXXXXXX----SEEEEEEEEEEEEE--TT.TS-EEEEEEEEEEEES-SS--GGGGGHHHHHHH.HS-SSEEG. CS
                            GCHY-1   1 lpDvqsekderkipldrVGvkgvklpvkvkdke.kkaqtlvaevdlfvdLpaekkGihmSRlvevle.eaeeelee. 74 
                                       lpD+q+ +++++++l+rVGv+gvk+++kv++ + +++  l++++++fvdLp+++kG+++SR++e+++   e++++  
  gi|330508962|ref|YP_004385390.1|   6 LPDIQACEPDFPFNLTRVGVTGVKKLIKVERGSdERPVVLISNFEVFVDLPSDRKGANLSRNFEAIDeVLEDAINLp 82 
                                       79****************************97625779*****************************5445555547 PP

                                       .GGHHH....HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE...TTE..EEEEEEEEEEE CS
                            GCHY-1  75 .kslee....ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaeler.kee..vkltvgvevpv 143
                                        +++ee    i+++ll+++eya+raev++k+ey++++++p ++++++e +++++ea ++    +  +++tvg+ev++
  gi|330508962|ref|YP_004385390.1|  83 vYEIEElcgeIAKRLLARHEYASRAEVKMKSEYIVRRQTPFTKVTCQEVVDIFAEAVARAgP-TgcLRKTVGAEVMG 158
                                       7777777778************************************************7743.236*********** PP

                                       EEE-HHHHHHS.........................SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE- CS
                            GCHY-1 144 ttlCPCskeisrell.....................eagaHnQRsvvtvkvelaeeekeveiedlielvessassev 199
                                       +t+CPC++ei+++++                     ++++HnQR++ +++ve+ ++++ v+i+++i+++e+s+ss+v
  gi|330508962|ref|YP_004385390.1| 159 MTACPCAQEIMKDQArgelikaglseevaldvlsrlPVATHNQRGRGSISVEV-RDRRCVSIDRIIKIIEESMSSKV 234
                                       ***********9999*************************************5.68999****************** PP

                                       -S---HHHHHHHHHHHHTS---HHHHHHHHHHHHHS-TTEEEE.........EEEEEEE-TTTSSEEEE CS
                            GCHY-1 200 yellKReDEkavtekayenpkFvEDvvRevaaaleeeerveef.........sveveneESiHnHnavA 259
                                       y llKR+DE+ v+ +a++npkFvED+vR++a++      ve+f         ++++ neESiH+Hna+A
  gi|330508962|ref|YP_004385390.1| 235 YGLLKRPDEALVVSRAHSNPKFVEDCVRTMAQKT-----VEAFsdlpddaavTLKQINEESIHQHNAFA 298
                                       *********************************9.....6666666999999****************8 PP

>> FolB  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     4e-05      0.36      31      97 ..      51     115 ..      37     129 .. 0.73
   2 ?    2.1   0.0     0.032   2.8e+02      46      70 ..     215     239 ..     185     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4e-05
                                       EEE-CHHHHHHTTGGGSS-HHHHHHHHHHHHHSSEES-HHHHHHHHHHHHHCHST.ESEEEEEEEETT CS
                              FolB  31 leldlskaaesddledtvdYaelakavkelvesssfkllEalaeriaealleefp.vekvevrveKpn 97 
                                       + +dl +  +  +l  + +++++ + +++ ++  ++  +E l+ +ia++ll++++ ++++ev+++   
  gi|330508962|ref|YP_004385390.1|  51 VFVDLPSDRKGANL--SRNFEAIDEVLEDAINL-PVYEIEELCGEIAKRLLARHEyASRAEVKMKSEY 115
                                       44444333333333..56778888888888876.9999*************99999999***998665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.032
                                       GSS-HHHHHHHHHHHHHSSEES-HH CS
                              FolB  46 dtvdYaelakavkelvesssfkllE 70 
                                       + v+ ++++k+++e ++s+ + ll 
  gi|330508962|ref|YP_004385390.1| 215 RCVSIDRIIKIIEESMSSKVYGLLK 239
                                       4588888888888888887887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2464.06
//
Query:       gi|330508963|ref|YP_004385391.1|  [L=258]
Description: hypothetical protein MCON_3314 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2002.37
//
Query:       gi|330508964|ref|YP_004385392.1|  [L=586]
Description: hypothetical protein MCON_3315 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 4075.10
//
Query:       gi|330508965|ref|YP_004385393.1|  [L=404]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete 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-141  469.5   0.0   4.6e-141  469.2   0.0    1.0  1  DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
    2.8e-06   27.5   0.0    8.9e-06   25.9   0.0    1.9  1  HTH_Tnp_Tc3_2    Transposase
    0.00039   20.5   0.0    0.00091   19.3   0.0    1.6  1  HTH_21           HTH-like domain
     0.0024   18.0   0.0     0.0038   17.3   0.0    1.3  1  GSH-S_N          Prokaryotic glutathione synthetase, N-termin
     0.0042   17.7   0.1      0.011   16.3   0.1    1.8  1  HTH_32           Homeodomain-like domain
  ------ inclusion threshold ------
      0.012   14.3   0.0       0.02   13.6   0.0    1.3  1  UPF0236          Uncharacterised protein family (UPF0236)
       0.02   14.5   0.3      0.073   12.7   0.1    2.0  3  HTH_33           Winged helix-turn helix
      0.031   14.2   0.4       0.11   12.4   0.1    2.1  2  HTH_12           Ribonuclease R winged-helix domain
      0.058   13.4   0.1       0.62   10.1   0.0    2.4  2  HTH_29           Winged helix-turn helix


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.2   0.0  2.3e-144  4.6e-141       1     308 []      91     398 ..      91     398 .. 1.00

  Alignments for each domain:
  == domain 1  score: 469.2 bits;  conditional E-value: 2.3e-144
                   DDE_Tnp_ISAZ013   1 dleelvepetrgdpesplrwttkslrklaeeLkeqghkvsaetvaelLkelgyslqsnrKtkegkkhpdrdaqFeki 77 
                                       dle+++e++t+gdp+s l+wt ks++++aeeL+++ghkvs++tv++lLke+gyslq+nrK+ egk+ p+rd+qF+++
  gi|330508965|ref|YP_004385393.1|  91 DLEKIMEESTAGDPMSLLKWTYKSTYAIAEELQSRGHKVSHDTVRRLLKESGYSLQANRKNLEGKSGPERDTQFRYV 167
                                       79*************************************************************************** PP

                   DDE_Tnp_ISAZ013  78 nekvkeaqeagqpvisvdtkkkeliGefkrsGkewrpkgepaevkdhdfvskeegkaipyGiydlaenegwvsvgtd 154
                                       +++++++ +ag+pvisvd+kkkel+G++k+sG++wr+kg+p+ v+++df+sk+ g+aipyG+yd+++neg+v++g++
  gi|330508965|ref|YP_004385393.1| 168 SSQAAKFIDAGDPVISVDAKKKELVGNYKNSGRTWRQKGQPELVNVYDFPSKAIGAAIPYGVYDPKRNEGVVNIGKS 244
                                       ***************************************************************************** PP

                   DDE_Tnp_ISAZ013 155 kdtaefavesirrwWqevgkarypkakrllitaDaggsnssrsrlwkkelqkladelgleiqvahfPpgtskwnkiE 231
                                       ++taefavesir+wW+ vgk+ry+ +k+lli+aD+ggsn+sr+r wk  lq+lade+g++i+v+hfPpgtskwnkiE
  gi|330508965|ref|YP_004385393.1| 245 HNTAEFAVESIRQWWNLVGKYRYAGCKNLLICADGGGSNGSRNRGWKFFLQQLADEIGITITVSHFPPGTSKWNKIE 321
                                       ***************************************************************************** PP

                   DDE_Tnp_ISAZ013 232 hRlfshitqnwrgrpltsvevvvnliaatttkkglkveaeldeksyetGikvskeemealeierdelhgewnytiap 308
                                       h++fs+i++nwrg+pl+s+e++++li++t+tkkgl++ea+ld+++yetGik+ +e+m++l+i+ +el++ wny+i+p
  gi|330508965|ref|YP_004385393.1| 322 HCMFSFISMNWRGKPLSSYETIIKLIGSTKTKKGLRIEARLDDRDYETGIKILDEDMARLKISVHELYPMWNYSIEP 398
                                       ***************************************************************************98 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.5e-09   8.9e-06      14      51 ..     113     150 ..      96     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.5e-09
                     HTH_Tnp_Tc3_2  14 itlreLanelkeeGksvsreTirrrLrkaglkkrkprk 51 
                                       ++  ++a+el+++G++vs+ T+rr L+++g++ +  rk
  gi|330508965|ref|YP_004385393.1| 113 KSTYAIAEELQSRGHKVSHDTVRRLLKESGYSLQANRK 150
                                       57779*****999******************9888777 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.5e-07   0.00091      26      59 ..     118     150 ..     116     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.5e-07
                            HTH_21  26 iwaeLrreggvrvnhkrVrRlMrelGLrgvqrrk 59 
                                       i+ eL+ +g+ +v+h +VrRl +e G+  + +rk
  gi|330508965|ref|YP_004385393.1| 118 IAEELQSRGH-KVSHDTVRRLLKESGYSLQANRK 150
                                       6789****99.5**************99888887 PP

>> GSH-S_N  Prokaryotic glutathione synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.9e-06    0.0038       8      60 ..     103     156 ..      96     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.9e-06
                           GSH-S_N   8 dplesikikkDttfalmleaqarghevfvleaadLslreg.katararkvevke 60 
                                       dp++ +k +  +t+a+++e q+rgh+v + ++++L  ++g +++a+ +++e k+
  gi|330508965|ref|YP_004385393.1| 103 DPMSLLKWTYKSTYAIAEELQSRGHKVSHDTVRRLLKESGySLQANRKNLEGKS 156
                                       9999***999*************************9987723455555555533 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   5.5e-06     0.011      20      73 .]      73     138 ..      51     138 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.5e-06
                            HTH_32  20 rprrgrpr..klsdevrariiallreep.........rWsprq...laarlaeregvkvShstvyriL 73 
                                       +p +gr+r     + +   + ++  ee+         +W+++    +a++l + +g kvSh tv+r+L
  gi|330508965|ref|YP_004385393.1|  73 KPGGGRKRvaDREPNLLNDLEKIM-EEStagdpmsllKWTYKStyaIAEEL-QSRGHKVSHDTVRRLL 138
                                       344557764435555666666666.433467779999997777777*****.888899********98 PP

>> UPF0236  Uncharacterised protein family (UPF0236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.9e-06      0.02     139     230 ..     119     216 ..     110     222 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.9e-06
                           UPF0236 139 aeklerivcqekvskeairqlvleigvalaaaekevkveikekrkvRvLyieaDg.lfvsrq......dgkkeeerl 208
                                       ae+l+++    kvs++++r+l  e g +l+a +k+ + + + +r+  + y+      f+         d kk+e   
  gi|330508965|ref|YP_004385393.1| 119 AEELQSR--GHKVSHDTVRRLLKESGYSLQANRKNLEGKSGPERDTQFRYVSSQAaKFIDAGdpvisvDAKKKELVG 193
                                       4555333..479***********************************999976531344433233322334444444 PP

                           UPF0236 209 lviheGrk.ekgsrleLvnrrdy 230
                                        +   Gr+ ++ ++ eLvn+ d+
  gi|330508965|ref|YP_004385393.1| 194 NYKNSGRTwRQKGQPELVNVYDF 216
                                       45666755356677778887665 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.4   2.9e+03      23      40 ..      97     114 ..      94     122 .. 0.83
   2 ?   12.7   0.1   3.7e-05     0.073      10      39 ..     118     146 ..     111     159 .. 0.85
   3 ?   -3.7   0.0       4.8   9.5e+03      13      26 ..     296     309 ..     295     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
                            HTH_33  23 svsgvyrlLkrlGfsyqk 40 
                                       ++s+ ++ +  l+++y++
  gi|330508965|ref|YP_004385393.1|  97 EESTAGDPMSLLKWTYKS 114
                                       6788888999999**997 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.7e-05
                            HTH_33  10 laqlieerfgvsysvsgvyrlLkrlGfsyq 39 
                                       +a+ ++ r g ++s+ +v+rlLk+ G+s q
  gi|330508965|ref|YP_004385393.1| 118 IAEELQSR-GHKVSHDTVRRLLKESGYSLQ 146
                                       66666666.999****************99 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.8
                            HTH_33  13 lieerfgvsysvsg 26 
                                        ++++ g++++vs+
  gi|330508965|ref|YP_004385393.1| 296 QLADEIGITITVSH 309
                                       5789999*999985 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.7e-05      0.11      17      40 ..     116     139 ..     107     149 .. 0.92
   2 ?   -2.9   0.0       3.5     7e+03      18      31 ..     357     370 ..     346     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.7e-05
                            HTH_12  17 keiaeeLkkrgydigeravRyrLr 40 
                                        +iaeeL+ rg +++  +vR+ L+
  gi|330508965|ref|YP_004385393.1| 116 YAIAEELQSRGHKVSHDTVRRLLK 139
                                       68*******************998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.5
                            HTH_12  18 eiaeeLkkrgydig 31 
                                       +i+  L +r+y+ g
  gi|330508965|ref|YP_004385393.1| 357 RIEARLDDRDYETG 370
                                       68888999998765 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00031      0.62       4      58 ..      27      82 ..      24      86 .. 0.78
   2 ?    0.2   0.0      0.39   7.8e+02      24      34 ..     129     139 ..     125     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00031
                            HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegG.laalld.rrrsgrprnrls 58
                                      a  +l+ G++ vs + +++g sr+t+++ +   e  + l+   + r+ +g +r+r+ 
  gi|330508965|ref|YP_004385393.1| 27 AAKALELGWGGVSKVSAITGFSRTTINKGIQELESNEdLKPPERlRK-PGGGRKRVA 82
                                      6678899999*****************98888776666888888554.676777654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.39
                            HTH_29  24 lsrrtvyrwlk 34 
                                       +s +tv+r lk
  gi|330508965|ref|YP_004385393.1| 129 VSHDTVRRLLK 139
                                       899*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.35s 00:00:01.04 Elapsed: 00:00:00.57
# Mc/sec: 2147.07
//
Query:       gi|330508966|ref|YP_004385394.1|  [L=75]
Description: hypothetical protein MCON_3320 [Methanosaeta concilii GP6]
Scores for complete 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-21   74.3   0.2    9.1e-21   74.2   0.2    1.0  1  Y1_Tnp    Transposase IS200 like


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.2   5.1e-25   9.1e-21      44     121 .]       2      72 ..       1      72 [. 0.94

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 5.1e-25
                            Y1_Tnp  44 elelmpDHvHllvelppklsiskivkalkgassrlinkefpelkkkklkkeslWqrgYfvstvgeasletvkrYIen 120
                                       +le+mpDH+Hl+++ pp++++s +++++kg s+r++n     ++++++k    W+++Y+v t+g++++et+k+YIe+
  gi|330508966|ref|YP_004385394.1|   2 SLEIMPDHIHLFISSPPQNAPSLLINWFKGISARMYN---YWYNETAIK----WTNSYYVGTAGTVTAETIKKYIEE 71 
                                       589**********************************...666667788....***********************9 PP

                            Y1_Tnp 121 q 121
                                       q
  gi|330508966|ref|YP_004385394.1|  72 Q 72 
                                       8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.54
# Mc/sec: 417.21
//
Query:       gi|330508967|ref|YP_004385395.1|  [L=267]
Description: fructose bisphosphate aldolase [Methanosaeta concilii GP6]
Scores for complete 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-61  205.4   0.0    1.2e-60  205.1   0.0    1.1  1  DeoC       DeoC/LacD family aldolase
    0.00077   18.8   0.7    0.00077   18.8   0.7    1.6  2  ThiG       Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
       0.02   14.8   0.3        1.3    8.9   0.1    2.9  3  ETF        Electron transfer flavoprotein domain
      0.049   12.8   0.1       0.11   11.7   0.0    1.7  2  DUF561     Protein of unknown function (DUF561)
      0.053   13.1   0.1       0.11   12.1   0.1    1.8  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil
       0.46    9.8   4.2       0.17   11.2   1.3    1.7  2  NMO        Nitronate monooxygenase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.1   0.0   3.9e-64   1.2e-60       1     235 []      23     239 ..      23     239 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.1 bits;  conditional E-value: 3.9e-64
                                       EEEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTT CS
                              DeoC   1 ivilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskq 77 
                                       +vi+++D++++ +++++       +dl ++v++++++ga+avl ++g++++++++y++d++l+v+++++t l ++++
  gi|330508967|ref|YP_004385395.1|  23 TVIIPLDHGISVGPIQGL------ADLPEMVNKVAKGGANAVLQQKGMVRHGHRGYGQDVGLIVHMSASTSLGPDPN 93 
                                       69****************......7***************************************************9 PP

                                       EEEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHH CS
                              DeoC  78 rdvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlva 154
                                        +v  v+ vee +++GAdav++++++   gse+e  +l   + v+e+c+ +g+pl++++y+r+++i + + d ++va
  gi|330508967|ref|YP_004385395.1|  94 NKVQ-VCLVEECLKMGADAVSIHINI---GSETESDQLSIMGCVSERCDFWGMPLVAMMYPRGKNIANPN-DVEVVA 165
                                       9999.*********************...*************************************9999.****** PP

                                       HHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEE CS
                              DeoC 155 eAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvls 228
                                       +Aar++aelGaDiiK++++        +d ++f++v+k++pvp vv++GG+   ++ +fl+++e A+ +aga Gv++
  gi|330508967|ref|YP_004385395.1| 166 HAARAGAELGADIIKTNYT--------GDPDSFRKVVKGCPVP-VVIAGGPkteTDMEFLKMIEGAL-QAGARGVAI 232
                                       *******************........****************.*******9988999*********.********* PP

                                       SHHHHTT CS
                              DeoC 229 GRaifqk 235
                                       GR++fq+
  gi|330508967|ref|YP_004385395.1| 233 GRNVFQH 239
                                       *****97 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.9   5.7e+03     192     206 ..     103     117 ..     101     123 .. 0.74
   2 !   18.8   0.7   2.6e-07   0.00077     163     235 ..     186     264 ..     160     267 .] 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.9
                                       HHHHTT-SEEEESHH CS
                              ThiG 192 qamelGadavllnta 206
                                       + +++Gadav +   
  gi|330508967|ref|YP_004385395.1| 103 ECLKMGADAVSIHIN 117
                                       568899999977655 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.6e-07
                                       -HHHHHHHHHH-SS-BEEES---SHHH......HHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHHHHHHH CS
                              ThiG 163 nkealkiiieeakvPvivDAGigspsd......aaqamelGadavllntavaeakdpvamArafklaveaGrlayla 233
                                       ++  ++ +++ + vPv++  G  + +d      +  a++ Ga +v +   v + kdpv+m ra+++ v+ G+ a +a
  gi|330508967|ref|YP_004385395.1| 186 DPDSFRKVVKGCPVPVVIAGGPKTETDmeflkmIEGALQAGARGVAIGRNVFQHKDPVKMTRAIAAIVNKGKNADEA 262
                                       566778888999999999999888877222222346999***********************************998 PP

                                       -- CS
                              ThiG 234 gr 235
                                        +
  gi|330508967|ref|YP_004385395.1| 263 IK 264
                                       65 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.081   2.4e+02      40      61 ..      88     112 ..      85     118 .. 0.74
   2 ?   -0.0   0.0      0.24   7.1e+02      10      34 ..     153     177 ..     148     181 .. 0.78
   3 ?    8.9   0.1   0.00043       1.3      32      88 ..     196     256 ..     191     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.081
                                       EES....S-....CHHHHHHCT-SEE CS
                               ETF  40 vGppeaeea....lrealaamGadkv 61 
                                       +Gp+  +++    ++e+l+ mGad v
  gi|330508967|ref|YP_004385395.1|  88 LGPDPNNKVqvclVEECLK-MGADAV 112
                                       6887777777794555666.****87 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.24
                                       CCCE-HHHHHHHHHHHHHHHHHT-- CS
                               ETF  10 dgklnpvdlealeaArrlkekagge 34 
                                       +++ np+d e ++ A r  +++g++
  gi|330508967|ref|YP_004385395.1| 153 KNIANPNDVEVVAHAARAGAELGAD 177
                                       6889999999999999987766655 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00043
                                       T--EEEEEEES....S-......CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHHHHHHHC CS
                               ETF  32 ggevtavvvGppeaeea......lrealaamGadkvilvddpalagydaeatakalaalikke 88 
                                       g++v +v++G p++e+       ++ al+  Ga + + +    +++ d+ ++++a+aa+++k 
  gi|330508967|ref|YP_004385395.1| 196 GCPVPVVIAGGPKTETDmeflkmIEGALQ-AGA-RGVAIGRNVFQHKDPVKMTRAIAAIVNKG 256
                                       6889999***9999988999886667777.999.999***********************996 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       1.6   4.8e+03      73      87 ..     100     114 ..      95     127 .. 0.67
   2 ?   11.7   0.0   3.5e-05      0.11     180     234 ..     192     253 ..     160     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.6
                            DUF561  73 llleavkaGadlvei 87 
                                       l+ e+ k Gad v i
  gi|330508967|ref|YP_004385395.1| 100 LVEECLKMGADAVSI 114
                                       455677777776655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.5e-05
                            DUF561 180 eiskkvslPvicasGlsdvt.......vplalslgasGiGigsavsklndeeemvallseik 234
                                       +++k   +Pv+ a G ++ t       ++ al++ga G+ ig++v + +d ++m  ++  i 
  gi|330508967|ref|YP_004385395.1| 192 KVVKGCPVPVVIAGGPKTETdmeflkmIEGALQAGARGVAIGRNVFQHKDPVKMTRAIAAIV 253
                                       5667777777777776554432232225669************************9998876 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 ?   12.1   0.1   3.6e-05      0.11     116     224 ..     142     248 ..      40     249 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
                                       EEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCCHTHHHHHHTTCSCEEEHHHTT...EEEEECTTC CS
                         OMPdecase 116 llilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqetlnateedaddfihltpgigl...eqggdgkgq 189
                                       + ++a+m   g+        + ++v +a+++ ae    G+   +t      d d f ++++g+ +        ++g 
  gi|330508967|ref|YP_004385395.1| 142 MPLVAMMYPRGKNIANP--NDVEVVAHAARAGAE---LGADIIKTNY--TGDPDSFRKVVKGCPVpvvI----AGGP 207
                                       55666666666665555..556666666666656...5666666633..344679*********95552....4444 PP

                                       CGGG......HHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 190 qynt......pekligiagadiiivGRgIlkagdpveeaer 224
                                       + +t      + + + +aga  + +GR +++ +dpv+ +++
  gi|330508967|ref|YP_004385395.1| 208 KTETdmeflkMIEGALQAGARGVAIGRNVFQHKDPVKMTRA 248
                                       4443111111333445699*****************98876 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.57   1.7e+03     150     172 ..      48      71 ..      37      88 .. 0.75
   2 ?   11.2   1.3   5.8e-05      0.17     180     227 ..     185     238 ..      96     261 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.57
                               NMO 150 rkvearGaDalivq.GpeaGGhqG 172
                                        kv++ Ga a+  q G+   Gh+G
  gi|330508967|ref|YP_004385395.1|  48 NKVAKGGANAVLQQkGMVRHGHRG 71 
                                       678888888888655999999999 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.8e-05
                               NMO 180 glfaLvpqvldavdiPviAaGGiidrrg......vaaaLalGAsgvqigtrfLl 227
                                       g      +v++   +Pv+ aGG  ++ +      ++ aL +GA gv+ig     
  gi|330508967|ref|YP_004385395.1| 185 GDPDSFRKVVKGCPVPVVIAGGPKTETDmeflkmIEGALQAGARGVAIGRNVFQ 238
                                       44444455666666********888866444444789************76655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1437.09
//
Query:       gi|330508968|ref|YP_004385396.1|  [L=173]
Description: hypothetical protein MCON_3322 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.078   11.9   0.0      0.087   11.7   0.0    1.1  1  Glyco_hydro_125  Metal-independent alpha-mannosidase (GH125)


Domain annotation for each model (and alignments):
>> Glyco_hydro_125  Metal-independent alpha-mannosidase (GH125)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.9e-06     0.087     222     292 ..      35     109 ..       9     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.9e-06
                                       SSE.EHHHHHHHHHHHHHHHHHHHHTS--....HHHHHHHHHHHHHHHHHHHSEEEETTTEEEE-SEE-SSS-EE CS
                   Glyco_hydro_125 222 fqf.lipaNmmlaveLeklaeileklaeke...lakearklakeiregiekhavvehkkfgkiyAyEvDGyGsal 292
                                       fq+ ++paN+++  +L ++   +++++++e      + r+ ++ i++ i+k  +++ ++  ++  yEvDG  + l
  gi|330508968|ref|YP_004385396.1|  35 FQYeITPANIIIDDKLGQIILEVHQMSTAEpmdEPISERDQSTGIEHCIQKSDMIHGSREMTMKEYEVDGHDGVL 109
                                       7773469***********98888878777774433344677889**************************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 953.36
//
Query:       gi|330508969|ref|YP_004385397.1|  [L=140]
Description: hypothetical protein MCON_3324 [Methanosaeta concilii GP6]
Scores for complete 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-17   62.6   0.0    6.7e-17   62.2   0.0    1.1  1  GyrI-like       GyrI-like small molecule binding domain
    2.1e-07   31.2   0.0    2.7e-07   30.9   0.0    1.1  1  Cass2           Integron-associated effector binding protein
  ------ inclusion threshold ------
       0.05   14.0   0.0      0.075   13.4   0.0    1.3  1  Minor_capsid_3  Minor capsid protein from bacteriophage
       0.15   12.1   0.0       0.19   11.7   0.0    1.3  1  DUF5016         Domain of unknown function (DUF5016)


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 !   62.2   0.0   1.5e-20   6.7e-17       7     140 ..       3     135 ..       1     139 [. 0.90

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.5e-20
                                       EE--EEEEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHCTT--SSEEEEEEEEE-....STTCCCEEEEEEEECCCCC CS
                         GyrI-like   7 elpafrvvgirhrgdyneeggipklweelyawaseiklsnavspligvssdepe....etedeelkydigvtveirv 79 
                                       + +++ v+g+r++g y+e   i+++ ++l++ a++ k   +++pl+       e    ++e++  + +++v + ++ 
  gi|330508969|ref|YP_004385397.1|   3 DEKPQLVAGMRRKGHYRE---IAEMLASLFEYAMSCKAIIVGHPLFLYHEKSVEeakrADEAGNADIEVCVPILKNI 76 
                                       668999************...*****************9766666655544433566799***************** PP

                                       CGBTTSEEEEE-SEEEEEEEEECEGGGHHHHHHHHHHTHHHHTT-EEEESEEEEEEECCCT CS
                         GyrI-like  80 egpeglefleipageyAvfrhkGpyddlqatyaklygewlpesgyerrdgpsiEiYlsdpr 140
                                       +++ ++  +e+ +g++A+  hkGpy +++ ty +l+  wl +++   + gp +E Y +dp 
  gi|330508969|ref|YP_004385397.1|  77 PENDMIRCYELAGGKMAKTVHKGPYQECESTYMELFD-WLQKNNH-KIIGPIREGYVNDPS 135
                                       *************************************.*******.*************96 PP

>> Cass2  Integron-associated effector binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   6.1e-11   2.7e-07       8     132 ..       7     129 ..       2     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 6.1e-11
                                       EEEEEEEEETTCCCCH...HHHHHHHHHHHHHHHCTTSBSTEEEEEEEC-TT.......-CCGEEEEEEEEE-TTSS CS
                             Cass2   8 ftvaGiryegskeeedlnkeigklwreflekgrlkkikkdkrvfgiyhdyes.......eenkfsyyagvevpsdse 77 
                                       + vaG+r+ g ++e    +++  l++  ++   +k i+  +  + +yh+          e+++ +++++v++ ++  
  gi|330508969|ref|YP_004385397.1|   7 QLVAGMRRKGHYREIA--EMLASLFEYAMS---CKAII-VGHPLFLYHEKSVeeakradEAGNADIEVCVPILKNIP 77 
                                       5678888888777773..555555555555...44443.33333333333323556778***************999 PP

                                       S-TT-EEEEE--EEEEEEEEESSSTT-HHHHHHHHHHCHCCHCTEEE-SSEEEEE CS
                             Cass2  78 vpeglvkkeiPggkYavftiegdfeedlaeaweaiygellpnsnyerrggpdfEv 132
                                        +++++  e+ ggk+a++ ++g+ +e  + ++ +++ +l++n++     gp  E 
  gi|330508969|ref|YP_004385397.1|  78 ENDMIRCYELAGGKMAKTVHKGPYQE-CESTYMELFDWLQKNNHKII--GPIREG 129
                                       9999*********************8.*************9877554..455555 PP

>> Minor_capsid_3  Minor capsid protein from bacteriophage
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.7e-05     0.075      10      53 ..      57     102 ..      51     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                    Minor_capsid_3  10 vlkeignldlklritalke..kdesivvlalpgssnkkeymDGtke 53 
                                       +  e+gn+d+++ + +lk+  +++ i+ ++l+g++  k+++ G ++
  gi|330508969|ref|YP_004385397.1|  57 RADEAGNADIEVCVPILKNipENDMIRCYELAGGKMAKTVHKGPYQ 102
                                       667899************99999******************99765 PP

>> DUF5016  Domain of unknown function (DUF5016)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.3e-05      0.19      70     105 ..      46      80 ..      29      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                           DUF5016  70 lfdeesvseevirtktsGtytgaifvPlykniPdGk 105
                                       l+ e+sv ee  r+   G  + ++ vP++kniP+ +
  gi|330508969|ref|YP_004385397.1|  46 LYHEKSV-EEAKRADEAGNADIEVCVPILKNIPEND 80 
                                       5555555.6788*********************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 782.36
//
Query:       gi|330508970|ref|YP_004385398.1|  [L=201]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (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  109.2   0.0    1.9e-31  108.8   0.0    1.1  1  DDE_3     DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.063   13.5   0.0       0.12   12.5   0.0    1.5  1  rve_2     Integrase core domain
       0.11   12.3   0.3        2.3    8.1   0.0    2.5  3  rve_3     Integrase core domain


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8   0.0   3.2e-35   1.9e-31      15     145 ..      10     171 ..       2     172 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 3.2e-35
                             DDE_3  15 vrrrawakkGkrer.leeygrrgrvnligaldekgglaf.vtfeetlnaedfaeflerlletalqakkivlilDnas 89 
                                         +  ++ +Gk er ++ey+r+g++++i+++ +++g++  + + +t+n++df+ ++++++e+ l+  +++++ Dn++
  gi|330508970|ref|YP_004385398.1|  10 KHPGLPMAPGKVERrEFEYIRHGTQSFIVSFAVANGKVDtISCGDTRNEDDFVSHIKEVVERSLSTSRWHFVADNLN 86 
                                       5666799********************************99************************************ PP

                             DDE_3  90 iHkseslrelveee.............................adrlellylPpySPelNpiEivwsklkrellkrr 137
                                       iHksesl+++v++                              +++++++y+P ++++ N++Ei++s+l+r+ll+r+
  gi|330508970|ref|YP_004385398.1|  87 IHKSESLVRYVADVsdldidlgikgrdgilksietresfladpSHSIVFHYTPIHASWMNQVEIWFSILVRKLLRRA 163
                                       ***************************************************************************** PP

                             DDE_3 138 sfksldeL 145
                                       sf s+ +L
  gi|330508970|ref|YP_004385398.1| 164 SFASINDL 171
                                       ****9998 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     2e-05      0.12       3      36 ..     151     184 ..     149     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
                             rve_2   3 fFgsLKtElvygetfktleeleaaiedYIewYNn 36 
                                        F +L ++l++ + f++++ l+a++  ++e++N+
  gi|330508970|ref|YP_004385398.1| 151 WFSILVRKLLRRASFASINDLNAKVLAFVEYFNK 184
                                       699999***************************7 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.04   2.4e+02       5      21 ..       7      23 ..       4      29 .. 0.88
   2 ?   -3.4   0.0       1.5   8.9e+03      19      33 ..      69      83 ..      67      93 .. 0.65
   3 ?    8.1   0.0   0.00038       2.3      24      55 ..     153     184 ..     131     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.04
                             rve_3  5 lsyiapgkPqqNglvEs 21
                                      l++ +pg P+  g+vE+
  gi|330508970|ref|YP_004385398.1|  7 LERKHPGLPMAPGKVER 23
                                      56789***********9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                             rve_3 19 vEsfngtlrdellne 33
                                      vE++  t r +++  
  gi|330508970|ref|YP_004385398.1| 69 VERSLSTSRWHFVAD 83
                                      677777766666554 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00038
                             rve_3  24 gtlrdellneelfrslaearekleawredYNt 55 
                                         l ++ll + +f s++++++k+ a++e++N+
  gi|330508970|ref|YP_004385398.1| 153 SILVRKLLRRASFASINDLNAKVLAFVEYFNK 184
                                       556678899999*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1400.33
//
Query:       gi|330508971|ref|YP_004385399.1|  [L=85]
Description: hypothetical protein MCON_3326 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 627.03
//
Query:       gi|330508972|ref|YP_004385400.1|  [L=374]
Description: transposase, Mutator family [Methanosaeta concilii GP6]
Scores for complete 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-105  352.7   1.9   2.6e-105  352.4   1.9    1.0  1  Transposase_mut  Transposase, Mutator family
    4.9e-08   33.3   0.1    1.3e-07   31.9   0.0    1.8  2  MULE             MULE transposase domain
  ------ inclusion threshold ------
      0.016   14.9   0.2      0.041   13.6   0.2    1.7  1  DDE_Tnp_ISL3     Transposase
        0.4   11.3   4.9        3.1    8.5   0.1    3.7  4  DUF5499          Family of unknown function (DUF5499)


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 !  352.4   1.9  5.8e-109  2.6e-105      21     380 ..      13     365 ..       2     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 352.4 bits;  conditional E-value: 5.8e-109
                   Transposase_mut  21 gkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspalleryk 97 
                                       + ++ +k+l+  +l+e+++ e++++++a  yer+++r+ +RnG r+rkl+T +g++el  P+ R+  F++a++er+ 
  gi|330508972|ref|YP_004385400.1|  13 DRKEGMKKLTAGFLNEVMQLEAENQIQARPYERTGKRRAHRNGTRSRKLKTIYGEIELDKPQIREFPFETAVFERFS 89 
                                       4568999********************************************************************** PP

                   Transposase_mut  98 RrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkv 174
                                       R e+ l  +v+e y +Gvstrkvek++ +++  k++S+sevS+i+k+ld+ v+ f +R++e +  p++f+Da y kv
  gi|330508972|ref|YP_004385400.1|  90 RVEDSLRVAVAESYFEGVSTRKVEKVFSKFGL-KNISASEVSRIAKKLDKLVKDFLNRPIEGS-IPYIFVDASYFKV 164
                                       *******************************9.88****************************.************* PP

                   Transposase_mut 175 ReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaa 251
                                       R +gr v+ka l+ ++++ dG+reiL+ +v+dsE+e+ W++ +esLk+rGlkgv+lv+sDahkG+++a++++f +a+
  gi|330508972|ref|YP_004385400.1| 165 RTDGRYVNKALLVVVAIHDDGYREILSATVDDSEDESCWENCFESLKARGLKGVKLVISDAHKGIQAAVQKSFLGAS 241
                                       ***************************************************************************** PP

                   Transposase_mut 252 vQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaedvlaflafpe 328
                                       +Q C vH++r +l+++pkk++++va +lk    a + e   ++l+ +l+   k ++k a+++d+ + d+ ++ +fp+
  gi|330508972|ref|YP_004385400.1| 242 WQMCNVHFMRAVLKNIPKKEKKEVAYMLKD---AIEDEFKMQELAVILD--DKGFKKSADTIDSFRFDLWNYKSFPR 313
                                       ****************************95...6677888889999998..56899********************* PP

                   Transposase_mut 329 qirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                        ++++i++tN+lEr+Nke++Rr+rv g + n++s+lr+ + ++++ +++w++
  gi|330508972|ref|YP_004385400.1| 314 SHWKRIRTTNVLERINKELKRRSRVAGAYSNDQSLLRVAVCIMMDINEDWIT 365
                                       **************************************************86 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0     3e-11   1.3e-07      14      95 ..     172     251 ..     154     252 .. 0.87
   2 ?   -3.6   0.0       3.6   1.6e+04      61      70 ..     351     360 ..     341     364 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3e-11
                              MULE  14 klplltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlCl 90 
                                       +  ll vv+++d g   +l  ++ +se+e+++e  +++l+++    +  k +i+D +k+++ a+++ f +a  ++C 
  gi|330508972|ref|YP_004385400.1| 172 NKALLVVVAIHDDGYREILSATVDDSEDESCWENCFESLKARGL--KGVKLVISDAHKGIQAAVQKSFLGASWQMCN 246
                                       56789999********************************9644..69***************************** PP

                              MULE  91 fHiak 95 
                                        H+++
  gi|330508972|ref|YP_004385400.1| 247 VHFMR 251
                                       ***96 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.6
                              MULE  61 spkviitDke 70 
                                         ++i++D +
  gi|330508972|ref|YP_004385400.1| 351 VAVCIMMDIN 360
                                       4578888865 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   9.1e-06     0.041      23     105 ..     183     268 ..     162     351 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.1e-06
                      DDE_Tnp_ISL3  23 vdg.grlldilpg..RkketlkafleslsekerekveavvmDmsaayksavkealPnAkivvDrFHvvklanealde 96 
                                        dg +++l ++ +   ++++ ++++esl+++  + v+ v+ D ++++++av++ +  A+  + + H+++ + + + +
  gi|330508972|ref|YP_004385400.1| 183 DDGyREILSATVDdsEDESCWENCFESLKARGLKGVKLVISDAHKGIQAAVQKSFLGASWQMCNVHFMRAVLKNIPK 259
                                       3446677666544115667889*******9***************************************99998877 PP

                      DDE_Tnp_ISL3  97 vRrreqkel 105
                                         ++e+  +
  gi|330508972|ref|YP_004385400.1| 260 KEKKEVAYM 268
                                       766666555 PP

>> DUF5499  Family of unknown function (DUF5499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.7   3.1e+03       9      25 ..      37      53 ..      33      68 .. 0.74
   2 ?    8.5   0.1   0.00069       3.1      25      64 ..     113     152 ..      94     187 .. 0.83
   3 ?    1.9   0.0     0.076   3.4e+02      29      54 ..     199     224 ..     179     238 .. 0.78
   4 ?   -1.0   0.3      0.63   2.8e+03      36      61 ..     310     333 ..     276     346 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.7
                           DUF5499  9 dlkvrdydyfgkrkapd 25
                                      +++ r y+  gkr+a  
  gi|330508972|ref|YP_004385400.1| 37 QIQARPYERTGKRRAHR 53
                                      57789999999999864 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00069
                           DUF5499  25 dgvshkdmvenifrsdkwrrmkgidsevkdelnrqlrgev 64 
                                       + v  k  ++ni  s+  r  k +d  vkd lnr + g +
  gi|330508972|ref|YP_004385400.1| 113 EKVFSKFGLKNISASEVSRIAKKLDKLVKDFLNRPIEGSI 152
                                       4556677789*************************99987 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.076
                           DUF5499  29 hkdmvenifrsdkwrrmkgidsevkd 54 
                                        +   en f s k r +kg+   + d
  gi|330508972|ref|YP_004385400.1| 199 DESCWENCFESLKARGLKGVKLVISD 224
                                       556779*************9877666 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.63
                           DUF5499  36 ifrsdkwrrmkgidsevkdelnrqlr 61 
                                        f   +w+r++  +  v + +n++l+
  gi|330508972|ref|YP_004385400.1| 310 SFPRSHWKRIRTTN--VLERINKELK 333
                                       45566788877643..3344444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 2847.03
//
Query:       gi|330508973|ref|YP_004385401.1|  [L=252]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-22   77.5   1.1    1.1e-21   76.5   0.1    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.6e-07   31.5   0.5    2.6e-07   30.9   0.5    1.3  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
       0.12   12.4   1.2       0.26   11.3   1.2    1.7  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.15   11.9   2.8       0.27   11.1   2.8    1.3  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.98    9.3   4.9        1.6    8.6   4.9    1.3  1  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
        1.3    9.2   5.2         12    5.9   0.0    2.3  3  DUF4337         Domain of unknown function (DUF4337)


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 ?   -1.5   0.1      0.82   2.5e+03      47      47 ..      86      86 ..      52     108 .. 0.61
   2 !   76.5   0.1   3.7e-25   1.1e-21       1      67 [.     154     218 ..     154     219 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.82
                    OrfB_Zn_ribbon 47 f 47
                                       
  gi|330508973|ref|YP_004385401.1| 86 R 86
                                      0 PP

  == domain 2  score: 76.5 bits;  conditional E-value: 3.7e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       f++lke+l+yka  +G+++++v+pa TS+tC++Cg+ + +  +g+ fkCp Cg + d+D+n+a Ni+
  gi|330508973|ref|YP_004385401.1| 154 FYQLKEFLSYKALAAGVPLVQVDPACTSQTCHQCGEHGIR--NGKSFKCPVCGWSGDADFNGAKNIA 218
                                       899*************************************..************************7 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.5   8.7e-11   2.6e-07      10     106 ..      27     121 ..      18     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 8.7e-11
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn..ykkasrklarlhrkr 84 
                                       +++    +++g+DlGi ++a++++++     + g+ +k  +  +a  +a lq+k+ k ++  ++++++ ++rl+ k 
  gi|330508973|ref|YP_004385401.1|  27 PEQIHVDTVLGVDLGITDIAVTSEGQ----KFGGKTIKLIKNHYASMRAVLQQKAVKGTRssRRRCRELQQRLSGKE 99 
                                       566667789****************9....78999999999***********9998888889*************** PP

                        OrfB_IS605  85 srrrkhllhklathliktlkev 106
                                       +r  +   h+++++++ + +e+
  gi|330508973|ref|YP_004385401.1| 100 ARYQRQINHEISKAIVTRAQEI 121
                                       ****************999987 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   1.2   8.7e-05      0.26      64      95 ..     175     206 ..     108     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.7e-05
                                       EEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  64 ieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       ++    + +C++Cg+++  + k+++Cp Cg +
  gi|330508973|ref|YP_004385401.1| 175 VDPACTSQTCHQCGEHGIRNGKSFKCPVCGWS 206
                                       555566789*****9998777789*****965 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 ?   11.1   2.8   8.9e-05      0.27      20      43 ..     179     203 ..     172     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.9e-05
                                       EEEEEE-HHHHHHHHH..TT-B-TTT CS
                        zf-C3HC4_3  20 CgHlvlCeeCaekllk..rkkkCpiC 43 
                                       C  + +C++C e+  +  ++ kCp+C
  gi|330508973|ref|YP_004385401.1| 179 CTSQ-TCHQCGEHGIRngKSFKCPVC 203
                                       7778.9*******99999******** PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.9   0.00054       1.6      17      40 .]     178     203 ..     171     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00054
                        zf-C3HC4_2  17 pCgHvfCqkCilrsLeekn..eCPlC 40 
                                       +C  ++C +C    +++++  +CP+C
  gi|330508973|ref|YP_004385401.1| 178 ACTSQTCHQCGEHGIRNGKsfKCPVC 203
                                       6999*********99998889***** PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       4.5   1.3e+04      79      93 ..      12      26 ..       8      29 .. 0.63
   2 ?    4.8   1.3    0.0091        27      46     105 ..      60     123 ..      57     132 .. 0.76
   3 ?    5.9   0.0    0.0041        12      25      47 ..     137     159 ..     125     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.5
                           DUF4337 79 iakykkkiarykkek 93
                                       a++++k+ ry++e 
  gi|330508973|ref|YP_004385401.1| 12 SANFTAKMIRYQSEA 26
                                      456666777777664 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0091
                           DUF4337  46 ksikehlaeleleqlelllkakaeelaaavdkkiakykkkiarykke.....kkeikkkAkelea 105
                                       k ik+h a++ +  l+ ++ ++++  +++ ++ +++++ k ary+++     +k+i ++A+e+ a
  gi|330508973|ref|YP_004385401.1|  60 KLIKNHYASM-RAVLQQKAVKGTRSSRRRCRELQQRLSGKEARYQRQinheiSKAIVTRAQEIPA 123
                                       5578888888.4444444444499999999****************9877777777778888765 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0041
                           DUF4337  25 aqteailaqaeasdqWafYQAks 47 
                                       ++++a  ++ + ++ WafYQ k+
  gi|330508973|ref|YP_004385401.1| 137 VNQKAGKNHRRRVNGWAFYQLKE 159
                                       5677888899**********886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1959.21
//
Query:       gi|330508974|ref|YP_004385402.1|  [L=349]
Description: hypothetical protein MCON_3328 [Methanosaeta concilii GP6]
Scores for complete 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   16.9   0.0       0.33   10.2   0.1    2.4  2  NosD      Periplasmic copper-binding protein (NosD)


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 !   10.2   0.1   1.8e-05      0.33      51      91 ..     145     186 ..     111     241 .. 0.59
   2 !    3.7   0.0    0.0017        30      25      82 ..     243     301 ..     231     334 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 1.8e-05
                              NosD  51 itgntienl.ryGihlensesntiedntlssnesGialmsss 91 
                                       +   + +n+ ++G +l++++++ + d+ + ++++G++l+ ++
  gi|330508974|ref|YP_004385402.1| 145 VFSVVAQNCgAEGFMLDTCHNSHVLDCAAWHCREGLCLHGNN 186
                                       222244444677777777777777777777777777776655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0017
                              NosD  25 egseisnneisnsrdgi..lldnssnntitgntienlryGihlensesntiedntlssne 82 
                                       + s+++n + ++ ++g   ++++ss + + ++++e    Gih ++ +++ ++++ l   +
  gi|330508974|ref|YP_004385402.1| 243 RRSVLKNDKAKTDSTGGatYIYESSRVLFDDCQLEGF-FGIHAVGRSHVEAKNCRLVAPG 301
                                       5567777788777777789*************99888.**********999999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2547.06
//
Query:       gi|330508975|ref|YP_004385403.1|  [L=360]
Description: transposase, IS605 OrfB family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-16   59.2   3.4    2.8e-16   59.2   3.4    2.3  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    1.4e-08   34.9   0.8    2.8e-08   34.0   0.8    1.4  1  OrfB_IS605       Probable transposase
     0.0015   17.8   9.3       0.23   10.9   5.3    3.4  2  zf-ribbon_3      zinc-ribbon domain
  ------ inclusion threshold ------
       0.03   14.3   6.2       0.37   10.8   0.8    2.7  2  zf-C2HC5         Putative zinc finger motif, C2HC5-type
       0.03   14.3   0.2       0.03   14.3   0.2    2.0  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.15   11.9   0.1       0.23   11.2   0.1    1.2  1  DASH_Spc34       DASH complex subunit Spc34
       0.15   11.8  11.4        2.2    8.1   0.5    3.4  3  zinc_ribbon_2    zinc-ribbon domain
        1.1    8.8   7.9        1.5    8.4   0.0    3.5  3  TF_Zn_Ribbon     TFIIB zinc-binding
        2.4    8.3  11.2        1.2    9.2   0.6    3.3  3  UPF0547          Uncharacterised protein family UPF0547
        2.9    8.0  13.6       0.21   11.6   2.5    2.8  2  DZR              Double zinc ribbon


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   1.8       5.3   9.5e+03      33      51 ..     112     127 ..     103     131 .. 0.71
   2 ?   -3.7   0.2       6.5   1.2e+04      29      36 ..     138     145 ..     137     155 .. 0.67
   3 !   59.2   3.4   1.6e-19   2.8e-16       9      67 ..     265     323 ..     263     324 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.3
                    OrfB_Zn_ribbon  33 eCgsknkealsgrtfkCpn 51 
                                       +C + +++   +r+++C +
  gi|330508975|ref|YP_004385403.1| 112 RCCYSQER---RREMVCHS 127
                                       45555555...89999975 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.5
                    OrfB_Zn_ribbon  29 ktCseCgs 36 
                                         C+ Cg+
  gi|330508975|ref|YP_004385403.1| 138 VFCAFCGE 145
                                       55777776 PP

  == domain 3  score: 59.2 bits;  conditional E-value: 1.6e-19
                    OrfB_Zn_ribbon   9 eykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                        yka+ + +k+++v+ + T ++Cs Cgs++k++ls r+++Cp Cgf++drD+ A++Nil
  gi|330508975|ref|YP_004385403.1| 265 TYKAQSADRKLIKVDHRDTTQRCSACGSIVKKDLSVRVHECPYCGFSCDRDYDASRNIL 323
                                       69********************************************************7 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.8   1.5e-11   2.8e-08      64     117 ..     172     225 ..     167     227 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.5e-11
                        OrfB_IS605  64 lkksknykkasrklarlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       + +++nyk  + k+a+lh++++++r+++l kl++  +++ + + ve+L+++++k
  gi|330508975|ref|YP_004385403.1| 172 QRRANNYKSLKDKIAKLHKRINCQRDDFLYKLSRTYVNKFYIICVEDLDIKGLK 225
                                       6789***********************************************998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.1     0.005       8.9      17      26 .]     138     147 ..     136     147 .. 0.86
   2 !   10.9   5.3   0.00013      0.23       2      23 ..     284     309 ..     283     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.005
                       zf-ribbon_3  17 nvCpyCGtkl 26 
                                       ++C+ CG++l
  gi|330508975|ref|YP_004385403.1| 138 VFCAFCGEPL 147
                                       69*****987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                       zf-ribbon_3   2 tvrCPnCGaplssddnv....CpyCG 23 
                                       t+rC++CG+++++d +v    CpyCG
  gi|330508975|ref|YP_004385403.1| 284 TQRCSACGSIVKKDLSVrvheCPYCG 309
                                       78*******889987777777****9 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 ?    5.5   0.5    0.0091        16      36      48 ..     139     151 ..     122     158 .. 0.76
   2 ?   10.8   0.8   0.00021      0.37      17      41 ..     284     309 ..     274     315 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0091
                          zf-C2HC5  36 pCsfCgspllsse 48 
                                        C fCg+pl s+ 
  gi|330508975|ref|YP_004385403.1| 139 FCAFCGEPLCSDP 151
                                       5999999999854 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00021
                          zf-C2HC5  17 apnClnCGkiiCakegls.kpCsfCg 41 
                                       +  C +CG i+ +   +  ++C++Cg
  gi|330508975|ref|YP_004385403.1| 284 TQRCSACGSIVKKDLSVRvHECPYCG 309
                                       678********98888889******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 ?   -4.0   2.1         8   1.4e+04      67      94 ..     134     145 ..     110     152 .. 0.55
   2 ?   14.3   0.2   1.7e-05      0.03      53     110 ..     267     327 ..     240     329 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 8
                                       E--EEEETTTS-EEECHHHHHS-TTTSS CS
                              HypA  67 vpvkvrCreCgkefeleekalrCpkCgs 94 
                                       + ++v                 C  Cg+
  gi|330508975|ref|YP_004385403.1| 134 IILSV----------------FCAFCGE 145
                                       22233................4555554 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.7e-05
                                       CC.TTTT-EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSSS.-EEEEESSSEEEEEE CS
                              HypA  53 egtvlegaeLeieevpvkvrCreCgkefeleek..alrCpkCgsa.dveivsGeellvksi 110
                                       + + ++++ +++++ + + rC+ Cg+ ++++ +    +Cp Cg + d +  + +++l++ +
  gi|330508975|ref|YP_004385403.1| 267 KAQSADRKLIKVDHRDTTQRCSACGSIVKKDLSvrVHECPYCGFScDRDYDASRNILITGM 327
                                       45556777789999***********9999776334679****9664777777777777665 PP

>> DASH_Spc34  DASH complex subunit Spc34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00013      0.23     171     208 ..     162     199 ..     155     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                        DASH_Spc34 171 yplleakekieelreeYeelseeieeleaeiaeQkkqL 208
                                       y l++  + i++  ++Y++l+++i++l+++i+ Q++++
  gi|330508975|ref|YP_004385403.1| 162 YSLPGLTHIIQRRANNYKSLKDKIAKLHKRINCQRDDF 199
                                       8888889999999*********************9986 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.5    0.0013       2.2      14      23 .]     138     147 ..     137     147 .. 0.90
   2 ?    3.5   0.2     0.036        64      10      21 ..     281     292 ..     279     294 .. 0.78
   3 ?    3.5   5.3     0.034        61       2      21 ..     287     310 ..     286     311 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                     zinc_ribbon_2  14 kFCpyCGtpl 23 
                                       +FC  CG+pl
  gi|330508975|ref|YP_004385403.1| 138 VFCAFCGEPL 147
                                       8*******97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.036
                     zinc_ribbon_2  10 qdnakFCpyCGt 21 
                                        d+ + C+ CG+
  gi|330508975|ref|YP_004385403.1| 281 RDTTQRCSACGS 292
                                       677888999996 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.034
                     zinc_ribbon_2   2 CpnCGaelq.d.nakF..CpyCGt 21 
                                       C+ CG  ++ d  ++   CpyCG+
  gi|330508975|ref|YP_004385403.1| 287 CSACGSIVKkDlSVRVheCPYCGF 310
                                       777777774365555577*****7 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.8      0.48   8.5e+02      21      27 ..     139     145 ..     137     152 .. 0.83
   2 ?    8.4   0.0   0.00081       1.5      12      32 ..     277     297 ..     272     300 .. 0.84
   3 ?    2.2   0.5     0.072   1.3e+02       2      10 ..     304     312 ..     303     323 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.48
                                       EESSSSB CS
                      TF_Zn_Ribbon  21 vCtdCGl 27 
                                       +C +CG+
  gi|330508975|ref|YP_004385403.1| 139 FCAFCGE 145
                                       7999996 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00081
                                       HEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon  12 veDpergelvCtdCGlVledn 32 
                                        +D+  ++ +C++CG+++  +
  gi|330508975|ref|YP_004385403.1| 277 KVDHRDTTQRCSACGSIVKKD 297
                                       689999999*******99865 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.072
                                       EETTTTCEE CS
                      TF_Zn_Ribbon   2 kCPnCgstn 10 
                                        CP+Cg + 
  gi|330508975|ref|YP_004385403.1| 304 ECPYCGFSC 312
                                       5****9665 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.7     0.054        97      15      21 ..     138     144 ..     137     144 .. 0.89
   2 ?    1.3   0.1      0.21   3.8e+02      14      21 ..     284     291 ..     283     293 .. 0.90
   3 ?    9.2   0.6    0.0007       1.2      11      23 ..     299     311 ..     295     312 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.054
                           UPF0547  15 qfCphCG 21 
                                       +fC++CG
  gi|330508975|ref|YP_004385403.1| 138 VFCAFCG 144
                                       69****9 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.21
                           UPF0547  14 aqfCphCG 21 
                                       +q+C+ CG
  gi|330508975|ref|YP_004385403.1| 284 TQRCSACG 291
                                       699****9 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0007
                           UPF0547  11 PvaaqfCphCGyv 23 
                                       +v + +Cp+CG++
  gi|330508975|ref|YP_004385403.1| 299 SVRVHECPYCGFS 311
                                       667889*****97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   3.0      0.19   3.3e+02      13      23 ..     138     148 ..     103     161 .. 0.71
   2 ?   11.6   2.5   0.00012      0.21      10      39 ..     282     313 ..     262     318 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.19
                               DZR  13 rfCseCgtklk 23 
                                        fC  Cg++l 
  gi|330508975|ref|YP_004385403.1| 138 VFCAFCGEPLC 148
                                       36777777765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00012
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvd 39 
                                       +  + Cs+Cg+ +k+  +   + Cp Cg ++d
  gi|330508975|ref|YP_004385403.1| 282 DTTQRCSACGSIVKKDLSvrVHECPYCGFSCD 313
                                       44556667776666554466666777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2624.18
//
Query:       gi|330508976|ref|YP_004385404.1|  [L=75]
Description: TRAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-12   46.0   0.7    4.3e-12   45.8   0.7    1.1  1  TRAM      TRAM domain
  ------ inclusion threshold ------
      0.079   12.9   0.0        0.1   12.6   0.0    1.3  1  Exc       Excisionase-like protein


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.7   4.8e-16   4.3e-12       2      61 ..      19      74 ..      18      75 .] 0.95

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.8e-16
                                      XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM  2 syvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61
                                      ++vG +++V +e+ + +eg+gi+r++ g+v+fv +++   Gd + ++I+kv r+++ G+ 
  gi|330508976|ref|YP_004385404.1| 19 VEVGGEYDVHIEDIA-REGDGIARVE-GFVIFVADTKV--GDDARIQIDKVMRRFAIGHK 74
                                      689***********9.**********.*********99..****************9986 PP

>> Exc  Excisionase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.1e-05       0.1      27      59 ..      10      42 ..       8      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                                      HTT-EES--EEETTEEEEETT-EE--SSX.... CS
                               Exc 27 reglitPaPvkdGreylveedavkvelerlprv 59
                                      r +l  PaPv  G ey v+ + + +e + + rv
  gi|330508976|ref|YP_004385404.1| 10 RSSLSAPAPVEVGGEYDVHIEDIAREGDGIARV 42
                                      667889********************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 526.03
//
Query:       gi|330508977|ref|YP_004385405.1|  [L=75]
Description: TRAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-13   49.3   0.7    4.2e-13   49.1   0.7    1.1  1  TRAM          TRAM domain
  ------ inclusion threshold ------
      0.092   12.4   0.0       0.11   12.2   0.0    1.1  1  ChitinaseA_N  Chitinase A, N-terminal 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 !   49.1   0.7   4.7e-17   4.2e-13       3      61 ..      20      74 ..      18      75 .] 0.95

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 4.7e-17
                                      XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM  3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61
                                       vG +++V++e+ + +eg+gi+r+d g+v+fv +++   Gd + V+I+kv r+++ G+ 
  gi|330508977|ref|YP_004385405.1| 20 AVGGEYDVKIEDIA-REGDGIARVD-GFVIFVADTNV--GDDARVQIDKVMRRFAIGHK 74
                                      6999*********9.**********.***********..****************9986 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 ?   12.2   0.0   1.2e-05      0.11      67     112 ..       7      54 ..       3      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.2e-05
                      ChitinaseA_N  67 gaasakesatfkvkkgGryqleve..lCdaeGCsksapkeivvaDtDG 112
                                       g+++  +   + v  gG+y++++e  + +++G ++ +   i vaDt+ 
  gi|330508977|ref|YP_004385405.1|   7 GSSNGGSAPAVPVAVGGEYDVKIEdiAREGDGIARVDGFVIFVADTNV 54 
                                       55554455588999*********93334667799************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 561.08
//
Query:       gi|330508978|ref|YP_004385406.1|  [L=301]
Description: NOL1/NOP2/sun family RNA methylase [Methanosaeta concilii GP6]
Scores for complete 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  177.8   0.0    2.5e-52  177.4   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    6.3e-06   26.6   0.0      1e-05   25.9   0.0    1.4  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
    4.4e-05   24.1   0.0     0.0014   19.2   0.0    2.2  2  Methyltransf_25  Methyltransferase domain
    0.00063   19.9   0.0     0.0015   18.7   0.0    1.6  1  FtsJ             FtsJ-like methyltransferase
     0.0019   18.0   0.0     0.0036   17.1   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
     0.0035   17.1   0.0     0.0052   16.6   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.085   13.5   0.0       0.75   10.5   0.0    2.1  1  Methyltransf_11  Methyltransferase domain
       0.22   10.8   0.0        3.3    7.0   0.0    2.0  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.4   0.0   1.1e-55   2.5e-52       2     199 ..      92     294 ..      91     295 .. 0.89

  Alignments for each domain:
  == domain 1  score: 177.4 bits;  conditional E-value: 1.1e-55
                                       HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgge 78 
                                       l+L+pq++e +lDlca+PG+KT  i+++mkn g+v+A++ +  R+  + +n +rLgv n+ ++++D+r++++   + 
  gi|330508978|ref|YP_004385406.1|  92 LVLDPQPGELVLDLCASPGSKTCQISQMMKNLGRVIANEPSLARIAPLRSNCERLGVMNVAITRYDGRRFPSRPVQ- 167
                                       68*********************************************************************99996. PP

                                       .EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHH CS
                   Methyltr_RsmB-F  79 lfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLk 155
                                        fDr+L+DaPCs+ g  rr p v  + + k  + l++lq +ll  ai l+k+gG++vYsTC+ ++eEne vie++L+
  gi|330508978|ref|YP_004385406.1| 168 -FDRVLVDAPCSSEGRERRGPGVLCKSSSKRSMDLHRLQADLLRNAIRLTKPGGIVVYSTCTYAPEENELVIESVLE 243
                                       .***************************************************************************9 PP

                                       H-TTEEEESSB......STTSTTSSECEEC......TSEEE-TTTTSS-SEEEEEE CS
                   Methyltr_RsmB-F 156 kredvelvete......lsepkglklgeea......gtlrllPhtenkdgffiakl 199
                                       +    +++         ++e  g+     +      +t r++Ph +++ gff+akl
  gi|330508978|ref|YP_004385406.1| 244 TARLERISIPGllacpgITEWGGI-----NlnheveKTARYYPHLNDTGGFFVAKL 294
                                       985555443321111113444444.....1444446799****************9 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.6e-09     1e-05       5      90 .]       3      88 ..       1      88 [. 0.87

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.6e-09
                                      HHHHHHHHHGGGHHHHHHHHH-----EEE--TTS..TTHHHH.HHH.-SS--B-TT-TTEEES---...TTSHHHHTTS CS
                   Methyltr_RsmF_N  5 FiekmkellgeeaeaflaaleeprkkglRvNtlKisveelek.lse.efelepvpwceeGfyleeeerpgkhplheaGl 81
                                      ++e++++l++ +++ f a  ++  +++ R+NtlKi++ +l + ++e +++ ++  w + G  l+ e +pgk ++  +G 
  gi|330508978|ref|YP_004385406.1|  3 WLERYRDLIP-DFDGFRAVQSQALPSSCRINTLKIERCALLDrFAEnGIDYQSFNWYPLGLKLDME-SPGKLVENLSGF 79
                                      6788888776.7999999999**************9877665155589****************99.9*********** PP

                                      -EE--TTTH CS
                   Methyltr_RsmF_N 82 yYiQEpSam 90
                                      ++iQE  +m
  gi|330508978|ref|YP_004385406.1| 80 IHIQEELSM 88
                                      *****8877 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   6.4e-07    0.0014       1      70 [.     102     173 ..     102     185 .. 0.94
   2 ?    2.7   0.0     0.092   2.1e+02      82      97 .]     205     220 ..     189     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.4e-07
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvs 70 
                                       vLdl++ +G  t ++++ + + ++v++ ++s + ++  r+++e+ g+ nv + + d +++p    +fD v++
  gi|330508978|ref|YP_004385406.1| 102 VLDLCASPGSKTCQISQMMkNLGRVIANEPSLARIAPLRSNCERLGVmNVAITRYDGRRFPSRPVQFDRVLV 173
                                       9****************99659**********************999**********************987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.092
                                       HHHHHHHHHHHEEEEE CS
                   Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                       ++++l+++ r++kpgG
  gi|330508978|ref|YP_004385406.1| 205 QADLLRNAIRLTKPGG 220
                                       3579***********9 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   6.6e-07    0.0015      20     145 ..      97     238 ..      77     252 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.6e-07
                                       -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEES..SSSHHH....TTEEEECS-CCCSSHHHHHCHCHHHSSEEE CS
                              FtsJ  20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDl..qpmapl....pgvttiqgditdpetiekikealserkvdl 90 
                                       +pg+ v+Dl+a+PG+ +  ++q +++ g+v+a       +apl    +++ +++  it+ + ++  ++     ++d 
  gi|330508978|ref|YP_004385406.1|  97 QPGELVLDLCASPGSKTCQISQMMKNLGRVIANEPslARIAPLrsncERLGVMNVAITRYDGRRFPSRP---VQFDR 170
                                       36788*******************888*****9763255677775556777779999999999988875...58999 PP

                                       EEE--S-...............SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCH..CCCHHHHH CS
                              FtsJ  91 vvsDgap...............dvsgvhdldeylqsqLllaalelalkllkpggtfvlkifr..geeteall 145
                                       v+ D                  + s ++        +L    l+ a++l kpgg++v  +++   ee e ++
  gi|330508978|ref|YP_004385406.1| 171 VLVDAPCssegrerrgpgvlckSSSKRSMDL----HRLQADLLRNAIRLTKPGGIVVYSTCTyaPEENELVI 238
                                       9999865455555555553332222222222....4444444555666699999999988886433333444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.6e-06    0.0036       7     127 ..     102     246 ..      96     280 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.6e-06
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlilsn. 81 
                                       vlDl +  G +t ++ + +   ++v+  + s   i   r+n+++lg+ nv   + d   +++  ++   fD +l + 
  gi|330508978|ref|YP_004385406.1| 102 VLDLCASPGSKTCQISQMMKNLGRVIANEPSLARIAPLRSNCERLGVMNVAITRYDGRRFPSRpVQ---FDRVLVDa 175
                                       7888888888888888655556778888888888888999*********************77666...***99995 PP

                   Methyltransf_31  82 ............evl.........naladpdkileeiervlkpggilliedpr...llaelp.akveeesk 127
                                                   +vl         ++   +++ l++++r+ kpggi++ +++     + el  ++v e+ +
  gi|330508978|ref|YP_004385406.1| 176 pcssegrerrgpGVLckssskrsmDLHRLQADLLRNAIRLTKPGGIVVYSTCTyapEENELViESVLETAR 246
                                       55555555555533377777888788899999********************9644333332566666655 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.3e-06    0.0052      72     150 ..      97     175 ..      86     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.3e-06
                                       -TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEE CS
                              PCMT  72 kkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihv 148
                                       ++g+ vL++ +  G +t  +++++++ grv++ e +   ++  + n ++l+++nv+++  DGr        +d+++v
  gi|330508978|ref|YP_004385406.1|  97 QPGELVLDLCASPGSKTCQISQMMKNLGRVIANEPSLARIAPLRSNCERLGVMNVAITRYDGRRFPSRPVQFDRVLV 173
                                       78999*************************998877777777799******************98888888888888 PP

                                       SS CS
                              PCMT 149 ga 150
                                        a
  gi|330508978|ref|YP_004385406.1| 174 DA 175
                                       76 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00033      0.75       2      95 ..     104     223 ..     103     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00033
                                       EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES..... CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvsse..... 69 
                                       d+ +  G+ ++++ +     +rv++ ++s + ++  +++ ++ g+ +v + + d +++p +  +fD v++       
  gi|330508978|ref|YP_004385406.1| 104 DLCASPGSKTCQISQMMknlGRVIANEPSLARIAPLRSNCERLGVmNVAITRYDGRRFPSRPVQFDRVLVDApcsse 180
                                       55555666666666333344899999999999999999999999999999999999999999999999998844444 PP

                                       .-CCC-C....................CHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  70 .vlhhve....................dpekalkeiaRvLkpgGllv 95 
                                             e                     ++++l+++ R+ kpgG++v
  gi|330508978|ref|YP_004385406.1| 181 gR----ErrgpgvlckssskrsmdlhrLQADLLRNAIRLTKPGGIVV 223
                                       40....24455555555566777777788999************987 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0015       3.3      46     120 ..      97     171 ..      91     175 .. 0.86
   2 ?    1.5   0.0     0.072   1.6e+02     135     150 ..     208     223 ..     203     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0015
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEE CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvv 120
                                       ++g+ vlD+++  g  + ++s+++++ g+v+  + +   +   +   ++ g++n+     ++ ++p     fD v
  gi|330508978|ref|YP_004385406.1|  97 QPGELVLDLCASPGSKTCQISQMMKNLGRVIANEPSLARIAPLRSNCERLGVMNVAITRYDGRRFPSRPVQFDRV 171
                                       678999***********************9999988888888889999999999999988888888888878776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.072
                                       HHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 135 aLkeayrvlkpGGrlv 150
                                        L++a r  kpGG++v
  gi|330508978|ref|YP_004385406.1| 208 LLRNAIRLTKPGGIVV 223
                                       699**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2261.52
//
Query:       gi|330508979|ref|YP_004385407.1|  [L=159]
Description: hypothetical protein MCON_3334 [Methanosaeta concilii GP6]
Scores for complete 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   46.6   0.0    3.5e-12   46.1   0.0    1.2  1  Methyltranf_PUA  RNA-binding PUA-like domain of methyltransfe
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.21   11.6   0.0    1.3  1  TruB-C_2         Pseudouridine synthase II TruB, C-terminal


Domain annotation for each model (and alignments):
>> Methyltranf_PUA  RNA-binding PUA-like domain of methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0     4e-16   3.5e-12       3      50 .]      84     131 ..      82     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 4e-16
                   Methyltranf_PUA   3 rYlkGetielepdlkkGwvlVcydgyplGwgKlvggrlKNkyPkglRr 50 
                                       +++ G+t+++e+d + G+v+V y+g++lG+g +++g+l ++ Pk++R+
  gi|330508979|ref|YP_004385407.1|  84 SFMEGKTLAIESDSESGYVVVFYRGEVLGCGLYSHGKLVSQIPKERRM 131
                                       79************99******************************96 PP

>> TruB-C_2  Pseudouridine synthase II TruB, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.4e-05      0.21       3      53 ..      75     122 ..      74     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                          TruB-C_2   3 veLseesakrflqGQrvklaaglpaeglVRvydeegrFlGvGeitddgvla 53 
                                       ++L+++ +++f+ G+++++ +++ ++g V v+  +g  lG G    +g+l+
  gi|330508979|ref|YP_004385407.1|  75 IHLDSANSRSFMEGKTLAI-ESDSESGYVVVF-YRGEVLGCGLYS-HGKLV 122
                                       79***************88.789999999999.999999999888.77765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1112.99
//
Query:       gi|330508980|ref|YP_004385408.1|  [L=353]
Description: 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit [Methanosaeta concilii GP6]
Scores for complete sequence (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   45.3   0.4      3e-11   44.0   0.1    1.8  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.19   11.8   0.0    1.3  1  UPF0154      Uncharacterised protein family (UPF0154)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.1   3.4e-15     3e-11       1     165 [.      60     228 ..      60     230 .. 0.89
   2 ?   -2.3   0.0      0.58   5.2e+03     124     136 ..     326     338 ..     313     349 .. 0.53

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 3.4e-15
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavp 76 
                                       +++t+ C + C+fC++++      + + ls+eeil  ++e+ +e+g ++ +++gg  p +  + +  +++++++ +p
  gi|330508980|ref|YP_004385408.1|  60 INFTNYCIGSCKFCSFKH-----SKRYRLSTEEILSRAREA-EERGaTEICLQGGLSPGMLLEDYCGILEIIHRSHP 130
                                       689**************8.....6*****************.9***9999999999999998888777777777778 PP

                                       TEEEEEEECSSCHG.........HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxx.........xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpd.........eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagi 142
                                        ++++  ++  ++          ++ l++l++ g        +e++ d  v+++++  + +  +++e + +++ + i
  gi|330508980|ref|YP_004385408.1| 131 RLHLHAYSPMEVLHmsrnsnvpvKDCLKELKRSGlGSMPGTAAEILVDS-VRQKICpEKLNAGQWKEIIVAAHHLKI 206
                                       88888888888888888888888***********888888888888888.9999998889999************** PP

                                       ETEEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 143 krvvdrivglpGendeeleelle 165
                                       + ++++i+ ++ e++e++ e+le
  gi|330508980|ref|YP_004385408.1| 207 P-STSTILFGHVESMEDRLEHLE 228
                                       *.99*************999987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.58
                                       TSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 124 ghtfeevlealek 136
                                       g + ee++e++e 
  gi|330508980|ref|YP_004385408.1| 326 GISAEEIKELIES 338
                                       3444444444443 PP

>> UPF0154  Uncharacterised protein family (UPF0154)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.1e-05      0.19      18      48 ..     315     345 ..     301     347 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                           UPF0154  18 kymkkqlkenPpinekmirammkqmGrkPSe 48 
                                         + +  ke P i+++ i+++ ++ Grk+ +
  gi|330508980|ref|YP_004385408.1| 315 ERIARNSKEEPGISAEEIKELIESCGRKAVQ 345
                                       55666779********************866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 2200.18
//
Query:       gi|330508981|ref|YP_004385409.1|  [L=281]
Description: hypothetical protein MCON_3336 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-38  129.1   9.6    6.4e-06   26.2   0.1    9.0  9  LRV          Leucine rich repeat variant
    4.4e-07   29.6  21.2        1.4    9.4   0.1    8.8  9  HEAT         HEAT repeat
     0.0015   18.2   0.2        2.4    7.9   0.0    4.8  6  XPC-binding  XPC-binding domain
     0.0043   17.4  18.0        7.5    7.0   0.3    7.1  4  HEAT_2       HEAT repeats


Domain annotation for each model (and alignments):
>> LRV  Leucine rich repeat variant
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00044         2       1      24 [.      25      48 ..      25      50 .. 0.96
   2 !   11.2   0.0     9e-05       0.4       3      25 ..      53      75 ..      52      76 .. 0.94
   3 !   18.7   0.0   3.5e-07    0.0016       3      25 ..      79     101 ..      77     102 .. 0.95
   4 !    7.5   0.0    0.0014       6.1       2      26 .]     115     139 ..     114     139 .. 0.94
   5 ?    1.0   0.0      0.16   7.1e+02       2      11 ..     141     150 ..     140     163 .. 0.83
   6 !   13.3   0.1   1.9e-05     0.084       1      24 [.     166     189 ..     166     190 .. 0.92
   7 !   25.1   1.5   3.1e-09   1.4e-05       2      25 ..     193     216 ..     192     217 .. 0.95
   8 !   12.5   0.0   3.5e-05      0.16       1      23 [.     218     240 ..     218     241 .. 0.95
   9 !   26.2   0.1   1.4e-09   6.4e-06       3      26 .]     246     269 ..     244     269 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00044
                               LRV  1 reVRaaVArrPdlPpeaLerLahD 24
                                      ++VR+ +A ++d++ + L  La+D
  gi|330508981|ref|YP_004385409.1| 25 WHVRRKLAWNSDTSEDILSYLARD 48
                                      99********************99 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9e-05
                               LRV  3 VRaaVArrPdlPpeaLerLahDP 25
                                      VR+aVA +  +P+  L +La D+
  gi|330508981|ref|YP_004385409.1| 53 VREAVAGNACTPSSNLAQLAEDS 75
                                      9********************97 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 3.5e-07
                               LRV   3 VRaaVArrPdlPpeaLerLahDP 25 
                                       VRaaVA++ ++ +e+Le+La D+
  gi|330508981|ref|YP_004385409.1|  79 VRAAVALNRQATSEMLESLAGDE 101
                                       9*********************7 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0014
                               LRV   2 eVRaaVArrPdlPpeaLerLahDPd 26 
                                        V +aVA  P+  p +Le La+D+d
  gi|330508981|ref|YP_004385409.1| 115 LVKEAVAKSPNINPQTLEFLARDSD 139
                                       699********************98 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.16
                               LRV   2 eVRaaVArrP 11 
                                       +VRa +A++P
  gi|330508981|ref|YP_004385409.1| 141 HVRACAASNP 150
                                       7********8 PP

  == domain 6  score: 13.3 bits;  conditional E-value: 1.9e-05
                               LRV   1 reVRaaVArrPdlPpeaLerLahD 24 
                                       + VR + Ar+P++P e L  La D
  gi|330508981|ref|YP_004385409.1| 166 WLVRNNIARNPSTPEELLAYLALD 189
                                       89****************999877 PP

  == domain 7  score: 25.1 bits;  conditional E-value: 3.1e-09
                               LRV   2 eVRaaVArrPdlPpeaLerLahDP 25 
                                       +VRa++A++P++P+e L++La+D 
  gi|330508981|ref|YP_004385409.1| 193 DVRATAALNPRTPAESLVTLARDR 216
                                       8**********************6 PP

  == domain 8  score: 12.5 bits;  conditional E-value: 3.5e-05
                               LRV   1 reVRaaVArrPdlPpeaLerLah 23 
                                       +e+R+a Ar+P l++  L +La 
  gi|330508981|ref|YP_004385409.1| 218 WEIREATARNPKLDGKLLDELAS 240
                                       9********************95 PP

  == domain 9  score: 26.2 bits;  conditional E-value: 1.4e-09
                               LRV   3 VRaaVArrPdlPpeaLerLahDPd 26 
                                       VR+aVA +P++ +e+LerLa+DPd
  gi|330508981|ref|YP_004385409.1| 246 VREAVAKNPNTLAETLERLATDPD 269
                                       9**********************9 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.64   2.9e+03      13      22 ..      24      33 ..      24      34 .. 0.82
   2 ?    3.0   0.0     0.035   1.6e+02       6      21 ..      42      58 ..      40      60 .. 0.81
   3 !    5.5   0.0    0.0056        25       5      22 ..      68      85 ..      66      86 .. 0.87
   4 !    5.5   0.1    0.0055        25       8      22 ..     134     148 ..     128     149 .. 0.79
   5 ?    4.0   0.1     0.016        72       6      22 ..     158     174 ..     153     175 .. 0.78
   6 ?    0.7   0.0      0.19   8.7e+02      10      22 ..     188     200 ..     181     201 .. 0.75
   7 !    9.4   0.1   0.00031       1.4       5      22 ..     209     226 ..     207     227 .. 0.87
   8 !    5.2   0.1    0.0066        30      13      23 ..     243     253 ..     233     261 .. 0.79
   9 ?    3.7   0.0     0.021        92       4      20 ..     260     276 ..     257     276 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.64
                                      SHHHHHHHHH CS
                              HEAT 13 speVReaAak 22
                                      +++VR+  a+
  gi|330508981|ref|YP_004385409.1| 24 DWHVRRKLAW 33
                                      7***998877 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.035
                                      HHHH.T-SSHHHHHHHH CS
                              HEAT  6 lkll.sDpspeVReaAa 21
                                      l+ l +D+   VRea+a
  gi|330508981|ref|YP_004385409.1| 42 LSYLaRDQVQWVREAVA 58
                                      556669*********98 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0056
                                      HHHHHT-SSHHHHHHHHH CS
                              HEAT  5 llkllsDpspeVReaAak 22
                                      l +l +D+s +VR+a+a+
  gi|330508981|ref|YP_004385409.1| 68 LAQLAEDSSGFVRAAVAL 85
                                      78889**********997 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.0055
                                       HHT-SSHHHHHHHHH CS
                              HEAT   8 llsDpspeVReaAak 22 
                                       l +D++ +VR+ Aa 
  gi|330508981|ref|YP_004385409.1| 134 LARDSDEHVRACAAS 148
                                       449**********97 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.016
                                       HHHHT-SSHHHHHHHHH CS
                              HEAT   6 lkllsDpspeVReaAak 22 
                                        ++ +D s+ VR + a+
  gi|330508981|ref|YP_004385409.1| 158 KRMVKDVSWLVRNNIAR 174
                                       4566********98876 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 0.19
                                       T-SSHHHHHHHHH CS
                              HEAT  10 sDpspeVReaAak 22 
                                        D   +VR++Aa+
  gi|330508981|ref|YP_004385409.1| 188 LDRIIDVRATAAL 200
                                       577789*****97 PP

  == domain 7  score: 9.4 bits;  conditional E-value: 0.00031
                                       HHHHHT-SSHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAak 22 
                                       l++l +D s+e+Rea+a+
  gi|330508981|ref|YP_004385409.1| 209 LVTLARDRSWEIREATAR 226
                                       77889**********997 PP

  == domain 8  score: 5.2 bits;  conditional E-value: 0.0066
                                       SHHHHHHHHHH CS
                              HEAT  13 speVReaAaka 23 
                                       s+ VRea+ak+
  gi|330508981|ref|YP_004385409.1| 243 SWMVREAVAKN 253
                                       8********97 PP

  == domain 9  score: 3.7 bits;  conditional E-value: 0.021
                                       HHHHHHT-SSHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaA 20 
                                       +l +l +Dp+ +V +aA
  gi|330508981|ref|YP_004385409.1| 260 TLERLATDPDQSVQKAA 276
                                       577888********998 PP

>> XPC-binding  XPC-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.38   1.7e+03       9      34 ..      49      74 ..      45      95 .. 0.71
   2 ?    0.1   0.0      0.15   6.9e+02      35      48 ..     127     140 ..     120     145 .. 0.85
   3 ?   -0.9   0.0      0.31   1.4e+03      12      30 ..     141     159 ..     131     163 .. 0.73
   4 ?   -0.6   0.0      0.26   1.1e+03      14      32 ..     169     187 ..     167     189 .. 0.80
   5 ?    1.5   0.0     0.056   2.5e+02      12      33 ..     219     240 ..     218     241 .. 0.88
   6 !    7.9   0.0   0.00055       2.4      13      33 ..     246     266 ..     244     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.38
                       XPC-binding  9 qFqqlRqlvqqnPqlLqplLqqlaqs 34
                                      q q +R++v+ n    ++ L qla++
  gi|330508981|ref|YP_004385409.1| 49 QVQWVREAVAGNACTPSSNLAQLAED 74
                                      77778888877765555555555554 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.15
                       XPC-binding  35 nPqllqlIqqnqee 48 
                                       nPq l+ ++++++e
  gi|330508981|ref|YP_004385409.1| 127 NPQTLEFLARDSDE 140
                                       99999999999887 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.31
                       XPC-binding  12 qlRqlvqqnPqlLqplLqq 30 
                                       ++R   ++nP l  +l+++
  gi|330508981|ref|YP_004385409.1| 141 HVRACAASNPLLTAELMKR 159
                                       5677778888887777766 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.26
                       XPC-binding  14 RqlvqqnPqlLqplLqqla 32 
                                       R  +++nP+  ++lL  la
  gi|330508981|ref|YP_004385409.1| 169 RNNIARNPSTPEELLAYLA 187
                                       7789999999999887765 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.056
                       XPC-binding  12 qlRqlvqqnPqlLqplLqqlaq 33 
                                       ++R++ ++nP+l  +lL +la 
  gi|330508981|ref|YP_004385409.1| 219 EIREATARNPKLDGKLLDELAS 240
                                       69*********99999999885 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.00055
                       XPC-binding  13 lRqlvqqnPqlLqplLqqlaq 33 
                                       +R++v++nP+ L + L++la 
  gi|330508981|ref|YP_004385409.1| 246 VREAVAKNPNTLAETLERLAT 266
                                       7*****************985 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.7     0.021        96      36      52 ..      42      58 ..      17      86 .. 0.51
   2 ?    2.9   0.0     0.033   1.5e+02      36      52 ..      68      84 ..      59     104 .. 0.68
   3 ?    2.8   4.4     0.034   1.5e+02      25      52 ..     198     225 ..     128     227 .. 0.63
   4 !    7.0   0.3    0.0017       7.5      21      51 ..     251     276 ..     230     278 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.021
                            HEAT_2 36 LvellededpavRraaa 52
                                      L  l++d+  +vR+a+a
  gi|330508981|ref|YP_004385409.1| 42 LSYLARDQVQWVREAVA 58
                                      44444555555555554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.033
                            HEAT_2 36 LvellededpavRraaa 52
                                      L +l+ed++  vR+a+a
  gi|330508981|ref|YP_004385409.1| 68 LAQLAEDSSGFVRAAVA 84
                                      44444444444444443 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.034
                            HEAT_2  25 grignpealpaLvellededpavRraaa 52 
                                       + +++++  + Lv l++d ++++R+a a
  gi|330508981|ref|YP_004385409.1| 198 AALNPRTPAESLVTLARDRSWEIREATA 225
                                       2344445577777777777777777766 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0017
                            HEAT_2  21 iraLgrignpealpaLvellededpavRraa 51 
                                       ++     ++ ++ ++L +l++d+d  v++aa
  gi|330508981|ref|YP_004385409.1| 251 AK-----NPNTLAETLERLATDPDQSVQKAA 276
                                       33.....344667889999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2062.13
//
Query:       gi|330508982|ref|YP_004385410.1|  [L=325]
Description: hypothetical protein MCON_3337 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-17   62.8   1.3    4.9e-17   62.4   0.1    1.7  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    7.1e-08   32.8   0.0    1.5e-07   31.8   0.0    1.5  1  eRF1_2          eRF1 domain 2
    8.3e-07   29.3   2.6    1.6e-06   28.4   0.1    2.1  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    0.00026   21.5   6.6    0.00026   21.5   6.6    2.4  2  SlyX            SlyX
     0.0045   17.0   9.3     0.0045   17.0   9.3    1.9  2  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
  ------ inclusion threshold ------
      0.075   13.1   0.1      0.075   13.1   0.1    1.8  2  baeRF_family2   Bacterial archaeo-eukaryotic release factor f
       0.11   12.5   5.5       0.29   11.1   5.5    1.8  1  Tnp_22_trimer   L1 transposable element trimerization domain
       0.12   12.2   6.4      0.058   13.2   4.0    1.6  2  Dynactin_p22    Dynactin subunit p22
       0.14   12.3   6.1        0.9    9.6   5.1    2.1  2  UPF0242         Uncharacterised protein family (UPF0242) N-te
       0.56   10.4  10.7        1.6    8.9   8.4    2.1  2  CENP-Q          CENP-Q, a CENPA-CAD centromere complex subuni
       0.88    9.7   5.4       0.62   10.3   2.1    2.1  2  Fib_alpha       Fibrinogen alpha/beta chain family
       0.99    9.5  12.1        7.8    6.6   8.4    2.2  2  ADIP            Afadin- and alpha -actinin-Binding
        1.6    8.6   9.2       0.18   11.7   4.7    1.6  2  Utp11           Utp11 protein
        1.7    8.5  11.3        0.3   10.9   6.1    2.0  2  DUF724          Protein of unknown function (DUF724)
        1.9    8.9   6.4        2.7    8.5   4.5    2.1  2  FlaC_arch       Flagella accessory protein C (FlaC)
        4.3    7.9   8.8       0.97   10.0   4.3    2.1  2  DUF16           Protein of unknown function DUF16
        4.5    7.4  11.4        1.8    8.7   8.3    1.8  2  DivIVA          DivIVA protein
          5    7.8   7.8        2.7    8.7   4.2    2.2  2  YabA            Initiation control protein YabA


Domain annotation for each model (and alignments):
>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.7   3.7e+03      56      56 ..      43      43 ..      12      94 .. 0.62
   2 !   62.4   0.1     5e-20   4.9e-17       4     119 ..     187     303 ..     184     307 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.7
                           acVLRF1 56 d 56
                                      +
  gi|330508982|ref|YP_004385410.1| 43 K 43
                                      2 PP

  == domain 2  score: 62.4 bits;  conditional E-value: 5e-20
                           acVLRF1   4 gvllvrrggfavgvve.ggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae... 76 
                                       +v+  ++g   +gv+   +     ++ +++v++++++GGwSq+Rf+R re+ ++++l+av+e++a l  ++ ++   
  gi|330508982|ref|YP_004385410.1| 187 LVVSAHAGSTFLGVALsREGFAVNEKVESQVKEKHSKGGWSQKRFERLREEDIKNHLDAVQEKLAGLQ-SKYGSivk 262
                                       5667778887788887455566678899*************************************987.44444588 PP

                           acVLRF1  77 .vvlgGdrslvaevledarlaplatlareelldvpdprravLed 119
                                         vlgG++ l+++++ +  l  ++++ ++  +d +dp  ++L++
  gi|330508982|ref|YP_004385410.1| 263 yAVLGGEEGLIRQIAPSISLPLVERRLKR--HDEKDP-DSLLRE 303
                                       9*************999776665555555..677777.666655 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   1.5e-10   1.5e-07      17      66 ..     202     251 ..     186     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.5e-10
                                       EESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHH CS
                            eRF1_2  17 lkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaan 66 
                                       l+++   v +k+e++v  Kh +Gg s++rfeRlree +++ l+ v e++ 
  gi|330508982|ref|YP_004385410.1| 202 LSREGFAVNEKVESQVKEKHSKGGWSQKRFERLREEDIKNHLDAVQEKLA 251
                                       566778899************************************99875 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 ?    0.7   0.4      0.57   5.7e+02      69     112 ..      44      87 ..      12      89 .. 0.67
   2 !   28.4   0.1   1.6e-09   1.6e-06      37     116 ..     208     288 ..     183     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.57
                    baeRF_family10  69 aerhlkevAellaklleergverlvlgGdeeetaalldrlpkal 112
                                       +   +++ A l+ k++e++ ++++  +  + et+  ++rlp+a+
  gi|330508982|ref|YP_004385410.1|  44 RLTSANQEANLALKAMEQKTATMVASSPEKTETERPKARLPEAW 87 
                                       22345667778888888888777777777888888888888876 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.6e-09
                    baeRF_family10  37 eeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellaklleerg..verlvlgGdeeetaalldrlpka 111
                                       +  e+ve++v++++ +ggw sq+rf+r +ee ++ hl++v e la l ++ g  v+  vlgG e  + +++   + +
  gi|330508982|ref|YP_004385410.1| 208 AVNEKVESQVKEKHSKGGW-SQKRFERLREEDIKNHLDAVQEKLAGLQSKYGsiVKYAVLGGEEGLIRQIAPSISLP 283
                                       567899*************.*********************************99*******998877777666666 PP

                    baeRF_family10 112 lrarv 116
                                       l +r 
  gi|330508982|ref|YP_004385410.1| 284 LVERR 288
                                       66555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   6.6   2.6e-07   0.00026       1      55 [.      10      64 ..      10      79 .. 0.87
   2 ?   -1.5   0.0       3.9   3.9e+03      37      52 ..     240     255 ..     229     259 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.6e-07
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX  1 leerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55
                                      le+r+ eLE+ +a qe+  eeL +++ + +++i+rl+   ++ +  lk++e++++
  gi|330508982|ref|YP_004385410.1| 10 LEDRISELEEAIAVQEREKEELVRTLQKREEKIKRLTSANQEANLALKAMEQKTA 64
                                      69*********************************************99999876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.9
                                       HHHHHHHHHT-XXXXX CS
                              SlyX  37 qrqlrllaerlkelee 52 
                                       + +l++++e+l+ l++
  gi|330508982|ref|YP_004385410.1| 240 KNHLDAVQEKLAGLQS 255
                                       5566666666666555 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   9.3   4.5e-06    0.0045      62     125 ..       8      71 ..       6      79 .. 0.91
   2 ?   -1.2   0.2       1.8   1.8e+03      55      67 ..     237     249 ..     209     261 .. 0.47

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.5e-06
                    CENP-F_leu_zip  62 eelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeesk 125
                                       ++l+ + +ele  ++   +ekeeL + lqk  e+++ L s+n + +  l+  Eq+ + m  +s 
  gi|330508982|ref|YP_004385410.1|   8 KKLEDRISELEEAIAVQEREKEELVRTLQKREEKIKRLTSANQEANLALKAMEQKTATMVASSP 71 
                                       6889999************************************************998876664 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                    CENP-F_leu_zip  55 etlkeeieelaee 67 
                                       e +k++++  +e+
  gi|330508982|ref|YP_004385410.1| 237 EDIKNHLDAVQEK 249
                                       2222222222222 PP

>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       3.8   3.8e+03      90      97 ..      30      37 ..       8      76 .. 0.55
   2 ?   13.1   0.1   7.5e-05     0.075      27      71 ..     212     254 ..     186     273 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.8
                     baeRF_family2 90 llrdeLpe 97
                                       l++ L++
  gi|330508982|ref|YP_004385410.1| 30 ELVRTLQK 37
                                      22222222 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.5e-05
                     baeRF_family2  27 tveGghdpvhkvraggwshrryqrraeeswerNaeavAeevdrlv 71 
                                       +ve + +  +k ++ggws++r++r  ee +++  +av e+++ l 
  gi|330508982|ref|YP_004385410.1| 212 KVESQVK--EKHSKGGWSQKRFERLREEDIKNHLDAVQEKLAGLQ 254
                                       4444444..56678***********************99998775 PP

>> Tnp_22_trimer  L1 transposable element trimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   5.5    0.0003      0.29       1      39 [.      13      51 ..      13      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Tnp_22_trimer  1 RidelEERvSaaEDeieeidrevKereKrkkileQslQv 39
                                      Ri elEE +   E e ee+ r+   re  +k+l+   Q+
  gi|330508982|ref|YP_004385410.1| 13 RISELEEAIAVQEREKEELVRTLQKREEKIKRLTSANQE 51
                                      9********************************987665 PP

>> Dynactin_p22  Dynactin subunit p22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   4.0   5.9e-05     0.058       4      62 ..       9      63 ..       7      84 .. 0.82
   2 ?   -2.3   0.0       3.4   3.4e+03      29      48 ..     238     257 ..     227     263 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.9e-05
                      Dynactin_p22  4 aLEeriaeLEkrvlGeekekekedesiidsLakvqkklssavskrekikellkkleele 62
                                      +LE+ri+eLE+ +  +e+e    +e+++ +L+k ++k+++++s +++++ +lk +e+ +
  gi|330508982|ref|YP_004385410.1|  9 KLEDRISELEEAIAVQERE----KEELVRTLQKREEKIKRLTSANQEANLALKAMEQKT 63
                                      7************665555....447***********************9999998755 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                      Dynactin_p22  29 siidsLakvqkklssavskr 48 
                                        i + L +vq+kl  + sk+
  gi|330508982|ref|YP_004385410.1| 238 DIKNHLDAVQEKLAGLQSKY 257
                                       33444444444444444433 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.1    0.0009       0.9      81     135 ..      11      65 ..       6      92 .. 0.81
   2 ?    1.5   0.0      0.28   2.8e+02     138     177 ..     211     255 ..     144     261 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0009
                           UPF0242  81 deglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfee 135
                                       ++ +++ eea+   + e+eeL + l+++ee+++rl+  nq+ +  l+a+ +  + 
  gi|330508982|ref|YP_004385410.1|  11 EDRISELEEAIAVQEREKEELVRTLQKREEKIKRLTSANQEANLALKAMEQKTAT 65 
                                       45688999999999999999*******************9888888877765554 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.28
                           UPF0242 138 leleeqLaekqellqeyqetieeqrsv.....lekrqdqieqLes 177
                                        ++e+q++ek+ +   +q+ +e +r++     l+  q++ + L+s
  gi|330508982|ref|YP_004385410.1| 211 EKVESQVKEKHSKGGWSQKRFERLREEdiknhLDAVQEKLAGLQS 255
                                       455666666666666666666555543211114444444444444 PP

>> CENP-Q  CENP-Q, a CENPA-CAD centromere complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   8.4    0.0016       1.6      34     110 ..       7      81 ..       4     112 .. 0.67
   2 ?    1.4   0.0      0.32   3.2e+02     117     148 ..     224     255 ..     199     262 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                            CENP-Q  34 kaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknakaeare.rkeklkkehvllqesdseelslleass 109
                                       k+ le+  s ++++++  e+e+e+++r+l++ +e++++L  +a+ ea+   k  ++k+  ++   +s+e+++ e ++
  gi|330508982|ref|YP_004385410.1|   7 KKKLEDRISELEEAIAVQEREKEELVRTLQKREEKIKRLT-SANQEANLaLKAMEQKTATMVA--SSPEKTETERPK 80 
                                       789************************************6.4555555535554444444444..333344444333 PP

                            CENP-Q 110 d 110
                                        
  gi|330508982|ref|YP_004385410.1|  81 A 81 
                                       3 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.32
                            CENP-Q 117 sgtvfsdlepeldeellpllqqLgshLesmrg 148
                                        g +++ +e   +e++++ l +++++L  +++
  gi|330508982|ref|YP_004385410.1| 224 GGWSQKRFERLREEDIKNHLDAVQEKLAGLQS 255
                                       33344444444466666666666666665555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.1   0.00062      0.62      83     124 ..       7      48 ..       6      58 .. 0.93
   2 ?   -0.1   0.1      0.95   9.5e+02      30      52 ..     236     258 ..     209     265 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00062
                                       HHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  83 skeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqd 124
                                       +k+le++i++l+e i  qe++ ++L  +l++ e+ki++L ++
  gi|330508982|ref|YP_004385410.1|   7 KKKLEDRISELEEAIAVQEREKEELVRTLQKREEKIKRLTSA 48 
                                       689************************************876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.95
                                       CCCCCHHHCCCCCCCCCCCCHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstk 52 
                                       e+d+k++l+ ++++l+ +++++ 
  gi|330508982|ref|YP_004385410.1| 236 EEDIKNHLDAVQEKLAGLQSKYG 258
                                       34444444444444444444443 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   8.4    0.0078       7.8      77     133 ..       8      64 ..       7      75 .. 0.92
   2 ?    4.2   0.1     0.042        42      53     104 ..     208     257 ..     200     260 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0078
                              ADIP  77 erlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktqya 133
                                       ++l+++ ++le  +a++++++ +l ++l++ e+k+k+++  +q  + al++++++ a
  gi|330508982|ref|YP_004385410.1|   8 KKLEDRISELEEAIAVQEREKEELVRTLQKREEKIKRLTSANQEANLALKAMEQKTA 64 
                                       6899***************************************99999999988765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.042
                              ADIP  53 eqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekkl 104
                                       +++e+++ +++++ +     q+++erl +  e+ ++ l++vq+k++ l+ k+
  gi|330508982|ref|YP_004385410.1| 208 AVNEKVESQVKEKHSKGGWSQKRFERLRE--EDIKNHLDAVQEKLAGLQSKY 257
                                       67899999999999999999*******76..799999*****9999999875 PP

>> Utp11  Utp11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   4.7   0.00019      0.18     182     228 ..      16      69 ..       4      92 .. 0.73
   2 ?   -2.2   0.1       3.1   3.1e+03     168     186 ..     224     242 ..     200     262 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                             Utp11 182 q.......kekkkeklykeLkarlerekqLkkaeqelelqralmkkgakkkvkk 228
                                       +       +e++ke+l++ L++r e+ k+L+ a+qe +l  + m++++ + v +
  gi|330508982|ref|YP_004385410.1|  16 EleeaiavQEREKEELVRTLQKREEKIKRLTSANQEANLALKAMEQKTATMVAS 69 
                                       13334433499********************************97665555444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.1
                             Utp11 168 eekeerkenrkkvkqkekk 186
                                          ++++++r ++++ +++
  gi|330508982|ref|YP_004385410.1| 224 GGWSQKRFERLREEDIKNH 242
                                       2333344444442222333 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   6.1    0.0003       0.3     125     186 ..       7      68 ..       4      70 .. 0.92
   2 ?   -0.1   0.2      0.72   7.1e+02     107     146 ..     218     257 ..     207     265 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                            DUF724 125 krkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFeavas 186
                                       k+kle+ i+ele++i+  er+++ l +  ++ +++i+rl s +++++ +l+++eq+  ++++
  gi|330508982|ref|YP_004385410.1|   7 KKKLEDRISELEEAIAVQEREKEELVRTLQKREEKIKRLTSANQEANLALKAMEQKTATMVA 68 
                                       6899******************99999999************************99877765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.72
                            DUF724 107 lleerkklekkieeeesekrkleeeidelekkilelerql 146
                                       +++++k+  ++ + e+ +++ +++++d +++k + l+ + 
  gi|330508982|ref|YP_004385410.1| 218 KEKHSKGGWSQKRFERLREEDIKNHLDAVQEKLAGLQSKY 257
                                       3444444445555556666667777777777777777664 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 ?    8.5   4.5    0.0027       2.7       4      40 ..       9      45 ..       8      47 .. 0.95
   2 ?   -1.9   0.0       4.7   4.7e+03       5      19 ..     239     253 ..     233     261 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0027
                         FlaC_arch  4 elEnklsklsteletvkkeneelsksveelkenVkdl 40
                                      +lE ++s+l+  ++  ++e eel  ++++ +e++k+l
  gi|330508982|ref|YP_004385410.1|  9 KLEDRISELEEAIAVQEREKEELVRTLQKREEKIKRL 45
                                      79*********************************98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.7
                         FlaC_arch   5 lEnklsklsteletv 19 
                                       + n l+ ++ +l+ +
  gi|330508982|ref|YP_004385410.1| 239 IKNHLDAVQEKLAGL 253
                                       333333333344433 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.3   0.00097      0.97      32      89 ..      10      68 ..       4      77 .. 0.75
   2 ?   -1.2   0.1       2.8   2.8e+03      80      88 ..     238     246 ..     207     262 .. 0.40

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00097
                                      BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH........HHHHHH CS
                             DUF16 32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvd.etlelil 89
                                       + r+ ++e+ +++++ + ++l  + +k +ekik+l+   +  + +l++++ +t  +++
  gi|330508982|ref|YP_004385410.1| 10 LEDRISELEEAIAVQEREKEELVRTLQKREEKIKRLTSANQEANLALKAMEqKTATMVA 68
                                      56789999999999999999999999999999999987666655557755414555554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.8
                                       ....HHHHH CS
                             DUF16  80 kvdetleli 88 
                                        +++ l+ +
  gi|330508982|ref|YP_004385410.1| 238 DIKNHLDAV 246
                                       222222222 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   8.3    0.0018       1.8      41     109 ..       7      74 ..       5      83 .. 0.84
   2 ?   -1.8   0.0         3     3e+03      19      34 ..     235     250 ..     210     259 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  41 neelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeea 109
                                       +++l+++++elee+++  +  +e+L +tl   +e  +++ ++a++ea+l +k+ e+k  ++v+ + e++
  gi|330508982|ref|YP_004385410.1|   7 KKKLEDRISELEEAIAVQEREKEELVRTLQKREEKIKRL-TSANQEANLALKAMEQKTATMVASSPEKT 74 
                                       5799*********************99995555555444.589******************98766654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                                       EHHHHHHHHHHHHHHH CS
                            DivIVA  19 dedeVdeFLdqvakdy 34 
                                       +e+++++ Ld v +++
  gi|330508982|ref|YP_004385410.1| 235 REEDIKNHLDAVQEKL 250
                                       3445555555555544 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.2    0.0028       2.7       3      62 ..       7      66 ..       5      84 .. 0.81
   2 ?   -0.1   0.1       1.5   1.5e+03      12      29 ..     238     255 ..     204     296 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0028
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXX CS
                              YabA  3 kkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekek 62
                                      kk+l d+++elee ++   +e eel ++l++  e+ ++L+  n++    l+  e+k+++ 
  gi|330508982|ref|YP_004385410.1|  7 KKKLEDRISELEEAIAVQEREKEELVRTLQKREEKIKRLTSANQEANLALKAMEQKTATM 66
                                      78999***************************************9998885444444333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHHHHH CS
                              YabA  12 eleeqleelleeleelke 29 
                                       +++++l++++e+l+ l++
  gi|330508982|ref|YP_004385410.1| 238 DIKNHLDAVQEKLAGLQS 255
                                       233444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1916  (0.106866); expected 358.6 (0.02)
Passed bias filter:                     1090  (0.0607954); expected 358.6 (0.02)
Passed Vit filter:                       163  (0.00909142); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 2223.11
//
Query:       gi|330508983|ref|YP_004385411.1|  [L=139]
Description: hypothetical protein MCON_3339 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1026.79
//
Query:       gi|330508984|ref|YP_004385412.1|  [L=53]
Description: hypothetical protein MCON_3340 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.027   14.5   3.0        2.1    8.4   0.1    2.0  2  CpXC           CpXC protein
      0.078   13.0   2.7       0.12   12.4   2.7    1.4  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
       0.12   12.4   4.4        1.2    9.2   0.1    2.4  2  UPF0547        Uncharacterised protein family UPF0547
       0.26   10.8   0.2       0.26   10.8   0.2    2.2  2  zn-ribbon_14   Zinc-ribbon
        6.3    6.3   7.2        6.8    6.2   1.2    2.1  2  Mu-like_Com    Mu-like prophage protein Com


Domain annotation for each model (and alignments):
>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1   0.00058       2.1      33      48 ..       3      18 ..       1      23 [. 0.83
   2 ?    7.9   0.3   0.00087       3.1      31      52 ..      22      43 ..      17      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00058
                              CpXC 33 gslfeatCpkCgatak 48
                                      g+ f + Cp+Cg+ a 
  gi|330508984|ref|YP_004385412.1|  3 GTHFLTNCPRCGYVAN 18
                                      788999******9876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00087
                              CpXC 31 ldgslfeatCpkCgatakleap 52
                                      +dg   ++ C  Cg+++++++p
  gi|330508984|ref|YP_004385412.1| 22 IDGLTVKVCCKMCGYEGTIPHP 43
                                      67778899**********9998 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.7   3.4e-05      0.12      20      45 ..       9      36 ..       2      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                     Zn_Tnp_IS1595 20 vCPhCgsr.kayrikt.rglfqCkeCrk 45
                                       CP+Cg+   a +i +   + +Ck C++
  gi|330508984|ref|YP_004385412.1|  9 NCPRCGYVaNAQSIDGlTVKVCCKMCGY 36
                                      5******99999999998999*****98 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00034       1.2      17      23 ..      10      16 ..       8      19 .. 0.87
   2 ?    4.3   1.1     0.012        44      17      23 ..      31      37 ..      26      37 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00034
                           UPF0547 17 CphCGyv 23
                                      Cp CGyv
  gi|330508984|ref|YP_004385412.1| 10 CPRCGYV 16
                                      9999997 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.012
                           UPF0547 17 CphCGyv 23
                                      C  CGy+
  gi|330508984|ref|YP_004385412.1| 31 CKMCGYE 37
                                      699**97 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   7.2e-05      0.26       2      11 ..       9      18 ..       8      21 .. 0.85
   2 ?    0.3   3.6      0.14     5e+02       3       8 ..      31      36 ..      29      37 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.2e-05
                      zn-ribbon_14  2 kCerCGylSS 11
                                      +C rCGy+++
  gi|330508984|ref|YP_004385412.1|  9 NCPRCGYVAN 18
                                      8******987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.14
                      zn-ribbon_14  3 CerCGy 8 
                                      C+ CGy
  gi|330508984|ref|YP_004385412.1| 31 CKMCGY 36
                                      9****9 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.2    0.0019       6.8      26      32 ..       9      15 ..       5      18 .. 0.83
   2 ?    4.6   0.3     0.006        22      15      31 ..      17      35 ..      15      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0019
                       Mu-like_Com 26 KCPRCGt 32
                                       CPRCG 
  gi|330508984|ref|YP_004385412.1|  9 NCPRCGY 15
                                      6*****5 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.006
                       Mu-like_Com 15 aKaeAlDeltiK..CPRCG 31
                                      a a+ +D lt+K  C  CG
  gi|330508984|ref|YP_004385412.1| 17 ANAQSIDGLTVKvcCKMCG 35
                                      789999*999998678887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 386.27
//
Query:       gi|330508985|ref|YP_004385413.1|  [L=102]
Description: hypothetical protein MCON_3341 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-17   62.7   0.0    5.1e-17   62.4   0.0    1.1  1  MJ1316    MJ1316 RNA cyclic group end recognition domain
  ------ inclusion threshold ------
      0.027   14.5   0.1       0.04   14.0   0.1    1.2  1  bPH_4     Bacterial PH domain


Domain annotation for each model (and alignments):
>> MJ1316  MJ1316 RNA cyclic group end recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0   5.7e-21   5.1e-17       1      76 []       1      80 [.       1      80 [. 0.92

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 5.7e-21
                            MJ1316  1 MrtaqdvlnRirWdkeldkskfvvgyldR..fkgikevpleeiswied.flleeeege.laIPlHRiryikrkgevvWd 75
                                      Mrt+  +l R+++d+ +d sk ++ yldR  +++i+ v++e+i + e  ++ + ++ +  +IP+HRir+i+++ge +W+
  gi|330508985|ref|YP_004385413.1|  1 MRTSYALLLRLIHDPGYDLSKASIEYLDRgaSGDISLVKGEDIISLESgIMEIRSDLKtKFIPIHRIRRISYQGEPLWE 79
                                      ******************************99*************99995555555555*******************9 PP

                            MJ1316 76 R 76
                                      +
  gi|330508985|ref|YP_004385413.1| 80 K 80
                                      7 PP

>> bPH_4  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.5e-06      0.04       5      37 ..      46      78 ..      43      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-06
                             bPH_4  5 itegvLliksGfirkkIpiedIkkirktkspls 37
                                      +++g ++i+s + +k Ipi++I+ i+++++pl 
  gi|330508985|ref|YP_004385413.1| 46 LESGIMEIRSDLKTKFIPIHRIRRISYQGEPLW 78
                                      5788999*********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 747.65
//
Query:       gi|330508986|ref|YP_004385414.1|  [L=246]
Description: beta-lactamase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-20   71.2   0.0    1.3e-19   70.5   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
    9.8e-07   29.0   1.9    1.8e-06   28.1   1.1    1.7  2  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.099   11.7   0.4       0.13   11.3   0.4    1.2  1  PDEase_II      cAMP phosphodiesterases class-II


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   2.2e-23   1.3e-19       3     201 .]      31     211 ..      29     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 2.2e-23
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EE.EEEEEEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkk.lplyapkgvlavleanfvyla 78 
                                       i++Dag ++ +   ++       d+      ++l+h H DH++gl  l +++ ++ l+++++kg+++vl++     +
  gi|330508986|ref|YP_004385414.1|  31 IILDAGNGISKA-DQYI-----DDD--LPVYLFLSHFHLDHIEGLHILNKFHFSQgLKIFGQKGTREVLNTIVNDPF 99 
                                       778888887655.5554.....444..44569******************888878**************9955444 PP

                                       CHTT....TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHH CS
                     Lactamase_B_2  79 leee....pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeig 151
                                       + +      +v+v el +g   ++  + le+++  + h+s+         tlG+r++ +gk ++y++Dtg +++++ 
  gi|330508986|ref|YP_004385414.1| 100 TVPLeklpYPVEVGELLPGP-YKMP-FALECEF--LLHASP---------TLGYRFDLEGKIIAYCPDTGICEGAVH 163
                                       33333344344444443332.2331.2333333..355555.........5**********************9987 PP

                                       HHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 152 erlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                        + g+ dll+ ++   ++ e +  + Hl+p++a+++a+++gakrl l+H+
  gi|330508986|ref|YP_004385414.1| 164 -LAGDSDLLIAECS-HKPGESSPAWPHLNPQDAADIARRAGAKRLALTHF 211
                                       .9999*******88.556565559*************************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 !   28.1   1.1     3e-10   1.8e-06       4      63 ..      17      69 ..      14      73 .. 0.92
   2 ?   -1.6   0.0      0.37   2.2e+03      59      98 ..     166     209 ..     165     240 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3e-10
                                      CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGG CS
                       Lactamase_B  4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgg 63
                                      +++ ++li  ++ +i+ D+G + ++a++       +++++ + +++l+H+HlDHi gl+ 
  gi|330508986|ref|YP_004385414.1| 17 GNTICTLINSEKYHIILDAGNGISKADQ-------YIDDDLPVYLFLSHFHLDHIEGLHI 69
                                      6788***********************7.......89******************99976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.37
                                       TTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH....T CS
                       Lactamase_B  59 Gglgglveatdvpvgavaeeapalfmeeaddaasrkgll....l 98 
                                       G+ + l+ +   ++g+ + ++p+l++  a d a r g++     
  gi|330508986|ref|YP_004385414.1| 166 GDSDLLIAECSHKPGESSPAWPHLNPQDAADIARRAGAKrlalT 209
                                       55566666677777777777777777777777777666544330 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   2.3e-05      0.13      72     105 ..      41      76 ..      22      99 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHTEEEE.E-S---GGGTHHH.HHHGGGGG CS
                         PDEase_II  72 kktyeiknniksy.lItHsHLDHvsgl.vinSaefy 105
                                       k+ + i + +  y +++H HLDH+ gl ++n  +f 
  gi|330508986|ref|YP_004385414.1|  41 KADQYIDDDLPVYlFLSHFHLDHIEGLhILNKFHFS 76 
                                       5667777888878468**********9455554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 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:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1763.85
//
Query:       gi|330508987|ref|YP_004385415.1|  [L=61]
Description: hypothetical protein MCON_3343 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.097   12.7   3.3        7.8    6.6   4.1    2.0  2  zinc_ribbon_6  Zinc-ribbon


Domain annotation for each model (and alignments):
>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   4.1   0.00044       7.8      27      53 ..      19      45 ..      13      48 .. 0.77
   2 ?    5.9   0.2   0.00074        13      30      39 ..      43      52 ..      38      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00044
                     zinc_ribbon_6 27 kvkilCnDCekksevkfhvlglkCkeC 53
                                      + + +C  C+k ++v+f+  g +   C
  gi|330508987|ref|YP_004385415.1| 19 MHDATCAECGKACQVPFKPDGSRPVYC 45
                                      56679************9988764444 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.00074
                     zinc_ribbon_6 30 ilCnDCekks 39
                                      ++C DC +k 
  gi|330508987|ref|YP_004385415.1| 43 VYCSDCYQKH 52
                                      89****9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 466.02
//
Query:       gi|330508988|ref|YP_004385416.1|  [L=762]
Description: DEAD/DEAH box helicase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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  101.1   0.0    1.1e-23   83.7   0.0    2.4  2  Helicase_C     Helicase conserved C-terminal domain
    7.5e-27   94.4   0.0    2.1e-26   93.0   0.0    1.8  1  ERCC4          ERCC4 domain
    2.8e-17   63.2   0.0    6.5e-17   62.1   0.0    1.6  1  ResIII         Type III restriction enzyme, res subunit
    8.6e-17   61.5   0.0    6.1e-16   58.7   0.0    2.2  2  DEAD           DEAD/DEAH box helicase
    1.5e-13   50.6   0.0    4.5e-13   49.1   0.0    1.9  1  HHH_2          Helix-hairpin-helix motif
    1.5e-10   41.5   0.1    5.9e-10   39.6   0.1    2.1  1  HHH_5          Helix-hairpin-helix domain
    1.7e-05   24.4   0.3     0.0018   18.0   0.1    3.2  2  HHH            Helix-hairpin-helix motif
     0.0013   19.1   0.1      0.081   13.3   0.1    3.2  3  HHH_8          Helix-hairpin-helix domain
     0.0035   17.9   0.0      0.015   15.9   0.0    2.1  1  5_3_exonuc     5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
      0.019   14.3   0.0      0.028   13.7   0.0    1.4  1  SecA_DEAD      SecA DEAD-like domain
      0.019   14.2   0.0      0.037   13.3   0.0    1.4  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
      0.041   14.1   0.0        0.4   11.0   0.0    2.6  1  HHH_3          Helix-hairpin-helix motif
      0.051   12.8   0.0       0.15   11.3   0.0    1.7  2  DUF2075        Uncharacterized conserved protein (DUF2075)


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 !   15.0   0.0   1.7e-05     0.023       7     100 ..      49     145 ..      43     158 .. 0.79
   2 !   83.7   0.0   7.8e-27   1.1e-23       7     110 ..     353     468 ..     347     469 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                                       HHHHHHTTTTSEEEEEESSHHHHHH.....HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH.TTSSSEEEESGGGT CS
                        Helicase_C   7 lellkleeeggkilifvntidrlek.....vklllekkgikvavlhgelpqnereeileqfn.kgesdvLiatdvae 77 
                                       + ll  + ++g++l  ++t+  +e+      ++l  k + +v++++ge+  ++r+++ e+ +   ++  +i  d ++
  gi|330508988|ref|YP_004385416.1|  49 MVLL-ARLDKGRVLFLAPTKPLVEQhaaflRRVL--KDEGEVTMMTGEMMPEKRKAAWEAARiTVSTPQVIENDLLS 122
                                       4455.788999**********9988634422333..34799*********************655666********* PP

                                       SSSTSTTESEEEESSSSSSHHHH CS
                        Helicase_C  78 rGidipkvnlVinfdlprnvtsy 100
                                       r id+++++l+i+ ++ r v +y
  gi|330508988|ref|YP_004385416.1| 123 RRIDLEDISLIIFDEAHRAVGNY 145
                                       ************99999887555 PP

  == domain 2  score: 83.7 bits;  conditional E-value: 7.8e-27
                                       HHHH...HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTT........STHHHHHHHHHHHHTTSSSEEE CS
                        Helicase_C   7 lell...kleeeggkilifvntidrlek.vklllekkgikvavlhge........lpqnereeileqfnkgesdvLi 71 
                                        ++l    + + +++i++f+n++d+++  +++l+e  +ik++++ g+        l+q+++ eil++f++ge++vLi
  gi|330508988|ref|YP_004385416.1| 353 RKILteqIEAKPESRIMVFTNYRDTASAlIRFLKEDPKIKAVRFVGQssraddegLSQKKQAEILQRFRAGEYNVLI 429
                                       444444458999************9977889998888*********999**************************** PP

                                       ESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  72 atdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       at+v+e+Gidip  ++V ++++  +  + iqr+GRtgRa
  gi|330508988|ref|YP_004385416.1| 430 ATSVGEEGIDIPATDMVLFYEPVPSEIRSIQRKGRTGRA 468
                                       **************************************8 PP

>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.0   1.5e-29   2.1e-26       1     156 []     557     676 ..     557     676 .. 0.97

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 1.5e-29
                                       EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCC..SH CS
                             ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikd..gr 75 
                                       +D+re  +g+ +  le +g+ev+ ++l++gdy ++   +++               v++erk+a+d+vasi+d  + 
  gi|330508988|ref|YP_004385416.1| 557 VDPRE--RGMARL-LEGRGLEVTLKNLEVGDY-VV---SDR---------------VAIERKTAQDFVASIIDpeRN 611
                                       79***..999999.******************.**...9**...............******************99* PP

                                       HHHHHHHHHH.H-SEEEEEEES-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHH CS
                             ERCC4  76 leeqvsrlkrngykkpillvegldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaew 152
                                       l++q+++l+r +y++p+l++eg d y+r+               +++++i++aL ++++d+gv+i+ te++++ta +
  gi|330508988|ref|YP_004385416.1| 612 LFRQIADLAR-SYERPVLILEGRDLYSRQ---------------VSASSIQGALTSVAVDYGVPIIPTEDQEDTASV 672
                                       **********.*****************9...............********************************9 PP

                                       HHHH CS
                             ERCC4 153 lanl 156
                                       ++ l
  gi|330508988|ref|YP_004385416.1| 673 ITML 676
                                       9865 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   4.7e-20   6.5e-17      25     169 ..      31     170 ..      14     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 4.7e-20
                                       SEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG......GEEEESSS-B--.. CS
                            ResIII  25 krglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayke..igkkvsgdkkkake 98 
                                          li+ +TG GKT++a + l +rl k     ++lfl+p+k l+eq    ++++l+++ +    ++++  +k+ka  
  gi|330508988|ref|YP_004385416.1|  31 SSSLIVVPTGLGKTVIAlMVLLARLDKG----RVLFLAPTKPLVEQHAAFLRRVLKDEGEVtmMTGEMMPEKRKA-- 101
                                       5689*************66666666664....8*************99988888888764455444444444444.. PP

                                       .....-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---....SEEEEEESS- CS
                            ResIII  99 kdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfke....avllglTATp 169
                                        + + ++i+v+t q + +d+      s + + + + +ii+DEaHr+ ++ ++  i+e + +     ++lg+TA p
  gi|330508988|ref|YP_004385416.1| 102 -AWEAARITVSTPQVIENDL-----LSRRIDLEDISLIIFDEAHRAVGNYAYVYIAERYARegtnPLVLGITASP 170
                                       .6999***************.....99999999999************889999866653335559*******88 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.0   4.4e-19   6.1e-16      15     136 ..      31     144 ..      19     176 .. 0.80
   2 ?   -0.7   0.0      0.78   1.1e+03      43      72 ..     596     625 ..     577     656 .. 0.77

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 4.4e-19
                                       CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardql 91 
                                        + l+  +TG GKT ++l+ +l+++      ++ ++l+++Pt+ L+eq++  l++++k  + +v +++g +   +++
  gi|330508988|ref|YP_004385416.1|  31 SSSLIVVPTGLGKTVIALMVLLARL------DKGRVLFLAPTKPLVEQHAAFLRRVLKDEG-EVTMMTG-EMMPEKR 99 
                                       4678999***************777......6679***********************755.5555555.5555555 PP

                                       HHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  92 skldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq 136
                                       ++  + ++i+v+tp+ + + l +++++l++++++++DEa+r   +
  gi|330508988|ref|YP_004385416.1| 100 KAAWEAARITVSTPQVIENDLLSRRIDLEDISLIIFDEAHRAVGN 144
                                       555499************96666999***************8877 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.78
                                       TTSTS-EEEEEESSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkk 72 
                                       k+ +   a i+ P r L +q+++ ++++  
  gi|330508988|ref|YP_004385416.1| 596 KTAQDFVASIIDPERNLFRQIADLARSYER 625
                                       6667778889**********9988777665 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   3.3e-16   4.5e-13       7      53 ..     708     754 ..     704     759 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 3.3e-16
                             HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsive 53 
                                        I+ VG ++A++L ++F+s+++  +as eeL+evd +G++iA+ i+e
  gi|330508988|ref|YP_004385416.1| 708 AIPSVGPSVARKLLRHFGSIEKVIAASKEELQEVDMVGPKIAERIRE 754
                                       59*******************************************97 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.1   4.3e-13   5.9e-10       3      53 ..     704     754 ..     702     755 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 4.3e-13
                                       HHHT.STT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5   3 eLls.vsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                       +L+s ++ +Gp++A++ll++ ++s+e+++aa++eeL+++  +G+k Aeri +
  gi|330508988|ref|YP_004385416.1| 704 YLISaIPSVGPSVARKLLRH-FGSIEKVIAASKEELQEVDMVGPKIAERIRE 754
                                       566559**************.*****************************75 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.08   1.1e+02      14      29 ..     707     722 ..     705     723 .. 0.84
   2 !   18.0   0.1   1.3e-06    0.0018       1      29 [.     726     754 ..     726     755 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.08
                                       HTSTT-SHHHHHHHHH CS
                               HHH  14 lalPGVGpktAeaIls 29 
                                        a+P VGp++A++ l 
  gi|330508988|ref|YP_004385416.1| 707 SAIPSVGPSVARKLLR 722
                                       57899*******9985 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.3e-06
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIls 29 
                                       s+e +i+as eeL+++  VGpk Ae+I++
  gi|330508988|ref|YP_004385416.1| 726 SIEKVIAASKEELQEVDMVGPKIAERIRE 754
                                       6899***********************86 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.6   6.4e+03      28      39 ..     332     343 ..     330     346 .. 0.83
   2 ?    1.9   0.0      0.21     3e+02      47      63 ..     702     720 ..     690     724 .. 0.71
   3 !   13.3   0.1   5.8e-05     0.081      40      67 ..     729     756 ..     721     757 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.6
                                       HHHHHCCCCC-S CS
                             HHH_8  28 YrrAaraiealp 39 
                                       +r A +a+e+l 
  gi|330508988|ref|YP_004385416.1| 332 FRQAMQALEDLQ 343
                                       899*****9997 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.21
                                       T..HCTTSTT--HHHHHHH CS
                             HHH_8  47 e..eltklpgiGkkiaaki 63 
                                       +   ++++p +G+++a+k+
  gi|330508988|ref|YP_004385416.1| 702 QeyLISAIPSVGPSVARKL 720
                                       2433478*********996 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 5.8e-05
                                       S-HHHHTTHCTTSTT--HHHHHHHHHHH CS
                             HHH_8  40 eeitsleeeltklpgiGkkiaakieeil 67 
                                       + i+  +eel++++++G+kia++i+e++
  gi|330508988|ref|YP_004385416.1| 729 KVIAASKEELQEVDMVGPKIAERIRELV 756
                                       555555556*****************86 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-05     0.015      20      58 ..     706     750 ..     702     756 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                        5_3_exonuc  20 ipGvpgiGektAakLlkeygsleeilenld.elke.....kklke 58 
                                       i  +p +G+  A kLl+++gs+e+++++ + el+e     +k++e
  gi|330508988|ref|YP_004385416.1| 706 ISAIPSVGPSVARKLLRHFGSIEKVIAASKeELQEvdmvgPKIAE 750
                                       6789***********************876444444333344444 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     2e-05     0.028      84     190 ..      24     129 ..      11     369 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SecA_DEAD  84 iGglvlhegkiaemkTGEGKtlvatlpaylnaltgkgvhvvtvndYLakrdaewmgpvyeflGlsvgvieselesee 160
                                       +++ +l++ ++  + TG GKt++a +  +l+ l +  v  ++    L ++ a+ +++v +  G +v +++ e+ +e+
  gi|330508988|ref|YP_004385416.1|  24 LAASALKSSSLIVVPTGLGKTVIALMV-LLARLDKGRVLFLAPTKPLVEQHAAFLRRVLKDEG-EVTMMTGEMMPEK 98 
                                       4677899999999********999775.567788888999999******************99.8999999****** PP

                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                         SecA_DEAD 161 rreaYea.ditYgtnnelgfdyLrDnlalsk 190
                                       r++a+ea  it  t + ++ d L  ++ l+ 
  gi|330508988|ref|YP_004385416.1|  99 RKAAWEAaRITVSTPQVIENDLLSRRIDLED 129
                                       *****86279*99*99999999988777665 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 ?   13.3   0.0   2.7e-05     0.037      90     155 ..     409     472 ..     404     502 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                     ERCC3_RAD25_C  90 seaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkks 155
                                       s++++ +ilq+f++  ++n+++   vg++ iD+P   +++     + s  +  qr Gr  ra++++
  gi|330508988|ref|YP_004385416.1| 409 SQKKQAEILQRFRAG-EYNVLIATSVGEEGIDIPATDMVLFY-EPVPSEIRSIQRKGRTGRARSGR 472
                                       788999*******87.789999999*********88877765.56777778899999999999864 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00029       0.4      11      30 ..     733     752 ..     703     756 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                             HHH_3  11 AsaeeLqklpGlgpklAknI 30 
                                       As+eeLq +  +gpk+A++I
  gi|330508988|ref|YP_004385416.1| 733 ASKEELQEVDMVGPKIAERI 752
                                       56666666666666666665 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   0.00011      0.15      10     101 ..      39     142 ..      33     162 .. 0.70
   2 ?   -3.3   0.0       2.9     4e+03     330     350 ..     405     429 ..     390     430 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                           DUF2075  10 aGtGKtvvllnllaeleddeeertavylsvNhplvl....vlrealakke.........ekkkkkeafeklssfinn 73 
                                       +G GKtv++l +l +     ++ ++ +l   +plv+     lr+ l+ +          +++k+k+a e  +  + +
  gi|330508988|ref|YP_004385416.1|  39 TGLGKTVIALMVLLAR---LDKGRVLFLAPTKPLVEqhaaFLRRVLKDEGevtmmtgemMPEKRKAAWEAARITVST 112
                                       588*****99988776...4666677777777777644443444444443666666666555555555555555555 PP

                           DUF2075  74 lsef..kkaeekkeepkedvvivDEAhrll 101
                                        +    +   ++ + +++ ++i+DEAhr+ 
  gi|330508988|ref|YP_004385416.1| 113 PQVIenDLLSRRIDLEDISLIIFDEAHRAV 142
                                       55435477888889999***********97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.9
                           DUF2075 330 k....kkeseekaqkllkNayrVLL 350
                                       +    +k+++e  q++   +y+VL+
  gi|330508988|ref|YP_004385416.1| 405 DeglsQKKQAEILQRFRAGEYNVLI 429
                                       12333668899999999*****995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (762 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.41
# Mc/sec: 5543.70
//
Query:       gi|330508989|ref|YP_004385417.1|  [L=266]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.7    8.6   4.9        2.8    7.9   4.9    1.4  1  LPAM_2    Prokaryotic lipoprotein-attachment site


Domain annotation for each model (and alignments):
>> LPAM_2  Prokaryotic lipoprotein-attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.9   0.00015       2.8       2      15 ..       6      19 ..       5      20 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00015
                            LPAM_2  2 llllallllLaGCG 15
                                      +++l+l+ +LaGCG
  gi|330508989|ref|YP_004385417.1|  6 IVALVLAIALAGCG 19
                                      799*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1958.46
//
Query:       gi|330508990|ref|YP_004385418.1|  [L=136]
Description: hypothetical protein MCON_3346 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1030.36
//
Query:       gi|330508991|ref|YP_004385419.1|  [L=50]
Description: hypothetical protein MCON_3347 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 391.48
//
Query:       gi|330508992|ref|YP_004385420.1|  [L=138]
Description: hypothetical protein MCON_3348 [Methanosaeta concilii GP6]
Scores for complete 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  133.8   0.0      5e-39  133.6   0.0    1.0  1  DUF2072      Zn-ribbon containing protein
  ------ inclusion threshold ------
      0.025   14.5   0.7      0.041   13.8   0.7    1.3  1  Prok-RING_1  Prokaryotic RING finger family 1
      0.039   14.1   0.9      0.089   12.9   0.9    1.6  1  Zn-ribbon_8  Zinc ribbon 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 !  133.6   0.0   8.4e-43     5e-39       1     133 []       2     134 ..       2     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 8.4e-43
                           DUF2072   1 PHkCtkCekvfedgskeilkGCpsCGgkkFlyvkeeekkedvseeke.elvaeaeee......ieevldaeeteeek 70 
                                       PH Ct+C++vfe+g++ ilkGCpsCG+kkF++v+++ +  d s+ ++ +++++a+++      +e+ l+++++e ++
  gi|330508992|ref|YP_004385420.1|   2 PHICTRCNSVFESGED-ILKGCPSCGWKKFMFVRKMPQGGDISSVSQdRIISRAMGVrmppkkREKPLAIDRDEPSI 77 
                                       9*************99.************************999998556666666677777788888888888888 PP

                           DUF2072  71 lekkekekaekekeeedrvesvrilepGsYelNlekLlerdelvmalkeegkYvvdlpsvlkk 133
                                        e       + ek e++++es++i+ pG+YelNl++L+er+el+ma+ke g+Y++dl+sv++k
  gi|330508992|ref|YP_004385420.1|  78 REF-----GDGEKLEGEKLESIKITAPGTYELNLPSLFEREELIMAVKE-GTYFIDLTSVFRK 134
                                       666.....5788999*******************************998.**********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 ?   13.8   0.7   6.8e-06     0.041       6      27 ..       4      26 ..       2      29 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.8e-06
                       Prok-RING_1  6 kCpvCgkelkeedDiVv.CpeCg 27
                                      +C+ C+  +++++Di   Cp Cg
  gi|330508992|ref|YP_004385420.1|  4 ICTRCNSVFESGEDILKgCPSCG 26
                                      7**************966****9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.9   1.5e-05     0.089       8      33 ..       5      26 ..       4      30 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                       Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCg 33
                                      C++C+++fe    + ++ l+ CP+Cg
  gi|330508992|ref|YP_004385420.1|  5 CTRCNSVFE----SGEDILKGCPSCG 26
                                      *********....45666777****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1169.45
//
Query:       gi|330508993|ref|YP_004385421.1|  [L=114]
Description: hypothetical protein MCON_3349 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-42  144.0   1.4    1.4e-42  143.8   1.4    1.0  1  DUF2073   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2073  Uncharacterized protein conserved in archaea (DUF2073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.8   1.4   7.9e-47   1.4e-42       1     105 []       9     111 ..       9     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 143.8 bits;  conditional E-value: 7.9e-47
                           DUF2073   1 lekmtsmekirlildkvkegkivvlEkgLtpeeeakliettmeeikpdeFsGieietypkkekdkgllekllgkkes 77 
                                       le+mtsmekirlildkvk+gkivvlE+gLtp+ee +lie+tm+ei++deFsGieie+yp+k+   ++l++++gk   
  gi|330508993|ref|YP_004385421.1|   9 LENMTSMEKIRLILDKVKTGKIVVLESGLTPDEEVRLIEMTMTEIRVDEFSGIEIESYPSKKG-GSFLDRIFGKG-L 83 
                                       799**********************************************************99.**********8.9 PP

                           DUF2073  78 eerltvigPanqlktlkkdkdlisalvs 105
                                       + r+tvigPanq++t++kd+  i + vs
  gi|330508993|ref|YP_004385421.1|  84 KGRMTVIGPANQIHTIEKDEFQIRTKVS 111
                                       ********************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 969.20
//
Query:       gi|330508994|ref|YP_004385422.1|  [L=212]
Description: small GTP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-16   58.9   0.0    5.7e-16   58.6   0.0    1.1  1  MMR_HSR1      50S ribosome-binding GTPase
    1.4e-13   50.8   0.0    2.1e-06   27.4   0.0    3.0  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    3.9e-06   26.4   0.0      0.018   14.5   0.0    2.4  2  Arf           ADP-ribosylation factor family
    2.2e-05   24.4   0.0      0.083   12.8   0.0    2.1  2  RsgA_GTPase   RsgA GTPase
    8.2e-05   23.0   0.0    0.00014   22.3   0.0    1.4  1  AAA           ATPase family associated with various cellular 
    0.00018   21.7   0.0      0.066   13.4   0.0    2.3  2  Roc           Ras of Complex, Roc, domain of DAPkinase
    0.00023   20.7   0.2     0.0024   17.4   0.2    2.4  1  FeoB_N        Ferrous iron transport protein B
    0.00044   19.6   0.0    0.00058   19.2   0.0    1.2  1  Septin        Septin
     0.0011   19.0   0.0     0.0017   18.3   0.0    1.3  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0015   18.0   0.0        0.2   11.0   0.0    2.3  2  SRPRB         Signal recognition particle receptor beta subun
     0.0025   17.6   0.0     0.0041   16.9   0.0    1.6  1  AAA_24        AAA domain
  ------ inclusion threshold ------
       0.01   15.4   0.0       0.02   14.5   0.0    1.6  1  AAA_25        AAA domain
       0.01   14.9   0.1      0.016   14.3   0.1    1.2  1  Parvo_NS1     Parvovirus non-structural protein NS1
       0.02   14.8   0.0      0.059   13.3   0.0    1.7  2  NACHT         NACHT domain
      0.046   14.3   0.0      0.094   13.3   0.0    1.7  1  AAA_18        AAA domain
      0.065   12.4   0.0       0.11   11.7   0.0    1.3  1  NB-ARC        NB-ARC domain
      0.072   13.0   0.0       0.12   12.3   0.0    1.5  1  ATPase_2      ATPase domain predominantly from Archaea
      0.075   13.4   0.0       0.15   12.4   0.0    1.5  1  RNA_helicase  RNA helicase
      0.084   13.4   0.0       0.11   13.0   0.0    1.2  1  ABC_tran      ABC transporter
      0.086   11.8   0.0        3.2    6.6   0.0    2.5  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
        0.1   13.0   0.0       0.15   12.4   0.0    1.4  1  AAA_16        AAA ATPase domain
       0.14   12.3   0.0         11    6.0   0.0    2.3  2  Dynamin_N     Dynamin family
       0.15   12.3   0.0       0.55   10.5   0.0    2.0  2  AAA_22        AAA domain


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   7.3e-19   5.7e-16       1     114 []      25     169 ..      25     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 7.3e-19
                                       EEEEEESTTSSHHHHHHHHHT.....S.TEEESSSTTSSSSEEEEE...EEETT..EEEEEEECGGC.......... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltg.....e.kaivsdkpgtTrdinegr...vklkg..keielvDtpGl.......... 56 
                                       +++++G pN+GK+tL n++++     +    vs +p  Tr   +++   ++ +g   e+ +vDtpG+          
  gi|330508994|ref|YP_004385422.1|  25 RIGLYGPPNAGKTTLANRILKdwstgDaIGTVSPIPHETRRAMRREglvINANGssIELDIVDTPGMatkidfkefm 101
                                       699*****************85544323679**********9777533333444347799******87776766665 PP

                                       ...S...S...HHHHHH...HHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  57 ...i...e...gaseek...glgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                          +   e   +a+  +   g+ +a++ l++ d +llv+d++e+ +++++ ++   +e +k pl++v+nk
  gi|330508994|ref|YP_004385422.1| 102 afgLsetEskkRAK--EateGVIEAIKWLDDLDGVLLVMDSTEDPYTQVNVTVIGNMEARKLPLLIVANK 169
                                       55414332322222..123578888888889*********8888************999*********98 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.8e-07   0.00069       4      94 ..      24     108 ..      21     123 .. 0.74
   2 !   27.4   0.0   2.7e-09   2.1e-06      87     191 ..     124     210 ..     118     212 .] 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.8e-07
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESS. CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPG. 79 
                                         ig+ g  ++GKtTL  r+l++ ++ +  g++          ++E +r +  +  +i+ +  +++ ++ ++DtPG 
  gi|330508994|ref|YP_004385422.1|  24 ARIGLYGPPNAGKTTLANRILKDWSTGDAIGTVS-------PIPHETRRAMRREGLVINAN--GSSIELDIVDTPGm 91 
                                       579999***************9999988877655.......45556555555555555555..66666********3 PP

                                       ..SGGGHHHHHHHHHT- CS
                          GTP_EFTU  80 ..HvdFskevirglrvl 94 
                                          +dF + +  gl+ +
  gi|330508994|ref|YP_004385422.1|  92 atKIDFKEFMAFGLSET 108
                                       33347877777777665 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.7e-09
                                       HHHHHHT-SEEEEEEETTTBSTHHHH.HHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  87 virglrvlDgavlvvdaveGvepqte.evlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekyge 162
                                        i+ l  lDg++lv+d++e++ +q + +v+  + ++++p+ ++ NKmD ++a+ ++i  +  q+             
  gi|330508994|ref|YP_004385422.1| 124 AIKWLDDLDGVLLVMDSTEDPYTQVNvTVIGNMEARKLPLLIVANKMDLPNASPSRISAAFPQHS------------ 188
                                       55668899************999975499*********************999999888777555............ PP

                                       TTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 163 kgekevpvvfgSalkgegvktllealvel 191
                                              +v++Sal+g ++++l +a+ ++
  gi|330508994|ref|YP_004385422.1| 189 -------IVPISALEGSNIDDLYQAIATH 210
                                       .......8999999999999999999987 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00056      0.44       5      37 ..      15      46 ..      11      75 .. 0.80
   2 !   14.5   0.0   2.3e-05     0.018      80     136 ..     129     180 ..     118     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00056
                                      HHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHS CS
                               Arf  5 laklklkkkelrilllGLDnaGKtTilkklkle 37
                                      ++k+++ kk +ri l G  naGKtT+ +++ ++
  gi|330508994|ref|YP_004385422.1| 15 IRKIFK-KKRARIGLYGPPNAGKTTLANRILKD 46
                                      677777.99****************99987654 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.3e-05
                                       TTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHH CS
                               Arf  80 ektdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeel 136
                                       ++ d+v+ v+Ds++    +       +++ + e ++ +ll++aNK+Dlp+a   + +
  gi|330508994|ref|YP_004385422.1| 129 DDLDGVLLVMDSTEDPYTQVN----VTVIGNMEARKLPLLIVANKMDLPNASP-SRI 180
                                       566777777777765433322....3567778999**************9854.444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00011     0.083     103     162 ..      27      92 ..      11      97 .. 0.80
   2 !    9.7   0.0   0.00097      0.75      17      98 ..     132     208 ..     116     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                       EEECSTTSSHHHHHHHHCT..T-----S--------------SEEEEEETTTEE....EESS-SSS CS
                       RsgA_GTPase 103 vlvGqSGvGKStLinallp..elelktgevseklgrGkhTTtavellelaeggl....liDtPGfr 162
                                        l G+  +GK+tL n++l   ++  ++g vs   ++ +   ++  l+  a+g+     ++DtPG+ 
  gi|330508994|ref|YP_004385422.1|  27 GLYGPPNAGKTTLANRILKdwSTGDAIGTVSPIPHETRRAMRREGLVINANGSSieldIVDTPGMA 92 
                                       5889999**********9945567899*****999999999999998877755423338*****96 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00097
                                       -EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHH CS
                       RsgA_GTPase  17 dqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleel 93 
                                       d +l+v+  +e+ +++  +  ++  +e+++++++iv nK+Dl + +   +++++++ +   +++ +sa +++++++l
  gi|330508994|ref|YP_004385422.1| 132 DGVLLVMDSTEDPYTQVNV-TVIGNMEARKLPLLIVANKMDLPNASP--SRISAAFPQH--SIVPISALEGSNIDDL 203
                                       6777777666444444333.58899*****************99988..5566666555..6677777777888887 PP

                                       HHHCT CS
                       RsgA_GTPase  94 kellk 98 
                                        ++++
  gi|330508994|ref|YP_004385422.1| 204 YQAIA 208
                                       77665 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 !   22.3   0.0   1.8e-07   0.00014       3     115 ..      28     173 ..      26     185 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.8e-07
                                       EESSTTSSHHHHHHHHHHHHTHE......................EEEEETTTCSSS.................STT CS
                               AAA   3 lyGppGtGKTllakavakelgve......................fleisgsellsk.................yvg 40 
                                       lyGpp  GKT+la+ + k++++                       +++ +gs++  +                  +g
  gi|330508994|ref|YP_004385422.1|  28 LYGPPNAGKTTLANRILKDWSTGdaigtvspiphetrramrreglVINANGSSIELDivdtpgmatkidfkefmAFG 104
                                       9******************8533334444556677777788888867777777664457777777777777777999 PP

                                       HHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHH.HHHHHHTTTSSSTEEEEEEESSGGGS CS
                               AAA  41 esekkirelfkeakekakp.silfiDEidalaksrsgseseeeervvnqL.lteldgvkkkeskvivigatnrpdkl 115
                                        se + ++  kea e      i ++D++d +         +++e+   q  +t++ +++   +k+ +++++n++d +
  gi|330508994|ref|YP_004385422.1| 105 LSETESKKRAKEATEGV-IeAIKWLDDLDGVLLVM-----DSTEDPYTQVnVTVIGNMEA--RKLPLLIVANKMDLP 173
                                       99999999999999998.55999******998888.....22223333321345555555..357888888888765 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   8.5e-05     0.066       2      66 ..      26      91 ..      25     102 .. 0.84
   2 ?    6.1   0.0     0.016        13      80     120 .]     131     172 ..     124     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.5e-05
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEETTTT.EEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SG CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstig.vdfltkevtkikgvendkkvkkvklniWDtaGq 66
                                      + l G  ++GKt+l++r+++d  + +   t++ +   t+++++ +g+  + + ++++l+i Dt G 
  gi|330508994|ref|YP_004385422.1| 26 IGLYGPPNAGKTTLANRILKDWSTGDAIGTVSpIPHETRRAMRREGLVINANGSSIELDIVDTPGM 91
                                      6688****************9999888877753667778888889999999999999999999885 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
                                       SCEEEEEEEGHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TTT CS
                               Roc  80 aalailvydsrssenlkeWlkelkkvag.kspvilvgnkiDl 120
                                        + ++lv+ds+++   +  ++ + ++   k p+++v+nk+Dl
  gi|330508994|ref|YP_004385422.1| 131 LDGVLLVMDSTEDPYTQVNVTVIGNMEArKLPLLIVANKMDL 172
                                       5678999999999888888999988755166*********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 !   17.4   0.2   3.1e-06    0.0024       2     156 .]      25     207 ..      24     207 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.1e-06
                                       EEEEEESTTSSHHHHHHHHHT...TSEEEEESTTSSSEEEEEEEEE......TT..EEEEEEE----.......... CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltg...akqkvgNwpGvtvekkegklkl......kg..keveivDlPGi.......... 57 
                                       ++ l G pn+Gkttl n++ +   +   +g  + +  e +++  +       +g   e++ivD PG+          
  gi|330508994|ref|YP_004385422.1|  25 RIGLYGPPNAGKTTLANRILKdwsTGDAIGTVSPIPHETRRAMRREglvinaNGssIELDIVDTPGMatkidfkefm 101
                                       57899*************9762223345665555554444333222222333442367889*****97777766655 PP

                                       .SSS.......SSSSHHHHHHHHHHHCTSSSEEEEEEEGGG...HHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTE CS
                            FeoB_N  58 .Ysl.......sayseeekvardflleeepdvvvnvvdatn...lernLyLtlqllelgvpvvlalnmideaekkgi 123
                                        + l        a    e v + +   ++ d v+ v+d+t+    + n++++ ++   ++p++++ n++d  +++  
  gi|330508994|ref|YP_004385422.1| 102 aFGLseteskkRAKEATEGVIEAIKWLDDLDGVLLVMDSTEdpyTQVNVTVIGNMEARKLPLLIVANKMDLPNASPS 178
                                       5555554433222223344555555578999*******9974435667777777777789999*******9999999 PP

                                       EE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N 124 eidlkkLsekLgvpvvktsakkkegieellkai 156
                                       +i ++  +      +v++sa ++++i++l +ai
  gi|330508994|ref|YP_004385422.1| 179 RISAAFPQ----HSIVPISALEGSNIDDLYQAI 207
                                       99876544....568999999999999998875 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.5e-07   0.00058      10      80 ..      29      99 ..      24     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.5e-07
                                      EEBTTSSCCCCCCTTSSSS------------------S-EEEEEEEEETTCEEEEEEEE---BSSSSSHHC CS
                            Septin 10 vGesglGkttlintlfetdlieeekleeasekkkktveikkkkvvieedgvklnltviDtpgfGdavdnsk 80
                                       G    Gkttl n ++++  + +   +     +++   ++++  vi+ +g  ++l ++Dtpg   ++d ++
  gi|330508994|ref|YP_004385422.1| 29 YGPPNAGKTTLANRILKDWSTGDAIGTVSPIPHETRRAMRREGLVINANGSSIELDIVDTPGMATKIDFKE 99
                                      577889**********999888865554445778888999************************9999765 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.2e-06    0.0017      56     101 ..     161     208 ..     136     212 .] 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.2e-06
                      MMR_HSR1_Xtn  56 ipclyvlNKiDl..isleeldelarepnsvviSaekelnldeLkekiw 101
                                       +p l+v NK+Dl  +s + +++   ++++v+iSa ++ n+d+L ++i 
  gi|330508994|ref|YP_004385422.1| 161 LPLLIVANKMDLpnASPSRISAAFPQHSIVPISALEGSNIDDLYQAIA 208
                                       799*********5555556655555789999************99985 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00026       0.2       3      59 ..      23      91 ..      21     102 .. 0.66
   2 ?    4.6   0.0     0.025        19      66     129 ..     121     177 ..     114     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                                      --EEEEE-STTSSHHHHHHHHHHS....S---B---S..S-EEETTG.........GGTT-SEEEETT- CS
                             SRPRB  3 kpavllvGlsdsGKTslftrLttd....svkktvtSq..essaalkv......ksekgskltliDfPGh 59
                                      + ++ l G+ ++GKT+l +r+++d     +  tv  +  e+  a +        +    +l+++D PG 
  gi|330508994|ref|YP_004385422.1| 23 RARIGLYGPPNAGKTTLANRILKDwstgDAIGTVSPIphETRRAMRReglvinANGSSIELDIVDTPGM 91
                                      5677799***************99865534444444432333333335666433445556678999985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.025
                                       HHHHHHHHGGEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT--- CS
                             SRPRB  66 lleklkaksslkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflaks 129
                                       ++e +k  + l g++ v+DSt dp    +v     +++    ++  ++++li  nK +l  a +
  gi|330508994|ref|YP_004385422.1| 121 VIEAIKWLDDLDGVLLVMDSTEDPYTQVNV-----TVI--GNMEARKLPLLIVANKMDLPNASP 177
                                       578888899999999999999999765544.....333..334467788888888888877654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.2e-06    0.0041       2      23 ..      23      52 ..      22     160 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.2e-06
                            AAA_24  2 klkiliyGpsgiGKTtlakel........g 23
                                       ++i +yGp+ +GKTtla+++         
  gi|330508994|ref|YP_004385422.1| 23 RARIGLYGPPNAGKTTLANRIlkdwstgdA 52
                                      579****************99655555550 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.6e-05      0.02      33      66 ..      23      63 ..      13     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
                            AAA_25 33 gelallaGapgtGKttlaldlalavatGkpwlg........p 66
                                       + + l+G+p +GKttla  +  +++tG+   g         
  gi|330508994|ref|YP_004385422.1| 23 RARIGLYGPPNAGKTTLANRILKDWSTGDAI-GtvspipheT 63
                                      566779*********************9965.6577553332 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 ?   14.3   0.1   2.1e-05     0.016     106     136 ..      14      45 ..       9      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                         Parvo_NS1 106 wlskql.gkrntvwfyGpantGktnlaeaIak 136
                                       w++k +  kr  +++yGp+n Gkt la+ I k
  gi|330508994|ref|YP_004385422.1|  14 WIRKIFkKKRARIGLYGPPNAGKTTLANRILK 45 
                                       555544145778****************9986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.6e-05     0.059       5      47 ..      28      68 ..      24      78 .. 0.79
   2 ?   -1.7   0.0         3   2.4e+03      82      99 ..     133     150 ..     112     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.6e-05
                                      EEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTT CS
                             NACHT  5 lqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsr 47
                                      l G++  GKTtL+ ++  +w +g+  +     ++ ++ r+  r
  gi|330508994|ref|YP_004385422.1| 28 LYGPPNAGKTTLANRILKDWSTGDAIGT--VSPIPHETRRAMR 68
                                      7788899****************98883..5666666666655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3
                                       CEEEEEE-STT-SS-TCH CS
                             NACHT  82 rlLlilDglDelvtdlgq 99 
                                        +Ll++D+ ++  t+ + 
  gi|330508994|ref|YP_004385422.1| 133 GVLLVMDSTEDPYTQVNV 150
                                       578889988877776555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00012     0.094       1      20 [.      26      45 ..      26     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                            AAA_18  1 IlltGtpGvGKttlakeLsk 20
                                      I+l G+p +GKttla+++ k
  gi|330508994|ref|YP_004385422.1| 26 IGLYGPPNAGKTTLANRILK 45
                                      89*************99844 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.11      20      45 ..      23      48 ..       9      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                                      SEEEEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC 20 slvvalvGmgGvGKttlakqilnksd 45
                                      +  ++l+G +  GKttla+ il++ +
  gi|330508994|ref|YP_004385422.1| 23 RARIGLYGPPNAGKTTLANRILKDWS 48
                                      3359******************9965 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015      0.12      14      44 ..      18      47 ..      13     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                          ATPase_2 14 ilerepneiyfiYGpegsGKtaLlkeiienl 44
                                      i ++++++ + +YGp + GKt+L ++i++  
  gi|330508994|ref|YP_004385422.1| 18 IFKKKRAR-IGLYGPPNAGKTTLANRILKDW 47
                                      55554433.457**************99865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00019      0.15       3      23 ..      28      48 ..      26      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                      RNA_helicase  3 lyGpsgeGKStlakeLakall 23
                                      lyGp++ GK+tla+++ k+++
  gi|330508994|ref|YP_004385422.1| 28 LYGPPNAGKTTLANRILKDWS 48
                                      8**************999876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014      0.11      10      67 ..      22      77 ..      19     152 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                                      TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67
                                      +  ++++ G+  aGK+tL++ +++  +   G+      ++ +++++ +r+e  v+  +
  gi|330508994|ref|YP_004385422.1| 22 KRARIGLYGPPNAGKTTLANRILKDWS--TGDAIGTVSPIPHETRRAMRREGLVINAN 77
                                      56789*****************98755..45443445777777777777766665555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0042       3.2      29      51 ..      23      45 ..      14      60 .. 0.84
   2 ?    2.7   0.0     0.065        51     205     229 ..     187     211 ..     132     212 .] 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0042
                                      SEEEEEEE-TTSSHHHHHHHHHH CS
                              MeaB 29 aqvvGltGvPGaGkstlvealgl 51
                                        ++Gl G P aGk tl +++  
  gi|330508994|ref|YP_004385422.1| 23 RARIGLYGPPNAGKTTLANRILK 45
                                      469**************999865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.065
                                       -EEEEEBCCCTBSHHHHHHHHHHHH CS
                              MeaB 205 pkvlktsavegeGidelvdaieehr 229
                                         ++ +sa+eg  id+l +ai  h+
  gi|330508994|ref|YP_004385422.1| 187 HSIVPISALEGSNIDDLYQAIATHF 211
                                       4678899999999999999999986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00019      0.15      29      93 ..      28     112 ..      16     210 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                            AAA_16  29 lsGesGvGKsslvrellralekd...................ggiflrgkcdqlesaipysa.laqalareellrql 85 
                                       l+G++  GK++l++++l+ +++                    +g++++++  + e +i   +  a+ ++++e+++  
  gi|330508994|ref|YP_004385422.1|  28 LYGPPNAGKTTLANRILKDWSTGdaigtvspiphetrramrrEGLVINANGSSIELDIVDTPgMATKIDFKEFMAFG 104
                                       8*****************99888666666666666666666546666666655544432244466666666666666 PP

                            AAA_16  86 ldeaesae 93 
                                       l+e+es++
  gi|330508994|ref|YP_004385422.1| 105 LSETESKK 112
                                       66655544 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.014        11       1      21 [.      26      46 ..      26      71 .. 0.79
   2 ?    4.3   0.0     0.048        38     103     120 ..      83     116 ..      74     170 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.014
                                      EEEEEBTTTTHHHHHHHHHTS CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlge 21
                                      i + G  ++GK++++n +l++
  gi|330508994|ref|YP_004385422.1| 26 IGLYGPPNAGKTTLANRILKD 46
                                      5678999***********976 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.048
                                       EEEEE---B-SSSGTTS................H CS
                         Dynamin_N 103 ltlvDlPGldsvnkrdq................e 120
                                       l +vD+PG+    + ++                e
  gi|330508994|ref|YP_004385422.1|  83 LDIVDTPGMATKIDFKEfmafglseteskkrakE 116
                                       789*****98765555445555555555555550 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0007      0.55      10      29 ..      28      47 ..      20     142 .. 0.69
   2 ?   -1.0   0.0       2.5     2e+03      34      64 ..     181     211 ..     167     212 .] 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0007
                            AAA_22 10 vtGesGtGKTtllrrlleql 29
                                      ++G++ +GKTtl++r+l+  
  gi|330508994|ref|YP_004385422.1| 28 LYGPPNAGKTTLANRILKDW 47
                                      89*************98754 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.5
                            AAA_22  34 kaeeerpevvfvtlpsstsskdllrellral 64 
                                       +a+ ++ ++v + + ++++ +dl+++++  +
  gi|330508994|ref|YP_004385422.1| 181 SAAFPQHSIVPISALEGSNIDDLYQAIATHF 211
                                       4444677888888999999999999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 1561.86
//
Query:       gi|330508995|ref|YP_004385423.1|  [L=373]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   0.3    3.3e-14   53.6   0.4    1.5  2  Radical_SAM  Radical SAM superfamily
     0.0014   19.1   0.1     0.0032   17.9   0.1    1.7  1  SPASM        Iron-sulfur cluster-binding domain
  ------ inclusion threshold ------
      0.031   14.5   0.1      0.064   13.5   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 !   53.6   0.4   5.5e-18   3.3e-14       1     166 [.      91     244 ..      91     245 .. 0.94
   2 ?   -3.2   0.0       1.6   9.6e+03      29      64 ..     261     296 ..     256     316 .. 0.64

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 5.5e-18
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       ++vtr C  +C +C ++e       + +ls eei++ ++++  ++g+  ++++ g+pll+ d+ el+++   +   +
  gi|330508995|ref|YP_004385423.1|  91 IEVTRSCGAKCDHCLIKE------GEGELSSEEIKRVIDQA-LDMGTCIITFTEGDPLLREDIFELIRHVDPE---K 157
                                       689**************7......7999*************.8********************9999999998...9 PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpG 154
                                         + + t+g+  + ek+ +l+e+g+  + +g+ ++++e++ +  +  +   + lea++++ + g+  v+  + +l G
  gi|330508995|ref|YP_004385423.1| 158 AVVNLFTPGLEMTVEKAVKLREAGLYNLIIGVYSINPEEHDRVRGVAGAHAKALEAIRIALDTGLL-VTMSCHILSG 233
                                       **************************************777777799*******************.9******999 PP

                                       TSHHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 155 endeeleellel 166
                                       + d+ + el+el
  gi|330508995|ref|YP_004385423.1| 234 QVDR-IMELYEL 244
                                       9999.7777776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHH CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  29 lsveeileevkelk.aekgvkevilgggepllypdfv 64 
                                       +s+e+ l ++++ k  +   + + ++ g p l ++ +
  gi|330508995|ref|YP_004385423.1| 261 KSPEQALTQIEREKiINI-YRKINSTPGGPRLFANTY 296
                                       677777877777765555.777777766666655555 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   5.4e-07    0.0032       1      46 [.     304     343 ..     304     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.4e-07
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwns 46 
                                       C+a++r + +++dG V  C ++      + +  +ire sl++ w+ 
  gi|330508995|ref|YP_004385423.1| 304 CMAGRRWMHVAVDGRVRACPYM------QDSYDDIREVSLKDAWKR 343
                                       99*****************444......24779***********54 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.1e-05     0.064      14      84 ..      96     158 ..      88     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                           Fer4_12  14 gCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekp 84 
                                        C  +C+ C      +   + e ++e ++++i+++ +     +t++ G+Pll   +e++ el+++v  ek 
  gi|330508995|ref|YP_004385423.1|  96 SCGAKCDHCL----IKEG-EGELSSEEIKRVIDQALDMGTCIITFTEGDPLL---REDIFELIRHVDPEKA 158
                                       6889999988....3333.34556677889999999****************...9999*****9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.58
# Mc/sec: 1950.47
//
Query:       gi|330508996|ref|YP_004385424.1|  [L=391]
Description: argininosuccinate synthase [Methanosaeta concilii GP6]
Scores for complete 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-162  539.4   0.0   6.6e-162  539.2   0.0    1.0  1  Arginosuc_synth  Arginosuccinate synthase
  ------ inclusion threshold ------
      0.072   12.2   0.0       0.11   11.6   0.0    1.2  1  NAD_synthase     NAD synthase
       0.16   11.5   0.0        0.3   10.6   0.0    1.5  1  QueC             Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  539.2   0.0  1.1e-165  6.6e-162       1     386 [.       5     385 ..       5     387 .. 0.99

  Alignments for each domain:
  == domain 1  score: 539.2 bits;  conditional E-value: 1.1e-165
                   Arginosuc_synth   1 vLaysGGlDtsviikllkeklg.eeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikana 76 
                                       vLaysGGlDtsv+i+ll+e++g +++++v+vdvGq++ d+++ + +a++l++ +++++Da+eefve+ +fp ikan+
  gi|330508996|ref|YP_004385424.1|   5 VLAYSGGLDTSVCIPLLRERYGfDKIVTVLVDVGQPRSDIERGNLRAKQLAD-EHYTIDAREEFVEKCLFPLIKANG 80 
                                       8*********************99**************************99.************************ PP

                   Arginosuc_synth  77 lYedrYllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeiey 153
                                        Ye+ Y+lgta+aRPlia k  e+a k g + +ahGctG+GnDq+Rfe+++r+++    viaP+Rel+l Re+ei+y
  gi|330508996|ref|YP_004385424.1|  81 SYEG-YVLGTAIARPLIASKSAEIADKLGIKNLAHGCTGRGNDQLRFEAIFRATD--CRVIAPMRELDLAREWEIDY 154
                                       ****.***********************************************998..9******************* PP

                   Arginosuc_synth 154 akekgipvevtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeel 230
                                       a+e+gi+v+vtk+kp+siDen+++rsie+g+Ledp ++ppe+iy +tk p++++ ++++vei+f++GvPv+ldg+++
  gi|330508996|ref|YP_004385424.1| 155 AREHGIDVPVTKDKPWSIDENIWSRSIEGGKLEDPYFEPPEEIYGWTKTPSSDR-SAQIVEIGFKEGVPVSLDGKQM 230
                                       ****************************************************99.99******************** PP

                   Arginosuc_synth 231 svlelieklneiagkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvY 307
                                       + +eliekln+i+g+hGvGR+D++edR++glk+Re+Ye+paa++L++ahkdle+l+l+r++++fk +v+e ++el Y
  gi|330508996|ref|YP_004385424.1| 231 NGMELIEKLNQIGGEHGVGRTDMIEDRVMGLKARENYEHPAATILLTAHKDLERLVLSRNELRFKVMVDEFWSELAY 307
                                       ***************************************************************************** PP

                   Arginosuc_synth 308 kGlwfsPlkealdafiektqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGfikihglqa 384
                                        Gl+ +Pl+++l+af++++q+rv+G+v++klf Gs++ +gR+s+ +lY+++++s+d ++++ qk+aeGf+k+hg+qa
  gi|330508996|ref|YP_004385424.1| 308 MGLVEDPLYADLNAFVDQSQKRVNGSVKIKLFCGSAISVGRQSPDALYSQDMVSFD-SQTLSQKDAEGFAKYHGFQA 383
                                       ********************************************************.99*****************9 PP

                   Arginosuc_synth 385 kl 386
                                       +l
  gi|330508996|ref|YP_004385424.1| 384 RL 385
                                       87 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.8e-05      0.11      19      82 ..       2      64 ..       1      72 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.8e-05
                                      SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---H CS
                      NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidik 82
                                      ++vvl  SGG+D s+   l ++  g ++++++l+ ++ ++++d+e     a++l +e  tid +
  gi|330508996|ref|YP_004385424.1|  2 SEVVLAYSGGLDTSVCIPLLRERYGFDKIVTVLV-DVGQPRSDIERGNLRAKQLADEHYTIDAR 64
                                      689******************************9.9999***************9999999865 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     5e-05       0.3       2      42 ..       4      47 ..       3      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5e-05
                                      EEEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-T.TSHHHH CS
                              QueC  2 avvllSGGlDSttvlalakkeg..kevealtfdYgqr.hkkele 42
                                      +v+  SGGlD ++++ l ++++  +++ ++ +d gq   ++e  
  gi|330508996|ref|YP_004385424.1|  4 VVLAYSGGLDTSVCIPLLRERYgfDKIVTVLVDVGQPrSDIERG 47
                                      57789**********9999987669**********963555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 2095.41
//
Query:       gi|330508997|ref|YP_004385425.1|  [L=138]
Description: hypothetical protein MCON_3353 [Methanosaeta concilii GP6]
Scores for complete 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-32  109.9   3.3    6.6e-32  109.4   3.3    1.2  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 !  109.4   3.3   3.7e-36   6.6e-32       2      83 .]      32     111 ..      31     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 3.7e-36
                           DUF2111   2 helvgklPvtirsknkkGvriekgkvvdedYtgpvLeevleegkvikkvpkeGaYkGvpvvvaPikekegkviaaiG 78 
                                       +e+v+ lPvt+r  + +Gvr+e+gkvvd +Ytgp+Leev+++gk+i+++pk+Ga+kGvpv vaPi   eg+++aaiG
  gi|330508997|ref|YP_004385425.1|  32 NEIVR-LPVTMRGLKYPGVRVENGKVVDGNYTGPILEEVIRTGKAIRTIPKSGAFKGVPVSVAPIVV-EGRTVAAIG 106
                                       56777.*************************************************************.********* PP

                           DUF2111  79 vVDit 83 
                                       +VD++
  gi|330508997|ref|YP_004385425.1| 107 IVDVI 111
                                       ***96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 769.36
//
Query:       gi|330508998|ref|YP_004385426.1|  [L=156]
Description: N-GNAT family acetyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-12   47.0   0.0    3.3e-12   46.7   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.1e-12   46.5   0.1    3.8e-12   46.2   0.1    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.7e-09   37.9   0.2    2.4e-09   37.5   0.2    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.5e-05   24.1   0.1    3.5e-05   23.7   0.1    1.2  1  FR47             FR47-like protein
    3.2e-05   24.0   0.0     0.0014   18.7   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.025   14.7   0.0      0.048   13.8   0.0    1.5  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
       0.13   10.7   0.0       0.16   10.4   0.0    1.0  1  Cellulose_synt   Cellulose synthase


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 !   46.7   0.0   1.3e-15   3.3e-12       3     117 .]      13     121 ..      11     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.3e-15
                                       HHHHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHH CS
                    Acetyltransf_1   3 dlvellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGs 79 
                                       ++v+++ ++f+  + +a+   ++ ++++ a  ++++e +++++Gfi ++   +     ++++ l V+  yr++G+G+
  gi|330508998|ref|YP_004385426.1|  13 QMVQIESLCFP--DDTAFPPGMFAYLIRYAVAIVACEPEDQILGFIIGYNSGN----AGAVYTLDVHTGYRRRGIGK 83 
                                       56777777754..34444444677777788888889999*******7777766....8******************* PP

                                       HHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  80 aLlealeerareegikkivlaveedndaairlYeklGF 117
                                       +Ll  le+r+   g+++i l+ +     ai+lY+k G+
  gi|330508998|ref|YP_004385426.1|  84 ELLLSLEKRLAMMGARAIRLEASLEKPEAIELYRKAGY 121
                                       *********************************88*98 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.1   1.5e-15   3.8e-12      32     126 ..      42     143 ..      32     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.5e-15
                   Acetyltransf_10  32 lllvaeeggkivGvi.elrdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYe 102
                                        ++++e +++i+G+i + ++++    ++ l V+  yr++Gigk+Ll  +e+++  +g +  +l++   + +a+++Y+
  gi|330508998|ref|YP_004385426.1|  42 AIVACEPEDQILGFIiG-YNSGnagAVYTLDVHTGYRRRGIGKELLLSLEKRLAMMGARAiRLEASLEKpEAIELYR 117
                                       6789999********53.4444477***************************999999966777665556******* PP

                   Acetyltransf_10 103 klGFkav..geeqeenGirfvpMeke 126
                                       k G+++    ++ +  G++ v+M k 
  gi|330508998|ref|YP_004385426.1| 118 KAGYREReiVRNYYGRGCHAVRMWKI 143
                                       ****99888999***********775 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.2   9.3e-13   2.4e-09       7      76 .]      45     123 ..      33     123 .. 0.69

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 9.3e-13
                                       EEEETTEEEEEEEEEEESTCTEEEE...E-GGGTTSSHHHHHHH.HTT....SEEE.EE.EEEETHHHHHHHHHHTT CS
                    Acetyltransf_7   7 VaeddgkivGfialslldaeitrla...VdpeyrgkGiGraLle.aae....kgii.le.qlelnaekaikfYeklG 73 
                                        +e +++i+Gfi+ + ++ + + ++   V++ yr++GiG++Ll  +++     g + +  ++ l++++ai++Y+k G
  gi|330508998|ref|YP_004385426.1|  45 ACEPEDQILGFIIGYNSG-NAGAVYtldVHTGYRRRGIGKELLLsLEKrlamMGARaIRlEASLEKPEAIELYRKAG 120
                                       355569999**9988887.333344445**************95332234454422223446665569********* PP

                                       EEE CS
                    Acetyltransf_7  74 Fee 76 
                                       ++e
  gi|330508998|ref|YP_004385426.1| 121 YRE 123
                                       *86 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   1.4e-08   3.5e-05      21      80 ..      64     124 ..      51     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.4e-08
                                       TSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EEE CS
                              FR47  21 ggelgalqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfeki 80 
                                        g+++ l v+   rrrG g+ l  +l k++a  g  ++ l +  +  ++i+ly k G++++
  gi|330508998|ref|YP_004385426.1|  64 AGAVYTLDVHTGYRRRGIGKELLLSLEKRLAMMGARAIrLEASLEKPEAIELYRKAGYRER 124
                                       4788888899999*******************8877652667788888***********98 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   5.4e-07    0.0014       1     126 [.       2     122 ..       2     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.4e-07
                                       .EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEE.TTEEEEEEEEEEEEEEETTEEEEEEEE CS
                    Acetyltransf_9   1 eirelteedldevlellkyaFqdeespleeireyfrklleesrvlgaed.ngelvgqlallplelnvpGktlkaagv 76 
                                       +ir+++++dl++++++ + +F d++         f +l+  + +++a + ++++ g +  +        ++ +a++v
  gi|330508998|ref|YP_004385426.1|   2 RIRKAEPKDLPQMVQIESLCFPDDTAFPP---GMFAYLIRYAVAIVACEpEDQILGFIIGY--------NSGNAGAV 67 
                                       58999999999999999999999998752...34667777776666666699999987655........67899*** PP

                                       EEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-E CS
                    Acetyltransf_9  77 tgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGye 126
                                       +   v+  +r+rg+ ++Ll  + ++++ +g++ + l +      +i++Yr+ Gy+
  gi|330508998|ref|YP_004385426.1|  68 YTLDVHTGYRRRGIGKELLLSLEKRLAMMGARAIRLEAslekpEAIELYRKAGYR 122
                                       *******************999999999999999999866655678********7 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         2   5.2e+03       1      15 [.       3      17 ..       3      19 .. 0.84
   2 ?   13.8   0.0   1.9e-05     0.048      87     144 ..      74     131 ..      46     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2
                    Acetyltransf_4  1 iraateeDakeilai 15
                                      ir a+++D+ ++ +i
  gi|330508998|ref|YP_004385426.1|  3 IRKAEPKDLPQMVQI 17
                                      8999****9998665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.9e-05
                    Acetyltransf_4  87 rdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkci 144
                                       +  + +g+g+el+ +le++l++++ + +  e   ++ ++i+++ + G++   i+++++
  gi|330508998|ref|YP_004385426.1|  74 TGYRRRGIGKELLLSLEKRLAMMGARAIRLEASLEKPEAIELYRKAGYREREIVRNYY 131
                                       5567899*********************999999999*************99999987 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.4e-05      0.16     388     461 ..      31     107 ..       9     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.4e-05
                    Cellulose_synt 388 aldaalvkeaisviscgyedktewGkeiGwiyGs...v.tedvltGfkmharGwrsvycvtkrdafkGsapinlsdr 460
                                        + a l++ a+++++c  ed+   G  iG+  G    v t dv tG++    G   +  + kr a+ G+  i l   
  gi|330508998|ref|YP_004385426.1|  31 GMFAYLIRYAVAIVACEPEDQI-LGFIIGYNSGNagaVyTLDVHTGYRRRGIGKELLLSLEKRLAMMGARAIRLEAS 106
                                       4557899************986.788888877642223499****************************99999876 PP

                    Cellulose_synt 461 l 461
                                       l
  gi|330508998|ref|YP_004385426.1| 107 L 107
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.33s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 860.31
//
Query:       gi|330508999|ref|YP_004385427.1|  [L=680]
Description: extracellular protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.5e-34  114.9 151.3      2e-05   24.4   2.4   13.0 13  Dicty_CTDC  Dictyostelium (slime mold) repeat


Domain annotation for each model (and alignments):
>> Dicty_CTDC  Dictyostelium (slime mold) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   7.6   1.2e-07    0.0021       1      21 [.      39      58 ..      39      58 .. 0.98
   2 ?   -1.3   0.1      0.12   2.2e+03      18      23 ..     103     108 ..     102     109 .. 0.89
   3 !   19.9   5.1   2.9e-08   0.00052       1      24 []     110     132 ..     110     132 .. 0.90
   4 !   20.4   9.5     2e-08   0.00036       1      24 []     133     155 ..     133     155 .. 0.94
   5 !   17.8   4.5   1.3e-07    0.0023       1      23 [.     156     177 ..     156     177 .. 0.96
   6 !   21.9  11.9   6.5e-09   0.00012       1      23 [.     179     200 ..     179     200 .. 0.97
   7 ?   -5.3   2.3         1   1.8e+04      21      24 .]     327     330 ..     326     330 .. 0.85
   8 !    3.3   8.6    0.0045        81       1      24 []     331     353 ..     331     353 .. 0.91
   9 !   17.8   5.3   1.3e-07    0.0023       6      24 .]     359     376 ..     357     376 .. 0.86
  10 !   16.4   4.8   3.5e-07    0.0063       1      24 []     377     399 ..     377     399 .. 0.92
  11 !   24.4   2.4   1.1e-09     2e-05       1      20 [.     400     419 ..     400     423 .. 0.91
  12 !    3.3   1.5    0.0043        77      12      24 .]     431     444 ..     422     444 .. 0.74
  13 !   22.9   0.5   3.2e-09   5.7e-05       1      19 [.     445     463 ..     445     464 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.2e-07
                        Dicty_CTDC  1 NpCTiDsCsnstGCvHTPisC 21
                                      NpCT D+C+ ++ C HTP sC
  gi|330508999|ref|YP_004385427.1| 39 NPCTKDFCNGTK-CEHTPQSC 58
                                      9********999.*******9 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.12
                        Dicty_CTDC  18 PisCDD 23 
                                       Pi C+D
  gi|330508999|ref|YP_004385427.1| 103 PIICED 108
                                       9****9 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 2.9e-08
                        Dicty_CTDC   1 NpCTiDsCsnstGCvHTPisCDDN 24 
                                       N CTiD+    +GC+H P+sCDD+
  gi|330508999|ref|YP_004385427.1| 110 NLCTIDYSG-PAGCTHDPVSCDDG 132
                                       99*****66.669**********7 PP

  == domain 4  score: 20.4 bits;  conditional E-value: 2e-08
                        Dicty_CTDC   1 NpCTiDsCsnstGCvHTPisCDDN 24 
                                       Np T D+C   tGC++ P++CDD+
  gi|330508999|ref|YP_004385427.1| 133 NPLTTDYCT-ATGCINDPVNCDDG 155
                                       9*******9.77***********7 PP

  == domain 5  score: 17.8 bits;  conditional E-value: 1.3e-07
                        Dicty_CTDC   1 NpCTiDsCsnstGCvHTPisCDD 23 
                                       NpCT D+ s+ +GC H P+sCDD
  gi|330508999|ref|YP_004385427.1| 156 NPCTSDY-SSLAGCMHDPVSCDD 177
                                       9******.7799**********9 PP

  == domain 6  score: 21.9 bits;  conditional E-value: 6.5e-09
                        Dicty_CTDC   1 NpCTiDsCsnstGCvHTPisCDD 23 
                                       NpCT DsC    GCv+ P++CDD
  gi|330508999|ref|YP_004385427.1| 179 NPCTTDSCGAM-GCVNDPVNCDD 200
                                       9********88.9*********9 PP

  == domain 7  score: -5.3 bits;  conditional E-value: 1
                        Dicty_CTDC  21 CDDN 24 
                                       CDD+
  gi|330508999|ref|YP_004385427.1| 327 CDDG 330
                                       ***7 PP

  == domain 8  score: 3.3 bits;  conditional E-value: 0.0045
                        Dicty_CTDC   1 NpCTiDsCsnstG.CvHTPisCDDN 24 
                                       +pCT D   + +G C H + +C+DN
  gi|330508999|ref|YP_004385427.1| 331 DPCTDDH--FVNGkCMHYTKTCNDN 353
                                       7999995..899************9 PP

  == domain 9  score: 17.8 bits;  conditional E-value: 1.3e-07
                        Dicty_CTDC   6 DsCsnstG.CvHTPisCDDN 24 
                                       D+C    G CvH+Pi+CDD+
  gi|330508999|ref|YP_004385427.1| 359 DYCY--QGdCVHSPINCDDG 376
                                       8886..488**********7 PP

  == domain 10  score: 16.4 bits;  conditional E-value: 3.5e-07
                        Dicty_CTDC   1 NpCTiDsCsnstGCvHTPisCDDN 24 
                                       ++CTiDs + ++ CvH+P +CDD+
  gi|330508999|ref|YP_004385427.1| 377 DKCTIDSYNGTA-CVHSPRNCDDG 399
                                       79*****99777.**********7 PP

  == domain 11  score: 24.4 bits;  conditional E-value: 1.1e-09
                        Dicty_CTDC   1 NpCTiDsCsnstGCvHTPis 20 
                                       NpCT DsC++ +GC++  i+
  gi|330508999|ref|YP_004385427.1| 400 NPCTEDSCNKLAGCQNMEIN 419
                                       9***************9998 PP

  == domain 12  score: 3.3 bits;  conditional E-value: 0.0043
                        Dicty_CTDC  12 tG.CvHTPisCDDN 24 
                                       +G  v++P+ CDD+
  gi|330508999|ref|YP_004385427.1| 431 NGnPVFKPLICDDG 444
                                       344799*******7 PP

  == domain 13  score: 22.9 bits;  conditional E-value: 3.2e-09
                        Dicty_CTDC   1 NpCTiDsCsnstGCvHTPi 19 
                                       Np T D+C++s GCvH+Pi
  gi|330508999|ref|YP_004385427.1| 445 NPWTKDYCDKSRGCVHVPI 463
                                       55699*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (680 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); 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:                         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: 0.83u 0.30s 00:00:01.12 Elapsed: 00:00:00.57
# Mc/sec: 3619.72
//
Query:       gi|330509000|ref|YP_004385428.1|  [L=535]
Description: hypothetical protein MCON_3356 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-37  127.3   0.0    1.9e-36  126.3   0.0    1.5  1  DUF87            Helicase HerA, central domain
    3.1e-09   36.9   0.1    8.2e-09   35.5   0.1    1.7  1  HAS-barrel       HAS barrel domain
      1e-06   27.7   0.0      0.013   14.2   0.0    2.2  2  DUF853           Bacterial protein of unknown function (DUF85
    8.4e-05   21.6   0.0     0.0015   17.6   0.0    2.3  2  AAA_10           AAA-like domain
    0.00013   21.0   0.0      0.023   13.6   0.0    2.2  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
     0.0024   17.0   0.0      0.038   13.1   0.0    2.2  2  T2SSE            Type II/IV secretion system protein
     0.0081   15.0   0.0      0.016   14.0   0.0    1.5  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
  ------ inclusion threshold ------
      0.015   15.6   0.0        9.4    6.5   0.0    3.1  3  AAA_22           AAA domain
      0.022   14.5   0.0        1.6    8.5   0.0    2.7  2  DEAD             DEAD/DEAH box helicase
      0.065   13.2   0.0       0.23   11.5   0.0    1.8  2  ResIII           Type III restriction enzyme, res subunit
        0.1   12.2   0.0       0.33   10.6   0.0    1.8  2  Zot              Zonular occludens toxin (Zot)


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 !  126.3   0.0   1.2e-39   1.9e-36       2     226 ..     125     342 ..     124     343 .. 0.88

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 1.2e-39
                             DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal.......... 68 
                                       +iG l +g +++v  d+n lv++H+ +l++TGsGKS+t+av+leell ++++ +l++DpHGEY++++          
  gi|330509000|ref|YP_004385428.1| 125 YIGML-KGYDIRVEMDANTLVQKHCSVLAKTGSGKSYTAAVILEELL-DRKVALLVIDPHGEYASMKepnnvgdfsk 199
                                       69999.9****************************************.*******************6666666666 PP

                             DUF87  69 ..ekllsekvkvitpspsa....kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklss 139
                                          k    ++ v+tp ++a     d+++++n  +l+ +e++++++   +++++ q  +l+ea++ ++   e   ++ 
  gi|330509000|ref|YP_004385428.1| 200 ykVKPRGYDITVYTPGEMAmnprADRPFRFNSLNLSAREVAKMIPN--ESSSSGQLGLLYEAISALR--AETDAYTL 272
                                       6633333445566666555***************************..888888************9..9******* PP

                             DUF87 140 depveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaq 216
                                       ++++e           ++ +++++ +++l  +le+ll+ g +   + t  ++ll     ++g+ ++id+ g+  + q
  gi|330509000|ref|YP_004385428.1| 273 EDIIE-----------QVVRSNSKVKWNLVGQLESLLELGLFS-GTATPCDELL-----RPGRAAVIDMTGIIPELQ 332
                                       *****...........4567899***************99998.7777777777.....****************** PP

                             DUF87 217 qlvvsvilrr 226
                                        ++v+ +l  
  gi|330509000|ref|YP_004385428.1| 333 AMIVARLLTD 342
                                       **99999875 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.1   5.1e-12   8.2e-09       1      88 [.       9      85 ..       9      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 5.1e-12
                        HAS-barrel  1 iGevigestssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalat 79
                                      +G ++ge+t++ + f +    +v+ G y++++++++e++l +++di+r     sn    v  l ++ +++   e ++a 
  gi|330509000|ref|YP_004385428.1|  9 VGTIVGETTPTAFKFLISK--EVGRGTYIKAKGDGREWILAQIEDIKR-----SNTAYTVNQLNDAARNYDSREMMIAE 80
                                      799***************8..9**************************.....66666666677777777777777766 PP

                        HAS-barrel 80 edtgvkvlG 88
                                           +v+G
  gi|330509000|ref|YP_004385428.1| 81 S----RVIG 85
                                      6....5555 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 !   11.4   0.0   5.5e-05      0.09      18      83 ..     142     207 ..     130     220 .. 0.88
   2 !   14.2   0.0   7.7e-06     0.013     289     403 ..     388     493 ..     328     509 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                            DUF853  18 klanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiakaGevkdklaarleeigl 83 
                                       +l+ +h  +   tG Gk  t  v+ e+l +  v+ ++ d  G+ +++ ++ +v d  + +++  g+
  gi|330509000|ref|YP_004385428.1| 142 TLVQKHCSVLAKTGSGKSYTAAVILEELLDRKVALLVIDPHGEYASMKEPNNVGDFSKYKVKPRGY 207
                                       56889999********************************************99999888887765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 7.7e-06
                            DUF853 289 rskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaadtfranpefdveeaiteLgvGealvsvLd 365
                                       r  G G+  ++q P+ + ++v++q  +  q  +r   p+d ka+ +  +++ +    d+ee i+ L  G a++ v +
  gi|330509000|ref|YP_004385428.1| 388 RKFGLGLMIISQRPARVDKNVISQCNT--QIIMRVTNPNDLKALSKGLEGMTT----DLEEEIKRLPAGVAML-VSN 457
                                       6679********************876..5579****************9975....89999*******9976.447 PP

                            DUF853 366 ekGaPsiveralvvpPasrlgplsee.eraalvqespva 403
                                       e  +P  v+   ++p +sr g +s e  +++ +++s+v+
  gi|330509000|ref|YP_004385428.1| 458 EIERPITVN---IRPRKSRHGGVSTEiVSREKAKASSVQ 493
                                       778888775...899999999987662445566666666 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     9e-07    0.0015      22     170 ..     146     300 ..     136     306 .. 0.65
   2 ?    1.2   0.0     0.085   1.4e+02     260     324 ..     378     444 ..     333     457 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9e-07
                            AAA_10  22 sasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketl.....peiakkinvvtLdseeenegvLdPl 93 
                                        ++ ++ ++G GKS++a ++   ++ ++  +l+iDp  e   +ke        +++ k +  +++  +  e +++P 
  gi|330509000|ref|YP_004385428.1| 146 KHCSVLAKTGSGKSYTAAVILEELLDRKVALLVIDPHGEYASMKEPNnvgdfSKYKVKPRGYDITVYTPGEMAMNPR 222
                                       6889999********************************66665543223221122222222333223333344443 PP

                            AAA_10  94 vllk.eekeaeslaedilelllgvkkkesekkaalseaveavl.egkqrgllavieelrkedekvareiarhlesvv 168
                                          + + +  +  a+++ +++ + +++  +   +l ea++a   e +   l+++ie++ ++++kv  ++   les+ 
  gi|330509000|ref|YP_004385428.1| 223 ADRPfRFNSLNLSAREVAKMIPNESSSSGQ-LGLLYEAISALRaETDAYTLEDIIEQVVRSNSKVKWNLVGQLESLL 298
                                       332222222333344444445555544444.4589999999763677799999999999999999999999998887 PP

                            AAA_10 169 kk 170
                                       + 
  gi|330509000|ref|YP_004385428.1| 299 EL 300
                                       65 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.085
                            AAA_10 260 kllkelvRiGRsynaavylvtqsadDvlkeelknniglklaFr...etdkeeikkvLeflgldveded 324
                                       ++++ +   GR++   +++++q +  v+k+ +++   ++++ r   ++d ++  k+Le +  d e+e+
  gi|330509000|ref|YP_004385428.1| 378 NIVRTIAAEGRKFGLGLMIISQRPARVDKNVISQC-NTQIIMRvtnPNDLKALSKGLEGMTTDLEEEI 444
                                       455666668******************99986543.33333331114666777788888888887655 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 !   13.6   0.0   1.4e-05     0.023      14      57 ..     144     187 ..     136     190 .. 0.92
   2 !    5.1   0.0    0.0055         9     262     323 ..     381     435 ..     376     483 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                     TrwB_AAD_bind  14 etqhilivGttGsGKtqalekllrairargdraivlDltGafvs 57 
                                        ++h  ++  tGsGK+ ++  +l+++  r+   +v+D++G++ s
  gi|330509000|ref|YP_004385428.1| 144 VQKHCSVLAKTGSGKSYTAAVILEELLDRKVALLVIDPHGEYAS 187
                                       688999999********************************975 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0055
                     TrwB_AAD_bind 262 ksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsdaetAeelsell.G 323
                                        +++aegRkfG  + +  q  a++         ++++s +nt++i+rv++ +  + ls+ l G
  gi|330509000|ref|YP_004385428.1| 381 RTIAAEGRKFGLGLMIISQRPARVD--------KNVISQCNTQIIMRVTNPNDLKALSKGLeG 435
                                       6778999999998888888888886........489999********9999988888887755 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   2.3e-05     0.038      25     170 ..      33     186 ..      23     202 .. 0.78
   2 ?    1.5   0.0     0.078   1.3e+02     137     178 ..     247     287 ..     208     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
                             T2SSE  25 vkvrervdg..ielreveelekaalerlisriaalakldiseerplqdarlp..ekgvrlrvvllPvvagealviR. 96 
                                         ++ + dg    l+++e+++++ +++ ++++  +a++  s+e ++ + r+   e++ +lr+ + P+  ge++ +  
  gi|330509000|ref|YP_004385428.1|  33 TYIKAKGDGreWILAQIEDIKRSNTAYTVNQLNDAARNYDSREMMIAESRVIgvESNGKLRLPTSPARPGESVFLAd 109
                                       56666666656678999*******************9999999999999999999999**************99994 PP

                             T2SSE  97 .kksakeltldd....lgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvE 168
                                        k  ++ l l++    +g+ +  + +++   ++ v++++++l    TgsGK+ ++ ++l+e+ +++  ++++    E
  gi|330509000|ref|YP_004385428.1| 110 eKLIKATLGLSKgdmyIGMLKGYDIRVEMDANTLVQKHCSVLA--KTGSGKSYTAAVILEELLDRKVALLVIDPHGE 184
                                       4334445555542222344444556666677888899999986..7******************9888888876667 PP

                             T2SSE 169 iq 170
                                       + 
  gi|330509000|ref|YP_004385428.1| 185 YA 186
                                       65 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.078
                             T2SSE 137 gTgsGKttllyallkeinksderivtvEDpvEiqleganqvq 178
                                         +sG   lly +++ + ++     t+ED +E  ++ + +v+
  gi|330509000|ref|YP_004385428.1| 247 SSSSGQLGLLYEAISALRAE-TDAYTLEDIIEQVVRSNSKVK 287
                                       56999999**********99.8999*******9988877776 PP

>> T4SS-DNA_transf  Type IV secretory system Conjugative DNA transfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0     1e-05     0.016      32      85 ..     132     188 ..     102     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                   T4SS-DNA_transf  32 lyaggllntdGdf.....ehvlvvAptrsgK..gvgvviPnllkwkqsiVvlDpkgElael 85 
                                       ++ +  ++          +h +v A t+sgK  +++v++  ll  k ++ v+Dp gE a +
  gi|330509000|ref|YP_004385428.1| 132 YDIRVEMD----AntlvqKHCSVLAKTGSGKsyTAAVILEELLDRKVALLVIDPHGEYASM 188
                                       33333222....1234569************5558999*******************8876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.9   4.8e+03      57      95 ..      42      77 ..      33      80 .. 0.75
   2 ?    6.5   0.0    0.0058       9.4       5      31 ..     145     171 ..     142     198 .. 0.78
   3 ?    5.6   0.0     0.011        18      70     115 ..     312     383 ..     229     429 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.9
                            AAA_22 57 lrellralglelkaerlsseellealeqalraraviell 95
                                      ++++l ++++ + +   ++   +++l++a+r+++ +e++
  gi|330509000|ref|YP_004385428.1| 42 REWILAQIEDIKRS---NTAYTVNQLNDAARNYDSREMM 77
                                      68899999976666...7777779999999988875555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0058
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqlde 31 
                                       ++++ v + +G+GK+++++ +le+l  
  gi|330509000|ref|YP_004385428.1| 145 QKHCSVLAKTGSGKSYTAAVILEELLD 171
                                       67888999***********99999863 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.011
                            AAA_22  70 a................erlsseellealeqalrarav....ielliiDEaqhlr..s....eealeeLrsl 115
                                       +                ++l+   + ++l++ ++ar++    +++++++Ea++ +  +    ++  + +r++
  gi|330509000|ref|YP_004385428.1| 312 EllrpgraavidmtgiiPELQAMIVARLLTDIFEARKRrlisPGMVVVEEAHNYIpeRgtgnAASTNIVRTI 383
                                       25555555666666666677777777899999999999999************6555145534444444555 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   0.00097       1.6      11      58 ..     142     184 ..     132     205 .. 0.72
   2 ?    3.1   0.0     0.042        69     108     136 ..     340     368 ..     274     429 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00097
                                       HHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  11 ilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtre 58 
                                       +l ++++ v a+TGsGK+  +++ + + +     +++   l++ P  e
  gi|330509000|ref|YP_004385428.1| 142 TLVQKHCSVLAKTGSGKSYTAAVILEELL-----DRKVALLVIDPHGE 184
                                       55678999**********99776555444.....56666777777655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.042
                                       HHHHHHCTSSHCTTEEEEEEETHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 108 lddllstgklnlsqvrflVlDEadrlldq 136
                                       l d+++ +k +l +  ++V+ Ea+++  +
  gi|330509000|ref|YP_004385428.1| 340 LTDIFEARKRRLISPGMVVVEEAHNYIPE 368
                                       456778888889999*********99876 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.23      24      60 ..     145     178 ..     111     201 .. 0.85
   2 ?   -3.9   0.0       7.4   1.2e+04     135     145 ..     356     366 ..     345     383 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                       TSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                            ResIII  24 dkrglikmaTGtGKTlvaaklierllkkgkeekflfl 60 
                                       +k+  + + TG+GK+++aa + e+ll     + +l++
  gi|330509000|ref|YP_004385428.1| 145 QKHCSVLAKTGSGKSYTAAVILEELLDR---KVALLV 178
                                       566678889****************996...233444 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7.4
                                       EEEEETGGGTT CS
                            ResIII 135 viiiDEaHrlg 145
                                       ++++ EaH++ 
  gi|330509000|ref|YP_004385428.1| 356 MVVVEEAHNYI 366
                                       89999999875 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         2   3.2e+03       9      17 ..     154     162 ..     146     213 .. 0.75
   2 ?   10.6   0.0    0.0002      0.33      80     138 ..     353     412 ..     332     422 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2
                               Zot   9 pGsgKtsga 17 
                                        GsgK++ a
  gi|330509000|ref|YP_004385428.1| 154 TGSGKSYTA 162
                                       567776655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0002
                               Zot  80 kgallviDEcqeifpvrakegrkdpevi.naftehRhlgwDivlltqdiskihkevrala 138
                                         +++v+ E+++  p+r + ++   +++    +e R++g  ++++ q +++++k+v   +
  gi|330509000|ref|YP_004385428.1| 353 SPGMVVVEEAHNYIPERGTGNAASTNIVrTIAAEGRKFGLGLMIISQRPARVDKNVISQC 412
                                       55799*******99999996666666677778899*******************996665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.81u 0.36s 00:00:01.17 Elapsed: 00:00:00.57
# Mc/sec: 2830.00
//
Query:       gi|330509001|ref|YP_004385429.1|  [L=75]
Description: hypothetical protein MCON_3357 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-26   92.2   0.3      2e-26   92.0   0.3    1.0  1  Dodecin   Dodecin


Domain annotation for each model (and alignments):
>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   0.3   1.1e-30     2e-26       1      64 []       8      71 ..       8      71 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 1.1e-30
                                      EEEEEEEEEEESS-HHHHHHHHHHHHHHH-SSEEEEEEEEEEEEECTTCCEEEEEEEEEEEE-S CS
                           Dodecin  1 VyKvielvGsSpkSwedAiqnAiaeAsktlrnirwveVketrahvedgkiaeYqvtlkvgFrle 64
                                      VyKvielvG+S++SwedA+++ +++A+ktlr++r++eVke+++++++gkiaeY++++ ++F++e
  gi|330509001|ref|YP_004385429.1|  8 VYKVIELVGTSTTSWEDAVKTVVDRATKTLRDLRIAEVKELDVRLDNGKIAEYRAKVCLSFKYE 71
                                      9************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 417.97
//
Query:       gi|330509002|ref|YP_004385430.1|  [L=465]
Description: HMG-CoA synthase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-27   96.6   0.0    2.5e-27   96.2   0.0    1.1  1  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
    1.6e-19   70.4   0.0      3e-19   69.5   0.0    1.4  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
  ------ inclusion threshold ------
      0.045   13.9   0.1       0.22   11.7   0.0    2.1  2  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha


Domain annotation for each model (and alignments):
>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.0   4.2e-31   2.5e-27       4     235 ..     203     430 ..     199     454 .. 0.82

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 4.2e-31
                                       -TT--EEEE----SEE---TT-S--EE-HHHHHHHHHHHHHHHHHHHHHH..HHHHHHH------GGG-SEEEE--S CS
                    HMG_CoA_synt_C   4 drklrashmehayDFykPdlaseYPvvDGklslscYlkaldrcYksyskk..vkkitkdadkeftlddfdyvifhsP 78 
                                       + ++ +++ ++  DF++P        v+Gk s +cYl a++ +++s+  k   k i + ++ e t d +d+++fh P
  gi|330509002|ref|YP_004385430.1| 203 E-QIYGCFTRDENDFFRPTG-CTMATVNGKHSNQCYLDAMQGAFASFAAKaaRKGIISPKNGECTTDWIDHLLFHIP 277
                                       4.899*************64.56789************************433445666899*************** PP

                                       SHHHHHHHHHHHHHHHHHH.S-.HHHHHHH-GGGGGGTT--GGGGGT-HHHHHHHHHHHHHH...HHHHTGGGGHHH CS
                    HMG_CoA_synt_C  79 fcklvqkslarllynDflanas.sdkeeevkekleekddlkldesltdkdlekallkiakel...fkkkvkpsllvp 151
                                       + ++++ + a ++ +D+++ ++ sd e+e+  + e+ +  +l+    d +  + + + ++++   ++++v  s  ++
  gi|330509002|ref|YP_004385430.1| 278 YPRMIEYASAAIFRQDWKNSSRwSDVEAEIGPEPEAGNYDDLERYRLDLARYARSFARSRQFleaYNARVIDSAALS 354
                                       *****************98554134444454444444444555555666666666666765433399********** PP

                                       HHH---GGGHHHHHHHHHHHHS-HHHHTT.-EEEEEEEETTTEEEEEEEEE-S--STTSHHHHHTTTTHHHHHHTSE CS
                    HMG_CoA_synt_C 152 tevGnmYtaslyaalasllskvsadelag.kriglfsYGsGlaaslfslrvkqdvsedsildiakvldlkkkLdsRk 227
                                       + +Gn+Yt s+y  lasll   + ++l+  +r+ + +YGsG +a +fs rv+ + s      + +  dl ++L++R+
  gi|330509002|ref|YP_004385430.1| 355 RSIGNIYTGSIYLGLASLL---ELQKLRAhERLCFGAYGSGCSALVFSARVSSEFSS-----VPSR-DLFERLEKRR 422
                                       *******************...67778775899999*****************9999.....7776.********** PP

                                       EE-HHHHH CS
                    HMG_CoA_synt_C 228 evtPeefe 235
                                       e++ ee+e
  gi|330509002|ref|YP_004385430.1| 423 EISLEEYE 430
                                       *****997 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 !   69.5   0.0   5.1e-23     3e-19       3     170 ..      22     194 ..      20     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 5.1e-23
                    HMG_CoA_synt_N   3 kdvgilaleiylpaqyvd.qaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrl 78 
                                       + vgi  l +y+p  y+  + e+ +  +++ gk t g+g  rm++ + +ed  +++   + +l++r +l  + ig++
  gi|330509002|ref|YP_004385430.1|  22 EAVGIDDLAVYIPQLYLPlEGEFSRRREIDPGKLTRGIGIERMAIPDAHEDAATMAAMSLLELMRRCDLLPEDIGKI 98 
                                       579*************973689******************************************************* PP

                    HMG_CoA_synt_N  79 evgtetiidksksvksvlmqlfee....sgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiy 151
                                        +gte+ +d +k++ + ++ ++e+     +      ++   ac g t al     w+ ++    r  +v+a d+a y
  gi|330509002|ref|YP_004385430.1|  99 HIGTESAVDEAKAIGTYVIGMLEKvygpGSFQHCSTVEFKSACIGTTLALESISYWVAADE-GERVGVVIASDVAKY 174
                                       *************9998776665521114456778888899*********99999998776.5699*********** PP

                    HMG_CoA_synt_N 152 dsgna.rptggagavallig 170
                                       + g++   t gag+v+ll+ 
  gi|330509002|ref|YP_004385430.1| 175 PLGSSgEYTQGAGSVSLLVK 194
                                       **9862679********986 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.66   3.9e+03       6      26 ..     264     284 ..     261     289 .. 0.83
   2 ?   11.7   0.0   3.6e-05      0.22      43      82 ..     355     394 ..     335     400 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.66
                                       --GGG-SEEEE-SSSHHHHHH CS
                     ACP_syn_III_C   6 ltpedidalvphqanlriida 26 
                                        t++ id+l++h    r+i+ 
  gi|330509002|ref|YP_004385430.1| 264 CTTDWIDHLLFHIPYPRMIEY 284
                                       57788*******999999986 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.6e-05
                                       HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEETTTE CS
                     ACP_syn_III_C  43 deyGntsaasiplaLdeaveegklkpgdlvllvgfGaGlt 82 
                                       + +Gn+ + si l L+ ++e +kl++ +++ + + G G +
  gi|330509002|ref|YP_004385430.1| 355 RSIGNIYTGSIYLGLASLLELQKLRAHERLCFGAYGSGCS 394
                                       679***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2643.33
//
Query:       gi|330509003|ref|YP_004385431.1|  [L=443]
Description: periplasmic binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-21   77.5   0.0    5.9e-21   75.1   0.0    1.9  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 !   75.1   0.0   3.3e-25   5.9e-21      48     234 ..     167     367 ..     138     370 .. 0.82

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 3.3e-25
                                       SSB-HHHHHHH--SEEEE-GGG...GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                      Peripla_BP_2  48 geidvEklaalkPDlvilskglgltdedeellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsk 124
                                       +e+d E ++ + PD+ ++ ++       +++  +gi+ +    +    +  + ir lg +l++e+eae++++++d+ 
  gi|330509003|ref|YP_004385431.1| 167 SELDNEYILSMNPDIFLGWYKE------DREKLPGINLIHSKLWG--LNSSRDIRKLGYILDKENEAEEYIKWHDNC 235
                                       5778888888888887776666......55555888888888887..9999************************** PP

                                       HHHHHHTS-TT...-EEEEEEEETTE..EEEE-TTSTTTHHHHT.S--EESTTT--...STT-EEE-HHHHHHH--S CS
                      Peripla_BP_2 125 laaaksaidse..kpkpvlvfggadeggyvvagsnsyigdllda.lgieniaaesk...kseyeeisaEqilasdpd 195
                                       + ++k+ +d++  +++p ++++   +gg++  +++ +++  +d+ + + ++ + ++   +++yee++ E++ +++pd
  gi|330509003|ref|YP_004385431.1| 236 INKIKEEVDEIplDDRPRVLVALPKPGGVFGVYRGEGGTTGMDDlMTLIPVNSIGQllpTKDYEEVDTEWVIEQNPD 312
                                       *************9999999999999888888888888887777777777766666778****************** PP

                                       EEEEEEH................HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 196 vifvsgr................aeadnktgleflkenpllaelpAvkngrVyal 234
                                       +i+++++                + ++     e+++++p+lae++AvkngrVy +
  gi|330509003|ref|YP_004385431.1| 313 IIIIASNlieakgggsfagydldDPSQMAREREDFLSRPELAEVNAVKNGRVYMM 367
                                       ********************99777777778899*******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 2442.58
//
Query:       gi|330509004|ref|YP_004385432.1|  [L=83]
Description: hypothetical protein MCON_3361 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 473.31
//
Query:       gi|330509005|ref|YP_004385433.1|  [L=295]
Description: oxidoreductase, NAD-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-12   47.0   2.2    1.6e-12   47.0   2.2    1.7  2  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
    0.00015   22.3   0.0    0.00047   20.8   0.0    1.8  1  NAD_binding_1    Oxidoreductase NAD-binding domain
     0.0016   18.4   0.1     0.0031   17.5   0.1    1.5  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
       0.21   11.6   1.2       0.41   10.6   0.3    1.9  2  Fer2             2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.8   1.3e+04      27      32 ..     153     158 ..     148     158 .. 0.73
   2 !   47.0   2.2   3.6e-16   1.6e-12       2      41 ..     213     248 ..     212     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.8
                                       EETTTT CS
                   DHODB_Fe-S_bind  27 krvCkd 32 
                                         vC+d
  gi|330509005|ref|YP_004385433.1| 153 LLVCTD 158
                                       679987 PP

  == domain 2  score: 47.0 bits;  conditional E-value: 3.6e-16
                                       ---SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   2 erMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                        +M +G+G+C++C+v+++g    +++ +C++GP+Fd+++v
  gi|330509005|ref|YP_004385433.1| 213 PIMIDGTGMCGSCRVEVDG----QMRLACVEGPEFDGHKV 248
                                       68***************76....59*************99 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 !   20.8   0.0     1e-07   0.00047       2     108 ..     105     197 ..     104     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1e-07
                                       EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHH CS
                     NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvq 78 
                                       ++gGtG+a ++ + r++  +     +v+ + G+r+ee +++r e+e+++ +l   +  + +      g  +++  v+
  gi|330509005|ref|YP_004385433.1| 105 VGGGTGVAVLYPIARKLKSR---GSRVISIIGARNEELIILRREMETVSDELLV-C--TDT------GTIERNALVT 169
                                       79***************997...6799999******************433333.2..222......2233456999 PP

                                       HHHHHHHHHHSSTTEEEEEECSHHHHHHHH CS
                     NAD_binding_1  79 dalleellslkkeethvyvCGppgMikavr 108
                                       d l+e l+   +  + v+  Gp +M+k v+
  gi|330509005|ref|YP_004385433.1| 170 DLLMEVLDR--ETPDVVVAIGPVPMMKRVS 197
                                       999998888..777888888******9886 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 !   17.5   0.1   6.9e-07    0.0031      54      74 ..     219     239 ..     215     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.9e-07
                            Fer2_3  54 egiCGscavainGkptlaCta 74 
                                        g+CGsc v+++G+ +laC +
  gi|330509005|ref|YP_004385433.1| 219 TGMCGSCRVEVDGQMRLACVE 239
                                       69*****************76 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   9.1e-05      0.41      38      74 ..     220     238 ..     217     247 .. 0.75
   2 ?   -3.2   0.0       1.8   8.2e+03      21      37 ..     266     281 ..     262     283 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.1e-05
                                       SSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGG CS
                              Fer2  38 ggCgtClvevlegevqsdetelegeeldegklrlaCq 74 
                                       g Cg+C+vev+            g++      rlaC+
  gi|330509005|ref|YP_004385433.1| 220 GMCGSCRVEVD------------GQM------RLACV 238
                                       55******988............554......57774 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.8
                                       HHHHHTTTTTSTTSSSS CS
                              Fer2  21 daaeenggidipysCgg 37 
                                       +a+e   g+   +sC++
  gi|330509005|ref|YP_004385433.1| 266 QALEAH-GVTELHSCRM 281
                                       566655.4444478875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 1890.04
//
Query:       gi|330509006|ref|YP_004385434.1|  [L=569]
Description: AMP-dependent synthetase and ligase [Methanosaeta concilii GP6]
Scores for complete 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-111  372.4   0.0   2.7e-111  372.2   0.0    1.0  1  AMP-binding      AMP-binding enzyme
    2.4e-19   70.1   0.0      7e-19   68.6   0.0    1.8  1  AMP-binding_C    AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
       0.16   12.3   0.0       0.38   11.1   0.0    1.6  1  AMP-binding_C_2  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 !  372.2   0.0  4.5e-115  2.7e-111       1     422 [.      27     460 ..      27     461 .. 0.87

  Alignments for each domain:
  == domain 1  score: 372.2 bits;  conditional E-value: 4.5e-115
                                       HHHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEE CS
                       AMP-binding   1 leeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpl 77 
                                       ++e a+k+pd  alv+ ++g+++TYrel+++ nr A+g+ +lG+kkgdr ai++ n +ew+++ +a++kaG++ v +
  gi|330509006|ref|YP_004385434.1|  27 FDEIAEKYPDNDALVSIHQGKRYTYRELQKELNRTAKGFIALGLKKGDRLAIWATNIAEWIITQYATAKAGIIMVNI 103
                                       68899***********889********************************************************** PP

                                       ETTS-HHHHHHHHHHHTESEEE............ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCC CS
                       AMP-binding  78 nptltaeelayiledseakvli............atvdselleklleaaakleavklvivldadellkeeelkeeee 142
                                       np+++ +el+y l++sea+vl+                     +++++a++  ++  +i++++ ++l+++ l ++ e
  gi|330509006|ref|YP_004385434.1| 104 NPAYRTHELEYSLRQSEAQVLLlmdrfkssdyvkM------FYEVCPEAQT--SKPGEIHSEKLPFLRTAVL-IRGE 171
                                       **********************9987655433330......4444444443..2333444555555555333.3333 PP

                                       CSCTTS.................-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT CS
                       AMP-binding 143 seekae.................kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklked 202
                                       ++++ +                  + ++++l+ dd+++i+YTSGTTG PKGV+l+h n+++n + +   ++ k++e+
  gi|330509006|ref|YP_004385434.1| 172 KQSSMYtweevlrmgeeipdevlAE-RQASLDFDDPINIQYTSGTTGFPKGVVLTHHNILNNGYFI--GECMKFTEE 245
                                       3333324455666777788888644.4558999*****************************7775..7889999** PP

                                       -EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHH CS
                       AMP-binding 203 dvvlsilplahifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakka 279
                                       d+++  +p++h+fg++l+ ++++++G ++vl+   +++dp   l ++ek+++t ++gvP+++ a le+++++    +
  gi|330509006|ref|YP_004385434.1| 246 DRLCIPVPFYHCFGMVLSNMASVTHGTAMVLPA--EHFDPVSTLSAVEKERCTAVHGVPTMFVAELEHPDFS----K 316
                                       *******************************66..667888899***********************99998....3 PP

                                       CCGTT-SEEEEESS-EBHHHHHHHHHHHTC.EEEEEEEEGGGSSECEE.CHCTTTCTSTTS-BEE-TTEEEEEE-TT CS
                       AMP-binding 280 kdlsslrlvllggeplspellrffralfge.evlegYGlTEttgvvtv.lpleedkkklgsvGkplpgvevkivDee 354
                                        dlsslr+ +++g+p++ e +++++ l+   ev+ +YG+TE ++ +t+  +++  + ++++vGkp+p++e+kivD++
  gi|330509006|ref|YP_004385434.1| 317 FDLSSLRTGIMAGSPCPIEFMKKVSTLMNMrEVVITYGQTESSPGITMsSTDDSLDLRVSTVGKPMPHTEMKIVDPK 393
                                       4***************************9999**************87744455556789***************** PP

                                       TSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 355 tgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       tg+ vp+ge+Ge++ rg  +m+ Y+++p at++ +d e++wl+TGDlg+lde+ y +i+gR+kd++++
  gi|330509006|ref|YP_004385434.1| 394 TGKIVPRGETGEICARGYMIMREYYNNPVATEQCID-EEGWLHTGDLGTLDENDYCKITGRLKDMVIR 460
                                       ***********************************9.657**************************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 !   68.6   0.0   1.2e-22     7e-19       1      76 []     469     544 ..     469     544 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 1.2e-22
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                       e+E+ l +hpa++++ V+Gvpd++ Ge l+a + lk+g +a +ee+ka+++ ++++++ p++++fvd++p+t sGK
  gi|330509006|ref|YP_004385434.1| 469 EIEEFLYTHPAISDVQVIGVPDKKYGEELMAWIKLKNGASANQEEIKAFCKGRIAHFKIPRYIKFVDDFPMTVSGK 544
                                       8**********************************99954468********************************9 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.3e-05      0.38       1      55 [.     462     516 ..     462     532 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.3e-05
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHH CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelea 55 
                                       G n++P +iee l + + +++   i v +++  +el   + +k+g+s + +e +a
  gi|330509006|ref|YP_004385434.1| 462 GENIYPREIEEFLYTHPAISDVQVIGVPDKKYGEELMAWIKLKNGASANQEEIKA 516
                                       78**********************************9999999998876555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3639.46
//
Query:       gi|330509007|ref|YP_004385435.1|  [L=535]
Description: hypothetical protein MCON_3367 [Methanosaeta concilii GP6]
Scores for complete 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   53.3   0.0    5.3e-10   39.0   0.0    2.1  2  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   4.5e-06     0.081      61     157 ..     114     238 ..     102     245 .. 0.83
   2 !   39.0   0.0   2.9e-14   5.3e-10     193     301 ..     291     402 ..     279     414 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-06
                                       HHHHHTTEE---B-TTTS-HHHHHHHHHHHHHHT-B-EETT..S---GGGGS-----.................... CS
                      Glu_synthase  61 alkikkriltsamSyGalseeahealakamnrlgtksntGE..GGedeerlktakdv.................... 115
                                       ++++k +i t+a+    ++++  e +a+++   g+++ +GE   G+d+e +  ++                      
  gi|330509007|ref|YP_004385435.1| 114 KVSMKLPIFTGALGSTDIARKNWEHFAIGAAISGITIVCGEnvCGVDPELVLDGHGQvqrspemdrrietyrrfheg 190
                                       57889999999999999************************55599999887766656999**************** PP

                                       ...SEEE..E-TT-TT--HHHHH..H-SEEEEE---TTSTTS--EE-GG CS
                      Glu_synthase 116 ...aikQ..vasgrFGvteeyLn..nakaleikiaQGakpgeGgqlpge 157
                                           ++Q  v   r Gv e++ +    + +e+k +QGak   Gg+++ +
  gi|330509007|ref|YP_004385435.1| 191 wgeILVQmnVEDTRLGVAEYVSSrhGLETIELKWGQGAKCI-GGEIKVD 238
                                       **95566226789****987654115799**********97.9998766 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 2.9e-14
                                       HHHHHHHH-TTSEEEEEEE-STTHHHHHHH..HHHTT-SEEEEE-TT---SSEEHHHHHHB---HHH..HHH.HHHH CS
                      Glu_synthase 193 liedLkevnkeakvsvKlvaeagvetiaag..vakanadiilidGleGGTGAspkssikhaGlPlel..ala.evdq 264
                                        +  L+ ++  ++++ K +a + +e   a    a+a+ d+++idG  GGTG sp+ ++++ G+P+    al+ e  +
  gi|330509007|ref|YP_004385435.1| 291 EVDRLRGLG-FKRITLKTGAYSMAELAMAIryGAEAKIDLLTIDGAPGGTGMSPWPMMNEWGIPTFYlqALVyEFAT 366
                                       566777777.67899999998888876554347999****************************9751144413344 PP

                                       HHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE CS
                      Glu_synthase 265 tlkeeglrdrvsliadGglktgadvvkalalGAdavg 301
                                       +l + g ++  ++ ++Gg+ t + v+k++a+GA +v+
  gi|330509007|ref|YP_004385435.1| 367 KLSRRG-KKVPDIAMAGGFSTEDGVFKSIAMGAPFVK 402
                                       444433.34458*********************8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); 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: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3701.34
//
Query:       gi|330509008|ref|YP_004385436.1|  [L=519]
Description: excinuclease ABC subunit C [Methanosaeta concilii GP6]
Scores for complete 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  180.4   0.6    4.1e-53  179.4   0.0    1.8  2  UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
    7.6e-10   38.9   0.0    2.4e-09   37.3   0.0    1.9  1  GIY-YIG     GIY-YIG catalytic domain
    2.9e-07   30.0   2.2    7.4e-07   28.7   2.2    1.8  1  UVR         UvrB/uvrC motif
  ------ inclusion threshold ------
      0.015   15.6   0.2      0.037   14.4   0.1    1.6  2  AIF_C       Apoptosis-inducing factor, mitochondrion-associat
      0.029   13.7   0.5      0.046   13.0   0.5    1.2  1  NOA36       NOA36 protein
      0.088   13.1   0.1       0.31   11.3   0.1    2.0  2  PPP5        PPP5 TPR repeat region


Domain annotation for each model (and alignments):
>> UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.5   4.4e+03     105     144 ..     194     231 ..     179     237 .. 0.59
   2 !  179.4   0.0   1.4e-56   4.1e-53       1     154 []     357     506 ..     357     506 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                                       --EEEEES............SSSEEEE--TT-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N 105 ipvvglaKdkkrktrakaeereeevlelkkssealkllqr 144
                                        ++++  K++++ ++++  ++ e+ +el+ + +al  lq+
  gi|330509008|ref|YP_004385436.1| 194 AELISSMKEEMTGRANR--QDFERAIELRDEINALDRLQE 231
                                       56666667555544443..444555777777777776665 PP

  == domain 2  score: 179.4 bits;  conditional E-value: 1.4e-56
                                       HHHTT-SS---EEEEEEEEEETTTEEEEEEEEEETTEE-GGG-EEEEEE.-SS--HHHHHHHHHHHHHTTS.....- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N   1 kellglkekpkriecyDiShiqgtntvgsmvvfedgkpkkseyRkfkiksvkegdDyaamrevlrRrfkrllkefsk 77 
                                       +e+l+l++kp+ iec+DiSh+ g+++vgsmv f+ gkp+ks+yR+fki++v++gdD+a+++ev+rRr++rl+ke+++
  gi|330509008|ref|YP_004385436.1| 357 QEALHLPKKPEVIECFDISHLAGSFAVGSMVQFRSGKPDKSNYRRFKIRDVQGGDDFASIAEVVRRRYSRLKKENKE 433
                                       689************************************************************************** PP

                                       --SEEEESSSHHHHHHHHHHHHHTT----EEEEES............SSSEE........EE--TT-HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N  78 lPdLiliDGGkgqlnaakevleelglkipvvglaKdkkrktrakaeereeev........lelkkssealkllqrir 146
                                       lPdLi+iDGG gql+ a + l+e+ +k+p+++laK +            ee+        l++kk+++a  +lq+ir
  gi|330509008|ref|YP_004385436.1| 434 LPDLIVIDGGAGQLSSALKELREMRVKVPIISLAKRE------------EEIyvpgldgpLDIKKNEKASLYLQEIR 498
                                       ***********************************33............333344445559**************** PP

                                       HHHHHHHH CS
                                       xxxxxxxx RF
                        UvrC_HhH_N 147 deaHrfAI 154
                                       deaHrfAI
  gi|330509008|ref|YP_004385436.1| 499 DEAHRFAI 506
                                       *******8 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   8.1e-13   2.4e-09       3      78 .]      12      89 ..      10      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 8.1e-13
                                      EEEEEEET...TT--EEEEEESSHHHHHHHHHHHHHHT--S-HS.STEEEEEEEE----HHHHHHHHHHHHHHTTSSSS CS
                           GIY-YIG  3 gvYiirsk...enkliYvGstknlekRlkqHnagkkakytrkkgkkpfeliileifptksealelEkklikkyksnkyn 78
                                      g+Y++r+     +++iYvG++++l+kR+++++++ ++  ++ + +   + + + +  t+ eal lE+ likk+++ +yn
  gi|330509008|ref|YP_004385436.1| 12 GCYLFRDSpeeWGNIIYVGKARDLKKRISNYFQKQNHSPRTAALVAAIKGVDFIVTNTEVEALLLENTLIKKHQP-RYN 89
                                      8999996666689999************************9975555555555666777777*************.998 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   2.2   2.5e-10   7.4e-07       2      34 ..     195     227 ..     194     229 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.5e-10
                               UVR   2 klikeLeeemeeAaenedFEkAAklRDqinalk 34 
                                       +li++++eem+  a+++dFE+A +lRD+inal 
  gi|330509008|ref|YP_004385436.1| 195 ELISSMKEEMTGRANRQDFERAIELRDEINALD 227
                                       79*****************************97 PP

>> AIF_C  Apoptosis-inducing factor, mitochondrion-associated, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.3     1e+04      99     120 ..      60      81 ..      39      91 .. 0.76
   2 ?   14.4   0.1   1.2e-05     0.037      59     119 ..     203     263 ..     172     270 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.3
                             AIF_C  99 kGvvfylrddkvvGivlwnvfn 120
                                       kGv f + + +v  ++l n + 
  gi|330509008|ref|YP_004385436.1|  60 KGVDFIVTNTEVEALLLENTLI 81 
                                       8999999999999888888765 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.2e-05
                             AIF_C  59 esseesksekeeeaskekseekseeekkkkekkeeeedygkGvvfylrddkvvGivlwnvf 119
                                       e++ +++ +  e+a + ++e ++ ++ +++++ e++ +y++ ++ yl d+++v ++l+ v+
  gi|330509008|ref|YP_004385436.1| 203 EMTGRANRQDFERAIELRDEINALDRLQERQRVEQNRKYDQDIISYLMDKEIVYLMLFKVY 263
                                       2222333333333344444444466777888889999*********************998 PP

>> NOA36  NOA36 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   1.6e-05     0.046     172     244 ..     143     214 ..     133     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                             NOA36 172 tfkcvscnrlgqysclrckacycedhvrrkgfkyeknkaipcpkcgyetqetkdlslstrslkfgrqkqadgs 244
                                       +f   +c+rl + +clr + c+c      k  k++ +  +   k +    +t +l  s+++   gr +++d +
  gi|330509008|ref|YP_004385436.1| 143 AFGLRTCKRLPKRACLRYHLCHCSGPCIGKITKKDYQARVQRAKSALSG-RTAELISSMKEEMTGRANRQDFE 214
                                       677889**********************************999998865.68888889999999998866543 PP

>> PPP5  PPP5 TPR repeat region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.3   9.8e+03      74      82 ..     135     143 ..      94     157 .. 0.67
   2 ?   11.3   0.1    0.0001      0.31       4      45 ..     204     246 ..     201     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.3
                              PPP5  74 yvyaillkv 82 
                                       +vy+i+ k+
  gi|330509008|ref|YP_004385436.1| 135 FVYQIVRKA 143
                                       344444433 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0001
                              PPP5   4 ceklirreaFekAIeveekesasetl.dlesieveksYdGprL 45 
                                       ++   +r+ Fe+AIe +++ +a+++l + + +e +++Yd   +
  gi|330509008|ref|YP_004385436.1| 204 MTGRANRQDFERAIELRDEINALDRLqERQRVEQNRKYDQDII 246
                                       5667799*******************55777888888997666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3496.69
//
Query:       gi|330509009|ref|YP_004385437.1|  [L=199]
Description: thiamine-phosphate pyrophosphorylase [Methanosaeta concilii GP6]
Scores for complete 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  205.6   0.1    4.2e-61  205.4   0.1    1.0  1  TMP-TENI      Thiamine monophosphate synthase
     0.0018   17.8   0.0     0.0029   17.1   0.0    1.4  1  His_biosynth  Histidine biosynthesis protein
     0.0042   16.4   0.2     0.0066   15.7   0.2    1.2  1  DHO_dh        Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.035   13.5   3.3        0.5    9.7   2.4    2.3  2  NMO           Nitronate monooxygenase
      0.068   12.3   0.1       0.28   10.3   0.1    1.8  2  DUF561        Protein of unknown function (DUF561)


Domain annotation for each model (and alignments):
>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.4   0.1   1.2e-64   4.2e-61       2     180 ..       5     181 ..       4     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 205.4 bits;  conditional E-value: 1.2e-64
                          TMP-TENI   2 ylvtdskldkneellevveealkggvtlvqlRekeldarellelaeklaalcrkygvpliindrvdlalavgadgvH 78 
                                       y++tds+l  ++  ++ v ea++ +v++vq+R+k++++re++e+a  l+++cr  +  ++indr+d+alavgadgvH
  gi|330509009|ref|YP_004385437.1|   5 YFITDSRLS-RAGNISDVMEAASCKVDAVQYRNKNAETREMYEEALHLREICR--DLTFLINDRIDIALAVGADGVH 78 
                                       9*****999.55566666778899****************************5..789******************* PP

                          TMP-TENI  79 lgqddlpvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkda.eplgleglkelaealeiPvv 154
                                       lgq+d+p+++are+lg+++iiG++vhsl ea+ a+++gadY+gv+pif+T+tK+da +p+g+++++e+++++ iP++
  gi|330509009|ref|YP_004385437.1|  79 LGQTDMPCKTAREMLGEEMIIGVTVHSLFEALVAKRDGADYLGVSPIFQTATKSDAgKPAGIALIEEIRRKIDIPLI 155
                                       ***************************************************************************** PP

                          TMP-TENI 155 aiGGitlenvaevleagadgvavvsa 180
                                       aiGGi+l+n++ev+ agadg++ +s 
  gi|330509009|ref|YP_004385437.1| 156 AIGGINLSNAPEVIGAGADGLCAISC 181
                                       ************************97 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   8.1e-07    0.0029      54     115 ..     132     192 ..     102     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.1e-07
                                       HCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHH CS
                      His_biosynth  54 akegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikel 115
                                       + +g++a ++l+eei+++++ip+   GGI+  + + e++ agad ++  +++v++ ++  ++
  gi|330509009|ref|YP_004385437.1| 132 SDAGKPAGIALIEEIRRKIDIPLIAIGGINLSN-APEVIGAGADGLCAISCVVESDDVSAQI 192
                                       44899999*********************9887.********************99998876 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.8e-06    0.0066     227     284 ..     136     189 ..     131     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHH CS
                            DHO_dh 227 kdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkia 284
                                       k+ ++++i e++++++  ip+I++GGi+ +  a e i aGA  +   +++v ++  + 
  gi|330509009|ref|YP_004385437.1| 136 KPAGIALIEEIRRKID--IPLIAIGGINLS-NAPEVIGAGADGLCAISCVVESD-DVS 189
                                       8999************..*********975.79********9888778875444.333 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.55     2e+03     268     295 ..      22      48 ..      11      58 .. 0.72
   2 ?    9.7   2.4   0.00014       0.5     134     204 ..      94     162 ..      63     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.55
                               NMO 268 leeleeakiatlalpeahelakkiraal 295
                                       +e   + k+ ++++++++ ++ ++ + +
  gi|330509009|ref|YP_004385437.1|  22 MEA-ASCKVDAVQYRNKNAETREMYEEA 48 
                                       333.348899999999998888876554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00014
                               NMO 134 eagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiid 204
                                         ++++ +t+ s  ea ++ + GaD l v    +   +   + g+   +aL+++++  +diP+iA GGi+ 
  gi|330509009|ref|YP_004385437.1|  94 GEEMIIGVTVHSLFEALVAKRDGADYLGVSPIFQTATKS--DAGKPAGIALIEEIRRKIDIPLIAIGGINL 162
                                       455667778888888888888888888777776665555..444466799******************985 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.17   6.1e+02     200     216 ..      66      82 ..      55     103 .. 0.80
   2 ?   10.3   0.1   7.8e-05      0.28     175     224 ..     140     189 ..     125     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.17
                            DUF561 200 vplalslgasGiGigsa 216
                                       +++al++ga G+ +g++
  gi|330509009|ref|YP_004385437.1|  66 IDIALAVGADGVHLGQT 82 
                                       67899999999988875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 7.8e-05
                            DUF561 175 lastyeiskkvslPvicasGlsdvtvplalslgasGiGigsavsklndee 224
                                       +a + ei +k+++P+i+  G++ + +p  + +ga G+   s v + +d  
  gi|330509009|ref|YP_004385437.1| 140 IALIEEIRRKIDIPLIAIGGINLSNAPEVIGAGADGLCAISCVVESDDVS 189
                                       56677899****************************98777776555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1307.56
//
Query:       gi|330509010|ref|YP_004385438.1|  [L=264]
Description: hydroxyethylthiazole kinase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-76  257.0   5.6    1.8e-76  256.8   5.6    1.0  1  HK            Hydroxyethylthiazole kinase family
    9.8e-07   28.5   1.3    1.2e-06   28.3   1.3    1.1  1  Carb_kinase   Carbohydrate kinase
      1e-05   25.0   2.7    1.3e-05   24.7   2.7    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
       0.14   12.5   0.0       0.89    9.9   0.0    2.1  3  eRF1_2        eRF1 domain 2


Domain annotation for each model (and alignments):
>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.8   5.6   3.9e-80   1.8e-76       1     246 []       9     254 ..       9     254 .. 0.99

  Alignments for each domain:
  == domain 1  score: 256.8 bits;  conditional E-value: 3.9e-80
                                       HHHHHHH--EEEEE--TTTHHHHHHHHHHHT-EEEE--STTTHHHHHHTSSEEEEE-TT--HHHHHHHHHHHHHHHH CS
                                HK   1 lkklreksPlvhhiTNkVaqnfsANvllAlgaSPimseaeeEvselakianaLllNiGtleekaiealkaAvksake 77 
                                       l+++r+ +Plv h+TN V+  + AN++   gaSP+m++a eEv+++akia++L+lNiGtl+++ +ea+  A+ sa+e
  gi|330509010|ref|YP_004385438.1|   9 LERVRRDKPLVCHLTNFVTIYDCANIVKVFGASPVMAHAREEVADMAKIASSLVLNIGTLTTEFVEAMLLAGISANE 85 
                                       6899************************************************************************* PP

                                       TT--EEEE-TTBTTBHHHHHHHHHHHHHS--SEEEEEHHHHHHHHTSSCCSCSSSSSS-SHHHHHHHHHHHHHHTSE CS
                                HK  78 vnrPvvlDPVgvgAtelRrelalellkevklavikGNasEilslaglelkvkGvDskeaataavaavqkvAqklrvv 154
                                       +++PvvlD  g+gAt++R e ++e+l  v++++ikGN sE++ +ag+++k++GvD+ + + +++ +++++A +++++
  gi|330509010|ref|YP_004385438.1|  86 KKIPVVLDVCGAGATRFRDEKCQEILDAVEVSIIKGNSSEVARIAGEDVKTRGVDAADIESNLLGVAHSLAGERGCT 162
                                       ***************************************************************************** PP

                                       EEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HHHHHHHTTHH CS
                                HK 155 vvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgkeaaarsegsgs 231
                                       vv+tG+ D+v+d k+ + ++nG++++++++++GC+ +sv++af+av++d++ a+v+++++y+vA++ aa    g+gs
  gi|330509010|ref|YP_004385438.1| 163 VVITGKDDIVADMKRAIWVHNGHPMMANVVGTGCMATSVIGAFAAVETDHVVASVSGLICYEVAAEIAALVAAGPGS 239
                                       ***************************************************************************** PP

                                       HHHHHHHHHHH--HH CS
                                HK 232 Fqvelldalsqltee 246
                                       F+ +l da+++l +e
  gi|330509010|ref|YP_004385438.1| 240 FKENLYDAVYNLDSE 254
                                       ***********9876 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   1.3   2.6e-10   1.2e-06      47     223 ..      42     228 ..      18     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.6e-10
                                       TCEECCTTHTTTS...--SSS-SEEEE-TT-SSSHCHHH...HCHHHCCCCS-EEEE...GGGGGSGGGG....TTT CS
                       Carb_kinase  47 evivhplledeqakileklerldavviGpGLgrdekikk...lleevlekdeplviD...AdgLnllaqkne.lser 116
                                        v++h ++     ++ + ++ ++ +v+  G  ++e +++   +   + ek+ p+v+D   A++  ++++k + + + 
  gi|330509010|ref|YP_004385438.1|  42 PVMAHARE-----EVADMAKIASSLVLNIGTLTTEFVEAmllAGISANEKKIPVVLDvcgAGATRFRDEKCQeILDA 113
                                       45555555.....3456667777777777777777766652233345566778**9988889999999998878899 PP

                                       TSSEEEE--HHHHHHHCTTTCH........HCCSHHHHHHHHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG- CS
                       Carb_kinase 117 kaeviLTPhkkEfkrLlkaivk........keddrlelarelaqklnavvllkgekdvivspegevlinstgssala 185
                                        +  i+  +  E +r+++  vk        +e++ l +a+ la + +++v++ g+ d++++ + +++  +    ++ 
  gi|330509010|ref|YP_004385438.1| 114 VEVSIIKGNSSEVARIAGEDVKtrgvdaadIESNLLGVAHSLAGERGCTVVITGKDDIVADMKRAIWVHNGHPMMAN 190
                                       9999**************99999**************************************9988888776666777 PP

                                       STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHH CS
                       Carb_kinase 186 kGGsGDvLaGligalLaqneasyeaaiaaawlhgaasd 223
                                       + G+G   + +iga+ a++ ++  a + + +    a++
  gi|330509010|ref|YP_004385438.1| 191 VVGTGCMATSVIGAFAAVETDHVVASVSGLICYEVAAE 228
                                       89******************999888877666555554 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   2.7     3e-09   1.3e-05      24     217 ..      24     212 ..      16     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3e-09
                                       EEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHHHH.HH.TTSSEEEE---SSC CS
                      Phos_pyr_kin  24 svitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiievvaekl.kk.ykvpvVlDPVmvak 98 
                                         +t   + n  +v +  p+ a+  e+ +++  +  +  ++ iG l+++ + +++ + + ++ +k+pvVlD   v+ 
  gi|330509010|ref|YP_004385438.1|  24 NFVTIYDCANIVKVFGASPVMAHAREEVADMA-KIASSLVLNIGTLTTEFVEAMLLAGIsANeKKIPVVLD---VCG 96 
                                       55666666666666666666666554444443.3445567889***99988888888887443677*****...899 PP

                                       TSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---S........SHHHHHHHHHHHHHTT-SEEEEEEGGS- CS
                      Phos_pyr_kin  99 sgselleeeavealkeeLlplatvitPNlpEaeaLlgekik........teedmkeaakkllklgakaVlikGghle 167
                                        g++ +++e ++ + +  + ++++i  N  E+++++ge++k         e+++  +a++l+     +V+i+G++  
  gi|330509010|ref|YP_004385438.1|  97 AGATRFRDEKCQEILD--AVEVSIIKGNSSEVARIAGEDVKtrgvdaadIESNLLGVAHSLAGERGCTVVITGKD-- 169
                                       9************999..778****************88884333222112233445556666455556667765.. PP

                                       SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSH CS
                      Phos_pyr_kin 168 geeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesl 217
                                              d++ d ++ +++++ +    n  GtGC   s+i a  a + + 
  gi|330509010|ref|YP_004385438.1| 170 -------DIVADMKRAIWVHNGHPMMANVVGTGCMATSVIGAFAAVETDH 212
                                       .......9999*************99****************99876654 PP

>> eRF1_2  eRF1 domain 2
   #    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      85     113 ..      65      95 ..      41     115 .. 0.51
   2 ?   -1.1   0.0      0.49   2.2e+03      87      88 ..      99     100 ..      64     129 .. 0.57
   3 ?    9.9   0.0    0.0002      0.89      71      98 ..     223     250 ..     209     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
                                       SSTHHHHHHHHHHHHHHHHT.CCEE.EEE-S CS
                            eRF1_2  85 pgfvkeefldkdlldaelkk.kvik.lvdvs 113
                                        g   +ef++ +ll    ++ k+i  ++dv+
  gi|330509010|ref|YP_004385438.1|  65 IGTLTTEFVEAMLLAGISANeKKIPvVLDVC 95 
                                       4555555555554443222212222133443 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.49
                                       TH CS
                            eRF1_2  87 fv 88 
                                        +
  gi|330509010|ref|YP_004385438.1|  99 AT 100
                                       32 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0002
                                       HCHTTTESEEEEEESSTHHHHHHHHHHH CS
                            eRF1_2  71 lvdkdklkgiilagpgfvkeefldkdll 98 
                                       +    ++++++ agpg +ke+++d  + 
  gi|330509010|ref|YP_004385438.1| 223 YEVAAEIAALVAAGPGSFKENLYDAVYN 250
                                       555678999***************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1891.39
//
Query:       gi|330509011|ref|YP_004385439.1|  [L=525]
Description: phosphoglycerate dehydrogenase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-60  203.3   0.1    3.7e-60  202.3   0.1    1.5  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    1.4e-42  144.6   0.0      5e-42  142.7   0.0    1.9  1  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    3.5e-05   23.9   0.9    0.00023   21.3   0.1    2.5  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
    0.00077   19.7   0.4    0.00077   19.7   0.4    3.0  3  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0013   18.3   0.1     0.0055   16.3   0.0    2.1  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0034   17.1   0.0      0.012   15.4   0.0    2.0  1  ACT             ACT domain
  ------ inclusion threshold ------
      0.026   14.9   0.0      0.092   13.2   0.0    1.9  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
      0.049   14.1   0.5       0.32   11.5   0.1    2.6  3  NAD_binding_7   Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.3   0.1   1.6e-63   3.7e-60       1     178 []     104     278 ..     104     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: 202.3 bits;  conditional E-value: 1.6e-63
                                       HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77 
                                       +a++lal+r++++a++++++gew ++k+++g e  +kt+G++GlGr+G +va r+k+fgm+++ayd++ ++e+ +++
  gi|330509011|ref|YP_004385439.1| 104 IAMMLALARNIPQANSALHQGEW-NRKKYTGVEFFNKTLGVVGLGRVGAEVATRMKSFGMRILAYDPFVTEEK-AQQ 178
                                       68*********************.9*******************************************99776.9** PP

                                       HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES-- CS
                      2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvf 154
                                       +g++l++le++l+e D++++h+plt+etr+li+++e++ mk+g+ ++N+aRGg+++e+aL++a+ +gk+agaa+Dvf
  gi|330509011|ref|YP_004385439.1| 179 MGLTLANLETVLREGDFITVHTPLTNETRNLIDDDEFKIMKDGVRIVNCARGGIINEAALAKAVAEGKVAGAAVDVF 255
                                       ***************************************************************************** PP

                                       SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 155 eeeplpedspllelpnviltPHia 178
                                        +ep++  +pll  +++i tPH++
  gi|330509011|ref|YP_004385439.1| 256 TKEPPT-GNPLLGQERIITTPHLG 278
                                       *****9.55*************97 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.7   0.0   2.2e-45     5e-42       1     134 []       3     310 ..       3     310 .. 0.99

  Alignments for each domain:
  == domain 1  score: 142.7 bits;  conditional E-value: 2.2e-45
                                       EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDl 77 
                                       vl++++l e+++++l+  g +v+v ++l+ eel++k++d+dal++rs tkvta+v++a+++Lkvi+ragvG+DnvD+
  gi|330509011|ref|YP_004385439.1|   3 VLVSDSLAEDGVKRLQS-GADVDVITNLSPEELIQKIPDYDALVIRSGTKVTADVINAAKRLKVIGRAGVGIDNVDV 78 
                                       7999*************.55********************************************************* PP

                                       HHHHHTT-EEEE-TTTTHHHHHHHH.................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                        2-Hacid_dh  78 daakerGilVtnvpgystesvAElt.................................................... 102
                                       +aa+++Gi+V n+pg +t+s+AE+t                                                    
  gi|330509011|ref|YP_004385439.1|  79 EAATKKGIIVLNTPGGNTISAAEHTiammlalarnipqansalhqgewnrkkytgveffnktlgvvglgrvgaevat 155
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|330509011|ref|YP_004385439.1| 156 rmksfgmrilaydpfvteekaqqmgltlanletvlregdfitvhtpltnetrnlidddefkimkdgvrivncarggi 232
                                       ***************************************************************************** PP

                                       ..............................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                       ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ..............................................aaTeeaqeniaeeaaenlvaflkgespanav 133
                                                                                     a+T eaq n+a  +a++++a++kg+ p+na+
  gi|330509011|ref|YP_004385439.1| 233 ineaalakavaegkvagaavdvftkepptgnpllgqeriittphlgASTAEAQVNVALAVADQILAIAKGGLPTNAI 309
                                       ***************************************************************************99 PP

                                       S CS
                                       x RF
                        2-Hacid_dh 134 n 134
                                       n
  gi|330509011|ref|YP_004385439.1| 310 N 310
                                       8 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 ?    0.1   0.1      0.33   7.4e+02      32      96 ..      69     102 ..      43     122 .. 0.58
   2 !   21.3   0.1     1e-07   0.00023      17     110 ..     132     228 ..     125     272 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.33
                                       SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-SSSSSSB-HHH CS
                     AdoHcyase_NAD  32 GdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvtttGnkdiitleh 96 
                                         v                               G + v +e ++kk+ iv+ t G + i  +eh
  gi|330509011|ref|YP_004385439.1|  69 AGV-------------------------------GIDNVDVEAATKKGIIVLNTPGGNTISAAEH 102
                                       333...............................3344455555555555555555555555555 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1e-07
                                       H-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHH.HHHHCTT-EE--HHHCTTT-SEEEE-S....SS CS
                     AdoHcyase_NAD  17 tdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPica.lqaameGfevvtleevvkkadivvttt....Gn 88 
                                       t v +  k+  v+G G vG   a+ +k++G r++    dP  +  +a   G+ +++le+v++++d++   t     +
  gi|330509011|ref|YP_004385439.1| 132 TGVEFFNKTLGVVGLGRVGAEVATRMKSFGMRILA--YDPFVTeEKAQQMGLTLANLETVLREGDFITVHTpltnET 206
                                       66777789999********************9875..7997651678889***************886554222257 PP

                                       SSSB-HHHHCCS-TTEEEEE-S CS
                     AdoHcyase_NAD  89 kdiitlehlkkmkddaivcniG 110
                                       +++i  +++k mkd + + n  
  gi|330509011|ref|YP_004385439.1| 207 RNLIDDDEFKIMKDGVRIVNCA 228
                                       89************98666653 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.43   9.7e+02      81     109 ..      40      68 ..      15     114 .. 0.61
   2 !   19.7   0.4   3.4e-07   0.00077       2     107 ..     141     245 ..     140     254 .. 0.88
   3 ?   -0.8   0.0       0.7   1.6e+03      34      79 ..     386     431 ..     375     441 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.43
                                       -TT-EEEE-S---HHHHHHHHHHHHHTT- CS
                     NAD_binding_2  81 kkgdilidgstsspedtrelakelkekgl 109
                                       + ++++i ++t   +d ++ ak+lk  g 
  gi|330509011|ref|YP_004385439.1|  40 DYDALVIRSGTKVTADVINAAKRLKVIGR 68 
                                       45566666666666666666666665443 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 3.4e-07
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       +g++GlG  G++ a+++++ g+++ +y+     +ee +++   +++++e ++++ d++ +  + +++++++i++  +
  gi|330509011|ref|YP_004385439.1| 141 LGVVGLGRVGAEVATRMKSFGMRILAYDP--FVTEEKAQQMGLTLANLETVLREGDFITVHTPLTNETRNLIDDdEF 215
                                       79**************************4..46777777777789999*************************9999 PP

                                       CC--TT-EEEE-S---HHHHHHHHHHHHHT CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakelkek 107
                                       + +k g  +++++   + +   lak+++e 
  gi|330509011|ref|YP_004385439.1| 216 KIMKDGVRIVNCARGGIINEAALAKAVAEG 245
                                       999999999999988888888888887775 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.7
                                       HHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC CS
                     NAD_binding_2  34 kveelvaegakaaesieelvasldvvitmvkagkavdeviegllea 79 
                                       ++++l + g+k++es  e +++    itm   ++ v ++++g ++ 
  gi|330509011|ref|YP_004385439.1| 386 ATTTLKEMGVKLLESKTESINGYSNAITMKLTKNGVINMVQGTVSG 431
                                       5666777777888888888887766666666666666666664443 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 ?   -1.5   0.0      0.74   1.7e+03      83     112 ..      36      65 ..      18     108 .. 0.64
   2 !   16.3   0.0   2.4e-06    0.0055       4      89 ..     138     222 ..     135     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.74
                                       GG--TT-EEEESSSHHHHTTSS---TTSEE CS
                              IlvN  83 pnlkegkalafahGfnihfglikppkdvdv 112
                                       +++ + +al+  +G ++  + i++ k+++v
  gi|330509011|ref|YP_004385439.1|  36 QKIPDYDALVIRSGTKVTADVINAAKRLKV 65 
                                       334444444445555555555555544444 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.4e-06
                                       TS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHH.HHHHHHH CS
                              IlvN   4 gkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDel.qkevyee 79 
                                       +k++ v+G G  G   a+ ++  g+ +    ++   + +kA++ g++ ++++ + ++ d++++ +P +   ++++++
  gi|330509011|ref|YP_004385439.1| 138 NKTLGVVGLGRVGAEVATRMKSFGMRILA--YDPFVTEEKAQQMGLTLANLETVLREGDFITVHTPLTNeTRNLIDD 212
                                       799*********************99763..4445589***************************965414556666 PP

                                       HTGGG--TT- CS
                              IlvN  80 eiepnlkegk 89 
                                       +  + +k+g 
  gi|330509011|ref|YP_004385439.1| 213 DEFKIMKDGV 222
                                       6666666664 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.3e-06     0.012      20      66 ..     471     515 ..     469     516 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.3e-06
                                       HHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  20 aladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                       +l++ +iNi s++++++++  +    +v+ vd+ ++++++++l +++
  gi|330509011|ref|YP_004385439.1| 471 VLGEGNINIGSMHVGRMDE--GQPQLMVLSVDQMVPDDLMKRLLQVP 515
                                       67777**************..9*********************9987 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.1   9.2e+03      64      72 ..      38      46 ..      13      88 .. 0.61
   2 ?   13.2   0.0   4.1e-05     0.092      21      76 ..     152     202 ..     150     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.1
                                      HTT-SEEEE CS
                    UDPG_MGDP_dh_C 64 lkgadaivi 72
                                      + ++da+vi
  gi|330509011|ref|YP_004385439.1| 38 IPDYDALVI 46
                                      333333333 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.1e-05
                                       HHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S-- CS
                    UDPG_MGDP_dh_C  21 diieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaivilteh 76 
                                       ++++++++ g+++ +yDP v+ee++++     g++++ +le+ l++ d i ++t+ 
  gi|330509011|ref|YP_004385439.1| 152 EVATRMKSFGMRILAYDPFVTEEKAQQ----MGLTLA-NLETVLREGDFITVHTPL 202
                                       688999****************99987....578887.79******9999999975 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 ?   -1.8   0.0       1.9   4.3e+03      27      46 ..      17      33 ..      14      88 .. 0.63
   2 ?   11.5   0.1   0.00014      0.32       6      70 ..     137     201 ..     134     260 .. 0.73
   3 ?   -2.0   0.0       2.3   5.1e+03      62      72 ..     451     461 ..     398     463 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.9
                     NAD_binding_7 27 leagakvtvvapevkeelee 46
                                      l++ga+v v+++ +    ee
  gi|330509011|ref|YP_004385439.1| 17 LQSGADVDVITNLS---PEE 33
                                      66778887766552...222 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00014
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatd 70 
                                        +k+  vvG G+v+a+ + ++ ++g ++  ++p v+ee  +++ l+  +le  l + d++ + t+
  gi|330509011|ref|YP_004385439.1| 137 FNKTLGVVGLGRVGAEVATRMKSFGMRILAYDPFVTEEKAQQMGLTLANLETVLREGDFITVHTP 201
                                       578999****************************9888776666665555555555444444443 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.3
                     NAD_binding_7  62 adlviaatddr 72 
                                        d+via++dd+
  gi|330509011|ref|YP_004385439.1| 451 GDMVIAVIDDK 461
                                       57999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3693.40
//
Query:       gi|330509012|ref|YP_004385440.1|  [L=230]
Description: flavoprotein [Methanosaeta concilii GP6]
Scores for complete 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-22   78.4   0.0    6.7e-22   77.9   0.0    1.3  1  FMN_red       NADPH-dependent FMN reductase
      2e-12   47.2   0.0      4e-12   46.3   0.0    1.4  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.75   10.0   0.0    2.1  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 !   77.9   0.0   1.1e-25   6.7e-22       1     114 [.       1     122 [.       1     144 [. 0.83

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 1.1e-25
                                       -EEEEEES--S.TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHT..CGGSHHHHHHHHHH CS
                           FMN_red   1 mkilvisGSlr.kgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlese..gqtsddvaelleki 70 
                                       m il+i+GS++  ++nt k+++ ++e lkeaga+veli   +l i pc   +   +++ ++  + ++dd++ +l ki
  gi|330509012|ref|YP_004385440.1|   1 MDILAINGSPHmNEGNTAKILNPFLEGLKEAGANVELIYSWKLnIEPCsgdM--SCWFVNPgtCAKDDDMKTILPKI 75 
                                       89*********677************************98888889999753..33444335599************ PP

                                       HH-SCEEEEEEECTTCE-HHHHHHHHCHT-....SSCHCCTT-EEEE CS
                           FMN_red  71 aaadaliivtPeYngsysgllKnalDrlsr...trgkkelrgKpval 114
                                       ++ad++++++P+Y  +++g+lK+++Dr  +   + ++++  +K+v++
  gi|330509012|ref|YP_004385440.1|  76 KNADVIVWASPVYYSGITGPLKTLMDRQLPayvMGQPRSKMQKAVLV 122
                                       **************************975556655555555555555 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   6.7e-16     4e-12       1     108 [.       1     108 [.       1     134 [. 0.82

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 6.7e-16
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCC.HHHHTTC.HHHHHHH.HHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaak.layeekp.adveseq.iek 74 
                                       m iL in++p+ ++ ++ ++++ f+e+l++ag ++v+ +  +++ +  ++  d+++   ++ + +  d +++  + k
  gi|330509012|ref|YP_004385440.1|   1 MDILAINGSPHMNEGNTAKILNPFLEGLKEAG-ANVELIYSWKLNIEPCSG-DMSCWfVNPGT-CaKDDDMKTiLPK 74 
                                       88******************************.899999999986666665.77775466666.6699999999*** PP

                                       HHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTT CS
                      Flavodoxin_2  75 llaadaivlqfPlwwfgvPailKgwiDrvltagf 108
                                       +++ad+iv+++P+++ g+   lK  +Dr l a  
  gi|330509012|ref|YP_004385440.1|  75 IKNADVIVWASPVYYSGITGPLKTLMDRQLPAYV 108
                                       ****************************776654 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.21   1.2e+03       8      31 ..      14      37 ..      13      44 .. 0.89
   2 ?   10.0   0.0   0.00013      0.75      39     120 ..      73     160 ..      61     171 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.21
                      Flavodoxin_5  8 dGqTkkiaeriaeelreegelvdv 31
                                      +G+T+ki +   e l+e+g+ v++
  gi|330509012|ref|YP_004385440.1| 14 EGNTAKILNPFLEGLKEAGANVEL 37
                                      8*********99999999998876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00013
                      Flavodoxin_5  39 edlesydavvigasvyygkllpelakFvekh..reaLstkpvalfsvsltarkpeksyvrkf.....lkeklrwqpk 108
                                       ++++++d +v +++vyy+++ + l+ + +++     + + ++ +    l+++ +++ +++ f       + + ++p+
  gi|330509012|ref|YP_004385440.1|  73 PKIKNADVIVWASPVYYSGITGPLKTLMDRQlpAYVMGQPRSKMQKAVLVSTCSAW-EISMFdpllvQMKAIYDNPQ 148
                                       6899*******************999999984433455566666666666666666.55555443321123344577 PP

                      Flavodoxin_5 109 lvgvfaGaldys 120
                                       +   faGal  +
  gi|330509012|ref|YP_004385440.1| 149 DGCEFAGALLRP 160
                                       777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1661.39
//
Query:       gi|330509013|ref|YP_004385441.1|  [L=184]
Description: hypothetical protein MCON_3373 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-17   64.3   0.0    2.1e-17   64.0   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 !   64.0   0.0   1.2e-21   2.1e-17       1     144 [.      11     172 ..      11     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 1.2e-21
                               NYN   1 rvavfiDgenlpvpak...gke.vdyrklleeirskgelvraraygn..........wedee.......qnkfqdal 56 
                                       r+avfiDg++l +  +   gk  +d+ ++ + +  + e   +++y n          +   e       + kf   l
  gi|330509013|ref|YP_004385441.1|  11 RAAVFIDGAYLTKILDvdfGKPkIDLARFSDILCGNYER-LRTYYYNcmpyqscpstD---EesrrfasMDKFVYTL 83 
                                       78*************966644456666666666665553.466777769999985431...2344555578888888 PP

                               NYN  57 sstgi.kvkhkplkkrg.gsgkkavDvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeas 131
                                       ++    +vk ++l + g +  +k vD++la d+++l   + +  +v+v+gD+DF p++e+++  g+ V+++++e +s
  gi|330509013|ref|YP_004385441.1|  84 RKLPRfEVKLGRLGRVGgEFVQKRVDIALAADLVRLSCGRMIGKAVIVTGDSDFLPAIEAAKDAGVLVTLFYSE-SS 159
                                       88888899999997777*********************9999************************99999955.8* PP

                               NYN 132 tsseLisaadefi 144
                                       + +eL sa+de +
  gi|330509013|ref|YP_004385441.1| 160 IHDELLSAVDERT 172
                                       *********9765 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:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1361.50
//
Query:       gi|330509014|ref|YP_004385442.1|  [L=313]
Description: crispr-associated protein, Csa1 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-61  208.2   0.0    2.5e-61  207.6   0.0    1.3  1  Csa1      CRISPR-associated exonuclease Csa1
     0.0004   20.4   0.0     0.0009   19.2   0.0    1.6  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> Csa1  CRISPR-associated exonuclease Csa1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.6   0.0   2.8e-65   2.5e-61       6     289 ..       7     312 ..       1     313 [] 0.89

  Alignments for each domain:
  == domain 1  score: 207.6 bits;  conditional E-value: 2.8e-65
                              Csa1   6 eevrlL.krlkklsaskeveeElRGWnwnePPvkprslvklslsdvvsgyCetkRdvYLkrvlgvrgeeekklllGa 81 
                                       ee + L k+l  +++++ + e+lRGWnw+   + p++ + +++ +v  +yCet+Rd+YL++v++v + ++++++ G+
  gi|330509014|ref|YP_004385442.1|   7 EERKYLlKKLIPSTRERGIAEDLRGWNWHCSELSPPHDILMPVWEVSDRYCETGRDTYLRHVQKVSVPASEEMVAGR 83 
                                       3445555********************************************************************** PP

                              Csa1  82 aiHeavakaleelkkliysg.ekldsslerllv...adeivalledvie...............kakelykylasrv 139
                                       + H+a+a+   ++k+liy++  ++  +l  +l+    d+iv++ e++ +               + ++l+ + +sr+
  gi|330509014|ref|YP_004385442.1|  84 IYHQAMAELYPTAKRLIYKEgMSICAELPGILMerlDDAIVEANEQLSQtkfspsaeagqsvsdNLRKLWSFEVSRI 160
                                       *****************975155555554454411157888888877778889999988888878889999999999 PP

                              Csa1 140 saelsevrskfekatedsvaarviPvlvefkvdGsllGlsslvrvDafililplvvelkvgsykeehelalaGYala 216
                                        +++    +k ++++ ds++ +++P++ve+k+dG+ lGls ++++Da+ +   l+ +lk+g+ ++ h+l+ +GYal+
  gi|330509014|ref|YP_004385442.1| 161 VSSIFAYLAKYKYLSDDSLINHALPFVVEHKLDGKYLGLSRNLSADAINMGGMLICDLKTGQKRDFHRLSATGYALV 237
                                       99998889***************************************888888************************ PP

                              Csa1 217 lEsqleiPvDfGvlisvtvngev...klkaelvaisdslRkefleeRdraidivekesDPGlakkCsskClflevC 289
                                        Es +e+P+ +G+ +++ + ++    +++ + + isd++R++f+eeRd ++d++++e+DPG  ++ + +C ++e+C
  gi|330509014|ref|YP_004385442.1| 238 YESLYEVPINIGCTVYLSFPKNHptpHIERDFFIISDEVRQWFIEERDSKQDLIFYERDPGRCPN-PGSCRYREFC 312
                                       *****************8866544489**********************************8776.678*999999 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 !   19.2   0.0     1e-07    0.0009      18     254 ..      64     312 ..      54     313 .] 0.63

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1e-07
                          PDDEXK_1  18 flryllgl..reeeeleapdlGtlvHaaleefye.....................wkkldke...dleelleeavee 68 
                                       +lr+++++  +++ee+ a   G+++H+a++e+y                       ++ld++   + e+l++   ++
  gi|330509014|ref|YP_004385442.1|  64 YLRHVQKVsvPASEEMVA---GRIYHQAMAELYPtakrliykegmsicaelpgilMERLDDAiveANEQLSQ---TK 134
                                       889999997777888888...**********************99998887666655555555544444444...23 PP

                          PDDEXK_1  69 lwpellleeeilessarlrylaeklkevleklverlaeeleakrg.frpvalelefggekvrLkGri.........D 135
                                       ++p+++  ++   s++  + ++ ++ +++++ + +la+++  ++  +  + + l f   + +L G++         D
  gi|330509014|ref|YP_004385442.1| 135 FSPSAEAGQS--VSDNLRKLWSFEVSRIVSSIFAYLAKYKYLSDDsL--INHALPFV-VEHKLDGKYlglsrnlsaD 206
                                       3333222222..34555577888889999999999999999999953..44444444.2234555553332222226 PP

                          PDDEXK_1 136 rvddkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkkma 212
                                        +  + g + i D Ktg+   k+       ++l  + Y+l+++    ++ +  ++g++ +          ++ ++ +
  gi|330509014|ref|YP_004385442.1| 207 AI--NMGGMLICDLKTGQ---KRD-----FHRLSATGYALVYESL--YEVPI-NIGCTVYLS-------FPKNHPTP 263
                                       66..34469*********...333.....4789999********9..66555.444444433.......12222222 PP

                          PDDEXK_1 213 lteeel....eallqeleel...aeeilagefparpskkC...eyCpyksvC 254
                                       + e ++    ++++q++ e+    + +    ++ +p++ C    +C y++ C
  gi|330509014|ref|YP_004385442.1| 264 HIERDFfiisDEVRQWFIEErdsKQDLI--FYERDPGR-CpnpGSCRYREFC 312
                                       2233331445555555555522244444..77777775.977788****999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2367.61
//
Query:       gi|330509015|ref|YP_004385443.1|  [L=197]
Description: crispr-associated protein Cas4 [Methanosaeta concilii GP6]
Scores for complete 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-21   75.0   0.1    1.1e-20   74.4   0.1    1.3  1  Cas_Cas4  Domain of unknown function DUF83
    2.2e-12   47.4   0.6    1.2e-10   41.8   0.3    2.1  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
     0.0003   20.2   0.1     0.0018   17.7   0.1    1.8  2  Csa1      CRISPR-associated exonuclease Csa1
  ------ inclusion threshold ------
      0.035   13.4   0.0      0.046   13.0   0.0    1.2  1  DUF2800   Protein of unknown function (DUF2800)


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 !   74.4   0.1   2.4e-24   1.1e-20       6     161 ..       2     186 ..       1     187 [. 0.83

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 2.4e-24
                          Cas_Cas4   6 qyyliCkrklwlisheitleensetvelGkllhe................esyerek.....kevelse........ 53 
                                       ++yl+C++ +++ ++   ++  +++++ G  +h+                      +     k              
  gi|330509015|ref|YP_004385443.1|   2 KQYLYCPKIIYFDHVLHIPKPPDQKLQTGIEMHDsitakekrrkgaifydP-----EldqaeK-----Mfrvemess 68 
                                       79*************99999999***********88754444444443331.....0333332.....033334466 PP

                          Cas_Cas4  54 ....sikiDvvekekeklvvvEvKkskkk....eeaaklQllyYlllLe.kkgveikeGvleypkekkreeveltee 121
                                           ++++D++ +++++ ++v++K +++     + ++k+Ql +Y+ll+e +    +++G+++y   +k++++ + +e
  gi|330509015|ref|YP_004385443.1|  69 tlglRGVLDYLVRTNREFIPVDYKFGQSHkgsiHLNHKYQLAAYALLVEeSFKTIVRRGFIHYSRDQKNVQIDFGDE 145
                                       8999********************9999855556789************877777788******************* PP

                          Cas_Cas4 122 lreelekaikeieeiisse.kppkvkkkkiCkkCayaelCl 161
                                        r+++ k+i++i +ii+ e +p  + ++ +C  C+y+++C+
  gi|330509015|ref|YP_004385443.1| 146 IRRRTLKMIEKIAQIIEDEiEPAGTRNSARCIDCEYRKYCV 186
                                       *******************8888899999***********7 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 !    5.0   0.0    0.0043        19       8      45 ..       2      38 ..       1      66 [. 0.75
   2 !   41.8   0.3   2.6e-14   1.2e-10     116     254 ..      60     185 ..      37     186 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0043
                          PDDEXK_1  8 etfleCplrfflryllglreeeeleapdlGtlvHaale 45
                                      +++l Cp   ++ ++l+++++++++  + G  +H+ + 
  gi|330509015|ref|YP_004385443.1|  2 KQYLYCPKIIYFDHVLHIPKPPDQKL-QTGIEMHDSIT 38
                                      799***************77555555.66*****9985 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 2.6e-14
                          PDDEXK_1 116 pvalelefggekvrLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepaga 192
                                       ++++e+e  ++++ L+G +D + ++++e+  +DyK g++++ s     l++  Ql++Y+l+++e    k     ++ 
  gi|330509015|ref|YP_004385443.1|  60 MFRVEME--SSTLGLRGVLDYLVRTNREFIPVDYKFGQSHKGSIH---LNHKYQLAAYALLVEES--FKT---IVRR 126
                                       2333322..24566*********99999**********7766665...99***************..443...3555 PP

                          PDDEXK_1 193 lylrleepkvkdeevvkkmalteeeleallqeleelaeeilagefparpskk...CeyCpyksvC 254
                                        ++++     +  ++  +++  +e ++++l+ +e+ +++i + e++++ +++   C  C+y+++C
  gi|330509015|ref|YP_004385443.1| 127 GFIHY-----SRDQKNVQIDFGDEIRRRTLKMIEK-IAQIIEDEIEPAGTRNsarCIDCEYRKYC 185
                                       56665.....1222223332333333555555555.4666678899999988999********** PP

>> Csa1  CRISPR-associated exonuclease Csa1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.064   2.9e+02      55     105 ..       7      55 ..       3      71 .. 0.74
   2 !   17.7   0.1     4e-07    0.0018     196     290 ..      95     186 ..      60     188 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.064
                              Csa1  55 CetkRdvYLkrvlgvrgeeekklllGaaiHeavakaleelkkliysgekld 105
                                       C+  + +Y  +vl +     +kl++G  +H+ ++   +  k  i+   +ld
  gi|330509015|ref|YP_004385443.1|   7 CP--KIIYFDHVLHIPKPPDQKLQTGIEMHDSITAKEKRRKGAIFYDPELD 55 
                                       55..4599999****999************998877666666665544444 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 4e-07
                              Csa1 196 elkvgsykeehelalaGYalalEsqleiPvDfGvlisvtvngevklkaelvaisdslRkefleeRdraidivekesD 272
                                       + + gs++ +h+  la Yal +E      v  G++ + + +++v      +  +d++R++ l + +++++i+e+e +
  gi|330509015|ref|YP_004385443.1|  95 QSHKGSIHLNHKYQLAAYALLVEESFKTIVRRGFIHYSRDQKNV-----QIDFGDEIRRRTLKMIEKIAQIIEDEIE 166
                                       3456788889***********************98776555544.....46789*********************** PP

                              Csa1 273 PGlakkCs..skClflevCk 290
                                       P  +++     +C ++++C 
  gi|330509015|ref|YP_004385443.1| 167 PAGTRNSArcIDCEYRKYCV 186
                                       *5544332114899999995 PP

>> DUF2800  Protein of unknown function (DUF2800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05     0.046     103     162 ..      62     123 ..      35     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                           DUF2800 103 rvdfskyvpegfGtaDvviiaddvLeviDlKyGkgvkVsaekNp..QlalYAlGAleefdll 162
                                       rv++++ +   +G  D ++ ++++   +D+K+G+  k s + N+  Qla+YAl   e+f+ +
  gi|330509015|ref|YP_004385443.1|  62 RVEMESSTLGLRGVLDYLVRTNREFIPVDYKFGQSHKGSIHLNHkyQLAAYALLVEESFKTI 123
                                       667777777799**********************988777666444*******888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1322.64
//
Query:       gi|330509016|ref|YP_004385444.1|  [L=92]
Description: crispr-associated protein Cas2 [Methanosaeta concilii GP6]
Scores for complete 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   70.5   0.2    1.3e-19   70.1   0.2    1.2  1  CRISPR_Cas2  CRISPR associated protein Cas2
  ------ inclusion threshold ------
      0.038   13.9   0.0       0.05   13.6   0.0    1.2  1  SeqA         SeqA protein C-terminal domain
      0.039   13.9   0.5      0.058   13.4   0.5    1.2  1  zf-A20       A20-like zinc finger
       0.14   12.2   0.0       0.16   12.1   0.0    1.1  1  ADK          Adenylate kinase
       0.18   11.8   0.0       0.23   11.5   0.0    1.1  1  GPP34        Golgi phosphoprotein 3 (GPP34)


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 !   70.1   0.2   3.7e-23   1.3e-19       1      74 [.       1      73 [.       1      75 [. 0.98

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 3.7e-23
                                      EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCHHH CS
                       CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekqfe 74
                                      m  +++YDi +d+  r++vak+l ++G++r+Q+S F g ++++  ekl+ rl+++++++e++i +y++++k+f+
  gi|330509016|ref|YP_004385444.1|  1 MDTIIIYDI-SDNSLRARVAKVLLDFGCIRIQKSAFWGIMNHNTREKLRLRLERMMHEKEGNIQFYPMCSKCFS 73
                                      788******.**************************************************************95 PP

>> SeqA  SeqA protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.4e-05      0.05      70      97 ..      29      57 ..      20      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                              SeqA 70 qipetpfWVitNnntarKrli.leevmes 97
                                      +i ++ fW i N nt  K  + le++m++
  gi|330509016|ref|YP_004385444.1| 29 RIQKSAFWGIMNHNTREKLRLrLERMMHE 57
                                      599************99955438888876 PP

>> zf-A20  A20-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   1.6e-05     0.058      11      23 ..      60      72 ..      60      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                            zf-A20 11 GnpatnglCSkCY 23
                                      Gn ++ ++CSkC+
  gi|330509016|ref|YP_004385444.1| 60 GNIQFYPMCSKCF 72
                                      899999******9 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.5e-05      0.16     103     147 ..       1      66 [.       1      70 [. 0.95

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.5e-05
                                       ESEEEEEE--HHHHHHHHHT.....................GSHHHHHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK 103 ldlvleldvpeevlveRltg.....................DneetvkkRletykkqtkplidyyk 147
                                       +d+++  d++++ l  R+++                     ++ e+++ Rle  +++ +  i++y 
  gi|330509016|ref|YP_004385444.1|   1 MDTIIIYDISDNSLRARVAKvlldfgciriqksafwgimnhNTREKLRLRLERMMHEKEGNIQFYP 66 
                                       58999***********************************999********************996 PP

>> GPP34  Golgi phosphoprotein 3 (GPP34)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.3e-05      0.23      89     141 ..      12      56 ..       3      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.3e-05
                             GPP34  89 ksvrervakgLvdkGilrtekrrflglfdmtthpvadtaakeavrrrvraalt 141
                                        s+r+rvak L d G++r +k+ f g++        + +++e++r r+++ ++
  gi|330509016|ref|YP_004385444.1|  12 NSLRARVAKVLLDFGCIRIQKSAFWGIM--------NHNTREKLRLRLERMMH 56 
                                       699**********************994........44557777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 617.58
//
Query:       gi|330509017|ref|YP_004385445.1|  [L=337]
Description: crispr-associated protein Cas1 [Methanosaeta concilii GP6]
Scores for 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-75  253.6   0.0    2.7e-75  253.1   0.0    1.1  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 !  253.1   0.0   1.5e-79   2.7e-75       2     281 ..       5     291 ..       4     292 .. 0.95

  Alignments for each domain:
  == domain 1  score: 253.1 bits;  conditional E-value: 1.5e-79
                                       EEESTEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEEST.EEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEE.S CS
                          Cas_Cas1   2 yvteqgaylrkkgerlvvekegeekkeiplediesivifge.vslstkalrllaekgipvvflsengkylgrlep.e 76 
                                       +++++g++l+k++e++++++++     +p++ +e+i+++g+ +s+s++a++++ e g++vvf s++gk+++rl+p +
  gi|330509017|ref|YP_004385445.1|   5 ILSDRGTFLGKSSEQFRITRKDLPDVLVPARGVEQILVLGSgISVSSDAIQMADELGVEVVFASYYGKPMARLIPaS 81 
                                       57889************************************************************************ PP

                                       SSSTHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHC.TT.....HHHHCHCHHHHHHHHHHHH-.. CS
                          Cas_Cas1  77 esgnvelrraQyraaddeekrlelakkivagklenqrkvlrrlkrdr.ee.....eeleeaieeleellekleka.. 145
                                         g+v++rr+Qy+a++d++ +++la+++v+gkl+nq+++l+ ++++  +e      e++++ +++eel+ +l+ +  
  gi|330509017|ref|YP_004385445.1|  82 LGGTVKTRREQYNAYNDSR-GTNLARSFVRGKLKNQASLLKSFAKKWkGErqdlwGEFRNNSNQIEELIPRLNLIkg 157
                                       ****************998.**********************999885224679999************99999999 PP

                                       ...HSHHHHHHHHHHHHHHHHHHHHHHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SS CS
                          Cas_Cas1 146 ...esleeLrgiEGeaakaYfeafdkllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfL 219
                                          + + e++g+EG  a++Y+++++kl++++++f gR    ++D++N+lL+fgY ll++ev++ai  +gLdPy+GfL
  gi|330509017|ref|YP_004385445.1| 158 kvdDVRGEIMGVEGIGAEIYWRTWAKLIPDDWSFPGRDYPAARDQINSLLNFGYYLLEQEVWAAILYAGLDPYAGFL 234
                                       9989999********************************************************************** PP

                                       S--TTSS-HHHHHHHHHHHHHHCHHHHHHHHHTTSS-GGGEEEETTEEEE-HHHHHHHHHHH CS
                          Cas_Cas1 220 HedrpgrpsLalDLmEefRpllvDrlvlslinkrqlkekdFekeengvlLteegrkkfleaf 281
                                       H+drpg++ L++D+mEefRpl+vDr+v+sl   r++++ +F+     +++t++g k+  +af
  gi|330509017|ref|YP_004385445.1| 235 HADRPGKEKLVYDMMEEFRPLVVDRVVVSLA--REMRQGHFQD---DCRMTKDGIKIASKAF 291
                                       *****************************98..5678899987...8********9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2364.38
//
Query:       gi|330509018|ref|YP_004385446.1|  [L=800]
Description: CRISPR-associated helicase Cas3 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-19   69.1   0.0    3.4e-17   62.8   0.0    2.6  2  DEAD             DEAD/DEAH box helicase
    2.6e-13   50.3   0.7    2.7e-12   47.0   0.3    2.4  2  Helicase_C       Helicase conserved C-terminal domain
    1.1e-07   32.0   0.0    2.7e-05   24.3   0.0    2.4  2  ResIII           Type III restriction enzyme, res subunit
    1.2e-05   25.6   0.0      2e-05   24.8   0.0    1.3  1  HD_6             HD domain
  ------ inclusion threshold ------
      0.022   13.9   0.1      0.076   12.2   0.0    1.8  2  Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransfera


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 !   62.8   0.0   9.4e-21   3.4e-17       2     174 ..      24     212 ..      23     214 .. 0.78
   2 ?    3.4   0.0     0.016        56      44     105 ..     258     318 ..     242     335 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 9.4e-21
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid... 75 
                                       ++Q++++ l+ +g++v+++a+TGsGKTl  ++p l    + ++k + ++++  P+r+La + +n + +  ++++   
  gi|330509018|ref|YP_004385446.1|  24 PYQEKVFSLLDRGKSVVLRAPTGSGKTLSVIMPYLYLRKN-NEKMADRIIYALPMRALAFDLYNSTIQTAEKAGfcv 99 
                                       89*********************************66644.899999************************877433 PP

                                       ...........SEEEEEETTSSHHHHHHHH.........HTT....CSEEEEEHHHHHH.HH........HCTSSHC CS
                                       ...........xxxxxxxxxxxxxxxxxxx.........xxx....xxxxxxxxxxxxx.xx........xxxxxxx RF
                              DEAD  76 ...........lrvlliiggvaardqlskl.........dng....vdivvgtpgrldd.ll........stgklnl 119
                                                                  s++         +n+     di+++t ++l++  l        + g++n+
  gi|330509018|ref|YP_004385446.1| 100 vedpekrsgedR--------------DSEIcitiqtgelQNDhffeGDIIFTTIDQLLSgYLtlpvslpdRLGNINI 162
                                       333333333331..............333333333333322234448999999999999655899999987788999 PP

                                       TTE..EEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSHHHH CS
                                       xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 120 sqv..rflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlpkdvk 174
                                         +  +++V+DE++ +  q    +  +++n++     +g +  q+ v++ATl++  +
  gi|330509018|ref|YP_004385446.1| 163 GAIigSLIVFDEVHLMEFQRSFLTATEMMNRF-----EGLA--QFFVMTATLTEPTQ 212
                                       9999999************8888888999999.....3444..5********96655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.016
                                       TSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCSEEEEEH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  44 gktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngvdivvgtp 105
                                       ++++ k+l+++     a+q++++lk+ + ++d ++ l+ ++   ++++s++++++++ +g  
  gi|330509018|ref|YP_004385446.1| 258 KNHRQKTLVICNRVDKAQQIYSELKEKLINADTKIALL-HSRFFKRDRSEIEKNLQLWFGKR 318
                                       4667799*********************9999777654.44555666677766666666655 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.3   7.5e-16   2.7e-12      13     110 ..     258     363 ..     251     364 .. 0.87
   2 ?    0.4   0.0      0.22   7.9e+02      33      70 ..     541     578 ..     526     583 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 7.5e-16
                                       TTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHH......TTSSS.EEEESGGGTS CS
                        Helicase_C  13 eeeggkilifvntidrlek.vklllekk...gikvavlhgelpqnereeileqfn......kgesd.vLiatdvaer 78 
                                       +++++k+l+++n++d++++  + l+ek    + k+a lh++  +++r ei ++ +      +++++ +L++t+v+e 
  gi|330509018|ref|YP_004385446.1| 258 KNHRQKTLVICNRVDKAQQiYSELKEKLinaDTKIALLHSRFFKRDRSEIEKNLQlwfgkrSEDVNaILVSTQVVEA 334
                                       67899**********88767455544446669**********************9998877788889********** PP

                                       SSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       Gidi ++n+++   +p n  s+iqr+GR++R+
  gi|330509018|ref|YP_004385446.1| 335 GIDI-SCNTMHTELAPAN--SLIQRAGRCARY 363
                                       ****.6999999999977..9**********6 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.22
                                       HHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEE CS
                        Helicase_C  33 klllekkgikvavlhgelpqnereeileqfnkgesdvL 70 
                                        l+  ++g ++++l+ + p ++ + + e+f++++++v+
  gi|330509018|ref|YP_004385446.1| 541 GLIFGEEGTRCIILNKKSPYKSYKYSCESFQEHTHRVI 578
                                       566667799*********************99988876 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   7.4e-09   2.7e-05      22     169 ..      34     207 ..      10     209 .. 0.71
   2 !    5.1   0.1    0.0059        21      51     103 ..     258     321 ..     252     349 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 7.4e-09
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH-S........-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEESSS CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkee...kflflvprkslleqtleefkkflseayke...igkkvsgd 92 
                                       +r k +++ ++TG+GKTl  +    +l+k+++ +   +++   p ++l   +++   +++++a        +k sg+
  gi|330509018|ref|YP_004385446.1|  34 DRGKSVVLRAPTGSGKTLSVIMPYLYLRKNNE-KmadRIIYALPMRALAFDLYNSTIQTAEKAGFCvveDPEKRSGE 109
                                       6788999**********988777777776644.44789999999998877777777555555533355555555555 PP

                                       -B--..................-SEEEEEHHHHHHTH........HHHTTT-S.......EEEEETGGGTTS.TTTH CS
                            ResIII  93 kkka...........kekdstnkkilvttiqsldadseeeeeeseellrdrfd.......viiiDEaHrlgakkswr 151
                                        +++           ++ +  + +i++tti++l +    +   s   + ++++       +i++DE+H +  + s+ 
  gi|330509018|ref|YP_004385446.1| 110 DRDSeicitiqtgelQNDHFFEGDIIFTTIDQLLSGY-LTLPVSLPDRLGNINigaiigsLIVFDEVHLMEFQRSFL 185
                                       55555777777777666888899*********99999.444444444444444779999*************97666 PP

                                       HHHHT---....SEEEEEESS- CS
                            ResIII 152 eilekfke....avllglTATp 169
                                        + e++++    a  + +TAT+
  gi|330509018|ref|YP_004385446.1| 186 TATEMMNRfeglAQFFVMTATL 207
                                       6666665555567777899997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0059
                                       .....-EEEEESSHHHHHHHHHHGGGGTGG........GEEEESSS-B--.............. CS
                            ResIII  51 kgkeekflflvprkslleqtleefkkflseayke....igkkvsgdkkka.......kekdstn 103
                                       k++++k+l++++r +  +q ++e+k+ l +a+++    ++ +++ d+ ++       + k+s++
  gi|330509018|ref|YP_004385446.1| 258 KNHRQKTLVICNRVDKAQQIYSELKEKLINADTKiallHSRFFKRDRSEIeknlqlwFGKRSED 321
                                       45788*********************99999988888866666666666645556663333333 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   5.6e-09     2e-05      38     128 ..     595     723 ..     556     769 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.6e-09
                                       HHHHC.TS-HHHHHHHHHHHHHCCCGGGSSHHHHTTS----TTS-.....-GGGT.....................- CS
                              HD_6  38 larllrgleeealrrllaflaalHDlGKaspaFqakvpelaekleeaglelekel.....................e 93 
                                       l++++r  ++ ++++++++ +alHD GK+s + q   ++ +   +++  ++ k l                     +
  gi|330509018|ref|YP_004385446.1| 595 LSKKMRLDRNHSIEKMILLACALHDTGKLSVRWQGAMNRWQGISNPNAEQFIKGLplahttydpvkdwirmqelkiQ 671
                                       45555234456678999999***************994444433333333333337788888899999999999999 PP

                                       ---HHHHHHHHHH..................HHHHHHHHHHHTTTS---HHHH CS
                              HD_6  94 karHdslgaalle..................evarslaaavggHHGkppkeee 128
                                       k +H++ ga+ +                   ++a  ++aa++ HHG p +++ 
  gi|330509018|ref|YP_004385446.1| 672 KGPHAAEGAYAVFtmifkgsqtmlgdgddtqNMAIGIMAAIARHHG-PRTSNL 723
                                       99******999556666666667777777778999***********.444443 PP

>> Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.45   1.6e+03      84     239 ..     198     228 ..     189     250 .. 0.59
   2 ?   12.2   0.0   2.1e-05     0.076      37      84 ..     288     335 ..     282     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.45
                   Lip_A_acyltrans  84 graivetirvafisdeeiakrveviglehikealaeeegvilllpHfanwelaglvlakqypglavvaenkknplln 160
                                       ++++v+t+++                                                                   
  gi|330509018|ref|YP_004385446.1| 198 AQFFVMTATLTE----------------------------------------------------------------- 209
                                       444444444444................................................................. PP

                   Lip_A_acyltrans 161 qliislRerfggkllprknaikelikalrkgevvvllpDqdlgrkdsvfvpfFgepaatttspaklalktkaavipv 237
                                                                                                   ++  +la+++ka+ i++
  gi|330509018|ref|YP_004385446.1| 210 ------------------------------------------------------------PTQKWLAKQIKAEPITC 226
                                       ............................................................45555555555555555 PP

                   Lip_A_acyltrans 238 ai 239
                                        i
  gi|330509018|ref|YP_004385446.1| 227 SI 228
                                       44 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.1e-05
                   Lip_A_acyltrans  37 ilkglgrlaakflkrrrkiarkNLalvfpekseaerekiidksfesvg 84 
                                       + ++++ l ++f kr r+++ kNL+l f+++se++   ++ +++ ++g
  gi|330509018|ref|YP_004385446.1| 288 ADTKIALLHSRFFKRDRSEIEKNLQLWFGKRSEDVNAILVSTQVVEAG 335
                                       5678999999*************************9988888776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (800 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 5373.32
//
Query:       gi|330509019|ref|YP_004385447.1|  [L=572]
Description: hypothetical protein MCON_3380 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   12.7   0.1       0.19   11.8   0.1    1.3  1  P2_Phage_GpR  P2 phage tail completion protein R (GpR)


Domain annotation for each model (and alignments):
>> P2_Phage_GpR  P2 phage tail completion protein R (GpR)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.1e-05      0.19      31      88 ..     457     517 ..     447     530 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                      P2_Phage_GpR  31 egelvat...gaqslsfeyrYtlvlviedfpgdpdalmvpvlaWlrenqpdllenpekrla 88 
                                       + ++ a+    ++ + ++++Y l   ++++ ++pd+l++++ ++++++  +  +++e++++
  gi|330509019|ref|YP_004385447.1| 457 RATVNAQyrkAQGRRDWDIKYGLAQDWKRVAEQPDKLVIAISEFVQQYNAENARHAEENKE 517
                                       55555556657778889******************************99998888766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); 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: 0.78u 0.36s 00:00:01.14 Elapsed: 00:00:00.59
# Mc/sec: 2935.14
//
Query:       gi|330509020|ref|YP_004385448.1|  [L=439]
Description: transposase, IS116/IS110/IS902 family [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-25   87.4   0.0    1.3e-24   86.3   0.0    1.6  1  Transposase_20  Transposase IS116/IS110/IS902 family
    9.3e-23   80.8   0.2    3.7e-22   78.9   0.0    2.0  2  DEDD_Tnp_IS110  Transposase
     0.0059   16.4   0.1      0.015   15.1   0.1    1.7  1  YfkB            YfkB-like domain
  ------ inclusion threshold ------
       0.12   11.3   0.1       0.79    8.6   0.0    2.1  2  UPF0261         Uncharacterised protein family (UPF0261)


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0     3e-28   1.3e-24       2      86 ..     249     334 ..     248     335 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 3e-28
                    Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaai.r 77 
                                       ++++sipGi ++  +++l+eig+ r f++++qla+++Gl+p en+S++kkr+ +i+krG++++R +L+eaA++++  
  gi|330509020|ref|YP_004385448.1| 249 AIVMSIPGIAFISGSVILSEIGNYRDFQTPEQLAKWCGLNPGENESAGKKRKCGITKRGSKYIRVVLVEAAQTIAnM 325
                                       589********************************************************************999955 PP

                    Transposase_20  78 anpelrayy 86 
                                       +n  l ++y
  gi|330509020|ref|YP_004385448.1| 326 KNTGLSRFY 334
                                       569999888 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   8.3e-26   3.7e-22       1     151 [.       9     150 ..       9     152 .. 0.93
   2 ?   -1.5   0.0      0.46     2e+03      28      70 ..     323     366 ..     312     370 .. 0.63

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 8.3e-26
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       +G Dv+kd ++a+++  ++   ++e++ +++++l+++ ++ +a+ ++ +v++eatg y+ +++ + l++ i+++v n
  gi|330509020|ref|YP_004385448.1|   9 CGADVHKDLIVATITG-DEVPSIRENFGTTKSELDRFRNW-LADNKCEQVAFEATGVYWIPIYDV-LSRTIDTIVAN 82 
                                       799******9999984.66666778999999999999999.88999*************999998.6789******* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLd 151
                                       pl++k +      ++K+D+kD+k IA l +  ++++ +++ +++ +eLr+ltr+r+ +vk+rt++knr+++ L 
  gi|330509020|ref|YP_004385448.1|  83 PLQIKSIP-----NDKSDSKDSKRIATLCL-NNQIKRSRVFSDEDRELRNLTRARSGYVKTRTQFKNRIHKYLS 150
                                       ******95.....8****************.****************************************996 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.46
                    DEDD_Tnp_IS110  28 pn.deeglealleklaakagevlvvveatghygallvaflleag 70 
                                       +n +  gl+++ ++l++k+++   +v    +   l++++l +++
  gi|330509020|ref|YP_004385448.1| 323 ANmKNTGLSRFYKRLSKKKEHNVAIVAVARKLICLIYHLLINQE 366
                                       44144678888888666666666666666666666666766665 PP

>> YfkB  YfkB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.4e-06     0.015      91     150 ..     317     377 ..     306     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-06
                              YfkB  91 gdeealgnikeekledvfekwke.sklakslnchcpavkclGpnvlvknayykevdfkkrk 150
                                         +++++n+k++ l+  +++ ++ ++ +  +     ++ cl   +l+++ +y+evd +krk
  gi|330509020|ref|YP_004385448.1| 317 EAAQTIANMKNTGLSRFYKRLSKkKEHNVAIVAVARKLICLIYHLLINQEFYQEVDCRKRK 377
                                       56789***************9873567788999999**********************998 PP

>> UPF0261  Uncharacterised protein family (UPF0261)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00018      0.79     195     224 ..      34      63 ..      30      64 .. 0.96
   2 ?   -0.4   0.1     0.096   4.3e+02     156     192 ..     311     347 ..     307     356 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00018
                           UPF0261 195 fGvttpavdairelLeeegyevlvFhAtGt 224
                                       fG+t+   d+ r+ L+++++e ++F AtG+
  gi|330509020|ref|YP_004385448.1|  34 FGTTKSELDRFRNWLADNKCEQVAFEATGV 63 
                                       9****************************6 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.096
                           UPF0261 156 lrkvLsnAaaaiaGmakaeekskeekeeeeekplvai 192
                                       +r vL +Aa+ ia m ++  ++  ++ ++++ + vai
  gi|330509020|ref|YP_004385448.1| 311 IRVVLVEAAQTIANMKNTGLSRFYKRLSKKKEHNVAI 347
                                       6889*************99999988877777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.56
# Mc/sec: 2347.97
//
Query:       gi|330509021|ref|YP_004385449.1|  [L=202]
Description: hypothetical protein MCON_3383 [Methanosaeta concilii GP6]
Scores for complete 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   18.3   0.0     0.0037   17.6   0.0    1.3  1  DDE_Tnp_IS1  IS1 transposase
  ------ inclusion threshold ------
       0.14   12.4   0.9         14    6.0   0.1    2.9  4  FAF          Fantastic Four meristem regulator


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS1  IS1 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.1e-07    0.0037      86     116 ..     107     137 ..     101     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.1e-07
                       DDE_Tnp_IS1  86 tqriernnltlrtrlkrlarkslsfsksvel 116
                                       t  +er nlt r+   r+ rk+lsfsk  e+
  gi|330509021|ref|YP_004385449.1| 107 TAYVERTNLTSRQMNGRMVRKTLSFSKEEEM 137
                                       6789***********************9886 PP

>> FAF  Fantastic Four meristem regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.39   3.5e+03       3      11 ..      29      36 ..      29      51 .. 0.68
   2 ?    6.0   0.1    0.0016        14      14      28 ..      71      85 ..      54      92 .. 0.83
   3 ?    3.6   0.0    0.0088        79      14      44 ..     111     141 ..     100     142 .. 0.82
   4 ?   -3.4   0.0       1.3   1.2e+04       5      12 ..     154     161 ..     154     169 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.39
                               FAF  3 PPPlpslsg 11
                                      PP+++s  g
  gi|330509021|ref|YP_004385449.1| 29 PPAISSD-G 36
                                      9999986.4 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0016
                               FAF 14 pwvllrshredGRLv 28
                                       ++++ +hr++GRL+
  gi|330509021|ref|YP_004385449.1| 71 RCLQVTKHRSGGRLI 85
                                      689999*******98 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.0088
                               FAF  14 pwvllrshredGRLvleevkvpsrheylrae 44 
                                       +++ l s++ +GR+v +  + ++++e+l+a+
  gi|330509021|ref|YP_004385449.1| 111 ERTNLTSRQMNGRMVRKTLSFSKEEEMLKAS 141
                                       5667889999*****9999999999999885 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 1.3
                               FAF   5 Plpslsgr 12 
                                       Pl+sl+++
  gi|330509021|ref|YP_004385449.1| 154 PLKSLREE 161
                                       88888633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1127.49
//
Query:       gi|330509022|ref|YP_004385450.1|  [L=155]
Description: hypothetical protein MCON_3384 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.021   14.5   1.0      0.036   13.8   1.0    1.4  1  Zn_Tnp_IS1  InsA N-terminal domain
      0.032   14.0   0.1       0.05   13.4   0.1    1.4  1  HTH_23      Homeodomain-like domain
      0.036   14.5   0.1      0.069   13.6   0.1    1.5  1  LtuA        Late transcription unit A
       0.12   12.9   0.2       0.16   12.4   0.2    1.2  1  HTH_40      Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.0   8.1e-06     0.036      15      34 ..      28      47 ..      17      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.1e-06
                        Zn_Tnp_IS1 15 dVyRhGkstagHeRfrCrdC 34
                                      +++R G+  +g +R +C+ C
  gi|330509022|ref|YP_004385450.1| 28 NIVRYGRTSKGTQRLKCKTC 47
                                      58****************** PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.1e-05      0.05       6      41 ..      68     103 ..      63     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                            HTH_23   6 eRlrillllaeGlsvreIAreLgvsrrTvyrwlkry 41 
                                       e l+ l +lae+ s ++I r  g+ + T+  wl++ 
  gi|330509022|ref|YP_004385450.1|  68 EILECLAMLAERNSLAAIHRVKGIKEETIVDWLRKA 103
                                       5578899*************************9984 PP

>> LtuA  Late transcription unit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.5e-05     0.069      19      43 ..      34      60 ..      26      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                              LtuA 19 aakkGeqvmksrss..vWvGarGaiFY 43
                                       + kG q +k +    v+vG +G+iFY
  gi|330509022|ref|YP_004385450.1| 34 RTSKGTQRLKCKTCgrVFVGNKGTIFY 60
                                      5889***999876434*********** PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   3.6e-05      0.16       5      45 ..      72     112 ..      69     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.6e-05
                            HTH_40   5 tlelleeglsieeIAkerglkesTIegHLaelieegeeidl 45 
                                        l +l e  s+++I +  g+ke TI++ L ++  + eei++
  gi|330509022|ref|YP_004385450.1|  72 CLAMLAERNSLAAIHRVKGIKEETIVDWLRKASAHVEEIEA 112
                                       5789****************************999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 866.05
//
Query:       gi|330509023|ref|YP_004385451.1|  [L=245]
Description: hypothetical protein MCON_3386 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1373.64
//
Query:       gi|330509024|ref|YP_004385452.1|  [L=263]
Description: hypothetical protein MCON_3387 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1483.89
//
Query:       gi|330509025|ref|YP_004385453.1|  [L=109]
Description: IS3/IS66 family element, Orf1 protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.9e-11   41.8   0.1    1.6e-10   41.1   0.0    1.5  1  HTH_Tnp_1  Transposase
      0.002   17.8   0.0     0.0044   16.8   0.0    1.6  1  HTH_23     Homeodomain-like domain
     0.0046   17.0   0.0     0.0099   16.0   0.0    1.6  1  HTH_28     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.033   14.1   0.3      0.074   12.9   0.3    1.6  1  PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein k
      0.062   13.8   0.1       0.13   12.7   0.0    1.5  2  DUF4733    Domain of unknown function (DUF4733)


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   4.4e-14   1.6e-10       2      74 ..       3      75 ..       2      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 4.4e-14
                         HTH_Tnp_1  2 rrrrrwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyr...egeeaspaefeltaleeenrelkrel 74
                                      ++rrr+++ fK+++++e  e+gk+ +++Ar++g++p+   +W+++     e  +a   +    + +++++el+r+l
  gi|330509025|ref|YP_004385453.1|  3 KTRRRYDRDFKISVLAEL-EAGKPLAQIAREYGIHPSLPCRWKAELAenpE--KAFMGNGNKYKDQAKIAELERLL 75
                                      79***************9.*************************9975332..33333333344466777777765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.2e-06    0.0044       8      40 ..      14      46 ..       2      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                      +++l  l  G++ ++IAre+g++++  +rw+  
  gi|330509025|ref|YP_004385453.1| 14 ISVLAELEAGKPLAQIAREYGIHPSLPCRWKAE 46
                                      567888888***************987777765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.8e-06    0.0099       1      27 [.      12      38 ..      12      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
                            HTH_28  1 qRleiikllaaGhsvreaArelgisrr 27
                                      +++ ++ +l aG++ +++Are+gi+++
  gi|330509025|ref|YP_004385453.1| 12 FKISVLAELEAGKPLAQIAREYGIHPS 38
                                      7999********************997 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.1e-05     0.074       9      28 ..      67      86 ..      61      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                         PKcGMP_CC  9 RIRELEkrlaekdeEIqELr 28
                                      +I+ELE+ l + ++EI  L+
  gi|330509025|ref|YP_004385453.1| 67 KIAELERLLGQAHAEIDLLK 86
                                      9***************9888 PP

>> DUF4733  Domain of unknown function (DUF4733)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.7e-05      0.13      29      67 ..       4      42 ..       1      51 [. 0.88
   2 ?   -2.0   0.0       1.4     5e+03      32      32 ..      91      91 ..      64     106 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                           DUF4733 29 qplrpqravleelsaplelsqplsgllddyGilPkhPrp 67
                                        +r+ r +   + a le  +pl+++  +yGi+P  P +
  gi|330509025|ref|YP_004385453.1|  4 TRRRYDRDFKISVLAELEAGKPLAQIAREYGIHPSLPCR 42
                                      56899999999***********************99976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                           DUF4733 32 r 32
                                       
  gi|330509025|ref|YP_004385453.1| 91 M 91
                                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 616.44
//
Query:       gi|330509026|ref|YP_004385454.1|  [L=292]
Description: transposase IS3 family protein integrase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-25   89.8   0.0    2.2e-25   89.1   0.0    1.3  1  rve            Integrase core domain
    2.7e-19   69.1   0.3    1.9e-18   66.3   0.3    2.1  2  HTH_21         HTH-like domain
    3.8e-16   58.6   0.1    9.1e-16   57.4   0.1    1.7  1  rve_3          Integrase core domain
    4.7e-08   33.1   3.6    9.4e-08   32.1   2.4    2.1  2  rve_2          Integrase core domain
    0.00016   21.9   0.3    0.00028   21.1   0.3    1.4  1  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.027   14.6   0.1         12    6.1   0.0    2.4  2  GP3_package    DNA-packaging protein gp3
      0.041   14.1   0.0       0.11   12.7   0.0    1.7  1  HTH_Tnp_Tc3_2  Transposase
      0.049   13.8   0.1       0.17   12.0   0.0    1.9  2  HTH_Tnp_1_2    Helix-turn-helix of insertion element transpos


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.0   9.9e-29   2.2e-25       5     117 ..     127     239 ..     124     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 9.9e-29
                               rve   5 gelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve..pervlsDngseyt 79 
                                       ++ w +D+t+v++      ++l+v++d +sr ++++ ls+++ ++++  +l +a++++ ++    ++++sD+g +y+
  gi|330509026|ref|YP_004385454.1| 127 NQAWASDITYVQLQHE--HIFLAVILDLYSRKCIGWELSRSIRSDLAMSALAKALKNRSKESleGLIHHSDQGVQYA 201
                                       899*********6655..5*****************************************8899************* PP

                               rve  80 skafrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                       sk++ + l+ ++i++s++r+g+p+dn+ +E+f++tlk 
  gi|330509026|ref|YP_004385454.1| 202 SKDYVDCLKAHDIQISMSRKGNPYDNAFAESFIKTLKV 239
                                       ************************************95 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.3   8.5e-22   1.9e-18       6      58 ..      49      99 ..      45     101 .. 0.90
   2 ?   -0.0   0.0      0.45     1e+03      13      33 ..     257     277 ..     248     292 .] 0.66

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 8.5e-22
                            HTH_21  6 llalireifeeskgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgvqrr 58
                                      l ++i+ei  e  + YGyrri+aeL+++g+ +vnhkrV RlMr+++L+++ ++
  gi|330509026|ref|YP_004385454.1| 49 LVNQIQEIALEF-PYYGYRRITAELQNRGY-AVNHKRVLRLMRQEKLLCYKKK 99
                                      7899********.9**************87.5*****************9544 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.45
                            HTH_21  13 ifeeskgrYGyrriwaeLrre 33 
                                       i++    +Y ++r++ +L+ +
  gi|330509026|ref|YP_004385454.1| 257 ICNFIENVYNHKRLHSALNYR 277
                                       555445577788888888854 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1   4.1e-19   9.1e-16       1      67 []     212     279 ..     212     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 4.1e-19
                             rve_3   1 lgielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawred.YNteRPHssLgykTP 67 
                                       ++i++s+++ g P++N+++Esf++tl+ e ++ + ++++++a +++ +++e  YN++R Hs+L+y++P
  gi|330509026|ref|YP_004385454.1| 212 HDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHSALNYRSP 279
                                       689***************************************99999999866*************99 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.4     3e+03      21      33 ..     196     208 ..     184     209 .. 0.74
   2 !   32.1   2.4   4.2e-11   9.4e-08       1      48 [.     231     283 ..     231     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                             rve_2  21 eeleaaiedYIew 33 
                                       + ++ a +dY+++
  gi|330509026|ref|YP_004385454.1| 196 QGVQYASKDYVDC 208
                                       556788999*986 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 4.2e-11
                             rve_2   1 EsfFgsLKtElvygetfktleeleaaiedYIew.YNnkRlk....glsPvqYr 48 
                                       Esf ++LK+E vy  +++t+e +   i ++Ie  YN+kRl+    + sPvq++
  gi|330509026|ref|YP_004385454.1| 231 ESFIKTLKVEEVYLNEYETFEDAFRNICNFIENvYNHKRLHsalnYRSPVQFE 283
                                       9******************************988*****988888*******8 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   1.3e-07   0.00028       2     139 ..     128     271 ..     127     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                     DDE_Tnp_IS240   2 kswrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkek.lepeeivtDkasayasalke 76 
                                       ++w+ D Tyv+ + +  +l  ++D  +r  +++ +s     + a  +l kalk+ + ++ e ++    +  + a k 
  gi|330509026|ref|YP_004385454.1| 128 QAWASDITYVQLQHEHIFLAVILDLYSRkCIGWELSRSIRSDLAMSALAKALKNRSkESLEGLIHHSDQGVQYASKD 204
                                       68************************************999************998455555665555555555555 PP

                     DDE_Tnp_IS240  77 lkr...egelfdevshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktl.agfeavknlrkgh 139
                                         +     + + ++s+   +y n   Es  +tlK++  + +  ++++ a + + + +e v+n+++ h
  gi|330509026|ref|YP_004385454.1| 205 YVDclkAHDIQISMSRKGNPYDNAFAESFIKTLKVEEVYLNEYETFEDAFRNIcNFIENVYNHKRLH 271
                                       44411123556788899999***************************99877625679999999977 PP

>> GP3_package  DNA-packaging protein gp3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0053        12      49      78 ..      19      55 ..      15      63 .. 0.82
   2 ?    6.1   0.0    0.0052        12      51      90 ..     236     275 ..     199     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0053
                                      HHHHT--HHHHHHHGG..SHHH.......HHHHHHHH CS
                       GP3_package 49 alyLgisrstlkeyekrkrefs.......etierikq 78
                                      +l+L++srs  +e+ kr+++f        +++++i++
  gi|330509026|ref|YP_004385454.1| 19 CLALDVSRSGYYEWLKRSEKFTaensessDLVNQIQE 55
                                      899***************9998666666666666555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0052
                                       HHT--HHHHHHHGG..SHHHHHHHHHHHHHHHHHHHHHHT CS
                       GP3_package  51 yLgisrstlkeyekrkrefsetierikqivenqqiegala 90 
                                        L + + +l+eye+ +  f ++ + i+++ +++++  al 
  gi|330509026|ref|YP_004385454.1| 236 TLKVEEVYLNEYETFEDAFRNICNFIENVYNHKRLHSALN 275
                                       6889999*******999****************9999876 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.9e-05      0.11       3      56 ..      52     105 ..      50     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                     HTH_Tnp_Tc3_2   3 rIvrlvrkdPritlreLanelkeeGksvsreTirrrLrkaglkkrkprkkplLs 56 
                                       +I +++ + P+  +r++++el+++G  v ++ + r +r+++l  +k + kp+ +
  gi|330509026|ref|YP_004385454.1|  52 QIQEIALEFPYYGYRRITAELQNRGYAVNHKRVLRLMRQEKLLCYKKKFKPVTT 105
                                       68888889999**********************************999999755 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.7e-05      0.17      33      61 ..      19      48 ..      13      58 .. 0.83
   2 ?   -2.7   0.1       2.7   6.1e+03      55      72 ..     225     243 ..     224     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.7e-05
                                      HHHHTS-HHHHHHHH.H-HHHHHHHHHHHH CS
                       HTH_Tnp_1_2 33 aeevgvsrsTlykWk.kkkeFieyvnelae 61
                                      +  + vsrs +y+W+ + ++F+++ +e ++
  gi|330509026|ref|YP_004385454.1| 19 CLALDVSRSGYYEWLkRSEKFTAENSESSD 48
                                      56789*********9889999999888765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHT.THHHHH CS
                       HTH_Tnp_1_2  55 yvnelaeeflee.eraevy 72 
                                       y n  ae+f+++ +++evy
  gi|330509026|ref|YP_004385454.1| 225 YDNAFAESFIKTlKVEEVY 243
                                       7899999999873557777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.34s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1605.59
//
Query:       gi|330509027|ref|YP_004385455.1|  [L=71]
Description: hypothetical protein MCON_3393 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 474.11
//
Query:       gi|330509028|ref|YP_004385456.1|  [L=374]
Description: transposase, Mutator family [Methanosaeta concilii GP6]
Scores for complete 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-105  352.7   1.9   2.6e-105  352.4   1.9    1.0  1  Transposase_mut  Transposase, Mutator family
    4.9e-08   33.3   0.1    1.3e-07   31.9   0.0    1.8  2  MULE             MULE transposase domain
  ------ inclusion threshold ------
      0.016   14.9   0.2      0.041   13.6   0.2    1.7  1  DDE_Tnp_ISL3     Transposase
        0.4   11.3   4.9        3.1    8.5   0.1    3.7  4  DUF5499          Family of unknown function (DUF5499)


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 !  352.4   1.9  5.8e-109  2.6e-105      21     380 ..      13     365 ..       2     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 352.4 bits;  conditional E-value: 5.8e-109
                   Transposase_mut  21 gkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspalleryk 97 
                                       + ++ +k+l+  +l+e+++ e++++++a  yer+++r+ +RnG r+rkl+T +g++el  P+ R+  F++a++er+ 
  gi|330509028|ref|YP_004385456.1|  13 DRKEGMKKLTAGFLNEVMQLEAENQIQARPYERTGKRRAHRNGTRSRKLKTIYGEIELDKPQIREFPFETAVFERFS 89 
                                       4568999********************************************************************** PP

                   Transposase_mut  98 RrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkv 174
                                       R e+ l  +v+e y +Gvstrkvek++ +++  k++S+sevS+i+k+ld+ v+ f +R++e +  p++f+Da y kv
  gi|330509028|ref|YP_004385456.1|  90 RVEDSLRVAVAESYFEGVSTRKVEKVFSKFGL-KNISASEVSRIAKKLDKLVKDFLNRPIEGS-IPYIFVDASYFKV 164
                                       *******************************9.88****************************.************* PP

                   Transposase_mut 175 ReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaa 251
                                       R +gr v+ka l+ ++++ dG+reiL+ +v+dsE+e+ W++ +esLk+rGlkgv+lv+sDahkG+++a++++f +a+
  gi|330509028|ref|YP_004385456.1| 165 RTDGRYVNKALLVVVAIHDDGYREILSATVDDSEDESCWENCFESLKARGLKGVKLVISDAHKGIQAAVQKSFLGAS 241
                                       ***************************************************************************** PP

                   Transposase_mut 252 vQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaedvlaflafpe 328
                                       +Q C vH++r +l+++pkk++++va +lk    a + e   ++l+ +l+   k ++k a+++d+ + d+ ++ +fp+
  gi|330509028|ref|YP_004385456.1| 242 WQMCNVHFMRAVLKNIPKKEKKEVAYMLKD---AIEDEFKMQELAVILD--DKGFKKSADTIDSFRFDLWNYKSFPR 313
                                       ****************************95...6677888889999998..56899********************* PP

                   Transposase_mut 329 qirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                        ++++i++tN+lEr+Nke++Rr+rv g + n++s+lr+ + ++++ +++w++
  gi|330509028|ref|YP_004385456.1| 314 SHWKRIRTTNVLERINKELKRRSRVAGAYSNDQSLLRVAVCIMMDINEDWIT 365
                                       **************************************************86 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0     3e-11   1.3e-07      14      95 ..     172     251 ..     154     252 .. 0.87
   2 ?   -3.6   0.0       3.6   1.6e+04      61      70 ..     351     360 ..     341     364 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3e-11
                              MULE  14 klplltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlCl 90 
                                       +  ll vv+++d g   +l  ++ +se+e+++e  +++l+++    +  k +i+D +k+++ a+++ f +a  ++C 
  gi|330509028|ref|YP_004385456.1| 172 NKALLVVVAIHDDGYREILSATVDDSEDESCWENCFESLKARGL--KGVKLVISDAHKGIQAAVQKSFLGASWQMCN 246
                                       56789999********************************9644..69***************************** PP

                              MULE  91 fHiak 95 
                                        H+++
  gi|330509028|ref|YP_004385456.1| 247 VHFMR 251
                                       ***96 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.6
                              MULE  61 spkviitDke 70 
                                         ++i++D +
  gi|330509028|ref|YP_004385456.1| 351 VAVCIMMDIN 360
                                       4578888865 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   9.1e-06     0.041      23     105 ..     183     268 ..     162     351 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.1e-06
                      DDE_Tnp_ISL3  23 vdg.grlldilpg..RkketlkafleslsekerekveavvmDmsaayksavkealPnAkivvDrFHvvklanealde 96 
                                        dg +++l ++ +   ++++ ++++esl+++  + v+ v+ D ++++++av++ +  A+  + + H+++ + + + +
  gi|330509028|ref|YP_004385456.1| 183 DDGyREILSATVDdsEDESCWENCFESLKARGLKGVKLVISDAHKGIQAAVQKSFLGASWQMCNVHFMRAVLKNIPK 259
                                       3446677666544115667889*******9***************************************99998877 PP

                      DDE_Tnp_ISL3  97 vRrreqkel 105
                                         ++e+  +
  gi|330509028|ref|YP_004385456.1| 260 KEKKEVAYM 268
                                       766666555 PP

>> DUF5499  Family of unknown function (DUF5499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.7   3.1e+03       9      25 ..      37      53 ..      33      68 .. 0.74
   2 ?    8.5   0.1   0.00069       3.1      25      64 ..     113     152 ..      94     187 .. 0.83
   3 ?    1.9   0.0     0.076   3.4e+02      29      54 ..     199     224 ..     179     238 .. 0.78
   4 ?   -1.0   0.3      0.63   2.8e+03      36      61 ..     310     333 ..     276     346 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.7
                           DUF5499  9 dlkvrdydyfgkrkapd 25
                                      +++ r y+  gkr+a  
  gi|330509028|ref|YP_004385456.1| 37 QIQARPYERTGKRRAHR 53
                                      57789999999999864 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00069
                           DUF5499  25 dgvshkdmvenifrsdkwrrmkgidsevkdelnrqlrgev 64 
                                       + v  k  ++ni  s+  r  k +d  vkd lnr + g +
  gi|330509028|ref|YP_004385456.1| 113 EKVFSKFGLKNISASEVSRIAKKLDKLVKDFLNRPIEGSI 152
                                       4556677789*************************99987 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.076
                           DUF5499  29 hkdmvenifrsdkwrrmkgidsevkd 54 
                                        +   en f s k r +kg+   + d
  gi|330509028|ref|YP_004385456.1| 199 DESCWENCFESLKARGLKGVKLVISD 224
                                       556779*************9877666 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.63
                           DUF5499  36 ifrsdkwrrmkgidsevkdelnrqlr 61 
                                        f   +w+r++  +  v + +n++l+
  gi|330509028|ref|YP_004385456.1| 310 SFPRSHWKRIRTTN--VLERINKELK 333
                                       45566788877643..3344444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2355.40
//
Query:       gi|330509029|ref|YP_004385457.1|  [L=65]
Description: hypothetical protein MCON_3395 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 452.27
//
Query:       gi|330509030|ref|YP_004385458.1|  [L=93]
Description: hypothetical protein MCON_3396 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   12.4   6.4         18    5.8   0.0    3.1  3  Romo1     Reactive mitochondrial oxygen species modulator 1


Domain annotation for each model (and alignments):
>> Romo1  Reactive mitochondrial oxygen species modulator 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.4    0.0016        29      55      65 ..       8      18 ..       4      19 .. 0.89
   2 ?    4.8   0.5     0.002        37      41      64 ..      18      42 ..      17      43 .. 0.82
   3 ?    5.8   0.0     0.001        18      55      65 ..      83      93 .]      65      93 .] 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0016
                             Romo1 55 GfFmsiGsviR 65
                                       +F++iGs+iR
  gi|330509030|ref|YP_004385458.1|  8 SLFIGIGSAIR 18
                                      58********9 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.002
                             Romo1 41 rtlgksmlgsaatF.GfFmsiGsvi 64
                                      r l k m++ + +F  +F++iGs++
  gi|330509030|ref|YP_004385458.1| 18 RGLVKGMVEPGNSFnSLFIGIGSAM 42
                                      56778899999999679******86 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.001
                             Romo1 55 GfFmsiGsviR 65
                                       +F++iGs+iR
  gi|330509030|ref|YP_004385458.1| 83 SLFIGIGSAIR 93
                                      68********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 636.25
//
Query:       gi|330509031|ref|YP_004385459.1|  [L=90]
Description: hypothetical protein MCON_3397 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 620.25
//
Query:       gi|330509032|ref|YP_004385460.1|  [L=93]
Description: hypothetical protein MCON_3398 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 618.23
//
Query:       gi|330509033|ref|YP_004385461.1|  [L=141]
Description: hypothetical protein MCON_3405 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 957.81
//
Query:       gi|330509034|ref|YP_004385462.1|  [L=77]
Description: hypothetical protein MCON_3406 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   13.2   0.0      0.079   12.9   0.0    1.1  1  Hum_adeno_E3A  Human adenovirus early E3A glycoprotein


Domain annotation for each model (and alignments):
>> Hum_adeno_E3A  Human adenovirus early E3A glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.4e-06     0.079       4      52 ..      20      71 ..      17      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.4e-06
                     Hum_adeno_E3A  4 stiaptvdtvnstatgltsaldlpqvsafvndwasldmwwfsi...almfvc 52
                                      s i p +d  ns   g+ sa  lp + + ++ w s++  ++ i    l++vc
  gi|330509034|ref|YP_004385462.1| 20 SRIDPETDCFNSLFIGIGSAILLPLILTRIQLWRSFNSLFIGIgsaILLLVC 71
                                      7899*******************************99998877221355555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 585.10
//
Query:       gi|330509035|ref|YP_004385463.1|  [L=57]
Description: hypothetical protein MCON_3407 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00046   20.3   0.0    0.00046   20.3   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.5e-08   0.00046      20      48 ..       9      36 ..       1      55 [. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.5e-08
                   HicB_lk_antitox 20 lpGcfsagdtleeaianakeaielhlegl 48
                                      + G  s g+t+eea++n kea el+le+ 
  gi|330509035|ref|YP_004385463.1|  9 V-GTASQGKTIEEAVKNLKEATELYLEEF 36
                                      4.899**********************84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); 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: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 454.67
//
Query:       gi|330509036|ref|YP_004385464.1|  [L=76]
Description: YcfA-like protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-14   53.5   0.1      2e-14   53.3   0.1    1.1  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.1   1.1e-18     2e-14       4      57 ..      12      66 ..       9      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1.1e-18
                                      HHHHHHH.TT-EEEEEETTEEEEE-..TTSS-EEEEE.S-SSS--CCCHHHHHHHCC CS
                        HicA_toxin  4 viklLek.lGfevvrqkGSHvrfkh..pdkrgivtvppHpgkelkpgtlksIlkqaG 57
                                      vik+L + +Gf v +q+GSHvr+ +    +++ ++vp+H  +elkpgtl+s+lk a+
  gi|330509036|ref|YP_004385464.1| 12 VIKVLCNhFGFMVSGQSGSHVRLSKvtAQGKIGTVVPMH--DELKPGTLRSVLKLAK 66
                                      89999999*****************665555589*****..*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 558.06
//
Query:       gi|330509037|ref|YP_004385465.1|  [L=325]
Description: hypothetical protein MCON_3409 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      7e-15   55.4   0.1    1.3e-14   54.6   0.1    1.4  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6


Domain annotation for each model (and alignments):
>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.1   7.1e-19   1.3e-14       1      86 []     195     321 ..     195     321 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 7.1e-19
                                       EEEEEEE-EE..TEEESS--HHHHHHHHHHHHHHHTSS.............................EECHHHHHH. CS
                       CRISPR_Cas6   1 lrfltPtrfk..krkgllpsprlvfssllrrwnalaglkgk..........................ptveeeleg. 48 
                                       +rfltP ++k  +r++  ps+r ++s ll r nala+++g                           +       + 
  gi|330509037|ref|YP_004385465.1| 195 VRFLTPAQIKedDRFTAAPSFRGLISRLLFRANALAEFYGSgmlydneqvlailgacrlvsiikantE-------Ev 264
                                       79********87777788*********************99999888777777777666665543330.......03 PP

                                       ..................EEEEEEEE--.HHHECCCHHHHHHHH-SSSTGGGTTT-E CS
                       CRISPR_Cas6  49 ..................GfvGevkysg.eleelekllrfaeylgvGkktafGlGkv 86 
                                                          fvGe++y+g  ++e++ ll+++ +++vGk ++fG G++
  gi|330509037|ref|YP_004385465.1| 265 iakryfhkqkmkklslppFFVGEITYRGeFSREVMALLELGRLIHVGKMATFGNGMY 321
                                       333344445555677777********8899*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2452.71
//
Query:       gi|330509038|ref|YP_004385466.1|  [L=223]
Description: lipoprotein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1462.30
//
Query:       gi|330509039|ref|YP_004385467.1|  [L=386]
Description: pentapeptide repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-77  252.8  33.3      5e-10   38.8   1.4   10.1 11  Pentapeptide    Pentapeptide repeats (8 copies)
    2.4e-46  155.8   0.0    1.1e-08   35.1   0.0    5.8  7  Pentapeptide_4  Pentapeptide repeats (9 copies)
    2.1e-27   95.0   0.0     0.0061   16.7   0.0    8.3  8  Pentapeptide_3  Pentapeptide repeats (9 copies)
    4.2e-08   33.3   0.0     0.0028   17.7   0.0    3.5  4  CfAFP           Choristoneura fumiferana antifreeze protein (


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   3.8     1e-12   4.6e-09       2      39 ..      37      74 ..      37      74 .. 0.98
   2 !   38.8   1.4   1.1e-13     5e-10       6      38 ..      81     113 ..      78     113 .. 0.86
   3 !   33.3   0.1   5.9e-12   2.6e-08       1      40 []     111     150 ..     111     150 .. 0.98
   4 !   30.1   0.0     6e-11   2.7e-07       1      40 []     151     190 ..     151     190 .. 0.94
   5 !   24.5   0.1   3.3e-09   1.5e-05      11      40 .]     186     215 ..     185     215 .. 0.93
   6 !   35.6   1.0   1.2e-12   5.3e-09       2      39 ..     202     239 ..     201     239 .. 0.95
   7 !   29.1   0.0   1.2e-10   5.5e-07       1      39 [.     221     259 ..     221     259 .. 0.95
   8 !   35.8   0.0     1e-12   4.5e-09       1      38 [.     241     278 ..     241     278 .. 0.97
   9 !   33.7   0.1   4.5e-12     2e-08       1      40 []     276     315 ..     276     315 .. 0.98
  10 !   25.5   0.2   1.6e-09   7.4e-06      11      39 ..     321     349 ..     318     350 .. 0.57
  11 ?    1.7   0.0     0.046   2.1e+02      22      33 ..     360     371 ..     355     373 .. 0.54

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1e-12
                                      B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide  2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39
                                      nLs AnLs  +L ga+l++++L+g+nl+g++L ga L+
  gi|330509039|ref|YP_004385467.1| 37 NLSYANLSAMDLAGAHLNQSDLQGCNLNGSNLDGAYLR 74
                                      9**********************************997 PP

  == domain 2  score: 38.8 bits;  conditional E-value: 1.1e-13
                                       -B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   6 AnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                         L g+ L++a+l+gA+Lt+A+l+gAdL+ganL
  gi|330509039|ref|YP_004385467.1|  81 SHLNGSTLENADLTGAVLTEADLTGADLTGANL 113
                                       568999999999999999999999999999997 PP

  == domain 3  score: 33.3 bits;  conditional E-value: 5.9e-12
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       AnL +++ s a+L+ga    A+Lt+A++s++dLs+a+L++
  gi|330509039|ref|YP_004385467.1| 111 ANLIRVQMSKAKLNGARIVKADLTEADISDSDLSDADLTD 150
                                       9*************************************97 PP

  == domain 4  score: 30.1 bits;  conditional E-value: 6e-11
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       A+L +++Lsga+L+g  l+ An++gA +s+Ad+s a Ls+
  gi|330509039|ref|YP_004385467.1| 151 ARLFRTDLSGAKLKGIYLTSANMIGAHISWADMSVAYLSQ 190
                                       7999*****************************9887775 PP

  == domain 5  score: 24.5 bits;  conditional E-value: 3.3e-09
                                       SCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide  11 anLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       a+Ls+  +s+A L+++nlsg+dLs+a++++
  gi|330509039|ref|YP_004385467.1| 186 AYLSQGQFSRAELYSTNLSGSDLSDADFTR 215
                                       6899999*********************95 PP

  == domain 6  score: 35.6 bits;  conditional E-value: 1.2e-12
                                       B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                       nLsg +Ls a++++a l ++nLtgAn+ +Ad+  a+L+
  gi|330509039|ref|YP_004385467.1| 202 NLSGSDLSDADFTRAYLMRSNLTGANIDWADMAYADLT 239
                                       9********************************99997 PP

  == domain 7  score: 29.1 bits;  conditional E-value: 1.2e-10
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                       +nL+gAn  +a++  a+l++A+LtgA+l  A++  ++L+
  gi|330509039|ref|YP_004385467.1| 221 SNLTGANIDWADMAYADLTEAVLTGASLKSAKMPYSDLT 259
                                       7*******************************9988886 PP

  == domain 8  score: 35.8 bits;  conditional E-value: 1e-12
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       A L+gA L  a++  ++l+ An+tgA+ls A L ga+L
  gi|330509039|ref|YP_004385467.1| 241 AVLTGASLKSAKMPYSDLTKANFTGADLSEAYLDGAIL 278
                                       779*********************************98 PP

  == domain 9  score: 33.7 bits;  conditional E-value: 4.5e-12
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       A+L gA L++a+L+++nl++ +L+g ++ gA L+++ L+g
  gi|330509039|ref|YP_004385467.1| 276 AILAGATLRNAKLDRVNLREVDLRGLEMGGASLKNSVLTG 315
                                       89************************************98 PP

  == domain 10  score: 25.5 bits;  conditional E-value: 1.6e-09
                                       SCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide  11 anLsganlsgAnLtgAnlsgAdLsganLs 39 
                                       ++L ga+l++A+L  ++++gA+Ls anL+
  gi|330509039|ref|YP_004385467.1| 321 TDLAGADLRDATLVQVEMTGANLSSANLE 349
                                       55556666666666666666666666554 PP

  == domain 11  score: 1.7 bits;  conditional E-value: 0.046
                                       EECT-B-TT-EE CS
                      Pentapeptide  22 nLtgAnlsgAdL 33 
                                       +L++A+l gA+ 
  gi|330509039|ref|YP_004385467.1| 360 SLSRAELDGAKI 371
                                       455555555544 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   8.8e-08   0.00039      31      73 ..      28      74 ..      14      78 .. 0.82
   2 !   27.6   0.0   5.4e-10   2.4e-06       5      76 ..      35     107 ..      34     108 .. 0.91
   3 !   35.1   0.0   2.5e-12   1.1e-08       1      69 [.     101     170 ..      76     177 .. 0.87
   4 !   22.2   0.0   2.5e-08   0.00011      11      74 ..     156     220 ..     155     223 .. 0.87
   5 !   24.3   0.0   5.7e-09   2.5e-05      11      74 ..     186     250 ..     176     252 .. 0.63
   6 !   31.1   0.0   4.2e-11   1.9e-07       4      73 ..     199     279 ..     192     283 .. 0.77
   7 !   29.2   0.0   1.7e-10   7.7e-07       6      75 ..     281     351 ..     276     362 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.8e-08
                    Pentapeptide_4 31 crl...snvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klk 73
                                       ++   + vn++ +nls  d+a+++l+ + ++gcnl+++n+++  l+
  gi|330509039|ref|YP_004385467.1| 28 LDInidDRVNLSYANLSAMDLAGAHLNQSDLQGCNLNGSNLDGaYLR 74
                                      444667889********************************984565 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 5.4e-10
                    Pentapeptide_4   5 rcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf.sdklkdid 76 
                                       r+ +  ++ls ++++ a+l+ +++++c+l+  n+d + l+++ +   +l+ +++++ +l+++++ ++ l+++d
  gi|330509039|ref|YP_004385467.1|  35 RVNLSYANLSAMDLAGAHLNQSDLQGCNLNGSNLDGAYLRSAWLMASHLNGSTLENADLTGAVLtEADLTGAD 107
                                       566777899*******************************************************556999887 PP

  == domain 3  score: 35.1 bits;  conditional E-value: 2.5e-12
                    Pentapeptide_4   1 aeftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf.s 69 
                                       a++t + + +++l +v++s+a+l++++++ ++l+++  ++++lsd+d+++++l+r+ +sg  lk++ + s
  gi|330509039|ref|YP_004385467.1| 101 ADLTGADLTGANLIRVQMSKAKLNGARIVKADLTEADISDSDLSDADLTDARLFRTDLSGAKLKGIYLtS 170
                                       5678888899999999999999999999999999999999999999999999999999999999988844 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 2.5e-08
                    Pentapeptide_4  11 cklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkd 74 
                                       ++ls++ ++ ++l ++n+ ++++s + ++ + ls+ +f+ ++l ++++sg++l+++ f +  l++
  gi|330509039|ref|YP_004385467.1| 156 TDLSGAKLKGIYLTSANMIGAHISWADMSVAYLSQGQFSRAELYSTNLSGSDLSDADFTRaYLMR 220
                                       68888999999999999999999***********************************5536776 PP

  == domain 5  score: 24.3 bits;  conditional E-value: 5.7e-09
                    Pentapeptide_4  11 cklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkd 74 
                                       + ls+ +Fs a+l ++n+++++ls++ F+++ l  ++++++++ +a     +l+++++ + +lk+
  gi|330509039|ref|YP_004385467.1| 186 AYLSQGQFSRAELYSTNLSGSDLSDADFTRAYLMRSNLTGANIDWADMAYADLTEAVLTGaSLKS 250
                                       55666677777777777777777777777777777777777777776666666666666545665 PP

  == domain 6  score: 31.1 bits;  conditional E-value: 4.2e-11
                    Pentapeptide_4   4 trcsfnncklsnvnFsearlrdcnFtecrl..........snvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd 70 
                                        +  + +++ls+++F+ a+l ++n+t++++          ++++++ ++l++++    dl++a+F+g +l+++ +++
  gi|330509039|ref|YP_004385467.1| 199 YSTNLSGSDLSDADFTRAYLMRSNLTGANIdwadmayadlTEAVLTGASLKSAKMPYSDLTKANFTGADLSEAYLDG 275
                                       55667899999999999999999999999977777777777777777777777777777777788888888888776 PP

                    Pentapeptide_4  71 .klk 73 
                                         l 
  gi|330509039|ref|YP_004385467.1| 276 aILA 279
                                       4555 PP

  == domain 7  score: 29.2 bits;  conditional E-value: 1.7e-10
                    Pentapeptide_4   6 csfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdi 75 
                                       ++++n+kl++vn++e++lr+  + ++ l+n +++      +d+a++dl++a++ +++ +++n+s   l++i
  gi|330509039|ref|YP_004385467.1| 281 ATLRNAKLDRVNLREVDLRGLEMGGASLKNSVLTGVFMAMTDLAGADLRDATLVQVEMTGANLSSaNLERI 351
                                       67788888888888888888888888888888888888888888888888888888888888854366655 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00034       1.5      19      47 ..      45      71 ..      31      78 .. 0.54
   2 !   15.8   0.0   2.6e-06     0.012       6      45 ..      83     119 ..      74     127 .. 0.59
   3 !   14.0   0.0   9.1e-06     0.041       4      46 ..     116     155 ..     113     162 .. 0.76
   4 ?    1.1   0.0       0.1   4.6e+02       2      31 ..     159     186 ..     157     190 .. 0.76
   5 !   15.5   0.0   3.3e-06     0.015       1      45 [.     193     234 ..     186     237 .. 0.85
   6 !   16.7   0.0   1.4e-06    0.0061      10      47 ..     236     271 ..     233     272 .. 0.95
   7 !   10.3   0.0   0.00013       0.6       2      47 ..     269     311 ..     268     312 .. 0.82
   8 !    9.2   0.0   0.00029       1.3       8      47 ..     305     341 ..     298     351 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00034
                    Pentapeptide_3 19 gaasFsnadFgsadFsgarFtgdvdFsga 47
                                       + +  +a+++ +d++g++ + +++++ga
  gi|330509039|ref|YP_004385467.1| 45 AM-DLAGAHLNQSDLQGCNLN-GSNLDGA 71
                                      44.444555555555555554.4444443 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.6e-06
                    Pentapeptide_3   6 FsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFs 45 
                                       + g+ ++++a  +ga+  ++ad+++ad+ ga+   +v++s
  gi|330509039|ref|YP_004385467.1|  83 LNGS-TLENADLTGAV-LTEADLTGADLTGANLI-RVQMS 119
                                       4555.55555555553.55555555555555555.54444 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 9.1e-06
                    Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsg 46 
                                       +++s+a  + ga+  +a + ++ad++++d+s+a  t d+++ +
  gi|330509039|ref|YP_004385467.1| 116 VQMSKA-KLNGARIVKA-DLTEADISDSDLSDADLT-DARLFR 155
                                       567777.8888888888.888888888888888888.887755 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.1
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsa 31 
                                       sga ++g  +++ a+ +ga   s ad++ a
  gi|330509039|ref|YP_004385467.1| 159 SGAKLKGI-YLTSANMIGA-HISWADMSVA 186
                                       78999999.9999999998.5677766655 PP

  == domain 5  score: 15.5 bits;  conditional E-value: 3.3e-06
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFs 45 
                                       Fs+a+++ + +++g+  s+a +F++a + ++++ ga+++ ++d+ 
  gi|330509039|ref|YP_004385467.1| 193 FSRAELYST-NLSGSDLSDA-DFTRAYLMRSNLTGANID-WADMA 234
                                       888889999.9999999999.999999999999999998.88876 PP

  == domain 6  score: 16.7 bits;  conditional E-value: 1.4e-06
                    Pentapeptide_3  10 adFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                       ad+++a+ +ga s ++a +  +d+ +a+Ft ++d+s+a
  gi|330509039|ref|YP_004385467.1| 236 ADLTEAVLTGA-SLKSAKMPYSDLTKANFT-GADLSEA 271
                                       69*********.******************.****986 PP

  == domain 7  score: 10.3 bits;  conditional E-value: 0.00013
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                       s+a ++ga  + gat ++a   ++ +++++d++g  +  +++++++
  gi|330509039|ref|YP_004385467.1| 269 SEAYLDGA-ILAGATLRNA-KLDRVNLREVDLRGLEMG-GASLKNS 311
                                       67888888.9999999999.699999999999999995.9998887 PP

  == domain 8  score: 9.2 bits;  conditional E-value: 0.00029
                    Pentapeptide_3   8 gaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                       g a++ +++ +g  ++  +d+ +ad+++a+    v+++ga
  gi|330509039|ref|YP_004385467.1| 305 G-ASLKNSVLTGV-FMAMTDLAGADLRDATLV-QVEMTGA 341
                                       4.49999999999.899999999999999976.6666665 PP

>> CfAFP  Choristoneura fumiferana antifreeze protein (CfAFP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0   0.00083       3.7      47     107 ..      26      86 ..      10     103 .. 0.82
   2 !   17.7   0.0   6.2e-07    0.0028      42     111 ..     116     185 ..      96     209 .. 0.88
   3 ?    1.8   0.0     0.048   2.1e+02      52      97 ..     206     251 ..     189     258 .. 0.74
   4 ?    3.6   0.0     0.014        63      34      99 ..     218     283 ..     206     292 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00083
                             CfAFP  47 selessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitsstttgtrisGp 107
                                       +el+ +i  r + s a++     + + +++s+l g    gs+ dG y++s+   ++++ G 
  gi|330509039|ref|YP_004385467.1|  26 AELDINIDDRVNLSYANLSAMDLAGAHLNQSDLQGCNLNGSNLDGAYLRSAWLMASHLNGS 86 
                                       67888999999999999999999***************************98888888775 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 6.2e-07
                             CfAFP  42 cyidnselessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitsstttgtrisGpgcsi 111
                                        ++ +++l+ + +++++ ++a + +s  +d+++ +++l+ t  +g++ +G+y+ts+   g++is    s+
  gi|330509039|ref|YP_004385467.1| 116 VQMSKAKLNGARIVKADLTEADISDSDLSDADLTDARLFRTDLSGAKLKGIYLTSANMIGAHISWADMSV 185
                                       56678889999999***********************************************999766555 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.048
                             CfAFP  52 sictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitss 97 
                                       s  + ++++ ay+++s  t +nid +++  +  t++   G  ++s+
  gi|330509039|ref|YP_004385467.1| 206 SDLSDADFTRAYLMRSNLTGANIDWADMAYADLTEAVLTGASLKSA 251
                                       4445667888888999999999998888877777777777776665 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.014
                             CfAFP  34 cvkstltncyidnselessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitsstt 99 
                                        ++s lt  +id +++  +  t +  ++a +k+++    ++ k+++ g+  +++  dG  +  +t 
  gi|330509039|ref|YP_004385467.1| 218 LMRSNLTGANIDWADMAYADLTEAVLTGASLKSAKMPYSDLTKANFTGADLSEAYLDGAILAGATL 283
                                       457788888888888877888888888888888888877777777777777777777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2933.82
//
Query:       gi|330509040|ref|YP_004385468.1|  [L=953]
Description: pentapeptide repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-105  343.9 143.4    3.1e-10   39.5   2.1   15.1 20  Pentapeptide    Pentapeptide repeats (8 copies)
    1.2e-51  172.8   6.4    2.6e-09   37.1   0.3    8.4  8  Pentapeptide_4  Pentapeptide repeats (9 copies)
    1.6e-42  143.4  11.8    0.00055   20.0   0.0   11.8 11  Pentapeptide_3  Pentapeptide repeats (9 copies)
    1.5e-09   37.5   0.0    3.6e-09   36.3   0.0    1.6  1  ABC_sub_bind    ABC transporter substrate binding protein
    1.1e-06   28.7   0.0       0.28   11.2   0.0    4.4  5  CfAFP           Choristoneura fumiferana antifreeze protein (


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   2.2   9.4e-11   3.4e-07       5      40 .]     417     452 ..     417     452 .. 0.97
   2 !   25.0   0.4   2.9e-09   1.1e-05       4      38 ..     461     495 ..     458     497 .. 0.90
   3 !   21.3   0.1   4.3e-08   0.00016       3      39 ..     500     536 ..     499     536 .. 0.94
   4 !   28.6   1.9   2.2e-10   7.7e-07       4      38 ..     541     575 ..     538     575 .. 0.94
   5 !   36.4   0.7   7.9e-13   2.8e-09       3      38 ..     560     595 ..     560     596 .. 0.77
   6 !   29.8   1.3   9.3e-11   3.3e-07       1      39 [.     598     636 ..     598     636 .. 0.97
   7 !   28.6   4.7   2.3e-10   8.1e-07       1      38 [.     628     665 ..     628     665 .. 0.94
   8 !   30.7   0.4     5e-11   1.8e-07       1      40 []     643     682 ..     643     682 .. 0.97
   9 !   30.9   0.2   4.1e-11   1.5e-07       1      40 []     663     702 ..     663     702 .. 0.95
  10 !   36.3   4.5   8.4e-13     3e-09       1      40 []     688     727 ..     688     727 .. 0.95
  11 !   34.0   1.7   4.6e-12   1.7e-08       1      39 [.     703     741 ..     703     741 .. 0.97
  12 !   26.8   0.1   8.4e-10     3e-06       3      37 ..     725     759 ..     723     760 .. 0.93
  13 !   38.3   3.6     2e-13   7.3e-10       1      40 []     738     777 ..     738     777 .. 0.97
  14 !   38.7   3.7   1.5e-13   5.5e-10       1      38 [.     758     795 ..     758     796 .. 0.97
  15 !   39.5   2.1   8.5e-14   3.1e-10       1      40 []     768     807 ..     768     807 .. 0.99
  16 !   32.8   0.7     1e-11   3.7e-08       1      36 [.     798     833 ..     798     834 .. 0.94
  17 !    7.0   0.0    0.0013       4.7      12      40 .]     839     867 ..     836     867 .. 0.92
  18 !   32.9   0.9     1e-11   3.6e-08       3      37 ..     860     894 ..     859     896 .. 0.92
  19 !   35.4   1.5   1.7e-12     6e-09       1      40 []     868     907 ..     868     907 .. 0.99
  20 ?   -2.2   0.0      0.96   3.4e+03      27      33 ..     927     933 ..     926     934 .. 0.33

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 9.4e-11
                                       T-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   5 gAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       +A+L + nLsg +ls+++L++++l g+dLsg+nLs+
  gi|330509040|ref|YP_004385468.1| 417 RADLNNRNLSGLDLSETDLSYSDLLGSDLSGTNLSR 452
                                       79********************************95 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 2.9e-09
                                       TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   4 sgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       s+  L  anLsga++  A L+g++lsgAdL+ga L
  gi|330509040|ref|YP_004385468.1| 461 SNSTLIRANLSGAFMPLAALDGSDLSGADLRGATL 495
                                       78899999999999999999999999999999987 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 4.3e-08
                                       -TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide   3 LsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                       L g n +ga+Lsg+ + +A +++++l +A++ ga L+
  gi|330509040|ref|YP_004385468.1| 500 LMGSNMTGADLSGSLMDQAMMDNSTLVDAKMDGASLW 536
                                       7899******************************995 PP

  == domain 4  score: 28.6 bits;  conditional E-value: 2.2e-10
                                       TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   4 sgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       s+AnL ga+L +a+l+++++ ++ l gA+L+ga L
  gi|330509040|ref|YP_004385468.1| 541 SDANLFGASLINAFLERSTFVNSQLKGANLTGASL 575
                                       79******************************987 PP

  == domain 5  score: 36.4 bits;  conditional E-value: 7.9e-13
                                       -TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   3 LsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       + + +L ganL+ga+l gAnL++A++++AdLsga+ 
  gi|330509040|ref|YP_004385468.1| 560 FVNSQLKGANLTGASLVGANLINATITDADLSGADI 595
                                       567788888888888888888888888888888875 PP

  == domain 6  score: 29.8 bits;  conditional E-value: 9.3e-11
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                       A++ gAnLs + L g+ +  +nL+gA+ls A+Lsg+ Ls
  gi|330509040|ref|YP_004385468.1| 598 ARCMGANLSRSRLVGSTMGFSNLNGADLSMANLSGSYLS 636
                                       789*********************************996 PP

  == domain 7  score: 28.6 bits;  conditional E-value: 2.3e-10
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       AnLsg +Ls + + ++nl++A+L++Anl+ A L++a+L
  gi|330509040|ref|YP_004385468.1| 628 ANLSGSYLSASVFANSNLTRADLSDANLESAFLNRAKL 665
                                       899****************************9999987 PP

  == domain 8  score: 30.7 bits;  conditional E-value: 5e-11
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       +nL++A+Ls anL+ a+l++A+L +A l ++ L +a L++
  gi|330509040|ref|YP_004385468.1| 643 SNLTRADLSDANLESAFLNRAKLVEAKLVNTSLPRAHLED 682
                                       7***********************************9986 PP

  == domain 9  score: 30.9 bits;  conditional E-value: 4.1e-11
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       A L +A L +++L +a+l++++L+++nl++AdL++a L g
  gi|330509040|ref|YP_004385468.1| 663 AKLVEAKLVNTSLPRAHLEDSDLSNSNLERADLTNALLGG 702
                                       7899********************************9866 PP

  == domain 10  score: 36.3 bits;  conditional E-value: 8.4e-13
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       +nL++A+L++a L g+nl gAnL+gA l gAdLs a +++
  gi|330509040|ref|YP_004385468.1| 688 SNLERADLTNALLGGCNLIGANLNGARLLGADLSLATMKD 727
                                       79********************************999875 PP

  == domain 11  score: 34.0 bits;  conditional E-value: 4.6e-12
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                       +nL gAnL ga L ga+ls A++ +A lsgA++ ga+++
  gi|330509040|ref|YP_004385468.1| 703 CNLIGANLNGARLLGADLSLATMKDAYLSGANMVGARMN 741
                                       9***********************************985 PP

  == domain 12  score: 26.8 bits;  conditional E-value: 8.4e-10
                                       -TT-B-CCSCCEECCCESEEECT-B-TT-EECCEE CS
                      Pentapeptide   3 LsgAnLsganLsganlsgAnLtgAnlsgAdLsgan 37 
                                       +++A+Lsgan+ ga ++ A+L+g++l+ +++s+a 
  gi|330509040|ref|YP_004385468.1| 725 MKDAYLSGANMVGARMNWADLSGSSLTESQFSRAE 759
                                       679*****************************995 PP

  == domain 13  score: 38.3 bits;  conditional E-value: 2e-13
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       A++++A+Lsg++L+++ +s+A L gAnl+++dLs++++++
  gi|330509040|ref|YP_004385468.1| 738 ARMNWADLSGSSLTESQFSRAELFGANLTNCDLSNSDFTR 777
                                       7899**********************************95 PP

  == domain 14  score: 38.7 bits;  conditional E-value: 1.5e-13
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       A+L gAnL++++Ls++++++A L ++nlsg+ L+ga+L
  gi|330509040|ref|YP_004385468.1| 758 AELFGANLTNCDLSNSDFTRAYLVRSNLSGCTLRGAKL 795
                                       899*********************************98 PP

  == domain 15  score: 39.5 bits;  conditional E-value: 8.5e-14
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       ++Ls+ +++ a+L ++nlsg++L+gA l +AdLs ++L++
  gi|330509040|ref|YP_004385468.1| 768 CDLSNSDFTRAYLVRSNLSGCTLRGAKLDFADLSSVDLRN 807
                                       9*************************************97 PP

  == domain 16  score: 32.8 bits;  conditional E-value: 1e-11
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCE CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsga 36 
                                       A+Ls ++L++++L+g+ + +  L++A+lsgAdL g+
  gi|330509040|ref|YP_004385468.1| 798 ADLSSVDLRNSDLNGVIFANVHLINADLSGADLAGS 833
                                       89******************************9875 PP

  == domain 17  score: 7.0 bits;  conditional E-value: 0.0013
                                       CCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide  12 nLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       nL+g++   A+L ++++ +  +s++++sg
  gi|330509040|ref|YP_004385468.1| 839 NLKGTSWHKASLKSSEMVRMVFSDVDFSG 867
                                       999************************98 PP

  == domain 18  score: 32.9 bits;  conditional E-value: 1e-11
                                       -TT-B-CCSCCEECCCESEEECT-B-TT-EECCEE CS
                      Pentapeptide   3 LsgAnLsganLsganlsgAnLtgAnlsgAdLsgan 37 
                                       +s++++sga+L++a +s++ +++ n+sgAdL+ga+
  gi|330509040|ref|YP_004385468.1| 860 FSDVDFSGADLKNARFSESFMNNLNFSGADLRGAI 894
                                       899*****************************997 PP

  == domain 19  score: 35.4 bits;  conditional E-value: 1.7e-12
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       A+L++A++s++ +++ n+sgA+L+gA ++++ ++ +++sg
  gi|330509040|ref|YP_004385468.1| 868 ADLKNARFSESFMNNLNFSGADLRGAIIEKTAFEKCDFSG 907
                                       89*************************************8 PP

  == domain 20  score: -2.2 bits;  conditional E-value: 0.96
                                       B-TT-EE CS
                      Pentapeptide  27 nlsgAdL 33 
                                       nl+gA++
  gi|330509040|ref|YP_004385468.1| 927 NLQGAKM 933
                                       3333333 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00029       1.1      22      64 ..     419     461 ..     406     478 .. 0.46
   2 !   11.8   0.0   5.8e-05      0.21       7      64 ..     484     546 ..     477     553 .. 0.64
   3 !   22.7   0.0   2.3e-08   8.4e-05      10      70 ..     552     612 ..     543     616 .. 0.87
   4 !   28.6   0.1   3.3e-10   1.2e-06       7      76 ..     619     694 ..     613     719 .. 0.56
   5 !   30.6   0.1   7.7e-11   2.8e-07       5      70 ..     712     777 ..     679     783 .. 0.73
   6 !   36.3   0.1   1.3e-12   4.6e-09       2      71 ..     764     833 ..     763     858 .. 0.76
   7 !   35.4   0.1   2.4e-12   8.7e-09       2      70 ..     799     877 ..     798     879 .. 0.89
   8 !   37.1   0.3   7.1e-13   2.6e-09       3      70 ..     850     917 ..     848     926 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00029
                    Pentapeptide_4  22 rlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlk 64 
                                       +l++ n+++ +ls++ ++ ++l  +d+++++l r+ + +  ++
  gi|330509040|ref|YP_004385468.1| 419 DLNNRNLSGLDLSETDLSYSDLLGSDLSGTNLSRSFLIQAVIS 461
                                       3333333333333333333333333333333333333333333 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.8e-05
                    Pentapeptide_4   7 sfnncklsnvnFsearlrdcnFtecrl.....snvnFdecnlsdvdfaevdlkrasFsgcnlk 64 
                                        + +++l ++++  ++l ++n+t+++l     +++++d+++l d++  +++l  a  s  nl 
  gi|330509040|ref|YP_004385468.1| 484 DLSGADLRGATLLGNYLMGSNMTGADLsgslmDQAMMDNSTLVDAKMDGASLWAAKVSDANLF 546
                                       345555555666666777777777777777777777777777777777777766666666664 PP

  == domain 3  score: 22.7 bits;  conditional E-value: 2.3e-08
                    Pentapeptide_4  10 ncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd 70 
                                       n+ l++ +F +++l+++n+t++ l+ +n+ ++++ d+d++++d+  a+  g nl+ +++ +
  gi|330509040|ref|YP_004385468.1| 552 NAFLERSTFVNSQLKGANLTGASLVGANLINATITDADLSGADISAARCMGANLSRSRLVG 612
                                       67789999999*************9999999999999999999999999999999988754 PP

  == domain 4  score: 28.6 bits;  conditional E-value: 3.3e-10
                    Pentapeptide_4   7 sfnncklsnvnFsearlrdcnFtecrl.....snvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdid 76 
                                        +n+++ls +n+s ++l ++ F +++l     s++n++++ l+ +++ e++l ++s+ +  l+++ +s+  l+++d
  gi|330509040|ref|YP_004385468.1| 619 NLNGADLSMANLSGSYLSASVFANSNLtradlSDANLESAFLNRAKLVEAKLVNTSLPRAHLEDSDLSNsNLERAD 694
                                       5666666666666666666666666665555555555555555555555555555555555555555443454443 PP

  == domain 5  score: 30.6 bits;  conditional E-value: 7.7e-11
                    Pentapeptide_4   5 rcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd 70 
                                        + +++++ls ++++ a+l ++n++++r++ + ++ ++l +++f+ ++l+ a++++c+l+n+ f +
  gi|330509040|ref|YP_004385468.1| 712 GARLLGADLSLATMKDAYLSGANMVGARMNWADLSGSSLTESQFSRAELFGANLTNCDLSNSDFTR 777
                                       445566666666777777777777777777777888888888888888888888888888888843 PP

  == domain 6  score: 36.3 bits;  conditional E-value: 1.3e-12
                    Pentapeptide_4   2 eftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsdk 71 
                                        +t+c + n++++++ +  ++l +c++++++l+ + +++ +l+++d+++v ++++ + + +l+++ + ++
  gi|330509040|ref|YP_004385468.1| 764 NLTNCDLSNSDFTRAYLVRSNLSGCTLRGAKLDFADLSSVDLRNSDLNGVIFANVHLINADLSGADLAGS 833
                                       5677777777777777777788888888888877778888888888888888888888888877777654 PP

  == domain 7  score: 35.4 bits;  conditional E-value: 2.4e-12
                    Pentapeptide_4   2 eftrcsfnncklsnvnFsearlrdcnFtecrl..........snvnFdecnlsdvdfaevdlkrasFsgcnlknvnf 68 
                                       +++++ ++n++l++v F++++l+++++++++l          + +++++++l++++   + + ++ Fsg +lkn++f
  gi|330509040|ref|YP_004385468.1| 799 DLSSVDLRNSDLNGVIFANVHLINADLSGADLagsyynsmnlKGTSWHKASLKSSEMVRMVFSDVDFSGADLKNARF 875
                                       6788888999999999999999999999999999888888889999******************************* PP

                    Pentapeptide_4  69 sd 70 
                                       s+
  gi|330509040|ref|YP_004385468.1| 876 SE 877
                                       86 PP

  == domain 8  score: 37.1 bits;  conditional E-value: 7.1e-13
                    Pentapeptide_4   3 ftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd 70 
                                       ++++ + +  +s+v+Fs a+l++++F+e++++n nF+ ++l+ + ++++ + +  Fsg nl++++ +d
  gi|330509040|ref|YP_004385468.1| 850 LKSSEMVRMVFSDVDFSGADLKNARFSESFMNNLNFSGADLRGAIIEKTAFEKCDFSGANLEGIKYDD 917
                                       6667777778****************************************************999877 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00051       1.8       2      48 .]     446     494 ..     435     494 .. 0.88
   2 !   13.9   0.0   1.2e-05     0.044       2      47 ..     481     523 ..     480     524 .. 0.91
   3 !    9.0   0.0   0.00042       1.5       3      37 ..     547     579 ..     541     580 .. 0.63
   4 !   18.9   0.0   3.4e-07    0.0012       1      42 [.     560     598 ..     560     614 .. 0.85
   5 !   14.2   0.2   1.1e-05     0.038       5      42 ..     619     658 ..     617     664 .. 0.64
   6 !   13.4   0.0   1.8e-05     0.064       2      44 ..     686     715 ..     657     734 .. 0.56
   7 !   13.9   0.0   1.3e-05     0.046       2      46 ..     711     757 ..     700     761 .. 0.55
   8 !   15.0   1.2   5.7e-06      0.02       6      46 ..     745     782 ..     743     784 .. 0.74
   9 !   20.0   0.0   1.5e-07   0.00055       1      47 [.     785     828 ..     780     829 .. 0.84
  10 !   15.3   0.1   4.7e-06     0.017       2      41 ..     841     877 ..     840     883 .. 0.86
  11 !   17.9   0.1   7.1e-07    0.0025       5      35 ..     884     912 ..     878     917 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00051
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaa....sFsnadFgsadFsgarFtgdvdFsgat 48 
                                       sg+n+s++ ++  a+ s+++    + s+a +  a ++g+  + ++d++gat
  gi|330509040|ref|YP_004385468.1| 446 SGTNLSRS-FLIQAVISNSTliraNLSGAFMPLAALDGSDLS-GADLRGAT 494
                                       78999999.999888888888877899999999999999999.99999986 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.2e-05
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                       +g+ +sga d+rgat  g  +  ++++++ad+sg+ ++  + ++++
  gi|330509040|ref|YP_004385468.1| 481 DGSDLSGA-DLRGATLLGN-YLMGSNMTGADLSGSLMD-QAMMDNS 523
                                       7999****.**********.9****************9.7777776 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00042
                    Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgar 37 
                                       ga++ +a +++++tF ++   ++a++++a++ ga+
  gi|330509040|ref|YP_004385468.1| 547 GASLINA-FLERSTFVNS-QLKGANLTGASLVGAN 579
                                       5555566.6677777777.3777777777776665 PP

  == domain 4  score: 18.9 bits;  conditional E-value: 3.4e-07
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdv 42 
                                       F++++++ga +++ga   ga +  na++++ad+sga ++ ++
  gi|330509040|ref|YP_004385468.1| 560 FVNSQLKGA-NLTGASLVGA-NLINATITDADLSGADIS-AA 598
                                       889999999.9999999999.899999999999999887.54 PP

  == domain 5  score: 14.2 bits;  conditional E-value: 1.1e-05
                    Pentapeptide_3   5 nFsgaadFrgatFsgaa.s...FsnadFgsadFsgarFtgdv 42 
                                       n+ ga d+++a+ sg+  s   F n+++++ad+s+a+ +  +
  gi|330509040|ref|YP_004385468.1| 619 NLNGA-DLSMANLSGSYlSasvFANSNLTRADLSDANLE-SA 658
                                       67777.**********44133466666666666666555.44 PP

  == domain 6  score: 13.4 bits;  conditional E-value: 1.8e-05
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdF 44 
                                       s++n+++a d++           na +g++++ ga+ + ++++
  gi|330509040|ref|YP_004385468.1| 686 SNSNLERA-DLT-----------NALLGGCNLIGANLN-GARL 715
                                       33444444.444...........333333333333333.2222 PP

  == domain 7  score: 13.9 bits;  conditional E-value: 1.3e-05
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaa....sFsnadFgsadFsgarFtgdvdFsg 46 
                                       +ga++ ga d++ at ++a     ++ +a+++ ad+sg+  t +++Fs+
  gi|330509040|ref|YP_004385468.1| 711 NGARLLGA-DLSLATMKDAYlsgaNMVGARMNWADLSGSSLT-ESQFSR 757
                                       44555555.555444444433333466666666666666666.666665 PP

  == domain 8  score: 15.0 bits;  conditional E-value: 5.7e-06
                    Pentapeptide_3   6 FsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsg 46 
                                       +sg+ +++++ Fs+a    +a+++++d+s++ Ft ++ + +
  gi|330509040|ref|YP_004385468.1| 745 LSGS-SLTESQFSRA-ELFGANLTNCDLSNSDFT-RAYLVR 782
                                       6788.8888888888.588888888888888888.777666 PP

  == domain 9  score: 20.0 bits;  conditional E-value: 1.5e-07
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                       +sg++++ga  +++a  s+  + +n+d++++ F++++   ++d+sga
  gi|330509040|ref|YP_004385468.1| 785 LSGCTLRGA-KLDFADLSSV-DLRNSDLNGVIFANVHLI-NADLSGA 828
                                       478888888.8888888888.899999999999999999.9999987 PP

  == domain 10  score: 15.3 bits;  conditional E-value: 4.7e-06
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgd 41 
                                       +g+++++a ++  +   +++ Fs+ dF++ad+ +arF+ +
  gi|330509040|ref|YP_004385468.1| 841 KGTSWHKA-SLKSSEMVRMV-FSDVDFSGADLKNARFS-E 877
                                       68999999.99999999996.9**************98.5 PP

  == domain 11  score: 17.9 bits;  conditional E-value: 7.1e-07
                    Pentapeptide_3   5 nFsgaadFrgatFsgaasFsnadFgsadFsg 35 
                                       nFsga d+rga  +++a F+ +dF++a+++g
  gi|330509040|ref|YP_004385468.1| 884 NFSGA-DLRGAIIEKTA-FEKCDFSGANLEG 912
                                       89999.99999999997.9999999999987 PP

>> ABC_sub_bind  ABC transporter substrate binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0     1e-12   3.6e-09      54     284 ..      93     327 ..      75     337 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1e-12
                                       HHHHTT--SEEEEESHHHHHHHHHH-SS....S-EEEEEES-TTTTTS-S-SSS--SSEEEEE----HHHHHHHHHH CS
                      ABC_sub_bind  54 rqlkaekpdlivgiatpaaqilksatkn....iPiVfaavtdpvgakLvksleapgenvTGvsdaekvektieLikk 126
                                       ++ k+ ++d+i      a q l +   +     P+Vf +v d       +++   g+n TGv +a ++  ti+L+ k
  gi|330509040|ref|YP_004385468.1|  93 NKYKDRHYDVITCLDDDAFQFLLNNRDElfssTPVVFCGV-DF----FEDQMLTAGKNFTGVVEAFDIPGTISLMLK 164
                                       5677777777777777777777776665555689999999.54....556777889********************* PP

                                       HSTT--EEEEEE-TT-HHHHHHHHHHHHHHHHTT-EEEEEE-SS...GGGHHHHHHHHHTT-SEEEE-S-HHHHHTH CS
                      ABC_sub_bind 127 llPnvkkigilyspgeansvslveelkklakkaglkvveaavkn...vndvesavsslaekvdaiyiltdnliasaf 200
                                       l P++k+i i+   + a s++  e + +++ +++  v ++ + n   v++++  +s+l e +  i  l+ n+  ++ 
  gi|330509040|ref|YP_004385468.1| 165 LHPDAKQIVIID-DQTATSKASQEAMNQTLSRFNTIV-SFVIWNdmtVEELQRNASALHEGSL-ILLLNYNNDREGR 238
                                       *******98875.5666799999***********655.4555331326788887777776555.5555555555554 PP

                                       HH.....HHHHHHHTT--EEESSHHHHHTT-SEEEE--HHHHHHHHHHHHHHHHTT--GGGS--EE----EEEE-HH CS
                      ABC_sub_bind 201 ea.....vvkaanqakiPviasddesvkegalaalgvnekelGvqagkvvvkiLkGkkpkdipvsrakslklvinkk 272
                                       +            ++ +P++   d +   g l    +  + +G  a++++ +iL+G +  dipv +   +  +    
  gi|330509040|ref|YP_004385468.1| 239 AVtheesAWILRSASSVPIYGTRDVYMGFGVLGGAIITGQVQGRLAADMAHRILQGVPADDIPVIKELPSSYIFDML 315
                                       4311222222235678****************7777777788*********************98877777777777 PP

                                       HHHHTT----HH CS
                      ABC_sub_bind 273 aakelgitikee 284
                                        +++++i ++ +
  gi|330509040|ref|YP_004385468.1| 316 ELRRFNISVQRS 327
                                       777777777665 PP

>> CfAFP  Choristoneura fumiferana antifreeze protein (CfAFP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.42   1.5e+03      47     106 ..     443     502 ..     433     513 .. 0.70
   2 !   11.2   0.0   7.9e-05      0.28      28     115 ..     514     601 ..     494     615 .. 0.89
   3 ?    4.3   0.0      0.01        37      29     109 ..     636     720 ..     618     727 .. 0.68
   4 !    6.4   0.0    0.0023       8.3      47      95 ..     743     791 ..     730     802 .. 0.79
   5 !    6.2   0.1    0.0026       9.3      24      68 ..     751     794 ..     745     849 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.42
                             CfAFP  47 selessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitsstttgtrisG 106
                                       s+l  +  +rs   +a + +s+   +n++ + + +++  gs   G  ++ +t  g  + G
  gi|330509040|ref|YP_004385468.1| 443 SDLSGTNLSRSFLIQAVISNSTLIRANLSGAFMPLAALDGSDLSGADLRGATLLGNYLMG 502
                                       666666777777777777777777777777777777777777777777777766665555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 7.9e-05
                             CfAFP  28 isanskcvkstltncyidnselessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitsstttgtri 104
                                       + + +   +stl    +d + l ++ ++ ++  +a ++++        +sql g+  tg+   G  +  +t t++ +
  gi|330509040|ref|YP_004385468.1| 514 LMDQAMMDNSTLVDAKMDGASLWAAKVSDANLFGASLINAFLERSTFVNSQLKGANLTGASLVGANLINATITDADL 590
                                       55566778999999999999999999999999999999999999999****************************** PP

                             CfAFP 105 sGpgcsissct 115
                                       sG   s ++c+
  gi|330509040|ref|YP_004385468.1| 591 SGADISAARCM 601
                                       *****999996 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.01
                             CfAFP  29 sanskcvkstltncyidnselessictrsqysdayvkks.....vttdcnidksqlygttctgsrydGvyitssttt 100
                                       s  s   +s lt   + +++les+   r++  +a+++++        d ++++s+l  +  t++   G  +  +   
  gi|330509040|ref|YP_004385468.1| 636 S-ASVFANSNLTRADLSDANLESAFLNRAKLVEAKLVNTslpraHLEDSDLSNSNLERADLTNALLGGCNLIGANLN 711
                                       3.567778888888888888888888888888887765411111445677777777777788888888777777777 PP

                             CfAFP 101 gtrisGpgc 109
                                       g+r++G   
  gi|330509040|ref|YP_004385468.1| 712 GARLLGADL 720
                                       777777655 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0023
                             CfAFP  47 selessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyit 95 
                                       ++l  s  t sq+s a++  +  t+c++++s++  +    s+  G +++
  gi|330509040|ref|YP_004385468.1| 743 ADLSGSSLTESQFSRAELFGANLTNCDLSNSDFTRAYLVRSNLSGCTLR 791
                                       5666777888999999999999999999998888777777777777665 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.0026
                             CfAFP  24 tnsqisanskcvkstltncyidnselessictrsqysdayvkksv 68 
                                       t+sq s  ++   + ltnc + ns+   +  +rs+ s++ ++ ++
  gi|330509040|ref|YP_004385468.1| 751 TESQFS-RAELFGANLTNCDLSNSDFTRAYLVRSNLSGCTLRGAK 794
                                       444444.34444455666666666665555555555555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (953 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.79u 0.35s 00:00:01.14 Elapsed: 00:00:00.53
# Mc/sec: 5369.13
//
Query:       gi|330509041|ref|YP_004385469.1|  [L=115]
Description: hypothetical protein MCON_3414 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 803.05
//
Query:       gi|330509042|ref|YP_004385470.1|  [L=1270]
Description: hypothetical protein MCON_3415 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.4e-36  122.2   0.0    3.5e-06   27.2   0.0    5.9  6  DUF11       Domain of unknown function DUF11
    0.00092   19.5   0.0        4.6    7.6   0.0    4.1  4  Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   6.6e-10   5.9e-06       8      51 ..     106     185 ..      98     227 .. 0.78
   2 !   21.2   0.0   2.9e-08   0.00026       5      78 ..     396     470 ..     392     483 .. 0.84
   3 !   19.4   0.0   1.1e-07   0.00095       3      78 ..     511     592 ..     509     609 .. 0.73
   4 !   19.5   0.1   9.7e-08   0.00087       1      71 [.     633     706 ..     633     755 .. 0.72
   5 ?   -3.2   0.0       1.3   1.1e+04      29      62 ..     766     799 ..     763     810 .. 0.73
   6 !   27.2   0.0   3.9e-10   3.5e-06      17      81 ..    1100    1166 ..    1094    1174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.6e-10
                             DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtl....................................Paglayvsv 48 
                                       ++vr Gdtv+yt  vtNtg+++++++ +tDt                                     Pa+ ++ + 
  gi|330509042|ref|YP_004385470.1| 106 PPVRVGDTVVYTYNVTNTGGVTLYEINLTDTHdwgpnchptrvgggggdealepgqswqyeclyeihdPANYTILRI 182
                                       489****************************9888777777777777777777777777777777777777777776 PP

                             DUF11  49 sas 51 
                                        as
  gi|330509042|ref|YP_004385470.1| 183 MAS 185
                                       666 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2.9e-08
                             DUF11   5 vdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas..qgtasaltsvgsLeagesatlsftvrv 78 
                                        ++ +v++ +t++yt+  +N+g+++a +v ++ t  ++l+++ +s +   gt+  ++++g+L   es ++++++r 
  gi|330509042|ref|YP_004385470.1| 396 DEPDPVQFNGTINYTIAYKNNGGQDAHEVMLKETYNESLEFIWASPApdPGTI-DAWTIGDLDKEESGKIAIQARL 470
                                       556699************************************99999754444.6677799999999888888875 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 1.1e-07
                             DUF11   3 KtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas.....qgtasaltsv.gsLeagesatls 73 
                                       K  +++ + pG+ ++yt+  +N+g ++ ++vv+ D l + + +  + +      +++++  +   g+L +g+  t++
  gi|330509042|ref|YP_004385470.1| 511 KRASSRIIFPGEHLNYTIDYRNNGSVKQTDVVIHDYLDEKVDFKYSLSDpllinESSGRHHWWYvGDLLPGSGGTIE 587
                                       666777788****************************7777754333335666644444444444777777776666 PP

                             DUF11  74 ftvrv 78 
                                       + v++
  gi|330509042|ref|YP_004385470.1| 588 IFVKA 592
                                       66655 PP

  == domain 4  score: 19.5 bits;  conditional E-value: 9.7e-08
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpa.sangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesat 71 
                                       ++K  ++++++ G+++tyt+   N+ ++ +a++v +tD+lP+ + +  ++      +  + ++ +g+L + +  t
  gi|330509042|ref|YP_004385470.1| 633 IKKEANATAAARGENITYTIKYGNSDTDfTAENVSITDMLPE-VDFLGATPHpniINGKNLTWMIGNLTPRANGT 706
                                       68999*********************99567*********84.23333332222222334444445555554444 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 1.3
                             DUF11  29 sangvvvtDtlPaglayvsvsasqgtasaltsvg 62 
                                       s++ vvvt +  ag+++ ++ +++g ++ + s++
  gi|330509042|ref|YP_004385470.1| 766 SSSSVVVTILGAAGTRITTSEHGSGHYEEDESSR 799
                                       5667888888889999999999988888777764 PP

  == domain 6  score: 27.2 bits;  conditional E-value: 3.9e-10
                             DUF11   17 tytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatlsftvrvtrt 81  
                                         + + vtN g ++++++ v+D lP+gl+++ +s +         ++++ sL  g + t+++++rv + 
  gi|330509042|ref|YP_004385470.1| 1100 LFLINVTNDGSRPLKKLDVSDRLPPGLSFIDSSQRpevD-GQFINWTISSLDIGRTMTIKLRARVENG 1166
                                        58899******************************7743.334667779*****99999888888764 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 !    7.6   0.0   0.00051       4.6      27      87 ..     408     466 ..     401     469 .. 0.87
   2 ?    0.8   0.0     0.067     6e+02      28      90 ..     526     591 ..     522     592 .. 0.77
   3 ?    0.9   0.0     0.062   5.6e+02      42      78 ..     665     700 ..     649     712 .. 0.79
   4 ?    3.4   0.0     0.011        95      30      85 ..    1103    1157 ..    1090    1162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00051
                        Chlam_OMP6  27 pypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqgekskitv 87 
                                        y i     g +d+ +v++ +      ef+ + pa  p +     w+i  l + e  ki++
  gi|330509042|ref|YP_004385470.1| 408 NYTIAYKNNGGQDAHEVMLKETYNESLEFIWASPAPDPGT--IDAWTIGDLDKEESGKIAI 466
                                       588888999*************************977744..4479**9999999999987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.067
                        Chlam_OMP6  28 ypieitavgkkdcvdvvitqqlpcevefv..rsdpastptadgklv.wkidrlgqgekskitvwvk 90 
                                       y i+    g     dvvi + l  +v+f    sdp     + g+   w +  l  g    i ++vk
  gi|330509042|ref|YP_004385470.1| 526 YTIDYRNNGSVKQTDVVIHDYLDEKVDFKysLSDPLLINESSGRHHwWYVGDLLPGSGGTIEIFVK 591
                                       77888888999999********99998862157999999999986515677777777777777776 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.062
                        Chlam_OMP6  42 dvvitqqlpcevefvrsdpastptadgklvwkidrlg 78 
                                       +v it+ lp ev+f+ + p     +  +l w i  l 
  gi|330509042|ref|YP_004385470.1| 665 NVSITDMLP-EVDFLGATPHPNIINGKNLTWMIGNLT 700
                                       788898888.899999999888888888999988775 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.011
                        Chlam_OMP6   30 ieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklv.wkidrlgqgekski 85  
                                        i++t  g +   ++ ++++lp    f+ s  +  p  dg+++ w+i  l  g    i
  gi|330509042|ref|YP_004385470.1| 1103 INVTNDGSRPLKKLDVSDRLPPGLSFIDS--SQRPEVDGQFInWTISSLDIGRTMTI 1157
                                        7778888888888889999*******966..679******988****9998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.84u 0.29s 00:00:01.12 Elapsed: 00:00:00.48
# Mc/sec: 7951.59
//
Query:       gi|330509043|ref|YP_004385471.1|  [L=289]
Description: hypothetical protein MCON_3416 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 2058.51
//
Query:       gi|330509044|ref|YP_004385472.1|  [L=122]
Description: hypothetical protein MCON_3417 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 797.44
//
Query:       gi|330509045|ref|YP_004385473.1|  [L=411]
Description: transposase, IS4 [Methanosaeta concilii GP6]
Scores for complete 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-14   51.9   0.0    1.1e-13   51.2   0.0    1.3  1  DDE_5      DDE superfamily endonuclease
    1.2e-12   47.7   6.1    3.8e-11   42.8   6.1    2.2  1  DDE_Tnp_2  Archaeal putative transposase ISC1217
      1e-07   31.8   1.0    1.5e-07   31.3   1.0    1.2  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.026   14.5   0.1      0.063   13.2   0.1    1.6  1  SeqA       SeqA protein C-terminal domain
       0.13   11.3   0.2       0.22   10.6   0.2    1.3  1  Colicin_M  Colicin M


Domain annotation for each model (and alignments):
>> DDE_5  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0     3e-17   1.1e-13       5     214 ..      21     222 ..      17     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 3e-17
                             DDE_5   5 altradrrrglllylrgllldggrksvepmaarl...ehdg.shqalqrflsrspwddaklrrrlarlvl.pllape 76 
                                        +t+ +  + ++ ++ +l  + + k+v ++  ++   + +  s+ ++  f+s+++wd+ ++ +r  +l +  l+ +e
  gi|330509045|ref|YP_004385473.1|  21 LFTKPSYGS-FRDLCGALSVCDKSKTVSNLCDTMadcSKGKkSRSSYNWFFSDANWDENEVAQRKVDLFIdSLCLKE 96 
                                       555444444.66777777777777***********9955555999*****************999999997777776 PP

                             DDE_5  77 aav..laiDdTgfpkdGkasvgvarqycgalgkadncqvavslglatervsapldwrlylpeswaqdlsarrrragv 151
                                       +    l+iDdT   k G ++ gv+++y++++   + ++ +v+  + ++  ++p +   y++              ++
  gi|330509045|ref|YP_004385473.1|  97 NDKllLIIDDTYNEKEGNQTDGVGKFYDHSKEAYIWGNNFVTSVVQSKGLFIPHKAKMYIK--------------ND 159
                                       66679************************************99999999999999999999..............34 PP

                             DDE_5 152 pddvtaktkpeial.elldraraagvplqvvvaDagYgdaaalrqglrelglhyvvrvrsdral 214
                                       ++   +ktk eia  e+++ ++  +  + ++v+D++  +++ +      lg ++v +++sd+++
  gi|330509045|ref|YP_004385473.1| 160 DENENFKTKMEIAFeEIIKPLVVPKSIDLYIVFDSWWFSSDLF-SKCLKLGHNIVCQIKSDKKV 222
                                       56669********96677888888888889*******9*****.888889***********987 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   6.1   1.1e-14   3.8e-11     147     306 ..     147     340 ..      87     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.1e-14
                         DDE_Tnp_2 147 yiprkvaeilkerGeksefktkiellle.ileilkeefnva.avvfdsWyvnskl....lk..gnvvgelksnarv. 214
                                       +ip+k +  +k+  e+ +fktk+e++ e i++ l     +   +vfdsW+++s l    lk   n+v ++ks+++v 
  gi|330509045|ref|YP_004385473.1| 147 FIPHKAKMYIKNDDENENFKTKMEIAFEeIIKPLVVPKSIDlYIVFDSWWFSSDLfskcLKlgHNIVCQIKSDKKVg 223
                                       799999999***************98752777776655554279******997552222433369**********95 PP

                         DDE_Tnp_2 215 ve...................gerhvpvaelPeGeylveyl...dtvikllvldd..ykkdgrrylfstdlndtded 267
                                       ++                    +  v v    +  y  e     d+v ++++++    k+   +y+ st+  ++  +
  gi|330509045|ref|YP_004385473.1| 224 INrdmyfqvrdlanqiedkffIKTTVSVRGKKKTYYAFEKKviiDKVGEVKLVISkrKKDSTTKYIISTNGSLSLKE 300
                                       449****************999999999999999999886555688877776665115667789************* PP

                         DDE_Tnp_2 268 iittWenrWdievlirel.kalGledssflkrvrnkGfll 306
                                       i + +e rWdie  +re  + lG++d  +  +   + f+ 
  gi|330509045|ref|YP_004385473.1| 301 ILSIYEDRWDIETAHREAnQKLGFKDYQLRDKHSIERFIQ 340
                                       ****************983469998877766666666665 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   1.0     4e-11   1.5e-07      78     212 ..     188     346 ..     154     348 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 4e-11
                         DDE_Tnp_1  78 klvlaDaGYasaelldtleekgvdyiirlkkntklyrk.....gaeskrrgrlrkhdrnkiltksqkrrnk...... 143
                                        +++ D++ +s +l+ ++ + g + + ++k+++k+ +         ++ ++++ k + + +++ + k++++      
  gi|330509045|ref|YP_004385473.1| 188 LYIVFDSWWFSSDLFSKCLKLGHNIVCQIKSDKKVGINrdmyfQVRDLANQIEDKFFIKTTVSVRGKKKTYyafekk 264
                                       5899******************************999999999888899**************************** PP

                         DDE_Tnp_1 144 ..............skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqll 206
                                                     + k + ++ y+ +tn  +ls +e+  +y  Rw iE+ +++  +k+g+   ++r++  +e+++ 
  gi|330509045|ref|YP_004385473.1| 265 viidkvgevklvisKRKKDSTTKYIISTNG-SLSLKEILSIYEDRWDIETAHREANQKLGFKDYQLRDKHSIERFIQ 340
                                       ************754555555555555555.899******************************************* PP

                         DDE_Tnp_1 207 llllal 212
                                       +++ ++
  gi|330509045|ref|YP_004385473.1| 341 MVFSVW 346
                                       998765 PP

>> SeqA  SeqA protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.8e-05     0.063      29      88 ..     236     300 ..     215     306 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                              SeqA  29 lyradpeaFakatekvkGrtRvYfakdeetllasgks.....tkpkqipetpfWVitNnntarKr 88 
                                         +++++ F k+t +v+G++++Y+a +++ ++++  +     +k k+ ++t + + tN + + K+
  gi|330509045|ref|YP_004385473.1| 236 ANQIEDKFFIKTTVSVRGKKKTYYAFEKKVIIDKVGEvklviSKRKKDSTTKYIISTNGSLSLKE 300
                                       4566778899999*****************99887776888889999999999999998766665 PP

>> Colicin_M  Colicin M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   6.2e-05      0.22     156     233 ..     231     316 ..     209     322 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.2e-05
                         Colicin_M 156 kindlkdiiksavvGettvst...ktsyatGddsvitriylGtitlki.......eGkltisasGsvsysGvvkayd 222
                                       ++ dl + i+     +ttvs+   k +y++ +++vi    +G++ l i       + k  is++Gs+s + ++  y+
  gi|330509045|ref|YP_004385473.1| 231 QVRDLANQIEDKFFIKTTVSVrgkKKTYYAFEKKVIIDK-VGEVKLVIskrkkdsTTKYIISTNGSLSLKEILSIYE 306
                                       667777777777777778876333678888888888653.566666442222222678899**************** PP

                         Colicin_M 223 dkydanasshr 233
                                       d++d+++ +hr
  gi|330509045|ref|YP_004385473.1| 307 DRWDIET-AHR 316
                                       ****986.466 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); 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:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2630.43
//
Query:       gi|330509046|ref|YP_004385474.1|  [L=436]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete 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   27.8   0.6    2.7e-05   23.8   0.6    2.1  1  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
       0.14   12.7   4.6       0.18   12.3   2.2    2.4  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.15   12.2   0.7        7.5    6.8   0.1    2.4  2  Zn-ribbon_8      Zinc ribbon domain
       0.21   11.2   0.6         12    5.6   0.1    2.4  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.27   11.3   2.8        1.3    9.1   3.1    1.9  2  DZR              Double zinc ribbon
       0.66   10.0   2.5        7.3    6.7   0.3    2.6  2  YhfH             YhfH-like protein
        6.2    6.4   5.5         77    2.9   5.5    2.4  1  TF_Zn_Ribbon     TFIIB zinc-binding


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 !   23.8   0.6     1e-08   2.7e-05     111     259 ..     188     381 ..     146     393 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1e-08
                      DDE_Tnp_IS66 111 sRggevaealLag.....fkGvlvsDgyagYnklae....eqvthalCwaHlrRkfvdaeeakkksqaaaealar.. 176
                                       s  ++++e +L        + ++v+D y gY+++ +    ++v h++C+ Hl   +v+   +k   ++ +e l++  
  gi|330509046|ref|YP_004385474.1| 188 SKDADTIEGFLRRnldtqKQIFIVTDLYRGYSNVFKrvfgNKVIHQFCLLHLNKLIVNDFPRKT--SIEQELLKYkm 262
                                       55566666666655554445699**********9999***************999887776643..44444444442 PP

                      DDE_Tnp_IS66 177 igklya.............ierearea...........eae.........erlalrqeesrpllaelea.wleeql. 218
                                       ++ +++              e+ +r +           e           + + +r++es+ l+++ ++  l++ + 
  gi|330509046|ref|YP_004385474.1| 263 LNIFFNreleieflstlieEEKMMR-QrsnkeykswiaE-AkhlfydfvrRLELRRRRESKNLEQRTYHeALNNFKf 337
                                       4444445555555555543233332.1233344334331.0333333442555666777788877655504444448 PP

                      DDE_Tnp_IS66 219 ...kkvlpksklgkairyllkrweallrfledgrvpidNNaaER 259
                                          ++ +    ++k ++++ + w++l+ f    + p +NN +E+
  gi|330509046|ref|YP_004385474.1| 338 lkmQSDSFMISVRKRLDKIEELWPNLTAFYFTDNAPATNNPIEN 381
                                       777666677789*******************************9 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2     7e-05      0.18       8      51 ..      44     118 ..      43     123 .. 0.62
   2 ?   -1.0   0.0      0.99   2.5e+03      14      29 ..     284     299 ..     282     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7e-05
                   Zn_ribbon_recom   8 CgeCGspmtr......rkrkgkr.......hyYrCstyrrkgk..................k.Csnh...sireekl 49 
                                       C eCG+pm++      +    kr         Y C+++ ++ +                  + C+     ++++e++
  gi|330509046|ref|YP_004385474.1|  44 CPECGHPMSHngfntcQ----KRhlgganvGKYLCGACGKSTEedrdfwiklktdffgivtEiCTRLrlnHVSYEVI 116
                                       **********5543322....22355558889999988766655556666666666665531466544556666666 PP

                   Zn_ribbon_recom  50 ee 51 
                                       e+
  gi|330509046|ref|YP_004385474.1| 117 ES 118
                                       65 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.99
                   Zn_ribbon_recom  14 pmtrrkrkgkrhyYrC 29 
                                       +m r+++++++  ++ 
  gi|330509046|ref|YP_004385474.1| 284 KMMRQRSNKEYKSWIA 299
                                       7999999999988875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0029       7.5      26      35 ..      40      50 ..      25      53 .. 0.60
   2 ?    3.3   0.1     0.035        90       6      17 ..      72      83 ..      71      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                       Zn-ribbon_8 26 lta.CPeCgse 35
                                       ++ CPeCg++
  gi|330509046|ref|YP_004385474.1| 40 VPPlCPECGHP 50
                                      3444****986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.035
                       Zn-ribbon_8  6 YrCeeCghefev 17
                                      Y C +Cg+  e+
  gi|330509046|ref|YP_004385474.1| 72 YLCGACGKSTEE 83
                                      89*****99885 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0046        12       4      14 ..      43      53 ..      43      57 .. 0.86
   2 ?    3.5   0.1     0.021        54       2      15 ..      71      84 ..      70      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0046
                            zf_UBZ  4 lCerCgkeipe 14
                                      lC++Cg+++++
  gi|330509046|ref|YP_004385474.1| 43 LCPECGHPMSH 53
                                      6*******987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.021
                            zf_UBZ  2 tylCerCgkeipes 15
                                       ylC  Cgk+ +e+
  gi|330509046|ref|YP_004385474.1| 71 KYLCGACGKSTEED 84
                                      69*******97765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.9     0.002         5      30      46 ..      43      60 ..      26      63 .. 0.76
   2 ?    9.1   3.1   0.00049       1.3      15      43 ..      44      86 ..      41     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.002
                               DZR 30 rCpsCgek.vdpearfCp 46
                                       Cp+Cg++  ++++++C+
  gi|330509046|ref|YP_004385474.1| 43 LCPECGHPmSHNGFNTCQ 60
                                      688888886666777775 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00049
                               DZR 15 CseCgtklkavaa................edrCpsCgekvdpear 43
                                      C+eCg++++   +                ++ C +Cg++++++  
  gi|330509046|ref|YP_004385474.1| 44 CPECGHPMSH--NgfntcqkrhlgganvgKYLCGACGKSTEEDRD 86
                                      5556655552..123555555555556669999999998877665 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0028       7.3       7      24 ..      35      52 ..      31      61 .. 0.85
   2 ?    2.6   0.1     0.055   1.4e+02      15      26 ..      73      84 ..      67      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0028
                              YhfH  7 FfrnLPkKkCteCGkeie 24
                                      +fr++ +  C+eCG  + 
  gi|330509046|ref|YP_004385474.1| 35 IFRKIVPPLCPECGHPMS 52
                                      799999999*****9986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.055
                              YhfH 15 kCteCGkeieEq 26
                                       C  CGk  eE 
  gi|330509046|ref|YP_004385474.1| 73 LCGACGKSTEED 84
                                      6******99995 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   5.5      0.03        77       3      32 ..      44      84 ..      43      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.03
                                      ETTTTCEEC...........HEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon  3 CPnCgstnl...........veDpergelvCtdCGlVledn 32
                                      CP+Cg+++            +  ++ g ++C++CG   e++
  gi|330509046|ref|YP_004385474.1| 44 CPECGHPMShngfntcqkrhLGGANVGKYLCGACGKSTEED 84
                                      99999987458888888777777999999999999877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2859.71
//
Query:       gi|330509047|ref|YP_004385475.1|  [L=71]
Description: hypothetical protein MCON_3420 [Methanosaeta concilii GP6]
Scores for complete 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-20   71.3   0.0    9.5e-20   71.0   0.0    1.0  1  DUF4277   Domain of unknown function (DUF4277)


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.0   5.3e-24   9.5e-20       3      62 ..       7      66 ..       5      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 5.3e-24
                           DUF4277  3 vksldhlglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfp 62
                                      +  ++hlg+vag++d+l++a++id+++pk+ ++++ ++ ++ka+ilngLg++ ++Lylfp
  gi|330509047|ref|YP_004385475.1|  7 SYLIGHLGIVAGTFDALNIADVIDQVLPKRGSRNLPHSVIIKAMILNGLGYTGQRLYLFP 66
                                      5679*******************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); 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 0.28s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 434.49
//
Query:       gi|330509048|ref|YP_004385476.1|  [L=129]
Description: HesB/YadR/YfhF family protein [Methanosaeta concilii GP6]
Scores for complete 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-08   33.1   0.0    7.7e-08   32.5   0.0    1.3  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 !   32.5   0.0   4.3e-12   7.7e-08       3      97 ..       2      84 ..       1      98 [. 0.90

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 4.3e-12
                                      EEE-HHHHHHHHHHHHCTTECEEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEEETTEEEEEEGGGHHHS.T CS
                       Fe-S_biosyn  3 itlteaAaeklkkllaedkkelrLdvddgggpyskggCsiggkyslvlvdeedeeydevlesnggkvyvksyslvflde 81
                                      i++t++Aa+ lk+++ edk  +r+++            s g++y + l d+e  ++d+ +es g+k++++++++++l  
  gi|330509048|ref|YP_004385476.1|  2 IEITKEAADMLKSKVVEDKV-IRMFLAAVD-------PS-GANYGMTLGDAE--KDDVIFESRGIKIHMEPKDAELL-A 68
                                      99*****************9.887777776.......55.********9976..***********************.9 PP

                                      TEEEEEEEETTEEEEE CS
                       Fe-S_biosyn 82 glvldfvedlgtlgLk 97
                                      ++ +d+v+d+ + g+ 
  gi|330509048|ref|YP_004385476.1| 69 ETIIDYVDDDRGTGFI 84
                                      9********9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 845.72
//
Query:       gi|330509049|ref|YP_004385477.1|  [L=339]
Description: FLAP endonuclease [Methanosaeta concilii GP6]
Scores for complete sequence (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   0.0    1.7e-25   89.2   0.0    1.3  1  XPG_I       XPG I-region
    1.6e-17   63.8   0.0    2.4e-17   63.2   0.0    1.3  1  XPG_N       XPG N-terminal domain
    9.4e-05   22.9   0.0    0.00018   22.0   0.0    1.5  1  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
      0.067   13.8   0.0       0.18   12.4   0.0    1.7  1  HHH_5       Helix-hairpin-helix domain


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 !   89.2   0.0   3.7e-29   1.7e-25       2      94 .]     142     237 ..     141     237 .. 0.94

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 3.7e-29
                                       HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHH CS
                             XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlk 75 
                                       +mg+p+++Ap+E+EAq+ay++++g+vd++ s+D+D+llFGap v+rnl  ++k+k    + ++++++evi+le  l 
  gi|330509049|ref|YP_004385477.1| 142 AMGLPVIQAPSEGEAQAAYMAARGDVDYAGSQDYDSLLFGAPLVVRNLAiTGKRKLPrkNIYVDVEPEVINLEVGLA 218
                                       59**********************************************965555544779999************** PP

                                       HHT--HHHHHHHHHHHCET CS
                             XPG_I  76 elgltreqlidlaillgcD 94 
                                       +lg+t++ql+++ i++g+D
  gi|330509049|ref|YP_004385477.1| 219 NLGITHKQLVEIGIMCGTD 237
                                       ******************9 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0   5.4e-21   2.4e-17      10     100 ..      12     103 ..       1     104 [. 0.92

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 5.4e-21
                                       HHHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE-- CS
                             XPG_N  10 lkevaairsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFdg 81 
                                       lk     ++++i+ l+g+ +aiDa   ly+fl  +r+++g+ l+      tshl gl++r+  l++ g+k  fVFdg
  gi|330509049|ref|YP_004385477.1|  12 LKR----KQIEIKDLSGRWVAIDAFNTLYQFLSIIRQRDGTPLMDrqgrvTSHLSGLLYRTTNLIEAGVKVAFVFDG 84 
                                       444....4599********************************9999****************************** PP

                                       S--GGGHHHHHHHHHHHHH CS
                             XPG_N  82 kapdlkkeelekrserrqe 100
                                       +ap++k+ +l+ rse+r++
  gi|330509049|ref|YP_004385477.1|  85 EAPTFKAVTLAERSEIRDK 103
                                       ****************987 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 !   22.0   0.0   4.1e-08   0.00018      20      55 ..     239     276 ..     222     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4.1e-08
                        5_3_exonuc  20 ipGvpgiGektAakLlkeygsleeilenld.elke.kk 55 
                                         G + +G+ktA kL++e g+le+il+  d ++++ +k
  gi|330509049|ref|YP_004385477.1| 239 NSGLERVGPKTALKLIREKGDLESILADRDdKIEDfEK 276
                                       4799***********************88755555344 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     4e-05      0.18       7      38 ..     242     275 ..     238     280 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-05
                                       STT--HHHHHHHHTTT--SHHHHHHS.-..HHHHH CS
                             HHH_5   7 vsGiGpktAlallsaGiesvedlaaa.d..veeLa 38 
                                       ++ +GpktAl+l++   + +e ++a  d  +e++ 
  gi|330509049|ref|YP_004385477.1| 242 LERVGPKTALKLIRE-KGDLESILADrDdkIEDFE 275
                                       788***********9.7899988665221245555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 2322.44
//
Query:       gi|330509050|ref|YP_004385478.1|  [L=313]
Description: diphthamide biosynthesis protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-72  244.9   0.0    1.4e-72  244.7   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 !  244.7   0.0   8.1e-77   1.4e-72       2     302 ..      15     305 ..      14     306 .. 0.96

  Alignments for each domain:
  == domain 1  score: 244.7 bits;  conditional E-value: 8.1e-77
                   Diphthamide_syn   2 Pegllpdsaeiadil.eefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvdrlpvlYvfveieldve 77 
                                       Pegl++  + +a ++ ee+gaev+i+gD+++GaC+vd+    +  +dl+ H Gh+ + + +  +v++  ++++ d++
  gi|330509050|ref|YP_004385478.1|  15 PEGLKRATPIVAARIaEETGAEVIISGDPCFGACDVDTRLSGE--VDLMLHLGHAGIGE-EPEKVIFLEARMNEDLR 88 
                                       **************************************99988..9************8.89*************** PP

                   Diphthamide_syn  78 hlvetlkknfkekkkivlvstiqyahaleevkeeleeegyevvkvpqsekplspgevlgctspklkeeeeevdaily 154
                                        +ve++  ++ ++k++++ +t+q++h+l+ + e l e+g+e +  p s ++++pg+vlgc ++++k+   +vd++l+
  gi|330509050|ref|YP_004385478.1|  89 GVVEKAIGEL-KSKRVGVSTTVQHVHKLDGALEVLAEHGIEGLLGPASGRIKYPGQVLGCCYASAKAL--DVDEYLF 162
                                       **********.7889*********************99*9999566666****************955..9****** PP

                   Diphthamide_syn 155 igdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelverlk 231
                                       ig+g+fh+l+++l++ k +v+++dp++   +  + d + +lrrR+aai++a+dak+++++v+++++q+r+el++r+ 
  gi|330509050|ref|YP_004385478.1| 163 IGTGQFHPLGIALATGK-RVLAADPVTC--EILEIDPDPMLRRRFAAISRAADAKSFAVLVSKKSGQKRMELARRMM 236
                                       ***************77.9*******97..56678899*************************************** PP

                   Diphthamide_syn 232 kllkeagkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalgerewteey 302
                                        l +++g++++lv++++++p++L n+    a V +aCpr+++dd+ +++ Pvltp E+ev++g+r+w+ +y
  gi|330509050|ref|YP_004385478.1| 237 ALGEARGREMFLVYLDNIEPDRLLNL-GARAAVSTACPRVALDDSAKYSIPVLTPPEFEVLVGKRKWE-DY 305
                                       **************************.9***************************************5.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1710.10
//
Query:       gi|330509051|ref|YP_004385479.1|  [L=362]
Description: methyltransferase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-56  190.0   0.0    5.3e-56  189.5   0.0    1.2  1  Met_10           Met-10+ like-protein
    4.4e-14   52.1   0.1      1e-13   50.9   0.1    1.7  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    3.7e-07   30.8   0.0    7.5e-07   29.8   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
      6e-07   29.4   0.0    9.6e-07   28.7   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    8.4e-07   28.7   0.0    1.4e-06   28.0   0.0    1.3  1  MTS              Methyltransferase small domain
      6e-06   25.9   0.0      1e-05   25.1   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      1e-05   24.9   0.0    1.3e-05   24.5   0.0    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    1.5e-05   24.7   0.0    2.3e-05   24.1   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    5.2e-05   23.0   0.0    8.9e-05   22.2   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
    6.4e-05   22.2   0.0    9.3e-05   21.6   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00069   18.7   0.0     0.0011   18.1   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
    0.00083   20.0   0.0     0.0017   19.0   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
     0.0036   17.0   0.0     0.0091   15.7   0.0    1.6  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
  ------ inclusion threshold ------
      0.036   13.5   0.0      0.059   12.8   0.0    1.3  1  TehB             Tellurite resistance protein TehB
      0.064   12.9   0.0       0.11   12.2   0.0    1.4  1  UPF0020          Putative RNA methylase family UPF0020
      0.079   12.1   0.0       0.13   11.4   0.0    1.2  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
      0.099   12.0   0.0       0.17   11.2   0.0    1.3  1  DNA_methylase    C-5 cytosine-specific DNA methylase
        0.1   12.0   0.0       0.18   11.3   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
       0.14   12.3   0.0       0.36   11.0   0.0    1.6  1  DUF4081          Domain of unknown function (DUF4081)


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 !  189.5   0.0   5.6e-59   5.3e-56       2     199 .]     113     308 ..     112     308 .. 0.95

  Alignments for each domain:
  == domain 1  score: 189.5 bits;  conditional E-value: 5.6e-59
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       +fei+Gd+++++  ee +   + ++ +++    ++ktv+   s vege+Rt++++++aG+++t+t hkE+g r+++D
  gi|330509051|ref|YP_004385479.1| 113 SFEIVGDIAMIEDLEEGEA--ERVASALMSSSnSIKTVIAPISDVEGEYRTRRYRHVAGEERTTTTHKEHGLRYRID 187
                                       69*********98777765..677888877776******************************************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                       +   yf ++l +Er r+a+lv + +vV+d+fAG+Gpf+i +ak  + + v+a+d+nP +v+yl+en +lNkve++  
  gi|330509051|ref|YP_004385479.1| 188 LEGAYFTPRLGTERLRIASLVGPTDVVLDMFAGVGPFSILMAK--RCRWVVAMDKNPVAVQYLRENARLNKVENI-D 261
                                       *******************************************..9**************************985.6 PP

                                       EEES-GGG---..TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 155 pileDgrevir..eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                        +++D++e++   +++ad+v+mnlp+sa  Fl +++ a+k gg++hy
  gi|330509051|ref|YP_004385479.1| 262 ILEGDANEIALryQNAADHVIMNLPHSASLFLPAAIGAAKPGGIVHY 308
                                       9********988999*******************************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 !   50.9   0.1   1.1e-16     1e-13       1      44 [.      33      76 ..      33      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 1.1e-16
                                      EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S--H CS
                            Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkeepe 44
                                      +ikV++k+gE+ R++L +++++d+++KI+sd+ ++y+Pv+e  e
  gi|330509051|ref|YP_004385479.1| 33 GIKVERKNGERFRRALVDLKAFDPGRKICSDGSQIYLPVRELSE 76
                                      7**************************************99776 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   7.9e-10   7.5e-07       1      91 [.     214     298 ..     214     304 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 7.9e-10
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSS.STTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpf.edgsfDlvvssgalh 75 
                                       vLd+ +G G +++ +akr+    v+++D ++ ++++ re+a+ +++ n+++++gda+++ +  ++  D v+++  l 
  gi|330509051|ref|YP_004385479.1| 214 VLDMFAGVGPFSILMAKRC--RWVVAMDKNPVAVQYLRENARLNKVeNIDILEGDANEIALrYQNAADHVIMN--LP 286
                                       8*****************9..9*******************99999************986356799***995..44 PP

                                       GSSHHHHHHHHHHHHH CS
                   Methyltransf_25  76 hlsdedlekalkeiar 91 
                                       h     +  +l  +  
  gi|330509051|ref|YP_004385479.1| 287 HS----ASLFLPAAIG 298
                                       42....2345555555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0     1e-09   9.6e-07       6      89 ..     213     292 ..     209     350 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1e-09
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlilsn 81 
                                       +vlD  +G G +++ +a++ +    vv  D ++ a+++ rena+ ++++n+   +gd++e+  l ++ +  D ++ n
  gi|330509051|ref|YP_004385479.1| 213 VVLDMFAGVGPFSILMAKRCRW---VVAMDKNPVAVQYLRENARLNKVENIDILEGDANEIA-LrYQ-NAADHVIMN 284
                                       79***************66443...***********************************88.4499.99***9999 PP

                   Methyltransf_31  82 evlnalad 89 
                                        +  a  +
  gi|330509051|ref|YP_004385479.1| 285 LPHSASLF 292
                                       55433322 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.5e-09   1.4e-06      32     107 ..     211     287 ..     197     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.5e-09
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST..TS-EEEEEE-- CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve..ekkfdlivsNP 105
                                       ++ vlD+ +G+G+ ++ +ak++    v+++d++  A++  +en++ nk+e +++++ d+ e +   ++  d++++N 
  gi|330509051|ref|YP_004385479.1| 211 TDVVLDMFAGVGPFSILMAKRCRW--VVAMDKNPVAVQYLRENARLNKVEnIDILEGDANEIALryQNAADHVIMNL 285
                                       5679****************9998..9************************9999999887544346999******8 PP

                                       -S CS
                               MTS 106 Pf 107
                                       P 
  gi|330509051|ref|YP_004385479.1| 286 PH 287
                                       85 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.1e-08     1e-05     158     255 ..     207     305 ..     194     311 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.1e-08
                              PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk.....eekadv 229
                                       lv +++ vlD+ +G G  +i  ak   + vva+D ++vAv+  +eNa+lNkve+     l++++ +     ++ ad 
  gi|330509051|ref|YP_004385479.1| 207 LVGPTDVVLDMFAGVGPFSILMAK-RCRWVVAMDKNPVAVQYLRENARLNKVENIDI--LEGDANEialryQNAADH 280
                                       56778899************9998.5689************************9553..4444443334567899** PP

                              PrmA 230 ivaNILaevlielaedikklvkeggl 255
                                       ++ N L +    +++ +  + k+gg+
  gi|330509051|ref|YP_004385479.1| 281 VIMN-LPHSASLFLPAAIGAAKPGGI 305
                                       ***9.566667777788888888876 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.4e-08   1.3e-05      53     150 ..     214     307 ..     151     312 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.4e-08
                                       EEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--S CS
                               TRM  53 vldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDPf 129
                                       vld +++ G  +i  a+     + v+a D ++ Av+ ++eN++ln+ve+ + i e+dAn +  + +++ d++ +   
  gi|330509051|ref|YP_004385479.1| 214 VLDMFAGVGPFSILMAKR---CRWVVAMDKNPVAVQYLRENARLNKVEN-IDILEGDANEIALRYQNAADHVIMNLP 286
                                       677777777777777776...78999***********************.788888***998888888888888877 PP

                                       S--GGGHHHHHHHEEEEEEEE CS
                               TRM 130 GspapfldsavqsvkekglLl 150
                                        s++ fl +a+ ++k +g++ 
  gi|330509051|ref|YP_004385479.1| 287 HSASLFLPAAIGAAKPGGIVH 307
                                       79**************99976 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 !   24.1   0.0   2.4e-08   2.3e-05       2      80 ..     212     286 ..     211     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.4e-08
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflS 78 
                                        v+lD+f+G G  +i +a+  + v+a+++n+  ++   +Na++  v ++i++  gd +e+  + + ++   d v++ 
  gi|330509051|ref|YP_004385479.1| 212 DVVLDMFAGVGPFSILMAKRCRWVVAMDKNPVAVQYLRENARLNKV-ENIDILEGDANEIALRYQNAA---DHVIMN 284
                                       589*****************999********************977.57*********9876654433...566665 PP

                   Methyltransf_15  79 pP 80 
                                        P
  gi|330509051|ref|YP_004385479.1| 285 LP 286
                                       55 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   9.4e-08   8.9e-05      42     135 ..     211     299 ..     202     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.4e-08
                                       C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                          vLD+faG G  ++  + R ++ +v+++k++ av+ l+en +  k+e+ +++l  da e +l+    ++  d v 
  gi|330509051|ref|YP_004385479.1| 211 TDVVLDMFAGVGPFSILMAKR-CRWVVAMDKNPVAVQYLRENARLNKVEN-IDILEGDANEIALRY---QNAADHVI 282
                                       5679************76665.7*********************999886.9****9999999888...34568899 PP

                                       E--SSSTTCH.HHHHHH CS
                     Cons_hypoth95 119 lDPPyakellieevlel 135
                                       ++ P  ++l++ +++ +
  gi|330509051|ref|YP_004385479.1| 283 MNLPHSASLFLPAAIGA 299
                                       99998888887777655 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   9.9e-08   9.3e-05      30     116 ..     210     291 ..     199     314 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 9.9e-08
                                       TTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHHHHCTTTCCCCEE CS
                            RrnaAD  30 ekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpeevtekdsihqef 104
                                       +++ vl++ +G+G ++  +akr++ vv++ + ++ ++ l+++ +  k e++ +++ D+ + ++ +       ++   
  gi|330509051|ref|YP_004385479.1| 210 PTDVVLDMFAGVGPFSILMAKRCRWVVAMDKNPVAVQYLRENARlnKVENIDILEGDANEIALRY-------QNAAD 279
                                       899************************************997777699**********9999888.......34444 PP

                                       EEEEE--TTTHH CS
                            RrnaAD 105 lvvanlPyeist 116
                                        v+ nlP+ +s 
  gi|330509051|ref|YP_004385479.1| 280 HVIMNLPHSASL 291
                                       566777777765 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0011     204     266 ..     213     275 ..     203     283 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                   tRNA_U5-meth_tr 204 dllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirlsaeeltealk 266
                                        +l+++ G G fs+ +a++ + v+a +    +v+  + n   nk++n++i+   a+e++  ++
  gi|330509051|ref|YP_004385479.1| 213 VVLDMFAGVGPFSILMAKRCRWVVAMDKNPVAVQYLRENARLNKVENIDILEGDANEIALRYQ 275
                                       5799***********************************************999999987665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.8e-06    0.0017       2      68 ..     216     284 ..     215     307 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-06
                                       EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-T.T-EEEEEEE CS
                   Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfed.nsfDlvvss 68 
                                       d+ +G G ++  +akr++ vv++D ++ ++++ +e+a+ +++ +++++++da ++ ++  n  D v+++
  gi|330509051|ref|YP_004385479.1| 216 DMFAGVGPFSILMAKRCRWVVAMDKNPVAVQYLRENARLNKVeNIDILEGDANEIALRYqNAADHVIMN 284
                                       66689999*********************************9************998875799999887 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.6e-06    0.0091       9      92 ..     211     290 ..     207     297 .. 0.86
   2 ?    0.4   0.0      0.46   4.3e+02     110     141 ..     282     313 ..     278     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.6e-06
                                       T-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEE CS
                   Methyltr_RsmB-F   9 eetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLl 85 
                                        + +lD+ a+ G    ++a   k    vvA+d+n   ++ + en +   v+n+ +le+Da++i      +  D++++
  gi|330509051|ref|YP_004385479.1| 211 TDVVLDMFAGVGPFSILMA---KRCRWVVAMDKNPVAVQYLRENARLNKVENIDILEGDANEIALRYQ-NAADHVIM 283
                                       5778999998887665554...55789*****************998899*************88877.599***** PP

                                       EE--CCG CS
                   Methyltr_RsmB-F  86 DaPCsgt 92 
                                         P s+ 
  gi|330509051|ref|YP_004385479.1| 284 NLPHSAS 290
                                       ***9986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHHHHHCCCEEEEEEEEEEES-- CS
                   Methyltr_RsmB-F 110 iaqlaklqkellsaaidllkkgGvlvYsTCsv 141
                                       i++l +  +  l aai   k+gG++ Y   s 
  gi|330509051|ref|YP_004385479.1| 282 IMNLPHSASLFLPAAIGAAKPGGIVHYYCISP 313
                                       778888888999*************9976665 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.2e-05     0.059      21      93 ..     200     273 ..     189     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.2e-05
                                       HHHHHCCCS-S-E.EEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG---- CS
                              TehB  21 evveavkivkpgk.vldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineakld 93 
                                       e +  + +v p+  vld+  g g  s+ ++     v a+dkn  ++++l+e +  ++++ni+    d ne+ l 
  gi|330509051|ref|YP_004385479.1| 200 ERLRIASLVGPTDvVLDMFAGVGPFSILMAKRCRWVVAMDKNPVAVQYLRENARLNKVENIDILEGDANEIALR 273
                                       5566677888886369*************************************999999999999999988764 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.11      78     134 ..     233     290 ..     184     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                       -.EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.STTS---EEEE------- CS
                           UPF0020  78 k.lygsDldrrvvqgareNaekagvgdliefsqadaakLr.lkegevdvivtnpPYGer 134
                                       + ++++D+++ +vq  reNa+  +v++ i++ + da ++  + ++  d ++ n+P   +
  gi|330509051|ref|YP_004385479.1| 233 RwVVAMDKNPVAVQYLRENARLNKVEN-IDILEGDANEIAlRYQNAADHVIMNLPHSAS 290
                                       3489*****************999976.677777777777546679*********8766 PP

>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.13      78     171 ..     167     257 ..     156     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                   Methyltrans_SAM  78 lvgeldespvvvesglkyqldigrnqnfglfldmrlgrdwvqena...kdknvlnlfaytcgfsvaaiaggaskvvn 151
                                       ++ge   +   +e+gl+y++d+      g ++  rlg + ++  +       vl++fa    fs+  +a  ++ vv 
  gi|330509051|ref|YP_004385479.1| 167 VAGEERTTTTHKEHGLRYRIDLE-----GAYFTPRLGTERLRIASlvgPTDVVLDMFAGVGPFSIL-MAKRCRWVVA 237
                                       67999999999**********96.....7777888888777655411146789***********95.79999***** PP

                   Methyltrans_SAM 152 vdmargslnkgrdnhrlngh 171
                                       +d    +++  r+n rln+ 
  gi|330509051|ref|YP_004385479.1| 238 MDKNPVAVQYLRENARLNKV 257
                                       *****************975 PP

>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018      0.17       3      59 ..     214     271 ..     213     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                       EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-GS- CS
                     DNA_methylase   3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk..kvsigDitkidkkklp 59 
                                       ++d+faG+G f++   a+  + v+a ++++ a++ ++ n +  kv++ Di + d ++++
  gi|330509051|ref|YP_004385479.1| 214 VLDMFAGVGPFSIL-MAKRCRWVVAMDKNPVAVQYLRENARlnKVENIDILEGDANEIA 271
                                       68**********95.556679999****************9999999999999988554 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019      0.18       4      65 ..     213     272 ..     210     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                                       EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHH CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvll 65 
                                       vvl++  G G f + +Ak+     +++++++   v+++ ++++ ++++N+ il+gda ++ l
  gi|330509051|ref|YP_004385479.1| 213 VVLDMFAGVGPFSILMAKRC--RWVVAMDKNPVAVQYLRENARLNKVENIDILEGDANEIAL 272
                                       78888999999999999975..5689*******************************77654 PP

>> DUF4081  Domain of unknown function (DUF4081)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00039      0.36      34      65 ..     192     223 ..     187     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
                           DUF4081  34 afAdralrrgrrcsSivGpaeavlaLwerLee 65 
                                       +f  r+ +++ r++S+vGp + vl++++ + +
  gi|330509051|ref|YP_004385479.1| 192 YFTPRLGTERLRIASLVGPTDVVLDMFAGVGP 223
                                       678899999******************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1960.40
//
Query:       gi|330509052|ref|YP_004385480.1|  [L=191]
Description: transcription factor TFIID [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-53  178.0   1.2    1.1e-25   89.4   0.1    2.1  2  TBP       Transcription factor TFIID (or TATA-binding protein
    3.4e-08   33.5   0.0     0.0028   17.8   0.0    2.2  2  DUF3378   Domain of unknown function (DUF3378)


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.1   3.4e-29     3e-25       3      84 ..       2      81 ..       1      82 [. 0.96
   2 !   89.4   0.1   1.2e-29   1.1e-25       2      83 ..      93     174 ..      92     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 3.4e-29
                                      EEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHH CS
                               TBP  3 kiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapi 81
                                      +++Nvvas++l  e+dL k++ ++  ++aeY++e+fpglvyr++ pk+++liF+sGk+v+tGak+ e++r+++ ++a+ 
  gi|330509052|ref|YP_004385480.1|  2 NVENVVASTKLADEFDLYKIEAEL--EGAEYKKEKFPGLVYRVKAPKAAFLIFTSGKIVCTGAKNIEDIRRVIITLAET 78
                                      79******************8777..**************************************************999 PP

                                      HHH CS
                               TBP 82 lkk 84
                                      lk 
  gi|330509052|ref|YP_004385480.1| 79 LKS 81
                                      986 PP

  == domain 2  score: 89.4 bits;  conditional E-value: 1.2e-29
                                       EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakki 78 
                                       + +qN+va+a+++++l+L+++ l + ++n+eYepe+fpg+v+r+++pkv++l+FssGk+v+tG k++++++e ++ i
  gi|330509052|ref|YP_004385480.1|  93 IIVQNIVATADFKVDLNLNAVVLGMGMENVEYEPEQFPGVVCRVKKPKVVVLVFSSGKLVVTGGKTVNDCEEGVQVI 169
                                       569******************999779**********************************************9988 PP

                                       HHHHH CS
                               TBP  79 apilk 83 
                                        + l+
  gi|330509052|ref|YP_004385480.1| 170 RKGLE 174
                                       87766 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   6.5e-06     0.058      22      54 ..      30      62 ..      11      67 .. 0.82
   2 !   17.8   0.0   3.1e-07    0.0028      24      55 ..     126     157 ..     120     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.5e-06
                           DUF3378 22 lrskkppyavfaakkndttItaYtSgKVlFQGk 54
                                       +++k p+ v++ k +++   ++tSgK++  G+
  gi|330509052|ref|YP_004385480.1| 30 YKKEKFPGLVYRVKAPKAAFLIFTSGKIVCTGA 62
                                      456679***********************8886 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.1e-07
                           DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGkn 55 
                                        ++ p++v + kk+++++ ++ SgK+++ G +
  gi|330509052|ref|YP_004385480.1| 126 PEQFPGVVCRVKKPKVVVLVFSSGKLVVTGGK 157
                                       5789***********************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1099.59
//
Query:       gi|330509053|ref|YP_004385481.1|  [L=977]
Description: hypothetical protein MCON_3428 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      0.007   16.6   0.0      0.017   15.4   0.0    1.7  1  CARDB        CARDB
  ------ inclusion threshold ------
        2.5    8.2   7.0         20    5.3   0.7    2.8  2  Phage_spike  Phage spike trimer


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 !   15.4   0.0   1.9e-06     0.017      18     100 ..     233     321 ..     207     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-06
                                       TSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.....EEEEESEE-CTEEEEEEEEEE-S-S-CEEE.EEEEESTT- CS
                             CARDB  18 geentitvtvkNqGtaasgatkvalyldgelv.....gtvtvpsLaagesttvsftwtteategevt.ltvvvDpdn 88 
                                        ++  + v+vkN Gt ++++++v+lyl + +      + ++v  + ag++++ ++ w  e +  e + l++++   n
  gi|330509053|ref|YP_004385481.1| 233 ADSQAVAVEVKNMGTVEAKDVRVQLYLKKGEDlqpigQPAYVGDIPAGSTKSGTAFWDLEGKNAEGAiLQAQAFMLN 309
                                       5667899********************877766788888999******************44444444999999999 PP

                                       SS--SSCCCSEE CS
                             CARDB  89 evaEsnEtNNel 100
                                       e +  +E+NN+ 
  gi|330509053|ref|YP_004385481.1| 310 EKDAIEEDNNAS 321
                                       999999999975 PP

>> Phage_spike  Phage spike trimer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.9    0.0028        25      29      50 ..     688     708 ..     684     714 .. 0.80
   2 ?    5.3   0.7    0.0022        20      29      50 ..     895     917 ..     887     920 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0028
                                       EEEEESSEEEEES-EEEESS-E CS
                       Phage_spike  29 gtltvqgGGtikGdithsgGnl 50 
                                       + ++vq+G++++G+i+  gG++
  gi|330509053|ref|YP_004385481.1| 688 QDMAVQTGAQMTGTIQ-AGGEI 708
                                       57899**********5.46665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0022
                                       EEEEESSEE.EEES-EEEESS-E CS
                       Phage_spike  29 gtltvqgGG.tikGdithsgGnl 50 
                                       gt+++q+ G +++G+ th +G +
  gi|330509053|ref|YP_004385481.1| 895 GTMQLQQSGdKVTGNYTHDQGRI 917
                                       48999*************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (977 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.83u 0.35s 00:00:01.18 Elapsed: 00:00:00.54
# Mc/sec: 5448.33
//
Query:       gi|330509054|ref|YP_004385482.1|  [L=104]
Description: hypothetical protein MCON_3429 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   0.0      0.018   14.3   0.0    1.1  1  NKAIN     Na,K-Atpase Interacting protein
        0.1   12.7   0.1       0.16   12.1   0.1    1.3  1  LAB_N     Lipid A Biosynthesis N-terminal domain


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 ?   14.3   0.0     2e-06     0.018     104     166 ..       4      68 ..       1      96 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-06
                             NKAIN 104 vswweenGpGckatevtnatse..kateskraetveGclldyqlievvhsavqillallglvyai 166
                                       + w++ +G G  ++   ++  +  +a +  ++e v+G l dy++  +  ++v illa   +  a 
  gi|330509054|ref|YP_004385482.1|   4 RNWYKSDGWGAFREFCIENRYDliSAKQIDEPEPVKGALYDYRFWPISTAGVFILLAYTVIHPAF 68 
                                       68********99998776555534667778899***********************987665554 PP

>> 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 ?   12.1   0.1   1.8e-05      0.16      30      50 ..      45      65 ..      35      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
                             LAB_N 30 vlFWvlSllGslllliYailr 50
                                        FW +S +G ++ll+Y +++
  gi|330509054|ref|YP_004385482.1| 45 YRFWPISTAGVFILLAYTVIH 65
                                      67***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 689.12
//
Query:       gi|330509055|ref|YP_004385483.1|  [L=162]
Description: TspO/MBR family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-41  140.1  20.9      5e-41  139.9  20.9    1.0  1  TspO_MBR     TspO/MBR family


Domain annotation for each model (and alignments):
>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9  20.9   2.8e-45     5e-41       2     134 ..      15     158 ..      14     159 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 2.8e-45
                                       HHHHHHHHHHHHHHHHHCCH.HHHHHS---TTS--HHHHTTHHHHHHHHHHHHHHHHHHH..........HHHHHHH CS
                          TspO_MBR   2 alalpllvgllgglftksee.ewykslrkPpwaPpdwvfppvWtvlyilmgvaaylvwka..........lalyavq 67 
                                       +++++ +vg+ g++ft++++ +wy ++ kP++aPpd ++p+vW++l++lmg++++lvw++          + ++a+q
  gi|330509055|ref|YP_004385483.1|  15 CIIICQAVGSSGSVFTNMSVkTWYPTMVKPWFAPPDGLIPVVWIILFTLMGISLFLVWREgldrpevkaaIYIFALQ 91 
                                       7899*************8888***********************************************9977***** PP

                                       HHHHHTSGGCTTTTTSGGGHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHCHHHHHHHHHHHHHHHHH CS
                          TspO_MBR  68 lvlnllwsplffglkspvlalvdivallglvvalilafskvdklaallllpyllWllfatylnasiw 134
                                       +v+n++ws +ffgl+sp  +l++iv+l+++++++i++f++v++ aalll+py+lW++fa++ln++i+
  gi|330509055|ref|YP_004385483.1|  92 FVFNIAWSGAFFGLRSPYYGLIVIVLLWLMILLTIFKFWQVSRNAALLLVPYILWVSFAMALNYNIM 158
                                       ****************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1124.07
//
Query:       gi|330509056|ref|YP_004385484.1|  [L=83]
Description: hypothetical protein MCON_3432 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.11   12.5   3.0       0.23   11.4   3.0    1.6  1  DUF4428      Domain of unknown function (DUF4428)
       0.14   12.3   2.0        0.2   11.8   2.0    1.3  1  Zn-ribbon_8  Zinc ribbon domain
       0.39   10.5   3.1       0.26   11.1   0.7    1.9  2  DUF1289      Protein of unknown function (DUF1289)
       0.78    9.9   3.1        6.7    6.9   0.3    2.3  2  DUF2256      Uncharacterized protein conserved in bacteria (D


Domain annotation for each model (and alignments):
>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.0   5.2e-05      0.23       2      32 ..      45      75 ..      44      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.2e-05
                           DUF4428  2 CaiCgkKigllkrlkleDg.yvCkdClkKlse 32
                                      C +Cg+  + +   +++ g  vC dC+kKl+e
  gi|330509056|ref|YP_004385484.1| 45 CQVCGEGFTEICG-RTASGlAVCMDCFKKLTE 75
                                      8888888887753.4555548********976 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.0   4.5e-05       0.2       6      35 ..      43      72 ..      42      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.5e-05
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgse 35
                                      + C+ Cg+ f++++  + + l +C +C ++
  gi|330509056|ref|YP_004385484.1| 43 FGCQVCGEGFTEICGRTASGLAVCMDCFKK 72
                                      77************888888888****774 PP

>> DUF1289  Protein of unknown function (DUF1289)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.4      0.25   1.1e+03      14      22 ..      51      59 ..      44      62 .. 0.50
   2 ?   11.1   0.7   5.7e-05      0.26      13      30 ..      63      80 ..      53      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.25
                           DUF1289 14 glClGCgRt 22
                                      g+ + CgRt
  gi|330509056|ref|YP_004385484.1| 51 GFTEICGRT 59
                                      333346666 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.7e-05
                           DUF1289 13 dglClGCgRtldEiaaWs 30
                                        +C+ C+  l E+ aW 
  gi|330509056|ref|YP_004385484.1| 63 LAVCMDCFKKLTERNAWP 80
                                      469**************6 PP

>> DUF2256  Uncharacterized protein conserved in bacteria (DUF2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.018        80       7      18 ..      42      53 ..      36      55 .. 0.81
   2 ?    6.9   0.3    0.0015       6.7       9      24 ..      65      80 ..      63      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.018
                           DUF2256  7 sKiCavCgrpft 18
                                      +  C vCg  ft
  gi|330509056|ref|YP_004385484.1| 42 TFGCQVCGEGFT 53
                                      556*****9997 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0015
                           DUF2256  9 iCavCgrpftwRkkWe 24
                                      +C+ C +++t R  W 
  gi|330509056|ref|YP_004385484.1| 65 VCMDCFKKLTERNAWP 80
                                      6**************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 541.41
//
Query:       gi|330509057|ref|YP_004385485.1|  [L=631]
Description: peptide ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-59  199.7   0.2    1.7e-29  103.0   0.0    2.2  2  ABC_tran         ABC transporter
    2.6e-24   85.5   0.0      1e-17   64.4   0.0    2.4  2  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    9.6e-14   51.9   2.2    0.00022   21.1   0.0    4.2  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    6.6e-13   48.6   1.4    4.8e-05   22.9   0.0    3.3  2  SMC_N            RecF/RecN/SMC N terminal domain
      2e-10   41.0   0.9    0.00031   21.0   0.1    3.5  3  AAA_22           AAA domain
    1.2e-06   28.2   3.3      0.014   15.2   0.3    2.5  2  AAA_29           P-loop containing region of AAA domain
    4.6e-06   26.6   0.0       0.02   14.8   0.0    2.6  2  NACHT            NACHT domain
    7.8e-06   25.9   1.2      0.041   13.8   0.1    2.4  2  RsgA_GTPase      RsgA GTPase
    2.7e-05   24.0   2.5       0.49   10.1   0.0    3.8  4  IstB_IS21        IstB-like ATP binding protein
    5.2e-05   23.8   0.0      0.092   13.2   0.0    2.2  2  AAA_23           AAA domain
    5.9e-05   23.5   6.2      0.018   15.5   0.4    2.9  2  AAA_16           AAA ATPase domain
    0.00069   19.8   0.0       0.32   11.2   0.0    3.0  3  AAA_33           AAA domain
     0.0013   18.4   0.2        1.6    8.2   0.0    2.9  3  AAA_25           AAA domain
     0.0017   17.6   0.7        0.5    9.5   0.1    3.2  3  NB-ARC           NB-ARC domain
     0.0023   18.0   1.3        1.3    9.2   0.1    2.4  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0029   18.1   0.2       0.84   10.2   0.0    2.8  2  AAA_18           AAA domain
     0.0032   17.2   0.2        2.2    8.0   0.0    2.2  2  AAA_24           AAA domain
     0.0034   17.5   1.2        2.4    8.2   0.1    2.3  2  DUF87            Helicase HerA, central domain
     0.0049   16.3   0.1       0.55    9.6   0.0    2.7  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0052   16.5   0.1       0.25   11.0   0.0    2.7  2  AAA_30           AAA domain
     0.0082   16.4   1.7          4    7.7   0.5    3.9  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
     0.0083   16.1   0.5        1.6    8.7   0.0    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0087   15.8   0.2        1.2    8.9   0.0    2.3  2  PRK              Phosphoribulokinase / Uridine kinase family
     0.0097   16.3   0.0          1    9.8   0.0    2.6  2  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.012   15.0   0.8        1.4    8.2   0.1    2.3  2  ATPase           KaiC
      0.014   15.4   0.5       0.77    9.8   0.0    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.014   14.0   0.0       0.89    8.1   0.0    2.6  3  AAA_13           AAA domain
      0.015   15.0   0.0          5    6.7   0.0    3.2  3  AAA_15           AAA ATPase domain
      0.024   14.6   0.8        3.9    7.4   0.1    2.9  3  NTPase_1         NTPase
      0.027   14.4   0.4          4    7.3   0.0    2.3  2  APS_kinase       Adenylylsulphate kinase
      0.037   14.1   3.9        4.2    7.4   0.1    2.6  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.038   13.7   1.3        1.7    8.4   0.0    3.0  3  Sigma54_activat  Sigma-54 interaction domain
      0.041   13.1   0.0        1.2    8.2   0.0    2.1  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.042   13.7   0.8        1.5    8.7   0.1    2.6  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.047   14.1   0.4        3.8    7.9   0.0    2.4  2  RNA_helicase     RNA helicase
      0.047   13.3   0.1        0.9    9.2   0.0    2.3  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.069   13.4   2.2          3    8.1   0.1    2.3  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.084   12.1   0.7          1    8.6   0.0    2.1  2  Septin           Septin
      0.085   11.1   0.1        6.5    4.8   0.1    2.1  2  Myosin_head      Myosin head (motor domain)
      0.088   12.3   0.1        3.4    7.2   0.0    2.2  2  AAA_7            P-loop containing dynein motor region
       0.09   13.1   0.2        6.4    7.1   0.0    3.2  3  AAA_19           AAA domain
       0.12   11.5   0.0        2.8    7.0   0.0    2.1  2  G-alpha          G-protein alpha subunit
       0.15   11.8   1.5        1.4    8.6   0.1    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.35   10.3   1.7        6.9    6.1   0.1    2.4  2  Pox_A32          Poxvirus A32 protein
        1.1    9.0   3.5        1.6    8.5   0.3    2.2  2  ATP_bind_1       Conserved hypothetical 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 !   94.7   0.1   1.6e-29   6.5e-27       1     137 []      17     198 ..      17     198 .. 0.89
   2 !  103.0   0.0   4.4e-32   1.7e-29       1     137 []     348     498 ..     348     498 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 1.6e-29
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke....qeleslrkeigvlpqe..pq 69 
                                       l+ ++l++ +g ++ai+Ge+GaGKStL   ++gll++  + Ge+ll+g+dl +    + ++    e+++++q+  + 
  gi|330509057|ref|YP_004385485.1|  17 LRGIDLDIDKGDCLAIIGESGAGKSTLGLSIMGLLSKgaARGEVLLNGRDLFRitedELRQLRGGEMAMVFQNieDA 93 
                                       57899******************************99999***********998885555566689*******9999 PP

                                       S-TTSBHHHH........................................HHHTCHHHHHHHSTTGGTTCBGESTTS CS
                                       xxxxxxxxxx........................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  70 lfpeltvren........................................esdeeiekalsklglkelkdtvvkssp 106
                                       l+p  +v+++                                          ++ + ++l+ +gl+e   +++   p
  gi|330509057|ref|YP_004385485.1|  94 LDPVQRVGDQiieaisihqkglqcllelgslgrlkglrglkggeesrgerSFQSGMIRLLRAVGLSE---EKAVAYP 167
                                       999999**********************************999876554444444888888888888...4444689 PP

                                       GGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 107 ssLSgGqkqrvalarallkkpkllllDEpta 137
                                       ++LSgG+kqr+++a+al+++p+ll+lDEpta
  gi|330509057|ref|YP_004385485.1| 168 HQLSGGEKQRISIAMALANDPDLLILDEPTA 198
                                       *****************************97 PP

  == domain 2  score: 103.0 bits;  conditional E-value: 4.4e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpelt 75 
                                       l+ v+l+l+ege++a+vGe+G+GK+tL ++++gl ++ +Ge+ l+g++l + +  s+ +++++++q+  +++  ++t
  gi|330509057|ref|YP_004385485.1| 348 LSGVDLTLYEGETLAVVGESGSGKTTLSRAIMGLCQQSSGEVFLEGNKLGK-RDVSFYSRVQMIFQNpkESVSHRMT 423
                                       5789*********************************************99.66677789*******8888999999 PP

                                       HHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       v +               e+ +++++++++ +l+   d+ + + p++LSgG+ qrva+aral+ +pkll++DEpt+
  gi|330509057|ref|YP_004385485.1| 424 VLDAvleplnvmrrgspeERVDRAKEVIRQAELPI-SDRFLAKYPHQLSGGEVQRVAIARALALRPKLLIADEPTS 498
                                       9999***********88777778999999999887.999999********************************96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   2.6e-20     1e-17       1      65 []     247     307 ..     247     307 .. 0.92
   2 !   18.8   0.0   4.5e-06    0.0018       1      26 [.     549     574 ..     549     596 .. 0.89

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 2.6e-20
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE+g++++++++p+HPYT++L+rs+p ++r kd l++i+g     ++  eGCpF++RC+++ e+C
  gi|330509057|ref|YP_004385485.1| 247 VETGDAQEIMKNPAHPYTRGLIRSYPAMNRAKD-LQGIPGM---MSHGLEGCPFHDRCTQRIEIC 307
                                       8********************************.5555555...688888**************9 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 4.5e-06
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvp 26 
                                       vE+g ++++++++  PYT++L++s+ 
  gi|330509057|ref|YP_004385485.1| 549 VEEGATDDILSNAVDPYTRGLIESAC 574
                                       8**********************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 ?    5.1   0.0     0.043        17       3      60 ..      31      87 ..      29     113 .. 0.70
   2 !   11.4   0.1   0.00052      0.21     233     282 ..     166     212 ..     153     231 .. 0.79
   3 !   11.0   0.0   0.00069      0.27       3      24 ..     362     383 ..     361     413 .. 0.74
   4 !   21.1   0.0   5.5e-07   0.00022     235     299 ..     468     530 ..     439     533 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.043
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfef 60
                                      ++iG  g+GKS+L   + +l +  + ++g+   +++    +  + l  l+  e++++f
  gi|330509057|ref|YP_004385485.1| 31 AIIGESGAGKSTLGLSIMGLLS-KGAARGEVLLNGRDLFRITEDELRQLRGGEMAMVF 87
                                      79***********777766655.55555555555555555555555555555555555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00052
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell 282
                                        +++lS G k+ + ++ al+ ++   +ll++DEp ++L+      +++ll
  gi|330509057|ref|YP_004385485.1| 166 YPHQLSGGEKQRISIAMALANDP---DLLILDEPTASLDAMTKMDIIRLL 212
                                       57899*******99999999999...9***********985555555555 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00069
                            AAA_21   3 vliGpNgsGKSnLLdaldllar 24 
                                       +++G  gsGK++L +a+ +l++
  gi|330509057|ref|YP_004385485.1| 362 AVVGESGSGKTTLSRAIMGLCQ 383
                                       689**************99976 PP

  == domain 4  score: 21.1 bits;  conditional E-value: 5.5e-07
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                                       ++lS G  +  a++ al+ ++   +ll+ DEp + L+P++++++l+ll ++ +r g  ++l+TH+ 
  gi|330509057|ref|YP_004385485.1| 468 HQLSGGEVQRVAIARALALRP---KLLIADEPTSALDPSVQAKILKLLmNLQERMGLGILLVTHDI 530
                                       566667655557777777777...89*******************9995666669*********95 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.8   5.4e-07   0.00022      26     204 ..      29     233 ..      17     247 .. 0.75
   2 !   22.9   0.0   1.2e-07   4.8e-05      25     212 ..     359     543 ..     341     550 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.4e-07
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEE.SSSSSSC.EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkk.lkiekee.vsi 99 
                                         ai+G+ G+GKs l  +i+ +L++ +a+     + +dl    ++e +++  +e++++f+n +++  ++++     i
  gi|330509057|ref|YP_004385485.1|  29 CLAIIGESGAGKSTLGLSIMGLLSKGAARGEVLLNGRDLFRItEDELRQLRGGEMAMVFQNIEDAlDPVQRVGdQII 105
                                       5689***************888887777655555667776554588899999*******998877533333221333 PP

                                       EEEEETTSEEEEEE....................TTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseyki....................ngkevtkkevsellesagiske.......lLSgGektLvalaL 149
                                       +   ++++  +  +                     g++  ++ + +ll+ +g+s+e       +LSgGek+ +++a+
  gi|330509057|ref|YP_004385485.1| 106 EAISIHQKGLQCLLelgslgrlkglrglkggeesRGERSFQSGMIRLLRAVGLSEEkavayphQLSGGEKQRISIAM 182
                                       3333444444555556777777888888887776677777788888888888888899***99*************9 PP

                                       HHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 150 lfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlek 204
                                        +A        l +lDe  a LD++    + +ll+++ +    + i+++  + ++
  gi|330509057|ref|YP_004385485.1| 183 ALAN----DPDLLILDEPTASLDAMTKMDIIRLLQSALHCRMSLLITHDISLAQR 233
                                       9873....44599**********************99988888888887666655 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.2e-07
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSC... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekee... 96 
                                       +  a+vG+ GSGK+ l  Ai   +G  +     +++ +  +      +++ +   +v+++f+n++++++ + +    
  gi|330509057|ref|YP_004385485.1| 359 ETLAVVGESGSGKTTLSRAI---MGLCQ-----QSSGEVFLEGnkLGKRDVSFYSRVQMIFQNPKESVSHRMTVlda 427
                                       5669****************...77322.....2344444444433455666779********99994444333111 PP

                                       EEEEEEEETTSEEEEEETTEEE..-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  97 vsisrrvkrkgeseykingkev..tkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                       v    +v+r g+ e ++++ +   +++e+    +    ++++LSgGe + va+a  +A++      l + De  +aL
  gi|330509057|ref|YP_004385485.1| 428 VLEPLNVMRRGSPEERVDRAKEviRQAELPISDRFLAKYPHQLSGGEVQRVAIARALALRP----KLLIADEPTSAL 500
                                       44456777888877778766540044554444444444689*************9999854....38899******* PP

                                       -HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 172 Deknvkkvaellkekskn..aQfivislreemlekadklvgvt 212
                                       D +  +k+ +ll + +++    ++ ++++  + +ka+  + v 
  gi|330509057|ref|YP_004385485.1| 501 DPSVQAKILKLLMNLQERmgLGILLVTHDIAVARKASDRIAVL 543
                                       *************888874467899999999999997776665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.5e-05     0.018       4      89 ..      26     111 ..      23     120 .. 0.73
   2 ?   -0.2   0.1       2.8   1.1e+03      59     120 ..     151     215 ..     139     233 .. 0.54
   3 !   21.0   0.1   7.9e-07   0.00031       8     128 ..     361     526 ..     356     533 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.5e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdl.lrellralglelkaerlsse 76 
                                       +  +l+++GesG+GK+tl   ++  l + a+  e   ++++++++t  ++  ++   + ++++++++ l+      +
  gi|330509057|ref|YP_004385485.1|  26 KGDCLAIIGESGAGKSTLGLSIMGLLSKGAARGEvllNGRDLFRITEDELRQLRGGeMAMVFQNIEDALDP----VQ 98 
                                       5679**************99999999877766668888888888888887766666677777777765544....66 PP

                            AAA_22  77 ellealeqalrar 89 
                                       ++ +++ +a++ +
  gi|330509057|ref|YP_004385485.1|  99 RVGDQIIEAISIH 111
                                       6666666665555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.8
                            AAA_22  59 ellralglelka...erlsseellealeqalrarav...ielliiDEaqh.lrseealeeLrsllnlsr 120
                                       +llra+gl+ ++   ++++++   ++    + a      + lli+DE    l+ ++ +  +r l+    
  gi|330509057|ref|YP_004385485.1| 151 RLLRAVGLSEEKavaYPHQLSGGEKQRISIAMA--LandPDLLILDEPTAsLDAMTKMDIIRLLQS--A 215
                                       566667766666555444444444222222222..2336899999997777753444444444444..3 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 7.9e-07
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka............. 70 
                                       l+v+GesG+GKTtl r ++   ++       +++ vf + ++++    ++++++  ++++++++             
  gi|330509057|ref|YP_004385485.1| 361 LAVVGESGSGKTTLSRAIMGLCQQ-------SSGEVFLEGNKLGkRDVSFYSRVQMIFQNPKESvshrmtvldavle 430
                                       89***************9998654.......6666677777777555566777777777777777777777777777 PP

                            AAA_22  71 ...................................erlsseell.ealeqalrarav...ielliiDEaqh.lr... 104
                                                                          +    ++l    +++ + ara    ++lli DE    l+   
  gi|330509057|ref|YP_004385485.1| 431 plnvmrrgspeervdrakevirqaelpisdrflakY---PHQLSgGEVQRVAIARALalrPKLLIADEPTSaLDpsv 504
                                       777787779999999999998888888888885441...33333344444444444466677******999998644 PP

                            AAA_22 105 seealeeLrsllnlsrkgvqliLv 128
                                       ++++l+ L +l++  r g+ ++Lv
  gi|330509057|ref|YP_004385485.1| 505 QAKILKLLMNLQE--RMGLGILLV 526
                                       4777777777777..999999998 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   3.4e-05     0.014      16      38 ..      21      43 ..      14      55 .. 0.83
   2 !   13.0   0.2   0.00016     0.064      17      43 ..     353     379 ..     345     387 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.4e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTl 38
                                      +++id  +   ++G+sG+GKSTl
  gi|330509057|ref|YP_004385485.1| 21 DLDIDKGDCLAIIGESGAGKSTL 43
                                      5788866699************9 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00016
                            AAA_29  17 ieidlkgatlltGpsGsGKSTllDAiq 43 
                                       +++ + ++  ++G+sGsGK+Tl  Ai+
  gi|330509057|ref|YP_004385485.1| 353 LTLYEGETLAVVGESGSGKTTLSRAIM 379
                                       5555444889************87776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0026       1.1       3      30 ..      30      57 ..      28     100 .. 0.90
   2 !   14.8   0.0     5e-05      0.02       2      28 ..     360     386 ..     359     437 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0026
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklp 30
                                      +++ Ge+G GK+tL  +++ ++ +g   
  gi|330509057|ref|YP_004385485.1| 30 LAIIGESGAGKSTLGLSIMGLLSKGAAR 57
                                      789***************9999998765 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5e-05
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegk 28 
                                       ++++ Ge+GsGKTtL + ++ + +++ 
  gi|330509057|ref|YP_004385485.1| 360 TLAVVGESGSGKTTLSRAIMGLCQQSS 386
                                       789****************98888765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1     0.001       0.4      99     116 ..      26      44 ..       6      60 .. 0.79
   2 !   13.8   0.1    0.0001     0.041      97     130 ..     356     389 ..     333     400 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.001
                                       T.SEEEEECSTTSSHHHHH CS
                       RsgA_GTPase  99 d.ktsvlvGqSGvGKStLi 116
                                       + ++ +++G+SG+GKStL 
  gi|330509057|ref|YP_004385485.1|  26 KgDCLAIIGESGAGKSTLG 44 
                                       448899***********95 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.0001
                                       CTTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpelelktgev 130
                                        +++t ++vG+SG GK+tL  a+++  +++ gev
  gi|330509057|ref|YP_004385485.1| 356 YEGETLAVVGESGSGKTTLSRAIMGLCQQSSGEV 389
                                       45699********************999998887 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    0.0012      0.49      44      67 ..      24      47 ..       8      60 .. 0.82
   2 ?    3.5   0.1      0.13        54      98     152 ..     177     231 ..     169     236 .. 0.79
   3 !    7.3   0.0    0.0089       3.5      46      67 ..     357     378 ..     343     402 .. 0.83
   4 ?   -1.2   0.0       3.7   1.5e+03     105     146 ..     484     527 ..     473     535 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                         IstB_IS21 44 iekkenivllGpsGvGKshlaial 67
                                      i+k ++++++G sG+GKs l  ++
  gi|330509057|ref|YP_004385485.1| 24 IDKGDCLAIIGESGAGKSTLGLSI 47
                                      899***************998775 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.13
                         IstB_IS21  98 klaralkrllkvdllilDdlgllpldqaeaellfeviekrye.rrsiiitsnlpfa 152
                                       +++ a++    +dllilD+  +  ld   + ++ ++++++   r s++it ++++a
  gi|330509057|ref|YP_004385485.1| 177 RISIAMALANDPDLLILDEP-TASLDAMTKMDIIRLLQSALHcRMSLLITHDISLA 231
                                       455556666788*******7.57899999999**9998765438899999998876 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0089
                         IstB_IS21  46 kkenivllGpsGvGKshlaial 67 
                                       + e ++++G sG GK+ l+ a+
  gi|330509057|ref|YP_004385485.1| 357 EGETLAVVGESGSGKTTLSRAI 378
                                       67899*************9997 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 3.7
                         IstB_IS21 105 rllkvdllilDdlgllpldqaeaellfevi...ekryerrsiiit 146
                                         l+++lli D+     ld   ++++++++   ++r +   +++t
  gi|330509057|ref|YP_004385485.1| 484 LALRPKLLIADEPT-SALDPSVQAKILKLLmnlQERMGLGILLVT 527
                                       4578999**99953.445555555555554000555554455555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1     0.007       2.8      16      35 ..      23      43 ..       2      59 .. 0.78
   2 !   13.2   0.0   0.00023     0.092      22      68 ..     361     406 ..     341     460 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.007
                            AAA_23 16 dFsk.gltlItGpNGaGKTTi 35
                                      d +k    +I+G+ GaGK+T+
  gi|330509057|ref|YP_004385485.1| 23 DIDKgDCLAIIGESGAGKSTL 43
                                      444425779***********8 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00023
                            AAA_23  22 tlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese 68 
                                        +++G+ G+GKTT+ +Ai   +   ++++   +g+++ k+dv++ s+
  gi|330509057|ref|YP_004385485.1| 361 LAVVGESGSGKTTLSRAIMGLCQQ-SSGEVFLEGNKLGKRDVSFYSR 406
                                       5789**************876665.4555556677788888877665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.8     0.002      0.79      25      66 ..      28      66 ..      14     241 .. 0.67
   2 !   15.5   0.4   4.4e-05     0.018      24      58 ..     358     393 ..     348     526 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.002
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesa 66
                                       ++ ++GesG GKs+l  +++  l+k    ++rg+   ++++
  gi|330509057|ref|YP_004385485.1| 28 DCLAIIGESGAGKSTLGLSIMGLLSKG---AARGEVLLNGRD 66
                                      6899************98888666555...355555555333 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.4e-05
                            AAA_16  24 pelvllsGesGvGKsslvrellralekd..ggiflrg 58 
                                       +e + ++GesG+GK++l r+++  l+++  g +fl+g
  gi|330509057|ref|YP_004385485.1| 358 GETLAVVGESGSGKTTLSRAIM-GLCQQssGEVFLEG 393
                                       57899****************9.56555342333333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.069        28       4      20 ..      32      48 ..      30     128 .. 0.72
   2 ?   -0.9   0.0       4.1   1.6e+03      69     118 ..     187     237 ..     137     240 .. 0.74
   3 !   11.2   0.0   0.00079      0.32       4      20 ..     363     379 ..     361     452 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.069
                            AAA_33  4 lvGlpGsGKstlaerll 20
                                      ++G +G+GKstl  +++
  gi|330509057|ref|YP_004385485.1| 32 IIGESGAGKSTLGLSIM 48
                                      689********976664 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.1
                            AAA_33  69 agrnvildatnlsrrerarflkl.arrlgvpvrivvvetdeetlkeRlakR 118
                                           +ild + +s +++ +++ + + +    +r+  + t +  l++Rla R
  gi|330509057|ref|YP_004385485.1| 187 DPDLLILDEPTASLDAMTKMDIIrLLQSALHCRMSLLITHDISLAQRLANR 237
                                       344488999999988886555553334677888999999999999999988 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00079
                            AAA_33   4 lvGlpGsGKstlaerll 20 
                                       +vG +GsGK+tl++ ++
  gi|330509057|ref|YP_004385485.1| 363 VVGESGSGKTTLSRAIM 379
                                       79***********9975 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0041       1.6      30      58 ..      24      52 ..       3      97 .. 0.84
   2 ?    6.7   0.0     0.012       4.7      30      50 ..     355     375 ..     349     395 .. 0.88
   3 ?   -2.6   0.0       8.8   3.5e+03     165     188 ..     504     528 ..     478     528 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0041
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava 58
                                      + +g+  +++G +g+GK+tl l+++  ++
  gi|330509057|ref|YP_004385485.1| 24 IDKGDCLAIIGESGAGKSTLGLSIMGLLS 52
                                      6899999**************99876555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.012
                            AAA_25  30 lpagelallaGapgtGKttla 50 
                                       l +ge+ +++G +g+GKttl 
  gi|330509057|ref|YP_004385485.1| 355 LYEGETLAVVGESGSGKTTLS 375
                                       5689***************95 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 8.8
                            AAA_25 165 v.galvealeriarrtgaavllvhH 188
                                       v +++++ l ++++r g  +llv H
  gi|330509057|ref|YP_004385485.1| 504 VqAKILKLLMNLQERMGLGILLVTH 528
                                       4477888899999999999999998 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.079        31      21      40 ..      28      47 ..      18      53 .. 0.84
   2 !    9.5   0.1    0.0012       0.5      22      42 ..     360     380 ..     353     390 .. 0.83
   3 ?    0.1   0.0      0.94   3.8e+02     120     173 ..     510     563 ..     478     572 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.079
                                      EEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqi 40
                                      + +a+ G  G GK+tl  +i
  gi|330509057|ref|YP_004385485.1| 28 DCLAIIGESGAGKSTLGLSI 47
                                      4799***********97666 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                                       EEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC  22 vvalvGmgGvGKttlakqiln 42 
                                        +a+vG  G+GKttl++ i+ 
  gi|330509057|ref|YP_004385485.1| 360 TLAVVGESGSGKTTLSRAIMG 380
                                       689*************99975 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.94
                                       ....HHHHCHTTSEEEEEESBCCCCCCS-S-.EEEEEESS--HHHHHHHHHHCCT CS
                            NB-ARC 120 kigvvlparenrlrvllTTRdeevanavsat.sekievelLekdeawellenkvf 173
                                       k+ + l+ +  +l +ll T d +va ++s++    ++ ++ e+    ++l+n v 
  gi|330509057|ref|YP_004385485.1| 510 KLLMNLQ-ERMGLGILLVTHDIAVARKASDRiAVLLKGRIVEEGATDDILSNAVD 563
                                       5566666.778999***************99999999999999888888888875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2     0.011       4.3       2      20 ..      30      48 ..      29      60 .. 0.81
   2 !    9.2   0.1    0.0032       1.3       2      21 ..     361     380 ..     360     401 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.011
                                      EEEEESTTSSHHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinalt 20
                                       ai+G + +GKStL  +++
  gi|330509057|ref|YP_004385485.1| 30 LAIIGESGAGKSTLGLSIM 48
                                      59***********966665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0032
                                       EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                        a+vG + +GK+tL +a++g
  gi|330509057|ref|YP_004385485.1| 361 LAVVGESGSGKTTLSRAIMG 380
                                       69****************97 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.077        31       3      52 ..      32      78 ..      30     113 .. 0.67
   2 !   10.2   0.0    0.0021      0.84       3      35 ..     363     393 ..     361     433 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.077
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrl 52
                                      + G +G+GK+tl+  +  +l + g   ++v+ +++ l+  +++   e ++l
  gi|330509057|ref|YP_004385485.1| 32 IIGESGAGKSTLGLSIMGLL-SkGAARGEVLLNGRDLFRITED---ELRQL 78
                                      8899********99885554.2477777777777777776666...44444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0021
                            AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvaken 35 
                                       + G +G+GKttl++++  ++   + +++v+ e+
  gi|330509057|ref|YP_004385485.1| 363 VVGESGSGKTTLSRAIMGLC--QQSSGEVFLEG 393
                                       7899************8776..55555555554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0095       3.8       5      22 ..      30      47 ..      26      75 .. 0.89
   2 !    8.0   0.0    0.0054       2.2       4      21 ..     360     377 ..     357     391 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0095
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++i+G+sg+GK+tl +++
  gi|330509057|ref|YP_004385485.1| 30 LAIIGESGAGKSTLGLSI 47
                                      79***********98765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0054
                            AAA_24   4 kiliyGpsgiGKTtlake 21 
                                        ++++G+sg+GKTtl + 
  gi|330509057|ref|YP_004385485.1| 360 TLAVVGESGSGKTTLSRA 377
                                       5799**********9875 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0059       2.4      25      49 ..      29      53 ..      11      62 .. 0.74
   2 !    7.7   0.1    0.0082       3.3      26      44 ..     361     379 ..     352     389 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0059
                             DUF87 25 HlAilgsTGsGKSntvavLleelle 49
                                       lAi+g++G+GKS++  +++  l +
  gi|330509057|ref|YP_004385485.1| 29 CLAIIGESGAGKSTLGLSIMGLLSK 53
                                      58************97777766664 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0082
                             DUF87  26 lAilgsTGsGKSntvavLl 44 
                                       lA++g++GsGK+++ + ++
  gi|330509057|ref|YP_004385485.1| 361 LAVVGESGSGKTTLSRAIM 379
                                       7*************99886 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.12        46      25      48 ..      30      53 ..      17      63 .. 0.87
   2 ?   -2.9   0.0       9.2   3.7e+03     174     199 ..     159     184 ..     154     189 .. 0.81
   3 !    9.6   0.0    0.0014      0.55      23      86 ..     359     419 ..     345     427 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpp 48
                                      l ++G +G+GK+ l   +++ll++
  gi|330509057|ref|YP_004385485.1| 30 LAIIGESGAGKSTLGLSIMGLLSK 53
                                      6789****************9986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.2
                      Mg_chelatase 174 sekeierYlsklsgplldRidlqvev 199
                                       se++   Y ++lsg    Ri + +++
  gi|330509057|ref|YP_004385485.1| 159 SEEKAVAYPHQLSGGEKQRISIAMAL 184
                                       56778899999999999999998876 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0014
                      Mg_chelatase  23 HnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpfraphhsas 86 
                                         l +vG +GsGKt l +++++l  + s e  le +k+     ++ +     +  f++p++s+s
  gi|330509057|ref|YP_004385485.1| 359 ETLAVVGESGSGKTTLSRAIMGLCQQSSGEVFLEGNKLGK---RDVSFYSRVQMIFQNPKESVS 419
                                       568899*****************99999999999887652...223333333445555555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.28   1.1e+02      20      35 ..      29      44 ..      23      62 .. 0.78
   2 !   11.0   0.0   0.00063      0.25      20      50 ..     360     390 ..     351     511 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.28
                            AAA_30 20 vavltGpAGtGKttal 35
                                      + ++ G  G+GK+t+ 
  gi|330509057|ref|YP_004385485.1| 29 CLAIIGESGAGKSTLG 44
                                      67899*********85 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00063
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrvi 50 
                                       + +++G  G+GKtt+ +a+  + +++ g+v+
  gi|330509057|ref|YP_004385485.1| 360 TLAVVGESGSGKTTLSRAIMGLCQQSSGEVF 390
                                       6789*******************99976665 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.5      0.01         4      32      88 ..     169     212 ..     153     214 .. 0.76
   2 ?    3.7   0.0      0.19        75      33      87 ..     470     511 ..     459     514 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.01
                           SbcCD_C  32 tlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       +lSGGek   +++a+a+a            ++++l++LDE  ++lD+ +   +++ll
  gi|330509057|ref|YP_004385485.1| 169 QLSGGEK-QRISIAMALA------------NDPDLLILDEPTASLDAMTKMDIIRLL 212
                                       6888888.4445555522............368999999999999999888888887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.19
                           SbcCD_C  33 lSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllel 87 
                                       lSGGe    +++a a+al            +++l++ DE  s lD+  +a++l+l
  gi|330509057|ref|YP_004385485.1| 470 LSGGEV-QRVAIARALAL------------RPKLLIADEPTSALDPSVQAKILKL 511
                                       666666.33334444444............3556666666666666666666665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.076        30       4      31 ..      32      62 ..      30      84 .. 0.72
   2 !    8.7   0.0     0.004       1.6       4      29 ..     363     388 ..     360     405 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.076
                                      EE--SSSSHHHHHHHGGGGB...S--EEEEE CS
                             AAA_5  4 LvGppGtgKselaerlaaal...nreveyvq 31
                                      ++G++G gKs+l  ++  +l    ++ e+ +
  gi|330509057|ref|YP_004385485.1| 32 IIGESGAGKSTLGLSIMGLLskgAARGEVLL 62
                                      79**********9999999877444444444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.004
                                       EE--SSSSHHHHHHHGGGGBS--EEE CS
                             AAA_5   4 LvGppGtgKselaerlaaalnrevey 29 
                                       +vG++G+gK++l++ +  + +++  +
  gi|330509057|ref|YP_004385485.1| 363 VVGESGSGKTTLSRAIMGLCQQSSGE 388
                                       79*************99999776655 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.051        20       3      24 ..      31      52 ..      29      82 .. 0.83
   2 !    8.9   0.0    0.0029       1.2       3      24 ..     362     383 ..     360     422 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.051
                               PRK  3 gvagsSGaGkttvarklekifg 24
                                      ++ g+SGaGk+t+   +  ++ 
  gi|330509057|ref|YP_004385485.1| 31 AIIGESGAGKSTLGLSIMGLLS 52
                                      899*********9888877776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0029
                               PRK   3 gvagsSGaGkttvarklekifg 24 
                                       +v g+SG+Gktt++r++  + +
  gi|330509057|ref|YP_004385485.1| 362 AVVGESGSGKTTLSRAIMGLCQ 383
                                       899************9987655 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 ?    3.6   0.0      0.21        83       3      52 ..      32      89 ..      30     114 .. 0.70
   2 !    9.8   0.0    0.0025         1       3      53 ..     363     414 ..     361     429 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.21
                                      EESSTTSSHHHHHHHHHHHH............THEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel............gvefleisgsellskyvgesekkirelfke 52
                                      ++G  G GK++l  +++  l            g+++++i   el+    + +  +++++f++
  gi|330509057|ref|YP_004385485.1| 32 IIGESGAGKSTLGLSIMGLLskgaargevllnGRDLFRITEDELR----QLRGGEMAMVFQN 89
                                      78***************9985544444444434667777777777....3344444444444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0025
                                       EESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSSSTTHHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakelgve..fleisgsellskyvgesekkirelfkea 53 
                                       ++G  G GKT+l +a++  ++++   + ++g +l  k      ++++++f++ 
  gi|330509057|ref|YP_004385485.1| 363 VVGESGSGKTTLSRAIMGLCQQSsgEVFLEGNKLG-KRDVSFYSRVQMIFQNP 414
                                       79**************9998644123445555554.43445566666666664 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.036        14      17      38 ..      25      46 ..      18      61 .. 0.81
   2 ?    8.2   0.1    0.0035       1.4      16      37 ..     355     376 ..     346     387 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.036
                            ATPase 17 pegrvvlitGepGtGKtifalq 38
                                       +g    i Ge+G+GK++++l 
  gi|330509057|ref|YP_004385485.1| 25 DKGDCLAIIGESGAGKSTLGLS 46
                                      5678899************975 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0035
                            ATPase  16 ipegrvvlitGepGtGKtifal 37 
                                       ++eg++  ++Ge+G+GKt+++ 
  gi|330509057|ref|YP_004385485.1| 355 LYEGETLAVVGESGSGKTTLSR 376
                                       67999**************985 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.21        84      19      38 ..      27      46 ..      10      57 .. 0.78
   2 ?    9.8   0.0    0.0019      0.77      19      41 ..     358     380 ..     336     389 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.21
                                      TEEEEEEESTTSSHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrg 38
                                      gd++++ G+ GaGK+tl  +
  gi|330509057|ref|YP_004385485.1| 27 GDCLAIIGESGAGKSTLGLS 46
                                      78899***********9655 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0019
                                       TEEEEEEESTTSSHHHHHHHHHH CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglak 41 
                                       g++++  G+ G+GKTtl+r+++ 
  gi|330509057|ref|YP_004385485.1| 358 GETLAVVGESGSGKTTLSRAIMG 380
                                       778999*************9975 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.5   1.4e+03      21      39 ..      32      50 ..      31      88 .. 0.80
   2 ?    2.7   0.0     0.099        40     527     580 ..     188     237 ..     164     254 .. 0.84
   3 ?    8.1   0.0    0.0022      0.89      23      48 ..     365     390 ..     362     417 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.5
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      i G  GaGK+tL   +  l
  gi|330509057|ref|YP_004385485.1| 32 IIGESGAGKSTLGLSIMGL 50
                                      56899*******8776665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.099
                            AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkn 580
                                           ++D P  SLD+   + ++ l++s l    + +  ++ TH +++ + + ++
  gi|330509057|ref|YP_004385485.1| 188 PDLLILDEPTASLDAMTKMDIIRLLQSAL----HCRMSLLITHDISLAQRLANR 237
                                       45689***********************9....889999999999998887765 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0022
                            AAA_13  23 GwNGaGKTtLSrllrslelgetepkf 48 
                                       G  G+GKTtLSr++  l +++  + f
  gi|330509057|ref|YP_004385485.1| 365 GESGSGKTTLSRAIMGLCQQSSGEVF 390
                                       788***********999776655544 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.12        46      17      43 ..      20      47 ..      17      95 .. 0.78
   2 ?   -0.2   0.0       1.6   6.3e+02     322     351 ..     186     215 ..     135     220 .. 0.83
   3 ?    6.7   0.0     0.013         5      25      65 ..     360     396 ..     341     421 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                            AAA_15 17 veidlsee.ltvliGkNnsGKSsileal 43
                                      +++d+++     +iG+ ++GKS++   +
  gi|330509057|ref|YP_004385485.1| 20 IDLDIDKGdCLAIIGESGAGKSTLGLSI 47
                                      45666666799************85444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkel 351
                                       +++++l+++EP a+L    ++ +i+ll+++
  gi|330509057|ref|YP_004385485.1| 186 NDPDLLILDEPTASLDAMTKMDIIRLLQSA 215
                                       57899**********999999999999986 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.013
                            AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedl 65 
                                       +  ++G+ +sGK+++ +a+  + +++    + ++++e ++l
  gi|330509057|ref|YP_004385485.1| 360 TLAVVGESGSGKTTLSRAIMGLCQQS----SGEVFLEGNKL 396
                                       6789***************9999988....56666666655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.091        36       2      25 ..      30      53 ..      29      63 .. 0.85
   2 ?   -1.3   0.0       4.4   1.8e+03      91     141 ..     183     235 ..     147     251 .. 0.64
   3 ?    7.4   0.1    0.0098       3.9       2      26 ..     361     385 ..     360     394 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.091
                                      EEEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellks 25
                                      ++i G++G GK+Tl   ++ ll++
  gi|330509057|ref|YP_004385485.1| 30 LAIIGESGAGKSTLGLSIMGLLSK 53
                                      5788**********9999999843 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.4
                                       HHHHHH-EEEE--.-STTGGG-H.HHHHHHHHHHTTTSEEEEE--SS--SHHH CS
                          NTPase_1  91 kalseadviviDE.iGkmElksk.kfkeaveevLksekpvlavihrrkdlalv 141
                                          +++d++++DE   ++   +k  +++ ++ +L++   +l++   +  ++l 
  gi|330509057|ref|YP_004385485.1| 183 ALANDPDLLILDEpTASLDAMTKmDIIRLLQSALHCRMSLLITHDISLAQRLA 235
                                       33478999999993345554433256677777777777777766665444444 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0098
                                       EEEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss 26 
                                       +++ G++G+GKtTl + ++ l+++s
  gi|330509057|ref|YP_004385485.1| 361 LAVVGESGSGKTTLSRAIMGLCQQS 385
                                       5789**************9999876 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.051        20       3      38 ..      28      64 ..      26      77 .. 0.75
   2 ?    7.3   0.0      0.01         4       2      40 ..     358     395 ..     357     407 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.051
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT.--EEEEEH CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekg.isvylLdG 38
                                       ++ + G sg+GKst+   +   L +   +  +lL+G
  gi|330509057|ref|YP_004385485.1| 28 DCLAIIGESGAGKSTLGLSIMGLLSKGAaRGEVLLNG 64
                                      567789***********99998777766233444555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.01
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdn 40 
                                       g ++ + G sgsGK+t+++a+   L ++    + L+G++
  gi|330509057|ref|YP_004385485.1| 358 GETLAVVGESGSGKTTLSRAIM-GLCQQSSGEVFLEGNK 395
                                       5678899*************98.6777777777788876 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 ?    6.8   0.6     0.016       6.5       5      26 ..      33      54 ..      30      62 .. 0.85
   2 ?    7.4   0.1     0.011       4.2       5      26 ..     364     385 ..     361     391 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.016
                                      ESSTTSSHHHHHHHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  5 stkGGvGKTtlaanLaralarr 26
                                       + +G+GK+tl ++++ +l+++
  gi|330509057|ref|YP_004385485.1| 33 IGESGAGKSTLGLSIMGLLSKG 54
                                      578****************995 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                                       ESSTTSSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   5 stkGGvGKTtlaanLaralarr 26 
                                        + +G+GKTtl+ +++ + ++ 
  gi|330509057|ref|YP_004385485.1| 364 VGESGSGKTTLSRAIMGLCQQS 385
                                       578*********9999887775 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.24        95      25      42 ..      30      47 ..      12      63 .. 0.81
   2 ?    8.4   0.0    0.0042       1.7      24      51 ..     360     387 ..     346     395 .. 0.80
   3 ?   -2.3   0.0         8   3.2e+03     104     119 ..     499     514 ..     491     522 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.24
                                      EEEECSTTSSHHHHHHHH CS
                   Sigma54_activat 25 vlitGesGtGKellarai 42
                                      + i GesG+GK++l  +i
  gi|330509057|ref|YP_004385485.1| 30 LAIIGESGAGKSTLGLSI 47
                                      5699*******9987655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0042
                                       -EEEECSTTSSHHHHHHHHHHHSTTTTS CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheaskrkek 51 
                                       ++ ++GesG+GK++l+rai    +++++
  gi|330509057|ref|YP_004385485.1| 360 TLAVVGESGSGKTTLSRAIMGLCQQSSG 387
                                       56799**************987776654 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8
                                       GS-HHHHHHHHHHHHH CS
                   Sigma54_activat 104 elplelQekLlrvlqe 119
                                        l++++Q+k+l++l +
  gi|330509057|ref|YP_004385485.1| 499 ALDPSVQAKILKLLMN 514
                                       688999**99998854 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0031       1.2       4      74 ..      30      97 ..      27     110 .. 0.79
   2 ?    2.6   0.0      0.16        63       5      37 ..     362     391 ..     359     425 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0031
                           DUF2075  4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnl 74
                                      + + G++G+GK+ ++l+++  l  ++   +  +l+  ++l ++ + +l++ + + +   +f++ +    ++
  gi|330509057|ref|YP_004385485.1| 30 LAIIGESGAGKSTLGLSIMGLL--SKGAARGEVLLNGRDLFRITEDELRQLR-GGEMAMVFQNIEDALDPV 97
                                      6688*****************9..8888888888888899998888886666.777666666666655555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.16
                           DUF2075   5 lVtGvaGtGKtvvllnllaeleddeeertavyl 37 
                                        V G++G+GKt +  +++  +   ++ + +v+l
  gi|330509057|ref|YP_004385485.1| 362 AVVGESGSGKTTLSRAIMGLC---QQSSGEVFL 391
                                       588*********999998888...444444444 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.24        96       2      25 ..      30      53 ..      29      63 .. 0.81
   2 ?    8.7   0.1    0.0039       1.5       2      22 ..     361     381 ..     360     389 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.24
                              MobB  2 lgivgksgsGKTtLleklipelka 25
                                      l+i+g sg+GK tL   ++  l++
  gi|330509057|ref|YP_004385485.1| 30 LAIIGESGAGKSTLGLSIMGLLSK 53
                                      79***********97777766654 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0039
                              MobB   2 lgivgksgsGKTtLleklipe 22 
                                       l++vg sgsGKTtL   ++  
  gi|330509057|ref|YP_004385485.1| 361 LAVVGESGSGKTTLSRAIMGL 381
                                       789**********98776655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.18        71       3      18 ..      32      47 ..      30      63 .. 0.81
   2 ?    7.9   0.0    0.0095       3.8       3      26 ..     363     385 ..     361     411 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.18
                      RNA_helicase  3 lyGpsgeGKStlakeL 18
                                      + G+sg GKStl  ++
  gi|330509057|ref|YP_004385485.1| 32 IIGESGAGKSTLGLSI 47
                                      89*********97665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0095
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkkl 26 
                                       ++G+sg GK+tl++ ++  l++++
  gi|330509057|ref|YP_004385485.1| 363 VVGESGSGKTTLSRAIM-GLCQQS 385
                                       89************944.444333 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 ?    1.5   0.0      0.48   1.9e+02      12      35 ..      25      48 ..      20      61 .. 0.84
   2 ?    9.2   0.0    0.0022       0.9      10      41 ..     354     385 ..     350     454 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.48
                                      BTT-EEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 12 vqGqrtlipgafgvGktvisqsls 35
                                       +G  ++i+g++g Gk+++  s++
  gi|330509057|ref|YP_004385485.1| 25 DKGDCLAIIGESGAGKSTLGLSIM 48
                                      589999***********9876664 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0022
                                       -EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  10 pivqGqrtlipgafgvGktvisqslskqsnsd 41 
                                       ++ +G++++++g++g Gkt++s++++  ++++
  gi|330509057|ref|YP_004385485.1| 354 TLYEGETLAVVGESGSGKTTLSRAIMGLCQQS 385
                                       7899******************8887665544 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3     0.083        33       3      20 ..      31      48 ..      30      55 .. 0.85
   2 ?    8.1   0.1    0.0076         3       2      20 ..     361     379 ..     360     399 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.083
                                      EEESSTTSSHHHHHHCHC CS
                               Roc  3 vlvGdsgvGKtsllkrfv 20
                                       ++G+sg+GK++l  +++
  gi|330509057|ref|YP_004385485.1| 31 AIIGESGAGKSTLGLSIM 48
                                      69**********976665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0076
                                       EEEESSTTSSHHHHHHCHC CS
                               Roc   2 vvlvGdsgvGKtsllkrfv 20 
                                       + +vG+sg+GKt+l + ++
  gi|330509057|ref|YP_004385485.1| 361 LAVVGESGSGKTTLSRAIM 379
                                       579***********99887 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.31   1.2e+02       7      21 ..      30      44 ..      27      58 .. 0.84
   2 ?    8.6   0.0    0.0025         1       6      31 ..     360     385 ..     357     428 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.31
                                      EEEEEBTTSSCCCCC CS
                            Septin  7 lmvvGesglGkttli 21
                                      l ++Gesg Gk+tl 
  gi|330509057|ref|YP_004385485.1| 30 LAIIGESGAGKSTLG 44
                                      6799*********95 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0025
                                       EEEEEEBTTSSCCCCCCTTSSSS--- CS
                            Septin   6 tlmvvGesglGkttlintlfetdlie 31 
                                       tl vvGesg Gkttl ++++    ++
  gi|330509057|ref|YP_004385485.1| 360 TLAVVGESGSGKTTLSRAIMGLCQQS 385
                                       799************87766543333 PP

>> Myosin_head  Myosin head (motor domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.03        12      84     111 ..      26      53 ..      19      92 .. 0.86
   2 ?    4.8   0.1     0.016       6.5      86     108 ..     359     381 ..     353     400 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.03
                                       SEEEEEEESSTTSSHHHHHHHHHHHHHH CS
                       Myosin_head  84 enqsilisGEsGAGKteatKkvlqylas 111
                                       +  ++ i GEsGAGK      ++  l+ 
  gi|330509057|ref|YP_004385485.1|  26 KGDCLAIIGESGAGKSTLGLSIMGLLSK 53 
                                       567999*********9998888887765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.016
                                       EEEEEESSTTSSHHHHHHHHHHH CS
                       Myosin_head  86 qsilisGEsGAGKteatKkvlqy 108
                                        ++ + GEsG GKt  ++ ++  
  gi|330509057|ref|YP_004385485.1| 359 ETLAVVGESGSGKTTLSRAIMGL 381
                                       567899**************975 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.18        73      27      54 ..      21      48 ..       9      57 .. 0.76
   2 ?    7.2   0.0    0.0084       3.4      26      55 ..     351     380 ..     341     390 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.18
                             AAA_7 27 elllknkkpvllvGptGtGKtviikdll 54
                                      +l ++++  + ++G++G GK+++  +++
  gi|330509057|ref|YP_004385485.1| 21 DLDIDKGDCLAIIGESGAGKSTLGLSIM 48
                                      555777888899*********9876665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0084
                             AAA_7  26 lelllknkkpvllvGptGtGKtviikdllk 55 
                                       ++l l ++  + +vG++G+GKt++ + ++ 
  gi|330509057|ref|YP_004385485.1| 351 VDLTLYEGETLAVVGESGSGKTTLSRAIMG 380
                                       567788889999***********9988765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.99   3.9e+02      10      36 ..      27      53 ..      23     103 .. 0.88
   2 ?    7.1   0.0     0.016       6.4      10      38 ..     358     386 ..     352     393 .. 0.86
   3 ?   -0.6   0.0       3.7   1.5e+03     100     129 ..     486     516 ..     444     527 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.99
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallve 36
                                       ++l++++  G GK+++   i+ ll +
  gi|330509057|ref|YP_004385485.1| 27 GDCLAIIGESGAGKSTLGLSIMGLLSK 53
                                      57899**********987777776665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.016
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelg 38 
                                        ++l+v++  G+GKT++ ++i+ l+++  
  gi|330509057|ref|YP_004385485.1| 358 GETLAVVGESGSGKTTLSRAIMGLCQQSS 386
                                       67899************999999888765 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.7
                            AAA_19 100 lqeeellivDE.fqdvd.elqyrLlkallgek 129
                                       l + +lli DE ++ +d  +q ++lk l++ +
  gi|330509057|ref|YP_004385485.1| 486 L-RPKLLIADEpTSALDpSVQAKILKLLMNLQ 516
                                       3.667999999778999999999999988555 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.18        72      26      89 ..      30     108 ..      21     238 .. 0.76
   2 ?    7.0   0.0    0.0069       2.8      26      51 ..     361     390 ..     354     470 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.18
                                       EEEEESTTSSHHHHHHHHH.HHCS--..............--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT..... CS
                           G-alpha  26 llllGqseSGKsTilkqlk.llykkg..............fseeelatwraviqlnivrsiktilealesleselse 87 
                                       l ++G+s+ GKsT+  ++  ll k++              ++e+el+++r   +  + ++i++ l+ +++ +++++e
  gi|330509057|ref|YP_004385485.1|  30 LAIIGESGAGKSTLGLSIMgLLSKGAargevllngrdlfrITEDELRQLRGGEMAMVFQNIEDALDPVQRVGDQIIE 106
                                       6789**********666552555555788888888888777777788888888888888888888888887777766 PP

                                       .. CS
                           G-alpha  88 sf 89 
                                        +
  gi|330509057|ref|YP_004385485.1| 107 AI 108
                                       55 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0069
                                       EEEEESTTSSHHHHHHHHHHHCS--....- CS
                           G-alpha  26 llllGqseSGKsTilkqlkllykkg....f 51 
                                       l ++G+s+SGK+T+ + +  l++++    f
  gi|330509057|ref|YP_004385485.1| 361 LAVVGESGSGKTTLSRAIMGLCQQSsgevF 390
                                       7789*************9988877645552 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.62   2.5e+02       6      21 ..      32      47 ..      28      52 .. 0.83
   2 ?    8.6   0.1    0.0036       1.4       5      23 ..     362     380 ..     359     385 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.62
                         PduV-EutP  6 liGkvgsGKttLtqal 21
                                      +iG++g+GK tL  ++
  gi|330509057|ref|YP_004385485.1| 32 IIGESGAGKSTLGLSI 47
                                      89*********97665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0036
                         PduV-EutP   5 lliGkvgsGKttLtqalkg 23 
                                        ++G++gsGKttL++a+ g
  gi|330509057|ref|YP_004385485.1| 362 AVVGESGSGKTTLSRAIMG 380
                                       589************9976 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2      0.15        61      16      35 ..      30      49 ..      24      55 .. 0.84
   2 ?    6.1   0.1     0.017       6.9      16      30 ..     361     375 ..     355     391 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.15
                           Pox_A32 16 lalvGgsGsGktvyLlsLlr 35
                                      la++G+sG+Gk +  ls++ 
  gi|330509057|ref|YP_004385485.1| 30 LAIIGESGAGKSTLGLSIMG 49
                                      89**********99888765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.017
                           Pox_A32  16 lalvGgsGsGktvyL 30 
                                       la+vG+sGsGkt+  
  gi|330509057|ref|YP_004385485.1| 361 LAVVGESGSGKTTLS 375
                                       89**********965 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2       0.8   3.2e+02       1      14 [.      32      45 ..      32      57 .. 0.82
   2 ?    8.5   0.3    0.0039       1.6       1      23 [.     363     385 ..     363     390 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.8
                        ATP_bind_1  1 vvGpaGsGKttfvg 14
                                      ++G  G+GK+t+  
  gi|330509057|ref|YP_004385485.1| 32 IIGESGAGKSTLGL 45
                                      79*********855 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0039
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelr 23 
                                       vvG  GsGKtt+ +a++ +++++
  gi|330509057|ref|YP_004385485.1| 363 VVGESGSGKTTLSRAIMGLCQQS 385
                                       89**************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 3842.50
//
Query:       gi|330509058|ref|YP_004385486.1|  [L=320]
Description: peptide ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete 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-19   68.8  12.1    4.9e-19   68.8  12.1    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
    9.5e-09   35.1  11.0    1.3e-08   34.7   0.1    3.7  3  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.5      0.13   1.2e+03     159     180 ..      15      36 ..      13      39 .. 0.63
   2 !   68.8  12.1   5.5e-23   4.9e-19       2     183 ..      93     275 ..      88     277 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.13
                      BPD_transp_1 159 lalviavlllnlvadilqrlld 180
                                       + l+i+vl+ +l++ i++ ll+
  gi|330509058|ref|YP_004385486.1|  15 ALLGILVLAAILLMAIFAPLLS 36 
                                       5566666666666666666655 PP

  == domain 2  score: 68.8 bits;  conditional E-value: 5.5e-23
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg.hlilpviillllsaapyvrlirraalr 77 
                                       +l+G+ +a   ++   ++ +++++v+ slP+++++il+        ++  +l l +++++++s+++ +r++r+++l 
  gi|330509058|ref|YP_004385486.1|  93 VLIGASSA-LVGGLYERFWMRIVDVMISLPTIIVMILIA------AYFRpNLPLLILLISAFSWPGGARIVRSQVLT 162
                                       78999999.9***********************999999......7888678888********************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                         +++++ aar+ Ga  ++i++++++P + p i++ +i  + +++   + l flg    ++   l +++g+++++++
  gi|330509058|ref|YP_004385486.1| 163 LKERMHIYAARTFGADQRHILKNHIVPDISPIIASMMIQDARRAVFMEAGLAFLG----VS-DPLIISWGKMMHQAL 234
                                       *******************************************************....55.556688999999999 PP

                      BPD_transp_1 155 ............nggvlalviavlllnlvadilqrlldprv 183
                                                     + ++l + ++ l+++   l ++ dpr+
  gi|330509058|ref|YP_004385486.1| 235 aftyldvwkwwlLPTGIFLSLTLVSLSFLGVSLEAAMDPRL 275
                                       9**********99999999999999*****99999999997 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 !   34.7   0.1   1.4e-12   1.3e-08      11      45 ..      10      44 ..       7      57 .. 0.85
   2 ?   -0.4   0.1      0.13   1.2e+03       1      10 [.      61      70 ..      61      72 .. 0.88
   3 ?    1.7   4.4      0.03   2.7e+02      17      33 ..     117     134 ..     116     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.4e-12
                            OppC_N 11 krNklAvvglvilllllliaifaPliaPydpqdli 45
                                      + +++A++g  +l+++ll+aifaPl++Py+p++++
  gi|330509058|ref|YP_004385486.1| 10 RHDRMALLGILVLAAILLMAIFAPLLSPYSPTEYT 44
                                      889***************************96665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.13
                            OppC_N  1 slwqdawrrF 10
                                      s++qd+w r+
  gi|330509058|ref|YP_004385486.1| 61 SMGQDIWTRL 70
                                      789****998 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.03
                            OppC_N  17 vvglvilllllliaif.a 33 
                                       +++l  +++++lia++  
  gi|330509058|ref|YP_004385486.1| 117 MISLPTIIVMILIAAYfR 134
                                       999999999999998732 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.45
# Mc/sec: 2155.86
//
Query:       gi|330509059|ref|YP_004385487.1|  [L=327]
Description: peptide ABC transporter permease [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-34  117.8   7.7    4.5e-34  117.8   7.7    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0     0.088   1.6e+03     157     172 ..      13      28 ..       5      39 .. 0.67
   2 !  117.8   7.7   2.5e-38   4.5e-34       1     184 [.     119     324 ..     115     325 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.088
                      BPD_transp_1 157 gvlalviavlllnlva 172
                                       +++++++a+++ln+++
  gi|330509059|ref|YP_004385487.1|  13 SYIIALLAIFALNFIL 28 
                                       4555556666666655 PP

  == domain 2  score: 117.8 bits;  conditional E-value: 2.5e-38
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.......................vilsilghlil 54 
                                       g++lGi ++++r+ ++d+ l+    +l +lP f l+i+l+l+f                        + +i+ hl+l
  gi|330509059|ref|YP_004385487.1| 119 GVMLGIESGYRRGERIDRGLLAGLMLLGGLPDFFLGIVLLLIFgvslnlfplsgaltpysglegfpLVADIARHLAL 195
                                       678888888*********************************************************9999******* PP

                      BPD_transp_1  55 pviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllefl 131
                                       p+++l+l+ ++++ +l+r+ ++ +l ++++ +ara+G+s++ + + ++ +nal p+ t  +l+++ l++ga+++e++
  gi|330509059|ref|YP_004385487.1| 196 PLAALVLVDLGGIYLLTRNTVVTILKEGFMLTARAKGCSEFCLRYSHAGRNALLPVTTATGLRIPQLITGALFIEII 272
                                       ***************************************************************************** PP

                      BPD_transp_1 132 gswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       +s+pGlg++l +a+ ++dy++i+ g++l +++ vl  nl++d +++ ldpr+r
  gi|330509059|ref|YP_004385487.1| 273 FSYPGLGLMLRTALDARDYPLIQ-GILLLVTVTVLFANLFVDQIYKRLDPRTR 324
                                       ***********************.***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2179.23
//
Query:       gi|330509060|ref|YP_004385488.1|  [L=152]
Description: hypothetical protein MCON_3436 [Methanosaeta concilii GP6]
Scores for complete 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-35  121.3   0.0    2.9e-35  121.1   0.0    1.1  1  TrmO      tRNA-methyltransferase O


Domain annotation for each model (and alignments):
>> TrmO  tRNA-methyltransferase O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.1   0.0   1.6e-39   2.9e-35       1     119 []      25     136 ..      25     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 121.1 bits;  conditional E-value: 1.6e-39
                                       TS-SSGGG--.-EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E-TT-.SS-E.EGGGS--S-SS CS
                              TrmO   1 giPrqpglaeeaeaeielepeynseealegleefshlwllfvfhenaekklkakvrpprlggnervGvfatRsphRp 77 
                                       +iPrq++l+e   ++ie++pey  ee+l+++e+++hl++lf++h   ++k + + +pp+ +g e+ GvfatRsp+Rp
  gi|330509060|ref|YP_004385488.1|  25 DIPRQGRLSE-EICQIEVFPEY--EEGLKDIEQCTHLFILFWLHLG-DRK-RLLATPPTSKG-EH-GVFATRSPNRP 94 
                                       69*******9.79*********..********************88.333.57777888887.56.*********** PP

                                       S-EEEEEEEEEEEETTEEEEES----TT-EEEEEEE--HHHH CS
                              TrmO  78 npiglsvvklekvegnvlevsgvDlldgtpvlDiKPYvpyaD 119
                                       npi++ +v+l kvegn+l+v+g+D+ldg+ +lDiKPY +++D
  gi|330509060|ref|YP_004385488.1|  95 NPIAIDIVQLLKVEGNRLTVKGMDALDGSVLLDIKPYSAEMD 136
                                       **************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1147.59
//
Query:       gi|330509061|ref|YP_004385489.1|  [L=511]
Description: family 5 extracellular solute-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-71  240.0   1.3    5.5e-71  239.5   1.3    1.2  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.5   1.3     3e-75   5.5e-71       2     363 ..      67     416 ..      66     423 .. 0.89

  Alignments for each domain:
  == domain 1  score: 239.5 bits;  conditional E-value: 3e-75
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       +vpaLAes we  +D k y f+LR+ v++ D +p+ A+Dv+f+++++ d+++++  +s++      +++e++dd+tv
  gi|330509061|ref|YP_004385489.1|  67 FVPALAES-WEYLADEKAYVFHLRDKVTWNDKEPFSAQDVAFTIDYIQDHPYQWVDSSTI------ESAEVLDDRTV 136
                                       79******.7*********************************************98886......8********** PP

                                       EEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTT.TSE-BSSSEEEEEEETTT.EEEEEE-TTSTTTSCSSSS CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiakkaaekeddkdkdtn.ekpvgtGPYklkefkpgq.kivlernpdYwgggkpkld 153
                                       ++tl++ +a+fl  +a + + ++++ ++  +d+ ++ + e++ gtGP++lk++++ q +  +e+n+dY+ +g+p+ +
  gi|330509061|ref|YP_004385489.1| 137 KITLTEEYAPFLDQVAGTLPILPEHIYDGVSDPASFMDsEALTGTGPFMLKSYDKAQgSYLYEANEDYY-QGAPRTK 212
                                       *************9999999999977777777766665156667***********887888*******9.******* PP

                                       EEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHH CS
                         SBP_bac_5 154 riefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyA 230
                                       +i+f  + +++ + a+l++G++ d+a +p + +++lk++    +  +++  +v  +++N++k+pf+d+++RqAl yA
  gi|330509061|ref|YP_004385489.1| 213 QIKFIKV-SQEMASASLEKGDV-DAAAVPGETVDSLKDDGFAVI--KGNHDWVAKIMVNHNKEPFSDIKFRQALYYA 285
                                       *******.999999999*****.99999*******977665555..******************************* PP

                                       S-HHHHHHHCTTTSSEEESSS.STTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETC...EEEEEEEE CS
                         SBP_bac_5 231 iDreeivkavlegyatpansl.lppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrek...klkltlll 303
                                       iDr+++vk+ l+gy+  + +   ++  ++++++ +++  a+dp+   klL+e Gy  +++g++ +    +  + ll+
  gi|330509061|ref|YP_004385489.1| 286 IDRDDLVKTGLRGYGLEGSAGlYASDNDWHNPSQEEY--AHDPARTGKLLEELGYAMDGEGEYYSIdgyPDGIELLA 360
                                       ***************9888884555555555555544..78***************999998877767655555554 PP

                                       ETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTH CS
                         SBP_bac_5 304 asgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpd 363
                                       +   ++ ++ aeli++ l+++Gik+++++vd+ +t ++ v ++++d++l+g g+  +dp 
  gi|330509061|ref|YP_004385489.1| 361 T---ADTERQAELIKKHLEDAGIKINLRSVDS-KTLDSLVGEWKYDLALSGHGGLGGDPA 416
                                       4...455789**********************.9**9***************99988885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3670.90
//
Query:       gi|330509062|ref|YP_004385490.1|  [L=156]
Description: hypothetical protein MCON_3439 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1198.99
//
Query:       gi|330509063|ref|YP_004385491.1|  [L=250]
Description: CoB--CoM heterodisulfide reductase subunit E [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00058   19.5   8.9    0.00058   19.5   8.9    3.3  3  Nitrate_red_gam  Nitrate reductase gamma subunit
  ------ inclusion threshold ------
       0.29   11.7   3.3       0.61   10.6   3.3    1.4  1  DUF4808          Domain of unknown function (DUF4808)


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 ?   -3.3   0.1      0.58   5.2e+03      11      23 ..      19      31 ..       9      40 .. 0.57
   2 ?    2.1   1.0     0.014   1.2e+02     103     148 ..      77     122 ..      54     138 .. 0.74
   3 !   19.5   8.9   6.5e-08   0.00058      91     208 ..     140     243 ..     120     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.58
                   Nitrate_red_gam 11 valavlvvgsllr 23
                                      ++lav++ g +++
  gi|330509063|ref|YP_004385491.1| 19 IVLAVWIYGIYFN 31
                                      4444444444444 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.014
                   Nitrate_red_gam 103 llLllRRltnkrvraatsasDkvvlllLllqillGllttlvsaldy 148
                                       +lLl R l+++ vr + ++s ++ +l+L++   lGl+  +v+++++
  gi|330509063|ref|YP_004385491.1|  77 VLLLRRTLARSPVRWVMHMSMFYGFLALAALSGLGLMLDIVEHFNL 122
                                       4555555788899999999999999999999999999999988866 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 6.5e-08
                   Nitrate_red_gam  91 GliagvlalvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlvsaldygseretispwlrslltlqp 167
                                         ++g l+l+G ++ + RR+  k vr +tsa D +++ +++l +++G+++ ++                 +  +l  
  gi|330509063|ref|YP_004385491.1| 140 FDVFGYLLLFGSTIAISRRILIKFVRDNTSAYDALLIGAVFLITVTGFYAEWMR----------------GNSFLVG 200
                                       3579***********************************999999999876654................3333444 PP

                   Nitrate_red_gam 168 d.aellaevplifklHvllglllfa.lfPFtrLvHvlsapleY 208
                                       +  e+   +p +  +H+ll+l lfa ++P+++ +Hv+++p++ 
  gi|330509063|ref|YP_004385491.1| 201 NmFEYPIYAPHFALIHTLLALGLFAlILPWSKYIHVIATPMTL 243
                                       436777788899999******9997368***********9975 PP

>> DUF4808  Domain of unknown function (DUF4808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.3   6.9e-05      0.61       7      29 ..      14      36 ..      10      39 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.9e-05
                           DUF4808  7 vlivvlvLilWvaaialFfnrWG 29
                                      +l+ v+vL +W+  i + f++WG
  gi|330509063|ref|YP_004385491.1| 14 ILLTVIVLAVWIYGIYFNFKKWG 36
                                      78899*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1813.13
//
Query:       gi|330509064|ref|YP_004385492.1|  [L=456]
Description: CoB--CoM heterodisulfide reductase iron-sulfur subunit D [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.7e-27   93.2   9.3    3.4e-13   49.6   0.1    2.7  3  CCG          Cysteine-rich domain
    9.9e-09   35.5   3.8    9.9e-09   35.5   3.8    2.8  3  Fer4_8       4Fe-4S dicluster domain
    1.5e-06   28.2   4.5    1.5e-06   28.2   4.5    2.9  3  Fer4_10      4Fe-4S dicluster domain
    2.8e-06   27.8   4.5    2.8e-06   27.8   4.5    3.0  4  Fer4_17      4Fe-4S dicluster domain
    3.3e-06   27.2   4.9    3.3e-06   27.2   4.9    3.0  3  Fer4_9       4Fe-4S dicluster domain
    8.7e-05   23.4   4.4    8.7e-05   23.4   4.4    2.5  2  Fer4_16      4Fe-4S double cluster binding domain
    0.00027   21.4   8.7    0.00027   21.4   8.7    2.8  2  Fer4_7       4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.16   12.8  10.0          7    7.6   0.1    4.3  4  Fer4_22      4Fe-4S dicluster domain
       0.54    9.8   0.0       0.54    9.8   0.0    3.2  4  zf-PHD-like  PHD/FYVE-zinc-finger like domain
        3.6    7.8   8.8         12    6.1   1.4    2.8  2  Fer4_18      4Fe-4S dicluster domain
        4.2    7.6  12.5        5.2    7.3   0.5    3.3  4  Fer4_21      4Fe-4S dicluster domain
        4.6    8.4  17.2       0.71   11.0   3.8    3.1  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 ?   -3.3   0.1       7.5   1.1e+04      72      81 ..      90      99 ..      77     101 .. 0.67
   2 !   48.9   1.1   3.9e-16   5.9e-13       2      80 ..     168     246 ..     167     249 .. 0.98
   3 !   49.6   0.1   2.3e-16   3.4e-13       1      83 [.     292     385 ..     292     387 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.5
                               CCG 72 aivtacpgCl 81
                                      + +t+c+ C 
  gi|330509064|ref|YP_004385492.1| 90 YYCTTCGVCG 99
                                      4568888886 PP

  == domain 2  score: 48.9 bits;  conditional E-value: 3.9e-16
                               CCG   2 ayfdgChllraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtac 77 
                                       +yf gC  + +++++++ a+ ++l++l++++  l ++e+CC ++ +r+g+ e++ + a +nv++++++ga+ ++ ac
  gi|330509064|ref|YP_004385492.1| 168 VYFAGC-TAAYRQQALGVATVRILNKLNADFAMLgKDEWCCASAMVRTGQREVMAEHAVHNVDALKDAGAKTVLFAC 243
                                       7*****.9********************************************************************* PP

                               CCG  78 pgC 80 
                                       +gC
  gi|330509064|ref|YP_004385492.1| 244 AGC 246
                                       *** PP

  == domain 3  score: 49.6 bits;  conditional E-value: 2.3e-16
                               CCG   1 vayfdgChllraa.........ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetae 66 
                                       v+y+d+Ch +r+           ++ r+ l+ +++ ++ ++ ++ e + CCGaggg++   + la+++ak +v   e
  gi|330509064|ref|YP_004385492.1| 292 VTYHDPCHNGRHLmheigkdwaFEASRECLESIPGLKFKDMLRNrELQRCCGAGGGVKAGIPdLALDMAKARVMDGE 368
                                       89*******99999********9*********************************9999777************** PP

                               CCG  67 etgadaivtacpgCllq 83 
                                       e++ad+i ++cp+C  +
  gi|330509064|ref|YP_004385492.1| 369 EVKADVISSTCPFCRRN 385
                                       **************876 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   3.8   6.6e-12   9.9e-09       2      65 .]      23     106 ..      22     106 .. 0.77
   2 ?   -1.4   0.2       2.2   3.2e+03      44      54 ..     233     246 ..     204     248 .. 0.57
   3 ?   -0.6   0.0       1.3   1.9e+03      13      30 ..     377     395 ..     374     428 .. 0.71

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 6.6e-12
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvlee.....................eealwsCttcgaC 57 
                                       ++ C++C+ C++ Cp++  + +++  ++  +++  ++e + ++                      e +++Cttcg C
  gi|330509064|ref|YP_004385492.1|  23 VDGCNRCQECMKWCPTFAVRPDRPGITPMYKNA-RWRELMAKNhslrakifggkpleedemklfTEDVYYCTTCGVC 98 
                                       678************999988766666666666.4444444445666677777777777777889************ PP

                            Fer4_8  58 tevCpvgi 65 
                                        +vC  gi
  gi|330509064|ref|YP_004385492.1|  99 GTVCEAGI 106
                                       ****9887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                            Fer4_8  44 e...eealwsCttc 54 
                                       +   ++ l++C +c
  gi|330509064|ref|YP_004385492.1| 233 DagaKTVLFACAGC 246
                                       14447778888887 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.3
                            Fer4_8  13 saCpvlrrtk.khlldarg 30 
                                       s+Cp++rr   + ++da+ 
  gi|330509064|ref|YP_004385492.1| 377 STCPFCRRNImDGRNDAKS 395
                                       6899999987333444443 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   4.5     1e-09   1.5e-06       5      55 ..      22     102 ..      19     103 .. 0.86
   2 ?   -2.5   0.0       3.9   5.8e+03      39      48 ..     237     246 ..     220     248 .. 0.63
   3 ?   -0.4   0.1      0.84   1.3e+03      32      49 ..     366     383 ..     339     395 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1e-09
                           Fer4_10   5 dddtCirCgkCvkaCPadl.............................tsvgakg.easeeeavrkkvekCtgcgaC 51 
                                       + d C rC++C+k CP+ +                             +  g+k+ e++e +   ++v+ Ct+cg C
  gi|330509064|ref|YP_004385492.1|  22 EVDGCNRCQECMKWCPTFAvrpdrpgitpmyknarwrelmaknhslraKIFGGKPlEEDEMKLFTEDVYYCTTCGVC 98 
                                       6789*************88*****************************555555505555555555*********** PP

                           Fer4_10  52 veaC 55 
                                         +C
  gi|330509064|ref|YP_004385492.1|  99 GTVC 102
                                       **** PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.9
                           Fer4_10  39 rkkvekCtgc 48 
                                       ++++ +C gc
  gi|330509064|ref|YP_004385492.1| 237 KTVLFACAGC 246
                                       4455666665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.84
                           Fer4_10  32 aseeeavrkkvekCtgcg 49 
                                       + ee + ++ ++ C++c 
  gi|330509064|ref|YP_004385492.1| 366 DGEEVKADVISSTCPFCR 383
                                       455555666778888885 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   4.5   1.9e-09   2.8e-06       2      60 ..      26     106 ..      25     107 .. 0.68
   2 ?   -0.2   0.3         1   1.5e+03      16      49 ..     211     246 ..     204     248 .. 0.57
   3 ?   -3.0   0.1       7.6   1.1e+04      35      49 ..     330     344 ..     317     346 .. 0.71
   4 ?   -3.2   0.1       9.1   1.4e+04      12      17 ..     379     384 ..     376     396 .. 0.65

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.9e-09
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepk.kllraakl..................glleeaeke....ekaslCieCgeCerk 55 
                                       C++C+ C++ Cp+++ ++++p  +++++ +                   + lee e +    e +  C++Cg C ++
  gi|330509064|ref|YP_004385492.1|  26 CNRCQECMKWCPTFAVRPDRPGiTPMYKNARwrelmaknhslrakifggKPLEEDE-MklftEDVYYCTTCGVCGTV 101
                                       ****************8887664455552223545555555666556542333332.2467789************* PP

                           Fer4_17  56 CPqgl 60 
                                       C +g+
  gi|330509064|ref|YP_004385492.1| 102 CEAGI 106
                                       *9987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1
                           Fer4_17  16 eaydnepkkllraaklglleeaeke...ekaslCieC 49 
                                       + +   +++++++ +++ +++ ++    ++   C++C
  gi|330509064|ref|YP_004385492.1| 211 MVRTG-QREVMAEHAVHNVDALKDAgakTVLFACAGC 246
                                       44444.4445555555555555444443789999999 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 7.6
                           Fer4_17  35 eeaekeekaslCieC 49 
                                       +++ ++++ ++C++ 
  gi|330509064|ref|YP_004385492.1| 330 KDMLRNRELQRCCGA 344
                                       456667788888875 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 9.1
                           Fer4_17  12 Cpsyea 17 
                                       Cp++++
  gi|330509064|ref|YP_004385492.1| 379 CPFCRR 384
                                       666655 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   4.9   2.2e-09   3.3e-06       2      49 ..      26     105 ..      25     108 .. 0.97
   2 ?   -0.9   0.4       1.3   1.9e+03      18      39 ..     221     246 ..     204     248 .. 0.51
   3 ?   -2.4   0.0       3.8   5.7e+03      34      40 ..     377     383 ..     358     393 .. 0.65

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.2e-09
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase................................eaCigCgaCveaC 46 
                                       C++C++C++ Cp+ +v++d+ + +  +++a++                                  C++Cg C  +C
  gi|330509064|ref|YP_004385492.1|  26 CNRCQECMKWCPTFAVRPDRPGITPMYKNARWrelmaknhslrakifggkpleedemklftedvYYCTTCGVCGTVC 102
                                       ***************************99999********************************89*********** PP

                            Fer4_9  47 pkg 49 
                                       + g
  gi|330509064|ref|YP_004385492.1| 103 EAG 105
                                       987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                            Fer4_9  18 vedaaerkarlraase.............eaCigC 39 
                                        e+a++         +              aC gC
  gi|330509064|ref|YP_004385492.1| 221 AEHAVH---------NvdalkdagaktvlFACAGC 246
                                       333333.........23333334447777778888 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.8
                            Fer4_9  34 eaCigCg 40 
                                       + C +C+
  gi|330509064|ref|YP_004385492.1| 377 STCPFCR 383
                                       3466664 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 !   23.4   4.4   5.9e-08   8.7e-05       2      65 ..      26     103 ..      25     105 .. 0.70
   2 ?   -2.4   0.1       6.6   9.9e+03      44      57 ..     233     246 ..     205     248 .. 0.44

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.9e-08
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy.............ntaekkdlaedeekckkq..eaitgCdiCqdv 63 
                                       C +C++C++ CPt a++ + ++ i +  + +              +  + k l+ede k   +  + +t C++C +v
  gi|330509064|ref|YP_004385492.1|  26 CNRCQECMKWCPTFAVRPD-RPGITPMYKNARwrelmaknhslraKIFGGKPLEEDEMKLFTEdvYYCTTCGVCGTV 101
                                       *****************88.233322222121234455566777788899999999988553333788********* PP

                           Fer4_16  64 CP 65 
                                       C 
  gi|330509064|ref|YP_004385492.1| 102 CE 103
                                       *6 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.6
                           Fer4_16  44 deekckkqeaitgC 57 
                                       d+ +++   a++gC
  gi|330509064|ref|YP_004385492.1| 233 DAGAKTVLFACAGC 246
                                       22222223333444 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   8.7   1.8e-07   0.00027       2      51 ..      26     105 ..      25     106 .. 0.64
   2 ?   -2.4   0.0         5   7.5e+03      30      42 ..     371     383 ..     353     387 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.8e-07
                            Fer4_7   2 CigCgaCvaaCpvkaield..........eeenek........................gtekveidpekClgCgaC 44 
                                       C  C+ C++ Cp+ a++ d               +                        +++  + d  +C++Cg+C
  gi|330509064|ref|YP_004385492.1|  26 CNRCQECMKWCPTFAVRPDrpgitpmyknA----RwrelmaknhslrakifggkpleedEMKLFTEDVYYCTTCGVC 98 
                                       ************999998844443322220....13333333334444444444443335555599999******** PP

                            Fer4_7  45 vavCPtg 51 
                                        +vC +g
  gi|330509064|ref|YP_004385492.1|  99 GTVCEAG 105
                                       ****987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5
                            Fer4_7  30 kveidpekClgCg 42 
                                       k+++ +++C +C+
  gi|330509064|ref|YP_004385492.1| 371 KADVISSTCPFCR 383
                                       4455566777775 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.3     0.019        29      78      94 ..      22      38 ..       5      43 .. 0.70
   2 ?    7.6   0.1    0.0047         7      78      96 .]      88     106 ..      47     106 .. 0.79
   3 ?    2.3   0.1      0.21   3.1e+02      53      88 ..     211     249 ..     186     254 .. 0.73
   4 ?    0.5   0.0      0.76   1.1e+03      37      86 ..     295     345 ..     286     351 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.019
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                      +  gC  C  C+++cp+
  gi|330509064|ref|YP_004385492.1| 22 EVDGCNRCQECMKWCPT 38
                                      55566666666666664 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0047
                           Fer4_22  78 gesgCvGCgRCieacpvki 96 
                                       + + C+ Cg C ++c ++i
  gi|330509064|ref|YP_004385492.1|  88 DVYYCTTCGVCGTVCEAGI 106
                                       6778999999999998765 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.21
                           Fer4_22  53 nvrkekkerlrqrllhklsefkekf...gesgCvGCgRC 88 
                                        vr+ ++e + ++ +h +  +k+        +C GC R 
  gi|330509064|ref|YP_004385492.1| 211 MVRTGQREVMAEHAVHNVDALKDAGaktVLFACAGCIRN 249
                                       678888888888889988877776621145577777764 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.76
                           Fer4_22  37 wdsClleeftkvaggenvr.kekkerlrqrllhklsefkekfgesgCvGCg 86 
                                       +d C+  ++ +++ g++   + ++e l++    k++++ ++ + + C+G g
  gi|330509064|ref|YP_004385492.1| 295 HDPCHNGRHLMHEIGKDWAfEASRECLESIPGLKFKDMLRNRELQRCCGAG 345
                                       56777777776666655441444455566667899999999******9988 PP

>> zf-PHD-like  PHD/FYVE-zinc-finger like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4       1.5   2.2e+03      70      86 ..      24      40 ..      18      45 .. 0.70
   2 ?   -3.2   0.2       3.7   5.6e+03      70      83 ..      90     103 ..      79     107 .. 0.75
   3 ?    9.8   0.0   0.00036      0.54       6      36 ..     158     188 ..     153     215 .. 0.81
   4 ?    1.3   0.1      0.15   2.2e+02     105     132 ..     223     250 ..     206     260 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                       zf-PHD-like 70 dvCqeCkeegksckpfr 86
                                      d C++C+e  k c +f 
  gi|330509064|ref|YP_004385492.1| 24 DGCNRCQECMKWCPTFA 40
                                      56777777777777665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.7
                       zf-PHD-like  70 dvCqeCkeegksck 83 
                                         C++C   g++c+
  gi|330509064|ref|YP_004385492.1|  90 YYCTTCGVCGTVCE 103
                                       46888888888886 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00036
                       zf-PHD-like   6 eskdeekgqlvyCqGCslsyhkaClGkRsaR 36 
                                        +k  e g++vy  GC+++y ++ lG  + R
  gi|330509064|ref|YP_004385492.1| 158 DAKVDESGEIVYFAGCTAAYRQQALGVATVR 188
                                       4556789*******************98877 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.15
                       zf-PHD-like 105 dPiteveeelinnaenvlfRCaeCkraw 132
                                         + +v++ +   a++vlf Ca C r  
  gi|330509064|ref|YP_004385492.1| 223 HAVHNVDALKDAGAKTVLFACAGCIRNS 250
                                       5556666666667899999999998865 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.0      0.02        31      57      73 ..      22      38 ..       3      44 .. 0.83
   2 ?    6.1   1.4     0.008        12      56      76 ..      87     107 ..      44     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.02
                           Fer4_18 57 gagdcidcescvkvcPt 73
                                      ++  c  c+ c+k cPt
  gi|330509064|ref|YP_004385492.1| 22 EVDGCNRCQECMKWCPT 38
                                      5678************9 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.008
                           Fer4_18  56 kgagdcidcescvkvcPtgid 76 
                                       +++  c++c++c +vc  gi 
  gi|330509064|ref|YP_004385492.1|  87 EDVYYCTTCGVCGTVCEAGIK 107
                                       55667***********99985 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.6    0.0036       5.3      39      53 ..      24      38 ..      14      42 .. 0.74
   2 ?    7.3   0.5    0.0035       5.2      40      51 ..      91     102 ..      76     113 .. 0.72
   3 ?   -1.4   0.1       1.8   2.8e+03      28      45 ..     230     247 ..     219     252 .. 0.64
   4 ?   -3.5   0.0       8.1   1.2e+04      36      44 ..     374     382 ..     362     387 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0036
                           Fer4_21 39 deCvGCnlCssvCPv 53
                                      d C  C+ C++ CP+
  gi|330509064|ref|YP_004385492.1| 24 DGCNRCQECMKWCPT 38
                                      678888888888885 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0035
                           Fer4_21  40 eCvGCnlCssvC 51 
                                        C+ C +C +vC
  gi|330509064|ref|YP_004385492.1|  91 YCTTCGVCGTVC 102
                                       688888888877 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.8
                           Fer4_21  28 idaktvlkvvedeCvGCn 45 
                                         +++ +k+v   C GC 
  gi|330509064|ref|YP_004385492.1| 230 ALKDAGAKTVLFACAGCI 247
                                       445556666777888885 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 8.1
                           Fer4_21  36 vvedeCvGC 44 
                                       v++++C  C
  gi|330509064|ref|YP_004385492.1| 374 VISSTCPFC 382
                                       444444444 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.8   0.00047      0.71       1      13 [.      26      38 ..      26      40 .. 0.93
   2 ?    1.9   5.5      0.37   5.6e+02       1      11 [.      92     102 ..      92     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00047
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+ C+ C+++CP+
  gi|330509064|ref|YP_004385492.1| 26 CNRCQECMKWCPT 38
                                      99**********7 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.37
                            Fer4_3   1 CtgCgaCvevC 11 
                                       Ct Cg C  vC
  gi|330509064|ref|YP_004385492.1|  92 CTTCGVCGTVC 102
                                       *********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); 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:                        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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3006.64
//
Query:       gi|330509065|ref|YP_004385493.1|  [L=384]
Description: cytidine deaminase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-58  198.1   0.0      2e-58  197.6   0.0    1.2  1  F420_ligase      F420-0:Gamma-glutamyl ligase
      7e-14   51.5   0.2    1.2e-13   50.7   0.2    1.4  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    5.7e-09   36.3   0.5    1.2e-08   35.3   0.5    1.5  1  dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-
  ------ inclusion threshold ------
      0.082   12.5   2.5        3.7    7.1   0.3    2.2  2  LmjF365940-deam  A distinct subfamily of CDD/CDA-like deamina


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.6   0.0   4.4e-62     2e-58       1     244 []       5     220 ..       5     220 .. 0.98

  Alignments for each domain:
  == domain 1  score: 197.6 bits;  conditional E-value: 4.4e-62
                                       -..-----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H..... CS
                       F420_ligase   1 giktplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrn 77 
                                       gik +l+ +gddl+e +v +++++g  ++dgDi+vv+e++va++eg++v+l++i+p++ A+++a ++ ++dp     
  gi|330509065|ref|YP_004385493.1|   5 GIKSDLLMPGDDLVEFLVRAMNRSGQAFQDGDILVVSESIVATSEGRVVDLDEIQPGDLAISLAGQY-KKDP----- 75 
                                       799****************************************************************.****..... PP

                                       .............HHHHHHHHTEEEEEE-...S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHH CS
                       F420_ligase  78 rfsliLkalakatrkvevvlsepsdevgn...qlidekytdevlvklGllgsnagidesnveegllkllPedpdksa 151
                                                    r++e++l+e++++vg    ++++ +         G+l  nagid+sn++ g+++l+P dp+ sa
  gi|330509065|ref|YP_004385493.1|  76 -------------REMELILRESDEIVGGipgVVLTLN--------NGFLFPNAGIDNSNAPPGHVVLFPADPKGSA 131
                                       .............***************9998888888........7****************************** PP

                                       HHHHHHHHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHH CS
                       F420_ligase 152 eeikkklkertgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladL 228
                                        +i++++++  gk+++V+i   D+++++++l++++va+++sglea+ d rg+kdl+g+el++t +av+d+l s+a++
  gi|330509065|ref|YP_004385493.1| 132 IAIRERMAN--GKKIGVII--GDSRTHPLRLGCVGVALACSGLEAVVDARGQKDLFGRELKITRKAVADNLVSAAQI 204
                                       *******76..********..******************************************************** PP

                                       HC-SSSS---EEEEES CS
                       F420_ligase 229 vsGsadegtPvvlvrg 244
                                       v+G++deg+P++++r+
  gi|330509065|ref|YP_004385493.1| 205 VMGEGDEGIPAAIIRD 220
                                       **************95 PP

>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.2   2.8e-17   1.2e-13       6      99 ..     259     357 ..     256     359 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 2.8e-17
                                       HHHHHHHHHHHHHH.TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEE.... CS
                   dCMP_cyt_deam_1   6 kllelalkaakeaq.kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyv.... 77 
                                       +l+e+a +a  +a+ ++s+f+VGa++++++  ++ + n e+a+    i+AE++Ai +a   g+ ++ +a+ +v    
  gi|330509065|ref|YP_004385493.1| 259 QLIECAGQAIARAYaPYSRFRVGAALLTKKGNVYSAGNIENASTGAGICAERVAISQAIASGEREF-EAIAIVgdgc 334
                                       78899999999*****************999****************************9965466.6777778*** PP

                                       .EE--BHHHHHHHHHHT-SEEEE CS
                   dCMP_cyt_deam_1  78 .tlePCsmCakaiiqsgikkvvv 99 
                                         ++PC+ C++ +i++g + +v+
  gi|330509065|ref|YP_004385493.1| 335 qPISPCGICRQSLIEFGEDIMVI 357
                                       9***************9766665 PP

>> dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.5   2.6e-12   1.2e-08      45     114 ..     258     328 ..     237     331 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.6e-12
                                       -HHHHHHHHHHTT-B-TTT---EEEEEEETTS-EEEEE-B--TTSTT-B-HHHHHHHHHHH.TT--GGGEE CS
                   dCMP_cyt_deam_2  45 delkeaAlaaanasyapyskcpsGvaLvtkdgkvyaGsyiEsaAfNpsLpPlqaAlvalvl.ggkefeeie 114
                                       d+l e A +a  ++yapys+   G aL tk+g+vy+   iE+a     + + ++A+ ++++ g++efe i 
  gi|330509065|ref|YP_004385493.1| 258 DQLIECAGQAIARAYAPYSRFRVGAALLTKKGNVYSAGNIENASTGAGICAERVAISQAIAsGEREFEAIA 328
                                       679999*******************************************************6667787775 PP

>> LmjF365940-deam  A distinct subfamily of CDD/CDA-like deaminases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3   0.00082       3.7      57      89 ..     288     320 ..     280     333 .. 0.79
   2 ?    5.1   0.1    0.0034        15     152     177 ..     335     357 ..     328     363 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00082
                   LmjF365940-deam  57 reelvrgvNlEvSmPtGSlCsErnaigkalasd 89 
                                       + +++ + N+E        C+Er ai++a+as 
  gi|330509065|ref|YP_004385493.1| 288 KGNVYSAGNIENASTGAGICAERVAISQAIASG 320
                                       5678889999976666679***********996 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0034
                   LmjF365940-deam 152 nPLkPCGaCeewLkkiaevnpdfkvl 177
                                        P+ PCG+C++ L    e + d++v+
  gi|330509065|ref|YP_004385493.1| 335 QPISPCGICRQSLI---EFGEDIMVI 357
                                       69********9885...444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2459.02
//
Query:       gi|330509066|ref|YP_004385494.1|  [L=421]
Description: dihydropteroate synthase [Methanosaeta concilii GP6]
Scores for complete 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-54  182.9   0.0      1e-53  182.5   0.0    1.2  1  Pterin_bind  Pterin binding enzyme
  ------ inclusion threshold ------
      0.018   14.5   0.1        3.1    7.2   0.1    2.5  2  PEP_mutase   Phosphoenolpyruvate phosphomutase


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 !  182.5   0.0   1.1e-57     1e-53       1     244 []      23     258 ..      23     258 .. 0.96

  Alignments for each domain:
  == domain 1  score: 182.5 bits;  conditional E-value: 1.1e-57
                                       EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEE CS
                       Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpis 77 
                                       mg++N++ +sf++g+ + + ++ala+ar++ +eGAdi+D+g+ st Pg+ +++ee e +r+   l++++d++d+ +s
  gi|330509066|ref|YP_004385494.1|  23 MGVINLSRESFYKGS-VASSNEALATARRLQDEGADIIDLGAVSTAPGSPPISEEVEKDRLFAALKEITDNLDIVVS 98 
                                       9***********955.569********************************************************** PP

                                       EE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHH CS
                       Pterin_bind  78 iDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearv 154
                                       +Dt +a++ae+Al++ga+ +Ndvsg+  dp+m++ vae++  +++m+++++p           ++ +++   l  +v
  gi|330509066|ref|YP_004385494.1|  99 VDTQRAKIAEKALSCGATCINDVSGLH-DPDMASKVAEYDGSLIIMASDQRP--------GDLPLLNQIIPLLGDKV 166
                                       ***************************.*********************433........5678999********** PP

                                       HHHHHTT--GGGEEEETTTTS...STTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHH CS
                       Pterin_bind 155 eaaeeaGvaperillDpgigf...gkteehnlellrrldelrealevpvllGvSrksflgrllelgkaeeRdagtaa 228
                                       ++a++aGva ++i +Dpgig      t+ ++l++l+ +d+l +a + pv+ ++Srk f+g+ l++ ++  R ag++a
  gi|330509066|ref|YP_004385494.1| 167 RQAVRAGVALNKISIDPGIGKwipVRTAAQDLAILDGFDRL-RAIGRPVVAALSRKTFIGESLNIPDPGGRLAGSLA 242
                                       *******************998899****************.99*****************998788********** PP

                                       HHHHHHHTT-SEEEES CS
                       Pterin_bind 229 flalaaaaGadivrVh 244
                                       +++ a+  Ga+ivr+h
  gi|330509066|ref|YP_004385494.1| 243 ATTVAVYLGAHIVRTH 258
                                       ***************9 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1   0.00034       3.1      21      78 ..      47     103 ..      44     109 .. 0.81
   2 ?    5.0   0.0    0.0016        14     163     201 ..     108     146 ..     102     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00034
                        PEP_mutase  21 sakiveeagfkalatsSlavaaslGvpDg.eelpleellaavraiaevvslPlivDled 78 
                                       +a+ +++ g++ + ++  av+++ G p + ee++ ++l+aa+++i++++++ ++vD + 
  gi|330509066|ref|YP_004385494.1|  47 TARRLQDEGADIIDLG--AVSTAPGSPPIsEEVEKDRLFAALKEITDNLDIVVSVDTQR 103
                                       6666666666666665..67888898887689************************875 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0016
                        PEP_mutase 163 raYaeAGAdgvfvpglqkdaeiaelvaavdvplnvvplk 201
                                       +  +  GA+++  +++ +d+++a+ va++d+ l++++++
  gi|330509066|ref|YP_004385494.1| 108 EKALSCGATCINDVSGLHDPDMASKVAEYDGSLIIMASD 146
                                       445667******************************953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 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:                        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 0.29s 00:00:00.85 Elapsed: 00:00:00.57
# Mc/sec: 2235.03
//
Query:       gi|330509067|ref|YP_004385495.1|  [L=261]
Description: ABC transporter [Methanosaeta concilii GP6]
Scores for complete 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  28.4    4.5e-11   42.6  28.4    1.3  1  ABC2_membrane  ABC-2 type transporter


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6  28.4   2.5e-15   4.5e-11      19     209 ..      30     218 ..      10     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 2.5e-15
                     ABC2_membrane  19 slgllwrliqplllalvfgtvfgnlgnsedglnr..pgllffsvlflafsaltsvapvferergvlerelvsplysl 93 
                                       +l+ +w+l++ l ++l+  ++  +    e+ +++  +g ++ ++l +a ++  + +++f++  ++++  + +p+ + 
  gi|330509067|ref|YP_004385495.1|  30 ELF-FWPLVNLLSIGLLTRFLMVD----ESMVSFllVGSIALTILQVA-QMDVAYVLLFDMWSKSIKNTFIAPI-HS 99 
                                       233.67777777777777777762....23333355************.8877888******************.99 PP

                     ABC2_membrane  94 sayvlakvlvelpvsllqalifllivyflvgldlsrf....flflllllltalaasslgllisalapsfedasqlas 166
                                          +++++++ ++++ ++ +i+  i+++l++++ +++     l++l+ ++++ a++++ ++is+l+  +  a + a 
  gi|330509067|ref|YP_004385495.1| 100 RHLIFGSLFFGIMRGSVVFAILASISFYLFDFRFQAGglipPLIFLAGVFSMAAIIGITVCISILTFGQ-KADVAAW 175
                                       9999******************************95513334444444555555556666777666554.4555555 PP

                     ABC2_membrane 167 lvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                        +  ++ll+sG+++p+d +p +lq +a++ Plty++e +rs++
  gi|330509067|ref|YP_004385495.1| 176 SLSGLILLFSGIYYPVDVLPFFLQVLARAIPLTYFLEYYRSIF 218
                                       6667778**********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.42
# Mc/sec: 1860.55
//
Query:       gi|330509068|ref|YP_004385496.1|  [L=345]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-27   97.1   0.0    2.4e-27   96.1   0.0    1.5  1  ABC_tran  ABC transporter
    1.5e-13   51.3   4.0    9.2e-08   32.2   0.3    2.3  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    9.1e-05   22.3   0.5       0.29   10.8   0.0    2.3  2  AAA_15    AAA ATPase domain
    9.8e-05   22.0   0.1    0.00019   21.1   0.1    1.4  1  AAA_29    P-loop containing region of AAA domain
    0.00076   20.0   0.1     0.0013   19.2   0.1    1.5  1  AAA_23    AAA domain
     0.0022   18.7   0.6     0.0075   17.0   0.6    2.0  1  DUF4162   Domain of unknown function (DUF4162)
  ------ inclusion threshold ------
      0.025   14.8   0.0      0.041   14.1   0.0    1.4  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
      0.051   13.0   0.1        1.5    8.2   0.1    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain
      0.056   13.8   0.0       0.15   12.5   0.0    1.7  1  AAA_16    AAA ATPase domain
      0.074   13.0   0.0       0.23   11.4   0.0    1.8  2  AAA_5     AAA domain (dynein-related subfamily)
        0.1   11.6   0.0        0.2   10.6   0.0    1.4  1  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.18   11.5   0.0       0.36   10.5   0.0    1.4  1  AAA_24    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   0.0   1.6e-30   2.4e-27       1     136 [.      33     176 ..      33     177 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 1.6e-30
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ +sl++ +ge+ +++G+nG+GK+tL+++++ l  p+eG++ + g + ++ ++ + rk i + + +p++   ltvr
  gi|330509068|ref|YP_004385496.1|  33 LEGISLDIDRGEIFGLLGPNGSGKTTLISIFSTLIYPEEGSLSILGLNARR-DRGEIRKIINISTAKPNFPWSLTVR 108
                                       6789*****************************************999999.9************************ PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en               ++ +e+ ++ ++l e +d +     ++LS G kqr++la+a+l++p+ll+lDEpt
  gi|330509068|ref|YP_004385496.1| 109 ENlvhysmlyglyglGLNRTVEDQIDAFELGEYRDVKF----ENLSTGLKQRLSLAKAMLNHPRLLFLDEPT 176
                                       **************9999**************999998....*****************************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 !   21.2   1.2   1.4e-07   0.00021       2      50 ..      46      96 ..      45     112 .. 0.78
   2 !   32.2   0.3   6.1e-11   9.2e-08     186     298 ..      81     208 ..      70     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.4e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl..drdvegltdelsggggirkipslld 50
                                       +l GpNgsGK++L+ +++ l      + ++ + + ++++g+irki++ ++
  gi|330509068|ref|YP_004385496.1| 46 FGLLGPNGSGKTTLISIFSTLIYPeeGSLSILGLNARRDRGEIRKIINIST 96
                                      689***************999665776666677777777777777776655 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 6.1e-11
                            AAA_21 186 qrlvrslklveielsdlgegeeliasvderlrer.....................gvvflengdgqelparelSdGt 241
                                        r+ r+  +  i++s+     + ++++++  re+                      +  +e g ++++ + +lS G 
  gi|330509068|ref|YP_004385496.1|  81 ARRDRGEIRKIINISTA----KPNFPWSLTVRENlvhysmlyglyglglnrtvedQIDAFELGEYRDVKFENLSTGL 153
                                       55555555555555555....46666667777777788888888888888888889999****************** PP

                            AAA_21 242 krllalltallralkkgsllliDEpEngLHP...kllrrllellkelsrngaQviltTHS 298
                                       k+ l l+ a+l  +   +ll++DEp +gL+P   + ++ l++ + ++  +g+ vi++TH 
  gi|330509068|ref|YP_004385496.1| 154 KQRLSLAKAMLNHP---RLLFLDEPTTGLDPdmsAKTHDLIRRIHDE--EGISVIMSTHY 208
                                       ***********877...**************4444446666555444..56********5 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.2   0.00054      0.81      18      46 ..      37      66 ..      32      73 .. 0.78
   2 !   10.8   0.0   0.00019      0.29     287     364 ..     136     207 ..      85     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00054
                            AAA_15 18 eidlsee.ltvliGkNnsGKSsilealdlF 46
                                      ++d++   +  l G+N+sGK++++ ++  +
  gi|330509068|ref|YP_004385496.1| 37 SLDIDRGeIFGLLGPNGSGKTTLISIFSTL 66
                                      5555555577899***********999766 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00019
                            AAA_15 287 k...ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQvi 360
                                       +   +  ++++++ ++G+++ l+l+   l+            +l+++EP + L p++    ++l++++ +++   vi
  gi|330509068|ref|YP_004385496.1| 136 FelgEYRDVKFENLSTGLKQRLSLAKAMLNHP---------RLLFLDEPTTGLDPDMSAKTHDLIRRIHDEEGISVI 203
                                       15667778999999999999998875555444.........56*****************************99*** PP

                            AAA_15 361 itTH 364
                                       ++TH
  gi|330509068|ref|YP_004385496.1| 204 MSTH 207
                                       **** PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   1.3e-07   0.00019      16      50 ..      37      71 ..      31      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +++id+ +++ l Gp+GsGK+Tl+  +++l++p++
  gi|330509068|ref|YP_004385496.1| 37 SLDIDRGEIFGLLGPNGSGKTTLISIFSTLIYPEE 71
                                      67888777999*********************986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1     9e-07    0.0013      16      46 ..      39      70 ..      25     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9e-07
                            AAA_23 16 dFsk.gltlItGpNGaGKTTildAiklaLyge 46
                                      d ++  ++ + GpNG+GKTT++  +    y e
  gi|330509068|ref|YP_004385496.1| 39 DIDRgEIFGLLGPNGSGKTTLISIFSTLIYPE 70
                                      554425999*************9888888765 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.6     5e-06    0.0075      30      80 ..     289     343 ..     232     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5e-06
                                       -EEEE-TT....S-EEEEE--.---------------EEEEEEEE---HHHHHHHH CS
                           DUF4162  30 veeveeeg....gelelkled.eeaanellkaltsgveirsFeeeePsLndIFiek 80 
                                       +e+ + ++    ++le+ +++ e++  ++lk   ++++i  ++ eeP L+d+F+e+
  gi|330509068|ref|YP_004385496.1| 289 IEVTKPAEgpvdRQLEILMDSnEDSLDRILKSF-QDAKILDINIEEPDLEDVFLEL 343
                                       5555444445657899999988***********.********************97 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.8e-05     0.041      47      89 ..     150     192 ..     139     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                           SbcCD_C  47 aaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                         +l + +s a++  +++rl+fLDE   +lD++++a+  +l++
  gi|330509068|ref|YP_004385496.1| 150 STGLKQRLSLAKAMLNHPRLLFLDEPTTGLDPDMSAKTHDLIR 192
                                       56788888887667899*******************9998876 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1     0.001       1.5      28      41 ..      47      60 ..      26      67 .. 0.83
   2 ?    2.5   0.0     0.055        82     134     201 ..     146     209 ..     118     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.001
                                      EEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxx RF
                             SMC_N 28 aivGpNGSGKsnll 41
                                       ++GpNGSGK+ l+
  gi|330509068|ref|YP_004385496.1| 47 GLLGPNGSGKTTLI 60
                                      689********987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.055
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreem 201
                                        e+LS G k+     L +A  + +   l +lDe    LD    +k  +l+++ +++  + vi  ++ m
  gi|330509068|ref|YP_004385496.1| 146 FENLSTGLKQ----RLSLAKAMLNHPRLLFLDEPTTGLDPDMSAKTHDLIRRIHDEEGISVIMSTHYM 209
                                       5566666665....4556677888888999********************987777665555554444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.8e-05      0.15      23      99 ..      42     143 ..      31     199 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.8e-05
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesa.........................ipysala 73 
                                       r+e+  l G+ G+GK++l+  + + +  ++g + + g + + +++                         ++ys+l 
  gi|330509068|ref|YP_004385496.1|  42 RGEIFGLLGPNGSGKTTLISIFSTLIYPEEGSLsILGLNARRDRGeirkiinistakpnfpwsltvrenlVHYSMLY 118
                                       5678889************9999877777433334444443323333344444444444444444444444555555 PP

                            AAA_16  74 qalareellrqlldeaesaeleawre 99 
                                        +    +l r ++d+ ++ el+++r+
  gi|330509068|ref|YP_004385496.1| 119 GLY-GLGLNRTVEDQIDAFELGEYRD 143
                                       555.3355555555544444444444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.23       4      48 ..      48      95 ..      46     108 .. 0.86
   2 ?   -2.2   0.0       2.6   3.9e+03      85      87 ..     187     189 ..     151     228 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                      EE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--. CS
                             AAA_5  4 LvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreik 48
                                      L+Gp G+gK++l+  ++ ++   + ++ +  l+++  + +++  ++i+
  gi|330509068|ref|YP_004385496.1| 48 LLGPNGSGKTTLISIFSTLIypeEGSLSILGLNARRDRGEIRKIINIS 95
                                      89******************9988888888888888888888888875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                                       HHH CS
                             AAA_5  85 Lls 87 
                                        + 
  gi|330509068|ref|YP_004385496.1| 187 THD 189
                                       333 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00014       0.2      14      53 ..      28      67 ..      15      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHH CS
                              MeaB 14 eakellerllakaGraqvvGltGvPGaGkstlvealglel 53
                                      +ak++le ++ +  r +  Gl G  G+Gk tl++ + + +
  gi|330509068|ref|YP_004385496.1| 28 SAKTVLEGISLDIDRGEIFGLLGPNGSGKTTLISIFSTLI 67
                                      899*******************************998765 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   0.00024      0.36       6      35 ..      47      74 ..      43     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                            AAA_24  6 liyGpsgiGKTtlakelgpkplfidtekGl 35
                                       + Gp+g+GKTtl++ +  ++l+   e++l
  gi|330509068|ref|YP_004385496.1| 47 GLLGPNGSGKTTLISIF--STLIYPEEGSL 74
                                      589*************9..77776666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2134.95
//
Query:       gi|330509069|ref|YP_004385497.1|  [L=326]
Description: hypothetical protein MCON_3447 [Methanosaeta concilii GP6]
Scores for complete 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   21.0   0.0       0.16   12.2   0.0    2.7  3  CARDB        CARDB
  ------ inclusion threshold ------
      0.051   13.8   0.0         13    6.1   0.0    2.5  2  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
       0.15   11.7   0.0       0.24   11.0   0.0    1.3  1  TraK         TraK protein


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 ?   -2.5   0.0       1.1   6.3e+03      23      33 ..      54      64 ..      37      66 .. 0.74
   2 !    5.8   0.0    0.0028        17      50      90 ..     110     151 ..      88     157 .. 0.84
   3 !   12.2   0.0   2.7e-05      0.16       4      76 ..     184     257 ..     181     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                                      EEEEEEE-SSS CS
                             CARDB 23 itvtvkNqGta 33
                                      ++++++NqG +
  gi|330509069|ref|YP_004385497.1| 54 LRISIANQGRI 64
                                      56788898865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0028
                                       EEEEESEE-CTEEEEEEEEEE-S.-S-CEEEEEEEESTT-SS CS
                             CARDB  50 gtvtvpsLaagesttvsftwtte.ategevtltvvvDpdnev 90 
                                       g + ++ L age ++ +f++ ++ +++g ++l + vD   +v
  gi|330509069|ref|YP_004385497.1| 110 GVQHIAILPAGEAKELQFNISIDqRASGWYDLPLRVDYVRQV 151
                                       56778999***************99************87776 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 2.7e-05
                                       EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S-S-C CS
                             CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtteateg 76 
                                       L +  +   s +++gee ++ + v+N G++  ++++++l++         + ++  L++ge ++ sf + +++ ++
  gi|330509069|ref|YP_004385497.1| 184 LRI--AGVQSHLYPGEEGSLIIAVENIGEDILPNCSASLIAAPPFRvksRDLPLGDLSPGEMASASFLVGVDRDAS 257
                                       555..55678899****************************9887777788999*************998884333 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 ?    6.1   0.0    0.0021        13      39      77 ..     109     146 ..     103     148 .. 0.85
   2 ?    5.3   0.0     0.004        24       3      73 ..     195     264 ..     193     269 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0021
                       NPCBM_assoc  39 vspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                       + ++ +a l++Ge+ e ++++++ ++a  G y++ +++ 
  gi|330509069|ref|YP_004385497.1| 109 SGVQHIAILPAGEAKELQFNISIDQRAS-GWYDLPLRVD 146
                                       55678889******************99.8998877765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.004
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaa..slapGetveatvkVtppagaaaGdyevt 73 
                                       pGe+ +l ++v n g++ + n s sl + +  +   v+ + ++  +l pGe ++a + V +  +a   +y++ 
  gi|330509069|ref|YP_004385497.1| 195 PGEEGSLIIAVENIGEDILPNCSASLIAAPPFR---VKSRDLPlgDLSPGEMASASFLVGVDRDASQEEYQLG 264
                                       566666666666666666666666666655566...3333344449*******************99999875 PP

>> TraK  TraK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.1e-05      0.24     159     230 ..     130     201 ..     119     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.1e-05
                              TraK 159 evrkrvvllkeaglrltrvreyeGeglrgeeyrlkNvskapmeLaekeflrpgvlavalerhnLapgettrv 230
                                       ++++r  ++ ++ lr+  vr+++ +   ge + l+  s++ ++L+   f +++ l +a  +++L pge+ ++
  gi|330509069|ref|YP_004385497.1| 130 SIDQRASGWYDLPLRVDYVRQVDVSVSDGEAFPLRQPSNQSLNLRVYAFGDKDDLRIAGVQSHLYPGEEGSL 201
                                       6789999*************************************************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.36s 00:00:01.04 Elapsed: 00:00:00.58
# Mc/sec: 1685.90
//
Query:       gi|330509070|ref|YP_004385498.1|  [L=268]
Description: cation ABC-3 transporter family protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-70  238.1  35.1    1.2e-70  238.0  35.1    1.0  1  ABC-3     ABC 3 transport family
    9.1e-08   31.5  35.9    1.3e-07   30.9  35.4    1.5  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.0  35.1   1.4e-74   1.2e-70       1     257 [.      10     266 ..      10     267 .. 0.99

  Alignments for each domain:
  == domain 1  score: 238.0 bits;  conditional E-value: 1.4e-74
                             ABC-3   1 qyeflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellkrk 77 
                                       qy+f++ al+a+++ ++ c+++g +v+l+++++++d+++Haa++G++l+y+lg+ +l+  + ++++ av++++++ +
  gi|330509070|ref|YP_004385498.1|  10 QYDFMRVALAAGLASAVLCGIIGIYVILNKIVFISDGIAHAAFGGIGLGYFLGFDPLIFGVGSAVLTAVGIGMVSGR 86 
                                       79*************************************************************************** PP

                             ABC-3  78 tklkedtaigivlsvflalglvlvslikkskvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfd 154
                                       ++++edtaig+ +++++alg++l++l+k+++ dl  yLfGnil+++ +d++li+ +++ ++ll+ +++ke+l+++fd
  gi|330509070|ref|YP_004385498.1|  87 ARVSEDTAIGVFMATGMALGVMLLTLSKGYARDLYGYLFGNILAVTINDVLLISGLTLAIMLLIYILYKEFLIMSFD 163
                                       ***************************************************************************** PP

                             ABC-3 155 eelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlll 231
                                       + + +++gl+vk l+lllla++a +vvv +++vG+i+viall+iP+a+ r+  r l s+++ +++lg ++v++Gl++
  gi|330509070|ref|YP_004385498.1| 164 PVYGEAIGLPVKSLRLLLLAMVAFSVVVLIKIVGIIMVIALLTIPGAISRQHLRGLPSIMAGSAVLGSIFVTVGLIV 240
                                       ***************************************************************************** PP

                             ABC-3 232 SyyldlatGavivlvatllfllallv 257
                                       Sy+ld+++Ga+i+l a+++f+l+ l+
  gi|330509070|ref|YP_004385498.1| 241 SYMLDVPSGATIILTAAIFFFLSTLY 266
                                       *********************99875 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9  35.4   1.5e-11   1.3e-07     104     307 ..      65     261 ..      20     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.5e-11
                             FecCD 104 plaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllneealesilfwllGslsgaswskvl 180
                                       pl++ +g+++ +++ + ++  +++a+      +G+ +++ + al  +ll+l ++  +++++ +l+G++  +++++vl
  gi|330509070|ref|YP_004385498.1|  65 PLIFGVGSAVLTAVGIGMV--SGRARVSEDTAIGVFMATGM-ALGVMLLTL-SKGYARDLYGYLFGNILAVTINDVL 137
                                       4444455544444444444..34444444455688877665.566666666.789********************** PP

                             FecCD 181 lllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltavavalvGpigFvGLi.vPhiarll 256
                                       l++ l+l+++ll+++l++++ +++++    +++G++v+ +rllll++va+ + v + +vG+i  ++L+ +P  +++ 
  gi|330509070|ref|YP_004385498.1| 138 LISGLTLAIMLLIYILYKEFLIMSFDPVYGEAIGLPVKSLRLLLLAMVAFSVVVLIKIVGIIMVIALLtIPGAISRQ 214
                                       ******************************************************************97357776666 PP

                             FecCD 257 vgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffi 307
                                         +   +++  sa+lG++++++  +++ +l    ++p g+ + l  a+ff+
  gi|330509070|ref|YP_004385498.1| 215 HLRGLPSIMAGSAVLGSIFVTVGLIVSYML----DVPSGATIILTAAIFFF 261
                                       66789999999***********99999988....67777777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1145  (0.063863); 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:                         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: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 1457.36
//
Query:       gi|330509071|ref|YP_004385499.1|  [L=253]
Description: cation ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete 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-29  100.8   0.0    1.8e-28   99.8   0.0    1.5  2  ABC_tran     ABC transporter
      3e-12   47.0   0.4    5.2e-05   23.2   0.1    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0024   18.0   0.1       0.11   12.8   0.1    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
     0.0028   17.4   0.0     0.0048   16.6   0.0    1.3  1  AAA_29       P-loop containing region of AAA domain
     0.0032   16.9   0.0       0.54    9.7   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
       0.02   14.6   0.1      0.087   12.5   0.0    1.8  2  AAA_15       AAA ATPase domain
       0.02   13.9   0.0      0.029   13.4   0.0    1.2  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.081   12.8   0.0       0.14   12.0   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
        0.1   13.1   0.0       0.15   12.5   0.0    1.2  1  AAA_23       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.8   0.0     9e-32   1.8e-28       1     137 []      21     167 ..      21     167 .. 0.90
   2 ?   -2.6   0.0       3.5     7e+03      46      67 ..     196     215 ..     178     234 .. 0.58

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 9e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS...--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe...pqlfpel 74 
                                       l++++lkl++   ++++G+nG GKStLlk+++gl kp++G+i++ g +      e +r ++g+lpq+   +q fp +
  gi|330509071|ref|YP_004385499.1|  21 LEDINLKLERADFLGLIGPNGGGKSTLLKVMLGLIKPDKGRIRIFGLEP-----EAARGRVGYLPQKtifDQNFPIK 92 
                                       689***************************************7776554.....66***********5444444444 PP

                                       BHHHH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                        v e                  ++++ ++ al+ +g+++ +d+ +      LSgG++qrv +ar+l+++p+llllDE
  gi|330509071|ref|YP_004385499.1|  93 -VLEVvqmgrfgrtglfrrygpADRNAAYCALEAVGMEDRADREI----GALSGGEQQRVFVARSLVSDPELLLLDE 164
                                       .5666999***********99888888************999999....**************************** PP

                                       TTT CS
                                       xxx RF
                          ABC_tran 135 pta 137
                                       pta
  gi|330509071|ref|YP_004385499.1| 165 PTA 167
                                       *97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.5
                                       TCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  46 gkdlkeqeleslrkeigvlpqe 67 
                                       ++d++   ++++  +i++l q 
  gi|330509071|ref|YP_004385499.1| 196 SHDITA--ISKYVGKIACLNQR 215
                                       444444..55555666666665 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 !   23.2   0.1   2.6e-08   5.2e-05       2      55 ..      34      81 ..      33     117 .. 0.76
   2 !   22.1   0.0   5.8e-08   0.00012     226     300 ..     128     200 ..     109     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.6e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpe 55
                                       +liGpNg GKS+LL+ + +l      +++++   + +g +++ ++   +y p 
  gi|330509071|ref|YP_004385499.1| 34 LGLIGPNGGGKSTLLKVMLGL------IKPDKGRIRIFGLEPEAARGRVGYLPQ 81
                                      68****************777......566666666666666666655555554 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 5.8e-08
                            AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                       ++d+ ++ +  lS G ++  +++ +l +++    lll+DEp +g + + +++++ell  l++  g+ ++l++H+ +
  gi|330509071|ref|YP_004385499.1| 128 MEDRADREIGALSGGEQQRVFVARSLVSDP---ELLLLDEPTAGVDSSQQTEFYELLCHLNQdMGIAIVLVSHDIT 200
                                       788999999999***999999999999999...9***********************88888899********965 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   5.5e-05      0.11      21      88 ..     127     181 ..     116     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.5e-05
                           SbcCD_C  21 gkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       g e + +r++g+lSGGe+q ++       +++l+s+       ++l++LDE  +++D+  +++  ell
  gi|330509071|ref|YP_004385499.1| 127 GMEDRADREIGALSGGEQQRVFV------ARSLVSD-------PELLLLDEPTAGVDSSQQTEFYELL 181
                                       56667899**********76553......2444444.......7899999999999998888877765 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 !   16.6   0.0   2.4e-06    0.0048      17      50 ..      26      59 ..      18      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.4e-06
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++++++++  l+Gp+G GKSTll  +  l+ p+k
  gi|330509071|ref|YP_004385499.1| 26 LKLERADFLGLIGPNGGGKSTLLKVMLGLIKPDK 59
                                      55666667779************88888888876 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   0.00027      0.54      25      44 ..      32      51 ..      20      64 .. 0.84
   2 !    5.6   0.0    0.0047       9.3     136     202 ..     138     200 ..      66     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00027
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                       f  ++GpNG GKs ll  +
  gi|330509071|ref|YP_004385499.1| 32 DFLGLIGPNGGGKSTLLKVM 51
                                      57889**********99866 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0047
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreeml 202
                                       +LSgGe++ v     +A   v+   l llDe  a  D ++ +++ ell + ++++ + ++ ++++++
  gi|330509071|ref|YP_004385499.1| 138 ALSGGEQQRVF----VARSLVSDPELLLLDEPTAGVDSSQQTEFYELLCHLNQDMGIAIVLVSHDIT 200
                                       79999987544....445556667799**********************999998777766655554 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   4.4e-05     0.087      16      50 ..      23      58 ..      19      95 .. 0.74
   2 ?   -0.4   0.0      0.38   7.5e+02     322     355 ..     155     188 ..     143     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.4e-05
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      d+ ++l+   +  liG+N+ GKS++l+++  +++ +
  gi|330509071|ref|YP_004385499.1| 23 DINLKLERAdFLGLIGPNGGGKSTLLKVMLGLIKPD 58
                                      5555555557889**************998777755 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.38
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandn 355
                                       +++ +ll++EP a    ++q+++++ll+ l +d 
  gi|330509071|ref|YP_004385499.1| 155 SDPELLLLDEPTAGVDSSQQTEFYELLCHLNQDM 188
                                       578899*********************9987765 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.5e-05     0.029      15      70 ..      17      72 ..       6      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 15 akellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                       +++le +  k  ra  +Gl G  G Gkstl++ +   ++    r+ +  ++P + 
  gi|330509071|ref|YP_004385499.1| 17 EHAILEDINLKLERADFLGLIGPNGGGKSTLLKVMLGLIKPDKGRIRIFGLEPEAA 72
                                      568999**************************988777777777888888888665 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   7.2e-05      0.14      85     122 ..      16      54 ..       3      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-05
                                       TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       ++++ le+++ +l+  ++  l+G+ G GKStL++++l+ 
  gi|330509071|ref|YP_004385499.1|  16 EEHAILEDINLKLERaDFLGLIGPNGGGKSTLLKVMLGL 54 
                                       56677899999999889999*************999875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.6e-05      0.15      15      37 ..      24      49 ..       6      54 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.6e-05
                            AAA_23 15 idF...skgltlItGpNGaGKTTild 37
                                      i++      +  ++GpNG GK+T+l 
  gi|330509071|ref|YP_004385499.1| 24 INLkleRADFLGLIGPNGGGKSTLLK 49
                                      44455555777899**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1398.83
//
Query:       gi|330509072|ref|YP_004385500.1|  [L=332]
Description: cation periplasmic solute binding protein [Methanosaeta concilii GP6]
Scores for 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-69  233.9   0.0    2.4e-69  233.6   0.0    1.1  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 !  233.6   0.0   1.3e-73   2.4e-69       1     255 [.      83     329 ..      83     330 .. 0.91

  Alignments for each domain:
  == domain 1  score: 233.6 bits;  conditional E-value: 1.3e-73
                                       EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTTCCCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssqatrvev 77 
                                       V +t+spl+ l++ ++Gd+ve+ +++ppga+pH+yeptp++++++a+Ad++++ng++lE w++k+l  +   +++ v
  gi|330509072|ref|YP_004385500.1|  83 VATTISPLAGLISLIGGDNVEIATIIPPGAEPHTYEPTPSQMKEIANADIYIMNGAGLEFWMEKALLVN---EDMLV 156
                                       89*************************************************************997333...34578 PP

                                       EETTTTCCSEBCSS...ESTGGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSG CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA  78 idlsegveeeeeee...DpHiWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireelaeipe 151
                                       +d segve   ee    DpHiWls++na+ +v+ni ++L+++d an d+y +n +a+ e++++ld+e+ +++a   +
  gi|330509072|ref|YP_004385500.1| 157 VDSSEGVELLSEEGgnaDPHIWLSLQNAAIQVDNICNGLIQVDSANRDYYLRNKDALLEEMKALDREFSQTFA--AK 231
                                       88888875444444566********************************************************..66 PP

                                       TEGEEEESSSTTHHHHHHTT-EEEEEESSSSS..HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHHHHT-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 152 ekrklvtthdafgylarayglevagiagiste..aaqiaalieeikeagvkaifveplaspklaetlaeeagvkvat 226
                                       e+++++++h+a++ylar+ygl ++ i++ ++e  ++ +a+li+++k++++++ifv+p+++pk+ae +a+e ++ +++
  gi|330509072|ref|YP_004385500.1| 232 ENKTFIVFHPAWSYLARDYGLVQVPIMEEEKEpgPQYLASLIDMAKKNDITTIFVDPQFNPKSAEVIAREMNATIVV 308
                                       7789********************9987777789******************************************* PP

                                       E-STSSSTSTTSTTSHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 227 lysldslgdegsaetYidmmranleslke 255
                                       l++l      +   +Y++ mr   e++ +
  gi|330509072|ref|YP_004385500.1| 309 LDPLA-----D---DYLQNMRRTGEEISK 329
                                       ***33.....3...8******99888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2111.61
//
Query:       gi|330509073|ref|YP_004385501.1|  [L=109]
Description: hypothetical protein MCON_3451 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 724.45
//
Query:       gi|330509074|ref|YP_004385502.1|  [L=244]
Description: hypothetical protein MCON_3454 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1632.75
//
Query:       gi|330509075|ref|YP_004385503.1|  [L=663]
Description: peptidyl-arginine deiminase/hydrolase fusion protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.3e-121  405.8   0.0   1.9e-121  405.3   0.0    1.2  1  PAD_porph     Porphyromonas-type peptidyl-arginine deiminase
    6.2e-55  186.3   0.0    8.9e-55  185.8   0.0    1.2  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> PAD_porph  Porphyromonas-type peptidyl-arginine deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.3   0.0  2.1e-125  1.9e-121       1     319 []     324     660 ..     324     660 .. 0.95

  Alignments for each domain:
  == domain 1  score: 405.3 bits;  conditional E-value: 2.1e-125
                                       EE--TTS-EEEEEEE--S.TTSGCGGGHHHHHHHHHHHHHHHHTTSEEEEEESSHH.HHHHHHHC.........EEE CS
                         PAD_porph   1 rmpaEwepqeavwlawPhkeesdweekleeaqeefaelakaiaefepvtllvedee.aeearell.........vel 67 
                                       +mpaEwe++ea+wl+wP+++e+    ++e++++++++++ka++++e v+llv+de   +++ e+l         +++
  gi|330509075|ref|YP_004385503.1| 324 HMPAEWEEHEAIWLSWPYDQET--FFDIEKVEDAYIAIIKAMHKSEMVNLLVRDEMmLSAVIERLreekvellrIRF 398
                                       59****************8864..579*************************887766666677789999******* PP

                                       EE---SSS-HHHHS-EEEE........ETEEEEEEE--HHHHTSSHHTTHHHHHHHHHH.TT-CEEEEEEE--GGGE CS
                         PAD_porph  68 veiptndlWlRDtgpifvv.......kkelaavdfrFnaWGgkyeeaekdnavarklae.aglerveadlvlEGGsi 136
                                       ++i++ d+W+RD+gp+fvv        ++ a+v ++FnaWG+ky  + +d++++  + + +++e++   +vlEGGsi
  gi|330509075|ref|YP_004385503.1| 399 HQINYADVWFRDYGPTFVVsrgenkgMDNIAMVAWTFNAWGEKYPGLMRDTRIPCLINDdLKMECFIPGIVLEGGSI 475
                                       *******************998876433667**************************9999*****9********** PP

                                       EEESSSEEEEEHHHHTCTTTSTTS-HHHHHHHHHHHHT-SEEEEESS-STTTTSSS-GGGTEEEEETTEEEEEE-S- CS
                         PAD_porph 137 evdGeGtllttescllnpnRNpglskeeieaeLkellgvekviwlkeGlagddtdgHiDtlarfvapgtvllaredd 213
                                       +v+G Gt+ltte+clln+nRNpgl+keeie++Lke+lg++kviwlkeG+agddtdgH+D++arfv+p tvl+a e+d
  gi|330509075|ref|YP_004385503.1| 476 DVNGSGTVLTTEQCLLNRNRNPGLNKEEIESYLKEYLGARKVIWLKEGIAGDDTDGHVDDIARFVDPTTVLCAFEED 552
                                       ***************************************************************************** PP

                                       TTSTTHHHHHHHHHHHHTTB-TTSSB-EEEEEEB-S--E...EEE--BTT--EEETTEEEEEE-SSTTCHHHHHHHH CS
                         PAD_porph 214 eedenyealkealeiLkaatdakgrklevvelplpeevr...erlpasYaNflivngavlvptfgdeekDekAleil 287
                                       ++deny+ lk+++e+L ++td++g++l+v++lp+p  v+    rlpasYaNf+i n++vlvp f++ e+D+kAl+i+
  gi|330509075|ref|YP_004385503.1| 553 PDDENYAPLKANYEQLCQETDQDGNPLKVIKLPMPGLVEnesGRLPASYANFYIGNDVVLVPLFRN-ENDQKALKII 628
                                       ***********************************87777656***********************.89******** PP

                                       HHHSTTSEEEEEETTTGGGGS--TGGGEEEEE CS
                         PAD_porph 288 qelfpdrevvgvdaralvlggGsiHCitqqvP 319
                                       q +fpdr vvg+d+r++v+g G+iHCi+qq+P
  gi|330509075|ref|YP_004385503.1| 629 QGAFPDRMVVGIDCREMVEGLGTIHCISQQQP 660
                                       *******************************9 PP

>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.8   0.0     1e-58   8.9e-55       5     260 ..      15     268 ..      11     269 .. 0.93

  Alignments for each domain:
  == domain 1  score: 185.8 bits;  conditional E-value: 1e-58
                                       EEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBS....SSHHHHHHHHBHSSSHHHHHHHHHHHHHTEE CS
                      CN_hydrolase   5 vQlpqkaadleanlqklleliaeAarkgadLivlPElfitgy....keeahfleaAeaglgetlallaalarkngia 77 
                                       +Q +  ++d++ nl+k+  +i+eAa+kga++++lPEl  t y    ++++  + +Ae+++ge++++++ lar++ i+
  gi|330509075|ref|YP_004385503.1|  15 IQSTA-SEDRDLNLKKAIGMIKEAAKKGAKIVCLPELYRTRYfpqwDQKDASH-LAETIPGESTDAFSILAREHEIV 89 
                                       55555.78999*******************************88864444444.678******************** PP

                                       EEEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGG CS
                      CN_hydrolase  78 vvigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCy 154
                                       +++++ e+  t+g++  +n+a ++d+dg+l+  yrK+h    +p  p ++e ++f+pgd+i ++dt+++++ + iCy
  gi|330509075|ref|YP_004385503.1|  90 IIVPIYEK--TEGDY--FNSAAVIDNDGSLLETYRKIH----IPHDPLFYEQSYFSPGDEIRIYDTRYARFAVFICY 158
                                       ********..*****..*********************....5899******************************* PP

                                       GGGSHHHHHHHHHTT-SEEEE......BH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE-- CS
                      CN_hydrolase 155 eigfpellralalkgaeilvn......lserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvgh 225
                                       +++fpe++r+ al ga+i+++      ++ +++  +  +++ we+++r +a+ n + v+a+n+vg   +++l+++g+
  gi|330509075|ref|YP_004385503.1| 159 DQWFPEAARVAALGGAQIIFYptaignIMDQGEPAEGDWHDAWETVQRGHAISNSICVAAVNRVGR--EESLSFWGS 233
                                       **********************998875577888899*****************************..********* PP

                                       EEEE-TTS-EEEECCSSSTEEEEEEEEHHHHHHHH CS
                      CN_hydrolase 226 SaiidpdGrilaglgeeeegvliaeidladvratr 260
                                       S++ d  G+i+a+++ + e+vl a++dla+ +++r
  gi|330509075|ref|YP_004385503.1| 234 SFVSDSFGNIVAKASGDREEVLLADLDLAKNKSVR 268
                                       **************999999********9877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (663 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 3994.92
//
Query:       gi|330509076|ref|YP_004385504.1|  [L=125]
Description: hypothetical protein MCON_3457 [Methanosaeta concilii GP6]
Scores for 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   34.8   0.1    2.3e-08   34.6   0.1    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.1   1.3e-12   2.3e-08       2     120 ..       5     119 ..       4     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.3e-12
                                       EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHH CS
                               PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeia 78 
                                       + DT +l+++l+g +  e++ +      el+ts+  + El+y   r   + ++ + +  l  l+s++++++  + ++
  gi|330509076|ref|YP_004385504.1|   5 FADTYALVEILKGNPAYEKYSQ-----KELITSEFNIFELAYAMYR---DFGRTDSINILSFLRSRIEVISPEDLDY 73 
                                       77*************8865555.....89*****************...9*************************** PP

                                       HHHHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  79 eeaaeialkyg.....llpnDaliaAtAkehgikliatfDedfrrva 120
                                       +ea++++l  +     l+++D l + + k+ +i+ + t D++f++++
  gi|330509076|ref|YP_004385504.1|  74 LEASRFRLSNNkkgkkLSLIDSLGYICSKRLKIRFL-TGDREFKDIE 119
                                       ********9999*********************999.*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 804.46
//
Query:       gi|330509077|ref|YP_004385505.1|  [L=62]
Description: hypothetical protein MCON_3458 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-12   47.3   0.4    2.4e-12   47.1   0.4    1.1  1  DUF104    Protein of unknown function DUF104
  ------ inclusion threshold ------
      0.042   13.6   0.1      0.062   13.0   0.1    1.4  1  DUF3945   Protein of unknown function (DUF3945)


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.4   2.7e-16   2.4e-12       4      55 ..       6      54 ..       4      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.7e-16
                            DUF104  4 vIeavYEnGvLKPLekvdLkEGeevkikIeeakeilkklkgilk..eadeeele 55
                                      +++a+YEn+ L+P ek+dLkEGeev i+I+      + ++g+lk  ++d+++l+
  gi|330509077|ref|YP_004385505.1|  6 IVKAIYENNLLRPQEKLDLKEGEEVDIEIKS-----RGIFGLLKdwKLDSQSLK 54
                                      89*****************************.....888888887756655555 PP

>> DUF3945  Protein of unknown function (DUF3945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   6.9e-06     0.062      34      57 ..      15      37 ..       4      38 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-06
                           DUF3945 34 kLteeqkqdLreGkavllegmtsk 57
                                       L +++k dL+eG++v +e ++s+
  gi|330509077|ref|YP_004385505.1| 15 LLRPQEKLDLKEGEEVDIE-IKSR 37
                                      5899**************8.7776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 424.18
//
Query:       gi|330509078|ref|YP_004385506.1|  [L=411]
Description: citrate transporter [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-32  113.0  34.1    2.2e-32  112.5  34.1    1.3  1  CitMHS    Citrate transporter


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.5  34.1   1.2e-36   2.2e-32      11     296 ..      31     358 ..       4     371 .. 0.81

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 1.2e-36
                                       xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  11 ldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrdllvllvllta 83 
                                       +  ++ll+++l+     +++ +a s+i  +++++l+g+++ig+a+ e+G    l +++  +a++  +ll+l+ ++++
  gi|330509078|ref|YP_004385506.1|  31 IWQIMLLGALLVllsgEISPVDAASAINPDVMIFLAGMFVIGEAMRESGYLFHLFNRIFCRAKNLDQLLLLILFAMG 107
                                       4455666666656666888888*****************************************9766********** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                            CitMHS  84 llsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnlll....... 153
                                       +lsa++ nd+ ++i +p++l la+ l  +p lll+ la+a  +g+a++piG+p            +nll+       
  gi|330509078|ref|YP_004385506.1| 108 FLSALLMNDTLAIIGTPLMLYLAQALRISPKLLLLTLAFAVTTGSAMSPIGNP------------QNLLIaingslt 172
                                       ************************98888888*********************............999998888889 PP

                                       ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                            CitMHS 154 ..............lalllvgllplvllfmfgvalalpvnapkvkkqkaiieaiarsllpvatillla......... 207
                                                     +a l+ + l l l++ ++ + + ++++pk      +++ i+r  +   +il+la         
  gi|330509078|ref|YP_004385506.1| 173 npflvffqylfiptVANLFLAYLLLRLFY-KSQFQQTAIEIPKECISDPTLANISRISIILLLILILAkvlavtvqs 248
                                       88777777777655444555555555555.77777777777777777777777777444444444444888888888 PP

                                       ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                            CitMHS 208 ...........................ykkveWsvlllfaGvfllvgaleqtGilealadllga.ggplvalalvlg 256
                                                                  +k+++W +l++fa++f+l++ + ++G  +++++   + g  + ++ ++l+
  gi|330509078|ref|YP_004385506.1| 249 sqhfsltyiaifsalpvilfssrrweiMKHIDWCTLVFFAAMFVLMDSVWRSGFFQSMMEES-SlG--FGSIPVILA 322
                                       88888888888888999999*********************************999998665.222..244445678 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 257 liallsafisnvavaalmapialgmapalgllspsplala 296
                                       l+++ls++isnv+++al+ p++++  p+++  ++++la  
  gi|330509078|ref|YP_004385506.1| 323 LSVFLSQIISNVPFVALFQPLLIN--PSAQ--DLMALAAG 358
                                       8888********************..7545..44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); 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:                         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 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2588.29
//
Query:       gi|330509079|ref|YP_004385507.1|  [L=385]
Description: cysteine desulfurase NifS [Methanosaeta concilii GP6]
Scores for complete 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-88  295.0   0.0    8.9e-88  294.7   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    2.1e-06   27.2   0.0    2.8e-06   26.8   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    4.4e-05   23.0   0.0    7.5e-05   22.2   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
       0.11   11.8   0.0       0.16   11.3   0.0    1.2  1  AroM             AroM protein


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 !  294.7   0.0     2e-91   8.9e-88       1     371 []       4     366 ..       4     366 .. 0.94

  Alignments for each domain:
  == domain 1  score: 294.7 bits;  conditional E-value: 2e-91
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlv 77 
                                       iy+d +Att++ +eVl+a+  y+ +  +n+ +s+h+ g ea++a+e+ rekva+l++a+  eeiiftsG+te+ nl+
  gi|330509079|ref|YP_004385507.1|   4 IYMDHSATTPVAPEVLAAMLPYFGEKFGNA-SSLHRSGREAKEALEDSREKVAALLGARA-EEIIFTSGGTESDNLA 78 
                                       8*****************************.****************************6.**************** PP

                                       HHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTT CS
                       Aminotran_5  78 alslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtG 153
                                       ++++ar+  k g++i++t++eh a l ++++l+ ++g++v+++p++ eg+++l++le+ ++++t l++++h++n+ G
  gi|330509079|ref|YP_004385507.1|  79 LKGIARKnRKLGKHIITTQIEHPAILETCRALE-KEGFEVTYLPVTGEGLVELSTLEASIRPDTILISVMHANNEVG 154
                                       *******9************************8.77***************************************** PP

                                       EB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTS CS
                       Aminotran_5 154 tiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggem 230
                                       tiqp+eeig+la +++++++ Da+q+vg+ip++v++lgvD+l++s+hKl+gP+G+G+ly+rk    kle +  gg+ 
  gi|330509079|ref|YP_004385507.1| 155 TIQPLEEIGRLAAERDIYLHSDAVQSVGKIPVNVDDLGVDLLSLSAHKLYGPKGVGALYIRK--GTKLESIIQGGG- 228
                                       **************************************************************..999999999999. PP

                                       EEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CT CS
                       Aminotran_5 231 veevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaer 307
                                             +e+        +++GT+n+ gi+gl+ a+e+ e+   +++e+ +      ++  l ++++  ++g + ++r
  gi|330509079|ref|YP_004385507.1| 229 ------HERR-------LRSGTENISGIVGLARAAELAERDMPREAERLAGLRDRLAELVLGKVKDAWING-TMKKR 291
                                       ......5665.......9*******************95555555555565566666778899****9999.689** PP

                                       CBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTT....HHHHHHTT.S.......-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 308 rasivsfnfkgvhaedvatlLdeegIavrsGhhca....qplmkrlale.......gtvRaSlyiynteeevdrl 371
                                        ++ ++f fk+v+ e +  +Ld++gI+v++G++c+    +p++++++l        g++R+ l++ nt +ev+++
  gi|330509079|ref|YP_004385507.1| 292 LPGNLNFGFKYVEGESLLLFLDSKGICVSTGSACSshklEPSHVLMSLGlkaeechGSLRITLGMSNTLDEVEYV 366
                                       ***********************************999999999888888899999****************975 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   6.2e-10   2.8e-06      38     168 ..      51     177 ..      37     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 6.2e-10
                                       HHHHHHHTT-..SEEEEES-HHHHHHHHHHHH--T....TEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTB CS
                   Beta_elim_lyase  38 edavaelfgk..eaalfvpqGtaAnsillkillqr....geevivtepahihfdetgaiaelagvklrdlknkeaGk 108
                                        ++va+l+g+  e ++f+  Gt +++++lk ++++    g+ +i t+  h    et  + e +g +++ l+   +G 
  gi|330509079|ref|YP_004385507.1|  51 REKVAALLGAraEEIIFTSGGTESDNLALKGIARKnrklGKHIITTQIEHPAILETCRALEKEGFEVTYLPVTGEGL 127
                                       5678888886225789*************9998651222456677777998887776666889999*****9999** PP

                                       E-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
                   Beta_elim_lyase 109 mdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                                       ++l  lea i+++      + lis+  +nn     v +++ l+e+  +a +++i lh D+
  gi|330509079|ref|YP_004385507.1| 128 VELSTLEASIRPD------TILISVMHANNE----VGTIQPLEEIGRLAAERDIYLHSDA 177
                                       ************4......56*********5....6677778889999**********97 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 !   22.2   0.0   1.7e-08   7.5e-05      30     150 ..      52     182 ..      34     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.7e-08
                                       HHHHHHHT..-SEEEEESSHHHHHHHHHHHTTTT...TT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTT..SSB CS
                   DegT_DnrJ_EryC1  30 kafaaylg..vkhaiavssGtaAlhlaLralgvg...pgdeVIvpsltFvatanavlelgakpvfvDvdpdt..yni 99 
                                       +++aa lg  ++  i +s Gt++  laL+ +  +    g+ +I++++   a  ++ + l  +   v   p t    +
  gi|330509079|ref|YP_004385507.1|  52 EKVAALLGarAEEIIFTSGGTESDNLALKGIARKnrkLGKHIITTQIEHPAILETCRALEKEGFEVTYLPVTgeGLV 128
                                       5778888866788999*************9555444489************77766666555555555555411689 PP

                                       -GGGCGGG--TTEEEEEEB-G...GGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1 100 dpaaieaaitertkaIlpVhl...yGqvadmdalkaiaakhglkvieDaAhAlG 150
                                       + +++ea i + t  I + h+   +G +  ++++ ++aa+ ++++ +Da +++G
  gi|330509079|ref|YP_004385507.1| 129 ELSTLEASIRPDTILISVMHAnneVGTIQPLEEIGRLAAERDIYLHSDAVQSVG 182
                                       *************99999998333588889999*******************99 PP

>> AroM  AroM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.6e-05      0.16      73     139 ..     101     165 ..      51     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.6e-05
                              AroM  73 prlqaaiakleeegvdlilllcTg.efpeleakapliepqrileslvaalvkkkqlgvivPleeqaeq 139
                                       p++ +  + le+eg+++++l  Tg  + el++    i+p++il s+++a   ++++g i Plee  + 
  gi|330509079|ref|YP_004385507.1| 101 PAILETCRALEKEGFEVTYLPVTGeGLVELSTLEASIRPDTILISVMHA---NNEVGTIQPLEEIGRL 165
                                       566678899***************559*****999*******9776655...677*******997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 2597.10
//
Query:       gi|330509080|ref|YP_004385508.1|  [L=82]
Description: hypothetical protein MCON_3461 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.9    8.0   5.1        1.4    8.9   0.9    2.1  2  DUF1201   Protein of unknown function (DUF1201)


Domain annotation for each model (and alignments):
>> DUF1201  Protein of unknown function (DUF1201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2     0.024   4.2e+02       9      20 ..      17      28 ..      11      37 .. 0.74
   2 ?    8.9   0.9     8e-05       1.4      17      33 ..      61      77 ..      47      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.024
                           DUF1201  9 lllafGfliclf 20
                                       l+ +Gfli  f
  gi|330509080|ref|YP_004385508.1| 17 ALIGLGFLIYPF 28
                                      578899*99776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 8e-05
                           DUF1201 17 iclflfclvvfiwfvyk 33
                                      + lf f +vv iw++y 
  gi|330509080|ref|YP_004385508.1| 61 LVLFGFTVVVGIWMMYV 77
                                      36999*********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 617.59
//
Query:       gi|330509081|ref|YP_004385509.1|  [L=366]
Description: hypothetical protein MCON_3463 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-37  127.7   0.0    5.4e-37  127.3   0.0    1.2  1  ATP-grasp_3      ATP-grasp domain
    3.7e-10   39.7   0.0    0.00046   19.7   0.0    2.2  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.5e-07   31.2   0.0    2.9e-07   30.3   0.0    1.4  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    6.5e-06   25.8   0.0    4.2e-05   23.2   0.0    2.1  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    1.8e-05   24.2   0.0      0.002   17.4   0.0    2.2  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
     0.0001   22.0   0.0    0.00018   21.2   0.0    1.3  1  RimK             RimK-like ATP-grasp domain
     0.0021   17.7   0.0       0.39   10.3   0.0    2.2  2  ATP-grasp        ATP-grasp domain
  ------ inclusion threshold ------
      0.037   13.8   0.1       0.19   11.5   0.1    2.1  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.3   0.0   2.4e-40   5.4e-37       1     161 []     102     260 ..     102     260 .. 0.94

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 2.4e-40
                                       HTSHHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEEE CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplSv 77 
                                       +sdKl  +++L+++g+++    +++++e  + ++ vKpr+Gagg + r++e+   +e   ee  ++qe ++G+ +Sv
  gi|330509081|ref|YP_004385509.1| 102 ISDKLYQARWLEKNGFPFI--RTETSAEDLNFPVMVKPRQGAGGVGCRIAEDSSRLE--WEEGLIAQEVVSGRAASV 174
                                       69************88776..667777888999********************7777..77777************* PP

                                       EEEE.SSSEEEEEEEEEEEET.......TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEE CS
                       ATP-grasp_3  78 sllsdgekvlvlavnrqliekaeke...fvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkdeepyv 151
                                       s+++dg++++ la n+qli+  +++   f+y+Gn+tp e   k+++ ++ae++v++l gl+G++GvD++l++e+p+v
  gi|330509081|ref|YP_004385509.1| 175 SVIGDGKDARALAANEQLIGESWTGakgFRYCGNITPLEPLPKNDIANMAERIVARL-GLLGSNGVDFLLTEEGPVV 250
                                       ********************99988999***********999***************.******************* PP

                                       EEEESS--GG CS
                       ATP-grasp_3 152 iEvNPRltts 161
                                       +EvN R+++s
  gi|330509081|ref|YP_004385509.1| 251 VEVNCRFQGS 260
                                       ********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 !   19.7   0.0   2.1e-07   0.00046      33      64 ..     125     156 ..     120     174 .. 0.90
   2 !   17.7   0.0   8.9e-07     0.002     139     198 ..     218     275 ..     210     281 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.1e-07
                                       HHHHH-SSEEEEETTCCTTTTEEEESSHHHHH CS
                       CPSase_L_D2  33 iakeigyPviikaafglGGkGmrvarneeela 64 
                                        a+++ +Pv++k+  g GG G r+a+++++l+
  gi|330509081|ref|YP_004385509.1| 125 SAEDLNFPVMVKPRQGAGGVGCRIAEDSSRLE 156
                                       699************************99875 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 8.9e-07
                                       HHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHH CS
                       CPSase_L_D2 139 qalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvke 198
                                       + + + a ++v  +g+ g   v+fll +  +  +v+EvN R + +    e+aTG+++ ++
  gi|330509081|ref|YP_004385509.1| 218 NDIANMAERIVARLGLLGSNGVDFLLTE--EGPVVVEVNCRFQGSLDTVECATGINVFEA 275
                                       56888999******************95..8889*********************98765 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 !   30.3   0.0   1.3e-10   2.9e-07      46     111 ..     217     283 ..     204     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.3e-10
                      ATPgrasp_Ter  46 deelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllgl 111
                                       ++++ ++aer++ ++gl g ++v +  +e+gp++ E+N R++G l+ + +++G+n+ ++ l+ + gl
  gi|330509081|ref|YP_004385509.1| 217 KNDIANMAERIVARLGLLGSNGVDFLLTEEGPVVVEVNCRFQGSLDtVECATGINVFEAHLNSFRGL 283
                                       578999***************************************8357999********9999886 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 !   23.2   0.0   1.9e-08   4.2e-05      29     173 ..     123     254 ..     110     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.9e-08
                                       HHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-SCEEEEE--ESEEEEEEEEETSS.CEEEEEEEE CS
                   Dala_Dala_lig_C  29 ekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkydekvlvEeaiegreievavlgnek.levsevgei 104
                                       e   e l++pv+VKp +    vG   +e  + l        +++e  +  e+++gr   v+v+g++k  +++ ++e 
  gi|330509081|ref|YP_004385509.1| 123 ETSAEDLNFPVMVKPRQGAGGVGCRIAEDSSRL--------EWEEGLIAQEVVSGRAASVSVIGDGKdARALAANEQ 191
                                       556789***********999****999998876........6999999****************9884667777776 PP

                                       E-SSSSS-HH.HHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEE CS
                   Dala_Dala_lig_C 105 vvkkgfydye.akysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvN 173
                                          +++   +  +y          + le+  ++ i ++a ++ + l+l G+  vDf+lteeg  v+ EvN
  gi|330509081|ref|YP_004385509.1| 192 LIGESWTGAKgFRYC------GNITPLEPLPKNDIANMAERIVARLGLLGSNGVDFLLTEEGP-VVVEVN 254
                                       666666543312443......33457899999***************************8775.567888 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 !    4.6   0.0    0.0074        17      58      83 ..     128     153 ..      93     173 .. 0.82
   2 !   17.4   0.0     9e-07     0.002     228     276 ..     220     269 ..     217     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0074
                       ATPgrasp_ST  58 eleegvviKpakgsgGkGilvitere 83 
                                       +l+  v++Kp +g gG G +++ + +
  gi|330509081|ref|YP_004385509.1| 128 DLNFPVMVKPRQGAGGVGCRIAEDSS 153
                                       4544499*************997654 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 9e-07
                       ATPgrasp_ST 228 vlelaakaaeklpglgylGwDivldeekgplllElNar..pglaivqiang 276
                                       + ++a ++ ++l  lg  G+D+ l+ee+ p+++E+N r   +l+ v+ a g
  gi|330509081|ref|YP_004385509.1| 220 IANMAERIVARLGLLGSNGVDFLLTEEG-PVVVEVNCRfqGSLDTVECATG 269
                                       67899***********************.*******997334666665555 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   7.8e-08   0.00018      38     180 ..     128     272 ..     111     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.8e-08
                                       -.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--EEEEE--SS-S........EEEEEEEETTEEEEEEEEE CS
                              RimK  38 klrfPvvvKsvegsqGikvvlakkeqklkqvlealkeailvqeyieeaen........ediRvlvvddevvaalrrv 106
                                       +l+fPv+vK  +g  G++  +a++  +l+   e+    ++ qe +             +d R l  +++ ++   + 
  gi|330509081|ref|YP_004385509.1| 128 DLNFPVMVKPRQGAGGVGCRIAEDSSRLEWE-EG----LIAQEVVSGRAAsvsvigdgKDARALAANEQLIGESWTG 199
                                       378***********************99977.55....45555544333223445556******************9 PP

                                       --SSS----TTTT-EEEE---.-HHHHHHHHHH.HHHCT-SEEEEEEEEETTEEEEEEEESS--..SHHHHHHHT-- CS
                              RimK 107 skeGdFRsnlhrGgvaeklql.seeekelAika.akamelvvaGvDllrakrgllvlEvnsspg..lekiektlgid 179
                                       +k   FR   + G+++    l +++  ++A ++ a++  l   GvD l +++g++v+Evn   +  l+ +e  +gi+
  gi|330509081|ref|YP_004385509.1| 200 AKG--FR---YCGNITPLEPLpKNDIANMAERIvARLGLLGSNGVDFLLTEEGPVVVEVNCRFQgsLDTVECATGIN 271
                                       999..88...566666555552334566666651566667799*****************98654488999999999 PP

                                       H CS
                              RimK 180 i 180
                                       +
  gi|330509081|ref|YP_004385509.1| 272 V 272
                                       7 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0066        15      21      54 ..     123     155 ..     110     168 .. 0.86
   2 !   10.3   0.0   0.00017      0.39     119     155 ..     217     252 ..     203     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0066
                                       HHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGH CS
                         ATP-grasp  21 eeaaeelglpvvvKarrlgydGkGqsvvrseedl 54 
                                       e  ae+l++pv+vK +r g  G G  + +++++l
  gi|330509081|ref|YP_004385509.1| 123 ETSAEDLNFPVMVK-PRQGAGGVGCRIAEDSSRL 155
                                       567899********.999******9999888766 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEE CS
                         ATP-grasp 119 qkkaeeiakkiveeLggvGvfavElFvledgellvnE 155
                                       ++ ++++a++iv++Lg +G  +v + ++e+g ++v E
  gi|330509081|ref|YP_004385509.1| 217 KNDIANMAERIVARLGLLGSNGVDFLLTEEGPVVV-E 252
                                       678999**********************9998765.4 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 ?   11.5   0.1   8.5e-05      0.19     136     190 ..     213     258 ..     125     261 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.5e-05
                                       TTS-HHHHHHHHHHTHHHHHHHHHCTT---EEEEE...EEEEEETTEEEEEEEESS-- CS
                            GARS_A 136 pvvteellekikeeileptveglkkegipfkGvLy...aglmlvedgpkvlefnvRfg 190
                                         ++++++ ++ e+i+ +             G+L    ++++l+e+gp v+e n+Rf 
  gi|330509081|ref|YP_004385509.1| 213 EPLPKNDIANMAERIVAR------------LGLLGsngVDFLLTEEGPVVVEVNCRFQ 258
                                       555555544444444433............333321114689**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); 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:                         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 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2768.54
//
Query:       gi|330509082|ref|YP_004385510.1|  [L=210]
Description: hypothetical protein MCON_3465 [Methanosaeta concilii GP6]
Scores for complete 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-50  169.2   0.0    3.5e-50  168.9   0.0    1.1  1  Trm56           tRNA ribose 2'-O-methyltransferase, aTrm56
  ------ inclusion threshold ------
       0.03   14.5   0.0      0.043   14.0   0.0    1.1  1  SpoU_methylase  SpoU rRNA Methylase family


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 !  168.9   0.0   3.9e-54   3.5e-50       1     119 []      49     165 ..      49     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 168.9 bits;  conditional E-value: 3.9e-54
                                       H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESSSS CS
                             Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkekdllvvvGaekvprevyeladynvsvgnq 77 
                                       wGg f+++ + s+k  i ++k++gg+vvhltmyG n+ +vi+ei+k+e d+l+vvGaekvp+evy+lad+nv+vgnq
  gi|330509082|ref|YP_004385510.1|  49 WGGAFRLTPNASWKGEIVRWKESGGQVVHLTMYGSNLPDVIDEIRKSE-DILIVVGAEKVPAEVYQLADWNVAVGNQ 124
                                       ********************************************9986.5*************************** PP

                                       ---HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EEE CS
                             Trm56  78 PhsevaalaifldrllegkelekefedaklkviPsergkkvv 119
                                       Phsevaala+fldrl++g+el +efe + lk++Ps+rgk+v+
  gi|330509082|ref|YP_004385510.1| 125 PHSEVAALAVFLDRLFQGEELGREFE-GGLKIVPSSRGKEVI 165
                                       *************************9.889*********995 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.8e-06     0.043      22     122 ..      21     121 ..      15     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-06
                                       HHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGC....CSHHH CS
                    SpoU_methylase  22 akafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgksls....eidlk 94 
                                       a+afga++++l+++++    ++ +  aa      ++l+  +s++  + ++ke+g ++v ++ +g++l     ei+ +
  gi|330509082|ref|YP_004385510.1|  21 ARAFGAEGMLLCGRDAH--VEESLNDAARRWGGAFRLTPNASWKGEIVRWKESGGQVVHLTMYGSNLPdvidEIRKS 95 
                                       77999*999**996554..788888888888888889999**********************999999555566888 PP

                                       TTEEEEEEBTTTBS-HHHHCTSSEEEE- CS
                    SpoU_methylase  95 ekvalvfGnEdkGlsnelleladrlvkI 122
                                       e +++v+G E+  ++ e+ +lad  v +
  gi|330509082|ref|YP_004385510.1|  96 EDILIVVGAEK--VPAEVYQLADWNVAV 121
                                       **********7..788888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1427.88
//
Query:       gi|330509083|ref|YP_004385511.1|  [L=718]
Description: hypothetical protein MCON_3466 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-08   34.4   0.0    1.9e-07   31.0   0.2    2.7  4  tRNA_anti-codon  OB-fold nucleic acid binding domain
    2.2e-08   34.3  11.2    2.2e-08   34.3  11.2    2.3  2  DnaJ_CXXCXGXG    DnaJ central domain
    2.9e-05   24.3   2.4      7e-05   23.1   0.1    2.6  2  S1               S1 RNA binding domain
    8.7e-05   22.6   0.1    0.00067   19.8   0.1    2.4  2  tRNA_anti_2      OB-fold nucleic acid binding domain
    0.00047   20.4   0.3    0.00086   19.5   0.3    1.4  1  DHH              DHH family
  ------ inclusion threshold ------
       0.01   15.8  14.0       0.09   12.8   1.4    2.9  2  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
      0.024   14.7   0.0       0.06   13.4   0.0    1.7  1  S1_2             S1 domain
       0.24   11.6  10.9        0.6   10.3   7.3    2.7  3  PHF5             PHF5-like protein
        1.3    9.2  17.6         63    3.7  17.4    2.8  1  DZR              Double zinc ribbon
        6.2    7.1  16.0         18    5.6   0.5    4.1  3  DUF5351          Family of unknown function (DUF5351)


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 ?   -2.9   0.0       3.8   6.8e+03      35      68 ..     146     175 ..     133     181 .. 0.65
   2 !   31.0   0.2   1.1e-10   1.9e-07       1      74 [.     208     278 ..     208     280 .. 0.96
   3 ?   -1.5   0.0       1.4   2.6e+03       8      32 ..     374     397 ..     371     410 .. 0.80
   4 ?   -2.7   0.0       3.5   6.3e+03      50      74 ..     575     601 ..     568     602 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.8
                                       ETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEE CS
                   tRNA_anti-codon  35 freeatklaenlkeGdvvrvtGrvkrrpggelel 68 
                                        +   ++l+++ + Gd + vt r    +g+ +el
  gi|330509083|ref|YP_004385511.1| 146 HN---KYLKSRPEAGDAIMVTVRNILPNGN-IEL 175
                                       44...5666677788888888776666666.665 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.1e-10
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveeie 74 
                                       V ++G+v+++  +++g+   ++l D++g + + +f  +  + + +++ ++ vrv G+v+ r+++ +++ +++++
  gi|330509083|ref|YP_004385511.1| 208 VMIKGEVIQV--KQTGGPTIFTLADDSGLVFCAAFERAGVRAYADIDSDMMVRVIGEVSLRNNQ-VQVEIKSMK 278
                                       679*******..***************************************************9.999999886 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.4
                                       EEEEEEEETTEEEEEEEETTEEEEE CS
                   tRNA_anti-codon   8 tsisdrsggkvifidlrDgtgriqv 32 
                                       ++++ r+ +k+ f++l+D t  ++ 
  gi|330509083|ref|YP_004385511.1| 374 HNYR-RAPSKAPFYELEDVTKDLTF 397
                                       5666.9999999******9987765 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 3.5
                                       SEEEEE.EEEEEC..TTSSEEEEEEEEE CS
                   tRNA_anti-codon  50 dvvrvt.Grvkrr..pggelelkveeie 74 
                                         +r++ G vk++  p+g + ++v ++e
  gi|330509083|ref|YP_004385511.1| 575 EQLRASmGNVKSTklPNG-IIMNVLDVE 601
                                       567889999999999999.888887776 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3  11.2   1.2e-11   2.2e-08       1      66 [.       4      74 ..       4      75 .. 0.78
   2 ?   -1.4   1.6       1.8   3.2e+03      44      64 ..      80      98 ..      76     101 .. 0.50

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.2e-11
                     DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkGsGvvree.....qkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGk 66
                                      C++C+G+g  +  +k C++C+G+G++++      +++ +++++++ + +C+ C+G+Gk+   ++ C++C+G 
  gi|330509083|ref|YP_004385511.1|  4 CERCQGRGVLTVGEKPCPNCNGKGTTESIslgeaSDKdMKSLIESGSAKCSVCQGSGKIP-ITEICPDCHGL 74
                                      ********97766889********533323554322358889999999**********76.5679*****95 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                     DnaJ_CXXCXGXG 44 CpeCeGtGkvikekdkCkkCk 64
                                      C  C+ +    ++k+ C++C 
  gi|330509083|ref|YP_004385511.1| 80 CVVCKTKLD--SKKELCERCA 98
                                      444444433..2244455554 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   3.9e-08     7e-05       4      58 ..     117     217 ..     114     221 .. 0.74
   2 ?   -1.2   0.2       1.5   2.7e+03      36      63 ..     250     277 ..     248     279 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.9e-08
                                       TTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS........................................ CS
                                S1   4 kgevveGeVtsvtkgGafVelgngvegfvpaselsrd........................................ 40 
                                       +ge+++G+V+ + ++GafV+l   v+g+ + + l+++                                        
  gi|330509083|ref|YP_004385511.1| 117 VGEIYQGKVSGLANFGAFVDLSDSVRGLAHNKYLKSRpeagdaimvtvrnilpngnielepaelkeyntvevekdlp 193
                                       8**********************************997777777777777777766666666666666666666666 PP

                                       ......CEESCHHHCEETTEEEEE CS
                                S1  41 ......arvedpdevlkvGdevkv 58 
                                              + +++++v  +G+ + v
  gi|330509083|ref|YP_004385511.1| 194 lskasdLHSQVGKTVMIKGEVIQV 217
                                       666666555555555555555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                                       GSSSSCEESCHHHCEETTEEEEEEEEEE CS
                                S1  36 elsrdarvedpdevlkvGdevkvkvlkv 63 
                                       ++++d++v++++ev   +++v v++  +
  gi|330509083|ref|YP_004385511.1| 250 DIDSDMMVRVIGEVSLRNNQVQVEIKSM 277
                                       68999999*************9999876 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.5   2.7e+03      55      77 ..     146     165 ..     118     170 .. 0.69
   2 !   19.8   0.1   3.7e-07   0.00067      14      93 ..     200     276 ..     194     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
                       tRNA_anti_2  55 frsraaklkftledGmkVlvkgr 77 
                                        +   + lk ++e G+ ++v++r
  gi|330509083|ref|YP_004385511.1| 146 HN---KYLKSRPEAGDAIMVTVR 165
                                       33...456778999999999886 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 3.7e-07
                       tRNA_anti_2  14 leaelkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgrlsvYeprGsyqli 90 
                                       l++++ k+v+++Ge+ ++k ++ g + ftL D++  + ++ f+++  +  ++++++m V v g++s+ ++  ++q+ 
  gi|330509083|ref|YP_004385511.1| 200 LHSQVGKTVMIKGEVIQVK-QTGGPTIFTLADDSGLVFCAAFERAGVRAYADIDSDMMVRVIGEVSLRNN--QVQVE 273
                                       45677889**********5.4689******************9887777789*************98544..45555 PP

                       tRNA_anti_2  91 ved 93 
                                       +++
  gi|330509083|ref|YP_004385511.1| 274 IKS 276
                                       555 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   4.8e-07   0.00086       3      61 ..     339     452 ..     337     491 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.8e-07
                                       EEE-ECSSSHHHHHHHHHHHH.......................................................C CS
                                       xxxxxxxxxxxxxxxxxxxxx.......................................................x RF
                               DHH   3 livghknpDtDsigSaialan.......................................................l 24 
                                       ++   ++ D+D+i +a+a++                                                        +
  gi|330509083|ref|YP_004385511.1| 339 VV--RHHADADGISAAVAIEMailpliaevsgpdaeyhnyrrapskapfyeledvtkdltfaledqsrhgqkmpliV 413
                                       44..7899***********9988888888888888888888888888888877777777777777777777777777 PP

                                       ECS--TCGGCGCCH..HCCCSEEEEEEE-S---SS---S CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  25 lvDhneksqavege..akeeaedviiiDHHrlgeefetl 61 
                                       l+D+++++++v +   a+  + +++++DHH +++ ++++
  gi|330509083|ref|YP_004385511.1| 414 LMDNGSTEEDVPAMrqAQVYGLEMLVVDHHHPHKIVDQF 452
                                       ********999876557777899********98533333 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 ?    6.7   5.3    0.0039       6.9      12      41 ..       3      28 ..       2      32 .. 0.81
   2 ?   12.8   1.4     5e-05      0.09      11      40 ..      51      75 ..      45      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0039
                                      E-TTTTTTSEETTE......E-TTTTTSSE CS
                         Anti-TRAP 12 kCdaCngsGkiepeeprasleCPkCsGkgl 41
                                      +C+ C+g G           +CP+C+Gkg 
  gi|330509083|ref|YP_004385511.1|  3 QCERCQGRGVLTVG----EKPCPNCNGKGT 28
                                      79999999988765....569999999985 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5e-05
                                      EE-TTTTTTSEETTE......E-TTTTTSS CS
                         Anti-TRAP 11 tkCdaCngsGkiepeeprasleCPkCsGkg 40
                                       kC  C+gsGki+ +       CP+C G g
  gi|330509083|ref|YP_004385511.1| 51 AKCSVCQGSGKIPIT-----EICPDCHGLG 75
                                      58***********99.....47*****976 PP

>> S1_2  S1 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      0.06       1      48 [.     117     164 ..     117     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                              S1_2   1 iGkintlkvlretdfgyfLqkdesgevlLpkkevpeeleiGdeveVFv 48 
                                       +G+i + kv    +fg+f++ ++s+  l ++k+++   e Gd + V v
  gi|330509083|ref|YP_004385511.1| 117 VGEIYQGKVSGLANFGAFVDLSDSVRGLAHNKYLKSRPEAGDAIMVTV 164
                                       69999***************************************9975 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       4.2   7.5e+03      23      31 ..       4      12 ..       2      28 .. 0.52
   2 ?   10.3   7.3   0.00034       0.6      17      77 ..      40      99 ..      25     102 .. 0.86
   3 ?    1.3   0.0      0.21   3.9e+02      13      32 ..     614     633 ..     605     640 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.2
                              PHF5 23 cekcdgkcp 31
                                      ce+c+g+ +
  gi|330509083|ref|YP_004385511.1|  4 CERCQGRGV 12
                                      555555543 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00034
                              PHF5 17 taigklcekcdgkcpicdslvkpatkvricdecsfgkleekciicgskgvsdayyclecvr 77
                                      +++  l e+   kc +c+    ++   +ic +c     e  c++c +k  s+   c+ c++
  gi|330509083|ref|YP_004385511.1| 40 KDMKSLIESGSAKCSVCQGSG-KIPITEICPDCHGLGREYLCVVCKTKLDSKKELCERCAK 99
                                      567788899999*****9885.567789*******************************86 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.21
                              PHF5  13 kqpGtaigklcekcdgkcpi 32 
                                       k++G    +lc+k dgk ++
  gi|330509083|ref|YP_004385511.1| 614 KTSGEVHDRLCQKYDGKPVV 633
                                       678888999*******9876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  17.4     0.035        63       1      48 [.      20      97 ..       4      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.035
                               DZR  1 CpqCgee...................lppdarfCseCgtklkavaa...........edrCpsCgekvdpearfCpeC 48
                                      Cp+C+ +                   +++++  Cs C+ + k + +           e+ C+ C++k+d++++ C  C
  gi|330509083|ref|YP_004385511.1| 20 CPNCNGKgttesislgeasdkdmkslIESGSAKCSVCQGSGKIPITeicpdchglgrEYLCVVCKTKLDSKKELCERC 97
                                      888888888888899999999999999999999999999855444468889999999********************* PP

>> DUF5351  Family of unknown function (DUF5351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   4.2     0.028        51       1      28 [.       4      28 ..       4      29 .. 0.80
   2 ?    5.6   0.5    0.0098        18      16      28 ..      49      61 ..      44      62 .. 0.87
   3 ?    2.8   0.2     0.074   1.3e+02      17      28 ..      65      76 ..      65      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.028
                           DUF5351  1 CpYCeGkGYfqLlLGGSETCesCeGtgk 28
                                      C+ C+G+G    l  G   C+ C+G+g+
  gi|330509083|ref|YP_004385511.1|  4 CERCQGRGV---LTVGEKPCPNCNGKGT 28
                                      888999994...4458899*******98 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0098
                           DUF5351 16 GSETCesCeGtgk 28
                                      GS  C  C+G+gk
  gi|330509083|ref|YP_004385511.1| 49 GSAKCSVCQGSGK 61
                                      9999*******97 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.074
                           DUF5351 17 SETCesCeGtgk 28
                                      +E C+ C+G g 
  gi|330509083|ref|YP_004385511.1| 65 TEICPDCHGLGR 76
                                      689******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (718 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); 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: 00:00:00.49
# Mc/sec: 4364.38
//
Query:       gi|330509084|ref|YP_004385512.1|  [L=1098]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-22   79.5  47.9    5.6e-08   33.0   2.3    5.1  7  TPR_12         Tetratricopeptide repeat
    3.3e-14   52.0   4.7     0.0013   18.4   0.1    4.3  4  TPR_1          Tetratricopeptide repeat
      5e-11   41.9   6.5     0.0085   16.2   0.2    4.8  4  TPR_8          Tetratricopeptide repeat
    4.4e-10   38.9  22.6      0.033   14.3   0.1    8.0  7  TPR_2          Tetratricopeptide repeat
    9.3e-09   34.9  17.6     0.0011   18.7   0.2    5.1  5  TPR_10         Tetratricopeptide repeat
    3.6e-07   29.9  17.1    4.9e-05   22.9   4.2    2.7  3  TPR_MalT       MalT-like TPR region
      2e-05   25.1   1.7      4e-05   24.1   0.2    2.3  2  AAA_16         AAA ATPase domain
      8e-05   22.4  19.5       0.99    9.6   0.1    6.6  6  TPR_7          Tetratricopeptide repeat
     0.0014   19.2   2.5     0.0014   19.2   2.5    6.3  5  TPR_16         Tetratricopeptide repeat
     0.0014   19.0  30.0       0.45   11.1   2.6    6.5  6  TPR_19         Tetratricopeptide repeat
     0.0053   16.8   2.4       0.96    9.6   0.2    2.8  2  ANAPC5         Anaphase-promoting complex subunit 5
  ------ inclusion threshold ------
      0.022   14.2   7.0      0.088   12.2   2.8    2.6  2  Coatomer_E     Coatomer epsilon subunit
      0.074   12.9   0.0       0.17   11.8   0.0    1.6  1  Helicase_RecD  Helicase
      0.078   12.7   7.6       0.81    9.4   0.6    4.4  4  TPR_11         TPR repeat
       0.12   12.3   0.1        1.5    8.8   0.0    2.6  2  NACHT          NACHT domain
       0.24   10.8  11.3        1.7    8.0   0.8    3.1  3  SNAP           Soluble NSF attachment protein, SNAP
       0.38   10.5   3.6         40    3.9   0.0    3.6  2  RPN7           26S proteasome subunit RPN7
       0.59   10.4   4.8         19    5.5   0.1    3.3  3  ANAPC3         Anaphase-promoting complex, cyclosome, subunit


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       6.9   6.9e+03      55      65 ..     737     747 ..     729     749 .. 0.63
   2 !   26.7   2.6   5.1e-09   5.1e-06       6      74 ..     783     842 ..     780     845 .. 0.94
   3 !   19.0   1.3   1.3e-06    0.0013       8      76 ..     818     884 ..     810     885 .. 0.83
   4 !   20.2   1.2   5.6e-07   0.00056       5      77 .]     856     925 ..     851     925 .. 0.90
   5 !   26.6   2.6   5.5e-09   5.4e-06       3      76 ..     894     964 ..     891     965 .. 0.93
   6 !   33.0   2.3   5.7e-11   5.6e-08       5      77 .]     935    1005 ..     931    1005 .. 0.93
   7 !   27.0   1.2   4.2e-09   4.1e-06       2      63 ..     972    1031 ..     971    1036 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.9
                            TPR_12  55 yralgryeeAl 65 
                                       y+++g+++eA+
  gi|330509084|ref|YP_004385512.1| 737 YLEAGDLAEAR 747
                                       44666666665 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 5.1e-09
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +n +a++++++ +++ A ++++kal++a     pd    a ++++Lg++++ +g+y+ A+e le+al+i
  gi|330509084|ref|YP_004385512.1| 783 MNWIAQAYAHQMDLENAAQWYKKALDMA-----PD----AFSYQGLGMIQLGRGEYDLAEESLEKALQI 842
                                       4579************************.....97....89**************************98 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 1.3e-06
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        l+++ + +g+yd A+e lekal+i+     +d  ++a++l++L+ +   ++   +A + le+a +i+e
  gi|330509084|ref|YP_004385512.1| 818 GLGMIQLGRGEYDLAEESLEKALQIHLGQ--KDQRGEAAVLQALASIDMSRKSGSAAKDKLERAARILE 884
                                       599999999*****************555..99999*********997566688888888888888876 PP

  == domain 4  score: 20.2 bits;  conditional E-value: 5.6e-07
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       ++  la++ + ++    A + le+a +i + l  +d+ ++a++l+ ++ +  ++g+y+ A+ +l ++l++a++
  gi|330509084|ref|YP_004385512.1| 856 LQ-ALASIDMSRKSGSAAKDKLERAARILEDL--GDRMGEAAVLQEMANIDMMQGHYDSAWPRLARSLELARE 925
                                       33.6899999999999999*************..9***************99******************986 PP

  == domain 5  score: 26.6 bits;  conditional E-value: 5.5e-09
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a ++ ++a++ + +g yd A   l ++le+ar++  +d++++a  l+ L+++ r++g+++ A e l  alai +
  gi|330509084|ref|YP_004385512.1| 894 AVLQ-EMANIDMMQGHYDSAWPRLARSLELAREA--KDRAGEAVLLFYLADVDRETGELARATEELDCALAITR 964
                                       3344.8****************************..***********************************976 PP

  == domain 6  score: 33.0 bits;  conditional E-value: 5.7e-11
                            TPR_12    5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77  
                                        +l  la+v r+ g+++ A e l+ al+i r l  +d+ + a++l++Lg++ +++g+ e A e+++eal+++++
  gi|330509084|ref|YP_004385512.1|  935 LLFYLADVDRETGELARATEELDCALAITRDL--GDRKGMAASLHGLGMISSQAGEMEMAAEHFREALQVYQE 1005
                                        4546**************************99..8888********************************985 PP

  == domain 7  score: 27.0 bits;  conditional E-value: 4.2e-09
                            TPR_12    2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryee 63  
                                        +a++l+ l+++  ++g+++ A e++++al+++++l  +d +++a +l+ Lg l  +++r +e
  gi|330509084|ref|YP_004385512.1|  972 MAASLHGLGMISSQAGEMEMAAEHFREALQVYQEL--KDQAGEAGALFQLGALAVQMDRIQE 1031
                                        688999*****************************..*******************999887 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   1.8e-06    0.0018       5      33 ..     784     812 ..     781     812 .. 0.92
   2 !   18.4   0.1   1.3e-06    0.0013       2      30 ..     814     842 ..     813     843 .. 0.93
   3 !   14.7   0.0     2e-05      0.02       1      32 [.     973    1004 ..     973    1006 .. 0.91
   4 ?   -2.5   0.0       5.3   5.3e+03       3      19 ..    1015    1031 ..    1013    1033 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   5 ynlGnayfklgkydeAleyyekALelnPn 33 
                                       + +++ay ++ +++ A + y+kAL   P+
  gi|330509084|ref|YP_004385512.1| 784 NWIAQAYAHQMDLENAAQWYKKALDMAPD 812
                                       679***********************997 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                        ++ +lG++ +  g+yd A+e  ekAL++
  gi|330509084|ref|YP_004385512.1| 814 FSYQGLGMIQLGRGEYDLAEESLEKALQI 842
                                       57899**********************98 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 2e-05
                                        HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1    1 akalynlGnayfklgkydeAleyyekALelnP 32  
                                        a +l +lG++  + g+ + A e++++AL+++ 
  gi|330509084|ref|YP_004385512.1|  973 AASLHGLGMISSQAGEMEMAAEHFREALQVYQ 1004
                                        567889**********************9875 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 5.3
                                        HHHHHHHHHHHTT-HHH CS
                             TPR_1    3 alynlGnayfklgkyde 19  
                                        al++lG++  ++ + +e
  gi|330509084|ref|YP_004385512.1| 1015 ALFQLGALAVQMDRIQE 1031
                                        8999**99999988876 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   8.5e-06    0.0085       3      33 ..     782     812 ..     781     812 .. 0.94
   2 !   14.5   0.2   3.1e-05     0.031       3      30 ..     815     842 ..     815     842 .. 0.95
   3 !   10.7   0.1   0.00051      0.51       2      30 ..     974    1002 ..     973    1005 .. 0.90
   4 ?   -2.6   0.0       9.5   9.5e+03       2      19 ..    1014    1031 ..    1013    1032 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.5e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++++++++y  + d+e+A ++y+kal+++pd
  gi|330509084|ref|YP_004385512.1| 782 SMNWIAQAYAHQMDLENAAQWYKKALDMAPD 812
                                       6789*************************97 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekalel 30 
                                       +y+ lg+i l  g+y+ A+e++ekal++
  gi|330509084|ref|YP_004385512.1| 815 SYQGLGMIQLGRGEYDLAEESLEKALQI 842
                                       6899*********************986 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00051
                                        CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8    2 eayynlgsiylklgdyeeAkeyyekalel 30  
                                         +++ lg+i ++ g++e+A e +++al+ 
  gi|330509084|ref|YP_004385512.1|  974 ASLHGLGMISSQAGEMEMAAEHFREALQV 1002
                                        57899*********************986 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 9.5
                                        CHHHHHHHHHHHTT-HHH CS
                             TPR_8    2 eayynlgsiylklgdyee 19  
                                         a+++lg +  ++ +++e
  gi|330509084|ref|YP_004385512.1| 1014 GALFQLGALAVQMDRIQE 1031
                                        6899***99999998876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.96   9.6e+02      11      22 ..     737     748 ..     733     752 .. 0.87
   2 !   14.0   0.7   4.2e-05     0.042       4      33 ..     783     812 ..     781     813 .. 0.93
   3 !   14.3   0.1   3.4e-05     0.033       2      30 ..     814     842 ..     813     843 .. 0.92
   4 ?    2.9   0.0      0.15   1.4e+02       1      20 [.     893     912 ..     893     925 .. 0.86
   5 ?    2.4   0.0      0.22   2.2e+02       3      28 ..     935     960 ..     933     965 .. 0.83
   6 !   13.6   0.1   5.4e-05     0.054       2      31 ..     974    1003 ..     973    1006 .. 0.91
   7 ?    0.2   0.1       1.1   1.1e+03       2      22 ..    1014    1034 ..    1013    1037 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.96
                             TPR_2  11 yyklgdyeeAle 22 
                                       y+++gd++eA++
  gi|330509084|ref|YP_004385512.1| 737 YLEAGDLAEARR 748
                                       8999******97 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.2e-05
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                        +++++ay+++ d+e A+++++kAl  +P+
  gi|330509084|ref|YP_004385512.1| 783 MNWIAQAYAHQMDLENAAQWYKKALDMAPD 812
                                       6899************************98 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 3.4e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAlel 30 
                                         +  lG++ + +g+y+ A+e +ekAl++
  gi|330509084|ref|YP_004385512.1| 814 FSYQGLGMIQLGRGEYDLAEESLEKALQI 842
                                       57889**********************97 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.15
                             TPR_2   1 aealynlGlayyklgdyeeA 20 
                                       a +l +++++ + +g+y+ A
  gi|330509084|ref|YP_004385512.1| 893 AAVLQEMANIDMMQGHYDSA 912
                                       568899************98 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.22
                             TPR_2   3 alynlGlayyklgdyeeAleafekAl 28 
                                       +l++l+++ ++ g++++A e ++ Al
  gi|330509084|ref|YP_004385512.1| 935 LLFYLADVDRETGELARATEELDCAL 960
                                       79****************99876555 PP

  == domain 6  score: 13.6 bits;  conditional E-value: 5.4e-05
                             TPR_2    2 ealynlGlayyklgdyeeAleafekAleld 31  
                                          l+ lG++  ++g+ e A+e+f++Al+ +
  gi|330509084|ref|YP_004385512.1|  974 ASLHGLGMISSQAGEMEMAAEHFREALQVY 1003
                                        67999**********************976 PP

  == domain 7  score: 0.2 bits;  conditional E-value: 1.1
                             TPR_2    2 ealynlGlayyklgdyeeAle 22  
                                         al++lG ++ ++++ +e l+
  gi|330509084|ref|YP_004385512.1| 1014 GALFQLGALAVQMDRIQEGLR 1034
                                        699************999776 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.4   3.5e-05     0.035       4      31 ..     782     809 ..     781     810 .. 0.95
   2 !   12.3   0.1   0.00012      0.12       4      32 ..     815     843 ..     813     844 .. 0.92
   3 ?   -2.7   0.2       6.1   6.1e+03       3      35 ..     894     926 ..     893     927 .. 0.70
   4 ?   -2.3   0.2       4.5   4.5e+03       8      33 ..     939     964 ..     938     966 .. 0.83
   5 !   18.7   0.2   1.1e-06    0.0011       2      35 ..     973    1006 ..     972    1009 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                            TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                                       s+n +a a+ ++ +++ A +++++al++
  gi|330509084|ref|YP_004385512.1| 782 SMNWIAQAYAHQMDLENAAQWYKKALDM 809
                                       8*************************87 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00012
                            TPR_10   4 slnNLanalrqrgrydeAealleealair 32 
                                       s+  L+++   rg+yd Ae+ le+al+i+
  gi|330509084|ref|YP_004385512.1| 815 SYQGLGMIQLGRGEYDLAEESLEKALQIH 843
                                       7788***********************97 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.1
                            TPR_10   3 sslnNLanalrqrgrydeAealleealairrrl 35 
                                       + l  +an+   +g yd A   l ++l++ r++
  gi|330509084|ref|YP_004385512.1| 894 AVLQEMANIDMMQGHYDSAWPRLARSLELAREA 926
                                       566677888888888888877777777777765 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4.5
                            TPR_10   8 LanalrqrgrydeAealleealairr 33 
                                       La + r++g++++A + l+ alai r
  gi|330509084|ref|YP_004385512.1| 939 LADVDRETGELARATEELDCALAITR 964
                                       66677899******999999999987 PP

  == domain 5  score: 18.7 bits;  conditional E-value: 1.1e-06
                            TPR_10    2 AsslnNLanalrqrgrydeAealleealairrrl 35  
                                        A+sl+ L+++ +q g+ + A ++++eal+++++l
  gi|330509084|ref|YP_004385512.1|  973 AASLHGLGMISSQAGEMEMAAEHFREALQVYQEL 1006
                                        89******************************98 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   7.7   2.6e-07   0.00026      19     195 ..     765     927 ..     751     931 .. 0.85
   2 !   22.9   4.2   4.9e-08   4.9e-05      85     193 ..     898    1005 ..     890    1011 .. 0.90
   3 !   13.4   1.4   3.8e-05     0.038      43     115 ..     936    1008 ..     928    1035 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.6e-07
                          TPR_MalT  19 ralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGr 95 
                                       + ++l r++L+l p++d  + ++a      a+ +q dle+A q++++a ++a +       ++++ ++++i+  +G+
  gi|330509084|ref|YP_004385512.1| 765 ELIRLNREILELEPDKD-SMNWIA-----QAYAHQMDLENAAQWYKKALDMAPD-------AFSYQGLGMIQLGRGE 828
                                       55667788888888888.444444.....7899*******************44.......4556699********* PP

                          TPR_MalT  96 LheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql.epeaaldayvllaria 171
                                        + A+e  e+alq    q+ q+      +l  la +   +    +A++ l+++ ++le+l ++   ++ ++ +a i 
  gi|330509084|ref|YP_004385512.1| 829 YDLAEESLEKALQIHLGQKDQR--GEAAVLQALASIDMSRKSGSAAKDKLERAARILEDLgDRMGEAAVLQEMANID 903
                                       *************776666665..444555677**************************9677889999******** PP

                          TPR_MalT 172 laqGdleeAetllekaeelaresn 195
                                       + qG  + A+  l++  elare++
  gi|330509084|ref|YP_004385512.1| 904 MMQGHYDSAWPRLARSLELAREAK 927
                                       *******************99875 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 4.9e-08
                          TPR_MalT   85 qqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql.epe 158 
                                          a+i ++qG+ + A+    ++l+la+e++ ++ ++  +ll +lad+ +E ++L +A + l+ +++++++l +++
  gi|330509084|ref|YP_004385512.1|  898 EMANIDMMQGHYDSAWPRLARSLELAREAKDRAGEA--VLLFYLADVDRETGELARATEELDCALAITRDLgDRK 970 
                                        45789***************************7554..555589**************************96678 PP

                          TPR_MalT  159 aaldayvllarialaqGdleeAetllekaeelare 193 
                                          ++++  l  i+ + G++e A++ +++a ++++e
  gi|330509084|ref|YP_004385512.1|  971 GMAASLHGLGMISSQAGEMEMAAEHFREALQVYQE 1005
                                        888999**************************986 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 3.8e-05
                          TPR_MalT   43 tavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqgl 115 
                                        ++ l+ +   +G+l++A++ l  a +++r+ +  + ++ +l ++++i  + G++++A+e++++alq+++e + 
  gi|330509084|ref|YP_004385512.1|  936 LFYLADVDRETGELARATEELDCALAITRDLGDRKGMAASLHGLGMISSQAGEMEMAAEHFREALQVYQELKD 1008
                                        4455555556677777777777777777777777777777777777777777777777777777777776554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.2     4e-08     4e-05      10     146 ..     388     504 ..     385     538 .. 0.69
   2 ?   -2.2   0.1       4.6   4.6e+03      89     106 ..     944     961 ..     848    1038 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4e-08
                            AAA_16  10 eqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysalaqalareellrq 84 
                                       + Ll+++ ++r+g  ++++++Ge G GKs+l++ l+r l ++ g+f    g + ++    p    a++++      q
  gi|330509084|ref|YP_004385512.1| 388 KDLLRLYPDLRQGAVNALIITGELGRGKSALANFLARMLAAS-GYFvlPLGGTAHN----PI-SSARLIE--AAGLQ 456
                                       67899999****************************999999.5555433444444....22.1333331..22223 PP

                            AAA_16  85 lldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqw 146
                                       l+++ e + le  ++ l+++              ++e l+ l++ll++  r ++++ Ddl+ 
  gi|330509084|ref|YP_004385512.1| 457 LAAAGEYQGLEGTKRLLDSS------------LPVNERLAVLMELLRS-NR-ILIFWDDLDL 504
                                       33333443444333333333............4599999999999998.88.********94 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.6
                            AAA_16  89 aesaeleawrekleeala 106
                                        e+ el+++ e+l+ ala
  gi|330509084|ref|YP_004385512.1| 944 RETGELARATEELDCALA 961
                                       233334444444444443 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.012        12      10      34 ..     758     782 ..     752     784 .. 0.86
   2 !    6.8   0.2    0.0079       7.9       5      31 ..     786     812 ..     786     815 .. 0.86
   3 !    9.0   0.2    0.0016       1.6       2      34 ..     816     848 ..     815     852 .. 0.84
   4 ?   -1.0   0.0       2.4   2.4e+03      12      34 ..     906     928 ..     899     930 .. 0.86
   5 ?   -1.1   0.2       2.5   2.5e+03       2      35 ..     936     969 ..     935     970 .. 0.77
   6 !    9.6   0.1   0.00099      0.99       1      28 [.     975    1002 ..     975    1010 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                             TPR_7  10 srlGdyeeAielyeqsLaltkdped 34 
                                        r+G+y e+i+l+++ L+l+ d + 
  gi|330509084|ref|YP_004385512.1| 758 DRRGYYTELIRLNREILELEPDKDS 782
                                       579****************999876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0079
                             TPR_7   5 LarlysrlGdyeeAielyeqsLaltkd 31 
                                       +a++y  + d e+A++ y+++L ++ d
  gi|330509084|ref|YP_004385512.1| 786 IAQAYAHQMDLENAAQWYKKALDMAPD 812
                                       6999****************7777765 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0016
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       +  L+ ++  +G+y+ A+e +e++L+++  + d
  gi|330509084|ref|YP_004385512.1| 816 YQGLGMIQLGRGEYDLAEESLEKALQIHLGQKD 848
                                       6679999999***************99966554 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 2.4
                             TPR_7  12 lGdyeeAielyeqsLaltkdped 34 
                                       +G+y+ A   + +sL+l+++  d
  gi|330509084|ref|YP_004385512.1| 906 QGHYDSAWPRLARSLELAREAKD 928
                                       79999999999****99987655 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 2.5
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       L++La++ ++ G+ ++A e +  +La+t+d +d+
  gi|330509084|ref|YP_004385512.1| 936 LFYLADVDRETGELARATEELDCALAITRDLGDR 969
                                       6777777777888888888777799999999886 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.00099
                             TPR_7    1 aLlnLarlysrlGdyeeAielyeqsLal 28  
                                        +L+ L+ + s+ G++e A+e+++++L++
  gi|330509084|ref|YP_004385512.1|  975 SLHGLGMISSQAGEMEMAAEHFREALQV 1002
                                        6999********************8865 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2         6     6e+03      20      62 ..     604     643 ..     601     648 .. 0.77
   2 !   19.2   2.5   1.4e-06    0.0014      22      67 ..     772     813 ..     731     814 .. 0.89
   3 ?    5.0   0.1     0.038        38       3      25 ..     819     841 ..     818     862 .. 0.71
   4 ?    0.2   1.1       1.2   1.2e+03      10      53 ..     906     952 ..     898     966 .. 0.75
   5 ?    3.4   0.6      0.13   1.2e+02       8      45 ..     991    1024 ..     967    1040 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6
                            TPR_16  20 leaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyraalr 62 
                                        + al+r+   P +++ l  l++++   + la+ + a+y+   +
  gi|330509084|ref|YP_004385512.1| 604 IRSALARG--LPKDVDPLARLAECLSPESLLALQRiAVYDV--A 643
                                       56677777..5888888889999999999999999888887..3 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.4e-06
                            TPR_16  22 aalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       + l++    P + +++++ ++a+++q +l+ Aa++y++al+ apda
  gi|330509084|ref|YP_004385512.1| 772 EILELE---P-DKDSMNWIAQAYAHQMDLENAAQWYKKALDMAPDA 813
                                       556666...6.799******************************97 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.038
                            TPR_16   3 laraalragdyddAaaaleaalk 25 
                                       l+++ l +g+yd A++ le al 
  gi|330509084|ref|YP_004385512.1| 819 LGMIQLGRGEYDLAEESLEKALQ 841
                                       56667777777777777777765 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.2
                            TPR_16  10 agdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeA 53 
                                       +g+yd A ++l + l+++++  d    a  l++l+d+  + g+la+A
  gi|330509084|ref|YP_004385512.1| 906 QGHYDSAWPRLARSLELAREAKDragEAVLLFYLADVDRETGELARA 952
                                       89999999999999999877777766666777777777777777777 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.13
                            TPR_16    8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaal 45  
                                        ++a ++++A+ ++ + lk++      a Al+ lg +a 
  gi|330509084|ref|YP_004385512.1|  991 MAAEHFREALQVY-QELKDQ---AGEAGALFQLGALAV 1024
                                        4677788888888.556666...556667777777665 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.7     7e+02      13      35 ..     607     626 ..     597     627 .. 0.74
   2 ?    6.1   0.0     0.016        16       7      54 ..     703     756 ..     699     768 .. 0.68
   3 !   11.1   2.6   0.00045      0.45       6      53 ..     795     841 ..     774     858 .. 0.89
   4 ?    5.3   0.4     0.029        29       5      53 ..     874     921 ..     871     929 .. 0.82
   5 !   10.2   1.2   0.00082      0.82       2      57 ..     904     965 ..     903     972 .. 0.75
   6 ?    3.9   3.1     0.076        76       2      48 ..     991    1036 ..     990    1039 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.7
                            TPR_19  13 lleqalqedpknaearllLAeal 35 
                                       +l++     pk+ + +++LAe+l
  gi|330509084|ref|YP_004385512.1| 607 ALAR---GLPKDVDPLARLAECL 626
                                       3333...39*************8 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
                            TPR_19   7 yaeAlalleqalqedpknaearl....lL...AeallalgqldeAealLdalpee 54 
                                       + +A ++le++ +e+  ++e+ l    +L      +l++g+l+eA+++ +++   
  gi|330509084|ref|YP_004385512.1| 703 HKRAGRFLEEM-AESGRSPELFLfrldGLleaRGHYLEAGDLAEARRVTARISSY 756
                                       56677777775.66555555555544422343778*************9999765 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00045
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       d+++A++ +++al+ +p+    + +L  ++l  g++d Ae+ L+++++
  gi|330509084|ref|YP_004385512.1| 795 DLENAAQWYKKALDMAPDAFSYQ-GLGMIQLGRGEYDLAEESLEKALQ 841
                                       99***************544444.5999***************99875 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.029
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                        ++++A+++le  l +  + a+++  +A++ + +g++d A   L++ +e
  gi|330509084|ref|YP_004385512.1| 874 DKLERAARILED-LGDRMGEAAVLQEMANIDMMQGHYDSAWPRLARSLE 921
                                       578999999999.6777889999999************99777766665 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.00082
                            TPR_19   2 laegdyaeAlalleqalqe......dpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       +++g y++A ++l++ l+        ++ a ++ +LA++  ++g+l+ A + Ld +++ ++d
  gi|330509084|ref|YP_004385512.1| 904 MMQGHYDSAWPRLARSLELareakdRAGEAVLLFYLADVDRETGELARATEELDCALAITRD 965
                                       789******888888775533332233355555589*****************977666655 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.076
                            TPR_19    2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealL 48  
                                        +a++ + eAl+ +++ l++ ++ a a+ +L  + +++ +++e  +l+
  gi|330509084|ref|YP_004385512.1|  991 MAAEHFREALQVYQE-LKDQAGEAGALFQLGALAVQMDRIQEGLRLM 1036
                                        688999*********.7999999999999***********9977765 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2   0.00097      0.96       7      87 ..     822     939 ..     820     946 .. 0.84
   2 !    6.3   0.2    0.0099       9.9      43      79 ..     975    1011 ..     943    1025 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00097
                            ANAPC5   7 nalrakdYqqaldsLhryFDyvlsqnessq....................................kksyqyalLn. 46 
                                        +l++ +Y+ a +sL +   + l+q++++                                      ++ + a+L+ 
  gi|330509084|ref|YP_004385512.1| 822 IQLGRGEYDLAEESLEKALQIHLGQKDQRGeaavlqalasidmsrksgsaakdkleraariledlgDRMGEAAVLQe 898
                                       57788899999999999999988888887778999999999999999999999999999999999888889998863 PP

                            ANAPC5  47 laslhadfghneeAvkaleeairlArenkDkscLalalawl 87 
                                       +a++ +  gh++ A  +l  + +lAre kD +  a+ l  l
  gi|330509084|ref|YP_004385512.1| 899 MANIDMMQGHYDSAWPRLARSLELAREAKDRAGEAVLLFYL 939
                                       78888888**********************98766666655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0099
                            ANAPC5   43 alLnlaslhadfghneeAvkaleeairlArenkDksc 79  
                                        +l  l +++++ g+ e A + ++ea ++ +e kD++ 
  gi|330509084|ref|YP_004385512.1|  975 SLHGLGMISSQAGEMEMAAEHFREALQVYQELKDQAG 1011
                                        455688999999**********************986 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.8   8.8e-05     0.088     112     233 ..     790     925 ..     764     956 .. 0.73
   2 ?    2.7   0.1     0.069        68     179     214 ..     992    1026 ..     988    1040 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.8e-05
                                       HHHTT-HHHHHHHHTT--SHHHHHHHHH..HHHHTT-..HHHHHHHHHHHHHH-........TT-HHHHHHHHHHHH CS
                        Coatomer_E 112 flkegdfddalkllkksenLeavAlkvq..illklhr..vdlAekelkkmqdid........edatltQLAqawvkl 176
                                       + ++ d ++a +  kk   +   A + q   +++l r   dlAe+ l k+ +i         e a+l  LA+  ++ 
  gi|330509084|ref|YP_004385512.1| 790 YAHQMDLENAAQWYKKALDMAPDAFSYQglGMIQLGRgeYDLAEESLEKALQIHlgqkdqrgEAAVLQALASIDMSR 866
                                       66677777777777777666666666652223444442267899998888877433333333667788899999988 PP

                                       HH-T...THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT CS
                        Coatomer_E 177 avgg...ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdak 233
                                        +g+   +k++ A  i ++l +++    ++l+ +A +++++g+y+ A   L  +L+   +
  gi|330509084|ref|YP_004385512.1| 867 KSGSaakDKLERAARILEDLGDRM-GEAAVLQEMANIDMMQGHYDSAWPRLARSLELARE 925
                                       888766789**************5.567899********************999975443 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.069
                                        -TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHT CS
                        Coatomer_E  179 ggekiqdAyyifqelsekykstplllngkAvvslll 214 
                                        ++e++++A+ ++qel ++  +  +l +  A   +++
  gi|330509084|ref|YP_004385512.1|  992 AAEHFREALQVYQELKDQAGEAGALFQLGAL-AVQM 1026
                                        78999*************9888877665443.3444 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.17       1      54 [.     406     461 ..     406     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                     Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegk..snilvtapskenvktlfeflakglealg 54 
                                       ++t++ GRGKSa++  ++  l+a+g+    +  ta ++ + ++l+e +  +l a g
  gi|330509084|ref|YP_004385512.1| 406 IITGELGRGKSALANFLARMLAASGYfvLPLGGTAHNPISSARLIEAAGLQLAAAG 461
                                       59999*********************7667777*************9988887765 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.6   0.00081      0.81       3      28 ..     789     814 ..     787     817 .. 0.83
   2 ?    2.3   0.1      0.13   1.3e+02       7      23 ..     826     842 ..     823     843 .. 0.95
   3 ?    0.3   0.0      0.57   5.7e+02       2      26 ..     941     965 ..     940     966 .. 0.90
   4 ?    0.1   0.1      0.65   6.5e+02       8      23 ..     987    1002 ..     985    1006 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00081
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdna 28 
                                       ay  q ++e+A ++YkkAl+  Pd  
  gi|330509084|ref|YP_004385512.1| 789 AYAHQMDLENAAQWYKKALDMAPDAF 814
                                       66667799************999975 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.13
                            TPR_11   7 qGkyeeAieaYkkAlkl 23 
                                       +G+y+ A e+++kAl++
  gi|330509084|ref|YP_004385512.1| 826 RGEYDLAEESLEKALQI 842
                                       7**************98 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.57
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPd 26 
                                       d+ +e G++  A e++  Al+++ d
  gi|330509084|ref|YP_004385512.1| 941 DVDRETGELARATEELDCALAITRD 965
                                       78899****************9876 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.65
                            TPR_11    8 GkyeeAieaYkkAlkl 23  
                                        G+ e A e++++Al+ 
  gi|330509084|ref|YP_004385512.1|  987 GEMEMAAEHFREALQV 1002
                                        6667777777777764 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0015       1.5       3      29 ..     405     431 ..     403     538 .. 0.79
   2 ?   -0.1   0.0      0.77   7.7e+02     116     142 ..     671     697 ..     655     712 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegkl 29 
                                       +i++Ge G GK++L+  la+ +a++ +
  gi|330509084|ref|YP_004385512.1| 405 LIITGELGRGKSALANFLARMLAASGY 431
                                       79*******************999874 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.77
                                       TTTT--EEEEEEECCCHHHHCTTSSCE CS
                             NACHT 116 kllpeasllltvrpralrdleeqleea 142
                                       +l+ ++  l++v+++a++ l+e+l+ +
  gi|330509084|ref|YP_004385512.1| 671 SLCYKTGNLWAVHSSARPALREGLSPE 697
                                       68889999***************9866 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4      0.38   3.8e+02     120     144 ..     786     809 ..     781     817 .. 0.85
   2 ?    7.7   1.0     0.002         2      54     176 ..     832     954 ..     825     960 .. 0.62
   3 ?    8.0   0.8    0.0017       1.7      91     170 ..     950    1028 ..     921    1048 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.38
                                       HHHHHHHTT--HHHHHHHHHHHHHH CS
                              SNAP 120 iaelyekelgdlekAieaYekAael 144
                                       ia+ y ++  dle+A + Y+kA ++
  gi|330509084|ref|YP_004385512.1| 786 IAQAYAHQ-MDLENAAQWYKKALDM 809
                                       78899988.9999999999999875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHHH.TT-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT- CS
                              SNAP  54 AgeaflkaAecqek.lkekdeaanayveAakcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelg 129
                                       A e  +ka +++    +++ eaa   + A+  ++++s ++A + le+A+ i+ + g     A   +e+a++   + g
  gi|330509084|ref|YP_004385512.1| 832 AEESLEKALQIHLGqKDQRGEAAVLQALASIDMSRKSGSAAKDKLERAARILEDLGDRMGEAAVLQEMANIDMMQ-G 907
                                       555555666666542333444444444444445555666777777777777777776666666777777777777.7 PP

                                       -HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHH CS
                              SNAP 130 dlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAie 176
                                       ++++A    ++  el ++ +  a    +l  +A++  e +++++A+e
  gi|330509084|ref|YP_004385512.1| 908 HYDSAWPRLARSLELAREAKDRAGEAVLLFYLADVDRETGELARATE 954
                                       77777777777777766666666666666667777666666666665 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0017
                                        HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                              SNAP   91 eeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAels 165 
                                        ++A e l+ A +i  + g  +  A     ++ +  ++ g++e A e++++A ++y++ + +a    +l ++  l+
  gi|330509084|ref|YP_004385512.1|  950 ARATEELDCALAITRDLGDRKGMAASLHGLGMISSQA-GEMEMAAEHFREALQVYQELKDQAGEAGALFQLGALA 1023
                                        5666777777777777666665555666677777666.7777777777777777777666666666666666666 PP

                                        HHTT- CS
                              SNAP  166 aelek 170 
                                         ++++
  gi|330509084|ref|YP_004385512.1| 1024 VQMDR 1028
                                        55555 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.04        40      44      66 ..     735     757 ..     727     769 .. 0.85
   2 ?    2.8   1.8     0.086        86      39     105 ..     783     845 ..     777    1013 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.04
                                       HHHHHCT-HHHHHHHHHTCCCC- CS
                              RPN7  44 ehYlkigdleeAlkaysrireyc 66 
                                        hYl++gdl+eA +  +ri  y+
  gi|330509084|ref|YP_004385512.1| 735 GHYLEAGDLAEARRVTARISSYL 757
                                       69****************99886 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.086
                                       HHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHCSSS- CS
                              RPN7  39 kldlaehYlkigdleeAlkaysrireyctslkhkidmllnlirvaiffndwdlvskylekakellek 105
                                       ++ +a+ Y+  +dle+A ++y+++++    +++     l +i++   ++++dl+++ leka ++   
  gi|330509084|ref|YP_004385512.1| 783 MNWIAQAYAHQMDLENAAQWYKKALDMA--PDAFSYQGLGMIQL--GRGEYDLAEESLEKALQIHLG 845
                                       6667888999999999999999988754..33433344444333..355555555555555555444 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.4     0.026        26      22      49 ..     779     806 ..     762     839 .. 0.80
   2 ?   -2.5   0.0       6.1   6.1e+03       2      44 ..     906     954 ..     905     975 .. 0.67
   3 ?    5.5   0.1     0.019        19      37      78 ..     994    1035 ..     991    1037 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.026
                                       -HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                            ANAPC3  22 spedayllAlclylngqykrAyellrka 49 
                                       + ++  + A+++ ++ + + A ++++ka
  gi|330509084|ref|YP_004385512.1| 779 DKDSMNWIAQAYAHQMDLENAAQWYKKA 806
                                       678899********************99 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.1
                                       TT-HHHHHHHHHHHH.....HHH--HHH..HHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerll....aaetesped..ayllAlclylngqykrAye 44 
                                       q++y++A   + r l    +a+ +  e+  +++lA +  ++g+  rA e
  gi|330509084|ref|YP_004385512.1| 906 QGHYDSAWPRLARSLelarEAKDRAGEAvlLFYLADVDRETGELARATE 954
                                       6677777777777773322233333333446777888888888888866 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.019
                                        T-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   37 gqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaa 78  
                                        + + +A+++++++k +    g+++ ++  ++++++++e++++
  gi|330509084|ref|YP_004385512.1|  994 EHFREALQVYQELKDQAGEAGALFQLGALAVQMDRIQEGLRL 1035
                                        5799*********9999**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1098 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.90u 0.31s 00:00:01.21 Elapsed: 00:00:00.54
# Mc/sec: 6155.49
//
Query:       gi|330509085|ref|YP_004385513.1|  [L=304]
Description: hypothetical protein MCON_3469 [Methanosaeta concilii GP6]
Scores for complete 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   50.7   0.0    3.2e-13   50.3   0.0    1.1  1  Peptidase_C1     Papain family cysteine protease
  ------ inclusion threshold ------
       0.14   12.7   0.0       0.26   11.8   0.0    1.4  1  Peptidase_C39_2  Peptidase_C39 like family


Domain annotation for each model (and alignments):
>> Peptidase_C1  Papain family cysteine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   3.5e-17   3.2e-13       1     200 [.      58     274 ..      58     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 3.5e-17
                                       STSCEETTTTTTGSG---B-TSSBTHHHHHHHHHHHHHHHHHHSSS---B-HHHHHHHST..TTSTGGGBB-HHHHH CS
                      Peptidase_C1   1 lpesvDwrekggavtpvkdqgsCGsCWafsavgaledrlaiktkkklvslSeqelvdCsk..eenegCnGGlmenaf 75 
                                       lp+svD r+    + p++dqg+ GsC a + vg++e     +  +++++ S   l   ++  ++++g +G +  +++
  gi|330509085|ref|YP_004385513.1|  58 LPTSVDLRK---WFPPIEDQGDLGSCTANAGVGVFEYFERRAF-GEHIDASRLFLYKVTRnlMQERGDTGAYIRTTM 130
                                       699*****9...489**********************999999.7***********9999756666*********** PP

                                       HHHHHTEBEBTTTS--SSSCS.........SS-CGCGGGSEEBEESEEEEEESSBHHHHHHHHHHHSSEEEEEECCS CS
                      Peptidase_C1  76 eyikkggivtekdypYkakeg.........gkCkkkkkkekvakikgygkvkenseealkkalakngPvsvaidase 143
                                         +   g+  e   pY  ++          g  ++ k   k+++ +  g+++ +  +++k+++a+  P    +++++
  gi|330509085|ref|YP_004385513.1| 131 GAMALFGVPPERYWPYDISKFdeepsaflfGFADNYKA-LKYVNLDPPGTTPTKLLSNIKTNIAAGIPSIFGFTVYD 206
                                       ************99***444345667777543344444.34799999999999999********************* PP

                                       HHHHTEESSEESSTSCET..SS-EEEEEEEEEEEET..........TEEEEEEE-SBTTTSTBTTEEEE CS
                      Peptidase_C1 144 edfqlYksGvyketecsk..telnhavlivGygven..........gkkyWivkNsWgtdwgekGYiri 200
                                       +  q+ ++G +    cs+   +  ha+ +vGy+ +           ++   +++NsWg+ wg++GY ++
  gi|330509085|ref|YP_004385513.1| 207 SISQAGSTGKIPY-PCSNesVQGGHAIIAVGYDDKMkiknsncgaeTTGALMIRNSWGELWGDEGYGWL 274
                                       8777777775555.5666447889*********9999********99999****************876 PP

>> Peptidase_C39_2  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.9e-05      0.26      87     135 ..     183     241 ..     165     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.9e-05
                   Peptidase_C39_2  87 ssieevkkeidagkPvvvsvttfkpl..............ndgeikftssgHlvvitGYdekg 135
                                       + ++++k++i+ag+P ++ +t+ + +              n    ++ ++gH+++ +GYd+k 
  gi|330509085|ref|YP_004385513.1| 183 KLLSNIKTNIAAGIPSIFGFTVYDSIsqagstgkipypcsN----ESVQGGHAIIAVGYDDKM 241
                                       56799***************875555799999888866543....67899**********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2141.19
//
Query:       gi|330509086|ref|YP_004385514.1|  [L=85]
Description: hypothetical protein MCON_3470 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-17   63.0   0.0    2.7e-17   63.0   0.0    1.0  1  Inhibitor_I42  Chagasin family peptidase inhibitor I42


Domain annotation for each model (and alignments):
>> Inhibitor_I42  Chagasin family peptidase inhibitor I42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.0   1.5e-21   2.7e-17       7      87 ..       2      79 ..       1      83 [. 0.89

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 1.5e-21
                                      EEEEEEEE-CCCT-EEEEEE--TTTEEE-TTTCECCECCESTTSSEEEEEEEEESSSEEEEEEEEEE-TTSTSS--SC. CS
                     Inhibitor_I42  7 tieieLpenpttGYsWtvdasdseglkllseeyipdesdelvGaggthvwtfkalkpGettiefkyarpwekateaeer 85
                                      +++++L++npttGY+W+  + d  +l+l ++e+++++ +  vG+gg+++ tf   k+G t+i+++ +r+we+ +  e+r
  gi|330509086|ref|YP_004385514.1|  2 EFTLSLESNPTTGYVWE-ATFDRAFLELKKKEFKESDGE-SVGSGGIETLTFVPIKAGRTEITMVHKRQWENIPL-ERR 77
                                      599**************.44568***************9.********************************944.444 PP

                                      EE CS
                     Inhibitor_I42 86 tf 87
                                      +f
  gi|330509086|ref|YP_004385514.1| 78 SF 79
                                      66 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 559.20
//
Query:       gi|330509087|ref|YP_004385515.1|  [L=210]
Description: 30S ribosomal protein S3Ae [Methanosaeta concilii GP6]
Scores for complete 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  223.1   2.5    2.8e-66  222.9   2.5    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.28   11.2   0.0    1.6  1  DUF4460         Domain of unknown function (DUF4460)


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.9   2.5   3.2e-70   2.8e-66       3     202 .]       5     193 ..       3     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 222.9 bits;  conditional E-value: 3.2e-70
                                       ----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCS.HTSSSEEEEEEEEEE CS
                    Ribosomal_S3Ae   3 kkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtnde.keqafrklklkieev 78 
                                       ++++ D+ k+K+Wy+v +P++fg++++G+t++       +++e ++gr++e++l+DLtn++ k+  ++klk+++++v
  gi|330509087|ref|YP_004385515.1|   5 SQRKADSRKAKQWYKVVSPEMFGRVPFGETIA-------NDPERIVGRIIETTLGDLTNNFsKQ--NTKLKFRVDRV 72 
                                       67899***************************.......**********************555..*********** PP

                                       ESSEEEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHH CS
                    Ribosomal_S3Ae  79 qgknaltnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilte 155
                                       +g++a+t+F g+e+t+D++rslv++++s+I+ ivdv+t+Dgy++r+++ +fT kr   a+++q+k Ir   + ++ e
  gi|330509087|ref|YP_004385515.1|  73 AGDSAYTKFLGHEMTTDYVRSLVKRRTSRIDSIVDVTTTDGYTVRIKPSCFTVKR---ARANQVKCIRDLSKSVVME 146
                                       *******************************************************...******************* PP

                                       HHHHS-HHHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE-S CS
                    Ribosomal_S3Ae 156 easeldlkelvkklipeslgkeiekeakkIyplrnveirKvkvlkkP 202
                                       + ++ldl++l+++++  +++ +i+keak Iyplr+ve+rK+++ ++P
  gi|330509087|ref|YP_004385515.1| 147 RSKNLDLNQLIQDVVGGKISLDIYKEAKVIYPLRRVEVRKTEIRTEP 193
                                       ****************77***********************997766 PP

>> DUF4460  Domain of unknown function (DUF4460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.1e-05      0.28       6      71 ..       7      71 ..       2     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                           DUF4460  6 skkelrnaLrpFYlavhPDlfgqyPkekkvNeeSLklLnsyleelkkeekksikpekkkLtFyvre 71
                                       k++ r+a +++Y+ v P++fg+ P   ++ ++  ++   ++e+     +++++++++kL+F v  
  gi|330509087|ref|YP_004385515.1|  7 RKADSRKA-KQWYKVVSPEMFGRVPFGETIANDPERIVGRIIETTLGDLTNNFSKQNTKLKFRVDR 71
                                      44444444.99*****************9999999*********99999999**********9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1516.88
//
Query:       gi|330509088|ref|YP_004385516.1|  [L=131]
Description: hypothetical protein MCON_3472 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0014   18.6   0.0     0.0021   18.0   0.0    1.2  1  BiPBP_C    Penicillin-Binding Protein C-terminus Family
  ------ inclusion threshold ------
      0.087   13.6   0.0       0.16   12.8   0.0    1.6  1  Big_7      Bacterial Ig domain
        0.2   11.7   0.4        0.2   11.7   0.4    2.2  3  Ibs_toxin  Toxin Ibs, type I toxin-antitoxin system


Domain annotation for each model (and alignments):
>> 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 !   18.0   0.0   3.6e-07    0.0021      10      88 ..      46     127 ..      38     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.6e-07
                           BiPBP_C  10 splrIafPadGailaldpdipkrqrlqlkarggea..plrWll..dgeplaetkrgrelawqpepGrhrLtv..vDa 80 
                                         ++I++P +G i++ d+di    ++  +a+gge+  +++W    dg++  + +++++  +++e+G h + +  +D+
  gi|330509088|ref|YP_004385516.1|  46 IKVTITSPDAGQIIKGDEDI----SFEGSAKGGEGdlSYEWSSsiDGKLS-TSRSFKQNPIELEKGGHIIILkaMDE 117
                                       5789***************9....888899999777988886444****9.889999999999*****987777*** PP

                           BiPBP_C  81 aGrvdd..vr 88 
                                       +G++ +  v+
  gi|330509088|ref|YP_004385516.1| 118 SGKSGQgsVQ 127
                                       **99776555 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.6e-05      0.16       3      27 ..      48      73 ..      47     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                                      EEEEE--TT--EB.TSEEEEEEEEE- CS
                             Big_7  3 vtitsPangatvs.ggtvtisasAsd 27
                                      vtitsP +g+ ++  +++++++sA  
  gi|330509088|ref|YP_004385516.1| 48 VTITSPDAGQIIKgDEDISFEGSAKG 73
                                      9************8889999999975 PP

>> Ibs_toxin  Toxin Ibs, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   3.4e-05       0.2       2      12 ..       1      11 [.       1      16 [. 0.83
   2 ?   -3.2   0.1       1.6   9.6e+03      14      16 ..      65      67 ..      65      68 .. 0.86
   3 ?   -2.8   2.1       1.2     7e+03       4       8 ..     108     112 ..     108     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                         Ibs_toxin  2 MKLVIILVVLL 12
                                      MKLVIIL + L
  gi|330509088|ref|YP_004385516.1|  1 MKLVIILAICL 11
                                      *******8765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                         Ibs_toxin 14 ISF 16
                                      ISF
  gi|330509088|ref|YP_004385516.1| 65 ISF 67
                                      9** PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.2
                         Ibs_toxin   4 LVIIL 8  
                                       ++IIL
  gi|330509088|ref|YP_004385516.1| 108 HIIIL 112
                                       88997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 969.24
//
Query:       gi|330509089|ref|YP_004385517.1|  [L=251]
Description: purine nucleoside phosphorylase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-34  119.1   0.1      2e-34  118.9   0.1    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 !  118.9   0.1   1.1e-38     2e-34       2     216 ..       5     218 ..       4     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 1.1e-38
                                       EEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--...SSHHHHHHHHHHHHHHHC--SEEEE CS
                         PNP_UDP_1   2 iaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstG...iGkpnaavvaeirllkefgvkaiir 75 
                                       ia+i+g +  +e +a++   +t +g++     f+ G   ++  +i ++G   + ++ ++++a i + k  g+  +i+
  gi|330509089|ref|YP_004385517.1|   5 IAVIGGVGFTLEGIADE--VDTAYGPV---PAFRSGIKSQRLAFIPRHGtghLPPHKVDYRAIISAAKKIGAQWVIS 76 
                                       9****************..99999999...77888999999********9999999********************* PP

                                       EEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEES CS
                         PNP_UDP_1  76 iGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatad 152
                                       ++++G++ ++ +vG +  p d++ f+  +  +++++  + ++d ++a ++p lr  l +aa+ l+ ++ +Gv+++a+
  gi|330509089|ref|YP_004385517.1|  77 VNSVGAM-ASQPVGSFFFPYDFVEFTKCRSNTFYEDR-AVHIDLSEA-YCPHLRGHLLAAAKSLDLETSEGVYVCAE 150
                                       *******.999*************9998888888887.*********.***************************** PP

                                       ESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH......HCCCH CS
                         PNP_UDP_1 153 gfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeath.....eevee 216
                                       g++ et+ ++r++r++g d+v+M+++++++lAre+++++a+i++++++aag ++ e+       e v++
  gi|330509089|ref|YP_004385517.1| 151 GPHLETPGQIRMMRQFG-DVVGMTGYPEVALAREAELCYASICIITNPAAGMGESESLSasdipEQVKK 218
                                       *****************.*****************************9998555444334333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1714.16
//
Query:       gi|330509090|ref|YP_004385518.1|  [L=338]
Description: methylthioribose-1-phosphate isomerase [Methanosaeta concilii GP6]
Scores for complete 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-84  282.8   0.0    2.9e-84  282.6   0.0    1.0  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.6   0.0   1.6e-88   2.9e-84       2     282 .]      47     332 ..      46     332 .. 0.98

  Alignments for each domain:
  == domain 1  score: 282.6 bits;  conditional E-value: 1.6e-88
                                       S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHH CS
                             IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakks 78 
                                       vrG+pa++ a++++++ ++++++++++ +++ el+ a+d+++++rPta++l++ ++r+l+   +    ++++e++++
  gi|330509090|ref|YP_004385518.1|  47 VRGAPALGAAGAYSIALAAERSHATNAFDMIAELEMAADMIRNSRPTAINLSWGVDRALQ---AARGGESTEEIREA 120
                                       89**********************************************************...789*********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH CS
                             IF-2B  79 liekikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG 147
                                       +++ ++ +++e+ + +++ig+++a+l++dgdtilT+cn++         +l+v+r+a++++kk++V+++E+rP  qG
  gi|330509090|ref|YP_004385518.1| 121 ALRSAEGIAEEDIRVNRAIGKNGAKLLEDGDTILTHCNAGRlacvgwgtALGVVRSAVEAGKKIEVYACETRPLHQG 197
                                       ***************************************************************************** PP

                                       .HTHHHHHHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGB CS
                             IF-2B 148 .rltakeLvqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkf 222
                                        rlta+eL++++ipvtli  s+ + +m++ ++dkvivGAdri+++  ++nkiGT++ AvlAk+++ip++v+a++++f
  gi|330509090|ref|YP_004385518.1| 198 sRLTAWELAEDKIPVTLICESMSGSLMRRgKIDKVIVGADRITRDV-VFNKIGTYNHAVLAKHHKIPFYVAAPLSTF 273
                                       *********************************************8.****************************** PP

                                       ESTSSSGGGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 223 servqldedifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       ++    +edi ieerdpee+   +g+r a+  ++v+npafD tP el++++ITe+Gv+ p
  gi|330509090|ref|YP_004385518.1| 274 DRI-YGEEDITIEERDPEEICTLAGVRLAPLGINVYNPAFDATPLELVSALITEKGVFRP 332
                                       *87.67888999*********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2374.98
//
Query:       gi|330509091|ref|YP_004385519.1|  [L=276]
Description: phosphate binding protein [Methanosaeta concilii GP6]
Scores for complete 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  113.1   2.7    1.6e-31  110.0   2.7    1.9  1  PBP_like_2  PBP superfamily domain
    1.8e-18   66.4   0.0    2.3e-18   66.0   0.0    1.2  1  PBP_like    PBP superfamily domain
     0.0005   19.9   0.0     0.0034   17.2   0.0    2.1  1  SBP_bac_11  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.053   12.9   0.0      0.079   12.4   0.0    1.2  1  SBP_bac_6   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.0   2.7   3.6e-35   1.6e-31       9     279 ..      30     260 ..      22     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 3.6e-35
                        PBP_like_2   9 vgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangaggl 85 
                                          +++ Gs+t+ p+ +++a+ f+ +++++ v ++++G+gagi+ + +  +d+a+++r +te+e     +  g   +
  gi|330509091|ref|YP_004385519.1|  30 D--VTIMGSSTVMPLAEAAAEVFNLEQNDYLVSVTAGGTGAGILGIVERKYDIAMASRAITEEEK----QMFG-DSF 99 
                                       4..899*********************************************************88....2334.669 PP

                        PBP_like_2  86 iqvpvaigaialvvnkd...npln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqg 158
                                        +++++ ++i ++v+ +    +++ lsr+++  I+sg+ItnWn+ +g+p d++I v++r+ gsgt++ f +a+    
  gi|330509091|ref|YP_004385519.1| 100 QEFKIGMDGISIAVSDEiyqEGVRdLSRDQVMRIYSGEITNWNE-VGGP-DKDIYVISREYGSGTRDDFNEAVIGDI 174
                                       ***************999999999********************.6666.***********************9885 PP

                        PBP_like_2 159 pwtasgigasg..segvasavsn.ngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnpla 232
                                        +++ g+ +      +v++a+s+ + aigy+  +y +   ++ +a+                    +          
  gi|330509091|ref|YP_004385519.1| 175 GTESPGVDTVAysGAEVKTAISGsDRAIGYLGFNYLGGG-VQGIAF--------------------NG--------- 221
                                       555555554445466677777777888888888866622.333332....................22......... PP

                        PBP_like_2 233 wslqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyll 279
                                         ++p++eni+ + y l r +y+++  ++       ++a+aF+d++l
  gi|330509091|ref|YP_004385519.1| 222 --IVPSYENIKLDFYELKRNLYFYTFGDP------TPGARAFIDFIL 260
                                       ..9999*********************99......**********98 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   5.2e-22   2.3e-18       2     168 ..      48     238 ..      47     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 5.2e-22
                                       HHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCH....HCCCCCEEEEEEEEEEE........E-C CS
                          PBP_like   2 eelaeknpgvrvavanvGsggGlkalrageadiagshlldketee....ynapalrkaldgievvl........vnl 66 
                                       e ++ +++++ v+v+  G+g+G+  + +++ dia++++ ++e+e+      +++++  +dgi +++        v+ 
  gi|330509091|ref|YP_004385519.1|  48 EVFNLEQNDYLVSVTAGGTGAGILGIVERKYDIAMASRAITEEEKqmfgDSFQEFKIGMDGISIAVsdeiyqegVRD 124
                                       56777788999********************************9955555667778899999999999999999999 PP

                                       C-HCHCCCCHCCHHHS--BGGGC..-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHC CS
                          PBP_like  67 arreqglvvakgnpkkitnwkdl..adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVa 141
                                       ++r q + +++g   +itnw+++  +d+++ ++ Re GSGtrd f+e++ +    + + +g++++a+s  +v++a++
  gi|330509091|ref|YP_004385519.1| 125 LSRDQVMRIYSG---EITNWNEVggPDKDIYVISREYGSGTRDDFNEAVIGD--IGTESPGVDTVAYSGAEVKTAIS 196
                                       999999999999...9*********************************664..56788999*************** PP

                                       CETTCCE................CCCGG-HCCCCCCECTTCE- CS
                          PBP_like 142 agradvg................vgieavaeelkgldfvplae 168
                                         + ++g                 gi +  e++  ldf +l++
  gi|330509091|ref|YP_004385519.1| 197 GSDRAIGylgfnylgggvqgiafNGIVPSYENI-KLDFYELKR 238
                                       *******55555555555554432444444444.555555555 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.6e-07    0.0034     199     229 ..     248     273 ..      31     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.6e-07
                                       EE-TT--HHHHHHHHHTTSHHHHHHHHHTT- CS
                        SBP_bac_11 199 lkkaakreaAraFlafLrspeaqailrkyGf 229
                                       ++       AraF++f+++p++q+i+++ Gf
  gi|330509091|ref|YP_004385519.1| 248 PT-----PGARAFIDFILGPKGQKIAAEEGF 273
                                       33.....46*********************9 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.8e-05     0.079     191     217 ..     250     275 ..     243     276 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                         SBP_bac_6 191 elakafidfllspevqailakaggvfP 217
                                       + a+afidf+l+p++q+i a++g+ +P
  gi|330509091|ref|YP_004385519.1| 250 PGARAFIDFILGPKGQKIAAEEGF-IP 275
                                       5699******************99.77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1823.04
//
Query:       gi|330509092|ref|YP_004385520.1|  [L=907]
Description: cation-transporting P-type ATPase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-50  171.0   0.6    1.7e-50  171.0   0.6    2.7  3  E1-E2_ATPase     E1-E2 ATPase
    3.1e-38  131.3   4.6    3.1e-38  131.3   4.6    1.9  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    8.2e-19   67.1   0.0      2e-18   65.8   0.0    1.7  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    3.5e-17   63.4   5.3    1.3e-16   61.5   5.3    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
    9.4e-14   51.3   0.0    2.1e-13   50.2   0.0    1.5  1  Cation_ATPase    Cation transport ATPase (P-type)
      4e-07   30.0   0.5    0.00019   21.2   0.6    2.3  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    8.4e-05   23.0   0.0    0.00019   21.9   0.0    1.7  1  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.35   11.1   3.1       0.87    9.9   0.4    3.1  3  DUF2530          Protein of unknown function (DUF2530)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2      0.18     4e+02     118     156 ..      57      93 ..      42      96 .. 0.64
   2 !  171.0   0.6   7.7e-54   1.7e-50       2     181 .]     115     308 ..     114     308 .. 0.98
   3 ?   -3.1   0.4       2.1   4.8e+03     119     155 ..     780     816 ..     767     819 .. 0.51

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHH CS
                      E1-E2_ATPase 118 lgkvlvpvvlliallvflialllgkslaeallralallv 156
                                       l ++++p++ +++l++++ +ll  ++++e+++ +++ll+
  gi|330509092|ref|YP_004385520.1|  57 LRQFYSPLIYILLLAAAISLLL--GDWQESIFIMIVLLL 93 
                                       4445777777777777766533..455599999999886 PP

  == domain 2  score: 171.0 bits;  conditional E-value: 7.7e-54
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-............. CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek............. 64 
                                       +  ++++virdg+e eid++elvpGDivll++g +vpaD+r++e ++  vdes+LTGEs p  k             
  gi|330509092|ref|YP_004385520.1| 115 MVRTKTRVIRDGEEFEIDSEELVPGDIVLLESGGKVPADIRLIEVQDlVVDESLLTGESIPDAKdpdlildrrtplg 191
                                       567899*********************************************************************** PP

                                       G-TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTT CS
                      E1-E2_ATPase  65 ekgdmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllg 141
                                       ++++m+f+Gt+vvsg+ ++v++at+++t +g +a++++ + ++k+pl   ++k+ + +++ v ++++++f++ +++g
  gi|330509092|ref|YP_004385520.1| 192 DRENMAFAGTIVVSGRGRGVAVATASNTAVGGLAASLAGKPETKPPLILRMEKFNSKIALGVAVAVAVIFAVEIYRG 268
                                       ***************************************************************************** PP

                                       SSTTHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 142 kslaeallralallvaaiPcaLplavplalalgarrlakk 181
                                       +++ +++l+++al+vaa+P++Lp+a+++al++g++r+ak+
  gi|330509092|ref|YP_004385520.1| 269 EPIYDIFLQSVALAVAAVPEGLPVAMTVALSIGMSRMAKR 308
                                       **************************************96 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHH CS
                      E1-E2_ATPase 119 gkvlvpvvlliallvflialllgkslaeallralall 155
                                       ++ +++vv  ++ ++f  ++++g+s+ ea   a+ ++
  gi|330509092|ref|YP_004385520.1| 780 VALVAVVVGGLTYAIFHWQMSMGRSIEEARNIAMIMM 816
                                       3444445555555555555556665554444444444 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 ?   -4.0   0.1       4.5     1e+04     130     176 ..     251     263 ..     239     281 .. 0.57
   2 !  131.3   4.6   1.4e-41   3.1e-38       1     182 []     727     899 ..     727     899 .. 0.96

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4.5
                   Cation_ATPase_C 130 laillslllqvlivyvpglnavfgtaplsleewlialllalvvllvd 176
                                       l++                                  ++a++v++ +
  gi|330509092|ref|YP_004385520.1| 251 LGV----------------------------------AVAVAVIFAV 263
                                       222..................................2333333333 PP

  == domain 2  score: 131.3 bits;  conditional E-value: 1.4e-41
                   Cation_ATPase_C   1 plplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfg 77 
                                       plpl a+q+Lw+nLvt ++  +aLa+ep+e + m+rpPr+ +e ++++ m+ ++++++++++ +t+++f + ++ +g
  gi|330509092|ref|YP_004385520.1| 727 PLPLLAVQLLWLNLVTNGIQDVALAFEPAEGGEMNRPPRPANEAIFNRLMVEKVALVAVVVGGLTYAIFHWQMS-MG 802
                                       89*******************************************************************66665.65 PP

                   Cation_ATPase_C  78 isekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgt 154
                                        s +e       a+ +a i++vl++ + ++++rs+ +s+f+ s+  +n+ll++++++++l+qv+ +y+pgl +v+++
  gi|330509092|ref|YP_004385520.1| 803 RSIEE-------ARNIAMIMMVLFENAVVFASRSELKSAFS-SSPLRNPLLVFGTIAAILIQVAAMYMPGLSDVLQI 871
                                       55555.......*****************************.99999****************************** PP

                   Cation_ATPase_C 155 aplsleewlialllalvvllvdelvKll 182
                                       +p+sl++w+ ++++alv ++  el Kl+
  gi|330509092|ref|YP_004385520.1| 872 HPVSLYQWVELVGVALVAFAAIELHKLI 899
                                       **************************96 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0     9e-22     2e-18       2      69 .]       8      75 ..       7      75 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 9e-22
                   Cation_ATPase_N  2 halsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                      h+ ++ +++e L+ + e GL ++e+aerl+ yGpN l+++k++s+ v +l+qf +pl+++Ll aa++s
  gi|330509092|ref|YP_004385520.1|  8 HSIPAYDAIEALKANTEGGLGKDEVAERLRIYGPNSLPKPKPTSIAVYFLRQFYSPLIYILLLAAAIS 75
                                      88899999**********************************************************98 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   5.3   5.7e-20   1.3e-16       3     209 ..     326     656 ..     324     657 .. 0.75

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 5.7e-20
                                       EEEEESBTTTBCHH.HHHHHHHHHH.............CHHHHHHHHHHHHCHHHHHHHHHHHHH....HHHHHHHH CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxx RF
                         Hydrolase   3 tvvfDkdGTLttge.psvedvivsa.............alalaaaletgsehpigkalvaaakar....sgaltgfa 61 
                                        ++ Dk+GTLt  +  + + vi+ +             ++a+ aa  +++e p g + + +  a+    + ++  ++
  gi|330509092|ref|YP_004385520.1| 326 FIASDKTGTLTVNQlTVTRAVIPGRdswnvidlaksprEVAEEAAGKMAAEGPVGSQSAGQTSALkalaRASVLANE 402
                                       6899*******777344444444447777777767777666666666667777776665555555555644444444 PP

                                       HETTTE...........................................................HHHHTHHHHHHH CS
                                       xxxxxx...........................................................xxxxxxxxxxxx RF
                         Hydrolase  62 tfigrg...........................................................ayaigkpewlta 79 
                                       +f g+                                                            a+a+g+pe + +
  gi|330509092|ref|YP_004385520.1| 403 AFSGFRdggwdyhgdavdvallmmaqetgvtqqeeqsnypriaqipfeskrqfsatlhqgpdgriAFAKGSPEKILK 479
                                       44444444588888999999999999999999999999999999999999999999999999999999999998888 PP

                                       H.........HCHHHHHHHHHHHHHHCHHHHHH..........................TTHHHHHHHHHHTHHBHT CS
                                       x.........xxxxxxxxxxxxxxxxxxxxxxx..........................xxxxxxxxxxxxxxxxxx RF
                         Hydrolase  80 l.........dippdlgaaigsaqsqgrtvall..........................qaralavftiadplkvkp 121
                                       +         +ip d + a+  a++                                      l+++ + dp  ++p
  gi|330509092|ref|YP_004385520.1| 480 MscrmatpdgEIPLDPQGADKVAEAL------AtagfrllalasgrfpenqefaedrleGLTFLGLVGMIDP--LRP 548
                                       88864555554444444444444444......255555599*********99998777655999999999**..*** PP

                                       THHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCES...................STTTSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx...................xxxxxxxx RF
                         Hydrolase 122 eaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdiet...................vakpspeg 178
                                       ea+ av++ k+ g++v+++tgd+p+ta ++ ++lG +d +d v+++ + +                    a ++p++
  gi|330509092|ref|YP_004385520.1| 549 EAKAAVEACKSSGVQVAMVTGDHPATAFAISRELGlADSVDQVVTGMELKdaeakgpeavdaltrkgrvYARVEPQQ 625
                                       ***********************************97777777777777756544555555555555656666**** PP

                                       HHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 179 kvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                       kv + + L  +++ va+ GDg+nDa+al aA
  gi|330509092|ref|YP_004385520.1| 626 KVLITNSLVRNGKLVAVTGDGANDAPALHAA 656
                                       ********988888***************99 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 !   50.2   0.0   9.1e-17   2.1e-13      14      87 ..     409     480 ..     398     484 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 9.1e-17
                     Cation_ATPase  14 kdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilkr 87 
                                       ++ ++++G++ ++ALl +a++ g  ++e +++++++++ipF+s+r + +++++     + +++ KG+pe ilk 
  gi|330509092|ref|YP_004385520.1| 409 DGGWDYHGDAVDVALLMMAQETGVTQQEEQSNYPRIAQIPFESKRQFSATLHQG--PDGRIAFAKGSPEKILKM 480
                                       678**************************************************5..6999************95 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0034       7.6      18      55 ..     548     585 ..     542     594 .. 0.90
   2 !   21.2   0.6   8.7e-08   0.00019     202     251 ..     636     686 ..     627     690 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0034
                                       HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                       Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                       +++k+a++ +k+ g++v+  TG ++ ++  + +elgl 
  gi|330509092|ref|YP_004385520.1| 548 PEAKAAVEACKSSGVQVAMVTGDHPATAFAISRELGLA 585
                                       7899*************************999999986 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 8.7e-08
                                       -GGGEEEEESSGGGHHHHHHSSEEEEETTS.-HHHHHHSSEEE--GGGTHH CS
                       Hydrolase_3 202 sleeviafGDgeNDieMLeaaglgvAmgna.seevkkaAdyvtksnnedGV 251
                                       + + v++ GDg ND + L aa +gvAmg + ++ +k+ Ad ++++ n  ++
  gi|330509092|ref|YP_004385520.1| 636 NGKLVAVTGDGANDAPALHAAHVGVAMGKGgTDVAKESADLIITDDNFASI 686
                                       55668899*******************985388899*****9999887666 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   8.4e-08   0.00019      86     187 ..     546     653 ..     486     654 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.4e-08
                               HAD  86 ldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalre.. 160
                                       l+p+a+++++a+++ G++v++v+g +   + ++ +elg    la +++   ++tg  +l +   +g + v+al +  
  gi|330509092|ref|YP_004385520.1| 546 LRPEAKAAVEACKSSGVQVAMVTGDHPATAFAISRELG----LADSVDQ--VVTGM-ELKDAEAKGPEAVDALTRkg 615
                                       469***********************************....7775444..89999.99999999999999999988 PP

                               HAD 161 ..........wlaaegegidlee..........vvay.GDspsDlpll 187
                                                 +                      +va+ GD+ +D p+l
  gi|330509092|ref|YP_004385520.1| 616 rvyarvepqqKV----------LitnslvrngkLVAVtGDGANDAPAL 653
                                       664444444422..........2334555555577777******9998 PP

>> DUF2530  Protein of unknown function (DUF2530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       4.4   9.8e+03      19      34 ..     248     263 ..     235     267 .. 0.56
   2 ?    9.9   0.4   0.00039      0.87      43      64 ..     779     800 ..     771     804 .. 0.86
   3 ?   -2.1   0.0       2.1   4.7e+03       8      31 ..     803     826 ..     799     837 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.4
                           DUF2530  19 vgtllWlvalvvllvv 34 
                                        ++l  +va+ v+++v
  gi|330509092|ref|YP_004385520.1| 248 KIALGVAVAVAVIFAV 263
                                       4555556666666654 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00039
                           DUF2530  43 pvclaGlvvGllGlaiflwQRr 64 
                                       +v+l+ +vvG l +aif wQ +
  gi|330509092|ref|YP_004385520.1| 779 KVALVAVVVGGLTYAIFHWQMS 800
                                       689999**************76 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.1
                           DUF2530   8 rrLtdprpvivvgtllWlvalvvl 31 
                                       r++++ r ++++ ++l+  a+v +
  gi|330509092|ref|YP_004385520.1| 803 RSIEEARNIAMIMMVLFENAVVFA 826
                                       678888999999999999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (907 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.45
# Mc/sec: 6039.52
//
Query:       gi|330509093|ref|YP_004385521.1|  [L=254]
Description: pantothenate synthetase [Methanosaeta concilii GP6]
Scores for complete 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-76  253.4   0.9      1e-75  253.1   0.9    1.1  1  PPS_PS        Phosphopantothenate/pantothenate synthetase
      0.005   16.6   0.6      0.032   14.0   0.2    2.2  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
       0.15   11.8   0.0       0.23   11.2   0.0    1.3  1  Collagen_mid  Bacterial collagen, middle region
       0.18   11.5   0.0          2    8.1   0.0    2.3  2  DUF5053       Domain of unknown function (DUF5053)


Domain annotation for each model (and alignments):
>> PPS_PS  Phosphopantothenate/pantothenate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.1   0.9   2.3e-79     1e-75       1     176 []      66     241 ..      66     241 .. 0.99

  Alignments for each domain:
  == domain 1  score: 253.1 bits;  conditional E-value: 2.3e-79
                            PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeagaeevlgleedaripeleseR 77 
                                       llla++p isvNGN+aaLv+ee+v+La+al+ +levNlf+r+e+Rv+kia+ll+e+gae+vlg++ d+++p+l+++R
  gi|330509093|ref|YP_004385521.1|  66 LLLAERPAISVNGNVAALVSEEMVALARALNIPLEVNLFHRSEDRVKKIADLLREKGAEDVLGERPDTSVPGLDHAR 142
                                       79*************************************************************************** PP

                            PPS_PS  78 akvskeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkske 154
                                       a +++ Giy+aDvvl+plEDGDR+eaL +mgK+viaiDLNPlsRta++at++ivdn+ Ra+p+lte+v++l++k  +
  gi|330509093|ref|YP_004385521.1| 143 ALATRGGIYDADVVLIPLEDGDRCEALLAMGKRVIAIDLNPLSRTAKKATVSIVDNILRAVPQLTEEVRQLSNKPLS 219
                                       ***************************************************************************** PP

                            PPS_PS 155 eleeivkefdnkkvlkealkei 176
                                       +le+i++e+dn+++l+ a++ei
  gi|330509093|ref|YP_004385521.1| 220 DLEKILNEYDNQETLAGAVQEI 241
                                       ****************999986 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 !   14.0   0.2   7.2e-06     0.032       4      42 ..      62      99 ..      59     107 .. 0.89
   2 ?    0.3   0.0      0.12   5.3e+02     104     136 ..     174     205 ..     122     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.2e-06
                                      HHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EE CS
                      TPP_enzyme_M  4 aaellkaakrpvilvGggvarsgaseelrelaeklgiPv 42
                                       a+ll  a+rp+i v g va + +see+++la++l+iP 
  gi|330509093|ref|YP_004385521.1| 62 GAALLLLAERPAISVNGNVA-ALVSEEMVALARALNIPL 99
                                      5899***************9.99***************7 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.12
                                       -EEEEEESSCCCCTTCC--SEEEECTHHHHHHH CS
                      TPP_enzyme_M 104 akiihididpaeigknyqvdlaivgdvketlea 136
                                       +++i id +p +    + ++++iv ++  ++ +
  gi|330509093|ref|YP_004385521.1| 174 KRVIAIDLNPLSRTAKK-ATVSIVDNILRAVPQ 205
                                       37888888887666654.678888877766665 PP

>> Collagen_mid  Bacterial collagen, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.2e-05      0.23      41     110 ..     181     250 ..     171     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.2e-05
                      Collagen_mid  41 anpvGtTla.stgnvvtelgeavssagslVsaLgtgplaplapvttpvggvvstvgqavtsagttLttals 110
                                        np+  T + +t ++v ++ +av ++ + V +L ++pl+ l+++     +  +t++ av+++ + L +++ 
  gi|330509093|ref|YP_004385521.1| 181 LNPLSRTAKkATVSIVDNILRAVPQLTEEVRQLSNKPLSDLEKILNEYDNQ-ETLAGAVQEIRDHLDEQFR 250
                                       58888887525779******************************9998664.8888899988888887765 PP

>> DUF5053  Domain of unknown function (DUF5053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00045         2      31      53 ..      74      96 ..      73      97 .. 0.94
   2 ?    0.3   0.0      0.12   5.6e+02      43      58 ..     229     244 ..     225     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00045
                           DUF5053 31 idvngkvatFteeeletLkeALq 53
                                      i vng+va++ +ee+  L++AL+
  gi|330509093|ref|YP_004385521.1| 74 ISVNGNVAALVSEEMVALARALN 96
                                      679******************96 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.12
                           DUF5053  43 eeletLkeALqdlskr 58 
                                       ++ etL+ A+q++ + 
  gi|330509093|ref|YP_004385521.1| 229 DNQETLAGAVQEIRDH 244
                                       5789********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      724  (0.0403815); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1646.68
//
Query:       gi|330509094|ref|YP_004385522.1|  [L=289]
Description: GHMP kinase ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-08   34.0   1.6      1e-07   32.1   1.6    2.0  2  GHMP_kinases_N  GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.036   14.4   1.9      0.079   13.3   0.1    2.2  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 !   32.1   1.6   1.1e-11     1e-07       2      66 .]      88     152 ..      87     152 .. 0.88
   2 ?   -1.6   0.0      0.36   3.2e+03       9      17 ..     228     236 ..     204     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.1e-11
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                       ++++ ++P g+G+G S+A a++ ++Al+++++l l   + a +a+ + ++ +++ gDv a   Gg
  gi|330509094|ref|YP_004385522.1|  88 VKTDMNMPFGSGFGASGAGALGCAYALNHHFDLGLTADQAASVAHAAEVVNRTGLGDVIAQNTGG 152
                                       6788899************************999876788888887777899******9987776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.36
                                       HTTSSSCHH CS
                    GHMP_kinases_N   9 PvgaGLGSS 17 
                                        + +GL+SS
  gi|330509094|ref|YP_004385522.1| 228 TMETGLASS 236
                                       456788887 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 ?   -0.4   0.3      0.17   1.5e+03      49      65 ..      98     114 ..      94     138 .. 0.70
   2 ?   13.3   0.1   8.8e-06     0.079       4      66 ..     211     265 ..     207     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.17
                    GHMP_kinases_C  49 lgaklsGaGgGptvfal 65 
                                        g++ sGaG  ++ +al
  gi|330509094|ref|YP_004385522.1|  98 SGFGASGAGALGCAYAL 114
                                       46777888555555555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.8e-06
                    GHMP_kinases_C   4 alergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalf 66 
                                       +l+r  le++ +l ++++      ++g  + +  +++ea ++ G   ++ s+ ++G++v+a++
  gi|330509094|ref|YP_004385522.1| 211 LLRRPTLEEFMRLSRRFTM-----ETGLASSWALDMIEAVEAEG---GRASMIMLGDAVYAFG 265
                                       5555555555555555555.....9**************99999...99999999******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); 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 0.29s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2043.83
//
Query:       gi|330509095|ref|YP_004385523.1|  [L=398]
Description: phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-50  171.7   0.1      3e-50  170.7   0.1    1.5  1  DFP           DNA / pantothenate metabolism flavoprotein
    2.4e-38  131.4   0.2    3.9e-38  130.7   0.2    1.3  1  Flavoprotein  Flavoprotein
  ------ inclusion threshold ------
      0.064   13.8   0.0       0.22   12.1   0.0    1.9  2  Pyr_redox     Pyridine nucleotide-disulphide oxidoreductase


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 !  170.7   0.1     5e-54     3e-50       1     186 []     190     370 ..     190     370 .. 0.91

  Alignments for each domain:
  == domain 1  score: 170.7 bits;  conditional E-value: 5e-54
                                       TTT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHH CS
                               DFP   1 legkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleave 77 
                                       l+gk++l+t+G+  E+iDp+R+++Nr+SGk+G+alA +a++rGa+Vtlv+   + + p  v+ v  +sa++ml+av+
  gi|330509095|ref|YP_004385523.1| 190 LKGKRILITSGSNAESIDPIRILTNRASGKTGVALALEARRRGADVTLVHRFIQ-DLP--VHQVYAQSASDMLDAVM 263
                                       689***********************************************9953.334..8899************* PP

                                       HHHTT-.SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-SS....-HH CS
                               DFP  78 ealkea.divimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaete....ell 149
                                       ++lk+  d++i+aAAvaDy+ +  +eeKik    + el+l+l+++++i++++ +++ ++  +vGF+aet+     ll
  gi|330509095|ref|YP_004385523.1| 264 SELKKGcDALISAAAVADYTLD-PSEEKIKS---GLELNLRLKPTRKIIKTV-REAYPDLKIVGFKAETDtgdeALL 335
                                       9996545*************97.6899**96...567***************.56667667*******9668889** PP

                                       HHHHHHHHHTT-SEEEEEEGGGTTGGG-SS-EEEEE. CS
                               DFP 150 enareklerkgldlivaNdvskeeagfgsdenevtll 186
                                       ++ar+ le  gldl+vaNdvs+   g+g+d+n+v++l
  gi|330509095|ref|YP_004385523.1| 336 ARARASLEGAGLDLVVANDVSRG--GMGTDDNRVLIL 370
                                       *********************98..*********985 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.7   0.2   6.5e-42   3.9e-38       1     156 [.      16     183 ..      16     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 130.7 bits;  conditional E-value: 6.5e-42
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHH...CTTESE CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhiel...rrwadl 67 
                                       k i++g+TGs+aa+ +++l++ L+++g+ev+++++ aA +++++  l+ a+       ++++++h+ +     +adl
  gi|330509095|ref|YP_004385523.1|  16 KTIVVGVTGSIAAVRVIDLIRDLIRRGAEVHCTMSHAAGQILHPYALEYASnhpviteITGRVEHVLFcgvGGKADL 92 
                                       679****************************************876666557778888888888887754455**** PP

                                       EEEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT.............. CS
                      Flavoprotein  68 lviaPasantlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigk 141
                                       +++aPa+ant++k+anGi d+++t+++    ++ kp+ ++Pam+ amy++p++++nl++l e gv +i+P   ++gk
  gi|330509095|ref|YP_004385523.1|  93 FLVAPATANTIGKMANGIDDTPVTTFATTalGSGKPVAVVPAMHEAMYRHPAVIRNLQILrEMGVALIDPR-IEEGK 168
                                       ***********************999944589****************************77*********.999** PP

                                       ..GHHHHHHHHHHCH CS
                      Flavoprotein 142 gkmaeieeivgkild 156
                                       +k+a+ +++v+++ +
  gi|330509095|ref|YP_004385523.1| 169 AKFADNQRVVQEVER 183
                                       ***********9986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.9   1.2e+04      16      39 ..     120     141 ..     118     161 .. 0.52
   2 ?   12.1   0.0   3.7e-05      0.22       8      38 ..     218     251 ..     217     271 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.9
                                       HHHHHTTSEEEEEESSSSSSTTSS CS
                         Pyr_redox  16 galaelgkkVtvversdkllrllD 39 
                                       +++   gk V vv ++ + +  + 
  gi|330509095|ref|YP_004385523.1| 120 TTALGSGKPVAVVPAMHEAM--YR 141
                                       55555667777777777666..33 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.7e-05
                                       SHHHHHHHHHHHHTTSEEEEEESSSSSS...TTS CS
                         Pyr_redox   8 GyiglElAgalaelgkkVtvversdkll...rll 38 
                                       G +g+ lA ++++ g++Vt+v+r  + l   +++
  gi|330509095|ref|YP_004385523.1| 218 GKTGVALALEARRRGADVTLVHRFIQDLpvhQVY 251
                                       899********************98888444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3004.16
//
Query:       gi|330509096|ref|YP_004385524.1|  [L=366]
Description: hypothetical protein MCON_3483 [Methanosaeta concilii GP6]
Scores for complete 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-08   32.5  47.5    1.9e-05   24.6  20.5    3.1  2  Apolipoprotein   Apolipoprotein A1/A4/E domain
    3.4e-07   30.5  33.5    0.00029   21.0   4.0    4.9  5  DUF4164          Domain of unknown function (DUF4164)
    1.4e-05   25.2  24.5      0.019   15.0   2.6    5.2  6  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    5.1e-05   22.8  25.4    0.00096   18.7  17.0    4.7  2  HBM              Helical bimodular sensor domain
    0.00046   17.9  29.7    0.00046   17.9  29.7    2.1  2  DUF3584          Protein of unknown function (DUF3584)
     0.0009   19.1  32.3       0.06   13.2   1.7    5.4  6  CdvA             CdvA-like coiled-coil domain
     0.0012   18.3  25.0       0.24   10.7  11.4    3.2  3  DUF4407          Domain of unknown function (DUF4407)
     0.0018   18.7   1.7        2.4    8.7   0.1    3.6  3  T7SS_ESX_EspC    Excreted virulence factor EspC, type VII ESX
     0.0034   17.9  31.7         17    6.1   0.4    5.8  2  Syntaxin-6_N     Syntaxin 6, N-terminal
     0.0048   17.2   1.4     0.0048   17.2   1.4    3.2  2  FCH              Fes/CIP4, and EFC/F-BAR homology domain
     0.0061   16.7  23.3       0.63   10.1   2.1    4.8  4  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
     0.0064   16.5  25.6       0.21   11.6   3.7    4.7  4  DUF1664          Protein of unknown function (DUF1664)
     0.0083   16.5  33.4      0.017   15.5   1.6    6.0  5  UPF0184          Uncharacterised protein family (UPF0184)
  ------ inclusion threshold ------
      0.013   15.7   4.9        2.5    8.4   0.2    3.4  3  Ribosomal_S15    Ribosomal protein S15
      0.013   15.7  19.7        3.5    7.9   0.8    6.9  5  WXG100           Proteins of 100 residues with WXG
      0.033   14.9   2.1        1.9    9.2   0.1    2.6  2  DUF4439          Domain of unknown function (DUF4439)
      0.033   13.5  32.9       0.32   10.3  11.1    3.1  3  SF-assemblin     SF-assemblin/beta giardin
      0.041   13.7   1.8      0.041   13.7   1.8    4.8  3  HSBP1            Heat shock factor binding protein 1
      0.059   13.3  18.2        1.4    8.8   2.1    4.6  5  Remorin_C        Remorin, C-terminal region
      0.085   13.4  37.5        0.2   12.2   2.9    5.0  5  FadA             Adhesion protein FadA
       0.17   12.2  35.0       0.35   11.2   2.2    5.0  4  YlqD             YlqD protein
       0.24   12.0  18.1    1.7e+02    2.8   4.4    5.6  2  YtxH             YtxH-like protein
       0.34   10.9  26.2        0.9    9.6   0.5    4.8  5  Laminin_II       Laminin Domain II
       0.42    9.1   5.5       0.27    9.7   0.4    2.2  2  FUSC             Fusaric acid resistance protein family
       0.43   10.6  25.3      0.079   13.0   5.6    3.7  3  Erp_C            Erp protein C-terminus
       0.44    8.5  26.6        0.5    8.2   6.9    2.7  3  Prominin         Prominin
       0.58   10.1  10.4         12    5.9   0.0    4.7  4  ApoO             Apolipoprotein O
       0.58   10.2  41.3       0.88    9.6   9.1    3.9  4  DUF1640          Protein of unknown function (DUF1640)
       0.65    9.7   9.3        7.3    6.3   0.5    3.6  3  DUF842           Eukaryotic protein of unknown function (DUF8
       0.68   10.4  19.3        2.7    8.5   1.0    5.7  5  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.89   10.0  31.6        1.2    9.5   9.5    4.4  4  DUF4600          Domain of unknown function (DUF4600)
       0.93   10.0   4.4        2.4    8.7   0.2    3.1  2  Tox-REase-5      Restriction endonuclease fold toxin 5
       0.94    9.0  31.7        7.9    5.9  20.8    3.0  2  Exonuc_VII_L     Exonuclease VII, large subunit
        1.1    8.1  13.7      0.072   12.1   0.7    2.9  3  Histidinol_dh    Histidinol dehydrogenase
        1.2    9.3  35.0        2.3    8.4   1.8    4.2  4  Fib_alpha        Fibrinogen alpha/beta chain family
        1.3    9.1   5.4         25    5.0   0.3    3.3  2  HJURP_C          Holliday junction regulator protein family C
        1.5    8.8   7.2        6.9    6.6   0.1    3.6  2  Matrilin_ccoil   Trimeric coiled-coil oligomerisation domain 
        1.5    8.5  42.5       0.47   10.1  31.2    2.8  2  SHE3             SWI5-dependent HO expression protein 3
        1.6    9.0  40.2        4.1    7.7  10.9    4.4  4  OmpH             Outer membrane protein (OmpH-like)
        1.9    8.1  11.3        1.4    8.6   0.7    3.5  4  DCB              Dimerisation and cyclophilin-binding domain 
          2    8.7  33.0       0.36   11.1   2.2    5.4  5  FliJ             Flagellar FliJ protein
        2.5    7.9  31.5        8.7    6.1   3.5    3.7  4  PIN_8            PIN like domain
        2.6    6.7  29.7      0.043   12.6   5.7    3.4  3  BshC             Bacillithiol biosynthesis BshC
        3.1    8.2  32.4        4.6    7.6   4.6    6.2  8  KxDL             Uncharacterized conserved protein
        3.2    8.0   9.6        9.4    6.5   0.1    3.9  3  Endonuc-dimeris  T4 recombination endonuclease VII, dimerisat
        4.3    7.4  13.4       0.87    9.6   1.0    4.1  4  DUF1515          Protein of unknown function (DUF1515)
        6.4    7.1  32.9       0.63   10.3   2.8    6.9  8  XhlA             Haemolysin XhlA
          7    7.3  22.8        8.4    7.1   2.1    5.4  5  DUF883           Bacterial protein of unknown function (DUF88
        8.2    7.0  38.9        7.2    7.2   9.7    5.4  4  DUF16            Protein of unknown function DUF16


Domain annotation for each model (and alignments):
>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6  20.5   5.2e-08   1.9e-05       3     185 ..      53     243 ..      51     248 .. 0.87
   2 !   21.6  19.0   4.5e-07   0.00017       3     185 ..     143     344 ..     141     349 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.2e-08
                                       HHCCCCHHHHHCCHHHCHHCH...HHHHHHHHHHHHHHHHHHH...HHHHHHHHHHCCCCHHHHHHCCCHHHHHHHH CS
                    Apolipoprotein   3 eesldelkayaeeleeqlapl...aqelrdrlskeleelrarl...raeleevrarlepyrdevqeqlgqnleelrq 73 
                                       +esld+l++y+ e+e++ + l   a+++ ++l +  +++ +     ++e+++   +l++++d ++ +l + l++l +
  gi|330509096|ref|YP_004385524.1|  53 SESLDKLDQYIIEVESRWSILepeARKILEQLKDTGNDIHNSFnelKQETDQRGTKLQEDTDKAKVELHAALDNLES 129
                                       699************997766443777777776666655543244499***************************** PP

                                       HCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..---- CS
                    Apolipoprotein  74 rlapyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaphaeevee 150
                                       +l+  ++  +++ + ++ e+ + l+     l ++ e+++++   +l++++++++ +l++ l +l+++l+++++ +++
  gi|330509096|ref|YP_004385524.1| 130 KLDQSLKYFQDKSEDRYTEINQNLDNHRSRL-DEFEKETDQRWMKLQEDTDKAKVELHAALNNLESKLDQSLKYFQD 205
                                       ***********99999999999999988777.5689999************************************** PP

                                       -SSSHHHHHHHTS-T...TSHHHHHS--XXXXXXXXXX CS
                    Apolipoprotein 151 rlssrveelreklee...qaeelrerleanleelkaql 185
                                       + ++r++e+++ l+     ++el+ ++++   +l++ +
  gi|330509096|ref|YP_004385524.1| 206 KSEDRYTEINQNLDNhrsRLDELEKEIDQRGMKLQEDI 243
                                       ***************99999999999999998888766 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 4.5e-07
                                       HHCCCCHHHHHCCHHHCHHCHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCC CS
                    Apolipoprotein   3 eesldelkayaeeleeqlaplaq...elrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrla 76 
                                       e++  e+++++++ +++l ++ +   + + +l +++++++ +l a l+++ ++l + +  +q + +++  e++q l+
  gi|330509096|ref|YP_004385524.1| 143 EDRYTEINQNLDNHRSRLDEFEKetdQRWMKLQEDTDKAKVELHAALNNLESKLDQSLKYFQDKSEDRYTEINQNLD 219
                                       6788899999999999999994434368999*********************************************9 PP

                                       HHHHHHHH...HHHHCHHCCHHCHCCHCHH.......HHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH---- CS
                    Apolipoprotein  77 pyteelre...rlaadaeelqeqlavyaee.......lrerlerhvealkarlapyveelrqklaerleelkeslap 143
                                       ++ ++l e    ++++  +lqe ++  + +       lr++l r + +l++  +  + e+ ++ +++ +e++e  + 
  gi|330509096|ref|YP_004385524.1| 220 NHRSRLDElekEIDQRGMKLQEDITNAQSDfqianrnLRNELVRMINDLRSESEIRFLEFNNSFDQQKDEFSEVTTG 296
                                       99877755444666666666666666665566666666666666655555555555555555555555555555444 PP

                                       -..---...--SSSHHHHHHHTS-T...TSHHHHHS--XXXXXXXXXX CS
                    Apolipoprotein 144 haeeve...erlssrveelreklee...qaeelrerleanleelkaql 185
                                        +++++   ++l+  +e  r++++e   +a e +  +e +++el++q+
  gi|330509096|ref|YP_004385524.1| 297 LKDSIQkmhDELTGDLEVSRQEYKEffrNAIEKNTTIESQIHELRKQV 344
                                       444333222455555555555555566666666666666666666665 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.2      0.44   1.6e+02       5      83 ..      13      91 ..       2      97 .. 0.71
   2 ?    1.1   0.1       1.4     5e+02       5      33 ..      83     111 ..      79     117 .. 0.78
   3 !   21.0   4.0     8e-07   0.00029       4      58 ..     111     167 ..     107     177 .. 0.81
   4 !   18.5   7.3     5e-06    0.0018       4      68 ..     176     242 ..     173     271 .. 0.74
   5 ?    3.2   0.3       0.3   1.1e+02       2      50 ..     286     343 ..     285     350 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.44
                           DUF4164  5 eleaaltrLeaaldsLEkavdrrleaerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaieti 83
                                      ele++  r ++ l++L++  d  le  + ++++e++++   e   +L++ + ++e r + le  +r + ++Lk + + i
  gi|330509096|ref|YP_004385524.1| 13 ELEDFRARSQETLKTLDQLADFILEFSKLEKDFESKLRGASESLDKLDQYIIEVESRWSILEPEARKILEQLKDTGNDI 91
                                      5666666666777777777777777777777777777777777777777777777777777777777777777666555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.4
                           DUF4164   5 eleaaltrLeaaldsLEkavdrrleaerk 33 
                                       +l++  +++++++++L +  d+r ++ ++
  gi|330509096|ref|YP_004385524.1|  83 QLKDTGNDIHNSFNELKQETDQRGTKLQE 111
                                       677888999999****9999999777655 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 8e-07
                           DUF4164   4 keleaaltrLeaaldsLEkavdrrleaerkr.deleaei.ealgedrsRLaeeLdqa 58 
                                       ++ ++a  +L+aald+LE+ +d+ l+  +++ +++ +ei + l++ rsRL+e   ++
  gi|330509096|ref|YP_004385524.1| 111 EDTDKAKVELHAALDNLESKLDQSLKYFQDKsEDRYTEInQNLDNHRSRLDEFEKET 167
                                       67789999******************98887678889999**********9744444 PP

  == domain 4  score: 18.5 bits;  conditional E-value: 5e-06
                           DUF4164   4 keleaaltrLeaaldsLEkavdrrleaerkr.deleaei.ealgedrsRLae...eLdqaearaarleev 68 
                                       ++ ++a  +L+aal++LE+ +d+ l+  +++ +++ +ei + l++ rsRL+e   e+dq+ ++   l+e 
  gi|330509096|ref|YP_004385524.1| 176 EDTDKAKVELHAALNNLESKLDQSLKYFQDKsEDRYTEInQNLDNHRSRLDElekEIDQRGMK---LQED 242
                                       67789999******************98887678889999*********98622255555544...4444 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.3
                           DUF4164   2 vtkeleaaltrLeaaldsLEkavdrrleaerkr............deleaei.ealgedrsR 50 
                                       +++e ++++t L+ +++++ + ++  le  r++                 +i ++++e r++
  gi|330509096|ref|YP_004385524.1| 286 QKDEFSEVTTGLKDSIQKMHDELTGDLEVSRQEykeffrnaieknT----TIeSQIHELRKQ 343
                                       678899999**********999999999998887777775432222....334444444444 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       1.2   4.4e+02      27      67 ..      19      58 ..       6      69 .. 0.54
   2 !   15.0   2.6   5.1e-05     0.019      21      99 ..      80     158 ..      70     165 .. 0.76
   3 !   13.0   0.8   0.00022     0.082      44     102 ..     168     226 ..     157     234 .. 0.84
   4 !    9.1   4.3    0.0033       1.2      30      94 ..     183     250 ..     180     277 .. 0.61
   5 ?    7.6   1.0      0.01       3.7      17      88 ..     242     313 ..     236     318 .. 0.89
   6 ?    0.7   0.1       1.3   4.9e+02      24      48 ..     326     349 ..     317     352 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.2
                      Baculo_PEP_C 27 lqnvqilaqlatlldaietqLnalsedlksllaeldtrldt 67
                                      + + ++l  l +l d i + +++l++d++s l   ++ ld+
  gi|330509096|ref|YP_004385524.1| 19 ARSQETLKTLDQLADFILE-FSKLEKDFESKLRGASESLDK 58
                                      4444444555555554444.555555555555444444443 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.1e-05
                      Baculo_PEP_C  21 vLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnL 97 
                                       +L++++     i +  ++l+++ +++ ++l+ed  ++  el+++ld+l ++L+++l+ +qd+ + + t +n++l n 
  gi|330509096|ref|YP_004385524.1|  80 ILEQLKDTGNDIHNSFNELKQETDQRGTKLQEDTDKAKVELHAALDNLESKLDQSLKYFQDKSEDRYTEINQNLDNH 156
                                       5555555555666666666666666666677777777777777****************************999986 PP

                      Baculo_PEP_C  98 ls 99 
                                        s
  gi|330509096|ref|YP_004385524.1| 157 RS 158
                                       65 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00022
                      Baculo_PEP_C  44 etqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvt 102
                                       +++  +l+ed  ++  el+++l++l ++L+++l+ +qd+ + + t +n++l n  s + 
  gi|330509096|ref|YP_004385524.1| 168 DQRWMKLQEDTDKAKVELHAALNNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLD 226
                                       5666789999999999*********************9999999999999999777665 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0033
                      Baculo_PEP_C  30 vqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsil 94 
                                       v++ a+l++l  +++++L+ ++++ ++  +e++++ld+  ++L++  +++     +l++++tn +s+ 
  gi|330509096|ref|YP_004385524.1| 183 VELHAALNNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDELEKEIDqrgMKLQEDITNAQSDF 250
                                       55666777777777777777777777666666666666666666666555544445555555555543 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.01
                      Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLt 88 
                                       d+tn+ ++ +  n ++ ++l ++++++ ++ +    +++++  ++++++++++t L+d+++++ d+l+ +L+
  gi|330509096|ref|YP_004385524.1| 242 DITNAQSDFQIANRNLRNELVRMINDLRSESEIRFLEFNNSFDQQKDEFSEVTTGLKDSIQKMHDELTGDLE 313
                                       89999999999999999999999999998877777899999999999*******************999886 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 1.3
                      Baculo_PEP_C  24 airlqnvqilaqlatlldaietqLn 48 
                                       ai  +n++i +q+ +l +++  qL 
  gi|330509096|ref|YP_004385524.1| 326 AI-EKNTTIESQIHELRKQVRAQLA 349
                                       56.6778888888888887777775 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7  17.0   2.6e-06   0.00096      47     226 ..      53     244 ..      36     271 .. 0.79
   2 ?    0.9   0.2      0.67   2.5e+02      23      60 ..     308     347 ..     296     351 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.6e-06
                                       HHHHHHHHHHHHHHHHH--..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHH CS
                               HBM  47 qkkldelkaqlqklkakfk..spenvrlLqeqlalvqeyrksfnelraayesr.naaRqeldsaaeraleaidelea 120
                                       +++ld+l++   +++ + +  +pe ++ L++  ++ + + +sfnel++ +++r  ++ +  d+a  ++ +a+d+le+
  gi|330509096|ref|YP_004385524.1|  53 SESLDKLDQYIIEVESRWSilEPEARKILEQLKDTGNDIHNSFNELKQETDQRgTKLQEDTDKAKVELHAALDNLES 129
                                       5667777777766666554348****************************9984688999999999*********** PP

                                       HHHCS-S-H....HHHHHHH.HHHHHHHHHHHHHHHHHHHHHHS...--HHHHHHHHHHHHHHHHHHHHHHHH-GG. CS
                               HBM 121 evlqtpead....serlaql.qaiaelkrqvqlaryqvrgYtfs...enedseqaavtaldaalaeldqlrqalasd 189
                                       ++ q++++     ++r++++ q++++ + ++ +   ++    ++   ++++++  + +al++  ++ldq  + ++++
  gi|330509096|ref|YP_004385524.1| 130 KLDQSLKYFqdksEDRYTEInQNLDNHRSRLDEFEKETDQRWMKlqeDTDKAKVELHAALNNLESKLDQSLKYFQDK 206
                                       **99998755577666655426788888888888888766655500044555556789******************* PP

                                       GHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHH CS
                               HBM 190 praalqqlesalskYRaaleqfkaavaai.eqarkemt 226
                                       +++++ ++++ l++ R+ l++++++++++  ++++ +t
  gi|330509096|ref|YP_004385524.1| 207 SEDRYTEINQNLDNHRSRLDELEKEIDQRgMKLQEDIT 244
                                       ***********************999876244555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHHHH..HTTT-HHHHHHHHHHHHHHHHHHHH CS
                               HBM  23 llkdLRiaRlqye..lsngdataaavqkkldelkaqlqkl 60 
                                       l+ dL ++R +y+   +n  ++++ ++ ++ el++q+ ++
  gi|330509096|ref|YP_004385524.1| 308 LTGDLEVSRQEYKefFRNAIEKNTTIESQIHELRKQVRAQ 347
                                       3457777777776323455555555777777777766655 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  29.7   1.2e-06   0.00046     308     534 ..       8     233 ..       4     251 .. 0.90
   2 ?    3.1   2.5     0.035        13     364     431 ..     280     347 ..     258     350 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.2e-06
                           DUF3584 308 delnqelsaakaklaakeselealeeqkkkyed..adie.klkadldqlpsirseleeleeeldaltekhqdvqeky 381
                                       +++n el++ +a  ++  + l++l +   ++ +  +d e kl+   + l+++ + + e+e +   l+ +++++ e++
  gi|330509096|ref|YP_004385524.1|   8 EQVNFELEDFRARSQETLKTLDQLADFILEFSKleKDFEsKLRGASESLDKLDQYIIEVESRWSILEPEARKILEQL 84 
                                       567889999999999999999999999999964336766368889999***************************** PP

                           DUF3584 382 drrkqkikeeleeeleklkerleaireekdrlkaaieealealesqlrkqleaqkeelneeekelesrlselklrld 458
                                       +     i+++++e  ++ ++r  +++e  d+ k + ++al++les+l + l+  + + +++  e++++l++   rld
  gi|330509096|ref|YP_004385524.1|  85 KDTGNDIHNSFNELKQETDQRGTKLQEDTDKAKVELHAALDNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLD 161
                                       *********************9************************************************9999999 PP

                           DUF3584 459 satateEeleqieeadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaerrleqlrqaleeleeqls 534
                                       +   ++E+ ++  + +e  +ka+ el++a ++ e+     + l+  +d+ +++++++++ l + r++l+ele+ ++
  gi|330509096|ref|YP_004385524.1| 162 EF--EKETDQRWMKLQEDTDKAKVELHAALNNLESK--LDQSLKYFQDKSEDRYTEINQNLDNHRSRLDELEKEID 233
                                       75..7888999999999***********99998765..456788899*************************9875 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.035
                           DUF3584 364 eeeldaltekhqdvqekydrrkqkikeeleeeleklker.leaireekdrlkaaieealealesqlrkq 431
                                       ++++d + ++  +v+  ++  +qk+++el  +le  +++ +e  r++ ++  ++ie++ ++l++q r+q
  gi|330509096|ref|YP_004385524.1| 280 NNSFDQQKDEFSEVTTGLKDSIQKMHDELTGDLEVSRQEyKEFFRNAIEK-NTTIESQIHELRKQVRAQ 347
                                       55666666777777777777777777777777777777656666666666.677777777777777766 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       5.6   2.1e+03      86     111 ..       9      34 ..       5      46 .. 0.67
   2 !   11.7   2.0   0.00047      0.17       4      58 ..      79     133 ..      77     138 .. 0.94
   3 !   13.2   1.7   0.00016      0.06       8      58 ..     148     198 ..     145     203 .. 0.93
   4 ?    6.5   1.5      0.02       7.2      21      70 ..     201     250 ..     197     256 .. 0.75
   5 ?    0.4   0.0       1.5   5.4e+02      23      52 ..     279     308 ..     255     313 .. 0.53
   6 ?    6.7   0.5     0.016       5.9       7      49 ..     306     348 ..     301     351 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.6
                              CdvA  86 airellesaleekeeikklleklskl 111
                                       +++ +le  +++ +e+ k+l++l++ 
  gi|330509096|ref|YP_004385524.1|   9 QVNFELEDFRARSQETLKTLDQLADF 34 
                                       55566677777777777777777654 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00047
                              CdvA   4 kALeeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqiks 58 
                                       k Le+L  +g+  +  ++e+k++ ++  +kl+e+ ++ k +l++ l+ le+++++
  gi|330509096|ref|YP_004385524.1|  79 KILEQLKDTGNDIHNSFNELKQETDQRGTKLQEDTDKAKVELHAALDNLESKLDQ 133
                                       679***********************************************98865 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00016
                              CdvA   8 eLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqiks 58 
                                       e+ ++ d  +s+ +e++++ ++  +kl+e+ ++ k +l++ l+ le+++++
  gi|330509096|ref|YP_004385524.1| 148 EINQNLDNHRSRLDEFEKETDQRWMKLQEDTDKAKVELHAALNNLESKLDQ 198
                                       78889999**************************************98875 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.02
                              CdvA  21 eeikekleealkklkekakelkeklkkrlkeledqikslekalanlkisy 70 
                                       + ++ k e+ +++++++ ++ +++l++  ke+++   +l++ ++n++  +
  gi|330509096|ref|YP_004385524.1| 201 KYFQDKSEDRYTEINQNLDNHRSRLDELEKEIDQRGMKLQEDITNAQSDF 250
                                       55677778888888888888888888888888888888888888887776 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 1.5
                              CdvA  23 ikekleealkklkekakelkeklkkrlkel 52 
                                       ++  ++++ ++  e    lk+ ++k  +el
  gi|330509096|ref|YP_004385524.1| 279 FNNSFDQQKDEFSEVTTGLKDSIQKMHDEL 308
                                       344444444444444444444444433333 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.016
                              CdvA   7 eeLvsegdipkstyeeikekleealkklkekakelkeklkkrl 49 
                                       +eL  + ++++++y+e+ ++  e++++++ +  el+++++++l
  gi|330509096|ref|YP_004385524.1| 306 DELTGDLEVSRQEYKEFFRNAIEKNTTIESQIHELRKQVRAQL 348
                                       78999999*****************************999987 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   4.8    0.0015      0.53     130     238 ..      32     150 ..       7     161 .. 0.60
   2 !   10.7  11.4   0.00067      0.24     107     227 ..     130     258 ..     127     264 .. 0.75
   3 !    7.5   0.3    0.0062       2.3     127     211 ..     268     347 ..     254     352 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                           DUF4407 130 a............ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaake.kkaqld 193
                                       a            ++++l+ + + +++l++ i + e+r++ l+ ea+k l++ k tg   ++    + k+  ++  +
  gi|330509096|ref|YP_004385524.1|  32 AdfilefsklekdFESKLRGASESLDKLDQYIIEVESRWSILEPEARKILEQLKDTGND-IHNSFNELKQeTDQRGT 107
                                       144555555555599************************************98877744.34443333332444445 PP

                           DUF4407 194 aaqaelaelkakldatarlaalraelaeleaerakeraasqaaaa 238
                                       ++q++ +++k +    a+l++l+++l++  +  +++ ++  ++++
  gi|330509096|ref|YP_004385524.1| 108 KLQEDTDKAKVE--LHAALDNLESKLDQSLKYFQDKSEDRYTEIN 150
                                       555555555555..5555555555555443333333333332222 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00067
                           DUF4407 107 eIdaelaeeqqeeakelkeqlaaa...ltaelaeleaqia....alqaeidaaearldalraeaqkeldgtkgtgtt 176
                                        +d+ l+ +q ++++++ ++++++    +++l+e e++++    +lq+  d+a+ +l a+ ++++++ld+       
  gi|330509096|ref|YP_004385524.1| 130 KLDQSLKYFQDKSEDRY-TEINQNldnHRSRLDEFEKETDqrwmKLQEDTDKAKVELHAALNNLESKLDQSL---KY 202
                                       56667777777777766.444444466677777777777788889999999999999999999999999765...23 PP

                           DUF4407 177 gvaGkgpaakekkaqldaaqaelaelkakld.....atarlaalraelaeleaera 227
                                            +++++e +++ld  + +l+el++++d      +++++++++  + ++++++
  gi|330509096|ref|YP_004385524.1| 203 FQDKSEDRYTEINQNLDNHRSRLDELEKEIDqrgmkLQEDITNAQSDFQIANRNLR 258
                                       35557899*********************877777777777777777766666555 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0062
                           DUF4407 127 laaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelk 203
                                       l+++++ +  e ++  ++ + e+++  + l++  +++ +el+g+       ++ + + ++++ +++++++ ++ el+
  gi|330509096|ref|YP_004385524.1| 268 LRSESEIRFLEFNNSFDQQKDEFSEVTTGLKDSIQKMHDELTGDLEVS---RQEYKEFFRNAIEKNTTIESQIHELR 341
                                       4555566667788888999***********************988666...8899********************** PP

                           DUF4407 204 akldatar 211
                                       ++   +a+
  gi|330509096|ref|YP_004385524.1| 342 KQ--VRAQ 347
                                       *9..4444 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0066       2.4      36      92 ..      87     143 ..      76     151 .. 0.81
   2 ?    4.3   0.1      0.15        54      56      92 ..     172     208 ..     162     216 .. 0.82
   3 ?    2.9   0.0       0.4   1.5e+02      56      88 ..     288     320 ..     240     322 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0066
                     T7SS_ESX_EspC  36 asaavldshGpicaatndavaaaeaarraagealaaasteLadkLraAAaaYeatDe 92 
                                       +++++ +s+  ++++t++  ++++++ ++a  +l+aa++ L+ kL+++ + +++  e
  gi|330509096|ref|YP_004385524.1|  87 TGNDIHNSFNELKQETDQRGTKLQEDTDKAKVELHAALDNLESKLDQSLKYFQDKSE 143
                                       566667777778899999999999**********************99999987655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.15
                     T7SS_ESX_EspC  56 aaaeaarraagealaaasteLadkLraAAaaYeatDe 92 
                                        +++++ ++a  +l+aa++ L+ kL+++ + +++  e
  gi|330509096|ref|YP_004385524.1| 172 MKLQEDTDKAKVELHAALNNLESKLDQSLKYFQDKSE 208
                                       577889999999****************999987655 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.4
                     T7SS_ESX_EspC  56 aaaeaarraagealaaasteLadkLraAAaaYe 88 
                                       +++ +  ++  ++++++++eL  +L ++ ++Y+
  gi|330509096|ref|YP_004385524.1| 288 DEFSEVTTGLKDSIQKMHDELTGDLEVSRQEYK 320
                                       466777777888999**************9997 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 ?    6.1   0.4     0.045        17      36      69 ..      35      68 ..       7      83 .. 0.72
   2 ?    4.3   1.5      0.17        61      35      64 ..     286     316 ..     256     350 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.045
                      Syntaxin-6_N 36 seeldetrteLrkalrsiewdledLeetvrivek 69
                                        e+++++++++++lr +++ l+ L++ +  ve+
  gi|330509096|ref|YP_004385524.1| 35 ILEFSKLEKDFESKLRGASESLDKLDQYIIEVES 68
                                      568999**********************965555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.17
                      Syntaxin-6_N  35 tseeldetrteLrkalrsiewdle.dLeetv 64 
                                       +++e++e +t L+ +++++  +l  dLe + 
  gi|330509096|ref|YP_004385524.1| 286 QKDEFSEVTTGLKDSIQKMHDELTgDLEVSR 316
                                       4555555555555555554444422333222 PP

>> FCH  Fes/CIP4, and EFC/F-BAR homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.4   1.3e-05    0.0048       3      73 ..      15     107 ..      13     111 .. 0.79
   2 ?   -0.3   0.9       3.6   1.3e+03      46      46 ..     198     198 ..     122     304 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT----TT-.............................. CS
                               FCH   3 kvlqkrleqgialledlqeflkeRaeiEkeYakkLqkLakkylkrrkkks.........................ee 54 
                                       + + +r +  +++l++l++f+ e +++Ek++  kL+  +++ +k    ++                          +
  gi|330509096|ref|YP_004385524.1|  15 EDFRARSQETLKTLDQLADFILEFSKLEKDFESKLRGASESLDKL---DQyiievesrwsilepearkileqlkdTG 88 
                                       56788999************************************6...33344444555555555555566666689 PP

                                       HHHHHHHHHHHHHHHHHHH CS
                               FCH  55 stlvtawtvlleeteklaq 73 
                                         +++++++l++et+++++
  gi|330509096|ref|YP_004385524.1|  89 NDIHNSFNELKQETDQRGT 107
                                       9999999999999999875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 3.6
                                       - CS
                               FCH  46 k 46 
                                       +
  gi|330509096|ref|YP_004385524.1| 198 Q 198
                                       1 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   2.1    0.0017      0.63      50     128 ..      46     127 ..      14     141 .. 0.51
   2 ?    6.1   4.1      0.03        11       6      90 ..      86     176 ..      85     181 .. 0.67
   3 !    8.7   1.7    0.0047       1.7      39     114 ..     190     261 ..     186     275 .. 0.51
   4 ?    5.2   0.7     0.055        20      48      98 ..     282     329 ..     275     349 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0017
                         ApoLp-III  50 kkksdeleealkevkkkieetadklseenPevkk...kaqelqekvQsgvqslvkesqklaeslkensqeakeklak 123
                                         k   + e+l+ + + i e+    s  +Pe+ k   +++++ + + ++ ++l +e+++ + +l+e++ +ak +l +
  gi|330509096|ref|YP_004385524.1|  46 ESKLRGASESLDKLDQYIIEVESRWSILEPEARKileQLKDTGNDIHNSFNELKQETDQRGTKLQEDTDKAKVELHA 122
                                       33333344555555555555555555555555441113333334566666666666666666666666666666665 PP

                         ApoLp-III 124 aikqa 128
                                       a+ ++
  gi|330509096|ref|YP_004385524.1| 123 ALDNL 127
                                       55544 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.03
                         ApoLp-III   6 elqksvkkqln..lpsqeevvetiKensenlvdqlk....qvikslqeelkkksdeleealkevkkkieetadklse 76 
                                       ++++ + +++n   +++++  + ++e ++++  +l     ++ ++l+++lk  +d+ e   +e+++++ + +  l e
  gi|330509096|ref|YP_004385524.1|  86 DTGNDIHNSFNelKQETDQRGTKLQEDTDKAKVELHaaldNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDE 162
                                       55666666666656777777788888888765555400005556667777778888888888888888888888888 PP

                         ApoLp-III  77 enPevkkkaqelqe 90 
                                        + e+ +   +lqe
  gi|330509096|ref|YP_004385524.1| 163 FEKETDQRWMKLQE 176
                                       77777777777776 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0047
                         ApoLp-III  39 kqvikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslkens 114
                                       +++ ++l+++lk  +d+ e   +e+++++ + +  l e    ++k++++   k+Q+ +++  ++ q +  +l ++ 
  gi|330509096|ref|YP_004385524.1| 190 NNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDE----LEKEIDQRGMKLQEDITNAQSDFQIANRNLRNEL 261
                                       45555556666666666666666666666666555555....5555555555555555554444444444443333 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.055
                         ApoLp-III  48 elkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQsgvqs 98 
                                       +  ++ de+ e+ + +k+ i+++ d+l+    +++ + qe++e + +++++
  gi|330509096|ref|YP_004385524.1| 282 SFDQQKDEFSEVTTGLKDSIQKMHDELTG---DLEVSRQEYKEFFRNAIEK 329
                                       55566777777777777777777777776...4444445555555555543 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2      0.14        51      49     115 ..       6      75 ..       4      84 .. 0.70
   2 !    9.6   2.1    0.0024      0.86      51     108 ..     107     165 ..      87     174 .. 0.79
   3 !   11.6   3.7   0.00057      0.21      50     119 ..     171     241 ..     157     247 .. 0.83
   4 ?    4.4   1.2       0.1        37      48     110 ..     281     344 ..     251     352 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.14
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkld...eqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       +leqv  +l++ + + ++ ++++d+  d   e +++ k+ ++++  ++e l+++++ + +v++  + le 
  gi|330509096|ref|YP_004385524.1|   6 DLEQVNFELEDFRARSQETLKTLDQLADfilEFSKLEKDFESKLRGASESLDKLDQYIIEVESRWSILEP 75 
                                       5788887777777666666555555444222777778888999999999999999988888887777765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0024
                           DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkei.skeikeevtevredlseigedvesvke 108
                                       ++++e+  ++k +L + +d++++kld++ +  + + ++  te++++l++ ++ +++ ++
  gi|330509096|ref|YP_004385524.1| 107 TKLQEDTDKAKVELHAALDNLESKLDQSLKYfQDKSEDRYTEINQNLDNHRSRLDEFEK 165
                                       467788889*****************987651667788899*****9999988887665 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00057
                           DUF1664  50 leqvseslaatkrhLssridrvdkkldeqke.iskeikeevtevredlseigedvesvkeavegleskler 119
                                         +++e+  ++k +L + ++++++kld++ +  + + ++  te++++l++ ++ ++++++ + + ++kl++
  gi|330509096|ref|YP_004385524.1| 171 WMKLQEDTDKAKVELHAALNNLESKLDQSLKyFQDKSEDRYTEINQNLDNHRSRLDELEKEIDQRGMKLQE 241
                                       5577889999*****************98761567788899*********************999999864 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.1
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikee.vtevredlseigedvesvkeav 110
                                       ++ +q +++ +++   L++ i+++ ++l    e+s++  +e   ++ e+ ++i+++++++++ v
  gi|330509096|ref|YP_004385524.1| 281 NSFDQQKDEFSEVTTGLKDSIQKMHDELTGDLEVSRQEYKEfFRNAIEKNTTIESQIHELRKQV 344
                                       4556666666777777777777777777777666655443314556666666666666666665 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3      0.69   2.5e+02      32      77 ..      53      98 ..      38     106 .. 0.78
   2 ?    3.0   1.0      0.37   1.3e+02      16      51 ..      98     133 ..      85     137 .. 0.70
   3 !   15.5   1.6   4.6e-05     0.017      21      58 ..     139     176 ..     133     191 .. 0.91
   4 !   11.5   6.3   0.00081       0.3      21      61 ..     204     244 ..     190     267 .. 0.82
   5 ?    0.4   0.0       2.3   8.6e+02      47      61 ..     328     342 ..     322     349 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.69
                           UPF0184 32 nsmLDqinsaLDalEernDdlnskLrELlesnRqiRlefaeqldea 77
                                       ++LD+++ ++ ++E r   l+   r +le  +++   +++  +e 
  gi|330509096|ref|YP_004385524.1| 53 SESLDKLDQYIIEVESRWSILEPEARKILEQLKDTGNDIHNSFNEL 98
                                      5789999999999999999999999999998888777777666555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.37
                           UPF0184  16 aeteedefgeeEyeainsmLDqinsaLDalEernDd 51 
                                       +++e d+ g +  e+ +    ++ +aLD+lE + D+
  gi|330509096|ref|YP_004385524.1|  98 LKQETDQRGTKLQEDTDKAKVELHAALDNLESKLDQ 133
                                       555666666666777777777888888988888775 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 4.6e-05
                           UPF0184  21 defgeeEyeainsmLDqinsaLDalEernDdlnskLrE 58 
                                       ++  e+ y +in+ LD+  s LD+ E+ +D+   kL+E
  gi|330509096|ref|YP_004385524.1| 139 QDKSEDRYTEINQNLDNHRSRLDEFEKETDQRWMKLQE 176
                                       6677899**************************9*999 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00081
                           UPF0184  21 defgeeEyeainsmLDqinsaLDalEernDdlnskLrELle 61 
                                       ++  e+ y +in+ LD+  s LD+lE+  D+   kL+E + 
  gi|330509096|ref|YP_004385524.1| 204 QDKSEDRYTEINQNLDNHRSRLDELEKEIDQRGMKLQEDIT 244
                                       6778899******************************9663 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 2.3
                           UPF0184  47 ernDdlnskLrELle 61 
                                       e+n  ++s+++EL +
  gi|330509096|ref|YP_004385524.1| 328 EKNTTIESQIHELRK 342
                                       79999*******965 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       8.1     3e+03      28      48 ..      76      96 ..      65     110 .. 0.68
   2 ?    7.6   0.2     0.012       4.5      48      78 ..     123     153 ..     107     155 .. 0.88
   3 ?    8.4   0.2    0.0069       2.5      48      78 ..     188     218 ..     170     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 8.1
                                      HHHHHHHHHHCTTT-HHHHHH CS
                     Ribosomal_S15 28 rInnltehlkenkkDkhsrrg 48
                                      +++++ e lk   +D h+  +
  gi|330509096|ref|YP_004385524.1| 76 EARKILEQLKDTGNDIHNSFN 96
                                      566677777777777777654 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHC CS
                     Ribosomal_S15  48 gLlklvskRrkllkYLkrkdverYkkliekl 78 
                                       +L +l+sk  + lkY + k+ +rY+++ ++l
  gi|330509096|ref|YP_004385524.1| 123 ALDNLESKLDQSLKYFQDKSEDRYTEINQNL 153
                                       68899********************998877 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0069
                                       HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHC CS
                     Ribosomal_S15  48 gLlklvskRrkllkYLkrkdverYkkliekl 78 
                                       +L +l+sk  + lkY + k+ +rY+++ ++l
  gi|330509096|ref|YP_004385524.1| 188 ALNNLESKLDQSLKYFQDKSEDRYTEINQNL 218
                                       7999*********************998877 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2      0.12        45      52      81 ..      69      98 ..      27     112 .. 0.69
   2 ?    3.9   0.9      0.17        64      18      74 ..     115     167 ..     108     179 .. 0.60
   3 ?    2.4   0.3       0.5   1.8e+02      54      83 ..     176     205 ..     161     208 .. 0.73
   4 ?    7.9   0.8    0.0097       3.5      17      82 ..     179     240 ..     175     242 .. 0.78
   5 ?    6.2   0.3     0.033        12      14      75 ..     281     345 ..     276     348 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.12
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100 52 efeewkqaaqklvdaLeeisealkqaanaf 81
                                       +  + ++a+k+ ++L+++++ ++++ n++
  gi|330509096|ref|YP_004385524.1| 69 RWSILEPEARKILEQLKDTGNDIHNSFNEL 98
                                      455555666666666666666555554444 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  18 kqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeiseal 74 
                                       k++ el+++l++l++++d+    ++ ++ d+    ++e++q++++    L+e ++++
  gi|330509096|ref|YP_004385524.1| 115 KAKVELHAALDNLESKLDQSLKYFQDKSEDR----YTEINQNLDNHRSRLDEFEKET 167
                                       5555666666666666666666665555544....4556666666666666555555 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  54 eewkqaaqklvdaLeeisealkqaanafed 83 
                                       e  ++a  +l++aL++++++l+q+ + f+d
  gi|330509096|ref|YP_004385524.1| 176 EDTDKAKVELHAALNNLESKLDQSLKYFQD 205
                                       455566667888888888888888777765 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0097
                                       HHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  17 qkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafe 82 
                                       +k++ el+++l++l++++d+    ++ ++ d     ++e++q++++    L+e++++++q + +++
  gi|330509096|ref|YP_004385524.1| 179 DKAKVELHAALNNLESKLDQSLKYFQDKSED----RYTEINQNLDNHRSRLDELEKEIDQRGMKLQ 240
                                       5667777778888888887777777766655....56899****************9999988877 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHHHHHHHHHHHHHCGCGCTHH...HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  14 arfqkqaeeledelqrlkaevdalqsgWsGa...aadafqaefeewkqaaqklvdaLeeisealk 75 
                                       ++f++q++e +++ + lk +++++++   G+   ++++++++f +  ++ +++  + +e++++++
  gi|330509096|ref|YP_004385524.1| 281 NSFDQQKDEFSEVTTGLKDSIQKMHDELTGDlevSRQEYKEFFRNAIEKNTTIESQIHELRKQVR 345
                                       57899999999999999999999999999987778889999999999999999999998888876 PP

>> DUF4439  Domain of unknown function (DUF4439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2      0.12        46      25      52 ..     143     170 ..     139     186 .. 0.83
   2 ?    9.2   0.1    0.0051       1.9      25      58 ..     208     241 ..     204     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.12
                           DUF4439  25 garraaarealaaHrarrdalaallsar 52 
                                       ++r ++++++l++Hr+r d+ ++ + +r
  gi|330509096|ref|YP_004385524.1| 143 EDRYTEINQNLDNHRSRLDEFEKETDQR 170
                                       6788999*************99876655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0051
                           DUF4439  25 garraaarealaaHrarrdalaallsargatppa 58 
                                       ++r ++++++l++Hr+r d+l++ + +rg + ++
  gi|330509096|ref|YP_004385524.1| 208 EDRYTEINQNLDNHRSRLDELEKEIDQRGMKLQE 241
                                       6788999******************999987665 PP

>> SF-assemblin  SF-assemblin/beta giardin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   5.7     0.014       5.1      88     185 ..      43     139 ..      14     156 .. 0.48
   2 ?    7.1   9.4    0.0081         3      52     141 ..     147     236 ..     139     246 .. 0.91
   3 ?   10.3  11.1   0.00088      0.32      19     133 ..     226     340 ..     216     347 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                      SF-assemblin  88 lelkkaveelnekinnveanvenekakrrdaieklakelvkelneleaaideEkaerkkkedqlnkkveEdlkklsa 164
                                        ++++ ++   e +  ++  +  e ++r + +e  a++++++l +    i++  +e k++ dq   k++Ed  k + 
  gi|330509096|ref|YP_004385524.1|  43 KDFESKLRGASESLDKLDQYII-EVESRWSILEPEARKILEQLKDTGNDIHNSFNELKQETDQRGTKLQEDTDKAKV 118
                                       3333333334444444443332.334444445555555555555555555555555555555555555555544444 PP

                      SF-assemblin 165 kidtEkniRdsevsaltaeve 185
                                       ++       +s+  +   + +
  gi|330509096|ref|YP_004385524.1| 119 ELHAALDNLESKLDQSLKYFQ 139
                                       444433333333333333333 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0081
                      SF-assemblin  52 aEvkkRaesdkdiqeefkkeikklqekikeevddlalelkkaveelnekinnveanvenekakrrdaieklakelvk 128
                                       +E+ +  ++++   +ef+ke ++   k +e+ d  ++el+ a+++l+ k+ +     +++ + r  +i++  ++   
  gi|330509096|ref|YP_004385524.1| 147 TEINQNLDNHRSRLDEFEKETDQRWMKLQEDTDKAKVELHAALNNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRS 223
                                       6778888888888899************************************************************* PP

                      SF-assemblin 129 elneleaaideEk 141
                                       +l ele  id+  
  gi|330509096|ref|YP_004385524.1| 224 RLDELEKEIDQRG 236
                                       *********9865 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00088
                      SF-assemblin  19 kelenEieqkrvdektrvklikeaiakleksveaEvkkRaesdkdiqeefkkeikklqekikeevddlalelkkave 95 
                                       +ele+Ei+q+ ++ ++ +   +   +  ++++ +E  + ++  +   e+   e ++ + ++k+e+ +++  lk++++
  gi|330509096|ref|YP_004385524.1| 226 DELEKEIDQRGMKLQEDITNAQSDFQIANRNLRNELVRMINDLRSESEIRFLEFNNSFDQQKDEFSEVTTGLKDSIQ 302
                                       79**************************************999999999999************************* PP

                      SF-assemblin  96 elnekin.nveanvenekakrrdaieklakelvkelnel 133
                                       ++ ++++ ++e   ++ k+  r+aiek  + +  ++ el
  gi|330509096|ref|YP_004385524.1| 303 KMHDELTgDLEVSRQEYKEFFRNAIEKN-TTIESQIHEL 340
                                       *****9879****************974.5555555555 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 ?    2.6   0.1      0.35   1.3e+02      34      41 ..       2       9 ..       1      11 [. 0.86
   2 ?    6.8   1.1     0.016       5.9       3      42 ..     127     166 ..     125     170 .. 0.88
   3 ?   13.7   1.8   0.00011     0.041       3      45 ..     192     234 ..     190     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.35
                             HSBP1 34 sriDdLEk 41
                                       riDdLE+
  gi|330509096|ref|YP_004385524.1|  2 ARIDDLEQ 9 
                                      59*****7 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                             HSBP1   3 LtavVenlLqqlqdkFqtmsdqilsriDdMssriDdLEks 42 
                                       L++  ++ L+  qdk ++  ++i + +D+  sr+D+ Ek 
  gi|330509096|ref|YP_004385524.1| 127 LESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDEFEKE 166
                                       77777888999999999999******************96 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 0.00011
                             HSBP1   3 LtavVenlLqqlqdkFqtmsdqilsriDdMssriDdLEksiad 45 
                                       L++  ++ L+  qdk ++  ++i + +D+  sr+D+LEk i++
  gi|330509096|ref|YP_004385524.1| 192 LESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDELEKEIDQ 234
                                       67777888999999999999********************985 PP

>> Remorin_C  Remorin, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       6.1   2.2e+03      44      63 ..       7      26 ..       2      35 .. 0.77
   2 ?    0.8   0.2       1.2   4.4e+02      14      55 ..      76     117 ..      67     120 .. 0.80
   3 ?    8.8   2.1    0.0039       1.4      33      87 ..     113     167 ..      93     178 .. 0.81
   4 ?    7.5   4.1    0.0099       3.6      27      85 ..     172     230 ..     157     255 .. 0.77
   5 ?    3.2   0.3      0.22        81      41      83 ..     302     347 ..     292     349 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 6.1
                         Remorin_C 44 lrkleeklEkkrakaleklk 63
                                      l+++  +lE  ra+++e lk
  gi|330509096|ref|YP_004385524.1|  7 LEQVNFELEDFRARSQETLK 26
                                      56666699999999999876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.2
                         Remorin_C  14 ekakikkrykreeakIaaWenekkakaeaelrkleeklEkkr 55 
                                       e  ki +++k + ++I +  ne k++  ++  kl+e+ +k +
  gi|330509096|ref|YP_004385524.1|  76 EARKILEQLKDTGNDIHNSFNELKQETDQRGTKLQEDTDKAK 117
                                       677888888888888888889999999999999998888877 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0039
                         Remorin_C  33 enekkakaeaelrkleeklEkkrakaleklknklariekkAeekRasaeakrree 87 
                                        ++ k ++ a+l++le+kl++  +  ++k +++ ++i+++ ++ R++  + ++e 
  gi|330509096|ref|YP_004385524.1| 113 TDKAKVELHAALDNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDEFEKET 167
                                       4556667789***********************************9887766554 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0099
                         Remorin_C  27 akIaaWenekkakaeaelrkleeklEkkrakaleklknklariekkAeekRasaeakrr 85 
                                        k ++  ++ k ++ a+l++le+kl++  +  ++k +++ ++i+++ ++ R++  + ++
  gi|330509096|ref|YP_004385524.1| 172 MKLQEDTDKAKVELHAALNNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDELEK 230
                                       44444455566677899********************************9998776554 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.22
                         Remorin_C  41 eaelrkleeklEkkrakaleklknkla...riekkAeekRasaeak 83 
                                       ++  ++l  +lE  r++++e ++n ++   +ie + +e R++++a+
  gi|330509096|ref|YP_004385524.1| 302 QKMHDELTGDLEVSRQEYKEFFRNAIEkntTIESQIHELRKQVRAQ 347
                                       44455666799*********99997752227999999999999886 PP

>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       5.7   2.1e+03      70      92 ..      37      59 ..       6      74 .. 0.57
   2 ?   10.1   5.2    0.0024      0.86       3      78 ..      89     160 ..      87     162 .. 0.79
   3 ?    9.5   9.2    0.0036       1.3       7      88 ..     158     238 ..     151     241 .. 0.79
   4 ?   12.2   2.9   0.00054       0.2       7      88 ..     223     307 ..     216     310 .. 0.84
   5 ?    2.7   0.3      0.47   1.7e+02      41      89 ..     298     344 ..     295     350 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 5.7
                              FadA 70 eyksllkelekeikekekkianf 92
                                      e+++l k+ e++ +  ++ ++++
  gi|330509096|ref|YP_004385524.1| 37 EFSKLEKDFESKLRGASESLDKL 59
                                      33333333333333333333333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0024
                              FadA   3 naLeaelqkLekkeeqrykkekakaeaaaaklak.kkelkakieeklakleadsevrfykdeYkellkeyksllkel 78 
                                       n + + +++L+++++qr  k ++  ++a+ +l +   +l+ k+++ l+  + +se     d Y e+ +++++ +++l
  gi|330509096|ref|YP_004385524.1|  89 NDIHNSFNELKQETDQRGTKLQEDTDKAKVELHAaLDNLESKLDQSLKYFQDKSE-----DRYTEINQNLDNHRSRL 160
                                       679999***********999999999999999651689999*******9777776.....45566666666555555 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0036
                              FadA   7 aelqkLekkeeqrykkekakaeaaaaklak.kkelkakieeklakleadsevrfykdeYkellkeyksllkelekei 82 
                                       + l++ ek+++qr +k ++  ++a+ +l +  ++l+ k+++ l+  + +se r+   e ++ l + +s l+elekei
  gi|330509096|ref|YP_004385524.1| 158 SRLDEFEKETDQRWMKLQEDTDKAKVELHAaLNNLESKLDQSLKYFQDKSEDRY--TEINQNLDNHRSRLDELEKEI 232
                                       56889999*******************975168999*********777777664..566777788888888899999 PP

                              FadA  83 kekekk 88 
                                        ++  k
  gi|330509096|ref|YP_004385524.1| 233 DQRGMK 238
                                       887655 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00054
                              FadA   7 aelqkLekkeeqrykkekakaeaaaakla.kkkelkakieeklakleadsevrf..ykdeYkellkeyksllkelek 80 
                                       + l++Lek+ +qr +k ++   +a+ + + ++++l++++   +++l ++se+rf  + + +++   e++++ + l  
  gi|330509096|ref|YP_004385524.1| 223 SRLDELEKEIDQRGMKLQEDITNAQSDFQiANRNLRNELVRMINDLRSESEIRFleFNNSFDQQKDEFSEVTTGLKD 299
                                       67899999*9***66666666666666654899********************98899******************9 PP

                              FadA  81 eikekekk 88 
                                       +i++   +
  gi|330509096|ref|YP_004385524.1| 300 SIQKMHDE 307
                                       99987665 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.47
                              FadA  41 kakieeklakleadsevrfykdeYkellkeyksllkelekeikekekki 89 
                                       k++i++  ++l+ d ev+  ++eYke   +  +  + +e++i e  k++
  gi|330509096|ref|YP_004385524.1| 298 KDSIQKMHDELTGDLEVS--RQEYKEFFRNAIEKNTTIESQIHELRKQV 344
                                       555555555555555555..55566665555555556666666655555 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   3.5      0.24        89      22      82 ..      56     112 ..       4     117 .. 0.81
   2 ?    8.5   5.2    0.0068       2.5      15      87 ..     103     175 ..     102     176 .. 0.92
   3 ?    7.1   6.0     0.019       6.8      19      87 ..     172     240 ..     167     241 .. 0.90
   4 ?   11.2   2.2   0.00097      0.35      20     104 ..     238     323 ..     236     329 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.24
                              YlqD  22 qqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqq 82 
                                       +++l++ i ++++ ++ Le +a+++++++k     + + i++++++ k+e  ++  +l+++
  gi|330509096|ref|YP_004385524.1|  56 LDKLDQYIIEVESRWSILEPEARKILEQLKD----TGNDIHNSFNELKQETDQRGTKLQED 112
                                       5678888899999999999999999999988....44556666666666665555555554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0068
                              YlqD  15 eklKeelqqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvq 87 
                                       ++  ++lq++ ++++ +l   l++Le ++ + +k  + +s+++ +ei++++++ +s++ e  k+ +q+  ++q
  gi|330509096|ref|YP_004385524.1| 103 DQRGTKLQEDTDKAKVELHAALDNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDEFEKETDQRWMKLQ 175
                                       556679999*******************************************************999988776 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.019
                              YlqD  19 eelqqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvq 87 
                                        +lq++ ++++ +l   l++Le ++ + +k  + +s+++ +ei++++++ +s++ e  k+++q+  ++q
  gi|330509096|ref|YP_004385524.1| 172 MKLQEDTDKAKVELHAALNNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDELEKEIDQRGMKLQ 240
                                       6899999999**************************************************999876665 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00097
                              YlqD  20 elqqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvq.kLelgsev 95 
                                       +lq++++++ + ++   ++L+ ++ r+i++++++s+ +  e +++++++k+e+ e    l++ +++++ +L+ + ev
  gi|330509096|ref|YP_004385524.1| 238 KLQEDITNAQSDFQIANRNLRNELVRMINDLRSESEIRFLEFNNSFDQQKDEFSEVTTGLKDSIQKMHdELTGDLEV 314
                                       578888888888888889*****************99*****************************97479999999 PP

                              YlqD  96 kqgqveslv 104
                                       ++++  +++
  gi|330509096|ref|YP_004385524.1| 315 SRQEYKEFF 323
                                       999988887 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   7.6       1.2   4.5e+02      28      62 ..      82     119 ..       8     183 .. 0.78
   2 ?    2.8   4.4      0.46   1.7e+02      29      73 ..     195     242 ..     173     349 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.2
                              YtxH  28 kdlkekaddlkekakelleeakeka...kekaedlkek 62 
                                       ++lk++ +d+ ++++el++e+ +++   +e ++++k +
  gi|330509096|ref|YP_004385524.1|  82 EQLKDTGNDIHNSFNELKQETDQRGtklQEDTDKAKVE 119
                                       66777777777777777777766666663333333333 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.46
                              YtxH  29 dlkekaddlkekakelleeakeka...kekaedlkekvkekadelkek 73 
                                       +l ++++ +++k ++ ++e++++    +++ ++l ++++++  +l+e+
  gi|330509096|ref|YP_004385524.1| 195 KLDQSLKYFQDKSEDRYTEINQNLdnhRSRLDELEKEIDQRGMKLQED 242
                                       444445555555555555555555555555555555555554444444 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.5    0.0025       0.9      11      91 ..      20     101 ..      10     110 .. 0.85
   2 ?    3.5   0.7      0.18        67      10      67 ..      79     123 ..      75     145 .. 0.45
   3 ?    6.7   2.8     0.019       6.8      16      76 ..     143     197 ..     129     209 .. 0.69
   4 ?    6.2   2.7     0.027       9.8      16      75 ..     208     268 ..     204     292 .. 0.78
   5 ?    1.6   0.6      0.72   2.6e+02      29      72 ..     297     341 ..     259     349 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH... CS
                        Laminin_II  11 takevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss 87 
                                         +e+l+ l +l+  + + ++  + ++++++   e ++++ + i ++++  + Le +a ++l++lk   +   +s +
  gi|330509096|ref|YP_004385524.1|  20 RSQETLKTLDQLADFILEFSKLEKDFESKLRGASESLDKLDQYIIEVESRWSILEPEARKILEQLKDTGNDIHNSFN 96 
                                       568899999999999999999999999999999*******************************9987777666655 PP

                                       .HHHH CS
                        Laminin_II  88 .lsdn 91 
                                        l+++
  gi|330509096|ref|YP_004385524.1|  97 eLKQE 101
                                       56665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.18
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--T CS
                        Laminin_II  10 etakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekl 67 
                                       +++++ ++  +++++  +++k++  +  ++++e ++k+k             ++L   
  gi|330509096|ref|YP_004385524.1|  79 KILEQLKDTGNDIHNSFNELKQETDQRGTKLQEDTDKAK-------------VELHAA 123
                                       344444444444444444444444444444444333333.............222222 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.019
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHH CS
                        Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklk 76 
                                       ++  ++++qnl+n ++ l e++++ ++        +k  +d  ++ ++L   +++L++kl 
  gi|330509096|ref|YP_004385524.1| 143 EDRYTEINQNLDNHRSRLDEFEKETDQR------WMKLQEDTDKAKVELHAALNNLESKLD 197
                                       567789***************9995444......444444444445555555555555553 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.027
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX--TTTTTGGGH CS
                        Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvk.dankairdArrsvkkLeklapqLldkl 75 
                                       ++  ++++qnl+n ++ l e+++++++   k++ d ++a  d + + ++L +++ ++++ l
  gi|330509096|ref|YP_004385524.1| 208 EDRYTEINQNLDNHRSRLDELEKEIDQRGMKLQeDITNAQSDFQIANRNLRNELVRMINDL 268
                                       567799******************9988877776777777777777777766666555554 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.72
                                       XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX--TTTTTG CS
                        Laminin_II  29 tkeklseinrsveetnekvk.dankairdArrsvkkLeklapqLl 72 
                                       +k++++++++++    e+ + ++++  r A ++  ++e ++ +L 
  gi|330509096|ref|YP_004385524.1| 297 LKDSIQKMHDELTGDLEVSRqEYKEFFRNAIEKNTTIESQIHELR 341
                                       333333333332222221112333344444444444444443333 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4   0.00074      0.27     203     328 ..       6     145 ..       2     169 .. 0.78
   2 ?    1.5   1.1      0.23        83     240     319 ..     169     230 ..     144     282 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00074
                              FUSC 203 lrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaal............. 266
                                        ++q+ +e +++rar++     l ++++++  +s+l++  +   +  +++ ++l++++ e+++              
  gi|330509096|ref|YP_004385524.1|   6 DLEQVNFELEDFRARSQETLKTLDQLADFILEFSKLEKDFESKLRGASESLDKLDQYIIEVESRwsilepearkile 82 
                                       6899**********************************999999999999899*********989*99999999999 PP

                              FUSC 267 eaaaaaealeaalaalrarlralrraleadadtaa.lllarlaellaelaqllaslraleaai 328
                                       + ++  ++++   ++l ++ ++  + l++d+d a  +l a+l++l ++l q l+ +++ ++++
  gi|330509096|ref|YP_004385524.1|  83 QLKDTGNDIHNSFNELKQETDQRGTKLQEDTDKAKvELHAALDNLESKLDQSLKYFQDKSEDR 145
                                       666778888888888888888888888855555541455555555555555555555555554 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.23
                              FUSC 240 rllarlraeeaaavpelaallaelaal..........eaaaaaealeaalaalrarlralrraleadadtaalllar 306
                                       +++  l++  ++a  el+a l  l++           +                            + d+  ++ ++
  gi|330509096|ref|YP_004385524.1| 169 QRWMKLQEDTDKAKVELHAALNNLESKldqslkyfqdK----------------------------SEDRYTEINQN 217
                                       34444444444444444444444444334433333331............................22222222222 PP

                              FUSC 307 laellaelaqlla 319
                                       l+++ ++l +l +
  gi|330509096|ref|YP_004385524.1| 218 LDNHRSRLDELEK 230
                                       2222222222222 PP

>> Erp_C  Erp protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   5.6   0.00022     0.079      63     135 ..      77     151 ..      63     156 .. 0.80
   2 ?    8.4   4.6    0.0057       2.1      69     135 ..     148     216 ..     144     221 .. 0.77
   3 ?    0.1   2.4         2   7.3e+02      49      74 ..     222     247 ..     208     319 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00022
                             Erp_C  63 lgkllkelsdtrdelrtklnegnkayivlekepklkenvnvs..eikedleklkskleevkkylkde..dkfeeikg 135
                                         k+l +l dt +++   +ne  ++  ++++  kl+e+ + +  e++  l++l skl++  ky++d+  d++ ei +
  gi|330509096|ref|YP_004385524.1|  77 ARKILEQLKDTGNDIHNSFNELKQE--TDQRGTKLQEDTDKAkvELHAALDNLESKLDQSLKYFQDKseDRYTEINQ 151
                                       4699****************97654..5777899999998762267899***************9972257888876 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0057
                             Erp_C  69 elsdtrdelrtklnegnkayivlekepklkenvnvs..eikedleklkskleevkkylkde..dkfeeikg 135
                                       e+ +  d+ r++l+e +k+  ++++  kl+e+ + +  e++  l++l skl++  ky++d+  d++ ei +
  gi|330509096|ref|YP_004385524.1| 148 EINQNLDNHRSRLDEFEKE--TDQRWMKLQEDTDKAkvELHAALNNLESKLDQSLKYFQDKseDRYTEINQ 216
                                       6667778999999998887..4566788998888652267899***************9972257888876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2
                             Erp_C  49 yktwgdledeedeglgkllkelsdtr 74 
                                       +   ++le+e d+   kl  ++++++
  gi|330509096|ref|YP_004385524.1| 222 RSRLDELEKEIDQRGMKLQEDITNAQ 247
                                       22333444444443344444444444 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  14.1    0.0016      0.57     183     381 ..      15     224 ..       7     227 .. 0.75
   2 ?    8.2   6.9    0.0014       0.5     612     723 ..     162     272 ..     157     285 .. 0.78
   3 ?    2.2   0.6     0.093        34     337     403 ..     281     346 ..     268     363 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0016
                          Prominin 183 edlrtflkdvpqhidhvlvq..nyeelekhvsddLddagkhlgl..dladtlesnvlpaLa.elerllenlkeakeq 254
                                       ed+r   +++ + +d++++   ++++lek+ +++L +a+++l +  +   ++es   + L+ e +++le+lk++ + 
  gi|330509096|ref|YP_004385524.1|  15 EDFRARSQETLKTLDQLADFilEFSKLEKDFESKLRGASESLDKldQYIIEVESR-WSILEpEARKILEQLKDTGND 90 
                                       5555555555555555554322499999999999999998874411222244555.445554889999999999988 PP

                          Prominin 255 Leq.vnklekeLrksgsqLrdglrgvkrdlnqalsn.lCqs.eeCskilssleiekldtskcl....dqlpnvdevl 324
                                       +++  n+l++e  + g++L++   ++k +l+ al n + +  ++ + +++++e  + + +++l    + l++ +++ 
  gi|330509096|ref|YP_004385524.1|  91 IHNsFNELKQETDQRGTKLQEDTDKAKVELHAALDNlESKLdQSLKYFQDKSEDRYTEINQNLdnhrSRLDEFEKET 167
                                       86537999999999999999999999999999999977774488899999999999999999987777788888888 PP

                          Prominin 325 ealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakk 381
                                       ++    l+++++++  e  a ln++++k+ + ++ +  +     ++++++++++ ++
  gi|330509096|ref|YP_004385524.1| 168 DQRWMKLQEDTDKAKVELHAALNNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSR 224
                                       888888899999999999999999999999999998888888888888888877665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0014
                          Prominin 612 lyleqlckkltkvnletlaekleelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksvkkldeens 688
                                       ++ ++++++++k++ +t ++k+ el  +l+n +++l qslk  + + ++ ++e++++l++  + l +  k++d+++ 
  gi|330509096|ref|YP_004385524.1| 162 EFEKETDQRWMKLQEDTDKAKV-ELHAALNNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDELEKEIDQRGM 237
                                       5666667777666555544443.333444444567999999999999999999999999999999999999999999 PP

                          Prominin 689 dlqesikkllaaveraenflkkngseiinneskkl 723
                                       +lqe i++  +  + a+  l+++  ++in+++++ 
  gi|330509096|ref|YP_004385524.1| 238 KLQEDITNAQSDFQIANRNLRNELVRMINDLRSES 272
                                       9************9999999999999999988765 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.093
                          Prominin 337 sivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprealdavisdlentersskt 403
                                       +   ++ +++ e+ + +k+ ++++  +l+ +l+  r++ k++ ++   e+  ++ s+++++ +++++
  gi|330509096|ref|YP_004385524.1| 281 NSFDQQKDEFSEVTTGLKDSIQKMHDELTGDLEVSRQEYKEFFRNA-IEKNTTIESQIHELRKQVRA 346
                                       4444555555555555555555555555555555555555555544.44445555555555555444 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.8      0.22        79      12      56 ..     105     150 ..      37     179 .. 0.73
   2 ?    2.4   0.3       0.4   1.5e+02      15      62 ..     173     221 ..     163     242 .. 0.67
   3 ?    5.9   0.0     0.033        12      12      62 ..     257     307 ..     241     314 .. 0.90
   4 ?    1.3   0.1      0.85   3.1e+02      11      31 ..     328     348 ..     314     353 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.22
                              ApoO  12 ptdrLeegvrslRkslepytsavqdelnkvkskvet.aeqsvtdti 56 
                                       + ++L+e   ++  +l+  ++ ++++l++  +++++ +e   t+  
  gi|330509096|ref|YP_004385524.1| 105 RGTKLQEDTDKAKVELHAALDNLESKLDQSLKYFQDkSEDRYTEIN 150
                                       4456666777777777777777777776666665541333444444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.4
                              ApoO  15 rLeegvrslRkslepytsavqdelnkvkskveta.eqsvtdtiasLkep 62 
                                       +L+e   ++  +l+  ++ ++++l++  ++++++ e   t+  ++L ++
  gi|330509096|ref|YP_004385524.1| 173 KLQEDTDKAKVELHAALNNLESKLDQSLKYFQDKsEDRYTEINQNLDNH 221
                                       5777777777778888888888877766666543144444444455544 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.033
                              ApoO  12 ptdrLeegvrslRkslepytsavqdelnkvkskvetaeqsvtdtiasLkep 62 
                                        +++L + ++ lR + e  + +++++++++k+ + +  + ++d+i+ ++++
  gi|330509096|ref|YP_004385524.1| 257 LRNELVRMINDLRSESEIRFLEFNNSFDQQKDEFSEVTTGLKDSIQKMHDE 307
                                       566788999*************************************99985 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.85
                              ApoO  11 eptdrLeegvrslRkslepyt 31 
                                       e+ +++e+++++lRk++  ++
  gi|330509096|ref|YP_004385524.1| 328 EKNTTIESQIHELRKQVRAQL 348
                                       46678999******9998776 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  12.1     0.083        30      71     155 ..      85     169 ..      19     173 .. 0.84
   2 ?    4.5   9.3     0.091        33      79     152 ..     158     231 ..     155     238 .. 0.79
   3 ?    4.2   3.7      0.11        41      75     116 ..     219     260 ..     215     272 .. 0.77
   4 ?    9.6   9.1    0.0024      0.88      46     146 ..     241     344 ..     231     364 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.083
                           DUF1640  71 rsefaalrseteklqreleklkqkLreeidklkadirldlnleKgrireelakleakiqelnnkidrevsalrteiE 147
                                       +   + ++++ ++l++e ++  +kL+e++dk k +    l++  ++  + l+++++k ++ ++ i++++ + r+ ++
  gi|330509096|ref|YP_004385524.1|  85 KDTGNDIHNSFNELKQETDQRGTKLQEDTDKAKVELHAALDNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLD 161
                                       5566778888999*************************************************************999 PP

                           DUF1640 148 svKldvik 155
                                       +   ++ +
  gi|330509096|ref|YP_004385524.1| 162 EFEKETDQ 169
                                       88777655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.091
                           DUF1640  79 seteklqreleklkqkLreeidklkadirldlnleKgrireelakleakiqelnnkidrevsalrteiEsvKld 152
                                       s  ++ ++e ++   kL+e++dk k +    ln+  ++  + l+++++k ++ ++ i++++ + r+ ++++  +
  gi|330509096|ref|YP_004385524.1| 158 SRLDEFEKETDQRWMKLQEDTDKAKVELHAALNNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDELEKE 231
                                       55667778888888899999999999999999999999999999999999999999999998888888876555 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.11
                           DUF1640  75 aalrseteklqreleklkqkLreeidklkadirldlnleKgr 116
                                        + rs  ++l++e+++   kL+e+i++ ++d+++   + +++
  gi|330509096|ref|YP_004385524.1| 219 DNHRSRLDELEKEIDQRGMKLQEDITNAQSDFQIANRNLRNE 260
                                       577888999**********************99865554444 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0024
                           DUF1640  46 selekseylqkaalselrkevqise.......rsefaalrseteklqreleklkqkLreeidklkadirldlnleKg 115
                                       +++ +++  ++ a  +lr+e++ +        +  f ++ ++ ++ + e+ ++++ L++ i+k+ ++   dl+  ++
  gi|330509096|ref|YP_004385524.1| 241 EDITNAQSDFQIANRNLRNELVRMIndlrsesEIRFLEFNNSFDQQKDEFSEVTTGLKDSIQKMHDELTGDLEVSRQ 317
                                       4444444445555555555444433344443388899999************************************9 PP

                           DUF1640 116 rireelakleakiqelnnkidrevsalrtei 146
                                       + +e + +  +k    n+ i+ ++++lr+++
  gi|330509096|ref|YP_004385524.1| 318 EYKEFFRNAIEK----NTTIESQIHELRKQV 344
                                       999977776665....555566666666554 PP

>> DUF842  Eukaryotic protein of unknown function (DUF842)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.4     0.024       8.9      54     101 ..     110     158 ..      99     174 .. 0.79
   2 ?    6.3   0.5      0.02       7.3      54     100 ..     175     222 ..     165     234 .. 0.80
   3 ?    0.8   0.1         1   3.7e+02      45      79 ..     238     272 ..     227     312 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.024
                            DUF842  54 seplqkaqkvvqqEleqfqerLqrcvmvCqdkakdklgp.nssekqtak 101
                                       +e + ka+  +   l++++++L ++++  qdk +d++++ n++ ++  +
  gi|330509096|ref|YP_004385524.1| 110 QEDTDKAKVELHAALDNLESKLDQSLKYFQDKSEDRYTEiNQNLDNHRS 158
                                       6788999999**************************9776554443333 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.02
                            DUF842  54 seplqkaqkvvqqEleqfqerLqrcvmvCqdkakdklgp.nssekqta 100
                                       +e + ka+  +   l++++++L ++++  qdk +d++++ n++ ++  
  gi|330509096|ref|YP_004385524.1| 175 QEDTDKAKVELHAALNNLESKLDQSLKYFQDKSEDRYTEiNQNLDNHR 222
                                       6788999999**************************977655444433 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1
                            DUF842  45 sveqCvekCseplqkaqkvvqqEleqfqerLqrcv 79 
                                       ++++ ++++++  q a++ + +El ++ + L +  
  gi|330509096|ref|YP_004385524.1| 238 KLQEDITNAQSDFQIANRNLRNELVRMINDLRSES 272
                                       55666777777777788888888777777766544 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.35   1.3e+02      39      66 ..      44      74 ..       5      86 .. 0.75
   2 ?    1.4   0.4       1.2   4.5e+02      15      45 ..     101     132 ..      79     143 .. 0.64
   3 ?    5.2   0.7      0.08        29      17      57 ..     128     166 ..     118     184 .. 0.77
   4 ?    8.5   1.0    0.0075       2.7      12      60 ..     188     234 ..     183     245 .. 0.80
   5 ?    2.8   0.4      0.46   1.7e+02      27      66 ..     265     309 ..     230     315 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.35
                           NPV_P10 39 elnekLdaqsaqLaelet...kvenIqdiLn 66
                                      + ++kL + s++L++l++   +ve+  +iL 
  gi|330509096|ref|YP_004385524.1| 44 DFESKLRGASESLDKLDQyiiEVESRWSILE 74
                                      4678999**********94444444445666 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.2
                           NPV_P10  15 avddkVdalqqqvddvqenlpd.vtelnekLd 45 
                                       ++d++ + lq+  d+ + +l   +++l++kLd
  gi|330509096|ref|YP_004385524.1| 101 ETDQRGTKLQEDTDKAKVELHAaLDNLESKLD 132
                                       45555566666666555554431445555555 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.08
                           NPV_P10  17 ddkVdalqqqvddvqenlpd.vtelnekLdaqsaqLaeletk 57 
                                       ++    l+q+++  q++++d  te+n++Ld+    L+e+e++
  gi|330509096|ref|YP_004385524.1| 128 ES---KLDQSLKYFQDKSEDrYTEINQNLDNHRSRLDEFEKE 166
                                       44...458888888888876468*************999874 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0075
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpd.vtelnekLdaqsaqLaeletkven 60 
                                       + +++++k+   +q+++  q++++d  te+n++Ld+    L+ele+++++
  gi|330509096|ref|YP_004385524.1| 188 ALNNLESKL---DQSLKYFQDKSEDrYTEINQNLDNHRSRLDELEKEIDQ 234
                                       555666665...7888888888876468*****************98875 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.46
                           NPV_P10  27 vddvqenlp.dvtelnekLdaqsaqLaelet....kvenIqdiLn 66 
                                       ++d++++++  + e n+ +d+q ++  e+ t    ++++ +d L+
  gi|330509096|ref|YP_004385524.1| 265 INDLRSESEiRFLEFNNSFDQQKDEFSEVTTglkdSIQKMHDELT 309
                                       556665554245678888888888888888854445555555555 PP

>> DUF4600  Domain of unknown function (DUF4600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.8    0.0065       2.4      27      97 ..      78     148 ..       7     151 .. 0.91
   2 ?    9.5   9.5    0.0034       1.2      28      99 ..     144     215 ..     141     242 .. 0.85
   3 ?    0.3   1.1       2.4   8.9e+02      14      65 ..     213     271 ..     211     308 .. 0.57
   4 ?    3.5   0.7      0.25        91       3      31 ..     317     345 ..     315     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0065
                           DUF4600  27 keklekirgnpsdrlasirvleklteeelnqllkqLekekkslenqlkdlelrleqEsKayhkandeRkay 97 
                                       ++ le++++  +d+ +s + l++ t++   +l +  +k k +l+  l +le +l+q  K ++  ++ R ++
  gi|330509096|ref|YP_004385524.1|  78 RKILEQLKDTGNDIHNSFNELKQETDQRGTKLQEDTDKAKVELHAALDNLESKLDQSLKYFQDKSEDRYTE 148
                                       4557778888888888888899999**99*********************************999999765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0034
                           DUF4600  28 eklekirgnpsdrlasirvleklteeelnqllkqLekekkslenqlkdlelrleqEsKayhkandeRkayla 99 
                                       ++  +i +n +++ + ++ +ek t++   +l +  +k k +l+  l +le +l+q  K ++  ++ R ++++
  gi|330509096|ref|YP_004385524.1| 144 DRYTEINQNLDNHRSRLDEFEKETDQRWMKLQEDTDKAKVELHAALNNLESKLDQSLKYFQDKSEDRYTEIN 215
                                       6777889999999************************************************99999976554 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.4
                           DUF4600  14 elNdqLekqiailkeklekir.......gnpsdrlasirvleklteeelnqllkqLeke 65 
                                       e+N++L +  ++l+e  ++i        ++ ++ ++  +  ++   +el ++++ L +e
  gi|330509096|ref|YP_004385524.1| 213 EINQNLDNHRSRLDELEKEIDqrgmklqEDITNAQSDFQIANRNLRNELVRMINDLRSE 271
                                       66666666666666655555522222223333333444444555555555555555444 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.25
                           DUF4600   3 newktrYetqlelNdqLekqiailkekle 31 
                                       +e+k  +    e+N+ +e qi  l++++ 
  gi|330509096|ref|YP_004385524.1| 317 QEYKEFFRNAIEKNTTIESQIHELRKQVR 345
                                       58888899999**************9875 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   0.1       1.3   4.6e+02       3      70 ..     238     305 ..     236     317 .. 0.71
   2 ?    8.7   0.2    0.0067       2.4      46      79 ..     317     350 ..     311     356 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1.3
                       Tox-REase-5   3 aYQaqitgvpkgteyrvkseewelldvdfDGfksaeclllEaKagYdqffdkkepklkksfkgadkll 70 
                                       + Q+ it+++ ++++++ + + el+++  D   ++e  +lE  + +dq  d+  ++++  +   +k+ 
  gi|330509096|ref|YP_004385524.1| 238 KLQEDITNAQSDFQIANRNLRNELVRMINDLRSESEIRFLEFNNSFDQQKDEFSEVTTGLKDSIQKMH 305
                                       56999999999999988888888887777777777777888877777766666665555555555554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0067
                       Tox-REase-5  46 agYdqffdkkepklkksfkgadklleqaerqara 79 
                                       ++Y++ff++ ++k +++ ++ ++l +q++ q+  
  gi|330509096|ref|YP_004385524.1| 317 QEYKEFFRNAIEKNTTIESQIHELRKQVRAQLAF 350
                                       79****************************9865 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  20.8     0.022       7.9     141     258 ..     116     234 ..       4     240 .. 0.80
   2 ?    5.2  13.5     0.036        13     143     240 ..     183     298 ..     180     353 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.022
                      Exonuc_VII_L 141 dkaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleel 217
                                        k el++ l++le++l++++k   ++++ r ++++++l + +++l++ +++ d+   +l++ ++k+  + +++l++l
  gi|330509096|ref|YP_004385524.1| 116 AKVELHAALDNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDEFEKETDQRWMKLQEDTDKAKVELHAALNNL 192
                                       34566777888888888888888888888888888888888888888888888888888887777777777777888 PP

                      Exonuc_VII_L 218 kerlkekleekkerlkklkerle.lleekkerleeleeklea 258
                                       +++l ++l+  +++ +++ ++++ +l+++++rl+ele+++++
  gi|330509096|ref|YP_004385524.1| 193 ESKLDQSLKYFQDKSEDRYTEINqNLDNHRSRLDELEKEIDQ 234
                                       877755555555555444444445688888888888888876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.036
                      Exonuc_VII_L 143 aeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelke 219
                                        el++ l++le++l++++k   ++++ r ++++++l + +++l++ ++++d+   +l++ ++++ +  + + ++l++
  gi|330509096|ref|YP_004385524.1| 183 VELHAALNNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDELEKEIDQRGMKLQEDITNAQSDFQIANRNLRN 259
                                       67899999999999999999999999999999999999899999999999998888888666654444444444443 PP

                      Exonuc_VII_L 220 rl.k.................ekleekkerlkklkerle 240
                                       +l +                 ++++++k++++++++ l+
  gi|330509096|ref|YP_004385524.1| 260 ELvRmindlrseseirflefnNSFDQQKDEFSEVTTGLK 298
                                       333333333334443333333333333333333322222 PP

>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   2.9      0.16        60      19      89 ..     106     172 ..      68     194 .. 0.63
   2 ?   -0.1   1.7      0.97   3.6e+02      44      76 ..     176     208 ..     141     255 .. 0.47
   3 ?   12.1   0.7    0.0002     0.072       8     100 ..     254     343 ..     247     356 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.16
                                       HHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC----EEE CS
                     Histidinol_dh  19 ledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaqkeseeev 89 
                                        ++ +e+ d+a +e+ + +D+++  ++l  s + ++++ e+  +e+ + l++  +++ +f +++ ++  ++
  gi|330509096|ref|YP_004385524.1| 106 GTKLQEDTDKAKVELHAALDNLE--SKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDEFEKETDQR--WM 172
                                       45566677777777777777553..345555555666666666666677777777777777777654..33 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.97
                                       GCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHH CS
                     Histidinol_dh  44 eslrvseeeieealekldeelkealeeaaenir 76 
                                       e+    + e+++al++l+++l ++l+  +++ +
  gi|330509096|ref|YP_004385524.1| 176 EDTDKAKVELHAALNNLESKLDQSLKYFQDKSE 208
                                       222222333333333333333333333222222 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.0002
                                       -HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC-- CS
                     Histidinol_dh   8 seeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaqke 84 
                                       +++++++  ++++d r+e +   le+++ FD+   +++++  ++ ++++++k+++el+  le++ ++ ++f ++  e
  gi|330509096|ref|YP_004385524.1| 254 NRNLRNELVRMINDLRSESEIRFLEFNNSFDQQ--KDEFSEVTTGLKDSIQKMHDELTGDLEVSRQEYKEFFRNAIE 328
                                       556777788899*******************44..46777777899*****************************98 PP

                                       --EEEEEECTTEEEEE CS
                     Histidinol_dh  85 seeevketepgvvlgq 100
                                       +++++ e++     +q
  gi|330509096|ref|YP_004385524.1| 329 KNTTI-ESQIHELRKQ 343
                                       76655.3333333333 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 ?    8.4   1.8    0.0064       2.3      36     129 ..       6     106 ..       3     111 .. 0.77
   2 ?    5.3   8.5     0.057        21      32     128 ..      76     170 ..      71     186 .. 0.73
   3 ?    5.6   8.9     0.046        17      33     125 ..     178     272 ..     172     278 .. 0.59
   4 ?    4.9   1.9     0.077        28      44      99 ..     287     346 ..     266     351 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0064
                                       HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHCCCHHHHH..HHCCH..HHHH CS
                         Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvik...ksskeleeeilrlket..idaqe..snir 105
                                       dle+++ ele+++ +++e+ ++  ++ d + e  k +kd ++ ++   +s ++l++ i++++ +  i + e  + ++
  gi|330509096|ref|YP_004385524.1|   6 DLEQVNFELEDFRARSQETLKTLDQLADFILEFSKLEKDFESKLRgasESLDKLDQYIIEVESRwsILEPEarKILE 82 
                                       78999999*********************999999999987666501155556667777777643377766656679 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 106 vLqnvlesneqkiqkLeqdidqke 129
                                       +L+++ ++ +++ ++L+q+ dq+ 
  gi|330509096|ref|YP_004385524.1|  83 QLKDTGNDIHNSFNELKQETDQRG 106
                                       999999999999999999999875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.057
                                       CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                         Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilrlketidaqesnirvL 107
                                       + +k le+l+++ ++i+ns +e ++ + +  ++l+e+  ++k +   ++ +++++l++   +++++    e +  ++
  gi|330509096|ref|YP_004385524.1|  76 EARKILEQLKDTGNDIHNSFNELKQETDQRGTKLQEDTDKAKVElHAALDNLESKLDQSLKYFQDKS---EDRYTEI 149
                                       5667788888888888888888888888888888888777776668888888888887777777654...4555555 PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 108 qnvlesneqkiqkLeqdidqk 128
                                        ++l++ ++++ + e++ dq+
  gi|330509096|ref|YP_004385524.1| 150 NQNLDNHRSRLDEFEKETDQR 170
                                       667888888888888877775 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.046
                                       CCHHHCCCCCCCCCCCCHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHH CS
                         Fib_alpha  33 vkkdlekleneleeisnstkeaeelvke.ikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLq 108
                                       ++k   +l+  l++++++  ++ ++ ++  +d ++e +++ +++ + + +++ke++++ ++l+e i++  s  +   
  gi|330509096|ref|YP_004385524.1| 178 TDKAKVELHAALNNLESKLDQSLKYFQDkSEDRYTEINQNLDNHRSRLDELEKEIDQRGMKLQEDITNAQSDFQIAN 254
                                       44444445555555554444444443330233333333333334778889999999999999999999999988877 PP

                                       HHHHHHH.HHHHHHHHHH CS
                         Fib_alpha 109 nvlesne.qkiqkLeqdi 125
                                        +l++   + i++L++++
  gi|330509096|ref|YP_004385524.1| 255 RNLRNELvRMINDLRSES 272
                                       666665404556676665 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.077
                                       CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHCCCHHHHHHHC CS
                         Fib_alpha  44 leeisnstkeaeelvkeikdslrekqkskkdn.....dnvikksskeleeeilrlketida 99 
                                        +e+s+ t+  ++ +++++d l+ + + ++++      n+i+k ++++e++i +l++++ a
  gi|330509096|ref|YP_004385524.1| 287 KDEFSEVTTGLKDSIQKMHDELTGDLEVSRQEykeffRNAIEK-NTTIESQIHELRKQVRA 346
                                       4455666666666666666666666666664222222222222.22334444444444443 PP

>> HJURP_C  Holliday junction regulator protein family C-terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.072        26      20      33 ..     142     155 ..     134     157 .. 0.90
   2 ?    5.0   0.3     0.068        25      20      33 ..     207     220 ..     199     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.072
                           HJURP_C  20 tenkYreIkeeFDk 33 
                                        e++Y+eI+   D+
  gi|330509096|ref|YP_004385524.1| 142 SEDRYTEINQNLDN 155
                                       69*******99996 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.068
                           HJURP_C  20 tenkYreIkeeFDk 33 
                                        e++Y+eI+   D+
  gi|330509096|ref|YP_004385524.1| 207 SEDRYTEINQNLDN 220
                                       69********9996 PP

>> Matrilin_ccoil  Trimeric coiled-coil oligomerisation domain of matrilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.071        26      16      43 ..     138     165 ..     133     167 .. 0.91
   2 ?    6.6   0.1     0.019       6.9      16      44 ..     203     231 ..     198     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.071
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Matrilin_ccoil  16 FQtkVeseiqaLtqkLeavtkRlealEn 43 
                                       FQ+k e++    +q+L++  +Rl  +E 
  gi|330509096|ref|YP_004385524.1| 138 FQDKSEDRYTEINQNLDNHRSRLDEFEK 165
                                       *******************9**999996 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Matrilin_ccoil  16 FQtkVeseiqaLtqkLeavtkRlealEnk 44 
                                       FQ+k e++    +q+L++  +Rl  lE  
  gi|330509096|ref|YP_004385524.1| 203 FQDKSEDRYTEINQNLDNHRSRLDELEKE 231
                                       **************************986 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  31.2    0.0013      0.47      11     205 ..      27     232 ..      19     251 .. 0.80
   2 ?   -2.1  13.6       6.9   2.5e+03      66     202 ..     209     343 ..     199     350 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHH CS
                              SHE3  11 qiDaLtktnlqLtqqsqeLleklelaqkkeskflenlaslkhENdnLsslLkRKerrlkd.lekelselkesveelk 86 
                                       ++D+L++ +l+  + +++  +kl  a     + l++l +   E +   s+L+   r++++ l +  ++ ++s++elk
  gi|330509096|ref|YP_004385524.1|  27 TLDQLADFILEFSKLEKDFESKLRGAS----ESLDKLDQYIIEVESRWSILEPEARKILEqLKDTGNDIHNSFNELK 99 
                                       689999999999999999999998875....46788888889999************986488889*********** PP

                                       HHHHHHHHHHHHCC.CHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHSSSXXXXX CS
                              SHE3  87 lekkqlkkrlenss.aseteleeelerlkvqYdalv.dsqkeYkehY...qqeieeLkesleklklenekqleelqe 158
                                       +e++q  ++l++ + + + el++ l++l+ + d  +   q +  ++Y   +q++++ + +l+++++e ++++ +lqe
  gi|330509096|ref|YP_004385524.1| 100 QETDQRGTKLQEDTdKAKVELHAALDNLESKLDQSLkYFQDKSEDRYteiNQNLDNHRSRLDEFEKETDQRWMKLQE 176
                                       *****999987665156789***********9955514566667777333578999999****************** PP

                                       XXXXXX.XXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXX.....X CS
                              SHE3 159 rissndkdidtkldsynnkk....knlesieeeknkkllkkleslaseld.....l 205
                                       ++ + + ++ + l+++++k     k +++ +e++ +++++ l++ +s+ld     +
  gi|330509096|ref|YP_004385524.1| 177 DTDKAKVELHAALNNLESKLdqslKYFQDKSEDRYTEINQNLDNHRSRLDelekeI 232
                                       *************99887752111667788899999********999998654443 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.9
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  66 rrlkdlekelselkesveelklekkqlkkrlenssaseteleeelerlk.vqYdalvdsqkeYkehYqqeieeLkes 141
                                        r  +++++l +++++ +el++e +q  ++l++   + +    +++  + +  + lv   +  ++  +    e ++s
  gi|330509096|ref|YP_004385524.1| 209 DRYTEINQNLDNHRSRLDELEKEIDQRGMKLQEDITNAQ---SDFQIANrNLRNELVRMINDLRSESEIRFLEFNNS 282
                                       455555566666666666655555554444444333322...22222220223556666666666666666666666 PP

                                       HHHHHHHHHSSSXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SHE3 142 leklklenekqleelqerissndkdidtkldsynnkkknlesieeeknkkllkkleslase 202
                                       +++ k e ++  + l+++i++ + ++   l+   + +k++ +   ekn+ +++++++l+++
  gi|330509096|ref|YP_004385524.1| 283 FDQQKDEFSEVTTGLKDSIQKMHDELTGDLEVSRQEYKEFFRNAIEKNTTIESQIHELRKQ 343
                                       6666666666666666666666666666666666666666666666666666666666665 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2       1.3   4.9e+02      84     107 ..      18      40 ..       2      69 .. 0.43
   2 ?    7.0  10.4     0.018       6.7      15      86 ..      75     152 ..      73     176 .. 0.62
   3 ?    7.7  10.9     0.011       4.1      21     100 ..     175     267 ..     162     272 .. 0.72
   4 ?    4.4   1.7      0.12        45      22      73 ..     281     341 ..     273     352 .. 0.48

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  84 qkkqqellkpildkinkaikevak 107
                                       ++++qe lk  ld++ ++i e+ k
  gi|330509096|ref|YP_004385524.1|  18 RARSQETLK-TLDQLADFILEFSK 40 
                                       333333333.23333333322222 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.......-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  15 pegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkle......keekeqelqkkeqelqqkqqqkaqelqk 85 
                                       pe++++ eql+++ +++ + ++++++e ++  ++lq+++ k++        + e +l++  + +q+k + ++ e+++
  gi|330509096|ref|YP_004385524.1|  75 PEARKILEQLKDTGNDIHNSFNELKQETDQRGTKLQEDTDKAKvelhaaLDNLESKLDQSLKYFQDKSEDRYTEINQ 151
                                       78889999999999999999999999999999999855544312333333333333444444444433333333333 PP

                                       H CS
                              OmpH  86 k 86 
                                       +
  gi|330509096|ref|YP_004385524.1| 152 N 152
                                       2 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..............-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  21 qeqlekkfkklqaeleakekelqklqeelqkkakkl.e............keekeqelqkkeqelqqkqqqkaqelq 84 
                                       qe+ +k + +l a+l+++e +l++  + +q+k+++  +              e e+e++++  +lq++  +++ ++q
  gi|330509096|ref|YP_004385524.1| 175 QEDTDKAKVELHAALNNLESKLDQSLKYFQDKSEDRyTeinqnldnhrsrLDELEKEIDQRGMKLQEDITNAQSDFQ 251
                                       555555555555555555555555555555555444335555566788888899999**********9999999999 PP

                                       HHHHHHHHHHHHHHHH CS
                              OmpH  85 kkqqellkpildkink 100
                                        +++ l+++++  in+
  gi|330509096|ref|YP_004385524.1| 252 IANRNLRNELVRMIND 267
                                       9999999998887775 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHH...........HHHHHHHHH CS
                              OmpH  22 eqlekkfkklqaeleakekelqklqeelqkkakkle.keekeqe...........lqkkeqelq 73 
                                       + +++++ ++ +  + +++++qk+ +el     +le ++++++e           ++ +  el+
  gi|330509096|ref|YP_004385524.1| 281 NSFDQQKDEFSEVTTGLKDSIQKMHDELT---GDLEvSRQEYKEffrnaieknttIESQIHELR 341
                                       44555666666666666666666666664...33213555555553222222222222222222 PP

>> DCB  Dimerisation and cyclophilin-binding domain of Mon2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.7    0.0038       1.4       8      56 ..      89     138 ..      82     145 .. 0.84
   2 ?    4.1   0.6     0.091        33       5      58 ..     126     179 ..     122     190 .. 0.84
   3 ?    3.0   1.3      0.19        69       5      56 ..     151     203 ..     147     227 .. 0.81
   4 ?    3.3   0.9      0.16        58       4      56 ..     190     242 ..     187     309 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0038
                               DCB   8 ealqsdlkalsseskrkhskvkeasekgilkLktikssseee.eqslaea 56 
                                       + + +++++l++e+ ++ +k++e ++k+ ++L+ + ++ e++ +qsl+++
  gi|330509096|ref|YP_004385524.1|  89 NDIHNSFNELKQETDQRGTKLQEDTDKAKVELHAALDNLESKlDQSLKYF 138
                                       568899**************************998887766668888876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.091
                               DCB   5 kllealqsdlkalsseskrkhskvkeasekgilkLktikssseeeeqslaease 58 
                                       +l ++l+++lk  +  s+ +++++++  ++  ++L + ++++++   +l+e ++
  gi|330509096|ref|YP_004385524.1| 126 NLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDEFEKETDQRWMKLQEDTD 179
                                       577889999999************************999999777777777654 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.19
                               DCB   5 kllealqsdlkalsseskrkhskvkeasekgilkLktikssseee.eqslaea 56 
                                       + l++  s l +  +e+ ++  k++e ++k+ ++L+ + ++ e++ +qsl+++
  gi|330509096|ref|YP_004385524.1| 151 QNLDNHRSRLDEFEKETDQRWMKLQEDTDKAKVELHAALNNLESKlDQSLKYF 203
                                       55677788899999************999999999988777755568888776 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.16
                               DCB   4 skllealqsdlkalsseskrkhskvkeasekgilkLktikssseeeeqslaea 56 
                                       ++l ++l+++lk  +  s+ +++++++  ++  ++L +++++ ++   +l+e 
  gi|330509096|ref|YP_004385524.1| 190 NNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDELEKEIDQRGMKLQED 242
                                       5678899999*********************9999999999886655555554 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   2.0      0.27     1e+02      45     106 ..      47     109 ..       8     117 .. 0.46
   2 ?    3.3   1.9      0.25        91      19      88 ..      54     115 ..      43     139 .. 0.52
   3 ?    5.8   2.5     0.042        15       1      61 [.     140     196 ..     140     204 .. 0.74
   4 ?   11.1   2.2   0.00098      0.36       1      53 [.     205     257 ..     205     274 .. 0.75
   5 ?    4.1   1.5      0.14        50       6      77 ..     275     346 ..     270     349 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.27
                              FliJ  45 aelrnyqafisaldeaiaqqkqelaqaekqvekareewqea.rqerkklekLkerekkeeqke 106
                                       ++lr  ++ +++ld+ i + ++  + +e +  k  e+++   +  ++++  Lk++  ++  k 
  gi|330509096|ref|YP_004385524.1|  47 SKLRGASESLDKLDQYIIEVESRWSILEPEARKILEQLKDTgNDIHNSFNELKQETDQRGTKL 109
                                       555555555555555555555555555555444444444431222334444444333333333 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.25
                              FliJ  19 ekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqe 88 
                                       e l++l qy+ e ++++s              ++ +++l+++ + ++++ + ++++ +++  ++qe   +
  gi|330509096|ref|YP_004385524.1|  54 ESLDKLDQYIIEVESRWSILE--------PEARKILEQLKDTGNDIHNSFNELKQETDQRGTKLQEDTDK 115
                                       455555555555555554444........23333444445555555555555555555555555443332 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.042
                              FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeai 61 
                                       d+ + ++ e++++l++++++l+e e++ ++   +l++++      +   ++a +++l++++
  gi|330509096|ref|YP_004385524.1| 140 DKSEDRYTEINQNLDNHRSRLDEFEKETDQRWMKLQEDT----DKAKVELHAALNNLESKL 196
                                       788999**********************99988888877....344444444444444444 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00098
                              FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqaf 53 
                                       d+ + ++ e++++l++++++l+ele+++++   +l+++ ++++   + + ++ 
  gi|330509096|ref|YP_004385524.1| 205 DKSEDRYTEINQNLDNHRSRLDELEKEIDQRGMKLQEDITNAQSDFQIANRNL 257
                                       78899**************************9999999943333333334444 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.14
                              FliJ   6 eLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvek 77 
                                       ++ e ++ ++q++ +  e++  +++  +++ +e +g      + y++f ++  e+ + ++++++ ++kqv +
  gi|330509096|ref|YP_004385524.1| 275 RFLEFNNSFDQQKDEFSEVTTGLKDSIQKMHDELTGDLEVSRQEYKEFFRNAIEKNTTIESQIHELRKQVRA 346
                                       555666666666666666666666666666666643335556778888888888888888999999988876 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   3.5     0.024       8.7      65     136 ..      58     133 ..       9     139 .. 0.47
   2 ?    4.4   8.6     0.082        30      50     126 ..      79     158 ..      40     170 .. 0.54
   3 ?    4.3  11.2     0.084        31      54     137 ..     141     235 ..     133     258 .. 0.51
   4 ?    4.1  13.8     0.097        35      18     139 ..     180     310 ..     178     351 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.024
                             PIN_8  65 eleklkkaaekkleealkkwakkkald.teelrkelkkqleelkeel.......kaeleelkksskadkeedpilkk 133
                                       +l++ + ++e  + ++l+ +a+k   +  +++ ++++++++elk+e+       +++++++k + +a    d++++k
  gi|330509096|ref|YP_004385524.1|  58 KLDQYIIEVES-RWSILEPEARKIL-EqLKDTGNDIHNSFNELKQETdqrgtklQEDTDKAKVELHAAL--DNLESK 130
                                       33222222221.1112222222222.2366666666666666666663333322444444444443333..555555 PP

                             PIN_8 134 lee 136
                                       l++
  gi|330509096|ref|YP_004385524.1| 131 LDQ 133
                                       544 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.082
                             PIN_8  50 sviskekkayedlekeleklkkaaekkleealkkwakkkald....teelrkelkkqleelkeelkaeleelkkssk 122
                                       +++++ k++ +d+++++++lk++++ ++ ++l+++  k++++     ++l+++l+++l+ ++++ +  ++e++++ +
  gi|330509096|ref|YP_004385524.1|  79 KILEQLKDTGNDIHNSFNELKQETD-QRGTKLQEDTDKAKVElhaaLDNLESKLDQSLKYFQDKSEDRYTEINQNLD 154
                                       3444555555555555555555444.233344444444444422224444444444444444444444455555554 PP

                             PIN_8 123 adke 126
                                       ++++
  gi|330509096|ref|YP_004385524.1| 155 NHRS 158
                                       4443 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.084
                             PIN_8  54 kekkayedlekeleklkkaaekkleealkkwakkkald..........teelrkelkkqleelkeelkaeleelkks 120
                                       k++++y++++++l++ ++++++ ++e +++w k ++ +           ++l+++l+++l+ ++++ +  ++e++++
  gi|330509096|ref|YP_004385524.1| 141 KSEDRYTEINQNLDNHRSRLDEFEKETDQRWMKLQEDTdkakvelhaaLNNLESKLDQSLKYFQDKSEDRYTEINQN 217
                                       34445555555555555555544444444444433322111111223355555555555555555556666777777 PP

                             PIN_8 121 skadkee.dpilkkleel 137
                                        ++++++ d+++k++++ 
  gi|330509096|ref|YP_004385524.1| 218 LDNHRSRlDELEKEIDQR 235
                                       777766667777777664 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.097
                             PIN_8  18 etrkdllkvlekladrlwvPhqvalEfqrnresviskekkayedlekeleklkkaaekkleealkkwakkkaldtee 94 
                                       +++ +l ++l++l+++l  +   ++  ++ r + i+++ +  ++  +elek ++++ +kl+e +++ + + ++++++
  gi|330509096|ref|YP_004385524.1| 180 KAKVELHAALNNLESKLDQSLKYFQDKSEDRYTEINQNLDNHRSRLDELEKEIDQRGMKLQEDITNAQSDFQIANRN 256
                                       56678888999999999888888888888899999999999999999999999999999999999999999999*** PP

                             PIN_8  95 lrkelkkqleelkeelkaeleelkksskadkee.........dpilkkleelle 139
                                       lr+el + +++l++e +    e+++s++++k+e         d+i k  +el++
  gi|330509096|ref|YP_004385524.1| 257 LRNELVRMINDLRSESEIRFLEFNNSFDQQKDEfsevttglkDSIQKMHDELTG 310
                                       *************99955555555555555533322222244555555555544 PP

>> BshC  Bacillithiol biosynthesis BshC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   5.7   0.00012     0.043     418     497 ..      74     153 ..      36     158 .. 0.84
   2 ?    2.5  10.9      0.13        47     410     537 ..     144     273 ..     138     274 .. 0.77
   3 ?    2.2   2.4      0.17        61     422     474 ..     277     329 ..     243     350 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                       HTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHH CS
                              BshC 418 easeleldelfeeakeeleeafealkelaakidktleklveanekkilkqlekLekkllkaekrkheeelrqlekik 494
                                       e +  ++ e+++++ + +++ f++lk++  +   +l++ +++ ++++  +l++Le+kl ++ k  ++++ +++++i+
  gi|330509096|ref|YP_004385524.1|  74 EPEARKILEQLKDTGNDIHNSFNELKQETDQRGTKLQEDTDKAKVELHAALDNLESKLDQSLKYFQDKSEDRYTEIN 150
                                       445667777999****************************************************************9 PP

                                       HHH CS
                              BshC 495 neL 497
                                       ++L
  gi|330509096|ref|YP_004385524.1| 151 QNL 153
                                       988 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                                       HHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHT CS
                              BshC 410 elkkklveeaseleldelfeeakeeleeafealkelaakidktleklveanekkilkqlekLekkllka...ekrkh 483
                                       +  +++ ++ ++++    ++e ++e ++   +l+e   k   +l+ ++++ e+k+ ++l++++ k +++    +++ 
  gi|330509096|ref|YP_004385524.1| 144 DRYTEINQNLDNHRSR--LDEFEKETDQRWMKLQEDTDKAKVELHAALNNLESKLDQSLKYFQDKSEDRyteINQNL 218
                                       4444555555566555..99999999999999999999999999999999999999999999999886511157788 PP

                                       HHHHHHHHHHHHHHSGGG.S-HHHH-BHHHHHHHHHHHHHHHHHHS----SS-EE CS
                              BshC 484 eeelrqlekikneLfPng.slQERvlnfleflnkygedliekllealepldgehk 537
                                       +++ ++l+++++e+   g +lQE ++n    +   +++l ++l+ +++ l +e +
  gi|330509096|ref|YP_004385524.1| 219 DNHRSRLDELEKEIDQRGmKLQEDITNAQSDFQIANRNLRNELVRMINDLRSESE 273
                                       8999999999999987664799999998887777788888888888888777665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHHHHHHHH CS
                              BshC 422 leldelfeeakeeleeafealkelaakidktleklveanekkilkqlekLekk 474
                                       le+++ f+++k+e++e+ + lk+ ++k+ ++l + +e ++++ ++ +++  +k
  gi|330509096|ref|YP_004385524.1| 277 LEFNNSFDQQKDEFSEVTTGLKDSIQKMHDELTGDLEVSRQEYKEFFRNAIEK 329
                                       45555666666666666666666666666666666665555555444433332 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.4      0.53   1.9e+02      25      48 ..       7      30 ..       4      68 .. 0.64
   2 ?    0.7   0.3       1.8   6.5e+02      31      72 ..      58      99 ..      39     108 .. 0.82
   3 ?    2.7   2.2      0.41   1.5e+02      28      82 ..      91     146 ..      76     148 .. 0.62
   4 ?    6.3   3.1     0.032        12      21      62 ..     123     165 ..     109     176 .. 0.67
   5 ?    5.7   3.7      0.05        18      19      83 ..     147     212 ..     140     213 .. 0.85
   6 ?    7.6   4.6     0.013       4.6      20      66 ..     187     234 ..     172     241 .. 0.73
   7 ?    3.6   0.8      0.22        79      24      66 ..     217     259 ..     214     270 .. 0.83
   8 ?    5.0   0.3     0.079        29      30      71 ..     263     304 ..     251     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.53
                              KxDL 25 lnkknreLlelnalsqerlaklra 48
                                      l++ n eL++++a sqe l+ l +
  gi|330509096|ref|YP_004385524.1|  7 LEQVNFELEDFRARSQETLKTLDQ 30
                                      666677777777777777776654 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.8
                              KxDL 31 eLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkir 72
                                      +L +++ ++++r + l+ + ++  + lk++ +d+ ++f  ++
  gi|330509096|ref|YP_004385524.1| 58 KLDQYIIEVESRWSILEPEARKILEQLKDTGNDIHNSFNELK 99
                                      677888888888888888888888888888888888887766 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.41
                              KxDL  28 knreLlelnalsqerlaklrarfkqgtkllkevkkdLes.ifkkirslkaklakky 82 
                                        ++   el +++++r +kl+++  + +  l+   ++Les + + ++ +++k +++y
  gi|330509096|ref|YP_004385524.1|  91 IHNSFNELKQETDQRGTKLQEDTDKAKVELHAALDNLESkLDQSLKYFQDKSEDRY 146
                                       34555667777777777777777777777777777777524555666666666665 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.032
                              KxDL  21 tsgrlnkk.nreLlelnalsqerlaklrarfkqgtkllkevkk 62 
                                        ++ l++k  + L+ ++++s+ r++++++++ ++   l e  k
  gi|330509096|ref|YP_004385524.1| 123 ALDNLESKlDQSLKYFQDKSEDRYTEINQNLDNHRSRLDEFEK 165
                                       4555555534667888888888888888888877766666554 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.05
                              KxDL  19 aqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLes.ifkkirslkaklakkyP 83 
                                       +++ + l +   +L e+ +++++r  kl+++  + +  l+   ++Les + + ++ +++k +++y 
  gi|330509096|ref|YP_004385524.1| 147 TEINQNLDNHRSRLDEFEKETDQRWMKLQEDTDKAKVELHAALNNLESkLDQSLKYFQDKSEDRYT 212
                                       677889999999**********************************96366778888888877775 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.013
                              KxDL  20 qtsgrlnkk.nreLlelnalsqerlaklrarfkqgtkllkevkkdLes 66 
                                         ++ l++k  + L+ ++++s+ r++++++++ ++   l e+ k++++
  gi|330509096|ref|YP_004385524.1| 187 AALNNLESKlDQSLKYFQDKSEDRYTEINQNLDNHRSRLDELEKEIDQ 234
                                       556666666356788888889999999988888888888888888775 PP

  == domain 7  score: 3.6 bits;  conditional E-value: 0.22
                              KxDL  24 rlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLes 66 
                                        l +   +L el ++ ++r  kl++++ + + + +  +++L++
  gi|330509096|ref|YP_004385524.1| 217 NLDNHRSRLDELEKEIDQRGMKLQEDITNAQSDFQIANRNLRN 259
                                       6777788999999999999999999999999999999999864 PP

  == domain 8  score: 5.0 bits;  conditional E-value: 0.079
                              KxDL  30 reLlelnalsqerlaklrarfkqgtkllkevkkdLesifkki 71 
                                       r++ +l+ +s+ r+ ++++ f q++   +ev   L+ + +k+
  gi|330509096|ref|YP_004385524.1| 263 RMINDLRSESEIRFLEFNNSFDQQKDEFSEVTTGLKDSIQKM 304
                                       89999**************************99997655544 PP

>> Endonuc-dimeris  T4 recombination endonuclease VII, dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1       0.1        38      19      41 ..      96     118 ..      94     123 .. 0.86
   2 ?    0.4   0.1       2.1   7.5e+02      16      41 ..     158     183 ..     155     187 .. 0.81
   3 ?    6.5   0.1     0.026       9.4      16      39 ..     223     246 ..     220     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.1
                                       HHHHHHHHHTT----TTS-HHHH CS
                   Endonuc-dimeris  19 eEqkeellslGikYnesdkKsdL 41 
                                       +E k+e +++G k  e   K+  
  gi|330509096|ref|YP_004385524.1|  96 NELKQETDQRGTKLQEDTDKAKV 118
                                       699***********999888765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2.1
                                       S-HHHHHHHHHHTT----TTS-HHHH CS
                   Endonuc-dimeris  16 LkkeEqkeellslGikYnesdkKsdL 41 
                                        +++E  +e +++ +k  e   K+  
  gi|330509096|ref|YP_004385524.1| 158 SRLDEFEKETDQRWMKLQEDTDKAKV 183
                                       457899999*******9999888765 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.026
                                       S-HHHHHHHHHHTT----TTS-HH CS
                   Endonuc-dimeris  16 LkkeEqkeellslGikYnesdkKs 39 
                                        +++E  +e++++G+k  e  + +
  gi|330509096|ref|YP_004385524.1| 223 SRLDELEKEIDQRGMKLQEDITNA 246
                                       5678999*********99987655 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.3       1.2   4.2e+02       7      62 ..     121     177 ..      76     184 .. 0.53
   2 ?    4.0   0.5      0.13        49       9      66 ..     188     246 ..     180     249 .. 0.53
   3 ?    9.6   1.0    0.0024      0.87       8      70 ..     234     315 ..     228     327 .. 0.78
   4 ?   -2.0   0.0       9.7   3.5e+03      11      25 ..     331     345 ..     322     348 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.2
                           DUF1515   7 lqqlgtllaevkelredlk....rsedrsdasrakmyrkmdelvervtalegsvvklkad 62 
                                       + +l++l +++ +    lk    +sedr   +  ++ ++   l e  + ++   +kl++d
  gi|330509096|ref|YP_004385524.1| 121 HAALDNLESKLDQ---SLKyfqdKSEDRYTEINQNLDNHRSRLDEFEKETDQRWMKLQED 177
                                       2233333322222...22222245555555555555554445555555555555666665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.13
                           DUF1515   9 qlgtllaevkelredlk....rsedrsdasrakmyrkmdelvervtalegsvvklkaditsv 66 
                                       +l++l +++    + lk    +sedr   +  ++ ++   l e  + ++   +kl++dit+ 
  gi|330509096|ref|YP_004385524.1| 188 ALNNLESKL---DQSLKyfqdKSEDRYTEINQNLDNHRSRLDELEKEIDQRGMKLQEDITNA 246
                                       444444333...33444222455555555555555444444444455556669999*99975 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0024
                           DUF1515   8 qqlgtllaevkelredlk...................rsedrsdasrakmyrkmdelvervtalegsvvklkadits 65 
                                       q+  +l+ ++++ + d++                   +se r      +  ++ de+ e  t l+ s+ k+++++t 
  gi|330509096|ref|YP_004385524.1| 234 QRGMKLQEDITNAQSDFQianrnlrnelvrmindlrsESEIRFLEFNNSFDQQKDEFSEVTTGLKDSIQKMHDELTG 310
                                       555566666777666666666666677777888885677788888999**************************997 PP

                           DUF1515  66 vkevt 70 
                                         ev+
  gi|330509096|ref|YP_004385524.1| 311 DLEVS 315
                                       66665 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 9.7
                           DUF1515  11 gtllaevkelredlk 25 
                                        t+ ++++elr++++
  gi|330509096|ref|YP_004385524.1| 331 TTIESQIHELRKQVR 345
                                       455566666666655 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       2.3   8.2e+02      19      44 ..       3      28 ..       1      36 [. 0.66
   2 ?    1.3   0.2       1.1     4e+02      12      32 ..      48      68 ..      43      99 .. 0.55
   3 ?    0.1   2.1       2.5   9.2e+02      19      42 ..     105     128 ..      79     138 .. 0.63
   4 ?    0.1   0.1       2.5   9.3e+02       8      26 ..     119     134 ..     118     144 .. 0.67
   5 ?    7.5   1.7     0.013       4.6       4      39 ..     144     176 ..     141     182 .. 0.72
   6 ?   -0.1   0.1         3   1.1e+03       8      25 ..     184     198 ..     180     210 .. 0.66
   7 ?   10.3   2.8    0.0017      0.63       4      42 ..     209     244 ..     206     251 .. 0.71
   8 ?    2.2   0.0       0.6   2.2e+02      31      66 ..     327     362 ..     298     363 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2.3
                              XhlA 19 rvdkleekaaeaeekiknleedlkkl 44
                                      r+d+le+ + e e      +e+lk l
  gi|330509096|ref|YP_004385524.1|  3 RIDDLEQVNFELEDFRARSQETLKTL 28
                                      78888888777666555555555554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.1
                              XhlA 12 kldnleervdkleekaaeaee 32
                                      kl   +e +dkl++   e+e+
  gi|330509096|ref|YP_004385524.1| 48 KLRGASESLDKLDQYIIEVES 68
                                      444444444444444444443 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2.5
                              XhlA  19 rvdkleekaaeaeekiknleedlk 42 
                                       r +kl+e+ ++a+ ++  + ++l+
  gi|330509096|ref|YP_004385524.1| 105 RGTKLQEDTDKAKVELHAALDNLE 128
                                       445677777777666665555553 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 2.5
                              XhlA   8 rietkldnleervdkleek 26 
                                       ++++ ldnle++   l++ 
  gi|330509096|ref|YP_004385524.1| 119 ELHAALDNLESK---LDQS 134
                                       577889999996...4444 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.013
                              XhlA   4 erlerietkldnleervdkleekaaeaeekiknlee 39 
                                       +r ++i+++ldn+ +r+d+    + e++++ + l+e
  gi|330509096|ref|YP_004385524.1| 144 DRYTEINQNLDNHRSRLDE---FEKETDQRWMKLQE 176
                                       66689**********9555...55555555555555 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 3
                              XhlA   8 rietkldnleervdklee 25 
                                       ++++ l+nle++   l++
  gi|330509096|ref|YP_004385524.1| 184 ELHAALNNLESK---LDQ 198
                                       567778888885...444 PP

  == domain 7  score: 10.3 bits;  conditional E-value: 0.0017
                              XhlA   4 erlerietkldnleervdkleekaaeaeekiknleedlk 42 
                                       +r ++i+++ldn+ +r+d+le+   e +++ + l+ed+ 
  gi|330509096|ref|YP_004385524.1| 209 DRYTEINQNLDNHRSRLDELEK---EIDQRGMKLQEDIT 244
                                       5668999999999999666665...55666666666665 PP

  == domain 8  score: 2.2 bits;  conditional E-value: 0.6
                              XhlA  31 eekiknleedlkklesnqkWlirtiiGalisaviyl 66 
                                        ek   +e ++ +l +++  ++ ++  ++i+++ y+
  gi|330509096|ref|YP_004385524.1| 327 IEKNTTIESQIHELRKQVRAQLAFVGLIVIVILLYI 362
                                       455566788999999999999999988888888876 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 ?    3.0   3.1      0.42   1.5e+02       9      49 ..      90     133 ..       5     144 .. 0.71
   2 ?    7.1   2.1     0.023       8.4       3      67 ..     120     180 ..     114     184 .. 0.66
   3 ?    6.9   1.7     0.025       9.3       2      59 ..     184     237 ..     179     251 .. 0.64
   4 ?    0.3   0.2       2.9   1.1e+03       2      46 ..     227     271 ..     226     295 .. 0.73
   5 ?    2.0   0.1      0.91   3.3e+02       2      40 ..     307     348 ..     303     351 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.42
                            DUF883   9 slladleellkea...adeageeaeelRerleerlerarerlrd 49 
                                       ++ ++ +el +e+   + + +e++++++ +l+++l+++ ++l++
  gi|330509096|ref|YP_004385524.1|  90 DIHNSFNELKQETdqrGTKLQEDTDKAKVELHAALDNLESKLDQ 133
                                       22222223322220002233444445555555555554444444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.023
                            DUF883   3 leaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67 
                                       l+a l++l ++l++ lk  +d++++ +     +++++l++ r+rl++ e++  +r  +  e++d+
  gi|330509096|ref|YP_004385524.1| 120 LHAALDNLESKLDQSLKYFQDKSEDRY----TEINQNLDNHRSRLDEFEKETDQRWMKLQEDTDK 180
                                       444455555555555555555555555....5567778888999999998888888888888875 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.025
                            DUF883   2 eleaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerak 59 
                                       el+a l++l ++l++ lk  +d++++ + e+ ++    l++ r+rl+++e+++ +r  
  gi|330509096|ref|YP_004385524.1| 184 ELHAALNNLESKLDQSLKYFQDKSEDRYTEINQN----LDNHRSRLDELEKEIDQRGM 237
                                       4566777778888888888888888888776655....55555555555555555443 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 2.9
                            DUF883   2 eleaeleslladleellkeaadeageeaeelRerleerlerarer 46 
                                       ele+e+++   +l+e + +a+++ +   ++lR++l  +++++r++
  gi|330509096|ref|YP_004385524.1| 227 ELEKEIDQRGMKLQEDITNAQSDFQIANRNLRNELVRMINDLRSE 271
                                       566777666677777777777777777778888888888877776 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.91
                            DUF883   2 eleaeleslladleellkeaadea...geeaeelRerleerl 40 
                                       el+ +le  +++ +e++++a ++    +++++elR++++++l
  gi|330509096|ref|YP_004385524.1| 307 ELTGDLEVSRQEYKEFFRNAIEKNttiESQIHELRKQVRAQL 348
                                       566777777777777777654332111567777777776665 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   5.2      0.43   1.6e+02      22      96 ..      92     128 ..      11     133 .. 0.61
   2 ?    0.5  11.7       2.2   8.2e+02      22      92 ..      92     153 ..      86     197 .. 0.54
   3 ?    7.2   9.7      0.02       7.2      27      85 ..     198     257 ..     193     309 .. 0.78
   4 ?    0.9   2.9       1.7   6.3e+02      44      74 ..     305     347 ..     272     355 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.43
                                       HHHHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHH CS
                             DUF16  22 rkqlnefkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkin 96 
                                       +  +ne k++++qr +k+++  dk ++                                       +  +L++++
  gi|330509096|ref|YP_004385524.1|  92 HNSFNELKQETDQRGTKLQEDTDKAKV--------------------------------------ELHAALDNLE 128
                                       344444555555544444444443333......................................3333444444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.2
                                       HHHHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHH.HHHHHHHHHHHHHHHHHH.......HHHHHHHHH CS
                             DUF16  22 rkqlnefkdsnkqrLkkieakvdklgeqinkleqkve.kqgekikelkveqkaqgeelnkvdetleliletL 92 
                                       +  +ne k++++qr +k+++  dk ++++++  ++ e k+++ +k  + + + +  e+n+           L
  gi|330509096|ref|YP_004385524.1|  92 HNSFNELKQETDQRGTKLQEDTDKAKVELHAALDNLEsKLDQSLKYFQDKSEDRYTEINQ----------NL 153
                                       678899999999999998888885444443333333213333444444444433333332..........11 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.02
                                       H....B-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HH CS
                             DUF16  27 e....fkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetl 85 
                                       +    f+d  + r ++i++++d +  ++++le+++++ g k++e   ++   + +++  ++ l
  gi|330509096|ref|YP_004385524.1| 198 QslkyFQDKSEDRYTEINQNLDNHRSRLDELEKEIDQRGMKLQE---DITNAQSDFQIANRNL 257
                                       444449999******************************99844...3333333365333332 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.7
                                       H...............HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DUF16  44 d............klgeqinkleqkvekqgekikelkveqkaq 74 
                                       +              +e + +  +k ++ + +i+el++++ aq
  gi|330509096|ref|YP_004385524.1| 305 HdeltgdlevsrqEYKEFFRNAIEKNTTIESQIHELRKQVRAQ 347
                                       1333355555444444445555556666677777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2386  (0.13308); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                        86  (0.0047967); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              49  [number of targets reported over threshold]
# CPU time: 1.45u 0.38s 00:00:01.83 Elapsed: 00:00:00.62
# Mc/sec: 1791.36
//
Query:       gi|330509097|ref|YP_004385525.1|  [L=1309]
Description: hypothetical protein MCON_3484 [Methanosaeta concilii GP6]
Scores for complete 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-17   61.7   0.0    1.2e-16   60.9   0.0    1.4  1  DEAD          DEAD/DEAH box helicase
    8.8e-07   29.3   0.0    2.7e-06   27.7   0.0    1.9  1  Helicase_C    Helicase conserved C-terminal domain
    0.00097   19.8   0.7     0.0062   17.2   0.7    2.5  1  RecQ_Zn_bind  RecQ zinc-binding
     0.0016   17.3   0.0       0.02   13.6   0.0    2.1  2  SNF2_N        SNF2 family N-terminal domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   2.8e-20   1.2e-16       4     175 ..     448     618 ..     445     619 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 2.8e-20
                                       HHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   4 QaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                       Q e +  il++++vl+  +T +GK+l+f++ +l  +          +l+++P+r+L++++++nl++ +  +  ++ +
  gi|330509097|ref|YP_004385525.1| 448 QFELLVKILNQESVLGILPTSYGKSLVFQLYAL--L------IPRTTLVICPLRSLIRDQIQNLQRQGLLCAESITS 516
                                       66778889*************************..3......34578*****************9999965533333 PP

                                       EETTSSHHHHHHHHH.TTCSEEEEEHHHHHH.HH...HCTSSHCTTEEEEEEETHHHHHHT..TTHHHHHHHHHHSH CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.xx...xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                              DEAD  81 iiggvaardqlskld.ngvdivvgtpgrldd.ll...stgklnlsqvrflVlDEadrlldq..gfsdfinrilnqlp 150
                                         + + +++++++l+ +++++++  p+rl +  +    + +l+ s v  +V+DEa++++++  +f++ + +i +  +
  gi|330509097|ref|YP_004385525.1| 517 YDNRSGKDKKYEDLQgHNYRLLYISPERLREkEFycqIKSTLENSPVGAIVVDEAHCVSEWghDFRPSYLQIDRFRK 593
                                       334555677788886445************9644786456688999***************9999**9999777766 PP

                                       HHCTTSTTTSEEEEEESSBSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 151 qitcdgklqrqvivlSATlpkdvkk 175
                                       +i++ ++    +i+l+AT++kdvk+
  gi|330509097|ref|YP_004385525.1| 594 TIEKATRRMVPIIALTATASKDVKE 618
                                       66666667777***********986 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 !   27.7   0.0     6e-10   2.7e-06      57     110 ..     800     853 ..     783     854 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 6e-10
                                       HHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  57 eileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       +  e+f + ++ +L+at+  ++Gid  +++++++ ++  +++ y q +GR+gR 
  gi|330509097|ref|YP_004385525.1| 800 QCQEEFHQSQFPLLVATKGFGMGIDKRNIRFIVHHSFASGLEGYYQEAGRAGRD 853
                                       56689999*********************************************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 !   17.2   0.7   1.4e-06    0.0062      23      65 ..    1062    1110 ..    1045    1111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                      RecQ_Zn_bind   23 aelekleamlaycentteCrrkllleyFgeeaaee.......eCgnCDnC 65  
                                         ++++l +  +y+ +++ Crr  l + F+ e+ ++       +C+ CD+C
  gi|330509097|ref|YP_004385525.1| 1062 MRYQMLTDEKNYAVSKQ-CRRITLRSIFDTEQNHSrlvdsnyHCNFCDVC 1110
                                        56677777789**8877.**********96544448999999******** 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   4.5e-06      0.02      98     190 ..     353     575 ..      84     665 .. 0.75
   2 ?    1.4   0.0     0.024   1.1e+02     250     302 ..    1127    1179 ..    1090    1207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.5e-06
                                       -............................................................................ CS
                                       x............................................................................ RF
                            SNF2_N  98 p............................................................................ 98 
                                       +                                                                            
  gi|330509097|ref|YP_004385525.1| 353 Aepgqgdqrvdfsmtpvnlyfndnlpdadyvfadeamnpckskdcisgaslerfpdmfleianrqiqlelpkmidre 429
                                       05555555555555555555555555555555555555566666666667777777777777777777777777777 PP

                                       ........................................................EEEE--H.HHHHHHHHHHHHH CS
                                       ........................................................xxxxxxx.xxxxxxxxxxxxx RF
                            SNF2_N  99 ........................................................tLivvPa.slldqWeneierh 118
                                                                                               tL+++P  sl++   ++++r 
  gi|330509097|ref|YP_004385525.1| 430 ildyfarryflvpelkerqfellvkilnqesvlgilptsygkslvfqlyalliprtTLVICPLrSLIRDQIQNLQRQ 506
                                       77777777777778888888888888888888888888888888888888888888*******9***9655555555 PP

                                       -TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 119 vsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlk 190
                                           a  +  y++   ++ k +k  + + ++y  + ++ ++l+++  + +++s+l++     +v+DE+h + 
  gi|330509097|ref|YP_004385525.1| 507 GLLCAESITSYDN---RSGKDKKYEDLQGHNYRLLYISPERLREKEFYCQIKSTLENSPVGAIVVDEAHCVS 575
                                       4444444444554...45777788999999*************888888********************986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.024
                                        HHHHHHHHHHHHTT-STTEE---GGGT--S---EEEEEEEEE--HHHHHHHH. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  250 eaqaekgrsrLlqllqrlmlrrakkdveknlPpkteeiiflklskverksYnr 302 
                                        ea+ ++ ++ ++ +l+r+ + ++kk v   + +k    ++++++ + ++ Yn+
  gi|330509097|ref|YP_004385525.1| 1127 EAELDEIAKSIHLILERFDVEAMKKAVRTVFEKKADTSLLVQMTYQLEQKYND 1179
                                        466788899999***************999999*************9999*94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); 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: 0.89u 0.33s 00:00:01.22 Elapsed: 00:00:00.49
# Mc/sec: 8103.65
//
Query:       gi|330509098|ref|YP_004385526.1|  [L=563]
Description: hypothetical protein MCON_3485 [Methanosaeta concilii GP6]
Scores for complete 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   1.8    8.4e-09   35.4   1.8    1.5  1  DDE_Tnp_1     Transposase DDE domain
  ------ inclusion threshold ------
       0.11   12.8   0.4          1    9.7   0.4    2.6  2  MADF_DNA_bdg  Alcohol dehydrogenase transcription factor Myb/


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 !   35.4   1.8   9.3e-13   8.4e-09      26     212 ..     208     487 ..     183     489 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 9.3e-13
                         DDE_Tnp_1  26 gykggk.ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYasaelldtleekg 99 
                                       gy+ ++ +++  +l i+v+ r +++ls  + +g++h + ++k ll++l ++  ++ +++ D+G  s+++++ ++e+g
  gi|330509098|ref|YP_004385526.1| 208 GYNPDRiRRRQANLAILVSKRDRYPLSHFVYNGSRHSISTVKNLLNRLSKMaiEPGTLIWDRGNVSKKHVQMVDESG 284
                                       888788899999************9999999********************************************** PP

                         DDE_Tnp_1 100 vdyiirlkkntklyrk.......gaeskrrgrlrkhdrnkiltksqkrrnk.......................... 143
                                       ++ i  ++k +k+ +        +++     r   +++  ++++++++++k                          
  gi|330509098|ref|YP_004385526.1| 285 WKLICGVPKTSKEAKEiigktkiPISPDSLVRSSHAGHIYAIKTENELFGKerstivyanrersvkdadarnealsv 361
                                       *******9999999889999999455555555566666666666666666666666668888888999999999*** PP

                         DDE_Tnp_1 144 .........................................................skkekgdvyyvtntnsells 163
                                                                                                +  ek+d+  + + ++ +l 
  gi|330509098|ref|YP_004385526.1| 362 igeslnelsqtgkdwsekrlhdriknivgqwsgfidasvrrkkdgpriewsydrqrlRSAEKYDGKWLILSTDYSLN 438
                                       *******************************************************99999999999999999999** PP

                         DDE_Tnp_1 164 aeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                       a   +++y  +  iE vF+ lk++   + +r+r   rv+a+l+ ++la+
  gi|330509098|ref|YP_004385526.1| 439 ANNAVNMYLEKDFIEKVFRVLKTHEEVEPVRHRLEHRVKAYLFVCMLAY 487
                                       ************************************************9 PP

>> MADF_DNA_bdg  Alcohol dehydrogenase transcription factor Myb/SANT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.28   2.5e+03       9      37 ..     264     293 ..     259     306 .. 0.70
   2 ?    9.7   0.4   0.00011         1       7      57 ..     337     393 ..     335     417 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.28
                      MADF_DNA_bdg   9 pvLwdrshpdyrnkek.rekaweeiaeeln 37 
                                       +++wdr + + ++++   e  w+ i+   +
  gi|330509098|ref|YP_004385526.1| 264 TLIWDRGNVSKKHVQMvDESGWKLICGVPK 293
                                       679***997777666636778988886655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00011
                      MADF_DNA_bdg   7 khpvLwdrshpdyrnkekrekaweeiaeelnekvd......veeckkkwknLRdryr 57 
                                       + ++ + ++ ++ ++ ++r++a++ i e+lne  +      +++++ ++kn+  + +
  gi|330509098|ref|YP_004385526.1| 337 RSTIVYANRERSVKDADARNEALSVIGESLNELSQtgkdwsEKRLHDRIKNIVGQWS 393
                                       56789*************************843333333324446667776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); 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: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3599.80
//
Query:       gi|330509099|ref|YP_004385527.1|  [L=492]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-44  144.3  24.2    2.6e-06   27.1   0.0   11.9 12  TPR_2            Tetratricopeptide repeat
    2.4e-43  144.2  18.6    1.5e-05   24.6   0.0   11.9 12  TPR_1            Tetratricopeptide repeat
    4.3e-38  126.3  18.6     0.0012   18.8   0.1   12.0 12  TPR_8            Tetratricopeptide repeat
    7.5e-34  115.9  21.9      1e-09   38.5   0.2    6.8  7  TPR_12           Tetratricopeptide repeat
    1.1e-29  102.8  22.7    6.9e-10   39.4   0.4    7.0  7  TPR_16           Tetratricopeptide repeat
    2.5e-27   93.2  26.1    0.00015   22.3   0.2    9.8 10  TPR_14           Tetratricopeptide repeat
    6.8e-25   86.5  22.5    1.9e-06   27.5   0.6    9.1  9  TPR_11           TPR repeat
    2.3e-23   82.5  20.4    3.8e-07   30.5   0.0    7.1  7  TPR_19           Tetratricopeptide repeat
    1.8e-19   68.6   3.1     0.0037   17.5   0.0    9.5  9  TPR_17           Tetratricopeptide repeat
    1.4e-16   60.3  14.1    5.3e-05   23.3   0.2    6.3  6  TPR_9            Tetratricopeptide repeat
    2.8e-12   45.7  13.7        0.6   10.3   0.0    8.8  9  TPR_7            Tetratricopeptide repeat
    4.3e-12   46.3  19.4      0.028   14.5   0.3    7.6  7  DUF3856          Domain of Unknown Function (DUF3856)
    4.2e-11   42.7   7.5          1   10.2   0.1    8.6  9  TPR_6            Tetratricopeptide repeat
    4.2e-10   39.7   9.5    0.00055   20.1   0.2    5.1  5  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    8.5e-10   38.2   9.7      0.062   12.2   1.2    4.9  4  NARP1            NMDA receptor-regulated protein 1
    9.8e-10   38.5  12.9      0.019   14.7   0.1    5.4  5  TPR_21           Tetratricopeptide repeat-like domain
    1.4e-09   37.8   5.0    0.00023   20.7   0.1    3.6  3  TPR_MalT         MalT-like TPR region
    1.9e-07   30.7  26.3       0.34   10.8   0.0    8.5  9  TPR_10           Tetratricopeptide repeat
      1e-06   29.2  15.7        0.2   12.1   0.9    5.7  6  BTAD             Bacterial transcriptional activator domain
      2e-05   23.8   1.2       0.22   10.5   0.1    3.1  3  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
  ------ inclusion threshold ------
      0.028   13.2   0.1      0.028   13.2   0.1    1.7  2  DUF3808          Protein of unknown function (DUF3808)
      0.056   13.9   5.5         54    4.2   0.0    4.3  6  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
      0.066   13.3   4.5         26    5.0   0.2    4.9  5  ANAPC5           Anaphase-promoting complex subunit 5
      0.066   13.4   3.3         16    5.7   0.1    3.7  3  DUF1510          Domain of unknown function (DUF1510)
      0.069   12.7   0.6         16    5.1   0.0    4.6  5  HTH_Bact         Helix-turn-helix bacterial domain
       0.13   12.9   0.1       0.13   12.9   0.1    6.8  5  TPR_4            Tetratricopeptide repeat
       0.26   11.4   2.8         51    4.1   0.2    4.5  5  DUF2802          Protein of unknown function (DUF2802)
        2.1    8.5  25.7         23    5.2   0.1    8.1  9  MIT              MIT (microtubule interacting and transport) 
        2.2    8.4   6.1        1.8    8.7   0.0    3.9  3  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.042        26       3      32 ..      50      79 ..      49      79 .. 0.87
   2 ?    2.0   0.0      0.45   2.8e+02      16      30 ..      97     111 ..      91     114 .. 0.81
   3 !   14.7   0.1   4.1e-05     0.025       2      31 ..     124     153 ..     123     156 .. 0.94
   4 !   27.1   0.0   4.2e-09   2.6e-06       1      32 [.     164     195 ..     164     197 .. 0.94
   5 !    9.1   0.0    0.0025       1.5       4      33 ..     201     230 ..     198     231 .. 0.84
   6 !   15.6   1.4   2.1e-05     0.013       1      33 [.     237     269 ..     237     270 .. 0.93
   7 !   18.6   0.0   2.2e-06    0.0014       3      34 .]     273     304 ..     271     304 .. 0.94
   8 !    7.4   0.1    0.0086       5.3       3      30 ..     307     334 ..     305     336 .. 0.90
   9 ?    5.0   0.0     0.051        32       8      30 ..     351     373 ..     344     374 .. 0.79
  10 !   20.1   0.0   7.1e-07   0.00044       6      33 ..     390     417 ..     387     418 .. 0.92
  11 !   23.9   0.2   4.6e-08   2.8e-05       3      33 ..     427     457 ..     425     458 .. 0.92
  12 ?   -0.1   0.1       2.2   1.3e+03       2      17 ..     460     475 ..     459     478 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.042
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldP 32
                                      ++ n+++ +++++  +eA+ a+  A + +P
  gi|330509099|ref|YP_004385527.1| 50 YWINRAEELMHNDSIDEAISACGMAQKKEP 79
                                      79*****************99877776665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.45
                             TPR_2  16 dyeeAleafekAlel 30 
                                         +e ++ +ekAl l
  gi|330509099|ref|YP_004385527.1|  97 MVNESAKTYEKALTL 111
                                       567889999999987 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 4.1e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                       ea+ + + +++ l++ +e  +a+ekAle+ 
  gi|330509099|ref|YP_004385527.1| 124 EAWQWKAIVLASLNREDESDQAYEKALEIF 153
                                       89**************************96 PP

  == domain 4  score: 27.1 bits;  conditional E-value: 4.2e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       a+ +  +++++++lg+++eA+e +++A el P
  gi|330509099|ref|YP_004385527.1| 164 ADSWIGRADVLLNLGRWDEARESYNRATELKP 195
                                       678***************************99 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.0025
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                       +++ +++    gd +e +ea++kA++l P 
  gi|330509099|ref|YP_004385527.1| 201 WWRKAEVISGIGDINESVEAYDKAISLIPA 230
                                       777777777789***************985 PP

  == domain 6  score: 15.6 bits;  conditional E-value: 2.1e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a+ + ++ ++ + ++eeAlea +k+lel+P+
  gi|330509099|ref|YP_004385527.1| 237 ALAYAAKAEDLAFAERWEEALEAVDKSLELNPK 269
                                       67899999999*********************7 PP

  == domain 7  score: 18.6 bits;  conditional E-value: 2.2e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +++  +  +++ g+ +eAl+af++Al+  P++
  gi|330509099|ref|YP_004385527.1| 273 WWHFKASTLMEIGRNDEALAAFDEALRQSPGD 304
                                       8999************************9986 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.0086
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                        + + + ++ +++ y+e ++a+++ lel
  gi|330509099|ref|YP_004385527.1| 307 SWLRKAGLLVEMKCYNESIKAYDRTLEL 334
                                       68889999999*************9998 PP

  == domain 9  score: 5.0 bits;  conditional E-value: 0.051
                             TPR_2   8 GlayyklgdyeeAleafekAlel 30 
                                       G a+ + g+ +eA+eaf+ +lel
  gi|330509099|ref|YP_004385527.1| 351 GTALNRIGRRKEAKEAFRMSLEL 373
                                       555557799*********99998 PP

  == domain 10  score: 20.1 bits;  conditional E-value: 7.1e-07
                             TPR_2   6 nlGlayyklgdyeeAleafekAleldPn 33 
                                       + Gl +y+lg+yee le ++++le  P+
  gi|330509099|ref|YP_004385527.1| 390 MKGLTLYNLGRYEESLEVYDQVLEASPR 417
                                       5799********************9995 PP

  == domain 11  score: 23.9 bits;  conditional E-value: 4.6e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       al   G+a+++l++ +eAlea+++A+el+P 
  gi|330509099|ref|YP_004385527.1| 427 ALEGKGDALRALNRNQEALEAYNEAIELAPS 457
                                       67789************************96 PP

  == domain 12  score: -0.1 bits;  conditional E-value: 2.2
                             TPR_2   2 ealynlGlayyklgdy 17 
                                        a++  G+a ++lg+ 
  gi|330509099|ref|YP_004385527.1| 460 AAWHGKGEAERALGQV 475
                                       699*********9996 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0049         3       4      32 ..      51      79 ..      50      81 .. 0.92
   2 ?    2.5   0.0      0.24   1.5e+02      11      30 ..      92     111 ..      86     113 .. 0.77
   3 !   12.3   0.1   0.00018      0.11       2      30 ..     124     152 ..     123     155 .. 0.94
   4 !   24.6   0.0   2.4e-08   1.5e-05       1      32 [.     164     195 ..     164     196 .. 0.97
   5 !    8.6   0.0    0.0028       1.7      15      32 ..     212     229 ..     210     231 .. 0.91
   6 !   12.8   0.6   0.00013     0.083       2      33 ..     238     269 ..     237     270 .. 0.85
   7 !   13.8   0.0   6.3e-05     0.039       4      33 ..     274     303 ..     272     304 .. 0.88
   8 !   10.7   0.1   0.00058      0.36       3      30 ..     307     334 ..     305     336 .. 0.93
   9 !    9.4   0.0    0.0015      0.94       3      30 ..     346     373 ..     344     374 .. 0.93
  10 !   17.2   0.0   5.4e-06    0.0033       7      32 ..     391     416 ..     390     417 .. 0.93
  11 !   24.4   0.1   2.8e-08   1.7e-05       3      33 ..     427     457 ..     425     458 .. 0.92
  12 ?   -0.5   0.0       2.1   1.3e+03       2      16 ..     460     474 ..     459     478 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0049
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1  4 lynlGnayfklgkydeAleyyekALelnP 32
                                      + n++  ++++   deA+ ++  A + +P
  gi|330509099|ref|YP_004385527.1| 51 WINRAEELMHNDSIDEAISACGMAQKKEP 79
                                      99********************9999888 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.24
                                       HHHTT-HHHHHHHHHHHHHH CS
                             TPR_1  11 yfklgkydeAleyyekALel 30 
                                       +   g+ +e  + yekAL+l
  gi|330509099|ref|YP_004385527.1|  92 LNIIGMVNESAKTYEKALTL 111
                                       5556777889999*****87 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                       +a+  ++ ++ +l++ de  ++yekALe+
  gi|330509099|ref|YP_004385527.1| 124 EAWQWKAIVLASLNREDESDQAYEKALEI 152
                                       89**************************8 PP

  == domain 4  score: 24.6 bits;  conditional E-value: 2.4e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+++ +++ ++++lg++deA e y++A el P
  gi|330509099|ref|YP_004385527.1| 164 ADSWIGRADVLLNLGRWDEARESYNRATELKP 195
                                       799***************************98 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0028
                                       T-HHHHHHHHHHHHHHST CS
                             TPR_1  15 gkydeAleyyekALelnP 32 
                                       g+ +e +e+y+kA++l P
  gi|330509099|ref|YP_004385527.1| 212 GDINESVEAYDKAISLIP 229
                                       899************988 PP

  == domain 6  score: 12.8 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                        a+  ++  +   ++++eAle+ +k LelnP+
  gi|330509099|ref|YP_004385527.1| 238 LAYAAKAEDLAFAERWEEALEAVDKSLELNPK 269
                                       577777777778899****************7 PP

  == domain 7  score: 13.8 bits;  conditional E-value: 6.3e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPn 33 
                                       +  ++ ++++ g+ deAl+++++AL+  P 
  gi|330509099|ref|YP_004385527.1| 274 WHFKASTLMEIGRNDEALAAFDEALRQSPG 303
                                       55678999*****************99986 PP

  == domain 8  score: 10.7 bits;  conditional E-value: 0.00058
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                       ++ +++ ++ +++ y+e +++y++ Lel
  gi|330509099|ref|YP_004385527.1| 307 SWLRKAGLLVEMKCYNESIKAYDRTLEL 334
                                       69999999******************98 PP

  == domain 9  score: 9.4 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                       ++  +G a+ + g+ +eA e+++  Lel
  gi|330509099|ref|YP_004385527.1| 346 IWLVKGTALNRIGRRKEAKEAFRMSLEL 373
                                       58889**********************8 PP

  == domain 10  score: 17.2 bits;  conditional E-value: 5.4e-06
                                       HHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnP 32 
                                       +G+++++lg+y+e le y+++Le  P
  gi|330509099|ref|YP_004385527.1| 391 KGLTLYNLGRYEESLEVYDQVLEASP 416
                                       79********************9777 PP

  == domain 11  score: 24.4 bits;  conditional E-value: 2.8e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       al ++G a++ l++ +eAle+y++A+el P+
  gi|330509099|ref|YP_004385527.1| 427 ALEGKGDALRALNRNQEALEAYNEAIELAPS 457
                                       66689*************************7 PP

  == domain 12  score: -0.5 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHTT- CS
                             TPR_1   2 kalynlGnayfklgk 16 
                                        a+ ++G a + lg+
  gi|330509099|ref|YP_004385527.1| 460 AAWHGKGEAERALGQ 474
                                       69*******999998 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.3   8.1e+02       3      23 ..      50      70 ..      48      72 .. 0.90
   2 ?    5.0   0.1     0.054        34       5      30 ..      86     111 ..      83     111 .. 0.87
   3 !   16.7   0.1   9.7e-06     0.006       2      30 ..     124     152 ..     123     155 .. 0.95
   4 !   18.3   0.0     3e-06    0.0019       1      32 [.     164     195 ..     164     195 .. 0.96
   5 !   14.7   0.0   4.2e-05     0.026       2      33 ..     199     230 ..     198     231 .. 0.91
   6 ?    3.5   0.2      0.16     1e+02      18      33 ..     254     269 ..     237     270 .. 0.92
   7 !   14.1   0.0   6.6e-05     0.041       4      32 ..     274     302 ..     274     304 .. 0.93
   8 ?    6.2   0.1     0.022        14       1      30 [.     305     334 ..     305     337 .. 0.91
   9 !    9.7   0.0    0.0017         1       2      29 ..     345     372 ..     344     373 .. 0.89
  10 !   17.4   0.0   5.8e-06    0.0036       6      32 ..     390     416 ..     390     418 .. 0.95
  11 !   18.8   0.1     2e-06    0.0012       4      33 ..     428     457 ..     425     458 .. 0.90
  12 ?    1.0   0.0       1.1   6.7e+02       3      29 ..     461     487 ..     459     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.3
                                      HHHHHHHHHHHTT-HHHHHHH CS
                             TPR_8  3 ayynlgsiylklgdyeeAkey 23
                                      ++ n +  ++    ++eA+++
  gi|330509099|ref|YP_004385527.1| 50 YWINRAEELMHNDSIDEAISA 70
                                      799***************987 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.054
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekalel 30 
                                       +++++ +   g  +e+ ++yekal+l
  gi|330509099|ref|YP_004385527.1|  86 VRKAMYLNIIGMVNESAKTYEKALTL 111
                                       5788888999999**********986 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 9.7e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                       ea+++++ ++ +l++ +e+ ++yekale+
  gi|330509099|ref|YP_004385527.1| 124 EAWQWKAIVLASLNREDESDQAYEKALEI 152
                                       89*************************98 PP

  == domain 4  score: 18.3 bits;  conditional E-value: 3e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+++   ++++l+lg+ +eA e+y++a+el+p
  gi|330509099|ref|YP_004385527.1| 164 ADSWIGRADVLLNLGRWDEARESYNRATELKP 195
                                       68999*************************98 PP

  == domain 5  score: 14.7 bits;  conditional E-value: 4.2e-05
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +++++++ + +  gd++e++e+y ka++l p+
  gi|330509099|ref|YP_004385527.1| 199 SVWWRKAEVISGIGDINESVEAYDKAISLIPA 230
                                       689999999999*****************997 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHH CS
                             TPR_8  18 eeAkeyyekaleldpd 33 
                                       eeA e+  k lel+p+
  gi|330509099|ref|YP_004385527.1| 254 EEALEAVDKSLELNPK 269
                                       89*************8 PP

  == domain 7  score: 14.1 bits;  conditional E-value: 6.6e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ++ ++s++++ g+ +eA +++ +al+ +p
  gi|330509099|ref|YP_004385527.1| 274 WHFKASTLMEIGRNDEALAAFDEALRQSP 302
                                       899**********************9888 PP

  == domain 8  score: 6.2 bits;  conditional E-value: 0.022
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+++++++ ++ +++ y+e++++y + lel
  gi|330509099|ref|YP_004385527.1| 305 AHSWLRKAGLLVEMKCYNESIKAYDRTLEL 334
                                       689*********************987776 PP

  == domain 9  score: 9.7 bits;  conditional E-value: 0.0017
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                        +++ +g ++   g+ +eAke+++  le
  gi|330509099|ref|YP_004385527.1| 345 GIWLVKGTALNRIGRRKEAKEAFRMSLE 372
                                       6899*******************97666 PP

  == domain 10  score: 17.4 bits;  conditional E-value: 5.8e-06
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldp 32 
                                       ++g+++ +lg+yee+ e+y ++le++p
  gi|330509099|ref|YP_004385527.1| 390 MKGLTLYNLGRYEESLEVYDQVLEASP 416
                                       689**********************99 PP

  == domain 11  score: 18.8 bits;  conditional E-value: 2e-06
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +  +g++++ l++ +eA e+y++a+el+p+
  gi|330509099|ref|YP_004385527.1| 428 LEGKGDALRALNRNQEALEAYNEAIELAPS 457
                                       5568************************96 PP

  == domain 12  score: 1.0 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekale 29 
                                       a++ +g + + lg+  +A  ++  a +
  gi|330509099|ref|YP_004385527.1| 461 AWHGKGEAERALGQVGNAGMSLLTADK 487
                                       89*************999888887765 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.3     4e-05     0.025       8      76 ..      87     154 ..      83     155 .. 0.88
   2 !   34.6   0.3   2.8e-11   1.7e-08       8      75 ..     128     194 ..     122     195 .. 0.90
   3 !   18.4   0.3   3.1e-06    0.0019       6      75 ..     201     267 ..     198     269 .. 0.91
   4 !   11.0   0.1   0.00066      0.41       6      40 ..     274     305 ..     270     310 .. 0.82
   5 !   22.2   0.2   2.1e-07   0.00013       4      74 ..     306     373 ..     303     374 .. 0.90
   6 !   38.5   0.2   1.7e-12     1e-09       9      76 ..     391     456 ..     385     457 .. 0.93
   7 ?   -0.9   0.0       3.3     2e+03       4      24 ..     460     480 ..     458     485 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-05
                            TPR_12   8 nlaavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       + a+ l+  g   e+ + +ekal +  ++l  ++++  +++ +  ++++  l+r +e  +++e+al+i+ 
  gi|330509099|ref|YP_004385527.1|  87 RKAMYLNIIGMVNESAKTYEKALTLLdEKL--KKNAIDVEAWQWKAIVLASLNREDESDQAYEKALEIFD 154
                                       6678888889999*************5555..778899*****************************986 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 2.8e-11
                            TPR_12   8 nlaavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                         a vl+ l r de+ + +ekalei+ +r+ ++     a + ++ +++++ lgr++eA+e +++a++++
  gi|330509099|ref|YP_004385527.1| 128 WKAIVLASLNREDESDQAYEKALEIFdQRIKND--SRDADSWIGRADVLLNLGRWDEARESYNRATELK 194
                                       5799**********************9999554..469****************************985 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 3.1e-06
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       + + a+v    g+  e+ e ++ka+ ++   +  d ++ a ++ + ++ +  ++r+eeAle+  ++l++ 
  gi|330509099|ref|YP_004385527.1| 201 WWRKAEVISGIGDINESVEAYDKAISLI---PAYDAAERALAYAAKAEDLAFAERWEEALEAVDKSLELN 267
                                       55789999999*****************...668999******************************985 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00066
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpd 40 
                                       ++  a++l++ gr deAl+ +++al++    +G+ 
  gi|330509099|ref|YP_004385527.1| 274 WHFKASTLMEIGRNDEALAAFDEALRQS---PGDA 305
                                       455899******************9876...6655 PP

  == domain 5  score: 22.2 bits;  conditional E-value: 2.1e-07
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        ++ + a +l +++ y e+++ +++ le++ ++   +  ++a +    g+++ + gr +eA e+++ +l++
  gi|330509099|ref|YP_004385527.1| 306 HSWLRKAGLLVEMKCYNESIKAYDRTLELIAES---NTKELAGIWLVKGTALNRIGRRKEAKEAFRMSLEL 373
                                       5677899***********************665...55579****************************97 PP

  == domain 6  score: 38.5 bits;  conditional E-value: 1.7e-12
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        +++l+ lgry+e+le ++++le+  r+  + +   +++l + g+++ral+r +eAle+++ea+++a+
  gi|330509099|ref|YP_004385527.1| 391 KGLTLYNLGRYEESLEVYDQVLEASPRI--EPYVIDVSALEGKGDALRALNRNQEALEAYNEAIELAP 456
                                       5899*********************888..6689*******************************986 PP

  == domain 7  score: -0.9 bits;  conditional E-value: 3.3
                            TPR_12   4 talnnlaavlrrlgrydeAle 24 
                                       +a++  ++++r+lg+   A  
  gi|330509099|ref|YP_004385527.1| 460 AAWHGKGEAERALGQVGNAGM 480
                                       688899999999999877765 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0087       5.4      13      64 ..     105     153 ..     100     156 .. 0.91
   2 !   31.3   0.1   3.8e-10   2.4e-07      13      65 ..     146     195 ..     142     198 .. 0.94
   3 !   27.1   0.1   7.8e-09   4.8e-06       3      62 ..     170     226 ..     168     235 .. 0.91
   4 !   27.3   0.8   6.8e-09   4.2e-06       2      68 .]     242     305 ..     241     305 .. 0.96
   5 ?    4.4   0.0       0.1        62       2      60 ..     310     370 ..     309     375 .. 0.80
   6 !   39.4   0.4   1.1e-12   6.9e-10       2      67 ..     390     458 ..     389     459 .. 0.97
   7 !   21.7   1.5   3.7e-07   0.00023       3      56 ..     431     482 ..     430     485 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0087
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                       y++A+ +l++ lk++     ++eA+ +++ +++ ++r +e  ++y++al+  
  gi|330509099|ref|YP_004385527.1| 105 YEKALTLLDEKLKKN---AIDVEAWQWKAIVLASLNREDESDQAYEKALEIF 153
                                       99*************...***********************99999999765 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 3.8e-10
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       y++A++ +++ +k+d   +++a+++ +++d++l +gr++eA++ y++a +  p
  gi|330509099|ref|YP_004385527.1| 146 YEKALEIFDQRIKND---SRDADSWIGRADVLLNLGRWDEARESYNRATELKP 195
                                       99*************...*****************************988877 PP

  == domain 3  score: 27.1 bits;  conditional E-value: 7.8e-09
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       +a+ +l++g++d+A++ +++a+++    P+++  ++ ++++    g+  e +++y++a+ 
  gi|330509099|ref|YP_004385527.1| 170 RADVLLNLGRWDEARESYNRATELK---PLDYSVWWRKAEVISGIGDINESVEAYDKAIS 226
                                       799**********************...****************************9984 PP

  == domain 4  score: 27.3 bits;  conditional E-value: 6.8e-09
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       a+a +++ a ++++A++a +  l+++p+s++   ++ +++  + + gr +eA+a++++alr++p+++
  gi|330509099|ref|YP_004385527.1| 242 AKAEDLAFAERWEEALEAVDKSLELNPKSSV---WWHFKASTLMEIGRNDEALAAFDEALRQSPGDA 305
                                       7899**********************88888...******************************986 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.1
                            TPR_16   2 alaraalragdyddAaaaleaalkr..dpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                        +a ++++ + y + ++a++++l++   + + + a  +l +g a+ r gr +eA +++r  
  gi|330509099|ref|YP_004385527.1| 310 RKAGLLVEMKCYNESIKAYDRTLELiaESNTKELAGIWLVKGTALNRIGRRKEAKEAFRMS 370
                                       678899999999999****999986114555669999999999999999999998888765 PP

  == domain 6  score: 39.4 bits;  conditional E-value: 1.1e-12
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd......aaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++++ ++++g+y++ +++++++l++    P+      ++ Al ++gda+ +++r +eA+++y++a++ ap++
  gi|330509099|ref|YP_004385527.1| 390 MKGLTLYNLGRYEESLEVYDQVLEAS---PRiepyviDVSALEGKGDALRALNRNQEALEAYNEAIELAPSS 458
                                       68999*********************...*****************************************87 PP

  == domain 7  score: 21.7 bits;  conditional E-value: 3.7e-07
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.al 56 
                                       +++a++++++ ++A++a+++a++++   P   +A+ ++g+a  ++g +  A   l
  gi|330509099|ref|YP_004385527.1| 431 KGDALRALNRNQEALEAYNEAIELA---PSSSAAWHGKGEAERALGQVGNAGmSL 482
                                       689**********************...88899*************998886555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.081        50       6      40 ..      53      87 ..      49      90 .. 0.86
   2 ?    0.7   0.0       2.1   1.3e+03      12      39 ..     100     127 ..      95     129 .. 0.82
   3 ?    7.0   0.2      0.02        12       1      31 [.     123     153 ..     123     160 .. 0.92
   4 !   22.3   0.2   2.4e-07   0.00015       3      43 ..     166     206 ..     164     207 .. 0.90
   5 ?    4.2   0.2      0.16        99      15      43 ..     212     240 ..     210     241 .. 0.90
   6 !   14.3   0.7   9.2e-05     0.057       3      42 ..     239     278 ..     235     280 .. 0.87
   7 !   17.9   0.2   6.4e-06     0.004       8      42 ..     278     312 ..     276     314 .. 0.92
   8 ?    6.7   0.0     0.025        15       3      32 ..     346     375 ..     344     392 .. 0.82
   9 !   10.3   0.0    0.0017         1       6      33 ..     390     417 ..     385     423 .. 0.87
  10 !   19.2   0.3   2.4e-06    0.0015       8      43 ..     432     467 ..     425     468 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.081
                            TPR_14  6 alaeallalGdpdeAiallrralalaPddaeawll 40
                                       +ae l++++  deAi ++  a ++ P+++ +  +
  gi|330509099|ref|YP_004385527.1| 53 NRAEELMHNDSIDEAISACGMAQKKEPWNDSIIVR 87
                                      58999**********************99876655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 2.1
                            TPR_14  12 lalGdpdeAiallrralalaPddaeawl 39 
                                       + +  +++A++ll++ l+++  d eaw 
  gi|330509099|ref|YP_004385527.1| 100 ESAKTYEKALTLLDEKLKKNAIDVEAWQ 127
                                       56777999*****999999999999985 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.02
                            TPR_14   1 peallalaeallalGdpdeAiallrralala 31 
                                       +ea++  a +l+ l + de+ +++++al+ +
  gi|330509099|ref|YP_004385527.1| 123 VEAWQWKAIVLASLNREDESDQAYEKALEIF 153
                                       589*************************986 PP

  == domain 4  score: 22.3 bits;  conditional E-value: 2.4e-07
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                        +  +a++ll+lG++deA++ ++ra +l P d  +w + a+
  gi|330509099|ref|YP_004385527.1| 166 SWIGRADVLLNLGRWDEARESYNRATELKPLDYSVWWRKAE 206
                                       57889*************************99999988776 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.16
                            TPR_14  15 GdpdeAiallrralalaPddaeawlllaq 43 
                                       Gd  e+++++++a++l P+ ++a ++la 
  gi|330509099|ref|YP_004385527.1| 212 GDINESVEAYDKAISLIPAYDAAERALAY 240
                                       778899**************999999986 PP

  == domain 6  score: 14.3 bits;  conditional E-value: 9.2e-05
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       a++a ae l+ +++++eA+++ ++ l+l+P++ ++w + a
  gi|330509099|ref|YP_004385527.1| 239 AYAAKAEDLAFAERWEEALEAVDKSLELNPKSSVWWHFKA 278
                                       566777888999************************9877 PP

  == domain 7  score: 17.9 bits;  conditional E-value: 6.4e-06
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                                       a+ l++ G+ deA+a++++al++ P+da  wl+ a
  gi|330509099|ref|YP_004385527.1| 278 ASTLMEIGRNDEALAAFDEALRQSPGDAHSWLRKA 312
                                       7789999*********************9999876 PP

  == domain 8  score: 6.7 bits;  conditional E-value: 0.025
                            TPR_14   3 allalaeallalGdpdeAiallrralalaP 32 
                                        +l  + al + G+ +eA +++r  l+l+ 
  gi|330509099|ref|YP_004385527.1| 346 IWLVKGTALNRIGRRKEAKEAFRMSLELHV 375
                                       5888899*******************9764 PP

  == domain 9  score: 10.3 bits;  conditional E-value: 0.0017
                            TPR_14   6 alaeallalGdpdeAiallrralalaPd 33 
                                       + +  l++lG+++e++++++++l++ P 
  gi|330509099|ref|YP_004385527.1| 390 MKGLTLYNLGRYEESLEVYDQVLEASPR 417
                                       5577899******************996 PP

  == domain 10  score: 19.2 bits;  conditional E-value: 2.4e-06
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       ++al+al + +eA++++++a++laP++ +aw   ++
  gi|330509099|ref|YP_004385527.1| 432 GDALRALNRNQEALEAYNEAIELAPSSSAAWHGKGE 467
                                       789****************************87765 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.53   3.3e+02      10      23 ..      98     111 ..      95     113 .. 0.85
   2 ?    4.1   0.1     0.061        38       9      42 .]     145     178 ..     132     178 .. 0.81
   3 !   19.5   0.0   9.1e-07   0.00056       2      32 ..     172     202 ..     171     208 .. 0.85
   4 !   10.6   1.9   0.00056      0.34       8      37 ..     212     241 ..     211     244 .. 0.88
   5 ?    3.4   0.0       0.1        62       9      26 ..     252     269 ..     250     271 .. 0.92
   6 !   11.9   0.0   0.00023      0.14       4      28 ..     281     305 ..     278     312 .. 0.87
   7 ?    1.9   0.0       0.3   1.8e+02      10      23 ..     321     334 ..     313     336 .. 0.82
   8 !   14.8   0.0   2.7e-05     0.017       1      25 [.     392     416 ..     392     417 .. 0.91
   9 !   27.5   0.6     3e-09   1.9e-06       1      37 [.     432     468 ..     432     473 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.53
                            TPR_11  10 yeeAieaYkkAlkl 23 
                                        +e+ + Y+kAl l
  gi|330509099|ref|YP_004385527.1|  98 VNESAKTYEKALTL 111
                                       589999*****976 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.061
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                        ye+A+e + + +k d+ +a+ + +++++++++G
  gi|330509099|ref|YP_004385527.1| 145 AYEKALEIFDQRIKNDSRDADSWIGRADVLLNLG 178
                                       5888888888888888888888888888888877 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 9.1e-07
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayy 32 
                                       d++  +G+++eA e+Y++A +l+P + ++++
  gi|330509099|ref|YP_004385527.1| 172 DVLLNLGRWDEARESYNRATELKPLDYSVWW 202
                                       788899******************7777666 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00056
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       G+++e++eaY kA+ l P +  a  +L++a
  gi|330509099|ref|YP_004385527.1| 212 GDINESVEAYDKAISLIPAYDAAERALAYA 241
                                       99****************999887777765 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.1
                            TPR_11   9 kyeeAieaYkkAlkldPd 26 
                                       ++eeA+ea  k l+l+P+
  gi|330509099|ref|YP_004385527.1| 252 RWEEALEAVDKSLELNPK 269
                                       79***************8 PP

  == domain 6  score: 11.9 bits;  conditional E-value: 0.00023
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdna 28 
                                       ++e G+++eA++a+ +Al+ +P +a
  gi|330509099|ref|YP_004385527.1| 281 LMEIGRNDEALAAFDEALRQSPGDA 305
                                       7899*****************9877 PP

  == domain 7  score: 1.9 bits;  conditional E-value: 0.3
                            TPR_11  10 yeeAieaYkkAlkl 23 
                                       y+e+i+aY + l+l
  gi|330509099|ref|YP_004385527.1| 321 YNESIKAYDRTLEL 334
                                       9*******998876 PP

  == domain 8  score: 14.8 bits;  conditional E-value: 2.7e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldP 25 
                                       G  +y +G+yee++e+Y + l+ +P
  gi|330509099|ref|YP_004385527.1| 392 GLTLYNLGRYEESLEVYDQVLEASP 416
                                       7789*****************9777 PP

  == domain 9  score: 27.5 bits;  conditional E-value: 3e-09
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       Gda+++++++ eA+eaY++A++l P++  a+++ G+a
  gi|330509099|ref|YP_004385527.1| 432 GDALRALNRNQEALEAYNEAIELAPSSSAAWHGKGEA 468
                                       9*****************************9999987 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       6.7   4.2e+03       3      28 ..      60      85 ..      58      89 .. 0.73
   2 !    9.3   0.1    0.0027       1.6       5      43 ..     103     141 ..     101     145 .. 0.93
   3 !   30.5   0.0   6.1e-10   3.8e-07       5      62 ..     144     202 ..     142     206 .. 0.93
   4 !   10.5   1.2    0.0011      0.65       5      66 ..     212     278 ..     212     279 .. 0.82
   5 !   19.2   0.1   2.1e-06    0.0013       2      53 ..     282     333 ..     281     343 .. 0.91
   6 !   12.6   0.0   0.00023      0.14      11      61 ..     371     422 ..     353     428 .. 0.82
   7 !    8.6   0.7    0.0043       2.6       5      41 ..     439     475 ..     433     482 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.7
                            TPR_19  3 aegdyaeAlalleqalqedpknaear 28
                                       +   +eA+++   a +++p n+ + 
  gi|330509099|ref|YP_004385527.1| 60 HNDSIDEAISACGMAQKKEPWNDSII 85
                                      56677889998888888888887766 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0027
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqlde 43 
                                       + y+ Al ll + l++++ + ea+ + A++l +l++ de
  gi|330509099|ref|YP_004385527.1| 103 KTYEKALTLLDEKLKKNAIDVEAWQWKAIVLASLNREDE 141
                                       689*********************************998 PP

  == domain 3  score: 30.5 bits;  conditional E-value: 6.1e-10
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.arya 62 
                                       + y+ Al+++ q ++ d  +a+ +++ A++ll+lg++deA++  +++ e +p d + ++
  gi|330509099|ref|YP_004385527.1| 144 QAYEKALEIFDQRIKNDSRDADSWIGRADVLLNLGRWDEARESYNRATELKPLDySVWW 202
                                       789*********999*************************************9877776 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.0011
                            TPR_19   5 gdyaeAlalleqalqedpknaearllL.....AeallalgqldeAealLdalpeedpddaryasLlA 66 
                                       gd  e ++++ +a++  p +++a  +L     Ae l  + +++eA +++d+ +e +p+++ ++  +A
  gi|330509099|ref|YP_004385527.1| 212 GDINESVEAYDKAISLIPAYDAAERALayaakAEDLAFAERWEEALEAVDKSLELNPKSSVWWHFKA 278
                                       6788889999999999999999999883333344455589******************999998887 PP

  == domain 5  score: 19.2 bits;  conditional E-value: 2.1e-06
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       ++ g+ +eAla++ +al ++p++a  +l+ A +l++++ ++e +++ d+ +e
  gi|330509099|ref|YP_004385527.1| 282 MEIGRNDEALAAFDEALRQSPGDAHSWLRKAGLLVEMKCYNESIKAYDRTLE 333
                                       566899***********************************99999988766 PP

  == domain 6  score: 12.6 bits;  conditional E-value: 0.00023
                            TPR_19  11 lalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd.dary 61 
                                       l+l  +a+ edp+++ ++      l++lg+++e  ++ d+++e+ p  ++++
  gi|330509099|ref|YP_004385527.1| 371 LELHVKAILEDPGDLSLKRMKGLTLYNLGRYEESLEVYDQVLEASPRiEPYV 422
                                       4455567788**********************************99855665 PP

  == domain 7  score: 8.6 bits;  conditional E-value: 0.0043
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgql 41 
                                       ++ +eAl+++ +a++ +p +++a+ +  ea  algq+
  gi|330509099|ref|YP_004385527.1| 439 NRNQEALEAYNEAIELAPSSSAAWHGKGEAERALGQV 475
                                       5679999999999999999999999999999999997 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.062        38       6      31 ..     116     141 ..     104     147 .. 0.79
   2 !   17.5   0.0     6e-06    0.0037       6      34 .]     157     185 ..     145     185 .. 0.85
   3 ?    1.3   0.0      0.91   5.6e+02       2      28 ..     187     213 ..     186     221 .. 0.79
   4 !    9.5   0.0    0.0022       1.4       4      33 ..     262     291 ..     260     292 .. 0.95
   5 ?    5.1   0.0     0.056        35       2      23 ..     294     315 ..     293     326 .. 0.83
   6 ?   -1.5   0.0       7.3   4.5e+03      13      33 ..     344     364 ..     335     365 .. 0.81
   7 ?    4.4   0.0     0.091        56       4      33 ..     376     405 ..     373     406 .. 0.88
   8 ?   -1.1   0.0       5.5   3.4e+03      14      33 ..     426     445 ..     408     446 .. 0.72
   9 !   14.6   0.0   5.2e-05     0.032       1      31 [.     447     477 ..     447     480 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.062
                            TPR_17   6 leldPnnadaynnLAelllknGdlmt 31 
                                       l+++  +++a++ +A +l+++++ ++
  gi|330509099|ref|YP_004385527.1| 116 LKKNAIDVEAWQWKAIVLASLNREDE 141
                                       5677778************8886544 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 6e-06
                            TPR_17   6 leldPnnadaynnLAelllknGdlmtArq 34 
                                       +++d  +ad++  +A +ll++G++++Ar+
  gi|330509099|ref|YP_004385527.1| 157 IKNDSRDADSWIGRADVLLNLGRWDEARE 185
                                       6778999********************96 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.91
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGd 28 
                                       y +a el P +  ++  +Ae+ + +Gd
  gi|330509099|ref|YP_004385527.1| 187 YNRATELKPLDYSVWWRKAEVISGIGD 213
                                       99**********999777777665555 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0022
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtAr 33 
                                       k+lel+P++++ ++ +A +l ++G+ ++A+
  gi|330509099|ref|YP_004385527.1| 262 KSLELNPKSSVWWHFKASTLMEIGRNDEAL 291
                                       99**************************97 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.056
                            TPR_17   2 ylkaleldPnnadaynnLAell 23 
                                       + +al++ P +a ++  +A ll
  gi|330509099|ref|YP_004385527.1| 294 FDEALRQSPGDAHSWLRKAGLL 315
                                       889************9998666 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 7.3
                            TPR_17  13 adaynnLAelllknGdlmtAr 33 
                                       a  +  ++++l ++G+ ++A+
  gi|330509099|ref|YP_004385527.1| 344 AGIWLVKGTALNRIGRRKEAK 364
                                       667999999**9999988887 PP

  == domain 7  score: 4.4 bits;  conditional E-value: 0.091
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtAr 33 
                                       ka+  dP +  +  +++ +l+++G++++ +
  gi|330509099|ref|YP_004385527.1| 376 KAILEDPGDLSLKRMKGLTLYNLGRYEESL 405
                                       899999999999999***********9865 PP

  == domain 8  score: -1.1 bits;  conditional E-value: 5.5
                            TPR_17  14 daynnLAelllknGdlmtAr 33 
                                        a+  ++ +l+ +++ ++A+
  gi|330509099|ref|YP_004385527.1| 426 SALEGKGDALRALNRNQEAL 445
                                       55556788888888888886 PP

  == domain 9  score: 14.6 bits;  conditional E-value: 5.2e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                       +y +a+el P+++ a++ ++e+ + +G+ + 
  gi|330509099|ref|YP_004385527.1| 447 AYNEAIELAPSSSAAWHGKGEAERALGQVGN 477
                                       599************************9765 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2   1.7e-07   0.00011       9      60 ..     144     195 ..     141     206 .. 0.94
   2 ?    5.1   0.0     0.041        25      18      69 ..     187     238 ..     185     244 .. 0.88
   3 !   23.3   0.2   8.5e-08   5.3e-05       8      63 ..     250     305 ..     247     307 .. 0.95
   4 !   15.3   0.1   2.7e-05     0.016       7      58 ..     283     334 ..     278     345 .. 0.88
   5 !   10.7   0.0   0.00071      0.44      25      60 ..     381     416 ..     354     429 .. 0.86
   6 ?    5.5   0.2     0.031        19       8      49 ..     438     479 ..     432     485 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.7e-07
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       + +e+al++ + ++  +++d++ +  R+ +l  lG++ +A++  +++ +l p
  gi|330509099|ref|YP_004385527.1| 144 QAYEKALEIFDQRIKNDSRDADSWIGRADVLLNLGRWDEARESYNRATELKP 195
                                       679*********************************************9998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.041
                             TPR_9  18 verllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeair 69 
                                       ++r   l+P d + ++  + +    G++++ +++ + +++l p+ ++ae++ 
  gi|330509099|ref|YP_004385527.1| 187 YNRATELKPLDYSVWWRKAEVISGIGDINESVEAYDKAISLIPAYDAAERAL 238
                                       689999*************************************777777664 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 8.5e-08
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       +e+we+al++v+  l l+P++   +   +  l++ G+  +Ala+++ +l+++p ++
  gi|330509099|ref|YP_004385527.1| 250 AERWEEALEAVDKSLELNPKSSVWWHFKASTLMEIGRNDEALAAFDEALRQSPGDA 305
                                       69***************************************************765 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 2.7e-05
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylal 58 
                                       +  ++++ala+ +  l   P d++ ++  + ll+++ c+++ +++ ++ l+l
  gi|330509099|ref|YP_004385527.1| 283 EIGRNDEALAAFDEALRQSPGDAHSWLRKAGLLVEMKCYNESIKAYDRTLEL 334
                                       55789****************************************9999876 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00071
                             TPR_9  25 aPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       +P d ++ r  Gl l+ lG++++ l+  ++ l+ +p
  gi|330509099|ref|YP_004385527.1| 381 DPGDLSLKRMKGLTLYNLGRYEESLEVYDQVLEASP 416
                                       9**************************999999998 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.031
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAl 49 
                                        +++++al++++  + laP +   +   G ++  lG++  A 
  gi|330509099|ref|YP_004385527.1| 438 LNRNQEALEAYNEAIELAPSSSAAWHGKGEAERALGQVGNAG 479
                                       578999***************999999999999999987775 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       0.7   4.3e+02      17      32 ..     100     115 ..      91     119 .. 0.70
   2 ?    4.0   0.2       0.1        62      12      34 ..     143     163 ..     133     165 .. 0.83
   3 !    9.5   0.0    0.0017       1.1       6      34 ..     171     197 ..     166     199 .. 0.87
   4 ?   -1.5   0.0       5.6   3.5e+03      11      21 ..     217     227 ..     209     228 .. 0.66
   5 ?   -0.3   0.1       2.2   1.4e+03      14      28 ..     252     266 ..     239     270 .. 0.85
   6 !    7.8   0.0    0.0061       3.7       5      35 ..     277     305 ..     274     305 .. 0.90
   7 ?    5.0   0.0     0.047        29      10      33 ..     355     383 ..     349     386 .. 0.79
   8 !   10.3   0.0   0.00097       0.6       8      32 ..     394     416 ..     391     420 .. 0.78
   9 !    7.3   0.1    0.0087       5.4       6      32 ..     432     456 ..     427     460 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.7
                             TPR_7  17 eAielyeqsLaltkdp 32 
                                       e ++ ye++L l ++ 
  gi|330509099|ref|YP_004385527.1| 100 ESAKTYEKALTLLDEK 115
                                       6778899977665554 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.1
                             TPR_7  12 lGdyeeAielyeqsLaltkdped 34 
                                       ++ ye+A+e++ q  ++ +d  d
  gi|330509099|ref|YP_004385527.1| 143 DQAYEKALEIFDQ--RIKNDSRD 163
                                       6779*********..99888655 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0017
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                       a++  +lG+++eA e y +  a++  p+d
  gi|330509099|ref|YP_004385527.1| 171 ADVLLNLGRWDEARESYNR--ATELKPLD 197
                                       78999**************..99888876 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 5.6
                             TPR_7  11 rlGdyeeAiel 21 
                                       ++  y++Ai+l
  gi|330509099|ref|YP_004385527.1| 217 SVEAYDKAISL 227
                                       45558888876 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 2.2
                             TPR_7  14 dyeeAielyeqsLal 28 
                                       ++eeA+e   +sL+l
  gi|330509099|ref|YP_004385527.1| 252 RWEEALEAVDKSLEL 266
                                       89****999998877 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0061
                             TPR_7   5 LarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                        a++  + G+ +eA+  + +  al+ +p+da
  gi|330509099|ref|YP_004385527.1| 277 KASTLMEIGRNDEALAAFDE--ALRQSPGDA 305
                                       69999***************..*****9985 PP

  == domain 7  score: 5.0 bits;  conditional E-value: 0.047
                             TPR_7  10 srlGdyeeAielyeqsLalt.....kdpe 33 
                                        r G+++eA e ++ sL+l+     +dp+
  gi|330509099|ref|YP_004385527.1| 355 NRIGRRKEAKEAFRMSLELHvkailEDPG 383
                                       578***************99666666665 PP

  == domain 8  score: 10.3 bits;  conditional E-value: 0.00097
                             TPR_7   8 lysrlGdyeeAielyeqsLaltkdp 32 
                                       +  +lG+yee +e+y q  +l+ +p
  gi|330509099|ref|YP_004385527.1| 394 TLYNLGRYEESLEVYDQ--VLEASP 416
                                       56689************..555555 PP

  == domain 9  score: 7.3 bits;  conditional E-value: 0.0087
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdp 32 
                                       +++ ++l++ +eA+e y +  a++ +p
  gi|330509099|ref|YP_004385527.1| 432 GDALRALNRNQEALEAYNE--AIELAP 456
                                       899****************..555555 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.016       9.8     101     133 ..      83     115 ..      12     122 .. 0.93
   2 !   14.5   0.3   4.6e-05     0.028      63     129 ..     131     193 ..     116     197 .. 0.90
   3 ?    0.1   0.0       1.2   7.5e+02     104     130 ..     202     228 ..     196     231 .. 0.80
   4 !    9.4   1.9    0.0017       1.1      54     126 ..     236     297 ..     216     301 .. 0.80
   5 ?    4.5   0.1     0.055        34     107     126 ..     278     297 ..     277     344 .. 0.61
   6 !   13.1   0.2   0.00012     0.074      58     129 ..     308     373 ..     295     390 .. 0.70
   7 !    8.4   0.1    0.0034       2.1      65     130 ..     395     455 ..     384     468 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH- CS
                           DUF3856 101 aavfsravaleelGrkdealkafrmagemiaer 133
                                       ++++++a+ l+ +G  +e+ k++++a  +++e+
  gi|330509099|ref|YP_004385527.1|  83 SIIVRKAMYLNIIGMVNESAKTYEKALTLLDEK 115
                                       57899*************************997 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.6e-05
                                       HHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  63 ealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                         la l r de+ ++ +kal+ f++r + ++ +   Wi     ra  l +lGr dea ++++ a+e+
  gi|330509099|ref|YP_004385527.1| 131 IVLASLNREDESDQAYEKALEIFDQRIKNDSRDADSWIG----RADVLLNLGRWDEARESYNRATEL 193
                                       56789999*****************************95....9********************996 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.2
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmagemi 130
                                       +++a  ++++G  +e+++a+ +a  +i
  gi|330509099|ref|YP_004385527.1| 202 WRKAEVISGIGDINESVEAYDKAISLI 228
                                       678888999999999999998887766 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  54 dalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                        al++a+ +e la   r++eale++dk+l       el+      W      +a +l e+Gr+deal af  a
  gi|330509099|ref|YP_004385527.1| 236 RALAYAAKAEDLAFAERWEEALEAVDKSL-------ELNPKSSVWW----HFKASTLMEIGRNDEALAAFDEA 297
                                       599************************99.......5776655555....469999***********999876 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.055
                                       HHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 107 avaleelGrkdealkafrma 126
                                       a +l e+Gr+deal af  a
  gi|330509099|ref|YP_004385527.1| 278 ASTLMEIGRNDEALAAFDEA 297
                                       45555555555555555443 PP

  == domain 6  score: 13.1 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  58 haglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                       +   ++ l++++ y+e++++ d++l+         + + k    + + +++al+ +Gr++ea +afrm+ e+
  gi|330509099|ref|YP_004385527.1| 308 WLRKAGLLVEMKCYNESIKAYDRTLELIA------ESNTKELAGIWLVKGTALNRIGRRKEAKEAFRMSLEL 373
                                       55555666666777777777666666543......3344444445568********************9986 PP

  == domain 7  score: 8.4 bits;  conditional E-value: 0.0034
                                       HHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                           DUF3856  65 laklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagemi 130
                                       l +lgry+e+le  d+ l+   r          + ++a+  ++ al  l r++eal+a++ a e+ 
  gi|330509099|ref|YP_004385527.1| 395 LYNLGRYEESLEVYDQVLEASPRIEPYV-----IDVSALEGKGDALRALNRNQEALEAYNEAIELA 455
                                       5678999999999999988877765444.....44899999*********************9975 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       5.1   3.1e+03       6      24 ..      95     113 ..      91     114 .. 0.74
   2 ?    2.8   0.1      0.36   2.2e+02       7      30 ..     130     153 ..     124     155 .. 0.74
   3 !    8.0   0.0    0.0077       4.8       6      27 ..     170     191 ..     165     195 .. 0.85
   4 ?   -0.4   0.0       3.7   2.3e+03      14      28 ..     212     226 ..     201     227 .. 0.80
   5 ?   -0.2   0.1       3.2     2e+03       9      32 ..     239     269 ..     235     270 .. 0.59
   6 ?    5.1   0.0     0.065        40      12      32 ..     283     303 ..     273     304 .. 0.78
   7 ?    0.6   0.0       1.8   1.1e+03       8      25 ..     352     369 ..     341     374 .. 0.81
   8 !    8.4   0.0     0.006       3.7       7      31 ..     392     416 ..     390     417 .. 0.90
   9 !   10.2   0.1    0.0016         1       6      33 .]     431     458 ..     426     458 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 5.1
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAleale 24 
                                       +++  ++++ ++kAl++l+
  gi|330509099|ref|YP_004385527.1|  95 IGMVNESAKTYEKALTLLD 113
                                       5777777777888888775 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeY 30 
                                       a  + +l++ d++ +a+e+ ++ +
  gi|330509099|ref|YP_004385527.1| 130 AIVLASLNREDESDQAYEKALEIF 153
                                       666667788999999999988866 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0077
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerli 27 
                                       +a  +++lg++d+A+e ++r  
  gi|330509099|ref|YP_004385527.1| 170 RADVLLNLGRWDEARESYNRAT 191
                                       577889999**********986 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHHHHHH CS
                             TPR_6  14 gdtdkAlealerlik 28 
                                       gd  +++ea+++ i+
  gi|330509099|ref|YP_004385527.1| 212 GDINESVEAYDKAIS 226
                                       799999****99885 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 3.2
                                       HHHH.H......HHHHHHHHHHHHHHHH-TT CS
                             TPR_6   9 syrk.l......gdtdkAlealerlikeYPd 32 
                                       +y + +       ++++Alea ++ ++  P+
  gi|330509099|ref|YP_004385527.1| 239 AYAAkAedlafaERWEEALEAVDKSLELNPK 269
                                       4443224444556999999986666666665 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.065
                                       HHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  12 klgdtdkAlealerlikeYPd 32 
                                       + g+ d+Al+a+++ +++ P+
  gi|330509099|ref|YP_004385527.1| 283 EIGRNDEALAAFDEALRQSPG 303
                                       3589************99985 PP

  == domain 7  score: 0.6 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAlealer 25 
                                        ++ + g+  +A+ea++ 
  gi|330509099|ref|YP_004385527.1| 352 TALNRIGRRKEAKEAFRM 369
                                       5556658999******86 PP

  == domain 8  score: 8.4 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       +l +++lg+++++le ++++++  P
  gi|330509099|ref|YP_004385527.1| 392 GLTLYNLGRYEESLEVYDQVLEASP 416
                                       88999*99*************9877 PP

  == domain 9  score: 10.2 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPdS 33 
                                        + ++r+l++ ++Alea+++ i+  P S
  gi|330509099|ref|YP_004385527.1| 431 KGDALRALNRNQEALEAYNEAIELAPSS 458
                                       588999999***************9987 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 !   20.1   0.2   8.8e-07   0.00055       4      80 ..     104     188 ..     101     190 .. 0.91
   2 !   15.8   0.4     2e-05     0.013      21      81 ..     235     296 ..     215     297 .. 0.83
   3 ?    0.4   0.0       1.2   7.6e+02      37      49 ..     326     338 ..     299     370 .. 0.56
   4 ?    3.1   0.1      0.18   1.1e+02      62      79 ..     391     408 ..     318     411 .. 0.74
   5 ?    4.8   0.1     0.054        33      29      78 ..     391     447 ..     369     451 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.8e-07
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-.......HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-H CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngq.......ykrAyellrka.klnskslgcrylfAqcllkLkky 72 
                                        y++A+ l++  l++++ + e+  ++A +l ++++       y++A+e++++  k +s++  +++  A +ll L+++
  gi|330509099|ref|YP_004385527.1| 104 TYEKALTLLDEKLKKNAIDVEAWQWKAIVLASLNRedesdqaYEKALEIFDQRiKNDSRDADSWIGRADVLLNLGRW 180
                                       699999999999999999999999999888888777788999*********************************** PP

                                       HHHHHHH- CS
                            ANAPC3  73 eeAiaaLe 80 
                                       +eA+  + 
  gi|330509099|ref|YP_004385527.1| 181 DEARESYN 188
                                       ***98765 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2e-05
                                       --HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  21 espedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       e++ +  ++A+ l  ++++++A+e ++k+ +ln+ks   +  +A +l ++++ +eA+aa+++
  gi|330509099|ref|YP_004385527.1| 235 ERALAYAAKAEDLAFAERWEEALEAVDKSlELNPKSSVWWHFKASTLMEIGRNDEALAAFDE 296
                                       44444445688888899******************************************987 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.2
                                       T-HHHHHHHHHCT CS
                            ANAPC3  37 gqykrAyellrka 49 
                                       + y+r +el+ ++
  gi|330509099|ref|YP_004385527.1| 326 KAYDRTLELIAES 338
                                       2355555555555 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.18
                                       HHHHHHHTT-HHHHHHHH CS
                            ANAPC3  62 fAqcllkLkkyeeAiaaL 79 
                                       ++ +l+ L++yee + ++
  gi|330509099|ref|YP_004385527.1| 391 KGLTLYNLGRYEESLEVY 408
                                       344555555555555554 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.054
                                       HHHHHHHTT-HHHHHHHHHCT.SHHHC-H......HHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  29 lAlclylngqykrAyellrka.klnsksl......gcrylfAqcllkLkkyeeAiaa 78 
                                       ++l+ly++g+y++ +e++++  +  ++ +       ++  ++ +l +L++ +eA+ a
  gi|330509099|ref|YP_004385527.1| 391 KGLTLYNLGRYEESLEVYDQVlEASPRIEpyvidvSALEGKGDALRALNRNQEALEA 447
                                       488888888888888888888554444445555555555555666666666666655 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   1.2    0.0001     0.062      12      67 ..      97     152 ..      88     161 .. 0.83
   2 !    8.6   0.1    0.0012      0.75      42     111 ..     168     236 ..     146     248 .. 0.68
   3 !    9.2   0.1   0.00079      0.49      17      69 ..     250     302 ..     240     345 .. 0.62
   4 !   10.6   0.3   0.00031      0.19      37     109 ..     384     461 ..     354     463 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                       HHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             NARP1  12 qiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLler 67 
                                       ++ e a ++e+Al  L+ek k+    ++  + ka +l  L+r++e+ ++ye+ le 
  gi|330509099|ref|YP_004385527.1|  97 MVNESAKTYEKALTLLDEKLKKNAIDVEAWQWKAIVLASLNREDESDQAYEKALEI 152
                                       456677899********98887777778889********************99876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH-T.T-CHHHHHHHHHT..SSS-HHHHHHHHHHTTTS-TT-SHHHH CS
                             NARP1  42 etkaelllkLgrkeeAeatyeaLlernp.enskYyeglekakklskedeeallalydelaekyprsdaprR 111
                                         +a++ll+Lgr +eA++ y++  e  p + s ++++ e   ++  +d+++ +++yd++ + +p  da++R
  gi|330509099|ref|YP_004385527.1| 168 IGRADVLLNLGRWDEARESYNRATELKPlDYSVWWRKAEVISGI--GDINESVEAYDKAISLIPAYDAAER 236
                                       45889999999999999999988887763666667776666664..4668889999999998888888887 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00079
                                       HTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-T CS
                             NARP1  17 agkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernp 69 
                                       a++ eeAle ++++ +       +  +ka+ l+++gr++eA a++ + l++ p
  gi|330509099|ref|YP_004385527.1| 250 AERWEEALEAVDKSLELNPKSSVWWHFKASTLMEIGRNDEALAAFDEALRQSP 302
                                       45556666666666666666666666666666666666666666666666655 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00031
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT........SSS-HHHHHHHHHHTTTS-TT-S CS
                             NARP1  37 klavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekak......klskedeeallalydelaekyprsd 107
                                        l++k +k+  l +Lgr+ee+ ++y + le  p  + Y  ++ + +      + + + +++ l++y+e+ e  p s+
  gi|330509099|ref|YP_004385527.1| 384 DLSLKRMKGLTLYNLGRYEESLEVYDQVLEASPRIEPYVIDVSALEgkgdalR-ALNRNQEALEAYNEAIELAPSSS 459
                                       47889999999999999999999999999999999999999988885444321.22355778888888888888887 PP

                                       HH CS
                             NARP1 108 ap 109
                                       a+
  gi|330509099|ref|YP_004385527.1| 460 AA 461
                                       75 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.9    0.0013      0.81     123     178 ..      99     155 ..      53     161 .. 0.86
   2 !    7.4   0.0    0.0051       3.1     152     174 ..     170     192 ..     157     198 .. 0.91
   3 ?    4.1   0.3     0.054        33     150     181 ..     275     310 ..     205     323 .. 0.71
   4 !    9.6   0.9    0.0011       0.7      79     174 ..     274     372 ..     230     380 .. 0.72
   5 !   14.7   0.1   3.1e-05     0.019     127     178 ..     406     457 ..     377     468 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                            TPR_21 123 llaekkydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAlaalee 178
                                          +k y++Al++L++k k++a ++++ + +  +l++ ++ de  +aY++Al+  ++
  gi|330509099|ref|YP_004385527.1|  99 NESAKTYEKALTLLDEKlKKNAIDVEAWQWKAIVLASLNREDESDQAYEKALEIFDQ 155
                                       456799********76537889******************************87665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0051
                            TPR_21 152 rGDilvaqgkldeAraaYqaAla 174
                                       r D+l++ g+ deAr+ Y++A +
  gi|330509099|ref|YP_004385527.1| 170 RADVLLNLGRWDEARESYNRATE 192
                                       56******************986 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.054
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAlaaleeka....r 181
                                         +   l++ g++deA aa+++Al++   +a    r
  gi|330509099|ref|YP_004385527.1| 275 HFKASTLMEIGRNDEALAAFDEALRQSPGDAhswlR 310
                                       556667889999************999888755551 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0011
                            TPR_21  79 aLllAkaaveagdlaaAkaqLewvlekakdeelkalarlRLarvllae.......kkydeAlktLeakkeeafaalv 148
                                         ++A + +e g  ++A a+++++l +++ ++ + l +  L   l+++       k+yd+ l++++++++++ a+  
  gi|330509099|ref|YP_004385527.1| 274 WHFKASTLMEIGRNDEALAAFDEALRQSPGDAHSWLRKAGL---LVEMkcynesiKAYDRTLELIAESNTKELAGIW 347
                                       55678888888999999999999999999998877666544...333311111226788888888888888888776 PP

                            TPR_21 149 aelrGDilvaqgkldeAraaYqaAla 174
                                         ++G +l + g+++eA++a++ +l+
  gi|330509099|ref|YP_004385527.1| 348 L-VKGTALNRIGRRKEAKEAFRMSLE 372
                                       5.9******************99886 PP

  == domain 5  score: 14.7 bits;  conditional E-value: 3.1e-05
                            TPR_21 127 kkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaalee 178
                                       + yd+ l++  + ++   ++++ e +GD+l a ++++eA +aY++A++   +
  gi|330509099|ref|YP_004385527.1| 406 EVYDQVLEASPRIEPYVIDVSALEGKGDALRALNRNQEALEAYNEAIELAPS 457
                                       55666666666777777888999***********************987665 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   3.7e-07   0.00023      83     191 ..      85     194 ..      50     208 .. 0.85
   2 ?    5.5   0.3     0.015       9.3      15      99 ..     212     297 ..     204     307 .. 0.65
   3 !   11.7   0.0    0.0002      0.12      49     114 ..     394     459 ..     387     477 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.7e-07
                          TPR_MalT  83 llqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql..ep 157
                                       +++ a+ l   G   e+++tye+al+l +e+  +++  v+    + a +l   n+ +e  q+ ++++e+ +q   + 
  gi|330509099|ref|YP_004385527.1|  85 IVRKAMYLNIIGMVNESAKTYEKALTLLDEKLKKNAIDVEAW-QWKAIVLASLNREDESDQAYEKALEIFDQRikND 160
                                       556677777779999*******************99888877.566************************9977666 PP

                          TPR_MalT 158 eaaldayvllarialaqGdleeAetllekaeela 191
                                        + +d+ +  a++ l  G+++eA +  ++a+el 
  gi|330509099|ref|YP_004385527.1| 161 SRDADSWIGRADVLLNLGRWDEARESYNRATELK 194
                                       999***************************9984 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
                          TPR_MalT  15 gdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadsl.hvallallqqaeil 90 
                                       gd+++++e   +A++l+p  d  +r++a+a+ +e    +++ e+Al+a  +  +l  +   + h+ + +l+ ++   
  gi|330509099|ref|YP_004385527.1| 212 GDINESVEAYDKAISLIPAYDAAERALAYAAKAEDLAFAERWEEALEAVDKSLELNPKSSVWwHFKASTLMEIGRND 288
                                       78888888888999999999999999999998888888888888887777766665333333244444444444444 PP

                          TPR_MalT  91 vaqGrLheA 99 
                                        a   ++eA
  gi|330509099|ref|YP_004385527.1| 289 EALAAFDEA 297
                                       444444444 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.0002
                          TPR_MalT  49 asllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqg 114
                                       +    G+ e++l+++ ++ +++ +++ + + + al + ++ l+a +r +eAle y++a++la+ ++
  gi|330509099|ref|YP_004385527.1| 394 TLYNLGRYEESLEVYDQVLEASPRIEPYVIDVSALEGKGDALRALNRNQEALEAYNEAIELAPSSS 459
                                       55567999******************************************************9876 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.6   3.5e+03       2      26 ..      89     113 ..      89     114 .. 0.64
   2 !    7.1   0.1    0.0081         5       9      31 ..     130     152 ..     129     163 .. 0.86
   3 ?    5.2   0.1     0.033        20      11      28 ..     173     190 ..     170     193 .. 0.82
   4 ?   -1.2   0.0       3.3     2e+03      16      30 ..     212     226 ..     209     228 .. 0.87
   5 ?   -0.1   0.7       1.6   9.6e+02      12      30 ..     247     265 ..     236     267 .. 0.71
   6 ?    6.0   0.1     0.019        12       9      30 ..     278     299 ..     278     299 .. 0.89
   7 ?    4.7   0.0     0.048        30       9      35 ..     351     377 ..     351     384 .. 0.87
   8 !   10.8   0.0   0.00056      0.34       9      31 ..     392     414 ..     391     415 .. 0.93
   9 !    8.0   0.9    0.0044       2.7       9      31 ..     432     454 ..     426     455 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.6
                            TPR_10   2 AsslnNLanalrqrgrydeAealle 26 
                                       A+ ln ++++  + + y++A+ ll+
  gi|330509099|ref|YP_004385527.1|  89 AMYLNIIGMVNESAKTYEKALTLLD 113
                                       5666666776666667777777765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0081
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       a++l +++r de+ + +e+al+i
  gi|330509099|ref|YP_004385527.1| 130 AIVLASLNREDESDQAYEKALEI 152
                                       899******************99 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.033
                            TPR_10  11 alrqrgrydeAealleea 28 
                                       +l ++gr+deA++ + +a
  gi|330509099|ref|YP_004385527.1| 173 VLLNLGRWDEARESYNRA 190
                                       7899********977666 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 3.3
                            TPR_10  16 grydeAealleeala 30 
                                       g+ +e+++ +++a++
  gi|330509099|ref|YP_004385527.1| 212 GDINESVEAYDKAIS 226
                                       7889*********97 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 1.6
                            TPR_10  12 lrqrgrydeAealleeala 30 
                                       l    r++eA++  +++l+
  gi|330509099|ref|YP_004385527.1| 247 LAFAERWEEALEAVDKSLE 265
                                       5556688888888888776 PP

  == domain 6  score: 6.0 bits;  conditional E-value: 0.019
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       a +l + gr deA+a ++eal+
  gi|330509099|ref|YP_004385527.1| 278 ASTLMEIGRNDEALAAFDEALR 299
                                       5678899*************95 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.048
                            TPR_10   9 analrqrgrydeAealleealairrrl 35 
                                       + al + gr++eA + ++ +l+++ ++
  gi|330509099|ref|YP_004385527.1| 351 GTALNRIGRRKEAKEAFRMSLELHVKA 377
                                       6789999***************99876 PP

  == domain 8  score: 10.8 bits;  conditional E-value: 0.00056
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + +l+++gry+e+++ ++++l++
  gi|330509099|ref|YP_004385527.1| 392 GLTLYNLGRYEESLEVYDQVLEA 414
                                       789*****************985 PP

  == domain 9  score: 8.0 bits;  conditional E-value: 0.0044
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + alr+++r +eA++ + ea+++
  gi|330509099|ref|YP_004385527.1| 432 GDALRALNRNQEALEAYNEAIEL 454
                                       5699****************986 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.47   2.9e+02      67     130 ..      53     116 ..      40     120 .. 0.86
   2 !   11.1   0.0   0.00063      0.39      36     122 ..     128     224 ..     118     229 .. 0.75
   3 !   12.1   0.9   0.00033       0.2      60     124 ..     235     299 ..     230     303 .. 0.91
   4 ?    1.6   0.0      0.55   3.4e+02      87     121 ..     333     369 ..     310     384 .. 0.71
   5 ?    2.1   0.0      0.39   2.4e+02     105     122 ..     394     411 ..     376     417 .. 0.86
   6 ?    6.9   1.2     0.013       7.9      74     123 ..     397     452 ..     389     458 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.47
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHH CS
                              BTAD  67 alaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeL 130
                                        +ae++++   ++ea++    + +++P+++         l   G  +e  ++Ye++  lL+e L
  gi|330509099|ref|YP_004385527.1|  53 NRAEELMHNDSIDEAISACGMAQKKEPWNDSIIVRKAMYLNIIGMVNESAKTYEKALTLLDEKL 116
                                       578888888899999999999999******9988888889999**************9999988 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00063
                                       --SSTTGGGTT........STTHHHHHHHHHHHHHHHHHHHHH..HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHH CS
                              BTAD  36 wrGpaladlea........gewleaererleelrlealealae..aelrlGraeealaelealvaehPlrErlhrql 102
                                       w++ +la l+         ++ le + +r++++  +a  ++ +   +l lGr++ea + ++++++++Pl+   +   
  gi|330509099|ref|YP_004385527.1| 128 WKAIVLASLNRedesdqayEKALEIFDQRIKNDSRDADSWIGRadVLLNLGRWDEARESYNRATELKPLDYSVWWRK 204
                                       555555555554555555555556666666665555555544422678999************************** PP

                                       HHHHHHTT-HHHHHHHHHHH CS
                              BTAD 103 mrAlarsGrqaeALevYerl 122
                                        +     G+ +e  e+Y+++
  gi|330509099|ref|YP_004385527.1| 205 AEVISGIGDINESVEAYDKA 224
                                       *****************987 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00033
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  60 lrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       +r  a++a ae ++  +r+eeal+  ++ ++++P     +      l+  Gr+ eAL++++++ r
  gi|330509099|ref|YP_004385527.1| 235 ERALAYAAKAEDLAFAERWEEALEAVDKSLELNPKSSVWWHFKASTLMEIGRNDEALAAFDEALR 299
                                       68889999999777788*******************************************99865 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.55
                                       HHHHHSTT-HHHHHHHH..HHHHHTT-HHHHHHHHHH CS
                              BTAD  87 alvaehPlrErlhrqlm..rAlarsGrqaeALevYer 121
                                       +l+ae +++E +   l   +Al r Gr+ eA e+++ 
  gi|330509099|ref|YP_004385527.1| 333 ELIAESNTKELAGIWLVkgTALNRIGRRKEAKEAFRM 369
                                       555555666555444442259999******9999985 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.39
                                       HHHHTT-HHHHHHHHHHH CS
                              BTAD 105 AlarsGrqaeALevYerl 122
                                        l+ +Gr +e LevY+++
  gi|330509099|ref|YP_004385527.1| 394 TLYNLGRYEESLEVYDQV 411
                                       5899***********987 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.013
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHH......HHHHTT-HHHHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmr......AlarsGrqaeALevYerlr 123
                                        lGr+ee l+ +++ +++ P  E ++  + +      Al++++r++eALe+Y+++ 
  gi|330509099|ref|YP_004385527.1| 397 NLGRYEESLEVYDQVLEASPRIEPYVIDVSAlegkgdALRALNRNQEALEAYNEAI 452
                                       678888888888888888888888766553222334499*************9975 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00036      0.22     180     287 ..     100     217 ..      88     238 .. 0.77
   2 !    6.9   0.1    0.0045       2.8     218     282 ..     255     319 ..     219     329 .. 0.89
   3 ?    3.9   0.0     0.037        23     244     290 ..     435     481 ..     410     486 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00036
                                       HHHT-HHHHHHHH.HHHHTT-GGGHHHHHHHH....HHTT-HH.....HHHHHHHHHH-SSS-HHHHHHHHHHHHHH CS
                             ChAPs 180 rltkrydralell.ekLkeeepevvillarvl....lladeEv.....davkllneeleeeekdaelLllqaeflls 246
                                       + +k y++al+ll ekLk++  +v +   + +    l  ++E      +a+++  + ++++++da+  + +a+ ll+
  gi|330509099|ref|YP_004385527.1| 100 ESAKTYEKALTLLdEKLKKNAIDVEAWQWKAIvlasLNREDESdqayeKALEIFDQRIKNDSRDADSWIGRADVLLN 176
                                       4567889999988457888877775443332200002223332112226899999999******************* PP

                                       SS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHH CS
                             ChAPs 247 kkkeelAlevakravksaPsefktWalLvkvYikledienA 287
                                         + + A e  +ra+++ P +++ W + ++v   ++di++ 
  gi|330509099|ref|YP_004385527.1| 177 LGRWDEARESYNRATELKPLDYSVWWRKAEVISGIGDINES 217
                                       ***************************99999988888765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0045
                                       HHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT CS
                             ChAPs 218 davkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikle 282
                                       +a++ + ++le ++k++   + +a  l++  +++ Al++ ++a + +P + + W + +   ++++
  gi|330509099|ref|YP_004385527.1| 255 EALEAVDKSLELNPKSSVWWHFKASTLMEIGRNDEALAAFDEALRQSPGDAHSWLRKAGLLVEMK 319
                                       678889999*********************************************99888877776 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.037
                                       HHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
                             ChAPs 244 llskkkeelAlevakravksaPsefktWalLvkvYikledienALlt 290
                                       l   ++++ Ale+ ++a+++aPs ++ W    +   +l+++ nA ++
  gi|330509099|ref|YP_004385527.1| 435 LRALNRNQEALEAYNEAIELAPSSSAAWHGKGEAERALGQVGNAGMS 481
                                       666678899*******************9877777777777777655 PP

>> DUF3808  Protein of unknown function (DUF3808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       1.9   1.2e+03     319     374 ..     100     154 ..      52     162 .. 0.53
   2 ?   13.2   0.1   4.5e-05     0.028     275     368 ..     204     296 ..     198     319 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.9
                           DUF3808 319 vylheykeaaesfleLlklskwSkalYtYlaaacllelgreekkaeakekaeelfk 374
                                          + y++a+   +e lk +      ++  +a++l++l re++ ++a eka e+f 
  gi|330509099|ref|YP_004385527.1| 100 ESAKTYEKALTLLDEKLKKNAIDVEAWQ-WKAIVLASLNREDESDQAYEKALEIFD 154
                                       4444444444444444444443333333.356666666666666666677666665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.5e-05
                           DUF3808 275 earieslkgnldeAlelleeiieesqselkqvkhlclfelaltlvylheykeaaesfleLlklskwSkalYtYlaaa 351
                                       +a + s  g+++e++e+++++i+         ++l +  +a  l++  +++ea+e++++ l+l+ +S  ++  ++a+
  gi|330509099|ref|YP_004385527.1| 204 KAEVISGIGDINESVEAYDKAISLIPAYDAAERALAYAAKAEDLAFAERWEEALEAVDKSLELNPKSSVWW-HFKAS 279
                                       56666777888888888888884333333344567777788888888888888888888888888886555.56888 PP

                           DUF3808 352 cllelgreekkaeakek 368
                                        l+e+gr++++ +a ++
  gi|330509099|ref|YP_004385527.1| 280 TLMEIGRNDEALAAFDE 296
                                       88888888665544443 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       6.4     4e+03      74     124 ..      53     103 ..      49     116 .. 0.81
   2 ?    2.2   0.1      0.38   2.3e+02      82     123 ..     102     143 ..      93     146 .. 0.88
   3 ?    4.0   0.0       0.1        63      76     122 ..     137     183 ..     128     193 .. 0.82
   4 ?    3.3   0.3      0.17   1.1e+02      73     123 ..     241     291 ..     217     298 .. 0.87
   5 ?    4.2   0.0     0.088        54      77     124 ..     359     406 ..     344     415 .. 0.88
   6 ?    3.2   0.0      0.18   1.1e+02      79     126 ..     395     448 ..     387     461 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.4
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  74 ekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                       ++a+e + ++ +  a++ + ++  ++p n++    ka  l+ +g  +esa 
  gi|330509099|ref|YP_004385527.1|  53 NRAEELMHNDSIDEAISACGMAQKKEPWNDSIIVRKAMYLNIIGMVNESAK 103
                                       678888888888889999999999999998888888888888888888876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.38
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  82 egdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       ++ y+ a++ll+  + ++  + ea + ka +l +l ++ es 
  gi|330509099|ref|YP_004385527.1| 102 AKTYEKALTLLDEKLKKNAIDVEAWQWKAIVLASLNREDESD 143
                                       5679999****************************9999986 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.1
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  76 akealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                        +e+ +++ y+ a+e+ ++ + +d+++a+    +ad+l +lg+  e+
  gi|330509099|ref|YP_004385527.1| 137 NREDESDQAYEKALEIFDQRIKNDSRDADSWIGRADVLLNLGRWDEA 183
                                       455566777*********************************97775 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.17
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  73 lekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       ++ka++ + ++  + a+e +++ ++ +p+ +   + ka++l ++g+  e+ 
  gi|330509099|ref|YP_004385527.1| 241 AAKAEDLAFAERWEEALEAVDKSLELNPKSSVWWHFKASTLMEIGRNDEAL 291
                                       567888888899999******************************999876 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.088
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  77 kealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                       +++ +++ +r+++el  +++ +dp + + k++k  +l +lg+ +es  
  gi|330509099|ref|YP_004385527.1| 359 RRKEAKEAFRMSLELHVKAILEDPGDLSLKRMKGLTLYNLGRYEESLE 406
                                       55667888**********************************999975 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.18
                                       HHHTT-HHHHHHHHHHHHHHSTT......-HHHHHHHHHHHHHHHHH-SSHHHH CS
                   Alkyl_sulf_dimr  79 alkegdyrwaaellnhlvfadpe......naeakelkadaleqlgyqaesatwR 126
                                        ++ g y+ ++e+ +++++a p+      + +a e k dal++l + +e+  + 
  gi|330509099|ref|YP_004385527.1| 395 LYNLGRYEESLEVYDQVLEASPRiepyviDVSALEGKGDALRALNRNQEALEAY 448
                                       567899**************9986665555788888999999999999987765 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.3   3.3e+03      65      90 ..       2      27 ..       1      29 [. 0.85
   2 ?    0.7   0.0      0.91   5.6e+02      12      37 ..     140     190 ..     131     235 .. 0.61
   3 ?    3.1   0.0      0.16     1e+02      49      69 ..     279     299 ..     275     306 .. 0.85
   4 ?    0.7   0.0      0.92   5.7e+02      44      75 ..     308     339 ..     304     350 .. 0.80
   5 ?    5.0   0.2     0.041        26      54      72 ..     438     456 ..     434     461 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.3
                            ANAPC5 65 eeairlArenkDkscLalalawlarl 90
                                      e+  ++A  ++D+  L  +l+ +++l
  gi|330509099|ref|YP_004385527.1|  2 ENNAKIAEIRHDHRQLPDILYAVFKL 27
                                      667799999*******9999999887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.91
                            ANAPC5  12 kdYqqaldsLhryFDyvlsqnessq.........................k 37 
                                       ++ +qa ++  ++FD  ++++++ +                         +
  gi|330509099|ref|YP_004385527.1| 140 DESDQAYEKALEIFDQRIKNDSRDAdswigradvllnlgrwdearesynrA 190
                                       556788888888999988888877544444444444444444443333330 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.16
                            ANAPC5  49 slhadfghneeAvkaleeair 69 
                                       s+ +++g n+eA++a+ ea r
  gi|330509099|ref|YP_004385527.1| 279 STLMEIGRNDEALAAFDEALR 299
                                       5567889************87 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.92
                            ANAPC5  44 lLnlaslhadfghneeAvkaleeairlArenk 75 
                                        L  a l  ++ +++e++ka   + +l  e++
  gi|330509099|ref|YP_004385527.1| 308 WLRKAGLLVEMKCYNESIKAYDRTLELIAESN 339
                                       6788899999*********9988887766665 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.041
                            ANAPC5  54 fghneeAvkaleeairlAr 72 
                                       ++ n+eA++a +eai+lA 
  gi|330509099|ref|YP_004385527.1| 438 LNRNQEALEAYNEAIELAP 456
                                       7899*************95 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.026        16      28      52 ..     180     204 ..     178     227 .. 0.88
   2 ?    3.8   0.1      0.11        65      28      52 ..     253     277 ..     248     290 .. 0.89
   3 ?    2.0   0.1      0.37   2.3e+02      29      65 ..     442     476 ..     438     481 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.026
                           DUF1510  28 wnEmekavskatglsednmivwwlg 52 
                                       w+E ++  ++at+l+  ++ vww +
  gi|330509099|ref|YP_004385527.1| 180 WDEARESYNRATELKPLDYSVWWRK 204
                                       9**********************76 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.11
                           DUF1510  28 wnEmekavskatglsednmivwwlg 52 
                                       w+E ++av k  +l+ ++++ w+ +
  gi|330509099|ref|YP_004385527.1| 253 WEEALEAVDKSLELNPKSSVWWHFK 277
                                       ***************9999988876 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.37
                           DUF1510  29 nEmekavskatglsednmivwwlgnggspqkaigtvs 65 
                                       +E ++a ++a++l  +++  w+ +  g++++a g+v 
  gi|330509099|ref|YP_004385527.1| 442 QEALEAYNEAIELAPSSSAAWHGK--GEAERALGQVG 476
                                       6999************99999865..56667887775 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 ?    0.1   0.0      0.99   6.1e+02       2      14 ..     146     158 ..     145     163 .. 0.89
   2 ?   -0.0   0.0       1.1   6.7e+02       1      15 [.     252     266 ..     252     269 .. 0.87
   3 ?   -1.9   0.0       4.2   2.6e+03       2      20 ..     321     339 ..     320     361 .. 0.78
   4 ?    5.1   0.0     0.026        16       1      19 [.     400     418 ..     400     421 .. 0.90
   5 ?   -1.6   0.0       3.3     2e+03       3      15 ..     442     454 ..     440     456 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.99
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAie 14 
                                       Ye+aLe  ++ i+
  gi|330509099|ref|YP_004385527.1| 146 YEKALEIFDQRIK 158
                                       9*******99987 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       r+eeaLe v+k +e+
  gi|330509099|ref|YP_004385527.1| 252 RWEEALEAVDKSLEL 266
                                       579********9885 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.2
                                       HHHHHHHHHHHHHHHHHTT CS
                          HTH_Bact   2 YeeaLeqvnkAieiSirin 20 
                                       Y+e+++  ++ +e+  + n
  gi|330509099|ref|YP_004385527.1| 321 YNESIKAYDRTLELIAESN 339
                                       8999999998888765555 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.026
                                       -HHHHHHHHHHHHHHHHHT CS
                          HTH_Bact   1 rYeeaLeqvnkAieiSiri 19 
                                       rYee+Le+ ++ +e S ri
  gi|330509099|ref|YP_004385527.1| 400 RYEESLEVYDQVLEASPRI 418
                                       7*************99776 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   3 eeaLeqvnkAiei 15 
                                       +eaLe  n Aie+
  gi|330509099|ref|YP_004385527.1| 442 QEALEAYNEAIEL 454
                                       5899999999986 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00021      0.13       4      22 ..     167     185 ..     164     189 .. 0.89
   2 ?    0.1   4.2       2.9   1.8e+03       2      25 ..     238     261 ..     232     262 .. 0.90
   3 ?    0.6   0.1         2   1.2e+03      15      26 .]     285     296 ..     278     296 .. 0.88
   4 ?    2.7   0.0      0.43   2.6e+02       8      26 .]     392     410 ..     387     410 .. 0.85
   5 ?    0.9   0.1       1.6     1e+03       3      23 ..     427     447 ..     425     450 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00021
                             TPR_4   4 llaLArallalGdldeAra 22 
                                        +++A +ll lG++deAr+
  gi|330509099|ref|YP_004385527.1| 167 WIGRADVLLNLGRWDEARE 185
                                       5789**************7 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.9
                             TPR_4   2 rallaLArallalGdldeAralle 25 
                                        a++a A+ l+ + +++eA+++++
  gi|330509099|ref|YP_004385527.1| 238 LAYAAKAEDLAFAERWEEALEAVD 261
                                       688999**************9875 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 2
                             TPR_4  15 GdldeAraller 26 
                                       G+ deA+a++++
  gi|330509099|ref|YP_004385527.1| 285 GRNDEALAAFDE 296
                                       999*****9875 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.43
                             TPR_4   8 ArallalGdldeAraller 26 
                                       + +l+ lG+++e +++ ++
  gi|330509099|ref|YP_004385527.1| 392 GLTLYNLGRYEESLEVYDQ 410
                                       678999******9998876 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 1.6
                             TPR_4   3 allaLArallalGdldeAral 23 
                                       al + + al al +  eA+++
  gi|330509099|ref|YP_004385527.1| 427 ALEGKGDALRALNRNQEALEA 447
                                       5666789***********986 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.5     4e+03      45      57 ..      63      75 ..      45      76 .. 0.85
   2 ?    4.1   0.2     0.083        51      23      41 ..     130     154 ..      98     156 .. 0.69
   3 ?   -2.0   0.0       6.6   4.1e+03      27      39 ..     181     193 ..     174     194 .. 0.85
   4 ?   -2.3   0.0       8.3   5.1e+03      30      40 ..     218     228 ..     213     230 .. 0.81
   5 ?    3.5   0.1      0.12        77      18      41 ..     433     456 ..     425     461 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.5
                           DUF2802 45 sveelaeecgLsr 57
                                      s++e +++cg+++
  gi|330509099|ref|YP_004385527.1| 63 SIDEAISACGMAQ 75
                                      7899999999976 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.083
                           DUF2802  23 l......eqqdpqsklYsqAiklvr 41 
                                              + +d++++ Y++A++   
  gi|330509099|ref|YP_004385527.1| 130 AivlaslNREDESDQAYEKALEIFD 154
                                       05555559999*********99765 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 6.6
                           DUF2802  27 dpqsklYsqAikl 39 
                                       d++  +Y++A +l
  gi|330509099|ref|YP_004385527.1| 181 DEARESYNRATEL 193
                                       678899****987 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 8.3
                           DUF2802  30 sklYsqAiklv 40 
                                          Y++Ai l+
  gi|330509099|ref|YP_004385527.1| 218 VEAYDKAISLI 228
                                       568*****997 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.12
                           DUF2802  18 erleeleqqdpqsklYsqAiklvr 41 
                                       + l++l+ ++++   Y++Ai+l+ 
  gi|330509099|ref|YP_004385527.1| 433 DALRALNRNQEALEAYNEAIELAP 456
                                       567788999999*********985 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 ?   -1.6   0.0       4.7   2.9e+03      56      63 ..      51      58 ..      43      60 .. 0.79
   2 ?    1.9   0.1      0.38   2.3e+02       9      39 ..      87     117 ..      84     131 .. 0.70
   3 ?    5.1   0.1     0.039        24      11      43 ..     130     160 ..     127     170 .. 0.73
   4 ?    2.1   0.0      0.34   2.1e+02      15      32 ..     175     192 ..     167     193 .. 0.83
   5 ?   -0.8   0.0       2.6   1.6e+03      18      33 ..     212     227 ..     211     229 .. 0.82
   6 ?    2.5   2.6      0.25   1.5e+02       2      32 ..     235     265 ..     234     266 .. 0.89
   7 ?   -0.8   0.0       2.7   1.6e+03      17      34 ..     318     335 ..     304     342 .. 0.78
   8 ?    0.1   0.1       1.4   8.4e+02      16      30 ..     397     411 ..     394     414 .. 0.82
   9 ?    5.2   0.1     0.036        23      21      33 ..     442     454 ..     437     457 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.7
                               MIT 56 YleRaeeL 63
                                      +++RaeeL
  gi|330509099|ref|YP_004385527.1| 51 WINRAEEL 58
                                      799***99 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.38
                               MIT   9 kkAveeDnagnyeeAlelYkealelLlqalk 39 
                                       +kA+ +   g   e  + Y++al lL + lk
  gi|330509099|ref|YP_004385527.1|  87 RKAMYLNIIGMVNESAKTYEKALTLLDEKLK 117
                                       5555555556667777888888888888777 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.039
                               MIT  11 AveeDnagnyeeAlelYkealelLlqalkekne 43 
                                       A+ + + +  +e  ++Y++ale++ q +k  n+
  gi|330509099|ref|YP_004385527.1| 130 AIVLASLNREDESDQAYEKALEIFDQRIK--ND 160
                                       5555666666777789********99999..32 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.34
                               MIT  15 DnagnyeeAlelYkeale 32 
                                        n g ++eA e Y  a e
  gi|330509099|ref|YP_004385527.1| 175 LNLGRWDEARESYNRATE 192
                                       57899*********9987 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 2.6
                               MIT  18 gnyeeAlelYkealel 33 
                                       g++ e +e+Y +a+ l
  gi|330509099|ref|YP_004385527.1| 212 GDINESVEAYDKAISL 227
                                       6778999999999976 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.25
                               MIT   2 dkAlelvkkAveeDnagnyeeAlelYkeale 32 
                                       ++Al+++ kA ++  a+ +eeAle+  ++le
  gi|330509099|ref|YP_004385527.1| 235 ERALAYAAKAEDLAFAERWEEALEAVDKSLE 265
                                       68*********************98777776 PP

  == domain 7  score: -0.8 bits;  conditional E-value: 2.7
                               MIT  17 agnyeeAlelYkealelL 34 
                                        + y e +++Y   lel+
  gi|330509099|ref|YP_004385527.1| 318 MKCYNESIKAYDRTLELI 335
                                       578999999999988876 PP

  == domain 8  score: 0.1 bits;  conditional E-value: 1.4
                               MIT  16 nagnyeeAlelYkea 30 
                                       n g yee le Y + 
  gi|330509099|ref|YP_004385527.1| 397 NLGRYEESLEVYDQV 411
                                       568999999999875 PP

  == domain 9  score: 5.2 bits;  conditional E-value: 0.036
                               MIT  21 eeAlelYkealel 33 
                                       +eAle+Y ea+el
  gi|330509099|ref|YP_004385527.1| 442 QEALEAYNEAIEL 454
                                       8**********97 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       4.6   2.8e+03      15      30 ..     103     118 ..     101     121 .. 0.83
   2 ?   -0.5   0.0       2.2   1.4e+03      17      33 ..     253     269 ..     250     271 .. 0.88
   3 ?    8.7   0.0     0.003       1.8      11      33 ..     395     417 ..     392     419 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.6
                                       T-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C  15 geYseArryvdalLei 30 
                                       + Y++A+ ++d  L++
  gi|330509099|ref|YP_004385527.1| 103 KTYEKALTLLDEKLKK 118
                                       679****999988876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  17 YseArryvdalLeiEPe 33 
                                        +eA++ vd  Le+ P+
  gi|330509099|ref|YP_004385527.1| 253 WEEALEAVDKSLELNPK 269
                                       689**********9996 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.003
                                       HHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPe 33 
                                        y lg+Y+e+++  d++Le  P+
  gi|330509099|ref|YP_004385527.1| 395 LYNLGRYEESLEVYDQVLEASPR 417
                                       699****************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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):              29  [number of targets reported over threshold]
# CPU time: 0.80u 0.34s 00:00:01.14 Elapsed: 00:00:00.57
# Mc/sec: 2586.85
//
Query:       gi|330509100|ref|YP_004385528.1|  [L=481]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-54  179.0  18.8    1.5e-09   37.2   0.1   12.2 12  TPR_1            Tetratricopeptide repeat
    2.8e-48  158.2  21.7    5.3e-08   32.4   0.0   12.0 12  TPR_2            Tetratricopeptide repeat
    5.6e-45  147.8  21.1      3e-05   23.9   0.4   12.0 12  TPR_8            Tetratricopeptide repeat
      4e-36  122.4  28.3    1.8e-09   37.1   0.4   11.4 11  TPR_11           TPR repeat
    1.8e-35  118.5  15.4    1.3e-05   25.6   0.2   10.4 10  TPR_14           Tetratricopeptide repeat
    6.2e-35  119.3  20.1    8.2e-10   38.8   0.1    6.7  6  TPR_12           Tetratricopeptide repeat
    5.4e-33  113.4  12.1    1.3e-09   38.5   0.0    6.8  7  TPR_16           Tetratricopeptide repeat
    5.4e-31  104.7   4.7     0.0075   16.6   0.0   10.9 10  TPR_17           Tetratricopeptide repeat
      1e-29  102.8  16.1    2.7e-06   27.8   0.0    7.5  7  TPR_19           Tetratricopeptide repeat
    1.4e-22   79.6   7.6    1.6e-06   28.2   0.1    6.8  8  TPR_9            Tetratricopeptide repeat
    1.6e-17   62.8  15.5      0.031   14.9   0.1    9.7  9  TPR_6            Tetratricopeptide repeat
    1.2e-14   53.7  20.9       0.28   11.1   0.1    9.8 10  TPR_10           Tetratricopeptide repeat
    1.2e-14   54.3   3.7     0.0014   18.8   0.0    5.8  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    1.1e-12   48.2  14.4    1.3e-05   25.3   0.4    6.5  6  DUF3856          Domain of Unknown Function (DUF3856)
    1.3e-12   46.8  14.0      0.027   14.5   0.1    9.2  9  TPR_7            Tetratricopeptide repeat
    7.6e-12   45.3  13.5      0.038   13.7   0.1    6.1  6  TPR_21           Tetratricopeptide repeat-like domain
    4.8e-11   42.3  11.1     0.0033   16.4   0.4    5.9  7  NARP1            NMDA receptor-regulated protein 1
    3.2e-10   40.6   6.6       0.28   11.6   0.0    6.7  7  BTAD             Bacterial transcriptional activator domain
    1.5e-08   34.4   8.5    1.8e-06   27.6   0.5    4.0  4  SNAP             Soluble NSF attachment protein, SNAP
    1.7e-07   31.8   0.5      0.036   14.5   0.0    4.2  4  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    2.1e-05   24.0   4.6     0.0019   17.7   0.2    3.7  4  TPR_MalT         MalT-like TPR region
    2.3e-05   24.3   1.7         41    4.7   0.0    7.1  6  PPR              PPR repeat
    0.00051   19.7   0.0       0.19   11.5   0.0    3.8  3  PPTA             Protein prenyltransferase alpha subunit repe
    0.00055   20.3  22.2        4.6    8.2   0.0    8.4  6  TPR_4            Tetratricopeptide repeat
    0.00058   19.4   7.1         17    4.7   0.0    5.4  6  Coatomer_E       Coatomer epsilon subunit
    0.00058   19.9  20.7        7.7    6.7   0.1    8.2  8  MIT              MIT (microtubule interacting and transport) 
    0.00072   19.6   1.2         10    6.3   0.0    5.7  5  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
     0.0015   18.8  10.3        3.2    8.2   0.5    6.2  6  TPR_20           Tetratricopeptide repeat
     0.0041   17.4   3.1        2.3    8.5   0.0    4.9  6  TPR_5            Tetratrico peptide repeat
     0.0045   17.0   3.5       0.65   10.1   0.0    5.0  5  TPR_3            Tetratricopeptide repeat
     0.0047   16.9   4.2         14    5.5   0.0    4.6  4  Wzy_C_2          Virulence factor membrane-bound polymerase, 
  ------ inclusion threshold ------
      0.012   15.7   2.2        4.7    7.4   0.3    5.0  4  ANAPC5           Anaphase-promoting complex subunit 5
      0.028   14.2   7.0       0.38   10.5   1.5    3.5  3  DUF2225          Uncharacterized protein conserved in bacteri
      0.069   13.0   0.8         41    4.1   0.1    3.8  3  BPS              BPS (Between PH and SH2)
      0.084   12.3   0.0         40    3.7   0.0    3.4  3  DUF2917          Protein of unknown function (DUF2917)
       0.12   12.0   3.5         17    5.1   0.1    5.0  5  HTH_Bact         Helix-turn-helix bacterial domain
       0.14   12.3   0.2         17    5.7   0.0    2.9  2  Pepsin-I3        Pepsin inhibitor-3-like repeated domain
        4.5    7.4  16.0        4.6    7.4   0.1    5.7  4  Strep_SA_rep     Streptococcal surface antigen repeat
        7.8    6.7   8.0         77    3.5   0.0    4.6  4  DUF1510          Domain of unknown function (DUF1510)


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     0.022        10       3      34 .]      38      69 ..      36      69 .. 0.92
   2 ?    1.5   0.0      0.63   2.9e+02      15      30 ..      84      99 ..      73     102 .. 0.83
   3 ?    7.1   0.2     0.011       5.1       1      29 [.     111     139 ..     111     141 .. 0.96
   4 !   37.2   0.1   3.3e-12   1.5e-09       2      34 .]     153     185 ..     152     185 .. 0.96
   5 ?    6.5   0.0     0.017       7.8       4      33 ..     189     218 ..     187     219 .. 0.82
   6 !    7.9   0.0    0.0062       2.8      15      33 ..     240     258 ..     235     259 .. 0.93
   7 !   18.5   0.0   2.7e-06    0.0012       7      34 .]     266     293 ..     263     293 .. 0.91
   8 !   22.5   0.3   1.5e-07   6.7e-05       1      30 [.     294     323 ..     294     327 .. 0.95
   9 !   15.8   0.0     2e-05    0.0091       4      31 ..     336     363 ..     333     365 .. 0.92
  10 !   25.9   0.1   1.2e-08   5.7e-06       4      29 ..     377     402 ..     374     404 .. 0.91
  11 !   28.0   0.0   2.8e-09   1.3e-06       2      34 .]     415     447 ..     414     447 .. 0.94
  12 ?    2.4   0.1      0.34   1.6e+02       2      16 ..     449     463 ..     448     467 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.022
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                                       +  ++  + ++  ++e +   ++AL+ +P n
  gi|330509100|ref|YP_004385528.1| 38 YWMDKAEEFAYNSSFEEVISSLDEALKTDPGN 69
                                      6889999999999*****************87 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.63
                                      T-HHHHHHHHHHHHHH CS
                             TPR_1 15 gkydeAleyyekALel 30
                                      gk +e  + yekAL++
  gi|330509100|ref|YP_004385528.1| 84 GKVNESSQTYEKALSI 99
                                      777888899*****87 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALe 29 
                                       a+a+  ++ ++ +l++ +e l++ye+ Le
  gi|330509100|ref|YP_004385528.1| 111 AEAWQKKASVLGSLNRQNESLAAYEETLE 139
                                       89************************997 PP

  == domain 4  score: 37.2 bits;  conditional E-value: 3.3e-12
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +a+ ++Gna+++lgk+deA ++y++A+e++P++
  gi|330509100|ref|YP_004385528.1| 153 DAWIGKGNALLNLGKWDEARDAYNEAIEVDPQD 185
                                       8******************************86 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPn 33 
                                       + +++ +  + g+ +e  e+y++ +el P 
  gi|330509100|ref|YP_004385528.1| 189 WGRKAEVIGRIGDINESMEAYDRTIELIPA 218
                                       666666666789***************985 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.0062
                                       T-HHHHHHHHHHHHHHSTT CS
                             TPR_1  15 gkydeAleyyekALelnPn 33 
                                       g++ eAle+ +  Le++P+
  gi|330509100|ref|YP_004385528.1| 240 GRWAEALEAINHSLEIDPE 258
                                       899***************7 PP

  == domain 7  score: 18.5 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnPnn 34 
                                       ++ ++ +lg+ deA+e+++++L  nP++
  gi|330509100|ref|YP_004385528.1| 266 KADILSQLGRKDEAIEAFDEVLNQNPED 293
                                       68899*********************86 PP

  == domain 8  score: 22.5 bits;  conditional E-value: 1.5e-07
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a+++  ++n++ ++++y+e +e+y+kA+el
  gi|330509100|ref|YP_004385528.1| 294 AESWLWKANLLVEMKRYNESVEAYDKAIEL 323
                                       799**************************9 PP

  == domain 9  score: 15.8 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALeln 31 
                                       +  +G a+ k g+ deA ++++k Le +
  gi|330509100|ref|YP_004385528.1| 336 WLSKGWALNKTGRTDEAQAAFQKSLEFY 363
                                       889**********************976 PP

  == domain 10  score: 25.9 bits;  conditional E-value: 1.2e-08
                                       HHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALe 29 
                                       l ++G+++f+lg+ydeA+e+y+++L+
  gi|330509100|ref|YP_004385528.1| 377 LQQKGLVLFELGRYDEAIEAYDQVLK 402
                                       6689********************97 PP

  == domain 11  score: 28.0 bits;  conditional E-value: 2.8e-09
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        a+ ++G  ++ +gk +eAle+y+kA+ l P++
  gi|330509100|ref|YP_004385528.1| 415 SAWIGKGDSLRLQGKNEEALEAYNKAIDLGPHY 447
                                       69***************************9986 PP

  == domain 12  score: 2.4 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHTT- CS
                             TPR_1   2 kalynlGnayfklgk 16 
                                       +a+ ++G a   +g+
  gi|330509100|ref|YP_004385528.1| 449 NAWHGRGEAQKAMGQ 463
                                       79************8 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.13        60       3      34 .]      38      69 ..      36      69 .. 0.87
   2 ?    2.7   0.0      0.36   1.7e+02      17      32 ..      93     108 ..      72     110 .. 0.57
   3 ?    6.1   0.3     0.031        14       1      29 [.     111     139 ..     111     143 .. 0.93
   4 !   32.4   0.0   1.2e-10   5.3e-08       2      34 .]     153     185 ..     152     185 .. 0.96
   5 ?    4.9   0.0     0.075        34       6      34 .]     191     219 ..     187     219 .. 0.81
   6 !   11.6   0.0   0.00051      0.24      13      33 ..     238     258 ..     234     259 .. 0.89
   7 !   20.8   0.0   5.7e-07   0.00026       4      34 .]     263     293 ..     262     293 .. 0.93
   8 !   18.9   0.3   2.3e-06    0.0011       1      30 [.     294     323 ..     294     327 .. 0.94
   9 !   12.1   0.1   0.00036      0.17       4      33 ..     336     365 ..     333     366 .. 0.87
  10 !   23.2   0.1   9.8e-08   4.5e-05       3      29 ..     376     402 ..     374     404 .. 0.91
  11 !   24.0   0.0   5.5e-08   2.5e-05       3      33 ..     416     446 ..     414     447 .. 0.94
  12 ?    0.4   0.1       2.1   9.6e+02       2      17 ..     449     464 ..     448     467 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.13
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                                      +++  ++  +++  +ee +  +++Al+ dP+n
  gi|330509100|ref|YP_004385528.1| 38 YWMDKAEEFAYNSSFEEVISSLDEALKTDPGN 69
                                      678888888888899***************87 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.36
                             TPR_2  17 yeeAleafekAleldP 32 
                                       ye+Al  +++ l  dP
  gi|330509100|ref|YP_004385528.1|  93 YEKALSILDEILLKDP 108
                                       5555555555555555 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.031
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAle 29 
                                       aea+   + ++  l++ +e l+a+e+ le
  gi|330509100|ref|YP_004385528.1| 111 AEAWQKKASVLGSLNRQNESLAAYEETLE 139
                                       79************************998 PP

  == domain 4  score: 32.4 bits;  conditional E-value: 1.2e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +a+   G+a+++lg+++eA++a+++A+e dP++
  gi|330509100|ref|YP_004385528.1| 153 DAWIGKGNALLNLGKWDEARDAYNEAIEVDPQD 185
                                       69*****************************86 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.075
                             TPR_2   6 nlGlayyklgdyeeAleafekAleldPnn 34 
                                       + +++  + gd +e  ea+++ +el P n
  gi|330509100|ref|YP_004385528.1| 191 RKAEVIGRIGDINESMEAYDRTIELIPAN 219
                                       5555666789***************9976 PP

  == domain 6  score: 11.6 bits;  conditional E-value: 0.00051
                             TPR_2  13 klgdyeeAleafekAleldPn 33 
                                       + g+++eAlea + +le+dP+
  gi|330509100|ref|YP_004385528.1| 238 AGGRWAEALEAINHSLEIDPE 258
                                       669*****************7 PP

  == domain 7  score: 20.8 bits;  conditional E-value: 5.7e-07
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +   ++++ +lg+ +eA+eaf+++l  +P++
  gi|330509100|ref|YP_004385528.1| 263 WRFKADILSQLGRKDEAIEAFDEVLNQNPED 293
                                       677899***********************86 PP

  == domain 8  score: 18.9 bits;  conditional E-value: 2.3e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       ae + + ++++ ++++y+e +ea++kA+el
  gi|330509100|ref|YP_004385528.1| 294 AESWLWKANLLVEMKRYNESVEAYDKAIEL 323
                                       799**************************9 PP

  == domain 9  score: 12.1 bits;  conditional E-value: 0.00036
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                       +   G+a+ k g+ +eA +af+k+le +++
  gi|330509100|ref|YP_004385528.1| 336 WLSKGWALNKTGRTDEAQAAFQKSLEFYET 365
                                       6778999999***************98865 PP

  == domain 10  score: 23.2 bits;  conditional E-value: 9.8e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                                       +l + Gl++++lg+y+eA+ea++++l+
  gi|330509100|ref|YP_004385528.1| 376 LLQQKGLVLFELGRYDEAIEAYDQVLK 402
                                       67889********************98 PP

  == domain 11  score: 24.0 bits;  conditional E-value: 5.5e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+   G++++ +g+ eeAlea++kA+ l P+
  gi|330509100|ref|YP_004385528.1| 416 AWIGKGDSLRLQGKNEEALEAYNKAIDLGPH 446
                                       89**************************997 PP

  == domain 12  score: 0.4 bits;  conditional E-value: 2.1
                             TPR_2   2 ealynlGlayyklgdy 17 
                                        a++ +G+a  ++g+ 
  gi|330509100|ref|YP_004385528.1| 449 NAWHGRGEAQKAMGQV 464
                                       59*******9999986 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       1.1     5e+02       3      33 ..      38      68 ..      36      69 .. 0.80
   2 ?    4.3   0.0      0.12        56      15      30 ..      84      99 ..      72      99 .. 0.85
   3 !   11.7   0.2   0.00053      0.24       1      28 [.     111     138 ..     111     141 .. 0.92
   4 !   21.5   0.0   3.7e-07   0.00017       2      34 .]     153     185 ..     152     185 .. 0.95
   5 ?    7.5   0.0     0.012       5.4       2      34 .]     187     219 ..     186     219 .. 0.90
   6 ?    5.3   0.0     0.059        27       2      33 ..     226     258 ..     225     259 .. 0.83
   7 !   18.9   0.0   2.5e-06    0.0012       7      34 .]     266     293 ..     263     293 .. 0.93
   8 !   23.9   0.4   6.5e-08     3e-05       1      32 [.     294     325 ..     294     327 .. 0.93
   9 !   15.9   0.0   2.4e-05     0.011       4      30 ..     336     362 ..     336     365 .. 0.92
  10 !   22.3   0.1   2.1e-07   9.5e-05       2      29 ..     375     402 ..     374     405 .. 0.93
  11 !   17.1   0.0   9.6e-06    0.0044       2      30 ..     415     443 ..     414     447 .. 0.92
  12 ?    0.7   0.0       1.8   8.3e+02       2      24 ..     449     471 ..     448     477 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1.1
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      +++ ++        +ee ++++ +al+ dp 
  gi|330509100|ref|YP_004385528.1| 38 YWMDKAEEFAYNSSFEEVISSLDEALKTDPG 68
                                      6777777777777899999********9996 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.12
                                      T-HHHHHHHHHHHHHH CS
                             TPR_8 15 gdyeeAkeyyekalel 30
                                      g+ +e+ ++yekal++
  gi|330509100|ref|YP_004385528.1| 84 GKVNESSQTYEKALSI 99
                                      8899**********97 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00053
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekal 28 
                                       aea+++++s++ +l++ +e+ ++ye+ l
  gi|330509100|ref|YP_004385528.1| 111 AEAWQKKASVLGSLNRQNESLAAYEETL 138
                                       79***********************855 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 3.7e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +a+  +g+++l+lg+ +eA  +y++a+e dp++
  gi|330509100|ref|YP_004385528.1| 153 DAWIGKGNALLNLGKWDEARDAYNEAIEVDPQD 185
                                       79*****************************86 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.012
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +a+ +++ +    gd++e++e+y + +el p+n
  gi|330509100|ref|YP_004385528.1| 187 HAWGRKAEVIGRIGDINESMEAYDRTIELIPAN 219
                                       6899999999999***************99976 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.059
                                       CHHHHHHHHH.HHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiy.lklgdyeeAkeyyekaleldpd 33 
                                       ++++ ++ ++ +  g+  eA e++++ le+dp+
  gi|330509100|ref|YP_004385528.1| 226 DYWMSKAEVLaIAGGRWAEALEAINHSLEIDPE 258
                                       678888866668888999**************7 PP

  == domain 7  score: 18.9 bits;  conditional E-value: 2.5e-06
                                       HHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +++i+++lg+++eA+e++ ++l  +p++
  gi|330509100|ref|YP_004385528.1| 266 KADILSQLGRKDEAIEAFDEVLNQNPED 293
                                       79********************999975 PP

  == domain 8  score: 23.9 bits;  conditional E-value: 6.5e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ae+++++++++ ++++y+e++e+y ka+el  
  gi|330509100|ref|YP_004385528.1| 294 AESWLWKANLLVEMKRYNESVEAYDKAIELIA 325
                                       79***************************976 PP

  == domain 9  score: 15.9 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekalel 30 
                                       ++ +g+++ k+g+ +eA+++++k le 
  gi|330509100|ref|YP_004385528.1| 336 WLSKGWALNKTGRTDEAQAAFQKSLEF 362
                                       7899********************996 PP

  == domain 10  score: 22.3 bits;  conditional E-value: 2.1e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                       ++++++g+++++lg+y+eA+e+y ++l+
  gi|330509100|ref|YP_004385528.1| 375 RLLQQKGLVLFELGRYDEAIEAYDQVLK 402
                                       7899*********************998 PP

  == domain 11  score: 17.1 bits;  conditional E-value: 9.6e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                       +a+  +g+ ++ +g+ eeA e+y+ka++l
  gi|330509100|ref|YP_004385528.1| 415 SAWIGKGDSLRLQGKNEEALEAYNKAIDL 443
                                       6999***********************98 PP

  == domain 12  score: 0.7 bits;  conditional E-value: 1.8
                                       CHHHHHHHHHHHTT-HHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyy 24 
                                        a++  g + + +g+  +A  ++
  gi|330509100|ref|YP_004385528.1| 449 NAWHGRGEAQKAMGQVGNAGMSF 471
                                       699************99996665 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.84   3.8e+02       9      30 ..      51      72 ..      44      74 .. 0.81
   2 ?    5.8   0.1     0.024        11       8      32 ..      84     115 ..      83     125 .. 0.77
   3 !    8.5   0.1    0.0035       1.6      10      42 .]     134     166 ..     120     166 .. 0.96
   4 !   25.1   0.3   2.2e-08   9.9e-06       1      27 [.     159     185 ..     159     189 .. 0.94
   5 ?    3.8   0.0       0.1        47       8      27 ..     200     219 ..     198     221 .. 0.92
   6 ?    3.9   0.0     0.096        44       6      26 ..     238     258 ..     237     259 .. 0.91
   7 !   20.0   0.0     9e-07   0.00041       2      40 ..     268     306 ..     267     308 .. 0.92
   8 !   14.4   0.2   4.9e-05     0.023       2      23 ..     302     323 ..     301     327 .. 0.91
   9 ?    1.0   0.0      0.74   3.4e+02       3      23 ..     342     362 ..     340     367 .. 0.85
  10 !   20.4   0.1   6.5e-07    0.0003       1      22 [.     381     402 ..     381     403 .. 0.94
  11 !   37.1   0.4   3.9e-12   1.8e-09       1      42 []     421     462 ..     421     462 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.84
                            TPR_11  9 kyeeAieaYkkAlkldPdnaea 30
                                       +ee i ++ +Alk dP n ++
  gi|330509100|ref|YP_004385528.1| 51 SFEEVISSLDEALKTDPGNETI 72
                                      5777788999*******98876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.024
                            TPR_11   8 GkyeeAieaYkkAlkl.......dPdnaeayy 32 
                                       Gk +e+ + Y+kAl +       dPd+aea+ 
  gi|330509100|ref|YP_004385528.1|  84 GKVNESSQTYEKALSIldeillkDPDDAEAWQ 115
                                       89999999*****9986666666777777775 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0035
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       yee +ea+++ ++ d+++ +a+ + G+a++++G
  gi|330509100|ref|YP_004385528.1| 134 YEETLEAFNRRIEKDSKDIDAWIGKGNALLNLG 166
                                       9999*************************9998 PP

  == domain 4  score: 25.1 bits;  conditional E-value: 2.2e-08
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdn 27 
                                       G+a+  +Gk++eA  aY++A++ dP++
  gi|330509100|ref|YP_004385528.1| 159 GNALLNLGKWDEARDAYNEAIEVDPQD 185
                                       9************************98 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.1
                            TPR_11   8 GkyeeAieaYkkAlkldPdn 27 
                                       G+++e++eaY + ++l P n
  gi|330509100|ref|YP_004385528.1| 200 GDINESMEAYDRTIELIPAN 219
                                       99*************98887 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.096
                            TPR_11   6 eqGkyeeAieaYkkAlkldPd 26 
                                       + G++ eA+ea +  l++dP+
  gi|330509100|ref|YP_004385528.1| 238 AGGRWAEALEAINHSLEIDPE 258
                                       67*****************97 PP

  == domain 7  score: 20.0 bits;  conditional E-value: 9e-07
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       d++ ++G+ +eAiea+ + l+ +P++ae +++ ++++ +
  gi|330509100|ref|YP_004385528.1| 268 DILSQLGRKDEAIEAFDEVLNQNPEDAESWLWKANLLVE 306
                                       78899***************************9998866 PP

  == domain 8  score: 14.4 bits;  conditional E-value: 4.9e-05
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkl 23 
                                       ++++e  +y+e++eaY kA++l
  gi|330509100|ref|YP_004385528.1| 302 NLLVEMKRYNESVEAYDKAIEL 323
                                       8899*****************8 PP

  == domain 9  score: 1.0 bits;  conditional E-value: 0.74
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkl 23 
                                       a+ + G+ +eA +a++k l++
  gi|330509100|ref|YP_004385528.1| 342 ALNKTGRTDEAQAAFQKSLEF 362
                                       67789**********999885 PP

  == domain 10  score: 20.4 bits;  conditional E-value: 6.5e-07
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlk 22 
                                       G +++e+G+y+eAieaY + lk
  gi|330509100|ref|YP_004385528.1| 381 GLVLFELGRYDEAIEAYDQVLK 402
                                       889****************987 PP

  == domain 11  score: 37.1 bits;  conditional E-value: 3.9e-12
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       Gd ++ qGk+eeA+eaY+kA++l P + +a++++G+a+ ++G
  gi|330509100|ref|YP_004385528.1| 421 GDSLRLQGKNEEALEAYNKAIDLGPHYSNAWHGRGEAQKAMG 462
                                       99************************************9998 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0094       4.3       4      40 ..      39      75 ..      37      81 .. 0.87
   2 !   14.2   0.0   0.00013     0.059       8      42 ..      84     118 ..      76     120 .. 0.87
   3 ?    4.6   0.0      0.16        72      14      41 ..     131     158 ..     124     161 .. 0.85
   4 !   25.6   0.2   2.8e-08   1.3e-05       2      43 ..     153     194 ..     152     195 .. 0.93
   5 !   13.1   0.0    0.0003      0.14       4      43 ..     228     268 ..     225     269 .. 0.86
   6 !   19.7   0.1   2.3e-06     0.001       7      42 ..     266     301 ..     263     303 .. 0.89
   7 ?    5.2   0.1       0.1        47       2      30 ..     295     323 ..     294     337 .. 0.83
   8 ?    8.0   0.0     0.013       5.8       4      31 ..     336     363 ..     333     369 .. 0.88
   9 !   14.5   0.0   0.00011     0.049       3      29 ..     376     402 ..     374     413 .. 0.89
  10 !   14.1   0.0   0.00014     0.063       3      42 ..     416     455 ..     414     457 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0094
                            TPR_14  4 llalaeallalGdpdeAiallrralalaPddaeawll 40
                                      +++ ae ++ +  ++e i  l++al+++P++++++++
  gi|330509100|ref|YP_004385528.1| 39 WMDKAEEFAYNSSFEEVISSLDEALKTDPGNETILIR 75
                                      7788888888999******************999875 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00013
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +++ + ++ +++A+ +l+++l ++Pddaeaw   a
  gi|330509100|ref|YP_004385528.1|  84 GKVNESSQTYEKALSILDEILLKDPDDAEAWQKKA 118
                                       5677888999*********************9877 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.16
                            TPR_14  14 lGdpdeAiallrralalaPddaeawlll 41 
                                       l  ++e +++++r+++++ +d +aw+  
  gi|330509100|ref|YP_004385528.1| 131 LAAYEETLEAFNRRIEKDSKDIDAWIGK 158
                                       56789999*****************865 PP

  == domain 4  score: 25.6 bits;  conditional E-value: 2.8e-08
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +a+   + all+lG++deA++++++a++ +P+d  aw + a+
  gi|330509100|ref|YP_004385528.1| 153 DAWIGKGNALLNLGKWDEARDAYNEAIEVDPQDYHAWGRKAE 194
                                       57888899******************************9997 PP

  == domain 5  score: 13.1 bits;  conditional E-value: 0.0003
                            TPR_14   4 llalaeall.alGdpdeAiallrralalaPddaeawlllaq 43 
                                       ++  ae+l+ a G+++eA+++ +  l+ +P++++ w++ a+
  gi|330509100|ref|YP_004385528.1| 228 WMSKAEVLAiAGGRWAEALEAINHSLEIDPESRVNWRFKAD 268
                                       7777999862678***********************99987 PP

  == domain 6  score: 19.7 bits;  conditional E-value: 2.3e-06
                            TPR_14   7 laeallalGdpdeAiallrralalaPddaeawllla 42 
                                        a++l +lG+ deAi++++++l ++P+dae wl  a
  gi|330509100|ref|YP_004385528.1| 266 KADILSQLGRKDEAIEAFDEVLNQNPEDAESWLWKA 301
                                       5899**************************998776 PP

  == domain 7  score: 5.2 bits;  conditional E-value: 0.1
                            TPR_14   2 eallalaeallalGdpdeAiallrralal 30 
                                       e +l  a +l +  ++ e+++++++a++l
  gi|330509100|ref|YP_004385528.1| 295 ESWLWKANLLVEMKRYNESVEAYDKAIEL 323
                                       789999********************995 PP

  == domain 8  score: 8.0 bits;  conditional E-value: 0.013
                            TPR_14   4 llalaeallalGdpdeAiallrralala 31 
                                       +l  ++al   G++deA a++++ l+ +
  gi|330509100|ref|YP_004385528.1| 336 WLSKGWALNKTGRTDEAQAAFQKSLEFY 363
                                       778899*****************99876 PP

  == domain 9  score: 14.5 bits;  conditional E-value: 0.00011
                            TPR_14   3 allalaeallalGdpdeAiallrrala 29 
                                       +l++ + +l++lG++deAi++++++l+
  gi|330509100|ref|YP_004385528.1| 376 LLQQKGLVLFELGRYDEAIEAYDQVLK 402
                                       7888999*****************998 PP

  == domain 10  score: 14.1 bits;  conditional E-value: 0.00014
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       a+   ++ l+ +G+ +eA++++++a++l+P    aw   +
  gi|330509100|ref|YP_004385528.1| 416 AWIGKGDSLRLQGKNEEALEAYNKAIDLGPHYSNAWHGRG 455
                                       66667788999**********************9998766 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   2.7e-06    0.0012      15      75 ..      82     141 ..      70     143 .. 0.88
   2 !   16.2   0.0   2.1e-05    0.0095       5      60 ..     154     208 ..     150     211 .. 0.77
   3 !   11.8   0.1    0.0005      0.23       5      76 ..     188     257 ..     184     258 .. 0.89
   4 !   14.4   0.1   7.7e-05     0.035      16      73 ..     239     288 ..     232     292 .. 0.87
   5 !   36.8   0.5   7.6e-12   3.5e-09       4      76 ..     295     364 ..     292     365 .. 0.91
   6 !   38.8   0.1   1.8e-12   8.2e-10       8      74 ..     379     443 ..     373     445 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.7e-06
                            TPR_12  15 rlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                         g+  e+ + +ekal i  ++l  + p+ a++ +  + ++  l+r+ e l+++ee+l+++
  gi|330509100|ref|YP_004385528.1|  82 IVGKVNESSQTYEKALSILDEILL-KDPDDAEAWQKKASVLGSLNRQNESLAAYEETLEAF 141
                                       568889999**********99986.579******************************987 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.1e-05
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgr 60 
                                       a+   +++l+ lg++deA++ +++a+e+  + +  + +   a++   +g++ + ++ 
  gi|330509100|ref|YP_004385528.1| 154 AWIGKGNALLNLGKWDEARDAYNEAIEVDpQDY--HAWGRKAEVIGRIGDINESMEA 208
                                       6778899*******************9987777..5566677777777776666655 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.0005
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyr.algryeeAlelleealaiae 76 
                                       a+ + a+v  r g+  e+ e +++ +e++   +  +  + a +    ++++  a gr++eAle+ +++l+i++
  gi|330509100|ref|YP_004385528.1| 188 AWGRKAEVIGRIGDINESMEAYDRTIELI---PANNTREQADYWMSKAEVLAiAGGRWAEALEAINHSLEIDP 257
                                       67789999999******************...66888899**********97477***************976 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 7.7e-05
                            TPR_12  16 lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                        gr++eAle  +++lei      p++       r  ++++++lgr +eA+e++ e+l+
  gi|330509100|ref|YP_004385528.1| 239 GGRWAEALEAINHSLEID-----PES---RVNWRFKADILSQLGRKDEAIEAFDEVLN 288
                                       699***************.....876...6788999*******************997 PP

  == domain 5  score: 36.8 bits;  conditional E-value: 7.6e-12
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        ++   a++l +++ry e+ e ++ka+e++ +    +++++a      g+++ ++gr++eA+++++++l+ +e
  gi|330509100|ref|YP_004385528.1| 295 ESWLWKANLLVEMKRYNESVEAYDKAIELIAE---NNSEDLALDWLSKGWALNKTGRTDEAQAAFQKSLEFYE 364
                                       566679************************44...67888******************************998 PP

  == domain 6  score: 38.8 bits;  conditional E-value: 1.8e-12
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       + ++vl++lgrydeA+e ++++l    +l  +    ++++ ++ g+ +r++g+ eeAle++++a+++
  gi|330509100|ref|YP_004385528.1| 379 QKGLVLFELGRYDEAIEAYDQVLKNSLSL--EFDTTAVSAWIGKGDSLRLQGKNEEALEAYNKAIDL 443
                                       689***********************999..66667****************************986 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1     0.013       5.9      13      63 ..      93     140 ..      89     144 .. 0.90
   2 !   24.3   0.6   7.8e-08   3.6e-05      14      67 ..     135     185 ..     131     186 .. 0.92
   3 !   26.2   0.0     2e-08     9e-06       3      65 ..     158     217 ..     156     220 .. 0.90
   4 !   11.2   0.0   0.00097      0.44      14      65 ..     203     257 ..     197     259 .. 0.76
   5 !   28.3   0.0   4.5e-09   2.1e-06       4      62 ..     267     322 ..     266     328 .. 0.94
   6 ?    5.1   0.1     0.078        36      37      64 ..     336     363 ..     322     367 .. 0.83
   7 !   38.5   0.0   2.8e-12   1.3e-09       3      67 ..     380     447 ..     379     448 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.013
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       y++A+  l++ l +d   Pd+aeA+  ++ ++  ++r  e +a+y++ l+a
  gi|330509100|ref|YP_004385528.1|  93 YEKALSILDEILLKD---PDDAEAWQKKASVLGSLNRQNESLAAYEETLEA 140
                                       999************...*******99999999999999999999987765 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 7.8e-08
                            TPR_16  14 ddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++ ++a+++ +++d   + + +A+ ++g+a+l +g ++eA+++y++a++ +p++
  gi|330509100|ref|YP_004385528.1| 135 EETLEAFNRRIEKD---SKDIDAWIGKGNALLNLGKWDEARDAYNEAIEVDPQD 185
                                       55579999999999...88999******************************97 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 2e-08
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +++a+l++g++d+A+ a+++a++ d   P++++A+  ++++  r g+  e  ++y++ ++  p
  gi|330509100|ref|YP_004385528.1| 158 KGNALLNLGKWDEARDAYNEAIEVD---PQDYHAWGRKAEVIGRIGDINESMEAYDRTIELIP 217
                                       799**********************...*************9999999999988888766555 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00097
                            TPR_16  14 ddAaaaleaalkrdpssPd.....aaeAllllgdaal.rqgrlaeAaalyraalraap 65 
                                        +  +a+++++++    P+      a+ ++ ++++++ + gr+aeA+++++  l+ +p
  gi|330509100|ref|YP_004385528.1| 203 NESMEAYDRTIELI---PAnntreQADYWMSKAEVLAiAGGRWAEALEAINHSLEIDP 257
                                       55556666666665...55555559************888*******99998888877 PP

  == domain 5  score: 28.3 bits;  conditional E-value: 4.5e-09
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       a+++ ++g+ d+A++a++++l ++   P++ae++l++++++ + +r+ e +++y++a++
  gi|330509100|ref|YP_004385528.1| 267 ADILSQLGRKDEAIEAFDEVLNQN---PEDAESWLWKANLLVEMKRYNESVEAYDKAIE 322
                                       89999*******************...****************************9985 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.078
                            TPR_16  37 llllgdaalrqgrlaeAaalyraalraa 64 
                                       +l +g+a+ + gr +eA a++++ l+ +
  gi|330509100|ref|YP_004385528.1| 336 WLSKGWALNKTGRTDEAQAAFQKSLEFY 363
                                       7888999999999999999998887665 PP

  == domain 7  score: 38.5 bits;  conditional E-value: 2.8e-12
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +++ ++++g+yd+A++a++++lk+  s  +   a+ A+ ++gd++  qg  +eA+++y++a++ +p +
  gi|330509100|ref|YP_004385528.1| 380 KGLVLFELGRYDEAIEAYDQVLKNSLSLEFdttAVSAWIGKGDSLRLQGKNEEALEAYNKAIDLGPHY 447
                                       5889*********************66666*********************************99975 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00039      0.18       4      30 ..     102     128 ..      92     132 .. 0.82
   2 !   16.6   0.0   1.6e-05    0.0075       2      33 ..     141     172 ..     140     173 .. 0.92
   3 !   11.1   0.0   0.00089      0.41       1      29 [.     174     202 ..     174     209 .. 0.84
   4 ?    3.0   0.0      0.36   1.6e+02       2      33 ..     209     246 ..     208     247 .. 0.81
   5 ?    3.7   0.0      0.22     1e+02       4      34 .]     251     281 ..     248     281 .. 0.87
   6 !   14.1   0.0    0.0001     0.046       2      31 ..     283     312 ..     282     315 .. 0.87
   7 ?    5.9   0.1     0.042        19       2      33 ..     317     353 ..     316     354 .. 0.78
   8 !   11.9   0.0    0.0005      0.23       1      34 []     362     395 ..     362     395 .. 0.97
   9 ?    2.4   0.0      0.57   2.6e+02       5      34 .]     406     435 ..     406     435 .. 0.91
  10 !   12.9   0.0   0.00024      0.11       1      31 [.     436     466 ..     436     469 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00039
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlm 30 
                                       + l +dP++a+a++ +A +l ++++  
  gi|330509100|ref|YP_004385528.1| 102 EILLKDPDDAEAWQKKASVLGSLNRQN 128
                                       55778***************9887655 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.6e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + + +e+d ++ da+  ++++ll++G++++Ar
  gi|330509100|ref|YP_004385528.1| 141 FNRRIEKDSKDIDAWIGKGNALLNLGKWDEAR 172
                                       56669**************************8 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00089
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdl 29 
                                       +y +a+e dP +  a+  +Ae+  ++Gd 
  gi|330509100|ref|YP_004385528.1| 174 AYNEAIEVDPQDYHAWGRKAEVIGRIGDI 202
                                       599******************99977763 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.36
                            TPR_17   2 ylkaleldPnn.....adaynnLAelllknG.dlmtAr 33 
                                       y + +el P n     ad +  +Ae+l+ +G ++++A+
  gi|330509100|ref|YP_004385528.1| 209 YDRTIELIPANntreqADYWMSKAEVLAIAGgRWAEAL 246
                                       7788888888778888************9973688886 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.22
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtArq 34 
                                        +le+dP + + +  +A +l+++G++++A++
  gi|330509100|ref|YP_004385528.1| 251 HSLEIDPESRVNWRFKADILSQLGRKDEAIE 281
                                       6889999999999999************986 PP

  == domain 6  score: 14.1 bits;  conditional E-value: 0.0001
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmt 31 
                                       + ++l ++P +a+++  +A+ll + +++ +
  gi|330509100|ref|YP_004385528.1| 283 FDEVLNQNPEDAESWLWKANLLVEMKRYNE 312
                                       7899******************98888766 PP

  == domain 7  score: 5.9 bits;  conditional E-value: 0.042
                            TPR_17   2 ylkalel..dPnn....adaynnLAelllknGdlmtAr 33 
                                       y ka+el  + nn    a  +  ++++l k G++++A+
  gi|330509100|ref|YP_004385528.1| 317 YDKAIELiaE-NNsedlALDWLSKGWALNKTGRTDEAQ 353
                                       7788888631.224557999*****************9 PP

  == domain 8  score: 11.9 bits;  conditional E-value: 0.0005
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y+ a+  +  n  ++++++ +l ++G++++A++
  gi|330509100|ref|YP_004385528.1| 362 FYETAISGNTGNIRLLQQKGLVLFELGRYDEAIE 395
                                       6*******************************86 PP

  == domain 9  score: 2.4 bits;  conditional E-value: 0.57
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmtArq 34 
                                       +le d + + a+  ++  l+ +G+ ++A++
  gi|330509100|ref|YP_004385528.1| 406 SLEFDTTAVSAWIGKGDSLRLQGKNEEALE 435
                                       5899999999*****************985 PP

  == domain 10  score: 12.9 bits;  conditional E-value: 0.00024
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                       +y ka++l P +++a++ ++e+++  G+ + 
  gi|330509100|ref|YP_004385528.1| 436 AYNKAIDLGPHYSNAWHGRGEAQKAMGQVGN 466
                                       59**********************9999765 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.3e-05    0.0061       7      66 ..      52     118 ..      46     120 .. 0.79
   2 !   22.3   0.1     3e-07   0.00014       7      62 ..     134     187 ..     127     195 .. 0.88
   3 !   27.8   0.0   5.8e-09   2.7e-06       2      66 ..     237     301 ..     236     303 .. 0.89
   4 !   23.0   0.3   1.8e-07   8.3e-05       8      53 ..     277     322 ..     277     332 .. 0.93
   5 !    9.5   0.2     0.003       1.4       1      52 [.     304     360 ..     304     365 .. 0.86
   6 !   17.8   0.1   7.6e-06    0.0035       5      53 ..     347     402 ..     343     405 .. 0.78
   7 !   16.7   0.2   1.7e-05    0.0076       3      41 ..     426     464 ..     424     467 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.3e-05
                            TPR_19   7 yaeAlalleqalqedpknaearl...lL....AeallalgqldeAealLdalpeedpddaryasLlA 66 
                                       ++e ++ l +al+ dp+n+ +++   l+     ++  ++  +++A  +Ld+++++dpdda++++ +A
  gi|330509100|ref|YP_004385528.1|  52 FEEVISSLDEALKTDPGNETILIreaLYlgivGKVNESSQTYEKALSILDEILLKDPDDAEAWQKKA 118
                                       66677778888888888766666554114668888889999******************99999888 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 3e-07
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       y+e l+++ + +++d k+ +a+++  +all+lg +deA+++ +++ e dp+d  y+
  gi|330509100|ref|YP_004385528.1| 134 YEETLEAFNRRIEKDSKDIDAWIGKGNALLNLGKWDEARDAYNEAIEVDPQD--YH 187
                                       66777888887899************************************95..44 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 5.8e-09
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66 
                                       +a g+ aeAl++    l+ dp++   +   A++l +lg+ deA+++ d++++++p da+ +  +A
  gi|330509100|ref|YP_004385528.1| 237 IAGGRWAEALEAINHSLEIDPESRVNWRFKADILSQLGRKDEAIEAFDEVLNQNPEDAESWLWKA 301
                                       67799*****************88888889**************************998776555 PP

  == domain 4  score: 23.0 bits;  conditional E-value: 1.8e-07
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       +eA++++ ++l ++p++ae +l+ A++l+++++++e  ++ d++ e
  gi|330509100|ref|YP_004385528.1| 277 DEAIEAFDEVLNQNPEDAESWLWKANLLVEMKRYNESVEAYDKAIE 322
                                       79***********************************999988765 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.003
                            TPR_19   1 llaegdyaeAlalleqalqe..dpknaearl.lL..AeallalgqldeAealLdalp 52 
                                       l+++++y e ++++ +a++   ++++++++l +L    al ++g++deA+a+ ++ +
  gi|330509100|ref|YP_004385528.1| 304 LVEMKRYNESVEAYDKAIELiaENNSEDLALdWLskGWALNKTGRTDEAQAAFQKSL 360
                                       689999**********99886677788888866689***************998866 PP

  == domain 6  score: 17.8 bits;  conditional E-value: 7.6e-06
                            TPR_19   5 gdyaeA.......lalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       g+ +eA       l+++e a++ + +n +++ +   +l++lg++deA+++ d++++
  gi|330509100|ref|YP_004385528.1| 347 GRTDEAqaafqksLEFYETAISGNTGNIRLLQQKGLVLFELGRYDEAIEAYDQVLK 402
                                       5566662233333666666888899999999999******************9986 PP

  == domain 7  score: 16.7 bits;  conditional E-value: 1.7e-05
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgql 41 
                                        +g+ +eAl+++ +a++  p++++a+ +  ea+ a+gq+
  gi|330509100|ref|YP_004385528.1| 426 LQGKNEEALEAYNKAIDLGPHYSNAWHGRGEAQKAMGQV 464
                                       699**********************************97 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   4.8e-05     0.022       8      54 ..      90     136 ..      87     140 .. 0.89
   2 !   18.9   0.1   2.8e-06    0.0013      11      63 ..     134     186 ..     130     196 .. 0.94
   3 !   10.3   0.1    0.0013      0.58      10      68 ..     167     225 ..     167     226 .. 0.95
   4 !   28.2   0.1   3.5e-09   1.6e-06       4      64 ..     235     295 ..     232     303 .. 0.93
   5 ?    5.6   0.0     0.039        18      24      58 ..     289     323 ..     284     333 .. 0.88
   6 ?    1.1   0.0      0.97   4.5e+02      18      58 ..     321     362 ..     309     368 .. 0.76
   7 !   10.2   0.1    0.0014      0.66      14      57 ..     359     402 ..     351     408 .. 0.80
   8 ?    5.5   0.0     0.042        20       9      48 ..     428     467 ..     424     471 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.8e-05
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLea 54 
                                       ++ +e+al +++ +ll +Pdd+e +   + +l  l++ ++ la+ e 
  gi|330509100|ref|YP_004385528.1|  90 SQTYEKALSILDEILLKDPDDAEAWQKKASVLGSLNRQNESLAAYEE 136
                                       6789****************************999999888888775 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.8e-06
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       +e++l++ +r++  +++d++ +   G +l  lG + +A+++ + +++++p++ 
  gi|330509100|ref|YP_004385528.1| 134 YEETLEAFNRRIEKDSKDIDAWIGKGNALLNLGKWDEARDAYNEAIEVDPQDY 186
                                       7899**********************************************985 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0013
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeai 68 
                                       +w++a  +++  + ++P+d + +   + +  + G++++ +++ ++ ++l p++ ++e++
  gi|330509100|ref|YP_004385528.1| 167 KWDEARDAYNEAIEVDPQDYHAWGRKAEVIGRIGDINESMEAYDRTIELIPANNTREQA 225
                                       5999***********************************************99999875 PP

  == domain 4  score: 28.2 bits;  conditional E-value: 3.5e-09
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       +ai   +w++al++++  l ++P++   +r  + +l qlG+  +A+++++  l ++p++++
  gi|330509100|ref|YP_004385528.1| 235 LAIAGGRWAEALEAINHSLEIDPESRVNWRFKADILSQLGRKDEAIEAFDEVLNQNPEDAE 295
                                       5788899**************************************************9976 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.039
                             TPR_9  24 laPddpeerrdRGlllaqlGclsaAladLeaylal 58 
                                        +P+d+e ++  + ll+++ ++++ +++ + +++l
  gi|330509100|ref|YP_004385528.1| 289 QNPEDAESWLWKANLLVEMKRYNESVEAYDKAIEL 323
                                       58**************************9999965 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.97
                             TPR_9  18 verllllaPdd.peerrdRGlllaqlGclsaAladLeaylal 58 
                                       +e++   +++d + +++  G +l + G++ +A a+++  l+ 
  gi|330509100|ref|YP_004385528.1| 321 IELIAENNSEDlALDWLSKGWALNKTGRTDEAQAAFQKSLEF 362
                                       5555555555426789*******************9987765 PP

  == domain 7  score: 10.2 bits;  conditional E-value: 0.0014
                             TPR_9  14 alavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57 
                                        l+ +e  +  +   ++++   Gl+l++lG++ +A+++ ++ l 
  gi|330509100|ref|YP_004385528.1| 359 SLEFYETAISGNTGNIRLLQQKGLVLFELGRYDEAIEAYDQVLK 402
                                       55666666666667789999*****************9998775 PP

  == domain 8  score: 5.5 bits;  conditional E-value: 0.042
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaA 48 
                                        ++e+al++++  + l P+    +  RG ++  +G++  A
  gi|330509100|ref|YP_004385528.1| 428 GKNEEALEAYNKAIDLGPHYSNAWHGRGEAQKAMGQVGNA 467
                                       6799******************************998766 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       1.3     6e+02      15      32 ..      92     109 ..      82     110 .. 0.84
   2 !   11.7   0.0    0.0007      0.32       6      32 ..     158     184 ..     153     185 .. 0.85
   3 ?   -0.8   0.0       6.7   3.1e+03      14      28 ..     200     214 ..     191     215 .. 0.82
   4 ?    0.9   0.0         2   9.1e+02      12      23 ..     235     249 ..     224     259 .. 0.67
   5 !   11.5   0.0   0.00084      0.39      10      32 ..     270     292 ..     266     293 .. 0.86
   6 ?    5.5   0.0     0.066        30       2      28 ..     296     322 ..     295     323 .. 0.90
   7 ?    7.9   0.1     0.012       5.5       7      25 ..     340     358 ..     337     363 .. 0.89
   8 !   14.9   0.1   6.7e-05     0.031       7      29 ..     381     403 ..     377     404 .. 0.91
   9 !    8.8   0.0    0.0061       2.8       7      28 ..     421     442 ..     416     443 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHH-TT CS
                             TPR_6  15 dtdkAlealerlikeYPd 32 
                                        ++kAl +l++++ + Pd
  gi|330509100|ref|YP_004385528.1|  92 TYEKALSILDEILLKDPD 109
                                       589*********999998 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0007
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                        + ++++lg++d+A++a+++ i+  P+
  gi|330509100|ref|YP_004385528.1| 158 KGNALLNLGKWDEARDAYNEAIEVDPQ 184
                                       588999999************998775 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 6.7
                                       HHHHHHHHHHHHHHH CS
                             TPR_6  14 gdtdkAlealerlik 28 
                                       gd  +++ea++r i+
  gi|330509100|ref|YP_004385528.1| 200 GDINESMEAYDRTIE 214
                                       799999****99875 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 2
                                       HH...HHHHHHHHHH CS
                             TPR_6  12 kl...gdtdkAleal 23 
                                        +   g++++Alea 
  gi|330509100|ref|YP_004385528.1| 235 LAiagGRWAEALEAI 249
                                       434449******985 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00084
                                       HHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  10 yrklgdtdkAlealerlikeYPd 32 
                                       + +lg++d+A+ea+++++++ P+
  gi|330509100|ref|YP_004385528.1| 270 LSQLGRKDEAIEAFDEVLNQNPE 292
                                       55689***************996 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.066
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                       + ++ a ++ +++++ +++ea+++ i+
  gi|330509100|ref|YP_004385528.1| 296 SWLWKANLLVEMKRYNESVEAYDKAIE 322
                                       678999999**9************997 PP

  == domain 7  score: 7.9 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealer 25 
                                       ++++ k+g+td+A +a+++
  gi|330509100|ref|YP_004385528.1| 340 GWALNKTGRTDEAQAAFQK 358
                                       89999999**********8 PP

  == domain 8  score: 14.9 bits;  conditional E-value: 6.7e-05
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlike 29 
                                       +l +++lg++d+A+ea+++++k+
  gi|330509100|ref|YP_004385528.1| 381 GLVLFELGRYDEAIEAYDQVLKN 403
                                       8999**99*************97 PP

  == domain 9  score: 8.8 bits;  conditional E-value: 0.0061
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       + s+r +g+ ++Alea+++ i+
  gi|330509100|ref|YP_004385528.1| 421 GDSLRLQGKNEEALEAYNKAID 442
                                       7899999************997 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.54   2.5e+02      11      37 ..      79     105 ..      77     110 .. 0.78
   2 ?   -0.0   0.0         2     9e+02      16      28 ..     106     118 ..     104     119 .. 0.88
   3 ?    5.6   0.1     0.034        16       9      31 ..     118     140 ..     117     149 .. 0.84
   4 !   11.1   0.1   0.00061      0.28       9      30 ..     159     180 ..     158     181 .. 0.95
   5 ?   -1.6   0.0       5.9   2.7e+03      16      30 ..     240     254 ..     238     255 .. 0.76
   6 !    7.6   0.0    0.0076       3.5      11      30 ..     269     288 ..     267     288 .. 0.90
   7 !    8.1   0.1    0.0055       2.5       9      31 ..     301     323 ..     298     327 .. 0.92
   8 !   11.1   0.0   0.00064      0.29       9      35 ..     340     366 ..     339     370 .. 0.93
   9 !   10.0   0.1    0.0013      0.61       9      29 ..     381     401 ..     377     402 .. 0.92
  10 ?    3.8   0.1      0.12        57      12      30 ..     424     442 ..     421     443 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.54
                            TPR_10  11 alrqrgrydeAealleealairrrllG 37 
                                       +l  +g+ +e+ + +e+al+i  ++l 
  gi|330509100|ref|YP_004385528.1|  79 YLGIVGKVNESSQTYEKALSILDEILL 105
                                       66778999999999******9888775 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2
                            TPR_10  16 grydeAealleea 28 
                                       ++ d+Aea++++a
  gi|330509100|ref|YP_004385528.1| 106 KDPDDAEAWQKKA 118
                                       689******9997 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.034
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       a +l +++r +e++a +ee+l++
  gi|330509100|ref|YP_004385528.1| 118 ASVLGSLNRQNESLAAYEETLEA 140
                                       6688999*************997 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00061
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       +nal ++g++deA++ + ea++
  gi|330509100|ref|YP_004385528.1| 159 GNALLNLGKWDEARDAYNEAIE 180
                                       89******************98 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 5.9
                            TPR_10  16 grydeAealleeala 30 
                                       gr++eA++   ++l+
  gi|330509100|ref|YP_004385528.1| 240 GRWAEALEAINHSLE 254
                                       8999*9987666665 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.0076
                            TPR_10  11 alrqrgrydeAealleeala 30 
                                       +l+q+gr deA + ++e+l+
  gi|330509100|ref|YP_004385528.1| 269 ILSQLGRKDEAIEAFDEVLN 288
                                       79***************985 PP

  == domain 7  score: 8.1 bits;  conditional E-value: 0.0055
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       an+l +++ry+e+++ +++a+++
  gi|330509100|ref|YP_004385528.1| 301 ANLLVEMKRYNESVEAYDKAIEL 323
                                       89999****************97 PP

  == domain 8  score: 11.1 bits;  conditional E-value: 0.00064
                            TPR_10   9 analrqrgrydeAealleealairrrl 35 
                                       + al ++gr deA a ++++l+ ++ +
  gi|330509100|ref|YP_004385528.1| 340 GWALNKTGRTDEAQAAFQKSLEFYETA 366
                                       78999*******************976 PP

  == domain 9  score: 10.0 bits;  conditional E-value: 0.0013
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       + +l+++grydeA + ++++l
  gi|330509100|ref|YP_004385528.1| 381 GLVLFELGRYDEAIEAYDQVL 401
                                       789***************998 PP

  == domain 10  score: 3.8 bits;  conditional E-value: 0.12
                            TPR_10  12 lrqrgrydeAealleeala 30 
                                       lr +g+ +eA++ + +a++
  gi|330509100|ref|YP_004385528.1| 424 LRLQGKNEEALEAYNKAID 442
                                       788***********99986 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.7e-05    0.0077       5      81 ..      93     177 ..      89     178 .. 0.76
   2 !   14.3   0.0   7.8e-05     0.036      18      81 ..     218     285 ..     201     286 .. 0.82
   3 !   18.8   0.0     3e-06    0.0014       5      81 ..     242     319 ..     239     320 .. 0.87
   4 !    8.5   0.1     0.005       2.3      15      49 ..     286     320 ..     283     359 .. 0.58
   5 !   10.1   0.0    0.0016      0.72      39      80 ..     356     398 ..     352     400 .. 0.73
   6 ?    0.4   0.0       1.7     8e+02      31      51 ..     422     443 ..     412     452 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-.......HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HH CS
                            ANAPC3   5 yknAiflaerllaaetespedayllAlclylngq.......ykrAyellrka.klnskslgcrylfAqcllkLkkye 73 
                                       y++A+ +++ +l ++++++e+   +A +l ++++       y++ +e +++  +++sk++ +++ ++ +ll L+k++
  gi|330509100|ref|YP_004385528.1|  93 YEKALSILDEILLKDPDDAEAWQKKASVLGSLNRqneslaaYEETLEAFNRRiEKDSKDIDAWIGKGNALLNLGKWD 169
                                       66777777776655566666655555555444444445777************************************ PP

                                       HHHHHH-S CS
                            ANAPC3  74 eAiaaLek 81 
                                       eA++a+ +
  gi|330509100|ref|YP_004385528.1| 170 EARDAYNE 177
                                       ****9876 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.8e-05
                                       HHH--HHHHHHH..HHHHHHT.T-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  18 aetespedayll..Alclyln.gqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       a++ ++++ y+   A++l  + g++ +A+e ++ + +++++s   +  +A  l +L++ +eAi a+++
  gi|330509100|ref|YP_004385528.1| 218 ANNTREQADYWMskAEVLAIAgGRWAEALEAINHSlEIDPESRVNWRFKADILSQLGRKDEAIEAFDE 285
                                       677777788885447777655167*****************************************987 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 3e-06
                                       HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       + +A+  ++  l+ ++es  +  ++A  l ++g+ ++A+e +++  ++n+++ ++++ +A  l+++k+y+e + a++
  gi|330509100|ref|YP_004385528.1| 242 WAEALEAINHSLEIDPESRVNWRFKADILSQLGRKDEAIEAFDEVlNQNPEDAESWLWKANLLVEMKRYNESVEAYD 318
                                       5566666666667777777777889**********************************************999988 PP

                                       S CS
                            ANAPC3  81 k 81 
                                       k
  gi|330509100|ref|YP_004385528.1| 319 K 319
                                       7 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.005
                                       HH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                            ANAPC3  15 llaaetespedayllAlclylngqykrAyellrka 49 
                                       +l++++e++e+ +++A  l ++++y++  e ++ka
  gi|330509100|ref|YP_004385528.1| 286 VLNQNPEDAESWLWKANLLVEMKRYNESVEAYDKA 320
                                       55567777777777788888877755544444444 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  39 ykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +++ +e++++a   n  +++ +  ++ +l++L++y+eAi a++
  gi|330509100|ref|YP_004385528.1| 356 FQKSLEFYETAiSGNTGNIRLLQQKGLVLFELGRYDEAIEAYD 398
                                       5555666677766677777777778899999999999999876 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1.7
                                       HHHHHTT-HHHHHHHHHCT.SH CS
                            ANAPC3  31 lclylngqykrAyellrka.kl 51 
                                        +l l+g+ ++A+e ++ka +l
  gi|330509100|ref|YP_004385528.1| 422 DSLRLQGKNEEALEAYNKAiDL 443
                                       6778888888888888888555 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.4   2.9e-08   1.3e-05      29     129 ..      90     181 ..      82     188 .. 0.84
   2 ?   -1.0   0.0       3.6   1.6e+03     105     131 ..     191     217 ..     186     227 .. 0.80
   3 ?    3.7   0.0      0.13        59     106     126 ..     266     286 ..     243     294 .. 0.88
   4 !   12.0   0.3   0.00037      0.17      62     129 ..     301     362 ..     293     373 .. 0.79
   5 ?    4.3   0.0     0.082        38     100     126 ..     374     400 ..     369     406 .. 0.77
   6 !    9.5   0.1    0.0022         1      65     128 ..     384     442 ..     378     446 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.9e-08
                                       HHHHHHHHHHHTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHH CS
                           DUF3856  29 aasyrkalevsrtipaeeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfs 105
                                       ++ y+kal +      +e +  +  da ++   ++ l  l r +e+l + +++l+ fnrr e ++ +   Wi     
  gi|330509100|ref|YP_004385528.1|  90 SQTYEKALSIL-----DEILLKDPDDAEAWQKKASVLGSLNRQNESLAAYEETLEAFNRRIEKDSKDIDAWI----G 157
                                       55555555443.....455556667888999999****************************9999988888....5 PP

                                       HHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 106 ravaleelGrkdealkafrmagem 129
                                       ++ al +lG+ dea +a++ a e+
  gi|330509100|ref|YP_004385528.1| 158 KGNALLNLGKWDEARDAYNEAIEV 181
                                       9******************99985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.6
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrmagemia 131
                                       ++a  +  +G  +e+++a+  + e+i 
  gi|330509100|ref|YP_004385528.1| 191 RKAEVIGRIGDINESMEAYDRTIELIP 217
                                       577788889999999999999999885 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.13
                                       HHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 106 ravaleelGrkdealkafrma 126
                                       +a  l++lGrkdea++af  +
  gi|330509100|ref|YP_004385528.1| 266 KADILSQLGRKDEAIEAFDEV 286
                                       678899**********99765 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00037
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  62 sealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                       ++ l++++ry+e++e+ dka++         +d    W    +s++ al+++Gr+dea  af+++ e 
  gi|330509100|ref|YP_004385528.1| 301 ANLLVEMKRYNESVEAYDKAIELIAEN--NSEDLALDW----LSKGWALNKTGRTDEAQAAFQKSLEF 362
                                       566789999999999999999887543..345555567....589******************99886 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.082
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 100 iaavfsravaleelGrkdealkafrma 126
                                       i+ + +++  l elGr+dea++a+ ++
  gi|330509100|ref|YP_004385528.1| 374 IRLLQQKGLVLFELGRYDEAIEAYDQV 400
                                       566677888888888888888888654 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.0022
                                       HHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  65 laklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       l +lgrydea+e+ d+ l+       l  +     ++a + ++ +l   G+++eal+a+++a +
  gi|330509100|ref|YP_004385528.1| 384 LFELGRYDEAIEAYDQVLKN-----SLSLEFDTTAVSAWIGKGDSLRLQGKNEEALEAYNKAID 442
                                       6789*************984.....33333334455666689******************9976 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       1.5     7e+02      15      35 ..      93     111 ..      88     112 .. 0.79
   2 ?   -1.4   0.0         7   3.2e+03       7      31 ..     119     144 ..     116     149 .. 0.73
   3 !   10.5   0.0    0.0011       0.5       6      34 ..     159     185 ..     154     187 .. 0.89
   4 ?   -0.3   0.0       3.1   1.4e+03      13      29 ..     240     256 ..     235     260 .. 0.83
   5 !   10.5   0.0    0.0011      0.51       6      35 ..     267     294 ..     264     295 .. 0.90
   6 ?    1.8   0.0      0.66     3e+02       6      28 ..     301     323 ..     300     331 .. 0.72
   7 ?    3.5   0.0      0.18        85       6      28 ..     340     362 ..     336     368 .. 0.79
   8 !   14.5   0.1   5.9e-05     0.027       6      31 ..     381     404 ..     376     410 .. 0.80
   9 ?    3.7   0.0      0.16        73       6      30 ..     421     443 ..     416     446 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.5
                             TPR_7  15 yeeAielyeqsLaltkdpeda 35 
                                       ye+A++++ +   l kdp+da
  gi|330509100|ref|YP_004385528.1|  93 YEKALSILDE--ILLKDPDDA 111
                                       8899999888..888888887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 7
                             TPR_7   7 rlysrlGdyeeAielyeqsL.altkd 31 
                                       ++  +l++  e +  ye+ L a+ ++
  gi|330509100|ref|YP_004385528.1| 119 SVLGSLNRQNESLAAYEETLeAFNRR 144
                                       55667888889999999988666655 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0011
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                       +++  +lG+++eA + y +  a++ dp+d
  gi|330509100|ref|YP_004385528.1| 159 GNALLNLGKWDEARDAYNE--AIEVDPQD 185
                                       8999***************..99999876 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 3.1
                             TPR_7  13 GdyeeAielyeqsLalt 29 
                                       G+++eA+e    sL+++
  gi|330509100|ref|YP_004385528.1| 240 GRWAEALEAINHSLEID 256
                                       99*****9988887776 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.0011
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       a++ s+lG+ +eAie + +  +l   peda
  gi|330509100|ref|YP_004385528.1| 267 ADILSQLGRKDEAIEAFDE--VLNQNPEDA 294
                                       89*****************..998888887 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.66
                             TPR_7   6 arlysrlGdyeeAielyeqsLal 28 
                                       a+l +++ +y e +e y ++++l
  gi|330509100|ref|YP_004385528.1| 301 ANLLVEMKRYNESVEAYDKAIEL 323
                                       67777888888888888885533 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.18
                             TPR_7   6 arlysrlGdyeeAielyeqsLal 28 
                                       + +  + G+++eA   +++sL++
  gi|330509100|ref|YP_004385528.1| 340 GWALNKTGRTDEAQAAFQKSLEF 362
                                       66677889999999999998876 PP

  == domain 8  score: 14.5 bits;  conditional E-value: 5.9e-05
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                       + + ++lG+y+eAie y q  +l ++
  gi|330509100|ref|YP_004385528.1| 381 GLVLFELGRYDEAIEAYDQ--VLKNS 404
                                       778899*************..65554 PP

  == domain 9  score: 3.7 bits;  conditional E-value: 0.16
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltk 30 
                                       ++  + +G+ eeA+e y +  a++ 
  gi|330509100|ref|YP_004385528.1| 421 GDSLRLQGKNEEALEAYNK--AIDL 443
                                       5667889**********99..7765 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2      0.96   4.4e+02     123     176 ..      87     141 ..      40     152 .. 0.79
   2 !   13.7   0.1   8.3e-05     0.038     152     178 ..     158     184 ..     146     197 .. 0.90
   3 !    9.7   0.0    0.0014      0.66     128     187 ..     241     308 ..     200     312 .. 0.79
   4 !   10.5   0.4   0.00076      0.35     127     176 ..     315     363 ..     309     381 .. 0.83
   5 ?    4.9   0.0     0.043        20     150     175 ..     378     403 ..     370     417 .. 0.87
   6 !   12.8   0.2   0.00015      0.07     122     175 ..     383     443 ..     383     450 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.96
                            TPR_21 123 llaekkydeAlktLeakk.eeafaalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                           + y++Al+ L++   ++  +a++ + +  +l + ++++e  aaY++ l+a 
  gi|330509100|ref|YP_004385528.1|  87 NESSQTYEKALSILDEILlKDPDDAEAWQKKASVLGSLNRQNESLAAYEETLEAF 141
                                       5556778888888877651444567777888888888888888888888888776 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.3e-05
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaalee 178
                                       +G++l++ gk deAr+aY++A++   +
  gi|330509100|ref|YP_004385528.1| 158 KGNALLNLGKWDEARDAYNEAIEVDPQ 184
                                       8********************987665 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0014
                            TPR_21 128 kydeAlktLeakkeeafaalva.elrGDilvaqgkldeAraaYqaAlaaleeka.......rellqlK 187
                                         +eAl++++++ e   +++v+   + Dil++ g++deA +a+++ l+++ e+a       + l+++K
  gi|330509100|ref|YP_004385528.1| 241 RWAEALEAINHSLEIDPESRVNwRFKADILSQLGRKDEAIEAFDEVLNQNPEDAeswlwkaNLLVEMK 308
                                       556666666666666666655534689**********************9999876776655566666 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.00076
                            TPR_21 127 kkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                       ++yd+A+++++++++e  a      +G +l ++g++deA+aa+q++l+  
  gi|330509100|ref|YP_004385528.1| 315 EAYDKAIELIAENNSEDLALDWL-SKGWALNKTGRTDEAQAAFQKSLEFY 363
                                       789*******9999999876665.7********************99855 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.043
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAlaa 175
                                       + +G +l++ g+ deA +aY++ l++
  gi|330509100|ref|YP_004385528.1| 378 QQKGLVLFELGRYDEAIEAYDQVLKN 403
                                       67999****************99876 PP

  == domain 6  score: 12.8 bits;  conditional E-value: 0.00015
                            TPR_21 122 vllaekkydeAlktLeakkeeafaalvael.......rGDilvaqgkldeAraaYqaAlaa 175
                                       vl++ + ydeA+++ +++ +++ + +++         +GD l  qgk++eA +aY++A++ 
  gi|330509100|ref|YP_004385528.1| 383 VLFELGRYDEAIEAYDQVLKNSLSLEFDTTavsawigKGDSLRLQGKNEEALEAYNKAIDL 443
                                       56777888888877666666655555444333334459********************985 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.9   1.4e+03     211     256 ..      21      66 ..      16      68 .. 0.81
   2 !    9.5   0.3   0.00088       0.4      13      66 ..      86     139 ..      77     146 .. 0.90
   3 !    8.8   0.0    0.0014      0.65     205     252 ..     165     212 ..     160     218 .. 0.90
   4 ?    2.1   0.0      0.15        70     207     260 ..     201     260 ..     196     264 .. 0.72
   5 !   16.4   0.4   7.1e-06    0.0033      18     106 ..     240     327 ..     222     346 .. 0.68
   6 !    7.8   0.1    0.0029       1.3      19      67 ..     355     403 ..     343     409 .. 0.82
   7 ?    0.9   0.0      0.36   1.7e+02     206     245 ..     428     467 ..     420     477 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 211 AleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       Al  + +++  + t +++++ Ka+ +     +++ ++ ++ea k D
  gi|330509100|ref|YP_004385528.1|  21 ALAALCACVTAQETTTDYWMDKAEEFAYNSSFEEVISSLDEALKTD 66 
                                       6667778999999999999999998888888888888888887666 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00088
                                       HHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1  13 iieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLle 66 
                                       + e ++++e+Al  L+e   +  D  +  ++ka++l  L+r++e+ a+ye+ le
  gi|330509100|ref|YP_004385528.1|  86 VNESSQTYEKALSILDEILLKDPDDAEAWQKKASVLGSLNRQNESLAAYEETLE 139
                                       56778899*****************************************99887 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0014
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                       lg+ ++A +  ++aie +p+    + +Ka+++ + Gd+++ +e+ +++
  gi|330509100|ref|YP_004385528.1| 165 LGKWDEARDAYNEAIEVDPQDYHAWGRKAEVIGRIGDINESMEAYDRT 212
                                       56778999999*******************************998875 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.15
                                       -SHHHHHHHHHHHHH-T.....T-HHHHHHHHHHHHHTT.-HHHHHHHHHHHHHCTTT-H CS
                             NARP1 207 srekAleyidkaiehtp.....tlvelyltKarilkhaG.dlkkAaevmeearklDlaDR 260
                                       + ++++e  d+ ie  p     +  ++++ Ka++l  aG    +A e+++++ ++D + R
  gi|330509100|ref|YP_004385528.1| 201 DINESMEAYDRTIELIPanntrEQADYWMSKAEVLAIAGgRWAEALEAINHSLEIDPESR 260
                                       5566666666666654411111679**********988626899*******999997766 PP

  == domain 5  score: 16.4 bits;  conditional E-value: 7.1e-06
                                       THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT...SSS-HHHHH CS
                             NARP1  18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekak.klskedeeall 93 
                                       g+  eAle ++++ +   +      +ka++l +Lgrk+eA +++ + l++npe+ + +  l ka+  ++ +  ++ +
  gi|330509100|ref|YP_004385528.1| 240 GRWAEALEAINHSLEIDPESRVNWRFKADILSQLGRKDEAIEAFDEVLNQNPEDAESW--LWKANlLVEMKRYNESV 314
                                       556677777766444333333334689*************************998755..44444234455567777 PP

                                       HHHHHTTTS-TT- CS
                             NARP1  94 alydelaekyprs 106
                                       ++yd++ e ++++
  gi|330509100|ref|YP_004385528.1| 315 EAYDKAIELIAEN 327
                                       8888777766554 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             NARP1  19 kleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLler 67 
                                         +++le  e++ +  + ++ ++++k+ +l++Lgr++eA ++y + l+ 
  gi|330509100|ref|YP_004385528.1| 355 AFQKSLEFYETAISGNTGNIRLLQQKGLVLFELGRYDEAIEAYDQVLKN 403
                                       456667777777777788999***********************99985 PP

  == domain 7  score: 0.9 bits;  conditional E-value: 0.36
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHH CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkA 245
                                       g+ e+Ale  +kai+  p   + +  +++  k +G++ +A
  gi|330509100|ref|YP_004385528.1| 428 GKNEEALEAYNKAIDLGPHYSNAWHGRGEAQKAMGQVGNA 467
                                       56789*****************999999999999999887 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.019       8.6      77     134 ..      51     108 ..      23     113 .. 0.80
   2 !    7.9   0.1    0.0084       3.9      78     125 ..      93     140 ..      89     150 .. 0.89
   3 !   11.6   0.0    0.0006      0.28      69     124 ..     159     214 ..     138     219 .. 0.89
   4 !    8.1   0.0    0.0071       3.3      73     122 ..     237     286 ..     229     293 .. 0.91
   5 ?   -0.2   0.1       2.6   1.2e+03     105     121 ..     342     358 ..     300     380 .. 0.68
   6 ?    3.9   0.0      0.15        69     105     132 ..     383     411 ..     373     417 .. 0.76
   7 ?    1.1   0.0         1   4.7e+02     107     122 ..     425     440 ..     421     445 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.019
                                       -HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS--- CS
                              BTAD  77 raeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvep 134
                                         ee+++ l+++++ +P +E+      + l  +G+ +e  ++Ye++ ++L+e L  +p
  gi|330509100|ref|YP_004385528.1|  51 SFEEVISSLDEALKTDPGNETILIREALYLGIVGKVNESSQTYEKALSILDEILLKDP 108
                                       6789*****************999888889999*************999999876666 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0084
                                       HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD  78 aeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                       +e+al+ l++++ ++P + +++++    l  ++rq+e L++Ye++ + 
  gi|330509100|ref|YP_004385528.1|  93 YEKALSILDEILLKDPDDAEAWQKKASVLGSLNRQNESLAAYEETLEA 140
                                       688999999**********************************98765 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.0006
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  69 aeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                        +a+l lG+++ea + ++++++ +P +  ++    +   r G+ +e +e+Y+r+ +
  gi|330509100|ref|YP_004385528.1| 159 GNALLNLGKWDEARDAYNEAIEVDPQDYHAWGRKAEVIGRIGDINESMEAYDRTIE 214
                                       5699************************************************9865 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0071
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       ++ Gr++eal+  +  ++ +P     +r     l ++Gr+ eA+e+++++
  gi|330509100|ref|YP_004385528.1| 237 IAGGRWAEALEAINHSLEIDPESRVNWRFKADILSQLGRKDEAIEAFDEV 286
                                       5679*******************************************987 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 2.6
                                       HHHHTT-HHHHHHHHHH CS
                              BTAD 105 AlarsGrqaeALevYer 121
                                       Al ++Gr+ eA +++++
  gi|330509100|ref|YP_004385528.1| 342 ALNKTGRTDEAQAAFQK 358
                                       55666666666666654 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.15
                                       HHHHTT-HHHHHHHHHHH.HHHHHHHHS- CS
                              BTAD 105 AlarsGrqaeALevYerl.rrlLaeeLgv 132
                                        l+ +Gr  eA+e+Y+++ +++L+ e+++
  gi|330509100|ref|YP_004385528.1| 383 VLFELGRYDEAIEAYDQVlKNSLSLEFDT 411
                                       68899**********88525667777766 PP

  == domain 7  score: 1.1 bits;  conditional E-value: 1
                                       HHTT-HHHHHHHHHHH CS
                              BTAD 107 arsGrqaeALevYerl 122
                                       + +G+++eALe+Y+++
  gi|330509100|ref|YP_004385528.1| 425 RLQGKNEEALEAYNKA 440
                                       5679999******987 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.9    0.0067       3.1      55     176 ..     111     247 ..      80     258 .. 0.60
   2 ?    5.8   0.1     0.018       8.2      84     183 ..     196     288 ..     166     292 .. 0.67
   3 !   27.6   0.5   3.8e-09   1.8e-06      69     187 ..     289     406 ..     275     418 .. 0.83
   4 ?   -0.2   0.0       1.2   5.4e+02     129     143 ..     428     442 ..     416     450 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0067
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT..-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT. CS
                              SNAP  55 geaflkaAecqeklkekdeaanayveAakcykkv..speeAvealekAieiytekgrfrraAklkkeiaelyekel. 128
                                       +ea++k A++  +l+ ++e+  ay e  +++++   + ++ ++a     + +++ g++++a + ++e  e+  ++  
  gi|330509100|ref|YP_004385528.1| 111 AEAWQKKASVLGSLNRQNESLAAYEETLEAFNRRieKDSKDIDAWIGKGNALLNLGKWDEARDAYNEAIEVDPQDYh 187
                                       45666666666666666666666666666666654344444555555566666666666666666666666666665 PP

                                       ............--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHH CS
                              SNAP 129 ............gdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAie 176
                                                   gd+++++eaY++  el   ++   +a   + k+  l+   +++++A+e
  gi|330509100|ref|YP_004385528.1| 188 awgrkaevigriGDINESMEAYDRTIELIPANNTREQADYWMSKAEVLAIAGGRWAEALE 247
                                       555555555555556666666666666666666666666655555555555556666655 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.018
                                       HHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              SNAP  84 cykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllk 160
                                       + +  +++e++ea++++ie+ + +++ r+ A++ ++ ae++  + g++ +A+ea ++  e+      +++    +  
  gi|330509100|ref|YP_004385528.1| 196 IGRIGDINESMEAYDRTIEL-IPANNTREQADYWMSKAEVLAIAGGRWAEALEAINHSLEIDP----ESRV--NWRF 265
                                       33444788899999999985.566778888899999999999988899999998888887522....2222..2344 PP

                                       HHHHHHHTT-HHHHHHHHHHHHH CS
                              SNAP 161 vAelsaelekyekAieiyekvak 183
                                        A++ ++l++ ++Aie++++v +
  gi|330509100|ref|YP_004385528.1| 266 KADILSQLGRKDEAIEAFDEVLN 288
                                       58888888888888888888865 PP

  == domain 3  score: 27.6 bits;  conditional E-value: 3.8e-09
                                       T-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHH CS
                              SNAP  69 kekdeaanayveAakcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaely 145
                                       +++++a + +++A   +++++ +e+vea++kAie+ +e+++ + a +   + +  ++k  g++++A +a++k  e+y
  gi|330509100|ref|YP_004385528.1| 289 QNPEDAESWLWKANLLVEMKRYNESVEAYDKAIELIAENNSEDLALDWLSK-GWALNKT-GRTDEAQAAFQKSLEFY 363
                                       5778899999*************************9999999998888776.4455555.8**************** PP

                                       HHTT-HHHHH.HHHHHHHHHHHHTT-HHHHHHHHHHHHHTTSS CS
                              SNAP 146 eqeeakalan.kcllkvAelsaelekyekAieiyekvakksle 187
                                       e+  +  + n  +l++   +  el++y++Aie+y++v k+sl+
  gi|330509100|ref|YP_004385528.1| 364 ETAISGNTGNiRLLQQKGLVLFELGRYDEAIEAYDQVLKNSLS 406
                                       ***9777766155555566699******************997 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.2
                                       --HHHHHHHHHHHHH CS
                              SNAP 129 gdlekAieaYekAae 143
                                       g+ e+A+eaY+kA +
  gi|330509100|ref|YP_004385528.1| 428 GKNEEALEAYNKAID 442
                                       334455555555544 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   7.9e-05     0.036      82     125 ..      90     133 ..      40     147 .. 0.92
   2 ?    0.9   0.0       1.2   5.6e+02      75     125 ..     158     208 ..     151     224 .. 0.83
   3 !   10.7   0.0    0.0012      0.55      81     124 ..     238     281 ..     225     292 .. 0.86
   4 ?    0.5   0.0       1.7   7.6e+02      88     124 ..     279     315 ..     277     321 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.9e-05
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHH CS
                   Alkyl_sulf_dimr  82 egdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatw 125
                                       ++ y+ a+++l+ ++ +dp++aea + ka++l +l +q+es ++
  gi|330509100|ref|YP_004385528.1|  90 SQTYEKALSILDEILLKDPDDAEAWQKKASVLGSLNRQNESLAA 133
                                       56799***********************************9876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.2
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHH CS
                   Alkyl_sulf_dimr  75 kakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatw 125
                                       k ++ l+ g+   a    n +++ dp++  a   ka++  ++g  +es+ +
  gi|330509100|ref|YP_004385528.1| 158 KGNALLNLGKWDEARDAYNEAIEVDPQDYHAWGRKAEVIGRIGDINESMEA 208
                                       5566677788888999999***********************999999764 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0012
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                       + g    a+e +nh ++ dpe +   + kad+l qlg++ e+  
  gi|330509100|ref|YP_004385528.1| 238 AGGRWAEALEAINHSLEIDPESRVNWRFKADILSQLGRKDEAIE 281
                                       567777899*****************************999865 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  88 aaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                       a+e  + ++ ++pe+ae    ka+ l ++ + +es  
  gi|330509100|ref|YP_004385528.1| 279 AIEAFDEVLNQNPEDAESWLWKANLLVEMKRYNESVE 315
                                       6788899999999999999999999999999998865 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         3   1.4e+03     154     197 ..      10      53 ..       5      65 .. 0.60
   2 ?    3.1   0.0      0.11        49      17     110 ..      93     182 ..      72     202 .. 0.68
   3 ?    3.4   0.1      0.09        41      27     109 ..     178     255 ..     155     296 .. 0.50
   4 !   17.7   0.2     4e-06    0.0019       7     163 ..     300     455 ..     295     461 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3
                          TPR_MalT 154 qlepeaald..ayvllarialaqGdleeAetllekaeelaresnfh 197
                                       +l+ + al   a+++l+    aq    + + +++kaee+a +s f 
  gi|330509100|ref|YP_004385528.1|  10 KLGAKLALTllALAALCACVTAQ--ETTTDYWMDKAEEFAYNSSFE 53 
                                       55444444400455555555555..456678999999998888774 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.11
                          TPR_MalT  17 aeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaek.larqadslhvallallqqaeilva 92 
                                        e+al +  ++L   p+d+  ++  a +vlG  +  +    ++l+a++e+ + + r++++    + a ++ ++ l  
  gi|330509100|ref|YP_004385528.1|  93 YEKALSILDEILLKDPDDAEAWQKKA-SVLGSLNRQN----ESLAAYEETLEaFNRRIEKDSKDIDAWIGKGNALLN 164
                                       44555555555555566777777777.7778444444....555666655431446666666667778888999999 PP

                          TPR_MalT  93 qGrLheAletyeqalqla 110
                                        G+ +eA + y++a+++ 
  gi|330509100|ref|YP_004385528.1| 165 LGKWDEARDAYNEAIEVD 182
                                       999999999999999853 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.09
                          TPR_MalT  27 ALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAlety 103
                                       A++  p+d + +   a  v+G      Gd +++ +a+  +++l+ + +   +a + + +   +++a Gr  eAle  
  gi|330509100|ref|YP_004385528.1| 178 AIEVDPQDYHAWGRKA-EVIG----RIGDINESMEAYDRTIELIPANNTREQADYWMSKAEVLAIAGGRWAEALEAI 249
                                       4444444444444444.3444....3345555555555555555444444444333333444455555555555555 PP

                          TPR_MalT 104 eqalql 109
                                       +++l+ 
  gi|330509100|ref|YP_004385528.1| 250 NHSLEI 255
                                       444443 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 4e-06
                          TPR_MalT   7 rAllaiasgdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallal 83 
                                       +A l + + + ++++e   +A++l+ e++    ++  ++ G a   +G++++A++a+q+  ++   a s ++    l
  gi|330509100|ref|YP_004385528.1| 300 KANLLVEMKRYNESVEAYDKAIELIAENNSEDLALDWLSKGWALNKTGRTDEAQAAFQKSLEFYETAISGNTGNIRL 376
                                       5677778888888889999999999999988888888899******************9999988888887767777 PP

                          TPR_MalT  84 lqqae.ilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlepea 159
                                       lqq   +l++ Gr +eA+e y q l+     +   + ++ ++  + +d l+ +++ eeA ++ +++i+l+ ++++++
  gi|330509100|ref|YP_004385528.1| 377 LQQKGlVLFELGRYDEAIEAYDQVLKNSLSLEFDTTAVSAWI--GKGDSLRLQGKNEEALEAYNKAIDLGPHYSNAW 451
                                       7665559*******************9999999999999998..88**************************99988 PP

                          TPR_MalT 160 alda 163
                                       + + 
  gi|330509100|ref|YP_004385528.1| 452 HGRG 455
                                       7655 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       2.4   1.1e+03      16      27 ..      93     104 ..      93     107 .. 0.85
   2 ?    4.1   0.0      0.14        64       8      26 ..     160     178 ..     160     181 .. 0.85
   3 ?    4.7   0.0      0.09        41       9      27 ..     269     287 ..     268     297 .. 0.89
   4 ?    0.7   0.0       1.7     8e+02       9      25 ..     342     358 ..     341     362 .. 0.83
   5 ?    3.6   0.0       0.2        94      12      29 ..     386     403 ..     383     405 .. 0.83
   6 ?    0.5   0.0         2   9.3e+02      13      28 ..     427     442 ..     422     444 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2.4
                               PPR  16 leeAlelfkeMk 27 
                                       +e+Al++++e++
  gi|330509100|ref|YP_004385528.1|  93 YEKALSILDEIL 104
                                       69*******986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.14
                               PPR   8 sgycknGkleeAlelfkeM 26 
                                       +++   Gk++eA + ++e 
  gi|330509100|ref|YP_004385528.1| 160 NALLNLGKWDEARDAYNEA 178
                                       578899********99985 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.09
                               PPR   9 gycknGkleeAlelfkeMk 27 
                                        +++ G+ +eA+e f+e +
  gi|330509100|ref|YP_004385528.1| 269 ILSQLGRKDEAIEAFDEVL 287
                                       5899************975 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.7
                               PPR   9 gycknGkleeAlelfke 25 
                                       ++ k G+ +eA   f++
  gi|330509100|ref|YP_004385528.1| 342 ALNKTGRTDEAQAAFQK 358
                                       56799******999886 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.2
                               PPR  12 knGkleeAlelfkeMkek 29 
                                         G+++eA+e +++ +++
  gi|330509100|ref|YP_004385528.1| 386 ELGRYDEAIEAYDQVLKN 403
                                       67**********998776 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 2
                               PPR  13 nGkleeAlelfkeMke 28 
                                        Gk eeAle +++ ++
  gi|330509100|ref|YP_004385528.1| 427 QGKNEEALEAYNKAID 442
                                       6999*****9998666 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.47   2.2e+02       6      18 ..      60      72 ..      58      72 .. 0.87
   2 ?    1.2   0.0      0.75   3.4e+02       2      20 ..      97     115 ..      96     115 .. 0.85
   3 !   11.5   0.0   0.00041      0.19       6      19 ..     176     189 ..     176     190 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.47
                                      HHHHHH-TT-CHH CS
                              PPTA  6 ekliekdpkNYsa 18
                                      ++++++dp N+++
  gi|330509100|ref|YP_004385528.1| 60 DEALKTDPGNETI 72
                                      589*******986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.75
                                       HHHHHHHHHH-TT-CHHHH CS
                              PPTA   2 LeltekliekdpkNYsaWn 20 
                                       L   ++++ kdp++  aW+
  gi|330509100|ref|YP_004385528.1|  97 LSILDEILLKDPDDAEAWQ 115
                                       667789*******999995 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00041
                                       HHHHHH-TT-CHHH CS
                              PPTA   6 ekliekdpkNYsaW 19 
                                       +++ie dp++Y+aW
  gi|330509100|ref|YP_004385528.1| 176 NEAIEVDPQDYHAW 189
                                       589*********** PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.014       6.5       4      23 ..     155     174 ..     153     177 .. 0.85
   2 ?    3.2   0.1      0.39   1.8e+02      10      23 ..     235     248 ..     234     250 .. 0.84
   3 ?    1.8   0.0       1.1   5.1e+02       7      25 ..     266     284 ..     263     285 .. 0.81
   4 !    8.2   0.0      0.01       4.6       8      24 ..     340     356 ..     336     358 .. 0.87
   5 ?    6.2   0.0     0.044        20       8      25 ..     381     398 ..     379     399 .. 0.83
   6 ?    2.1   0.0       0.9   4.1e+02       3      23 ..     416     436 ..     414     438 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.014
                             TPR_4   4 llaLArallalGdldeAral 23 
                                        ++ + all lG +deAr++
  gi|330509100|ref|YP_004385528.1| 155 WIGKGNALLNLGKWDEARDA 174
                                       567799************86 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.39
                             TPR_4  10 allalGdldeAral 23 
                                       ++ a G+++eA+++
  gi|330509100|ref|YP_004385528.1| 235 LAIAGGRWAEALEA 248
                                       57899******985 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 1.1
                             TPR_4   7 LArallalGdldeAralle 25 
                                        A  l +lG+ deA ++++
  gi|330509100|ref|YP_004385528.1| 266 KADILSQLGRKDEAIEAFD 284
                                       588999********77665 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.01
                             TPR_4   8 ArallalGdldeArall 24 
                                       ++al  +G+ deA+a++
  gi|330509100|ref|YP_004385528.1| 340 GWALNKTGRTDEAQAAF 356
                                       89************987 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.044
                             TPR_4   8 ArallalGdldeAralle 25 
                                       + +l++lG++deA ++ +
  gi|330509100|ref|YP_004385528.1| 381 GLVLFELGRYDEAIEAYD 398
                                       679**********77665 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.9
                             TPR_4   3 allaLArallalGdldeAral 23 
                                       a ++ +  l ++G  +eA+++
  gi|330509100|ref|YP_004385528.1| 416 AWIGKGDSLRLQGKNEEALEA 436
                                       67788999**********985 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.037        17     206     256 ..      41      91 ..      30      93 .. 0.79
   2 ?    4.5   0.3     0.042        19     215     238 ..      91     114 ..      85     139 .. 0.83
   3 ?    4.3   0.0     0.048        22     195     237 ..     146     188 ..     120     216 .. 0.78
   4 ?   -0.5   0.0       1.4   6.5e+02     209     233 ..     234     258 ..     217     263 .. 0.82
   5 ?    4.4   0.1     0.046        21     213     268 ..     272     330 ..     259     339 .. 0.84
   6 ?    1.2   0.1      0.44     2e+02     160     228 ..     328     401 ..     324     413 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.037
                                       HHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 206 gkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                        kA       ++ee  s+L eaL+ d+ +e  Li        +gk +e+s+
  gi|330509100|ref|YP_004385528.1|  41 DKAEEFAYNSSFEEVISSLDEALKTDPGNETILIREALYLGIVGKVNESSQ 91 
                                       55555556789**********************998888888888877765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.042
                                       T-HHHHHHHHHHHHHH-TT-HHHH CS
                        Coatomer_E 215 gryeeAeslLkeaLdkdakdeetL 238
                                       + ye+A s+L e L kd+ d+e+ 
  gi|330509100|ref|YP_004385528.1|  91 QTYEKALSILDEILLKDPDDAEAW 114
                                       78*******************986 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.048
                                       HHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHH CS
                        Coatomer_E 195 ekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeet 237
                                       ek ++  +   gk  + l lg+++eA    +ea++ d++d+ +
  gi|330509100|ref|YP_004385528.1| 146 EKDSKDIDAWIGKGNALLNLGKWDEARDAYNEAIEVDPQDYHA 188
                                       4545555666788888899999999999999999999999876 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.4
                                       HHHHHTT-HHHHHHHHHHHHHH-TT CS
                        Coatomer_E 209 vvslllgryeeAeslLkeaLdkdak 233
                                       v  ++ gr++eA + ++ +L+ d++
  gi|330509100|ref|YP_004385528.1| 234 VLAIAGGRWAEALEAINHSLEIDPE 258
                                       7789999*************98875 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.046
                                       HTT-HHHHHHHHHHHHHH-TT-HHHH...HHHHHHHHHTT--HHHHHHHHHHHHHH-TT CS
                        Coatomer_E 213 llgryeeAeslLkeaLdkdakdeetL...iNlvvaaqhlgkdaevsernlsqlklshpe 268
                                       +lgr +eA +   e L+++++d+e     +Nl+v ++  + + e+ ++ ++ + ++ +e
  gi|330509100|ref|YP_004385528.1| 272 QLGRKDEAIEAFDEVLNQNPEDAESWlwkANLLVEMKRYNESVEAYDKAIELIAENNSE 330
                                       68999*******************854558*********99999999999877766654 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 0.44
                                       H-TT-HHHHHHHHHHHHHH-T.THHHHHHHHHHHHHHHS....---HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                        Coatomer_E 160 idedatltQLAqawvklavgg.ekiqdAyyifqelseky....kstplllngkAvvslllgryeeAeslLkeaL 228
                                        +ed  l  L + w    +g  ++ q A+    e+ e+       +  ll+ k  v   lgry+eA +   + L
  gi|330509100|ref|YP_004385528.1| 328 NSEDLALDWLSKGWALNKTGRtDEAQAAFQKSLEFYETAisgnTGNIRLLQQKGLVLFELGRYDEAIEAYDQVL 401
                                       566777777777774444333367777776555555553111145678999999**********9965443333 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.057        26      10      53 ..      76     118 ..      72     126 .. 0.82
   2 ?    0.5   0.1       1.5   6.7e+02      10      48 ..     117     154 ..     109     164 .. 0.76
   3 ?    6.2   0.1     0.024        11      16      32 ..     164     180 ..     154     181 .. 0.88
   4 ?   -0.7   0.0       3.3   1.5e+03      29      48 ..     278     296 ..     277     306 .. 0.76
   5 ?    4.1   0.2      0.11        49      18      34 ..     308     324 ..     300     327 .. 0.89
   6 ?    1.7   0.0       0.6   2.8e+02       4      39 ..     333     368 ..     330     383 .. 0.65
   7 ?    3.3   0.2      0.18        85      17      29 ..     387     399 ..     379     405 .. 0.86
   8 ?    6.7   0.1     0.017       7.7      18      33 ..     428     443 ..     426     447 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.057
                               MIT  10 kAveeDnagnyeeAlelYkealelLlqalkekneerrellreki 53 
                                       +A  +   g+  e  + Y++al +L ++l  k++ + e++++k+
  gi|330509100|ref|YP_004385528.1|  76 EALYLGIVGKVNESSQTYEKALSILDEILL-KDPDDAEAWQKKA 118
                                       555555668899999************997.7889999988886 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.5
                               MIT  10 kAveeDnagnyeeAlelYkealelLlqalkekneerrel 48 
                                       kA  + + +   e l +Y+e le ++  +  k++++ ++
  gi|330509100|ref|YP_004385528.1| 117 KASVLGSLNRQNESLAAYEETLEAFNRRIE-KDSKDIDA 154
                                       56666666778899999******9999885.66666665 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.024
                               MIT  16 nagnyeeAlelYkeale 32 
                                       n g+++eA ++Y ea+e
  gi|330509100|ref|YP_004385528.1| 164 NLGKWDEARDAYNEAIE 180
                                       789*************8 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 3.3
                               MIT  29 ealelLlqalkekneerrel 48 
                                       ea+e + ++l+ +n+e+ e 
  gi|330509100|ref|YP_004385528.1| 278 EAIEAFDEVLN-QNPEDAES 296
                                       799*******8.56666554 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.11
                               MIT  18 gnyeeAlelYkealelL 34 
                                       + y e +e+Y +a+el+
  gi|330509100|ref|YP_004385528.1| 308 KRYNESVEAYDKAIELI 324
                                       78************986 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.6
                               MIT   4 AlelvkkAveeDnagnyeeAlelYkealelLlqalk 39 
                                       Al+ ++k   + + g  +eA  +++++le   +a++
  gi|330509100|ref|YP_004385528.1| 333 ALDWLSKGWALNKTGRTDEAQAAFQKSLEFYETAIS 368
                                       555566666666677777777777777777777766 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.18
                               MIT  17 agnyeeAlelYke 29 
                                        g y+eA+e+Y +
  gi|330509100|ref|YP_004385528.1| 387 LGRYDEAIEAYDQ 399
                                       589********87 PP

  == domain 8  score: 6.7 bits;  conditional E-value: 0.017
                               MIT  18 gnyeeAlelYkealel 33 
                                       g+ eeAle+Y +a++l
  gi|330509100|ref|YP_004385528.1| 428 GKNEEALEAYNKAIDL 443
                                       789***********96 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.023        10      15      37 ..      91     113 ..      75     117 .. 0.79
   2 ?    3.0   0.0      0.24   1.1e+02      11      34 ..     162     185 ..     159     189 .. 0.88
   3 ?    0.9   0.0         1   4.8e+02      16      34 ..     241     259 ..     239     260 .. 0.87
   4 ?   -1.1   0.1       4.6   2.1e+03      14      34 ..     307     327 ..     305     330 .. 0.82
   5 ?    1.1   0.0      0.95   4.4e+02      14      29 ..     387     402 ..     384     404 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.023
                                       T-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenrQa 37 
                                       + Y++A+  +d +L ++P+   a
  gi|330509100|ref|YP_004385528.1|  91 QTYEKALSILDEILLKDPDDAEA 113
                                       68****************98776 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.24
                                       HHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPen 34 
                                        + lg+ +eAr   +  +e++P+ 
  gi|330509100|ref|YP_004385528.1| 162 LLNLGKWDEARDAYNEAIEVDPQD 185
                                       5789******************86 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1
                                       -HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPen 34 
                                       +  eA++ ++  Lei+Pe 
  gi|330509100|ref|YP_004385528.1| 241 RWAEALEAINHSLEIDPES 259
                                       6789*************85 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 4.6
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                       +++Y+e+ +  d  +e+  en
  gi|330509100|ref|YP_004385528.1| 307 MKRYNESVEAYDKAIELIAEN 327
                                       799***999999988876666 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.95
                                       HT-HHHHHHHHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLe 29 
                                       lg+Y+eA +  d++L+
  gi|330509100|ref|YP_004385528.1| 387 LGRYDEAIEAYDQVLK 402
                                       89**********9998 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.84   3.9e+02      23      64 ..      37      78 ..      18     100 .. 0.55
   2 ?    3.2   0.1      0.24   1.1e+02      10      59 ..      58     114 ..      52     134 .. 0.61
   3 ?    4.3   0.1      0.11        52       4      52 ..     134     182 ..     131     193 .. 0.84
   4 ?   -1.4   0.0       6.7   3.1e+03      31      52 ..     235     256 ..     202     261 .. 0.69
   5 !    8.2   0.5     0.007       3.2       4      44 ..     276     316 ..     273     361 .. 0.83
   6 ?    3.2   0.1      0.24   1.1e+02       5      53 ..     357     405 ..     353     464 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.84
                            TPR_20 23 darldlAlallaagryeeAleqLleilkrdrkweddaarkql 64
                                      d  +d A+  + ++  ee ++ L e lk+d + e+  +r++l
  gi|330509100|ref|YP_004385528.1| 37 DYWMDKAEEFAYNSSFEEVISSLDEALKTDPGNETILIREAL 78
                                      555555555555555555556665555555555555555444 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.24
                            TPR_20  10 eleaalaanpddldarldlAlallaagr.......yeeAleqLleilkrdrkwedda 59 
                                       +l++al+++p +  + +  Al l   g+       ye+Al+ L eil +d ++++  
  gi|330509100|ref|YP_004385528.1|  58 SLDEALKTDPGNETILIREALYLGIVGKvnessqtYEKALSILDEILLKDPDDAEAW 114
                                       566666666666666666555554443311111117788888888888877765544 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.11
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrd 52 
                                        +++l+++ ++++++ +d+da +   +all  g+ +eA ++  e ++ d
  gi|330509100|ref|YP_004385528.1| 134 YEETLEAFNRRIEKDSKDIDAWIGKGNALLNLGKWDEARDAYNEAIEVD 182
                                       567899************************9999999988877777666 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 6.7
                            TPR_20  31 allaagryeeAleqLleilkrd 52 
                                       + +a+gr +eAle++ + l+ d
  gi|330509100|ref|YP_004385528.1| 235 LAIAGGRWAEALEAINHSLEID 256
                                       3467888888988877766665 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.007
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                       +++ ++++++ l++np+d +  l  A++l++ +ry e++e+
  gi|330509100|ref|YP_004385528.1| 276 KDEAIEAFDEVLNQNPEDAESWLWKANLLVEMKRYNESVEA 316
                                       5678999***************************9976543 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.24
                            TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                                       +++l+  e+a+  n  ++ +  +  l+l++ gry+eA+e+  ++lk+ +
  gi|330509100|ref|YP_004385528.1| 357 QKSLEFYETAISGNTGNIRLLQQKGLVLFELGRYDEAIEAYDQVLKNSL 405
                                       5667777888888888888888888899999999999988777776655 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.63   2.9e+02      13      65 ..      82     138 ..      71     154 .. 0.65
   2 ?    1.4   0.1      0.76   3.5e+02       8      68 ..     118     182 ..     109     215 .. 0.68
   3 ?   -0.6   0.0       3.3   1.5e+03      15      34 ..     166     185 ..     153     256 .. 0.66
   4 ?    2.2   0.1      0.43     2e+02      65      65 ..     287     287 ..     192     321 .. 0.70
   5 ?   -1.9   0.0       8.2   3.8e+03      10      29 ..     342     361 ..     337     367 .. 0.78
   6 !    8.5   0.0     0.005       2.3      14      66 ..     387     442 ..     378     452 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.63
                             TPR_5  13 stGhedkavplYrraL....aeGLagarrrratiqLassLRnlGeaeealaLLrael 65 
                                        +G+ +++ + Y++aL    +  L++     a  + as L  l + +e+la  ++ l
  gi|330509100|ref|YP_004385528.1|  82 IVGKVNESSQTYEKALsildEILLKDPDDAEAWQKKASVLGSLNRQNESLAAYEETL 138
                                       567777777777777622222245666666666666777777777777666665555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.76
                             TPR_5   8 agarDstGhedkavplYrraLaeGL....agarrrratiqLassLRnlGeaeealaLLraeleap 68 
                                       a++  s  +++++   Y++ L++      ++++   a i    +L nlG+ +ea    ++ +e  
  gi|330509100|ref|YP_004385528.1| 118 ASVLGSLNRQNESLAAYEETLEAFNrrieKDSKDIDAWIGKGNALLNLGKWDEARDAYNEAIEVD 182
                                       56666666667777777776665431111355556667777777888888877776666665554 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.3
                             TPR_5  15 GhedkavplYrraLaeGLag 34 
                                       G+ d+a   Y++a++   ++
  gi|330509100|ref|YP_004385528.1| 166 GKWDEARDAYNEAIEVDPQD 185
                                       55555555555555543333 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.43
                             TPR_5  65 l 65 
                                       l
  gi|330509100|ref|YP_004385528.1| 287 L 287
                                       2 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 8.2
                             TPR_5  10 arDstGhedkavplYrraLa 29 
                                       a + tG+ d+a   ++++L+
  gi|330509100|ref|YP_004385528.1| 342 ALNKTGRTDEAQAAFQKSLE 361
                                       55678888888888888775 PP

  == domain 6  score: 8.5 bits;  conditional E-value: 0.005
                             TPR_5  14 tGhedkavplYrraLaeGLa...garrrratiqLassLRnlGeaeealaLLraele 66 
                                        G+ d+a++ Y + L++ L+   ++ +  a i    sLR  G+ eeal+  ++ ++
  gi|330509100|ref|YP_004385528.1| 387 LGRYDEAIEAYDQVLKNSLSlefDTTAVSAWIGKGDSLRLQGKNEEALEAYNKAID 442
                                       6999**************9865678889999****************987776655 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.85   3.9e+02      13      26 ..     164     175 ..     161     183 .. 0.84
   2 ?    0.6   0.0       1.3     6e+02      16      30 ..     275     288 ..     272     289 .. 0.78
   3 ?   -0.4   0.0       2.7   1.2e+03      17      23 ..     317     323 ..     306     325 .. 0.66
   4 !   10.1   0.0    0.0014      0.65       9      25 ..     382     398 ..     381     402 .. 0.87
   5 ?   -1.0   0.1       4.1   1.9e+03      14      26 ..     427     437 ..     426     443 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.85
                                       HTT-HHHHHHH..H CS
                             TPR_3  13 nkkkyqeArelfsY 26 
                                       n +k +eAr++  Y
  gi|330509100|ref|YP_004385528.1| 164 NLGKWDEARDA--Y 175
                                       67899999999..4 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.3
                                       -HHHHHHH..HHHHH CS
                             TPR_3  16 kyqeArelfsYalla 30 
                                       + +eA+e+f+ ++l+
  gi|330509100|ref|YP_004385528.1| 275 RKDEAIEAFD-EVLN 288
                                       559******9.7775 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.7
                                       HHHHHHH CS
                             TPR_3  17 yqeArel 23 
                                       y++A+el
  gi|330509100|ref|YP_004385528.1| 317 YDKAIEL 323
                                       6666665 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0014
                                       HHHHHTT-HHHHHHH.. CS
                             TPR_3   9 aefynkkkyqeArelfs 25 
                                        +++  ++y+eA+e+++
  gi|330509100|ref|YP_004385528.1| 382 LVLFELGRYDEAIEAYD 398
                                       689999*********87 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 4.1
                                       TT-HHHHHHH..H CS
                             TPR_3  14 kkkyqeArelfsY 26 
                                       ++k +eA+e+  Y
  gi|330509100|ref|YP_004385528.1| 427 QGKNEEALEA--Y 437
                                       5666677777..3 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.49   2.3e+02      49      89 ..      12      54 ..       2     148 .. 0.67
   2 ?    4.1   0.1     0.083        38     152     180 ..     161     189 ..     160     194 .. 0.89
   3 ?    5.5   0.0     0.031        14     126     180 ..     242     297 ..     212     302 .. 0.82
   4 ?    3.2   0.0      0.15        71     152     181 ..     423     452 ..     417     458 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.49
                           Wzy_C_2 49 pklvlrvvalvlallglalllsilhdyq..rleqlyltsepne 89
                                       + +++ + +++al+++++   +  dy+  ++e + ++s+ +e
  gi|330509100|ref|YP_004385528.1| 12 GAKLALTLLALAALCACVTAQETTTDYWmdKAEEFAYNSSFEE 54
                                      4556677777888888888888888888888888888776554 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.083
                           Wzy_C_2 152 slallGdedeAeqilararalfpeedakw 180
                                       +l  lG+ deA++ + +a+ + p+++++w
  gi|330509100|ref|YP_004385528.1| 161 ALLNLGKWDEARDAYNEAIEVDPQDYHAW 189
                                       57789************************ PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.031
                           Wzy_C_2 126 laaklalarklihlsPepavierl.ilslallGdedeAeqilararalfpeedakw 180
                                        a+ l++ +  ++  Pe +v  r  ++ l +lG++deA    +++ ++ pe++++w
  gi|330509100|ref|YP_004385528.1| 242 WAEALEAINHSLEIDPESRVNWRFkADILSQLGRKDEAIEAFDEVLNQNPEDAESW 297
                                       566777777778888888887664388999*************************9 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.15
                           Wzy_C_2 152 slallGdedeAeqilararalfpeedakwv 181
                                       sl l+G+ +eA+  + +a+ l p +  +w+
  gi|330509100|ref|YP_004385528.1| 423 SLRLQGKNEEALEAYNKAIDLGPHYSNAWH 452
                                       899******************999999994 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.49   2.3e+02      53      70 ..     164     181 ..     154     185 .. 0.89
   2 ?    1.3   0.0      0.77   3.5e+02      52      69 ..     271     288 ..     266     298 .. 0.82
   3 ?    7.4   0.3      0.01       4.7      24      78 ..     282     331 ..     277     339 .. 0.82
   4 ?   -1.0   0.0       4.1   1.9e+03      55      70 ..     428     443 ..     423     447 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.49
                            ANAPC5  53 dfghneeAvkaleeairl 70 
                                       ++g+++eA +a +eai++
  gi|330509100|ref|YP_004385528.1| 164 NLGKWDEARDAYNEAIEV 181
                                       6899************87 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.77
                            ANAPC5  52 adfghneeAvkaleeair 69 
                                       +++g ++eA++a+ e+ +
  gi|330509100|ref|YP_004385528.1| 271 SQLGRKDEAIEAFDEVLN 288
                                       6899**********9865 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.01
                            ANAPC5  24 yFDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleeairlArenkDks 78 
                                        FD vl+qn +        + L  a+l  ++  ++e+v+a   ai+l  en+++ 
  gi|330509100|ref|YP_004385528.1| 282 AFDEVLNQNPED-----AESWLWKANLLVEMKRYNESVEAYDKAIELIAENNSED 331
                                       577777777777.....6678999**********************999998764 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 4.1
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                       g+neeA++a + ai l
  gi|330509100|ref|YP_004385528.1| 428 GKNEEALEAYNKAIDL 443
                                       789********99986 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 ?    5.0   0.3     0.037        17      90     160 ..      83     153 ..      42     232 .. 0.86
   2 ?   -1.5   0.0       3.9   1.8e+03     148     195 ..     242     290 ..     218     298 .. 0.71
   3 ?   10.5   1.5   0.00082      0.38      82     169 ..     299     384 ..     276     444 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.037
                           DUF2225  90 ertldeaiesYkLallcyelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelykeayekesfpve 160
                                         +++e  ++Y  al   + +  k+   A  + + A +   ++ +++++  +++ le +++ +ek+s++++
  gi|330509100|ref|YP_004385528.1|  83 VGKVNESSQTYEKALSILDEILLKDPDDAEAWQKKASVLGSLNRQNESLAAYEETLEAFNRRIEKDSKDID 153
                                       45789999*********************************************************999877 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.9
                           DUF2225 148 ykeayekesfpvegideatvlYL.iaeLerrlgnkeealrwlskvigsk 195
                                       + ea+e  + + e+  e++v +   a+   +lg+k+ea++++ +v++++
  gi|330509100|ref|YP_004385528.1| 242 WAEALEAINHSLEIDPESRVNWRfKADILSQLGRKDEAIEAFDEVLNQN 290
                                       5666666666666666666665414777888999999999999998875 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00082
                           DUF2225  82 wksrdfskertldeaiesYkLallcyelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelykeayekesfp 158
                                       wk++   +   ++e +e+Y  a++   + ++++   A  +l  +W  ++++  ++ +   +k le+y++a++ ++ +
  gi|330509100|ref|YP_004385528.1| 299 WKANLLVEMKRYNESVEAYDKAIEL--IAENNSEDLALDWLSKGWALNKTGRTDEAQAAFQKSLEFYETAISGNTGN 373
                                       5555566677899999999999864..456666699*************************************9999 PP

                           DUF2225 159 vegideatvlY 169
                                       ++ ++++ +++
  gi|330509100|ref|YP_004385528.1| 374 IRLLQQKGLVL 384
                                       99888876544 PP

>> BPS  BPS (Between PH and SH2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.47   2.2e+02      26      43 ..     102     119 ..      99     123 .. 0.83
   2 ?    2.3   0.0      0.34   1.6e+02      25      42 ..     176     193 ..     172     196 .. 0.88
   3 ?    4.1   0.1     0.088        41      15      41 ..     274     300 ..     273     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.47
                               BPS  26 EalsaaleegqaWRkkss 43 
                                       E l  +++++ aW kk s
  gi|330509100|ref|YP_004385528.1| 102 EILLKDPDDAEAWQKKAS 119
                                       666678899*******87 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.34
                               BPS  25 tEalsaaleegqaWRkks 42 
                                        Ea  +++++ +aW +k 
  gi|330509100|ref|YP_004385528.1| 176 NEAIEVDPQDYHAWGRKA 193
                                       69************9885 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.088
                               BPS  15 GqkgrvIeNptEalsaaleegqaWRkk 41 
                                       G+k   Ie   E+l+ ++e++ +W  k
  gi|330509100|ref|YP_004385528.1| 274 GRKDEAIEAFDEVLNQNPEDAESWLWK 300
                                       6777789*****************666 PP

>> DUF2917  Protein of unknown function (DUF2917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.27   1.2e+02      28      47 ..      29      48 ..      16      59 .. 0.78
   2 ?    1.7   0.0      0.37   1.7e+02      34      51 ..     224     241 ..     220     246 .. 0.86
   3 ?    3.7   0.0     0.086        40      38      57 ..     417     436 ..     416     438 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.27
                           DUF2917 28 vTregdpeDhwLqaGqslrl 47
                                      vT+++   D+w+ + + ++ 
  gi|330509100|ref|YP_004385528.1| 29 VTAQETTTDYWMDKAEEFAY 48
                                      899*********99888765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.37
                           DUF2917  34 peDhwLqaGqslrlargq 51 
                                         D+w+ + + l++a+g+
  gi|330509100|ref|YP_004385528.1| 224 QADYWMSKAEVLAIAGGR 241
                                       68**********999985 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.086
                           DUF2917  38 wLqaGqslrlargqrvvlea 57 
                                       w ++G+slrl+++++  lea
  gi|330509100|ref|YP_004385528.1| 417 WIGKGDSLRLQGKNEEALEA 436
                                       99*********999887777 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       6.8   3.1e+03       2      14 ..     134     146 ..     133     148 .. 0.88
   2 ?   -1.9   0.0       5.8   2.7e+03       2      15 ..     242     255 ..     241     256 .. 0.76
   3 ?    5.1   0.1     0.037        17       1      21 [.     309     329 ..     309     332 .. 0.90
   4 ?    1.8   0.1      0.39   1.8e+02       1      18 [.     389     406 ..     389     408 .. 0.89
   5 ?    0.7   0.0      0.83   3.8e+02       3      15 ..     431     443 ..     429     449 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.8
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAie 14 
                                       Yee Le  n+ ie
  gi|330509100|ref|YP_004385528.1| 134 YEETLEAFNRRIE 146
                                       9*****9999887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.8
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                       ++eaLe +n  +ei
  gi|330509100|ref|YP_004385528.1| 242 WAEALEAINHSLEI 255
                                       67899999888776 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.037
                                       -HHHHHHHHHHHHHHHHHTTB CS
                          HTH_Bact   1 rYeeaLeqvnkAieiSirins 21 
                                       rY+e+ e  +kAie+  ++ns
  gi|330509100|ref|YP_004385528.1| 309 RYNESVEAYDKAIELIAENNS 329
                                       7*************9888876 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.39
                                       -HHHHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiSir 18 
                                       rY+ea+e  ++ ++ S+ 
  gi|330509100|ref|YP_004385528.1| 389 RYDEAIEAYDQVLKNSLS 406
                                       7***********999986 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.83
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   3 eeaLeqvnkAiei 15 
                                       eeaLe  nkAi +
  gi|330509100|ref|YP_004385528.1| 431 EEALEAYNKAIDL 443
                                       89*********75 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 ?    3.4   0.0       0.2        90      46      71 ..     306     331 ..     301     333 .. 0.85
   2 ?    5.7   0.0     0.038        17      46      66 ..     386     406 ..     383     411 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.2
                         Pepsin-I3  46 ELktydaevtkYkeelksslqervkg 71 
                                       E+k y++ v++Y ++++ + ++  + 
  gi|330509100|ref|YP_004385528.1| 306 EMKRYNESVEAYDKAIELIAENNSED 331
                                       99*************99888877665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.038
                         Pepsin-I3  46 ELktydaevtkYkeelksslq 66 
                                       EL  yd+  ++Y + lk+sl+
  gi|330509100|ref|YP_004385528.1| 386 ELGRYDEAIEAYDQVLKNSLS 406
                                       999****************97 PP

>> Strep_SA_rep  Streptococcal surface antigen repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.32   1.5e+02       7      17 ..     131     141 ..     128     146 .. 0.64
   2 ?    7.4   0.1      0.01       4.6      13      24 ..     306     317 ..     305     318 .. 0.95
   3 ?    2.7   0.2      0.29   1.3e+02      13      24 ..     386     397 ..     386     399 .. 0.83
   4 ?    1.9   0.2       0.5   2.3e+02      14      21 ..     434     441 ..     430     442 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHH CS
                      Strep_SA_rep   7 LakYeaeLAaV 17 
                                       La+Ye  L+a 
  gi|330509100|ref|YP_004385528.1| 131 LAAYEETLEAF 141
                                       66666666665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHH- CS
                      Strep_SA_rep  13 eLAaVQKanady 24 
                                       e++++++ +++y
  gi|330509100|ref|YP_004385528.1| 306 EMKRYNESVEAY 317
                                       8**********9 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHH- CS
                      Strep_SA_rep  13 eLAaVQKanady 24 
                                       eL ++ +a+++y
  gi|330509100|ref|YP_004385528.1| 386 ELGRYDEAIEAY 397
                                       678999999998 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.5
                                       HHHHHHHH CS
                      Strep_SA_rep  14 LAaVQKan 21 
                                       L+a++Ka+
  gi|330509100|ref|YP_004385528.1| 434 LEAYNKAI 441
                                       89999987 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.17        77      28      50 ..     168     190 ..     165     215 .. 0.83
   2 ?    2.6   0.0      0.33   1.5e+02      28      52 ..     242     266 ..     238     290 .. 0.88
   3 ?   -0.5   0.1         3   1.4e+03      29      52 ..     311     338 ..     306     364 .. 0.53
   4 ?    1.1   0.0      0.96   4.4e+02      29      66 ..     431     466 ..     428     470 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.17
                           DUF1510  28 wnEmekavskatglsednmivww 50 
                                       w+E ++a ++a++++ +++  w 
  gi|330509100|ref|YP_004385528.1| 168 WDEARDAYNEAIEVDPQDYHAWG 190
                                       *******************9994 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.33
                           DUF1510  28 wnEmekavskatglsednmivwwlg 52 
                                       w E ++a+++  +++ ++ + w+ +
  gi|330509100|ref|YP_004385528.1| 242 WAEALEAINHSLEIDPESRVNWRFK 266
                                       *******************999976 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 3
                           DUF1510  29 nEmekavskatgl....sednmivwwlg 52 
                                       nE ++a  ka++l    +++++ + wl+
  gi|330509100|ref|YP_004385528.1| 311 NESVEAYDKAIELiaenNSEDLALDWLS 338
                                       5555555555554111133344444443 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.96
                           DUF1510  29 nEmekavskatglsednmivwwlgnggspqkaigtvss 66 
                                       +E ++a +ka++l    +  w+ g+ g++qka+g+v +
  gi|330509100|ref|YP_004385528.1| 431 EEALEAYNKAIDLGPHYSNAWH-GR-GEAQKAMGQVGN 466
                                       688999999***9877666665.43.678899999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.92u 0.33s 00:00:01.25 Elapsed: 00:00:00.62
# Mc/sec: 2350.39
//
Query:       gi|330509101|ref|YP_004385529.1|  [L=206]
Description: hypothetical protein MCON_3488 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       365  (0.0203581); 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:                         0  (0); expected 0.2 (1e-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: 1334.18
//
Query:       gi|330509102|ref|YP_004385530.1|  [L=406]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete 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-76  255.3   1.4    1.1e-75  254.4   0.6    1.7  2  DDE_Tnp_ISL3  Transposase
    3.3e-14   52.0   0.1    6.3e-14   51.1   0.1    1.5  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
    1.9e-10   41.2   6.3      5e-10   39.9   6.3    1.7  1  zf-ISL3       zinc-finger of transposase IS204/IS1001/IS1096/
  ------ inclusion threshold ------
        0.1   13.0   0.2       0.24   11.8   0.0    1.8  2  MULE          MULE transposase domain


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 ?   -1.1   0.0      0.28   1.3e+03     185     211 ..     121     147 ..     102     150 .. 0.81
   2 !  254.4   0.6   2.5e-79   1.1e-75       1     240 []     159     393 ..     159     393 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.28
                      DDE_Tnp_ISL3 185 efkklaktlknhreeIlnyfdsrlsng 211
                                        +  +a+++++h ++I +++++++  +
  gi|330509102|ref|YP_004385530.1| 121 TVTAIAEMIDEHDTRIWRVLQHYVAEA 147
                                       567789999999999999999987766 PP

  == domain 2  score: 254.4 bits;  conditional E-value: 2.5e-79
                      DDE_Tnp_ISL3   1 lgiDEislkkghkyvtvvvdllvdggrlldilpgRkketlkafleslsek..erekveavvmDmsaayksavkealP 75 
                                       +g+DE+s  kghkyv+v++dl  d++r++++++g++++t+ +f ++l+++    e++e +++Dms+a++s +++ +P
  gi|330509102|ref|YP_004385530.1| 159 IGVDETSRAKGHKYVSVFIDL--DESRVIHVCEGKNASTIGSFKDDLEQHngSSENIENFCCDMSPAFISGIENSFP 233
                                       8********************..************************8888899*********************** PP

                      DDE_Tnp_ISL3  76 nAkivvDrFHvvklanealdevRrreqkelreekrkklkrsrrlllknpenlteeqkqrldelleaspelekaYelk 152
                                       nA+i++D+FHv+kl+nea+d+vRr+eq++        lkr+r+++lknpenlt +q + l  l +   ++ +aY++k
  gi|330509102|ref|YP_004385530.1| 234 NASITFDKFHVMKLMNEAVDKVRREEQSHNA-----LLKRTRYIWLKNPENLTANQNKMLTPLKSIRLKTMRAYNIK 305
                                       ****************************865.....6***********************99*************** PP

                      DDE_Tnp_ISL3 153 eelrevfrkkdkeearkalkewiekaersglkefkklaktlknhreeIlnyfdsrlsngpvEgiNnkikaikrrayG 229
                                        +lr+++ ++ +++a+ +lk+w+ +a++s+l+++ ++ak++knh+++++ny+++++ ng++Eg+N+ i+a+k +a+G
  gi|330509102|ref|YP_004385530.1| 306 LALRDFWSYEYRKSAEDYLKRWYYWATHSRLDPVIECAKMIKNHWNGVTNYIKTKIDNGILEGTNSLIQAAKDSARG 382
                                       ********99*******************************************99********************** PP

                      DDE_Tnp_ISL3 230 frnfenfrlri 240
                                       fr+++nf+++i
  gi|330509102|ref|YP_004385530.1| 383 FRSTKNFITII 393
                                       ********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 !   51.1   0.1   1.4e-17   6.3e-14       2      52 .]      95     144 ..      94     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.4e-17
                      HTH_Tnp_ISL3   2 elPwarrrsriTlrleayilelllesrsvkavArqlgvSwtTVwrildryv 52 
                                       ++Pwar++s++Tl+++  i+ +++ + +v+a+A++ + ++t++wr+l +yv
  gi|330509102|ref|YP_004385530.1|  95 KVPWARKGSGFTLLMDSLIVLMAQYM-TVTAIAEMIDEHDTRIWRVLQHYV 144
                                       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 !   39.9   6.3   1.1e-13     5e-10       5      47 .]      47      89 ..      44      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.1e-13
                           zf-ISL3  5 CPnCgsktvvkhgkkerrvrhlpiggkrvyLrlrkrRyrCkeC 47
                                      C +Cg++   +h++ er++rhl+++++++y+++r++R  C +C
  gi|330509102|ref|YP_004385530.1| 47 CAKCGNPGCSVHDTIERTWRHLNFFQFKTYIHCRVPRTICEDC 89
                                      *******99*********************************9 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         2   8.8e+03      29      51 ..     121     143 ..     107     156 .. 0.56
   2 ?   11.8   0.0   5.4e-05      0.24      36      95 ..     187     246 ..     163     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2
                              MULE  29 lvplafalveseneesyewllqe 51 
                                       +v ++  ++++ ++ ++++l + 
  gi|330509102|ref|YP_004385530.1| 121 TVTAIAEMIDEHDTRIWRVLQHY 143
                                       44444445555555666555444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.4e-05
                              MULE  36 lveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClfHiak 95 
                                       + e +n +++  + ++l +++++ ++ + + +D   a+++ +e+ fp+a   +  fH++k
  gi|330509102|ref|YP_004385530.1| 187 VCEGKNASTIGSFKDDLEQHNGSSENIENFCCDMSPAFISGIENSFPNASITFDKFHVMK 246
                                       568899999999999******************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2703.24
//
Query:       gi|330509103|ref|YP_004385531.1|  [L=263]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (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  142.2  23.8    4.6e-10   38.9   0.0    8.2  9  TPR_1            Tetratricopeptide repeat
    1.5e-39  133.4  15.6    8.2e-08   31.8   0.2    6.3  6  TPR_11           TPR repeat
    4.4e-38  126.3  17.8    4.2e-07   29.6   0.0    7.8  8  TPR_2            Tetratricopeptide repeat
    1.5e-36  121.5  12.3      7e-07   29.0   0.0    7.5  7  TPR_8            Tetratricopeptide repeat
    2.3e-34  115.3   7.5    7.3e-06   26.0   0.1    6.4  6  TPR_17           Tetratricopeptide repeat
    3.2e-27   92.9   5.4    2.2e-05   24.9   0.5    7.2  7  TPR_14           Tetratricopeptide repeat
    1.4e-25   89.6   0.3    2.1e-09   37.9   0.0    5.4  6  TPR_16           Tetratricopeptide repeat
    1.3e-21   76.7   6.9    5.8e-05   23.3   0.0    5.3  5  TPR_12           Tetratricopeptide repeat
    3.6e-21   75.4   3.7    2.1e-08   34.5   0.1    5.0  5  TPR_19           Tetratricopeptide repeat
    1.5e-19   69.9   0.0    1.1e-06   28.7   0.2    4.2  5  TPR_9            Tetratricopeptide repeat
    1.9e-14   53.2   5.3       0.17   12.6   0.0    7.5  7  TPR_6            Tetratricopeptide repeat
    1.2e-13   51.1   1.8    7.8e-08   32.4   0.1    4.0  4  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    4.2e-10   39.1   0.1     0.0006   18.9   0.0    4.0  4  NARP1            NMDA receptor-regulated protein 1
    2.7e-07   30.2   6.6       0.53   10.4   0.0    6.4  7  TPR_7            Tetratricopeptide repeat
    2.2e-06   27.3   8.3        4.2    7.4   0.1    7.0  7  TPR_10           Tetratricopeptide repeat
    5.8e-06   26.3   4.8        5.5    7.1   0.0    5.3  5  MIT              MIT (microtubule interacting and transport) 
    8.6e-06   25.9   3.7        1.1    9.3   0.4    5.4  4  DUF3856          Domain of Unknown Function (DUF3856)
    3.1e-05   24.5   1.6      0.025   15.0   0.2    3.2  3  BTAD             Bacterial transcriptional activator domain
    0.00029   20.5   0.6       0.18   11.6   0.0    3.1  2  PPTA             Protein prenyltransferase alpha subunit repe
     0.0017   17.6   6.0       0.13   11.4   0.8    3.6  2  FAT              FAT domain
     0.0032   17.5   2.3        8.1    6.6   0.0    4.6  4  Ribosomal_S16    Ribosomal protein S16
     0.0042   17.1   0.4        7.1    6.8   0.0    4.4  5  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
     0.0066   17.0   2.9         18    6.3   0.0    4.9  5  TPR_4            Tetratricopeptide repeat
     0.0089   16.5   0.8        6.7    7.2   0.0    3.3  3  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
  ------ inclusion threshold ------
      0.026   13.9   0.1        2.3    7.5   0.0    2.6  2  TPR_MalT         MalT-like TPR region
      0.027   14.5   0.0         19    5.3   0.0    3.7  2  DUF627           Protein of unknown function (DUF627)
      0.085   12.3   0.2        7.7    6.1   0.0    3.2  3  SHNi-TPR         SHNi-TPR
       0.12   12.5   0.4        1.2    9.2   0.0    2.8  3  ANAPC5           Anaphase-promoting complex subunit 5
        4.5    6.9   9.6         39    3.9   0.6    5.2  5  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 !   15.7   0.2   1.6e-05      0.01      18      33 ..      36      51 ..      35      52 .. 0.92
   2 ?   -2.6   0.0       9.6   5.9e+03       1      10 [.      53      62 ..      53      64 .. 0.65
   3 !   22.4   0.1   1.2e-07   7.4e-05      14      34 .]      67      87 ..      65      87 .. 0.95
   4 !   38.9   0.0   7.5e-13   4.6e-10       1      33 [.      88     120 ..      88     121 .. 0.98
   5 !   33.2   0.0   4.7e-11   2.9e-08       2      33 ..     123     154 ..     122     155 .. 0.96
   6 ?    3.3   0.0      0.13        78       2      30 ..     157     185 ..     156     187 .. 0.90
   7 !    8.4   0.0    0.0032         2      17      33 ..     179     195 ..     176     196 .. 0.90
   8 !   25.2   0.0   1.6e-08     1e-05       3      32 ..     199     228 ..     197     230 .. 0.94
   9 !    9.9   0.7     0.001      0.64       2      29 ..     232     259 ..     231     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHHHHHHSTT CS
                             TPR_1 18 deAleyyekALelnPn 33
                                      +eA e+y+kA+e++P+
  gi|330509103|ref|YP_004385531.1| 36 QEAREAYDKAIEIDPQ 51
                                      89*************7 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9.6
                                      HHHHHHHHHH CS
                             TPR_1  1 akalynlGna 10
                                      a a++ +G +
  gi|330509103|ref|YP_004385531.1| 53 ASAWFKKGEL 62
                                      5677777754 PP

  == domain 3  score: 22.4 bits;  conditional E-value: 1.2e-07
                                      TT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1 14 lgkydeAleyyekALelnPnn 34
                                      lg+y+eAl +++k +++nP++
  gi|330509103|ref|YP_004385531.1| 67 LGNYEEALNAFNKSIQINPQF 87
                                      8******************86 PP

  == domain 4  score: 38.9 bits;  conditional E-value: 7.5e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+a+y++G ++   g+++eAle y+k Le+nPn
  gi|330509103|ref|YP_004385531.1|  88 ADAWYQKGKTLTGYGDFEEALESYNKSLEINPN 120
                                       89******************************9 PP

  == domain 5  score: 33.2 bits;  conditional E-value: 4.7e-11
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                       +a+y ++ ++ +l++++eA+ +y+kA+el+P+
  gi|330509103|ref|YP_004385531.1| 123 DAWYWKAGVLAELNRHEEAIPAYDKAIELDPT 154
                                       8******************************7 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                         +  +G a+ +l++ + A + + +A+el
  gi|330509103|ref|YP_004385531.1| 157 SYWLDRGGALNRLNRTEGANASFTRAVEL 185
                                       579999*********************99 PP

  == domain 7  score: 8.4 bits;  conditional E-value: 0.0032
                                       HHHHHHHHHHHHHHSTT CS
                             TPR_1  17 ydeAleyyekALelnPn 33 
                                       +  A+e +++A+e nP+
  gi|330509103|ref|YP_004385531.1| 179 FTRAVELCDEAIEQNPK 195
                                       567*************7 PP

  == domain 8  score: 25.2 bits;  conditional E-value: 1.6e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                       a+ ++G a+++l++++e +++++k++el P
  gi|330509103|ref|YP_004385531.1| 199 AWQGKGTAFYHLERLNESIQCFDKVIELAP 228
                                       899**************************9 PP

  == domain 9  score: 9.9 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALe 29 
                                       +++y +G a++ lg+  eA+e + +  e
  gi|330509103|ref|YP_004385531.1| 232 RSYYYKGKALQDLGREVEAEELFARSKE 259
                                       78*******************9987655 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   5.5e-09   3.4e-06      11      37 ..      36      62 ..      35      64 .. 0.93
   2 !   31.8   0.2   1.3e-10   8.2e-08       7      37 ..      67      97 ..      67     100 .. 0.95
   3 !   27.2   0.2   3.8e-09   2.3e-06       8      39 ..     102     133 ..     101     136 .. 0.90
   4 !   29.4   0.2   7.6e-10   4.7e-07       4      38 ..     132     166 ..     129     170 .. 0.91
   5 ?    3.9   0.0     0.072        44      13      39 ..     182     208 ..     163     210 .. 0.74
   6 !   24.5   0.2   2.6e-08   1.6e-05       1      42 []     204     245 ..     204     245 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5.5e-09
                            TPR_11 11 eeAieaYkkAlkldPdnaeayynLGla 37
                                       eA eaY kA+++dP++a+a+++ G++
  gi|330509103|ref|YP_004385531.1| 36 QEAREAYDKAIEIDPQSASAWFKKGEL 62
                                      79*********************9986 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.3e-10
                            TPR_11  7 qGkyeeAieaYkkAlkldPdnaeayynLGla 37
                                      +G+yeeA++a++k ++++P++a+a+y  G++
  gi|330509103|ref|YP_004385531.1| 67 LGNYEEALNAFNKSIQINPQFADAWYQKGKT 97
                                      69**************************987 PP

  == domain 3  score: 27.2 bits;  conditional E-value: 3.8e-09
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       G++eeA+e+Y+k l+++P++ +a+y+ + +++
  gi|330509103|ref|YP_004385531.1| 102 GDFEEALESYNKSLEINPNSSDAWYWKAGVLA 133
                                       99***********************9876665 PP

  == domain 4  score: 29.4 bits;  conditional E-value: 7.6e-10
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       + e+++ eeAi aY kA++ldP++a+ ++ +G a+
  gi|330509103|ref|YP_004385531.1| 132 LAELNRHEEAIPAYDKAIELDPTQASYWLDRGGAL 166
                                       6799**************************99776 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.072
                            TPR_11  13 AieaYkkAlkldPdnaeayynLGlayy 39 
                                       A+e   +A++ +P++  a+ + G a+y
  gi|330509103|ref|YP_004385531.1| 182 AVELCDEAIEQNPKSIMAWQGKGTAFY 208
                                       555556888888888888877777776 PP

  == domain 6  score: 24.5 bits;  conditional E-value: 2.6e-08
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G a+y + +++e+i+++ k ++l P + + yy  G+a++ +G
  gi|330509103|ref|YP_004385531.1| 204 GTAFYHLERLNESIQCFDKVIELAPMYYRSYYYKGKALQDLG 245
                                       6799**********************************9998 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.5e-05     0.015      18      33 ..      36      51 ..      34      52 .. 0.92
   2 !   20.4   0.0   5.9e-07   0.00036      14      33 ..      67      86 ..      53      87 .. 0.93
   3 !   29.6   0.0   6.8e-10   4.2e-07       1      33 [.      88     120 ..      88     121 .. 0.97
   4 !   29.0   0.1   1.1e-09   6.6e-07       2      33 ..     123     154 ..     122     155 .. 0.96
   5 ?    7.0   0.0     0.012       7.1       2      32 ..     157     187 ..     156     189 .. 0.89
   6 ?    5.9   0.0     0.025        16      18      33 ..     180     195 ..     178     196 .. 0.89
   7 !   19.4   0.0   1.2e-06   0.00075       3      32 ..     199     228 ..     197     230 .. 0.95
   8 !   11.2   1.0   0.00052      0.32       3      30 ..     233     260 ..     231     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                             TPR_2 18 eeAleafekAleldPn 33
                                      +eA+ea++kA+e+dP+
  gi|330509103|ref|YP_004385531.1| 36 QEAREAYDKAIEIDPQ 51
                                      8**************7 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 5.9e-07
                             TPR_2 14 lgdyeeAleafekAleldPn 33
                                      lg+yeeAl+af+k+++++P+
  gi|330509103|ref|YP_004385531.1| 67 LGNYEEALNAFNKSIQINPQ 86
                                      8******************7 PP

  == domain 3  score: 29.6 bits;  conditional E-value: 6.8e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+a+y+ G+ +   gd+eeAle ++k+le++Pn
  gi|330509103|ref|YP_004385531.1|  88 ADAWYQKGKTLTGYGDFEEALESYNKSLEINPN 120
                                       79******************************9 PP

  == domain 4  score: 29.0 bits;  conditional E-value: 1.1e-09
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +a+y+ + ++++l+++eeA+ a++kA+eldP+
  gi|330509103|ref|YP_004385531.1| 123 DAWYWKAGVLAELNRHEEAIPAYDKAIELDPT 154
                                       79*****************************7 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.012
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                        ++  +G a+ +l++ e A + f +A+el+ 
  gi|330509103|ref|YP_004385531.1| 157 SYWLDRGGALNRLNRTEGANASFTRAVELCD 187
                                       678899999999****************985 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.025
                             TPR_2  18 eeAleafekAleldPn 33 
                                        +A+e++++A+e +P+
  gi|330509103|ref|YP_004385531.1| 180 TRAVELCDEAIEQNPK 195
                                       68*************7 PP

  == domain 7  score: 19.4 bits;  conditional E-value: 1.2e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                       a+   G a y+l +++e +++f+k++el+P
  gi|330509103|ref|YP_004385531.1| 199 AWQGKGTAFYHLERLNESIQCFDKVIELAP 228
                                       89999************************9 PP

  == domain 8  score: 11.2 bits;  conditional E-value: 0.00052
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                        +y+ G+a+  lg+  eA+e+f ++ el
  gi|330509103|ref|YP_004385531.1| 233 SYYYKGKALQDLGREVEAEELFARSKEL 260
                                       79********************998665 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.2   0.00021      0.13      18      33 ..      36      51 ..      35      52 .. 0.92
   2 !   24.6   0.0   2.9e-08   1.8e-05       1      33 [.      53      86 ..      53      87 .. 0.96
   3 !   28.0   0.1   2.4e-09   1.5e-06       1      33 [.      88     120 ..      88     121 .. 0.97
   4 !   29.0   0.0   1.1e-09     7e-07       2      33 ..     123     154 ..     122     155 .. 0.96
   5 !    7.5   0.0    0.0089       5.5       1      30 [.     156     185 ..     156     195 .. 0.93
   6 !   15.4   0.0   2.5e-05     0.016       3      32 ..     199     228 ..     199     228 .. 0.96
   7 ?    6.2   0.6     0.023        14       1      27 [.     231     257 ..     231     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                                      HHHHHHHHHHHHHHHH CS
                             TPR_8 18 eeAkeyyekaleldpd 33
                                      +eA e+y ka+e+dp+
  gi|330509103|ref|YP_004385531.1| 36 QEAREAYDKAIEIDPQ 51
                                      79*************7 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 2.9e-08
                                      CCHHHHHHHHH.HHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  1 aeayynlgsiy.lklgdyeeAkeyyekaleldpd 33
                                      a+a++++g +  + lg+yeeA  +++k ++++p+
  gi|330509103|ref|YP_004385531.1| 53 ASAWFKKGELQiDFLGNYEEALNAFNKSIQINPQ 86
                                      689******************************7 PP

  == domain 3  score: 28.0 bits;  conditional E-value: 2.4e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+a+y++g+++   gd+eeA e+y+k le++p+
  gi|330509103|ref|YP_004385531.1|  88 ADAWYQKGKTLTGYGDFEEALESYNKSLEINPN 120
                                       79******************************8 PP

  == domain 4  score: 29.0 bits;  conditional E-value: 1.1e-09
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a+y+++ ++ +l+++eeA+ +y ka+eldp+
  gi|330509103|ref|YP_004385531.1| 123 DAWYWKAGVLAELNRHEEAIPAYDKAIELDPT 154
                                       79*****************************6 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.0089
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a++++  g ++  l++ e A +++ +a+el
  gi|330509103|ref|YP_004385531.1| 156 ASYWLDRGGALNRLNRTEGANASFTRAVEL 185
                                       678999**********************98 PP

  == domain 6  score: 15.4 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a++ +g +   l++++e+++++ k++el+p
  gi|330509103|ref|YP_004385531.1| 199 AWQGKGTAFYHLERLNESIQCFDKVIELAP 228
                                       69999***********************98 PP

  == domain 7  score: 6.2 bits;  conditional E-value: 0.023
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyeka 27 
                                       +++yy +g+++++lg+  eA+e + + 
  gi|330509103|ref|YP_004385531.1| 231 YRSYYYKGKALQDLGREVEAEELFARS 257
                                       589******************999776 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   4.5e-08   2.8e-05       1      33 [.      41      74 ..      41      75 .. 0.92
   2 !   21.6   0.0   3.1e-07   0.00019       2      34 .]      77     109 ..      76     109 .. 0.94
   3 !   26.0   0.1   1.2e-08   7.3e-06       2      33 ..     111     142 ..     110     142 .. 0.97
   4 !   13.8   0.0   9.5e-05     0.059       1      32 [.     144     175 ..     144     175 .. 0.91
   5 !   15.0   0.0   3.9e-05     0.024       1      33 [.     185     217 ..     185     218 .. 0.90
   6 !   13.9   0.0   8.6e-05     0.053       1      34 []     219     252 ..     219     252 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.5e-08
                            TPR_17  1 lylkaleldPnnadaynnLAelll.knGdlmtAr 33
                                      +y ka+e+dP +a a++ ++el+   +G++++A+
  gi|330509103|ref|YP_004385531.1| 41 AYDKAIEIDPQSASAWFKKGELQIdFLGNYEEAL 74
                                      59********************95499****996 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 3.1e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + k+++++P  ada+++++++l   Gd+++A++
  gi|330509103|ref|YP_004385531.1|  77 FNKSIQINPQFADAWYQKGKTLTGYGDFEEALE 109
                                       89**************************99975 PP

  == domain 3  score: 26.0 bits;  conditional E-value: 1.2e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y k+le++Pn++da++ +A +l++++++++A+
  gi|330509103|ref|YP_004385531.1| 111 YNKSLEINPNSSDAWYWKAGVLAELNRHEEAI 142
                                       99***************************996 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 9.5e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y ka+eldP+ a  +  ++ +l ++++++ A
  gi|330509103|ref|YP_004385531.1| 144 AYDKAIELDPTQASYWLDRGGALNRLNRTEGA 175
                                       59******************999999988765 PP

  == domain 5  score: 15.0 bits;  conditional E-value: 3.9e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       l+ +a+e++P++  a++ ++++++++ +l + +
  gi|330509103|ref|YP_004385531.1| 185 LCDEAIEQNPKSIMAWQGKGTAFYHLERLNESI 217
                                       689*********************999887766 PP

  == domain 6  score: 13.9 bits;  conditional E-value: 8.6e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       ++ k++el P +  +y++++++l  +G+  +A++
  gi|330509103|ref|YP_004385531.1| 219 CFDKVIELAPMYYRSYYYKGKALQDLGREVEAEE 252
                                       799*************************999986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   3.5e-05     0.021      17      44 .]      35      62 ..      26      62 .. 0.92
   2 !   17.3   0.0   9.4e-06    0.0058      14      43 ..      67      96 ..      66      97 .. 0.94
   3 !   22.5   0.0     2e-07   0.00012       2      40 ..      89     127 ..      88     129 .. 0.94
   4 !   24.9   0.5   3.6e-08   2.2e-05       2      39 ..     123     160 ..     122     165 .. 0.94
   5 !   16.1   0.0   2.3e-05     0.014       4      41 ..     159     203 ..     158     206 .. 0.79
   6 ?    5.9   0.0     0.044        27       3      32 ..     199     228 ..     197     228 .. 0.93
   7 ?    2.1   0.1      0.72   4.5e+02       4      27 ..     234     257 ..     232     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.5e-05
                            TPR_14 17 pdeAiallrralalaPddaeawlllaql 44
                                      ++eA++++++a++ +P++a aw+  ++l
  gi|330509103|ref|YP_004385531.1| 35 LQEAREAYDKAIEIDPQSASAWFKKGEL 62
                                      689*******************998875 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 9.4e-06
                            TPR_14 14 lGdpdeAiallrralalaPddaeawlllaq 43
                                      lG+++eA++++++ ++ +P++a+aw++ ++
  gi|330509103|ref|YP_004385531.1| 67 LGNYEEALNAFNKSIQINPQFADAWYQKGK 96
                                      79***********************99876 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 2e-07
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       +a+++ ++ l   Gd++eA++ +++ l+ +P++ +aw+ 
  gi|330509103|ref|YP_004385531.1|  89 DAWYQKGKTLTGYGDFEEALESYNKSLEINPNSSDAWYW 127
                                       79**********************************985 PP

  == domain 4  score: 24.9 bits;  conditional E-value: 3.6e-08
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +a++  a +l++l +++eAi ++++a++l+P++a +wl
  gi|330509103|ref|YP_004385531.1| 123 DAWYWKAGVLAELNRHEEAIPAYDKAIELDPTQASYWL 160
                                       69**********************************98 PP

  == domain 5  score: 16.1 bits;  conditional E-value: 2.3e-05
                            TPR_14   4 llalaeallalGd.......pdeAiallrralalaPddaeawlll 41 
                                       +l+++ al +l +       + +A++l+++a++++P++  aw   
  gi|330509103|ref|YP_004385531.1| 159 WLDRGGALNRLNRteganasFTRAVELCDEAIEQNPKSIMAWQGK 203
                                       78888888888774444444667*******************865 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.044
                            TPR_14   3 allalaeallalGdpdeAiallrralalaP 32 
                                       a++  + a+++l+++ e+i++++++++laP
  gi|330509103|ref|YP_004385531.1| 199 AWQGKGTAFYHLERLNESIQCFDKVIELAP 228
                                       7888999********************998 PP

  == domain 7  score: 2.1 bits;  conditional E-value: 0.72
                            TPR_14   4 llalaeallalGdpdeAiallrra 27 
                                       ++  ++al  lG+  eA++l+ r 
  gi|330509103|ref|YP_004385531.1| 234 YYYKGKALQDLGREVEAEELFARS 257
                                       6778999*************9985 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   4.5e-07   0.00028      14      65 ..      36      85 ..      34      86 .. 0.87
   2 !   24.5   0.0   5.2e-08   3.2e-05      10      67 ..      67     121 ..      66     122 .. 0.96
   3 !   37.9   0.0   3.3e-12   2.1e-09      11      67 ..     102     155 ..      94     156 .. 0.95
   4 ?    7.4   0.1     0.012       7.1      25      63 ..     150     185 ..     148     197 .. 0.82
   5 !    9.5   0.0    0.0024       1.5      13      65 ..     179     228 ..     175     228 .. 0.93
   6 !   17.2   0.1   9.9e-06    0.0061       4      60 ..     204     257 ..     202     261 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.5e-07
                            TPR_16 14 ddAaaaleaalkrdpssPdaaeAllllgdaalrq.grlaeAaalyraalraap 65
                                      ++A++a++ a++ d   P+ a A++ +g++   + g+++eA+ ++++ ++  p
  gi|330509103|ref|YP_004385531.1| 36 QEAREAYDKAIEID---PQSASAWFKKGELQIDFlGNYEEALNAFNKSIQINP 85
                                      89************...***************999*******66655556555 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 5.2e-08
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +g+y++A++a++  +  +   P+ a+A++ +g  +   g+++eA++ y++ l+  p++
  gi|330509103|ref|YP_004385531.1|  67 LGNYEEALNAFNKSIQIN---PQFADAWYQKGKTLTGYGDFEEALESYNKSLEINPNS 121
                                       69****************...*******************************999987 PP

  == domain 3  score: 37.9 bits;  conditional E-value: 3.3e-12
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       gd+++A++ ++  l+ +   P   +A+++++ ++++++r++eA+ +y++a++ +p  
  gi|330509103|ref|YP_004385531.1| 102 GDFEEALESYNKSLEIN---PNSSDAWYWKAGVLAELNRHEEAIPAYDKAIELDPTQ 155
                                       8****************...88888***************************99975 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.012
                            TPR_16  25 krdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       ++d   P  a  +l +g a+ r++r ++A a + +a++ 
  gi|330509103|ref|YP_004385531.1| 150 ELD---PTQASYWLDRGGALNRLNRTEGANASFTRAVEL 185
                                       566...778999***********9999999999988854 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0024
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +++A+++ ++a++++   P    A+ ++g a++++ rl e ++ +++ ++ ap
  gi|330509103|ref|YP_004385531.1| 179 FTRAVELCDEAIEQN---PKSIMAWQGKGTAFYHLERLNESIQCFDKVIELAP 228
                                       899************...99999*******************99999988887 PP

  == domain 6  score: 17.2 bits;  conditional E-value: 9.9e-06
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                       ++a++ + +  + +  ++ +++++   P  +++++++g a+  +gr  eA++l+++ 
  gi|330509103|ref|YP_004385531.1| 204 GTAFYHLERLNESIQCFDKVIELA---PMYYRSYYYKGKALQDLGREVEAEELFARS 257
                                       7888999999**************...*************************99986 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   3.6e-06    0.0023      20      75 ..      36      84 ..      32      86 .. 0.79
   2 !   21.0   0.0   4.8e-07    0.0003      16      75 ..      67     118 ..      66     120 .. 0.90
   3 !   14.7   0.0   4.6e-05     0.028       4      32 ..     123     151 ..     120     155 .. 0.88
   4 !   23.3   0.0   9.3e-08   5.8e-05       5      75 ..     158     227 ..     154     229 .. 0.91
   5 ?    6.7   0.2     0.015       9.1       6      31 ..     234     259 ..     230     261 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.6e-06
                            TPR_12 20 deAlellekaleiarrllGpdhpltattlrnLgrly.ralgryeeAlelleealaia 75
                                      +eA+e ++ka+ei      p   + a++ +  g+l+ + lg+yeeAl++++++++i 
  gi|330509103|ref|YP_004385531.1| 36 QEAREAYDKAIEID-----P---QSASAWFKKGELQiDFLGNYEEALNAFNKSIQIN 84
                                      55666666665555.....5...5799********97799*************9986 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 4.8e-07
                            TPR_12  16 lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       lg+y+eAl  ++k+++i      p+    a + +  g ++   g++eeAle ++++l+i 
  gi|330509103|ref|YP_004385531.1|  67 LGNYEEALNAFNKSIQIN-----PQ---FADAWYQKGKTLTGYGDFEEALESYNKSLEIN 118
                                       89************9999.....65...57789999**********************95 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 4.6e-05
                            TPR_12   4 talnnlaavlrrlgrydeAlellekalei 32 
                                        a++  a vl++l r++eA+  ++ka+e+
  gi|330509103|ref|YP_004385531.1| 123 DAWYWKAGVLAELNRHEEAIPAYDKAIEL 151
                                       57788999*****************9997 PP

  == domain 4  score: 23.3 bits;  conditional E-value: 9.3e-08
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                        +  ++ +l+rl r + A + + +a+e++ +++  +++p  + + ++ g++++ l+r+ e ++ + +++++a
  gi|330509103|ref|YP_004385531.1| 158 YWLDRGGALNRLNRTEGANASFTRAVELCdEAI--EQNPKSIMAWQGKGTAFYHLERLNESIQCFDKVIELA 227
                                       455799***********************6666..89********************************997 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.015
                            TPR_12   6 lnnlaavlrrlgrydeAlellekale 31 
                                       ++  + +l+ lgr  eA+el+ ++ e
  gi|330509103|ref|YP_004385531.1| 234 YYYKGKALQDLGREVEAEELFARSKE 259
                                       45567777777777777777777765 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.4   4.9e-06     0.003       7      57 ..      35      86 ..      35      90 .. 0.92
   2 !   21.1   0.1   5.4e-07   0.00034       5      46 ..      68     109 ..      67     109 .. 0.97
   3 !   34.5   0.1   3.4e-11   2.1e-08       4      62 ..     101     159 ..      98     162 .. 0.94
   4 !   15.2   0.0   3.8e-05     0.023       6      62 ..     178     232 ..     161     241 .. 0.91
   5 ?    4.8   0.0     0.066        41      11      51 ..     217     257 ..     212     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.9e-06
                            TPR_19  7 yaeAlalleqalqedpknaearllLAeallal.gqldeAealLdalpeedpd 57
                                      ++eA +++ +a++ dp++a a+    e+++   g+++eA ++ ++  + +p+
  gi|330509103|ref|YP_004385531.1| 35 LQEAREAYDKAIEIDPQSASAWFKKGELQIDFlGNYEEALNAFNKSIQINPQ 86
                                      689****************************88********99998887776 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 5.4e-07
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                       g+y+eAl+++ + +q +p+ a+a+++  + l   g+++eA +
  gi|330509103|ref|YP_004385531.1|  68 GNYEEALNAFNKSIQINPQFADAWYQKGKTLTGYGDFEEALE 109
                                       89**************************************75 PP

  == domain 3  score: 34.5 bits;  conditional E-value: 3.4e-11
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                        gd++eAl+ + + l+ +p++++a+++ A +l +l++ +eA+ + d++ e dp +a y+
  gi|330509103|ref|YP_004385531.1| 101 YGDFEEALESYNKSLEINPNSSDAWYWKAGVLAELNRHEEAIPAYDKAIELDPTQASYW 159
                                       69***************************************************987776 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 3.8e-05
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                        +++A++l  +a++++pk+  a+ +   a + l +l+e +++ d++ e +p   +y+
  gi|330509103|ref|YP_004385531.1| 178 SFTRAVELCDEAIEQNPKSIMAWQGKGTAFYHLERLNESIQCFDKVIELAPM--YYR 232
                                       6899*******************************************99998..444 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.066
                            TPR_19  11 lalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                       ++ + ++++ +p + +  ++  +al  lg+  eAe+l ++ 
  gi|330509103|ref|YP_004385531.1| 217 IQCFDKVIELAPMYYRSYYYKGKALQDLGREVEAEELFARS 257
                                       66688999999999999**99***************99875 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     3e-05     0.018      12      65 ..      36      90 ..      29      91 .. 0.92
   2 !   18.1   0.0   3.7e-06    0.0023      10      65 ..      69     124 ..      67     129 .. 0.95
   3 !   19.6   0.0   1.2e-06   0.00076       9      61 ..     102     154 ..      97     156 .. 0.95
   4 !   28.7   0.2   1.8e-09   1.1e-06       5      62 ..     132     189 ..     128     192 .. 0.94
   5 !    8.8   0.0    0.0027       1.7      25      60 ..     193     228 ..     189     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-05
                             TPR_9 12 eralavverllllaPddpeerrdRGlllaq.lGclsaAladLeaylalapdapda 65
                                      ++a ++++  + ++P++++ ++  G l+   lG++++Al++++  ++++p+ +da
  gi|330509103|ref|YP_004385531.1| 36 QEAREAYDKAIEIDPQSASAWFKKGELQIDfLGNYEEALNAFNKSIQINPQFADA 90
                                      679999***********************879***************99987665 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.7e-06
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       ++e+al + +  ++++P+ ++ ++  G  l   G++++Al+  +  l+++p+  da
  gi|330509103|ref|YP_004385531.1|  69 NYEEALNAFNKSIQINPQFADAWYQKGKTLTGYGDFEEALESYNKSLEINPNSSDA 124
                                       5899***********************************************99887 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 1.2e-06
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                        d+e+al+ ++  l ++P++ + ++  + +la+l++ ++A+ + + +++l+p 
  gi|330509103|ref|YP_004385531.1| 102 GDFEEALESYNKSLEINPNSSDAWYWKAGVLAELNRHEEAIPAYDKAIELDPT 154
                                       69*************************************************96 PP

  == domain 4  score: 28.7 bits;  conditional E-value: 1.8e-09
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       +++ +++e+a+ +++  + l+P +++ ++dRG +l +l+++++A a + ++++l+++a
  gi|330509103|ref|YP_004385531.1| 132 LAELNRHEEAIPAYDKAIELDPTQASYWLDRGGALNRLNRTEGANASFTRAVELCDEA 189
                                       577899*************************************************987 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0027
                             TPR_9  25 aPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       +P+++  +   G + ++l++l++ +++++  ++lap
  gi|330509103|ref|YP_004385531.1| 193 NPKSIMAWQGKGTAFYHLERLNESIQCFDKVIELAP 228
                                       699999***************************999 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2     0.023        14      17      33 .]      36      52 ..      22      52 .. 0.94
   2 !   12.6   0.0   0.00027      0.17       2      31 ..      55      85 ..      54      86 .. 0.93
   3 !   10.0   0.0    0.0018       1.1       1      33 []      89     121 ..      89     121 .. 0.91
   4 !    9.4   0.0    0.0028       1.7       1      31 [.     123     153 ..     123     154 .. 0.86
   5 ?    2.7   0.0      0.39   2.4e+02      17      33 .]     180     196 ..     164     196 .. 0.84
   6 ?    3.8   0.0      0.17   1.1e+02       7      31 ..     204     228 ..     200     228 .. 0.89
   7 ?    2.7   0.2      0.38   2.4e+02       2      25 ..     233     256 ..     232     258 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.023
                                      HHHHHHHHHHHHH-TT- CS
                             TPR_6 17 dkAlealerlikeYPdS 33
                                      ++A+ea+++ i+  P+S
  gi|330509103|ref|YP_004385531.1| 36 QEAREAYDKAIEIDPQS 52
                                      69*************98 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00027
                                      HHHHHHHHHHH.HHHHHHHHHHHHHHHHH-T CS
                             TPR_6  2 Alyklalsyrk.lgdtdkAlealerlikeYP 31
                                      A +k +++++  lg++++Al a+++ i+  P
  gi|330509103|ref|YP_004385531.1| 55 AWFKKGELQIDfLGNYEEALNAFNKSIQINP 85
                                      89********99*************999888 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPdS 33 
                                       dA y+ ++ +   gd ++Ale +++ ++  P+S
  gi|330509103|ref|YP_004385531.1|  89 DAWYQKGKTLTGYGDFEEALESYNKSLEINPNS 121
                                       68899999999868*****************98 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                       dA y+ a  + +l+++++A+ a+++ i+  P
  gi|330509103|ref|YP_004385531.1| 123 DAWYWKAGVLAELNRHEEAIPAYDKAIELDP 153
                                       68888888888888*************9888 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHH-TT- CS
                             TPR_6  17 dkAlealerlikeYPdS 33 
                                       ++A+e+ ++ i++ P+S
  gi|330509103|ref|YP_004385531.1| 180 TRAVELCDEAIEQNPKS 196
                                       68999999999999988 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       + +++ l +  ++++ ++++i+  P
  gi|330509103|ref|YP_004385531.1| 204 GTAFYHLERLNESIQCFDKVIELAP 228
                                       789999779************9877 PP

  == domain 7  score: 2.7 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealer 25 
                                       ++y+ +++++ lg+  +A e++ r
  gi|330509103|ref|YP_004385531.1| 233 SYYYKGKALQDLGREVEAEELFAR 256
                                       689********99*****999976 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00083      0.52      41      81 ..      37      79 ..      35      80 .. 0.86
   2 !   32.4   0.1   1.3e-10   7.8e-08       4      81 ..      69     147 ..      68     148 .. 0.97
   3 !   11.2   0.0   0.00053      0.33      36      81 ..     176     222 ..     174     223 .. 0.95
   4 ?    1.2   0.1      0.69   4.3e+02      21      49 ..     229     257 ..     218     261 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00083
                                      HHHHHHHCT.SHHHC-HHHHHHHHHHHH.HTT-HHHHHHHH-S CS
                            ANAPC3 41 rAyellrka.klnskslgcrylfAqcll.kLkkyeeAiaaLek 81
                                      +A e ++ka +++++s  +++ +++ ++  L++yeeA++a+ k
  gi|330509103|ref|YP_004385531.1| 37 EAREAYDKAiEIDPQSASAWFKKGELQIdFLGNYEEALNAFNK 79
                                      566677777788****************778*********987 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 1.3e-10
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       ny++A+  +++  + +++ +++ y ++++l   g++++A+e ++k+ ++n++s  ++y +A +l +L+++eeAi a+
  gi|330509103|ref|YP_004385531.1|  69 NYEEALNAFNKSIQINPQFADAWYQKGKTLTGYGDFEEALESYNKSlEINPNSSDAWYWKAGVLAELNRHEEAIPAY 145
                                       8*************************************************************************998 PP

                                       -S CS
                            ANAPC3  80 ek 81 
                                       +k
  gi|330509103|ref|YP_004385531.1| 146 DK 147
                                       87 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00053
                                       TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       n  ++rA el+++a ++n+ks+ ++  ++ + + L++++e i++++k
  gi|330509103|ref|YP_004385531.1| 176 NASFTRAVELCDEAiEQNPKSIMAWQGKGTAFYHLERLNESIQCFDK 222
                                       5679****************************************998 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.69
                                       --HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                            ANAPC3  21 espedayllAlclylngqykrAyellrka 49 
                                         + + y+++++l  +g+  +A el+ ++
  gi|330509103|ref|YP_004385531.1| 229 MYYRSYYYKGKALQDLGREVEAEELFARS 257
                                       44445555566666666666666665555 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.7e-07    0.0006     201     252 ..      63     114 ..      14     121 .. 0.81
   2 ?    3.2   0.0     0.054        33      44      75 ..     128     159 ..     120     176 .. 0.70
   3 !   10.0   0.0   0.00048       0.3     207     251 ..     178     222 ..     168     226 .. 0.89
   4 !    6.2   0.0    0.0065         4     204     255 ..     209     260 ..     204     262 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.7e-07
                                       HHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 201 hydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                         d lg++e+Al+  +k i+ +p++ + +++K++ l  +Gd+++A e  +++
  gi|330509103|ref|YP_004385531.1|  63 QIDFLGNYEEALNAFNKSIQINPQFADAWYQKGKTLTGYGDFEEALESYNKS 114
                                       46999*****************************************998876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.054
                                       HHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHH CS
                             NARP1  44 kaelllkLgrkeeAeatyeaLlernpenskYy 75 
                                       ka +l +L+r+eeA  +y + +e  p + +Y+
  gi|330509103|ref|YP_004385531.1| 128 KAGVLAELNRHEEAIPAYDKAIELDPTQASYW 159
                                       56666677777777777777777666666665 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00048
                                       -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                             NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmee 251
                                       s ++A+e+ d+aie++p+++  ++ K++ + h   l++ +++ ++
  gi|330509103|ref|YP_004385531.1| 178 SFTRAVELCDEAIEQNPKSIMAWQGKGTAFYHLERLNESIQCFDK 222
                                       5679****************************9999999988877 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0065
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                       +l++ ++++++ dk ie  p     y+ K++ l+  G   +A e+  ++++l
  gi|330509103|ref|YP_004385531.1| 209 HLERLNESIQCFDKVIELAPMYYRSYYYKGKALQDLGREVEAEELFARSKEL 260
                                       6778899***********************************9999988877 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.6     1e+03      16      31 ..      36      49 ..      35      54 .. 0.58
   2 ?    4.6   0.0     0.061        37       6      26 ..      60      81 ..      53      90 .. 0.77
   3 !    7.8   0.0    0.0059       3.6      13      29 ..     102     118 ..      88     124 .. 0.82
   4 !   10.4   0.0   0.00086      0.53       9      34 ..     132     155 ..     128     157 .. 0.83
   5 ?    0.2   0.0       1.6     1e+03      15      31 ..     179     193 ..     165     197 .. 0.79
   6 ?   -1.8   0.0       6.9   4.3e+03      12      28 ..     210     226 ..     204     228 .. 0.68
   7 ?    3.3   0.1      0.16        98       1      25 [.     233     257 ..     233     261 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.6
                             TPR_7 16 eeAielyeqsLaltkd 31
                                      +eA e y +  a++ d
  gi|330509103|ref|YP_004385531.1| 36 QEAREAYDK--AIEID 49
                                      566666666..55544 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.061
                             TPR_7  6 arlysr.lGdyeeAielyeqsL 26
                                      ++l+ + lG+yeeA+  + +s+
  gi|330509103|ref|YP_004385531.1| 60 GELQIDfLGNYEEALNAFNKSI 81
                                      55666679******99887765 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0059
                             TPR_7  13 GdyeeAielyeqsLalt 29 
                                       Gd+eeA+e y +sL++ 
  gi|330509103|ref|YP_004385531.1| 102 GDFEEALESYNKSLEIN 118
                                       9***********99986 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00086
                             TPR_7   9 ysrlGdyeeAielyeqsLaltkdped 34 
                                         +l+++eeAi  y +  a++ dp+ 
  gi|330509103|ref|YP_004385531.1| 132 LAELNRHEEAIPAYDK--AIELDPTQ 155
                                       5789************..88888865 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 1.6
                             TPR_7  15 yeeAielyeqsLaltkd 31 
                                       + +A+el+ +  a++  
  gi|330509103|ref|YP_004385531.1| 179 FTRAVELCDE--AIEQN 193
                                       5688888888..77655 PP

  == domain 6  score: -1.8 bits;  conditional E-value: 6.9
                             TPR_7  12 lGdyeeAielyeqsLal 28 
                                       l +  e i+++ ++++l
  gi|330509103|ref|YP_004385531.1| 210 LERLNESIQCFDKVIEL 226
                                       55666889999986555 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.16
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqs 25 
                                       ++++ + + ++lG+  eA+el+ +s
  gi|330509103|ref|YP_004385531.1| 233 SYYYKGKALQDLGREVEAEELFARS 257
                                       688999****************985 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2      0.21   1.3e+02      18      31 ..      35      48 ..      34      49 .. 0.91
   2 ?    4.3   0.0     0.061        38      15      31 ..      67      83 ..      66      84 .. 0.91
   3 ?    2.6   0.0      0.21   1.3e+02      24      38 ..     103     117 ..     101     123 .. 0.69
   4 !    7.4   0.1    0.0068       4.2       9      30 ..     129     150 ..     128     151 .. 0.91
   5 ?    2.8   0.0      0.18   1.1e+02       9      37 ..     163     191 ..     161     194 .. 0.75
   6 ?   -0.2   0.0       1.7     1e+03      10      31 ..     205     226 ..     204     227 .. 0.85
   7 ?    4.5   0.1     0.053        33       9      28 ..     238     257 ..     232     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.21
                            TPR_10 18 ydeAealleealai 31
                                      ++eA++ +++a++i
  gi|330509103|ref|YP_004385531.1| 35 LQEAREAYDKAIEI 48
                                      59**********97 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.061
                            TPR_10 15 rgrydeAealleealai 31
                                      +g+y+eA++ + ++++i
  gi|330509103|ref|YP_004385531.1| 67 LGNYEEALNAFNKSIQI 83
                                      69*********999987 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.21
                            TPR_10  24 lleealairrrllGp 38 
                                       ++eeal+ + + l+ 
  gi|330509103|ref|YP_004385531.1| 103 DFEEALESYNKSLEI 117
                                       467777777777763 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0068
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       a +l +++r++eA   +++a++
  gi|330509103|ref|YP_004385531.1| 129 AGVLAELNRHEEAIPAYDKAIE 150
                                       66899***************98 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.18
                            TPR_10   9 analrqrgrydeAealleealairrrllG 37 
                                       + al +++r ++A a + +a++++ ++ +
  gi|330509103|ref|YP_004385531.1| 163 GGALNRLNRTEGANASFTRAVELCDEAIE 191
                                       56788888888888888888888877765 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 1.7
                            TPR_10  10 nalrqrgrydeAealleealai 31 
                                        a +++ r++e+ + +++++++
  gi|330509103|ref|YP_004385531.1| 205 TAFYHLERLNESIQCFDKVIEL 226
                                       5678899***********9986 PP

  == domain 7  score: 4.5 bits;  conditional E-value: 0.053
                            TPR_10   9 analrqrgrydeAealleea 28 
                                       + al+++gr  eAe+l+ ++
  gi|330509103|ref|YP_004385531.1| 238 GKALQDLGREVEAEELFARS 257
                                       779*************9875 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 ?    2.9   0.1      0.19   1.2e+02      21      32 ..      36      47 ..      19      48 .. 0.79
   2 !    7.1   0.0    0.0089       5.5       8      32 ..      57      82 ..      51      86 .. 0.77
   3 ?    6.6   0.1     0.013       8.2      18      32 ..     102     116 ..     100     117 .. 0.92
   4 ?    5.2   0.1     0.036        22      16      33 ..     134     151 ..     128     151 .. 0.83
   5 ?    1.4   0.0      0.56   3.4e+02      21      46 ..     173     197 ..     166     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.19
                               MIT 21 eeAlelYkeale 32
                                      +eA e+Y +a+e
  gi|330509103|ref|YP_004385531.1| 36 QEAREAYDKAIE 47
                                      788888888887 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0089
                               MIT  8 vkkA.veeDnagnyeeAlelYkeale 32
                                      +kk   + D  gnyeeAl+++ ++++
  gi|330509103|ref|YP_004385531.1| 57 FKKGeLQIDFLGNYEEALNAFNKSIQ 82
                                      555556668889*********99997 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.013
                               MIT  18 gnyeeAlelYkeale 32 
                                       g++eeAle Y ++le
  gi|330509103|ref|YP_004385531.1| 102 GDFEEALESYNKSLE 116
                                       799**********98 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.036
                               MIT  16 nagnyeeAlelYkealel 33 
                                       + +  eeA+ +Y +a+el
  gi|330509103|ref|YP_004385531.1| 134 ELNRHEEAIPAYDKAIEL 151
                                       56789***********96 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.56
                               MIT  21 eeAlelYkealelLlqalkekneerr 46 
                                       e A   ++ a+el+ +a+  +n+++ 
  gi|330509103|ref|YP_004385531.1| 173 EGANASFTRAVELCDEAIE-QNPKSI 197
                                       6677788899999999995.666665 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   0.4    0.0018       1.1      62     129 ..      53     117 ..      13     122 .. 0.78
   2 !    8.2   0.0    0.0039       2.4      77     129 ..     103     151 ..      88     157 .. 0.72
   3 ?    4.9   0.0      0.04        25      80     132 ..     140     188 ..     133     196 .. 0.77
   4 ?    4.8   0.0     0.045        28     101     128 ..     232     259 ..     187     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                                       HHHHHHTT-HH.HHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  62 sealaklgryd.ealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                       ++a+ k g+ + + l   ++al+ fn+  +++ +    W    ++++++l + G  +eal++++++ e+
  gi|330509103|ref|YP_004385531.1|  53 ASAWFKKGELQiDFLGNYEEALNAFNKSIQINPQFADAW----YQKGKTLTGYGDFEEALESYNKSLEI 117
                                       556666666653456778899999999999987666666....89******************998875 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0039
                                       HHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  77 sadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                         ++al+ +n+  e++ +    W    + +a  l+el r++ea+ a+ +a e+
  gi|330509103|ref|YP_004385531.1| 103 DFEEALESYNKSLEINPNSSDAW----YWKAGVLAELNRHEEAIPAYDKAIEL 151
                                       34556666677777888888777....56888899999999999999998885 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.04
                                       HHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                           DUF3856  80 kalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagemiae 132
                                       +a+  +++  el+  + + W+    +r+ al+ l r++ a  +f  a+e+ +e
  gi|330509103|ref|YP_004385531.1| 140 EAIPAYDKAIELDPTQASYWL----DRGGALNRLNRTEGANASFTRAVELCDE 188
                                       555555566666666666664....7999*******************99988 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.045
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 101 aavfsravaleelGrkdealkafrmage 128
                                       +  + +++al++lGr+ ea + f  ++e
  gi|330509103|ref|YP_004385531.1| 232 RSYYYKGKALQDLGREVEAEELFARSKE 259
                                       5567899999999999999999988776 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.063        39      75     121 ..      67     113 ..      33     117 .. 0.86
   2 !   15.0   0.2   4.1e-05     0.025      70     135 ..     130     195 ..     122     199 .. 0.91
   3 ?    2.3   0.1      0.33     2e+02      73     123 ..     208     258 ..     195     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.063
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                       lG +eeal   ++ ++ +P   +++ q  + l   G+ +eALe Y++
  gi|330509103|ref|YP_004385531.1|  67 LGNYEEALNAFNKSIQINPQFADAWYQKGKTLTGYGDFEEALESYNK 113
                                       7999*****************************************86 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.1e-05
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS---- CS
                              BTAD  70 eaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepg 135
                                         +++l+r+eea++ ++++++++P++  ++     Al r++r++ A + + r+++l +e +   p+
  gi|330509103|ref|YP_004385531.1| 130 GVLAELNRHEEAIPAYDKAIELDPTQASYWLDRGGALNRLNRTEGANASFTRAVELCDEAIEQNPK 195
                                       56789*************************************************999998877775 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.33
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                        +l+r +e ++  ++ +++ P+  r++    +Al  +Gr+ eA e + r +
  gi|330509103|ref|YP_004385531.1| 208 YHLERLNESIQCFDKVIELAPMYYRSYYYKGKALQDLGREVEAEELFARSK 258
                                       56788888888888899999999999999999999******9999998865 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.015       9.3       7      20 ..      44      57 ..      43      57 .. 0.92
   2 !   11.6   0.0   0.00029      0.18       3      20 ..     184     201 ..     182     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                                      HHHHH-TT-CHHHH CS
                              PPTA  7 kliekdpkNYsaWn 20
                                      k+ie dp++ saW+
  gi|330509103|ref|YP_004385531.1| 44 KAIEIDPQSASAWF 57
                                      89***********5 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00029
                                       HHHHHHHHH-TT-CHHHH CS
                              PPTA   3 eltekliekdpkNYsaWn 20 
                                       el++++ie++pk+  aW+
  gi|330509103|ref|YP_004385531.1| 184 ELCDEAIEQNPKSIMAWQ 201
                                       8****************6 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.8   0.00021      0.13     203     291 ..      18      93 ..       7      99 .. 0.75
   2 !    6.3   0.6    0.0077       4.8     259     303 ..     102     139 ..      92     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                       HHHHSSCCHHHHCCTSSCCCSS-SS---............HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCH CS
                               FAT 203 qkealqkLreftsellekkeelqsgleaqkeptnleeftkllarcylkkGewqealqkldwseekieeilqsysaat 279
                                       ++ a+++++ +t +      e+  + + +   ++  e+  + a + +kkGe q+ +        + ee+l+++ ++ 
  gi|330509103|ref|YP_004385531.1|  18 REMAINEMQNQTAR------EIFLQEARE-AYDKAIEIDPQSASAWFKKGELQIDFLG------NYEEALNAFNKSI 81 
                                       56677777777773......333343333.55666677777799**********9998......39*********** PP

                                       HCTCCCHSTTCC CS
                               FAT 280 eidpswykawht 291
                                       +i+p+ ++aw++
  gi|330509103|ref|YP_004385531.1|  82 QINPQFADAWYQ 93 
                                       **********86 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0077
                                       CCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHH CS
                               FAT 259 qkldwseekieeilqsysaateidpswykawhtwalfnfevvske 303
                                       ++       +ee+l+sy ++ ei+p++ +aw+  a +  e  ++e
  gi|330509103|ref|YP_004385531.1| 102 GD-------FEEALESYNKSLEINPNSSDAWYWKAGVLAELNRHE 139
                                       44.......889999999999999999999976555555555555 PP

>> Ribosomal_S16  Ribosomal protein S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.62   3.8e+02      47      58 ..       3      14 ..       2      17 .. 0.85
   2 ?    4.3   0.1     0.066        41      26      58 ..      64      95 ..      23      99 .. 0.78
   3 ?    6.6   0.0     0.013       8.1      43      58 ..     140     163 ..     102     166 .. 0.69
   4 ?   -1.8   0.0       5.4   3.3e+03      44      59 ..     190     205 ..     179     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.62
                                      -HHHHHHHHHTT CS
                     Ribosomal_S16 47 neerikyWlgvG 58
                                      +e+ + yWl++G
  gi|330509103|ref|YP_004385531.1|  3 KEDTAGYWLNKG 14
                                      578899*****9 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.066
                                      SEEEEEEETTTTSSTS.SEEE-HHHHHHHHHTT CS
                     Ribosomal_S16 26 iEklGtYdPlakkkekkevelneerikyWlgvG 58
                                      i+ lG Y+   +  +k ++++n + +  W ++G
  gi|330509103|ref|YP_004385531.1| 64 IDFLGNYEEALNAFNK-SIQINPQFADAWYQKG 95
                                      6778888873333333.4889999999998888 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.013
                                       S........EEE-HHHHHHHHHTT CS
                     Ribosomal_S16  43 e........velneerikyWlgvG 58 
                                       e        +el+ +++ yWl  G
  gi|330509103|ref|YP_004385531.1| 140 EaipaydkaIELDPTQASYWLDRG 163
                                       044555555************998 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 5.4
                                       EEE-HHHHHHHHHTTE CS
                     Ribosomal_S16  44 velneerikyWlgvGA 59 
                                       +e n + i  W g+G 
  gi|330509103|ref|YP_004385531.1| 190 IEQNPKSIMAWQGKGT 205
                                       6777888999999995 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      0.71   4.4e+02      18      34 ..      36      52 ..      35      56 .. 0.86
   2 ?    6.8   0.0     0.011       7.1      14      37 ..      67      90 ..      67      91 .. 0.92
   3 ?    2.8   0.0      0.21   1.3e+02      14      35 ..     101     122 ..      97     125 .. 0.88
   4 ?   -1.3   0.0       3.9   2.4e+03      17      32 ..     179     194 ..     177     196 .. 0.85
   5 ?   -1.9   0.0         6   3.7e+03      11      32 ..     207     228 ..     205     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.71
                                      HHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C 18 seArryvdalLeiEPen 34
                                      +eAr+  d  +ei+P+ 
  gi|330509103|ref|YP_004385531.1| 36 QEAREAYDKAIEIDPQS 52
                                      58*************86 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.011
                                      HT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPenrQa 37
                                      lg+Y+eA++  +  ++i P++  a
  gi|330509103|ref|YP_004385531.1| 67 LGNYEEALNAFNKSIQINPQFADA 90
                                      79*****************98765 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.21
                                       HT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenr 35 
                                        g+++eA++  +  Lei P+ +
  gi|330509103|ref|YP_004385531.1| 101 YGDFEEALESYNKSLEINPNSS 122
                                       589****************966 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.9
                                       HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C  17 YseArryvdalLeiEP 32 
                                       +++A +++d  +e  P
  gi|330509103|ref|YP_004385531.1| 179 FTRAVELCDEAIEQNP 194
                                       78999****9999887 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 6
                                       HHHHT-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEP 32 
                                        y l + +e+ ++ d ++e+ P
  gi|330509103|ref|YP_004385531.1| 207 FYHLERLNESIQCFDKVIELAP 228
                                       5788889999999999888777 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       2.3   1.4e+03      14      21 ..      67      74 ..      65      77 .. 0.85
   2 ?    0.9   0.0       1.7     1e+03      15      22 ..     102     109 ..      94     111 .. 0.92
   3 ?    4.0   0.1      0.16     1e+02       3      20 ..     124     141 ..     123     146 .. 0.88
   4 ?   -0.9   0.2       6.4   3.9e+03       4      20 ..     159     175 ..     156     177 .. 0.81
   5 ?    6.3   0.0     0.029        18       7      26 .]     237     256 ..     232     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.3
                             TPR_4 14 lGdldeAr 21
                                      lG+++eA+
  gi|330509103|ref|YP_004385531.1| 67 LGNYEEAL 74
                                      8******8 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.7
                             TPR_4  15 GdldeAra 22 
                                       Gd++eA++
  gi|330509103|ref|YP_004385531.1| 102 GDFEEALE 109
                                       9*****96 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.16
                             TPR_4   3 allaLArallalGdldeA 20 
                                       a ++ A +l++l +++eA
  gi|330509103|ref|YP_004385531.1| 124 AWYWKAGVLAELNRHEEA 141
                                       5688899**********9 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 6.4
                             TPR_4   4 llaLArallalGdldeA 20 
                                        l+++ al +l + + A
  gi|330509103|ref|YP_004385531.1| 159 WLDRGGALNRLNRTEGA 175
                                       57788899999999988 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.029
                             TPR_4   7 LArallalGdldeAraller 26 
                                        + al++lG+  eA++l++r
  gi|330509103|ref|YP_004385531.1| 237 KGKALQDLGREVEAEELFAR 256
                                       5789************9876 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.37   2.3e+02     118     136 ..      23      41 ..      15      44 .. 0.85
   2 ?    7.2   0.0     0.011       6.7      71     123 ..      90     142 ..      58     146 .. 0.90
   3 ?    3.7   0.0      0.13        79      81     123 ..     175     217 ..     163     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.37
                                       HH-SSHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr 118 yqaesatwRniYlsgakel 136
                                       +++++ t+R+i+l++a+e 
  gi|330509103|ref|YP_004385531.1|  23 NEMQNQTAREIFLQEAREA 41 
                                       5789************996 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  71 kvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       +  +k k+    gd++ a+e  n+ ++ +p+ ++a   ka +l +l +++e+ 
  gi|330509103|ref|YP_004385531.1|  90 AWYQKGKTLTGYGDFEEALESYNKSLEINPNSSDAWYWKAGVLAELNRHEEAI 142
                                       5567788888899*********************************9999876 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.13
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       ++  +  a+el++ +++++p+   a + k  a+ +l + +es 
  gi|330509103|ref|YP_004385531.1| 175 ANASFTRAVELCDEAIEQNPKSIMAWQGKGTAFYHLERLNESI 217
                                       5566888**************9999999999988888888775 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.06        37      55     113 ..      69     121 ..      55     152 .. 0.67
   2 ?    7.5   0.0    0.0037       2.3      14      72 ..     176     229 ..     171     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.06
                          TPR_MalT  55 dleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateq 113
                                       + e+Al+a+++ +++       ++ + a +q +++l+  G+++eAle y+++l+  + +
  gi|330509103|ref|YP_004385531.1|  69 NYEEALNAFNKSIQIN------PQFADAWYQKGKTLTGYGDFEEALESYNKSLEINPNS 121
                                       5555555555555554......3445566788899999999999999999988865544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0037
                          TPR_MalT  14 sgdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarq 72 
                                          ++ra+el+ +A+++ p++ + +++      G+a+ + ++l+++ q + ++++la +
  gi|330509103|ref|YP_004385531.1| 176 NASFTRAVELCDEAIEQNPKSIMAWQGK-----GTAFYHLERLNESIQCFDKVIELAPM 229
                                       56789****************9999987.....6777999***********99999843 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.03        19      48     104 ..      24      81 ..      12     119 .. 0.69
   2 ?    3.5   0.0      0.12        72      59      86 ..     213     240 ..     174     258 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.03
                            DUF627  48 ktedpdvkfayllasvecfseavelsrfyArsLfelas.qlgsklyYkkavkkakraL 104
                                       ++++++++  +l+ + e++ +a e+   +A+  f+ ++ q++    Y++a++  ++++
  gi|330509103|ref|YP_004385531.1|  24 EMQNQTAREIFLQEAREAYDKAIEIDPQSASAWFKKGElQIDFLGNYEEALNAFNKSI 81 
                                       5667777777777777777777777777777777777633444446666665554444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
                            DUF627  59 llasvecfseavelsrfyArsLfelasq 86 
                                       l  s++cf +  el+ +y rs +  ++ 
  gi|330509103|ref|YP_004385531.1| 213 LNESIQCFDKVIELAPMYYRSYYYKGKA 240
                                       4568888888888886666666555554 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0       0.2   1.2e+02      15      30 ..      68      83 ..      68      86 .. 0.91
   2 ?    6.1   0.0     0.013       7.7      17      30 ..     104     117 ..     102     118 .. 0.95
   3 ?   -2.1   0.0       4.5   2.8e+03      16      30 ..     137     151 ..     134     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.2
                          SHNi-TPR 15 enFpqAveDlrkaLeL 30
                                      +n+++A+  ++k++++
  gi|330509103|ref|YP_004385531.1| 68 GNYEEALNAFNKSIQI 83
                                      59***********997 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                          SHNi-TPR  17 FpqAveDlrkaLeL 30 
                                       F++A+e ++k+Le+
  gi|330509103|ref|YP_004385531.1| 104 FEEALESYNKSLEI 117
                                       9***********98 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.5
                          SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                       + ++A+  ++ka+eL
  gi|330509103|ref|YP_004385531.1| 137 RHEEAIPAYDKAIEL 151
                                       668899899999997 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0     0.002       1.2      41      72 ..      53      85 ..      22      92 .. 0.84
   2 ?   -0.4   0.0         2   1.2e+03      51      70 ..     132     151 ..      99     156 .. 0.79
   3 ?   -2.2   0.0         7   4.3e+03      52      71 ..     208     227 ..     203     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.002
                            ANAPC5 41 qyalLnlaslhadf.ghneeAvkaleeairlAr 72
                                       +a ++   l+ df g++eeA++a++ +i++  
  gi|330509103|ref|YP_004385531.1| 53 ASAWFKKGELQIDFlGNYEEALNAFNKSIQINP 85
                                      568899999****99**************9965 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2
                            ANAPC5  51 hadfghneeAvkaleeairl 70 
                                        a+++ +eeA+ a   ai+l
  gi|330509103|ref|YP_004385531.1| 132 LAELNRHEEAIPAYDKAIEL 151
                                       46778888888888888875 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7
                            ANAPC5  52 adfghneeAvkaleeairlA 71 
                                       ++++  +e+++ +  +i+lA
  gi|330509103|ref|YP_004385531.1| 208 YHLERLNESIQCFDKVIELA 227
                                       67788888888888888887 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         7   4.3e+03       9      15 ..      42      48 ..      37      54 .. 0.66
   2 ?    3.9   0.6     0.064        39       2      16 ..      70      84 ..      69     111 .. 0.86
   3 ?    0.2   0.0      0.94   5.8e+02       2      15 ..     104     117 ..     103     122 .. 0.84
   4 ?    0.2   0.0       0.9   5.6e+02       2       9 ..     138     145 ..     124     157 .. 0.57
   5 ?    2.6   0.3      0.17     1e+02      29      42 ..     234     247 ..     232     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7
                                      HHHHHHH CS
                          HTH_Bact  9 vnkAiei 15
                                       +kAiei
  gi|330509103|ref|YP_004385531.1| 42 YDKAIEI 48
                                      5667766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.064
                                      HHHHHHHHHHHHHHH CS
                          HTH_Bact  2 YeeaLeqvnkAieiS 16
                                      YeeaL+  nk i+i 
  gi|330509103|ref|YP_004385531.1| 70 YEEALNAFNKSIQIN 84
                                      99*******999985 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.94
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                       +eeaLe  nk +ei
  gi|330509103|ref|YP_004385531.1| 104 FEEALESYNKSLEI 117
                                       68999999999987 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.9
                                       HHHHHHHH CS
                          HTH_Bact   2 YeeaLeqv 9  
                                        eea+   
  gi|330509103|ref|YP_004385531.1| 138 HEEAIPAY 145
                                       34444444 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHTT-- CS
                          HTH_Bact  29 yYqkgecleklgfs 42 
                                       yY+kg+ l  lg +
  gi|330509103|ref|YP_004385531.1| 234 YYYKGKALQDLGRE 247
                                       9*******999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 1583.64
//
Query:       gi|330509104|ref|YP_004385532.1|  [L=438]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-47  155.9  26.0    8.4e-08   31.7   0.0   12.1 12  TPR_1            Tetratricopeptide repeat
      3e-42  139.3  27.0    5.5e-06   26.1   0.1   11.6 12  TPR_2            Tetratricopeptide repeat
    2.7e-39  132.6  27.4    2.3e-07   30.4   2.5   10.2 10  TPR_11           TPR repeat
      2e-37  124.3  26.2    4.8e-05   23.2   0.1   12.1 12  TPR_8            Tetratricopeptide repeat
    4.1e-32  110.3   9.1    2.9e-08   33.9   0.0    6.5  6  TPR_12           Tetratricopeptide repeat
    1.2e-29  102.6  14.7    1.6e-07   31.9   0.0    7.5  8  TPR_16           Tetratricopeptide repeat
    6.9e-28   95.0  12.4     0.0022   18.7   0.1   10.1 10  TPR_14           Tetratricopeptide repeat
    2.9e-24   85.4  14.0    0.00023   21.6   0.0    7.5  7  TPR_19           Tetratricopeptide repeat
    1.2e-23   81.8  11.2     0.0028   17.9   0.0    8.2  7  TPR_17           Tetratricopeptide repeat
    9.8e-18   64.1   0.4    0.00041   20.4   0.0    5.5  5  TPR_9            Tetratricopeptide repeat
    1.9e-13   49.8  12.7      0.011   15.6   0.0    7.8  8  TPR_10           Tetratricopeptide repeat
    1.2e-12   47.9   1.0      0.018   15.3   0.0    5.5  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
      3e-11   43.2   5.1     0.0032   17.5   0.0    6.3  7  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    3.3e-10   39.2   8.7      0.078   13.0   0.0    7.8  8  TPR_7            Tetratricopeptide repeat
    6.4e-10   39.3  13.5        0.1   12.7   0.6    6.2  6  DUF3856          Domain of Unknown Function (DUF3856)
    1.7e-09   37.7  14.6      0.017   14.9   0.1    5.8  5  TPR_21           Tetratricopeptide repeat-like domain
    6.1e-08   32.0   5.0     0.0089   15.0   0.1    4.1  4  NARP1            NMDA receptor-regulated protein 1
    7.1e-08   32.6  13.3        9.1    7.2   0.0    9.4 10  TPR_6            Tetratricopeptide repeat
    3.8e-07   30.6   4.5     0.0073   16.8   0.0    4.3  4  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    6.9e-07   29.8   8.9     0.0002   21.8   0.0    5.5  5  BTAD             Bacterial transcriptional activator domain
    3.6e-05   23.3   7.6         14    5.4   0.0    7.6  9  HTH_Bact         Helix-turn-helix bacterial domain
    4.5e-05   23.0  10.5    0.00058   19.4   2.1    4.1  4  SNAP             Soluble NSF attachment protein, SNAP
    9.5e-05   21.8   2.2      0.099   11.8   1.7    3.7  3  FAT              FAT domain
    0.00099   18.6   1.5       0.85    9.0   0.0    3.0  3  Coatomer_E       Coatomer epsilon subunit
     0.0011   18.8   0.5        3.4    7.3   0.0    4.2  4  RPN7             26S proteasome subunit RPN7
     0.0026   17.8  17.7        3.1    7.9   0.5    7.7  9  MIT              MIT (microtubule interacting and transport) 
     0.0035   16.8   3.2         10    5.6   0.0    5.5  7  SHNi-TPR         SHNi-TPR
  ------ inclusion threshold ------
      0.014   15.4   4.9        4.6    7.4   0.2    5.6  5  ANAPC5           Anaphase-promoting complex subunit 5
      0.027   14.2   5.0       0.35   10.6   0.9    4.1  4  TOM20_plant      Plant specific mitochondrial import receptor
      0.045   13.6   6.8         11    5.7   0.0    5.7  8  DUF5113          Domain of unknown function (DUF5113)
      0.054   13.0   1.0         13    5.2   0.0    3.9  4  14-3-3           14-3-3 protein
      0.093   13.0   2.6        2.9    8.2   0.0    4.4  5  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
       0.11   12.8   0.0       0.19   12.0   0.0    1.3  1  PBP_N            Penicillin-binding protein N-terminus


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1   1.7e-08     9e-06       1      34 []      43      76 ..      43      76 .. 0.97
   2 !   18.1   0.0   3.1e-06    0.0017       1      31 [.      77     107 ..      77     109 .. 0.92
   3 !   17.9   0.0   3.5e-06    0.0019       1      34 []     118     151 ..     118     151 .. 0.93
   4 ?    3.6   0.2      0.12        65       1      12 [.     152     163 ..     152     165 .. 0.87
   5 !   11.3   0.1   0.00043      0.23      17      34 .]     178     195 ..     176     195 .. 0.95
   6 ?    0.8   0.1      0.94   5.1e+02       2      17 ..     197     212 ..     196     213 .. 0.85
   7 !    9.3   0.0    0.0019         1      15      30 ..     218     233 ..     216     235 .. 0.94
   8 !   18.9   0.1   1.8e-06   0.00096      14      34 .]     271     291 ..     269     291 .. 0.92
   9 ?    4.4   0.0     0.065        35       7      25 ..     300     318 ..     295     322 .. 0.83
  10 !   17.7   0.0   4.1e-06    0.0022      11      34 .]     343     366 ..     341     366 .. 0.93
  11 !   31.7   0.0   1.5e-10   8.4e-08       2      33 ..     368     399 ..     367     400 .. 0.95
  12 ?    4.5   0.1      0.06        32       1      30 [.     405     434 ..     405     434 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.7e-08
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a+++y+ G+ ++ + +y +Al +++kA+e++P+n
  gi|330509104|ref|YP_004385532.1| 43 ADSWYQEGLKLMGNDNYRDALIAFDKAIEIDPEN 76
                                      799*****************************97 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.1e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                       a ++ ++G ++ ++g+y+e l+ ye ALe  
  gi|330509104|ref|YP_004385532.1|  77 ASIWMGKGDVLVRMGDYNESLKIYENALEMA 107
                                       678**************************86 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 3.5e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+ +  +G ++ +  k deA+ +y++A elnP++
  gi|330509104|ref|YP_004385532.1| 118 ARGWLVKGELFIRIFKNDEAINAYSRATELNPKY 151
                                       678999999999999*****************97 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayf 12 
                                       a+a+y++G+a+ 
  gi|330509104|ref|YP_004385532.1| 152 AEAWYQKGAALN 163
                                       89******9985 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.00043
                                       HHHHHHHHHHHHHHSTTH CS
                             TPR_1  17 ydeAleyyekALelnPnn 34 
                                       y+eA  + +kA+el+P +
  gi|330509104|ref|YP_004385532.1| 178 YEEAFTALNKAIELDPGY 195
                                       9***************76 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 0.94
                                       HHHHHHHHHHHHTT-H CS
                             TPR_1   2 kalynlGnayfklgky 17 
                                       ka++ +G+++++l ++
  gi|330509104|ref|YP_004385532.1| 197 KAWNDKGYTLLSLARF 212
                                       79*******9998665 PP

  == domain 7  score: 9.3 bits;  conditional E-value: 0.0019
                                       T-HHHHHHHHHHHHHH CS
                             TPR_1  15 gkydeAleyyekALel 30 
                                       ++y+e le++++A+el
  gi|330509104|ref|YP_004385532.1| 218 NRYNESLEAFDRAIEL 233
                                       69*************8 PP

  == domain 8  score: 18.9 bits;  conditional E-value: 1.8e-06
                                       TT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  14 lgkydeAleyyekALelnPnn 34 
                                        ++y+eAl ++++++el+P++
  gi|330509104|ref|YP_004385532.1| 271 RERYEEALTACDRVIELDPDF 291
                                       579****************97 PP

  == domain 9  score: 4.4 bits;  conditional E-value: 0.065
                                       HHHHHHHTT-HHHHHHHHH CS
                             TPR_1   7 lGnayfklgkydeAleyye 25 
                                       ++ ++ +lg+y+e l +y+
  gi|330509104|ref|YP_004385532.1| 300 KAGILSELGRYNESLVAYD 318
                                       6668999**********96 PP

  == domain 10  score: 17.7 bits;  conditional E-value: 4.1e-06
                                       HHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  11 yfklgkydeAleyyekALelnPnn 34 
                                       + k+g+y+eAl   + AL+++P+n
  gi|330509104|ref|YP_004385532.1| 343 LVKMGEYEEALTTINAALKIDPTN 366
                                       569*******************98 PP

  == domain 11  score: 31.7 bits;  conditional E-value: 1.5e-10
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                        a++n+G a+ + g+y+eA+ +y+kA+el P+
  gi|330509104|ref|YP_004385532.1| 368 IAWKNKGEALNYTGRYEEAVSAYDKAVELSPE 399
                                       69****************************96 PP

  == domain 12  score: 4.5 bits;  conditional E-value: 0.06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a ++ ++G a+   g+  eA +++ +A el
  gi|330509104|ref|YP_004385532.1| 405 ASSWQGKGDALKASGRQVEAAAAFARAKEL 434
                                       568999********************9886 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1     1e-08   5.5e-06       1      34 []      43      76 ..      43      76 .. 0.96
   2 !   17.8   0.0   4.6e-06    0.0025       2      32 ..      78     108 ..      77     110 .. 0.91
   3 !   15.1   0.0   3.5e-05     0.019       1      34 []     118     151 ..     118     151 .. 0.91
   4 ?   -0.1   0.2       2.5   1.4e+03       1      11 [.     152     162 ..     152     163 .. 0.74
   5 !   11.1   0.1   0.00065      0.36      17      33 ..     178     194 ..     175     195 .. 0.95
   6 ?   -1.9   0.0       9.1   4.9e+03       2      17 ..     197     212 ..     196     213 .. 0.81
   7 !    8.2   0.0    0.0054         3      15      30 ..     218     233 ..     216     235 .. 0.93
   8 !   14.4   0.1   5.5e-05      0.03      14      33 ..     271     290 ..     268     291 .. 0.91
   9 ?    4.5   0.0     0.084        46       8      32 ..     301     325 ..     295     327 .. 0.81
  10 !   17.3   0.0   6.5e-06    0.0035      10      34 .]     342     366 ..     335     366 .. 0.92
  11 !   24.7   0.1   2.9e-08   1.6e-05       2      33 ..     368     399 ..     367     400 .. 0.95
  12 !    8.9   0.5    0.0032       1.7       3      30 ..     407     434 ..     405     436 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1e-08
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      a+ +y+ Gl ++ +++y +Al af+kA+e+dP+n
  gi|330509104|ref|YP_004385532.1| 43 ADSWYQEGLKLMGNDNYRDALIAFDKAIEIDPEN 76
                                      689*****************************97 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 4.6e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                        +++  G+++ ++gdy+e l+ +e Ale ++
  gi|330509104|ref|YP_004385532.1|  78 SIWMGKGDVLVRMGDYNESLKIYENALEMAE 108
                                       6899***********************9875 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 3.5e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+++   G++ ++  + +eA++a+ +A el+P++
  gi|330509104|ref|YP_004385532.1| 118 ARGWLVKGELFIRIFKNDEAINAYSRATELNPKY 151
                                       567888999999999*****************85 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 2.5
                             TPR_2   1 aealynlGlay 11 
                                       aea+y+ G a+
  gi|330509104|ref|YP_004385532.1| 152 AEAWYQKGAAL 162
                                       68888888765 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.00065
                             TPR_2  17 yeeAleafekAleldPn 33 
                                       yeeA  a++kA+eldP+
  gi|330509104|ref|YP_004385532.1| 178 YEEAFTALNKAIELDPG 194
                                       9***************7 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 9.1
                             TPR_2   2 ealynlGlayyklgdy 17 
                                       +a++  G+ ++ l ++
  gi|330509104|ref|YP_004385532.1| 197 KAWNDKGYTLLSLARF 212
                                       699*****99987665 PP

  == domain 7  score: 8.2 bits;  conditional E-value: 0.0054
                             TPR_2  15 gdyeeAleafekAlel 30 
                                       ++y+e leaf++A+el
  gi|330509104|ref|YP_004385532.1| 218 NRYNESLEAFDRAIEL 233
                                       69************98 PP

  == domain 8  score: 14.4 bits;  conditional E-value: 5.5e-05
                             TPR_2  14 lgdyeeAleafekAleldPn 33 
                                       + +yeeAl a+++++eldP+
  gi|330509104|ref|YP_004385532.1| 271 RERYEEALTACDRVIELDPD 290
                                       689****************8 PP

  == domain 9  score: 4.5 bits;  conditional E-value: 0.084
                             TPR_2   8 GlayyklgdyeeAleafekAleldP 32 
                                       + ++ +lg+y+e l a++ A++  P
  gi|330509104|ref|YP_004385532.1| 301 AGILSELGRYNESLVAYDGAISSVP 325
                                       557889***********98887655 PP

  == domain 10  score: 17.3 bits;  conditional E-value: 6.5e-06
                             TPR_2  10 ayyklgdyeeAleafekAleldPnn 34 
                                       ++ k+g+yeeAl   ++Al++dP+n
  gi|330509104|ref|YP_004385532.1| 342 VLVKMGEYEEALTTINAALKIDPTN 366
                                       6789*******************98 PP

  == domain 11  score: 24.7 bits;  conditional E-value: 2.9e-08
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                        a+ n G+a+ + g+yeeA+ a++kA+el P+
  gi|330509104|ref|YP_004385532.1| 368 IAWKNKGEALNYTGRYEEAVSAYDKAVELSPE 399
                                       79****************************97 PP

  == domain 12  score: 8.9 bits;  conditional E-value: 0.0032
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                        +   G+a+ ++g+  eA++af +A el
  gi|330509104|ref|YP_004385532.1| 407 SWQGKGDALKASGRQVEAAAAFARAKEL 434
                                       68999********************887 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.5e-07   0.00019       9      42 .]      58      91 ..      50      91 .. 0.93
   2 !   11.5   0.0   0.00034      0.19       1      22 [.      84     105 ..      84     109 .. 0.95
   3 !   30.4   2.5   4.3e-10   2.3e-07       9      38 ..     133     162 ..     133     164 .. 0.95
   4 !   16.1   0.2   1.3e-05    0.0069      10      38 ..     178     206 ..     175     209 .. 0.90
   5 ?    5.5   0.1     0.024        13       8      23 ..     218     233 ..     218     236 .. 0.94
   6 !   10.1   0.0   0.00091      0.49       7      27 ..     271     291 ..     270     292 .. 0.92
   7 ?    6.2   0.0     0.016       8.4       6      22 ..     306     322 ..     303     327 .. 0.84
   8 !   29.0   0.0   1.1e-09     6e-07       3      38 ..     342     377 ..     341     378 .. 0.94
   9 !   20.3   0.1   6.1e-07   0.00033       1      26 [.     374     399 ..     374     400 .. 0.93
  10 ?    0.3   0.3         1   5.6e+02       1      20 [.     412     431 ..     412     434 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.5e-07
                            TPR_11  9 kyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      +y +A+ a+ kA+++dP+na+++ + G+++ ++G
  gi|330509104|ref|YP_004385532.1| 58 NYRDALIAFDKAIEIDPENASIWMGKGDVLVRMG 91
                                      68899999**********************9998 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00034
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlk 22 
                                       Gd+++  G+y+e+++ Y++Al+
  gi|330509104|ref|YP_004385532.1|  84 GDVLVRMGDYNESLKIYENALE 105
                                       9*******************98 PP

  == domain 3  score: 30.4 bits;  conditional E-value: 4.3e-10
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       k++eAi+aY++A +l+P++aea+y  G+a+
  gi|330509104|ref|YP_004385532.1| 133 KNDEAINAYSRATELNPKYAEAWYQKGAAL 162
                                       689************************996 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 1.3e-05
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       yeeA +a++kA++ldP +  a++  G+++
  gi|330509104|ref|YP_004385532.1| 178 YEEAFTALNKAIELDPGYGKAWNDKGYTL 206
                                       9***************9999999999876 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.024
                            TPR_11   8 GkyeeAieaYkkAlkl 23 
                                       ++y+e++ea+ +A++l
  gi|330509104|ref|YP_004385532.1| 218 NRYNESLEAFDRAIEL 233
                                       69************98 PP

  == domain 6  score: 10.1 bits;  conditional E-value: 0.00091
                            TPR_11   7 qGkyeeAieaYkkAlkldPdn 27 
                                       + +yeeA++a  + ++ldPd+
  gi|330509104|ref|YP_004385532.1| 271 RERYEEALTACDRVIELDPDF 291
                                       779****************95 PP

  == domain 7  score: 6.2 bits;  conditional E-value: 0.016
                            TPR_11   6 eqGkyeeAieaYkkAlk 22 
                                       e+G+y+e++ aY  A+ 
  gi|330509104|ref|YP_004385532.1| 306 ELGRYNESLVAYDGAIS 322
                                       89**********99996 PP

  == domain 8  score: 29.0 bits;  conditional E-value: 1.1e-09
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       ++++ G+yeeA++  ++Alk+dP+n+ a+ n G+a+
  gi|330509104|ref|YP_004385532.1| 342 VLVKMGEYEEALTTINAALKIDPTNPIAWKNKGEAL 377
                                       68999****************************985 PP

  == domain 9  score: 20.3 bits;  conditional E-value: 6.1e-07
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPd 26 
                                       G a+   G+yeeA+ aY kA++l+P+
  gi|330509104|ref|YP_004385532.1| 374 GEALNYTGRYEEAVSAYDKAVELSPE 399
                                       7889999*****************96 PP

  == domain 10  score: 0.3 bits;  conditional E-value: 1
                            TPR_11   1 GdayyeqGkyeeAieaYkkA 20 
                                       Gda+ + G+  eA +a+ +A
  gi|330509104|ref|YP_004385532.1| 412 GDALKASGRQVEAAAAFARA 431
                                       9************9999887 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   8.7e-05     0.047       1      34 []      43      76 ..      43      76 .. 0.95
   2 !   20.7   0.0     6e-07   0.00032       1      33 [.      77     109 ..      77     110 .. 0.94
   3 !   16.2   0.0   1.7e-05     0.009       1      33 [.     118     150 ..     118     151 .. 0.95
   4 ?    0.0   0.1       2.4   1.3e+03       1      11 [.     152     162 ..     152     169 .. 0.78
   5 !   11.6   0.1   0.00049      0.27      15      32 ..     176     193 ..     172     195 .. 0.89
   6 ?    5.6   0.3     0.039        21      12      30 ..     215     233 ..     196     236 .. 0.83
   7 ?    5.2   0.1     0.052        28       8      29 ..     258     279 ..     253     281 .. 0.86
   8 !    8.9   0.0    0.0036       1.9      15      33 ..     272     290 ..     269     291 .. 0.92
   9 !    7.5   0.0      0.01       5.4       2      29 ..     295     322 ..     294     327 .. 0.88
  10 !   18.3   0.0   3.4e-06    0.0018       5      34 .]     337     366 ..     333     366 .. 0.90
  11 !   23.2   0.1   8.9e-08   4.8e-05       6      33 ..     372     399 ..     369     400 .. 0.93
  12 ?    5.0   0.1     0.062        34       1      30 [.     405     434 ..     405     434 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.7e-05
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      a+++y+ g+ ++   +y  A  ++ ka+e+dp+n
  gi|330509104|ref|YP_004385532.1| 43 ADSWYQEGLKLMGNDNYRDALIAFDKAIEIDPEN 76
                                      689*****************************86 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 6e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++++ +g+++  +gdy+e+ + ye ale++++
  gi|330509104|ref|YP_004385532.1|  77 ASIWMGKGDVLVRMGDYNESLKIYENALEMAEK 109
                                       679***************************987 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.7e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+ ++ +g + +   + +eA+ +y +a+el+p+
  gi|330509104|ref|YP_004385532.1| 118 ARGWLVKGELFIRIFKNDEAINAYSRATELNPK 150
                                       689*****************************8 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 2.4
                                       CCHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiy 11 
                                       aea+y++g ++
  gi|330509104|ref|YP_004385532.1| 152 AEAWYQKGAAL 162
                                       79999999765 PP

  == domain 5  score: 11.6 bits;  conditional E-value: 0.00049
                                       T-HHHHHHHHHHHHHHHH CS
                             TPR_8  15 gdyeeAkeyyekaleldp 32 
                                       + yeeA  +++ka+eldp
  gi|330509104|ref|YP_004385532.1| 176 KTYEEAFTALNKAIELDP 193
                                       569**************9 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.039
                                       HHTT-HHHHHHHHHHHHHH CS
                             TPR_8  12 lklgdyeeAkeyyekalel 30 
                                       ++ ++y+e+ e++ +a+el
  gi|330509104|ref|YP_004385532.1| 215 KNFNRYNESLEAFDRAIEL 233
                                       566899**********998 PP

  == domain 7  score: 5.2 bits;  conditional E-value: 0.052
                                       HHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyyekale 29 
                                       ++ + ++ +++eA e ye+al+
  gi|330509104|ref|YP_004385532.1| 258 SNMLNDMDRKDEARERYEEALT 279
                                       567889**************97 PP

  == domain 8  score: 8.9 bits;  conditional E-value: 0.0036
                                       T-HHHHHHHHHHHHHHHHH CS
                             TPR_8  15 gdyeeAkeyyekaleldpd 33 
                                       ++yeeA  ++ +++eldpd
  gi|330509104|ref|YP_004385532.1| 272 ERYEEALTACDRVIELDPD 290
                                       69****************8 PP

  == domain 9  score: 7.5 bits;  conditional E-value: 0.01
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                       ea ++++ i+++lg+y+e+  +y  a++
  gi|330509104|ref|YP_004385532.1| 295 EARLLKAGILSELGRYNESLVAYDGAIS 322
                                       57789999**************999987 PP

  == domain 10  score: 18.3 bits;  conditional E-value: 3.4e-06
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                         ++s++ k+g+yeeA  +++ al++dp+n
  gi|330509104|ref|YP_004385532.1| 337 ADKSSVLVKMGEYEEALTTINAALKIDPTN 366
                                       67899***********************86 PP

  == domain 11  score: 23.2 bits;  conditional E-value: 8.9e-08
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpd 33 
                                       n+g ++  +g+yeeA+++y ka+el+p+
  gi|330509104|ref|YP_004385532.1| 372 NKGEALNYTGRYEEAVSAYDKAVELSPE 399
                                       89************************96 PP

  == domain 12  score: 5.0 bits;  conditional E-value: 0.062
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a++++ +g++++  g+  eA +++ +a el
  gi|330509104|ref|YP_004385532.1| 405 ASSWQGKGDALKASGRQVEAAAAFARAKEL 434
                                       679*********************999775 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.25   1.3e+02      52      75 ..      50      73 ..      36      75 .. 0.62
   2 !   33.9   0.0   5.3e-11   2.9e-08       3      75 ..      77     148 ..      75     150 .. 0.93
   3 !   12.5   0.2   0.00024      0.13      17      74 ..     176     233 ..     173     238 .. 0.92
   4 !   11.5   0.1   0.00053      0.29      44      75 ..     250     281 ..     240     287 .. 0.71
   5 !   18.1   0.0   4.6e-06    0.0025       6      75 ..     299     363 ..     294     365 .. 0.90
   6 !   31.1   0.2     4e-10   2.2e-07       4      72 ..     368     432 ..     367     435 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.25
                            TPR_12 52 grlyralgryeeAlelleealaia 75
                                      g  +   ++y++Al ++ +a++i+
  gi|330509104|ref|YP_004385532.1| 50 GLKLMGNDNYRDALIAFDKAIEID 73
                                      444445567777777777777765 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 5.3e-11
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a+++   ++vl r+g+y e+l+++e ale+a+++   d+p  a+     g+l+ +  + +eA++++ +a+++ 
  gi|330509104|ref|YP_004385532.1|  77 ASIWMGKGDVLVRMGDYNESLKIYENALEMAEKTT-QDNPHDARGWLVKGELFIRIFKNDEAINAYSRATELN 148
                                       6788899************************9994.78999****************************9985 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00024
                            TPR_12  17 grydeAlellekaleiarrllGpdhpltattlrnLgrlyral.gryeeAlelleealai 74 
                                       + y+eA++ l+ka+e+    +G+ + +   tl  L+r   +  +ry e le++ +a+++
  gi|330509104|ref|YP_004385532.1| 176 KTYEEAFTALNKAIELD-PGYGKAWNDKGYTLLSLARFNGKNfNRYNESLEAFDRAIEL 233
                                       569**************.778******************7666*************997 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00053
                            TPR_12  44 tattlrnLgrlyralgryeeAlelleealaia 75 
                                        a +  +++ ++  ++r +eA+e++eeal ++
  gi|330509104|ref|YP_004385532.1| 250 KALAFVGMSNMLNDMDRKDEARERYEEALTAC 281
                                       56666666777777777777777777777665 PP

  == domain 5  score: 18.1 bits;  conditional E-value: 4.6e-06
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       l   a +l +lgry e+l  ++ a+  +   + +  +ltat + + + ++ ++g+yeeAl   + al+i+
  gi|330509104|ref|YP_004385532.1| 299 L--KAGILSELGRYNESLVAYDGAISSV---PADLVLLTATFMADKSSVLVKMGEYEEALTTINAALKID 363
                                       4..899******************5555...88999****************************999986 PP

  == domain 6  score: 31.1 bits;  conditional E-value: 4e-10
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       +a+ n +++l++ gry+eA + ++ka+e+  +l     +l a++ ++ g+++ a+gr+ eA +++ +a 
  gi|330509104|ref|YP_004385532.1| 368 IAWKNKGEALNYTGRYEEAVSAYDKAVELSPEL----GLLKASSWQGKGDALKASGRQVEAAAAFARAK 432
                                       57889*************************444....689*************************9995 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.9e-07    0.0001       2      63 ..      48     106 ..      47     109 .. 0.89
   2 !    8.8   0.0    0.0048       2.6       4      29 ..      84     109 ..      83     131 .. 0.79
   3 !   20.4   0.9   1.1e-06   0.00061      12      65 ..     133     193 ..     122     195 .. 0.80
   4 ?    7.3   0.1     0.014       7.5      13      62 ..     178     232 ..     173     238 .. 0.87
   5 ?    1.6   0.1      0.82   4.4e+02      11      26 ..     218     233 ..     216     254 .. 0.62
   6 !   16.7   0.1   1.6e-05    0.0089      10      63 ..     271     323 ..     269     327 .. 0.90
   7 !   31.9   0.0   2.9e-10   1.6e-07       6      65 ..     342     398 ..     338     401 .. 0.94
   8 !   17.6   4.0   8.4e-06    0.0046      11      61 ..     381     432 ..     381     435 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.9e-07
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       ++++ ++ + +y+dA+ a++ a++ d   P++a  ++++gd++ r g++ e +  y+ al+ 
  gi|330509104|ref|YP_004385532.1|  48 QEGLKLMGNDNYRDALIAFDKAIEID---PENASIWMGKGDVLVRMGDYNESLKIYENALEM 106
                                       6677789999****************...**********************99777777665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0048
                            TPR_16   4 araalragdyddAaaaleaalkrdps 29 
                                       ++ ++r gdy + ++ +e al+++ +
  gi|330509104|ref|YP_004385532.1|  84 GDVLVRMGDYNESLKIYENALEMAEK 109
                                       8899*****************99855 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 1.1e-06
                            TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrq..........grlaeAaalyraalraap 65 
                                       + d+A++a+ +a++++   P  aeA++ +g a+  +          + ++eA  ++++a++ +p
  gi|330509104|ref|YP_004385532.1| 133 KNDEAINAYSRATELN---PKYAEAWYQKGAALNLKagelpeqesaKTYEEAFTALNKAIELDP 193
                                       679*************...**************9667677777777777777766666666666 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.014
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrq........grlaeAaalyraalr 62 
                                       y++A  al+ a+++d   P    A++ +g  +l +        +r+ e ++++++a++
  gi|330509104|ref|YP_004385532.1| 178 YEEAFTALNKAIELD---PGYGKAWNDKGYTLLSLarfngknfNRYNESLEAFDRAIE 232
                                       899999*********...**************99988888888888888888888875 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.82
                            TPR_16  11 gdyddAaaaleaalkr 26 
                                       ++y + ++a+++a+++
  gi|330509104|ref|YP_004385532.1| 218 NRYNESLEAFDRAIEL 233
                                       5788888888888764 PP

  == domain 6  score: 16.7 bits;  conditional E-value: 1.6e-05
                            TPR_16  10 agdyddAaaaleaalkrdpssPd..aaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       + +y++A+ a ++++++d   Pd    eA+ll++ ++ ++gr+ e + +y+ a+  
  gi|330509104|ref|YP_004385532.1| 271 RERYEEALTACDRVIELD---PDftGQEARLLKAGILSELGRYNESLVAYDGAISS 323
                                       689***************...9999**********************888888755 PP

  == domain 7  score: 31.9 bits;  conditional E-value: 2.9e-10
                            TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                        +++ g+y++A+   +aalk d   P ++ A+ ++g+a+   gr++eA+ +y++a++ +p
  gi|330509104|ref|YP_004385532.1| 342 VLVKMGEYEEALTTINAALKID---PTNPIAWKNKGEALNYTGRYEEAVSAYDKAVELSP 398
                                       5899******************...99999**************************9998 PP

  == domain 8  score: 17.6 bits;  conditional E-value: 8.4e-06
                            TPR_16  11 gdyddAaaaleaalkrdpssPd....aaeAllllgdaalrqgrlaeAaalyraal 61 
                                       g+y++A+ a++ a+++    P+     a ++ ++gda+ + gr  eAaa++++a 
  gi|330509104|ref|YP_004385532.1| 381 GRYEEAVSAYDKAVELS---PElgllKASSWQGKGDALKASGRQVEAAAAFARAK 432
                                       8****************...777779***********************999986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00046      0.25      11      42 ..      53      84 ..      43      86 .. 0.83
   2 !   12.2   0.0   0.00047      0.25       4      44 .]      80     127 ..      79     127 .. 0.86
   3 !   18.7   0.1     4e-06    0.0022       4      42 ..     121     159 ..     118     162 .. 0.86
   4 !    8.7   0.0    0.0063       3.4      14      38 ..     175     199 ..     164     207 .. 0.87
   5 ?    0.8   0.0       2.2   1.2e+03      15      30 ..     218     233 ..     203     251 .. 0.71
   6 !   11.2   0.3     0.001      0.55      12      41 ..     269     300 ..     268     301 .. 0.84
   7 ?    6.4   0.0     0.035        19       2      39 ..     295     332 ..     294     338 .. 0.90
   8 !   16.8   0.0   1.6e-05    0.0084       9      43 ..     341     375 ..     333     376 .. 0.90
   9 !   10.3   0.0    0.0019         1       3      33 ..     369     399 ..     368     404 .. 0.90
  10 ?    3.0   0.4      0.43   2.3e+02       4      27 ..     408     431 ..     405     435 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00046
                            TPR_14 11 llalGdpdeAiallrralalaPddaeawllla 42
                                      l+ ++++++A+ ++++a++ +P++a +w+  +
  gi|330509104|ref|YP_004385532.1| 53 LMGNDNYRDALIAFDKAIEIDPENASIWMGKG 84
                                      677899**********************9766 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00047
                            TPR_14   4 llalaeallalGdpdeAiallrrala.......laPddaeawlllaql 44 
                                       ++  +++l + Gd+ e++++++ al+       ++P da+ wl  ++l
  gi|330509104|ref|YP_004385532.1|  80 WMGKGDVLVRMGDYNESLKIYENALEmaekttqDNPHDARGWLVKGEL 127
                                       56668999*****9999999999999999888789*******998875 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 4e-06
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +l  +e++ +  + deAi+++ ra +l+P+ aeaw++ +
  gi|330509104|ref|YP_004385532.1| 121 WLVKGELFIRIFKNDEAINAYSRATELNPKYAEAWYQKG 159
                                       77777888888889*********************9986 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0063
                            TPR_14  14 lGdpdeAiallrralalaPddaeaw 38 
                                       +  ++eA ++l++a++l+P+   aw
  gi|330509104|ref|YP_004385532.1| 175 AKTYEEAFTALNKAIELDPGYGKAW 199
                                       66799***************99998 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 2.2
                            TPR_14  15 GdpdeAiallrralal 30 
                                        ++ e++++++ra++l
  gi|330509104|ref|YP_004385532.1| 218 NRYNESLEAFDRAIEL 233
                                       5677888888888874 PP

  == domain 6  score: 11.2 bits;  conditional E-value: 0.001
                            TPR_14  12 lalGdpdeAiallrralalaPdd..aeawlll 41 
                                       +a+++++eA+++++r+++l+Pd+  +ea+ll 
  gi|330509104|ref|YP_004385532.1| 269 EARERYEEALTACDRVIELDPDFtgQEARLLK 300
                                       57899*****************9555787765 PP

  == domain 7  score: 6.4 bits;  conditional E-value: 0.035
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       ea+l+ a +l +lG++ e++ +++ a++  P+d+++++
  gi|330509104|ref|YP_004385532.1| 295 EARLLKAGILSELGRYNESLVAYDGAISSVPADLVLLT 332
                                       689999*************************9998764 PP

  == domain 8  score: 16.8 bits;  conditional E-value: 1.6e-05
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       ++l   G+++eA++  ++al+ +P+++ aw   ++
  gi|330509104|ref|YP_004385532.1| 341 SVLVKMGEYEEALTTINAALKIDPTNPIAWKNKGE 375
                                       789999************************98775 PP

  == domain 9  score: 10.3 bits;  conditional E-value: 0.0019
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPd 33 
                                       a++  +eal   G+++eA+ ++++a++l P+
  gi|330509104|ref|YP_004385532.1| 369 AWKNKGEALNYTGRYEEAVSAYDKAVELSPE 399
                                       6777799999******************997 PP

  == domain 10  score: 3.0 bits;  conditional E-value: 0.43
                            TPR_14   4 llalaeallalGdpdeAiallrra 27 
                                       ++  ++al a+G+  eA+a++ ra
  gi|330509104|ref|YP_004385532.1| 408 WQGKGDALKASGRQVEAAAAFARA 431
                                       6677899*************9998 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   4.3e-07   0.00023       1      47 [.      53      99 ..      53     101 .. 0.94
   2 ?    6.0   0.0     0.031        17       7      32 ..     100     125 ..      99     130 .. 0.86
   3 !   12.8   0.4   0.00025      0.13       8      41 ..     135     169 ..     133     171 .. 0.87
   4 !    9.0   0.0    0.0037         2       5      41 ..     176     212 ..     174     214 .. 0.90
   5 !   17.4   0.1   8.9e-06    0.0048       3      49 ..     270     318 ..     261     329 .. 0.89
   6 !   19.9   0.0   1.4e-06   0.00077       1      56 [.     343     398 ..     343     405 .. 0.93
   7 !   10.1   0.6    0.0016      0.87       5      53 ..     381     433 ..     377     437 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.3e-07
                            TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47
                                      l+ + +y +Al ++ +a++ dp+na ++++  ++l+ +g+++e  ++
  gi|330509104|ref|YP_004385532.1| 53 LMGNDNYRDALIAFDKAIEIDPENASIWMGKGDVLVRMGDYNESLKI 99
                                      68899*************************************98776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.031
                            TPR_19   7 yaeAlalleqalqedpknaearllLA 32 
                                       y++Al++ e+  q++p++a+ +l   
  gi|330509104|ref|YP_004385532.1| 100 YENALEMAEKTTQDNPHDARGWLVKG 125
                                       899****************9998655 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00025
                            TPR_19   8 aeAlalleqalqedpknaearllL.Aeallalgql 41 
                                       +eA++++++a + +pk+aea+++  A + l++g+l
  gi|330509104|ref|YP_004385532.1| 135 DEAINAYSRATELNPKYAEAWYQKgAALNLKAGEL 169
                                       89********************9878888888877 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0037
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgql 41 
                                       + y+eA  +l +a++ dp+++ a+ +    ll+l ++
  gi|330509104|ref|YP_004385532.1| 176 KTYEEAFTALNKAIELDPGYGKAWNDKGYTLLSLARF 212
                                       689*********************9999999998877 PP

  == domain 5  score: 17.4 bits;  conditional E-value: 8.9e-06
                            TPR_19   3 aegdyaeAlalleqalqedpk..naearllLAeallalgqldeAealLd 49 
                                       a+++y+eAl +  ++++ dp+   +earll A +l +lg+++e   + d
  gi|330509104|ref|YP_004385532.1| 270 ARERYEEALTACDRVIELDPDftGQEARLLKAGILSELGRYNESLVAYD 318
                                       57899*************************************9877666 PP

  == domain 6  score: 19.9 bits;  conditional E-value: 1.4e-06
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                       l+++g y+eAl    +al+ dp n+ a+ +  eal  +g+++eA  + d++ e  p
  gi|330509104|ref|YP_004385532.1| 343 LVKMGEYEEALTTINAALKIDPTNPIAWKNKGEALNYTGRYEEAVSAYDKAVELSP 398
                                       689******************************************99999887766 PP

  == domain 7  score: 10.1 bits;  conditional E-value: 0.0016
                            TPR_19   5 gdyaeAlalleqalqedpk....naearllLAeallalgqldeAealLdalpe 53 
                                       g+y+eA++++ +a + +p+     a  + +  +al a+g+  eA a+ +++ e
  gi|330509104|ref|YP_004385532.1| 381 GRYEEAVSAYDKAVELSPElgllKASSWQGKGDALKASGRQVEAAAAFARAKE 433
                                       9******************99888888889*************9999998765 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     1e-05    0.0056       2      32 ..      66      96 ..      65      98 .. 0.92
   2 ?    0.0   0.0       2.7   1.5e+03       3      32 ..     108     137 ..      99     138 .. 0.69
   3 !   17.9   0.3   5.1e-06    0.0028       2      30 ..     141     170 ..     140     174 .. 0.86
   4 !   17.6   0.2   6.7e-06    0.0036       2      25 ..     185     212 ..     184     225 .. 0.82
   5 ?    3.9   0.0      0.16        85       2      31 ..     281     312 ..     280     314 .. 0.86
   6 !   17.9   0.0   5.1e-06    0.0028       3      33 ..     357     387 ..     355     388 .. 0.93
   7 ?    6.0   0.0     0.033        18       1      32 [.     389     424 ..     389     426 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1e-05
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtA 32
                                      + ka+e+dP na  +  ++ +l + Gd+ + 
  gi|330509104|ref|YP_004385532.1| 66 FDKAIEIDPENASIWMGKGDVLVRMGDYNES 96
                                      89*************************9875 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.7
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +k  + +P +a  +  ++el+ ++ + ++A
  gi|330509104|ref|YP_004385532.1| 108 EKTTQDNPHDARGWLVKGELFIRIFKNDEA 137
                                       555566899999999999888766555555 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 5.1e-06
                            TPR_17   2 ylkaleldPnnadaynnLAell.lknGdlm 30 
                                       y +a el+P++a+a+++++ +l lk+G+l 
  gi|330509104|ref|YP_004385532.1| 141 YSRATELNPKYAEAWYQKGAALnLKAGELP 170
                                       89******************9966888865 PP

  == domain 4  score: 17.6 bits;  conditional E-value: 6.7e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelll....k 25 
                                       + ka+eldP + +a+n ++++ll     
  gi|330509104|ref|YP_004385532.1| 185 LNKAIELDPGYGKAWNDKGYTLLslarF 212
                                       579*******************956553 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.16
                            TPR_17   2 ylkaleldPnn..adaynnLAelllknGdlmt 31 
                                       + +++eldP+    +a  ++A +l+++G++ +
  gi|330509104|ref|YP_004385532.1| 281 CDRVIELDPDFtgQEARLLKAGILSELGRYNE 312
                                       789*******9999999999999999998865 PP

  == domain 6  score: 17.9 bits;  conditional E-value: 5.1e-06
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtAr 33 
                                         al++dP+n+ a+ n++e+l   G++++A+
  gi|330509104|ref|YP_004385532.1| 357 NAALKIDPTNPIAWKNKGEALNYTGRYEEAV 387
                                       579*************************996 PP

  == domain 7  score: 6.0 bits;  conditional E-value: 0.033
                            TPR_17   1 lylkaleldPnn....adaynnLAelllknGdlmtA 32 
                                       +y ka+el P      a +++ ++ +l+  G+  +A
  gi|330509104|ref|YP_004385532.1| 389 AYDKAVELSPELgllkASSWQGKGDALKASGRQVEA 424
                                       599****************************98887 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     2e-06    0.0011       6      61 ..      54     109 ..      51     120 .. 0.88
   2 ?    6.3   0.0     0.019        11       6      38 ..     129     161 ..     124     164 .. 0.89
   3 ?   -0.2   0.0       2.1   1.2e+03      10      42 ..     177     209 ..     173     214 .. 0.65
   4 !   10.6   0.1   0.00092       0.5       7      53 ..     270     318 ..     269     334 .. 0.76
   5 !   20.4   0.0   7.6e-07   0.00041      10      61 ..     348     399 ..     341     427 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2e-06
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       + ++++  al + +  + ++P+ ++ ++  G +l+++G++++ l+  e +l++a++
  gi|330509104|ref|YP_004385532.1|  54 MGNDNYRDALIAFDKAIEIDPENASIWMGKGDVLVRMGDYNESLKIYENALEMAEK 109
                                       56789999*******************************************99983 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.019
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGll 38 
                                       ir  ++++a+ ++ r   l+P+ +e ++  G +
  gi|330509104|ref|YP_004385532.1| 129 IRIFKNDEAINAYSRATELNPKYAEAWYQKGAA 161
                                       6677899**********************9987 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.1
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaql 42 
                                        +e+a  +++  + l+P     + d G  l  l
  gi|330509104|ref|YP_004385532.1| 177 TYEEAFTALNKAIELDPGYGKAWNDKGYTLLSL 209
                                       566677777777777777777777777666655 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00092
                             TPR_9   7 reedweralavverllllaPddp..eerrdRGlllaqlGclsaAladLe 53 
                                        +e++e+al +++r++ l+Pd    e r+  + +l +lG++++ l + +
  gi|330509104|ref|YP_004385532.1| 270 ARERYEEALTACDRVIELDPDFTgqEARLLKAGILSELGRYNESLVAYD 318
                                       589*****************96522467777777788887777766555 PP

  == domain 5  score: 20.4 bits;  conditional E-value: 7.6e-07
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       ++e+al +++  l ++P  p  +   G +l   G++++A+ + + +++l+p+
  gi|330509104|ref|YP_004385532.1| 348 EYEEALTTINAALKIDPTNPIAWKNKGEALNYTGRYEEAVSAYDKAVELSPE 399
                                       689***********************************************96 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         7   3.8e+03      17      31 ..      58      72 ..      55      72 .. 0.86
   2 !   14.9   0.0   3.3e-05     0.018      11      41 ..      86     116 ..      84     117 .. 0.87
   3 ?    3.6   0.0      0.12        66       8      31 ..     209     233 ..     204     235 .. 0.80
   4 !   15.6   0.0     2e-05     0.011       9      37 ..     258     286 ..     255     292 .. 0.88
   5 ?    3.7   0.0      0.11        62       9      29 ..     301     321 ..     301     323 .. 0.86
   6 ?    2.3   0.0      0.31   1.7e+02       1      22 [.     332     353 ..     332     363 .. 0.82
   7 !   10.4   0.1   0.00089      0.48       9      31 ..     374     396 ..     372     397 .. 0.90
   8 ?   -2.1   0.2       7.3   3.9e+03      11      28 ..     414     431 ..     412     435 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 7
                            TPR_10 17 rydeAealleealai 31
                                      +y +A+  +++a++i
  gi|330509104|ref|YP_004385532.1| 58 NYRDALIAFDKAIEI 72
                                      799999999999986 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.3e-05
                            TPR_10  11 alrqrgrydeAealleealairrrllGpdHP 41 
                                       +l ++g+y+e+++++e al++ +++  +++ 
  gi|330509104|ref|YP_004385532.1|  86 VLVRMGDYNESLKIYENALEMAEKTTQDNPH 116
                                       6789********************9887766 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.12
                            TPR_10   8 Lanal.rqrgrydeAealleealai 31 
                                       La+    + +ry+e+++ +++a+++
  gi|330509104|ref|YP_004385532.1| 209 LARFNgKNFNRYNESLEAFDRAIEL 233
                                       5555556889************986 PP

  == domain 4  score: 15.6 bits;  conditional E-value: 2e-05
                            TPR_10   9 analrqrgrydeAealleealairrrllG 37 
                                       +n+l ++ r deA++ +eeal ++ r+ +
  gi|330509104|ref|YP_004385532.1| 258 SNMLNDMDRKDEARERYEEALTACDRVIE 286
                                       799*********************99977 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.11
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       a +l+++gry+e++  ++ a+
  gi|330509104|ref|YP_004385532.1| 301 AGILSELGRYNESLVAYDGAI 321
                                       5689*********99998887 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.31
                            TPR_10   1 tAsslnNLanalrqrgrydeAe 22 
                                       tA+ + + + +l ++g+y+eA+
  gi|330509104|ref|YP_004385532.1| 332 TATFMADKSSVLVKMGEYEEAL 353
                                       6777777788899999999997 PP

  == domain 7  score: 10.4 bits;  conditional E-value: 0.00089
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al  +gry+eA+  +++a+++
  gi|330509104|ref|YP_004385532.1| 374 GEALNYTGRYEEAVSAYDKAVEL 396
                                       88999***************986 PP

  == domain 8  score: -2.1 bits;  conditional E-value: 7.3
                            TPR_10  11 alrqrgrydeAealleea 28 
                                       al + gr  eA a + +a
  gi|330509104|ref|YP_004385532.1| 414 ALKASGRQVEAAAAFARA 431
                                       788999999999988777 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 !   11.9   0.0   0.00037       0.2      30      81 ..      50     102 ..      28     103 .. 0.55
   2 !   15.3   0.0   3.3e-05     0.018       2      80 ..      56     142 ..      55     144 .. 0.74
   3 !    7.9   0.3    0.0065       3.5       5      70 ..     100     167 ..      98     188 .. 0.79
   4 ?    0.0   0.0       1.9     1e+03      37      49 ..     176     188 ..     173     213 .. 0.71
   5 !    8.0   0.0    0.0061       3.3      38      80 ..     273     318 ..     270     320 .. 0.74
   6 !   15.2   0.0   3.5e-05     0.019      30      81 ..     340     392 ..     331     393 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00037
                                       HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +l l  n +y  A+  ++ka ++++++  +++ ++ +l+ ++ y+e ++++e+
  gi|330509104|ref|YP_004385532.1|  50 GLKLMGNDNYRDALIAFDKAiEIDPENASIWMGKGDVLVRMGDYNESLKIYEN 102
                                       55555555555555555555555555555555555555555555555555544 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.3e-05
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-.......HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngq.......ykrAyellrka.klnskslgcrylfAqcllkLk 70 
                                       + ny++A++ ++++ + ++e+++  + ++ +l ++g+       y+ A+e ++k+ + n+++ + ++++++  + + 
  gi|330509104|ref|YP_004385532.1|  56 NDNYRDALIAFDKAIEIDPENASIWMGKGDVLVRMGDyneslkiYENALEMAEKTtQDNPHDARGWLVKGELFIRIF 132
                                       679************5555555555557*********5555555556666666666666666688888888888888 PP

                                       -HHHHHHHH- CS
                            ANAPC3  71 kyeeAiaaLe 80 
                                       k +eAi+a++
  gi|330509104|ref|YP_004385532.1| 133 KNDEAINAYS 142
                                       8888888876 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0065
                                       HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHH.HHTT CS
                            ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcl.lkLk 70 
                                       y+nA+ +ae+  + +++++   + +++ + +  + ++A++ +++a +ln+k  +++y ++ +l lk +
  gi|330509104|ref|YP_004385532.1| 100 YENALEMAEKTTQDNPHDARGWLVKGELFIRIFKNDEAINAYSRAtELNPKYAEAWYQKGAALnLKAG 167
                                       88999999999966676666677779999999999999999999999999999999988877655655 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 1.9
                                       T-HHHHHHHHHCT CS
                            ANAPC3  37 gqykrAyellrka 49 
                                       + y++A++ l+ka
  gi|330509104|ref|YP_004385532.1| 176 KTYEEAFTALNKA 188
                                       4555555555555 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.0061
                                       -HHHHHHHHHCT.SHHHC-H..HHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  38 qykrAyellrka.klnsksl..gcrylfAqcllkLkkyeeAiaaLe 80 
                                       +y++A++ +++  +l++     ++r+l+A  l +L++y+e + a++
  gi|330509104|ref|YP_004385532.1| 273 RYEEALTACDRViELDPDFTgqEARLLKAGILSELGRYNESLVAYD 318
                                       6777777777776665543344999999999999999999988765 PP

  == domain 6  score: 15.2 bits;  conditional E-value: 3.5e-05
                                       HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       + +l ++g+y++A++ ++ a k++++++ ++  ++++l   ++yeeA++a++k
  gi|330509104|ref|YP_004385532.1| 340 SSVLVKMGEYEEALTTINAAlKIDPTNPIAWKNKGEALNYTGRYEEAVSAYDK 392
                                       56899********************************************9987 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.043        23      15      35 ..      57      77 ..      47      79 .. 0.91
   2 !    7.2   0.0    0.0095       5.2      12      33 ..      88     109 ..      87     113 .. 0.86
   3 ?   -1.3   0.0       4.3   2.4e+03      15      33 ..     176     194 ..     175     198 .. 0.85
   4 ?   -1.6   0.0       5.5     3e+03      15      29 ..     218     232 ..     206     245 .. 0.75
   5 !    8.6   0.0    0.0036         2      16      35 ..     273     292 ..     271     307 .. 0.82
   6 !   17.5   0.0   5.9e-06    0.0032      12      34 ..     344     366 ..     343     369 .. 0.94
   7 ?   -1.0   0.0       3.5   1.9e+03      15      33 ..     381     399 ..     380     400 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.043
                                      T-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C 15 geYseArryvdalLeiEPenr 35
                                       +Y++A+   d  +ei+Pen 
  gi|330509104|ref|YP_004385532.1| 57 DNYRDALIAFDKAIEIDPENA 77
                                      69******************6 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0095
                                       HHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPe 33 
                                        ++g+Y+e+++  +  Le+  +
  gi|330509104|ref|YP_004385532.1|  88 VRMGDYNESLKIYENALEMAEK 109
                                       69***************98765 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.3
                                       T-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPe 33 
                                       + Y+eA   ++  +e++P+
  gi|330509104|ref|YP_004385532.1| 176 KTYEEAFTALNKAIELDPG 194
                                       6799999999999999997 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 5.5
                                       T-HHHHHHHHHHHHH CS
                        Fis1_TPR_C  15 geYseArryvdalLe 29 
                                        +Y+e+++  d+ +e
  gi|330509104|ref|YP_004385532.1| 218 NRYNESLEAFDRAIE 232
                                       468888888887665 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0036
                                       -HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPenr 35 
                                       +Y+eA+  +d+++e++P++ 
  gi|330509104|ref|YP_004385532.1| 273 RYEEALTACDRVIELDPDFT 292
                                       7****************984 PP

  == domain 6  score: 17.5 bits;  conditional E-value: 5.9e-06
                                       HHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPen 34 
                                        k+geY+eA+  ++a L+i+P n
  gi|330509104|ref|YP_004385532.1| 344 VKMGEYEEALTTINAALKIDPTN 366
                                       69*******************99 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 3.5
                                       T-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPe 33 
                                       g+Y+eA    d   e+ Pe
  gi|330509104|ref|YP_004385532.1| 381 GRYEEAVSAYDKAVELSPE 399
                                       89*****999999999886 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       4.1   2.3e+03      14      34 ..      58      76 ..      57      78 .. 0.72
   2 !   13.0   0.0   0.00014     0.078       6      30 ..      84     108 ..      82     118 .. 0.87
   3 ?    0.2   0.0       1.8     1e+03       6      30 ..     125     147 ..     122     150 .. 0.80
   4 ?   -0.5   0.0         3   1.6e+03      13      28 ..     218     233 ..     205     240 .. 0.67
   5 ?    4.6   0.1     0.069        38      12      32 ..     271     291 ..     263     295 .. 0.75
   6 ?   -0.9   0.0       4.1   2.3e+03       6      19 ..     301     314 ..     298     326 .. 0.78
   7 ?    6.1   0.0     0.024        13       8      32 ..     342     364 ..     340     368 .. 0.77
   8 !   10.5   0.0    0.0009      0.49       1      32 [.     369     398 ..     369     401 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.1
                             TPR_7 14 dyeeAielyeqsLaltkdped 34
                                      +y++A+  + +  a++ dpe+
  gi|330509104|ref|YP_004385532.1| 58 NYRDALIAFDK--AIEIDPEN 76
                                      68888888888..77777766 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00014
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltk 30 
                                       +++ +r+Gdy e +++ye +L++++
  gi|330509104|ref|YP_004385532.1|  84 GDVLVRMGDYNESLKIYENALEMAE 108
                                       78899**************999985 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.8
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltk 30 
                                       ++l+ r  + +eAi  y +  a++ 
  gi|330509104|ref|YP_004385532.1| 125 GELFIRIFKNDEAINAYSR--ATEL 147
                                       6778888899******999..7765 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 3
                             TPR_7  13 GdyeeAielyeqsLal 28 
                                       ++y e +e + ++++l
  gi|330509104|ref|YP_004385532.1| 218 NRYNESLEAFDRAIEL 233
                                       6677777777775544 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.069
                             TPR_7  12 lGdyeeAielyeqsLaltkdp 32 
                                       + +yeeA++ + ++++l+ d 
  gi|330509104|ref|YP_004385532.1| 271 RERYEEALTACDRVIELDPDF 291
                                       468999999999977776665 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 4.1
                             TPR_7   6 arlysrlGdyeeAi 19 
                                       a + s+lG+y e +
  gi|330509104|ref|YP_004385532.1| 301 AGILSELGRYNESL 314
                                       66889999998876 PP

  == domain 7  score: 6.1 bits;  conditional E-value: 0.024
                             TPR_7   8 lysrlGdyeeAielyeqsLaltkdp 32 
                                       + +++G+yeeA++   +  al  dp
  gi|330509104|ref|YP_004385532.1| 342 VLVKMGEYEEALTTINA--ALKIDP 364
                                       5689*********9999..655555 PP

  == domain 8  score: 10.5 bits;  conditional E-value: 0.0009
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       a+ n +++    G+yeeA++ y +  a++ +p
  gi|330509104|ref|YP_004385532.1| 369 AWKNKGEALNYTGRYEEAVSAYDK--AVELSP 398
                                       567888899999************..887776 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2   0.00071      0.39      45     129 ..      67     147 ..      35     175 .. 0.84
   2 ?    5.0   0.2     0.044        24      20      83 ..     173     232 ..     156     247 .. 0.70
   3 !   12.7   0.6   0.00019       0.1      23     126 ..     218     320 ..     201     325 .. 0.79
   4 ?    6.7   0.0     0.013       6.9      58      83 ..     336     361 ..     329     364 .. 0.87
   5 !    9.1   0.0    0.0024       1.3     105     129 ..     372     396 ..     367     404 .. 0.89
   6 ?    2.0   0.1      0.37     2e+02     105     129 ..     410     434 ..     401     436 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00071
                                       TS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                           DUF3856  45 eeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealk 121
                                       + a + +  +a ++ g  + l+++g+y+e+l+  ++al+  ++  + +  + + W+     ++  +  + ++dea++
  gi|330509104|ref|YP_004385532.1|  67 DKAIEIDPENASIWMGKGDVLVRMGDYNESLKIYENALEMAEKTTQDNPHDARGWL----VKGELFIRIFKNDEAIN 139
                                       55555666677788888999999***************999999999999999996....47888888888888888 PP

                                       HHHHHHHH CS
                           DUF3856 122 afrmagem 129
                                       a+  a+e+
  gi|330509104|ref|YP_004385532.1| 140 AYSRATEL 147
                                       88888885 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.044
                                       HHHT-HHHHHHHHHHHHHHHTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  20 leegayeeaaasyrkalevsrtipaeeafdheGfdalchaglsealaklgrydealesadkalr 83 
                                        ++++yeea    +ka+e+      + a++ +G+  l  a + +   ++ ry+e+le+ d+a++
  gi|330509104|ref|YP_004385532.1| 173 ESAKTYEEAFTALNKAIELDPG--YGKAWNDKGYTLLSLARFNGK--NFNRYNESLEAFDRAIE 232
                                       4456677777777777777654..456777777777777777664..56788888888888765 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00019
                                       T-HHHHHHHHHHHHHHHTTS-..TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHH CS
                           DUF3856  23 gayeeaaasyrkalevsrtip..aeeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGk 97 
                                       ++y+e+ + + +a+e+  +    +  a+ +eG  al++ g+s+ l  + r dea e  ++al   +r  el+ d   
  gi|330509104|ref|YP_004385532.1| 218 NRYNESLEAFDRAIELISAEDsrQFSALAWEG-KALAFVGMSNMLNDMDRKDEARERYEEALTACDRVIELDPDFTG 293
                                       57899999999999975443300345677777.69*************************************99776 PP

                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  98 lWiaavfsravaleelGrkdealkafrma 126
                                       +   a + +a  l+elGr++e+l a+  a
  gi|330509104|ref|YP_004385532.1| 294 Q--EARLLKAGILSELGRYNESLVAYDGA 320
                                       6..466779999*********99998765 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  58 haglsealaklgrydealesadkalr 83 
                                        a  s+ l+k+g+y+eal++++ al+
  gi|330509104|ref|YP_004385532.1| 336 MADKSSVLVKMGEYEEALTTINAALK 361
                                       5777999***************9997 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.0024
                                       HHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrmagem 129
                                       +++ al+ +Gr++ea+ a+ +a+e+
  gi|330509104|ref|YP_004385532.1| 372 NKGEALNYTGRYEEAVSAYDKAVEL 396
                                       899********************97 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.37
                                       HHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrmagem 129
                                        ++ al+  Gr+ ea  af  a+e+
  gi|330509104|ref|YP_004385532.1| 410 GKGDALKASGRQVEAAAAFARAKEL 434
                                       5899****************99986 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0022       1.2     151     180 ..      82     111 ..      51     120 .. 0.84
   2 !    6.8   0.2    0.0093       5.1     129     180 ..     100     152 ..     100     171 .. 0.73
   3 !    9.9   0.2     0.001      0.56     127     177 ..     225     282 ..     219     297 .. 0.83
   4 !   14.9   0.1   3.1e-05     0.017     121     175 ..     341     396 ..     293     405 .. 0.87
   5 ?    5.2   0.9     0.027        15     148     174 ..     407     433 ..     400     437 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0022
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaaleeka 180
                                        +GD+lv++g+ +e  + Y++Al+  e+++
  gi|330509104|ref|YP_004385532.1|  82 GKGDVLVRMGDYNESLKIYENALEMAEKTT 111
                                       59*********************9888765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0093
                            TPR_21 129 ydeAlktLeakk.eeafaalvaelrGDilvaqgkldeAraaYqaAlaaleeka 180
                                       y++Al++ e+++ ++  +a+   ++G+++++  k+deA +aY++A + + + a
  gi|330509104|ref|YP_004385532.1| 100 YENALEMAEKTTqDNPHDARGWLVKGELFIRIFKNDEAINAYSRATELNPKYA 152
                                       567777775554155688888899*********************98776655 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.001
                            TPR_21 127 kkydeAlktLeakkeeafaalvaelr.....G..DilvaqgkldeAraaYqaAlaale 177
                                       +++d+A+++++a+++ +f+al+ e +     G  ++l  ++++deAr+ Y++Al+a +
  gi|330509104|ref|YP_004385532.1| 225 EAFDRAIELISAEDSRQFSALAWEGKalafvGmsNMLNDMDRKDEARERYEEALTACD 282
                                       67899999999999999999998877333333447888999*************9876 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 3.1e-05
                            TPR_21 121 rvllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       +vl+++++y+eAl+t++a+ + +  +  +   +G++l  +g+ +eA +aY++A++ 
  gi|330509104|ref|YP_004385532.1| 341 SVLVKMGEYEEALTTINAALKiDPTNPIAWKNKGEALNYTGRYEEAVSAYDKAVEL 396
                                       79**************887652667778889**********************975 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.027
                            TPR_21 148 vaelrGDilvaqgkldeAraaYqaAla 174
                                         + +GD+l a g++ eA aa+ +A +
  gi|330509104|ref|YP_004385532.1| 407 SWQGKGDALKASGRQVEAAAAFARAKE 433
                                       55679******************9975 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   7.8e-05     0.043     207     256 ..      58     107 ..      27     114 .. 0.89
   2 ?    3.0   0.6     0.069        37      41     103 ..     121     185 ..     101     192 .. 0.61
   3 ?    0.6   0.0      0.38   2.1e+02     205     246 ..     271     314 ..     258     327 .. 0.76
   4 !   15.0   0.1   1.6e-05    0.0089     187     255 ..     325     396 ..     310     399 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.8e-05
                                       -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       ++  Al   dkaie +p+   +++ K+ +l ++Gd ++  ++ e+a ++ 
  gi|330509104|ref|YP_004385532.1|  58 NYRDALIAFDKAIEIDPENASIWMGKGDVLVRMGDYNESLKIYENALEMA 107
                                       46689999************************************998875 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.069
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT....SSS-HHHHHHHHHHTTTS- CS
                             NARP1  41 ketkaelllkLgrkeeAeatyeaLlernpenskYyeglekak..klskedeeallalydelaeky 103
                                         +k+el +++ +++eA ++y++  e np   + + +  +a+  k  +  e++  ++y+e+ +++
  gi|330509104|ref|YP_004385532.1| 121 WLVKGELFIRIFKNDEAINAYSRATELNPKYAEAWYQKGAALnlKAGELPEQESAKTYEEAFTAL 185
                                       45789999999999999999999999999877644444444412433445566666666665555 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.38
                                       HT-SHHHHHHHHHHHHH-TT-H..HHHHHHHHHHHHTT-HHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlv..elyltKarilkhaGdlkkAa 246
                                        +++e+Al+  d+ ie +p ++  e  l Ka il   G  ++  
  gi|330509104|ref|YP_004385532.1| 271 RERYEEALTACDRVIELDPDFTgqEARLLKAGILSELGRYNESL 314
                                       45678999999999999997653488888999998888877765 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 1.6e-05
                                       -SSHHHHHHHHHHHHHHH...HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 187 pesallwvlyflAqhydk...lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                       p+  +l + +f+A        +g++e+Al++i++a++ +pt    + +K++ l  +G  ++A+++ ++a +l
  gi|330509104|ref|YP_004385532.1| 325 PADLVLLTATFMADKSSVlvkMGEYEEALTTINAALKIDPTNPIAWKNKGEALNYTGRYEEAVSAYDKAVEL 396
                                       556678888888877654333999*******************************************99776 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.11        61      10      32 ..      46      75 ..      35      76 .. 0.75
   2 ?    4.4   0.0      0.13        70       2      27 ..      86     111 ..      82     117 .. 0.56
   3 ?    2.2   0.0      0.64   3.5e+02       9      32 ..     127     150 ..     124     151 .. 0.78
   4 ?    2.3   0.1      0.59   3.2e+02      14      31 ..     176     193 ..     153     195 .. 0.76
   5 ?    1.5   0.0       1.1   5.7e+02       8      28 ..     209     232 ..     204     233 .. 0.74
   6 ?    5.2   0.0     0.072        39      15      32 ..     273     290 ..     253     290 .. 0.78
   7 ?   -0.6   0.0       4.8   2.6e+03       4      29 ..     299     323 ..     295     326 .. 0.67
   8 ?    3.1   0.0      0.34   1.8e+02      12      32 ..     345     365 ..     341     366 .. 0.86
   9 ?    7.2   0.0     0.017       9.1       7      31 ..     374     398 ..     372     399 .. 0.83
  10 ?   -1.5   0.2       9.4   5.1e+03       8      26 ..     413     431 ..     410     434 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.11
                                      HHH.H......HHHHHHHHHHHHHHHH-TT CS
                             TPR_6 10 yrk.l......gdtdkAlealerlikeYPd 32
                                       ++ +      +++++Al a+++ i+  P+
  gi|330509104|ref|YP_004385532.1| 46 WYQeGlklmgnDNYRDALIAFDKAIEIDPE 75
                                      444236667767**************9996 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerli 27 
                                       +l +++   ++l+ +++Ale+ e+  
  gi|330509104|ref|YP_004385532.1|  86 VLVRMGDYNESLKIYENALEMAEKTT 111
                                       45555555555555566666555555 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                                       ++++  + d+A+ a+ r  +  P+
  gi|330509104|ref|YP_004385532.1| 127 LFIRIFKNDEAINAYSRATELNPK 150
                                       555634789*********999986 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.59
                                       HHHHHHHHHHHHHHHH-T CS
                             TPR_6  14 gdtdkAlealerlikeYP 31 
                                       + +++A +al++ i+  P
  gi|330509104|ref|YP_004385532.1| 176 KTYEEAFTALNKAIELDP 193
                                       6799*********99888 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 1.1
                                       HHHHHH...HHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrkl...gdtdkAlealerlik 28 
                                       l+++++   +++ ++lea++r i+
  gi|330509104|ref|YP_004385532.1| 209 LARFNGknfNRYNESLEAFDRAIE 232
                                       5555555568999*******9986 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.072
                                       HHHHHHHHHHHHHHH-TT CS
                             TPR_6  15 dtdkAlealerlikeYPd 32 
                                       ++++Al+a +r+i+  Pd
  gi|330509104|ref|YP_004385532.1| 273 RYEEALTACDRVIELDPD 290
                                       788888888888888886 PP

  == domain 7  score: -0.6 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlike 29 
                                       +k++ +  +lg++ ++l a++  i++
  gi|330509104|ref|YP_004385532.1| 299 LKAGILS-ELGRYNESLVAYDGAISS 323
                                       4444444.467****99999877765 PP

  == domain 8  score: 3.1 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  12 klgdtdkAlealerlikeYPd 32 
                                       k+g++++Al++ +  +k  P+
  gi|330509104|ref|YP_004385532.1| 345 KMGEYEEALTTINAALKIDPT 365
                                       789********9999998886 PP

  == domain 9  score: 7.2 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       ++++  +g++++A+ a+++ ++  P
  gi|330509104|ref|YP_004385532.1| 374 GEALNYTGRYEEAVSAYDKAVELSP 398
                                       56666679************99877 PP

  == domain 10  score: -1.5 bits;  conditional E-value: 9.4
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAlealerl 26 
                                        ++++ g+  +A +a+ r 
  gi|330509104|ref|YP_004385532.1| 413 DALKASGRQVEAAAAFARA 431
                                       5666656788899999886 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.033        18      77     126 ..      51     100 ..      34     113 .. 0.84
   2 ?    0.1   0.0       1.9     1e+03      79     118 ..     172     211 ..     144     222 .. 0.70
   3 !   16.8   0.0   1.3e-05    0.0073      62     124 ..     251     315 ..     243     322 .. 0.89
   4 ?    6.2   0.1     0.024        13      76     123 ..     340     387 ..     332     427 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.033
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHH CS
                   Alkyl_sulf_dimr  77 kealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwR 126
                                        + + +++yr a+   +++++ dpena+    k d+l ++g  +es    
  gi|330509104|ref|YP_004385532.1|  51 LKLMGNDNYRDALIAFDKAIEIDPENASIWMGKGDVLVRMGDYNESLKIY 100
                                       56678899**********************************99998755 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.9
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  79 alkegdyrwaaellnhlvfadpenaeakelkadaleqlgy 118
                                       + +++ y+ a + ln++++ dp   +a + k  +l +l++
  gi|330509104|ref|YP_004385532.1| 172 QESAKTYEEAFTALNKAIELDPGYGKAWNDKGYTLLSLAR 211
                                       3345567777777777777777777777766666666666 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 1.3e-05
                                       HHHHTTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT..-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  62 lvelmGgaekvlekakealkegdyrwaaellnhlvfadpe..naeakelkadaleqlgyqaesat 124
                                        ++++G ++ + ++ +++ +++ y+ a++ ++ +++ dp+   +ea+ lka +l +lg+ +es +
  gi|330509104|ref|YP_004385532.1| 251 ALAFVGMSNMLNDMDRKDEARERYEEALTACDRVIELDPDftGQEARLLKAGILSELGRYNESLV 315
                                       56788888888899999999*******************95568*****************9976 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.024
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  76 akealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                        +  +k g+y+ a++ +n ++  dp+n  a + k +al+  g+ +e+ 
  gi|330509104|ref|YP_004385532.1| 340 SSVLVKMGEYEEALTTINAALKIDPTNPIAWKNKGEALNYTGRYEEAV 387
                                       55567899**********************999999999999988865 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.32   1.7e+02      78     123 ..      59     104 ..      37     110 .. 0.83
   2 ?    1.0   0.0      0.97   5.3e+02      36      76 ..     156     196 ..     130     212 .. 0.67
   3 ?    2.1   0.1      0.44   2.4e+02      73     122 ..     269     320 ..     259     330 .. 0.76
   4 !   21.8   0.0   3.7e-07    0.0002      70     132 ..     341     402 ..     325     409 .. 0.87
   5 ?    1.5   0.4      0.66   3.6e+02     105     124 ..     414     433 ..     412     436 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  78 aeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       +++al   +++++ +P +   +      l r+G+ +e L+ Ye++ 
  gi|330509104|ref|YP_004385532.1|  59 YRDALIAFDKAIEIDPENASIWMGKGDVLVRMGDYNESLKIYENAL 104
                                       55666677778888888888888888899*************9975 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.97
                                       --SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                              BTAD  36 wrGpaladleagewleaererleelrlealealaeaelrlG 76 
                                       ++  a  +l+age  e+e ++  e++++al + +e++  +G
  gi|330509104|ref|YP_004385532.1| 156 YQKGAALNLKAGELPEQESAKTYEEAFTALNKAIELDPGYG 196
                                       44445555566666666666666666666666666665555 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.44
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHH..HHHTT-HHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrA..larsGrqaeALevYerl 122
                                        + +r+eeal+  ++ ++++P      + l++A  l  +Gr +e L +Y+ +
  gi|330509104|ref|YP_004385532.1| 269 EARERYEEALTACDRVIELDPDFTGQEARLLKAgiLSELGRYNESLVAYDGA 320
                                       4567888888888888888888888888888886677888888888888765 PP

  == domain 4  score: 21.8 bits;  conditional E-value: 3.7e-07
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS- CS
                              BTAD  70 eaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgv 132
                                         ++++G++eeal++ +a+++ +P++  +++   +Al ++Gr +eA  +Y+++++ L+ eLg+
  gi|330509104|ref|YP_004385532.1| 341 SVLVKMGEYEEALTTINAALKIDPTNPIAWKNKGEALNYTGRYEEAVSAYDKAVE-LSPELGL 402
                                       467899**********************************************975.7778886 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.66
                                       HHHHTT-HHHHHHHHHHHHH CS
                              BTAD 105 AlarsGrqaeALevYerlrr 124
                                       Al +sGrq eA +++ r+++
  gi|330509104|ref|YP_004385532.1| 414 ALKASGRQVEAAAAFARAKE 433
                                       8999***********99976 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   0.0      0.51   2.8e+02       2      21 ..      59      78 ..      58      81 .. 0.83
   2 ?    0.5   0.0      0.88   4.8e+02       2      15 ..      93     106 ..      92     111 .. 0.82
   3 ?   -2.4   0.0         7   3.8e+03      29      36 ..     155     162 ..     154     167 .. 0.83
   4 ?    3.6   0.0     0.091        50       2      15 ..     178     191 ..     177     192 .. 0.92
   5 ?    5.4   0.0     0.025        14       1      15 [.     219     233 ..     219     239 .. 0.89
   6 ?    0.4   0.0      0.88   4.8e+02       1      14 [.     273     286 ..     273     288 .. 0.90
   7 ?   -2.1   0.0       5.4     3e+03       1      14 [.     309     322 ..     309     323 .. 0.84
   8 ?    3.1   0.0      0.13        70       1      15 [.     348     362 ..     348     364 .. 0.92
   9 ?    3.7   0.0     0.085        46       1      16 [.     382     397 ..     382     401 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.51
                                      HHHHHHHHHHHHHHHHHTTB CS
                          HTH_Bact  2 YeeaLeqvnkAieiSirins 21
                                      Y  aL   +kAiei  +++s
  gi|330509104|ref|YP_004385532.1| 59 YRDALIAFDKAIEIDPENAS 78
                                      999**********9766665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.88
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                       Y+e+L+  + A+e+
  gi|330509104|ref|YP_004385532.1|  93 YNESLKIYENALEM 106
                                       99999999999886 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 7
                                       HHHHHHHH CS
                          HTH_Bact  29 yYqkgecl 36 
                                       +Yqkg  l
  gi|330509104|ref|YP_004385532.1| 155 WYQKGAAL 162
                                       6***9866 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.091
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                       Yeea+   nkAie+
  gi|330509104|ref|YP_004385532.1| 178 YEEAFTALNKAIEL 191
                                       ************95 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.025
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rY+e+Le  ++Aie+
  gi|330509104|ref|YP_004385532.1| 219 RYNESLEAFDRAIEL 233
                                       7************95 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 0.88
                                       -HHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAie 14 
                                       rYeeaL   ++ ie
  gi|330509104|ref|YP_004385532.1| 273 RYEEALTACDRVIE 286
                                       7********99998 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 5.4
                                       -HHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAie 14 
                                       rY+e+L   + Ai 
  gi|330509104|ref|YP_004385532.1| 309 RYNESLVAYDGAIS 322
                                       7*****99988885 PP

  == domain 8  score: 3.1 bits;  conditional E-value: 0.13
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +YeeaL  +n A++i
  gi|330509104|ref|YP_004385532.1| 348 EYEEALTTINAALKI 362
                                       6***********997 PP

  == domain 9  score: 3.7 bits;  conditional E-value: 0.085
                                       -HHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiS 16 
                                       rYeea    +kA+e+S
  gi|330509104|ref|YP_004385532.1| 382 RYEEAVSAYDKAVELS 397
                                       7*************99 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.21   1.1e+02      67     103 ..      36      72 ..      31      84 .. 0.87
   2 !   19.4   2.1   1.1e-06   0.00058      51     194 ..      93     243 ..      89     247 .. 0.84
   3 ?    1.4   0.0      0.32   1.8e+02      51      87 ..     247     283 ..     244     303 .. 0.80
   4 ?    2.3   0.2      0.17        94     124     144 ..     377     396 ..     369     434 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.21
                                       HTT-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHH CS
                              SNAP  67 klkekdeaanayveAakcykkvspeeAvealekAiei 103
                                        + ++++a + y+e  k + +++  +A  a++kAiei
  gi|330509104|ref|YP_004385532.1|  36 AVAQENTADSWYQEGLKLMGNDNYRDALIAFDKAIEI 72 
                                       56788999999***********************998 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.1e-06
                                       THHHHHHHHHHHHHHHH..TT-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHH..TT-HHHHHHHHHHHHHH CS
                              SNAP  51 weeAgeaflkaAecqek..lkekdeaanayveAakcykkvspeeAvealekAieiyte..kgrfrraAklkkeiael 123
                                       ++e+ +++++a e+ ek   +++++a   +v+    ++  +++eA++a+++A e+  +  +   +++A l+ + +el
  gi|330509104|ref|YP_004385532.1|  93 YNESLKIYENALEMAEKttQDNPHDARGWLVKGELFIRIFKNDEAINAYSRATELNPKyaEAWYQKGAALNLKAGEL 169
                                       6677789999999999965678899999999999999999**************965411566899*********** PP

                                       HHHTT--.HHHHHHHHHHHHHHHHHTT.-HHHHHHHHHHHHHHHHHTT.-HHHHHHHHHHHHHTTSS-TTTGGG CS
                              SNAP 124 yekelgd.lekAieaYekAaelyeqee.akalankcllkvAelsaele.kyekAieiyekvakkslennllkys 194
                                        e+e ++ +e+A  a +kA el  + + a  +    ll +A ++ ++  +y++++e++++ ++    +   ++s
  gi|330509104|ref|YP_004385532.1| 170 PEQESAKtYEEAFTALNKAIELDPGYGkAWNDKGYTLLSLARFNGKNFnRYNESLEAFDRAIELISAEDSRQFS 243
                                       ***974459************99888856777777899*****999977**********999887777766666 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.32
                                       THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              SNAP  51 weeAgeaflkaAecqeklkekdeaanayveAakcykk 87 
                                       we  + af+ ++++ ++++ kdea + y eA ++  +
  gi|330509104|ref|YP_004385532.1| 247 WEGKALAFVGMSNMLNDMDRKDEARERYEEALTACDR 283
                                       5555678888888889999999999999999877665 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.17
                                       HHHTT--HHHHHHHHHHHHHH CS
                              SNAP 124 yekelgdlekAieaYekAael 144
                                       ++   g++e+A++aY+kA el
  gi|330509104|ref|YP_004385532.1| 377 LNYT-GRYEEAVSAYDKAVEL 396
                                       4444.5666666666666553 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.34   1.8e+02     265     298 ..      56      96 ..      38     113 .. 0.75
   2 !   11.8   1.7   0.00018     0.099     204     306 ..     101     223 ..      92     264 .. 0.60
   3 ?   -1.6   0.0       2.3   1.2e+03     265     284 ..     380     399 ..     330     415 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.34
                                       ...-SSCCHHHHCCHHCTCCCHSTTCC.......CCHHHHH CS
                               FAT 265 eekieeilqsysaateidpswykawht.......walfnfe 298
                                       +++ +++l ++ +a eidp+ +  w+        ++++n+ 
  gi|330509104|ref|YP_004385532.1|  56 NDNYRDALIAFDKAIEIDPENASIWMGkgdvlvrMGDYNES 96 
                                       456789999****************9766665556666655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00018
                                       HHHSSCCHHHHCCTSSCCC..........SS-SS---...................HH.HHCCCTCCCCCCCCCCCT CS
                               FAT 204 kealqkLreftsellekke..........elqsgleaq.......keptnleeftkll.arcylkkGewqealqkld 262
                                       ++al+++++ t+   ++++          ++ ++ ea+       + + + +e   ++ a ++lk Ge    l + +
  gi|330509104|ref|YP_004385532.1| 101 ENALEMAEKTTQDNPHDARgwlvkgelfiRIFKNDEAInaysratELNPKYAEAWYQKgAALNLKAGE----LPE-Q 172
                                       55666666666666666556655566666444444444222233322222222222222333444444....333.4 PP

                                       .S...-SSCCHHHHCCHHCTCCCHSTTCC.......CCHHHHHCCHHHHHH CS
                               FAT 263 wseekieeilqsysaateidpswykawht.......walfnfevvskeeeq 306
                                       +s ++ ee++ +  +a e+dp+  kaw+        +a+fn ++++++ e+
  gi|330509104|ref|YP_004385532.1| 173 ESAKTYEEAFTALNKAIELDPGYGKAWNDkgytllsLARFNGKNFNRYNES 223
                                       445557777777777777777777777777777777777777777777544 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.3
                                       ...-SSCCHHHHCCHHCTCC CS
                               FAT 265 eekieeilqsysaateidps 284
                                       + + ee++++y +a+e++p+
  gi|330509104|ref|YP_004385532.1| 380 TGRYEEAVSAYDKAVELSPE 399
                                       33356666777777766665 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0016      0.85     178     233 ..      54     109 ..      41     113 .. 0.90
   2 ?   -0.5   0.0       1.2   6.5e+02     215     237 ..     176     198 ..     162     242 .. 0.67
   3 !    6.7   0.0    0.0076       4.1     201     251 ..     333     383 ..     326     400 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                                       H-TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT CS
                        Coatomer_E 178 vggekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdak 233
                                        g ++++dA+  f+   e  +++  + +gk  v + +g+y+e  ++ ++aL+  +k
  gi|330509104|ref|YP_004385532.1|  54 MGNDNYRDALIAFDKAIEIDPENASIWMGKGDVLVRMGDYNESLKIYENALEMAEK 109
                                       58899**************9*******************************98766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                                       T-HHHHHHHHHHHHHH-TT-HHH CS
                        Coatomer_E 215 gryeeAeslLkeaLdkdakdeet 237
                                       + yeeA + L++a++ d+ +  +
  gi|330509104|ref|YP_004385532.1| 176 KTYEEAFTALNKAIELDPGYGKA 198
                                       67999999999999998877554 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0076
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-- CS
                        Coatomer_E 201 plllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkd 251
                                          +  k  v +++g+yeeA + ++ aL+ d+ ++ +  N   a + +g+ 
  gi|330509104|ref|YP_004385532.1| 333 ATFMADKSSVLVKMGEYEEALTTINAALKIDPTNPIAWKNKGEALNYTGRY 383
                                       556677889999******************999987777766666666555 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.052        28      30      66 ..      71     107 ..      61     114 .. 0.82
   2 !    7.3   0.0    0.0063       3.4      36      64 ..     118     146 ..     108     149 .. 0.90
   3 ?    0.9   0.0       0.6   3.3e+02      37      63 ..     334     360 ..     330     366 .. 0.86
   4 ?   -0.2   0.0       1.3   6.9e+02      39      64 ..     370     395 ..     362     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.052
                                       T-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC- CS
                              RPN7  30 lgkeeirrakldlaehYlkigdleeAlkaysrireyc 66 
                                       +++ e +  +  +++  +++gd++e+lk y+ ++e  
  gi|330509104|ref|YP_004385532.1|  71 EIDPENASIWMGKGDVLVRMGDYNESLKIYENALEMA 107
                                       5677778888999******************998865 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0063
                                       HHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  36 rrakldlaehYlkigdleeAlkaysrire 64 
                                       +r++l ++e +++i + +eA++aysr+ e
  gi|330509104|ref|YP_004385532.1| 118 ARGWLVKGELFIRIFKNDEAINAYSRATE 146
                                       578899********************875 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.6
                                       HHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  37 rakldlaehYlkigdleeAlkaysrir 63 
                                         + d+    +k+g++eeAl + ++++
  gi|330509104|ref|YP_004385532.1| 334 TFMADKSSVLVKMGEYEEALTTINAAL 360
                                       66889999999*********9999875 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  39 kldlaehYlkigdleeAlkaysrire 64 
                                       +++++e    +g +eeA+ ay +++e
  gi|330509104|ref|YP_004385532.1| 370 WKNKGEALNYTGRYEEAVSAYDKAVE 395
                                       5677888888999********99987 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 ?   -1.1   0.0       3.8   2.1e+03      18      32 ..      57      71 ..      48      72 .. 0.78
   2 ?   -1.0   0.0       3.5   1.9e+03      19      32 ..      58      71 ..      56      77 .. 0.62
   3 ?    3.8   0.0      0.11        62      18      33 ..      91     106 ..      89     121 .. 0.83
   4 ?   -0.3   0.0       2.2   1.2e+03      21      33 ..     135     147 ..     133     148 .. 0.84
   5 ?    3.8   0.4      0.11        62      13      33 ..     171     191 ..     156     192 .. 0.87
   6 ?    1.8   0.0      0.46   2.5e+02      25      44 ..     218     238 ..     215     243 .. 0.65
   7 ?    4.2   0.0     0.085        46      20      41 ..     267     289 ..     250     321 .. 0.78
   8 ?   -0.7   0.0       2.7   1.5e+03      27      40 ..     349     363 ..     346     378 .. 0.69
   9 !    7.9   0.5    0.0056       3.1      17      33 ..     380     396 ..     372     434 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.8
                               MIT 18 gnyeeAlelYkeale 32
                                       ny +Al ++ +a+e
  gi|330509104|ref|YP_004385532.1| 57 DNYRDALIAFDKAIE 71
                                      578888888888776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.5
                               MIT 19 nyeeAlelYkeale 32
                                      ny +Al ++ +a+e
  gi|330509104|ref|YP_004385532.1| 58 NYRDALIAFDKAIE 71
                                      56666666666655 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.11
                               MIT  18 gnyeeAlelYkealel 33 
                                       g+y e l+ Y++ale 
  gi|330509104|ref|YP_004385532.1|  91 GDYNESLKIYENALEM 106
                                       89************96 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.2
                               MIT  21 eeAlelYkealel 33 
                                       +eA+++Y+ a el
  gi|330509104|ref|YP_004385532.1| 135 DEAINAYSRATEL 147
                                       79*****999875 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.11
                               MIT  13 eeDnagnyeeAlelYkealel 33 
                                       e+++a+ yeeA+ +  +a+el
  gi|330509104|ref|YP_004385532.1| 171 EQESAKTYEEAFTALNKAIEL 191
                                       6799999****9999999885 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.46
                               MIT  25 elYkealelLlqalke.knee 44 
                                       + Y e+le +  a+   ++e 
  gi|330509104|ref|YP_004385532.1| 218 NRYNESLEAFDRAIELiSAED 238
                                       568888888888776335544 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.085
                               MIT  20 yeeAlelYkealelLlqalk.ek 41 
                                        +eA e Y+eal  +  ++    
  gi|330509104|ref|YP_004385532.1| 267 KDEARERYEEALTACDRVIElDP 289
                                       589*********99999987333 PP

  == domain 8  score: -0.7 bits;  conditional E-value: 2.7
                               MIT  27 YkealelLlqalk.e 40 
                                       Y+eal  ++ alk  
  gi|330509104|ref|YP_004385532.1| 349 YEEALTTINAALKiD 363
                                       777777777777744 PP

  == domain 9  score: 7.9 bits;  conditional E-value: 0.0056
                               MIT  17 agnyeeAlelYkealel 33 
                                        g yeeA+++Y +a+el
  gi|330509104|ref|YP_004385532.1| 380 TGRYEEAVSAYDKAVEL 396
                                       689************97 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   5.5e+02      14      30 ..      56      72 ..      54      72 .. 0.89
   2 ?    4.0   0.0     0.061        33      23      36 ..      92     105 ..      91     107 .. 0.89
   3 ?    0.2   0.0      0.98   5.3e+02      17      30 ..     178     191 ..     176     191 .. 0.94
   4 ?   -2.1   0.1       5.1   2.8e+03      16      30 ..     219     233 ..     218     233 .. 0.85
   5 ?   -0.9   0.0       2.1   1.1e+03      14      22 ..     271     279 ..     270     280 .. 0.87
   6 ?   -2.3   0.0       5.7   3.1e+03      17      30 ..     349     362 ..     347     362 .. 0.82
   7 ?    5.6   0.0     0.019        10      15      30 ..     381     396 ..     380     400 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1
                          SHNi-TPR 14 nenFpqAveDlrkaLeL 30
                                      n+n+ +A+  ++ka+e+
  gi|330509104|ref|YP_004385532.1| 56 NDNYRDALIAFDKAIEI 72
                                      89******999999987 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.061
                          SHNi-TPR  23 DlrkaLeLreqllp 36 
                                       D++++L+++e+ l+
  gi|330509104|ref|YP_004385532.1|  92 DYNESLKIYENALE 105
                                       9*********9776 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.98
                          SHNi-TPR  17 FpqAveDlrkaLeL 30 
                                       +++A++ l+ka+eL
  gi|330509104|ref|YP_004385532.1| 178 YEEAFTALNKAIEL 191
                                       89**********98 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 5.1
                          SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                       ++++ +e +++a+eL
  gi|330509104|ref|YP_004385532.1| 219 RYNESLEAFDRAIEL 233
                                       899999999999987 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 2.1
                          SHNi-TPR  14 nenFpqAve 22 
                                       +e++++A++
  gi|330509104|ref|YP_004385532.1| 271 RERYEEALT 279
                                       69*****86 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 5.7
                          SHNi-TPR  17 FpqAveDlrkaLeL 30 
                                       +++A++  ++aL++
  gi|330509104|ref|YP_004385532.1| 349 YEEALTTINAALKI 362
                                       88999988899886 PP

  == domain 7  score: 5.6 bits;  conditional E-value: 0.019
                          SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                       +++++Av+ ++ka+eL
  gi|330509104|ref|YP_004385532.1| 381 GRYEEAVSAYDKAVEL 396
                                       69*************9 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.84   4.6e+02      52      74 ..      88     110 ..      78     123 .. 0.85
   2 ?    7.4   0.2    0.0086       4.6      41      72 ..     203     235 ..     171     248 .. 0.73
   3 ?   -1.2   0.0         4   2.1e+03      44      68 ..     254     278 ..     239     282 .. 0.82
   4 ?    2.0   0.0      0.41   2.2e+02      50      70 ..     342     362 ..     328     366 .. 0.85
   5 ?   -0.8   0.0       3.1   1.7e+03      55      71 ..     381     397 ..     376     400 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.84
                            ANAPC5  52 adfghneeAvkaleeairlAren 74 
                                        ++g+++e++k  e+a ++A ++
  gi|330509104|ref|YP_004385532.1|  88 VRMGDYNESLKIYENALEMAEKT 110
                                       57999***********9999765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0086
                            ANAPC5  41 qyalLnlaslh.adfghneeAvkaleeairlAr 72 
                                        y lL+la++   +f+ ++e+++a+  ai+l  
  gi|330509104|ref|YP_004385532.1| 203 GYTLLSLARFNgKNFNRYNESLEAFDRAIELIS 235
                                       4889*****98467***************9854 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4
                            ANAPC5  44 lLnlaslhadfghneeAvkaleeai 68 
                                        + + ++  d++ ++eA ++ eea 
  gi|330509104|ref|YP_004385532.1| 254 FVGMSNMLNDMDRKDEARERYEEAL 278
                                       5556677788999999999999996 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.41
                            ANAPC5  50 lhadfghneeAvkaleeairl 70 
                                       +  ++g++eeA+ +++ a ++
  gi|330509104|ref|YP_004385532.1| 342 VLVKMGEYEEALTTINAALKI 362
                                       56789**********999887 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 3.1
                            ANAPC5  55 ghneeAvkaleeairlA 71 
                                       g +eeAv+a   a++l+
  gi|330509104|ref|YP_004385532.1| 381 GRYEEAVSAYDKAVELS 397
                                       7899*****99999986 PP

>> TOM20_plant  Plant specific mitochondrial import receptor subunit TOM20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       1.1   6.2e+02      52     113 ..      60      76 ..      49      83 .. 0.62
   2 ?   10.6   0.9   0.00064      0.35       2     112 ..      95     194 ..      94     201 .. 0.88
   3 ?    0.2   0.0      0.98   5.4e+02      89     112 ..     267     290 ..     203     301 .. 0.74
   4 ?   -0.7   0.0       1.9     1e+03      52      78 ..     350     376 ..     343     399 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT- CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqavdedPdn 113
                                       +da+  +++a+ idP+                                             n
  gi|330509104|ref|YP_004385532.1|  60 RDALIAFDKAIEIDPE---------------------------------------------N 76 
                                       3555555555555554.............................................4 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00064
                                       HHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHH CS
                       TOM20_plant   2 drlllfeearkdaeatykknPldadnllrWggallelsqfqsvaeakqmiqdaiskleeallidPkkhdalWcigna 78 
                                       + l ++e+a + ae+t ++nP da   l  g+ ++ +  f++        ++ai  +  a  ++Pk  +a +  g a
  gi|330509104|ref|YP_004385532.1|  95 ESLKIYENALEMAEKTTQDNPHDARGWLVKGELFIRI--FKN--------DEAINAYSRATELNPKYAEAWYQKGAA 161
                                       67999*******************9999888876654..777........79999999************9999999 PP

                                       HHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT CS
                       TOM20_plant  79 ytsfafltpdeeeakenfekatqffqqavdedPd 112
                                           a   p++e ak+ +e a   +++a++ dP+
  gi|330509104|ref|YP_004385532.1| 162 LNLKAGELPEQESAKT-YEEAFTALNKAIELDPG 194
                                       9999999999988875.78999999999999996 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.98
                                       HHHHHHHHHHHHHHHHHHHHH-TT CS
                       TOM20_plant  89 eeeakenfekatqffqqavdedPd 112
                                       ++ea+e +e a    ++ ++ dPd
  gi|330509104|ref|YP_004385532.1| 267 KDEARERYEEALTACDRVIELDPD 290
                                       467888888888888888888877 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHH CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWcigna 78 
                                       ++a++ ++ al idP+   a    g+a
  gi|330509104|ref|YP_004385532.1| 350 EEALTTINAALKIDPTNPIAWKNKGEA 376
                                       588889999999999876554444444 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         5   2.7e+03     125     154 ..       3      32 ..       3      37 .. 0.61
   2 ?    0.7   0.0      0.77   4.2e+02       8      37 ..      43      72 ..      40     103 .. 0.79
   3 ?   -0.4   0.0       1.7   9.1e+02      20      39 ..      89     108 ..      75     126 .. 0.73
   4 ?   -2.4   0.0       6.9   3.8e+03      22      36 ..     176     190 ..     171     215 .. 0.80
   5 ?   -2.1   0.0       5.3   2.9e+03      22      38 ..     218     234 ..     209     240 .. 0.83
   6 ?   -0.8   0.0       2.2   1.2e+03      19      36 ..     269     286 ..     255     287 .. 0.80
   7 ?    3.9   0.0     0.079        43      11      36 ..     336     361 ..     327     363 .. 0.77
   8 ?    5.7   0.0     0.021        11      11      36 ..     370     395 ..     367     398 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5
                           DUF5113 125 esycrqlersaknknvllilvvlllvvllv 154
                                       e++++ l+ +ak++ +++ + ++l v++++
  gi|330509104|ref|YP_004385532.1|   3 EKRVNDLRANAKKMRAWMRIPLILAVLFVL 32 
                                       678888888888887766554443333332 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.77
                           DUF5113  8 andYanlayylnvegeyeeALeyldsaley 37
                                      a+ + + + +l  +++y++AL  +d+a+e+
  gi|330509104|ref|YP_004385532.1| 43 ADSWYQEGLKLMGNDNYRDALIAFDKAIEI 72
                                      666777778888899************986 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.7
                           DUF5113  20 vegeyeeALeyldsaleylN 39 
                                         g+y+e+L++ ++ale+  
  gi|330509104|ref|YP_004385532.1|  89 RMGDYNESLKIYENALEMAE 108
                                       56788888888888887654 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 6.9
                           DUF5113  22 geyeeALeyldsale 36 
                                       ++yeeA + l++a+e
  gi|330509104|ref|YP_004385532.1| 176 KTYEEAFTALNKAIE 190
                                       679999999999887 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 5.3
                           DUF5113  22 geyeeALeyldsaleyl 38 
                                       ++y+e+Le +d a+e++
  gi|330509104|ref|YP_004385532.1| 218 NRYNESLEAFDRAIELI 234
                                       47999999999999876 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 2.2
                           DUF5113  19 nvegeyeeALeyldsale 36 
                                        ++++yeeAL+  d ++e
  gi|330509104|ref|YP_004385532.1| 269 EARERYEEALTACDRVIE 286
                                       56789*****99999876 PP

  == domain 7  score: 3.9 bits;  conditional E-value: 0.079
                           DUF5113  11 YanlayylnvegeyeeALeyldsale 36 
                                        a+  + l   geyeeAL++++ al+
  gi|330509104|ref|YP_004385532.1| 336 MADKSSVLVKMGEYEEALTTINAALK 361
                                       55666677788*************97 PP

  == domain 8  score: 5.7 bits;  conditional E-value: 0.021
                           DUF5113  11 YanlayylnvegeyeeALeyldsale 36 
                                       ++n + +ln++g+yeeA++  d+a+e
  gi|330509104|ref|YP_004385532.1| 370 WKNKGEALNYTGRYEEAVSAYDKAVE 395
                                       678999*****************986 PP

>> 14-3-3  14-3-3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.76   4.1e+02     136     154 ..      94     112 ..      91     117 .. 0.78
   2 ?   -0.7   0.0       1.5   8.3e+02       6      38 ..     173     209 ..     171     237 .. 0.75
   3 ?    5.2   0.0     0.023        13       6      38 ..     269     301 ..     266     314 .. 0.90
   4 ?    1.8   0.0      0.26   1.4e+02     141     184 ..     348     396 ..     335     403 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.76
                                       HHHHHHHHHHHHHHHTTTG CS
                            14-3-3 136 ekakeaYeeAleiakkelq 154
                                       +++ + Ye+Ale+a+k+ q
  gi|330509104|ref|YP_004385532.1|  94 NESLKIYENALEMAEKTTQ 112
                                       5788999999999977654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                                       HHCCHHHHHHHHHCHHHHC....SS---HCHHHHHHH CS
                            14-3-3   6 eqaeryddmveymkkvvel....keeLskeernlLsv 38 
                                       e+a+ y++++++++k++el    ++  +++  +lLs 
  gi|330509104|ref|YP_004385532.1| 173 ESAKTYEEAFTALNKAIELdpgyGKAWNDKGYTLLSL 209
                                       6778888888888888887665555556666666655 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.023
                                       HHCCHHHHHHHHHCHHHHCSS---HCHHHHHHH CS
                            14-3-3   6 eqaeryddmveymkkvvelkeeLskeernlLsv 38 
                                       e  ery++++++  +v+el+++++ +e +lL+ 
  gi|330509104|ref|YP_004385532.1| 269 EARERYEEALTACDRVIELDPDFTGQEARLLKA 301
                                       5679**************************986 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.26
                                       HHHHHHHHH..HTTTGCC-HHHH...HHHHHHHHHHHCTT--HHHHHHH CS
                            14-3-3 141 aYeeAleia..kkelqpthpirL...glaLNySVflyeilnspekAcel 184
                                        YeeAl++     +++pt+pi     g aLNy+  + e +   +kA+el
  gi|330509104|ref|YP_004385532.1| 348 EYEEALTTInaALKIDPTNPIAWknkGEALNYTGRYEEAVSAYDKAVEL 396
                                       5777777762233445677775433366777777777777777777766 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       9.3     5e+03      14      36 ..      83     105 ..      81     112 .. 0.77
   2 ?   -2.1   0.0       8.4   4.6e+03      21      35 ..     175     189 ..     163     191 .. 0.83
   3 ?    0.4   0.0       1.4   7.8e+02      14      31 ..     339     356 ..     327     362 .. 0.79
   4 ?    8.2   0.0    0.0053       2.9      14      37 ..     373     396 ..     367     410 .. 0.81
   5 ?   -1.6   0.0       5.9   3.2e+03      13      35 ..     410     432 ..     399     435 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.3
                         NRBF2_MIT  14 kadrllaaGkyeeaischkkaaa 36 
                                       k d l+  G y+e++  ++ a +
  gi|330509104|ref|YP_004385532.1|  83 KGDVLVRMGDYNESLKIYENALE 105
                                       56788899999999988887755 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8.4
                         NRBF2_MIT  21 aGkyeeaischkkaa 35 
                                       a  yeea +  +ka 
  gi|330509104|ref|YP_004385532.1| 175 AKTYEEAFTALNKAI 189
                                       678999999988885 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.4
                         NRBF2_MIT  14 kadrllaaGkyeeaisch 31 
                                       k+  l+  G yeea++  
  gi|330509104|ref|YP_004385532.1| 339 KSSVLVKMGEYEEALTTI 356
                                       66778999******9765 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0053
                         NRBF2_MIT  14 kadrllaaGkyeeaischkkaaay 37 
                                       k + l  +G+yeea+s + ka + 
  gi|330509104|ref|YP_004385532.1| 373 KGEALNYTGRYEEAVSAYDKAVEL 396
                                       67788889************9875 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 5.9
                         NRBF2_MIT  13 rkadrllaaGkyeeaischkkaa 35 
                                        k d l a+G+  ea +   +a 
  gi|330509104|ref|YP_004385532.1| 410 GKGDALKASGRQVEAAAAFARAK 432
                                       57899999999999999888775 PP

>> PBP_N  Penicillin-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00035      0.19      72     133 ..      10      72 ..       2      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00035
                             PBP_N  72 haaakkkarkgrwvwgtllvvvllavlsvas.gaayvwfky.lkdtpalpsrealfavnrapgv 133
                                        a+akk  r +  +   l+v ++l++++va   +a  w++  lk       r+al+a ++a  +
  gi|330509104|ref|YP_004385532.1|  10 RANAKK-MRAWMRIPLILAVLFVLCLAAVAQeNTADSWYQEgLKLMGNDNYRDALIAFDKAIEI 72 
                                       466666.99*******************997256889997449999999999999999998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.63
# Mc/sec: 2110.23
//
Query:       gi|330509105|ref|YP_004385533.1|  [L=339]
Description: hypothetical protein MCON_3492 [Methanosaeta concilii GP6]
Scores for complete 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   18.2   0.0      0.004   17.0   0.0    1.6  1  MarR_2           MarR family
     0.0073   16.1   0.0      0.014   15.2   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.018   15.0   0.1      0.033   14.1   0.1    1.5  1  MarR             MarR family
      0.021   14.4   0.1      0.041   13.5   0.1    1.5  1  GntR             Bacterial regulatory proteins, gntR family
      0.025   14.9   0.4      0.043   14.2   0.4    1.3  1  Penicillinase_R  Penicillinase repressor
      0.029   13.9   0.0        0.1   12.1   0.0    1.9  1  SieB             Super-infection exclusion protein B
      0.037   13.9   0.1       0.07   13.0   0.1    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm


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 !   17.0   0.0   1.6e-06     0.004       3      54 ..     268     318 ..     266     323 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.6e-06
                                       --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       ltp ++ ++  L  ++g+ + + +   ++g++ks+++ +l  L+++ Lv+r+
  gi|330509105|ref|YP_004385533.1| 268 LTPRERSIMEILIKNGGK-MKQMDMRYETGVPKSTLTMVLISLEKRNLVTRK 318
                                       89**************97.9*****************************997 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.4e-06     0.014       8      50 ..     275     317 ..     272     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.4e-06
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       i+++l + ++ ++  ++  +tg+pkSt    L +L+++ +v++
  gi|330509105|ref|YP_004385533.1| 275 IMEILIKNGGKMKQMDMRYETGVPKSTLTMVLISLEKRNLVTR 317
                                       999999***********************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.3e-05     0.033       1      50 [.     268     318 ..     268     320 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                                       --HHHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR   1 ltltqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                       lt+ + +i++il  +g+ +++ ++    gv kst+t vl  Lek++l++R+
  gi|330509105|ref|YP_004385533.1| 268 LTPRERSIMEILIKNGGkMKQMDMRYETGVPKSTLTMVLISLEKRNLVTRK 318
                                       6777888888877777769999****************************7 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.6e-05     0.041      11      62 ..     273     323 ..     271     325 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                                       HHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR  11 edIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGt 62 
                                       + I++  ++ G k+ ++++ + e gV ++t+  +L+ Le ++lv+r+  + t
  gi|330509105|ref|YP_004385533.1| 273 RSIMEILIKNGGKM-KQMDMRYETGVPKSTLTMVLISLEKRNLVTRKEWGRT 323
                                       5688888999****.*******************************986666 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   1.7e-05     0.043       1      60 [.     268     324 ..     268     327 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                                       ---S-SHHHHHHHHHS-.EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEE CS
                   Penicillinase_R   1 lgelEaevmeilwekge.atvkevveeleeekelaysTVktllrrLvkKgllsrekegraf 60 
                                       l+++E+ +meil ++g  +  k+   + e    + +sT + +l  L+k++l++r++ gr+ 
  gi|330509105|ref|YP_004385533.1| 268 LTPRERSIMEILIKNGGkM--KQMDMRYETG--VPKSTLTMVLISLEKRNLVTRKEWGRTN 324
                                       6899**********99844..5555555555..77*********************99985 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.1e-05       0.1      28     101 ..     187     291 ..     173     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.1e-05
                              SieB  28 leeyglwiglvflisiayllaqvvskllaeikekik...............................kkreqkkvek 73 
                                        +++ +w++ ++++++ +++ +v+++++ + +++++                               ++    + ++
  gi|330509105|ref|YP_004385533.1| 187 SSSNNFWLVGGAILFLVLFIGSVFTFMMRWRRNEMQpvkkdllegdhllgiesqdaskpidavrslgEIEVGSELNA 263
                                       57899*************************************************************99999****** PP

                              SieB  74 klknLteeekavLreflnqgksvltlpl 101
                                       +l++Lt++e+ ++  ++++g ++ ++++
  gi|330509105|ref|YP_004385533.1| 264 VLETLTPRERSIMEILIKNGGKMKQMDM 291
                                       *******************999988776 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   0.1   2.7e-05      0.07      16      57 ..     278     321 ..     268     330 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                                       HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.S CS
                              TrmB  16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek.g 57 
                                        L+ + g+++  +   e+gvp+s+   vL sLe++ lV+r++ g
  gi|330509105|ref|YP_004385533.1| 278 ILIkNGGKMKQMDMRYETGVPKSTLTMVLISLEKRNLVTRKEwG 321
                                       56633456778888899**********************99844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.72u 0.37s 00:00:01.08 Elapsed: 00:00:00.59
# Mc/sec: 1721.20
//
Query:       gi|330509106|ref|YP_004385534.1|  [L=249]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (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   75.1   5.7    6.3e-05   22.8   0.6    5.7  6  TPR_2        Tetratricopeptide repeat
    2.4e-19   68.3   4.2    0.00038   20.2   0.0    5.4  5  TPR_1        Tetratricopeptide repeat
    9.1e-18   63.7   3.6    1.3e-05   24.7   0.0    5.1  5  TPR_11       TPR repeat
    2.1e-15   55.5   8.3     0.0012   18.8   0.0    5.4  5  TPR_8        Tetratricopeptide repeat
    1.1e-13   50.6   3.1     0.0018   18.5   0.0    5.3  5  TPR_17       Tetratricopeptide repeat
      2e-13   50.7   6.0    0.00031   21.2   0.2    4.2  4  TPR_19       Tetratricopeptide repeat
    8.6e-12   44.8   5.3      0.093   13.6   0.0    6.0  6  TPR_14       Tetratricopeptide repeat
    6.6e-11   42.7   0.4    0.00027   21.5   0.0    4.1  4  TPR_16       Tetratricopeptide repeat
    2.4e-09   37.4   8.1    0.00045   20.4   0.2    4.6  5  TPR_12       Tetratricopeptide repeat
    1.2e-08   34.9   0.0     0.0028   17.8   0.0    3.6  4  TPR_9        Tetratricopeptide repeat
    4.5e-06   25.9   1.5     0.0011   18.0   0.1    2.4  2  NARP1        NMDA receptor-regulated protein 1
    5.8e-05   23.2   0.6      0.012   15.8   0.0    3.1  3  ANAPC3       Anaphase-promoting complex, cyclosome, subunit 3
    0.00013   22.5   0.5       0.17   12.4   0.1    2.9  2  BTAD         Bacterial transcriptional activator domain
    0.00016   21.2   3.7     0.0008   18.9   0.6    2.2  2  SNAP         Soluble NSF attachment protein, SNAP
    0.00024   20.9   2.3        4.3    7.6   0.0    4.5  4  TPR_7        Tetratricopeptide repeat
     0.0028   17.7   4.3        0.2   11.7   0.1    3.6  4  DUF3856      Domain of Unknown Function (DUF3856)
     0.0041   17.7   4.4        1.4    9.7   0.0    4.8  5  TPR_6        Tetratricopeptide repeat
     0.0073   16.0   2.5        1.2    9.0   0.1    4.0  4  PPTA         Protein prenyltransferase alpha subunit repeat
  ------ inclusion threshold ------
       0.03   15.2   0.3       0.15   12.9   0.1    2.1  2  Csm2_III-A   Csm2 Type III-A
      0.038   13.7   1.6       0.18   11.6   0.6    2.4  2  TOM20_plant  Plant specific mitochondrial import receptor sub
      0.042   13.7  11.5        1.1    9.2   0.1    5.3  6  TPR_10       Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0014       1.2      17      34 .]      52      69 ..      44      69 .. 0.84
   2 !    9.0   0.1    0.0019       1.6       1      32 [.     106     137 ..     106     139 .. 0.88
   3 !    9.7   0.0    0.0011      0.96       3      34 .]     115     146 ..     113     146 .. 0.87
   4 !   22.8   0.6   7.4e-08   6.3e-05       3      31 ..     149     177 ..     147     178 .. 0.96
   5 !   20.3   0.0   4.6e-07    0.0004       2      34 .]     183     215 ..     182     215 .. 0.95
   6 !    9.9   0.0   0.00095      0.81       3      30 ..     218     245 ..     216     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                             TPR_2 17 yeeAleafekAleldPnn 34
                                      + eAl+a++kAl+ d +n
  gi|330509106|ref|YP_004385534.1| 52 LTEALNAYDKALQMDSQN 69
                                      679**********99776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0019
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       a a+ ++G a+ +l   +eA + fekA+e++ 
  gi|330509106|ref|YP_004385534.1| 106 ALAWQARGVALNYLSIEQEATQSFEKAIEIYD 137
                                       67899999999999999************985 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0011
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       al++l    ++ + +e+A+e +++ ++ dP+n
  gi|330509106|ref|YP_004385534.1| 115 ALNYLSIEQEATQSFEKAIEIYDQEIQKDPKN 146
                                       68888889999999999999999999999987 PP

  == domain 4  score: 22.8 bits;  conditional E-value: 7.4e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                       a+++ ++ +++l+++eeAl a+ek++eld
  gi|330509106|ref|YP_004385534.1| 149 AWWYKAENLANLQRFEEALIAYEKVIELD 177
                                       8**************************98 PP

  == domain 5  score: 20.3 bits;  conditional E-value: 4.6e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +al   G ++++ g++ee + a++kA eldPn+
  gi|330509106|ref|YP_004385534.1| 183 DALSTKGGILMQYGRLEESISALDKATELDPNH 215
                                       689999*************************97 PP

  == domain 6  score: 9.9 bits;  conditional E-value: 0.00095
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                        ++  G+a+ ++g+ +e ++a  kA el
  gi|330509106|ref|YP_004385534.1| 218 SWFTKGQALKEMGRNAESEAATAKAREL 245
                                       69***********************987 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00046      0.39      18      34 .]      53      69 ..      48      69 .. 0.89
   2 !   13.0   0.2     8e-05     0.068       1      31 [.     106     136 ..     106     138 .. 0.94
   3 !   15.7   0.2   1.2e-05    0.0098      11      31 ..     157     177 ..     150     178 .. 0.90
   4 !   20.2   0.0   4.4e-07   0.00038       2      34 .]     183     215 ..     182     215 .. 0.95
   5 ?    5.7   0.0     0.017        14       3      29 ..     218     244 ..     216     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00046
                                      HHHHHHHHHHHHHSTTH CS
                             TPR_1 18 deAleyyekALelnPnn 34
                                       eAl +y+kAL+ + +n
  gi|330509106|ref|YP_004385534.1| 53 TEALNAYDKALQMDSQN 69
                                      69***********9876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8e-05
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                       a a+  +G+a+ +l   +eA + +ekA+e++
  gi|330509106|ref|YP_004385534.1| 106 ALAWQARGVALNYLSIEQEATQSFEKAIEIY 136
                                       679**************************96 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.2e-05
                                       HHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1  11 yfklgkydeAleyyekALeln 31 
                                       + +l++++eAl +yek++el+
  gi|330509106|ref|YP_004385534.1| 157 LANLQRFEEALIAYEKVIELD 177
                                       57899***************9 PP

  == domain 4  score: 20.2 bits;  conditional E-value: 4.4e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +al  +G ++++ g+++e + + +kA el+Pn+
  gi|330509106|ref|YP_004385534.1| 183 DALSTKGGILMQYGRLEESISALDKATELDPNH 215
                                       89999**************************97 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALe 29 
                                       +++ +G+a+ ++g+  e +++  kA e
  gi|330509106|ref|YP_004385534.1| 218 SWFTKGQALKEMGRNAESEAATAKARE 244
                                       699***********9999998888766 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.2e-06    0.0044       8      31 ..      50      73 ..      47      76 .. 0.88
   2 ?    1.1   0.0      0.38   3.3e+02      24      38 ..     102     116 ..      99     117 .. 0.87
   3 !    8.2   0.2    0.0024         2       8      33 ..     127     152 ..     125     161 .. 0.88
   4 !    9.6   0.1   0.00086      0.73       7      24 ..     160     177 ..     156     185 .. 0.91
   5 !   24.7   0.0   1.6e-08   1.3e-05       3      42 .]     191     230 ..     189     230 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.2e-06
                            TPR_11  8 GkyeeAieaYkkAlkldPdnaeay 31
                                        ++eA++aY kAl+ d++n +++
  gi|330509106|ref|YP_004385534.1| 50 ESLTEALNAYDKALQMDSQNESIL 73
                                      5799****************9986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.38
                            TPR_11  24 dPdnaeayynLGlay 38 
                                       +P++a a+ ++G+a+
  gi|330509106|ref|YP_004385534.1| 102 NPQDALAWQARGVAL 116
                                       8***********986 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0024
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayyn 33 
                                       + +e+Aie Y + ++ dP+n +a++ 
  gi|330509106|ref|YP_004385534.1| 127 QSFEKAIEIYDQEIQKDPKNGTAWWY 152
                                       579*****************999985 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00086
                            TPR_11   7 qGkyeeAieaYkkAlkld 24 
                                       ++++eeA+ aY+k ++ld
  gi|330509106|ref|YP_004385534.1| 160 LQRFEEALIAYEKVIELD 177
                                       679**************9 PP

  == domain 5  score: 24.7 bits;  conditional E-value: 1.6e-08
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ++++ G++ee+i a+ kA +ldP+  + ++  G+a+ ++G
  gi|330509106|ref|YP_004385534.1| 191 ILMQYGRLEESISALDKATELDPNHITSWFTKGQALKEMG 230
                                       78999********************************998 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.017        15      16      34 .]      51      69 ..      47      69 .. 0.86
   2 !    7.0   0.2     0.009       7.7       4      31 ..     109     136 ..     106     139 .. 0.75
   3 !   14.7   0.2   3.1e-05     0.026       7      31 ..     153     177 ..     148     178 .. 0.87
   4 !   18.8   0.0   1.5e-06    0.0012       3      34 .]     184     215 ..     182     215 .. 0.91
   5 !   10.0   0.0   0.00098      0.84       2      23 ..     217     238 ..     216     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
                                      -HHHHHHHHHHHHHHHHH. CS
                             TPR_8 16 dyeeAkeyyekaleldpdn 34
                                       + eA  +y kal++d +n
  gi|330509106|ref|YP_004385534.1| 51 SLTEALNAYDKALQMDSQN 69
                                      5789***********9875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.009
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleld 31 
                                       ++  g ++  l   +eA +++eka+e+ 
  gi|330509106|ref|YP_004385534.1| 109 WQARGVALNYLSIEQEATQSFEKAIEIY 136
                                       6666666666666789**********96 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekaleld 31 
                                       ++  + +l+++eeA  +yek++eld
  gi|330509106|ref|YP_004385534.1| 153 KAENLANLQRFEEALIAYEKVIELD 177
                                       6777899****************98 PP

  == domain 4  score: 18.8 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+  +g i+++ g++ee+++++ ka+eldp++
  gi|330509106|ref|YP_004385534.1| 184 ALSTKGGILMQYGRLEESISALDKATELDPNH 215
                                       66778999**********************97 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.00098
                                       CHHHHHHHHHHHTT-HHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkey 23 
                                        +++ +g++++++g+  e++++
  gi|330509106|ref|YP_004385534.1| 217 TSWFTKGQALKEMGRNAESEAA 238
                                       58****************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       2.4     2e+03       1      12 [.      58      69 ..      58      75 .. 0.83
   2 !   11.3   0.1   0.00044      0.38       4      24 ..      97     117 ..      95     134 .. 0.84
   3 !   10.5   0.3   0.00079      0.67       2      33 ..     136     167 ..     128     168 .. 0.93
   4 ?    5.9   0.0     0.023        19       1      31 [.     169     200 ..     169     203 .. 0.82
   5 !   18.5   0.0   2.2e-06    0.0018       2      32 ..     205     235 ..     204     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.4
                            TPR_17  1 lylkaleldPnn 12
                                      +y kal+ d  n
  gi|330509106|ref|YP_004385534.1| 58 AYDKALQMDSQN 69
                                      599***999887 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00044
                            TPR_17   4 kaleldPnnadaynnLAelll 24 
                                       k le++P +a a++ ++++l 
  gi|330509106|ref|YP_004385534.1|  97 KKLENNPQDALAWQARGVALN 117
                                       669**************9985 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00079
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y + +++dP+n  a+ ++Ae l+++ ++++A+
  gi|330509106|ref|YP_004385534.1| 136 YDQEIQKDPKNGTAWWYKAENLANLQRFEEAL 167
                                       889999********************999995 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.023
                            TPR_17   1 lylkaleld.PnnadaynnLAelllknGdlmt 31 
                                       +y+k++eld P  +da+  ++ +l + G+l++
  gi|330509106|ref|YP_004385534.1| 169 AYEKVIELDhPRKVDALSTKGGILMQYGRLEE 200
                                       5*******66******9999988887777765 PP

  == domain 5  score: 18.5 bits;  conditional E-value: 2.2e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       + ka eldPn+  +++ ++++l++ G+ ++ 
  gi|330509106|ref|YP_004385534.1| 205 LDKATELDPNHITSWFTKGQALKEMGRNAES 235
                                       579*********************9998765 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0    0.0002      0.17       2      30 ..      47      75 ..      46      80 .. 0.91
   2 ?    4.3   0.0     0.066        57       5      29 ..      86     110 ..      85     116 .. 0.85
   3 !   21.2   0.2   3.6e-07   0.00031       5      57 ..     127     179 ..     123     188 .. 0.88
   4 !   13.0   0.1   0.00013      0.11       1      53 [.     192     244 ..     192     248 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                            TPR_19  2 laegdyaeAlalleqalqedpknaearll 30
                                      +a++ ++eAl+++ +alq d +n+ ++l+
  gi|330509106|ref|YP_004385534.1| 47 MASESLTEALNAYDKALQMDSQNESILLR 75
                                      68899*******************99985 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.066
                            TPR_19   5 gdyaeAlalleqalqedpknaearl 29 
                                       g  +eAl + e+ l+ +p++a a+ 
  gi|330509106|ref|YP_004385534.1|  86 GTATEALGIVEKKLENNPQDALAWQ 110
                                       67899**************999986 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 3.6e-07
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       + ++ A++++ q +q+dpkn+ a+ + Ae l +l +++eA  + +++ e d+ 
  gi|330509106|ref|YP_004385534.1| 127 QSFEKAIEIYDQEIQKDPKNGTAWWYKAENLANLQRFEEALIAYEKVIELDHP 179
                                       67999***********************************9888888877765 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 0.00013
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       l++ g+++e +++l +a + dp++   +    +al ++g+ +e ea+ +++ e
  gi|330509106|ref|YP_004385534.1| 192 LMQYGRLEESISALDKATELDPNHITSWFTKGQALKEMGRNAESEAATAKARE 244
                                       7899***************************************9998887765 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.033        29      13      40 ..      48      75 ..      27      79 .. 0.88
   2 ?    5.3   0.1     0.051        44      17      42 ..      88     113 ..      84     116 .. 0.86
   3 !   11.0   0.0   0.00073      0.62      11      42 ..     123     154 ..     114     155 .. 0.85
   4 !    9.5   0.3    0.0023         2       3      31 ..     149     177 ..     148     185 .. 0.87
   5 !   13.6   0.0   0.00011     0.093       3      43 ..     184     224 ..     182     225 .. 0.86
   6 ?    1.7   0.0      0.72   6.1e+02       4      29 ..     219     244 ..     217     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.033
                            TPR_14 13 alGdpdeAiallrralalaPddaeawll 40
                                      a++ + eA++++++al+ + +++ ++l+
  gi|330509106|ref|YP_004385534.1| 48 ASESLTEALNAYDKALQMDSQNESILLR 75
                                      677899***********99999888876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.051
                            TPR_14  17 pdeAiallrralalaPddaeawllla 42 
                                         eA+ + ++ l+ +P+da aw + +
  gi|330509106|ref|YP_004385534.1|  88 ATEALGIVEKKLENNPQDALAWQARG 113
                                       67899999999***********9876 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00073
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawllla 42 
                                        +a + +++Ai+++++ ++++P++ +aw + a
  gi|330509106|ref|YP_004385534.1| 123 QEATQSFEKAIEIYDQEIQKDPKNGTAWWYKA 154
                                       578899**********************8877 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0023
                            TPR_14   3 allalaeallalGdpdeAiallrralala 31 
                                       a++  ae l++l++++eA+ +++++++l+
  gi|330509106|ref|YP_004385534.1| 149 AWWYKAENLANLQRFEEALIAYEKVIELD 177
                                       7999999*******************963 PP

  == domain 5  score: 13.6 bits;  conditional E-value: 0.00011
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       al   + +l++ G+++e+i +l++a +l+P++ + w+  +q
  gi|330509106|ref|YP_004385534.1| 184 ALSTKGGILMQYGRLEESISALDKATELDPNHITSWFTKGQ 224
                                       56667889***********************9998887666 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.72
                            TPR_14   4 llalaeallalGdpdeAiallrrala 29 
                                       +   ++al + G+ +e++a+  +a +
  gi|330509106|ref|YP_004385534.1| 219 WFTKGQALKEMGRNAESEAATAKARE 244
                                       6667999*********9999888865 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0       0.3   2.6e+02      13      27 ..      52      66 ..      47      76 .. 0.71
   2 ?    0.1   0.1       1.5   1.3e+03      24      44 ..      99     116 ..      87     125 .. 0.75
   3 !   21.5   0.0   3.2e-07   0.00027      12      61 ..     128     174 ..     119     181 .. 0.91
   4 !   13.2   0.0   0.00013      0.11       3      61 ..     188     243 ..     186     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.3
                            TPR_16 13 yddAaaaleaalkrd 27
                                       ++A++a++ al +d
  gi|330509106|ref|YP_004385534.1| 52 LTEALNAYDKALQMD 66
                                      567777777777666 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.5
                            TPR_16  24 lkrdpssPdaaeAllllgdaa 44 
                                       l+++   P++a A+ ++g+a+
  gi|330509106|ref|YP_004385534.1|  99 LENN---PQDALAWQARGVAL 116
                                       4556...88888888888776 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 3.2e-07
                            TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                        +++A++ +++ + +d   P +  A++++++ ++ ++r++eA+ +y++ +
  gi|330509106|ref|YP_004385534.1| 128 SFEKAIEIYDQEIQKD---PKNGTAWWYKAENLANLQRFEEALIAYEKVI 174
                                       5999************...************************9998876 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.00013
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       ++ ++++ g+ ++ + al+ a+++d   P +  +++ +g+a+ + gr ae +a+ ++a 
  gi|330509106|ref|YP_004385534.1| 188 KGGILMQYGRLEESISALDKATELD---PNHITSWFTKGQALKEMGRNAESEAATAKAR 243
                                       57889999*****************...************************8887775 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1       0.1        89      61      74 ..      52      65 ..      46      70 .. 0.58
   2 !   10.4   0.1    0.0007       0.6      27      76 ..      89     137 ..      85     138 .. 0.91
   3 !   15.3   2.2   2.2e-05     0.018      19      74 ..     122     176 ..     106     177 .. 0.78
   4 !   20.4   0.2   5.3e-07   0.00045       9      76 ..     153     213 ..     147     214 .. 0.79
   5 !   13.8   0.1   6.3e-05     0.054       5      73 ..     184     244 ..     182     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.1
                            TPR_12 61 yeeAlelleealai 74
                                      + eAl+++ +al++
  gi|330509106|ref|YP_004385534.1| 52 LTEALNAYDKALQM 65
                                      34555555555555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0007
                            TPR_12  27 ekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        +al i+++ l +++p+ a + ++ g ++ +l   +eA + +e+a++i+ 
  gi|330509106|ref|YP_004385534.1|  89 TEALGIVEKKL-ENNPQDALAWQARGVALNYLSIEQEATQSFEKAIEIYD 137
                                       58999998887.699*********************************97 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 2.2e-05
                            TPR_12  19 ydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        +eA + +eka+ei+ ++++ + + +ta+ + +   +  +  r+eeAl ++e+++++
  gi|330509106|ref|YP_004385534.1| 122 EQEATQSFEKAIEIYdQEIQKDPKNGTAWWYKAENLAN-L-QRFEEALIAYEKVIEL 176
                                       479************99997777778888887776665.4.49**********9997 PP

  == domain 4  score: 20.4 bits;  conditional E-value: 5.3e-07
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        a+ l+ l+r++eAl  +ek+        + dhp  + +l + g ++ + gr+ee +++l +a+++++
  gi|330509106|ref|YP_004385534.1| 153 KAENLANLQRFEEALIAYEKV-------IELDHPRKVDALSTKGGILMQYGRLEESISALDKATELDP 213
                                       566666666666666666666.......4556***************999**************9975 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 6.3e-05
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       al+  + +l++ gr++e+++ l+ka e+      p+h   +t+ ++ g+++ ++gr +e +++  +a +
  gi|330509106|ref|YP_004385534.1| 184 ALSTKGGILMQYGRLEESISALDKATELD-----PNH---ITSWFTKGQALKEMGRNAESEAATAKARE 244
                                       56678999*****************8888.....998...9******************9998777766 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       3.8   3.2e+03      11      25 ..      52      66 ..      44      73 .. 0.58
   2 !   11.5   0.0    0.0003      0.25      13      62 ..      90     139 ..      86     149 .. 0.89
   3 !   17.8   0.0   3.3e-06    0.0028       6      61 ..     158     214 ..     154     218 .. 0.94
   4 ?    6.4   0.0     0.012       9.8      21      45 ..     208     232 ..     204     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.8
                             TPR_9 11 weralavverlllla 25
                                        +al +++  l+++
  gi|330509106|ref|YP_004385534.1| 52 LTEALNAYDKALQMD 66
                                      444555555555444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0003
                             TPR_9  13 ralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       +al +ve  l  +P+d+  +  RG++l  l   ++A + +e ++++ ++ 
  gi|330509106|ref|YP_004385534.1|  90 EALGIVEKKLENNPQDALAWQARGVALNYLSIEQEATQSFEKAIEIYDQE 139
                                       69999**************************************9877654 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 3.3e-06
                             TPR_9   6 ireedweralavverllll.aPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       ++ +++e+al ++e ++ l +P+ ++ +   G +l+q G+l++ + +L+ + +l+p+
  gi|330509106|ref|YP_004385534.1| 158 ANLQRFEEALIAYEKVIELdHPRKVDALSTKGGILMQYGRLEESISALDKATELDPN 214
                                       6779***************99**********************************96 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.012
                             TPR_9  21 llllaPddpeerrdRGlllaqlGcl 45 
                                          l+P+++  ++  G++l ++G+ 
  gi|330509106|ref|YP_004385534.1| 208 ATELDPNHITSWFTKGQALKEMGRN 232
                                       5689******************985 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.9   0.00053      0.45     161     256 ..      78     177 ..      55     178 .. 0.70
   2 !   18.0   0.1   1.2e-06    0.0011     196     280 ..     151     239 ..     147     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00053
                                       HHHHHHTTTTTSSSSTTGG.GSS----SSHHHH.....HHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHH CS
                             NARP1 161 lvegyvkslktsgklsesdnedsekepesallw.....vlyflAqhydklgsrekAleyidkaiehtptlvelyltK 232
                                       +v+++++  ++++ l   + ++ e++p+ al w     +l++l+   + ++s ekA+e+ d+ i+++p+    +  K
  gi|330509106|ref|YP_004385534.1|  78 VVLDIITIGTATEALGIVE-KKLENNPQDALAWqargvALNYLSIEQEATQSFEKAIEIYDQEIQKDPKNGTAWWYK 153
                                       5555555555555444433.6778999999999333333566666666677788****************9999999 PP

                                       HHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 233 arilkhaGdlkkAaevmeearklD 256
                                       a+ l     +++A  + e+  +lD
  gi|330509106|ref|YP_004385534.1| 154 AENLANLQRFEEALIAYEKVIELD 177
                                       988877777777777777766666 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHHHT-SHHHHHHHHHHHHH-.TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT...-HHHHHHHHH CS
                             NARP1 196 yflAqhydklgsrekAleyidkaieht.ptlvelyltKarilkhaGdlkkAaevmeearklDla...DRyiNskcak 268
                                       ++ A    +l++ e+Al   +k ie + p  v+   tK+ il ++G l++ ++++++a +lD +     +  +++ k
  gi|330509106|ref|YP_004385534.1| 151 WYKAENLANLQRFEEALIAYEKVIELDhPRKVDALSTKGGILMQYGRLEESISALDKATELDPNhitSWFTKGQALK 227
                                       5778888899999************877**********************************751114577777777 PP

                                       HHHHTT-HHHHH CS
                             NARP1 269 ymLradeveeAe 280
                                        m r+ e e A 
  gi|330509106|ref|YP_004385534.1| 228 EMGRNAESEAAT 239
                                       777777777665 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2       0.3   2.6e+02      35      80 ..      84     130 ..      48     132 .. 0.51
   2 !   11.9   0.3   0.00024      0.21      30      81 ..     115     172 ..      84     173 .. 0.74
   3 !   15.8   0.0   1.4e-05     0.012       3      78 ..     161     238 ..     159     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.3
                                       HTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  35 lngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                         g  ++A+ +++k+ + n+++  ++   + +l  L+  +eA + +e
  gi|330509106|ref|YP_004385534.1|  84 TIGTATEALGIVEKKlENNPQDALAWQARGVALNYLSIEQEATQSFE 130
                                       44566677777777766666666665555555556666666665555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00024
                                       HHHHHHTT-.....HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  30 Alclylngq.....ykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       Al +++ +q     +++A+e++++  ++++k+  ++  +A+ l  L+++eeA+ a+ek
  gi|330509106|ref|YP_004385534.1| 115 ALNYLSIEQeatqsFEKAIEIYDQEiQKDPKNGTAWWYKAENLANLQRFEEALIAYEK 172
                                       66666655555566****************************************9998 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1.4e-05
                                       T-HHHHHHHHHHHH..HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   3 nnyknAiflaerlla.aetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       +++++A++ +e++ +  +++  +++  ++  l + g+ ++ +  l+ka +l+++++ ++++++q+l ++++  e +a
  gi|330509106|ref|YP_004385534.1| 161 QRFEEALIAYEKVIElDHPRKVDALSTKGGILMQYGRLEESISALDKAtELDPNHITSWFTKGQALKEMGRNAESEA 237
                                       6899**********97778888888889****************************************999988777 PP

                                       H CS
                            ANAPC3  78 a 78 
                                       a
  gi|330509106|ref|YP_004385534.1| 238 A 238
                                       6 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0069       5.9      72     138 ..      82     148 ..      27     154 .. 0.89
   2 !   12.4   0.1   0.00019      0.17      39     118 ..     155     238 ..     149     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0069
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH CS
                              BTAD  72 elrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepgpel 138
                                        +++G a eal+  e+ ++++P +  ++++   Al ++  ++eA + +e++ ++ ++e+  +p+  +
  gi|330509106|ref|YP_004385534.1|  82 IITIGTATEALGIVEKKLENNPQDALAWQARGVALNYLSIEQEATQSFEKAIEIYDQEIQKDPKNGT 148
                                       5689999*****************************************************9999877 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00019
                                       STTGGGTTSTTHHHHHHHH....HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT- CS
                              BTAD  39 paladleagewleaererl....eelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGr 111
                                       + la+l+ +e++  + e++    + ++++al +    ++++Gr ee ++ l+++++++P + +++    +Al  +Gr
  gi|330509106|ref|YP_004385534.1| 155 ENLANLQRFEEALIAYEKVieldHPRKVDALSTKGGILMQYGRLEESISALDKATELDPNHITSWFTKGQALKEMGR 231
                                       5566666655555555444111134689999999******************************************* PP

                                       HHHHHHH CS
                              BTAD 112 qaeALev 118
                                       +ae  ++
  gi|330509106|ref|YP_004385534.1| 232 NAESEAA 238
                                       **98876 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.064        54     246     276 ..      45      75 ..      29      82 .. 0.79
   2 !   18.9   0.6   9.4e-07    0.0008     132     196 ..     123     188 ..     113     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.064
                                       HTT-TTTHHHHHHHHTTSS---HHHHHHHHH CS
                              SNAP 246 eegdvekfteavkefDkiskldkWkttlLlk 276
                                       ++  +e +tea+  +Dk  ++d+ + ++Ll+
  gi|330509106|ref|YP_004385534.1|  45 NSMASESLTEALNAYDKALQMDSQNESILLR 75 
                                       4556688888888888888888888888876 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 9.4e-07
                                       HHHHHHHHHHHHHHHHTT-HHHHH.HHHHHHHHHHHHTT-HHHHHHHHHHHHHTTSS-TTTGGGHH CS
                              SNAP 132 ekAieaYekAaelyeqeeakalan.kcllkvAelsaelekyekAieiyekvakkslennllkysvk 196
                                       ++A++++ekA e+y+qe +k   n +++   Ae  a+l+++e+A+ +yekv++     ++   s k
  gi|330509106|ref|YP_004385534.1| 123 QEATQSFEKAIEIYDQEIQKDPKNgTAWWYKAENLANLQRFEEALIAYEKVIELDHPRKVDALSTK 188
                                       78***************98777772567889********************987776666666665 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.1     9e+02      17      31 ..      54      68 ..      52      72 .. 0.75
   2 !    7.6   0.0    0.0051       4.3      15      32 ..     129     144 ..     115     147 .. 0.85
   3 ?    5.9   0.0     0.017        15      11      29 ..     159     177 ..     151     183 .. 0.86
   4 ?    2.6   0.0      0.19   1.6e+02       8      35 ..     191     216 ..     184     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
                             TPR_7 17 eAielyeqsLaltkd 31
                                      eA+  y ++L+++++
  gi|330509106|ref|YP_004385534.1| 54 EALNAYDKALQMDSQ 68
                                      788889998888765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0051
                             TPR_7  15 yeeAielyeqsLaltkdp 32 
                                       +e+Aie+y q  ++ kdp
  gi|330509106|ref|YP_004385534.1| 129 FEKAIEIYDQ--EIQKDP 144
                                       8*********..999998 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.017
                             TPR_7  11 rlGdyeeAielyeqsLalt 29 
                                       +l+++eeA+  ye++++l+
  gi|330509106|ref|YP_004385534.1| 159 NLQRFEEALIAYEKVIELD 177
                                       799***********77775 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.19
                             TPR_7   8 lysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +  + G+ ee i+ + +  a++ dp+++
  gi|330509106|ref|YP_004385534.1| 191 ILMQYGRLEESISALDK--ATELDPNHI 216
                                       55666999*********..******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 ?   -1.0   0.0         2   1.7e+03      26      76 ..      53      64 ..      20      76 .. 0.62
   2 !   11.7   0.1   0.00024       0.2      48     134 ..      99     181 ..      89     188 .. 0.88
   3 ?    2.0   0.0      0.23     2e+02      69     128 ..     161     175 ..     154     214 .. 0.46
   4 ?    4.7   0.1     0.035        30     100     128 ..     216     244 ..     209     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                                      HHHHHHHHHHHHHHTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                           DUF3856 26 eeaaasyrkalevsrtipaeeafdheGfdalchaglsealaklgrydeale 76
                                       ea                                       l  yd+al+
  gi|330509106|ref|YP_004385534.1| 53 TEA---------------------------------------LNAYDKALQ 64
                                      222.......................................333333333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00024
                                       --HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                           DUF3856  48 fdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafr 124
                                       ++ +  dal++ +   al  l   +ea +s +ka++ +++  + +  +G  W    + +a  l++l r +eal a++
  gi|330509106|ref|YP_004385534.1|  99 LENNPQDALAWQARGVALNYLSIEQEATQSFEKAIEIYDQEIQKDPKNGTAW----WYKAENLANLQRFEEALIAYE 171
                                       5667789********************************9998888999999....579****************** PP

                                       HHHHHHHH-- CS
                           DUF3856 125 magemiaerk 134
                                       ++ e+ + rk
  gi|330509106|ref|YP_004385534.1| 172 KVIELDHPRK 181
                                       *999877766 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.23
                                       T-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  69 grydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       +r++eal + +k +                                             e
  gi|330509106|ref|YP_004385534.1| 161 QRFEEALIAYEKVI---------------------------------------------E 175
                                       44444443333322.............................................2 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.035
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 100 iaavfsravaleelGrkdealkafrmage 128
                                       i+  f++++al+e+Gr++e+  a  +a e
  gi|330509106|ref|YP_004385534.1| 216 ITSWFTKGQALKEMGRNAESEAATAKARE 244
                                       778899***********998777777766 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.7   3.2e+03      17      27 ..      53      63 ..      44      65 .. 0.63
   2 ?    2.6   0.0      0.29   2.5e+02      15      32 ..     128     145 ..     114     146 .. 0.72
   3 !    9.7   0.0    0.0017       1.4       2      29 ..     149     176 ..     148     180 .. 0.86
   4 ?    2.4   0.0      0.36     3e+02      11      33 .]     194     215 ..     188     215 .. 0.81
   5 ?   -1.4   0.1       5.6   4.8e+03       8      20 ..     224     236 ..     220     245 .. 0.48

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.7
                                      HHHHHHHHHHH CS
                             TPR_6 17 dkAlealerli 27
                                      ++Al a+++ +
  gi|330509106|ref|YP_004385534.1| 53 TEALNAYDKAL 63
                                      45666665554 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHH-TT CS
                             TPR_6  15 dtdkAlealerlikeYPd 32 
                                         +kA+e++++ i++ P+
  gi|330509106|ref|YP_004385534.1| 128 SFEKAIEIYDQEIQKDPK 145
                                       567899998887777665 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlike 29 
                                       A ++ a+ + +l++ ++Al a+e++i+ 
  gi|330509106|ref|YP_004385534.1| 149 AWWYKAENLANLQRFEEALIAYEKVIEL 176
                                       7788899999977*************85 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6  11 rklgdtdkAlealerlikeYPdS 33 
                                       +  g+ ++++ al++  +  P++
  gi|330509106|ref|YP_004385534.1| 194 QY-GRLEESISALDKATELDPNH 215
                                       43.599************99985 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 5.6
                                       HHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAl 20 
                                       ++++++g+ +++ 
  gi|330509106|ref|YP_004385534.1| 224 QALKEMGRNAESE 236
                                       5555554443332 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.78   6.6e+02       7      18 ..      61      72 ..      60      72 .. 0.89
   2 ?    2.1   0.0       0.2   1.7e+02       2      15 ..      92     105 ..      91     110 .. 0.85
   3 !    9.0   0.1    0.0014       1.2       9      21 ..     140     152 ..     138     153 .. 0.94
   4 ?    0.6   0.0      0.62   5.3e+02       7      20 ..     207     220 ..     205     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.78
                                      HHHHH-TT-CHH CS
                              PPTA  7 kliekdpkNYsa 18
                                      k++++d +N+s+
  gi|330509106|ref|YP_004385534.1| 61 KALQMDSQNESI 72
                                      89*******996 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.2
                                       HHHHHHHHHH-TT- CS
                              PPTA   2 LeltekliekdpkN 15 
                                       L  +ek++e++p++
  gi|330509106|ref|YP_004385534.1|  92 LGIVEKKLENNPQD 105
                                       6789********86 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0014
                                       HHH-TT-CHHHHH CS
                              PPTA   9 iekdpkNYsaWny 21 
                                       i+kdpkN +aW y
  gi|330509106|ref|YP_004385534.1| 140 IQKDPKNGTAWWY 152
                                       89*********99 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.62
                                       HHHHH-TT-CHHHH CS
                              PPTA   7 kliekdpkNYsaWn 20 
                                       k+ e+dp + + W+
  gi|330509106|ref|YP_004385534.1| 207 KATELDPNHITSWF 220
                                       67799********5 PP

>> Csm2_III-A  Csm2 Type III-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.9   3.3e+03     100     111 ..      51      62 ..      26      66 .. 0.72
   2 ?   12.9   0.1   0.00018      0.15      66     111 ..     118     173 ..     107     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.9
                                       HHHHHHHHHHHC CS
                        Csm2_III-A 100 dffEAivAYhky 111
                                        ++EA+ AY k+
  gi|330509106|ref|YP_004385534.1|  51 SLTEALNAYDKA 62 
                                       578999999887 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHHHHHHHHHHH--SH...........HHHHHHHHHHHHHHHHHHC CS
                        Csm2_III-A  66 Yaagreeavkelsevlkkaidkvkksk..........ekfkrfvdffEAivAYhky 111
                                       Y +  +ea++ +++ ++ + ++++k++          e++ ++ +f EA++AY+k+
  gi|330509106|ref|YP_004385534.1| 118 YLSIEQEATQSFEKAIEIYDQEIQKDPkngtawwykaENLANLQRFEEALIAYEKV 173
                                       5666688999999999999999999988999999999*****************97 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 ?   11.6   0.6   0.00021      0.18      28     115 ..      56     148 ..      43     160 .. 0.67
   2 ?    0.4   0.0      0.54   4.6e+02      51      66 ..     198     213 ..     154     242 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHHHHS-HHHHHHHHHHHHH..HHHHHHHH-TT-HHHHHHHHHHHHHHH...HH---HHHHHHHHHHH CS
                       TOM20_plant  28 llrWggallelsqfqsvaeakqmiqdais..kleeallidPkkhdalWcignaytsfa...fltpdeeeakenfeka 99 
                                       l  + +al   sq +s+   k ++ d i+     eal i  kk +     + a+ + +    + + e+ea + feka
  gi|330509106|ref|YP_004385534.1|  56 LNAYDKALQMDSQNESILLRKTVVLDIITigTATEALGIVEKKLENNPQDALAWQARGvalNYLSIEQEATQSFEKA 132
                                       5556666666677777777777777765422566777776666544433333333322111355668899******* PP

                                       HHHHHHHHHH-TT-HH CS
                       TOM20_plant 100 tqffqqavdedPdndl 115
                                        ++++q +++dP+n +
  gi|330509106|ref|YP_004385534.1| 133 IEIYDQEIQKDPKNGT 148
                                       ************9964 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHHHHH-T CS
                       TOM20_plant  51 iqdaiskleeallidP 66 
                                       ++++is l++a  +dP
  gi|330509106|ref|YP_004385534.1| 198 LEESISALDKATELDP 213
                                       3444444444444444 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.16   1.4e+02      18      31 ..      52      65 ..      48      68 .. 0.87
   2 ?   -0.7   0.0       1.6   1.4e+03      16      30 ..     101     115 ..      90     118 .. 0.78
   3 ?    3.9   0.1     0.062        53      19      35 ..     123     139 ..     122     144 .. 0.84
   4 ?    9.2   0.1    0.0013       1.1      25      41 ..     163     179 ..     154     180 .. 0.80
   5 ?   -2.8   0.0         8   6.8e+03      10      28 ..     190     208 ..     184     210 .. 0.67
   6 ?    1.1   0.2      0.47     4e+02       9      23 ..     223     237 ..     223     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.16
                            TPR_10 18 ydeAealleealai 31
                                      ++eA++ +++al++
  gi|330509106|ref|YP_004385534.1| 52 LTEALNAYDKALQM 65
                                      57999999999986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                            TPR_10  16 grydeAealleeala 30 
                                       ++ ++A+a++ + +a
  gi|330509106|ref|YP_004385534.1| 101 NNPQDALAWQARGVA 115
                                       678899998877665 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.062
                            TPR_10  19 deAealleealairrrl 35 
                                       +eA + +e+a++i+ + 
  gi|330509106|ref|YP_004385534.1| 123 QEATQSFEKAIEIYDQE 139
                                       7999*********9765 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0013
                            TPR_10  25 leealairrrllGpdHP 41 
                                       +eeal +++++ + dHP
  gi|330509106|ref|YP_004385534.1| 163 FEEALIAYEKVIELDHP 179
                                       78899999999888888 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 8
                            TPR_10  10 nalrqrgrydeAealleea 28 
                                        +l q gr++e+   l++a
  gi|330509106|ref|YP_004385534.1| 190 GILMQYGRLEESISALDKA 208
                                       5666668888877666665 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.47
                            TPR_10   9 analrqrgrydeAea 23 
                                       + al ++gr +e+ea
  gi|330509106|ref|YP_004385534.1| 223 GQALKEMGRNAESEA 237
                                       6799********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1062  (0.0592336); expected 358.6 (0.02)
Passed bias filter:                      724  (0.0403815); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.76u 0.37s 00:00:01.12 Elapsed: 00:00:00.60
# Mc/sec: 1247.35
//
Query:       gi|330509107|ref|YP_004385535.1|  [L=395]
Description: hypothetical protein MCON_3494 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-05   24.1   0.1    4.9e-05   23.1   0.1    1.5  1  MarR_2    MarR family
    0.00017   21.3   0.2    0.00036   20.3   0.2    1.6  1  HTH_IclR  IclR helix-turn-helix domain
     0.0049   16.7   0.0     0.0086   15.9   0.0    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.026   14.6   0.0      0.049   13.7   0.0    1.4  1  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d
        0.1   12.2   0.2       0.18   11.4   0.2    1.4  1  HTH_24    Winged helix-turn-helix DNA-binding
       0.34   10.9   0.0       0.34   10.9   0.0    1.8  2  CbiN      Cobalt transport protein component CbiN


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 !   23.1   0.1   1.6e-08   4.9e-05       2      54 ..     323     374 ..     322     379 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.6e-08
                                       T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       +lt  ++ ++ aL  ++gr  t++e+  ++gl++s+++ +l  L+++ L++++
  gi|330509107|ref|YP_004385535.1| 323 ALTHRERSIIEALIKHGGR-TTQAEIRYETGLPRSSLTMVLVSLERRNLITKK 374
                                       58999*************8.6*****************************976 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   1.2e-07   0.00036       7      50 ..     330     373 ..     320     375 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.2e-07
                                       HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       +i++al +++++ t +e+  +tglp+S+    L +L+++ ++++
  gi|330509107|ref|YP_004385535.1| 330 SIIEALIKHGGRTTQAEIRYETGLPRSSLTMVLVSLERRNLITK 373
                                       599************************************99876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.9e-06    0.0086       7      56 ..     325     375 ..     323     385 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.9e-06
                                       HHHCCCHCHHHHHHCCCHH.CHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB   7 seyEakvYlaLlklgpata.deiaeelgvprskvYevLrsLedkGlVerek 56 
                                       +  E ++  aL+k+g  t+  ei  e+g+prs+   vL sLe++ l+++++
  gi|330509107|ref|YP_004385535.1| 325 THRERSIIEALIKHGGRTTqAEIRYETGLPRSSLTMVLVSLERRNLITKKE 375
                                       6667777789998877665279*************************9987 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.6e-05     0.049      17      57 ..     330     371 ..     323     372 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHSSBEHH.HHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9  17 kVvetLlrkgrltlr.elvkktkLsldqVkksLvvLiqhrlV 57 
                                        ++e L+++g +t + e+  +t+L++++   +Lv+L +++l+
  gi|330509107|ref|YP_004385535.1| 330 SIIEALIKHGGRTTQaEIRYETGLPRSSLTMVLVSLERRNLI 371
                                       799******97776439**********************998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   5.9e-05      0.18       3      47 ..     326     371 ..     324     372 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.9e-05
                            HTH_24   3 etdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       + +r I+e+L k+++ ++q+e+  ++gl++s ++  l  Le+  lI
  gi|330509107|ref|YP_004385535.1| 326 HRERSIIEALIKHGGrTTQAEIRYETGLPRSSLTMVLVSLERRNLI 371
                                       6789********8877*************99988777777777766 PP

>> CbiN  Cobalt transport protein component CbiN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.34       6      30 ..      23      47 ..      22      51 .. 0.90
   2 ?   -3.6   0.5       3.7   1.1e+04       3      12 ..     207     216 ..     205     224 .. 0.43

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                              CbiN  6 llvvllavvplflvkgaeFgGaDdq 30
                                      l+v+ll++v+++l +g+eF G+D+q
  gi|330509107|ref|YP_004385535.1| 23 LIVALLLLVSIALTSGQEFDGTDEQ 47
                                      6899999999*************98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.7
                              CbiN   3 lllllvvlla 12 
                                       l+++++++++
  gi|330509107|ref|YP_004385535.1| 207 LMVAAFIFIL 216
                                       2333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2613.69
//
Query:       gi|330509108|ref|YP_004385536.1|  [L=355]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-38  126.5  20.2    2.3e-05   24.0   0.0    9.4  9  TPR_1            Tetratricopeptide repeat
    4.9e-34  113.7  19.9    0.00034   20.5   0.1    8.7  8  TPR_2            Tetratricopeptide repeat
    2.2e-28   98.6   8.7    1.6e-08   35.1   0.0    7.5  7  TPR_16           Tetratricopeptide repeat
    6.1e-28   94.7  16.3     0.0095   16.1   0.3    8.8  8  TPR_8            Tetratricopeptide repeat
      1e-26   92.3  25.9    7.9e-07   28.7   0.1    7.8  8  TPR_11           TPR repeat
    2.2e-26   90.3  18.1    0.00039   21.0   0.0    8.1  8  TPR_14           Tetratricopeptide repeat
    6.1e-25   85.8   5.8     0.0006   20.0   0.0    8.1  7  TPR_17           Tetratricopeptide repeat
    9.7e-19   67.7  17.9    5.3e-05   23.6   1.0    6.2  6  TPR_19           Tetratricopeptide repeat
    2.9e-17   62.7  18.6    9.5e-05   22.6   0.5    5.9  5  TPR_12           Tetratricopeptide repeat
    9.5e-16   57.7   4.9      0.028   14.6   0.1    6.0  6  TPR_9            Tetratricopeptide repeat
    1.6e-11   43.9   1.8     0.0068   15.4   0.0    4.9  5  NARP1            NMDA receptor-regulated protein 1
    4.3e-10   38.9  13.3      0.065   13.3   0.2    7.8  8  TPR_7            Tetratricopeptide repeat
    1.2e-08   34.9   7.5      0.014   15.5   0.1    5.6  6  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    8.2e-08   32.4  10.2    0.00099   19.2   0.2    4.7  4  DUF3856          Domain of Unknown Function (DUF3856)
    1.9e-07   31.2   2.2     0.0097   16.1   0.1    4.3  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    5.5e-07   29.5   6.5       0.01   15.6   0.2    4.3  5  TOM20_plant      Plant specific mitochondrial import receptor
    1.5e-06   28.5  11.4        3.2    8.6   0.0    7.2  8  TPR_6            Tetratricopeptide repeat
    3.7e-06   26.6  24.1       0.02   14.8   0.2    7.4  8  TPR_10           Tetratricopeptide repeat
    3.6e-05   24.2   3.4        1.3    9.5   0.0    4.6  5  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0001   22.3   0.2        1.2    9.1   0.0    3.3  3  DUF4919          Domain of unknown function (DUF4919)
    0.00025   21.5   4.9        1.1    9.7   0.1    3.9  4  BTAD             Bacterial transcriptional activator domain
    0.00056   19.4   1.8        1.4    8.2   0.0    3.3  3  Coatomer_E       Coatomer epsilon subunit
     0.0039   16.9  18.1       0.21   11.3   0.2    4.5  5  TPR_21           Tetratricopeptide repeat-like domain
     0.0053   16.8  12.9        1.3    9.1   0.2    6.2  7  MIT              MIT (microtubule interacting and transport) 
  ------ inclusion threshold ------
      0.013   15.0   2.6        2.3    7.9   0.0    4.8  6  HTH_Bact         Helix-turn-helix bacterial domain
      0.022   14.5   1.5         13    5.7   0.0    4.4  5  PPTA             Protein prenyltransferase alpha subunit repe
      0.038   14.3   0.1        8.8    6.7   0.0    2.9  3  preATP-grasp_3   pre ATP-grasp 3 domain
      0.039   14.0   0.0          3    7.9   0.0    3.7  4  DUF627           Protein of unknown function (DUF627)
      0.066   12.3   6.1        1.6    7.8   0.2    2.6  3  NRDE-2           NRDE-2, necessary for RNA interference
        0.1   11.8   4.1        1.5    8.0   0.9    3.5  2  FAT              FAT domain
       0.11   12.2   1.3       0.24   11.1   0.1    2.0  2  ADP_ribosyl_GH   ADP-ribosylglycohydrolase
       0.22   11.3   1.7         33    4.3   0.1    4.4  5  DUF5113          Domain of unknown function (DUF5113)
       0.27   10.9   4.8       0.49   10.1   0.5    3.0  3  DUF2225          Uncharacterized protein conserved in bacteri
       0.63   10.2   5.6         29    4.9   0.0    4.1  4  DUF2802          Protein of unknown function (DUF2802)
        4.5    7.4  11.9         11    6.1   0.1    4.9  4  TPR_3            Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   4.5e-08   2.3e-05       2      34 .]      39      71 ..      38      71 .. 0.96
   2 !   14.8   0.3   3.8e-05     0.019      17      34 .]     109     126 ..     108     126 .. 0.95
   3 !   13.7   0.1   8.1e-05     0.041      18      34 .]     151     167 ..     146     167 .. 0.89
   4 ?   -0.2   0.0         2     1e+03       1      11 [.     168     178 ..     168     186 .. 0.85
   5 !   17.0   0.2   7.5e-06    0.0038      15      33 ..     189     207 ..     183     208 .. 0.92
   6 ?    6.6   0.1     0.014       7.3       4      31 ..     212     239 ..     209     245 .. 0.76
   7 !   19.5   0.0   1.2e-06   0.00062       2      32 ..     254     284 ..     253     286 .. 0.91
   8 !   23.3   0.0   7.4e-08   3.8e-05      12      34 .]     299     321 ..     289     321 .. 0.92
   9 !   13.7   0.1   7.8e-05      0.04       3      30 ..     324     351 ..     322     351 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.5e-08
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                       a+  +G  + +++ y+eA +++++ALe +P+n
  gi|330509108|ref|YP_004385536.1| 39 VAWIKRGIELSSNESYEEATQAFDRALEQDPQN 71
                                      69*****************************97 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHHHHHHHHSTTH CS
                             TPR_1  17 ydeAleyyekALelnPnn 34 
                                       +d+A+e+ e+A+e+ P+n
  gi|330509108|ref|YP_004385536.1| 109 FDKAIEAHERAIEIAPEN 126
                                       8***************97 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 8.1e-05
                                       HHHHHHHHHHHHHSTTH CS
                             TPR_1  18 deAleyyekALelnPnn 34 
                                       +e l++++kALelnP++
  gi|330509108|ref|YP_004385536.1| 151 NESLQAFDKALELNPED 167
                                       789************86 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2
                                       HHHHHHHHHHH CS
                             TPR_1   1 akalynlGnay 11 
                                       a+a+ ++G a+
  gi|330509108|ref|YP_004385536.1| 168 ADAWHGKGIAL 178
                                       89******997 PP

  == domain 5  score: 17.0 bits;  conditional E-value: 7.5e-06
                                       T-HHHHHHHHHHHHHHSTT CS
                             TPR_1  15 gkydeAleyyekALelnPn 33 
                                        +y+eAl y ++ALe++P+
  gi|330509108|ref|YP_004385536.1| 189 SRYEEALRYIDRALEIDPQ 207
                                       58****************6 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALeln 31 
                                       l n++ ++ +lg+ +e  + y++ALel+
  gi|330509108|ref|YP_004385536.1| 212 LENKAGILSELGRQNESDKLYSEALELY 239
                                       5577778888888888888888888885 PP

  == domain 7  score: 19.5 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       +a+  +G +++ +gky++A+++   A   +P
  gi|330509108|ref|YP_004385536.1| 254 EAWLSKGFILQAQGKYEDAVKALGNATDADP 284
                                       8*********************999988888 PP

  == domain 8  score: 23.3 bits;  conditional E-value: 7.4e-08
                                       HHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  12 fklgkydeAleyyekALelnPnn 34 
                                       ++l++yd+A+ +++kAL++nP++
  gi|330509108|ref|YP_004385536.1| 299 RELKEYDDAVNAFDKALQINPKD 321
                                       789******************86 PP

  == domain 9  score: 13.7 bits;  conditional E-value: 7.8e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                       ++ n+G a+  lg+  eA e+y kA el
  gi|330509108|ref|YP_004385536.1| 324 TWMNKGDALKALGRQAEADEAYAKAREL 351
                                       8************************886 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.4e-06    0.0007       3      34 .]      40      71 ..      38      71 .. 0.95
   2 ?    6.7   0.2     0.017       8.7      17      34 .]     109     126 ..     107     126 .. 0.95
   3 !   11.7   0.1   0.00043      0.22      18      34 .]     151     167 ..     149     167 .. 0.91
   4 !   18.2   0.0   3.5e-06    0.0018       3      33 ..     177     207 ..     168     208 .. 0.90
   5 !   10.5   0.1    0.0011      0.55       3      33 ..     211     241 ..     209     242 .. 0.90
   6 !   17.6   0.0   5.6e-06    0.0029       2      32 ..     254     284 ..     253     286 .. 0.93
   7 !   20.5   0.1   6.6e-07   0.00034      11      34 .]     298     321 ..     296     321 .. 0.92
   8 !   16.2   0.2   1.6e-05    0.0081       2      30 ..     323     351 ..     322     352 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-06
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                                      a+  +G  +  +  yeeA +af++Ale dP+n
  gi|330509108|ref|YP_004385536.1| 40 AWIKRGIELSSNESYEEATQAFDRALEQDPQN 71
                                      89****************************97 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.017
                             TPR_2  17 yeeAleafekAleldPnn 34 
                                       +++A+ea e+A+e++P+n
  gi|330509108|ref|YP_004385536.1| 109 FDKAIEAHERAIEIAPEN 126
                                       79**************97 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00043
                             TPR_2  18 eeAleafekAleldPnn 34 
                                       +e l+af+kAlel+P++
  gi|330509108|ref|YP_004385536.1| 151 NESLQAFDKALELNPED 167
                                       699************86 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 3.5e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       al ++ +  +   +yeeAl++ ++Ale+dP+
  gi|330509108|ref|YP_004385536.1| 177 ALVYISQTREDTSRYEEALRYIDRALEIDPQ 207
                                       6777788888889*****************7 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.0011
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       al n + ++ +lg+ +e  +++ +Alel+ +
  gi|330509108|ref|YP_004385536.1| 211 ALENKAGILSELGRQNESDKLYSEALELYNT 241
                                       78899999********************975 PP

  == domain 6  score: 17.6 bits;  conditional E-value: 5.6e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       ea+   G ++ ++g+ye+A++a+  A   dP
  gi|330509108|ref|YP_004385536.1| 254 EAWLSKGFILQAQGKYEDAVKALGNATDADP 284
                                       89************************99998 PP

  == domain 7  score: 20.5 bits;  conditional E-value: 6.6e-07
                             TPR_2  11 yyklgdyeeAleafekAleldPnn 34 
                                       +++l++y++A++af+kAl+++P++
  gi|330509108|ref|YP_004385536.1| 298 WRELKEYDDAVNAFDKALQINPKD 321
                                       6799******************86 PP

  == domain 8  score: 16.2 bits;  conditional E-value: 1.6e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAlel 30 
                                         ++n G+a+ +lg+ +eA ea+ kA el
  gi|330509108|ref|YP_004385536.1| 323 LTWMNKGDALKALGRQAEADEAYAKAREL 351
                                       579***********************987 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   0.00014      0.07       4      48 ..      45      86 ..      42      88 .. 0.86
   2 ?    7.4   0.0     0.013       6.7      13      57 ..     109     150 ..     106     155 .. 0.88
   3 !    8.4   0.0    0.0066       3.4      15      44 ..     152     178 ..     150     179 .. 0.88
   4 !   16.4   0.1   2.1e-05     0.011       9      49 ..     187     224 ..     183     228 .. 0.93
   5 !    8.6   0.0    0.0058         3      13      43 ..     232     262 ..     227     264 .. 0.93
   6 !   35.1   0.0   3.1e-11   1.6e-08       7      68 .]     263     322 ..     260     322 .. 0.95
   7 !   23.5   1.1   1.3e-07   6.4e-05       9      61 ..     300     349 ..     299     353 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00014
                            TPR_16  4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqg 48
                                      + ++  +  y++A  a+++al++d   P++  A+l++  a+  +g
  gi|330509108|ref|YP_004385536.1| 45 GIELSSNESYEEATQAFDRALEQD---PQNLNAWLFKSMALTSLG 86
                                      566667788***************...*********999988776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.013
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaaly 57 
                                       +d+A++a e+a++ +   P++a  + ++++ +++ g +++ +  +
  gi|330509108|ref|YP_004385536.1| 109 FDKAIEAHERAIEIA---PENATVWTYKANNLAKIGSFTDNLSIL 150
                                       799************...****************99999887444 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0066
                            TPR_16  15 dAaaaleaalkrdpssPdaaeAllllgdaa 44 
                                       + + a++ al+++   P++a+A+ ++g a+
  gi|330509108|ref|YP_004385536.1| 152 ESLQAFDKALELN---PEDADAWHGKGIAL 178
                                       6789*********...*******9988775 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 2.1e-05
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgr 49 
                                       +  +y++A+++ ++al+ d   P++a Al +++ ++ ++gr
  gi|330509108|ref|YP_004385536.1| 187 DTSRYEEALRYIDRALEID---PQTAGALENKAGILSELGR 224
                                       5679***************...****************998 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0058
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgda 43 
                                       y +A++++++ ++  +s+ d +eA+l +g +
  gi|330509108|ref|YP_004385536.1| 232 YSEALELYNTSIETEKSTEDLVEAWLSKGFI 262
                                       89************************99987 PP

  == domain 6  score: 35.1 bits;  conditional E-value: 3.1e-11
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaal.rqgrlaeAaalyraalraapdap 68 
                                       + ++g+y+dA++al  a+++d   P +  A+  +g++++ +++++++A+ ++++al+  p++p
  gi|330509108|ref|YP_004385536.1| 263 LQAQGKYEDAVKALGNATDAD---PMNGLAWKVKGVLLWrELKEYDDAVNAFDKALQINPKDP 322
                                       789******************...***************666*******999999*****998 PP

  == domain 7  score: 23.5 bits;  conditional E-value: 1.3e-07
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       ++++yddA++a++ al  +   P ++  ++++gda+ ++gr aeA ++y++a 
  gi|330509108|ref|YP_004385536.1| 300 ELKEYDDAVNAFDKALQIN---PKDPLTWMNKGDALKALGRQAEADEAYAKAR 349
                                       5789***************...66666******************98888875 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00025      0.13       3      34 .]      40      71 ..      39      71 .. 0.93
   2 ?    7.2   0.0     0.013       6.7      17      34 .]     109     126 ..     104     126 .. 0.92
   3 !    8.1   0.0    0.0067       3.4      17      34 .]     150     167 ..     134     167 .. 0.80
   4 !   13.2   0.0   0.00016     0.082       8      33 ..     182     207 ..     177     208 .. 0.88
   5 !   11.7   0.2   0.00047      0.24       3      31 ..     211     239 ..     209     242 .. 0.90
   6 !   14.2   0.0   7.3e-05     0.037       2      32 ..     254     284 ..     253     286 .. 0.95
   7 !   15.4   0.0   3.1e-05     0.016       8      34 .]     294     321 ..     289     321 .. 0.87
   8 !   16.1   0.3   1.9e-05    0.0095       4      27 ..     325     348 ..     323     351 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00025
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      a+ + g  +++ + yeeA +++ +ale dp+n
  gi|330509108|ref|YP_004385536.1| 40 AWIKRGIELSSNESYEEATQAFDRALEQDPQN 71
                                      7889999999********************96 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHHHH. CS
                             TPR_8  17 yeeAkeyyekaleldpdn 34 
                                       +++A+e+ e+a+e++p+n
  gi|330509108|ref|YP_004385536.1| 109 FDKAIEAHERAIEIAPEN 126
                                       79**************86 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0067
                                       HHHHHHHHHHHHHHHHH. CS
                             TPR_8  17 yeeAkeyyekaleldpdn 34 
                                       ++e+ +++ kalel+p++
  gi|330509108|ref|YP_004385536.1| 150 LNESLQAFDKALELNPED 167
                                       68999***********86 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.00016
                                       HHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyyekaleldpd 33 
                                       +++ +++ +yeeA  y+ +ale+dp+
  gi|330509108|ref|YP_004385536.1| 182 SQTREDTSRYEEALRYIDRALEIDPQ 207
                                       67778889*****************8 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.00047
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a+ n++ i+++lg+ +e+ + y +alel 
  gi|330509108|ref|YP_004385536.1| 211 ALENKAGILSELGRQNESDKLYSEALELY 239
                                       78899**********************97 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 7.3e-05
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ea++ +g i++ +g+ye A++++  a+++dp
  gi|330509108|ref|YP_004385536.1| 254 EAWLSKGFILQAQGKYEDAVKALGNATDADP 284
                                       89**********************9999998 PP

  == domain 7  score: 15.4 bits;  conditional E-value: 3.1e-05
                                       HHHH.HHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   8 gsiy.lklgdyeeAkeyyekaleldpdn 34 
                                       g ++ ++l++y+ A+ ++ kal+++p++
  gi|330509108|ref|YP_004385536.1| 294 GVLLwRELKEYDDAVNAFDKALQINPKD 321
                                       5566679*******************96 PP

  == domain 8  score: 16.1 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyeka 27 
                                       ++n+g++++ lg+  eA e+y ka
  gi|330509108|ref|YP_004385536.1| 325 WMNKGDALKALGRQAEADEAYAKA 348
                                       9*********************98 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   3.1e-05     0.016       8      31 ..      52      75 ..      47      76 .. 0.90
   2 !   13.3   0.2   9.5e-05     0.048      10      35 ..     109     134 ..     108     141 .. 0.84
   3 !   20.8   0.0   4.4e-07   0.00022      10      38 ..     150     178 ..     150     179 .. 0.94
   4 !   10.0   0.2    0.0011      0.55       9      35 ..     190     216 ..     187     223 .. 0.84
   5 ?    6.2   0.1     0.016         8      10      42 .]     232     267 ..     216     267 .. 0.71
   6 !   15.2   0.1   2.6e-05     0.013       6      28 ..     265     287 ..     260     299 .. 0.85
   7 !   28.7   0.1   1.5e-09   7.9e-07       5      42 .]     299     336 ..     296     336 .. 0.95
   8 ?    5.2   0.3     0.033        17       1      21 [.     329     349 ..     329     351 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                            TPR_11  8 GkyeeAieaYkkAlkldPdnaeay 31
                                        yeeA +a+ +Al+ dP+n +a+
  gi|330509108|ref|YP_004385536.1| 52 ESYEEATQAFDRALEQDPQNLNAW 75
                                      68******************9997 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 9.5e-05
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLG 35 
                                       +++Aiea ++A+++ P+na+++   +
  gi|330509108|ref|YP_004385536.1| 109 FDKAIEAHERAIEIAPENATVWTYKA 134
                                       79******************997655 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 4.4e-07
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       ++e+++a+ kAl+l+P++a+a+++ G a+
  gi|330509108|ref|YP_004385536.1| 150 LNESLQAFDKALELNPEDADAWHGKGIAL 178
                                       689*********************99986 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0011
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLG 35 
                                       +yeeA+    +Al++dP+ a a+ n +
  gi|330509108|ref|YP_004385536.1| 190 RYEEALRYIDRALEIDPQTAGALENKA 216
                                       89******************9998866 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.016
                            TPR_11  10 yeeAieaYkkAlkl...dPdnaeayynLGlayykqG 42 
                                       y eA+e Y++ ++    ++d +ea++  G+++++qG
  gi|330509108|ref|YP_004385536.1| 232 YSEALELYNTSIETeksTEDLVEAWLSKGFILQAQG 267
                                       678888888887652224567777777777777776 PP

  == domain 6  score: 15.2 bits;  conditional E-value: 2.6e-05
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdna 28 
                                       +qGkye+A++a+ +A + dP n 
  gi|330509108|ref|YP_004385536.1| 265 AQGKYEDAVKALGNATDADPMNG 287
                                       8*******************995 PP

  == domain 7  score: 28.7 bits;  conditional E-value: 1.5e-09
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +e+ +y++A++a+ kAl+++P+++  + n G+a+ ++G
  gi|330509108|ref|YP_004385536.1| 299 RELKEYDDAVNAFDKALQINPKDPLTWMNKGDALKALG 336
                                       6789******************************9998 PP

  == domain 8  score: 5.2 bits;  conditional E-value: 0.033
                            TPR_11   1 GdayyeqGkyeeAieaYkkAl 21 
                                       Gda+ ++G+  eA eaY kA 
  gi|330509108|ref|YP_004385536.1| 329 GDALKALGRQAEADEAYAKAR 349
                                       9****************9995 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     9e-07   0.00046       2      40 ..      39      77 ..      38      80 .. 0.93
   2 !   16.6   0.0     2e-05      0.01      17      42 ..     109     134 ..     101     135 .. 0.90
   3 !   11.2   0.1    0.0011      0.55      19      40 ..     152     173 ..     150     177 .. 0.88
   4 !   12.5   0.1   0.00041      0.21      11      41 ..     185     215 ..     175     218 .. 0.82
   5 ?    3.4   0.0      0.35   1.8e+02       6      36 ..     221     251 ..     216     258 .. 0.68
   6 !   11.5   0.0   0.00083      0.42       1      41 [.     253     293 ..     253     296 .. 0.88
   7 !   21.0   0.0   7.7e-07   0.00039       8      42 ..     294     329 ..     287     331 .. 0.82
   8 ?    1.7   1.1       1.2   6.2e+02       9      29 ..     330     350 ..     328     352 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 9e-07
                            TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeawll 40
                                       a+ +++  l  ++ ++eA ++++ral+++P+++ awl+
  gi|330509108|ref|YP_004385536.1| 39 VAWIKRGIELSSNESYEEATQAFDRALEQDPQNLNAWLF 77
                                      589999*******************************86 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2e-05
                            TPR_14  17 pdeAiallrralalaPddaeawllla 42 
                                       +d+Ai++ +ra++ aP++a++w++ a
  gi|330509108|ref|YP_004385536.1| 109 FDKAIEAHERAIEIAPENATVWTYKA 134
                                       9*********************9987 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0011
                            TPR_14  19 eAiallrralalaPddaeawll 40 
                                       e+++++++al+l+P+da+aw  
  gi|330509108|ref|YP_004385536.1| 152 ESLQAFDKALELNPEDADAWHG 173
                                       6899****************76 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00041
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawlll 41 
                                        +   +++eA+++ +ral+ +P+ a a+   
  gi|330509108|ref|YP_004385536.1| 185 REDTSRYEEALRYIDRALEIDPQTAGALENK 215
                                       5666799****************99998765 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.35
                            TPR_14   6 alaeallalGdpdeAiallrralalaPddae 36 
                                       +l++  +    + eA++l++  +++  + ++
  gi|330509108|ref|YP_004385536.1| 221 ELGRQNESDKLYSEALELYNTSIETEKSTED 251
                                       5677777777789999999999998764433 PP

  == domain 6  score: 11.5 bits;  conditional E-value: 0.00083
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       +ea+l  + +l a+G++++A+++l  a +++P +  aw   
  gi|330509108|ref|YP_004385536.1| 253 VEAWLSKGFILQAQGKYEDAVKALGNATDADPMNGLAWKVK 293
                                       589***************************99777777665 PP

  == domain 7  score: 21.0 bits;  conditional E-value: 7.7e-07
                            TPR_14   8 aealla.lGdpdeAiallrralalaPddaeawllla 42 
                                       + +l++ l ++d+A++++++al+ +P+d+ +w+  +
  gi|330509108|ref|YP_004385536.1| 294 GVLLWReLKEYDDAVNAFDKALQINPKDPLTWMNKG 329
                                       55666438************************9876 PP

  == domain 8  score: 1.7 bits;  conditional E-value: 1.2
                            TPR_14   9 eallalGdpdeAiallrrala 29 
                                       +al alG+ +eA +++ +a +
  gi|330509108|ref|YP_004385536.1| 330 DALKALGRQAEADEAYAKARE 350
                                       566666666666666666544 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0079         4       2      16 ..      61      75 ..      60      96 .. 0.88
   2 !   16.8   0.0   1.2e-05    0.0063       2      27 ..     116     141 ..     115     145 .. 0.91
   3 !   17.8   0.0     6e-06    0.0031       2      24 ..     157     179 ..     156     195 .. 0.84
   4 ?    6.8   0.0     0.019       9.8       3      30 ..     199     226 ..     197     230 .. 0.89
   5 !    9.1   0.0    0.0036       1.8       2      33 ..     239     273 ..     231     274 .. 0.75
   6 ?    1.6   0.0       0.9   4.6e+02       9      21 ..     278     290 ..     275     308 .. 0.73
   7 !   20.0   0.0   1.2e-06    0.0006       2      32 ..     311     341 ..     310     343 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0079
                            TPR_17  2 ylkaleldPnnaday 16
                                      + +ale+dP n +a+
  gi|330509108|ref|YP_004385536.1| 61 FDRALEQDPQNLNAW 75
                                      89*********8888 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.2e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknG 27 
                                        ++a+e+ P na +++++A+ l+k+G
  gi|330509108|ref|YP_004385536.1| 116 HERAIEIAPENATVWTYKANNLAKIG 141
                                       69******************999988 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 6e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelll 24 
                                       + kalel+P +ada++ ++ +l 
  gi|330509108|ref|YP_004385536.1| 157 FDKALELNPEDADAWHGKGIALV 179
                                       89****************99986 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.019
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlm 30 
                                        +ale+dP  a a+ n+A +l+++G+  
  gi|330509108|ref|YP_004385536.1| 199 DRALEIDPQTAGALENKAGILSELGRQN 226
                                       79********************999765 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.0036
                            TPR_17   2 ylkaleld...PnnadaynnLAelllknGdlmtAr 33 
                                       y  ++e +    + ++a+  ++ +l  +G++++A+
  gi|330509108|ref|YP_004385536.1| 239 YNTSIETEkstEDLVEAWLSKGFILQAQGKYEDAV 273
                                       455555533224459******************97 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 0.9
                            TPR_17   9 dPnnadaynnLAe 21 
                                       + ++ad++n LA+
  gi|330509108|ref|YP_004385536.1| 278 NATDADPMNGLAW 290
                                       6677888887776 PP

  == domain 7  score: 20.0 bits;  conditional E-value: 1.2e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       + kal+++P+++  + n++ +l+ +G+ ++A
  gi|330509108|ref|YP_004385536.1| 311 FDKALQINPKDPLTWMNKGDALKALGRQAEA 341
                                       89*************************9998 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   5.2e-05     0.027       4      30 ..      51      77 ..      48      86 .. 0.85
   2 !    9.3   0.0     0.003       1.6       6      49 ..     108     151 ..     103     156 .. 0.86
   3 ?    7.2   0.1     0.014       7.1      11      35 ..     154     178 ..     150     187 .. 0.78
   4 !   11.7   0.4   0.00056      0.29       6      53 ..     190     237 ..     185     245 .. 0.88
   5 !    9.6   0.1    0.0025       1.3       3      28 ..     265     290 ..     263     300 .. 0.87
   6 !   23.6   1.0     1e-07   5.3e-05       5      53 ..     302     350 ..     298     354 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.2e-05
                            TPR_19  4 egdyaeAlalleqalqedpknaearll 30
                                      ++ y+eA +++ +al++dp+n++a+l 
  gi|330509108|ref|YP_004385536.1| 51 NESYEEATQAFDRALEQDPQNLNAWLF 77
                                      678*********************995 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.003
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLd 49 
                                        ++ A+++ e+a++ +p+na ++ + A+ l + g +++   +L+
  gi|330509108|ref|YP_004385536.1| 108 AFDKAIEAHERAIEIAPENATVWTYKANNLAKIGSFTDNLSILN 151
                                       6899********************99*99999999887666665 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.014
                            TPR_19  11 lalleqalqedpknaearllLAeal 35 
                                       l+++ +al+ +p++a+a+ +  +al
  gi|330509108|ref|YP_004385536.1| 154 LQAFDKALELNPEDADAWHGKGIAL 178
                                       899**************98664444 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00056
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       +y+eAl++  +al+ dp+ a a+ + A +l +lg+ +e  +l ++++e
  gi|330509108|ref|YP_004385536.1| 190 RYEEALRYIDRALEIDPQTAGALENKAGILSELGRQNESDKLYSEALE 237
                                       79********************************98887777766665 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.0025
                            TPR_19   3 aegdyaeAlalleqalqedpknaear 28 
                                       a+g+y++A+++l +a ++dp n+ a+
  gi|330509108|ref|YP_004385536.1| 265 AQGKYEDAVKALGNATDADPMNGLAW 290
                                       89*****************9888776 PP

  == domain 6  score: 23.6 bits;  conditional E-value: 1e-07
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       + y++A++++ +alq +pk++  +++  +al alg+ +eA ++ +++ e
  gi|330509108|ref|YP_004385536.1| 302 KEYDDAVNAFDKALQINPKDPLTWMNKGDALKALGRQAEADEAYAKARE 350
                                       68**************************************999888765 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.047        24      17      33 ..      52      68 ..      27      87 .. 0.63
   2 ?    7.2   0.1     0.012       6.3      19      47 ..     109     131 ..     105     143 .. 0.70
   3 !   19.0   0.4   2.5e-06    0.0013      20      76 ..     151     206 ..     134     207 .. 0.94
   4 !   22.6   0.5   1.9e-07   9.5e-05       1      69 [.     207     277 ..     207     284 .. 0.88
   5 !   18.3   0.5   4.3e-06    0.0022      10      74 ..     294     351 ..     288     353 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.047
                            TPR_12 17 grydeAlellekaleia 33
                                      + y+eA + +++ale+ 
  gi|330509108|ref|YP_004385536.1| 52 ESYEEATQAFDRALEQD 68
                                      44666666666666655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                            TPR_12  19 ydeAlellekaleiarrllGpdhpltatt 47 
                                       +d+A+e +e+a+eia     p++ +t++t
  gi|330509108|ref|YP_004385536.1| 109 FDKAIEAHERAIEIA-----PEN-ATVWT 131
                                       688888888888888.....444.44444 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 2.5e-06
                            TPR_12  20 deAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        e+l+ ++kale+  + +  + +++  ++l  ++++ + + ryeeAl++  +al+i++
  gi|330509108|ref|YP_004385536.1| 151 NESLQAFDKALELNpEDA--DAWHGKGIALVYISQTREDTSRYEEALRYIDRALEIDP 206
                                       699***********7777..99*********************************986 PP

  == domain 4  score: 22.6 bits;  conditional E-value: 1.9e-07
                            TPR_12   1 dvatalnnlaavlrrlgrydeAlellekaleia.rrl.lGpdhpltattlrnLgrlyralgryeeAlelle 69 
                                       ++a al n a +l +lgr  e+ +l+ +ale++ +++  ++  ++++++    g +++a+g+ye+A+++l 
  gi|330509108|ref|YP_004385536.1| 207 QTAGALENKAGILSELGRQNESDKLYSEALELYnTSIeTEKSTEDLVEAWLSKGFILQAQGKYEDAVKALG 277
                                       5788999**************************7777555555***********************99875 PP

  == domain 5  score: 18.3 bits;  conditional E-value: 4.3e-06
                            TPR_12  10 aavl.rrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +++l r+l++yd+A   ++kal+i      p+ pl   t  n g+++ algr++eA e++ +a ++
  gi|330509108|ref|YP_004385536.1| 294 GVLLwRELKEYDDAVNAFDKALQIN-----PKDPL---TWMNKGDALKALGRQAEADEAYAKAREL 351
                                       6677355******************.....*9999...6************************986 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00094      0.48      27      65 ..      36      74 ..      20      81 .. 0.87
   2 ?    5.9   0.0     0.028        14      11      65 ..     109     170 ..     106     170 .. 0.75
   3 ?    4.1   0.0       0.1        53      15      39 ..     154     178 ..     150     186 .. 0.73
   4 !   14.6   0.1   5.4e-05     0.028       9      44 ..     189     224 ..     181     238 .. 0.91
   5 !    9.6   0.0    0.0019      0.99      28      62 ..     252     286 ..     230     296 .. 0.87
   6 !   12.1   0.0   0.00033      0.17       9      50 ..     302     343 ..     293     351 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00094
                             TPR_9 27 ddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                                      ++p  +  RG+ l   + +++A ++++++l+++p++  a
  gi|330509108|ref|YP_004385536.1| 36 NTPVAWIKRGIELSSNESYEEATQAFDRALEQDPQNLNA 74
                                      67889999**************************98666 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.028
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGcl.......saAladLeaylalapdapda 65 
                                       +++a+++ er + +aP+ +  +   +  la+ G +       ++ l++++ +l+l+p+++da
  gi|330509108|ref|YP_004385536.1| 109 FDKAIEAHERAIEIAPENATVWTYKANNLAKIGSFtdnlsilNESLQAFDKALELNPEDADA 170
                                       78999999999999999999998888888888876222222256777778888888888876 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.1
                             TPR_9  15 lavverllllaPddpeerrdRGlll 39 
                                       l++ +  l l+P+d++ +   G++l
  gi|330509108|ref|YP_004385536.1| 154 LQAFDKALELNPEDADAWHGKGIAL 178
                                       5666777788888888887777766 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 5.4e-05
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGc 44 
                                        ++e+al++++r l ++P++++ +   + +l +lG+
  gi|330509108|ref|YP_004385536.1| 189 SRYEEALRYIDRALEIDPQTAGALENKAGILSELGR 224
                                       689**********************99999999997 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.0019
                             TPR_9  28 dpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                        +e ++  G++l+ +G ++ A+++L  + + +p +
  gi|330509108|ref|YP_004385536.1| 252 LVEAWLSKGFILQAQGKYEDAVKALGNATDADPMN 286
                                       5789***********************99999965 PP

  == domain 6  score: 12.1 bits;  conditional E-value: 0.00033
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAla 50 
                                       ++++ a  + +  l+++P+dp  ++  G +l  lG+ ++A +
  gi|330509108|ref|YP_004385536.1| 302 KEYDDAVNAFDKALQINPKDPLTWMNKGDALKALGRQAEADE 343
                                       678999*****************************9988866 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.19     1e+02     206     236 ..      52      82 ..      46      95 .. 0.86
   2 ?    4.2   0.1     0.032        16     206     252 ..     107     153 ..      99     160 .. 0.86
   3 !   15.4   0.0   1.3e-05    0.0068     195     254 ..     178     237 ..     166     240 .. 0.89
   4 !    7.0   0.0    0.0046       2.4     208     256 ..     232     283 ..     226     286 .. 0.83
   5 !   12.1   0.0   0.00013     0.065     204     255 ..     300     351 ..     295     354 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.19
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHH CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKaril 236
                                       +s+e+A++  d+a+e++p+ ++ +l K+  l
  gi|330509108|ref|YP_004385536.1|  52 ESYEEATQAFDRALEQDPQNLNAWLFKSMAL 82 
                                       6899*******************99998766 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.032
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                          +kA+e  ++aie  p+   +++ Ka+ l + G +++  ++++e+
  gi|330509108|ref|YP_004385536.1| 107 TAFDKAIEAHERAIEIAPENATVWTYKANNLAKIGSFTDNLSILNES 153
                                       5578********************************99999999886 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1 195 lyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeeark 254
                                       l +++q  + + ++e+Al+yid+a+e +p+      +Ka il   G  ++  ++  ea +
  gi|330509108|ref|YP_004385536.1| 178 LVYISQTREDTSRYEEALRYIDRALEIDPQTAGALENKAGILSELGRQNESDKLYSEALE 237
                                       679999999999999**************************9999999998888887765 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0046
                                       SHHHHHHHHHHHH...H-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 208 rekAleyidkaie...htptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       +++Ale+ ++ ie   +t  lve +l K+ il+ +G  ++A++++ +a   D
  gi|330509108|ref|YP_004385536.1| 232 YSEALELYNTSIEtekSTEDLVEAWLSKGFILQAQGKYEDAVKALGNATDAD 283
                                       568899999999722246889**********************999987766 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 0.00013
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                       +l++++ A++  dka++ +p+    +++K+  lk  G   +A e+  +ar+l
  gi|330509108|ref|YP_004385536.1| 300 ELKEYDDAVNAFDKALQINPKDPLTWMNKGDALKALGRQAEADEAYAKAREL 351
                                       67899*********************************************98 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       1.3   6.6e+02      15      34 ..      54      71 ..      51      73 .. 0.88
   2 ?    6.6   0.0     0.018       9.1      15      34 ..     109     126 ..     106     128 .. 0.78
   3 ?   -1.8   0.0       8.2   4.2e+03      11      21 ..     153     163 ..     146     167 .. 0.76
   4 !   13.3   0.2   0.00013     0.065       1      30 [.     177     206 ..     177     212 .. 0.86
   5 ?    4.2   0.1     0.098        50       2      28 ..     212     238 ..     211     252 .. 0.61
   6 ?    5.5   0.0      0.04        21       8      31 ..     262     283 ..     255     284 .. 0.81
   7 ?    7.1   0.0     0.012         6       8      28 ..     297     317 ..     294     323 .. 0.83
   8 ?    2.7   0.1      0.32   1.6e+02       2      24 ..     325     347 ..     324     352 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.3
                             TPR_7 15 yeeAielyeqsLaltkdped 34
                                      yeeA + + +  al+ dp++
  gi|330509108|ref|YP_004385536.1| 54 YEEATQAFDR--ALEQDPQN 71
                                      8999999***..99999976 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.018
                             TPR_7  15 yeeAielyeqsLaltkdped 34 
                                       +++Aie +e+  a++ +pe+
  gi|330509108|ref|YP_004385536.1| 109 FDKAIEAHER--AIEIAPEN 126
                                       89********..66655555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 8.2
                             TPR_7  11 rlGdyeeAiel 21 
                                       +l+ +++A+el
  gi|330509108|ref|YP_004385536.1| 153 SLQAFDKALEL 163
                                       56678888886 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00013
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       aL+++ +++++  +yeeA+++  ++L+++ 
  gi|330509108|ref|YP_004385536.1| 177 ALVYISQTREDTSRYEEALRYIDRALEIDP 206
                                       789999******************777765 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.098
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLal 28 
                                       L n a + s+lG+  e  +ly ++L+l
  gi|330509108|ref|YP_004385536.1| 212 LENKAGILSELGRQNESDKLYSEALEL 238
                                       556666677777776666666665555 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.04
                             TPR_7   8 lysrlGdyeeAielyeqsLaltkd 31 
                                       + +++G+ye+A++ +    a++ d
  gi|330509108|ref|YP_004385536.1| 262 ILQAQGKYEDAVKALGN--ATDAD 283
                                       6799********98887..77666 PP

  == domain 7  score: 7.1 bits;  conditional E-value: 0.012
                             TPR_7   8 lysrlGdyeeAielyeqsLal 28 
                                       l+++l +y++A+  + ++L++
  gi|330509108|ref|YP_004385536.1| 297 LWRELKEYDDAVNAFDKALQI 317
                                       6999*************8866 PP

  == domain 8  score: 2.7 bits;  conditional E-value: 0.32
                             TPR_7   2 LlnLarlysrlGdyeeAielyeq 24 
                                       + n +++  +lG+ +eA e y +
  gi|330509108|ref|YP_004385536.1| 325 WMNKGDALKALGRQAEADEAYAK 347
                                       678899*************9988 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1    0.0012       0.6      16      37 ..      53      74 ..      51      81 .. 0.88
   2 ?   -0.3   0.0       2.2   1.1e+03      16      34 ..     108     126 ..     105     129 .. 0.86
   3 ?   -0.1   0.0         2     1e+03      18      36 ..     151     169 ..     147     171 .. 0.86
   4 !   15.5   0.1   2.6e-05     0.014      16      35 ..     190     209 ..     188     216 .. 0.87
   5 ?   -1.6   0.1         6   3.1e+03      17      31 ..     232     246 ..     230     251 .. 0.83
   6 ?    6.8   0.0     0.014       7.1      14      33 ..     301     320 ..     300     322 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                                      -HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C 16 eYseArryvdalLeiEPenrQa 37
                                       Y+eA +  d+ Le +P+n +a
  gi|330509108|ref|YP_004385536.1| 53 SYEEATQAFDRALEQDPQNLNA 74
                                      6******************998 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.2
                                       -HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPen 34 
                                        +++A +  ++ +ei Pen
  gi|330509108|ref|YP_004385536.1| 108 AFDKAIEAHERAIEIAPEN 126
                                       588999999*********9 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C  18 seArryvdalLeiEPenrQ 36 
                                       +e+++  d  Le+ Pe   
  gi|330509108|ref|YP_004385536.1| 151 NESLQAFDKALELNPEDAD 169
                                       789999*********9765 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 2.6e-05
                                       -HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPenr 35 
                                       +Y+eA+ry+d+ Lei+P+  
  gi|330509108|ref|YP_004385536.1| 190 RYEEALRYIDRALEIDPQTA 209
                                       7****************865 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 6
                                       HHHHHHHHHHHHHHT CS
                        Fis1_TPR_C  17 YseArryvdalLeiE 31 
                                       YseA+++ ++ +e E
  gi|330509108|ref|YP_004385536.1| 232 YSEALELYNTSIETE 246
                                       999999999888877 PP

  == domain 6  score: 6.8 bits;  conditional E-value: 0.014
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       l+eY++A +  d  L+i P+
  gi|330509108|ref|YP_004385536.1| 301 LKEYDDAVNAFDKALQINPK 320
                                       89****************97 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.9   9.6e+02     107     128 ..      45      66 ..      33      71 .. 0.62
   2 !   19.2   0.2   1.9e-06   0.00099      40     140 ..     111     215 ..      80     218 .. 0.83
   3 !    9.1   0.1    0.0025       1.3      62     127 ..     216     280 ..     211     287 .. 0.87
   4 ?    7.0   0.3     0.011       5.7      94     129 ..     320     351 ..     277     353 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.9
                                       HHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 107 avaleelGrkdealkafrmage 128
                                       +  l++  +++ea +af  a e
  gi|330509108|ref|YP_004385536.1|  45 GIELSSNESYEEATQAFDRALE 66 
                                       5555555555555555555443 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.9e-06
                                       TTS-.TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHH....HHHHHHHHHHHH CS
                           DUF3856  40 rtip.aeeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklW....iaavfsravale 111
                                       ++i  +e a + +  +a +++  ++ lak+g++ + l+  +++l+ f++  el+ ++   W    ia v   +++ e
  gi|330509108|ref|YP_004385536.1| 111 KAIEaHERAIEIAPENATVWTYKANNLAKIGSFTDNLSILNESLQAFDKALELNPEDADAWhgkgIALV-YISQTRE 186
                                       455414567888888999*******************************************65555555.567889* PP

                                       HTT-HHHHHHHHHHHHHHHHH--S--TTH CS
                           DUF3856 112 elGrkdealkafrmagemiaerkGelkgk 140
                                       ++ r++eal++   a e+  +  G l++k
  gi|330509108|ref|YP_004385536.1| 187 DTSRYEEALRYIDRALEIDPQTAGALENK 215
                                       ****************9988888888776 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0025
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  62 sealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       ++ l +lgr +e+ +   +al+ +n   e e+      + a +s++  l+  G++++a+ka+  a+
  gi|330509108|ref|YP_004385536.1| 216 AGILSELGRQNESDKLYSEALELYNTSIETEKSTE-DLVEAWLSKGFILQAQGKYEDAVKALGNAT 280
                                       5678899*******************999887765.568999******************987765 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.011
                                       THHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  94 deGklWiaavfsravaleelGrkdealkafrmagem 129
                                        +   W    ++++ al+ lGr++ea +a+ +a e+
  gi|330509108|ref|YP_004385536.1| 320 KDPLTW----MNKGDALKALGRQAEADEAYAKAREL 351
                                       444455....589*****************999985 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 ?    4.3   0.0     0.091        47       2      32 ..      51      81 ..      48      88 .. 0.54
   2 ?   -1.6   0.0       6.6   3.4e+03      39      74 ..     109     145 ..     107     153 .. 0.54
   3 !    7.6   0.0    0.0089       4.6      12      74 ..     157     227 ..     144     235 .. 0.77
   4 !   13.1   0.1   0.00016     0.083       2      81 ..     188     278 ..     187     279 .. 0.75
   5 !   16.1   0.1   1.9e-05    0.0097       4      81 ..     231     313 ..     228     314 .. 0.79
   6 ?    4.5   0.0      0.08        41      36      75 ..     301     341 ..     296     348 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.091
                                      TT-HHHHHHHHHHHH.HHH--HHHHHHHHHH CS
                            ANAPC3  2 qnnyknAiflaerllaaetespedayllAlc 32
                                      ++ y++A   ++r+l+++++++++ ++++ +
  gi|330509108|ref|YP_004385536.1| 51 NESYEEATQAFDRALEQDPQNLNAWLFKSMA 81
                                      4455666666666666666666555544333 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.6
                                       HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHH CS
                            ANAPC3  39 ykrAyellrka.klnskslgcrylfAqcllkLkkyee 74 
                                       +++A+e  ++a ++++++  ++  +A  l k++++ +
  gi|330509108|ref|YP_004385536.1| 109 FDKAIEAHERAiEIAPENATVWTYKANNLAKIGSFTD 145
                                       4555555555555555555555555555555555554 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0089
                                       HHHHH.HHH--HHHHHHH..HHHHHHTT-.....HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHH CS
                            ANAPC3  12 aerllaaetespedayll..Alclylngq.....ykrAyellrka.klnskslgcrylfAqcllkLkkyee 74 
                                       ++++l+ ++e++++ + +  Al++ ++ +     y++A++++++a ++++++ g++  +A  l +L++ +e
  gi|330509108|ref|YP_004385536.1| 157 FDKALELNPEDADAWHGKgiALVYISQTRedtsrYEEALRYIDRAlEIDPQTAGALENKAGILSELGRQNE 227
                                       6777777777777755544466666554444445************************9999999999887 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 0.00016
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-.......HHHHHHHHHCT.SHHHC-H...HHHHHHHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngq.......ykrAyellrka.klnsksl...gcrylfAqcll 67 
                                       + +y++A+ +++r+l+ +++ + ++  +A  l ++g+       y +A+el++++ +++++++   ++++ ++  l 
  gi|330509108|ref|YP_004385536.1| 188 TSRYEEALRYIDRALEIDPQTAGALENKAGILSELGRqnesdklYSEALELYNTSiETEKSTEdlvEAWLSKGFILQ 264
                                       67899999999999975555555544444444443333333566***********77777777999*********** PP

                                       HTT-HHHHHHHH-S CS
                            ANAPC3  68 kLkkyeeAiaaLek 81 
                                       +++kye+A++aL++
  gi|330509108|ref|YP_004385536.1| 265 AQGKYEDAVKALGN 278
                                       ************97 PP

  == domain 5  score: 16.1 bits;  conditional E-value: 1.9e-05
                                       -HHHHHHHHHHHH...HHH--HHHHHH.HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHH.HTT-HHHH CS
                            ANAPC3   4 nyknAiflaerlla..aetespedayl.lAlclylngqykrAyellrka.klnskslgcrylfAqcll.kLkkyeeA 75 
                                        y +A+ l++   +  ++te++  a l ++  l  +g+y+ A + l +a + ++ +  ++ +++  l  +Lk+y++A
  gi|330509108|ref|YP_004385536.1| 231 LYSEALELYNTSIEteKSTEDLVEAWLsKGFILQAQGKYEDAVKALGNAtDADPMNGLAWKVKGVLLWrELKEYDDA 307
                                       67777777777773223444444444435889999**************99999999*******99988******** PP

                                       HHHH-S CS
                            ANAPC3  76 iaaLek 81 
                                       ++a++k
  gi|330509108|ref|YP_004385536.1| 308 VNAFDK 313
                                       ***998 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.08
                                       TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHH CS
                            ANAPC3  36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeA 75 
                                       +++y+ A + ++ka ++n+k++  ++ ++ +l +L++  eA
  gi|330509108|ref|YP_004385536.1| 301 LKEYDDAVNAFDKAlQINPKDPLTWMNKGDALKALGRQAEA 341
                                       57777777777777777777777777777777777777776 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 !   10.0   0.1    0.0011      0.54      92     139 ..      50      99 ..      32     112 .. 0.78
   2 ?    2.1   0.1      0.28   1.4e+02      93     115 ..     106     128 ..      90     138 .. 0.81
   3 !   15.6   0.2     2e-05      0.01      25     113 ..     124     208 ..     106     215 .. 0.78
   4 ?    2.0   0.0      0.29   1.5e+02      47     115 ..     228     288 ..     205     295 .. 0.62
   5 ?    2.4   0.1      0.23   1.2e+02      52      82 ..     305     335 ..     298     351 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHH-TT-..HHHHHHHHHHHTHHHHHHHHHHSSS- CS
                       TOM20_plant  92 akenfekatqffqqavdedPdn..dlyrkslelaakaPelhteihkqgll 139
                                       ++e +e atq f++a ++dP+n      ks+ l++   ++  e ++ g+ 
  gi|330509108|ref|YP_004385536.1|  50 SNESYEEATQAFDRALEQDPQNlnAWLFKSMALTSLGTKIALENKNLGIK 99 
                                       56789***************973245679998888777777766666655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHHHH-TT-HH CS
                       TOM20_plant  93 kenfekatqffqqavdedPdndl 115
                                        + f+ka +  ++a++  P+n +
  gi|330509108|ref|YP_004385536.1| 106 MTAFDKAIEAHERAIEIAPENAT 128
                                       4689***************9975 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH CS
                       TOM20_plant  25 adnllrWggallelsqfqsvaeakqmiqdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatq 101
                                        +n + W+    +l++  s ++   +++++++ +++al ++P+  da    g a +    + + + e  + +e a +
  gi|330509108|ref|YP_004385536.1| 124 PENATVWTYKANNLAKIGSFTDNLSILNESLQAFDKALELNPEDADAWHGKGIALV----YISQTREDTSRYEEALR 196
                                       4788889999999999999999**********************999776666543....33444555677899999 PP

                                       HHHHHHHH-TT- CS
                       TOM20_plant 102 ffqqavdedPdn 113
                                       + ++a + dP+ 
  gi|330509108|ref|YP_004385536.1| 197 YIDRALEIDPQT 208
                                       999999999975 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT-HH CS
                       TOM20_plant  47 akqmiqdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqavdedPdndl 115
                                       + ++ ++a+  ++ ++  + + +d    + +a++s +f+     +a+ ++e a + +++a+d+dP n l
  gi|330509108|ref|YP_004385536.1| 228 SDKLYSEALELYNTSIETEKSTED----LVEAWLSKGFIL----QAQGKYEDAVKALGNATDADPMNGL 288
                                       555555555555555444444444....345666666664....6888899999999999999998865 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHH-TT-HHHHHH.HHHHHHHH CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWc.ignaytsf 82 
                                       +da+  +++al i+Pk     W+  g+a  + 
  gi|330509108|ref|YP_004385536.1| 305 DDAVNAFDKALQINPKDP-LTWMnKGDALKAL 335
                                       799999999****99643.3343145555554 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.65   3.3e+02      16      32 ..      54      70 ..      40      71 .. 0.88
   2 ?    0.5   0.0       2.3   1.2e+03      14      32 ..     107     125 ..      95     126 .. 0.82
   3 ?   -1.4   0.0       9.8     5e+03      18      32 ..     152     166 ..     150     167 .. 0.78
   4 ?    5.4   0.0     0.066        34       2      33 .]     177     208 ..     175     208 .. 0.77
   5 ?   -0.8   0.0       6.2   3.2e+03      14      24 ..     230     240 ..     216     244 .. 0.60
   6 ?    6.3   0.0     0.034        17       2      29 ..     255     282 ..     254     284 .. 0.79
   7 !    8.6   0.0    0.0062       3.2       9      32 ..     297     320 ..     293     321 .. 0.85
   8 ?    4.7   0.5      0.11        56       6      27 ..     328     349 ..     325     351 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.65
                                      HHHHHHHHHHHHHH-TT CS
                             TPR_6 16 tdkAlealerlikeYPd 32
                                      +++A +a++r +++ P+
  gi|330509108|ref|YP_004385536.1| 54 YEEATQAFDRALEQDPQ 70
                                      789999******99997 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHHHH-TT CS
                             TPR_6  14 gdtdkAlealerlikeYPd 32 
                                       +  dkA+ea er i+  P+
  gi|330509108|ref|YP_004385536.1| 107 TAFDKAIEAHERAIEIAPE 125
                                       5678999999999998886 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 9.8
                                       HHHHHHHHHHHH-TT CS
                             TPR_6  18 kAlealerlikeYPd 32 
                                       ++l+a+++ ++  P+
  gi|330509108|ref|YP_004385536.1| 152 ESLQAFDKALELNPE 166
                                       678899999988885 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.066
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPdS 33 
                                       Al ++ + ++ + ++++Al++ +r ++  P++
  gi|330509108|ref|YP_004385536.1| 177 ALVYISQTREDTSRYEEALRYIDRALEIDPQT 208
                                       5555566666657*************999975 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 6.2
                                       HHHHHHHHHHH CS
                             TPR_6  14 gdtdkAleale 24 
                                       + +++Ale+++
  gi|330509108|ref|YP_004385536.1| 230 KLYSEALELYN 240
                                       34566666665 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlike 29 
                                       A +  +  ++++g++++A++al +  + 
  gi|330509108|ref|YP_004385536.1| 255 AWLSKGFILQAQGKYEDAVKALGNATDA 282
                                       5666678889999*********987765 PP

  == domain 7  score: 8.6 bits;  conditional E-value: 0.0062
                                       HHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                                       + r+l+++d+A+ a+++ ++  P+
  gi|330509108|ref|YP_004385536.1| 297 LWRELKEYDDAVNAFDKALQINPK 320
                                       456699**************9997 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerli 27 
                                        + ++++lg+ ++A ea+ + +
  gi|330509108|ref|YP_004385536.1| 328 KGDALKALGRQAEADEAYAKAR 349
                                       588999999*********9976 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       1.7   8.5e+02      12      30 ..      48      66 ..      45      66 .. 0.81
   2 ?    0.6   0.1       1.1   5.8e+02      19      31 ..     110     122 ..     107     124 .. 0.65
   3 ?   -2.4   0.0       9.8     5e+03      19      30 ..     151     162 ..     145     164 .. 0.63
   4 ?    5.0   0.2     0.047        24      17      31 ..     190     204 ..     186     204 .. 0.90
   5 !   14.8   0.2   3.8e-05      0.02       1      33 [.     208     240 ..     208     246 .. 0.94
   6 ?    5.2   0.0     0.038        20       9      24 ..     260     275 ..     259     279 .. 0.86
   7 !    8.4   0.0    0.0038       1.9      12      31 ..     298     317 ..     294     318 .. 0.88
   8 ?    3.1   0.9      0.18        91       9      30 ..     329     350 ..     326     354 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.7
                            TPR_10 12 lrqrgrydeAealleeala 30
                                      l++   y+eA + +++al+
  gi|330509108|ref|YP_004385536.1| 48 LSSNESYEEATQAFDRALE 66
                                      6667779*********996 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                            TPR_10  19 deAealleealai 31 
                                       d+A + +e+a++i
  gi|330509108|ref|YP_004385536.1| 110 DKAIEAHERAIEI 122
                                       5666666666665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 9.8
                            TPR_10  19 deAealleeala 30 
                                       +e+++ +++al+
  gi|330509108|ref|YP_004385536.1| 151 NESLQAFDKALE 162
                                       466666666665 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.047
                            TPR_10  17 rydeAealleealai 31 
                                       ry+eA+++ ++al+i
  gi|330509108|ref|YP_004385536.1| 190 RYEEALRYIDRALEI 204
                                       9************97 PP

  == domain 5  score: 14.8 bits;  conditional E-value: 3.8e-05
                            TPR_10   1 tAsslnNLanalrqrgrydeAealleealairr 33 
                                       tA +l N a +l+++gr +e+ +l+ eal+++ 
  gi|330509108|ref|YP_004385536.1| 208 TAGALENKAGILSELGRQNESDKLYSEALELYN 240
                                       89****************************995 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.038
                            TPR_10   9 analrqrgrydeAeal 24 
                                       + +l+++g+y++A++ 
  gi|330509108|ref|YP_004385536.1| 260 GFILQAQGKYEDAVKA 275
                                       6789*********986 PP

  == domain 7  score: 8.4 bits;  conditional E-value: 0.0038
                            TPR_10  12 lrqrgrydeAealleealai 31 
                                        r++++yd+A++ +++al+i
  gi|330509108|ref|YP_004385536.1| 298 WRELKEYDDAVNAFDKALQI 317
                                       4899**************98 PP

  == domain 8  score: 3.1 bits;  conditional E-value: 0.18
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       + al ++gr +eA + + +a +
  gi|330509108|ref|YP_004385536.1| 329 GDALKALGRQAEADEAYAKARE 350
                                       7799************999976 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.084        43      77     119 ..      46      88 ..      37      96 .. 0.87
   2 ?    3.0   0.0      0.25   1.3e+02      86     127 ..     110     151 ..      92     164 .. 0.83
   3 !    9.5   0.0    0.0025       1.3      78     123 ..     184     229 ..     169     241 .. 0.87
   4 ?   -0.8   0.0       3.7   1.9e+03      80     109 ..     264     293 ..     253     309 .. 0.83
   5 ?    3.8   0.0      0.14        73      83     122 ..     302     341 ..     298     347 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.084
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  77 kealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyq 119
                                        e  +++ y+ a +  + ++++dp+n +a   k  al++lg +
  gi|330509108|ref|YP_004385536.1|  46 IELSSNESYEEATQAFDRALEQDPQNLNAWLFKSMALTSLGTK 88 
                                       56667899******************************99975 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHH CS
                   Alkyl_sulf_dimr  86 rwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRn 127
                                         a+e  + +++  pena+  + ka+ l ++g ++ +    n
  gi|330509108|ref|YP_004385536.1| 110 DKAIEAHERAIEIAPENATVWTYKANNLAKIGSFTDNLSILN 151
                                       5578888889999********************999987655 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0025
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       +  +   y+ a+  ++ +++ dp+ a a e ka +l +lg+q+es 
  gi|330509108|ref|YP_004385536.1| 184 TREDTSRYEEALRYIDRALEIDPQTAGALENKAGILSELGRQNESD 229
                                       445677899**********************************995 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3.7
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHH CS
                   Alkyl_sulf_dimr  80 lkegdyrwaaellnhlvfadpenaeakelk 109
                                        ++g+y+ a++ l ++  adp n  a ++k
  gi|330509108|ref|YP_004385536.1| 264 QAQGKYEDAVKALGNATDADPMNGLAWKVK 293
                                       478999999999999999999998887775 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.14
                                       T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  83 gdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       ++y  a++  +++++ +p++  +   k dal++lg+qae+
  gi|330509108|ref|YP_004385536.1| 302 KEYDDAVNAFDKALQINPKDPLTWMNKGDALKALGRQAEA 341
                                       5788899999***************************997 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.041        21      67     108 ..      48      89 ..      32      99 .. 0.88
   2 !    9.1   0.0    0.0023       1.2      62     125 ..     180     243 ..     159     255 .. 0.85
   3 ?    4.3   0.0     0.065        33      71     119 ..     302     350 ..     297     352 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.041
                           DUF4919  67 elseeelkeiislaeealkknPfdlkqlnllayaykalgkke 108
                                         s+e+++e+ ++  +al+++P +l++  + ++a+ +lg k 
  gi|330509108|ref|YP_004385536.1|  48 LSSNESYEEATQAFDRALEQDPQNLNAWLFKSMALTSLGTKI 89 
                                       56899*****************************99999875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0023
                           DUF4919  62 kldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkllkail 125
                                       + +++  +++ ++e++++  +al+ +P    +l++ a ++++lg+++e+ ++++   +l ++ +
  gi|330509108|ref|YP_004385536.1| 180 YISQTREDTSRYEEALRYIDRALEIDPQTAGALENKAGILSELGRQNESDKLYSEALELYNTSI 243
                                       678888999*************************************999888888777777655 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.065
                           DUF4919  71 eelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnk 119
                                       +e+++++++  +al+ nP d+ + ++   a+kalg++ ea + + + ++
  gi|330509108|ref|YP_004385536.1| 302 KEYDDAVNAFDKALQINPKDPLTWMNKGDALKALGRQAEADEAYAKARE 350
                                       799**********************************999998887765 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0         4     2e+03      16      91 ..      48      67 ..      39      88 .. 0.59
   2 ?    2.4   0.1      0.39     2e+02      83     136 ..     155     208 ..     145     211 .. 0.81
   3 !    9.3   0.1    0.0029       1.5      60     138 ..     207     288 ..     199     297 .. 0.83
   4 !    9.7   0.1    0.0021       1.1      75     124 ..     301     350 ..     295     353 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4
                                      HHHTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD 16 alaagdpeeaaelleaAlalwrGpaladleagewleaererleelrlealealaeaelrlGraeealaelealvae 91
                                      +++++  eea +++++Al                                                        ++
  gi|330509108|ref|YP_004385536.1| 48 LSSNESYEEATQAFDRAL--------------------------------------------------------EQ 67
                                      444444455555555544........................................................44 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.39
                                       HHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----H CS
                              BTAD  83 aelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepgp 136
                                       +  +++++++P + +++     Al +  ++ e   +Ye++ r+ ++ L ++p++
  gi|330509108|ref|YP_004385536.1| 155 QAFDKALELNPEDADAWHGKGIALVYISQTREDTSRYEEALRYIDRALEIDPQT 208
                                       556677788888888888888888888888888999999999999999999986 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHHHHHTT-HH...HHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS-- CS
                              BTAD  60 lrlealealaeaelrlGrae...ealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgve 133
                                       +   ale  a  +++lGr +   ++ +e+ +l +     E++ + l +A    G   +A ++Ye++++ L +  + +
  gi|330509108|ref|YP_004385536.1| 207 QTAGALENKAGILSELGRQNesdKLYSEALELYNTSIETEKSTEDLVEAWLSKGFILQAQGKYEDAVKALGNATDAD 283
                                       556789999999999996662237777777777777789*******************************9999999 PP

                                       --HHH CS
                              BTAD 134 pgpel 138
                                       p   l
  gi|330509108|ref|YP_004385536.1| 284 PMNGL 288
                                       87655 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0021
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       l ++++a+   +++++ +P +  ++     Al ++GrqaeA e+Y ++r+
  gi|330509108|ref|YP_004385536.1| 301 LKEYDDAVNAFDKALQINPKDPLTWMNKGDALKALGRQAEADEAYAKARE 350
                                       66889999999999999999999999999******************997 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.12        61     215     259 ..      52      96 ..      36     123 .. 0.77
   2 !    8.2   0.0    0.0028       1.4     214     259 ..     188     233 ..     174     248 .. 0.86
   3 ?    6.2   0.1     0.012       5.9     163     256 ..     246     343 ..     235     351 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.12
                                       T-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHH CS
                        Coatomer_E 215 gryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernl 259
                                       ++yeeA +    aL++d+++ ++      a + lg      ++nl
  gi|330509108|ref|YP_004385536.1|  52 ESYEEATQAFDRALEQDPQNLNAWLFKSMALTSLGTKIALENKNL 96 
                                       789**************9998876666666666666666666666 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0028
                                       TT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHH CS
                        Coatomer_E 214 lgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernl 259
                                       + ryeeA   +  aL+ d++ + +L N      +lg+++e+ + + 
  gi|330509108|ref|YP_004385536.1| 188 TSRYEEALRYIDRALEIDPQTAGALENKAGILSELGRQNESDKLYS 233
                                       579**********************************988866554 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.012
                                       T-HHHHHHHHHHH...HHH-TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHH.HTT-HHHHHHHHHHHHHH-TT-H CS
                        Coatomer_E 163 datltQLAqawvk...lavggekiqdAyyifqelsekykstplllngkAvvsl.llgryeeAeslLkeaLdkdakde 235
                                       ++    L +aw++   + ++ +k++dA     + ++  +++ l  + k v     l++y++A +   +aL+ ++kd+
  gi|330509108|ref|YP_004385536.1| 246 EKSTEDLVEAWLSkgfILQAQGKYEDAVKALGNATDADPMNGLAWKVKGVLLWrELKEYDDAVNAFDKALQINPKDP 322
                                       5555678889997666789999999999999999999999999999999876526899******************* PP

                                       HHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 236 etLiNlvvaaqhlgkdaevse 256
                                        t +N   a + lg++ae+ e
  gi|330509108|ref|YP_004385536.1| 323 LTWMNKGDALKALGRQAEADE 343
                                       *****9999999999988876 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.56   2.9e+02     156     179 ..      48      71 ..      43      85 .. 0.79
   2 ?   -1.5   0.1       3.3   1.7e+03     161     192 ..     108     138 ..     103     139 .. 0.79
   3 ?    5.3   0.5     0.028        15     112     176 ..     174     239 ..     148     255 .. 0.80
   4 !   11.3   0.2    0.0004      0.21     122     177 ..     262     319 ..     241     327 .. 0.78
   5 !    8.9   1.7    0.0022       1.2     152     174 ..     328     350 ..     324     355 .] 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.56
                            TPR_21 156 lvaqgkldeAraaYqaAlaaleek 179
                                       l++++  +eA +a+++Al++  ++
  gi|330509108|ref|YP_004385536.1|  48 LSSNESYEEATQAFDRALEQDPQN 71 
                                       567788899999999999998776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.3
                            TPR_21 161 kldeAraaYqaAlaaleekarellqlKlddLa 192
                                        +d+A +a ++A++   e+   +   K ++La
  gi|330509108|ref|YP_004385536.1| 108 AFDKAIEAHERAIEIAPEN-ATVWTYKANNLA 138
                                       5689999999999988888.588888888887 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.028
                            TPR_21 112 kalarlRLarvllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                       k +a + + +   ++  y+eAl+ ++++ e +  +a + e +  il++ g+++e  + Y++Al+  
  gi|330509108|ref|YP_004385536.1| 174 KGIALVYISQTREDTSRYEEALRYIDRALEiDPQTAGALENKAGILSELGRQNESDKLYSEALELY 239
                                       56677777777788999********8775537899999999999******************9865 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.0004
                            TPR_21 122 vllaekkydeAlktLeakk.eeafaalvaelrGDilva.qgkldeAraaYqaAlaale 177
                                       +l a++ky++A+k+L +++ ++  ++l+  ++G +l +  ++ d+A +a+++Al+ + 
  gi|330509108|ref|YP_004385536.1| 262 ILQAQGKYEDAVKALGNATdADPMNGLAWKVKGVLLWReLKEYDDAVNAFDKALQINP 319
                                       7899***********665516679*********9987516889**********98655 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0022
                            TPR_21 152 rGDilvaqgkldeAraaYqaAla 174
                                       +GD+l a g+++eA +aY +A +
  gi|330509108|ref|YP_004385536.1| 328 KGDALKALGRQAEADEAYAKARE 350
                                       9*******************976 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 ?    4.4   0.0     0.075        38       8      32 ..      42      66 ..      39      70 .. 0.87
   2 ?   -1.6   0.0       5.8     3e+03      20      32 ..     109     121 ..     107     123 .. 0.70
   3 ?   -0.6   0.0       2.7   1.4e+03      29      49 ..     152     171 ..     133     178 .. 0.66
   4 ?    3.4   0.1      0.16        83      26      39 ..     190     203 ..     173     221 .. 0.65
   5 !    9.1   0.2    0.0026       1.3      11      32 ..     223     244 ..     213     245 .. 0.81
   6 ?   -1.5   0.1       5.5   2.8e+03      17      26 ..     266     275 ..     262     282 .. 0.68
   7 ?    2.8   0.0      0.24   1.2e+02      25      43 ..     302     322 ..     301     335 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.075
                               MIT  8 vkkAveeDnagnyeeAlelYkeale 32
                                      +k+ +e+ +++ yeeA +++  ale
  gi|330509108|ref|YP_004385536.1| 42 IKRGIELSSNESYEEATQAFDRALE 66
                                      7888999999999999999999997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.8
                               MIT  20 yeeAlelYkeale 32 
                                       +++A+e+ + a+e
  gi|330509108|ref|YP_004385536.1| 109 FDKAIEAHERAIE 121
                                       5677777777776 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.7
                               MIT  29 ealelLlqalkekneerrell 49 
                                       e+l+ + +al   n+e+ +++
  gi|330509108|ref|YP_004385536.1| 152 ESLQAFDKALE-LNPEDADAW 171
                                       56666666664.455555555 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.16
                               MIT  26 lYkealelLlqalk 39 
                                        Y+eal+++  al 
  gi|330509108|ref|YP_004385536.1| 190 RYEEALRYIDRALE 203
                                       46666666666664 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.0026
                               MIT  11 AveeDnagnyeeAlelYkeale 32 
                                         ++++ + y+eAlelY +++e
  gi|330509108|ref|YP_004385536.1| 223 GRQNESDKLYSEALELYNTSIE 244
                                       56889999***********998 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 5.5
                               MIT  17 agnyeeAlel 26 
                                       +g+ye+A+++
  gi|330509108|ref|YP_004385536.1| 266 QGKYEDAVKA 275
                                       5777777664 PP

  == domain 7  score: 2.8 bits;  conditional E-value: 0.24
                               MIT  25 elYkealelLlqalk.e.kne 43 
                                       + Y +a++ + +al+ + k++
  gi|330509108|ref|YP_004385536.1| 302 KEYDDAVNAFDKALQiNpKDP 322
                                       558899999999998656665 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 ?   -1.4   0.0       3.4   1.8e+03       2      15 ..      54      67 ..      53      76 .. 0.81
   2 ?    2.1   0.0      0.29   1.5e+02       2      16 ..     109     123 ..     108     129 .. 0.85
   3 ?   -1.6   0.0       4.1   2.1e+03       3      15 ..     151     163 ..     151     166 .. 0.86
   4 ?    7.9   0.0    0.0045       2.3       1      15 [.     190     204 ..     190     209 .. 0.90
   5 ?   -2.2   0.1       6.3   3.2e+03       2      15 ..     232     245 ..     232     248 .. 0.83
   6 ?   -1.3   0.0       3.3   1.7e+03       1      15 [.     303     317 ..     303     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.4
                                      HHHHHHHHHHHHHH CS
                          HTH_Bact  2 YeeaLeqvnkAiei 15
                                      Yeea +  ++A+e 
  gi|330509108|ref|YP_004385536.1| 54 YEEATQAFDRALEQ 67
                                      99999999999875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAieiS 16 
                                       +++a+e  ++Aiei 
  gi|330509108|ref|YP_004385536.1| 109 FDKAIEAHERAIEIA 123
                                       699**********97 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   3 eeaLeqvnkAiei 15 
                                       +e+L+  +kA+e+
  gi|330509108|ref|YP_004385536.1| 151 NESLQAFDKALEL 163
                                       689******9985 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0045
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rYeeaL ++++A+ei
  gi|330509108|ref|YP_004385536.1| 190 RYEEALRYIDRALEI 204
                                       7************98 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 6.3
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                       Y eaLe  n  ie+
  gi|330509108|ref|YP_004385536.1| 232 YSEALELYNTSIET 245
                                       88999999988875 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 3.3
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y+ a +  +kA++i
  gi|330509108|ref|YP_004385536.1| 303 EYDDAVNAFDKALQI 317
                                       69*********9986 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0       0.2     1e+02       7      19 ..      63      75 ..      62      83 .. 0.87
   2 ?    5.7   0.0     0.025        13       6      21 ..     117     132 ..     117     133 .. 0.91
   3 ?   -1.1   0.0       3.4   1.7e+03       7      20 ..     159     172 ..     158     172 .. 0.79
   4 ?    0.5   0.0       1.1   5.5e+02       2      13 ..     195     206 ..     194     207 .. 0.90
   5 ?   -1.5   0.1       4.7   2.4e+03       7      15 ..     313     321 ..     312     322 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.2
                                      HHHHH-TT-CHHH CS
                              PPTA  7 kliekdpkNYsaW 19
                                       ++e+dp+N  aW
  gi|330509108|ref|YP_004385536.1| 63 RALEQDPQNLNAW 75
                                      689******9999 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.025
                                       HHHHHH-TT-CHHHHH CS
                              PPTA   6 ekliekdpkNYsaWny 21 
                                       e +ie  p N ++W y
  gi|330509108|ref|YP_004385536.1| 117 ERAIEIAPENATVWTY 132
                                       579***********99 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.4
                                       HHHHH-TT-CHHHH CS
                              PPTA   7 kliekdpkNYsaWn 20 
                                       k++e++p +  aW+
  gi|330509108|ref|YP_004385536.1| 159 KALELNPEDADAWH 172
                                       79999999877776 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.1
                                       HHHHHHHHHH-T CS
                              PPTA   2 Leltekliekdp 13 
                                       L +++ ++e dp
  gi|330509108|ref|YP_004385536.1| 195 LRYIDRALEIDP 206
                                       89*********9 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 4.7
                                       HHHHH-TT- CS
                              PPTA   7 kliekdpkN 15 
                                       k+++ +pk+
  gi|330509108|ref|YP_004385536.1| 313 KALQINPKD 321
                                       899****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 ?    4.1   0.1      0.11        56      23      51 ..      97     126 ..      81     131 .. 0.79
   2 ?   -1.1   0.0       4.5   2.3e+03      18      52 ..     134     168 ..     127     171 .. 0.82
   3 ?    6.7   0.0     0.017       8.8      14      67 ..     171     224 ..     156     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.11
                    preATP-grasp_3  23 vvdseedvd.etfrrlaaeaDaVlvIAPEt 51 
                                        ++++e    ++f +++++++    IAPE 
  gi|330509108|ref|YP_004385536.1|  97 GIKDREASGmTAFDKAIEAHERAIEIAPEN 126
                                       555555555589*****************6 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.5
                    preATP-grasp_3  18 avevlvvdseedvdetfrrlaaeaDaVlvIAPEtd 52 
                                       a+++  + s+ d+ +++++ +++ D  l   PE  
  gi|330509108|ref|YP_004385536.1| 134 ANNLAKIGSFTDNLSILNESLQAFDKALELNPEDA 168
                                       46778899999999999999999999998888865 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.017
                    preATP-grasp_3  14 ltlpavevlvvdseedvdetfrrlaaeaDaVlvIAPEtdgiLarltrlveaagk 67 
                                       ++ ++++++ +++ ++ +++++++++  D  l I P t g L++ + ++ + g+
  gi|330509108|ref|YP_004385536.1| 171 WHGKGIALVYISQTREDTSRYEEALRYIDRALEIDPQTAGALENKAGILSELGR 224
                                       444478899999999999**************************9999988776 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       5.3   2.7e+03      85     105 ..      46      66 ..      40      68 .. 0.82
   2 ?    7.9   0.0    0.0059         3      59     106 ..     150     204 ..     110     206 .. 0.90
   3 ?    0.8   0.0      0.96   4.9e+02      80      98 ..     219     237 ..     212     273 .. 0.65
   4 ?   -2.0   0.0       7.1   3.7e+03       7      15 ..     327     335 ..     303     351 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5.3
                            DUF627  85 sqlgsklyYkkavkkakraLs 105
                                        +l s+  Y++a +   raL 
  gi|330509108|ref|YP_004385536.1|  46 IELSSNESYEEATQAFDRALE 66 
                                       578899999999999999885 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0059
                            DUF627  59 llasvecfseavels.......rfyArsLfelasqlgsklyYkkavkkakraLsv 106
                                       l  s+++f +a el        ++    L+ + +  + ++ Y++a++   raL +
  gi|330509108|ref|YP_004385536.1| 150 LNESLQAFDKALELNpedadawHGKGIALVYISQTREDTSRYEEALRYIDRALEI 204
                                       6789************************************************987 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.96
                            DUF627  80 LfelasqlgsklyYkkavk 98 
                                       L el++q +s + Y +a++
  gi|330509108|ref|YP_004385536.1| 219 LSELGRQNESDKLYSEALE 237
                                       5666666666666666554 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 7.1
                            DUF627   7 argnhikAL 15 
                                       ++g+  kAL
  gi|330509108|ref|YP_004385536.1| 327 NKGDALKAL 335
                                       344444444 PP

>> NRDE-2  NRDE-2, necessary for RNA interference
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0031       1.6       3      63 ..      58     125 ..      56     140 .. 0.75
   2 ?    7.5   0.3    0.0039         2       4      88 ..     155     249 ..     152     304 .. 0.68
   3 ?   -2.6   0.0       4.4   2.3e+03       4      21 ..     309     326 ..     306     330 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0031
                            NRDE-2   3 naelnraveenPedidaWl....elvefQdellsaeee...slskserkalaeiklsilekAleknks 63 
                                       ++ ++ra+e++P++++aWl    +l ++  +++ ++++   + +++      ++ ++  e+A+e +++
  gi|330509108|ref|YP_004385536.1|  58 TQAFDRALEQDPQNLNAWLfksmALTSLGTKIALENKNlgiKDREASGMTAFDKAIEAHERAIEIAPE 125
                                       67899*************64433788888877765666876545555666889999999999998843 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0039
                            NRDE-2   4 aelnraveenPedidaW....lelvefQdellsaeee.............slskserkalaeiklsilekAleknks 63 
                                       + +++a+e nPed+daW    ++lv + ++  +   +             +    +++  +e k  il++  ++n  
  gi|330509108|ref|YP_004385536.1| 155 QAFDKALELNPEDADAWhgkgIALVYISQTRED--TSryeealryidralE-IDPQTAGALENKAGILSELGRQN-- 226
                                       57899************5555578888774332..1123344555555321.12223335566666665555555.. PP

                            NRDE-2  64 npdserLllelLklgseiwdsekla 88 
                                         +s++L  e L+l++   ++ek +
  gi|330509108|ref|YP_004385536.1| 227 --ESDKLYSEALELYNTSIETEKST 249
                                       ..78899999999998887777533 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.4
                            NRDE-2   4 aelnraveenPedidaWl 21 
                                         +++a++ nP+d  +W+
  gi|330509108|ref|YP_004385536.1| 309 NAFDKALQINPKDPLTWM 326
                                       568899999********8 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.23   1.2e+02     264     290 ..      50      76 ..      39      83 .. 0.87
   2 ?    8.0   0.9    0.0029       1.5     245     307 ..     127     189 ..      80     347 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.23
                                       S...-SSCCHHHHCCHHCTCCCHSTTC CS
                               FAT 264 seekieeilqsysaateidpswykawh 290
                                       s+e+ ee++q++ +a e dp+  +aw 
  gi|330509108|ref|YP_004385536.1|  50 SNESYEEATQAFDRALEQDPQNLNAWL 76 
                                       567789*******************95 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0029
                                       HHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHHHHHS CS
                               FAT 245 arcylkkGewqealqkldwseekieeilqsysaateidpswykawhtwalfnfevvskeeeqk 307
                                       a + + k+  ++++++++ +    +e lq++ +a e++p+ ++awh  + +   + ++ e+++
  gi|330509108|ref|YP_004385536.1| 127 ATVWTYKANNLAKIGSFTDNLSILNESLQAFDKALELNPEDADAWHGKGIALVYISQTREDTS 189
                                       4445555555566666666666699*********************84444444444443333 PP

>> ADP_ribosyl_GH  ADP-ribosylglycohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00047      0.24     162     235 ..      18      90 ..      13     117 .. 0.88
   2 ?   -0.6   0.1       1.7   8.5e+02     237     237 ..     246     246 ..     156     347 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00047
                                       HHHHHHHHHHHHHHHHTT--STHHHHHH..HHHHTTT-HHHHHHHGGGGG---HHH........HHHHH--SSB CS
                    ADP_ribosyl_GH 162 avagaaayaaliaaalrgksleealdaaeeelavapaeeelaaalrkalaladsdkdvdvdaeeavdelgsggy 235
                                       a+  a++ a+++aaa++ +++ ++++++  el+ +++ ee ++a ++al+++ ++ +++ +++ a+ +lg+ ++
  gi|330509108|ref|YP_004385536.1|  18 AMVLAVFSALCLAAAAEDNTPVAWIKRG-IELSSNESYEEATQAFDRALEQDPQNLNAWLFKSMALTSLGTKIA 90 
                                       667899*********************9.99*******************999999877777777777776655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                                       H CS
                    ADP_ribosyl_GH 237 v 237
                                       +
  gi|330509108|ref|YP_004385536.1| 246 E 246
                                       2 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0         1   5.1e+02      15      36 ..      45      66 ..      38      88 .. 0.80
   2 ?   -1.6   0.0         4   2.1e+03       7      36 ..     133     162 ..     127     166 .. 0.74
   3 ?    4.3   0.1     0.064        33      21      37 ..     188     204 ..     169     246 .. 0.84
   4 ?   -0.9   0.0       2.5   1.3e+03      10      34 ..     255     279 ..     249     282 .. 0.79
   5 ?    0.8   0.0      0.73   3.7e+02      22      64 ..     302     343 ..     295     349 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1
                           DUF5113 15 ayylnvegeyeeALeyldsale 36
                                      + +l  +++yeeA + +d ale
  gi|330509108|ref|YP_004385536.1| 45 GIELSSNESYEEATQAFDRALE 66
                                      6667778899999999999986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsale 36 
                                       +an+ a++++++      +e+L+ +d+ale
  gi|330509108|ref|YP_004385536.1| 133 KANNLAKIGSFTDNLSILNESLQAFDKALE 162
                                       567777777777777777888888888886 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.064
                           DUF5113  21 egeyeeALeyldsaley 37 
                                       + +yeeAL+y+d ale+
  gi|330509108|ref|YP_004385536.1| 188 TSRYEEALRYIDRALEI 204
                                       579***********985 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 2.5
                           DUF5113  10 dYanlayylnvegeyeeALeyldsa 34 
                                       ++ + +  l ++g+ye+A++ l +a
  gi|330509108|ref|YP_004385536.1| 255 AWLSKGFILQAQGKYEDAVKALGNA 279
                                       566677788999******9988776 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.73
                           DUF5113  22 geyeeALeyldsaleylNahyekYakkkadtldklkmllegeg 64 
                                       +ey++A++ +d+al++  +   ++++k  d l+ l   +e ++
  gi|330509108|ref|YP_004385536.1| 302 KEYDDAVNAFDKALQINPKDPLTWMNKG-DALKALGRQAEADE 343
                                       689***********98777777777766.67766665555555 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 ?   -1.3   0.0       2.9   1.5e+03     136     157 ..      49      70 ..      31      78 .. 0.72
   2 ?    1.2   0.2      0.49   2.5e+02      82     154 ..      98     163 ..      74     205 .. 0.61
   3 ?   10.1   0.5   0.00096      0.49     116     163 ..     207     254 ..     180     322 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.9
                           DUF2225 136 keklflkkAlelykeayekesf 157
                                       ++++ +++A++ +++a+e++ +
  gi|330509108|ref|YP_004385536.1|  49 SSNESYEEATQAFDRALEQDPQ 70 
                                       5566788899999998888765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.49
                           DUF2225  82 wksrdfskertldeaiesYkLallcyelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelykeayek 154
                                       +k r+ s+   +d+aie++  a++ +  +    + kA ++ +++ + +++         l++ l+ +++a+e 
  gi|330509108|ref|YP_004385536.1|  98 IKDREASGMTAFDKAIEAHERAIEIAPENATVWTYKANNLAKIGSFTDNLSI-------LNESLQAFDKALEL 163
                                       5555666777777777777777777666666666666666666655444444.......44444444444444 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00096
                           DUF2225 116 kkAklalrlAWlyrdkedeekeklflkkAlelykeayekesfpvegid 163
                                       + A+ + + A + ++++ ++++++++ +Alely++++e+e+++++ ++
  gi|330509108|ref|YP_004385536.1| 207 QTAGALENKAGILSELGRQNESDKLYSEALELYNTSIETEKSTEDLVE 254
                                       556666666667778888999********************9766544 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.065        34      20      47 ..     154     205 ..     138     206 .. 0.69
   2 ?    4.9   0.0     0.056        29      20      42 ..     219     241 ..     207     252 .. 0.83
   3 ?   -2.3   0.1       9.5   4.9e+03      28      46 ..     264     282 ..     263     283 .. 0.76
   4 ?    0.3   0.0       1.6     8e+02      20      43 ..     332     355 .]     300     355 .] 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.065
                           DUF2802  20 leel........................eqqdpqsklYsqAiklvrqGasve 47 
                                       l+++                        +q+ +++ +Y++A++ + + ++++
  gi|330509108|ref|YP_004385536.1| 154 LQAFdkalelnpedadawhgkgialvyiSQTREDTSRYEEALRYIDRALEID 205
                                       444444444445555555777777787788889***********99887765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.056
                           DUF2802  20 leeleqqdpqsklYsqAiklvrq 42 
                                       l+el  q++++klYs+A++l + 
  gi|330509108|ref|YP_004385536.1| 219 LSELGRQNESDKLYSEALELYNT 241
                                       678888999**********9765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 9.5
                           DUF2802  28 pqsklYsqAiklvrqGasv 46 
                                       +++++Y+ A+k ++   ++
  gi|330509108|ref|YP_004385536.1| 264 QAQGKYEDAVKALGNATDA 282
                                       57899**999987766665 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 1.6
                           DUF2802  20 leeleqqdpqsklYsqAiklvrqG 43 
                                       l++l  q +++  Y +A +l  qG
  gi|330509108|ref|YP_004385536.1| 332 LKALGRQAEADEAYAKARELGYQG 355
                                       555567778999999999986665 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       8.9   4.6e+03      17      25 ..      54      62 ..      51      65 .. 0.86
   2 ?    1.1   0.0      0.83   4.2e+02      17      26 ..     232     239 ..     228     242 .. 0.63
   3 ?    6.1   0.1     0.021        11       8      23 ..     260     275 ..     255     277 .. 0.87
   4 ?    4.7   0.1     0.058        30      15      25 ..     302     312 ..     300     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 8.9
                                      HHHHHHH.. CS
                             TPR_3 17 yqeArelfs 25
                                      y+eA ++f+
  gi|330509108|ref|YP_004385536.1| 54 YEEATQAFD 62
                                      999*99987 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.83
                                       HHHHHHH..H CS
                             TPR_3  17 yqeArelfsY 26 
                                       y+eA+el  Y
  gi|330509108|ref|YP_004385536.1| 232 YSEALEL--Y 239
                                       7777777..3 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.021
                                       HHHHHHTT-HHHHHHH CS
                             TPR_3   8 AaefynkkkyqeArel 23 
                                       ++ ++ ++ky++A+ +
  gi|330509108|ref|YP_004385536.1| 260 GFILQAQGKYEDAVKA 275
                                       5789*********865 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.058
                                       T-HHHHHHH.. CS
                             TPR_3  15 kkyqeArelfs 25 
                                       k+y++A+++f+
  gi|330509108|ref|YP_004385536.1| 302 KEYDDAVNAFD 312
                                       99*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.54
# Mc/sec: 1974.42
//
Query:       gi|330509109|ref|YP_004385537.1|  [L=371]
Description: hypothetical protein MCON_3496 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-06   28.3   0.1    2.4e-06   27.3   0.1    1.5  1  MarR_2           MarR family
    0.00029   20.6   0.1    0.00029   20.6   0.1    2.0  2  HTH_IclR         IclR helix-turn-helix domain
     0.0027   17.5   0.1     0.0053   16.6   0.1    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0056   16.6   0.3      0.013   15.4   0.4    1.6  1  MarR             MarR family
     0.0087   15.6   0.6      0.017   14.6   0.6    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.013   15.0   0.2      0.028   14.0   0.2    1.6  1  Sigma70_r4       Sigma-70, region 4
      0.015   15.6   0.2      0.028   14.8   0.2    1.4  1  Penicillinase_R  Penicillinase repressor
      0.027   14.6   0.0      0.057   13.5   0.0    1.5  1  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
      0.034   14.6   0.2      0.059   13.9   0.2    1.4  1  HTH_27           Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.1   1.2e-09   2.4e-06       2      54 ..     298     349 ..     297     354 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.2e-09
                                       T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       +ltp ++ +  aL  r+gr +t++e+  +++l++s+++ il  L+++ L++++
  gi|330509109|ref|YP_004385537.1| 298 ALTPRERSIVEALIKRGGR-MTQAEIRYETNLPRSTLTTILVSLERRNLITKK 349
                                       69***************97.9*****************************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 ?   -2.6   0.2       2.5   4.9e+03       3      14 ..       1      12 [.       1      16 [. 0.73
   2 !   20.6   0.1   1.4e-07   0.00029       8      50 ..     306     348 ..     293     350 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.5
                                      HHHHHHHCT-CT CS
                          HTH_IclR  3 dRalaiLdalae 14
                                      +R +a+L++l +
  gi|330509109|ref|YP_004385537.1|  1 MRSVALLRMLVR 12
                                      688888888755 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.4e-07
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       i +al ++++++t +e+  +t lp+St   +L +L+++ ++++
  gi|330509109|ref|YP_004385537.1| 306 IVEALIKRGGRMTQAEIRYETNLPRSTLTTILVSLERRNLITK 348
                                       77889999999***************************99876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.7e-06    0.0053       8      56 ..     301     350 ..     298     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
                                       HHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB   8 eyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56 
                                         E ++  aL+ + g++t  ei  e+++prs+   +L sLe++ l+++++
  gi|330509109|ref|YP_004385537.1| 301 PRERSIVEALIkRGGRMTQAEIRYETNLPRSTLTTILVSLERRNLITKKE 350
                                       55666667888445789*****************************9987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   6.6e-06     0.013      11      50 ..     310     349 ..     299     350 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.6e-06
                                       HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                       ++++ g ++++e+    ++ +st+t++l  Le+++li+++
  gi|330509109|ref|YP_004385537.1| 310 LIKRGGRMTQAEIRYETNLPRSTLTTILVSLERRNLITKK 349
                                       4666677******************************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 !   14.6   0.6   8.7e-06     0.017       4      48 .]     302     347 ..     299     347 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.7e-06
                            HTH_24   4 tdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                        +r I e+L k  +r++q+e+  +++l++st+++ l  Le+  lI+
  gi|330509109|ref|YP_004385537.1| 302 RERSIVEALIKrGGRMTQAEIRYETNLPRSTLTTILVSLERRNLIT 347
                                       678999888885677*************************999996 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   1.4e-05     0.028       1      36 [.     295     332 ..     295     338 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                                       HHHHS-HHHHHHHHHHH..TTT--HHHHHHHHTS-HHH CS
                        Sigma70_r4   1 aLasLpererevlelrf..geglTleEIgerlgiSrer 36 
                                       +++ L++rer ++e     g  +T++EI  + +++r++
  gi|330509109|ref|YP_004385537.1| 295 VMDALTPRERSIVEALIkrGGRMTQAEIRYETNLPRST 332
                                       589***********9999**********8888888876 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   1.4e-05     0.028       1      60 [.     299     355 ..     299     357 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                                       ---S-SHHHHHHHHHS-.EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEE CS
                   Penicillinase_R   1 lgelEaevmeilwekge.atvkevveeleeekelaysTVktllrrLvkKgllsrekegraf 60 
                                       l+++E+ + e+l ++g  +t +e++ e + +    +sT +t+l  L++++l+++++ gr+ 
  gi|330509109|ref|YP_004385537.1| 299 LTPRERSIVEALIKRGGrMTQAEIRYETNLP----RSTLTTILVSLERRNLITKKEWGRTN 355
                                       6899**********99989999998877666....*********************99975 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.9e-05     0.057      17      57 ..     305     346 ..     300     347 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHHS.SBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9  17 kVvetLlrkg.rltlrelvkktkLsldqVkksLvvLiqhrlV 57 
                                        +ve L+++g r t  e+  +t+L+++   ++Lv+L +++l+
  gi|330509109|ref|YP_004385537.1| 305 SIVEALIKRGgRMTQAEIRYETNLPRSTLTTILVSLERRNLI 346
                                       6888998875278999***********************998 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   2.9e-05     0.059       1      52 [.     299     350 ..     299     362 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-05
                            HTH_27   1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertg 52 
                                       lt+ ++ +++ +  r++r+++a+++  +n+  s+   +l  L+++ L+++++
  gi|330509109|ref|YP_004385537.1| 299 LTPRERSIVEALIKRGGRMTQAEIRYETNLPRSTLTTILVSLERRNLITKKE 350
                                       67888888888888**********************************5443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 2268.37
//
Query:       gi|330509110|ref|YP_004385538.1|  [L=722]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-72  234.1  51.2    8.9e-09   34.8   0.1   15.1 15  TPR_1            Tetratricopeptide repeat
    7.4e-68  219.3  53.7    1.2e-07   31.2   0.2   15.2 14  TPR_2            Tetratricopeptide repeat
    9.7e-55  178.3  45.5    1.5e-05   24.9   0.0   14.8 14  TPR_8            Tetratricopeptide repeat
    2.7e-47  158.2  56.2    3.4e-09   36.2   0.8   14.4 14  TPR_11           TPR repeat
      4e-40  133.1  34.7    0.00052   20.6   1.7   13.5 13  TPR_14           Tetratricopeptide repeat
    9.2e-39  131.8  41.8    1.5e-09   38.3   0.6   10.0 11  TPR_16           Tetratricopeptide repeat
    5.5e-37  125.9  47.4    9.4e-09   35.4   1.4   11.4 12  TPR_12           Tetratricopeptide repeat
    1.9e-32  109.3  33.2     0.0013   19.0   0.0   13.9 13  TPR_17           Tetratricopeptide repeat
      4e-32  110.5  38.1    1.6e-07   31.7   1.9    9.3  9  TPR_19           Tetratricopeptide repeat
    8.6e-19   66.9  36.3      0.065   13.9   0.1   13.5 13  TPR_6            Tetratricopeptide repeat
    1.5e-18   66.7  27.6     0.0004   20.5   1.4    9.5 10  TPR_9            Tetratricopeptide repeat
      1e-14   53.4  25.0      0.016   15.2   0.5   11.1 11  TPR_7            Tetratricopeptide repeat
    1.1e-14   54.7  18.2      0.031   14.4   0.1    9.3  6  DUF3856          Domain of Unknown Function (DUF3856)
    1.6e-14   53.9  15.6    0.00036   20.7   0.2    6.3  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    9.9e-11   41.2  51.6     0.0038   17.0   0.0   12.6 13  TPR_10           Tetratricopeptide repeat
    2.1e-08   34.7  24.9      0.048   14.1   0.1    8.1  9  BTAD             Bacterial transcriptional activator domain
    3.8e-08   32.7  11.6       0.83    8.5   0.0    7.1  7  NARP1            NMDA receptor-regulated protein 1
    3.4e-07   30.2  14.5       0.75    9.9   0.1    7.3  7  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    3.4e-07   30.5  10.4       0.16   12.2   0.3    6.4  6  TPR_5            Tetratrico peptide repeat
    3.9e-05   23.5  24.9     0.0058   16.4   0.4    7.1  6  TPR_21           Tetratricopeptide repeat-like domain
    8.3e-05   22.6   1.6          2    8.5   0.0    4.8  4  SRP_TPR_like     Putative TPR-like repeat
    0.00024   21.1   0.3        6.2    6.7   0.0    4.0  4  DUF4919          Domain of unknown function (DUF4919)
    0.00033   20.6  10.1       0.21   11.6   0.1    5.5  4  TPR_3            Tetratricopeptide repeat
    0.00049   20.6  11.4        1.2    9.5   0.1    5.7  6  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    0.00051   20.1  34.6       0.35   11.0   0.5   10.5 12  MIT              MIT (microtubule interacting and transport) 
    0.00077   18.8   8.4        1.4    8.1   0.1    5.1  5  FAT              FAT domain
     0.0039   17.2   3.7          4    7.5   0.0    5.0  4  DUF3775          Protein of unknown function (DUF3775)
  ------ inclusion threshold ------
      0.021   15.0   1.5        6.8    7.2   0.0    5.3  4  PPR              PPR repeat
      0.033   14.1   0.4        3.7    7.5   0.0    3.1  3  SLATT_1          SMODS and SLOG-associating 2TM effector doma
      0.039   13.7   7.6         10    5.9   0.1    5.7  5  DUF5113          Domain of unknown function (DUF5113)
      0.049   13.9   0.7          1    9.6   0.0    3.2  3  Bep_C_terminal   BID domain of Bartonella effector protein (B
      0.051   14.1   0.6         15    6.2   0.1    3.8  3  Peptidase_M15_4  D-alanyl-D-alanine carboxypeptidase
      0.086   13.2   0.1         17    5.8   0.0    3.7  4  TruB_N           TruB family pseudouridylate synthase (N term
       0.09   12.6   2.5         16    5.4   0.0    4.3  4  LemA             LemA family
       0.15   12.6   5.4       0.33   11.6   0.1    3.9  2  DUF5344          Family of unknown function (DUF5344)
       0.32   10.5  12.4        1.3    8.5   0.2    5.6  4  SHNi-TPR         SHNi-TPR
       0.41   10.4  12.1       0.63    9.8   0.6    5.1  5  TOM20_plant      Plant specific mitochondrial import receptor
       0.52   10.1   8.5        1.3    8.9   0.1    4.6  4  PPTA             Protein prenyltransferase alpha subunit repe
        1.6    8.6  12.7        1.2    9.1   0.4    5.0  4  Wzy_C_2          Virulence factor membrane-bound polymerase, 
        2.8    8.3  18.4         18    5.7   0.1    6.4  6  TPR_20           Tetratricopeptide repeat
        3.2    7.4  20.3        5.2    6.7   0.1    7.9  8  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 !   13.0   0.3   0.00015     0.067      16      34 .]      44      62 ..      44      62 .. 0.94
   2 ?    5.4   0.1     0.039        17       2      28 ..      64      90 ..      63      92 .. 0.92
   3 !   13.0   0.0   0.00016     0.069       3      30 ..     106     133 ..     104     135 .. 0.96
   4 !   15.4   0.0   2.7e-05     0.012      10      32 ..     154     176 ..     139     178 .. 0.85
   5 !   26.8   0.1   6.9e-09     3e-06       2      34 .]     330     362 ..     329     362 .. 0.93
   6 !   34.8   0.1     2e-11   8.9e-09       1      33 [.     363     395 ..     363     396 .. 0.96
   7 !   12.4   0.1   0.00024       0.1       7      31 ..     406     430 ..     403     432 .. 0.91
   8 !   10.1   0.0    0.0013      0.56       2      23 ..     447     468 ..     446     478 .. 0.93
   9 !   20.7   0.0   5.8e-07   0.00025      13      34 .]     493     514 ..     489     514 .. 0.93
  10 !   31.3   0.5   2.6e-10   1.1e-07       6      33 ..     520     547 ..     517     548 .. 0.89
  11 !   24.0   0.1   5.1e-08   2.2e-05       1      29 [.     549     577 ..     549     581 .. 0.94
  12 !   25.1   0.3   2.3e-08     1e-05       3      29 ..     586     612 ..     585     612 .. 0.95
  13 !   13.3   0.2   0.00012     0.054      14      34 .]     604     624 ..     604     624 .. 0.95
  14 !   28.8   0.2   1.6e-09   6.8e-07       1      34 []     625     658 ..     625     658 .. 0.95
  15 ?   -1.8   0.0       7.4   3.2e+03       2      19 ..     660     677 ..     659     681 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                                      -HHHHHHHHHHHHHHSTTH CS
                             TPR_1 16 kydeAleyyekALelnPnn 34
                                      + deAle+++ A++++P+n
  gi|330509110|ref|YP_004385538.1| 44 NIDEALEAFDNAIQIEPQN 62
                                      679**************97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.039
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekAL 28
                                      +a+ +++  + ++ + +e le+++  L
  gi|330509110|ref|YP_004385538.1| 64 DAWLGKAKSLAYMDEKNESLEAFRNIL 90
                                      8**********************9876 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                       a+  +G a+ +lg+  eA +++e+ +el
  gi|330509110|ref|YP_004385538.1| 106 AWQSKGIALASLGREAEATDAFERSIEL 133
                                       899***********************98 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 2.7e-05
                                       HHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1  10 ayfklgkydeAleyyekALelnP 32 
                                        +  lg+ d Ale+y+k++eln 
  gi|330509110|ref|YP_004385538.1| 154 NLELLGRTDSALEAYDKVIELNS 176
                                       5788*****************97 PP

  == domain 5  score: 26.8 bits;  conditional E-value: 6.9e-09
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       + ++n+G+ ++++  ++eAl++++kA+e+n ++
  gi|330509110|ref|YP_004385538.1| 330 EDWFNRGQELQRNDSHEEALQAFDKAIEINQSY 362
                                       56****************************986 PP

  == domain 6  score: 34.8 bits;  conditional E-value: 2e-11
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a a+ ++G++++++g+y+eA+++ ++A+el+P+
  gi|330509110|ref|YP_004385538.1| 363 AFAWGGKGYVLYNMGRYEEAIAAWDRAIELEPD 395
                                       679*****************************8 PP

  == domain 7  score: 12.4 bits;  conditional E-value: 0.00024
                                       HHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   7 lGnayfklgkydeAleyyekALeln 31 
                                       +G ++  lg+ +e  ++ye+ALel 
  gi|330509110|ref|YP_004385538.1| 406 KGKVLAILGRNEESAQAYERALELA 430
                                       799999*****************96 PP

  == domain 8  score: 10.1 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHTT-HHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAley 23 
                                        a+  +G+++  +g+y eAle+
  gi|330509110|ref|YP_004385538.1| 447 AAWGFKGQLLDDQGRYVEALEA 468
                                       69999***************97 PP

  == domain 9  score: 20.7 bits;  conditional E-value: 5.8e-07
                                       HTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  13 klgkydeAleyyekALelnPnn 34 
                                       +lg+y+e +e y+k Le++P+n
  gi|330509110|ref|YP_004385538.1| 493 RLGRYNESIESYNKSLEIDPKN 514
                                       79******************98 PP

  == domain 10  score: 31.3 bits;  conditional E-value: 2.6e-10
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   6 nlGnayfklgkydeAleyyekALelnPn 33 
                                       + G+a+ +lg+y+eAleyy++ALe++  
  gi|330509110|ref|YP_004385538.1| 520 GEGYALASLGRYEEALEYYNRALEIDSR 547
                                       5699*********************975 PP

  == domain 11  score: 24.0 bits;  conditional E-value: 5.1e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALe 29 
                                       a+a+ +lG a++++g+y+e +++y++A+ 
  gi|330509110|ref|YP_004385538.1| 549 ARAWQGLGDALRNMGMYNESIQAYDRAIA 577
                                       89*************************97 PP

  == domain 12  score: 25.1 bits;  conditional E-value: 2.3e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALe 29 
                                       al ++G+a+ +lg+ydeA e+ye+AL+
  gi|330509110|ref|YP_004385538.1| 586 ALIGKGMALDSLGRYDEAQEDYEQALK 612
                                       8999*********************97 PP

  == domain 13  score: 13.3 bits;  conditional E-value: 0.00012
                                       TT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  14 lgkydeAleyyekALelnPnn 34 
                                       +++y++Al++y+ +++ nP n
  gi|330509110|ref|YP_004385538.1| 604 QEDYEQALKDYDDVIKKNPRN 624
                                       78*****************87 PP

  == domain 14  score: 28.8 bits;  conditional E-value: 1.6e-09
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a++ yn Gna++ l++++e l++y++A+elnP +
  gi|330509110|ref|YP_004385538.1| 625 AQVMYNQGNALRGLQRHNESLQAYDRAIELNPGY 658
                                       6788****************************76 PP

  == domain 15  score: -1.8 bits;  conditional E-value: 7.4
                                       HHHHHHHHHHHHTT-HHH CS
                             TPR_1   2 kalynlGnayfklgkyde 19 
                                       +a+ +++ +++ lg   e
  gi|330509110|ref|YP_004385538.1| 660 DAWRGKAIVLRALGGNAE 677
                                       79999***9999985555 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.2   0.00063      0.28      16      34 .]      44      62 ..      26      62 .. 0.83
   2 ?    7.2   0.1     0.014       6.2       2      30 ..      64      92 ..      63      95 .. 0.92
   3 !   13.1   0.0   0.00018      0.08       3      31 ..     106     134 ..     104     137 .. 0.92
   4 !   19.5   0.1   1.6e-06   0.00071       1      31 [.     145     175 ..     145     177 .. 0.96
   5 !   22.5   0.2   1.8e-07   7.9e-05       1      32 [.     329     360 ..     329     362 .. 0.94
   6 !   31.2   0.2   2.9e-10   1.2e-07       1      33 [.     363     395 ..     363     396 .. 0.95
   7 !   15.8   0.3   2.5e-05     0.011       4      32 ..     403     431 ..     401     433 .. 0.92
   8 !   10.2   0.0    0.0015      0.67       3      34 .]     448     479 ..     446     479 .. 0.88
   9 !   18.1   0.0   4.6e-06     0.002      12      34 .]     492     514 ..     481     514 .. 0.93
  10 !   28.1   1.3   2.8e-09   1.2e-06       3      32 ..     517     546 ..     516     548 .. 0.92
  11 !   23.2   0.1   1.1e-07   4.7e-05       1      33 [.     549     581 ..     549     582 .. 0.95
  12 !   22.5   0.2   1.7e-07   7.6e-05       3      29 ..     586     612 ..     584     624 .. 0.91
  13 !   25.2   0.2   2.4e-08     1e-05       1      33 [.     625     657 ..     625     658 .. 0.95
  14 ?   -1.5   0.1       8.7   3.8e+03       2      23 ..     660     681 ..     659     688 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00063
                             TPR_2 16 dyeeAleafekAleldPnn 34
                                      + +eAleaf+ A++++P+n
  gi|330509110|ref|YP_004385538.1| 44 NIDEALEAFDNAIQIEPQN 62
                                      78***************97 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.014
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAlel 30
                                      +a+   +++++++++ +e leaf+  l l
  gi|330509110|ref|YP_004385538.1| 64 DAWLGKAKSLAYMDEKNESLEAFRNILNL 92
                                      69999*******************99987 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00018
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                       a+   G a++ lg+ +eA +afe+++el 
  gi|330509110|ref|YP_004385538.1| 106 AWQSKGIALASLGREAEATDAFERSIELL 134
                                       79999**********************95 PP

  == domain 4  score: 19.5 bits;  conditional E-value: 1.6e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       aea++  ++ ++ lg+ + Alea++k++el+
  gi|330509110|ref|YP_004385538.1| 145 AEAWWLKAENLELLGRTDSALEAYDKVIELN 175
                                       89****************************9 PP

  == domain 5  score: 22.5 bits;  conditional E-value: 1.8e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       ae ++n+G+ + +++ +eeAl+af+kA+e++ 
  gi|330509110|ref|YP_004385538.1| 329 AEDWFNRGQELQRNDSHEEALQAFDKAIEINQ 360
                                       688***************************96 PP

  == domain 6  score: 31.2 bits;  conditional E-value: 2.9e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a+   G+++y++g+yeeA++a+++A+el+P+
  gi|330509110|ref|YP_004385538.1| 363 AFAWGGKGYVLYNMGRYEEAIAAWDRAIELEPD 395
                                       67999***************************7 PP

  == domain 7  score: 15.8 bits;  conditional E-value: 2.5e-05
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldP 32 
                                       + + G++++ lg+ ee ++a+e+Alel+ 
  gi|330509110|ref|YP_004385538.1| 403 WEMKGKVLAILGRNEESAQAYERALELAD 431
                                       7789**********************985 PP

  == domain 8  score: 10.2 bits;  conditional E-value: 0.0015
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+   G+++  +g+y eAlea   + + +P++
  gi|330509110|ref|YP_004385538.1| 448 AWGFKGQLLDDQGRYVEALEAVANSSKANPED 479
                                       88899***************999888888875 PP

  == domain 9  score: 18.1 bits;  conditional E-value: 4.6e-06
                             TPR_2  12 yklgdyeeAleafekAleldPnn 34 
                                        +lg+y+e +e ++k+le+dP+n
  gi|330509110|ref|YP_004385538.1| 492 DRLGRYNESIESYNKSLEIDPKN 514
                                       689******************97 PP

  == domain 10  score: 28.1 bits;  conditional E-value: 2.8e-09
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                       al   G+a++ lg+yeeAle++++Ale+d 
  gi|330509110|ref|YP_004385538.1| 517 ALRGEGYALASLGRYEEALEYYNRALEIDS 546
                                       67889**********************995 PP

  == domain 11  score: 23.2 bits;  conditional E-value: 1.1e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+a+  lG+a++++g y+e ++a+++A++  P+
  gi|330509110|ref|YP_004385538.1| 549 ARAWQGLGDALRNMGMYNESIQAYDRAIAEMPQ 581
                                       789**************************9996 PP

  == domain 12  score: 22.5 bits;  conditional E-value: 1.7e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                                       al   G+a+  lg+y+eA e++e+Al+
  gi|330509110|ref|YP_004385538.1| 586 ALIGKGMALDSLGRYDEAQEDYEQALK 612
                                       78999*********************8 PP

  == domain 13  score: 25.2 bits;  conditional E-value: 2.4e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a++ yn+G+a++ l++++e l+a+++A+el+P+
  gi|330509110|ref|YP_004385538.1| 625 AQVMYNQGNALRGLQRHNESLQAYDRAIELNPG 657
                                       6789****************************7 PP

  == domain 14  score: -1.5 bits;  conditional E-value: 8.7
                             TPR_2   2 ealynlGlayyklgdyeeAlea 23 
                                       +a+   + ++++lg  +eA+ea
  gi|330509110|ref|YP_004385538.1| 660 DAWRGKAIVLRALGGNAEAEEA 681
                                       6899999999999988888876 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.047        21      16      34 .]      44      62 ..      29      62 .. 0.76
   2 ?    2.1   0.1      0.67   2.9e+02       2      30 ..      64      92 ..      63      96 .. 0.88
   3 !    9.4   0.0    0.0029       1.3       2      30 ..     105     133 ..     104     133 .. 0.95
   4 !   17.9   0.1   5.7e-06    0.0025       1      32 [.     145     176 ..     145     178 .. 0.95
   5 ?   -1.4   0.0       8.8   3.9e+03      15      26 ..     247     258 ..     244     262 .. 0.82
   6 !   16.5   0.0   1.6e-05    0.0071       4      33 ..     332     361 ..     330     362 .. 0.96
   7 !   20.2   0.0     1e-06   0.00045       3      33 ..     365     395 ..     365     396 .. 0.95
   8 !   15.4   0.3   3.6e-05     0.016       4      31 ..     403     430 ..     403     433 .. 0.93
   9 ?    6.8   0.0     0.021         9       3      33 ..     448     478 ..     446     479 .. 0.88
  10 !   24.9   0.0   3.3e-08   1.5e-05       3      34 .]     482     514 ..     482     514 .. 0.95
  11 !   22.6   0.4   1.7e-07   7.5e-05       8      32 ..     522     546 ..     521     548 .. 0.94
  12 !   18.7   0.1   3.1e-06    0.0014       1      28 [.     549     576 ..     549     579 .. 0.96
  13 !   20.3   0.5   9.9e-07   0.00043       4      29 ..     587     612 ..     585     612 .. 0.91
  14 !   19.4   0.0   1.9e-06   0.00081       1      32 [.     625     656 ..     625     658 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.047
                                      -HHHHHHHHHHHHHHHHH. CS
                             TPR_8 16 dyeeAkeyyekaleldpdn 34
                                      +++eA e++  a++++p+n
  gi|330509110|ref|YP_004385538.1| 44 NIDEALEAFDNAIQIEPQN 62
                                      89***************86 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.67
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekalel 30
                                      +a++ +++ +  + +++e+ e+++  l l
  gi|330509110|ref|YP_004385538.1| 64 DAWLGKAKSLAYMDEKNESLEAFRNILNL 92
                                      7999*******************988876 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0029
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                       +a++ +g ++ +lg+  eA  ++e+ +el
  gi|330509110|ref|YP_004385538.1| 105 SAWQSKGIALASLGREAEATDAFERSIEL 133
                                       589************************97 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 5.7e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       aea+++++  ++ lg+ ++A e+y k++el+ 
  gi|330509110|ref|YP_004385538.1| 145 AEAWWLKAENLELLGRTDSALEAYDKVIELNS 176
                                       79****************************96 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 8.8
                                       T-HHHHHHHHHH CS
                             TPR_8  15 gdyeeAkeyyek 26 
                                       g+y+ ++++y  
  gi|330509110|ref|YP_004385538.1| 247 GRYNRSIQAYDD 258
                                       99******9975 PP

  == domain 6  score: 16.5 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++n g+ ++    +eeA +++ ka+e++++
  gi|330509110|ref|YP_004385538.1| 332 WFNRGQELQRNDSHEEALQAFDKAIEINQS 361
                                       9**************************975 PP

  == domain 7  score: 20.2 bits;  conditional E-value: 1e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+  +g+++ ++g+yeeA+++  +a+el+pd
  gi|330509110|ref|YP_004385538.1| 365 AWGGKGYVLYNMGRYEEAIAAWDRAIELEPD 395
                                       68899*************************8 PP

  == domain 8  score: 15.4 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleld 31 
                                       + ++g+++  lg+ ee+ ++ye+alel+
  gi|330509110|ref|YP_004385538.1| 403 WEMKGKVLAILGRNEESAQAYERALELA 430
                                       6799**********************98 PP

  == domain 9  score: 6.8 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+  +g++++++g+y eA e+     +++p+
  gi|330509110|ref|YP_004385538.1| 448 AWGFKGQLLDDQGRYVEALEAVANSSKANPE 478
                                       899****************998888888886 PP

  == domain 10  score: 24.9 bits;  conditional E-value: 3.3e-08
                                       HHHHHHHHH.HHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiy.lklgdyeeAkeyyekaleldpdn 34 
                                       a+  +g+i+ + lg+y+e++e+y+k le+dp+n
  gi|330509110|ref|YP_004385538.1| 482 AWAVMGDILaDRLGRYNESIESYNKSLEIDPKN 514
                                       69999*9999*********************97 PP

  == domain 11  score: 22.6 bits;  conditional E-value: 1.7e-07
                                       HHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyyekaleldp 32 
                                       g+++ +lg+yeeA eyy++ale+d 
  gi|330509110|ref|YP_004385538.1| 522 GYALASLGRYEEALEYYNRALEIDS 546
                                       8999*******************96 PP

  == domain 12  score: 18.7 bits;  conditional E-value: 3.1e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekal 28 
                                       a+a++ lg++++++g y+e++++y +a+
  gi|330509110|ref|YP_004385538.1| 549 ARAWQGLGDALRNMGMYNESIQAYDRAI 576
                                       79************************98 PP

  == domain 13  score: 20.3 bits;  conditional E-value: 9.9e-07
                                       HHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekale 29 
                                       +  +g+++++lg+y+eA+e ye+al+
  gi|330509110|ref|YP_004385538.1| 587 LIGKGMALDSLGRYDEAQEDYEQALK 612
                                       6679********************97 PP

  == domain 14  score: 19.4 bits;  conditional E-value: 1.9e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+++yn g++++ l++++e+ ++y +a+el+p
  gi|330509110|ref|YP_004385538.1| 625 AQVMYNQGNALRGLQRHNESLQAYDRAIELNP 656
                                       6899***************************9 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.5   5.9e-06    0.0026      10      36 ..      45      71 ..      44      75 .. 0.89
   2 ?    3.8   0.1      0.11        47      10      33 ..     127     150 ..     125     153 .. 0.89
   3 !    9.2   0.0    0.0021      0.94       7      26 ..     158     177 ..     157     179 .. 0.90
   4 ?    0.0   0.0       1.6   7.1e+02       8      18 ..     247     257 ..     242     261 .. 0.85
   5 !   19.3   0.4   1.5e-06   0.00067      10      42 .]     345     377 ..     336     377 .. 0.93
   6 !   25.6   0.2   1.6e-08   7.1e-06       1      26 [.     370     395 ..     370     398 .. 0.95
   7 !   12.3   0.4   0.00024       0.1       1      23 [.     407     429 ..     407     435 .. 0.93
   8 ?    1.2   0.0      0.68     3e+02      11      28 ..     431     448 ..     430     451 .. 0.83
   9 ?    1.3   0.1      0.63   2.8e+02       3      31 ..     455     483 ..     453     492 .. 0.70
  10 !   22.3   0.1   1.7e-07   7.4e-05       7      30 ..     494     517 ..     487     520 .. 0.87
  11 !   36.2   0.8   7.9e-12   3.4e-09       1      42 []     522     563 ..     522     563 .. 0.96
  12 !   14.4   0.2     5e-05     0.022       1      28 [.     556     583 ..     556     585 .. 0.90
  13 !   18.8   1.5   2.1e-06   0.00094       6      38 ..     603     635 ..     593     636 .. 0.95
  14 !   22.4   0.2   1.6e-07   6.9e-05       1      38 [.     632     669 ..     632     673 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.9e-06
                            TPR_11 10 yeeAieaYkkAlkldPdnaeayynLGl 36
                                      ++eA+ea+ +A+++ P+n +a+++ ++
  gi|330509110|ref|YP_004385538.1| 45 IDEALEAFDNAIQIEPQNIDAWLGKAK 71
                                      79*******************987665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.11
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayyn 33 
                                       +e +ie +++ l  dP++aea++ 
  gi|330509110|ref|YP_004385538.1| 127 FERSIELLNQSLLNDPKDAEAWWL 150
                                       688999****************96 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0021
                            TPR_11   7 qGkyeeAieaYkkAlkldPd 26 
                                       +G+ + A+eaY k ++l+++
  gi|330509110|ref|YP_004385538.1| 158 LGRTDSALEAYDKVIELNSS 177
                                       699**************987 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 1.6
                            TPR_11   8 GkyeeAieaYk 18 
                                       G+y+ +i+aY 
  gi|330509110|ref|YP_004385538.1| 247 GRYNRSIQAYD 257
                                       9*********6 PP

  == domain 5  score: 19.3 bits;  conditional E-value: 1.5e-06
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                        eeA++a+ kA+++++++a a+ + G+++y++G
  gi|330509110|ref|YP_004385538.1| 345 HEEALQAFDKAIEINQSYAFAWGGKGYVLYNMG 377
                                       79*****************************98 PP

  == domain 6  score: 25.6 bits;  conditional E-value: 1.6e-08
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPd 26 
                                       G+++y  G+yeeAi+a+ +A++l Pd
  gi|330509110|ref|YP_004385538.1| 370 GYVLYNMGRYEEAIAAWDRAIELEPD 395
                                       899**********************9 PP

  == domain 7  score: 12.3 bits;  conditional E-value: 0.00024
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                       G+++  +G++ee+ +aY++Al+l
  gi|330509110|ref|YP_004385538.1| 407 GKVLAILGRNEESAQAYERALEL 429
                                       889999***************98 PP

  == domain 8  score: 1.2 bits;  conditional E-value: 0.68
                            TPR_11  11 eeAieaYkkAlkldPdna 28 
                                       ++A+++Yk+  +l+ + a
  gi|330509110|ref|YP_004385538.1| 431 DKAVTEYKTSTDLNLSAA 448
                                       79*******999986655 PP

  == domain 9  score: 1.3 bits;  conditional E-value: 0.63
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeay 31 
                                       ++ +qG+y eA+ea  +  k +P++a a+
  gi|330509110|ref|YP_004385538.1| 455 LLDDQGRYVEALEAVANSSKANPEDAFAW 483
                                       5558********98766666666666665 PP

  == domain 10  score: 22.3 bits;  conditional E-value: 1.7e-07
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaea 30 
                                       +G+y+e+ie+Y+k l++dP+n  a
  gi|330509110|ref|YP_004385538.1| 494 LGRYNESIESYNKSLEIDPKNIGA 517
                                       6********************866 PP

  == domain 11  score: 36.2 bits;  conditional E-value: 7.9e-12
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+a+ ++G+yeeA+e Y++Al++d+ +a+a+ +LG+a+ ++G
  gi|330509110|ref|YP_004385538.1| 522 GYALASLGRYEEALEYYNRALEIDSRFARAWQGLGDALRNMG 563
                                       899**********************************97776 PP

  == domain 12  score: 14.4 bits;  conditional E-value: 5e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdna 28 
                                       Gda++  G y+e+i+aY +A++  P+++
  gi|330509110|ref|YP_004385538.1| 556 GDALRNMGMYNESIQAYDRAIAEMPQQP 583
                                       9********************9777766 PP

  == domain 13  score: 18.8 bits;  conditional E-value: 2.1e-06
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       +q +ye+A+++Y   +k +P na + yn G+a+
  gi|330509110|ref|YP_004385538.1| 603 AQEDYEQALKDYDDVIKKNPRNAQVMYNQGNAL 635
                                       5889**************************996 PP

  == domain 14  score: 22.4 bits;  conditional E-value: 1.6e-07
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       G+a++ +++ +e+++aY +A++l+P + +a+ + + ++
  gi|330509110|ref|YP_004385538.1| 632 GNALRGLQRHNESLQAYDRAIELNPGYIDAWRGKAIVL 669
                                       9*****************************98877776 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     5e-05     0.022       3      43 ..      28      71 ..      26      72 .. 0.88
   2 !   13.5   0.9   0.00022     0.098       8      42 ..     111     152 ..     104     154 .. 0.61
   3 !   14.9   0.2   7.9e-05     0.035       1      42 [.     145     187 ..     145     189 .. 0.88
   4 ?    0.4   0.0       3.8   1.7e+03      14      42 ..     246     276 ..     241     278 .. 0.74
   5 !    9.2   0.0    0.0055       2.4       3      39 ..     331     367 ..     329     372 .. 0.85
   6 !   14.0   0.1   0.00015     0.068       8      34 ..     370     396 ..     365     398 .. 0.90
   7 !   10.2   0.1    0.0026       1.2       6      32 ..     405     431 ..     402     438 .. 0.87
   8 !   10.6   0.1    0.0019      0.85       4      43 ..     449     488 ..     446     489 .. 0.89
   9 !   10.7   0.0    0.0018       0.8       3      39 ..     482     519 ..     482     524 .. 0.88
  10 !   20.6   1.7   1.2e-06   0.00052       8      43 ..     522     557 ..     516     558 .. 0.91
  11 !   15.6   0.2   4.8e-05     0.021       2      36 ..     550     584 ..     549     589 .. 0.89
  12 !   13.2   0.1   0.00029      0.12       3      37 ..     593     627 ..     592     632 .. 0.90
  13 !   13.8   0.1   0.00019     0.082       8      42 ..     632     666 ..     626     669 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5e-05
                            TPR_14  3 allalaeallalG...dpdeAiallrralalaPddaeawlllaq 43
                                       +++ ++ l a G   + deA+++++ a++  P++ +awl  a+
  gi|330509110|ref|YP_004385538.1| 28 DWYKKGQSLIATGfgyNIDEALEAFDNAIQIEPQNIDAWLGKAK 71
                                      68888999999886667**********************99886 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00022
                            TPR_14   8 aeallalGdpdeAiallrrala.......laPddaeawllla 42 
                                       + al+ lG+ +eA ++++r ++        +P+daeaw l a
  gi|330509110|ref|YP_004385538.1| 111 GIALASLGREAEATDAFERSIEllnqsllNDPKDAEAWWLKA 152
                                       5555555555555555555555444444389*******8777 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 7.9e-05
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPdda.eawllla 42 
                                       +ea+++ ae l+ lG++d A+++++++++l+ ++a  aw++  
  gi|330509110|ref|YP_004385538.1| 145 AEAWWLKAENLELLGRTDSALEAYDKVIELNSSEAvGAWIRKS 187
                                       589***************************9877637998865 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 3.8
                            TPR_14  14 lGdpdeAiallrralalaPdd..aeawllla 42 
                                        G++ ++i+++++++++  ++   +aw   +
  gi|330509110|ref|YP_004385538.1| 246 FGRYNRSIQAYDDLVQTRTKSglFAAWQNKG 276
                                       6899999*******99987773346666655 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0055
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                        +  +++ l +++ ++eA++++++a++ + + a aw 
  gi|330509110|ref|YP_004385538.1| 331 DWFNRGQELQRNDSHEEALQAFDKAIEINQSYAFAWG 367
                                       6777899999*****************9999888886 PP

  == domain 6  score: 14.0 bits;  conditional E-value: 0.00015
                            TPR_14   8 aeallalGdpdeAiallrralalaPdd 34 
                                       + +l++ G+++eAia+ +ra++l Pd+
  gi|330509110|ref|YP_004385538.1| 370 GYVLYNMGRYEEAIAAWDRAIELEPDE 396
                                       7899*********************96 PP

  == domain 7  score: 10.2 bits;  conditional E-value: 0.0026
                            TPR_14   6 alaeallalGdpdeAiallrralalaP 32 
                                       + +++l+ lG+ +e++++++ral+la 
  gi|330509110|ref|YP_004385538.1| 405 MKGKVLAILGRNEESAQAYERALELAD 431
                                       6689*******************9875 PP

  == domain 8  score: 10.6 bits;  conditional E-value: 0.0019
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +   +++l  +G++ eA+++     +++P+da aw  +++
  gi|330509110|ref|YP_004385538.1| 449 WGFKGQLLDDQGRYVEALEAVANSSKANPEDAFAWAVMGD 488
                                       555689999***************************9987 PP

  == domain 9  score: 10.7 bits;  conditional E-value: 0.0018
                            TPR_14   3 allalaeall.alGdpdeAiallrralalaPddaeawl 39 
                                       a++ ++++l+ +lG++ e+i+ +++ l+ +P++  a++
  gi|330509110|ref|YP_004385538.1| 482 AWAVMGDILAdRLGRYNESIESYNKSLEIDPKNIGALR 519
                                       7888999886489********************98875 PP

  == domain 10  score: 20.6 bits;  conditional E-value: 1.2e-06
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       + al+ lG+++eA+++++ral+ +  +a+aw  l++
  gi|330509110|ref|YP_004385538.1| 522 GYALASLGRYEEALEYYNRALEIDSRFARAWQGLGD 557
                                       68999***************************9986 PP

  == domain 11  score: 15.6 bits;  conditional E-value: 4.8e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddae 36 
                                       +a++ l++al++ G + e+i++++ra+a  P++++
  gi|330509110|ref|YP_004385538.1| 550 RAWQGLGDALRNMGMYNESIQAYDRAIAEMPQQPQ 584
                                       89**************************8888775 PP

  == domain 12  score: 13.2 bits;  conditional E-value: 0.00029
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaea 37 
                                       al  l+++ +a++d+++A++ ++++++++P +a++
  gi|330509110|ref|YP_004385538.1| 593 ALDSLGRYDEAQEDYEQALKDYDDVIKKNPRNAQV 627
                                       677899*************************9976 PP

  == domain 13  score: 13.8 bits;  conditional E-value: 0.00019
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                                       + al+ l+++ e++++++ra++l+P+  +aw+  a
  gi|330509110|ref|YP_004385538.1| 632 GNALRGLQRHNESLQAYDRAIELNPGYIDAWRGKA 666
                                       7899999************************9876 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.077        34      12      44 ..      44      73 ..      44      74 .. 0.91
   2 ?    8.0   0.0      0.01       4.4      21      62 ..      94     132 ..      90     137 .. 0.86
   3 !   23.6   0.5   1.3e-07   5.9e-05       3      64 ..     117     175 ..     116     179 .. 0.88
   4 ?   -1.3   0.0       8.3   3.6e+03       8      25 ..     244     261 ..     242     277 .. 0.73
   5 !   22.8   0.7   2.5e-07   0.00011       2      65 ..     334     394 ..     333     397 .. 0.87
   6 !   27.3   1.3   9.7e-09   4.2e-06       4      66 ..     370     432 ..     368     434 .. 0.93
   7 !   13.6   0.5   0.00019     0.083      14      64 ..     431     476 ..     430     480 .. 0.80
   8 !   21.6   0.1   5.9e-07   0.00026       4      67 ..     453     514 ..     452     515 .. 0.94
   9 !   28.8   3.9   3.2e-09   1.4e-06       3      68 .]     521     583 ..     519     586 .. 0.93
  10 !   38.3   0.6   3.4e-12   1.5e-09       3      66 ..     597     657 ..     588     659 .. 0.96
  11 !   17.1   2.8   1.5e-05    0.0066       1      56 [.     629     682 ..     629     687 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.077
                            TPR_16 12 dyddAaaaleaalkrdpssPdaaeAllllgdaa 44
                                      + d+A++a++ a+      P++ +A+l+++ ++
  gi|330509110|ref|YP_004385538.1| 44 NIDEALEAFDNAIQIE---PQNIDAWLGKAKSL 73
                                      579*************...*********99876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.01
                            TPR_16  21 eaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       ++++k +   P++  A+  +g a++ +gr aeA +++++ ++
  gi|330509110|ref|YP_004385538.1|  94 NETIKEN---PEDTSAWQSKGIALASLGREAEATDAFERSIE 132
                                       6788999...************************99998765 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 1.3e-07
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                       l+r+a +   +++ +++l++ l +d   P +aeA++l+++ +  +gr + A+++y++ ++  
  gi|330509110|ref|YP_004385538.1| 117 LGREAEATDAFERSIELLNQSLLND---PKDAEAWWLKAENLELLGRTDSALEAYDKVIELN 175
                                       56777777779**************...***************************9987665 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 8.3
                            TPR_16   8 lragdyddAaaaleaalk 25 
                                       ++ g+y + + a++ ++ 
  gi|330509110|ref|YP_004385538.1| 244 VDFGRYNRSIQAYDDLVQ 261
                                       567888888888887765 PP

  == domain 5  score: 22.8 bits;  conditional E-value: 2.5e-07
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyraalraap 65 
                                       ++++++ r+   ++A+ a++ a++ +      a A+ ++g +++  gr++eA+ a+ r a++  p
  gi|330509110|ref|YP_004385538.1| 334 NRGQELQRNDSHEEALQAFDKAIEIN---QSYAFAWGGKGYVLYNMGRYEEAIaAWDR-AIELEP 394
                                       68999999999***************...************************55555.556555 PP

  == domain 6  score: 27.3 bits;  conditional E-value: 9.7e-09
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++ +++ g+y++A+aa+++a+++    Pd       +  +g +++ +gr +e a++y++al+ a +
  gi|330509110|ref|YP_004385538.1| 370 GYVLYNMGRYEEAIAAWDRAIELE---PDefySGSKWEMKGKVLAILGRNEESAQAYERALELADK 432
                                       8899********************...998989999*************************98865 PP

  == domain 7  score: 13.6 bits;  conditional E-value: 0.00019
                            TPR_16  14 ddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyraalraa 64 
                                       d+A+  +++ ++++       +A+ ++g+++  qgr+ eA+ a+ ++  +a 
  gi|330509110|ref|YP_004385538.1| 431 DKAVTEYKTSTDLN-----LSAAWGFKGQLLDDQGRYVEALeAVANSS-KAN 476
                                       56778888888888.....889*******************7777766.444 PP

  == domain 8  score: 21.6 bits;  conditional E-value: 5.9e-07
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaal.rqgrlaeAaalyraalraapda 67 
                                       ++++ ++g+y +A++a     k++   P++a A+   gd+++ r+gr+ e ++ y++ l+ +p++
  gi|330509110|ref|YP_004385538.1| 453 GQLLDDQGRYVEALEAVANSSKAN---PEDAFAWAVMGDILAdRLGRYNESIESYNKSLEIDPKN 514
                                       78999*******************...88888**********888****************9986 PP

  == domain 9  score: 28.8 bits;  conditional E-value: 3.2e-09
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       +++a++ +g+y++A++++++al+ d   ++ a+A+ +lgda+   g + e +++y++a+++ p+ p
  gi|330509110|ref|YP_004385538.1| 521 EGYALASLGRYEEALEYYNRALEID---SRFARAWQGLGDALRNMGMYNESIQAYDRAIAEMPQQP 583
                                       6899*********************...******************************97766655 PP

  == domain 10  score: 38.3 bits;  conditional E-value: 3.4e-12
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       l+r+  ++ dy++A++ ++ ++k++   P++a+ +++ g+a+  ++r+ e +++y++a++  p+
  gi|330509110|ref|YP_004385538.1| 597 LGRYDEAQEDYEQALKDYDDVIKKN---PRNAQVMYNQGNALRGLQRHNESLQAYDRAIELNPG 657
                                       7899999******************...*******************************99998 PP

  == domain 11  score: 17.1 bits;  conditional E-value: 1.5e-05
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.al 56 
                                       +++++a++ +++  + + a+++a++++   P   +A+ +++ ++ ++g  aeA+ a 
  gi|330509110|ref|YP_004385538.1| 629 YNQGNALRGLQRHNESLQAYDRAIELN---PGYIDAWRGKAIVLRALGGNAEAEeAS 682
                                       89*************************...*****************9999999555 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       1.8   7.7e+02      19      45 ..      45      70 ..      44      76 .. 0.74
   2 !   15.4   0.2   3.8e-05     0.016      10      76 ..      70     135 ..      61     136 .. 0.85
   3 !   23.4   1.0   1.2e-07   5.5e-05       8      74 ..     109     174 ..     102     177 .. 0.89
   4 !   10.0   0.1    0.0019      0.82      44      76 ..     328     360 ..     315     361 .. 0.77
   5 !   22.3   1.4   2.6e-07   0.00012       5      76 ..     365     431 ..     361     432 .. 0.90
   6 !   14.4   1.6   7.8e-05     0.034       9      66 ..     406     467 ..     398     470 .. 0.79
   7 !   18.7   0.0   3.7e-06    0.0016       9      76 ..     452     512 ..     444     513 .. 0.78
   8 !   34.1   1.4   5.8e-11   2.5e-08       9      75 ..     486     545 ..     478     547 .. 0.89
   9 !   26.9   4.5     1e-08   4.5e-06      10      73 ..     522     577 ..     515     581 .. 0.85
  10 !   27.5   1.9   6.7e-09   2.9e-06       3      73 ..     549     612 ..     547     616 .. 0.91
  11 !   35.4   1.4   2.2e-11   9.4e-09       6      74 ..     587     654 ..     581     656 .. 0.92
  12 ?    5.4   0.1      0.05        22       5      32 ..     661     688 ..     657     690 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.8
                            TPR_12 19 ydeAlellekaleia.rrllGpdhplta 45
                                       deAle ++ a++i  +++  + +++ a
  gi|330509110|ref|YP_004385538.1| 45 IDEALEAFDNAIQIEpQNI--DAWLGKA 70
                                      69*********99976666..5555555 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 3.8e-05
                            TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a  l+++ +  e+le ++  l++ +++  +++p+  ++ +  g+++  lgr +eA +++e++++++ 
  gi|330509110|ref|YP_004385538.1|  70 AKSLAYMDEKNESLEAFRNILNLTNETI-KENPEDTSAWQSKGIALASLGREAEATDAFERSIELLN 135
                                       55555555556*************8886.789********************************976 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 1.2e-07
                            TPR_12   8 nlaavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                         + +l+ lgr +eA + +e+++e+  ++l   + p  a++    ++ +++lgr++ Ale++ +++++
  gi|330509110|ref|YP_004385538.1| 109 SKGIALASLGREAEATDAFERSIELLnQSL--LNDPKDAEAWWLKAENLELLGRTDSALEAYDKVIEL 174
                                       579999********************5555..67899***************************9987 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0019
                            TPR_12  44 tattlrnLgrlyralgryeeAlelleealaiae 76 
                                        a+  +n g+ +++ + +eeAl+++ +a++i +
  gi|330509110|ref|YP_004385538.1| 328 SAEDWFNRGQELQRNDSHEEALQAFDKAIEINQ 360
                                       577788999999999999999999999999865 PP

  == domain 5  score: 22.3 bits;  conditional E-value: 2.6e-07
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a+   + vl+ +gry+eA++  ++a+e+      pd  +  +     g ++  lgr ee  +++e+al++a 
  gi|330509110|ref|YP_004385538.1| 365 AWGGKGYVLYNMGRYEEAIAAWDRAIELE-----PDEFYSGSKWEMKGKVLAILGRNEESAQAYERALELAD 431
                                       677899*******************9999.....77777888899************************986 PP

  == domain 6  score: 14.4 bits;  conditional E-value: 7.8e-05
                            TPR_12   9 laavlrrlgrydeAlellekaleia.rrl...lGpdhpltattlrnLgrlyralgryeeAle 66 
                                        + vl+ lgr +e+ + +e+ale+a +++      + ++++++    g+l++ +gry eAle
  gi|330509110|ref|YP_004385538.1| 406 KGKVLAILGRNEESAQAYERALELAdKAVteyKTSTDLNLSAAWGFKGQLLDDQGRYVEALE 467
                                       578999999999999999999999944442102344588899999999*********99998 PP

  == domain 7  score: 18.7 bits;  conditional E-value: 3.7e-06
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrly.ralgryeeAlelleealaiae 76 
                                        +++l  +gry eAle    +         + +p+ a +   +g+++ ++lgry e +e ++++l+i++
  gi|330509110|ref|YP_004385538.1| 452 KGQLLDDQGRYVEALEAVANSS--------KANPEDAFAWAVMGDILaDRLGRYNESIESYNKSLEIDP 512
                                       6667777777777777777772........556778**********857*****************986 PP

  == domain 8  score: 34.1 bits;  conditional E-value: 5.8e-11
                            TPR_12   9 laavlrr.lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       ++++l+  lgry e++e ++k+lei      p++   + +lr+ g ++  lgryeeAle++++al+i+
  gi|330509110|ref|YP_004385538.1| 486 MGDILADrLGRYNESIESYNKSLEID-----PKN---IGALRGEGYALASLGRYEEALEYYNRALEID 545
                                       67777444******************.....998...559**************************96 PP

  == domain 9  score: 26.9 bits;  conditional E-value: 1e-08
                            TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       + +l+ lgry+eAle++++alei +r         a++ ++Lg+++r +g y e ++++ +a+a
  gi|330509110|ref|YP_004385538.1| 522 GYALASLGRYEEALEYYNRALEIDSRF--------ARAWQGLGDALRNMGMYNESIQAYDRAIA 577
                                       678999******************887........67888888888888888888888888875 PP

  == domain 10  score: 27.5 bits;  conditional E-value: 6.7e-09
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       a+a+  l+++lr +g y e+++ +++a++ +     p+ p++  +l++ g++++ lgry+eA+e +e+al+
  gi|330509110|ref|YP_004385538.1| 549 ARAWQGLGDALRNMGMYNESIQAYDRAIAEM-----PQQPQY--ALIGKGMALDSLGRYDEAQEDYEQALK 612
                                       677757*********************7777.....999998..*************************97 PP

  == domain 11  score: 35.4 bits;  conditional E-value: 2.2e-11
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       l   +++l  lgrydeA+e +e+al  +  +  +++p  a++++n g ++r l r+ e l+++ +a+++
  gi|330509110|ref|YP_004385538.1| 587 LIGKGMALDSLGRYDEAQEDYEQALKDYDDVI-KKNPRNAQVMYNQGNALRGLQRHNESLQAYDRAIEL 654
                                       5578999999******************8885.789******************************997 PP

  == domain 12  score: 5.4 bits;  conditional E-value: 0.05
                            TPR_12   5 alnnlaavlrrlgrydeAlellekalei 32 
                                       a++  a vlr+lg  +eA+e   ka+++
  gi|330509110|ref|YP_004385538.1| 661 AWRGKAIVLRALGGNAEAEEASAKAMDL 688
                                       5666788888888888888888888875 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0057       2.5       2      25 ..      52      78 ..      51      86 .. 0.80
   2 !    8.0   0.0    0.0094       4.1       5      32 ..      96     123 ..      93     124 .. 0.91
   3 !   10.0   0.2    0.0021      0.92       2      34 .]     134     166 ..     133     166 .. 0.92
   4 ?    2.9   0.0      0.39   1.7e+02      11      34 .]     327     350 ..     324     350 .. 0.90
   5 !   18.1   0.0   5.8e-06    0.0025       2      33 ..     352     383 ..     351     384 .. 0.95
   6 ?   -0.7   0.0       5.7   2.5e+03       3      13 ..     387     397 ..     385     421 .. 0.70
   7 ?    0.3   0.0       2.6   1.1e+03      19      34 .]     452     467 ..     444     467 .. 0.87
   8 ?    5.4   0.0     0.065        29       7      33 ..     474     501 ..     470     502 .. 0.84
   9 !   15.0   0.0   5.4e-05     0.024       2      34 .]     504     536 ..     503     536 .. 0.97
  10 !   15.6   0.1   3.5e-05     0.015       1      34 []     537     570 ..     537     570 .. 0.94
  11 ?    1.9   0.1      0.85   3.7e+02      15      34 .]     586     605 ..     571     605 .. 0.82
  12 !   15.0   0.1   5.4e-05     0.024       2      29 ..     614     641 ..     613     646 .. 0.83
  13 !   19.0   0.0   2.9e-06    0.0013       1      34 []     647     680 ..     647     680 .. 0.96

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0057
                            TPR_17  2 ylkaleldPnnadaynnLAelll...k 25
                                      + +a++++P n da+  +A+ l+   +
  gi|330509110|ref|YP_004385538.1| 52 FDNAIQIEPQNIDAWLGKAKSLAymdE 78
                                      789****************99884443 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0094
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmtA 32 
                                        ++ +P +  a++ ++ +l+++G+ ++A
  gi|330509110|ref|YP_004385538.1|  96 TIKENPEDTSAWQSKGIALASLGREAEA 123
                                       6999*******************98877 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0021
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + ++l +dP++a+a+ ++Ae l+ +G+++ A++
  gi|330509110|ref|YP_004385538.1| 134 LNQSLLNDPKDAEAWWLKAENLELLGRTDSALE 166
                                       6789************************99975 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.39
                            TPR_17  11 nnadaynnLAelllknGdlmtArq 34 
                                       n+a+ ++n+++ l +n  +++A+q
  gi|330509110|ref|YP_004385538.1| 327 NSAEDWFNRGQELQRNDSHEEALQ 350
                                       78999**********999999987 PP

  == domain 5  score: 18.1 bits;  conditional E-value: 5.8e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + ka+e++ ++a a+  ++++l++ G++++A+
  gi|330509110|ref|YP_004385538.1| 352 FDKAIEINQSYAFAWGGKGYVLYNMGRYEEAI 383
                                       89*****************************8 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 5.7
                            TPR_17   3 lkaleldPnna 13 
                                        +a+el+P+ +
  gi|330509110|ref|YP_004385538.1| 387 DRAIELEPDEF 397
                                       58888888754 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 2.6
                            TPR_17  19 LAelllknGdlmtArq 34 
                                       +++ll  +G++ +A++
  gi|330509110|ref|YP_004385538.1| 452 KGQLLDDQGRYVEALE 467
                                       699**********985 PP

  == domain 8  score: 5.4 bits;  conditional E-value: 0.065
                            TPR_17   7 eldPnnadaynnLAelll.knGdlmtAr 33 
                                       + +P +a a+  ++ +l+ ++G++ + +
  gi|330509110|ref|YP_004385538.1| 474 KANPEDAFAWAVMGDILAdRLGRYNESI 501
                                       78***************86779998765 PP

  == domain 9  score: 15.0 bits;  conditional E-value: 5.4e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y k+le+dP+n  a+   +++l+++G++++A++
  gi|330509110|ref|YP_004385538.1| 504 YNKSLEIDPKNIGALRGEGYALASLGRYEEALE 536
                                       99*****************************85 PP

  == domain 10  score: 15.6 bits;  conditional E-value: 3.5e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +ale+d   a a++ L+ +l++ G + + +q
  gi|330509110|ref|YP_004385538.1| 537 YYNRALEIDSRFARAWQGLGDALRNMGMYNESIQ 570
                                       69*************************9998776 PP

  == domain 11  score: 1.9 bits;  conditional E-value: 0.85
                            TPR_17  15 aynnLAelllknGdlmtArq 34 
                                       a+  ++ +l ++G++++A++
  gi|330509110|ref|YP_004385538.1| 586 ALIGKGMALDSLGRYDEAQE 605
                                       666789999*********96 PP

  == domain 12  score: 15.0 bits;  conditional E-value: 5.4e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdl 29 
                                       y  +++++P na +++n +++l+ + ++
  gi|330509110|ref|YP_004385538.1| 614 YDDVIKKNPRNAQVMYNQGNALRGLQRH 641
                                       8999*****************9855544 PP

  == domain 13  score: 19.0 bits;  conditional E-value: 2.9e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a+el+P + da+  +A +l+ +G+ ++A++
  gi|330509110|ref|YP_004385538.1| 647 AYDRAIELNPGYIDAWRGKAIVLRALGGNAEAEE 680
                                       59*****************************986 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   5.8e-05     0.025       6      48 ..      44      86 ..      36      95 .. 0.83
   2 ?    3.5   0.0      0.23     1e+02       9      50 ..      88     129 ..      83     132 .. 0.83
   3 !   16.6   0.4   1.9e-05    0.0084       9      56 ..     129     176 ..     124     182 .. 0.88
   4 !   22.4   0.1   2.9e-07   0.00013       5      57 ..     343     395 ..     339     401 .. 0.93
   5 !   12.2   0.6   0.00047       0.2       4      66 ..     420     487 ..     419     489 .. 0.83
   6 !   15.6   0.0   3.9e-05     0.017       3      57 ..     458     513 ..     455     522 .. 0.93
   7 !   31.7   1.9   3.7e-10   1.6e-07       5      62 ..     529     586 ..     525     594 .. 0.95
   8 !    9.9   0.6    0.0023         1       3      39 ..     603     639 ..     596     646 .. 0.71
   9 !   16.8   0.4   1.6e-05     0.007       5      51 ..     639     685 ..     635     690 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.8e-05
                            TPR_19  6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealL 48
                                      + +eAl+++ +a+q +p+n +a+l+ A+ l  + + +e  ++ 
  gi|330509110|ref|YP_004385538.1| 44 NIDEALEAFDNAIQIEPQNIDAWLGKAKSLAYMDEKNESLEAF 86
                                      689**********************999887777777766665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.23
                            TPR_19   9 eAlalleqalqedpknaearllLAeallalgqldeAealLda 50 
                                       + l+l  + ++e+p++  a+    +al +lg+ +eA ++ ++
  gi|330509110|ref|YP_004385538.1|  88 NILNLTNETIKENPEDTSAWQSKGIALASLGREAEATDAFER 129
                                       55666667789*************************887765 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 1.9e-05
                            TPR_19   9 eAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                       + ++ll q l  dpk+aea+ l Ae l  lg++d A ++ d++ e + 
  gi|330509110|ref|YP_004385538.1| 129 RSIELLNQSLLNDPKDAEAWWLKAENLELLGRTDSALEAYDKVIELNS 176
                                       5589************************************99988765 PP

  == domain 4  score: 22.4 bits;  conditional E-value: 2.9e-07
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                         ++eAl+++ +a++ +  +a a+ +   +l+++g+++eA+a+ d++ e +pd
  gi|330509110|ref|YP_004385538.1| 343 DSHEEALQAFDKAIEINQSYAFAWGGKGYVLYNMGRYEEAIAAWDRAIELEPD 395
                                       5799************************************************9 PP

  == domain 5  score: 12.2 bits;  conditional E-value: 0.00047
                            TPR_19   4 egdyaeAlalleqalqedpknaearl....lL.AeallalgqldeAealLdalpeedpddaryasLlA 66 
                                       ++ y++Al+l  +a +e+  + ++ l    +   ++l  +g++ eA ++++   +++p da ++++++
  gi|330509110|ref|YP_004385538.1| 420 AQAYERALELADKAVTEYKTSTDLNLsaawGFkGQLLDDQGRYVEALEAVANSSKANPEDAFAWAVMG 487
                                       5789*************9997776664333337*************************9988877776 PP

  == domain 6  score: 15.6 bits;  conditional E-value: 3.9e-05
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallal.gqldeAealLdalpeedpd 57 
                                       ++g+y eAl++ ++  +++p++a a++ + ++l    g+++e ++  ++ +e dp+
  gi|330509110|ref|YP_004385538.1| 458 DQGRYVEALEAVANSSKANPEDAFAWAVMGDILADRlGRYNESIESYNKSLEIDPK 513
                                       69*******************************9888***************9998 PP

  == domain 7  score: 31.7 bits;  conditional E-value: 3.7e-10
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       g+y+eAl+++ +al+ d   a+a+ +L +al ++g ++e +++ d++ +e p++++ya
  gi|330509110|ref|YP_004385538.1| 529 GRYEEALEYYNRALEIDSRFARAWQGLGDALRNMGMYNESIQAYDRAIAEMPQQPQYA 586
                                       9********************************************************8 PP

  == domain 8  score: 9.9 bits;  conditional E-value: 0.0023
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalg 39 
                                       a++dy++Al+ +  +++++p na + ++  +al  l 
  gi|330509110|ref|YP_004385538.1| 603 AQEDYEQALKDYDDVIKKNPRNAQVMYNQGNALRGLQ 639
                                       5677777777777777889999998887666665555 PP

  == domain 9  score: 16.8 bits;  conditional E-value: 1.6e-05
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                       +++ e l+++ +a++ +p++ +a+ + A++l alg  +eAe++ +++
  gi|330509110|ref|YP_004385538.1| 639 QRHNESLQAYDRAIELNPGYIDAWRGKAIVLRALGGNAEAEEASAKA 685
                                       688899***********************************986655 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2     0.027        12       4      32 ..      30      61 ..       7      62 .. 0.85
   2 ?    3.1   0.1      0.41   1.8e+02       1      28 [.      64      91 ..      64      92 .. 0.92
   3 ?   -0.8   0.0       6.9     3e+03       8      26 ..     112     130 ..     110     133 .. 0.81
   4 !   10.5   0.0    0.0018      0.77       1      28 [.     146     173 ..     146     176 .. 0.91
   5 ?    0.4   0.0       2.9   1.3e+03      14      29 ..     247     262 ..     234     266 .. 0.85
   6 ?    1.8   0.0       1.1   4.7e+02      10      28 ..     339     357 ..     332     359 .. 0.72
   7 !   10.9   0.0    0.0013      0.58       7      32 ..     370     395 ..     368     396 .. 0.92
   8 ?    5.3   0.1     0.082        36       5      33 .]     412     440 ..     408     440 .. 0.82
   9 ?    0.2   0.0       3.4   1.5e+03      11      32 ..     491     513 ..     486     514 .. 0.77
  10 !    8.5   0.3    0.0081       3.5       7      28 ..     522     543 ..     517     545 .. 0.87
  11 ?    7.8   0.1     0.013       5.6       5      29 ..     554     578 ..     550     581 .. 0.89
  12 !   13.9   0.1   0.00015     0.065       1      32 [.     585     616 ..     585     622 .. 0.92
  13 !   11.2   0.1     0.001      0.46       1      32 [.     626     657 ..     626     658 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.027
                                      HHHHHHHHHH..H.HHHHHHHHHHHHHHH-TT CS
                             TPR_6  4 yklalsyrkl..g.dtdkAlealerlikeYPd 32
                                      yk ++s++++  g + d+Alea+++ i+  P+
  gi|330509110|ref|YP_004385538.1| 30 YKKGQSLIATgfGyNIDEALEAFDNAIQIEPQ 61
                                      777888887459779************99997 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.41
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  1 dAlyklalsyrklgdtdkAlealerlik 28
                                      dA +  a+s+  ++++ ++lea++++++
  gi|330509110|ref|YP_004385538.1| 64 DAWLGKAKSLAYMDEKNESLEAFRNILN 91
                                      789999*******9**********9986 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 6.9
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAlealerl 26 
                                        ++ +lg+ ++A +a+er 
  gi|330509110|ref|YP_004385538.1| 112 IALASLGREAEATDAFERS 130
                                       5677789*********985 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                       +A ++ a+ ++ lg+td Alea++++i+
  gi|330509110|ref|YP_004385538.1| 146 EAWWLKAENLELLGRTDSALEAYDKVIE 173
                                       68899999999999************98 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHHHHHHH CS
                             TPR_6  14 gdtdkAlealerlike 29 
                                       g++ ++++a+++l++ 
  gi|330509110|ref|YP_004385538.1| 247 GRYNRSIQAYDDLVQT 262
                                       7999*********986 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlealerlik 28 
                                       +++ + +++Al+a+++ i+
  gi|330509110|ref|YP_004385538.1| 339 LQRNDSHEEALQAFDKAIE 357
                                       44445789*******9997 PP

  == domain 7  score: 10.9 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       ++ ++++g++++A++a++r i+  Pd
  gi|330509110|ref|YP_004385538.1| 370 GYVLYNMGRYEEAIAAWDRAIELEPD 395
                                       78899999**************9998 PP

  == domain 8  score: 5.3 bits;  conditional E-value: 0.082
                                       HHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   5 klalsyrklgdtdkAlealerlikeYPdS 33 
                                        l++  ++++ +++Ale+ ++ ++eY +S
  gi|330509110|ref|YP_004385538.1| 412 ILGRNEESAQAYERALELADKAVTEYKTS 440
                                       67888888669************999665 PP

  == domain 9  score: 0.2 bits;  conditional E-value: 3.4
                                       HH.HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  11 rk.lgdtdkAlealerlikeYPd 32 
                                          lg++ +++e +++ ++  P+
  gi|330509110|ref|YP_004385538.1| 491 ADrLGRYNESIESYNKSLEIDPK 513
                                       43389*********998887776 PP

  == domain 10  score: 8.5 bits;  conditional E-value: 0.0081
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       ++++ +lg++++Ale+++r ++
  gi|330509110|ref|YP_004385538.1| 522 GYALASLGRYEEALEYYNRALE 543
                                       77888899***********986 PP

  == domain 11  score: 7.8 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlike 29 
                                        l+ ++r++g + ++++a++r i e
  gi|330509110|ref|YP_004385538.1| 554 GLGDALRNMGMYNESIQAYDRAIAE 578
                                       589******************9986 PP

  == domain 12  score: 13.9 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       +Al   ++++ +lg++d+A e +e+ +k+Y d
  gi|330509110|ref|YP_004385538.1| 585 YALIGKGMALDSLGRYDEAQEDYEQALKDYDD 616
                                       6888889*****99**************9965 PP

  == domain 13  score: 11.2 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       +++y+++ ++r l+++ ++l+a++r i+  P+
  gi|330509110|ref|YP_004385538.1| 626 QVMYNQGNALRGLQRHNESLQAYDRAIELNPG 657
                                       58*********977**************9985 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.16        71      12      56 ..      46      90 ..      42      99 .. 0.83
   2 !   10.4   0.0    0.0013      0.58      25      58 ..     100     133 ..      81     136 .. 0.88
   3 !   10.2   0.1    0.0015      0.65      11      60 ..     127     176 ..     126     185 .. 0.89
   4 ?    6.1   0.0     0.027        12      27      58 ..     327     358 ..     324     362 .. 0.91
   5 !   17.8   0.2   6.1e-06    0.0027       5      61 ..     339     395 ..     337     399 .. 0.97
   6 ?    1.9   0.1      0.55   2.4e+02      35      63 ..     406     434 ..     401     444 .. 0.82
   7 ?    3.9   0.0      0.14        60       8      62 ..     459     514 ..     454     521 .. 0.88
   8 !   20.5   1.4   9.2e-07    0.0004       6      68 ..     526     588 ..     522     590 .. 0.93
   9 ?    3.6   0.1      0.17        75      37      58 ..     592     613 ..     590     629 .. 0.59
  10 !    8.4   0.3    0.0053       2.3       9      48 ..     639     678 ..     631     688 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.16
                             TPR_9 12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl 56
                                      ++al++ +  +++ P+ ++ ++  +  la ++  ++ l+++   l
  gi|330509110|ref|YP_004385538.1| 46 DEALEAFDNAIQIEPQNIDAWLGKAKSLAYMDEKNESLEAFRNIL 90
                                      789999999999999999999999998888888888888877655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0013
                             TPR_9  25 aPddpeerrdRGlllaqlGclsaAladLeaylal 58 
                                       +P+d + +   G++la lG+ ++A +++e+ ++l
  gi|330509110|ref|YP_004385538.1| 100 NPEDTSAWQSKGIALASLGREAEATDAFERSIEL 133
                                       7****************************98775 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0015
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       +er ++ ++  ll +P+d+e ++  +  l+ lG++  Al++ +  ++l+ 
  gi|330509110|ref|YP_004385538.1| 127 FERSIELLNQSLLNDPKDAEAWWLKAENLELLGRTDSALEAYDKVIELNS 176
                                       57778889999******************************999998765 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.027
                             TPR_9  27 ddpeerrdRGlllaqlGclsaAladLeaylal 58 
                                       +++e+++ RG+ l++ +  ++Al++++ ++++
  gi|330509110|ref|YP_004385538.1| 327 NSAEDWFNRGQELQRNDSHEEALQAFDKAIEI 358
                                       789************************99986 PP

  == domain 5  score: 17.8 bits;  conditional E-value: 6.1e-06
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       ++r++ +e+al++ +  + ++   +  +   G +l+ +G++++A+a+ +++++l+pd
  gi|330509110|ref|YP_004385538.1| 339 LQRNDSHEEALQAFDKAIEINQSYAFAWGGKGYVLYNMGRYEEAIAAWDRAIELEPD 395
                                       5899****************************************************8 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.55
                             TPR_9  35 RGlllaqlGclsaAladLeaylalapdap 63 
                                        G +la lG+ ++ +++ e++l+la++a 
  gi|330509110|ref|YP_004385538.1| 406 KGKVLAILGRNEESAQAYERALELADKAV 434
                                       57788999999999999999999998765 PP

  == domain 7  score: 3.9 bits;  conditional E-value: 0.14
                             TPR_9   8 eedweralavverllllaPddpeerrdRGllla.qlGclsaAladLeaylalapda 62 
                                       + ++ +al++v      +P+d+  +   G +la +lG++++ ++  +  l+++p++
  gi|330509110|ref|YP_004385538.1| 459 QGRYVEALEAVANSSKANPEDAFAWAVMGDILAdRLGRYNESIESYNKSLEIDPKN 514
                                       5688999**********************9998689************99999976 PP

  == domain 8  score: 20.5 bits;  conditional E-value: 9.2e-07
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeai 68 
                                       ++  ++e+al++++r l ++++ ++ +   G +l  +G +++ +++ ++++a  p+ p+ ++i
  gi|330509110|ref|YP_004385538.1| 526 ASLGRYEEALEYYNRALEIDSRFARAWQGLGDALRNMGMYNESIQAYDRAIAEMPQQPQYALI 588
                                       566799**************************************************9997766 PP

  == domain 9  score: 3.6 bits;  conditional E-value: 0.17
                             TPR_9  37 lllaqlGclsaAladLeaylal 58 
                                       ++l  lG++ +A +d e++l  
  gi|330509110|ref|YP_004385538.1| 592 MALDSLGRYDEAQEDYEQALKD 613
                                       5566677777777777776633 PP

  == domain 10  score: 8.4 bits;  conditional E-value: 0.0053
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaA 48 
                                       +++ + l++++r + l+P  ++ +r  +++l  lG  ++A
  gi|330509110|ref|YP_004385538.1| 639 QRHNESLQAYDRAIELNPGYIDAWRGKAIVLRALGGNAEA 678
                                       788899************************9988865555 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.4   6.2e+02      14      35 ..     126     145 ..     108     146 .. 0.62
   2 ?    2.3   0.0      0.47   2.1e+02      12      31 ..     158     177 ..     153     180 .. 0.83
   3 ?   -1.3   0.0       6.9     3e+03      12      22 ..     349     359 ..     344     361 .. 0.66
   4 ?    4.1   0.0      0.13        56      10      31 ..     374     395 ..     365     397 .. 0.76
   5 ?    4.9   0.2     0.073        32      12      30 ..     413     431 ..     410     439 .. 0.89
   6 ?    1.9   0.1      0.64   2.8e+02       2      20 ..     449     467 ..     448     470 .. 0.86
   7 !    7.9   0.0    0.0078       3.4       5      29 ..     486     511 ..     482     515 .. 0.82
   8 !   15.2   0.5   3.7e-05     0.016       8      30 ..     524     546 ..     522     549 .. 0.87
   9 !    9.4   0.0    0.0026       1.1       2      27 ..     552     578 ..     551     584 .. 0.82
  10 !   11.0   0.1   0.00082      0.36       6      28 ..     591     611 ..     586     619 .. 0.83
  11 ?    1.9   0.0      0.64   2.8e+02       3      30 ..     629     654 ..     627     657 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.4
                             TPR_7  14 dyeeAielyeqsLaltkdpeda 35 
                                        +e+ iel+ q   l +dp da
  gi|330509110|ref|YP_004385538.1| 126 AFERSIELLNQ--SLLNDPKDA 145
                                       46677777777..666777665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.47
                             TPR_7  12 lGdyeeAielyeqsLaltkd 31 
                                       lG+++ A+e y ++++l ++
  gi|330509110|ref|YP_004385538.1| 158 LGRTDSALEAYDKVIELNSS 177
                                       89***********8887766 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 6.9
                             TPR_7  12 lGdyeeAiely 22 
                                       l+ +++Aie++
  gi|330509110|ref|YP_004385538.1| 349 LQAFDKAIEIN 359
                                       56678888765 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.13
                             TPR_7  10 srlGdyeeAielyeqsLaltkd 31 
                                        ++G+yeeAi    ++++l+ d
  gi|330509110|ref|YP_004385538.1| 374 YNMGRYEEAIAAWDRAIELEPD 395
                                       579*******998886666655 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.073
                             TPR_7  12 lGdyeeAielyeqsLaltk 30 
                                       lG+ ee ++ ye++L+l++
  gi|330509110|ref|YP_004385538.1| 413 LGRNEESAQAYERALELAD 431
                                       7999*********998874 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.64
                             TPR_7   2 LlnLarlysrlGdyeeAie 20 
                                       +   ++l  ++G+y eA+e
  gi|330509110|ref|YP_004385538.1| 449 WGFKGQLLDDQGRYVEALE 467
                                       5667999**********97 PP

  == domain 7  score: 7.9 bits;  conditional E-value: 0.0078
                             TPR_7   5 Larlysr.lGdyeeAielyeqsLalt 29 
                                       ++++  + lG+y e ie y +sL+++
  gi|330509110|ref|YP_004385538.1| 486 MGDILADrLGRYNESIESYNKSLEID 511
                                       77886666*************99986 PP

  == domain 8  score: 15.2 bits;  conditional E-value: 3.7e-05
                             TPR_7   8 lysrlGdyeeAielyeqsLaltk 30 
                                       +  +lG+yeeA+e+y ++L++++
  gi|330509110|ref|YP_004385538.1| 524 ALASLGRYEEALEYYNRALEIDS 546
                                       6789*************999886 PP

  == domain 9  score: 9.4 bits;  conditional E-value: 0.0026
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsL.a 27 
                                       +  L+++ +++G y e i+ y +++ +
  gi|330509110|ref|YP_004385538.1| 552 WQGLGDALRNMGMYNESIQAYDRAIaE 578
                                       5679*******************6544 PP

  == domain 10  score: 11.0 bits;  conditional E-value: 0.00082
                             TPR_7   6 arlysrlGdyeeAielyeqsLal 28 
                                       + +  +lG+y+eA e yeq  al
  gi|330509110|ref|YP_004385538.1| 591 GMALDSLGRYDEAQEDYEQ--AL 611
                                       567889*************..55 PP

  == domain 11  score: 1.9 bits;  conditional E-value: 0.64
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltk 30 
                                       +n +++ + l+++ e ++ y +  a++ 
  gi|330509110|ref|YP_004385538.1| 629 YNQGNALRGLQRHNESLQAYDR--AIEL 654
                                       5778888888888888888888..5544 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.2    0.0019      0.83      62     131 ..      70     135 ..      50     138 .. 0.78
   2 ?    3.3   0.0      0.18        80     105     129 ..     150     174 ..     143     184 .. 0.87
   3 !   10.0   2.9    0.0016      0.69      14     133 ..     313     433 ..     304     443 .. 0.73
   4 !   14.4   0.1     7e-05     0.031      54     129 ..     479     544 ..     467     549 .. 0.86
   5 !    9.9   0.0    0.0017      0.75      57     126 ..     551     610 ..     545     621 .. 0.82
   6 !   11.9   0.1   0.00042      0.18      63     129 ..     592     654 ..     585     666 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0019
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                           DUF3856  62 sealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagemia 131
                                       +++la + + +e+le+  + l+  n   + + ++ + W     s++ al++lGr++ea +af+ + e+++
  gi|330509110|ref|YP_004385538.1|  70 AKSLAYMDEKNESLEAFRNILNLTNETIKENPEDTSAW----QSKGIALASLGREAEATDAFERSIELLN 135
                                       55566666777777777777777777766666666666....68*********************99986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.18
                                       HHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrmagem 129
                                        +a  le lGr+d al+a+ ++ e+
  gi|330509110|ref|YP_004385538.1| 150 LKAENLELLGRTDSALEAYDKVIEL 174
                                       58999***************99987 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHT-HHHHHHH..HHHHHHHHTTS-TTS-...--H....HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  14 seaekqleegayeeaaas..yrkalevsrtipaeea...fdh....eGfdalchaglsealaklgrydealesadka 81 
                                        ++   l+eg++e+ +a+  +++  e+ r  ++eea   fd     +   a+++ g    l ++gry+ea+ + d+a
  gi|330509110|ref|YP_004385538.1| 313 INGSADLQEGSFEDNSAEdwFNRGQELQRNDSHEEAlqaFDKaieiNQSYAFAWGGKGYVLYNMGRYEEAIAAWDRA 389
                                       57888999****9865543379999****999999633355422223455777778888888888888888877777 PP

                                       HHHHHHH--TTSTH...HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH- CS
                           DUF3856  82 lryfnrrGeleqde...GklWiaavfsravaleelGrkdealkafrmagemiaer 133
                                       +       ele de   G++W      +++ l+ lGr++e+ +a++ a e+ +  
  gi|330509110|ref|YP_004385538.1| 390 I-------ELEPDEfysGSKWE----MKGKVLAILGRNEESAQAYERALELADKA 433
                                       6.......67777644488884....6999999**************99987655 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 7e-05
                                       HHHHHHHHHHHHH.HTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  54 dalchaglseala.klgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                       da+++a++ + la +lgry+e++es +k+l+        +     + i a+   + al++lGr++eal++++ a e+
  gi|330509110|ref|YP_004385538.1| 479 DAFAWAVMGDILAdRLGRYNESIESYNKSLEI-------DP----KNIGALRGEGYALASLGRYEEALEYYNRALEI 544
                                       9*********98757*********98888753.......32....359999999******************99985 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  57 chaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       ++ gl +al ++g y+e++++ d+a+       e+ q+       a++ +++al++lGr+dea + +++a
  gi|330509110|ref|YP_004385538.1| 551 AWQGLGDALRNMGMYNESIQAYDRAIA------EMPQQ----PQYALIGKGMALDSLGRYDEAQEDYEQA 610
                                       677899999999999999999999986......44443....3357899**************9999887 PP

  == domain 6  score: 11.9 bits;  conditional E-value: 0.00042
                                       HHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  63 ealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                        al  lgrydea e  ++al+ ++   + +        +++++++ al +l r++e+l+a+  a e+
  gi|330509110|ref|YP_004385538.1| 592 MALDSLGRYDEAQEDYEQALKDYDDVIKKNP----RNAQVMYNQGNALRGLQRHNESLQAYDRAIEL 654
                                       58889***************99975433333....346799********************999986 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.2     0.003       1.3       8      81 ..      13      88 ..       8      89 .. 0.85
   2 ?    4.2   0.0      0.12        50      39      81 ..     127     170 ..     112     206 .. 0.72
   3 !   12.4   0.1   0.00031      0.14      19      78 ..     325     385 ..     317     389 .. 0.86
   4 !   20.7   0.2   8.3e-07   0.00036       3      80 ..     421     505 ..     419     507 .. 0.87
   5 !   11.3   0.2   0.00072      0.32       3      75 ..     529     603 ..     527     610 .. 0.91
   6 ?    2.6   0.1      0.36   1.6e+02      36      81 ..     604     650 ..     602     651 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.003
                                      HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-...HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  8 AiflaerllaaetespedayllAlclylngq...ykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                      A+++a+ +  a+ + ++d y ++++l  +g     ++A+e +++a +++++++ +++ +A++l  +++ +e + a+ +
  gi|330509110|ref|YP_004385538.1| 13 AMLCASAM--AQEDTANDWYKKGQSLIATGFgynIDEALEAFDNAiQIEPQNIDAWLGKAKSLAYMDEKNESLEAFRN 88
                                      44444444..588889999999******99665599************************************999876 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.12
                                       HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  39 ykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++r +ell+++   ++k+ +++ l+A+ l  L++ + A+ a++k
  gi|330509110|ref|YP_004385538.1| 127 FERSIELLNQSlLNDPKDAEAWWLKAENLELLGRTDSALEAYDK 170
                                       55556666666555555556666666666666666666666554 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00031
                                       HH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  19 etespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       e +s+ed +  ++ l +n  +++A++ ++ka ++n +   ++  ++ +l+ +++yeeAiaa
  gi|330509110|ref|YP_004385538.1| 325 EDNSAEDWFNRGQELQRNDSHEEALQAFDKAiEINQSYAFAWGGKGYVLYNMGRYEEAIAA 385
                                       567777888889999****************888888888888888*************98 PP

  == domain 4  score: 20.7 bits;  conditional E-value: 8.3e-07
                                       T-HHHHHHHHHHHH....HHH--HHHHHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHH.HTT-H CS
                            ANAPC3   3 nnyknAiflaerll...aaetespedayl..lAlclylngqykrAyellrka.klnskslgcrylfAqcll.kLkky 72 
                                       ++y+ A+ la++++   +++t+ + +a +  +++ l  +g+y +A+e + ++ k n+++  ++ +++  l   L++y
  gi|330509110|ref|YP_004385538.1| 421 QAYERALELADKAVteyKTSTDLNLSAAWgfKGQLLDDQGRYVEALEAVANSsKANPEDAFAWAVMGDILAdRLGRY 497
                                       68************544466666666777767**************************************9899*** PP

                                       HHHHHHH- CS
                            ANAPC3  73 eeAiaaLe 80 
                                       +e i  + 
  gi|330509110|ref|YP_004385538.1| 498 NESIESYN 505
                                       **998776 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.00072
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHH.HTT-HHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcll.kLkkyeeA 75 
                                       ++y++A+ +++r+l+ +++ + +   l+ +l ++g y++ ++ +++a  + ++ ++++++    +l  L++y+eA
  gi|330509110|ref|YP_004385538.1| 529 GRYEEALEYYNRALEIDSRFARAWQGLGDALRNMGMYNESIQAYDRAiAEMPQQPQYALIGKGMALdSLGRYDEA 603
                                       689***********9999999999999********************9999999999999998888688*****9 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.36
                                       TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +++y++A++ +++  k+n+++ ++ y  + +l  L++++e ++a+++
  gi|330509110|ref|YP_004385538.1| 604 QEDYEQALKDYDDViKKNPRNAQVMYNQGNALRGLQRHNESLQAYDR 650
                                       78999********99999**999999999999999999999998875 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       6.9     3e+03      17      31 ..      44      58 ..      43      58 .. 0.87
   2 ?    6.5   0.0     0.019       8.2       9      36 ..     111     138 ..     110     144 .. 0.86
   3 ?    1.0   0.0         1   4.4e+02      15      31 ..     158     174 ..     153     182 .. 0.85
   4 ?    3.8   0.1      0.13        58      11      33 ..     338     360 ..     334     361 .. 0.82
   5 !   10.0   0.3    0.0015      0.64       9      31 ..     370     392 ..     370     393 .. 0.92
   6 ?    5.7   0.3     0.032        14      11      34 ..     409     432 ..     407     434 .. 0.84
   7 ?    0.3   0.1       1.6   6.8e+02      10      23 ..     454     467 ..     453     469 .. 0.85
   8 ?   -1.4   0.0       5.3   2.3e+03      14      31 ..     493     510 ..     489     510 .. 0.84
   9 !   12.7   0.7    0.0002     0.086       9      31 ..     522     544 ..     522     547 .. 0.93
  10 ?    2.9   0.2      0.24   1.1e+02       8      30 ..     555     577 ..     553     578 .. 0.95
  11 !   17.0   0.0   8.7e-06    0.0038       9      35 ..     591     617 ..     586     624 .. 0.87
  12 !    7.9   1.3    0.0066       2.9       4      31 ..     627     654 ..     625     655 .. 0.88
  13 ?    0.2   0.2       1.7   7.3e+02       9      29 ..     666     686 ..     666     688 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6.9
                            TPR_10 17 rydeAealleealai 31
                                      + deA++ ++ a++i
  gi|330509110|ref|YP_004385538.1| 44 NIDEALEAFDNAIQI 58
                                      789******999986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.019
                            TPR_10   9 analrqrgrydeAealleealairrrll 36 
                                       ++al ++gr +eA + +e+++++  + l
  gi|330509110|ref|YP_004385538.1| 111 GIALASLGREAEATDAFERSIELLNQSL 138
                                       89*******************9955544 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1
                            TPR_10  15 rgrydeAealleealai 31 
                                       +gr d A++ +++++++
  gi|330509110|ref|YP_004385538.1| 158 LGRTDSALEAYDKVIEL 174
                                       69************997 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.13
                            TPR_10  11 alrqrgrydeAealleealairr 33 
                                        l++   ++eA++ +++a++i +
  gi|330509110|ref|YP_004385538.1| 338 ELQRNDSHEEALQAFDKAIEINQ 360
                                       57778889************965 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.0015
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + +l+++gry+eA a  ++a+++
  gi|330509110|ref|YP_004385538.1| 370 GYVLYNMGRYEEAIAAWDRAIEL 392
                                       679*****************985 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.032
                            TPR_10  11 alrqrgrydeAealleealairrr 34 
                                       +l  +gr +e+ + +e+al++  +
  gi|330509110|ref|YP_004385538.1| 409 VLAILGRNEESAQAYERALELADK 432
                                       67789**************98765 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 1.6
                            TPR_10  10 nalrqrgrydeAea 23 
                                        +l ++gry eA++
  gi|330509110|ref|YP_004385538.1| 454 QLLDDQGRYVEALE 467
                                       67889*******97 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 5.3
                            TPR_10  14 qrgrydeAealleealai 31 
                                       ++gry+e+ + + ++l+i
  gi|330509110|ref|YP_004385538.1| 493 RLGRYNESIESYNKSLEI 510
                                       689****99999888876 PP

  == domain 9  score: 12.7 bits;  conditional E-value: 0.0002
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al ++gry+eA++++ +al+i
  gi|330509110|ref|YP_004385538.1| 522 GYALASLGRYEEALEYYNRALEI 544
                                       6799*****************97 PP

  == domain 10  score: 2.9 bits;  conditional E-value: 0.24
                            TPR_10   8 LanalrqrgrydeAealleeala 30 
                                       L+ alr++g y+e+ + +++a+a
  gi|330509110|ref|YP_004385538.1| 555 LGDALRNMGMYNESIQAYDRAIA 577
                                       899******************97 PP

  == domain 11  score: 17.0 bits;  conditional E-value: 8.7e-06
                            TPR_10   9 analrqrgrydeAealleealairrrl 35 
                                       ++al ++grydeA +++e+al  +  +
  gi|330509110|ref|YP_004385538.1| 591 GMALDSLGRYDEAQEDYEQALKDYDDV 617
                                       899******************988655 PP

  == domain 12  score: 7.9 bits;  conditional E-value: 0.0066
                            TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                                        + N +nalr ++r++e+++ +++a+++
  gi|330509110|ref|YP_004385538.1| 627 VMYNQGNALRGLQRHNESLQAYDRAIEL 654
                                       566779*******************986 PP

  == domain 13  score: 0.2 bits;  conditional E-value: 1.7
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       a++lr++g  +eAe+   +a+
  gi|330509110|ref|YP_004385538.1| 666 AIVLRALGGNAEAEEASAKAM 686
                                       899***********9766665 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.29   1.3e+02     100     146 .]      11      57 ..       8      57 .. 0.92
   2 ?    3.9   0.0      0.15        67      77     122 ..      44      89 ..      35      95 .. 0.89
   3 !   14.1   0.1   0.00011     0.048      75     135 ..      83     143 ..      69     147 .. 0.87
   4 ?    0.4   0.0       1.8   8.1e+02     100     124 ..     149     173 ..     139     178 .. 0.73
   5 ?    1.7   0.1      0.74   3.2e+02      11      34 ..     334     357 ..     327     368 .. 0.86
   6 ?    0.2   0.0         2   8.9e+02     106     125 ..     373     392 ..     371     406 .. 0.71
   7 !   11.3   3.4   0.00078      0.34      13     123 ..     414     542 ..     408     547 .. 0.71
   8 !   12.8   0.5   0.00028      0.12      67     123 ..     520     576 ..     510     582 .. 0.89
   9 !    9.3   0.2    0.0032       1.4      68     123 ..     597     652 ..     592     656 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.29
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHHHHHHHH CS
                              BTAD 100 rqlmrAlarsGrqaeALevYerlrrlLaeeLgvepgpelralheeil 146
                                       +  m++  ++ ++ +A   Y++ ++l a+ +g   +++l a  ++i+
  gi|330509110|ref|YP_004385538.1|  11 AIAMLCASAMAQEDTANDWYKKGQSLIATGFGYNIDEALEAFDNAIQ 57 
                                       568*************************************9999985 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.15
                                       -HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  77 raeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        ++eal+  +++++ +P + +++    + la++++++e Le+++++
  gi|330509110|ref|YP_004385538.1|  44 NIDEALEAFDNAIQIEPQNIDAWLGKAKSLAYMDEKNESLEAFRNI 89 
                                       5689999999*********************************987 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 0.00011
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS---- CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepg 135
                                       l+  +++l   ++ ++e+P +  +++    Ala +Gr+aeA  ++er  +lL++ L  +p+
  gi|330509110|ref|YP_004385538.1|  83 LEAFRNILNLTNETIKENPEDTSAWQSKGIALASLGREAEATDAFERSIELLNQSLLNDPK 143
                                       566677788889999***************************************9987776 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.8
                                       HHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD 100 rqlmrAlarsGrqaeALevYerlrr 124
                                        +  + l  +Gr+  ALe+Y+++ +
  gi|330509110|ref|YP_004385538.1| 149 WLKAENLELLGRTDSALEAYDKVIE 173
                                       5555667779**********99866 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.74
                                       HHHHHHHHTT-HHHHHHHHHHHHT CS
                              BTAD  11 aagraalaagdpeeaaelleaAla 34 
                                       ++g+++++++ +eea++++++A++
  gi|330509110|ref|YP_004385538.1| 334 NRGQELQRNDSHEEALQAFDKAIE 357
                                       6899999999********999986 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 2
                                       HHHTT-HHHHHHHHHHHHHH CS
                              BTAD 106 larsGrqaeALevYerlrrl 125
                                       l+ +Gr +eA+++++r+ +l
  gi|330509110|ref|YP_004385538.1| 373 LYNMGRYEEAIAAWDRAIEL 392
                                       67777777777777766554 PP

  == domain 7  score: 11.3 bits;  conditional E-value: 0.00078
                                       HHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTT...................STTHHHHHHHHHHHHHHHHHHHHH CS
                              BTAD  13 graalaagdpeeaaelleaAlalwrGpaladlea...................gewleaererleelrlealealae 70 
                                       gr++ +a + e+a+el+++A+ +++ +   +l+a                   +  +++  +              +
  gi|330509110|ref|YP_004385538.1| 414 GRNEESAQAYERALELADKAVTEYKTSTDLNLSAawgfkgqllddqgryvealEAVANSSKA--------------N 476
                                       56666677777777777777777777777777776666644444433444433333333333..............2 PP

                                       .............HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  71 .............aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                                    +  rlGr++e ++ +++ ++ +P +  + r    Ala +Gr +eALe+Y+r+ 
  gi|330509110|ref|YP_004385538.1| 477 pedafawavmgdiLADRLGRYNESIESYNKSLEIDPKNIGALRGEGYALASLGRYEEALEYYNRAL 542
                                       33444444444444569**********************************************985 PP

  == domain 8  score: 12.8 bits;  conditional E-value: 0.00028
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  67 alaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                           a+++lGr+eeal++++++++ +    r+++ l  Al+ +G  +e +++Y+r+ 
  gi|330509110|ref|YP_004385538.1| 520 GEGYALASLGRYEEALEYYNRALEIDSRFARAWQGLGDALRNMGMYNESIQAYDRAI 576
                                       55568899*********************************************9985 PP

  == domain 9  score: 9.3 bits;  conditional E-value: 0.0032
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  68 laeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       l + + + +++e+al+++++ ++++P + + +     Al+ + r +e L++Y+r+ 
  gi|330509110|ref|YP_004385538.1| 597 LGRYDEAQEDYEQALKDYDDVIKKNPRNAQVMYNQGNALRGLQRHNESLQAYDRAI 652
                                       55556677899******************************************985 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.028        12     208     241 ..      45      78 ..      35      89 .. 0.84
   2 ?    2.6   0.0      0.11        50     206     255 ..     125     174 ..      81     180 .. 0.70
   3 ?    3.9   0.0     0.046        20     203     256 ..     340     393 ..     332     402 .. 0.85
   4 ?    4.7   0.2     0.027        12      16      68 ..     375     430 ..     371     444 .. 0.70
   5 !    6.3   0.0    0.0084       3.7       6      72 ..     448     515 ..     443     520 .. 0.80
   6 ?    3.8   0.4      0.05        22      48     117 ..     525     597 ..     515     627 .. 0.60
   7 !    8.5   0.0    0.0019      0.83     206     254 ..     639     687 ..     625     691 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.028
                                       SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT- CS
                             NARP1 208 rekAleyidkaiehtptlvelyltKarilkhaGd 241
                                        ++Ale  d+ai+ +p+ ++ +l Ka+ l  + +
  gi|330509110|ref|YP_004385538.1|  45 IDEALEAFDNAIQIEPQNIDAWLGKAKSLAYMDE 78 
                                       579***********************97766655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                          e+++e++++ + ++p+  e +  Ka+ l+  G  + A e+ ++  +l
  gi|330509110|ref|YP_004385538.1| 125 DAFERSIELLNQSLLNDPKDAEAWWLKAENLELLGRTDSALEAYDKVIEL 174
                                       34557788888888888888888888888888888888887777776555 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.046
                                       HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       ++  s e+Al+  dkaie + +    +  K+ +l  +G  ++A+++ ++a +l 
  gi|330509110|ref|YP_004385538.1| 340 QRNDSHEEALQAFDKAIEINQSYAFAWGGKGYVLYNMGRYEEAIAAWDRAIELE 393
                                       556678899999999999999999999999999999999999999999998876 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.027
                                       HHTHHHHHHHHHHH...HGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH- CS
                             NARP1  16 eagkleeAlehLee...kekqivDklavketkaelllkLgrkeeAeatyeaLlern 68 
                                       + g++eeA++  ++    e + +   +  e+k+++l  Lgr+ee++++ye+ le  
  gi|330509110|ref|YP_004385538.1| 375 NMGRYEEAIAAWDRaieLEPDEFYSGSKWEMKGKVLAILGRNEESAQAYERALELA 430
                                       5666676666665522234444555667899******************9888755 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.0084
                                       HHHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHH.HTT-HHHHHHHHHHHHHH-TT-C CS
                             NARP1   6 llLyknqiieeagkleeAlehLeekekqivDklavketkaelll.kLgrkeeAeatyeaLlernpens 72 
                                       +  +k q++ ++g++ eAle + +++k   +      +++++l  +Lgr++e+ + y++ le  p n 
  gi|330509110|ref|YP_004385538.1| 448 AWGFKGQLLDDQGRYVEALEAVANSSKANPEDAFAWAVMGDILAdRLGRYNESIESYNKSLEIDPKNI 515
                                       556999****************998877665555555666665439*************999998875 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.05
                                       HHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT.....SSS-HHHHHHHHHHTTTS-TT-SHHHHTHHHH- CS
                             NARP1  48 llkLgrkeeAeatyeaLlernpenskYyeglekak...klskedeeallalydelaekyprsdaprRlpLdfl 117
                                       l  Lgr+eeA ++y++ le  +   + ++gl  a+   ++ +e+++a+  + +e+ ++ +++ + + ++Ld l
  gi|330509110|ref|YP_004385538.1| 525 LASLGRYEEALEYYNRALEIDSRFARAWQGLGDALrnmGMYNESIQAYDRAIAEMPQQPQYALIGKGMALDSL 597
                                       5667777777777777777777777777777777744434444555555555555555566666666666654 PP

  == domain 7  score: 8.5 bits;  conditional E-value: 0.0019
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeeark 254
                                       ++ +++l+  d+aie +p  ++ +  Ka +l+  G   +A e+  +a  
  gi|330509110|ref|YP_004385538.1| 639 QRHNESLQAYDRAIELNPGYIDAWRGKAIVLRALGGNAEAEEASAKAMD 687
                                       566799999**************************99999987665544 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.15        66      18      36 ..      46      64 ..      44      67 .. 0.89
   2 ?    6.6   0.0     0.019       8.3      12      33 ..     374     395 ..     371     396 .. 0.95
   3 ?    6.2   0.0     0.026        11      13      35 ..     493     515 ..     492     519 .. 0.92
   4 !    9.9   0.1    0.0017      0.75      10      34 ..     524     548 ..     522     553 .. 0.85
   5 ?   -2.0   0.1         9   3.9e+03      13      36 ..     561     584 ..     558     586 .. 0.83
   6 ?    6.7   0.1     0.017       7.5      15      37 ..     605     627 ..     603     629 .. 0.94
   7 ?   -0.2   0.0       2.5   1.1e+03      13      33 ..     637     657 ..     626     661 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.15
                                      HHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C 18 seArryvdalLeiEPenrQ 36
                                      +eA++  d  ++iEP+n  
  gi|330509110|ref|YP_004385538.1| 46 DEALEAFDNAIQIEPQNID 64
                                      689**************66 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.019
                                       HHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPe 33 
                                       y +g+Y+eA    d+ +e+EP+
  gi|330509110|ref|YP_004385538.1| 374 YNMGRYEEAIAAWDRAIELEPD 395
                                       99*******************7 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.026
                                       HHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPenr 35 
                                       +lg+Y+e+ +  +  Lei+P+n 
  gi|330509110|ref|YP_004385538.1| 493 RLGRYNESIESYNKSLEIDPKNI 515
                                       89*******************96 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0017
                                       HHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPen 34 
                                       + + lg+Y+eA++y ++ Lei+ ++
  gi|330509110|ref|YP_004385538.1| 524 ALASLGRYEEALEYYNRALEIDSRF 548
                                       66779****************9765 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 9
                                       HHT-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQ 36 
                                        +g Y+e+ +  d+ ++  P+  Q
  gi|330509110|ref|YP_004385538.1| 561 NMGMYNESIQAYDRAIAEMPQQPQ 584
                                       5899****9999999988887766 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.017
                                       T-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenrQa 37 
                                        +Y++A++  d ++++ P+n Q+
  gi|330509110|ref|YP_004385538.1| 605 EDYEQALKDYDDVIKKNPRNAQV 627
                                       69********************8 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 2.5
                                       HHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPe 33 
                                        l++++e+++  d+ +e+ P+
  gi|330509110|ref|YP_004385538.1| 637 GLQRHNESLQAYDRAIELNPG 657
                                       68999**********999997 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.84   3.7e+02      10      27 ..     113     130 ..      49     183 .. 0.65
   2 ?    0.4   0.0       1.7   7.3e+02     105     117 ..     246     258 ..     241     260 .. 0.84
   3 ?    1.1   0.1         1   4.5e+02      13      29 ..     412     428 ..     370     442 .. 0.56
   4 ?    6.4   0.1     0.024        10      76     119 .]     463     508 ..     402     508 .. 0.85
   5 !    9.2   0.1    0.0031       1.3      11      65 ..     525     576 ..     519     589 .. 0.83
   6 !   12.2   0.3   0.00038      0.16       5     100 ..     588     685 ..     583     691 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.84
                             TPR_5  10 arDstGhedkavplYrra 27 
                                       a  s G+e++a   ++r+
  gi|330509110|ref|YP_004385538.1| 113 ALASLGREAEATDAFERS 130
                                       334455555555555544 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.7
                             TPR_5 105 lprYqRsvtnYar 117
                                       + rY+Rs+++Y +
  gi|330509110|ref|YP_004385538.1| 246 FGRYNRSIQAYDD 258
                                       579********76 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1
                             TPR_5  13 stGhedkavplYrraLa 29 
                                         G+++++++ Y+raL+
  gi|330509110|ref|YP_004385538.1| 412 ILGRNEESAQAYERALE 428
                                       34555555555555554 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.024
                             TPR_5  76 laaflaLvLsdlgrereavsivl..lalaehlprYqRsvtnYareL 119
                                       ++a+ a++ s++  +++a + ++  + la+ l rY+ s+++Y + L
  gi|330509110|ref|YP_004385538.1| 463 VEALEAVANSSKANPEDAFAWAVmgDILADRLGRYNESIESYNKSL 508
                                       6677788888889999988877622469**************9876 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0031
                             TPR_5  11 rDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLrael 65 
                                         s G+ ++a + Y+raL+    ++r  ra   L  +LRn+G  +e+++  +  +
  gi|330509110|ref|YP_004385538.1| 525 LASLGRYEEALEYYNRALEI---DSRFARAWQGLGDALRNMGMYNESIQAYDRAI 576
                                       5689**************95...8999999999************9987665554 PP

  == domain 6  score: 12.2 bits;  conditional E-value: 0.00038
                             TPR_5   5 FeragarDstGhedkavplYrraLaeGLa....garrrratiqLassLRnlGeaeealaLLraeleapsdelddala 77 
                                         ++ a Ds G+ d+a + Y++aL++  +    + r+ +++     +LR l + +e+l+  +  +e  + ++ da +
  gi|330509110|ref|YP_004385538.1| 588 IGKGMALDSLGRYDEAQEDYEQALKDYDDvikkNPRNAQVMYNQGNALRGLQRHNESLQAYDRAIEL-NPGYIDAWR 663
                                       5677899*****************87543111144555555667889**********9998877765.457888888 PP

                             TPR_5  78 aflaLvLsdlgrereavsivlla 100
                                       +  a+vL +lg ++ea   + +a
  gi|330509110|ref|YP_004385538.1| 664 G-KAIVLRALGGNAEAEEASAKA 685
                                       7.688999999988886665555 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.36   1.6e+02     150     179 ..     108     137 ..      91     156 .. 0.84
   2 !    7.1   0.2    0.0088       3.9     126     174 ..     342     391 ..     336     397 .. 0.80
   3 !   16.4   0.4   1.3e-05    0.0058     122     180 ..     372     434 ..     371     447 .. 0.82
   4 ?    3.6   0.1      0.11        47     122     176 ..     455     511 ..     453     524 .. 0.80
   5 !    8.5   0.3    0.0033       1.5     125     182 ..     527     585 ..     522     599 .. 0.74
   6 ?    3.9   1.0     0.088        38     124     171 ..     602     650 ..     590     657 .. 0.50

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.36
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAlaaleek 179
                                       + +G +l++ g+ +eA +a++++++ l+++
  gi|330509110|ref|YP_004385538.1| 108 QSKGIALASLGREAEATDAFERSIELLNQS 137
                                       679999****************99988776 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0088
                            TPR_21 126 ekkydeAlktLeakkeeafa.alvaelrGDilvaqgkldeAraaYqaAla 174
                                       ++ ++eAl++ +++ e + + a +   +G +l+++g+ +eA aa+++A++
  gi|330509110|ref|YP_004385538.1| 342 NDSHEEALQAFDKAIEINQSyAFAWGGKGYVLYNMGRYEEAIAAWDRAIE 391
                                       577899999998776655541555689*********************97 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 1.3e-05
                            TPR_21 122 vllaekkydeAlktL....eakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaaleeka 180
                                       vl +++ y+eA+++     e +++e ++++  e++G +l+  g+++e  +aY++Al+  ++  
  gi|330509110|ref|YP_004385538.1| 372 VLYNMGRYEEAIAAWdraiELEPDEFYSGSKWEMKGKVLAILGRNEESAQAYERALELADKAV 434
                                       78889999999986422227789999******************************9888764 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.11
                            TPR_21 122 vllaekkydeAlktLeakkeeafaalva.elrGDilv.aqgkldeAraaYqaAlaal 176
                                       +l +++ y eAl++++++++++ + ++a  + GDil+ + g+ +e  + Y+++l+  
  gi|330509110|ref|YP_004385538.1| 455 LLDDQGRYVEALEAVANSSKANPEDAFAwAVMGDILAdRLGRYNESIESYNKSLEID 511
                                       67799**********88777766555543899****93479*********9999765 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0033
                            TPR_21 125 aekkydeAlktLea..kkeeafaalvaelrGDilvaqgkldeAraaYqaAlaaleekare 182
                                         + y+eAl+  ++  + ++ fa + + l GD+l ++g  +e  +aY++A+a++ ++ + 
  gi|330509110|ref|YP_004385538.1| 527 SLGRYEEALEYYNRalEIDSRFARAWQGL-GDALRNMGMYNESIQAYDRAIAEMPQQPQY 585
                                       55778888887754114566776666665.************************998743 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.088
                            TPR_21 124 laekkydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqa 171
                                        a+++y++Alk  +++ k++  +a+v   +G++l    + +e  +aY++
  gi|330509110|ref|YP_004385538.1| 602 EAQEDYEQALKDYDDViKKNPRNAQVMYNQGNALRGLQRHNESLQAYDR 650
                                       3455555555555443133344455555555555555555555555555 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.5   2.4e+03       3      35 ..      84     125 ..      51     137 .. 0.75
   2 !    8.5   0.0    0.0045         2      28      66 ..     343     384 ..     337     396 .. 0.86
   3 ?    1.1   0.0      0.89   3.9e+02       3      44 ..     421     476 ..     419     488 .. 0.69
   4 ?    7.0   0.2     0.013       5.8       3      52 ..     502     551 ..     500     655 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.5
                      SRP_TPR_like   3 eeyekilrlegkelkkf.........kvvaliklekyeeaLk 35 
                                       e++ +il+l ++++k+          k +al +l++ +ea  
  gi|330509110|ref|YP_004385538.1|  84 EAFRNILNLTNETIKENpedtsawqsKGIALASLGREAEATD 125
                                       456667777777776666666666668888888887777755 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0045
                      SRP_TPR_like  28 ekyeeaLkllkkgsalsedvrfE...kaYvlYklkkykkalk 66 
                                       + +eeaL++ +k+ +++++  f    k YvlY + +y++a  
  gi|330509110|ref|YP_004385538.1| 343 DSHEEALQAFDKAIEINQSYAFAwggKGYVLYNMGRYEEAIA 384
                                       6789**********9****999544499***********976 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.89
                      SRP_TPR_like   3 eeyekilrlegkelkkf..............kvvaliklekyeeaLkllkkgsals 44 
                                       ++ye+ l+l++k ++++              k   l   ++y eaL+++++ s+ +
  gi|330509110|ref|YP_004385538.1| 421 QAYERALELADKAVTEYktstdlnlsaawgfKGQLLDDQGRYVEALEAVANSSKAN 476
                                       67777777777777777666666666666666666667788888888888777544 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.013
                      SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsalsedvrfEka 52 
                                       e+y+k l+++ k++        al +l++yeeaL++ + +   + d rf +a
  gi|330509110|ref|YP_004385538.1| 502 ESYNKSLEIDPKNIGALrgEGYALASLGRYEEALEYYNRAL--EIDSRFARA 551
                                       6788888888888887733468999***********98765..445555555 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.033        14      58     120 ..      70     133 ..      59     137 .. 0.84
   2 ?    0.8   0.0      0.92     4e+02      66     120 ..     120     174 ..     108     176 .. 0.86
   3 ?    3.3   0.0      0.15        68      72     120 ..     496     544 ..     491     556 .. 0.91
   4 ?    6.7   0.0     0.014       6.2      65     117 ..     599     651 ..     583     656 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.033
                           DUF4919  58 leel.kldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkl 120
                                       +++l ++d+k+ s e +++i++l +e +k+nP d  + +   +a+ +lg++ ea    +r  +l
  gi|330509110|ref|YP_004385538.1|  70 AKSLaYMDEKNESLEAFRNILNLTNETIKENPEDTSAWQSKGIALASLGREAEATDAFERSIEL 133
                                       4444578999999*********************************999999988776666555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.92
                           DUF4919  66 kelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkl 120
                                       +   +  +++ i+l +++l ++P d ++  l a  +++lg++++a + ++++ +l
  gi|330509110|ref|YP_004385538.1| 120 EAEATDAFERSIELLNQSLLNDPKDAEAWWLKAENLELLGRTDSALEAYDKVIEL 174
                                       55566788999********************************999999988765 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.15
                           DUF4919  72 elkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkl 120
                                        ++e i+  +++l+ +P ++ +l    ya+ +lg+ eea +y++r  ++
  gi|330509110|ref|YP_004385538.1| 496 RYNESIESYNKSLEIDPKNIGALRGEGYALASLGRYEEALEYYNRALEI 544
                                       578889999***********************************98776 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.014
                           DUF4919  65 kkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrl 117
                                       + +  +e+++++++   +++kknP + + ++++ +a++ l++++e+ + ++r 
  gi|330509110|ref|YP_004385538.1| 599 RYDEAQEDYEQALKDYDDVIKKNPRNAQVMYNQGNALRGLQRHNESLQAYDRA 651
                                       5667899*********************************9998877766665 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.7   7.3e+02      16      25 ..      44      53 ..      44      62 .. 0.78
   2 !   11.6   0.1   0.00048      0.21       8      23 ..     370     385 ..     358     393 .. 0.80
   3 !    9.6   0.1    0.0021      0.91       8      30 ..     522     542 ..     517     546 .. 0.83
   4 ?   -0.2   0.3       2.4     1e+03      15      29 ..     598     610 ..     596     615 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.7
                                      -HHHHHHH.. CS
                             TPR_3 16 kyqeArelfs 25
                                      +++eA+e+f+
  gi|330509110|ref|YP_004385538.1| 44 NIDEALEAFD 53
                                      69******98 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00048
                                       HHHHHHTT-HHHHHHH CS
                             TPR_3   8 AaefynkkkyqeArel 23 
                                       ++++yn+++y+eA+ +
  gi|330509110|ref|YP_004385538.1| 370 GYVLYNMGRYEEAIAA 385
                                       9************976 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0021
                                       HHHHHHTT-HHHHHHH..HHHHH CS
                             TPR_3   8 AaefynkkkyqeArelfsYalla 30 
                                       ++++ + ++y+eA+e+  Y  + 
  gi|330509110|ref|YP_004385538.1| 522 GYALASLGRYEEALEY--YNRAL 542
                                       7999************..65555 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.4
                                       T-HHHHHHH..HHHH CS
                             TPR_3  15 kkyqeArelfsYall 29 
                                       ++y+eA e   Y+++
  gi|330509110|ref|YP_004385538.1| 598 GRYDEAQED--YEQA 610
                                       666666665..5554 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.099        43      85     129 ..      45      90 ..      15     100 .. 0.79
   2 !    9.5   0.1    0.0028       1.2      72     121 ..     114     163 ..     104     169 .. 0.88
   3 ?    0.6   0.1       1.7   7.3e+02      80     126 ..     374     423 ..     353     435 .. 0.81
   4 ?    0.0   0.1       2.4   1.1e+03      80     102 ..     418     440 ..     403     506 .. 0.65
   5 ?    2.8   0.0      0.35   1.5e+02      81     125 ..     527     571 ..     517     579 .. 0.90
   6 ?    4.8   0.1      0.08        35      75     124 ..     597     646 ..     583     654 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.099
                                       HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHH.HHHH CS
                   Alkyl_sulf_dimr  85 yrwaaellnhlvfadpenaeakelkadaleqlgyqaesatw.RniY 129
                                       +  a+e  +++++ +p+n +a   ka++l  + +++es  + Rni 
  gi|330509110|ref|YP_004385538.1|  45 IDEALEAFDNAIQIEPQNIDAWLGKAKSLAYMDEKNESLEAfRNIL 90 
                                       567999*******************************987526654 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
                   Alkyl_sulf_dimr  72 vlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                                       +++  +ea + + ++ ++elln+ + +dp++aea  lka+ le lg+  +
  gi|330509110|ref|YP_004385538.1| 114 LASLGREAEATDAFERSIELLNQSLLNDPKDAEAWWLKAENLELLGRTDS 163
                                       55667777888899********************************9865 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.7
                                       HHTT-HHHHHHHHHHHHHHSTT-...HHHHHHHHHHHHHHHHH-SSHHHH CS
                   Alkyl_sulf_dimr  80 lkegdyrwaaellnhlvfadpen...aeakelkadaleqlgyqaesatwR 126
                                       ++ g y+ a+   + +++ +p++    +  e+k ++l  lg+ +esa++ 
  gi|330509110|ref|YP_004385538.1| 374 YNMGRYEEAIAAWDRAIELEPDEfysGSKWEMKGKVLAILGRNEESAQAY 423
                                       67788899999999999999985443688899999999999999999875 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 2.4
                                       HHTT-HHHHHHHHHHHHHHSTT- CS
                   Alkyl_sulf_dimr  80 lkegdyrwaaellnhlvfadpen 102
                                        +++ y+ a+el++++v++ ++ 
  gi|330509110|ref|YP_004385538.1| 418 ESAQAYERALELADKAVTEYKTS 440
                                       45666888888888888864332 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.35
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHH CS
                   Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatw 125
                                       + g y+ a+e  n +++ d++ a+a + + dal+++g  +es ++
  gi|330509110|ref|YP_004385538.1| 527 SLGRYEEALEYYNRALEIDSRFARAWQGLGDALRNMGMYNESIQA 571
                                       56899*********************************9999865 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.08
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  75 kakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                         + + +++dy+ a++  + ++ ++p+na+    + +al+ l +++es +
  gi|330509110|ref|YP_004385538.1| 597 LGRYDEAQEDYEQALKDYDDVIKKNPRNAQVMYNQGNALRGLQRHNESLQ 646
                                       555666899**********************************9999976 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.4   6.3e+02      21      39 ..      46      57 ..      43      85 .. 0.62
   2 ?    4.0   0.0      0.12        53      14      48 ..     114     147 ..     108     160 .. 0.78
   3 ?   -0.1   0.0       2.3     1e+03      10      32 ..     151     173 ..     147     174 .. 0.87
   4 ?    0.9   0.0       1.1   4.9e+02      11      32 ..     336     357 ..     328     361 .. 0.78
   5 ?    0.8   0.1       1.2   5.4e+02      17      33 ..     376     392 ..     369     394 .. 0.89
   6 ?    2.8   0.1      0.28   1.2e+02      21      40 ..     417     436 ..     410     446 .. 0.64
   7 ?   -1.2   0.0       5.1   2.2e+03      13      25 ..     455     467 ..     452     470 .. 0.86
   8 ?    5.4   0.0     0.042        19      12      32 ..     489     509 ..     478     510 .. 0.86
   9 !    8.6   0.9    0.0046         2      17      32 ..     528     543 ..     521     544 .. 0.88
  10 ?   -0.7   0.0       3.6   1.6e+03      18      32 ..     563     577 ..     561     581 .. 0.82
  11 !   11.0   0.5   0.00081      0.35       7      45 ..     587     624 ..     585     635 .. 0.84
  12 ?   -1.9   0.0       8.5   3.7e+03      20      33 ..     641     654 ..     638     654 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.4
                               MIT 21 eeAlelYkealelLlqalk 39
                                      +eAle++ +a       ++
  gi|330509110|ref|YP_004385538.1| 46 DEALEAFDNA-------IQ 57
                                      4555555555.......55 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.12
                               MIT  14 eDnagnyeeAlelYkealelLlqalkekneerrel 48 
                                       + + g  +eA ++++ ++elL+q l  +++++ e+
  gi|330509110|ref|YP_004385538.1| 114 LASLGREAEATDAFERSIELLNQSLL-NDPKDAEA 147
                                       55667889***************997.56666665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.3
                               MIT  10 kAveeDnagnyeeAlelYkeale 32 
                                       kA +++  g  + Ale+Y + +e
  gi|330509110|ref|YP_004385538.1| 151 KAENLELLGRTDSALEAYDKVIE 173
                                       7889999999********98666 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.1
                               MIT  11 AveeDnagnyeeAlelYkeale 32 
                                         e+ ++   eeAl+++ +a+e
  gi|330509110|ref|YP_004385538.1| 336 GQELQRNDSHEEALQAFDKAIE 357
                                       5666677788999999999998 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 1.2
                               MIT  17 agnyeeAlelYkealel 33 
                                        g yeeA+ +   a+el
  gi|330509110|ref|YP_004385538.1| 376 MGRYEEAIAAWDRAIEL 392
                                       589*****999999986 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.28
                               MIT  21 eeAlelYkealelLlqalke 40 
                                       ee  ++Y+ alel  +a++e
  gi|330509110|ref|YP_004385538.1| 417 EESAQAYERALELADKAVTE 436
                                       45556666666666666654 PP

  == domain 7  score: -1.2 bits;  conditional E-value: 5.1
                               MIT  13 eeDnagnyeeAle 25 
                                        +D +g y eAle
  gi|330509110|ref|YP_004385538.1| 455 LLDDQGRYVEALE 467
                                       5899*******98 PP

  == domain 8  score: 5.4 bits;  conditional E-value: 0.042
                               MIT  12 veeDnagnyeeAlelYkeale 32 
                                       + +D+ g y e +e Y ++le
  gi|330509110|ref|YP_004385538.1| 489 ILADRLGRYNESIESYNKSLE 509
                                       5689***************98 PP

  == domain 9  score: 8.6 bits;  conditional E-value: 0.0046
                               MIT  17 agnyeeAlelYkeale 32 
                                        g yeeAle+Y  ale
  gi|330509110|ref|YP_004385538.1| 528 LGRYEEALEYYNRALE 543
                                       689***********98 PP

  == domain 10  score: -0.7 bits;  conditional E-value: 3.6
                               MIT  18 gnyeeAlelYkeale 32 
                                       g y e +++Y  a+ 
  gi|330509110|ref|YP_004385538.1| 563 GMYNESIQAYDRAIA 577
                                       679999****99986 PP

  == domain 11  score: 11.0 bits;  conditional E-value: 0.00081
                               MIT   7 lvkkAveeDnagnyeeAlelYkealelLlqalkekneer 45 
                                       l+ k + +D+ g y+eA e Y++al+    ++k kn++ 
  gi|330509110|ref|YP_004385538.1| 587 LIGKGMALDSLGRYDEAQEDYEQALKDYDDVIK-KNPRN 624
                                       788999*******************99999998.55554 PP

  == domain 12  score: -1.9 bits;  conditional E-value: 8.5
                               MIT  20 yeeAlelYkealel 33 
                                         e l++Y  a+el
  gi|330509110|ref|YP_004385538.1| 641 HNESLQAYDRAIEL 654
                                       56788888888875 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.11        48     267     291 ..      44      68 ..      23     153 .. 0.83
   2 ?    4.1   0.1     0.051        23     254     289 ..     332     366 ..     314     380 .. 0.83
   3 ?    0.0   0.0      0.88   3.8e+02       3      59 ..     443     508 ..     441     528 .. 0.77
   4 ?    4.0   0.0     0.054        24     260     299 ..     530     562 ..     517     588 .. 0.82
   5 !    8.1   0.1    0.0032       1.4     231     289 ..     610     662 ..     566     666 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                                       .-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 267 kieeilqsysaateidpswykawht 291
                                       +i+e+l+++  a +i p+ ++aw  
  gi|330509110|ref|YP_004385538.1|  44 NIDEALEAFDNAIQIEPQNIDAWLG 68 
                                       699********************64 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.051
                                       CCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTT CS
                               FAT 254 wqealqkldwseekieeilqsysaateidpswykaw 289
                                       w ++ q+l +++++ ee+lq++ +a ei++s + aw
  gi|330509110|ref|YP_004385538.1| 332 WFNRGQEL-QRNDSHEEALQAFDKAIEINQSYAFAW 366
                                       77777776.46778***************9998888 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.88
                                       CTTCCCCTSS.S.GHHCCCCT..........TSSSS--CCCHCCC.CHH--CCHCHHCCCHCCCCC CS
                               FAT   3 laaeaaWrlg.q.Wdsmeeylsvlk......kdspdkaffeaila.lhrnqfdeakeliekarqll 59 
                                       l + aaW+ + q  d++ +y++ l+      k +p+ af  a++  +  + + + +e+ie  ++ l
  gi|330509110|ref|YP_004385538.1| 443 LNLSAAWGFKgQlLDDQGRYVEALEavanssKANPEDAFAWAVMGdILADRLGRYNESIESYNKSL 508
                                       788999*99877788899999999999999999999999999998877788888777777766655 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.054
                                       CCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHC CS
                               FAT 260 kldwseekieeilqsysaateidpswykawhtwalfnfev 299
                                       +        ee+l++y +a eid + + aw  ++++  ++
  gi|330509110|ref|YP_004385538.1| 530 R-------YEEALEYYNRALEIDSRFARAWQGLGDALRNM 562
                                       4.......79**********************99987765 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0032
                                       .............HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTT CS
                               FAT 231 q.keptnleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykaw 289
                                         k+ + + +++ + a+++  +G  ++ lq+        +e lq+y +a e++p+ ++aw
  gi|330509110|ref|YP_004385538.1| 610 AlKDYDDVIKKNPRNAQVMYNQGNALRGLQR-------HNESLQAYDRAIELNPGYIDAW 662
                                       25566777777777799**************.......99******************** PP

>> DUF3775  Protein of unknown function (DUF3775)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.7   1.2e+03      20      39 ..     112     131 ..     107     137 .. 0.84
   2 ?   -0.8   0.1       3.8   1.6e+03      21      40 ..     372     391 ..     371     392 .. 0.87
   3 ?    5.2   0.0      0.05        22      21      51 ..     409     439 ..     405     446 .. 0.88
   4 !    7.5   0.0    0.0091         4      20      41 ..     592     613 ..     570     629 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.7
                           DUF3775  20 vALmwiGRgdfeaeewdeav 39 
                                       +AL+ +GR+ ++ + +++ +
  gi|330509110|ref|YP_004385538.1| 112 IALASLGREAEATDAFERSI 131
                                       79*******99999888765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.8
                           DUF3775  21 ALmwiGRgdfeaeewdeave 40 
                                       +L  +GR +++   wd+a+e
  gi|330509110|ref|YP_004385538.1| 372 VLYNMGRYEEAIAAWDRAIE 391
                                       57789***********9986 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.05
                           DUF3775  21 ALmwiGRgdfeaeewdeaveeAreeeserta 51 
                                       +L+ +GR +++a+ +++a+e A ++ +e+++
  gi|330509110|ref|YP_004385538.1| 409 VLAILGRNEESAQAYERALELADKAVTEYKT 439
                                       6899******************999887765 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0091
                           DUF3775  20 vALmwiGRgdfeaeewdeavee 41 
                                       +AL  +GR d+++e++++a+++
  gi|330509110|ref|YP_004385538.1| 592 MALDSLGRYDEAQEDYEQALKD 613
                                       48999**************986 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       5.4   2.4e+03      14      29 ..     159     174 ..     157     176 .. 0.86
   2 ?   -0.1   0.0       3.4   1.5e+03      12      27 ..     341     356 ..     339     359 .. 0.82
   3 ?    0.1   0.0       2.7   1.2e+03      12      25 ..     375     388 ..     372     392 .. 0.79
   4 ?    7.2   0.0     0.016       6.8       9      25 ..     524     540 ..     523     545 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 5.4
                               PPR  14 GkleeAlelfkeMkek 29 
                                       G+ + Ale +++ +e 
  gi|330509110|ref|YP_004385538.1| 159 GRTDSALEAYDKVIEL 174
                                       999*******998876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.4
                               PPR  12 knGkleeAlelfkeMk 27 
                                       +n  +eeAl+ f++ +
  gi|330509110|ref|YP_004385538.1| 341 RNDSHEEALQAFDKAI 356
                                       67889*******9866 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2.7
                               PPR  12 knGkleeAlelfke 25 
                                         G++eeA+  +++
  gi|330509110|ref|YP_004385538.1| 375 NMGRYEEAIAAWDR 388
                                       68******998876 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.016
                               PPR   9 gycknGkleeAlelfke 25 
                                       ++++ G++eeAle++++
  gi|330509110|ref|YP_004385538.1| 524 ALASLGRYEEALEYYNR 540
                                       7899***********98 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 ?   -2.0   0.1       7.6   3.3e+03      31      65 ..       6      40 ..       3      53 .. 0.71
   2 ?    7.5   0.0    0.0084       3.7       5      92 ..     530     618 ..     528     627 .. 0.91
   3 ?    3.0   0.0      0.22        95       4      67 ..     639     704 ..     638     716 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 7.6
                           SLATT_1 31 lillellalllaalrafgelsvdlvgvlaavaaal 65
                                      +++l ++a+l+a + a +++  d+ +   +++a++
  gi|330509110|ref|YP_004385538.1|  6 VVALLAIAMLCASAMAQEDTANDWYKKGQSLIATG 40
                                      45666777777777766666667877666666665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0084
                           SLATT_1   5 RveeqldwYrkkaeeneraakrwrlllillellalllaalrafgelsv.dlvgvlaavaaallaWlelkqyeelaaa 80 
                                       R+ee l++Y + +e  +r a++w+ l  +l  +++    ++a+  +    + +   a+++ ++a   l +y+e  + 
  gi|330509110|ref|YP_004385538.1| 530 RYEEALEYYNRALEIDSRFARAWQGLGDALRNMGMYNESIQAYDRAIAeMPQQPQYALIGKGMALDSLGRYDEAQED 606
                                       99***************************************99888777889999999******************* PP

                           SLATT_1  81 YslaaeeLeiir 92 
                                       Y++a ++ +++ 
  gi|330509110|ref|YP_004385538.1| 607 YEQALKDYDDVI 618
                                       **9998877665 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.22
                           SLATT_1   4 eRveeqldwYrkkaeeneraakrwrlllillellalllaalr.afgelsv.dlvgvlaavaaalla 67 
                                       +R +e l+ Y +  e n    ++wr   i+l +l+  + a +  ++++++  + g+++ava+++l 
  gi|330509110|ref|YP_004385538.1| 639 QRHNESLQAYDRAIELNPGYIDAWRGKAIVLRALGGNAEAEEaSAKAMDLgYMSGMVTAVAGSGLI 704
                                       5888889999999999999999*************999999977888888999********99875 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.044        19       7      40 ..     328     360 ..     326     366 .. 0.87
   2 ?    0.8   0.1      0.85   3.7e+02      14      36 ..     369     391 ..     360     422 .. 0.87
   3 ?   -0.4   0.0       2.1   9.1e+02      19      35 ..     418     434 ..     402     439 .. 0.82
   4 ?    5.9   0.1     0.024        10      11      57 ..     518     563 ..     497     580 .. 0.79
   5 ?   -0.3   0.1       1.9   8.1e+02      14      37 ..     597     620 ..     589     654 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.044
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsaleylNa 40 
                                        a+d+ n +++l  ++++eeAL+ +d+a+e+ N+
  gi|330509110|ref|YP_004385538.1| 328 SAEDWFNRGQELQRNDSHEEALQAFDKAIEI-NQ 360
                                       689999***********************85.54 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.85
                           DUF5113  14 layylnvegeyeeALeyldsale 36 
                                        +y l+  g+yeeA++  d a+e
  gi|330509110|ref|YP_004385538.1| 369 KGYVLYNMGRYEEAIAAWDRAIE 391
                                       67889999************997 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.1
                           DUF5113  19 nvegeyeeALeyldsal 35 
                                          + ye+ALe++d+a+
  gi|330509110|ref|YP_004385538.1| 418 ESAQAYERALELADKAV 434
                                       56789*********997 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.024
                           DUF5113  11 YanlayylnvegeyeeALeyldsaleylNahyekYakkkadtldklk 57 
                                        +  +y+l   g+yeeALey + ale+  ++ + +     d l ++ 
  gi|330509110|ref|YP_004385538.1| 518 LRGEGYALASLGRYEEALEYYNRALEIDSRFARAWQGLG-DALRNMG 563
                                       56678899999**************98777777766665.5665555 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 1.9
                           DUF5113  14 layylnvegeyeeALeyldsaley 37 
                                       l+ y  ++++ye+AL+  d +++ 
  gi|330509110|ref|YP_004385538.1| 597 LGRYDEAQEDYEQALKDYDDVIKK 620
                                       677788899999999999988875 PP

>> Bep_C_terminal  BID domain of Bartonella effector protein (Bep)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       5.3   2.3e+03      53      87 ..      59      93 ..      47     138 .. 0.58
   2 ?    9.6   0.0    0.0024         1      33      69 ..     486     527 ..     456     534 .. 0.72
   3 ?   -0.3   0.1       2.8   1.2e+03      36      82 ..     638     684 ..     620     690 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5.3
                    Bep_C_terminal 53 epesigaLaGkkgllakraekqeRkaAeanvpaLa 87
                                      ep+ i a  Gk   la   ek+e  +A +n+  L 
  gi|330509110|ref|YP_004385538.1| 59 EPQNIDAWLGKAKSLAYMDEKNESLEAFRNILNLT 93
                                      55555555555555555555555555554444443 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0024
                    Bep_C_terminal  33 i.....davlkdpalakellqkiaaepesigaLaGkkgllak 69 
                                       +     d + + +++ ++  + ++ +p+ igaL+G+++ la+
  gi|330509110|ref|YP_004385538.1| 486 MgdilaDRLGRYNESIESYNKSLEIDPKNIGALRGEGYALAS 527
                                       2333445555556788889999****************9997 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.8
                    Bep_C_terminal  36 vlkdpalakellqkiaaepesigaLaGkkgllakraekqeRkaAean 82 
                                       +++ +++ ++  ++i+ +p+ i a +Gk  +l     + e ++A a+
  gi|330509110|ref|YP_004385538.1| 638 LQRHNESLQAYDRAIELNPGYIDAWRGKAIVLRALGGNAEAEEASAK 684
                                       56677788888899999***********9999877777777776665 PP

>> Peptidase_M15_4  D-alanyl-D-alanine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.43   1.9e+02       7      30 ..     199     223 ..     194     273 .. 0.66
   2 ?    6.2   0.1     0.034        15      29      55 ..     343     369 ..     323     371 .. 0.75
   3 ?   -0.2   0.0       3.3   1.5e+03       7      27 ..     643     665 ..     639     703 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.43
                   Peptidase_M15_4   7 lSnHsyGlAiDinplvnp..ywkalk 30 
                                       +S+ ++G A+D+  +  +  +++ + 
  gi|330509110|ref|YP_004385538.1| 199 QSQDAFGKAVDLMEVN-StsFISFWY 223
                                       8999********9773.222333333 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.034
                   Peptidase_M15_4  29 lkpengeayadevvkifkklGfeWGgd 55 
                                        ++e++ + +d++++i +++ f WGg+
  gi|330509110|ref|YP_004385538.1| 343 DSHEEALQAFDKAIEINQSYAFAWGGK 369
                                       3455555556****************7 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 3.3
                   Peptidase_M15_4   7 lSnHsyGlAiDinplvnpyw..k 27 
                                        S  +y +Ai +np + + w  k
  gi|330509110|ref|YP_004385538.1| 643 ESLQAYDRAIELNPGYIDAWrgK 665
                                       56668999999**9965555441 PP

>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.038        17      70     130 ..      79     139 ..      51     150 .. 0.87
   2 ?   -0.8   0.0       4.1   1.8e+03      74     125 ..     342     393 ..     322     411 .. 0.80
   3 ?   -0.8   0.0       4.1   1.8e+03      79     126 ..     499     546 ..     493     554 .. 0.87
   4 ?    1.4   0.0      0.88   3.8e+02      73     125 ..     603     655 ..     553     671 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.038
                                       TT--HHHHHHHHHHC-EEE---------------------------------EEEEEEEEE CS
                            TruB_N  70 eklteekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelell 130
                                       ++ + e+++++l+  + +i+  p   SA + +G  l +l re e+++  +r++++ + +ll
  gi|330509110|ref|YP_004385538.1|  79 KNESLEAFRNILNLTNETIKENPEDTSAWQSKGIALASLGREAEATDAFERSIELLNQSLL 139
                                       45567889999999999*****************************999999988776666 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHC-EEE---------------------------------EEEE CS
                            TruB_N  74 eekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiy 125
                                       +++ ee+l++f  +ie   +   A   +G  ly++ r +e++    r ++++
  gi|330509110|ref|YP_004385538.1| 342 NDSHEEALQAFDKAIEINQSYAFAWGGKGYVLYNMGRYEEAIAAWDRAIELE 393
                                       45678999999999999999999999999999**999999999888888765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 4.1
                                       HHHHHC-EEE---------------------------------EEEEE CS
                            TruB_N  79 evlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiye 126
                                       e +++++ ++e  p  + A++ +G  l +l r +e++e  +r  +i++
  gi|330509110|ref|YP_004385538.1| 499 ESIESYNKSLEIDPKNIGALRGEGYALASLGRYEEALEYYNRALEIDS 546
                                       66788888889999999**********************999999976 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.88
                                       -HHHHHHHHHHC-EEE---------------------------------EEEE CS
                            TruB_N  73 teekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiy 125
                                        +e+ e++lk++   i++ p     +  +G+ l  l r++e+++   r ++++
  gi|330509110|ref|YP_004385538.1| 603 AQEDYEQALKDYDDVIKKNPRNAQVMYNQGNALRGLQRHNESLQAYDRAIELN 655
                                       568899*****************999****************99999998876 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.8   2.5e+03     103     117 ..     248     262 ..     242     274 .. 0.80
   2 ?    5.4   0.0     0.036        16     102     124 ..     495     517 ..     486     521 .. 0.87
   3 ?    2.2   0.0      0.33   1.4e+02     103     121 ..     564     582 ..     559     590 .. 0.89
   4 ?    0.3   0.1       1.3   5.5e+02     100     121 ..     603     624 ..     598     634 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.8
                              LemA 103 rYneavreyntkies 117
                                       rYn+++++y+  +++
  gi|330509110|ref|YP_004385538.1| 248 RYNRSIQAYDDLVQT 262
                                       79*******999887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.036
                              LemA 102 rrYneavreyntkiesfpsniva 124
                                        rYne++++yn+++e  p+ni a
  gi|330509110|ref|YP_004385538.1| 495 GRYNESIESYNKSLEIDPKNIGA 517
                                       58****************99976 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.33
                              LemA 103 rYneavreyntkiesfpsn 121
                                        Yne++++y+ +i ++p++
  gi|330509110|ref|YP_004385538.1| 564 MYNESIQAYDRAIAEMPQQ 582
                                       6****************86 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 1.3
                              LemA 100 aRrrYneavreyntkiesfpsn 121
                                       a+++Y +a ++y+  i++ p n
  gi|330509110|ref|YP_004385538.1| 603 AQEDYEQALKDYDDVIKKNPRN 624
                                       7899*************99988 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       2.2   9.5e+02      31      52 ..     341     362 ..     336     365 .. 0.78
   2 ?   11.6   0.1   0.00075      0.33      34      70 ..     589     625 ..     566     631 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2.2
                           DUF5344  31 etisgknsldvvekineleeel 52 
                                          s+++ l++ +k+ e+++++
  gi|330509110|ref|YP_004385538.1| 341 RNDSHEEALQAFDKAIEINQSY 362
                                       5667788899999999999988 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00075
                           DUF5344  34 sgknsldvvekineleeeleellkaYktlllknvedt 70 
                                       ++   ld + ++ e +e++e++lk+Y ++++kn   +
  gi|330509110|ref|YP_004385538.1| 589 GKGMALDSLGRYDEAQEDYEQALKDYDDVIKKNPRNA 625
                                       44456999999*********************96655 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       3.6   1.6e+03      18      32 ..     346     360 ..     342     362 .. 0.84
   2 ?    1.5   0.0      0.47     2e+02      16      30 ..     496     510 ..     495     511 .. 0.93
   3 ?    3.8   0.0     0.093        40      16      30 ..     530     544 ..     528     544 .. 0.93
   4 ?    8.5   0.2     0.003       1.3      16      29 ..     599     612 ..     597     614 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.6
                          SHNi-TPR  18 pqAveDlrkaLeLre 32 
                                       ++A++ ++ka+e+ +
  gi|330509110|ref|YP_004385538.1| 346 EEALQAFDKAIEINQ 360
                                       799********9966 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.47
                          SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                       ++++ +e ++k+Le+
  gi|330509110|ref|YP_004385538.1| 496 RYNESIESYNKSLEI 510
                                       89***********98 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.093
                          SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                       ++++A+e +++aLe+
  gi|330509110|ref|YP_004385538.1| 530 RYEEALEYYNRALEI 544
                                       9************98 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.003
                          SHNi-TPR  16 nFpqAveDlrkaLe 29 
                                       ++++A+eD++ aL+
  gi|330509110|ref|YP_004385538.1| 599 RYDEAQEDYEQALK 612
                                       9***********96 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 ?    4.0   0.5     0.082        36      51     114 ..      45     104 ..      41     109 .. 0.80
   2 ?    9.8   0.6    0.0014      0.63       2      76 ..      81     152 ..      78     161 .. 0.85
   3 ?   -0.4   0.0       1.8     8e+02     108     127 ..     415     434 ..     383     491 .. 0.76
   4 ?    0.2   0.0       1.2   5.3e+02      52      99 ..     498     541 ..     488     579 .. 0.76
   5 ?    1.3   0.1      0.56   2.5e+02       7      41 ..     607     641 ..     602     654 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.082
                                       HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT-H CS
                       TOM20_plant  51 iqdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqavdedPdnd 114
                                       i++a+  +++a+ i+P+  da W +g a  s a + ++++e+ e f    ++ +++++e+P+++
  gi|330509110|ref|YP_004385538.1|  45 IDEALEAFDNAIQIEPQNIDA-W-LGKAK-SLA-YMDEKNESLEAFRNILNLTNETIKENPEDT 104
                                       7899***************99.5.57764.444.456778888889988888899999998876 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHH CS
                       TOM20_plant   2 drlllfeearkdaeatykknPldadnllrWggallelsqfqsvaeakqmiqdaiskleeallidPkkhdalWcig 76 
                                       + l  f ++ + +++t k+nP+d+      g al  l +    aea    + +i  l+++ll dPk  +a W+ +
  gi|330509110|ref|YP_004385538.1|  81 ESLEAFRNILNLTNETIKENPEDTSAWQSKGIALASLGR---EAEATDAFERSIELLNQSLLNDPKDAEAWWLKA 152
                                       5677899999999***********987777777766665...568889999*********************865 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.8
                                       HH-TT-HHHHHHHHHHHTHH CS
                       TOM20_plant 108 dedPdndlyrkslelaakaP 127
                                        ++ + + y+++lela+ka 
  gi|330509110|ref|YP_004385538.1| 415 RNEESAQAYERALELADKAV 434
                                       56667889999999999985 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHH CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfeka 99 
                                       +++i  ++++l idPk   al   g a  s +++     ea e++++a
  gi|330509110|ref|YP_004385538.1| 498 NESIESYNKSLEIDPKNIGALRGEGYALASLGRYE----EALEYYNRA 541
                                       78888899999999999999999888888888874....444444444 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.56
                                       HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH CS
                       TOM20_plant   7 feearkdaeatykknPldadnllrWggallelsqf 41 
                                       +e+a kd ++  kknP +a+ +   g+al  l + 
  gi|330509110|ref|YP_004385538.1| 607 YEQALKDYDDVIKKNPRNAQVMYNQGNALRGLQRH 641
                                       68899999999999999999999999998777554 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0029       1.3       2      20 ..      90     108 ..      90     108 .. 0.96
   2 ?    1.1   0.2      0.83   3.6e+02       3      19 ..     132     148 ..     131     149 .. 0.88
   3 ?   -1.2   0.0       4.2   1.8e+03       7      15 ..     506     514 ..     505     517 .. 0.80
   4 ?    1.3   0.0      0.71   3.1e+02       7      17 ..     616     626 ..     615     627 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHH-TT-CHHHH CS
                              PPTA   2 LeltekliekdpkNYsaWn 20 
                                       L+lt++ i+++p + saW+
  gi|330509110|ref|YP_004385538.1|  90 LNLTNETIKENPEDTSAWQ 108
                                       89****************6 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.83
                                       HHHHHHHHH-TT-CHHH CS
                              PPTA   3 eltekliekdpkNYsaW 19 
                                       el ++ + +dpk+  aW
  gi|330509110|ref|YP_004385538.1| 132 ELLNQSLLNDPKDAEAW 148
                                       899999*******9999 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.2
                                       HHHHH-TT- CS
                              PPTA   7 kliekdpkN 15 
                                       k +e dpkN
  gi|330509110|ref|YP_004385538.1| 506 KSLEIDPKN 514
                                       56899**** PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.71
                                       HHHHH-TT-CH CS
                              PPTA   7 kliekdpkNYs 17 
                                       ++i+k+p+N +
  gi|330509110|ref|YP_004385538.1| 616 DVIKKNPRNAQ 626
                                       78*******66 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.24     1e+02     127     170 ..      87     131 ..      64     140 .. 0.82
   2 ?    0.5   0.1       1.1     5e+02     156     181 ..     459     484 ..     454     488 .. 0.89
   3 ?    0.2   0.0       1.4     6e+02     151     169 ..     523     541 ..     500     552 .. 0.91
   4 ?    9.1   0.4    0.0027       1.2     113     180 ..     594     662 ..     564     667 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.24
                           Wzy_C_2 127 aaklalarklihlsPepav.ierlilslallGdedeAeqilarar 170
                                          l l++++i+  Pe +   +   ++la lG+e+eA++  +r +
  gi|330509110|ref|YP_004385538.1|  87 RNILNLTNETIKENPEDTSaWQSKGIALASLGREAEATDAFERSI 131
                                       567888999999999987624667799************999866 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.1
                           Wzy_C_2 156 lGdedeAeqilararalfpeedakwv 181
                                       +G+  eA+  +a   ++ pe++++w+
  gi|330509110|ref|YP_004385538.1| 459 QGRYVEALEAVANSSKANPEDAFAWA 484
                                       89***********************5 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.4
                           Wzy_C_2 151 lslallGdedeAeqilara 169
                                       ++la lG+ +eA+ ++ ra
  gi|330509110|ref|YP_004385538.1| 523 YALASLGRYEEALEYYNRA 541
                                       68999***********998 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0027
                           Wzy_C_2 113 llelgllplspenlaaklalarklihlsPepa.vierlilslallGdedeAeqilararalfpeedakw 180
                                       l  lg++   +e++++ l+ + ++i+  P+ a v++++  +l +l+++ e +q ++ra+ l p +  +w
  gi|330509110|ref|YP_004385538.1| 594 LDSLGRYDEAQEDYEQALKDYDDVIKKNPRNAqVMYNQGNALRGLQRHNESLQAYDRAIELNPGYIDAW 662
                                       5678899999*******************975499**************************99998888 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.042        18       7      50 ..      48      91 ..      44      99 .. 0.90
   2 ?    1.2   0.0       1.1   4.6e+02      13      45 ..      95     127 ..      90     132 .. 0.89
   3 ?    3.7   0.2      0.18        78       7      49 ..     130     172 ..     122     183 .. 0.85
   4 ?   -1.3   0.0       6.6   2.9e+03      66      85 ..     408     427 ..     370     430 .. 0.53
   5 ?    5.1   0.0     0.067        29       6      56 ..     499     549 ..     496     580 .. 0.79
   6 ?    1.0   0.1       1.3   5.6e+02       7      43 ..     610     646 ..     596     678 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.042
                            TPR_20  7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50
                                       l+++++a++ +p+++da l  A+ l+   ++ e+le++ +il 
  gi|330509110|ref|YP_004385538.1| 48 ALEAFDNAIQIEPQNIDAWLGKAKSLAYMDEKNESLEAFRNILN 91
                                      68999*******************************99988886 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.1
                            TPR_20  13 aalaanpddldarldlAlallaagryeeAleqL 45 
                                       +++++np+d  a      al++ gr++eA +++
  gi|330509110|ref|YP_004385538.1|  95 ETIKENPEDTSAWQSKGIALASLGREAEATDAF 127
                                       7899************************99875 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.18
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleil 49 
                                       +++ l + l ++p+d +a    A+ l   gr + Ale+  +++
  gi|330509110|ref|YP_004385538.1| 130 SIELLNQSLLNDPKDAEAWWLKAENLELLGRTDSALEAYDKVI 172
                                       678899999**************************99865555 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 6.6
                            TPR_20  66 kifealgsqdplvakyRrkL 85 
                                       k++++lg +++ +++y r L
  gi|330509110|ref|YP_004385538.1| 408 KVLAILGRNEESAQAYERAL 427
                                       56666777777777666665 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.067
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwe 56 
                                       +++++  + l+ +p+++ a      al++ gryeeAle   + l+ d+ ++
  gi|330509110|ref|YP_004385538.1| 499 ESIESYNKSLEIDPKNIGALRGEGYALASLGRYEEALEYYNRALEIDSRFA 549
                                       6788899999****************************9999888888873 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 1.3
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAle 43 
                                        l++ ++ +++np + + +++  +al   +r+ e+l+
  gi|330509110|ref|YP_004385538.1| 610 ALKDYDDVIKKNPRNAQVMYNQGNALRGLQRHNESLQ 646
                                       4566667778888888888888887777777776665 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 ?    1.5   0.0      0.49   2.2e+02       3      15 ..     346     358 ..     344     361 .. 0.90
   2 ?    1.4   0.0      0.53   2.3e+02       1      15 [.     378     392 ..     378     393 .. 0.93
   3 ?   -0.4   0.1         2   8.8e+02       2      14 ..     423     435 ..     422     440 .. 0.91
   4 ?    0.5   0.0       1.1   4.8e+02       1      15 [.     496     510 ..     496     513 .. 0.91
   5 ?    6.7   0.1     0.012       5.2       1      15 [.     530     544 ..     530     549 .. 0.91
   6 ?    2.9   0.1      0.18        80       2      26 ..     565     589 ..     564     590 .. 0.91
   7 ?   -2.4   0.1       8.7   3.8e+03       1      14 [.     599     612 ..     599     613 .. 0.84
   8 ?   -0.0   0.0       1.5   6.6e+02       2      14 ..     641     653 ..     626     655 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.49
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   3 eeaLeqvnkAiei 15 
                                       eeaL+  +kAiei
  gi|330509110|ref|YP_004385538.1| 346 EEALQAFDKAIEI 358
                                       89*********98 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.53
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rYeea+   ++Aie+
  gi|330509110|ref|YP_004385538.1| 378 RYEEAIAAWDRAIEL 392
                                       7************95 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAie 14 
                                       Ye aLe  +kA+ 
  gi|330509110|ref|YP_004385538.1| 423 YERALELADKAVT 435
                                       9**********85 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.1
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rY+e++e  nk +ei
  gi|330509110|ref|YP_004385538.1| 496 RYNESIESYNKSLEI 510
                                       7**********9987 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.012
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rYeeaLe+ n+A+ei
  gi|330509110|ref|YP_004385538.1| 530 RYEEALEYYNRALEI 544
                                       7************98 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHTTB-TTHH CS
                          HTH_Bact   2 YeeaLeqvnkAieiSirinsMsLlG 26 
                                       Y+e+++  ++Ai+   ++   +L+G
  gi|330509110|ref|YP_004385538.1| 565 YNESIQAYDRAIAEMPQQPQYALIG 589
                                       9************999999999888 PP

  == domain 7  score: -2.4 bits;  conditional E-value: 8.7
                                       -HHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAie 14 
                                       rY+ea e  ++A++
  gi|330509110|ref|YP_004385538.1| 599 RYDEAQEDYEQALK 612
                                       79999999999986 PP

  == domain 8  score: -0.0 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAie 14 
                                        +e+L+  ++Aie
  gi|330509110|ref|YP_004385538.1| 641 HNESLQAYDRAIE 653
                                       5788888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (722 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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):              41  [number of targets reported over threshold]
# CPU time: 0.97u 0.28s 00:00:01.25 Elapsed: 00:00:00.53
# Mc/sec: 4074.98
//
Query:       gi|330509111|ref|YP_004385539.1|  [L=788]
Description: extracellular protein [Methanosaeta concilii GP6]
Scores for complete 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-48  161.6 130.1    8.6e-07   28.8   7.9   10.9 10  Dicty_CTDC  Dictyostelium (slime mold) repeat
    0.00018   21.5  17.8    0.00018   21.5  17.8    4.8  5  Mucin-like  Mucin-like


Domain annotation for each model (and alignments):
>> Dicty_CTDC  Dictyostelium (slime mold) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   7.9   9.6e-11   8.6e-07       1      22 [.      37      57 ..      37      58 .. 0.96
   2 !   21.7   1.9   1.6e-08   0.00014       1      23 [.     414     435 ..     414     435 .. 0.95
   3 !   21.6  10.5   1.7e-08   0.00015       1      23 [.     437     458 ..     437     458 .. 0.96
   4 !   16.7   3.1   5.7e-07    0.0051       1      24 []     460     482 ..     460     482 .. 0.89
   5 !   20.5   6.1   3.6e-08   0.00032       1      24 []     483     505 ..     483     505 .. 0.90
   6 !   22.4   8.1     9e-09   8.1e-05       1      24 []     506     528 ..     506     528 .. 0.92
   7 !   17.9   8.4   2.3e-07    0.0021       1      24 []     529     551 ..     529     551 .. 0.92
   8 !   19.0   6.6   1.1e-07   0.00095       1      24 []     552     574 ..     552     574 .. 0.92
   9 !   23.1   2.0   5.4e-09   4.9e-05       1      24 []     575     598 ..     575     598 .. 0.93
  10 !   25.6   4.6   9.5e-10   8.5e-06       1      21 [.     599     619 ..     599     619 .. 0.98

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 9.6e-11
                        Dicty_CTDC  1 NpCTiDsCsnstGCvHTPisCD 22
                                      NpCT D+C ++ GCvH Pi CD
  gi|330509111|ref|YP_004385539.1| 37 NPCTKDYCGPN-GCVHEPIDCD 57
                                      9********99.9********9 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.6e-08
                        Dicty_CTDC   1 NpCTiDsCsnstGCvHTPisCDD 23 
                                       N+CT D  + +  CvHTP++CDD
  gi|330509111|ref|YP_004385539.1| 414 NACTADAWNGKE-CVHTPVNCDD 435
                                       9*******9887.*********9 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 1.7e-08
                        Dicty_CTDC   1 NpCTiDsCsnstG.CvHTPisCDD 23 
                                       NpCTiDsC   +G C+H++  CDD
  gi|330509111|ref|YP_004385539.1| 437 NPCTIDSCE--NGvCTHKQKDCDD 458
                                       9*******8..799*********9 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 5.7e-07
                        Dicty_CTDC   1 NpCTiDsCsnstG.CvHTPisCDDN 24 
                                       N  TiD+C   +G CvH+   CDD+
  gi|330509111|ref|YP_004385539.1| 460 NESTIDYCL--NGvCVHSSKKCDDG 482
                                       666*****6..799**********7 PP

  == domain 5  score: 20.5 bits;  conditional E-value: 3.6e-08
                        Dicty_CTDC   1 NpCTiDsCsnstGCvHTPisCDDN 24 
                                       N+CTiD+ + +  CvHTP +CDD+
  gi|330509111|ref|YP_004385539.1| 483 NACTIDTWNGNE-CVHTPGNCDDG 505
                                       9******88555.**********7 PP

  == domain 6  score: 22.4 bits;  conditional E-value: 9e-09
                        Dicty_CTDC   1 NpCTiDsCsnstGCvHTPisCDDN 24 
                                       N+CT DsC n t C+H + +C+D+
  gi|330509111|ref|YP_004385539.1| 506 NACTADSCENGT-CTHRQKNCNDG 528
                                       9*******9666.**********7 PP

  == domain 7  score: 17.9 bits;  conditional E-value: 2.3e-07
                        Dicty_CTDC   1 NpCTiDsCsnstG.CvHTPisCDDN 24 
                                       NpCT+DsC   +G C+H   +C+D+
  gi|330509111|ref|YP_004385539.1| 529 NPCTVDSCV--NGeCYHMGKNCNDG 551
                                       9*******4..688**********7 PP

  == domain 8  score: 19.0 bits;  conditional E-value: 1.1e-07
                        Dicty_CTDC   1 NpCTiDsCsnstG.CvHTPisCDDN 24 
                                       NpCT DsC   +G C+H   +CDD+
  gi|330509111|ref|YP_004385539.1| 552 NPCTADSCV--NGeCYHRGKNCDDG 574
                                       9*******4..688**********7 PP

  == domain 9  score: 23.1 bits;  conditional E-value: 5.4e-09
                        Dicty_CTDC   1 NpCTiDsCsnstG.CvHTPisCDDN 24 
                                       N+CTiD C+   G C H   +CDD+
  gi|330509111|ref|YP_004385539.1| 575 NACTIDACDGR-GkCMHLRRNCDDG 598
                                       9********55.99**********7 PP

  == domain 10  score: 25.6 bits;  conditional E-value: 9.5e-10
                        Dicty_CTDC   1 NpCTiDsCsnstGCvHTPisC 21 
                                       NpCTiD C++  GC HTP+ C
  gi|330509111|ref|YP_004385539.1| 599 NPCTIDECDPYWGCSHTPVVC 619
                                       9********999*******99 PP

>> Mucin-like  Mucin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2  21.0   1.9e-06     0.017       7      98 ..      61     152 ..      51     154 .. 0.65
   2 !   21.5  17.8     2e-08   0.00018       3      95 ..     134     226 ..     133     231 .. 0.67
   3 !    8.9  21.0   0.00017       1.5       3      67 ..     211     277 ..     209     310 .. 0.82
   4 ?   -1.5   0.7      0.29   2.6e+03      67      85 ..     367     385 ..     327     404 .. 0.43
   5 ?   -2.1   0.7      0.46   4.2e+03      76      86 ..     636     646 ..     631     652 .. 0.41

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-06
                        Mucin-like   7 tqppaspsssygepsraPsssytapsrapsssygepprdpsssytapqsapsssytappstpsssygeppaapsssy 83 
                                       t+pp+ +   ++ p++ +s+++t+p++ +s  ++ pp  +s  + +p++  s s+ +pp+  s s++ pp+ +s s+
  gi|330509111|ref|YP_004385539.1|  61 TSPPEVTGPGITSPPEVTSPGITSPPEVTSPGITSPPDITSPGIANPPEVTSPSIANPPEITSPSITNPPEVTSPSI 137
                                       55666666666666666666666666666666666666666666666666666666666666666666666666666 PP

                        Mucin-like  84 tapprdpsssytapp 98 
                                       t+p +  s  + +pp
  gi|330509111|ref|YP_004385539.1| 138 TNPLEVTSPGIANPP 152
                                       666666666666665 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2e-08
                        Mucin-like   3 sssstqppaspsssygepsraPsssytapsrapsssygepprdpsssytapqsapsssytappstpsssygeppaap 79 
                                       s+s+t p + +s  + +p++ +s+++ +p++  s s+++p + +s s+t+p++  s s+t+pp+  s ++  p + +
  gi|330509111|ref|YP_004385539.1| 134 SPSITNPLEVTSPGIANPPEVTSPGIANPPEVASPSITNPLEVTSPSITNPPEVTSPSITNPPEVTSPGIANPLEVT 210
                                       45666666777777777777777777777777777777777777777777777777777777777777777777777 PP

                        Mucin-like  80 sssytapprdpsssyt 95 
                                       s s+t pp+  s  + 
  gi|330509111|ref|YP_004385539.1| 211 SPSITSPPEATSPGIA 226
                                       7777777776665555 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00017
                        Mucin-like   3 sssstqppaspsssygepsraPsssytapsrapsssygepprdpsssytapqsapsssytapps..t 67 
                                       s+s+t+pp+++s  + +p + + +++t+p+  +s +++ p++ +s ++t p++  s ++t+pp+   
  gi|330509111|ref|YP_004385539.1| 211 SPSITSPPEATSPGIANPLEVTGPGITSPPDITSPDITSPSEISSPDITSPSENRSPDITNPPEitS 277
                                       7899999999999999999999999999999999999999999999999999999999999988552 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.29
                        Mucin-like  67 tpsssygeppaapsssyta 85 
                                       +++s +  +p++ +ss+ +
  gi|330509111|ref|YP_004385539.1| 367 ANTSFIESMPTQGNSSILQ 385
                                       2222222223333333332 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 0.46
                        Mucin-like  76 paapsssytap 86 
                                       p+a +ssyt p
  gi|330509111|ref|YP_004385539.1| 636 PRAAPSSYTIP 646
                                       22222223222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (788 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.46
# Mc/sec: 5117.32
//
Query:       gi|330509112|ref|YP_004385540.1|  [L=598]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-43  143.1  37.4    8.8e-05   22.3   0.1   13.3 13  TPR_2            Tetratricopeptide repeat
    2.9e-42  139.4  32.9    0.00055   19.9   0.0   12.6 12  TPR_8            Tetratricopeptide repeat
    4.5e-42  140.2  40.0    3.2e-06   26.7   0.1   13.4 13  TPR_1            Tetratricopeptide repeat
    1.1e-34  117.9  36.2    3.2e-05   23.5   0.2   12.2 12  TPR_11           TPR repeat
    8.1e-24   83.7  28.9    6.5e-07   29.5   0.8    7.9  8  TPR_12           Tetratricopeptide repeat
    1.2e-23   81.7  20.0       0.13   12.7   0.0   11.4 10  TPR_17           Tetratricopeptide repeat
    1.8e-23   81.2  26.5    0.00031   21.3   0.1   12.2 13  TPR_14           Tetratricopeptide repeat
    3.6e-19   69.1  29.3      2e-07   31.6   1.6    8.1  9  TPR_16           Tetratricopeptide repeat
    1.7e-10   40.9  25.4       0.22   12.2   0.0   10.5 11  TPR_6            Tetratricopeptide repeat
    1.8e-10   41.2  27.0      0.014   15.9   0.5    8.3  9  TPR_19           Tetratricopeptide repeat
    5.7e-09   36.0  12.4      0.059   13.5   0.1    8.1  9  TPR_9            Tetratricopeptide repeat
    3.4e-07   30.4  18.6      0.037   14.1   1.4    6.4  4  DUF3856          Domain of Unknown Function (DUF3856)
    4.4e-05   23.6  15.5       0.59   10.4   0.4    5.8  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    0.00011   21.7   1.9        6.5    6.4   0.0    5.9  6  HTH_Bact         Helix-turn-helix bacterial domain
    0.00023   20.8   0.0        9.8    6.1   0.0    4.5  4  PPTA             Protein prenyltransferase alpha subunit repe
    0.00029   21.3   6.8       0.55   10.6   0.1    5.1  5  BTAD             Bacterial transcriptional activator domain
    0.00065   19.5  17.0        5.3    7.3   0.1    9.3 10  TPR_7            Tetratricopeptide repeat
    0.00073   19.6   6.6         20    5.3   0.0    6.4  7  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    0.00084   19.4   4.6        7.3    6.8   0.1    5.1  5  DUF1510          Domain of unknown function (DUF1510)
     0.0045   16.9   1.0        5.2    6.9   0.0    5.0  5  LemA             LemA family
  ------ inclusion threshold ------
      0.056   13.5   0.6         31    4.7   0.0    4.3  5  MAS20            MAS20 protein import receptor
      0.059   13.3  25.6        5.2    7.1   0.0    8.9 10  TPR_10           Tetratricopeptide repeat
      0.061   13.0   0.1      0.061   13.0   0.1    5.2  6  TPR_21           Tetratricopeptide repeat-like domain
       0.14   12.4   2.3        1.7    8.9   0.0    3.5  3  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
       0.16   12.4  11.5        4.1    7.9   0.5    4.8  5  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
       0.21   11.9   1.8         33    5.0   0.0    4.6  3  PPR              PPR repeat
       0.52   10.4   8.7         14    5.9   0.0    5.6  4  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 ?    1.8   0.0      0.51   3.4e+02      24      34 .]      48      58 ..      42      58 .. 0.91
   2 !   10.7   0.0    0.0007      0.46       1      29 [.      59      87 ..      59      90 .. 0.92
   3 !   12.5   0.1   0.00018      0.12       1      31 [.     100     130 ..     100     133 .. 0.94
   4 !    8.2   0.1    0.0045         3       4      31 ..     144     171 ..     141     173 .. 0.86
   5 !   11.8   0.0   0.00032      0.21       3      34 .]     178     210 ..     176     210 .. 0.84
   6 !   17.3   0.0   5.5e-06    0.0037       3      34 .]     296     327 ..     294     327 .. 0.95
   7 !    9.4   0.0    0.0018       1.2      16      34 .]     350     368 ..     347     368 .. 0.93
   8 !   15.8   0.1   1.7e-05     0.011      17      32 ..     394     409 ..     390     411 .. 0.94
   9 !    8.8   0.1    0.0029       1.9      13      34 .]     425     446 ..     413     446 .. 0.83
  10 !   22.3   0.1   1.3e-07   8.8e-05       2      31 ..     455     484 ..     454     487 .. 0.94
  11 !   20.3   0.1   5.8e-07   0.00038       1      33 [.     489     521 ..     489     522 .. 0.94
  12 !   10.8   0.2   0.00064      0.42       7      33 ..     534     560 ..     528     561 .. 0.81
  13 !   10.5   0.3   0.00083      0.55       1      30 [.     565     594 ..     565     596 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.51
                             TPR_2 24 fekAleldPnn 34
                                      ++ Al+ldP+n
  gi|330509112|ref|YP_004385540.1| 48 YDHALQLDPGN 58
                                      899******87 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0007
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAle 29
                                      a a+   +++   lg+  e +e+f+kAl 
  gi|330509112|ref|YP_004385540.1| 59 ASAWLGKAQVSQILGNQIESREYFQKALD 87
                                      579999*********************96 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00018
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       a+a+ ++G a++ l + eeA+ a+e+++e+ 
  gi|330509112|ref|YP_004385540.1| 100 AKAWQAMGVALAGLARNEEAIGALERSIEIS 130
                                       79**************************986 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0045
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleld 31 
                                       l++ + +y++l     A++a+ek++el+
  gi|330509112|ref|YP_004385540.1| 144 LWQKAVSYEALYMDYAAIKAYEKVIELN 171
                                       6778889999999999***********9 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 0.00032
                             TPR_2   3 alynlGlayyklgdy.eeAleafekAleldPnn 34 
                                       a+ +++++++++ +  +e +eaf++A++l P+n
  gi|330509112|ref|YP_004385540.1| 178 AWIRIADILFAKANGyNESVEAFNEAIRLMPDN 210
                                       6777777777777766***************98 PP

  == domain 6  score: 17.3 bits;  conditional E-value: 5.5e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++y   + ++k+  yee +ea+++A+eldP+n
  gi|330509112|ref|YP_004385540.1| 296 GWYKTSQELFKKASYEESVEALNRAIELDPQN 327
                                       799999************************97 PP

  == domain 7  score: 9.4 bits;  conditional E-value: 0.0018
                             TPR_2  16 dyeeAleafekAleldPnn 34 
                                       +y+e l+a +kA+eldP+n
  gi|330509112|ref|YP_004385540.1| 350 QYNESLKAQDKAIELDPGN 368
                                       8****************97 PP

  == domain 8  score: 15.8 bits;  conditional E-value: 1.7e-05
                             TPR_2  17 yeeAleafekAleldP 32 
                                       yeeA++ f+kAleldP
  gi|330509112|ref|YP_004385540.1| 394 YEEAIKEFDKALELDP 409
                                       9**************9 PP

  == domain 9  score: 8.8 bits;  conditional E-value: 0.0029
                             TPR_2  13 klgdyeeAleafekAleldPnn 34 
                                       +l++ +eAl a++kA+ ld +n
  gi|330509112|ref|YP_004385540.1| 425 RLNKSAEALLAYDKAIDLDGEN 446
                                       67888*************9775 PP

  == domain 10  score: 22.3 bits;  conditional E-value: 1.3e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                        a+   G a++klg+y+e  eaf+kA+el+
  gi|330509112|ref|YP_004385540.1| 455 NAWSGKGTALAKLGRYNESFEAFDKAIELN 484
                                       589**************************8 PP

  == domain 11  score: 20.3 bits;  conditional E-value: 5.8e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a ++ + G+a+ ++g+yeeA+ a++k++e +P+
  gi|330509112|ref|YP_004385540.1| 489 AFVWLAKGDALNQSGRYEEAAFAYDKVVEQNPD 521
                                       678999**************************8 PP

  == domain 12  score: 10.8 bits;  conditional E-value: 0.00064
                             TPR_2   7 lGlayyklgdyeeAleafekAleldPn 33 
                                        G+a+ + g+y+eA+ a++ A+e +P 
  gi|330509112|ref|YP_004385540.1| 534 KGDALSAWGKYDEAVIAYDNAIENYPS 560
                                       666666679**************9995 PP

  == domain 13  score: 10.5 bits;  conditional E-value: 0.00083
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a+ ++  G a+ +lg+  +A +af kA el
  gi|330509112|ref|YP_004385540.1| 565 AQTWHKKGIALQALGRTSDADAAFAKAKEL 594
                                       678************************887 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00019      0.12       1      30 [.      59      88 ..      59      91 .. 0.93
   2 !   11.0   0.1   0.00061       0.4       1      32 [.     100     131 ..     100     133 .. 0.94
   3 !    9.1   0.8    0.0025       1.6       3      32 ..     143     172 ..     141     174 .. 0.85
   4 !    9.4   0.0     0.002       1.4       3      34 .]     178     210 ..     176     210 .. 0.88
   5 !   18.5   0.0   2.5e-06    0.0016       3      34 .]     296     327 ..     294     327 .. 0.93
   6 ?    7.1   0.0     0.011       7.1      16      33 ..     350     367 ..     342     368 .. 0.92
   7 !   12.2   0.1   0.00025      0.17      16      32 ..     393     409 ..     386     411 .. 0.90
   8 !    7.3   0.2    0.0097       6.4       3      33 ..     414     445 ..     412     446 .. 0.82
   9 !   18.9   0.1   1.8e-06    0.0012       3      31 ..     456     484 ..     454     486 .. 0.92
  10 !   19.9   0.0   8.3e-07   0.00055       3      33 ..     491     521 ..     491     522 .. 0.96
  11 !   17.7   0.2   4.3e-06    0.0029       1      32 [.     528     559 ..     528     561 .. 0.93
  12 !    9.4   0.1     0.002       1.3       1      30 [.     565     594 ..     565     594 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekalel 30
                                      a+a++ ++++ + lg+  e+ ey++kal++
  gi|330509112|ref|YP_004385540.1| 59 ASAWLGKAQVSQILGNQIESREYFQKALDA 88
                                      689************************985 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00061
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+a++ +g ++  l + eeA+ ++e+ +e++ 
  gi|330509112|ref|YP_004385540.1| 100 AKAWQAMGVALAGLARNEEAIGALERSIEISD 131
                                       79***************************985 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ++++++  y+ l    +A+++yek++el+ 
  gi|330509112|ref|YP_004385540.1| 143 SLWQKAVSYEALYMDYAAIKAYEKVIELNS 172
                                       67788888888888899***********96 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.002
                                       HHHHHHHHH.HHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiy.lklgdyeeAkeyyekaleldpdn 34 
                                       a+ ++++i+  k + y+e++e++++a++l pdn
  gi|330509112|ref|YP_004385540.1| 178 AWIRIADILfAKANGYNESVEAFNEAIRLMPDN 210
                                       899***999788888*************98875 PP

  == domain 5  score: 18.5 bits;  conditional E-value: 2.5e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        +y+ ++ ++k+  yee++e++++a+eldp+n
  gi|330509112|ref|YP_004385540.1| 296 GWYKTSQELFKKASYEESVEALNRAIELDPQN 327
                                       68999999**********************96 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.011
                                       -HHHHHHHHHHHHHHHHH CS
                             TPR_8  16 dyeeAkeyyekaleldpd 33 
                                       +y+e+ ++  ka+eldp 
  gi|330509112|ref|YP_004385540.1| 350 QYNESLKAQDKAIELDPG 367
                                       79**************96 PP

  == domain 7  score: 12.2 bits;  conditional E-value: 0.00025
                                       -HHHHHHHHHHHHHHHH CS
                             TPR_8  16 dyeeAkeyyekaleldp 32 
                                        yeeA++ + kaleldp
  gi|330509112|ref|YP_004385540.1| 393 LYEEAIKEFDKALELDP 409
                                       59**************9 PP

  == domain 8  score: 7.3 bits;  conditional E-value: 0.0097
                                       HHHHHHHHH.HHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiy.lklgdyeeAkeyyekaleldpd 33 
                                       a+  ++s++   l++  eA  +y ka++ld +
  gi|330509112|ref|YP_004385540.1| 414 AWTYKASVLdTRLNKSAEALLAYDKAIDLDGE 445
                                       555667777789*****************976 PP

  == domain 9  score: 18.9 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a+  +g ++ klg+y+e+ e++ ka+el+
  gi|330509112|ref|YP_004385540.1| 456 AWSGKGTALAKLGRYNESFEAFDKAIELN 484
                                       78899**********************98 PP

  == domain 10  score: 19.9 bits;  conditional E-value: 8.3e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +++ +g+++ + g+yeeA  +y k++e +pd
  gi|330509112|ref|YP_004385540.1| 491 VWLAKGDALNQSGRYEEAAFAYDKVVEQNPD 521
                                       699**************************98 PP

  == domain 11  score: 17.7 bits;  conditional E-value: 4.3e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+ay  +g++++  g+y+eA+ +y  a+e  p
  gi|330509112|ref|YP_004385540.1| 528 AHAYGSKGDALSAWGKYDEAVIAYDNAIENYP 559
                                       689*************************9877 PP

  == domain 12  score: 9.4 bits;  conditional E-value: 0.002
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+ ++++g +++ lg+   A +++ ka el
  gi|330509112|ref|YP_004385540.1| 565 AQTWHKKGIALQALGRTSDADAAFAKAKEL 594
                                       689************************876 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0       0.3     2e+02      24      34 .]      48      58 ..      41      58 .. 0.83
   2 !    8.0   0.1     0.004       2.6       1      29 [.      59      87 ..      59      88 .. 0.95
   3 !    9.6   0.1    0.0012      0.82       1      30 [.     100     129 ..     100     132 .. 0.96
   4 !    9.7   0.2    0.0012      0.77      19      32 ..     159     172 ..     147     174 .. 0.91
   5 !    7.3   0.0    0.0068       4.5      17      34 .]     193     210 ..     178     210 .. 0.91
   6 !   14.1   0.2   4.5e-05      0.03      11      34 .]     304     327 ..     302     327 .. 0.88
   7 ?    6.3   0.1     0.013       8.8      15      34 .]     349     368 ..     347     368 .. 0.89
   8 !   15.1   0.2   2.3e-05     0.015      17      34 .]     394     411 ..     388     411 .. 0.88
   9 !    9.6   0.1    0.0013      0.84      14      33 ..     426     445 ..     424     446 .. 0.88
  10 !   26.7   0.1   4.8e-09   3.2e-06       2      31 ..     455     484 ..     454     485 .. 0.97
  11 !   22.7   0.0   8.8e-08   5.9e-05       2      33 ..     490     521 ..     489     522 .. 0.94
  12 !   20.2   0.2   5.3e-07   0.00035       3      33 ..     530     560 ..     528     561 .. 0.94
  13 !    8.4   0.1    0.0029       1.9       1      30 [.     565     594 ..     565     594 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.3
                                      HHHHHHHSTTH CS
                             TPR_1 24 yekALelnPnn 34
                                      y+ AL+l+P n
  gi|330509112|ref|YP_004385540.1| 48 YDHALQLDPGN 58
                                      999******87 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.004
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALe 29
                                      a a+ +++++ + lg+  e  ey++kAL 
  gi|330509112|ref|YP_004385540.1| 59 ASAWLGKAQVSQILGNQIESREYFQKALD 87
                                      689************************95 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       aka+  +G+a+  l + +eA+ + e+ +e+
  gi|330509112|ref|YP_004385540.1| 100 AKAWQAMGVALAGLARNEEAIGALERSIEI 129
                                       89***************************8 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHST CS
                             TPR_1  19 eAleyyekALelnP 32 
                                        A+++yek++eln 
  gi|330509112|ref|YP_004385540.1| 159 AAIKAYEKVIELNS 172
                                       6***********97 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.0068
                                       HHHHHHHHHHHHHHSTTH CS
                             TPR_1  17 ydeAleyyekALelnPnn 34 
                                       y+e +e++++A++l P+n
  gi|330509112|ref|YP_004385540.1| 193 YNESVEAFNEAIRLMPDN 210
                                       99**************98 PP

  == domain 6  score: 14.1 bits;  conditional E-value: 4.5e-05
                                       HHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  11 yfklgkydeAleyyekALelnPnn 34 
                                       +fk+  y+e +e+ ++A+el+P+n
  gi|330509112|ref|YP_004385540.1| 304 LFKKASYEESVEALNRAIELDPQN 327
                                       567777****************97 PP

  == domain 7  score: 6.3 bits;  conditional E-value: 0.013
                                       T-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  15 gkydeAleyyekALelnPnn 34 
                                        +y+e l++ +kA+el+P n
  gi|330509112|ref|YP_004385540.1| 349 SQYNESLKAQDKAIELDPGN 368
                                       5899999999********87 PP

  == domain 8  score: 15.1 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHHHHHHHSTTH CS
                             TPR_1  17 ydeAleyyekALelnPnn 34 
                                       y+eA++ ++kALel+P n
  gi|330509112|ref|YP_004385540.1| 394 YEEAIKEFDKALELDPMN 411
                                       9***************65 PP

  == domain 9  score: 9.6 bits;  conditional E-value: 0.0013
                                       TT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  14 lgkydeAleyyekALelnPn 33 
                                       l+k  eAl +y+kA+ l+ +
  gi|330509112|ref|YP_004385540.1| 426 LNKSAEALLAYDKAIDLDGE 445
                                       88999************976 PP

  == domain 10  score: 26.7 bits;  conditional E-value: 4.8e-09
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                       +a+ ++G a+ klg+y+e  e+++kA+eln
  gi|330509112|ref|YP_004385540.1| 455 NAWSGKGTALAKLGRYNESFEAFDKAIELN 484
                                       79***************************8 PP

  == domain 11  score: 22.7 bits;  conditional E-value: 8.8e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                        ++  +G a+ + g+y+eA  +y+k++e nP+
  gi|330509112|ref|YP_004385540.1| 490 FVWLAKGDALNQSGRYEEAAFAYDKVVEQNPD 521
                                       68999**************************8 PP

  == domain 12  score: 20.2 bits;  conditional E-value: 5.3e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+  +G a+   gkydeA+ +y+ A+e +P+
  gi|330509112|ref|YP_004385540.1| 530 AYGSKGDALSAWGKYDEAVIAYDNAIENYPS 560
                                       899************************9996 PP

  == domain 13  score: 8.4 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a+++  +G a++ lg+  +A +++ kA el
  gi|330509112|ref|YP_004385540.1| 565 AQTWHKKGIALQALGRTSDADAAFAKAKEL 594
                                       789***********************9886 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0025       1.7      17      37 ..      48      68 ..      44      73 .. 0.85
   2 ?    0.4   0.0      0.83   5.5e+02      21      39 ..      93     111 ..      92     113 .. 0.89
   3 ?   -0.3   0.0       1.3   8.7e+02       9      24 ..     115     130 ..     115     132 .. 0.88
   4 ?    6.1   0.3     0.014         9      12      26 ..     159     173 ..     158     174 .. 0.91
   5 !   13.3   0.0   7.8e-05     0.052       7      28 ..     190     211 ..     184     212 .. 0.88
   6 !   23.5   0.2   4.8e-08   3.2e-05       3      31 ..     303     331 ..     302     334 .. 0.91
   7 !    9.0   0.0    0.0017       1.1       8      35 ..     349     376 ..     347     378 .. 0.86
   8 !   21.9   0.1   1.5e-07    0.0001      10      32 ..     394     416 ..     393     422 .. 0.92
   9 !    9.2   0.3    0.0015      0.98       7      28 ..     426     447 ..     423     448 .. 0.87
  10 !   10.9   0.2   0.00043      0.28       1      24 [.     461     484 ..     461     487 .. 0.93
  11 !   18.8   0.3   1.4e-06   0.00095       1      27 [.     496     522 ..     496     530 .. 0.93
  12 !   11.6   0.2   0.00026      0.17       1      25 [.     535     559 ..     535     579 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0025
                            TPR_11 17 YkkAlkldPdnaeayynLGla 37
                                      Y  Al+ldP na+a+++ +++
  gi|330509112|ref|YP_004385540.1| 48 YDHALQLDPGNASAWLGKAQV 68
                                      999***********9877665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.83
                            TPR_11  21 lkldPdnaeayynLGlayy 39 
                                       lk d+++a a+ ++G+a++
  gi|330509112|ref|YP_004385540.1|  93 LKDDSQDAKAWQAMGVALA 111
                                       6789************986 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.3
                            TPR_11   9 kyeeAieaYkkAlkld 24 
                                       ++eeAi a+++ ++++
  gi|330509112|ref|YP_004385540.1| 115 RNEEAIGALERSIEIS 130
                                       589*********9996 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.014
                            TPR_11  12 eAieaYkkAlkldPd 26 
                                       +Ai+aY+k ++l+++
  gi|330509112|ref|YP_004385540.1| 159 AAIKAYEKVIELNSS 173
                                       6***********975 PP

  == domain 5  score: 13.3 bits;  conditional E-value: 7.8e-05
                            TPR_11   7 qGkyeeAieaYkkAlkldPdna 28 
                                        + y+e++ea+++A++l Pdna
  gi|330509112|ref|YP_004385540.1| 190 ANGYNESVEAFNEAIRLMPDNA 211
                                       567******************9 PP

  == domain 6  score: 23.5 bits;  conditional E-value: 4.8e-08
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeay 31 
                                       +++++  yee++ea+++A++ldP+na+++
  gi|330509112|ref|YP_004385540.1| 303 ELFKKASYEESVEALNRAIELDPQNATLW 331
                                       6788889*******************975 PP

  == domain 7  score: 9.0 bits;  conditional E-value: 0.0017
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLG 35 
                                        +y+e+++a  kA++ldP n +++ + G
  gi|330509112|ref|YP_004385540.1| 349 SQYNESLKAQDKAIELDPGNSTLHIHKG 376
                                       69****************9988886655 PP

  == domain 8  score: 21.9 bits;  conditional E-value: 1.5e-07
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayy 32 
                                       yeeAi+++ kAl+ldP n ea+ 
  gi|330509112|ref|YP_004385540.1| 394 YEEAIKEFDKALELDPMNEEAWT 416
                                       9*******************986 PP

  == domain 9  score: 9.2 bits;  conditional E-value: 0.0015
                            TPR_11   7 qGkyeeAieaYkkAlkldPdna 28 
                                       ++k  eA+ aY kA++ld +na
  gi|330509112|ref|YP_004385540.1| 426 LNKSAEALLAYDKAIDLDGENA 447
                                       56778*************9987 PP

  == domain 10  score: 10.9 bits;  conditional E-value: 0.00043
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkld 24 
                                       G a+ ++G+y+e+ ea+ kA++l+
  gi|330509112|ref|YP_004385540.1| 461 GTALAKLGRYNESFEAFDKAIELN 484
                                       66899*****************97 PP

  == domain 11  score: 18.8 bits;  conditional E-value: 1.4e-06
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdn 27 
                                       Gda+ + G+yeeA  aY k ++ +Pd+
  gi|330509112|ref|YP_004385540.1| 496 GDALNQSGRYEEAAFAYDKVVEQNPDS 522
                                       9************************97 PP

  == domain 12  score: 11.6 bits;  conditional E-value: 0.00026
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldP 25 
                                       Gda+ + Gky+eA+ aY +A++  P
  gi|330509112|ref|YP_004385540.1| 535 GDALSAWGKYDEAVIAYDNAIENYP 559
                                       8888899**************9544 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.8   9.8e-10   6.5e-07       3      75 ..      59     130 ..      58     132 .. 0.94
   2 !    8.4   0.0    0.0039       2.6      21      76 ..     152     208 ..     143     209 .. 0.90
   3 ?    3.2   0.4      0.17   1.1e+02      18      73 ..     309     363 ..     304     367 .. 0.62
   4 !    7.8   1.2     0.006         4      19      74 ..     394     442 ..     381     445 .. 0.83
   5 !   20.7   0.6   5.7e-07   0.00038       6      74 ..     415     483 ..     410     486 .. 0.89
   6 !   23.2   0.2   9.4e-08   6.2e-05       3      72 ..     454     516 ..     452     517 .. 0.90
   7 !   26.5   0.5   8.5e-09   5.7e-06       6      76 ..     492     559 ..     485     560 .. 0.92
   8 ?    6.4   0.0     0.017        11       4      31 ..     566     593 ..     562     597 .. 0.61

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 9.8e-10
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a+a+   a+v + lg+  e++e+++kal++ + +l +d+ + a + +++g ++  l r eeA+ +le++++i 
  gi|330509112|ref|YP_004385540.1|  59 ASAWLGKAQVSQILGNQIESREYFQKALDATNGTLKDDS-QDAKAWQAMGVALAGLARNEEAIGALERSIEIS 130
                                       6788899****************************9988.99****************************996 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0039
                            TPR_12  21 eAlellekaleiarrllGpdhpltattlrnLgrly.ralgryeeAlelleealaiae 76 
                                       eAl +  +a+ +++++ + ++   + + + +++++  +++ y e +e+++ea+++++
  gi|330509112|ref|YP_004385540.1| 152 EALYMDYAAIKAYEKVIELNSSKSVGAWIRIADILfAKANGYNESVEAFNEAIRLMP 208
                                       8999999999999999999999999*********83599**************9875 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.17
                            TPR_12  18 rydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                        y+e+ e l++a+e+  +++  + +++ a++l   +     + +y e l++  +a++
  gi|330509112|ref|YP_004385540.1| 309 SYEESVEALNRAIELDpQNA--TLWDAKASSLGIAASFDGNRSQYNESLKAQDKAIE 363
                                       57888888888888876666..66766666665555544444566666666666655 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.006
                            TPR_12  19 ydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       y+eA++ ++kale+      p + ++a+t+ +      +l++ +eAl ++ +a+++
  gi|330509112|ref|YP_004385540.1| 394 YEEAIKEFDKALELD-----PMN-EEAWTYKASVLD-TRLNKSAEALLAYDKAIDL 442
                                       9**************.....445.578888765555.6999**********99987 PP

  == domain 5  score: 20.7 bits;  conditional E-value: 5.7e-07
                            TPR_12   6 lnnlaavl.rrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       ++  a+vl +rl + +eAl  ++ka+++  +++   d++ ++++  + g+++ +lgry e  e++ +a+++
  gi|330509112|ref|YP_004385540.1| 415 WTYKASVLdTRLNKSAEALLAYDKAIDLDgENA--IDNESLSNAWSGKGTALAKLGRYNESFEAFDKAIEL 483
                                       33478888899******************7777..99999****************************997 PP

  == domain 6  score: 23.2 bits;  conditional E-value: 9.4e-08
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       ++a++  +++l++lgry e++e ++ka+e+       +    a +  + g+++ ++gryeeA  ++ +++
  gi|330509112|ref|YP_004385540.1| 454 SNAWSGKGTALAKLGRYNESFEAFDKAIELNL-----QA--SAFVWLAKGDALNQSGRYEEAAFAYDKVV 516
                                       789999*************************3.....33..8********************99998876 PP

  == domain 7  score: 26.5 bits;  conditional E-value: 8.5e-09
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +   +++l++ gry+eA   ++k++e+    ++   +l a ++   g++++a+g+y+eA+ ++  a++ ++
  gi|330509112|ref|YP_004385540.1| 492 WLAKGDALNQSGRYEEAAFAYDKVVEQN---PDSSQALIAHAYGSKGDALSAWGKYDEAVIAYDNAIENYP 559
                                       55799*******************9999...99999***************************99999886 PP

  == domain 8  score: 6.4 bits;  conditional E-value: 0.017
                            TPR_12   4 talnnlaavlrrlgrydeAlellekale 31 
                                       +++++ + +l++lgr  +A + + ka e
  gi|330509112|ref|YP_004385540.1| 566 QTWHKKGIALQALGRTSDADAAFAKAKE 593
                                       4555666666666666666666666655 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0    0.0002      0.13       2      33 ..      48      79 ..      48      80 .. 0.91
   2 ?    4.5   0.0      0.08        53       6      32 ..      93     119 ..      82     124 .. 0.84
   3 ?    5.9   0.0     0.029        19       1      31 [.     163     195 ..     163     198 .. 0.80
   4 !    9.3   0.1    0.0023       1.5       2      23 ..     317     338 ..     316     355 .. 0.83
   5 !    8.8   0.0    0.0034       2.3       3      28 ..     359     384 ..     357     390 .. 0.87
   6 !   11.9   0.1   0.00034      0.23       2      32 ..     401     432 ..     400     433 .. 0.91
   7 !    7.4   0.1    0.0094       6.2       2      31 ..     436     472 ..     435     475 .. 0.91
   8 ?    6.2   0.1     0.024        16       2      32 ..     477     508 ..     476     509 .. 0.94
   9 !    9.4   0.0    0.0022       1.4       1      32 [.     511     547 ..     511     549 .. 0.93
  10 !    8.6   0.0    0.0039       2.6       1      32 [.     550     584 ..     550     586 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0002
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      y  al+ldP na a+  +A++   +G+  + r
  gi|330509112|ref|YP_004385540.1| 48 YDHALQLDPGNASAWLGKAQVSQILGNQIESR 79
                                      899*******************9999987765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.08
                            TPR_17   6 leldPnnadaynnLAelllknGdlmtA 32 
                                       l+ d  +a+a++ ++++l+ + + ++A
  gi|330509112|ref|YP_004385540.1|  93 LKDDSQDAKAWQAMGVALAGLARNEEA 119
                                       567899************966666665 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.029
                            TPR_17   1 lylkaleld.PnnadaynnLAell.lknGdlmt 31 
                                       +y+k++el+  +++ a+   A +l +k++++ +
  gi|330509112|ref|YP_004385540.1| 163 AYEKVIELNsSKSVGAWIRIADILfAKANGYNE 195
                                       5*******95669*********87468787765 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0023
                            TPR_17   2 ylkaleldPnnadaynnLAell 23 
                                       + +a+eldP na ++  +A  l
  gi|330509112|ref|YP_004385540.1| 317 LNRAIELDPQNATLWDAKASSL 338
                                       579************8888665 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0034
                            TPR_17   3 lkaleldPnnadaynnLAelllknGd 28 
                                        ka+eldP n+ ++  ++ + +++ d
  gi|330509112|ref|YP_004385540.1| 359 DKAIELDPGNSTLHIHKGFFIANLAD 384
                                       69************999998887655 PP

  == domain 6  score: 11.9 bits;  conditional E-value: 0.00034
                            TPR_17   2 ylkaleldPnnadaynnLAelll.knGdlmtA 32 
                                       + kaleldP n +a++++A +l  +++++++A
  gi|330509112|ref|YP_004385540.1| 401 FDKALELDPMNEEAWTYKASVLDtRLNKSAEA 432
                                       89********************8688999988 PP

  == domain 7  score: 7.4 bits;  conditional E-value: 0.0094
                            TPR_17   2 ylkaleldPnn.......adaynnLAelllknGdlmt 31 
                                       y ka++ld  n       ++a+  ++++l+k+G++ +
  gi|330509112|ref|YP_004385540.1| 436 YDKAIDLDGENaidneslSNAWSGKGTALAKLGRYNE 472
                                       999999999999999999***************9976 PP

  == domain 8  score: 6.2 bits;  conditional E-value: 0.024
                            TPR_17   2 ylkaleld.PnnadaynnLAelllknGdlmtA 32 
                                       + ka+el+   +a ++  ++ +l + G++++A
  gi|330509112|ref|YP_004385540.1| 477 FDKAIELNlQASAFVWLAKGDALNQSGRYEEA 508
                                       89*****9999*******************98 PP

  == domain 9  score: 9.4 bits;  conditional E-value: 0.0022
                            TPR_17   1 lylkaleldPnn.....adaynnLAelllknGdlmtA 32 
                                       +y k++e++P++     a ay  ++ +l+  G++++A
  gi|330509112|ref|YP_004385540.1| 511 AYDKVVEQNPDSsqaliAHAYGSKGDALSAWGKYDEA 547
                                       59**********9999999999999999999999999 PP

  == domain 10  score: 8.6 bits;  conditional E-value: 0.0039
                            TPR_17   1 lylkaleldPnn...adaynnLAelllknGdlmtA 32 
                                       +y +a+e++P+    a  ++ ++ +l  +G++ +A
  gi|330509112|ref|YP_004385540.1| 550 AYDNAIENYPSEpmgAQTWHKKGIALQALGRTSDA 584
                                       599***************************99877 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.032        21      24      43 ..      48      67 ..      39      68 .. 0.87
   2 ?    3.4   0.1      0.27   1.8e+02       3      30 ..      61      88 ..      59      95 .. 0.89
   3 !   11.4   0.4    0.0007      0.46       2      31 ..     101     130 ..     100     150 .. 0.85
   4 ?    5.6   0.0      0.05        33       6      43 ..     146     184 ..     141     185 .. 0.81
   5 ?    5.3   0.0     0.067        45       2      36 ..     177     212 ..     176     215 .. 0.89
   6 !   15.0   0.0   4.9e-05     0.032       4      42 ..     297     335 ..     295     337 .. 0.86
   7 ?    0.9   0.0       1.7   1.1e+03      25      42 ..     359     376 ..     341     378 .. 0.79
   8 !   11.4   0.0   0.00069      0.46      16      42 ..     393     419 ..     382     422 .. 0.88
   9 ?    2.3   0.2      0.58   3.8e+02       2      34 ..     413     446 ..     413     448 .. 0.84
  10 ?    6.7   0.0     0.024        16       2      32 ..     455     485 ..     454     491 .. 0.87
  11 !   21.3   0.1   4.6e-07   0.00031       3      42 ..     491     530 ..     489     532 .. 0.92
  12 ?    4.9   0.0     0.085        56      15      36 ..     542     563 ..     534     570 .. 0.85
  13 ?    1.7   0.2      0.92   6.1e+02       3      27 ..     567     591 ..     565     595 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.032
                            TPR_14 24 lrralalaPddaeawlllaq 43
                                      ++ al+l+P++a awl  aq
  gi|330509112|ref|YP_004385540.1| 48 YDHALQLDPGNASAWLGKAQ 67
                                      7789************9998 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.27
                            TPR_14  3 allalaeallalGdpdeAiallrralal 30
                                      a+l  a++   lG+  e+++++++al++
  gi|330509112|ref|YP_004385540.1| 61 AWLGKAQVSQILGNQIESREYFQKALDA 88
                                      89999999999**************986 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.0007
                            TPR_14   2 eallalaeallalGdpdeAiallrralala 31 
                                       +a++a++ al+ l + +eAi +l+r ++  
  gi|330509112|ref|YP_004385540.1| 101 KAWQAMGVALAGLARNEEAIGALERSIEIS 130
                                       79***********************99954 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.05
                            TPR_14   6 alaeallalGdpdeAiallrralalaP.ddaeawlllaq 43 
                                       + a  ++al    +Ai++++++++l+  ++  aw++ a+
  gi|330509112|ref|YP_004385540.1| 146 QKAVSYEALYMDYAAIKAYEKVIELNSsKSVGAWIRIAD 184
                                       55667888888899**********975389999999886 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.067
                            TPR_14   2 eallalaeallalGd.pdeAiallrralalaPddae 36 
                                        a+ ++a++l+a  + + e+++++++a++l Pd+a 
  gi|330509112|ref|YP_004385540.1| 177 GAWIRIADILFAKANgYNESVEAFNEAIRLMPDNAS 212
                                       589999*99999999788***************985 PP

  == domain 6  score: 15.0 bits;  conditional E-value: 4.9e-05
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +++  + l+    ++e++++l+ra++l+P++a++w + a
  gi|330509112|ref|YP_004385540.1| 297 WYKTSQELFKKASYEESVEALNRAIELDPQNATLWDAKA 335
                                       66677778888899*********************8776 PP

  == domain 7  score: 0.9 bits;  conditional E-value: 1.7
                            TPR_14  25 rralalaPddaeawllla 42 
                                       ++a++l+P++ +++++ +
  gi|330509112|ref|YP_004385540.1| 359 DKAIELDPGNSTLHIHKG 376
                                       789*********999887 PP

  == domain 8  score: 11.4 bits;  conditional E-value: 0.00069
                            TPR_14  16 dpdeAiallrralalaPddaeawllla 42 
                                        ++eAi+ +++al+l+P ++eaw++ a
  gi|330509112|ref|YP_004385540.1| 393 LYEEAIKEFDKALELDPMNEEAWTYKA 419
                                       589********************9988 PP

  == domain 9  score: 2.3 bits;  conditional E-value: 0.58
                            TPR_14   2 eallalaeal.lalGdpdeAiallrralalaPdd 34 
                                       ea+   a++l  +l + +eA+ ++++a++l+ ++
  gi|330509112|ref|YP_004385540.1| 413 EAWTYKASVLdTRLNKSAEALLAYDKAIDLDGEN 446
                                       577777888757999**************99877 PP

  == domain 10  score: 6.7 bits;  conditional E-value: 0.024
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaP 32 
                                       +a+   + al+ lG++ e+ +++++a++l+ 
  gi|330509112|ref|YP_004385540.1| 455 NAWSGKGTALAKLGRYNESFEAFDKAIELNL 485
                                       57888899*******************9875 PP

  == domain 11  score: 21.3 bits;  conditional E-value: 4.6e-07
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       ++la ++al ++G+++eA+ +++++++++Pd+ +a+++ a
  gi|330509112|ref|YP_004385540.1| 491 VWLAKGDALNQSGRYEEAAFAYDKVVEQNPDSSQALIAHA 530
                                       699*****************************99998755 PP

  == domain 12  score: 4.9 bits;  conditional E-value: 0.085
                            TPR_14  15 GdpdeAiallrralalaPddae 36 
                                       G++deA+ +++ a++ +P+++ 
  gi|330509112|ref|YP_004385540.1| 542 GKYDEAVIAYDNAIENYPSEPM 563
                                       89****************9874 PP

  == domain 13  score: 1.7 bits;  conditional E-value: 0.92
                            TPR_14   3 allalaeallalGdpdeAiallrra 27 
                                        + + + al alG++ +A a++ +a
  gi|330509112|ref|YP_004385540.1| 567 TWHKKGIALQALGRTSDADAAFAKA 591
                                       6888999**********99999887 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.015        10      23      64 ..      51      89 ..      48      92 .. 0.89
   2 !   10.4   0.5    0.0012      0.81      13      62 ..      82     128 ..      73     133 .. 0.87
   3 ?    7.4   0.0     0.011       7.2      15      67 ..     159     210 ..     159     214 .. 0.83
   4 !    8.3   0.1    0.0055       3.7       5      59 ..     302     360 ..     298     369 .. 0.63
   5 !   17.3   0.2   8.5e-06    0.0056      13      64 ..     394     443 ..     390     451 .. 0.92
   6 ?    5.9   0.1     0.031        21      35      62 ..     455     482 ..     445     488 .. 0.83
   7 !   22.5   0.6     2e-07   0.00014       3      67 ..     460     522 ..     458     523 .. 0.90
   8 !   31.6   1.6     3e-10     2e-07       1      68 []     493     562 ..     493     562 .. 0.95
   9 !   15.2   0.6   3.8e-05     0.025       4      61 ..     535     592 ..     533     595 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.015
                            TPR_16 23 alkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64
                                      al +d   P +a A+l+++++   +g+  e ++++++al+a 
  gi|330509112|ref|YP_004385540.1| 51 ALQLD---PGNASAWLGKAQVSQILGNQIESREYFQKALDAT 89
                                      77788...*****************************99875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0012
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       +++A+ a + +lk+d   +++a A+ + g+a++ + r +eA+ ++++ ++
  gi|330509112|ref|YP_004385540.1|  82 FQKALDATNGTLKDD---SQDAKAWQAMGVALAGLARNEEAIGALERSIE 128
                                       899************...************************66666555 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.011
                            TPR_16  15 dAaaaleaalkrdpssPdaaeAllllgdaalrq.grlaeAaalyraalraapda 67 
                                       +A++a+e ++++++  +  + A+   +d+++++ + + e ++++++a+r  pd+
  gi|330509112|ref|YP_004385540.1| 159 AAIKAYEKVIELNS--SKSVGAWIRIADILFAKaNGYNESVEAFNEAIRLMPDN 210
                                       5999*********5..6688***********55488999999999988877766 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0055
                            TPR_16   5 raalragdyddAaaaleaalkrdpssPd......aaeAllllgdaal.rqgrlaeAaalyra 59 
                                       +++++   y++ ++al++a+++d   P+      a +++l+ + ++   ++ + e + + ++
  gi|330509112|ref|YP_004385540.1| 302 QELFKKASYEESVEALNRAIELD---PQnatlwdAKASSLGIAASFDgNRSQYNESLKAQDK 360
                                       56788888***************...995555555555555555555444555555544444 PP

  == domain 5  score: 17.3 bits;  conditional E-value: 8.5e-06
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaal.rqgrlaeAaalyraalraa 64 
                                       y++A++ ++ al++d   P + eA+ +++ ++  r++  aeA+ +y++a++ +
  gi|330509112|ref|YP_004385540.1| 394 YEEAIKEFDKALELD---PMNEEAWTYKASVLDtRLNKSAEALLAYDKAIDLD 443
                                       9**************...***************888************99765 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.031
                            TPR_16  35 eAllllgdaalrqgrlaeAaalyraalr 62 
                                        A+ ++g a++++gr+ e  +++++a++
  gi|330509112|ref|YP_004385540.1| 455 NAWSGKGTALAKLGRYNESFEAFDKAIE 482
                                       6899999999999999999999999875 PP

  == domain 7  score: 22.5 bits;  conditional E-value: 2e-07
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +++a++++g+y +  +a++ a++++    + a  +l++gda+ + gr++eAa +y++ +++ pd+
  gi|330509112|ref|YP_004385540.1| 460 KGTALAKLGRYNESFEAFDKAIELN--LQASAFVWLAKGDALNQSGRYEEAAFAYDKVVEQNPDS 522
                                       689**********************..3668889******************7777778999987 PP

  == domain 8  score: 31.6 bits;  conditional E-value: 3e-10
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPd..aaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       la+++a+ ++g+y++Aa a++ +++++p+s++   a+A+  +gda+ + g ++eA+ +y+ a++++p++p
  gi|330509112|ref|YP_004385540.1| 493 LAKGDALNQSGRYEEAAFAYDKVVEQNPDSSQalIAHAYGSKGDALSAWGKYDEAVIAYDNAIENYPSEP 562
                                       689999*********************99999999*********************9999999****997 PP

  == domain 9  score: 15.2 bits;  conditional E-value: 3.8e-05
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       ++a+ + g+yd+A+ a++ a++++ps+P  a+ +  +g a+ ++gr  +A a++++a 
  gi|330509112|ref|YP_004385540.1| 535 GDALSAWGKYDEAVIAYDNAIENYPSEPMGAQTWHKKGIALQALGRTSDADAAFAKAK 592
                                       56666669****************************************9988888875 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.41   2.7e+02       5      28 ..      62      87 ..      59      88 .. 0.82
   2 ?   -0.0   0.1       2.7   1.8e+03       6      26 ..     106     126 ..     102     129 .. 0.77
   3 !    8.3   0.2    0.0059       3.9       1      28 [.     142     169 ..     142     172 .. 0.88
   4 ?    3.9   0.0      0.15        99       5      31 ..     181     208 ..     178     210 .. 0.83
   5 ?    4.5   0.0     0.098        65       9      32 ..     304     326 ..     295     327 .. 0.75
   6 ?   -1.0   0.0       5.3   3.5e+03      16      28 ..     394     406 ..     390     409 .. 0.62
   7 ?   -0.3   0.1       3.3   2.2e+03      12      28 ..     425     441 ..     413     443 .. 0.73
   8 ?    2.5   0.0      0.42   2.8e+02       7      28 ..     461     482 ..     459     484 .. 0.89
   9 !   10.5   0.0    0.0012      0.77       9      33 .]     498     522 ..     489     522 .. 0.83
  10 !   12.2   0.0   0.00033      0.22      13      32 ..     535     560 ..     524     561 .. 0.77
  11 ?    3.5   0.1      0.19   1.3e+02       5      26 ..     570     591 ..     567     594 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.41
                                      HHHHHHHHH..HHHHHHHHHHHHHHH CS
                             TPR_6  5 klalsyrkl..gdtdkAlealerlik 28
                                      +l++++ ++  g+  +++e++++ ++
  gi|330509112|ref|YP_004385540.1| 62 WLGKAQVSQilGNQIESREYFQKALD 87
                                      788888866679999*******9886 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerl 26 
                                       ++ ++  l + ++A+ aler 
  gi|330509112|ref|YP_004385540.1| 106 MGVALAGLARNEEAIGALERS 126
                                       5677777558999*9999985 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0059
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                       d+l++ a sy++l    +A++a+e++i+
  gi|330509112|ref|YP_004385540.1| 142 DSLWQKAVSYEALYMDYAAIKAYEKVIE 169
                                       789********9876668********98 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.15
                                       HHHHHHHH.HHHHHHHHHHHHHHHHH-T CS
                             TPR_6   5 klalsyrk.lgdtdkAlealerlikeYP 31 
                                       ++a  +++ ++ + +++ea+++ i+  P
  gi|330509112|ref|YP_004385540.1| 181 RIADILFAkANGYNESVEAFNEAIRLMP 208
                                       8998999879************998655 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.098
                                       HHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                                       +++k+  +++++eal+r i+  P+
  gi|330509112|ref|YP_004385540.1| 304 LFKKA-SYEESVEALNRAIELDPQ 326
                                       34447.99************9997 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 5.3
                                       HHHHHHHHHHHHH CS
                             TPR_6  16 tdkAlealerlik 28 
                                       +++A++ +++ ++
  gi|330509112|ref|YP_004385540.1| 394 YEEAIKEFDKALE 406
                                       5566666666655 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHHHHHHH CS
                             TPR_6  12 klgdtdkAlealerlik 28 
                                       +l+++++Al a+++ i+
  gi|330509112|ref|YP_004385540.1| 425 RLNKSAEALLAYDKAID 441
                                       56889999999999986 PP

  == domain 8  score: 2.5 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       + ++ klg++ ++ ea+++ i+
  gi|330509112|ref|YP_004385540.1| 461 GTALAKLGRYNESFEAFDKAIE 482
                                       77899999**********9997 PP

  == domain 9  score: 10.5 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   9 syrklgdtdkAlealerlikeYPdS 33 
                                       ++ + g++++A  a+++++++ PdS
  gi|330509112|ref|YP_004385540.1| 498 ALNQSGRYEEAAFAYDKVVEQNPDS 522
                                       455547******************9 PP

  == domain 10  score: 12.2 bits;  conditional E-value: 0.00033
                                       H......HHHHHHHHHHHHHHHH-TT CS
                             TPR_6  13 l......gdtdkAlealerlikeYPd 32 
                                       +      g++d+A+ a+++ i++YP 
  gi|330509112|ref|YP_004385540.1| 535 GdalsawGKYDEAVIAYDNAIENYPS 560
                                       35556667*****************5 PP

  == domain 11  score: 3.5 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerl 26 
                                       k + ++++lg+t++A +a+ + 
  gi|330509112|ref|YP_004385540.1| 570 KKGIALQALGRTSDADAAFAKA 591
                                       5688999999*********986 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0      0.03        20      14      34 ..      48      68 ..      41      74 .. 0.86
   2 !    8.7   0.5    0.0037       2.4       7      53 ..      82     128 ..      78     140 .. 0.88
   3 !    7.9   0.0    0.0064       4.2       9      62 ..     159     214 ..     159     216 .. 0.90
   4 ?    4.5   0.2     0.076        51      40      66 ..     309     335 ..     301     336 .. 0.66
   5 ?   -1.8   0.0       7.2   4.8e+03       6      28 ..     350     372 ..     348     375 .. 0.77
   6 !    8.0   0.5    0.0062       4.1       7      35 ..     394     422 ..     391     448 .. 0.78
   7 ?   -0.1   0.4       2.1   1.4e+03       8      44 ..     430     473 ..     423     486 .. 0.63
   8 !   15.9   0.5   2.1e-05     0.014       5      61 ..     468     525 ..     464     531 .. 0.77
   9 ?    2.9   0.2      0.24   1.6e+02       5      51 ..     542     591 ..     538     596 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.03
                            TPR_19 14 leqalqedpknaearllLAea 34
                                      +  alq dp+na a+l+ A++
  gi|330509112|ref|YP_004385540.1| 48 YDHALQLDPGNASAWLGKAQV 68
                                      6789************99986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0037
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       ++ Al++    l++d ++a a+ ++  al  l + +eA+ +L++  e
  gi|330509112|ref|YP_004385540.1|  82 FQKALDATNGTLKDDSQDAKAWQAMGVALAGLARNEEAIGALERSIE 128
                                       56777777888999****************************98765 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0064
                            TPR_19   9 eAlalleqalqe.dpknaearllLAeallal.gqldeAealLdalpeedpddarya 62 
                                       +A++++e++++  + k+  a+++ A++l+a  + ++e  ++ +++ +  pd+a +a
  gi|330509112|ref|YP_004385540.1| 159 AAIKAYEKVIELnSSKSVGAWIRIADILFAKaNGYNESVEAFNEAIRLMPDNASWA 214
                                       69********996667*************99899******9999999999987765 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.076
                            TPR_19  40 qldeAealLdalpeedpddaryasLlA 66 
                                        ++e  ++L+++ e dp++a +++++A
  gi|330509112|ref|YP_004385540.1| 309 SYEESVEALNRAIELDPQNATLWDAKA 335
                                       566777777777777777776666665 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 7.2
                            TPR_19   6 dyaeAlalleqalqedpknaear 28 
                                       +y e l++  +a++ dp+n+ + 
  gi|330509112|ref|YP_004385540.1| 350 QYNESLKAQDKAIELDPGNSTLH 372
                                       67777777788999999998765 PP

  == domain 6  score: 8.0 bits;  conditional E-value: 0.0062
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeal 35 
                                       y+eA++ + +al+ dp n+ea+ + A +l
  gi|330509112|ref|YP_004385540.1| 394 YEEAIKEFDKALELDPMNEEAWTYKASVL 422
                                       89*******************99776555 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 2.1
                            TPR_19   8 aeAlalleqalqedpk.......naearllLAeallalgqldeA 44 
                                       aeAl ++ +a++ d +        ++a+ +   al +lg+++e 
  gi|330509112|ref|YP_004385540.1| 430 AEALLAYDKAIDLDGEnaidnesLSNAWSGKGTALAKLGRYNES 473
                                       67777777777776663343333445555666677777777765 PP

  == domain 8  score: 15.9 bits;  conditional E-value: 2.1e-05
                            TPR_19   5 gdyaeAlalleqalqedpk.naearllLAeallalgqldeAealLdalpeedpddary 61 
                                       g+y e  +++ +a++ + + +a ++l+  +al ++g+++eA  + d++ e++pd++++
  gi|330509112|ref|YP_004385540.1| 468 GRYNESFEAFDKAIELNLQaSAFVWLAKGDALNQSGRYEEAAFAYDKVVEQNPDSSQA 525
                                       778888888888887755534445556699************************7664 PP

  == domain 9  score: 2.9 bits;  conditional E-value: 0.24
                            TPR_19   5 gdyaeAlalleqalqedpk...naearllLAeallalgqldeAealLdal 51 
                                       g+y+eA+ ++ +a++ +p     a  +    +al alg++ +A a+ +++
  gi|330509112|ref|YP_004385540.1| 542 GKYDEAVIAYDNAIENYPSepmGAQTWHKKGIALQALGRTSDADAAFAKA 591
                                       89999999999999998886655556666799999999999999988876 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0034       2.2      18      67 ..      48     102 ..      36     106 .. 0.82
   2 !   11.1   0.2   0.00052      0.35       8      62 ..      79     133 ..      76     146 .. 0.90
   3 ?    2.0   0.0      0.36   2.4e+02      12      58 ..     124     170 ..     115     177 .. 0.78
   4 ?    2.7   0.0      0.22   1.4e+02      45      64 ..     310     329 ..     306     336 .. 0.76
   5 ?    1.1   0.0      0.67   4.5e+02      45      64 ..     394     413 ..     347     427 .. 0.78
   6 ?    2.9   0.0      0.18   1.2e+02      34      59 ..     459     484 ..     425     490 .. 0.89
   7 !   13.5   0.1   8.8e-05     0.059      32      69 ..     492     529 ..     485     532 .. 0.92
   8 ?    0.4   0.0       1.1   7.5e+02      35      63 ..     534     562 ..     528     568 .. 0.86
   9 ?    0.6   0.1      0.97   6.5e+02      29      53 ..     565     589 ..     543     594 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0034
                             TPR_9  18 verllllaPddpeerrdRGlllaqlGclsaAladLeaylalap.....dapdaea 67 
                                       ++  l+l+P  ++ ++  +++ + lG+  + ++ ++ +l+ +      d +da a
  gi|330509112|ref|YP_004385540.1|  48 YDHALQLDPGNASAWLGKAQVSQILGNQIESREYFQKALDATNgtlkdDSQDAKA 102
                                       6789***********************************7665555557777765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00052
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       +e +++al + +  l  +++d+  +   G++la l + ++A+ +Le+ +++++++
  gi|330509112|ref|YP_004385540.1|  79 REYFQKALDATNGTLKDDSQDAKAWQAMGVALAGLARNEEAIGALERSIEISDQR 133
                                       677999******************************************9887754 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.36
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylal 58 
                                       er +++++ +l  +P+d++ ++  ++ ++ l    aA+++ e  ++l
  gi|330509112|ref|YP_004385540.1| 124 ERSIEISDQRLEENPEDIDSLWQKAVSYEALYMDYAAIKAYEKVIEL 170
                                       66777888888889***999999999998887777777777766665 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.22
                             TPR_9  45 lsaAladLeaylalapdapd 64 
                                       +++ +++L+++++l+p++++
  gi|330509112|ref|YP_004385540.1| 310 YEESVEALNRAIELDPQNAT 329
                                       67778888888888888765 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.67
                             TPR_9  45 lsaAladLeaylalapdapd 64 
                                       +++A+++++ +l+l+p +++
  gi|330509112|ref|YP_004385540.1| 394 YEEAIKEFDKALELDPMNEE 413
                                       67788888888888885555 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.18
                             TPR_9  34 dRGlllaqlGclsaAladLeaylala 59 
                                         G +la+lG++++  ++++ +++l+
  gi|330509112|ref|YP_004385540.1| 459 GKGTALAKLGRYNESFEAFDKAIELN 484
                                       57999***************999876 PP

  == domain 7  score: 13.5 bits;  conditional E-value: 8.8e-05
                             TPR_9  32 rrdRGlllaqlGclsaAladLeaylalapdapdaeair 69 
                                       ++  G +l q+G++++A+++ +  ++++pd  +a  + 
  gi|330509112|ref|YP_004385540.1| 492 WLAKGDALNQSGRYEEAAFAYDKVVEQNPDSSQALIAH 529
                                       8899****************************998765 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 1.1
                             TPR_9  35 RGlllaqlGclsaAladLeaylalapdap 63 
                                        G +l  +G + +A+ + + ++++ p+ p
  gi|330509112|ref|YP_004385540.1| 534 KGDALSAWGKYDEAVIAYDNAIENYPSEP 562
                                       68888999****************99765 PP

  == domain 9  score: 0.6 bits;  conditional E-value: 0.97
                             TPR_9  29 peerrdRGlllaqlGclsaAladLe 53 
                                       ++ +   G++l+ lG++s A a++ 
  gi|330509112|ref|YP_004385540.1| 565 AQTWHKKGIALQALGRTSDADAAFA 589
                                       5678899*********999977765 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.3   0.00079      0.53      30     129 ..      80     170 ..      57     177 .. 0.70
   2 ?    3.7   0.4     0.091        60      22     128 ..     307     406 ..     297     413 .. 0.54
   3 !   14.1   1.4   5.6e-05     0.037      40     128 ..     432     517 ..     410     523 .. 0.64
   4 !    8.8   1.7    0.0024       1.6       9     130 ..     489     595 ..     487     598 .] 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00079
                                       HHHHHHHHHHTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHH CS
                           DUF3856  30 asyrkalevsrtipaeeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsr 106
                                       + ++kal++++      ++  +  da ++ ++  ala+l r +ea+ + +++++  ++r e + ++    i  ++++
  gi|330509112|ref|YP_004385540.1|  80 EYFQKALDATNG-----TLKDDSQDAKAWQAMGVALAGLARNEEAIGALERSIEISDQRLEENPED----IDSLWQK 147
                                       555555555544.....34445667888888899999****************9999997655433....4555566 PP

                                       HHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 107 avaleelGrkdealkafrmagem 129
                                       av++e l     a+ka++++ e+
  gi|330509112|ref|YP_004385540.1| 148 AVSYEALYMDYAAIKAYEKVIEL 170
                                       66666666677777777777765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.091
                                       HT-HHHHHHHHHHHHHHHTTS-TTS---HHHHHHHH.HHHHHHHHHH.TT-HHHHHHHHHHHHHHHHHH--TTSTHH CS
                           DUF3856  22 egayeeaaasyrkalevsrtipaeeafdheGfdalc.haglsealak.lgrydealesadkalryfnrrGeleqdeG 96 
                                       +++yee+++  ++a+e+    p++ ++    +da +   g++ ++ +   +y+e+l++ dka++       l+  +G
  gi|330509112|ref|YP_004385540.1| 307 KASYEESVEALNRAIELD---PQNATL----WDAKAsSLGIAASFDGnRSQYNESLKAQDKAIELDPGNSTLHIHKG 376
                                       555555555555555543...222221....2222201233333333145688888888888777777777777766 PP

                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  97 klWiaavfsravaleelGrkdealkafrmage 128
                                         +ia + +   + ++   ++ea+k+f +a e
  gi|330509112|ref|YP_004385540.1| 377 -FFIANLADL-SGHKNESLYEEAIKEFDKALE 406
                                       .455555443.345555667777777777766 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 5.6e-05
                                       TTS-TTS---HHHHHHHHHHHHHH.......HHHHTT-HHHHHHHHHHHHHHHHHH--TT.STHHHHHHHHHHHHHH CS
                           DUF3856  40 rtipaeeafdheGfdalchaglse.......alaklgrydealesadkalryfnrrGele.qdeGklWiaavfsrav 108
                                         ++ + a d +G +a+   +ls+       alaklgry+e++e+ dka+       el+ q+    W+a    ++ 
  gi|330509112|ref|YP_004385540.1| 432 ALLAYDKAIDLDGENAIDNESLSNawsgkgtALAKLGRYNESFEAFDKAI-------ELNlQASAFVWLA----KGD 497
                                       34455555566666665555555400001116677777777777777766.......5552556667865....99* PP

                                       HHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 109 aleelGrkdealkafrmage 128
                                       al++ Gr++ea  a+ +++e
  gi|330509112|ref|YP_004385540.1| 498 ALNQSGRYEEAAFAYDKVVE 517
                                       ***********999999887 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0024
                                       HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                           DUF3856   9 aylalseaekqleegayeeaaasyrkalevsrtipaeeafdheGfdalchaglsealaklgrydealesadkalryf 85 
                                       a++ l++++   + g+yeeaa  y k +e             + + a ++ +  +al   g+ydea+ + d+a++ +
  gi|330509112|ref|YP_004385540.1| 489 AFVWLAKGDALNQSGRYEEAAFAYDKVVEQNPD-------SSQALIAHAYGSKGDALSAWGKYDEAVIAYDNAIENY 558
                                       666666777766777777777777766654332.......2344567778888899999999999999999999877 PP

                                       HHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                           DUF3856  86 nrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagemi 130
                                             e  + + W     +++ al+ lGr+++a  af +a+e+ 
  gi|330509112|ref|YP_004385540.1| 559 PS----EPMGAQTW----HKKGIALQALGRTSDADAAFAKAKELG 595
                                       54....33444556....689999999999999999999999975 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.024        16      38      81 ..      81     125 ..      47     126 .. 0.92
   2 ?    4.0   0.0     0.087        58      37      81 ..     158     202 ..     129     203 .. 0.71
   3 ?    0.1   0.2       1.4   9.4e+02      18      55 ..     289     327 ..     276     338 .. 0.73
   4 !    9.5   0.4    0.0017       1.1       3      81 ..     392     479 ..     390     480 .. 0.74
   5 !   10.4   0.4   0.00088      0.59      33      76 ..     499     548 ..     468     554 .. 0.61
   6 !   10.0   0.2    0.0012       0.8       3      47 ..     503     545 ..     501     590 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.024
                                       -HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  38 qykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                        +++A++ ++ + k +s++ +++  ++ +l  L + eeAi aLe+
  gi|330509112|ref|YP_004385540.1|  81 YFQKALDATNGTlKDDSQDAKAWQAMGVALAGLARNEEAIGALER 125
                                       4899***************************************96 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.087
                                       T-HHHHHHHHHCTSHHHC-HHHHHHHHHHHH.HTT-HHHHHHHH-S CS
                            ANAPC3  37 gqykrAyellrkaklnskslgcrylfAqcll.kLkkyeeAiaaLek 81 
                                           +Aye + ++   sks g+++ +A  l+ k + y+e + a+ +
  gi|330509112|ref|YP_004385540.1| 158 YAAIKAYEKVIEL-NSSKSVGAWIRIADILFaKANGYNESVEAFNE 202
                                       3344555555555.446677**********9899*****9999876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.4
                                       HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC- CS
                            ANAPC3  18 aetespedayllAlclylngqykrAyellrka.klnsks 55 
                                       +++e  +  y  ++ l++   y++  e l++a +l++++
  gi|330509112|ref|YP_004385540.1| 289 RMQEKTDGWYKTSQELFKKASYEESVEALNRAiELDPQN 327
                                       445666666777888999999999999999998887776 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0017
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHH.HHTT-.......HHHHHHHHHCTSHHHC-H.......HHHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlcl.ylngq.......ykrAyellrkaklnsksl.......gcrylfAq 64 
                                         y++Ai  ++++l+ ++ ++e+  ++A +l  ++++       y++A++l  ++              +++  ++ 
  gi|330509112|ref|YP_004385540.1| 392 SLYEEAIKEFDKALELDPMNEEAWTYKASVLdTRLNKsaeallaYDKAIDLDGEN------AidneslsNAWSGKGT 462
                                       6799*******************99999998434455344555566666665555......4443333599999999 PP

                                       HHHHTT-HHHHHHHH-S CS
                            ANAPC3  65 cllkLkkyeeAiaaLek 81 
                                       +l kL++y+e   a++k
  gi|330509112|ref|YP_004385540.1| 463 ALAKLGRYNESFEAFDK 479
                                       999*******9999887 PP

  == domain 5  score: 10.4 bits;  conditional E-value: 0.00088
                                       HHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHH.....HHHHHTT-HHHHH CS
                            ANAPC3  33 lylngqykrAyellrka.klnskslgcrylfA.....qcllkLkkyeeAi 76 
                                       l ++g+y++A   ++k  ++n+ s ++++ +A      +l + +ky+eA+
  gi|330509112|ref|YP_004385540.1| 499 LNQSGRYEEAAFAYDKVvEQNPDSSQALIAHAygskgDALSAWGKYDEAV 548
                                       55555555555555555555555555555555555545555555555555 PP

  == domain 6  score: 10.0 bits;  conditional E-value: 0.0012
                                       T-HHHHHHHHHHHH.HHH--HHHHHHH.HHHHHHTT-HHHHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayll.AlclylngqykrAyellr 47 
                                       ++y++A f +++++    ++p+++ +l A ++ + g+  +A   ++
  gi|330509112|ref|YP_004385540.1| 503 GRYEEAAFAYDKVV---EQNPDSSQALiAHAYGSKGDALSAWGKYD 545
                                       78999999999999...34444433333666666666666654444 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.9   3.2e+03       3      16 ..     117     130 ..     116     133 .. 0.69
   2 ?   -1.6   0.0       3.2   2.1e+03       2      14 ..     193     205 ..     192     210 .. 0.91
   3 ?    3.3   0.0     0.091        60       2      15 ..     310     323 ..     309     329 .. 0.89
   4 ?    4.1   0.0     0.053        35       1      15 [.     350     364 ..     350     366 .. 0.93
   5 ?    0.4   0.0      0.73   4.9e+02       2      14 ..     394     406 ..     393     408 .. 0.92
   6 !    6.4   0.0    0.0098       6.5       1      20 [.     469     488 ..     469     493 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.9
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   3 eeaLeqvnkAieiS 16 
                                       eea+   ++ ieiS
  gi|330509112|ref|YP_004385540.1| 117 EEAIGALERSIEIS 130
                                       56677777777777 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAie 14 
                                       Y+e+ e  n Ai 
  gi|330509112|ref|YP_004385540.1| 193 YNESVEAFNEAIR 205
                                       9**********97 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.091
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                       Yee+ e  n+Aie+
  gi|330509112|ref|YP_004385540.1| 310 YEESVEALNRAIEL 323
                                       ************97 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.053
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y+e+L+  +kAie+
  gi|330509112|ref|YP_004385540.1| 350 QYNESLKAQDKAIEL 364
                                       7************95 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.73
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAie 14 
                                       Yeea++  +kA+e
  gi|330509112|ref|YP_004385540.1| 394 YEEAIKEFDKALE 406
                                       9**********98 PP

  == domain 6  score: 6.4 bits;  conditional E-value: 0.0098
                                       -HHHHHHHHHHHHHHHHHTT CS
                          HTH_Bact   1 rYeeaLeqvnkAieiSirin 20 
                                       rY+e++e  +kAie+ ++ +
  gi|330509112|ref|YP_004385540.1| 469 RYNESFEAFDKAIELNLQAS 488
                                       7*************999875 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.04        27       8      19 ..      51      62 ..      49      63 .. 0.90
   2 ?    4.0   0.0     0.067        44       6      19 ..     318     331 ..     315     332 .. 0.90
   3 ?   -0.9   0.0       2.4   1.6e+03       7      15 ..     360     368 ..     359     370 .. 0.88
   4 ?    6.1   0.0     0.015       9.8       7      22 ..     403     418 ..     402     424 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.04
                                      HHHH-TT-CHHH CS
                              PPTA  8 liekdpkNYsaW 19
                                      ++++dp N saW
  gi|330509112|ref|YP_004385540.1| 51 ALQLDPGNASAW 62
                                      899********* PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.067
                                       HHHHHH-TT-CHHH CS
                              PPTA   6 ekliekdpkNYsaW 19 
                                       + +ie+dp+N + W
  gi|330509112|ref|YP_004385540.1| 318 NRAIELDPQNATLW 331
                                       689*********99 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.4
                                       HHHHH-TT- CS
                              PPTA   7 kliekdpkN 15 
                                       k+ie+dp N
  gi|330509112|ref|YP_004385540.1| 360 KAIELDPGN 368
                                       89*****99 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.015
                                       HHHHH-TT-CHHHHHH CS
                              PPTA   7 kliekdpkNYsaWnyR 22 
                                       k++e+dp N+ aW y 
  gi|330509112|ref|YP_004385540.1| 403 KALELDPMNEEAWTYK 418
                                       89************96 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.083        55      79     135 ..      83     139 ..      68     144 .. 0.85
   2 ?    1.5   0.0      0.56   3.7e+02      66     100 ..     299     332 ..     264     375 .. 0.71
   3 !   10.6   0.1   0.00083      0.55      78     123 ..     394     440 ..     379     446 .. 0.90
   4 ?    1.7   0.1      0.49   3.2e+02      70     113 ..     497     538 ..     460     563 .. 0.59
   5 ?    3.2   0.1      0.16   1.1e+02      62     124 ..     528     593 ..     505     597 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.083
                                       HHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS---- CS
                              BTAD  79 eealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepg 135
                                       ++al+  ++ ++ +  + ++++++  Ala + r++eA+++ er  ++ ++ L   p+
  gi|330509112|ref|YP_004385540.1|  83 QKALDATNGTLKDDSQDAKAWQAMGVALAGLARNEEAIGALERSIEISDQRLEENPE 139
                                       577788888888888999999999999***********9999999999999887775 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.56
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHH CS
                              BTAD  66 ealaeaelrlGraeealaelealvaehPlrErlhr 100
                                       ++   ++++ + +ee ++ l+++++++P + +l+ 
  gi|330509112|ref|YP_004385540.1| 299 KTSQ-ELFKKASYEESVEALNRAIELDPQNATLWD 332
                                       4433.477788888888888999998888887775 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00083
                                       HHHHHHHHHHHHHHSTT-HHHHHHHHHHH.HHTT-HHHHHHHHHHHH CS
                              BTAD  78 aeealaelealvaehPlrErlhrqlmrAl.arsGrqaeALevYerlr 123
                                       +eea++e +++++++P++E+++      l  r+++ aeAL +Y+++ 
  gi|330509112|ref|YP_004385540.1| 394 YEEAIKEFDKALELDPMNEEAWTYKASVLdTRLNKSAEALLAYDKAI 440
                                       689********************999998579***********9875 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.49
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HH CS
                              BTAD  70 eaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqa 113
                                       +a+ + Gr+eea+  +++ v+++P    + +++  A+   G+  
  gi|330509112|ref|YP_004385540.1| 497 DALNQSGRYEEAAFAYDKVVEQNPDS--SQALIAHAYGSKGDAL 538
                                       35556677777777777777777633..3333334444444433 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST...T-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  62 lealealaeaelrlGraeealaelealvaehP...lrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                        +a+ +  +a+++ G+++ea+  ++++++++P   +  +++ +   Al ++Gr+++A +++ ++++
  gi|330509112|ref|YP_004385540.1| 528 AHAYGSKGDALSAWGKYDEAVIAYDNAIENYPsepMGAQTWHKKGIALQALGRTSDADAAFAKAKE 593
                                       5666677789999999999999999999876511155688888899***********999988865 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.2   8.1e+02       6      29 ..      64      89 ..      63      99 .. 0.71
   2 !    7.3   0.1     0.008       5.3       1      33 [.     102     134 ..     102     137 .. 0.87
   3 ?   -0.8   0.0         3     2e+03      18      31 ..     160     173 ..     159     176 .. 0.78
   4 ?   -0.4   0.0       2.4   1.6e+03      15      35 ..     310     328 ..     305     329 .. 0.88
   5 ?    4.7   0.1     0.055        37       4      29 ..     381     408 ..     379     420 .. 0.78
   6 ?   -0.7   0.0       2.9   1.9e+03      11      33 ..     425     445 ..     414     448 .. 0.77
   7 ?    1.2   0.0      0.71   4.7e+02      15      25 ..     477     487 ..     461     490 .. 0.73
   8 ?    3.3   0.0      0.15     1e+02       2      24 ..     492     514 ..     491     523 .. 0.78
   9 ?    2.3   0.0      0.31   2.1e+02       2      29 ..     531     556 ..     530     562 .. 0.78
  10 ?   -0.1   0.0       1.9   1.2e+03       6      24 ..     572     590 ..     567     597 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.2
                             TPR_7  6 arlysr..lGdyeeAielyeqsLalt 29
                                      + ++++  lG+  e  e+++++L  t
  gi|330509112|ref|YP_004385540.1| 64 GKAQVSqiLGNQIESREYFQKALDAT 89
                                      66666667888888999****77433 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.008
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       a+ +++++   l + eeAi+ +e+s+++ ++ +
  gi|330509112|ref|YP_004385540.1| 102 AWQAMGVALAGLARNEEAIGALERSIEISDQRL 134
                                       67899*******************999987765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3
                             TPR_7  18 AielyeqsLaltkd 31 
                                       Ai+ ye++++l ++
  gi|330509112|ref|YP_004385540.1| 160 AIKAYEKVIELNSS 173
                                       9999***8887665 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.4
                             TPR_7  15 yeeAielyeqsLaltkdpeda 35 
                                       yee +e + +  a++ dp++a
  gi|330509112|ref|YP_004385540.1| 310 YEESVEALNR--AIELDPQNA 328
                                       899999999*..999999886 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.055
                             TPR_7   4 nLarl..ysrlGdyeeAielyeqsLalt 29 
                                       nLa+l  + ++  yeeAi+ + ++L+l+
  gi|330509112|ref|YP_004385540.1| 381 NLADLsgHKNESLYEEAIKEFDKALELD 408
                                       5555555777889**********66654 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 2.9
                             TPR_7  11 rlGdyeeAielyeqsLaltkdpe 33 
                                       rl++ +eA+  y +  a++ d e
  gi|330509112|ref|YP_004385540.1| 425 RLNKSAEALLAYDK--AIDLDGE 445
                                       57888888888888..7776655 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 0.71
                             TPR_7  15 yeeAielyeqs 25 
                                       +++Aiel+ q+
  gi|330509112|ref|YP_004385540.1| 477 FDKAIELNLQA 487
                                       89999999883 PP

  == domain 8  score: 3.3 bits;  conditional E-value: 0.15
                             TPR_7   2 LlnLarlysrlGdyeeAielyeq 24 
                                       +l+ +++  + G+yeeA+  y +
  gi|330509112|ref|YP_004385540.1| 492 WLAKGDALNQSGRYEEAAFAYDK 514
                                       678899999********866555 PP

  == domain 9  score: 2.3 bits;  conditional E-value: 0.31
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLalt 29 
                                       +   +++ s+ G+y+eA+  y    a++
  gi|330509112|ref|YP_004385540.1| 531 YGSKGDALSAWGKYDEAVIAYDN--AIE 556
                                       66678888888*******99988..555 PP

  == domain 10  score: -0.1 bits;  conditional E-value: 1.9
                             TPR_7   6 arlysrlGdyeeAielyeq 24 
                                       + + ++lG++++A   + +
  gi|330509112|ref|YP_004385540.1| 572 GIALQALGRTSDADAAFAK 590
                                       7788899999999877766 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       8.6   5.7e+03      25      37 ..      49      61 ..      48      61 .. 0.81
   2 ?   -2.0   0.0       5.9   3.9e+03      13      35 ..     189     211 ..     188     213 .. 0.86
   3 ?    3.3   0.1      0.13        87      13      34 ..     306     327 ..     298     329 .. 0.90
   4 ?    3.3   0.0      0.14        90      16      35 ..     350     369 ..     348     371 .. 0.93
   5 ?    5.3   0.0      0.03        20      17      37 ..     394     414 ..     387     423 .. 0.89
   6 ?    2.6   0.0      0.21   1.4e+02      10      29 ..     463     482 ..     461     489 .. 0.82
   7 ?    1.3   0.0      0.56   3.7e+02      15      38 ..     503     526 ..     498     527 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.6
                                      HHHHHHTTS-HHH CS
                        Fis1_TPR_C 25 dalLeiEPenrQa 37
                                      d  L+++P+n  a
  gi|330509112|ref|YP_004385540.1| 49 DHALQLDPGNASA 61
                                      6689*****9866 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.9
                                       HHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPenr 35 
                                       k   Y+e+ +  +  +++ P+n 
  gi|330509112|ref|YP_004385540.1| 189 KANGYNESVEAFNEAIRLMPDNA 211
                                       677899**999999999999995 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.13
                                       HHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPen 34 
                                       k   Y+e+ + +++ +e++P+n
  gi|330509112|ref|YP_004385540.1| 306 KKASYEESVEALNRAIELDPQN 327
                                       6678*****************9 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.14
                                       -HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPenr 35 
                                       +Y+e+++  d  +e++P+n+
  gi|330509112|ref|YP_004385540.1| 350 QYNESLKAQDKAIELDPGNS 369
                                       7*****************95 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.03
                                       HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  17 YseArryvdalLeiEPenrQa 37 
                                       Y+eA +  d  Le++P n+ a
  gi|330509112|ref|YP_004385540.1| 394 YEEAIKEFDKALELDPMNEEA 414
                                       9*****************998 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.21
                                       HHHHHT-HHHHHHHHHHHHH CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLe 29 
                                       + +klg+Y+e+ +  d  +e
  gi|330509112|ref|YP_004385540.1| 463 ALAKLGRYNESFEAFDKAIE 482
                                       789********999888776 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.56
                                       T-HHHHHHHHHHHHHHTTS-HHHH CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenrQaq 38 
                                       g+Y+eA    d + e  P+ +Qa+
  gi|330509112|ref|YP_004385540.1| 503 GRYEEAAFAYDKVVEQNPDSSQAL 526
                                       89********************96 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       6.4   4.3e+03      19      51 ..     149     180 ..     145     183 .. 0.78
   2 ?    0.3   0.0       1.2   7.7e+02      27      47 ..     192     212 ..     187     243 .. 0.75
   3 ?    6.8   0.1     0.011       7.3      26      52 ..     308     334 ..     290     339 .. 0.83
   4 ?    6.6   0.0     0.013       8.5      19      49 ..     342     372 ..     335     377 .. 0.90
   5 ?    2.2   0.0      0.29     2e+02      28      56 ..     470     498 ..     468     509 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.4
                           DUF1510  19 ssydkgsvDwnEmekavskatglsednmivwwl 51 
                                       +sy+    D+    ka +k+++l++++++  w+
  gi|330509112|ref|YP_004385540.1| 149 VSYEALYMDYAA-IKAYEKVIELNSSKSVGAWI 180
                                       667777777765.58999999999999998887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.2
                           DUF1510  27 DwnEmekavskatglsednmi 47 
                                        +nE ++a+++a+ l  dn  
  gi|330509112|ref|YP_004385540.1| 192 GYNESVEAFNEAIRLMPDNAS 212
                                       699************999865 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.011
                           DUF1510  26 vDwnEmekavskatglsednmivwwlg 52 
                                         ++E ++a+++a++l+ +n ++w  +
  gi|330509112|ref|YP_004385540.1| 308 ASYEESVEALNRAIELDPQNATLWDAK 334
                                       4589********************875 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.013
                           DUF1510  19 ssydkgsvDwnEmekavskatglsednmivw 49 
                                       +s+d + + +nE +ka  ka++l+  n++++
  gi|330509112|ref|YP_004385540.1| 342 ASFDGNRSQYNESLKAQDKAIELDPGNSTLH 372
                                       78999**********************9987 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.29
                           DUF1510  28 wnEmekavskatglsednmivwwlgnggs 56 
                                       +nE  +a+ ka++l+ + + ++wl +g++
  gi|330509112|ref|YP_004385540.1| 470 YNESFEAFDKAIELNLQASAFVWLAKGDA 498
                                       899********************998865 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.6     4e+02      92     130 ..      30      67 ..      14      84 .. 0.75
   2 !    6.9   0.0    0.0079       5.2      99     122 ..     188     211 ..     128     220 .. 0.78
   3 ?   -0.5   0.0       1.5   9.8e+02     100     122 ..     306     328 ..     290     350 .. 0.89
   4 ?   -0.9   0.0         2   1.3e+03     100     123 ..     347     370 ..     339     378 .. 0.82
   5 ?    1.4   0.0      0.39   2.6e+02     103     123 ..     543     563 ..     521     584 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.6
                              LemA  92 gtEnriavaRrrYneavreyntkiesfpsnivaklfgfk 130
                                       g+  +i+ +R+ +++ v+ y+ +++  p+n  a l + +
  gi|330509112|ref|YP_004385540.1|  30 GISGNIS-ERNPFQDVVQGYDHALQLDPGNASAWLGKAQ 67 
                                       5555554.799**************99999988776665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0079
                              LemA  99 vaRrrYneavreyntkiesfpsni 122
                                       ++ + Yne+v+++n++i+ +p+n 
  gi|330509112|ref|YP_004385540.1| 188 AKANGYNESVEAFNEAIRLMPDNA 211
                                       45578****************985 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.5
                              LemA 100 aRrrYneavreyntkiesfpsni 122
                                       ++  Y e+v+++n +ie  p+n 
  gi|330509112|ref|YP_004385540.1| 306 KKASYEESVEALNRAIELDPQNA 328
                                       6789************9988875 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 2
                              LemA 100 aRrrYneavreyntkiesfpsniv 123
                                       +R++Yne+ ++ +++ie  p+n +
  gi|330509112|ref|YP_004385540.1| 347 NRSQYNESLKAQDKAIELDPGNST 370
                                       7999******99999998888765 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.39
                              LemA 103 rYneavreyntkiesfpsniv 123
                                       +Y eav +y+++ie++ps+ +
  gi|330509112|ref|YP_004385540.1| 543 KYDEAVIAYDNAIENYPSEPM 563
                                       7****************9755 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.9   1.2e+03      85     108 ..     186     210 ..     178     212 .. 0.80
   2 ?    4.7   0.0     0.046        31      82     112 ..     301     331 ..     288     339 .. 0.89
   3 ?   -2.4   0.0       7.2   4.8e+03      73     104 ..     376     407 ..     347     414 .. 0.66
   4 ?   -1.6   0.0         4   2.6e+03      82     107 ..     461     486 ..     458     493 .. 0.81
   5 ?    2.5   0.0      0.22   1.4e+02      65     107 ..     517     560 ..     493     563 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.9
                             MAS20  85 llaq.geeeeaaehlynAlkvcpqP 108
                                       l+a+ + ++e++e++  A++++p  
  gi|330509112|ref|YP_004385540.1| 186 LFAKaNGYNESVEAFNEAIRLMPDN 210
                                       666668899***********99875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.046
                             MAS20  82 GEellaqgeeeeaaehlynAlkvcpqPqeLl 112
                                        +el++++++ee++e+l +A+ + pq + L 
  gi|330509112|ref|YP_004385540.1| 301 SQELFKKASYEESVEALNRAIELDPQNATLW 331
                                       5789999*******************99886 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 7.2
                             MAS20  73 kfFleevqlGEellaqgeeeeaaehlynAlkv 104
                                        fF+ +++      +++ +eea++ + +Al +
  gi|330509112|ref|YP_004385540.1| 376 GFFIANLADLSGHKNESLYEEAIKEFDKALEL 407
                                       46666666666666667788888888888876 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 4
                             MAS20  82 GEellaqgeeeeaaehlynAlkvcpq 107
                                       G  l++ g+++e+ e++ +A+ +  q
  gi|330509112|ref|YP_004385540.1| 461 GTALAKLGRYNESFEAFDKAIELNLQ 486
                                       66677779************987655 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.22
                             MAS20  65 ptdaeevekfFleev.qlGEellaqgeeeeaaehlynAlkvcpq 107
                                        +++++ ++   +   ++G+ l+a g+++ea+ +  nA+  +p+
  gi|330509112|ref|YP_004385540.1| 517 EQNPDSSQALIAHAYgSKGDALSAWGKYDEAVIAYDNAIENYPS 560
                                       4555666666655542589999999**************99986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.029        19      14      41 ..      71      98 ..      66      99 .. 0.84
   2 ?    5.9   0.2     0.019        12       8      40 ..     106     138 ..     105     140 .. 0.90
   3 ?   -1.1   0.1       2.9     2e+03      20      36 ..     152     168 ..     152     172 .. 0.78
   4 ?   -0.7   0.0       2.3   1.5e+03      14      30 ..     347     363 ..     341     364 .. 0.88
   5 ?   -1.3   0.1       3.4   2.3e+03      18      30 ..     394     406 ..     391     407 .. 0.74
   6 ?   -2.2   0.0       6.5   4.3e+03      13      30 ..     424     441 ..     419     442 .. 0.79
   7 ?    7.1   0.0    0.0078       5.2       9      31 ..     461     483 ..     460     487 .. 0.91
   8 ?    1.7   0.1       0.4   2.6e+02      11      22 ..     498     509 ..     496     517 .. 0.80
   9 ?    1.2   0.0      0.56   3.7e+02       5      29 ..     531     555 ..     527     556 .. 0.76
  10 ?    2.2   0.1      0.26   1.7e+02       9      29 ..     572     592 ..     569     598 .] 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.029
                            TPR_10 14 qrgrydeAealleealairrrllGpdHP 41
                                       +g+  e+++++++al++   +l +d+ 
  gi|330509112|ref|YP_004385540.1| 71 ILGNQIESREYFQKALDATNGTLKDDSQ 98
                                      6899*************99888888875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.019
                            TPR_10   8 LanalrqrgrydeAealleealairrrllGpdH 40 
                                       +++al  + r +eA   le++++i  + l++++
  gi|330509112|ref|YP_004385540.1| 106 MGVALAGLARNEEAIGALERSIEISDQRLEENP 138
                                       68999999*****************99999886 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.9
                            TPR_10  20 eAealleealairrrll 36 
                                       eA+ +   a+ +++++ 
  gi|330509112|ref|YP_004385540.1| 152 EALYMDYAAIKAYEKVI 168
                                       68888888999999985 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.3
                            TPR_10  14 qrgrydeAealleeala 30 
                                       +r +y+e+++ +++a++
  gi|330509112|ref|YP_004385540.1| 347 NRSQYNESLKAQDKAIE 363
                                       6779***********98 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 3.4
                            TPR_10  18 ydeAealleeala 30 
                                       y+eA + +++al+
  gi|330509112|ref|YP_004385540.1| 394 YEEAIKEFDKALE 406
                                       6788888888876 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 6.5
                            TPR_10  13 rqrgrydeAealleeala 30 
                                       +++++ +eA+  +++a++
  gi|330509112|ref|YP_004385540.1| 424 TRLNKSAEALLAYDKAID 441
                                       677888999999999986 PP

  == domain 7  score: 7.1 bits;  conditional E-value: 0.0078
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al ++gry+e+ + +++a+++
  gi|330509112|ref|YP_004385540.1| 461 GTALAKLGRYNESFEAFDKAIEL 483
                                       7899*****************97 PP

  == domain 8  score: 1.7 bits;  conditional E-value: 0.4
                            TPR_10  11 alrqrgrydeAe 22 
                                       al q gry+eA 
  gi|330509112|ref|YP_004385540.1| 498 ALNQSGRYEEAA 509
                                       899*******96 PP

  == domain 9  score: 1.2 bits;  conditional E-value: 0.56
                            TPR_10   5 lnNLanalrqrgrydeAealleeal 29 
                                       +   + al++ g+ydeA+  ++ a+
  gi|330509112|ref|YP_004385540.1| 531 YGSKGDALSAWGKYDEAVIAYDNAI 555
                                       555567788889******9998887 PP

  == domain 10  score: 2.2 bits;  conditional E-value: 0.26
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       ++al+++gr  +A a + +a 
  gi|330509112|ref|YP_004385540.1| 572 GIALQALGRTSDADAAFAKAK 592
                                       89***********99998885 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       7.6     5e+03     160     177 ..      73      90 ..      64     115 .. 0.69
   2 ?    0.2   0.2      0.79   5.3e+02     158     180 ..     425     447 ..     395     466 .. 0.75
   3 ?   -2.2   0.1       4.1   2.8e+03     152     174 ..     460     482 ..     435     491 .. 0.82
   4 ?    7.6   0.6    0.0044       2.9     151     184 ..     494     527 ..     464     531 .. 0.84
   5 ?   13.0   0.1   9.2e-05     0.061     141     177 ..     523     559 ..     519     567 .. 0.86
   6 ?    0.7   0.1      0.54   3.6e+02     149     174 ..     568     593 ..     558     598 .] 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.6
                            TPR_21 160 gkldeAraaYqaAlaale 177
                                       g++ e r+ +q+Al+a +
  gi|330509112|ref|YP_004385540.1|  73 GNQIESREYFQKALDATN 90 
                                       555566666777766654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.79
                            TPR_21 158 aqgkldeAraaYqaAlaaleeka 180
                                       + +k +eA  aY++A++  +e+a
  gi|330509112|ref|YP_004385540.1| 425 RLNKSAEALLAYDKAIDLDGENA 447
                                       5789999999****999888776 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.1
                            TPR_21 152 rGDilvaqgkldeAraaYqaAla 174
                                       +G +l++ g+ +e  +a+++A++
  gi|330509112|ref|YP_004385540.1| 460 KGTALAKLGRYNESFEAFDKAIE 482
                                       88899999999999999999987 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0044
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaaleekarell 184
                                        +GD+l + g+ +eA  aY++ ++++ +++++l+
  gi|330509112|ref|YP_004385540.1| 494 AKGDALNQSGRYEEAAFAYDKVVEQNPDSSQALI 527
                                       59*********************99998877665 PP

  == domain 5  score: 13.0 bits;  conditional E-value: 9.2e-05
                            TPR_21 141 eeafaalvaelrGDilvaqgkldeAraaYqaAlaale 177
                                       ++a  a++   +GD+l+a gk deA  aY++A+++  
  gi|330509112|ref|YP_004385540.1| 523 SQALIAHAYGSKGDALSAWGKYDEAVIAYDNAIENYP 559
                                       56677888899**********************9866 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 0.54
                            TPR_21 149 aelrGDilvaqgkldeAraaYqaAla 174
                                          +G +l a g++ +A aa+ +A +
  gi|330509112|ref|YP_004385540.1| 568 WHKKGIALQALGRTSDADAAFAKAKE 593
                                       5668999****************976 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       9.7   6.4e+03      16      37 ..     462     483 ..     453     491 .. 0.74
   2 ?    0.6   0.0         1   6.9e+02      14      34 ..     495     515 ..     489     524 .. 0.82
   3 ?    8.9   0.0    0.0025       1.7       7      42 ..     527     563 ..     521     584 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 9.7
                         NRBF2_MIT  16 drllaaGkyeeaischkkaaay 37 
                                         l   G+y+e+     ka + 
  gi|330509112|ref|YP_004385540.1| 462 TALAKLGRYNESFEAFDKAIEL 483
                                       5566679999999999988765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1
                         NRBF2_MIT  14 kadrllaaGkyeeaischkka 34 
                                       k d l  +G+yeea   + k 
  gi|330509112|ref|YP_004385540.1| 495 KGDALNQSGRYEEAAFAYDKV 515
                                       67889999******8877776 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0025
                         NRBF2_MIT   7 lahqqsrkadrllaaGkyeeaischkkaaa.ylseam 42 
                                       +ah    k d l a Gky+ea+  +  a + y se m
  gi|330509112|ref|YP_004385540.1| 527 IAHAYGSKGDALSAWGKYDEAVIAYDNAIEnYPSEPM 563
                                       699999***************9888777542666666 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.18   1.2e+02      85     123 ..      41      79 ..      17      92 .. 0.86
   2 ?   -1.3   0.0       4.1   2.7e+03      63     116 ..     103     154 ..      91     166 .. 0.75
   3 ?    7.9   0.5    0.0061       4.1      73     119 ..     298     344 ..     277     360 .. 0.85
   4 ?    2.9   0.1      0.21   1.4e+02      82     116 ..     391     425 ..     380     435 .. 0.81
   5 ?    2.2   0.1      0.36   2.4e+02      73     118 ..     493     543 ..     457     553 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  85 yrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       ++ +++  +h+++ dp na+a   ka++ + lg+q es 
  gi|330509112|ref|YP_004385540.1|  41 FQDVVQGYDHALQLDPGNASAWLGKAQVSQILGNQIESR 79 
                                       677888899**************************9985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.1
                                       HHHTTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  63 velmGgaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleql 116
                                        ++mG   +++  a+++ + g ++ ++e+ ++ ++++pe+ +    ka ++e+l
  gi|330509112|ref|YP_004385540.1| 103 WQAMG--VALAGLARNEEAIGALERSIEISDQRLEENPEDIDSLWQKAVSYEAL 154
                                       55666..56677788888889999999999999999999877777777777765 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0061
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  73 lekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyq 119
                                        +  +e +k+  y+ ++e ln +++ dp+na+  ++ka++l   + +
  gi|330509112|ref|YP_004385540.1| 298 YKTSQELFKKASYEESVEALNRAIELDPQNATLWDAKASSLGIAASF 344
                                       56789999*****************************9998766655 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.21
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  82 egdyrwaaellnhlvfadpenaeakelkadaleql 116
                                       e  y+ a++  +++++ dp n+ea + ka++l+ +
  gi|330509112|ref|YP_004385540.1| 391 ESLYEEAIKEFDKALELDPMNEEAWTYKASVLDTR 425
                                       555888999999*******************9865 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.36
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHH.....HHHHHHHHHH CS
                   Alkyl_sulf_dimr  73 lekakealkegdyrwaaellnhlvfadpenaeakel.....kadaleqlgy 118
                                       l+k  +  ++g y+ aa   +++v+++p+ ++a  +     k dal + g+
  gi|330509112|ref|YP_004385540.1| 493 LAKGDALNQSGRYEEAAFAYDKVVEQNPDSSQALIAhaygsKGDALSAWGK 543
                                       455555668999**************9997554332222335566655555 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0      0.05        33       9      30 ..     463     484 ..     462     485 .. 0.88
   2 ?    1.2   0.0      0.83   5.5e+02       9      27 ..     498     516 ..     497     519 .. 0.78
   3 ?    0.4   0.0       1.5   9.9e+02       8      20 ..     536     548 ..     529     556 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.05
                               PPR   9 gycknGkleeAlelfkeMkekG 30 
                                       +++k G++ e +e f++ +e +
  gi|330509112|ref|YP_004385540.1| 463 ALAKLGRYNESFEAFDKAIELN 484
                                       89**************988765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.83
                               PPR   9 gycknGkleeAlelfkeMk 27 
                                       ++ ++G++eeA   +++ +
  gi|330509112|ref|YP_004385540.1| 498 ALNQSGRYEEAAFAYDKVV 516
                                       7889*******87777765 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.5
                               PPR   8 sgycknGkleeAl 20 
                                       ++++  Gk++eA+
  gi|330509112|ref|YP_004385540.1| 536 DALSAWGKYDEAV 548
                                       5778888888886 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.2   8.3e+02      54      73 ..     113     132 ..      67     137 .. 0.79
   2 ?    5.9   0.0      0.02        14      49      74 ..     185     210 ..     145     215 .. 0.83
   3 ?    1.6   2.1      0.44   2.9e+02      36      68 ..     447     481 ..     302     494 .. 0.67
   4 ?   -1.8   0.0       5.2   3.5e+03      52      68 ..     539     555 ..     510     556 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.2
                            ANAPC5  54 fghneeAvkaleeairlAre 73 
                                       +  neeA+ ale +i+++ +
  gi|330509112|ref|YP_004385540.1| 113 LARNEEAIGALERSIEISDQ 132
                                       567999*****999999866 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                            ANAPC5  49 slhadfghneeAvkaleeairlAren 74 
                                       +l a+ + ++e+v+a++eairl  +n
  gi|330509112|ref|YP_004385540.1| 185 ILFAKANGYNESVEAFNEAIRLMPDN 210
                                       567777899************97666 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.44
                            ANAPC5  36 q..kksyqyalLnlaslhadfghneeAvkaleeai 68 
                                       +  ++s+  a     +  a++g ++e+ +a+  ai
  gi|330509112|ref|YP_004385540.1| 447 AidNESLSNAWSGKGTALAKLGRYNESFEAFDKAI 481
                                       22334444444444444555556666666665555 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 5.2
                            ANAPC5  52 adfghneeAvkaleeai 68 
                                       ++ g+++eAv a  +ai
  gi|330509112|ref|YP_004385540.1| 539 SAWGKYDEAVIAYDNAI 555
                                       56789999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.55
# Mc/sec: 3250.15
//
Query:       gi|330509113|ref|YP_004385541.1|  [L=462]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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  168.6  12.6    9.8e-07   28.3   0.0   12.5 13  TPR_1            Tetratricopeptide repeat
    2.8e-50  164.4  23.9    5.5e-07   29.2   0.0   12.5 13  TPR_2            Tetratricopeptide repeat
    2.8e-48  158.1  18.0    3.7e-05   23.6   0.0   11.9 12  TPR_8            Tetratricopeptide repeat
    5.5e-41  138.7  21.5    5.1e-10   39.5   0.0    7.1  7  TPR_12           Tetratricopeptide repeat
    9.7e-36  122.2  16.5    3.2e-08   34.1   0.5    8.2  8  TPR_16           Tetratricopeptide repeat
    1.9e-34  115.4  23.9    5.4e-05   23.7   0.1   11.1 11  TPR_14           Tetratricopeptide repeat
    3.4e-34  116.2  26.2    2.7e-10   39.8   0.1   11.5 11  TPR_11           TPR repeat
    1.8e-26   92.4  19.6    2.7e-06   27.8   0.2    7.3  7  TPR_19           Tetratricopeptide repeat
    9.1e-24   82.1  16.8    0.00044   20.4   0.0   10.7 10  TPR_17           Tetratricopeptide repeat
    1.1e-22   80.0   7.6    1.8e-05   24.8   0.0    7.4  8  TPR_9            Tetratricopeptide repeat
      2e-16   60.3  20.3      3e-05   24.1   2.7    7.2  6  DUF3856          Domain of Unknown Function (DUF3856)
      2e-16   59.9  10.1     0.0062   16.7   0.0    7.4  8  ANAPC3           Anaphase-promoting complex, cyclosome, subun
      2e-15   56.7  12.9     0.0045   16.0   0.9    6.4  7  NARP1            NMDA receptor-regulated protein 1
    4.7e-12   46.6  15.4       0.12   12.8   0.1    6.2  6  BTAD             Bacterial transcriptional activator domain
    1.5e-10   40.3  20.0       0.15   12.1   0.0   10.2 11  TPR_7            Tetratricopeptide repeat
    2.1e-10   40.5  11.5        9.7    7.1   0.1   10.8 12  TPR_6            Tetratricopeptide repeat
    7.8e-10   38.4  23.3       0.22   10.7   0.8    6.4  6  TPR_15           Tetratricopeptide repeat
      6e-09   35.5  33.7       0.67    9.9   0.1   10.2 11  TPR_10           Tetratricopeptide repeat
    8.8e-08   31.9  14.6    6.4e-05   22.5   0.7    3.7  5  SNAP             Soluble NSF attachment protein, SNAP
    2.2e-06   26.9   1.9        0.4    9.6   0.0    3.6  3  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
    5.5e-06   25.9   0.6      0.074   12.7   0.0    5.3  5  HTH_Bact         Helix-turn-helix bacterial domain
    6.2e-06   26.1  18.8       0.36   10.5   2.9    6.1  5  TPR_21           Tetratricopeptide repeat-like domain
    2.9e-05   23.6   8.4     0.0063   15.9   1.4    3.9  2  TPR_MalT         MalT-like TPR region
    4.4e-05   23.5   4.2        1.5    8.9   0.7    4.9  4  SRP_TPR_like     Putative TPR-like repeat
    6.1e-05   22.6  11.8       0.67    9.3   0.1    4.3  4  Coatomer_E       Coatomer epsilon subunit
    9.8e-05   22.6   5.9        6.3    7.1   0.0    5.4  5  TPR_5            Tetratrico peptide repeat
    0.00018   21.5   3.3        1.4    9.0   0.0    5.4  4  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    0.00036   20.8  16.1        2.6    8.4   0.0    7.3  8  TPR_20           Tetratricopeptide repeat
     0.0012   18.8   7.3        3.1    7.9   0.2    5.8  5  ANAPC5           Anaphase-promoting complex subunit 5
      0.002   18.6  17.0       0.59   10.9   0.8    6.5  6  TPR_4            Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.014   15.1  10.0        1.6    8.4   0.2    4.8  4  TOM20_plant      Plant specific mitochondrial import receptor
      0.029   14.1   8.7       0.08   12.6   0.4    3.0  2  DUF2225          Uncharacterized protein conserved in bacteri
      0.087   11.5   4.8       0.44    9.2   0.8    3.1  4  DUF3808          Protein of unknown function (DUF3808)
       0.12   12.6   3.1        2.6    8.4   0.7    3.4  2  UPF0122          Putative helix-turn-helix protein, YlxM / p1
       0.14   12.8   0.5       0.59   10.8   0.1    2.3  1  Bin3             Bicoid-interacting protein 3 (Bin3)
       0.15   12.5  11.9         13    6.3   1.4    4.7  4  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
       0.42   11.0  10.8         60    4.2   0.0    6.9  5  PPR              PPR repeat
        1.1    9.6   9.1       0.88   10.0   0.5    4.1  3  CCDC-167         Coiled-coil domain-containing protein 167
        2.7    8.3   6.2        1.1    9.6   0.3    3.2  3  Retrotrans_gag   Retrotransposon gag protein
        3.5    7.8  15.7        1.7    8.8   0.2    5.6  6  DUF1510          Domain of unknown function (DUF1510)


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 !   12.4   0.0   0.00023       0.1       3      34 .]      20      51 ..      18      51 .. 0.88
   2 ?    1.0   0.0      0.96   4.3e+02       8      24 ..      66      82 ..      59      84 .. 0.78
   3 !   18.7   0.4   2.4e-06    0.0011       1      30 [.      93     122 ..      93     125 .. 0.95
   4 !   28.3   0.0   2.2e-09   9.8e-07       1      34 []     134     167 ..     134     167 .. 0.97
   5 ?    5.9   0.0     0.027        12      15      32 ..     182     199 ..     180     201 .. 0.89
   6 !    9.9   0.0    0.0015      0.68      15      33 ..     221     239 ..     217     240 .. 0.89
   7 !   14.5   0.0   5.2e-05     0.023       4      34 .]     244     274 ..     242     274 .. 0.90
   8 !   17.8   0.2   4.7e-06    0.0021       7      31 ..     281     305 ..     278     308 .. 0.86
   9 !   17.6   0.0   5.5e-06    0.0025       1      31 [.     314     344 ..     314     347 .. 0.95
  10 ?    1.8   0.0      0.54   2.4e+02      21      33 ..     341     353 ..     340     354 .. 0.78
  11 !   10.6   0.0   0.00087      0.39       7      29 ..     361     383 ..     358     387 .. 0.88
  12 !   22.4   0.0   1.7e-07   7.4e-05       3      34 .]     397     428 ..     395     428 .. 0.95
  13 ?    3.2   0.0      0.19        86       3      20 ..     431     448 ..     429     449 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                                       +  ++  + ++g ++eA+ + ++AL ++P+n
  gi|330509113|ref|YP_004385541.1| 20 YWMDKAEGLTHNGSFEEAISALDEALNIEPEN 51
                                      577777788999******************97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.96
                                      HHHHHHTT-HHHHHHHH CS
                             TPR_1  8 GnayfklgkydeAleyy 24
                                      G+a  + ++y+ Al + 
  gi|330509113|ref|YP_004385541.1| 66 GMANESAKEYERALSFL 82
                                      78888999999999765 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a+a+  ++ a+ +l++ +e +++yekALe+
  gi|330509113|ref|YP_004385541.1|  93 AEAWEKKASALNSLNRNEESIKAYEKALEV 122
                                       799*************************97 PP

  == domain 4  score: 28.3 bits;  conditional E-value: 2.2e-09
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a+ +++n++++lg++deA e+y+++ el P++
  gi|330509113|ref|YP_004385541.1| 134 ADAWMGRANVLLNLGRWDEAHEAYDEVTELKPQD 167
                                       89******************************86 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.027
                                       T-HHHHHHHHHHHHHHST CS
                             TPR_1  15 gkydeAleyyekALelnP 32 
                                       g+ +e +e+y++A+ l P
  gi|330509113|ref|YP_004385541.1| 182 GDINESVEAYDRAIGLIP 199
                                       899***********9988 PP

  == domain 6  score: 9.9 bits;  conditional E-value: 0.0015
                                       T-HHHHHHHHHHHHHHSTT CS
                             TPR_1  15 gkydeAleyyekALelnPn 33 
                                        ++++Ale+ +k LelnP 
  gi|330509113|ref|YP_004385541.1| 221 DRWEDALEAVNKSLELNPR 239
                                       589***************6 PP

  == domain 7  score: 14.5 bits;  conditional E-value: 5.2e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +  ++ ++ +l + +eAl+++++A+  nP++
  gi|330509113|ref|YP_004385541.1| 244 WHFKAFILTELDRKEEALAAFNEAIGQNPED 274
                                       55688999*********************86 PP

  == domain 8  score: 17.8 bits;  conditional E-value: 4.7e-06
                                       HHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   7 lGnayfklgkydeAleyyekALeln 31 
                                       ++ ++ ++++y+e le+y+kA+el 
  gi|330509113|ref|YP_004385541.1| 281 KASLLVEMKRYNESLEAYDKAIELA 305
                                       6788899****************97 PP

  == domain 9  score: 17.6 bits;  conditional E-value: 5.5e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                       a++++ ++ a+ k g+ +eA +++++ L+l+
  gi|330509113|ref|YP_004385541.1| 314 AQTWFSKASALNKTGRNEEATDAFQRSLKLY 344
                                       789**************************96 PP

  == domain 10  score: 1.8 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHSTT CS
                             TPR_1  21 leyyekALelnPn 33 
                                       l+ y++A+  nP 
  gi|330509113|ref|YP_004385541.1| 341 LKLYDEAIAENPG 353
                                       6789999999886 PP

  == domain 11  score: 10.6 bits;  conditional E-value: 0.00087
                                       HHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   7 lGnayfklgkydeAleyyekALe 29 
                                       +G ++f+l++ydeA++ y+  Le
  gi|330509113|ref|YP_004385541.1| 361 KGRVLFNLERYDEAIAIYDHILE 383
                                       6999************9987776 PP

  == domain 12  score: 22.4 bits;  conditional E-value: 1.7e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++  +G a++ lg+ +eAle y+kA+   Pn+
  gi|330509113|ref|YP_004385541.1| 397 TWIARGDALRALGRNEEALEEYNKAIDMSPNF 428
                                       6999**************************97 PP

  == domain 13  score: 3.2 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHTT-HHHH CS
                             TPR_1   3 alynlGnayfklgkydeA 20 
                                       a+ +lG a + lg+   A
  gi|330509113|ref|YP_004385541.1| 431 AWHGLGEAQRALGQTHNA 448
                                       9************97766 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.1e-05    0.0095       2      34 .]      19      51 ..      18      51 .. 0.94
   2 ?    4.9   0.0     0.075        34       4      30 ..      62      88 ..      54      92 .. 0.72
   3 !   11.9   0.5   0.00042      0.19       1      30 [.      93     122 ..      93     125 .. 0.91
   4 !   29.2   0.0   1.2e-09   5.5e-07       1      34 []     134     167 ..     134     167 .. 0.96
   5 ?    5.7   0.0     0.042        19       3      33 ..     170     200 ..     168     201 .. 0.82
   6 !   13.0   0.1    0.0002     0.088       3      33 ..     209     239 ..     207     240 .. 0.84
   7 !   17.4   0.0   7.6e-06    0.0034       3      34 .]     243     274 ..     241     274 .. 0.94
   8 !   16.0   0.5   2.1e-05    0.0094       4      32 ..     278     306 ..     277     308 .. 0.90
   9 !   12.2   0.0   0.00036      0.16       2      32 ..     315     345 ..     314     347 .. 0.89
  10 !   10.7   0.1     0.001      0.46       3      33 ..     323     353 ..     321     354 .. 0.64
  11 !   14.4   0.0   6.7e-05      0.03       4      32 ..     358     386 ..     355     387 .. 0.88
  12 !   25.8   0.0   1.6e-08     7e-06       3      33 ..     397     427 ..     395     428 .. 0.95
  13 ?    2.8   0.0      0.36   1.6e+02       3      18 ..     431     446 ..     429     449 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-05
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPnn 34
                                      ++++  ++ + ++g +eeA+ a+++Al ++P+n
  gi|330509113|ref|YP_004385541.1| 19 DYWMDKAEGLTHNGSFEEAISALDEALNIEPEN 51
                                      589999999**********************97 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.075
                             TPR_2  4 lynlGlayyklgdyeeAleafekAlel 30
                                      l   G+a + +++ye+Al ++++ l+ 
  gi|330509113|ref|YP_004385541.1| 62 LSVVGMANESAKEYERALSFLDEDLKK 88
                                      455677777888888888888776665 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00042
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       aea+   + a+  l++ ee ++a+ekAle 
  gi|330509113|ref|YP_004385541.1|  93 AEAWEKKASALNSLNRNEESIKAYEKALEV 122
                                       7899999999999***************96 PP

  == domain 4  score: 29.2 bits;  conditional E-value: 1.2e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+a++ +++++++lg+++eA+ea++++ el P++
  gi|330509113|ref|YP_004385541.1| 134 ADAWMGRANVLLNLGRWDEAHEAYDEVTELKPQD 167
                                       79******************************86 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.042
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       ++++ +++    gd +e +ea+++A+ l P 
  gi|330509113|ref|YP_004385541.1| 170 VWWRKAEVISGIGDINESVEAYDRAIGLIPA 200
                                       577777777788*************988776 PP

  == domain 6  score: 13.0 bits;  conditional E-value: 0.0002
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+    + ++  +++e+Alea +k+lel+P+
  gi|330509113|ref|YP_004385541.1| 209 AYASKSENLASVDRWEDALEAVNKSLELNPR 239
                                       6666677788889*****************7 PP

  == domain 7  score: 17.4 bits;  conditional E-value: 7.6e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +++  + ++ +l++ eeAl+af++A+  +P++
  gi|330509113|ref|YP_004385541.1| 243 WWHFKAFILTELDRKEEALAAFNEAIGQNPED 274
                                       89************************999986 PP

  == domain 8  score: 16.0 bits;  conditional E-value: 2.1e-05
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldP 32 
                                       + + + ++ ++++y+e lea++kA+el+ 
  gi|330509113|ref|YP_004385541.1| 278 WQWKASLLVEMKRYNESLEAYDKAIELAA 306
                                       778899999*****************985 PP

  == domain 9  score: 12.2 bits;  conditional E-value: 0.00036
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       + ++  + a+ k g+ eeA +af+++l+l+ 
  gi|330509113|ref|YP_004385541.1| 315 QTWFSKASALNKTGRNEEATDAFQRSLKLYD 345
                                       67999999999******************86 PP

  == domain 10  score: 10.7 bits;  conditional E-value: 0.001
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       al+  G+  ++ + +++ l+++++A++ +P+
  gi|330509113|ref|YP_004385541.1| 323 ALNKTGRNEEATDAFQRSLKLYDEAIAENPG 353
                                       5666666666666777777777777777775 PP

  == domain 11  score: 14.4 bits;  conditional E-value: 6.7e-05
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldP 32 
                                       l + G+++++l +y+eA++ ++  le  P
  gi|330509113|ref|YP_004385541.1| 358 LEAKGRVLFNLERYDEAIAIYDHILETTP 386
                                       6789******************9998776 PP

  == domain 12  score: 25.8 bits;  conditional E-value: 1.6e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                        + ++G+a+++lg+ eeAle ++kA+   Pn
  gi|330509113|ref|YP_004385541.1| 397 TWIARGDALRALGRNEEALEEYNKAIDMSPN 427
                                       599***************************8 PP

  == domain 13  score: 2.8 bits;  conditional E-value: 0.36
                             TPR_2   3 alynlGlayyklgdye 18 
                                       a++ lG+a ++lg+  
  gi|330509113|ref|YP_004385541.1| 431 AWHGLGEAQRALGQTH 446
                                       9************975 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00059      0.26       4      34 .]      21      51 ..      18      51 .. 0.83
   2 ?   -0.0   0.0       3.1   1.4e+03      17      29 ..      68      80 ..      55      84 .. 0.66
   3 !   22.8   0.4   1.5e-07   6.6e-05       1      30 [.      93     122 ..      93     125 .. 0.95
   4 !   15.2   0.0     4e-05     0.018       1      34 []     134     167 ..     134     167 .. 0.96
   5 !   11.7   0.0   0.00054      0.24       2      34 .]     169     201 ..     168     201 .. 0.91
   6 ?    1.5   0.1         1   4.5e+02      18      32 ..     224     238 ..     207     240 .. 0.86
   7 !   14.3   0.0   7.8e-05     0.035       4      34 .]     244     274 ..     243     274 .. 0.94
   8 !   20.8   0.4   6.4e-07   0.00029       4      34 .]     278     308 ..     275     308 .. 0.93
   9 !   16.2   0.0   1.9e-05    0.0086       1      31 [.     314     344 ..     314     346 .. 0.94
  10 !   14.3   0.0   7.8e-05     0.035       5      32 ..     359     386 ..     355     387 .. 0.86
  11 !   23.6   0.0   8.2e-08   3.7e-05       3      33 ..     397     427 ..     395     428 .. 0.94
  12 ?    5.5   0.0     0.051        23       2      24 ..     430     452 ..     429     458 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00059
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  4 yynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      ++ ++  +   g +eeA++++ +al ++p+n
  gi|330509113|ref|YP_004385541.1| 21 WMDKAEGLTHNGSFEEAISALDEALNIEPEN 51
                                      666666667789*****************86 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 3.1
                                      HHHHHHHHHHHHH CS
                             TPR_8 17 yeeAkeyyekale 29
                                       +e+ + ye+al+
  gi|330509113|ref|YP_004385541.1| 68 ANESAKEYERALS 80
                                      4455555666654 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 1.5e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       aea+ +++s++ +l++ ee++++yekale 
  gi|330509113|ref|YP_004385541.1|  93 AEAWEKKASALNSLNRNEESIKAYEKALEV 122
                                       79**************************95 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 4e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+a++  ++++l+lg+ +eA e+y +++el+p++
  gi|330509113|ref|YP_004385541.1| 134 ADAWMGRANVLLNLGRWDEAHEAYDEVTELKPQD 167
                                       789*****************************86 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.00054
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        ++++++ + +  gd++e++e+y +a+ l p+n
  gi|330509113|ref|YP_004385541.1| 169 NVWWRKAEVISGIGDINESVEAYDRAIGLIPAN 201
                                       579999999999*****************9986 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHH CS
                             TPR_8  18 eeAkeyyekaleldp 32 
                                       e A e+ +k lel+p
  gi|330509113|ref|YP_004385541.1| 224 EDALEAVNKSLELNP 238
                                       679999********9 PP

  == domain 7  score: 14.3 bits;  conditional E-value: 7.8e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++ ++ i+ +l ++eeA +++++a+  +p++
  gi|330509113|ref|YP_004385541.1| 244 WHFKAFILTELDRKEEALAAFNEAIGQNPED 274
                                       889999********************99975 PP

  == domain 8  score: 20.8 bits;  conditional E-value: 6.4e-07
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +++++s++ ++++y+e+ e+y ka+el+ +n
  gi|330509113|ref|YP_004385541.1| 278 WQWKASLLVEMKRYNESLEAYDKAIELAAEN 308
                                       999************************9875 PP

  == domain 9  score: 16.2 bits;  conditional E-value: 1.9e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a+ ++ ++s++ k+g+ eeA  ++++ l+l 
  gi|330509113|ref|YP_004385541.1| 314 AQTWFSKASALNKTGRNEEATDAFQRSLKLY 344
                                       789*************************985 PP

  == domain 10  score: 14.3 bits;  conditional E-value: 7.8e-05
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldp 32 
                                         +g+++++l++y+eA++ y + le  p
  gi|330509113|ref|YP_004385541.1| 359 EAKGRVLFNLERYDEAIAIYDHILETTP 386
                                       579*****************99988665 PP

  == domain 11  score: 23.6 bits;  conditional E-value: 8.2e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        +   g++++ lg+ eeA e y+ka++++p+
  gi|330509113|ref|YP_004385541.1| 397 TWIARGDALRALGRNEEALEEYNKAIDMSPN 427
                                       6999**************************8 PP

  == domain 12  score: 5.5 bits;  conditional E-value: 0.051
                                       CHHHHHHHHHHHTT-HHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyy 24 
                                        a++ lg + + lg+ ++A  ++
  gi|330509113|ref|YP_004385541.1| 430 TAWHGLGEAQRALGQTHNASMSL 452
                                       59*****************8766 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   8.9e-06     0.004       9      69 ..      24      83 ..      17      84 .. 0.91
   2 !   34.9   0.9   3.1e-11   1.4e-08       3      76 ..      93     165 ..      91     166 .. 0.93
   3 !   13.9   0.0   0.00011     0.051       6      74 ..     171     236 ..     168     239 .. 0.92
   4 ?    4.1   0.1      0.13        58      10      71 ..     248     267 ..     237     270 .. 0.60
   5 !   36.3   0.9   1.1e-11   5.1e-09       9      76 ..     281     345 ..     274     346 .. 0.91
   6 !   39.5   0.0   1.1e-12   5.1e-10       6      75 ..     358     425 ..     354     427 .. 0.91
   7 ?    2.2   0.1      0.51   2.3e+02       4      22 ..     430     448 ..     428     453 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.9e-06
                            TPR_12  9 laavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelle 69
                                       a+ l++ g ++eA++ l++al+i  ++   +     a++l   g++ + +++ye Al++l 
  gi|330509113|ref|YP_004385541.1| 24 KAEGLTHNGSFEEAISALDEALNIEpENE--TVLIRKAWYLSVVGMANESAKEYERALSFLD 83
                                      78999********************6666..999************************9986 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 3.1e-11
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a a+ + a++l+ l r +e+++ +ekale++ +r+  + + l a +  + + +++ lgr++eA+e++ e++++++
  gi|330509113|ref|YP_004385541.1|  93 AEAWEKKASALNSLNRNEESIKAYEKALEVFdQRI--ERNQLDADAWMGRANVLLNLGRWDEAHEAYDEVTELKP 165
                                       678989*************************8888..78889*****************************9976 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 0.00011
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       + + a+v    g+  e+ e +++a+ ++   +  d +++a ++   ++ +   +r+e+Ale+ +++l++
  gi|330509113|ref|YP_004385541.1| 171 WWRKAEVISGIGDINESVEAYDRAIGLI---PANDTDELALAYASKSENLASVDRWEDALEAVNKSLEL 236
                                       66789999999*****************...779999******************************98 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.13
                            TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                       a                                           ++ +l+r eeAl++++ea
  gi|330509113|ref|YP_004385541.1| 248 AF------------------------------------------ILTELDRKEEALAAFNEA 267
                                       44..........................................455566666666666666 PP

  == domain 5  score: 36.3 bits;  conditional E-value: 1.1e-11
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        a++l +++ry e+le ++ka+e+a +    + +++a+t +  + ++ ++gr eeA ++++++l+++ 
  gi|330509113|ref|YP_004385541.1| 281 KASLLVEMKRYNESLEAYDKAIELAAE---NNTEELAQTWFSKASALNKTGRNEEATDAFQRSLKLYD 345
                                       699999*******************43...68899******************************996 PP

  == domain 6  score: 39.5 bits;  conditional E-value: 1.1e-12
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       l   + vl+ l+rydeA++++++ le   ++  + ++  +tt ++ g+++ralgr eeAle +++a+++ 
  gi|330509113|ref|YP_004385541.1| 358 LEAKGRVLFNLERYDEAIAIYDHILETTPSV--EPRLTHITTWIARGDALRALGRNEEALEEYNKAIDMS 425
                                       44789***********************778..66899*****************************996 PP

  == domain 7  score: 2.2 bits;  conditional E-value: 0.51
                            TPR_12   4 talnnlaavlrrlgrydeA 22 
                                       ta++ l+++ r+lg+ + A
  gi|330509113|ref|YP_004385541.1| 430 TAWHGLGEAQRALGQTHNA 448
                                       4555555555555555444 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.034        15      35      61 ..      19      45 ..      13      52 .. 0.84
   2 !   12.7   0.5   0.00034      0.15      10      61 ..      72     120 ..      65     122 .. 0.91
   3 !   34.1   0.5   7.2e-11   3.2e-08      13      67 ..     116     167 ..     114     168 .. 0.96
   4 !   26.4   0.0   1.8e-08   8.1e-06       4      66 ..     141     200 ..     140     202 .. 0.95
   5 !   21.4   0.0   6.5e-07   0.00029      12      67 ..     222     274 ..     215     275 .. 0.94
   6 !   14.7   0.2   8.1e-05     0.036       4      61 ..     282     341 ..     281     343 .. 0.90
   7 !   24.9   0.0   5.1e-08   2.3e-05      13      65 ..     337     386 ..     334     389 .. 0.93
   8 !   17.5   0.4   1.1e-05    0.0049       2      49 ..     400     444 ..     399     448 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.034
                            TPR_16 35 eAllllgdaalrqgrlaeAaalyraal 61
                                      + ++ +++ + ++g ++eA+ ++++al
  gi|330509113|ref|YP_004385541.1| 19 DYWMDKAEGLTHNGSFEEAISALDEAL 45
                                      68999999999*********9999887 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00034
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       a++y++A+  l++ lk++     +aeA+  ++ a+  ++r +e + +y++al
  gi|330509113|ref|YP_004385541.1|  72 AKEYERALSFLDEDLKKN---ASDAEAWEKKASALNSLNRNEESIKAYEKAL 120
                                       67899999999999****...99999*******************9999998 PP

  == domain 3  score: 34.1 bits;  conditional E-value: 7.2e-11
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       y++A++++++ ++r+    ++a+A++++++++l +gr++eA ++y++  +  p++
  gi|330509113|ref|YP_004385541.1| 116 YEKALEVFDQRIERN---QLDADAWMGRANVLLNLGRWDEAHEAYDEVTELKPQD 167
                                       99*************...*****************************99999987 PP

  == domain 4  score: 26.4 bits;  conditional E-value: 1.8e-08
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       a+ +l++g++d+A +a+++++++    P+++  ++ ++++    g+  e +++y++a++  p 
  gi|330509113|ref|YP_004385541.1| 141 ANVLLNLGRWDEAHEAYDEVTELK---PQDYNVWWRKAEVISGIGDINESVEAYDRAIGLIPA 200
                                       899*********************...******************************998776 PP

  == domain 5  score: 21.4 bits;  conditional E-value: 6.5e-07
                            TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +++dA++a +  l+++   P+   ++ +++ ++ ++ r +eA+a++++a+++ p +
  gi|330509113|ref|YP_004385541.1| 222 RWEDALEAVNKSLELN---PRSSTWWHFKAFILTELDRKEEALAAFNEAIGQNPED 274
                                       89**************...*******************************999976 PP

  == domain 6  score: 14.7 bits;  conditional E-value: 8.1e-05
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraal 61 
                                       a ++++ ++y + ++a++ a++++    +      a+ ++ ++ a+ + gr +eA +++++ l
  gi|330509113|ref|YP_004385541.1| 282 ASLLVEMKRYNESLEAYDKAIELA---AEnnteeLAQTWFSKASALNKTGRNEEATDAFQRSL 341
                                       7899*****************999...6666677**********************9999876 PP

  == domain 7  score: 24.9 bits;  conditional E-value: 5.1e-08
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +++ ++++++a++ +   P ++  l ++g++++ + r++eA+a y+  l+  p
  gi|330509113|ref|YP_004385541.1| 337 FQRSLKLYDEAIAEN---PGDVSLLEAKGRVLFNLERYDEAIAIYDHILETTP 386
                                       7999***********...**************************998887776 PP

  == domain 8  score: 17.5 bits;  conditional E-value: 1.1e-05
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgr 49 
                                       a+++a++++g+ ++A++ ++ a+++    P    A+ +lg+a  ++g 
  gi|330509113|ref|YP_004385541.1| 400 ARGDALRALGRNEEALEEYNKAIDMS---PNFSTAWHGLGEAQRALGQ 444
                                       799***********************...*************999885 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.8e-06    0.0021       3      42 ..      20      59 ..      18      61 .. 0.94
   2 ?    3.4   0.1       0.4   1.8e+02      12      42 ..      70     100 ..      58     101 .. 0.67
   3 !   10.6   0.1    0.0019      0.86       2      31 ..      94     123 ..      93     128 .. 0.91
   4 !   23.5   0.3   1.3e-07   5.9e-05       2      43 ..     135     176 ..     134     177 .. 0.93
   5 ?    1.8   0.1       1.3   5.7e+02      15      42 ..     182     209 ..     180     213 .. 0.72
   6 !   10.5   0.1     0.002      0.91      11      43 ..     217     249 ..     204     250 .. 0.81
   7 !    9.2   0.1    0.0053       2.4      10      42 ..     250     282 ..     247     284 .. 0.85
   8 ?    5.1   0.1      0.11        51       4      34 ..     278     308 ..     275     321 .. 0.83
   9 !    9.8   0.1    0.0035       1.6      11      40 ..     331     360 ..     314     363 .. 0.55
  10 !   13.3   0.0   0.00026      0.12       6      33 ..     360     387 ..     355     394 .. 0.87
  11 !   23.7   0.1   1.2e-07   5.4e-05       3      43 ..     397     437 ..     395     448 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.8e-06
                            TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawllla 42
                                       +++ ae l ++G ++eAi +l++al   P++++++++ a
  gi|330509113|ref|YP_004385541.1| 20 YWMDKAEGLTHNGSFEEAISALDEALNIEPENETVLIRKA 59
                                      59999******************************99877 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.4
                            TPR_14  12 lalGdpdeAiallrralalaPddaeawllla 42 
                                       + + ++++A+  l++ l+++ +daeaw   a
  gi|330509113|ref|YP_004385541.1|  70 ESAKEYERALSFLDEDLKKNASDAEAWEKKA 100
                                       4455666666666665669999999998766 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0019
                            TPR_14   2 eallalaeallalGdpdeAiallrralala 31 
                                       ea+ + a+al  l + +e+i+++++al+ +
  gi|330509113|ref|YP_004385541.1|  94 EAWEKKASALNSLNRNEESIKAYEKALEVF 123
                                       8999***********************976 PP

  == domain 4  score: 23.5 bits;  conditional E-value: 1.3e-07
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +a++ +a +ll+lG++deA ++++++ +l P+d  +w + a+
  gi|330509113|ref|YP_004385541.1| 135 DAWMGRANVLLNLGRWDEAHEAYDEVTELKPQDYNVWWRKAE 176
                                       79*******************************999988876 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 1.3
                            TPR_14  15 GdpdeAiallrralalaPddaeawllla 42 
                                       Gd  e++++++ra+ l P++++  l+la
  gi|330509113|ref|YP_004385541.1| 182 GDINESVEAYDRAIGLIPANDTDELALA 209
                                       7788999*******99887754333333 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.002
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawlllaq 43 
                                       l+  +++++A+++ ++ l+l+P + ++w + a+
  gi|330509113|ref|YP_004385541.1| 217 LASVDRWEDALEAVNKSLELNPRSSTWWHFKAF 249
                                       4556799*********************99886 PP

  == domain 7  score: 9.2 bits;  conditional E-value: 0.0053
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawllla 42 
                                       +l +l++ +eA+a++++a+ ++P+d   w   a
  gi|330509113|ref|YP_004385541.1| 250 ILTELDRKEEALAAFNEAIGQNPEDIGNWQWKA 282
                                       57788999****************998887655 PP

  == domain 8  score: 5.1 bits;  conditional E-value: 0.11
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPdd 34 
                                       ++  a++l +  ++ e+++++++a++la ++
  gi|330509113|ref|YP_004385541.1| 278 WQWKASLLVEMKRYNESLEAYDKAIELAAEN 308
                                       677799999****************987654 PP

  == domain 9  score: 9.8 bits;  conditional E-value: 0.0035
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawll 40 
                                       ++a + ++++++l+++a+a +P+d  ++ +
  gi|330509113|ref|YP_004385541.1| 331 EEATDAFQRSLKLYDEAIAENPGDVSLLEA 360
                                       333444555666666666677777776665 PP

  == domain 10  score: 13.3 bits;  conditional E-value: 0.00026
                            TPR_14   6 alaeallalGdpdeAiallrralalaPd 33 
                                       a +++l++l+++deAia+++ +l++ P+
  gi|330509113|ref|YP_004385541.1| 360 AKGRVLFNLERYDEAIAIYDHILETTPS 387
                                       6799*********************997 PP

  == domain 11  score: 23.7 bits;  conditional E-value: 1.2e-07
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                        + a+++al+alG+ +eA++ +++a++  P++ +aw  l++
  gi|330509113|ref|YP_004385541.1| 397 TWIARGDALRALGRNEEALEEYNKAIDMSPNFSTAWHGLGE 437
                                       5899*********************************9987 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.2e-05     0.023       7      30 ..      31      54 ..      28      56 .. 0.90
   2 ?    0.4   0.1       1.2   5.3e+02      12      22 ..      70      80 ..      68     103 .. 0.68
   3 !   12.9   0.2   0.00014     0.064       3      22 ..     102     121 ..     100     122 .. 0.91
   4 !   17.1   0.0     7e-06    0.0032       2      35 ..     142     175 ..     141     178 .. 0.89
   5 !    7.8   0.2    0.0057       2.6       8      27 ..     182     201 ..     181     211 .. 0.90
   6 ?    2.2   0.0      0.33   1.5e+02       9      26 ..     222     239 ..     220     242 .. 0.92
   7 ?    6.8   0.1     0.012       5.4       5      27 ..     252     274 ..     250     276 .. 0.83
   8 !   13.4   0.4    0.0001     0.047       3      26 ..     284     307 ..     282     309 .. 0.86
   9 ?    3.6   0.1      0.12        52       3      23 ..     323     343 ..     321     358 .. 0.87
  10 ?    5.4   0.0     0.033        15       1      17 [.     362     378 ..     362     386 .. 0.91
  11 !   39.8   0.1     6e-13   2.7e-10       1      42 []     402     443 ..     402     443 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.2e-05
                            TPR_11  7 qGkyeeAieaYkkAlkldPdnaea 30
                                       G +eeAi a+ +Al++ P+n ++
  gi|330509113|ref|YP_004385541.1| 31 NGSFEEAISALDEALNIEPENETV 54
                                      699******************875 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
                            TPR_11 12 eAieaYkkAlk 22
                                      e+ ++Y++Al 
  gi|330509113|ref|YP_004385541.1| 70 ESAKEYERALS 80
                                      66677777764 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00014
                            TPR_11   3 ayyeqGkyeeAieaYkkAlk 22 
                                       a+ +++++ee+i+aY+kAl+
  gi|330509113|ref|YP_004385541.1| 102 ALNSLNRNEESIKAYEKALE 121
                                       7889***************8 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 7e-06
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLG 35 
                                       +++  +G+++eA eaY +  +l+P++ ++++  +
  gi|330509113|ref|YP_004385541.1| 142 NVLLNLGRWDEAHEAYDEVTELKPQDYNVWWRKA 175
                                       788999********************99998755 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0057
                            TPR_11   8 GkyeeAieaYkkAlkldPdn 27 
                                       G+++e++eaY +A+ l P n
  gi|330509113|ref|YP_004385541.1| 182 GDINESVEAYDRAIGLIPAN 201
                                       99************998887 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.33
                            TPR_11   9 kyeeAieaYkkAlkldPd 26 
                                       ++e+A+ea +k l+l+P 
  gi|330509113|ref|YP_004385541.1| 222 RWEDALEAVNKSLELNPR 239
                                       79**************96 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.012
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdn 27 
                                       +e+ + eeA++a+++A+  +P++
  gi|330509113|ref|YP_004385541.1| 252 TELDRKEEALAAFNEAIGQNPED 274
                                       5666679************9987 PP

  == domain 8  score: 13.4 bits;  conditional E-value: 0.0001
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPd 26 
                                       +++e  +y+e++eaY kA++l  +
  gi|330509113|ref|YP_004385541.1| 284 LLVEMKRYNESLEAYDKAIELAAE 307
                                       578999**************9665 PP

  == domain 9  score: 3.6 bits;  conditional E-value: 0.12
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkl 23 
                                       a+ + G++eeA  a+++ lkl
  gi|330509113|ref|YP_004385541.1| 323 ALNKTGRNEEATDAFQRSLKL 343
                                       677889999999999999987 PP

  == domain 10  score: 5.4 bits;  conditional E-value: 0.033
                            TPR_11   1 GdayyeqGkyeeAieaY 17 
                                       G++++ + +y+eAi+ Y
  gi|330509113|ref|YP_004385541.1| 362 GRVLFNLERYDEAIAIY 378
                                       8999**********977 PP

  == domain 11  score: 39.8 bits;  conditional E-value: 6e-13
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       Gda++++G++eeA+e+Y+kA++ +P++ +a+++LG+a+ ++G
  gi|330509113|ref|YP_004385541.1| 402 GDALRALGRNEEALEEYNKAIDMSPNFSTAWHGLGEAQRALG 443
                                       9************************************97776 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.4   0.00028      0.13       4      66 ..      31     100 ..      28     102 .. 0.85
   2 ?    6.0   1.6     0.039        17       5      54 ..      73     122 ..      67     132 .. 0.88
   3 !   27.8   0.2   6.1e-09   2.7e-06       6      61 ..     115     171 ..     110     175 .. 0.86
   4 ?    5.0   0.0     0.078        35      25      66 ..     204     248 ..     182     250 .. 0.69
   5 !   12.6   0.4   0.00033      0.15       8      55 ..     258     305 ..     251     317 .. 0.92
   6 !   24.1   0.0   8.5e-08   3.8e-05       7      57 ..     337     387 ..     328     394 .. 0.89
   7 !   17.2   0.1   1.2e-05    0.0053       2      44 ..     406     448 ..     405     458 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00028
                            TPR_19   4 egdyaeAlalleqalqedpknaearllL.......AeallalgqldeAealLdalpeedpddaryasLlA 66 
                                       +g ++eA+++l +al  +p+n+ ++++          a  ++++++ A   Ld+ +++++ da+++  +A
  gi|330509113|ref|YP_004385541.1|  31 NGSFEEAISALDEALNIEPENETVLIRKawylsvvGMANESAKEYERALSFLDEDLKKNASDAEAWEKKA 100
                                       799******************9999954333567788888999999999999999999999999998877 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.039
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpee 54 
                                       + y++Al++l + l++++ +aea+   A al +l++ +e +++ ++++e 
  gi|330509113|ref|YP_004385541.1|  73 KEYERALSFLDEDLKKNASDAEAWEKKASALNSLNRNEESIKAYEKALEV 122
                                       68999999999999999999999999999999999999999998888775 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 6.1e-09
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.ary 61 
                                        y+ Al+ + q ++ +  +a+a+++ A++ll+lg++deA ++ d++ e +p+d   +
  gi|330509113|ref|YP_004385541.1| 115 AYEKALEVFDQRIERNQLDADAWMGRANVLLNLGRWDEAHEAYDEVTELKPQDyNVW 171
                                       477888888887788888**********************************84544 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.078
                            TPR_19  25 aearllL...AeallalgqldeAealLdalpeedpddaryasLlA 66 
                                       +e++l++    e l +  ++++A +++++ +e +p ++ ++  +A
  gi|330509113|ref|YP_004385541.1| 204 DELALAYaskSENLASVDRWEDALEAVNKSLELNPRSSTWWHFKA 248
                                       4555545445566777789*****************999998877 PP

  == domain 5  score: 12.6 bits;  conditional E-value: 0.00033
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55 
                                       +eAla++ +a+ ++p++   + + A +l+++++++e  ++ d++ e +
  gi|330509113|ref|YP_004385541.1| 258 EEALAAFNEAIGQNPEDIGNWQWKASLLVEMKRYNESLEAYDKAIELA 305
                                       69*************************************999988765 PP

  == domain 6  score: 24.1 bits;  conditional E-value: 8.5e-08
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       +++ l+l+ +a++e+p++  ++ +  ++l++l ++deA+a+ d ++e +p 
  gi|330509113|ref|YP_004385541.1| 337 FQRSLKLYDEAIAENPGDVSLLEAKGRVLFNLERYDEAIAIYDHILETTPS 387
                                       45559******************************************9997 PP

  == domain 7  score: 17.2 bits;  conditional E-value: 1.2e-05
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeA 44 
                                        a g+ +eAl+ + +a++ +p+ + a+ +L ea+ algq+  A
  gi|330509113|ref|YP_004385541.1| 406 RALGRNEEALEEYNKAIDMSPNFSTAWHGLGEAQRALGQTHNA 448
                                       567999*********************************8766 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.082        37       3      31 ..      42      77 ..      40      80 .. 0.77
   2 ?    5.7   0.2      0.05        22       6      32 ..      86     112 ..      82     114 .. 0.88
   3 !   18.6   0.2   3.8e-06    0.0017       6      34 .]     127     155 ..     115     155 .. 0.92
   4 ?    2.0   0.0      0.73   3.3e+02       2      28 ..     157     183 ..     156     190 .. 0.79
   5 ?    3.9   0.0      0.19        85       4      33 ..     232     261 ..     230     262 .. 0.90
   6 ?    4.3   0.0      0.14        62       2      31 ..     264     293 ..     263     296 .. 0.87
   7 ?    7.0   0.2     0.019       8.6       1      32 [.     297     333 ..     297     335 .. 0.91
   8 !   13.8   0.0   0.00013     0.056       1      33 [.     343     375 ..     343     376 .. 0.97
   9 ?    1.7   0.0      0.95   4.2e+02      15      34 .]     397     416 ..     393     416 .. 0.87
  10 !   20.4   0.0   9.7e-07   0.00044       2      32 ..     418     448 ..     417     449 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.082
                            TPR_17  3 lkaleldPnnadaynnLAelll.......knGdlmt 31
                                       +al ++P n  ++  +A++l+       +++++++
  gi|330509113|ref|YP_004385541.1| 42 DEALNIEPENETVLIRKAWYLSvvgmaneSAKEYER 77
                                      689*******************66655554455555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.05
                            TPR_17   6 leldPnnadaynnLAelllknGdlmtA 32 
                                       l+++ ++a+a+  +A +l ++++ ++ 
  gi|330509113|ref|YP_004385541.1|  86 LKKNASDAEAWEKKASALNSLNRNEES 112
                                       78999*************999988775 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 3.8e-06
                            TPR_17   6 leldPnnadaynnLAelllknGdlmtArq 34 
                                       +e++  +ada+  +A++ll++G++++A++
  gi|330509113|ref|YP_004385541.1| 127 IERNQLDADAWMGRANVLLNLGRWDEAHE 155
                                       899************************86 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.73
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGd 28 
                                       y ++ el P + +++  +Ae+ + +Gd
  gi|330509113|ref|YP_004385541.1| 157 YDEVTELKPQDYNVWWRKAEVISGIGD 183
                                       9999***********887777665555 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.19
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtAr 33 
                                       k+lel+P ++  ++ +A +l ++ ++++A+
  gi|330509113|ref|YP_004385541.1| 232 KSLELNPRSSTWWHFKAFILTELDRKEEAL 261
                                       99*********9999999999999999986 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.14
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmt 31 
                                       + +a+ ++P +   ++ +A ll + +++ +
  gi|330509113|ref|YP_004385541.1| 264 FNEAIGQNPEDIGNWQWKASLLVEMKRYNE 293
                                       789999****************98888766 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.019
                            TPR_17   1 lylkaleldPnn.....adaynnLAelllknGdlmtA 32 
                                       +y ka+el   n     a  ++ +A +l k G+ ++A
  gi|330509113|ref|YP_004385541.1| 297 AYDKAIELAAENnteelAQTWFSKASALNKTGRNEEA 333
                                       599*****877779999***************99988 PP

  == domain 8  score: 13.8 bits;  conditional E-value: 0.00013
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       ly +a++ +P ++ ++  ++++l ++ ++++A+
  gi|330509113|ref|YP_004385541.1| 343 LYDEAIAENPGDVSLLEAKGRVLFNLERYDEAI 375
                                       7*******************************8 PP

  == domain 9  score: 1.7 bits;  conditional E-value: 0.95
                            TPR_17  15 aynnLAelllknGdlmtArq 34 
                                        +  ++ +l+ +G+ ++A++
  gi|330509113|ref|YP_004385541.1| 397 TWIARGDALRALGRNEEALE 416
                                       69999************985 PP

  == domain 10  score: 20.4 bits;  conditional E-value: 9.7e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       y ka++  Pn + a++ L+e+++ +G++  A
  gi|330509113|ref|YP_004385541.1| 418 YNKAIDMSPNFSTAWHGLGEAQRALGQTHNA 448
                                       9**************************9765 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0057       2.5      30      65 ..      19      54 ..      11      59 .. 0.89
   2 ?    5.7   0.2     0.036        16       7      68 ..      71     132 ..      67     136 .. 0.91
   3 !   16.9   0.3   1.1e-05    0.0051      10      62 ..     115     167 ..     111     170 .. 0.95
   4 !   13.2   0.0   0.00017     0.074       4      64 ..     143     203 ..     141     210 .. 0.89
   5 !   24.8   0.0   3.9e-08   1.8e-05       6      62 ..     218     274 ..     215     276 .. 0.95
   6 !    7.7   0.0    0.0086       3.9      25      66 ..     271     312 ..     270     318 .. 0.89
   7 !   12.1   0.0   0.00037      0.16      13      61 ..     332     387 ..     320     395 .. 0.79
   8 !    8.1   0.0    0.0066         3      28      61 ..     394     427 ..     391     442 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0057
                             TPR_9 30 eerrdRGlllaqlGclsaAladLeaylalapdapda 65
                                      + ++d +  l + G +++A+ +L+ +l ++p+++++
  gi|330509113|ref|YP_004385541.1| 19 DYWMDKAEGLTHNGSFEEAISALDEALNIEPENETV 54
                                      6699***************************99886 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.036
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeai 68 
                                       +++++eral  ++  l  +  d+e +   + +l  l++ ++ +++ e +l++ +++ ++ ++
  gi|330509113|ref|YP_004385541.1|  71 SAKEYERALSFLDEDLKKNASDAEAWEKKASALNSLNRNEESIKAYEKALEVFDQRIERNQL 132
                                       5788999*******************************************999998888776 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 1.1e-05
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                        +e+al+v + ++  +  d++ ++ R+ +l  lG++ +A ++ +   +l p++
  gi|330509113|ref|YP_004385541.1| 115 AYEKALEVFDQRIERNQLDADAWMGRANVLLNLGRWDEAHEAYDEVTELKPQD 167
                                       689******************************************99999987 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.00017
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       ++++  +w++a ++++ +  l+P+d   ++  + +    G++++ +++ ++++ l p++++
  gi|330509113|ref|YP_004385541.1| 143 VLLNLGRWDEAHEAYDEVTELKPQDYNVWWRKAEVISGIGDINESVEAYDRAIGLIPANDT 203
                                       678889**********************************************988885554 PP

  == domain 5  score: 24.8 bits;  conditional E-value: 3.9e-08
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       ++ ++we al++v+  l l+P++   +   +++l +l++ ++Ala+++ ++ ++p++
  gi|330509113|ref|YP_004385541.1| 218 ASVDRWEDALEAVNKSLELNPRSSTWWHFKAFILTELDRKEEALAAFNEAIGQNPED 274
                                       5679*************************************************9987 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.0086
                             TPR_9  25 aPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                                       +P+d++ +   + ll+++ ++++ l++ + +++la ++ + e
  gi|330509113|ref|YP_004385541.1| 271 NPEDIGNWQWKASLLVEMKRYNESLEAYDKAIELAAENNTEE 312
                                       69******************************9998776655 PP

  == domain 7  score: 12.1 bits;  conditional E-value: 0.00037
                             TPR_9  13 ralavverllll.......aPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       +a  + +r l l       +P d++++   G++l+ l+++ +A+a  ++ l+ +p+
  gi|330509113|ref|YP_004385541.1| 332 EATDAFQRSLKLydeaiaeNPGDVSLLEAKGRVLFNLERYDEAIAIYDHILETTPS 387
                                       5555555555555555555**************************99999998884 PP

  == domain 8  score: 8.1 bits;  conditional E-value: 0.0066
                             TPR_9  28 dpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       ++  +  RG +l  lG+ ++Al++ + +++++p+
  gi|330509113|ref|YP_004385541.1| 394 HITTWIARGDALRALGRNEEALEEYNKAIDMSPN 427
                                       677899**************************95 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.46     2e+02     102     131 ..      54      83 ..      20      88 .. 0.63
   2 !   24.1   2.7   6.8e-08     3e-05      27     129 ..      70     163 ..      64     167 .. 0.88
   3 ?   -0.4   0.0       2.5   1.1e+03     104     130 ..     172     198 ..     166     206 .. 0.80
   4 !    9.2   0.3    0.0027       1.2      55     126 ..     207     267 ..     193     284 .. 0.77
   5 !   19.5   0.6   1.8e-06   0.00082      63     137 ..     283     355 ..     277     361 .. 0.72
   6 !   12.4   0.0   0.00027      0.12     100     129 ..     395     424 ..     362     435 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmagemia 131
                                       +++++a  l+ +G  +e+ k+++ a   ++
  gi|330509113|ref|YP_004385541.1|  54 VLIRKAWYLSVVGMANESAKEYERALSFLD 83 
                                       455666666667777777777766666655 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 6.8e-08
                                       HHHHHHHHHHHHHTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHH CS
                           DUF3856  27 eaaasyrkalevsrtipaeeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaav 103
                                       e+a++y++al +      +e +  +  da ++   ++al  l r +e++++ +kal+ f++r e +q +   W+   
  gi|330509113|ref|YP_004385541.1|  70 ESAKEYERALSF-----LDEDLKKNASDAEAWEKKASALNSLNRNEESIKAYEKALEVFDQRIERNQLDADAWM--- 138
                                       455555555544.....5788899999********************************************996... PP

                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmagem 129
                                         ra  l +lGr dea +a+  ++e+
  gi|330509113|ref|YP_004385541.1| 139 -GRANVLLNLGRWDEAHEAYDEVTEL 163
                                       .69*****************999986 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.5
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmagemi 130
                                       +++a  ++++G  +e+++a+  a  +i
  gi|330509113|ref|YP_004385541.1| 172 WRKAEVISGIGDINESVEAYDRAIGLI 198
                                       578888999999999999998887766 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  55 alchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       al++a+ se la + r+++ale+++k+l+       l+      W      +a  l el rk+eal af+ a
  gi|330509113|ref|YP_004385541.1| 207 ALAYASKSENLASVDRWEDALEAVNKSLE-------LNPRSSTWW----HFKAFILTELDRKEEALAAFNEA 267
                                       8999999999*******999999999995.......444444444....34777788888888888888776 PP

  == domain 5  score: 19.5 bits;  conditional E-value: 1.8e-06
                                       HHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH....HHHHHH--S CS
                           DUF3856  63 ealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma....gemiaerkG 135
                                       + l++++ry+e+le+ dka++      e + +      ++ fs+a al+++Gr++ea +af+ +    +e iae  G
  gi|330509113|ref|YP_004385541.1| 283 SLLVEMKRYNESLEAYDKAIELAA---ENNTE---ELAQTWFSKASALNKTGRNEEATDAFQRSlklyDEAIAENPG 353
                                       6688999***********997643...22222...23345599***************9998762222566666666 PP

                                       -- CS
                           DUF3856 136 el 137
                                       ++
  gi|330509113|ref|YP_004385541.1| 354 DV 355
                                       65 PP

  == domain 6  score: 12.4 bits;  conditional E-value: 0.00027
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 100 iaavfsravaleelGrkdealkafrmagem 129
                                       i++ + r+ al  lGr++eal+++++a +m
  gi|330509113|ref|YP_004385541.1| 395 ITTWIARGDALRALGRNEEALEEYNKAIDM 424
                                       666778*********************999 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.036        16      24      59 ..      17      55 ..       4      63 .. 0.74
   2 !   11.6   0.7   0.00054      0.24      36      82 .]      72     119 ..      70     119 .. 0.96
   3 !   12.5   0.0   0.00028      0.13      37      81 ..     114     159 ..     112     160 .. 0.92
   4 !   14.2   0.0   8.8e-05     0.039      34      81 ..     218     266 ..     182     267 .. 0.77
   5 !   16.7   0.0   1.4e-05    0.0062       4      81 ..     222     300 ..     219     301 .. 0.90
   6 ?    7.2   0.1     0.013       5.7      37      81 ..     296     339 ..     270     340 .. 0.64
   7 !   12.5   0.0   0.00029      0.13      39      81 ..     337     380 ..     318     381 .. 0.85
   8 ?   -0.8   0.0       4.2   1.9e+03      69      74 ..     415     420 ..     391     456 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.036
                                      HHHHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHH CS
                            ANAPC3 24 edayl..lAlclylngqykrAyellrka.klnskslgcr 59
                                         y+  +A+ l +ng +++A+  l++a +++++++ ++
  gi|330509113|ref|YP_004385541.1| 17 TTDYWmdKAEGLTHNGSFEEAISALDEAlNIEPENETVL 55
                                      3445523599999***************99988887544 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00054
                                       TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
                            ANAPC3  36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLekl 82 
                                       +++y+rA+ +l++  k+n ++ +++  +A +l  L++ ee i+a+ek+
  gi|330509113|ref|YP_004385541.1|  72 AKEYERALSFLDEDlKKNASDAEAWEKKASALNSLNRNEESIKAYEKA 119
                                       799*****************************************9985 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00028
                                       T-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  37 gqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       + y++A+e++++  + n  +  +++  A +ll L++++eA  a+++
  gi|330509113|ref|YP_004385541.1| 114 KAYEKALEVFDQRiERNQLDADAWMGRANVLLNLGRWDEAHEAYDE 159
                                       569**********99999999*******************998876 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 8.8e-05
                                       HHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  34 ylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                        +  +++ A+e ++k+ +ln++s   +  +A  l +L++ eeA+aa+ +
  gi|330509113|ref|YP_004385541.1| 218 ASVDRWEDALEAVNKSlELNPRSSTWWHFKAFILTELDRKEEALAAFNE 266
                                       344569****************************************976 PP

  == domain 5  score: 16.7 bits;  conditional E-value: 1.4e-05
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       ++++A+   ++ l+ +++s+   +++A  l ++ + ++A+  +++a ++n++++g +  +A  l+++k+y+e + a+
  gi|330509113|ref|YP_004385541.1| 222 RWEDALEAVNKSLELNPRSSTWWHFKAFILTELDRKEEALAAFNEAiGQNPEDIGNWQWKASLLVEMKRYNESLEAY 298
                                       68899999999999999999999999999999999999999999999999999999999999999999999999998 PP

                                       -S CS
                            ANAPC3  80 ek 81 
                                       +k
  gi|330509113|ref|YP_004385541.1| 299 DK 300
                                       87 PP

  == domain 6  score: 7.2 bits;  conditional E-value: 0.013
                                       T-HHHHHHHHHCTSHHHC-H.....HHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  37 gqykrAyellrkaklnsksl.....gcrylfAqcllkLkkyeeAiaaLek 81 
                                       + y++A+el+ ++            + ++ +A +l k ++ eeA +a+++
  gi|330509113|ref|YP_004385541.1| 296 EAYDKAIELAAEN------NteelaQTWFSKASALNKTGRNEEATDAFQR 339
                                       3355555555555......3334459999999999999999999999875 PP

  == domain 7  score: 12.5 bits;  conditional E-value: 0.00029
                                       HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  39 ykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++r ++l+++a  +n+ +   +  ++++l+ L++y+eAia++++
  gi|330509113|ref|YP_004385541.1| 337 FQRSLKLYDEAiAENPGDVSLLEAKGRVLFNLERYDEAIAIYDH 380
                                       67778888888888888889999999*************99875 PP

  == domain 8  score: -0.8 bits;  conditional E-value: 4.2
                                       TT-HHH CS
                            ANAPC3  69 Lkkyee 74 
                                       L++y++
  gi|330509113|ref|YP_004385541.1| 415 LEEYNK 420
                                       222332 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0037       1.7     217     254 ..       9      46 ..       2      51 .. 0.88
   2 !    9.2   2.2    0.0011      0.51      15      66 ..      70     121 ..      61     134 .. 0.88
   3 !   12.3   0.0   0.00013     0.057      20     107 ..     116     202 ..     115     223 .. 0.73
   4 !   15.1   0.6   1.8e-05    0.0082       7      71 ..     244     308 ..     205     314 .. 0.69
   5 !   16.0   0.9     1e-05    0.0045       8      73 ..     245     310 ..     239     352 .. 0.73
   6 !   11.1   0.1   0.00031      0.14      17      69 ..     334     386 ..     312     390 .. 0.72
   7 !    6.5   0.0    0.0072       3.2      43      91 ..     400     448 ..     391     458 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0037
                                       HHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1 217 kaiehtptlvelyltKarilkhaGdlkkAaevmeeark 254
                                       +++  + + +++++ Ka+ l h G +++A+++++ea +
  gi|330509113|ref|YP_004385541.1|   9 ACVTAQENTTDYWMDKAEGLTHNGSFEEAISALDEALN 46 
                                       678889999**************************965 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
                                       HHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1  15 eeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLle 66 
                                       e a ++e+Al  L+e  k+     +  e+ka+ l  L+r+ee+ ++ye+ le
  gi|330509113|ref|YP_004385541.1|  70 ESAKEYERALSFLDEDLKKNASDAEAWEKKASALNSLNRNEESIKAYEKALE 121
                                       567899*********9999988899999********************9887 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHH.HGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CH.HHHHHHHHT..SSS-HHHHHH CS
                             NARP1  20 leeAlehLee.kekqivDklavketkaelllkLgrkeeAeatyeaLlernpensk.Yyeglekakklskedeealla 94 
                                       +e+Ale +++  e++ +D  a++  +a++ll+Lgr +eA+++y +  e  p++++ ++++ e   +   +d+++ ++
  gi|330509113|ref|YP_004385541.1| 116 YEKALEVFDQrIERNQLDADAWMG-RANVLLNLGRWDEAHEAYDEVTELKPQDYNvWWRKAEVISG--IGDINESVE 189
                                       689999998757889999999985.89*******************99998766514454444444..445677777 PP

                                       HHHHTTTS-TT-S CS
                             NARP1  95 lydelaekyprsd 107
                                       +yd++   +p +d
  gi|330509113|ref|YP_004385541.1| 190 AYDRAIGLIPAND 202
                                       7777666666554 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT- CS
                             NARP1   7 lLyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpen 71 
                                         +k+ i++e ++ eeAl+ ++e+  q  + +   + ka+ll++++r++e+ ++y + +e  +en
  gi|330509113|ref|YP_004385541.1| 244 WHFKAFILTELDRKEEALAAFNEAIGQNPEDIGNWQWKASLLVEMKRYNESLEAYDKAIELAAEN 308
                                       34666677777777777777777766666666666777777777777777777777766666666 PP

  == domain 5  score: 16.0 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CH CS
                             NARP1   8 LyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpensk 73 
                                        +k+ i++e ++ eeAl+ ++e+  q  + +   + ka+ll++++r++e+ ++y + +e  +en +
  gi|330509113|ref|YP_004385541.1| 245 HFKAFILTELDRKEEALAAFNEAIGQNPEDIGNWQWKASLLVEMKRYNESLEAYDKAIELAAENNT 310
                                       5999****************************************************9999998864 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.00031
                                       HTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-T CS
                             NARP1  17 agkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernp 69 
                                       ++  +++l+  +e+  +    ++++e+k+++l++L+r++eA a+y ++le  p
  gi|330509113|ref|YP_004385541.1| 334 TDAFQRSLKLYDEAIAENPGDVSLLEAKGRVLFNLERYDEAIAIYDHILETTP 386
                                       23334444444444444455799**************************9876 PP

  == domain 7  score: 6.5 bits;  conditional E-value: 0.0072
                                       HHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHH CS
                             NARP1  43 tkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeea 91 
                                       ++++ l +Lgr+eeA + y++ +++ p+ s+ ++gl +a++   ++++a
  gi|330509113|ref|YP_004385541.1| 400 ARGDALRALGRNEEALEEYNKAIDMSPNFSTAWHGLGEAQRALGQTHNA 448
                                       68999**************************999999998644444444 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00049      0.22      62     131 ..      18      87 ..       7      95 .. 0.87
   2 ?    2.8   0.1      0.32   1.5e+02      98     129 ..      95     126 ..      89     131 .. 0.78
   3 !   12.8   0.1   0.00028      0.12      47     122 ..     117     194 ..      99     200 .. 0.84
   4 !    8.8   0.0    0.0046       2.1      63     122 ..     208     267 ..     199     277 .. 0.88
   5 ?    7.2   0.6     0.015       6.5      74     134 ..     290     352 ..     279     355 .. 0.75
   6 !   10.9   0.1     0.001      0.45      63     123 ..     356     422 ..     351     427 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00049
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS CS
                              BTAD  62 lealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLg 131
                                        +   + ae +++ G  eea++ l+++++ +P +E+        l  +G  +e  + Yer+ + L+e+L 
  gi|330509113|ref|YP_004385541.1|  18 TDYWMDKAEGLTHNGSFEEAISALDEALNIEPENETVLIRKAWYLSVVGMANESAKEYERALSFLDEDLK 87 
                                       555566677888999****************************************************996 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH CS
                              BTAD  98 lhrqlmrAlarsGrqaeALevYerlrrlLaee 129
                                       ++++   Al  ++r++e +++Ye++ ++ ++ 
  gi|330509113|ref|YP_004385541.1|  95 AWEKKASALNSLNRNEESIKAYEKALEVFDQR 126
                                       67777788999999999999999888776665 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00028
                                       STTHHHHHHHHHHHHHHHHHHHHH..HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  47 gewleaererleelrlealealae..aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                       ++ le + +r+e+  l+a +++ +   +l lGr++ea + +++ ++++P + + +    +     G+ +e  e+Y+r
  gi|330509113|ref|YP_004385541.1| 117 EKALEVFDQRIERNQLDADAWMGRanVLLNLGRWDEAHEAYDEVTELKPQDYNVWWRKAEVISGIGDINESVEAYDR 193
                                       56777788889988888887776622578999*******************************************98 PP

                                       H CS
                              BTAD 122 l 122
                                       +
  gi|330509113|ref|YP_004385541.1| 194 A 194
                                       7 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0046
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  63 ealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        a+++  e ++++ r+e+al+  ++ ++++P   + +      l  ++r++eAL++++++
  gi|330509113|ref|YP_004385541.1| 208 LAYASKSENLASVDRWEDALEAVNKSLELNPRSSTWWHFKAFILTELDRKEEALAAFNEA 267
                                       4666777889999********************************************987 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.015
                                       HTT-HHHHHHHHHHHHHHSTT-H..HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS--- CS
                              BTAD  74 rlGraeealaelealvaehPlrE..rlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvep 134
                                       r+++  ea +++ +l+ae+++ E  +++     Al ++Gr++eA  +++r  +l +e +   p
  gi|330509113|ref|YP_004385541.1| 290 RYNESLEAYDKAIELAAENNTEElaQTWFSKASALNKTGRNEEATDAFQRSLKLYDEAIAENP 352
                                       566666778888888888888884445667778999999999999999999888887776666 PP

  == domain 6  score: 10.9 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHH......HHHHTT-HHHHHHHHHHHH CS
                              BTAD  63 ealealaeaelrlGraeealaelealvaehPlrErlhrqlmr......AlarsGrqaeALevYerlr 123
                                       + lea  + ++ l+r++ea+a ++ +++  P  E    ++ +      Al+++Gr++eALe Y+++ 
  gi|330509113|ref|YP_004385541.1| 356 SLLEAKGRVLFNLERYDEAIAIYDHILETTPSVEPRLTHITTwiargdALRALGRNEEALEEYNKAI 422
                                       6788889999999******************99986655543333344***************9875 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.4   1.1e+03      15      31 ..      34      48 ..      29      53 .. 0.72
   2 ?    1.2   0.2       1.1   4.7e+02      14      34 ..      74      92 ..      70      94 .. 0.73
   3 ?    7.3   0.1     0.012       5.4       6      28 ..     100     123 ..      95     134 .. 0.77
   4 ?    5.7   0.0     0.039        18       6      33 ..     141     166 ..     136     169 .. 0.82
   5 ?   -1.8   0.0       9.7   4.4e+03      12      20 ..     188     196 ..     179     203 .. 0.57
   6 ?   -1.1   0.0       5.7   2.5e+03      12      28 ..     220     236 ..     204     240 .. 0.76
   7 ?    2.0   0.1      0.57   2.5e+02       6      29 ..     282     305 ..     281     312 .. 0.74
   8 ?    3.5   0.0       0.2        90       6      29 ..     321     344 ..     313     356 .. 0.67
   9 !   12.1   0.0   0.00034      0.15       3      32 ..     359     388 ..     357     391 .. 0.86
  10 !    8.9   0.0    0.0036       1.6       2      33 ..     398     427 ..     397     430 .. 0.88
  11 ?    2.1   0.1      0.54   2.4e+02       1      18 [.     431     448 ..     431     448 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.4
                             TPR_7 15 yeeAielyeqsLaltkd 31
                                      +eeAi+ + ++L +  +
  gi|330509113|ref|YP_004385541.1| 34 FEEAISALDEALNI--E 48
                                      89999999995544..3 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.1
                             TPR_7 14 dyeeAielyeqsLaltkdped 34
                                      +ye+A++++ +   l k  +d
  gi|330509113|ref|YP_004385541.1| 74 EYERALSFLDE--DLKKNASD 92
                                      79999999988..66665555 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.012
                             TPR_7   6 arlysrlGdyeeAielyeqsL.al 28 
                                       a++  +l++ ee i+ ye++L ++
  gi|330509113|ref|YP_004385541.1| 100 ASALNSLNRNEESIKAYEKALeVF 123
                                       677778999999999999977444 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.039
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpe 33 
                                       a++  +lG+++eA e y +  +++  p+
  gi|330509113|ref|YP_004385541.1| 141 ANVLLNLGRWDEAHEAYDE--VTELKPQ 166
                                       88999********999999..7776665 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 9.7
                             TPR_7  12 lGdyeeAie 20 
                                       +  y++Ai+
  gi|330509113|ref|YP_004385541.1| 188 VEAYDRAIG 196
                                       333555554 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 5.7
                             TPR_7  12 lGdyeeAielyeqsLal 28 
                                       + ++e+A+e   +sL+l
  gi|330509113|ref|YP_004385541.1| 220 VDRWEDALEAVNKSLEL 236
                                       56899999877776665 PP

  == domain 7  score: 2.0 bits;  conditional E-value: 0.57
                             TPR_7   6 arlysrlGdyeeAielyeqsLalt 29 
                                       a+l +++ +y e +e y ++++l+
  gi|330509113|ref|YP_004385541.1| 282 ASLLVEMKRYNESLEAYDKAIELA 305
                                       677788888999999999966665 PP

  == domain 8  score: 3.5 bits;  conditional E-value: 0.2
                             TPR_7   6 arlysrlGdyeeAielyeqsLalt 29 
                                       a++  + G+ eeA + +++sL l 
  gi|330509113|ref|YP_004385541.1| 321 ASALNKTGRNEEATDAFQRSLKLY 344
                                       666667777777777777777554 PP

  == domain 9  score: 12.1 bits;  conditional E-value: 0.00034
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                        + +r+ ++l +y+eAi +y   L++t + 
  gi|330509113|ref|YP_004385541.1| 359 EAKGRVLFNLERYDEAIAIYDHILETTPSV 388
                                       56799*****************99998765 PP

  == domain 10  score: 8.9 bits;  conditional E-value: 0.0036
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       + + +++ ++lG+ eeA+e y +  a++ +p+
  gi|330509113|ref|YP_004385541.1| 398 WIARGDALRALGRNEEALEEYNK--AIDMSPN 427
                                       56779******************..9998886 PP

  == domain 11  score: 2.1 bits;  conditional E-value: 0.54
                             TPR_7   1 aLlnLarlysrlGdyeeA 18 
                                       a++ L++++++lG++ +A
  gi|330509113|ref|YP_004385541.1| 431 AWHGLGEAQRALGQTHNA 448
                                       6899*********99887 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       2.9   1.3e+03      14      32 ..      32      50 ..      22      51 .. 0.84
   2 ?    0.2   0.0       3.3   1.5e+03       7      24 ..      66      83 ..      65      84 .. 0.84
   3 ?    2.6   0.0      0.59   2.6e+02       7      28 ..     100     121 ..      94     125 .. 0.76
   4 ?    6.0   0.0     0.049        22       1      28 [.     135     162 ..     135     167 .. 0.88
   5 ?   -0.7   0.0       6.5   2.9e+03      14      27 ..     182     195 ..     171     196 .. 0.81
   6 ?   -1.3   0.0       9.8   4.4e+03       6      25 ..     206     232 ..     205     240 .. 0.66
   7 ?    4.0   0.0      0.21        93      12      32 ..     253     273 ..     244     274 .. 0.84
   8 ?    2.9   0.1      0.46     2e+02       7      28 ..     282     303 ..     280     307 .. 0.84
   9 ?    2.9   0.0      0.46   2.1e+02       9      30 ..     323     344 ..     315     353 .. 0.75
  10 ?    3.4   0.0      0.31   1.4e+02       7      26 ..     362     381 ..     361     386 .. 0.83
  11 ?    7.1   0.1     0.022       9.7       7      32 ..     402     427 ..     400     427 .. 0.89
  12 ?    3.4   0.0      0.33   1.5e+02       2      20 ..     431     449 ..     430     455 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.9
                                      HHHHHHHHHHHHHHHH-TT CS
                             TPR_6 14 gdtdkAlealerlikeYPd 32
                                      g  ++A+ al++ ++  P+
  gi|330509113|ref|YP_004385541.1| 32 GSFEEAISALDEALNIEPE 50
                                      5679********9998886 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 3.3
                                      HHHHHHHHHHHHHHHHHH CS
                             TPR_6  7 alsyrklgdtdkAleale 24
                                      +++ ++++++++Al  l+
  gi|330509113|ref|YP_004385541.1| 66 GMANESAKEYERALSFLD 83
                                      88999999*****98875 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.59
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       a ++ +l++ +++++a+e+ ++
  gi|330509113|ref|YP_004385541.1| 100 ASALNSLNRNEESIKAYEKALE 121
                                       5566668899999999999987 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.049
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                       dA + +a  +++lg++d+A ea++++ +
  gi|330509113|ref|YP_004385541.1| 135 DAWMGRANVLLNLGRWDEAHEAYDEVTE 162
                                       68888999999999*********99976 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 6.5
                                       HHHHHHHHHHHHHH CS
                             TPR_6  14 gdtdkAlealerli 27 
                                       gd  +++ea++r i
  gi|330509113|ref|YP_004385541.1| 182 GDINESVEAYDRAI 195
                                       799999****9986 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 9.8
                                       HHHHHHHH.......HHHHHHHHHHHH CS
                             TPR_6   6 lalsyrkl.......gdtdkAlealer 25 
                                       lal+y +        +++++Alea ++
  gi|330509113|ref|YP_004385541.1| 206 LALAYASKsenlasvDRWEDALEAVNK 232
                                       677777655677777889999987555 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  12 klgdtdkAlealerlikeYPd 32 
                                       +l+++++Al+a+++ i + P+
  gi|330509113|ref|YP_004385541.1| 253 ELDRKEEALAAFNEAIGQNPE 273
                                       56799***********99986 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       a ++ +++++ ++lea+++ i+
  gi|330509113|ref|YP_004385541.1| 282 ASLLVEMKRYNESLEAYDKAIE 303
                                       55677899**********9997 PP

  == domain 9  score: 2.9 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6   9 syrklgdtdkAlealerlikeY 30 
                                       ++ k+g+ ++A +a++r +k Y
  gi|330509113|ref|YP_004385541.1| 323 ALNKTGRNEEATDAFQRSLKLY 344
                                       5566778888888888877777 PP

  == domain 10  score: 3.4 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerl 26 
                                       ++ +++l ++d+A+++++ +
  gi|330509113|ref|YP_004385541.1| 362 GRVLFNLERYDEAIAIYDHI 381
                                       78899977********9865 PP

  == domain 11  score: 7.1 bits;  conditional E-value: 0.022
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + ++r+lg+ ++Ale +++ i+  P+
  gi|330509113|ref|YP_004385541.1| 402 GDALRALGRNEEALEEYNKAIDMSPN 427
                                       88999*99************997775 PP

  == domain 12  score: 3.4 bits;  conditional E-value: 0.33
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAl 20 
                                       A   l++++r+lg+t +A 
  gi|330509113|ref|YP_004385541.1| 431 AWHGLGEAQRALGQTHNAS 449
                                       66789******99**9985 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   3.9   0.00052      0.23     146     239 ..      18     118 ..      11     121 .. 0.78
   2 !    8.1   0.1    0.0031       1.4     143     180 ..     131     168 ..     118     170 .. 0.85
   3 !   10.7   0.8   0.00048      0.22     145     248 ..     167     275 ..     165     283 .. 0.75
   4 !    7.2   7.7    0.0058       2.6     157     268 ..     218     334 ..     203     342 .. 0.62
   5 !   10.6   2.6   0.00051      0.23     115     241 ..     287     422 ..     280     427 .. 0.66
   6 !    8.5   0.0    0.0023         1     147     182 ..     396     431 ..     383     442 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00052
                            TPR_15 146 aafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrrae....Lrellkawkara...esdas 215
                                         +++  ae  + +g  ++A+ ++ eAl+ +p+++++  +  W+l   g ++e      ++l+ + ++    +sda+
  gi|330509113|ref|YP_004385541.1|  18 TDYWMDKAEGLTHNGSFEEAISALDEALNIEPENETVLIRKAWYLSVVGMANEsakeYERALSFLDEDLkknASDAE 94 
                                       56899999999999999999999999999999999999999999977787777522233344444444377799999 PP

                            TPR_15 216 LwgplaaAlllLgrpkkALeylrk 239
                                        w+  a+Al  L+r+++  + ++k
  gi|330509113|ref|YP_004385541.1|  95 AWEKKASALNSLNRNEESIKAYEK 118
                                       999999999999999998887776 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0031
                            TPR_15 143 eqsaafllaraelyrqegqtdaAlrdyreAlalapdss 180
                                       + +a  ++ ra++ ++ g++d+A ++y e+ +l+p++ 
  gi|330509113|ref|YP_004385541.1| 131 QLDADAWMGRANVLLNLGRWDEAHEAYDEVTELKPQDY 168
                                       468889*****************************985 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00048
                            TPR_15 145 saafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara..........e 211
                                       +  ++ + ae+ +  g+ ++++++y +A+ l p++++   al +++  +++ a     + +w+++            
  gi|330509113|ref|YP_004385541.1| 167 DYNVWWRKAEVISGIGDINESVEAYDRAIGLIPANDTDELALAYASK-SENLA----SVDRWEDALeavnkslelnP 238
                                       56789999999999999999999999999999998887777777653.33333....24555544444555556658 PP

                            TPR_15 212 sdasLwgplaaAlllLgrpkkALeylrkqakenrkdp 248
                                       ++++ w   a+ l  L r+++AL+ ++    +n++d+
  gi|330509113|ref|YP_004385541.1| 239 RSSTWWHFKAFILTELDRKEEALAAFNEAIGQNPEDI 275
                                       8999999999999999999999999999999999985 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0058
                            TPR_15 157 rqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgplaaAlllLgrp 230
                                          +++++Al+++ + l+l+p ss+      ++l +l+r++e   +l+a++++     +d   w+  a+ l+ ++r+
  gi|330509113|ref|YP_004385541.1| 218 ASVDRWEDALEAVNKSLELNPRSSTWWHFKAFILTELDRKEE---ALAAFNEAIgqnPEDIGNWQWKASLLVEMKRY 291
                                       345667777777777777777777777777777777777775...66666655553355555577777777777777 PP

                            TPR_15 231 kkALeylrk...qakenrkdplwllaY..ADaleqagradeAw 268
                                       ++ Le + k    a+en+ + l +  +  A al++ gr +eA 
  gi|330509113|ref|YP_004385541.1| 292 NESLEAYDKaieLAAENNTEELAQTWFskASALNKTGRNEEAT 334
                                       7777777765545566666666665554466777777777764 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00051
                            TPR_15 115 salellerakdydriaellksleeeeaae...qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallW 188
                                       ++  + e +++yd+  el ++   ee a+   + a  l   ++ ++++++ +++l++y eA+a +p++ +l +a   
  gi|330509113|ref|YP_004385541.1| 287 EMKRYNESLEAYDKAIELAAENNTEELAQtwfSKASALNKTGRNEEATDAFQRSLKLYDEAIAENPGDVSLLEAKGR 363
                                       55555566666666666655533333333333555555555555555555566677777888889999999999888 PP

                            TPR_15 189 lliDlgrraeLrellkawkara......esdasLwgplaaAlllLgrpkkALeylrkqa 241
                                       +l +l+r++e+ ++  +  + +       +  + w + + Al +Lgr+++ALe ++k  
  gi|330509113|ref|YP_004385541.1| 364 VLFNLERYDEAIAIYDHILETTpsveprLTHITTWIARGDALRALGRNEEALEEYNKAI 422
                                       88888999985555555554448777777777789999999999999999999888765 PP

  == domain 6  score: 8.5 bits;  conditional E-value: 0.0023
                            TPR_15 147 afllaraelyrqegqtdaAlrdyreAlalapdssel 182
                                       + ++ar+ + r+ g++++Al+ y +A++++p+ s++
  gi|330509113|ref|YP_004385541.1| 396 TTWIARGDALRALGRNEEALEEYNKAIDMSPNFSTA 431
                                       57****************************997765 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.39   1.8e+02      11      31 ..      27      47 ..      24      48 .. 0.87
   2 ?   -1.1   0.0       4.3   1.9e+03      12      24 ..      69      81 ..      59      87 .. 0.56
   3 ?    5.9   0.1     0.027        12       9      31 ..     100     122 ..      99     132 .. 0.89
   4 !    9.8   0.1    0.0016      0.72       9      28 ..     141     160 ..     140     164 .. 0.91
   5 ?   -1.9   0.1       7.6   3.4e+03      12      25 ..     217     230 ..     206     236 .. 0.65
   6 ?    2.4   0.1      0.35   1.5e+02       9      29 ..     248     268 ..     248     269 .. 0.89
   7 ?    6.4   0.2     0.019       8.6      10      31 ..     283     304 ..     281     307 .. 0.87
   8 !    7.4   0.0    0.0092       4.1       9      35 ..     321     347 ..     320     354 .. 0.88
   9 !    9.9   0.1    0.0015      0.67       9      31 ..     362     384 ..     358     385 .. 0.93
  10 !    8.3   0.2    0.0049       2.2      10      31 ..     403     424 ..     401     425 .. 0.91
  11 ?   -1.7   0.1       6.7     3e+03      33      40 ..     439     446 ..     433     448 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.39
                            TPR_10 11 alrqrgrydeAealleealai 31
                                       l++ g ++eA   l+eal+i
  gi|330509113|ref|YP_004385541.1| 27 GLTHNGSFEEAISALDEALNI 47
                                      5888999***********997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.3
                            TPR_10 12 lrqrgrydeAeal 24
                                        + ++y++A+ +
  gi|330509113|ref|YP_004385541.1| 69 NESAKEYERALSF 81
                                      4444555555555 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.027
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       a al +++r +e+ + +e+al++
  gi|330509113|ref|YP_004385541.1| 100 ASALNSLNRNEESIKAYEKALEV 122
                                       678999**************986 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0016
                            TPR_10   9 analrqrgrydeAealleea 28 
                                       an+l ++gr+deA + ++e+
  gi|330509113|ref|YP_004385541.1| 141 ANVLLNLGRWDEAHEAYDEV 160
                                       89**************9997 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 7.6
                            TPR_10  12 lrqrgrydeAeall 25 
                                       l ++ r+++A++  
  gi|330509113|ref|YP_004385541.1| 217 LASVDRWEDALEAV 230
                                       55667777777655 PP

  == domain 6  score: 2.4 bits;  conditional E-value: 0.35
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       a +l+++ r +eA+a + ea+
  gi|330509113|ref|YP_004385541.1| 248 AFILTELDRKEEALAAFNEAI 268
                                       56899**********999997 PP

  == domain 7  score: 6.4 bits;  conditional E-value: 0.019
                            TPR_10  10 nalrqrgrydeAealleealai 31 
                                        +l +++ry+e+++ +++a+++
  gi|330509113|ref|YP_004385541.1| 283 SLLVEMKRYNESLEAYDKAIEL 304
                                       567899**************97 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.0092
                            TPR_10   9 analrqrgrydeAealleealairrrl 35 
                                       a al ++gr +eA + ++++l ++ ++
  gi|330509113|ref|YP_004385541.1| 321 ASALNKTGRNEEATDAFQRSLKLYDEA 347
                                       678999*****************9887 PP

  == domain 9  score: 9.9 bits;  conditional E-value: 0.0015
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       +++l+++ rydeA a++++ l++
  gi|330509113|ref|YP_004385541.1| 362 GRVLFNLERYDEAIAIYDHILET 384
                                       899***************99987 PP

  == domain 10  score: 8.3 bits;  conditional E-value: 0.0049
                            TPR_10  10 nalrqrgrydeAealleealai 31 
                                        alr++gr +eA++ + +a+++
  gi|330509113|ref|YP_004385541.1| 403 DALRALGRNEEALEEYNKAIDM 424
                                       689****************986 PP

  == domain 11  score: -1.7 bits;  conditional E-value: 6.7
                            TPR_10  33 rrllGpdH 40 
                                       +r+lG+ H
  gi|330509113|ref|YP_004385541.1| 439 QRALGQTH 446
                                       66666666 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   3.1     0.016         7     129     181 ..      66     119 ..       8     123 .. 0.77
   2 !   13.7   3.4   6.9e-05     0.031      91     183 ..      69     162 ..      33     172 .. 0.77
   3 !   14.3   2.6   4.6e-05     0.021      54     159 ..      92     212 ..      85     236 .. 0.63
   4 !   22.5   0.7   1.4e-07   6.4e-05      62     184 ..     262     384 ..     256     397 .. 0.84
   5 ?   -2.0   0.0       4.3   1.9e+03     130     143 ..     410     423 ..     402     430 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.016
                                       --HHHHHHHHHHHHHHHHHTT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              SNAP 129 gdlekAieaYekAaelyeqee.akalankcllkvAelsaelekyekAieiyekv 181
                                       g  +++ + Ye+A  + +++  ++a+  ++++k A+   +l++ e++i++yek 
  gi|330509113|ref|YP_004385541.1|  66 GMANESAKEYERALSFLDEDLkKNASDAEAWEKKASALNSLNRNEESIKAYEKA 119
                                       456677788999999988887788888999999998888888889999999875 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.9e-05
                                       HHHHHHHHHHHHHHHHTT-HHHH.HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT.-HHHHHHHHHHHHHHH CS
                              SNAP  91 eeAvealekAieiytekgrfrra.AklkkeiaelyekelgdlekAieaYekAaelyeqee.akalankcllkvAels 165
                                       +e+++ +e+A +++ e  + + + A+  ++ a  +++  ++ e++i+aYekA e+++q    + l   +++  A++ 
  gi|330509113|ref|YP_004385541.1|  69 NESAKEYERALSFLDEDLKKNASdAEAWEKKASALNSL-NRNEESIKAYEKALEVFDQRIeRNQLDADAWMGRANVL 144
                                       56666777777665443322222244445555555544.88999999999999999998768888999999999999 PP

                                       HHTT-HHHHHHHHHHHHH CS
                              SNAP 166 aelekyekAieiyekvak 183
                                        +l+++++A e+y++v +
  gi|330509113|ref|YP_004385541.1| 145 LNLGRWDEAHEAYDEVTE 162
                                       999999999999999975 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 4.6e-05
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT...-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT CS
                              SNAP  54 AgeaflkaAecqeklkekdeaanayveAakcykkv...speeAvealekAieiytekgrfrraAklkkeiaelyeke 127
                                        +ea++k A++ ++l+ ++e+ +ay +A +++ +    ++ +A + + + ++++++ gr+++a + + e+ el  ++
  gi|330509113|ref|YP_004385541.1|  92 DAEAWEKKASALNSLNRNEESIKAYEKALEVFDQRierNQLDADAWMGR-ANVLLNLGRWDEAHEAYDEVTELKPQD 167
                                       4577777777777777777777777777777776655333344444444.466777777777777777777777777 PP

                                       T.............--HHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                              SNAP 128 l.............gdlekAieaYekAaelyeqeeakalankcll 159
                                                     gd+++++eaY++A  l   ++   la     
  gi|330509113|ref|YP_004385541.1| 168 YnvwwrkaevisgiGDINESVEAYDRAIGLIPANDTDELALAYAS 212
                                       666666666666666677777777777776666665555555555 PP

  == domain 4  score: 22.5 bits;  conditional E-value: 1.4e-07
                                       HHHHHH.TT-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHH CS
                              SNAP  62 Aecqek.lkekdeaanayveAakcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAiea 137
                                       A+++e   +++++ +n  ++A+  +++++ +e+ ea++kAie+ + +++ ++ A+  ++ a  ++k  g+ e+A++a
  gi|330509113|ref|YP_004385541.1| 262 AAFNEAiGQNPEDIGNWQWKASLLVEMKRYNESLEAYDKAIELAA-ENNTEELAQTWFSKASALNKT-GRNEEATDA 336
                                       555555578999******************************765.567788889999999999998.9******** PP

                                       HHHHHHHHHHTT-HHHHHHHHHHHH.HHHHHTT-HHHHHHHHHHHHHT CS
                              SNAP 138 YekAaelyeqeeakalankcllkvA.elsaelekyekAieiyekvakk 184
                                       +++  +ly++  a+      ll++   +  +le+y++Ai+iy+++ ++
  gi|330509113|ref|YP_004385541.1| 337 FQRSLKLYDEAIAENPGDVSLLEAKgRVLFNLERYDEAIAIYDHILET 384
                                       *********999877766655554438999*************99764 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 4.3
                                       -HHHHHHHHHHHHH CS
                              SNAP 130 dlekAieaYekAae 143
                                       + e+A+e Y+kA +
  gi|330509113|ref|YP_004385541.1| 410 RNEEALEEYNKAID 423
                                       45566666666655 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0085       3.8     218     288 ..     118     188 ..      61     219 .. 0.83
   2 !    7.9   0.2    0.0029       1.3     218     288 ..     225     295 ..     214     301 .. 0.90
   3 !    9.6   0.0   0.00089       0.4     181     291 ..     333     452 ..     329     455 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0085
                                       HHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                             ChAPs 218 davkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienAL 288
                                       +a+++  + +e ++ da+  + +a+ ll+  + + A e+ ++ +++ P +++ W + ++v   ++di++ +
  gi|330509113|ref|YP_004385541.1| 118 KALEVFDQRIERNQLDADAWMGRANVLLNLGRWDEAHEAYDEVTELKPQDYNVWWRKAEVISGIGDINESV 188
                                       5788999999***********************************************99999999988765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                             ChAPs 218 davkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienAL 288
                                       da++ +n++le +++++   + +a  l + +++e Al++ ++a+   P +   W   +   ++++ +++ L
  gi|330509113|ref|YP_004385541.1| 225 DALEAVNKSLELNPRSSTWWHFKAFILTELDRKEEALAAFNEAIGQNPEDIGNWQWKASLLVEMKRYNESL 295
                                       789999******************9999***************************9999999999888877 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00089
                                       HHT-HHHHHHHHHHHHTT-GGGHHHH.H..HHHHHTT-HHHHHHHHHHHH-SSS-H......HHHHHHHHHHHHHSS CS
                             ChAPs 181 ltkrydralellekLkeeepevvill.a..rvllladeEvdavkllneeleeeekd......aelLllqaefllskk 248
                                        t  ++r+l+l ++ ++e+p  v+ll a  rvl+  ++  +a+ +  + le +++           +++ + l    
  gi|330509113|ref|YP_004385541.1| 333 ATDAFQRSLKLYDEAIAENPGDVSLLeAkgRVLFNLERYDEAIAIYDHILETTPSVeprlthITTWIARGDALRALG 409
                                       57889999999999999998777777343367777777789999988888666665444433444555666777777 PP

                                       --HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                             ChAPs 249 keelAlevakravksaPsefktWalLvkvYikledienALltL 291
                                       ++e Ale  ++a++++P+ ++ W  L +   +l++++nA ++L
  gi|330509113|ref|YP_004385541.1| 410 RNEEALEEYNKAIDMSPNFSTAWHGLGEAQRALGQTHNASMSL 452
                                       8899********************************9998876 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.1   2.7e+03      32      48 ..      99     115 ..      98     116 .. 0.85
   2 ?    2.3   0.0      0.29   1.3e+02       2      15 ..     116     129 ..     115     131 .. 0.91
   3 ?    0.1   0.0       1.4   6.2e+02       1      15 [.     222     236 ..     222     241 .. 0.85
   4 !   12.7   0.0   0.00016     0.074       1      44 [.     290     332 ..     290     336 .. 0.86
   5 ?    3.2   0.0      0.15        67       3      16 ..     412     425 ..     410     429 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.1
                                       HHHHHHHTT--HHHHHH CS
                          HTH_Bact  32 kgecleklgfseeeIke 48 
                                       k++ l  l+ +ee+Ik 
  gi|330509113|ref|YP_004385541.1|  99 KASALNSLNRNEESIKA 115
                                       88999999999999985 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                       Ye+aLe+ ++ ie+
  gi|330509113|ref|YP_004385541.1| 116 YEKALEVFDQRIER 129
                                       **********9985 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.4
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       r+e aLe vnk +e+
  gi|330509113|ref|YP_004385541.1| 222 RWEDALEAVNKSLEL 236
                                       5799*******9986 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00016
                                       -HHHHHHHHHHHHHHHHHTTB-TTHHHHHHHHHHHHHHTT--HH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiSirinsMsLlGQLyYqkgecleklgfsee 44 
                                       rY+e+Le  +kAie+  ++n    l Q ++ k++ l k g +ee
  gi|330509113|ref|YP_004385541.1| 290 RYNESLEAYDKAIELAAENNTE-ELAQTWFSKASALNKTGRNEE 332
                                       7**************9987665.568999999999999987776 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   3 eeaLeqvnkAieiS 16 
                                       eeaLe  nkAi +S
  gi|330509113|ref|YP_004385541.1| 412 EEALEEYNKAIDMS 425
                                       89*********998 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   2.9   0.00079      0.36      82     180 ..      24     127 ..      15     136 .. 0.77
   2 ?    4.0   0.0     0.082        37     154     174 ..     142     162 ..     129     178 .. 0.83
   3 ?    1.6   0.0      0.44     2e+02     155     186 ..     250     288 ..     215     293 .. 0.81
   4 ?    3.2   1.8      0.14        63     127     178 ..     296     346 ..     282     361 .. 0.66
   5 !   10.0   0.1    0.0011       0.5     152     175 ..     401     424 ..     396     430 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00079
                            TPR_21  82 lAkaaveagdlaaAkaqLewvlekakdeelkalarl.RLarvlla...ekkydeAlktLeak.keeafaalvaelrG 153
                                       +A+    +g +++A ++L+++l+ ++++e   + +   L  v +a   +k+y++Al+ L+++ k++a +a++ e + 
  gi|330509113|ref|YP_004385541.1|  24 KAEGLTHNGSFEEAISALDEALNIEPENETVLIRKAwYLSVVGMAnesAKEYERALSFLDEDlKKNASDAEAWEKKA 100
                                       566677888899999999999988877776666554134444443112589********7652778999******** PP

                            TPR_21 154 DilvaqgkldeAraaYqaAlaaleeka 180
                                        +l + ++++e  +aY++Al+  +++ 
  gi|330509113|ref|YP_004385541.1| 101 SALNSLNRNEESIKAYEKALEVFDQRI 127
                                       ********************9888765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.082
                            TPR_21 154 DilvaqgkldeAraaYqaAla 174
                                       ++l++ g+ deA++aY++  +
  gi|330509113|ref|YP_004385541.1| 142 NVLLNLGRWDEAHEAYDEVTE 162
                                       7999************99765 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.44
                            TPR_21 155 ilvaqgkldeAraaYqaAlaaleeka.......rellql 186
                                       il++ ++++eA aa+++A+ ++ e+        + l+++
  gi|330509113|ref|YP_004385541.1| 250 ILTELDRKEEALAAFNEAIGQNPEDIgnwqwkaSLLVEM 288
                                       7889999***********999888765555554445555 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.14
                            TPR_21 127 kkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaalee 178
                                       ++yd+A+++ +++++e+  a+    +  +l ++g+++eA +a+q++l+  +e
  gi|330509113|ref|YP_004385541.1| 296 EAYDKAIELAAENNTEEL-AQTWFSKASALNKTGRNEEATDAFQRSLKLYDE 346
                                       456666554444444443.444556888999999999999999999876665 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.0011
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaa 175
                                       rGD+l a g+++eA ++Y++A++ 
  gi|330509113|ref|YP_004385541.1| 401 RGDALRALGRNEEALEEYNKAIDM 424
                                       9********************986 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.7    0.0049       2.2      88     196 ..      61     168 ..      25     179 .. 0.55
   2 !   15.9   1.4   1.4e-05    0.0063       7     208 ..     247     440 ..     245     457 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0049
                          TPR_MalT  88 eilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql..epeaald 162
                                        + v  G   e+++ ye+al + +e   +++  ++    + a  l   n+ ee  ++ ++++e+ +q    ++  +d
  gi|330509113|ref|YP_004385541.1|  61 YLSVV-GMANESAKEYERALSFLDEDLKKNASDAEAWE-KKASALNSLNRNEESIKAYEKALEVFDQRieRNQLDAD 135
                                       33333.44456666666666666666666666666553.33666666666677777777777777775323344455 PP

                          TPR_MalT 163 ayvllarialaqGdleeAetllekaeelaresnf 196
                                       a +  a + l  G+++eA+++ ++ +el   +++
  gi|330509113|ref|YP_004385541.1| 136 AWMGRANVLLNLGRWDEAHEAYDEVTELKP-QDY 168
                                       666667777777777777777777777643.444 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.4e-05
                          TPR_MalT   7 rAllaiasgdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallal 83 
                                       +A++ +   + e+al+  ++A+ + ped   +++ a+++  e   +    +++l+a+ +a++la + +     + + 
  gi|330509113|ref|YP_004385541.1| 247 KAFILTELDRKEEALAAFNEAIGQNPEDIGNWQWKASLL-VEMKRY----NESLEAYDKAIELAAENNTEE-LAQTW 317
                                       788899999999999999******************666.444444....56788*********6555555.55666 PP

                          TPR_MalT  84 lqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlep.ea 159
                                        + a  l + Gr +eA++ ++++l+l++e+  ++ p    ll   +++l+   + +eA    +  +e + ++ep  +
  gi|330509113|ref|YP_004385541.1| 318 FSKASALNKTGRNEEATDAFQRSLKLYDEAIAEN-PGDVSLLEAKGRVLFNLERYDEAIAIYDHILETTPSVEPrLT 393
                                       6678888888*******************99998.66555666779**99999999999999888888888855233 PP

                          TPR_MalT 160 aldayvllarialaqGdleeAetllekaeelaresnfhvdwlanaeevr 208
                                       ++   ++  +   a G++eeA++  +ka  +    nf+++w+   e+ r
  gi|330509113|ref|YP_004385541.1| 394 HITTWIARGDALRALGRNEEALEEYNKAIDMSP--NFSTAWHGLGEAQR 440
                                       334444444455678888888877777655544..66667765555555 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 ?    4.1   0.1       0.1        45      19      68 ..      89     157 ..      64     171 .. 0.54
   2 ?    2.4   0.0      0.34   1.5e+02       3      40 ..     114     160 ..     112     197 .. 0.68
   3 ?    7.3   0.0      0.01       4.6      20      71 ..     213     267 ..     153     275 .. 0.75
   4 !    8.9   0.7    0.0033       1.5      18      94 ..     279     374 ..     265     385 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.1
                      SRP_TPR_like  19 f.........kvvaliklekyeeaLkllkkgs..........alsedvrfEkaYvlYklkkykkalkil 68 
                                                 k+ al +l++ ee++k+ +k+           +l+ d  + +a vl  l ++ +a +  
  gi|330509113|ref|YP_004385541.1|  89 NasdaeawekKASALNSLNRNEESIKAYEKALevfdqriernQLDADAWMGRANVLLNLGRWDEAHEAY 157
                                       444444444455555555555555555555544555555555555555555555555555555555444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.34
                      SRP_TPR_like   3 eeyekilrlegkelkkf.........kvvaliklekyeeaLkllkkg 40 
                                       ++yek l++ ++ +++          ++  l++l++++ea ++ ++ 
  gi|330509113|ref|YP_004385541.1| 114 KAYEKALEVFDQRIERNqldadawmgRANVLLNLGRWDEAHEAYDEV 160
                                       45555555555555555555556666666666666666666555544 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.01
                      SRP_TPR_like  20 kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkv 71 
                                       k   l +++++e+aL++++k       s+     ka++l  l + ++al  ++++
  gi|330509113|ref|YP_004385541.1| 213 KSENLASVDRWEDALEAVNKSLelnPRSSTWWHFKAFILTELDRKEEALAAFNEA 267
                                       5556778999999999999987333234555566999999999999999888775 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0033
                      SRP_TPR_like  18 kfkvvaliklekyeeaLkllkkgs........alsedvrfEkaYvlYklkkykka.......lkilkkveaee..kv 77 
                                       ++k+  l+++ +y+e+L++ +k+         +   ++ f ka +l k+ + ++a       lk+ +++ ae+   v
  gi|330509113|ref|YP_004385541.1| 279 QWKASLLVEMKRYNESLEAYDKAIelaaenntEELAQTWFSKASALNKTGRNEEAtdafqrsLKLYDEAIAENpgDV 355
                                       56888999**********99998877777755333467899999999988766651111000444444444444344 PP

                      SRP_TPR_like  78 kvlks..qvlYrlgsyekA 94 
                                       + l++   vl+ l+ y++A
  gi|330509113|ref|YP_004385541.1| 356 SLLEAkgRVLFNLERYDEA 374
                                       4443311466666666666 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0029       1.3     199     240 ..      16      57 ..      12      72 .. 0.85
   2 ?    3.6   1.0     0.083        37     214     255 ..      72     113 ..      62     120 .. 0.79
   3 !    9.3   0.1    0.0015      0.67     182     237 ..     115     170 ..      99     195 .. 0.87
   4 ?    6.6   1.0      0.01       4.6      76     237 ..     217     391 ..     189     418 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0029
                                       --HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHH CS
                        Coatomer_E 199 stplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiN 240
                                       +t++  + kA    + g++eeA s L eaL+ ++++e +Li 
  gi|330509113|ref|YP_004385541.1|  16 NTTDYWMDKAEGLTHNGSFEEAISALDEALNIEPENETVLIR 57 
                                       5777788888889999********************999985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.083
                                       TT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHH CS
                        Coatomer_E 214 lgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevs 255
                                        ++ye A s L e L+k+a d+e+      a + l++++e++
  gi|330509113|ref|YP_004385541.1|  72 AKEYERALSFLDEDLKKNASDAEAWEKKASALNSLNRNEESI 113
                                       578********************9877777766666666655 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHH CS
                        Coatomer_E 182 kiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeet 237
                                        ++ A+ +f++  e+ +   +  +g+A v l lgr++eA +   e  + +++d+++
  gi|330509113|ref|YP_004385541.1| 115 AYEKALEVFDQRIERNQLDADAWMGRANVLLNLGRWDEAHEAYDEVTELKPQDYNV 170
                                       567899***********************************999998888888775 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.01
                                       HH-STTHHHHHHHHHHHHHS----S-HHHHHHHHHHHHHTT-HHHHHHHHTT-.....-SHHHHHHHHHHHHHTT-H CS
                        Coatomer_E  76 lnspsrkeeilaelkeeladseiesnevlrllaaivflkegdfddalkllkks.....enLeavAlkvqillklhrv 147
                                       l+s +r e++l+ +++ l  +    ++++    a ++++ +  ++al + ++      e +     k  +l+ ++r 
  gi|330509113|ref|YP_004385541.1| 217 LASVDRWEDALEAVNKSLELNPR--SSTWWHFKAFILTELDRKEEALAAFNEAigqnpEDIGNWQWKASLLVEMKRY 291
                                       45556666777777776655444..5678888899999999999999888764432235566677889999****** PP

                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHH-....T..THHHHHHH....HHHHHHHHS---HHHHHHHHHHHHHT CS
                        Coatomer_E 148 dlAekelkkmqdidedatltQLAqawvklavg....g..ekiqdAyy....ifqelsekykstplllngkAvvslll 214
                                       +   +   k+ +++ ++    LAq+w + a++    g  e+  dA+     +++e     +    ll  k  v   l
  gi|330509113|ref|YP_004385541.1| 292 NESLEAYDKAIELAAENNTEELAQTWFSKASAlnktGrnEEATDAFQrslkLYDEAIAENPGDVSLLEAKGRVLFNL 368
                                       **************************9988763332234566777743333888876666889999999999***** PP

                                       T-HHHHHHHHHHHHHH-TT-HHH CS
                        Coatomer_E 215 gryeeAeslLkeaLdkdakdeet 237
                                       +ry+eA  +    L+  +  e  
  gi|330509113|ref|YP_004385541.1| 369 ERYDEAIAIYDHILETTPSVEPR 391
                                       *****998888887776665555 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.042        19       6      65 ..      98     161 ..      93     170 .. 0.75
   2 ?    7.1   0.0     0.014       6.3       8     101 ..     175     268 ..     169     273 .. 0.79
   3 ?   -1.2   0.0       5.3   2.4e+03     101     118 ..     284     301 ..     280     302 .. 0.81
   4 ?    5.5   0.2     0.045        20       3      29 ..     316     342 ..     314     422 .. 0.63
   5 ?    1.3   0.0      0.85   3.8e+02      47      64 ..     404     421 ..     396     455 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.042
                             TPR_5   6 eragarDstGhedkavplYrraLaeGLagarrrr....atiqLassLRnlGeaeealaLLrael 65 
                                       ++a+a +s  +++++++ Y++aL+   + + r +    a +  a  L nlG+ +ea +  ++ +
  gi|330509113|ref|YP_004385541.1|  98 KKASALNSLNRNEESIKAYEKALEVFDQRIERNQldadAWMGRANVLLNLGRWDEAHEAYDEVT 161
                                       578999999**************98888888877222245667999999999999877666555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.014
                             TPR_5   8 agarDstGhedkavplYrraLaeGL.agarrrratiqLassLRnlGeaeealaLLraelea.psdelddalaaflaL 82 
                                       a +   +G+ +++v+ Y ra+  GL        + +  as   nl  +++ +  L+a  ++ + +  +     f a 
  gi|330509113|ref|YP_004385541.1| 175 AEVISGIGDINESVEAYDRAI--GLiPANDTDELALAYASKSENLASVDRWEDALEAVNKSlELNPRSSTWWHFKAF 249
                                       556667889999999999987..55144556778899999999999998888888888777566777888999**** PP

                             TPR_5  83 vLsdlgrereavsivllal 101
                                       +L++l+r++ea++   +a+
  gi|330509113|ref|YP_004385541.1| 250 ILTELDRKEEALAAFNEAI 268
                                       ************9876665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.3
                             TPR_5 101 laehlprYqRsvtnYare 118
                                       l   + rY+ s+++Y ++
  gi|330509113|ref|YP_004385541.1| 284 LLVEMKRYNESLEAYDKA 301
                                       667899*******99875 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.045
                             TPR_5   3 aaFeragarDstGhedkavplYrraLa 29 
                                       + F +a+a + tG++++a   ++r+L+
  gi|330509113|ref|YP_004385541.1| 316 TWFSKASALNKTGRNEEATDAFQRSLK 342
                                       679999999999999999999998885 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.85
                             TPR_5  47 sLRnlGeaeealaLLrae 64 
                                       +LR lG+ eeal+  ++ 
  gi|330509113|ref|YP_004385541.1| 404 ALRALGRNEEALEEYNKA 421
                                       455555555555433333 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0031       1.4       9      35 ..      26      52 ..      24      55 .. 0.88
   2 ?    4.1   0.0      0.11        50      11      33 ..      69      91 ..      57      97 .. 0.77
   3 ?    2.4   0.1      0.37   1.7e+02      14      35 ..     288     309 ..     286     322 .. 0.85
   4 ?    1.2   0.0      0.86   3.9e+02      13      33 ..     367     387 ..     365     389 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0031
                                      HHHHHHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  9 lGhyklgeYseArryvdalLeiEPenr 35
                                       G +  g ++eA   +d  L+iEPen+
  gi|330509113|ref|YP_004385541.1| 26 EGLTHNGSFEEAISALDEALNIEPENE 52
                                      57778899******************7 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.11
                                      HHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C 11 hyklgeYseArryvdalLeiEPe 33
                                      +   +eY++A+ ++d  L++  +
  gi|330509113|ref|YP_004385541.1| 69 NESAKEYERALSFLDEDLKKNAS 91
                                      55579**********98888665 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.37
                                       HT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenr 35 
                                       +++Y+e+++  d  +e+  en+
  gi|330509113|ref|YP_004385541.1| 288 MKRYNESLEAYDKAIELAAENN 309
                                       89**************998886 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.86
                                       HHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPe 33 
                                        l +Y+eA    d +Le  P+
  gi|330509113|ref|YP_004385541.1| 367 NLERYDEAIAIYDHILETTPS 387
                                       6899*************9986 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0058       2.6      15      86 ..      11      80 ..       3      82 .. 0.88
   2 ?    2.5   1.0       0.4   1.8e+02       9      43 ..      80     114 ..      76     121 .. 0.89
   3 ?    3.3   0.1      0.23     1e+02       6      43 ..     118     155 ..     114     164 .. 0.89
   4 ?   -1.7   0.1       8.6   3.8e+03      28      43 ..     213     228 ..     186     237 .. 0.59
   5 ?    3.8   0.0      0.16        72       4      43 ..     257     296 ..     255     298 .. 0.88
   6 ?    4.0   0.2      0.14        62      11      48 ..     302     340 ..     297     343 .. 0.79
   7 ?    3.0   0.0      0.29   1.3e+02      11      43 ..     344     376 ..     336     389 .. 0.85
   8 ?    0.5   0.0       1.7   7.8e+02      29      53 ..     402     426 ..     394     453 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0058
                            TPR_20 15 laanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllkifealgsqdplvakyRrkLs 86
                                      ++a+ +  d  +d A+ l ++g  eeA+++L e l  + + e+  +rk+   +++++g +++ +++y r Ls
  gi|330509113|ref|YP_004385541.1| 11 VTAQENTTDYWMDKAEGLTHNGSFEEAISALDEALNIEPENETVLIRKAW--YLSVVGMANESAKEYERALS 80
                                      66777777888999***************************999999985..8999*********9999997 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.4
                            TPR_20   9 aeleaalaanpddldarldlAlallaagryeeAle 43 
                                       + l+++l++n +d +a  + A al++ +r+ee+++
  gi|330509113|ref|YP_004385541.1|  80 SFLDEDLKKNASDAEAWEKKASALNSLNRNEESIK 114
                                       568899*************************9986 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.23
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAle 43 
                                       + l+ ++++++ n  d da +  A++ll  gr +eA e
  gi|330509113|ref|YP_004385541.1| 118 KALEVFDQRIERNQLDADAWMGRANVLLNLGRWDEAHE 155
                                       5678899*************************999976 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 8.6
                            TPR_20  28 lAlallaagryeeAle 43 
                                        ++ l++  r e+Ale
  gi|330509113|ref|YP_004385541.1| 213 KSENLASVDRWEDALE 228
                                       2344555555556555 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.16
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAle 43 
                                       +++ la++ +a+ +np+d+      A +l++ +ry e+le
  gi|330509113|ref|YP_004385541.1| 257 KEEALAAFNEAIGQNPEDIGNWQWKASLLVEMKRYNESLE 296
                                       5678999************999999999999999999987 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.14
                            TPR_20  11 leaalaanpddl.darldlAlallaagryeeAleqLlei 48 
                                       +e a+++n ++l ++ +  A al++ gr+eeA +++ + 
  gi|330509113|ref|YP_004385541.1| 302 IELAAENNTEELaQTWFSKASALNKTGRNEEATDAFQRS 340
                                       5666777777765778999*************9987655 PP

  == domain 7  score: 3.0 bits;  conditional E-value: 0.29
                            TPR_20  11 leaalaanpddldarldlAlallaagryeeAle 43 
                                        ++a+a+np d+ +  +  ++l+  +ry+eA++
  gi|330509113|ref|YP_004385541.1| 344 YDEAIAENPGDVSLLEAKGRVLFNLERYDEAIA 376
                                       6789**************************986 PP

  == domain 8  score: 0.5 bits;  conditional E-value: 1.7
                            TPR_20  29 AlallaagryeeAleqLleilkrdr 53 
                                        +al a gr+eeAle+  + +    
  gi|330509113|ref|YP_004385541.1| 402 GDALRALGRNEEALEEYNKAIDMSP 426
                                       5677788888888887655555444 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.24   1.1e+02      55      74 ..      32      51 ..      22      63 .. 0.85
   2 ?    2.1   0.0      0.44     2e+02      15      69 ..     113     162 ..     100     167 .. 0.71
   3 ?    3.6   0.0      0.15        67      51      68 ..     251     268 ..     243     274 .. 0.85
   4 !    7.9   0.2    0.0068       3.1      48      82 ..     282     316 ..     280     328 .. 0.82
   5 ?   -0.2   0.0       2.4   1.1e+03      45      70 ..     318     343 ..     310     370 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.24
                            ANAPC5 55 ghneeAvkaleeairlAren 74
                                      g  eeA++al ea ++  en
  gi|330509113|ref|YP_004385541.1| 32 GSFEEAISALDEALNIEPEN 51
                                      7889**********997776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.44
                            ANAPC5  15 qqaldsLhryFDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleeair 69 
                                        +a ++  + FD  ++ n+         a +  a++  ++g ++eA +a  e+++
  gi|330509113|ref|YP_004385541.1| 113 IKAYEKALEVFDQRIERNQLD-----ADAWMGRANVLLNLGRWDEAHEAYDEVTE 162
                                       455666666777777777777.....67788888888888889999888888876 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.15
                            ANAPC5  51 hadfghneeAvkaleeai 68 
                                        ++++ +eeA++a++eai
  gi|330509113|ref|YP_004385541.1| 251 LTELDRKEEALAAFNEAI 268
                                       4678999**********9 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0068
                            ANAPC5  48 aslhadfghneeAvkaleeairlArenkDkscLal 82 
                                       asl  ++  ++e+++a   ai+lA en+ ++  + 
  gi|330509113|ref|YP_004385541.1| 282 ASLLVEMKRYNESLEAYDKAIELAAENNTEELAQT 316
                                       788999*********************98876555 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 2.4
                            ANAPC5  45 LnlaslhadfghneeAvkaleeairl 70 
                                       ++ as   + g neeA++a++ + +l
  gi|330509113|ref|YP_004385541.1| 318 FSKASALNKTGRNEEATDAFQRSLKL 343
                                       55666667779999999999988765 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.8    0.0013      0.59       3      25 ..     136     158 ..     134     159 .. 0.86
   2 ?   -0.9   0.0       8.4   3.8e+03       8      24 ..     248     264 ..     245     266 .. 0.78
   3 ?    0.3   0.0       3.7   1.6e+03       7      25 ..     320     338 ..     314     339 .. 0.78
   4 ?   -0.8   0.0       7.9   3.5e+03       6      23 ..     360     377 ..     356     379 .. 0.80
   5 !    9.2   0.2    0.0047       2.1       4      22 ..     398     416 ..     396     419 .. 0.90
   6 ?    3.1   0.4      0.45     2e+02       3      17 ..     431     445 ..     429     448 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0013
                             TPR_4   3 allaLArallalGdldeAralle 25 
                                       a  ++A +ll lG++deA ++ +
  gi|330509113|ref|YP_004385541.1| 136 AWMGRANVLLNLGRWDEAHEAYD 158
                                       66789*************99876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 8.4
                             TPR_4   8 ArallalGdldeArall 24 
                                       A  l +l + +eA+a++
  gi|330509113|ref|YP_004385541.1| 248 AFILTELDRKEEALAAF 264
                                       66677889999**9975 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 3.7
                             TPR_4   7 LArallalGdldeAralle 25 
                                        A al  +G+ +eA ++++
  gi|330509113|ref|YP_004385541.1| 320 KASALNKTGRNEEATDAFQ 338
                                       57799999******87765 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 7.9
                             TPR_4   6 aLArallalGdldeAral 23 
                                       a +r+l+ l ++deA a+
  gi|330509113|ref|YP_004385541.1| 360 AKGRVLFNLERYDEAIAI 377
                                       56899999999***9775 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0047
                             TPR_4   4 llaLArallalGdldeAra 22 
                                        +a++ al alG+ +eA++
  gi|330509113|ref|YP_004385541.1| 398 WIARGDALRALGRNEEALE 416
                                       589**************97 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.45
                             TPR_4   3 allaLArallalGdl 17 
                                       a ++L++a+ alG+ 
  gi|330509113|ref|YP_004385541.1| 431 AWHGLGEAQRALGQT 445
                                       678999999999985 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 ?    8.4   0.2    0.0036       1.6      52     110 ..      35      89 ..      30     107 .. 0.70
   2 ?    4.4   0.2     0.061        27       4      48 ..     113     157 ..     110     164 .. 0.86
   3 ?    3.0   0.1      0.17        77     114     147 ..     289     322 ..     253     331 .. 0.80
   4 ?   -2.6   0.0       8.7   3.9e+03      56     142 ..     416     441 ..     403     457 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH- CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqavded 110
                                       ++ais l+eal i+P+ +  l +    y+s + +    +e+ +++e+a  f+++  +++
  gi|330509113|ref|YP_004385541.1|  35 EEAISALDEALNIEPENETVL-IRKAWYLSVVGM---ANESAKEYERALSFLDEDLKKN 89 
                                       79*************987654.344445665544...4455567888888887766554 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.061
                                       HHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHHS-HHHHH CS
                       TOM20_plant   4 lllfeearkdaeatykknPldadnllrWggallelsqfqsvaeak 48 
                                       +  +e+a +  +++ ++n ldad  +  +++ll+l ++++  ea 
  gi|330509113|ref|YP_004385541.1| 113 IKAYEKALEVFDQRIERNQLDADAWMGRANVLLNLGRWDEAHEAY 157
                                       677899999999999*********************999888875 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHTHHHHHHHHHHSSS-XXXXXXXX CS
                       TOM20_plant 114 dlyrkslelaakaPelhteihkqgllsqllgaea 147
                                       + y+ sle  +ka el +e   + l +   ++  
  gi|330509113|ref|YP_004385541.1| 289 KRYNESLEAYDKAIELAAENNTEELAQTWFSKAS 322
                                       6799999999999999998888888877766654 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 8.7
                                       HHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHTHHHHHHH CS
                       TOM20_plant  56 skleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqavdedPdndlyrkslelaakaPelhte 132
                                                                                                   y+k+++++   P++ t 
  gi|330509113|ref|YP_004385541.1| 416 E----------------------------------------------------------EYNKAIDMS---PNFSTA 431
                                       2..........................................................333333332...333333 PP

                                       HHHSSS-XXX CS
                       TOM20_plant 133 ihkqgllsql 142
                                        h  g  ++ 
  gi|330509113|ref|YP_004385541.1| 432 WHGLGEAQRA 441
                                       3333333333 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   0.00018      0.08      93     161 ..      68     136 ..      40     202 .. 0.86
   2 ?    3.6   2.6       0.1        46      82     160 ..     280     356 ..     272     431 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                           DUF2225  93 ldeaiesYkLallcyelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelykeayekesfpveg 161
                                       ++e +++Y  al   +   +k+++ A  + + A   + ++ +e++ + ++kAle++++ +e ++ + + 
  gi|330509113|ref|YP_004385541.1|  68 ANESAKEYERALSFLDEDLKKNASDAEAWEKKASALNSLNRNEESIKAYEKALEVFDQRIERNQLDADA 136
                                       68999********************************************************99987764 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.1
                           DUF2225  82 wksrdfskertldeaiesYkLallcyelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelykeayekesfp 158
                                       wk+    +   ++e +e+Y  a++ +   +++  + A ++   A   ++++ +e+ ++  ++ l+ly+ea+ ++  +
  gi|330509113|ref|YP_004385541.1| 280 WKASLLVEMKRYNESLEAYDKAIELA--AENNTEELAQTWFSKASALNKTGRNEEATDAFQRSLKLYDEAIAENPGD 354
                                       55666666778889999999998765..46667789999999999999999999999999999****9999887766 PP

                           DUF2225 159 ve 160
                                       v+
  gi|330509113|ref|YP_004385541.1| 355 VS 356
                                       55 PP

>> DUF3808  Protein of unknown function (DUF3808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3         1   4.7e+02     280     373 ..      29     123 ..      21     140 .. 0.59
   2 ?   -1.5   0.4       1.8     8e+02     284     334 ..     108     160 ..      59     166 .. 0.60
   3 ?    9.2   0.8   0.00097      0.44     252     330 ..     224     304 ..     171     348 .. 0.60
   4 ?    1.8   0.0      0.17        77     274     312 ..     360     398 ..     330     433 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1
                           DUF3808 280 slkgnldeAlelleeiieesqselkqvkhlclfelaltlvy...lheykeaaesfle.LlklskwSkalYtYlaaac 352
                                         +g ++eA+++l+e++ + + e + v     + l+++ +     +ey++a+   +e L k+ +   a+    +a+ 
  gi|330509113|ref|YP_004385541.1|  29 THNGSFEEAISALDEAL-NIEPENETVLIRKAWYLSVVGMAnesAKEYERALSFLDEdLKKNASDAEAWE--KKASA 102
                                       56777888888888887.6677777766666666665555411146777777776651333333344433..35555 PP

                           DUF3808 353 llelgreekkaeakekaeelf 373
                                       l +l r+e+  +a eka e+f
  gi|330509113|ref|YP_004385541.1| 103 LNSLNRNEESIKAYEKALEVF 123
                                       555555555544445555554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.8
                           DUF3808 284 nldeAlelleeiie..esqselkqvkhlclfelaltlvylheykeaaesfleL 334
                                       + +e+++++e+++e   +++e  q+ +     +a +l+ l +++ea e+ +e+
  gi|330509113|ref|YP_004385541.1| 108 RNEESIKAYEKALEvfDQRIERNQLDADAWMGRANVLLNLGRWDEAHEAYDEV 160
                                       33444444444443112345556666666667777777777777666666655 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00097
                           DUF3808 252 eeleelLlksrkrfPksalwllfearieslkgnldeAlelleeiieesqsel..kqvkhlclfelaltlvylheyke 326
                                       e + e++ ks+++ P+s+ w  f+a i+    + +eAl++++e+i ++ +++   q k+ +l e    +  l  y++
  gi|330509113|ref|YP_004385541.1| 224 EDALEAVNKSLELNPRSSTWWHFKAFILTELDRKEEALAAFNEAIGQNPEDIgnWQWKASLLVEMKRYNESLEAYDK 300
                                       34455666777788888888888888888888888888888888865555441134455555555444444444444 PP

                           DUF3808 327 aaes 330
                                       a+e 
  gi|330509113|ref|YP_004385541.1| 301 AIEL 304
                                       4443 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.17
                           DUF3808 274 fearieslkgnldeAlelleeiieesqselkqvkhlclf 312
                                        ++r+++   + deA++++++i+e + s    + h+  +
  gi|330509113|ref|YP_004385541.1| 360 AKGRVLFNLERYDEAIAIYDHILETTPSVEPRLTHITTW 398
                                       589*******************97777777777777776 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.7    0.0057       2.6      46      80 ..      98     132 ..      71     137 .. 0.83
   2 ?    2.2   0.1      0.48   2.1e+02      53      77 ..     287     311 ..     280     336 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0057
                           UPF0122  46 srqavydnikrtekllekyEekLkllekykkreel 80 
                                       ++ +  ++++r e+ ++ yE++L+++++  +r++l
  gi|330509113|ref|YP_004385541.1|  98 KKASALNSLNRNEESIKAYEKALEVFDQRIERNQL 132
                                       45666789************************998 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.48
                           UPF0122  53 nikrtekllekyEekLkllekykkr 77 
                                       ++kr ++ le y+++++l +++++ 
  gi|330509113|ref|YP_004385541.1| 287 EMKRYNESLEAYDKAIELAAENNTE 311
                                       6899**************9887654 PP

>> Bin3  Bicoid-interacting protein 3 (Bin3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0013      0.59      52     107 ..     288     345 ..     276     346 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0013
                              Bin3  52 kkklseelkenykelklrpedfeevLleevgfesveeleekeee...skgfkRpilvyr 107
                                        k+++e+l++  k+++l  e+ +e L + + f++ + l+++ ++   +++f+R++ +y 
  gi|330509113|ref|YP_004385541.1| 288 MKRYNESLEAYDKAIELAAENNTEELAQ-TWFSKASALNKTGRNeeaTDAFQRSLKLYD 345
                                       56777788887888**************.99***9999998887777888******995 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.4     0.028        13      81     124 ..      71     114 ..      17     119 .. 0.90
   2 ?    1.5   0.1      0.84   3.8e+02      82     122 ..     113     153 ..     108     158 .. 0.88
   3 ?    6.3   1.6     0.028        13      41     124 ..     242     335 ..     238     343 .. 0.80
   4 ?    0.2   0.0       2.1   9.3e+02      67     123 ..     353     415 ..     345     422 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.028
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                       ++++y+ a+++l+  + ++ ++aea e ka+al++l + +es  
  gi|330509113|ref|YP_004385541.1|  71 SAKEYERALSFLDEDLKKNASDAEAWEKKASALNSLNRNEESIK 114
                                       467899999999999999999*****************999976 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.84
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  82 egdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                        + y+ a+e+ ++ ++ ++ +a+a   +a++l +lg+  e+
  gi|330509113|ref|YP_004385541.1| 113 IKAYEKALEVFDQRIERNQLDADAWMGRANVLLNLGRWDEA 153
                                       567999*****************************997765 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.028
                                       -S--S-GGGTS---HHHHH.HHHHHHTT....SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-.....HHHHH CS
                   Alkyl_sulf_dimr  41 GWfdgnPanLnplppeeka.krlvelmG....gaekvlekakealkegdyrwaaellnhlvfadpen.....aeake 107
                                       +W+  ++  L +l ++e+a + ++e++G    +  +   ka+  ++ + y+ ++e  +++++   en     a++  
  gi|330509113|ref|YP_004385541.1| 242 TWWHFKAFILTELDRKEEAlAAFNEAIGqnpeDIGNWQWKASLLVEMKRYNESLEAYDKAIELAAENnteelAQT-- 316
                                       799999999****9999884678999**77777777888899999****************97555434322344.. PP

                                       H..HHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr 108 l..kadaleqlgyqaesat 124
                                          ka+al++ g+ +e++ 
  gi|330509113|ref|YP_004385541.1| 317 WfsKASALNKTGRNEEATD 335
                                       266**********999875 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 2.1
                                       TSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT......-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  67 Ggaekvlekakealkegdyrwaaellnhlvfadpe......naeakelkadaleqlgyqaesa 123
                                       G+++ + +k +  ++ + y  a+ + +h+++ +p+      + ++  ++ dal++lg+ +e+ 
  gi|330509113|ref|YP_004385541.1| 353 GDVSLLEAKGRVLFNLERYDEAIAIYDHILETTPSveprltHITTWIARGDALRALGRNEEAL 415
                                       666667778888889999999999******998873333323444455889999999888865 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.16        71       9      25 ..      27      43 ..      26      46 .. 0.89
   2 ?    0.4   0.1       2.3     1e+03      16      24 ..     116     124 ..     114     125 .. 0.88
   3 ?    4.2   0.0      0.13        60       9      27 ..     143     161 ..     141     164 .. 0.83
   4 ?    0.7   0.0       1.7   7.8e+02       8      25 ..     322     339 ..     321     344 .. 0.86
   5 ?    0.1   0.0       2.7   1.2e+03      12      26 ..     367     381 ..     363     383 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.16
                               PPR  9 gycknGkleeAlelfke 25
                                      g+ +nG +eeA++ ++e
  gi|330509113|ref|YP_004385541.1| 27 GLTHNGSFEEAISALDE 43
                                      7899********99988 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2.3
                               PPR  16 leeAlelfk 24 
                                       +e+Ale+f+
  gi|330509113|ref|YP_004385541.1| 116 YEKALEVFD 124
                                       79******8 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.13
                               PPR   9 gycknGkleeAlelfkeMk 27 
                                       ++   G+++eA e ++e  
  gi|330509113|ref|YP_004385541.1| 143 VLLNLGRWDEAHEAYDEVT 161
                                       56779**********9975 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.7
                               PPR   8 sgycknGkleeAlelfke 25 
                                       s++ k G+ eeA + f++
  gi|330509113|ref|YP_004385541.1| 322 SALNKTGRNEEATDAFQR 339
                                       68889*******999986 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 2.7
                               PPR  12 knGkleeAlelfkeM 26 
                                          +++eA+ +++ +
  gi|330509113|ref|YP_004385541.1| 367 NLERYDEAIAIYDHI 381
                                       56799******9976 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 ?   -1.2   0.0       5.8   2.6e+03      10      31 ..      69      90 ..      64     107 .. 0.65
   2 ?   10.0   0.5     0.002      0.88       6      37 ..     106     149 ..     101     193 .. 0.79
   3 ?    2.2   0.9      0.53   2.4e+02      15      56 ..     222     300 ..     214     316 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.8
                          CCDC-167 10 eeklascrerLeaverrlrkee 31
                                      +e+ +++++ L  ++  l+k+ 
  gi|330509113|ref|YP_004385541.1| 69 NESAKEYERALSFLDEDLKKNA 90
                                      5566666666666666666655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.002
                          CCDC-167   6 IdkleeklascrerLeaverrlrkeelseee............R 37 
                                       +++ ee+++++++ Le  ++r+++++l  ++            R
  gi|330509113|ref|YP_004385541.1| 106 LNRNEESIKAYEKALEVFDQRIERNQLDADAwmgranvllnlgR 149
                                       5789***********************99876665555555550 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.53
                          CCDC-167  15 screrLeaverrlrkeelseee.....................................ResleeEeaslkeqleen 54 
                                       + ++ Leav+++l+ +  s+                                       + sl  E++  +e le +
  gi|330509113|ref|YP_004385541.1| 222 RWEDALEAVNKSLELNPRSSTWwhfkafilteldrkeealaafneaigqnpedignwqwKASLLVEMKRYNESLEAY 298
                                       66788888888888777666656666666666666666666666666666666666666555555555555555555 PP

                          CCDC-167  55 ek 56 
                                       +k
  gi|330509113|ref|YP_004385541.1| 299 DK 300
                                       54 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3    0.0025       1.1      31      82 ..      81     133 ..      57     142 .. 0.81
   2 ?   -0.8   0.2       4.3   1.9e+03      14      36 ..     229     249 ..     215     266 .. 0.59
   3 ?   -1.1   0.1       5.4   2.4e+03       9      42 ..     312     330 ..     286     344 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0025
                    Retrotrans_gag  31 dlkkaflktflpserkdqleeelsslrQgtesvreYvtrfktladqlde.vlt 82 
                                        l++ ++k+  + e ++++ + l sl+ ++es++ Y + ++ + +++++ +l+
  gi|330509113|ref|YP_004385541.1|  81 FLDEDLKKNASDAEAWEKKASALNSLNRNEESIKAYEKALEVFDQRIERnQLD 133
                                       588999*********************************99998888875555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 4.3
                    Retrotrans_gag  14 wlkslvarsidasesWkdlkkaf 36 
                                        ++++ + +++ s++W+++k+ f
  gi|330509113|ref|YP_004385541.1| 229 AVNKSLELNPR-SSTWWHFKA-F 249
                                       33334444444.788888874.4 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 5.4
                    Retrotrans_gag   9 gaAkswlkslvarsidasesWkdlkkaflktflp 42 
                                       + A               ++W    +a++kt  +
  gi|330509113|ref|YP_004385541.1| 312 ELA---------------QTWFSKASALNKTGRN 330
                                       234...............4444444444444444 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       2.2   9.8e+02      28      49 ..      34      55 ..      12      78 .. 0.83
   2 ?    8.8   0.2    0.0039       1.7      28      52 ..     150     174 ..     148     190 .. 0.90
   3 ?   -0.9   0.0       4.1   1.8e+03      26      44 ..     182     200 ..     174     220 .. 0.81
   4 ?    2.9   0.1      0.26   1.2e+02      27      51 ..     221     246 ..     190     249 .. 0.85
   5 ?   -0.3   0.0       2.6   1.2e+03      29      51 ..     258     280 ..     247     283 .. 0.80
   6 ?    1.5   0.1      0.76   3.4e+02      28      58 ..     291     321 ..     286     345 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 2.2
                           DUF1510 28 wnEmekavskatglsednmivw 49
                                      ++E  +a+ +a +++ +n +v+
  gi|330509113|ref|YP_004385541.1| 34 FEEAISALDEALNIEPENETVL 55
                                      7899999999*99999998775 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0039
                           DUF1510  28 wnEmekavskatglsednmivwwlg 52 
                                       w+E ++a  ++t+l+ +++ vww +
  gi|330509113|ref|YP_004385541.1| 150 WDEAHEAYDEVTELKPQDYNVWWRK 174
                                       ***********************76 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 4.1
                           DUF1510  26 vDwnEmekavskatglsed 44 
                                        D nE ++a  +a+gl   
  gi|330509113|ref|YP_004385541.1| 182 GDINESVEAYDRAIGLIPA 200
                                       589999*******998544 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.26
                           DUF1510  27 D.wnEmekavskatglsednmivwwl 51 
                                       D w++ ++av+k  +l+  +++ w+ 
  gi|330509113|ref|YP_004385541.1| 221 DrWEDALEAVNKSLELNPRSSTWWHF 246
                                       4499***************9999986 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 2.6
                           DUF1510  29 nEmekavskatglsednmivwwl 51 
                                       +E + a+++a+g + +++  w  
  gi|330509113|ref|YP_004385541.1| 258 EEALAAFNEAIGQNPEDIGNWQW 280
                                       4678999*********9999975 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.76
                           DUF1510  28 wnEmekavskatglsednmivwwlgnggspq 58 
                                       +nE ++a  ka++l  +n +    +   s+ 
  gi|330509113|ref|YP_004385541.1| 291 YNESLEAYDKAIELAAENNTEELAQTWFSKA 321
                                       8999999999999999988876666554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        44  (0.00245412); 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: 0.96u 0.35s 00:00:01.31 Elapsed: 00:00:00.63
# Mc/sec: 2202.56
//
Query:       gi|330509114|ref|YP_004385542.1|  [L=801]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-65  210.3  29.2    4.8e-06   26.3   0.0   15.2 15  TPR_2            Tetratricopeptide repeat
    5.4e-61  197.8  27.9    9.9e-06   25.4   0.1   15.4 15  TPR_8            Tetratricopeptide repeat
      8e-60  196.4  18.8    1.2e-07   31.3   0.3   15.3 15  TPR_1            Tetratricopeptide repeat
      8e-44  147.1  23.3    1.6e-08   34.1   0.1   12.8 13  TPR_11           TPR repeat
    3.8e-36  123.5  24.0    8.3e-09   36.0   0.1   10.1 12  TPR_16           Tetratricopeptide repeat
    1.8e-35  121.0  25.4    1.2e-07   31.9   0.3   10.2 11  TPR_12           Tetratricopeptide repeat
    3.4e-32  108.4  26.0      0.016   16.0   0.1   13.8 14  TPR_14           Tetratricopeptide repeat
      1e-26   91.3  10.8    0.00013   22.1   0.3   10.9 10  TPR_17           Tetratricopeptide repeat
    3.1e-26   91.3   9.5     0.0088   16.2   0.3    9.0 10  TPR_9            Tetratricopeptide repeat
    1.9e-24   85.9  23.6    4.4e-05   23.9   0.2    9.7  9  TPR_19           Tetratricopeptide repeat
    1.1e-17   64.4  21.7    1.9e-08   34.5   0.1    8.6  8  DUF3856          Domain of Unknown Function (DUF3856)
      9e-13   48.0  16.0       0.22   12.2   0.0   11.1 11  TPR_6            Tetratricopeptide repeat
    7.8e-12   45.3  10.2     0.0018   18.5   0.1    6.8  7  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    1.3e-11   45.1  11.3      0.017   15.5   0.1    8.0 11  BTAD             Bacterial transcriptional activator domain
    4.2e-10   38.9   6.9       0.84    9.8   0.0   10.0 11  TPR_7            Tetratricopeptide repeat
    1.3e-07   31.2  27.0       0.21   11.5   0.0   10.4 10  TPR_10           Tetratricopeptide repeat
    3.1e-06   27.5   0.0    8.2e-06   26.2   0.0    1.8  1  LTD              Lamin Tail Domain
    4.3e-06   25.9   8.4       0.68    8.8   0.0    5.4  6  NARP1            NMDA receptor-regulated protein 1
    4.7e-06   26.1   1.0      0.012   15.3   0.0    4.3  4  PPTA             Protein prenyltransferase alpha subunit repe
    5.3e-06   26.4   1.0      0.025   14.6   0.1    3.6  2  SRP_TPR_like     Putative TPR-like repeat
    8.7e-06   25.6  17.6     0.0019   18.0   0.0    6.8  7  TPR_21           Tetratricopeptide repeat-like domain
    2.4e-05   24.3   8.6        1.1    9.4   0.0    7.1  8  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    0.00037   20.0   5.4        2.5    7.4   0.4    4.4  4  TPR_MalT         MalT-like TPR region
     0.0011   19.4   3.8        2.9    8.4   0.0    5.1  6  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0035   17.6  16.3        1.8    9.0   0.8    6.6  6  TPR_20           Tetratricopeptide repeat
      0.004   16.9   8.5        1.1    9.0   0.2    4.0  3  TOM20_plant      Plant specific mitochondrial import receptor
  ------ inclusion threshold ------
       0.11   12.4   0.1        0.9    9.4   0.0    2.5  2  LemA             LemA family
       0.19   12.0   8.7         15    6.1   0.0    6.8  7  PPR              PPR repeat
       0.66    9.1  10.1        8.2    5.5   0.0    4.9  5  FAT              FAT domain


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 !    8.6   0.0    0.0035       2.2      14      34 .]       1      21 [.       1      21 [. 0.94
   2 !   11.0   0.0   0.00063      0.39       1      30 [.      22      51 ..      22      54 .. 0.94
   3 !    7.3   0.2    0.0095       5.9       2      32 ..      64      94 ..      63      96 .. 0.84
   4 !   17.2   0.0   6.2e-06    0.0038       2      34 .]      99     131 ..      98     131 .. 0.96
   5 !   11.9   0.0   0.00031      0.19       1      34 []     394     427 ..     394     427 .. 0.95
   6 ?    5.3   0.0     0.042        26       3      33 ..     430     460 ..     428     468 .. 0.74
   7 !   13.1   0.2   0.00013     0.079       1      30 [.     469     498 ..     469     500 .. 0.95
   8 !   20.7   0.0   4.6e-07   0.00029       2      32 ..     511     541 ..     510     543 .. 0.94
   9 ?    1.2   0.0      0.81     5e+02       1      30 [.     546     575 ..     546     579 .. 0.81
  10 !   17.2   0.2   6.3e-06    0.0039       1      34 []     585     618 ..     585     618 .. 0.94
  11 !   18.6   0.0   2.2e-06    0.0014       4      33 ..     622     651 ..     620     652 .. 0.94
  12 !   26.3   0.1   7.8e-09   4.8e-06       1      31 [.     653     683 ..     653     685 .. 0.95
  13 !   26.3   0.0   7.7e-09   4.8e-06       6      33 ..     700     727 ..     696     728 .. 0.91
  14 !   24.9   0.2   2.2e-08   1.4e-05       1      33 [.     734     766 ..     734     767 .. 0.96
  15 ?    6.9   0.0     0.013       7.9       2      30 ..     769     797 ..     768     798 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0035
                             TPR_2 14 lgdyeeAleafekAleldPnn 34
                                      +g+ eeA+ af++ l+ dP+n
  gi|330509114|ref|YP_004385542.1|  1 MGRNEEAISAFDEGLKTDPQN 21
                                      5999***************97 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00063
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAlel 30
                                      a a++ +G+a++ +g+ +eA +  +kA el
  gi|330509114|ref|YP_004385542.1| 22 ASAWHHRGMALAGMGHGAEANQSIQKAMEL 51
                                      679************************998 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0095
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldP 32
                                      eal+ +++     g+ eeAlea+ ++ el+ 
  gi|330509114|ref|YP_004385542.1| 64 EALWLRAEEMDLFGKSEEALEAYGRVAELNS 94
                                      6777777777888999*************96 PP

  == domain 4  score: 17.2 bits;  conditional E-value: 6.2e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ea+ +  ++++++g+y++ +e f +A +l P n
  gi|330509114|ref|YP_004385542.1|  99 EAWIRESDILAAQGRYNQSVESFSRAMALVPAN 131
                                       79***************************9976 PP

  == domain 5  score: 11.9 bits;  conditional E-value: 0.00031
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+ +y  G  +++++ +ee + a+e++++ldP+n
  gi|330509114|ref|YP_004385542.1| 394 ADDWYKKGTELFENDSLEESVLAMERVIQLDPEN 427
                                       567*****************************97 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.042
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+  ++  +  +g+  e  +a+ekAl l  n
  gi|330509114|ref|YP_004385542.1| 430 AWLSIAITLGIMGNGSESSKAYEKALNLIDN 460
                                       5666677777778888888888888887555 PP

  == domain 7  score: 13.1 bits;  conditional E-value: 0.00013
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a+a+ +  +a++ lg+ ee l+a ekAle+
  gi|330509114|ref|YP_004385542.1| 469 ARAWEAKSDALIGLGRQEESLDAIEKALEI 498
                                       789*************************97 PP

  == domain 8  score: 20.7 bits;  conditional E-value: 4.6e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       ea++  ++++y  g+ +eAl+a+ek++el+ 
  gi|330509114|ref|YP_004385542.1| 511 EAWWSKANVLYGIGRSDEALQAYEKVIELNH 541
                                       89***************************95 PP

  == domain 9  score: 1.2 bits;  conditional E-value: 0.81
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a+al   G+  + +g+y+e +e f++A+ l
  gi|330509114|ref|YP_004385542.1| 546 ADALLIKGYDFAIKGNYDEFKETFNQAIGL 575
                                       678888999999******988888888755 PP

  == domain 10  score: 17.2 bits;  conditional E-value: 6.3e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+ ++  G a+++lg+ eeA eafek  +l P++
  gi|330509114|ref|YP_004385542.1| 585 ARTWNSAGFALAELGKEEEAFEAFEKYAQLSPGD 618
                                       67899***************************86 PP

  == domain 11  score: 18.6 bits;  conditional E-value: 2.2e-06
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                       + + G+ + +lg+y+  +ea+++Al++dP+
  gi|330509114|ref|YP_004385542.1| 622 WRMKGDMASELGRYNVSIEAYDQALRIDPK 651
                                       8899*************************7 PP

  == domain 12  score: 26.3 bits;  conditional E-value: 7.8e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       ae++y  G+a++k++++++Al+afekA+e+ 
  gi|330509114|ref|YP_004385542.1| 653 AEVWYKKGNALAKMDNHNDALKAFEKAVEIS 683
                                       79**************************986 PP

  == domain 13  score: 26.3 bits;  conditional E-value: 7.7e-09
                             TPR_2   6 nlGlayyklgdyeeAleafekAleldPn 33 
                                         G+a++kl++y+eA+ea+++Ale++P 
  gi|330509114|ref|YP_004385542.1| 700 IKGYALIKLNRYDEAIEALDRALEIAPS 727
                                       57************************96 PP

  == domain 14  score: 24.9 bits;  conditional E-value: 2.2e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       aea++  G+++++lg+ e+Alea++k++e +P 
  gi|330509114|ref|YP_004385542.1| 734 AEAWNGKGDILLALGKNEDALEAYNKSIEFNPA 766
                                       89*****************************95 PP

  == domain 15  score: 6.9 bits;  conditional E-value: 0.013
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAlel 30 
                                       +a++  Gla  +lg++ eA   f+ A +l
  gi|330509114|ref|YP_004385542.1| 769 RAWHGKGLAQSALGQFSEADLSFRVARKL 797
                                       69*****************9999877765 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0     0.006       3.7      14      34 .]       1      21 [.       1      21 [. 0.95
   2 ?    6.4   0.0     0.019        12       1      30 [.      22      51 ..      22      54 .. 0.94
   3 ?    3.2   0.0      0.21   1.3e+02      15      33 ..      77      95 ..      64      96 .. 0.88
   4 !    9.4   0.0    0.0021       1.3       2      30 ..      99     127 ..      98     131 .. 0.90
   5 !   11.1   0.0    0.0006      0.37       4      34 .]     397     427 ..     397     427 .. 0.97
   6 ?    7.2   0.0     0.011       6.8       2      31 ..     429     458 ..     428     461 .. 0.90
   7 !   15.3   0.1   2.7e-05     0.017       1      30 [.     469     498 ..     469     498 .. 0.97
   8 !   18.2   0.0   3.2e-06     0.002       2      31 ..     511     540 ..     510     542 .. 0.96
   9 !   11.0   0.0   0.00064      0.39       8      33 ..     553     578 ..     546     579 .. 0.80
  10 !   17.7   0.0   4.6e-06    0.0028       1      33 [.     585     617 ..     585     618 .. 0.95
  11 !   18.1   0.0   3.5e-06    0.0021       4      33 ..     622     651 ..     620     651 .. 0.92
  12 !   22.9   0.2     1e-07   6.3e-05       1      31 [.     653     683 ..     653     685 .. 0.96
  13 !   25.4   0.1   1.6e-08   9.9e-06       3      33 ..     697     727 ..     695     728 .. 0.93
  14 !   23.4   0.1   7.1e-08   4.4e-05       1      33 [.     734     766 ..     734     767 .. 0.96
  15 ?    5.7   0.0     0.034        21       2      25 ..     769     792 ..     768     794 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.006
                                      TT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8 14 lgdyeeAkeyyekaleldpdn 34
                                      +g+ eeA++++ + l+ dp+n
  gi|330509114|ref|YP_004385542.1|  1 MGRNEEAISAFDEGLKTDPQN 21
                                      79*****************86 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekalel 30
                                      a+a+++ g+++  +g   eA ++++ka el
  gi|330509114|ref|YP_004385542.1| 22 ASAWHHRGMALAGMGHGAEANQSIQKAMEL 51
                                      689************************998 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.21
                                      T-HHHHHHHHHHHHHHHHH CS
                             TPR_8 15 gdyeeAkeyyekaleldpd 33
                                      g+ eeA e+y ++ el+ +
  gi|330509114|ref|YP_004385542.1| 77 GKSEEALEAYGRVAELNSS 95
                                      89*************9976 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0021
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                       ea+ + ++i+  +g+y++++e++ +a  l
  gi|330509114|ref|YP_004385542.1|  99 EAWIRESDILAAQGRYNQSVESFSRAMAL 127
                                       89*********************999866 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.0006
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +y++g  +++   +ee++ ++e++++ldp+n
  gi|330509114|ref|YP_004385542.1| 397 WYKKGTELFENDSLEESVLAMERVIQLDPEN 427
                                       9****************************86 PP

  == domain 6  score: 7.2 bits;  conditional E-value: 0.011
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                       +a++ ++ ++  +g+  e+ ++yekal l 
  gi|330509114|ref|YP_004385542.1| 429 SAWLSIAITLGIMGNGSESSKAYEKALNLI 458
                                       69999**********************985 PP

  == domain 7  score: 15.3 bits;  conditional E-value: 2.7e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+a+  ++++++ lg+ ee+  ++ekale+
  gi|330509114|ref|YP_004385542.1| 469 ARAWEAKSDALIGLGRQEESLDAIEKALEI 498
                                       79**************************97 PP

  == domain 8  score: 18.2 bits;  conditional E-value: 3.2e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                       ea++ +++++   g+ +eA ++yek++el+
  gi|330509114|ref|YP_004385542.1| 511 EAWWSKANVLYGIGRSDEALQAYEKVIELN 540
                                       79**************************97 PP

  == domain 9  score: 11.0 bits;  conditional E-value: 0.00064
                                       HHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyyekaleldpd 33 
                                       g+    +g+y+e ke++++a+ l p+
  gi|330509114|ref|YP_004385542.1| 553 GYDFAIKGNYDEFKETFNQAIGLIPA 578
                                       5556679***************9886 PP

  == domain 10  score: 17.7 bits;  conditional E-value: 4.6e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+ ++  g ++ +lg+ eeA e++ek+ +l+p 
  gi|330509114|ref|YP_004385542.1| 585 ARTWNSAGFALAELGKEEEAFEAFEKYAQLSPG 617
                                       799***************************995 PP

  == domain 11  score: 18.1 bits;  conditional E-value: 3.5e-06
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       + ++g+  ++lg+y+ ++e+y +al++dp+
  gi|330509114|ref|YP_004385542.1| 622 WRMKGDMASELGRYNVSIEAYDQALRIDPK 651
                                       5589*************************7 PP

  == domain 12  score: 22.9 bits;  conditional E-value: 1e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                       ae++y++g+++ k+ +++ A +++eka+e++
  gi|330509114|ref|YP_004385542.1| 653 AEVWYKKGNALAKMDNHNDALKAFEKAVEIS 683
                                       79***************************97 PP

  == domain 13  score: 25.4 bits;  conditional E-value: 1.6e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++  +g++++kl++y+eA+e++ +ale++p+
  gi|330509114|ref|YP_004385542.1| 697 ICIIKGYALIKLNRYDEAIEALDRALEIAPS 727
                                       68889************************96 PP

  == domain 14  score: 23.4 bits;  conditional E-value: 7.1e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       aea++ +g+i+l lg+ e A e+y+k +e +p+
  gi|330509114|ref|YP_004385542.1| 734 AEAWNGKGDILLALGKNEDALEAYNKSIEFNPA 766
                                       79*****************************97 PP

  == domain 15  score: 5.7 bits;  conditional E-value: 0.034
                                       CHHHHHHHHHHHTT-HHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyye 25 
                                       +a++ +g++ + lg++ eA  +++
  gi|330509114|ref|YP_004385542.1| 769 RAWHGKGLAQSALGQFSEADLSFR 792
                                       89*****************87775 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0023       1.4      14      34 .]       1      21 [.       1      21 [. 0.95
   2 ?    2.9   0.0      0.17     1e+02       1      30 [.      22      51 ..      22      52 .. 0.85
   3 !    7.5   0.0    0.0063       3.9      15      33 ..      77      95 ..      76      96 .. 0.91
   4 !    7.1   0.0     0.008         5      10      32 ..     107     129 ..     100     131 .. 0.89
   5 !    7.1   0.0    0.0081         5       2      34 .]     395     427 ..     394     427 .. 0.94
   6 !    8.2   0.0    0.0036       2.2       2      30 ..     429     457 ..     428     461 .. 0.91
   7 ?    5.0   0.1     0.038        23      12      30 ..     480     498 ..     477     499 .. 0.88
   8 !   21.5   0.0   2.3e-07   0.00014       6      33 ..     515     542 ..     511     543 .. 0.91
   9 ?    1.9   0.1      0.36   2.3e+02       1      30 [.     546     575 ..     546     578 .. 0.83
  10 !   12.5   0.1   0.00017       0.1       1      33 [.     585     617 ..     585     618 .. 0.93
  11 !   13.1   0.0    0.0001     0.065       4      33 ..     622     651 ..     621     651 .. 0.90
  12 !   29.6   0.2   6.5e-10     4e-07       1      30 [.     653     682 ..     653     685 .. 0.96
  13 !   27.7   0.1   2.5e-09   1.6e-06       7      33 ..     701     727 ..     697     728 .. 0.94
  14 !   31.3   0.3   1.9e-10   1.2e-07       1      33 [.     734     766 ..     734     767 .. 0.96
  15 !    7.7   0.0    0.0053       3.3       2      20 ..     769     787 ..     768     792 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
                                      TT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1 14 lgkydeAleyyekALelnPnn 34
                                      +g+ +eA+ ++++ L+ +P+n
  gi|330509114|ref|YP_004385542.1|  1 MGRNEEAISAFDEGLKTDPQN 21
                                      7999***************97 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.17
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALel 30
                                      a a+  +G+a+  +g   eA +  +kA el
  gi|330509114|ref|YP_004385542.1| 22 ASAWHHRGMALAGMGHGAEANQSIQKAMEL 51
                                      689************988888888877776 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0063
                                      T-HHHHHHHHHHHHHHSTT CS
                             TPR_1 15 gkydeAleyyekALelnPn 33
                                      gk +eAle+y ++ eln +
  gi|330509114|ref|YP_004385542.1| 77 GKSEEALEAYGRVAELNSS 95
                                      789**************87 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.008
                                       HHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1  10 ayfklgkydeAleyyekALelnP 32 
                                       ++  +g+y++ +e +++A  l P
  gi|330509114|ref|YP_004385542.1| 107 ILAAQGRYNQSVESFSRAMALVP 129
                                       6789**************98866 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.0081
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       + +y +G  +f++  ++e + + e++++l+P+n
  gi|330509114|ref|YP_004385542.1| 395 DDWYKKGTELFENDSLEESVLAMERVIQLDPEN 427
                                       56*****************************97 PP

  == domain 6  score: 8.2 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                        a+  ++ ++  +g+  e  ++yekAL l
  gi|330509114|ref|YP_004385542.1| 429 SAWLSIAITLGIMGNGSESSKAYEKALNL 457
                                       59*************************77 PP

  == domain 7  score: 5.0 bits;  conditional E-value: 0.038
                                       HHTT-HHHHHHHHHHHHHH CS
                             TPR_1  12 fklgkydeAleyyekALel 30 
                                         lg+ +e l++ ekALe+
  gi|330509114|ref|YP_004385542.1| 480 IGLGRQEESLDAIEKALEI 498
                                       568999***********98 PP

  == domain 8  score: 21.5 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   6 nlGnayfklgkydeAleyyekALelnPn 33 
                                        ++n+++  g+ deAl++yek++eln++
  gi|330509114|ref|YP_004385542.1| 515 SKANVLYGIGRSDEALQAYEKVIELNHT 542
                                       689***********************86 PP

  == domain 9  score: 1.9 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a+al  +G+ +  +g+yde  e +++A+ l
  gi|330509114|ref|YP_004385542.1| 546 ADALLIKGYDFAIKGNYDEFKETFNQAIGL 575
                                       7899999***********977777777766 PP

  == domain 10  score: 12.5 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a++++  G a+ +lgk +eA e++ek  +l P 
  gi|330509114|ref|YP_004385542.1| 585 ARTWNSAGFALAELGKEEEAFEAFEKYAQLSPG 617
                                       789***********************9999986 PP

  == domain 11  score: 13.1 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPn 33 
                                       +  +G +  +lg+y+  +e+y++AL+++P+
  gi|330509114|ref|YP_004385542.1| 622 WRMKGDMASELGRYNVSIEAYDQALRIDPK 651
                                       6668899999*******************6 PP

  == domain 12  score: 29.6 bits;  conditional E-value: 6.5e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a+++y +Gna+ k+ ++++Al+++ekA+e+
  gi|330509114|ref|YP_004385542.1| 653 AEVWYKKGNALAKMDNHNDALKAFEKAVEI 682
                                       89**************************98 PP

  == domain 13  score: 27.7 bits;  conditional E-value: 2.5e-09
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnPn 33 
                                       +G+a+ kl++ydeA+e+ ++ALe+ P+
  gi|330509114|ref|YP_004385542.1| 701 KGYALIKLNRYDEAIEALDRALEIAPS 727
                                       79************************7 PP

  == domain 14  score: 31.3 bits;  conditional E-value: 1.9e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+a++++G +++ lgk ++Ale+y+k +e nP 
  gi|330509114|ref|YP_004385542.1| 734 AEAWNGKGDILLALGKNEDALEAYNKSIEFNPA 766
                                       89******************************5 PP

  == domain 15  score: 7.7 bits;  conditional E-value: 0.0053
                                       HHHHHHHHHHHHTT-HHHH CS
                             TPR_1   2 kalynlGnayfklgkydeA 20 
                                       +a+ ++G+a   lg++ eA
  gi|330509114|ref|YP_004385542.1| 769 RAWHGKGLAQSALGQFSEA 787
                                       79****************9 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.1e-07   0.00013       8      42 .]       2      36 ..       1      36 [. 0.96
   2 ?    5.7   0.0     0.019        12       8      26 ..      77      95 ..      77      98 .. 0.89
   3 !   12.8   0.0   0.00011     0.069       2      27 ..     106     131 ..     106     132 .. 0.95
   4 !    9.3   0.0    0.0014      0.89       1      37 [.     401     437 ..     401     442 .. 0.88
   5 ?    1.5   0.2      0.39   2.4e+02      11      23 ..     445     457 ..     440     474 .. 0.78
   6 ?    2.0   0.1      0.28   1.7e+02      10      41 ..     492     523 ..     477     524 .. 0.60
   7 !   12.0   0.1   0.00021      0.13       2      25 ..     518     541 ..     517     548 .. 0.91
   8 ?    0.4   0.1      0.86   5.3e+02       1      27 [.     553     579 ..     553     599 .. 0.71
   9 ?   -1.2   0.1       2.7   1.7e+03       3      19 ..     594     610 ..     592     616 .. 0.79
  10 !   34.1   0.1   2.6e-11   1.6e-08       1      41 [.     626     666 ..     626     667 .. 0.92
  11 !    6.6   0.1      0.01       6.2       1      24 [.     660     683 ..     660     685 .. 0.95
  12 !   20.6   0.0   4.3e-07   0.00027       1      27 [.     702     728 ..     702     731 .. 0.95
  13 !   29.4   0.3   7.7e-10   4.8e-07       1      42 []     741     782 ..     741     782 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.1e-07
                            TPR_11  8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      G++eeAi a+ + lk dP+na+a++++G a++ +G
  gi|330509114|ref|YP_004385542.1|  2 GRNEEAISAFDEGLKTDPQNASAWHHRGMALAGMG 36
                                      9****************************999887 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.019
                            TPR_11  8 GkyeeAieaYkkAlkldPd 26
                                      Gk eeA+eaY +  +l+++
  gi|330509114|ref|YP_004385542.1| 77 GKSEEALEAYGRVAELNSS 95
                                      788*************987 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00011
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdn 27 
                                       d++ +qG+y++++e++++A +l P n
  gi|330509114|ref|YP_004385542.1| 106 DILAAQGRYNQSVESFSRAMALVPAN 131
                                       7899*******************987 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0014
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       G +++e   +ee++ a ++ ++ldP+n +a++ ++ +
  gi|330509114|ref|YP_004385542.1| 401 GTELFENDSLEESVLAMERVIQLDPENSSAWLSIAIT 437
                                       567899999**********************998866 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.39
                            TPR_11  11 eeAieaYkkAlkl 23 
                                        e+ +aY+kAl+l
  gi|330509114|ref|YP_004385542.1| 445 SESSKAYEKALNL 457
                                       5778899999987 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.28
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       +e+A+e ++   + +P++ ea++  ++++y  
  gi|330509114|ref|YP_004385542.1| 492 IEKALEILNLSTERNPKDGEAWWSKANVLYGI 523
                                       34444444444455788888888888888765 PP

  == domain 7  score: 12.0 bits;  conditional E-value: 0.00021
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldP 25 
                                       +++y  G+ +eA++aY+k ++l+ 
  gi|330509114|ref|YP_004385542.1| 518 NVLYGIGRSDEALQAYEKVIELNH 541
                                       889999****************96 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 0.86
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdn 27 
                                       G+ +  +G+y+e  e +++A+ l P +
  gi|330509114|ref|YP_004385542.1| 553 GYDFAIKGNYDEFKETFNQAIGLIPAS 579
                                       667788899999888888888776654 PP

  == domain 9  score: -1.2 bits;  conditional E-value: 2.7
                            TPR_11   3 ayyeqGkyeeAieaYkk 19 
                                       a+ e+Gk eeA ea++k
  gi|330509114|ref|YP_004385542.1| 594 ALAELGKEEEAFEAFEK 610
                                       68899******999887 PP

  == domain 10  score: 34.1 bits;  conditional E-value: 2.6e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       Gd+  e+G+y+ +ieaY +Al++dP+ ae++y+ G+a++k+
  gi|330509114|ref|YP_004385542.1| 626 GDMASELGRYNVSIEAYDQALRIDPKWAEVWYKKGNALAKM 666
                                       5666689*******************************997 PP

  == domain 11  score: 6.6 bits;  conditional E-value: 0.01
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkld 24 
                                       G+a+ +  + ++A++a++kA++++
  gi|330509114|ref|YP_004385542.1| 660 GNALAKMDNHNDALKAFEKAVEIS 683
                                       99********************96 PP

  == domain 12  score: 20.6 bits;  conditional E-value: 4.3e-07
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdn 27 
                                       G+a+ ++++y+eAiea+ +Al++ P++
  gi|330509114|ref|YP_004385542.1| 702 GYALIKLNRYDEAIEALDRALEIAPSS 728
                                       89*********************9986 PP

  == domain 13  score: 29.4 bits;  conditional E-value: 7.7e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       Gd++ ++Gk+e+A+eaY+k ++++P + +a+++ Gla+ ++G
  gi|330509114|ref|YP_004385542.1| 741 GDILLALGKNEDALEAYNKSIEFNPAFGRAWHGKGLAQSALG 782
                                       9************************************99887 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00091      0.56      11      46 ..       2      34 ..       1      41 [. 0.89
   2 ?    4.6   0.2     0.083        51       4      42 ..      36      71 ..      33      71 .. 0.89
   3 !   14.7   0.4     6e-05     0.037      11      60 ..      77     124 ..      76     131 .. 0.86
   4 ?    3.5   0.0      0.18   1.1e+02       1      41 [.     398     435 ..     398     438 .. 0.92
   5 !   16.4   0.2   1.7e-05      0.01      13      62 ..     451     497 ..     446     502 .. 0.93
   6 !   13.9   0.0   0.00011     0.066      25      61 ..     504     537 ..     501     540 .. 0.89
   7 !   17.7   0.0     7e-06    0.0043       3      65 ..     516     577 ..     515     582 .. 0.89
   8 !    8.1   0.5    0.0066       4.1      33      67 ..     584     618 ..     578     619 .. 0.88
   9 !   20.6   0.4   8.6e-07   0.00053       7      65 ..     595     650 ..     589     651 .. 0.88
  10 !   19.8   0.1   1.5e-06    0.0009       4      63 ..     626     682 ..     623     685 .. 0.91
  11 !   36.0   0.1   1.4e-11   8.3e-09       4      65 ..     702     765 ..     701     768 .. 0.92
  12 !   15.2   0.0   4.2e-05     0.026       3      53 ..     740     787 ..     738     794 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00091
                            TPR_16 11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalr 46
                                      g+ ++A+ a+++ lk d   P++a A+ ++g a++ 
  gi|330509114|ref|YP_004385542.1|  2 GRNEEAISAFDEGLKTD---PQNASAWHHRGMALAG 34
                                      999**************...************9985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.083
                            TPR_16  4 araalragdyddAaaaleaalkrdpssPdaaeAllllgd 42
                                      ++ a +++  ++A ++ ++ l  +   P++ eAl+l+++
  gi|330509114|ref|YP_004385542.1| 36 GHGAEANQSIQKAMELIDQRLQEN---PEDQEALWLRAE 71
                                      67778888899*************...*********995 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 6e-05
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                       g+ ++A++a+ ++ ++++s+  a eA+    d++++qgr+   ++ + +a
  gi|330509114|ref|YP_004385542.1|  77 GKSEEALEAYGRVAELNSSH--ALEAWIRESDILAAQGRYNQSVESFSRA 124
                                       899**************755..88****************8888777776 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.18
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllg 41 
                                       ++++++++++   ++ + a e+++ +d   P++  A+l  +
  gi|330509114|ref|YP_004385542.1| 398 YKKGTELFENDSLEESVLAMERVIQLD---PENSSAWLSIA 435
                                       78999**********************...**999**9766 PP

  == domain 5  score: 16.4 bits;  conditional E-value: 1.7e-05
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       y++A+++ +  lk++   P++a+A+ ++ da+  +gr +e ++++++al+
  gi|330509114|ref|YP_004385542.1| 451 YEKALNLIDNDLKKN---PQDARAWEAKSDALIGLGRQEESLDAIEKALE 497
                                       99*************...**************************999986 PP

  == domain 6  score: 13.9 bits;  conditional E-value: 0.00011
                            TPR_16  25 krdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       +r+   P + eA++ ++++++  gr +eA+++y++ +
  gi|330509114|ref|YP_004385542.1| 504 ERN---PKDGEAWWSKANVLYGIGRSDEALQAYEKVI 537
                                       567...99***********************999865 PP

  == domain 7  score: 17.7 bits;  conditional E-value: 7e-06
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +a+ ++  g+ d+A+ a+e +++++  +P+ a+All +g  ++ +g+++e  + ++ a++  p
  gi|330509114|ref|YP_004385542.1| 516 KANVLYGIGRSDEALQAYEKVIELN-HTPRLADALLIKGYDFAIKGNYDEFKETFNQAIGLIP 577
                                       6999*********************.999*******************998777777766555 PP

  == domain 8  score: 8.1 bits;  conditional E-value: 0.0066
                            TPR_16  33 aaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                        a+ ++  g a++++g  +eA ++++++++ +p++
  gi|330509114|ref|YP_004385542.1| 584 LARTWNSAGFALAELGKEEEAFEAFEKYAQLSPGD 618
                                       56778999*************************97 PP

  == domain 9  score: 20.6 bits;  conditional E-value: 8.6e-07
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       ++++g+ ++A +a+e +  +    P +++++  +gd+a ++gr+   +++y+ alr +p
  gi|330509114|ref|YP_004385542.1| 595 LAELGKEEEAFEAFEKYAQLS---PGDRHSWRMKGDMASELGRYNVSIEAYDQALRIDP 650
                                       677777888888888888888...********************************999 PP

  == domain 10  score: 19.8 bits;  conditional E-value: 1.5e-06
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       ++ a ++g+y   ++a+++al+ d   P  ae ++ +g+a+++  ++ +A+ ++++a++ 
  gi|330509114|ref|YP_004385542.1| 626 GDMASELGRYNVSIEAYDQALRID---PKWAEVWYKKGNALAKMDNHNDALKAFEKAVEI 682
                                       5557789*****************...************************999999875 PP

  == domain 11  score: 36.0 bits;  conditional E-value: 1.4e-11
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       ++a++++++yd+A++al++al+ +   P       aeA++++gd++l++g  ++A+++y++ ++  p
  gi|330509114|ref|YP_004385542.1| 702 GYALIKLNRYDEAIEALDRALEIA---PSsvpvfPAEAWNGKGDILLALGKNEDALEAYNKSIEFNP 765
                                       889*********************...7767789**********************99999877665 PP

  == domain 12  score: 15.2 bits;  conditional E-value: 4.2e-05
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeA 53 
                                       +++++l++g+ +dA++a++  ++ +   P+  +A+ ++g+a  ++g + eA
  gi|330509114|ref|YP_004385542.1| 740 KGDILLALGKNEDALEAYNKSIEFN---PAFGRAWHGKGLAQSALGQFSEA 787
                                       699**********************...******************99998 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.8   2.3e+03      59      72 ..       2      15 ..       1      19 [. 0.55
   2 !   13.8   2.1   8.9e-05     0.055       3      74 ..      22      92 ..      20      95 .. 0.93
   3 !    7.7   0.0    0.0071       4.4      10      33 ..     105     128 ..      96     135 .. 0.79
   4 ?   -2.4   0.0       9.8     6e+03      59      74 ..     247     262 ..     245     263 .. 0.82
   5 !   23.3   0.1   9.6e-08   5.9e-05       4      75 ..     429     499 ..     426     501 .. 0.92
   6 !   10.3   0.0    0.0011      0.67       8      32 ..     515     539 ..     502     542 .. 0.58
   7 !   16.9   0.1   9.3e-06    0.0058      10      73 ..     553     613 ..     544     617 .. 0.88
   8 !    9.5   0.0    0.0019       1.2      47      76 ..     621     650 ..     615     651 .. 0.83
   9 !   31.9   0.3     2e-10   1.2e-07       4      76 ..     654     726 ..     653     727 .. 0.93
  10 !   29.0   0.1   1.5e-09   9.6e-07      10      73 ..     702     762 ..     697     766 .. 0.91
  11 !   14.5   0.1   5.4e-05     0.034       3      64 ..     734     787 ..     732     797 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.8
                            TPR_12 59 gryeeAlelleeal 72
                                      gr eeA++++ e l
  gi|330509114|ref|YP_004385542.1|  2 GRNEEAISAFDEGL 15
                                      55555555555554 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.9e-05
                            TPR_12  3 atalnnlaavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74
                                      a+a+++++++l+ +g  +eA +  +ka+e++ +rl   ++p+  ++l   ++  +++g+ eeAle++ ++ ++
  gi|330509114|ref|YP_004385542.1| 22 ASAWHHRGMALAGMGHGAEANQSIQKAMELIdQRL--QENPEDQEALWLRAEEMDLFGKSEEALEAYGRVAEL 92
                                      789*9**************************9999..77999999**********************998775 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0071
                            TPR_12  10 aavlrrlgrydeAlellekaleia 33 
                                        ++l+++gry ++ e + +a++++
  gi|330509114|ref|YP_004385542.1| 105 SDILAAQGRYNQSVESFSRAMALV 128
                                       567889999999999999998875 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 9.8
                            TPR_12  59 gryeeAlelleealai 74 
                                       ++++eA++l + +l+i
  gi|330509114|ref|YP_004385542.1| 247 DNLKEAVSLQNWSLEI 262
                                       5789999999999987 PP

  == domain 5  score: 23.3 bits;  conditional E-value: 9.6e-08
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +a+  +a +l  +g+  e+ + +ekal+++ + l +++p+ a++  + ++++  lgr+ee l++ e+al+i+
  gi|330509114|ref|YP_004385542.1| 429 SAWLSIAITLGIMGNGSESSKAYEKALNLIDNDL-KKNPQDARAWEAKSDALIGLGRQEESLDAIEKALEIL 499
                                       567789999*********************5555.89*********************************96 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.0011
                            TPR_12   8 nlaavlrrlgrydeAlellekalei 32 
                                         a+vl+  gr deAl+ +ek++e+
  gi|330509114|ref|YP_004385542.1| 515 SKANVLYGIGRSDEALQAYEKVIEL 539
                                       4455555555555555555555544 PP

  == domain 7  score: 16.9 bits;  conditional E-value: 9.3e-06
                            TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       +   +  g+yde  e +++a+ ++   +  d + +a+t +  g ++ +lg+ eeA e++e+  +
  gi|330509114|ref|YP_004385542.1| 553 GYDFAIKGNYDEFKETFNQAIGLI---PASDTAKLARTWNSAGFALAELGKEEEAFEAFEKYAQ 613
                                       5556678*****************...889******************************9766 PP

  == domain 8  score: 9.5 bits;  conditional E-value: 0.0019
                            TPR_12  47 tlrnLgrlyralgryeeAlelleealaiae 76 
                                       + r  g++ ++lgry   +e++ +al+i++
  gi|330509114|ref|YP_004385542.1| 621 SWRMKGDMASELGRYNVSIEAYDQALRIDP 650
                                       55667999999**************99976 PP

  == domain 9  score: 31.9 bits;  conditional E-value: 2e-10
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        ++++ +++l+++ ++ +Al+ +eka+ei  ++  +d  +++ + +  g ++ +l+ry+eA+e+l +al+ia+
  gi|330509114|ref|YP_004385542.1| 654 EVWYKKGNALAKMDNHNDALKAFEKAVEISDEVIQKDAGNASGICIIKGYALIKLNRYDEAIEALDRALEIAP 726
                                       67889*************************99999999999999999999999******************97 PP

  == domain 10  score: 29.0 bits;  conditional E-value: 1.5e-09
                            TPR_12  10 aavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       + +l +l rydeA+e l++aleia +++  p     a++ ++ g++++alg+ e+Ale+++++++
  gi|330509114|ref|YP_004385542.1| 702 GYALIKLNRYDEAIEALDRALEIApSSV--P--VFPAEAWNGKGDILLALGKNEDALEAYNKSIE 762
                                       677889******************7777..6..589***************************98 PP

  == domain 11  score: 14.5 bits;  conditional E-value: 5.4e-05
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeA 64 
                                       a a+n  +++l++lg+ ++Ale ++k++e    ++G        + ++ g +++alg++ eA
  gi|330509114|ref|YP_004385542.1| 734 AEAWNGKGDILLALGKNEDALEAYNKSIEFN-PAFGR-------AWHGKGLAQSALGQFSEA 787
                                       6789889999999999999999999997766.44444.......445555555555555555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00025      0.15      15      41 ..       2      28 ..       1      31 [. 0.92
   2 !   11.5   0.3   0.00072      0.45       3      41 ..      31      69 ..      30      71 .. 0.84
   3 ?    4.3   0.5      0.14        87       2      40 ..      64     103 ..      64     107 .. 0.86
   4 ?    3.9   0.1       0.2   1.2e+02       2      34 ..      99     131 ..      98     134 .. 0.88
   5 !    8.1   0.0    0.0089       5.5       3      39 ..     396     432 ..     394     437 .. 0.90
   6 ?    4.5   0.3      0.13        80       4      41 ..     431     475 ..     430     478 .. 0.67
   7 !    9.2   0.0     0.004       2.4       3      38 ..     478     513 ..     476     519 .. 0.90
   8 !   10.6   0.1    0.0014      0.86       2      37 ..     511     546 ..     511     554 .. 0.80
   9 ?   -0.0   0.0       3.5   2.2e+03       3      39 ..     548     584 ..     546     587 .. 0.80
  10 !   12.0   0.1   0.00048       0.3       4      43 ..     588     627 ..     585     628 .. 0.88
  11 !   11.3   0.0   0.00083      0.51       4      41 ..     622     659 ..     619     662 .. 0.90
  12 !    9.1   0.0    0.0041       2.5       2      30 ..     654     682 ..     653     688 .. 0.92
  13 !   15.4   0.0     4e-05     0.025       8      34 ..     702     728 ..     700     732 .. 0.90
  14 !   16.0   0.1   2.6e-05     0.016       2      40 ..     735     773 ..     734     787 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00025
                            TPR_14 15 GdpdeAiallrralalaPddaeawlll 41
                                      G+ +eAi ++++ l+++P++a aw + 
  gi|330509114|ref|YP_004385542.1|  2 GRNEEAISAFDEGLKTDPQNASAWHHR 28
                                      899*********************875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00072
                            TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawlll 41
                                      al+ +++  +a++  ++A++l +++l+ +P+d+ea+ l 
  gi|330509114|ref|YP_004385542.1| 31 ALAGMGHGAEANQSIQKAMELIDQRLQENPEDQEALWLR 69
                                      56778899999*******************998766444 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.14
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPdda.eawll 40 
                                       eal+++ae +   G+ +eA++++ r+ +l+ ++a eaw++
  gi|330509114|ref|YP_004385542.1|  64 EALWLRAEEMDLFGKSEEALEAYGRVAELNSSHAlEAWIR 103
                                       5788888888999***************998876589976 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.2
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPdd 34 
                                       ea+ +  ++l+a+G++ ++++ + ra al P++
  gi|330509114|ref|YP_004385542.1|  99 EAWIRESDILAAQGRYNQSVESFSRAMALVPAN 131
                                       688888899*****************9988876 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0089
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                        +++ +  l++++ ++e++ + +r+++l+P++  awl
  gi|330509114|ref|YP_004385542.1| 396 DWYKKGTELFENDSLEESVLAMERVIQLDPENSSAWL 432
                                       68888999999*************************8 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.13
                            TPR_14   4 llalaeallalGdpdeAiallrrala.......laPddaeawlll 41 
                                       +l +a  l   G+  e+ +++++al        ++P+da+aw + 
  gi|330509114|ref|YP_004385542.1| 431 WLSIAITLGIMGNGSESSKAYEKALNlidndlkKNPQDARAWEAK 475
                                       6666666666666666677777775555555559********876 PP

  == domain 7  score: 9.2 bits;  conditional E-value: 0.004
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       al  l++ ++ l+  ++A+++l+   +++P+d eaw
  gi|330509114|ref|YP_004385542.1| 478 ALIGLGRQEESLDAIEKALEILNLSTERNPKDGEAW 513
                                       67779999999***********************99 PP

  == domain 8  score: 10.6 bits;  conditional E-value: 0.0014
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaea 37 
                                       ea++  a +l+  G+ deA+++++++++l+ +++ a
  gi|330509114|ref|YP_004385542.1| 511 EAWWSKANVLYGIGRSDEALQAYEKVIELNHTPRLA 546
                                       699999**********************86444333 PP

  == domain 9  score: -0.0 bits;  conditional E-value: 3.5
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       all  +  ++  G++de  + +++a+ l P++++a l
  gi|330509114|ref|YP_004385542.1| 548 ALLIKGYDFAIKGNYDEFKETFNQAIGLIPASDTAKL 584
                                       555556667788**************99999998876 PP

  == domain 10  score: 12.0 bits;  conditional E-value: 0.00048
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +  ++ al++lG+ +eA ++++++ +l P+d+  w++ ++
  gi|330509114|ref|YP_004385542.1| 588 WNSAGFALAELGKEEEAFEAFEKYAQLSPGDRHSWRMKGD 627
                                       55677899***********************999999875 PP

  == domain 11  score: 11.3 bits;  conditional E-value: 0.00083
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       +++ ++   +lG++  +i+++++al+ +P+ ae+w+  
  gi|330509114|ref|YP_004385542.1| 622 WRMKGDMASELGRYNVSIEAYDQALRIDPKWAEVWYKK 659
                                       8888999999*************************876 PP

  == domain 12  score: 9.1 bits;  conditional E-value: 0.0041
                            TPR_14   2 eallalaeallalGdpdeAiallrralal 30 
                                       e++++ + al+  +++ +A++++++a++ 
  gi|330509114|ref|YP_004385542.1| 654 EVWYKKGNALAKMDNHNDALKAFEKAVEI 682
                                       89************************986 PP

  == domain 13  score: 15.4 bits;  conditional E-value: 4e-05
                            TPR_14   8 aeallalGdpdeAiallrralalaPdd 34 
                                       + al  l ++deAi++l+ral+ aP++
  gi|330509114|ref|YP_004385542.1| 702 GYALIKLNRYDEAIEALDRALEIAPSS 728
                                       578999*******************87 PP

  == domain 14  score: 16.0 bits;  conditional E-value: 2.6e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       ea+   +++llalG+ ++A++++++ ++ +P++ +aw  
  gi|330509114|ref|YP_004385542.1| 735 EAWNGKGDILLALGKNEDALEAYNKSIEFNPAFGRAWHG 773
                                       78888899*****************************54 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00058      0.36       2      28 ..      11      43 ..      10      50 .. 0.79
   2 !   10.5   0.0     0.001      0.64       3      28 ..     418     443 ..     416     450 .. 0.88
   3 ?    2.5   0.0      0.37   2.3e+02       6      30 ..     462     486 ..     450     493 .. 0.81
   4 !   10.6   0.0   0.00095      0.59       6      34 .]     503     531 ..     499     531 .. 0.95
   5 ?    2.8   0.0       0.3   1.9e+02       1      21 [.     532     554 ..     532     564 .. 0.73
   6 ?   -0.3   0.0       2.9   1.8e+03      13      32 ..     585     604 ..     581     606 .. 0.86
   7 !   22.1   0.3   2.1e-07   0.00013       1      33 [.     641     673 ..     641     674 .. 0.93
   8 ?    0.1   0.0       2.2   1.4e+03      20      34 .]     702     716 ..     701     716 .. 0.90
   9 !   11.0   0.0   0.00071      0.44       3      34 .]     719     755 ..     717     755 .. 0.94
  10 !   13.2   0.0   0.00014     0.088       1      32 [.     756     787 ..     756     788 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00058
                            TPR_17  2 ylkaleldPnnadaynnLAelll......knGd 28
                                      + + l+ dP na a++ ++ +l+      ++++
  gi|330509114|ref|YP_004385542.1| 11 FDEGLKTDPQNASAWHHRGMALAgmghgaEANQ 43
                                      77899*****************96655554444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.001
                            TPR_17   3 lkaleldPnnadaynnLAelllknGd 28 
                                       +++++ldP n+ a+   A +l   G+
  gi|330509114|ref|YP_004385542.1| 418 ERVIQLDPENSSAWLSIAITLGIMGN 443
                                       89*****************9987764 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.37
                            TPR_17   6 leldPnnadaynnLAelllknGdlm 30 
                                       l+++P +a a+  +  +l  +G+ +
  gi|330509114|ref|YP_004385542.1| 462 LKKNPQDARAWEAKSDALIGLGRQE 486
                                       7899*******99888888777665 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00095
                            TPR_17   6 leldPnnadaynnLAelllknGdlmtArq 34 
                                        e++P++ +a+  +A++l+ +G++++A+q
  gi|330509114|ref|YP_004385542.1| 503 TERNPKDGEAWWSKANVLYGIGRSDEALQ 531
                                       69*************************97 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.3
                            TPR_17   1 lylkaleld..PnnadaynnLAe 21 
                                       +y+k++el+  P  ada+  +++
  gi|330509114|ref|YP_004385542.1| 532 AYEKVIELNhtPRLADALLIKGY 554
                                       5*******966778888876665 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 2.9
                            TPR_17  13 adaynnLAelllknGdlmtA 32 
                                       a  +n  + +l+++G+ ++A
  gi|330509114|ref|YP_004385542.1| 585 ARTWNSAGFALAELGKEEEA 604
                                       6789999********99988 PP

  == domain 7  score: 22.1 bits;  conditional E-value: 2.1e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y +al++dP+ a++++ ++++l+k  ++ +A+
  gi|330509114|ref|YP_004385542.1| 641 AYDQALRIDPKWAEVWYKKGNALAKMDNHNDAL 673
                                       59***********************99999987 PP

  == domain 8  score: 0.1 bits;  conditional E-value: 2.2
                            TPR_17  20 AelllknGdlmtArq 34 
                                       +++l k++++++A++
  gi|330509114|ref|YP_004385542.1| 702 GYALIKLNRYDEAIE 716
                                       89999********86 PP

  == domain 9  score: 11.0 bits;  conditional E-value: 0.00071
                            TPR_17   3 lkaleldPnn.....adaynnLAelllknGdlmtArq 34 
                                        +ale+ P++     a+a+n ++ +ll +G+ ++A++
  gi|330509114|ref|YP_004385542.1| 719 DRALEIAPSSvpvfpAEAWNGKGDILLALGKNEDALE 755
                                       79*******************************9975 PP

  == domain 10  score: 13.2 bits;  conditional E-value: 0.00014
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y k++e +P    a++ ++ +++ +G++ +A
  gi|330509114|ref|YP_004385542.1| 756 AYNKSIEFNPAFGRAWHGKGLAQSALGQFSEA 787
                                       59**************************9877 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   1.4e-05    0.0088      10      69 ..       3      69 ..       2      71 .. 0.86
   2 !    7.5   0.0    0.0073       4.5      11      61 ..      79     130 ..      77     137 .. 0.84
   3 ?    0.6   0.0       1.1   6.5e+02      27      63 ..     392     428 ..     389     432 .. 0.69
   4 ?    5.8   0.0     0.024        15       9      66 ..     408     470 ..     402     476 .. 0.79
   5 !    7.1   0.0    0.0095       5.8       8      56 ..     448     496 ..     442     497 .. 0.93
   6 !   16.0   0.0   1.6e-05      0.01      10      67 ..     491     550 ..     487     553 .. 0.86
   7 !   12.2   0.0   0.00024      0.15      30      65 ..     586     621 ..     582     629 .. 0.86
   8 !   15.1   0.0     3e-05     0.018      10      60 ..     634     684 ..     626     695 .. 0.88
   9 !    8.0   0.0     0.005       3.1      36      61 ..     702     727 ..     701     731 .. 0.84
  10 ?    5.9   0.0     0.023        14       6      48 ..     745     787 ..     742     791 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-05
                             TPR_9 10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl.......alapdapdaeair 69
                                      ++e+a+ + +  l  +P+ ++ +  RG++la +G+ ++A +  + ++       + +p++++a  +r
  gi|330509114|ref|YP_004385542.1|  3 RNEEAISAFDEGLKTDPQNASAWHHRGMALAGMGHGAEANQSIQKAMelidqrlQENPEDQEALWLR 69
                                      688999999999***********************************77777666677777776655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0073
                             TPR_9  11 weralavverllllaPddp.eerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       +e+al+++ r+  l++ ++ e +     +la +G++++ ++ + +++al p+
  gi|330509114|ref|YP_004385542.1|  79 SEEALEAYGRVAELNSSHAlEAWIRESDILAAQGRYNQSVESFSRAMALVPA 130
                                       789***********76665156777899*******************99986 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.1
                             TPR_9  27 ddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       +++++++  G  l++ + l++ + ++e+ ++l+p++ 
  gi|330509114|ref|YP_004385542.1| 392 NTADDWYKKGTELFENDSLEESVLAMERVIQLDPENS 428
                                       5667777777777777777777777777777777654 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.024
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl.....alapdapdae 66 
                                       +  e+   + er+++l+P+  + ++  ++ l  +G+ s+  ++ e +l     +l  +++da+
  gi|330509114|ref|YP_004385542.1| 408 DSLEESVLAMERVIQLDPENSSAWLSIAITLGIMGNGSESSKAYEKALnlidnDLKKNPQDAR 470
                                       5556666689*******************************9999999777774444555544 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.0095
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl 56 
                                       ++ +e+al  ++  l  +P+d++ +     +l  lG+ ++ l++ e +l
  gi|330509114|ref|YP_004385542.1| 448 SKAYEKALNLIDNDLKKNPQDARAWEAKSDALIGLGRQEESLDAIEKAL 496
                                       6789***************************************999887 PP

  == domain 6  score: 16.0 bits;  conditional E-value: 1.6e-05
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl..alapdapdaea 67 
                                         e+al+++++    +P+d e ++  + +l+  G+  +Al++ e  +   ++p  +da +
  gi|330509114|ref|YP_004385542.1| 491 AIEKALEILNLSTERNPKDGEAWWSKANVLYGIGRSDEALQAYEKVIelNHTPRLADALL 550
                                       579********************************************4445555555555 PP

  == domain 7  score: 12.2 bits;  conditional E-value: 0.00024
                             TPR_9  30 eerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       + +   G++la+lG  ++A +++e y++l+p ++  
  gi|330509114|ref|YP_004385542.1| 586 RTWNSAGFALAELGKEEEAFEAFEKYAQLSPGDRHS 621
                                       667789*************************77665 PP

  == domain 8  score: 15.1 bits;  conditional E-value: 3e-05
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       ++ + +++++  l ++P+ +e ++  G +la++++ + Al+++e ++++++
  gi|330509114|ref|YP_004385542.1| 634 RYNVSIEAYDQALRIDPKWAEVWYKKGNALAKMDNHNDALKAFEKAVEISD 684
                                       66777899***************************************9987 PP

  == domain 9  score: 8.0 bits;  conditional E-value: 0.005
                             TPR_9  36 GlllaqlGclsaAladLeaylalapd 61 
                                       G +l +l+++ +A+++L+++l++ap+
  gi|330509114|ref|YP_004385542.1| 702 GYALIKLNRYDEAIEALDRALEIAPS 727
                                       67888999999999999999999996 PP

  == domain 10  score: 5.9 bits;  conditional E-value: 0.023
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaA 48 
                                       +   ++e al++++  + ++P   + +   Gl++  lG++s+A
  gi|330509114|ref|YP_004385542.1| 745 LALGKNEDALEAYNKSIEFNPAFGRAWHGKGLAQSALGQFSEA 787
                                       6667899**********************************98 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00064      0.39       4      53 ..       1      50 [.       1      51 [. 0.94
   2 ?    6.0   0.6     0.028        17       3      32 ..      41      70 ..      39      72 .. 0.88
   3 !    9.6   0.1     0.002       1.2       5      54 ..      77     127 ..      76     136 .. 0.88
   4 ?    5.7   0.1     0.034        21       2      60 ..     405     470 ..     404     477 .. 0.61
   5 ?    6.6   1.0     0.018        11       5      53 ..     449     497 ..     445     500 .. 0.88
   6 !   14.9   0.1   4.7e-05     0.029       8      64 ..     493     548 ..     489     552 .. 0.90
   7 !   11.5   0.0   0.00054      0.34       5      64 ..     599     658 ..     595     662 .. 0.92
   8 !   23.9   0.2   7.1e-08   4.4e-05       2      57 ..     664     727 ..     663     732 .. 0.81
   9 !   11.9   0.1    0.0004      0.25       1      44 [.     744     787 ..     744     796 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00064
                            TPR_19  4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53
                                      +g+ +eA++++ + l+ dp+na a+     al  +g+ +eA + +++++e
  gi|330509114|ref|YP_004385542.1|  1 MGRNEEAISAFDEGLKTDPQNASAWHHRGMALAGMGHGAEANQSIQKAME 50
                                      68999*************************************99998876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.028
                            TPR_19  3 aegdyaeAlalleqalqedpknaearllLA 32
                                      a++  + A++l  q lqe+p+++ea+ l A
  gi|330509114|ref|YP_004385542.1| 41 ANQSIQKAMELIDQRLQENPEDQEALWLRA 70
                                      6789999**************999998776 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.002
                            TPR_19   5 gdyaeAlalleqalqe.dpknaearllLAeallalgqldeAealLdalpee 54 
                                       g+ +eAl+++ ++ +  + + +ea+++  ++l a+g++++  +  +++++ 
  gi|330509114|ref|YP_004385542.1|  77 GKSEEALEAYGRVAELnSSHALEAWIRESDILAAQGRYNQSVESFSRAMAL 127
                                       6789********99887778*********************9999998875 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.034
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeal.......lalgqldeAealLdalpeedpddar 60 
                                       +++  ++e + ++e+++q dp+n+ a+l  A+ l        +++ +++A +l+d  ++++p+dar
  gi|330509114|ref|YP_004385542.1| 405 FENDSLEESVLAMERVIQLDPENSSAWLSIAITLgimgngsESSKAYEKALNLIDNDLKKNPQDAR 470
                                       566667777778999999999999999988877722222223344455555555555555555555 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.018
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       + y+ Al+l  + l+++p++a+a+ +  +al+ lg+ +e  +++++++e
  gi|330509114|ref|YP_004385542.1| 449 KAYEKALNLIDNDLKKNPQDARAWEAKSDALIGLGRQEESLDAIEKALE 497
                                       56999999999999**********************9998888887765 PP

  == domain 6  score: 14.9 bits;  conditional E-value: 4.7e-05
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL 64 
                                       + Al++l    + +pk++ea+   A++l+  g+ deA ++ +++ e ++  +r+a++
  gi|330509114|ref|YP_004385542.1| 493 EKALEILNLSTERNPKDGEAWWSKANVLYGIGRSDEALQAYEKVIELNHT-PRLADA 548
                                       6789999999999**********************************999.888754 PP

  == domain 7  score: 11.5 bits;  conditional E-value: 0.00054
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL 64 
                                       g+ +eA +++e+  q +p++   +    +   +lg+++  +++ d++++ dp++a+++  
  gi|330509114|ref|YP_004385542.1| 599 GKEEEAFEAFEKYAQLSPGDRHSWRMKGDMASELGRYNVSIEAYDQALRIDPKWAEVWYK 658
                                       67789*******99****************************************999865 PP

  == domain 8  score: 23.9 bits;  conditional E-value: 7.1e-08
                            TPR_19   2 laegdyaeAlalleqalqe........dpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                        ++ ++ +Al+++e+a +         + + + + +    al++l+++deA+++Ld+++e +p 
  gi|330509114|ref|YP_004385542.1| 664 AKMDNHNDALKAFEKAVEIsdeviqkdAGNASGICIIKGYALIKLNRYDEAIEALDRALEIAPS 727
                                       5788999********98553334444355588888889**********************9997 PP

  == domain 9  score: 11.9 bits;  conditional E-value: 0.0004
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeA 44 
                                       lla g+ ++Al+++ + ++ +p  ++a+ +   a+ algq+ eA
  gi|330509114|ref|YP_004385542.1| 744 LLALGKNEDALEAYNKSIEFNPAFGRAWHGKGLAQSALGQFSEA 787
                                       78999**************************************9 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00042      0.26     102     138 ..      24      60 ..      18      66 .. 0.86
   2 ?    1.0   0.0      0.65     4e+02     102     129 ..      65      92 ..      62     100 .. 0.86
   3 ?   -0.9   0.0       2.6   1.6e+03      97     132 ..     429     460 ..     408     467 .. 0.75
   4 !   34.5   0.1   3.1e-11   1.9e-08      50     129 ..     464     539 ..     442     544 .. 0.89
   5 ?    3.9   0.1     0.081        50     104     126 ..     589     611 ..     545     620 .. 0.83
   6 !   11.6   0.4   0.00036      0.22      98     132 ..     651     685 ..     621     696 .. 0.83
   7 ?    4.9   0.0     0.041        25      64      83 ..     704     723 ..     697     726 .. 0.88
   8 ?    3.0   0.1      0.16     1e+02      63     126 ..     735     794 ..     731     798 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00042
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH--S--T CS
                           DUF3856 102 avfsravaleelGrkdealkafrmagemiaerkGelk 138
                                       a  +r++al+++G+ +ea ++ ++a e+i++r  e +
  gi|330509114|ref|YP_004385542.1|  24 AWHHRGMALAGMGHGAEANQSIQKAMELIDQRLQENP 60 
                                       56789**************************987765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmagem 129
                                       a++ ra  ++  G+++eal+a+  ++e+
  gi|330509114|ref|YP_004385542.1|  65 ALWLRAEEMDLFGKSEEALEAYGRVAEL 92 
                                       56679999999***********999886 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                           DUF3856  97 klWiaavfsravaleelGrkdealkafrmagemiae 132
                                       + W+    s a +l  +G+ +e+ ka+++a ++i++
  gi|330509114|ref|YP_004385542.1| 429 SAWL----SIAITLGIMGNGSESSKAYEKALNLIDN 460
                                       5554....4577888899999999999999999975 PP

  == domain 4  score: 34.5 bits;  conditional E-value: 3.1e-11
                                       HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  50 heGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                        +  da ++ + s+al++lgr +e+l +++kal+ +n   e +  +G+ W    +s+a  l ++Gr+deal+a++++
  gi|330509114|ref|YP_004385542.1| 464 KNPQDARAWEAKSDALIGLGRQEESLDAIEKALEILNLSTERNPKDGEAW----WSKANVLYGIGRSDEALQAYEKV 536
                                       56679999999**************************************9....68*******************99 PP

                                       HHH CS
                           DUF3856 127 gem 129
                                        e+
  gi|330509114|ref|YP_004385542.1| 537 IEL 539
                                       986 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.081
                                       HHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrma 126
                                        s + al+elG+++ea++af++ 
  gi|330509114|ref|YP_004385542.1| 589 NSAGFALAELGKEEEAFEAFEKY 611
                                       46689**************9875 PP

  == domain 6  score: 11.6 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                           DUF3856  98 lWiaavfsravaleelGrkdealkafrmagemiae 132
                                       +W  + ++++ al+++ ++++alkaf++a+e+ +e
  gi|330509114|ref|YP_004385542.1| 651 KWAEVWYKKGNALAKMDNHNDALKAFEKAVEISDE 685
                                       69999*************************98776 PP

  == domain 7  score: 4.9 bits;  conditional E-value: 0.041
                                       HHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkalr 83 
                                       al+kl rydea+e+ d+al+
  gi|330509114|ref|YP_004385542.1| 704 ALIKLNRYDEAIEALDRALE 723
                                       899*************9996 PP

  == domain 8  score: 3.0 bits;  conditional E-value: 0.16
                                       HHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  63 ealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       ea+ + g+   al   + al+ +n+  e++ + G+ W      ++ a + lG+ +ea  +fr+a
  gi|330509114|ref|YP_004385542.1| 735 EAWNGKGDILLALGKNEDALEAYNKSIEFNPAFGRAW----HGKGLAQSALGQFSEADLSFRVA 794
                                       5666667777788888888888888888888888888....46788888888888888888777 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.025        16       1      28 [.      64      91 ..      64      95 .. 0.87
   2 ?   -1.2   0.0       6.6   4.1e+03      11      26 ..     109     124 ..     102     129 .. 0.83
   3 ?    0.0   0.0       2.8   1.7e+03      11      32 ..     405     426 ..     397     427 .. 0.74
   4 ?    0.7   0.0       1.7     1e+03       1      31 [.     477     507 ..     477     509 .. 0.80
   5 !    8.3   0.0    0.0065         4       6      28 ..     516     538 ..     511     540 .. 0.79
   6 ?    5.5   0.1     0.049        30       7      31 ..     592     616 ..     590     618 .. 0.87
   7 ?   -0.3   0.0       3.5   2.2e+03      12      31 ..     631     650 ..     625     651 .. 0.82
   8 !    8.8   0.0    0.0046       2.8       1      28 [.     654     681 ..     654     683 .. 0.92
   9 !   12.2   0.0   0.00036      0.22       7      33 .]     702     728 ..     700     728 .. 0.94
  10 ?    2.3   0.0      0.53   3.3e+02       7      26 ..     741     760 ..     739     765 .. 0.82
  11 ?   -0.7   0.0       4.5   2.8e+03       6      26 ..     774     794 ..     770     797 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.025
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  1 dAlyklalsyrklgdtdkAlealerlik 28
                                      +Al+++a+ +   g++++Alea+ r+ +
  gi|330509114|ref|YP_004385542.1| 64 EALWLRAEEMDLFGKSEEALEAYGRVAE 91
                                      68999999999857***********976 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 6.6
                                       HHHHHHHHHHHHHHHH CS
                             TPR_6  11 rklgdtdkAlealerl 26 
                                        ++g++ +++e + r 
  gi|330509114|ref|YP_004385542.1| 109 AAQGRYNQSVESFSRA 124
                                       5689*******99886 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  11 rklgdtdkAlealerlikeYPd 32 
                                       ++ +  ++++ a+er+i+  P+
  gi|330509114|ref|YP_004385542.1| 405 FENDSLEESVLAMERVIQLDPE 426
                                       44456789999*******9996 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                       dAl  l++  ++l+  +kAle+l+   ++ P
  gi|330509114|ref|YP_004385542.1| 477 DALIGLGRQEESLDAIEKALEILNLSTERNP 507
                                       68888899888899999***99987766666 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0065
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                        a  ++  g++d+Al+a+e++i+
  gi|330509114|ref|YP_004385542.1| 516 KANVLYGIGRSDEALQAYEKVIE 538
                                       566677768************97 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.049
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       + ++ +lg+ ++A ea+e+  +  P
  gi|330509114|ref|YP_004385542.1| 592 GFALAELGKEEEAFEAFEKYAQLSP 616
                                       67889999***********998877 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  12 klgdtdkAlealerlikeYP 31 
                                       +lg++  ++ea+++ ++  P
  gi|330509114|ref|YP_004385542.1| 631 ELGRYNVSIEAYDQALRIDP 650
                                       47899999******999888 PP

  == domain 8  score: 8.8 bits;  conditional E-value: 0.0046
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                       ++ yk + ++ k++++ +Al+a+e+ ++
  gi|330509114|ref|YP_004385542.1| 654 EVWYKKGNALAKMDNHNDALKAFEKAVE 681
                                       578**********************986 PP

  == domain 9  score: 12.2 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPdS 33 
                                       +++++kl+++d+A+eal+r ++  P S
  gi|330509114|ref|YP_004385542.1| 702 GYALIKLNRYDEAIEALDRALEIAPSS 728
                                       88999*99***************9987 PP

  == domain 10  score: 2.3 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerl 26 
                                       +  +++lg+ ++Alea+++ 
  gi|330509114|ref|YP_004385542.1| 741 GDILLALGKNEDALEAYNKS 760
                                       56678899*********985 PP

  == domain 11  score: -0.7 bits;  conditional E-value: 4.5
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerl 26 
                                        +l++ +lg+ ++A   ++  
  gi|330509114|ref|YP_004385542.1| 774 KGLAQSALGQFSEADLSFRVA 794
                                       589999999*****9888765 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.012       7.1       2      77 ..      42     119 ..      41     124 .. 0.79
   2 !   10.0   0.1    0.0012      0.76      36      82 .]     448     495 ..     406     495 .. 0.92
   3 ?    5.6   0.0      0.03        19      40      81 ..     493     535 ..     492     536 .. 0.93
   4 ?   -0.8   0.0         3   1.9e+03      57      82 .]     586     611 ..     567     611 .. 0.72
   5 !    9.5   0.1    0.0018       1.1       7      82 .]     603     679 ..     597     679 .. 0.87
   6 !   18.5   0.1   2.9e-06    0.0018      38      81 ..     675     720 ..     674     721 .. 0.89
   7 ?   -0.3   0.0         2   1.3e+03      64      81 ..     742     759 ..     735     760 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H.HHHHHHHHHHHHTT-HHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnsksl.gcrylfAqcllkLkkyeeAi 76 
                                       ++ +++A+ l++  l+ ++e+ e++ l A+ + l g+ ++A+e + +  +lns++  ++++     l ++++y++ +
  gi|330509114|ref|YP_004385542.1|  42 NQSIQKAMELIDQRLQENPEDQEALWLRAEEMDLFGKSEEALEAYGRVaELNSSHAlEAWIRESDILAAQGRYNQSV 118
                                       6778999999999996777777777777********************99999998777776667777777777766 PP

                                       H CS
                            ANAPC3  77 a 77 
                                        
  gi|330509114|ref|YP_004385542.1| 119 E 119
                                       5 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0012
                                       TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
                            ANAPC3  36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLekl 82 
                                       ++ y++A++l+++  k+n+++ +++  +  +l+ L++ ee ++a+ek+
  gi|330509114|ref|YP_004385542.1| 448 SKAYEKALNLIDNDlKKNPQDARAWEAKSDALIGLGRQEESLDAIEKA 495
                                       678******************************************985 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.03
                                       HHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  40 krAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++A+e+l+ + + n+k+ +++  +A +l+ +++ +eA++a+ek
  gi|330509114|ref|YP_004385542.1| 493 EKALEILNLStERNPKDGEAWWSKANVLYGIGRSDEALQAYEK 535
                                       689999999999999999**********************998 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHTT-HHHHHHHH-SS CS
                            ANAPC3  57 gcrylfAqcllkLkkyeeAiaaLekl 82 
                                       + +  ++ +l +L+k eeA  a+ek+
  gi|330509114|ref|YP_004385542.1| 586 RTWNSAGFALAELGKEEEAFEAFEKY 611
                                       566667788899*********99986 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
                            ANAPC3   7 nAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLekl 82 
                                       +A   +e++ + ++ +  +  +++    ++g+y+  +e +++a ++++k  +++y ++ +l k++++++A++a+ek+
  gi|330509114|ref|YP_004385542.1| 603 EAFEAFEKYAQLSPGDRHSWRMKGDMASELGRYNVSIEAYDQAlRIDPKWAEVWYKKGNALAKMDNHNDALKAFEKA 679
                                       66667778887888888888888888889999**999******999****************************985 PP

  == domain 6  score: 18.5 bits;  conditional E-value: 2.9e-06
                                       -HHHHHHHHHCT.SHHHC-H.HHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  38 qykrAyellrka.klnsksl.gcrylfAqcllkLkkyeeAiaaLek 81 
                                        +++A e+ ++  +++  +  g++++++ +l+kL++y+eAi aL++
  gi|330509114|ref|YP_004385542.1| 675 AFEKAVEISDEViQKDAGNAsGICIIKGYALIKLNRYDEAIEALDR 720
                                       589999999999977777777***********************87 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 2
                                       HHHHHTT-HHHHHHHH-S CS
                            ANAPC3  64 qcllkLkkyeeAiaaLek 81 
                                         ll+L+k e+A+ a+ k
  gi|330509114|ref|YP_004385542.1| 742 DILLALGKNEDALEAYNK 759
                                       6799*********99876 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00096       0.6      76     135 ..       2      61 ..       1      65 [. 0.95
   2 ?   -1.7   0.0       5.8   3.6e+03     110     124 ..      77      91 ..      61      98 .. 0.81
   3 ?   -1.2   0.0       4.1   2.6e+03       6      35 ..      98     127 ..      94     132 .. 0.73
   4 ?    3.4   0.0      0.16        96      76     135 ..     408     467 ..     377     471 .. 0.87
   5 ?    6.3   0.0      0.02        12      78     126 ..     451     499 ..     444     507 .. 0.88
   6 !   11.1   0.0   0.00064      0.39      66     123 ..     473     537 ..     466     542 .. 0.70
   7 ?   -2.4   0.0       9.3   5.7e+03     118     143 ..     561     586 ..     560     587 .. 0.89
   8 ?    0.4   0.0       1.3     8e+02     104     124 ..     593     613 ..     585     617 .. 0.83
   9 !   15.5   0.1   2.8e-05     0.017      69     130 ..     626     687 ..     592     694 .. 0.85
  10 ?    1.0   0.1      0.82   5.1e+02     106     120 ..     744     758 ..     701     763 .. 0.50
  11 ?    0.7   0.0         1   6.3e+02      73      91 ..     745     763 ..     734     798 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00096
                                       T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS---- CS
                              BTAD  76 GraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepg 135
                                       Gr eea++  ++ ++ +P +  ++ +   Ala +G  aeA +  +++++l ++ L   p+
  gi|330509114|ref|YP_004385542.1|   2 GRNEEAISAFDEGLKTDPQNASAWHHRGMALAGMGHGAEANQSIQKAMELIDQRLQENPE 61 
                                       99***************************************************9988886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.8
                                       T-HHHHHHHHHHHHH CS
                              BTAD 110 GrqaeALevYerlrr 124
                                       G+ +eALe+Y r+ +
  gi|330509114|ref|YP_004385542.1|  77 GKSEEALEAYGRVAE 91 
                                       788999999988755 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHTT CS
                              BTAD   6 fealvaagraalaagdpeeaaelleaAlal 35 
                                       +ea  ++++ ++a+g+ ++ +e++++A+al
  gi|330509114|ref|YP_004385542.1|  98 LEAWIRESDILAAQGRYNQSVESFSRAMAL 127
                                       555566777778888888888888888887 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.16
                                       T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS---- CS
                              BTAD  76 GraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepg 135
                                          ee +  +e+ ++++P +  ++  +   l  +G+ +e  ++Ye++ +l +++L   p+
  gi|330509114|ref|YP_004385542.1| 408 DSLEESVLAMERVIQLDPENSSAWLSIAITLGIMGNGSESSKAYEKALNLIDNDLKKNPQ 467
                                       55677788899************************************9999999977775 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                              BTAD  78 aeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlL 126
                                       +e+al   ++ ++++P + r++++   Al  +Grq+e L + e++ ++L
  gi|330509114|ref|YP_004385542.1| 451 YEKALNLIDNDLKKNPQDARAWEAKSDALIGLGRQEESLDAIEKALEIL 499
                                       5778888889999**************************9999888877 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.00064
                                       HHHHHHHHHTT-HH.......HHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  66 ealaeaelrlGrae.......ealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       ea  +a++ lGr e       +al+ l+  ++ +P + +++      l+  Gr  eAL++Ye++ 
  gi|330509114|ref|YP_004385542.1| 473 EAKSDALIGLGRQEesldaieKALEILNLSTERNPKDGEAWWSKANVLYGIGRSDEALQAYEKVI 537
                                       55555555555554111111155556666677899999************************986 PP

  == domain 7  score: -2.4 bits;  conditional E-value: 9.3
                                       HHHHHHHHHHHHHS----HHHHHHHH CS
                              BTAD 118 vYerlrrlLaeeLgvepgpelralhe 143
                                        Y++++++ ++ +g+ p++++ +l +
  gi|330509114|ref|YP_004385542.1| 561 NYDEFKETFNQAIGLIPASDTAKLAR 586
                                       599****************9999865 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 1.3
                                       HHHHHTT-HHHHHHHHHHHHH CS
                              BTAD 104 rAlarsGrqaeALevYerlrr 124
                                        Ala +G+++eA e++e++ +
  gi|330509114|ref|YP_004385542.1| 593 FALAELGKEEEAFEAFEKYAQ 613
                                       599*************99865 PP

  == domain 9  score: 15.5 bits;  conditional E-value: 2.8e-05
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHH CS
                              BTAD  69 aeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeL 130
                                        ++ ++lGr++  ++ ++++++ +P   + + +   Ala++++ ++AL+++e+++++ +e +
  gi|330509114|ref|YP_004385542.1| 626 GDMASELGRYNVSIEAYDQALRIDPKWAEVWYKKGNALAKMDNHNDALKAFEKAVEISDEVI 687
                                       447899************************************************99887765 PP

  == domain 10  score: 1.0 bits;  conditional E-value: 0.82
                                       HHHTT-HHHHHHHHH CS
                              BTAD 106 larsGrqaeALevYe 120
                                       l ++G++++ALe+Y+
  gi|330509114|ref|YP_004385542.1| 744 LLALGKNEDALEAYN 758
                                       455666666666665 PP

  == domain 11  score: 0.7 bits;  conditional E-value: 1
                                       HHTT-HHHHHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvae 91 
                                       l+lG+ e+al+ +++ ++ 
  gi|330509114|ref|YP_004385542.1| 745 LALGKNEDALEAYNKSIEF 763
                                       4555555555555555555 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.34   2.1e+02      12      35 ..       1      22 [.       1      23 [. 0.90
   2 ?   -0.3   0.0       2.4   1.5e+03      13      28 ..      77      92 ..      74      97 .. 0.83
   3 ?    2.4   0.0      0.31   1.9e+02       8      29 ..     107     128 ..     105     136 .. 0.79
   4 ?   -1.1   0.0       4.1   2.5e+03      15      34 ..     451     468 ..     437     470 .. 0.65
   5 ?   -1.7   0.0       6.3   3.9e+03      12      28 ..     482     498 ..     474     506 .. 0.81
   6 ?    3.1   0.0      0.19   1.2e+02      12      30 ..     523     541 ..     512     549 .. 0.80
   7 ?    5.0   0.0     0.048        30       6      29 ..     626     649 ..     621     651 .. 0.82
   8 ?    1.1   0.0      0.82   5.1e+02       6      29 ..     660     681 ..     655     690 .. 0.81
   9 !    9.8   0.0    0.0014      0.84       8      29 ..     704     725 ..     701     729 .. 0.84
  10 ?    4.7   0.0     0.057        35       2      28 ..     737     763 ..     736     769 .. 0.85
  11 ?   -1.0   0.0       3.9   2.4e+03       3      18 ..     772     787 ..     770     792 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.34
                             TPR_7 12 lGdyeeAielyeqsLaltkdpeda 35
                                      +G+ eeAi+ + +  +l  dp++a
  gi|330509114|ref|YP_004385542.1|  1 MGRNEEAISAFDE--GLKTDPQNA 22
                                      5999*********..****99987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.4
                             TPR_7 13 GdyeeAielyeqsLal 28
                                      G+ eeA+e y ++ +l
  gi|330509114|ref|YP_004385542.1| 77 GKSEEALEAYGRVAEL 92
                                      7889******997766 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.31
                             TPR_7   8 lysrlGdyeeAielyeqsLalt 29 
                                       +  ++G+y + +e + +++al 
  gi|330509114|ref|YP_004385542.1| 107 ILAAQGRYNQSVESFSRAMALV 128
                                       6788*************66554 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 4.1
                             TPR_7  15 yeeAielyeqsLaltkdped 34 
                                       ye+A+ l      l k p+d
  gi|330509114|ref|YP_004385542.1| 451 YEKALNLIDN--DLKKNPQD 468
                                       6666666666..66666665 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 6.3
                             TPR_7  12 lGdyeeAielyeqsLal 28 
                                       lG+ ee ++  e++L++
  gi|330509114|ref|YP_004385542.1| 482 LGRQEESLDAIEKALEI 498
                                       78999999999998876 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.19
                             TPR_7  12 lGdyeeAielyeqsLaltk 30 
                                        G+ +eA++ ye++++l  
  gi|330509114|ref|YP_004385542.1| 523 IGRSDEALQAYEKVIELNH 541
                                       6999*********888765 PP

  == domain 7  score: 5.0 bits;  conditional E-value: 0.048
                             TPR_7   6 arlysrlGdyeeAielyeqsLalt 29 
                                       +++ s+lG+y   ie y q+L+++
  gi|330509114|ref|YP_004385542.1| 626 GDMASELGRYNVSIEAYDQALRID 649
                                       778899*************55543 PP

  == domain 8  score: 1.1 bits;  conditional E-value: 0.82
                             TPR_7   6 arlysrlGdyeeAielyeqsLalt 29 
                                       +++  ++ ++ +A++ +e+  a++
  gi|330509114|ref|YP_004385542.1| 660 GNALAKMDNHNDALKAFEK--AVE 681
                                       88999999***********..555 PP

  == domain 9  score: 9.8 bits;  conditional E-value: 0.0014
                             TPR_7   8 lysrlGdyeeAielyeqsLalt 29 
                                       +  +l++y+eAie + ++L+++
  gi|330509114|ref|YP_004385542.1| 704 ALIKLNRYDEAIEALDRALEIA 725
                                       6679*************88876 PP

  == domain 10  score: 4.7 bits;  conditional E-value: 0.057
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLal 28 
                                       ++  +++  +lG+ e+A+e y +s+++
  gi|330509114|ref|YP_004385542.1| 737 WNGKGDILLALGKNEDALEAYNKSIEF 763
                                       666799***************997765 PP

  == domain 11  score: -1.0 bits;  conditional E-value: 3.9
                             TPR_7   3 lnLarlysrlGdyeeA 18 
                                       +  + ++s+lG+++eA
  gi|330509114|ref|YP_004385542.1| 772 HGKGLAQSALGQFSEA 787
                                       55688999******99 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.14        89       6      40 ..      26      60 ..      22      62 .. 0.85
   2 ?    0.4   0.0       1.1   6.6e+02      11      30 ..     107     126 ..     106     127 .. 0.83
   3 ?    4.8   0.0     0.045        28       8      31 ..     434     457 ..     432     458 .. 0.92
   4 ?    1.2   0.1      0.57   3.6e+02      14      31 ..     481     498 ..     477     500 .. 0.86
   5 !    8.2   0.0    0.0036       2.2       9      31 ..     517     539 ..     516     541 .. 0.93
   6 ?    1.2   0.1      0.58   3.6e+02       4      27 ..     587     610 ..     584     611 .. 0.84
   7 ?    0.1   0.0       1.3     8e+02      12      31 ..     629     648 ..     626     648 .. 0.87
   8 !   11.5   0.0   0.00033      0.21       9      36 ..     660     687 ..     659     690 .. 0.91
   9 !    8.0   0.5    0.0043       2.7       9      31 ..     702     724 ..     702     725 .. 0.91
  10 ?   -0.2   0.0       1.6     1e+03      11      30 ..     743     762 ..     740     763 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.14
                            TPR_10  6 nNLanalrqrgrydeAealleealairrrllGpdH 40
                                      ++ ++al  +g ++eA +  ++a+++  + l +++
  gi|330509114|ref|YP_004385542.1| 26 HHRGMALAGMGHGAEANQSIQKAMELIDQRLQENP 60
                                      6679********************99888887765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                            TPR_10  11 alrqrgrydeAealleeala 30 
                                       +l ++gry+++++ + +a+a
  gi|330509114|ref|YP_004385542.1| 107 ILAAQGRYNQSVESFSRAMA 126
                                       5889******9998877776 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.045
                            TPR_10   8 LanalrqrgrydeAealleealai 31 
                                       +a++l  +g++ e+ + +e+al++
  gi|330509114|ref|YP_004385542.1| 434 IAITLGIMGNGSESSKAYEKALNL 457
                                       799******************985 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.57
                            TPR_10  14 qrgrydeAealleealai 31 
                                        +gr +e+++  e+al+i
  gi|330509114|ref|YP_004385542.1| 481 GLGRQEESLDAIEKALEI 498
                                       68999**********998 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.0036
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       an+l+  gr deA++ +e+++++
  gi|330509114|ref|YP_004385542.1| 517 ANVLYGIGRSDEALQAYEKVIEL 539
                                       899*****************986 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 0.58
                            TPR_10   4 slnNLanalrqrgrydeAeallee 27 
                                       + n  + al ++g+ +eA + +e+
  gi|330509114|ref|YP_004385542.1| 587 TWNSAGFALAELGKEEEAFEAFEK 610
                                       5577899************99986 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 1.3
                            TPR_10  12 lrqrgrydeAealleealai 31 
                                        +++gry+ + + +++al+i
  gi|330509114|ref|YP_004385542.1| 629 ASELGRYNVSIEAYDQALRI 648
                                       6899*************986 PP

  == domain 8  score: 11.5 bits;  conditional E-value: 0.00033
                            TPR_10   9 analrqrgrydeAealleealairrrll 36 
                                       +nal ++ ++++A++ +e+a++i  ++ 
  gi|330509114|ref|YP_004385542.1| 660 GNALAKMDNHNDALKAFEKAVEISDEVI 687
                                       89*********************88875 PP

  == domain 9  score: 8.0 bits;  conditional E-value: 0.0043
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al +++rydeA + l++al+i
  gi|330509114|ref|YP_004385542.1| 702 GYALIKLNRYDEAIEALDRALEI 724
                                       668899***************98 PP

  == domain 10  score: -0.2 bits;  conditional E-value: 1.6
                            TPR_10  11 alrqrgrydeAealleeala 30 
                                       +l ++g+ ++A++ + ++++
  gi|330509114|ref|YP_004385542.1| 743 ILLALGKNEDALEAYNKSIE 762
                                       68899*******99988886 PP

>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.3e-08   8.2e-06       8     110 ..     230     324 ..     223     326 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.3e-08
                               LTD   8 vvIsevmedgagnnanefvelyNtsskavdLsgwkledasgeytfpngtgtlaageyvvvwsgsgttsasngskass 84 
                                       + I+++++++   +  +f+ ++ +  +av+L++w+le + ++  +p+ +  l +g+ v v+  sg+++ ++    +s
  gi|330509114|ref|YP_004385542.1| 230 LTITKINPKE---D--DFIDIADNLKEAVSLQNWSLEIQGSKVSLPEYS--LLPGKAVRVHLRSGQENETDL-FLDS 298
                                       7788888877...3..9***********************777777775..************988877777.4679 PP

                               LTD  85 savwnnggdavaLydasgevvdsvgy 110
                                       ++ +n++  +v+L+d sg  v+s++y
  gi|330509114|ref|YP_004385542.1| 299 NLGLNDTVGSVSLRDGSGAKVASLDY 324
                                       999999999*************9988 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.078        48     205     249 ..      42      86 ..       4      95 .. 0.84
   2 ?   -3.2   0.1       4.7   2.9e+03     441     493 ..     381     432 ..     373     435 .. 0.78
   3 ?    2.8   0.1      0.07        43      17      66 ..     448     497 ..     443     505 .. 0.79
   4 !    8.8   0.0    0.0011      0.68      18      72 ..     490     544 ..     485     584 .. 0.70
   5 !    8.3   0.1    0.0016      0.96      16     252 ..     597     679 ..     592     690 .. 0.55
   6 !    6.1   0.0    0.0073       4.5      29      69 ..     723     765 ..     694     788 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.078
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevm 249
                                        +s +kA+e+id+ ++++p+  e    +a+ +   G  ++A e+ 
  gi|330509114|ref|YP_004385542.1|  42 NQSIQKAMELIDQRLQENPEDQEALWLRAEEMDLFGKSEEALEAY 86 
                                       45678******************9999999999999999998875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.7
                                       ....-------------S-SSSTTTT-S-HHHHHHHHHTTTGGGTTT-THHHH CS
                             NARP1 441 aekkakkedeeakkededplgekLvkteepLeeAlkflkpLlklaaeniethl 493
                                       +++++k+e +e++++d    g++L + +  Lee +  ++ + +l +en +++l
  gi|330509114|ref|YP_004385542.1| 381 HNHSNKDELQENTADDWYKKGTELFEND-SLEESVLAMERVIQLDPENSSAWL 432
                                       5556667777777777778999999866.999999999999999999988876 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.07
                                       HTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1  17 agkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLle 66 
                                       +  +e+Al+ +++  k+        e+k++ l+ Lgr+ee+  ++e+ le
  gi|330509114|ref|YP_004385542.1| 448 SKAYEKALNLIDNDLKKNPQDARAWEAKSDALIGLGRQEESLDAIEKALE 497
                                       66788899999888888877778888899999999999998888877666 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0011
                                       THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-C CS
                             NARP1  18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpens 72 
                                       + +e+Ale L+ + ++     +    ka++l  +gr +eA ++ye+ +e n+  +
  gi|330509114|ref|YP_004385542.1| 490 DAIEKALEILNLSTERNPKDGEAWWSKANVLYGIGRSDEALQAYEKVIELNHTPR 544
                                       6788999999988887777777778899999999999999999999999887655 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0016
                                       HHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHH CS
                             NARP1  16 eagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeal 92 
                                       e gk+eeA+e +e++++          +k+++  +Lgr++ + ++y + l+  p   +                   
  gi|330509114|ref|YP_004385542.1| 597 ELGKEEEAFEAFEKYAQLSPGDRHSWRMKGDMASELGRYNVSIEAYDQALRIDPKWAEV------------------ 655
                                       66666666666666665554444444566666666666666666666666666665544.................. PP

                                       HHHHHHTTTS-TT-SHHHHTHHHH--HHHHHHHHHHHHHHHHHCT-TTHHHHHGGGGGGSCHHHHHHHHHHHHHTTT CS
                             NARP1  93 lalydelaekyprsdaprRlpLdfleGeeFkelvdkYlrkaLrkgvPslfanlksLYedkeKvkileelvegyvksl 169
                                                                                                                    
  gi|330509114|ref|YP_004385542.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       TTSSSSTTGG.GSS----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                             NARP1 170 ktsgklsesdnedsekepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAa 246
                                                                                                  ++ K++ l ++ + ++A 
  gi|330509114|ref|YP_004385542.1| 656 -----------------------------------------------------------WYKKGNALAKMDNHNDAL 673
                                       ...........................................................444444444444444444 PP

                                       HHHHHH CS
                             NARP1 247 evmeea 252
                                       ++ e+a
  gi|330509114|ref|YP_004385542.1| 674 KAFEKA 679
                                       333333 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.0073
                                       HHGGG---HH..HHHHHHHHHHHHTT-HHHHHHHHHHHHHH-T CS
                             NARP1  29 ekekqivDkl..avketkaelllkLgrkeeAeatyeaLlernp 69 
                                       e + + v +   +  + k+++ll+Lg++e+A ++y++ +e np
  gi|330509114|ref|YP_004385542.1| 723 EIAPSSVPVFpaEAWNGKGDILLALGKNEDALEAYNKSIEFNP 765
                                       3444444444113446789999999999999999999999887 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.9e-05     0.012       9      22 ..      15      28 ..      12      28 .. 0.93
   2 ?   -1.5   0.0       3.8   2.4e+03       2      16 ..      49      63 ..      48      65 .. 0.87
   3 ?    5.5   0.0     0.023        14       6      19 ..     418     431 ..     417     432 .. 0.91
   4 ?   -0.4   0.1       1.7     1e+03       2      15 ..     455     468 ..     454     472 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                                      HHH-TT-CHHHHHH CS
                              PPTA  9 iekdpkNYsaWnyR 22
                                      +++dp+N saW++R
  gi|330509114|ref|YP_004385542.1| 15 LKTDPQNASAWHHR 28
                                      899**********9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.8
                                      HHHHHHHHHH-TT-C CS
                              PPTA  2 LeltekliekdpkNY 16
                                      +el+++ ++++p ++
  gi|330509114|ref|YP_004385542.1| 49 MELIDQRLQENPEDQ 63
                                      799*********986 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.023
                                       HHHHHH-TT-CHHH CS
                              PPTA   6 ekliekdpkNYsaW 19 
                                       e +i++dp N saW
  gi|330509114|ref|YP_004385542.1| 418 ERVIQLDPENSSAW 431
                                       678*********** PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.7
                                       HHHHHHHHHH-TT- CS
                              PPTA   2 LeltekliekdpkN 15 
                                       L+l+++ ++k+p++
  gi|330509114|ref|YP_004385542.1| 455 LNLIDNDLKKNPQD 468
                                       899*********86 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0041       2.6       2      71 ..     448     536 ..     447     557 .. 0.88
   2 !   14.6   0.1   4.1e-05     0.025       3      70 ..     640     720 ..     638     728 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0041
                      SRP_TPR_like   2 neeyekilrlegkelkkf.........kvvaliklekyeeaLkllkkgs..........alsedvrfEkaYvlYklk 59 
                                       +++yek l+l ++ lkk          k  ali l++ ee+L +++k+             +++  + ka vlY + 
  gi|330509114|ref|YP_004385542.1| 448 SKAYEKALNLIDNDLKKNpqdaraweaKSDALIGLGRQEESLDAIEKALeilnlsternPKDGEAWWSKANVLYGIG 524
                                       6899***********99999******9********************988999998887677889999999999999 PP

                      SRP_TPR_like  60 kykkalkilkkv 71 
                                       +  +al+  +kv
  gi|330509114|ref|YP_004385542.1| 525 RSDEALQAYEKV 536
                                       999999888776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.1e-05
                      SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgs...........alsedvrfEkaYvlYklkkykkalk 66 
                                       e+y++ lr++ k  + +  k  al k++ +++aLk+ +k+            + ++ +   k Y+l kl++y +a +
  gi|330509114|ref|YP_004385542.1| 640 EAYDQALRIDPKWAEVWykKGNALAKMDNHNDALKAFEKAVeisdeviqkdaGNASGICIIKGYALIKLNRYDEAIE 716
                                       6788888888776665566899*****************998999999998855666777899************99 PP

                      SRP_TPR_like  67 ilkk 70 
                                        l++
  gi|330509114|ref|YP_004385542.1| 717 ALDR 720
                                       9877 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2      0.36   2.2e+02     131     179 ..       6      55 ..       1      74 [. 0.77
   2 ?   -0.0   0.1      0.98   6.1e+02     153     180 ..     105     132 ..      76     140 .. 0.74
   3 ?    6.3   0.1     0.012       7.1     126     176 ..     448     499 ..     441     509 .. 0.87
   4 ?   -0.3   0.0       1.2   7.2e+02     154     178 ..     518     542 ..     515     555 .. 0.77
   5 ?    1.9   0.2      0.26   1.6e+02     150     174 ..     623     647 ..     559     655 .. 0.77
   6 ?    2.7   0.1      0.14        88     152     177 ..     659     684 ..     652     691 .. 0.88
   7 !   18.0   0.0     3e-06    0.0019     125     174 ..     707     762 ..     700     770 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.36
                            TPR_21 131 eAlktL.eakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaaleek 179
                                       eA+++  e+ k++  +a++   rG +l+ +g+ +eA +  q+A++ ++++
  gi|330509114|ref|YP_004385542.1|   6 EAISAFdEGLKTDPQNASAWHHRGMALAGMGHGAEANQSIQKAMELIDQR 55 
                                       55555533456677788888899999999*********999999988775 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.98
                            TPR_21 153 GDilvaqgkldeAraaYqaAlaaleeka 180
                                        Dil+aqg+ ++  + +++A+a   +++
  gi|330509114|ref|YP_004385542.1| 105 SDILAAQGRYNQSVESFSRAMALVPANK 132
                                       4999999999999999999998776665 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.012
                            TPR_21 126 ekkydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                        k+y++Al++++++ k++  +a++ e + D+l+  g+++e  +a ++Al+ l
  gi|330509114|ref|YP_004385542.1| 448 SKAYEKALNLIDNDlKKNPQDARAWEAKSDALIGLGRQEESLDAIEKALEIL 499
                                       689********7762667899***************************9866 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.2
                            TPR_21 154 DilvaqgkldeAraaYqaAlaalee 178
                                       ++l+  g+ deA +aY++ ++ +++
  gi|330509114|ref|YP_004385542.1| 518 NVLYGIGRSDEALQAYEKVIELNHT 542
                                       5777889999999999998876655 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.26
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAla 174
                                        ++GD++++ g+ +   +aY++Al+
  gi|330509114|ref|YP_004385542.1| 623 RMKGDMASELGRYNVSIEAYDQALR 647
                                       4789999999999999999999986 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.14
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaale 177
                                       +G++l+++++ ++A +a+++A++  +
  gi|330509114|ref|YP_004385542.1| 659 KGNALAKMDNHNDALKAFEKAVEISD 684
                                       9********************98655 PP

  == domain 7  score: 18.0 bits;  conditional E-value: 3e-06
                            TPR_21 125 aekkydeAlktL......eakkeeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       + + ydeA+++L      + ++   f a++ + +GDil+a gk+++A +aY+++++
  gi|330509114|ref|YP_004385542.1| 707 KLNRYDEAIEALdraleiAPSSVPVFPAEAWNGKGDILLALGKNEDALEAYNKSIE 762
                                       4566777777662222224455678***************************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 ?   -1.9   0.0       5.9   3.7e+03      18      37 ..       5      24 ..       1      25 [. 0.79
   2 ?    2.6   0.4      0.23   1.4e+02      19      41 ..      47      69 ..      45      72 .. 0.92
   3 ?   -1.5   0.0       4.3   2.7e+03      14      39 ..     111     136 ..     109     137 .. 0.85
   4 ?   -0.8   0.0       2.8   1.7e+03      19      37 ..     412     430 ..     409     431 .. 0.82
   5 ?    3.0   0.0      0.18   1.1e+02      15      34 ..     449     468 ..     444     473 .. 0.88
   6 ?    4.3   0.0     0.069        43      14      36 ..     632     654 ..     630     656 .. 0.92
   7 ?    1.5   0.0      0.51   3.2e+02      10      32 ..     662     684 ..     653     691 .. 0.82
   8 !    9.4   0.0    0.0018       1.1       9      33 ..     703     727 ..     702     728 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.9
                                      HHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C 18 seArryvdalLeiEPenrQa 37
                                      +eA    d  L+ +P+n  a
  gi|330509114|ref|YP_004385542.1|  5 EEAISAFDEGLKTDPQNASA 24
                                      6777788888*******876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.23
                                      HHHHHHHHHHHHTTS-HHHHHHH CS
                        Fis1_TPR_C 19 eArryvdalLeiEPenrQaqsLk 41
                                      +A++++d+ L+  Pe + a+ L+
  gi|330509114|ref|YP_004385542.1| 47 KAMELIDQRLQENPEDQEALWLR 69
                                      89*****************9987 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.3
                                       HT-HHHHHHHHHHHHHHTTS-HHHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaqs 39 
                                       +g+Y+++ +   + +++ P n+   +
  gi|330509114|ref|YP_004385542.1| 111 QGRYNQSVESFSRAMALVPANKSESQ 136
                                       589*************9999987655 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  19 eArryvdalLeiEPenrQa 37 
                                       e+   ++++++++Pen+ a
  gi|330509114|ref|YP_004385542.1| 412 ESVLAMERVIQLDPENSSA 430
                                       666778999*******987 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.18
                                       T-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPen 34 
                                       + Y++A++++d  L++ P+ 
  gi|330509114|ref|YP_004385542.1| 449 KAYEKALNLIDNDLKKNPQD 468
                                       67****************86 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.069
                                       HT-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQ 36 
                                       lg+Y+ + +  d+ L+i+P++  
  gi|330509114|ref|YP_004385542.1| 632 LGRYNVSIEAYDQALRIDPKWAE 654
                                       899*****************975 PP

  == domain 7  score: 1.5 bits;  conditional E-value: 0.51
                                       HHHHHT-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEP 32 
                                       + +k+ ++++A++  +   ei  
  gi|330509114|ref|YP_004385542.1| 662 ALAKMDNHNDALKAFEKAVEISD 684
                                       789**********9999888865 PP

  == domain 8  score: 9.4 bits;  conditional E-value: 0.0018
                                       HHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPe 33 
                                       ++ +kl +Y+eA + +d+ Lei P+
  gi|330509114|ref|YP_004385542.1| 703 YALIKLNRYDEAIEALDRALEIAPS 727
                                       5789******************996 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.4     0.004       2.5      53     115 ..      76     133 ..      36     140 .. 0.72
   2 ?    5.8   0.0     0.012       7.6      14     146 ..     485     613 ..     478     617 .. 0.78
   3 ?    4.5   0.0     0.031        19     282     311 ..     697     726 ..     672     732 .. 0.87
   4 ?   -1.5   0.0       2.1   1.3e+03      21      41 ..     774     794 ..     766     797 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.004
                          TPR_MalT  53 qGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqgl 115
                                        G+   +++al++  ++a + +s+h al a ++ ++il aqGr  +++e + +a++l++ ++ 
  gi|330509114|ref|YP_004385542.1|  76 FGK---SEEALEAYGRVA-ELNSSH-ALEAWIRESDILAAQGRYNQSVESFSRAMALVPANKS 133
                                       455...445555555555.667777.999999************************9988765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
                          TPR_MalT  14 sgdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeil 90 
                                       +++  +a+e A ++L+l+ e++ +  + a ++ + +    G+ ++Alqa++++++l     ++++ + all  +   
  gi|330509114|ref|YP_004385542.1| 485 QEESLDAIEKALEILNLSTERN-PKDGEAWWSKANVLYGIGRSDEALQAYEKVIELN----HTPRLADALLIKGYDF 556
                                       5556678888889998888888.7788888996766666667777777776666654....6666777888888877 PP

                          TPR_MalT  91 vaqGrLheAletyeqalqlateqglqql.plvgfllvlladllyEwndLeeAeqhlq 146
                                         +G  +e  et++qa+ l++ ++ ++l ++++ +   la+l  E   +e+ e+++q
  gi|330509114|ref|YP_004385542.1| 557 AIKGNYDEFKETFNQAIGLIPASDTAKLaRTWNSAGFALAELGKEEEAFEAFEKYAQ 613
                                       777********************9999955999999999999999999988888887 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.031
                          TPR_MalT 282 iliLqalalqaqgreeeAlaaLeqALeLAe 311
                                       i i   +al  ++r +eA++aL++ALe+A 
  gi|330509114|ref|YP_004385542.1| 697 ICIIKGYALIKLNRYDEAIEALDRALEIAP 726
                                       56777889999****************995 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 2.1
                          TPR_MalT  21 lelArqALallpeddllaria 41 
                                       + lA+ AL +++e dl +r+a
  gi|330509114|ref|YP_004385542.1| 774 KGLAQSALGQFSEADLSFRVA 794
                                       557888888888888888875 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.056        35      75     123 ..      35      83 ..      19      99 .. 0.86
   2 ?    2.7   0.0      0.27   1.6e+02      71     124 ..     396     449 ..     355     451 .. 0.89
   3 !    8.4   0.0    0.0046       2.9      82     123 ..     448     489 ..     441     493 .. 0.91
   4 ?    0.2   0.0       1.5   9.6e+02      86     124 ..     493     531 ..     489     537 .. 0.89
   5 ?   -1.2   0.0       4.2   2.6e+03      75     117 ..     625     667 ..     594     681 .. 0.71
   6 ?   -2.0   0.0       7.3   4.5e+03      80     121 ..     706     752 ..     669     758 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.056
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  75 kakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       + + a +++ ++ a+el+++ ++++pe++ea  l+a+ ++  g+ +e+ 
  gi|330509114|ref|YP_004385542.1|  35 MGHGAEANQSIQKAMELIDQRLQENPEDQEALWLRAEEMDLFGKSEEAL 83 
                                       55566678899*************************9999999988875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  71 kvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                          +k +e ++++ ++ ++  ++ +++ dpen++a    a +l  +g+++es  
  gi|330509114|ref|YP_004385542.1| 396 DWYKKGTELFENDSLEESVLAMERVIQLDPENSSAWLSIAITLGIMGNGSESSK 449
                                       55678889999999*****************************99999999975 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0046
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  82 egdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       ++ y+ a++l+++ + ++p++a+a e+k dal  lg+q+es 
  gi|330509114|ref|YP_004385542.1| 448 SKAYEKALNLIDNDLKKNPQDARAWEAKSDALIGLGRQEESL 489
                                       567999**********************************97 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  86 rwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                       + a+e+ln   + +p++ ea   ka++l  +g+  e+ +
  gi|330509114|ref|YP_004385542.1| 493 EKALEILNLSTERNPKDGEAWWSKANVLYGIGRSDEALQ 531
                                       6799*************************9999988765 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 4.2
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  75 kakealkegdyrwaaellnhlvfadpenaeakelkadaleqlg 117
                                       k   a + g y++++e  ++++  dp+ ae    k +al ++ 
  gi|330509114|ref|YP_004385542.1| 625 KGDMASELGRYNVSIEAYDQALRIDPKWAEVWYKKGNALAKMD 667
                                       3444556788999999999999999997777777776666665 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 7.3
                                       HHTT-HHHHHHHHHHHHHHSTT-.....HHHHHHHHHHHHHHHHH-S CS
                   Alkyl_sulf_dimr  80 lkegdyrwaaellnhlvfadpen.....aeakelkadaleqlgyqae 121
                                       +k + y  a+e l+ +++  p+      aea + k d+l +lg+ + 
  gi|330509114|ref|YP_004385542.1| 706 IKLNRYDEAIEALDRALEIAPSSvpvfpAEAWNGKGDILLALGKNED 752
                                       45566777778888888877775556657888888888888887765 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.63   3.9e+02       5      43 ..       5      43 ..       2      49 .. 0.86
   2 !    9.0   0.8    0.0028       1.8       7      44 ..      48      85 ..      42     128 .. 0.87
   3 ?    6.6   0.4     0.016       9.7       7      46 ..     454     493 ..     448     502 .. 0.82
   4 ?    4.7   0.0     0.063        39      13      49 ..     501     537 ..     493     580 .. 0.87
   5 ?    0.9   0.1      0.92   5.7e+02       7      50 ..     638     681 ..     634     693 .. 0.85
   6 ?   -1.4   0.0       4.8     3e+03      31      55 ..     743     767 ..     735     784 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.63
                            TPR_20  5 apelaeleaalaanpddldarldlAlallaagryeeAle 43
                                      ++ ++++++ l+++p++  a +    al+  g+ +eA +
  gi|330509114|ref|YP_004385542.1|  5 EEAISAFDEGLKTDPQNASAWHHRGMALAGMGHGAEANQ 43
                                      5678999999*************9999999999999865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0028
                            TPR_20  7 elaeleaalaanpddldarldlAlallaagryeeAleq 44
                                       ++ ++++l++np+d +a    A+     g+ eeAle+
  gi|330509114|ref|YP_004385542.1| 48 AMELIDQRLQENPEDQEALWLRAEEMDLFGKSEEALEA 85
                                      677899******************************96 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.016
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLl 46 
                                        l  ++++l++np+d  a  + ++al+  gr+ee+l+++ 
  gi|330509114|ref|YP_004385542.1| 454 ALNLIDNDLKKNPQDARAWEAKSDALIGLGRQEESLDAIE 493
                                       56668899*************************9887654 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.063
                            TPR_20  13 aalaanpddldarldlAlallaagryeeAleqLleil 49 
                                          + np+d +a    A++l+  gr +eAl++  +++
  gi|330509114|ref|YP_004385542.1| 501 LSTERNPKDGEAWWSKANVLYGIGRSDEALQAYEKVI 537
                                       56789*************************9765555 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.92
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                       ++++ ++al  +p+  +  ++  +al++  ++ +Al+++ + ++
  gi|330509114|ref|YP_004385542.1| 638 SIEAYDQALRIDPKWAEVWYKKGNALAKMDNHNDALKAFEKAVE 681
                                       68999999***************************998877666 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 4.8
                            TPR_20  31 allaagryeeAleqLleilkrdrkw 55 
                                        lla g++e+Ale+  + ++ + ++
  gi|330509114|ref|YP_004385542.1| 743 ILLALGKNEDALEAYNKSIEFNPAF 767
                                       5778899999999877666666555 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 !    9.0   0.2    0.0017       1.1      24      77 ..      18      71 ..       4     129 .. 0.80
   2 ?    5.8   0.5     0.017        10       7      79 ..     451     520 ..     446     540 .. 0.85
   3 ?    4.6   0.1      0.04        25      55     113 ..     639     693 ..     632     696 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                                      -HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHH CS
                       TOM20_plant 24 dadnllrWggallelsqfqsvaeakqmiqdaiskleeallidPkkhdalWcign 77
                                      d +n   W    + l+ +   aea q iq+a+  +++ l  +P+ ++alW+ ++
  gi|330509114|ref|YP_004385542.1| 18 DPQNASAWHHRGMALAGMGHGAEANQSIQKAMELIDQRLQENPEDQEALWLRAE 71
                                      445556666666677777777899999999999999999999999999998765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHH CS
                       TOM20_plant   7 feearkdaeatykknPldadnllrWggallelsqfqsvaeakqmiqdaiskleeallidPkkhdalWcignay 79 
                                       +e+a +  ++  kknP da      ++al+ l + +   e+   i++a+  l+ +   +Pk  +a W  +n  
  gi|330509114|ref|YP_004385542.1| 451 YEKALNLIDNDLKKNPQDARAWEAKSDALIGLGRQE---ESLDAIEKALEILNLSTERNPKDGEAWWSKANVL 520
                                       677777788999********************9754...69999***********************988864 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.04
                                       HHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT- CS
                       TOM20_plant  55 iskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqavdedPdn 113
                                       i  +++al idPk  +  +  gna        +++++a + feka ++ ++ +++d +n
  gi|330509114|ref|YP_004385542.1| 639 IEAYDQALRIDPKWAEVWYKKGNALAK----MDNHNDALKAFEKAVEISDEVIQKDAGN 693
                                       677899******999988899999764....467789999******9999999988877 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0015       0.9      94     133 ..     104     143 ..      74     152 .. 0.89
   2 ?   -1.0   0.0       2.4   1.5e+03     103     139 ..     561     597 ..     557     605 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                              LemA  94 EnriavaRrrYneavreyntkiesfpsnivaklfgfkeke 133
                                       E++i +a+ rYn++v+++  ++  +p+n   + +gf++++
  gi|330509114|ref|YP_004385542.1| 104 ESDILAAQGRYNQSVESFSRAMALVPANKSESQLGFQRRS 143
                                       889*****************************99999865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.4
                              LemA 103 rYneavreyntkiesfpsnivaklfgfkekelfeaee 139
                                       +Y e  +++n++i  +p++ +akl +  + + f ++e
  gi|330509114|ref|YP_004385542.1| 561 NYDEFKETFNQAIGLIPASDTAKLARTWNSAGFALAE 597
                                       68888999*************9999988888777744 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       5.9   3.7e+03      14      25 ..       2      13 ..       1      15 [. 0.89
   2 ?   -1.2   0.0         5   3.1e+03      14      25 ..      77      88 ..      76      93 .. 0.82
   3 ?    0.0   0.0       2.1   1.3e+03      14      29 ..     524     539 ..     519     541 .. 0.87
   4 ?    6.1   0.0     0.025        15       2      25 ..     587     610 ..     586     611 .. 0.93
   5 ?    1.6   0.0      0.68   4.2e+02       8      25 ..     661     678 ..     661     682 .. 0.88
   6 ?    1.1   0.0      0.99   6.1e+02       9      25 ..     704     720 ..     703     723 .. 0.85
   7 ?   -2.0   0.0       9.4   5.8e+03      13      25 ..     747     759 ..     743     764 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.9
                               PPR 14 GkleeAlelfke 25
                                      G+ eeA++ f+e
  gi|330509114|ref|YP_004385542.1|  2 GRNEEAISAFDE 13
                                      889*******98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5
                               PPR 14 GkleeAlelfke 25
                                      Gk eeAle + +
  gi|330509114|ref|YP_004385542.1| 77 GKSEEALEAYGR 88
                                      899****98876 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 2.1
                               PPR  14 GkleeAlelfkeMkek 29 
                                       G+ +eAl+ +++ +e 
  gi|330509114|ref|YP_004385542.1| 524 GRSDEALQAYEKVIEL 539
                                       899*******998886 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.025
                               PPR   2 tynslIsgycknGkleeAlelfke 25 
                                       t+ns   +++  Gk eeA+e f++
  gi|330509114|ref|YP_004385542.1| 587 TWNSAGFALAELGKEEEAFEAFEK 610
                                       9999999*************9986 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.68
                               PPR   8 sgycknGkleeAlelfke 25 
                                       ++++k  ++ +Al+ f++
  gi|330509114|ref|YP_004385542.1| 661 NALAKMDNHNDALKAFEK 678
                                       699*************98 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.99
                               PPR   9 gycknGkleeAlelfke 25 
                                       ++ k ++++eA+e +++
  gi|330509114|ref|YP_004385542.1| 704 ALIKLNRYDEAIEALDR 720
                                       67899*******99886 PP

  == domain 7  score: -2.0 bits;  conditional E-value: 9.4
                               PPR  13 nGkleeAlelfke 25 
                                        Gk e+Ale +++
  gi|330509114|ref|YP_004385542.1| 747 LGKNEDALEAYNK 759
                                       5777888888776 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3      0.32     2e+02     269     295 ..       5      33 ..       2     103 .. 0.45
   2 ?    0.6   0.0      0.43   2.7e+02     144     204 ..      95     160 ..      75     191 .. 0.75
   3 ?   -0.9   0.1       1.2   7.4e+02     242     290 ..     465     514 ..     443     542 .. 0.72
   4 ?    3.8   0.2     0.045        28     241     287 ..     649     688 ..     594     692 .. 0.71
   5 ?    5.5   0.0     0.013       8.2     246     291 ..     735     773 ..     727     788 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.32
                                       SSCCHHHHCCHHCTCCCHSTTCC..CCHH CS
                               FAT 269 eeilqsysaateidpswykawht..walf 295
                                       ee+ +++ +  ++dp+ + awh+  +al+
  gi|330509114|ref|YP_004385542.1|   5 EEAISAFDEGLKTDPQNASAWHHrgMALA 33 
                                       56666666666666666666665442222 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.43
                                       S-STTCCCCCCCCHCHHHHCCSTTHHCCCCCHCTT............TT.TSSCCCHHHHHHHCCHHH CS
                               FAT 144 gvkaemwlkfanlarksgrlslAekaLkelleedp....eewlp...rappevvyaylKylwssgeqk 204
                                       +  +e+w++ +++   +gr++++ ++ ++++   p    e+  +   ++ +e ++   K ++ +g+++
  gi|330509114|ref|YP_004385542.1|  95 SHALEAWIRESDILAAQGRYNQSVESFSRAMALVPanksES--QlgfQRRSENTFIFTKAWLINGQIH 160
                                       556899******************99999999999653222..2456777777777777777777764 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.2
                                       .HH.HHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTC CS
                               FAT 242 kll.arcylkkGewqealqkldwseekieeilqsysaateidpswykawh 290
                                       + + ar+   k++ ++ l++ ++s + ie++l+   ++te +p+  +aw 
  gi|330509114|ref|YP_004385542.1| 465 NPQdARAWEAKSDALIGLGRQEESLDAIEKALEILNLSTERNPKDGEAWW 514
                                       33447777777777778888777778888888888888888888888774 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.045
                                       ..HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHS CS
                               FAT 241 tkllarcylkkGewqealqkldwseekieeilqsysaateidpswyk 287
                                         + a++  kkG  ++++ +        +++l+++ +a+ei++++++
  gi|330509114|ref|YP_004385542.1| 649 DPKWAEVWYKKGNALAKMDN-------HNDALKAFEKAVEISDEVIQ 688
                                       44446777777777777777.......78888888888888888776 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.013
                                       HCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 246 rcylkkGewqealqkldwseekieeilqsysaateidpswykawht 291
                                       ++ + kG+ + al+k       +e++l++y ++ e++p    awh 
  gi|330509114|ref|YP_004385542.1| 735 EAWNGKGDILLALGK-------NEDALEAYNKSIEFNPAFGRAWHG 773
                                       556668889999999.......9*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (801 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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):              29  [number of targets reported over threshold]
# CPU time: 0.96u 0.33s 00:00:01.29 Elapsed: 00:00:00.62
# Mc/sec: 3900.59
//
Query:       gi|330509115|ref|YP_004385543.1|  [L=1140]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-86  283.5  43.4    3.6e-08   33.0   0.1   19.9 19  TPR_11           TPR repeat
    2.2e-86  277.2  53.6    0.00016   21.5   0.0   21.9 22  TPR_2            Tetratricopeptide repeat
    2.4e-86  280.3  45.6      3e-07   30.0   0.0   23.2 24  TPR_1            Tetratricopeptide repeat
      1e-71  231.2  34.9    2.5e-05   24.1   0.0   21.4 21  TPR_8            Tetratricopeptide repeat
    3.8e-58  193.9  50.2    5.4e-10   39.8   0.0   14.8 14  TPR_16           Tetratricopeptide repeat
    3.9e-52  171.0  16.2    0.00095   19.4   0.0   16.4 15  TPR_17           Tetratricopeptide repeat
      2e-51  168.2  63.2    0.00041   20.9   0.2   20.0 20  TPR_14           Tetratricopeptide repeat
      3e-39  133.2  55.6    7.8e-06   26.1   0.3   15.7 17  TPR_12           Tetratricopeptide repeat
    3.7e-39  133.1  43.5    0.00016   22.1   0.2   14.6 15  TPR_19           Tetratricopeptide repeat
    4.3e-30  103.7  26.8    0.00023   21.2   1.2   12.7 13  TPR_9            Tetratricopeptide repeat
    1.3e-18   65.6  35.7       0.02   14.9   0.1   15.7 14  TPR_7            Tetratricopeptide repeat
    6.4e-18   65.2  33.1     0.0011   19.0   1.1   10.5 10  DUF3856          Domain of Unknown Function (DUF3856)
    3.7e-17   62.4   6.2      0.035   13.0   0.1    9.4  9  NARP1            NMDA receptor-regulated protein 1
    9.4e-16   57.3  39.7       0.47   11.2   0.0   17.9 19  TPR_6            Tetratricopeptide repeat
    3.5e-14   52.8  16.7       0.01   16.1   0.0    9.0  9  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    2.4e-10   40.7   0.5    2.5e-09   37.5   0.1    2.6  2  LTD              Lamin Tail Domain
    3.4e-09   36.3  68.0       0.12   12.3   0.4   18.9 21  TPR_10           Tetratricopeptide repeat
    4.3e-08   33.1   6.5        0.2   11.4   0.1    6.4  7  TOM20_plant      Plant specific mitochondrial import receptor
    1.4e-06   28.8  35.2     0.0066   16.9   0.4    8.9  8  BTAD             Bacterial transcriptional activator domain
    2.6e-06   27.4   1.4       0.54   10.4   0.0    6.8  5  ANAPC5           Anaphase-promoting complex subunit 5
    4.6e-06   26.6  14.7         22    5.2   0.1   10.3 12  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    1.4e-05   25.6  16.1       0.01   16.3   0.1    6.7  7  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
      4e-05   23.2  30.7       0.39   10.1   0.4    7.7  7  SNAP             Soluble NSF attachment protein, SNAP
    0.00018   21.0   8.8         14    5.3   0.0    8.5  8  HTH_Bact         Helix-turn-helix bacterial domain
     0.0011   18.6   0.6          3    7.7   0.0    4.1  3  PPTA             Protein prenyltransferase alpha subunit repe
     0.0022   17.9   1.9        1.3    9.0   0.1    4.0  3  YfdX             YfdX protein
     0.0029   17.9  11.0        3.7    8.0   0.0    6.0  5  TPR_20           Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.018   15.2  14.5        1.3    9.3   0.0    7.8  8  DUF1510          Domain of unknown function (DUF1510)
      0.026   14.5   0.1    1.1e+02    2.9   0.0    5.5  5  MCC-bdg_PDZ      PDZ domain of MCC-2 bdg protein for Usher sy
      0.058   14.1   2.7         22    5.9   0.1    3.9  2  Sel1             Sel1 repeat
      0.078   13.0   3.7        2.1    8.5   0.0    5.3  6  TPR_3            Tetratricopeptide repeat
       0.14   11.7   6.0      1e+02    2.5   0.0    6.1  5  SHNi-TPR         SHNi-TPR
       0.22   11.8  11.8        6.5    7.0   0.5    5.3  5  TPR_5            Tetratrico peptide repeat
       0.62    9.9   6.9         19    5.0   0.1    6.4  8  DUF5113          Domain of unknown function (DUF5113)


Domain annotation for each model (and alignments):
>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   1.6e-05    0.0086       4      31 ..      53      80 ..      51      84 .. 0.92
   2 !   21.0   0.0   3.7e-07   0.00019       7      38 ..      97     128 ..      96     130 .. 0.92
   3 !   20.3   0.0   5.9e-07   0.00031      10      36 ..     144     170 ..     143     171 .. 0.92
   4 !   10.5   1.0   0.00072      0.38       9      29 ..     184     204 ..     181     214 .. 0.85
   5 !   12.5   0.1   0.00017     0.091      10      27 ..     238     255 ..     222     257 .. 0.89
   6 !   10.7   0.2   0.00059      0.31      10      42 .]     281     313 ..     267     313 .. 0.96
   7 !   25.5   0.0   1.4e-08   7.6e-06       6      37 ..     311     342 ..     307     346 .. 0.90
   8 !   33.0   0.1   6.8e-11   3.6e-08       6      37 ..     346     377 ..     345     378 .. 0.95
   9 !   30.6   0.0   3.6e-10   1.9e-07       1      38 [.     375     412 ..     375     412 .. 0.97
  10 !   15.8   0.2   1.6e-05    0.0082       1      33 [.     409     441 ..     409     445 .. 0.91
  11 !   27.9   0.2   2.6e-09   1.4e-06      10      39 ..     473     502 ..     472     504 .. 0.95
  12 !    8.8   0.0    0.0024       1.3       7      36 ..     511     540 ..     510     546 .. 0.86
  13 !    9.3   0.1    0.0017       0.9       7      28 ..     545     566 ..     544     568 .. 0.90
  14 !   11.8   0.0   0.00027      0.14       2      26 ..     575     599 ..     575     601 .. 0.92
  15 ?   -1.6   0.0       4.2   2.2e+03       7      18 ..     672     683 ..     672     684 .. 0.86
  16 !    9.4   0.2    0.0016      0.85       1      21 [.     710     730 ..     710     731 .. 0.97
  17 ?    5.6   0.2     0.024        13       8      33 ..     769     794 ..     762     796 .. 0.90
  18 !   15.7   0.0   1.7e-05    0.0087       7      42 .]     802     837 ..     798     837 .. 0.90
  19 !   19.7   0.0   9.1e-07   0.00048       7      42 .]     875     910 ..     871     910 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                            TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeay 31
                                      +y  G +ee+++a  kA++ldP+na+++
  gi|330509115|ref|YP_004385543.1| 53 LYNNGSLEESLQAVDKAIELDPENATLW 80
                                      6889*********************987 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 3.7e-07
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       q +++e++++Y +A++ldP+n + +++ G+a+
  gi|330509115|ref|YP_004385543.1|  97 QSRFDESLQVYDRAIELDPENTTYLLWKGFAL 128
                                       5689***********************99986 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 5.9e-07
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGl 36 
                                       +eeAie + +Al++dP++aea+ + G+
  gi|330509115|ref|YP_004385543.1| 144 FEEAIETFDRALEIDPKFAEAWAGKGV 170
                                       69*******************988775 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.00072
                            TPR_11   9 kyeeAieaYkkAlkldPdnae 29 
                                       +y+++++aY kA++l P+n +
  gi|330509115|ref|YP_004385543.1| 184 RYNDSLAAYDKAIELAPTNDS 204
                                       79****************975 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 0.00017
                            TPR_11  10 yeeAieaYkkAlkldPdn 27 
                                       ++eA+++Y k ++ldPd+
  gi|330509115|ref|YP_004385543.1| 238 LKEAVKNYDKVIDLDPDF 255
                                       579*************97 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.00059
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ye+Aie++++ ++ + +n  a+ n + ++++qG
  gi|330509115|ref|YP_004385543.1| 281 YEKAIEQLNRSIEVNLNNSGAWVNKAILFQEQG 313
                                       9***************************99998 PP

  == domain 7  score: 25.5 bits;  conditional E-value: 1.4e-08
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       eqG+yeeAi+a+++A k++P+++ a+  +G++
  gi|330509115|ref|YP_004385543.1| 311 EQGRYEEAITALNNATKITPEYVMAWEMMGEI 342
                                       8**********************999888876 PP

  == domain 8  score: 33.0 bits;  conditional E-value: 6.8e-11
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       ++G+y+e+ieaY +Al+ldP++a+a+   G+a
  gi|330509115|ref|YP_004385543.1| 346 DLGRYDESIEAYDRALQLDPSDARAWTSKGHA 377
                                       79*************************99998 PP

  == domain 9  score: 30.6 bits;  conditional E-value: 3.6e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       G+a++++G++ eA+ aY +Alk+dP+ a+a+++ G+a+
  gi|330509115|ref|YP_004385543.1| 375 GHALRSLGRNREAVLAYDRALKIDPNRATAWSGKGAAL 412
                                       99********************************9985 PP

  == domain 10  score: 15.8 bits;  conditional E-value: 1.6e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayyn 33 
                                       G a+++qG+y+e+++aY + l+  + +++  y 
  gi|330509115|ref|YP_004385543.1| 409 GAALRDQGRYNESVQAYDEVLRAVERDPTYRYS 441
                                       6699******************99999999885 PP

  == domain 11  score: 27.9 bits;  conditional E-value: 2.6e-09
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       y+e+++aY+kA+++dP++a+a+ ++G+a++
  gi|330509115|ref|YP_004385543.1| 473 YNESLQAYEKAIQIDPESARAWIGRGNALL 502
                                       9***************************86 PP

  == domain 12  score: 8.8 bits;  conditional E-value: 0.0024
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                       +  ye A+e+++  l+ dP++aea++  ++
  gi|330509115|ref|YP_004385543.1| 511 KEAYERAVEVLNGSLEEDPEDAEAWWLKAE 540
                                       567**********************98765 PP

  == domain 13  score: 9.3 bits;  conditional E-value: 0.0017
                            TPR_11   7 qGkyeeAieaYkkAlkldPdna 28 
                                       +G+ +eA++aY + ++l+++ a
  gi|330509115|ref|YP_004385543.1| 545 LGRSNEALQAYDRVIELNSSKA 566
                                       68899*************9876 PP

  == domain 14  score: 11.8 bits;  conditional E-value: 0.00027
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPd 26 
                                       d+++++G+y+e++ea+  Al+l P+
  gi|330509115|ref|YP_004385543.1| 575 DIFVSLGRYNESVEAFDSALNLLPT 599
                                       79*******************9775 PP

  == domain 15  score: -1.6 bits;  conditional E-value: 4.2
                            TPR_11   7 qGkyeeAieaYk 18 
                                       +G+ +eA++a++
  gi|330509115|ref|YP_004385543.1| 672 LGRHDEALQALS 683
                                       69******9975 PP

  == domain 16  score: 9.4 bits;  conditional E-value: 0.0016
                            TPR_11   1 GdayyeqGkyeeAieaYkkAl 21 
                                       G+a++  + +e+A eaY+kA+
  gi|330509115|ref|YP_004385543.1| 710 GRALFRSQSFEGAAEAYEKAI 730
                                       89******************8 PP

  == domain 17  score: 5.6 bits;  conditional E-value: 0.024
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayyn 33 
                                         +e+A+  + + l++ P+na a++n
  gi|330509115|ref|YP_004385543.1| 769 ESLEKALDYFDQVLEIYPENAGAWLN 794
                                       579********************988 PP

  == domain 18  score: 15.7 bits;  conditional E-value: 1.7e-05
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                        G+  eA+ a  +A++l+P+n ++++ +++++ ++G
  gi|330509115|ref|YP_004385543.1| 802 MGRTGEALDAVDRAVELNPENIDFHWQRAELLSMLG 837
                                       58899999999******************9998777 PP

  == domain 19  score: 19.7 bits;  conditional E-value: 9.1e-07
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       q+++eeA++a++k  +ldP+ ++ ++  G+++ ++G
  gi|330509115|ref|YP_004385543.1| 875 QNNNEEALKAFEKVTELDPQEPTGWLYKGEVLKALG 910
                                       89******************************9998 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   1.5e-06   0.00079       1      34 []      43      76 ..      43      76 .. 0.96
   2 !   14.0   0.0   7.8e-05     0.041       5      34 .]      88     117 ..      84     117 .. 0.83
   3 !   12.4   0.0   0.00026      0.14      17      33 ..     144     160 ..     139     161 .. 0.92
   4 !   10.8   0.2   0.00085      0.45      16      34 .]     184     202 ..     182     202 .. 0.95
   5 !    8.5   0.1    0.0045       2.4       2      30 ..     216     244 ..     215     247 .. 0.90
   6 ?    6.5   0.0      0.02        10      18      33 ..     239     254 ..     225     255 .. 0.90
   7 !   10.2   0.9    0.0013       0.7       2      29 ..     259     286 ..     258     290 .. 0.92
   8 !   19.5   0.0   1.3e-06    0.0007       3      33 ..     301     331 ..     299     332 .. 0.95
   9 !   20.0   0.0   9.5e-07    0.0005      14      34 .]     347     367 ..     346     367 .. 0.94
  10 !   21.5   0.0     3e-07   0.00016       1      33 [.     368     400 ..     368     401 .. 0.96
  11 !   16.1   0.1   1.7e-05     0.009       1      29 [.     402     430 ..     402     435 .. 0.92
  12 !   10.4   0.1    0.0011      0.58      17      33 ..     473     489 ..     472     490 .. 0.94
  13 !   18.3   0.1   3.3e-06    0.0017       1      29 [.     491     519 ..     491     523 .. 0.95
  14 !   18.8   0.1   2.3e-06    0.0012       1      31 [.     532     562 ..     532     564 .. 0.96
  15 !   13.2   0.0   0.00014     0.076       3      33 ..     569     599 ..     567     600 .. 0.94
  16 ?   -1.2   0.0       5.8   3.1e+03      14      24 ..     672     682 ..     672     683 .. 0.87
  17 !   12.3   0.1   0.00026      0.14       2      28 ..     704     730 ..     703     732 .. 0.92
  18 !   11.1   0.1   0.00065      0.34      17      34 .]     771     788 ..     762     788 .. 0.88
  19 !   16.6   0.0   1.2e-05    0.0062       2      34 .]     790     822 ..     789     822 .. 0.95
  20 !    9.2   0.0    0.0028       1.5       3      34 .]     825     856 ..     823     856 .. 0.91
  21 !   20.4   0.0     7e-07   0.00037       1      33 [.     862     894 ..     862     895 .. 0.96
  22 !   12.9   0.3   0.00018     0.095       3      32 ..     898     927 ..     896     929 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.5e-06
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      a ++y+  l +y++g +ee l+a +kA+eldP+n
  gi|330509115|ref|YP_004385543.1| 43 ANYWYEKSLDLYNNGSLEESLQAVDKAIELDPEN 76
                                      679*****************************97 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 7.8e-05
                             TPR_2   5 ynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +  G +  ++ +++e l+ +++A+eldP+n
  gi|330509115|ref|YP_004385543.1|  88 NLAGVITQNQSRFDESLQVYDRAIELDPEN 117
                                       55566667889*****************97 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00026
                             TPR_2  17 yeeAleafekAleldPn 33 
                                       +eeA+e f++Ale+dP+
  gi|330509115|ref|YP_004385543.1| 144 FEEAIETFDRALEIDPK 160
                                       8***************7 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00085
                             TPR_2  16 dyeeAleafekAleldPnn 34 
                                       +y++ l+a++kA+el+P+n
  gi|330509115|ref|YP_004385543.1| 184 RYNDSLAAYDKAIELAPTN 202
                                       799**************98 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0045
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAlel 30 
                                        al  +G+ ++++g+ ee ++ +++A++ 
  gi|330509115|ref|YP_004385543.1| 216 VALSHMGQDLAARGQIEESRAVLKEAVKN 244
                                       58999*********************986 PP

  == domain 6  score: 6.5 bits;  conditional E-value: 0.02
                             TPR_2  18 eeAleafekAleldPn 33 
                                       +eA++ ++k++ ldP+
  gi|330509115|ref|YP_004385543.1| 239 KEAVKNYDKVIDLDPD 254
                                       79************98 PP

  == domain 7  score: 10.2 bits;  conditional E-value: 0.0013
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                       ea  n++ ++ +lg+ +eA++ +ekA+e
  gi|330509115|ref|YP_004385543.1| 259 EAQQNRAGVLKELGRRDEAAAGYEKAIE 286
                                       678899*********************8 PP

  == domain 8  score: 19.5 bits;  conditional E-value: 1.3e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+ n + +  ++g+yeeA+ a++ A ++ P+
  gi|330509115|ref|YP_004385543.1| 301 AWVNKAILFQEQGRYEEAITALNNATKITPE 331
                                       89***************************98 PP

  == domain 9  score: 20.0 bits;  conditional E-value: 9.5e-07
                             TPR_2  14 lgdyeeAleafekAleldPnn 34 
                                       lg+y+e +ea+++Al+ldP +
  gi|330509115|ref|YP_004385543.1| 347 LGRYDESIEAYDRALQLDPSD 367
                                       8******************86 PP

  == domain 10  score: 21.5 bits;  conditional E-value: 3e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+a+   G a++ lg+  eA+ a+++Al++dPn
  gi|330509115|ref|YP_004385543.1| 368 ARAWTSKGHALRSLGRNREAVLAYDRALKIDPN 400
                                       7899****************************8 PP

  == domain 11  score: 16.1 bits;  conditional E-value: 1.7e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAle 29 
                                       a a+   G a++ +g+y+e ++a++++l+
  gi|330509115|ref|YP_004385543.1| 402 ATAWSGKGAALRDQGRYNESVQAYDEVLR 430
                                       679************************98 PP

  == domain 12  score: 10.4 bits;  conditional E-value: 0.0011
                             TPR_2  17 yeeAleafekAleldPn 33 
                                       y+e l+a+ekA+++dP+
  gi|330509115|ref|YP_004385543.1| 473 YNESLQAYEKAIQIDPE 489
                                       89**************7 PP

  == domain 13  score: 18.3 bits;  conditional E-value: 3.3e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAle 29 
                                       a+a+  +G+a++ l +y + +ea+e+A+e
  gi|330509115|ref|YP_004385543.1| 491 ARAWIGRGNALLSLEKYSDSKEAYERAVE 519
                                       78*************************98 PP

  == domain 14  score: 18.8 bits;  conditional E-value: 2.3e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       aea++  ++++ +lg+ +eAl+a+++++el+
  gi|330509115|ref|YP_004385543.1| 532 AEAWWLKAESLDNLGRSNEALQAYDRVIELN 562
                                       89****************************9 PP

  == domain 15  score: 13.2 bits;  conditional E-value: 0.00014
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+ +  ++   lg+y+e +eaf+ Al l P+
  gi|330509115|ref|YP_004385543.1| 569 AWIRKSDIFVSLGRYNESVEAFDSALNLLPT 599
                                       89999***********************997 PP

  == domain 16  score: -1.2 bits;  conditional E-value: 5.8
                             TPR_2  14 lgdyeeAleaf 24 
                                       lg+++eAl+a+
  gi|330509115|ref|YP_004385543.1| 672 LGRHDEALQAL 682
                                       79******986 PP

  == domain 17  score: 12.3 bits;  conditional E-value: 0.00026
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAl 28 
                                       + + + G+a+++++ +e A+ea+ekA+
  gi|330509115|ref|YP_004385543.1| 704 DDWVQTGRALFRSQSFEGAAEAYEKAI 730
                                       668899********************7 PP

  == domain 18  score: 11.1 bits;  conditional E-value: 0.00065
                             TPR_2  17 yeeAleafekAleldPnn 34 
                                       +e+Al++f+++le++P+n
  gi|330509115|ref|YP_004385543.1| 771 LEKALDYFDQVLEIYPEN 788
                                       79**************97 PP

  == domain 19  score: 16.6 bits;  conditional E-value: 1.2e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        a+ n   +++ +g+  eAl+a ++A+el+P+n
  gi|330509115|ref|YP_004385543.1| 790 GAWLNKSFILRWMGRTGEALDAVDRAVELNPEN 822
                                       69*****************************97 PP

  == domain 20  score: 9.2 bits;  conditional E-value: 0.0028
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                        ++++++++  lg+y+e  +af++ +e  P n
  gi|330509115|ref|YP_004385543.1| 825 FHWQRAELLSMLGRYNESDQAFDETIEMIPAN 856
                                       6899********************99998865 PP

  == domain 21  score: 20.4 bits;  conditional E-value: 7e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       ae++   G   + +++ eeAl+afek+ eldP+
  gi|330509115|ref|YP_004385543.1| 862 AEVWTFKGFNFMGQNNNEEALKAFEKVTELDPQ 894
                                       79999***************************7 PP

  == domain 22  score: 12.9 bits;  conditional E-value: 0.00018
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                       ++ + G+++ +lg+ +eA ea+ +A eld 
  gi|330509115|ref|YP_004385543.1| 898 GWLYKGEVLKALGRRAEADEAYARAGELDN 927
                                       799**********************99986 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.3   0.00055      0.29      10      34 .]      52      76 ..      43      76 .. 0.85
   2 !   16.0   0.0   1.5e-05    0.0078      12      34 .]      95     117 ..      84     117 .. 0.88
   3 !   16.1   0.0   1.4e-05    0.0073      17      34 .]     144     161 ..     141     161 .. 0.95
   4 ?   -1.2   0.0         4   2.1e+03       1      12 [.     162     173 ..     162     175 .. 0.86
   5 !   11.7   0.3   0.00034      0.18      16      34 .]     184     202 ..     183     202 .. 0.95
   6 ?   -1.1   0.0       3.7   1.9e+03       7      16 ..     214     223 ..     208     235 .. 0.54
   7 !    9.9   0.1    0.0013      0.67      18      34 .]     239     255 ..     238     255 .. 0.93
   8 !    8.6   0.1    0.0032       1.7       3      29 ..     260     286 ..     259     294 .. 0.92
   9 !   21.3   0.0   3.2e-07   0.00017       3      33 ..     301     331 ..     299     332 .. 0.93
  10 !   23.4   0.0   6.9e-08   3.6e-05      13      34 .]     346     367 ..     344     367 .. 0.94
  11 !   30.0   0.0   5.8e-10     3e-07       1      33 [.     368     400 ..     368     401 .. 0.98
  12 !   19.5   0.0   1.2e-06   0.00062       1      29 [.     402     430 ..     402     437 .. 0.95
  13 !   13.2   0.3   0.00011     0.059      17      33 ..     473     489 ..     472     490 .. 0.94
  14 !   23.3   0.1   7.5e-08   3.9e-05       1      30 [.     491     520 ..     491     521 .. 0.96
  15 !   16.8   0.0     8e-06    0.0042       1      32 [.     532     563 ..     532     565 .. 0.89
  16 !    8.3   0.0     0.004       2.1      10      33 ..     576     599 ..     569     600 .. 0.88
  17 ?    0.6   0.0       1.1   5.6e+02      14      24 ..     672     682 ..     672     684 .. 0.88
  18 ?    6.1   0.0     0.019        10       7      28 ..     709     730 ..     703     732 .. 0.87
  19 ?   -0.4   0.0       2.3   1.2e+03       1      12 [.     741     752 ..     741     755 .. 0.87
  20 !   12.9   0.3   0.00014     0.072      17      34 .]     771     788 ..     766     788 .. 0.91
  21 !   12.9   0.0   0.00014     0.072       3      34 .]     791     822 ..     789     822 .. 0.89
  22 ?    3.9   0.0       0.1        53       7      32 ..     829     854 ..     828     856 .. 0.89
  23 !   18.1   0.0   3.3e-06    0.0017       1      33 [.     862     894 ..     862     895 .. 0.95
  24 ?    4.7   0.1     0.056        29       3      27 ..     898     922 ..     896     927 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00055
                                      HHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1 10 ayfklgkydeAleyyekALelnPnn 34
                                       ++++g ++e l++ +kA+el+P+n
  gi|330509115|ref|YP_004385543.1| 52 DLYNNGSLEESLQAVDKAIELDPEN 76
                                      58999******************97 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.5e-05
                                       HHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  12 fklgkydeAleyyekALelnPnn 34 
                                       +++ ++de l+ y++A+el+P+n
  gi|330509115|ref|YP_004385543.1|  95 QNQSRFDESLQVYDRAIELDPEN 117
                                       6899*****************97 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHHHHSTTH CS
                             TPR_1  17 ydeAleyyekALelnPnn 34 
                                       ++eA+e +++ALe++P++
  gi|330509115|ref|YP_004385543.1| 144 FEEAIETFDRALEIDPKF 161
                                       89**************96 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 4
                                       HHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayf 12 
                                       a+a+ ++G+++ 
  gi|330509115|ref|YP_004385543.1| 162 AEAWAGKGVICD 173
                                       89*******986 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.00034
                                       -HHHHHHHHHHHHHHSTTH CS
                             TPR_1  16 kydeAleyyekALelnPnn 34 
                                       +y++ l++y+kA+el P+n
  gi|330509115|ref|YP_004385543.1| 184 RYNDSLAAYDKAIELAPTN 202
                                       799**************98 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 3.7
                                       HHHHHHHTT- CS
                             TPR_1   7 lGnayfklgk 16 
                                       +++a+ ++g+
  gi|330509115|ref|YP_004385543.1| 214 KAVALSHMGQ 223
                                       5555555554 PP

  == domain 7  score: 9.9 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHSTTH CS
                             TPR_1  18 deAleyyekALelnPnn 34 
                                       +eA++ y+k++ l+P++
  gi|330509115|ref|YP_004385543.1| 239 KEAVKNYDKVIDLDPDF 255
                                       79*************97 PP

  == domain 8  score: 8.6 bits;  conditional E-value: 0.0032
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALe 29 
                                       a  n++ ++ +lg+ deA + yekA+e
  gi|330509115|ref|YP_004385543.1| 260 AQQNRAGVLKELGRRDEAAAGYEKAIE 286
                                       5669999*******************9 PP

  == domain 9  score: 21.3 bits;  conditional E-value: 3.2e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+ n++ +++++g+y+eA+ + + A ++ P+
  gi|330509115|ref|YP_004385543.1| 301 AWVNKAILFQEQGRYEEAITALNNATKITPE 331
                                       8************************999876 PP

  == domain 10  score: 23.4 bits;  conditional E-value: 6.9e-08
                                       HTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  13 klgkydeAleyyekALelnPnn 34 
                                        lg+yde +e+y++AL+l+P++
  gi|330509115|ref|YP_004385543.1| 346 DLGRYDESIEAYDRALQLDPSD 367
                                       59******************86 PP

  == domain 11  score: 30.0 bits;  conditional E-value: 5.8e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+a+  +G+a+++lg+  eA+ +y++AL+++Pn
  gi|330509115|ref|YP_004385543.1| 368 ARAWTSKGHALRSLGRNREAVLAYDRALKIDPN 400
                                       89******************************9 PP

  == domain 12  score: 19.5 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALe 29 
                                       a a+ ++G+a++ +g+y+e +++y+++L+
  gi|330509115|ref|YP_004385543.1| 402 ATAWSGKGAALRDQGRYNESVQAYDEVLR 430
                                       679***********************995 PP

  == domain 13  score: 13.2 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHSTT CS
                             TPR_1  17 ydeAleyyekALelnPn 33 
                                       y+e l++yekA++++P+
  gi|330509115|ref|YP_004385543.1| 473 YNESLQAYEKAIQIDPE 489
                                       99**************7 PP

  == domain 14  score: 23.3 bits;  conditional E-value: 7.5e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a+a+ ++Gna+++l+ky +  e+ye+A+e+
  gi|330509115|ref|YP_004385543.1| 491 ARAWIGRGNALLSLEKYSDSKEAYERAVEV 520
                                       89*************************995 PP

  == domain 15  score: 16.8 bits;  conditional E-value: 8e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+a+  ++  + +lg+ +eAl++y++++eln 
  gi|330509115|ref|YP_004385543.1| 532 AEAWWLKAESLDNLGRSNEALQAYDRVIELNS 563
                                       56677789999*******************97 PP

  == domain 16  score: 8.3 bits;  conditional E-value: 0.004
                                       HHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  10 ayfklgkydeAleyyekALelnPn 33 
                                       ++ +lg+y+e +e+++ AL l P+
  gi|330509115|ref|YP_004385543.1| 576 IFVSLGRYNESVEAFDSALNLLPT 599
                                       5678***************99986 PP

  == domain 17  score: 0.6 bits;  conditional E-value: 1.1
                                       TT-HHHHHHHH CS
                             TPR_1  14 lgkydeAleyy 24 
                                       lg++deAl++ 
  gi|330509115|ref|YP_004385543.1| 672 LGRHDEALQAL 682
                                       79******986 PP

  == domain 18  score: 6.1 bits;  conditional E-value: 0.019
                                       HHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1   7 lGnayfklgkydeAleyyekAL 28 
                                        G a+f+ + ++ A e+yekA+
  gi|330509115|ref|YP_004385543.1| 709 TGRALFRSQSFEGAAEAYEKAI 730
                                       5889999999***********8 PP

  == domain 19  score: -0.4 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayf 12 
                                       a+a++++G a++
  gi|330509115|ref|YP_004385543.1| 741 AEAWKGKGEAFL 752
                                       89*******987 PP

  == domain 20  score: 12.9 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHHHSTTH CS
                             TPR_1  17 ydeAleyyekALelnPnn 34 
                                       +++Al+y++++Le++P+n
  gi|330509115|ref|YP_004385543.1| 771 LEKALDYFDQVLEIYPEN 788
                                       79**************97 PP

  == domain 21  score: 12.9 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+ n+  +++ +g+  eAl++ ++A+elnP+n
  gi|330509115|ref|YP_004385543.1| 791 AWLNKSFILRWMGRTGEALDAVDRAVELNPEN 822
                                       67777779999*******************97 PP

  == domain 22  score: 3.9 bits;  conditional E-value: 0.1
                                       HHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnP 32 
                                       ++ ++  lg+y+e  +++++ +e  P
  gi|330509115|ref|YP_004385543.1| 829 RAELLSMLGRYNESDQAFDETIEMIP 854
                                       789999***************99887 PP

  == domain 23  score: 18.1 bits;  conditional E-value: 3.3e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+++  +G  ++ +++ +eAl+++ek+ el+P+
  gi|330509115|ref|YP_004385543.1| 862 AEVWTFKGFNFMGQNNNEEALKAFEKVTELDPQ 894
                                       7899999*************************6 PP

  == domain 24  score: 4.7 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekA 27 
                                        +  +G ++  lg+  eA e+y +A
  gi|330509115|ref|YP_004385543.1| 898 GWLYKGEVLKALGRRAEADEAYARA 922
                                       6999******************998 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.2    0.0013      0.71       2      34 .]      44      76 ..      43      76 .. 0.90
   2 !   10.2   0.0    0.0014      0.71       4      34 .]      87     117 ..      84     117 .. 0.87
   3 !   10.5   0.0    0.0011      0.57      17      33 ..     144     160 ..     144     161 .. 0.94
   4 ?    7.1   0.1     0.013         7      12      34 .]     180     202 ..     162     202 .. 0.85
   5 ?    6.2   0.0     0.027        14      17      33 ..     238     254 ..     225     255 .. 0.87
   6 !    8.4   0.2    0.0054       2.9       2      29 ..     259     286 ..     258     287 .. 0.92
   7 !   18.9   0.0   2.2e-06    0.0012       3      33 ..     301     331 ..     299     332 .. 0.95
   8 !   22.1   0.0   2.1e-07   0.00011       3      34 .]     335     367 ..     335     367 .. 0.94
   9 !   24.1   0.0   4.7e-08   2.5e-05       1      33 [.     368     400 ..     368     401 .. 0.97
  10 !    9.8   0.0    0.0019         1       1      29 [.     402     430 ..     402     431 .. 0.91
  11 !    8.5   0.3    0.0049       2.6      17      33 ..     473     489 ..     472     490 .. 0.93
  12 !   14.4   0.1     6e-05     0.032       1      29 [.     491     519 ..     491     520 .. 0.96
  13 !   19.4   0.1   1.6e-06   0.00082       1      32 [.     532     563 ..     532     565 .. 0.95
  14 !   13.7   0.0    0.0001     0.054       3      30 ..     569     596 ..     567     599 .. 0.93
  15 ?   -1.7   0.0         9   4.8e+03      14      24 ..     672     682 ..     670     683 .. 0.86
  16 ?    7.0   0.0     0.015       7.7       5      31 ..     707     733 ..     706     736 .. 0.86
  17 ?    5.6   0.1     0.042        22      15      34 .]     769     788 ..     762     788 .. 0.82
  18 !    8.9   0.0    0.0036       1.9       1      34 []     789     822 ..     789     822 .. 0.95
  19 ?    5.2   0.0     0.056        30       4      34 .]     826     856 ..     823     856 .. 0.87
  20 !   16.9   0.0   9.8e-06    0.0052       1      33 [.     862     894 ..     862     895 .. 0.95
  21 ?    6.4   0.1     0.023        12       7      31 ..     902     926 ..     897     928 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0013
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                       ++y +++ + + g +ee+ ++  ka+eldp+n
  gi|330509115|ref|YP_004385543.1| 44 NYWYEKSLDLYNNGSLEESLQAVDKAIELDPEN 76
                                      678888888899*******************86 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +++ g i +++ +++e+ ++y +a+eldp+n
  gi|330509115|ref|YP_004385543.1|  87 LNLAGVITQNQSRFDESLQVYDRAIELDPEN 117
                                       677788889999*****************86 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHH CS
                             TPR_8  17 yeeAkeyyekaleldpd 33 
                                       +eeA+e++ +ale+dp+
  gi|330509115|ref|YP_004385543.1| 144 FEEAIETFDRALEIDPK 160
                                       69**************8 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.013
                                       HHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  12 lklgdyeeAkeyyekaleldpdn 34 
                                        +  +y+ + ++y ka+el+p+n
  gi|330509115|ref|YP_004385543.1| 180 NDSARYNDSLAAYDKAIELAPTN 202
                                       56779999*************86 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHHHHHH CS
                             TPR_8  17 yeeAkeyyekaleldpd 33 
                                       ++eA++ y k+++ldpd
  gi|330509115|ref|YP_004385543.1| 238 LKEAVKNYDKVIDLDPD 254
                                       589************98 PP

  == domain 6  score: 8.4 bits;  conditional E-value: 0.0054
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                       ea +n + ++++lg+ +eA + yeka+e
  gi|330509115|ref|YP_004385543.1| 259 EAQQNRAGVLKELGRRDEAAAGYEKAIE 286
                                       577899999*****************98 PP

  == domain 7  score: 18.9 bits;  conditional E-value: 2.2e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++n++ + +++g+yeeA+ +++ a+++ p+
  gi|330509115|ref|YP_004385543.1| 301 AWVNKAILFQEQGRYEEAITALNNATKITPE 331
                                       8***************************997 PP

  == domain 8  score: 22.1 bits;  conditional E-value: 2.1e-07
                                       HHHHHHHHH.HHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiy.lklgdyeeAkeyyekaleldpdn 34 
                                       a+ ++g i+  +lg+y+e++e+y +al+ldp++
  gi|330509115|ref|YP_004385543.1| 335 AWEMMGEILsNDLGRYDESIEAYDRALQLDPSD 367
                                       68999*9999*********************85 PP

  == domain 9  score: 24.1 bits;  conditional E-value: 4.7e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+a+  +g+++++lg+  eA+ +y +al++dp+
  gi|330509115|ref|YP_004385543.1| 368 ARAWTSKGHALRSLGRNREAVLAYDRALKIDPN 400
                                       79******************************8 PP

  == domain 10  score: 9.8 bits;  conditional E-value: 0.0019
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekale 29 
                                       a a+  +g +++++g+y+e++++y ++l+
  gi|330509115|ref|YP_004385543.1| 402 ATAWSGKGAALRDQGRYNESVQAYDEVLR 430
                                       5689999******************9986 PP

  == domain 11  score: 8.5 bits;  conditional E-value: 0.0049
                                       HHHHHHHHHHHHHHHHH CS
                             TPR_8  17 yeeAkeyyekaleldpd 33 
                                       y+e+ ++yeka+++dp+
  gi|330509115|ref|YP_004385543.1| 473 YNESLQAYEKAIQIDPE 489
                                       8999************7 PP

  == domain 12  score: 14.4 bits;  conditional E-value: 6e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekale 29 
                                       a+a+   g+++l+l++y  +ke+ye+a+e
  gi|330509115|ref|YP_004385543.1| 491 ARAWIGRGNALLSLEKYSDSKEAYERAVE 519
                                       79*************************98 PP

  == domain 13  score: 19.4 bits;  conditional E-value: 1.6e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       aea+++++  +++lg+ +eA ++y +++el+ 
  gi|330509115|ref|YP_004385543.1| 532 AEAWWLKAESLDNLGRSNEALQAYDRVIELNS 563
                                       79****************************96 PP

  == domain 14  score: 13.7 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+ ++++i  +lg+y+e++e++  al l
  gi|330509115|ref|YP_004385543.1| 569 AWIRKSDIFVSLGRYNESVEAFDSALNL 596
                                       8**********************99976 PP

  == domain 15  score: -1.7 bits;  conditional E-value: 9
                                       TT-HHHHHHHH CS
                             TPR_8  14 lgdyeeAkeyy 24 
                                       lg+++eA +++
  gi|330509115|ref|YP_004385543.1| 672 LGRHDEALQAL 682
                                       8******9876 PP

  == domain 16  score: 7.0 bits;  conditional E-value: 0.015
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleld 31 
                                       ++ g++++  + +e A e+yeka+ ++
  gi|330509115|ref|YP_004385543.1| 707 VQTGRALFRSQSFEGAAEAYEKAIGAA 733
                                       55699999****************876 PP

  == domain 17  score: 5.6 bits;  conditional E-value: 0.042
                                       T-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  15 gdyeeAkeyyekaleldpdn 34 
                                       + +e+A  y+ ++le+ p+n
  gi|330509115|ref|YP_004385543.1| 769 ESLEKALDYFDQVLEIYPEN 788
                                       56799999999999999976 PP

  == domain 18  score: 8.9 bits;  conditional E-value: 0.0036
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a a++n++ i++ +g+  eA  +  +a+el+p+n
  gi|330509115|ref|YP_004385543.1| 789 AGAWLNKSFILRWMGRTGEALDAVDRAVELNPEN 822
                                       569*****************************86 PP

  == domain 19  score: 5.2 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +++ + +++ lg+y+e+ +++ + +e+ p+n
  gi|330509115|ref|YP_004385543.1| 826 HWQRAELLSMLGRYNESDQAFDETIEMIPAN 856
                                       6788999999*************99999875 PP

  == domain 20  score: 16.9 bits;  conditional E-value: 9.8e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ae++  +g   + +++ eeA +++ek++eldp+
  gi|330509115|ref|YP_004385543.1| 862 AEVWTFKGFNFMGQNNNEEALKAFEKVTELDPQ 894
                                       789999**************************7 PP

  == domain 21  score: 6.4 bits;  conditional E-value: 0.023
                                       HHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekaleld 31 
                                       +g +++ lg+  eA e+y +a eld
  gi|330509115|ref|YP_004385543.1| 902 KGEVLKALGRRAEADEAYARAGELD 926
                                       7999**************9997776 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2     0.019        10      33      67 ..      42      76 ..      34      84 .. 0.65
   2 !   13.4   0.0   0.00018     0.095       9      46 ..      96     130 ..      90     135 .. 0.93
   3 !    9.8   0.0    0.0024       1.3      13      44 ..     144     172 ..     142     178 .. 0.93
   4 ?    7.7   2.8      0.01       5.5      11      59 ..     183     233 ..     181     237 .. 0.87
   5 !    7.8   1.3    0.0096         5       4      62 ..     222     286 ..     221     291 .. 0.78
   6 !   39.8   0.0     1e-12   5.4e-10       2      68 .]     304     368 ..     303     368 .. 0.96
   7 !   35.9   1.7   1.6e-11   8.7e-09       3      66 ..     374     434 ..     372     436 .. 0.94
   8 !   15.5   0.1     4e-05     0.021      13      61 ..     473     518 ..     472     519 .. 0.93
   9 !   25.5   0.5   2.9e-08   1.5e-05      13      63 ..     514     561 ..     507     566 .. 0.92
  10 ?    0.4   0.0         2   1.1e+03       5      24 ..     575     594 ..     571     598 .. 0.82
  11 !   15.6   0.1   3.6e-05     0.019       4      47 ..     710     754 ..     707     759 .. 0.93
  12 !   15.2   0.0   4.7e-05     0.025      10      66 ..     768     821 ..     762     823 .. 0.91
  13 !   11.6   0.0   0.00063      0.33      11      62 ..     803     851 ..     798     857 .. 0.87
  14 !   23.6   0.2   1.1e-07   5.9e-05       8      60 ..     873     922 ..     871     927 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.019
                            TPR_16 33 aaeAllllgdaalrqgrlaeAaalyraalraapda 67
                                       a  ++++ + ++ +g l+e ++++++a++ +p +
  gi|330509115|ref|YP_004385543.1| 42 SANYWYEKSLDLYNNGSLEESLQAVDKAIELDPEN 76
                                      56666666666777777777777777777766654 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00018
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalr 46 
                                       ++ ++d+ + ++++a+++d   P++   ll++g a+ +
  gi|330509115|ref|YP_004385543.1|  96 NQSRFDESLQVYDRAIELD---PENTTYLLWKGFALRQ 130
                                       799****************...*************987 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0024
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaa 44 
                                       +++A++ +++al+ d   P  aeA+ ++g+++
  gi|330509115|ref|YP_004385543.1| 144 FEEAIETFDRALEID---PKFAEAWAGKGVIC 172
                                       79*************...***********987 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.01
                            TPR_16  11 gdyddAaaaleaalkrdpssPd..aaeAllllgdaalrqgrlaeAaalyra 59 
                                        +y d +aa++ a++++p       a+A+ ++++a+ + g   +A+ ++++
  gi|330509115|ref|YP_004385543.1| 183 ARYNDSLAAYDKAIELAPTNDSrnLAQAYEGKAVALSHMGQDLAARGQIEE 233
                                       69***************8877799*************99999999866554 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0096
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPd.........aaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       +++++++g+ ++ +a+l++a+k++                eA+ +++ ++ ++gr +eAaa y++a++
  gi|330509115|ref|YP_004385543.1| 222 GQDLAARGQIEESRAVLKEAVKNY---DKvidldpdfvGQEAQQNRAGVLKELGRRDEAAAGYEKAIE 286
                                       677777788888888888888777...334666666999*********************88877765 PP

  == domain 6  score: 39.8 bits;  conditional E-value: 1e-12
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaal.rqgrlaeAaalyraalraapdap 68 
                                       ++a ++ ++g+y++A+ al+ a+k     P+ + A+   g+++   +gr++e +++y++al+ +p+++
  gi|330509115|ref|YP_004385543.1| 304 NKAILFQEQGRYEEAITALNNATKIT---PEYVMAWEMMGEILSnDLGRYDESIEAYDRALQLDPSDA 368
                                       578999********************...***************888******************985 PP

  == domain 7  score: 35.9 bits;  conditional E-value: 1.6e-11
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       +++a++ +g+ ++A+ a+++alk d   P +a A+ ++g a+  qgr+ e +++y++ lra   
  gi|330509115|ref|YP_004385543.1| 374 KGHALRSLGRNREAVLAYDRALKID---PNRATAWSGKGAALRDQGRYNESVQAYDEVLRAVER 434
                                       79***********************...*****************************9988655 PP

  == domain 8  score: 15.5 bits;  conditional E-value: 4e-05
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       y + + a+e a+  d   P+ a+A+ ++g+a+l +  + +  ++y++a+
  gi|330509115|ref|YP_004385543.1| 473 YNESLQAYEKAIQID---PESARAWIGRGNALLSLEKYSDSKEAYERAV 518
                                       778999*********...*********************9999999986 PP

  == domain 9  score: 25.5 bits;  conditional E-value: 2.9e-08
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       y++A+++l+  l+ d   P++aeA++l+++++  +gr  eA+++y++ ++ 
  gi|330509115|ref|YP_004385543.1| 514 YERAVEVLNGSLEED---PEDAEAWWLKAESLDNLGRSNEALQAYDRVIEL 561
                                       9**************...****************************98765 PP

  == domain 10  score: 0.4 bits;  conditional E-value: 2
                            TPR_16   5 raalragdyddAaaaleaal 24 
                                       ++++ +g+y + ++a++ al
  gi|330509115|ref|YP_004385543.1| 575 DIFVSLGRYNESVEAFDSAL 594
                                       67788999999999999887 PP

  == domain 11  score: 15.6 bits;  conditional E-value: 3.6e-05
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPd.aaeAllllgdaalrq 47 
                                       +ra++r++ ++ Aa+a+e a+ +++s     aeA+ ++g+a+l++
  gi|330509115|ref|YP_004385543.1| 710 GRALFRSQSFEGAAEAYEKAIGAAGSNKIlLAEAWKGKGEAFLVL 754
                                       89**********************888879***********9986 PP

  == domain 12  score: 15.2 bits;  conditional E-value: 4.7e-05
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       +   ++A+ +++++l+ +   P++a A+l++  ++   gr  eA++++++a++  p 
  gi|330509115|ref|YP_004385543.1| 768 NESLEKALDYFDQVLEIY---PENAGAWLNKSFILRWMGRTGEALDAVDRAVELNPE 821
                                       556899************...*******************************99886 PP

  == domain 13  score: 11.6 bits;  conditional E-value: 0.00063
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       g+  +A+ a ++a++++   P++ ++++ +++++  +gr+ e  +++++ ++
  gi|330509115|ref|YP_004385543.1| 803 GRTGEALDAVDRAVELN---PENIDFHWQRAELLSMLGRYNESDQAFDETIE 851
                                       78889************...********************887777776655 PP

  == domain 14  score: 23.6 bits;  conditional E-value: 1.1e-07
                            TPR_16   8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                       + +++ ++A++a+e ++++d   P+ +  +l++g+++ ++gr aeA ++y++a
  gi|330509115|ref|YP_004385543.1| 873 MGQNNNEEALKAFEKVTELD---PQEPTGWLYKGEVLKALGRRAEADEAYARA 922
                                       789*****************...***********************9777776 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0012      0.65       4      20 ..      68      84 ..      66      97 .. 0.93
   2 !    9.1   0.0    0.0035       1.8       2      25 ..     107     130 ..     106     142 .. 0.84
   3 !   11.4   0.0   0.00063      0.33       2      25 ..     151     178 ..     150     184 .. 0.79
   4 !   11.0   0.1   0.00085      0.45       1      33 [.     191     228 ..     191     229 .. 0.93
   5 ?    2.6   0.0      0.42   2.2e+02       2      32 ..     245     277 ..     244     279 .. 0.85
   6 !   13.9   0.0    0.0001     0.053       3      33 ..     289     319 ..     288     320 .. 0.94
   7 !    8.3   0.0     0.006       3.2       3      33 ..     323     354 ..     321     355 .. 0.87
   8 !   19.4   0.0   1.8e-06   0.00095       1      32 [.     356     387 ..     356     388 .. 0.96
   9 !   15.4   0.0   3.4e-05     0.018       1      33 [.     390     422 ..     390     423 .. 0.93
  10 ?   -0.5   0.0       3.9   2.1e+03       3      12 ..     429     438 ..     428     466 .. 0.76
  11 !   18.3   0.0   4.1e-06    0.0022       1      31 [.     479     509 ..     479     516 .. 0.88
  12 !   12.1   0.1    0.0004      0.21       5      34 .]     524     553 ..     521     553 .. 0.96
  13 !    9.9   0.0    0.0019         1       2      32 ..     778     808 ..     777     810 .. 0.86
  14 !   10.8   0.0     0.001      0.53       4      31 ..     814     841 ..     811     845 .. 0.91
  15 !    9.0   0.0    0.0037       1.9       2      32 ..     885     915 ..     884     918 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0012
                            TPR_17  4 kaleldPnnadaynnLA 20
                                      ka+eldP na ++ ++A
  gi|330509115|ref|YP_004385543.1| 68 KAIELDPENATLWAYKA 84
                                      9*************998 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0035
                            TPR_17   2 ylkaleldPnnadaynnLAelllk 25 
                                       y +a+eldP n   +  ++ +l++
  gi|330509115|ref|YP_004385543.1| 107 YDRAIELDPENTTYLLWKGFALRQ 130
                                       99*****************99983 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00063
                            TPR_17   2 ylkaleldPnnadaynnLAelll....k 25 
                                       + +ale+dP+ a+a+  ++++       
  gi|330509115|ref|YP_004385543.1| 151 FDRALEIDPKFAEAWAGKGVICDdlatF 178
                                       89**************999987655554 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00085
                            TPR_17   1 lylkaleldPnn.....adaynnLAelllknGdlmtAr 33 
                                       +y ka+el P+n     a ay  +A++l++ G+   Ar
  gi|330509115|ref|YP_004385543.1| 191 AYDKAIELAPTNdsrnlAQAYEGKAVALSHMGQDLAAR 228
                                       59******************************987775 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.42
                            TPR_17   2 ylkaleldPnn..adaynnLAelllknGdlmtA 32 
                                       y k+++ldP+    +a +n+A +l+++G+ ++A
  gi|330509115|ref|YP_004385543.1| 245 YDKVIDLDPDFvgQEAQQNRAGVLKELGRRDEA 277
                                       99********98999999999999988876665 PP

  == domain 6  score: 13.9 bits;  conditional E-value: 0.0001
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtAr 33 
                                        +++e + nn+ a+ n+A l+ ++G++++A+
  gi|330509115|ref|YP_004385543.1| 289 NRSIEVNLNNSGAWVNKAILFQEQGRYEEAI 319
                                       58999999*********************97 PP

  == domain 7  score: 8.3 bits;  conditional E-value: 0.006
                            TPR_17   3 lkaleldPnnadaynnLAelll.knGdlmtAr 33 
                                        +a ++ P ++ a+ +++e+l+  +G++++ +
  gi|330509115|ref|YP_004385543.1| 323 NNATKITPEYVMAWEMMGEILSnDLGRYDESI 354
                                       679999***************95669999876 PP

  == domain 8  score: 19.4 bits;  conditional E-value: 1.8e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y +al+ldP++a a++ ++ +l+++G+ ++A
  gi|330509115|ref|YP_004385543.1| 356 AYDRALQLDPSDARAWTSKGHALRSLGRNREA 387
                                       59**************************9998 PP

  == domain 9  score: 15.4 bits;  conditional E-value: 3.4e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y +al++dPn a a+  ++ +l+ +G++ + +
  gi|330509115|ref|YP_004385543.1| 390 AYDRALKIDPNRATAWSGKGAALRDQGRYNESV 422
                                       59**************************98866 PP

  == domain 10  score: -0.5 bits;  conditional E-value: 3.9
                            TPR_17   3 lkaleldPnn 12 
                                       l+a+e+dP++
  gi|330509115|ref|YP_004385543.1| 429 LRAVERDPTY 438
                                       69******98 PP

  == domain 11  score: 18.3 bits;  conditional E-value: 4.1e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                       +y+ka+++dP +a a+  ++++ll++ ++ +
  gi|330509115|ref|YP_004385543.1| 479 AYEKAIQIDPESARAWIGRGNALLSLEKYSD 509
                                       5***********************9887654 PP

  == domain 12  score: 12.1 bits;  conditional E-value: 0.0004
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmtArq 34 
                                       +le dP +a+a+ ++Ae l ++G++ +A+q
  gi|330509115|ref|YP_004385543.1| 524 SLEEDPEDAEAWWLKAESLDNLGRSNEALQ 553
                                       79**************************87 PP

  == domain 13  score: 9.9 bits;  conditional E-value: 0.0019
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       + ++le++P na a+ n+  +l+  G++++A
  gi|330509115|ref|YP_004385543.1| 778 FDQVLEIYPENAGAWLNKSFILRWMGRTGEA 808
                                       889****************999977777777 PP

  == domain 14  score: 10.8 bits;  conditional E-value: 0.001
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmt 31 
                                       +a+el+P n d++ ++Aell+++G++ +
  gi|330509115|ref|YP_004385543.1| 814 RAVELNPENIDFHWQRAELLSMLGRYNE 841
                                       89**********************9876 PP

  == domain 15  score: 9.0 bits;  conditional E-value: 0.0037
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       ++k+ eldP  +  + +++e+l+ +G+ ++A
  gi|330509115|ref|YP_004385543.1| 885 FEKVTELDPQEPTGWLYKGEVLKALGRRAEA 915
                                       89**********************9986655 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   9.8e-05     0.052       4      42 ..      46      84 ..      43      85 .. 0.87
   2 !   11.4   0.0   0.00089      0.47      14      40 ..      97     123 ..      89     128 .. 0.85
   3 !   15.3   0.1   4.9e-05     0.026      17      41 ..     144     168 ..     126     171 .. 0.80
   4 ?    5.0   0.2       0.1        55       6      35 ..     174     203 ..     173     211 .. 0.85
   5 ?    7.3   0.0     0.018       9.7       4      31 ..     218     245 ..     215     256 .. 0.80
   6 !    8.7   0.4    0.0067       3.5       3      37 ..     260     294 ..     259     306 .. 0.69
   7 !   19.8   0.0   1.8e-06   0.00093       3      43 ..     301     341 ..     299     342 .. 0.91
   8 !   20.9   0.2   7.9e-07   0.00041      13      39 ..     346     372 ..     341     375 .. 0.92
   9 !   15.4   0.4   4.6e-05     0.024       8      39 ..     375     406 ..     373     411 .. 0.92
  10 ?    7.9   0.3     0.012       6.5       4      39 ..     405     440 ..     404     447 .. 0.85
  11 !    9.9   0.1    0.0027       1.4      18      40 ..     474     496 ..     465     500 .. 0.86
  12 !   11.3   0.2   0.00094       0.5      16      43 ..     513     540 ..     496     541 .. 0.76
  13 !   12.0   0.2   0.00057       0.3       1      41 [.     532     573 ..     532     576 .. 0.85
  14 ?    1.7   0.0       1.2   6.3e+02       3      32 ..     569     598 ..     567     602 .. 0.86
  15 ?   -0.8   0.0       7.3   3.8e+03      14      24 ..     672     682 ..     672     684 .. 0.88
  16 !   10.8   0.2    0.0014      0.72       3      38 ..     705     744 ..     703     750 .. 0.81
  17 !   13.8   0.0   0.00015      0.08      11      41 ..     765     795 ..     762     798 .. 0.88
  18 !    9.6   0.1    0.0033       1.8      11      43 ..     799     831 ..     796     838 .. 0.88
  19 !   11.9   0.0   0.00063      0.33      14      43 ..     875     904 ..     864     905 .. 0.91
  20 ?    5.0   0.4     0.099        52       3      29 ..     898     924 ..     896     942 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.8e-05
                            TPR_14  4 llalaeallalGdpdeAiallrralalaPddaeawllla 42
                                      +++    l+++G ++e++++ ++a++l+P++a++w + a
  gi|330509115|ref|YP_004385543.1| 46 WYEKSLDLYNNGSLEESLQAVDKAIELDPENATLWAYKA 84
                                      5666666899*************************9987 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00089
                            TPR_14  14 lGdpdeAiallrralalaPddaeawll 40 
                                       + ++de++++++ra++l+P++ +++l 
  gi|330509115|ref|YP_004385543.1|  97 QSRFDESLQVYDRAIELDPENTTYLLW 123
                                       679*****************9987765 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 4.9e-05
                            TPR_14  17 pdeAiallrralalaPddaeawlll 41 
                                       ++eAi+ ++ral+ +P++aeaw   
  gi|330509115|ref|YP_004385543.1| 144 FEEAIETFDRALEIDPKFAEAWAGK 168
                                       89********************866 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.1
                            TPR_14   6 alaeallalGdpdeAiallrralalaPdda 35 
                                       +la +   + ++ +++a++++a++laP+++
  gi|330509115|ref|YP_004385543.1| 174 DLATFNNDSARYNDSLAAYDKAIELAPTND 203
                                       6788888899999**************986 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.018
                            TPR_14   4 llalaeallalGdpdeAiallrralala 31 
                                       l  +++ l+a+G+ +e++a+l++a++ +
  gi|330509115|ref|YP_004385543.1| 218 LSHMGQDLAARGQIEESRAVLKEAVKNY 245
                                       66788999999**999999999998854 PP

  == domain 6  score: 8.7 bits;  conditional E-value: 0.0067
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaea 37 
                                       a++ +a +l +lG+ deA+a +++a+++   + e+
  gi|330509115|ref|YP_004385543.1| 260 AQQNRAGVLKELGRRDEAAAGYEKAIEQLNRSIEV 294
                                       67778999999999888777777777765544443 PP

  == domain 7  score: 19.8 bits;  conditional E-value: 1.8e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       a+   a ++ ++G+++eAi++l+ a +  P+   aw ++++
  gi|330509115|ref|YP_004385543.1| 301 AWVNKAILFQEQGRYEEAITALNNATKITPEYVMAWEMMGE 341
                                       6666789999*****************************98 PP

  == domain 8  score: 20.9 bits;  conditional E-value: 7.9e-07
                            TPR_14  13 alGdpdeAiallrralalaPddaeawl 39 
                                        lG++de+i++++ral+l+P+da+aw+
  gi|330509115|ref|YP_004385543.1| 346 DLGRYDESIEAYDRALQLDPSDARAWT 372
                                       58************************7 PP

  == domain 9  score: 15.4 bits;  conditional E-value: 4.6e-05
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawl 39 
                                       ++al+ lG+ +eA+ +++ral+ +P+ a+aw 
  gi|330509115|ref|YP_004385543.1| 375 GHALRSLGRNREAVLAYDRALKIDPNRATAWS 406
                                       689***************************95 PP

  == domain 10  score: 7.9 bits;  conditional E-value: 0.012
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +   ++al+ +G++ e++++++++l++   d+++++
  gi|330509115|ref|YP_004385543.1| 405 WSGKGAALRDQGRYNESVQAYDEVLRAVERDPTYRY 440
                                       666789********************9988888775 PP

  == domain 11  score: 9.9 bits;  conditional E-value: 0.0027
                            TPR_14  18 deAiallrralalaPddaeawll 40 
                                        e+++++++a++ +P++a+aw+ 
  gi|330509115|ref|YP_004385543.1| 474 NESLQAYEKAIQIDPESARAWIG 496
                                       5889*****************86 PP

  == domain 12  score: 11.3 bits;  conditional E-value: 0.00094
                            TPR_14  16 dpdeAiallrralalaPddaeawlllaq 43 
                                        +++A+++l+  l+ +P+daeaw l a+
  gi|330509115|ref|YP_004385543.1| 513 AYERAVEVLNGSLEEDPEDAEAWWLKAE 540
                                       46788888888888*********88775 PP

  == domain 13  score: 12.0 bits;  conditional E-value: 0.00057
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaP.ddaeawlll 41 
                                       +ea+++ ae l +lG+  eA+++++r+++l+  +   aw++ 
  gi|330509115|ref|YP_004385543.1| 532 AEAWWLKAESLDNLGRSNEALQAYDRVIELNSsKAIGAWIRK 573
                                       58***************************9752566788775 PP

  == domain 14  score: 1.7 bits;  conditional E-value: 1.2
                            TPR_14   3 allalaeallalGdpdeAiallrralalaP 32 
                                       a+ +  +++  lG++ e++++++ al l P
  gi|330509115|ref|YP_004385543.1| 569 AWIRKSDIFVSLGRYNESVEAFDSALNLLP 598
                                       67777889999**************98777 PP

  == domain 15  score: -0.8 bits;  conditional E-value: 7.3
                            TPR_14  14 lGdpdeAiall 24 
                                       lG++deA+++l
  gi|330509115|ref|YP_004385543.1| 672 LGRHDEALQAL 682
                                       69*******98 PP

  == domain 16  score: 10.8 bits;  conditional E-value: 0.0014
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPdd....aeaw 38 
                                        + + ++al++++ +++A++++++a+ +a ++    aeaw
  gi|330509115|ref|YP_004385543.1| 705 DWVQTGRALFRSQSFEGAAEAYEKAIGAAGSNkillAEAW 744
                                       68899*********************99887754444555 PP

  == domain 17  score: 13.8 bits;  conditional E-value: 0.00015
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawlll 41 
                                       ++a++ +++A+++++++l+ +P++a awl  
  gi|330509115|ref|YP_004385543.1| 765 EEANESLEKALDYFDQVLEIYPENAGAWLNK 795
                                       5788899*********************976 PP

  == domain 18  score: 9.6 bits;  conditional E-value: 0.0033
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawlllaq 43 
                                       l+  G++ eA+++ +ra++l+P++ +++ + a+
  gi|330509115|ref|YP_004385543.1| 799 LRWMGRTGEALDAVDRAVELNPENIDFHWQRAE 831
                                       66789*******************988877666 PP

  == domain 19  score: 11.9 bits;  conditional E-value: 0.00063
                            TPR_14  14 lGdpdeAiallrralalaPddaeawlllaq 43 
                                       + + +eA+++++++ +l+P++++ wl+ ++
  gi|330509115|ref|YP_004385543.1| 875 QNNNEEALKAFEKVTELDPQEPTGWLYKGE 904
                                       6789**********************9886 PP

  == domain 20  score: 5.0 bits;  conditional E-value: 0.099
                            TPR_14   3 allalaeallalGdpdeAiallrrala 29 
                                        +l  +e+l alG+ +eA +++ ra +
  gi|330509115|ref|YP_004385543.1| 898 GWLYKGEVLKALGRRAEADEAYARAGE 924
                                       589999****************99954 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.48   2.5e+02      47      76 ..      24      55 ..      22      56 .. 0.73
   2 !   13.5   0.2   0.00012     0.065       6      76 ..      46     115 ..      41     116 .. 0.89
   3 !   12.4   0.1   0.00028      0.15       4      76 ..      85     159 ..      82     160 .. 0.84
   4 !    9.5   0.3    0.0023       1.2      19      75 ..     144     199 ..     139     201 .. 0.92
   5 !   16.4   1.6   1.5e-05    0.0081       9      76 ..     175     239 ..     170     247 .. 0.86
   6 !   25.9   0.8   1.7e-08   8.9e-06       8      74 ..     263     328 ..     258     331 .. 0.91
   7 !   26.1   0.3   1.5e-08   7.8e-06       6      76 ..     336     399 ..     332     400 .. 0.89
   8 !   14.4   2.9   6.4e-05     0.034       2      42 ..     401     439 ..     400     482 .. 0.76
   9 !   14.8   2.4   5.1e-05     0.027      18      75 ..     465     521 ..     447     523 .. 0.88
  10 !   22.8   0.8   1.6e-07   8.5e-05       2      74 ..     490     561 ..     489     564 .. 0.94
  11 !   11.2   0.1   0.00068      0.36       3      67 ..     532     596 ..     530     599 .. 0.70
  12 ?   -0.4   0.0       2.7   1.4e+03      16      26 ..     672     682 ..     671     684 .. 0.59
  13 ?    1.6   0.1      0.64   3.4e+02      10      52 ..     710     748 ..     705     756 .. 0.65
  14 ?    5.7   0.0     0.035        19      19      33 ..     771     785 ..     765     791 .. 0.59
  15 !   14.6   0.0   5.9e-05     0.031       5      74 ..     791     852 ..     787     855 .. 0.85
  16 !    9.4   0.0    0.0023       1.2       8      76 ..     828     893 ..     824     894 .. 0.86
  17 ?    2.8   0.3      0.28   1.5e+02       9      29 ..     902     922 ..     894     931 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.48
                            TPR_12 47 tlrnLgrlyr.al.gryeeAlelleealaiae 76
                                      +++ L++l+  a  ++ + A +++e++l+++ 
  gi|330509115|ref|YP_004385543.1| 24 AMISLAILCIgAVaEDEKSANYWYEKSLDLYN 55
                                      5666666664133589999**********996 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00012
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +++  + l+  g ++e+l+  +ka+e+  +++  + +++ a+ l+  g + + + r++e l+ + +a+++++
  gi|330509115|ref|YP_004385543.1|  46 WYEKSLDLYNNGSLEESLQAVDKAIELDpENA--TLWAYKASGLNLAGVITQNQSRFDESLQVYDRAIELDP 115
                                       55666778999*****************8888..99**************99999*************9975 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00028
                            TPR_12   4 talnnlaavl.rrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgr...yeeAlelleealaia 75 
                                       + l nla v  + + r+de+l+ +++a+e+  +++  ++ ++   +lr     +r ++r   +eeA+e + +al+i+
  gi|330509115|ref|YP_004385543.1|  85 SGL-NLAGVItQNQSRFDESLQVYDRAIELDpENT--TYLLWKGFALRQAVNGLRGQERiqiFEEAIETFDRALEID 158
                                       556.666666477******************9999..9999999999999999999999666789999999999997 PP

                            TPR_12  76 e 76 
                                       +
  gi|330509115|ref|YP_004385543.1| 159 P 159
                                       6 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0023
                            TPR_12  19 ydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       ++eA+e +++alei    + + +++   +  +L++    + ry + l+++ +a+++a
  gi|330509115|ref|YP_004385543.1| 144 FEEAIETFDRALEID-PKFAEAWAGKGVICDDLATFNNDSARYNDSLAAYDKAIELA 199
                                       69*************.556699***************9999*************997 PP

  == domain 5  score: 16.4 bits;  conditional E-value: 1.5e-05
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       la++ +   ry ++l+ ++ka+e+a   +  d+ ++a+++ + + +++ +g+  +A+   ee+ a+++
  gi|330509115|ref|YP_004385543.1| 175 LATFNNDSARYNDSLAAYDKAIELA---PTNDSRNLAQAYEGKAVALSHMGQDLAARGQIEESRAVLK 239
                                       889999999****************...5588888999999999999999998888888888888776 PP

  == domain 6  score: 25.9 bits;  conditional E-value: 1.7e-08
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       n+a vl +lgr deA + +eka+e+ +r+ +  +++ + +  n ++l++++gryeeA+ +l+ a++i
  gi|330509115|ref|YP_004385543.1| 263 NRAGVLKELGRRDEAAAGYEKAIEQLNRSIE-VNLNNSGAWVNKAILFQEQGRYEEAITALNNATKI 328
                                       89************************88875.578**************************999887 PP

  == domain 7  score: 26.1 bits;  conditional E-value: 1.5e-08
                            TPR_12   6 lnnlaavl.rrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +  ++++l + lgryde++e +++al++      p     a++    g ++r lgr +eA+ ++ +al+i++
  gi|330509115|ref|YP_004385543.1| 336 WEMMGEILsNDLGRYDESIEAYDRALQLD-----PS---DARAWTSKGHALRSLGRNREAVLAYDRALKIDP 399
                                       43589999888******************.....74...69999999**********************975 PP

  == domain 8  score: 14.4 bits;  conditional E-value: 6.4e-05
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhp 42 
                                       +ata++  +a+lr +gry e+ + ++++l++++r   p++ 
  gi|330509115|ref|YP_004385543.1| 401 RATAWSGKGAALRDQGRYNESVQAYDEVLRAVERD--PTYR 439
                                       6899*99*************************987..5442 PP

  == domain 9  score: 14.8 bits;  conditional E-value: 5.1e-05
                            TPR_12  18 rydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       + +eA   ++++l++++++     p+ a++ ++ g +++ l++y +  e++e+a++++
  gi|330509115|ref|YP_004385543.1| 465 KAEEAAIAYNESLQAYEKAIQI-DPESARAWIGRGNALLSLEKYSDSKEAYERAVEVL 521
                                       6789999999999999999877.5999***************************9975 PP

  == domain 10  score: 22.8 bits;  conditional E-value: 1.6e-07
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        a+a+  ++++l+ l++y ++ e +e+a+e+ + +l+ + p+ a++    ++ ++ lgr  eAl+++ +++++
  gi|330509115|ref|YP_004385543.1| 490 SARAWIGRGNALLSLEKYSDSKEAYERAVEVLNGSLE-EDPEDAEAWWLKAESLDNLGRSNEALQAYDRVIEL 561
                                       589999**************************99986.579****************************9987 PP

  == domain 11  score: 11.2 bits;  conditional E-value: 0.00068
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlel 67 
                                       a a+   a+ l  lgr  eAl+ +++++e+ ++   + +   + +   Lgr+ +  + ++ Al+l
  gi|330509115|ref|YP_004385543.1| 532 AEAWWLKAESLDNLGRSNEALQAYDRVIELNSSKAIGAWIRKSDIFVSLGRYNESVEAFDSALNL 596
                                       6677789999999**************99995553344666666666666555555555555554 PP

  == domain 12  score: -0.4 bits;  conditional E-value: 2.7
                            TPR_12  16 lgrydeAlell 26 
                                       lgr+deAl+ l
  gi|330509115|ref|YP_004385543.1| 672 LGRHDEALQAL 682
                                       46666666544 PP

  == domain 13  score: 1.6 bits;  conditional E-value: 0.64
                            TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLg 52 
                                       + +l+r + ++ A e +eka+ +a    G ++ l+a++  + g
  gi|330509115|ref|YP_004385543.1| 710 GRALFRSQSFEGAAEAYEKAIGAA----GSNKILLAEAWKGKG 748
                                       566777777777777777776666....566666666665555 PP

  == domain 14  score: 5.7 bits;  conditional E-value: 0.035
                            TPR_12  19 ydeAlellekaleia 33 
                                       +++Al++++++lei+
  gi|330509115|ref|YP_004385543.1| 771 LEKALDYFDQVLEIY 785
                                       555666666666655 PP

  == domain 15  score: 14.6 bits;  conditional E-value: 5.9e-05
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       a+ n   +lr++gr  eAl+  ++a+e+      p++   +      ++l+++lgry e  +++ e++++
  gi|330509115|ref|YP_004385543.1| 791 AWLNKSFILRWMGRTGEALDAVDRAVELN-----PEN---IDFHWQRAELLSMLGRYNESDQAFDETIEM 852
                                       778999*******************9999.....665...667788899999999999988888888887 PP

  == domain 16  score: 9.4 bits;  conditional E-value: 0.0023
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       ++a++l  lgry e+ + +++ +e++   +   +  +a++    g  +  +++ eeAl+++e+++++++
  gi|330509115|ref|YP_004385543.1| 828 QRAELLSMLGRYNESDQAFDETIEMI---PANSSRKLAEVWTFKGFNFMGQNNNEEALKAFEKVTELDP 893
                                       6899999*******************...44556679999999999998999***********999875 PP

  == domain 17  score: 2.8 bits;  conditional E-value: 0.28
                            TPR_12   9 laavlrrlgrydeAlelleka 29 
                                        ++vl +lgr +eA e + +a
  gi|330509115|ref|YP_004385543.1| 902 KGEVLKALGRRAEADEAYARA 922
                                       677777777777777777776 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.032        17       4      58 ..      56     117 ..      53     124 .. 0.74
   2 !    9.3   0.0    0.0029       1.5       7      30 ..     144     167 ..     143     176 .. 0.88
   3 ?    1.7   0.6      0.73   3.9e+02      20      53 ..     210     243 ..     181     247 .. 0.70
   4 !    8.2   0.2    0.0065       3.4       8      45 ..     239     278 ..     225     280 .. 0.92
   5 !   16.7   0.1   1.4e-05    0.0076       7      57 ..     281     331 ..     277     342 .. 0.92
   6 !   20.7   0.4   8.1e-07   0.00043       5      62 ..     348     405 ..     344     406 .. 0.94
   7 !   17.5   0.4   8.5e-06    0.0045       5      63 ..     382     440 ..     378     446 .. 0.92
   8 !   14.3   0.2   8.2e-05     0.043       7      47 ..     473     513 ..     465     515 .. 0.91
   9 !   22.1   0.2   3.1e-07   0.00016       6      54 ..     513     561 ..     510     567 .. 0.93
  10 ?   -0.4   0.0       3.1   1.6e+03      27      56 ..     569     598 ..     562     604 .. 0.80
  11 ?   -1.0   0.0       4.8   2.5e+03       5      15 ..     673     683 ..     672     696 .. 0.64
  12 ?   -0.2   0.1       2.9   1.5e+03       2      23 ..     714     735 ..     713     749 .. 0.75
  13 !   15.2   0.1   4.5e-05     0.024       4      48 ..     768     812 ..     766     813 .. 0.92
  14 !   16.9   0.0   1.2e-05    0.0066       4      55 ..     802     853 ..     799     862 .. 0.90
  15 !   20.8   0.3   7.5e-07    0.0004       2      56 ..     873     927 ..     872     935 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.032
                            TPR_19   4 egdyaeAlalleqalqedpknaearl......lLAeallal.gqldeAealLdalpeedpdd 58 
                                       +g ++e l++  +a++ dp+na +++      +LA +  ++  ++de  ++ d++ e dp +
  gi|330509115|ref|YP_004385543.1|  56 NGSLEESLQAVDKAIELDPENATLWAykasglNLAGVITQNqSRFDESLQVYDRAIELDPEN 117
                                       789999999999********888888666655555555555488888888888888888875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0029
                            TPR_19   7 yaeAlalleqalqedpknaearll 30 
                                       ++eA++ + +al+ dpk aea+++
  gi|330509115|ref|YP_004385543.1| 144 FEEAIETFDRALEIDPKFAEAWAG 167
                                       689*****************9987 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.73
                            TPR_19  20 edpknaearllLAeallalgqldeAealLdalpe 53 
                                       ++ + a a+  + + l a gq++e +a+L+++ +
  gi|330509115|ref|YP_004385543.1| 210 AYEGKAVALSHMGQDLAARGQIEESRAVLKEAVK 243
                                       3555556666667777888999999999988766 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0065
                            TPR_19   8 aeAlalleqalqedpk..naearllLAeallalgqldeAe 45 
                                        eA++ + ++++ dp+   +ea+ + A +l +lg+ deA 
  gi|330509115|ref|YP_004385543.1| 239 KEAVKNYDKVIDLDPDfvGQEAQQNRAGVLKELGRRDEAA 278
                                       68999999999****************************6 PP

  == domain 5  score: 16.7 bits;  conditional E-value: 1.4e-05
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       y+ A++ l + ++ + +n+ a+ + A++  ++g+++eA+ +L+ + + +p 
  gi|330509115|ref|YP_004385543.1| 281 YEKAIEQLNRSIEVNLNNSGAWVNKAILFQEQGRYEEAITALNNATKITPE 331
                                       889****************************************99998886 PP

  == domain 6  score: 20.7 bits;  conditional E-value: 8.1e-07
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       g+y+e ++++ +alq dp +a+a+     al +lg+  eA  + d++++ dp+ a ++
  gi|330509115|ref|YP_004385543.1| 348 GRYDESIEAYDRALQLDPSDARAWTSKGHALRSLGRNREAVLAYDRALKIDPNRATAW 405
                                       99***************************************************77665 PP

  == domain 7  score: 17.5 bits;  conditional E-value: 8.5e-06
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryas 63 
                                       g+  eA+ ++ +al+ dp+ a a+ +   al  +g+++e  ++ d+++++   d+ y+ 
  gi|330509115|ref|YP_004385543.1| 382 GRNREAVLAYDRALKIDPNRATAWSGKGAALRDQGRYNESVQAYDEVLRAVERDPTYRY 440
                                       77889***********************************************9999985 PP

  == domain 8  score: 14.3 bits;  conditional E-value: 8.2e-05
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAeal 47 
                                       y e l+++e+a+q dp++a+a+++  +all+l  + + +++
  gi|330509115|ref|YP_004385543.1| 473 YNESLQAYEKAIQIDPESARAWIGRGNALLSLEKYSDSKEA 513
                                       66779*****************************9998875 PP

  == domain 9  score: 22.1 bits;  conditional E-value: 3.1e-07
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpee 54 
                                        y++A++ l   l+edp++aea+ l Ae l +lg+ +eA ++ d++ e 
  gi|330509115|ref|YP_004385543.1| 513 AYERAVEVLNGSLEEDPEDAEAWWLKAESLDNLGRSNEALQAYDRVIEL 561
                                       699*****************************************99876 PP

  == domain 10  score: -0.4 bits;  conditional E-value: 3.1
                            TPR_19  27 arllLAeallalgqldeAealLdalpeedp 56 
                                       a+++  ++ ++lg+++e  ++ d +++  p
  gi|330509115|ref|YP_004385543.1| 569 AWIRKSDIFVSLGRYNESVEAFDSALNLLP 598
                                       566667888999****99999999887665 PP

  == domain 11  score: -1.0 bits;  conditional E-value: 4.8
                            TPR_19   5 gdyaeAlalle 15 
                                       g+++eAl++l+
  gi|330509115|ref|YP_004385543.1| 673 GRHDEALQALS 683
                                       45555555554 PP

  == domain 12  score: -0.2 bits;  conditional E-value: 2.9
                            TPR_19   2 laegdyaeAlalleqalqedpk 23 
                                       + ++ ++ A++++e+a+ ++  
  gi|330509115|ref|YP_004385543.1| 714 FRSQSFEGAAEAYEKAIGAAGS 735
                                       678999*********9765444 PP

  == domain 13  score: 15.2 bits;  conditional E-value: 4.5e-05
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealL 48 
                                       ++ ++ Al+++ q+l+ +p+na a+l+   +l  +g++ eA +++
  gi|330509115|ref|YP_004385543.1| 768 NESLEKALDYFDQVLEIYPENAGAWLNKSFILRWMGRTGEALDAV 812
                                       67899**********************************998875 PP

  == domain 14  score: 16.9 bits;  conditional E-value: 1.2e-05
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55 
                                       +g+  eAl++  +a + +p+n +   + Ae+l  lg+++e  ++ d+  e+ 
  gi|330509115|ref|YP_004385543.1| 802 MGRTGEALDAVDRAVELNPENIDFHWQRAELLSMLGRYNESDQAFDETIEMI 853
                                       799*************************************999988776665 PP

  == domain 15  score: 20.8 bits;  conditional E-value: 7.5e-07
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                       + +++ +eAl+++e++ + dp+ +  +l+  e+l alg+ +eA ++ ++++e d 
  gi|330509115|ref|YP_004385543.1| 873 MGQNNNEEALKAFEKVTELDPQEPTGWLYKGEVLKALGRRAEADEAYARAGELDN 927
                                       789999*******************************************999875 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.66   3.5e+02      31      64 ..      45      78 ..      22      84 .. 0.67
   2 ?    3.8   0.0      0.13        66       5      33 ..      94     122 ..      90     131 .. 0.80
   3 ?    1.5   0.0      0.62   3.2e+02      11      36 ..     144     169 ..     138     175 .. 0.78
   4 ?    0.7   0.0       1.1     6e+02      30      61 ..     223     254 ..     202     271 .. 0.80
   5 !   14.2   0.0     7e-05     0.037      11      61 ..     281     331 ..     273     338 .. 0.93
   6 !   21.2   1.2   4.4e-07   0.00023      10      65 ..     349     404 ..     346     405 .. 0.95
   7 !   11.7   0.9   0.00042      0.22       9      64 ..     382     437 ..     376     446 .. 0.87
   8 !   16.4   0.1   1.5e-05    0.0077      14      66 ..     476     533 ..     472     539 .. 0.86
   9 !    9.6   0.0    0.0019         1      10      61 ..     547     599 ..     542     606 .. 0.89
  10 ?    2.8   0.0      0.25   1.3e+02      29      59 ..     703     733 ..     701     741 .. 0.87
  11 !   20.8   0.0   5.9e-07   0.00031       8      64 ..     768     824 ..     764     826 .. 0.95
  12 !   15.3   0.1   3.2e-05     0.017      13      67 ..     807     861 ..     803     864 .. 0.89
  13 !   12.7   0.1    0.0002      0.11       8      59 ..     875     926 ..     872     940 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.66
                             TPR_9 31 errdRGlllaqlGclsaAladLeaylalapdapd 64
                                       +++  l l+  G l++ l++ + +++l+p++++
  gi|330509115|ref|YP_004385543.1| 45 YWYEKSLDLYNNGSLEESLQAVDKAIELDPENAT 78
                                      5666666666666666666666666666666554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.13
                             TPR_9   5 aireedweralavverllllaPddpeerr 33 
                                        +++ ++++ l+v++r + l+P+    ++
  gi|330509115|ref|YP_004385543.1|  94 TQNQSRFDESLQVYDRAIELDPENTTYLL 122
                                       578999****************9876555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.62
                             TPR_9  11 weralavverllllaPddpeerrdRG 36 
                                       +e+a+++ +r l ++P+ +e +   G
  gi|330509115|ref|YP_004385543.1| 144 FEEAIETFDRALEIDPKFAEAWAGKG 169
                                       67888888888888888888876555 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.1
                             TPR_9  30 eerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       +++  RG++++ +  l++A++  +  ++l+pd
  gi|330509115|ref|YP_004385543.1| 223 QDLAARGQIEESRAVLKEAVKNYDKVIDLDPD 254
                                       56678999999999999999999999999994 PP

  == domain 5  score: 14.2 bits;  conditional E-value: 7e-05
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       +e+a++ ++r + ++ +  + +   ++l +++G++++A+ +L+ +  ++p+
  gi|330509115|ref|YP_004385543.1| 281 YEKAIEQLNRSIEVNLNNSGAWVNKAILFQEQGRYEEAITALNNATKITPE 331
                                       78999**************************************99988885 PP

  == domain 6  score: 21.2 bits;  conditional E-value: 4.4e-07
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       ++++ +++++r l+l+P d++ +   G +l  lG+ ++A+ + +++l ++p++++a
  gi|330509115|ref|YP_004385543.1| 349 RYDESIEAYDRALQLDPSDARAWTSKGHALRSLGRNREAVLAYDRALKIDPNRATA 404
                                       6778899*********************************************9987 PP

  == domain 7  score: 11.7 bits;  conditional E-value: 0.00042
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                        ++ +a  +++r l ++P+++  +   G +l  +G++++ +++ +  l+  + +p+
  gi|330509115|ref|YP_004385543.1| 382 GRNREAVLAYDRALKIDPNRATAWSGKGAALRDQGRYNESVQAYDEVLRAVERDPT 437
                                       57888999***********************************9999977666665 PP

  == domain 8  score: 16.4 bits;  conditional E-value: 1.5e-05
                             TPR_9  14 alavverllllaPddpeerrdRGlllaqlGclsaAladLeayl.....alapdapdae 66 
                                        l+++e  ++++P++++ +  RG +l  l+ +s   ++ e+++     +l++d++dae
  gi|330509115|ref|YP_004385543.1| 476 SLQAYEKAIQIDPESARAWIGRGNALLSLEKYSDSKEAYERAVevlngSLEEDPEDAE 533
                                       58999**************************************777774444666665 PP

  == domain 9  score: 9.6 bits;  conditional E-value: 0.0019
                             TPR_9  10 dweralavverllll.aPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       ++ +al++++r++ l  +++++ +     + + lG++++ +++++ +l l p 
  gi|330509115|ref|YP_004385543.1| 547 RSNEALQAYDRVIELnSSKAIGAWIRKSDIFVSLGRYNESVEAFDSALNLLPT 599
                                       6789***********556789***************************99984 PP

  == domain 10  score: 2.8 bits;  conditional E-value: 0.25
                             TPR_9  29 peerrdRGlllaqlGclsaAladLeaylala 59 
                                       ++++   G++l+++  +++A+++ e ++  a
  gi|330509115|ref|YP_004385543.1| 703 ADDWVQTGRALFRSQSFEGAAEAYEKAIGAA 733
                                       57899********************998555 PP

  == domain 11  score: 20.8 bits;  conditional E-value: 5.9e-07
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       +e  e+al + + +l + P+ ++ ++   ++l  +G++ +Al++ +++++l+p++ d
  gi|330509115|ref|YP_004385543.1| 768 NESLEKALDYFDQVLEIYPENAGAWLNKSFILRWMGRTGEALDAVDRAVELNPENID 824
                                       7899*************************************************9766 PP

  == domain 12  score: 15.3 bits;  conditional E-value: 3.2e-05
                             TPR_9  13 ralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaea 67 
                                       +al +v+r + l+P+ ++ ++ R+ ll  lG++++  ++++  +++ p++  + +
  gi|330509115|ref|YP_004385543.1| 807 EALDAVDRAVELNPENIDFHWQRAELLSMLGRYNESDQAFDETIEMIPANSSRKL 861
                                       79***********************************999999999887766655 PP

  == domain 13  score: 12.7 bits;  conditional E-value: 0.0002
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                       ++++e+al++ e +  l+P++p  ++  G +l  lG+ ++A ++  ++ +l+
  gi|330509115|ref|YP_004385543.1| 875 QNNNEEALKAFEKVTELDPQEPTGWLYKGEVLKALGRRAEADEAYARAGELD 926
                                       7899*************************************99888876665 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0071       3.7       3      34 ..      88     117 ..      87     119 .. 0.84
   2 ?    3.5   0.0      0.16        86      15      29 ..     144     158 ..     138     164 .. 0.83
   3 ?    4.1   0.1      0.11        56       6      28 ..     265     288 ..     262     295 .. 0.77
   4 !   10.6   0.0   0.00092      0.48       1      21 [.     301     321 ..     301     327 .. 0.90
   5 !   14.9   0.1   3.7e-05      0.02       2      35 ..     336     368 ..     335     369 .. 0.82
   6 !    7.3   0.0    0.0099       5.2       4      33 ..     373     400 ..     370     403 .. 0.81
   7 !    8.6   0.0    0.0039       2.1       6      32 ..     409     436 ..     404     437 .. 0.89
   8 ?    3.5   0.1      0.16        84       6      35 ..     498     532 ..     493     533 .. 0.65
   9 ?    1.2   0.0      0.89   4.7e+02       8      29 ..     541     562 ..     534     567 .. 0.65
  10 ?    3.2   0.0      0.21   1.1e+02       7      28 ..     575     596 ..     569     604 .. 0.81
  11 ?    3.0   0.0      0.23   1.2e+02       6      26 ..     710     730 ..     706     740 .. 0.86
  12 ?    0.4   0.0       1.6   8.5e+02      16      28 ..     772     784 ..     771     791 .. 0.84
  13 ?    3.9   0.0      0.13        67      12      35 ..     875     896 ..     872     897 .. 0.90
  14 ?    3.2   0.4       0.2   1.1e+02       4      31 ..     901     926 ..     899     938 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0071
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       +  +++ +++ +++e +++y +  a++ dpe+
  gi|330509115|ref|YP_004385543.1|  88 NLAGVITQNQSRFDESLQVYDR--AIELDPEN 117
                                       566777899*************..98888875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.16
                             TPR_7  15 yeeAielyeqsLalt 29 
                                       +eeAie + ++L+++
  gi|330509115|ref|YP_004385543.1| 144 FEEAIETFDRALEID 158
                                       89********77776 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.11
                             TPR_7   6 arlysrlGdyeeAielyeqsL.al 28 
                                       a +  +lG+++eA+  ye+++ +l
  gi|330509115|ref|YP_004385543.1| 265 AGVLKELGRRDEAAAGYEKAIeQL 288
                                       556789*************66555 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00092
                             TPR_7   1 aLlnLarlysrlGdyeeAiel 21 
                                       a++n a l++++G+yeeAi+ 
  gi|330509115|ref|YP_004385543.1| 301 AWVNKAILFQEQGRYEEAITA 321
                                       68999**************85 PP

  == domain 5  score: 14.9 bits;  conditional E-value: 3.7e-05
                             TPR_7   2 LlnLarlysr.lGdyeeAielyeqsLaltkdpeda 35 
                                       +  ++++ s+ lG+y+e ie y +  al  dp+da
  gi|330509115|ref|YP_004385543.1| 336 WEMMGEILSNdLGRYDESIEAYDR--ALQLDPSDA 368
                                       55799999999*************..666666665 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.0099
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                         +++ ++lG+ +eA+  y +  al  dp+
  gi|330509115|ref|YP_004385543.1| 373 SKGHALRSLGRNREAVLAYDR--ALKIDPN 400
                                       66999****************..7766665 PP

  == domain 7  score: 8.6 bits;  conditional E-value: 0.0039
                             TPR_7   6 arlysrlGdyeeAielyeqsL.altkdp 32 
                                       + + +++G+y e ++ y ++L a+++dp
  gi|330509115|ref|YP_004385543.1| 409 GAALRDQGRYNESVQAYDEVLrAVERDP 436
                                       7899*****************9999998 PP

  == domain 8  score: 3.5 bits;  conditional E-value: 0.16
                             TPR_7   6 arlysrlGdyeeAielyeqsLalt.......kdpeda 35 
                                       +++  +l +y++  e ye+  a++       +dpeda
  gi|330509115|ref|YP_004385543.1| 498 GNALLSLEKYSDSKEAYER--AVEvlngsleEDPEDA 532
                                       6777777788888888888..4443345555777766 PP

  == domain 9  score: 1.2 bits;  conditional E-value: 0.89
                             TPR_7   8 lysrlGdyeeAielyeqsLalt 29 
                                          +lG+  eA++ y ++++l 
  gi|330509115|ref|YP_004385543.1| 541 SLDNLGRSNEALQAYDRVIELN 562
                                       4556777777777777755554 PP

  == domain 10  score: 3.2 bits;  conditional E-value: 0.21
                             TPR_7   7 rlysrlGdyeeAielyeqsLal 28 
                                       +++++lG+y e +e +  +L l
  gi|330509115|ref|YP_004385543.1| 575 DIFVSLGRYNESVEAFDSALNL 596
                                       799************9997755 PP

  == domain 11  score: 3.0 bits;  conditional E-value: 0.23
                             TPR_7   6 arlysrlGdyeeAielyeqsL 26 
                                       +r+ +r + +e A+e ye+++
  gi|330509115|ref|YP_004385543.1| 710 GRALFRSQSFEGAAEAYEKAI 730
                                       789999999**********55 PP

  == domain 12  score: 0.4 bits;  conditional E-value: 1.6
                             TPR_7  16 eeAielyeqsLal 28 
                                       e+A++++ q+L++
  gi|330509115|ref|YP_004385543.1| 772 EKALDYFDQVLEI 784
                                       89*******9987 PP

  == domain 13  score: 3.9 bits;  conditional E-value: 0.13
                             TPR_7  12 lGdyeeAielyeqsLaltkdpeda 35 
                                       +++ eeA++ +e+  +++ dp+++
  gi|330509115|ref|YP_004385543.1| 875 QNNNEEALKAFEK--VTELDPQEP 896
                                       7999*********..*****9987 PP

  == domain 14  score: 3.2 bits;  conditional E-value: 0.2
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkd 31 
                                       + +++  +lG+++eA e y +  a + d
  gi|330509115|ref|YP_004385543.1| 901 YKGEVLKALGRRAEADEAYAR--AGELD 926
                                       66888999*************..87766 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       4.1   2.2e+03      73      99 ..      61      80 ..      47     122 .. 0.47
   2 !   14.9   1.3   3.9e-05     0.021      22     131 ..     182     289 ..     176     299 .. 0.88
   3 !   15.2   0.4   3.1e-05     0.016      62     130 ..     265     329 ..     260     342 .. 0.90
   4 !    7.3   0.1    0.0088       4.6      67     128 ..     346     396 ..     333     409 .. 0.81
   5 ?    1.7   0.0      0.46   2.4e+02      58      86 ..     405     433 ..     397     441 .. 0.66
   6 !   19.0   1.1   2.2e-06    0.0011       5     129 ..     446     561 ..     442     568 .. 0.86
   7 ?    3.2   0.0      0.16        83      62      84 ..     574     596 ..     569     610 .. 0.86
   8 !   18.5   0.4   3.2e-06    0.0017      19     130 ..     713     819 ..     698     824 .. 0.87
   9 ?    2.5   0.0      0.27   1.4e+02     104     131 ..     827     854 ..     820     863 .. 0.88
  10 !    7.5   0.1    0.0077         4      77     129 ..     877     925 ..     861     938 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.1
                                      HHHHHHHHHHHHHHHH--TTSTHHHHH CS
                           DUF3856 73 ealesadkalryfnrrGeleqdeGklW 99
                                      e+l+++d       +  el+ ++  lW
  gi|330509115|ref|YP_004385543.1| 61 ESLQAVD-------KAIELDPENATLW 80
                                      3333333.......3334444444444 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.9e-05
                                       HT-HHHHHHHHHHHHHHHTTS-TTS.---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHH CS
                           DUF3856  22 egayeeaaasyrkalevsrtipaee.afdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGk 97 
                                        ++y+++ a y ka+e++ t  + + a  +eG  a++ + + + la  g+ +e+    ++a++ +++  +l+ d   
  gi|330509115|ref|YP_004385543.1| 182 SARYNDSLAAYDKAIELAPTNDSRNlAQAYEG-KAVALSHMGQDLAARGQIEESRAVLKEAVKNYDKVIDLDPDFVG 257
                                       578***************99876552777888.68999999999***************************999755 PP

                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                           DUF3856  98 lWiaavfsravaleelGrkdealkafrmagemia 131
                                       +   a  +ra  l+elGr+dea   +++a e ++
  gi|330509115|ref|YP_004385543.1| 258 Q--EAQQNRAGVLKELGRRDEAAAGYEKAIEQLN 289
                                       4..6889**********************99875 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 3.1e-05
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                           DUF3856  62 sealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagemi 130
                                       ++ l +lgr dea    +ka++ +nr  e++ ++   W+    ++a  ++e Gr++ea+ a++ a+ + 
  gi|330509115|ref|YP_004385543.1| 265 AGVLKELGRRDEAAAGYEKAIEQLNRSIEVNLNNSGAWV----NKAILFQEQGRYEEAITALNNATKIT 329
                                       677899*****************************9996....89*****************9998765 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0088
                                       HTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  67 klgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                        lgryde++e+ d+al+       l+  + + W     s+++al +lGr+ ea+ a+  a  
  gi|330509115|ref|YP_004385543.1| 346 DLGRYDESIEAYDRALQ-------LDPSDARAW----TSKGHALRSLGRNREAVLAYDRALK 396
                                       58888888888888884.......888888888....589*************999988865 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                           DUF3856  58 haglsealaklgrydealesadkalryfn 86 
                                       ++g   al   gry+e++++ d+ lr  +
  gi|330509115|ref|YP_004385543.1| 405 WSGKGAALRDQGRYNESVQAYDEVLRAVE 433
                                       55555666666666666666666666554 PP

  == domain 6  score: 19.0 bits;  conditional E-value: 2.2e-06
                                       HHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856   5 evaeaylalseaekqleegayeeaaasyrkalevsrtipaeeafdheGfdalchaglsealaklgrydealesadka 81 
                                        va+a+l  s+ae  +  ++ eeaa  y+++l++      e a   +   a ++ g  +al+ l +y ++ e+ ++a
  gi|330509115|ref|YP_004385543.1| 446 AVADAWLGKSKAESLMGPDKAEEAAIAYNESLQA-----YEKAIQIDPESARAWIGRGNALLSLEKYSDSKEAYERA 517
                                       5899999999999999999999999999998875.....57888888889999************************ PP

                                       HHHHHHH--TTST..HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  82 lryfnrrGeleqd..eGklWiaavfsravaleelGrkdealkafrmagem 129
                                       ++ +n  G le+d  + + W    + +a +l++lGr++eal+a+  + e+
  gi|330509115|ref|YP_004385543.1| 518 VEVLN--GSLEEDpeDAEAW----WLKAESLDNLGRSNEALQAYDRVIEL 561
                                       ****9..5565551155555....679*****************999987 PP

  == domain 7  score: 3.2 bits;  conditional E-value: 0.16
                                       HHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  62 sealaklgrydealesadkalry 84 
                                       s+ ++ lgry+e++e+ d+al+ 
  gi|330509115|ref|YP_004385543.1| 574 SDIFVSLGRYNESVEAFDSALNL 596
                                       678999**********9999975 PP

  == domain 8  score: 18.5 bits;  conditional E-value: 3.2e-06
                                       HHHHT-HHHHHHHHHHHHHH..HTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTS CS
                           DUF3856  19 qleegayeeaaasyrkalev..srtipaeeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleq 93 
                                        ++ +++e aa+ y+ka+ +  s+ i   ea+  +G    ++ +ls++    g+ +ea es +kal yf++  e+  
  gi|330509115|ref|YP_004385543.1| 713 LFRSQSFEGAAEAYEKAIGAagSNKILLAEAWKGKGE---AFLVLSGSEKSPGKREEANESLEKALDYFDQVLEIYP 786
                                       567899************9823467889999988884...56799******************************** PP

                                       THHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                           DUF3856  94 deGklWiaavfsravaleelGrkdealkafrmagemi 130
                                       ++   W+    +++  l  +Gr+ eal+a   a+e+ 
  gi|330509115|ref|YP_004385543.1| 787 ENAGAWL----NKSFILRWMGRTGEALDAVDRAVELN 819
                                       **99996....79999**************9999975 PP

  == domain 9  score: 2.5 bits;  conditional E-value: 0.27
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmagemia 131
                                       ++ra  l+ lGr++e+ +af  + emi 
  gi|330509115|ref|YP_004385543.1| 827 WQRAELLSMLGRYNESDQAFDETIEMIP 854
                                       5799999*******************95 PP

  == domain 10  score: 7.5 bits;  conditional E-value: 0.0077
                                       HHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  77 sadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                         ++al+ f++  el+ +e   W+     ++  l+ lGr++ea +a+  age+
  gi|330509115|ref|YP_004385543.1| 877 NNEEALKAFEKVTELDPQEPTGWL----YKGEVLKALGRRAEADEAYARAGEL 925
                                       5689*******************7....69********************997 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.014       7.5     205     252 ..      56     103 ..      37     114 .. 0.81
   2 ?    5.1   0.0     0.017       8.7     183     236 ..     113     172 ..      92     175 .. 0.79
   3 ?    2.8   0.1     0.082        43     198     254 ..     175     236 ..     172     241 .. 0.87
   4 ?    2.1   0.1      0.14        74      40      67 ..     260     287 ..     239     293 .. 0.67
   5 !   13.0   0.1   6.7e-05     0.035       3      72 ..     298     368 ..     296     440 .. 0.84
   6 !    8.5   0.0    0.0016      0.82     199     255 ..     505     561 ..     466     602 .. 0.64
   7 !    8.8   0.0    0.0013      0.69     206     255 ..     769     818 ..     763     826 .. 0.92
   8 !   11.3   0.0   0.00022      0.12       3      72 ..     788     857 ..     786     864 .. 0.85
   9 ?    5.1   0.0     0.016       8.7     205     258 ..     873     928 ..     861     935 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.014
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                        gs e++l+ +dkaie +p+   l+  Ka  l  aG +++  +  +e+
  gi|330509115|ref|YP_004385543.1|  56 NGSLEESLQAVDKAIELDPENATLWAYKASGLNLAGVITQNQSRFDES 103
                                       467899***********************9999999888877777765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.017
                                       S----SSHHHHHHHHHHHHHHHHT-SH......HHHHHHHHHHHH-TT-HHHHHHHHHHH CS
                             NARP1 183 sekepesallwvlyflAqhydklgsre......kAleyidkaiehtptlvelyltKaril 236
                                          e  + llw  + l q  + l+ +e      +A+e+ d+a+e +p++ e +  K+ i+
  gi|330509115|ref|YP_004385543.1| 113 LDPENTTYLLWKGFALRQAVNGLRGQEriqifeEAIETFDRALEIDPKFAEAWAGKGVIC 172
                                       4567788899999999999999777444445559********************999886 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.082
                                       HHHHHHHHT-SHHHHHHHHHHHHH-TT.....-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1 198 lAqhydklgsrekAleyidkaiehtpt.....lvelyltKarilkhaGdlkkAaevmeeark 254
                                       lA + +   +++ +l   dkaie  pt     l + y  Ka  l h+G+  +A   +ee+r+
  gi|330509115|ref|YP_004385543.1| 175 LATFNNDSARYNDSLAAYDKAIELAPTndsrnLAQAYEGKAVALSHMGQDLAARGQIEESRA 236
                                       678888889999999999****9999855555789999***************999999996 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             NARP1  40 vketkaelllkLgrkeeAeatyeaLler 67 
                                        ++++a +l +Lgr++eA+a ye+ +e+
  gi|330509115|ref|YP_004385543.1| 260 AQQNRAGVLKELGRRDEAAAGYEKAIEQ 287
                                       4567777777777777777777776665 PP

  == domain 5  score: 13.0 bits;  conditional E-value: 6.7e-05
                                       HHHHHHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHH.HTT-HHHHHHHHHHHHHH-TT-C CS
                             NARP1   3 esellLyknqiieeagkleeAlehLeekekqivDklavketkaelll.kLgrkeeAeatyeaLlernpens 72 
                                       +s +   k+ +++e+g++eeA+  L+++ k   + +   e+++e+l   Lgr++e+ ++y + l+  p + 
  gi|330509115|ref|YP_004385543.1| 298 NSGAWVNKAILFQEQGRYEEAITALNNATKITPEYVMAWEMMGEILSnDLGRYDESIEAYDRALQLDPSDA 368
                                       5677778999******************9999999*********98636***********98888766554 PP

  == domain 6  score: 8.5 bits;  conditional E-value: 0.0016
                                       HHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 199 AqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                        ++ d  + +e+A+e+++  +e++p+  e +  Ka+ l   G  ++A ++ ++  +l
  gi|330509115|ref|YP_004385543.1| 505 EKYSDSKEAYERAVEVLNGSLEEDPEDAEAWWLKAESLDNLGRSNEALQAYDRVIEL 561
                                       345555555566666666666666666666666666666666666665555544333 PP

  == domain 7  score: 8.8 bits;  conditional E-value: 0.0013
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                       +s ekAl+y d+ +e  p+    +l+K+ il+ +G   +A +++++a +l
  gi|330509115|ref|YP_004385543.1| 769 ESLEKALDYFDQVLEIYPENAGAWLNKSFILRWMGRTGEALDAVDRAVEL 818
                                       6789******************************************9887 PP

  == domain 8  score: 11.3 bits;  conditional E-value: 0.00022
                                       HHHHHHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-C CS
                             NARP1   3 esellLyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpens 72 
                                       ++ + L k  i++  g++ eAl+ ++++ +   +++ ++ ++aell  Lgr++e+ +++ + +e+ p ns
  gi|330509115|ref|YP_004385543.1| 788 NAGAWLNKSFILRWMGRTGEALDAVDRAVELNPENIDFHWQRAELLSMLGRYNESDQAFDETIEMIPANS 857
                                       5667788889999999999999999999999999999999999999999999999999999999888776 PP

  == domain 9  score: 5.1 bits;  conditional E-value: 0.016
                                       HT-SH..HHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT CS
                             NARP1 205 lgsre..kAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDla 258
                                       +g+ +  +Al+  +k  e +p+    +l K+++lk  G   +A e+  +a +lD++
  gi|330509115|ref|YP_004385543.1| 873 MGQNNneEALKAFEKVTELDPQEPTGWLYKGEVLKALGRRAEADEAYARAGELDNH 928
                                       44433338999999999999999999999999999999999999999999998876 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       3.3   1.7e+03      13      32 ..      97     116 ..      87     117 .. 0.84
   2 ?    2.3   0.0      0.61   3.2e+02      15      31 ..     143     159 ..     121     160 .. 0.78
   3 ?   -1.1   0.1       7.5   3.9e+03      15      32 ..     184     201 ..     180     202 .. 0.82
   4 ?    4.3   0.1      0.14        73       5      30 ..     220     245 ..     206     250 .. 0.75
   5 ?    2.1   0.4       0.7   3.7e+02       7      28 ..     265     286 ..     259     287 .. 0.78
   6 ?    7.9   0.0      0.01       5.4       4      28 ..     303     327 ..     301     331 .. 0.84
   7 ?    7.7   0.0     0.012       6.1       5      31 ..     338     365 ..     335     367 .. 0.88
   8 ?    3.9   0.0      0.19     1e+02       8      32 ..     376     400 ..     374     400 .. 0.89
   9 ?    2.7   0.1      0.47   2.5e+02       8      28 ..     410     430 ..     407     431 .. 0.85
  10 ?    2.1   0.0      0.69   3.6e+02      16      33 .]     473     490 ..     459     490 .. 0.88
  11 ?    1.5   0.0       1.1   5.6e+02       6      28 ..     497     519 ..     493     520 .. 0.84
  12 !   11.2   0.0   0.00089      0.47       1      28 [.     533     560 ..     533     563 .. 0.94
  13 ?   -0.6   0.0         5   2.6e+03      12      29 ..     579     596 ..     572     599 .. 0.82
  14 ?   -1.3   0.0       8.9   4.7e+03      12      23 ..     670     682 ..     668     684 .. 0.82
  15 ?    2.5   0.1      0.51   2.7e+02       5      27 ..     708     730 ..     706     732 .. 0.88
  16 ?    7.7   0.1     0.012       6.2      16      32 ..     771     787 ..     764     788 .. 0.88
  17 ?   -0.0   0.0       3.3   1.8e+03       4      27 ..     827     850 ..     825     851 .. 0.86
  18 ?    5.4   0.0     0.062        33      13      32 ..     875     894 ..     868     895 .. 0.85
  19 ?    2.8   0.3      0.43   2.3e+02       4      26 ..     900     922 ..     898     925 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  13 lgdtdkAlealerlikeYPd 32 
                                       + + d++l+ ++r i+  P+
  gi|330509115|ref|YP_004385543.1|  97 QSRFDESLQVYDRAIELDPE 116
                                       4578999********99886 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.61
                                       HHHHHHHHHHHHHHH-T CS
                             TPR_6  15 dtdkAlealerlikeYP 31 
                                         ++A+e+++r ++  P
  gi|330509115|ref|YP_004385543.1| 143 IFEEAIETFDRALEIDP 159
                                       679*********99888 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 7.5
                                       HHHHHHHHHHHHHHH-TT CS
                             TPR_6  15 dtdkAlealerlikeYPd 32 
                                       ++ ++l+a+++ i+  P+
  gi|330509115|ref|YP_004385543.1| 184 RYNDSLAAYDKAIELAPT 201
                                       677889999999998886 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6   5 klalsyrklgdtdkAlealerlikeY 30 
                                       ++++ + + g+ +++++ l++ +k+Y
  gi|330509115|ref|YP_004385543.1| 220 HMGQDLAARGQIEESRAVLKEAVKNY 245
                                       4444445549***************9 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.7
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       a  +++lg+ d+A + +e+ i+
  gi|330509115|ref|YP_004385543.1| 265 AGVLKELGRRDEAAAGYEKAIE 286
                                       44566788***********998 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlik 28 
                                        + a +++++g++++A++al++  k
  gi|330509115|ref|YP_004385543.1| 303 VNKAILFQEQGRYEEAITALNNATK 327
                                       567899999***********98765 PP

  == domain 7  score: 7.7 bits;  conditional E-value: 0.012
                                       HHHHHHHH.HHHHHHHHHHHHHHHHH-T CS
                             TPR_6   5 klalsyrk.lgdtdkAlealerlikeYP 31 
                                       ++++ + + lg++d+++ea++r ++  P
  gi|330509115|ref|YP_004385543.1| 338 MMGEILSNdLGRYDESIEAYDRALQLDP 365
                                       6889999989**************9888 PP

  == domain 8  score: 3.9 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   8 lsyrklgdtdkAlealerlikeYPd 32 
                                        ++r+lg+ ++A+ a++r +k  P+
  gi|330509115|ref|YP_004385543.1| 376 HALRSLGRNREAVLAYDRALKIDPN 400
                                       5788899**************9997 PP

  == domain 9  score: 2.7 bits;  conditional E-value: 0.47
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAlealerlik 28 
                                        ++r +g++ ++++a++++++
  gi|330509115|ref|YP_004385543.1| 410 AALRDQGRYNESVQAYDEVLR 430
                                       5677799**********9986 PP

  == domain 10  score: 2.1 bits;  conditional E-value: 0.69
                                       HHHHHHHHHHHHHH-TT- CS
                             TPR_6  16 tdkAlealerlikeYPdS 33 
                                       + ++l+a+e+ i+  P+S
  gi|330509115|ref|YP_004385543.1| 473 YNESLQAYEKAIQIDPES 490
                                       678899999999999987 PP

  == domain 11  score: 1.5 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                       ++ ++++l ++++++ea+er ++
  gi|330509115|ref|YP_004385543.1| 497 RGNALLSLEKYSDSKEAYERAVE 519
                                       6788888779**********875 PP

  == domain 12  score: 11.2 bits;  conditional E-value: 0.00089
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                       +A ++ a+s+ +lg++ +Al+a++r+i+
  gi|330509115|ref|YP_004385543.1| 533 EAWWLKAESLDNLGRSNEALQAYDRVIE 560
                                       699999******99************98 PP

  == domain 13  score: -0.6 bits;  conditional E-value: 5
                                       HHHHHHHHHHHHHHHHHH CS
                             TPR_6  12 klgdtdkAlealerlike 29 
                                       +lg++ +++ea+++ ++ 
  gi|330509115|ref|YP_004385543.1| 579 SLGRYNESVEAFDSALNL 596
                                       679*********999875 PP

  == domain 14  score: -1.3 bits;  conditional E-value: 8.9
                                       H.HHHHHHHHHHH CS
                             TPR_6  12 k.lgdtdkAleal 23 
                                       k lg++d+Al+al
  gi|330509115|ref|YP_004385543.1| 670 KpLGRHDEALQAL 682
                                       55799******98 PP

  == domain 15  score: 2.5 bits;  conditional E-value: 0.51
                                       HHHHHHHH.HHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrk.lgdtdkAlealerli 27 
                                       + ++++++ +   + A ea+e+ i
  gi|330509115|ref|YP_004385543.1| 708 QTGRALFRsQ-SFEGAAEAYEKAI 730
                                       6799999977.**********987 PP

  == domain 16  score: 7.7 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHH-TT CS
                             TPR_6  16 tdkAlealerlikeYPd 32 
                                        +kAl++++++++ YP+
  gi|330509115|ref|YP_004385543.1| 771 LEKALDYFDQVLEIYPE 787
                                       589*************7 PP

  == domain 17  score: -0.0 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   4 yklalsyrklgdtdkAlealerli 27 
                                       +++a+++ +lg++ ++ +a+++ i
  gi|330509115|ref|YP_004385543.1| 827 WQRAELLSMLGRYNESDQAFDETI 850
                                       68899999999********98766 PP

  == domain 18  score: 5.4 bits;  conditional E-value: 0.062
                                       HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  13 lgdtdkAlealerlikeYPd 32 
                                       +++ ++Al+a+e++ +  P+
  gi|330509115|ref|YP_004385543.1| 875 QNNNEEALKAFEKVTELDPQ 894
                                       7899**********999886 PP

  == domain 19  score: 2.8 bits;  conditional E-value: 0.43
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   4 yklalsyrklgdtdkAlealerl 26 
                                       ++ ++ +++lg+ ++A ea+ r 
  gi|330509115|ref|YP_004385543.1| 900 LYKGEVLKALGRRAEADEAYARA 922
                                       67799999999*********985 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.045        24       8      56 ..      29      77 ..      23      87 .. 0.78
   2 ?   -1.4   0.0       5.3   2.8e+03       2      33 ..      97     128 ..      96     133 .. 0.82
   3 !   14.5   0.1   5.9e-05     0.031      39      81 ..     281     324 ..     277     325 .. 0.95
   4 !   10.3   0.0    0.0012      0.63       3      81 ..     348     427 ..     346     428 .. 0.95
   5 ?    1.1   0.0      0.91   4.8e+02      39      78 ..     473     513 ..     470     516 .. 0.83
   6 !   16.1   0.0   1.9e-05      0.01       3      80 ..     512     591 ..     510     593 .. 0.70
   7 ?   -1.4   0.0       5.4   2.8e+03      27      54 ..     707     735 ..     698     743 .. 0.75
   8 ?    4.4   0.0     0.085        45      32      80 ..     798     847 ..     767     849 .. 0.73
   9 ?    3.9   0.0      0.12        62       2      60 ..     875     933 ..     874     937 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.045
                                      HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H CS
                            ANAPC3  8 AiflaerllaaetespedayllAlclylngqykrAyellrka.klnsksl 56
                                      Ai+++  +   + +s++  y ++l ly+ng  ++ ++ ++ka +l++++ 
  gi|330509115|ref|YP_004385543.1| 29 AILCIGAVA-EDEKSANYWYEKSLDLYNNGSLEESLQAVDKAiELDPENA 77
                                      666777777.667777777778*******************977776664 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.3
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlcl 33 
                                       q ++++ + +++r+ + ++e+   +++++ +l
  gi|330509115|ref|YP_004385543.1|  97 QSRFDESLQVYDRAIELDPENTTYLLWKGFAL 128
                                       77888999999999999999999999986555 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 5.9e-05
                                       HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  39 ykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       y++A+e l+++ + n ++ g+++ +A    ++++yeeAi+aL +
  gi|330509115|ref|YP_004385543.1| 281 YEKAIEQLNRSiEVNLNNSGAWVNKAILFQEQGRYEEAITALNN 324
                                       99****************************************87 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.0012
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       ++y++ i  ++r+l+ ++ ++ +   ++ +l ++g+  +A   +++a k++++   ++  ++ +l ++++y+e ++a
  gi|330509115|ref|YP_004385543.1| 348 GRYDESIEAYDRALQLDPSDARAWTSKGHALRSLGRNREAVLAYDRAlKIDPNRATAWSGKGAALRDQGRYNESVQA 424
                                       6899**********999*99999999***********************************************9999 PP

                                       H-S CS
                            ANAPC3  79 Lek 81 
                                       +++
  gi|330509115|ref|YP_004385543.1| 425 YDE 427
                                       876 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.91
                                       HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  39 ykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       y++ ++ ++ka +++++s ++++  + +ll L+ky +   a
  gi|330509115|ref|YP_004385543.1| 473 YNESLQAYEKAiQIDPESARAWIGRGNALLSLEKYSDSKEA 513
                                       6677778888888899*******************986555 PP

  == domain 6  score: 16.1 bits;  conditional E-value: 1.9e-05
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H.HHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnsksl.gcrylfAqcllkLkkyeeAia 77 
                                       ++y+ A+ +++  l+ ++e++e+  l+A++l ++g+ ++A++ +++  +lns+   g+++ +    + L++y+e + 
  gi|330509115|ref|YP_004385543.1| 512 EAYERAVEVLNGSLEEDPEDAEAWWLKAESLDNLGRSNEALQAYDRViELNSSKAiGAWIRKSDIFVSLGRYNESVE 588
                                       56777777777777777777777777788888888888888888887777666666777777777777777777777 PP

                                       HH- CS
                            ANAPC3  78 aLe 80 
                                       a++
  gi|330509115|ref|YP_004385543.1| 589 AFD 591
                                       765 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 5.4
                                       HHHHHHHHHTT-HHHHHHHHHCT.SHHHC CS
                            ANAPC3  27 yllAlclylngqykrAyellrka.klnsk 54 
                                          + +l++++ ++ A e ++ka + +++
  gi|330509115|ref|YP_004385543.1| 707 VQTGRALFRSQSFEGAAEAYEKAiGAAGS 735
                                       55678999999999999999998555444 PP

  == domain 8  score: 4.4 bits;  conditional E-value: 0.085
                                       HHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  32 clylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                        l  +g+  +A++ +++a +ln++++  +   A+ l  L++y+e  +a++
  gi|330509115|ref|YP_004385543.1| 798 ILRWMGRTGEALDAVDRAvELNPENIDFHWQRAELLSMLGRYNESDQAFD 847
                                       4555688899*********************************9877766 PP

  == domain 9  score: 3.9 bits;  conditional E-value: 0.12
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcry 60 
                                       qnn ++A+  +e++ + +++ p   ++++++l  +g+  +A e + +a++ +++l++++
  gi|330509115|ref|YP_004385543.1| 875 QNNNEEALKAFEKVTELDPQEPTGWLYKGEVLKALGRRAEADEAYARAGELDNHLRSLL 933
                                       7999********************************99999999999988899988765 PP

>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0         2   1.1e+03       9      39 ..      32      64 ..      29      67 .. 0.81
   2 !   37.5   0.1   4.7e-12   2.5e-09       2     110 ..     962    1070 ..     961    1071 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 2
                               LTD  9 vIsevmedgagnnan..efvelyNtsskavdLs 39
                                       I  v ed+++ n    + + lyN++s + +L+
  gi|330509115|ref|YP_004385543.1| 32 CIGAVAEDEKSANYWyeKSLDLYNNGSLEESLQ 64
                                      57778888877766699*********9988886 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 4.7e-12
                               LTD    2 aaaagdvvIsevmedgagnnanefvelyNtsskavdLsgwkledasge.......ytfpngtgtlaageyvvvws 69  
                                        +++++ + I+++m+ g +    efv ++N+  +a +L+gw+l  + g+        t+p+   tl ++e + ++ 
  gi|330509115|ref|YP_004385543.1|  962 SSTPKMLAITRIMATGED----EFVVVANSRAAAQSLNGWTLDVSDGRngssnqsVTLPDL--TLGPNERINIHL 1030
                                        56777899******8844....*********************999777666666666666..7*********** PP

                               LTD   70 gsgttsasngskasssavwnnggdavaLydasgevvdsvgy 110 
                                        g g+++ ++    +s+ ++n+++ +++L+d +g +v+s+gy
  gi|330509115|ref|YP_004385543.1| 1031 GRGESNETDV-FLNSAITLNDTAGNIILKDETGMIVASFGY 1070
                                        *876655555.5889999999******************99 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       6.5   3.5e+03      11      30 ..      52      71 ..      42      72 .. 0.78
   2 ?    4.9   0.0     0.049        26       6      30 ..      88     112 ..      84     113 .. 0.82
   3 ?    2.9   0.0       0.2     1e+02      17      39 ..     136     158 ..     135     159 .. 0.88
   4 ?    1.1   0.1      0.73   3.8e+02       6      31 ..     173     198 ..     170     199 .. 0.86
   5 !    8.2   0.0    0.0042       2.2       2      29 ..     215     242 ..     215     249 .. 0.93
   6 !   10.8   0.7   0.00067      0.35       4      30 ..     260     286 ..     259     286 .. 0.93
   7 ?    2.8   0.1      0.23   1.2e+02       9      22 ..     306     319 ..     303     325 .. 0.84
   8 ?    4.9   0.1     0.048        25      13      30 ..     345     362 ..     338     363 .. 0.86
   9 ?    6.2   0.1     0.019        10       9      31 ..     375     397 ..     372     397 .. 0.94
  10 !   12.3   0.4   0.00022      0.12       9      32 ..     409     432 ..     407     434 .. 0.91
  11 ?    0.9   0.2      0.88   4.7e+02      18      31 ..     473     486 ..     465     488 .. 0.66
  12 ?    2.8   0.0      0.21   1.1e+02       9      39 ..     498     528 ..     497     531 .. 0.85
  13 ?    2.2   0.1      0.33   1.7e+02      12      31 ..     542     561 ..     539     566 .. 0.86
  14 ?    0.1   0.0       1.6   8.3e+02      15      30 ..     580     595 ..     578     597 .. 0.88
  15 ?   -1.5   0.0         5   2.7e+03      15      23 ..     672     680 ..     672     682 .. 0.84
  16 ?    1.3   0.3      0.66   3.5e+02       9      29 ..     710     730 ..     710     733 .. 0.90
  17 ?    0.6   0.1         1   5.5e+02      18      32 ..     771     785 ..     762     785 .. 0.64
  18 ?    2.1   0.0      0.37   1.9e+02      10      31 ..     797     818 ..     793     819 .. 0.88
  19 ?    2.3   0.0      0.31   1.7e+02       9      31 ..     830     852 ..     829     853 .. 0.90
  20 ?   -0.7   0.0       2.8   1.5e+03      15      28 ..     875     888 ..     873     891 .. 0.87
  21 ?    1.0   0.9      0.81   4.2e+02       9      28 ..     903     922 ..     903     922 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.5
                            TPR_10 11 alrqrgrydeAealleeala 30
                                       l++ g ++e+++  ++a++
  gi|330509115|ref|YP_004385543.1| 52 DLYNNGSLEESLQAVDKAIE 71
                                      47788888888888888876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.049
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       n  +++ +++ r+de+++ +++a++
  gi|330509115|ref|YP_004385543.1|  88 NLAGVITQNQSRFDESLQVYDRAIE 112
                                       4446666****************98 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.2
                            TPR_10  17 rydeAealleealairrrllGpd 39 
                                       r++e  +++eea+++  r+l+ d
  gi|330509115|ref|YP_004385543.1| 136 RGQERIQIFEEAIETFDRALEID 158
                                       789999*********99999876 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.73
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                        +La    +  ry++++a +++a+++
  gi|330509115|ref|YP_004385543.1| 173 DDLATFNNDSARYNDSLAAYDKAIEL 198
                                       57888888999*************86 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.0042
                            TPR_10   2 AsslnNLanalrqrgrydeAealleeal 29 
                                       A +l++++  l +rg+ +e++a l+ea+
  gi|330509115|ref|YP_004385543.1| 215 AVALSHMGQDLAARGQIEESRAVLKEAV 242
                                       6799***********************8 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.00067
                            TPR_10   4 slnNLanalrqrgrydeAealleeala 30 
                                       ++ N a +l ++gr+deA a +e+a++
  gi|330509115|ref|YP_004385543.1| 260 AQQNRAGVLKELGRRDEAAAGYEKAIE 286
                                       67899********************96 PP

  == domain 7  score: 2.8 bits;  conditional E-value: 0.23
                            TPR_10   9 analrqrgrydeAe 22 
                                       a++ +++gry+eA 
  gi|330509115|ref|YP_004385543.1| 306 AILFQEQGRYEEAI 319
                                       78889********6 PP

  == domain 8  score: 4.9 bits;  conditional E-value: 0.048
                            TPR_10  13 rqrgrydeAealleeala 30 
                                        ++gryde+ + +++al+
  gi|330509115|ref|YP_004385543.1| 345 NDLGRYDESIEAYDRALQ 362
                                       689*************98 PP

  == domain 9  score: 6.2 bits;  conditional E-value: 0.019
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       ++alr++gr  eA+  +++al i
  gi|330509115|ref|YP_004385543.1| 375 GHALRSLGRNREAVLAYDRALKI 397
                                       899*****************986 PP

  == domain 10  score: 12.3 bits;  conditional E-value: 0.00022
                            TPR_10   9 analrqrgrydeAealleealair 32 
                                       ++alr++gry+e+++ ++e+l++ 
  gi|330509115|ref|YP_004385543.1| 409 GAALRDQGRYNESVQAYDEVLRAV 432
                                       799******************875 PP

  == domain 11  score: 0.9 bits;  conditional E-value: 0.88
                            TPR_10  18 ydeAealleealai 31 
                                       y+e+++ +e+a++i
  gi|330509115|ref|YP_004385543.1| 473 YNESLQAYEKAIQI 486
                                       56666777777665 PP

  == domain 12  score: 2.8 bits;  conditional E-value: 0.21
                            TPR_10   9 analrqrgrydeAealleealairrrllGpd 39 
                                       +nal ++ +y ++ + +e+a+++    l++d
  gi|330509115|ref|YP_004385543.1| 498 GNALLSLEKYSDSKEAYERAVEVLNGSLEED 528
                                       8999*****************9876666665 PP

  == domain 13  score: 2.2 bits;  conditional E-value: 0.33
                            TPR_10  12 lrqrgrydeAealleealai 31 
                                       l ++gr +eA++ +++++++
  gi|330509115|ref|YP_004385543.1| 542 LDNLGRSNEALQAYDRVIEL 561
                                       6689999********99986 PP

  == domain 14  score: 0.1 bits;  conditional E-value: 1.6
                            TPR_10  15 rgrydeAealleeala 30 
                                       +gry+e+++ ++ al+
  gi|330509115|ref|YP_004385543.1| 580 LGRYNESVEAFDSALN 595
                                       79********999997 PP

  == domain 15  score: -1.5 bits;  conditional E-value: 5
                            TPR_10  15 rgrydeAea 23 
                                       +gr+deA++
  gi|330509115|ref|YP_004385543.1| 672 LGRHDEALQ 680
                                       59*****98 PP

  == domain 16  score: 1.3 bits;  conditional E-value: 0.66
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       ++al++ + +++A + +e+a+
  gi|330509115|ref|YP_004385543.1| 710 GRALFRSQSFEGAAEAYEKAI 730
                                       7899999999*********98 PP

  == domain 17  score: 0.6 bits;  conditional E-value: 1
                            TPR_10  18 ydeAealleealair 32 
                                       +++A+++++++l+i+
  gi|330509115|ref|YP_004385543.1| 771 LEKALDYFDQVLEIY 785
                                       456777777777766 PP

  == domain 18  score: 2.1 bits;  conditional E-value: 0.37
                            TPR_10  10 nalrqrgrydeAealleealai 31 
                                        +lr +gr  eA++  ++a+++
  gi|330509115|ref|YP_004385543.1| 797 FILRWMGRTGEALDAVDRAVEL 818
                                       689***********99999985 PP

  == domain 19  score: 2.3 bits;  conditional E-value: 0.31
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       a +l+ +gry+e+ + ++e++++
  gi|330509115|ref|YP_004385543.1| 830 AELLSMLGRYNESDQAFDETIEM 852
                                       567999**************987 PP

  == domain 20  score: -0.7 bits;  conditional E-value: 2.8
                            TPR_10  15 rgrydeAealleea 28 
                                       +++ +eA++ +e++
  gi|330509115|ref|YP_004385543.1| 875 QNNNEEALKAFEKV 888
                                       8999*******997 PP

  == domain 21  score: 1.0 bits;  conditional E-value: 0.81
                            TPR_10   9 analrqrgrydeAealleea 28 
                                       + +l ++gr++eA + + +a
  gi|330509115|ref|YP_004385543.1| 903 GEVLKALGRRAEADEAYARA 922
                                       67899********9998876 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 ?   -1.2   0.0       2.7   1.4e+03     105     122 ..      36      53 ..      22      59 .. 0.75
   2 !    9.7   0.0    0.0013      0.67      52     117 ..      60     121 ..      54     133 .. 0.80
   3 ?    5.6   0.2     0.023        12      46     122 ..     139     211 ..     136     244 .. 0.69
   4 ?   -2.2   0.0       5.4   2.9e+03      43      66 ..     230     253 ..     217     256 .. 0.86
   5 ?   -1.6   0.0       3.6   1.9e+03      52      71 ..     385     404 ..     352     425 .. 0.82
   6 !   11.4   0.1   0.00038       0.2      49     114 ..     471     532 ..     460     550 .. 0.79
   7 ?    2.4   0.0      0.22   1.1e+02      89     114 ..     764     789 ..     748     797 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.7
                                       HHHHH-TT-HHHHHHHHH CS
                       TOM20_plant 105 qavdedPdndlyrkslel 122
                                        a+de+  n  y+ksl+l
  gi|330509115|ref|YP_004385543.1|  36 VAEDEKSANYWYEKSLDL 53 
                                       578888999999999987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT-HHHH CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqavdedPdndlyr 117
                                       +++++ +++a+ +dP+   +lW    + +    l+   ++ ++ f+ + q++++a++ dP+n++y 
  gi|330509115|ref|YP_004385543.1|  60 EESLQAVDKAIELDPEN-ATLWAYKASGL---NLAGVITQNQSRFDESLQVYDRAIELDPENTTYL 121
                                       66777788899999975.57886544433...45556688899*********************95 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHH CS
                       TOM20_plant  46 eakqmiqdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqavdedPdndlyrkslel 122
                                       e  q+ ++ai  ++ al idPk  +a    g   ++    t +++ a+ n  +a   +++a++  P nd  + +   
  gi|330509115|ref|YP_004385543.1| 139 ERIQIFEEAIETFDRALEIDPKFAEAWA--GKGVICDDLATFNNDSARYNDSLA--AYDKAIELAPTNDSRNLAQAY 211
                                       56688999*************9999843..445555555555555666554444..577777777777765555444 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 5.4
                                       -HHHHHHHHHHHHHHHHHHHHH-T CS
                       TOM20_plant  43 svaeakqmiqdaiskleeallidP 66 
                                       ++ e++ ++++a+  +++ + +dP
  gi|330509115|ref|YP_004385543.1| 230 QIEESRAVLKEAVKNYDKVIDLDP 253
                                       6899999******99999999998 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHHHH-TT-HHH CS
                       TOM20_plant  52 qdaiskleeallidPkkhda 71 
                                       ++a+  ++ al idP++  a
  gi|330509115|ref|YP_004385543.1| 385 REAVLAYDRALKIDPNRATA 404
                                       57888999999999998776 PP

  == domain 6  score: 11.4 bits;  conditional E-value: 0.00038
                                       HHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT-H CS
                       TOM20_plant  49 qmiqdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqavdedPdnd 114
                                          +++++ +e+a+ idP+   a    gna +s   ++    ++ke +e+a ++++ + +edP++ 
  gi|330509115|ref|YP_004385543.1| 471 IAYNESLQAYEKAIQIDPESARAWIGRGNALLSLEKYS----DSKEAYERAVEVLNGSLEEDPEDA 532
                                       55678888899999999999999888899999988875....356668999999999999999864 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHHHHHHHHHH-TT-H CS
                       TOM20_plant  89 eeeakenfekatqffqqavdedPdnd 114
                                       +eea+e +eka ++f+q  +  P+n 
  gi|330509115|ref|YP_004385543.1| 764 REEANESLEKALDYFDQVLEIYPENA 789
                                       689*****************999985 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.7     3e+03      76     138 ..      57     119 ..      46     124 .. 0.76
   2 ?    1.1   0.2      0.93   4.9e+02     106     132 ..     268     294 ..     258     308 .. 0.78
   3 !   16.9   0.4   1.2e-05    0.0066      55     123 ..     326     395 ..     313     404 .. 0.85
   4 ?    2.5   0.1      0.35   1.8e+02      87     125 ..     393     431 ..     392     436 .. 0.86
   5 !   14.0   0.8   9.9e-05     0.052      75     124 ..     511     560 ..     457     565 .. 0.88
   6 ?   -1.2   0.1       4.8   2.5e+03       9      33 ..     706     730 ..     699     732 .. 0.83
   7 !    9.4   0.1    0.0026       1.4      11      95 ..     760     856 ..     755     895 .. 0.81
   8 ?    2.9   0.7      0.27   1.4e+02      78     122 ..     878     922 ..     873     938 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.7
                                       T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH CS
                              BTAD  76 GraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepgpel 138
                                       G  ee l+  +++++++P + +l++     l   G   +   ++++  ++ ++ + ++p+ ++
  gi|330509115|ref|YP_004385543.1|  57 GSLEESLQAVDKAIELDPENATLWAYKASGLNLAGVITQNQSRFDESLQVYDRAIELDPENTT 119
                                       677788888888899999999998888888888877777777777777777777777777665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.93
                                       HHHTT-HHHHHHHHHHHHHHHHHHHS- CS
                              BTAD 106 larsGrqaeALevYerlrrlLaeeLgv 132
                                       l  +Gr+ eA + Ye++ ++L++ + v
  gi|330509115|ref|YP_004385543.1| 268 LKELGRRDEAAAGYEKAIEQLNRSIEV 294
                                       567889999999999998888887766 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHHHHHH.HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  55 erleelrlealealae.aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       ++++ + + a e + e +   lGr++e ++ ++++++++P + r++     Al+ +Gr+ eA  +Y+r+ 
  gi|330509115|ref|YP_004385543.1| 326 TKITPEYVMAWEMMGEiLSNDLGRYDESIEAYDRALQLDPSDARAWTSKGHALRSLGRNREAVLAYDRAL 395
                                       556666677777777744457*********************************************9985 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.35
                                       HHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD  87 alvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                       ++++ +P r +++    +Al+ +Gr +e  ++Y+++ r 
  gi|330509115|ref|YP_004385543.1| 393 RALKIDPNRATAWSGKGAALRDQGRYNESVQAYDEVLRA 431
                                       567889999999999999****************98765 PP

  == domain 5  score: 14.0 bits;  conditional E-value: 9.9e-05
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                        + +e+a++ l++ ++e+P + +++ +  + l  +Gr +eAL++Y+r+ +
  gi|330509115|ref|YP_004385543.1| 511 KEAYERAVEVLNGSLEEDPEDAEAWWLKAESLDNLGRSNEALQAYDRVIE 560
                                       5578999***************************************9865 PP

  == domain 6  score: -1.2 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD   9 lvaagraalaagdpeeaaelleaAl 33 
                                        v++gra+ +   +e+aae++e+A+
  gi|330509115|ref|YP_004385543.1| 706 WVQTGRALFRSQSFEGAAEAYEKAI 730
                                       5889999999999999999999986 PP

  == domain 7  score: 9.4 bits;  conditional E-value: 0.0026
                                       HHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTT............STTHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                              BTAD  11 aagraalaagdpeeaaelleaAlalwrGpaladlea............gewleaererleelrlealealaeaelrl 75 
                                       + g+++ a++  e+a++ +++ l+++ + a a l++               + +++++l+ + ++ + ++ae+++ l
  gi|330509115|ref|YP_004385543.1| 760 SPGKREEANESLEKALDYFDQVLEIYPENAGAWLNKsfilrwmgrtgeALDAVDRAVELNPENIDFHWQRAELLSML 836
                                       5678888899999*****************9999999******9998778889999********************* PP

                                       T-HHHHHHHHHHHHHHSTT- CS
                              BTAD  76 GraeealaelealvaehPlr 95 
                                       Gr++e  +  ++ +++ P +
  gi|330509115|ref|YP_004385543.1| 837 GRYNESDQAFDETIEMIPAN 856
                                       *9997777766666666654 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  78 aeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        eeal+  e+ ++++P   + +    + l ++Gr+aeA e+Y r+
  gi|330509115|ref|YP_004385543.1| 878 NEEALKAFEKVTELDPQEPTGWLYKGEVLKALGRRAEADEAYARA 922
                                       567888888888888888888888888899999999999999886 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.95     5e+02      13      68 ..     184     242 ..     169     246 .. 0.62
   2 !   10.4   0.0     0.001      0.54      39      71 ..     297     329 ..     254     333 .. 0.78
   3 ?   -2.3   0.0       9.4     5e+03      58      86 ..     419     451 ..     414     457 .. 0.44
   4 ?   -0.3   0.0       2.1   1.1e+03      24      70 ..     554     596 ..     541     609 .. 0.73
   5 ?    5.4   0.0     0.037        20      15      76 ..     768     824 ..     763     876 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.95
                            ANAPC5  13 dYqqaldsLhryFDyvlsqnessqkksyqyalLnlaslhadf...ghneeAvkaleeai 68 
                                       +Y+++l +  +    + ++++++ ++ y+  +++l  + +d+   g+ ee+ + l+ea+
  gi|330509115|ref|YP_004385543.1| 184 RYNDSLAAYDKAIELAPTNDSRNLAQAYEGKAVALSHMGQDLaarGQIEESRAVLKEAV 242
                                       44444444444444455555555566666667777777666666677777777777777 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.001
                            ANAPC5  39 syqyalLnlaslhadfghneeAvkaleeairlA 71 
                                       +   a +n a+l ++ g +eeA+ al++a+++ 
  gi|330509115|ref|YP_004385543.1| 297 NNSGAWVNKAILFQEQGRYEEAITALNNATKIT 329
                                       4456899***********************996 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 9.4
                            ANAPC5  58 eeAvkaleeairlAre....nkDkscLalalaw 86 
                                       +e+v+a  e+ r +      + +++ La+a+aw
  gi|330509115|ref|YP_004385543.1| 419 NESVQAYDEVLRAVERdptyRYSSAALAVADAW 451
                                       455555555444332211112334444444444 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.1
                            ANAPC5  24 yFDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleeairl 70 
                                        +D+v++ n+s+       a +    +  ++g ++e+v+a+  a +l
  gi|330509115|ref|YP_004385543.1| 554 AYDRVIELNSSK----AIGAWIRKSDIFVSLGRYNESVEAFDSALNL 596
                                       556666666555....3346677777788899999999999998876 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.037
                            ANAPC5  15 qqaldsLhryFDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleeairlArenkD 76 
                                       +++l++   yFD vl+   ++       a Ln   +   +g   eA++a+  a++l  en D
  gi|330509115|ref|YP_004385543.1| 768 NESLEKALDYFDQVLEIYPEN-----AGAWLNKSFILRWMGRTGEALDAVDRAVELNPENID 824
                                       566777777777777777777.....788999999999999999999999999998888766 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.042        22       8      34 ..      50      76 ..      44      79 .. 0.86
   2 ?    2.2   0.0      0.37     2e+02      16      35 ..      99     118 ..      95     121 .. 0.90
   3 ?    5.1   0.0     0.044        23      12      37 ..     139     164 ..     137     176 .. 0.84
   4 ?   -1.9   0.1       6.9   3.7e+03      16      35 ..     184     203 ..     182     213 .. 0.86
   5 ?    3.8   0.0      0.12        62      14      34 ..     347     367 ..     346     371 .. 0.91
   6 ?   -2.2   0.0       8.4   4.4e+03      18      33 ..     385     400 ..     381     404 .. 0.80
   7 ?   -0.2   0.1         2   1.1e+03      17      33 ..     473     489 ..     472     493 .. 0.91
   8 ?    1.9   0.0      0.45   2.4e+02      17      42 ..     514     539 ..     511     547 .. 0.88
   9 ?   -1.8   0.0       6.7   3.5e+03      14      30 ..     580     596 ..     579     600 .. 0.86
  10 ?    4.7   0.0     0.061        32      18      35 ..     772     789 ..     768     792 .. 0.89
  11 ?   -1.3   0.0       4.4   2.3e+03      19      34 ..     807     822 ..     802     825 .. 0.89
  12 ?   -1.2   0.0       4.1   2.2e+03      14      35 ..     836     857 ..     834     860 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.042
                                      HHHHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  8 AlGhyklgeYseArryvdalLeiEPen 34
                                      +l  y  g  +e+++ vd  +e++Pen
  gi|330509115|ref|YP_004385543.1| 50 SLDLYNNGSLEESLQAVDKAIELDPEN 76
                                      55679999******************9 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.37
                                       -HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPenr 35 
                                       +++e+++  d+ +e++Pen 
  gi|330509115|ref|YP_004385543.1|  99 RFDESLQVYDRAIELDPENT 118
                                       799***************95 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.044
                                       HHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQa 37 
                                        +++ ++eA +  d+ Lei+P++  a
  gi|330509115|ref|YP_004385543.1| 139 ERIQIFEEAIETFDRALEIDPKFAEA 164
                                       588889****************9887 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 6.9
                                       -HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPenr 35 
                                       +Y++++   d  +e+ P n 
  gi|330509115|ref|YP_004385543.1| 184 RYNDSLAAYDKAIELAPTND 203
                                       799999999*9999999996 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.12
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                       lg+Y+e+ +  d+ L+++P+ 
  gi|330509115|ref|YP_004385543.1| 347 LGRYDESIEAYDRALQLDPSD 367
                                       79*****************86 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 8.4
                                       HHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  18 seArryvdalLeiEPe 33 
                                       +eA    d+ L+i+P+
  gi|330509115|ref|YP_004385543.1| 385 REAVLAYDRALKIDPN 400
                                       5778888999****97 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  17 YseArryvdalLeiEPe 33 
                                       Y+e+++  +  ++i+Pe
  gi|330509115|ref|YP_004385543.1| 473 YNESLQAYEKAIQIDPE 489
                                       9***************8 PP

  == domain 8  score: 1.9 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHHHTTS-HHHHHHHH CS
                        Fis1_TPR_C  17 YseArryvdalLeiEPenrQaqsLke 42 
                                       Y++A + ++  Le +Pe   a  Lk+
  gi|330509115|ref|YP_004385543.1| 514 YERAVEVLNGSLEEDPEDAEAWWLKA 539
                                       *****************999987775 PP

  == domain 9  score: -1.8 bits;  conditional E-value: 6.7
                                       HT-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLei 30 
                                       lg+Y+e+ +  d  L++
  gi|330509115|ref|YP_004385543.1| 580 LGRYNESVEAFDSALNL 596
                                       799*******9999986 PP

  == domain 10  score: 4.7 bits;  conditional E-value: 0.061
                                       HHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  18 seArryvdalLeiEPenr 35 
                                       ++A+ y d++Lei Pen 
  gi|330509115|ref|YP_004385543.1| 772 EKALDYFDQVLEIYPENA 789
                                       89**************96 PP

  == domain 11  score: -1.3 bits;  conditional E-value: 4.4
                                       HHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  19 eArryvdalLeiEPen 34 
                                       eA+  vd+  e+ Pen
  gi|330509115|ref|YP_004385543.1| 807 EALDAVDRAVELNPEN 822
                                       899************9 PP

  == domain 12  score: -1.2 bits;  conditional E-value: 4.1
                                       HT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenr 35 
                                       lg+Y+e+ +  d  +e+ P n+
  gi|330509115|ref|YP_004385543.1| 836 LGRYNESDQAFDETIEMIPANS 857
                                       89***********999999996 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.28   1.5e+02      76     117 ..      50      91 ..      39     106 .. 0.85
   2 !    8.5   0.4    0.0049       2.6      52     123 ..     197     278 ..     193     280 .. 0.73
   3 ?   -0.3   0.1       2.5   1.3e+03      84     127 ..     280     323 ..     274     333 .. 0.87
   4 ?    2.0   0.0       0.5   2.7e+02      83     122 ..     348     387 ..     335     393 .. 0.89
   5 !   16.3   0.1   1.9e-05      0.01      65     124 ..     494     553 ..     475     563 .. 0.89
   6 ?   -0.2   0.0       2.4   1.3e+03     118     118 ..     804     804 ..     703     846 .. 0.61
   7 ?   -2.2   0.0       9.8   5.2e+03      84     122 ..     877     915 ..     871     923 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.28
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  76 akealkegdyrwaaellnhlvfadpenaeakelkadaleqlg 117
                                         + +++g ++ +++ ++++++ dpena+  + ka+ l+  g
  gi|330509115|ref|YP_004385543.1|  50 SLDLYNNGSLEESLQAVDKAIELDPENATLWAYKASGLNLAG 91 
                                       5578999*********************99999999887666 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0049
                                       ---HHHHHHHHHHHTTSHHHHH.HHHHHHHHTT-HHHHHHHHHHHHHH.......STT..-HHHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  52 plppeekakrlvelmGgaekvl.ekakealkegdyrwaaellnhlvfa.......dpe..naeakelkadaleqlgy 118
                                       +l+p++ +++l+++  g++  l  + ++ +++g+++ +  +l+ +v +       dp+   +ea++ +a +l++lg+
  gi|330509115|ref|YP_004385543.1| 197 ELAPTNDSRNLAQAYEGKAVALsHMGQDLAARGQIEESRAVLKEAVKNydkvidlDPDfvGQEAQQNRAGVLKELGR 273
                                       57888899999988766666550566667799998888888888888622222225555459*************** PP

                                       H-SSH CS
                   Alkyl_sulf_dimr 119 qaesa 123
                                       + e+a
  gi|330509115|ref|YP_004385543.1| 274 RDEAA 278
                                       99876 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.5
                                       -HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHH CS
                   Alkyl_sulf_dimr  84 dyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRn 127
                                        y+ a+e+ln  ++ + +n+ a   ka  +++ g+ +e+ t+ n
  gi|330509115|ref|YP_004385543.1| 280 GYEKAIEQLNRSIEVNLNNSGAWVNKAILFQEQGRYEEAITALN 323
                                       5889999****************99**99999999999988755 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.5
                                       T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  83 gdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       g y  ++e  + +++ dp++a+a + k +al++lg+  e+
  gi|330509115|ref|YP_004385543.1| 348 GRYDESIEAYDRALQLDPSDARAWTSKGHALRSLGRNREA 387
                                       778889999**************************99886 PP

  == domain 5  score: 16.3 bits;  conditional E-value: 1.9e-05
                                       HTTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  65 lmGgaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                        +G  +++l+  k + +++ y+ a+e+ln  +++dpe+aea  lka++l++lg+ +e+ +
  gi|330509115|ref|YP_004385543.1| 494 WIGRGNALLSLEKYSDSKEAYERAVEVLNGSLEEDPEDAEAWWLKAESLDNLGRSNEALQ 553
                                       56777788888888888999**********************************999865 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 2.4
                                       H CS
                   Alkyl_sulf_dimr 118 y 118
                                       +
  gi|330509115|ref|YP_004385543.1| 804 R 804
                                       3 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 9.8
                                       -HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  84 dyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       + + a++  +++ + dp++ +    k ++l++lg++ae+
  gi|330509115|ref|YP_004385543.1| 877 NNEEALKAFEKVTELDPQEPTGWLYKGEVLKALGRRAEA 915
                                       5667888899999999999999999999*****999986 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2      0.02        10      70     178 ..      38     151 ..      27     156 .. 0.67
   2 ?    1.2   0.2      0.38     2e+02     131     184 ..     144     198 ..     132     211 .. 0.65
   3 !    9.3   0.9    0.0013      0.69     116     180 ..     260     324 ..     225     336 .. 0.78
   4 ?    4.2   0.0     0.045        24     120     144 ..     339     363 ..     333     397 .. 0.85
   5 ?   -0.1   0.1      0.97   5.1e+02     167     194 ..     414     441 ..     380     452 .. 0.80
   6 !    6.7   1.3    0.0083       4.4      89     196 ..     465     573 ..     454     581 .. 0.71
   7 !   10.1   0.4   0.00074      0.39      22     181 ..     712     888 ..     695     897 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.02
                                       -HHHHHHH.HHHHHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHH CS
                              SNAP  70 ekdeaana.yveAakcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaely 145
                                       e++++an  y ++   y++ s ee+ +a++kAie+  e+  +        ++a ++ ++ ++++++++ Y++A el 
  gi|330509115|ref|YP_004385543.1|  38 EDEKSANYwYEKSLDLYNNGSLEESLQAVDKAIELDPENATLWAYKASGLNLAGVITQNQSRFDESLQVYDRAIELD 114
                                       45555555145578899999999999999999999887777766555666777777777799999999999999975 PP

                                       HHTT-HHHHHHHHHHHH..HHHHHTT..-HHHHHHHH CS
                              SNAP 146 eqeeakalankcllkvA..elsaele..kyekAieiy 178
                                        +++   l + + l+ A   l  +++   +e+Aie +
  gi|330509115|ref|YP_004385543.1| 115 PENTTYLLWKGFALRQAvnGLRGQERiqIFEEAIETF 151
                                       5555555555555555533455555444555666655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHHHHHHTT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHT CS
                              SNAP 131 lekAieaYekAaelyeqee.akalankcllkvAelsaelekyekAieiyekvakk 184
                                       +e+Aie +++A e+  +   a a    +  ++A ++ + ++y++++++y+k ++ 
  gi|330509115|ref|YP_004385543.1| 144 FEEAIETFDRALEIDPKFAeAWAGKGVICDDLATFNNDSARYNDSLAAYDKAIEL 198
                                       5667777777777644333244444445667777777777777777777776654 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              SNAP 116 lkkeiaelyekelgdlekAieaYekAaelyeqee.akalankcllkvAelsaelekyekAieiyek 180
                                        +++ a +++ elg+ ++A + YekA e  +    ++ + + ++++ A l  e+++ye+Ai++ ++
  gi|330509115|ref|YP_004385543.1| 260 AQQNRAGVLK-ELGRRDEAAAGYEKAIEQLNRSIeVNLNNSGAWVNKAILFQEQGRYEEAITALNN 324
                                       5566666666.56999***********999887659999999*******************98766 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.045
                                       HHHHHHHTT--HHHHHHHHHHHHHH CS
                              SNAP 120 iaelyekelgdlekAieaYekAael 144
                                       ++e++ ++lg+++++ieaY++A +l
  gi|330509115|ref|YP_004385543.1| 339 MGEILSNDLGRYDESIEAYDRALQL 363
                                       89********************876 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.97
                                       HTT-HHHHHHHHHHHHHTTSS-TTTGGG CS
                              SNAP 167 elekyekAieiyekvakkslennllkys 194
                                       ++++y++++++y++v ++  +    +ys
  gi|330509115|ref|YP_004385543.1| 414 DQGRYNESVQAYDEVLRAVERDPTYRYS 441
                                       56799*********99999888888887 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.0083
                                       -HHHHHHHHHHHHHHHHHTT-HH.HHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHH..TT-HHHHHHHHHHHH CS
                              SNAP  89 speeAvealekAieiytekgrfr.raAklkkeiaelyekelgdlekAieaYekAaelyeq..eeakalankcllkvA 162
                                       ++eeA+ a++++ + y ++ +++ ++A+     ++ + +  ++++++ eaYe+A e+ ++  ee   +a+  +lk A
  gi|330509115|ref|YP_004385543.1| 465 KAEEAAIAYNESLQAYEKAIQIDpESARAWIGRGNALLSL-EKYSDSKEAYERAVEVLNGslEEDPEDAEAWWLK-A 539
                                       5666777777777777777666535677777777777665.8899999999999999987335566677777777.5 PP

                                       HHHHHTT-HHHHHHHHHHHHHTTSS-TTTGGGHH CS
                              SNAP 163 elsaelekyekAieiyekvakkslennllkysvk 196
                                       e   +l++ ++A+++y++v++   ++ +  +  k
  gi|330509115|ref|YP_004385543.1| 540 ESLDNLGRSNEALQAYDRVIELNSSKAIGAWIRK 573
                                       5556789999999999999998888877777655 PP

  == domain 7  score: 10.1 bits;  conditional E-value: 0.00074
                                       HHH--SHHHHHHHHHHHHHH.....HHHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT...-H CS
                              SNAP  22 slfgsksskaeeAadlyeqA.....AnayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv...sp 90 
                                        lf s  + +e Aa+ ye+A      n+  la++w+  geafl ++  +++ ++++ea +++ +A   + +v    p
  gi|330509115|ref|YP_004385543.1| 712 ALFRS--QSFEGAAEAYEKAigaagSNKILLAEAWKGKGEAFLVLSGSEKSPGKREEANESLEKALDYFDQVleiYP 786
                                       46644..569999999998755544467778***************************************9999999 PP

                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT.............--HHHHHHHHHHHHHHHHHTT-HHHH CS
                              SNAP  91 eeAvealekAieiytekgrfrraAklkkeiaelyekel.............gdlekAieaYekAaelyeqeeakala 154
                                       e+A + l+k++ i+  +gr  +a +      el  +++             g+++++ +a+++  e+   +++  la
  gi|330509115|ref|YP_004385543.1| 787 ENAGAWLNKSF-ILRWMGRTGEALDAVDRAVELNPENIdfhwqraellsmlGRYNESDQAFDETIEMIPANSSRKLA 862
                                       ****9999986.78888888888888777777777665444444333333333555555555555555555555555 PP

                                       HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              SNAP 155 nkcllkvAelsaelekyekAieiyekv 181
                                       +    k  ++  ++ + e+A++++ekv
  gi|330509115|ref|YP_004385543.1| 863 EVWTFKGFNFMGQN-NNEEALKAFEKV 888
                                       55555554444444.335666666666 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.24   1.3e+02       3      15 ..      60      72 ..      58      78 .. 0.89
   2 ?    2.4   0.0      0.22   1.2e+02       1      15 [.      99     113 ..      99     119 .. 0.90
   3 ?    2.0   0.0       0.3   1.6e+02       1      16 [.     184     199 ..     184     208 .. 0.86
   4 ?    5.3   0.0     0.027        14       2      19 ..     281     298 ..     280     300 .. 0.90
   5 ?   -0.9   0.0       2.4   1.3e+03       1      16 [.     314     329 ..     314     332 .. 0.90
   6 ?   -0.3   0.1       1.5   8.2e+02       1      14 [.     349     362 ..     349     364 .. 0.90
   7 ?    3.1   0.1      0.13        70       2      15 ..     473     486 ..     472     491 .. 0.92
   8 ?   -0.9   0.0       2.4   1.2e+03      28      40 ..     825     837 ..     806     843 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.24
                                      HHHHHHHHHHHHH CS
                          HTH_Bact  3 eeaLeqvnkAiei 15
                                      ee+L+ v+kAie+
  gi|330509115|ref|YP_004385543.1| 60 EESLQAVDKAIEL 72
                                      89*********96 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.22
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       r++e+L++ ++Aie+
  gi|330509115|ref|YP_004385543.1|  99 RFDESLQVYDRAIEL 113
                                       689**********96 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.3
                                       -HHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiS 16 
                                       rY+ +L   +kAie+ 
  gi|330509115|ref|YP_004385543.1| 184 RYNDSLAAYDKAIELA 199
                                       7************986 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHHHHHHT CS
                          HTH_Bact   2 YeeaLeqvnkAieiSiri 19 
                                       Ye+a+eq n+ ie+ +++
  gi|330509115|ref|YP_004385543.1| 281 YEKAIEQLNRSIEVNLNN 298
                                       *************98876 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 2.4
                                       -HHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiS 16 
                                       rYeea+   n A +i+
  gi|330509115|ref|YP_004385543.1| 314 RYEEAITALNNATKIT 329
                                       7**********99986 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 1.5
                                       -HHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAie 14 
                                       rY+e++e  ++A++
  gi|330509115|ref|YP_004385543.1| 349 RYDESIEAYDRALQ 362
                                       7**********986 PP

  == domain 7  score: 3.1 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                       Y+e+L+  +kAi+i
  gi|330509115|ref|YP_004385543.1| 473 YNESLQAYEKAIQI 486
                                       ************97 PP

  == domain 8  score: -0.9 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHTT CS
                          HTH_Bact  28 LyYqkgecleklg 40 
                                       + +q++e+l  lg
  gi|330509115|ref|YP_004385543.1| 825 FHWQRAELLSMLG 837
                                       4567777777666 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0057         3       5      21 ..      66      82 ..      63      83 .. 0.90
   2 ?   -2.0   0.0       6.4   3.4e+03       7      19 ..     153     165 ..     152     166 .. 0.84
   3 ?    6.3   0.1     0.016       8.5       2      28 .]     775     801 ..     774     801 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0057
                                      HHHHHHH-TT-CHHHHH CS
                              PPTA  5 tekliekdpkNYsaWny 21
                                      ++k+ie+dp N + W y
  gi|330509115|ref|YP_004385543.1| 66 VDKAIELDPENATLWAY 82
                                      789************99 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.4
                                       HHHHH-TT-CHHH CS
                              PPTA   7 kliekdpkNYsaW 19 
                                        ++e dpk   aW
  gi|330509115|ref|YP_004385543.1| 153 RALEIDPKFAEAW 165
                                       5899****98888 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.016
                                       HHHHHHHHHH-TT-CHHHHHHHHHHCH CS
                              PPTA   2 LeltekliekdpkNYsaWnyRrwllek 28 
                                       L++ ++++e +p N  aW   +++l++
  gi|330509115|ref|YP_004385543.1| 775 LDYFDQVLEIYPENAGAWLNKSFILRW 801
                                       89999*******************986 PP

>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3      0.18        98      21     104 ..     141     248 ..     129     253 .. 0.68
   2 !    9.0   0.1    0.0024       1.3     106     140 ..     292     326 ..     258     328 .. 0.85
   3 ?    2.3   0.0      0.28   1.5e+02      15      41 ..     762     788 ..     760     864 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHTS-HHHHHCCB-...........S--SSSS....................-EEEEEEEEEEE---- CS
                              YfdX  21 kkllekAqgkleaaladdpklvk...........kapasad....................alvPvdaevividdla 66 
                                       ++  e+A + +++al+ dpk+                   +                    +l P + + ++++ ++
  gi|330509115|ref|YP_004385543.1| 141 IQIFEEAIETFDRALEIDPKFAEawagkgvicddL-----AtfnndsaryndslaaydkaiELAPTNDSRNLAQAYE 212
                                       56678999999**********55666555555441.....0444445555666777788888888888888888883 PP

                                       --HHHHHHHHHHHHHHHTT-HHHHHHHHHHTT-EEEEE CS
                              YfdX  67 dtpekkaaikkanellkkgdtqaArelLkllgseidit 104
                                          ++ a     ++l + g+ ++ r++Lk++ ++ d +
  gi|330509115|ref|YP_004385543.1| 213 --GKAVALSHMGQDLAARGQIEESRAVLKEAVKNYDKV 248
                                       ..333333333466777788999999999888777655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0024
                                       EEEEHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              YfdX 106 allPLatypaavkkAaelleegkyyeAkeaLkeal 140
                                       + ++L++  a v+kA+ + e+g y+eA +aL++a 
  gi|330509115|ref|YP_004385543.1| 292 IEVNLNNSGAWVNKAILFQEQGRYEEAITALNNAT 326
                                       46899999************************995 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.28
                                       T-HHHHHHHHHHHHHHHTS-HHHHHCC CS
                              YfdX  15 gdtkeAkkllekAqgkleaaladdpkl 41 
                                       g+ +eA + lekA   ++ +l+ +p+ 
  gi|330509115|ref|YP_004385543.1| 762 GKREEANESLEKALDYFDQVLEIYPEN 788
                                       789999999999999999999999987 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0      0.01       5.3       5      50 ..     282     327 ..     278     334 .. 0.88
   2 ?    0.0   0.1         2   1.1e+03       6      43 ..     352     389 ..     349     404 .. 0.84
   3 ?    2.4   0.2      0.38     2e+02       7      43 ..     517     553 ..     472     557 .. 0.77
   4 ?    3.9   0.1      0.12        66       7      56 ..     517     566 ..     511     597 .. 0.75
   5 !    8.0   0.0     0.007       3.7       6      53 ..     807     857 ..     803     889 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.01
                            TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                       ++ +++l + ++ n ++  a ++ A +  ++gryeeA+++L +  k
  gi|330509115|ref|YP_004385543.1| 282 EKAIEQLNRSIEVNLNNSGAWVNKAILFQEQGRYEEAITALNNATK 327
                                       56899**********************************9977655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAle 43 
                                       +++++ ++al+ +p+d  a      al + gr++eA+ 
  gi|330509115|ref|YP_004385543.1| 352 ESIEAYDRALQLDPSDARAWTSKGHALRSLGRNREAVL 389
                                       67899999***********9999999999999999975 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.38
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAle 43 
                                        ++ l   l+++p+d +a    A+ l   gr  eAl+
  gi|330509115|ref|YP_004385543.1| 517 AVEVLNGSLEEDPEDAEAWWLKAESLDNLGRSNEALQ 553
                                       4556666778888888888888888888888888776 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.12
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwe 56 
                                        ++ l   l+++p+d +a    A+ l   gr  eAl++  ++++ +++ +
  gi|330509115|ref|YP_004385543.1| 517 AVEVLNGSLEEDPEDAEAWWLKAESLDNLGRSNEALQAYDRVIELNSSKA 566
                                       567788899***************************98777776666555 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.007
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryee...AleqLleilkrdr 53 
                                       + l+++++a++ np+++d + + A++l + gry e   A+++ +e++ +++
  gi|330509115|ref|YP_004385543.1| 807 EALDAVDRAVELNPENIDFHWQRAELLSMLGRYNEsdqAFDETIEMIPANS 857
                                       578999***********************9998652227888777777665 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0024       1.3      29      67 ..      60      96 ..      39     123 .. 0.80
   2 ?   -0.7   0.1       3.2   1.7e+03      19      44 ..     176     201 ..     173     215 .. 0.88
   3 ?    0.7   0.1       1.1   5.9e+02      28      51 ..     315     338 ..     305     353 .. 0.87
   4 ?   -2.0   0.0       7.8   4.1e+03      28      52 ..     350     374 ..     344     380 .. 0.87
   5 ?    3.5   0.1      0.15        77      25      54 ..     470     498 ..     464     523 .. 0.75
   6 ?   -1.1   0.0         4   2.1e+03      29      53 ..     549     573 ..     547     576 .. 0.91
   7 ?   -0.2   0.0       2.2   1.2e+03      30      51 ..     807     828 ..     805     833 .. 0.90
   8 ?    1.7   0.0      0.55   2.9e+02      23      52 ..     873     902 ..     865     917 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0024
                           DUF1510 29 nEmekavskatglsednmivwwlgnggspqkaigtvssk 67
                                      +E ++av ka++l+ +n ++w  + +g +    g+++++
  gi|330509115|ref|YP_004385543.1| 60 EESLQAVDKAIELDPENATLWAYKASGLNL--AGVITQN 96
                                      799*********************999855..4444333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.2
                           DUF1510  19 ssydkgsvDwnEmekavskatglsed 44 
                                       ++++++s  +n+ + a  ka++l   
  gi|330509115|ref|YP_004385543.1| 176 ATFNNDSARYNDSLAAYDKAIELAPT 201
                                       6899*****************99765 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.1
                           DUF1510  28 wnEmekavskatglsednmivwwl 51 
                                       ++E   a+++at ++ + ++ w +
  gi|330509115|ref|YP_004385543.1| 315 YEEAITALNNATKITPEYVMAWEM 338
                                       8999***********999999976 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 7.8
                           DUF1510  28 wnEmekavskatglsednmivwwlg 52 
                                       ++E  +a  +a +l+ ++   w  +
  gi|330509115|ref|YP_004385543.1| 350 YDESIEAYDRALQLDPSDARAWTSK 374
                                       78999*************9999765 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.15
                           DUF1510  25 svDwnEmekavskatglsednmivwwlgng 54 
                                          +nE ++a +ka++++ ++   w +g+g
  gi|330509115|ref|YP_004385543.1| 470 AIAYNESLQAYEKAIQIDPESARAW-IGRG 498
                                       5679**************9887766.4444 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 4
                           DUF1510  29 nEmekavskatglsednmivwwlgn 53 
                                       nE ++a  ++++l++++ i  w+++
  gi|330509115|ref|YP_004385543.1| 549 NEALQAYDRVIELNSSKAIGAWIRK 573
                                       8999******************986 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 2.2
                           DUF1510  30 Emekavskatglsednmivwwl 51 
                                       E ++av +a++l+ +n+ ++w 
  gi|330509115|ref|YP_004385543.1| 807 EALDAVDRAVELNPENIDFHWQ 828
                                       7889*************99996 PP

  == domain 8  score: 1.7 bits;  conditional E-value: 0.55
                           DUF1510  23 kgsvDwnEmekavskatglsednmivwwlg 52 
                                       +g+++ +E +ka++k+t+l+ ++ + w  +
  gi|330509115|ref|YP_004385543.1| 873 MGQNNNEEALKAFEKVTELDPQEPTGWLYK 902
                                       57788899*************999988765 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 ?    2.5   0.0      0.28   1.5e+02      28      49 ..     341     362 ..     338     373 .. 0.85
   2 ?   -0.4   0.0       2.3   1.2e+03      31      49 ..     577     595 ..     573     604 .. 0.82
   3 ?    2.9   0.0      0.22   1.1e+02      35      58 ..     762     785 ..     760     788 .. 0.86
   4 ?   -1.5   0.0       4.8   2.6e+03      26      38 ..     828     840 ..     823     858 .. 0.79
   5 ?   -2.1   0.0       7.8   4.1e+03      27      42 ..    1023    1038 ..    1021    1039 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.28
                       MCC-bdg_PDZ  28 eeLsldlgkaEsnatALvlALe 49 
                                       e Ls+dlg++     A+  AL+
  gi|330509115|ref|YP_004385543.1| 341 EILSNDLGRYDESIEAYDRALQ 362
                                       679*******988889888888 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.3
                       MCC-bdg_PDZ  31 sldlgkaEsnatALvlALe 49 
                                        + lg+++  + A  +AL+
  gi|330509115|ref|YP_004385543.1| 577 FVSLGRYNESVEAFDSALN 595
                                       5789****99999999998 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.22
                       MCC-bdg_PDZ  35 gkaEsnatALvlALeyserlkeay 58 
                                       gk+E  +  L  AL+y ++++e+y
  gi|330509115|ref|YP_004385543.1| 762 GKREEANESLEKALDYFDQVLEIY 785
                                       666667778**************9 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 4.8
                       MCC-bdg_PDZ  26 qseeLsldlgkaE 38 
                                       q +eL   lg+++
  gi|330509115|ref|YP_004385543.1| 828 QRAELLSMLGRYN 840
                                       4567777799999 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 7.8
                       MCC-bdg_PDZ   27 seeLsldlgkaEsnat 42  
                                        +e++ + lg+ Esn t
  gi|330509115|ref|YP_004385543.1| 1023 NERINIHLGRGESNET 1038
                                        5889999******976 PP

>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.041        22      14      35 ..      32      52 ..      22      55 .. 0.73
   2 ?    5.9   0.1     0.041        22       5      37 ..     514     543 ..     513     544 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.041
                              Sel1 14 lnGlgvpkDpekAiewyekAAe 35
                                      + G  v  D+++A +wyek+ +
  gi|330509115|ref|YP_004385543.1| 32 CIGA-VAEDEKSANYWYEKSLD 52
                                      4555.7779**********876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.041
                              Sel1   5 yrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                       y  +     lnG  ++ Dpe A+ w+ kA +++
  gi|330509115|ref|YP_004385543.1| 514 YERA--VEVLNGS-LEEDPEDAEAWWLKAESLD 543
                                       6666..4448998.999************8876 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         7   3.7e+03      12      36 .]      95     117 ..      93     117 .. 0.78
   2 ?   -1.4   0.0       4.9   2.6e+03      17      34 ..     144     159 ..     144     160 .. 0.78
   3 ?    8.5   0.0    0.0039       2.1       8      34 ..     306     330 ..     306     331 .. 0.82
   4 ?   -1.3   0.0       4.5   2.4e+03      15      34 ..     348     365 ..     346     367 .. 0.75
   5 ?   -2.3   0.0       9.4     5e+03      13      25 ..     414     426 ..     409     429 .. 0.79
   6 ?   -1.2   0.0         4   2.1e+03      17      28 ..     771     780 ..     769     788 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7
                                       HHTT-HHHHHHH..HHHHHHH-TT- CS
                             TPR_3  12 ynkkkyqeArelfsYallaildken 36 
                                       +n+ +++e +++++   +  ld+en
  gi|330509115|ref|YP_004385543.1|  95 QNQSRFDESLQVYD--RAIELDPEN 117
                                       77888888888866..888888887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.9
                                       HHHHHHH..HHHHHHH-T CS
                             TPR_3  17 yqeArelfsYallaildk 34 
                                       ++eA+e+f+   +  +d+
  gi|330509115|ref|YP_004385543.1| 144 FEEAIETFD--RALEIDP 159
                                       589****98..7777776 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0039
                                       HHHHHHTT-HHHHHHH..HHHHHHH-T CS
                             TPR_3   8 AaefynkkkyqeArelfsYallaildk 34 
                                       A  f+ +++y+eA+ ++    ++++++
  gi|330509115|ref|YP_004385543.1| 306 AILFQEQGRYEEAITALN--NATKITP 330
                                       567***********9977..7777766 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 4.5
                                       T-HHHHHHH..HHHHHHH-T CS
                             TPR_3  15 kkyqeArelfsYallaildk 34 
                                       ++y+e +e+++   +  ld+
  gi|330509115|ref|YP_004385543.1| 348 GRYDESIEAYD--RALQLDP 365
                                       899*9999977..6666665 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 9.4
                                       HTT-HHHHHHH.. CS
                             TPR_3  13 nkkkyqeArelfs 25 
                                       ++++y+e +++++
  gi|330509115|ref|YP_004385543.1| 414 DQGRYNESVQAYD 426
                                       79*****999987 PP

  == domain 6  score: -1.2 bits;  conditional E-value: 4
                                       HHHHHHH..HHH CS
                             TPR_3  17 yqeArelfsYal 28 
                                       +++A+++f+  +
  gi|330509115|ref|YP_004385543.1| 771 LEKALDYFD--Q 780
                                       589****99..4 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.1   5.6e+02      13      30 ..      96     113 ..      93     114 .. 0.89
   2 ?    1.8   0.1      0.32   1.7e+02      17      30 ..     144     157 ..     144     158 .. 0.96
   3 ?    2.1   0.0      0.25   1.3e+02      11      25 ..     309     323 ..     308     328 .. 0.82
   4 ?    0.2   0.0         1   5.4e+02      16      30 ..     349     363 ..     347     363 .. 0.93
   5 ?    2.5   0.0      0.19     1e+02       9      31 ..     575     597 ..     574     599 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.1
                          SHNi-TPR  13 EnenFpqAveDlrkaLeL 30 
                                        +++F++ ++ +++a+eL
  gi|330509115|ref|YP_004385543.1|  96 NQSRFDESLQVYDRAIEL 113
                                       589************998 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.32
                          SHNi-TPR  17 FpqAveDlrkaLeL 30 
                                       F++A+e +++aLe+
  gi|330509115|ref|YP_004385543.1| 144 FEEAIETFDRALEI 157
                                       9***********98 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.25
                          SHNi-TPR  11 slEnenFpqAveDlr 25 
                                       ++E++++++A++ l+
  gi|330509115|ref|YP_004385543.1| 309 FQEQGRYEEAITALN 323
                                       78*********9776 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1
                          SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                       ++++ +e +++aL+L
  gi|330509115|ref|YP_004385543.1| 349 RYDESIEAYDRALQL 363
                                       8************98 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.19
                          SHNi-TPR   9 EislEnenFpqAveDlrkaLeLr 31 
                                       +i++  +++++ ve +++aL+L 
  gi|330509115|ref|YP_004385543.1| 575 DIFVSLGRYNESVEAFDSALNLL 597
                                       6777779**************95 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1         6   3.2e+03      10      66 ..     185     243 ..     176     250 .. 0.64
   2 ?    7.0   0.5     0.012       6.5       3      94 ..     260     354 ..     258     361 .. 0.68
   3 ?    6.0   0.6     0.027        14      14     114 ..     347     444 ..     335     449 .. 0.68
   4 ?    3.0   0.0      0.21   1.1e+02       7      58 ..     538     587 ..     503     604 .. 0.66
   5 ?   -1.8   0.0       6.7   3.5e+03       9      63 ..     756     814 ..     749     844 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6
                             TPR_5  10 arDstGhedkavplYrraLaeGLagarrrrati..qLassLRnlGeaeealaLLraele 66 
                                         Ds    dka++l      + La+a  ++a+    +   L   G++ee+ a+L++ ++
  gi|330509115|ref|YP_004385543.1| 185 YNDSLAAYDKAIELAPTNDSRNLAQAYEGKAVAlsHMGQDLAARGQIEESRAVLKEAVK 243
                                       55666667777777666666666666666654322455667777888888888887765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                             TPR_5   3 aaFeragarDstGhedkavplYrraLaeGLa....garrrratiqLassLRnlGeaeealaLLraeleapsdeldda 75 
                                       a+ +rag+    G+ d+a+ +Y++a+++  +    + ++  a +  a      G+ eea++ L++  ++ + e+  a
  gi|330509115|ref|YP_004385543.1| 260 AQQNRAGVLKELGRRDEAAAGYEKAIEQLNRsievNLNNSGAWVNKAILFQEQGRYEEAITALNNA-TKITPEYVMA 335
                                       56689********************98744311123345567777777777777777777777654.3445566666 PP

                             TPR_5  76 laaflaLvLsdlgrereav 94 
                                        +++  +   dlgr  e++
  gi|330509115|ref|YP_004385543.1| 336 WEMMGEILSNDLGRYDESI 354
                                       6666666666666666665 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.027
                             TPR_5  14 tGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgre 90 
                                        G+ d++++ Y raL+   ++    ra      +LR lG+  ea+   +  l+  ++    a +     +L d+gr 
  gi|330509115|ref|YP_004385543.1| 347 LGRYDESIEAYDRALQLDPSD---ARAWTSKGHALRSLGRNREAVLAYDRALKIDPNRA-TAWS-GKGAALRDQGRY 418
                                       688999999999999854444...44556668899999999998866666655554443.3444.445578999999 PP

                             TPR_5  91 reavsi...vllalaehlprYqRsvtn 114
                                       +e+v+    vl a+ e  p Y+ s ++
  gi|330509115|ref|YP_004385543.1| 419 NESVQAydeVLRAV-ERDPTYRYSSAA 444
                                       99887522155554.455777776665 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.21
                             TPR_5   7 ragarDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeeal 58 
                                       +a + D  G++++a + Y r ++  L+ +++  a i  +     lG+ +e++
  gi|330509115|ref|YP_004385543.1| 538 KAESLDNLGRSNEALQAYDRVIE--LNSSKAIGAWIRKSDIFVSLGRYNESV 587
                                       45556666666666666666665..555555555555555555555555544 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 6.7
                             TPR_5   9 garDstGhedkavplYrraLa..eGLagarrrrat..iqLassLRnlGeaeealaLLra 63 
                                       g++ s G+ ++a +  ++aL+  + + ++   +a   +  +  LR +G++ eal  ++ 
  gi|330509115|ref|YP_004385543.1| 756 GSEKSPGKREEANESLEKALDyfDQVLEIYPENAGawLNKSFILRWMGRTGEALDAVDR 814
                                       67777788888888888887622222233333333003333346666666666655555 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         7   3.7e+03       8      36 ..      43      71 ..      41      73 .. 0.79
   2 ?   -1.2   0.0       2.9   1.6e+03      14      35 ..     175     196 ..     141     201 .. 0.58
   3 ?    5.0   0.1     0.036        19       5      38 ..     296     329 ..     292     345 .. 0.86
   4 ?   -1.1   0.0       2.8   1.5e+03      11      40 ..     405     434 ..     399     449 .. 0.75
   5 ?   -2.2   0.0       5.8   3.1e+03      17      74 ..     507     539 ..     493     545 .. 0.53
   6 ?   -1.4   0.0       3.4   1.8e+03      21      38 ..     580     597 ..     566     602 .. 0.74
   7 ?    0.4   0.0      0.95     5e+02      19      45 ..     766     785 ..     750     833 .. 0.66
   8 ?   -1.4   0.0       3.4   1.8e+03       7      62 ..     788     842 ..     778     849 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7
                           DUF5113  8 andYanlayylnvegeyeeALeyldsale 36
                                      an + +    l+ +g+ ee+L+ +d+a+e
  gi|330509115|ref|YP_004385543.1| 43 ANYWYEKSLDLYNNGSLEESLQAVDKAIE 71
                                      55566666778889999********9997 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.9
                           DUF5113  14 layylnvegeyeeALeyldsal 35 
                                       la++ n + +y+++L+  d+a+
  gi|330509115|ref|YP_004385543.1| 175 LATFNNDSARYNDSLAAYDKAI 196
                                       4455555556666666666555 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.036
                           DUF5113   5 lqiandYanlayylnvegeyeeALeyldsaleyl 38 
                                       l+ +++++n a     +g+yeeA++ l++a ++ 
  gi|330509115|ref|YP_004385543.1| 296 LNNSGAWVNKAILFQEQGRYEEAITALNNATKIT 329
                                       78899***********************998765 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2.8
                           DUF5113  11 YanlayylnvegeyeeALeyldsaleylNa 40 
                                       +   + +l  +g+y+e+++  d++l+ + +
  gi|330509115|ref|YP_004385543.1| 405 WSGKGAALRDQGRYNESVQAYDEVLRAVER 434
                                       555666777789999999999999988865 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 5.8
                           DUF5113  17 ylnvegeyeeALeyldsaleylNahyekYakkkadtldklkmllegegeaaelkWlkd 74 
                                       y+  ++ ye+A+e+l                         + +le++ e ae  Wlk 
  gi|330509115|ref|YP_004385543.1| 507 YSDSKEAYERAVEVL-------------------------NGSLEEDPEDAEAWWLKA 539
                                       344444444444444.........................344455555555555555 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 3.4
                           DUF5113  21 egeyeeALeyldsaleyl 38 
                                        g+y+e++e +dsal++l
  gi|330509115|ref|YP_004385543.1| 580 LGRYNESVEAFDSALNLL 597
                                       478888888888888876 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 0.95
                           DUF5113  19 nvegeyeeALeyldsaleylNahyekY 45 
                                        ++++ e+AL+y+d++le+       Y
  gi|330509115|ref|YP_004385543.1| 766 EANESLEKALDYFDQVLEI-------Y 785
                                       4455556666666666654.......3 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 3.4
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtldklkmlleg 62 
                                        a+++ n    l   g+  eAL+ +d a+e+ N     +  ++a+ l+ l  + e+
  gi|330509115|ref|YP_004385543.1| 788 NAGAWLNKSFILRWMGRTGEALDAVDRAVEL-NPENIDFHWQRAELLSMLGRYNES 842
                                       5778888888888899999999999999984.444444444444566666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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: 1.11u 0.35s 00:00:01.46 Elapsed: 00:00:00.66
# Mc/sec: 5244.95
//
Query:       gi|330509116|ref|YP_004385544.1|  [L=228]
Description: hypothetical protein MCON_3506 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1565.07
//
Query:       gi|330509117|ref|YP_004385545.1|  [L=282]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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   87.7  11.0      1e-06   28.3   0.0    6.4  6  TPR_1            Tetratricopeptide repeat
    7.4e-25   85.1  13.5    1.1e-05   25.3   0.0    6.6  6  TPR_8            Tetratricopeptide repeat
    2.4e-23   80.3   8.5    7.6e-06   25.7   0.0    7.0  6  TPR_2            Tetratricopeptide repeat
    4.8e-23   80.6   9.7    6.6e-07   28.9   0.1    6.0  6  TPR_11           TPR repeat
    1.9e-19   68.6   3.7    0.00028   21.1   0.0    6.7  6  TPR_17           Tetratricopeptide repeat
    1.8e-17   62.5   0.1     0.0033   18.1   0.0    6.2  6  TPR_14           Tetratricopeptide repeat
    2.1e-17   63.5   0.0    3.7e-05   24.3   0.5    4.7  4  TPR_16           Tetratricopeptide repeat
    2.6e-12   46.8   6.5     0.0027   18.0   0.1    5.3  5  TPR_12           Tetratricopeptide repeat
    1.1e-11   45.1   4.4      0.013   16.0   0.0    5.3  5  TPR_19           Tetratricopeptide repeat
    1.1e-09   38.3   3.5    3.3e-05   24.0   0.0    3.6  4  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    1.8e-07   31.2   0.0       0.01   15.9   0.0    4.3  6  TPR_9            Tetratricopeptide repeat
    8.1e-07   28.6   6.8       0.21   11.4   0.0    4.3  4  PPTA             Protein prenyltransferase alpha subunit repe
    8.6e-07   29.2   5.1         25    5.8   0.0    6.3  6  TPR_6            Tetratricopeptide repeat
    1.6e-06   27.4   3.8     0.0098   14.8   0.1    3.2  3  NARP1            NMDA receptor-regulated protein 1
    3.3e-05   24.0   0.4        7.6    6.6   0.0    4.7  5  DUF3856          Domain of Unknown Function (DUF3856)
    0.00015   22.2   0.1      0.097   13.1   0.0    3.4  3  BTAD             Bacterial transcriptional activator domain
    0.00025   21.1   0.2        1.5    9.0   0.0    4.0  4  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
     0.0004   20.4   0.9      0.001   19.0   0.3    1.9  2  DUF4919          Domain of unknown function (DUF4919)
    0.00055   19.7   7.8       0.55   10.2   0.0    5.4  5  TPR_10           Tetratricopeptide repeat
    0.00081   19.7   4.9       0.85   10.0   0.7    3.9  4  TPR_20           Tetratricopeptide repeat
     0.0014   18.5   4.7        4.2    7.6   0.0    6.0  6  TPR_7            Tetratricopeptide repeat
     0.0016   18.9   0.4        1.4    9.4   0.0    3.8  4  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0039   17.2   0.4        2.5    8.1   0.0    3.4  3  DUF627           Protein of unknown function (DUF627)
  ------ inclusion threshold ------
      0.019   15.1   2.5         14    5.9   0.0    4.1  5  DUF1510          Domain of unknown function (DUF1510)
      0.039   13.7   4.2       0.55    9.9   0.2    3.2  3  TPR_21           Tetratricopeptide repeat-like domain
       0.24   11.1   4.0       0.38   10.4   0.1    2.7  3  DUF2225          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   2.2e-07   0.00015      11      34 .]      45      68 ..      43      68 .. 0.91
   2 ?    0.8   0.0       0.7   4.8e+02       8      30 ..     112     134 ..     106     137 .. 0.79
   3 !    9.6   0.0    0.0012      0.83      18      31 ..     163     176 ..     162     179 .. 0.92
   4 !   28.3   0.0   1.5e-09     1e-06       2      34 .]     182     214 ..     181     214 .. 0.96
   5 !   19.5   0.1     9e-07   0.00062       2      33 ..     216     247 ..     215     248 .. 0.94
   6 !    9.8   0.3   0.00099      0.68       1      30 [.     249     278 ..     249     281 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.2e-07
                                      HHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1 11 yfklgkydeAleyyekALelnPnn 34
                                      +f++ ++ eAle yekA+++nP+n
  gi|330509117|ref|YP_004385545.1| 45 FFNKSNPLEALESYEKAIQINPDN 68
                                      78888999**************98 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.7
                                       HHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   8 GnayfklgkydeAleyyekALel 30 
                                       ++a+ +lg+ +e  ++ +kA+ +
  gi|330509117|ref|YP_004385545.1| 112 AMALASLGNREESNQFLKKAIDV 134
                                       67888888888888888888875 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHS CS
                             TPR_1  18 deAleyyekALeln 31 
                                       +eA+ +y+k++eln
  gi|330509117|ref|YP_004385545.1| 163 EEAISAYDKVIELN 176
                                       8************9 PP

  == domain 4  score: 28.3 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +al  +Gn++++lg+y+e ++  +kA++l+P+n
  gi|330509117|ref|YP_004385545.1| 182 DALITKGNILLNLGRYNESIDTIDKAIQLDPEN 214
                                       79999**************************97 PP

  == domain 5  score: 19.5 bits;  conditional E-value: 9e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                        ++y ++  y  lgky+e l++ye   +l+P+
  gi|330509117|ref|YP_004385545.1| 216 SVWYEKATYYNVLGKYNESLDAYEMITKLEPE 247
                                       58**************************9996 PP

  == domain 6  score: 9.8 bits;  conditional E-value: 0.00099
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a a+  +Gn++  lg+  +A ++y kA el
  gi|330509117|ref|YP_004385545.1| 249 ASAWLFKGNVLKALGRQTDADAAYAKAKEL 278
                                       679************************987 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   2.1e-06    0.0015       1      34 []      34      68 ..      34      68 .. 0.95
   2 !   11.1   0.1   0.00054      0.38       2      30 ..     106     134 ..     105     137 .. 0.91
   3 !   11.1   0.0   0.00054      0.37       2      31 ..     147     176 ..     146     179 .. 0.88
   4 !   25.3   0.0   1.6e-08   1.1e-05       2      34 .]     182     214 ..     181     214 .. 0.94
   5 !   10.1   0.1    0.0012       0.8       2      33 ..     216     247 ..     215     248 .. 0.92
   6 !   13.5   0.2     9e-05     0.062       1      30 [.     249     278 ..     249     278 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.1e-06
                                      CCHHHHHH.HHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  1 aeayynlg.siylklgdyeeAkeyyekaleldpdn 34
                                      a+++  +g ++ +++ +  eA e+yeka++++pdn
  gi|330509117|ref|YP_004385545.1| 34 AKYWIAKGdDLFFNKSNPLEALESYEKAIQINPDN 68
                                      68999***9************************97 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00054
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                       ea++  ++++ +lg+ ee+ ++++ka++ 
  gi|330509117|ref|YP_004385545.1| 106 EALQTSAMALASLGNREESNQFLKKAIDV 134
                                       788899********************985 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00054
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                        a+++++ + + l+  eeA+++y k++el+
  gi|330509117|ref|YP_004385545.1| 147 TAWFLKAGLISILNGSEEAISAYDKVIELN 176
                                       6889999888999999*************8 PP

  == domain 4  score: 25.3 bits;  conditional E-value: 1.6e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +a+  +g+i+l+lg+y+e++ ++ ka++ldp+n
  gi|330509117|ref|YP_004385545.1| 182 DALITKGNILLNLGRYNESIDTIDKAIQLDPEN 214
                                       68899**************************86 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.0012
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +++y ++  y  lg+y+e+  +ye  ++l+p+
  gi|330509117|ref|YP_004385545.1| 216 SVWYEKATYYNVLGKYNESLDAYEMITKLEPE 247
                                       58**********************99999986 PP

  == domain 6  score: 13.5 bits;  conditional E-value: 9e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+a++ +g++++ lg+   A ++y ka el
  gi|330509117|ref|YP_004385545.1| 249 ASAWLFKGNVLKALGRQTDADAAYAKAKEL 278
                                       689************************876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   6.2e-06    0.0042      12      34 .]      46      68 ..      34      68 .. 0.81
   2 !    9.1   0.0    0.0022       1.5       2      31 ..     106     135 ..     105     145 .. 0.87
   3 ?    6.6   0.0     0.013       9.3      18      31 ..     163     176 ..     162     178 .. 0.93
   4 !   25.7   0.0   1.1e-08   7.6e-06       2      34 .]     182     214 ..     181     214 .. 0.96
   5 !   10.6   0.0   0.00074      0.51       3      33 ..     217     247 ..     215     248 .. 0.92
   6 !    9.8   0.5    0.0013      0.89       1      30 [.     249     278 ..     249     280 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.2e-06
                             TPR_2 12 yklgdyeeAleafekAleldPnn 34
                                      +++ ++ eAle +ekA++++P+n
  gi|330509117|ref|YP_004385545.1| 46 FNKSNPLEALESYEKAIQINPDN 68
                                      4555679**************98 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0022
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                       eal   ++a++ lg+ ee  ++++kA+  +
  gi|330509117|ref|YP_004385545.1| 106 EALQTSAMALASLGNREESNQFLKKAIDVY 135
                                       677888999999999999999999999765 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.013
                             TPR_2  18 eeAleafekAleld 31 
                                       eeA+ a++k++el+
  gi|330509117|ref|YP_004385545.1| 163 EEAISAYDKVIELN 176
                                       8************8 PP

  == domain 4  score: 25.7 bits;  conditional E-value: 1.1e-08
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +al   G+++++lg+y+e ++  +kA++ldP+n
  gi|330509117|ref|YP_004385545.1| 182 DALITKGNILLNLGRYNESIDTIDKAIQLDPEN 214
                                       68999**************************97 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00074
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       ++y+ +  y  lg+y+e l+a+e   +l+P+
  gi|330509117|ref|YP_004385545.1| 217 VWYEKATYYNVLGKYNESLDAYEMITKLEPE 247
                                       8999999999*************99999996 PP

  == domain 6  score: 9.8 bits;  conditional E-value: 0.0013
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a a+   G+++ +lg+  +A +a+ kA el
  gi|330509117|ref|YP_004385545.1| 249 ASAWLFKGNVLKALGRQTDADAAYAKAKEL 278
                                       57999**********************887 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.2e-07   8.6e-05      12      32 ..      53      73 ..      43      75 .. 0.91
   2 !   11.2   0.1   0.00032      0.22      10      32 ..     128     150 ..     119     153 .. 0.89
   3 ?    5.9   0.0     0.015        10      11      24 ..     163     176 ..     160     179 .. 0.94
   4 !   28.9   0.1   9.5e-10   6.6e-07       1      35 [.     188     222 ..     188     227 .. 0.92
   5 !   13.9   0.2   4.6e-05     0.032       7      42 .]     228     263 ..     224     263 .. 0.95
   6 ?    3.6   0.1     0.076        52       1      20 [.     256     275 ..     256     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.2e-07
                            TPR_11 12 eAieaYkkAlkldPdnaeayy 32
                                      eA+e+Y+kA++++Pdn +a++
  gi|330509117|ref|YP_004385545.1| 53 EALESYEKAIQINPDNMTAWN 73
                                      8****************9997 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00032
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayy 32 
                                       +++Ai +Y + +k +P+na+a++
  gi|330509117|ref|YP_004385545.1| 128 LKKAIDVYDQEIKDNPKNATAWF 150
                                       689******************98 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.015
                            TPR_11  11 eeAieaYkkAlkld 24 
                                       eeAi aY k ++l+
  gi|330509117|ref|YP_004385545.1| 163 EEAISAYDKVIELN 176
                                       8***********98 PP

  == domain 4  score: 28.9 bits;  conditional E-value: 9.5e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLG 35 
                                       G+++  +G+y+e+i    kA++ldP+n++++y+ +
  gi|330509117|ref|YP_004385545.1| 188 GNILLNLGRYNESIDTIDKAIQLDPENPSVWYEKA 222
                                       9*******************************876 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 4.6e-05
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +Gky+e++ aY+   kl P+ a+a++  G+++ ++G
  gi|330509117|ref|YP_004385545.1| 228 LGKYNESLDAYEMITKLEPEKASAWLFKGNVLKALG 263
                                       7******************************99988 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.076
                            TPR_11   1 GdayyeqGkyeeAieaYkkA 20 
                                       G+++ ++G+ ++A +aY kA
  gi|330509117|ref|YP_004385545.1| 256 GNVLKALGRQTDADAAYAKA 275
                                       9****************999 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00016      0.11       2      20 ..      58      76 ..      57      86 .. 0.88
   2 ?    3.2   0.0       0.2   1.4e+02       6      28 ..      98     120 ..      95     126 .. 0.89
   3 !   14.5   0.0   5.2e-05     0.036       2      33 ..     135     166 ..     134     167 .. 0.93
   4 !    8.5   0.0    0.0043       2.9       1      32 [.     168     200 ..     168     202 .. 0.90
   5 !   21.1   0.0   4.1e-07   0.00028       3      31 ..     205     233 ..     203     236 .. 0.91
   6 ?    3.1   0.1      0.22   1.5e+02       2      32 ..     238     268 ..     237     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                            TPR_17  2 ylkaleldPnnadaynnLA 20
                                      y+ka++++P+n  a+n + 
  gi|330509117|ref|YP_004385545.1| 58 YEKAIQINPDNMTAWNGKS 76
                                      9**************9765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.2
                            TPR_17   6 leldPnnadaynnLAelllknGd 28 
                                       l+++P + +a++  A +l+++G+
  gi|330509117|ref|YP_004385545.1|  98 LAKNPQDIEALQTSAMALASLGN 120
                                       789***************99987 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 5.2e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y + ++ +P+na a++++A l + ++++++A+
  gi|330509117|ref|YP_004385545.1| 135 YDQEIKDNPKNATAWFLKAGLISILNGSEEAI 166
                                       88889********************9999997 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0043
                            TPR_17   1 lylkaleldPnn.adaynnLAelllknGdlmtA 32 
                                       +y k++el+ +   da+  ++++ll++G++ + 
  gi|330509117|ref|YP_004385545.1| 168 AYDKVIELNGSKmIDALITKGNILLNLGRYNES 200
                                       5999*****8888****************9875 PP

  == domain 5  score: 21.1 bits;  conditional E-value: 4.1e-07
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmt 31 
                                        ka++ldP n+ +++++A+++  +G++ +
  gi|330509117|ref|YP_004385545.1| 205 DKAIQLDPENPSVWYEKATYYNVLGKYNE 233
                                       79***********************9976 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.22
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       y+   +l+P  a a+  ++++l+ +G+  +A
  gi|330509117|ref|YP_004385545.1| 238 YEMITKLEPEKASAWLFKGNVLKALGRQTDA 268
                                       6666788999999999999999999976655 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00028       0.2      11      38 ..      45      72 ..      34      76 .. 0.86
   2 !   16.1   0.0   2.1e-05     0.014       3      42 ..     114     153 ..     105     155 .. 0.86
   3 ?   -1.3   0.0         8   5.5e+03      18      31 ..     163     176 ..     162     178 .. 0.85
   4 !   18.1   0.0   4.9e-06    0.0033       4      42 ..     184     222 ..     181     224 .. 0.90
   5 !   10.8   0.0    0.0011      0.76       3      42 ..     217     256 ..     216     258 .. 0.93
   6 ?    3.3   0.2      0.27   1.8e+02       3      27 ..     251     275 ..     249     279 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00028
                            TPR_14 11 llalGdpdeAiallrralalaPddaeaw 38
                                      +++  +p eA++ +++a++ +Pd+ +aw
  gi|330509117|ref|YP_004385545.1| 45 FFNKSNPLEALESYEKAIQINPDNMTAW 72
                                      556678889******************9 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.1e-05
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       al+ l+  ++ ++ +++Ai+++++ ++++P++a+aw+l a
  gi|330509117|ref|YP_004385545.1| 114 ALASLGNREESNQFLKKAIDVYDQEIKDNPKNATAWFLKA 153
                                       56667777788888999*******************9987 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 8
                            TPR_14  18 deAiallrralala 31 
                                       +eAi +++++++l+
  gi|330509117|ref|YP_004385545.1| 163 EEAISAYDKVIELN 176
                                       799*****999986 PP

  == domain 4  score: 18.1 bits;  conditional E-value: 4.9e-06
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       l   + +ll+lG++ e+i+  ++a++l+P+++ +w++ a
  gi|330509117|ref|YP_004385545.1| 184 LITKGNILLNLGRYNESIDTIDKAIQLDPENPSVWYEKA 222
                                       5566889****************************9987 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.0011
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       ++++ a ++  lG++ e++++++ + +l P+ a awl+ +
  gi|330509117|ref|YP_004385545.1| 217 VWYEKATYYNVLGKYNESLDAYEMITKLEPEKASAWLFKG 256
                                       59999*******************************9865 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.27
                            TPR_14   3 allalaeallalGdpdeAiallrra 27 
                                       a+l  + +l alG+  +A a++ +a
  gi|330509117|ref|YP_004385545.1| 251 AWLFKGNVLKALGRQTDADAAYAKA 275
                                       89999*********99999999887 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     0.003         2       6      44 ..      44      79 ..      38      83 .. 0.85
   2 !   13.5   0.0   0.00013     0.086       7      61 ..     122     173 ..     116     179 .. 0.85
   3 !   18.8   0.0   2.8e-06    0.0019       3      58 ..     187     239 ..     185     240 .. 0.94
   4 !   24.3   0.5   5.3e-08   3.7e-05       1      61 [.     219     276 ..     219     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.003
                            TPR_16  6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaa 44
                                      ++++  ++ +A++ +e a+  +   Pd+  A++++  ++
  gi|330509117|ref|YP_004385545.1| 44 LFFNKSNPLEALESYEKAIQIN---PDNMTAWNGKSMVL 79
                                      567777899*************...*******9987665 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00013
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                          ++   +A+ ++++ +k++   P +a A++l++ +   ++  +eA+ +y++ +
  gi|330509117|ref|YP_004385545.1| 122 EESNQFLKKAIDVYDQEIKDN---PKNATAWFLKAGLISILNGSEEAISAYDKVI 173
                                       555666789************...*************999999999998888765 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 2.8e-06
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyr 58 
                                       +++++l++g+y + +   + a+ +d   P+++  +++++  + ++g + e +++y+
  gi|330509117|ref|YP_004385545.1| 187 KGNILLNLGRYNESIDTIDKAIQLD---PENPSVWYEKATYYNVLGKYNESLDAYE 239
                                       799**********************...9999******************998886 PP

  == domain 4  score: 24.3 bits;  conditional E-value: 5.3e-08
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       +++a+++  +g+y + + a+e  +k+    P+ a A+l++g+++ ++gr ++A a+y++a 
  gi|330509117|ref|YP_004385545.1| 219 YEKATYYNVLGKYNESLDAYEMITKLE---PEKASAWLFKGNVLKALGRQTDADAAYAKAK 276
                                       6788999999*****************...***********************99998885 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.036        25      45      74 ..      34      64 ..      11      68 .. 0.63
   2 !   16.2   0.1   1.4e-05    0.0097      22      76 ..      83     136 ..      81     137 .. 0.90
   3 !   18.0   0.1   3.9e-06    0.0027       8      74 ..     110     175 ..     103     176 .. 0.92
   4 !   16.0   0.0   1.6e-05     0.011       5      61 ..     183     238 ..     179     244 .. 0.83
   5 !    9.6   0.5    0.0016       1.1       5      71 ..     217     275 ..     214     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.036
                            TPR_12 45 attlrnLgrlyral.gryeeAlelleealai 74
                                      a + ++ g+ ++    ++ eAle +e+a++i
  gi|330509117|ref|YP_004385545.1| 34 AKYWIAKGDDLFFNkSNPLEALESYEKAIQI 64
                                      5555555555433335556666666666655 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.4e-05
                            TPR_12  22 AlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       + + + k l++ +  l  ++p+ +++l++ ++++  lg+ ee  ++l++a++++ 
  gi|330509117|ref|YP_004385545.1|  83 SVQTYSKILNLSETKL-AKNPQDIEALQTSAMALASLGNREESNQFLKKAIDVYD 136
                                       578899******6555.789********************************996 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 3.9e-06
                            TPR_12   8 nlaavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                         a++l+ lg+ +e+ ++l+ka++++ +++  +d+p  at+ +  + l + l+  eeA++++ +++++
  gi|330509117|ref|YP_004385545.1| 110 TSAMALASLGNREESNQFLKKAIDVYdQEI--KDNPKNATAWFLKAGLISILNGSEEAISAYDKVIEL 175
                                       57999*********************8888..9******************************99986 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 1.6e-05
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgry 61 
                                       al   +++l+ lgry e+++  +ka+++  + +   +++ at+++ Lg + + l+ y
  gi|330509117|ref|YP_004385545.1| 183 ALITKGNILLNLGRYNESIDTIDKAIQLDPENP-SVWYEKATYYNVLGKYNESLDAY 238
                                       67789************************5554.66899999999999887776655 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.0016
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                       ++++ a+ ++ lg+y e+l+ +e      ++l +p+    a++    g ++ algr+ +A +++ +a
  gi|330509117|ref|YP_004385545.1| 217 VWYEKATYYNVLGKYNESLDAYEMI----TKL-EPE---KASAWLFKGNVLKALGRQTDADAAYAKA 275
                                       5667888899999999999988888....333.254...7999999999999999999999999988 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.018        12       7      28 ..      51      72 ..      47      79 .. 0.86
   2 !    9.7   0.2    0.0018       1.2       9      53 ..      89     133 ..      82     138 .. 0.85
   3 ?    4.0   0.0      0.11        74       8      32 ..     129     153 ..     128     156 .. 0.86
   4 !   16.0   0.0   1.8e-05     0.013       8      62 ..     163     218 ..     160     224 .. 0.91
   5 !    8.4   0.3    0.0043         3       5      52 ..     229     276 ..     226     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.018
                            TPR_19  7 yaeAlalleqalqedpknaear 28
                                      + eAl+ +e+a+q +p+n  a+
  gi|330509117|ref|YP_004385545.1| 51 PLEALESYEKAIQINPDNMTAW 72
                                      569**************98776 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0018
                            TPR_19   9 eAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                         l+l e  l+++p++ ea+   A al +lg+ +e  + L+++ +
  gi|330509117|ref|YP_004385545.1|  89 KILNLSETKLAKNPQDIEALQTSAMALASLGNREESNQFLKKAID 133
                                       55666666799*****************************99876 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.11
                            TPR_19   8 aeAlalleqalqedpknaearllLA 32 
                                         A++ + q ++++pkna a+ l A
  gi|330509117|ref|YP_004385545.1| 129 KKAIDVYDQEIKDNPKNATAWFLKA 153
                                       579999***9********9998765 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 1.8e-05
                            TPR_19   8 aeAlalleqalqedpk.naearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       +eA++++ ++++ +   + +a++   ++ll+lg+++e ++++d++ + dp ++ ++
  gi|330509117|ref|YP_004385545.1| 163 EEAISAYDKVIELNGSkMIDALITKGNILLNLGRYNESIDTIDKAIQLDPENPSVW 218
                                       69*********997777*********************************998776 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0043
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalp 52 
                                       g+y e l+++e + + +p+ a a+l   ++l alg+ ++A a+ +++ 
  gi|330509117|ref|YP_004385545.1| 229 GKYNESLDAYEMITKLEPEKASAWLFKGNVLKALGRQTDADAAYAKAK 276
                                       7899999999999999************************99887765 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       0.6   4.2e+02      17      57 ..      26      70 ..      11      73 .. 0.67
   2 !   14.6   0.2   4.1e-05     0.028       5      81 ..      87     171 ..      83     172 .. 0.90
   3 !   24.0   0.0   4.7e-08   3.3e-05       7      80 ..     164     239 ..     163     241 .. 0.93
   4 ?   -2.4   0.0       8.4   5.8e+03      19      30 ..     264     275 ..     243     278 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.6
                                      .HHH--HHHHHHH...HHHHHHTT-HHHHHHHHHCT.SHHHC-HH CS
                            ANAPC3 17 aaetespedayll...AlclylngqykrAyellrka.klnskslg 57
                                      +a ++ + + y+       +++ ++  +A+e ++ka ++n+ ++ 
  gi|330509117|ref|YP_004385545.1| 26 SAAAQENTAKYWIakgDDLFFNKSNPLEALESYEKAiQINPDNMT 70
                                      466777777777633334677777788888888888777777765 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.1e-05
                                       HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-.......HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HH CS
                            ANAPC3   5 yknAiflaerllaaetespedayllAlclylngq.......ykrAyellrka.klnskslgcrylfAqcllkLkkye 73 
                                       y +++ l+e  la+++++ e++   A +l ++g+        k+A++++++  k n+k+  +++l+A     L+  e
  gi|330509117|ref|YP_004385545.1|  87 YSKILNLSETKLAKNPQDIEALQTSAMALASLGNreesnqfLKKAIDVYDQEiKDNPKNATAWFLKAGLISILNGSE 163
                                       888899999999999999999999888888888777999999*********************************** PP

                                       HHHHHH-S CS
                            ANAPC3  74 eAiaaLek 81 
                                       eAi+a++k
  gi|330509117|ref|YP_004385545.1| 164 EAISAYDK 171
                                       ****9987 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 4.7e-08
                                       HHHHHHHHHH..HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3   7 nAiflaerlla.aetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +Ai  ++++ +   +++ +++  ++  l+++g+y++ ++ ++ka +l+++++ ++y +A  +  L+ky+e ++a+e
  gi|330509117|ref|YP_004385545.1| 164 EAISAYDKVIElNGSKMIDALITKGNILLNLGRYNESIDTIDKAiQLDPENPSVWYEKATYYNVLGKYNESLDAYE 239
                                       688889999985669999*******************************************************987 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 8.4
                                       HH--HHHHHHHH CS
                            ANAPC3  19 etespedayllA 30 
                                        + ++++ay++A
  gi|330509117|ref|YP_004385545.1| 264 RQTDADAAYAKA 275
                                       344555555555 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1         4   2.8e+03      12      48 ..      12      28 ..       3      35 .. 0.50
   2 ?    1.6   0.0      0.44     3e+02      45      65 ..      51      71 ..      43      76 .. 0.67
   3 ?    6.8   0.0     0.011       7.4      10      60 ..      86     136 ..      82     148 .. 0.85
   4 !    8.2   0.0    0.0038       2.6      12      63 ..     163     215 ..     160     217 .. 0.87
   5 !   15.9   0.0   1.5e-05      0.01       4      64 ..     190     250 ..     188     255 .. 0.91
   6 ?    5.3   0.0      0.03        21      13      44 ..     233     264 ..     229     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4
                             TPR_9 12 eralavverllllaPddpeerrdRGlllaqlGclsaA 48
                                      ++al                    Gll     c+saA
  gi|330509117|ref|YP_004385545.1| 12 AVAL--------------------GLLALAALCVSAA 28
                                      4444....................3444444444444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.44
                             TPR_9 45 lsaAladLeaylalapdapda 65
                                      + +Al+  e +++++pd+ +a
  gi|330509117|ref|YP_004385545.1| 51 PLEALESYEKAIQINPDNMTA 71
                                      456666666666666665554 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.011
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                        +++ l  +e  l+ +P+d+e +   +++la lG+ ++  + L  ++++ +
  gi|330509117|ref|YP_004385545.1|  86 TYSKILNLSETKLAKNPQDIEALQTSAMALASLGNREESNQFLKKAIDVYD 136
                                       567778888888999*********************999999999988766 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0038
                             TPR_9  12 eralavverllll.aPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       e+a+ +++ ++ l  ++ ++ +   G +l  lG++++ ++  + +++l+p++p
  gi|330509117|ref|YP_004385545.1| 163 EEAISAYDKVIELnGSKMIDALITKGNILLNLGRYNESIDTIDKAIQLDPENP 215
                                       677788888888867888999999**************************988 PP

  == domain 5  score: 15.9 bits;  conditional E-value: 1.5e-05
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       i+++  ++ + + +++  ++l+P+ p+ +++ +  +  lG +++ l++ e    l+p+ + 
  gi|330509117|ref|YP_004385545.1| 190 ILLNLGRYNESIDTIDKAIQLDPENPSVWYEKATYYNVLGKYNESLDAYEMITKLEPEKAS 250
                                       7788888999999*************************************99999998765 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.03
                             TPR_9  13 ralavverllllaPddpeerrdRGlllaqlGc 44 
                                       + l ++e++  l P+ ++ ++  G +l  lG+
  gi|330509117|ref|YP_004385545.1| 233 ESLDAYEMITKLEPEKASAWLFKGNVLKALGR 264
                                       56899****************99999988887 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2    0.0011      0.74       6      20 ..      59      73 ..      59      73 .. 0.95
   2 ?   -0.5   0.1       1.7   1.2e+03       2      14 ..      91     103 ..      91     105 .. 0.88
   3 !    7.9   0.1    0.0037       2.5       9      20 ..     139     150 ..     136     151 .. 0.92
   4 !   11.4   0.0   0.00031      0.21       6      20 ..     205     219 ..     202     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                                      HHHHHH-TT-CHHHH CS
                              PPTA  6 ekliekdpkNYsaWn 20
                                      ek+i+ +p+N +aWn
  gi|330509117|ref|YP_004385545.1| 59 EKAIQINPDNMTAWN 73
                                      699***********9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                                       HHHHHHHHHH-TT CS
                              PPTA   2 Leltekliekdpk 14 
                                       L+l e ++ k+p+
  gi|330509117|ref|YP_004385545.1|  91 LNLSETKLAKNPQ 103
                                       78999*******7 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0037
                                       HHH-TT-CHHHH CS
                              PPTA   9 iekdpkNYsaWn 20 
                                       i+++pkN +aW+
  gi|330509117|ref|YP_004385545.1| 139 IKDNPKNATAWF 150
                                       89*********5 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00031
                                       HHHHHH-TT-CHHHH CS
                              PPTA   6 ekliekdpkNYsaWn 20 
                                       +k+i++dp N s+W+
  gi|330509117|ref|YP_004385545.1| 205 DKAIQLDPENPSVWY 219
                                       79************7 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.036        25      15      33 .]      50      68 ..      33      68 .. 0.85
   2 ?    4.0   0.1      0.13        91       6      30 ..     111     135 ..     106     137 .. 0.86
   3 ?    5.3   0.0     0.052        36       4      28 ..     151     174 ..     148     176 .. 0.79
   4 ?    2.9   0.0       0.3     2e+02       7      32 ..     188     213 ..     182     214 .. 0.83
   5 ?    5.8   0.0     0.037        26      10      31 ..     224     246 ..     217     247 .. 0.85
   6 ?    1.2   0.2         1   7.2e+02       9      26 ..     258     275 ..     251     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.036
                                      HHHHHHHHHHHHHHH-TT- CS
                             TPR_6 15 dtdkAlealerlikeYPdS 33
                                      ++ +Ale +e+ i+  Pd+
  gi|330509117|ref|YP_004385545.1| 50 NPLEALESYEKAIQINPDN 68
                                      6669*************95 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeY 30 
                                        a+++ +lg+ +++ + l++ i+ Y
  gi|330509117|ref|YP_004385545.1| 111 SAMALASLGNREESNQFLKKAIDVY 135
                                       6999***99************9987 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.052
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlik 28 
                                       +k++l  +    +++A+ a++++i+
  gi|330509117|ref|YP_004385545.1| 151 LKAGLISILN-GSEEAISAYDKVIE 174
                                       6666666655.99**********97 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       +  +++lg++ +++++ ++ i+  P+
  gi|330509117|ref|YP_004385545.1| 188 GNILLNLGRYNESIDTIDKAIQLDPE 213
                                       67788999*************99986 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.037
                                       HHH.HHHHHHHHHHHHHHHHH-T CS
                             TPR_6  10 yrk.lgdtdkAlealerlikeYP 31 
                                       y++ lg++ ++l+a+e + k  P
  gi|330509117|ref|YP_004385545.1| 224 YYNvLGKYNESLDAYEMITKLEP 246
                                       77779************999877 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHHHHH CS
                             TPR_6   9 syrklgdtdkAlealerl 26 
                                        +++lg+ ++A +a+ + 
  gi|330509117|ref|YP_004385545.1| 258 VLKALGRQTDADAAYAKA 275
                                       566778899999999876 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.15     1e+02      53      94 ..      50      92 ..      19     115 .. 0.68
   2 !   14.8   0.1   1.4e-05    0.0098     181     257 ..     137     212 ..     100     215 .. 0.79
   3 !   10.5   0.1   0.00029       0.2     196     257 ..     219     280 ..     213     282 .] 0.92

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.15
                                      -HHHHHHHHHHHHHH-TT-CHHHHHHHHHT...SSS-HHHHHH CS
                             NARP1 53 rkeeAeatyeaLlernpenskYyeglekak.klskedeealla 94
                                      +  eA + ye+ ++ np+n++ ++g   ++  ls ++ +++l+
  gi|330509117|ref|YP_004385545.1| 50 NPLEALESYEKAIQINPDNMTAWNGKSMVLdTLSVQTYSKILN 92
                                      4457888899999999999888887777763233334444444 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.4e-05
                                       GSS----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-.TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 181 edsekepesallwvlyflAqhydklgsrekAleyidkaieht.ptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       ++ +++p++a  w  ++ A     l+  e+A++  dk ie +  ++++  +tK++il   G  ++ ++++++a +lD
  gi|330509117|ref|YP_004385545.1| 137 QEIKDNPKNATAW--FLKAGLISILNGSEEAISAYDKVIELNgSKMIDALITKGNILLNLGRYNESIDTIDKAIQLD 211
                                       4556677777333..55577778888899***********99789*******************************9 PP

                                       T CS
                             NARP1 257 l 257
                                        
  gi|330509117|ref|YP_004385545.1| 212 P 212
                                       5 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00029
                                       HHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                             NARP1 196 yflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                       y  A +y+ lg+++++l+  +   + +p+    +l K+++lk  G  ++A ++  +a++l +
  gi|330509117|ref|YP_004385545.1| 219 YEKATYYNVLGKYNESLDAYEMITKLEPEKASAWLFKGNVLKALGRQTDADAAYAKAKELGH 280
                                       55699****************************************************99865 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   0.0       1.6   1.1e+03      93     121 ..      31      63 ..      20      70 .. 0.74
   2 ?    6.1   0.0     0.015        11      98     130 ..     103     135 ..      91     146 .. 0.85
   3 ?    6.6   0.0     0.011       7.6      95     127 ..     176     208 ..     156     216 .. 0.72
   4 ?    6.1   0.0     0.016        11      64     129 ..     190     244 ..     181     252 .. 0.72
   5 ?    3.1   0.1      0.13        92      97     129 ..     250     278 ..     222     281 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.6
                                       STHHHHHHH....HHHHHHHHHHHTT-HHHHHH CS
                           DUF3856  93 qdeGklWia....avfsravaleelGrkdealk 121
                                       ++  k Wia      f+++  le l ++++a++
  gi|330509117|ref|YP_004385545.1|  31 ENTAKYWIAkgddLFFNKSNPLEALESYEKAIQ 63 
                                       566778887333347888888888888888876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                           DUF3856  98 lWiaavfsravaleelGrkdealkafrmagemi 130
                                       + i a+ + a+al++lG+++e+ + +++a ++ 
  gi|330509117|ref|YP_004385545.1| 103 QDIEALQTSAMALASLGNREESNQFLKKAIDVY 135
                                       56889999*******************998865 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  95 eGklWiaavfsravaleelGrkdealkafrmag 127
                                       +G++ i a+++++  l +lGr++e++++  +a 
  gi|330509117|ref|YP_004385545.1| 176 NGSKMIDALITKGNILLNLGRYNESIDTIDKAI 208
                                       477888888888888888888888888777665 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.016
                                       HHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                        l++lgry+e++ ++dka++       l+ ++ + W    +++a+ ++ lG+++e+l+a++m++ +
  gi|330509117|ref|YP_004385545.1| 190 ILLNLGRYNESIDTIDKAIQ-------LDPENPSVW----YEKATYYNVLGKYNESLDAYEMITKL 244
                                       57788999999999998885.......666666666....56777778888888888888777665 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  97 klWiaavfsravaleelGrkdealkafrmagem 129
                                       + W    + ++  l+ lGr+ +a  a+ +a+e+
  gi|330509117|ref|YP_004385545.1| 250 SAW----LFKGNVLKALGRQTDADAAYAKAKEL 278
                                       444....35788899999999999999998885 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.13        91      74     138 ..      83     147 ..      75     153 .. 0.76
   2 !   13.1   0.0   0.00014     0.097      62     123 ..     181     242 ..     157     247 .. 0.91
   3 ?    5.9   0.2     0.024        17      75     125 ..     228     278 ..     228     282 .] 0.90

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.13
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepgpel 138
                                       ++  ++++l   e  +a++P + ++ +    Ala +G+++e  +  +++ ++ ++e+   p+ ++
  gi|330509117|ref|YP_004385545.1|  83 SVQTYSKILNLSETKLAKNPQDIEALQTSAMALASLGNREESNQFLKKAIDVYDQEIKDNPKNAT 147
                                       55667777778888888888887777777779999999998888888888888888777776665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  62 lealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       ++al +  + +l lGr++e +++ +++++++P +   + +  + +  +G+ +e L +Ye + 
  gi|330509117|ref|YP_004385545.1| 181 IDALITKGNILLNLGRYNESIDTIDKAIQLDPENPSVWYEKATYYNVLGKYNESLDAYEMIT 242
                                       66777778899***********************************************9775 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.024
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                       lG+++e l+ +e +++++P +  ++      l ++Grq +A ++Y ++++l
  gi|330509117|ref|YP_004385545.1| 228 LGKYNESLDAYEMITKLEPEKASAWLFKGNVLKALGRQTDADAAYAKAKEL 278
                                       6889999999999******99999999999****************99876 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.54   3.7e+02      19      39 ..      53      73 ..      52      84 .. 0.79
   2 ?   -2.2   0.0       6.7   4.6e+03      16      38 ..      86     108 ..      81     118 .. 0.76
   3 !    9.0   0.0    0.0021       1.5      13      35 ..     193     215 ..     191     217 .. 0.92
   4 ?    5.3   0.0     0.029        20      14      36 ..     228     250 ..     224     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.54
                                      HHHHHHHHHHHHTTS-HHHHH CS
                        Fis1_TPR_C 19 eArryvdalLeiEPenrQaqs 39
                                      eA++  +  ++i P+n+ a +
  gi|330509117|ref|YP_004385545.1| 53 EALESYEKAIQINPDNMTAWN 73
                                      6888889999******98865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.7
                                       -HHHHHHHHHHHHHHTTS-HHHH CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPenrQaq 38 
                                        Ys+ +++ ++ L++ P+   a+
  gi|330509117|ref|YP_004385545.1|  86 TYSKILNLSETKLAKNPQDIEAL 108
                                       57777788888888888876665 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0021
                                       HHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPenr 35 
                                        lg+Y+e+   +d  ++++Pen 
  gi|330509117|ref|YP_004385545.1| 193 NLGRYNESIDTIDKAIQLDPENP 215
                                       69*******************96 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.029
                                       HT-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQ 36 
                                       lg+Y+e++   +++ ++EPe   
  gi|330509117|ref|YP_004385545.1| 228 LGKYNESLDAYEMITKLEPEKAS 250
                                       89*****************9765 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.3   1.5e-06     0.001      63     118 ..      77     132 ..      55     139 .. 0.83
   2 ?   -1.9   0.0       4.1   2.8e+03      72     110 ..     196     234 ..     168     246 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-06
                           DUF4919  63 ldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrln 118
                                       +  ++ls +++ +i++l+e  l+knP d+++l+  a+a+ +lg+ ee++++ k+  
  gi|330509117|ref|YP_004385545.1|  77 MVLDTLSVQTYSKILNLSETKLAKNPQDIEALQTSAMALASLGNREESNQFLKKAI 132
                                       45688999*************************************99999888765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.1
                           DUF4919  72 elkeiislaeealkknPfdlkqlnllayaykalgkkeea 110
                                        ++e i++  +a++ +P ++   +  a  y+ lgk +e+
  gi|330509117|ref|YP_004385545.1| 196 RYNESIDTIDKAIQLDPENPSVWYEKATYYNVLGKYNES 234
                                       566777777777777777777776666666666666554 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.53   3.6e+02      20      31 ..      53      64 ..      50      65 .. 0.84
   2 !   10.2   0.0   0.00079      0.55       9      35 ..     112     138 ..     106     143 .. 0.89
   3 ?    3.7   0.0     0.088        61       8      23 ..     187     202 ..     181     210 .. 0.76
   4 ?    0.3   0.0         1     7e+02       9      26 ..     222     239 ..     221     240 .. 0.82
   5 ?    3.3   0.2      0.11        77       9      29 ..     256     276 ..     256     282 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.53
                            TPR_10 20 eAealleealai 31
                                      eA++ +e+a++i
  gi|330509117|ref|YP_004385545.1| 53 EALESYEKAIQI 64
                                      789999999987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00079
                            TPR_10   9 analrqrgrydeAealleealairrrl 35 
                                       a+al ++g+++e+ ++l++a++++ + 
  gi|330509117|ref|YP_004385545.1| 112 AMALASLGNREESNQFLKKAIDVYDQE 138
                                       89********************99765 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.088
                            TPR_10   8 LanalrqrgrydeAea 23 
                                        +n+l ++gry+e+ +
  gi|330509117|ref|YP_004385545.1| 187 KGNILLNLGRYNESID 202
                                       599**********876 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 1
                            TPR_10   9 analrqrgrydeAealle 26 
                                       a ++  +g+y+e+++ +e
  gi|330509117|ref|YP_004385545.1| 222 ATYYNVLGKYNESLDAYE 239
                                       567888999999998876 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.11
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       +n+l ++gr ++A a + +a 
  gi|330509117|ref|YP_004385545.1| 256 GNVLKALGRQTDADAAYAKAK 276
                                       89*************999985 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.6   2.5e+03       7      24 ..      54      71 ..      49      72 .. 0.82
   2 !   10.0   0.7    0.0012      0.85      12      50 ..      95     133 ..      88     153 .. 0.82
   3 ?    1.2   0.0      0.67   4.6e+02       8      43 ..     132     167 ..     128     176 .. 0.82
   4 !    7.8   0.0    0.0061       4.2       5      44 ..     198     237 ..     196     251 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.6
                            TPR_20  7 elaeleaalaanpddlda 24
                                       l++ e+a++ npd++ a
  gi|330509117|ref|YP_004385545.1| 54 ALESYEKAIQINPDNMTA 71
                                      678899999****99865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0012
                            TPR_20  12 eaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                       e++la+np+d++a    A al++ g++ee+ + L + + 
  gi|330509117|ref|YP_004385545.1|  95 ETKLAKNPQDIEALQTSAMALASLGNREESNQFLKKAID 133
                                       789*************************99777666555 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.67
                            TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAle 43 
                                       ++  ++++++np++  a +  A +    +  eeA++
  gi|330509117|ref|YP_004385545.1| 132 IDVYDQEIKDNPKNATAWFLKAGLISILNGSEEAIS 167
                                       5566899*********99999988888888888875 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0061
                            TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                       +++++++++a++ +p++    ++ A+ ++  g+y e+l++
  gi|330509117|ref|YP_004385545.1| 198 NESIDTIDKAIQLDPENPSVWYEKATYYNVLGKYNESLDA 237
                                       578999******************************9986 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.68   4.7e+02      17      27 ..      53      63 ..      43      70 .. 0.72
   2 ?    3.7   0.0      0.11        76      16      34 ..     129     145 ..     110     147 .. 0.80
   3 ?   -0.2   0.0       1.9   1.3e+03      16      28 ..     163     175 ..     162     179 .. 0.77
   4 !    7.6   0.0    0.0061       4.2       5      35 ..     187     215 ..     183     216 .. 0.85
   5 ?    0.3   0.1       1.4   9.5e+02      12      32 ..     228     246 ..     219     250 .. 0.74
   6 ?   -0.6   0.1       2.5   1.8e+03       2      24 ..     252     274 ..     251     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.68
                             TPR_7 17 eAielyeqsLa 27
                                      eA+e ye++++
  gi|330509117|ref|YP_004385545.1| 53 EALESYEKAIQ 63
                                      79999999544 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                             TPR_7  16 eeAielyeqsLaltkdped 34 
                                       ++Ai++y q  ++ + p +
  gi|330509117|ref|YP_004385545.1| 129 KKAIDVYDQ--EIKDNPKN 145
                                       688888888..88887766 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.9
                             TPR_7  16 eeAielyeqsLal 28 
                                       eeAi+ y ++++l
  gi|330509117|ref|YP_004385545.1| 163 EEAISAYDKVIEL 175
                                       7999999996554 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0061
                             TPR_7   5 LarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                        +++  +lG+y e i+   +  a+  dpe++
  gi|330509117|ref|YP_004385545.1| 187 KGNILLNLGRYNESIDTIDK--AIQLDPENP 215
                                       599*****************..888888876 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1.4
                             TPR_7  12 lGdyeeAielyeqsLaltkdp 32 
                                       lG+y e ++ ye    +  +p
  gi|330509117|ref|YP_004385545.1| 228 LGKYNESLDAYEM--ITKLEP 246
                                       899*9*9999998..555555 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 2.5
                             TPR_7   2 LlnLarlysrlGdyeeAielyeq 24 
                                       +l  +++  +lG+  +A   y +
  gi|330509117|ref|YP_004385545.1| 252 WLFKGNVLKALGRQTDADAAYAK 274
                                       66778999999999999998887 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.32   2.2e+02      87     122 ..      53      88 ..      34      92 .. 0.85
   2 ?    2.2   0.2      0.32   2.2e+02      89     124 ..      91     126 ..      80     142 .. 0.81
   3 !    9.4   0.0     0.002       1.4      70     125 ..     182     237 ..     159     247 .. 0.85
   4 ?   -0.1   0.0       1.8   1.2e+03      94     121 ..     240     267 ..     234     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  87 waaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                        a+e  +++++ +p+n +a + k  +l+ l+ q+ s
  gi|330509117|ref|YP_004385545.1|  53 EALESYEKAIQINPDNMTAWNGKSMVLDTLSVQTYS 88 
                                       58899999*********************9999876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  89 aellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                       ++l +  ++++p++ ea +  a al +lg+++es +
  gi|330509117|ref|YP_004385545.1|  91 LNLSETKLAKNPQDIEALQTSAMALASLGNREESNQ 126
                                       566666777899999**************9999865 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHH CS
                   Alkyl_sulf_dimr  70 ekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatw 125
                                       +++++k +  l+ g y+ ++  ++++++ dpen +    ka  ++ lg+ +es  +
  gi|330509117|ref|YP_004385545.1| 182 DALITKGNILLNLGRYNESIDTIDKAIQLDPENPSVWYEKATYYNVLGKYNESLDA 237
                                       67888888899999************************************999765 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.8
                                       HHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
                   Alkyl_sulf_dimr  94 hlvfadpenaeakelkadaleqlgyqae 121
                                       ++   +pe+a+a   k ++l++lg+q+ 
  gi|330509117|ref|YP_004385545.1| 240 MITKLEPEKASAWLFKGNVLKALGRQTD 267
                                       556679999999999*********9986 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.38   2.6e+02       5      29 ..      45      69 ..      42      75 .. 0.83
   2 !    8.1   0.0    0.0037       2.5      62      99 ..      83     134 ..      80     141 .. 0.91
   3 ?    3.1   0.0      0.14        96      62      98 ..     234     277 ..     228     282 .] 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.38
                            DUF627  5 llargnhikALeiiedlisrhgede 29
                                      ++++ n  +ALe  e++i+ + ++ 
  gi|330509117|ref|YP_004385545.1| 45 FFNKSNPLEALESYEKAIQINPDNM 69
                                      5789999*********999887765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0037
                            DUF627  62 svecfseavels..............rfyArsLfelasqlgsklyYkkavkk 99 
                                       sv+ +s+  +ls              + +A+ L  l+++ +s+++ kka+  
  gi|330509117|ref|YP_004385545.1|  83 SVQTYSKILNLSetklaknpqdiealQTSAMALASLGNREESNQFLKKAIDV 134
                                       899999999999999*********99**********************9875 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.14
                            DUF627  62 svecfseavels.......rfyArsLfelasqlgsklyYkkavk 98 
                                       s++++++ ++l         f  + L  l++q +    Y ka +
  gi|330509117|ref|YP_004385545.1| 234 SLDAYEMITKLEpekasawLFKGNVLKALGRQTDADAAYAKAKE 277
                                       88999999999999999999999999999999999999999865 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0      0.02        14      30      53 ..      53      76 ..      46      95 .. 0.79
   2 ?   -2.3   0.0       7.5   5.2e+03      43      59 ..     110     126 ..     104     140 .. 0.56
   3 ?   -1.7   0.0       4.8   3.3e+03      30      53 ..     164     187 ..     162     190 .. 0.82
   4 ?    3.1   0.0      0.15   1.1e+02      28      50 ..     197     219 ..     195     225 .. 0.92
   5 ?    2.9   0.0      0.18   1.2e+02      26      54 ..     229     257 ..     220     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                           DUF1510 30 Emekavskatglsednmivwwlgn 53
                                      E ++  +ka++++ dnm+ w  ++
  gi|330509117|ref|YP_004385545.1| 53 EALESYEKAIQINPDNMTAWNGKS 76
                                      7889999*************7655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.5
                           DUF1510  43 ednmivwwlgnggspqk 59 
                                       ++ m +  lgn+ ++++
  gi|330509117|ref|YP_004385545.1| 110 TSAMALASLGNREESNQ 126
                                       55566666666544443 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.8
                           DUF1510  30 Emekavskatglsednmivwwlgn 53 
                                       E  +a  k+++l+ ++mi   +++
  gi|330509117|ref|YP_004385545.1| 164 EAISAYDKVIELNGSKMIDALITK 187
                                       77889999999**99999877765 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.15
                           DUF1510  28 wnEmekavskatglsednmivww 50 
                                       +nE  +++ ka++l+ +n  vw+
  gi|330509117|ref|YP_004385545.1| 197 YNESIDTIDKAIQLDPENPSVWY 219
                                       89*******************98 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.18
                           DUF1510  26 vDwnEmekavskatglsednmivwwlgng 54 
                                         +nE ++a +  t l+ ++   w  + +
  gi|330509117|ref|YP_004385545.1| 229 GKYNESLDAYEMITKLEPEKASAWLFKGN 257
                                       569*******************9998754 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.44     3e+02     143     178 ..      31      67 ..      18      84 .. 0.72
   2 ?    1.9   0.1      0.22   1.5e+02      52     136 ..     122     204 ..      94     211 .. 0.57
   3 ?    9.9   0.2   0.00079      0.55     151     177 ..     254     280 ..     226     282 .] 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.44
                            TPR_21 143 afaalvaelrGD.ilvaqgkldeAraaYqaAlaalee 178
                                       + +a++   +GD +++++ +  eA + Y++A++ + +
  gi|330509117|ref|YP_004385545.1|  31 ENTAKYWIAKGDdLFFNKSNPLEALESYEKAIQINPD 67 
                                       5556666678853888999999*********986655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.22
                            TPR_21  52 akdaakakeaaeeladeyggtaYaalaaLllAkaaveagdlaaAkaqLewvlekakdeelkalarlRLarvllaekk 128
                                       +++++ +k+a++   +e ++++  a a +l+A      +  ++A +++++v+e + ++ ++al++    ++ll+ + 
  gi|330509117|ref|YP_004385545.1| 122 EESNQFLKKAIDVYDQEIKDNPKNATAWFLKAGLISILNGSEEAISAYDKVIELNGSKMIDALITK--GNILLNLGR 196
                                       344444556666666666666666666666666666666666666666666666666666666554..345555555 PP

                            TPR_21 129 ydeAlktL 136
                                       y+e + t+
  gi|330509117|ref|YP_004385545.1| 197 YNESIDTI 204
                                       55555444 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00079
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaale 177
                                        +G++l a g++++A aaY +A + ++
  gi|330509117|ref|YP_004385545.1| 254 FKGNVLKALGRQTDADAAYAKAKELGH 280
                                       69********************87665 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 ?    0.2   0.0      0.78   5.4e+02     143     166 ..      53      76 ..      39      86 .. 0.85
   2 ?   10.4   0.1   0.00055      0.38     126     198 ..     113     179 ..      81     188 .. 0.77
   3 ?   -0.6   0.2       1.4   9.3e+02      86     125 ..     217     256 ..     196     278 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.78
                           DUF2225 143 kAlelykeayekesfpvegideat 166
                                       +Ale y++a++ + ++++  + ++
  gi|330509117|ref|YP_004385545.1|  53 EALESYEKAIQINPDNMTAWNGKS 76 
                                       699********9999998877665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00055
                           DUF2225 126 WlyrdkedeekeklflkkAlelykeayekesfpvegideatvlYLiaeLerrlgnkeealrwlskvigskkas 198
                                            +++ e++++flkkA+++y++ ++ + +      +at  +L a L   l   eea+ ++ kvi+ + ++
  gi|330509117|ref|YP_004385545.1| 113 MALASLGNREESNQFLKKAIDVYDQEIKDNPK------NATAWFLKAGLISILNGSEEAISAYDKVIELNGSK 179
                                       44567899****************99887766......78899999999999999999999999999987766 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.4
                           DUF2225  86 dfskertldeaiesYkLallcyelkkekkskkAklalrlA 125
                                        ++++ t+ + + +Y  +l  ye++ + + +kA  +l  +
  gi|330509117|ref|YP_004385545.1| 217 VWYEKATYYNVLGKYNESLDAYEMITKLEPEKASAWLFKG 256
                                       4566677777777777777777777777777776655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1774.92
//
Query:       gi|330509118|ref|YP_004385546.1|  [L=468]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-58  192.0  16.7    1.4e-07   31.1   0.0   11.2 11  TPR_1            Tetratricopeptide repeat
    3.3e-57  186.1  23.6    1.2e-07   31.3   0.1   12.2 13  TPR_2            Tetratricopeptide repeat
    5.8e-47  154.0  15.6      4e-05   23.5   0.0   10.7 10  TPR_8            Tetratricopeptide repeat
    4.3e-38  129.4  22.5    2.1e-11   43.9   0.1    7.6  7  TPR_12           Tetratricopeptide repeat
    1.3e-37  127.2  25.1    1.1e-07   31.4   0.1   10.4 10  TPR_11           TPR repeat
    1.3e-34  115.9  25.5    3.7e-05   24.2   0.2   10.9 10  TPR_14           Tetratricopeptide repeat
    1.6e-32  111.8  21.1    1.2e-05   25.9   0.5    8.3 10  TPR_16           Tetratricopeptide repeat
    8.7e-31  106.3  29.8    3.2e-06   27.6   1.4    7.9 10  TPR_19           Tetratricopeptide repeat
    2.1e-28   96.6  10.4      0.001   19.3   0.1    9.9  9  TPR_17           Tetratricopeptide repeat
    1.8e-19   69.8  12.3    0.00012   22.2   0.2    5.7  5  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    1.6e-18   66.6   9.8    0.00066   19.8   0.2    6.9  6  TPR_9            Tetratricopeptide repeat
    1.6e-17   62.9  18.5     0.0066   17.0   0.1   10.5 10  TPR_6            Tetratricopeptide repeat
    1.8e-16   60.5  12.6    5.2e-05   23.3   0.3    6.8  6  DUF3856          Domain of Unknown Function (DUF3856)
      2e-15   56.1  21.9     0.0021   17.8   0.1    9.2  9  TPR_10           Tetratricopeptide repeat
    1.3e-10   40.5  15.7       0.11   12.6   0.0    8.7  8  TPR_7            Tetratricopeptide repeat
    2.1e-08   33.7  19.9      0.009   15.3   0.9    4.1  3  TPR_15           Tetratricopeptide repeat
    1.4e-07   31.5  17.4       0.12   13.0   0.2    7.7  6  TPR_4            Tetratricopeptide repeat
    2.3e-07   30.7  21.9      0.015   15.0   0.1    6.6  6  TPR_21           Tetratricopeptide repeat-like domain
      9e-07   29.4  17.5        0.6   10.5   0.0    6.6  6  BTAD             Bacterial transcriptional activator domain
    3.5e-06   26.7   4.0    6.7e-05   22.4   0.5    3.1  2  TPR_MalT         MalT-like TPR region
    5.2e-06   25.7  15.1       0.49    9.2   0.0    6.1  6  NARP1            NMDA receptor-regulated protein 1
      3e-05   23.9   1.5       0.16   12.0   0.1    5.5  6  TPR_3            Tetratricopeptide repeat
    3.3e-05   23.3   8.5       0.11   11.6   0.9    3.6  3  FAT              FAT domain
    0.00013   21.5   0.0        8.3    6.3   0.0    4.9  4  PPTA             Protein prenyltransferase alpha subunit repe
    0.00015   21.8  13.6      0.026   14.6   0.1    7.4  9  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    0.00016   21.7   5.4       0.39   10.6   0.2    5.5  5  Wzy_C_2          Virulence factor membrane-bound polymerase, 
     0.0004   19.9  14.4       0.62    9.4   1.2    5.2  6  Coatomer_E       Coatomer epsilon subunit
     0.0043   17.1   2.7       0.26   11.4   0.3    3.4  3  MAS20            MAS20 protein import receptor
  ------ inclusion threshold ------
      0.029   13.4   1.9        9.6    5.1   0.1    3.3  3  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
      0.039   14.4  11.5         22    5.5   0.3    5.5  6  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
      0.049   13.7   4.4        3.1    7.9   0.0    4.9  4  DUF3775          Protein of unknown function (DUF3775)
      0.077   13.2   3.4         17    5.7   0.0    4.6  4  DUF5388          Family of unknown function (DUF5388)
       0.11   12.1   5.5         28    4.4   0.0    5.6  6  HTH_Bact         Helix-turn-helix bacterial domain
       0.14   11.9   8.4         24    4.6   0.1    4.5  4  TOM20_plant      Plant specific mitochondrial import receptor
       0.36   10.9  19.8         16    5.7   0.2    7.6  8  MIT              MIT (microtubule interacting and transport) 
       0.51   10.0   4.7        1.3    8.7   0.6    3.0  2  DUF2225          Uncharacterized protein conserved in bacteri
        1.1    9.7  16.4        1.3    9.4   1.0    5.5  7  TPR_20           Tetratricopeptide repeat
        1.9    8.5   9.3         15    5.6   0.1    4.1  4  GldM_N           GldM N-terminal 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 !   15.9   0.0   1.7e-05    0.0082       3      34 .]      28      59 ..      26      59 .. 0.94
   2 ?    5.6   0.0     0.033        16       3      30 ..      62      89 ..      61      93 .. 0.92
   3 !   19.1   0.6   1.8e-06   0.00083       1      30 [.     101     130 ..     101     133 .. 0.96
   4 !   23.2   0.0   8.9e-08   4.2e-05       3      34 .]     144     175 ..     142     175 .. 0.94
   5 !   10.4   0.0   0.00099      0.47       3      32 ..     178     207 ..     176     209 .. 0.93
   6 !   24.3   0.1     4e-08   1.9e-05       2      34 .]     250     282 ..     250     282 .. 0.92
   7 !   22.6   0.0   1.4e-07   6.5e-05       1      33 [.     283     315 ..     283     316 .. 0.94
   8 !   12.3   0.0   0.00025      0.12       2      30 ..     326     354 ..     325     357 .. 0.93
   9 !   26.3   0.1     9e-09   4.2e-06       7      29 ..     372     394 ..     368     397 .. 0.93
  10 !   31.1   0.0   2.9e-10   1.4e-07       2      33 ..     405     436 ..     404     437 .. 0.95
  11 ?    1.1   0.0      0.81   3.8e+02       2      16 ..     439     453 ..     438     461 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-05
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                                       +  ++n++ ++   +eA+ +y+++L+l+P+n
  gi|330509118|ref|YP_004385546.1| 28 YWMDRANVLIHKDLEEEAVFAYDEVLKLDPKN 59
                                      7999**************************98 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.033
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1  3 alynlGnayfklgkydeAleyyekALel 30
                                      al +++ +++ lgk de    ye+AL l
  gi|330509118|ref|YP_004385546.1| 62 ALLRKASTLYTLGKEDEGQRTYERALLL 89
                                      7999*********************976 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       aka+ n++ a+  lg+ deA e+ e+AL +
  gi|330509118|ref|YP_004385546.1| 101 AKAWQNKAIALSGLGRKDEAKEANEEALAI 130
                                       89**************************87 PP

  == domain 4  score: 23.2 bits;  conditional E-value: 8.9e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                        +++++ ++  lg+++eAl++y+k+ e++P++
  gi|330509118|ref|YP_004385546.1| 144 LWKGKADVLAFLGRWEEALQAYSKVTEIDPED 175
                                       699***************************86 PP

  == domain 5  score: 10.4 bits;  conditional E-value: 0.00099
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                       a+ ++G  +   g+y+e l + +kA+e  P
  gi|330509118|ref|YP_004385546.1| 178 AWGRKGEFLGMIGRYNESLLALDKAIETIP 207
                                       8*************************9766 PP

  == domain 6  score: 24.3 bits;  conditional E-value: 4e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ka+  +G+   klg+y+e le+ye++L+l+P++
  gi|330509118|ref|YP_004385546.1| 250 KAWSLMGYDMAKLGRYNESLEAYEEVLKLDPKD 282
                                       68888888899********************86 PP

  == domain 7  score: 22.6 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+a+  ++  + ++++ydeA e+++kA+el P 
  gi|330509118|ref|YP_004385546.1| 283 AQAWSTKARQLVEMKRYDEAQEAFDKAIELMPG 315
                                       789***************************886 PP

  == domain 8  score: 12.3 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                       +++  +G a+ + g+ d+A ++++kALe+
  gi|330509118|ref|YP_004385546.1| 326 QIWLDKGDALNETGNGDDAGKAFQKALEV 354
                                       68999**********************97 PP

  == domain 9  score: 26.3 bits;  conditional E-value: 9e-09
                                       HHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   7 lGnayfklgkydeAleyyekALe 29 
                                       +Gna+f+lg+ydeA e+y++A++
  gi|330509118|ref|YP_004385546.1| 372 KGNALFNLGRYDEAREAYDQAIK 394
                                       8*********************8 PP

  == domain 10  score: 31.1 bits;  conditional E-value: 2.9e-10
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                        a+ + G a++ lg+ +eAle++++ALe+nP+
  gi|330509118|ref|YP_004385546.1| 405 SAWIGEGKALLALGRNEEALEAFRQALEINPT 436
                                       69*****************************7 PP

  == domain 11  score: 1.1 bits;  conditional E-value: 0.81
                                       HHHHHHHHHHHHTT- CS
                             TPR_1   2 kalynlGnayfklgk 16 
                                       +a++++G     lg+
  gi|330509118|ref|YP_004385546.1| 439 EAWKGKGDSQKALGR 453
                                       89********99998 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.8e-06    0.0018       2      34 .]      27      59 ..      26      59 .. 0.96
   2 !    8.4   0.1    0.0053       2.5       3      33 ..      62      92 ..      61      93 .. 0.91
   3 !   14.6   0.5   5.6e-05     0.027       1      31 [.     101     131 ..     101     134 .. 0.93
   4 ?    2.8   0.0      0.34   1.6e+02      18      34 .]     125     141 ..     124     141 .. 0.94
   5 !   20.6   0.0   6.7e-07   0.00032       3      34 .]     144     175 ..     142     175 .. 0.93
   6 ?    7.3   0.0     0.012       5.8       3      32 ..     178     207 ..     176     209 .. 0.87
   7 ?    1.2   0.0       1.1   5.3e+02      13      34 .]     227     248 ..     223     248 .. 0.86
   8 !   29.5   0.1   9.7e-10   4.6e-07       2      34 .]     250     282 ..     249     282 .. 0.96
   9 !   26.0   0.0   1.3e-08     6e-06       1      34 []     283     316 ..     283     316 .. 0.96
  10 ?    7.5   0.0      0.01         5       3      30 ..     327     354 ..     325     358 .. 0.86
  11 !   25.8   0.1   1.4e-08   6.8e-06       7      29 ..     372     394 ..     368     399 .. 0.91
  12 !   31.3   0.1   2.5e-10   1.2e-07       2      33 ..     405     436 ..     404     437 .. 0.95
  13 ?    0.5   0.0       1.8   8.6e+02       2      24 ..     439     461 ..     438     467 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.8e-06
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPnn 34
                                      ++++ +++++++++  eeA+ a++++l+ldP+n
  gi|330509118|ref|YP_004385546.1| 27 DYWMDRANVLIHKDLEEEAVFAYDEVLKLDPKN 59
                                      689****************************97 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0053
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPn 33
                                      al + +  +y lg+ +e  + +e+Al l ++
  gi|330509118|ref|YP_004385546.1| 62 ALLRKASTLYTLGKEDEGQRTYERALLLMEE 92
                                      7889999*******************99876 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 5.6e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       a+a+ n + a+  lg+ +eA+ea e+Al++ 
  gi|330509118|ref|YP_004385546.1| 101 AKAWQNKAIALSGLGRKDEAKEANEEALAIF 131
                                       79**************************986 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.34
                             TPR_2  18 eeAleafekAleldPnn 34 
                                       eeAl+ f+ +l  dP+n
  gi|330509118|ref|YP_004385546.1| 125 EEALAIFNHSLDKDPEN 141
                                       8**************97 PP

  == domain 5  score: 20.6 bits;  conditional E-value: 6.7e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++   +++++ lg++eeAl+a+ k+ e+dP++
  gi|330509118|ref|YP_004385546.1| 144 LWKGKADVLAFLGRWEEALQAYSKVTEIDPED 175
                                       688899************************86 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.012
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                       a+ + G+ +   g+y+e l a++kA+e  P
  gi|330509118|ref|YP_004385546.1| 178 AWGRKGEFLGMIGRYNESLLALDKAIETIP 207
                                       788889999999**************9766 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 1.1
                             TPR_2  13 klgdyeeAleafekAleldPnn 34 
                                        +++  eAl +++    l+P+n
  gi|330509118|ref|YP_004385546.1| 227 SSNQIGEALSLLDNLTDLYPQN 248
                                       678889**************97 PP

  == domain 8  score: 29.5 bits;  conditional E-value: 9.7e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +a+  +G+  +klg+y+e lea+e++l+ldP++
  gi|330509118|ref|YP_004385546.1| 250 KAWSLMGYDMAKLGRYNESLEAYEEVLKLDPKD 282
                                       69*****************************86 PP

  == domain 9  score: 26.0 bits;  conditional E-value: 1.3e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+a+   ++ + ++++y+eA eaf+kA+el P++
  gi|330509118|ref|YP_004385546.1| 283 AQAWSTKARQLVEMKRYDEAQEAFDKAIELMPGD 316
                                       689*****************************86 PP

  == domain 10  score: 7.5 bits;  conditional E-value: 0.01
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                       ++   G+a+ + g+ ++A +af+kAle 
  gi|330509118|ref|YP_004385546.1| 327 IWLDKGDALNETGNGDDAGKAFQKALEV 354
                                       678888999999**************96 PP

  == domain 11  score: 25.8 bits;  conditional E-value: 1.4e-08
                             TPR_2   7 lGlayyklgdyeeAleafekAle 29 
                                        G+a+++lg+y+eA+ea+++A++
  gi|330509118|ref|YP_004385546.1| 372 KGNALFNLGRYDEAREAYDQAIK 394
                                       7********************98 PP

  == domain 12  score: 31.3 bits;  conditional E-value: 2.5e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                        a+   G+a+++lg+ eeAleaf++Ale++P+
  gi|330509118|ref|YP_004385546.1| 405 SAWIGEGKALLALGRNEEALEAFRQALEINPT 436
                                       69*****************************8 PP

  == domain 13  score: 0.5 bits;  conditional E-value: 1.8
                             TPR_2   2 ealynlGlayyklgdyeeAleaf 24 
                                       ea+   G++  +lg+  +A   f
  gi|330509118|ref|YP_004385546.1| 439 EAWKGKGDSQKALGRARDASLSF 461
                                       899999********999887666 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.1e-05     0.015       2      34 .]      27      59 ..      26      59 .. 0.95
   2 !    9.6   0.1    0.0023       1.1       3      29 ..      62      88 ..      60      92 .. 0.93
   3 !   16.3   0.3   1.7e-05     0.008       1      30 [.     101     130 ..     101     133 .. 0.94
   4 !   12.3   0.0   0.00033      0.16       7      34 .]     148     175 ..     143     175 .. 0.93
   5 ?    6.0   0.0     0.034        16       3      33 ..     178     208 ..     176     209 .. 0.89
   6 !   18.0   0.1   4.7e-06    0.0022      13      34 .]     261     282 ..     250     282 .. 0.91
   7 !   17.5   0.0   6.9e-06    0.0032       1      30 [.     283     312 ..     283     316 .. 0.91
   8 !   12.3   0.0   0.00032      0.15       2      31 ..     326     355 ..     325     357 .. 0.93
   9 !   23.5   0.0   8.4e-08     4e-05       3      30 ..     368     395 ..     366     399 .. 0.90
  10 !   23.2   0.0   1.1e-07     5e-05       3      33 ..     406     436 ..     404     437 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-05
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      ++++  +++++ +   eeA+ +y ++l+ldp+n
  gi|330509118|ref|YP_004385546.1| 27 DYWMDRANVLIHKDLEEEAVFAYDEVLKLDPKN 59
                                      6899***************************97 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0023
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8  3 ayynlgsiylklgdyeeAkeyyekale 29
                                      a+++++s++ +lg+ +e + +ye+al 
  gi|330509118|ref|YP_004385546.1| 62 ALLRKASTLYTLGKEDEGQRTYERALL 88
                                      7899*********************95 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 1.7e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+a++n++ +++ lg+++eAke+ e+al +
  gi|330509118|ref|YP_004385546.1| 101 AKAWQNKAIALSGLGRKDEAKEANEEALAI 130
                                       79*********************9999976 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00033
                                       HHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +++++  lg+ eeA ++y k++e+dp++
  gi|330509118|ref|YP_004385546.1| 148 KADVLAFLGRWEEALQAYSKVTEIDPED 175
                                       689999********************86 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+ ++g  +   g+y+e+  ++ ka+e  p+
  gi|330509118|ref|YP_004385546.1| 178 AWGRKGEFLGMIGRYNESLLALDKAIETIPA 208
                                       89999999999***************98776 PP

  == domain 6  score: 18.0 bits;  conditional E-value: 4.7e-06
                                       HTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  13 klgdyeeAkeyyekaleldpdn 34 
                                       klg+y+e+ e+ye++l+ldp++
  gi|330509118|ref|YP_004385546.1| 261 KLGRYNESLEAYEEVLKLDPKD 282
                                       8*******************96 PP

  == domain 7  score: 17.5 bits;  conditional E-value: 6.9e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+a+  +++ + ++++y+eA+e++ ka+el
  gi|330509118|ref|YP_004385546.1| 283 AQAWSTKARQLVEMKRYDEAQEAFDKAIEL 312
                                       68999999999******************8 PP

  == domain 8  score: 12.3 bits;  conditional E-value: 0.00032
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                       ++++ +g+++ ++g+ + A ++++kale +
  gi|330509118|ref|YP_004385546.1| 326 QIWLDKGDALNETGNGDDAGKAFQKALEVS 355
                                       79*************************976 PP

  == domain 9  score: 23.5 bits;  conditional E-value: 8.4e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekalel 30 
                                       +++++g+++++lg+y+eA e+y +a++ 
  gi|330509118|ref|YP_004385546.1| 368 SMLLKGNALFNLGRYDEAREAYDQAIKT 395
                                       6789**********************95 PP

  == domain 10  score: 23.2 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+   g+++l lg+ eeA e++++ale++p+
  gi|330509118|ref|YP_004385546.1| 406 AWIGEGKALLALGRNEEALEAFRQALEINPT 436
                                       788889***********************95 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   3.4   4.4e-10   2.1e-07       4      75 ..      61     131 ..      59     133 .. 0.92
   2 !   13.5   0.0   0.00014     0.067       6      33 ..     145     172 ..     140     179 .. 0.81
   3 !   10.9   0.0   0.00092      0.43       6      75 ..     179     245 ..     176     247 .. 0.83
   4 !   19.5   0.9   1.9e-06   0.00089       5      74 ..     251     312 ..     249     312 .. 0.89
   5 !   13.8   0.1   0.00011     0.054       3      38 ..     283     315 ..     281     321 .. 0.85
   6 !   15.7   0.0   2.9e-05     0.014       4      46 ..     326     368 ..     323     371 .. 0.84
   7 !   43.9   0.1   4.5e-14   2.1e-11       2      74 ..     366     433 ..     365     436 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4.4e-10
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       tal + a++l+ lg+ de ++ +e+al ++++ l ++  + a + +n +++++ lgr +eA e+ eealai+
  gi|330509118|ref|YP_004385546.1|  61 TALLRKASTLYTLGKEDEGQRTYERALLLMEEDL-KNTSQNAKAWQNKAIALSGLGRKDEAKEANEEALAIF 131
                                       577799************************8887.566699*****************************97 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00014
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleia 33 
                                       +   a+vl+ lgr++eAl+ + k+ ei 
  gi|330509118|ref|YP_004385546.1| 145 WKGKADVLAFLGRWEEALQAYSKVTEID 172
                                       5468999999999999999999998875 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00092
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       + + +++l   gry e+l  l+ka+e +  + + d +l a++    + l+  +++  eAl+ll   ++++
  gi|330509118|ref|YP_004385546.1| 179 WGRKGEFLGMIGRYNESLLALDKAIETI-PADN-DEDLQAWSFAKVAVLH-SSNQIGEALSLLDNLTDLY 245
                                       66789999999*****************.4433.4469***********8.677******9997666666 PP

  == domain 4  score: 19.5 bits;  conditional E-value: 1.9e-06
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       a++ ++   ++lgry e+le +e++l +      p+    a++  + +r + +++ry+eA+e++ +a+++
  gi|330509118|ref|YP_004385546.1| 251 AWSLMGYDMAKLGRYNESLEAYEEVLKLD-----PK---DAQAWSTKARQLVEMKRYDEAQEAFDKAIEL 312
                                       566788899999**999999999999999.....86...5999999999999***************985 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 0.00011
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllG 38 
                                       a+a++  a  l +++rydeA+e ++ka+e++   +G
  gi|330509118|ref|YP_004385546.1| 283 AQAWSTKARQLVEMKRYDEAQEAFDKAIELM---PG 315
                                       6778888999999***************997...55 PP

  == domain 6  score: 15.7 bits;  conditional E-value: 2.9e-05
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltat 46 
                                       +++   +++l++ g+ d+A + ++kale+  ++l  d+++t++
  gi|330509118|ref|YP_004385546.1| 326 QIWLDKGDALNETGNGDDAGKAFQKALEVSDEALLNDSEQTSS 368
                                       677789************************7776678888866 PP

  == domain 7  score: 43.9 bits;  conditional E-value: 4.5e-14
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       ++++l   +++l+ lgrydeA+e +++a+  a  +++  h  + ++ ++ g +++algr eeAle++++al+i
  gi|330509118|ref|YP_004385546.1| 366 TSSML-LKGNALFNLGRYDEAREAYDQAIKTA--SPNSFH--VPSAWIGEGKALLALGRNEEALEAFRQALEI 433
                                       67788.99********************9999..555777..******************************9 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.7e-05     0.013      11      42 .]      43      74 ..      43      74 .. 0.94
   2 ?    3.0   0.0      0.17        82       9      31 ..     123     145 ..     120     153 .. 0.84
   3 !   19.8   0.0   9.8e-07   0.00046       5      27 ..     153     175 ..     149     183 .. 0.86
   4 ?    3.5   0.0      0.12        55       8      22 ..     190     204 ..     189     210 .. 0.90
   5 ?    4.9   0.0     0.045        21       4      42 .]     225     263 ..     224     263 .. 0.90
   6 !   26.0   0.3   1.1e-08   5.3e-06       5      31 ..     260     286 ..     256     288 .. 0.90
   7 !    8.5   0.0    0.0034       1.6       3      25 ..     292     314 ..     290     317 .. 0.89
   8 ?    4.6   0.1     0.055        26       1      23 [.     332     354 ..     332     358 .. 0.94
   9 !   21.0   0.6   4.1e-07   0.00019       1      22 [.     373     394 ..     373     396 .. 0.97
  10 !   31.4   0.1   2.4e-10   1.1e-07       1      42 []     411     452 ..     411     452 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-05
                            TPR_11 11 eeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      eeA+ aY + lkldP+n +a++  + ++y +G
  gi|330509118|ref|YP_004385546.1| 43 EEAVFAYDEVLKLDPKNETALLRKASTLYTLG 74
                                      89********************9999999887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.17
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeay 31 
                                        +eeA++ ++  l+ dP+n++++
  gi|330509118|ref|YP_004385546.1| 123 ANEEALAIFNHSLDKDPENVSLW 145
                                       689****************9987 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 9.8e-07
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdn 27 
                                         +G++eeA++aY+k  ++dP++
  gi|330509118|ref|YP_004385546.1| 153 AFLGRWEEALQAYSKVTEIDPED 175
                                       558******************98 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.12
                            TPR_11   8 GkyeeAieaYkkAlk 22 
                                       G+y+e++ a+ kA++
  gi|330509118|ref|YP_004385546.1| 190 GRYNESLLALDKAIE 204
                                       9*************8 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.045
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +++ +++ eA+  + +  +l P+n  a++ +G+ ++k+G
  gi|330509118|ref|YP_004385546.1| 225 LHSSNQIGEALSLLDNLTDLYPQNKKAWSLMGYDMAKLG 263
                                       7899***************************98666665 PP

  == domain 6  score: 26.0 bits;  conditional E-value: 1.1e-08
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeay 31 
                                        ++G+y+e++eaY++ lkldP++a a+
  gi|330509118|ref|YP_004385546.1| 260 AKLGRYNESLEAYEEVLKLDPKDAQAW 286
                                       689**********************98 PP

  == domain 7  score: 8.5 bits;  conditional E-value: 0.0034
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldP 25 
                                        ++e  +y+eA ea+ kA++l P
  gi|330509118|ref|YP_004385546.1| 292 QLVEMKRYDEAQEAFDKAIELMP 314
                                       678999**************976 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.055
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                       Gda+ e G+ ++A +a++kAl+ 
  gi|330509118|ref|YP_004385546.1| 332 GDALNETGNGDDAGKAFQKALEV 354
                                       9********************97 PP

  == domain 9  score: 21.0 bits;  conditional E-value: 4.1e-07
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlk 22 
                                       G+a++ +G+y+eA eaY +A+k
  gi|330509118|ref|YP_004385546.1| 373 GNALFNLGRYDEAREAYDQAIK 394
                                       9********************8 PP

  == domain 10  score: 31.4 bits;  conditional E-value: 2.4e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+a+ ++G++eeA+ea+++Al+++P+ +ea+ + G+ + ++G
  gi|330509118|ref|YP_004385546.1| 411 GKALLALGRNEEALEAFRQALEINPTLVEAWKGKGDSQKALG 452
                                       89*****************************99999888877 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   9.8e-06    0.0046       3      42 ..      28      67 ..      26      69 .. 0.95
   2 ?    5.6   0.1     0.073        34       3      28 ..      62      87 ..      61      96 .. 0.91
   3 ?    8.2   0.1     0.011       5.1       8      43 ..     108     150 ..     101     151 .. 0.66
   4 !   19.6   0.0   2.3e-06    0.0011       3      43 ..     144     184 ..     142     185 .. 0.92
   5 !    8.5   0.0    0.0083       3.9       6      42 ..     220     256 ..     214     259 .. 0.87
   6 !   19.2   0.2   3.2e-06    0.0015       3      39 ..     251     287 ..     249     291 .. 0.91
   7 !   11.0   0.2    0.0014      0.65       3      35 ..     285     317 ..     284     319 .. 0.91
   8 !    9.0   0.0    0.0061       2.9       2      30 ..     326     354 ..     325     361 .. 0.89
   9 !   16.4   0.1   2.5e-05     0.012       7      33 ..     372     399 ..     368     408 .. 0.82
  10 !   24.2   0.2   7.9e-08   3.7e-05       3      41 ..     406     444 ..     404     447 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.8e-06
                            TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawllla 42
                                       ++++a +l + +  +eA+ +++++l+l+P++++a+l+ a
  gi|330509118|ref|YP_004385546.1| 28 YWMDRANVLIHKDLEEEAVFAYDEVLKLDPKNETALLRKA 67
                                      599**********************************998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.073
                            TPR_14  3 allalaeallalGdpdeAiallrral 28
                                      all+ a+ l++lG+ de  + ++ral
  gi|330509118|ref|YP_004385546.1| 62 ALLRKASTLYTLGKEDEGQRTYERAL 87
                                      78999********************8 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.011
                            TPR_14   8 aeallalGd.......pdeAiallrralalaPddaeawlllaq 43 
                                       a al  lG+        +eA+a+++  l+++P++  +w   a+
  gi|330509118|ref|YP_004385546.1| 108 AIALSGLGRkdeakeaNEEALAIFNHSLDKDPENVSLWKGKAD 150
                                       55555555522222225679999999999********988775 PP

  == domain 4  score: 19.6 bits;  conditional E-value: 2.3e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +++  a++l+ lG+++eA++++ ++ + +P+d  aw + ++
  gi|330509118|ref|YP_004385546.1| 144 LWKGKADVLAFLGRWEEALQAYSKVTEIDPEDYGAWGRKGE 184
                                       688889******************************99876 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0083
                            TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       a +++l  + +  eA+ ll+ + +l+P++  aw l++
  gi|330509118|ref|YP_004385546.1| 220 AKVAVLHSSNQIGEALSLLDNLTDLYPQNKKAWSLMG 256
                                       557899999************************8876 PP

  == domain 6  score: 19.2 bits;  conditional E-value: 3.2e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       a+ +++  ++ lG++ e++++++++l+l+P+da+aw 
  gi|330509118|ref|YP_004385546.1| 251 AWSLMGYDMAKLGRYNESLEAYEEVLKLDPKDAQAWS 287
                                       89999999****************************5 PP

  == domain 7  score: 11.0 bits;  conditional E-value: 0.0014
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPdda 35 
                                       a+   a+ l +  ++deA +++++a++l P+d+
  gi|330509118|ref|YP_004385546.1| 285 AWSTKARQLVEMKRYDEAQEAFDKAIELMPGDD 317
                                       89999**********************999875 PP

  == domain 8  score: 9.0 bits;  conditional E-value: 0.0061
                            TPR_14   2 eallalaeallalGdpdeAiallrralal 30 
                                       + +l+ ++al + G+ d+A +++++al+ 
  gi|330509118|ref|YP_004385546.1| 326 QIWLDKGDALNETGNGDDAGKAFQKALEV 354
                                       579***********************995 PP

  == domain 9  score: 16.4 bits;  conditional E-value: 2.5e-05
                            TPR_14   7 laeallalGdpdeAiallrralala.Pd 33 
                                        + al++lG++deA++++++a+++a P+
  gi|330509118|ref|YP_004385546.1| 372 KGNALFNLGRYDEAREAYDQAIKTAsPN 399
                                       5899*******************74265 PP

  == domain 10  score: 24.2 bits;  conditional E-value: 7.9e-08
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       a+   ++allalG+ +eA++++r+al+ +P+  eaw   
  gi|330509118|ref|YP_004385546.1| 406 AWIGEGKALLALGRNEEALEAFRQALEINPTLVEAWKGK 444
                                       6677789*****************************866 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.14        67      35      67 ..      27      59 ..      21      60 .. 0.84
   2 ?    5.9   0.1     0.043        20      15      53 ..      44      79 ..      38      87 .. 0.82
   3 !    9.7   0.5    0.0027       1.3       2      63 ..      72     130 ..      64     134 .. 0.78
   4 !   18.5   0.1   4.9e-06    0.0023      14      66 ..     125     174 ..     121     176 .. 0.93
   5 !   18.0   0.0   7.2e-06    0.0034       3      67 ..     148     209 ..     146     211 .. 0.91
   6 ?    0.7   0.0       1.9   8.8e+02      12      37 ..     230     252 ..     227     257 .. 0.85
   7 !   16.3   0.1   2.5e-05     0.012       6      37 ..     258     286 ..     253     287 .. 0.89
   8 !   22.5   0.2   2.9e-07   0.00014       3      62 ..     289     353 ..     287     358 .. 0.92
   9 !   24.7   0.1     6e-08   2.8e-05      13      66 ..     348     398 ..     348     400 .. 0.87
  10 !   25.9   0.5   2.5e-08   1.2e-05       3      53 ..     410     457 ..     408     459 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.14
                            TPR_16 35 eAllllgdaalrqgrlaeAaalyraalraapda 67
                                      + ++ +++++ ++   +eA+ +y++ l+ +p++
  gi|330509118|ref|YP_004385546.1| 27 DYWMDRANVLIHKDLEEEAVFAYDEVLKLDPKN 59
                                      789*******99977777778888889999987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.043
                            TPR_16 15 dAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeA 53
                                      +A+ a++++lk+d   P +  All ++  ++ +g  +e 
  gi|330509118|ref|YP_004385546.1| 44 EAVFAYDEVLKLD---PKNETALLRKASTLYTLGKEDEG 79
                                      6777999******...*************9999987776 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0027
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                        l+++   ++ y++A+ + e+ lk+    +++a A+ +++ a+  +gr +eA ++ ++al+ 
  gi|330509118|ref|YP_004385546.1|  72 TLGKEDEGQRTYERALLLMEEDLKNT---SQNAKAWQNKAIALSGLGRKDEAKEANEEALAI 130
                                       45555555666777777777777777...77*********************9999999865 PP

  == domain 4  score: 18.5 bits;  conditional E-value: 4.9e-06
                            TPR_16  14 ddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++A+a ++  l++d   P+++  + +++d+++ +gr++eA+++y +  + +p 
  gi|330509118|ref|YP_004385546.1| 125 EEALAIFNHSLDKD---PENVSLWKGKADVLAFLGRWEEALQAYSKVTEIDPE 174
                                       7999999999****...***************************999888886 PP

  == domain 5  score: 18.0 bits;  conditional E-value: 7.2e-06
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +a+ ++ +g++++A+ a+  +++ d   P+++ A+  +g+ +   gr+ e + ++++a++  p +
  gi|330509118|ref|YP_004385546.1| 148 KADVLAFLGRWEEALQAYSKVTEID---PEDYGAWGRKGEFLGMIGRYNESLLALDKAIETIPAD 209
                                       6899999******************...99999*******************9999998776654 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 1.9
                            TPR_16  12 dyddAaaaleaalkrdpssPdaaeAl 37 
                                       +  +A+ +l+ +++++   P++  A+
  gi|330509118|ref|YP_004385546.1| 230 QIGEALSLLDNLTDLY---PQNKKAW 252
                                       6679************...9999998 PP

  == domain 7  score: 16.3 bits;  conditional E-value: 2.5e-05
                            TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAl 37 
                                       + +++g+y + ++a+e++lk+d   P +a+A+
  gi|330509118|ref|YP_004385546.1| 258 DMAKLGRYNESLEAYEEVLKLD---PKDAQAW 286
                                       55789*****************...9999998 PP

  == domain 8  score: 22.5 bits;  conditional E-value: 2.9e-07
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       +ar +++ ++yd+A++a++ a+++ p++ +      ++ +l +gda+ + g+ ++A  ++++al+
  gi|330509118|ref|YP_004385546.1| 289 KARQLVEMKRYDEAQEAFDKAIELMPGDDLkeleqIVQIWLDKGDALNETGNGDDAGKAFQKALE 353
                                       68899********************88888*******************************9996 PP

  == domain 9  score: 24.7 bits;  conditional E-value: 6e-08
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       +++A+++ ++al +d   ++   ++ll+g+a++ +gr++eA+++y+ a++ a+ 
  gi|330509118|ref|YP_004385546.1| 348 FQKALEVSDEALLND---SEQTSSMLLKGNALFNLGRYDEAREAYDQAIKTASP 398
                                       688999999999999...99999*******************999999955544 PP

  == domain 10  score: 25.9 bits;  conditional E-value: 2.5e-08
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeA 53 
                                       +++a+l++g+ ++A++a+++al+ +   P  +eA+ ++gd+  ++gr  +A
  gi|330509118|ref|YP_004385546.1| 410 EGKALLALGRNEEALEAFRQALEIN---PTLVEAWKGKGDSQKALGRARDA 457
                                       799**********************...****************9998766 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   2.4e-05     0.011       9      53 ..      44      88 ..      42      93 .. 0.93
   2 !   11.9   0.8   0.00052      0.25       4      47 ..      80     123 ..      78     125 .. 0.93
   3 !   25.8   0.0   2.5e-08   1.2e-05       8      58 ..     125     175 ..     123     181 .. 0.94
   4 !   11.2   0.0   0.00089      0.42       8      57 ..     159     208 ..     158     219 .. 0.92
   5 !    9.3   0.3    0.0033       1.6      32      65 ..     222     255 ..     188     262 .. 0.65
   6 !   26.0   0.6   2.1e-08   9.9e-06       4      67 ..     228     291 ..     225     292 .. 0.95
   7 !   27.6   1.4   6.7e-09   3.2e-06       5      57 ..     263     315 ..     259     324 .. 0.92
   8 !   13.0   0.7   0.00023      0.11       1      52 [.     293     352 ..     293     353 .. 0.87
   9 !   18.1   1.1     6e-06    0.0028       7      53 ..     341     394 ..     335     400 .. 0.76
  10 !   15.8   0.2   3.1e-05     0.015       1      45 [.     414     458 ..     414     464 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.4e-05
                            TPR_19  9 eAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53
                                      eA+ ++ ++l+ dpkn+ a+l+ A  l+ lg  de +++ +++++
  gi|330509118|ref|YP_004385546.1| 44 EAVFAYDEVLKLDPKNETALLRKASTLYTLGKEDEGQRTYERALL 88
                                      89***********************************99998875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00052
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47 
                                       +  y++Al l+e+ l+   +na a+ + A+al  lg+ deA+++
  gi|330509118|ref|YP_004385546.1|  80 QRTYERALLLMEEDLKNTSQNAKAWQNKAIALSGLGRKDEAKEA 123
                                       778999*******99999************************85 PP

  == domain 3  score: 25.8 bits;  conditional E-value: 2.5e-08
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       +eAla++   l++dp+n  ++ + A++l  lg+++eA ++ +++ e dp d
  gi|330509118|ref|YP_004385546.1| 125 EEALAIFNHSLDKDPENVSLWKGKADVLAFLGRWEEALQAYSKVTEIDPED 175
                                       69**********************************************985 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00089
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       +eAl++++++ + dp++  a+ +  e l   g+++e   +Ld++ e  p 
  gi|330509118|ref|YP_004385546.1| 159 EEALQAYSKVTEIDPEDYGAWGRKGEFLGMIGRYNESLLALDKAIETIPA 208
                                       69****************************************99988776 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.0033
                            TPR_19  32 AeallalgqldeAealLdalpeedpddaryasLl 65 
                                       + +l +++q+ eA  lLd l + +p++  ++sL+
  gi|330509118|ref|YP_004385546.1| 222 VAVLHSSNQIGEALSLLDNLTDLYPQNKKAWSLM 255
                                       6677788888888888888888888888888886 PP

  == domain 6  score: 26.0 bits;  conditional E-value: 2.1e-08
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAk 67 
                                       +++  eAl+ll ++ + +p+n  a+ l+   + +lg+++e  ++ +++++ dp+da+++s +A+
  gi|330509118|ref|YP_004385546.1| 228 SNQIGEALSLLDNLTDLYPQNKKAWSLMGYDMAKLGRYNESLEAYEEVLKLDPKDAQAWSTKAR 291
                                       57899******************************************************98885 PP

  == domain 7  score: 27.6 bits;  conditional E-value: 6.7e-09
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       g+y e l+++e++l+ dpk+a a+   A+ l++++++deA+++ d++ e  p 
  gi|330509118|ref|YP_004385546.1| 263 GRYNESLEAYEEVLKLDPKDAQAWSTKARQLVEMKRYDEAQEAFDKAIELMPG 315
                                       99*******************************************99987776 PP

  == domain 8  score: 13.0 bits;  conditional E-value: 0.00023
                            TPR_19   1 llaegdyaeAlalleqalqedpk........naearllLAeallalgqldeAealLdalp 52 
                                       l+++++y+eA++++ +a++  p+           ++l+  +al ++g+ d+A ++ ++++
  gi|330509118|ref|YP_004385546.1| 293 LVEMKRYDEAQEAFDKAIELMPGddlkeleqIVQIWLDKGDALNETGNGDDAGKAFQKAL 352
                                       6899**************999998877777788888888999999999999998888776 PP

  == domain 9  score: 18.1 bits;  conditional E-value: 6e-06
                            TPR_19   7 yaeAlalleqalqe.......dpknaearllLAeallalgqldeAealLdalpe 53 
                                        ++A +++++al+        d ++    ll  +al++lg++deA+++ d++ +
  gi|330509118|ref|YP_004385546.1| 341 GDDAGKAFQKALEVsdeallnDSEQTSSMLLKGNALFNLGRYDEAREAYDQAIK 394
                                       55666666666655444444488899999999****************999876 PP

  == domain 10  score: 15.8 bits;  conditional E-value: 3.1e-05
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAe 45 
                                       lla g+ +eAl++++qal+ +p   ea+ +  + + alg+  +A 
  gi|330509118|ref|YP_004385546.1| 414 LLALGRNEEALEAFRQALEINPTLVEAWKGKGDSQKALGRARDAS 458
                                       7899************************************99995 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00048      0.23       1      31 [.      48      78 ..      48      81 .. 0.91
   2 !   14.3   0.1   8.8e-05     0.041       6      34 .]      94     122 ..      89     122 .. 0.90
   3 !   13.8   0.0   0.00012     0.057       2      34 .]     131     163 ..     130     163 .. 0.95
   4 !    9.7   0.0    0.0025       1.2       2      31 ..     165     194 ..     164     196 .. 0.92
   5 ?    0.7   0.2       1.9   8.9e+02       4      31 ..     240     267 ..     237     270 .. 0.78
   6 !   19.3   0.1   2.2e-06     0.001       1      34 []     271     304 ..     271     304 .. 0.97
   7 !    9.3   0.1    0.0033       1.5       4      34 .]     357     387 ..     356     387 .. 0.92
   8 ?    2.3   0.0      0.56   2.7e+02       2      34 .]     389     425 ..     388     425 .. 0.85
   9 !   10.9   0.0    0.0011       0.5       2      32 ..     427     457 ..     426     458 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00048
                            TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmt 31
                                      +y ++l+ldP+n  a+  +A +l+ +G+ ++
  gi|330509118|ref|YP_004385546.1| 48 AYDEVLKLDPKNETALLRKASTLYTLGKEDE 78
                                      599***********************98765 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.8e-05
                            TPR_17   6 leldPnnadaynnLAelllknGdlmtArq 34 
                                       l++   na+a++n+A +l+ +G++++A++
  gi|330509118|ref|YP_004385546.1|  94 LKNTSQNAKAWQNKAIALSGLGRKDEAKE 122
                                       788899*********************86 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 0.00012
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +  +l++dP n+ ++  +A +l+ +G++++A+q
  gi|330509118|ref|YP_004385546.1| 131 FNHSLDKDPENVSLWKGKADVLAFLGRWEEALQ 163
                                       7789***************************97 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0025
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmt 31 
                                       y k+ e+dP +  a+  ++e+l ++G++ +
  gi|330509118|ref|YP_004385546.1| 165 YSKVTEIDPEDYGAWGRKGEFLGMIGRYNE 194
                                       899***********************9976 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 1.9
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmt 31 
                                       +  +l+P n +a+ ++++ ++k+G++ +
  gi|330509118|ref|YP_004385546.1| 240 NLTDLYPQNKKAWSLMGYDMAKLGRYNE 267
                                       566889*******999998888887766 PP

  == domain 6  score: 19.3 bits;  conditional E-value: 2.2e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y+++l+ldP++a a+  +A+ l + +++++A++
  gi|330509118|ref|YP_004385546.1| 271 AYEEVLKLDPKDAQAWSTKARQLVEMKRYDEAQE 304
                                       5*******************************96 PP

  == domain 7  score: 9.3 bits;  conditional E-value: 0.0033
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +al +d     ++ +++++l ++G++++Ar+
  gi|330509118|ref|YP_004385546.1| 357 EALLNDSEQTSSMLLKGNALFNLGRYDEARE 387
                                       68889999999******************96 PP

  == domain 8  score: 2.3 bits;  conditional E-value: 0.56
                            TPR_17   2 ylkalel.dPnn...adaynnLAelllknGdlmtArq 34 
                                       y +a++   Pn+   + a+   +++ll +G+ ++A++
  gi|330509118|ref|YP_004385546.1| 389 YDQAIKTaSPNSfhvPSAWIGEGKALLALGRNEEALE 425
                                       88888886688888999999999*********99975 PP

  == domain 9  score: 10.9 bits;  conditional E-value: 0.0011
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +++ale++P+ ++a+  ++  ++ +G+ ++A
  gi|330509118|ref|YP_004385546.1| 427 FRQALEINPTLVEAWKGKGDSQKALGRARDA 457
                                       899**************99999999998887 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.1   2.7e-05     0.013       5      77 ..      42     122 ..      38     127 .. 0.93
   2 !    9.7   0.0    0.0021      0.97      40      81 ..     125     167 ..     121     168 .. 0.92
   3 !   17.7   0.2   6.5e-06     0.003       4      81 ..     191     274 ..     188     275 .. 0.83
   4 !   22.2   0.2   2.6e-07   0.00012       4      81 ..     230     308 ..     229     309 .. 0.92
   5 !   21.5   0.1   4.2e-07    0.0002       4      80 ..     347     428 ..     344     430 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-.......HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HH CS
                            ANAPC3   5 yknAiflaerllaaetespedayllAlclylngq.......ykrAyellrka.klnskslgcrylfAqcllkLkkye 73 
                                        ++A+f ++ +l+ +++++ +++ +A +ly +g+       y+rA+ l ++  k  s++ +++  +A +l  L++ +
  gi|330509118|ref|YP_004385546.1|  42 EEEAVFAYDEVLKLDPKNETALLRKASTLYTLGKedegqrtYERALLLMEEDlKNTSQNAKAWQNKAIALSGLGRKD 118
                                       589*******************************99****************99999******************** PP

                                       HHHH CS
                            ANAPC3  74 eAia 77 
                                       eA  
  gi|330509118|ref|YP_004385546.1| 119 EAKE 122
                                       9965 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0021
                                       HHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  40 krAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++A+ +++ + ++++++   +  +A +l  L+++eeA++a++k
  gi|330509118|ref|YP_004385546.1| 125 EEALAIFNHSlDKDPENVSLWKGKADVLAFLGRWEEALQAYSK 167
                                       589999999999999************************9987 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 6.5e-06
                                       -HHHHHHHHHHHH.HHH--HHH.....HHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHH CS
                            ANAPC3   4 nyknAiflaerllaaetesped.....ayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyee 74 
                                       +y++ ++ ++++ ++ + +++      ++++  +l +++q  +A+ ll+++ +l++++++++ l++    kL++y+e
  gi|330509118|ref|YP_004385546.1| 191 RYNESLLALDKAIETIPADNDEdlqawSFAKVAVLHSSNQIGEALSLLDNLtDLYPQNKKAWSLMGYDMAKLGRYNE 267
                                       78888999999997554333333554666677789999*************************************** PP

                                       HHHHH-S CS
                            ANAPC3  75 AiaaLek 81 
                                        + a+e+
  gi|330509118|ref|YP_004385546.1| 268 SLEAYEE 274
                                       ***9987 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 2.6e-07
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       ++ +A+ l++ l    +++ ++  l ++ + ++g+y++ +e +++  kl++k+ +++ ++A+ l+++k+y+eA  a+
  gi|330509118|ref|YP_004385546.1| 230 QIGEALSLLDNLTDLYPQNKKAWSLMGYDMAKLGRYNESLEAYEEVlKLDPKDAQAWSTKARQLVEMKRYDEAQEAF 306
                                       6677888888888777999999999************************************************9999 PP

                                       -S CS
                            ANAPC3  80 ek 81 
                                       +k
  gi|330509118|ref|YP_004385546.1| 307 DK 308
                                       87 PP

  == domain 5  score: 21.5 bits;  conditional E-value: 4.2e-07
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H....HHHHHHHHHHHHTT-HHHH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnsksl....gcrylfAqcllkLkkyeeA 75 
                                       ++++A+ +++ +l  ++e  ++ +l++ +l+++g+y++A e +++a k++s +      +++  +++ll+L++ eeA
  gi|330509118|ref|YP_004385546.1| 347 AFQKALEVSDEALLNDSEQTSSMLLKGNALFNLGRYDEAREAYDQAiKTASPNSfhvpSAWIGEGKALLALGRNEEA 423
                                       68999999999996667777777778********************9998888888889999999************ PP

                                       HHHH- CS
                            ANAPC3  76 iaaLe 80 
                                       + a+ 
  gi|330509118|ref|YP_004385546.1| 424 LEAFR 428
                                       *9986 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.017         8      25      66 ..      22      63 ..       7      68 .. 0.84
   2 ?    1.5   0.0      0.69   3.3e+02      17      49 ..      82     121 ..      76     123 .. 0.75
   3 !   19.1   0.0   2.4e-06    0.0011       8      62 ..     121     175 ..     119     214 .. 0.96
   4 !   19.8   0.2   1.4e-06   0.00066      10      63 ..     264     317 ..     259     326 .. 0.90
   5 !   14.3   0.0   7.1e-05     0.034      10      57 ..     347     394 ..     344     404 .. 0.93
   6 ?    5.7   0.0     0.035        17      29      61 ..     404     436 ..     400     457 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.017
                             TPR_9 25 aPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66
                                      + ++ + ++dR+ +l + +  ++A+++ +  l l+p++++a 
  gi|330509118|ref|YP_004385546.1| 22 QENTTDYWMDRANVLIHKDLEEEAVFAYDEVLKLDPKNETAL 63
                                      5677788*****************************999986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.69
                             TPR_9  17 vverllll.......aPddpeerrdRGlllaqlGclsaAl 49 
                                       ++er lll        ++ +  +   +++l  lG+  +A 
  gi|330509118|ref|YP_004385546.1|  82 TYERALLLmeedlknTSQNAKAWQNKAIALSGLGRKDEAK 121
                                       5566666656666658899999999999999999988886 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 2.4e-06
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       +e +e+ala+ +  l  +P+ ++++   + +la lG++++Al++     +++p++
  gi|330509118|ref|YP_004385546.1| 121 KEANEEALAIFNHSLDKDPENVSLWKGKADVLAFLGRWEEALQAYSKVTEIDPED 175
                                       6889*******************************************99999986 PP

  == domain 4  score: 19.8 bits;  conditional E-value: 1.4e-06
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       ++ + l+++e +l l+P+d++ +   ++ l+++ ++ +A ++++ +++l p ++
  gi|330509118|ref|YP_004385546.1| 264 RYNESLEAYEEVLKLDPKDAQAWSTKARQLVEMKRYDEAQEAFDKAIELMPGDD 317
                                       5677899******************************************99664 PP

  == domain 5  score: 14.3 bits;  conditional E-value: 7.1e-05
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57 
                                        +++al+v++  ll ++++ +  +  G +l+ lG++ +A+++ ++++ 
  gi|330509118|ref|YP_004385546.1| 347 AFQKALEVSDEALLNDSEQTSSMLLKGNALFNLGRYDEAREAYDQAIK 394
                                       689****************************************99985 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.035
                             TPR_9  29 peerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       p+ +   G +l  lG+ ++Al+++ ++l+++p 
  gi|330509118|ref|YP_004385546.1| 404 PSAWIGEGKALLALGRNEEALEAFRQALEINPT 436
                                       666777788899999999999999999999883 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       1.7   7.9e+02      16      32 ..      42      58 ..      30      59 .. 0.83
   2 ?    4.4   0.2      0.15        70       2      26 ..      62      86 ..      61      88 .. 0.92
   3 ?   -0.3   0.0       4.5   2.1e+03      10      22 ..     111     123 ..     102     139 .. 0.78
   4 !    8.3   0.0    0.0084         4      12      32 ..     154     174 ..     144     175 .. 0.84
   5 ?    5.9   0.0      0.05        24       7      32 ..     216     247 ..     214     248 .. 0.80
   6 !    9.6   0.0    0.0033       1.5       6      32 ..     255     281 ..     251     282 .. 0.89
   7 ?    6.4   0.1     0.035        16      10      28 ..     293     311 ..     289     315 .. 0.84
   8 ?    1.4   0.0       1.3   6.1e+02       7      28 ..     332     353 ..     328     354 .. 0.84
   9 !   17.0   0.1   1.4e-05    0.0066       2      33 .]     368     400 ..     367     400 .. 0.89
  10 !   10.2   0.0    0.0021      0.98       7      31 ..     411     435 ..     406     436 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.7
                                      HHHHHHHHHHHHHH-TT CS
                             TPR_6 16 tdkAlealerlikeYPd 32
                                       ++A+ a+++++k  P+
  gi|330509118|ref|YP_004385546.1| 42 EEEAVFAYDEVLKLDPK 58
                                      579**********9997 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.15
                                      HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  2 AlyklalsyrklgdtdkAlealerl 26
                                      Al++ a  ++ lg+ d+  +++er 
  gi|330509118|ref|YP_004385546.1| 62 ALLRKASTLYTLGKEDEGQRTYERA 86
                                      99********999**********97 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 4.5
                                       HHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlea 22 
                                       +  lg++d+A+ea
  gi|330509118|ref|YP_004385546.1| 111 LSGLGRKDEAKEA 123
                                       4446899999986 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0084
                                       HHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  12 klgdtdkAlealerlikeYPd 32 
                                        lg++++Al+a+ ++ +  P+
  gi|330509118|ref|YP_004385546.1| 154 FLGRWEEALQAYSKVTEIDPE 174
                                       478************999886 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.05
                                       HHHHHH.H.....HHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrk.l.....gdtdkAlealerlikeYPd 32 
                                       a+s+ k +     ++  +Al +l++l + YP+
  gi|330509118|ref|YP_004385546.1| 216 AWSFAKvAvlhssNQIGEALSLLDNLTDLYPQ 247
                                       66677655777767999**************8 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.0033
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                       +++ + klg++ ++lea+e+++k  P+
  gi|330509118|ref|YP_004385546.1| 255 MGYDMAKLGRYNESLEAYEEVLKLDPK 281
                                       777789999**************9997 PP

  == domain 7  score: 6.4 bits;  conditional E-value: 0.035
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlealerlik 28 
                                       + +++++d+A ea+++ i+
  gi|330509118|ref|YP_004385546.1| 293 LVEMKRYDEAQEAFDKAIE 311
                                       55789***********997 PP

  == domain 8  score: 1.4 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       + ++ ++g+ d+A +a+++ ++
  gi|330509118|ref|YP_004385546.1| 332 GDALNETGNGDDAGKAFQKALE 353
                                       6677788899********9875 PP

  == domain 9  score: 17.0 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH.-TT- CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlike.YPdS 33 
                                       ++++ + ++++lg++d+A+ea+++ ik   P+S
  gi|330509118|ref|YP_004385546.1| 368 SMLLKGNALFNLGRYDEAREAYDQAIKTaSPNS 400
                                       68999******9**************9866665 PP

  == domain 10  score: 10.2 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       ++++++lg+ ++Alea+++ ++  P
  gi|330509118|ref|YP_004385546.1| 411 GKALLALGRNEEALEAFRQALEINP 435
                                       78999999*************9988 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.22     1e+02     102     133 ..      62      93 ..      58     103 .. 0.86
   2 !   21.2   0.3   5.1e-07   0.00024      54     136 ..     100     178 ..      88     185 .. 0.85
   3 ?    0.3   0.0       1.4   6.6e+02      67      83 ..     188     204 ..     182     216 .. 0.76
   4 ?    3.7   0.0      0.13        60      64      83 ..     258     277 ..     250     279 .. 0.83
   5 !   23.3   0.3   1.1e-07   5.2e-05      45     132 ..     273     357 ..     270     366 .. 0.89
   6 !   12.3   0.2   0.00028      0.13      63     129 ..     374     433 ..     368     451 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH- CS
                           DUF3856 102 avfsravaleelGrkdealkafrmagemiaer 133
                                       a++++a +l  lG++de  ++++ a  +++e 
  gi|330509118|ref|YP_004385546.1|  62 ALLRKASTLYTLGKEDEGQRTYERALLLMEED 93 
                                       7899*******************999888875 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 5.1e-07
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                           DUF3856  54 dalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagemi 130
                                       +a ++   + al +lgr dea e+ ++al  fn   + + ++ +lW      +a  l+ lGr +eal+a+ +++e+ 
  gi|330509118|ref|YP_004385546.1| 100 NAKAWQNKAIALSGLGRKDEAKEANEEALAIFNHSLDKDPENVSLWK----GKADVLAFLGRWEEALQAYSKVTEID 172
                                       6667778899************************9999999999995....69**********************97 PP

                                       HH--S- CS
                           DUF3856 131 aerkGe 136
                                        e  G 
  gi|330509118|ref|YP_004385546.1| 173 PEDYGA 178
                                       776665 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.4
                                       HTT-HHHHHHHHHHHHH CS
                           DUF3856  67 klgrydealesadkalr 83 
                                        +gry+e+l + dka++
  gi|330509118|ref|YP_004385546.1| 188 MIGRYNESLLALDKAIE 204
                                       46888888888888764 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.13
                                       HHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkalr 83 
                                        +aklgry+e+le+ ++ l+
  gi|330509118|ref|YP_004385546.1| 258 DMAKLGRYNESLEAYEEVLK 277
                                       5799*********9999876 PP

  == domain 5  score: 23.3 bits;  conditional E-value: 1.1e-07
                                       TS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                           DUF3856  45 eeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealk 121
                                       ee++  +  da ++++ +  l++++rydea e+ dka++ +    +l++   ++ +++ ++++ al+e+G+ d+a k
  gi|330509118|ref|YP_004385546.1| 273 EEVLKLDPKDAQAWSTKARQLVEMKRYDEAQEAFDKAIELMP-GDDLKEL--EQIVQIWLDKGDALNETGNGDDAGK 346
                                       888899999*****************************9875.3466654..57888899***************** PP

                                       HHHHHHHHHHH CS
                           DUF3856 122 afrmagemiae 132
                                       af++a e+ +e
  gi|330509118|ref|YP_004385546.1| 347 AFQKALEVSDE 357
                                       ******99877 PP

  == domain 6  score: 12.3 bits;  conditional E-value: 0.00028
                                       HHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  63 ealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                       +al +lgrydea e+ d+a++       ++    + Wi      ++al  lGr++eal+afr+a e+
  gi|330509118|ref|YP_004385546.1| 374 NALFNLGRYDEAREAYDQAIKTASPN-SFH--VPSAWI----GEGKALLALGRNEEALEAFRQALEI 433
                                       68999999999999999999865432.233..345676....589*******************995 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       3.6   1.7e+03       9      33 ..      67      91 ..      62      94 .. 0.67
   2 !   11.9   0.0   0.00034      0.16       7      31 ..     106     130 ..     105     139 .. 0.90
   3 ?    2.6   0.0      0.29   1.3e+02      11      25 ..     151     165 ..     149     171 .. 0.79
   4 ?    0.6   0.0       1.2   5.8e+02      16      31 ..     190     205 ..     183     206 .. 0.86
   5 ?    6.5   0.1     0.017         8      14      30 ..     261     277 ..     255     278 .. 0.87
   6 ?    5.7   0.2     0.029        14      14      31 ..     295     312 ..     292     313 .. 0.90
   7 ?    6.9   0.0     0.013         6      11      36 ..     334     359 ..     331     364 .. 0.87
   8 !   17.8   0.1   4.5e-06    0.0021       9      31 ..     373     395 ..     367     396 .. 0.90
   9 !   10.4   0.3   0.00098      0.46      10      31 ..     412     433 ..     411     434 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.6
                            TPR_10  9 analrqrgrydeAealleealairr 33
                                      a +l+ +g+ de  + +e+al + +
  gi|330509118|ref|YP_004385546.1| 67 ASTLYTLGKEDEGQRTYERALLLME 91
                                      5567777777777776777765544 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00034
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N a+al+ +gr deA +  eealai
  gi|330509118|ref|YP_004385546.1| 106 NKAIALSGLGRKDEAKEANEEALAI 130
                                       669********************98 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.29
                            TPR_10  11 alrqrgrydeAeall 25 
                                       +l  +gr++eA++ +
  gi|330509118|ref|YP_004385546.1| 151 VLAFLGRWEEALQAY 165
                                       67789******9977 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.2
                            TPR_10  16 grydeAealleealai 31 
                                       gry+e++  l++a+++
  gi|330509118|ref|YP_004385546.1| 190 GRYNESLLALDKAIET 205
                                       9************997 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.017
                            TPR_10  14 qrgrydeAealleeala 30 
                                       ++gry+e+++ +ee+l 
  gi|330509118|ref|YP_004385546.1| 261 KLGRYNESLEAYEEVLK 277
                                       78************996 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.029
                            TPR_10  14 qrgrydeAealleealai 31 
                                       +++rydeA + +++a+++
  gi|330509118|ref|YP_004385546.1| 295 EMKRYDEAQEAFDKAIEL 312
                                       789************986 PP

  == domain 7  score: 6.9 bits;  conditional E-value: 0.013
                            TPR_10  11 alrqrgrydeAealleealairrrll 36 
                                       al ++g++d+A + +++al++  ++l
  gi|330509118|ref|YP_004385546.1| 334 ALNETGNGDDAGKAFQKALEVSDEAL 359
                                       8999*****************98887 PP

  == domain 8  score: 17.8 bits;  conditional E-value: 4.5e-06
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       +nal+++grydeA++ +++a+ +
  gi|330509118|ref|YP_004385546.1| 373 GNALFNLGRYDEAREAYDQAIKT 395
                                       9*******************986 PP

  == domain 9  score: 10.4 bits;  conditional E-value: 0.00098
                            TPR_10  10 nalrqrgrydeAealleealai 31 
                                        al ++gr +eA++ +++al+i
  gi|330509118|ref|YP_004385546.1| 412 KALLALGRNEEALEAFRQALEI 433
                                       68999***************98 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1         4   1.9e+03      21      33 ..      82      94 ..      80      97 .. 0.65
   2 ?    6.0   0.0     0.028        13       1      30 [.     103     137 ..     103     143 .. 0.77
   3 ?    4.9   0.0     0.065        31       9      34 ..     152     175 ..     147     178 .. 0.76
   4 !    7.7   0.1    0.0084         4      11      34 ..     261     282 ..     251     284 .. 0.82
   5 ?    1.3   0.1      0.96   4.5e+02      13      29 ..     297     313 ..     290     320 .. 0.75
   6 ?    0.2   0.0       2.1     1e+03       6      31 ..     332     355 ..     327     362 .. 0.76
   7 !   12.6   0.0   0.00022      0.11       4      26 ..     371     393 ..     368     400 .. 0.83
   8 !    8.8   0.1    0.0037       1.8       6      28 ..     411     433 ..     411     448 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 4
                             TPR_7 21 lyeqsLaltkdpe 33
                                       ye++L l ++++
  gi|330509118|ref|YP_004385546.1| 82 TYERALLLMEEDL 94
                                      6999885555544 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.028
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt.....k 30 
                                       a+ n a + s lG+ +eA e +e++La+      k
  gi|330509118|ref|YP_004385546.1| 103 AWQNKAIALSGLGRKDEAKEANEEALAIFnhsldK 137
                                       56788999999*************77765444444 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.065
                             TPR_7   9 ysrlGdyeeAielyeqsLaltkdped 34 
                                          lG++eeA++ y +  +++ dped
  gi|330509118|ref|YP_004385546.1| 152 LAFLGRWEEALQAYSK--VTEIDPED 175
                                       5559**********99..66666654 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0084
                             TPR_7  11 rlGdyeeAielyeqsLaltkdped 34 
                                       +lG+y e +e ye+  +l  dp d
  gi|330509118|ref|YP_004385546.1| 261 KLGRYNESLEAYEE--VLKLDPKD 282
                                       79************..77766655 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.96
                             TPR_7  13 GdyeeAielyeqsLalt 29 
                                        +y+eA e + ++++l 
  gi|330509118|ref|YP_004385546.1| 297 KRYDEAQEAFDKAIELM 313
                                       58999999999976665 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 2.1
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                       +++  + G+ ++A + ++++L  + +
  gi|330509118|ref|YP_004385546.1| 332 GDALNETGNGDDAGKAFQKAL--EVS 355
                                       6777788999999999***55..433 PP

  == domain 7  score: 12.6 bits;  conditional E-value: 0.00022
                             TPR_7   4 nLarlysrlGdyeeAielyeqsL 26 
                                         +++ ++lG+y+eA e y q++
  gi|330509118|ref|YP_004385546.1| 371 LKGNALFNLGRYDEAREAYDQAI 393
                                       5699*****************54 PP

  == domain 8  score: 8.8 bits;  conditional E-value: 0.0037
                             TPR_7   6 arlysrlGdyeeAielyeqsLal 28 
                                       + +  +lG+ eeA+e ++q+L++
  gi|330509118|ref|YP_004385546.1| 411 GKALLALGRNEEALEAFRQALEI 433
                                       567889*************8776 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   5.8   0.00023      0.11     140     269 ..      20     163 ..       6     171 .. 0.77
   2 !   14.8   1.2   2.6e-05     0.012     123     202 ..     225     305 ..     209     311 .. 0.89
   3 !   15.3   0.9   1.9e-05     0.009     138     245 ..     317     435 ..     293     442 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                            TPR_15 140 eaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdssel...raallWlli..DlgrraeLrellkawkara. 210
                                       +a e+   +++ ra++   ++ +++A+ +y e+l+l+p+++++   +a  l++l   D g+r+  r+ll   +++  
  gi|330509118|ref|YP_004385546.1|  20 QAQENTTDYWMDRANVLIHKDLEEEAVFAYDEVLKLDPKNETAllrKASTLYTLGkeDEGQRTYERALL-LMEEDLk 95 
                                       44557778*******************************999844457788888533555555455544.2222224 PP

                            TPR_15 211 ..esdasLwgplaaAlllLgr.......pkkALeylrkqakenrkdplwllaYADaleqagradeAwr 269
                                         +++a+ w+  a Al+ Lgr       +++AL+ ++  +++ +++++     AD+l   gr +eA +
  gi|330509118|ref|YP_004385546.1|  96 ntSQNAKAWQNKAIALSGLGRkdeakeaNEEALAIFNHSLDKDPENVSLWKGKADVLAFLGRWEEALQ 163
                                       559****************9933333335679************999988899***********9986 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.6e-05
                            TPR_15 123 akdydriaellksleeeea.aeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrrae 198
                                       ++ +++i+e l  l ++ + + q+   +++++    + g+ +++l++y+e+l+l+p+++++ ++    l++++r++e
  gi|330509118|ref|YP_004385546.1| 225 LHSSNQIGEALSLLDNLTDlYPQNKKAWSLMGYDMAKLGRYNESLEAYEEVLKLDPKDAQAWSTKARQLVEMKRYDE 301
                                       577788889998888877746699****************************************************9 PP

                            TPR_15 199 Lrel 202
                                       ++e+
  gi|330509118|ref|YP_004385546.1| 302 AQEA 305
                                       9887 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.9e-05
                            TPR_15 138 eeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalap.....dsselraall..WlliDlgrraeLrellkawk 207
                                        ++++eq  +++l  + +  ++g+ d+A +++++Al++++     ds++  + ll   +l +lgr++e+re+  +  
  gi|330509118|ref|YP_004385546.1| 317 DLKELEQIVQIWLDKGDALNETGNGDDAGKAFQKALEVSDeallnDSEQTSSMLLkgNALFNLGRYDEAREAYDQAI 393
                                       45668899999*************************98763333256666666665558999******999877666 PP

                            TPR_15 208 ara....esdasLwgplaaAlllLgrpkkALeylrkqakenr 245
                                       + a       +s w   + All+Lgr+++ALe +r+ ++ n+
  gi|330509118|ref|YP_004385546.1| 394 KTAspnsFHVPSAWIGEGKALLALGRNEEALEAFRQALEINP 435
                                       665666688889999999*****************9998876 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.74   3.5e+02       8      21 ..     108     121 ..     106     123 .. 0.86
   2 !    8.9   0.2    0.0055       2.6       8      23 ..     149     164 ..     147     165 .. 0.90
   3 ?   -0.6   0.1       6.4     3e+03       8      25 ..     290     307 ..     283     308 .. 0.66
   4 ?   -0.6   0.0       6.7   3.1e+03       6      20 ..     330     344 ..     326     345 .. 0.85
   5 !   11.5   0.0   0.00082      0.39       5      26 .]     370     391 ..     367     391 .. 0.86
   6 !   13.0   0.2   0.00026      0.12       1      26 []     404     429 ..     404     429 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.74
                             TPR_4   8 ArallalGdldeAr 21 
                                       A al  lG+ deA 
  gi|330509118|ref|YP_004385546.1| 108 AIALSGLGRKDEAK 121
                                       99**********96 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0055
                             TPR_4   8 ArallalGdldeAral 23 
                                       A +l+ lG+++eA+++
  gi|330509118|ref|YP_004385546.1| 149 ADVLAFLGRWEEALQA 164
                                       89***********985 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 6.4
                             TPR_4   8 ArallalGdldeAralle 25 
                                       Ar l +  ++deA+++++
  gi|330509118|ref|YP_004385546.1| 290 ARQLVEMKRYDEAQEAFD 307
                                       555555558999998765 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 6.7
                             TPR_4   6 aLArallalGdldeA 20 
                                       + + al ++G+ d+A
  gi|330509118|ref|YP_004385546.1| 330 DKGDALNETGNGDDA 344
                                       56899********99 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00082
                             TPR_4   5 laLArallalGdldeAraller 26 
                                       l+ + al+ lG++deAr++ ++
  gi|330509118|ref|YP_004385546.1| 370 LLKGNALFNLGRYDEAREAYDQ 391
                                       56789************99876 PP

  == domain 6  score: 13.0 bits;  conditional E-value: 0.00026
                             TPR_4   1 arallaLArallalGdldeAraller 26 
                                       + a ++ + allalG+ +eA++++++
  gi|330509118|ref|YP_004385546.1| 404 PSAWIGEGKALLALGRNEEALEAFRQ 429
                                       56889999***************997 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.8     0.082        39      96     172 ..      91     168 ..      38     178 .. 0.82
   2 ?    5.2   0.6     0.033        16     110     187 ..     210     297 ..     190     300 .. 0.73
   3 ?    5.4   0.0     0.029        14     156     189 ..     293     330 ..     292     331 .. 0.89
   4 !   11.5   0.4   0.00038      0.18     125     178 ..     302     357 ..     301     370 .. 0.78
   5 !   15.0   0.1   3.3e-05     0.015     151     179 ..     371     399 ..     361     408 .. 0.90
   6 ?    3.0   0.0      0.15        70     153     174 ..     411     432 ..     409     440 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.082
                            TPR_21  96 kaqLewvlekakdeelkalarlRLarvllaekkydeAlktLeakkeeaf.aalvaelrGDilvaqgkldeAraaYqa 171
                                       ++ L++  ++ak  + ka+a   L r   a+++ +eAl+  +++ ++   +++    + D+l+  g+ +eA +aY++
  gi|330509118|ref|YP_004385546.1|  91 EEDLKNTSQNAKAWQNKAIALSGLGRKDEAKEANEEALAIFNHSLDKDPeNVSLWKGKADVLAFLGRWEEALQAYSK 167
                                       56788888888888888888888999889999999999988777665541455667777999999999999999987 PP

                            TPR_21 172 A 172
                                        
  gi|330509118|ref|YP_004385546.1| 168 V 168
                                       5 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.033
                            TPR_21 110 elkalarlRLar..vllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAlaaleeka... 180
                                       + ++l     a+  vl   +++ eAl++L++ ++    + ++  l G  +++ g+ +e  +aY++ l+   ++a   
  gi|330509118|ref|YP_004385546.1| 210 NDEDLQAWSFAKvaVLHSSNQIGEALSLLDNLTDlYPQNKKAWSLMGYDMAKLGRYNESLEAYEEVLKLDPKDAqaw 286
                                       444444444443116778899999999998877624567777899999999**************999888877889 PP

                            TPR_21 181 ....rellqlK 187
                                           r+l+++K
  gi|330509118|ref|YP_004385546.1| 287 stkaRQLVEMK 297
                                       99999999999 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.029
                            TPR_21 156 lvaqgkldeAraaYqaAlaaleeka....rellqlKld 189
                                       lv++++ deA++a+++A++ +  ++    ++++q+ ld
  gi|330509118|ref|YP_004385546.1| 293 LVEMKRYDEAQEAFDKAIELMPGDDlkelEQIVQIWLD 330
                                       6788999*************999999999999999887 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00038
                            TPR_21 125 aekkydeAlktLeakkeeafaalva..elrGDilvaqgkldeAraaYqaAlaalee 178
                                       a++++d+A++++ +++ ++ +  v+    +GD+l ++g+ d+A +a+q+Al+  +e
  gi|330509118|ref|YP_004385546.1| 302 AQEAFDKAIELMPGDDLKELEQIVQiwLDKGDALNETGNGDDAGKAFQKALEVSDE 357
                                       577888888888777666666555511459*********************98776 PP

  == domain 5  score: 15.0 bits;  conditional E-value: 3.3e-05
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaaleek 179
                                       l+G++l++ g+ deAr+aY++A+++ +++
  gi|330509118|ref|YP_004385546.1| 371 LKGNALFNLGRYDEAREAYDQAIKTASPN 399
                                       79*********************998876 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.15
                            TPR_21 153 GDilvaqgkldeAraaYqaAla 174
                                       G +l+a g+++eA +a+++Al+
  gi|330509118|ref|YP_004385546.1| 411 GKALLALGRNEEALEAFRQALE 432
                                       899*****************97 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.9     0.006       2.8      55     130 ..      19      94 ..      12     101 .. 0.88
   2 !    7.9   0.0    0.0084         4      68     124 ..     114     170 ..      96     178 .. 0.79
   3 ?    3.3   0.0      0.21     1e+02      73      95 ..     153     175 ..     140     206 .. 0.70
   4 !   10.5   0.0    0.0013       0.6      73     123 ..     226     276 ..     192     280 .. 0.89
   5 ?    1.6   1.9      0.72   3.4e+02      11      46 ..     288     323 ..     278     395 .. 0.62
   6 ?    5.9   0.0     0.035        16     104     123 ..     412     431 ..     404     457 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHH CS
                              BTAD  55 erleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeL 130
                                       ++ +e   +   ++a+ +++   +eea+  +++ ++++P +E++       l+ +G++ e  ++Yer+  l +e+L
  gi|330509118|ref|YP_004385546.1|  19 TQAQENTTDYWMDRANVLIHKDLEEEAVFAYDEVLKLDPKNETALLRKASTLYTLGKEDEGQRTYERALLLMEEDL 94 
                                       5666777777778888889999999******************************************987777776 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0084
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  68 laeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       l +++ + +  eeala  +  ++++P +  l++     la +Gr +eAL++Y ++ +
  gi|330509118|ref|YP_004385546.1| 114 LGRKDEAKEANEEALAIFNHSLDKDPENVSLWKGKADVLAFLGRWEEALQAYSKVTE 170
                                       4455556667778888888889999999999***9*****************98765 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.21
                                       HHTT-HHHHHHHHHHHHHHSTT- CS
                              BTAD  73 lrlGraeealaelealvaehPlr 95 
                                       + lGr+eeal+ +++ ++ +P +
  gi|330509118|ref|YP_004385546.1| 153 AFLGRWEEALQAYSKVTEIDPED 175
                                       44566666666666666666655 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.0013
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                        + +++ eal+ l++l++++P + +++ ++    a++Gr +e Le+Ye++ 
  gi|330509118|ref|YP_004385546.1| 226 HSSNQIGEALSLLDNLTDLYPQNKKAWSLMGYDMAKLGRYNESLEAYEEVL 276
                                       45678899**********************9*****************986 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.72
                                       HHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTT CS
                              BTAD  11 aagraalaagdpeeaaelleaAlalwrGpaladlea 46 
                                       +++r++ +  + +ea e++++A++l  G+ l++le+
  gi|330509118|ref|YP_004385546.1| 288 TKARQLVEMKRYDEAQEAFDKAIELMPGDDLKELEQ 323
                                       556666666666666666666666666666666655 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.035
                                       HHHHHTT-HHHHHHHHHHHH CS
                              BTAD 104 rAlarsGrqaeALevYerlr 123
                                       +Al ++Gr++eALe+++++ 
  gi|330509118|ref|YP_004385546.1| 412 KALLALGRNEEALEAFRQAL 431
                                       47777777777777777654 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.073        35      83     186 ..      63     167 ..      55     175 .. 0.63
   2 !   22.4   0.5   1.4e-07   6.7e-05      40     229 ..     249     431 ..     232     441 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.073
                          TPR_MalT  83 llqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql..ep 157
                                       ll+ a +l + G+ +e  +tye+al l++e        ++  + + a  l   ++ +eA+++ +e++++  +   + 
  gi|330509118|ref|YP_004385546.1|  63 LLRKASTLYTLGKEDEGQRTYERALLLMEEDLKNTSQNAKAWQNK-AIALSGLGRKDEAKEANEEALAIFNHSldKD 138
                                       566666666667777777777777777766666655555555444.6666666777777777777777666643433 PP

                          TPR_MalT 158 eaaldayvllarialaqGdleeAetllek 186
                                          +      a++ +  G++eeA+++  k
  gi|330509118|ref|YP_004385546.1| 139 PENVSLWKGKADVLAFLGRWEEALQAYSK 167
                                       55566666667777777777777666555 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.4e-07
                          TPR_MalT  40 iaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglq 116
                                         a +++G+ +   G+ +++l+a++e+ kl    +  +++ +  +q++e+ +     +eA e + +a++l++  +l+
  gi|330509118|ref|YP_004385546.1| 249 KKAWSLMGYDMAKLGRYNESLEAYEEVLKLD--PKDAQAWSTKARQLVEMKRY----DEAQEAFDKAIELMPGDDLK 319
                                       5677899999999999999999999998875..55555555666666677666....9999999999*****99999 PP

                          TPR_MalT 117 qlp.lvgfllvlladllyEwndLeeAeqhlqeGielleql..epeaaldayvllarialaqGdleeAetllekaeel 190
                                       +l+ +v++     +d l E ++ + A ++ q+++e++++   +   ++ + +l     +  G+ +eA ++ ++a ++
  gi|330509118|ref|YP_004385546.1| 320 ELEqIVQIW-LDKGDALNETGNGDDAGKAFQKALEVSDEAllNDSEQTSSMLLKGNALFNLGRYDEAREAYDQAIKT 395
                                       996355555.555**********************99996545566777777777777899**************** PP

                          TPR_MalT 191 aresnfhvdwlanaeevrvrlwlaqgdlaaaerwleaae 229
                                       a  + fhv   a++ e +   +la g++++a+++ ++a 
  gi|330509118|ref|YP_004385546.1| 396 ASPNSFHVP-SAWIGEGKA--LLALGRNEEALEAFRQAL 431
                                       999999954.446666774..367788877777777663 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.26   1.2e+02     210     258 ..      10      58 ..       4      60 .. 0.87
   2 ?    3.4   0.5      0.06        28      19      62 ..      82     125 ..      69     128 .. 0.84
   3 !    9.2   0.0     0.001      0.49      18     259 ..     122     175 ..     117     177 .. 0.55
   4 !    6.3   0.5    0.0084         4      42     252 ..     253     309 ..     217     317 .. 0.51
   5 ?    5.6   0.1     0.013       6.1      21      71 ..     349     399 ..     326     403 .. 0.78
   6 !    6.5   0.0    0.0073       3.4     205     246 ..     417     458 ..     410     467 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT CS
                             NARP1 210 kAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDla 258
                                        Al +i ++ + + + +++++ +a++l h+   ++A+ + +e  klD +
  gi|330509118|ref|YP_004385546.1|  10 LALAMICTCTQAQENTTDYWMDRANVLIHKDLEEEAVFAYDEVLKLDPK 58 
                                       589999999999999**************98888999999999999965 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.06
                                       HHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHH CS
                             NARP1  19 kleeAlehLeekekqivDklavketkaelllkLgrkeeAeatye 62 
                                       ++e+Al  +ee  k+   + +  ++ka  l  Lgrk+eA+++ e
  gi|330509118|ref|YP_004385546.1|  82 TYERALLLMEEDLKNTSQNAKAWQNKAIALSGLGRKDEAKEANE 125
                                       57999999999999999999999999999999999999998765 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.001
                                       THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHH CS
                             NARP1  18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeealla 94 
                                       + +e                                                                         
  gi|330509118|ref|YP_004385546.1| 122 EANE------------------------------------------------------------------------- 125
                                       3444......................................................................... PP

                                       HHHHTTTS-TT-SHHHHTHHHH--HHHHHHHHHHHHHHHHHCT-TTHHHHHGGGGGGSCHHHHHHHHHHHHHTTTTT CS
                             NARP1  95 lydelaekyprsdaprRlpLdfleGeeFkelvdkYlrkaLrkgvPslfanlksLYedkeKvkileelvegyvkslkt 171
                                                                                                                    
  gi|330509118|ref|YP_004385546.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       SSSSTTGG.GSS----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
                             NARP1 172 sgklsesdnedsekepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaev 248
                                                                             +Al + ++ ++++p+ v l+  Ka +l   G  ++A ++
  gi|330509118|ref|YP_004385546.1| 126 --------------------------------------EALAIFNHSLDKDPENVSLWKGKADVLAFLGRWEEALQA 164
                                       ......................................555555666666666666666666666666666666555 PP

                                       HHHHHHCTTT- CS
                             NARP1 249 meearklDlaD 259
                                         +  ++D +D
  gi|330509118|ref|YP_004385546.1| 165 YSKVTEIDPED 175
                                       55555555544 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0084
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHHTTTS-TT-SHHHHTHHHH-- CS
                             NARP1  42 etkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalydelaekyprsdaprRlpLdfle 118
                                         ++  + kLgr++e+ ++ye+                                                       
  gi|330509118|ref|YP_004385546.1| 253 SLMGYDMAKLGRYNESLEAYEEV------------------------------------------------------ 275
                                       44444444555555555555555...................................................... PP

                                       HHHHHHHHHHHHHHHHHCT-TTHHHHHGGGGGGSCHHHHHHHHHHHHHTTTTTSSSSTTGG.GSS----SSHHHHHH CS
                             NARP1 119 GeeFkelvdkYlrkaLrkgvPslfanlksLYedkeKvkileelvegyvkslktsgklsesdnedsekepesallwvl 195
                                                                                                                    
  gi|330509118|ref|YP_004385546.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 196 yflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                                              ++ +p+  + + tKar l  +   ++A e+ ++a
  gi|330509118|ref|YP_004385546.1| 276 -----------------------LKLDPKDAQAWSTKARQLVEMKRYDEAQEAFDKA 309
                                       .......................5555555555555555444444444444444444 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT- CS
                             NARP1  21 eeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpen 71 
                                       ++Ale  +e+  +  ++ + +  k++ l++Lgr++eA+++y + ++  + n
  gi|330509118|ref|YP_004385546.1| 349 QKALEVSDEALLNDSEQTSSMLLKGNALFNLGRYDEAREAYDQAIKTASPN 399
                                       55555555555555667788889*******************999887655 PP

  == domain 6  score: 6.5 bits;  conditional E-value: 0.0073
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAa 246
                                       lg+ e+Ale   +a+e +ptlve +  K+   k  G  ++A 
  gi|330509118|ref|YP_004385546.1| 417 LGRNEEALEAFRQALEINPTLVEAWKGKGDSQKALGRARDAS 458
                                       456677888888888888888888888877777777776665 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.8   1.3e+03      15      28 ..     156     167 ..     152     175 .. 0.74
   2 ?   -1.6   0.0         6   2.8e+03       9      25 ..     223     239 ..     223     244 .. 0.85
   3 ?   -1.1   0.0       4.3     2e+03       8      34 ..     256     280 ..     253     282 .. 0.71
   4 ?    3.9   0.1      0.11        53      14      25 ..     296     307 ..     290     312 .. 0.89
   5 !   12.0   0.1   0.00033      0.16      10      29 ..     375     392 ..     373     396 .. 0.87
   6 ?   -0.6   0.0       2.9   1.4e+03      18      32 ..     421     433 ..     416     435 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.8
                                       T-HHHHHHH..HHH CS
                             TPR_3  15 kkyqeArelfsYal 28 
                                       ++ +eA++++s   
  gi|330509118|ref|YP_004385546.1| 156 GRWEEALQAYS--K 167
                                       66789****98..4 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6
                                       HHHHHTT-HHHHHHH.. CS
                             TPR_3   9 aefynkkkyqeArelfs 25 
                                       a+++++ ++ eA+ l++
  gi|330509118|ref|YP_004385546.1| 223 AVLHSSNQIGEALSLLD 239
                                       6899999**9**99977 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.3
                                       HHHHHHTT-HHHHHHH..HHHHHHH-T CS
                             TPR_3   8 AaefynkkkyqeArelfsYallaildk 34 
                                       +++    ++y+e +e+  Y+   +ld+
  gi|330509118|ref|YP_004385546.1| 256 GYDMAKLGRYNESLEA--YEEVLKLDP 280
                                       6777788999999999..665555555 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.11
                                       TT-HHHHHHH.. CS
                             TPR_3  14 kkkyqeArelfs 25 
                                       +k+y+eA e+f+
  gi|330509118|ref|YP_004385546.1| 296 MKRYDEAQEAFD 307
                                       8********988 PP

  == domain 5  score: 12.0 bits;  conditional E-value: 0.00033
                                       HHHHTT-HHHHHHH..HHHH CS
                             TPR_3  10 efynkkkyqeArelfsYall 29 
                                       +++n ++y+eAre+++  ++
  gi|330509118|ref|YP_004385546.1| 375 ALFNLGRYDEAREAYD--QA 392
                                       689***********77..76 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 2.9
                                       HHHHHH..HHHHHHH CS
                             TPR_3  18 qeArelfsYallail 32 
                                       +eA+e+  ++++  +
  gi|330509118|ref|YP_004385546.1| 421 EEALEA--FRQALEI 433
                                       79****..8899876 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.9   0.00024      0.11     144     289 ..      23     179 ..       9     186 .. 0.76
   2 !    8.3   0.7    0.0024       1.2     164     281 ..     193     312 ..     186     359 .. 0.66
   3 ?    5.5   0.0     0.017       8.2     252     290 ..     411     442 ..     364     448 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                                       S-STTCCCCCCCCHCHHHHCCSTTHHCCCCCHCTT......TT.TSSCCCHHHHHHHCCHHHHHSSCCHHHHCCTSS CS
                               FAT 144 gvkaemwlkfanlarksgrlslAekaLkelleedp.eewlprappevvyaylKylwssgeqkealqkLreftselle 219
                                       + +++ w+  an+   ++  + A  a  e+l+ dp +e +  ++   +y+  K +  +   + al+ ++e ++++++
  gi|330509118|ref|YP_004385546.1|  23 ENTTDYWMDRANVLIHKDLEEEAVFAYDEVLKLDPkNETALLRKASTLYTLGKEDEGQRTYERALLLMEEDLKNTSQ 99 
                                       34788899999999999888888888888888898433333555566666666666666689*************** PP

                                       CCCSS-SS---................HHHHCCCTCCC.......CCCCCCCCT.S...-SSCCHHHHCCHHCTCCC CS
                               FAT 220 kkeelqsgleaq....keptnleeftkllarcylkkGe.......wqealqkldwseekieeilqsysaateidpsw 285
                                       ++++ q++ +a     ++ + +e +++ la +++ + +       w  +   l     + ee+lq+ys+ teidp+ 
  gi|330509118|ref|YP_004385546.1| 100 NAKAWQNKAIALsglgRKDEAKEANEEALAIFNHSLDKdpenvslWKGKADVL-AFLGRWEEALQAYSKVTEIDPED 175
                                       *9977777777778886777777777777888877777888888866666664.3444599**************** PP

                                       HSTT CS
                               FAT 286 ykaw 289
                                       y aw
  gi|330509118|ref|YP_004385546.1| 176 YGAW 179
                                       *999 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0024
                                       CSTTHHCCCCCHCTT........TT.TSSCCCHHHHHHHCCHHHHHSSCCHHHHCCTSSCCC........SS-SS-- CS
                               FAT 164 slAekaLkelleedp...eewlprappevvyaylKylwssgeqkealqkLreftsellekke........elqsgle 229
                                       + +  aL +++e+ p   +    +    + +a++ +l+ss+++ eal+ L   t+ + ++k+               
  gi|330509118|ref|YP_004385546.1| 193 NESLLALDKAIETIPadnD----EDLQAWSFAKVAVLHSSNQIGEALSLLDNLTDLYPQNKKawslmgydM------ 259
                                       5555556666565564222....34558**********************999998888876654443331...... PP

                                       -...............HHHHCCCTCCC.CCCCCCCCT.S...-SSCCHHHHCCHHC CS
                               FAT 230 aq...keptnleeftkllarcylkkGe.wqealqkldwseekieeilqsysaatei 281
                                            + +++le +++ l ++  k ++ w ++ ++l ++++  +e+ +++ +a e+
  gi|330509118|ref|YP_004385546.1| 260 -AklgRYNESLEAYEEVL-KLDPKDAQaWSTKARQLVEMKR-YDEAQEAFDKAIEL 312
                                       .13444555555555555.4444444456666666544443.66666666666654 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.017
                                       CCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTC CS
                               FAT 252 Gewqealqkldwseekieeilqsysaateidpswykawh 290
                                       G+ + al++       +ee+l+++++a ei+p++ +aw 
  gi|330509118|ref|YP_004385546.1| 411 GKALLALGR-------NEEALEAFRQALEINPTLVEAWK 442
                                       555566666.......9*********************6 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.098        46       7      18 ..      51      62 ..      50      62 .. 0.88
   2 ?    1.0   0.1      0.79   3.7e+02       9      19 ..     135     145 ..     128     145 .. 0.88
   3 ?    3.3   0.0      0.15        73       9      19 ..     169     179 ..     166     180 .. 0.84
   4 ?    6.3   0.0     0.018       8.3       6      20 ..     273     287 ..     273     287 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.098
                                      HHHHH-TT-CHH CS
                              PPTA  7 kliekdpkNYsa 18
                                      +++++dpkN++a
  gi|330509118|ref|YP_004385546.1| 51 EVLKLDPKNETA 62
                                      689******997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.79
                                       HHH-TT-CHHH CS
                              PPTA   9 iekdpkNYsaW 19 
                                       ++kdp N s W
  gi|330509118|ref|YP_004385546.1| 135 LDKDPENVSLW 145
                                       89*******99 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.15
                                       HHH-TT-CHHH CS
                              PPTA   9 iekdpkNYsaW 19 
                                        e dp +Y aW
  gi|330509118|ref|YP_004385546.1| 169 TEIDPEDYGAW 179
                                       578******** PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.018
                                       HHHHHH-TT-CHHHH CS
                              PPTA   6 ekliekdpkNYsaWn 20 
                                       e+++++dpk+ +aW+
  gi|330509118|ref|YP_004385546.1| 273 EEVLKLDPKDAQAWS 287
                                       6899**********6 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 ?    0.2   0.0       1.7   8.2e+02      23      37 ..      48      62 ..      43      67 .. 0.79
   2 ?   -2.0   0.0       8.5     4e+03      16      30 ..     116     130 ..     108     141 .. 0.54
   3 ?   -1.2   0.0       4.8   2.3e+03      14      34 ..     155     175 ..     155     178 .. 0.88
   4 ?   -0.7   0.0       3.3   1.6e+03      14      32 ..     189     207 ..     189     213 .. 0.76
   5 ?   -0.8   0.0       3.4   1.6e+03      19      40 ..     233     254 ..     232     258 .. 0.89
   6 !   14.6   0.1   5.4e-05     0.026      12      37 ..     260     285 ..     255     291 .. 0.94
   7 ?    1.8   0.0      0.55   2.6e+02      14      34 ..     296     316 ..     293     331 .. 0.82
   8 ?    4.9   0.0     0.057        27      10      30 ..     375     395 ..     373     400 .. 0.84
   9 ?   -0.4   0.0       2.6   1.2e+03      14      33 ..     417     436 ..     413     440 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.7
                                      HHHHHHHHTTS-HHH CS
                        Fis1_TPR_C 23 yvdalLeiEPenrQa 37
                                        d +L+++P+n+ a
  gi|330509118|ref|YP_004385546.1| 48 AYDEVLKLDPKNETA 62
                                      67899*******977 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.5
                                       -HHHHHHHHHHHHHH CS
                        Fis1_TPR_C  16 eYseArryvdalLei 30 
                                       + +eA++ ++  L+i
  gi|330509118|ref|YP_004385546.1| 116 RKDEAKEANEEALAI 130
                                       555666665555543 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.8
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                       lg+ +eA++    + ei+Pe 
  gi|330509118|ref|YP_004385546.1| 155 LGRWEEALQAYSKVTEIDPED 175
                                       68999*******999999986 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 3.3
                                       HT-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEP 32 
                                       +g+Y+e++  +d  +e  P
  gi|330509118|ref|YP_004385546.1| 189 IGRYNESLLALDKAIETIP 207
                                       5789998888888877666 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHHHTTS-HHHHHH CS
                        Fis1_TPR_C  19 eArryvdalLeiEPenrQaqsL 40 
                                       eA+ ++d l  + P+n+ a sL
  gi|330509118|ref|YP_004385546.1| 233 EALSLLDNLTDLYPQNKKAWSL 254
                                       799999***********99888 PP

  == domain 6  score: 14.6 bits;  conditional E-value: 5.4e-05
                                       HHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQa 37 
                                       +klg+Y+e+++  + +L+++P+  Qa
  gi|330509118|ref|YP_004385546.1| 260 AKLGRYNESLEAYEEVLKLDPKDAQA 285
                                       7************************9 PP

  == domain 7  score: 1.8 bits;  conditional E-value: 0.55
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                       +++Y+eA +  d  +e+ P+ 
  gi|330509118|ref|YP_004385546.1| 296 MKRYDEAQEAFDKAIELMPGD 316
                                       89***********99999875 PP

  == domain 8  score: 4.9 bits;  conditional E-value: 0.057
                                       HHHHHT-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLei 30 
                                       + + lg+Y+eAr+  d+ ++ 
  gi|330509118|ref|YP_004385546.1| 375 ALFNLGRYDEAREAYDQAIKT 395
                                       5678**********9998875 PP

  == domain 9  score: -0.4 bits;  conditional E-value: 2.6
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       lg+ +eA++  ++ Lei P 
  gi|330509118|ref|YP_004385546.1| 417 LGRNEEALEAFRQALEINPT 436
                                       56668999999999999995 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.2   0.00082      0.39      52     177 ..       5     135 ..       2     143 .. 0.82
   2 ?    2.8   0.0       0.2        96     150     180 ..     149     179 ..     143     183 .. 0.90
   3 ?    1.6   0.0      0.49   2.3e+02     160     180 ..     232     252 ..     222     258 .. 0.88
   4 ?   -1.1   0.0       3.3   1.6e+03     154     185 ..     260     291 ..     255     294 .. 0.81
   5 ?    3.2   0.0      0.16        74     105     180 ..     368     441 ..     347     447 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00082
                           Wzy_C_2  52 vlrvvalvlallglalllsilhdyq..rleqlyltsepneaalrevtnpkvwkdr..flfrayadllelgllplspe 124
                                       ++ v+ ++++++++     +  dy+  r+ +l+ +  ++ea+++ ++  k+  ++   l+r+ ++l  lg     + 
  gi|330509118|ref|YP_004385546.1|   5 LSTVMLALAMICTCTQAQENTTDYWmdRANVLIHKDLEEEAVFAYDEVLKLDPKNetALLRKASTLYTLGKEDEGQR 81 
                                       55677888889999999999999999999999999999999999998777766556799999999999999998888 PP

                           Wzy_C_2 125 nlaaklal.arklihlsPepavierlilslallGdedeAeqilararalfpeed 177
                                       ++++ l l +++l  +s  ++  ++ +++l +lG++deA+   ++a a+f  + 
  gi|330509118|ref|YP_004385546.1|  82 TYERALLLmEEDLKNTSQNAKAWQNKAIALSGLGRKDEAKEANEEALAIFNHSL 135
                                       88877665155666677788899*************************997665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.2
                           Wzy_C_2 150 ilslallGdedeAeqilararalfpeedakw 180
                                       ++ la+lG+ +eA+q ++++  + pe++ +w
  gi|330509118|ref|YP_004385546.1| 149 ADVLAFLGRWEEALQAYSKVTEIDPEDYGAW 179
                                       56799******************99999999 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.49
                           Wzy_C_2 160 deAeqilararalfpeedakw 180
                                        eA+  l+ +  l+p+++++w
  gi|330509118|ref|YP_004385546.1| 232 GEALSLLDNLTDLYPQNKKAW 252
                                       69999**************** PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3.3
                           Wzy_C_2 154 allGdedeAeqilararalfpeedakwvqlva 185
                                       a lG+  e +  ++++ +l p+++++w+  ++
  gi|330509118|ref|YP_004385546.1| 260 AKLGRYNESLEAYEEVLKLDPKDAQAWSTKAR 291
                                       56899999999999999999999999966555 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.16
                           Wzy_C_2 105 flfrayadllelgllplspenlaaklalarklihlsPepavierlilslallGdedeAeqilararalfpeedakw 180
                                         + + ++l++lg++   +e +++ ++ a+  + + P + + e  +l+  +lG+ +eA+   ++a  + p   ++w
  gi|330509118|ref|YP_004385546.1| 368 SMLLKGNALFNLGRYDEAREAYDQAIKTASPNSFHVPSAWIGEGKALL--ALGRNEEALEAFRQALEINPTLVEAW 441
                                       455566778888999999999999999999999999988888887665..58999999999998877766665555 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.3      0.16        77     198     258 ..      23      83 ..      18     105 .. 0.86
   2 ?    1.2   0.2      0.41   1.9e+02     214     256 ..      80     122 ..      44     124 .. 0.88
   3 !    9.0   0.0    0.0018      0.85     181     234 ..     122     175 ..      98     179 .. 0.86
   4 !    9.4   1.2    0.0013      0.62     161     239 ..     209     287 ..     197     313 .. 0.83
   5 ?    3.6   0.8     0.078        37     179     229 ..     344     394 ..     288     400 .. 0.69
   6 ?   -1.4   0.0       2.6   1.2e+03     210     232 ..     413     435 ..     404     442 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.16
                                       ---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHH CS
                        Coatomer_E 198 kstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsern 258
                                       ++t++  + +A v ++ +  eeA     e L+ d+k+e +L     +   lgk++e +  +
  gi|330509118|ref|YP_004385546.1|  23 ENTTDYWMDRANVLIHKDLEEEAVFAYDEVLKLDPKNETALLRKASTLYTLGKEDEGQRTY 83 
                                       5688899999*******************************************99877554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.41
                                       TT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 214 lgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                       +  ye A  l++e L+  ++++ +  N  +a   lg+ +e++e
  gi|330509118|ref|YP_004385546.1|  80 QRTYERALLLMEEDLKNTSQNAKAWQNKAIALSGLGRKDEAKE 122
                                       5679999999999999999999999999999999999988865 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0018
                                       THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT- CS
                        Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakd 234
                                       e  ++A+ if+   +k +++  l +gkA v   lgr+eeA +   +  + d++d
  gi|330509118|ref|YP_004385546.1| 122 EANEEALAIFNHSLDKDPENVSLWKGKADVLAFLGRWEEALQAYSKVTEIDPED 175
                                       56689***********************************99877766666665 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0013
                                       -TT-HHHHHHHHHHHHHH-TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHH CS
                        Coatomer_E 161 dedatltQLAqawvklavggekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeet 237
                                       d+d+ l     a v++  ++++i +A+ + ++l++ y+++      +     +lgry+e  +  +e L+ d+kd+++
  gi|330509118|ref|YP_004385546.1| 209 DNDEDLQAWSFAKVAVLHSSNQIGEALSLLDNLTDLYPQNKKAWSLMGYDMAKLGRYNESLEAYEEVLKLDPKDAQA 285
                                       7788888888899***************************99887777777789*******************9987 PP

                                       HH CS
                        Coatomer_E 238 Li 239
                                        +
  gi|330509118|ref|YP_004385546.1| 286 WS 287
                                       55 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.078
                                       -TTHHHHHHHHHHH..HHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                        Coatomer_E 179 ggekiqdAyyifqe..lsekykstplllngkAvvslllgryeeAeslLkeaLd 229
                                       +g+ +q A+ + +e  l++  ++ ++ll+g+A     lgry+eA +   +a++
  gi|330509118|ref|YP_004385546.1| 344 AGKAFQKALEVSDEalLNDSEQTSSMLLKGNALF--NLGRYDEAREAYDQAIK 394
                                       4566777777777766788888999999999986..56899999998888875 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 2.6
                                       HHHHTT-HHHHHHHHHHHHHH-T CS
                        Coatomer_E 210 vslllgryeeAeslLkeaLdkda 232
                                       + l+lgr eeA +  ++aL+ ++
  gi|330509118|ref|YP_004385546.1| 413 ALLALGRNEEALEAFRQALEINP 435
                                       4578999***********99765 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       4.9   2.3e+03      81     107 ..     182     208 ..     181     214 .. 0.86
   2 !   11.4   0.3   0.00055      0.26      41     106 ..     289     356 ..     267     366 .. 0.74
   3 ?    3.8   0.0      0.13        59      79     106 ..     408     435 ..     372     439 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.9
                             MAS20  81 lGEellaqgeeeeaaehlynAlkvcpq 107
                                       +GE l + g+++e++++l +A+  +p 
  gi|330509118|ref|YP_004385546.1| 182 KGEFLGMIGRYNESLLALDKAIETIPA 208
                                       688899999************998876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00055
                             MAS20  41 keeeeaekaekkk.kealeeakeelp.tdaeevekfFleevqlGEellaqgeeeeaaehlynAlkvcp 106
                                       k ++  e ++  + +ea ++a e +p +d +e+e+++   + +G+ l + g+ ++a +++ +Al v +
  gi|330509118|ref|YP_004385546.1| 289 KARQLVEMKRYDEaQEAFDKAIELMPgDDLKELEQIVQIWLDKGDALNETGNGDDAGKAFQKALEVSD 356
                                       222222222222256677777777999999***********************************976 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.13
                             MAS20  79 vqlGEellaqgeeeeaaehlynAlkvcp 106
                                       +  G  lla g++eea+e++ +Al + p
  gi|330509118|ref|YP_004385546.1| 408 IGEGKALLALGRNEEALEAFRQALEINP 435
                                       6789999*****************9876 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.11        52     218     291 ..     126     199 ..     119     203 .. 0.76
   2 ?    5.1   0.1      0.02       9.6     181     284 ..     227     334 ..     219     337 .. 0.72
   3 ?    2.5   0.0      0.12        57     219     289 ..     351     425 ..     348     430 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
                                       HHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                             ChAPs 218 davkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienALltL 291
                                       +a+ + n++l++++++++l + +a+ l    + e Al++ ++ +++ P ++  W +  +    ++ +++ Ll+L
  gi|330509118|ref|YP_004385546.1| 126 EALAIFNHSLDKDPENVSLWKGKADVLAFLGRWEEALQAYSKVTEIDPEDYGAWGRKGEFLGMIGRYNESLLAL 199
                                       67888888888888888888888888888888888888888888888888888877766666666666666665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.02
                                       HHT-HHHHHHHHHHHHTT-GG...GHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHH CS
                             ChAPs 181 ltkrydralellekLkeeepe...vvillarvllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAl 254
                                        ++++ +al+ll++L++ +p+   + +l+   +    +  ++++  +e l+ ++kda+  +++a  l++ k+++ A+
  gi|330509118|ref|YP_004385546.1| 227 SSNQIGEALSLLDNLTDLYPQnkkAWSLMGYDMAKLGRYNESLEAYEEVLKLDPKDAQAWSTKARQLVEMKRYDEAQ 303
                                       55566666666666665554311144454444444444556667777889999************************ PP

                                       HHHHHHHHH-TT.-HHHHHHHHHHHHHTT-H CS
                             ChAPs 255 evakravksaPs.efktWalLvkvYikledi 284
                                       e+ ++a+++ P  + k   ++v+++++ +d 
  gi|330509118|ref|YP_004385546.1| 304 EAFDKAIELMPGdDLKELEQIVQIWLDKGDA 334
                                       ***********62578888999999988875 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.12
                                       HHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHH.H-TT-HH...HHHHHHHHHHHTT-HHHHHH CS
                             ChAPs 219 avkllneeleeeekdaelLllqaefllskkkeelAlevakravk.saPsefk...tWalLvkvYikledienALl 289
                                       a+++  e+l +++++++ +ll+ + l +  +++ A e+ ++a+k ++P+ f+    W+   k  ++l+  e+AL 
  gi|330509118|ref|YP_004385546.1| 351 ALEVSDEALLNDSEQTSSMLLKGNALFNLGRYDEAREAYDQAIKtASPNSFHvpsAWIGEGKALLALGRNEEALE 425
                                       6666677774444443333355666777888999********983579*99633369988899999999998885 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.33   1.6e+02      86     122 ..      43      79 ..      27      96 .. 0.79
   2 ?    4.5   0.5     0.097        46      72     123 ..      70     121 ..      59     125 .. 0.76
   3 ?    4.2   0.0      0.12        55      84     123 ..     123     162 ..     116     167 .. 0.86
   4 ?    5.5   0.3     0.047        22      78     121 ..     258     301 ..     220     307 .. 0.80
   5 ?    2.8   0.1      0.32   1.5e+02      80     122 ..     343     385 ..     306     397 .. 0.74
   6 ?   -1.1   0.0       5.2   2.5e+03      67     116 ..     409     451 ..     405     465 .. 0.55

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.33
                                       HHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  86 rwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       + a+   + ++  dp+n++a   ka++l  lg++ e 
  gi|330509118|ref|YP_004385546.1|  43 EEAVFAYDEVLKLDPKNETALLRKASTLYTLGKEDEG 79 
                                       5566678899999*******************98875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.097
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  72 vlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       + +  ke+  +  y+ a+ l++  + ++++na+a + ka al  lg++ e+ 
  gi|330509118|ref|YP_004385546.1|  70 LYTLGKEDEGQRTYERALLLMEEDLKNTSQNAKAWQNKAIALSGLGRKDEAK 121
                                       334444444555599999999999**********************998875 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.12
                                       -HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  84 dyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                         + a+ + nh + +dpen +  + kad+l  lg+ +e+ 
  gi|330509118|ref|YP_004385546.1| 123 ANEEALAIFNHSLDKDPENVSLWKGKADVLAFLGRWEEAL 162
                                       55679999**************************998876 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.047
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
                   Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                                       + +k g y+ ++e  + ++  dp++a+a + ka+ l ++ +  e
  gi|330509118|ref|YP_004385546.1| 258 DMAKLGRYNESLEAYEEVLKLDPKDAQAWSTKARQLVEMKRYDE 301
                                       55677889999999999999999999999999999998887766 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.32
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  80 lkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                        + + ++ a+e+ + ++ +d+e+++   lk +al +lg+  e+
  gi|330509118|ref|YP_004385546.1| 343 DAGKAFQKALEVSDEALLNDSEQTSSMLLKGNALFNLGRYDEA 385
                                       3344599***************************999998775 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 5.2
                                       TSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  67 Ggaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleql 116
                                       G+ +++l+  +++ + + +r a+e+   lv+a        + k d+ ++l
  gi|330509118|ref|YP_004385546.1| 409 GEGKALLALGRNEEALEAFRQALEINPTLVEA-------WKGKGDSQKAL 451
                                       55555555555555555555666655555555.......33333333333 PP

>> DUF3775  Protein of unknown function (DUF3775)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.64     3e+02      16      39 ..     105     128 ..     101     139 .. 0.83
   2 ?   -2.1   0.0       8.8   4.1e+03      26      40 ..     339     353 ..     303     374 .. 0.58
   3 ?    7.9   0.0    0.0066       3.1      21      43 ..     375     397 ..     358     403 .. 0.90
   4 ?    1.1   0.0      0.83   3.9e+02      21      40 ..     413     432 ..     408     435 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.64
                           DUF3775  16 qaeLvALmwiGRgdfeaeewdeav 39 
                                       q + +AL  +GR d+++e  +ea+
  gi|330509118|ref|YP_004385546.1| 105 QNKAIALSGLGRKDEAKEANEEAL 128
                                       556799********9988777665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8.8
                           DUF3775  26 GRgdfeaeewdeave 40 
                                       G gd + + +++a+e
  gi|330509118|ref|YP_004385546.1| 339 GNGDDAGKAFQKALE 353
                                       444444444555554 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0066
                           DUF3775  21 ALmwiGRgdfeaeewdeaveeAr 43 
                                       AL+ +GR d++ e +d+a+++A 
  gi|330509118|ref|YP_004385546.1| 375 ALFNLGRYDEAREAYDQAIKTAS 397
                                       999*****************996 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.83
                           DUF3775  21 ALmwiGRgdfeaeewdeave 40 
                                       AL+ +GR +++ e + +a+e
  gi|330509118|ref|YP_004385546.1| 413 ALLALGRNEEALEAFRQALE 432
                                       99*********999999976 PP

>> DUF5388  Family of unknown function (DUF5388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.037        17      19      52 ..     105     138 ..     103     144 .. 0.89
   2 ?    3.1   0.0      0.24   1.1e+02      39      64 ..     303     329 ..     296     335 .. 0.83
   3 ?   -1.6   0.0         7   3.3e+03      23      52 ..     333     362 ..     330     368 .. 0.76
   4 ?    0.6   0.0       1.4   6.5e+02      23      43 ..     374     394 ..     372     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.037
                           DUF5388  19 rNklqALaaiGlaksqkeavkklveslidsLses 52 
                                       +Nk+ AL+ +G +  +kea ++++  +  sL+++
  gi|330509118|ref|YP_004385546.1| 105 QNKAIALSGLGRKDEAKEANEEALAIFNHSLDKD 138
                                       6*********************999888888765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.24
                           DUF5388  39 kklveslidsLsesdkkrfkkqlei.L 64 
                                       +++ ++ i+ ++ +d k+++++++i L
  gi|330509118|ref|YP_004385546.1| 303 QEAFDKAIELMPGDDLKELEQIVQIwL 329
                                       578899****************99844 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 7
                           DUF5388  23 qALaaiGlaksqkeavkklveslidsLses 52 
                                        AL+ +G +  + +a +k++e   + L ++
  gi|330509118|ref|YP_004385546.1| 333 DALNETGNGDDAGKAFQKALEVSDEALLND 362
                                       689999999999999999998877776555 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.4
                           DUF5388  23 qALaaiGlaksqkeavkklve 43 
                                       +AL ++G +  ++ea +++++
  gi|330509118|ref|YP_004385546.1| 374 NALFNLGRYDEAREAYDQAIK 394
                                       69*************999986 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 ?    4.4   0.0      0.06        28       1      15 [.     191     205 ..     191     209 .. 0.94
   2 ?   -2.7   0.1       9.5   4.5e+03       1      10 [.     264     273 ..     264     277 .. 0.78
   3 ?    1.1   0.0      0.64     3e+02       1      15 [.     298     312 ..     298     314 .. 0.93
   4 ?    1.3   0.0      0.54   2.6e+02       3      26 ..     349     373 ..     347     377 .. 0.80
   5 ?    1.3   0.0      0.55   2.6e+02       1      15 [.     381     395 ..     381     399 .. 0.91
   6 ?   -0.2   0.0       1.7   7.8e+02       3      15 ..     421     433 ..     419     434 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.06
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rY+e+L   +kAie+
  gi|330509118|ref|YP_004385546.1| 191 RYNESLLALDKAIET 205
                                       7************95 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.5
                                       -HHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvn 10 
                                       rY+e+Le  +
  gi|330509118|ref|YP_004385546.1| 264 RYNESLEAYE 273
                                       799**99765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.64
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rY+ea e  +kAie+
  gi|330509118|ref|YP_004385546.1| 298 RYDEAQEAFDKAIEL 312
                                       7************95 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHH.HHHHHTTB-TTHH CS
                          HTH_Bact   3 eeaLeqvnkAi.eiSirinsMsLlG 26 
                                       ++aLe+++ A+ + S +++sM L G
  gi|330509118|ref|YP_004385546.1| 349 QKALEVSDEALlNDSEQTSSMLLKG 373
                                       799*****99736788999998865 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.55
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rY+ea e  ++Ai++
  gi|330509118|ref|YP_004385546.1| 381 RYDEAREAYDQAIKT 395
                                       7************97 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   3 eeaLeqvnkAiei 15 
                                       eeaLe  ++A+ei
  gi|330509118|ref|YP_004385546.1| 421 EEALEAFRQALEI 433
                                       89********997 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 ?    2.9   0.0      0.17        80      48     106 ..      39      93 ..      33     112 .. 0.73
   2 ?    4.6   0.1     0.051        24      89     115 ..     117     143 ..     105     151 .. 0.89
   3 ?    4.0   0.5     0.076        36      11      77 ..     269     340 ..     259     350 .. 0.70
   4 ?    1.7   0.0       0.4   1.9e+02      47     100 ..     344     393 ..     341     401 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH CS
                       TOM20_plant  48 kqmiqdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqa 106
                                       k + ++a+  ++e l +dPk + al  +  a t ++   +d  e ++ +e+a  ++++ 
  gi|330509118|ref|YP_004385546.1|  39 KDLEEEAVFAYDEVLKLDPKNETAL--LRKASTLYTLGKED--EGQRTYERALLLMEED 93 
                                       56668999**************997..66777777665444..5566677776666555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.051
                                       HHHHHHHHHHHHHHHHHHHHH-TT-HH CS
                       TOM20_plant  89 eeeakenfekatqffqqavdedPdndl 115
                                       ++eake  e a  +f+++ d+dP+n  
  gi|330509118|ref|YP_004385546.1| 117 KDEAKEANEEALAIFNHSLDKDPENVS 143
                                       689*********************965 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.076
                                       HHHHHHHHHH-TT-HHHHHHHHHHHHHHHHHS-HHHH.....HHHHHHHHHHHHHHHHH-TT-HHHHHHHHH CS
                       TOM20_plant  11 rkdaeatykknPldadnllrWggallelsqfqsvaea.....kqmiqdaiskleeallidPkkhdalWcign 77 
                                        +  e+  k +P da+     +  l+e+ ++++ +ea       m  d +  le+ + i   k dal   gn
  gi|330509118|ref|YP_004385546.1| 269 LEAYEEVLKLDPKDAQAWSTKARQLVEMKRYDEAQEAfdkaiELMPGDDLKELEQIVQIWLDKGDALNETGN 340
                                       455677888888888888888888888888888777632222345567777788888887777777766666 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHH CS
                       TOM20_plant  47 akqmiqdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekat 100
                                       a +  q+a+   +eall d ++  ++ + gna    +++    +ea+e +++a 
  gi|330509118|ref|YP_004385546.1| 344 AGKAFQKALEVSDEALLNDSEQTSSMLLKGNALFNLGRY----DEAREAYDQAI 393
                                       556677888888899999999999999999998887776....46666666664 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   0.1       7.7   3.6e+03      12      35 ..      75      91 ..      63     109 .. 0.52
   2 ?    3.4   0.2      0.17        81       3      52 ..     100     148 ..      98     152 .. 0.81
   3 ?   -0.1   0.0       2.1     1e+03      18      29 ..     156     167 ..     155     169 .. 0.88
   4 ?    0.7   0.2       1.2   5.6e+02      19      50 ..     264     287 ..     257     295 .. 0.57
   5 ?    3.3   0.2      0.18        86       9      34 ..     288     313 ..     281     326 .. 0.83
   6 ?    1.8   0.0      0.53   2.5e+02       2      18 ..     349     365 ..     335     374 .. 0.77
   7 ?    5.7   0.2     0.033        16      17      32 ..     379     394 ..     378     397 .. 0.90
   8 ?    2.6   0.0      0.31   1.5e+02      19      33 ..     419     433 ..     410     455 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.7
                               MIT 12 veeDnagnyeeAlelYkealelLl 35
                                       e + +       + Y+ al l+ 
  gi|330509118|ref|YP_004385546.1| 75 KEDEGQ-------RTYERALLLME 91
                                      333334.......44555554444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.17
                               MIT   3 kAlelvkkAveeDnagnyeeAlelYkealelLlqalkekneerrellrek 52 
                                       +A +  +kA+ +   g  +eA e+ +eal ++++ l  k++e   l++ k
  gi|330509118|ref|YP_004385546.1| 100 NAKAWQNKAIALSGLGRKDEAKEANEEALAIFNHSLD-KDPENVSLWKGK 148
                                       5666778888888999999999999999999999998.777777777766 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.1
                               MIT  18 gnyeeAlelYke 29 
                                       g +eeAl++Y++
  gi|330509118|ref|YP_004385546.1| 156 GRWEEALQAYSK 167
                                       689*******85 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.2
                               MIT  19 nyeeAlelYkealelLlqalkekneerrellr 50 
                                               Y e+le   ++lk  ++++ +++ 
  gi|330509118|ref|YP_004385546.1| 264 R-------YNESLEAYEEVLK-LDPKDAQAWS 287
                                       4.......6666666666666.3445555555 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.18
                               MIT   9 kkAveeDnagnyeeAlelYkealelL 34 
                                       +kA ++ + + y+eA e++ +a+el+
  gi|330509118|ref|YP_004385546.1| 288 TKARQLVEMKRYDEAQEAFDKAIELM 313
                                       5666777779999**99999999985 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.53
                               MIT   2 dkAlelvkkAveeDnag 18 
                                       +kAle+  +A  +D+++
  gi|330509118|ref|YP_004385546.1| 349 QKALEVSDEALLNDSEQ 365
                                       67777777777777766 PP

  == domain 7  score: 5.7 bits;  conditional E-value: 0.033
                               MIT  17 agnyeeAlelYkeale 32 
                                        g y+eA e+Y +a++
  gi|330509118|ref|YP_004385546.1| 379 LGRYDEAREAYDQAIK 394
                                       689***********96 PP

  == domain 8  score: 2.6 bits;  conditional E-value: 0.31
                               MIT  19 nyeeAlelYkealel 33 
                                         eeAle++++ale+
  gi|330509118|ref|YP_004385546.1| 419 RNEEALEAFRQALEI 433
                                       457777777777774 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 ?    8.7   0.6    0.0027       1.3      92     161 ..      75     144 ..      51     173 .. 0.84
   2 ?    1.2   0.1      0.53   2.5e+02     142     193 ..     342     394 ..     283     406 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0027
                           DUF2225  92 tldeaiesYkLallcyelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelykeayekesfpveg 161
                                       + de+  +Y  all +e   ++ s+ Ak + + A   + ++ +++ k+  ++Al ++++++ k+ ++v+ 
  gi|330509118|ref|YP_004385546.1|  75 KEDEGQRTYERALLLMEEDLKNTSQNAKAWQNKAIALSGLGRKDEAKEANEEALAIFNHSLDKDPENVSL 144
                                       678999*******************************************************999887764 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.53
                           DUF2225 142 kkAlelykeayekesfpve.gideatvlYLiaeLerrlgnkeealrwlskvig 193
                                         A + +++a+e  ++      ++++ ++L ++    lg+++ea +++ + i+
  gi|330509118|ref|YP_004385546.1| 342 DDAGKAFQKALEVSDEALLnDSEQTSSMLLKGNALFNLGRYDEAREAYDQAIK 394
                                       33444455555444443331333444566666666666666666666666655 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2         1   4.9e+02      22      85 ..      26      87 ..      17      90 .. 0.74
   2 ?   -0.5   0.2       3.3   1.6e+03      18      61 ..      56     102 ..      48     120 .. 0.61
   3 ?   -0.5   0.3       3.5   1.6e+03      10      43 ..      96     129 ..      84     141 .. 0.48
   4 ?    2.6   0.0      0.36   1.7e+02       4      48 ..     124     168 ..     121     182 .. 0.83
   5 ?    0.0   0.1       2.4   1.1e+03       9      45 ..     197     238 ..     191     250 .. 0.60
   6 ?    9.4   1.0    0.0028       1.3       5      45 ..     266     306 ..     264     353 .. 0.88
   7 ?    2.3   0.0      0.47   2.2e+02      30      52 ..     412     434 ..     405     456 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1
                            TPR_20 22 ldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllkifealgsqdplvakyRrkL 85
                                       d  +d A++l+++  +eeA+ +  e+lk d k e+   rk+    +  lg++d+  ++y r L
  gi|330509118|ref|YP_004385546.1| 26 TDYWMDRANVLIHKDLEEEAVFAYDEVLKLDPKNETALLRKA--STLYTLGKEDEGQRTYERAL 87
                                      456788999999999999999999999998888888877775..56667777777666666655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.3
                            TPR_20  18 npddldarldlAlallaagryeeA...leqLleilkrdrkweddaar 61 
                                       +p++  a l  A  l+  g+++e     e+ l ++++d+k + + a+
  gi|330509118|ref|YP_004385546.1|  56 DPKNETALLRKASTLYTLGKEDEGqrtYERALLLMEEDLKNTSQNAK 102
                                       66666666666666666555544322256666666666666555555 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 3.5
                            TPR_20  10 eleaalaanpddldarldlAlallaagryeeAle 43 
                                       +  ++++a  +   a   l +++ a++ +eeAl+
  gi|330509118|ref|YP_004385546.1|  96 NTSQNAKAWQNKAIALSGLGRKDEAKEANEEALA 129
                                       3333333333333334444444444444454444 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.36
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleqLlei 48 
                                       +++ la +   l ++p+++ +    A++l+  gr eeAl++  ++
  gi|330509118|ref|YP_004385546.1| 124 NEEALAIFNHSLDKDPENVSLWKGKADVLAFLGRWEEALQAYSKV 168
                                       5667777888999*************************9976555 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 2.4
                            TPR_20   9 aeleaalaanpddldarldl.....AlallaagryeeAleqL 45 
                                        +l++a+++ p+d+d  l+        +l++ ++  eAl++L
  gi|330509118|ref|YP_004385546.1| 197 LALDKAIETIPADNDEDLQAwsfakVAVLHSSNQIGEALSLL 238
                                       566667776666665544321110145566666666776655 PP

  == domain 6  score: 9.4 bits;  conditional E-value: 0.0028
                            TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleqL 45 
                                       +++l++ e+ l+ +p+d +a    A++l++ +ry+eA e++
  gi|330509118|ref|YP_004385546.1| 266 NESLEAYEEVLKLDPKDAQAWSTKARQLVEMKRYDEAQEAF 306
                                       5789999***************************9886654 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.47
                            TPR_20  30 lallaagryeeAleqLleilkrd 52 
                                       +alla gr+eeAle++ + l+ +
  gi|330509118|ref|YP_004385546.1| 412 KALLALGRNEEALEAFRQALEIN 434
                                       67888999999999988777765 PP

>> GldM_N  GldM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       2.4   1.1e+03      28      51 ..      87     110 ..      77     117 .. 0.78
   2 ?    5.6   0.1     0.032        15      18      51 ..     118     151 ..     114     154 .. 0.92
   3 ?    0.8   1.1      0.94   4.4e+02      28      76 ..     269     315 ..     260     368 .. 0.59
   4 ?    4.0   0.0     0.099        47      23      52 ..     419     448 ..     415     454 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.4
                            GldM_N  28 yasleakaeenpekakewlekAke 51 
                                       +  +e+ ++++ ++ak+w +kA +
  gi|330509118|ref|YP_004385546.1|  87 LLLMEEDLKNTSQNAKAWQNKAIA 110
                                       556788889999999999999866 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.032
                            GldM_N  18 enasekNaalyasleakaeenpekakewlekAke 51 
                                       ++a+e N++++a ++ ++ ++pe++  w+ kA+ 
  gi|330509118|ref|YP_004385546.1| 118 DEAKEANEEALAIFNHSLDKDPENVSLWKGKADV 151
                                       67899**************************985 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.94
                            GldM_N  28 yasleakaeenpekakewlekAkevkkksdelynyiealKeeivkeagg 76 
                                       +++ e+ ++ +p+ a++w +kA ++ ++    y+  ++  ++ ++ + g
  gi|330509118|ref|YP_004385546.1| 269 LEAYEEVLKLDPKDAQAWSTKARQLVEMK--RYDEAQEAFDKAIELMPG 315
                                       55566777888999999999999988763..344444444444444444 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.099
                            GldM_N  23 kNaalyasleakaeenpekakewlekAkev 52 
                                       +N+++++++++++e np+ +++w+ k +  
  gi|330509118|ref|YP_004385546.1| 419 RNEEALEAFRQALEINPTLVEAWKGKGDSQ 448
                                       79**********************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.89u 0.34s 00:00:01.23 Elapsed: 00:00:00.59
# Mc/sec: 2373.13
//
Query:       gi|330509119|ref|YP_004385547.1|  [L=90]
Description: hypothetical protein MCON_3510 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.22   11.6   0.6       0.43   10.7   0.6    1.6  1  Plasmod_dom_1  Plasmodium protein of unknown function (Plasmo


Domain annotation for each model (and alignments):
>> Plasmod_dom_1  Plasmodium protein of unknown function (Plasmod_dom_1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   2.4e-05      0.43      10      25 ..       4      19 ..       2      48 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.4e-05
                     Plasmod_dom_1 10 ldifDnifidklidnn 25
                                       di+Dni++ kl dn+
  gi|330509119|ref|YP_004385547.1|  4 EDILDNIHSKKLNDNQ 19
                                      59**********9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 648.81
//
Query:       gi|330509120|ref|YP_004385548.1|  [L=420]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-60  198.5  20.3    3.1e-10   39.4   0.0   11.0 11  TPR_1            Tetratricopeptide repeat
    1.3e-52  171.7  18.5    1.9e-09   36.9   0.1   10.6 10  TPR_2            Tetratricopeptide repeat
    3.7e-45  151.3  29.1    7.4e-12   44.8   0.4    9.7 10  TPR_11           TPR repeat
    9.3e-42  137.8  17.7    2.8e-07   30.2   0.0    9.7 10  TPR_8            Tetratricopeptide repeat
      9e-36  122.3   2.5      4e-13   49.8   0.0    7.4  8  TPR_16           Tetratricopeptide repeat
    2.9e-30  102.3   8.3    6.6e-05   23.4   0.0    9.4  9  TPR_14           Tetratricopeptide repeat
    2.1e-29   99.8  13.4    8.3e-06   25.8   0.0   10.4  9  TPR_17           Tetratricopeptide repeat
    3.1e-28   97.9  16.5    6.7e-08   32.7   0.0    8.0  8  TPR_12           Tetratricopeptide repeat
    1.6e-26   92.6   5.2    1.6e-06   28.5   0.1    5.7  5  TPR_19           Tetratricopeptide repeat
    2.9e-22   78.6   0.0    9.1e-07   28.9   0.0    5.0  5  TPR_9            Tetratricopeptide repeat
    1.1e-16   60.8   0.8    0.00091   19.4   0.0    5.7  5  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    4.3e-15   56.0  13.0     0.0071   16.4   0.3    6.4  6  DUF3856          Domain of Unknown Function (DUF3856)
    1.5e-14   53.3  17.5     0.0048   16.7   0.1    8.2  8  TPR_10           Tetratricopeptide repeat
    2.3e-14   52.3   3.5       0.05   13.7   0.0    7.9  8  TPR_7            Tetratricopeptide repeat
      1e-13   50.9  12.3       0.43   11.3   0.0    8.3  8  TPR_6            Tetratricopeptide repeat
      2e-08   34.0   4.3       0.53   10.3   0.0    6.1  6  TPR_3            Tetratricopeptide repeat
    1.7e-07   31.8   5.5     0.0027   18.1   0.0    4.9  5  BTAD             Bacterial transcriptional activator domain
    6.2e-07   29.4  21.2        1.2    9.2   0.1    7.6  8  MIT              MIT (microtubule interacting and transport) 
      2e-06   27.9   0.2         10    6.4   0.0    6.0  6  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
    3.4e-06   26.3   1.7        1.2    7.9   0.0    3.9  4  NARP1            NMDA receptor-regulated protein 1
    4.2e-06   26.8   3.4       0.31   11.1   0.1    4.1  3  SRP_TPR_like     Putative TPR-like repeat
    6.8e-06   25.4   5.0       0.93    9.0   0.0    5.8  6  SHNi-TPR         SHNi-TPR
    1.5e-05   25.0   5.5        3.4    7.8   0.0    6.1  6  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    8.3e-05   23.1   2.8       0.14   12.6   0.1    4.7  5  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    0.00075   18.3   0.3     0.0061   15.3   0.1    2.3  2  DUF3808          Protein of unknown function (DUF3808)
     0.0017   18.7   0.7        9.5    6.6   0.0    4.2  4  TPR_20           Tetratricopeptide repeat
     0.0026   17.5  13.7        1.3    8.7   0.1    6.5  7  TPR_21           Tetratricopeptide repeat-like domain
      0.004   17.3   1.4         47    4.5   0.0    5.9  5  PPR              PPR repeat
     0.0096   15.7   4.2       0.43   10.3   0.1    3.3  4  TOM20_plant      Plant specific mitochondrial import receptor
  ------ inclusion threshold ------
      0.012   15.4   6.4       0.16   11.6   0.3    3.8  3  DUF2225          Uncharacterized protein conserved in bacteri
      0.055   12.9   0.3        1.9    7.8   0.1    3.3  3  Coatomer_E       Coatomer epsilon subunit
      0.063   12.9   2.0        4.6    6.9   0.0    3.3  3  UFC1             Ubiquitin-fold modifier-conjugating enzyme 1
      0.071   13.2   0.7         58    3.9   0.0    4.6  4  ANAPC5           Anaphase-promoting complex subunit 5
       0.18   11.4  13.6         18    5.0   0.1    6.5  7  HTH_Bact         Helix-turn-helix bacterial domain
        1.6    7.8   7.6       0.45    9.6   1.6    2.7  3  NRDE-2           NRDE-2, necessary for RNA interference


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 !   32.6   0.2   8.7e-11   4.5e-08       2      34 .]      45      77 ..      44      77 .. 0.96
   2 ?    4.4   0.1     0.072        37       1      30 [.      78     107 ..      78     108 .. 0.94
   3 ?    4.8   0.0     0.051        26       1      19 [.     119     137 ..     119     141 .. 0.82
   4 !   10.2   0.1     0.001      0.53      19      34 .]     144     159 ..     143     159 .. 0.95
   5 !   21.1   0.0   3.6e-07   0.00018       3      33 ..     162     192 ..     160     193 .. 0.94
   6 ?   -0.1   0.1       1.9   9.7e+02       1      12 [.     195     206 ..     195     207 .. 0.89
   7 !   27.5   0.0   3.5e-09   1.8e-06       3      33 ..     237     267 ..     235     268 .. 0.94
   8 !   17.4   0.1   5.5e-06    0.0028       4      34 .]     275     305 ..     274     305 .. 0.94
   9 !   36.4   0.1   5.6e-12   2.9e-09       7      34 .]     312     339 ..     308     339 .. 0.96
  10 !   39.4   0.0   6.1e-13   3.1e-10       3      33 ..     342     372 ..     340     373 .. 0.95
  11 !    8.1   0.2    0.0046       2.4       1      30 [.     387     416 ..     387     416 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 8.7e-11
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                      + ++++G+ ++ +g y+eA+++y+ A+++nP+n
  gi|330509120|ref|YP_004385548.1| 45 EYWCQKGQELQVNGSYEEAIQAYNMAIQINPEN 77
                                      57*****************************97 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.072
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a+a+ +++ +  +  k+deA   ye ALe+
  gi|330509120|ref|YP_004385548.1|  78 ADAWLGKAGISSRIDKHDEAKREYEIALEI 107
                                       7999999999999***************97 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.051
                                       HHHHHHHHHHHHHTT-HHH CS
                             TPR_1   1 akalynlGnayfklgkyde 19 
                                       a a+ n+G+a+  lg+  e
  gi|330509120|ref|YP_004385548.1| 119 ASAWINKGVALSCLGRDIE 137
                                       78*********99998555 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHSTTH CS
                             TPR_1  19 eAleyyekALelnPnn 34 
                                       +Ale y++AL+ nPn+
  gi|330509120|ref|YP_004385548.1| 144 KALEIYNQALQKNPND 159
                                       8*************97 PP

  == domain 5  score: 21.1 bits;  conditional E-value: 3.6e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       ++ n+++++  +g++++A+e+y+k++e  P+
  gi|330509120|ref|YP_004385548.1| 162 TWENKALVLVGMGRWEDAVEAYDKVIEFSPS 192
                                       799************************9996 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayf 12 
                                       a+a+  ++ +y 
  gi|330509120|ref|YP_004385548.1| 195 AYAWIDKAICYS 206
                                       79********96 PP

  == domain 7  score: 27.5 bits;  conditional E-value: 3.5e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       ++ ++G  +    +y+eA+++y+kA+eln +
  gi|330509120|ref|YP_004385548.1| 237 IWSGIGKSLSTASRYEEAIKAYDKAIELNSK 267
                                       699**************************87 PP

  == domain 8  score: 17.4 bits;  conditional E-value: 5.5e-06
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                       + ++++a++ lg+y+e + +++ ALe  P++
  gi|330509120|ref|YP_004385548.1| 275 WSGKAYALYALGRYNESINAFDIALEMMPEF 305
                                       899***********************98875 PP

  == domain 9  score: 36.4 bits;  conditional E-value: 5.6e-12
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnPnn 34 
                                       +Gna+f+ g+y+eA+++y+kA+ lnP++
  gi|330509120|ref|YP_004385548.1| 312 KGNALFQIGRYEEAIKAYDKAIALNPKD 339
                                       7*************************86 PP

  == domain 10  score: 39.4 bits;  conditional E-value: 6.1e-13
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       a++++G++++++g+y+eA+e+y++A++  P 
  gi|330509120|ref|YP_004385548.1| 342 AWNGKGMVLYNMGRYEEAIEDYDRAIKFAPF 372
                                       9**************************9996 PP

  == domain 11  score: 8.1 bits;  conditional E-value: 0.0046
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a a+ ++Gna+  lg+  e +++y+kA el
  gi|330509120|ref|YP_004385548.1| 387 ATAWTGKGNALKALGRQSEMEAAYSKAKEL 416
                                       679*************99988888888776 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   9.5e-08   4.9e-05       2      34 .]      45      77 ..      44      77 .. 0.97
   2 ?    6.8   0.1     0.016       8.4       1      30 [.      78     107 ..      78     110 .. 0.87
   3 ?    3.8   0.0      0.14        74       1      22 [.     119     140 ..     119     141 .. 0.89
   4 !    9.5   0.0    0.0022       1.1      19      34 .]     144     159 ..     142     159 .. 0.94
   5 !   17.7   0.0   5.4e-06    0.0028       3      32 ..     162     191 ..     160     193 .. 0.93
   6 !   21.9   0.0   2.4e-07   0.00012       3      33 ..     237     267 ..     235     268 .. 0.91
   7 !   20.4   0.1   7.3e-07   0.00037       4      33 ..     275     304 ..     272     305 .. 0.93
   8 !   36.9   0.1   3.7e-12   1.9e-09       2      34 .]     307     339 ..     306     339 .. 0.95
   9 !   32.0   0.0   1.4e-10     7e-08       3      33 ..     342     372 ..     340     373 .. 0.94
  10 ?    2.9   0.2      0.28   1.4e+02       1      29 [.     387     415 ..     387     417 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 9.5e-08
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPnn 34
                                      e++++ G+ +  +g yeeA++a++ A++++P+n
  gi|330509120|ref|YP_004385548.1| 45 EYWCQKGQELQVNGSYEEAIQAYNMAIQINPEN 77
                                      79*****************************97 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a+a+   + +  + ++++eA++ +e Ale+
  gi|330509120|ref|YP_004385548.1|  78 ADAWLGKAGISSRIDKHDEAKREYEIALEI 107
                                       678888888888999*************98 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.14
                             TPR_2   1 aealynlGlayyklgdyeeAle 22 
                                       a a+ n G a+  lg+  eA e
  gi|330509120|ref|YP_004385548.1| 119 ASAWINKGVALSCLGRDIEAFE 140
                                       679*************999976 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0022
                             TPR_2  19 eAleafekAleldPnn 34 
                                       +Ale +++Al+ +Pn+
  gi|330509120|ref|YP_004385548.1| 144 KALEIYNQALQKNPND 159
                                       8*************97 PP

  == domain 5  score: 17.7 bits;  conditional E-value: 5.4e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                        + n +l++  +g++e+A+ea++k++e  P
  gi|330509120|ref|YP_004385548.1| 162 TWENKALVLVGMGRWEDAVEAYDKVIEFSP 191
                                       6999***********************998 PP

  == domain 6  score: 21.9 bits;  conditional E-value: 2.4e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       ++  +G+++  + +yeeA++a++kA+el+ +
  gi|330509120|ref|YP_004385548.1| 237 IWSGIGKSLSTASRYEEAIKAYDKAIELNSK 267
                                       699999**********************976 PP

  == domain 7  score: 20.4 bits;  conditional E-value: 7.3e-07
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                       +   ++a+y+lg+y+e ++af+ Ale  P+
  gi|330509120|ref|YP_004385548.1| 275 WSGKAYALYALGRYNESINAFDIALEMMPE 304
                                       8889***********************997 PP

  == domain 8  score: 36.9 bits;  conditional E-value: 3.7e-12
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +++ + G+a+++ g+yeeA++a++kA++l+P++
  gi|330509120|ref|YP_004385548.1| 307 DIWDWKGNALFQIGRYEEAIKAYDKAIALNPKD 339
                                       789****************************86 PP

  == domain 9  score: 32.0 bits;  conditional E-value: 1.4e-10
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a++  G+++y++g+yeeA+e++++A++ +P 
  gi|330509120|ref|YP_004385548.1| 342 AWNGKGMVLYNMGRYEEAIEDYDRAIKFAPF 372
                                       8**************************9995 PP

  == domain 10  score: 2.9 bits;  conditional E-value: 0.28
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAle 29 
                                       a a+   G+a+ +lg+  e ++a+ kA e
  gi|330509120|ref|YP_004385548.1| 387 ATAWTGKGNALKALGRQSEMEAAYSKAKE 415
                                       679999*********99887777777766 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.6   1.7e-10   8.9e-08       7      32 ..      57      82 ..      51      85 .. 0.91
   2 ?    3.8   0.1     0.092        47       9      38 ..     100     129 ..      96     133 .. 0.88
   3 !   12.7   0.1   0.00015     0.075      12      42 .]     144     174 ..     143     174 .. 0.93
   4 !   16.4   0.0     1e-05    0.0052       7      28 ..     173     194 ..     167     198 .. 0.88
   5 ?   -1.0   0.0       2.9   1.5e+03      11      26 ..     213     228 ..     212     230 .. 0.86
   6 !   21.6   0.0   2.4e-07   0.00013       9      29 ..     250     270 ..     242     274 .. 0.90
   7 !   24.3   0.0   3.5e-08   1.8e-05       2      40 ..     280     318 ..     279     319 .. 0.96
   8 !   44.8   0.4   1.4e-14   7.4e-12       1      42 []     313     354 ..     313     354 .. 0.99
   9 !   23.4   0.1   6.9e-08   3.6e-05       3      29 ..     349     375 ..     347     380 .. 0.86
  10 ?   -0.1   0.1       1.5   7.5e+02       1      20 [.     394     413 ..     386     416 .. 0.64

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.7e-10
                            TPR_11  7 qGkyeeAieaYkkAlkldPdnaeayy 32
                                       G yeeAi+aY+ A++++P+na+a++
  gi|330509120|ref|YP_004385548.1| 57 NGSYEEAIQAYNMAIQINPENADAWL 82
                                      69**********************97 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.092
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       +ye A+e ++k l+ +++na+a+ n G+a+
  gi|330509120|ref|YP_004385548.1| 100 EYEIALEILNKRLEENSQNASAWINKGVAL 129
                                       688899999999999************997 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00015
                            TPR_11  12 eAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +A+e Y++Al+ +P++ + + n +l++  +G
  gi|330509120|ref|YP_004385548.1| 144 KALEIYNQALQKNPNDGNTWENKALVLVGMG 174
                                       799********************99998877 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 1e-05
                            TPR_11   7 qGkyeeAieaYkkAlkldPdna 28 
                                        G++e+A+eaY k ++++P+ a
  gi|330509120|ref|YP_004385548.1| 173 MGRWEDAVEAYDKVIEFSPSKA 194
                                       7******************988 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 2.9
                            TPR_11  11 eeAieaYkkAlkldPd 26 
                                       +e+i+a+ +A +l P+
  gi|330509120|ref|YP_004385548.1| 213 NESIAAWITAAQLIPT 228
                                       799*******999776 PP

  == domain 6  score: 21.6 bits;  conditional E-value: 2.4e-07
                            TPR_11   9 kyeeAieaYkkAlkldPdnae 29 
                                       +yeeAi+aY kA++l++++++
  gi|330509120|ref|YP_004385548.1| 250 RYEEAIKAYDKAIELNSKDVS 270
                                       8****************9987 PP

  == domain 7  score: 24.3 bits;  conditional E-value: 3.5e-08
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       +a+y++G+y+e+i+a+  Al+  P++++++ + G+a+++
  gi|330509120|ref|YP_004385548.1| 280 YALYALGRYNESINAFDIALEMMPEFPDIWDWKGNALFQ 318
                                       79**********************************997 PP

  == domain 8  score: 44.8 bits;  conditional E-value: 1.4e-14
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+a+++ G+yeeAi+aY kA++l+P++ +a+++ G ++y++G
  gi|330509120|ref|YP_004385548.1| 313 GNALFQIGRYEEAIKAYDKAIALNPKDGSAWNGKGMVLYNMG 354
                                       9***************************************98 PP

  == domain 9  score: 23.4 bits;  conditional E-value: 6.9e-08
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnae 29 
                                       ++y  G+yeeAie+Y +A+k+ P n++
  gi|330509120|ref|YP_004385548.1| 349 VLYNMGRYEEAIEDYDRAIKFAPFNVT 375
                                       7999****************9997765 PP

  == domain 10  score: -0.1 bits;  conditional E-value: 1.5
                            TPR_11   1 GdayyeqGkyeeAieaYkkA 20 
                                       G+a+ ++G+  e  +aY+kA
  gi|330509120|ref|YP_004385548.1| 394 GNALKALGRQSEMEAAYSKA 413
                                       66666666666655555555 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   1.3e-06   0.00064       2      34 .]      45      77 ..      44      77 .. 0.96
   2 ?    5.8   0.1     0.037        19       1      30 [.      78     107 ..      78     107 .. 0.93
   3 ?    4.4   0.0       0.1        54       1      31 [.     119     149 ..     119     151 .. 0.92
   4 ?    0.9   0.1       1.3   6.9e+02      19      33 ..     144     158 ..     137     159 .. 0.86
   5 !   12.8   0.0    0.0002       0.1       3      33 ..     162     192 ..     160     193 .. 0.94
   6 !   19.4   0.1   1.6e-06   0.00083       3      34 .]     237     268 ..     235     268 .. 0.90
   7 !    9.3   0.0    0.0028       1.5       4      30 ..     275     301 ..     273     305 .. 0.86
   8 !   30.2   0.0   5.4e-10   2.8e-07       2      34 .]     307     339 ..     306     339 .. 0.95
   9 !   27.7   0.0   3.6e-09   1.9e-06       2      33 ..     341     372 ..     340     373 .. 0.94
  10 !   12.2   0.3   0.00032      0.16       1      30 [.     387     416 ..     387     416 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-06
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      e+++++g+ ++  g yeeA+++y+ a++++p+n
  gi|330509120|ref|YP_004385548.1| 45 EYWCQKGQELQVNGSYEEAIQAYNMAIQINPEN 77
                                      79*****************************86 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.037
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+a++ ++ i +   +++eAk  ye ale+
  gi|330509120|ref|YP_004385548.1|  78 ADAWLGKAGISSRIDKHDEAKREYEIALEI 107
                                       6899*********************99886 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.1
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a+a+ n+g +++ lg+  eA e+  kale+ 
  gi|330509120|ref|YP_004385548.1| 119 ASAWINKGVALSCLGRDIEAFEARGKALEIY 149
                                       689********************99999986 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHH CS
                             TPR_8  19 eAkeyyekaleldpd 33 
                                       +A e y++al+ +p+
  gi|330509120|ref|YP_004385548.1| 144 KALEIYNQALQKNPN 158
                                       7999*****987776 PP

  == domain 5  score: 12.8 bits;  conditional E-value: 0.0002
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        + n+++++  +g+ e A+e+y k++e +p+
  gi|330509120|ref|YP_004385548.1| 162 TWENKALVLVGMGRWEDAVEAYDKVIEFSPS 192
                                       699************************9996 PP

  == domain 6  score: 19.4 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++  +g+ +++  +yeeA+++y ka+el+ ++
  gi|330509120|ref|YP_004385548.1| 237 IWSGIGKSLSTASRYEEAIKAYDKAIELNSKD 268
                                       6778999999999***************9875 PP

  == domain 7  score: 9.3 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekalel 30 
                                       +  +++++  lg+y+e++ ++  ale+
  gi|330509120|ref|YP_004385548.1| 275 WSGKAYALYALGRYNESINAFDIALEM 301
                                       55689****************988887 PP

  == domain 8  score: 30.2 bits;  conditional E-value: 5.4e-10
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +++ ++g+++++ g+yeeA+++y ka+ l+p++
  gi|330509120|ref|YP_004385548.1| 307 DIWDWKGNALFQIGRYEEAIKAYDKAIALNPKD 339
                                       68999**************************96 PP

  == domain 9  score: 27.7 bits;  conditional E-value: 3.6e-09
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a++ +g+++ ++g+yeeA+e y +a++ +p 
  gi|330509120|ref|YP_004385548.1| 341 SAWNGKGMVLYNMGRYEEAIEDYDRAIKFAPF 372
                                       59***************************997 PP

  == domain 10  score: 12.2 bits;  conditional E-value: 0.00032
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a a+  +g++++ lg+  e++++y ka el
  gi|330509120|ref|YP_004385548.1| 387 ATAWTGKGNALKALGRQSEMEAAYSKAKEL 416
                                       679************************876 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.3e-06    0.0032       2      52 ..      49      96 ..      48      97 .. 0.88
   2 ?    6.9   0.0     0.019       9.7      11      49 ..      99     134 ..      93     159 .. 0.85
   3 !   12.6   0.0   0.00031      0.16      15      66 ..     144     192 ..     142     194 .. 0.91
   4 !   11.4   0.0   0.00077      0.39       3      45 ..     166     206 ..     164     224 .. 0.85
   5 !   10.4   0.0    0.0016      0.82       4      31 ..     242     266 ..     236     272 .. 0.64
   6 !   23.5   0.0   1.3e-07   6.6e-05       3      52 ..     278     324 ..     276     324 .. 0.95
   7 !   49.8   0.0   7.9e-16     4e-13       4      67 ..     313     373 ..     312     374 .. 0.97
   8 ?    2.4   0.4      0.48   2.5e+02      33      60 ..     386     413 ..     377     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.3e-06
                            TPR_16  2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlae 52
                                      ++++++  +g y++A+ a++ a+  +   P++a+A+l+++ +  r   ++e
  gi|330509120|ref|YP_004385548.1| 49 QKGQELQVNGSYEEAIQAYNMAIQIN---PENADAWLGKAGISSRIDKHDE 96
                                      57999*********************...**********988776666665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.019
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgr 49 
                                       ++y+ A++ l+  l+ +   +++a A+ ++g+a+  +gr
  gi|330509120|ref|YP_004385548.1|  99 REYEIALEILNKRLEEN---SQNASAWINKGVALSCLGR 134
                                       679**************...*************985554 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00031
                            TPR_16  15 dAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       +A++ +++al ++   P +   + ++++++   gr+++A+++y++ ++ +p+
  gi|330509120|ref|YP_004385548.1| 144 KALEIYNQALQKN---PNDGNTWENKALVLVGMGRWEDAVEAYDKVIEFSPS 192
                                       59999********...99999*********999**********999998886 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00077
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaal 45 
                                       +a+ ++  g+++dA++a++ +++  p  + aa A+  ++ ++ 
  gi|330509120|ref|YP_004385548.1| 166 KALVLVGMGRWEDAVEAYDKVIEFSP--SKAAYAWIDKAICYS 206
                                       79999****************99995..449999988888886 PP

  == domain 5  score: 10.4 bits;  conditional E-value: 0.0016
                            TPR_16   4 araalragdyddAaaaleaalkrdpssP 31 
                                       ++++  a +y++A++a++ a++++   +
  gi|330509120|ref|YP_004385548.1| 242 GKSLSTASRYEEAIKAYDKAIELN---S 266
                                       445556677777777777777776...3 PP

  == domain 6  score: 23.5 bits;  conditional E-value: 1.3e-07
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlae 52 
                                       +a+a++++g+y + ++a+++al++    P+ ++ + ++g+a+++ gr++e
  gi|330509120|ref|YP_004385548.1| 278 KAYALYALGRYNESINAFDIALEMM---PEFPDIWDWKGNALFQIGRYEE 324
                                       699**********************...88888***************96 PP

  == domain 7  score: 49.8 bits;  conditional E-value: 7.9e-16
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++a+++ g+y++A++a++ a++++   P +  A++++g +++  gr++eA++ y++a++ ap++
  gi|330509120|ref|YP_004385548.1| 313 GNALFQIGRYEEAIKAYDKAIALN---PKDGSAWNGKGMVLYNMGRYEEAIEDYDRAIKFAPFN 373
                                       89**********************...**********************************986 PP

  == domain 8  score: 2.4 bits;  conditional E-value: 0.48
                            TPR_16  33 aaeAllllgdaalrqgrlaeAaalyraa 60 
                                        a A+ ++g+a+ ++gr  e +a+y +a
  gi|330509120|ref|YP_004385548.1| 386 SATAWTGKGNALKALGRQSEMEAAYSKA 413
                                       799*************998888888776 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.6e-06    0.0013      13      42 ..      56      85 ..      45      86 .. 0.86
   2 ?    6.6   0.0     0.033        17      13      42 ..      97     126 ..      93     129 .. 0.87
   3 !    8.9   0.0    0.0057       2.9      17      42 ..     142     167 ..     127     169 .. 0.80
   4 !    9.5   0.0    0.0038         2       8      41 ..     167     201 ..     165     204 .. 0.82
   5 !   10.6   0.0    0.0017      0.86       6      36 ..     240     270 ..     236     276 .. 0.83
   6 !    9.7   0.0    0.0031       1.6       7      38 ..     278     309 ..     272     313 .. 0.87
   7 !   23.4   0.0   1.3e-07   6.6e-05       1      38 [.     306     343 ..     306     348 .. 0.92
   8 !   10.6   0.0    0.0016      0.83       8      34 ..     347     373 ..     342     383 .. 0.83
   9 ?    2.1   0.1      0.87   4.5e+02       3      27 ..     389     413 ..     387     417 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.6e-06
                            TPR_14 13 alGdpdeAiallrralalaPddaeawllla 42
                                       +G ++eAi++++ a++ +P++a+awl  a
  gi|330509120|ref|YP_004385548.1| 56 VNGSYEEAIQAYNMAIQINPENADAWLGKA 85
                                      5799**********************9765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.033
                            TPR_14  13 alGdpdeAiallrralalaPddaeawllla 42 
                                       a ++++ A+++l+++l+ + ++a aw+  +
  gi|330509120|ref|YP_004385548.1|  97 AKREYEIALEILNKRLEENSQNASAWINKG 126
                                       6678999*******************9765 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0057
                            TPR_14  17 pdeAiallrralalaPddaeawllla 42 
                                         +A++++++al+++P+d  +w   a
  gi|330509120|ref|YP_004385548.1| 142 RGKALEIYNQALQKNPNDGNTWENKA 167
                                       568***************99997665 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0038
                            TPR_14   8 aeallalGdpdeAiallrralalaP.ddaeawlll 41 
                                       a +l   G++++A+++++++++  P + a aw+  
  gi|330509120|ref|YP_004385548.1| 167 ALVLVGMGRWEDAVEAYDKVIEFSPsKAAYAWIDK 201
                                       5678889******************4466788765 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.0017
                            TPR_14   6 alaeallalGdpdeAiallrralalaPddae 36 
                                        +++ l ++ +++eAi+++++a++l+ +d  
  gi|330509120|ref|YP_004385548.1| 240 GIGKSLSTASRYEEAIKAYDKAIELNSKDVS 270
                                       5678899999**************9988765 PP

  == domain 6  score: 9.7 bits;  conditional E-value: 0.0031
                            TPR_14   7 laeallalGdpdeAiallrralalaPddaeaw 38 
                                        a al+alG++ e+i++++ al+  P+++++w
  gi|330509120|ref|YP_004385548.1| 278 KAYALYALGRYNESINAFDIALEMMPEFPDIW 309
                                       5899*******************888888877 PP

  == domain 7  score: 23.4 bits;  conditional E-value: 1.3e-07
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       p+ +   + al++ G+++eAi+++++a+al+P+d  aw
  gi|330509120|ref|YP_004385548.1| 306 PDIWDWKGNALFQIGRYEEAIKAYDKAIALNPKDGSAW 343
                                       56788899**************************9999 PP

  == domain 8  score: 10.6 bits;  conditional E-value: 0.0016
                            TPR_14   8 aeallalGdpdeAiallrralalaPdd 34 
                                       + +l++ G+++eAi+ ++ra++ aP +
  gi|330509120|ref|YP_004385548.1| 347 GMVLYNMGRYEEAIEDYDRAIKFAPFN 373
                                       66899*****************99955 PP

  == domain 9  score: 2.1 bits;  conditional E-value: 0.87
                            TPR_14   3 allalaeallalGdpdeAiallrra 27 
                                       a+   + al alG+  e++a++ +a
  gi|330509120|ref|YP_004385548.1| 389 AWTGKGNALKALGRQSEMEAAYSKA 413
                                       56667899*************9987 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       1.2   6.3e+02      15      34 .]      46      65 ..      42      65 .. 0.90
   2 !   13.6   0.0   0.00013     0.066       2      33 ..      67      98 ..      66      99 .. 0.91
   3 !   10.3   0.0    0.0015      0.77       6      32 ..     112     138 ..     107     140 .. 0.88
   4 !   17.5   0.0   7.5e-06    0.0038       2      33 ..     149     180 ..     148     181 .. 0.94
   5 ?    6.8   0.0      0.02        10       1      24 [.     182     206 ..     182     218 .. 0.88
   6 !   10.4   0.1    0.0014       0.7       1      31 [.     257     290 ..     257     292 .. 0.91
   7 ?    6.8   0.0     0.019       9.8       6      34 .]     299     327 ..     295     327 .. 0.89
   8 !   25.8   0.0   1.6e-08   8.3e-06       1      34 []     328     361 ..     328     361 .. 0.96
   9 ?    4.0   0.1      0.16        80      12      28 ..     384     402 ..     362     408 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.2
                            TPR_17 15 aynnLAelllknGdlmtArq 34
                                       ++++++ l  nG +++A+q
  gi|330509120|ref|YP_004385548.1| 46 YWCQKGQELQVNGSYEEAIQ 65
                                      69999999**********97 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00013
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      y  a++++P nada+  +A + +++ ++++A+
  gi|330509120|ref|YP_004385548.1| 67 YNMAIQINPENADAWLGKAGISSRIDKHDEAK 98
                                      888****************9999999999996 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0015
                            TPR_17   6 leldPnnadaynnLAelllknGdlmtA 32 
                                       le +  na a+ n++++l+ +G+  +A
  gi|330509120|ref|YP_004385548.1| 112 LEENSQNASAWINKGVALSCLGRDIEA 138
                                       899****************99998777 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 7.5e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y +al+++Pn+ + + n+A +l   G++++A+
  gi|330509120|ref|YP_004385548.1| 149 YNQALQKNPNDGNTWENKALVLVGMGRWEDAV 180
                                       99*********************999999997 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.02
                            TPR_17   1 lylkaleldPnn.adaynnLAelll 24 
                                       +y k++e  P+  a+a+  +A +++
  gi|330509120|ref|YP_004385548.1| 182 AYDKVIEFSPSKaAYAWIDKAICYS 206
                                       59*********88**********98 PP

  == domain 6  score: 10.4 bits;  conditional E-value: 0.0014
                            TPR_17   1 lylkaleldPnn...adaynnLAelllknGdlmt 31 
                                       +y ka+el+ ++   ++ +  +A++l+ +G++ +
  gi|330509120|ref|YP_004385548.1| 257 AYDKAIELNSKDvssWPNWSGKAYALYALGRYNE 290
                                       59**********99999999******99999976 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.019
                            TPR_17   6 leldPnnadaynnLAelllknGdlmtArq 34 
                                       le  P  +d +  ++++l ++G++++A++
  gi|330509120|ref|YP_004385548.1| 299 LEMMPEFPDIWDWKGNALFQIGRYEEAIK 327
                                       5666999********************85 PP

  == domain 8  score: 25.8 bits;  conditional E-value: 1.6e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y ka++l+P++  a+n ++ +l++ G++++A++
  gi|330509120|ref|YP_004385548.1| 328 AYDKAIALNPKDGSAWNGKGMVLYNMGRYEEAIE 361
                                       59******************************86 PP

  == domain 9  score: 4.0 bits;  conditional E-value: 0.16
                            TPR_17  12 n..adaynnLAelllknGd 28 
                                       n  a a++ ++++l+ +G+
  gi|330509120|ref|YP_004385548.1| 384 NlsATAWTGKGNALKALGR 402
                                       1447778888888877775 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.045        23      58      74 ..      57      73 ..      40      76 .. 0.71
   2 !   22.6   0.6   1.9e-07   9.9e-05       4      77 .]      79     151 ..      76     151 .. 0.90
   3 !   32.7   0.0   1.3e-10   6.7e-08       3      74 ..     119     189 ..     117     192 .. 0.92
   4 !   12.6   0.0   0.00024      0.13       3      32 ..     235     264 ..     195     267 .. 0.72
   5 !    8.5   0.1    0.0047       2.4       8      32 ..     277     301 ..     269     307 .. 0.86
   6 !   15.3   0.1   3.6e-05     0.018       9      32 ..     312     335 ..     304     339 .. 0.85
   7 !   19.5   0.0   1.8e-06   0.00091       4      31 ..     341     368 ..     338     370 .. 0.90
   8 ?    2.0   0.1      0.51   2.6e+02       3      32 ..     387     416 ..     385     418 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.045
                            TPR_12 58 lgryeeAlelleealai 74
                                       g yeeA+++++ a++i
  gi|330509120|ref|YP_004385548.1| 57 NGSYEEAIQAYNMAIQI 73
                                      57788888888888776 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.9e-07
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                        a+   a +  r  ++deA + +e alei ++ l++++ + a++ +n g +++ lgr  eA e+  +al+i+ +
  gi|330509120|ref|YP_004385548.1|  79 DAWLGKAGISSRIDKHDEAKREYEIALEILNKRLEENS-QNASAWINKGVALSCLGRDIEAFEARGKALEIYNQ 151
                                       566677888888999***************88888888.99******************************975 PP

  == domain 3  score: 32.7 bits;  conditional E-value: 1.3e-10
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       a+a+ n +++l  lgr  eA+e   kalei++++l  ++p+  +t  n + ++  +gr+e+A+e++ ++++ 
  gi|330509120|ref|YP_004385548.1| 119 ASAWINKGVALSCLGRDIEAFEARGKALEIYNQAL-QKNPNDGNTWENKALVLVGMGRWEDAVEAYDKVIEF 189
                                       78999**************************6665.679****************************99885 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00024
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                       +t+++ ++  l  + ry+eA++ ++ka+e+
  gi|330509120|ref|YP_004385548.1| 235 STIWSGIGKSLSTASRYEEAIKAYDKAIEL 264
                                       355555666666666666666666666665 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0047
                            TPR_12   8 nlaavlrrlgrydeAlellekalei 32 
                                         a +l++lgry e++  ++ ale+
  gi|330509120|ref|YP_004385548.1| 277 GKAYALYALGRYNESINAFDIALEM 301
                                       6788999999999999999999987 PP

  == domain 6  score: 15.3 bits;  conditional E-value: 3.6e-05
                            TPR_12   9 laavlrrlgrydeAlellekalei 32 
                                        +++l++ gry+eA++ ++ka+++
  gi|330509120|ref|YP_004385548.1| 312 KGNALFQIGRYEEAIKAYDKAIAL 335
                                       799999999999999999999876 PP

  == domain 7  score: 19.5 bits;  conditional E-value: 1.8e-06
                            TPR_12   4 talnnlaavlrrlgrydeAlellekale 31 
                                       +a+n  ++vl+ +gry+eA+e +++a+ 
  gi|330509120|ref|YP_004385548.1| 341 SAWNGKGMVLYNMGRYEEAIEDYDRAIK 368
                                       58988********************986 PP

  == domain 8  score: 2.0 bits;  conditional E-value: 0.51
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                       ata++  +++l +lgr  e ++ + ka e+
  gi|330509120|ref|YP_004385548.1| 387 ATAWTGKGNALKALGRQSEMEAAYSKAKEL 416
                                       889999999999999999999999999775 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.4e-06   0.00073       4      46 ..      57      99 ..      56     102 .. 0.93
   2 ?    3.1   0.1      0.27   1.4e+02       6      35 ..     100     129 ..      97     138 .. 0.79
   3 !   23.9   0.0   8.9e-08   4.6e-05       9      61 ..     144     196 ..     140     202 .. 0.93
   4 !   15.1   0.0   4.9e-05     0.025       5      60 ..     249     307 ..     246     314 .. 0.86
   5 !   28.5   0.1   3.2e-09   1.6e-06       4      51 ..     319     366 ..     316     383 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.4e-06
                            TPR_19  4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46
                                      +g y+eA++++  a+q +p+na+a+l+ A +       deA++
  gi|330509120|ref|YP_004385548.1| 57 NGSYEEAIQAYNMAIQINPENADAWLGKAGISSRIDKHDEAKR 99
                                      699**************************99999999999986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.27
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeal 35 
                                        y+ Al++l + l+e+ +na a+++   al
  gi|330509120|ref|YP_004385548.1| 100 EYEIALEILNKRLEENSQNASAWINKGVAL 129
                                       566799999999999999999998776666 PP

  == domain 3  score: 23.9 bits;  conditional E-value: 8.9e-08
                            TPR_19   9 eAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                        Al+++ qalq++p++++ + + A +l+ +g++++A ++ d++ e  p  a+y
  gi|330509120|ref|YP_004385548.1| 144 KALEIYNQALQKNPNDGNTWENKALVLVGMGRWEDAVEAYDKVIEFSPSKAAY 196
                                       79*****************************************9999987666 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 4.9e-05
                            TPR_19   5 gdyaeAlalleqalqedpk...naearllLAeallalgqldeAealLdalpeedpddar 60 
                                        +y+eA++++ +a++ + k   ++  + + A al+alg+++e +++ d ++e+ p  ++
  gi|330509120|ref|YP_004385548.1| 249 SRYEEAIKAYDKAIELNSKdvsSWPNWSGKAYALYALGRYNESINAFDIALEMMPEFPD 307
                                       58**************99977666777799***************99999888877665 PP

  == domain 5  score: 28.5 bits;  conditional E-value: 3.2e-09
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                        g+y+eA++++ +a++ +pk++ a+ +   +l+++g+++eA++  d++
  gi|330509120|ref|YP_004385548.1| 319 IGRYEEAIKAYDKAIALNPKDGSAWNGKGMVLYNMGRYEEAIEDYDRA 366
                                       59***************************************9866655 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0017      0.88       8      58 ..      57     107 ..      51     121 .. 0.87
   2 ?    1.7   0.0      0.56   2.9e+02       8      44 ..      98     134 ..      94     141 .. 0.87
   3 !   21.9   0.0   2.7e-07   0.00014      12      64 ..     143     195 ..     137     203 .. 0.91
   4 !   11.5   0.0   0.00051      0.26       7      64 ..     247     307 ..     241     309 .. 0.84
   5 !   28.9   0.0   1.8e-09   9.1e-07       6      60 ..     317     371 ..     313     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0017
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylal 58 
                                       +  +e+a++++++ ++++P+ ++ ++  + +  + +   +A ++ e +l++
  gi|330509120|ref|YP_004385548.1|  57 NGSYEEAIQAYNMAIQINPENADAWLGKAGISSRIDKHDEAKREYEIALEI 107
                                       67899************************9999999999999999988865 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.56
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGc 44 
                                       ++++e al++++ +l  +++ ++ +   G++l  lG+
  gi|330509120|ref|YP_004385548.1|  98 KREYEIALEILNKRLEENSQNASAWINKGVALSCLGR 134
                                       5678889***********************9988886 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 2.7e-07
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                        +al++++  l+ +P+d   +   +l+l+ +G+++ A+++ +  ++ +p+ ++
  gi|330509120|ref|YP_004385548.1| 143 GKALEIYNQALQKNPNDGNTWENKALVLVGMGRWEDAVEAYDKVIEFSPSKAA 195
                                       58*********************************************998765 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00051
                             TPR_9   7 reedweralavverllllaPddpe...errdRGlllaqlGclsaAladLeaylalapdapd 64 
                                        + ++e+a+++++  + l+++d++    +   + +l+ lG++++ +++++ +l++ p+ pd
  gi|330509120|ref|YP_004385548.1| 247 TASRYEEAIKAYDKAIELNSKDVSswpNWSGKAYALYALGRYNESINAFDIALEMMPEFPD 307
                                       67899*************88876611156779**********************9998666 PP

  == domain 5  score: 28.9 bits;  conditional E-value: 1.8e-09
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                        +  ++e+a+++++  ++l+P+d + +   G++l+ +G++++A++d ++++  ap
  gi|330509120|ref|YP_004385548.1| 317 FQIGRYEEAIKAYDKAIALNPKDGSAWNGKGMVLYNMGRYEEAIEDYDRAIKFAP 371
                                       566799*********************************************9988 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 !   10.3   0.1    0.0012      0.63      20      75 ..      39      97 ..      25     102 .. 0.84
   2 ?    3.0   0.0      0.24   1.2e+02      38      64 ..     100     127 ..      98     141 .. 0.81
   3 !    8.8   0.0    0.0036       1.9      41      81 ..     144     185 ..     142     186 .. 0.94
   4 !   13.5   0.1   0.00013     0.066      30      80 ..     242     296 ..     195     298 .. 0.85
   5 !   19.4   0.0   1.8e-06   0.00091      20      77 ..     303     361 ..     294     366 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0012
                                      H--HHHHHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHH CS
                            ANAPC3 20 tespedayl..lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeA 75
                                      ++ +   y+  +++ l  ng y++A++ ++ a ++n+++  +++ +A  +  ++k++eA
  gi|330509120|ref|YP_004385548.1| 39 AQENTTEYWcqKGQELQVNGSYEEAIQAYNMAiQINPENADAWLGKAGISSRIDKHDEA 97
                                      444444555337999*******************************************9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.24
                                       -HHHHHHHHHCT.SHHHC-HHHHHHHHH CS
                            ANAPC3  38 qykrAyellrka.klnskslgcrylfAq 64 
                                       +y+ A+e+l+k  ++ns++  +++ ++ 
  gi|330509120|ref|YP_004385548.1| 100 EYEIALEILNKRlEENSQNASAWINKGV 127
                                       7999********9999999998876665 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0036
                                       HHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  41 rAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +A+e++++a ++n+++ + +  +A +l+ ++++e+A+ a++k
  gi|330509120|ref|YP_004385548.1| 144 KALEIYNQAlQKNPNDGNTWENKALVLVGMGRWEDAVEAYDK 185
                                       799******9999*************************9987 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 0.00013
                                       HHHHHHTT-HHHHHHHHHCT.SHHHC-H...HHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  30 AlclylngqykrAyellrka.klnsksl...gcrylfAqcllkLkkyeeAiaaLe 80 
                                       +++l  +++y++A++ ++ka +lnsk+      +  +A +l++L++y+e i+a++
  gi|330509120|ref|YP_004385548.1| 242 GKSLSTASRYEEAIKAYDKAiELNSKDVsswPNWSGKAYALYALGRYNESINAFD 296
                                       677788899****************9996666778888*************9985 PP

  == domain 5  score: 19.4 bits;  conditional E-value: 1.8e-06
                                       H--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3  20 tespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       +e p+   +++ +l++ g+y++A++ ++ka  ln+k+  ++  ++ +l+ +++yeeAi 
  gi|330509120|ref|YP_004385548.1| 303 PEFPDIWDWKGNALFQIGRYEEAIKAYDKAiALNPKDGSAWNGKGMVLYNMGRYEEAIE 361
                                       55555556999**********************************************96 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.014         7     104     129 ..      48      73 ..      44      86 .. 0.87
   2 !   16.4   0.3   1.4e-05    0.0071      61     129 ..      84     148 ..      77     161 .. 0.88
   3 !   12.8   0.1   0.00018     0.091      64     129 ..     128     189 ..     126     195 .. 0.92
   4 !   14.7   0.1   4.8e-05     0.025      67     132 ..     247     304 ..     232     306 .. 0.78
   5 ?    6.2   0.0      0.02        10     106     127 ..     312     333 ..     308     348 .. 0.74
   6 !   10.5   0.2   0.00091      0.47      63     129 ..     348     416 ..     337     417 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.014
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmagem 129
                                       +++++ l+  G+++ea++a++ma ++
  gi|330509120|ref|YP_004385548.1|  48 CQKGQELQVNGSYEEAIQAYNMAIQI 73 
                                       689999****************9876 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  61 lsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                        ++   ++ ++dea +  + al+ +n+r e ++++ + Wi    +++val+ lGr  ea++a  +a e+
  gi|330509120|ref|YP_004385548.1|  84 KAGISSRIDKHDEAKREYEIALEILNKRLEENSQNASAWI----NKGVALSCLGRDIEAFEARGKALEI 148
                                       5666778999*****************************8....79**************998888886 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00018
                                       HHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                       al  lgr  ea+e+  kal+ +n+  + + ++G+ W     ++a  l ++Gr ++a++a+ ++ e 
  gi|330509120|ref|YP_004385548.1| 128 ALSCLGRDIEAFEARGKALEIYNQALQKNPNDGNTW----ENKALVLVGMGRWEDAVEAYDKVIEF 189
                                       677899999***************************....58******************999885 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 4.8e-05
                                       HTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                           DUF3856  67 klgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagemiae 132
                                          ry       ++a++ +++  el++ + + W +    +a al  lGr++e+++af +a em+ e
  gi|330509120|ref|YP_004385548.1| 247 TASRY-------EEAIKAYDKAIELNSKDVSSWPN-WSGKAYALYALGRYNESINAFDIALEMMPE 304
                                       44444.......4566666666699********76.578************************976 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.02
                                       HHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 106 ravaleelGrkdealkafrmag 127
                                       ++ al ++Gr++ea+ka+ +a 
  gi|330509120|ref|YP_004385548.1| 312 KGNALFQIGRYEEAIKAYDKAI 333
                                       5677777777777777777664 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.00091
                                       HHHHHTT-HHHHHHHHHHHHHH..HHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  63 ealaklgrydealesadkalry..fnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                         l ++gry+ea+e  d+a+++  fn     +    +l  +a   ++ al+ lGr++e   a+ +a+e+
  gi|330509120|ref|YP_004385548.1| 348 MVLYNMGRYEEAIEDYDRAIKFapFNVTPLADLYAKNLSATAWTGKGNALKALGRQSEMEAAYSKAKEL 416
                                       567899**************9877887655455555677788899**************999*999985 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.9   2.5e+03      25      32 ..      60      67 ..      55      74 .. 0.63
   2 ?    2.3   0.1      0.33   1.7e+02      16      40 ..      92     116 ..      85     118 .. 0.85
   3 !   10.1   0.0    0.0012      0.59       7      40 ..     124     157 ..     119     159 .. 0.90
   4 !    7.7   0.0    0.0066       3.4       8      30 ..     166     188 ..     164     190 .. 0.89
   5 ?    4.4   0.0     0.069        35      12      31 ..     245     264 ..     240     267 .. 0.83
   6 ?    4.3   0.1     0.076        39       9      26 ..     279     296 ..     278     302 .. 0.82
   7 !   12.9   0.1   0.00015     0.076       9      31 ..     313     335 ..     311     336 .. 0.95
   8 !   16.7   0.1   9.4e-06    0.0048       9      30 ..     347     368 ..     344     370 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.9
                            TPR_10 25 leealair 32
                                      +eea++++
  gi|330509120|ref|YP_004385548.1| 60 YEEAIQAY 67
                                      46666655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.33
                            TPR_10  16 grydeAealleealairrrllGpdH 40 
                                        ++deA + +e al+i  + l++++
  gi|330509120|ref|YP_004385548.1|  92 DKHDEAKREYEIALEILNKRLEENS 116
                                       689*************999988875 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0012
                            TPR_10   7 NLanalrqrgrydeAealleealairrrllGpdH 40 
                                       N ++al+ +gr  eA +   +al+i+ ++l  ++
  gi|330509120|ref|YP_004385548.1| 124 NKGVALSCLGRDIEAFEARGKALEIYNQALQKNP 157
                                       7799**************************9886 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0066
                            TPR_10   8 LanalrqrgrydeAealleeala 30 
                                        a +l  +gr+++A++ ++++++
  gi|330509120|ref|YP_004385548.1| 166 KALVLVGMGRWEDAVEAYDKVIE 188
                                       5889999*************997 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.069
                            TPR_10  12 lrqrgrydeAealleealai 31 
                                       l+   ry+eA + +++a+++
  gi|330509120|ref|YP_004385548.1| 245 LSTASRYEEAIKAYDKAIEL 264
                                       677789***********986 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.076
                            TPR_10   9 analrqrgrydeAealle 26 
                                       a al+++gry+e+ + ++
  gi|330509120|ref|YP_004385548.1| 279 AYALYALGRYNESINAFD 296
                                       789*********998776 PP

  == domain 7  score: 12.9 bits;  conditional E-value: 0.00015
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       +nal+q gry+eA + +++a+a+
  gi|330509120|ref|YP_004385548.1| 313 GNALFQIGRYEEAIKAYDKAIAL 335
                                       89*******************96 PP

  == domain 8  score: 16.7 bits;  conditional E-value: 9.4e-06
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       +++l+++gry+eA +++++a+ 
  gi|330509120|ref|YP_004385548.1| 347 GMVLYNMGRYEEAIEDYDRAIK 368
                                       89******************96 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       4.5   2.3e+03      15      24 ..      60      69 ..      57      78 .. 0.78
   2 ?    0.4   0.0       1.7   8.5e+02       8      32 ..      87     111 ..      80     115 .. 0.76
   3 ?    0.8   0.0       1.2   6.2e+02      17      31 ..     144     156 ..     121     160 .. 0.64
   4 !    9.5   0.0     0.002         1       3      33 ..     164     192 ..     162     195 .. 0.77
   5 ?    7.1   0.0     0.012       6.2       6      28 ..     242     264 ..     238     270 .. 0.76
   6 ?    1.1   0.0      0.99   5.1e+02      10      30 ..     283     303 ..     277     308 .. 0.78
   7 !   13.7   0.0   9.7e-05      0.05       6      30 ..     313     337 ..     312     342 .. 0.82
   8 !   10.2   0.0    0.0013      0.65       9      33 ..     350     372 ..     342     375 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.5
                             TPR_7 15 yeeAielyeq 24
                                      yeeAi+ y  
  gi|330509120|ref|YP_004385548.1| 60 YEEAIQAYNM 69
                                      99***99966 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.7
                             TPR_7   8 lysrlGdyeeAielyeqsLaltkdp 32 
                                       + sr  +++eA + ye +L++ +  
  gi|330509120|ref|YP_004385548.1|  87 ISSRIDKHDEAKREYEIALEILNKR 111
                                       667788999*******999887665 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.2
                             TPR_7  17 eAielyeqsLaltkd 31 
                                       +A+e+y q  al k 
  gi|330509120|ref|YP_004385548.1| 144 KALEIYNQ--ALQKN 156
                                       56777777..55555 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.002
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                        n a + + +G++e+A+e y +  +++ +p+
  gi|330509120|ref|YP_004385548.1| 164 ENKALVLVGMGRWEDAVEAYDK--VIEFSPS 192
                                       5667788889************..6666655 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.012
                             TPR_7   6 arlysrlGdyeeAielyeqsLal 28 
                                       +   s   +yeeAi+ y ++++l
  gi|330509120|ref|YP_004385548.1| 242 GKSLSTASRYEEAIKAYDKAIEL 264
                                       555666789**********6665 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.99
                             TPR_7  10 srlGdyeeAielyeqsLaltk 30 
                                        +lG+y e i  +  +L++  
  gi|330509120|ref|YP_004385548.1| 283 YALGRYNESINAFDIALEMMP 303
                                       469*******99999888765 PP

  == domain 7  score: 13.7 bits;  conditional E-value: 9.7e-05
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltk 30 
                                       +++ ++ G+yeeAi+ y +++al  
  gi|330509120|ref|YP_004385548.1| 313 GNALFQIGRYEEAIKAYDKAIALNP 337
                                       7899***************666544 PP

  == domain 8  score: 10.2 bits;  conditional E-value: 0.0013
                             TPR_7   9 ysrlGdyeeAielyeqsLaltkdpe 33 
                                         ++G+yeeAie y +  a+  +p+
  gi|330509120|ref|YP_004385548.1| 350 LYNMGRYEEAIEDYDR--AIKFAPF 372
                                       5689************..8776666 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.018         9      13      32 ..      52      76 ..      37      77 .. 0.80
   2 ?   -1.5   0.0       9.9   5.1e+03      16      27 ..      94     105 ..      86     110 .. 0.68
   3 ?    5.1   0.1     0.079        40      18      32 ..     144     158 ..     138     159 .. 0.92
   4 !    9.2   0.0    0.0039         2       8      28 ..     168     188 ..     165     192 .. 0.82
   5 ?    5.2   0.0     0.073        37       6      28 ..     241     263 ..     240     267 .. 0.81
   6 ?    2.3   0.1      0.65   3.3e+02       7      25 ..     279     297 ..     277     301 .. 0.82
   7 !   11.3   0.0   0.00084      0.43       7      32 ..     313     338 ..     309     339 .. 0.89
   8 !   10.3   0.0    0.0018      0.93       7      28 ..     347     368 ..     345     371 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.018
                                      H.....HHHHHHHHHHHHHHHH-TT CS
                             TPR_6 13 l.....gdtdkAlealerlikeYPd 32
                                      +     g +++A++a++  i+  P+
  gi|330509120|ref|YP_004385548.1| 52 QelqvnGSYEEAIQAYNMAIQINPE 76
                                      24445579*************9997 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 9.9
                                       HHHHHHHHHHHH CS
                             TPR_6  16 tdkAlealerli 27 
                                       +d+A++ +e  +
  gi|330509120|ref|YP_004385548.1|  94 HDEAKREYEIAL 105
                                       667777666544 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.079
                                       HHHHHHHHHHHH-TT CS
                             TPR_6  18 kAlealerlikeYPd 32 
                                       kAle++++ +++ P+
  gi|330509120|ref|YP_004385548.1| 144 KALEIYNQALQKNPN 158
                                       8*************9 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0039
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAlealerlik 28 
                                       l +  +g++++A+ea++++i+
  gi|330509120|ref|YP_004385548.1| 168 LVLVGMGRWEDAVEAYDKVIE 188
                                       5566689************98 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.073
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                       +++s+  + ++++A++a+++ i+
  gi|330509120|ref|YP_004385548.1| 241 IGKSLSTASRYEEAIKAYDKAIE 263
                                       5666666679**********997 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealer 25 
                                       a+++++lg++ +++ a++ 
  gi|330509120|ref|YP_004385548.1| 279 AYALYALGRYNESINAFDI 297
                                       7899999999999999975 PP

  == domain 7  score: 11.3 bits;  conditional E-value: 0.00084
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + ++++ g++++A++a+++ i   P+
  gi|330509120|ref|YP_004385548.1| 313 GNALFQIGRYEEAIKAYDKAIALNPK 338
                                       78999988*************99996 PP

  == domain 8  score: 10.3 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       ++ ++++g++++A+e ++r ik
  gi|330509120|ref|YP_004385548.1| 347 GMVLYNMGRYEEAIEDYDRAIK 368
                                       8999**99***********998 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.088        45      11      36 .]      54      77 ..      48      77 .. 0.80
   2 ?   -1.4   0.0       4.9   2.5e+03      14      25 ..     173     184 ..     172     185 .. 0.84
   3 ?    1.3   0.1      0.71   3.6e+02      17      25 ..     251     259 ..     250     268 .. 0.52
   4 !    7.6   0.0    0.0075       3.9       8      30 ..     279     299 ..     274     304 .. 0.84
   5 ?    5.8   0.1     0.028        14      11      35 ..     316     338 ..     313     339 .. 0.78
   6 !   10.3   0.0     0.001      0.53       9      25 ..     348     364 ..     347     367 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.088
                                      HHHTT-HHHHHHH..HHHHHHH-TT- CS
                             TPR_3 11 fynkkkyqeArelfsYallaildken 36
                                      ++  + y+eA+++  Y  +  + +en
  gi|330509120|ref|YP_004385548.1| 54 LQVNGSYEEAIQA--YNMAIQINPEN 77
                                      666789*******..76887777776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.9
                                       TT-HHHHHHH.. CS
                             TPR_3  14 kkkyqeArelfs 25 
                                       +++ ++A+e+++
  gi|330509120|ref|YP_004385548.1| 173 MGRWEDAVEAYD 184
                                       578899****77 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.71
                                       HHHHHHH.. CS
                             TPR_3  17 yqeArelfs 25 
                                       y+eA+ +++
  gi|330509120|ref|YP_004385548.1| 251 YEEAIKAYD 259
                                       555555544 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0075
                                       HHHHHHTT-HHHHHHH..HHHHH CS
                             TPR_3   8 AaefynkkkyqeArelfsYalla 30 
                                       A+++y  ++y+e +++f+   + 
  gi|330509120|ref|YP_004385548.1| 279 AYALYALGRYNESINAFD--IAL 299
                                       9***************98..665 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.028
                                       HHHTT-HHHHHHH..HHHHHHH-TT CS
                             TPR_3  11 fynkkkyqeArelfsYallaildke 35 
                                       +++ ++y+eA+ +++   + +l ++
  gi|330509120|ref|YP_004385548.1| 316 LFQIGRYEEAIKAYD--KAIALNPK 338
                                       6788*********77..77777666 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.001
                                       HHHHHTT-HHHHHHH.. CS
                             TPR_3   9 aefynkkkyqeArelfs 25 
                                        ++yn+++y+eA+e ++
  gi|330509120|ref|YP_004385548.1| 348 MVLYNMGRYEEAIEDYD 364
                                       589**********9755 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.23   1.2e+02      74     131 ..      56     113 ..      33     121 .. 0.84
   2 ?    7.2   0.0     0.013       6.5      75     122 ..     139     186 ..     125     190 .. 0.86
   3 ?   -0.4   0.1       2.7   1.4e+03     104     119 ..     280     295 ..     242     303 .. 0.64
   4 !   18.1   0.0   5.3e-06    0.0027      69     123 ..     313     367 ..     298     369 .. 0.93
   5 ?    0.9   0.1       1.1   5.6e+02     104     124 ..     395     415 ..     378     417 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.23
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLg 131
                                         G +eea++ ++ +++ +P + +++        r ++  eA + Ye + ++L++ L 
  gi|330509120|ref|YP_004385548.1|  56 VNGSYEEAIQAYNMAIQINPENADAWLGKAGISSRIDKHDEAKREYEIALEILNKRLE 113
                                       4478999999999999999999999999999999999999999999999999998875 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.013
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       ++ + +al+ ++++++++P + ++++   + l  +Gr ++A e+Y+++
  gi|330509120|ref|YP_004385548.1| 139 FEARGKALEIYNQALQKNPNDGNTWENKALVLVGMGRWEDAVEAYDKV 186
                                       55667888899999*******************************987 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.7
                                       HHHHHTT-HHHHHHHH CS
                              BTAD 104 rAlarsGrqaeALevY 119
                                        Al+++Gr +e ++++
  gi|330509120|ref|YP_004385548.1| 280 YALYALGRYNESINAF 295
                                       3666666666666665 PP

  == domain 4  score: 18.1 bits;  conditional E-value: 5.3e-06
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  69 aeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                        +a++++Gr+eea++ +++++a++P +  ++      l+ +Gr +eA+e Y+r+ 
  gi|330509120|ref|YP_004385548.1| 313 GNALFQIGRYEEAIKAYDKAIALNPKDGSAWNGKGMVLYNMGRYEEAIEDYDRAI 367
                                       578999*********************************************9975 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 1.1
                                       HHHHHTT-HHHHHHHHHHHHH CS
                              BTAD 104 rAlarsGrqaeALevYerlrr 124
                                        Al ++Grq+e  ++Y ++++
  gi|330509120|ref|YP_004385548.1| 395 NALKALGRQSEMEAAYSKAKE 415
                                       69999***********99876 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.2    0.0034       1.7       9      32 ..      49      72 ..      48      73 .. 0.87
   2 ?    4.2   0.3     0.089        46      19      43 ..      93     117 ..      90     128 .. 0.82
   3 ?    2.9   0.1      0.22   1.1e+02       4      47 ..     119     161 ..     117     168 .. 0.67
   4 ?   -1.4   0.0       5.1   2.6e+03      18      30 ..     174     186 ..     172     189 .. 0.81
   5 !    9.2   0.1    0.0024       1.2      17      33 ..     248     264 ..     244     268 .. 0.91
   6 ?    0.4   0.0       1.4     7e+02      23      39 ..     284     300 ..     281     305 .. 0.85
   7 !    7.3   0.2    0.0099         5      18      32 ..     320     334 ..     318     335 .. 0.89
   8 ?    5.6   0.0     0.033        17      16      32 ..     352     368 ..     346     369 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0034
                               MIT  9 kkAveeDnagnyeeAlelYkeale 32
                                      +k  e+  +g yeeA+++Y  a++
  gi|330509120|ref|YP_004385548.1| 49 QKGQELQVNGSYEEAIQAYNMAIQ 72
                                      567788899***********9997 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.089
                               MIT  19 nyeeAlelYkealelLlqalkekne 43 
                                       + +eA + Y+ ale+L++ l e+++
  gi|330509120|ref|YP_004385548.1|  93 KHDEAKREYEIALEILNKRLEENSQ 117
                                       6799**************9986433 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.22
                               MIT   4 AlelvkkAveeDnagnyeeAlelYkealelLlqalkekneerre 47 
                                       A + ++k v +   g   eA+e+  +ale+ +qal+ kn+++ +
  gi|330509120|ref|YP_004385548.1| 119 ASAWINKGVALSCLGRDIEAFEARGKALEIYNQALQ-KNPNDGN 161
                                       666666666666677777888888888888888887.5555554 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 5.1
                               MIT  18 gnyeeAlelYkea 30 
                                       g +e+A+e+Y + 
  gi|330509120|ref|YP_004385548.1| 174 GRWEDAVEAYDKV 186
                                       67999*****875 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0024
                               MIT  17 agnyeeAlelYkealel 33 
                                       a  yeeA+++Y +a+el
  gi|330509120|ref|YP_004385548.1| 248 ASRYEEAIKAYDKAIEL 264
                                       678************97 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1.4
                               MIT  23 AlelYkealelLlqalk 39 
                                       Al  Y e+++ +  al 
  gi|330509120|ref|YP_004385548.1| 284 ALGRYNESINAFDIALE 300
                                       78899999999999985 PP

  == domain 7  score: 7.3 bits;  conditional E-value: 0.0099
                               MIT  18 gnyeeAlelYkeale 32 
                                       g yeeA+++Y +a+ 
  gi|330509120|ref|YP_004385548.1| 320 GRYEEAIKAYDKAIA 334
                                       79***********96 PP

  == domain 8  score: 5.6 bits;  conditional E-value: 0.033
                               MIT  16 nagnyeeAlelYkeale 32 
                                       n g yeeA+e Y  a++
  gi|330509120|ref|YP_004385548.1| 352 NMGRYEEAIEDYDRAIK 368
                                       5689**********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 ?    3.1   0.0      0.21   1.1e+02      13      35 ..      49      71 ..      40     100 .. 0.86
   2 ?   -0.5   0.0       2.8   1.5e+03      14      36 ..     166     188 ..     159     195 .. 0.83
   3 ?    4.9   0.0      0.06        30      18      37 ..     245     264 ..     239     270 .. 0.84
   4 ?    2.2   0.0      0.41   2.1e+02      12      37 ..     276     301 ..     274     305 .. 0.81
   5 ?    6.4   0.0      0.02        10      14      36 ..     312     334 ..     309     338 .. 0.86
   6 ?    1.5   0.0      0.67   3.4e+02      18      34 ..     350     366 ..     343     371 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.21
                         NRBF2_MIT 13 rkadrllaaGkyeeaischkkaa 35
                                      +k + l   G yeeai  ++ a 
  gi|330509120|ref|YP_004385548.1| 49 QKGQELQVNGSYEEAIQAYNMAI 71
                                      577788999*******9988775 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.8
                         NRBF2_MIT  14 kadrllaaGkyeeaischkkaaa 36 
                                       ka  l+  G++e+a+  + k  +
  gi|330509120|ref|YP_004385548.1| 166 KALVLVGMGRWEDAVEAYDKVIE 188
                                       67778999*******99988755 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.06
                         NRBF2_MIT  18 llaaGkyeeaischkkaaay 37 
                                       l +a +yeeai  + ka + 
  gi|330509120|ref|YP_004385548.1| 245 LSTASRYEEAIKAYDKAIEL 264
                                       67899***********9876 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.41
                         NRBF2_MIT  12 srkadrllaaGkyeeaischkkaaay 37 
                                       s ka  l a G+y+e+i     a ++
  gi|330509120|ref|YP_004385548.1| 276 SGKAYALYALGRYNESINAFDIALEM 301
                                       568999***********988777665 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.02
                         NRBF2_MIT  14 kadrllaaGkyeeaischkkaaa 36 
                                       k + l+  G+yeeai  + ka a
  gi|330509120|ref|YP_004385548.1| 312 KGNALFQIGRYEEAIKAYDKAIA 334
                                       56778999***********9976 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.67
                         NRBF2_MIT  18 llaaGkyeeaischkka 34 
                                       l   G+yeeai  + +a
  gi|330509120|ref|YP_004385548.1| 350 LYNMGRYEEAIEDYDRA 366
                                       6778*******877776 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.1    0.0095       4.9     204     250 ..      56     102 ..      44     110 .. 0.84
   2 !    6.0   0.0    0.0092       4.7     204     251 ..     138     185 ..     109     192 .. 0.80
   3 !    7.9   0.0    0.0024       1.2      19      74 ..     141     196 ..     134     258 .. 0.73
   4 !    7.6   0.0    0.0029       1.5     205     252 ..     319     366 ..     314     371 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0095
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevme 250
                                         gs+e+A++  + ai+ +p+  + +l Ka i  +    ++A +  e
  gi|330509120|ref|YP_004385548.1|  56 VNGSYEEAIQAYNMAIQINPENADAWLGKAGISSRIDKHDEAKREYE 102
                                       568999************************99998888888877655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0092
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmee 251
                                         + r kAle+ ++a++++p+  + + +Ka +l  +G  ++A+e+ ++
  gi|330509120|ref|YP_004385548.1| 138 AFEARGKALEIYNQALQKNPNDGNTWENKALVLVGMGRWEDAVEAYDK 185
                                       455667999999999999999999999999999999999999888776 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0024
                                       HHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHH CS
                             NARP1  19 kleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskY 74 
                                          +Ale  +++ ++  +  +  e+ka +l+ +gr e+A ++y + +e  p + +Y
  gi|330509120|ref|YP_004385548.1| 141 ARGKALEIYNQALQKNPNDGNTWENKALVLVGMGRWEDAVEAYDKVIEFSPSKAAY 196
                                       45567777777777777777888888888888888888888888888888888777 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0029
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                       +g++e+A++  dkai+ +p+    +  K+ +l  +G  ++A+e  ++a
  gi|330509120|ref|YP_004385548.1| 319 IGRYEEAIKAYDKAIALNPKDGSAWNGKGMVLYNMGRYEEAIEDYDRA 366
                                       7899**************************************998887 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.22   1.1e+02      11      41 ..     148     187 ..     139     213 .. 0.75
   2 !   11.1   0.1   0.00061      0.31      27      68 ..     248     295 ..     243     302 .. 0.73
   3 !   10.8   0.0   0.00071      0.36      19      65 ..     311     360 ..     294     369 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.22
                      SRP_TPR_like  11 legkelkkf.........kvvaliklekyeeaLkllkkgs 41 
                                       + ++ l+k          k++ l+ ++++e+a+++ +k  
  gi|330509120|ref|YP_004385548.1| 148 IYNQALQKNpndgntwenKALVLVGMGRWEDAVEAYDKVI 187
                                       444555555566666677999************9999876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00061
                      SRP_TPR_like  27 lekyeeaLkllkkgs.....alsed.vrfEkaYvlYklkkykkalkil 68 
                                       + +yeea+k+ +k+       +s+      kaY+lY l +y+++ + +
  gi|330509120|ref|YP_004385548.1| 248 ASRYEEAIKAYDKAIelnskDVSSWpNWSGKAYALYALGRYNESINAF 295
                                       679******9999883333322222134579***********998765 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00071
                      SRP_TPR_like  19 fkvvaliklekyeeaLkllkkgsals...edvrfEkaYvlYklkkykkal 65 
                                       +k  al ++++yeea+k+ +k+ al+   ++    k  vlY + +y++a 
  gi|330509120|ref|YP_004385548.1| 311 WKGNALFQIGRYEEAIKAYDKAIALNpkdGSAWNGKGMVLYNMGRYEEAI 360
                                       57789****************9977632256778899*********9996 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.2   1.1e+03      15      30 ..      58      73 ..      56      76 .. 0.85
   2 ?    1.1   0.0      0.54   2.7e+02      10      34 ..      87     111 ..      85     114 .. 0.79
   3 ?   -0.9   0.0       2.3   1.2e+03      26      35 ..     144     153 ..     137     155 .. 0.78
   4 !    6.7   0.1    0.0097         5      14      30 ..     248     264 ..     247     267 .. 0.92
   5 ?    4.0   0.0     0.068        35      15      30 ..     320     335 ..     317     336 .. 0.90
   6 !    9.0   0.0    0.0018      0.93      15      29 ..     354     368 ..     353     369 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.2
                          SHNi-TPR 15 enFpqAveDlrkaLeL 30
                                      + +++A++ ++ a+++
  gi|330509120|ref|YP_004385548.1| 58 GSYEEAIQAYNMAIQI 73
                                      569*****99999887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.54
                          SHNi-TPR  10 islEnenFpqAveDlrkaLeLreql 34 
                                       is   ++ ++A  +++ aLe+ ++ 
  gi|330509120|ref|YP_004385548.1|  87 ISSRIDKHDEAKREYEIALEILNKR 111
                                       5555678899999********9885 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.3
                          SHNi-TPR  26 kaLeLreqll 35 
                                       kaLe+++q l
  gi|330509120|ref|YP_004385548.1| 144 KALEIYNQAL 153
                                       8999999866 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0097
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A++ ++ka+eL
  gi|330509120|ref|YP_004385548.1| 248 ASRYEEAIKAYDKAIEL 264
                                       69*************98 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.068
                          SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                       +++++A++ ++ka++L
  gi|330509120|ref|YP_004385548.1| 320 GRYEEAIKAYDKAIAL 335
                                       79***********987 PP

  == domain 6  score: 9.0 bits;  conditional E-value: 0.0018
                          SHNi-TPR  15 enFpqAveDlrkaLe 29 
                                       +++++A+eD+++a++
  gi|330509120|ref|YP_004385548.1| 354 GRYEEAIEDYDRAIK 368
                                       59**********986 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.011       5.5      15      39 ..      58      82 ..      57      97 .. 0.81
   2 ?    0.6   0.1       1.2   6.2e+02      13      30 ..      90     107 ..      88     121 .. 0.69
   3 ?   -1.9   0.0       7.4   3.8e+03      19      33 ..     144     158 ..     143     161 .. 0.81
   4 !    7.8   0.0    0.0067       3.4       8      34 ..     279     305 ..     278     308 .. 0.93
   5 ?    2.9   0.0      0.22   1.1e+02      12      34 ..     317     339 ..     314     344 .. 0.85
   6 ?    2.9   0.0      0.23   1.2e+02      12      34 ..     351     373 ..     347     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                                      T-HHHHHHHHHHHHHHTTS-HHHHH CS
                        Fis1_TPR_C 15 geYseArryvdalLeiEPenrQaqs 39
                                      g Y+eA +  ++ ++i Pen  a  
  gi|330509120|ref|YP_004385548.1| 58 GSYEEAIQAYNMAIQINPENADAWL 82
                                      78******************98865 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.2
                                       HHT-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C  13 klgeYseArryvdalLei 30 
                                       ++ +++eA+r  +  Lei
  gi|330509120|ref|YP_004385548.1|  90 RIDKHDEAKREYEIALEI 107
                                       666777777777777765 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 7.4
                                       HHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  19 eArryvdalLeiEPe 33 
                                       +A++  ++ L++ P+
  gi|330509120|ref|YP_004385548.1| 144 KALEIYNQALQKNPN 158
                                       688888999999997 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0067
                                       HHHHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C   8 AlGhyklgeYseArryvdalLeiEPen 34 
                                       A++ y lg+Y+e+ +  d  Le+ Pe+
  gi|330509120|ref|YP_004385548.1| 279 AYALYALGRYNESINAFDIALEMMPEF 305
                                       8899*******************9997 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.22
                                       HHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPen 34 
                                       + +g+Y+eA +  d  +++ P+ 
  gi|330509120|ref|YP_004385548.1| 317 FQIGRYEEAIKAYDKAIALNPKD 339
                                       679************99999986 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.23
                                       HHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPen 34 
                                       y +g+Y+eA +  d+ ++  P n
  gi|330509120|ref|YP_004385548.1| 351 YNMGRYEEAIEDYDRAIKFAPFN 373
                                       99*******99999999988876 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.15        75      74     112 ..      49      87 ..      42      98 .. 0.84
   2 !   12.6   0.1   0.00028      0.14      78     127 ..      94     143 ..      81     155 .. 0.85
   3 ?   -0.6   0.0       3.3   1.7e+03      88     119 ..     145     176 ..     143     184 .. 0.87
   4 ?   -0.3   0.0       2.6   1.4e+03      81     130 ..     247     299 ..     233     306 .. 0.74
   5 ?    2.9   0.0      0.28   1.4e+02      77     122 ..     314     359 ..     310     410 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.15
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHH CS
                   Alkyl_sulf_dimr  74 ekakealkegdyrwaaellnhlvfadpenaeakelkada 112
                                       +k +e   +g y+ a++  n++++ +pena+a   ka +
  gi|330509120|ref|YP_004385548.1|  49 QKGQELQVNGSYEEAIQAYNMAIQINPENADAWLGKAGI 87 
                                       778889999*********************998777665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00028
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHH CS
                   Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRn 127
                                       ++ ++ +y++a+e+ln+ ++++++na+a   k  al +lg+  e+  +R 
  gi|330509120|ref|YP_004385548.1|  94 HDEAKREYEIALEILNKRLEENSQNASAWINKGVALSCLGRDIEAFEARG 143
                                       4457889*************************************999996 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  88 aaellnhlvfadpenaeakelkadaleqlgyq 119
                                       a+e+ n++++++p++ ++ e ka +l  +g+ 
  gi|330509120|ref|YP_004385548.1| 145 ALEIYNQALQKNPNDGNTWENKALVLVGMGRW 176
                                       8999***********99999999999888875 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.6
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHH...HHHHHHHHHHH-SSHHHHHHHH CS
                   Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakel...kadaleqlgyqaesatwRniYl 130
                                       ++  y+ a++  +++++ ++++ +       ka al +lg+ +es ++  i l
  gi|330509120|ref|YP_004385548.1| 247 TASRYEEAIKAYDKAIELNSKDVSSWPNwsgKAYALYALGRYNESINAFDIAL 299
                                       56678888888888888888765444333559999999999999999876655 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.28
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  77 kealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       ++ ++ g y+ a++  +++++ +p++ +a + k  +l ++g+ +e+
  gi|330509120|ref|YP_004385548.1| 314 NALFQIGRYEEAIKAYDKAIALNPKDGSAWNGKGMVLYNMGRYEEA 359
                                       5677889999999999999999999999998888888888887775 PP

>> DUF3808  Protein of unknown function (DUF3808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.2e-05    0.0061     242     361 ..      92     213 ..      67     236 .. 0.81
   2 ?    0.2   0.0      0.48   2.4e+02     276     333 ..     242     297 ..     234     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                           DUF3808 242 diddglkapleeleelLlksrkrfPksalwllfearieslkgnldeAlelleeiiee.sqselkqvkhlclfe.lal 316
                                       d +d+ k + e++ e+L k ++  ++ a   ++++ ++s  g+  eA e+  +++e  +q  +k  +    +e +al
  gi|330509120|ref|YP_004385548.1|  92 DKHDEAKREYEIALEILNKRLEENSQNASAWINKGVALSCLGRDIEAFEARGKALEIyNQALQKNPNDGNTWEnKAL 168
                                       44466788999999999999999999999999999999999999999999888874325666788889999973689 PP

                           DUF3808 317 tlvylheykeaaesfleLlklskwSkalYtYl.aaacllelgreek 361
                                       +lv + ++++a+e+ +++++ s  Ska Y+++ +a+c++e   +++
  gi|330509120|ref|YP_004385548.1| 169 VLVGMGRWEDAVEAYDKVIEFSP-SKAAYAWIdKAICYSEGLSMTN 213
                                       9*******************997.9******9789***99887733 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.48
                           DUF3808 276 arieslkgnldeAlelleeiieesqselkqvkhlclfe.laltlvylheykeaaesfle 333
                                       ++ +s+ ++ +eA+++++++i   + + k+v +   +  +a +l  l +y+e++++f+ 
  gi|330509120|ref|YP_004385548.1| 242 GKSLSTASRYEEAIKAYDKAI---ELNSKDVSSWPNWSgKAYALYALGRYNESINAFDI 297
                                       5667889999********988...67778888888886255566667788888888775 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3         1   5.3e+02       7      56 ..      63     115 ..      58     122 .. 0.69
   2 ?   -0.3   0.0       2.6   1.3e+03       8      43 ..     105     140 ..      98     149 .. 0.82
   3 ?    6.6   0.0     0.019       9.5       6      44 ..     144     182 ..     139     192 .. 0.88
   4 ?    5.3   0.0      0.05        25       7      43 ..     325     361 ..     320     368 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeA...leqLleilkrdrkwe 56 
                                        +++   a++ np++ da l  A       +++eA    e  leil + ++++
  gi|330509120|ref|YP_004385548.1|  63 AIQAYNMAIQINPENADAWLGKAGISSRIDKHDEAkreYEIALEILNKRLEEN 115
                                       67888889999999999988888877777777777333344566665555554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.6
                            TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAle 43 
                                       l+ l ++l++n ++  a ++   al   gr  eA+e
  gi|330509120|ref|YP_004385548.1| 105 LEILNKRLEENSQNASAWINKGVALSCLGRDIEAFE 140
                                       667889999999999999998888888888888887 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.019
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                       + l+   +al++np+d ++  + Al+l+  gr e+A+e+
  gi|330509120|ref|YP_004385548.1| 144 KALEIYNQALQKNPNDGNTWENKALVLVGMGRWEDAVEA 182
                                       56677789****************************996 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.05
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAle 43 
                                        +++ ++a+a np+d  a      +l+  gryeeA+e
  gi|330509120|ref|YP_004385548.1| 325 AIKAYDKAIALNPKDGSAWNGKGMVLYNMGRYEEAIE 361
                                       6889999****************************98 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.14        73     152     180 ..      50      78 ..      39      87 .. 0.84
   2 ?    1.1   0.0      0.53   2.7e+02     157     178 ..      89     110 ..      84     120 .. 0.82
   3 ?   -0.7   0.0       1.9   9.6e+02     155     174 ..     169     188 ..     143     200 .. 0.74
   4 ?    0.5   0.0      0.84   4.3e+02     157     178 ..     246     267 ..     241     273 .. 0.78
   5 !    8.7   0.1    0.0026       1.3     150     177 ..     310     337 ..     306     343 .. 0.88
   6 ?    3.6   0.1     0.092        47     151     174 ..     345     368 ..     339     387 .. 0.84
   7 ?    2.8   0.3      0.16        82     144     174 ..     385     415 ..     373     419 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.14
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaaleeka 180
                                       +G  l  +g  +eA +aY+ A++ + e+a
  gi|330509120|ref|YP_004385548.1|  50 KGQELQVNGSYEEAIQAYNMAIQINPENA 78 
                                       78888999*************99877765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.53
                            TPR_21 157 vaqgkldeAraaYqaAlaalee 178
                                       ++ +k deA+ +Y+ Al+ l++
  gi|330509120|ref|YP_004385548.1|  89 SRIDKHDEAKREYEIALEILNK 110
                                       566899**********987765 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.9
                            TPR_21 155 ilvaqgkldeAraaYqaAla 174
                                       +lv +g+ ++A +aY++ ++
  gi|330509120|ref|YP_004385548.1| 169 VLVGMGRWEDAVEAYDKVIE 188
                                       67788888888888887665 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.84
                            TPR_21 157 vaqgkldeAraaYqaAlaalee 178
                                       +   + +eA +aY++A++ +++
  gi|330509120|ref|YP_004385548.1| 246 STASRYEEAIKAYDKAIELNSK 267
                                       56678899999**999986655 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0026
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAlaale 177
                                       + +G++l++ g+ +eA +aY++A+a + 
  gi|330509120|ref|YP_004385548.1| 310 DWKGNALFQIGRYEEAIKAYDKAIALNP 337
                                       88*********************98665 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.092
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAla 174
                                        +G +l+++g+ +eA + Y++A++
  gi|330509120|ref|YP_004385548.1| 345 GKGMVLYNMGRYEEAIEDYDRAIK 368
                                       5899******************97 PP

  == domain 7  score: 2.8 bits;  conditional E-value: 0.16
                            TPR_21 144 faalvaelrGDilvaqgkldeAraaYqaAla 174
                                        +a +   +G++l a g++ e  aaY++A +
  gi|330509120|ref|YP_004385548.1| 385 LSATAWTGKGNALKALGRQSEMEAAYSKAKE 415
                                       556666679*******************975 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       4.2   2.2e+03      13      24 ..      57      68 ..      56      72 .. 0.83
   2 ?    2.6   0.0      0.37   1.9e+02      13      28 ..     173     188 ..     169     190 .. 0.85
   3 ?    1.9   0.0      0.64   3.3e+02       8      28 ..     243     263 ..     236     266 .. 0.77
   4 ?    4.5   0.0     0.092        47       8      25 ..     314     331 ..     314     336 .. 0.87
   5 ?   -0.3   0.0       3.1   1.6e+03      11      21 ..     351     361 ..     348     361 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 4.2
                               PPR 13 nGkleeAlelfk 24
                                      nG +eeA++ ++
  gi|330509120|ref|YP_004385548.1| 57 NGSYEEAIQAYN 68
                                      899****98876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.37
                               PPR  13 nGkleeAlelfkeMke 28 
                                        G++e+A+e +++ +e
  gi|330509120|ref|YP_004385548.1| 173 MGRWEDAVEAYDKVIE 188
                                       79*********99876 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.64
                               PPR   8 sgycknGkleeAlelfkeMke 28 
                                       ++++ + ++eeA++ +++ +e
  gi|330509120|ref|YP_004385548.1| 243 KSLSTASRYEEAIKAYDKAIE 263
                                       67777899******9998776 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.092
                               PPR   8 sgycknGkleeAlelfke 25 
                                       +++ + G++eeA++ +++
  gi|330509120|ref|YP_004385548.1| 314 NALFQIGRYEEAIKAYDK 331
                                       689999********9987 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 3.1
                               PPR  11 cknGkleeAle 21 
                                          G++eeA+e
  gi|330509120|ref|YP_004385548.1| 351 YNMGRYEEAIE 361
                                       568******86 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 !   10.3   0.1   0.00084      0.43      52     114 ..      61     119 ..      54     130 .. 0.87
   2 ?   -0.7   0.0       2.1   1.1e+03      91     113 ..     137     159 ..     124     171 .. 0.77
   3 ?   -2.9   0.0       9.3   4.7e+03      53      66 ..     253     266 ..     245     301 .. 0.54
   4 ?    4.8   0.1     0.042        21      52     124 ..     323     389 ..     317     413 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00084
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT-H CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqavdedPdnd 114
                                       ++ai+ ++ a+ i+P+  da W +g a +s       ++eak+++e a +++++  +e+ +n 
  gi|330509120|ref|YP_004385548.1|  61 EEAIQAYNMAIQINPENADA-W-LGKAGISSRID--KHDEAKREYEIALEILNKRLEENSQNA 119
                                       69****************99.5.79999987655..5568*************9999998875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHHHHHH-TT- CS
                       TOM20_plant  91 eakenfekatqffqqavdedPdn 113
                                       ea e  +ka ++++qa +++P++
  gi|330509120|ref|YP_004385548.1| 137 EAFEARGKALEIYNQALQKNPND 159
                                       66677789999999999999975 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 9.3
                                       HHHHHHHHHHHH-T CS
                       TOM20_plant  53 daiskleeallidP 66 
                                       +ai  +++a+ ++ 
  gi|330509120|ref|YP_004385548.1| 253 EAIKAYDKAIELNS 266
                                       33333333333332 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHH CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqavdedPdndlyrkslelaa 124
                                       ++ai  +++a+ ++Pk   a W   n      +     eea e +++a +f    ++  P  dly k l  +a
  gi|330509120|ref|YP_004385548.1| 323 EEAIKAYDKAIALNPKDGSA-W---NGKGMVLYNMGRYEEAIEDYDRAIKFA--PFNVTPLADLYAKNLSATA 389
                                       689999999*****976665.5...3333333444556899*******9995..5777899******998876 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 ?    2.7   0.0      0.17        87      76     108 ..      41      75 ..      37      92 .. 0.71
   2 ?   11.6   0.3   0.00032      0.16      92     168 ..      93     169 ..      84     204 .. 0.85
   3 ?    1.8   0.3      0.33   1.7e+02     141     185 ..     322     367 ..     234     375 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.17
                           DUF2225  76 ekiskkwksr..dfskertldeaiesYkLallcye 108
                                       e++++ w ++  + + + +++eai++Y +a++   
  gi|330509120|ref|YP_004385548.1|  41 ENTTEYWCQKgqELQVNGSYEEAIQAYNMAIQINP 75 
                                       66777776666577778899**********98754 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00032
                           DUF2225  92 tldeaiesYkLallcyelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelykeayekesfpvegideatvl 168
                                       + dea  +Y +al+  + + e++s+ A  +++ +   + ++ + +  +   kAle+y++a++k+ ++ +  +++ ++
  gi|330509120|ref|YP_004385548.1|  93 KHDEAKREYEIALEILNKRLEENSQNASAWINKGVALSCLGRDIEAFEARGKALEIYNQALQKNPNDGNTWENKALV 169
                                       6799***********************************************************99988776665544 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.33
                           DUF2225 141 lkkAlelykeayekesfpvegideat.vlYLiaeLerrlgnkeeal 185
                                       +++A++ y++a+  + ++ +  + +  vlY ++  e  ++++++a+
  gi|330509120|ref|YP_004385548.1| 322 YEEAIKAYDKAIALNPKDGSAWNGKGmVLYNMGRYEEAIEDYDRAI 367
                                       5556666666665555555544443335666666666666666555 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0037       1.9     142     221 ..      89     180 ..      57     194 .. 0.62
   2 ?   -1.6   0.0       2.7   1.4e+03     204     229 ..     275     300 ..     243     309 .. 0.54
   3 ?   -0.8   0.0       1.6   8.3e+02     201     222 ..     340     361 ..     313     374 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0037
                                       HHTT-HHHHHHHHHHHHHH-TT-H..HHHHHHHHHHHHH-....TTHHH......HHHHHHHHHHHHS---HHHHHH CS
                        Coatomer_E 142 lklhrvdlAekelkkmqdidedat..ltQLAqawvklavg....gekiq......dAyyifqelsekykstplllng 206
                                        ++++ d A++e  ++ +i +      +Q A+aw++  v+    g  i+       A+ i+++  +k ++   +   
  gi|330509120|ref|YP_004385548.1|  89 SRIDKHDEAKREYEIALEILNKRLeeNSQNASAWINKGVAlsclGRDIEafeargKALEIYNQALQKNPNDGNTWEN 165
                                       56777777777777777776654311567777777654431111222211111115667777777777777777777 PP

                                       HHHHHHHTT-HHHHH CS
                        Coatomer_E 207 kAvvslllgryeeAe 221
                                       kA v + +gr+e+A 
  gi|330509120|ref|YP_004385548.1| 166 KALVLVGMGRWEDAV 180
                                       777777777777775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHTT-HHHHHHHHHHHHH CS
                        Coatomer_E 204 lngkAvvslllgryeeAeslLkeaLd 229
                                         gkA +  +lgry+e  +    aL+
  gi|330509120|ref|YP_004385548.1| 275 WSGKAYALYALGRYNESINAFDIALE 300
                                       45556666666666665555555555 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHTT-HHHHHH CS
                        Coatomer_E 201 plllngkAvvslllgryeeAes 222
                                           ngk +v   +gryeeA +
  gi|330509120|ref|YP_004385548.1| 340 GSAWNGKGMVLYNMGRYEEAIE 361
                                       4456788888888888888855 PP

>> UFC1  Ubiquitin-fold modifier-conjugating enzyme 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.3   2.2e+03      68      79 ..      94     105 ..      59     125 .. 0.52
   2 ?    3.8   0.0     0.081        41      49      83 ..     262     299 ..     234     309 .. 0.67
   3 ?    6.9   0.0    0.0089       4.6      54      78 ..     337     361 ..     314     396 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.3
                              UFC1  68 helkkyefdlef 79 
                                       h+ +k e+++ +
  gi|330509120|ref|YP_004385548.1|  94 HDEAKREYEIAL 105
                                       222222333333 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.081
                              UFC1  49 fklesnkegt..kwkGkcwyvhelkkyefdle.fdipv 83 
                                       ++l+s++ ++  +w+Gk + ++ l +y+ +++ fdi+ 
  gi|330509120|ref|YP_004385548.1| 262 IELNSKDVSSwpNWSGKAYALYALGRYNESINaFDIAL 299
                                       5555555433228**************86653355543 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0089
                              UFC1  54 nkegtkwkGkcwyvhelkkyefdle 78 
                                        k+g+ w Gk  +++++ +ye  +e
  gi|330509120|ref|YP_004385548.1| 337 PKDGSAWNGKGMVLYNMGRYEEAIE 361
                                       478*****************98875 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.11        58      55      77 ..      58      80 ..      52      82 .. 0.91
   2 ?   -1.1   0.0         4     2e+03      56      70 ..     250     264 ..     246     270 .. 0.83
   3 ?    1.5   0.0      0.63   3.2e+02      53      70 ..     318     335 ..     314     343 .. 0.85
   4 ?    0.9   0.0      0.96   4.9e+02      49      71 ..     348     370 ..     345     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.11
                            ANAPC5 55 ghneeAvkaleeairlArenkDk 77
                                      g +eeA++a + ai++  en+D 
  gi|330509120|ref|YP_004385548.1| 58 GSYEEAIQAYNMAIQINPENADA 80
                                      789*****************995 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4
                            ANAPC5  56 hneeAvkaleeairl 70 
                                        +eeA+ka   ai+l
  gi|330509120|ref|YP_004385548.1| 250 RYEEAIKAYDKAIEL 264
                                       689999999999987 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.63
                            ANAPC5  53 dfghneeAvkaleeairl 70 
                                       ++g +eeA+ka   ai+l
  gi|330509120|ref|YP_004385548.1| 318 QIGRYEEAIKAYDKAIAL 335
                                       5699***********987 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.96
                            ANAPC5  49 slhadfghneeAvkaleeairlA 71 
                                       ++ +++g +eeA++    ai+ A
  gi|330509120|ref|YP_004385548.1| 348 MVLYNMGRYEEAIEDYDRAIKFA 370
                                       667899********999999987 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.25   1.3e+02       2      16 ..      60      74 ..      59      82 .. 0.86
   2 ?   -1.4   0.0       3.5   1.8e+03       1      18 [.     100     117 ..     100     123 .. 0.78
   3 ?   -0.9   0.0       2.4   1.2e+03       8      17 ..     122     131 ..     115     134 .. 0.86
   4 ?   -2.6   0.0       8.3   4.2e+03       4      14 ..     144     154 ..     143     156 .. 0.79
   5 ?    5.0   0.1     0.035        18       1      15 [.     250     264 ..     250     270 .. 0.91
   6 ?    4.1   0.0     0.067        34       1      15 [.     321     335 ..     321     341 .. 0.91
   7 ?    3.4   0.1      0.11        55       1      15 [.     355     369 ..     355     370 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.25
                                      HHHHHHHHHHHHHHH CS
                          HTH_Bact  2 YeeaLeqvnkAieiS 16
                                      Yeea++  n Ai+i 
  gi|330509120|ref|YP_004385548.1| 60 YEEAIQAYNMAIQIN 74
                                      9***********985 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.5
                                       -HHHHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiSir 18 
                                       +Ye aLe  nk +e   +
  gi|330509120|ref|YP_004385548.1| 100 EYEIALEILNKRLEENSQ 117
                                       6999****9998876555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.4
                                       HHHHHHHHHH CS
                          HTH_Bact   8 qvnkAieiSi 17 
                                        +nk++++S+
  gi|330509120|ref|YP_004385548.1| 122 WINKGVALSC 131
                                       69*******9 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 8.3
                                       HHHHHHHHHHH CS
                          HTH_Bact   4 eaLeqvnkAie 14 
                                       +aLe  n+A++
  gi|330509120|ref|YP_004385548.1| 144 KALEIYNQALQ 154
                                       68899999875 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.035
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rYeea++  +kAie+
  gi|330509120|ref|YP_004385548.1| 250 RYEEAIKAYDKAIEL 264
                                       7************97 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.067
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rYeea++  +kAi++
  gi|330509120|ref|YP_004385548.1| 321 RYEEAIKAYDKAIAL 335
                                       7************86 PP

  == domain 7  score: 3.4 bits;  conditional E-value: 0.11
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rYeea+e  ++Ai+ 
  gi|330509120|ref|YP_004385548.1| 355 RYEEAIEDYDRAIKF 369
                                       7************85 PP

>> NRDE-2  NRDE-2, necessary for RNA interference
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.6   0.00089      0.45       4     106 ..      65     164 ..      62     170 .. 0.75
   2 ?    4.7   0.4     0.028        14       6      64 ..     108     159 ..     104     190 .. 0.67
   3 ?   -0.2   0.5      0.85   4.3e+02      45      64 ..     249     268 ..     204     369 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00089
                            NRDE-2   4 aelnraveenPedidaWlelvefQdellsaeeeslskserkalaeiklsilekAleknksn...pdserLllelL.k 76 
                                       + +n a++ nPe++daWl  + +   +        + +e k  +ei l+il+k le+n++n     ++ + l  L +
  gi|330509120|ref|YP_004385548.1|  65 QAYNMAIQINPENADAWLGKAGISSRID-------KHDEAKREYEIALEILNKRLEENSQNasaWINKGVALSCLgR 134
                                       56899999***********999999664.......345577789**************8884432344555555524 PP

                            NRDE-2  77 lgseiwdseklakeWeellkenpnsvkLWr 106
                                        ++ + +  k  + ++++l++npn+ + W+
  gi|330509120|ref|YP_004385548.1| 135 DIEAFEARGKALEIYNQALQKNPNDGNTWE 164
                                       455556777888888888888888888886 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.028
                            NRDE-2   6 lnraveenPedidaWlel.vefQdellsaeeeslskserkalaeiklsilekAleknksn 64 
                                       ln+++een ++++aW++  v++    l   +      e  +   + l+i+++Al+kn+++
  gi|330509120|ref|YP_004385548.1| 108 LNKRLEENSQNASAWINKgVALSC--LG--R----DIEAFEARGKALEIYNQALQKNPND 159
                                       899999999999999863133322..21..1....2234556778888888888888554 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.85
                            NRDE-2  45 alaeiklsilekAleknksn 64 
                                       + +e  ++ ++kA+e n+++
  gi|330509120|ref|YP_004385548.1| 249 SRYEEAIKAYDKAIELNSKD 268
                                       45666666666666666443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.81u 0.29s 00:00:01.10 Elapsed: 00:00:00.54
# Mc/sec: 2354.13
//
Query:       gi|330509121|ref|YP_004385549.1|  [L=210]
Description: hypothetical protein MCON_3513, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.02   14.5   0.1      0.023   14.4   0.1    1.2  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 ?   14.4   0.1   1.3e-06     0.023       5     106 ..      12     127 ..       8     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-06
                         DDE_Tnp_1   5 evlivDattvrvpgtk.......edarw.......gykggkykygyk..lhiavdtrsglilsvvitpgnvhdskgl 65 
                                       +++ vD t++ v+g+        +            +k g+    +k  +  +v  + gl+   + ++gn++d k l
  gi|330509121|ref|YP_004385549.1|  12 QLIHVDTTNFSVHGKYendapdsT---DsiritfgHAKDGR--TDLKrfVLGLVTNQFGLPFFTEAFSGNESDKKSL 83 
                                       567799999999999966555553...04447553222444..34430034456666699***************** PP

                         DDE_Tnp_1  66 kqlldelrpr....kgklvlaDaGYasaelldtleekgvdyiirl 106
                                       + +++  ++     ++++ ++D++  ++++++ l    +++i r+
  gi|330509121|ref|YP_004385549.1|  84 IKMIQKTQQAinldDNRYWIVDSALYTEDNIKLLG-TDMQWITRA 127
                                       ******99999************977677777666.888889888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1331.75
//
Query:       gi|330509122|ref|YP_004385550.1|  [L=52]
Description: hypothetical protein MCON_3514 [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   12.0   4.1       0.23   11.4   4.1    1.3  1  AT_hook   AT hook motif


Domain annotation for each model (and alignments):
>> AT_hook  AT hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.1   1.3e-05      0.23       2      11 ..      41      50 ..      40      52 .] 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.3e-05
                           AT_hook  2 RkRGRPrKaa 11
                                      ++RGRP+K++
  gi|330509122|ref|YP_004385550.1| 41 KRRGRPKKDE 50
                                      99******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 354.22
//
Query:       gi|330509123|ref|YP_004385551.1|  [L=54]
Description: hypothetical protein MCON_3515, partial [Methanosaeta concilii GP6]
Scores for complete 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   27.2   0.1    2.9e-06   27.1   0.1    1.0  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.025   14.4   0.0    1.3  1  DUF3511    Domain of unknown function (DUF3511)


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 !   27.1   0.1   3.2e-10   2.9e-06     169     213 ..       3      48 ..       1      49 [. 0.95

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.2e-10
                         DDE_Tnp_1 169 elyrlRwqiErvFkwlkrk.fgldrlryrglnrveaqllllllaln 213
                                       ++y+ + ++Er F++lk+k f+   +++++  r+ea  ++++l+l+
  gi|330509123|ref|YP_004385551.1|   3 RYYKGQQTVERGFRFLKDKcFHVSEVYLKKEGRIEALCMIMALSLL 48 
                                       79*****************************************987 PP

>> DUF3511  Domain of unknown function (DUF3511)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.8e-06     0.025      25      43 ..       8      26 ..       5      28 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-06
                           DUF3511 25 KsSlrksfrWiKnkcskiv 43
                                       +++ ++fr +K+kc ++ 
  gi|330509123|ref|YP_004385551.1|  8 QQTVERGFRFLKDKCFHVS 26
                                      5899***********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 373.58
//
Query:       gi|330509124|ref|YP_004385552.1|  [L=49]
Description: transposase domain-containing protein, partial [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.7e-05   23.2   0.5    5.4e-05   23.0   0.5    1.1  1  IstB_IS21  IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.5     3e-09   5.4e-05     156     178 .]       3      25 ..       1      25 [. 0.91

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3e-09
                         IstB_IS21 156 evlgdatlatAilDRlvHhahvv 178
                                       ++++d+++a AilDR++Hh++ v
  gi|330509124|ref|YP_004385552.1|   3 DIFKDHVIAAAILDRILHHCTTV 25 
                                       79******************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 267.62
//
Query:       gi|330509125|ref|YP_004385553.1|  [L=107]
Description: transposase domain-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-05   24.6   0.1    3.9e-05   23.5   0.0    1.6  2  IstB_IS21  IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       0.1   1.8e+03       7      26 ..      28      47 ..       8      55 .. 0.59
   2 !   23.5   0.0   2.2e-09   3.9e-05       2      42 ..      57      97 ..      56     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.1
                         IstB_IS21  7 rlrlaklpaqktledidfra 26
                                      +l+ a+ +++ t+e +d+  
  gi|330509125|ref|YP_004385553.1| 28 YLEIAAKEKKSTIEILDYLV 47
                                      33344444444444444444 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 2.2e-09
                         IstB_IS21  2 rrletrlrlaklpaqktledidfraarsldkrkvkeLatls 42
                                      r+l+ r+r+a +p++k l+d+df++++sldk  ++e+a+l+
  gi|330509125|ref|YP_004385553.1| 57 RSLALRTRKAGFPMEKRLDDFDFEFQPSLDKSVINEIASLK 97
                                      8999*********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 586.21
//
Query:       gi|330509126|ref|YP_004385554.1|  [L=411]
Description: transposase [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-26   93.0   0.0    2.3e-26   92.3   0.0    1.4  1  rve           Integrase core domain
    1.6e-05   24.6   0.0    8.1e-05   22.3   0.0    2.2  3  rve_3         Integrase core domain
     0.0013   18.7   0.1      0.031   14.3   0.0    2.5  2  HTH_29        Winged helix-turn helix
     0.0042   17.1   0.0      0.013   15.6   0.0    1.9  1  HTH_7         Helix-turn-helix domain of resolvase
     0.0057   15.7   0.0     0.0085   15.1   0.0    1.2  1  TnsD          Tn7-like transposition protein D
      0.006   16.2   0.0      0.012   15.3   0.0    1.4  1  Sigma70_r4_2  Sigma-70, region 4
     0.0078   16.0   0.0      0.019   14.8   0.0    1.6  1  HTH_IclR      IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   14.9   0.1      0.035   13.6   0.1    1.6  1  Sigma70_r4    Sigma-70, region 4
      0.015   15.3   0.1      0.045   13.7   0.1    1.8  1  HTH_11        HTH domain
      0.032   14.3   0.0       0.11   12.6   0.0    1.9  1  HTH_Mga       M protein trans-acting positive regulator (MGA)
       0.04   14.0   0.0       0.11   12.5   0.0    1.7  1  HTH_3         Helix-turn-helix
      0.077   13.5   0.0       0.24   11.9   0.0    1.9  1  HTH_40        Helix-turn-helix domain
      0.078   12.6   0.0       0.19   11.3   0.0    1.6  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.094   12.5   0.2       0.31   10.9   0.0    2.0  2  HTH_38        Helix-turn-helix domain
      0.098   13.1   0.0       0.17   12.3   0.0    1.4  1  GcrA          GcrA cell cycle regulator
       0.14   12.2   0.0       0.28   11.2   0.0    1.5  1  DUF2089       Protein of unknown function (DUF2089)


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.0     2e-29   2.3e-26       2     118 ..     111     240 ..     110     241 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 2e-29
                               rve   2 trpgelwqvDvt...vvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDng 75 
                                       t+pg + qvD+    +++i + ++++y++++v+ +sr+ +ae++ +  d  t+++++ +a+ +fgg  p+++l+Dn 
  gi|330509126|ref|YP_004385554.1| 111 TKPGVQAQVDWAecgYIDIDGEKRRLYCFTMVLGYSRMRYAEFTLRI-DVYTLIQCHINAFGYFGGY-PQELLYDNI 185
                                       79**********777777777777*********************99.******************9.********* PP

                               rve  76 seytsk............afrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                       ++++ k            +f++f +++g+ ++++rp+rpq++Gk+Er+++ +k++
  gi|330509126|ref|YP_004385554.1| 186 TQIVKKrapkssdstwnsHFQDFFEHYGFIPRLCRPYRPQTKGKIERTVGFVKKD 240
                                       ****99********************************************99976 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.9   3.2e+03      36      53 ..     195     212 ..     186     215 .. 0.78
   2 !   22.3   0.0   7.2e-08   8.1e-05       7      54 ..     218     265 ..     212     267 .. 0.92
   3 ?   -2.8   0.0       5.2   5.8e+03      19      40 ..     277     298 ..     272     307 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.9
                             rve_3  36 frslaearekleawredY 53 
                                       ++s ++ +++ ++++e+Y
  gi|330509126|ref|YP_004385554.1| 195 KSSDSTWNSHFQDFFEHY 212
                                       6677888999999**999 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 7.2e-08
                             rve_3   7 yiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYN 54 
                                       + +p++Pq+ g++E+  g +++ +     f+s+++++++l++w+ + N
  gi|330509126|ref|YP_004385554.1| 218 LCRPYRPQTKGKIERTVGFVKKDFFMGGRFTSFTDLNSQLQKWLSRVN 265
                                       679****************************************98755 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.2
                             rve_3  19 vEsfngtlrdellneelfrsla 40 
                                       +E+f +   +++ n++++ + +
  gi|330509126|ref|YP_004385554.1| 277 IERFKQEGLQKIGNAPSYHNRR 298
                                       7888887777777777755444 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.8e-05     0.031       9      54 ..      12      51 ..       9      58 .. 0.75
   2 ?    1.4   0.1      0.29   3.3e+02      33      50 ..     277     294 ..     277     303 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-05
                            HTH_29  9 aeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrpr 54
                                      +e++s +s+iA+++g sr tv+++l+          l+++rs+ p+
  gi|330509126|ref|YP_004385554.1| 12 NEELS-ISEIARQTGHSRVTVRKYLNS-----QVPPLPQKRSKKPS 51
                                      68897.*******************98.....33455555555555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.29
                            HTH_29  33 lkrfeegGlaalldrrrs 50 
                                       ++rf ++Gl+++ + ++ 
  gi|330509126|ref|YP_004385554.1| 277 IERFKQEGLQKIGNAPSY 294
                                       79******9888776543 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   0.0   1.2e-05     0.013      13      44 ..       6      37 ..       1      38 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                                      GGGSSTTTT--STTTSSSS---SSSS--SS-- CS
                             HTH_7 13 rvvkLleeGisiskIAkevnisRsTvYRylad 44
                                      +++ L +e  sis+IA++++ sR Tv +yl+ 
  gi|330509126|ref|YP_004385554.1|  6 TLRDLFNEELSISEIARQTGHSRVTVRKYLNS 37
                                      6677888889********************97 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.6e-06    0.0085     191     269 ..       7      78 ..       4     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.6e-06
                              TnsD 191 lkeLveeeglslkeiAkelgvdiktVlryakklgllkekkkqkkesrelsskdrekkrkewleliksypdlgktelr 267
                                       l+ L++ e+ls+ eiA++ g +  tV++y++++    ++k +kk s+      ++ +r+  ++ +k++p +  ++ r
  gi|330509126|ref|YP_004385554.1|   7 LRDLFN-EELSISEIARQTGHSRVTVRKYLNSQVPPLPQKRSKKPSK------LDGHREYIIDRLKEFPLSASRIYR 76 
                                       789999.************************9997776655555543......588888888888888855555555 PP

                              TnsD 268 kl 269
                                       + 
  gi|330509126|ref|YP_004385554.1|  77 EI 78 
                                       55 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     1e-05     0.012      25      47 ..      13      35 ..       5      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                                      S---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 25 eglsykEIAellgisegtVksrl 47
                                      e+ls+ EIA+++g s +tV+++l
  gi|330509126|ref|YP_004385554.1| 13 EELSISEIARQTGHSRVTVRKYL 35
                                      79*******************98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.7e-05     0.019      17      41 ..      13      37 ..      12      37 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                      SS-BHHHHHHHHTS-HHHHHHHHHH CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqt 41
                                      +el++se+Ar+tg ++ tv+ +L++
  gi|330509126|ref|YP_004385554.1| 13 EELSISEIARQTGHSRVTVRKYLNS 37
                                      799*******************985 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.1e-05     0.035      13      39 ..       5      33 ..       2      36 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                                      HHHHH..TTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 13 lelrf..geglTleEIgerlgiSrerVrq 39
                                      l+lr    e+l+ +EI+++ g Sr +Vr 
  gi|330509126|ref|YP_004385554.1|  5 LTLRDlfNEELSISEIARQTGHSRVTVRK 33
                                      5566666********************96 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     4e-05     0.045      14      36 ..      13      35 ..       5      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-05
                            HTH_11 14 gpisgeeLAeeLnvSrrtvrrdI 36
                                      + +s++e+A++++ Sr tvr+++
  gi|330509126|ref|YP_004385554.1| 13 EELSISEIARQTGHSRVTVRKYL 35
                                      349******************98 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.7e-05      0.11      18      42 ..      12      36 ..      10      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.7e-05
                           HTH_Mga 18 eksltldelakeLglseltlqsdis 42
                                      +++l+++e+a ++g s++t++++++
  gi|330509126|ref|YP_004385554.1| 12 NEELSISEIARQTGHSRVTVRKYLN 36
                                      6899*******************96 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0001      0.11       9      36 ..      14      41 ..       7      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                                      THHHHHHHHHHTSSHHHHHHHHTTSSCS CS
                             HTH_3  9 glsqeeLAeklGvsrstisriEnGernP 36
                                       ls+ e+A+ +G sr t++++ n +  P
  gi|330509126|ref|YP_004385554.1| 14 ELSISEIARQTGHSRVTVRKYLNSQVPP 41
                                      58999******************97655 PP

>> HTH_40  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   0.00022      0.24       7      34 ..       9      36 ..       5      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                            HTH_40  7 elleeglsieeIAkerglkesTIegHLa 34
                                      +l++e lsi eIA++ g ++ T+ ++L 
  gi|330509126|ref|YP_004385554.1|  9 DLFNEELSISEIARQTGHSRVTVRKYLN 36
                                      799**********************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 ?   11.3   0.0   0.00017      0.19      15      39 ..      12      36 ..       6      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                            HTH_24 15 nprisqreLAerlglSpstvnrrlk 39
                                      n  +s++e+A+++g S+ tv+++l+
  gi|330509126|ref|YP_004385554.1| 12 NEELSISEIARQTGHSRVTVRKYLN 36
                                      7889******************997 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00027      0.31      13      39 ..       7      33 ..       2      36 .. 0.88
   2 ?   -3.0   0.1       5.6   6.3e+03      35      41 ..      72      78 ..      70      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                            HTH_38 13 IerllaeGlslreIArrLgrspsTIsR 39
                                      + +l +e ls++eIAr+ g s+ T+ +
  gi|330509126|ref|YP_004385554.1|  7 LRDLFNEELSISEIARQTGHSRVTVRK 33
                                      56899*****************99976 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.6
                            HTH_38 35 sTIsREl 41
                                      s I+RE+
  gi|330509126|ref|YP_004385554.1| 72 SRIYREI 78
                                      5599*98 PP

>> GcrA  GcrA cell cycle regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015      0.17       8      36 ..       4      31 ..       1      37 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                              GcrA  8 velLkklwleGlSasqiaaqlggvsRnAV 36
                                        +L++l++e lS+s+ia+q g  sR  V
  gi|330509126|ref|YP_004385554.1|  4 FLTLRDLFNEELSISEIARQTG-HSRVTV 31
                                      568*****************99.777655 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00025      0.28      51     107 ..      16      72 ..       2      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                           DUF2089  51 nlkevekelgisYpTvrnrldeileaLgyeeeeeeeeeeeerkeileklekgeisve 107
                                       +++e++++ g s  Tvr+ l++ +  L  + +++ ++ + +r+ i+++l++  +s++
  gi|330509126|ref|YP_004385554.1|  16 SISEIARQTGHSRVTVRKYLNSQVPPLPQKRSKKPSKLDGHREYIIDRLKEFPLSAS 72 
                                       799*************************9999774454689********99877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2402.60
//
Query:       gi|330509127|ref|YP_004385555.1|  [L=379]
Description: hypothetical protein MCON_3520 [Methanosaeta concilii GP6]
Scores for complete 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   29.5   0.1    1.4e-06   28.8   0.1    1.3  1  Radical_SAM  Radical SAM superfamily
     0.0043   17.3   1.3      0.011   15.9   0.5    2.1  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 !   28.8   0.1   1.5e-10   1.4e-06       3      83 ..      99     187 ..      97     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.5e-10
                                       EESEESS--TTTSCCTT.........HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.........vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerl 70 
                                       + + Cn++C+fC  +            ++++ gr ls+e+ +e ++el ++ ++  ++++gg+ +l +d + +++ +
  gi|330509127|ref|YP_004385555.1|  99 INNSCNRNCWFCGHNGIkrslgcmgcNKWNENGRPLSIERWKEVIDEL-KDLNCMDIFITGGDLTLEWDRTIDILDY 174
                                       6678***********99*******************************.6888*****************9999999 PP

                                       HHTCCCTEEEEEE CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM  71 aklavpgiritve 83 
                                         ++  +i it+ 
  gi|330509127|ref|YP_004385555.1| 175 TNRKFTNIYITLH 187
                                       8887555555554 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.27   2.4e+03      90     123 ..      39      70 ..      19      80 .. 0.64
   2 !   15.9   0.5   1.3e-06     0.011      14      88 ..     102     184 ..      93     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.27
                           Fer4_12  90 lytgytleelskkekeellkeidvlvdGkfeesl 123
                                       +++  +++ ++    +++l+e++ l  G+f  ++
  gi|330509127|ref|YP_004385555.1|  39 VTSCEKNNSIQ--GERKFLNELKQLCLGNFYSNR 70 
                                       44445555555..457888888888888876655 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.3e-06
                           Fer4_12  14 gCnlsCkgCfnketw..........sfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevk 80 
                                        Cn++C +C  + ++            ++g++ + e  +e+i++lk+ +  ++ ++GG+  l  + +  ++++++  
  gi|330509127|ref|YP_004385555.1| 102 SCNRNCWFCGHNGIKrslgcmgcnkWNENGRPLSIERWKEVIDELKDLNCMDIFITGGDLTL--EWDRTIDILDYTN 176
                                       6********9999995555555444344999*******************************..9999999999999 PP

                           Fer4_12  81 eekpekdi 88 
                                       +++ +  i
  gi|330509127|ref|YP_004385555.1| 177 RKFTNIYI 184
                                       99886554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2504.54
//
Query:       gi|330509128|ref|YP_004385556.1|  [L=495]
Description: radical SAM domain-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-12   45.9   0.1    1.5e-11   44.9   0.1    1.4  1  Radical_SAM  Radical SAM superfamily
    6.8e-11   42.6   0.1    3.5e-10   40.3   0.0    2.2  2  Fer4_12      4Fe-4S single cluster domain
    2.8e-05   24.2   0.0    2.8e-05   24.2   0.0    2.3  3  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.11   12.3   0.4        8.8    6.3   0.0    2.8  2  DUF3116      Protein of unknown function (DUF3116)
       0.17   12.4   4.7       0.49   11.0   4.7    1.9  1  SPASM        Iron-sulfur cluster-binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.1   4.3e-15   1.5e-11       2     143 ..     104     259 ..     103     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 4.3e-15
                                       EEESEESS--TTTSCCTT.........HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHH CS
                                       xxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet.........vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvell 67 
                                       +vt+ Cn+rC++Ca++           +++  + + + +++   ++ke++ +++     + + ggepll+ +++++ 
  gi|330509128|ref|YP_004385556.1| 104 SVTEDCNFRCKYCAFSDLyeytrsqsnKYMKSDTAKRAIDYYFSLLKEGArYNPKrQPALAFYGGEPLLNFNLIKIC 180
                                       68999***********98**9999998777777788888888888888877666558888999************** PP

                                       HHHHHTC..CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH..HHHHHHTCTSHHHHHHHHHHHHHHT CS
                                       xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  68 erlakla..vpgiritvetngtlpdeeklerllelgvdrvslgleaadde..kvlklmnrghtfeevlealeklrea 140
                                        + ++++  + + r t++tng l+d+ek+  l e     ++++l+ + +e  + + + n+++tf ev+ ++  + + 
  gi|330509128|ref|YP_004385556.1| 181 VEHIENEygNCKTRYTLTTNGSLLDKEKANWLMEHD-FSIAVSLDGPEEEhnRLRVYPNGKGTFREVMGNVTSILKT 256
                                       **********************************88.*************77666666799*******999999998 PP

                                       TSE CS
                                       xxx RF
                       Radical_SAM 141 gik 143
                                       g  
  gi|330509128|ref|YP_004385556.1| 257 GYT 259
                                       876 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   5.5e+03      73      94 ..      43      65 ..      33      79 .. 0.72
   2 !   40.3   0.0   9.7e-14   3.5e-10      12     126 ..     106     230 ..      94     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                           Fer4_12 73 lelvkevkeekp.ekdiwlytgy 94
                                       ++v ++  +++ e  i++y++ 
  gi|330509128|ref|YP_004385556.1| 43 DDIVFHLSDKFSkEDLIFCYNWL 65
                                      56777777888877789999985 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 9.7e-14
                           Fer4_12  12 vsgCnlsCkgCfnketw..............sfksgkeftkelleeiiedlkk......esiegltllGGEPllpen 68 
                                       +++Cn++Ck+C   ++                        k +++  +  lk+      ++++ l + GGEPll  n
  gi|330509128|ref|YP_004385556.1| 106 TEDCNFRCKYCAFSDLYeytrsqsnkymksdT-------AKRAIDYYFSLLKEgarynpKRQPALAFYGGEPLL--N 173
                                       689********999888343333222222222.......24444444444544444333777************..9 PP

                           Fer4_12  69 aeallelvkevkeekpekdiwlytgytleelskkekeellkeidvlvdGkfeeslede 126
                                        + +   v+++++e+ +   + yt +t+  l++kek + l e+d+ + + ++  +e++
  gi|330509128|ref|YP_004385556.1| 174 FNLIKICVEHIENEYGN-CKTRYTLTTNGSLLDKEKANWLMEHDFSIAVSLDGPEEEH 230
                                       9999999********96.789***********************99999988544443 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   7.8e-09   2.8e-05       5      97 ..     106     208 ..     103     226 .. 0.57
   2 ?   -3.2   0.0       2.5   8.9e+03      25      69 ..     329     339 ..     319     367 .. 0.49
   3 ?   -4.5   1.9         5   1.8e+04       8      18 ..     427     439 ..     421     466 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7.8e-09
                           Fer4_14   5 lsgCnlsCkgCd.......nketwkselgkpqteelleqilk.....dlkkseikiqglvltGGePLhyenkkellk 69 
                                       +  Cn+ Ck C        ++++ ++ ++   +++ ++  ++       ++ + ++  l + GGePL+    + +  
  gi|330509128|ref|YP_004385556.1| 106 TEDCNFRCKYCAfsdlyeyTRSQSNKYMKSDTAKRAIDYYFSllkegARYNPKRQP-ALAFYGGEPLLN--FNLIKI 179
                                       578********977766663333333333333344444444332232222223333.5*********55..444444 PP

                           Fer4_14  70 lvkrlkeey..pekkiwletngtleielek 97 
                                        v+++ +ey   + + +l tng+l  + ek
  gi|330509128|ref|YP_004385556.1| 180 CVEHIENEYgnCKTRYTLTTNGSLL-DKEK 208
                                       5788888885556777888888876.4333 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.5
                           Fer4_14  25 lgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellk 69 
                                       l ++++++ l                                  +
  gi|330509128|ref|YP_004385556.1| 329 LDHQKQRDKL----------------------------------T 339
                                       3333333333..................................2 PP

  == domain 3  score: -4.5 bits;  conditional E-value: 5
                           Fer4_14   8 Cnl..sCkgCdnk 18 
                                       C++  +C  C+ k
  gi|330509128|ref|YP_004385556.1| 427 CKVrrNCSQCYPK 439
                                       4432268888855 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0025       8.8      24      69 ..      38      81 ..      26      93 .. 0.80
   2 ?    3.0   0.1     0.026        95      64      81 ..     189     206 ..     184     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0025
                           DUF3116 24 knlqleeldeksvkkltkneLLytvYWLElkgyilRkeekannkkr 69
                                      k+l+l+ + ++ ++k++k +L+++  WL   g i  +++  ++++ 
  gi|330509128|ref|YP_004385556.1| 38 KSLSLDDIVFHLSDKFSKEDLIFCYNWLKKWGKIRPMKQ--KSSTS 81
                                      57888889999999**************98887765555..34444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.026
                           DUF3116  64 annkkrYelTekGellyk 81 
                                        n k+rY+lT +G ll k
  gi|330509128|ref|YP_004385556.1| 189 GNCKTRYTLTTNGSLLDK 206
                                       47799********99976 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.7   0.00014      0.49       1      64 [.     372     427 ..     372     437 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnirees.leeIwnseeyqefrkskkfplielC 64 
                                       C +p r +f+++dG+ + C    +++++ + +Gn++e   +e+I+  e + +   s   + +++C
  gi|330509128|ref|YP_004385556.1| 372 C-IPGRKIFVDVDGNFHIC----EKINSFFPIGNVNEGLnFENIC--ELLSNYI-S-SMDKCPSC 427
                                       6.6899*************....677666******7643488887..5555533.2.22223344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3220.61
//
Query:       gi|330509129|ref|YP_004385557.1|  [L=614]
Description: ABC transporter ATP-binding protein [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-34  118.6   0.0    4.9e-34  117.8   0.0    1.4  1  ABC_tran      ABC transporter
    6.9e-08   32.6   0.0     0.0042   16.9   0.0    2.6  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.2e-05   24.2   9.3      5e-05   23.1   1.8    2.3  2  ABC_membrane  ABC transporter transmembrane region
    2.3e-05   24.3   0.0     0.0017   18.2   0.0    2.6  3  AAA_15        AAA ATPase domain
    0.00018   21.0   0.4       0.28   10.6   0.0    2.3  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0032   17.2   0.0     0.0068   16.1   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0073   15.9   0.1      0.014   15.0   0.1    1.4  1  SRP54         SRP54-type protein, GTPase domain
     0.0078   16.0   0.1      0.027   14.2   0.1    1.9  1  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.011   16.3   0.0       0.02   15.4   0.0    1.4  1  AAA_23        AAA domain
      0.014   14.7   0.0      0.026   13.8   0.0    1.4  1  Zeta_toxin    Zeta toxin
      0.019   15.3   0.1      0.042   14.2   0.1    1.7  1  AAA_19        AAA domain
      0.022   15.2   0.0      0.056   13.9   0.0    1.7  1  AAA           ATPase family associated with various cellular 
      0.027   13.1   0.0        1.8    7.1   0.0    2.2  2  AAA_13        AAA domain
      0.027   15.0   0.0      0.067   13.7   0.0    1.7  1  AAA_18        AAA domain
      0.035   14.4   0.0       0.13   12.5   0.0    1.9  2  AAA_22        AAA domain
      0.036   14.1   0.0       0.12   12.4   0.0    1.9  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.038   12.8   0.0      0.057   12.2   0.0    1.2  1  DLIC          Dynein light intermediate chain (DLIC)
      0.089   13.0   0.1       0.19   11.9   0.1    1.5  1  AAA_28        AAA domain
       0.11   12.9   0.1       0.28   11.5   0.1    1.8  1  AAA_16        AAA ATPase domain
       0.11   12.1   0.0       0.19   11.3   0.0    1.4  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.16   11.9   0.1       0.35   10.8   0.1    1.5  1  RsgA_GTPase   RsgA GTPase
       0.17   11.8   0.0        0.7    9.8   0.0    1.9  2  NTPase_1      NTPase
        0.2   10.8   0.0       0.37    9.9   0.0    1.5  2  G-alpha       G-protein alpha subunit
       0.77    9.5   2.4        9.1    6.0   0.2    2.4  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   0.0   6.5e-37   4.9e-34       1     137 []     385     539 ..     385     539 .. 0.91

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 6.5e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+++s+k+k+g+++a+vG nG+GK+tL+kll++l++p++G+i +dg dlk+ + + lr+ei+v++q+   +++l+++
  gi|330509129|ref|YP_004385557.1| 385 LNDISVKIKPGQVIALVGGNGSGKTTLIKLLCRLYDPQKGRIAIDGVDLKDMRVSDLRREISVVFQD-YAQYNLSLA 460
                                       799****************************************************************.778888899 PP

                                       HH..................HHHTCHHHHHHHSTTGGTTCBGESTTS...GGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xx..................xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..................esdeeiekalsklglkelkdtvvkssp...ssLSgGqkqrvalarallkkpkllllD 133
                                       en                  ++d+ ++++l++l+  +  +t++++     + LS G++q+valara++++++++++D
  gi|330509129|ref|YP_004385557.1| 461 ENiwlgsaagpldmgkvakaARDSGVDRILKRLETGY--ETTLGKWFdkgTDLSIGEWQKVALARAFIRDSQIIIMD 535
                                       ***************9987777777********9988..44443332344*************************** PP

                                       STTT CS
                                       xxxx RF
                          ABC_tran 134 Epta 137
                                       Ept+
  gi|330509129|ref|YP_004385557.1| 536 EPTS 539
                                       **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 ?   -3.3   0.0       8.2   6.2e+03      47      86 ..     225     264 ..     220     273 .. 0.68
   2 !   16.9   0.0   5.7e-06    0.0042       2      22 ..     398     418 ..     397     457 .. 0.82
   3 !   13.0   0.0   8.9e-05     0.066     236     285 ..     510     556 ..     469     569 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 8.2
                            AAA_21  47 slldlydpeipfefeieeflsqgvryryglrlersqv.eek 86 
                                       ++l +  ++++f+ ei+ +++ g+ +r +++  r+q+ +ek
  gi|330509129|ref|YP_004385557.1| 225 WYLHWLLTDKSFAKEIR-LFDLGSIFRDRYTALREQLrKEK 264
                                       55566666777777777.77777777777777777774443 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 5.7e-06
                            AAA_21   2 nvliGpNgsGKSnLLdaldll 22 
                                        +l+G NgsGK++L+++l  l
  gi|330509129|ref|YP_004385557.1| 398 IALVGGNGSGKTTLIKLLCRL 418
                                       68***************9544 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 8.9e-05
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkel 285
                                       +lS G  +  al+ a++r+     +++ DEp ++L+Pk+ ++++  ++el
  gi|330509129|ref|YP_004385557.1| 510 DLSIGEWQKVALARAFIRDS---QIIIMDEPTSSLDPKAEAEVFAKFREL 556
                                       6799*****9*******999...9*************9988877444444 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.0     0.018        14       4      73 ..      44     114 ..      41     128 .. 0.79
   2 !   23.1   1.8   6.7e-08     5e-05     116     270 ..     161     314 ..     159     317 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHSS.TCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   4 iillailagvlsplfplvlgrildtlldk.gdpetealnvysllllllglaqfilallqsyllnvtgerls 73 
                                       +i l i +gvl ++  +v++ i+d + +  +++++ea++  +l++++l++++ +l++l ++  n+++e +s
  gi|330509129|ref|YP_004385557.1|  44 SIALVIPQGVLPLASLYVMKLIVDCVATGySSADSEAVTGQLLMFVALAILVELLSILIQSAANIASEFQS 114
                                       677888899999************99887555555778888888888888888888888887788777555 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 6.7e-08
                                       CHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHTH CS
                      ABC_membrane 116 geklglffqslltfvgglivmfylgwkltlvllailpliilvsaviakilk..klkkkeqkavakassvaeEslsgi 190
                                        ++l ++ q+ +++ ++++++f+ +w + ++ll  ++  ilv+ +++ +l   +++++e+++ +     +  + s  
  gi|330509129|ref|YP_004385557.1| 161 VRSLTQLAQNAISMASTVALLFLASWAIVVALLMASIPGILVQMIYSGKLYrwQVSRTEKDRKSWYLHWLLTDKSFA 237
                                       667899**********************9999988888888888888777524677888888888999999****** PP

                                       HHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHH CS
                      ABC_membrane 191 rtVkafgreeyflekfekaleeakkagikkaianglligitqllgllsyalalwfGttlvisgelsvgdlvvflslf 267
                                       + +++f   ++f+++++  +e+ +k  +   ++ +  + ++q++ + +++  l f +   ++g++++gd   ++++f
  gi|330509129|ref|YP_004385557.1| 238 KEIRLFDLGSIFRDRYTALREQLRKEKLDLSVSKSKANLAAQAIESMAVFGSLAFLAMEGMKGNITIGD---ITMYF 311
                                       *********************************************************************...66666 PP

                                       HHH CS
                      ABC_membrane 268 ail 270
                                         l
  gi|330509129|ref|YP_004385557.1| 312 GAL 314
                                       644 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.1   1.6e+03      65     102 ..     118     152 ..      94     172 .. 0.68
   2 !   18.2   0.0   2.2e-06    0.0017      15      78 ..     386     446 ..     384     493 .. 0.80
   3 ?    2.8   0.0       0.1        77     323     354 ..     528     559 ..     518     565 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.1
                            AAA_15  65 leifeniseskdikIdvefaekekakeyektlkskekk 102
                                        +++++i + k++ Id+e+    ++ +y +tl++ +++
  gi|330509129|ref|YP_004385557.1| 118 SDHTQDILHAKSVAIDLEY---YESPKYYDTLHRAQQE 152
                                       4567788899999999999...5678888888877665 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.2e-06
                            AAA_15  15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdik 78 
                                        d+++++++  +  l+G N+sGK++++++l  + + +    k  i i+  dl++++  +  ++i 
  gi|330509129|ref|YP_004385557.1| 386 NDISVKIKPGqVIALVGGNGSGKTTLIKLLCRLYDPQ----KGRIAIDGVDLKDMRVSDLRREIS 446
                                       677888888789******************9999988....777888888887775544444443 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.1
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkeland 354
                                       ++ i++++EP  +L p+a  +++ +++ela+ 
  gi|330509129|ref|YP_004385557.1| 528 DSQIIIMDEPTSSLDPKAEAEVFAKFRELAKG 559
                                       569**************************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 !    8.3   0.2    0.0019       1.4      25      42 ..     396     413 ..     382     419 .. 0.79
   2 !   10.6   0.0   0.00038      0.28     146     209 ..     520     579 ..     417     586 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0019
                                       SEEEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlld 42 
                                       ++ a+vG NGSGK+ l+ 
  gi|330509129|ref|YP_004385557.1| 396 QVIALVGGNGSGKTTLIK 413
                                       4789**********9986 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00038
                                       HHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 146 alaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklv 209
                                       ala       ++ + + ++De  + LD k  ++v   ++e  k    ivi +r  +++ ad ++
  gi|330509129|ref|YP_004385557.1| 520 ALA----RAFIRDSQIIIMDEPTSSLDPKAEAEVFAKFRELAKGKTAIVIGHRLSTVRMADCIY 579
                                       443....344688899****************************************99998776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   9.1e-06    0.0068      13      39 ..     386     412 ..     383     427 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.1e-06
                            AAA_29  13 dghtieidlkgatlltGpsGsGKSTll 39 
                                       ++ +++i++ +++ l+G +GsGK+Tl+
  gi|330509129|ref|YP_004385557.1| 386 NDISVKIKPGQVIALVGGNGSGKTTLI 412
                                       55678999888***************9 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.9e-05     0.014       2      38 ..     396     432 ..     395     438 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaD 38 
                                       +vi+lvG +G+GKTt +  L +l+  ++ ++++  +D
  gi|330509129|ref|YP_004385557.1| 396 QVIALVGGNGSGKTTLIKLLCRLYDPQKGRIAIDGVD 432
                                       589*********************9999999887777 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   3.6e-05     0.027      18      50 ..     395     427 ..     389     569 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-05
                            AAA_30  18 drvavltGpAGtGKttalkalreaweaaggrvi 50 
                                        +v +l+G+ G+GKtt++k l ++++ ++gr++
  gi|330509129|ref|YP_004385557.1| 395 GQVIALVGGNGSGKTTLIKLLCRLYDPQKGRIA 427
                                       57999****************999999966654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.7e-05      0.02      20      40 ..     396     416 ..     376     458 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-05
                            AAA_23  20 gltlItGpNGaGKTTildAik 40 
                                        + +++G NG+GKTT++  ++
  gi|330509129|ref|YP_004385557.1| 396 QVIALVGGNGSGKTTLIKLLC 416
                                       57899************9988 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.5e-05     0.026      18      57 ..     397     436 ..     385     454 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                        Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57 
                                       +i l+G+ G+GK++l++ll +  ++q++ + +d+ dl+ +
  gi|330509129|ref|YP_004385557.1| 397 VIALVGGNGSGKTTLIKLLCRLYDPQKGRIAIDGVDLKDM 436
                                       78899****************************9998865 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   5.6e-05     0.042       9      38 ..     394     423 ..     387     566 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.6e-05
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelg 38 
                                       + +v+++++G G+GKT+++k  ++l+  ++
  gi|330509129|ref|YP_004385557.1| 394 PGQVIALVGGNGSGKTTLIKLLCRLYDPQK 423
                                       67899***************9999887665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.5e-05     0.056       2      54 ..     399     453 ..     398     463 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.5e-05
                                       EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelfkeak 54 
                                        l+G  G GKT+l+k +++  +     + i+g +l ++ v++  ++i+ +f++  
  gi|330509129|ref|YP_004385557.1| 399 ALVGGNGSGKTTLIKLLCRLYDpqKGRIAIDGVDLKDMRVSDLRREISVVFQDYA 453
                                       699*****************96325569999999999999999999999999854 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0024       1.8      23      41 ..     402     420 ..     396     470 .. 0.63
   2 ?    3.6   0.0     0.029        21     525     554 ..     527     556 ..     517     575 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0024
                            AAA_13  23 GwNGaGKTtLSrllrslel 41 
                                       G NG+GKTtL +ll  l  
  gi|330509129|ref|YP_004385557.1| 402 GGNGSGKTTLIKLLCRLYD 420
                                       99**********9988843 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.029
                            AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksr 554
                                          +i+++D P SSLD ++   vf   ++ 
  gi|330509129|ref|YP_004385557.1| 527 RDSQIIIMDEPTSSLDPKAEAEVFAKFREL 556
                                       5679************99877777666655 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     9e-05     0.067       1      67 [.     398     463 ..     398     495 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf....gvnlrdvakenglllevdpealdeskrldedkldklldaleen 67 
                                       I+l G  G+GKttl k L ++  +    g++ +d +  ++++ ++      e  ++ +d+ +++l++ e++
  gi|330509129|ref|YP_004385557.1| 398 IALVGGNGSGKTTLIKLLCRL--YdpqkGRIAIDGVDLKDMRVSDLRR---EISVVFQDYAQYNLSLAENI 463
                                       8899**************776..5667899999999999999999888...99999999999988887765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00018      0.13       4      32 ..     394     422 ..     390     459 .. 0.78
   2 ?   -2.7   0.0       8.5   6.4e+03      91     117 ..     526     558 ..     489     565 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldee 32 
                                         ++++++G  G+GKTtl++ l + +d +
  gi|330509129|ref|YP_004385557.1| 394 PGQVIALVGGNGSGKTTLIKLLCRLYDPQ 422
                                       56899****************99998754 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.5
                            AAA_22  91 v..ielliiDEaqh.lr...seealeeLrslln 117
                                           +++i DE    l+   ++e++ ++r+l++
  gi|330509129|ref|YP_004385557.1| 526 IrdSQIIIMDEPTSsLDpkaEAEVFAKFRELAK 558
                                       144468888887777765433777777766665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015      0.12      13      42 ..     391     418 ..     380     427 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                       HHHHCHTEEEEEEESTTSSHHHHHHHHHHH CS
                              TsaE  13 klakalgdvilLeGdLGaGKTtlvrglaka 42 
                                       k++   g+vi+L G  G+GKTtl++ l++ 
  gi|330509129|ref|YP_004385557.1| 391 KIKP--GQVIALVGGNGSGKTTLIKLLCRL 418
                                       3333..899****************99986 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.7e-05     0.057      19      74 ..     389     443 ..     381     460 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.7e-05
                              DLIC  19 ssklPsgksvlvlGedgsGkttliaklqGveeekkGrGleylyldvkdedrddltr 74 
                                       s k+  g+ + ++G +gsGkttli  l  + +++kGr +    +d+kd    dl r
  gi|330509129|ref|YP_004385557.1| 389 SVKIKPGQVIALVGGNGSGKTTLIKLLCRLYDPQKGR-IAIDGVDLKDMRVSDLRR 443
                                       56888899999*************************9.445566666666666655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00026      0.19       2      19 ..     398     415 ..     397     425 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                            AAA_28   2 ivitGgestGKTtlleaL 19 
                                       i+++Gg ++GKTtl++ L
  gi|330509129|ref|YP_004385557.1| 398 IALVGGNGSGKTTLIKLL 415
                                       89*************988 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00038      0.28      25      52 ..     396     435 ..     385     565 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00038
                            AAA_16  25 elvllsGesGvGKsslvrellralekd............g 52 
                                       +++ l+G  G+GK++l++ l r +  +            +
  gi|330509129|ref|YP_004385557.1| 396 QVIALVGGNGSGKTTLIKLLCRLYDPQkgriaidgvdlkD 435
                                       6899*****************9888885444444444440 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00026      0.19       2      31 ..     397     428 ..     396     440 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEE CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklav 31 
                                       v+ l+G  GsGKTtL++ l+   + ++ ++a+
  gi|330509129|ref|YP_004385557.1| 397 VIALVGGNGSGKTTLIKLLCrlYDPQKGRIAI 428
                                       7889999**********999665556666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00047      0.35      89     121 ..     384     417 ..     372     441 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00047
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       +l++++ ++k  ++++lvG  G GK+tLi+ l  
  gi|330509129|ref|YP_004385557.1| 384 TLNDISVKIKPgQVIALVGGNGSGKTTLIKLLCR 417
                                       567788888877*****************99975 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00094       0.7       2      44 ..     398     442 ..     397     458 .. 0.79
   2 ?   -1.4   0.0       2.6   1.9e+03      88     103 ..     520     536 ..     484     537 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00094
                                       EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE------ CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfyteevreggrr 44 
                                       +++ G  G+GKtTl+k +++l + +   + ++G+  +++r  + r
  gi|330509129|ref|YP_004385557.1| 398 IALVGGNGSGKTTLIKLLCRLYDPQkgRIAIDGVDLKDMRVSDLR 442
                                       7889*************9999865522577889988888866555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.6
                                       HHHHHH.HHH-EEEE-- CS
                          NTPase_1  88 alrkal.seadviviDE 103
                                       al +a+ +++++i++DE
  gi|330509129|ref|YP_004385557.1| 520 ALARAFiRDSQIIIMDE 536
                                       4455555999******9 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.7   4.2e+03      97     109 ..     120     132 ..      89     176 .. 0.52
   2 ?    9.9   0.0    0.0005      0.37      26      50 ..     398     422 ..     383     585 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.7
                                       -SCCCS-HCHHHH CS
                           G-alpha  97 rldplkkveasli 109
                                       + ++++++++  i
  gi|330509129|ref|YP_004385557.1| 120 HTQDILHAKSVAI 132
                                       3333333333322 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0005
                                       EEEEESTTSSHHHHHHHHHHHCS-- CS
                           G-alpha  26 llllGqseSGKsTilkqlkllykkg 50 
                                       + l+G ++SGK+T++k l +ly+++
  gi|330509129|ref|YP_004385557.1| 398 IALVGGNGSGKTTLIKLLCRLYDPQ 422
                                       89********************886 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.12        87      26      75 ..     116     166 ..     107     182 .. 0.75
   2 ?    6.0   0.2     0.012       9.1       4      21 ..     398     415 ..     395     419 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                         PduV-EutP  26 lkYkktqaiefsdev.iDtPGeylenrklysalivtsaeadv..ialvqdate 75 
                                       l  + tq i + ++v iD   ey e+ k+y +l  +  ea    i +v + t+
  gi|330509129|ref|YP_004385557.1| 116 LVSDHTQDILHAKSVaIDL--EYYESPKYYDTLHRAQQEAAYrpIHIVRSLTQ 166
                                       5667899887666555997..9***********99998886433666666554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                         PduV-EutP   4 illiGkvgsGKttLtqal 21 
                                       i l+G  gsGKttL + l
  gi|330509129|ref|YP_004385557.1| 398 IALVGGNGSGKTTLIKLL 415
                                       789***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); 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: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 3666.66
//
Query:       gi|330509130|ref|YP_004385558.1|  [L=122]
Description: hypothetical protein MCON_3523 [Methanosaeta concilii GP6]
Scores for complete 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   29.3   0.0      1e-06   28.5   0.0    1.3  1  TrmB          Sugar-specific transcriptional regulator TrmB
    3.5e-05   23.8   0.0    6.7e-05   22.9   0.0    1.4  2  HTH_20        Helix-turn-helix domain
    5.2e-05   23.0   1.4      6e-05   22.8   0.7    1.5  2  HTH_5         Bacterial regulatory protein, arsR family
    6.4e-05   23.4   0.0    0.00011   22.6   0.0    1.4  1  HTH_27        Winged helix DNA-binding domain
     0.0002   21.1   0.4     0.0005   19.8   0.1    1.9  2  DUF1495       Winged helix DNA-binding domain (DUF1495)
     0.0014   18.4   0.1     0.0029   17.4   0.0    1.6  2  HTH_IclR      IclR helix-turn-helix domain
     0.0072   16.3   0.0     0.0099   15.8   0.0    1.3  1  PadR          Transcriptional regulator PadR-like family
     0.0079   16.2   1.4      0.012   15.6   1.4    1.3  1  HTH_45        Winged helix-turn-helix
  ------ inclusion threshold ------
      0.017   14.9   0.2      0.025   14.3   0.2    1.4  1  DUF4364       Domain of unknown function (DUF4364)
        0.1   12.6   0.0       0.13   12.3   0.0    1.1  1  Replic_Relax  Replication-relaxation


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 !   28.5   0.0   5.7e-10     1e-06      15      64 ..      25      75 ..      22      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 5.7e-10
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT.EEEE CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk.lYra 64
                                      l Llkl +++ + ++++l +p+s+ Y+ L  L++ GlV +e+ + k +Y  
  gi|330509130|ref|YP_004385558.1| 25 LQLLKLRNMNLTNLSKMLSIPKSSTYKNLTILIESGLVIKEPTNNKwRYYK 75
                                      579***************************************984434433 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   3.7e-08   6.7e-05       3      54 ..      12      62 ..      10      68 .. 0.94
   2 ?   -3.1   0.0       4.8   8.7e+03      35      46 ..      96     107 ..      92     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.7e-08
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                       ++AL++  R+ il++L   + + ++ l + l+++k++ +++L +L e gLv
  gi|330509130|ref|YP_004385558.1| 12 TLRALSSSNRLFILQLL-KLRNMNLTNLSKMLSIPKSSTYKNLTILIESGLV 62
                                      589**************.*********************************8 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.8
                                       TS-HHHHHHHHH CS
                            HTH_20  35 dlskntlsyHLr 46 
                                       d+sk+++++ L+
  gi|330509130|ref|YP_004385558.1|  96 DISKSSVRFALK 107
                                       789999988765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.7   3.4e-08     6e-05       2      47 .]      19      64 ..      18      64 .. 0.96
   2 ?   -3.6   0.0       6.1   1.1e+04      27      33 ..      97     103 ..      96     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.4e-08
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      ++Rl IL+lL  +++  + l+++l +++s +   L +L e+GLV k
  gi|330509130|ref|YP_004385558.1| 19 SNRLFILQLLKLRNMNLTNLSKMLSIPKSSTYKNLTILIESGLVIK 64
                                      78******************************************86 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.1
                                       S-HHHHH CS
                             HTH_5  27 lsqstvS 33 
                                       +s+s v+
  gi|330509130|ref|YP_004385558.1|  97 ISKSSVR 103
                                       8999886 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   6.3e-08   0.00011       7      68 .]      23      80 ..      17      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.3e-08
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      ++L l++  +r + l+ l+++l + +s++ ++l  L+e GLv   + +++ + + ++lT+kG
  gi|330509130|ref|YP_004385558.1| 23 FILQLLK--LRNMNLTNLSKMLSIPKSSTYKNLTILIESGLV--IKEPTNNKWRYYKLTPKG 80
                                      6788888..999******************************..8889*************9 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 !   19.8   0.1   2.8e-07    0.0005      51      85 ..      48      82 ..      12      86 .. 0.85
   2 ?   -3.5   0.0       5.2   9.4e+03       4      12 ..      96     104 ..      93     106 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.8e-07
                           DUF1495 51 krynsessLielGLveeeeeseglklYklteeGie 85
                                        y++ + Lie GLv +e  ++  ++Yklt++G  
  gi|330509130|ref|YP_004385558.1| 48 STYKNLTILIESGLVIKEPTNNKWRYYKLTPKGAM 82
                                      56888889*************************86 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.2
                           DUF1495   4 slnkSkvRk 12 
                                        + kS+vR 
  gi|330509130|ref|YP_004385558.1|  96 DISKSSVRF 104
                                       577888885 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 !   17.4   0.0   1.6e-06    0.0029      18      48 ..      32      62 ..      13      66 .. 0.84
   2 ?   -2.6   0.0       2.8     5e+03      30      36 ..      97     103 ..      96     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                                      S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyv 48
                                       ++l+ l++ + +pkS+++  L  L+e G+v
  gi|330509130|ref|YP_004385558.1| 32 NMNLTNLSKMLSIPKSSTYKNLTILIESGLV 62
                                      399***************************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.8
                                       S-HHHHH CS
                          HTH_IclR  30 lpkStvh 36 
                                       ++kS+v+
  gi|330509130|ref|YP_004385558.1|  97 ISKSSVR 103
                                       799*997 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.5e-06    0.0099      21      70 ..      37      81 ..      24      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.5e-06
                                      CCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCC CS
                              PadR 21 elsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGr 70
                                      +ls  +l + ++s Y++L+ L ++glv +e ++     + +yY+lT++G 
  gi|330509130|ref|YP_004385558.1| 37 NLS-KMLSIPKSSTYKNLTILIESGLVIKEPTN----NKWRYYKLTPKGA 81
                                      554.35778899*****************9776....599********97 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   1.4   6.8e-06     0.012      11      68 ..      24      86 ..      22      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.8e-06
                            HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli.....kkskekYvlTekGlellek 68
                                      IL+ ++  + + T++ +   +  + + k L +L+e gl+     +++   Y+lT kG  l ++
  gi|330509130|ref|YP_004385558.1| 24 ILQLLKLRNMNLTNLSKMLSIPKSSTYKNLTILIESGLVikeptNNKWRYYKLTPKGAMLFSN 86
                                      8999999999****************************9999977788899******998765 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   1.4e-05     0.025      39      85 ..      52     101 ..      20     121 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                           DUF4364  39 alseLvesglieee.ekenktlykiTekGketlelfenr..ipksireki 85 
                                        l+ L+esgl+ +e ++++  +yk+T+kG+   +   +   i+++i +  
  gi|330509130|ref|YP_004385558.1|  52 NLTILIESGLVIKEpTNNKWRYYKLTPKGAMLFSNESKMliISNDISKSS 101
                                       46789*********888999*********998876655422445555555 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.1e-05      0.13       6      74 ..      29      89 ..      25     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                      Replic_Relax  6 ehrvlTtrqiarllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaaqra 74
                                      ++r ++  ++ ++l   +++ +++ L++L e gl+ + ++  ++ r       Y LtpkGa l++++ +
  gi|330509130|ref|YP_004385558.1| 29 KLRNMNLTNLSKMLSIPKSS-TYKNLTILIESGLVIK-EPTNNKWR------YYKLTPKGAMLFSNESK 89
                                      67888999999999999999.**************99.33323344......59*******99966655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 939.00
//
Query:       gi|330509131|ref|YP_004385559.1|  [L=189]
Description: hypothetical protein MCON_3526 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0014   18.4   1.3      0.012   15.4   0.1    2.4  2  DivIC           Septum formation initiator
  ------ inclusion threshold ------
      0.011   15.8   2.9      0.011   15.8   2.9    2.2  2  bZIP_2          Basic region leucine zipper
      0.067   12.1   0.1      0.079   11.8   0.1    1.1  1  DUF677          Protein of unknown function (DUF677)
       0.11   12.9   0.7        1.9    9.0   0.0    2.5  3  Latarcin        Latarcin precursor
       0.18   11.9   2.5       0.97    9.5   2.5    2.0  1  Mod_r           Modifier of rudimentary (Mod(r)) protein
       0.85    9.7   3.5          4    7.6   1.1    2.4  2  PspB            Phage shock protein B
          2    8.5   8.3       0.68   10.0   5.0    1.9  2  ADIP            Afadin- and alpha -actinin-Binding
        6.7    6.9   6.3        3.9    7.7   0.8    2.9  3  NYD-SP28_assoc  Sperm tail C-terminal domain


Domain annotation for each model (and alignments):
>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   5.2e-06     0.012      19      50 ..      24      55 ..       7      64 .. 0.89
   2 ?    1.4   0.1      0.12   2.8e+02      34      50 ..     113     129 ..     103     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.2e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkdL 50
                                      ++ql qe+++l ae+++l a++e+Lea  +++
  gi|330509131|ref|YP_004385559.1| 24 LRQLLQEVQDLRAENQRLIARIEALEALHELY 55
                                      68999**********************98887 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHCC- CS
                             DivIC  34 aklkaeneeLeaevkdL 50 
                                       +k + ++e+L++ +kd+
  gi|330509131|ref|YP_004385559.1| 113 KKTRRRIEKLKELLKDY 129
                                       68899999999999998 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   2.9   4.8e-06     0.011      29      52 ..      26      49 ..      25      50 .. 0.93
   2 ?   -1.2   0.8      0.99   2.2e+03      22      35 ..     114     127 ..     106     129 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.8e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2 29 eleervkeLeeeNaqLrqkveqLe 52
                                      +l ++v++L++eN++L +++e+Le
  gi|330509131|ref|YP_004385559.1| 26 QLLQEVQDLRAENQRLIARIEALE 49
                                      7889*******************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.99
                                       HHHHHHHHHHHHHH CS
                            bZIP_2  22 kkkakeeeleervk 35 
                                       k + + e+l+e +k
  gi|330509131|ref|YP_004385559.1| 114 KTRRRIEKLKELLK 127
                                       66666666666555 PP

>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.5e-05     0.079      18     176 ..       2     163 ..       1     184 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.5e-05
                            DUF677  18 slateaktrslsedslkeltkcllelnqdvvkviieikedvwenqdLksLveaYFestkktldlcetlekcveraer 94 
                                       s+a +++++s  ++  ++++  l +l q+v ++  e +  +   ++L +L e Y        +   +l++ + r ++
  gi|330509131|ref|YP_004385559.1|   2 SFALRQDIQSQTFAFAMDFGIILRQLLQEVQDLRAENQRLIARIEALEALHELYHGPIPEDKNW-PSLKETLARQKD 77 
                                       7889999***********************************************9988877765.678888888888 PP

                            DUF677  95 se.llireAlaqFEkeklekdvG.....kkkkky..ekTleeLkkFkamgdpfdgeefltkFksvykeqvllleklr 163
                                          +l+  Al+q +  + +++ G     kk+ k+  +kT + + k k++ + + g    + F++++ ++ l   + +
  gi|330509131|ref|YP_004385559.1|  78 ASpVLLASALEQDDVVQ-HQGRGidataKKEMKHigKKTRRRIEKLKELLKDYGGS---QTFEQLQIDLNLSPSQFS 150
                                       777*******9866544.23334557676666665689*****************9...889999999999999999 PP

                            DUF677 164 ktkkkldkklrni 176
                                       ++ +kldk++  i
  gi|330509131|ref|YP_004385559.1| 151 QLVRKLDKRIFEI 163
                                       9999999998666 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00083       1.9      22      53 ..      23      54 ..       5      78 .. 0.90
   2 ?    2.0   0.1      0.13   2.8e+02      59      80 ..      97     118 ..      81     139 .. 0.72
   3 ?   -3.6   0.0       6.8   1.5e+04      33      43 ..     153     163 ..     147     164 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00083
                          Latarcin 22 inrklmemvnnlRkvqgRLeemvenlrkvedl 53
                                      i r+l++ v +lR  ++RL   +e+l+++++l
  gi|330509131|ref|YP_004385559.1| 23 ILRQLLQEVQDLRAENQRLIARIEALEALHEL 54
                                      679************************99876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.13
                          Latarcin  59 ARgafkklkdkfkkmgeklkkk 80 
                                        Rg+ ++ k+++k++g+k  ++
  gi|330509131|ref|YP_004385559.1|  97 GRGIDATAKKEMKHIGKKTRRR 118
                                       4666667777777777776655 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 6.8
                          Latarcin  33 lRkvqgRLeem 43 
                                       +Rk  +R+ e+
  gi|330509131|ref|YP_004385559.1| 153 VRKLDKRIFEI 163
                                       56777776665 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.5   0.00043      0.97      27     103 ..      30     141 ..      18     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00043
                             Mod_r  27 evkqlkeekeellaenesla..................................eknlslepeleelrselqekle. 68 
                                       ev++l++e + l+a +e+l                                    + l++ + ++++   + ++ + 
  gi|330509131|ref|YP_004385559.1|  30 EVQDLRAENQRLIARIEALEalhelyhgpipedknwpslketlarqkdaspvllASALEQDDVVQHQGRGIDATAKk 106
                                       55555555555555555555556666666666666666655555555555555599999999**********99998 PP

                             Mod_r  69 elkelekefeekeqeldellqkfspdallarLqta 103
                                       e+k++ k+ ++  ++l+ell++++ + + ++Lq  
  gi|330509131|ref|YP_004385559.1| 107 EMKHIGKKTRRRIEKLKELLKDYGGSQTFEQLQID 141
                                       9***********************99999999865 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.1    0.0018         4      41      63 ..      29      51 ..      24      56 .. 0.90
   2 ?    1.6   0.0      0.13     3e+02      35      64 ..     100     126 ..      93     130 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0018
                              PspB 41 krLeellekAekleeRietLEri 63
                                      +++++l+ + ++l +Rie+LE++
  gi|330509131|ref|YP_004385559.1| 29 QEVQDLRAENQRLIARIEALEAL 51
                                      7899*****************86 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.13
                              PspB  35 lsaedekrLeellekAekleeRietLEriL 64 
                                       ++a+ +k+++++    +k ++Rie L ++L
  gi|330509131|ref|YP_004385559.1| 100 IDATAKKEMKHIG---KKTRRRIEKLKELL 126
                                       5555555555444...45556888887776 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.0   0.00031      0.68      57     151 ..      26     127 ..      24     128 .. 0.81
   2 ?   -3.4   0.1       4.2   9.4e+03      71      90 ..     137     156 ..     133     160 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00031
                              ADIP  57 slnetirkleaeierlqskierlktqleql.....erela.lvqakerqlekklktleqklknekeelqrlknalqq 127
                                       +l +++++l+ae++rl ++ie l++  e +     e ++  +++++++ ++ +   l + + ++ + +q + + +++
  gi|330509131|ref|YP_004385559.1|  26 QLLQEVQDLRAENQRLIARIEALEALHELYhgpipEDKNWpSLKETLARQKDASPVLLASALEQDDVVQHQGRGIDA 102
                                       578999******************99998833333355556888899988888899999999************998 PP

                              ADIP 128 iktq.yahelkkkdreiekLkeklk 151
                                       ++++ ++h  kk  r+iekLke lk
  gi|330509131|ref|YP_004385559.1| 103 TAKKeMKHIGKKTRRRIEKLKELLK 127
                                       8666155556777789******987 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.2
                              ADIP  71 rlqskierlktqleqlerel 90 
                                       +lq + +    q +ql r+l
  gi|330509131|ref|YP_004385559.1| 137 QLQIDLNLSPSQFSQLVRKL 156
                                       44444444444444444443 PP

>> NYD-SP28_assoc  Sperm tail C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.8    0.0017       3.9      37      56 ..      26      45 ..      25      48 .. 0.88
   2 ?    0.0   0.1      0.42   9.4e+02      45      59 ..     115     129 ..     105     129 .. 0.76
   3 ?   -0.6   0.0      0.63   1.4e+03      30      43 ..     174     187 ..     170     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0017
                    NYD-SP28_assoc 37 klieetesLekqNeeLrnlL 56
                                      +l++e++ L+++N+ L  ++
  gi|330509131|ref|YP_004385559.1| 26 QLLQEVQDLRAENQRLIARI 45
                                      79**************8765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.42
                    NYD-SP28_assoc  45 LekqNeeLrnlLkqy 59 
                                        ++  e+L++lLk y
  gi|330509131|ref|YP_004385559.1| 115 TRRRIEKLKELLKDY 129
                                       567778999999887 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.63
                    NYD-SP28_assoc  30 evLteRaklieete 43 
                                       +vL++Ra + e++e
  gi|330509131|ref|YP_004385559.1| 174 KVLKRRAVIGENVE 187
                                       89****99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1269  (0.0707792); expected 358.6 (0.02)
Passed bias filter:                      847  (0.0472419); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1361.57
//
Query:       gi|330509132|ref|YP_004385560.1|  [L=73]
Description: IS3/IS66 family element, Orf1 protein [Methanosaeta concilii GP6]
Scores for complete sequence (score 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   0.0      0.066   13.5   0.0    1.4  1  HTH_Tnp_1  Transposase


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.7e-06     0.066       9      48 ..       3      39 ..       2      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-06
                         HTH_Tnp_1  9 defKariVreslepgksvsevArrhgvspnqLykWrrqyr 48
                                      +efK+++V e  e+gk+  ++A +hg++ +  y+W  +  
  gi|330509132|ref|YP_004385560.1|  3 REFKISVVSEL-ESGKP--QIATEHGIHSSIPYQWQYELA 39
                                      59********9.***98..79**************87764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 537.68
//
Query:       gi|330509133|ref|YP_004385561.1|  [L=83]
Description: hypothetical protein MCON_3528 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 615.15
//
Query:       gi|330509134|ref|YP_004385562.1|  [L=314]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete 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-22   76.1   1.0    7.6e-08   31.9   0.1    5.8  5  TPR_1            Tetratricopeptide repeat
    2.7e-16   58.3   5.4      7e-07   28.9   0.1    5.8  6  TPR_2            Tetratricopeptide repeat
      2e-14   52.5   8.8    6.8e-05   22.8   0.2    5.3  5  TPR_8            Tetratricopeptide repeat
    7.2e-14   51.2   8.9    5.1e-05   22.9   1.5    6.7  6  TPR_11           TPR repeat
      7e-12   45.1   0.4    3.4e-05   24.3   0.2    4.6  4  TPR_14           Tetratricopeptide repeat
    7.1e-12   44.8   3.7     0.0018   18.5   0.0    5.1  4  TPR_17           Tetratricopeptide repeat
    1.4e-11   44.5   1.3    2.2e-07   31.1   0.2    3.4  4  TPR_12           Tetratricopeptide repeat
    9.6e-09   35.8   1.1    1.3e-05   25.8   0.2    3.9  4  TPR_16           Tetratricopeptide repeat
    4.1e-07   30.0   0.0      0.022   14.9   0.0    3.5  3  TPR_9            Tetratricopeptide repeat
    5.5e-07   29.7   0.6     0.0017   18.4   0.1    3.3  3  DUF3856          Domain of Unknown Function (DUF3856)
    1.2e-06   28.1   0.1    0.00096   18.9   0.0    2.8  2  TPR_10           Tetratricopeptide repeat
    1.9e-06   27.1   0.9     0.0034   16.4   0.3    2.2  2  NARP1            NMDA receptor-regulated protein 1
    3.1e-05   24.3   0.3       0.76   10.5   0.1    4.3  4  TPR_6            Tetratricopeptide repeat
    6.8e-05   22.5   2.7       0.54   10.1   0.0    3.4  3  PPTA             Protein prenyltransferase alpha subunit repe
    6.9e-05   22.8   2.2       0.11   12.6   0.2    3.7  4  MIT              MIT (microtubule interacting and transport) 
    0.00012   22.2   0.4       0.15   12.3   0.0    2.8  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    0.00044   20.7   5.9      0.021   15.3   0.2    3.6  3  TPR_19           Tetratricopeptide repeat
     0.0018   18.2   0.2      0.035   14.1   0.0    3.0  3  TPR_7            Tetratricopeptide repeat
     0.0018   18.7   0.0     0.0051   17.2   0.0    1.7  2  BTAD             Bacterial transcriptional activator domain
     0.0073   16.8   0.2        1.2    9.6   0.1    2.5  2  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
  ------ inclusion threshold ------
      0.051   13.6   0.2        3.3    7.8   0.0    3.2  3  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
       0.12   11.9   0.3        1.5    8.4   0.2    2.8  3  HTH_Bact         Helix-turn-helix bacterial domain
       0.14   12.2   0.6         23    5.0   0.1    3.3  4  DUF627           Protein of unknown function (DUF627)
       0.65    9.4   4.9       0.57    9.6   1.1    2.2  2  SNAP             Soluble NSF attachment protein, SNAP


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 !   12.5   0.0   0.00013     0.099       3      30 ..      81     108 ..      79     111 .. 0.94
   2 !   31.9   0.1     1e-10   7.6e-08       2      30 ..     121     149 ..     120     159 .. 0.96
   3 !   15.4   0.0   1.6e-05     0.012       1      32 [.     161     192 ..     161     194 .. 0.90
   4 !    6.7   0.0     0.009       6.7      14      32 ..     205     223 ..     203     224 .. 0.89
   5 ?    3.1   0.0      0.13        95      14      33 ..     263     282 ..     261     283 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                        + n+++ + +lg+++e  e  +kAL l
  gi|330509134|ref|YP_004385562.1|  81 LWINRALNLTYLGRLNESMESHQKALDL 108
                                       69************************98 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1e-10
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                       +a++  G a+ +lg+yd+A++ yekA+e+
  gi|330509134|ref|YP_004385562.1| 121 DAWKMQGTALAYLGQYDDAIKSYEKAIEI 149
                                       89**************************8 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+a+  ++  +  lgk   A+ +y+k++eln 
  gi|330509134|ref|YP_004385562.1| 161 ADAWWHKAESLEILGKSMAAINAYNKVIELNS 192
                                       67777899999*******************97 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.009
                                       TT-HHHHHHHHHHHHHHST CS
                             TPR_1  14 lgkydeAleyyekALelnP 32 
                                       l +y++ +e+++kA el P
  gi|330509134|ref|YP_004385562.1| 205 LSEYNDSVEAFDKATELMP 223
                                       789*************987 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.13
                                       TT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  14 lgkydeAleyyekALelnPn 33 
                                       lg y++  + y++ L++n +
  gi|330509134|ref|YP_004385562.1| 263 LGSYNKSSKSYDRTLTINSK 282
                                       799**************975 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0027         2       3      30 ..      81     108 ..      79     112 .. 0.92
   2 ?    6.4   0.1     0.015        11       4      34 .]      89     119 ..      86     119 .. 0.89
   3 !   28.9   0.1   9.4e-10     7e-07       2      31 ..     121     150 ..     120     153 .. 0.93
   4 !   10.1   0.0     0.001      0.75       1      31 [.     161     191 ..     161     193 .. 0.95
   5 !    7.3   0.0    0.0078       5.8      16      33 ..     207     224 ..     203     224 .. 0.89
   6 ?   -0.2   0.0         2   1.5e+03      14      32 ..     263     281 ..     261     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0027
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                       ++ n++l + +lg+++e  e  +kAl l
  gi|330509134|ref|YP_004385562.1|  81 LWINRALNLTYLGRLNESMESHQKALDL 108
                                       79*******************9999988 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                       l +lG++ + +  +++Al++ +  l+ dP+n
  gi|330509134|ref|YP_004385562.1|  89 LTYLGRLNESMESHQKALDLIDDILKKDPKN 119
                                       6789999999999****************97 PP

  == domain 3  score: 28.9 bits;  conditional E-value: 9.4e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                       +a+ ++G a+++lg+y++A++ +ekA+e+ 
  gi|330509134|ref|YP_004385562.1| 121 DAWKMQGTALAYLGQYDDAIKSYEKAIEIS 150
                                       69**************************96 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.001
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       a+a++  +++++ lg+   A++a++k++el+
  gi|330509134|ref|YP_004385562.1| 161 ADAWWHKAESLEILGKSMAAINAYNKVIELN 191
                                       789***************************9 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.0078
                             TPR_2  16 dyeeAleafekAleldPn 33 
                                       +y++ +eaf+kA el P+
  gi|330509134|ref|YP_004385562.1| 207 EYNDSVEAFDKATELMPK 224
                                       899************996 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 2
                             TPR_2  14 lgdyeeAleafekAleldP 32 
                                       lg y++  + +++ l ++ 
  gi|330509134|ref|YP_004385562.1| 263 LGSYNKSSKSYDRTLTINS 281
                                       7899*********999885 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0027         2       2      30 ..      80     108 ..      79     111 .. 0.92
   2 !   22.8   0.2     9e-08   6.8e-05       3      33 ..     122     152 ..     120     153 .. 0.89
   3 !   16.9   0.2     7e-06    0.0053       1      32 [.     161     192 ..     161     194 .. 0.95
   4 ?    3.7   0.0      0.12        90      13      31 ..     204     222 ..     199     224 .. 0.86
   5 ?    1.6   0.0      0.55   4.1e+02      13      32 ..     262     281 ..     261     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0027
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                       +++ n ++ +  lg+++e++e+ +kal+l
  gi|330509134|ref|YP_004385562.1|  80 SLWINRALNLTYLGRLNESMESHQKALDL 108
                                       6899***********************98 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 9e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+ + g ++  lg+y+ A+++yeka+e++ +
  gi|330509134|ref|YP_004385562.1| 122 AWKMQGTALAYLGQYDDAIKSYEKAIEISNQ 152
                                       666889999*******************976 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 7e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+a+++++  ++ lg+  +A+ +y+k++el+ 
  gi|330509134|ref|YP_004385562.1| 161 ADAWWHKAESLEILGKSMAAINAYNKVIELNS 192
                                       78****************************96 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.12
                                       HTT-HHHHHHHHHHHHHHH CS
                             TPR_8  13 klgdyeeAkeyyekaleld 31 
                                       +l +y+ ++e++ ka+el 
  gi|330509134|ref|YP_004385562.1| 204 DLSEYNDSVEAFDKATELM 222
                                       5678999*********985 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.55
                                       HTT-HHHHHHHHHHHHHHHH CS
                             TPR_8  13 klgdyeeAkeyyekaleldp 32 
                                        lg y+++ ++y + l+++ 
  gi|330509134|ref|YP_004385562.1| 262 GLGSYNKSSKSYDRTLTINS 281
                                       599*********99998886 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.022        17       5      23 ..      90     108 ..      87     111 .. 0.91
   2 ?   -0.9   0.0       1.8   1.4e+03      21      31 ..     113     123 ..     113     123 .. 0.87
   3 !   22.9   1.5   6.8e-08   5.1e-05       1      26 [.     127     152 ..     127     175 .. 0.86
   4 !   11.3   0.1   0.00028      0.21       8      28 ..     175     195 ..     172     197 .. 0.86
   5 ?    5.9   0.0     0.014        10       6      28 ..     204     226 ..     202     227 .. 0.87
   6 ?    2.5   0.0      0.15   1.1e+02       7      27 ..     263     283 ..     263     287 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.022
                            TPR_11   5 yeqGkyeeAieaYkkAlkl 23 
                                       + +G+++e++e+ +kAl+l
  gi|330509134|ref|YP_004385562.1|  90 TYLGRLNESMESHQKALDL 108
                                       679**************97 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.8
                            TPR_11  21 lkldPdnaeay 31 
                                       lk dP+n +a+
  gi|330509134|ref|YP_004385562.1| 113 LKKDPKNIDAW 123
                                       688******97 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 6.8e-08
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPd 26 
                                       G a+  +G+y++Ai++Y+kA++++++
  gi|330509134|ref|YP_004385562.1| 127 GTALAYLGQYDDAIKSYEKAIEISNQ 152
                                       668899*****************865 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00028
                            TPR_11   8 GkyeeAieaYkkAlkldPdna 28 
                                       Gk  +Ai+aY+k ++l+++ a
  gi|330509134|ref|YP_004385562.1| 175 GKSMAAINAYNKVIELNSSKA 195
                                       66668************9876 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.014
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdna 28 
                                       ++ +y++++ea+ kA +l P+ a
  gi|330509134|ref|YP_004385562.1| 204 DLSEYNDSVEAFDKATELMPKGA 226
                                       5679**************99865 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.15
                            TPR_11   7 qGkyeeAieaYkkAlkldPdn 27 
                                       +G y+++ ++Y + l +++++
  gi|330509134|ref|YP_004385562.1| 263 LGSYNKSSKSYDRTLTINSKS 283
                                       69***********99999876 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       1.1   8.1e+02      25      42 ..      69      86 ..      57      89 .. 0.83
   2 !   14.3   0.0   7.2e-05     0.054       6      40 ..      91     125 ..      85     128 .. 0.89
   3 !   24.3   0.2   4.6e-08   3.4e-05       2      43 ..     121     169 ..     120     170 .. 0.93
   4 !    9.7   0.0    0.0023       1.7       2      44 .]     162     205 ..     161     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.1
                            TPR_14 25 rralalaPddaeawllla 42
                                      ++al+ +P+d  +w+  a
  gi|330509134|ref|YP_004385562.1| 69 DDALQNDPGDYSLWINRA 86
                                      489*******99998765 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.2e-05
                            TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawll 40 
                                        l+++ +  + +++A++l +++l+++P++ +aw +
  gi|330509134|ref|YP_004385562.1|  91 YLGRLNESMESHQKALDLIDDILKKDPKNIDAWKM 125
                                       57888899999**********************88 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 4.6e-08
                            TPR_14   2 eallalaeallalGdpdeAiallrrala.......laPddaeawlllaq 43 
                                       +a+++ + al+ lG++d+Ai+ +++a++       ++P da+aw + a+
  gi|330509134|ref|YP_004385562.1| 121 DAWKMQGTALAYLGQYDDAIKSYEKAIEisnqtleRNPRDADAWWHKAE 169
                                       79************************99999998899*******88876 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0023
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaP.ddaeawlllaql 44 
                                       +a++  ae l+ lG+  +Ai++++++++l+  +   aw++ a+l
  gi|330509134|ref|YP_004385562.1| 162 DAWWHKAESLEILGKSMAAINAYNKVIELNSsKAIGAWIRKADL 205
                                       79**************************9853778999999975 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0038       2.8       4      32 ..      70     101 ..      69     103 .. 0.76
   2 !   18.5   0.0   2.4e-06    0.0018       5      34 .]     112     141 ..     108     141 .. 0.92
   3 !   13.9   0.1     7e-05     0.052       5      33 ..     153     181 ..     142     182 .. 0.92
   4 ?   -0.2   0.0       2.3   1.7e+03       1      12 [.     183     194 ..     183     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0038
                            TPR_17   4 kaleldPnnadaynnLAelll...knGdlmtA 32 
                                        al++dP +  ++ n+A  l    +++++m+ 
  gi|330509134|ref|YP_004385562.1|  70 DALQNDPGDYSLWINRALNLTylgRLNESMES 101
                                       59***************977634555566665 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.4e-06
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmtArq 34 
                                        l++dP+n da+ + +++l+ +G++++A++
  gi|330509134|ref|YP_004385562.1| 112 ILKKDPKNIDAWKMQGTALAYLGQYDDAIK 141
                                       699*************************85 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 7e-05
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmtAr 33 
                                        le++P +ada+  +Ae l+ +G++m A+
  gi|330509134|ref|YP_004385562.1| 153 TLERNPRDADAWWHKAESLEILGKSMAAI 181
                                       6899**********************996 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.3
                            TPR_17   1 lylkaleldPnn 12 
                                       +y k++el+ + 
  gi|330509134|ref|YP_004385562.1| 183 AYNKVIELNSSK 194
                                       599*****9765 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1    0.0015       1.1       5      36 ..      81     112 ..      79     122 .. 0.85
   2 !   31.1   0.2   2.9e-10   2.2e-07       9      74 ..     126     190 ..     119     193 .. 0.92
   3 ?   -0.8   0.0       2.6   1.9e+03      60      75 ..     207     222 ..     198     232 .. 0.66
   4 ?   -2.0   0.0       6.2   4.6e+03      16      34 ..     263     281 ..     261     286 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrl 36 
                                       ++ n+a+ l++lgr+ e+ e ++kal+++  +
  gi|330509134|ref|YP_004385562.1|  81 LWINRALNLTYLGRLNESMESHQKALDLIDDI 112
                                       5779999*******************998655 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 2.9e-10
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        +++l++lg+yd+A++ +eka+ei +++l + +p  a +    ++ ++ lg+  +A++++++++++
  gi|330509134|ref|YP_004385562.1| 126 QGTALAYLGQYDDAIKSYEKAIEISNQTL-ERNPRDADAWWHKAESLEILGKSMAAINAYNKVIEL 190
                                       7999*********************9998.579******************************997 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.6
                            TPR_12  60 ryeeAlelleealaia 75 
                                       +y + +e++ +a++++
  gi|330509134|ref|YP_004385562.1| 207 EYNDSVEAFDKATELM 222
                                       4555555555555554 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 6.2
                            TPR_12  16 lgrydeAlellekaleiar 34 
                                       lg y ++ + +++ l i +
  gi|330509134|ref|YP_004385562.1| 263 LGSYNKSSKSYDRTLTINS 281
                                       6778888888888888765 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.2   9.2e+02      40      66 ..      92     118 ..      66     120 .. 0.63
   2 !   16.2   0.0   1.6e-05     0.012      14      62 ..     103     148 ..      90     152 .. 0.74
   3 !   25.8   0.2   1.7e-08   1.3e-05       2      60 ..     125     187 ..     124     195 .. 0.81
   4 ?   -1.2   0.0       4.5   3.3e+03       9      26 ..     204     221 ..     200     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.2
                            TPR_16  40 lgdaalrqgrlaeAaalyraalraapd 66 
                                       lg++      +++A++l++  l+ +p+
  gi|330509134|ref|YP_004385562.1|  92 LGRLNESMESHQKALDLIDDILKKDPK 118
                                       444444445566666666666666665 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.6e-05
                            TPR_16  14 ddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       ++A+ + +  lk+d   P + +A+   g a++ +g +++A+  y++a++
  gi|330509134|ref|YP_004385562.1| 103 QKALDLIDDILKKD---PKNIDAWKMQGTALAYLGQYDDAIKSYEKAIE 148
                                       66777777777777...77777777777777777777777777777765 PP

  == domain 3  score: 25.8 bits;  conditional E-value: 1.7e-08
                            TPR_16   2 alaraalragdyddAaaaleaa.......lkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                       ++++a++++g+yddA++ +e a       l+r+   P++a+A++++++++  +g   +A+ +y++ 
  gi|330509134|ref|YP_004385562.1| 125 MQGTALAYLGQYDDAIKSYEKAieisnqtLERN---PRDADAWWHKAESLEILGKSMAAINAYNKV 187
                                       79*****************97622222226778...99*****************99999555554 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 4.5
                            TPR_16   9 ragdyddAaaaleaalkr 26 
                                       ++ +y d ++a++ a+++
  gi|330509134|ref|YP_004385562.1| 204 DLSEYNDSVEAFDKATEL 221
                                       677899999999988875 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.048        36      22      49 ..      72      99 ..      65     101 .. 0.86
   2 !   14.9   0.0     3e-05     0.022       9      58 ..     100     149 ..      97     150 .. 0.95
   3 !   11.9   0.0   0.00025      0.19      10      60 ..     142     192 ..     141     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.048
                             TPR_9 22 lllaPddpeerrdRGlllaqlGclsaAl 49
                                      l+ +P d +++  R+l l  lG+l++ +
  gi|330509134|ref|YP_004385562.1| 72 LQNDPGDYSLWINRALNLTYLGRLNESM 99
                                      7779***************999998765 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3e-05
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylal 58 
                                       e +++al  ++ +l  +P+ ++ +   G +la lG++  A++  e ++++
  gi|330509134|ref|YP_004385562.1| 100 ESHQKALDLIDDILKKDPKNIDAWKMQGTALAYLGQYDDAIKSYEKAIEI 149
                                       789******************************************99985 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00025
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                        +e+a+++++  l  +P+d++ ++  +  l+ lG   aA+++ +  ++l+ 
  gi|330509134|ref|YP_004385562.1| 142 SYEKAIEISNQTLERNPRDADAWWHKAESLEILGKSMAAINAYNKVIELNS 192
                                       689**************************************9999888775 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0051       3.8      91     132 ..      72     111 ..      33     121 .. 0.81
   2 !   18.4   0.1   2.3e-06    0.0017      62     129 ..     127     190 ..     116     198 .. 0.90
   3 ?   -1.3   0.0       2.8   2.1e+03      66      83 ..     261     278 ..     253     284 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0051
                                       TTSTHH..HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                           DUF3856  91 leqdeG..klWiaavfsravaleelGrkdealkafrmagemiae 132
                                       l++d G  +lWi    +ra  l  lGr +e+++++++a ++i++
  gi|330509134|ref|YP_004385562.1|  72 LQNDPGdySLWI----NRALNLTYLGRLNESMESHQKALDLIDD 111
                                       666666223554....89*********************99986 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.3e-06
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  62 sealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                         ala lg+yd+a++s +ka++  n+  e +  +   W    +++a +le lG++  a++a++++ e+
  gi|330509134|ref|YP_004385562.1| 127 GTALAYLGQYDDAIKSYEKAIEISNQTLERNPRDADAW----WHKAESLEILGKSMAAINAYNKVIEL 190
                                       468999*************************9999999....689*******************9997 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.8
                                       HHTT-HHHHHHHHHHHHH CS
                           DUF3856  66 aklgrydealesadkalr 83 
                                        +lg+y+++ +s d++l 
  gi|330509134|ref|YP_004385562.1| 261 EGLGSYNKSSKSYDRTLT 278
                                       578888888888888775 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.013       9.6       7      36 ..      84     113 ..      83     117 .. 0.83
   2 !   18.9   0.0   1.3e-06   0.00096       9      42 .]     127     160 ..     127     160 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.013
                            TPR_10   7 NLanalrqrgrydeAealleealairrrll 36 
                                       N a  l+ +gr++e+++ +++al++   +l
  gi|330509134|ref|YP_004385562.1|  84 NRALNLTYLGRLNESMESHQKALDLIDDIL 113
                                       6688899****************9765555 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.3e-06
                            TPR_10   9 analrqrgrydeAealleealairrrllGpdHPd 42 
                                       + al  +g+yd+A + +e+a++i  ++l+++++d
  gi|330509134|ref|YP_004385562.1| 127 GTALAYLGQYDDAIKSYEKAIEISNQTLERNPRD 160
                                       67999*************************9987 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00062      0.46     195     233 ..      89     127 ..      60     131 .. 0.75
   2 !   16.4   0.3   4.5e-06    0.0034     195     256 ..     130     191 ..     128     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00062
                                       HHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHH CS
                             NARP1 195 lyflAqhydklgsrekAleyidkaiehtptlvelyltKa 233
                                       l++l    + ++s +kAl++id  ++++p+ ++ + + +
  gi|330509134|ref|YP_004385562.1|  89 LTYLGRLNESMESHQKALDLIDDILKKDPKNIDAWKMQG 127
                                       5677778888999********************997765 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.5e-06
                                       HHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 195 lyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       l +l q+ d ++s+ekA+e+ ++ +e++p   + +  Ka+ l+  G   +A+++ ++  +l 
  gi|330509134|ref|YP_004385562.1| 130 LAYLGQYDDAIKSYEKAIEISNQTLERNPRDADAWWHKAESLEILGKSMAAINAYNKVIELN 191
                                       679*************************************************9999988776 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.14   1.1e+02       5      32 ..      91     118 ..      89     119 .. 0.90
   2 !   10.5   0.1     0.001      0.76       6      28 ..     126     148 ..     122     150 .. 0.88
   3 ?    4.2   0.0      0.11        82       1      28 [.     162     189 ..     162     192 .. 0.81
   4 ?   -1.0   0.0         5   3.7e+03       7      27 ..     198     219 ..     197     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   5 klalsyrklgdtdkAlealerlikeYPd 32 
                                       +l+++ +++  ++kAl++ ++++k+ P+
  gi|330509134|ref|YP_004385562.1|  91 YLGRLNESMESHQKALDLIDDILKKDPK 118
                                       6899999987999************998 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                       ++ ++  lg++d+A++ +e+ i+
  gi|330509134|ref|YP_004385562.1| 126 QGTALAYLGQYDDAIKSYEKAIE 148
                                       677888889***********997 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                       dA ++ a+s++ lg++ +A+ a++++i+
  gi|330509134|ref|YP_004385562.1| 162 DAWWHKAESLEILGKSMAAINAYNKVIE 189
                                       56777777777567999*********98 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 5
                                       HHHHHH.HHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrk.lgdtdkAlealerli 27 
                                       a+ +++ l ++ +++ea+++  
  gi|330509134|ref|YP_004385562.1| 198 AWIRKAdLSEYNDSVEAFDKAT 219
                                       5667776778999999999875 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00073      0.54       7      22 ..      70      85 ..      69      86 .. 0.92
   2 !   10.0   0.1   0.00076      0.56       2      15 ..     106     119 ..     105     123 .. 0.88
   3 ?    0.4   0.1      0.81     6e+02       5      21 ..     150     166 ..     146     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00073
                                      HHHHH-TT-CHHHHHH CS
                              PPTA  7 kliekdpkNYsaWnyR 22
                                      +++++dp +Ys W  R
  gi|330509134|ref|YP_004385562.1| 70 DALQNDPGDYSLWINR 85
                                      799**********988 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00076
                                       HHHHHHHHHH-TT- CS
                              PPTA   2 LeltekliekdpkN 15 
                                       L+l++++++kdpkN
  gi|330509134|ref|YP_004385562.1| 106 LDLIDDILKKDPKN 119
                                       9************* PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.81
                                       HHHHHHH-TT-CHHHHH CS
                              PPTA   5 tekliekdpkNYsaWny 21 
                                        ++ +e++p++  aW +
  gi|330509134|ref|YP_004385562.1| 150 SNQTLERNPRDADAWWH 166
                                       6778999**99888888 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0088       6.6       9      50 ..      84     124 ..      82     130 .. 0.84
   2 !   12.6   0.2   0.00014      0.11      17      49 ..     133     164 ..     126     171 .. 0.81
   3 ?    0.6   0.0      0.81     6e+02       9      32 ..     166     189 ..     163     190 .. 0.87
   4 ?   -1.5   0.0       3.6   2.7e+03      27      39 ..     208     220 ..     204     231 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0088
                               MIT   9 kkAveeDnagnyeeAlelYkealelLlqalkekneerrellr 50 
                                       ++A ++   g   e +e  ++al+l+  +lk k+++  ++++
  gi|330509134|ref|YP_004385562.1|  84 NRALNLTYLGRLNESMESHQKALDLIDDILK-KDPKNIDAWK 124
                                       6677777778999*****************9.7888887766 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                               MIT  17 agnyeeAlelYkealelLlqalkekneerrell 49 
                                        g+y++A++ Y++a+e+ +q l   n+++ +++
  gi|330509134|ref|YP_004385562.1| 133 LGQYDDAIKSYEKAIEISNQTLE-RNPRDADAW 164
                                       599**************999996.577777665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.81
                               MIT   9 kkAveeDnagnyeeAlelYkeale 32 
                                       +kA  ++  g+  +A+++Y + +e
  gi|330509134|ref|YP_004385562.1| 166 HKAESLEILGKSMAAINAYNKVIE 189
                                       799999999**********98666 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 3.6
                               MIT  27 YkealelLlqalk 39 
                                       Y +++e + +a  
  gi|330509134|ref|YP_004385562.1| 208 YNDSVEAFDKATE 220
                                       6666666666654 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0    0.0002      0.15      35      81 ..      98     145 ..      83     145 .. 0.88
   2 !   10.0   0.0    0.0011      0.79      38      81 ..     142     186 ..     141     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                                       HTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  35 lngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +++ +++A++l+++  k+++k++ ++   + +l  L++y++Ai+ +ek
  gi|330509134|ref|YP_004385562.1|  98 SMESHQKALDLIDDIlKKDPKNIDAWKMQGTALAYLGQYDDAIKSYEK 145
                                       567799*************************************99876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                                       -HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  38 qykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                        y++A+e+ +++ + n+++  ++  +A++l  L+k   Ai+a+ k
  gi|330509134|ref|YP_004385562.1| 142 SYEKAIEISNQTlERNPRDADAWWHKAESLEILGKSMAAINAYNK 186
                                       79**********************************999999877 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0         2   1.5e+03      17      43 ..      71      97 ..      65     101 .. 0.80
   2 !   15.3   0.2   2.8e-05     0.021       4      47 ..      99     142 ..      96     145 .. 0.93
   3 !   11.0   0.3   0.00064      0.48       4      36 ..     133     172 ..     130     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2
                            TPR_19 17 alqedpknaearllLAeallalgqlde 43
                                      alq dp++  ++++ A  l  lg+l+e
  gi|330509134|ref|YP_004385562.1| 71 ALQNDPGDYSLWINRALNLTYLGRLNE 97
                                      8999***99999998887777777777 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.8e-05
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47 
                                       ++ ++ Al+l   +l++dpkn +a+     al  lgq+d+A++ 
  gi|330509134|ref|YP_004385562.1|  99 MESHQKALDLIDDILKKDPKNIDAWKMQGTALAYLGQYDDAIKS 142
                                       6789**********************99*************986 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00064
                            TPR_19   4 egdyaeAlalleqalqe.......dpknaearllLAeall 36 
                                        g+y++A++ +e+a++        +p +a+a+   Ae l 
  gi|330509134|ref|YP_004385562.1| 133 LGQYDDAIKSYEKAIEIsnqtlerNPRDADAWWHKAESLE 172
                                       5999999999999886644444448889999988887665 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0         2   1.5e+03      12      31 ..      92     111 ..      89     117 .. 0.68
   2 !   14.1   0.0   4.7e-05     0.035       6      32 ..     127     153 ..     122     160 .. 0.80
   3 ?   -1.6   0.0         5   3.8e+03      11      28 ..     204     219 ..     198     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2
                             TPR_7  12 lGdyeeAielyeqsLaltkd 31 
                                       lG+  e  e ++++L l +d
  gi|330509134|ref|YP_004385562.1|  92 LGRLNESMESHQKALDLIDD 111
                                       67777888888886655555 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.7e-05
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdp 32 
                                       + +   lG+y++Ai+ ye+++++ ++ 
  gi|330509134|ref|YP_004385562.1| 127 GTALAYLGQYDDAIKSYEKAIEISNQT 153
                                       5677789************88777655 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5
                             TPR_7  11 rlGdyeeAielyeqsLal 28 
                                       +l +y + +e + +  a+
  gi|330509134|ref|YP_004385562.1| 204 DLSEYNDSVEAFDK--AT 219
                                       48899999999988..55 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.9e-06    0.0051      70     135 ..      94     159 ..      83     162 .. 0.89
   2 ?   -0.8   0.0       2.5   1.9e+03      89     122 ..     154     187 ..     152     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.9e-06
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS---- CS
                              BTAD  70 eaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepg 135
                                       +++ +++ +++al+  +++++++P + ++++   +Ala++G+  +A++ Ye++ ++ ++ L   p 
  gi|330509134|ref|YP_004385562.1|  94 RLNESMESHQKALDLIDDILKKDPKNIDAWKMQGTALAYLGQYDDAIKSYEKAIEISNQTLERNPR 159
                                       45557789*************************************************999999886 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.5
                                       HHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  89 vaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       ++ +P + +++ +  + l  +G+  +A+++Y+++
  gi|330509134|ref|YP_004385562.1| 154 LERNPRDADAWWHKAESLEILGKSMAAINAYNKV 187
                                       566788888888888889999999*******987 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.037        28      84     119 ..     101     136 ..      88     141 .. 0.88
   2 !    9.6   0.1    0.0016       1.2      82     127 ..     140     185 ..     134     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.037
                                       -HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  84 dyrwaaellnhlvfadpenaeakelkadaleqlgyq 119
                                         + a+ l++ ++ +dp+n +a +++  al  lg+ 
  gi|330509134|ref|YP_004385562.1| 101 SHQKALDLIDDILKKDPKNIDAWKMQGTALAYLGQY 136
                                       57889**********************999999975 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0016
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHH CS
                   Alkyl_sulf_dimr  82 egdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRn 127
                                        + y+ a+e+ n+ ++ +p++a+a   ka++le lg+ + + ++ n
  gi|330509134|ref|YP_004385562.1| 140 IKSYEKAIEISNQTLERNPRDADAWWHKAESLEILGKSMAAINAYN 185
                                       567999*******************************999888765 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0045       3.3      16      37 ..     101     122 ..      98     131 .. 0.86
   2 ?    1.8   0.1      0.34   2.6e+02      14      34 ..     140     160 ..     128     171 .. 0.75
   3 ?   -1.9   0.0       4.8   3.6e+03      14      30 ..     263     279 ..     262     281 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0045
                                       -HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPenrQa 37 
                                        +++A+ ++d +L+++P+n  a
  gi|330509134|ref|YP_004385562.1| 101 SHQKALDLIDDILKKDPKNIDA 122
                                       6889***************877 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.34
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                       ++ Y++A +  ++ Le  P+ 
  gi|330509134|ref|YP_004385562.1| 140 IKSYEKAIEISNQTLERNPRD 160
                                       466777777777777777765 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.8
                                       HT-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLei 30 
                                       lg Y+++ +  d+ L i
  gi|330509134|ref|YP_004385562.1| 263 LGSYNKSSKSYDRTLTI 279
                                       799**999999988866 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 ?    8.4   0.2     0.002       1.5       1      18 [.     135     152 ..     135     155 .. 0.91
   2 ?   -0.9   0.0       1.7   1.3e+03      31      47 ..     166     182 ..     164     184 .. 0.80
   3 ?   -2.7   0.0       5.9   4.4e+03       1      14 [.     207     220 ..     207     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.002
                                       -HHHHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiSir 18 
                                       +Y+ a++  +kAieiS +
  gi|330509134|ref|YP_004385562.1| 135 QYDDAIKSYEKAIEISNQ 152
                                       7**************976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                                       HHHHHHHHTT--HHHHH CS
                          HTH_Bact  31 qkgecleklgfseeeIk 47 
                                        k+e le lg s + I+
  gi|330509134|ref|YP_004385562.1| 166 HKAESLEILGKSMAAIN 182
                                       79999999999988876 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5.9
                                       -HHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAie 14 
                                       +Y+ + e  +kA e
  gi|330509134|ref|YP_004385562.1| 207 EYNDSVEAFDKATE 220
                                       6999**99999976 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.031        23      10      33 ..     101     124 ..      98     137 .. 0.79
   2 ?    2.4   0.0       0.2   1.5e+02      79     105 ..     129     155 ..     124     158 .. 0.85
   3 ?    2.3   0.0      0.23   1.7e+02      10      38 ..     142     170 ..     137     188 .. 0.76
   4 ?   -0.3   0.0       1.4   1.1e+03      62      74 ..     211     224 ..     205     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.031
                            DUF627  10 nhikALeiiedlisrhgedeksal 33 
                                        h kAL +i+d++++  ++ +++ 
  gi|330509134|ref|YP_004385562.1| 101 SHQKALDLIDDILKKDPKNIDAWK 124
                                       699**********99998766654 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.2
                            DUF627  79 sLfelasqlgsklyYkkavkkakraLs 105
                                        L  l++  +  + Y+ka++ ++++L 
  gi|330509134|ref|YP_004385562.1| 129 ALAYLGQYDDAIKSYEKAIEISNQTLE 155
                                       6888999888999**********9995 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.23
                            DUF627  10 nhikALeiiedlisrhgedeksallhrlq 38 
                                        + kA+ei + ++ r+ +d +++ ++ + 
  gi|330509134|ref|YP_004385562.1| 142 SYEKAIEISNQTLERNPRDADAWWHKAES 170
                                       56789999999999988888888877665 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.4
                            DUF627  62 svecfseavels.r 74 
                                       sve+f +a+el+ +
  gi|330509134|ref|YP_004385562.1| 211 SVEAFDKATELMpK 224
                                       99******999842 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.9    0.0038       2.8     105     185 ..      46     150 ..      31     154 .. 0.65
   2 ?    9.6   1.1   0.00076      0.57     129     192 ..     134     198 ..      86     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0038
                                       HHTT-HHHHHHHHHHHHHHHHHTT--........................HHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                              SNAP 105 tekgrfrraAklkkeiaelyekelgd........................lekAieaYekAaelyeqeeakalankc 157
                                       t+ g ++  A+++   +e y+ e  d                        l++++e+ +kA +l ++  +k   n  
  gi|330509134|ref|YP_004385562.1|  46 TDFGMMKSDATFNVAFGESYQAED-DalqndpgdyslwinralnltylgrLNESMESHQKALDLIDDILKKDPKNID 121
                                       566666677777777777777764.2344444445555555555555555999999999999887665555444444 PP

                                       HHHHH.HHHHHTT-HHHHHHHHHHHHHTT CS
                              SNAP 158 llkvA.elsaelekyekAieiyekvakks 185
                                         k+     a l++y++Ai+ yek ++ s
  gi|330509134|ref|YP_004385562.1| 122 AWKMQgTALAYLGQYDDAIKSYEKAIEIS 150
                                       4444315578899**********998766 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00076
                                       --HHHHHHHHHHHHHHHHHTT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTTSS-TTTG CS
                              SNAP 129 gdlekAieaYekAaelyeqee.akalankcllkvAelsaelekyekAieiyekvakkslennllk 192
                                       g++++Ai++YekA e+ +q    + +   ++   Ae    l+k  +Ai++y+kv++   ++ +  
  gi|330509134|ref|YP_004385562.1| 134 GQYDDAIKSYEKAIEISNQTLeRNPRDADAWWHKAESLEILGKSMAAINAYNKVIELNSSKAIGA 198
                                       67888888888888887776545666666666667666777788888888888887776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2029.21
//
Query:       gi|330509135|ref|YP_004385563.1|  [L=300]
Description: hypothetical protein MCON_3530 [Methanosaeta concilii GP6]
Scores for complete 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  118.4   0.0    3.5e-34  117.6   0.0    1.5  1  PatG_D    PatG Domain
    1.6e-28   98.9   1.1    2.1e-28   98.6   0.4    1.5  2  PatG_C    PatG C-terminal
  ------ inclusion threshold ------
       0.11   12.1   0.0        0.9    9.2   0.0    2.0  2  MIX       Mitochondrial membrane-anchored proteins


Domain annotation for each model (and alignments):
>> PatG_D  PatG Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6   0.0   5.9e-38   3.5e-34       1      99 [.      50     226 ..      50     270 .. 0.93

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 5.9e-38
                            PatG_D   1 lvYviGrieadFpnearekefvqalaraktanpedqqalakvLsnrenrylaralsWiLtiegipiYvllPn..... 72 
                                       +vYv+G+iea+Fpn+++eke+vq+++r+k+an ++qqa+++vLs++enrylar+lsWiLt+eg+piY+llP+     
  gi|330509135|ref|YP_004385563.1|  50 FVYVLGQIEARFPNRSIEKEYVQIIERSKSANLDHQQAFHSVLSQPENRYLARKLSWILTMEGVPIYILLPTgpedl 126
                                       8**************************************************************************** PP

                            PatG_D  73 ..................................................................kpfalelfarl 83 
                                                                                                         k++a e f r+
  gi|330509135|ref|YP_004385563.1| 127 nilleairppacpldrqvvvgrkgpvappemcglevpmvlvdhlysleyndfiksirsesvtdekfKAIARETFLRM 203
                                       ***************************************************************************** PP

                            PatG_D  84 iealdnqedteesra.......d 99 
                                       ++ +dn ++t+++ra       +
  gi|330509135|ref|YP_004385563.1| 204 MQLADNIGSTDKHRAlnylsvrY 226
                                       *************9966555550 PP

>> PatG_C  PatG C-terminal
   #    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      54      72 ..      78      96 ..      66     102 .. 0.64
   2 !   98.6   0.4   3.6e-32   2.1e-28       3     115 .]     188     297 ..     186     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.5
                            PatG_C 54 eslsLdsveveksplsrad 72
                                      +s++Ld  ++ +s ls+++
  gi|330509135|ref|YP_004385563.1| 78 KSANLDHQQAFHSVLSQPE 96
                                      4446666666666666664 PP

  == domain 2  score: 98.6 bits;  conditional E-value: 3.6e-32
                            PatG_C   3 qeeeftkairevLdrvlqelrNlGatdedRAlNylatrapdiyretaelileslsLdsveveksplsradsdcvdVk 79 
                                       ++e+f++ +re + r++q ++N G td++RAlNyl++r+p iy ++ae+ ++++ L+sv++  s+ls   +++v+V+
  gi|330509135|ref|YP_004385563.1| 188 TDEKFKAIARETFLRMMQLADNIGSTDKHRALNYLSVRYPAIYVKAAEELERNFLLTSVNAIFSRLSDN-RKIVSVI 263
                                       67999***************************************************************9.******* PP

                            PatG_C  80 ltftnkenssraekkyrvtvDVseelPflvtkvqsy 115
                                        +ftnk  +++a +ky+v+vD +ee+Pf+vtk+ +y
  gi|330509135|ref|YP_004385563.1| 264 QSFTNK--ETGAVEKYFVRVDLTEEFPFIVTKMAPY 297
                                       ******..9************************998 PP

>> MIX  Mitochondrial membrane-anchored proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.081   4.8e+02      28      52 ..     133     157 ..     121     179 .. 0.78
   2 ?    9.2   0.0   0.00015       0.9      73     114 ..     215     256 ..     198     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.081
                               MIX  28 rrppwpllhqrvvllregkaapedl 52 
                                        rpp   l ++vv+ r+g  ap ++
  gi|330509135|ref|YP_004385563.1| 133 IRPPACPLDRQVVVGRKGPVAPPEM 157
                                       5888888888888899987666554 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00015
                               MIX  73 ltqvlkytsgaylqnyvadpdqlrkevllqllnvkygrvkdp 114
                                         + l+y s +y   yv+  ++l ++ ll  +n  + r++d 
  gi|330509135|ref|YP_004385563.1| 215 KHRALNYLSVRYPAIYVKAAEELERNFLLTSVNAIFSRLSDN 256
                                       567899********************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1962.79
//
Query:       gi|330509136|ref|YP_004385564.1|  [L=163]
Description: hypothetical protein MCON_3531 [Methanosaeta concilii GP6]
Scores for complete 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-09   36.0   0.0    1.2e-08   35.5   0.0    1.3  1  ABC_tran  ABC transporter
  ------ inclusion threshold ------
       0.17   11.7   0.0       0.19   11.5   0.0    1.1  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
       0.17   11.3   0.0       0.23   10.9   0.0    1.1  1  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 !   35.5   0.0     2e-12   1.2e-08      72     137 .]       4      88 ..       1      88 [. 0.78

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 2e-12
                                       TTSBHHHH..................HHHTCHHHHHHHSTTGGTTCBGESTTS...GGS-HHHHHHHHHHHHHHHTS CS
                                       xxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  72 peltvren..................esdeeiekalsklglkelkdtvvkssp...ssLSgGqkqrvalarallkkp 127
                                       ++lt++en                  ++d+ ++++l++l+  +  +t++++     + LS G++q+valara++ ++
  gi|330509136|ref|YP_004385564.1|   4 YNLTLAENiwlgsaarpldmgkvakaAKDSGADRVLRRLEAGY--ETTLGKWFdngTDLSIGEWQKVALARAFIWDS 78 
                                       6677777777777777877777777677777999999999887..33333322344********************* PP

                                       SEEEEESTTT CS
                                       xxxxxxxxxx RF
                          ABC_tran 128 kllllDEpta 137
                                       +++++DEpt+
  gi|330509136|ref|YP_004385564.1|  79 QIIIMDEPTS 88 
                                       ********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 ?   11.5   0.0   3.1e-05      0.19     236     287 ..      59     107 ..      16     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.1e-05
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                       +lS G  +  al+ a++ +     +++ DEp ++L+Pk+ ++++  ++el++
  gi|330509136|ref|YP_004385564.1|  59 DLSIGEWQKVALARAFIWDS---QIIIMDEPTSSLDPKAEAEVFAKFRELAK 107
                                       45777777777777777666...89************998888755555444 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   0.0   3.8e-05      0.23     159     208 ..      78     127 ..      57     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.8e-05
                                       -SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 159 aplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadkl 208
                                       + + ++De  + LD k  ++v   ++e  k    ivi +r  +++ ad +
  gi|330509136|ref|YP_004385564.1|  78 SQIIIMDEPTSSLDPKAEAEVFAKFRELAKGKTAIVIGHRLSTVRMADCI 127
                                       56899************************************999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.42
# Mc/sec: 1157.58
//
Query:       gi|330509137|ref|YP_004385565.1|  [L=317]
Description: hypothetical protein MCON_3532 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2138.51
//
Query:       gi|330509138|ref|YP_004385566.1|  [L=300]
Description: hypothetical protein MCON_3533 [Methanosaeta concilii GP6]
Scores for complete sequence (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  118.9   0.0    2.6e-34  118.0   0.0    1.5  1  PatG_D    PatG Domain
    1.1e-28   99.4   0.4    2.1e-28   98.6   0.4    1.4  1  PatG_C    PatG C-terminal


Domain annotation for each model (and alignments):
>> PatG_D  PatG Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.0   0.0   2.9e-38   2.6e-34       1      99 [.      50     226 ..      50     268 .. 0.93

  Alignments for each domain:
  == domain 1  score: 118.0 bits;  conditional E-value: 2.9e-38
                            PatG_D   1 lvYviGrieadFpnearekefvqalaraktanpedqqalakvLsnrenrylaralsWiLtiegipiYvllPn..... 72 
                                       +vYv+G++ea+Fpn+++ekefvq+++r+k+ n+e+qqa+++vLs++enrylar+lsW+Lt+eg+piY+llP+     
  gi|330509138|ref|YP_004385566.1|  50 FVYVLGQVEARFPNRSIEKEFVQIIERSKSTNFEHQQAFHSVLSQPENRYLARKLSWVLTKEGVPIYILLPTgpedl 126
                                       8**************************************************************************** PP

                            PatG_D  73 ..................................................................kpfalelfarl 83 
                                                                                                         k++a e f r+
  gi|330509138|ref|YP_004385566.1| 127 dilleairpsacpldrqvvvgrkgpvappemcglevpmvlvdhlysleyndfiksirsesvtdekfKAIARETFLRM 203
                                       ***************************************************************************** PP

                            PatG_D  84 iealdnqedteesra.......d 99 
                                       ++ +dn ++t+++ra       +
  gi|330509138|ref|YP_004385566.1| 204 MQLADNIGSTDKHRAlnylsvrY 226
                                       *************9966555550 PP

>> PatG_C  PatG C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.4   2.4e-32   2.1e-28       3     115 .]     188     297 ..     186     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 2.4e-32
                            PatG_C   3 qeeeftkairevLdrvlqelrNlGatdedRAlNylatrapdiyretaelileslsLdsveveksplsradsdcvdVk 79 
                                       ++e+f++ +re + r++q ++N G td++RAlNyl++r+p iy ++ae+ ++++ L+sv++  s+ls   +++v+V+
  gi|330509138|ref|YP_004385566.1| 188 TDEKFKAIARETFLRMMQLADNIGSTDKHRALNYLSVRYPAIYVKAAEELERNFLLTSVNAIFSRLSDN-RKIVSVI 263
                                       67999***************************************************************9.******* PP

                            PatG_C  80 ltftnkenssraekkyrvtvDVseelPflvtkvqsy 115
                                        +ftnk  +++a +ky+v+vD +ee+Pf+vtk+ +y
  gi|330509138|ref|YP_004385566.1| 264 QSFTNK--ETGAVEKYFVRVDLTEEFPFIVTKMAPY 297
                                       ******..9************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2111.58
//
Query:       gi|330509139|ref|YP_004385567.1|  [L=179]
Description: hypothetical protein MCON_3534 [Methanosaeta concilii GP6]
Scores for complete 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-10   39.7   0.0    8.7e-10   39.2   0.0    1.2  1  ABC_tran  ABC transporter
     0.0046   16.8   0.0     0.0051   16.7   0.0    1.1  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
  ------ inclusion threshold ------
      0.038   13.4   0.0      0.043   13.2   0.0    1.1  1  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 !   39.2   0.0   1.5e-13   8.7e-10      60     137 .]       9     104 ..       2     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.5e-13
                                       CEEEE-SS--S-TTSBHHHH..................HHHTCHHHHHHHSTTGGTTCBGESTTS...GGS-HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx RF
                          ABC_tran  60 eigvlpqepqlfpeltvren..................esdeeiekalsklglkelkdtvvkssp...ssLSgGqkq 115
                                       e +vl+q    +++l+++en                  ++d+ ++++l++l+  +  +t++++     + LS G++q
  gi|330509139|ref|YP_004385567.1|   9 EKSVLFQY-YAQYNLSLAENiwlgsadrpldmgkvakaARDSGVDRILKRLEAGY--ETTLGKWFdngTDLSIGEWQ 82 
                                       55677777.5666777888889988888888888876667777********9888..44443322344********* PP

                                       HHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 116 rvalarallkkpkllllDEpta 137
                                       +valara++++++++++DEpt+
  gi|330509139|ref|YP_004385567.1|  83 KVALARAFIRDSQIIIMDEPTS 104
                                       ********************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 !   16.7   0.0   8.5e-07    0.0051     235     286 ..      74     122 ..      14     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.5e-07
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkels 286
                                       ++lS G  +  al+ a++r+     +++ DEp ++L+Pk+ ++++  ++el+
  gi|330509139|ref|YP_004385567.1|  74 TDLSIGEWQKVALARAFIRDS---QIIIMDEPTSSLDPKAEAEVFAKFRELA 122
                                       356***************999...9*************99888875554444 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.3e-06     0.043     152     209 ..      87     144 ..      43     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.3e-06
                                       HHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 152 AiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklv 209
                                       A   ++ + + ++De  + LD k  ++v   ++e  k    ivi +r  +++ ad ++
  gi|330509139|ref|YP_004385567.1|  87 ARAFIRDSQIIIMDEPTSSLDPKAEAEVFAKFRELAKGKTAIVIGHRLSTVRMADCIY 144
                                       3444678889*****************************************9999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1294.71
//
Query:       gi|330509140|ref|YP_004385568.1|  [L=293]
Description: TPR-repeat-containing protein [Methanosaeta concilii GP6]
Scores for complete sequence (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  176.8   8.6      1e-08   34.6   0.5    7.2  7  TPR_1            Tetratricopeptide repeat
    2.8e-48  158.1  13.3      7e-08   32.1   0.0    7.1  7  TPR_8            Tetratricopeptide repeat
    2.8e-48  158.2   4.8    3.8e-08   32.8   0.4    7.2  7  TPR_2            Tetratricopeptide repeat
    3.2e-37  125.9  14.3    4.9e-07   29.3   0.0    6.7  7  TPR_11           TPR repeat
    7.3e-31  106.6   0.0    4.4e-11   43.2   0.0    4.3  4  TPR_16           Tetratricopeptide repeat
      1e-29  102.7   3.8    1.7e-13   50.7   0.0    4.7  4  TPR_12           Tetratricopeptide repeat
    2.4e-29   99.5   0.2    1.6e-05   25.4   0.0    7.1  7  TPR_14           Tetratricopeptide repeat
    9.3e-23   78.9   0.1     0.0036   17.6   0.0    7.1  7  TPR_17           Tetratricopeptide repeat
    5.7e-21   74.8   0.2    2.6e-05   24.6   0.0    4.7  5  TPR_19           Tetratricopeptide repeat
      1e-18   67.2   0.0    4.4e-05   23.5   0.0    4.3  4  TPR_9            Tetratricopeptide repeat
      2e-16   59.5   3.2       0.51   11.1   0.0    7.2  7  TPR_6            Tetratricopeptide repeat
    7.3e-13   47.6   0.1      0.094   12.8   0.0    6.3  6  TPR_7            Tetratricopeptide repeat
    4.5e-12   46.2   9.7     0.0054   16.8   0.2    6.7  6  DUF3856          Domain of Unknown Function (DUF3856)
    1.1e-10   41.5   3.3     0.0094   16.2   0.0    4.4  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    7.1e-09   35.3   8.9       0.59   10.1   0.0    6.4  7  TPR_10           Tetratricopeptide repeat
    7.8e-09   35.0   3.2      0.059   12.3   0.1    3.7  4  NARP1            NMDA receptor-regulated protein 1
    2.8e-07   31.1   2.6       0.32   11.4   0.1    4.6  3  BTAD             Bacterial transcriptional activator domain
    6.9e-07   29.2   6.3      0.063   13.0   0.0    4.7  5  TPR_21           Tetratricopeptide repeat-like domain
    7.8e-07   29.0   5.4       0.19   11.4   0.1    4.6  5  RPN7             26S proteasome subunit RPN7
    5.8e-06   25.9   6.2    0.00014   21.4   0.0    3.3  3  SNAP             Soluble NSF attachment protein, SNAP
    1.9e-05   24.8   2.1          8    6.8   0.0    4.9  5  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
    0.00013   21.9  18.6      0.018   15.1   1.1    5.3  5  MIT              MIT (microtubule interacting and transport) 
    0.00016   22.0   0.0       0.11   12.8   0.0    3.5  3  TPR_20           Tetratricopeptide repeat
    0.00016   21.7   3.8       0.91    9.6   0.1    5.5  6  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    0.00028   21.4   0.5          1    9.8   0.0    3.7  4  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    0.00031   20.7   0.7       0.15   12.1   0.0    3.2  3  SRP_TPR_like     Putative TPR-like repeat
    0.00033   20.5   0.3        3.3    7.5   0.0    4.2  5  DUF5113          Domain of unknown function (DUF5113)
     0.0011   18.2   1.5       0.51    9.5   0.0    3.2  3  FAT              FAT domain
      0.002   18.0   1.5         22    4.9   0.1    4.9  5  LemA             LemA family
     0.0027   17.8   6.0         27    5.3   0.0    5.9  6  PPR              PPR repeat
     0.0059   15.9   0.4      0.079   12.2   0.2    2.5  3  TPR_15           Tetratricopeptide repeat
     0.0064   16.7   0.6         23    5.3   0.0    4.0  4  TPR_5            Tetratrico peptide repeat
  ------ inclusion threshold ------
      0.011   15.8   3.9        1.2    9.3   0.1    3.9  4  Ribosomal_S16    Ribosomal protein S16
      0.015   14.8   0.0        7.6    6.1   0.0    3.8  4  SHNi-TPR         SHNi-TPR
      0.025   14.4   0.3        1.2    8.9   0.0    2.5  2  NACHT_N          N-terminal domain of NWD NACHT-NTPase
       0.04   12.6   0.1       0.97    8.1   0.0    2.1  2  PknG_TPR         Protein kinase G tetratricopeptide repeat
      0.042   13.9   0.0      0.075   13.1   0.0    1.4  1  FixH             FixH
      0.046   13.8   0.0        1.6    8.8   0.0    2.4  2  MAS20            MAS20 protein import receptor
      0.051   13.3   0.0        7.2    6.5   0.0    2.7  2  PPTA             Protein prenyltransferase alpha subunit repe
      0.057   13.0   1.7        5.9    6.4   0.0    3.5  5  MscS_porin       Mechanosensitive ion channel porin domain
       0.11   12.4   0.0         11    5.9   0.0    2.8  2  DELLA            Transcriptional regulator DELLA protein N te
       0.21   11.1   0.3        1.2    8.6   0.3    2.3  1  NAPRTase         Nicotinate phosphoribosyltransferase (NAPRTa
       0.67    9.6   3.7        1.8    8.3   0.5    2.8  2  DUF2225          Uncharacterized protein conserved in bacteri
        1.5    8.5  13.8         32    4.2   0.1    5.9  7  HTH_Bact         Helix-turn-helix bacterial domain
        1.5    9.0   4.2         18    5.6   0.0    3.6  3  DUF1510          Domain of unknown function (DUF1510)


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 !   34.6   0.5   2.6e-11     1e-08       2      34 .]      48      80 ..      47      80 .. 0.94
   2 !   25.1   0.0   2.7e-08   1.1e-05       3      33 ..      83     113 ..      81     114 .. 0.95
   3 !   23.7   0.0     7e-08   2.8e-05       2      33 ..     116     147 ..     115     148 .. 0.95
   4 !   30.7   0.1   4.6e-10   1.8e-07       1      31 [.     149     179 ..     149     181 .. 0.95
   5 !   28.9   0.0   1.7e-09   6.7e-07       3      30 ..     192     219 ..     190     221 .. 0.94
   6 !   26.7   0.0   8.2e-09   3.3e-06       3      33 ..     228     258 ..     227     259 .. 0.97
   7 ?    5.6   0.3     0.037        15       2      27 ..     262     287 ..     261     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.6e-11
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                      + +y +G+ + ++g y+eA+++y+kA+elnP++
  gi|330509140|ref|YP_004385568.1| 48 EDWYKKGQELERKGSYEEAVKAYDKAIELNPKD 80
                                      56*****************************86 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 2.7e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       ++  +G ++  l++++e +e+ye A+e++P+
  gi|330509140|ref|YP_004385568.1|  83 VWLSKGIILSGLEQHNESIEAYETAIEIDPK 113
                                       799***************************7 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 7e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                       +a+  ++  +++lg+y+e l +y+++L+ +P+
  gi|330509140|ref|YP_004385568.1| 116 QAWGTMADELYHLGRYNESLNAYNRVLQMDPH 147
                                       79*****************************7 PP

  == domain 4  score: 30.7 bits;  conditional E-value: 4.6e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                       a+a+  +G ++ k g+++eA+++++kALe++
  gi|330509140|ref|YP_004385568.1| 149 ARAWVEKGDILNKTGRHEEAIKAFNKALEIY 179
                                       89***************************97 PP

  == domain 5  score: 28.9 bits;  conditional E-value: 1.7e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                       a+ ++G ++ k+g+y+eA++ y+k++e 
  gi|330509140|ref|YP_004385568.1| 192 AWQGKGITLEKMGRYEEAIKSYDKVIEM 219
                                       9*************************96 PP

  == domain 6  score: 26.7 bits;  conditional E-value: 8.2e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+  +G ++   gky+e +++y+k++e+ P+
  gi|330509140|ref|YP_004385568.1| 228 AWTAKGDIFKAIGKYEESIKAYNKVIEIAPK 258
                                       899**************************97 PP

  == domain 7  score: 5.6 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekA 27 
                                       +a+ ++G+a+  lg+  eA +++++A
  gi|330509140|ref|YP_004385568.1| 262 YAWEGKGLALEALGRNSEANAAFSEA 287
                                       6999**************97777776 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.5   3.1e-10   1.2e-07       4      34 .]      50      80 ..      47      80 .. 0.97
   2 !   23.1   0.0   1.4e-07   5.4e-05       3      33 ..      83     113 ..      83     114 .. 0.95
   3 !   17.2   0.0   1.1e-05    0.0042       2      32 ..     116     146 ..     115     148 .. 0.95
   4 !   32.1   0.0   1.8e-10     7e-08       1      32 [.     149     180 ..     149     182 .. 0.94
   5 !   24.2   0.0   6.1e-08   2.4e-05       3      31 ..     192     220 ..     190     223 .. 0.93
   6 !   28.7   0.1   2.2e-09   8.7e-07       3      33 ..     228     258 ..     226     259 .. 0.95
   7 ?    4.9   0.3     0.091        36       3      27 ..     263     287 ..     261     290 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.1e-10
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  4 yynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      +y++g+ ++ +g yeeA+++y ka+el+p++
  gi|330509140|ref|YP_004385568.1| 50 WYKKGQELERKGSYEEAVKAYDKAIELNPKD 80
                                      9****************************96 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +++ +g i++ l++++e++e+ye a+e+dp+
  gi|330509140|ref|YP_004385568.1|  83 VWLSKGIILSGLEQHNESIEAYETAIEIDPK 113
                                       6999**************************8 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 1.1e-05
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +a+  +++ +  lg+y+e+  +y+++l++dp
  gi|330509140|ref|YP_004385568.1| 116 QAWGTMADELYHLGRYNESLNAYNRVLQMDP 146
                                       79****************************9 PP

  == domain 4  score: 32.1 bits;  conditional E-value: 1.8e-10
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+a++ +g+i+ k+g++eeA+++++kale+  
  gi|330509140|ref|YP_004385568.1| 149 ARAWVEKGDILNKTGRHEEAIKAFNKALEIYD 180
                                       79***************************975 PP

  == domain 5  score: 24.2 bits;  conditional E-value: 6.1e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a++ +g +++k+g+yeeA+++y k++e++
  gi|330509140|ref|YP_004385568.1| 192 AWQGKGITLEKMGRYEEAIKSYDKVIEMS 220
                                       79999**********************97 PP

  == domain 6  score: 28.7 bits;  conditional E-value: 2.2e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+  +g+i +  g+yee++++y+k++e++p+
  gi|330509140|ref|YP_004385568.1| 228 AWTAKGDIFKAIGKYEESIKAYNKVIEIAPK 258
                                       8*****************************8 PP

  == domain 7  score: 4.9 bits;  conditional E-value: 0.091
                                       HHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyeka 27 
                                       a+  +g++++ lg+  eA +++ +a
  gi|330509140|ref|YP_004385568.1| 263 AWEGKGLALEALGRNSEANAAFSEA 287
                                       78889*************9999887 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.4   9.5e-11   3.8e-08       1      34 []      47      80 ..      47      80 .. 0.96
   2 !   17.4   0.0   8.4e-06    0.0033       4      33 ..      84     113 ..      82     114 .. 0.92
   3 !   23.3   0.0   1.1e-07   4.5e-05       3      33 ..     117     147 ..     115     148 .. 0.94
   4 !   24.1   0.0   6.2e-08   2.5e-05       1      33 [.     149     181 ..     149     182 .. 0.94
   5 !   22.8   0.0   1.6e-07   6.3e-05       3      30 ..     192     219 ..     190     222 .. 0.93
   6 !   21.0   0.0   5.8e-07   0.00023       3      33 ..     228     258 ..     227     259 .. 0.95
   7 !   11.3   0.4   0.00077      0.31       2      28 ..     262     288 ..     261     292 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 9.5e-11
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      ae +y  G+ ++++g yeeA++a++kA+el+P++
  gi|330509140|ref|YP_004385568.1| 47 AEDWYKKGQELERKGSYEEAVKAYDKAIELNPKD 80
                                      688*****************************86 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 8.4e-06
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                       +   G ++  l +++e +ea+e A+e+dP+
  gi|330509140|ref|YP_004385568.1|  84 WLSKGIILSGLEQHNESIEAYETAIEIDPK 113
                                       778899***********************7 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 1.1e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+  +++ +y+lg+y+e l+a++++l+ dP+
  gi|330509140|ref|YP_004385568.1| 117 AWGTMADELYHLGRYNESLNAYNRVLQMDPH 147
                                       8999*************************96 PP

  == domain 4  score: 24.1 bits;  conditional E-value: 6.2e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+a+ + G+++ k g++eeA++af+kAle++ n
  gi|330509140|ref|YP_004385568.1| 149 ARAWVEKGDILNKTGRHEEAIKAFNKALEIYDN 181
                                       789***************************976 PP

  == domain 5  score: 22.8 bits;  conditional E-value: 1.6e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                       a+   G  ++k+g+yeeA++ ++k++e 
  gi|330509140|ref|YP_004385568.1| 192 AWQGKGITLEKMGRYEEAIKSYDKVIEM 219
                                       8999*********************986 PP

  == domain 6  score: 21.0 bits;  conditional E-value: 5.8e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+ + G++  + g+yee ++a++k++e++P+
  gi|330509140|ref|YP_004385568.1| 228 AWTAKGDIFKAIGKYEESIKAYNKVIEIAPK 258
                                       79999************************97 PP

  == domain 7  score: 11.3 bits;  conditional E-value: 0.00077
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAl 28 
                                       +a+   Gla+++lg+  eA +af +A 
  gi|330509140|ref|YP_004385568.1| 262 YAWEGKGLALEALGRNSEANAAFSEAK 288
                                       6999*********************96 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.2e-09   4.9e-07       4      37 ..      57      90 ..      54      95 .. 0.85
   2 !   19.4   0.2   1.5e-06    0.0006       9      31 ..      96     118 ..      93     118 .. 0.91
   3 !   21.1   0.0   4.6e-07   0.00018       2      31 ..     123     152 ..     122     155 .. 0.92
   4 !   19.4   0.0   1.5e-06   0.00062       1      23 [.     156     178 ..     156     204 .. 0.89
   5 !   15.2   0.0   3.2e-05     0.013       7      23 ..     203     219 ..     197     226 .. 0.87
   6 !   26.6   0.5   8.4e-09   3.4e-06       1      42 []     233     275 ..     233     275 .. 0.86
   7 ?   -1.1   0.0       3.9   1.6e+03       2      20 ..     269     287 ..     268     287 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.2e-09
                            TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37
                                      +  +G yeeA++aY kA++l+P++  +++  G +
  gi|330509140|ref|YP_004385568.1| 57 LERKGSYEEAVKAYDKAIELNPKDIMVWLSKGII 90
                                      5579********************9988887765 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.5e-06
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeay 31 
                                       + +e+ieaY++A+++dP++  a+
  gi|330509140|ref|YP_004385568.1|  96 QHNESIEAYETAIEIDPKSIQAW 118
                                       899***************99886 PP

  == domain 3  score: 21.1 bits;  conditional E-value: 4.6e-07
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeay 31 
                                       d++y +G+y+e+++aY++ l+ dP  a+a+
  gi|330509140|ref|YP_004385568.1| 123 DELYHLGRYNESLNAYNRVLQMDPHMARAW 152
                                       899*********************888876 PP

  == domain 4  score: 19.4 bits;  conditional E-value: 1.5e-06
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                       Gd++ + G+ eeAi+a++kAl++
  gi|330509140|ref|YP_004385568.1| 156 GDILNKTGRHEEAIKAFNKALEI 178
                                       9********************98 PP

  == domain 5  score: 15.2 bits;  conditional E-value: 3.2e-05
                            TPR_11   7 qGkyeeAieaYkkAlkl 23 
                                        G+yeeAi++Y k ++ 
  gi|330509140|ref|YP_004385568.1| 203 MGRYEEAIKSYDKVIEM 219
                                       7*************996 PP

  == domain 6  score: 26.6 bits;  conditional E-value: 8.4e-09
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnae.ayynLGlayykqG 42 
                                       Gd++ + Gkyee+i+aY+k +++ P+ a+ a+ + Gla+ ++G
  gi|330509140|ref|YP_004385568.1| 233 GDIFKAIGKYEESIKAYNKVIEIAPKEASyAWEGKGLALEALG 275
                                       9************************999636777777777666 PP

  == domain 7  score: -1.1 bits;  conditional E-value: 3.9
                            TPR_11   2 dayyeqGkyeeAieaYkkA 20 
                                        a+ ++G++ eA +a+++A
  gi|330509140|ref|YP_004385568.1| 269 LALEALGRNSEANAAFSEA 287
                                       5666899999998888877 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   2.2e-08   8.8e-06       1      67 [.      51     114 ..      51     115 .. 0.97
   2 !   43.2   0.0   1.1e-13   4.4e-11       3      65 ..     121     180 ..     120     182 .. 0.95
   3 !   25.0   0.0   5.5e-08   2.2e-05       5      67 ..     198     259 ..     195     260 .. 0.93
   4 !   21.1   0.1   9.3e-07   0.00037       2      60 ..     231     287 ..     230     290 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.2e-08
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +++++++ r g y++A++a++ a++++   P +   +l +g ++  +  + e +++y+ a++ +p++
  gi|330509140|ref|YP_004385568.1|  51 YKKGQELERKGSYEEAVKAYDKAIELN---PKDIMVWLSKGIILSGLEQHNESIEAYETAIEIDPKS 114
                                       7899***********************...**********************************975 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 1.1e-13
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +a++++ +g+y + ++a++++l +d   P  a+A+ ++gd++ + gr++eA+ ++++al+ + 
  gi|330509140|ref|YP_004385568.1| 121 MADELYHLGRYNESLNAYNRVLQMD---PHMARAWVEKGDILNKTGRHEEAIKAFNKALEIYD 180
                                       6999*********************...******************************99875 PP

  == domain 3  score: 25.0 bits;  conditional E-value: 5.5e-08
                            TPR_16   5 raalragdyddAaaaleaalkrdpssPd.aaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                         + + g+y++A++ ++ ++++   sPd a  A+ ++gd++ + g ++e + +y++ ++ ap++
  gi|330509140|ref|YP_004385568.1| 198 ITLEKMGRYEEAIKSYDKVIEMS--SPDyALGAWTAKGDIFKAIGKYEESIKAYNKVIEIAPKE 259
                                       567899*****************..699899*******************************87 PP

  == domain 4  score: 21.1 bits;  conditional E-value: 9.3e-07
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                       a+++++ + g+y++ ++a++ +++ +p   +a  A+ ++g+a+ ++gr  eA a++ +a
  gi|330509140|ref|YP_004385568.1| 231 AKGDIFKAIGKYEESIKAYNKVIEIAP--KEASYAWEGKGLALEALGRNSEANAAFSEA 287
                                       678889999*****************6..4499*******************9999887 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   8.8e-06    0.0035      13      76 ..      57     112 ..      47     113 .. 0.91
   2 !   24.8   0.1   4.8e-08   1.9e-05       8      75 ..      86     145 ..      80     146 .. 0.91
   3 !   50.7   0.0   4.2e-16   1.7e-13       2      74 ..     148     219 ..     147     221 .. 0.95
   4 !   16.2   0.1   2.4e-05    0.0096       5      71 ..     228     287 ..     224     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.8e-06
                            TPR_12  13 lrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       l r g y+eA + ++ka+e+      p+    + +    g++++ l+++ e +e++e a++i++
  gi|330509140|ref|YP_004385568.1|  57 LERKGSYEEAVKAYDKAIELN-----PK---DIMVWLSKGIILSGLEQHNESIEAYETAIEIDP 112
                                       67899************9888.....86...59****************************986 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 4.8e-08
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                         + +l  l+++ e++e +e+a+ei      p++   +++  ++++ ++ lgry e l++++++l+++
  gi|330509140|ref|YP_004385568.1|  86 SKGIILSGLEQHNESIEAYETAIEID-----PKS---IQAWGTMADELYHLGRYNESLNAYNRVLQMD 145
                                       678899999****************9.....876...99**************************996 PP

  == domain 3  score: 50.7 bits;  conditional E-value: 4.2e-16
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +a+a+++ +++l++ gr++eA++ ++kalei+ ++   ++p+ +++ ++ g++++++gryeeA++ + +++++
  gi|330509140|ref|YP_004385568.1| 148 MARAWVEKGDILNKTGRHEEAIKAFNKALEIYDNTI-QENPEDIIAWQGKGITLEKMGRYEEAIKSYDKVIEM 219
                                       6899****************************8886.679******************************998 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 2.4e-05
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                       a++  +++  + g+y+e+++ ++k++eia     p+   ++ +  + g +++algr  eA +++ ea
  gi|330509140|ref|YP_004385568.1| 228 AWTAKGDIFKAIGKYEESIKAYNKVIEIA-----PKE--ASYAWEGKGLALEALGRNSEANAAFSEA 287
                                       66678999999******************.....665..6667788888888888888887777665 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   3.9e-08   1.6e-05       2      39 ..      48      85 ..      47      90 .. 0.93
   2 !   14.8   0.0   9.3e-05     0.037       4      42 ..      84     122 ..      83     124 .. 0.90
   3 !   19.1   0.1     4e-06    0.0016       3      43 ..     117     157 ..     116     158 .. 0.93
   4 !   15.9   0.0   4.4e-05     0.017       2      30 ..     150     185 ..     149     195 .. 0.78
   5 !   13.9   0.0   0.00018     0.073       3      43 ..     192     234 ..     190     235 .. 0.86
   6 !   13.7   0.0   0.00022     0.089       3      38 ..     228     264 ..     226     269 .. 0.87
   7 ?    1.3   0.2       2.1   8.2e+02       8      27 ..     268     287 ..     263     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.9e-08
                            TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeawl 39
                                      e +++ ++ l++ G ++eA++++++a++l+P+d  +wl
  gi|330509140|ref|YP_004385568.1| 48 EDWYKKGQELERKGSYEEAVKAYDKAIELNPKDIMVWL 85
                                      789*********************************98 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 9.3e-05
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +l  + +l  l+++ e+i++++ a++ +P++ +aw  +a
  gi|330509140|ref|YP_004385568.1|  84 WLSKGIILSGLEQHNESIEAYETAIEIDPKSIQAWGTMA 122
                                       67778889999************************8887 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 4e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       a+  +a+ l++lG++ e++++++r+l+ +P  a+aw + ++
  gi|330509140|ref|YP_004385568.1| 117 AWGTMADELYHLGRYNESLNAYNRVLQMDPHMARAWVEKGD 157
                                       7889999*****************************99876 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 4.4e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrrala.......l 30 
                                       +a+ + +++l   G+++eAi+++++al+        
  gi|330509140|ref|YP_004385568.1| 150 RAWVEKGDILNKTGRHEEAIKAFNKALEiydntiqE 185
                                       79999**********************955444444 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 0.00018
                            TPR_14   3 allalaeallalGdpdeAiallrralal.aPdda.eawlllaq 43 
                                       a++  +  l+  G+++eAi+ ++++++   Pd a  aw++ ++
  gi|330509140|ref|YP_004385568.1| 192 AWQGKGITLEKMGRYEEAIKSYDKVIEMsSPDYAlGAWTAKGD 234
                                       78888999*******************6379987579998775 PP

  == domain 6  score: 13.7 bits;  conditional E-value: 0.00022
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPdda.eaw 38 
                                       a+ a ++++ a G+++e+i++++++++ aP++a  aw
  gi|330509140|ref|YP_004385568.1| 228 AWTAKGDIFKAIGKYEESIKAYNKVIEIAPKEAsYAW 264
                                       899999************************9983455 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 2.1
                            TPR_14   8 aeallalGdpdeAiallrra 27 
                                       + al+alG+  eA a++ +a
  gi|330509140|ref|YP_004385568.1| 268 GLALEALGRNSEANAAFSEA 287
                                       7799*********9999876 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       3.1   1.2e+03      16      33 ..      50      67 ..      47      68 .. 0.86
   2 !   17.6   0.0     9e-06    0.0036       1      31 [.      69      99 ..      69     102 .. 0.88
   3 !   14.7   0.0   7.5e-05      0.03       1      31 [.     103     133 ..     103     135 .. 0.93
   4 !    9.5   0.0    0.0034       1.4       1      34 []     137     170 ..     137     170 .. 0.95
   5 !   16.2   0.0   2.4e-05    0.0096       2      34 .]     179     211 ..     178     211 .. 0.95
   6 ?    3.9   0.0      0.21        83       2      33 ..     213     246 ..     212     247 .. 0.84
   7 ?    6.6   0.0     0.029        12       1      32 [.     248     280 ..     248     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 3.1
                            TPR_17 16 ynnLAelllknGdlmtAr 33
                                      ++ +++ l+++G +++A+
  gi|330509140|ref|YP_004385568.1| 50 WYKKGQELERKGSYEEAV 67
                                      9999999*****999997 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 9e-06
                            TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmt 31
                                      +y ka+el+P++  ++  ++ +l+ + ++ +
  gi|330509140|ref|YP_004385568.1| 69 AYDKAIELNPKDIMVWLSKGIILSGLEQHNE 99
                                      59*********************98887766 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 7.5e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                       +y+ a+e+dP++  a+  +A  l+++G++ +
  gi|330509140|ref|YP_004385568.1| 103 AYETAIEIDPKSIQAWGTMADELYHLGRYNE 133
                                       5************************999976 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0034
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y ++l+ dP  a a+ +++ +l k G++++A++
  gi|330509140|ref|YP_004385568.1| 137 AYNRVLQMDPHMARAWVEKGDILNKTGRHEEAIK 170
                                       599*****************************85 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 2.4e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y + ++ +P +  a++ ++ +l+k G++++A++
  gi|330509140|ref|YP_004385568.1| 179 YDNTIQENPEDIIAWQGKGITLEKMGRYEEAIK 211
                                       9999***************************85 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.21
                            TPR_17   2 ylkalel.dPnn.adaynnLAelllknGdlmtAr 33 
                                       y k++e   P++   a++ ++ +++ +G++++ +
  gi|330509140|ref|YP_004385568.1| 213 YDKVIEMsSPDYaLGAWTAKGDIFKAIGKYEESI 246
                                       7888888458887789*************99876 PP

  == domain 7  score: 6.6 bits;  conditional E-value: 0.029
                            TPR_17   1 lylkaleldPnn.adaynnLAelllknGdlmtA 32 
                                       +y k++e+ P+  ++a+  ++ +l+ +G+  +A
  gi|330509140|ref|YP_004385568.1| 248 AYNKVIEIAPKEaSYAWEGKGLALEALGRNSEA 280
                                       59*********77************99987665 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.2e-06   0.00048       5      66 ..      61     122 ..      57     123 .. 0.95
   2 !   15.8   0.0   3.8e-05     0.015       6      49 ..      96     139 ..      90     141 .. 0.91
   3 !   24.6   0.0   6.6e-08   2.6e-05       5      52 ..     129     176 ..     125     177 .. 0.94
   4 !   22.2   0.0   3.8e-07   0.00015       7      57 ..     172     222 ..     170     235 .. 0.90
   5 ?    4.7   0.2      0.11        44       5      49 ..     240     285 ..     236     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-06
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66 
                                       g y+eA++++ +a++ +pk+  ++l   ++l  l q +e +++ +++ e dp++ ++++ +A
  gi|330509140|ref|YP_004385568.1|  61 GSYEEAVKAYDKAIELNPKDIMVWLSKGIILSGLEQHNESIEAYETAIEIDPKSIQAWGTMA 122
                                       99***************************************************999888777 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.8e-05
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLd 49 
                                       ++ e ++++e a++ dpk+  a+  +A+ l+ lg+++e  ++ +
  gi|330509140|ref|YP_004385568.1|  96 QHNESIEAYETAIEIDPKSIQAWGTMADELYHLGRYNESLNAYN 139
                                       788999*******************************9887766 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 6.6e-08
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalp 52 
                                       g+y e l+++ ++lq dp++a+a+    ++l ++g+ +eA+++ ++++
  gi|330509140|ref|YP_004385568.1| 129 GRYNESLNAYNRVLQMDPHMARAWVEKGDILNKTGRHEEAIKAFNKAL 176
                                       99*****************************************99887 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 3.8e-07
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       +  Al+++ + +qe+p++  a+ +  + l ++g+++eA++  d++ e+   
  gi|330509140|ref|YP_004385568.1| 172 FNKALEIYDNTIQENPEDIIAWQGKGITLEKMGRYEEAIKSYDKVIEMSSP 222
                                       678***************************************999887655 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.11
                            TPR_19   5 gdyaeAlalleqalqedpk.naearllLAeallalgqldeAealLd 49 
                                       g+y+e ++++ ++++ +pk  ++a+ +   al alg+  eA a+ +
  gi|330509140|ref|YP_004385568.1| 240 GKYEESIKAYNKVIEIAPKeASYAWEGKGLALEALGRNSEANAAFS 285
                                       7899999999999999999888888899999999999999988765 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.8e-07   0.00011       6      65 ..      58     117 ..      55     123 .. 0.94
   2 !   23.5   0.0   1.1e-07   4.4e-05      11      59 ..     131     179 ..     127     184 .. 0.91
   3 !   18.6   0.0   3.9e-06    0.0016      11      59 ..     172     220 ..     170     232 .. 0.92
   4 ?    3.3   0.0      0.23        91      11      52 ..     242     284 ..     238     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.8e-07
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                        r+  +e+a ++++  + l+P+d+  ++  G++l  l++ ++ +++ e++++++p+  +a
  gi|330509140|ref|YP_004385568.1|  58 ERKGSYEEAVKAYDKAIELNPKDIMVWLSKGIILSGLEQHNESIEAYETAIEIDPKSIQA 117
                                       578899*************************************************88776 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.1e-07
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                       + + l +++r+l+++P+ ++ + + G +l + G+ ++A+++++ +l++ 
  gi|330509140|ref|YP_004385568.1| 131 YNESLNAYNRVLQMDPHMARAWVEKGDILNKTGRHEEAIKAFNKALEIY 179
                                       667799***************************************9876 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 3.9e-06
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                       + +al++++  ++ +P+d+  +   G+ l+++G++++A++  +  ++++
  gi|330509140|ref|YP_004385568.1| 172 FNKALEIYDNTIQENPEDIIAWQGKGITLEKMGRYEEAIKSYDKVIEMS 220
                                       789*************************************999988775 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.23
                             TPR_9  11 weralavverllllaPddp.eerrdRGlllaqlGclsaAladL 52 
                                       +e+ +++++ ++ +aP+++ + +   Gl+l+ lG+ s+A a++
  gi|330509140|ref|YP_004385568.1| 242 YEESIKAYNKVIEIAPKEAsYAWEGKGLALEALGRNSEANAAF 284
                                       5667788899999998877468888**********99998876 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1    0.0024      0.94       4      32 ..      51      79 ..      45      80 .. 0.82
   2 ?    5.1   0.0       0.1        40      15      33 .]      96     114 ..      87     114 .. 0.89
   3 ?    4.7   0.0      0.14        57      10      30 ..     125     145 ..     121     147 .. 0.81
   4 !   11.1   0.0    0.0013      0.51       7      33 .]     156     182 ..     148     182 .. 0.81
   5 !    9.7   0.0    0.0036       1.4       8      28 ..     198     218 ..     195     221 .. 0.89
   6 !    9.7   0.0    0.0035       1.4       9      32 ..     235     258 ..     231     259 .. 0.86
   7 ?    1.6   0.1       1.3   5.2e+02       7      25 ..     268     286 ..     262     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0024
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  4 yklalsyrklgdtdkAlealerlikeYPd 32
                                      yk ++ +++ g +++A++a+++ i+  P+
  gi|330509140|ref|YP_004385568.1| 51 YKKGQELERKGSYEEAVKAYDKAIELNPK 79
                                      55665555657**************9997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHH-TT- CS
                             TPR_6  15 dtdkAlealerlikeYPdS 33 
                                       ++ +++ea+e  i+  P+S
  gi|330509140|ref|YP_004385568.1|  96 QHNESIEAYETAIEIDPKS 114
                                       8899*************98 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6  10 yrklgdtdkAlealerlikeY 30 
                                       ++ lg++ ++l a++r+++  
  gi|330509140|ref|YP_004385568.1| 125 LYHLGRYNESLNAYNRVLQMD 145
                                       56678************9855 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPdS 33 
                                       +  + k+g++++A++a+++ ++ Y ++
  gi|330509140|ref|YP_004385568.1| 156 GDILNKTGRHEEAIKAFNKALEIYDNT 182
                                       55666779****************875 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAlealerlik 28 
                                         ++k+g++++A++ ++++i+
  gi|330509140|ref|YP_004385568.1| 198 ITLEKMGRYEEAIKSYDKVIE 218
                                       567899*************96 PP

  == domain 6  score: 9.7 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                                        +++ g+++++++a++++i+  P+
  gi|330509140|ref|YP_004385568.1| 235 IFKAIGKYEESIKAYNKVIEIAPK 258
                                       667778**************9996 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealer 25 
                                       +l++++lg+ ++A +a+ +
  gi|330509140|ref|YP_004385568.1| 268 GLALEALGRNSEANAAFSE 286
                                       89999999*****999975 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.044        18      11      32 ..      59      78 ..      57      81 .. 0.77
   2 ?    3.1   0.0      0.28   1.1e+02       5      31 ..      87     111 ..      83     115 .. 0.76
   3 ?    0.9   0.0       1.5   6.1e+02      12      29 ..     128     145 ..     117     150 .. 0.84
   4 !    7.8   0.0    0.0089       3.6       3      28 ..     153     178 ..     147     189 .. 0.83
   5 !   12.8   0.0   0.00024     0.094       6      29 ..     197     220 ..     192     224 .. 0.83
   6 !    8.2   0.0    0.0067       2.7       1      29 [.     228     256 ..     228     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.044
                             TPR_7 11 rlGdyeeAielyeqsLaltkdp 32
                                      r G yeeA++ y +  a++  p
  gi|330509140|ref|YP_004385568.1| 59 RKGSYEEAVKAYDK--AIELNP 78
                                      7788**********..666555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.28
                             TPR_7   5 LarlysrlGdyeeAielyeqsLaltkd 31 
                                        + + s l ++ e ie ye   a++ d
  gi|330509140|ref|YP_004385568.1|  87 KGIILSGLEQHNESIEAYET--AIEID 111
                                       577888899999********..55544 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.5
                             TPR_7  12 lGdyeeAielyeqsLalt 29 
                                       lG+y e +  y ++L+++
  gi|330509140|ref|YP_004385568.1| 128 LGRYNESLNAYNRVLQMD 145
                                       89*********9977765 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0089
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLal 28 
                                       +  +++  + G++eeAi+ + ++L++
  gi|330509140|ref|YP_004385568.1| 153 VEKGDILNKTGRHEEAIKAFNKALEI 178
                                       556888999*************7765 PP

  == domain 5  score: 12.8 bits;  conditional E-value: 0.00024
                             TPR_7   6 arlysrlGdyeeAielyeqsLalt 29 
                                       + + +++G+yeeAi+ y +++++ 
  gi|330509140|ref|YP_004385568.1| 197 GITLEKMGRYEEAIKSYDKVIEMS 220
                                       67899**************76665 PP

  == domain 6  score: 8.2 bits;  conditional E-value: 0.0067
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       a+ + ++++ + G+yee i+ y ++++++
  gi|330509140|ref|YP_004385568.1| 228 AWTAKGDIFKAIGKYEESIKAYNKVIEIA 256
                                       567889****************9966665 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.016       6.4     104     129 ..      51      76 ..      42      81 .. 0.88
   2 ?    1.8   0.0      0.57   2.3e+02     100     129 ..      81     110 ..      77     114 .. 0.87
   3 !   16.8   0.2   1.4e-05    0.0054      58     132 ..     118     181 ..     113     189 .. 0.82
   4 !   11.5   0.0    0.0006      0.24     102     129 ..     192     219 ..     182     223 .. 0.87
   5 ?    4.0   0.0      0.12        47     104     129 ..     230     255 ..     224     262 .. 0.84
   6 ?    4.5   0.1     0.084        33     106     128 ..     267     289 ..     262     293 .] 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.016
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmagem 129
                                       +++++ le  G+++ea+ka+ +a e+
  gi|330509140|ref|YP_004385568.1|  51 YKKGQELERKGSYEEAVKAYDKAIEL 76 
                                       68999999999999999999999986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 100 iaavfsravaleelGrkdealkafrmagem 129
                                       i + +s++  l++l +++e+++a+++a e+
  gi|330509140|ref|YP_004385568.1|  81 IMVWLSKGIILSGLEQHNESIEAYETAIEI 110
                                       667789999999999********9999885 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                           DUF3856  58 haglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagemiae 132
                                       + ++++ l +lgry+e+l++       +nr  +++    + W+    +++  l+++Gr++ea+kaf++a e+ ++
  gi|330509140|ref|YP_004385568.1| 118 WGTMADELYHLGRYNESLNA-------YNRVLQMDPHMARAWV----EKGDILNKTGRHEEAIKAFNKALEIYDN 181
                                       56788889999999998876.......6777677888888885....79*********************98765 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.0006
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmagem 129
                                       a   ++ +le++Gr++ea+k++ ++ em
  gi|330509140|ref|YP_004385568.1| 192 AWQGKGITLEKMGRYEEAIKSYDKVIEM 219
                                       5567999********************9 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.12
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmagem 129
                                         ++  ++ +G+++e++ka++++ e+
  gi|330509140|ref|YP_004385568.1| 230 TAKGDIFKAIGKYEESIKAYNKVIEI 255
                                       567888999************99986 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.084
                                       HHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 106 ravaleelGrkdealkafrmage 128
                                       ++ ale lGr++ea  af  a+ 
  gi|330509140|ref|YP_004385568.1| 267 KGLALEALGRNSEANAAFSEAKM 289
                                       899***************98864 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 !   10.5   0.0    0.0014      0.56      23      80 ..      47     105 ..      30     107 .. 0.89
   2 !   16.2   0.0   2.4e-05    0.0094       3      80 ..      61     139 ..      60     141 .. 0.84
   3 !   13.8   0.0   0.00013     0.051       4      81 ..      96     174 ..      94     175 .. 0.66
   4 !   12.5   0.0   0.00033      0.13      38      81 ..     171     215 ..     137     216 .. 0.72
   5 !   13.1   0.1   0.00022     0.086       4      79 ..     164     249 ..     161     252 .. 0.51
   6 ?    0.4   0.1         2     8e+02      70      81 ..     240     251 ..     231     287 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  23 pedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +ed y +++ l + g y++A + ++ka +ln+k++ +++ ++  l  L++++e i a+e
  gi|330509140|ref|YP_004385568.1|  47 AEDWYKKGQELERKGSYEEAVKAYDKAiELNPKDIMVWLSKGIILSGLEQHNESIEAYE 105
                                       6788888999999*****************************************99987 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.4e-05
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       + y++A+  ++++ + ++++    + ++  l  ++q+++ +e +++a ++++ks++++ ++A  l+ L++y+e ++a
  gi|330509140|ref|YP_004385568.1|  61 GSYEEAVKAYDKAIELNPKDIMVWLSKGIILSGLEQHNESIEAYETAiEIDPKSIQAWGTMADELYHLGRYNESLNA 137
                                       679999999999995555444444445888888899***************************************99 PP

                                       H- CS
                            ANAPC3  79 Le 80 
                                       + 
  gi|330509140|ref|YP_004385568.1| 138 YN 139
                                       86 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 0.00013
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       ++++ i  +e + + +++s ++    A  ly++g+y++ ++ +++  + +++  ++++ ++  l k +++eeAi+a+
  gi|330509140|ref|YP_004385568.1|  96 QHNESIEAYETAIEIDPKSIQAWGTMADELYHLGRYNESLNAYNRVlQMDPHMARAWVEKGDILNKTGRHEEAIKAF 172
                                       55555666666666666666666666777777777777777777776666666677777777777777777777777 PP

                                       -S CS
                            ANAPC3  80 ek 81 
                                        k
  gi|330509140|ref|YP_004385568.1| 173 NK 174
                                       65 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00033
                                       -HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  38 qykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                        +++A+e+++++ ++n++++ ++  ++ +l k+++yeeAi+ ++k
  gi|330509140|ref|YP_004385568.1| 171 AFNKALEIYDNTiQENPEDIIAWQGKGITLEKMGRYEEAIKSYDK 215
                                       3677777777777777777788888899999*********99877 PP

  == domain 5  score: 13.1 bits;  conditional E-value: 0.00022
                                       -HHHHHHHHHHHH.....HHH--HHHHHH...HHHHHHHTT-HHHHHHHHHCTSHHHC-H....HHHHHHHHHHHHT CS
                            ANAPC3   4 nyknAiflaerlla....aetespedayl...lAlclylngqykrAyellrkaklnsksl....gcrylfAqcllkL 69 
                                       ++++Ai  ++++l+    + +e+ped+ +   ++ +l ++g+y++A++ ++k  ++ +s+    g++  ++    ++
  gi|330509140|ref|YP_004385568.1| 164 RHEEAIKAFNKALEiydnTIQENPEDIIAwqgKGITLEKMGRYEEAIKSYDKV-IEMSSPdyalGAWTAKGDIFKAI 239
                                       56666666666663333355666666444233366666666666666666666.33333333445555555555555 PP

                                       T-HHHHHHHH CS
                            ANAPC3  70 kkyeeAiaaL 79 
                                       +kyee i+a+
  gi|330509140|ref|YP_004385568.1| 240 GKYEESIKAY 249
                                       6666666655 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 2
                                       T-HHHHHHHH-S CS
                            ANAPC3  70 kkyeeAiaaLek 81 
                                       +kyee i+a+ k
  gi|330509140|ref|YP_004385568.1| 240 GKYEESIKAYNK 251
                                       677777776655 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.077        31      15      31 ..      60      76 ..      54      77 .. 0.87
   2 ?    4.4   0.0     0.089        36       9      31 ..      88     110 ..      87     110 .. 0.94
   3 ?    6.2   0.1     0.025       9.8      12      31 ..     125     144 ..     120     144 .. 0.89
   4 !   10.1   0.0    0.0015      0.59      11      38 ..     158     185 ..     156     189 .. 0.83
   5 !    8.8   0.0    0.0038       1.5       9      31 ..     197     219 ..     197     220 .. 0.92
   6 ?   -0.4   0.0       2.9   1.1e+03      16      31 ..     240     255 ..     235     256 .. 0.74
   7 ?   -1.9   0.1       8.7   3.5e+03       9      23 ..     268     282 ..     268     287 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.077
                            TPR_10 15 rgrydeAealleealai 31
                                       g y+eA++ +++a+++
  gi|330509140|ref|YP_004385568.1| 60 KGSYEEAVKAYDKAIEL 76
                                      6889**********986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.089
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       +++l+ + +++e+ + +e a++i
  gi|330509140|ref|YP_004385568.1|  88 GIILSGLEQHNESIEAYETAIEI 110
                                       78999****************97 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.025
                            TPR_10  12 lrqrgrydeAealleealai 31 
                                       l+++gry+e+++ + ++l++
  gi|330509140|ref|YP_004385568.1| 125 LYHLGRYNESLNAYNRVLQM 144
                                       899***********999986 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0015
                            TPR_10  11 alrqrgrydeAealleealairrrllGp 38 
                                       +l ++gr++eA + + +al+i+  +  +
  gi|330509140|ref|YP_004385568.1| 158 ILNKTGRHEEAIKAFNKALEIYDNTIQE 185
                                       68899****************9766655 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0038
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       +++l ++gry+eA + +++++++
  gi|330509140|ref|YP_004385568.1| 197 GITLEKMGRYEEAIKSYDKVIEM 219
                                       789999**************997 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 2.9
                            TPR_10  16 grydeAealleealai 31 
                                       g+y+e+ + + ++++i
  gi|330509140|ref|YP_004385568.1| 240 GKYEESIKAYNKVIEI 255
                                       7788887777777776 PP

  == domain 7  score: -1.9 bits;  conditional E-value: 8.7
                            TPR_10   9 analrqrgrydeAea 23 
                                       + al ++gr  eA a
  gi|330509140|ref|YP_004385568.1| 268 GLALEALGRNSEANA 282
                                       567778888888865 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   0.00015     0.059     200     257 ..      55     112 ..      48     115 .. 0.91
   2 !   11.0   0.3   0.00036      0.14     198     253 ..     121     176 ..      94     182 .. 0.80
   3 !   10.8   0.1    0.0004      0.16     200     255 ..     164     219 ..     162     226 .. 0.90
   4 !   10.8   0.1   0.00041      0.16      14      75 ..     200     263 ..     196     289 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                                       HHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                             NARP1 200 qhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                       q  ++ gs+e+A++  dkaie +p+ + ++l K+ il    + ++ +e+ e+a ++D 
  gi|330509140|ref|YP_004385568.1|  55 QELERKGSYEEAVKAYDKAIELNPKDIMVWLSKGIILSGLEQHNESIEAYETAIEIDP 112
                                       6678899******************************999999999999999998885 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00036
                                       HHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             NARP1 198 lAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeear 253
                                       +A    +lg+++++l+  ++ ++ +p +   ++ K+ il ++G  ++A+++ ++a 
  gi|330509140|ref|YP_004385568.1| 121 MADELYHLGRYNESLNAYNRVLQMDPHMARAWVEKGDILNKTGRHEEAIKAFNKAL 176
                                       5777779999****************************************999985 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0004
                                       HHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 200 qhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                        h + ++  +kAle+ d+ i+++p+ +  ++ K+  l+++G  ++A++  ++  ++
  gi|330509140|ref|YP_004385568.1| 164 RHEEAIKAFNKALEIYDNTIQENPEDIIAWQGKGITLEKMGRYEEAIKSYDKVIEM 219
                                       588899999**************************************999987766 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00041
                                       HHHHTHHHHHHHHHHHHGGG---H..HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHH CS
                             NARP1  14 ieeagkleeAlehLeekekqivDk..lavketkaelllkLgrkeeAeatyeaLlernpenskYy 75 
                                       +e+ g++eeA++  +++ +       l   ++k+++  ++g++ee+ ++y++ +e  p + +Y 
  gi|330509140|ref|YP_004385568.1| 200 LEKMGRYEEAIKSYDKVIEMSSPDyaLGAWTAKGDIFKAIGKYEESIKAYNKVIEIAPKEASYA 263
                                       688999999999999976666665125567899***********************99999994 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.53   2.1e+02       9      35 ..      50      76 ..      44      78 .. 0.85
   2 !   11.0   0.1    0.0011      0.43      74     123 ..      93     142 ..      88     144 .. 0.93
   3 !   11.4   0.1    0.0008      0.32       2     122 ..     145     287 ..     144     293 .] 0.62

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.53
                                      HHHHHHHHHHTT-HHHHHHHHHHHHTT CS
                              BTAD  9 lvaagraalaagdpeeaaelleaAlal 35
                                       +++g+++ ++g  eea++++++A++l
  gi|330509140|ref|YP_004385568.1| 50 WYKKGQELERKGSYEEAVKAYDKAIEL 76
                                      578899999999999999999999876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0011
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                        l++++e ++ +e +++ +P   +++  +   l+++Gr +e L++Y+r+ 
  gi|330509140|ref|YP_004385568.1|  93 GLEQHNESIEAYETAIEIDPKSIQAWGTMADELYHLGRYNESLNAYNRVL 142
                                       5789*******************************************985 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.0008
                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTT.....................STTHHHHHHHH CS
                              BTAD   2 DlarfealvaagraalaagdpeeaaelleaAlalwrGpaladlea.....................gewleaererl 57 
                                       D +  +a v++g+ + + g++eea++++++Al++++ +  ++ e+                     ++  +      
  gi|330509140|ref|YP_004385568.1| 145 DPHMARAWVEKGDILNKTGRHEEAIKAFNKALEIYDNTIQENPEDiiawqgkgitlekmgryeeaiKSYDKVIEMSS 221
                                       5566777899999999********************99999977677777555555554444333222222222222 PP

                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HH.HHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  58 eelrlealealaeaelrlGraeealaelealvaehPlrEr.lhrqlmrAlarsGrqaeALevYerl 122
                                        + +l a +a  +   ++G++ee ++ +++ ++  P     +++   +Al ++Gr++eA +++ ++
  gi|330509140|ref|YP_004385568.1| 222 PDYALGAWTAKGDIFKAIGKYEESIKAYNKVIEIAPKEASyAWEGKGLALEALGRNSEANAAFSEA 287
                                       234444444444455566666666666666666666543324566666777777777776666665 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.084        34     152     176 ..      53      77 ..      44      85 .. 0.87
   2 ?   -1.0   0.0         3   1.2e+03     152     176 ..      87     111 ..      85     125 .. 0.84
   3 !   13.0   0.0   0.00016     0.063     151     178 ..     154     181 ..     120     192 .. 0.80
   4 !    9.0   0.1    0.0025         1     125     176 ..     202     256 ..     185     263 .. 0.80
   5 ?    2.3   0.1       0.3   1.2e+02     150     173 ..     265     288 ..     259     292 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.084
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaal 176
                                       +G  l ++g  +eA +aY++A++ +
  gi|330509140|ref|YP_004385568.1|  53 KGQELERKGSYEEAVKAYDKAIELN 77 
                                       7888899**************9865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaal 176
                                       +G il+  ++ +e  +aY+ A++  
  gi|330509140|ref|YP_004385568.1|  87 KGIILSGLEQHNESIEAYETAIEID 111
                                       788899999999999****999865 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00016
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaalee 178
                                        +GDil ++g+ +eA +a+++Al+  ++
  gi|330509140|ref|YP_004385568.1| 154 EKGDILNKTGRHEEAIKAFNKALEIYDN 181
                                       59********************987665 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0025
                            TPR_21 125 aekkydeAlktLeak...keeafaalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                       +++ y+eA+k  +++   ++  +a  +   +GDi+ a gk +e  +aY++ ++  
  gi|330509140|ref|YP_004385568.1| 202 KMGRYEEAIKSYDKViemSSPDYALGAWTAKGDIFKAIGKYEESIKAYNKVIEIA 256
                                       567888888877655111566788888899*******************988755 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.3
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAl 173
                                       e +G +l a g++ eA aa+++A 
  gi|330509140|ref|YP_004385568.1| 265 EGKGLALEALGRNSEANAAFSEAK 288
                                       6799999**************996 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.031        12      32      64 ..      43      75 ..      39      79 .. 0.90
   2 ?   -0.3   0.0       1.8   7.3e+02      36      64 ..     115     143 ..      94     147 .. 0.74
   3 !   11.4   0.1   0.00048      0.19      30      64 ..     143     177 ..     127     186 .. 0.84
   4 ?    2.0   0.0      0.37   1.5e+02      46      65 ..     200     219 ..     191     225 .. 0.82
   5 !    8.6   0.0    0.0034       1.4      38      64 ..     228     254 ..     224     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.031
                                      HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7 32 keeirrakldlaehYlkigdleeAlkaysrire 64
                                      +e i++ ++++++   + g +eeA+kay +++e
  gi|330509140|ref|YP_004385568.1| 43 QEMIAEDWYKKGQELERKGSYEEAVKAYDKAIE 75
                                      57799999*********************9876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  36 rrakldlaehYlkigdleeAlkaysrire 64 
                                        +a+   a+  +  g ++e+l+ay+r+++
  gi|330509140|ref|YP_004385568.1| 115 IQAWGTMADELYHLGRYNESLNAYNRVLQ 143
                                       46777788888899999999999999875 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00048
                                       T-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  30 lgkeeirrakldlaehYlkigdleeAlkaysrire 64 
                                       +++  ++ra+ ++++   k+g +eeA+ka+++++e
  gi|330509140|ref|YP_004385568.1| 143 QMDPHMARAWVEKGDILNKTGRHEEAIKAFNKALE 177
                                       567789**************************876 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.37
                                       HHHCT-HHHHHHHHHTCCCC CS
                              RPN7  46 YlkigdleeAlkaysrirey 65 
                                         k+g +eeA+k y +++e 
  gi|330509140|ref|YP_004385568.1| 200 LEKMGRYEEAIKSYDKVIEM 219
                                       578999********998875 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0034
                                       HHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  38 akldlaehYlkigdleeAlkaysrire 64 
                                       a+ ++++ +  ig++ee++kay++++e
  gi|330509140|ref|YP_004385568.1| 228 AWTAKGDIFKAIGKYEESIKAYNKVIE 254
                                       6789*******************9875 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.5     0.042        17     121     151 ..      54      83 ..      36     113 .. 0.59
   2 !   21.4   0.0   3.5e-07   0.00014     115     202 ..     150     238 ..     146     240 .. 0.81
   3 ?    0.2   0.1         1     4e+02     168     196 ..     239     267 ..     234     274 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.042
                                       HHHHHHTT--HHHHHHHHHHHHHHHHHTT-H CS
                              SNAP 121 aelyekelgdlekAieaYekAaelyeqeeak 151
                                       ++ +e + g +e+A++aY+kA el  ++   
  gi|330509140|ref|YP_004385568.1|  54 GQELERK-GSYEEAVKAYDKAIELNPKDIMV 83 
                                       3334444.66888888888888876655544 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 3.5e-07
                                       HHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH.HHHTT-HHHHHHHHHHHHHTTS.S-T CS
                              SNAP 115 klkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAel.saelekyekAieiyekvakksl.enn 189
                                       +   e +++++k  g+ e+Ai+a++kA e+y++  ++     +  +   +   ++++ye+Ai+ y+kv++ s  +  
  gi|330509140|ref|YP_004385568.1| 150 RAWVEKGDILNKT-GRHEEAIKAFNKALEIYDNTIQENPEDIIAWQGKGItLEKMGRYEEAIKSYDKVIEMSSpDYA 225
                                       5566778999988.*******************99888777776666666155666*************97652778 PP

                                       TTGGGHHHHHHHH CS
                              SNAP 190 llkysvkeyflka 202
                                       l  + +k+  +ka
  gi|330509140|ref|YP_004385568.1| 226 LGAWTAKGDIFKA 238
                                       9999999887777 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1
                                       TT-HHHHHHHHHHHHHTTSS-TTTGGGHH CS
                              SNAP 168 lekyekAieiyekvakkslennllkysvk 196
                                        +kye++i++y+kv++ + ++    +  k
  gi|330509140|ref|YP_004385568.1| 239 IGKYEESIKAYNKVIEIAPKEASYAWEGK 267
                                       46788888888888876666666666555 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 ?    4.8   0.0     0.081        32      13      38 ..      52      77 ..      43     109 .. 0.76
   2 ?   -1.2   0.0       6.3   2.5e+03      14      32 ..     121     139 ..     116     145 .. 0.83
   3 ?    5.8   0.0     0.039        16      13      40 ..     154     181 ..     142     189 .. 0.83
   4 ?    3.0   0.0      0.29   1.2e+02      20      37 ..     202     219 ..     194     227 .. 0.82
   5 ?    6.8   0.0      0.02         8      14      36 ..     232     254 ..     219     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.081
                         NRBF2_MIT 13 rkadrllaaGkyeeaischkkaaayl 38
                                      +k + l   G yeea+  + ka +  
  gi|330509140|ref|YP_004385568.1| 52 KKGQELERKGSYEEAVKAYDKAIELN 77
                                      677788889************98764 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 6.3
                         NRBF2_MIT  14 kadrllaaGkyeeaischk 32 
                                        ad l   G+y+e++  ++
  gi|330509140|ref|YP_004385568.1| 121 MADELYHLGRYNESLNAYN 139
                                       58999999*****988765 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.039
                         NRBF2_MIT  13 rkadrllaaGkyeeaischkkaaaylse 40 
                                        k d l  +G++eeai   +ka ++  +
  gi|330509140|ref|YP_004385568.1| 154 EKGDILNKTGRHEEAIKAFNKALEIYDN 181
                                       67888999**************887665 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.29
                         NRBF2_MIT  20 aaGkyeeaischkkaaay 37 
                                         G+yeeai  + k  ++
  gi|330509140|ref|YP_004385568.1| 202 KMGRYEEAIKSYDKVIEM 219
                                       579******999997665 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.02
                         NRBF2_MIT  14 kadrllaaGkyeeaischkkaaa 36 
                                       k d + a Gkyee+i  ++k  +
  gi|330509140|ref|YP_004385568.1| 232 KGDIFKAIGKYEESIKAYNKVIE 254
                                       6788889*********9999766 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 !   15.1   1.1   4.4e-05     0.018       9      33 ..      52      76 ..      47      76 .. 0.92
   2 ?    0.7   0.1       1.5   5.8e+02      19      32 ..      96     109 ..      94     110 .. 0.83
   3 ?    5.9   0.0     0.033        13      16      44 ..     161     188 ..     149     197 .. 0.82
   4 ?    7.4   0.0     0.011       4.4      11      30 ..     197     216 ..     191     219 .. 0.85
   5 ?    2.3   0.1      0.46   1.8e+02      18      29 ..     240     251 ..     231     262 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.4e-05
                               MIT  9 kkAveeDnagnyeeAlelYkealel 33
                                      kk  e++++g yeeA+++Y +a+el
  gi|330509140|ref|YP_004385568.1| 52 KKGQELERKGSYEEAVKAYDKAIEL 76
                                      7899*******************96 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.5
                               MIT  19 nyeeAlelYkeale 32 
                                       +  e +e+Y++a+e
  gi|330509140|ref|YP_004385568.1|  96 QHNESIEAYETAIE 109
                                       56799999*99998 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.033
                               MIT  16 nagnyeeAlelYkealelLlqalkeknee 44 
                                       + g  eeA++++ +ale+    ++e n+e
  gi|330509140|ref|YP_004385568.1| 161 KTGRHEEAIKAFNKALEIYDNTIQE-NPE 188
                                       56889************99999986.334 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.011
                               MIT  11 AveeDnagnyeeAlelYkea 30 
                                        + +++ g yeeA++ Y + 
  gi|330509140|ref|YP_004385568.1| 197 GITLEKMGRYEEAIKSYDKV 216
                                       6788999**********875 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.46
                               MIT  18 gnyeeAlelYke 29 
                                       g+yee +++Y +
  gi|330509140|ref|YP_004385568.1| 240 GKYEESIKAYNK 251
                                       456666665554 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00028      0.11       3      54 ..      96     147 ..      94     155 .. 0.91
   2 ?    2.5   0.0      0.48   1.9e+02      17      49 ..     144     176 ..     138     182 .. 0.79
   3 ?    4.0   0.0      0.15        61       8      76 ..     176     244 ..     170     253 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00028
                            TPR_20   3 adapelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                       ++++++++ e+a++ +p+ ++a   +A+ l++ gry e+l++  ++l+ d +
  gi|330509140|ref|YP_004385568.1|  96 QHNESIEAYETAIEIDPKSIQAWGTMADELYHLGRYNESLNAYNRVLQMDPH 147
                                       6899*************************************99999888765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.48
                            TPR_20  17 anpddldarldlAlallaagryeeAleqLleil 49 
                                        +p    a ++  + l++ gr+eeA++++ + l
  gi|330509140|ref|YP_004385568.1| 144 MDPHMARAWVEKGDILNKTGRHEEAIKAFNKAL 176
                                       5677777778889999*********99887666 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.15
                            TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllkifealgsqdp 76 
                                       l+  ++++++np+d+ a       l + gryeeA++   ++++  + +    a ++  +if+a+g+ ++
  gi|330509140|ref|YP_004385568.1| 176 LEIYDNTIQENPEDIIAWQGKGITLEKMGRYEEAIKSYDKVIEMSSPDYALGAWTAKGDIFKAIGKYEE 244
                                       5666789999*****999999*************99877777666655555555555666666666555 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 ?    1.7   0.0      0.68   2.7e+02      14      33 ..      60      79 ..      58      81 .. 0.88
   2 ?    1.5   0.0       0.8   3.2e+02      14      37 ..      94     117 ..      92     118 .. 0.90
   3 !    9.6   0.1    0.0023      0.91      12      33 ..     126     147 ..     125     151 .. 0.92
   4 ?   -0.4   0.0       3.1   1.2e+03      15      30 ..     163     178 ..     160     189 .. 0.56
   5 ?    2.4   0.0      0.43   1.7e+02      13      29 ..     202     218 ..     198     222 .. 0.86
   6 ?    0.4   0.0       1.7     7e+02      14      33 ..     239     258 ..     238     261 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.68
                                      HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPe 33
                                       g Y+eA +  d  +e+ P+
  gi|330509140|ref|YP_004385568.1| 60 KGSYEEAVKAYDKAIELNPK 79
                                      589***********999996 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.8
                                       HT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQa 37 
                                       l +++e+ +  ++ +ei+P+  Qa
  gi|330509140|ref|YP_004385568.1|  94 LEQHNESIEAYETAIEIDPKSIQA 117
                                       67899999***********99997 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0023
                                       HHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPe 33 
                                       y lg+Y+e+++  +++L+++P 
  gi|330509140|ref|YP_004385568.1| 126 YHLGRYNESLNAYNRVLQMDPH 147
                                       88*******************7 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 3.1
                                       T-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C  15 geYseArryvdalLei 30 
                                       g+++eA +  +  Lei
  gi|330509140|ref|YP_004385568.1| 163 GRHEEAIKAFNKALEI 178
                                       5666666666655555 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.43
                                       HHT-HHHHHHHHHHHHH CS
                        Fis1_TPR_C  13 klgeYseArryvdalLe 29 
                                       k+g+Y+eA +  d ++e
  gi|330509140|ref|YP_004385568.1| 202 KMGRYEEAIKSYDKVIE 218
                                       9*******999888776 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1.7
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       +g+Y+e+ +  + ++ei P+
  gi|330509140|ref|YP_004385568.1| 239 IGKYEESIKAYNKVIEIAPK 258
                                       699**********9999996 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.037        15      87     131 ..      99     143 ..      42     150 .. 0.71
   2 !    9.8   0.0    0.0026         1      74     127 ..     120     173 ..     114     181 .. 0.91
   3 ?    3.2   0.0      0.28   1.1e+02      80     123 ..     167     210 ..     155     217 .. 0.85
   4 ?    5.1   0.0     0.072        29      81     122 ..     238     280 ..     193     286 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHHHHH CS
                   Alkyl_sulf_dimr  87 waaellnhlvfadpenaeakelkadaleqlgyqaesatwRniYls 131
                                        ++e  + +++ dp+  +a    ad l +lg+ +es ++ n  l+
  gi|330509140|ref|YP_004385568.1|  99 ESIEAYETAIEIDPKSIQAWGTMADELYHLGRYNESLNAYNRVLQ 143
                                       3445555566678888999999**********9999999887665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0026
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHH CS
                   Alkyl_sulf_dimr  74 ekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRn 127
                                       ++a e +  g y+ +++  n +++ dp+ a+a   k d+l++ g+++e+  + n
  gi|330509140|ref|YP_004385568.1| 120 TMADELYHLGRYNESLNAYNRVLQMDPHMARAWVEKGDILNKTGRHEEAIKAFN 173
                                       588999999**************************************9988766 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.28
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  80 lkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                        + + ++ a+e+ ++ ++++pe+  a + k  +le++g+ +e+ 
  gi|330509140|ref|YP_004385568.1| 167 EAIKAFNKALEIYDNTIQENPEDIIAWQGKGITLEKMGRYEEAI 210
                                       45677899******************************998865 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.072
                                       HTT-HHHHHHHHHHHHHHSTT-H.HHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpena.eakelkadaleqlgyqaes 122
                                       + g+y+ +++  n++++  p++a  a e k  ale+lg+ +e+
  gi|330509140|ref|YP_004385568.1| 238 AIGKYEESIKAYNKVIEIAPKEAsYAWEGKGLALEALGRNSEA 280
                                       5567888888888888888887657888888888888888876 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       6.9   2.7e+03      29      38 ..      62      71 ..      47      85 .. 0.58
   2 !   12.1   0.0   0.00037      0.15       3      71 ..     102     175 ..     100     186 .. 0.84
   3 ?    5.6   0.1      0.04        16      20      45 ..     196     221 ..     176     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6.9
                      SRP_TPR_like 29 kyeeaLkllk 38
                                       yeea+k+ +
  gi|330509140|ref|YP_004385568.1| 62 SYEEAVKAYD 71
                                      2333333333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00037
                      SRP_TPR_like   3 eeyekilrlegkelkkfkvva..liklekyeeaLkllkkgsalsedvr...fEkaYvlYklkkykkalkilkkv 71 
                                       e+ye  ++++ k ++ +  +a  l +l++y+e+L++ +   +++ ++    +Ek  +l k+ + ++a k ++k+
  gi|330509140|ref|YP_004385568.1| 102 EAYETAIEIDPKSIQAWGTMAdeLYHLGRYNESLNAYNRVLQMDPHMArawVEKGDILNKTGRHEEAIKAFNKA 175
                                       7899999999999999977766699**********99988877777643339*****************99875 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.04
                      SRP_TPR_like  20 kvvaliklekyeeaLkllkkgsalse 45 
                                       k ++l k+++yeea+k  +k  ++s+
  gi|330509140|ref|YP_004385568.1| 196 KGITLEKMGRYEEAIKSYDKVIEMSS 221
                                       77888899999999999988775654 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.023       9.3       7      36 ..      46      75 ..      43      88 .. 0.92
   2 ?   -0.1   0.0       1.7     7e+02      10      36 ..     117     143 ..     113     150 .. 0.73
   3 !    7.5   0.0    0.0083       3.3       7      37 ..     148     178 ..     138     187 .. 0.87
   4 ?    0.5   0.0       1.2   4.6e+02      17      37 ..     199     219 ..     191     225 .. 0.83
   5 ?   -2.4   0.0       8.8   3.5e+03      15      36 ..     233     254 ..     224     259 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.023
                           DUF5113  7 iandYanlayylnvegeyeeALeyldsale 36
                                      ia+d+ + +++l  +g+yeeA++  d+a+e
  gi|330509140|ref|YP_004385568.1| 46 IAEDWYKKGQELERKGSYEEAVKAYDKAIE 75
                                      7999999*********************97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.7
                           DUF5113  10 dYanlayylnvegeyeeALeyldsale 36 
                                       ++ ++a +l+  g+y+e+L+  + +l+
  gi|330509140|ref|YP_004385568.1| 117 AWGTMADELYHLGRYNESLNAYNRVLQ 143
                                       566677777788888888888887776 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0083
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsaley 37 
                                       +a ++++ +  ln +g++eeA++ +++ale+
  gi|330509140|ref|YP_004385568.1| 148 MARAWVEKGDILNKTGRHEEAIKAFNKALEI 178
                                       6889999**********************97 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.2
                           DUF5113  17 ylnvegeyeeALeyldsaley 37 
                                       +l   g+yeeA++  d+++e+
  gi|330509140|ref|YP_004385568.1| 199 TLEKMGRYEEAIKSYDKVIEM 219
                                       566789**********99975 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 8.8
                           DUF5113  15 ayylnvegeyeeALeyldsale 36 
                                       +    + g+yee+++  ++++e
  gi|330509140|ref|YP_004385568.1| 233 GDIFKAIGKYEESIKAYNKVIE 254
                                       5555666777777777777665 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.45   1.8e+02     254     289 ..      50      84 ..      37      87 .. 0.75
   2 !    9.5   0.0    0.0013      0.51     255     294 ..      91     123 ..      83     136 .. 0.82
   3 ?    5.2   0.1     0.026        10     236     285 ..     140     182 ..     125     252 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.45
                                       CCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTT CS
                               FAT 254 wqealqkldwseekieeilqsysaateidpswykaw 289
                                       w ++ q+l +++ + ee++++y +a e++p+ +  w
  gi|330509140|ref|YP_004385568.1|  50 WYKKGQEL-ERKGSYEEAVKAYDKAIELNPKDIMVW 84 
                                       66666664.56677999********99999765555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                                       CCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCH CS
                               FAT 255 qealqkldwseekieeilqsysaateidpswykawhtwal 294
                                       ++ l++        +e  ++y +a eidp++++aw t+a+
  gi|330509140|ref|YP_004385568.1|  91 LSGLEQ-------HNESIEAYETAIEIDPKSIQAWGTMAD 123
                                       555555.......89999********************97 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.026
                                       .......HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCC CS
                               FAT 236 nleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpsw 285
                                        + +    +ar+  +kG+ ++++++        ee+ +++ +a ei ++ 
  gi|330509140|ref|YP_004385568.1| 140 RVLQMDPHMARAWVEKGDILNKTGR-------HEEAIKAFNKALEIYDNT 182
                                       4455555667777777777777777.......445555555554444443 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.23        91     101     123 ..      60      82 ..      56      87 .. 0.86
   2 ?    0.7   0.0       1.1   4.4e+02     103     124 ..      96     117 ..      90     128 .. 0.87
   3 ?    1.2   0.1      0.74   2.9e+02     103     121 ..     130     148 ..     126     155 .. 0.85
   4 ?    4.9   0.1     0.055        22     100     125 ..     168     193 ..     159     216 .. 0.86
   5 ?    1.9   0.0      0.47   1.9e+02     100     121 ..     238     259 ..     231     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.23
                              LemA 101 RrrYneavreyntkiesfpsniv 123
                                       +  Y eav++y+++ie  p+ i+
  gi|330509140|ref|YP_004385568.1|  60 KGSYEEAVKAYDKAIELNPKDIM 82 
                                       458*************9999886 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.1
                              LemA 103 rYneavreyntkiesfpsniva 124
                                       ++ne++++y+t+ie  p++i a
  gi|330509140|ref|YP_004385568.1|  96 QHNESIEAYETAIEIDPKSIQA 117
                                       78************99999977 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.74
                              LemA 103 rYneavreyntkiesfpsn 121
                                       rYne+ ++yn  +++ p+ 
  gi|330509140|ref|YP_004385568.1| 130 RYNESLNAYNRVLQMDPHM 148
                                       7**********99988875 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.055
                              LemA 100 aRrrYneavreyntkiesfpsnivak 125
                                       a +++n+a + y+++i++ p+ i+a 
  gi|330509140|ref|YP_004385568.1| 168 AIKAFNKALEIYDNTIQENPEDIIAW 193
                                       5579*******************995 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.47
                              LemA 100 aRrrYneavreyntkiesfpsn 121
                                       a  +Y e++++yn+ ie  p++
  gi|330509140|ref|YP_004385568.1| 238 AIGKYEESIKAYNKVIEIAPKE 259
                                       5568************999875 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0       0.3   1.2e+02      12      28 ..      59      75 ..      57      77 .. 0.84
   2 ?   -1.1   0.0       7.5     3e+03       5      21 ..      89     105 ..      88     106 .. 0.86
   3 ?    1.5   0.1       1.1   4.5e+02       3      26 ..     118     141 ..     117     145 .. 0.85
   4 ?    5.3   0.0     0.069        27      10      25 ..     159     174 ..     157     178 .. 0.84
   5 ?    4.0   0.1      0.18        71      12      28 ..     202     218 ..     200     220 .. 0.85
   6 ?   -0.4   0.0       4.4   1.8e+03      14      27 ..     240     253 ..     232     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.3
                               PPR 12 knGkleeAlelfkeMke 28
                                      ++G +eeA++ +++ +e
  gi|330509140|ref|YP_004385568.1| 59 RKGSYEEAVKAYDKAIE 75
                                      89********9998766 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 7.5
                               PPR   5 slIsgycknGkleeAle 21 
                                       +++sg+ ++++  eA e
  gi|330509140|ref|YP_004385568.1|  89 IILSGLEQHNESIEAYE 105
                                       5799999***9999986 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 1.1
                               PPR   3 ynslIsgycknGkleeAlelfkeM 26 
                                       + ++ + + + G++ e l  +++ 
  gi|330509140|ref|YP_004385568.1| 118 WGTMADELYHLGRYNESLNAYNRV 141
                                       999999999*******99988875 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.069
                               PPR  10 ycknGkleeAlelfke 25 
                                       + k G++eeA++ f++
  gi|330509140|ref|YP_004385568.1| 159 LNKTGRHEEAIKAFNK 174
                                       5699**********98 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.18
                               PPR  12 knGkleeAlelfkeMke 28 
                                       k G++eeA++ +++ +e
  gi|330509140|ref|YP_004385568.1| 202 KMGRYEEAIKSYDKVIE 218
                                       89*******99998776 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 4.4
                               PPR  14 GkleeAlelfkeMk 27 
                                       Gk+ee ++ +++ +
  gi|330509140|ref|YP_004385568.1| 240 GKYEESIKAYNKVI 253
                                       88999998888765 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.2    0.0002     0.079     149     269 ..      50     170 ..      42     176 .. 0.84
   2 ?    0.6   0.0      0.64   2.5e+02     231     252 ..     173     194 ..     168     216 .. 0.73
   3 ?   -1.5   0.0       2.9   1.2e+03     149     177 ..     229     257 ..     196     265 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                            TPR_15 149 llaraelyrqegqtdaAlrdyreAlalapdsse..lraallWlliDlgrraeLrellkawkara...esdasLwgpl 220
                                       ++  ++  +++g  ++A+++y +A++l+p++    l ++++   ++  ++      ++a++ +     ++ + wg +
  gi|330509140|ref|YP_004385568.1|  50 WYKKGQELERKGSYEEAVKAYDKAIELNPKDIMvwLSKGIILSGLEQHNE-----SIEAYETAIeidPKSIQAWGTM 121
                                       66677778999*******************96522567777777755544.....599999998777788889**** PP

                            TPR_15 221 aaAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAwr 269
                                       a  l  Lgr+++ L+ +++ ++  +  +   +   D+l++ gr +eA +
  gi|330509140|ref|YP_004385568.1| 122 ADELYHLGRYNESLNAYNRVLQMDPHMARAWVEKGDILNKTGRHEEAIK 170
                                       *******************9998888888888889**********9976 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.64
                            TPR_15 231 kkALeylrkqakenrkdplwll 252
                                       +kALe + +  +en++d+    
  gi|330509140|ref|YP_004385568.1| 173 NKALEIYDNTIQENPEDIIAWQ 194
                                       699************9986444 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.9
                            TPR_15 149 llaraelyrqegqtdaAlrdyreAlalap 177
                                       + a + + ++ g+ ++++++y ++++ ap
  gi|330509140|ref|YP_004385568.1| 229 WTAKGDIFKAIGKYEESIKAYNKVIEIAP 257
                                       44444444455555555555555555555 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         5     2e+03      13      29 ..      59      75 ..      50      81 .. 0.77
   2 ?    2.2   0.1      0.52   2.1e+02     103     119 .]     126     142 ..     117     142 .. 0.85
   3 ?    4.8   0.0     0.079        31       5      31 ..     153     179 ..     149     231 .. 0.64
   4 ?    5.3   0.0     0.057        23      13      95 ..     202     282 ..     191     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 5
                             TPR_5 13 stGhedkavplYrraLa 29
                                        G  ++av+ Y +a++
  gi|330509140|ref|YP_004385568.1| 59 RKGSYEEAVKAYDKAIE 75
                                      56888899999998876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.52
                             TPR_5 103 ehlprYqRsvtnYareL 119
                                        hl rY+ s+++Y r L
  gi|330509140|ref|YP_004385568.1| 126 YHLGRYNESLNAYNRVL 142
                                       499**********9876 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.079
                             TPR_5   5 FeragarDstGhedkavplYrraLaeG 31 
                                        e++ + + tG++++a++ +++aL+  
  gi|330509140|ref|YP_004385568.1| 153 VEKGDILNKTGRHEEAIKAFNKALEIY 179
                                       567777889999999999999999743 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.057
                             TPR_5  13 stGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgr 89 
                                        +G+ ++a++ Y + ++    ++  +  t +     + +G+ ee+++  ++ +e  ++e + a ++   L+L +lgr
  gi|330509140|ref|YP_004385568.1| 202 KMGRYEEAIKSYDKVIEMSSPDYALGAWTAK-GDIFKAIGKYEESIKAYNKVIEIAPKEASYAWEG-KGLALEALGR 276
                                       5677777888888877777777776655544.6678999****************99999999987.689999**** PP

                             TPR_5  90 ereavs 95 
                                       + ea +
  gi|330509140|ref|YP_004385568.1| 277 NSEANA 282
                                       999965 PP

>> Ribosomal_S16  Ribosomal protein S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0029       1.2      22      58 ..      53      88 ..      45      92 .. 0.82
   2 ?    4.7   0.0     0.079        31      28      58 ..     127     156 ..      97     157 .. 0.85
   3 ?   -1.4   0.0       6.6   2.6e+03      34      58 ..     181     197 ..     161     200 .. 0.61
   4 ?   -0.1   0.1       2.5   9.9e+02      26      38 ..     200     213 ..     194     268 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0029
                                      TSSESEEEEEEETTTTSSTS.SEEE-HHHHHHHHHTT CS
                     Ribosomal_S16 22 dgrpiEklGtYdPlakkkekkevelneerikyWlgvG 58
                                      +g+ +E+ G+Y+   k  +k  +eln + i  Wl++G
  gi|330509140|ref|YP_004385568.1| 53 KGQELERKGSYEEAVKAYDK-AIELNPKDIMVWLSKG 88
                                      68899999****95544444.5**************9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.079
                                       EEEEEET.TTTSSTS.SEEE-HHHHHHHHHTT CS
                     Ribosomal_S16  28 klGtYdP.lakkkekkevelneerikyWlgvG 58 
                                       +lG Y+  l+   +  +++++ + ++ W+++G
  gi|330509140|ref|YP_004385568.1| 127 HLGRYNEsLNA-YN-RVLQMDPHMARAWVEKG 156
                                       78999983443.33.47************999 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 6.6
                                       TTTTSSTS.SEEE-HHHHHHHHHTT CS
                     Ribosomal_S16  34 PlakkkekkevelneerikyWlgvG 58 
                                                +++ n e i  W g+G
  gi|330509140|ref|YP_004385568.1| 181 N--------TIQENPEDIIAWQGKG 197
                                       2........3666777777777777 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 2.5
                                       SEEEEEEET.TTTS CS
                     Ribosomal_S16  26 iEklGtYdP.lakk 38 
                                       +Ek+G Y+  +++ 
  gi|330509140|ref|YP_004385568.1| 200 LEKMGRYEEaIKSY 213
                                       56666665423222 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.17        67      17      30 ..      63      76 ..      60      77 .. 0.93
   2 ?    6.1   0.0     0.019       7.6      15      33 ..     163     181 ..     156     185 .. 0.85
   3 ?   -0.6   0.0       2.3   9.3e+02      15      26 ..     204     215 ..     203     218 .. 0.84
   4 ?   -1.6   0.0         5     2e+03       8      26 ..     233     251 ..     233     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.17
                          SHNi-TPR 17 FpqAveDlrkaLeL 30
                                      +++Av+ ++ka+eL
  gi|330509140|ref|YP_004385568.1| 63 YEEAVKAYDKAIEL 76
                                      99**********98 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.019
                          SHNi-TPR  15 enFpqAveDlrkaLeLreq 33 
                                       ++ ++A++ ++kaLe++ +
  gi|330509140|ref|YP_004385568.1| 163 GRHEEAIKAFNKALEIYDN 181
                                       6779************986 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.3
                          SHNi-TPR  15 enFpqAveDlrk 26 
                                       +++++A++ ++k
  gi|330509140|ref|YP_004385568.1| 204 GRYEEAIKSYDK 215
                                       59*****98876 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 5
                          SHNi-TPR   8 GEislEnenFpqAveDlrk 26 
                                       G+i+   +++++ ++ ++k
  gi|330509140|ref|YP_004385568.1| 233 GDIFKAIGKYEESIKAYNK 251
                                       7777788999999998877 PP

>> NACHT_N  N-terminal domain of NWD NACHT-NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0031       1.2      16     115 ..      98     202 ..      92     216 .. 0.68
   2 ?    3.2   0.0      0.17        69      93     125 ..     250     283 ..     223     287 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0031
                           NACHT_N  16 aelvkeYekils.....eeeekesskkeeeseekeeeseeekrqeqlkrlvekglkrvekkkkakegiaeaaevvla 87 
                                       +e +++Ye  ++      +   + +++  +    +e+ ++ +r  q++  + ++     +  + + + +ea+++ ++
  gi|330509140|ref|YP_004385568.1|  98 NESIEAYETAIEidpksIQAWGTMADELYHLGRYNESLNAYNRVLQMDPHMARAWVEKGDILNKTGRHEEAIKAFNK 174
                                       556677777776533211111122222222334455556667777777776666644444457888899******** PP

                           NACHT_N  88 vkdlideavkaspeaalaWagvclvlei 115
                                       + ++ d+ ++  pe  +aW g  ++le 
  gi|330509140|ref|YP_004385568.1| 175 ALEIYDNTIQENPEDIIAWQGKGITLEK 202
                                       *********************9999886 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.17
                           NACHT_N  93 deavkasp.eaalaWagvclvleiltnpvtaaka 125
                                       +++++ +p ea+ aW g  l+le l + ++a++a
  gi|330509140|ref|YP_004385568.1| 250 NKVIEIAPkEASYAWEGKGLALEALGRNSEANAA 283
                                       4555555526***************999998876 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 ?    8.1   0.0    0.0024      0.97     131     232 ..      49     152 ..      21     171 .. 0.85
   2 ?    2.6   0.0      0.11        46     134     168 ..     196     226 ..     168     286 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0024
                                       HHHHHHHHHH.HT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT---T.T-HHHHHHHH-TT-HHHHHHHHHHH CS
                          PknG_TPR 131 dWyrglaeLl.egdyeeAaaeFdevlaalpGEiaPklaLAataElagetde.ekyYrtVwrtdrgvvsAaFGlaRql 205
                                       dWy+   eL  +g yeeA++++d+ +++ p +i   l+  +     ++++e  + Y+t    d   + A   +a +l
  gi|330509140|ref|YP_004385568.1|  49 DWYKKGQELErKGSYEEAVKAYDKAIELNPKDIMVWLSKGIILSGLEQHNEsIEAYETAIEIDPKSIQAWGTMADEL 125
                                       89*98889862689*******************9999999887766665541699*************9999***** PP

                                       HHTT-HHHHHHHHHTS-TTSTTHHHHH CS
                          PknG_TPR 206 aaagdraaAvaaLdeVpatSrhyttAr 232
                                        + g+ ++ ++a + V +   h ++A 
  gi|330509140|ref|YP_004385568.1| 126 YHLGRYNESLNAYNRVLQMDPHMARAW 152
                                       ************999998888887775 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                                       HHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHH CS
                          PknG_TPR 134 rglaeLlegdyeeAaaeFdevlaalpGEiaPklaL 168
                                       +g++   +g+yeeA++++d+v+++     +P  aL
  gi|330509140|ref|YP_004385568.1| 196 KGITLEKMGRYEEAIKSYDKVIEMS----SPDYAL 226
                                       4555556778888888888888763....344444 PP

>> FixH  FixH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00019     0.075      14      66 ..      24      74 ..      17     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00019
                              FixH 14 alfavvvvvnltmlylAvstkdglvvddyYkkGkainqelarakaaqalglsa 66
                                      a fa+v+++ +++ + Av +   + ++d+YkkG++  ++ + ++a +a +  +
  gi|330509140|ref|YP_004385568.1| 24 ARFALVMIALVILCVSAVAQE--MIAEDWYKKGQELERKGSYEEAVKAYDKAI 74
                                      668999999999999999765..6************99988887777766555 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.37   1.5e+02      80     107 ..      52      79 ..      36      87 .. 0.84
   2 ?    8.8   0.0    0.0041       1.6      79     107 ..     153     181 ..     130     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.37
                             MAS20  80 qlGEellaqgeeeeaaehlynAlkvcpq 107
                                       ++G+el ++g++eea+++  +A+ + p+
  gi|330509140|ref|YP_004385568.1|  52 KKGQELERKGSYEEAVKAYDKAIELNPK 79 
                                       789999999*************998654 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0041
                             MAS20  79 vqlGEellaqgeeeeaaehlynAlkvcpq 107
                                       v++G+ l + g++eea++++ +Al ++++
  gi|330509140|ref|YP_004385568.1| 153 VEKGDILNKTGRHEEAIKAFNKALEIYDN 181
                                       899************************87 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.11        44       7      19 ..      72      84 ..      71      85 .. 0.91
   2 ?    6.5   0.0     0.018       7.2       7      19 ..     106     118 ..     105     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                                      HHHHH-TT-CHHH CS
                              PPTA  7 kliekdpkNYsaW 19
                                      k+ie++pk+  +W
  gi|330509140|ref|YP_004385568.1| 72 KAIELNPKDIMVW 84
                                      89*******9999 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.018
                                       HHHHH-TT-CHHH CS
                              PPTA   7 kliekdpkNYsaW 19 
                                        +ie dpk+ +aW
  gi|330509140|ref|YP_004385568.1| 106 TAIEIDPKSIQAW 118
                                       79*********** PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       6.1   2.4e+03      29      51 ..      57      79 ..      54      81 .. 0.79
   2 ?   -1.4   0.0       3.5   1.4e+03      32      55 ..      94     117 ..      90     126 .. 0.81
   3 ?    3.1   0.1      0.14        58      28      61 ..     158     191 ..     155     203 .. 0.71
   4 ?   -2.1   0.0       5.7   2.3e+03      29      47 ..     200     218 ..     194     220 .. 0.88
   5 ?    6.4   0.0     0.015       5.9      29      53 ..     236     260 ..     233     266 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.1
                        MscS_porin 29 LdkidkskkkaeelqkaiddaPk 51
                                      L+ +  +++  +++ kai+  Pk
  gi|330509140|ref|YP_004385568.1| 57 LERKGSYEEAVKAYDKAIELNPK 79
                                      66777899999999999987776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.5
                        MscS_porin  32 idkskkkaeelqkaiddaPkelre 55 
                                        +++++ +e++++ai+  Pk +++
  gi|330509140|ref|YP_004385568.1|  94 LEQHNESIEAYETAIEIDPKSIQA 117
                                       578899999999999988888875 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.14
                        MscS_porin  28 lLdkidkskkkaeelqkaiddaPkelrelqqele 61 
                                        L+k+ ++++ +++++ka++ + ++++e  +++ 
  gi|330509140|ref|YP_004385568.1| 158 ILNKTGRHEEAIKAFNKALEIYDNTIQENPEDII 191
                                       5677777777777777777777777777666554 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 5.7
                        MscS_porin  29 Ldkidkskkkaeelqkaid 47 
                                       L+k  ++++ ++ + k+i+
  gi|330509140|ref|YP_004385568.1| 200 LEKMGRYEEAIKSYDKVIE 218
                                       8899999999999999997 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.015
                        MscS_porin  29 LdkidkskkkaeelqkaiddaPkel 53 
                                        ++i k+++ +++++k+i+ aPke 
  gi|330509140|ref|YP_004385568.1| 236 FKAIGKYEESIKAYNKVIEIAPKEA 260
                                       57899******************96 PP

>> DELLA  Transcriptional regulator DELLA protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.19        75      40      65 ..      68      95 ..      55     100 .. 0.74
   2 ?    5.9   0.0     0.029        11      27      56 ..     166     193 ..     156     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.19
                             DELLA 40 qlasdtvhynPSdlsswves..mLseln 65
                                      +  + ++  nP d++ w+    +Ls l+
  gi|330509140|ref|YP_004385568.1| 68 KAYDKAIELNPKDIMVWLSKgiILSGLE 95
                                      556778999********97533566665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.029
                             DELLA  27 emvlgaaqedglsqlasdtvhynPSdlssw 56 
                                       e+++ a   +++ ++ ++t+  nP d+ +w
  gi|330509140|ref|YP_004385568.1| 166 EEAIKAF--NKALEIYDNTIQENPEDIIAW 193
                                       5555222..33678999************* PP

>> NAPRTase  Nicotinate phosphoribosyltransferase (NAPRTase) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.3    0.0031       1.2     124     167 ..     169     212 ..      38     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHHHHCTCTTTCCCSEEEEESS-SHHHHHHHHHHHHH CS
                          NAPRTase 124 vevieklaahygstlnskgytkrlifsDgldvekiieilealkk 167
                                       +++ +k++++y +t++ ++  ++  ++ g+++ek+ ++ ea+k+
  gi|330509140|ref|YP_004385568.1| 169 IKAFNKALEIYDNTIQENPEDIIAWQGKGITLEKMGRYEEAIKS 212
                                       458899*******************************9999886 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 ?    1.3   0.3      0.59   2.4e+02     131     156 ..      53      78 ..      38     149 .. 0.79
   2 ?    8.3   0.5    0.0045       1.8     118     195 ..     149     220 ..     122     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.59
                           DUF2225 131 kedeekeklflkkAlelykeayekes 156
                                       k++e ++k  +++A++ y++a+e + 
  gi|330509140|ref|YP_004385568.1|  53 KGQELERKGSYEEAVKAYDKAIELNP 78 
                                       44455666667777777777777654 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0045
                           DUF2225 118 AklalrlAWlyrdkedeekeklflkkAlelykeayekesfpvegideatvlYLiaeLerrlgnkeealrwlskvigs 194
                                       A  ++  + + ++++ +e+  +  +kAle+y+++++++ +++   + + +++       ++g++eea++ + kvi++
  gi|330509140|ref|YP_004385568.1| 149 ARAWVEKGDILNKTGRHEEAIKAFNKALEIYDNTIQENPEDIIAWQGKGITL------EKMGRYEEAIKSYDKVIEM 219
                                       4455555555555556677777777777777777777666666666665543......6889999999999999887 PP

                           DUF2225 195 k 195
                                       +
  gi|330509140|ref|YP_004385568.1| 220 S 220
                                       6 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 ?    0.8   0.7      0.94   3.7e+02      29      47 ..      50      68 ..      50      70 .. 0.74
   2 ?    2.7   0.1      0.23        92       2      15 ..      63      76 ..      62      79 .. 0.92
   3 ?   -0.7   0.0       2.8   1.1e+03       2      15 ..      97     110 ..      87     116 .. 0.77
   4 ?   -0.9   0.1       3.2   1.3e+03       1      12 [.     130     141 ..     130     144 .. 0.82
   5 ?    1.6   0.0      0.53   2.1e+02       2      15 ..     165     178 ..     154     186 .. 0.72
   6 ?    3.6   0.0      0.13        51       1      16 [.     205     220 ..     196     222 .. 0.89
   7 ?    4.2   0.1      0.08        32       1      19 [.     241     259 ..     241     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.94
                                      HHHHHHHHHHTT--HHHHH CS
                          HTH_Bact 29 yYqkgecleklgfseeeIk 47
                                      +Y kg+ le+ g  ee +k
  gi|330509140|ref|YP_004385568.1| 50 WYKKGQELERKGSYEEAVK 68
                                      69*******9776665554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.23
                                      HHHHHHHHHHHHHH CS
                          HTH_Bact  2 YeeaLeqvnkAiei 15
                                      Yeea +  +kAie+
  gi|330509140|ref|YP_004385568.1| 63 YEEAVKAYDKAIEL 76
                                      ************96 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                        +e++e  + Aiei
  gi|330509140|ref|YP_004385568.1|  97 HNESIEAYETAIEI 110
                                       46777777777776 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 3.2
                                       -HHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkA 12 
                                       rY+e+L+  n+ 
  gi|330509140|ref|YP_004385568.1| 130 RYNESLNAYNRV 141
                                       7*****999886 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                        eea++  nkA+ei
  gi|330509140|ref|YP_004385568.1| 165 HEEAIKAFNKALEI 178
                                       46777777777765 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.13
                                       -HHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiS 16 
                                       rYeea++  +k ie+S
  gi|330509140|ref|YP_004385568.1| 205 RYEEAIKSYDKVIEMS 220
                                       7999999999999988 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.08
                                       -HHHHHHHHHHHHHHHHHT CS
                          HTH_Bact   1 rYeeaLeqvnkAieiSiri 19 
                                       +Yee+++  nk iei  + 
  gi|330509140|ref|YP_004385568.1| 241 KYEESIKAYNKVIEIAPKE 259
                                       6*************97665 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.044        18      28      50 ..      63      85 ..      49      89 .. 0.89
   2 ?    1.9   0.1      0.63   2.5e+02      26      49 ..      95     118 ..      90     125 .. 0.87
   3 ?    0.2   0.0       2.1   8.5e+02      28      52 ..     242     266 ..     205     282 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.044
                           DUF1510 28 wnEmekavskatglsednmivww 50
                                      ++E +ka  ka++l+ ++++vw 
  gi|330509140|ref|YP_004385568.1| 63 YEEAVKAYDKAIELNPKDIMVWL 85
                                      89******************996 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.63
                           DUF1510  26 vDwnEmekavskatglsednmivw 49 
                                       +  nE  +a ++a++++ ++++ w
  gi|330509140|ref|YP_004385568.1|  95 EQHNESIEAYETAIEIDPKSIQAW 118
                                       5679**************999998 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 2.1
                           DUF1510  28 wnEmekavskatglsednmivwwlg 52 
                                       ++E  ka +k++++  ++  + w g
  gi|330509140|ref|YP_004385568.1| 242 YEESIKAYNKVIEIAPKEASYAWEG 266
                                       6777777777777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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):              45  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.53
# Mc/sec: 1671.93
//
Query:       gi|330509141|ref|YP_004385569.1|  [L=300]
Description: hypothetical protein MCON_3537 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-39  132.4   0.0    1.5e-38  131.7   0.0    1.3  1  PatG_D    PatG Domain
    7.9e-31  106.4   0.3    1.4e-30  105.6   0.3    1.4  1  PatG_C    PatG C-terminal


Domain annotation for each model (and alignments):
>> PatG_D  PatG Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.7   0.0   1.6e-42   1.5e-38       1     108 [.      50     235 ..      50     239 .. 0.98

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 1.6e-42
                            PatG_D   1 lvYviGrieadFpnearekefvqalaraktanpedqqalakvLsnrenrylaralsWiLtiegipiYvllPn..... 72 
                                       +vYv+G+iea+Fpn+++eke+vq+l+r+k+an+e+qqa+++vLs++enrylar+lsWiLt+eg+piY+llP+     
  gi|330509141|ref|YP_004385569.1|  50 YVYVLGQIEARFPNRSIEKEYVQILERSKSANFEHQQAFYSVLSQPENRYLARKLSWILTKEGVPIYILLPTgpedl 126
                                       8**************************************************************************** PP

                            PatG_D  73 ..................................................................kpfalelfarl 83 
                                                                                                         k++alelf+r+
  gi|330509141|ref|YP_004385569.1| 127 dilldairpsacsldrqvvvgrkgpvappemcgqevpmvlvdhlysleynnfmksihpelvadekfKAAALELFRRM 203
                                       ***************************************************************************** PP

                            PatG_D  84 iealdnqedteesra.......diervsiagv 108
                                       ++++dn+++te++ra       +++++s+a++
  gi|330509141|ref|YP_004385569.1| 204 MQIADNTGSTEKHRAlnylavrYLAIYSTAAE 235
                                       ***************99999998999998876 PP

>> PatG_C  PatG C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.6   0.3   1.6e-34   1.4e-30       4     115 .]     189     297 ..     187     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 1.6e-34
                            PatG_C   4 eeeftkairevLdrvlqelrNlGatdedRAlNylatrapdiyretaelileslsLdsveveksplsradsdcvdVkl 80 
                                       +e+f++a+ e++ r++q ++N+G t+++RAlNyla+r+  iy+++ae  ++s+sL+s e+ +s+ls   +++ +V++
  gi|330509141|ref|YP_004385569.1| 189 DEKFKAAALELFRRMMQIADNTGSTEKHRALNYLAVRYLAIYSTAAEKLENSFSLTSAEAIPSRLSDS-RKIISVVF 264
                                       68999**************************************************************9.******** PP

                            PatG_C  81 tftnkenssraekkyrvtvDVseelPflvtkvqsy 115
                                       +ftn+  +++  +ky+v+vDV+ee+Pf+vtk+ +y
  gi|330509141|ref|YP_004385569.1| 265 SFTNR--ETGIMEKYFVRVDVTEEFPFIVTKMAPY 297
                                       *****..9************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2027.24
//
Query:       gi|330509142|ref|YP_004385570.1|  [L=45]
Description: hypothetical protein MCON_3538 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       189  (0.0105416); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 341.32
//
Query:       gi|330509143|ref|YP_004385571.1|  [L=176]
Description: hypothetical protein MCON_3541 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.032   13.9   1.4      0.078   12.6   1.4    1.6  1  RPA_interact_N  Replication protein A interacting N-terminal


Domain annotation for each model (and alignments):
>> RPA_interact_N  Replication protein A interacting N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.4   4.4e-06     0.078      24      38 ..      30      44 ..      28      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-06
                    RPA_interact_N 24 RlresRsqLLwklRq 38
                                      +lre+R+qLL klR+
  gi|330509143|ref|YP_004385571.1| 30 NLREERQQLLAKLRD 44
                                      79************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1189.80
//
Query:       gi|330509144|ref|YP_004385572.1|  [L=502]
Description: hypothetical protein MCON_3543 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-11   44.5   2.4    1.6e-10   41.6   0.1    2.4  2  Radical_SAM  Radical SAM superfamily
    7.9e-09   35.9   0.0    7.9e-09   35.9   0.0    2.2  2  Fer4_12      4Fe-4S single cluster domain
    0.00035   20.7   0.0    0.00035   20.7   0.0    2.8  3  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 !   41.6   0.1   2.7e-14   1.6e-10       3     150 ..     106     266 ..     104     272 .. 0.82
   2 ?    2.3   0.3     0.034     2e+02       9      24 ..     432     446 ..     426     483 .. 0.72

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.7e-14
                                       EESEESS--TTTSCCTT.........HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHH CS
                                       xxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.........vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvelle 68 
                                       +t+ Cn+rC++C+++           +++  + + + +++ + ++ e+k +++  +  + + ggepll+  ++++  
  gi|330509144|ref|YP_004385572.1| 106 TTEDCNFRCRYCSFSDFyeynrgysdKYMDFDTAKKAIDYFISLLNEGKkYNPIrKPALGFYGGEPLLNFGLIKKCI 182
                                       6889***********99**9998888777777777777777777778875455446677777*******77777777 PP

                                       HHHHTC..CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH.HHHHHHT.CTSHHHHHHHHHHHHHHTT CS
                                       xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  69 rlakla..vpgiritvetngtlpdeeklerllelgvdrvslgleaadde.kvlklmn.rghtfeevlealeklreag 141
                                       ++++    + +i  t++tng ++d++ +  l e     + ++l+ + de + l++ + ++++f +v++++ ++ ++g
  gi|330509144|ref|YP_004385572.1| 183 EYIESIynDYEIIYTITTNGSMLDKKRANWLMEHD-FIIFVSLDGPEDEhDRLRIYEnGKGSFRDVIKNVTRIIRKG 258
                                       7777667779***********************88.*************856666667******************* PP

                                       SETEEEEEE CS
                                       xxxxxxxxx RF
                       Radical_SAM 142 ikrvvdriv 150
                                        k+ ++ ++
  gi|330509144|ref|YP_004385572.1| 259 YKE-IYCMP 266
                                       995.44444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.034
                                       S--TTTSCCTTHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM   9 lrCsfCarpetvrreg 24 
                                       ++C++C+++++  ++g
  gi|330509144|ref|YP_004385572.1| 432 RKCTYCYQNFM-TDNG 446
                                       68******996.3333 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 !   35.9   0.0   1.3e-12   7.9e-09      12     125 ..     107     231 ..      99     243 .. 0.76
   2 ?   -1.5   0.9      0.47   2.8e+03      17      34 ..     432     449 ..     425     475 .. 0.68

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.3e-12
                           Fer4_12  12 vsgCnlsCkgCfnketwsfk..sgkef...t..kelleeiiedlkkesi......egltllGGEPllpenaeallel 75 
                                       +++Cn++C++C   +  + +  +++++   +  k++++  i  l++ ++      + l + GGEPll  n   + + 
  gi|330509144|ref|YP_004385572.1| 107 TEDCNFRCRYCSFSDFYEYNrgYSDKYmdfDtaKKAIDYFISLLNEGKKynpirkPALGFYGGEPLL--NFGLIKKC 181
                                       689********88887766544333333332348888888888887444456777************..**999999 PP

                           Fer4_12  76 vkevkeekpekdiwlytgytleelskkekeellkeidvlvdGkfe.esled 125
                                       ++++++ + +   ++yt +t+  +++k++ + l e+d+++ + ++  + e+
  gi|330509144|ref|YP_004385572.1| 182 IEYIESIYND-YEIIYTITTNGSMLDKKRANWLMEHDFIIFVSLDgPEDEH 231
                                       9999998875.7899**********999*********98888877333333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.47
                           Fer4_12  17 lsCkgCfnketwsfksgk 34 
                                       ++C +C+++ + +   + 
  gi|330509144|ref|YP_004385572.1| 432 RKCTYCYQNFMTDNGFSP 449
                                       59*****88766655444 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 ?   -0.8   0.1      0.27   1.6e+03      10      45 ..      54      89 ..      51      97 .. 0.59
   2 !   20.7   0.0   5.8e-08   0.00035       5      96 ..     107     208 ..     104     226 .. 0.61
   3 ?   -2.1   1.4      0.68   4.1e+03       8      19 ..     428     441 ..     424     471 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.27
                           Fer4_14 10 lsCk...gCdnketwkselgkpqteelleqilkdlkkse 45
                                      ++C    +C+n  ++ ++ + p+ + ++ +++   +kse
  gi|330509144|ref|YP_004385572.1| 54 FNCDdisFCYNWLKKWEKIHVPDYKSQIPKEI---DKSE 89
                                      66776668998665555555555555555555...3333 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 5.8e-08
                           Fer4_14   5 lsgCnlsCkgCd..........nketwkselgkpqteelleqilk.dlkkseikiqglvltGGePLhyenkkellkl 70 
                                       +  Cn+ C+ C            ++++++  + +++ +   + l+  +k++ i++  l + GGePL   n   + k 
  gi|330509144|ref|YP_004385572.1| 107 TEDCNFRCRYCSfsdfyeynrgYSDKYMDFDTAKKAIDYFISLLNeGKKYNPIRKPALGFYGGEPL--LNFGLIKKC 181
                                       568********9666666544322222222222222222333444467777888888*********..666666666 PP

                           Fer4_14  71 vkrlkeeypekki..wletngtleiele 96 
                                       ++++   y++++i  ++ tng++  + +
  gi|330509144|ref|YP_004385572.1| 182 IEYIESIYNDYEIiyTITTNGSML-DKK 208
                                       666655555544423889999875.444 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.68
                           Fer4_14   8 Cnl..sCkgCdnke 19 
                                       C++  +C+ C+++ 
  gi|330509144|ref|YP_004385572.1| 428 CKVsrKCTYCYQNF 441
                                       65522699999543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3322.18
//
Query:       gi|330509145|ref|YP_004385573.1|  [L=383]
Description: hypothetical protein MCON_3544 [Methanosaeta concilii GP6]
Scores for complete sequence (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   25.6   0.0    1.9e-05   25.1   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    0.00063   20.2   3.1     0.0025   18.3   3.1    2.0  1  SPASM        Iron-sulfur cluster-binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   2.1e-09   1.9e-05       5      97 ..     105     203 ..     101     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.1e-09
                                       SEESS--TTTSCCTT.........HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   5 rgCnlrCsfCarpet.........vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlak 72 
                                       + Cn++C+fC  +            ++ + g  ls+e+ +  ++ l+ + +++ ++++gg+ +l +d + +++ +a 
  gi|330509145|ref|YP_004385573.1| 105 NSCNRDCWFCGYHGIkrslgcmgcNKWKENGSALSIEKWKIVIDGLR-DLRCRDIFITGGDLTLAWDNTLEILDYAS 180
                                       78***********99*******************************6.888********************999999 PP

                                       TCCCTEEEEEEECSSCHGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  73 lavpgiritvetngtlpdeeklerl 97 
                                       ++ ++i + +    +    ekl+ l
  gi|330509145|ref|YP_004385573.1| 181 RKFSNIYTILHQQSIS--SEKLDNL 203
                                       9766666666555555..3555554 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.1   2.8e-07    0.0025       5      67 ..     289     347 ..     287     356 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.8e-07
                             SPASM   5 srslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse..eyqefrkskkfplielCrnC 67 
                                        ++l+I ++G+V+pC        ++ k+Gn+r+ ++  + ++e   + ef    + + i+ C+ C
  gi|330509145|ref|YP_004385573.1| 289 GHTLAICHNGNVTPCP-----LMRRHKFGNVRNSEIYTVFEKEwrSIYEFW-GLNLDKIDRCTGC 347
                                       67899**********3.....34569*******999999877743334455.3344445668887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2628.51
//
Query:       gi|330509146|ref|YP_004385574.1|  [L=563]
Description: ABC transporter ATP-binding protein/permease [Methanosaeta concilii GP6]
Scores for complete 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   99.4   0.0    4.5e-28   98.5   0.0    1.5  1  ABC_tran      ABC transporter
    2.2e-27   96.4  13.5    3.1e-27   95.9  13.5    1.2  1  ABC_membrane  ABC transporter transmembrane region
    2.2e-11   43.6   3.2    3.5e-07   29.9   0.4    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    6.4e-11   42.6   0.1    2.3e-05   24.3   0.0    2.5  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.7e-06   28.0   0.0    4.6e-06   26.6   0.0    1.7  2  AAA_15        AAA ATPase domain
    1.2e-05   25.9   0.9      3e-05   24.6   0.0    1.9  2  AAA_23        AAA domain
    0.00043   20.7   1.5     0.0052   17.2   0.4    2.6  2  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.016   13.9   1.0       0.37    9.4   0.0    2.1  2  AAA_13        AAA domain
      0.023   14.6   0.7        6.9    6.5   0.4    2.3  2  NTPase_1      NTPase
      0.027   14.2   0.0      0.059   13.1   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.042   14.1   0.0       0.25   11.6   0.0    2.1  2  AAA_22        AAA domain
      0.061   13.2   0.2       0.22   11.4   0.0    2.0  2  RsgA_GTPase   RsgA GTPase
      0.088   11.9   0.1        2.3    7.3   0.0    2.3  2  MCM           MCM P-loop domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   0.0   3.3e-31   4.5e-28       4     136 ..     352     496 ..     349     497 .. 0.86

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 3.3e-31
                                       EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                          ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                        + ++k+g    +vG+nG+GKSt+lkll+  +  ++G+i++dg+d+ e ++e lrk++++++ +p lf+++ ++en 
  gi|330509146|ref|YP_004385574.1| 352 FNATFKKGLN-YVVGDNGTGKSTILKLLCSFYPLEQGKITIDGQDIFEVRREDLRKNVSMIFSDPYLFDGT-IYENi 426
                                       5666666655.479*********************************************************.9**** PP

                                       ...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                      ++ +++++++++l + +  +t v++++ +LS G+kq++alara+lk+++++llDE t
  gi|330509146|ref|YP_004385574.1| 427 hignllaskeeiikaAKLVRVHEFITSLPQGY--ETQVGEGGLKLSSGEKQKIALARAVLKDSPIVLLDEVT 496
                                       ******55555555555555666666666665..99999999****************************98 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9  13.5   2.2e-30   3.1e-27       2     273 ..      21     290 ..      20     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 2.2e-30
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   2 iliillailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrr 78 
                                        ++++l +++ +  ++ pl+ ++++d+++    +e     +++l  ++ +++++++++l+ y   ++   l +++ +
  gi|330509146|ref|YP_004385574.1|  21 AFLLVLEFIGMLFTFVSPLLAKSLIDDVFIGRRTEL--FGYILLGTAATYIISAVSTYLSGYGKGKLDLVLFNDVTK 95 
                                       56789999**********************999999..*************************************** PP

                                       HHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHH CS
                      ABC_membrane  79 klfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailplii 155
                                       ++f+++ ++ ++  ++++vG+llsr+  ++++   ++++ + +f+ +++ +++ + +m+++ wkltl+++  ++ ++
  gi|330509146|ref|YP_004385574.1|  96 EAFDAVQSAYIKKTQEMKVGDLLSRIVANTRSAIIIFTQIVPQFVVNVARIITPFTIMLFYDWKLTLIVTTPALFFL 172
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 156 lvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitq 232
                                       l + +++k+l++ +k   ++++ ++s++ Esl+ i  +k fg e+  ++kf+++ ++++  +i +++ n+  ++++ 
  gi|330509146|ref|YP_004385574.1| 173 LPMLFFGKRLEQTQKISLEKTGSIYSFLKESLTMIPLIKVFGLERWSRDKFNEQMKDYYDVSIDYTKNNSMGSSVNS 249
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 233 llgllsyalalwfGttlvisgelsvgdlvvflslfailfga 273
                                       l+  + +al ++fG+ +vi+g l++g+++ f++  a++fg+
  gi|330509146|ref|YP_004385574.1| 250 LIYGVPIALLILFGGPMVIQGSLTIGTFTLFMTNVALVFGP 290
                                       **************************************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 !   14.4   0.1   1.4e-05      0.02      17      42 ..     351     376 ..     342     389 .. 0.87
   2 !   29.9   0.4   2.5e-10   3.5e-07     111     213 ..     416     541 ..     380     548 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                                       EEEEETTSSEEEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  17 tvilpfsksftaivGpNGSGKsnlld 42 
                                       +    f+k+++ +vG NG GKs +l 
  gi|330509146|ref|YP_004385574.1| 351 RFNATFKKGLNYVVGDNGTGKSTILK 376
                                       566789*****************986 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 2.5e-10
                                       EEETTEEE-HHHHHHHHHCTT-STT...........................CS-HHHHHHHHHHHHHHHHCCS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx...........................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 111 ykingkevtkkevsellesagiske...........................lLSgGektLvalaLlfAiqkvkpap 160
                                       y ++g+  ++  + +ll+s++  ++                            LS Gek+ +ala        k +p
  gi|330509146|ref|YP_004385574.1| 416 YLFDGTIYENIHIGNLLASKEEIIKaaklvrvhefitslpqgyetqvgegglKLSSGEKQKIALA----RAVLKDSP 488
                                       55566666666666666544322224677888888888888888888888889******977765....456899** PP

                                       EEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 161 lyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtk 213
                                       ++llDe+    D+  +k + e++k+ +++  +i+i+++   +e+ ++++ + +
  gi|330509146|ref|YP_004385574.1| 489 IVLLDEVTKSVDADSRKSINEVIKNFKNKKTIIIITHNPSEIEQDSNIIDLGQ 541
                                       ****************************************9999998887766 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   1.2e-05     0.017       2      19 ..     361     378 ..     360     423 .. 0.78
   2 !   24.3   0.0   1.7e-08   2.3e-05     237     302 ..     469     530 ..     467     531 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                            AAA_21   2 nvliGpNgsGKSnLLdal 19 
                                       n ++G+Ng+GKS++L++l
  gi|330509146|ref|YP_004385574.1| 361 NYVVGDNGTGKSTILKLL 378
                                       779*************99 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 1.7e-08
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                                       lS+G k+ +al+ a+l +    +++l+DE+  + +    +++ e++k+ ++ +  +i+ TH+p+ +
  gi|330509146|ref|YP_004385574.1| 469 LSSGEKQKIALARAVLKDS---PIVLLDEVTKSVDADSRKSINEVIKNFKN-KKTIIIITHNPSEI 530
                                       8*******99999999988...***************************99.9**********876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2       5.5   7.6e+03     193     224 ..     206     237 ..     182     246 .. 0.54
   2 !   26.6   0.0   3.4e-09   4.6e-06      15     168 ..     350     543 ..     348     559 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.5
                            AAA_15 193 aiiklllisakRnvsdedsekkssllgklkek 224
                                        i++++++  +R++ d+++e+ +++++  ++ 
  gi|330509146|ref|YP_004385574.1| 206 MIPLIKVFGLERWSRDKFNEQMKDYYDVSIDY 237
                                       34455566666666666666666666555554 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 3.4e-09
                            AAA_15  15 kdveidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef........ 83 
                                       + +   +++ l+ ++G N++GKS+il++l  F   +    + +i+i+ +d+ + + ++  k++   +          
  gi|330509146|ref|YP_004385574.1| 350 QRFNATFKKGLNYVVGDNGTGKSTILKLLCSFYPLE----QGKITIDGQDIFEVRREDLRKNVSMIFSDpylfdgti 422
                                       6677889999**********************9988....88999********999999999999999899999999 PP

                            AAA_15  84 ..............................................................aekekakeyektlks 98 
                                                                                                     +              
  gi|330509146|ref|YP_004385574.1| 423 yenihignllaskeeiikaaklvrvhefitslpqgyetqvgegglklssgekqkialaravlK-------------- 485
                                       999999999999999999999999999999999988888877766544433333333333330.............. PP

                            AAA_15  99 kekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidked 168
                                          +++ +ll++  ++ +          ++ + ++e i+++k+k++ ++ + + ++ e++++ +++ +e+
  gi|330509146|ref|YP_004385574.1| 486 ---DSPIVLLDEVTKSVDA---------DSRKSINEVIKNFKNKKTIIIITHNPSEIEQDSNIIDLGQES 543
                                       ...3333333333332222.........233334444555555555555555555555555555555554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.2e-08     3e-05      11      40 ..     350     379 ..     342     382 .. 0.88
   2 ?   -2.2   0.1       3.7   5.1e+03     119     132 ..     505     518 ..     464     548 .. 0.54

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.2e-08
                            AAA_23  11 rdqeidFskgltlItGpNGaGKTTildAik 40 
                                       ++++  F+kgl+ ++G+NG+GK+Til  ++
  gi|330509146|ref|YP_004385574.1| 350 QRFNATFKKGLNYVVGDNGTGKSTILKLLC 379
                                       777889********************9887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.7
                            AAA_23 119 qfisellgskkiil 132
                                       + i+e ++++k+  
  gi|330509146|ref|YP_004385574.1| 505 KSINEVIKNFKNKK 518
                                       22222222222211 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.9   8.1e+03      38      57 ..     105     125 ..      63     135 .. 0.47
   2 !   17.2   0.4   3.8e-06    0.0052       2     117 ..     362     532 ..     361     538 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.9
                                       STTH.HHHHHHHHHHHHHHTS CS
                               AAA  38 yvge.sekkirelfkeakeka 57 
                                       y+++ +e+k+ +l++++ ++ 
  gi|330509146|ref|YP_004385574.1| 105 YIKKtQEMKVGDLLSRIVANT 125
                                       333203444555555543333 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.8e-06
                                       EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS............................... CS
                               AAA   2 llyGppGtGKTllakavakel..........gvefleisgsellsk............................... 37 
                                       +++G  GtGK+++ k +++            g++++e+   +l+++                               
  gi|330509146|ref|YP_004385574.1| 362 YVVGDNGTGKSTILKLLCSFYpleqgkitidGQDIFEVRREDLRKNvsmifsdpylfdgtiyenihignllaskeei 438
                                       689****************96555554445556788888888884489999999*********************** PP

                                       .............................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHH CS
                               AAA  38 .............................yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeerv 85 
                                                                        s +k +  +++a  k +  i+++DE+ + + ++           
  gi|330509146|ref|YP_004385574.1| 439 ikaaklvrvhefitslpqgyetqvgegglK-LSSGEKQKIALARAVLK-DSPIVLLDEVTKSVDAD----------S 503
                                       ********************9977777632.33333333333343333.259*******9999988..........4 PP

                                       HHHHHHHHHHTTTSSSTEEEEEEESSGGGSTH CS
                               AAA  86 vnqLlteldgvkkkeskvivigatnrpdkldp 117
                                        + + ++++++k+k    ++i++t++p+++++
  gi|330509146|ref|YP_004385574.1| 504 RKSINEVIKNFKNK---KTIIIITHNPSEIEQ 532
                                       55666677777773...358888888888875 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00027      0.37      17      39 ..     359     381 ..     345     427 .. 0.78
   2 ?    3.0   0.2     0.022        30     499     572 ..     468     528 ..     450     553 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00027
                            AAA_13  17 riNliYGwNGaGKTtLSrllrsl 39 
                                         N++ G NG+GK+t+ +ll s+
  gi|330509146|ref|YP_004385574.1| 359 GLNYVVGDNGTGKSTILKLLCSF 381
                                       47**************9999887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.022
                            AAA_13 499 tLSeGEktaIaflYFlkslkeddseigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnle 572
                                       +LS GEk  Ia+           + ++   iv +D    S D++s  ++   ik+     k+ k ++i THn +
  gi|330509146|ref|YP_004385574.1| 468 KLSSGEKQKIALA---------RAVLKDSPIVLLDEVTKSVDADSRKSINEVIKNF----KNKKTIIIITHNPS 528
                                       5666666666654.........2223356789999999999****99999999998....69999*******65 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    0.0071       9.8       4      44 ..     363     405 ..     361     412 .. 0.82
   2 ?    6.5   0.4     0.005       6.9      66     154 ..     457     538 ..     436     551 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0071
                                       EE--TTSSHHHHHHHHHHH..H...GGGEEEEEEEEE------ CS
                          NTPase_1   4 iTGppGvGKtTlvkkvlel..lkssgvkvgGfyteevreggrr 44 
                                       + G  G+GK+T++k +++   l++  ++++G    evr+++ r
  gi|330509146|ref|YP_004385574.1| 363 VVGDNGTGKSTILKLLCSFypLEQGKITIDGQDIFEVRREDLR 405
                                       6799**********99985338888899999999999987766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.005
                                       --SSEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE---ST.TGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHH CS
                          NTPase_1  66 kreprvgkyvvdvesfeelalealrkalseadviviDEiGk.mElkskkfkeaveevLksekpvlavihrrkdlalv 141
                                         e +vg+  +++ s e+  ++  r  l+++ ++++DE+ k     s+k +++v + +k++k ++++ h+++     
  gi|330509146|ref|YP_004385574.1| 457 GYETQVGEGGLKLSSGEKQKIALARAVLKDSPIVLLDEVTKsVDADSRKSINEVIKNFKNKKTIIIITHNPS----- 528
                                       56778999999999999999999988889999*******975899**************9999999999995..... PP

                                       HHHHT-TT-EEEE CS
                          NTPase_1 142 eeirerkdvkvfe 154
                                        ei++  d ++++
  gi|330509146|ref|YP_004385574.1| 529 -EIEQ--DSNIID 538
                                       .3443..244444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.3e-05     0.059      19      39 ..     356     375 ..     340     380 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-05
                            AAA_29  19 idlkgatlltGpsGsGKSTll 39 
                                       ++ kg   ++G++G+GKST+l
  gi|330509146|ref|YP_004385574.1| 356 FK-KGLNYVVGDNGTGKSTIL 375
                                       44.667899**********98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.25       4      31 ..     357     384 ..     354     415 .. 0.82
   2 ?   -0.7   0.0       1.2   1.6e+03      91     127 ..     483     523 ..     447     532 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqlde 31 
                                       ++g+ +v+G  GtGK+t l+ l + ++ 
  gi|330509146|ref|YP_004385574.1| 357 KKGLNYVVGDNGTGKSTILKLLCSFYPL 384
                                       678889**************99888765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                            AAA_22  91 v...ielliiDEaqh.lr..seealeeLrsllnlsrkgvqliL 127
                                       v    +++++DE+ + ++  s + ++e+ + ++   k++ +i+
  gi|330509146|ref|YP_004385574.1| 483 VlkdSPIVLLDEVTKsVDadSRKSINEVIKNFK--NKKTIIII 523
                                       334456889999988777776888888833333..44444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.3   3.1e+03       9      33 ..     118     142 ..     105     148 .. 0.76
   2 ?   11.4   0.0   0.00016      0.22      83     130 ..     342     389 ..     318     395 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.3
                                       TTTTEES--EEEEEEESTTTT--HH CS
                       RsgA_GTPase   9 vrpkvaNvdqllivvslkepelsln 33 
                                       + + vaN   ++i+++   p++ +n
  gi|330509146|ref|YP_004385574.1| 118 LSRIVANTRSAIIIFTQIVPQFVVN 142
                                       4455999999999999888887655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00016
                                       -TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  83 saktkegleelkellkdktsvlvGqSGvGKStLinallpelelktgev 130
                                       s +++  l++ ++ +k+ +  +vG  G GKSt+++ l +   l+ g++
  gi|330509146|ref|YP_004385574.1| 342 SYDNRPILQRFNATFKKGLNYVVGDNGTGKSTILKLLCSFYPLEQGKI 389
                                       55566678889999999*******************998766666655 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0017       2.3      62      83 ..     363     384 ..     357     394 .. 0.89
   2 ?    1.9   0.0     0.071        98     118     145 ..     483     511 ..     459     522 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0017
                                       EEESSTSTHHHHHHHHHHHSSS CS
                               MCM  62 lvgdpgtaKsqlLkyveklapr 83 
                                       +vgd gt+Ks++Lk ++++ p 
  gi|330509146|ref|YP_004385574.1| 363 VVGDNGTGKSTILKLLCSFYPL 384
                                       79**************998875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.071
                                       HHTTTSEEEEESGGGSTC.HHHHHHHHHH CS
                               MCM 118 vladkGvcciDefdkmke.edrsalhEam 145
                                       vl d+ ++++De+ k  + + r+++ E++
  gi|330509146|ref|YP_004385574.1| 483 VLKDSPIVLLDEVTKSVDaDSRKSINEVI 511
                                       8999**********976615578899987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); 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: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 3701.67
//
Query:       gi|330509147|ref|YP_004385575.1|  [L=1273]
Description: peptidase families S8 and S53 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-30  103.8   0.3    2.3e-29  102.6   0.3    1.6  1  Peptidase_S8  Subtilase family
  ------ inclusion threshold ------
      0.038   14.3   0.1       0.13   12.6   0.1    1.9  1  Invasin_D3    Invasin, domain 3
       0.17   12.3   0.7        1.1    9.7   0.2    2.6  2  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 !  102.6   0.3   3.9e-33   2.3e-29       1     298 []      52     482 ..      52     482 .. 0.76

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 3.9e-33
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegag..................................... 40 
                                       gkgv vav+D+G+d   pdl  t   ++++   ++                                          
  gi|330509147|ref|YP_004385575.1|  52 GKGVNVAVIDSGIDFATPDLIGT---QAHIS-NKSS---Lyygwpividldsliqyqqdsnhlfirsryantsstdv 121
                                       89*****************9944...33332.2222...1446999999*******9**999999977666666666 PP

                                       .................................................GGEETT-SS-TT-SC-S........... CS
                                       .................................................xxxxxxxxxxxxxxxxx........... RF
                      Peptidase_S8  41 .................................................fngadsettstnwardd........... 57 
                                                                                        +               d           
  gi|330509147|ref|YP_004385575.1| 122 rgyqttgtsksdiyhigdhpdmhltqfhgqpvkvllvdekspniydtvyV---------------Dlnnnhdfrddk 183
                                       66666666666666666666666666666666666555555555554440...............045555555555 PP

                                       ..........................................................SS....HHHHHHHHHH-B. CS
                                       ..........................................................xxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  58 ..........................................................ngnsieHGthvAGiaaana 76 
                                                                                                 + ++  HGt + Gi+aa+ 
  gi|330509147|ref|YP_004385575.1| 184 pcrkgdeisywdrdndgypdesggmiyfiadgktplplsrmlygedtkipkngelvafHYDDGSHGTMCTGIIAAQ- 259
                                       5666666666666778888889999999999999999999998888888886665555444445************. PP

                                       .SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                      Peptidase_S8  77 peegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsiealainravn. 152
                                          ++++g+ap+aki+ +++  +++      + l        +d++d+i+ s g  + l + g +    ++++++  
  gi|330509147|ref|YP_004385575.1| 260 --GKNIKGIAPDAKIIPIQNSRENDMLLYFLASLGYDGVPNTRDEADIISKSGG-FSYLFNKGADEGSTFLEYLITn 333
                                       ..**************9999987776664333333333344458999*******.5555555555555544444330 PP

                                       .CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES........TTSSB-TT--B-TT.......-EEEE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 153 .kkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayt........tegkiapfSsrGpssdgklkpdivap 220
                                        +  + +++++GN+g      +   + ++ps s+ vi vga+           +++  fSsrGp++ g++kp ++a 
  gi|330509147|ref|YP_004385575.1| 334 iSPFTTMIFANGNDG------SGYGTSQSPS-SEHVINVGAIYdlwwnnssYSEDVVCFSSRGPNALGQVKPNVLAT 403
                                       035899*********......8889999999.678*******99******9778899******************** PP

                                       -S-...CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT.....--HHHHHHHHHCCS-EE..... CS
                                       xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 221 Ggn...ivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpk.....ltpetvraallntAqdlgkadn 289
                                       G     +++ w+++s  ++ +   ++  GTS A+P++a+++Al+ +a+++      t e+ r++l+ +A+d+     
  gi|330509147|ref|YP_004385575.1| 404 GYLaprVLPLWDTHS--GKAAW-NNNCGGTSGATPHVAAVMALIYQAYKEkygefPTSEKARDILMSSATDI----D 473
                                       *99999*********..33333.479*********************99999*999*************998....4 PP

                                       .SSSSSSTT CS
                                       xxxxxxxxx RF
                      Peptidase_S8 290 iesfaqGaG 298
                                        e+f qG G
  gi|330509147|ref|YP_004385575.1| 474 EEVFVQGSG 482
                                       578888887 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.2e-05      0.13      23      79 ..    1083    1138 ..    1064    1151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                        Invasin_D3   23 tltvtlkDangnpvsglt...vtfsttsagtlsavtdngdGtytatLta.ttagtatitpt 79  
                                         +t++++D++gn v + t   v+f+   + t ++v d  +G+ +  Lta ++ag ++++++
  gi|330509147|ref|YP_004385575.1| 1083 EVTLKVQDKFGNLVENTTtagVEFN---DAT-KKV-DLVKGIGSINLTApNKAGRYKVKVQ 1138
                                        59***********998552234444...333.455.8888*********999***999887 PP

>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.51     3e+03      15      33 ..     762     777 ..     761     778 .. 0.87
   2 ?    9.7   0.2   0.00018       1.1       5      83 ..    1193    1262 ..    1189    1264 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.51
                                       EEEEEEE-CSSSSSTEEEE CS
                               fn3  15 sltvsWeppkdgggpitgY 33 
                                       ++ v+We p   + +i+ Y
  gi|330509147|ref|YP_004385575.1| 762 TIDVTWEDP---NTDIDVY 777
                                       5789*****...9999988 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00018
                                        EEEEEEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEETS CS
                               fn3    5 nlsvsevtstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavngg 79  
                                         +sv +  s +++++W+++      +++Y+v   ++g +  ++   v++++    +++ +  + Y++r+ avn +
  gi|330509147|ref|YP_004385575.1| 1193 SVSVLS-DSGNIRLTWQAS----EGVDHYNVYRLKDGAP--EKLAEVKSPE---YIKKGELWKSYTFRISAVNSE 1257
                                        455555.6779999***99....6899999966666555..5667777777...566668899************ PP

                                        E.EEE CS
                               fn3   80 g.egp 83  
                                        g e++
  gi|330509147|ref|YP_004385575.1| 1258 GnESE 1262
                                        86655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1273 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:                        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: 0.80u 0.28s 00:00:01.08 Elapsed: 00:00:00.44
# Mc/sec: 8621.86
//
Query:       gi|330509148|ref|YP_004385576.1|  [L=1249]
Description: peptidase families S8 and S53 [Methanosaeta concilii GP6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-32  111.6   1.8    7.9e-32  110.7   1.8    1.4  1  Peptidase_S8  Subtilase family
  ------ inclusion threshold ------
      0.023   15.0   1.4       0.04   14.3   0.4    1.9  2  fn3           Fibronectin type III domain
      0.033   14.5   3.1      0.038   14.3   0.3    2.6  3  DUF4959       Domain of unknown function (DUF4959)
       0.57    9.5   3.9        5.5    6.2   0.0    3.5  4  DUF4097       Putative adhesin


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 !  110.7   1.8   1.8e-35   7.9e-32       1     298 []      30     460 ..      30     468 .. 0.79

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 1.8e-35
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegag..................................... 40 
                                       g+gv+vav+D+Gvd   pdl  t    +  v+  +   +g                                     
  gi|330509148|ref|YP_004385576.1|  30 GEGVKVAVMDSGVDFATPDLIGT----QARVTNASSPYYGwplvididslahyiqgsenflvqsqyadttstnvsgy 102
                                       79*****************9944....222333333344499*******************9977777777777777 PP

                                       ..............................................GGEETT-SS-TT-SC-S.............. CS
                                       ..............................................xxxxxxxxxxxxxxxxx.............. RF
                      Peptidase_S8  41 ..............................................fngadsettstnwardd.............. 57 
                                                                                     +               d              
  gi|330509148|ref|YP_004385576.1| 103 qvtgtsksgiyhigahpdshlaqfygqpikvlledertpntydtvyV---------------Dlnnnhdfrddkpcr 164
                                       77777777777777777777777777777766666655555444441...............044444555556666 PP

                                       ................................................SS...........HHHHHHHHHH-B..SS CS
                                       ................................................xxxxxx.......xxxxxxxxxxxxxxxx RF
                      Peptidase_S8  58 ................................................ngnsie.......HGthvAGiaaanapee 79 
                                                                                       ng++i+       HGt +AGi+aa+    
  gi|330509148|ref|YP_004385576.1| 165 kgdeisywdrendgypdesggmiyfiadgkthlplseilygekakipkNGELIAfeyddsgHGTMCAGIIAAQ---G 238
                                       6666777777778888889999999999999999999999999999996655556666777************...9 PP

                                       SSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHH..HHHHHH.CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                      Peptidase_S8  80 gekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsieal..ainravnkk 154
                                        +++g+ap+aki  v++  +s+      t + +       d++dv+n s g  + l + g +   +  ++ +++ + 
  gi|330509148|ref|YP_004385576.1| 239 RNIKGIAPDAKIMPVRNSIESDMLLYLLTSIGSDGVPNTGDEADVVNRSGG-FSYLFNKGADEGSAflEYLTTIISP 314
                                       ******************9999999887999999999999***********.5555555555555556555556599 PP

                                       T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES........TTSSB-TT--B-TT.......-EEEE-S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 155 gvlvviSaGNngktgsslqagspvgtpstsknvitvgayt........tegkiapfSsrGpssdgklkpdivapGgn 223
                                        + +v+++GN+g      +   + ++ps s+ vi  ga+           g++a+fSsrGp++ g++kp ++a G  
  gi|330509148|ref|YP_004385576.1| 315 STTIVTANGNDG------SGYGTCSSPS-SEHVINAGAIYdlwwnnssYSGDLASFSSRGPNALGQIKPNVLAVGYL 384
                                       ************......8889999999.678******999******9999************************99 PP

                                       ...CCCCCCCCCHHHTTTHH.EEEE-SHHHCHHHHHHHHHHHHHHHTT.....--HHHHHHHHHCCS-EE......S CS
                                       ...xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 224 ...ivstwsrqsnnsaglss.yqsmsGTSmAsPnaagaaAlllsalpk.....ltpetvraallntAqdlgkadnie 291
                                          +++  ++++    g++   ++  GTS A+P++a+++Al+ +a+++      t e+ r++l+ +A+d+      e
  gi|330509148|ref|YP_004385576.1| 385 aprVLPLFETHN----GKTAwNDMGGGTSSATPHVASVVALIYQAYKDahgkfPTSEKARDILMSSATDI----DEE 453
                                       555455544444....3333368999*********************99***99*************998....335 PP

                                       SSSSSTT CS
                                       xxxxxxx RF
                      Peptidase_S8 292 sfaqGaG 298
                                        faqG G
  gi|330509148|ref|YP_004385576.1| 454 IFAQGSG 460
                                       6777766 PP

>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         4   1.8e+04      15      33 ..     740     755 ..     739     755 .. 0.76
   2 ?   14.3   0.4   8.9e-06      0.04       7      83 ..    1169    1238 ..    1164    1240 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4
                                       EEEEEEE-CSSSSSTEEEE CS
                               fn3  15 sltvsWeppkdgggpitgY 33 
                                       s+ v+We     + +i+ Y
  gi|330509148|ref|YP_004385576.1| 740 SIEVTWEDQ---DTDIDVY 755
                                       789999998...6777666 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.9e-06
                                        EEEEE.SSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEETSE CS
                               fn3    7 svsev.tstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavnggg 80  
                                        svs++ ts +++++W+++     + ++Y+v yr kg  + ++   v++++  +t++g +  + Y++rV avn +g
  gi|330509148|ref|YP_004385576.1| 1169 SVSSIlTSGNISLTWQAS----EDADHYNV-YRLKGVSS-EKLAEVKSPE--YTMKG-ELWKSYTFRVSAVNSEG 1234
                                        57778899**********....799*****.77777776.7777777777..99999.8899************8 PP

                                        .EEE CS
                               fn3   81 .egp 83  
                                         e++
  gi|330509148|ref|YP_004385576.1| 1235 nESE 1238
                                        6655 PP

>> DUF4959  Domain of unknown function (DUF4959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.74   3.3e+03      57      90 ..      80     115 ..      75     121 .. 0.72
   2 ?   -3.4   0.0       2.7   1.2e+04      36      57 ..     533     557 ..     532     565 .. 0.70
   3 ?   14.3   0.3   8.5e-06     0.038      13     106 .]    1158    1249 .]    1150    1249 .] 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.74
                           DUF4959  57 nGkerevkaSvykds..ltveGFgdtkeyevklyav 90 
                                       +G+e     S y+d+    v+G++ t++ +  +y +
  gi|330509148|ref|YP_004385576.1|  80 QGSENFLVQSQYADTtsTNVSGYQVTGTSKSGIYHI 115
                                       466666667788776558899999999988877776 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.7
                           DUF4959  36 isytlPdde...dLlyvkaeYklkn 57 
                                       i ++lP+d    dLl ++  Y+++ 
  gi|330509148|ref|YP_004385576.1| 533 IRFKLPKDMldcDLLKISSYYQREA 557
                                       7788898643339999999998654 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 8.5e-06
                           DUF4959   13 etdkaaPgkvtnvkvknlpGgavisytlPddedLlyvkaeYklknGkerevkaSvykdsltveGFgdtkeyevkl 87  
                                        +++++ P+kv+ v+   ++G+  ++++ ++d d   v   Y+lk G++ e+ a v + + t++G +  k+y++++
  gi|330509148|ref|YP_004385576.1| 1158 KEKADHPKKVESVSSILTSGNISLTWQASEDADHYNV---YRLK-GVSSEKLAEVKSPEYTMKG-ELWKSYTFRV 1227
                                        456889***************************8765...9975.*******************.7899****** PP

                           DUF4959   88 yavsrseneSe...pvevkitP 106 
                                        +av++++neSe   pv + +tP
  gi|330509148|ref|YP_004385576.1| 1228 SAVNSEGNESElsdPVGIVVTP 1249
                                        ******9998622266666655 PP

>> DUF4097  Putative adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2     0.034   1.5e+02     104     133 ..      83     112 ..      77     116 .. 0.90
   2 ?   -3.1   0.0      0.86   3.9e+03      90     131 ..     862     903 ..     847     904 .. 0.75
   3 ?    6.2   0.0    0.0012       5.5     173     211 ..    1081    1120 ..    1076    1126 .. 0.92
   4 ?   -0.8   0.0      0.17   7.6e+02      71      97 ..    1152    1183 ..    1144    1218 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.034
                           DUF4097 104 etlelksssGdltlsnvsaktltvksesGd 133
                                       e++ ++s++ d+t +nvs+ ++t +s+sG 
  gi|330509148|ref|YP_004385576.1|  83 ENFLVQSQYADTTSTNVSGYQVTGTSKSGI 112
                                       78999*********************9996 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.86
                           DUF4097  90 sGdlsvekatklkaetlelksssGdltlsnvsaktltvkses 131
                                       s +l+ + +++l+ + ++++s  G++t   +++++l ++s s
  gi|330509148|ref|YP_004385576.1| 862 SIELKAKAVDRLTIQPTHMDSIIGFSTGDEIKGEDLGFNSRS 903
                                       335556668888888899999999999999999999998865 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0012
                           DUF4097  173 tlsntklegsltitassGdvdlslpee.kkaavdassesG 211 
                                        t++++ +++++ +   sG+++l++p + ++ +++a+s++G
  gi|330509148|ref|YP_004385576.1| 1081 TVEFDNVSQKVNLVNGSGYINLTAPHKyGTCQIKAKSSYG 1120
                                        67888999999999*************************9 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.17
                           DUF4097   71 itiylPkkt.....kledlqvkassGdlsvek 97  
                                        +t  lPk++     k+e+++    sG++s++ 
  gi|330509148|ref|YP_004385576.1| 1152 MTAELPKEKadhpkKVESVSSILTSGNISLTW 1183
                                        56667877766666778999999999999653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.46
# Mc/sec: 8128.88
//
[ok]
